Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009539.1 Kokia drynarioides strain JFW-HI SEQ_124251, 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: 107024
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 174 characters in sequence are not A, C, G, or T
Found at i:4405 original size:23 final size:23
Alignment explanation
Indices: 4375--4477 Score: 113
Period size: 23 Copynumber: 4.5 Consensus size: 23
4365 ACGCTAGCGC
*
4375 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTTGTGT
4398 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * *
4421 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* *
4443 GCCTACTGGATT-GCA-TTGTGTGT
1 GCTTACT-GTTTCGCACTT-TGTGT
4466 GCTTACTGTTTC
1 GCTTACTGTTTC
4478 CCCAGCACTT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
22 21 0.30
23 49 0.70
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:11331 original size:23 final size:23
Alignment explanation
Indices: 11282--11381 Score: 98
Period size: 23 Copynumber: 4.4 Consensus size: 23
11272 CTAGCGCGCT
* * *
11282 TACTGTTTCGTACT-TCGTTTGCT
1 TACTGTTTCGCACTGT-GTGTGCC
*
11305 TACTGTTTCGCACTTTGTGTGCC
1 TACTGTTTCGCACTGTGTGTGCC
*
11328 TACTGATT-GCACTGTGTGTGCC
1 TACTGTTTCGCACTGTGTGTGCC
* *
11350 TACTGGATT-GCACTGTGTGTGCT
1 TACT-GTTTCGCACTGTGTGTGCC
11373 TACTGTTTC
1 TACTGTTTC
11382 CCCAGCACTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
22 20 0.30
23 46 0.69
24 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (23 bp):
TACTGTTTCGCACTGTGTGTGCC
Found at i:11345 original size:22 final size:22
Alignment explanation
Indices: 11305--11377 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 22
11295 TTCGTTTGCT
* *
11305 TACTGTTTCGCACTTTGTGTGCC
1 TACTGATT-GCACTGTGTGTGCC
11328 TACTGATTGCACTGTGTGTGCC
1 TACTGATTGCACTGTGTGTGCC
*
11350 TACTGGATTGCACTGTGTGTGCT
1 TACT-GATTGCACTGTGTGTGCC
11373 TACTG
1 TACTG
11378 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (22 bp):
TACTGATTGCACTGTGTGTGCC
Found at i:12668 original size:20 final size:20
Alignment explanation
Indices: 12645--12695 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
12635 ATTTTTATGT
12645 TTGTATCATCGTTTTATTGG
1 TTGTATCATCGTTTTATTGG
12665 TTGTATCATCGTTTTATTGG
1 TTGTATCATCGTTTTATTGG
*
12685 TTATA-CATCGT
1 TTGTATCATCGT
12696 CTCATTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (20 bp):
TTGTATCATCGTTTTATTGG
Found at i:12958 original size:14 final size:16
Alignment explanation
Indices: 12929--12960 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
12919 AGGGTTTTGT
12929 AATTTGTAAGGGTTTA
1 AATTTGTAAGGGTTTA
12945 AATTT-TAA-GGTTTA
1 AATTTGTAAGGGTTTA
12959 AA
1 AA
12961 GTGATGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
AATTTGTAAGGGTTTA
Found at i:17095 original size:19 final size:19
Alignment explanation
Indices: 17068--17110 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
17058 CGTCAAATAT
* * *
17068 ATTAATAAATAATTTTAAA
1 ATTAATAAAAAAATTAAAA
*
17087 ATTATTAAAAAAATTAAAA
1 ATTAATAAAAAAATTAAAA
17106 ATTAA
1 ATTAA
17111 ATACTCAAAG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAATAAAAAAATTAAAA
Found at i:17567 original size:18 final size:20
Alignment explanation
Indices: 17531--17575 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
17521 AAAATTTATA
17531 TTTAAAAAAACTATAAAAAT
1 TTTAAAAAAACTATAAAAAT
*
17551 TTTAAAAAAAGT-T-AAAAT
1 TTTAAAAAAACTATAAAAAT
17569 TTTAAAA
1 TTTAAAA
17576 CTTTTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
20 11 0.46
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TTTAAAAAAACTATAAAAAT
Found at i:19597 original size:28 final size:29
Alignment explanation
Indices: 19560--19615 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
19550 AATAGAATAT
*
19560 AATTACTAACGCAATACAA-T-AAATTATA
1 AATTACTAAC-AAATACAATTAAAATTATA
*
19588 AATTATTAACAAATACAATTAAAATTAT
1 AATTACTAACAAATACAATTAAAATTAT
19616 TTTTAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 10 0.42
29 7 0.29
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (29 bp):
AATTACTAACAAATACAATTAAAATTATA
Found at i:28731 original size:2 final size:2
Alignment explanation
Indices: 28724--28758 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28714 GCTTTAACAC
28724 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28759 ACAAATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:33535 original size:23 final size:24
Alignment explanation
Indices: 33509--33556 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
33499 CAACCAATCA
*
33509 AATTCGCCAGC-CTTTCGCTTCTT
1 AATTCGCCAACGCTTTCGCTTCTT
*
33532 AATTGGCCAACTGCTTTCGCTTCTT
1 AATTCGCCAAC-GCTTTCGCTTCTT
33557 CCTATAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
25 12 0.57
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTCGCCAACGCTTTCGCTTCTT
Found at i:35143 original size:127 final size:127
Alignment explanation
Indices: 35003--35249 Score: 350
Period size: 127 Copynumber: 1.9 Consensus size: 127
34993 ATTTATATTT
* * * * *
35003 ATATTTTATTATTTTACATCTAAAAATTGAAATATATAATGAAAATATTGGATGAAATAGATACA
1 ATATTTTATTATTTTACATCTAAAAATTAAAATATATAAGGAAAATATTAGATAAAATAGAGACA
* * * * *
35068 TCGCATCATCTTATATATTTTATTAATTCTTTAATATCATTTTAACATATTTTTTCATGTTA
66 TCACAGCATCTTATATATTTTACTAATTATTTAATATCATTTCAACATATTTTTTCATGTTA
* *
35130 ATATTTTATTATTTTACATCTAAAAATTAAAATATATAAGGAAAATATTATATAAAATAGAGACG
1 ATATTTTATTATTTTACATCTAAAAATTAAAATATATAAGGAAAATATTAGATAAAATAGAGACA
* * * *
35195 TCATAGCATCTTATGTCTTTTACTAATTATTTAATATCATTTCAACATTTTTTTT
66 TCACAGCATCTTATATATTTTACTAATTATTTAATATCATTTCAACATATTTTTT
35250 ATACTACTGA
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
127 104 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (127 bp):
ATATTTTATTATTTTACATCTAAAAATTAAAATATATAAGGAAAATATTAGATAAAATAGAGACA
TCACAGCATCTTATATATTTTACTAATTATTTAATATCATTTCAACATATTTTTTCATGTTA
Found at i:35457 original size:2 final size:2
Alignment explanation
Indices: 35450--35488 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
35440 CAATCCTTTC
* * *
35450 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35489 TTAATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35465 original size:10 final size:10
Alignment explanation
Indices: 35450--35488 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
35440 CAATCCTTTC
*
35450 TATATATATA
1 TATATATATG
35460 TATATATATG
1 TATATATATG
35470 TATATATATG
1 TATATATATG
*
35480 TATGTATAT
1 TATATATAT
35489 TTAATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (10 bp):
TATATATATG
Found at i:44396 original size:5 final size:6
Alignment explanation
Indices: 44382--44417 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
44372 AATCTCCTCG
* *
44382 AAAACA AAAACA AAAATA AAAATA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
44418 CTATAGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (6 bp):
AAAACA
Found at i:46546 original size:19 final size:21
Alignment explanation
Indices: 46524--46586 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
46514 TTTAAAAAAG
46524 TTATTAATTTTTAG-AT-TTT
1 TTATTAATTTTTAGAATATTT
46543 TTATT--TTTTT-GAATATTT
1 TTATTAATTTTTAGAATATTT
*
46561 TTA-TAATTTTTAAAATATTT
1 TTATTAATTTTTAGAATATTT
46581 TT-TTAA
1 TTATTAA
46587 CATGAAGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 1 0.03
17 8 0.22
18 6 0.16
19 10 0.27
20 12 0.32
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TTATTAATTTTTAGAATATTT
Found at i:47013 original size:23 final size:24
Alignment explanation
Indices: 46965--47013 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
46955 AGATTTAGAA
* *
46965 TTTAGTCCTTTTTATTTTTAAGAT
1 TTTAGTCCTTCTTATTTTCAAGAT
46989 TTTAGTCC-TCTTACTTTTCAA-AT
1 TTTAGTCCTTCTTA-TTTTCAAGAT
47012 TT
1 TT
47014 CAAAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTAGTCCTTCTTATTTTCAAGAT
Found at i:52491 original size:2 final size:2
Alignment explanation
Indices: 52479--52517 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
52469 AGTGTTTTAA
52479 AT AT GAT 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 AT AT AT
52518 GTTTATGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57411 original size:20 final size:20
Alignment explanation
Indices: 57386--57427 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
57376 CTTATTGGAG
57386 AAAGAAGGTAGTGATATAGT
1 AAAGAAGGTAGTGATATAGT
57406 AAAGAAGGTAGTGATATAGT
1 AAAGAAGGTAGTGATATAGT
57426 AA
1 AA
57428 CGATGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (20 bp):
AAAGAAGGTAGTGATATAGT
Found at i:58478 original size:17 final size:18
Alignment explanation
Indices: 58439--58480 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58429 ATAATTCTTT
* *
58439 TTAAAAGTATTTTTGACA
1 TTAAAAGTAATTTTGAAA
58457 TTAAAAGTAATTTT-AAA
1 TTAAAAGTAATTTTGAAA
58474 TTAAAAG
1 TTAAAAG
58481 CAATGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (18 bp):
TTAAAAGTAATTTTGAAA
Found at i:58909 original size:13 final size:14
Alignment explanation
Indices: 58883--58922 Score: 66
Period size: 13 Copynumber: 3.0 Consensus size: 14
58873 CAAAAGTATC
58883 TTTCAAAATCACTT
1 TTTCAAAATCACTT
58897 TTTCAAAAT-ACTT
1 TTTCAAAATCACTT
58910 TTT-AAAATCACTT
1 TTTCAAAATCACTT
58923 CTCAAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 9 0.36
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTCAAAATCACTT
Found at i:58916 original size:26 final size:27
Alignment explanation
Indices: 58869--58922 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
58859 TAAACCAAAC
58869 TTTTCAAAAGTATCTTTCAAAATCACT
1 TTTTCAAAAGTATCTTTCAAAATCACT
*
58896 TTTTCAAAA-TA-CTTTTTAAAATCACT
1 TTTTCAAAAGTATC-TTTCAAAATCACT
58922 T
1 T
58923 CTCAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 15 0.60
27 9 0.36
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTTCAAAAGTATCTTTCAAAATCACT
Found at i:58929 original size:13 final size:13
Alignment explanation
Indices: 58883--58929 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
58873 CAAAAGTATC
58883 TTTCAAAATCACTT
1 TTTCAAAATCAC-T
58897 TTTCAAAAT-ACT
1 TTTCAAAATCACT
*
58909 TTTTAAAATCACT
1 TTTCAAAATCACT
*
58922 TCTCAAAA
1 TTTCAAAA
58930 ACAATACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 9 0.31
13 11 0.38
14 9 0.31
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTCAAAATCACT
Found at i:60541 original size:102 final size:100
Alignment explanation
Indices: 60422--60612 Score: 242
Period size: 101 Copynumber: 1.9 Consensus size: 100
60412 GCAAAATTAT
* *
60422 CATTTAAAAATAATTTTAATAATTTTAG-AAATAAATTATGAACTTTTCAGT-TTTTTATAATTT
1 CATTTAAAAATAATTTTAATAATTTTAGCAAATAAATTATGAA-TTTT--GTAGTTTTAGAATTT
60485 TCTAAATTTCTACATTTTTAGGGATTTTTTTTAATTCTG
63 TCTAAATTTCTACATTTTTAGGG-TTTTTTTTAATTCTG
* * * *
60524 CATTTTAAAATATTTTTAATAGTTTTTGCAAATAAATTATGAATTTTGTAGTTTTAGAATTTTCT
1 CATTTAAAAATAATTTTAATAATTTTAGCAAATAAATTATGAATTTTGTAGTTTTAGAATTTTCT
* * * *
60589 AAGTTTTTAGATTTTTTGGGTTTT
66 AAATTTCTACATTTTTAGGGTTTT
60613 GGCCTTTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
100 6 0.08
101 29 0.38
102 28 0.36
103 14 0.18
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.53
Consensus pattern (100 bp):
CATTTAAAAATAATTTTAATAATTTTAGCAAATAAATTATGAATTTTGTAGTTTTAGAATTTTCT
AAATTTCTACATTTTTAGGGTTTTTTTTAATTCTG
Found at i:67486 original size:28 final size:28
Alignment explanation
Indices: 67411--67768 Score: 180
Period size: 29 Copynumber: 12.5 Consensus size: 28
67401 AGAACTTTCC
*
67411 AAAATTCCATTTTTGA-CCCTAAATTTTCTA
1 AAAATTCCA-TTTT-ACCCCTAAA-CTTCTA
**
67441 AAAATTATAATTTTACCCCTAAACTTCT-
1 AAAATT-CCATTTTACCCCTAAACTTCTA
*
67469 AAAATTCCATTTTAACCCTAAACTTTCTA
1 AAAATTCCATTTTACCCCTAAAC-TTCTA
* * * * *
67498 AAAATTACA-TTTACCCC-GAATTTTTC
1 AAAATTCCATTTTACCCCTAAACTTCTA
** * *
67524 AAAATTTTATTTTTGACCTC-GAACTT-TA
1 AAAATTCCA-TTTT-ACCCCTAAACTTCTA
* *
67552 CAAAATTACCATTTTACCCTTAAACTT-TCC
1 -AAAATT-CCATTTTACCCCTAAACTTCT-A
* * * *
67582 AAAATTCCATTTTAACCCTGAACTTTTC
1 AAAATTCCATTTTACCCCTAAACTTCTA
*
67610 AAAATTACCATTCTACCCCTAAA-TGTCTA
1 AAAATT-CCATTTTACCCCTAAACT-TCTA
* * * *
67639 AAAATTCCATTTTTGACCTCGAACCTTCCA
1 AAAATTCCA-TTTT-ACCCCTAAACTTCTA
67669 AAAATTACCATTTTACCCCTAAA-TGTCTA
1 AAAATT-CCATTTTACCCCTAAACT-TCTA
* * * *
67698 AAAATACCATTTTTAACCCCGAACCTTC-C
1 AAAATTCCA-TTTT-ACCCCTAAACTTCTA
* **
67727 AAAATTACCATTTTACCCTCGAATGTT-TA
1 AAAATT-CCATTTTACCC-CTAAACTTCTA
67756 AAAATTCCATTTT
1 AAAATTCCATTTT
67769 TAACCTCGAA
Statistics
Matches: 255, Mismatches: 48, Indels: 52
0.72 0.14 0.15
Matches are distributed among these distances:
26 10 0.04
27 16 0.06
28 66 0.26
29 108 0.42
30 49 0.19
31 6 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTAAACTTCTA
Found at i:67496 original size:57 final size:58
Alignment explanation
Indices: 67411--67799 Score: 322
Period size: 57 Copynumber: 6.8 Consensus size: 58
67401 AGAACTTTCC
* * * **
67411 AAAATTCCATTTTTGACCCTAAATTTTCTAAAAATTATAATTTTACCCCTAAACTTCT-
1 AAAATTCCATTTTTAACCCTGAACTTTCTAAAAATTACCATTTTACCCCTAAA-TTCTA
* * * * *
67469 AAAATTCCA-TTTTAACCCTAAACTTTCTAAAAATTA-CA-TTTACCCCGAATTTTTC
1 AAAATTCCATTTTTAACCCTGAACTTTCTAAAAATTACCATTTTACCCCTAAATTCTA
** * * *
67524 AAAATTTTATTTTTGA-CCTCGAAC-TT-TACAAAATTACCATTTTACCCTTAAACTT-TCC
1 AAAATTCCATTTTTAACCCT-GAACTTTCTA-AAAATTACCATTTTACCCCTAAA-TTCT-A
* *
67582 AAAATTCCA-TTTTAACCCTGAACTTT-TCAAAATTACCATTCTACCCCTAAATGTCTA
1 AAAATTCCATTTTTAACCCTGAACTTTCTAAAAATTACCATTTTACCCCTAAAT-TCTA
* * *
67639 AAAATTCCATTTTTGA-CCTCGAACCTTCCAAAAATTACCATTTTACCCCTAAATGTCTA
1 AAAATTCCATTTTTAACCCT-GAACTTTCTAAAAATTACCATTTTACCCCTAAAT-TCTA
* * * * * *
67698 AAAATACCATTTTTAACCCCGAACCTTC-CAAAATTACCATTTTA-CCCTCGAATGTTTA
1 AAAATTCCATTTTTAACCCTGAACTTTCTAAAAATTACCATTTTACCCCT-AAAT-TCTA
*
67756 AAAATTCCATTTTTAA-CCTCGAATCTTTC-GAAAATTACCATTTT
1 AAAATTCCATTTTTAACCCT-GAA-CTTTCTAAAAATTACCATTTT
67800 GTTCCAAGAA
Statistics
Matches: 277, Mismatches: 35, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
54 5 0.02
55 29 0.10
56 12 0.04
57 84 0.30
58 77 0.28
59 68 0.25
60 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCTGAACTTTCTAAAAATTACCATTTTACCCCTAAATTCTA
Found at i:73390 original size:31 final size:31
Alignment explanation
Indices: 73355--73418 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
73345 GAGCTTTGCC
* *
73355 TCCAATAATTTCATTTGCCTTGTGACCATGT
1 TCCAATAATTTCATTTACCTTATGACCATGT
73386 TCCAATAATTTCATTTACCTTATGACCATGT
1 TCCAATAATTTCATTTACCTTATGACCATGT
73417 TC
1 TC
73419 AAGCAATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.42
Consensus pattern (31 bp):
TCCAATAATTTCATTTACCTTATGACCATGT
Found at i:74026 original size:49 final size:49
Alignment explanation
Indices: 73948--74626 Score: 391
Period size: 49 Copynumber: 13.8 Consensus size: 49
73938 ACAGGTTTCG
* *
73948 GTACCACGAAG-TATGAAGGGAAAGATTTAAGTTGCAACGACGAATCTA
1 GTACCACGAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
* * * * * * *
73996 GTACCACGAAGATATGGAGGGAAAGTTTTAAGTCGCAACAGCGAACCTT
1 GTACCACGAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
* *** *
74045 GTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCA
1 GTACCAC-GAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
* * ** * * * * * *
74094 GTACCGCGAAGATACAAAAGGAAAGGTTTAAGTCGCAATGGCAAACCTTA
1 GTACCACGAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATC-TA
* * * *
74144 -TACCTC-AGAGACATGAAGGGAAAGATTTAAGCTGCAGCGGCAAATCTA
1 GTACCACGA-AGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
** * * * * *
74192 GTACCACGAAGACACAAAAAGGAAAGGTTTAAGATGCAATGGCGAACCTTA
1 GTACCACGAAGACA-TGAAGGGAAAGATTTAAGTTGCAACGGCGAATC-TA
** * *
74243 -TACC-TTATAGACATGAAGGGAAAGATTTAAGTTGCAATGGCGAATCCA
1 GTACCACGA-AGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
* * ** *
74291 GTACCACGAAGATACA-AAAGGGAAAGGTTTAAGTTGCAATAGCGAACCTTA
1 GTACCACGAAG--ACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATC-TA
* **
74342 -TACCTCAGAAG-CATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 GTACCAC-GAAGACATG-AAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
** * ** * *
74391 GTACCACGAAGACACAAAAGGGAAAGCTTTAAGTCACAATGGCGAACCTTA
1 GTACCACGAAGACA-TGAAGGGAAAGATTTAAGTTGCAACGGCGAATC-TA
* ** * *
74442 -TACCTTA-G-AGACATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCCA
1 GTACC--ACGAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
* * ** * * * *
74490 ATACCACGAATACACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTA
1 GTACCACGAAGACA-TGAAGGGAAAGATTTAAGTTGCAACGGCGAATC-TA
* * * *
74541 -TACCTTA-AAAG-CATGAAAGGGAAATATTTAAGCTGCAACGGCGAATCCA
1 GTACC--ACGAAGACATG-AAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
** * *
74590 GTACCACGAA-ACACAAAGGGAAAGGTTTAAGTCGCAA
1 GTACCACGAAGACATGAAGGGAAAGATTTAAGTTGCAA
74627 TGGCAAACCT
Statistics
Matches: 484, Mismatches: 112, Indels: 70
0.73 0.17 0.11
Matches are distributed among these distances:
47 1 0.00
48 42 0.09
49 219 0.45
50 204 0.42
51 16 0.03
52 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (49 bp):
GTACCACGAAGACATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCTA
Found at i:74255 original size:99 final size:100
Alignment explanation
Indices: 73960--74691 Score: 914
Period size: 99 Copynumber: 7.4 Consensus size: 100
73950 ACCACGAAGT
* * * * *** *
73960 ATGAAGGGAAAGATTTAAGTTGCAACGACGAATCTAGTACCACGAAGATA-TGGAGGGAAAGTTT
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
** *
74024 TAAGTCGCAACAGCGAACCTTGTACCTCAGA-AGC
66 TAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
** * *
74058 ATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCGCGAAGATACAAAA-GGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
*
74122 TAAGTCGCAATGGCAAACCTTATACCTCAGAGA-C
66 TAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
* * * *
74156 ATGAAGGGAAAGATTTAAGCTGCAGCGGCAAATCTAGTACCACGAAGACACAAAAAGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
* *
74221 TAAGAT-GCAATGGCGAACCTTATACCTTATAGA-C
66 TAAG-TCGCAATGGCGAACCTTATACCTCAGAGAGC
* * *
74255 ATGAAGGGAAAGATTTAAGTTGCAATGGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
* *
74320 TAAGTTGCAATAGCGAACCTTATACCTCAGA-AGC
66 TAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
* * *
74354 ATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGAAAGCT
1 ATG-AAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGT
* *
74419 TTAAGTCACAATGGCGAACCTTATACCTTAGAGA-C
65 TTAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
* * * * *
74454 ATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAATACCACGAATACACAAAAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
* *
74519 TAAGTCGCAATGGCGAACCTTATACCTTA-AAAGC
66 TAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
*
74553 ATGAAAGGGAAATATTTAAGCTGCAACGGCGAATCCAGTACCACGAA-ACAC-AAAGGGAAAGGT
1 ATG-AAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGT
*
74616 TTAAGTCGCAATGGCAAACCTTATACCTCAGA-AGC
65 TTAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
* * * * * **
74651 ATGAA-AGAAAAATTAAAGCCGCAACTGCGAATTTAGTACCA
1 ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCA
74692 TGCGTTTTGA
Statistics
Matches: 557, Mismatches: 66, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
96 29 0.05
97 2 0.00
98 178 0.32
99 221 0.40
100 126 0.23
101 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (100 bp):
ATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAAGGGAAAGGTT
TAAGTCGCAATGGCGAACCTTATACCTCAGAGAGC
Found at i:74438 original size:199 final size:198
Alignment explanation
Indices: 73955--74691 Score: 963
Period size: 199 Copynumber: 3.7 Consensus size: 198
73945 TCGGTACCAC
* * * * ***
73955 GAAGTATGAAGGGAAAGATTTAAGTTGCAACGACGAATCTAGTACCACGAAGATA-TGGAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGAA
* ** * * *
74019 AGTTTTAAGTCGCAACAGCGAACCTTGTACCTCAGA-AGCATGAAGGGAAAGATTTAAGCCACAA
66 AGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGA-CATGAAGGGAAAGATTTAAGCCGCAA
* * *
74083 CGGCGAATCCAGTACCGCGAAGATACAAAA-GGAAAGGTTTAAGTCGCAATGGCAAACCTTATAC
130 TGGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATAC
74147 CTCA
195 CTCA
* * *
74151 G-AGACATGAAGGGAAAGATTTAAGCTGCAGCGGCAAATCTAGTACCACGAAGACACAAAAAGGA
1 GAAG-CATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGA
* **
74215 AAGGTTTAAGAT-GCAATGGCGAACCTTATACCTTATAGACATGAAGGGAAAGATTTAAGTTGCA
65 AAGGTTTAAG-TCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAAGCCGCA
* *
74279 ATGGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTTTAAGTTGCAATAGCGAACCTTATA
129 ATGGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATA
74344 CCTCA
194 CCTCA
*
74349 GAAGCATGAAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGA
1 GAAGCATG-AAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGA
* * *
74414 AAGCTTTAAGTCACAATGGCGAACCTTATACCTTAGAGACATAAAGGGAAAGATTTAAGCCGCAA
65 AAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAAGCCGCAA
* * *
74479 TGGCGAATCCAATACCACGAATACACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATAC
130 TGGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATAC
*
74544 CTTA
195 CTCA
* * *
74548 AAAGCATGAAAGGGAAATATTTAAGCTGCAACGGCGAATCCAGTACCACGAA-ACAC-AAAGGGA
1 GAAGCATG-AAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGA
* * * * *
74611 AAGGTTTAAGTCGCAATGGCAAACCTTATACCTCAGA-AGCATGAA-AGAAAAATTAAAGCCGCA
65 AAGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGA-CATGAAGGGAAAGATTTAAGCCGCA
**
74674 ACT-GCGAATTTAGTACCA
129 A-TGGCGAATCCAGTACCA
74692 TGCGTTTTGA
Statistics
Matches: 476, Mismatches: 55, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
195 2 0.00
196 75 0.16
197 130 0.27
198 47 0.10
199 222 0.47
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (198 bp):
GAAGCATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGACACAAAAGGGAA
AGGTTTAAGTCGCAATGGCGAACCTTATACCTTAGAGACATGAAGGGAAAGATTTAAGCCGCAAT
GGCGAATCCAGTACCACGAAGATACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACC
TCA
Found at i:75044 original size:39 final size:39
Alignment explanation
Indices: 75001--75185 Score: 169
Period size: 39 Copynumber: 4.7 Consensus size: 39
74991 ATTCGATCTT
*
75001 TTACCCCGAGCCTAGGGCAGATCACCATCAACCATACTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAACCATACTC
* * * *
75040 TTACCCCGAGCCTGGGGCAGATTACTATAAACCA-ATGTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAACCATA-CTC
* * *** * * *
75079 TTACCCCGAGCTTGGGGTAGAT-TGTAGTCATTCGAT-CTT
1 TTACCCCGAGCCTGGGGCAGATCACCA-TCA-ACCATACTC
* * *
75118 TTACCCCGAGCCCGGGGCAGATCACCATAAACCAAACTC
1 TTACCCCGAGCCTGGGGCAGATCACCATCAACCATACTC
*
75157 TTACCCCGAGCCTGGGGCAGATCATCATC
1 TTACCCCGAGCCTGGGGCAGATCACCATC
75186 GATCAATCTC
Statistics
Matches: 112, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
38 5 0.04
39 104 0.93
40 3 0.03
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (39 bp):
TTACCCCGAGCCTGGGGCAGATCACCATCAACCATACTC
Found at i:75126 original size:117 final size:117
Alignment explanation
Indices: 74920--75180 Score: 387
Period size: 117 Copynumber: 2.2 Consensus size: 117
74910 AAACCCCGAT
* ***
74920 CTCTTACCTCGAGCCTGGGGCAGATCACTATAAGTTAATCTCTTACCACGAGCTTGGGGAAAATT
1 CTCTTACCCCGAGCCTGGGGCAGATCACTATAAACCAATCTCTTACCACGAGCTTGGGGAAAATT
* * *
74985 GCAGCCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAACCATA
66 GCAGCCATTCGATCTTTTACCCCGAGCCCAGGGCAGATCACCATAAACCAAA
* * * * *
75037 CTCTTACCCCGAGCCTGGGGCAGATTACTATAAACCAATGTCTTACCCCGAGCTTGGGGTAGATT
1 CTCTTACCCCGAGCCTGGGGCAGATCACTATAAACCAATCTCTTACCACGAGCTTGGGGAAAATT
* * *
75102 GTAGTCATTCGATCTTTTACCCCGAGCCCGGGGCAGATCACCATAAACCAAA
66 GCAGCCATTCGATCTTTTACCCCGAGCCCAGGGCAGATCACCATAAACCAAA
75154 CTCTTACCCCGAGCCTGGGGCAGATCA
1 CTCTTACCCCGAGCCTGGGGCAGATCA
75181 TCATCGATCA
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 128 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (117 bp):
CTCTTACCCCGAGCCTGGGGCAGATCACTATAAACCAATCTCTTACCACGAGCTTGGGGAAAATT
GCAGCCATTCGATCTTTTACCCCGAGCCCAGGGCAGATCACCATAAACCAAA
Found at i:75215 original size:78 final size:77
Alignment explanation
Indices: 75001--75217 Score: 220
Period size: 78 Copynumber: 2.8 Consensus size: 77
74991 ATTCGATCTT
* * * * * *
75001 TTACCCCGAGCCTAGGGCAGATCACCATCAACCATACTCTTACCCCGAGCCTGGGGCAGATTACT
1 TTACCCCGAGCCTGGGGCAGATCATCATCATCAAT-CTCTTACCCCGAGCCTGGGGCAGATCACC
**
75066 ATAAACCAATGTC
65 ATAAACCAAACTC
* * ** * * *
75079 TTACCCCGAGCTTGGGGTAGATTGT-AGTCATTCGATCTTTTACCCCGAGCCCGGGGCAGATCAC
1 TTACCCCGAGCCTGGGGCAGATCATCA-TCA-TCAATCTCTTACCCCGAGCCTGGGGCAGATCAC
75143 CATAAACCAAACTC
64 CATAAACCAAACTC
* * * *
75157 TTACCCCGAGCCTGGGGCAGATCATCATCGATCAATCTCCTACCTCGAGTCTGAGGCAGAT
1 TTACCCCGAGCCTGGGGCAGATCATCATC-ATCAATCTCTTACCCCGAGCCTGGGGCAGAT
75218 TGCAATTATC
Statistics
Matches: 110, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
77 1 0.01
78 104 0.95
79 5 0.05
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (77 bp):
TTACCCCGAGCCTGGGGCAGATCATCATCATCAATCTCTTACCCCGAGCCTGGGGCAGATCACCA
TAAACCAAACTC
Found at i:75745 original size:18 final size:18
Alignment explanation
Indices: 75722--75757 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
75712 TTCCTGTTAC
*
75722 ACAACAACAAGCAAAGAG
1 ACAACAACAAGAAAAGAG
*
75740 ACAACAACGAGAAAAGAG
1 ACAACAACAAGAAAAGAG
75758 GGGCAGCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.19, G:0.19, T:0.00
Consensus pattern (18 bp):
ACAACAACAAGAAAAGAG
Found at i:75846 original size:17 final size:17
Alignment explanation
Indices: 75826--75932 Score: 70
Period size: 17 Copynumber: 5.9 Consensus size: 17
75816 TTGAATTTGT
*
75826 TTTTAAATTCAAATTTA
1 TTTTAAATTTAAATTTA
* *
75843 TTTTAAGTTTAAGTTTAAA
1 TTTTAAATTTAAATTT--A
75862 TTTATTTTAAATTTAAATTTA
1 --T--TTTAAATTTAAATTTA
* *
75883 ATTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
75900 TTATCAAATTTAAATTTA
1 TT-TTAAATTTAAATTTA
** *
75918 TCCTAAATATAAATT
1 TTTTAAATTTAAATT
75933 AATAAGGTCC
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
17 39 0.57
18 14 0.20
19 1 0.01
21 2 0.03
23 13 0.19
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:75853 original size:6 final size:6
Alignment explanation
Indices: 75827--75917 Score: 75
Period size: 6 Copynumber: 15.7 Consensus size: 6
75817 TGAATTTGTT
* * * * *
75827 TTTAAA TTCAAA TTT-AT TTTAAG TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
75873 TTTAAA TTT-AA TTTAAG TTTAAA TTT--A TTATCAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTA
75918 TCCTAAATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.04
5 14 0.20
6 48 0.70
7 1 0.01
8 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:75853 original size:23 final size:23
Alignment explanation
Indices: 75827--75899 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
75817 TGAATTTGTT
*
75827 TTTAAATTCAAATTTATTTTAAG
1 TTTAAATTCAAATTTATTTTAAA
* *
75850 TTTAAGTTTAAATTTATTTTAAA
1 TTTAAATTCAAATTTATTTTAAA
* *
75873 TTTAAATT-TAATTTAAGTTTAAA
1 TTTAAATTCAAATTT-ATTTTAAA
75896 TTTA
1 TTTA
75900 TTATCAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.12
23 38 0.88
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAAATTCAAATTTATTTTAAA
Found at i:77767 original size:28 final size:28
Alignment explanation
Indices: 77668--77977 Score: 318
Period size: 28 Copynumber: 10.8 Consensus size: 28
77658 GAGATCCTCG
* *
77668 AACTTTCCAAAATTTCATTTTTTACCCCA
1 AACTTTCCAAAATTCCA-TTTTAACCCCA
* * *
77697 AACTTTCTAAAACTTACATTTTTACCCCCTA
1 AACTTTCCAAAA-TTCCA-TTTTAACCCC-A
77728 AACTTTCCAAAATTCCATTTTAACCCCA
1 AACTTTCCAAAATTCCATTTTAACCCCA
* * * *
77756 AACTTTCTAAAATTACATTTTTACTCCTA
1 AACTTTCCAAAATTCCATTTTAAC-CCCA
*
77785 AACTTTCCAAAATTCCATTTTAACCCTA
1 AACTTTCCAAAATTCCATTTTAACCCCA
* * *
77813 AACTTTCTAAAATTACATTTT-ACCCTTA
1 AACTTTCCAAAATTCCATTTTAACCC-CA
* * *
77841 AACTTTCTAAAATTCCATTTTTTATCCCA
1 AACTTTCCAAAATTCCA-TTTTAACCCCA
* *
77870 AACTTTACAAAATTACCATTTT-ACCCTA
1 AACTTTCCAAAATT-CCATTTTAACCCCA
* * *
77898 AACTTTCCAAAATTACATTTTGACCCTA
1 AACTTTCCAAAATTCCATTTTAACCCCA
*
77926 AACTTTCCAAAATTACCATTTTACCCCCTA
1 AACTTTCCAAAATT-CCATTTTAACCCC-A
77956 AACTTTCCAAAATTCCATTTTA
1 AACTTTCCAAAATTCCATTTTA
77978 TGTCCTTGGA
Statistics
Matches: 242, Mismatches: 29, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.04
28 100 0.41
29 82 0.34
30 38 0.16
31 12 0.05
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (28 bp):
AACTTTCCAAAATTCCATTTTAACCCCA
Found at i:77800 original size:57 final size:55
Alignment explanation
Indices: 77668--77977 Score: 397
Period size: 57 Copynumber: 5.4 Consensus size: 55
77658 GAGATCCTCG
* *
77668 AACTTTCCAAAATTTCATTTTTTACCCCAAACTTTCTAAAACTTACATTTTTACCCCCTA
1 AACTTTCCAAAATTCCA-TTTTAACCCCAAACTTTCTAAAA-TTACA-TTTTA--CCCTA
77728 AACTTTCCAAAATTCCATTTTAACCCCAAACTTTCTAAAATTACATTTTTACTCCTA
1 AACTTTCCAAAATTCCATTTTAACCCCAAACTTTCTAAAATTACA-TTTTAC-CCTA
*
77785 AACTTTCCAAAATTCCATTTTAACCCTAAACTTTCTAAAATTACATTTTACCCTTA
1 AACTTTCCAAAATTCCATTTTAACCCCAAACTTTCTAAAATTACATTTTACCC-TA
* * *
77841 AACTTTCTAAAATTCCATTTTTTATCCCAAACTTTAC-AAAATTACCATTTTACCCTA
1 AACTTTCCAAAATTCCA-TTTTAACCCCAAACTTT-CTAAAATTA-CATTTTACCCTA
* * * *
77898 AACTTTCCAAAATTACATTTTGACCCTAAACTTTCCAAAATTACCATTTTACCCCCTA
1 AACTTTCCAAAATTCCATTTTAACCCCAAACTTTCTAAAATTA-CATTTTA--CCCTA
77956 AACTTTCCAAAATTCCATTTTA
1 AACTTTCCAAAATTCCATTTTA
77978 TGTCCTTGGA
Statistics
Matches: 228, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
55 3 0.01
56 54 0.24
57 86 0.38
58 47 0.21
59 22 0.10
60 16 0.07
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (55 bp):
AACTTTCCAAAATTCCATTTTAACCCCAAACTTTCTAAAATTACATTTTACCCTA
Found at i:77844 original size:85 final size:86
Alignment explanation
Indices: 77668--77977 Score: 382
Period size: 85 Copynumber: 3.6 Consensus size: 86
77658 GAGATCCTCG
* * * *
77668 AACTTTCCAAAATTTCATTTTTTAC-CCCAAACTTTCTAAAACTTACATTTTTACCCCCTAAACT
1 AACTTTCCAAAATTACATTTTTTACTCCCAAACTTTCCAAAA-TTCCA-TTTTA-ACCCTAAACT
* *
77732 TTCCAAAATTCCATTTTAACCCCA
63 TTCCAAAATTACATTTTAACCCTA
* *
77756 AACTTTCTAAAATTACA-TTTTTACTCCTAAACTTTCCAAAATTCCATTTTAACCCTAAACTTTC
1 AACTTTCCAAAATTACATTTTTTACTCCCAAACTTTCCAAAATTCCATTTTAACCCTAAACTTTC
*
77820 TAAAATTACATTTT-ACCCTTA
66 CAAAATTACATTTTAACCC-TA
* * *
77841 AACTTTCTAAAATTCCATTTTTTA-TCCCAAACTTTACAAAATTACCATTTT-ACCCTAAACTTT
1 AACTTTCCAAAATTACATTTTTTACTCCCAAACTTTCCAAAATT-CCATTTTAACCCTAAACTTT
*
77904 CCAAAATTACATTTTGACCCTA
65 CCAAAATTACATTTTAACCCTA
*
77926 AACTTTCCAAAATTACCA--TTTTACCCCCTAAACTTTCCAAAATTCCATTTTA
1 AACTTTCCAAAATTA-CATTTTTTACTCCC-AAACTTTCCAAAATTCCATTTTA
77978 TGTCCTTGGA
Statistics
Matches: 196, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
84 9 0.05
85 109 0.56
86 38 0.19
87 11 0.06
88 29 0.15
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (86 bp):
AACTTTCCAAAATTACATTTTTTACTCCCAAACTTTCCAAAATTCCATTTTAACCCTAAACTTTC
CAAAATTACATTTTAACCCTA
Found at i:83220 original size:17 final size:17
Alignment explanation
Indices: 83200--83238 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
83190 ATTTTCTATA
*
83200 AATTTCTATTTTTAAAT
1 AATTTCTAGTTTTAAAT
* *
83217 AATTTTTAGTTTTGAAT
1 AATTTCTAGTTTTAAAT
83234 AATTT
1 AATTT
83239 TCATATAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
AATTTCTAGTTTTAAAT
Found at i:87922 original size:29 final size:28
Alignment explanation
Indices: 87890--87951 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
87880 AAAATGAGGC
* **
87890 TTTTCGAATACCCGGGGGTGAAATGGTAA
1 TTTT-GAATACCCAGGGGCAAAATGGTAA
*
87919 TTTTGAATCCCCAGGGGCAAAATGGTAA
1 TTTTGAATACCCAGGGGCAAAATGGTAA
87947 TTTTG
1 TTTTG
87952 GGAAAATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (28 bp):
TTTTGAATACCCAGGGGCAAAATGGTAA
Found at i:88098 original size:30 final size:30
Alignment explanation
Indices: 88054--88335 Score: 225
Period size: 30 Copynumber: 9.5 Consensus size: 30
88044 ATCCAAGGGC
88054 AAATGGTAATTTTTGGAAGTTTTTGGGGT-AA
1 AAATGG-AATTTTTGGAAG-TTTTGGGGTCAA
* * * *
88085 AATTGGATTTTTTGAAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
* **
88115 AAATGGGATTTTTGGAAGTTCGAGGGGTC-A
1 AAATGGAATTTTTGGAAGTT-TTGGGGTCAA
* * * * * * *
88145 GAATGGATTTTTTGAAAATTTTAGGGACGA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
* **
88175 AAATGGGATTTTTGGAAGTTCGGGGGT-AA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
*** *
88204 AAATGGAATTTTCAAAAGTTTTGCGGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
* *
88234 AAATGGAATTTTTGGAAG-CTCGAGGGT-AA
1 AAATGGAATTTTTGGAAGTTTTG-GGGTCAA
* * *
88263 AAATGGAATTTTTGGAAATTTTGGGATCGA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
**
88293 AAATGGAATTTTTGGAAGTTCGGGGGT-AA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
*
88322 AAATGTAATTTTTG
1 AAATGGAATTTTTG
88336 AACAGTTTAA
Statistics
Matches: 190, Mismatches: 54, Indels: 16
0.73 0.21 0.06
Matches are distributed among these distances:
29 71 0.37
30 109 0.57
31 10 0.05
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTCAA
Found at i:88334 original size:59 final size:60
Alignment explanation
Indices: 88054--88343 Score: 331
Period size: 59 Copynumber: 4.8 Consensus size: 60
88044 ATCCAAGGGC
** * *
88054 AAATGGTAATTTTTGGAAGTTTTTGGGGTAAAATTGGATTTTTTG-AAAGTTTTAGGGTCAA
1 AAATGG-AATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGAAAAGTTTTAGGGTCAA
* * * * * *
88115 AAATGGGATTTTTGGAAGTTCGAGGGGTCAGAATGGATTTTTTGAAAA-TTTTAGGGACGA
1 AAATGGAATTTTTGGAAGTTCG-GGGGTAAAAATGGAATTTTTGAAAAGTTTTAGGGTCAA
* *
88175 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAA-TTTTCAAAAGTTTT-GCGGTCAA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAAGTTTTAG-GGTCAA
* * * *
88234 AAATGGAATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAA-TTTT-GGGATCGA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAAGTTTTAGGG-TCAA
* *
88293 AAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGAACAGTTT
1 AAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAAGTTT
88344 AAGGACCTCC
Statistics
Matches: 197, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
58 11 0.06
59 106 0.54
60 71 0.36
61 9 0.05
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (60 bp):
AAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAAGTTTTAGGGTCAA
Found at i:89427 original size:3 final size:3
Alignment explanation
Indices: 89419--89529 Score: 114
Period size: 3 Copynumber: 35.3 Consensus size: 3
89409 TTTTCCTTTT
* * * *
89419 TTA TTA TTAA TGA TTA ATA ATA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
89465 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TGA GACA GTTA TTA CTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA -TTA TTA -TTA TTA
89514 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
89530 ACTACTTATG
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
3 85 0.89
4 10 0.11
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:90234 original size:17 final size:17
Alignment explanation
Indices: 90212--90308 Score: 72
Period size: 17 Copynumber: 5.6 Consensus size: 17
90202 ATTTAATTTT
90212 AATTTAAAATAAACTT-A
1 AATTTAAAATAAA-TTCA
*
90229 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTCA
* * * **
90246 AACTCAAAATGAATTTTG
1 AATTTAAAAT-AAATTCA
90264 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* *
90281 AATTTATTTAA-AAATTAA
1 AATTTA--AAATAAATTCA
90299 AATTTAAAAT
1 AATTTAAAAT
90309 TTGGACTCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
16 4 0.07
17 30 0.50
18 24 0.40
19 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:96936 original size:18 final size:17
Alignment explanation
Indices: 96904--96944 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
96894 TTTAAGTTTA
*
96904 TAATATTTAATATTATG
1 TAATTTTTAATATTATG
*
96921 TTATTTTTATATATTATG
1 TAATTTTTA-ATATTATG
96939 TAATTT
1 TAATTT
96945 AGAACTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TAATTTTTAATATTATG
Found at i:97950 original size:189 final size:189
Alignment explanation
Indices: 97630--98007 Score: 711
Period size: 189 Copynumber: 2.0 Consensus size: 189
97620 AAAATTAAAT
* *
97630 AAAGAAATAAAATGATTTTTTTGTAAAAGTTCAAAGGCCAAATAAGTTATTATACCAGATTCTTG
1 AAAGAAATAAAATGATTTTTTTATAAAAATTCAAAGGCCAAATAAGTTATTATACCAGATTCTTG
97695 ATTGAAATGAAAATCCGCTGTTCCAAGAATTCTTATACGTTAAAAAGAAATTAGTGCATAAGTCA
66 ATTGAAATGAAAATCCGCTGTTCCAAGAATTCTTATACGTTAAAAAGAAATTAGTGCATAAGTCA
97760 AAATTGATAAATTGTGAACCTAAAAATAAGACTTCGTTTGTTTTATTGAAATGATTTTC
131 AAATTGATAAATTGTGAACCTAAAAATAAGACTTCGTTTGTTTTATTGAAATGATTTTC
97819 AAAGAAATAAAATGATTTTTTTATAAAAATTCAAAGGCCAAATAAGTTATTATACCAGATTCTTG
1 AAAGAAATAAAATGATTTTTTTATAAAAATTCAAAGGCCAAATAAGTTATTATACCAGATTCTTG
* *
97884 ATTGAAATGAAAATCTGTTGTTCCAAGAATTCTTATACGTTAAAAAGAAATTAGTGCATAAGTCA
66 ATTGAAATGAAAATCCGCTGTTCCAAGAATTCTTATACGTTAAAAAGAAATTAGTGCATAAGTCA
*
97949 AAATTGATAAATTGTGAACCTAAAAATAAGACTTTGTTTGTTTTATTGAAATGATTTTC
131 AAATTGATAAATTGTGAACCTAAAAATAAGACTTCGTTTGTTTTATTGAAATGATTTTC
98008 TTAAAATAAT
Statistics
Matches: 184, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 184 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (189 bp):
AAAGAAATAAAATGATTTTTTTATAAAAATTCAAAGGCCAAATAAGTTATTATACCAGATTCTTG
ATTGAAATGAAAATCCGCTGTTCCAAGAATTCTTATACGTTAAAAAGAAATTAGTGCATAAGTCA
AAATTGATAAATTGTGAACCTAAAAATAAGACTTCGTTTGTTTTATTGAAATGATTTTC
Found at i:98916 original size:2 final size:2
Alignment explanation
Indices: 98909--98940 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
98899 AGTGGACTTT
98909 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
98941 AAGACTGTTT
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):
TA
Found at i:101893 original size:36 final size:36
Alignment explanation
Indices: 101846--101919 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
101836 ACGTGACTGA
*
101846 TCCAACTCGAACTCAGATCATACCTATAATTATTTC
1 TCCAACTCGAACTCAGATCACACCTATAATTATTTC
101882 TCCAACTCGAACTCAGATCACACCTATAATTATTTC
1 TCCAACTCGAACTCAGATCACACCTATAATTATTTC
101918 TC
1 TC
101920 TTTAATAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (36 bp):
TCCAACTCGAACTCAGATCACACCTATAATTATTTC
Found at i:106500 original size:47 final size:46
Alignment explanation
Indices: 106399--106500 Score: 177
Period size: 46 Copynumber: 2.2 Consensus size: 46
106389 ACAACAACAA
*
106399 GAAATAAAACAACCTTGATTTTGAAAATTAGCTAATTCAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
*
106445 GAAATAAAACAACCTTGATTTTGAAAAATATCTAATTCAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
106491 GAAAATAAAA
1 G-AAATAAAA
106501 AAATATTAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
46 45 0.85
47 8 0.15
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (46 bp):
GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
Done.