Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014729.1 Corchorus olitorius cultivar O-4 contig14762, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24880
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1998 original size:334 final size:333
Alignment explanation
Indices: 1--3944 Score: 4557
Period size: 333 Copynumber: 11.9 Consensus size: 333
* * ** *
1 AAAAAATTAAGCAAAACTGAATCGGGGCCCCGGAACGCGTTTTTAG-CAAAAACTGTGATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * *
65 GTACACGATTACGGCAAAAATTTTGCAAAAATTGACCCGAAAGGTTTGCGCTCAATTTTTTGCCA
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCA
* ** *
130 CAAT-ATCGTCTACCATATATAACTCAATGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
131 CAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
* * * * * *
194 TCAATTTTCCAATTTTGTT-TTAATTAAGATTTTATTTAAATCAGAAAAAGTTTCTGATGCTCGT
196 TCATTTTTCCAATTTT-TTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
* * * * *
258 AAAAACAACTCCTTAAATCCAATGTGGATGAGATTTTGTTAGAAGAATACAGATACTTTAATGAG
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAG
*
323 TCCTGACGT
325 TCTTGACGT
*
332 AAAAAATCATGCAAAACTGAGTC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
*
396 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCCCAATTTTTTGCCA
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCA
* *
461 CAATAATCGTATAAAATATAAAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCCAATA
131 CAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
* * * **
526 TTATTTTTCCAATTTTCTCTTACTTCGAATTCTAATTAAATCGGAAATAA-ATTCTGATGCTCGT
196 TCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAA-AAGATTCTGATGCTCGT
* * *
590 AAAAACAAATCCTTAAATCCAATGAGGCTGAGATTTCGATAGATGGATACAGATATTTTAATGAG
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAG
655 TCTTGACG-
325 TCTTGACGT
* * *
663 AAAAAATTCATGCAAAACTTAGCCGGGGCCCCGAAACGCGTTTTGAGCCAAAAACCGTGAT-G--
1 AAAAAA-TCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
725 -GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
65 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
* * *
789 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAA-ATTTTAGGGCTTTTAACGCGTCTAAT
130 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
* * * * *** * * *
853 ATCAATTTTCCAAGTTTTTCTAAATTAAAATTCTAGTCGTATTGGTAAACGATTCTGATGCTCGT
195 ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
* * *
918 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTCGATAGATGAATACATATATTTTAATGAG
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAG
*
983 TCTTGACGC
325 TCTTGACGT
* *
992 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTGAGCCAAAAACCGTGATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
*
1057 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGGTTTGCGCTCAATTTTTTGCCA
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCA
* * * *
1122 CAATAATCGTATAACATATATAATTCAATGTCAAAAAGATTTTATGGCCTTTCACGCTTCTAATA
131 CAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
* * * * * * *
1187 TCATTTTACGAATTTTTTTTTAATTAAGATTTTATTTAAATCAGAAAAAGATTCTGATGCTCGTA
196 TCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGTA
* * * * * * *
1252 AAAACAAGTTCTTAAATCCAATGTGGCTGAGATTTTGTTAGAAGAATAAAGATACTTTCATGAGT
261 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAGT
1317 CTTGACGT
326 CTTGACGT
* * *
1325 AAAAAATCATGCAAAACTGAGTC-GGGCCCCGGAACACGTTTTTAGCCAAAAAACCGTGATTGTT
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTT
*
1389 AGTACACGATTCCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
65 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
*
1454 ACAATAATCGTATAAAATATAAAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
130 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
* ** * * *
1519 ATTATTTTTCCAATTTTTTCTTAATTCGAATTCTAATTAACTCGGAAAAAAATTCTGATGCTCAT
195 ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
*
1584 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGATT-GATGGATACAGATATTTTAATGA
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCG-TTAGATGAATACAGATATTTTAATGA
* *
1648 GTCTTGATGA
324 GTCTTGACGT
* *
1658 AAAAAATCATGCAAAACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * *
1723 GTATACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGTTTTGCGCTTAATTTTTTGCCA
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCA
* *
1788 CAATAATCATATAAAATATATAACTCAACGTCAAAAAGATTTTAGAGCCTTTCACGCTTCTAATA
131 CAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
* * *
1853 TCATTTTTTCCATTTTTTTCTGAATTAAAATTCTAATTAAATCGGAAAAAGATTCCGATGCTCGT
196 TCA-TTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
* * * *
1918 AAAAACAAATCCTT-AATACCAATATGGCTGAGATTTTGTTAGGTGAATACATATATTTTAATGA
260 AAAAACAAATCCTTAAAT-CCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGA
* *
1982 GTCCTGCCGT
324 GTCTTGACGT
* * * * ** *
1992 AAAAAATCATGTATAACTGAGGCAGGGCCATGGATCGCGTTTTTAGCCAAAAACCGTGATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * *
2057 GTGCACGATTTCAGCTAAAATTTTGCAAAAATAGACTC-AAATGTTTTGCGCTCAATTTTTTCCC
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-GTTTTGCGCTCAATTTTTTGCC
*
2121 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAATATTTTAGGGCCTTTCACGCTTCTAAT
130 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
* * *
2186 ATCATTTTTCCAATTTTTTCTAAACTAAAATACTAATTAAATCGGAAAAAGATTCTGATGCTCGT
195 ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
** * * * * *
2251 AAAAACAAATCCTTAAATTTAA-GATGGCTGAGATTTCGATAAATGAAGACGGATATTTTAATAA
260 AAAAACAAATCCTTAAATCCAATG-TGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGA
* *
2315 GTTTTGACGC
324 GTCTTGACGT
* *
2325 AAAAAATCATGCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAAACGTGATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
*
2390 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGGTTTGCGCTCAATTTTTTTGCC
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAA-TTTTTTGCC
* * * *
2455 ACAATAATTGTATAACATATATAACTCAATGTCAAAAAGATTTTATGGCCTTTCACGCTTCTAAT
130 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
* * * * * *
2520 ATCA-TTTTACAAATTTTT-TTAATTAAGATTTTATTTAAATCAGAAAAAGATTCTGATGCTCGT
195 ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
* ** * * *
2583 AAAAACAAGTCCAGAAATCCAATGTGGCTGAGATTTTGTTAGAAGAATACAGATACTTTAATGAG
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAG
2648 TCTTGACGT
325 TCTTGACGT
* * * *
2657 AAAAAATCATGCAAAACTGAGTC-GGGCCCTGGAACACGTTTTTAGCCAAAAACCGTGAT--TAA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
*
2719 CGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
66 -GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCC
*
2784 ACAATAATCGTATAAAATATAAAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
130 ACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAAT
* *
2849 ATTATTTTTCCAATTTTTTCTTACTTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
195 ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGT
* *
2914 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGATAGATGGATACAGATATTTTAATGAG
260 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAG
*
2979 TCTTGACGCA
325 TCTTGACG-T
* * * *
2989 AAAAAATCATACAAAACTGAGCCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCTTTATGGTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * * * * *
3054 GTACACAATTTTGTCTAAAATTTTGCAAAAAATGACCCAAAAATGTTT-C-CTTAA-TTTTTG-A
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGT-TTTGCGCTCAATTTTTTGCC
* * * * ** * * * *
3115 ATAA-AATAC-TCATAATATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGTTTT
130 ACAATAAT-CGT-ATAA-A-ATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTC
* * * * * * *
3178 TAATATTATTTTT-CATATTTTTTCTGAATT-AATTTATAAGTAAATC-GAAACAAAATTCAGAT
191 TAATATCATTTTTCCA-ATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAA-AAGATTCTGAT
** * * * * ** * *
3240 GCTCGTAAGGACAAATTCTT-AATTCAATGTGGCTGAGATTT-GATTTGATGTATATGGACATCT
254 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCG-TTAGATGAATACAGATATTT
* * * ** *
3303 CAAGGATTCTTGGTGC
318 TAATGAGTCTTGACGT
* *** * * *
3319 CAAAAATCATGCAAAACTGA--------ATTGGAACGCTTTTTTAGCCAAAAACTGTGATGCTTA
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * *
3376 TTACATGATTTCAGCTAAAATTTTGTAAAAATTGACCC-AAATGATATTT-C-CTCAATTTTTGG
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-G-T-TTTGCGCTCAATTTTTTG
* * * * * * * * ** * * *
3438 CTAAAATACTCATA-AAAATATATAATTCAACGCCGAAAACATTGAAGGGCTTTTGACGTTTCTA
128 CCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTA
** * * ** * * * *
3502 ATATTGTTTTTCCTATTTCTTC-CGATTTAATTTCTAATTAAATC-GAAACAAGATTCAGATGAT
193 ATATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAA-AAGATTCTGATGCT
* * * *
3565 CGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATCT-GATTAGATGAATATAGATATTTCAA
257 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCG-TTAGATGAATACAGATATTTTAA
** *
3629 -GTAGTCTCAAAGCT
321 TG-AGTCTTGACG-T
* ** * * * * * ** *
3643 -AAAAATCATGCAAAATTGAGGTGAGTCCACGGAACGCATTTTTAGGCAAAAA-TTTAGATAGTT
1 AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGT-GATGGTT
* * * * * *
3706 AGTACACGATTTCGGCTAAAATTTTGGAAAAAATGACTC-AAAATATTT-CTCCTCAATTTTTGG
65 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGT-TTTGC-GCTCAATTTTTTG
* * * * * * * * ** * *
3769 CTAAAATACTCTTA-AAAATATATAATTGAACGCCAAAAACATTGGAGGG-CTTTCCATGCTTTT
128 CCACAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTT-CACGCTTCT
* * * ** * *
3832 AATGGTCGTATTTCTTATTTTTTCTAAATT-AATTTCTAATTAAAT-GGAAACAAGATT-TAGAT
192 AAT-ATCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAA-AAGATTCT-GAT
* * * * **
3894 GCTCGTAAAAA-AAATTCTTAAATCCTATGTTGCTAAGATTTAATTAGATGA
254 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGA
3945 TGTAAAGTAT
Statistics
Matches: 3122, Mismatches: 423, Indels: 136
0.85 0.11 0.04
Matches are distributed among these distances:
321 6 0.00
322 163 0.05
323 73 0.02
324 7 0.00
325 5 0.00
326 3 0.00
327 1 0.00
328 192 0.06
329 187 0.06
330 115 0.04
331 461 0.15
332 541 0.17
333 936 0.30
334 427 0.14
335 5 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (333 bp):
AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCA
CAATAATCGTATAAAATATATAACTCAACGTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATA
TCATTTTTCCAATTTTTTCTTAATTAAAATTCTAATTAAATCGGAAAAAGATTCTGATGCTCGTA
AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGAATACAGATATTTTAATGAGT
CTTGACGT
Found at i:3766 original size:654 final size:652
Alignment explanation
Indices: 32--3914 Score: 2336
Period size: 667 Copynumber: 5.9 Consensus size: 652
22 TCGGGGCCCC
* * * * * *
32 GGAACGCGTTTTTAG-CAAAAACTGTGATGGTTA-GTACACGATTACGGCAAAAATTTTGCAAAA
1 GGAACACGTTTTTAGCCAAAAACCGTGAT--TAACGTACACGATTTCAGCTAAAATTTTGCAAAA
* * * * * ** * *
95 ATTGACCCGAAAGGTTTGCGCTCAATTTTTTGCCACAAT-ATCGTCTACCATATATAACTCAATG
64 ATTGACCCGAAAGTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCAACG
* * ** * * *** * *
159 TCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATATCAATTTTCCAATTT-TGTTTTAATTAAGA
129 CCAAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCT-TCCGACTTAAAA
* * * * * * * *
223 TTTTATTTAAATCAGAAAAAGTTTCTGATGCTCGTAAAAACAACTCCTTAAATCCAATGTGGATG
193 TTCTAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * * ** * *
288 AGATTTTGTTAGAAGAATACAGATACTTT-AATGAGTC-CTGA-CGTAAAAAATCATGCAAAACT
258 AGATCTCGATAGATGAATACAGATA-TTTCAATGAGTCTCAAAGC-AAAAAAATCATACAAAACT
* * * * * *
350 GAGTCGG-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
321 GAG-CGGAGTCCCGGAACGCATTTTTAGCCAAAAA-CTTTATAGTTAGTACACAATTTCGGCTAA
* * * * ** * * *
414 AATTTTGCAAAAATTGACCCGAAAGT-TTTGCGCCCAATTTTTTG-CCACAATAATCGTATAAAA
384 AATTTTGCAAAAAATGACCCAAAAATGTTT-C-CTCAA-TTTTTGAATAAAATACTCATA-AAAA
* * * * * ** * ** * *
477 TATAAAACTCAACGTCAAAAAGATTTTAGGGCCTTT-CACGCTTCCAAT-ATTATTTTTCCA-AT
445 TATATAATTGAACGCCAAAAACATTGGA-GGACTTTCCACGCTTTTAATGATCATATTT-CATAT
* * * * * * * *
539 TTTCTCTTACTTCGAA-TTCTAATTAAATCGGAAA-TAAATTCTGATGCTCGTAAAAACAAATCC
508 TTTTTCTAAATT--AATTTATAAGTAAATC-GAAACAAAATTCAGATGCTCGTAAAAA-AAATTC
* * * * ** * * * * * ** *
602 TTAAATCCAATGAGGCTGAGATTTCGA-TAGATGGATACAGATATTTTAATGAGTCTTGACG-AA
569 TT-AATTCAATGTGGCTGAGATTT-GATTTGATGTATATGGACATCTCAAGGATTCTTGGTGCCA
****
665 AAAATTCATGCAAAACTTAGCCGGG
632 AAAA-TCATGCAAAAC-T-G-AATT
* * * *
690 GCCCCGAAACGCGTTTTGAGCCAAAAACCGTGA-T--GGTACACGATTTCGGCTAAAATTTTGCA
1 G----G-AACACGTTTTTAGCCAAAAACCGTGATTAACGTACACGATTTCAGCTAAAATTTTGCA
* * * *
752 AAAATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATATAACTCA
61 AAAATTGACCCGAAAGTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCA
* ** * * * * * ** *
817 ACGTCAAAAA-ATTTTAGGGCTTTTAACGCGTCTAATATCAATTTTCCAAGTTT-TTCTAAATTA
126 ACGCCAAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAA-TTTCTTCCGACTTA
* *** * * * * * *
880 AAATTCTAGTCGTATTGGTAAACGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGG
190 AAATTCTAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * ** * *
945 CTGAGATTTCGATAGATGAATACATATATTTTAATGAGTCTTGACGC-AAAAAATCATGCAAAAC
255 CTGAGATCTCGATAGATGAATACAGATATTTCAATGAGTCTCAAAGCAAAAAAATCATACAAAAC
* * * * * * * * *
1009 TGAGCCGGGGCCCCGAAACGCGTTTTGAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
320 TGAG-CGGAGTCCCGGAACGCATTTTTAGCCAAAAA-CTTTATAGTTAGTACACAATTTCGGCTA
* * * ** * * * *
1074 AAATTTTGCAAAAATTGACCC-GAAAGGTTTGCGCTCAATTTTTTG-CCACAATAATCGTATAAC
383 AAATTTTGCAAAAAATGACCCAAAAATGTTT-C-CTCAA-TTTTTGAATAAAATACTCATA-AAA
* * * * ** * *
1137 ATATATAATTCAATGTCAAAAAGATTTTATGGCCTTT-CACGCTTCTAAT-ATCAT-TTTACGA-
444 ATATATAATTGAACGCCAAAAACATTGGA-GGACTTTCCACGCTTTTAATGATCATATTT-C-AT
* * ** * * *
1198 ATTTTTTTTTAATTAAGATTT-TATTTAAATCAGAAA-AAGATTCTGATGCTCGTAAAAACAAGT
506 ATTTTTTCTAAATT-A-ATTTATAAGTAAATC-GAAACAAAATTCAGATGCTCGTAAAAA-AAAT
* * * * ** * * * * **
1261 TCTTAAATCCAATGTGGCTGAGATTTTG-TTAGAAGAATAAAGATACTTTC-ATGAGTCTTGACG
567 TCTT-AATTCAATGTGGCTGAGA-TTTGATTTGATGTATATGGACA-TCTCAAGGATTCTTGGTG
** * *
1324 TAAAAAATCATGCAAAACTGAGTCGGGCCCC
629 CCAAAAATCATGCAAAACTGAAT-------T
* * *
1355 GGAACACGTTTTTAGCCAAAAAACCGTGATTGTTA-GTACACGATTCCGGCTAAAATTTTGCAAA
1 GGAACACGTTTTTAGCC-AAAAACCGTGA-T-TAACGTACACGATTTCAGCTAAAATTTTGCAAA
* * *
1419 AATTGACCCGAAAGTTTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATAAAACTCAAC
63 AATTGACCCGAAAGTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCAAC
* * ** * ** * **
1484 GTCAAAAAGATTTTAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTTTTCTTAATTCGAA
128 GCCAAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCTTCCGACTTAAAA
* * * * *
1549 TTCTAATTAACTCGGAAAAAAATTCTGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTG
193 TTCTAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * * ** * *
1614 AGATTTCGATTGATGGATACAGATATTTTAATGAGTCTTGATG-AAAAAAATCATGCAAAACTGA
258 AGATCTCGATAGATGAATACAGATATTTCAATGAGTCTCAAAGCAAAAAAATCATACAAAACTGA
* * * * * *
1678 GCCGG-GGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGAT-GATTAGTATACGATTTCGGCTAA
323 G-CGGAGTCCC-GGAACGCATTTTTAGCCAAAAA-CTTTATAG-TTAGTACACAATTTCGGCTAA
* * * * * ** * *
1741 AATTTTGCAAAAATTGATCCGAAAGT-TTTGCGCTTAATTTTTTG-CCACAATAATCATATAAAA
384 AATTTTGCAAAAAATGACCCAAAAATGTTT-C-CTCAA-TTTTTGAATAAAATACTCATA-AAAA
* * * * ** * * *
1804 TATATAACTCAACGTCAAAAAGATTTTAGAGCCTTT-CACGCTTCTAAT-ATCATTTTTTCCAT-
445 TATATAATTGAACGCCAAAAACATTGGAG-GACTTTCCACGCTTTTAATGATCA-TATTT-CATA
* * * * * * *
1866 TTTTTTCTGAATTAAAATTCTAATTAAATCGGAAA-AAGATTCCGATGCTCGTAAAAACAAATCC
507 TTTTTTCTAAATT-AATTTATAAGTAAATC-GAAACAAAATTCAGATGCTCGTAAAAA-AAATTC
* * * * * *** * * * * * * ** **
1930 TTAATACCAATATGGCTGAGATTTTG-TTAGGTGAATACATATATTTTAATGAGTCCTGCCGTAA
569 TTAAT-TCAATGTGGCTGAGA-TTTGATTTGATGTATATGGACATCTCAAGGATTCTTGGTGCCA
* * *
1994 AAAATCATGTATAACTGAGGCAGGGCCAT
632 AAAATCATGCAAAACTGA---A-----TT
* * * *
2023 GGATCGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTGCACGATTTCAGCTAAAATTTTGCAAAA
1 GGAACACGTTTTTAGCCAAAAACCGTGAT--TAACGTACACGATTTCAGCTAAAATTTTGCAAAA
* * ** * * *
2087 ATAGACTC-AAATGTTTTGCGCTCAATTTTTTCCCACAATAATCGTATAAAATATATAACTCAAC
64 ATTGACCCGAAA-GTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCAAC
* * ** * * **
2151 GTCAAAAATATTTTAGGGCCTTTCACGCTTCTAATATCATTTTTCCAATTTTTTCTAAAC-TAAA
128 GCCAAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCTTC-CGACTTAAA
* * * **
2215 ATACTAATTAAATCGGAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATTTAA-GATGGC
192 ATTCTAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATG-TGGC
* * * * * * * ** * *
2279 TGAGATTTCGATAAATGAAGACGGATATTTTAATAAGTTTTGACGC-AAAAAATCATGCAAAACT
256 TGAGATCTCGATAGATGAATACAGATATTTCAATGAGTCTCAAAGCAAAAAAATCATACAAAACT
* * * * * * *
2343 GAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAA
321 GAGCGGA-GTCCCGGAACGCATTTTTAGCC-AAAAACTTTATAGTTAGTACACAATTTCGGCTAA
* * * * * **
2408 AATTTTGCAAAAATTGACCC-GAAAGGTTTGCGCTCAATTTTTTTGCCACAATAATTGT-AT-AA
384 AATTTTGCAAAAAATGACCCAAAAATGTTT-C-CTCAA--TTTTTG-AATAA-AATACTCATAAA
* * * * * * ** * * *
2470 CATATATAACTCAATGTCAAAAAGATTTTATGGCCTTT-CACGCTTCTAAT-ATCAT-TTTACAA
443 AATATATAATTGAACGCCAAAAACATTGGA-GGACTTTCCACGCTTTTAATGATCATATTT-CAT
** * * *
2532 ATTTTTT-T-AATTAAGATTT-TATTTAAATCAGAAA-AAGATTCTGATGCTCGTAAAAACAAGT
506 ATTTTTTCTAAATT-A-ATTTATAAGTAAATC-GAAACAAAATTCAGATGCTCGTAAAAA-AAAT
* ** * * * * ** * * * * **
2593 CCAGAAATCCAATGTGGCTGAGATTTTG-TTAGAAGAATACAGATA-CTTTAATGAGTCTTGACG
567 TC-TTAATTCAATGTGGCTGAGA-TTTGATTTGATGTATATGGACATC-TCAAGGATTCTTGGTG
** *
2656 TAAAAAATCATGCAAAACTGAGTCGGGCCCT
629 CCAAAAATCATGCAAAACTGAAT-------T
2687 GGAACACGTTTTTAGCCAAAAACCGTGATTAACGTACACGATTTCAGCTAAAATTTTGCAAAAAT
1 GGAACACGTTTTTAGCCAAAAACCGTGATTAACGTACACGATTTCAGCTAAAATTTTGCAAAAAT
* * * *
2752 TGACCCGAAAGTTTTGCGCTCAATTTTTTGCCACAATAATCGTATAAAATATAAAACTCAACGTC
66 TGACCCGAAAGTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCAACGCC
* ** * **
2817 AAAAAGATTTTAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTTTTCTTACTTAAAATTC
131 AAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCTTCCGACTTAAAATTC
* *
2882 TAATTAAATCGGAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
196 TAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * ** *
2947 TTTCGATAGATGGATACAGATATTTTAATGAGTCTTGACGCAAAAAAATCATACAAAACTGAGCC
261 TCTCGATAGATGAATACAGATATTTCAATGAGTCTCAAAGCAAAAAAATCATACAAAACTGAG-C
* * * * *
3012 GGGGTCCCGGAACGCGTTTTTAGCCAAAAACCTTTATGGTTAGTACACAATTTTGTCTAAAATTT
325 GGAGTCCCGGAACGCATTTTTAGCCAAAAA-CTTTATAGTTAGTACACAATTTCGGCTAAAATTT
* *
3077 TGCAAAAAATGACCCAAAAATGTTTCCTTAATTTTTGAATAAAATACTCATAATATATATATAAT
389 TGCAAAAAATGACCCAAAAATGTTTCCTCAATTTTTGAATAAAATACTCATAA-AAATATATAAT
* * * * * * *
3142 TTAACGCCAAAAAGATTGGAGGACTTTTCACGTTTTTAAT-ATTATTTTTCATATTTTTTCTGAA
453 TGAACGCCAAAAACATTGGAGGACTTTCCACGCTTTTAATGATCATATTTCATATTTTTTCTAAA
* *
3206 TTAATTTATAAGTAAATCGAAACAAAATTCAGATGCTCGTAAGGACAAATTCTTAATTCAATGTG
518 TTAATTTATAAGTAAATCGAAACAAAATTCAGATGCTCGTAA-AAAAAATTCTTAATTCAATGTG
3271 GCTGAGATTTGATTTGATGTATATGGACATCTCAAGGATTCTTGGTGCCAAAAATCATGCAAAAC
582 GCTGAGATTTGATTTGATGTATATGGACATCTCAAGGATTCTTGGTGCCAAAAATCATGCAAAAC
3336 TGAATT
647 TGAATT
* * * * * * *
3342 GGAACGCTTTTTTAGCCAAAAACTGTGATGCTTA-TTACATGATTTCAGCTAAAATTTTGTAAAA
1 GGAACACGTTTTTAGCCAAAAACCGTGAT--TAACGTACACGATTTCAGCTAAAATTTTGCAAAA
* * * *
3406 ATTGACCC-AAATGATATTT-C-CTCAATTTTTGGCTAAAATACTCATA-AAAATATATAATTCA
64 ATTGACCCGAAA-G-T-TTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCA
* * * * * * *
3467 ACGCCGAAAACATTGAAGGGCTTTTGACGTTTCTAATATTGTTTTTCCTATTTCTTCCGA-TTTA
126 ACGCCAAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCTTCCGACTTAA
* *
3531 ATTTCTAATTAAATC-GAAACAAGATTCAGATGATCGTAAAAACAAATTCTTAAATCCAATGTGG
191 AATTCTAATTAAATCGGAAA-AAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
3595 CTGAGATCT-GATTAGATGAATATAGATATTTCAA-GTAGTCTCAAAGC-TAAAAATCATGCAAA
255 CTGAGATCTCGA-TAGATGAATACAGATATTTCAATG-AGTCTCAAAGCAAAAAAATCATACAAA
* * *
3657 ATTGAG-GTGAGTCCACGGAACGCATTTTTAGGCAAAAA-TTTAGATAGTTAGTACACGATTTCG
318 ACTGAGCG-GAGTCC-CGGAACGCATTTTTAGCCAAAAACTTT--ATAGTTAGTACACAATTTCG
* * ** *
3720 GCTAAAATTTTGGAAAAAATGACTCAAAATAT-TTCTCCTCAATTTTTGGCTAAAATACTCTTAA
379 GCTAAAATTTTGCAAAAAATGACCCAAAA-ATGTT-TCCTCAATTTTTGAATAAAATACTCATAA
* * * * *
3784 AAATATATAATTGAACGCCAAAAACATTGGAGGGCTTTCCATGCTTTTAATGGTCGTATTTCTTA
442 AAATATATAATTGAACGCCAAAAACATTGGAGGACTTTCCACGCTTTTAATGATCATATTTCATA
* * * * *
3849 TTTTTTCTAAATTAATTTCTAATTAAATGGAAACAAGATTTAGATGCTCGTAAAAAAAATTCTTA
507 TTTTTTCTAAATTAATTTATAAGTAAATCGAAACAAAATTCAGATGCTCGTAAAAAAAATTCTTA
3914 A
572 A
3915 ATCCTATGTT
Statistics
Matches: 2764, Mismatches: 345, Indels: 237
0.83 0.10 0.07
Matches are distributed among these distances:
651 4 0.00
652 5 0.00
653 146 0.05
654 175 0.06
655 90 0.03
656 57 0.02
657 4 0.00
658 5 0.00
659 8 0.00
660 242 0.09
661 328 0.12
662 134 0.05
663 297 0.11
664 134 0.05
665 231 0.08
666 340 0.12
667 466 0.17
668 89 0.03
669 1 0.00
670 4 0.00
671 4 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (652 bp):
GGAACACGTTTTTAGCCAAAAACCGTGATTAACGTACACGATTTCAGCTAAAATTTTGCAAAAAT
TGACCCGAAAGTTTTGCGCTCAATTTTTGGCCAAAATAATCATATAAAATATAAAACTCAACGCC
AAAAACATTGAAGGGCCTTTCACGCTTCTAATATTATTTTTCCAATTTCTTCCGACTTAAAATTC
TAATTAAATCGGAAAAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
TCTCGATAGATGAATACAGATATTTCAATGAGTCTCAAAGCAAAAAAATCATACAAAACTGAGCG
GAGTCCCGGAACGCATTTTTAGCCAAAAACTTTATAGTTAGTACACAATTTCGGCTAAAATTTTG
CAAAAAATGACCCAAAAATGTTTCCTCAATTTTTGAATAAAATACTCATAAAAATATATAATTGA
ACGCCAAAAACATTGGAGGACTTTCCACGCTTTTAATGATCATATTTCATATTTTTTCTAAATTA
ATTTATAAGTAAATCGAAACAAAATTCAGATGCTCGTAAAAAAAATTCTTAATTCAATGTGGCTG
AGATTTGATTTGATGTATATGGACATCTCAAGGATTCTTGGTGCCAAAAATCATGCAAAACTGAA
TT
Found at i:4316 original size:15 final size:16
Alignment explanation
Indices: 4298--4327 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4288 ATAAATATTA
4298 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
4313 ATATTATAATCTAAA
1 ATATTATAATCTAAA
4328 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:4878 original size:42 final size:42
Alignment explanation
Indices: 4809--4893 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
4799 GACAGATCCG
4809 AATTAATCTAGGGTAAAAAATATATATATAATCCAACAATTA
1 AATTAATCTAGGGTAAAAAATATATATATAATCCAACAATTA
* * *
4851 AATTGATCTGGGGTAAAAAGTATATATATAATCCAACAATTA
1 AATTAATCTAGGGTAAAAAATATATATATAATCCAACAATTA
4893 A
1 A
4894 CACAATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (42 bp):
AATTAATCTAGGGTAAAAAATATATATATAATCCAACAATTA
Found at i:14603 original size:11 final size:11
Alignment explanation
Indices: 14587--14618 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
14577 GCTCGATTAA
14587 TGTTCGTTTAG
1 TGTTCGTTTAG
*
14598 TGTTCGTTTAT
1 TGTTCGTTTAG
14609 TGTTCGTTTA
1 TGTTCGTTTA
14619 ATAGATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (11 bp):
TGTTCGTTTAG
Found at i:14701 original size:23 final size:27
Alignment explanation
Indices: 14649--14698 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
14639 TTATGTTCGT
14649 TTATATTATATATTATATATATAATAA
1 TTATATTATATATTATATATATAATAA
*
14676 TTATATT-TTTATT-TATATA-AATA
1 TTATATTATATATTATATATATAATA
14699 TTAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 5 0.23
27 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATTATATATTATATATATAATAA
Found at i:14747 original size:40 final size:41
Alignment explanation
Indices: 14663--14749 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 41
14653 ATTATATATT
* *
14663 ATATATATAATAATTATATTTTTATTTATATAAATATTAAA
1 ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
*
14704 ATATGTAT-ATAATTATA-TTTTATTCCATAT-AATATAAATA
1 ATATATATAATAATTATATTTTTATT-CATATAAATATAAA-A
14744 ATATAT
1 ATATAT
14750 TTATTTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.35
40 19 0.47
41 7 0.17
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (41 bp):
ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
Found at i:19868 original size:38 final size:38
Alignment explanation
Indices: 19817--19890 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
19807 AATCCCTAAT
*
19817 AATCTCAAACATTAAAAGATAATAAGGAAAATTATTCC
1 AATCTCAAACATTAAAAAATAATAAGGAAAATTATTCC
19855 AATCTCAAACATTAAAAAATAATAAGGAAAATTATT
1 AATCTCAAACATTAAAAAATAATAAGGAAAATTATT
19891 TCATACACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (38 bp):
AATCTCAAACATTAAAAAATAATAAGGAAAATTATTCC
Found at i:23973 original size:21 final size:19
Alignment explanation
Indices: 23933--23987 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
23923 TTAGCAATTA
23933 TACAGATGAGATTATACTG
1 TACAGATGAGATTATACTG
*
23952 TACAGATTAGATTAGGTACTG
1 TACAGATGAGATTA--TACTG
*
23973 TACATATGAGATTAT
1 TACAGATGAGATTAT
23988 TAGAGCAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 14 0.45
21 17 0.55
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (19 bp):
TACAGATGAGATTATACTG
Found at i:24509 original size:21 final size:21
Alignment explanation
Indices: 24483--24522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24473 ACTAATGGAC
24483 TTTCCTTTCATCATTTTTTTT
1 TTTCCTTTCATCATTTTTTTT
**
24504 TTTCCTTTTTTCATTTTTT
1 TTTCCTTTCATCATTTTTT
24523 CAAATTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCCTTTCATCATTTTTTTT
Done.