Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024679.1 Corchorus olitorius cultivar O-4 contig24712, 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: 60407
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:8478 original size:36 final size:36
Alignment explanation
Indices: 8438--8551 Score: 142
Period size: 36 Copynumber: 3.1 Consensus size: 36
8428 AGGAGCTAAA
*
8438 AAAAAATGGACCTAAAATAGAAAGAGGTCGAAAGAG
1 AAAAAATGGACCTAAAATAGAAAGAGGTCGAAAAAG
*
8474 AAAAACTGGACCTAAAATAGAAAGAGGTC-AAAAAG
1 AAAAAATGGACCTAAAATAGAAAGAGGTCGAAAAAG
* *
8509 AAAAAACTTGG-CCTAAAACAGAGAGAGGTCAGAAAAAAG
1 AAAAAA--TGGACCTAAAATAGAAAGAGGTC-G-AAAAAG
8548 AAAA
1 AAAA
8552 TAAATAAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
35 10 0.15
36 45 0.66
37 3 0.04
39 10 0.15
ACGTcount: A:0.57, C:0.11, G:0.22, T:0.11
Consensus pattern (36 bp):
AAAAAATGGACCTAAAATAGAAAGAGGTCGAAAAAG
Found at i:9439 original size:59 final size:59
Alignment explanation
Indices: 9372--10058 Score: 1144
Period size: 59 Copynumber: 11.6 Consensus size: 59
9362 CTTCCTTTTC
* *
9372 TGTTTTTAAAAATCCTGTTCGAGGTCTCTGTTATAGAGTTTTCAATTCAAAATCCTATCT
1 TGTTTTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
*
9432 TG-TTTTAAAATCATGTTCGAGGTCTCTGTTAGAGAGTTTTTCAATTCAAAATCTTATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAG-TTTTCAATTCAAAATCTTATCT
* * *
9491 TGTTCTTAAAATCTTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
9550 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
* * **
9609 TGTTTTCAAAATCCTGTTCGAGGTCTTTGTTAGAGAGTTTTCAATTCAAAATCACATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
9668 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
* * *
9727 TGTTTTTAAAATCCAGTTCGAGCTCTCTGTTAGAGAGTTTTCAATTCAAAATCTGATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
*
9786 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
*
9845 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATCTTATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
* *
9904 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTCAGAGAGTTTTCAATTCAAAATCTTATTT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
* * *
9963 TGTTTTTAAAATCCTGTTCGAGGTCTCCGTTAGAGAGTTTTCAATTGAAAATTTTATCT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
* *
10022 TG-TTTTAAAATCCTGGTCGAGGTCTCTGTTTGAGAGT
1 TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
10059 CTATATTTCT
Statistics
Matches: 588, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
58 60 0.10
59 494 0.84
60 34 0.06
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (59 bp):
TGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCT
Found at i:10373 original size:29 final size:29
Alignment explanation
Indices: 10295--10450 Score: 117
Period size: 29 Copynumber: 5.4 Consensus size: 29
10285 TTGACCATTC
* *
10295 GCACGCTC-AGGGGCATTTTGGCCA-TTTT
1 GCACACTCTAGGGGCA-TTTGGTCATTTTT
* *
10323 GCACA-TCCAGAGGCATTTTGGTCATTTTT
1 GCACACTCTAGGGGCA-TTTGGTCATTTTT
* *
10352 GCATA-TCTAGGGGTATTATGGTCATTTTT
1 GCACACTCTAGGGGCATT-TGGTCATTTTT
* * *
10381 GCACA-TCCAAGGGCATTTTGGTCATCTTT
1 GCACACTCTAGGGGCA-TTTGGTCATTTTT
* *
10410 ACACATTCT-GGGGCAGTTTGGTCATTTTT
1 GCACACTCTAGGGGCA-TTTGGTCATTTTT
*
10439 GCATACTCTAGG
1 GCACACTCTAGG
10451 TTCTCTTTGG
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.02
28 20 0.20
29 74 0.73
30 6 0.06
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (29 bp):
GCACACTCTAGGGGCATTTGGTCATTTTT
Found at i:10396 original size:58 final size:58
Alignment explanation
Indices: 10304--10441 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
10294 CGCACGCTCA
* * * * *
10304 GGGGCATTTTGGCCA-TTTTGCACATCCAGAGGCATTTTGGTCATTTTTGCATA-TCT
1 GGGGCAGTTTGGTCATTTTTGCACATCCAGAGGCATTTTGGTCATCTTTACACATTCT
*
10360 AGGGGTA-TTATGGTCATTTTTGCACATCCA-AGGGCATTTTGGTCATCTTTACACATTCT
1 -GGGGCAGTT-TGGTCATTTTTGCACATCCAGA-GGCATTTTGGTCATCTTTACACATTCT
10419 GGGGCAGTTTGGTCATTTTTGCA
1 GGGGCAGTTTGGTCATTTTTGCA
10442 TACTCTAGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
56 2 0.03
57 11 0.16
58 52 0.74
59 5 0.07
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (58 bp):
GGGGCAGTTTGGTCATTTTTGCACATCCAGAGGCATTTTGGTCATCTTTACACATTCT
Found at i:15637 original size:21 final size:22
Alignment explanation
Indices: 15613--15653 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
15603 TTTACGTAAG
15613 TTTGTCCATTTTTT-TTTTGGA
1 TTTGTCCATTTTTTATTTTGGA
*
15634 TTTGTGCATTTTTTATTTTG
1 TTTGTCCATTTTTTATTTTG
15654 AATGTTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.10, C:0.07, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTGTCCATTTTTTATTTTGGA
Found at i:15646 original size:22 final size:21
Alignment explanation
Indices: 15613--15653 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15603 TTTACGTAAG
*
15613 TTTGTCCATTTTTTTTTTGGA
1 TTTGTCCATTTTTATTTTGGA
*
15634 TTTGTGCATTTTTTATTTTG
1 TTTGTCCA-TTTTTATTTTG
15654 AATGTTGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.10, C:0.07, G:0.15, T:0.68
Consensus pattern (21 bp):
TTTGTCCATTTTTATTTTGGA
Found at i:17433 original size:16 final size:16
Alignment explanation
Indices: 17412--17443 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17402 AAAAGGAGAT
17412 TAATATAATGAATTTA
1 TAATATAATGAATTTA
*
17428 TAATATAATGACTTTA
1 TAATATAATGAATTTA
17444 ATACCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TAATATAATGAATTTA
Found at i:18343 original size:455 final size:451
Alignment explanation
Indices: 17487--18397 Score: 1639
Period size: 455 Copynumber: 2.0 Consensus size: 451
17477 TTAAGTACGA
17487 TTTATGTAAAGATATCAGATGGCAGCTTTTTAACTTAAGAATACCTCTCAAGAGTCAGTTTTTAA
1 TTTATGTAAAGATATCAGATGGCAGCTTTTTAACTTAAGAATACCTCTCAAGAGTCAGTTTTTAA
*
17552 ACTTTTTCGCCTCATGATTCTAACTTTAAACTCCTTTAAATATATTTATCAAAACGCAGAAGCTA
66 ACATTTTCGCCTCATGATTCTAACTTTAAACTCCTTTAAATATATTTATCAAAACGCAGAAGCTA
* *
17617 AGAGTTGTCAAGAAAGTTAAGCAATAATAAGCTGTGAAGAAAATTTGATTATTCCAACAAAAAAC
131 AGAGTTGTCAAGAAAGTTAAGCAATAATAAGCTGTGAAGAAAAATTGACTATTCCAACAAAAAAC
17682 AGAAACATTAAGACTAAACAAACTTACCCAGCTATGATTGAAAGGCTTTTAGATTCTAAAACTTA
196 AGAAACATTAAGACTAAACAAACTTACCCAGCTATGATTGAAAGGCTTTTAGATTCTAAAACTTA
17747 AAAATTCTTCAAAAAAATTAACCATTATGAATTTATAATAACGACTTTAATACCAATCAAATGGA
261 AAAATTCTTCAAAAAAATTAACCATTATGAATTTATAATAACGACTTTAATACCAATCAAATGGA
*
17812 ACAGGTTAATTGGAGATTTAAGTACGATTTATGTAAAGATATAGGATGGCTAACTTTTTTAACTT
326 ACAGGTTAATTGGAGATTTAAGTACGATTTATGTAAAGATATAGGATGACTAACTTTTTTAACTT
17877 TTCAAAATCTAAAACTAGAAAAAAATTCTTCAAATTCCAATGTTTAGTGGACATTAATTTCACC
391 TTCAAAATCTAAAACT-G-AAAAAATTCTTCAAATTCCAATGTTTAGTGGACATTAA-TTCACC
17941 TTTATGTAAAGATATCAGATGGCAGCTTTTTAACTTAAGAATACCTCTCAAGAGTCAGTTTTTAA
1 TTTATGTAAAGATATCAGATGGCAGCTTTTTAACTTAAGAATACCTCTCAAGAGTCAGTTTTTAA
** *
18006 ACATTTTCGCCTCATGATTCTAACTTTAAACTTGTTTAAATATATTTATCAAAACGCAGAAGTTA
66 ACATTTTCGCCTCATGATTCTAACTTTAAACTCCTTTAAATATATTTATCAAAACGCAGAAGCTA
18071 AGAAGTTGTCAAGAAAGTTAAGCAATAATAAGCTGTGAAGAAAAATTGACTATTCCAACAAAAAA
131 AG-AGTTGTCAAGAAAGTTAAGCAATAATAAGCTGTGAAGAAAAATTGACTATTCCAACAAAAAA
*
18136 TAGAAACATTAAGACTAAACAAACTTACCCAGCTATGATTGAAAGGCTTTTAGATTCTAAAAACT
195 CAGAAACATTAAGACTAAACAAACTTACCCAGCTATGATTGAAAGGCTTTTAGATTCT-AAAACT
* *
18201 TAAAAAATT-TTCAAAAAAAATTAACCGTTATGAATTTATAATAATGACTTTAATACCAATCAAA
259 T-AAAAATTCTTC-AAAAAAATTAACCATTATGAATTTATAATAACGACTTTAATACCAATCAAA
18265 TGGAACAGGTTAATTGGAGATTTAAGTACGATTTATGTAAAGATATAGGATGAC-AAC-TTTTTA
322 TGGAACAGGTTAATTGGAGATTTAAGTACGATTTATGTAAAGATATAGGATGACTAACTTTTTTA
*
18328 ACTTTTCAGAATCTAAAACTGAAAAAATTCTTCAAATTCCAATGTTTAGTGGACATTAATTCACC
387 ACTTTTCAAAATCTAAAACTGAAAAAATTCTTCAAATTCCAATGTTTAGTGGACATTAATTCACC
18393 TTTAT
1 TTTAT
18398 TTATAATAAT
Statistics
Matches: 442, Mismatches: 11, Indels: 10
0.95 0.02 0.02
Matches are distributed among these distances:
452 11 0.02
453 38 0.09
454 129 0.29
455 142 0.32
456 13 0.03
457 109 0.25
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (451 bp):
TTTATGTAAAGATATCAGATGGCAGCTTTTTAACTTAAGAATACCTCTCAAGAGTCAGTTTTTAA
ACATTTTCGCCTCATGATTCTAACTTTAAACTCCTTTAAATATATTTATCAAAACGCAGAAGCTA
AGAGTTGTCAAGAAAGTTAAGCAATAATAAGCTGTGAAGAAAAATTGACTATTCCAACAAAAAAC
AGAAACATTAAGACTAAACAAACTTACCCAGCTATGATTGAAAGGCTTTTAGATTCTAAAACTTA
AAAATTCTTCAAAAAAATTAACCATTATGAATTTATAATAACGACTTTAATACCAATCAAATGGA
ACAGGTTAATTGGAGATTTAAGTACGATTTATGTAAAGATATAGGATGACTAACTTTTTTAACTT
TTCAAAATCTAAAACTGAAAAAATTCTTCAAATTCCAATGTTTAGTGGACATTAATTCACC
Found at i:20267 original size:2 final size:2
Alignment explanation
Indices: 20260--20305 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
20250 AGGGCGTTTC
* * *
20260 AT AT AT AT AT AC AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20302 AT AT
1 AT AT
20306 GTATGTTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:20280 original size:16 final size:16
Alignment explanation
Indices: 20259--20302 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
20249 AAGGGCGTTT
20259 CATATATATATACATA
1 CATATATATATACATA
20275 CATATATATATACATA
1 CATATATATATACATA
*
20291 TATATATATATA
1 CATATATATATA
20303 TATGTATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
CATATATATATACATA
Found at i:21430 original size:19 final size:19
Alignment explanation
Indices: 21393--21436 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
21383 TGAAATTAAC
21393 TAATTA-TTAATTAAATAA
1 TAATTATTTAATTAAATAA
* *
21411 TAATTATTTTATTGAATAA
1 TAATTATTTAATTAAATAA
*
21430 TTATTAT
1 TAATTAT
21437 CAAAAATCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTATTTAATTAAATAA
Found at i:23925 original size:19 final size:18
Alignment explanation
Indices: 23892--23927 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23882 TTGAAATTAT
*
23892 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
23910 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
23928 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:31530 original size:52 final size:52
Alignment explanation
Indices: 31469--31579 Score: 222
Period size: 52 Copynumber: 2.1 Consensus size: 52
31459 AATTCAAGGT
31469 TTTTTGGTGAATTAAGAAATTAAACTTAATTTGACCTAAACCTAAACTTCAA
1 TTTTTGGTGAATTAAGAAATTAAACTTAATTTGACCTAAACCTAAACTTCAA
31521 TTTTTGGTGAATTAAGAAATTAAACTTAATTTGACCTAAACCTAAACTTCAA
1 TTTTTGGTGAATTAAGAAATTAAACTTAATTTGACCTAAACCTAAACTTCAA
31573 TTTTTGG
1 TTTTTGG
31580 CTAAGTATGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTTTGGTGAATTAAGAAATTAAACTTAATTTGACCTAAACCTAAACTTCAA
Found at i:32931 original size:13 final size:13
Alignment explanation
Indices: 32913--32938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32903 CTTGGCATGA
32913 GTGATGATTTTTG
1 GTGATGATTTTTG
32926 GTGATGATTTTTG
1 GTGATGATTTTTG
32939 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:33332 original size:19 final size:18
Alignment explanation
Indices: 33295--33338 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
33285 TGAAATTAAG
33295 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
*
33313 TAATTATTATATTGAATAA
1 TAATTATTA-ATTAAATAA
*
33332 TTATTAT
1 TAATTAT
33339 AAAAAATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Found at i:57332 original size:439 final size:439
Alignment explanation
Indices: 56509--57336 Score: 1198
Period size: 439 Copynumber: 1.9 Consensus size: 439
56499 GGTCCCATTA
* * *
56509 TCCATAAACAAATCATTTTTTTGTCGAGATATTTATCGAATGATCGTCATACTCTTATGCTTTAT
1 TCCATAAACAAATCATTTTTTTGTCGAGATATTTATCAAATGATCCTCATACTCTTATACTTTAT
* *
56574 GTTATTTAATCATTTACAATTATGAGTTGGACGATTTAAGGCTTCGGTTTTTATTATTGTATTTT
66 GTTATTTAATCATTTACAATTATGAGTTGGACGATTTAACGCTTCGGTCTTTATTATTGTATTTT
* * *
56639 TTGTTCTATTTATCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTACAAC
131 TTGTTCTATTTATCCGATTAAGATGATCCAAGTGTCTATTAAAAGGTGATTTCAAGATCTACAAC
* * *
56704 TTTCATGAAGAACTCGGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTATGAAGTTTTAT
196 TTTCATGAAGAACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAAGGCTTATGAAATTTTAT
*
56769 GGTCTCAATTGCCGGTCTATCTAATATCGTATAATTTTCAGGCCACTTGTCCGATTGAGGTTGTT
261 GGTCTCAATTACCGGTCTATCTAATATCGTATAATTTTCAGGCCACTTGTCCGATTGAGGTTGTT
* * ** * *
56834 CAAGTGTCGGTCAAAAGTTTATTGTGTGATCTACGACTTTCATTAAGGGCCTAAAAGCTGAATTT
326 CAAGTGTCGCTCAAAAGGTTATTGCATGATCTAAGACTTTCATGAAGGGCCTAAAAGCTGAATTT
56899 AATTAATGAGTTTCATGGAGGGTTAAAGAGGGGATTTTTATGTTTCGTC
391 AATTAATGAGTTTCATGGAGGGTTAAAGAGGGGATTTTTATGTTTCGTC
* * * *
56948 TCCATAAACAAATTATTTTTTTGTTG-GATTATTTATCAAATGATCCTCATACTTTTCATATTTT
1 TCCATAAACAAATCATTTTTTTGTCGAGA-TATTTATCAAATGATCCTCATACTCTT-ATACTTT
* * * * *
57012 ATGTTATTTAATCCTTTACAATTATGGGTTGGACGATTTAACGTTTTGG-CTTTATTTTTGTATT
64 ATGTTATTTAATCATTTACAATTATGAGTTGGACGATTTAACGCTTCGGTCTTTATTATTGTATT
* *
57076 TTTTGTTCTATTTGTCCGATTAAGATGATCCAGGTGTCTATTAAAAGGTGATTTCAAGATCTACA
129 TTTTGTTCTATTTATCCGATTAAGATGATCCAAGTGTCTATTAAAAGGTGATTTCAAGATCTACA
* * * *
57141 ACTTTTATGAAGAACTCAGAAGCCAATTTTAATGTTTTGGTTCTACAAAAGGCTTCTGAAATTTT
194 ACTTTCATGAAGAACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAAGGCTTATGAAATTTT
* * *** * *
57206 GTGGTTTTGGTTACCGGTCTATTTAATATCGTATAATTTTC-GGTTCACTTGTCCGATTGAGGTT
259 ATGGTCTCAATTACCGGTCTATCTAATATCGTATAATTTTCAGG-CCACTTGTCCGATTGAGGTT
* *
57270 GTTCAAGTGTCAGCT-AAAAGGTTATTGCATGATTTAAGACTTTCATGAAGGAGCC-GAAAGCTG
323 GTTCAAGTGTC-GCTCAAAAGGTTATTGCATGATCTAAGACTTTCATGAAGG-GCCTAAAAGCTG
57333 AATT
386 AATT
57337 GTATTTACAG
Statistics
Matches: 342, Mismatches: 42, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
438 4 0.01
439 284 0.83
440 54 0.16
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (439 bp):
TCCATAAACAAATCATTTTTTTGTCGAGATATTTATCAAATGATCCTCATACTCTTATACTTTAT
GTTATTTAATCATTTACAATTATGAGTTGGACGATTTAACGCTTCGGTCTTTATTATTGTATTTT
TTGTTCTATTTATCCGATTAAGATGATCCAAGTGTCTATTAAAAGGTGATTTCAAGATCTACAAC
TTTCATGAAGAACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAAGGCTTATGAAATTTTAT
GGTCTCAATTACCGGTCTATCTAATATCGTATAATTTTCAGGCCACTTGTCCGATTGAGGTTGTT
CAAGTGTCGCTCAAAAGGTTATTGCATGATCTAAGACTTTCATGAAGGGCCTAAAAGCTGAATTT
AATTAATGAGTTTCATGGAGGGTTAAAGAGGGGATTTTTATGTTTCGTC
Found at i:59311 original size:18 final size:19
Alignment explanation
Indices: 59273--59311 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
59263 GTGCTTCCGT
59273 TGTGATGCTCCCACTTTCAA
1 TGTGATGCTCCCAC-TTCAA
*
59293 TGTGGTGCTCCCA-TTCAA
1 TGTGATGCTCCCACTTCAA
59311 T
1 T
59312 TCTGACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTGATGCTCCCACTTCAA
Found at i:59529 original size:31 final size:33
Alignment explanation
Indices: 59469--59530 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
59459 GATATCAACT
*
59469 ACTTTTTTTACTTGATTTATTATTTTTTTCTCTA
1 ACTTTTTTTA-TTGATTTATTATTCTTTTCTCTA
*
59503 ACTTTTTTT-TT-ATTTTTTATTCTTTTCT
1 ACTTTTTTTATTGATTTATTATTCTTTTCT
59531 TCTCCGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.58
32 2 0.08
34 9 0.35
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (33 bp):
ACTTTTTTTATTGATTTATTATTCTTTTCTCTA
Found at i:59943 original size:2 final size:2
Alignment explanation
Indices: 59936--59967 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59926 TTATATGCGA
59936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59968 TGTATTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.