Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024799.1 Corchorus olitorius cultivar O-4 contig24832, 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: 55405
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:546 original size:19 final size:19
Alignment explanation
Indices: 506--542 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
496 AATTTTTAAG
506 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
525 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
543 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:5329 original size:13 final size:13
Alignment explanation
Indices: 5308--5338 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5298 AGTCGTAAAC
*
5308 TTTTAATATTGAT
1 TTTTGATATTGAT
5321 TTTTGATATTGAT
1 TTTTGATATTGAT
5334 TTTTG
1 TTTTG
5339 GTGGCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (13 bp):
TTTTGATATTGAT
Found at i:15875 original size:2 final size:2
Alignment explanation
Indices: 15868--15906 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
15858 AAAAGTGTTA
15868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15907 CAAGTTAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18401 original size:2 final size:2
Alignment explanation
Indices: 18394--18431 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18384 TATAGTGCTT
18394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18432 GATTCATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23984 original size:49 final size:47
Alignment explanation
Indices: 23883--24024 Score: 180
Period size: 49 Copynumber: 3.0 Consensus size: 47
23873 GAGCGTGCCA
* * *
23883 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
23930 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* *
23979 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
24025 GGATTGCTTG
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
47 20 0.24
48 22 0.26
49 42 0.49
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:28547 original size:128 final size:128
Alignment explanation
Indices: 28319--28574 Score: 485
Period size: 128 Copynumber: 2.0 Consensus size: 128
28309 CACATAACAC
28319 AAGCCTCACTATAACAGGTTTGATGACTAGACTGAAAGTTTCATTACAGTCAAGTCCAGGTCTTT
1 AAGCCTCACTATAACAGGTTTGATGACTAGACTGAAAGTTTCATTACAGTCAAGTCCAGGTCTTT
*
28384 GGCTAAACCCCTTAGCAACAGGCCTGGCTTTGTATCTCAATACTGAACCATCTGAGTTTGTTT
66 GGCTAAACCCCTTAGCAACAAGCCTGGCTTTGTATCTCAATACTGAACCATCTGAGTTTGTTT
* *
28447 AAGCCTCACTGTAACAGGTTTGATGACTAGACTGAAAGTTTCATTACAGTCAAGTCCATGTCTTT
1 AAGCCTCACTATAACAGGTTTGATGACTAGACTGAAAGTTTCATTACAGTCAAGTCCAGGTCTTT
28512 GGCTAAACCCCTTAGCAACAAGCCTGGCTTTGTATCTCAATACTGAACCATCTGAGTTTGTTT
66 GGCTAAACCCCTTAGCAACAAGCCTGGCTTTGTATCTCAATACTGAACCATCTGAGTTTGTTT
28575 TGATCCGGAA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 125 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (128 bp):
AAGCCTCACTATAACAGGTTTGATGACTAGACTGAAAGTTTCATTACAGTCAAGTCCAGGTCTTT
GGCTAAACCCCTTAGCAACAAGCCTGGCTTTGTATCTCAATACTGAACCATCTGAGTTTGTTT
Found at i:31950 original size:125 final size:125
Alignment explanation
Indices: 31587--31950 Score: 647
Period size: 125 Copynumber: 2.9 Consensus size: 125
31577 TCTGATGCAC
* * *
31587 AACGCCGCTATATATAATCTTCTACAAATAATAGAAATTTGGTGAAACTAACAACACCATTTATT
1 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATT
* * * * *
31652 TGTTATGAATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTA
66 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTA
31712 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATT
1 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATT
31777 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTA
66 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTA
*
31837 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGTTGAAACTAAAAACACCATTTATT
1 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATT
31902 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCG
66 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCG
31951 TTTTCCATGA
Statistics
Matches: 230, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 230 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (125 bp):
AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATT
TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTA
Found at i:31951 original size:32 final size:32
Alignment explanation
Indices: 31909--31981 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
31899 ATTTGTTATG
* * *
31909 AATAGCGGCGTTTTTCATGACAGACGCCGCTA
1 AATAGTGGCGTTTTCCATGACAAACGCCGCTA
* *
31941 AATAGTGGCGTTTTCCATGATAAACGTCGCTA
1 AATAGTGGCGTTTTCCATGACAAACGCCGCTA
31973 AATAGTGGC
1 AATAGTGGC
31982 ACTTCTAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (32 bp):
AATAGTGGCGTTTTCCATGACAAACGCCGCTA
Found at i:32104 original size:156 final size:157
Alignment explanation
Indices: 31784--32106 Score: 576
Period size: 157 Copynumber: 2.1 Consensus size: 157
31774 ATTTGTTATG
* * * *
31784 AATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
1 AATAGTGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
*
31849 TTTAATCTTCTACAAACAATAGAAATTTGTTGAAACTAAAAACACCATTTATTTGTTATGAATAG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
31914 CGGCGTTTTTCATGACAGACGCCGCTA
131 CGGCGTTTTTCATGACAGACGCCGCTA
* *
31941 AATAGTGGCGTTTTCCATGATAAACGTCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
1 AATAGTGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
32006 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACT-AAAACACCATTTATTTGTTATGAATAG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
32070 CGGCGTTTTTCATGACAGACGCCGCTA
131 CGGCGTTTTTCATGACAGACGCCGCTA
32097 AATAGTGGCG
1 AATAGTGGCG
32107 CTTCTAAAGT
Statistics
Matches: 159, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 64 0.40
157 95 0.60
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (157 bp):
AATAGTGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
CGGCGTTTTTCATGACAGACGCCGCTA
Found at i:32166 original size:281 final size:282
Alignment explanation
Indices: 31659--32231 Score: 1094
Period size: 281 Copynumber: 2.0 Consensus size: 282
31649 ATTTGTTATG
31659 AATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
1 AATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
31724 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
31789 CGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAA
131 CGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAA
*
31854 TCTTCTACAAACAATAGAAATTTGTTGAAACTAAAAACACCATTTATTTGTTATGAATAGCGGCG
196 TCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAGCGGCG
*
31919 TTTTTCATGACAGACGCCGCTA
261 TTTTTCATGACAAACGCCGCTA
*
31941 AATAGTGGCGTTTTCCATGATAAACGTCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
1 AATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
32006 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACT-AAAACACCATTTATTTGTTATGAATAG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
32070 CGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAA
131 CGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAA
*
32135 TCTTTTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAGCGGCG
196 TCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAGCGGCG
*
32200 TTTTTCATGATAAACGCCGCTA
261 TTTTTCATGACAAACGCCGCTA
32222 AATAGTGGCG
1 AATAGTGGCG
32232 CTTCTAAAGT
Statistics
Matches: 286, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
281 185 0.65
282 101 0.35
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (282 bp):
AATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAG
CGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATATTTAA
TCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAATAGCGGCG
TTTTTCATGACAAACGCCGCTA
Found at i:32233 original size:125 final size:125
Alignment explanation
Indices: 31941--32399 Score: 787
Period size: 125 Copynumber: 3.7 Consensus size: 125
31931 GACGCCGCTA
* * * * *
31941 AATAGTGGCGTTTTCCATGATAAACGTCGCTAAATAGTGGCACTTCTAAAGTAAACGCCGCTATA
1 AATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
32006 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACT-AAAACACCATTTATTTGTTATG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
*
32065 AATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
1 AATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
*
32130 TTTAATCTTTTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
* *
32190 AATAGCGGCGTTTTTCATGATAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAATGCCGCTATA
1 AATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
32255 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
66 TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
* * *
32315 AATAACGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCACTATA
1 AATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
32380 TTTAATCATT-TACAAACAAT
66 TTTAATC-TTCTACAAACAAT
32400 TTTTTCTGTC
Statistics
Matches: 317, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
124 95 0.30
125 220 0.69
126 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (125 bp):
AATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTATA
TTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATG
Found at i:32340 original size:406 final size:407
Alignment explanation
Indices: 31587--32356 Score: 1416
Period size: 406 Copynumber: 1.9 Consensus size: 407
31577 TCTGATGCAC
*
31587 AACGCCGCTATATATAATCTTCTACAAATAATAGAAATTTGGTGAAACTAACAACACCATTTATT
1 AACGCCGCTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAACAACACCATTTATT
* *
31652 TGTTATGAATAGTGGCGTTTTCCATGATAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGC
66 TGTTATGAATAGCGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGC
31717 CGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTA
131 CGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTA
*
31782 TGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTA
196 TGAATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTA
*
31847 TATTTAATCTTCTACAAACAATAGAAATTTGTTGAAACTAAAAACACCATTTATTTGTTATGAAT
261 TATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAAT
*
31912 AGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGTTTTCCATGATAAACGTCGCTAAATA
326 AACGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGTTTTCCATGATAAACGTCGCTAAATA
31977 GTGGCACTTCTAAAGTA
391 GTGGCACTTCTAAAGTA
*
31994 AACGCCGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAA-AACACCATTTATT
1 AACGCCGCTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAACAACACCATTTATT
* * *
32058 TGTTATGAATAGCGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGC
66 TGTTATGAATAGCGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGC
*
32123 CGCTATATTTAATCTTTTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTA
131 CGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTA
* *
32188 TGAATAGCGGCGTTTTTCATGATAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAATGCCGCTA
196 TGAATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTA
32253 TATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAAT
261 TATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAAT
32318 AACGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCG
326 AACGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCG
32357 CTTCTAAAGT
Statistics
Matches: 350, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
406 301 0.86
407 49 0.14
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (407 bp):
AACGCCGCTATATATAATCTTCTACAAACAATAGAAATTTGGTGAAACTAACAACACCATTTATT
TGTTATGAATAGCGGCGTTTTCCATGACAAACGCCGCTAAATAGTGGCACTTCTAAAGTAAACGC
CGCTATATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTA
TGAATAGCGGCGTTTTTCATGACAAACGCCGCTAAATAGTGGCGCTTCTAAAGTAAACGCCGCTA
TATTTAATCTTCTACAAACAATAGAAATTTGGTGAAACTAAAAACACCATTTATTTGTTATGAAT
AACGGCGTTTTTCATGACAGACGCCGCTAAATAGTGGCGTTTTCCATGATAAACGTCGCTAAATA
GTGGCACTTCTAAAGTA
Found at i:32551 original size:28 final size:26
Alignment explanation
Indices: 32509--32565 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
32499 CTGCTTAATT
*
32509 AAATTTGCTTCTTCATTTTCTACCCA
1 AAATTTGCTTCTTCATTTTCGACCCA
*
32535 AAATTTGTTCTTCTTCATTTTCGACTCA
1 AAATTTG--CTTCTTCATTTTCGACCCA
32563 AAA
1 AAA
32566 GCAAAAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (26 bp):
AAATTTGCTTCTTCATTTTCGACCCA
Found at i:37643 original size:46 final size:48
Alignment explanation
Indices: 37591--37695 Score: 151
Period size: 48 Copynumber: 2.2 Consensus size: 48
37581 ACTCCAAGCA
***
37591 ATCTTTTACTTTT-C-TGCACTTTTTCTCAATTTTTGCTACAAAATTG
1 ATCTTTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTG
* *
37637 ATCTTTTATTTTTCCTTGCACTTTTTCTCAATTTTTAAGATAAAATTG
1 ATCTTTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTG
37685 ATCTTTTACTT
1 ATCTTTTACTT
37696 GTTATTGTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
46 12 0.24
47 1 0.02
48 38 0.75
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (48 bp):
ATCTTTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTG
Found at i:38579 original size:22 final size:21
Alignment explanation
Indices: 38554--38601 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
38544 CCCATGCTAG
38554 GGTG-AATGGTGCAAACAACAAT
1 GGTGAAATGGT-C-AACAACAAT
38576 GGTGCAAATGGTCAACAACAAT
1 GGTG-AAATGGTCAACAACAAT
38598 GGTG
1 GGTG
38602 TGAACAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 17 0.71
23 1 0.04
24 6 0.25
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.19
Consensus pattern (21 bp):
GGTGAAATGGTCAACAACAAT
Found at i:52698 original size:23 final size:23
Alignment explanation
Indices: 52671--52717 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52661 ATCAATGATT
52671 TAAACACGTTTGTGTGACTTTGA
1 TAAACACGTTTGTGTGACTTTGA
52694 TAAACACGTTTGTGTGACTTTGA
1 TAAACACGTTTGTGTGACTTTGA
52717 T
1 T
52718 TCAGGACTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (23 bp):
TAAACACGTTTGTGTGACTTTGA
Found at i:52821 original size:46 final size:48
Alignment explanation
Indices: 52769--52873 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
52759 ACTCCAAGCA
***
52769 ATCTTTTACTTTT-C-TACACTTTTTCTCAATTTTTGCTACAAAATTG
1 ATCTTTTACTTTTCCTTACACTTTTTCTCAATTTTTAAGACAAAATTG
* * *
52815 ATCTTTTATTTTTCCTTGCACTTTTTCTCAATTTTTAAGATAAAATTG
1 ATCTTTTACTTTTCCTTACACTTTTTCTCAATTTTTAAGACAAAATTG
52863 ATCTTTTACTT
1 ATCTTTTACTT
52874 GTTATTGTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 12 0.24
47 1 0.02
48 37 0.74
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.54
Consensus pattern (48 bp):
ATCTTTTACTTTTCCTTACACTTTTTCTCAATTTTTAAGACAAAATTG
Found at i:54352 original size:2 final size:2
Alignment explanation
Indices: 54341--54370 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
54331 CATTTTCTTT
54341 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54371 CTTTTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54965 original size:211 final size:213
Alignment explanation
Indices: 54725--55252 Score: 918
Period size: 211 Copynumber: 2.5 Consensus size: 213
54715 GAGGGTAGTG
54725 TAAATGAAATCATATATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTT
1 TAAA-GAAATCATATATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTT
54790 TAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGAT
65 TAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGAT
54855 ATATTGATTAGAAAAAAG-CTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTT
130 ATATTGATTAGAAAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTT
54919 TAAGATTTTAATTAAAAAA
195 TAAGATTTTAATTAAAAAA
54938 TAAAGAAATCAT-TATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTT
1 TAAAGAAATCATATATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTT
55002 AAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATA
66 AAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATA
55067 TATTGATTAGAAAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTT
131 TATTGATTAGAAAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTT
55132 AAGATTTTAATTAAAAAA
196 AAGATTTTAATTAAAAAA
** *
55150 TAAAGAAATCATATATCATATCATATATATATAATGATAACAATGTACACTTTGAAA-ATGGTAA
1 TAAAGAAATC----AT-ATATCATATATATATAATGATAACAATGTACAC-TACAAATATGGAAA
* * *
55214 CTCATTAAATGTTAAGGCCTCCAAATCTCGACAAGTGTC
60 CTCTTTAAATGTTGAGGCCTCCAAATCTCGACACGTGTC
55253 ATGCCCATTT
Statistics
Matches: 301, Mismatches: 6, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
211 134 0.45
212 83 0.28
213 4 0.01
216 2 0.01
218 74 0.25
219 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (213 bp):
TAAAGAAATCATATATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTT
AAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATA
TATTGATTAGAAAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTT
AAGATTTTAATTAAAAAA
Done.