Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010262.1 Corchorus capsularis cultivar CVL-1 contig10283, 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: 66696
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:149 original size:17 final size:17
Alignment explanation
Indices: 124--159 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
114 TCCCTCACCC
*
124 ATATTTTTTTTAAAAAT
1 ATATATTTTTTAAAAAT
141 ATATATTTTTTAAAAAT
1 ATATATTTTTTAAAAAT
158 AT
1 AT
160 TTTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTTTTTAAAAAT
Found at i:172 original size:17 final size:15
Alignment explanation
Indices: 128--176 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
118 TCACCCATAT
128 TTTTTTTAAAAATATA
1 TTTTTTTAAAAA-ATA
144 TATTTTTT-AAAAATA
1 T-TTTTTTAAAAAATA
159 TTTTTTAATAAAAAATA
1 TTTTTT--TAAAAAATA
176 T
1 T
177 GACGTGGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 4 0.14
16 6 0.21
17 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTTTAAAAAATA
Found at i:606 original size:17 final size:17
Alignment explanation
Indices: 584--616 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
574 CTCTAATGTT
584 TTATTATTATTATATTA
1 TTATTATTATTATATTA
*
601 TTATTATTGTTATATT
1 TTATTATTATTATATT
617 TTTGTTACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATTATTATTATATTA
Found at i:735 original size:14 final size:14
Alignment explanation
Indices: 716--746 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
706 TTCTCACGCG
716 GTGTCAGATCTCAA
1 GTGTCAGATCTCAA
730 GTGTCAGATCTCAA
1 GTGTCAGATCTCAA
744 GTG
1 GTG
747 AGAGACTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (14 bp):
GTGTCAGATCTCAA
Found at i:6584 original size:39 final size:39
Alignment explanation
Indices: 6541--6623 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
6531 CATCAAGAGG
* * *
6541 AAGAAGAACAGAAACA-AGTTCAACAACATCAA-AAACATC
1 AAGAAGAACAAAAACAGA-ATCAACAACAACAACAAA-ATC
*
6580 AAGAAGAAGAAAAACAGAATCAACAACAACAACAAAATC
1 AAGAAGAACAAAAACAGAATCAACAACAACAACAAAATC
6619 AAGAA
1 AAGAA
6624 CATGAAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.64, C:0.18, G:0.11, T:0.07
Consensus pattern (39 bp):
AAGAAGAACAAAAACAGAATCAACAACAACAACAAAATC
Found at i:6610 original size:45 final size:46
Alignment explanation
Indices: 6531--6637 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 46
6521 AACCCATCAT
* * ***
6531 CATCAAGAGGAAGAAGAACAGAAACAAGTTCAACAAC-ATCAAAAA
1 CATCAAGAAGAAGAAAAACAGAAACAACAACAACAACAATCAAAAA
* *
6576 CATCAAGAAGAAGAAAAACAGAATCAACAACAACAACAAAATCAAGAA
1 CATCAAGAAGAAGAAAAACAGAAACAACAACAACAAC--AATCAAAAA
*
6624 CATGAAGAAGAAGA
1 CATCAAGAAGAAGA
6638 GAATCATCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 31 0.61
48 20 0.39
ACGTcount: A:0.61, C:0.17, G:0.15, T:0.07
Consensus pattern (46 bp):
CATCAAGAAGAAGAAAAACAGAAACAACAACAACAACAATCAAAAA
Found at i:10557 original size:15 final size:15
Alignment explanation
Indices: 10537--10569 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10527 TACGAAACCA
*
10537 ACTGTTTGATTTAAT
1 ACTGTTGGATTTAAT
10552 ACTGTTGGATTTAAT
1 ACTGTTGGATTTAAT
10567 ACT
1 ACT
10570 CTTTCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (15 bp):
ACTGTTGGATTTAAT
Found at i:11261 original size:58 final size:58
Alignment explanation
Indices: 11191--11306 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
11181 CTGAACCATG
11191 AGGTCTTGGGTTCTATTCTCACGGAATGTGAGTTACTCTCATGCAATTGTGAGTTTTC
1 AGGTCTTGGGTTCTATTCTCACGGAATGTGAGTTACTCTCATGCAATTGTGAGTTTTC
11249 AGGTCTTGGGTTCTATTCTCACGGAATGTGAGTTACTCTCATGCAATTGTGAGTTTTC
1 AGGTCTTGGGTTCTATTCTCACGGAATGTGAGTTACTCTCATGCAATTGTGAGTTTTC
11307 GTGTGGTGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (58 bp):
AGGTCTTGGGTTCTATTCTCACGGAATGTGAGTTACTCTCATGCAATTGTGAGTTTTC
Found at i:14176 original size:6 final size:6
Alignment explanation
Indices: 14165--14189 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14155 TATTATTTAC
14165 TACTAG TACTAG TACTAG TACTAG T
1 TACTAG TACTAG TACTAG TACTAG T
14190 TCTTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TACTAG
Found at i:15843 original size:2 final size:2
Alignment explanation
Indices: 15836--15893 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
15826 TCTACAGCTC
* * *
15836 AT AT AT AT CT AT CT ACT AT AT AT AT AT AT AT -T A- AT -T AT GT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15876 AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT
15894 TTAATCTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
1 3 0.07
2 39 0.89
3 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18865 original size:178 final size:174
Alignment explanation
Indices: 18537--18906 Score: 392
Period size: 178 Copynumber: 2.1 Consensus size: 174
18527 ACAAACTATG
* *
18537 TAATATTAAGTAGATCGTCTATTTCCATTAACCAAAACAACTAATTCTTTGGAAGCAATTTTTAT
1 TAATATTAAGTAGACCGTCTATTCCCATTAACCAAAACAACTAATTCTTTGGAAGCAATTTTTAT
* * *
18602 ACCTTGAATATTAAAATTTTCGAGCCCTTCATGAAAGTTGTAGATCATTGAAAAACCTTTCAAGA
66 ACCTTGAACATTAAAATTTTCAAGCCCTTCATGAAAGTTGTAGATCATGGAAAAACCTTTCAAGA
* * *
18667 GACAGTTGAATCATCTTAATCAGACATCTGGAGTAAAAGTTATA
131 GACACTTGAACCACCTTAATCAGACATCTGGAGTAAAAGTTATA
* * * *
18711 TAATATTAAGTGGACCGTCTATTCCCGTTAATCGAAACAA-TAAATT-TTTCGGAAGC-ATTTTT
1 TAATATTAAGTAGACCGTCTATTCCCATTAACCAAAACAACT-AATTCTTT-GGAAGCAATTTTT
** * *
18773 GATA-CTTGAAACATTAAATTTAGTTTTCAAGTTCTTCATGAAAGTTGTAGATCATGGAACAATC
64 -ATACCTTG-AACATTAAA---A-TTTTCAAGCCCTTCATGAAAGTTGTAGATCATGGAAAAACC
* * * * * *
18837 TTTTAATAGATACTTGAACCACCTTAATCGGATAATC-GGAG-AGAAAATTATA
123 TTTCAAGAGACACTTGAACCACCTTAATCAGA-CATCTGGAGTA-AAAGTTATA
* *
18889 TAATGTTAAATAGACCGT
1 TAATATTAAGTAGACCGT
18907 TTAGCCAAAC
Statistics
Matches: 161, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
173 14 0.09
174 55 0.34
177 2 0.01
178 87 0.54
179 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (174 bp):
TAATATTAAGTAGACCGTCTATTCCCATTAACCAAAACAACTAATTCTTTGGAAGCAATTTTTAT
ACCTTGAACATTAAAATTTTCAAGCCCTTCATGAAAGTTGTAGATCATGGAAAAACCTTTCAAGA
GACACTTGAACCACCTTAATCAGACATCTGGAGTAAAAGTTATA
Found at i:19731 original size:23 final size:23
Alignment explanation
Indices: 19705--19778 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
19695 TTCTCACACA
19705 AATATATAGAATAATAACAAATT
1 AATATATAGAATAATAACAAATT
* * *
19728 AATAGAT-GATGATAAAAACAATTT
1 AATATATAGA--ATAATAACAAATT
*
19752 AATATGTAGAATAATAACAAATT
1 AATATATAGAATAATAACAAATT
19775 AATA
1 AATA
19779 GATGATGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.05
23 21 0.51
24 16 0.39
25 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (23 bp):
AATATATAGAATAATAACAAATT
Found at i:19762 original size:47 final size:46
Alignment explanation
Indices: 19705--19802 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 46
19695 TTCTCACACA
19705 AATATATAGAATAATAACAAATTAATAGATGATGATAAAAACAATTT
1 AATATATAGAATAATAACAAATTAATAGATGATGAT-AAAACAATTT
*
19752 AATATGTAGAATAATAACAAATTAATAGATGATGATAAAACAATTT
1 AATATATAGAATAATAACAAATTAATAGATGATGATAAAACAATTT
19798 AATAT
1 AATAT
19803 TATAATATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 15 0.30
47 35 0.70
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (46 bp):
AATATATAGAATAATAACAAATTAATAGATGATGATAAAACAATTT
Found at i:19793 original size:23 final size:24
Alignment explanation
Indices: 19715--19801 Score: 101
Period size: 23 Copynumber: 3.7 Consensus size: 24
19705 AATATATAGA
19715 ATAATAACAAATTAATAGATGATG
1 ATAATAACAAATTAATAGATGATG
* *
19739 ATAAAAACAATTTAAT--ATG-TAG
1 ATAATAACAAATTAATAGATGAT-G
19761 AATAATAACAAATTAATAGATGATG
1 -ATAATAACAAATTAATAGATGATG
*
19786 ATAA-AACAATTTAATA
1 ATAATAACAAATTAATA
19802 TTATAATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 4 0.08
23 25 0.47
24 18 0.34
25 4 0.08
26 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (24 bp):
ATAATAACAAATTAATAGATGATG
Found at i:20369 original size:17 final size:18
Alignment explanation
Indices: 20340--20373 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20330 CTTTCGTGTC
20340 TGTGTTTCTTTGTTTTTT
1 TGTGTTTCTTTGTTTTTT
20358 TGTGTTTC-TTGTTTTT
1 TGTGTTTCTTTGTTTTT
20374 GTAGGTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.06, G:0.18, T:0.76
Consensus pattern (18 bp):
TGTGTTTCTTTGTTTTTT
Found at i:20381 original size:17 final size:18
Alignment explanation
Indices: 20341--20386 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
20331 TTTCGTGTCT
*
20341 GTGTTTCTTTGTTTTTTT
1 GTGTTTCTTTGTTTTTTA
20359 GTGTTTC-TTGTTTTTGTA
1 GTGTTTCTTTGTTTTT-TA
20377 G-GTTTGCTTT
1 GTGTTT-CTTT
20387 TAATTCCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 12 0.50
18 10 0.42
19 2 0.08
ACGTcount: A:0.02, C:0.07, G:0.22, T:0.70
Consensus pattern (18 bp):
GTGTTTCTTTGTTTTTTA
Found at i:20975 original size:2 final size:2
Alignment explanation
Indices: 20962--21002 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20952 ATAATTTATT
*
20962 TA TA TT TA TA TA TA TA TA 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 TA TA TA TA TA T
21003 TTCTTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21648 original size:88 final size:89
Alignment explanation
Indices: 21522--21708 Score: 299
Period size: 88 Copynumber: 2.1 Consensus size: 89
21512 AGGATTCATG
*
21522 TAAAATAATAAAATTTGTAAAGAGAATATTTTCTAAATCTTGCCAAATTGTAGGAGATTTAGAAG
1 TAAAGTAATAAAATTTGTAAAGAGAATATTTTCTAAATCTTGCCAAATTGTAGGAGATTTAGAAG
21587 ATATTTTAAGAAAATAAATAAATTA
66 ATATTTTAAG-AAATAAATAAATTA
* * *
21612 TGAAGTAATAAAATTTGT-AA-AGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAG
1 TAAAGTAATAAAATTTGTAAAGAGAATATTTTCTAAATCTTGCCAAATTGTAGGAGATTTAGAAG
*
21675 ATATTTTAAGAAATAAATAAGTTA
66 ATATTTTAAGAAATAAATAAATTA
21699 TAAAG-AATAA
1 TAAAGTAATAA
21709 GAATATTTCT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
86 5 0.05
87 17 0.19
88 51 0.56
89 2 0.02
90 16 0.18
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.34
Consensus pattern (89 bp):
TAAAGTAATAAAATTTGTAAAGAGAATATTTTCTAAATCTTGCCAAATTGTAGGAGATTTAGAAG
ATATTTTAAGAAATAAATAAATTA
Found at i:21788 original size:77 final size:76
Alignment explanation
Indices: 21631--21775 Score: 192
Period size: 77 Copynumber: 1.9 Consensus size: 76
21621 AAAATTTGTA
* * *
21631 AAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAAG
1 AAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGAAATATCAAGAAATAAATAAG
* *
21696 TTATAAAGAAT
66 TAAAAAAGAAT
21707 AAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTA-GA-AAATATCAA-ATAAT-AATA
1 AAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGAAATATCAAGA-AATAAATA
21768 A-TAAAAAA
64 AGTAAAAAA
21776 TAATTGACAA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
73 5 0.08
74 6 0.10
75 9 0.15
76 12 0.19
77 30 0.48
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (76 bp):
AAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGAAATATCAAGAAATAAATAAG
TAAAAAAGAAT
Found at i:33086 original size:17 final size:17
Alignment explanation
Indices: 33064--33097 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
33054 TCCTTATAAG
33064 TTTGTTTATATTTAGAT
1 TTTGTTTATATTTAGAT
33081 TTTGTTTATATTTAGAT
1 TTTGTTTATATTTAGAT
33098 GATATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTGTTTATATTTAGAT
Found at i:35903 original size:6 final size:6
Alignment explanation
Indices: 35892--35921 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35882 TTACACCATT
*
35892 GTGTGA GTGTGA GTGTGA CTGTGA GTGTGA
1 GTGTGA GTGTGA GTGTGA GTGTGA GTGTGA
35922 TGGCAAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (6 bp):
GTGTGA
Found at i:37360 original size:12 final size:12
Alignment explanation
Indices: 37343--37367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37333 AATTGCTTCT
37343 AACATAAAATTA
1 AACATAAAATTA
37355 AACATAAAATTA
1 AACATAAAATTA
37367 A
1 A
37368 CCTCTCGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AACATAAAATTA
Found at i:38482 original size:6 final size:6
Alignment explanation
Indices: 38481--38505 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38471 TTTTTTTGTT
38481 TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG T
38506 CTCTCTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:39370 original size:17 final size:18
Alignment explanation
Indices: 39343--39380 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
39333 CCCTCATCAT
39343 GGTACCTAGGTAGCATGA
1 GGTACCTAGGTAGCATGA
39361 GGTA-CTAGGTAGCATGA
1 GGTACCTAGGTAGCATGA
39378 GGT
1 GGT
39381 GCTGGATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (18 bp):
GGTACCTAGGTAGCATGA
Found at i:41554 original size:26 final size:26
Alignment explanation
Indices: 41525--41591 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
41515 GATCTCCTTA
41525 TTTTTATCAAACCCTAGCCACCACAT
1 TTTTTATCAAACCCTAGCCACCACAT
41551 TTTTTATCAAACCCTAGCCACCACAT
1 TTTTTATCAAACCCTAGCCACCACAT
41577 TTTTTATCAAACCCT
1 TTTTTATCAAACCCT
41592 TCTTCTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34
Consensus pattern (26 bp):
TTTTTATCAAACCCTAGCCACCACAT
Found at i:41633 original size:87 final size:89
Alignment explanation
Indices: 41504--41751 Score: 367
Period size: 89 Copynumber: 2.8 Consensus size: 89
41494 ATTTTCTTTT
* * * *
41504 TTCTTCTATTTGATCTCCTTATTTTTATCAAACCCTAGCCACCACA-TTTTTTATCAAACCCTAG
1 TTCTTCTATTTGCTCTCTTTATTTTTATCAAACCCTAGCCACCGCATTTTTTTATCGAACCCTAG
41568 CCACCACA-TTTTTTATCAAACCC
66 CCACCACATTTTTTTATCAAACCC
* * *
41591 TTCTTCTATTCGCTCTCTTTATTTTTGTCAAACCCTAGCCACCGCATTTTTTTATCGAA-CCTAA
1 TTCTTCTATTTGCTCTCTTTATTTTTATCAAACCCTAGCCACCGCATTTTTTTATCGAACCCTAG
41655 CCACCACATTTTTTTTATCAAACCC
66 CCACCACA-TTTTTTTATCAAACCC
* *
41680 TTCTTCTATTTGCTCTCTTTATTTTTATCTAACCCTATCCACCGCAATTTTTTTTATCGAACCCT
1 TTCTTCTATTTGCTCTCTTTATTTTTATCAAACCCTAGCCACCGC-A-TTTTTTTATCGAACCCT
41745 AGCCACC
64 AGCCACC
41752 GCCTTTTAGT
Statistics
Matches: 143, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
87 53 0.37
88 11 0.08
89 56 0.39
90 1 0.01
91 13 0.09
92 9 0.06
ACGTcount: A:0.23, C:0.31, G:0.05, T:0.42
Consensus pattern (89 bp):
TTCTTCTATTTGCTCTCTTTATTTTTATCAAACCCTAGCCACCGCATTTTTTTATCGAACCCTAG
CCACCACATTTTTTTATCAAACCC
Found at i:41653 original size:26 final size:27
Alignment explanation
Indices: 41612--41678 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
41602 GCTCTCTTTA
* * *
41612 TTTTTGTCAAACCCTAGCCACCGCA-TT
1 TTTTTATCAAA-CCTAACCACCACATTT
*
41639 TTTTTATCGAACCTAACCACCACATTT
1 TTTTTATCAAACCTAACCACCACATTT
41666 TTTTTATCAAACC
1 TTTTTATCAAACC
41679 CTTCTTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.27, C:0.30, G:0.06, T:0.37
Consensus pattern (27 bp):
TTTTTATCAAACCTAACCACCACATTT
Found at i:44912 original size:19 final size:19
Alignment explanation
Indices: 44868--44914 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
44858 ATGAGGGCAG
*
44868 TAAAAAAATACAGAAAAAA
1 TAAAAAAACACAGAAAAAA
*
44887 TACAAAAACACAG-AAAAA
1 TAAAAAAACACAGAAAAAA
*
44905 TGAAAAAACA
1 TAAAAAAACA
44915 GAGGTAGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (19 bp):
TAAAAAAACACAGAAAAAA
Found at i:46214 original size:49 final size:49
Alignment explanation
Indices: 46087--46472 Score: 422
Period size: 49 Copynumber: 7.9 Consensus size: 49
46077 TATTTTTCAG
* **
46087 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACATAAGGCATTTA
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * * * * *
46136 TTTTTACCTG-TTTTTCCCAAAACGCCCTTCCAGGACGGAAGGCACTGA
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
*
46184 TTTTCACTTGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * *
46233 TTGTT-ACTTACTATTTCCCAAAATACCCTTCCCGTACTGAAGGCATTTA
1 TT-TTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * *
46282 CTTTCAGC-TACTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA-ATA
1 TTTTCA-CTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
** * *
46330 TTTTTGCTTGCTCTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTG
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * * *
46379 TTTTTACCTGCTATTCCCCAAAACGCCCTTCCCGGACGGAAGGTATTTA
1 TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * * *
46428 TTCTT-ACCTGCCATTTCCCAAAATGCCTTTTCCGGACGAAAGGCA
1 TT-TTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA
46473 AGTTCATTTT
Statistics
Matches: 282, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.00
48 80 0.28
49 196 0.70
50 5 0.02
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (49 bp):
TTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
Found at i:46361 original size:146 final size:144
Alignment explanation
Indices: 46092--46473 Score: 453
Period size: 146 Copynumber: 2.6 Consensus size: 144
46082 TTCAGTTTTC
* *
46092 ACTTGCTATTTCCCAAAATGCCCTTCCCAGACAT-AAGGCATTTATTTTTACCTGTTTTTCCCAA
1 ACTTGCTATTTCCCAAAATGCCCTTCCC-GAC-TGAAGGCATTTA-TTTTACCTCTATTTCCCAA
* * * *
46156 AACGCCCTTCCAGGACGGAAGGCACTGATTTTCACTTGTTATTTCCCAAAATGCCCTTCCCGGAC
63 AATGCCCTTCCCGGACGGAAGGCAATGATTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGAC
46221 GGAAGGCATTTATTGTT
128 GGAAGGCATTTATTGTT
* * * *
46238 ACTTACTATTTCCCAAAATACCCTTCCCGTACTGAAGGCATTTACTTTCAGCTACTATTTCCCAA
1 ACTTGCTATTTCCCAAAATGCCCTTCCCG-ACTGAAGGCATTTA-TTTTACCT-CTATTTCCCAA
** *
46303 AATGCCCTTCCCGGACGGAAGGCAAT-ATTTTTGCTTGCTCTTTCCCAAAATGCCCTTCCCGGAC
63 AATGCCCTTCCCGGACGGAAGGCAATGATTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGAC
* *
46367 GGAAGGCATTTGTTTTT
128 GGAAGGCATTTATTGTT
* * * * * *
46384 ACCTGCTATTCCCCAAAACGCCCTTCCCGGACGGAAGGTATTTATTCTTACCTGCCATTTCCCAA
1 ACTTGCTATTTCCCAAAATGCCCTTCCC-GACTGAAGGCATTTATT-TTACCT-CTATTTCCCAA
* * *
46449 AATGCCTTTTCCGGACGAAAGGCAA
63 AATGCCCTTCCCGGACGGAAGGCAA
46474 GTTCATTTTT
Statistics
Matches: 201, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
145 4 0.02
146 164 0.82
147 33 0.16
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (144 bp):
ACTTGCTATTTCCCAAAATGCCCTTCCCGACTGAAGGCATTTATTTTACCTCTATTTCCCAAAAT
GCCCTTCCCGGACGGAAGGCAATGATTTTCACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGA
AGGCATTTATTGTT
Found at i:46393 original size:97 final size:98
Alignment explanation
Indices: 46086--46472 Score: 440
Period size: 97 Copynumber: 4.0 Consensus size: 98
46076 CTATTTTTCA
* * ** *
46086 GTTTTCACTTGCTATTTCCCAAAATGCCCTTCCCAGACATAAGGCATTTATTTTTACCTG-TTTT
1 GTTTTCACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTCTT
* * *
46150 TCCCAAAACGCCCTTCCAGGACGGAAGGCA-CT
66 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTT
* * * * * *
46182 GATTTTCACTTGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTGTTACTTACTAT
1 G-TTTTCACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTCT
* * *
46247 TTCCCAAAATACCCTTCCCGTACTGAAGGCATTT
65 TTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT
** * * * * *
46281 ACTTTCAGCTACTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA-ATATTTTTGCTTGCTCTT
1 GTTTTCACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTCTT
46345 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTT
66 TCCCAAAATGCCCTTCCCGGACGGAAGGCATTT
* * * * *
46378 GTTTTTACCTGCTATTCCCCAAAACGCCCTTCCCGGACGGAAGGTATTTATTCTTACCTGC-CAT
1 GTTTTCACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTC-T
* * *
46442 TTCCCAAAATGCCTTTTCCGGACGAAAGGCA
65 TTCCCAAAATGCCCTTCCCGGACGGAAGGCA
46473 AGTTCATTTT
Statistics
Matches: 243, Mismatches: 43, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
96 1 0.00
97 134 0.55
98 107 0.44
99 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (98 bp):
GTTTTCACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTCTT
TCCCAAAATGCCCTTCCCGGACGGAAGGCATTT
Found at i:52417 original size:35 final size:35
Alignment explanation
Indices: 52371--52571 Score: 270
Period size: 35 Copynumber: 5.8 Consensus size: 35
52361 TTCTTACTAA
*
52371 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTC
* *
52406 ACTTAATTACCCTAAATTAAGTT-ACT-C-GACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
52438 ACTTAATTACCCCGAATTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTC
*
52474 ACTTAATTACCCTGAATTAAGTTGATTACTGGA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTACT-GACTC
52509 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
52544 ACTCAATTACCCTGAATTAAGTTGATTA
1 ACTTAATTACCCTGAATTAAGTTGATTA
52572 TTACCCTGAA
Statistics
Matches: 149, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.02
32 17 0.11
33 5 0.03
34 5 0.03
35 95 0.64
36 24 0.16
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:52575 original size:22 final size:22
Alignment explanation
Indices: 52549--52593 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52539 GACTCACTCA
52549 ATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATT
52571 ATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATT
52593 A
1 A
52594 CTGAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATTACCCTGAATTAAGTTGATT
Found at i:52575 original size:57 final size:57
Alignment explanation
Indices: 52514--52626 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
52504 GGATTACTTA
*
52514 ATTACCCTGAATTAAGTTGATTACTGACTCACTCAATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTGAATTAAGTTGATT
* *
52571 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGAT
1 ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTGAATTAAGTTGAT
52627 CACTGACTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (57 bp):
ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTGAATTAAGTTGATT
Found at i:52585 original size:92 final size:92
Alignment explanation
Indices: 52479--52838 Score: 363
Period size: 92 Copynumber: 4.0 Consensus size: 92
52469 GACTCACTTA
* *
52479 ATTACCCTGAATTAAGTTGATTACTGGATTACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATCACTGACTC
52544 ACTCAATTACCCTGAATTAAGTTGATT
66 ACTCAATTACCCTGAATTAAGTTGATT
52571 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATCACTGACTC
1 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATCACTGACTC
*
52636 ACTTAATTACCCTGAATTAAGTTGATT
66 ACTCAATTACCCTGAATTAAGTTGATT
* * * * * * * * * *
52663 A-T----TGAATT-ACTTAATTACCCTGAGTTAAGTTGATTACTGACTCACTCAA-TT-A-CCCT
1 ATTACCCTGAATTAAGTTGATTA--CTGAATT-ACTTAATTAC--CCTGAATTAAGTTGATCACT
* * * * * * *
52719 GAATTAAGTTAATTA--CTG-ACTCACTT-A--
61 G-ACTCACTCAATTACCCTGAATTAAGTTGATT
*
52746 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATCACTGACTC
*
52811 ACTCAATTACCCTGAATTAAGTTAATT
66 ACTCAATTACCCTGAATTAAGTTGATT
52838 A
1 A
52839 CTGACTTACT
Statistics
Matches: 210, Mismatches: 37, Indels: 42
0.73 0.13 0.15
Matches are distributed among these distances:
83 1 0.00
84 7 0.03
85 3 0.01
86 30 0.14
87 18 0.09
88 19 0.09
89 31 0.15
90 3 0.01
91 7 0.03
92 91 0.43
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (92 bp):
ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTGATCACTGACTC
ACTCAATTACCCTGAATTAAGTTGATT
Found at i:52613 original size:35 final size:35
Alignment explanation
Indices: 52571--52980 Score: 649
Period size: 35 Copynumber: 11.7 Consensus size: 35
52561 TAAGTTGATT
*
52571 ATTACCCTGAATTAAGTTGATTACTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52606 ATTACCCTGAATTAAGTTGATCACTGACTCACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52641 ATTACCCTGAATTAAGTTGATTATTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* * *
52676 ATTACCCTGAGTTAAGTTGATTACTGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52711 ATTACCCTGAATTAAGTTAATTACTGACTCACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
*
52746 ATTACCCTGAATTAAGTTGATTACTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52781 ATTACCCTGAATTAAGTTGATTACTGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
*
52816 ATTACCCTGAATTAAGTTAATTACTGACTTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52851 ATTACCCTGAATTAAGTTGATTACTGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
52886 ATTACCCTGAATTAAGTTAATTACTAACTTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
*
52921 ATTACCCTGAATTAAGTTGATTACTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
52956 ATTACCCTGAATTAAGTTGATTACT
1 ATTACCCTGAATTAAGTTGATTACT
52981 ACTGACTCAC
Statistics
Matches: 341, Mismatches: 34, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 341 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (35 bp):
ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
Found at i:53447 original size:22 final size:22
Alignment explanation
Indices: 53422--53467 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
53412 ATAAGATCTA
*
53422 CTCATTAATCATAAACTAAAAG
1 CTCATAAATCATAAACTAAAAG
53444 CTCATAAATCATAAACTAAAAG
1 CTCATAAATCATAAACTAAAAG
53466 CT
1 CT
53468 AAATTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.20, G:0.04, T:0.26
Consensus pattern (22 bp):
CTCATAAATCATAAACTAAAAG
Found at i:56479 original size:36 final size:36
Alignment explanation
Indices: 56432--56593 Score: 138
Period size: 36 Copynumber: 4.5 Consensus size: 36
56422 AAAATAAGTT
56432 ACTGAAGAAAGACCACCCTAGATCATTCCGAATTGA
1 ACTGAAGAAAGACCACCCTAGATCATTCCGAATTGA
*
56468 ACTGAAGAAAGACCACCCTGGATCATTCCG-A-TGCTA
1 ACTGAAGAAAGACCACCCTAGATCATTCCGAATTG--A
* * * *
56504 ACTGAAGGAAA-ACCACCCTCAG-TCA-ACCAAAATAA
1 ACTGAA-GAAAGACCACCCT-AGATCATTCCGAATTGA
** * * *
56539 ACTGAAGATCGACCACCCTTGACCATTCCGACTCT-A
1 ACTGAAGAAAGACCACCCTAGATCATTCCGAAT-TGA
*
56575 ACTGAAGAAGGACCACCCT
1 ACTGAAGAAAGACCACCCT
56594 GGGTCATTGA
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
34 5 0.05
35 20 0.20
36 69 0.68
37 7 0.07
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (36 bp):
ACTGAAGAAAGACCACCCTAGATCATTCCGAATTGA
Found at i:56590 original size:71 final size:71
Alignment explanation
Indices: 56432--56593 Score: 177
Period size: 71 Copynumber: 2.3 Consensus size: 71
56422 AAAATAAGTT
* * * * *
56432 ACTGAAGAAAGACCACCCTAGATCATTCCGAATTGAACTGAAGAAAGACCACCCTGGATCATTCC
1 ACTGAAG-AAGACCACCCTAGATCATACCAAAATAAACTGAAGAAAGACCACCCTGGACCATTCC
56497 GATGCTA
65 GATGCTA
* ** *
56504 ACTGAAGGAAAACCACCCTCAG-TCA-ACCAAAATAAACTGAAGATCGACCACCCTTGACCATTC
1 ACTGAA-GAAGACCACCCT-AGATCATACCAAAATAAACTGAAGAAAGACCACCCTGGACCATTC
56567 CGACT-CTA
64 CGA-TGCTA
56575 ACTGAAGAAGGACCACCCT
1 ACTGAAGAA-GACCACCCT
56594 GGGTCATTGA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
70 3 0.04
71 50 0.66
72 20 0.26
73 3 0.04
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (71 bp):
ACTGAAGAAGACCACCCTAGATCATACCAAAATAAACTGAAGAAAGACCACCCTGGACCATTCCG
ATGCTA
Found at i:56801 original size:34 final size:35
Alignment explanation
Indices: 56760--56861 Score: 136
Period size: 34 Copynumber: 2.9 Consensus size: 35
56750 TTTGAAAGCA
* *
56760 ACTGAAGAAAGACCGCCCTGGGTTAATTGAAA-TT
1 ACTGAAGAGAGACCGCCCTGGGTCAATTGAAATTT
* *
56794 ATTGAAGAGAGACCGCCCTGGATCAATTGAAATTT
1 ACTGAAGAGAGACCGCCCTGGGTCAATTGAAATTT
56829 ACTGAATG-GAGACCGCCCTGGGTCAATTTGAAA
1 ACTGAA-GAGAGACCGCCCTGGGTCAA-TTGAAA
56862 CCTTTGAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.47
35 24 0.41
36 7 0.12
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (35 bp):
ACTGAAGAGAGACCGCCCTGGGTCAATTGAAATTT
Found at i:58019 original size:16 final size:16
Alignment explanation
Indices: 57998--58043 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
57988 TAGAGCTTCA
57998 TCTCTTTTCTTCTTTT-
1 TCTCTTTTCTT-TTTTC
*
58014 TCTCTTTCCTTTTTTC
1 TCTCTTTTCTTTTTTC
*
58030 TTTCTTTTCTTTTT
1 TCTCTTTTCTTTTT
58044 CGATCGCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTCTTTTCTTTTTTC
Found at i:58773 original size:14 final size:14
Alignment explanation
Indices: 58751--58796 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
58741 CTTAAAAACC
58751 TTTTTGAAAACTCA
1 TTTTTGAAAACTCA
*
58765 TTTTGGAAAAC-CA
1 TTTTTGAAAACTCA
58778 TTTCTTGAAAA-TCA
1 TTT-TTGAAAACTCA
58792 TTTTT
1 TTTTT
58797 TTTGAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (14 bp):
TTTTTGAAAACTCA
Found at i:58916 original size:39 final size:39
Alignment explanation
Indices: 58873--58950 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
58863 CTTTTTATTC
*
58873 TCTTTTTGCAACCTCTTTCTTTTTTAGGCCCAGTTTTTT
1 TCTTTTTGCAACCTCTTTCTTTTTTAGGCCCAATTTTTT
*
58912 TCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAATTTTTT
1 TCTTTTTGCAACCTCTTTCTTTTTTAGGCCCAATTTTTT
58951 CTTCTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.10, C:0.23, G:0.10, T:0.56
Consensus pattern (39 bp):
TCTTTTTGCAACCTCTTTCTTTTTTAGGCCCAATTTTTT
Found at i:60892 original size:15 final size:16
Alignment explanation
Indices: 60861--60893 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60851 AGAAGAATTA
*
60861 AAAATTAAATCTAACT
1 AAAAGTAAATCTAACT
60877 AAAAGTAAAT-TAACT
1 AAAAGTAAATCTAACT
60892 AA
1 AA
60894 GAAATCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAGTAAATCTAACT
Found at i:62406 original size:20 final size:21
Alignment explanation
Indices: 62374--62412 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
62364 TAGAAAATAA
*
62374 GGTAAAAATGTATATAAAAGT
1 GGTAAAAATGTATAGAAAAGT
62395 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGTATAGAAAA
62413 ATAGCCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (21 bp):
GGTAAAAATGTATAGAAAAGT
Found at i:62413 original size:21 final size:21
Alignment explanation
Indices: 62374--62413 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62364 TAGAAAATAA
*
62374 GGTAAAAATGTATATAAAAGT
1 GGTAAAAATGTATAAAAAAGT
62395 GGTAAAAA-GTATAGAAAAA
1 GGTAAAAATGTATA-AAAAA
62414 TAGCCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (21 bp):
GGTAAAAATGTATAAAAAAGT
Found at i:63620 original size:35 final size:35
Alignment explanation
Indices: 63574--64207 Score: 544
Period size: 35 Copynumber: 18.7 Consensus size: 35
63564 TTCTTACTAA
*
63574 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTACTG-ACTC
*
63609 ACTTAATTACCCTGAATTAATTTAC-T-C-GACTC
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
*
63641 ACTTAATTACCCCGAATTAAAGTTGA-TTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACTC
* *
63677 ACTTAATTACCCTGAATTAAGTTAC-T--GGA-TT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
63708 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* *
63743 ACTCAATTACCCTGAATTAAGTTGA-TTA-TTAC-C
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* *** * * *
63776 -CTGAATTAAGTTG-ATTACTGAATTACTTAATTAC-C
1 ACTTAATTACCCTGAATTA---AGTTACTTACTGACTC
* * *
63811 -CTAAATTA---AG--TT--G--A-TCACTGACTC
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
* * *
63835 ACTTAATTACCCTGAATTAAGTTGA-TTATTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* *
63870 ACTTAGTTACCCTGAATTAAGTTGA-TTACCGACTC
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* *
63905 ACTCAATTACCCTGAATTAAGTTAATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
63940 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* * *
63975 ACTCAATTACCCTGAATTAAGTTAATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
* * *
64010 ACTCAATTACCCTGAATTAAGTTAATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
*
64045 ACTTAATTACCCTGAATTAAGTTGA-TTACTGAAAT-
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTG-ACTC
*
64080 ACTTAATTACCCTGAATTAAGTTGA-ATACTGACTC
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
* * * *
64115 ACTCAATTACCCCGAATTAAGTTAATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
* * *
64150 ACTTAATTAACCTGAATTAAGTTGA-TTACTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGACTC
64185 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
64208 GATTACTACT
Statistics
Matches: 510, Mismatches: 52, Indels: 74
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.01
24 2 0.00
25 7 0.01
28 1 0.00
30 2 0.00
31 33 0.06
32 33 0.06
33 6 0.01
34 21 0.04
35 373 0.73
36 27 0.05
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGACTC
Found at i:63774 original size:22 final size:22
Alignment explanation
Indices: 63748--63792 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
63738 GACTCACTCA
63748 ATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATT
63770 ATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATT
63792 A
1 A
63793 CTGAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATTACCCTGAATTAAGTTGATT
Found at i:63782 original size:57 final size:57
Alignment explanation
Indices: 63713--63825 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
63703 GGATTACTTA
* *
63713 ATTACCCTGAATTAAGTTGATTACTGACTCACTCAATTACCCTGAATTAAGTTGATT
1 ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTAAATTAAGTTGATT
* *
63770 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTAAATTAAGTTGAT
1 ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTAAATTAAGTTGAT
63826 CACTGACTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38
Consensus pattern (57 bp):
ATTACCCTGAATTAAGTTGATTACTGAATCACTCAATTACCCTAAATTAAGTTGATT
Found at i:63812 original size:92 final size:88
Alignment explanation
Indices: 63682--63864 Score: 294
Period size: 92 Copynumber: 2.0 Consensus size: 88
63672 GACTCACTTA
* * *
63682 ATTACCCTGAATTAAGTTACTGGATTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTC
1 ATTACCCTGAATTAAGTTACTGAATTACTTAATTACCCTAAATTAAGTTGATCACTGACTCACTC
63747 AATTACCCTGAATTAAGTTGATT
66 AATTACCCTGAATTAAGTTGATT
63770 ATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTAAATTAAGTTGATCACTGACTC
1 ATTACCCTGAATTAA---G-TTACTGAATTACTTAATTACCCTAAATTAAGTTGATCACTGACTC
*
63835 ACTTAATTACCCTGAATTAAGTTGATT
62 ACTCAATTACCCTGAATTAAGTTGATT
63862 ATT
1 ATT
63865 GAATTACTTA
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
88 15 0.17
91 1 0.01
92 71 0.82
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (88 bp):
ATTACCCTGAATTAAGTTACTGAATTACTTAATTACCCTAAATTAAGTTGATCACTGACTCACTC
AATTACCCTGAATTAAGTTGATT
Found at i:64208 original size:35 final size:35
Alignment explanation
Indices: 63770--64214 Score: 656
Period size: 35 Copynumber: 12.7 Consensus size: 35
63760 TAAGTTGATT
*
63770 ATTACCCTGAATTAAGTTGATTACTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* * *
63805 ATTACCCTAAATTAAGTTGATCACTGACTCACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
63840 ATTACCCTGAATTAAGTTGATTATTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* * * *
63875 GTTACCCTGAATTAAGTTGATTACCGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
63910 ATTACCCTGAATTAAGTTAATTACTGACTCACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
63945 ATTACCCTGAATTAAGTTGATTACTGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
63980 ATTACCCTGAATTAAGTTAATTACTGACTTACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
*
64015 ATTACCCTGAATTAAGTTAATTACTGACTTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
**
64050 ATTACCCTGAATTAAGTTGATTACTGAAATACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* * *
64085 ATTACCCTGAATTAAGTTGAATACTGACTCACTCA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
64120 ATTACCCCGAATTAAGTTAATTACTGACTTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
* *
64155 ATTAACCTGAATTAAGTTGATTACTGAATTACTTA
1 ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
64190 ATTACCCTGAATTAAGTTGATTACT
1 ATTACCCTGAATTAAGTTGATTACT
64215 ACTGACTCAC
Statistics
Matches: 368, Mismatches: 42, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 368 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (35 bp):
ATTACCCTGAATTAAGTTGATTACTGACTTACTTA
Found at i:64680 original size:22 final size:22
Alignment explanation
Indices: 64655--64698 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
64645 AATAAGATCT
*
64655 ACTCATTAATCATAAACTAAAA
1 ACTCATAAATCATAAACTAAAA
*
64677 ACTCATAAATCTTAAACTAAAA
1 ACTCATAAATCATAAACTAAAA
64699 GCCAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
ACTCATAAATCATAAACTAAAA
Done.