Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 1 of 207
Found at i:4371 original size:21 final size:21
Alignment explanation
Indices: 4329--4371 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4319 TTCACTATAC
*
4329 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
4350 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
4371 A
1 A
4372 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:5483 original size:39 final size:37
Alignment explanation
Indices: 5416--5508 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
5406 ACCAGAATGG
* *
5416 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
5455 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
5492 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5509 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:5871 original size:3 final size:3
Alignment explanation
Indices: 5863--5907 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5853 ATTCCCACTC
* * * *
5863 ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5908 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5908 original size:18 final size:18
Alignment explanation
Indices: 5863--5909 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5853 ATTCCCACTC
*
5863 ATAATAATAATAATACTA
1 ATAATAATACTAATACTA
5881 ATAATAATACTAATACTA
1 ATAATAATACTAATACTA
*
5899 ATATTAATACT
1 ATAATAATACT
5910 TACCTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATACTAATACTA
Found at i:5909 original size:12 final size:12
Alignment explanation
Indices: 5867--5907 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5857 CCACTCATAA
5867 TAATAATAATAC
1 TAATAATAATAC
5879 TAATAATAATAC
1 TAATAATAATAC
* *
5891 TAATACTAATAT
1 TAATAATAATAC
5903 TAATA
1 TAATA
5908 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:6618 original size:15 final size:15
Alignment explanation
Indices: 6600--6637 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6590 TGTTCCTTTG
6600 TTCTTTCTATTCTGT
1 TTCTTTCTATTCTGT
* *
6615 TTCTTTCTGTTTTGT
1 TTCTTTCTATTCTGT
6630 TTCTTTCT
1 TTCTTTCT
6638 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.18, G:0.08, T:0.71
Consensus pattern (15 bp):
TTCTTTCTATTCTGT
Found at i:6819 original size:31 final size:28
Alignment explanation
Indices: 6783--6850 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
6773 TTGTCTTTAT
**
6783 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
6813 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
6842 TTAATTTAT
1 TTAATTTAT
6851 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:6867 original size:21 final size:20
Alignment explanation
Indices: 6829--6867 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6819 TAATTTAATA
*
6829 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
6849 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
6868 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:15738 original size:19 final size:19
Alignment explanation
Indices: 15714--15753 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
15704 ATGAAAAGAA
*
15714 AATTCACTATGTCAAATTC
1 AATTCACTACGTCAAATTC
15733 AATTCACTACGTCAAATTC
1 AATTCACTACGTCAAATTC
15752 AA
1 AA
15754 ATGATACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (19 bp):
AATTCACTACGTCAAATTC
Found at i:16506 original size:6 final size:6
Alignment explanation
Indices: 16495--16522 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16485 TATCATCACT
16495 TTAAAA TTAAAA TTAAAA TTAAAA TTAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAA
16523 TTTTCAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:35576 original size:17 final size:17
Alignment explanation
Indices: 35554--35587 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35544 ATCCACTAAT
*
35554 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
35571 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
35588 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:40215 original size:17 final size:17
Alignment explanation
Indices: 40193--40226 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40183 ATCCACTAAT
*
40193 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
40210 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
40227 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:46652 original size:31 final size:33
Alignment explanation
Indices: 46617--46685 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 33
46607 TTTTTAATCT
* *
46617 AAATTTGGCCTTCAACCTTTT-AAAAAAAGTC-
1 AAATTTGACCATCAACCTTTTGAAAAAAAGTCG
* *
46648 AAATTTGACCATCAACTTTTTGAAAAATAGTCG
1 AAATTTGACCATCAACCTTTTGAAAAAAAGTCG
46681 AAATT
1 AAATT
46686 AATGGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 18 0.56
32 9 0.28
33 5 0.16
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (33 bp):
AAATTTGACCATCAACCTTTTGAAAAAAAGTCG
Found at i:50642 original size:12 final size:13
Alignment explanation
Indices: 50610--50645 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
50600 AAATTATCCA
*
50610 ACCCAACCTAATT
1 ACCCAACCCAATT
50623 ACCCAACCCAATT
1 ACCCAACCCAATT
50636 A-CCAACCCAA
1 ACCCAACCCAA
50646 CCCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:50739 original size:38 final size:39
Alignment explanation
Indices: 50640--50746 Score: 171
Period size: 39 Copynumber: 2.8 Consensus size: 39
50630 CCAATTACCA
*
50640 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCCAATT
1 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCAAATT
*
50679 ACCCATCCCAATAAAACTAAAACTAAAGTCTACCAAATT
1 ACCCAACCCAATAAAACTAAAACTAAAGTCTACCAAATT
* *
50718 A-CCAACCTAATAAAAATAAAACTAAAGTC
1 ACCCAACCCAATAAAACTAAAACTAAAGTC
50747 CAACTCTAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
38 25 0.40
39 38 0.60
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.19
Consensus pattern (39 bp):
ACCCAACCCAATAAAACTAAAACTAAAGTCTACCAAATT
Found at i:50924 original size:37 final size:37
Alignment explanation
Indices: 50880--50988 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
50870 TGTTAATTTC
50880 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
*
50917 AATACTTATG---TGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
* *
50951 AAGATTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
50988 A
1 A
50989 TTCAGGTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
34 32 0.49
37 33 0.51
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.48
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:53562 original size:2 final size:2
Alignment explanation
Indices: 53555--53583 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53545 TGCTTAGGGG
53555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53584 GTCTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:103135 original size:23 final size:22
Alignment explanation
Indices: 103109--103154 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
103099 ATCCAAGATC
103109 AAAACAA-CTCAAACCCAAAATTT
1 AAAACAATC-CAAA-CCAAAATTT
*
103132 AAAACAATCCAAATCAAAATTT
1 AAAACAATCCAAACCAAAATTT
103154 A
1 A
103155 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 11 0.52
24 1 0.05
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAACAATCCAAACCAAAATTT
Found at i:105555 original size:20 final size:22
Alignment explanation
Indices: 105515--105556 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
105505 AATTATTAAA
*
105515 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
105537 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
105557 AATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:105570 original size:18 final size:18
Alignment explanation
Indices: 105547--105581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105537 TAATAAATTA
* *
105547 TTTAATATTTAATTTTAT
1 TTTAATAATAAATTTTAT
105565 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
105582 AAAATAGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:113274 original size:22 final size:22
Alignment explanation
Indices: 113249--113294 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
113239 TACCGATTAC
*
113249 AGAAAGTATCTGTTAGGAGTTT
1 AGAAAGTATCTGCTAGGAGTTT
*
113271 AGAAAGTATCTGCTAGTAGTTT
1 AGAAAGTATCTGCTAGGAGTTT
113293 AG
1 AG
113295 GGGACAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (22 bp):
AGAAAGTATCTGCTAGGAGTTT
Found at i:113494 original size:27 final size:27
Alignment explanation
Indices: 113447--113498 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
113437 TAAATTTTAA
**
113447 AATTATATATAAACTTTAATTTGATAC
1 AATTATATATAAACTAAAATTTGATAC
113474 AATTATATATAAA-TGAAAATTTGAT
1 AATTATATATAAACT-AAAATTTGAT
113499 TATGATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (27 bp):
AATTATATATAAACTAAAATTTGATAC
Found at i:114523 original size:19 final size:20
Alignment explanation
Indices: 114489--114526 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
114479 AATTTTTTTA
*
114489 AAATAATAATGATTAAATTT
1 AAATAATAAGGATTAAATTT
114509 AAATAA-AAGGATTAAATT
1 AAATAATAAGGATTAAATT
114527 GATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
AAATAATAAGGATTAAATTT
Found at i:117100 original size:2 final size:2
Alignment explanation
Indices: 117095--117137 Score: 50
Period size: 2 Copynumber: 20.0 Consensus size: 2
117085 ATTATAGCTC
*
117095 TA TA TA TA TA TA TA TA TA TA TGA TG TA TGA TA TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA T-A TA TA TA
117138 ACTTGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 30 0.83
3 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (2 bp):
TA
Found at i:117125 original size:7 final size:7
Alignment explanation
Indices: 117098--117136 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
117088 ATAGCTCTAT
117098 ATATAT-
1 ATATATG
117104 ATATAT-
1 ATATATG
117110 ATATATG
1 ATATATG
*
117117 ATGTATG
1 ATATATG
117124 ATATATG
1 ATATATG
117131 ATATAT
1 ATATAT
117137 AACTTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (7 bp):
ATATATG
Found at i:119356 original size:50 final size:50
Alignment explanation
Indices: 119277--119441 Score: 204
Period size: 50 Copynumber: 3.2 Consensus size: 50
119267 GAACTTATAG
* **
119277 GGGACCTCTCATCTCGGTGCCAACCCCATGTCCCAGACATGGTCTTACAT
1 GGGACCTCTCGTCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAT
* *
119327 GGGACCTCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAG
1 GGGACCTCTCGTCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAT
* *
119377 GGGACTTCTCATGATCTTAAGGATGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 GGGACCTCTC--G-TC-T-CGG-TGCCAATGCCATGTCCCAGACATGGTCTTACAT
*
119433 GGGATCTCT
1 GGGACCTCT
119442 TTACCCAAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
50 54 0.55
52 1 0.01
53 2 0.02
54 1 0.01
55 2 0.02
56 38 0.39
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
GGGACCTCTCGTCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAT
Found at i:119557 original size:13 final size:13
Alignment explanation
Indices: 119536--119567 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
119526 GCTTGGATCA
*
119536 TCATCAAATAAAT
1 TCATAAAATAAAT
119549 TCATAAAATAAAT
1 TCATAAAATAAAT
119562 TCATAA
1 TCATAA
119568 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:125145 original size:18 final size:18
Alignment explanation
Indices: 125118--125210 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
125108 CCCAACTACT
* *
125118 GTATACGTGAACAGTACC
1 GTATATGTGAATAGTACC
125136 GTATATGTGAATAGTACC
1 GTATATGTGAATAGTACC
* *
125154 ATATGTGTGAATAGTACC
1 GTATATGTGAATAGTACC
*
125172 GTATATGTGAATAGTGCC
1 GTATATGTGAATAGTACC
* *
125190 GTATACGTAAATAGTACC
1 GTATATGTGAATAGTACC
125208 GTA
1 GTA
125211 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATATGTGAATAGTACC
Found at i:139084 original size:17 final size:17
Alignment explanation
Indices: 139048--139086 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
139038 ACAGTTAAAT
*
139048 TAATAATTTTGACAACA
1 TAATAATTTTAACAACA
* *
139065 TAATAATTTTAATAATA
1 TAATAATTTTAACAACA
139082 TAATA
1 TAATA
139087 TTATAATTTG
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:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATAATTTTAACAACA
Found at i:141116 original size:2 final size:2
Alignment explanation
Indices: 141082--141106 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141072 AATCTCTTCA
141082 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
141107 TTTGCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:146986 original size:60 final size:60
Alignment explanation
Indices: 146893--147018 Score: 252
Period size: 60 Copynumber: 2.1 Consensus size: 60
146883 ATTAAGGACA
146893 ATTAATCATGGTGTTCACATTTTCCGTCAATTTATCTTACTTTTGATTGATATAATTGCC
1 ATTAATCATGGTGTTCACATTTTCCGTCAATTTATCTTACTTTTGATTGATATAATTGCC
146953 ATTAATCATGGTGTTCACATTTTCCGTCAATTTATCTTACTTTTGATTGATATAATTGCC
1 ATTAATCATGGTGTTCACATTTTCCGTCAATTTATCTTACTTTTGATTGATATAATTGCC
147013 ATTAAT
1 ATTAAT
147019 GTCAACACAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (60 bp):
ATTAATCATGGTGTTCACATTTTCCGTCAATTTATCTTACTTTTGATTGATATAATTGCC
Found at i:153161 original size:27 final size:27
Alignment explanation
Indices: 153101--153161 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
153091 ATAAAAAATA
153101 ACTAAAATATTATAATTTTTTTTATTT
1 ACTAAAATATTATAATTTTTTTTATTT
*
153128 ACCAAAATATTATAATTTTTTTTATTT
1 ACTAAAATATTATAATTTTTTTTATTT
*
153155 ATTAAAA
1 ACTAAAA
153162 AATACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
ACTAAAATATTATAATTTTTTTTATTT
Found at i:153240 original size:27 final size:27
Alignment explanation
Indices: 153210--153282 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
153200 TCACATGGGA
*
153210 GGCACCAAAGGTGCCAATGAGATCGGC
1 GGCACCAAAGGTGCCAAAGAGATCGGC
* * *
153237 GGCACCAATGATGCCAAAGAGATTGGC
1 GGCACCAAAGGTGCCAAAGAGATCGGC
153264 GGCA-CAAATGGTGCCAAAG
1 GGCACCAAA-GGTGCCAAAG
153283 GATTAAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.08
27 36 0.92
ACGTcount: A:0.33, C:0.23, G:0.32, T:0.12
Consensus pattern (27 bp):
GGCACCAAAGGTGCCAAAGAGATCGGC
Found at i:153892 original size:19 final size:19
Alignment explanation
Indices: 153834--153892 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
153824 ACTTAATTTT
153834 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * * *
153853 TTTAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
153871 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
153890 TTA
1 TTA
153893 CTTAATTAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:153897 original size:18 final size:18
Alignment explanation
Indices: 153837--153897 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
153827 TAATTTTTTA
153837 AATTAAAATAGAGTTATTT
1 AATTAAAATAGAGTTA-TT
* * *
153856 AATGAGAATAG-TTTATT
1 AATTAAAATAGAGTTATT
153873 AAATTAAAATAGAGTTATT
1 -AATTAAAATAGAGTTATT
*
153892 ACTTAA
1 AATTAA
153898 TTAGAATTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 2 0.06
18 17 0.52
19 14 0.42
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (18 bp):
AATTAAAATAGAGTTATT
Found at i:154446 original size:27 final size:27
Alignment explanation
Indices: 154408--154471 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
154398 CATTTTAGTC
* *
154408 CTTTAGCACCATTCGTGCCGCCAATCT
1 CTTTGGCACCATTCGTGCCCCCAATCT
* *
154435 CTTTGGCACCATTGGTGCCCCCAATTT
1 CTTTGGCACCATTCGTGCCCCCAATCT
*
154462 TTTTGGCACC
1 CTTTGGCACC
154472 TTTAGTGTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTCGTGCCCCCAATCT
Found at i:154574 original size:26 final size:28
Alignment explanation
Indices: 154545--154608 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
154535 TTTTTTTGGT
154545 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
*
154571 ATATTTTGATAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
154599 ATATTTTGGT
1 ATATTTTGGT
154609 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 7 0.21
28 14 0.41
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:154599 original size:28 final size:26
Alignment explanation
Indices: 154545--154606 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
154535 TTTTTTTGGT
*
154545 ATATTTTGGTAAATAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAATTATA
154571 ATATTTTGATAAATAAAAAAAAGTTATA
1 ATATTTTGATAAAT-AAAAAAA-TTATA
154599 ATATTTTG
1 ATATTTTG
154607 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 13 0.39
27 7 0.21
28 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
ATATTTTGATAAATAAAAAAATTATA
Found at i:175707 original size:14 final size:14
Alignment explanation
Indices: 175688--175722 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
175678 ACAGAACAGG
175688 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
*
175702 AAAAAA-GAAAAGA
1 AAAAAAGGAAAAAA
175715 AAAAAAGG
1 AAAAAAGG
175723 GATTTCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAAAA
Found at i:184018 original size:27 final size:27
Alignment explanation
Indices: 183988--184073 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
183978 GTGGCTGAAG
** *
183988 AGGTGGGACCTTTGAAGGTGCCTTCAC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
*
184015 AGGTGGGACCTTCAAAGGTGCCTCCGC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
*
184042 AGGTGGGACCTTCAAAGGCGCCTTCGC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
184069 AGGTG
1 AGGTG
184074 TCTAAACCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.21
Consensus pattern (27 bp):
AGGTGGGACCTTCAAAGGTGCCTTCGC
Found at i:184626 original size:13 final size:14
Alignment explanation
Indices: 184599--184627 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
184589 TATTTGGTTA
184599 TTGGTTTAGTTAGG
1 TTGGTTTAGTTAGG
184613 TTGGTTTA-TTAGG
1 TTGGTTTAGTTAGG
184626 TT
1 TT
184628 ATGTTGGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.55
Consensus pattern (14 bp):
TTGGTTTAGTTAGG
Found at i:190496 original size:19 final size:19
Alignment explanation
Indices: 190471--190508 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
190461 ATTCCATGTT
190471 ATTTTTTTT-TAATTTTTA
1 ATTTTTTTTATAATTTTTA
*
190489 ATTTTTTTTATATTTTTTA
1 ATTTTTTTTATAATTTTTA
190508 A
1 A
190509 ATTATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTTTTATAATTTTTA
Found at i:196251 original size:21 final size:21
Alignment explanation
Indices: 196225--196265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
196215 ATCTGCTCAA
* *
196225 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
196246 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
196266 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:201369 original size:18 final size:18
Alignment explanation
Indices: 201346--201384 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
201336 TTACACGTTG
201346 TGTAATTTGATCTTTT-TT
1 TGTAATTT-ATCTTTTCTT
*
201364 TGTAATTTTTCTTTTCTT
1 TGTAATTTATCTTTTCTT
201382 TGT
1 TGT
201385 GACCCTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.13, C:0.08, G:0.10, T:0.69
Consensus pattern (18 bp):
TGTAATTTATCTTTTCTT
Found at i:202436 original size:6 final size:6
Alignment explanation
Indices: 202425--202468 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
202415 CTTTCAGTAC
*
202425 ATACAT ATACAT ATGCAT GCAATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ---ATACAT ATACAT ATACAT ATACA
202469 AAGATTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 28 0.85
9 5 0.15
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (6 bp):
ATACAT
Found at i:212488 original size:23 final size:23
Alignment explanation
Indices: 212458--212504 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
212448 CTGAACCTAC
212458 TATAACCCATCAATAAAATAAAT
1 TATAACCCATCAATAAAATAAAT
212481 TATAACCCATCAATAAAATAAAT
1 TATAACCCATCAATAAAATAAAT
212504 T
1 T
212505 CATTCAATGT
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:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TATAACCCATCAATAAAATAAAT
Found at i:212700 original size:21 final size:21
Alignment explanation
Indices: 212674--212824 Score: 79
Period size: 21 Copynumber: 7.2 Consensus size: 21
212664 CTGAAGGTTG
* *
212674 AACAGAAGCACATAAGTGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * *
212695 AACAGAAACTCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
*
212716 AACGGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * * *
212737 AACGGAAACCCATACGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * * *
212758 AACAGAGGCTCAAAAGAGTTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
212779 AACGGTAA-CTCATATGAGTTG
1 AACAG-AAGCTCATAAGAGCTA
* *
212800 AACAGAAGCTCGTGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
212821 AACA
1 AACA
212825 AAAAGTAAAC
Statistics
Matches: 95, Mismatches: 33, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
20 2 0.02
21 92 0.97
22 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:212730 original size:42 final size:42
Alignment explanation
Indices: 212669--212824 Score: 159
Period size: 42 Copynumber: 3.7 Consensus size: 42
212659 AAAGTCTGAA
* *
212669 GGTTGAACAGAAGCACATAAGTGCTAAACAGAAACTCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * * *
212711 GGTTGAACGGAAGCTCATAAGAGCTAAACGGAAACCCATACG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * * * * * * *
212753 GGTTAAACAGAGGCTCAAAAGAGTTGAACGGTAACTCATATG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * *
212795 AGTTGAACAGAAGCTCGTGAGAGCTAAACA
1 GGTTGAACAGAAGCTCATAAGAGCTAAACA
212825 AAAAGTAAAC
Statistics
Matches: 90, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
Found at i:240550 original size:16 final size:17
Alignment explanation
Indices: 240518--240560 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
240508 TTTTATCTCG
240518 AATTATTTTAAATTTAA-
1 AATT-TTTTAAATTTAAT
240535 AATATTTTTAAA-TTAAT
1 AAT-TTTTTAAATTTAAT
240552 AATTTTTTA
1 AATTTTTTA
240561 TAATCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.42
17 13 0.54
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTTTAAATTTAAT
Found at i:249084 original size:16 final size:16
Alignment explanation
Indices: 249065--249098 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
249055 TATATATATA
*
249065 TATATAGACACACACT
1 TATATACACACACACT
*
249081 TATATACATACACACT
1 TATATACACACACACT
249097 TA
1 TA
249099 ACAGAAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (16 bp):
TATATACACACACACT
Found at i:249086 original size:2 final size:2
Alignment explanation
Indices: 249038--249070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
249028 ACAACTCATA
249038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
249071 GACACACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:249519 original size:152 final size:152
Alignment explanation
Indices: 249239--249522 Score: 335
Period size: 152 Copynumber: 1.9 Consensus size: 152
249229 CCCAAATTTA
* * * *
249239 ACAATTAGGTCCAATTTGATACCTGTACTATTTTTTTTTGTCTACTTTGGTACTTGAACTTGACA
1 ACAATTAGGTCCAATTTGATACCTGTACTATTTTTTTTGGTCCACTTTGGTACCTCAACTTGACA
* * * *
249304 ACTAGATCCATTTTGGTCCATGGACTTGGCATGTAAAATTTTGATCATGTATGACGCGGCACAAT
66 ACTAGATCCATTTTGGTCCATGAACTTGACATGTAAAAGTTTGATCATGTATGACGCGACACAAT
249369 CTTAGAGTTTGCCTTTGATTAG
131 CTTAGAGTTTGCCTTTGATTAG
* * *
249391 ACAATTAGGTCTAATTTGGTACTTGTA-T-TGTTTTTTTGGTCCACTTTGGTACCTCAACTTGAC
1 ACAATTAGGTCCAATTTGATACCTGTACTAT-TTTTTTTGGTCCACTTTGGTACCTCAACTTGAC
* * * * * *
249454 -ACTAGGTCTATTTTGGT-CACTGAATTTGACAAATGTAAAAGTTTGCT-AGTGTATGATGTGAC
65 AACTAGATCCATTTTGGTCCA-TGAACTTGAC--ATGTAAAAGTTTGATCA-TGTATGACGCGAC
249516 ACAATCT
126 ACAATCT
249523 CAGAATACTA
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
149 2 0.02
150 23 0.21
151 31 0.28
152 54 0.49
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (152 bp):
ACAATTAGGTCCAATTTGATACCTGTACTATTTTTTTTGGTCCACTTTGGTACCTCAACTTGACA
ACTAGATCCATTTTGGTCCATGAACTTGACATGTAAAAGTTTGATCATGTATGACGCGACACAAT
CTTAGAGTTTGCCTTTGATTAG
Found at i:251613 original size:24 final size:23
Alignment explanation
Indices: 251575--251619 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
251565 GAAAACTTAA
251575 AATAATTATGATAAATTTAAAAT
1 AATAATTATGATAAATTTAAAAT
*
251598 AATAATATGTGATAAATTTAAA
1 AATAAT-TATGATAAATTTAAA
251620 CAACATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AATAATTATGATAAATTTAAAAT
Found at i:266143 original size:3 final size:3
Alignment explanation
Indices: 266135--266171 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
266125 AACCAAACAA
* *
266135 AAT AAT AAT AAT AAC AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
266172 GTCCAAAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:266158 original size:18 final size:17
Alignment explanation
Indices: 266130--266166 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
266120 CAAAAAACCA
266130 AACAAAATAATAATAAT
1 AACAAAATAATAATAAT
266147 AACAACAATAATAATAAT
1 AACAA-AATAATAATAAT
266165 AA
1 AA
266167 TAATAGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (17 bp):
AACAAAATAATAATAAT
Found at i:279658 original size:37 final size:37
Alignment explanation
Indices: 279608--279685 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
279598 TTCTACAGGC
* *
279608 TAAATTTGTTAAAT-TATGACTAATTTGACAGAATGTG
1 TAAATTTGTTAAATCAATAAC-AATTTGACAGAATGTG
* *
279645 TAAATTTTTTAAATCAATAACAATTTGATAGAATGTG
1 TAAATTTGTTAAATCAATAACAATTTGACAGAATGTG
279682 TAAA
1 TAAA
279686 CTTTAAAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (37 bp):
TAAATTTGTTAAATCAATAACAATTTGACAGAATGTG
Found at i:315851 original size:97 final size:97
Alignment explanation
Indices: 315735--315925 Score: 364
Period size: 97 Copynumber: 2.0 Consensus size: 97
315725 AATCCTCACA
*
315735 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCGTC
1 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
315800 GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
66 GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
*
315832 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCATCTTAGAACCAGAAATCGCATC
1 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
315897 GTTTCCTCTGCTTCGAAGCCTTCTTTTTC
66 GTTTCCTCTGCTTCGAAGCCTTCTTTTTC
315926 TCCGGGCTGC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (97 bp):
CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
Found at i:320277 original size:59 final size:58
Alignment explanation
Indices: 320159--320281 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 58
320149 CTCTAGGTCT
* * * *
320159 TTCAAGGACTAACTTGGACAAAAAAATTTCAAGCCCCAATATAGGAATAATTGTCAAG
1 TTCAAGGACTAACTTGAAAAAAAAAATTTCAAGCCCCAATATAGGAACAATTATCAAG
* * * * *
320217 TTCAAGGCCTAACTTGAATAAAAAAAAGTTT-AATCCCCAGTGTGGGAACAATTATCAAG
1 TTCAAGGACTAACTTGAA-AAAAAAAA-TTTCAAGCCCCAATATAGGAACAATTATCAAG
320276 TT-AAGG
1 TTCAAGG
320282 GCCTTTAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 20 0.37
59 31 0.57
60 3 0.06
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (58 bp):
TTCAAGGACTAACTTGAAAAAAAAAATTTCAAGCCCCAATATAGGAACAATTATCAAG
Found at i:321772 original size:31 final size:31
Alignment explanation
Indices: 321737--321812 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
321727 ATAAAGGAAT
* *
321737 AATTGCCAAGTTCA-GACCTCAATGTGAGAAC
1 AATTGCCAAGTTCAGGACC-CAATATAAGAAC
* *
321768 AATTGCTAAGTTCAGGTCCCAATATAAGAAC
1 AATTGCCAAGTTCAGGACCCAATATAAGAAC
*
321799 AATTACCAAGTTCA
1 AATTGCCAAGTTCA
321813 AATATTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (31 bp):
AATTGCCAAGTTCAGGACCCAATATAAGAAC
Found at i:328952 original size:21 final size:20
Alignment explanation
Indices: 328920--328967 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
328910 AAGCTAAATT
***
328920 TTCTTTTTTAAATTTTATTA
1 TTCTTTTTTAAAAAATATTA
328940 TTCTTTGTTTAAAAAATATTA
1 TTCTTT-TTTAAAAAATATTA
328961 TTCTTTT
1 TTCTTTT
328968 CAATTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTCTTTTTTAAAAAATATTA
Found at i:329888 original size:18 final size:18
Alignment explanation
Indices: 329861--329953 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
329851 TACGACCGTT
329861 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* * *
329879 TACGGCACTATTTATGTA
1 TACGGTACTATTCACGTA
*
329897 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
329915 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
329933 TACGGTACTGTTCAAGTA
1 TACGGTACTATTCACGTA
329951 TAC
1 TAC
329954 AGTAGTTGGG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:342866 original size:30 final size:29
Alignment explanation
Indices: 342821--342912 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 29
342811 AATTCAAATG
**
342821 TATATGTTTTATATATTGCCGAATTGATT
1 TATATGTAATATATATTGCCGAATTGATT
342850 TATATGTAGATATATATATTGCCGAATTGATTT
1 TATATGT--A-ATATATATTGCCGAATTGA-TT
*
342883 GTATATGT-ATATATATTGCCAAATTGATT
1 -TATATGTAATATATATTGCCGAATTGATT
342912 T
1 T
342913 GAGATCCCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.02
29 9 0.16
30 18 0.33
32 18 0.33
33 2 0.04
34 7 0.13
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (29 bp):
TATATGTAATATATATTGCCGAATTGATT
Found at i:342913 original size:30 final size:31
Alignment explanation
Indices: 342819--342913 Score: 129
Period size: 32 Copynumber: 3.1 Consensus size: 31
342809 TGAATTCAAA
* *
342819 TGTATATGTTTTATATATTGCCGAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
* *
342850 TATATGTAGATATATATATTGCCGAATTGATT
1 TGTATAT-GATATATATATTGCCGAATTGATT
*
342882 TGTATATG-TATATATATTGCCAAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
342912 TG
1 TG
342914 AGATCCCGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
30 23 0.41
31 6 0.11
32 27 0.48
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (31 bp):
TGTATATGATATATATATTGCCGAATTGATT
Found at i:343143 original size:48 final size:48
Alignment explanation
Indices: 342908--343142 Score: 330
Period size: 48 Copynumber: 4.9 Consensus size: 48
342898 TTGCCAAATT
* * *
342908 GATTTGAGATCCCGTATAAGACTATATTTGGGATATGACATCGGCATC
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
*
342956 GATTTGAGATC-CTGTATAAGACCATGTCTGGGATAT-AGCATCGGCATC
1 GATTTGAGATCTC-GTATAAGACCATATCTGGGATATGA-CATCGGCATC
* * *
343004 GATTTGAGATCTCGTATAATACCATGTCTAGGATATGACATCGGCATC
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
* * *
343052 GATTTGAGATCTCGTATAAGACCATATCTTGGATATGACATCGACATT
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
* *
343100 GATTTGAGATTTCGTATAAGACCATATCTGGGATATGAGATCG
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCG
343143 ATGTGAGACT
Statistics
Matches: 170, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
47 2 0.01
48 166 0.98
49 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (48 bp):
GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
Found at i:343163 original size:42 final size:42
Alignment explanation
Indices: 343049--343197 Score: 131
Period size: 48 Copynumber: 3.4 Consensus size: 42
343039 TGACATCGGC
* * * *
343049 ATCGATTTGAGATCTCGTATAAGACCATATCTTGGATATGAC
1 ATCGATGTGAGATTTCGTATAAGACCATATCTGGGATATGAG
343091 ATCGACATTGATTTGAGATTTCGTATAAGACCATATCTGGGATATGAG
1 ATCG--A-TG---TGAGATTTCGTATAAGACCATATCTGGGATATGAG
* * *
343139 ATCGATGTGAGACTTCGTGTAAGACCATAGT-TGGGCTATTG-G
1 ATCGATGTGAGATTTCGTATAAGACCATA-TCTGGGATA-TGAG
*
343181 CATCGATATGAGATTTC
1 -ATCGATGTGAGATTTC
343198 CATGTAAGAC
Statistics
Matches: 89, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
42 31 0.35
43 17 0.19
44 1 0.01
45 3 0.03
46 1 0.01
48 36 0.40
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
ATCGATGTGAGATTTCGTATAAGACCATATCTGGGATATGAG
Found at i:350444 original size:38 final size:38
Alignment explanation
Indices: 350393--350468 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
350383 GTGTAAGGTG
350393 TCTAATAGAAAATCTCAATTGATAGAATCAAAAGCTTT
1 TCTAATAGAAAATCTCAATTGATAGAATCAAAAGCTTT
350431 TCTAATAGAAAATCTCAATTGATAGAATCAAAAGCTTT
1 TCTAATAGAAAATCTCAATTGATAGAATCAAAAGCTTT
350469 CCTTCACTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (38 bp):
TCTAATAGAAAATCTCAATTGATAGAATCAAAAGCTTT
Found at i:357095 original size:14 final size:15
Alignment explanation
Indices: 357066--357098 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
357056 TCAAAAGTTT
*
357066 AATTTATTTCATCTA
1 AATTTATTTAATCTA
357081 AATTTA-TTAATCTA
1 AATTTATTTAATCTA
357095 AATT
1 AATT
357099 CAATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTATTTAATCTA
Found at i:357436 original size:17 final size:17
Alignment explanation
Indices: 357414--357446 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
357404 CATTTACTTT
*
357414 ATAATATTTTATAAAAA
1 ATAATATTTCATAAAAA
357431 ATAATATTTCATAAAA
1 ATAATATTTCATAAAA
357447 TAATTGAATA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATATTTCATAAAAA
Found at i:358416 original size:17 final size:18
Alignment explanation
Indices: 358377--358416 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
358367 AATAAATTTT
358377 TTATTTGAAAATAAATAC
1 TTATTTGAAAATAAATAC
358395 TTATTTGAATAA-AAAT-C
1 TTATTTGAA-AATAAATAC
358412 TTATT
1 TTATT
358417 CGAGTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TTATTTGAAAATAAATAC
Found at i:364217 original size:30 final size:31
Alignment explanation
Indices: 364171--364234 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
364161 ATTTCTTATG
364171 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
*
364202 CCAATAT-TTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
364232 CCA
1 CCA
364235 TAAATATGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATCTTTGACTTT
Found at i:364226 original size:15 final size:15
Alignment explanation
Indices: 364181--364227 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
364171 CCAATATCTC
364181 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
364196 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
364211 GATACCCATATCTTT
1 GATACCCATATCTTT
364226 GA
1 GA
364228 CTTTCCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:367712 original size:18 final size:19
Alignment explanation
Indices: 367679--367714 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
367669 TTCTTTTATT
*
367679 TGAAAATGATATAAATGTA
1 TGAAAATGATAAAAATGTA
367698 TGAAAA-GATAAAAATGT
1 TGAAAATGATAAAAATGT
367715 CATCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.28
Consensus pattern (19 bp):
TGAAAATGATAAAAATGTA
Found at i:371359 original size:44 final size:43
Alignment explanation
Indices: 371211--371360 Score: 113
Period size: 44 Copynumber: 3.3 Consensus size: 43
371201 GTTAAATATG
* *
371211 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTT
1 AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
** **** * * *
371254 AATTAATTTTAATTAAAT-AGTTAATTTTTTTCGTATTAGTATTGAGTC
1 AATT-ATTTTAATT-AATCACAT-ATGAAGTTC--ATTAGCAAT-AGTT
* *
371302 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTT
1 AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
371345 AATTGATTTTAATTAA
1 AATT-ATTTTAATTAA
371361 ATAGTTAATT
Statistics
Matches: 75, Mismatches: 24, Indels: 15
0.66 0.21 0.13
Matches are distributed among these distances:
43 11 0.15
44 25 0.33
45 8 0.11
46 8 0.11
47 16 0.21
48 7 0.09
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (43 bp):
AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
Found at i:371366 original size:91 final size:91
Alignment explanation
Indices: 371211--371392 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
371201 GTTAAATATG
371211 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
1 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
371276 AATTTTTTTCGTATTAGTATTGAGTC
66 AATTTTTTTCGTATTAGTATTGAGTC
*
371302 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTGATTTTAATTAAATAGTT
1 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
371367 AATTTTTTTCGTATTAGTATTGAGTC
66 AATTTTTTTCGTATTAGTATTGAGTC
371393 GATTGTTAAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (91 bp):
AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
AATTTTTTTCGTATTAGTATTGAGTC
Found at i:372823 original size:20 final size:19
Alignment explanation
Indices: 372788--372825 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
372778 TTTTGCATCA
372788 TAAAAAATTAAAATTAATT
1 TAAAAAATTAAAATTAATT
*
372807 TAAATAATTATAAATTAAT
1 TAAAAAATTA-AAATTAAT
372826 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAAATTAAAATTAATT
Found at i:372831 original size:20 final size:19
Alignment explanation
Indices: 372789--372833 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
372779 TTTGCATCAT
*
372789 AAAA-AATTAAAATTAATT
1 AAAATAATTAAAATTAATA
*
372807 TAAATAATTATAAATTAATA
1 AAAATAATTA-AAATTAATA
372827 AAAATAA
1 AAAATAA
372834 AATTAACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 5 0.23
20 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAATTAAAATTAATA
Found at i:377566 original size:29 final size:29
Alignment explanation
Indices: 377529--377598 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
377519 AAACGGAATC
377529 AAATCAAAATTTCATATATAAAATTGCACA
1 AAAT-AAAATTTCATATATAAAATTGCACA
* * * * *
377559 AAATAAAAGTTCATGTATGACATTGTACA
1 AAATAAAATTTCATATATAAAATTGCACA
*
377588 AAATCAAATTT
1 AAATAAAATTT
377599 ATCCCATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATAAAATTTCATATATAAAATTGCACA
Found at i:383867 original size:12 final size:13
Alignment explanation
Indices: 383838--383883 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
383828 AAAAACAATC
*
383838 TAAAGATTAAATAT
1 TAAATATTAAA-AT
383852 TAAATATT-AAAT
1 TAAATATTAAAAT
383864 TAAA-ATTAAAAT
1 TAAATATTAAAAT
383876 TAATATAT
1 TAA-ATAT
383884 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 3 0.11
12 13 0.46
13 3 0.11
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
TAAATATTAAAAT
Found at i:390693 original size:6 final size:6
Alignment explanation
Indices: 390682--390706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
390672 AAAAATATAT
390682 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
390707 GTTTTATGTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:392060 original size:30 final size:30
Alignment explanation
Indices: 392024--392086 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
392014 GGCTTTGACA
392024 TTAAGTTTATGGACCATTTATGAAATTACC
1 TTAAGTTTATGGACCATTTATGAAATTACC
392054 TTAAGTTTATGGACCATTTATGAAATTACC
1 TTAAGTTTATGGACCATTTATGAAATTACC
392084 TTA
1 TTA
392087 GCAATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (30 bp):
TTAAGTTTATGGACCATTTATGAAATTACC
Found at i:408785 original size:25 final size:26
Alignment explanation
Indices: 408753--408807 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
408743 TTATTAAATT
*
408753 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
408778 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
408803 A-ATAT
1 ATATAT
408808 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:408994 original size:44 final size:45
Alignment explanation
Indices: 408945--409039 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
408935 TTACACCTCT
* *
408945 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
408989 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
409034 ATTACA
1 ATTACA
409040 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:409039 original size:16 final size:16
Alignment explanation
Indices: 409020--409087 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
409010 GATTTGCTAT
* *
409020 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
409036 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
409052 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
409068 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
409084 TACA
1 TACA
409088 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:409599 original size:30 final size:30
Alignment explanation
Indices: 409563--409736 Score: 287
Period size: 30 Copynumber: 5.8 Consensus size: 30
409553 ACTTTTCTCA
*
409563 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
409593 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
409623 ACTAG-CACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
409652 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
409682 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
409712 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
409737 CTTGTACCTA
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
29 27 0.20
30 106 0.80
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:409638 original size:59 final size:60
Alignment explanation
Indices: 409563--409736 Score: 323
Period size: 59 Copynumber: 2.9 Consensus size: 60
409553 ACTTTTCTCA
*
409563 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
409623 ACTAG-CACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
*
409682 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
409737 CTTGTACCTA
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
59 58 0.52
60 53 0.48
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:409714 original size:89 final size:90
Alignment explanation
Indices: 409563--409736 Score: 287
Period size: 89 Copynumber: 1.9 Consensus size: 90
409553 ACTTTTCTCA
*
409563 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCACTAG
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCACTAG
* * *
409628 -CACTCTTTTTCCACCACCAACTCC
66 CCACACCTTCTCCACCACCAACTCC
* *
409652 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACTCTTTTTCCACCACCAACTCCACTAG
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCACTAG
409717 CCACACCTTCTCCACCACCA
66 CCACACCTTCTCCACCACCA
409737 CTTGTACCTA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 62 0.79
90 16 0.21
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.22
Consensus pattern (90 bp):
ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCACTAG
CCACACCTTCTCCACCACCAACTCC
Found at i:410257 original size:23 final size:23
Alignment explanation
Indices: 410220--410351 Score: 65
Period size: 25 Copynumber: 5.5 Consensus size: 23
410210 TTTTTTTTGT
410220 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
410243 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
410265 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* * *
410288 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
410315 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
*
410340 TATTATTTATAT
1 TATTATATATAT
410352 ATATATATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
21 3 0.04
22 15 0.19
23 18 0.22
24 4 0.05
25 30 0.37
26 1 0.01
27 6 0.07
28 3 0.04
29 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:410325 original size:25 final size:25
Alignment explanation
Indices: 410234--410355 Score: 74
Period size: 25 Copynumber: 5.0 Consensus size: 25
410224 ATTATATTTC
* * *
410234 TTAATATTATATTATATATAT-TCT
1 TTAATACTATATTATGTATATATAT
* *
410258 TT--TAATATATTAGGTATAT-T-T
1 TTAATACTATATTATGTATATATAT
* * *
410279 TAAATTCTATATTACGTATATATATAT
1 TTAATACTATATTA--TGTATATATAT
* * *
410306 TTTATACTATTTTATGTATATATCT
1 TTAATACTATATTATGTATATATAT
* *
410331 TTAATATTATATTATTTATATATAT
1 TTAATACTATATTATGTATATATAT
410356 ATATTTTTTT
Statistics
Matches: 73, Mismatches: 19, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
21 2 0.03
22 15 0.21
23 8 0.11
24 2 0.03
25 34 0.47
26 1 0.01
27 11 0.15
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:410347 original size:30 final size:30
Alignment explanation
Indices: 410307--410390 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
410297 TATATATATT
*
410307 TTATACTATTTTATGTATATATCTTTAATA
1 TTATATTATTTTATGTATATATCTTTAATA
* **
410337 TTATATTATTTATATATATATAT-TTTTTTA
1 TTATATTATTT-TATGTATATATCTTTAATA
* * *
410367 -CATGTTATCTTATGTATATATCTT
1 TTATATTATTTTATGTATATATCTT
410391 AACTATATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 10 0.23
29 9 0.20
30 15 0.34
31 10 0.23
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (30 bp):
TTATATTATTTTATGTATATATCTTTAATA
Found at i:410404 original size:22 final size:24
Alignment explanation
Indices: 410376--410434 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
410366 ACATGTTATC
410376 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
410398 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
410423 TTATGTACATAT
1 TTATGTATATAT
410435 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:410424 original size:25 final size:25
Alignment explanation
Indices: 410392--410440 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
410382 ATATATCTTA
**
410392 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
410417 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
410441 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:410621 original size:16 final size:14
Alignment explanation
Indices: 410602--410635 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
410592 TATTATTCTA
410602 ATATTTTGATATTTT
1 ATATTTT-ATATTTT
410617 GATATTTTATATTTT
1 -ATATTTTATATTTT
410632 ATAT
1 ATAT
410636 ATTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
ATATTTTATATTTT
Found at i:410630 original size:7 final size:8
Alignment explanation
Indices: 410602--410635 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
410592 TATTATTCTA
410602 ATATTTTG
1 ATATTTTG
410610 ATATTTTG
1 ATATTTTG
410618 ATATTTT-
1 ATATTTTG
410625 ATATTTT-
1 ATATTTTG
410632 ATAT
1 ATAT
410636 ATTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (8 bp):
ATATTTTG
Found at i:410637 original size:16 final size:15
Alignment explanation
Indices: 410602--410642 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
410592 TATTATTCTA
410602 ATATTTTGATATTTTG
1 ATATTTT-ATATTTTG
*
410618 ATATTTTATATTTTAT
1 ATATTTTATATTTT-G
410634 ATATTTTAT
1 ATATTTTAT
410643 TATTCACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
ATATTTTATATTTTG
Found at i:419110 original size:69 final size:71
Alignment explanation
Indices: 418934--419110 Score: 214
Period size: 72 Copynumber: 2.5 Consensus size: 71
418924 CTTTCCAAGG
* ** * *
418934 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTTA
*
418999 TTTTTT
66 TGTTTT
* ** *
419005 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT-AGTTT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTT
419069 ATGTTTT
65 ATGTTTT
** *
419076 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
419111 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
69 31 0.34
71 9 0.10
72 51 0.56
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAAGTTTA
TGTTTT
Found at i:419251 original size:72 final size:72
Alignment explanation
Indices: 419114--419462 Score: 416
Period size: 72 Copynumber: 4.7 Consensus size: 72
419104 TAAGCCTTTT
* ** *
419114 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACA-GCTGAGG
1 AATTTCTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
419178 TAATTTC
66 TAATTTC
**
419185 AATTTCTGTTGTTAAAAAATCAACTCATA-TGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTT-TTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
419249 GTAATTTC
65 GTAATTTC
* * * ** * *
419257 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
*
419322 TATTTTC
66 TAATTTC
*
419329 AATTTCTGTTTTCAAAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCAC
1 AATTTCTGTTTT------AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---AC
* *
419393 ATGCTGAGGTATTTTC
57 ACGCTGAGGTAATTTC
*
419409 AATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AATTTCTG-TTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
419463 ATTACCACTG
Statistics
Matches: 243, Mismatches: 21, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
71 49 0.20
72 92 0.38
75 37 0.15
76 1 0.00
77 1 0.00
78 35 0.14
80 24 0.10
81 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTC
Found at i:419544 original size:126 final size:123
Alignment explanation
Indices: 419349--419711 Score: 360
Period size: 126 Copynumber: 2.9 Consensus size: 123
419339 TTCAAAAAAA
* * *
419349 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTAATTTCAATTT
419414 CTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACCACTGTGTTT
63 CTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACCACT-T-TTT
*** * *
419478 -TTTTCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTAATTTCAATTTCT
* * * * * * *
419542 GTTTGTCAAGAATCAACT-AT-TATGCGAGAGGTGGGTTGAACCTTTTA-ATTTCTACTTTTT
65 GTTT-TTAAAAATCAACTCATAT-TGCGAGAGGTGAGTTG-AGC-TTCAGATTACCACTTTTT
* * * * *
419602 CAAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT-ATTTCATTTTG
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTAATTTCAATTTC
** *
419666 TGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
64 TGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
419712 GACACGCTGA
Statistics
Matches: 190, Mismatches: 34, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
122 2 0.01
123 9 0.05
124 22 0.12
125 33 0.17
126 87 0.46
127 4 0.02
128 31 0.16
129 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (123 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTAATTTCAATTTCTG
TTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACCACTTTTT
Found at i:419688 original size:70 final size:72
Alignment explanation
Indices: 419611--419748 Score: 219
Period size: 70 Copynumber: 1.9 Consensus size: 72
419601 TCAAAATCAG
* *
419611 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTA-TTTC-ATTTT-GTGTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGT-TTTTT
419673 AATTTCAA
65 AATTTCAA
*
419681 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTA
419746 ATT
66 ATT
419749 ATGTTTCAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
70 42 0.68
71 4 0.06
72 14 0.23
73 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (72 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTA
ATTTCAA
Found at i:419955 original size:73 final size:71
Alignment explanation
Indices: 419757--420003 Score: 321
Period size: 73 Copynumber: 3.5 Consensus size: 71
419747 TTATGTTTCA
* * *
419757 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA-AGACGCTGAGGTAATTTCAATTTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGA-GTATTTTCAATTTT
*
419821 GTTTT-C
65 CTTTTAC
*
419827 -AAAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGTATTTTCAATCTAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGTATTTTCAAT-TTT
419890 CTTTTAC
65 CTTTTAC
*
419897 AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT-AGGGACACGCTGAGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--GACACGCTGAGTATTTTCAATTT
419961 T-TGCTTTA-
64 TCT--TTTAC
419969 AAAAGAATCAACTCATATTGCGAGA-GTGAGTTGAG
1 AAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAG
420004 TCTCGGCCAC
Statistics
Matches: 159, Mismatches: 8, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
68 34 0.21
69 27 0.17
70 1 0.01
71 15 0.09
72 38 0.24
73 44 0.28
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (71 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGTATTTTCAATTTTC
TTTTAC
Found at i:420275 original size:69 final size:69
Alignment explanation
Indices: 420151--420282 Score: 187
Period size: 69 Copynumber: 1.9 Consensus size: 69
420141 TTCTGTTTAA
* * *
420151 AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAACCTCAAGTGCACATGAGTATTTTCAATTAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGTACACATAAGTATTTTCAATTAT
420216 CATC
66 CATC
* *
420220 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAA-CTCAAG-ACCCGTTAAGGTATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGTACAC-ATAA-GTATTTTCAATT
420283 TCTGTCAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 2 0.04
68 8 0.14
69 46 0.82
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (69 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGTACACATAAGTATTTTCAATTAT
CATC
Found at i:420497 original size:76 final size:74
Alignment explanation
Indices: 420335--420513 Score: 197
Period size: 76 Copynumber: 2.4 Consensus size: 74
420325 GTGATTGAGC
* * *
420335 CTCACATGCTGAGGTGTTTTCAA-TTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
1 CTCACATGCTGAGGTTTTTTCAATTTCT-GTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGT
*
420399 TGACCTTTGG
65 TGACCTTCGG
* *
420409 CT-ACACGCCTGAGGTATTTTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGTGA-AGGTG
1 CTCACATG-CTGAGGT-TTTTTCAATTTCTGTTGTC--AAAAATCAACTCATATTGCGAGAGGTG
*
420472 AGTTGA-GTCTCGG
62 AGTTGACCT-TCGG
420485 CTCACATGCTGAGGTCTTTTT-AATTTCTG
1 CTCACATGCTGAGGT-TTTTTCAATTTCTG
420514 CTTTTCAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
73 4 0.04
74 9 0.10
75 20 0.22
76 32 0.36
77 24 0.27
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (74 bp):
CTCACATGCTGAGGTTTTTTCAATTTCTGTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
GACCTTCGG
Found at i:420523 original size:14 final size:15
Alignment explanation
Indices: 420498--420539 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
420488 ACATGCTGAG
*
420498 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
420513 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
420527 GTTTTTTCAATTT
1 GTCTTTTCAATTT
420540 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:420535 original size:15 final size:14
Alignment explanation
Indices: 420501--420550 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
420491 TGCTGAGGTC
420501 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
420514 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
420528 TTTTTTCAATTTATA
1 -TTTTTCAATTTCTG
420543 TTTTTCAA
1 TTTTTCAA
420551 AAAAATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:420654 original size:178 final size:179
Alignment explanation
Indices: 420351--420763 Score: 601
Period size: 178 Copynumber: 2.3 Consensus size: 179
420341 TGCTGAGGTG
* * *
420351 TTTTCAA-TTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CCTTTGGCTACA
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGCGACA
* * *
420414 CGCCTGAGGTATTTTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGTGAAGGTGAGTTGAG
65 CGCCTGAGGTATATTTCAATTTCTGTTGGC-AAAAAATCAACTCATATTGCGAAGGTGAGTTGAG
420479 TCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTT
129 TCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTT
420530 TTTTCAATTTATATTTTTCAAAAAAATCAAC-CATATTGCCGA-AGGTGAGTTGAGCCTCGG-GA
1 TTTTCAATTTATATTTTTC--AAAAATCAACTCATATTG-CGAGAGGTGAGTTGAGCCTCGGCGA
*
420592 CACG-CTGAGGGTA-ATTTC-ATTTCTGTTTGGC-AAAAATTAACTCATATTGCGAGAGGTGAGT
63 CACGCCTGA-GGTATATTTCAATTTCTG-TTGGCAAAAAATCAACTCATATTGCGA-AGGTGAGT
420653 TGAGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTT
125 TGAGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTT
* * *
420708 TTTTCAATTTATATTTTTTAAAAATCAACTCATATTTCGAGATGTGAGTTGAGCCT
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
420764 TGGTTCAACA
Statistics
Matches: 214, Mismatches: 10, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
176 13 0.06
177 39 0.18
178 88 0.41
179 19 0.09
180 19 0.09
181 21 0.10
182 15 0.07
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (179 bp):
TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGACAC
GCCTGAGGTATATTTCAATTTCTGTTGGCAAAAAATCAACTCATATTGCGAAGGTGAGTTGAGTC
TCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTT
Found at i:420701 original size:14 final size:15
Alignment explanation
Indices: 420676--420717 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
420666 ACATGCTGAG
*
420676 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
420691 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
420705 GTTTTTTCAATTT
1 GTCTTTTCAATTT
420718 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:420713 original size:15 final size:14
Alignment explanation
Indices: 420679--420717 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
420669 TGCTGAGGTC
420679 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
420692 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
420706 TTTTTTCAATTT
1 -TTTTTCAATTT
420718 ATATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:420724 original size:15 final size:15
Alignment explanation
Indices: 420693--420726 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
420683 TAATTTCTGC
* *
420693 TTTTCAATTTCTGTT
1 TTTTCAATTTATATT
420708 TTTTCAATTTATATT
1 TTTTCAATTTATATT
420723 TTTT
1 TTTT
420727 AAAAATCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:420986 original size:77 final size:75
Alignment explanation
Indices: 420870--421053 Score: 246
Period size: 77 Copynumber: 2.5 Consensus size: 75
420860 ATTCTGTTCG
* * *
420870 AAAAAAATAAACTCATAGTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAAA
1 AAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-ATTT-AAA
*
420935 TTTCTGTTTTTC
64 TTTCTGTTTGTC
* * * * *
420947 AAAAAAATCAACTCATATTTCGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATT
421012 TCTGTTTGTC
66 TCTGTTTGTC
*
421022 --AAAAATTAACTCATATTGCGAGAGGTGAGTTG
1 AAAAAAATAAACTCATATTGCGAGAGGTGAGTTG
421054 GAGTCTCGGC
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
73 29 0.31
75 13 0.14
76 3 0.03
77 50 0.53
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (75 bp):
AAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATT
TCTGTTTGTC
Found at i:421899 original size:29 final size:30
Alignment explanation
Indices: 421866--422034 Score: 217
Period size: 29 Copynumber: 5.8 Consensus size: 30
421856 ACTTTTCTCA
*
421866 ACTAGCCACTCCTTTTCCACCACCAA-TCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
421895 ACTAGCCACACC-TTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* * *
421924 ACTAGCTACTCTTTTTCCACCA-CAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
421953 ACTAG-CAC-TCTTTTTCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
421981 ACTTAGCC-CACC-TTTCCACCACCAACTCC
1 AC-TAGCCACACCTTTTCCACCACCAACTCC
*
422010 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
422035 CTTGTACCTA
Statistics
Matches: 121, Mismatches: 11, Indels: 15
0.82 0.07 0.10
Matches are distributed among these distances:
27 9 0.07
28 29 0.24
29 61 0.50
30 22 0.18
ACGTcount: A:0.25, C:0.48, G:0.04, T:0.23
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:421980 original size:57 final size:57
Alignment explanation
Indices: 421866--422034 Score: 211
Period size: 57 Copynumber: 2.9 Consensus size: 57
421856 ACTTTTCTCA
421866 ACTAGCCACTCCTTTTCCACCACCAA-TCCACTAGCCACACCTTTCCACCACCAACTCC
1 ACTAGCCACT-CTTTTCCACCACCAACTCCACTAG-CACACCTTTCCACCACCAACTCC
* * * *
421924 ACTAGCTACTCTTTTTCCACCA-CAACTCCACTAGCACTCTTTTTCACCACCAACTCC
1 ACTAGCCACTC-TTTTCCACCACCAACTCCACTAGCACACCTTTCCACCACCAACTCC
421981 ACTTAGCCCAC-C-TTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 AC-TAG-CCACTCTTTTCCACCACCAACTCCACTAG-CACACCTT-TCCACCACCA
422035 CTTGTACCTA
Statistics
Matches: 96, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
56 9 0.09
57 38 0.40
58 37 0.39
59 12 0.12
ACGTcount: A:0.25, C:0.48, G:0.04, T:0.23
Consensus pattern (57 bp):
ACTAGCCACTCTTTTCCACCACCAACTCCACTAGCACACCTTTCCACCACCAACTCC
Found at i:422029 original size:86 final size:87
Alignment explanation
Indices: 421866--422032 Score: 250
Period size: 86 Copynumber: 1.9 Consensus size: 87
421856 ACTTTTCTCA
*
421866 ACTAGCCACTCCTTTTCCACCACCAATCCACTAGCCACACCTTTCCACCACCAACTCCACTAGCT
1 ACTAGCCACTCCTTTTCCACCACCAATCCACTAGCCACACCTTTCCACCACCAACTCCACTAGCC
* * *
421931 ACTCTTTTTCCACCACAACTCC
66 ACACCTTCTCCACCACAACTCC
*
421953 ACTAG-CACT-CTTTTTCACCACCAACTCCACTTAGCC-CACCTTTCCACCACCAACTCCACTAG
1 ACTAGCCACTCCTTTTCCACCACCAA-TCCAC-TAGCCACACCTTTCCACCACCAACTCCACTAG
422015 CCACACCTTCTCCACCAC
64 CCACACCTTCTCCACCAC
422033 CACTTGTACC
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
85 14 0.19
86 49 0.67
87 10 0.14
ACGTcount: A:0.25, C:0.48, G:0.04, T:0.23
Consensus pattern (87 bp):
ACTAGCCACTCCTTTTCCACCACCAATCCACTAGCCACACCTTTCCACCACCAACTCCACTAGCC
ACACCTTCTCCACCACAACTCC
Found at i:422653 original size:29 final size:28
Alignment explanation
Indices: 422592--422666 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
422582 TATATATATT
* *
422592 TTATACTATTTTATGTATATATCTTAATA
1 TTATATTA-TTTATATATATATCTTAATA
*
422621 TTATATTATTTAATATATATAT-TTACATG
1 TTATATTATTT-ATATATATATCTTA-ATA
* *
422650 TTATCTTATGTATATAT
1 TTATATTATTTATATAT
422667 CTTAACTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (28 bp):
TTATATTATTTATATATATATCTTAATA
Found at i:422869 original size:22 final size:21
Alignment explanation
Indices: 422844--422884 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
422834 TATTTCTATT
* *
422844 TTATTTTTATTGTCAATATTAA
1 TTATTATTATTCT-AATATTAA
422866 TTATTATTATTCTAATATT
1 TTATTATTATTCTAATATT
422885 TTGATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTATTATTCTAATATTAA
Found at i:422895 original size:14 final size:15
Alignment explanation
Indices: 422878--422912 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
422868 ATTATTATTC
422878 TAATATTTT-GATTT
1 TAATATTTTAGATTT
*
422892 TAATATTTTATATTT
1 TAATATTTTAGATTT
422907 TAATAT
1 TAATAT
422913 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TAATATTTTAGATTT
Found at i:422908 original size:15 final size:14
Alignment explanation
Indices: 422862--422920 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
422852 ATTGTCAATA
*
422862 TTAATTATTATTATT
1 TTAA-TATTTTTATT
* *
422877 CTAATATTTTGATT
1 TTAATATTTTTATT
422891 TTAATATTTTATATT
1 TTAATATTTT-TATT
422906 TTAATATATTTTATT
1 TTAATAT-TTTTATT
422921 ATTCCCTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 17 0.46
15 17 0.46
16 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
TTAATATTTTTATT
Found at i:435115 original size:251 final size:249
Alignment explanation
Indices: 434570--435116 Score: 652
Period size: 251 Copynumber: 2.2 Consensus size: 249
434560 GGATAATAAT
* * * * * * *
434570 AAAACATCTCCAAAAAGCTAGCTTACGTGCAAACTAACCATGTTAACATCAGTAATTCATTCTAG
1 AAAACAACTCCAAACA-C-AGCTTAAGTGCAAACTAACCATATCAACATCAATAATTCATTCAAG
* * *
434635 ATTCTAATGACTAGTAGTACAATAATAAGCACATGAAGGACAAATGATTAAATAGGAAAGCCCTA
64 ATTCTAATGACTAGTAGTAAAATAACAAGCACATGAAGGACAAATGATTAAATAGGAAAACCCTA
* * ** *
434700 TCCAAAATTCTACTAAAAAAACTAGCTAGTACCCACTTCAAGGAAACTAAAGGACATCCAGCATC
129 TCCAAAATTCTACTAAAAAAACTAGCTACTACCCACTACAAAAAAACTAAAGCACATCCAGCATC
*
434765 CCATCAATTCACTCCAAGCTTAAGAACACAATCAAATTCGCAGTAACAATAAGAAT
194 CCATCAATTCACTCCAAGCTTAAGAACACAATCAAATTCGCAGTAACAATAAGAAA
* ** **
434821 AAAACAACTCCAAACAGCTAGCTTATGCCCAAACTGGCCATATCAACATCAATAATTCATTCAAG
1 AAAACAACTCCAAACA-C-AGCTTAAGTGCAAACTAACCATATCAACATCAATAATTCATTCAAG
* * * *
434886 ATTGTAATGACTAGTAGTAAAATAACGAGCACATGAAGGAGAAGTGATTAAATAGGAAAACCC-A
64 ATTCTAATGACTAGTAGTAAAATAACAAGCACATGAAGGACAAATGATTAAATAGGAAAACCCTA
* * ** *
434950 TTCCAAGATTCTGCTCGAAAAACTAGCTACTACCCACTACAAAAAAACTAAAGCACGTCCTCAAG
129 -TCCAAAATTCTACTAAAAAAACTAGCTACTACCCACTACAAAAAAACTAAAGCACAT-C-C-AG
* * *
435015 CATGCCATTAATTCACTCCAAGCTTAAGAACACAATCAAATTTGCAGTAAC-ATCAAGAAAA
190 CATCCCATCAATTCACTCCAAGCTTAAGAACACAATCAAATTCGCAGTAACAAT-AAG-AAA
* * *
435076 AAAACATCTCC-AATA-AGCTTAAGTGCAAATTAACCATATCA
1 AAAACAACTCCAAACACAGCTTAAGTGCAAACTAACCATATCA
435117 TTCAAGATTC
Statistics
Matches: 250, Mismatches: 40, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
250 1 0.00
251 177 0.71
252 1 0.00
253 3 0.01
254 56 0.22
255 12 0.05
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (249 bp):
AAAACAACTCCAAACACAGCTTAAGTGCAAACTAACCATATCAACATCAATAATTCATTCAAGAT
TCTAATGACTAGTAGTAAAATAACAAGCACATGAAGGACAAATGATTAAATAGGAAAACCCTATC
CAAAATTCTACTAAAAAAACTAGCTACTACCCACTACAAAAAAACTAAAGCACATCCAGCATCCC
ATCAATTCACTCCAAGCTTAAGAACACAATCAAATTCGCAGTAACAATAAGAAA
Found at i:451073 original size:16 final size:16
Alignment explanation
Indices: 451054--451085 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
451044 AAATGATACA
451054 AACCCAAAATGACATG
1 AACCCAAAATGACATG
*
451070 AACCCGAAATGACATG
1 AACCCAAAATGACATG
451086 TGCAAGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
AACCCAAAATGACATG
Found at i:456125 original size:14 final size:15
Alignment explanation
Indices: 456095--456128 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
456085 TCAACATGTT
456095 TTTTA-ATATTTACA
1 TTTTATATATTTACA
456109 TTTTATATATTTA-A
1 TTTTATATATTTACA
456123 TTTTAT
1 TTTTAT
456129 GTGATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATATTTACA
Found at i:460150 original size:15 final size:15
Alignment explanation
Indices: 460132--460165 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
460122 TAAAGTCCTC
*
460132 TCAATAATGTCGATT
1 TCAACAATGTCGATT
460147 TCAACAATGTCGATT
1 TCAACAATGTCGATT
460162 TCAA
1 TCAA
460166 GATTCGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (15 bp):
TCAACAATGTCGATT
Found at i:466182 original size:3 final size:3
Alignment explanation
Indices: 466174--466202 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
466164 TTCACTCTCC
466174 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
466203 TAAAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.