Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 189 of 202
Found at i:57819433 original size:45 final size:45
Alignment explanation
Indices: 57819374--57819526 Score: 218
Period size: 45 Copynumber: 3.4 Consensus size: 45
57819364 CACCAGTATA
* *
57819374 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
* * *
57819420 CTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
* *
57819465 CGGTAACGGTAACAGTAACAGTATTCGACACACAAAGTG-TCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAAT
57819510 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
57819527 GTCGGCACAT
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
45 90 0.95
46 5 0.05
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
Found at i:57819471 original size:39 final size:41
Alignment explanation
Indices: 57819381--57819543 Score: 161
Period size: 45 Copynumber: 3.9 Consensus size: 41
57819371 ATACAGTAAT
* *
57819381 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCG-A-C-GT-A
57819426 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGA--C-GT-A
* * *
57819471 CGGTAACAGTAACAGTATTCGACACACAAAGTGTCGA-AT-
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGACGTA
* * *
57819510 CAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCC
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCC
57819544 TGATCAGTAA
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
38 6 0.06
39 23 0.22
41 1 0.01
44 1 0.01
45 74 0.70
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGACGTA
Found at i:57819814 original size:39 final size:40
Alignment explanation
Indices: 57819728--57819815 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
57819718 AATTCTTTAC
* *
57819728 TTCAGTAATTTCACAATTCAATGCATTATGCATAACAATA
1 TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
*
57819768 TTCAGTATTTTCACAATTCACT-CAGTAAT-CA-AGACAATA
1 TTCAGTATTTTCACAATTCAATGCA-TAATGCATA-ACAATA
57819807 TTCAGTATT
1 TTCAGTATT
57819816 CCATAATTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.44
40 23 0.53
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (40 bp):
TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
Found at i:57820549 original size:11 final size:11
Alignment explanation
Indices: 57820535--57820560 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57820525 CTTTTTCTTC
57820535 TTTCTCCCCTG
1 TTTCTCCCCTG
57820546 TTTCTCCCCTG
1 TTTCTCCCCTG
57820557 TTTC
1 TTTC
57820561 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:57822953 original size:2 final size:2
Alignment explanation
Indices: 57822946--57822988 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57822936 CCCTCTTTGA
57822946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57822988 A
1 A
57822989 ATACAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57824906 original size:2 final size:2
Alignment explanation
Indices: 57824899--57824953 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
57824889 TGTTCTAAGA
* *
57824899 AT AT AT AT AT AT AT AT AT AT -T CT A- AG A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57824938 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
57824954 TATTTTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57824929 original size:27 final size:27
Alignment explanation
Indices: 57824891--57824945 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
57824881 AAAAGCTTTG
57824891 TTCTAAGAATATATATATATATATATA
1 TTCTAAGAATATATATATATATATATA
57824918 TTCTAAGAATATATATATATATATATA
1 TTCTAAGAATATATATATATATATATA
57824945 T
1 T
57824946 ATATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (27 bp):
TTCTAAGAATATATATATATATATATA
Found at i:57825129 original size:16 final size:16
Alignment explanation
Indices: 57825104--57825144 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
57825094 GTGGTGTAAA
* *
57825104 ATTTTGAAAATATTTT
1 ATTTTAAAAATATTAT
*
57825120 TTTTTAAAAATATTAT
1 ATTTTAAAAATATTAT
57825136 ATTTTAAAA
1 ATTTTAAAA
57825145 TAATAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTAAAAATATTAT
Found at i:57838489 original size:16 final size:18
Alignment explanation
Indices: 57838456--57838489 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
57838446 TCATTTTAGT
57838456 TCTCTATTTAATTATTTA
1 TCTCTATTTAATTATTTA
57838474 TCTCT-TTTAA-TATTTA
1 TCTCTATTTAATTATTTA
57838490 AACTTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTCTATTTAATTATTTA
Found at i:57839792 original size:43 final size:43
Alignment explanation
Indices: 57839744--57839831 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 43
57839734 AATTTTCCAA
*
57839744 AACTTTAAT-A-TCACTTTTTATAAATAA-TATAATTTTTTGTCAT
1 AACTTTAATAAGTCA-TTTTTATAAATAAGTAT-ATTATTTGT-AT
*
57839787 AACTTTAATAAGTTATTTTTATAAATAAGTATATTATTTGTAT
1 AACTTTAATAAGTCATTTTTATAAATAAGTATATTATTTGTAT
57839830 AA
1 AA
57839832 TATATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
43 13 0.32
44 22 0.55
45 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (43 bp):
AACTTTAATAAGTCATTTTTATAAATAAGTATATTATTTGTAT
Found at i:57842476 original size:2 final size:2
Alignment explanation
Indices: 57842469--57842500 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
57842459 ATAAAGTTGG
*
57842469 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57842501 GGATCTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57844545 original size:29 final size:29
Alignment explanation
Indices: 57844513--57844571 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
57844503 TATCCATCTA
57844513 TATTTTATACTATTATTTAAGCCTGAGAT
1 TATTTTATACTATTATTTAAGCCTGAGAT
57844542 TATTTTATACTATTATTTAAGCCTGAGAT
1 TATTTTATACTATTATTTAAGCCTGAGAT
57844571 T
1 T
57844572 GAGTTGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
TATTTTATACTATTATTTAAGCCTGAGAT
Found at i:57846393 original size:19 final size:19
Alignment explanation
Indices: 57846351--57846395 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
57846341 TTTAAAAAAT
** *
57846351 AAAATTTAAAATCTTAAGC
1 AAAATTTAAAAAATTAACC
57846370 AAAATTTAAAAAATTAACC
1 AAAATTTAAAAAATTAACC
*
57846389 TAAATTT
1 AAAATTT
57846396 TTAAGTAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAAATTAACC
Found at i:57848581 original size:24 final size:22
Alignment explanation
Indices: 57848533--57848587 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
57848523 CTTATTTTCT
57848533 TTTTATTTTTAAATTTTAATTAA
1 TTTTATTTTTAAATTTT-ATTAA
57848556 TTTTATTTGTTAAATATTT-TTCAA
1 TTTTATTT-TTAAAT-TTTATT-AA
57848580 -TTTATTTT
1 TTTTATTTT
57848588 GTATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 1 0.03
23 17 0.59
24 8 0.28
25 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTAAATTTTATTAA
Found at i:57853406 original size:43 final size:43
Alignment explanation
Indices: 57853357--57853444 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
57853347 ATCCTTCAAA
57853357 AACAGATGAAGAGTCGGAGTAAAATAGTTTTAATCCATATGAG
1 AACAGATGAAGAGTCGGAGTAAAATAGTTTTAATCCATATGAG
*
57853400 AACAGATGAAGAGTCGGAGTAATATAGTTTTAATCCATATGAG
1 AACAGATGAAGAGTCGGAGTAAAATAGTTTTAATCCATATGAG
57853443 AA
1 AA
57853445 ACAGGCAAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (43 bp):
AACAGATGAAGAGTCGGAGTAAAATAGTTTTAATCCATATGAG
Found at i:57855259 original size:18 final size:18
Alignment explanation
Indices: 57855233--57855303 Score: 99
Period size: 18 Copynumber: 3.9 Consensus size: 18
57855223 TGTTCGTTCT
57855233 AGGATTTCTCCTCCTCCC
1 AGGATTTCTCCTCCTCCC
*
57855251 AGGACTTCTCCTCCT-CC
1 AGGATTTCTCCTCCTCCC
*
57855268 TGGCATTTCTCCTCCTCCC
1 AGG-ATTTCTCCTCCTCCC
*
57855287 AGGATTTCTCCTTCTCC
1 AGGATTTCTCCTCCTCC
57855304 AATTATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 4 0.09
18 38 0.83
19 4 0.09
ACGTcount: A:0.10, C:0.44, G:0.11, T:0.35
Consensus pattern (18 bp):
AGGATTTCTCCTCCTCCC
Found at i:57855312 original size:36 final size:36
Alignment explanation
Indices: 57855236--57855316 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
57855226 TCGTTCTAGG
**
57855236 ATTTCTCCTCCTCCCAGGACTTCTCCTCCTCCTGGC
1 ATTTCTCCTCCTCCCAGGACTTCTCCTCCTCCAAGC
* * **
57855272 ATTTCTCCTCCTCCCAGGATTTCTCCTTCTCCAATT
1 ATTTCTCCTCCTCCCAGGACTTCTCCTCCTCCAAGC
57855308 ATTTCTCCT
1 ATTTCTCCT
57855317 TCCATGTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.11, C:0.42, G:0.07, T:0.40
Consensus pattern (36 bp):
ATTTCTCCTCCTCCCAGGACTTCTCCTCCTCCAAGC
Found at i:57856965 original size:21 final size:23
Alignment explanation
Indices: 57856928--57856974 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
57856918 TTTTAAAAAA
*
57856928 TTTAAAAATATTGTTTT-CAATT
1 TTTAAAAATAATGTTTTACAATT
*
57856950 TTTAAAAATAAT-TTTTATAATT
1 TTTAAAAATAATGTTTTACAATT
57856972 TTT
1 TTT
57856975 TTGAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTAAAAATAATGTTTTACAATT
Found at i:57864783 original size:23 final size:22
Alignment explanation
Indices: 57864731--57864786 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
57864721 CACCTCTACT
*
57864731 TTTATTTTTAGGAATTTAATTTA
1 TTTATTTTTAGGAATTTAA-TAA
57864754 TTTATTTTTAGGAATTTAA-AA
1 TTTATTTTTAGGAATTTAATAA
*
57864775 TTTCAATTTTAG
1 TTT-ATTTTTAG
57864787 TTGTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 19 0.63
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTATTTTTAGGAATTTAATAA
Found at i:57865452 original size:17 final size:17
Alignment explanation
Indices: 57865427--57865461 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
57865417 TAATCCACAA
57865427 ATTGGTATTTAAGCTAT
1 ATTGGTATTTAAGCTAT
*
57865444 ATTGTTATTTAAGCTAT
1 ATTGGTATTTAAGCTAT
57865461 A
1 A
57865462 CCCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (17 bp):
ATTGGTATTTAAGCTAT
Found at i:57871129 original size:26 final size:28
Alignment explanation
Indices: 57871100--57871164 Score: 71
Period size: 32 Copynumber: 2.2 Consensus size: 28
57871090 TGATTGAAAT
*
57871100 TAAATTA-TCAATA-AATTATAAAGATA
1 TAAATTATTCAAAATAATTATAAAGATA
57871126 TAAATTAGACTTTCAAAATAATTATAAAGATA
1 TAAATT--A--TTCAAAATAATTATAAAGATA
57871158 TAAATTA
1 TAAATTA
57871165 ATATAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 6 0.19
28 1 0.03
30 1 0.03
31 5 0.16
32 19 0.59
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (28 bp):
TAAATTATTCAAAATAATTATAAAGATA
Found at i:57871943 original size:93 final size:93
Alignment explanation
Indices: 57871846--57872035 Score: 346
Period size: 93 Copynumber: 2.0 Consensus size: 93
57871836 TGTTAACACA
57871846 GTATACAAGAATGATCCACCCACCAGTC-TAGTTGAAACTTAAATATAATGGTTGTAACCTGTCT
1 GTATACAAGAATGATCCACCCACCAGTCTTA-TTGAAACTTAAATATAATGGTTGTAACCTGTCT
57871910 GCAGAAAAATGCATATATAGACAAATATG
65 GCAGAAAAATGCATATATAGACAAATATG
* *
57871939 GTATACAAGAATTATCCACCCACCATTCTTATTGAAACTTAAATATAATGGTTGTAACCTGTCTG
1 GTATACAAGAATGATCCACCCACCAGTCTTATTGAAACTTAAATATAATGGTTGTAACCTGTCTG
57872004 CAGAAAAATGCATATATAGACAAATATG
66 CAGAAAAATGCATATATAGACAAATATG
57872032 GTAT
1 GTAT
57872036 CACAGCTTTT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
93 92 0.98
94 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (93 bp):
GTATACAAGAATGATCCACCCACCAGTCTTATTGAAACTTAAATATAATGGTTGTAACCTGTCTG
CAGAAAAATGCATATATAGACAAATATG
Found at i:57878250 original size:17 final size:17
Alignment explanation
Indices: 57878228--57878276 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
57878218 TTTTTAGAAT
*
57878228 ATTTTAATAAATTTTTC
1 ATTTTAATAAATTTTTA
* * *
57878245 ATTTT-ATTAATATATA
1 ATTTTAATAAATTTTTA
57878261 ATTTTAATAAATTTTT
1 ATTTTAATAAATTTTT
57878277 TATGTGAATC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAATAAATTTTTA
Found at i:57894675 original size:45 final size:48
Alignment explanation
Indices: 57894606--57894713 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 48
57894596 GCTTTCCCTG
*
57894606 GTGGTTGGGGTGCTTCTGGAACTGAAAGTGG-A-GG-TGGCAGCGGCA
1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAATGGATGGCAGCGGCA
57894651 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCA
1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGG-AATGG--ATGGCAGCGGCA
57894702 GTGGCTGGGGTG
1 GTGGCTGGGGTG
57894714 GCAGTGGCGG
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
45 30 0.54
47 1 0.02
48 2 0.04
51 23 0.41
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (48 bp):
GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAATGGATGGCAGCGGCA
Found at i:57894716 original size:27 final size:27
Alignment explanation
Indices: 57894685--57894740 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
57894675 AAAGTGGAAA
57894685 TGGCAATGGCAGCGGCAGTGGCTGGGG
1 TGGCAATGGCAGCGGCAGTGGCTGGGG
* * * *
57894712 TGGCAGTGGCGGTGGCAGTGGTTGGGG
1 TGGCAATGGCAGCGGCAGTGGCTGGGG
57894739 TG
1 TG
57894741 CTTCTGGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.11, C:0.14, G:0.55, T:0.20
Consensus pattern (27 bp):
TGGCAATGGCAGCGGCAGTGGCTGGGG
Found at i:57894718 original size:15 final size:15
Alignment explanation
Indices: 57894698--57894740 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
57894688 CAATGGCAGC
57894698 GGCAGTGGCTGGGGT
1 GGCAGTGGCTGGGGT
57894713 GGCAGTGGC---GGT
1 GGCAGTGGCTGGGGT
*
57894725 GGCAGTGGTTGGGGT
1 GGCAGTGGCTGGGGT
57894740 G
1 G
57894741 CTTCTGGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 11 0.46
15 13 0.54
ACGTcount: A:0.07, C:0.12, G:0.60, T:0.21
Consensus pattern (15 bp):
GGCAGTGGCTGGGGT
Found at i:57894767 original size:78 final size:78
Alignment explanation
Indices: 57894647--57894792 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
57894637 AGGTGGCAGC
57894647 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
57894712 TGGCAGTGGCGGT
66 TGGCAGTGGCGGT
* ** *
57894725 GGCAGTGGTTGGGGTGCTTCTGGAACTGAAAGTGGAGGTGGCAATGGCAGCGGCAGTGGTTGGGG
1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
57894790 TGG
66 TGG
57894793 TGGTAGTGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.17, C:0.14, G:0.49, T:0.21
Consensus pattern (78 bp):
GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
TGGCAGTGGCGGT
Found at i:57899012 original size:19 final size:19
Alignment explanation
Indices: 57898974--57899017 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
57898964 AAAATGACAA
57898974 AAAATTTCTTTAAAATAAT
1 AAAATTTCTTTAAAATAAT
* *
57898993 ATAATTTACTTTATAA-AAT
1 AAAATTT-CTTTAAAATAAT
57899012 AAAATT
1 AAAATT
57899018 ATTGTGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTTCTTTAAAATAAT
Found at i:57902902 original size:2 final size:2
Alignment explanation
Indices: 57902895--57902937 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57902885 AGGGAAGGAA
57902895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57902937 A
1 A
57902938 ATGAGACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57905804 original size:15 final size:15
Alignment explanation
Indices: 57905785--57905814 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57905775 AACCTTTTAT
57905785 ATTTTT-TAATTTTG
1 ATTTTTATAATTTTG
57905799 ATTTTTATAATTTTG
1 ATTTTTATAATTTTG
57905814 A
1 A
57905815 ATTGTTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTTTATAATTTTG
Found at i:57907436 original size:32 final size:30
Alignment explanation
Indices: 57907368--57907442 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 30
57907358 CTTTTTTTAG
* *
57907368 CTTTAAAGGG-CCCAAAATTTTTTTATCAA
1 CTTTTAAGGGACCTAAAATTTTTTTATCAA
* *
57907397 CTCTTAAGGGACCTAAAATTTTTTTTCTCCAA
1 CTTTTAAGGGACCTAAAA-TTTTTTTAT-CAA
*
57907429 CTTTTAAGGAACCT
1 CTTTTAAGGGACCT
57907443 CAAACGCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.22
30 6 0.16
31 8 0.22
32 15 0.41
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (30 bp):
CTTTTAAGGGACCTAAAATTTTTTTATCAA
Found at i:57912339 original size:3 final size:3
Alignment explanation
Indices: 57912292--57912326 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
57912282 TAAAATGCAC
*
57912292 TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57912327 TGATGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:57916138 original size:62 final size:57
Alignment explanation
Indices: 57916051--57916182 Score: 165
Period size: 62 Copynumber: 2.2 Consensus size: 57
57916041 TTCAAAAATA
* * *
57916051 ATATTATTTTAATAGTTTAACATTAAATTTAATTTTATGTTTATCTTGTAGATAAATATT
1 ATATTATTTTAATAGTTTAACATTAAATTTAATCTAATATTTATC-T-T-GATAAATATT
* *
57916111 TTATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTATTTTAAT-AG-TTTAACATTAAATTTAATCTAATATTTATCTTGATAAATATT
*
57916170 ATATTATATTAAT
1 ATATTATTTTAAT
57916183 TGAATATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 21 0.33
60 13 0.21
61 3 0.05
62 26 0.41
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (57 bp):
ATATTATTTTAATAGTTTAACATTAAATTTAATCTAATATTTATCTTGATAAATATT
Found at i:57925260 original size:17 final size:17
Alignment explanation
Indices: 57925213--57925260 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
57925203 TGATTTGATA
57925213 AAAAATAAATATAATATT
1 AAAAATAAATA-AATATT
**
57925231 AAATTTAAATAAATATT
1 AAAAATAAATAAATATT
*
57925248 AAAAATAATTAAA
1 AAAAATAAATAAA
57925261 AAATAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATAAATAAATATT
Found at i:57926199 original size:19 final size:19
Alignment explanation
Indices: 57926153--57926208 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 19
57926143 AATCTTTAAG
57926153 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
57926172 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
57926193 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
57926209 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:57926230 original size:23 final size:22
Alignment explanation
Indices: 57926153--57926231 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 22
57926143 AATCTTTAAG
*
57926153 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
57926175 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
57926193 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
57926215 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
57926232 GATTTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 12 0.24
22 8 0.16
23 12 0.24
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:57926914 original size:4 final size:4
Alignment explanation
Indices: 57926905--57926934 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
57926895 TGTATATTTA
57926905 TATT TATT TATT TATT TATT TATT T-TT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
57926935 AATTCACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:57927161 original size:3 final size:3
Alignment explanation
Indices: 57927155--57927199 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
57927145 TTATCTTTTC
57927155 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
57927200 GTTCTTGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:57930256 original size:3 final size:3
Alignment explanation
Indices: 57930245--57930289 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
57930235 ATTGGAAAAA
*
57930245 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57930290 TGTTGGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:57934010 original size:19 final size:19
Alignment explanation
Indices: 57933988--57934024 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
57933978 TACTTGAAAA
57933988 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
57934007 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
57934025 AGATAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:57934935 original size:47 final size:46
Alignment explanation
Indices: 57934884--57935045 Score: 136
Period size: 47 Copynumber: 3.5 Consensus size: 46
57934874 AGTGTATTGT
* *
57934884 ATATTATTATTTTAGATTTATCATGTTTTATTATTTGTAATTTATCA
1 ATATTATTATTTTAAATTTATCATGTTATATTATTT-TAATTTATCA
* *
57934931 ATATTATTATTTTAAATTCAT--TGTTAACATTATTTTAAATTTATC-
1 ATATTATTATTTTAAATTTATCATGTT-ATATTATTTT-AATTTATCA
* * * *
57934976 ATATATATCTATTTCAAATTTATCAT-TAATATT-TTTAAATTTATTA
1 ATAT-TAT-TATTTTAAATTTATCATGTTATATTATTTTAATTTATCA
* **
57935022 TATACTATTATTTTGGATTTATCA
1 -ATATTATTATTTTAAATTTATCA
57935046 CATATGATTA
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
45 29 0.31
46 24 0.26
47 38 0.41
48 1 0.01
49 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (46 bp):
ATATTATTATTTTAAATTTATCATGTTATATTATTTTAATTTATCA
Found at i:57934963 original size:70 final size:69
Alignment explanation
Indices: 57934883--57935050 Score: 171
Period size: 70 Copynumber: 2.4 Consensus size: 69
57934873 AAGTGTATTG
* * * ** *
57934883 TATATTATTATTTTAGATTTATCATGTTTTAT-TATTTGTAATTTATCAATATTATTATTTTAAA
1 TATACTATTATTTTAGATTTATCAT-ATATATCTATTTCAAATTTATCAATAATA-T-TTTTAAA
*
57934947 TTCATTG
63 TTCATTA
* *
57934954 T-TAAC-ATTATTTTAAATTTATCATATATATCTATTTCAAATTTATCATTAATATTTTTAAATT
1 TAT-ACTATTATTTTAGATTTATCATATATATCTATTTCAAATTTATCAATAATATTTTTAAATT
*
57935017 TATTA
65 CATTA
* *
57935022 TATACTATTATTTTGGATTTATCACATAT
1 TATACTATTATTTTAGATTTATCATATAT
57935051 GATTATTATA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
68 15 0.19
69 26 0.32
70 37 0.46
71 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (69 bp):
TATACTATTATTTTAGATTTATCATATATATCTATTTCAAATTTATCAATAATATTTTTAAATTC
ATTA
Found at i:57935128 original size:24 final size:24
Alignment explanation
Indices: 57934883--57935139 Score: 144
Period size: 24 Copynumber: 10.8 Consensus size: 24
57934873 AAGTGTATTG
*
57934883 TATATTATTATTTTAGATTTATCA
1 TATATTATTATTTTAAATTTATCA
* *
57934907 TGTTTTATTATTTGT-AATTTATCA
1 TATATTATTATTT-TAAATTTATCA
* **
57934931 -ATATTATTATTTTAAATTCATTG
1 TATATTATTATTTTAAATTTATCA
**
57934954 T-TAACATTATTTTAAATTTATCA
1 TATATTATTATTTTAAATTTATCA
*
57934977 TATA-TATCTATTTCAAATTTATCA
1 TATATTAT-TATTTTAAATTTATCA
* *
57935001 T-TAATA-T-TTTTAAATTTATTA
1 TATATTATTATTTTAAATTTATCA
* **
57935022 TATACTATTATTTTGGATTTATCACA
1 TATATTATTATTTTAAATTTAT--CA
57935048 TATGATTATTATATTCTAGAA-TTATCA
1 TAT-ATTATTAT-TT-TA-AATTTATCA
*
57935075 TCA-A--AAT-TTTTAAATTTTAT-A
1 T-ATATTATTATTTTAAA-TTTATCA
* * * *
57935096 TGTACTATTATTTCAAATTTATTA
1 TATATTATTATTTTAAATTTATCA
*
57935120 TATATTATTTATTGTAAATT
1 TATATTA-TTATTTTAAATT
57935140 ATCCAATTCA
Statistics
Matches: 177, Mismatches: 32, Indels: 47
0.69 0.12 0.18
Matches are distributed among these distances:
20 2 0.01
21 18 0.10
22 12 0.07
23 47 0.27
24 63 0.36
25 11 0.06
26 5 0.03
27 10 0.06
28 3 0.02
29 5 0.03
30 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (24 bp):
TATATTATTATTTTAAATTTATCA
Found at i:57935236 original size:25 final size:23
Alignment explanation
Indices: 57935188--57935232 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
57935178 AATTGTACAT
*
57935188 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
*
57935211 TCATATATATTGTTTATTTTAA
1 TCATATATATTATTTATTTTAA
57935233 AACTTTGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:57936751 original size:16 final size:16
Alignment explanation
Indices: 57936730--57936765 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
57936720 AGACGAAAAT
* *
57936730 GAAAGAAAGGAAAGGG
1 GAAAGAAAAGAAAAGG
57936746 GAAAGAAAAGAAAAGG
1 GAAAGAAAAGAAAAGG
57936762 GAAA
1 GAAA
57936766 AACTAGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAAGG
Found at i:57937219 original size:40 final size:40
Alignment explanation
Indices: 57937175--57937252 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
57937165 AATTGAATCG
* *
57937175 AAGTGAAATT-ATTTGAACTGTGTATTGACTAGAAAGTGGA
1 AAGTGAAATTGAATTGAACTGTG-ATTGAATAGAAAGTGGA
* *
57937215 AAGTGAAATTGAATTGAATTGTGATTGAATTGAAAGTG
1 AAGTGAAATTGAATTGAACTGTGATTGAATAGAAAGTG
57937253 AATTTGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (40 bp):
AAGTGAAATTGAATTGAACTGTGATTGAATAGAAAGTGGA
Found at i:57938175 original size:2 final size:2
Alignment explanation
Indices: 57938168--57938194 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57938158 AGAAACTATT
57938168 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57938195 TATTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57946059 original size:4 final size:4
Alignment explanation
Indices: 57946050--57946080 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
57946040 ATGACGGCAT
*
57946050 GTAG GTAG GTAG GTAG GTAG GTAG GCAG GTA
1 GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTA
57946081 CAACACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.48, T:0.23
Consensus pattern (4 bp):
GTAG
Found at i:57946541 original size:24 final size:24
Alignment explanation
Indices: 57946488--57946541 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
57946478 AATTAGTAAG
* *
57946488 CCAAATAAACTATGCTAATAAATG
1 CCAAATAAACTATACTAATAAATA
* * *
57946512 CTAAATATATTATACTAATAAATA
1 CCAAATAAACTATACTAATAAATA
57946536 CCAAAT
1 CCAAAT
57946542 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.30
Consensus pattern (24 bp):
CCAAATAAACTATACTAATAAATA
Found at i:57947975 original size:21 final size:21
Alignment explanation
Indices: 57947951--57947990 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57947941 TGACATTAAA
* *
57947951 TACTATAGTGGTGAGATTAGT
1 TACTATAGTGATAAGATTAGT
57947972 TACTATAGTGATAAGATTA
1 TACTATAGTGATAAGATTA
57947991 AAATCAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (21 bp):
TACTATAGTGATAAGATTAGT
Found at i:57949018 original size:44 final size:43
Alignment explanation
Indices: 57948903--57949104 Score: 117
Period size: 44 Copynumber: 4.6 Consensus size: 43
57948893 TAACATCACT
* * *
57948903 CGAAGCAGATCGAAGATACAAACCTTGCCTCTCT-CGGTTG-TAG
1 CGAAGCAGATCGAAGACACAAACCTTGCCT-TCTGC-ATTGACAG
* * * * * * *
57948946 TGGAGCTGGTTGAAGACAACAGATCTTGCCTTCATGCATTGACAG
1 CGAAGCAGATCGAAGAC-ACAAACCTTGCCTTC-TGCATTGACAG
* * *
57948991 CGAAGCAGATCAAAGACACAAACCTTGCCTCTCT-CGGTAGTA-A-
1 CGAAGCAGATCGAAGACACAAACCTTGCCT-TCTGC-ATTG-ACAG
* * * * * *
57949034 CGGAGCTGGTTGAAGATAACAAATCTTGCCTTCCTGCATTGACAG
1 CGAAGCAGATCGAAGA-CACAAACCTTGCCTT-CTGCATTGACAG
57949079 CGAAGCAGATCGAAGACACAAACCTT
1 CGAAGCAGATCGAAGACACAAACCTT
57949105 ATCTCCCTAA
Statistics
Matches: 112, Mismatches: 35, Indels: 23
0.66 0.21 0.14
Matches are distributed among these distances:
43 27 0.24
44 55 0.49
45 30 0.27
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (43 bp):
CGAAGCAGATCGAAGACACAAACCTTGCCTTCTGCATTGACAG
Found at i:57949147 original size:88 final size:88
Alignment explanation
Indices: 57948903--57949104 Score: 332
Period size: 88 Copynumber: 2.3 Consensus size: 88
57948893 TAACATCACT
* *
57948903 CGAAGCAGATCGAAGATACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAG
1 CGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAA
57948968 ATCTTGCCTTCATGCATTGACAG
66 ATCTTGCCTTCATGCATTGACAG
* * ** *
57948991 CGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTAGTAACGGAGCTGGTTGAAGATAACAA
1 CGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAA
*
57949056 ATCTTGCCTTCCTGCATTGACAG
66 ATCTTGCCTTCATGCATTGACAG
57949079 CGAAGCAGATCGAAGACACAAACCTT
1 CGAAGCAGATCGAAGACACAAACCTT
57949105 ATCTCCCTAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 105 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (88 bp):
CGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAA
ATCTTGCCTTCATGCATTGACAG
Found at i:57950624 original size:12 final size:12
Alignment explanation
Indices: 57950609--57950641 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57950599 CATTACCTTT
57950609 TTATATATTATA
1 TTATATATTATA
57950621 TTATAT-TATATA
1 TTATATAT-TATA
57950633 TTATATATT
1 TTATATATT
57950642 TCTTTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATATTATA
Found at i:57950742 original size:3 final size:3
Alignment explanation
Indices: 57950734--57950777 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
57950724 ATGATTTCAA
57950734 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57950778 GTTTATACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57952822 original size:13 final size:13
Alignment explanation
Indices: 57952804--57952828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57952794 TATCGCAAAG
57952804 AAAAATAAAAAAT
1 AAAAATAAAAAAT
57952817 AAAAATAAAAAA
1 AAAAATAAAAAA
57952829 CACACAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:57953725 original size:11 final size:11
Alignment explanation
Indices: 57953709--57953734 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57953699 CTTTCTCTCA
57953709 AAAAAAATTAC
1 AAAAAAATTAC
57953720 AAAAAAATTAC
1 AAAAAAATTAC
57953731 AAAA
1 AAAA
57953735 TATTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAC
Found at i:57954731 original size:23 final size:23
Alignment explanation
Indices: 57954705--57954750 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
57954695 TTATAACTTT
57954705 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
57954728 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
57954751 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:57954858 original size:27 final size:27
Alignment explanation
Indices: 57954828--57954902 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
57954818 CGCCAATGGG
*
57954828 ATTGGCGGCACCAAAGGTGCCAA-AGCC
1 ATTGGCGGCACCAATGGTGCCAATA-CC
57954855 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
57954882 ATTGGCGGCACCAATGGTGCC
1 ATTGGCGGCACCAATGGTGCC
57954903 GTATTGATTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:57955027 original size:10 final size:11
Alignment explanation
Indices: 57955003--57955032 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
57954993 GTTACTGCGT
57955003 AAAAGAAGAGA
1 AAAAGAAGAGA
*
57955014 AAAAGAGGAGA
1 AAAAGAAGAGA
57955025 AAAAGAAG
1 AAAAGAAG
57955033 GTATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:57955094 original size:19 final size:21
Alignment explanation
Indices: 57955056--57955094 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
57955046 AATAATTGAT
*
57955056 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
57955077 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
57955095 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:57955156 original size:3 final size:3
Alignment explanation
Indices: 57955140--57955192 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
57955130 AAAATAATAG
*
57955140 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57955186 TAT TAT T
1 TAT TAT T
57955193 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:57955197 original size:3 final size:3
Alignment explanation
Indices: 57955191--57955228 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
57955181 ATTATTATTA
57955191 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
57955229 AGTATTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:57956054 original size:18 final size:17
Alignment explanation
Indices: 57956014--57956056 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
57956004 GACATGGTTG
*
57956014 GTGGTGAAGAAGAAGGT
1 GTGGCGAAGAAGAAGGT
57956031 GCTGGCGAAGAAGAAGGT
1 G-TGGCGAAGAAGAAGGT
57956049 AGTGGCGA
1 -GTGGCGA
57956057 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.47, T:0.14
Consensus pattern (17 bp):
GTGGCGAAGAAGAAGGT
Found at i:57961554 original size:22 final size:22
Alignment explanation
Indices: 57961528--57961590 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
57961518 CCTTCCTTCC
57961528 CTCTTCTTCTTCTTCTTTTTTT
1 CTCTTCTTCTTCTTCTTTTTTT
* *
57961550 CTCTTCTCCTTTCTT-TTTCTTT
1 CTCTTCTTC-TTCTTCTTTTTTT
57961572 C-CTTC-T-TTCTTTCTTTTTT
1 CTCTTCTTCTTC-TTCTTTTTT
57961591 CTTATCCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 5 0.15
21 4 0.12
22 15 0.44
23 5 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
CTCTTCTTCTTCTTCTTTTTTT
Found at i:57961572 original size:4 final size:4
Alignment explanation
Indices: 57961540--57961711 Score: 119
Period size: 4 Copynumber: 42.8 Consensus size: 4
57961530 CTTCTTCTTC
* * *
57961540 TTCT TTTT TTCT CTTC- TCCT TTC- TT-T TTCT TTCC TTCT TTCT TTCT
1 TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
57961586 TT-T TTCT TATCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT TTTT
1 TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
* *
57961631 TTCT CTTC- TCCT TTCCTT TTCT TTCC TTC- TT-T TTCT TTCT TTCAT
1 TTCT -TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTC-T
* *
57961676 CTCCT TTCT TTCT TTTT TTCT TTCT TTCT TTCT TTC
1 -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
57961712 CCTCTCCTTC
Statistics
Matches: 135, Mismatches: 15, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
3 19 0.14
4 91 0.67
5 17 0.13
6 8 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:57961585 original size:34 final size:34
Alignment explanation
Indices: 57961539--57961720 Score: 97
Period size: 34 Copynumber: 5.6 Consensus size: 34
57961529 TCTTCTTCTT
*
57961539 CTTCTTTTTTTCTCTTCTCCTTTCTTTTTCTTTC
1 CTTCTTTCTTTCTCTTCTCCTTTCTTTTTCTTTC
* * * * *
57961573 CTTCTTTCTTTCT-TTTTTCTTATCCTTTCCTTTT
1 CTTCTTTCTTTCTCTTCTCCTT-TCTTTTTCTTTC
*
57961607 CTTC-TTCTTTCT-TTCTTTCTTT-TTTTCTCTTCTC
1 CTTCTTTCTTTCTCTTC-TCCTTTCTTTT-TCTT-TC
*
57961641 C-T-TTCCTTT-TCTT-TCC-TTCTTTTTCTTTC
1 CTTCTTTCTTTCTCTTCTCCTTTCTTTTTCTTTC
* * *
57961670 TTTCATCTCCTT-TCTT-T-C-TT-TTTTTCTTTC
1 CTTC-TTTCTTTCTCTTCTCCTTTCTTTTTCTTTC
* *
57961700 TTTCTTTCTTTC-CCTCTCCTT
1 CTTCTTTCTTTCTCTTCTCCTT
57961721 CTGGTCCCCC
Statistics
Matches: 115, Mismatches: 19, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
29 9 0.08
30 22 0.19
31 10 0.09
32 14 0.12
33 28 0.24
34 32 0.28
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (34 bp):
CTTCTTTCTTTCTCTTCTCCTTTCTTTTTCTTTC
Found at i:57961627 original size:49 final size:48
Alignment explanation
Indices: 57961560--57961673 Score: 149
Period size: 49 Copynumber: 2.4 Consensus size: 48
57961550 CTCTTCTCCT
* * * *
57961560 TTCTTTTTCTTTCCTTCTTTCTTTCT-TTTTTCTTATCCTTTCCTTTTC
1 TTCTTTTTCTTTCTTTCTTTCTTTCTCTTCTCCTT-TCCTTTCCTTTCC
* *
57961608 TTCTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTT-TTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTTTCCTTTCC
57961657 TTCTTTTTCTTTCTTTC
1 TTCTTTTTCTTTCTTTC
57961674 ATCTCCTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
48 17 0.29
49 35 0.60
50 6 0.10
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (48 bp):
TTCTTTTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTTTCCTTTCC
Found at i:57961644 original size:44 final size:42
Alignment explanation
Indices: 57961533--57961710 Score: 194
Period size: 41 Copynumber: 4.4 Consensus size: 42
57961523 CTTCCCTCTT
*
57961533 CTTC-TTC-TTCTTTTTTTCTCTTCTCCTTTCTTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
57961573 CTTCTTTCTTTC--TTTTT-TCTTATCCTTTCCTTTTCTTCTTC
1 CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTC-T-TTC
*
57961614 TTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* * *
57961656 CTTC-TT-TTTCTTTCTTTCATCTCCTTTCTTT-CTTTT-TTTC
1 CTTCTTTCTTTCTTTTTTTC-TCTTC-TCCTTTCCTTTTCTTTC
*
57961696 TTTCTTTCTTTCTTT
1 CTTCTTTCTTTCTTT
57961711 CCCTCTCCTT
Statistics
Matches: 118, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
39 16 0.14
40 28 0.24
41 30 0.25
42 21 0.18
43 6 0.05
44 17 0.14
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (42 bp):
CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:57961696 original size:30 final size:30
Alignment explanation
Indices: 57961617--57961703 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 30
57961607 CTTCTTCTTT
* *
57961617 CTTTCTTTCTTTTTTTC--TCTTCTCCTTTC
1 CTTTCTTTCTTTTTTTCTTTCTT-TCATCTC
57961646 CTTTTCTTTCCTTCTTTTTCTTTCTTTCATCTC
1 C-TTTCTTT-CTT-TTTTTCTTTCTTTCATCTC
57961679 CTTTCTTTCTTTTTTTCTTTCTTTC
1 CTTTCTTTCTTTTTTTCTTTCTTTC
57961704 TTTCTTTCCC
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.02
30 21 0.41
31 6 0.12
32 13 0.25
33 6 0.12
34 4 0.08
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (30 bp):
CTTTCTTTCTTTTTTTCTTTCTTTCATCTC
Found at i:57961791 original size:27 final size:27
Alignment explanation
Indices: 57961753--57961822 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
57961743 CCCCCATAAA
57961753 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCTA-TGGCAC
*
57961780 CATTAGTGCCGCCAATGGCTATGGCAC
1 CATTGGTGCCGCCAATGGCTATGGCAC
*
57961807 CTTTGGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
57961823 CCCATTGGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 37 0.95
28 2 0.05
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.26
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTATGGCAC
Found at i:57961831 original size:27 final size:27
Alignment explanation
Indices: 57961753--57961831 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
57961743 CCCCCATAAA
*
57961753 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
*
57961780 CATTAGTGCCGCCAATGGC-TATGGCAC
1 CATTGGTGCCGCCAATGGCAT-TGGCAC
* **
57961807 CTTTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
57961832 GTGACCAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 42 0.95
28 1 0.02
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:57961920 original size:21 final size:24
Alignment explanation
Indices: 57961895--57961942 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
57961885 TGGTTTTTTT
57961895 TATA-TATTTTGGTAAATAAAAAA
1 TATATTATTTTGGTAAATAAAAAA
57961918 TATATTTATTTTGGTAAATAAAAAA
1 TATA-TTATTTTGGTAAATAAAAAA
57961943 AGTTATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.17
25 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
TATATTATTTTGGTAAATAAAAAA
Found at i:57961955 original size:27 final size:25
Alignment explanation
Indices: 57961895--57961961 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
57961885 TGGTTTTTTT
*
57961895 TATATATTTTGGTAAATAAAAAATA
1 TATACATTTTGGTAAATAAAAAATA
**
57961920 TATTTATTTTGGTAAATAAAAAA-A
1 TATACATTTTGGTAAATAAAAAATA
57961944 GTTATAACATTTTGGTAA
1 --TAT-ACATTTTGGTAA
57961962 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 22 0.61
26 3 0.08
27 10 0.28
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.42
Consensus pattern (25 bp):
TATACATTTTGGTAAATAAAAAATA
Found at i:57962952 original size:4 final size:4
Alignment explanation
Indices: 57962943--57962985 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
57962933 ATGACGGCAT
*
57962943 GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTAG GCAG GTA
1 GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTAG GTA
57962986 CAACACTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.02, G:0.49, T:0.23
Consensus pattern (4 bp):
GTAG
Found at i:57964229 original size:13 final size:13
Alignment explanation
Indices: 57964211--57964235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57964201 TTTTACTTTG
57964211 TTTTAATTTTAAT
1 TTTTAATTTTAAT
57964224 TTTTAATTTTAA
1 TTTTAATTTTAA
57964236 AATCTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:57966316 original size:43 final size:42
Alignment explanation
Indices: 57966259--57966479 Score: 134
Period size: 43 Copynumber: 5.0 Consensus size: 42
57966249 TTTTAAATGT
57966259 TTTATAATATTATTTTTTAAATATTTTAAATATATTTTTCTAAA
1 TTTA-AATATTATTTTTTAAATATTTTAAATATATTTTT-TAAA
57966303 TTTAAATATTATTTTTT-AAT-TTTTAAATATTATTTTTTAATA
1 TTTAAATATTATTTTTTAAATATTTTAAATA-TATTTTTTAA-A
** * ** *
57966345 TTATAAA-A-TATTTAAAATATATTATTTTTAAAATTATGAGCTTTCAAA
1 TT-TAAATATTATTT--TTTA-AATA-TTTT-AAA-TAT-ATTTTTTAAA
* * **
57966393 TTT-ATTATT-TGTTTTATAATATTTTAAATATATATTTAAAAA
1 TTTAAATATTATTTTTTA-AATATTTTAAATATAT-TTTTTAAA
*
57966435 TTTTTAAATA-TATTTTTTAAA-ATTTTACATATATATTTTTAAA
1 --TTTAAATATTATTTTTTAAATATTTTAAATATAT-TTTTTAAA
57966478 TT
1 TT
57966480 ATTTTTAAAG
Statistics
Matches: 138, Mismatches: 20, Indels: 41
0.69 0.10 0.21
Matches are distributed among these distances:
41 20 0.14
42 22 0.16
43 40 0.29
44 14 0.10
45 17 0.12
46 1 0.01
47 8 0.06
48 8 0.06
49 8 0.06
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (42 bp):
TTTAAATATTATTTTTTAAATATTTTAAATATATTTTTTAAA
Found at i:57966357 original size:20 final size:22
Alignment explanation
Indices: 57966249--57966356 Score: 125
Period size: 21 Copynumber: 4.9 Consensus size: 22
57966239 CAAATGTATA
* *
57966249 TTTTAAATGTTTTATAATATTAT
1 TTTTTAATATTTTA-AATATTAT
57966272 TTTTTAAATATTTTAAATA-TAT
1 TTTTT-AATATTTTAAATATTAT
57966294 TTTTCTAA-A-TTTAAATATTAT
1 TTTT-TAATATTTTAAATATTAT
57966315 TTTTTAAT-TTTTAAATATTAT
1 TTTTTAATATTTTAAATATTAT
*
57966336 TTTTTAATATTATAAAATATT
1 TTTTTAATATT-TTAAATATT
57966357 TAAAATATAT
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.15
21 28 0.37
22 11 0.15
23 17 0.23
24 8 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (22 bp):
TTTTTAATATTTTAAATATTAT
Found at i:57966429 original size:13 final size:13
Alignment explanation
Indices: 57966411--57966455 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
57966401 TTGTTTTATA
57966411 ATATTTTAAATAT
1 ATATTTTAAATAT
57966424 ATA-TTTAAA-A-
1 ATATTTTAAATAT
57966434 AT-TTTTAAATAT
1 ATATTTTAAATAT
*
57966446 ATTTTTTAAA
1 ATATTTTAAA
57966456 ATTTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 8 0.29
13 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:57966430 original size:22 final size:22
Alignment explanation
Indices: 57966405--57966477 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
57966395 TATTATTTGT
*
57966405 TTTATAATATTTTAAATATATA
1 TTTATAAAATTTTAAATATATA
57966427 TTTA-AAAATTTTTAAATATAT-
1 TTTATAAAA-TTTTAAATATATA
* *
57966448 TTTTTAAAATTTTACATATATA
1 TTTATAAAATTTTAAATATATA
*
57966470 TTTTTAAA
1 TTTATAAA
57966478 TTATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 17 0.38
22 28 0.62
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATAAAATTTTAAATATATA
Found at i:57966493 original size:23 final size:21
Alignment explanation
Indices: 57966404--57966494 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 21
57966394 TTATTATTTG
*
57966404 TTTTATAATATTTTAAATATAT
1 TTTTAAAAT-TTTTAAATATAT
*
57966426 ATTTAAAAATTTTTAAATATATT
1 -TTTTAAAATTTTTAAATATA-T
57966449 TTTTAAAA-TTTTACATATATAT
1 TTTTAAAATTTTTA-A-ATATAT
*
57966471 TTTTAAATTATTTTTAAAGATAT
1 TTTTAAA--ATTTTTAAATATAT
57966494 T
1 T
57966495 CAAACATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
21 5 0.09
22 27 0.47
23 19 0.33
24 2 0.03
25 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (21 bp):
TTTTAAAATTTTTAAATATAT
Found at i:57966507 original size:33 final size:33
Alignment explanation
Indices: 57966434--57966523 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
57966424 ATATTTAAAA
* * *
57966434 ATTTTTAAATATATTTTTTAAAATTTTACATATAT
1 ATTTTTAAAT-TA-TTTTTAAAATATTACAAACAT
57966469 ATTTTTAAATTATTTTTAAAGATATT-CAAACAT
1 ATTTTTAAATTATTTTTAAA-ATATTACAAACAT
* * * *
57966502 TTTTTTTAATTCTATTTAAAAT
1 ATTTTTAAATTATTTTTAAAAT
57966524 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 2 0.04
33 29 0.62
34 6 0.13
35 10 0.21
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (33 bp):
ATTTTTAAATTATTTTTAAAATATTACAAACAT
Found at i:57969970 original size:20 final size:20
Alignment explanation
Indices: 57969945--57969983 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
57969935 ATGTAGTTAA
57969945 CATTATTTATAAATATATTT
1 CATTATTTATAAATATATTT
57969965 CATTATTTATAAATATATT
1 CATTATTTATAAATATATT
57969984 ATTTGAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
CATTATTTATAAATATATTT
Found at i:57972159 original size:22 final size:22
Alignment explanation
Indices: 57972131--57972174 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57972121 AATAATATAC
*
57972131 AATAAATTTAAACAATGTTAAT
1 AATAAATATAAACAATGTTAAT
* *
57972153 AATAAATATAAATAATTTTAAT
1 AATAAATATAAACAATGTTAAT
57972175 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAAATATAAACAATGTTAAT
Found at i:57977375 original size:25 final size:24
Alignment explanation
Indices: 57977334--57977385 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
57977324 TCCTTGCTAC
57977334 TGTTAACTATTGTTTGCTATTATAT
1 TGTTAACTATTGTTTGCTATTAT-T
*
57977359 TGTT-ACTATTTTGTTGCTATTATT
1 TGTTAACTATTGT-TTGCTATTATT
57977383 TGT
1 TGT
57977386 ATATTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.19, C:0.08, G:0.13, T:0.60
Consensus pattern (24 bp):
TGTTAACTATTGTTTGCTATTATT
Found at i:57977409 original size:19 final size:17
Alignment explanation
Indices: 57977387--57977421 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
57977377 ATTATTTGTA
57977387 TATTGTATAATTATTGCTT
1 TATTGT-TAATT-TTGCTT
57977406 TATTGTTAATTTTGCT
1 TATTGTTAATTTTGCT
57977422 ACTATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TATTGTTAATTTTGCTT
Found at i:57977427 original size:18 final size:19
Alignment explanation
Indices: 57977387--57977427 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
57977377 ATTATTTGTA
*
57977387 TATTGTATAATTATTGCTT
1 TATTGTATAATTATTGCTC
57977406 TATTGT-TAATT-TTGCTAC
1 TATTGTATAATTATTGCT-C
57977424 TATT
1 TATT
57977428 TTCAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTGTATAATTATTGCTC
Found at i:57979629 original size:21 final size:22
Alignment explanation
Indices: 57979590--57979638 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
57979580 TTAAATGATT
57979590 TTATTTATATTTTTAATTA-TA
1 TTATTTATATTTTTAATTAGTA
57979611 TTATTTATA-TTTTATATTAGTTA
1 TTATTTATATTTTTA-ATTAG-TA
57979634 TTATT
1 TTATT
57979639 GATTTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
23 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTTATATTTTTAATTAGTA
Found at i:57982873 original size:20 final size:20
Alignment explanation
Indices: 57982814--57982910 Score: 99
Period size: 20 Copynumber: 4.6 Consensus size: 20
57982804 ATTTTAAATG
57982814 TTTTATAATATTACTTTTTAAAA
1 TTTTA-AATATT--TTTTTAAAA
*
57982837 TTTTTAAATATATTTTTCT-ATA
1 -TTTTAAATAT-TTTTT-TAAAA
57982859 -TTTAAATATTTTTTTAAAA
1 TTTTAAATATTTTTTTAAAA
57982878 TTTTAAATATTTTTTTAAAA
1 TTTTAAATATTTTTTTAAAA
*
57982898 TTATAAAATATTT
1 TT-TTAAATATTT
57982911 AAAATATATT
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
18 1 0.02
19 7 0.11
20 30 0.46
21 9 0.14
22 6 0.09
23 6 0.09
24 6 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATATTTTTTTAAAA
Found at i:57982907 original size:41 final size:41
Alignment explanation
Indices: 57982828--57983033 Score: 109
Period size: 45 Copynumber: 4.8 Consensus size: 41
57982818 ATAATATTAC
*
57982828 TTTTTAAAATTTTTAAATATATTTTTCTATATTTAAATATT
1 TTTTTAAAATTTTTAAATATATTTTTCTAAATTTAAATATT
57982869 TTTTTAAAA-TTTTAAATAT-TTTTT-TAAAATTATAAAATATT
1 TTTTTAAAATTTTTAAATATATTTTTCT-AAATT-T-AAATATT
* * ** ** *
57982910 TAAAATATATTATTTTTAATGATATGACCTTTC-AAATTT-ATTATT
1 T---TTTTAAAATTTTTAA--ATAT-ATTTTTCTAAATTTAAATATT
* * * **
57982955 TGTTTTATAATATTTTAAATGTATATTTAAAAATTTTTAAATATAT
1 T-TTTTAAAAT-TTTTAAATATATTTTTCTAAA--TTTAAATAT-T
*
57983001 TTTTTAAAA-TTTTAAATATATATTTTTTAAATT
1 TTTTTAAAATTTTTAAATATAT-TTTTCTAAATT
57983034 ATTTTTAAAG
Statistics
Matches: 124, Mismatches: 22, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
38 1 0.01
39 9 0.07
40 11 0.09
41 21 0.17
42 8 0.06
43 17 0.14
44 19 0.15
45 23 0.19
46 2 0.02
47 5 0.04
48 5 0.04
49 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (41 bp):
TTTTTAAAATTTTTAAATATATTTTTCTAAATTTAAATATT
Found at i:57983021 original size:23 final size:23
Alignment explanation
Indices: 57982957--57983031 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 23
57982947 TTATTATTTG
* * *
57982957 TTTTATAATATTTTAAATGTATA
1 TTTTTTAAAATTTTAAATATATA
* *
57982980 --TTTAAAAATTTTTAA-ATATA
1 TTTTTTAAAATTTTAAATATATA
57983000 TTTTTTAAAATTTTAAATATATA
1 TTTTTTAAAATTTTAAATATATA
57983023 TTTTTTAAA
1 TTTTTTAAA
57983032 TTATTTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.10
21 11 0.26
22 13 0.31
23 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTTTTAAAATTTTAAATATATA
Found at i:57983026 original size:22 final size:22
Alignment explanation
Indices: 57982957--57983033 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
57982947 TTATTATTTG
* *
57982957 TTTTATAATATTTTAAATGTATA
1 TTTT-TAAAATTTTAAATATATA
*
57982980 -TTTAAAAATTTTTAAATATAT-
1 TTTTTAAAA-TTTTAAATATATA
57983001 TTTTTAAAATTTTAAATATATA
1 TTTTTAAAATTTTAAATATATA
*
57983023 TTTTTTAAATT
1 TTTTTAAAATT
57983034 ATTTTTAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
TTTTTAAAATTTTAAATATATA
Found at i:57984908 original size:7 final size:7
Alignment explanation
Indices: 57984896--57984921 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57984886 TGGCCTCTCC
57984896 TTTTTCT
1 TTTTTCT
57984903 TTTTTCT
1 TTTTTCT
57984910 TTTTTCT
1 TTTTTCT
57984917 TTTTT
1 TTTTT
57984922 ATTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:57988638 original size:2 final size:2
Alignment explanation
Indices: 57988631--57988673 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57988621 CATTACCAGT
57988631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57988673 T
1 T
57988674 CCATATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57989372 original size:43 final size:43
Alignment explanation
Indices: 57989325--57989419 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
57989315 TGCAAGACAA
57989325 GGTCTTACACGTAAACACAAGTCGATGCCAACATCCCAGACGT
1 GGTCTTACACGTAAACACAAGTCGATGCCAACATCCCAGACGT
* * *
57989368 GGTCTTACACGTAATCACAAGTCGATGTCAACGTCCCAGACGT
1 GGTCTTACACGTAAACACAAGTCGATGCCAACATCCCAGACGT
57989411 GGTCTTACA
1 GGTCTTACA
57989420 GAAAATCACA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
GGTCTTACACGTAAACACAAGTCGATGCCAACATCCCAGACGT
Found at i:57995874 original size:21 final size:20
Alignment explanation
Indices: 57995827--57995871 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
57995817 CAAACCCCAC
57995827 CTTCTTAAATAGAATGTTCTT
1 CTTCTTAAATA-AATGTTCTT
57995848 CTTCTTAAAT-AATGTTCTT
1 CTTCTTAAATAAATGTTCTT
57995867 CTTCT
1 CTTCT
57995872 CTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.58
21 10 0.42
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (20 bp):
CTTCTTAAATAAATGTTCTT
Found at i:57995978 original size:18 final size:19
Alignment explanation
Indices: 57995957--57995998 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
57995947 ATTTGGGTAA
57995957 AATCGA-AAAAATTCGGTT
1 AATCGATAAAAATTCGGTT
*
57995975 AATCTATAAAAATTCGGTT
1 AATCGATAAAAATTCGGTT
57995994 AATCG
1 AATCG
57995999 GTCGGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (19 bp):
AATCGATAAAAATTCGGTT
Found at i:57996269 original size:9 final size:9
Alignment explanation
Indices: 57996257--57996294 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
57996247 AAATATAATT
57996257 TTCGGTTAA
1 TTCGGTTAA
*
57996266 TTCGGGTAA
1 TTCGGTTAA
57996275 TTCGGTTAA
1 TTCGGTTAA
57996284 TTCGGTTAA
1 TTCGGTTAA
57996293 TT
1 TT
57996295 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.45
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:57996620 original size:24 final size:24
Alignment explanation
Indices: 57996576--57996621 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
57996566 TTTCCACTTT
*
57996576 TTTAAATAAAATATTTTAAAAAAA
1 TTTAAATAAAATATTTGAAAAAAA
*
57996600 TTTAAATAGAAT-TTTAGAAAAA
1 TTTAAATAAAATATTT-GAAAAA
57996622 CTTTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTAAATAAAATATTTGAAAAAAA
Found at i:57996671 original size:16 final size:15
Alignment explanation
Indices: 57996638--57996683 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
57996628 GAATATCTTT
57996638 AAAA-ATAATTTT-A
1 AAAATATAATTTTAA
57996651 AAAATCATAATTTTAA
1 AAAAT-ATAATTTTAA
57996667 AAAATAT-ATATTTAA
1 AAAATATAAT-TTTAA
57996682 AA
1 AA
57996684 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 17 0.59
16 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATATAATTTTAA
Found at i:57996695 original size:19 final size:20
Alignment explanation
Indices: 57996666--57996704 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
57996656 CATAATTTTA
57996666 AAAAATATATATTTAAAATT
1 AAAAATATATATTTAAAATT
57996686 AAAAAT-TATATTTAAAATT
1 AAAAATATATATTTAAAATT
57996705 TTTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATATATATTTAAAATT
Found at i:57996858 original size:72 final size:72
Alignment explanation
Indices: 57996723--57996858 Score: 156
Period size: 72 Copynumber: 1.9 Consensus size: 72
57996713 ATGCATTTAA
* * *
57996723 AATATTATAAAACAAATAATAAATATATCTTTAAAAATAATATATTTTAAATATTTTATAATATT
1 AATATTATAAAACAAATAATAAATATATCTTTAAAAATAATATATTTAAAACATTTCATAATATT
57996788 AAAAAAT
66 AAAAAAT
*
57996795 AATATT-TAAAATTAAA-AATAATATATAGT-TTTAAAAA-AATAATATTATAAAACATTTCA-A
1 AATATTATAAAA-CAAATAATAA-ATATA-TCTTTAAAAATAAT-ATATT-TAAAACATTTCATA
57996855 ATAT
61 ATAT
57996859 ACATTTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
71 13 0.24
72 32 0.58
73 10 0.18
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (72 bp):
AATATTATAAAACAAATAATAAATATATCTTTAAAAATAATATATTTAAAACATTTCATAATATT
AAAAAAT
Found at i:57996901 original size:25 final size:23
Alignment explanation
Indices: 57996884--57996929 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
57996874 TAAAACCAAT
*
57996884 AATAAATAAA-ACAAATAAAATA
1 AATAAATAAAGACAAATAAAAAA
57996906 AATAAATAAAGGACAAATAAAAAA
1 AATAAATAAA-GACAAATAAAAAA
57996930 CTTAAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
24 11 0.52
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (23 bp):
AATAAATAAAGACAAATAAAAAA
Found at i:57998365 original size:20 final size:20
Alignment explanation
Indices: 57998340--57998378 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
57998330 ATGTATTTAA
57998340 CATTATTTATAAATATATTT
1 CATTATTTATAAATATATTT
57998360 CATTATTTATAAATATATT
1 CATTATTTATAAATATATT
57998379 ATTTGAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
CATTATTTATAAATATATTT
Found at i:58001626 original size:13 final size:13
Alignment explanation
Indices: 58001608--58001635 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58001598 GCACGTTCCC
58001608 TGCATGGCCACCT
1 TGCATGGCCACCT
58001621 TGCATGGCCACCT
1 TGCATGGCCACCT
58001634 TG
1 TG
58001636 GCTGCTACAT
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:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (13 bp):
TGCATGGCCACCT
Found at i:58002775 original size:21 final size:21
Alignment explanation
Indices: 58002743--58002783 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58002733 AGGCTCGAGG
58002743 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
58002764 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
58002784 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:58006126 original size:13 final size:13
Alignment explanation
Indices: 58006108--58006135 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58006098 GCACGTTCCC
58006108 TGCATGGCCACCT
1 TGCATGGCCACCT
58006121 TGCATGGCCACCT
1 TGCATGGCCACCT
58006134 TG
1 TG
58006136 GCTGCTGCAT
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:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (13 bp):
TGCATGGCCACCT
Found at i:58006900 original size:22 final size:22
Alignment explanation
Indices: 58006864--58006931 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
58006854 GGCCCGGCCC
*
58006864 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATAACAAAA
*
58006886 ATTTATTTTAAAAATAATAAAA
1 ATTTATTTTAAAAATAACAAAA
** *
58006908 AAGTATTTTAAAATTAA-AAAA
1 ATTTATTTTAAAAATAACAAAA
58006929 ATT
1 ATT
58006932 AAAAAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 5 0.13
22 27 0.71
23 6 0.16
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (22 bp):
ATTTATTTTAAAAATAACAAAA
Found at i:58009359 original size:24 final size:25
Alignment explanation
Indices: 58009290--58009368 Score: 133
Period size: 25 Copynumber: 3.2 Consensus size: 25
58009280 ACTTTAGCGC
58009290 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
58009315 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
**
58009340 GCTCTCTGATT-TTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTGGT
58009364 GCTCT
1 GCTCT
58009369 TTGTTTAGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
24 16 0.31
25 36 0.69
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:58009375 original size:22 final size:22
Alignment explanation
Indices: 58009302--58009417 Score: 88
Period size: 22 Copynumber: 5.0 Consensus size: 22
58009292 TCTCTGATTA
**
58009302 TTAGCACGTTGGTGCTCTCTGATT
1 TTAGCACGTCAGTGCTCTCTG--T
**
58009326 ATTAGCACGTTGGTGCTCTCTGATT
1 -TTAGCACGTCAGTGCTCTCTG--T
*
58009351 TTAGCACGTCAGTGCTCTTTGT
1 TTAGCACGTCAGTGCTCTCTGT
** *
58009373 TTAGCACACCTGTGCTCTCTGT
1 TTAGCACGTCAGTGCTCTCTGT
* * *
58009395 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACGTCAGTGCTCTCTGT
58009417 T
1 T
58009418 CATTAGTGCA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
22 36 0.46
24 18 0.23
25 24 0.31
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (22 bp):
TTAGCACGTCAGTGCTCTCTGT
Found at i:58015869 original size:22 final size:26
Alignment explanation
Indices: 58015843--58015896 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
58015833 TTATAAATTC
58015843 AATTTAAAAG-ATA-TT-AT-ACAAT
1 AATTTAAAAGCATATTTAATAACAAT
*
58015865 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATATTTAATAACAAT
58015890 AATTTAA
1 AATTTAA
58015897 TCATACAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 2 0.08
24 2 0.08
25 10 0.40
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (26 bp):
AATTTAAAAGCATATTTAATAACAAT
Found at i:58017776 original size:44 final size:44
Alignment explanation
Indices: 58017726--58017812 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
58017716 CCCCATCCTC
58017726 GTTGTTTGGTTTCCAAGTTGTGACCCAAAGTCAAGATTGATTTG
1 GTTGTTTGGTTTCCAAGTTGTGACCCAAAGTCAAGATTGATTTG
*
58017770 GTTGTTTGGTTTTCAAGTTGTGACCCAAAGTCAAGATTGATTT
1 GTTGTTTGGTTTCCAAGTTGTGACCCAAAGTCAAGATTGATTT
58017813 TAAAATTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (44 bp):
GTTGTTTGGTTTCCAAGTTGTGACCCAAAGTCAAGATTGATTTG
Found at i:58018011 original size:9 final size:9
Alignment explanation
Indices: 58017987--58018062 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
58017977 TTTAGTTAAA
*
58017987 AATTAATCG
1 AATTAACCG
*
58017996 AACTAACCG
1 AATTAACCG
58018005 AATTAACCG
1 AATTAACCG
* *
58018014 AATTACCCA
1 AATTAACCG
*
58018023 AATTAACCA
1 AATTAACCG
*
58018032 AATTATCCG
1 AATTAACCG
*
58018041 AATTAATCG
1 AATTAACCG
58018050 AATTAACCG
1 AATTAACCG
58018059 AATT
1 AATT
58018063 GAATCACTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:58018210 original size:18 final size:18
Alignment explanation
Indices: 58018171--58018210 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58018161 TATGATTGAG
**
58018171 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAA
*
58018189 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAA
58018207 TTGG
1 TTGG
58018211 ATTTGGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.45, T:0.40
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAA
Found at i:58018898 original size:46 final size:46
Alignment explanation
Indices: 58018848--58018997 Score: 122
Period size: 48 Copynumber: 3.2 Consensus size: 46
58018838 AATAAGGGTC
*
58018848 TAGGGTTTCTTAATTAAATTAATTATAAATTTTAAAAAAATTAGAT
1 TAGGGTTTCTTGATTAAATTAATTATAAATTTTAAAAAAATTAGAT
** * ** * * ** * *
58018894 TAGGGTTTAGTGTTTATGGTT-TTTAAGAAAAAATTAAATAAATTAGGGTT
1 TAGGGTTTCTTGATTA-AATTAATT-A-TAAATTTTAAAAAAATTA--GAT
* *
58018944 TAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGAT
1 TAGGGTTTCTTGATTAAATTAATTATAAATTTTAAAAAAATTAGAT
58018990 TAGGGTTT
1 TAGGGTTT
58018998 AGTGTTCAGG
Statistics
Matches: 72, Mismatches: 26, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
46 23 0.32
47 3 0.04
48 28 0.39
49 3 0.04
50 15 0.21
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (46 bp):
TAGGGTTTCTTGATTAAATTAATTATAAATTTTAAAAAAATTAGAT
Found at i:58018936 original size:96 final size:96
Alignment explanation
Indices: 58018809--58019132 Score: 497
Period size: 96 Copynumber: 3.4 Consensus size: 96
58018799 GTTTGTAGAT
* * * * * * *
58018809 TTTAGGGTTTTAAAGAAAAAAATTAAATAAATAAGGGTCTAGGGTTTCTTAATTAAATTAATTAT
1 TTTAGGGTTTTTAAG-AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
58018874 AAATTTTAAAAAAATTAGATTAGGGTTTAGTG
65 AAATTTTAAAAAAATTAGATTAGGGTTTAGTG
* *
58018906 TTTATGGTTTTTAAGAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
1 TTTAGGGTTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
58018971 AATTTTAAAAAAATTAGATTAGGGTTTAGTG
66 AATTTTAAAAAAATTAGATTAGGGTTTAGTG
* *
58019002 TTCAGGGTTTTTAATG-AAAAATCAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAA-GAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
* *
58019066 AAATTTTAAAAAAATTAGATTGGGGTTTAGTA
65 AAATTTTAAAAAAATTAGATTAGGGTTTAGTG
58019098 TTTAGGGTTTTTAAGAAAAAATCAAATAAAATTAG
1 TTTAGGGTTTTTAAGAAAAAATCAAAT-AAATTAG
58019133 TTGTTATTCG
Statistics
Matches: 210, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
95 1 0.00
96 188 0.90
97 21 0.10
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (96 bp):
TTTAGGGTTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
AATTTTAAAAAAATTAGATTAGGGTTTAGTG
Found at i:58018999 original size:53 final size:53
Alignment explanation
Indices: 58018935--58019095 Score: 153
Period size: 53 Copynumber: 3.2 Consensus size: 53
58018925 AATTAAATAA
58018935 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
* * * ** * ** *
58018988 ATTAGGGTTTAGTGTT-C-AGGGT-TTTTAA-T-GAAA----AATCAAA-TAA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
*
58019031 ATTAGGGTTTAGGATTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
*
58019084 ATTGGGGTTTAG
1 ATTAGGGTTTAG
58019096 TATTTAGGGT
Statistics
Matches: 78, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
43 16 0.21
44 6 0.08
45 3 0.04
46 4 0.05
47 1 0.01
48 6 0.08
49 1 0.01
50 4 0.05
51 3 0.04
52 6 0.08
53 28 0.36
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.39
Consensus pattern (53 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAG
Found at i:58020755 original size:45 final size:45
Alignment explanation
Indices: 58020691--58020980 Score: 429
Period size: 45 Copynumber: 6.4 Consensus size: 45
58020681 TTGTTGGATA
* *
58020691 GAAGATATCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
58020736 GAAGATAGCAGGTCTTGTCTTCTTGTATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
58020781 GAAGATAGCAAATCTTGTCTTCCTGTATTGGCATG-GAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCA-GCGAAGTAGATC
*
58020826 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGGGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
58020871 GAAGATAGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
58020916 GAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
58020961 GAAGATTGTAGATCATGTCT
1 GAAGATAGCAGATCTTGTCT
58020981 CCCTAAGCAG
Statistics
Matches: 223, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
44 1 0.00
45 221 0.99
46 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:58021288 original size:132 final size:132
Alignment explanation
Indices: 58020961--58021288 Score: 491
Period size: 132 Copynumber: 2.5 Consensus size: 132
58020951 AAAGTAGATT
58020961 GAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAA-G-ATGATAAATCTTATC
1 GAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA-G-TAAATCTTATC
* *
58021024 TTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTAGCAGTGGAGTA
64 TTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTA
*
58021089 GGTT
129 GGTC
* * * *
58021093 GAAGATTGTAAATCATGTCTCCCTAAGCAGTAGTGGAGCAGATGGAAGGCAGCAAATCCTATCTT
1 GAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGTAAATCTTATCTT
58021158 CCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCCT-TCTCCCTGAGCAGCAGTGGAGTAG
66 CCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT-CCTATCTCCCTGAGCAGCAGTGGAGTAG
58021222 GTC
130 GTC
* * * * * *
58021225 GAAGATTGTAGATCATGTATCCTTAAACAGTAATAGAGCAGATCGAAGGCAGTGAATCTTATCT
1 GAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGTAAATCTTATCT
58021289 CTTTGGCGTT
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
132 170 0.97
133 5 0.03
134 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
GAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGTAAATCTTATCTT
CCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGG
TC
Found at i:58021767 original size:19 final size:19
Alignment explanation
Indices: 58021743--58021796 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
58021733 CTTGAAAAAG
*
58021743 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
58021762 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
58021781 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
58021797 AGATAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:58022777 original size:24 final size:21
Alignment explanation
Indices: 58022734--58022788 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
58022724 TTAACATTAC
*
58022734 TTTAAATTTATCTTGTATATCT
1 TTTAAATTTATCTTGAATAT-T
58022756 ATTTCAAATTTATCATT-AATATT
1 -TTT-AAATTTATC-TTGAATATT
58022779 TTTAAATTTA
1 TTTAAATTTA
58022789 GTATATACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 7 0.24
22 3 0.10
23 4 0.14
24 13 0.45
25 2 0.07
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAAATTTATCTTGAATATT
Done.