Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010012.1 Corchorus capsularis cultivar CVL-1 contig10033, 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: 19113
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:1343 original size:22 final size:22
Alignment explanation
Indices: 1318--1421 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 22
1308 AAATGAAGTA
1318 TTCATACGAAATTATGATAACG
1 TTCATACGAAATTATGATAACG
**
1340 TTCATATTAAATTATGATAA--
1 TTCATACGAAATTATGATAACG
* * * *
1360 TT-ACAC-TATTTTTGATAACG
1 TTCATACGAAATTATGATAACG
* * * *
1380 TCCTTACGAAATTTTGATAACC
1 TTCATACGAAATTATGATAACG
* *
1402 TTCCTATGAAATTATGATAA
1 TTCATACGAAATTATGATAA
1422 TTACTATATT
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
18 9 0.15
19 2 0.03
20 3 0.05
21 2 0.03
22 45 0.74
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (22 bp):
TTCATACGAAATTATGATAACG
Found at i:1419 original size:62 final size:62
Alignment explanation
Indices: 1322--1476 Score: 222
Period size: 62 Copynumber: 2.5 Consensus size: 62
1312 GAAGTATTCA
* * * *
1322 TACGAAATTATGATAACGTTCATATTAAATTATGATAATTAC-ACTATTTTTGATAACGTCCT
1 TACGAAATTTTGATAACATTCCTATGAAATTATGATAATTACTA-TATTTTTGATAACGTCCT
* * *
1384 TACGAAATTTTGATAACCTTCCTATGAAATTATGATAATTACTATATTTTTTATGACGTCCT
1 TACGAAATTTTGATAACATTCCTATGAAATTATGATAATTACTATATTTTTGATAACGTCCT
*
1446 TATGAAATTTTGATAACATTCCTATGAAATT
1 TACGAAATTTTGATAACATTCCTATGAAATT
1477 TCAATAACGA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 83 0.99
63 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (62 bp):
TACGAAATTTTGATAACATTCCTATGAAATTATGATAATTACTATATTTTTGATAACGTCCT
Found at i:1471 original size:22 final size:21
Alignment explanation
Indices: 1369--1939 Score: 132
Period size: 22 Copynumber: 26.3 Consensus size: 21
1359 ATTACACTAT
* *
1369 TTTTGATAACGTCCTTACGAAA
1 TTTTGATAACTTCC-TATGAAA
1391 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAA-CTTCCTATGAAA
* * *
1413 TTATGATAA-TTACTAT--AT
1 TTTTGATAACTTCCTATGAAA
* * *
1431 TTTTTATGACGTCCTTATGAAA
1 TTTTGATAACTTCC-TATGAAA
1453 TTTTGATAACATTCCTATGAAA
1 TTTTGATAAC-TTCCTATGAAA
** * * *
1475 TTTCAATAACGATACTATGGAA
1 TTTTGATAAC-TTCCTATGAAA
* * **
1497 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAA-CTTCCTATGAAA
* *
1518 TTTTGTTTTAACCTTCTTATGAAA
1 TTTTG--ATAA-CTTCCTATGAAA
* * * * *
1542 TTTTGTTTACCTCCCTAAGGAA
1 TTTTG-ATAACTTCCTATGAAA
*
1564 TTTTGA-AGACCTCACTATGAAA
1 TTTTGATA-ACTTC-CTATGAAA
*
1586 TTTTGATAACTTCCAAATGAAA
1 TTTTGATAACTTCC-TATGAAA
**
1608 TTTTGATAACCAACACTAT-AAGA
1 TTTTGATAA-CTTC-CTATGAA-A
* * * *
1631 TGTTGATAGCCTCCATATGATA
1 TTTTGATAACTTCC-TATGAAA
*
1653 TATTGATAA--TCACGTTATGAAA
1 TTTTGATAACTTC-C--TATGAAA
* * * * *
1675 ATTTAAAAACCTCAATATG-AA
1 TTTTGATAACTTC-CTATGAAA
* * * *
1696 TTGTCAGTAA-TCACACTCTGAAA
1 TTTTGA-TAACT-TC-CTATGAAA
*
1719 TTTTGATAA-TCACACTATGAAA
1 TTTTGATAACT-TC-CTATGAAA
* * *
1741 TTGTGATAACCTCGTTATGAAA
1 TTTTGATAACTTC-CTATGAAA
*
1763 TTTTGATAAATCTTCCTATAAAA
1 TTTTGAT-AA-CTTCCTATGAAA
* * *
1786 TTCTGATAAATCTCCCTATAAAA
1 TTTTGAT-AA-CTTCCTATGAAA
*
1809 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACTTCC-TATGAAA
* *
1831 TCTTGATAA----CTA-CAAA
1 TTTTGATAACTTCCTATGAAA
* **
1847 TTTTGATAACCTCCCTATGATT
1 TTTTGATAA-CTTCCTATGAAA
* * *
1869 TTTTGATAACCTCATTATGAGA
1 TTTTGATAACTTC-CTATGAAA
* *
1891 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAA-CTTCCTATGAAA
* * *
1913 TTTTGATATCCTCC-CTGAAA
1 TTTTGATAACTTCCTATGAAA
1933 TTTTGAT
1 TTTTGAT
1940 TACTCCATAA
Statistics
Matches: 404, Mismatches: 107, Indels: 78
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 8 0.02
19 2 0.00
20 24 0.06
21 27 0.07
22 236 0.58
23 79 0.20
24 15 0.04
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (21 bp):
TTTTGATAACTTCCTATGAAA
Found at i:1531 original size:23 final size:24
Alignment explanation
Indices: 1504--1549 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1494 GAATTTCGAG
*
1504 AACCTTTTTAT-AAATTTTGTTTT
1 AACCTTCTTATGAAATTTTGTTTT
1527 AACCTTCTTATGAAATTTTGTTT
1 AACCTTCTTATGAAATTTTGTTT
1550 ACCTCCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (24 bp):
AACCTTCTTATGAAATTTTGTTTT
Found at i:2054 original size:22 final size:22
Alignment explanation
Indices: 2021--2119 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
2011 GAAGTACCAC
*
2021 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGGTAACCAC-TT
* * *
2044 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGGTAACCACTT
* *
2065 TATGAAATTTTGGTAACCGCTC
1 TATGAAATTTTGGTAACCACTT
* * * *
2087 TATAAAATTTTGTTGACC-CTC
1 TATGAAATTTTGGTAACCACTT
2108 TATGAAATTTTG
1 TATGAAATTTTG
2120 ATAATCAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 17 0.27
22 45 0.71
23 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACTT
Found at i:2074 original size:21 final size:21
Alignment explanation
Indices: 2045--2123 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
2035 AATCACATTT
* *
2045 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACC-CTCTA
*
2067 TGAAATTTTGGTAACCGCTCTA
1 TGAAATTTTGATAACC-CTCTA
* * *
2089 TAAAATTTTGTTGACCCTCTA
1 TGAAATTTTGATAACCCTCTA
2110 TGAAATTTTGATAA
1 TGAAATTTTGATAA
2124 TCAAATTATA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 16 0.34
22 31 0.66
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACCCTCTA
Found at i:2311 original size:37 final size:37
Alignment explanation
Indices: 2224--2317 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 37
2214 CTAAGCTCGG
* * *
2224 ATAGGACGTTGGAGACGAAGACAAAAAGCAAAATTAA
1 ATAGGACGTTGGAAACAAAGACAAAAAGAAAAATTAA
** * *
2261 ATATAAAGATTGGAAACAAAGACAAAAGGAAAAATTAA
1 ATAGGACG-TTGGAAACAAAGACAAAAAGAAAAATTAA
2299 ATAGGACGTTGGAAACAAA
1 ATAGGACGTTGGAAACAAA
2318 AAGTTAAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
37 16 0.35
38 30 0.65
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (37 bp):
ATAGGACGTTGGAAACAAAGACAAAAAGAAAAATTAA
Found at i:5483 original size:31 final size:31
Alignment explanation
Indices: 5425--5483 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
5415 AAGACCATTC
* **
5425 AAATATCGTGTAACATAATTTTCAAAAAAAA
1 AAATATCGTGTAACATAACTTAAAAAAAAAA
* *
5456 AAATATCTTGTAACATACCTTAAAAAAA
1 AAATATCGTGTAACATAACTTAAAAAAA
5484 TGCAAAAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (31 bp):
AAATATCGTGTAACATAACTTAAAAAAAAAA
Found at i:5626 original size:53 final size:53
Alignment explanation
Indices: 5568--5673 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
5558 GATTTACAGG
*
5568 GTAAGTCCCTAAATTTAGGACATTAATTTACCAGAATTTTAAAAATTGTAGGA
1 GTAAGTCCCTAAATTTAGAACATTAATTTACCAGAATTTTAAAAATTGTAGGA
*
5621 GTAAGTCCCTAAATTTAGAACATTAATTTGCCAGAATTTTAAAAATTGTAGGA
1 GTAAGTCCCTAAATTTAGAACATTAATTTACCAGAATTTTAAAAATTGTAGGA
5674 AAAAATTTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (53 bp):
GTAAGTCCCTAAATTTAGAACATTAATTTACCAGAATTTTAAAAATTGTAGGA
Found at i:6847 original size:437 final size:435
Alignment explanation
Indices: 6074--6930 Score: 1130
Period size: 437 Copynumber: 2.0 Consensus size: 435
6064 TTAAATCGAA
* * *
6074 TAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGTATGAAGGTCATTTGATAACT
1 TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAAGGTCATTTGATAAAT
* * *
6139 AATTATGATAAGAAAATATTTCTTAATAGATATCTTGAAACATAAAAATTCCCTTTTGAACCCTT
66 AATTATAATAAGAAAATATTTCTTAATAGAGATCTTGAAACATAAAAATTCCATTTTGAACCCTT
* * * * *
6204 CATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAGATCATACAGTAACC
131 CATGAAACTCGTAGATAAAATTAACTTTCGGATCCTTCATGAAAGTCGTAAATCATACAATAACC
* * * * *** *
6269 TTTTAACTGACACTTGAATAACTTTAATCGGACATATGGATTGAAAATTATATGGTATTAAATAG
196 TTTTAACTGAAACTTCAATAACTTCAATCGGACATATAGACAAAAAATTATATGATATTAAATAG
* * * * *
6334 ACCAACAATCGAAACGAAAAATTTAGAAAGCATTTTTTTGAATTAAAACATAAAAGTTTACTATT
261 ACCAACAATCAAAACCAAAAATTTAGAAAGCATTTTTTAGAATCAAAACATAAAAGTTGACTATT
* * *
6399 GAGCCCTTCATGAAAGTTGTAGATCATGAAATTACTTTTTAATAGACA-TATGAATCAACTTAAC
326 GAGCCCTTCATGAAAATTGTAGATCATGAAATTACCTTTCAATAGACACT-TGAATCAACTTAAC
6463 CAGACAAATA-GAACAAATAATAAAAAAATAAATCTTAAACGTTAGAT
390 CAGACAAATAGGAA-AAA-AATAAAAAAATAAATCTTAAACGTTAGAT
* * *
6510 TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCATTTGATAAAT
1 TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAAGGTCATTTGATAAAT
* * * * *
6575 AATCTA-AATAAGAAAATGTTTGTTAAT-GAAGATCTTGAAGCATAAAAATTCCATTTTGAGCTC
66 AAT-TATAATAAGAAAATATTTCTTAATAG-AGATCTTGAAACATAAAAATTCCATTTTGAACCC
*
6638 TTCATGAAACTCGTAGATAAAATTTAACTTTCGGATCCTTCATGAAAGTCGTAAATCATGCAATA
129 TTCATGAAACTCGTAGATAAAA-TTAACTTTCGGATCCTTCATGAAAGTCGTAAATCATACAATA
* * *
6703 TCCTTTTAACTGAAACTTCAATAACTTCAATCGGACATGTATACAAAAAATTATATGATATTAAA
193 ACCTTTTAACTGAAACTTCAATAACTTCAATCGGACATATAGACAAAAAATTATATGATATTAAA
* ** * * * *
6768 TTGACCGGCAATCAAAACCACAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAA-TTGGC
258 TAGACCAACAATCAAAACCAAAAATTTAGAAAGCATTTTTTAGAATCAAAACA-TAAAAGTTGAC
* ** * *
6832 TTTTGAGTTCTTCATGAAAATTGTAGATGATGAAATTACCTTTCAATAGACACTTGAATCACCTT
322 TATTGAGCCCTTCATGAAAATTGTAGATCATGAAATTACCTTTCAATAGACACTTGAATCAACTT
* * *
6897 AATCAGATAAATAGGAAAAAAATACAAAAATAAA
387 AACCAGACAAATAGGAAAAAAATAAAAAAATAAA
6931 AGTCAACGCG
Statistics
Matches: 361, Mismatches: 54, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
435 1 0.00
436 143 0.40
437 208 0.58
438 9 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (435 bp):
TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAAGGTCATTTGATAAAT
AATTATAATAAGAAAATATTTCTTAATAGAGATCTTGAAACATAAAAATTCCATTTTGAACCCTT
CATGAAACTCGTAGATAAAATTAACTTTCGGATCCTTCATGAAAGTCGTAAATCATACAATAACC
TTTTAACTGAAACTTCAATAACTTCAATCGGACATATAGACAAAAAATTATATGATATTAAATAG
ACCAACAATCAAAACCAAAAATTTAGAAAGCATTTTTTAGAATCAAAACATAAAAGTTGACTATT
GAGCCCTTCATGAAAATTGTAGATCATGAAATTACCTTTCAATAGACACTTGAATCAACTTAACC
AGACAAATAGGAAAAAAATAAAAAAATAAATCTTAAACGTTAGAT
Found at i:10442 original size:22 final size:21
Alignment explanation
Indices: 10417--11016 Score: 348
Period size: 22 Copynumber: 27.8 Consensus size: 21
10407 TGTCACATTT
10417 TATGAAATTTTGGTAACTACAC
1 TATGAAATTTTGGTAACT-CAC
*
10439 TATGAAATTTTGGTAATCTGAC
1 TATGAAATTTTGGTAA-CTCAC
*
10461 TATGAAATTTTGGTAACCTCAT
1 TATGAAATTTTGGTAA-CTCAC
*
10483 TATGAAATTTGGGTAACGTCAC
1 TATGAAATTTTGGTAAC-TCAC
* * * *
10505 TATAAAAATTCTGGCAACCTTC-T
1 TAT-GAAATTTTGGTAA-C-TCAC
* * * *
10528 TATTAAATTTTAGTAACCCCC
1 TATGAAATTTTGGTAACTCAC
*
10549 TATGAAATTTTGGAAACCTC-C
1 TATGAAATTTTGGTAA-CTCAC
* *
10570 ATATGAAATTTTGGTTAC-CCC
1 -TATGAAATTTTGGTAACTCAC
* *
10591 TATGAAAATTTGGTAACAGCAC
1 TATGAAATTTTGGTAAC-TCAC
* *
10613 TATTAAATTTTTGTAACCTCAC
1 TATGAAATTTTGGTAA-CTCAC
* *
10635 TATGAAA-TTCGGATAAC-CCC
1 TATGAAATTTTGG-TAACTCAC
10655 TTATGAAATTTTGGTAACCTCAC
1 -TATGAAATTTTGGTAA-CTCAC
* * *
10678 AATTAAATTTTTGTAAGCTCAC
1 TATGAAATTTTGGTAA-CTCAC
* *
10700 TATGAAATTTTTGTAGCCTTC-C
1 TATGAAATTTTGGTA-AC-TCAC
* * *
10722 TATAAAATATTGGTAAC-CCC
1 TATGAAATTTTGGTAACTCAC
*
10742 TATGAAATATTGGTAACCTCAC
1 TATGAAATTTTGGTAA-CTCAC
* * *
10764 AATGAAATTTTGGTAATGTCTC
1 TATGAAATTTTGGTAA-CTCAC
* *
10786 TATGAAATTTTTGTAACCTCCC
1 TATGAAATTTTGGTAA-CTCAC
* * * *
10808 TGTGAAATTTTTGTAGCCTGAC
1 TATGAAATTTTGGTA-ACTCAC
*
10830 TATGAAATTGAT-GTAACCTCAC
1 TATGAAATT-TTGGTAA-CTCAC
10852 TATGAAAATTTT-GTAAACTCAC
1 TATG-AAATTTTGGT-AACTCAC
* *
10874 TAT--AATTTTGATAAC-CTAT
1 TATGAAATTTTGGTAACTC-AC
* * *
10893 TTTGAAATATTGGTAAC-CCC
1 TATGAAATTTTGGTAACTCAC
*
10913 ATATGAAATTTTGGTAACTTCCC
1 -TATGAAATTTTGGTAAC-TCAC
* *
10936 CATGAAATTTTGGTAAAC-CCC
1 TATGAAATTTTGGT-AACTCAC
* * *
10957 TATGAGATTTTAGTAACCCCAC
1 TATGAAATTTTGGTAA-CTCAC
*
10979 TAT-AAAATTTGGTAACCTCAC
1 TATGAAATTTTGGTAA-CTCAC
*
11000 TATGAAATTTTTGTAAC
1 TATGAAATTTTGGTAAC
11017 CCCCAATATT
Statistics
Matches: 452, Mismatches: 89, Indels: 75
0.73 0.14 0.12
Matches are distributed among these distances:
18 1 0.00
19 13 0.03
20 38 0.08
21 93 0.21
22 271 0.60
23 33 0.07
24 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGGTAACTCAC
Found at i:10467 original size:44 final size:43
Alignment explanation
Indices: 10417--11017 Score: 426
Period size: 44 Copynumber: 13.9 Consensus size: 43
10407 TGTCACATTT
* *
10417 TATGAAATTTTGGTAACTACACTATGAAATTTTGGTAATCTGAC
1 TATGAAATTTTGGTAACT-CACTATGAAATTTTGGTAACCTCAC
* * *
10461 TATGAAATTTTGGTAACCTCATTATGAAATTTGGGTAACGTCAC
1 TATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACCTCAC
* * * * * * *
10505 TATAAAAATTCTGGCAACCTTC-TTATTAAATTTTAGTAACC-CCC
1 TAT-GAAATTTTGGTAA-C-TCACTATGAAATTTTGGTAACCTCAC
* *
10549 TATGAAATTTTGGAAACCTC-CATATGAAATTTTGGTTACC-C-C
1 TATGAAATTTTGGTAA-CTCAC-TATGAAATTTTGGTAACCTCAC
* * * *
10591 TATGAAAATTTGGTAACAGCACTATTAAATTTTTGTAACCTCAC
1 TATGAAATTTTGGTAAC-TCACTATGAAATTTTGGTAACCTCAC
* *
10635 TATGAAA-TTCGGATAAC-CCCTTATGAAATTTTGGTAACCTCAC
1 TATGAAATTTTGG-TAACTCAC-TATGAAATTTTGGTAACCTCAC
* * * * *
10678 AATTAAATTTTTGTAAGCTCACTATGAAATTTTTGTAGCCTTC-C
1 TATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACC-TCAC
* * * *
10722 TATAAAATATTGGTAAC-CCCTATGAAATATTGGTAACCTCAC
1 TATGAAATTTTGGTAACTCACTATGAAATTTTGGTAACCTCAC
* * * * *
10764 AATGAAATTTTGGTAATGTCTCTATGAAATTTTTGTAACCTCCC
1 TATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACCTCAC
* * * * *
10808 TGTGAAATTTTTGTAGCCTGACTATGAAATTGAT-GTAACCTCAC
1 TATGAAATTTTGGTA-ACTCACTATGAAATT-TTGGTAACCTCAC
* *
10852 TATGAAAATTTT-GTAAACTCACTAT--AATTTTGATAACCT-AT
1 TATG-AAATTTTGGT-AACTCACTATGAAATTTTGGTAACCTCAC
* * * * *
10893 TTTGAAATATTGGTAAC-CCCATATGAAATTTTGGTAACTTCCC
1 TATGAAATTTTGGTAACTCAC-TATGAAATTTTGGTAACCTCAC
* * * * *
10936 CATGAAATTTTGGTAAAC-CCCTATGAGATTTTAGTAACCCCAC
1 TATGAAATTTTGGT-AACTCACTATGAAATTTTGGTAACCTCAC
* *
10979 TAT-AAAATTTGGTAACCTCACTATGAAATTTTTGTAACC
1 TATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACC
11018 CCCAATATTC
Statistics
Matches: 439, Mismatches: 88, Indels: 61
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.00
40 12 0.03
41 12 0.03
42 98 0.22
43 111 0.25
44 160 0.36
45 42 0.10
46 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGGTAACTCACTATGAAATTTTGGTAACCTCAC
Found at i:10621 original size:42 final size:42
Alignment explanation
Indices: 10528--10641 Score: 113
Period size: 42 Copynumber: 2.6 Consensus size: 42
10518 GCAACCTTCT
* **
10528 TATTAAATTTTAGTAACCCCCTATGAAATTTTGGAAACCTCCA
1 TATTAAATTTTAGTAA-CCCCTATGAAAATTTGGAAACAGCCA
* * * *
10571 TATGAAATTTTGGTTACCCCTATGAAAATTTGGTAACAG-CA
1 TATTAAATTTTAGTAACCCCTATGAAAATTTGGAAACAGCCA
*
10612 CTATTAAATTTTTGTAACCTCACTATGAAA
1 -TATTAAATTTTAGTAACC-C-CTATGAAA
10642 TTCGGATAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.03
42 34 0.59
43 14 0.24
44 8 0.14
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (42 bp):
TATTAAATTTTAGTAACCCCTATGAAAATTTGGAAACAGCCA
Found at i:10621 original size:64 final size:62
Alignment explanation
Indices: 10417--11017 Score: 290
Period size: 64 Copynumber: 9.3 Consensus size: 62
10407 TGTCACATTT
* ** *
10417 TATGAAATTTTGGTAA-CTACACTATGAAATTTTGGTAATCTGACTATGAAATTTTGGTAACCTC
1 TATGAAATTTTGGTAACCT-CACTATGAAATTTTGGTTA-C-CCCTATGAAAATTTGGTAA-C-C
*
10481 AT
61 AC
* * * * ** * * * * *
10483 TATGAAATTTGGGTAACGTCACTATAAAAATTCTGGCAACCTTCTTATTAAATTTTAGTAACCCC
1 TATGAAATTTTGGTAACCTCACTAT-GAAATTTTGGTTACC--CCTATGAAAATTTGGTAA-CCA
10548 C
62 C
*
10549 TATGAAATTTTGGAAACCTC-CATATGAAATTTTGGTTACCCCTATGAAAATTTGGTAACAGCAC
1 TATGAAATTTTGGTAACCTCAC-TATGAAATTTTGGTTACCCCTATGAAAATTTGGTAAC--CAC
* * * * *
10613 TATTAAATTTTTGTAACCTCACTATGAAA-TTCGGATAACCCCTTATGAAATTTTGGTAACCTCA
1 TATGAAATTTTGGTAACCTCACTATGAAATTTTGG-TTACCCC-TATGAAAATTTGGTAA-C-CA
10677 C
62 C
* * * * * *
10678 AATTAAATTTTTGTAAGCTCACTATGAAATTTTTG-TAGCCTTCCTAT-AAAATATTGGTAACCC
1 TATGAAATTTTGGTAACCTCACTATGAAATTTTGGTTA-CC--CCTATGAAAAT-TTGGTAACCA
10741 C
62 C
* * ** * * * *
10742 TATGAAATATTGGTAACCTCACAATGAAATTTTGGTAATGTCTCTATGAAATTTTTGTAACCTCC
1 TATGAAATTTTGGTAACCTCACTATGAAATTTTGGT--TACCCCTATGAAAATTTGGTAA-C-CA
10807 C
62 C
* * * * * * *
10808 TGTGAAATTTTTGTAGCCTGACTATGAAATTGAT-GTAACCTCACTATGAAAATTTTGTAAACTC
1 TATGAAATTTTGGTAACCTCACTATGAAATT-TTGGTTACC-C-CTATGAAAATTTGGT-AAC-C
10872 AC
61 AC
* * * * * * *
10874 TAT--AATTTTGATAACCT-ATTTTGAAATATTGGTAACCCCATATGAAATTTTGGTAACTTCCC
1 TATGAAATTTTGGTAACCTCACTATGAAATTTTGGTTACCCC-TATGAAAATTTGGTAAC--CAC
* * * *
10936 CATGAAATTTTGGTAAACC-C-CTATGAGATTTTAGTAACCCCACTAT-AAAATTTGGTAACCTC
1 TATGAAATTTTGGT-AACCTCACTATGAAATTTTGGTTA-CCC-CTATGAAAATTTGGTAA-C-C
10998 AC
61 AC
*
11000 TATGAAATTTTTGTAACC
1 TATGAAATTTTGGTAACC
11018 CCCAATATTC
Statistics
Matches: 414, Mismatches: 85, Indels: 75
0.72 0.15 0.13
Matches are distributed among these distances:
61 4 0.01
62 20 0.05
63 36 0.09
64 131 0.32
65 81 0.20
66 109 0.26
67 33 0.08
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (62 bp):
TATGAAATTTTGGTAACCTCACTATGAAATTTTGGTTACCCCTATGAAAATTTGGTAACCAC
Found at i:10761 original size:86 final size:85
Alignment explanation
Indices: 10418--11017 Score: 413
Period size: 86 Copynumber: 6.9 Consensus size: 85
10408 GTCACATTTT
* * **
10418 ATGAAATTTTGGT-AACTACACTATGAAATTTTGGTAATCTGACTATGAAATTTTGGTAACCTCA
1 ATGAAATTTTGGTAAACT-CACTATGAAATTTTTGTAACCTTCCTATGAAA-TTTGGTAACC-C-
* * * *
10482 TTATGAAATTTGGGTAACGTCACT
62 CTATGAAATTTTGGTAACCTCACA
* * * * * * * * *
10506 ATAAAAATTCTGGCAACCTTC-TTATTAAATTTTAGTAACC-CCCTATGAAATTTTGGAAACCTC
1 AT-GAAATTTTGGTAAAC-TCACTATGAAATTTTTGTAACCTTCCTATGAAA-TTTGGTAACC-C
* *
10569 CATATGAAATTTTGGTTACC-C-CT
62 C-TATGAAATTTTGGTAACCTCACA
* * * *
10592 ATGAAAATTTGGT-AACAGCACTATTAAATTTTTGTAACC-TCACTATGAAATTCGGATAACCCC
1 ATGAAATTTTGGTAAAC-TCACTATGAAATTTTTGTAACCTTC-CTATGAAATTTGG-TAACCCC
10655 TTATGAAATTTTGGTAACCTCACA
63 -TATGAAATTTTGGTAACCTCACA
* * * * *
10679 ATTAAATTTTTGTAAGCTCACTATGAAATTTTTGTAGCCTTCCTATAAAATATTGGTAACCCCTA
1 ATGAAATTTTGGTAAACTCACTATGAAATTTTTGTAACCTTCCTATGAAAT-TTGGTAACCCCTA
*
10744 TGAAATATTGGTAACCTCACA
65 TGAAATTTTGGTAACCTCACA
** * * * * * *
10765 ATGAAATTTTGGTAATGTCTCTATGAAATTTTTGTAACCTCCCTGTGAAATTTTTGTAGCCTGAC
1 ATGAAATTTTGGTAAACTCACTATGAAATTTTTGTAACCTTCCTATGAAA-TTTGGTAACC--CC
* *
10830 TATGAAATTGAT-GTAACCTCACT
63 TATGAAATT-TTGGTAACCTCACA
*
10853 ATGAAAATTTT-GTAAACTCACTAT--AA-TTTTGATAACCTAT--TTTGAAATATTGGTAACCC
1 ATG-AAATTTTGGTAAACTCACTATGAAATTTTTG-TAACCT-TCCTATGAAAT-TTGGTAACCC
* * *
10912 CATATGAAATTTTGGTAACTTCCCC
62 C-TATGAAATTTTGGTAACCTCACA
* * * * *
10937 ATGAAATTTTGGTAAAC-CCCTATGAGATTTTAGTAACC-CCACTATAAAATTTGGTAACCTCAC
1 ATGAAATTTTGGTAAACTCACTATGAAATTTTTGTAACCTTC-CTATGAAATTTGGTAACC-C-C
*
11000 TATGAAATTTTTGTAACC
63 TATGAAATTTTGGTAACC
11018 CCCAATATTC
Statistics
Matches: 406, Mismatches: 75, Indels: 64
0.74 0.14 0.12
Matches are distributed among these distances:
83 14 0.03
84 30 0.07
85 81 0.20
86 122 0.30
87 48 0.12
88 76 0.19
89 31 0.08
90 3 0.01
91 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (85 bp):
ATGAAATTTTGGTAAACTCACTATGAAATTTTTGTAACCTTCCTATGAAATTTGGTAACCCCTAT
GAAATTTTGGTAACCTCACA
Found at i:10881 original size:108 final size:107
Alignment explanation
Indices: 10682--11017 Score: 252
Period size: 108 Copynumber: 3.1 Consensus size: 107
10672 CCTCACAATT
* **
10682 AAATTTTTGTAAGCTCACTATGAAATTTTTGTAGCCTTCCTATAAAATATTGGTAACCCCTATGA
1 AAATTTTTGTAACCTCACTATGAAATTTTTGTAGCCTGACTATAAAATATTGGTAACCCCTATGA
*
10747 AATATTGGTAACCTCACAATGAAATTTTGGTAATGTCTCTATG
66 AATATTGGTAAACTCACAAT-AAATTTTGGTAATGTCTCTATG
* * *
10790 AAATTTTTGTAACCTCCCTGTGAAATTTTTGTAGCCTGACTAT-GAA-ATTGATGTAACCTCACT
1 AAATTTTTGTAACCTCACTATGAAATTTTTGTAGCCTGACTATAAAATATTG--GTAACC-C-CT
* * * ** * *
10853 ATGAAA-ATTTTGTAAACTCACTAT-AATTTTGATAACCTAT-TTTG
62 ATGAAATA-TTGGTAAACTCACAATAAATTTTGGTAATGTCTCTATG
* * * * * * ** * * *
10897 AAATATTGGTAACCCCA-TATGAAATTTTGGTAACTTCCCCATGAAATTTTGGTAAACCCCTATG
1 AAATTTTTGTAACCTCACTATGAAATTTTTGTAGCCTGACTATAAAATATTGGT-AACCCCTATG
* * * * * * * ** *
10961 AGATTTTAGTAACCCCACTATAAAATTTGGTAACCTCACTATG
65 AAATATTGGTAAACTCACAATAAATTTTGGTAATGTCTCTATG
11004 AAATTTTTGTAACC
1 AAATTTTTGTAACC
11018 CCCAATATTC
Statistics
Matches: 178, Mismatches: 39, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
105 20 0.11
106 37 0.21
107 39 0.22
108 59 0.33
109 2 0.01
110 21 0.12
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (107 bp):
AAATTTTTGTAACCTCACTATGAAATTTTTGTAGCCTGACTATAAAATATTGGTAACCCCTATGA
AATATTGGTAAACTCACAATAAATTTTGGTAATGTCTCTATG
Found at i:11511 original size:86 final size:85
Alignment explanation
Indices: 11406--11727 Score: 273
Period size: 86 Copynumber: 3.8 Consensus size: 85
11396 TGTCCTATGG
* * * *
11406 AATTTTACTAACCTCCTTATGAAATTTTGGTAACCTCACAATCAAATTTTTGTAACCTCCCTATA
1 AATTTTAGTAACCTCCCTATGAAATTTTGGTAACCTCACAATGAAATTTTTGTAACCTCCCTATG
11471 AAATTTTGGTAACCCCCTAGA
66 AAATTTTGGTAA-CCCCTAGA
* * * ** * * * *
11492 AATGTTCGTAACCTCCTTATGAAATTTCAGTAACCTTA-ATATGAAAATTTGGTAACCTCACTAT
1 AATTTTAGTAACCTCCCTATGAAATTTTGGTAACCTCACA-ATGAAATTTTTGTAACCTCCCTAT
* *
11556 GAAATTTTGCTAA---AT-GA
65 GAAATTTTGGTAACCCCTAGA
* * * * * * * *
11573 AATTTTGGTAACATCCCGATGAAAATTTGATAACAC-C-CTATGAAATTTTTGTAAACTCCTTAT
1 AATTTTAGTAACCTCCCTATGAAATTTTGGTAAC-CTCACAATGAAATTTTTGTAACCTCCCTAT
*
11636 GAAATTTTAGTAACCCCTATGA
65 GAAATTTTGGTAACCCCTA-GA
* * * * * *
11658 AATTTTAGTAATCCTCCCTGTGAAATTTTGGTAACC-CCCTATGAAAATTTTGTAAACTTCCTAT
1 AATTTTAGTAA-CCTCCCTATGAAATTTTGGTAACCTCACAATGAAATTTTTGTAACCTCCCTAT
11722 GAAATT
65 GAAATT
11728 GTTGTCTAAG
Statistics
Matches: 185, Mismatches: 41, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
80 30 0.16
81 27 0.15
82 2 0.01
83 1 0.01
85 15 0.08
86 110 0.59
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (85 bp):
AATTTTAGTAACCTCCCTATGAAATTTTGGTAACCTCACAATGAAATTTTTGTAACCTCCCTATG
AAATTTTGGTAACCCCTAGA
Found at i:11638 original size:43 final size:43
Alignment explanation
Indices: 11569--11725 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
11559 ATTTTGCTAA
* *
11569 ATGAAATTTTGGT-AACATCCCGATGAAAATTTGATAACACCCT
1 ATGAAATTTTTGTAAACATCCCTATGAAAATTTGATAAC-CCCT
* *
11612 ATGAAATTTTTGTAAAC-TCCTTATG-AAATTTTAGTAACCCCT
1 ATGAAATTTTTGTAAACATCCCTATGAAAATTTGA-TAACCCCT
* * * * * *
11654 ATGAAATTTTAGTAATCCTCCCTGTGAAATTTTGGTAACCCCCT
1 ATGAAATTTTTGTAAACATCCCTATGAAAATTTGATAA-CCCCT
* *
11698 ATGAAAATTTTGTAAAC-TTCCTATGAAA
1 ATGAAATTTTTGTAAACATCCCTATGAAA
11726 TTGTTGTCTA
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
42 26 0.28
43 40 0.43
44 27 0.29
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (43 bp):
ATGAAATTTTTGTAAACATCCCTATGAAAATTTGATAACCCCT
Found at i:11691 original size:145 final size:144
Alignment explanation
Indices: 11424--11713 Score: 320
Period size: 145 Copynumber: 2.0 Consensus size: 144
11414 TAACCTCCTT
* * *
11424 ATGAAATTTTGGTAACCTCACAATCAAATTTTTGTAACCTCCCTATAAAATTTTGGTAACCCCCT
1 ATGAAATTTTGGTAACATCACAATCAAATATTTGTAACCACCCTATAAAATTTTGGTAACCCCCT
* *
11489 AGAAATGTTCGTAACCTCCTTATGAAATTTCAGTAACCTTAATATGAAAATTTGGTAACCTCACT
66 AGAAATGTTAGTAACCTCCTTATGAAATTTCAGTAACCTCAATATGAAAATTTGGTAACC-CACT
11554 ATG-AAATTTTGCTAA
130 ATGAAAATTTTG-TAA
* * * * * *
11569 ATGAAATTTTGGTAACATCCCGATGAAA-ATTTGATAA-CACCCTATGAAATTTTTGTAAACTCC
1 ATGAAATTTTGGTAACATCACAATCAAATATTTG-TAACCACCCTATAAAATTTTGGT-AACCCC
* * * ** * *
11632 TTATGAAATTTTAGTAACC-CC-TATGAAATTTTAGTAATCCTCCCTGTGAAATTTTGGTAACCC
64 CTA-GAAATGTTAGTAACCTCCTTATGAAATTTCAGTAA-CCTCAATATGAAAATTTGGTAACCC
*
11695 CCTATGAAAATTTTGTAA
127 ACTATGAAAATTTTGTAA
11713 A
1 A
11714 CTTCCTATGA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
144 45 0.37
145 63 0.52
146 13 0.11
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (144 bp):
ATGAAATTTTGGTAACATCACAATCAAATATTTGTAACCACCCTATAAAATTTTGGTAACCCCCT
AGAAATGTTAGTAACCTCCTTATGAAATTTCAGTAACCTCAATATGAAAATTTGGTAACCCACTA
TGAAAATTTTGTAA
Found at i:11709 original size:22 final size:21
Alignment explanation
Indices: 11399--11727 Score: 190
Period size: 22 Copynumber: 15.5 Consensus size: 21
11389 AGATAATTGT
* **
11399 CCTATGGAATTTTACTAACCTC
1 CCTATGAAATTTTGGTAACC-C
*
11421 CTTATGAAATTTTGGTAACCTC
1 CCTATGAAATTTTGGTAACC-C
* * * *
11443 ACAATCAAATTTTTGTAACCTC
1 CCTATGAAATTTTGGTAACC-C
*
11465 CCTATAAAATTTTGGTAACCC
1 CCTATGAAATTTTGGTAACCC
* *
11486 CCTA-GAAATGTTCGTAACCTC
1 CCTATGAAATTTTGGTAACC-C
* ** *
11507 CTTATGAAATTTCAGTAACCTT
1 CCTATGAAATTTTGGTAACC-C
** *
11529 AATATGAAAATTTGGTAACCTC
1 CCTATGAAATTTTGGTAACC-C
* *
11551 ACTATGAAATTTTGCTAA---
1 CCTATGAAATTTTGGTAACCC
*
11569 ---ATGAAATTTTGGTAACATC
1 CCTATGAAATTTTGGTAAC-CC
* * * *
11588 CCGATGAAAATTTGATAACAC
1 CCTATGAAATTTTGGTAACCC
* *
11609 CCTATGAAATTTTTGTAAACTC
1 CCTATGAAATTTTGGT-AACCC
* *
11631 CTTATGAAATTTTAGTAA-CC
1 CCTATGAAATTTTGGTAACCC
*
11651 CCTATGAAATTTTAGTAATCCTC
1 CCTATGAAATTTTGGTAA-CC-C
*
11674 CCTGTGAAATTTTGGTAACCC
1 CCTATGAAATTTTGGTAACCC
**
11695 CCTATGAAAATTTT-GTAAACTT
1 CCTATG-AAATTTTGGT-AACCC
11717 CCTATGAAATT
1 CCTATGAAATT
11728 GTTGTCTAAG
Statistics
Matches: 244, Mismatches: 48, Indels: 31
0.76 0.15 0.10
Matches are distributed among these distances:
15 14 0.06
20 30 0.12
21 37 0.15
22 146 0.60
23 17 0.07
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
CCTATGAAATTTTGGTAACCC
Found at i:11726 original size:43 final size:43
Alignment explanation
Indices: 11591--11727 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 43
11581 TAACATCCCG
* * * *
11591 ATGAAAATTTGATAACACCCTATGAAATTTTTGTAAAC-TCCTT
1 ATGAAATTTTGGTAACCCCCTATGAAAATTTTGTAAACTTCC-T
* * *
11634 ATGAAATTTTAGTAA-CCCCTATG-AAATTTTAGTAATCCTCCCT
1 ATGAAATTTTGGTAACCCCCTATGAAAATTTT-GTAA-ACTTCCT
*
11677 GTGAAATTTTGGTAACCCCCTATGAAAATTTTGTAAACTTCCT
1 ATGAAATTTTGGTAACCCCCTATGAAAATTTTGTAAACTTCCT
11720 ATGAAATT
1 ATGAAATT
11728 GTTGTCTAAG
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
41 6 0.08
42 11 0.14
43 39 0.51
44 14 0.18
45 7 0.09
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (43 bp):
ATGAAATTTTGGTAACCCCCTATGAAAATTTTGTAAACTTCCT
Done.