Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012436.1 Corchorus capsularis cultivar CVL-1 contig12457, 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: 17383
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:1959 original size:641 final size:639
Alignment explanation
Indices: 5--2936 Score: 3339
Period size: 641 Copynumber: 4.6 Consensus size: 639
1 CAAG
* * *
5 AAAATGAGGAAAAACTTTTCGGGTCAACTTTTAGCCGAAATCGTGTACTAACCATCACATTTTTT
1 AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACA-GTTTT
** * * * * * * *
70 TCCCTCAAAATGCGTTTCGGGGCCCCGGCAT-AATTTTTCATGATTTTTGGCAGAAAGACTCTTT
65 TGGCTAAAAACGCATTTCGGGGCCCCAGC-TCAATTTTGCATGATTTTTGGCTGAAAGACTCCTT
* ** *
134 GAAATATCTATATTCATATAACCAAATGTCAGCCAATTTAGATTTTATTATTTGATTTTACGAGC
129 GAAATATCTATATTCATATAACCAAATCTCAGCCAATTT-GATTTTAGGATTTGTTTTTACGAGC
* * *
199 ATCTCAATCTTGTTTCGATTTAATTTGAAATAAATTCAGAAAAAAATTGG-AAAATGATATTGGA
193 ATCTAAATCTTGTTTCGATTTAATTT-AAATAAATTAAGAAAAAAA-TGGAAAAACGATATTGGA
* * *
263 AGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTCTATAT-TTTCTTAGAGTTGTGTGGCA
256 AGCGTGAAAAACCCTTCAA-TTTTTTT-G-GTTGAATTATATATATTT-TTAAAGTAGTGTGGCA
* * *
327 AAAAAATGAAGAAAAAGTTTTCGGGTCAATTTTTAGTCGAAATC-GT-GT----ATCACGGTTTT
317 AAAAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCG-AATCTGTACTAAAAATCACGG-TTT
* * * * * * * * *
386 TTTGCTAAAAACGCGTTTCGTGGCCCCGGCTTAATTTTGCATGATTTTCGGCAGAAAAACTCATT
380 TTCGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
* * * *
451 GAAATATCTATATTCGTATAATCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGC
445 GAAATATCTATATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACGAGC
* * ** * *
516 AT-TCAATCTTGTCTCGATTTAATTTGATATAAATTCTGGAAAAAAAAATGGGAAAACGATATTG
510 ATCTCAATTTTGT-TCGATTTAATTTGAAATAAATTC-AAAAAAAAAAAAGGAAAAACGATATTG
* * * *
580 GAAGCGTGAAAAAACTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTTCGAGTTGTGTGGCA
573 GAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCA
645 AA
638 AA
* * * **
647 CAAATGA-GAAAGAAGTTTTCAGGTCAGTTTTTAATCGAAATCGTGTACTAACCATCACAGTTTT
1 AAAATGAGGAAA-AAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTT
* * * * * * *
711 TAGCTTGAAAACGCGTTTTGGGGCCCCAGCT-AAGTTTTGCATGATTATTGACTGAAAGACCCCT
65 TGGC-TAAAAACGCATTTCGGGGCCCCAGCTCAA-TTTTGCATGATTTTTGGCTGAAAGACTCCT
*
775 TGAAATATCTATATTCATAT-ACAAAAATCTCAGCCAATTTAGATTTTAGGATTT-TTTTTACGA
128 TGAAATATCTATATTCATATAAC-CAAATCTCAGCCAATTT-GATTTTAGGATTTGTTTTTACGA
* *
838 GCATCTGAAATCTTGTTTCGATTTAATTATAAATAAATT-CGAAAATAAATTGAAAAACGATATT
191 GCATCT-AAATCTTGTTTCGATTTAATT-TAAATAAATTAAGAAAA-AAATGGAAAAACGATATT
* * * *
902 GGAAGCGTGAAAAAGCCTTCAATTTTTTTGTGTGTTGAATTATATATTTTTTTAAAGTATTCTGG
253 GGAAGCGTGAAAAACCCTTCAA-TTTTTT-TG-GTTGAATTATATATATTTTTAAAGTAGTGTGG
* * * * *
967 CAAAAAAAT-A-GAAAATATTTTTCGGGTTATTTTTTAGTCGATTTCGTGTACT---AATCA---
315 CAAAAAAATGAGGAAAA-AGTTTTCGGGTCAATTTTTAGCCGA-ATC-TGTACTAAAAATCACGG
*
1024 ----T--C-----ACG-GTTTTGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
377 TTTTTCGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
*
1077 CTTGAAATATCTGTATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACG
442 CTTGAAATATCTATATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACG
**
1142 AGCATCTCAATTTTGTTCGATTTAATTTGAAATAAATTCTGAAAAAAAAAATGGGAAAAACGATA
507 AGCATCTCAATTTTGTTCGATTTAATTTGAAATAAATTC--AAAAAAAAAAAAGGAAAAACGATA
* * *
1207 TTGGAAGCGTAGAAAAAAACCTTCAATTTTGTTGGCGTTGAA-T-TATATTTTTTTAGAGTTATG
570 TTGGAAGCGT-G-AAAAACCCTTCAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTG
1270 TGGCAAA
633 TGGCAAA
* ** *
1277 CAAATGA-GAAAGAAGTTTTCGGGTCAGA-TTTTAATCGAAATCGTTTACTAACCATCACAGTTT
1 AAAATGAGGAAA-AAGTTTTCGGGTCA-ATTTTTAGCCGAAATCGTGTACTAACCATCACAGTTT
* * * *
1340 TTGGCTAGAAAACGTATTTTGGGGCCCCAGCT-AAGTTTTGCATGATTTTTGACTGAAAGACCCC
64 TTGGCTA-AAAACGCATTTCGGGGCCCCAGCTCAA-TTTTGCATGATTTTTGGCTGAAAGACTCC
*
1404 TTGAAATATCTATATTCATAT-ACAAAAATCTCAGCCAATTTAGATTTTAGGATTT-TTTTTACG
127 TTGAAATATCTATATTCATATAAC-CAAATCTCAGCCAATTT-GATTTTAGGATTTGTTTTTACG
* *
1467 AGCATCTGAAATCTTGTTTCGATTTAATTATAAATAAATT-TGAAAAAAATTGAAAAACGATATT
190 AGCATCT-AAATCTTGTTTCGATTTAATT-TAAATAAATTAAGAAAAAAATGGAAAAACGATATT
* *
1531 GGAAGCGTGAAAAAGCCTTCAATTTTTTT-GTTGAATTATATATATTTTTAAAGTAGTGTGGGAA
253 GGAAGCGTGAAAAACCCTTCAATTTTTTTGGTTGAATTATATATATTTTTAAAGTAGTGTGGCAA
* * *
1595 AAAAAT-A-GAAAATATTTTTCTGGTTAATTTTTAGCCG-AT-TGTACTAATAAAATCACGGTTT
318 AAAAATGAGGAAAA-AGTTTTCGGGTCAATTTTTAGCCGAATCTGTACT-A-AAAATCACGGTTT
1656 TTCGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
380 TTCGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
* *
1721 AAAATATCTATATCCATATAACCAAATCTCAGCTAATTTGGGTTTCATTATTTGTTTTTACGAGC
445 GAAATATCTATATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACGAGC
*
1786 ATCTCAATTTTGTTCGATTTAATTTGAAATAAATTCAAACAAAAAAAAAGGAAAAACGATATTTG
510 ATCTCAATTTTGTTCGATTTAATTTGAAATAAATTCAAA-AAAAAAAAAGGAAAAACGATATTGG
* *
1851 AAGAGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGAA
574 AAGCGTGAAAAACCCTTCAA-TTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCA
1916 AA
638 AA
*
1918 AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
1 AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * * * * * *
1983 TGCTAAAAACGCATTTCGGGGCCCCGGCTCAATTCTGCATGATTTTCGGCAGAAAGGCTCCTTAA
66 GGCTAAAAACGCATTTCGGGGCCCCAGCTCAATTTTGCATGATTTTTGGCTGAAAGACTCCTTGA
* * ** *
2048 AATATCTATATTCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGCTTTTACGAGCAT
131 AATATCTATATTCATATAACCAAATCTCAGCCAATTT-GATTTTAGGATTTGTTTTTACGAGCAT
* * * * *
2113 CTCAATTTTG-TTCGATTTAATTTGAAATAAATTCAAACACAAAAAAAGGAAAAACGATATTTGA
195 CTAAATCTTGTTTCGATTTAATTT-AAATAAATT--AAGA-AAAAAATGGAAAAACGATATTGGA
* * * *
2177 AGCGTGAAAAAACCCTTCAATTTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCA
256 AGCGTG-AAAAACCCTTCAA-TTTTTTT-G-GTTGAATTATATATATTTTTAAAGTAGTGTGGCA
** *
2242 AAAAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATTACGGTTT
317 AAAAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCG-AATC-TGTACTAAAAATCACGGTTT
* * * * * * * * * *
2307 TTTGCTAAAAATGCATTTCGGGGCCTCGGCTCAATTTTGCATGATTTTCGGCAG-AACACTCCTT
380 TTCGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
* * *
2371 GAAATATCTATATTCATATAACCAAATCTCAGCCAA-TTAGATTTCATTATTTGTTTTTACGAGC
445 GAAATATCTATATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACGAGC
* *** * *
2435 ATCTCAATCTTGTTTCGATTTAATTTGAAATAAATT--TGGAAAAAAAATGAGAAAACAATATTG
510 ATCTCAATTTTG-TTCGATTTAATTTGAAATAAATTCAAAAAAAAAAAAGGA-AAAACGATATTG
2498 GAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCA
573 GAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCA
2563 AA
638 AA
* * * *
2565 TAAATGAGGAAAAAGATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAAAACCATAACTGTTT
1 AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACT--AACCATCACAGTTT
* * * * *
2630 TTGGCTAAAAACGCGTTTCGTGGCCCCAGCTCAATTTTGCATGATTTTTGGGTGAATGACTCGTT
64 TTGGCTAAAAACGCATTTCGGGGCCCCAGCTCAATTTTGCATGATTTTTGGCTGAAAGACTCCTT
* * *
2695 GAAATATCTATACTCATATAACCAAATCTCAGCCAATTTGAAATTTAGGATTTGTTTTTACTAGC
129 GAAATATCTATATTCATATAACCAAATCTCAGCCAATTTG-ATTTTAGGATTTGTTTTTACGAGC
* * **
2760 ATCTAATATCTTATTTCGATTTAATTCGAAATAAATTCGGAAAAAAATGGAAAAACGATATTGGA
193 ATCTAA-ATCTTGTTTCGATTTAATT-TAAATAAATTAAGAAAAAAATGGAAAAACGATATTGGA
* ****** * *
2825 AGCGTGAAAAATCCTTCAA-TTAAAAAATT-AAATAGTATAT-TTTTTCAGAGTAGTGTGGCAAA
256 AGCGTGAAAAACCCTTCAATTTTTTTGGTTGAATTA-TATATATTTTT-AAAGTAGTGTGGCAAA
* *
2887 AAAATGAGAAAAAAGTTTTCGGGTCAATTTTTAGTCGATATCATGTACTA
319 AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGA-ATC-TGTACTA
2937 TTAGAAAGCT
Statistics
Matches: 2004, Mismatches: 208, Indels: 155
0.85 0.09 0.07
Matches are distributed among these distances:
621 6 0.00
623 1 0.00
625 65 0.03
626 5 0.00
627 1 0.00
628 6 0.00
629 167 0.08
630 290 0.14
631 2 0.00
632 27 0.01
633 1 0.00
635 2 0.00
637 1 0.00
638 13 0.01
639 40 0.02
640 133 0.07
641 308 0.15
642 256 0.13
643 101 0.05
644 13 0.01
645 13 0.01
647 114 0.06
648 95 0.05
649 185 0.09
650 74 0.04
651 78 0.04
652 1 0.00
653 6 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (639 bp):
AAAATGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTT
GGCTAAAAACGCATTTCGGGGCCCCAGCTCAATTTTGCATGATTTTTGGCTGAAAGACTCCTTGA
AATATCTATATTCATATAACCAAATCTCAGCCAATTTGATTTTAGGATTTGTTTTTACGAGCATC
TAAATCTTGTTTCGATTTAATTTAAATAAATTAAGAAAAAAATGGAAAAACGATATTGGAAGCGT
GAAAAACCCTTCAATTTTTTTGGTTGAATTATATATATTTTTAAAGTAGTGTGGCAAAAAAATGA
GGAAAAAGTTTTCGGGTCAATTTTTAGCCGAATCTGTACTAAAAATCACGGTTTTTCGCTAAAAA
CGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTAT
ATCCATATAACCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTT
GTTCGATTTAATTTGAAATAAATTCAAAAAAAAAAAAGGAAAAACGATATTGGAAGCGTGAAAAA
CCCTTCAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAA
Found at i:2350 original size:326 final size:322
Alignment explanation
Indices: 1036--2936 Score: 2321
Period size: 325 Copynumber: 5.9 Consensus size: 322
1026 ACGGTTTTGA
* * *
1036 GGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTGTATCCATATAA
1 GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
*
1101 CCAAATCTCAGCTAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
66 CCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
*
1166 ATTTGAAATAAATTCTGAA-AAAAAAAATGGGAAAAACGATATTGGAAGCGTAGAAAAAAACCTT
131 ATTTGAAATAAATTC--AAGAAAAAAAA--GGAAAAACGATATTGGAAGCGT-G-AAAAACCCTT
* * *
1230 CAATTTTGTTGGCGTTGAA-T-TATATTTTTTTAGAGTTATGTGGCAAACAAATGA-GAAAGAAG
190 CAATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAA-AAG
** * * *
1292 TTTTCGGGTCAGA-TTTTAATCGAAATCGTTTACTAACCATCACAGTTTTTGGCTAGAAAACGTA
254 TTTTCGGGTCA-ATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA-AAAACGCA
*
1356 TTTTGG
317 TTTCGG
* *
1362 GGCCCCAGCT-AAGTTTTGCATGATTTTTGACTGAAAGACCCCTTGAAATATCTATATTCATAT-
1 GGCCCCAGCTCAA-TTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATA
* * * ** * *
1425 ACAAAAATCTCAGCCAATTTAGATTTTAGGATTT-TTTTTACGAGCATCTGAAATCTTGTTTCGA
65 AC-CAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCT-CAATTTTG-TTCGA
* ** *
1489 TTTAATTAT-AAATAAATT--TGAAAAAAATTGAAAAACGATATTGGAAGCGTGAAAAAGCCTTC
127 TTTAATT-TGAAATAAATTCAAGAAAAAAAAGGAAAAACGATATTGGAAGCGTGAAAAACCCTTC
* * * * * *
1551 AATTTTTTT---GTTGAATTATATATATTTTTAAAGTAGTGTGGGAAAAAAAT-A-GAAAATATT
191 AATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAA-AGT
* * ** * *
1611 TTTCTGGTTAATTTTTAGCCG--AT--TGTACTAATAAAATCACGGTTTTTCGCTAAAAACGCGT
255 TTTCGGGTCAATTTTTAGCCGAAATCGTGTACT-A-ACCATCACGGTTTTTGGCTAAAAACGCAT
*
1672 TTCGA
318 TTCGG
* * *
1677 GGCCCCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTTAAAATATCTATATCCATATAA
1 GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
* *
1742 CCAAATCTCAGCTAATTTGGGTTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
66 CCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
* * *
1807 ATTTGAAATAAATTCAAACAAAAAAAAAGGAAAAACGATATTTGAAGAGTGAAAAACCCTTCAAT
131 ATTTGAAATAAATTC-AA-GAAAAAAAAGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAA-
*
1872 TTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGAAAAAAAATGAGGAAAAAGTTTT
193 TTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTTT
*
1937 CGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCATTTCGG
258 CGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGG
* * * * * *
2002 GGCCCCGGCTCAATTCTGCATGATTTTCGGCAGAAAGGCTCCTTAAAATATCTATATTCATATAA
1 GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
* *
2067 CCAAATCTCAGCTAATTTGGATTTCATTATTTGCTTTTACGAGCATCTCAATTTTGTTCGATTTA
66 CCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
* *
2132 ATTTGAAATAAATTCAAACACAAAAAAAGGAAAAACGATATTTGAAGCGTGAAAAAACCCTTCAA
131 ATTTGAAATAAATTC-AAGA-AAAAAAAGGAAAAACGATATTGGAAGCGTG-AAAAACCCTTCAA
2197 TTTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTT
193 -TTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTT
* * *
2262 TCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATTACGGTTTTTTGCTAAAAATGCATTTCG
257 TCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCG
2327 G
322 G
* * * * *
2328 GGCCTCGGCTCAATTTTGCATGATTTTCGGCAG-AACACTCCTTGAAATATCTATATTCATATAA
1 GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
* *
2392 CCAAATCTCAGCCAA-TTAGATTTCATTATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTT
66 CCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTG-TTCGATTT
** * *
2456 AATTTGAAATAAATT-TGGAAAAAAAATGAGAAAACAATATTGGAAGCGTGAAAAACCCTTCAAT
130 AATTTGAAATAAATTCAAGAAAAAAAAGGA-AAAACGATATTGGAAGCGTGAAAAACCCTTCAAT
* *
2520 TTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAATAAATGAGGAAAAAGATTTC
194 TTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTTTC
* * *
2585 GGGTCAATTTTTAGCCGAAATCGTGTACTAAAACCATAACTGTTTTTGGCTAAAAACGCGTTTCG
259 GGGTCAATTTTTAGCCGAAATCGTGTACT--AACCATCACGGTTTTTGGCTAAAAACGCATTTCG
*
2650 T
322 G
*** * * *
2651 GGCCCCAGCTCAATTTTGCATGATTTTTGGGTGAATGACTCGTTGAAATATCTATACTCATATAA
1 GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
* ** * *
2716 CCAAATCTCAGCCAATTTGAAATTT-AGGATTTGTTTTTACTAGCATCT-AATATCTTATTTCGA
66 CCAAATCTCAGCCAATTTG-GATTTCATTATTTGTTTTTACGAGCATCTCAAT-T-TT-GTTCGA
* * * *
2779 TTTAATTCGAAATAAATTC-GGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAATCCTTCA
127 TTTAATTTGAAATAAATTCAAGAAAAAAAAGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCA
****** * ** * * *
2843 A---TTAAAAAATTAAATAGTATATTTTTTCAGAGTAGTGTGGCAAAAAAATGAGAAAAAAGTTT
192 ATTTTTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTT
* * *
2905 TCGGGTCAATTTTTAGTCGATATCATGTACTA
257 TCGGGTCAATTTTTAGCCGAAATCGTGTACTA
2937 TTAGAAAGCT
Statistics
Matches: 1385, Mismatches: 147, Indels: 92
0.85 0.09 0.06
Matches are distributed among these distances:
313 1 0.00
314 26 0.02
315 97 0.07
316 36 0.03
317 8 0.01
318 62 0.04
319 33 0.02
320 19 0.01
321 94 0.07
322 154 0.11
323 98 0.07
324 95 0.07
325 335 0.24
326 299 0.22
327 27 0.02
328 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (322 bp):
GGCCCCAGCTCAATTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATATAA
CCAAATCTCAGCCAATTTGGATTTCATTATTTGTTTTTACGAGCATCTCAATTTTGTTCGATTTA
ATTTGAAATAAATTCAAGAAAAAAAAGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTT
TTTTGGCGTTGAATTCTATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGGAAAAAGTTTTCGG
GTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGG
Found at i:3904 original size:40 final size:41
Alignment explanation
Indices: 3859--3969 Score: 125
Period size: 49 Copynumber: 2.5 Consensus size: 41
3849 CAACACGCGA
3859 AGACACGAAGATACACGAGAAG-CCGCAGTGAGGCGAGGCC
1 AGACACGAAGATACACGAGAAGCCCGCAGTGAGGCGAGGCC
*
3899 AGACACAAAGATACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGATACAC--G-AG--A-AG-C-CCGCAGTGAGGCGAGGCC
*
3948 AGACACGAAGGTACACGAGAAG
1 AGACACGAAGATACACGAGAAG
3970 ACACACAACA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
40 15 0.25
42 1 0.02
43 4 0.07
44 1 0.02
45 1 0.02
46 4 0.07
47 1 0.02
49 32 0.54
ACGTcount: A:0.38, C:0.24, G:0.32, T:0.06
Consensus pattern (41 bp):
AGACACGAAGATACACGAGAAGCCCGCAGTGAGGCGAGGCC
Found at i:3991 original size:68 final size:68
Alignment explanation
Indices: 3917--4261 Score: 622
Period size: 68 Copynumber: 5.1 Consensus size: 68
3907 AGATACACGA
3917 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
3982 CAC
66 CAC
*
3985 GAAGAC--AGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGCGAAGACACACAACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
4048 CAC
66 CAC
* *
4051 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACGATACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
4116 CAC
66 CAC
* **
4119 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACATGAGAAGACACATGACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
4184 CAC
66 CAC
4187 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
4252 CAC
66 CAC
4255 GAAGACA
1 GAAGACA
4262 GACACAAAGG
Statistics
Matches: 265, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
66 65 0.25
68 200 0.75
ACGTcount: A:0.38, C:0.29, G:0.27, T:0.06
Consensus pattern (68 bp):
GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
CAC
Found at i:4156 original size:37 final size:37
Alignment explanation
Indices: 4115--4227 Score: 96
Period size: 37 Copynumber: 3.2 Consensus size: 37
4105 CACACGATAC
4115 ACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
* * * * * * * *
4152 ACACGAAG--GTA-CAT--G-AG-AAGACACATGACAC
1 ACACGAAGACATAGCCTCCGCAGTGAGGC-GAGGCCAG
4183 ACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
4220 ACACGAAG
1 ACACGAAG
4228 GTACACGAGA
Statistics
Matches: 52, Mismatches: 16, Indels: 16
0.62 0.19 0.19
Matches are distributed among these distances:
30 3 0.06
31 14 0.27
32 1 0.02
33 2 0.04
34 4 0.08
35 2 0.04
36 1 0.02
37 22 0.42
38 3 0.06
ACGTcount: A:0.35, C:0.27, G:0.29, T:0.08
Consensus pattern (37 bp):
ACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
Done.