What is the difference between LTR Unknown and NA Unknown?

[jia-wu-feng]

Dear Shujun,

I use the new version LTR_retriever, and a lot of results are NA Unknown. I am curious what is the difference between LTR Unknown and NA Unknown in the results?

Thanks, Jia-Wu

[oushujun]

Hello Jia-Wu,

Sorry I just saw your message. Can you give some examples of these sequence IDs?

Shujun

[jia-wu-feng]

chr1H_3:293323..296892_LTR#LTR/unknown TGTAGCGACCCGACTCAAAACGAGTCAAGCCTCTGTGTATCTGTGCCATCCCTGGATCAGTATGCTGGCACACACAGTACATCAATGTATTTATCAAAGTGCAATCACATGTAAATAGCGTAAAACTGATATATACCTTAAATATCGCAGCGGAAACAGTCAAGGGAGTGGAGTCCCAATAAACACCAACGGCAAGTTGAGTGCGGACCGTAACCCTGAATCGTACTCTTACTCGTCGAGAAAAATATCTGCAACATAAGACGTTGCAGCCGTGTAGGTCAGCATATTGAATATGCTGGCAAGTCACCAAAGAGAGGGGTGAAAATGTAATCATCTATACTATATGCATATATGGCAGGAGGGGTTGTAAGTTTTTAGCGTAAAGCAAATTTTCTCCTACAACAAGAGGGGCTAAAAGCAAAACATTACTACAAGGTTGGTTGTTAACGAGATGGTTCCGCCAACCAATTCTCGTACCCGAGTTGTCAGTAACACCCACATCAATATTATTATAATGGTGTTGAGAATTTCAGATAACTTCAGTTCCTTTGGCTCAAGTTGTCCATGACCGTGGACACGGCTAATCGATTAGGTTTGAGTACTCTGCAGAGTTTTGCACACGTTCCCCACAAGATTTGATCGCCTCCGTGTATGTCCTCGCACTTCAGGGTGTTTGAAGACCGGAAGATCAAAACATGGTCTTTCAACGGGTCCCTCTGAATCCCTGTCGGTGCCCATCCAAATCCTACCGTTCTTCTACATCTGCTAGCACCGCCTGTCCAGAGTCGCCACGTTGTCCAACCAAGCCAGAGCCCATAATGGCTTGTGGCTGTGCAGGTAAGCCTTGGGTCTTGAAAATATCCGTCCGTCTCTTTGAGCCTGGGTGAAGCTTTCCGCAAGATGTCATGGCACGTCTCCAGCATCCCGGGCATCCACTGGTTTCTCCAGGGAGCCGATCAACCGTCCTTCACCCAGAGTTGCATTGCATCACAAGGTCTTGAAAAGTCTTGACTTAACCGGTCTTGGTTATTAAATTATTCTCGCATCACTCGTGATAAACTCTCAACCAGAATCCCGTCTACTCACGCATAGCAATATGAAATTTGTCGTCCCGGGCCAAGTGACGGGGTTGTTGGATGCCTACCACATGATACTACAATATGTAACCATAATTTCCAAGTACCTACTCAGCATGCAATTGGGCAAAGAAAGGTGGAACTACCATGCATAGAAAACATAGGTGATAGTATGATCAAAGTGACTTGCCTGGTGATGTTGACGAAGAAGAATTATCGTTCTCGAGAAAATAACTTGATAGACTACTCGTCACTCTCCGATGAAATCTATATAACAAACATATCATTCACATAAGCACTCACACTAACAATCAAAACAAAAGAGAGAGCGAATAAGAATCCGAAGAACTTCAAATAAAACTAGTGAGTCTTCTTCTACATCAAACACTAAATAGTTTTTGTTCTAACTGAAAGTAAAACATTAAAATAACAGAGAACTAAGATATAAATTTAACTAAGATAAAATAAAGTATTTTTCATAAAACTAATTGAAAGTATTTTCAAATGGGAGTTGAAACCGTAGAGAAATCAATTGCAAGTTATTAGCAAACTTGAATTGATTTCACGATAAAAAATAAAATTAAAATAAAAACTTGTTGAACACCTACTGTTTAACTAACAGAAACTAAACATAAACTTTCTGAAATATAAAAGAAATTAATTTAAAAACAACTAAAGAAAGAGACTTTAGTCACAATCCTAAAAGAGGTGAAACAGAAATTGTTTCACATGAAATAATGAGTTAAAATGCTCAAACAATTCTGAAATTTTTACCACTGATAAACAAGATCACTAGTGATCAGTAGCAAAAGAATTAATTTAAAATCTATTTTTAAACTCCCGGAATAAGCAAAACAAGCTTTAAATCAAATCTGATCTAACTAAATTTTTATAAATCCAAATATAGACAAATTATATATTTTCGGAAACTACAAGAAAATTGTGATCTAACGCAAAACGAATCAGCATCATTGGACTTCTAGATCAAAAGTTATGGCCAAAACAAAATTGGAACTTTCTGTTTTTTGCAATTTAGACAGAAAAACTGAAGTTGACTAGCTAACAAATAGGGGTACACGTGGCGCACTACTATAGGCTGCGGGGGGTGTTTGTTGCAACGTTTGGAGCAAACGGCCGAGGCTAACAAAATTTTTCGGTTAAAACATAAGTGAATTAAAACCGCCGGTTTTCTACTCTAAACCGAAGGGGTATACTAGGGATCTAATCTACACCATCTAAATATGATCTAAGGGCTACTAAAGAAAAACAAAAAGAAACAGGAGGAGGGGATGGAGCCTTACCGTGGTTGGAGATGCTCCCGTGGCTGCTGGTGGCGAGGTGGAGGGGGGGGCTCCGGTGGGGTGGGGAGGGGCCGGCGGGAGGAGGGGGAGTGGCAGGGGGCGGTGGGGCTCCTGGGGGGGGGAAGGGAGGCGAGGTGGAGGGGGTCTGCAGGGGGGGGCGAGGGGGGGGGGGGAACTGCTGGTGTGCTGCTGCTCGTGGCAATGGCGATGGGGAGATGGAGAAAGGGCAGCAGGGGGCGGTGGAGGGGGTGCAGGAGGGTGCGGCAGGGGTGCCAGGGGGCGAGGTGGGGCTGGGGCGAGGTGGATTCAGCTCCTGCCGAGCTCCTGTCAACAGAGAAGATGGCGACGGTGGCGCCGAGGCTACGGGCGGGGAAACGGAGATTTTTTTAGGGGAATGGAACGAGGAGAGGCGGGGCATTCTTATAGAGGCGACGGGAGGCGCCGGGAGGAAGTATAGCTCGCGAATCCCGGAGGGGAAGCTTCTTGGGAAGCTTCTGCCATGGTACAGAAGGCAACGCTTGAGGTAGAAGAAGAAGGTGCGTTATGGGCCTGGTCTGTTTCCTAAGGTGGCCCAGGTACATTCCTAAAATAAGAGAGCTCTTTCCTTTTTTATTAAATCAGGGGTTAATACTATTAAAAGCAAATGGAATATTCCTCGGAATATAGGGGTATAATATATTAAAATTTTCAGAAAAATAAATCCAAAAAGATGGGCATTTTTCCACTACCAAAATAAAAACTTCAGAAAAAATTATTTTCACAAAATGGCCTAAAAGATTTATTTTCTTTTGCAAATAATTTTCAAATGACCCTCTAGGTTTTAGGGTTCAAATAACTTTCAAAATGTCCATGGGTTTGAGGGTCATGTTCCTCCTCTCTTTTTTCTGTTTGACAGAAAGTATTTCCCGGCATTTCTTGCACGAAGAAAACAAGTAAAAATGCAAGAGAATTCAAATGCAAATATCTCCGTTCAAATTCTTTATAGTTGAAGAAGTCATGTCATCTTCTCTCGTTGCTTTTAAAAGATTGAATTTGAACTCATCGGAGAAGGGGAAAGTCATTTTATTCCCTCTCATTCAAAAGTTTCGAAAAGTTTCAAATTCCACTCAAGTTTCAATCACTCATTCAAACAAACAAACAATTCTAATAATTATTTTTTTTTTTTTTAACATTCCAAAATTTGGGATGTTACA chr1H_3:296893..300367_INT#LTR/unknown AACCTACCACACTTAAAAATGAATCTCGTCCTCGAGATTCGAAGAGGCTAGAAAGAAAGGTTAGGGTTTGGGGTCTTCTAACAAATCCGATCTCTTGCAAAAGTGGGATGCTACCACACTTAAAATGAAGGTTACTGGTCCCTTAAAATTTTAACAATCCTCTGGGGTTTTGGCATCTGACTCCTCACAGTCTTCATACTAACTCCTCTGGTGATGCTCTTCCGTTATACTCATAACGTTCCCATCAAAATCGAGGGTTCTTCTGTTGATATAAGCTACTTCCGTTTACTGGGTCTTCTTAACTGACAGTCTCGTGGTCAATTCTAAATAACCTATCGATGATTCTCATGGTGGTCTACCATTTGTGGTTATCCTGCAGAGGGAGAGGTCTTGTCTTCATCCTCACCGTAAAATTTCCTACGCGTGACAACAAGTGCCATGTACATGGGCTTTTCCTATACCATTCTAAGGCTTAAACAAAAGCTTCAAAGAACGTCGACTCTCACTATGGGTAAGTCTCTCAGATTTACCATTCCGAATAGCAAGAGAATGATAATAGTAAGTCGTCATGGTGGCCAAGCCATGTCGCACTGAAATCATTACCTTGTATAAGGCTTAGGGAATCTCGTATTCTAACACTTGGGCATCCTCACAAGCATTGCGGAATTTCTCTTGTCCACGAACGAAGTTCGGATAATCCATTGGTTCTGCAAGCTGAACAAAACATCTATCGTAACTTCACAACTCTCAGGTTTTCGTATGCTCCTAAGAAAACGTTTTGCTGATCCGTCATAACTTCTTCCAAGTTTCTTTCATCATCAAGGTAGTGTTGGATCCTTATTAGTCCTTGGGTCTGTGGGTTGCAGGCATACTTGGAATTACTCCGCCTTTAAATTCCATAGTATTTCATTCCATCATATTCTTGGGGTAACCATCATATAATAATAATTCCTCAGACTTATTTTTGGTTCACACACCACTCTGTGGGATGCTTTCCATTGGTGTGTTTACCATGAAAAGGTATTGGTTCATCCATAAATCATATTCATTTCATAATCAATCCTTTATTACATCCTTCATTTCTTCTCAAAAACTCTAATTCAAAAGTACTTTATTACAAATGCTGCCATCCACATTGTTCGGTATGGTCGAGCATTTTTGCCAACTTTATTCATTAGTCTCCCTTGGAGATACTTTAGTTCCACTGGAACTTTCCAATGTGCTCCTTGAAATCATCCATCTTTTGCTTCATCATGGTGGCCATAAGCTTCATCTCCATCATCTCTGCACGTACCTCACTCAGGTATTCCAGGGTATGACGGAGTCTTGCTTCCAGTATTTCTCCAATCTGACGTATGGCTTCCATGGCAGCTTCACGAACAGCATCAAAGAAGGTTGCTCGTGGTACACGTGAAATGAAAAAGTATTGCCCCATAGTCTTTGGACAAACTCCTTTCACATGGTGGAGGTGTACTTCCACATACCAAAGTTCCGCTCCATTTTCCATGAACGGGTAGCCTTTGTAGACTGCATCTCCTTCAAGATGAATGTGCTTCATCGTGTCCTTCAGGATTTTTGGGTAATCATGATCACTGGTCAGGGTCATGATCGTTTCTGGGCCCTTGAGGAATGACTCGTAGAGAGTTGTCATCTGCAGGTGTCAGAAAATAGGTACTCAGAGGAATGTATGTGTCTCCTTGGTAATTATGGTACATTCCTACTCAGTGGATCCTGTGGGTTTACCGATTACTACCACACTTAAAATGAATTATACTTATGCCTGCATAGACCATATTTTCTCATATCCTCATAATTGTTCAGAGACCTTTGTTCGGAGAGAACAACGCATACAGTTTCAACATAGGCAATCATGAGACAATAAATTCCATTTATTCATGATGTTATTACAATCTCAGGGACTTCTGTTACAAAAATTTCACTCCATGATCTCATGAAAAACAAGAGTTCTTCAGATTACAGTAATTGCCGCGGTCAAAACTTAACTACTCCTTTTAGCTTTCTTCCTTTGTGGACAATCATTAGCAAAATGTCCTGCTTCCTTGCAACGAAAGCAAATGAGTTCTGACAAGTCTCGAGGCATCTTAGTGTTTGCTTTTGCTCCTTGGGTTTCCGGCTTCCTTCCTGAGCACATGTATTTGTGGTGGCCAAATTCCATACACTTGTAACATCTGTCATGACTCAGGTCTTTATCTACAGAGAGTTGGCTCTTTCGAGGGTTCTTTTTCTTCTTTCCGGACTCCTTTGTTTTGGCCAGTTCTTCTATTTCAAGTGGATCAAACTCCACTTTTTCTGCCGGGAAGTTTCCCAGATACTCTTGGCTTCCCTTCGTGCAATCCTGTGAATAATGTCCTTCTTCTCCACATGAGTAGCATGCATTGGAGAAAAATCTGGTCAGACCTTGTCCATCAGGGTCTTCTATATTTTCATTCTTCACAGGTTCTTCTGGAGTCTTCTTCTTGAGGGTTTCCTTCAGTGCATCTTTCTGCTGCTTGACAACTTGTTGCACCTTGGGGTAAATGTGACACTGAGCTGGATAGTGGTTGGTTCCTTCACAAAGGAAACAAGTCACCTGACTACTTGGGCACTCCTCAGCTGGGTGATTTTCTTCACAATGAGTGCATCCACCCTTGTGTTCTTCCTGGGTGTGTCCTATTTCTCCACAGATCTTGCATGCACAAGGCTTCTTCATCGGATTATCATAGCACTTCCGAATGAGACGGGATCTTAACAGAGTCTTCTTGAATTTGTCCCAGGTTTCTGCTCCACTAAATCCTTGTATGGCATGGTGCATTTTCCACCAGATAGCAGCACTTTGGGTAAAGTACTGGAGAGCGTGCTCCATTTCATACTTCCTTGAGATCAAGTTGCTCCCGAAGTGGTTTTCCATGTTCTGAATCCATATTTCAGCTTCCAGCTGGGTCATTGGTCCAGAGACTACAAGTCCAGCTTCATACTCCATCTGGTAGGGTTGAGGTTTTGGGGATGAGACGGGTAAGAGAGAGAGGGAGATACACACAATACAAACAACATTTTTGAGAATAGGTTTTATTTGTGGCCGTCGGAAAACACACGCCAATGACGGCTCACAAATCATCGTAACTAACGTGGGTATATAACAGGGATTTGGACTTCTAATGGTCATATAAATATTCGAACGCTTCAGGGTCTTTGAATTCTTCAGGTCTTGAGAGTCTTCAATGGGTGTAGCTTCAACTCTTCAAATGCATGGTGAAATCCTCTTTACTTTGAAGTAGAACTCCATTGATTCTTCATGTGGTCAAAGAGAAAGGCATTGTCTAACTATTTGAGGTGAGAGAGAAACATTTGATGAAATCAGGAGAGATGAGGAGTAAAAGGTGTTCTTTAAAATAAAAAATTTGAGAGATCCTTTCCTAAGAAATTTCCAGTTTCTAGGGTCACGTCCTACAGTCAACATGTGCTCTGATACCATCTC chr1H_3:300368..303934_LTR#LTR/unknown TGTAGCGACCCGACTCAAAACGAGTCAAGCCTCTGTGTATCTGTGCCATCCCTGGATCAGTATGCTGGCACACACAGTACATCAATGTATTTATCAAAGTGCAATCACATGTAAATAGCGTAAAACTGATATATACCTTAAATATCGCAGCGGAAACAGTCAAGGGAGTGGAGTCCCAATAAACACCAACGGCAAGTTGAGTGCGGACCGTAACCCTGAATCGTACTCTTACTCGTCGAGAAAAATATCTGCAACATAAGACGTTGCAGCCGTGTAGGTCAGCATATTGAATATGCTGGCAAGTCACCAAAGAGAGGGGTGAAAATGTAATC ATCTATACTATATGCATATATGGCAGGAGGGGTTGTAAGTTTTTAGCGTAAAGCAAATTTTCTCCTACAACAAGAGGGGCTAAAAGCAAAACATTACTACAAGGTTGGTTGTTAACGAGATGGTTCCGCCAACCAATTCTCGTACCCGAGTTGTCAGTAACACCCA CATCAATATTATTATAATGGTGTTGAGAATTTCAGATAACTTCAGTTCCTTTGGCTCAAGTTGTCCATGACCGTGGACACGGCTAATCGATTAGGTTTGAGTACTCTGCAGAGTTTTGCACACGTTCCCCACAAGATTTGATCGCCTCCATGTATGTCCTCGCACT TCAGGGTGTTTGAAGACCGGAAGATCAAAACATGGTCTTTCAACGGGTCCCTCTGAATCCCTGTCGGTGCCCATCCAAATCCTACCGTTCTTCTACATCTGCTAGCACCGCCTGTCCAGAGTCGCCACGTTGTCCAACCAAGCCAGAGCCCATAATGGCTTGTGGC TGTGCAGGTAAGCCTTGGGTCTTGAAAATATCCGTCCGTCTCTTTGAGCCTGGGTGAAGCTTTCCGCAAGATGTCATGGCACGTCTCCAGCATCCCGGGCATCCACTGGTTTCTCCAGGGAGCCGATCAACCGTCCTTCACCCAGAGTTGCATTGCATCACAAGGT CTTGAAAAGTCTTGACTTAACCGGTCTTGGTTATTAAATTATTCTCGCATCACTCGTGATAAACTCTCAACCAGAATCCCGTCTACTCACGCATAGCAATATGAAATTTGTCGTCCCGGGCCAAGTGACGGGGTTGTTGGATGCCTACCACATGATACTACAATAT GTAACCATAATTTCCAAGTACCTACTCAGCATGCAATTGGGCAAAGAAAGGTGGAACTACCATGCATAGAAAACATAGGTGATAGTATGATCAAAGTGACTTGCCTGGTGATGTTGACGAAGAAGAATTATCGTTCTCGAGAAAATAACTTGATAGACTACTCGTC ACTCTCCGATGAAATCTATATAACAAACATATCATTCACATAAGCACTCACACTAACAATCAAAACAAAAGAGAGAGCGAATAAGAATCCGAAGAACTTCAAATAAAACTAGTGAGTCTTCTTCTACATCAAACACTAAATAGTTTTTGTTCTAACTGAAAGTAAA ACATTAAAATAACAGAGAACTAAGATATAAATTTAACTAAGATAAAATAAAGTATTTTTCATAAAACTAATTGAAAGTATTTTCAAATGGGAGTTGAAACCGTAGAGAAATCAATTGCAAGTTATTAGCAAACTTGAATTGATTTCACGATAAAAAATAAAATTAA AATAAAAACTTGTTGAACACCTACTGTTTAACTAACAGAAACTAAACATAAACTTTCTGAAATATAAAAGAAATTAATTTAAAAACAACTAAAGAAAGAGACTTTAGTCACAATCCTAAAAGAGGTGAAACAGAAATTGTTTCACATGAAATAATGAGTTAAAATG CTCAAACAATTCTGAAATTTTTACCACTGATAAACAAGATCACTAGTGATCAGTAGCAAAAGAATTAATTTAAAATCTATTTTTAAACTCCCAGAATAAGCAAAACAAGCTTTAAGTCAAATCTGATCTAACTAAATTTTTATAAATCCAAATATAGACAAATTAT ATATTTTCGGAAACTACAAGAAAATTGTGATCTAACGCAAAACGAATCAGCATCATTGGACTTCTAGATCAAAAGTTATGGCCAAAACAAAATTGGAATTTTCTGTTTTTTGCAATTTAGACAGAAAAACTGAAGTTGACTAGCTAACAAATAGGGGTACACGTGG CGCACTACTATAGGCTGCGGGGGGTGTTTGTTGCAACGTTTGGAGCAAACGGCCGAGGCTAACAAAAATTTTCGGTTAAAACATAAGTGAATTAAAACCGCCGGTTTTCTACTCTAAACCGAAGGGGTATACTAGGGATCTAATCTACACCATCTAAATATGATCT AAGGGCTACTAAAGAAAAACAAAAAGAAACAGGAGGAGGGGATGGAGCCTTACCGTGGTTGGAGATGCTCCCGTGGCTGCTGGTGGCGAGGTGGAGGGGGGGGGCTCCGGTGGGGTGGGGAGGGGCCGGCGGGAGGAGGGGGAGTGGCAGGGGGCGGTGGGGCTCC TGGGGGGGGAAGGGAGGCGAGGTGGAGGGGGTCTGCAGGGGGGGCGAGGGGGGGGGGAACTGCTGGTGTGCTGCTGCTCGTGGCAATGGCGATGGGGAGATGGAGAAAGGGCAGCAGGGGGCGGTGGAGGGGGTGCAGGAGGGTGCGGCAGGGGTGCCAGGGGGCG AGGTGGGGCTGGGGCGAGGTGGATTCAGCTCCTGCCGAGCTCCTGTCAACAGAGAAGATGGCGACGGTGGCGCCGAGGCTACGGGCGGGGAAACGGAGATTTTTTTAGGGGAATGGAACGAGGAGAGGCGGGGCATTCTTATAGAGGCGACGGGAGGCGCCGGGAG GAAGTATAGCTCGCGAATCCCGGAGGGGAAGCTTCTTGGGAAGCTTCTGCCATGGTACAGAAGGCAACGCTTGAGGTAGAAGAAGAAGGTGCGTTATGGGCCTGGTCTGTTTCCTAAGGTGGCCCAGGTACATTCCTAAAATAAGAGAGCTCTTTCCTTTTTTATT AAATCAGGGGTTAATACTATTAAAAGCAAATGGAATATTCCTCGGAATATAGGGGTATAATATATTAAAATTTTCAGAAAAATAAATCCAAAAAGATGGGCATTTTTCCACTACCAAAATAAAAACTTCAGAAAAAATTATTTTCACAAAATGGCCTAAAAGATTT ATTTTCTTTTGCAAATAATTTTCAAATGACCCTCTAGGTTTTAGGGTTCAAATAACTTTCAAAATGTCCATGGGTTTGAGGGTCATGTTCCTCCTCGCTTTTTTCTGTTTGACAGAAAGTATTTCCCGGCATTTCTTGCACGAAGAAAACAAGTAAAAATGCAAGA GAATTCAAATGCAAATATCTCCGTTCAAATTCTTTATAGTTGAAGAAGTCATGTCATCTTCTCTCGTTGCTTTTAAAAGATTGAATTTGAACTCACCGGAGAAGGGGAAAGTCATTTTATTCCCTCTCATTCAAAAGTTTCGAAAAGTTTCAAATTCCACTCAAGT TTCAATCACTCATTCAAACAAACAAACAATTCTAATAATTATTATTATTTTTTTTAACATTCCAAAATTTGGGATGTTACA

[jia-wu-feng]

@oushujun It seems that it is three sequences combined. chr1H_3:293323..303934 , I found that it contains three sequences ： chr1H_3:293323..296892_LTR#LTR/unknown chr1H_3:296893..300367_INT#LTR/unknown chr1H_3:300368..303934_LTR#LTR/unknown

[oushujun]

This is a good question. I have to go back to the codes to find out why it's reported differently. So here is the answer. The screenshot is from the pass.list file, which header is this: #LTR_loc Category Motif TSD 5_TSD 3_TSD Internal Identity Strand SuperFamily TE_type Insertion_Time eg., M82_chr1:3661667..3667580 pass motif:TGCA TSD:TAT 3661664..3661666 3667581..3667583 IN:3662364..3666878 0.9900 - Copia LTR 388320

Column 10 is superfamily and 11 is TE type (class), which are deterined by HMM profile matching.

For column 11,

• The default is "NA" (no HMM alignment).
• If all HMMs aligned to this candidates are LTR profiles, then column 11 will be assigned "LTR".
• If both LTR and nonLTR profiles are aligned, then col 11 will be assigned "mixture" and this entry will be determined "false" (column 2).

Column 10 is determined with the following rules:

• The default is "unknown" (no HMM alignment), if there are alignments, depending on the number of gypsy and copia profiles:
• $family="Gypsy" if ($gypsy>$copia and $copia/$gypsy<0.3);
• $family="Copia" if ($copia>$gypsy and $gypsy/$copia<0.9);
• if none of the matched profiles are specific to Copia or Gypsy, then column 10 remains "unknown".

Column 9 is determined with the following rules:

• The default is "?" (no HMM alignment), if there are alignments, depending on the number of "+" and "-" directions:
• $strand="+" if ($pos_strand>$neg_strand and $neg_strand/$pos_strand<0.4);
• $strand="-" if ($neg_strand>$pos_strand and $pos_strand/$neg_strand<0.4);

So for "unknown NA", there's no rice LTR related HMM profiles matched to this candidate. For "unknown LTR", there are some rice LTR related HMM profiles matched, but we could not tell if this is a Copia or Gypsy.

For all LTR elements identified, the 5' LTR region, internal region, and 3' LTR region are separated into three sequences by default, as in your example.

Hope this helps!

Best, Shujun

[jia-wu-feng]

Thanks, I will close the issue.