Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 44 of 125
Found at i:13597751 original size:40 final size:40
Alignment explanation
Indices: 13597647--13597980 Score: 435
Period size: 40 Copynumber: 8.4 Consensus size: 40
13597637 AAAAATCGAA
* ** *
13597647 TGGTGTATCTTCAATCTGCCCTC-TGATTAGGGTAAAAGAT
1 TGGTGTGTCTTCAATCTGCCC-CATGATCGGGGTAAGAGAT
* * *
13597687 CGG-ATG-CTTCAATCTGCCCCATGATTGGGGTAAGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
* * *
13597725 TGGTGTGTCTTCAATCTACCCTATGATCGGGATAAGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
* * *
13597765 TAGTGTGTCTTCAATTTGCCCCATGATCGGGGTAGGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
* * *
13597805 TGGTGTGTCTTCAATCTACCCTATGATCGGGATAAGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
*
13597845 TGGTGTGTCTTCAATCTGCCCCATGATCAGGGTAAGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
13597885 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
* *
13597925 TGGTGTGTCTTAAATCTGCCCTATGATCGGGGT-A-AGAT
1 TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
* *
13597963 TTGTGTGTTTTCAATCTG
1 TGGTGTGTCTTCAATCTG
13597981 AGGGTGAGAC
Statistics
Matches: 258, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
37 1 0.00
38 49 0.19
39 4 0.02
40 204 0.79
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
TGGTGTGTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT
Found at i:13609248 original size:28 final size:28
Alignment explanation
Indices: 13609212--13609265 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13609202 GGTAACAAGT
* *
13609212 ATGACCTTTGAGTCAATAGGGGGTAAGC
1 ATGACCTTTGAGTCAACAGGGAGTAAGC
* *
13609240 ATGATCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTGAGTCAACAGGGAGTAA
13609266 ATCGGATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (28 bp):
ATGACCTTTGAGTCAACAGGGAGTAAGC
Found at i:13614664 original size:2 final size:2
Alignment explanation
Indices: 13614657--13614697 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
13614647 CCAAAAGTAA
13614657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13614698 CTTCAATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13615490 original size:29 final size:29
Alignment explanation
Indices: 13615443--13615498 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
13615433 AATTTAATTT
* *
13615443 TTTAATAATACATGGATTAAATTGATCCA
1 TTTAATAATACAAGAATTAAATTGATCCA
* *
13615472 TTTAATAATAGAAGAATTAATTTGATC
1 TTTAATAATACAAGAATTAAATTGATC
13615499 AAATCTCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTAATAATACAAGAATTAAATTGATCCA
Found at i:13623537 original size:18 final size:17
Alignment explanation
Indices: 13623514--13623555 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
13623504 AGTGCTTTTT
13623514 AAAAGTACTTTTGATATA
1 AAAAGTACTTTTGA-ATA
* *
13623532 AAAAGTGCTTTTGAATC
1 AAAAGTACTTTTGAATA
13623549 AAAAGTA
1 AAAAGTA
13623556 ATAATAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (17 bp):
AAAAGTACTTTTGAATA
Found at i:13623951 original size:13 final size:15
Alignment explanation
Indices: 13623933--13623978 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 15
13623923 AAACCAAACA
13623933 TTCAAAAAT-AC-TT
1 TTCAAAAATCACTTT
13623946 TTC-AAAATCACTTT
1 TTCAAAAATCACTTT
13623960 TTC-AAAA-CACTTT
1 TTCAAAAATCACTTT
13623973 TT-AAAA
1 TTCAAAA
13623979 GCATTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.17
13 16 0.53
14 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (15 bp):
TTCAAAAATCACTTT
Found at i:13623963 original size:14 final size:13
Alignment explanation
Indices: 13623944--13623991 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
13623934 TCAAAAATAC
13623944 TTTTCAAAATCACT
1 TTTTCAAAA-CACT
13623958 TTTTCAAAACACT
1 TTTTCAAAACACT
13623971 TTTT-AAAAGCA-T
1 TTTTCAAAA-CACT
*
13623983 TTATCAAAA
1 TTTTCAAAA
13623992 ACAATGCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (13 bp):
TTTTCAAAACACT
Found at i:13623992 original size:26 final size:27
Alignment explanation
Indices: 13623934--13623994 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
13623924 AACCAAACAT
* * *
13623934 TCAAAAATACTTTTCAAAATCACTTTT
1 TCAAAAACACTTTTCAAAAGCACTTTA
*
13623961 TC-AAAACACTTTTTAAAAGCA-TTTA
1 TCAAAAACACTTTTCAAAAGCACTTTA
13623986 TCAAAAACA
1 TCAAAAACA
13623995 ATGCTAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 22 0.76
27 2 0.07
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (27 bp):
TCAAAAACACTTTTCAAAAGCACTTTA
Found at i:13624103 original size:58 final size:58
Alignment explanation
Indices: 13624025--13624149 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 58
13624015 TACATAACCT
* * * *
13624025 ATTTTACCAAATGAGAATACTTCAAAAATTTGAAATTTTTTACTATCTAAATGAGTCA
1 ATTTAACCAAATGAGAATACTTCAAAAATTTGAAATCTTTTACTATCCAAATGAATCA
* *
13624083 ATTTAACCAAATGA-AGATACTTCAAAAATTTGTAATCTTTTACTATCCAAATGAATTA
1 ATTTAACCAAATGAGA-ATACTTCAAAAATTTGAAATCTTTTACTATCCAAATGAATCA
13624141 ATTTAACCA
1 ATTTAACCA
13624150 GTTTATCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.02
58 59 0.98
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (58 bp):
ATTTAACCAAATGAGAATACTTCAAAAATTTGAAATCTTTTACTATCCAAATGAATCA
Found at i:13629017 original size:125 final size:125
Alignment explanation
Indices: 13628779--13629031 Score: 454
Period size: 125 Copynumber: 2.0 Consensus size: 125
13628769 GGAAAAATAG
*
13628779 TAAAAATGAGTTGTGCAGGTTAGGATGGCTGTACTTCCCTTTTCCTTTGGATACAAAATAGAAAT
1 TAAAAATGAGTTGCGCAGGTTAGGATGGCTGTACTTCCCTTTTCCTTTGGATACAAAATAGAAAT
13628844 ATTATGCGTTACCTAATTATTCCAGCATCAATGGGCTACTGTTAAAAAGGAATTTCCTTC
66 ATTATGCGTTACCTAATTATTCCAGCATCAATGGGCTACTGTTAAAAAGGAATTTCCTTC
*
13628904 TAAAAATGAGTTGCGCAGGTTAGGATGGCTGTACTTTCCTTTTCCTTTGGATACAAAATAGAAAT
1 TAAAAATGAGTTGCGCAGGTTAGGATGGCTGTACTTCCCTTTTCCTTTGGATACAAAATAGAAAT
* *
13628969 ATTTATGCGTTACCTAGTTATTCCTGCATCAATGGGCTACTGTT-AAAAGGAATTTCCTTC
66 A-TTATGCGTTACCTAATTATTCCAGCATCAATGGGCTACTGTTAAAAAGGAATTTCCTTC
13629029 TAA
1 TAA
13629032 CTGTCTAAAT
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
125 83 0.67
126 40 0.33
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (125 bp):
TAAAAATGAGTTGCGCAGGTTAGGATGGCTGTACTTCCCTTTTCCTTTGGATACAAAATAGAAAT
ATTATGCGTTACCTAATTATTCCAGCATCAATGGGCTACTGTTAAAAAGGAATTTCCTTC
Found at i:13630378 original size:18 final size:18
Alignment explanation
Indices: 13630357--13630392 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13630347 TTTCAAATTT
*
13630357 TATTGTTTTCTTCTAGCA
1 TATTGTTTTCTCCTAGCA
13630375 TATTGTTTTCTCCTAGCA
1 TATTGTTTTCTCCTAGCA
13630393 AATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (18 bp):
TATTGTTTTCTCCTAGCA
Found at i:13638192 original size:50 final size:52
Alignment explanation
Indices: 13638074--13638223 Score: 175
Period size: 50 Copynumber: 2.9 Consensus size: 52
13638064 CAAAATAATA
* * * *
13638074 TAAACAAACATTTATATTTATGTAAAAACACCATATCTTAAACAAAAACATAT
1 TAAATAAATATTTATATTTAT-TTAAAACATCATATCTTAAACAAAAACATAT
* *
13638127 TAAATAAATATTTATATTTATTTAAAACATCATAT-TTGAACAAAGTA-A-AT
1 TAAATAAATATTTATATTTATTTAAAACATCATATCTTAAACAAA-AACATAT
* *
13638177 TAAATAAATGTTTATATTTATTTAAAACATCAGATC-TAAA-AAAAACA
1 TAAATAAATATTTATATTTATTTAAAACATCATATCTTAAACAAAAACA
13638224 ATTTATTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
48 1 0.01
49 4 0.05
50 38 0.45
51 9 0.11
52 13 0.15
53 19 0.23
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (52 bp):
TAAATAAATATTTATATTTATTTAAAACATCATATCTTAAACAAAAACATAT
Found at i:13639621 original size:37 final size:37
Alignment explanation
Indices: 13639453--13639609 Score: 242
Period size: 37 Copynumber: 4.2 Consensus size: 37
13639443 ATTCTTCTAT
* *
13639453 CACCGACACAAAGGCCTGCTAGGCACAAAGCCCGAATA
1 CACCGGCACAAA-GCCTGCTAGGCACATAGCCCGAATA
* *
13639491 CATCGGCACAAAGCCTGCTAGGCACATAGCTCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
13639528 CACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
**
13639565 CACCGATACAAAGCCTGCTAGGCACATAGCCCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
13639602 CACCGGCA
1 CACCGGCA
13639610 TGAATCCTGC
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 97 0.91
38 10 0.09
ACGTcount: A:0.34, C:0.33, G:0.21, T:0.12
Consensus pattern (37 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
Found at i:13644748 original size:37 final size:37
Alignment explanation
Indices: 13644691--13644944 Score: 328
Period size: 37 Copynumber: 6.8 Consensus size: 37
13644681 TCCATCCCTA
* * *
13644691 GCACAAAGGCCTGCTTGGCACAAAGCCCGAATACATCG
1 GCACAAA-GCCTGCTAGGCACATAGCCCGAATACACCG
* *
13644729 GCACAAAGCCTGCTAGGCACATAGCCTGAATACACTG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
* * *
13644766 GCACAAATCCTGCTAGGCACATAGCCTGAATACGCCG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
*
13644803 TCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
* *
13644840 GCACAAGGCCTGCTAGGCACATAGCCCGAATACAACG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
* * * *
13644877 ACACAAAGCCTACTAAGCACATAGCCCGGATACACCG
1 GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
** * *
13644914 ATACGAAGCCTGCTAGGCATATAGCCCGAAT
1 GCACAAAGCCTGCTAGGCACATAGCCCGAAT
13644945 TCTTAGAAGC
Statistics
Matches: 189, Mismatches: 27, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
37 182 0.96
38 7 0.04
ACGTcount: A:0.33, C:0.32, G:0.21, T:0.14
Consensus pattern (37 bp):
GCACAAAGCCTGCTAGGCACATAGCCCGAATACACCG
Found at i:13644749 original size:16 final size:16
Alignment explanation
Indices: 13644728--13644828 Score: 58
Period size: 16 Copynumber: 5.7 Consensus size: 16
13644718 CGAATACATC
13644728 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
* *
13644744 GGCACATAGCCTGAATACA
1 GGCACAAAGCCTG-CT--A
*
13644763 CTGGCACAAATCCTGCTA
1 --GGCACAAAGCCTGCTA
* *
13644781 GGCACATAGCCTGAATA
1 GGCACAAAGCCTG-CTA
13644798 CGCCGTCACAAAGCCTGCTA
1 -G--G-CACAAAGCCTGCTA
*
13644818 GGCACATAGCC
1 GGCACAAAGCC
13644829 CGAATACACC
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
16 31 0.48
17 4 0.06
18 2 0.03
19 2 0.03
20 4 0.06
21 21 0.33
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.16
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:13646460 original size:15 final size:15
Alignment explanation
Indices: 13646440--13646493 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
13646430 AGGAGTCTTT
13646440 AAATCAAATTGAATA
1 AAATCAAATTGAATA
13646455 AAATCAAATTGAATA
1 AAATCAAATTGAATA
*
13646470 AAATCAAATTAAATCGA
1 AAATCAAATTGAAT--A
13646487 AAATCAA
1 AAATCAA
13646494 TTTAATTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 28 0.78
17 8 0.22
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (15 bp):
AAATCAAATTGAATA
Found at i:13646505 original size:17 final size:17
Alignment explanation
Indices: 13646440--13646505 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 17
13646430 AGGAGTCTTT
*
13646440 AAATCAAATTGAAT--A
1 AAATCAAATTAAATAGA
*
13646455 AAATCAAATTGAAT--A
1 AAATCAAATTAAATAGA
*
13646470 AAATCAAATTAAATCGA
1 AAATCAAATTAAATAGA
* *
13646487 AAATCAATTTAATTAGA
1 AAATCAAATTAAATAGA
13646504 AA
1 AA
13646506 CAAAATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 28 0.62
17 17 0.38
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATCAAATTAAATAGA
Found at i:13648817 original size:53 final size:53
Alignment explanation
Indices: 13648737--13648928 Score: 264
Period size: 53 Copynumber: 3.6 Consensus size: 53
13648727 CGTAAATGCA
* *
13648737 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTGTCTCATCGTGAGTTATATGAATCCTATTACGGATT
* * *
13648790 AAAGGTTCGATGACTCTATACT-ATCGTGAGTTATATGAATCCTACTACGGATT
1 AAAGGTCCGATGACTCTGT-CTCATCGTGAGTTATATGAATCCTATTACGGATT
* *
13648843 AAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTCTCATCGTGAGTTATATGAATCCTATTACGGATT
* *
13648896 AAAGGGTTCGATGA--CTGTGTCATCGTGAGTTAT
1 AAA-GGTCCGATGACTCTGTCTCATCGTGAGTTAT
13648929 CAAACGTGAA
Statistics
Matches: 124, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
52 19 0.15
53 95 0.77
54 10 0.08
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTCTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:13649889 original size:21 final size:21
Alignment explanation
Indices: 13649865--13649908 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13649855 ACCAGTACCT
* *
13649865 GTATTAGTTCTACCGATACAA
1 GTATGAGTTCTACCGACACAA
*
13649886 GTATGATTTCTACCGACACAA
1 GTATGAGTTCTACCGACACAA
13649907 GT
1 GT
13649909 CATGCAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (21 bp):
GTATGAGTTCTACCGACACAA
Found at i:13661451 original size:27 final size:27
Alignment explanation
Indices: 13661402--13661453 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
13661392 TTCTTTGATA
*
13661402 TCACAATTGAAACTATAATTTAAGCTT
1 TCACAATTGAAACCATAATTTAAGCTT
*
13661429 TCACAATTTAAAGCCATAA-TTAAGC
1 TCACAATTGAAA-CCATAATTTAAGC
13661454 CCACAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (27 bp):
TCACAATTGAAACCATAATTTAAGCTT
Found at i:13661780 original size:166 final size:166
Alignment explanation
Indices: 13661594--13662037 Score: 540
Period size: 166 Copynumber: 2.7 Consensus size: 166
13661584 ATTTAAGTAT
* * *
13661594 TTCTTGTTTTGAAACAAAATCAAAATCAAATCAAATTTGTTAAATGACGAGAATAAATCTCGAAA
1 TTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATTTGTTGAACGACGAGAATAAATCTCGAAA
* * * *
13661659 CAAAATTATTCAATTAATTCTTATTTGGAAACAAAATCAAAATCAAATCAAATCTATTTAATGAC
66 CAAAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATCCATTGAACGAC
13661724 GGAAATAAATTCC-AAAACAAAATTATTCAATTTTAA
131 GGAAATAAA-TCCGAAAACAAAATTATTCAATTTTAA
* *
13661760 TTCTTGTTTGGAATCAAAATCAAAATCAAATCAAATTTGTTGAACGGCGAGAATAAATCTCGAAT
1 TTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATTTGTTGAACGACGAGAATAAATCTCGAA-
* * * *
13661825 A-AGAATTATTTAATTTTAATTCTTGTTT-GAAAAAAAATCAAAATCAAATCAAATCCGTTGAAC
65 ACAAAATTATTCAA--TTAATTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATCCATTGAAC
* * *
13661888 GGCGGGAATAAATCCTGAAAACAAAATTATTTAATTTTAA
128 GACGGAAATAAATCC-GAAAACAAAATTATTCAATTTTAA
* * * * *
13661928 TTCTTGTTTGGAAACAAAATAAAAAAAAT-AGAATAAAATCTGTTGAACAACGGGAATAAATC-C
1 TTCTTGTTTGGAAACAAAAT---CAAAATCA-AATCAAATTTGTTGAACGACGAGAATAAATCTC
* * *
13661991 TAAAACAAAATTATTCACTTAATTCTTGGTTGGAAAC-AAATCAAAAT
62 -GAAACAAAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAAT
13662038 ATTTGTTGAA
Statistics
Matches: 237, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
166 72 0.30
167 41 0.17
168 53 0.22
169 22 0.09
170 7 0.03
171 42 0.18
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (166 bp):
TTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATTTGTTGAACGACGAGAATAAATCTCGAAA
CAAAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATCCATTGAACGAC
GGAAATAAATCCGAAAACAAAATTATTCAATTTTAA
Found at i:13661891 original size:83 final size:84
Alignment explanation
Indices: 13661532--13662037 Score: 502
Period size: 82 Copynumber: 6.1 Consensus size: 84
13661522 AATTCTGAAA
* * * * * * *
13661532 CAAAATAAAATCAATTCTGTTGAACGAC-AGGATTAAATCTTGAAACAGAATTATTTAA--GTAT
1 CAAAATCAAATCAAATCTGTTGAACGACGA-GAATAAATCTCGAAACAAAATTATTTAATTTTAA
*
13661594 TTCTTGTTTTGAAACAAAAT
65 TTCTTGTTTGGAAACAAAAT
* * * *
13661614 CAAAATCAAATCAAATTTGTTAAATGACGAGAATAAATCTCGAAACAAAATTATTCAA--TTAAT
1 CAAAATCAAATCAAATCTGTTGAACGACGAGAATAAATCTCGAAACAAAATTATTTAATTTTAAT
*
13661677 TCTTATTTGGAAACAAAAT
66 TCTTGTTTGGAAACAAAAT
* * * * *
13661696 CAAAATCAAATCAAATCTATTTAATGACG-GAAATAAAT-TCCAAAACAAAATTATTCAATTTTA
1 CAAAATCAAATCAAATCTGTTGAACGACGAG-AATAAATCT-CGAAACAAAATTATTTAATTTTA
*
13661759 ATTCTTGTTTGGAATCAAAAT
64 ATTCTTGTTTGGAAACAAAAT
* * *
13661780 CAAAATCAAATCAAATTTGTTGAACGGCGAGAATAAATCTCGAATA-AGAATTATTTAATTTTAA
1 CAAAATCAAATCAAATCTGTTGAACGACGAGAATAAATCTCGAA-ACAAAATTATTTAATTTTAA
*
13661844 TTCTTGTTT-GAAAAAAAAT
65 TTCTTGTTTGGAAACAAAAT
* * *
13661863 CAAAATCAAATCAAATCCGTTGAACGGCGGGAATAAATC-CTGAAAACAAAATTATTTAATTTTA
1 CAAAATCAAATCAAATCTGTTGAACGACGAGAATAAATCTC-G-AAACAAAATTATTTAATTTTA
13661927 ATTCTTGTTTGGAAACAAAAT
64 ATTCTTGTTTGGAAACAAAAT
* * * * * * *
13661948 AAAAAAAAT-AGAATAAAATCTGTTGAACAACGGGAATAAATC-CTAAAACAAAATTA-TTCA-C
1 ---CAAAATCA-AATCAAATCTGTTGAACGACGAGAATAAATCTC-GAAACAAAATTATTTAATT
*
13662009 TTAATTCTTGGTTGGAAAC-AAAT
61 TTAATTCTTGTTTGGAAACAAAAT
13662032 CAAAAT
1 CAAAAT
13662038 ATTTGTTGAA
Statistics
Matches: 364, Mismatches: 44, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
81 7 0.02
82 118 0.32
83 47 0.13
84 113 0.31
85 30 0.08
86 3 0.01
87 12 0.03
88 34 0.09
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (84 bp):
CAAAATCAAATCAAATCTGTTGAACGACGAGAATAAATCTCGAAACAAAATTATTTAATTTTAAT
TCTTGTTTGGAAACAAAAT
Found at i:13662335 original size:53 final size:50
Alignment explanation
Indices: 13662277--13662438 Score: 123
Period size: 50 Copynumber: 3.2 Consensus size: 50
13662267 CATAATAATA
*
13662277 TAAATAAACATTCATGTTTATGTAAAAACACCAGATCGTAAACAAAAACAAAT
1 TAAATAAACATTCATATTTAT-TAAAAACACCAGAT-GTAAAC-AAAACAAAT
* * * ** * *
13662330 TAAATAAATATTTATATTTATTTAAAACATTAGATTTAAGCAAAACAAAT
1 TAAATAAACATTCATATTTATTAAAAACACCAGATGTAAACAAAACAAAT
* * * * * * *
13662380 TAAAT-AACTGTTTATATTTATTTAAAACATCATATCTAAA-AAAATAAA-
1 TAAATAAAC-ATTCATATTTATTAAAAACACCAGATGTAAACAAAACAAAT
13662428 TAAATTAAACA
1 TAAA-TAAACA
13662439 ATATCTGAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
48 4 0.04
49 10 0.11
50 43 0.48
51 4 0.04
52 11 0.12
53 18 0.20
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (50 bp):
TAAATAAACATTCATATTTATTAAAAACACCAGATGTAAACAAAACAAAT
Found at i:13662850 original size:17 final size:17
Alignment explanation
Indices: 13662828--13662878 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
13662818 CAATTTGAAT
13662828 AAAATCAAATCAAATTG
1 AAAATCAAATCAAATTG
**
13662845 AAAATC-AATTTAATTG
1 AAAATCAAATCAAATTG
*
13662861 GAAA-CAAAATCAAATTG
1 AAAATC-AAATCAAATTG
13662878 A
1 A
13662879 GACATTTGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
17 14 0.54
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (17 bp):
AAAATCAAATCAAATTG
Found at i:13673639 original size:3 final size:3
Alignment explanation
Indices: 13673631--13673682 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
13673621 GGGCCTTAAA
* * * * *
13673631 AAT AAT AAT AAT ATTT AAT AGT AAT AAT AAT AGT AGT AAT GAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13673677 AAT AAT
1 AAT AAT
13673683 TTGGACCCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:13674178 original size:42 final size:42
Alignment explanation
Indices: 13674131--13674388 Score: 365
Period size: 42 Copynumber: 6.1 Consensus size: 42
13674121 CCTTCATATA
** * * * *
13674131 CAATGAAAAAAAAATGGACCTCTACGCTTCGGCTTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
*
13674173 CAATGAAAAGTAAATGGACCTCCACA-TCTGGGCTTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACT-TGGGCCTCTAAATG
* * *
13674215 CAATGAAAAGTAAATGGACCTCTACACCTAGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
* *
13674257 CAATGAAAAGTAAATGGAACTCCACACTTGAGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
*
13674299 CAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
* *
13674341 CAATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
13674383 CAATGA
1 CAATGA
13674389 GTGCTTTCCT
Statistics
Matches: 194, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 1 0.01
42 193 0.99
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
Found at i:13675269 original size:19 final size:20
Alignment explanation
Indices: 13675224--13675271 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
13675214 AAATGGTCTT
13675224 TTAAGGGTTGTAACGTGGAC
1 TTAAGGGTTGTAACGTGGAC
13675244 TTAAGGGTTGTAACGTGGAC
1 TTAAGGGTTGTAACGTGGAC
13675264 -TAAGGGTT
1 TTAAGGGTT
13675272 AAAGGTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.25, C:0.08, G:0.35, T:0.31
Consensus pattern (20 bp):
TTAAGGGTTGTAACGTGGAC
Found at i:13683619 original size:10 final size:10
Alignment explanation
Indices: 13683604--13683632 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13683594 AGACACATCC
13683604 AAAAGAAAGA
1 AAAAGAAAGA
13683614 AAAAGAAAGA
1 AAAAGAAAGA
13683624 AAAAGAAAG
1 AAAAGAAAG
13683633 CGTTCCAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:13683852 original size:17 final size:17
Alignment explanation
Indices: 13683797--13683876 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
13683787 TGTTAGTAAG
* *
13683797 CATTGTCATCACA-TTC
1 CATTGTCATTATATTTC
* *
13683813 CTATTGTCATTACATTTT
1 C-ATTGTCATTATATTTC
* *
13683831 AATTGTCATTATATTTG
1 CATTGTCATTATATTTC
* *
13683848 CATTGTTATTGTATTTC
1 CATTGTCATTATATTTC
13683865 CATTTGTCATTA
1 CA-TTGTCATTA
13683877 GAATTTAGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
16 1 0.02
17 40 0.80
18 9 0.18
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (17 bp):
CATTGTCATTATATTTC
Found at i:13684446 original size:14 final size:15
Alignment explanation
Indices: 13684427--13684456 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13684417 AGTCACATTT
13684427 ATAAAAAA-AAAAAA
1 ATAAAAAAGAAAAAA
13684441 ATAAAAAAGAAAAAA
1 ATAAAAAAGAAAAAA
13684456 A
1 A
13684457 AAGATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (15 bp):
ATAAAAAAGAAAAAA
Found at i:13685820 original size:16 final size:16
Alignment explanation
Indices: 13685799--13685829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13685789 TTGGGGACTC
13685799 CATTTCATTATTATTG
1 CATTTCATTATTATTG
*
13685815 CATTTCATTTTTATT
1 CATTTCATTATTATT
13685830 TTCGTATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (16 bp):
CATTTCATTATTATTG
Found at i:13700838 original size:55 final size:55
Alignment explanation
Indices: 13700772--13700882 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
13700762 AAGATGATCA
13700772 AATGGGAACAAACTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGCT
1 AATGGGAACAAACTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGCT
*
13700827 AATGGGAACAAATTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGCT
1 AATGGGAACAAACTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGCT
13700882 A
1 A
13700883 TCACATCCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.30
Consensus pattern (55 bp):
AATGGGAACAAACTATACTATAAGTAAGGAGAAATCAATGGTTCTTTCTAATGCT
Found at i:13704288 original size:13 final size:13
Alignment explanation
Indices: 13704272--13704299 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13704262 AAACTCTATT
13704272 TTTAGGATTAATA
1 TTTAGGATTAATA
13704285 TTTAGGATTAATA
1 TTTAGGATTAATA
13704298 TT
1 TT
13704300 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:13705511 original size:14 final size:13
Alignment explanation
Indices: 13705487--13705554 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
13705477 TTACTTGAGC
13705487 ATTTTTTATTTTT
1 ATTTTTTATTTTT
13705500 ATTTTCTTATTTTT
1 ATTTT-TTATTTTT
*
13705514 -TGTTTTTA-ATTT
1 AT-TTTTTATTTTT
* * *
13705526 AATTTTTACATTTA
1 ATTTTTTA-TTTTT
13705540 ATTTTTTATTTTT
1 ATTTTTTATTTTT
13705553 AT
1 AT
13705555 AGGTTCTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
12 9 0.21
13 14 0.33
14 20 0.47
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:13705538 original size:13 final size:12
Alignment explanation
Indices: 13705516--13705550 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
13705506 TTATTTTTTG
13705516 TTTTTAATTTAA
1 TTTTTAATTTAA
13705528 TTTTTACATTTAA
1 TTTTTA-ATTTAA
*
13705541 TTTTTTATTT
1 TTTTTAATTT
13705551 TTATAGGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:13708354 original size:13 final size:13
Alignment explanation
Indices: 13708336--13708361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13708326 TGTTCTATTC
13708336 ATTAACCCATGAT
1 ATTAACCCATGAT
13708349 ATTAACCCATGAT
1 ATTAACCCATGAT
13708362 CCATATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
ATTAACCCATGAT
Found at i:13711307 original size:12 final size:12
Alignment explanation
Indices: 13711290--13711341 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
13711280 CAGGTTCAAT
13711290 TTCTTCCTTCTC
1 TTCTTCCTTCTC
13711302 TTCTTCCTT-TCC
1 TTCTTCCTTCT-C
*
13711314 TTCTTCTTCTTTTC
1 TTCTTC--CTTCTC
*
13711328 TTCATCCTTCTC
1 TTCTTCCTTCTC
13711340 TT
1 TT
13711342 GATCACCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 23 0.68
14 9 0.26
15 1 0.03
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:13718505 original size:20 final size:19
Alignment explanation
Indices: 13718467--13718515 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
13718457 GAAAAAGTCG
*
13718467 AAAAGAAAAATTGAAAAAA
1 AAAAGAAAAATGGAAAAAA
*
13718486 AAAAGAGAAAATGGAGAAAA
1 AAAAGA-AAAATGGAAAAAA
13718506 AAAAGAAAAA
1 AAAAGAAAAA
13718516 AATGTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAATGGAAAAAA
Found at i:13718509 original size:33 final size:31
Alignment explanation
Indices: 13718439--13718517 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 31
13718429 TTTATTATTT
*
13718439 AGAAAAAGAAAAAAAAAGGAAAAAGTCGAAA
1 AGAAAAAGAAAAAAAAAAGAAAAAGTCGAAA
*
13718470 AGAAAAATTGAAAAAAAAAAGAGAAAA-TGGAGAA
1 AGAAAAA--GAAAAAAAAAAGA-AAAAGTCGA-AA
13718504 A-AAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
13718518 TGTATTTGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 15 0.36
33 20 0.48
34 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (31 bp):
AGAAAAAGAAAAAAAAAAGAAAAAGTCGAAA
Found at i:13719464 original size:13 final size:13
Alignment explanation
Indices: 13719446--13719473 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13719436 AACTATATTT
13719446 TTTAGGATTAATA
1 TTTAGGATTAATA
13719459 TTTAGGATTAATA
1 TTTAGGATTAATA
13719472 TT
1 TT
13719474 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:13727560 original size:18 final size:20
Alignment explanation
Indices: 13727523--13727560 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13727513 TAAGCTTCAT
13727523 TAAGTTAGAAAATGTAATAAC
1 TAAGTTAGAAAA-GTAATAAC
13727544 TAAGTTA-AAAA-TAATAA
1 TAAGTTAGAAAAGTAATAA
13727561 AAATGTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (20 bp):
TAAGTTAGAAAAGTAATAAC
Found at i:13727996 original size:12 final size:13
Alignment explanation
Indices: 13727972--13728014 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
13727962 GTAGAACATG
13727972 AGGAAACAGAGGA
1 AGGAAACAGAGGA
13727985 AGGAAA-AGAGGA
1 AGGAAACAGAGGA
* *
13727997 A-GAAAGAAAGGA
1 AGGAAACAGAGGA
13728009 AGGAAA
1 AGGAAA
13728015 AGATGTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 13 0.48
13 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.00
Consensus pattern (13 bp):
AGGAAACAGAGGA
Found at i:13728472 original size:34 final size:34
Alignment explanation
Indices: 13728429--13728498 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
13728419 GTAGCTGTAA
* * *
13728429 TTTAATTGTCACCACATTTCCTTTGTCTTTGCAT
1 TTTAATTGTCACCACATGTCCATTGTCATTGCAT
* *
13728463 TTTAATTGTCACTACATGTGCATTGTCATTGCAT
1 TTTAATTGTCACCACATGTCCATTGTCATTGCAT
13728497 TT
1 TT
13728499 CCATGTGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (34 bp):
TTTAATTGTCACCACATGTCCATTGTCATTGCAT
Found at i:13728987 original size:15 final size:15
Alignment explanation
Indices: 13728967--13728997 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13728957 TGTGTGTCGG
13728967 CTTAATTACATACTC
1 CTTAATTACATACTC
13728982 CTTAATTACATACTC
1 CTTAATTACATACTC
13728997 C
1 C
13728998 CTAGGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (15 bp):
CTTAATTACATACTC
Found at i:13741553 original size:12 final size:13
Alignment explanation
Indices: 13741529--13741571 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
13741519 GTAGGACATG
*
13741529 AGGAAATAGAGGA
1 AGGAAAGAGAGGA
13741542 AGGAAA-AGAGGA
1 AGGAAAGAGAGGA
*
13741554 A-GAAAGAAAGGA
1 AGGAAAGAGAGGA
13741566 AGGAAA
1 AGGAAA
13741572 AGATGTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 13 0.48
13 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.02
Consensus pattern (13 bp):
AGGAAAGAGAGGA
Found at i:13752673 original size:9 final size:9
Alignment explanation
Indices: 13752659--13752685 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13752649 ATTTGTTGAT
13752659 GAAAATTAA
1 GAAAATTAA
13752668 GAAAATTAA
1 GAAAATTAA
13752677 GAAAATTAA
1 GAAAATTAA
13752686 AGAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (9 bp):
GAAAATTAA
Found at i:13755262 original size:21 final size:22
Alignment explanation
Indices: 13755232--13755277 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
13755222 TCTTCCTTCA
*
13755232 CTCCTTCTTT-TCCTTTTTTTTT
1 CTCCTTCTTTCT-CTTCTTTTTT
13755254 CTCC-TCTTTCTCTTCTTTTTT
1 CTCCTTCTTTCTCTTCTTTTTT
13755275 CTC
1 CTC
13755278 TTCCTCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
CTCCTTCTTTCTCTTCTTTTTT
Found at i:13759016 original size:3 final size:3
Alignment explanation
Indices: 13759008--13759042 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
13758998 TGTGCCCGTG
* *
13759008 GTT GTT GTT GTT ATT GTT GTT GTT TTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
13759043 CGTTCTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
GTT
Found at i:13759024 original size:12 final size:12
Alignment explanation
Indices: 13759009--13759042 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
13758999 GTGCCCGTGG
13759009 TTGTTGTTGTTA
1 TTGTTGTTGTTA
*
13759021 TTGTTGTTGTTT
1 TTGTTGTTGTTA
13759033 TTGTTGTTGT
1 TTGTTGTTGT
13759043 CGTTCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.71
Consensus pattern (12 bp):
TTGTTGTTGTTA
Found at i:13760343 original size:23 final size:22
Alignment explanation
Indices: 13760302--13760351 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
13760292 TATTTCGTTT
13760302 TTTAATTAAATTAAATTTACAAC
1 TTTAATTAAATTAAATTTA-AAC
* * * *
13760325 TTTAATTTAATTTATTTTAAAT
1 TTTAATTAAATTAAATTTAAAC
13760347 TTTAA
1 TTTAA
13760352 AATTAAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATTAAATTAAATTTAAAC
Found at i:13761469 original size:43 final size:43
Alignment explanation
Indices: 13761405--13761511 Score: 196
Period size: 43 Copynumber: 2.5 Consensus size: 43
13761395 TAACTCGCTT
*
13761405 AACCCTTAAAAAAGGATAATACGCTTTAGCACAGTCGATCTCTC
1 AACCCTT-AAAAAGGAGAATACGCTTTAGCACAGTCGATCTCTC
13761449 AACCCTTAAAAAGGAGAATACGCTTTAGCACAGTCGATCTCTC
1 AACCCTTAAAAAGGAGAATACGCTTTAGCACAGTCGATCTCTC
13761492 AACCCTTAAAAAGGAGAATA
1 AACCCTTAAAAAGGAGAATA
13761512 ATGTGCTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
43 55 0.89
44 7 0.11
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.22
Consensus pattern (43 bp):
AACCCTTAAAAAGGAGAATACGCTTTAGCACAGTCGATCTCTC
Found at i:13762690 original size:42 final size:42
Alignment explanation
Indices: 13762631--13762723 Score: 186
Period size: 42 Copynumber: 2.2 Consensus size: 42
13762621 CTCCCTCTCT
13762631 ACAAGAAGAAGAATATGATGACGATGATGAACAGCGAAGGCA
1 ACAAGAAGAAGAATATGATGACGATGATGAACAGCGAAGGCA
13762673 ACAAGAAGAAGAATATGATGACGATGATGAACAGCGAAGGCA
1 ACAAGAAGAAGAATATGATGACGATGATGAACAGCGAAGGCA
13762715 ACAAGAAGA
1 ACAAGAAGA
13762724 GGAGCCGTCG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.49, C:0.12, G:0.28, T:0.11
Consensus pattern (42 bp):
ACAAGAAGAAGAATATGATGACGATGATGAACAGCGAAGGCA
Found at i:13764545 original size:17 final size:18
Alignment explanation
Indices: 13764511--13764545 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13764501 ATAAAGCATT
13764511 GACTAACCAGTCTGCAGA
1 GACTAACCAGTCTGCAGA
*
13764529 GACTAATCAGT-TGCAGA
1 GACTAACCAGTCTGCAGA
13764546 TTTACCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (18 bp):
GACTAACCAGTCTGCAGA
Found at i:13765980 original size:18 final size:18
Alignment explanation
Indices: 13765957--13765992 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13765947 AAAACTTACA
13765957 ATTCAAAAGGATGATCTT
1 ATTCAAAAGGATGATCTT
13765975 ATTCAAAAGGATGATCTT
1 ATTCAAAAGGATGATCTT
13765993 TCATTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
ATTCAAAAGGATGATCTT
Found at i:13770860 original size:29 final size:30
Alignment explanation
Indices: 13770818--13770893 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
13770808 ACATGGCCTA
** *
13770818 TCACACGACCTACCACACTA-TCGTTTAGC
1 TCACACGGTCTACCACACTAGTCGTATAGC
*
13770847 TCACACGGTCTACCACA-TAGTCGTATGGC
1 TCACACGGTCTACCACACTAGTCGTATAGC
13770876 TCACACGGTCTACCACAC
1 TCACACGGTCTACCACAC
13770894 GTCCGTGTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 2 0.05
29 39 0.95
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.22
Consensus pattern (30 bp):
TCACACGGTCTACCACACTAGTCGTATAGC
Found at i:13776042 original size:16 final size:17
Alignment explanation
Indices: 13776018--13776050 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13776008 TAATCCCAAC
*
13776018 ATTACAAGTCT-AAAAA
1 ATTAAAAGTCTCAAAAA
13776034 ATTAAAAGTCTCAAAAA
1 ATTAAAAGTCTCAAAAA
13776051 CACTTTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (17 bp):
ATTAAAAGTCTCAAAAA
Found at i:13786490 original size:22 final size:22
Alignment explanation
Indices: 13786462--13786515 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
13786452 CTACTTGCTT
13786462 TGTCGCGACACAAGTCCTGGCG
1 TGTCGCGACACAAGTCCTGGCG
13786484 TGTCGCGACACAAGTCCTGGCG
1 TGTCGCGACACAAGTCCTGGCG
13786506 TGTCGCGACA
1 TGTCGCGACA
13786516 TTGAACCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (22 bp):
TGTCGCGACACAAGTCCTGGCG
Found at i:13787593 original size:21 final size:21
Alignment explanation
Indices: 13787568--13787630 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
13787558 GATGCCTAAT
*
13787568 AAAAGGTATCAATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
13787589 AAAAGGTATCGATA-TGTTTTG
1 AAAAGGTATCGATACT-TTTTG
*
13787610 AAATGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
13787631 TCATTGTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:13788022 original size:33 final size:34
Alignment explanation
Indices: 13787968--13788031 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
13787958 AATAGATTAC
* *
13787968 TCTCCCTTAATAAAAGACATTTTGAATTTAAACT
1 TCTCCCATAATAAAAGACATTTTCAATTTAAACT
13788002 TCTCCCAT-ATAAAA-ATCATTTTCAATTTAA
1 TCTCCCATAATAAAAGA-CATTTTCAATTTAA
13788032 GGCATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 1 0.04
33 19 0.70
34 7 0.26
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (34 bp):
TCTCCCATAATAAAAGACATTTTCAATTTAAACT
Found at i:13790715 original size:21 final size:21
Alignment explanation
Indices: 13790690--13790731 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13790680 GATACCTGAT
13790690 AAAAGGCATCGATACTTTTTG
1 AAAAGGCATCGATACTTTTTG
*
13790711 AAAAGGTATCGATACTTTTTG
1 AAAAGGCATCGATACTTTTTG
13790732 TCATTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (21 bp):
AAAAGGCATCGATACTTTTTG
Found at i:13794049 original size:25 final size:25
Alignment explanation
Indices: 13794020--13794069 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13794010 ACACTGGAAG
13794020 GTGTGGTTAATGTGCATGTTTAAGT
1 GTGTGGTTAATGTGCATGTTTAAGT
13794045 GTGTGGTTAATGTGCATGTTTAAGT
1 GTGTGGTTAATGTGCATGTTTAAGT
13794070 CGTAGATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.32, T:0.44
Consensus pattern (25 bp):
GTGTGGTTAATGTGCATGTTTAAGT
Found at i:13802675 original size:21 final size:20
Alignment explanation
Indices: 13802628--13802704 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
13802618 ATAGTGCAGA
*
13802628 CTTCTATCGATACAAGTAACT
1 CTTCTACCGATACAAGT-ACT
**
13802649 GGTCTACCGATACAAGTGACT
1 CTTCTACCGATACAAGT-ACT
* * *
13802670 CTTCTACTGGAAACAAGTATT
1 CTTCTAC-CGATACAAGTACT
13802691 ACTTCTACCGATAC
1 -CTTCTACCGATAC
13802705 TAAAAACTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 28 0.65
22 15 0.35
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (20 bp):
CTTCTACCGATACAAGTACT
Found at i:13803533 original size:52 final size:52
Alignment explanation
Indices: 13803437--13803675 Score: 325
Period size: 52 Copynumber: 4.6 Consensus size: 52
13803427 ATTTCCTTTA
* ** * ** * *
13803437 ATACTGACGATGACACATAGTCATCAAACCTCTTGTTCCTTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
13803489 ACACTCACGATAACACATAGTCATTGGACCTCATAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
13803541 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
13803593 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
13803645 ATACTAACGATGACACAAAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
13803676 TTTTCATTTA
Statistics
Matches: 165, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 165 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:13804535 original size:16 final size:15
Alignment explanation
Indices: 13804502--13804535 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
13804492 TTTAACTTAC
*
13804502 CTAATTTTAAAATTA
1 CTAATTTTAAAATCA
13804517 CTAATTTTAAAATCCA
1 CTAATTTTAAAAT-CA
13804533 CTA
1 CTA
13804536 TACCTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (15 bp):
CTAATTTTAAAATCA
Found at i:13813220 original size:18 final size:19
Alignment explanation
Indices: 13813197--13813241 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
13813187 CCAAAGGCCT
*
13813197 TATTTTAATTTTTTTAT-A
1 TATTTTAATTTTGTTATGA
*
13813215 TATTTTTATTTTGTTATGGA
1 TATTTTAATTTTGTTAT-GA
13813235 TATTTTA
1 TATTTTA
13813242 TTACTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
20 7 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (19 bp):
TATTTTAATTTTGTTATGA
Found at i:13814991 original size:17 final size:18
Alignment explanation
Indices: 13814954--13814991 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
13814944 GGAGATAGTA
*
13814954 AAATATTAGAAAATAAAT
1 AAATATTAGAAAACAAAT
*
13814972 AAATATTA-AAAACAATT
1 AAATATTAGAAAACAAAT
13814989 AAA
1 AAA
13814992 GGTATTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATATTAGAAAACAAAT
Found at i:13828814 original size:18 final size:18
Alignment explanation
Indices: 13828778--13828819 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13828768 CATTTTAAAT
13828778 ATGACAAGTGATATCTTA
1 ATGACAAGTGATATCTTA
*
13828796 ATGATAAGTGA-ATCGTTAA
1 ATGACAAGTGATATC-TT-A
13828815 ATGAC
1 ATGAC
13828820 TCAAAAGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (18 bp):
ATGACAAGTGATATCTTA
Found at i:13829197 original size:26 final size:28
Alignment explanation
Indices: 13829168--13829223 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
13829158 AAAGGAGGAA
*
13829168 GATA-TGGTCATTT-TTGGCAAATATGT
1 GATAGTGGTCATTTCATGGCAAATATGT
*
13829194 GATATGTGGTCATTTCATGGTAAATATGT
1 GATA-GTGGTCATTTCATGGCAAATATGT
13829223 G
1 G
13829224 GCAGTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
28 9 0.36
29 12 0.48
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (28 bp):
GATAGTGGTCATTTCATGGCAAATATGT
Found at i:13829244 original size:48 final size:47
Alignment explanation
Indices: 13829192--13829298 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
13829182 TGGCAAATAT
*
13829192 GTGATATGTGGTC-ATTTCATGGTAAATATGTGGCAG-TTTATCTGCAAA
1 GTGATATGTGG-CAATTT-ATGGCAAATATGTGGCAGTTTTA-CTGCAAA
*
13829240 GTGATTATGTGGCAATTTATGGCAATTATGTGGCAGTTTTACTGCAAA
1 GTGA-TATGTGGCAATTTATGGCAAATATGTGGCAGTTTTACTGCAAA
*
13829288 ATGAATATGTG
1 GTG-ATATGTG
13829299 ACTATGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
48 36 0.69
49 16 0.31
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.37
Consensus pattern (47 bp):
GTGATATGTGGCAATTTATGGCAAATATGTGGCAGTTTTACTGCAAA
Found at i:13829519 original size:17 final size:17
Alignment explanation
Indices: 13829472--13829519 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
13829462 GCATAGCATC
*
13829472 ATTGATGATATATGTGAT
1 ATTGATG-TGTATGTGAT
* *
13829490 CTT-ATGAGTATGTGAT
1 ATTGATGTGTATGTGAT
13829506 ATTGATGTGTATGT
1 ATTGATGTGTATGT
13829520 TGTTCTATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 10 0.42
17 12 0.50
18 2 0.08
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (17 bp):
ATTGATGTGTATGTGAT
Found at i:13830595 original size:21 final size:23
Alignment explanation
Indices: 13830555--13830600 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
13830545 TTTTCTCCCA
*
13830555 TTTTCTCTCTTGCCAAACACCAT
1 TTTTCTCTCTTGCAAAACACCAT
13830578 TTTTCT-TCTT-CAAAACACCAT
1 TTTTCTCTCTTGCAAAACACCAT
13830599 TT
1 TT
13830601 ATAAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTCTCTCTTGCAAAACACCAT
Found at i:13833007 original size:52 final size:52
Alignment explanation
Indices: 13832944--13833048 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
13832934 CACTCTGCAA
13832944 CTTCTACCGATACAAGTACATAAAATACCGATACTTCTAAGTACAGAACTAC
1 CTTCTACCGATACAAGTACATAAAATACCGATACTTCTAAGTACAGAACTAC
*
13832996 CTTCTATCGATACAAGTACATAAAATACCGATACTTCTAAGTACAGAACTAC
1 CTTCTACCGATACAAGTACATAAAATACCGATACTTCTAAGTACAGAACTAC
13833048 C
1 C
13833049 AATACCTACT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.26
Consensus pattern (52 bp):
CTTCTACCGATACAAGTACATAAAATACCGATACTTCTAAGTACAGAACTAC
Found at i:13833040 original size:25 final size:25
Alignment explanation
Indices: 13832957--13833040 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
13832947 CTACCGATAC
13832957 AAGTACATAAAATACCGATACTTCT
1 AAGTACATAAAATACCGATACTTCT
* * *
13832982 AAGTACA-GAACTACC--TTCTATCGAT
1 AAGTACATAAAATACCGATACT-TC--T
13833007 ACAAGTACATAAAATACCGATACTTCT
1 --AAGTACATAAAATACCGATACTTCT
13833034 AAGTACA
1 AAGTACA
13833041 GAACTACCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
22 3 0.07
23 2 0.04
24 6 0.13
25 15 0.33
27 8 0.18
28 6 0.13
29 2 0.04
30 3 0.07
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (25 bp):
AAGTACATAAAATACCGATACTTCT
Found at i:13844915 original size:7 final size:7
Alignment explanation
Indices: 13844903--13844927 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13844893 TCCCTTAACC
13844903 TTCCCAA
1 TTCCCAA
13844910 TTCCCAA
1 TTCCCAA
13844917 TTCCCAA
1 TTCCCAA
13844924 TTCC
1 TTCC
13844928 TAAATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (7 bp):
TTCCCAA
Found at i:13844984 original size:20 final size:20
Alignment explanation
Indices: 13844956--13845016 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
13844946 AAAAAAAAAC
* *
13844956 CTAAATGCTTCCATCCATTG
1 CTAAGTGCTTCCATCAATTG
13844976 CTAAGTGCTTCCATCAATTG
1 CTAAGTGCTTCCATCAATTG
* *
13844996 CTAAGTCCTTCCATCAGTTG
1 CTAAGTGCTTCCATCAATTG
13845016 C
1 C
13845017 AAATCGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (20 bp):
CTAAGTGCTTCCATCAATTG
Found at i:13845483 original size:40 final size:39
Alignment explanation
Indices: 13845421--13845503 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
13845411 TCTTATTGTA
*
13845421 TTTTCAATTTGTTTGTTATTTTACGAATTGTTTTAATAT
1 TTTTCAATTTGTTTGTTATTTTAAGAATTGTTTTAATAT
* * * *
13845460 CTTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 -TTTTCAATTTGTTTGTTATTTTAAGAATTGTTTTAATAT
13845500 TTTT
1 TTTT
13845504 AAGTGTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.66
Consensus pattern (39 bp):
TTTTCAATTTGTTTGTTATTTTAAGAATTGTTTTAATAT
Found at i:13845493 original size:12 final size:12
Alignment explanation
Indices: 13845476--13845501 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13845466 AATTTGTTTG
13845476 TTGTTTTAATAT
1 TTGTTTTAATAT
13845488 TTGTTTTAATAT
1 TTGTTTTAATAT
13845500 TT
1 TT
13845502 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:13846374 original size:117 final size:115
Alignment explanation
Indices: 13846072--13846550 Score: 486
Period size: 117 Copynumber: 4.1 Consensus size: 115
13846062 AAAAAATTTG
* * *
13846072 GTGTTGGCCATTGCATGGTCGACACCACCTTTTTGTTAGAT---AAATTTTTTTTTCTGGTGTTG
1 GTGTTGGCCATTGCATGGTCGACACCCCCTTTTTGTCAGATAAAAAATATTTTTTT-TGGTGTTG
* * * *
13846134 GCCATGCATT-AGCCGACACCACCTTTTTATTTGATAAAAAATCAATTTTTTT
65 GTCATGCCTTGA-CCGACACCACTTTTTTATCTGA-AAAAAATCAATTTTTTT
** * *
13846186 GTGTTGGTTATTGTATGGTCGACACCCCCTTTTTGTCAAATAAAAAATATTTTTTTTGGTGTTGG
1 GTGTTGGCCATTGCATGGTCGACACCCCCTTTTTGTCAGATAAAAAATATTTTTTTTGGTGTTGG
*
13846251 TCATGCCTTGACCGGCACCATCTTTTTTATCTGTAAAAAAATCAATTTTTTTT
66 TCATGCCTTGACCGACACCA-CTTTTTTATCTG-AAAAAAATCAA-TTTTTTT
* * * *
13846304 GTATTGGCCATTGCATGG-CTAACATCCCCTTTTTGTCAGATAAAAGATATTTTTTTT-GTGTTG
1 GTGTTGGCCATTGCATGGTC-GACACCCCCTTTTTGTCAGATAAAAAATATTTTTTTTGGTGTTG
*
13846367 GTCATGCCTTGATCGACACCACATTTTTTATCTGGAAAAAAATCAAATTTTTTT
65 GTCATGCCTTGACCGACACCAC-TTTTTTATCT-GAAAAAAATC-AATTTTTTT
* * * * *
13846421 GTGTGGGTCATTACATGGCCGACACCCCCTTTTTGTCAGATAAAAAATATTCAAATTTTTTTTGT
1 GTGTTGGCCATTGCATGGTCGACACCCCCTTTTTGTCAGATAAAAAATA-T----TTTTTTTGGT
* ** * * *
13846486 GTTGGCCATTACATG-GCGACACCACCTTTTTATCTGATAAAAAATTCAAATTTTTTTT
61 GTTGGTCATGCCTTGACCGACACCACTTTTTTATCTGA-AAAAAA-TC-AA-TTTTTTT
13846544 GTGTTGG
1 GTGTTGG
13846551 TCATACATTG
Statistics
Matches: 308, Mismatches: 36, Indels: 33
0.82 0.10 0.09
Matches are distributed among these distances:
114 35 0.11
116 25 0.08
117 124 0.40
118 60 0.19
120 2 0.01
121 15 0.05
122 21 0.07
123 26 0.08
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (115 bp):
GTGTTGGCCATTGCATGGTCGACACCCCCTTTTTGTCAGATAAAAAATATTTTTTTTGGTGTTGG
TCATGCCTTGACCGACACCACTTTTTTATCTGAAAAAAATCAATTTTTTT
Found at i:13846514 original size:62 final size:59
Alignment explanation
Indices: 13846147--13846575 Score: 310
Period size: 60 Copynumber: 7.2 Consensus size: 59
13846137 ATGCATTAGC
** * **
13846147 CGACACCACCTTTTTATTTGATAAAAAATC-AA-TTTTTTTGTGTTGGTTATTGTATGG
1 CGACACCACCTTTTTATCAGATAAAAAATCAAATTTTTTTTGTGTTGGTCATTACATGG
* * * ** * *
13846204 TCGACACCCCCTTTTTGTCAAATAAAAAAT---ATTTTTTTTGGTGTTGGTCATGCCTTGAC
1 -CGACACCACCTTTTTATCAGATAAAAAATCAAATTTTTTTT-GTGTTGGTCATTACATG-G
* * * * * *
13846263 CGGCACCATCTTTTTTATCTG-TAAAAAAATC-AATTTTTTTTGTATTGGCCATTGCATGG
1 CGACACCA-CCTTTTTATCAGAT-AAAAAATCAAATTTTTTTTGTGTTGGTCATTACATGG
* * * ** * *
13846322 CTAACATCC-CCTTTTTGTCAGATAAAAGAT---ATTTTTTTTGTGTTGGTCATGCCTTGAT
1 C-GACA-CCACCTTTTTATCAGATAAAAAATCAAATTTTTTTTGTGTTGGTCATTACATG-G
* * *
13846380 CGACACCACATTTTTTATCTGGA-AAAAAATCAAA-TTTTTTTGTGTGGGTCATTACATGG
1 CGACACCAC-CTTTTTATC-AGATAAAAAATCAAATTTTTTTTGTGTTGGTCATTACATGG
* * *
13846439 CCGACACCCCCTTTTTGTCAGATAAAAAATATTCAAATTTTTTTTGTGTTGGCCATTACATGG
1 -CGACACCACCTTTTTATCAGAT-AAAAA-A-TCAAATTTTTTTTGTGTTGGTCATTACATGG
*
13846502 CGACACCACCTTTTTATCTGATAAAAAATTCAAATTTTTTTTGTGTTGGTCA-TACATTGG
1 CGACACCACCTTTTTATCAGATAAAAAA-TCAAATTTTTTTTGTGTTGGTCATTACA-TGG
*
13846562 CCGACACCAACTTT
1 -CGACACCACCTTT
13846576 CCCTCATTTC
Statistics
Matches: 290, Mismatches: 56, Indels: 47
0.74 0.14 0.12
Matches are distributed among these distances:
56 3 0.01
57 32 0.11
58 59 0.20
59 44 0.15
60 75 0.26
61 30 0.10
62 24 0.08
63 23 0.08
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (59 bp):
CGACACCACCTTTTTATCAGATAAAAAATCAAATTTTTTTTGTGTTGGTCATTACATGG
Found at i:13847441 original size:18 final size:17
Alignment explanation
Indices: 13847420--13847483 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
13847410 AATTAGAAAT
13847420 GAAATTTAAAATATAAAC
1 GAAA-TTAAAATATAAAC
13847438 GAAATTACAAAT-T--A-
1 GAAATTA-AAATATAAAC
13847452 -AAATTAAAATATAAAC
1 GAAATTAAAATATAAAC
13847468 GAAATTACAAAT-TAAA
1 GAAATTA-AAATATAAA
13847484 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.10
13 7 0.18
15 2 0.05
17 14 0.36
18 12 0.31
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (17 bp):
GAAATTAAAATATAAAC
Found at i:13847459 original size:30 final size:30
Alignment explanation
Indices: 13847410--13847498 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
13847400 AAAAAATAAT
* * *
13847410 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTACAAATTAAAATTAAAATATAAACGA
13847440 AATTACAAATTAAAATTAAAATATAAACGA
1 AATTACAAATTAAAATTAAAATATAAACGA
*
13847470 AATTACAAATT-AAATTAAAAAAATAAACG
1 AATTACAAATTAAAATT-AAAATATAAACG
13847499 GAAAAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.09
30 49 0.91
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (30 bp):
AATTACAAATTAAAATTAAAATATAAACGA
Found at i:13849114 original size:60 final size:60
Alignment explanation
Indices: 13848864--13849608 Score: 623
Period size: 61 Copynumber: 12.6 Consensus size: 60
13848854 GAAAGGAGGG
* * * * * *
13848864 AAAGTTGGTGTCGACCAATGC-ATGGCTAACACCAAAAAAAATT-ATTTTTTTATCTGACAA
1 AAAGGTGGTGTCGGCC-ATGCAATGGCCAACACC-AAAAAATTTGATTTTTTTATCAGATAA
13848924 CCAATA-GTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAATTTGAATTTTTTTATCAGATAA
1 --AA-AGGTGGTGTCGGCC-ATGCAATGGCCAACACCAAAAAATTTG-ATTTTTTTATCAGATAA
* * *
13848987 AAAGGTGGTGTCGACCATGCAATGGCCAACACTAAAAAATTTGATTTTTTTTATTAGATAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGA-TTTTTTTATCAGATAA
* * * * *
13849048 AAAGGTGGTGTCGACCATTCAATGTCTAATACCAAAAAATTTGATTTTTTTATCAGATAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
* * * * * *
13849108 ATAGGTGGTGTCGGTCATGCAATTGCCAACA-CAAAAAA-AT-ATTTTTTTATCTGACAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
* * *
13849165 AAAGAG-GATGTCGGCCATGCAATGGCCAACACCAAAAAA-ATGATTTTTTTCT-AGATAAA
1 AAAG-GTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGAT-AA
* * * * * *
13849224 AAATGTGGTGTCGGCCAAGGC-ATGGCTAACACCAAAAAA-AT-A-TTGTTTATCTA-ACAA
1 AAAGGTGGTGTCGGCC-ATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATC-AGATAA
* * *
13849281 AAAGG-GAGTGTCGACCATG-AGATGGCCAACATCAAAAAAATTTGA-TTTTTTACCAGATAAA
1 AAAGGTG-GTGTCGGCCATGCA-ATGGCCAACA-CCAAAAAATTTGATTTTTTTATCAGAT-AA
* * *
13849342 AAAGATGGTATCGGCCATGCAATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
* * * ** * *
13849402 ATAAAG-GGTGTCGGTCATGCAATGGTCAACACCAAAAAAAAT-A-TTTTTTATCTGACAA
1 A-AAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
* * * * *
13849460 AAAGGGGGTGTCGGCCATGCAATGGCAAATA-CAAAAAAATT-AATTTTTTATCAGATAAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGAT-AA
* ** * * *
13849519 AAAGGTGGTGTCAGCCAATGC-ATGGCCAACA-CAAAAAA--AAAATTTATT-T--GACAA
1 AAAGGTGGTGTCGGCC-ATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
*
13849573 AAAGGTGGTGTCGGCCATGCAATGGGCAACACCAAA
1 AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAA
13849609 TTTTTTTTCA
Statistics
Matches: 570, Mismatches: 80, Indels: 73
0.79 0.11 0.10
Matches are distributed among these distances:
53 4 0.01
54 26 0.05
55 6 0.01
56 3 0.01
57 83 0.15
58 76 0.13
59 84 0.15
60 106 0.19
61 136 0.24
62 30 0.05
63 16 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (60 bp):
AAAGGTGGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAA
Found at i:13849497 original size:294 final size:296
Alignment explanation
Indices: 13848872--13849604 Score: 872
Period size: 294 Copynumber: 2.5 Consensus size: 296
13848862 GGAAAGTTGG
* * * * * *
13848872 TGTCGACCAATGC-ATGGCTAACACCAAAAAAAATTATTTTTTTATCTGACAACCAATA-GTGGT
1 TGTCGGCC-ATGCAATGGCAAACACC-AAAAAAATTAATTTTTTATCAGATAA--AAAAGGTGGT
* * *
13848935 GTCGGCCAATGCATGGCCAACACCAAAAAATTTGAATTTTTTTATCAGATAAAAAGGTGGTGTCG
62 GTCGGCCAATGCATGGCCAACACCAAAAAA-AT-AATTTGTTTATCAGACAAAAAGGTGGTGTCG
* ** * *
13849000 ACCATGCAATGGCCAACACTAAAAAATTTGATTTTTTTTATTAGATAAAAAGGTGGTGTCGACCA
125 ACCATGCAATGGCCAACACAAAAAAATTTGA-TTTTTTTACCAGATAAAAAGATGGTATCGACCA
* * * * * *
13849065 TTCAATGTCTAATACCAAAAAATTTGATTTTTTTATCAGATAAATAGGTGGTGTCGGTCATGCAA
189 TGCAATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAATAAGTGGTGTCGGTCATGCAA
*
13849130 TTGCCAACACAAAAAAATATTTTTTTATCTGACAAAAAGAGGA
254 TGGCCAACACAAAAAAATATTTTTTTATCTGACAAAAAGAGGA
* * *
13849173 TGTCGGCCATGCAATGGCCAACACCAAAAAAA-TGATTTTTT-TCTAGATAAAAAATGTGGTGTC
1 TGTCGGCCATGCAATGGCAAACACCAAAAAAATTAATTTTTTATC-AGATAAAAAAGGTGGTGTC
* *
13849236 GGCCAAGGCATGGCTAACACCAAAAAAAT-A-TTGTTTATCTA-ACAAAAAGG-GAGTGTCGACC
65 GGCCAATGCATGGCCAACACCAAAAAAATAATTTGTTTATC-AGACAAAAAGGTG-GTGTCGACC
*
13849297 ATG-AGATGGCCAACATCAAAAAAATTTGA-TTTTTTACCAGATAAAAAAGATGGTATCGGCCAT
128 ATGCA-ATGGCCAACA-CAAAAAAATTTGATTTTTTTACCAGAT-AAAAAGATGGTATCGACCAT
13849360 GCAATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAATAAAG-GGTGTCGGTCATGCAA
190 GCAATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAAT-AAGTGGTGTCGGTCATGCAA
* * *
13849424 TGGTCAACACCAAAAAAA-ATATTTTTTATCTGACAAAAAGGGGG
254 TGGCCAACA-CAAAAAAATAT-TTTTTTATCTGACAAAAAGAGGA
* *
13849468 TGTCGGCCATGCAATGGCAAATA-CAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGTGTCA
1 TGTCGGCCATGCAATGGCAAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGTGTCG
* * *
13849532 GCCAATGCATGGCCAACA-CAAAAAAAAAATTT-ATT-T--GACAAAAAGGTGGTGTCGGCCATG
66 GCCAATGCATGGCCAACACCAAAAAAATAATTTGTTTATCAGACAAAAAGGTGGTGTCGACCATG
*
13849592 CAATGGGCAACAC
131 CAATGGCCAACAC
13849605 CAAATTTTTT
Statistics
Matches: 375, Mismatches: 39, Indels: 46
0.82 0.08 0.10
Matches are distributed among these distances:
291 1 0.00
292 29 0.08
293 15 0.04
294 136 0.36
295 111 0.30
296 4 0.01
297 4 0.01
298 35 0.09
299 11 0.03
300 11 0.03
301 18 0.05
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (296 bp):
TGTCGGCCATGCAATGGCAAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGTGTCG
GCCAATGCATGGCCAACACCAAAAAAATAATTTGTTTATCAGACAAAAAGGTGGTGTCGACCATG
CAATGGCCAACACAAAAAAATTTGATTTTTTTACCAGATAAAAAGATGGTATCGACCATGCAATG
GCCAACACCAAAAAAATTGATTTTTTTATCAGATAAATAAGTGGTGTCGGTCATGCAATGGCCAA
CACAAAAAAATATTTTTTTATCTGACAAAAAGAGGA
Found at i:13849593 original size:113 final size:117
Alignment explanation
Indices: 13848864--13849608 Score: 435
Period size: 116 Copynumber: 6.3 Consensus size: 117
13848854 GAAAGGAGGG
* * * * * * **
13848864 AAAGTTGGTGTCGACCAATGC-ATGGCTAACACCAAAAAAAATT-ATTTTTTTATCTGACAACCA
1 AAAGGTGGTGTCGGCC-ATGCAATGGCAAACACC-AAAAAAATTGAATTTTTTATCAGATAAATA
* * * * *
13848927 ATAGTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAATTTGAATTTTTTTATCAGATAA
64 A-AG-GGTGTCAGCC-ATGCAATGGCCAACACCAAAAAA----AATATATTTATCTGACAA
* * * * * *
13848987 AAAGGTGGTGTCGACCATGCAATGGCCAACACTAAAAAATTTGATTTTTTTTATTAGATAAA-AA
1 AAAGGTGGTGTCGGCCATGCAATGGCAAACACCAAAAAAATTGA-ATTTTTTATCAGATAAATAA
* * * * * * * * * *
13849051 GGTGGTGTC-GACCATTCAATGTCTAATACCAAAAAATTTGATTTTTTTATCAGATAA
65 AG-GGTGTCAG-CCATGCAATGGCCAACACCAAAAAA---AATATATTTATCTGACAA
* * * * * * *
13849108 ATAGGTGGTGTCGGTCATGCAATTGCCAACA-CAAAAAAA-T-ATTTTTTTATCTGACAAA-AAG
1 AAAGGTGGTGTCGGCCATGCAATGGCAAACACCAAAAAAATTGAATTTTTTATCAGATAAATAA-
* * * * *
13849169 AGGATGTCGGCCATGCAATGGCCAACACC-AAAAAAATGATTTTTTTCTAGATAAA
65 AGGGTGTCAGCCATGCAATGGCCAACACCAAAAAAAAT-ATATTTATCT-GA-CAA
* * * * *
13849224 AAATGTGGTGTCGGCCAAGGC-ATGGCTAACACCAAAAAAA-T--ATTGTTTATCTA-ACAAA-A
1 AAAGGTGGTGTCGGCC-ATGCAATGGCAAACACCAAAAAAATTGAATTTTTTATC-AGATAAATA
* * * * * * *
13849283 AGGGAGTGTC-GACCATG-AGATGGCCAACATCAAAAAAATTTGATTTTTTACCAGATAAA
64 AAGG-GTGTCAG-CCATGCA-ATGGCCAACACCAAAAAAA-AT-A-TATTTATCTGA-CAA
* * * *
13849342 AAAGATGGTATCGGCCATGCAATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAATAAA
1 AAAGGTGGTGTCGGCCATGCAATGGCAAACACCAAAAAAATTGAATTTTTTATCAGATAAATAAA
* * * *
13849407 GGGTGTCGGTCATGCAATGGTCAACACCAAAAAAAATATTTTTTATCTGACAA
66 GGGTGTCAGCCATGCAATGGCCAACACCAAAAAAAATA-TATTTATCTGACAA
* *
13849460 AAAGGGGGTGTCGGCCATGCAATGGCAAATA-CAAAAAAATT-AATTTTTTATCAGATAAA-AAA
1 AAAGGTGGTGTCGGCCATGCAATGGCAAACACCAAAAAAATTGAATTTTTTATCAGATAAATAAA
*
13849522 GGTGGTGTCAGCCAATGC-ATGGCCAACA-CAAAAAAAA-A-ATTTATTTGACAA
66 -G-GGTGTCAGCC-ATGCAATGGCCAACACCAAAAAAAATATATTTATCTGACAA
13849573 AAAGGTGGTGTCGGCCATGCAATGGGC-AACACCAAA
1 AAAGGTGGTGTCGGCCATGCAAT-GGCAAACACCAAA
13849609 TTTTTTTTCA
Statistics
Matches: 510, Mismatches: 80, Indels: 73
0.77 0.12 0.11
Matches are distributed among these distances:
113 38 0.07
114 14 0.03
115 10 0.02
116 90 0.18
117 84 0.16
118 75 0.15
119 19 0.04
120 8 0.02
121 88 0.17
122 43 0.08
123 28 0.05
124 13 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (117 bp):
AAAGGTGGTGTCGGCCATGCAATGGCAAACACCAAAAAAATTGAATTTTTTATCAGATAAATAAA
GGGTGTCAGCCATGCAATGGCCAACACCAAAAAAAATATATTTATCTGACAA
Found at i:13849603 original size:54 final size:54
Alignment explanation
Indices: 13849408--13849604 Score: 182
Period size: 59 Copynumber: 3.5 Consensus size: 54
13849398 ATAAATAAAG
* * * * *
13849408 GGTGTCGGTCATGCAATGGTCAACACCAAAAAAAATATTTTTTATCTGACAAAAAGGG
1 GGTGTCGGCCATGCAATGGGCAACA-CAAAAAAAA-A--ATTTATTTGACAAAAAGGT
* * * *
13849466 GGTGTCGGCCATGCAAT-GGCAAATACAAAAAAATTAATTTTTTATCAGATAAAAAAGGT
1 GGTGTCGGCCATGCAATGGGC-AACACAAAAAAA-AAATTTATT-T--GA-CAAAAAGGT
* *
13849525 GGTGTCAGCCAATGC-ATGGCCAACACAAAAAAAAAATTTATTTGACAAAAAGGT
1 GGTGTCGGCC-ATGCAATGGGCAACACAAAAAAAAAATTTATTTGACAAAAAGGT
13849579 GGTGTCGGCCATGCAATGGGCAACAC
1 GGTGTCGGCCATGCAATGGGCAACAC
13849605 CAAATTTTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 22
0.74 0.11 0.14
Matches are distributed among these distances:
53 4 0.04
54 27 0.24
55 6 0.05
56 1 0.01
57 12 0.11
58 28 0.25
59 29 0.26
60 6 0.05
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (54 bp):
GGTGTCGGCCATGCAATGGGCAACACAAAAAAAAAATTTATTTGACAAAAAGGT
Found at i:13850166 original size:21 final size:21
Alignment explanation
Indices: 13850128--13850177 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
13850118 TCAAACATTA
*
13850128 AACCCCAAACTCATAACTTGT
1 AACCCCAAACTCATAACTCGT
*
13850149 AACCCCAAA-TCTTGAACTCGT
1 AACCCCAAACTCAT-AACTCGT
*
13850170 AAGCCCAA
1 AACCCCAA
13850178 GCCATTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.38, C:0.34, G:0.08, T:0.20
Consensus pattern (21 bp):
AACCCCAAACTCATAACTCGT
Found at i:13850434 original size:18 final size:17
Alignment explanation
Indices: 13850405--13850438 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
13850395 TTGCTTATAA
13850405 TTTAAAATTTTAATTAT
1 TTTAAAATTTTAATTAT
13850422 TTTAAATATTTTAATTA
1 TTTAAA-ATTTTAATTA
13850439 AAGTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAAATTTTAATTAT
Found at i:13851179 original size:28 final size:28
Alignment explanation
Indices: 13851147--13851202 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
13851137 ACCTATTCAG
13851147 GGCCTAAGTCAATGAACCAAATAAAAAA
1 GGCCTAAGTCAATGAACCAAATAAAAAA
13851175 GGCCTAAGTCAATGAACCAAATAAAAAA
1 GGCCTAAGTCAATGAACCAAATAAAAAA
13851203 ACAGTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.18, G:0.14, T:0.14
Consensus pattern (28 bp):
GGCCTAAGTCAATGAACCAAATAAAAAA
Found at i:13851589 original size:29 final size:28
Alignment explanation
Indices: 13851543--13851602 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
13851533 TGTTCATATT
* *
13851543 AAATAAAAAATTTATTAAAAATCA-TAA
1 AAATAAAAAAATTATTAAAAACCATTAA
13851570 AAATAAAAAAAATTATTTAAAAACCATTAA
1 AAAT-AAAAAAATTA-TTAAAAACCATTAA
13851600 AAA
1 AAA
13851603 ATTATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 9 0.32
29 9 0.32
30 6 0.21
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (28 bp):
AAATAAAAAAATTATTAAAAACCATTAA
Found at i:13853967 original size:1 final size:1
Alignment explanation
Indices: 13853961--13853995 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
13853951 CTTCATGAAA
* *
13853961 GGGGGGGGGGGGGGGGGGGCGGGGGGGGGGAGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
13853996 ATTCTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.03, G:0.94, T:0.00
Consensus pattern (1 bp):
G
Found at i:13859252 original size:63 final size:63
Alignment explanation
Indices: 13859174--13859294 Score: 215
Period size: 63 Copynumber: 1.9 Consensus size: 63
13859164 CTACATGCTA
* *
13859174 ATACAAGCATAAACACATATTCCAAAAGAATATGTATATACACACATACACAGACATAAGTAT
1 ATACAAGCATAAACACATATTCCAAAAGAATATGCATATACACACATACAAAGACATAAGTAT
*
13859237 ATACAAGCATAAACACATATTCCAAAAGAATATGCATATGCACACATACAAAGACATA
1 ATACAAGCATAAACACATATTCCAAAAGAATATGCATATACACACATACAAAGACATA
13859295 TAAGTTGTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.51, C:0.20, G:0.08, T:0.21
Consensus pattern (63 bp):
ATACAAGCATAAACACATATTCCAAAAGAATATGCATATACACACATACAAAGACATAAGTAT
Found at i:13868406 original size:16 final size:17
Alignment explanation
Indices: 13868380--13868411 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13868370 TTAATTTAAA
13868380 TAAATTAATTTTTCAAT
1 TAAATTAATTTTTCAAT
13868397 TAAA-TAATTTTTCAA
1 TAAATTAATTTTTCAA
13868412 CCCAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATTTTTCAAT
Found at i:13870396 original size:23 final size:21
Alignment explanation
Indices: 13870354--13870403 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
13870344 AATATAACAA
13870354 TAATTAAAACAAATAAATAAGGT
1 TAATTAAAACAAATAAATAA--T
*
13870377 TAATTAAAACATAA-ACATAAT
1 TAATTAAAACA-AATAAATAAT
13870398 TAATTA
1 TAATTA
13870404 TTTTAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
23 16 0.64
24 2 0.08
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (21 bp):
TAATTAAAACAAATAAATAAT
Found at i:13874302 original size:6 final size:6
Alignment explanation
Indices: 13874291--13874329 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
13874281 TGATCAAAAT
* * *
13874291 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
13874330 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:13874526 original size:37 final size:38
Alignment explanation
Indices: 13874429--13874535 Score: 90
Period size: 37 Copynumber: 2.8 Consensus size: 38
13874419 CTTCGACCTT
** *
13874429 GAGTCGATGAGACACTGGTTGTTATTATTTTACTTCGGATA
1 GAGTCGATGAGACACTGG--G-TACCACTTTACTTCGGATA
* ** * *
13874470 GATTCGATGAGGTATTGGGTACCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
**
13874508 G-GTCGATGAGACACTGGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTACCACTTTA
13874536 TTGCTTCGAA
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 21 0.40
38 16 0.31
39 1 0.02
41 14 0.27
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
Found at i:13875324 original size:13 final size:14
Alignment explanation
Indices: 13875299--13875327 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13875289 ATTTGCCCTG
13875299 TTTTGAGTAAAAAT
1 TTTTGAGTAAAAAT
13875313 TTTTGAGTAAAAAT
1 TTTTGAGTAAAAAT
13875327 T
1 T
13875328 ACATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TTTTGAGTAAAAAT
Found at i:13885892 original size:12 final size:12
Alignment explanation
Indices: 13885871--13885902 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
13885861 CCAAAAAGAG
13885871 AGAAACAAAGAAA
1 AGAAA-AAAGAAA
13885884 AGAAAAAAGAAA
1 AGAAAAAAGAAA
13885896 AGAAAAA
1 AGAAAAA
13885903 TGAGTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:13885911 original size:18 final size:19
Alignment explanation
Indices: 13885890--13885935 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
13885880 GAAAAGAAAA
13885890 AAGAAAAGAA-AA-ATGAGT
1 AAGAAAA-AAGAACATGAGT
13885908 AAGAACAAAAGAATCATGAGT
1 AAGAA-AAAAGAA-CATGAGT
13885929 AAGAAAA
1 AAGAAAA
13885936 CCTGTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 2 0.08
21 11 0.46
ACGTcount: A:0.65, C:0.04, G:0.20, T:0.11
Consensus pattern (19 bp):
AAGAAAAAAGAACATGAGT
Found at i:13885919 original size:21 final size:21
Alignment explanation
Indices: 13885893--13885933 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13885883 AAGAAAAAAG
13885893 AAAAGAAAAATGAGTAAGAAC
1 AAAAGAAAAATGAGTAAGAAC
**
13885914 AAAAGAATCATGAGTAAGAA
1 AAAAGAAAAATGAGTAAGAA
13885934 AACCTGTTGT
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:0.63, C:0.05, G:0.20, T:0.12
Consensus pattern (21 bp):
AAAAGAAAAATGAGTAAGAAC
Found at i:13891380 original size:46 final size:46
Alignment explanation
Indices: 13891313--13891408 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
13891303 ACTACTAATT
* ** *
13891313 TGTAATATTAGTTATGCACTTGGACGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
13891359 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
13891405 TGTA
1 TGTA
13891409 CTATTAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
Found at i:13893653 original size:24 final size:24
Alignment explanation
Indices: 13893620--13893666 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13893610 GGTTTCTTGA
*
13893620 AATGAAGAGAAAAGGATGGTGAGAG
1 AATGAAGAGAAAAGG-GGGTGAGAG
*
13893645 AATG-AGAGATAAGGGGGTGAGA
1 AATGAAGAGAAAAGGGGGTGAGA
13893667 TGGAGTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.13
Consensus pattern (24 bp):
AATGAAGAGAAAAGGGGGTGAGAG
Found at i:13894792 original size:21 final size:21
Alignment explanation
Indices: 13894737--13894792 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
13894727 TTTGTGATAG
*
13894737 TTCTATCGATACAAGTGTAAC
1 TTCTATCGATACTAGTGTAAC
* * * *
13894758 ATCTACCGAAACTAGT-TATGC
1 TTCTATCGATACTAGTGTA-AC
13894779 TTCTATCGATACTA
1 TTCTATCGATACTA
13894793 AAAACTCCAG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (21 bp):
TTCTATCGATACTAGTGTAAC
Found at i:13895470 original size:42 final size:42
Alignment explanation
Indices: 13895414--13895598 Score: 223
Period size: 42 Copynumber: 4.4 Consensus size: 42
13895404 TATACTCTAA
* * *
13895414 CGAGTCATAAGTCTTCCTTTAATCGT-ATCCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCATAAT-CTCATTCTCATCC
* *
13895456 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
* * *
13895498 TGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
* *
13895540 CGAGACATGAGTCTTCCTTT-ATACA-AATCCTCATGCTCAACC
1 CGAGACATGAGTCTTCCTTTAAT-CATAAT-CTCATTCTCATCC
*
13895582 TGAGACATGAGTCTTCC
1 CGAGACATGAGTCTTCC
13895599 CTTTTATACA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
41 5 0.04
42 121 0.95
43 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
Found at i:13902619 original size:41 final size:42
Alignment explanation
Indices: 13902565--13902668 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
13902555 TATGCTCCAA
* * *
13902565 CGAGTCATAAGTCTTCCTTTAATC-ATAT-TC-TTCTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCAAAATCTCATTCTCT--TCC
*
13902606 CGAGACATGAGTCTTCCTTTAATCAAAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAATCAAAATCTCATTCTCTTCC
13902648 CGAGACATGAGTCTTCCTTTA
1 CGAGACATGAGTCTTCCTTTA
13902669 CAAAAATCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 22 0.39
42 26 0.46
43 2 0.04
44 6 0.11
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCAAAATCTCATTCTCTTCC
Found at i:13902694 original size:42 final size:41
Alignment explanation
Indices: 13902565--13902706 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 41
13902555 TATGCTCCAA
* * * *
13902565 CGAGTCATAAGTCTTCCTTTAATCATATTCTTC-T-CTCATCC
1 CGAGACATGAGTCTTCCTTTAA-CAAAATC-TCATGCTCATCC
* * *
13902606 CGAGACATGAGTCTTCCTTTAATCAAAATCTCATTCTCTTCT
1 CGAGACATGAGTCTTCCTTTAA-CAAAATCTCATGCTCATCC
*
13902648 CGAGACATGAGTCTTCCTTT-ACAAAAATCCTCATGCTCAACC
1 CGAGACATGAGTCTTCCTTTAAC-AAAAT-CTCATGCTCATCC
* *
13902690 CGAGACTTAAGTCTTCC
1 CGAGACATGAGTCTTCC
13902707 CTTTTATACA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
41 33 0.39
42 49 0.58
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.35
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTTAACAAAATCTCATGCTCATCC
Found at i:13908143 original size:21 final size:21
Alignment explanation
Indices: 13908117--13908176 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
13908107 AATAGTGCAG
*
13908117 ACTTCTACTGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
13908138 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
13908159 TCTTCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
13908177 CTTATTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:13908992 original size:52 final size:52
Alignment explanation
Indices: 13908919--13909037 Score: 211
Period size: 52 Copynumber: 2.3 Consensus size: 52
13908909 CATTTCATTA
13908919 ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
* *
13908971 ATACTCACGATGACCCATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
*
13909023 ATACTCACAATGACA
1 ATACTCACGATGACA
13909038 TATACTCACG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
Found at i:13909041 original size:16 final size:16
Alignment explanation
Indices: 13909020--13909053 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13909010 GTAAAGGATT
13909020 CATATACTCACAATGA
1 CATATACTCACAATGA
*
13909036 CATATACTCACGATGA
1 CATATACTCACAATGA
13909052 CA
1 CA
13909054 CATAGTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (16 bp):
CATATACTCACAATGA
Found at i:13910452 original size:9 final size:9
Alignment explanation
Indices: 13910438--13910483 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
13910428 TAAATAGTTT
13910438 GAGTTATTC
1 GAGTTATTC
*
13910447 GAGTTAATC
1 GAGTTATTC
13910456 GAGTTATTC
1 GAGTTATTC
*
13910465 GAGTTAATC
1 GAGTTATTC
13910474 GAGTTATTC
1 GAGTTATTC
13910483 G
1 G
13910484 GATAAAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (9 bp):
GAGTTATTC
Found at i:13910461 original size:18 final size:18
Alignment explanation
Indices: 13910438--13910483 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
13910428 TAAATAGTTT
13910438 GAGTTATTCGAGTTAATC
1 GAGTTATTCGAGTTAATC
13910456 GAGTTATTCGAGTTAATC
1 GAGTTATTCGAGTTAATC
13910474 GAGTTATTCG
1 GAGTTATTCG
13910484 GATAAAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (18 bp):
GAGTTATTCGAGTTAATC
Found at i:13911446 original size:29 final size:28
Alignment explanation
Indices: 13911392--13911503 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 28
13911382 TTCGAAATCG
13911392 CCACAAAGGCATGTCCTTTCG-G-GGTTTTT
1 CCACAAAGGCAT-TCCTTT-GAGAGG-TTTT
* *
13911421 CCACAAAAGCATTCCTTTGAGAGGTTTG
1 CCACAAAGGCATTCCTTTGAGAGGTTTT
* *
13911449 CCACAAAGGCGTTCCTTTTTAGAGGTTTT
1 CCACAAAGGCATTCC-TTTGAGAGGTTTT
* * *
13911478 CCACAAAGGTAGTCCTTTAAGAGGTT
1 CCACAAAGGCATTCCTTTGAGAGGTT
13911504 CACCATAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 33 0.47
29 36 0.51
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (28 bp):
CCACAAAGGCATTCCTTTGAGAGGTTTT
Found at i:13914411 original size:17 final size:18
Alignment explanation
Indices: 13914389--13914426 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13914379 ATTAAATATT
*
13914389 TTAAATT-ATTGGAATGA
1 TTAAATTGATGGGAATGA
*
13914406 TTAAATTGATGGGAATTA
1 TTAAATTGATGGGAATGA
13914424 TTA
1 TTA
13914427 TCTAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (18 bp):
TTAAATTGATGGGAATGA
Found at i:13915020 original size:24 final size:24
Alignment explanation
Indices: 13914986--13915127 Score: 167
Period size: 24 Copynumber: 5.9 Consensus size: 24
13914976 TTTATCTGAA
*
13914986 TGGCTGACGAGCATAAACATAAAG
1 TGGCTGACGAGCATAAACGTAAAG
* * *
13915010 TAGCTGACGAGCGTAAACGCAAAG
1 TGGCTGACGAGCATAAACGTAAAG
*
13915034 TGGCTGACGAGCATAAATGTAAAG
1 TGGCTGACGAGCATAAACGTAAAG
* * * *
13915058 TGGTTGATGAGCATAAATGTATAG
1 TGGCTGACGAGCATAAACGTAAAG
*
13915082 TGACTGACGAGCATAAACGTAAAG
1 TGGCTGACGAGCATAAACGTAAAG
* * *
13915106 TGGCCGATGAGCATAAATGTAA
1 TGGCTGACGAGCATAAACGTAA
13915128 TTGAAACTTG
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 98 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.20
Consensus pattern (24 bp):
TGGCTGACGAGCATAAACGTAAAG
Found at i:13916994 original size:42 final size:42
Alignment explanation
Indices: 13916912--13917023 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
13916902 ATGCTCTATC
* * * *
13916912 GAGTCATAAGTCTTCCTTTTTAAACATAATCTCACACTCATTCT
1 GAGTCATGAGTCTTCC--TTTAATCATATTCTCACACTCATCCT
*
13916956 GAGTCATGAGTCTTCCTTTAATCATATTCTCACTCTCATCCT
1 GAGTCATGAGTCTTCCTTTAATCATATTCTCACACTCATCCT
*
13916998 GAGACATGAGTCTTCCTTTAAT-ATAT
1 GAGTCATGAGTCTTCCTTTAATCATAT
13917024 CATCATGCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
41 4 0.06
42 43 0.69
44 15 0.24
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (42 bp):
GAGTCATGAGTCTTCCTTTAATCATATTCTCACACTCATCCT
Found at i:13917093 original size:43 final size:40
Alignment explanation
Indices: 13916882--13917102 Score: 142
Period size: 42 Copynumber: 5.2 Consensus size: 40
13916872 GATTCACAAA
* * * * *
13916882 TCTTCCTTTAATACAATCTTATGCTCTAT-CGAGTCATAAG
1 TCTTCCTTTAATATATTCTCATGCTC-ATCCGAGACATGAG
* * ** * *
13916922 TCTTCCTTTTTAAACATAATCTCACACTCATTCTGAGTCATGAG
1 TCTTCC--TTT-AATATATTCTCATGCTCA-TCCGAGACATGAG
13916966 TCTTCCTTTAATCATATTCTCACT-CTCATCCTGAGACATGAG
1 TCTTCCTTTAAT-ATATTCTCA-TGCTCATCC-GAGACATGAG
* * * *
13917008 TCTTCCTTTAATATA-TCATCATGCTCGTTTCGAGTCACGAG
1 TCTTCCTTTAATATATTC-TCATGCTC-ATCCGAGACATGAG
* *
13917049 TCTTCCATTCATATAAATTCTCATGCTCAATCCGAGACATGAG
1 TCTTCC-TTTA-ATATATTCTCATGCTC-ATCCGAGACATGAG
13917092 TCTTCCATTTA
1 TCTTCC-TTTA
13917103 TACATCAAGT
Statistics
Matches: 143, Mismatches: 24, Indels: 25
0.74 0.12 0.13
Matches are distributed among these distances:
40 9 0.06
41 27 0.19
42 45 0.31
43 45 0.31
44 17 0.12
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (40 bp):
TCTTCCTTTAATATATTCTCATGCTCATCCGAGACATGAG
Found at i:13919494 original size:27 final size:27
Alignment explanation
Indices: 13919463--13919517 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
13919453 CCTATACCTT
13919463 GACTCGATGATTAAATCGAGTATAGGA
1 GACTCGATGATTAAATCGAGTATAGGA
*
13919490 GACTCGATGATTAAATCGGGTATAGGA
1 GACTCGATGATTAAATCGAGTATAGGA
13919517 G
1 G
13919518 TGTTACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (27 bp):
GACTCGATGATTAAATCGAGTATAGGA
Found at i:13923747 original size:7 final size:8
Alignment explanation
Indices: 13923716--13923788 Score: 55
Period size: 8 Copynumber: 9.2 Consensus size: 8
13923706 GTTAACAAAC
13923716 AATTATAA
1 AATTATAA
13923724 AATTATAA
1 AATTATAA
* *
13923732 AAATCTAA
1 AATTATAA
13923740 AATT-TAA
1 AATTATAA
*
13923747 AGCA-AATCAA
1 A--ATTAT-AA
13923757 AA-T-TAA
1 AATTATAA
*
13923763 AATTAAAA
1 AATTATAA
13923771 AATTATAA
1 AATTATAA
13923779 AATTATAA
1 AATTATAA
13923787 AA
1 AA
13923789 ATTCAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 4 0.08
7 6 0.12
8 37 0.71
9 2 0.04
10 3 0.06
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (8 bp):
AATTATAA
Found at i:13924078 original size:19 final size:19
Alignment explanation
Indices: 13924038--13924078 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
13924028 AGGTAAATCG
* *
13924038 AAAGCTAATGGAAGATAAA
1 AAAGATAATGGAAGAAAAA
*
13924057 AAAGATAATTGAAGAAAAA
1 AAAGATAATGGAAGAAAAA
13924076 AAA
1 AAA
13924079 ATCAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (19 bp):
AAAGATAATGGAAGAAAAA
Found at i:13939272 original size:24 final size:24
Alignment explanation
Indices: 13939245--13939292 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13939235 GGAAAGTAAC
*
13939245 AACAAAGATGTTATGCTAATAAAT
1 AACAAAGATATTATGCTAATAAAT
*
13939269 AACAAATATATTATGCTAATAAAT
1 AACAAAGATATTATGCTAATAAAT
13939293 TCTAAATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
AACAAAGATATTATGCTAATAAAT
Found at i:13939428 original size:25 final size:24
Alignment explanation
Indices: 13939394--13939465 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
13939384 AATCTTTAGA
* *
13939394 CAGTTCGCATGTTTTATTGCGACCT
1 CAGTTTGCAT-TTTTCTTGCGACCT
* *
13939419 CAGTTTGCATCTTTCTTGCGAGCT
1 CAGTTTGCATTTTTCTTGCGACCT
*
13939443 TAGTTTGCATTTTTCTTGCGACC
1 CAGTTTGCATTTTTCTTGCGACC
13939466 CTAGTCGCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (24 bp):
CAGTTTGCATTTTTCTTGCGACCT
Done.