Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 96 of 126
Found at i:29496753 original size:22 final size:24
Alignment explanation
Indices: 29496728--29496785 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
29496718 TATATATTGT
29496728 TTTGAATTTTTAGAAA-TTTAGA-
1 TTTGAATTTTTAGAAATTTTAGAC
29496750 TTTGTTAA-TTTT-GAAATTTTAGAC
1 TTTG--AATTTTTAGAAATTTTAGAC
*
29496774 TTTAAATTTTTA
1 TTTGAATTTTTA
29496786 AAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
22 10 0.34
23 14 0.48
24 5 0.17
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTGAATTTTTAGAAATTTTAGAC
Found at i:29501223 original size:27 final size:27
Alignment explanation
Indices: 29501185--29501238 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29501175 CTAACATAGC
29501185 TAACTATCACAACACTCTATAGCATTG
1 TAACTATCACAACACTCTATAGCATTG
29501212 TAACTATCACAACACTCTATAGCATTG
1 TAACTATCACAACACTCTATAGCATTG
29501239 ATTTCAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (27 bp):
TAACTATCACAACACTCTATAGCATTG
Found at i:29505818 original size:57 final size:58
Alignment explanation
Indices: 29505703--29505838 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 58
29505693 AATTTTTACT
* *
29505703 AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTACATATTATTTTATTA
1 AATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAAATTAAATATTATTTTATTA
* *
29505763 AATTGTATTTAATAATAATTATGTT-AAAATATAATTAAA-TAAATTAATT-TTTTATTA
1 AATTATATTTAATAATAATTATATTAAAAATATAATTAAATTAAA-T-ATTATTTTATTA
29505820 AATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
29505839 CATTAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 3 0.04
57 40 0.58
58 20 0.29
59 2 0.03
60 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAAATATAATTAAATTAAATATTATTTTATTA
Found at i:29506024 original size:46 final size:44
Alignment explanation
Indices: 29505932--29506025 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
29505922 ATTTCAGCAT
* *
29505932 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
29505976 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
29506022 CATT
1 CATT
29506026 ACAGTTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:29506028 original size:16 final size:16
Alignment explanation
Indices: 29506007--29506094 Score: 140
Period size: 16 Copynumber: 5.5 Consensus size: 16
29505997 TGAATTACTG
29506007 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
29506023 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
29506039 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
*
29506055 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
29506071 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
29506087 ATTACAGC
1 ATTACAGC
29506095 GAACCAAACG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:29506050 original size:32 final size:32
Alignment explanation
Indices: 29506007--29506093 Score: 165
Period size: 32 Copynumber: 2.7 Consensus size: 32
29505997 TGAATTACTG
*
29506007 ATTACAGCTCTATTCCATTACAGTTCTATTCC
1 ATTACACCTCTATTCCATTACAGTTCTATTCC
29506039 ATTACACCTCTATTCCATTACAGTTCTATTCC
1 ATTACACCTCTATTCCATTACAGTTCTATTCC
29506071 ATTACACCTCTATTCCATTACAG
1 ATTACACCTCTATTCCATTACAG
29506094 CGAACCAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.26, C:0.30, G:0.05, T:0.39
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACAGTTCTATTCC
Found at i:29507750 original size:20 final size:20
Alignment explanation
Indices: 29507711--29507811 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
29507701 GTTTGAAACA
*
29507711 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAA-CAAGTCAAAATG
29507733 ATTTTAAACAAGTCAAAAT-
1 ATTTTAAACAAGTCAAAATG
* * *
29507752 AATTTGAACTAAGTCAAAATC
1 ATTTTAAAC-AAGTCAAAATG
**
29507773 ATTTT-AACACTTCAAAATG
1 ATTTTAAACAAGTCAAAATG
*
29507792 TTTTTCAAACAAGTCAAAAT
1 ATTTT-AAACAAGTCAAAAT
29507812 AGCTCCAGGC
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 19 0.29
20 23 0.35
21 18 0.28
22 5 0.08
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (20 bp):
ATTTTAAACAAGTCAAAATG
Found at i:29509793 original size:59 final size:58
Alignment explanation
Indices: 29509724--29509981 Score: 374
Period size: 59 Copynumber: 4.4 Consensus size: 58
29509714 TGGATACCTG
* * * *
29509724 GGGGAAAAATGGTAAATTTTAGTGAAATCGAGGTTAAGAATGGAATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
* *
29509782 GGGAGTAAAATGGTAATTTTTGGTAAAATC-AGGGTTAAGAATGGAATTTTGGAAAGTTC
1 GGG-GTAAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTC
*
29509841 GGGGGTAAAATGCTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
* * *
29509900 AGGGGGAAAATGGTAATTTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
29509959 GAGGGTAAAATGGTAATTTTTGG
1 G-GGGTAAAATGGTAATTTTTGG
29509982 AAGTTTCGAG
Statistics
Matches: 181, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
58 5 0.03
59 172 0.95
60 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:29509804 original size:30 final size:27
Alignment explanation
Indices: 29509762--29509983 Score: 139
Period size: 30 Copynumber: 7.6 Consensus size: 27
29509752 CGAGGTTAAG
29509762 AATGGAATTTTGGAAAGTTCGGGAGTAA
1 AATGGAATTTTGGAAAGTTCGGG-GTAA
* *
29509790 AATGGTAATTTTTGGTAAA-ATCAGGGTTAA
1 AATGG-AA-TTTTGG-AAAGTTC-GGGGTAA
29509820 GAATGGAATTTTGGAAAGTTCGGGGGTAA
1 -AATGGAATTTTGGAAAGTTC-GGGGTAA
* *
29509849 AATGCTAATTTTTGGTGAAA--TCGAGGTTAAA
1 AATG-GAA-TTTT-G-GAAAGTTCG-GGGT-AA
*
29509880 AATGGAATTTTGGAAAGTTCAGGGGGAA
1 AATGGAATTTTGGAAAGTTC-GGGGTAA
*
29509908 AATGGTAATTTTTTGTGAAA--TCGAGGTTAAA
1 AATGG-AA--TTTTG-GAAAGTTCG-GGGT-AA
*
29509939 AATGGAATTTTGGAAAGTTTGAGGGTAA
1 AATGGAATTTTGGAAAGTTCG-GGGTAA
29509967 AATGGTAATTTTTGGAA
1 AATGG-AA-TTTTGGAA
29509984 GTTTCGAGGT
Statistics
Matches: 155, Mismatches: 14, Indels: 48
0.71 0.06 0.22
Matches are distributed among these distances:
27 8 0.05
28 32 0.21
29 38 0.25
30 39 0.25
31 30 0.19
32 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (27 bp):
AATGGAATTTTGGAAAGTTCGGGGTAA
Found at i:29509985 original size:29 final size:30
Alignment explanation
Indices: 29509753--29510040 Score: 141
Period size: 29 Copynumber: 9.8 Consensus size: 30
29509743 TAGTGAAATC
* *
29509753 GAGGTTAAGAATGG-AA-TTTTGGAAAGTTC
1 GAGGGTAA-AATGGTAATTTTTGGAAAGTTT
*
29509782 G-GGAGTAAAATGGTAATTTTTGGTAAA--AT
1 GAGG-GTAAAATGGTAATTTTTGG-AAAGTTT
* *
29509811 CAGGGTTAAGAATGG-AA-TTTTGGAAAGTTC
1 GAGGG-TAA-AATGGTAATTTTTGGAAAGTTT
* * *
29509841 GGGGGTAAAATGCTAATTTTTGGTGAAA--TC
1 GAGGGTAAAATGGTAATTTTT-G-GAAAGTTT
*
29509871 GAGGTTAAAAATGG-AA-TTTTGGAAAG-TT
1 GAGGGT-AAAATGGTAATTTTTGGAAAGTTT
* * *
29509899 CAGGGGGAAAATGGTAATTTTTTGTGAAA--TC
1 GA-GGGTAAAATGGTAA-TTTTTG-GAAAGTTT
*
29509930 GAGGTTAAAAATGG-AA-TTTTGGAAAGTTT
1 GAGGGT-AAAATGGTAATTTTTGGAAAGTTT
29509959 GAGGGTAAAATGGTAATTTTTGG-AAGTTT
1 GAGGGTAAAATGGTAATTTTTGGAAAGTTT
* *
29509988 CGA-GGTCAAAAT-ATAATTTTTTGAAA-TTT
1 -GAGGGT-AAAATGGTAATTTTTGGAAAGTTT
* *
29510017 TAGGGTTAAAAT-GTAATTTCTGGA
1 GAGGG-TAAAATGGTAATTTTTGGA
29510041 CTATTTGGGG
Statistics
Matches: 201, Mismatches: 28, Indels: 60
0.70 0.10 0.21
Matches are distributed among these distances:
27 8 0.04
28 37 0.18
29 71 0.35
30 48 0.24
31 29 0.14
32 8 0.04
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
GAGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:29510306 original size:162 final size:162
Alignment explanation
Indices: 29510106--29510447 Score: 605
Period size: 162 Copynumber: 2.1 Consensus size: 162
29510096 CACAGGCATC
* *
29510106 CAAA-AGTCAAAGGACTAATTTGTAAATCTTGAAAAATTCTTCGGCCAATTTTGTAATTAAACAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTCGGCCAATTTTGTAATTAAACAA
29510170 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
29510235 AAAAGGTGACACGTGGCGGCCTCTGGTGCAAT
131 AAAAGGTGACACGTGGCGGCCTCTGGTGCAAT
* * * *
29510267 CAAACAGTTAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCTAATTTTGTAATTAAGCAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTCGGCCAATTTTGTAATTAAACAA
*
29510332 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGATAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
*
29510397 AAAAGGTGACACGTGGCGGCCTCTGGTGCAGT
131 AAAAGGTGACACGTGGCGGCCTCTGGTGCAAT
29510429 CAAACAGTCAAAGGATTAA
1 CAAACAGTCAAAGGATTAA
29510448 ATTGAAAACC
Statistics
Matches: 171, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
161 4 0.02
162 167 0.98
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (162 bp):
CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTCGGCCAATTTTGTAATTAAACAA
AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
AAAAGGTGACACGTGGCGGCCTCTGGTGCAAT
Found at i:29510515 original size:162 final size:161
Alignment explanation
Indices: 29510182--29510488 Score: 395
Period size: 162 Copynumber: 1.9 Consensus size: 161
29510172 GTTGATTTTG
29510182 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
1 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
* * * * *
29510247 GTGGCGGCCTCTGGTGCAATCAAACAGTTAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGG
66 GTGGCGGCCTCTGGTGCAATCAAACAGTCAAAGGATTAATTGATAAACCTT-AAAAATTATCGGG
** ** * ** ****
29510312 CTAATTTTGTAATTAAGCAAAAGTTGATTTTG
130 CTAAAATTACAAATAAGCAAAAGAAGATAAAA
*
29510344 GGACTAAATTAAAACAAATTAAAAATGATAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
1 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
*
29510409 GTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATTAAATTGA-AAACCAATT-AAAATTATCG
66 GTGGCGGCCTCTGGTGCAATCAAACAGTCAAAGGATT-AATTGATAAACC--TTAAAAATTATCG
29510472 GG-TAAAATTACAAATAA
128 GGCTAAAATTACAAATAA
29510489 TTACAAGAAA
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
161 10 0.08
162 113 0.87
163 5 0.04
164 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (161 bp):
GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
GTGGCGGCCTCTGGTGCAATCAAACAGTCAAAGGATTAATTGATAAACCTTAAAAATTATCGGGC
TAAAATTACAAATAAGCAAAAGAAGATAAAA
Found at i:29511283 original size:10 final size:10
Alignment explanation
Indices: 29511270--29511329 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
29511260 TTTTTATTTA
29511270 TTAATATTAT
1 TTAATATTAT
29511280 TTAATATTAT
1 TTAATATTAT
* *
29511290 TT-TTATTAC
1 TTAATATTAT
** *
29511299 CAAATATTAA
1 TTAATATTAT
**
29511309 TTAATGCTAT
1 TTAATATTAT
29511319 TTAATATTAT
1 TTAATATTAT
29511329 T
1 T
29511330 ATTATCATCA
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
9 5 0.14
10 31 0.86
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (10 bp):
TTAATATTAT
Found at i:29514704 original size:29 final size:30
Alignment explanation
Indices: 29514625--29514756 Score: 89
Period size: 29 Copynumber: 4.5 Consensus size: 30
29514615 GTTCAGGGGG
* * * *
29514625 AAAATGGTAATTTTTTGTGAA-ATCGAGGTTA
1 AAAATGGTAA-TTTTT-TGAAGTTTGAGGGTC
*
29514656 AAAATGG-AA-TTTTGGAAAGTTTGAGGGT-
1 AAAATGGTAATTTTTTG-AAGTTTGAGGGTC
29514684 AAAATGGTAATTTTTTGAAGTTTCG-GGGTC
1 AAAATGGTAATTTTTTGAAGTTT-GAGGGTC
* * * * *
29514714 AAAAT-ATAATTTTCTAAAATTTTAGGGTC
1 AAAATGGTAATTTTTTGAAGTTTGAGGGTC
29514743 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
29514757 GGACTGTTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 13 0.16
29 48 0.59
30 13 0.16
31 7 0.09
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (30 bp):
AAAATGGTAATTTTTTGAAGTTTGAGGGTC
Found at i:29515019 original size:162 final size:162
Alignment explanation
Indices: 29514825--29515328 Score: 814
Period size: 162 Copynumber: 3.1 Consensus size: 162
29514815 CACAGGCATC
* * * *
29514825 CAAA-AGTCAAAGGACTAATTTGTAAATCTTGAAAAATTCTTGGGCCAATTTTATAATTAAACAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
29514889 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
* * * * *
29514954 AAACGGTGACAAGTGGCGACTTCTGGTGCAGT
131 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
* *
29514986 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATGCTTGGGCTAATTTTGTAATTAAGCAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
*
29515051 AAGTTAATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
29515116 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
131 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
* *
29515148 CAAACAGTCAAATGATTAGTTTATAAATCTTGAAAAAATT-TTGGGCCAATTTTGTAATTAAGCA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTG-AAAAATTCTTGGGCCAATTTTGTAATTAAGCA
* *
29515212 AAAGTTGATTTTGGGACTAAATTAAATCAAATTAAAAATGATAGGGACTAAATGCATAAATAAAC
65 AAAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
* * *
29515277 CAAAAAGTGACACGTGGTGGCCTCTGGTACAAT
130 CAAAAGGTGACACGTGGCGGCCTCTGGTACAGT
29515310 CAAACAGTCAAAGGATTAA
1 CAAACAGTCAAAGGATTAA
29515329 ATTGAAAACC
Statistics
Matches: 317, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
161 4 0.01
162 307 0.97
163 6 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (162 bp):
CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
Found at i:29515393 original size:162 final size:157
Alignment explanation
Indices: 29514901--29515411 Score: 438
Period size: 162 Copynumber: 3.2 Consensus size: 157
29514891 GTTGATTTTG
** *
29514901 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAACGGTGACAA
1 GGACTAAATT-AAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
* * * * * *
29514966 GTGGCGACTTCTGGTGCAGTCAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATGCTT-GG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTT-AAAAAT--TTCGG
** *** * ****
29515030 GCTAATTTTGTAATTAAGCAAAAGTTAATTTTG
127 GAAAATTAAATAATTAAGCAAAA-TGAA-AAAA
*
29515063 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
1 GGACTAAATT-AAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
* * * * * *
29515128 GTGGCGGCCTCTGGTACAGTCAAACAGTCAAATGATTAGTTTATAAATCTTGAAAAAATTTTGGG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTT--AAAAATTTCGGG
** *** *****
29515193 CCAATTTTGTAATTAAGCAAAAGTTGATTTTG
128 AAAATTAAATAATTAAGCAAAA--TGAAAAAA
*
29515225 GGACTAAATTAAATCAAATTAAAAATGATAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
1 GGACTAAATTAAA-CAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
*
29515290 GTGGTGGCCTCTGGTACAATCAAACAGTCAAAGGATTAAATTGA-AAACCAATT-AAAATTATCG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATT-AATTGATAAACC--TTAAAAATT-TCG
*
29515353 GGTAAAATTACAAATAATTTCAG-AAAA-GAAAAAA
126 GG-AAAATT--AAATAA-TTAAGCAAAATGAAAAAA
*
29515387 GGACTAAATTGAAACAAATAAAAAA
1 GGACTAAATT-AAACAAATTAAAAA
29515412 GCGAAAGGAC
Statistics
Matches: 303, Mismatches: 33, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
161 11 0.04
162 260 0.86
163 19 0.06
164 2 0.01
165 7 0.02
166 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (157 bp):
GGACTAAATTAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACACG
TGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTTAAAAATTTCGGGAAA
ATTAAATAATTAAGCAAAATGAAAAAA
Found at i:29517174 original size:59 final size:59
Alignment explanation
Indices: 29517075--29517544 Score: 552
Period size: 59 Copynumber: 8.0 Consensus size: 59
29517065 GAAGAAACGA
* * * * * * * * * **
29517075 TGAAATTGGGGTTGAAAATGGGACTTTTGGATA-TCCGGGGGCAAAATGTTAAATTTCAG
1 TGAAATCGAGGTTAAAAAT-GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * *
29517134 TGAAATCGAGGTTAAGAATAGAATTTTGGAAAGCTCGGGGGTAAAAATGGAAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT-AAAATGGTAATTTTTGG
*
29517194 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * **
29517253 TAAAAT-TAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* ** *
29517312 TGAAATCGAGGTTAAAAATGGAAATTTGGAAAGTTCGGTAGTAAAATGGTAATTTTCGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* ** * *
29517371 TAAAATTAAGGTT-AAAATGGAATTTTGGAAAGTTCAGGGGTAAAACGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* **
29517429 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * **
29517488 TGAAATCG-GGATTAAACATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
1 TGAAATCGAGG-TTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTT
29517545 TGAAGTTTCG
Statistics
Matches: 353, Mismatches: 52, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
58 61 0.17
59 241 0.68
60 51 0.14
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:29517423 original size:176 final size:176
Alignment explanation
Indices: 29517133--29517543 Score: 585
Period size: 176 Copynumber: 2.3 Consensus size: 176
29517123 TTAAATTTCA
* * * * *
29517133 GTGAAATCGAGGTTAAGAATAGAATTTTGGAAAGCTCGGGGGTAAAAATGGAAATTTTTGGTGAA
1 GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTC-GGGGT-AAAATGGTAATTTTCGGTAAA
* * *
29517198 ATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTAGG
64 ATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAACGGTAATTTTTGGTAAAATCAGG
* *
29517263 GTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTG
129 GTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTG
* * *
29517311 GTGAAATCGAGGTTAAAAATGGAAATTTGGAAAGTTCGGTAGTAAAATGGTAATTTTCGGTAAAA
1 GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCGG-GGTAAAATGGTAATTTTCGGTAAAA
* * *
29517376 TTAAGGTT-AAAATGGAATTTTGGAAAGTTC-AGGGGTAAAACGGTAATTTTTGGTGAAATCGGG
65 TCAAGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAACGGTAATTTTTGGTAAAATCAGG
29517439 GTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTG
129 GTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTG
* *
29517487 GTGAAATCG-GGATTAAACATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT
1 GTGAAATCGAGG-TTAAAAATAGAATTTTGGAAAG-TTCGGGGTAAAATGGTAATTTT
29517544 TTGAAGTTTC
Statistics
Matches: 208, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
175 3 0.01
176 139 0.67
177 31 0.15
178 35 0.17
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (176 bp):
GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTCGGTAAAAT
CAAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAACGGTAATTTTTGGTAAAATCAGGGT
TAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTG
Found at i:29517550 original size:29 final size:29
Alignment explanation
Indices: 29517517--29517602 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
29517507 AGAATTTTGG
*
29517517 AAAGTTTAGGGGT-AAAATGGTAATTTTTT
1 AAAGTTTAGGGGTCAAAAT-GTAATTTTTA
* * *
29517546 GAAGTTTCGGGGTCAAAATATAATTTTCTA
1 AAAGTTTAGGGGTCAAAATGTAATTTT-TA
*
29517576 AAATTTTA-GGGTCAAAATGTAATTTTT
1 AAAGTTTAGGGGTCAAAATGTAATTTTT
29517603 GGACTGTTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 35 0.74
30 11 0.23
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.41
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTTA
Found at i:29517865 original size:162 final size:162
Alignment explanation
Indices: 29517671--29518174 Score: 814
Period size: 162 Copynumber: 3.1 Consensus size: 162
29517661 CACAGGCATC
* * * *
29517671 CAAA-AGTCAAAGGACTAATTTGTAAATCTTGAAAAATTCTTGGGCCAATTTTATAATTAAACAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
29517735 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
* * * * *
29517800 AAACGGTGACAAGTGGCGACTTCTGGTGCAGT
131 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
* *
29517832 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATGCTTGGGCTAATTTTGTAATTAAGCAA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
*
29517897 AAGTTAATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
66 AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
29517962 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
131 AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
* *
29517994 CAAACAGTCAAATGATTAGTTTATAAATCTTGAAAAAATT-TTGGGCCAATTTTGTAATTAAGCA
1 CAAACAGTCAAAGGATTAATTTATAAATCTTG-AAAAATTCTTGGGCCAATTTTGTAATTAAGCA
* *
29518058 AAAGTTGATTTTGGGACTAAATTAAATCAAATTAAAAATGATAGGGACTAAATGCATAAATAAAC
65 AAAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
* * *
29518123 CAAAAAGTGACACGTGGTGGCCTCTGGTACAAT
130 CAAAAGGTGACACGTGGCGGCCTCTGGTACAGT
29518156 CAAACAGTCAAAGGATTAA
1 CAAACAGTCAAAGGATTAA
29518175 ATTGAAAACC
Statistics
Matches: 317, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
161 4 0.01
162 307 0.97
163 6 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (162 bp):
CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
AAGTTGATTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACC
AAAAGGTGACACGTGGCGGCCTCTGGTACAGT
Found at i:29518239 original size:162 final size:157
Alignment explanation
Indices: 29517747--29518257 Score: 438
Period size: 162 Copynumber: 3.2 Consensus size: 157
29517737 GTTGATTTTG
** *
29517747 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAACGGTGACAA
1 GGACTAAATT-AAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
* * * * * *
29517812 GTGGCGACTTCTGGTGCAGTCAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATGCTT-GG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTT-AAAAAT--TTCGG
** *** * ****
29517876 GCTAATTTTGTAATTAAGCAAAAGTTAATTTTG
127 GAAAATTAAATAATTAAGCAAAA-TGAA-AAAA
*
29517909 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
1 GGACTAAATT-AAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
* * * * * *
29517974 GTGGCGGCCTCTGGTACAGTCAAACAGTCAAATGATTAGTTTATAAATCTTGAAAAAATTTTGGG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTT--AAAAATTTCGGG
** *** *****
29518039 CCAATTTTGTAATTAAGCAAAAGTTGATTTTG
128 AAAATTAAATAATTAAGCAAAA--TGAAAAAA
*
29518071 GGACTAAATTAAATCAAATTAAAAATGATAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
1 GGACTAAATTAAA-CAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACAC
*
29518136 GTGGTGGCCTCTGGTACAATCAAACAGTCAAAGGATTAAATTGA-AAACCAATT-AAAATTATCG
65 GTGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATT-AATTGATAAACC--TTAAAAATT-TCG
*
29518199 GGTAAAATTACAAATAATTTCAG-AAAA-GAAAAAA
126 GG-AAAATT--AAATAA-TTAAGCAAAATGAAAAAA
*
29518233 GGACTAAATTGAAACAAATAAAAAA
1 GGACTAAATT-AAACAAATTAAAAA
29518258 GCGAAAGGAC
Statistics
Matches: 303, Mismatches: 33, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
161 11 0.04
162 260 0.86
163 19 0.06
164 2 0.01
165 7 0.02
166 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (157 bp):
GGACTAAATTAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAAGTGACACG
TGGCGGCCTCTGGTACAATCAAACAGTCAAAGGATTAATTGATAAACCTTAAAAATTTCGGGAAA
ATTAAATAATTAAGCAAAATGAAAAAA
Found at i:29520020 original size:59 final size:58
Alignment explanation
Indices: 29519963--29520213 Score: 306
Period size: 59 Copynumber: 4.3 Consensus size: 58
29519953 ATCCGGGGGC
* * * *
29519963 AAAATGTTAAATTTCAGTGAAATCGAGGTTAAGAATAGAATTTTGGAAAGCTCGGGGGT
1 AAAATGGTAAATTTTAGTGAAATCGAGGTTAA-AATAGAATTTTGGAAAGTTCGAGGGT
* * *
29520022 AAAATGGTAATTTTTGGTGAAATCGAGGTTTAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAAATTTTAGTGAAATCGAGG-TTAAAATAGAATTTTGGAAAGTTCGAGGGT
* * * *
29520081 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGAGT
1 AAAATGGTAAATTTTAGTGAAATCGAGGTT-AAAATAGAATTTTGGAAAGTTCGAGGGT
* * * *
29520140 AAAATGGT-AATTTATGGTAAAATCGGGGTTAAACATAGAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAAATTT-TAGTGAAATCGAGGTTAAA-ATAGAATTTTGGAAAGTTCGAGGGT
*
29520199 AAAATGGTAATTTTT
1 AAAATGGTAAATTTT
29520214 GAAGTTTCGG
Statistics
Matches: 172, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
58 9 0.05
59 155 0.90
60 8 0.05
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (58 bp):
AAAATGGTAAATTTTAGTGAAATCGAGGTTAAAATAGAATTTTGGAAAGTTCGAGGGT
Found at i:29520033 original size:29 final size:29
Alignment explanation
Indices: 29520001--29520212 Score: 181
Period size: 29 Copynumber: 7.2 Consensus size: 29
29519991 TTAAGAATAG
* *
29520001 AATTTTGGAAAGCTCGGGGGTAAAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
*
29520030 AATTTTTGGTGAAA--TCGAGGTTTAAAATGG-
1 AA-TTTT-G-GAAAGTTCGAGG-GTAAAATGGT
29520060 AATTTTGGAAAGTTCGAGGGTAAAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
*
29520089 AATTTTTGGTGAAA--TCGAGGTTAAAAATGG-
1 AA-TTTT-G-GAAAGTTCGAGGGT-AAAATGGT
*
29520119 AATTTTGGAAAGTTCGAGAGTAAAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
* *
29520148 AATTTATGGTAAA-ATCG-GGGTTAAACATAG-
1 AATTT-TGG-AAAGTTCGAGGG-TAAA-ATGGT
*
29520178 AATTTTAGAAAGTTCGAGGGTAAAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
29520207 AATTTT
1 AATTTT
29520213 TGAAGTTTCG
Statistics
Matches: 150, Mismatches: 12, Indels: 42
0.74 0.06 0.21
Matches are distributed among these distances:
27 8 0.05
28 23 0.15
29 46 0.31
30 42 0.28
31 23 0.15
32 8 0.05
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
AATTTTGGAAAGTTCGAGGGTAAAATGGT
Found at i:29520038 original size:30 final size:30
Alignment explanation
Indices: 29520003--29520272 Score: 180
Period size: 29 Copynumber: 9.2 Consensus size: 30
29519993 AAGAATAGAA
* *
29520003 TTTTGGAAAGCTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
*
29520033 TTTTGGTGAAA--TCGAGGTTTAAAATGG-AA-
1 TTTT-G-GAAAGTTCGAGG-GTAAAATGGTAAT
29520062 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
*
29520092 TTTTGGTGAAA--TCGAGGTTAAAAATGG-AA-
1 TTTT-G-GAAAGTTCGAGGGT-AAAATGGTAAT
*
29520121 TTTTGGAAAGTTCGAGAGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
* * *
29520151 TTATGGTAAA-ATCG-GGGTTAAACATAG-AA-
1 TTTTGG-AAAGTTCGAGGG-TAAA-ATGGTAAT
*
29520180 TTTTAGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
* *
29520210 TTTT-G-AAGTTTCG-GGGTTAAAT-ATAAT
1 TTTTGGAAAG-TTCGAGGGTAAAATGGTAAT
* ** *
29520237 TTTTTGAAA-TTTTAGGGTCAAAAT-GCAAT
1 TTTTGGAAAGTTCGAGGGT-AAAATGGTAAT
29520266 TTTTGGA
1 TTTTGGA
29520273 CTATTTGGGG
Statistics
Matches: 192, Mismatches: 22, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
27 18 0.09
28 39 0.20
29 59 0.31
30 45 0.23
31 23 0.12
32 8 0.04
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAGTTCGAGGGTAAAATGGTAAT
Found at i:29520129 original size:118 final size:118
Alignment explanation
Indices: 29519979--29520214 Score: 366
Period size: 118 Copynumber: 2.0 Consensus size: 118
29519969 TTAAATTTCA
* * * * *
29519979 GTGAAATCGAGGTTAAGAATAGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGCTCGAGAGTAAAATGGTAATTTATGGTAAAA
* * *
29520044 TCGAGGTTTAAA-ATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTG
66 TCG-GGGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTG
* *
29520097 GTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTATGGTAAAA
1 GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGCTCGAGAGTAAAATGGTAATTTATGGTAAAA
29520162 TCGGGGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTG
66 TCGGGGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTG
29520215 AAGTTTCGGG
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
117 7 0.07
118 100 0.93
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (118 bp):
GTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGCTCGAGAGTAAAATGGTAATTTATGGTAAAA
TCGGGGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTG
Found at i:29520267 original size:56 final size:58
Alignment explanation
Indices: 29519989--29520270 Score: 180
Period size: 59 Copynumber: 4.8 Consensus size: 58
29519979 GTGAAATCGA
* * * * ** **
29519989 GGTTAAGA-ATAGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAG
1 GGTTAA-ACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGCAATTTTTGAAG-TTTCG-G
* * * * ** ** *
29520049 GTTTAAA-ATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGA
1 GGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGCAATTTTTGAAG-TTTCGG
* * * * * * **
29520107 GGTTAAAAATGGAATTTTGGAAAGTTCGAGAGTAAAATGGTAATTTATGGTAA-AATCGG
1 GGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGCAATTT-TTG-AAGTTTCGG
*
29520166 GGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAGTTTCGG
1 GGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGCAATTTTTGAAGTTTCGG
* * * **
29520224 GGTTAAATATA-ATTTTTTGAAA-TTTTAGGGTCAAAAT-GCAATTTTTG
1 GGTTAAACATAGAATTTTAGAAAGTTCGAGGGT-AAAATGGCAATTTTTG
29520271 GACTATTTGG
Statistics
Matches: 193, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
56 16 0.08
57 16 0.08
58 22 0.11
59 132 0.68
60 7 0.04
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
GGTTAAACATAGAATTTTAGAAAGTTCGAGGGTAAAATGGCAATTTTTGAAGTTTCGG
Found at i:29520604 original size:162 final size:163
Alignment explanation
Indices: 29520337--29520670 Score: 573
Period size: 162 Copynumber: 2.1 Consensus size: 163
29520327 CACAGGCATC
* * *
29520337 CAAA-AGTCAAAGGACTAATTTGTAAATCTTGAAAAATTCTTGGGGCAATTTTGTAATTAAATAA
1 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAACAA
* *
29520401 AAGTTAATTTTTGGGACTAAATTAAAACAAATTAAAAATGACAGGGATTAAATGCATAAATAAAC
66 AAGTTAATTTTTAGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
*
29520466 CAAAAGGTGACACGTGGCGGCTTCTGGTGCAGT
131 CAAAAGGTGACACGTGGCGGCCTCTGGTGCAGT
* *
29520499 CAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAA
1 CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAACAA
*
29520564 AAGTTGA-TTTTAGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
66 AAGTTAATTTTTAGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
29520628 CAAAAGGTGACACGTGGCGGCCTCTGGTGCAGT
131 CAAAAGGTGACACGTGGCGGCCTCTGGTGCAGT
29520661 CAAACAGTCA
1 CAAACAGTCA
29520671 CGCGCGTGAG
Statistics
Matches: 162, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
162 101 0.62
163 61 0.38
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (163 bp):
CAAACAGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAACAA
AAGTTAATTTTTAGGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAAC
CAAAAGGTGACACGTGGCGGCCTCTGGTGCAGT
Found at i:29521895 original size:17 final size:16
Alignment explanation
Indices: 29521869--29521946 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 16
29521859 AATTTAATTT
29521869 ATAAATTTAAATTTATA
1 ATAAA-TTAAATTTATA
*
29521886 ATAAACTTAAATTTTTA
1 ATAAA-TTAAATTTATA
*
29521903 AGTAAATTTAAATTTAAA
1 A-TAAA-TTAAATTTATA
*
29521921 ATAAATTTAATTT-TA
1 ATAAATTAAATTTATA
29521936 A-AAATTAAATT
1 ATAAATTAAATT
29521947 ATCTCATTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 7 0.13
17 20 0.38
18 14 0.27
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATAAATTAAATTTATA
Found at i:29522417 original size:76 final size:76
Alignment explanation
Indices: 29522291--29522971 Score: 1060
Period size: 76 Copynumber: 9.0 Consensus size: 76
29522281 GCTTTGTCTA
* * * *
29522291 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
29522356 GAAATGATGTT
66 GAAATGATGTT
*
29522367 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
29522432 GAAATGACGTT
66 GAAATGATGTT
29522443 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
29522508 GAAATGATCTG
66 GAAATGATGTT
* * * * *
29522519 GCTCTTACTTCAATTTCAGAGGTAAAGACTTGATATCTAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
29522584 GAAATGACGTT
66 GAAATGATGTT
*
29522595 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
29522660 GAAATGACGTT
66 GAAATGATGTT
* *
29522671 GCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAAGGGGATA
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC-AAGAGGATA
* **
29522735 GGAAAACGATCCT
65 GG-AAATGATGTT
*
29522748 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
29522812 GAAAAGATCTT
66 GAAATGATGTT
* * * *
29522823 GCTCTTACTTCAATTTCAGAGATAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
29522888 GAAATGAGGTT
66 GAAATGATGTT
*
29522899 GCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
29522964 GAAATGAT
66 GAAATGAT
29522972 CTTGGATTGA
Statistics
Matches: 554, Mismatches: 48, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
75 59 0.11
76 436 0.79
77 59 0.11
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
GAAATGATGTT
Found at i:29535125 original size:59 final size:59
Alignment explanation
Indices: 29535061--29535318 Score: 381
Period size: 59 Copynumber: 4.4 Consensus size: 59
29535051 TTTGGATATC
* * * * * *
29535061 CGGGGGCAAAATGGTAAATTTTAGTCAAATCGGGGTTAAGAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* *
29535120 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAGAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
**
29535179 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* * *
29535238 CAGTGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
* *
29535297 TGGGGGTAAATTGGTAATTTTT
1 CGGGGGTAAAATGGTAATTTTT
29535319 TGAAGTTTCG
Statistics
Matches: 184, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 184 1.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:29535315 original size:29 final size:29
Alignment explanation
Indices: 29535090--29535317 Score: 161
Period size: 29 Copynumber: 7.8 Consensus size: 29
29535080 TTTAGTCAAA
*
29535090 TCGGGGTTAAGAATGG-AATTTTGGAAAGT
1 TCGGGGGTAA-AATGGTAATTTTGGAAAGT
29535119 TCGGGGGTAAAATGGTAATTTTTGGTGAAA--
1 TCGGGGGTAAAATGGTAA-TTTT-G-GAAAGT
*
29535149 TCGGGGTTAAGAATGG-AATTTTGGAAAGT
1 TCGGGGGTAA-AATGGTAATTTTGGAAAGT
**
29535178 TTAGGGGTAAAATGGTAATTTTTGGTGAAA--
1 TCGGGGGTAAAATGGTAA-TTTT-G-GAAAGT
* *
29535208 TCGAGGTTAAAAATGG-AATTTTGGAAAGT
1 TCGGGGGT-AAAATGGTAATTTTGGAAAGT
* *
29535237 TCAGTGGTAAAATGGTAATTTTTGGTGAAA-T
1 TCGGGGGTAAAATGGTAA-TTTT-G-GAAAGT
* *
29535268 T-GAGGTTAAAAATGG-AATTTTGGAAAGT
1 TCGGGGGT-AAAATGGTAATTTTGGAAAGT
* *
29535296 TTGGGGGTAAATTGGTAATTTT
1 TCGGGGGTAAAATGGTAATTTT
29535318 TTGAAGTTTC
Statistics
Matches: 157, Mismatches: 20, Indels: 44
0.71 0.09 0.20
Matches are distributed among these distances:
27 12 0.08
28 28 0.18
29 48 0.31
30 33 0.21
31 24 0.15
32 12 0.08
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGAAAGT
Found at i:29535367 original size:118 final size:115
Alignment explanation
Indices: 29535063--29535378 Score: 332
Period size: 118 Copynumber: 2.7 Consensus size: 115
29535053 TGGATATCCG
* * * * * * * *
29535063 GGGGCAAAATGGTAAATTTTAGTCAAATCGGGGTTAAGAATGGAATTTTGGAAAGTTCGGGGGTA
1 GGGGTAAAATGGT-AATTTTTGTGAAATCGAGGTCAAAAAT-GAATTTTGAAAAGTTC-AGGGTA
* *
29535128 AAATGGTAATTTTTGGTGAAATCGGGGTTAAGAATGGAATTTTGGAAAGTTTA
63 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
29535181 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAGTGGTA
1 GGGGTAAAATGGTAATTTTT-GTGAAATCGAGGTCAAAAAT-GAATTTTGAAAAGTTCAG-GGTA
* *
29535246 AAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTG
63 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * * *
29535299 GGGGTAAATTGGTAATTTTT-TGAAGTTTCGAGGTCAAAATAT-AATTTTCTAAAATTTTAGGGT
1 GGGGTAAAATGGTAATTTTTGTGAA--ATCGAGGTCAAAA-ATGAATTTT-GAAAAGTTCAGGGT
*
29535362 CAAAAT-GCAATTTTTGG
62 -AAAATGGTAATTTTTGG
29535379 ACTGTTTGGG
Statistics
Matches: 173, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
116 4 0.02
117 26 0.15
118 141 0.82
119 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTTGTGAAATCGAGGTCAAAAATGAATTTTGAAAAGTTCAGGGTAAAA
TGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:29535642 original size:162 final size:162
Alignment explanation
Indices: 29535460--29535786 Score: 568
Period size: 162 Copynumber: 2.0 Consensus size: 162
29535450 GTTAAAAGAC
* * *
29535460 TAATTTGTAAATCTTGAAAAATTCTTGGGCCAATTT-TGTAATTAAATAAAAGTTGATTTTGGGA
1 TAATTTATAAATCTTGAAAAAATCTTGGGCCAATTTAT-TAATTAAACAAAAGTTGATTTTGGGA
29535524 CTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCA-AAAGGTGACACGT
65 CTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAGAAA-GTGACACGT
29535588 GGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGAT
129 GGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGAT
*
29535622 TAATTTATAAATCTTGAAAAAATCTTGGGCCAATTTATTAATTAAGCAAAAGTTGATTTTGGGAC
1 TAATTTATAAATCTTGAAAAAATCTTGGGCCAATTTATTAATTAAACAAAAGTTGATTTTGGGAC
* *
29535687 TAAATTAAAACAAATTAAGAATGACATGGACTAAATGCATAAATAAACCAGAAAGTGACACGTGG
66 TAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAGAAAGTGACACGTGG
29535752 CGGCCTCTGGTGCAGTCAAACAGTCAAAGGAT
131 CGGCCTCTGGTGCAGTCAAACAGTCAAAGGAT
29535784 TAA
1 TAA
29535787 ATTGAAAACC
Statistics
Matches: 157, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
162 153 0.97
163 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (162 bp):
TAATTTATAAATCTTGAAAAAATCTTGGGCCAATTTATTAATTAAACAAAAGTTGATTTTGGGAC
TAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAGAAAGTGACACGTGG
CGGCCTCTGGTGCAGTCAAACAGTCAAAGGAT
Found at i:29535851 original size:162 final size:160
Alignment explanation
Indices: 29535521--29535869 Score: 397
Period size: 162 Copynumber: 2.2 Consensus size: 160
29535511 GTTGATTTTG
29535521 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
1 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
* *
29535586 GTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATTAATTTATAAATCTTGAAAAAATCTTGGG
66 GTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATTAATTGATAAACCTTGAAAAAATC-TGGG
* * * * * ****
29535651 CCAATTTATTAATTAAGCAAAAGTTGATTTTG
130 CAAATTAAATAATTAAGAAAAAG-TCATAAAA
* *
29535683 GGACTAAATTAAAACAAATTAAGAATGACATGGACTAAATGCATAAATAAACCAGAAA-GTGACA
1 GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCA-AAAGGTGACA
*
29535747 CGTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATTAAATTGA-AAACCAATT-AAAATTATC
65 CGTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATT-AATTGATAAACC--TTGAAAA-AATC
29535810 -GGGCAAAATTACAAATAATTACA-AAAAAG-CA-AAAA
126 TGGGC-AAATT--AAATAATTA-AGAAAAAGTCATAAAA
* * *
29535845 GGACTAAATTGAAGCAAATAAAAAA
1 GGACTAAATTAAAACAAATTAAAAA
29535870 GCGGAAGGAC
Statistics
Matches: 160, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
162 125 0.78
163 17 0.11
164 5 0.03
165 12 0.08
166 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.22
Consensus pattern (160 bp):
GGACTAAATTAAAACAAATTAAAAATGACAGGGACTAAATGCATAAATAAACCAAAAGGTGACAC
GTGGCGGCCTCTGGTGCAGTCAAACAGTCAAAGGATTAATTGATAAACCTTGAAAAAATCTGGGC
AAATTAAATAATTAAGAAAAAGTCATAAAA
Found at i:29537443 original size:17 final size:16
Alignment explanation
Indices: 29537417--29537494 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 16
29537407 AATTTAATTT
29537417 ATAAATTTAAATTTATA
1 ATAAA-TTAAATTTATA
*
29537434 ATAAACTTAAATTTTTA
1 ATAAA-TTAAATTTATA
*
29537451 AGTAAATTTAAATTTAAA
1 A-TAAA-TTAAATTTATA
*
29537469 ATAAATTTAATTT-TA
1 ATAAATTAAATTTATA
29537484 A-AAATTAAATT
1 ATAAATTAAATT
29537495 ATCTCATTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 7 0.13
17 20 0.38
18 14 0.27
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATAAATTAAATTTATA
Found at i:29540371 original size:21 final size:21
Alignment explanation
Indices: 29540346--29540385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29540336 ACTACTTGAA
*
29540346 ATCTAAATATAAATTTGAAGT
1 ATCTAAACATAAATTTGAAGT
*
29540367 ATCTAAACATGAATTTGAA
1 ATCTAAACATAAATTTGAA
29540386 ATATTTGAAA
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:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCTAAACATAAATTTGAAGT
Found at i:29541792 original size:11 final size:11
Alignment explanation
Indices: 29541773--29541804 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29541763 ATTTTGATTC
*
29541773 ATAATTAATAT
1 ATAAATAATAT
29541784 ATAAATAATAT
1 ATAAATAATAT
29541795 ATAAATAATA
1 ATAAATAATA
29541805 AAACAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:29541839 original size:5 final size:5
Alignment explanation
Indices: 29541831--29541871 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
29541821 CAACAATTAA
*
29541831 ATAAT ATAAT ATAAT ATAA- ATAAT GATAAT ATTA- ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT AT
29541872 TAATTCATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 7 0.23
5 19 0.61
6 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:29541943 original size:26 final size:22
Alignment explanation
Indices: 29541913--29541966 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
29541903 CAAGCATGAC
29541913 ATAATTGAAAATAATAAACTAAAAAA
1 ATAATT-AAAAT-ATAAA--AAAAAA
*
29541939 ATAATTAAAATATGAAAAAAAA
1 ATAATTAAAATATAAAAAAAAA
29541961 ATAATT
1 ATAATT
29541967 TAAAGGGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 12 0.44
24 4 0.15
25 5 0.19
26 6 0.22
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (22 bp):
ATAATTAAAATATAAAAAAAAA
Found at i:29542075 original size:12 final size:13
Alignment explanation
Indices: 29542044--29542076 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29542034 TAGATAAAAT
29542044 AAATAAAATAAAC
1 AAATAAAATAAAC
*
29542057 AAATAAAATAAGC
1 AAATAAAATAAAC
29542070 -AATAAAA
1 AAATAAAA
29542077 GGGACTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (13 bp):
AAATAAAATAAAC
Found at i:29542223 original size:23 final size:23
Alignment explanation
Indices: 29542171--29542227 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
29542161 TTAAAATTGT
*
29542171 AAACAAATTAAAGGCATAAATTA
1 AAACAAAATAAAGGCATAAATTA
29542194 AAA-AAAATAAAGG-ATTAAATTA
1 AAACAAAATAAAGGCA-TAAATTA
29542216 AAACAAAATAAA
1 AAACAAAATAAA
29542228 AATGCAGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 19 0.61
23 11 0.35
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.19
Consensus pattern (23 bp):
AAACAAAATAAAGGCATAAATTA
Found at i:29543320 original size:18 final size:16
Alignment explanation
Indices: 29543292--29543354 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
29543282 TTGTATTTTT
29543292 ATTTGTTATTTGTAAATGG
1 ATTT-TTATTT-T-AATGG
29543311 ATTTTTATTTTAATGG
1 ATTTTTATTTTAATGG
* *
29543327 ACTTTTTAATTTAAT-T
1 A-TTTTTATTTTAATGG
*
29543343 TTTTTTATTTTA
1 ATTTTTATTTTA
29543355 TTTGGTTGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 10 0.26
16 6 0.15
17 13 0.33
18 6 0.15
19 4 0.10
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (16 bp):
ATTTTTATTTTAATGG
Found at i:29550131 original size:16 final size:16
Alignment explanation
Indices: 29550110--29550144 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29550100 CTCATAATAT
29550110 AATAAACATATT-TAAA
1 AATAAACAT-TTATAAA
29550126 AATAAACATTTATAAA
1 AATAAACATTTATAAA
29550142 AAT
1 AAT
29550145 TTAATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAACATTTATAAA
Found at i:29550609 original size:15 final size:17
Alignment explanation
Indices: 29550588--29550628 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
29550578 TTAATTTTTA
29550588 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
29550604 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
29550620 AAAATTATA
1 AAAATTATA
29550629 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:29554568 original size:90 final size:89
Alignment explanation
Indices: 29554414--29554867 Score: 408
Period size: 90 Copynumber: 5.1 Consensus size: 89
29554404 TTAAAAATAT
* * * * * *
29554414 ATTTTGACCCCCAAATCTTTCCAAAATCACCTTTTGACCCTTAAACCTTT-CAAAAATCCTATTT
1 ATTTTGACCCCCAAACCTTTCCAAAATCACATTTTAACCCCTAAA-CTTTCCAAAATTAC-ATTT
*
29554478 TGACACTCAAACCTT-TCCAAAATC-C
64 TGACCCTCAAA-CTTCTCCAAAATCAC
* * * * *
29554503 TATTTTGACCTCTAAACCTTTCCAAAATCATATTTTGACCCCTAAACTTCTCTAAAATTACATTT
1 -ATTTTGACCCCCAAACCTTTCCAAAATCACATTTTAACCCCTAAACTT-TCCAAAATTACATTT
* *
29554568 TGACCCTTAAACTTCTCTAAAATCAC
64 TGACCCTCAAACTTCTCCAAAATCAC
* * * *
29554594 ATTTTAACCCCCAAACTTTTCCAAAATCACATTTTAACCCCCAAACTTTTCCAAAATCACATTTT
1 ATTTTGACCCCCAAACCTTTCCAAAATCACATTTTAACCCCTAAAC-TTTCCAAAATTACATTTT
*
29554659 AACCC-CAAACTTCTCC-AAA--AC
65 GACCCTCAAACTTCTCCAAAATCAC
* ** *
29554680 ATTTTGACTCTTAAA-TTTTCCTAAAATCACATTTTAACCCCTAAACTTCTCCAAAATTACATTT
1 ATTTTGACCCCCAAACCTTTCC-AAAATCACATTTTAACCCCTAAACTT-TCCAAAATTACATTT
* * * *
29554744 TAACCCTCAAATTTTTTCAAAATCAC
64 TGACCCTCAAACTTCTCCAAAATCAC
* * * * * * *
29554770 ATTTT-AACCACAAACCTTCCCAAAATCACATTTTAA-CCTTAAACTTTCATAAAAATACCTTTT
1 ATTTTGACCCCCAAACCTTTCCAAAATCACATTTTAACCCCTAAACTTTC-CAAAATTACATTTT
* *
29554833 GACCCTTAAA-TTCTTCCAAAATTAC
65 GACCCTCAAACTTC-TCCAAAATCAC
*
29554858 ATTTTAACCC
1 ATTTTGACCC
29554868 TAAATTCTTT
Statistics
Matches: 300, Mismatches: 49, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
85 8 0.03
86 56 0.19
87 12 0.04
88 48 0.16
89 38 0.13
90 129 0.43
91 9 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (89 bp):
ATTTTGACCCCCAAACCTTTCCAAAATCACATTTTAACCCCTAAACTTTCCAAAATTACATTTTG
ACCCTCAAACTTCTCCAAAATCAC
Found at i:29554868 original size:30 final size:31
Alignment explanation
Indices: 29554432--29554876 Score: 318
Period size: 30 Copynumber: 15.1 Consensus size: 31
29554422 CCCCAAATCT
* * *
29554432 TTCCAAAATCACCTTTTGACCCTTAAACCT-
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
* * * * *
29554462 TTCAAAAATC-CTATTTTGACACTCAAACCT-
1 TTCCAAAATCAC-ATTTTAACCCTTAAACTTC
* *
29554492 TTCCAAAATC-CTATTTTGA-CCTCTAAACCT-
1 TTCCAAAATCAC-ATTTTAACCCT-TAAACTTC
* * *
29554522 TTCCAAAATCATATTTTGACCCCTAAACTTC
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
* * *
29554553 -TCTAAAATTACATTTTGACCCTTAAACTTC
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
* **
29554583 -TCTAAAATCACATTTTAACCCCCAAACTT-
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
**
29554612 TTCCAAAATCACATTTTAACCCCCAAACTT-
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
*
29554642 TTCCAAAATCACATTTTAACCC-CAAACTTC
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
* *
29554672 -TCC-AAA--ACATTTTGACTCTTAAA-TT-
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
*
29554697 TTCCTAAAATCACATTTTAACCCCTAAACTTC
1 TTCC-AAAATCACATTTTAACCCTTAAACTTC
* * *
29554729 -TCCAAAATTACATTTTAACCCTCAAA-TTT
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
*
29554758 TTTCAAAATCACATTTTAACCAC--AAAC--C
1 TTCCAAAATCACATTTTAACC-CTTAAACTTC
29554786 TTCCCAAAATCACATTTTAA-CCTTAAACTTTC
1 TT-CCAAAATCACATTTTAACCCTTAAAC-TTC
* * * *
29554818 AT-AAAAAT-ACCTTTTGACCCTTAAA-TTC
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
*
29554846 TTCCAAAATTACATTTTAACCC-TAAA-TTC
1 TTCCAAAATCACATTTTAACCCTTAAACTTC
29554875 TT
1 TT
29554877 TGAAACTTCA
Statistics
Matches: 347, Mismatches: 41, Indels: 55
0.78 0.09 0.12
Matches are distributed among these distances:
26 15 0.04
27 4 0.01
28 13 0.04
29 59 0.17
30 246 0.71
31 8 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.35
Consensus pattern (31 bp):
TTCCAAAATCACATTTTAACCCTTAAACTTC
Found at i:29560796 original size:49 final size:49
Alignment explanation
Indices: 29560666--29561648 Score: 609
Period size: 49 Copynumber: 20.0 Consensus size: 49
29560656 GATGAACTAA
* * * *
29560666 GGTACCATGAAGATATAAAGGGAAAGGTTGAGGCCGTAATGGCGAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
** * * * *
29560715 ATTACCTTAGAAGATGTGATGGGAAAAGTTGAGGCCGCAACGGTGAACCC
1 GGTACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * *
29560765 GGTACCATGAAGATATAAAGGGAAAGATTGAGGTCGCAAGGGCAAACTC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * *
29560814 GGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGCGAACTC
1 GGTACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * *
29560864 GGTACTATGAATATTTGAAGGGAAAGGTTGAGGCCTCAACGACAAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * ** * *
29560913 GGTACCTTAGAAGACGTGATGGG-AAGGATTAAGGTCGCAACAACGAATCT
1 GGTACCAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCC
** * * * *
29560963 GACACCATGAAG-TATGATGGGAAAGGTTGAGGTCGCAACGGTGAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* ** ** * *
29561011 GGTACCATGAAGATTTGAAGGGAAATATTGAGGTTGCAACGACAAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * ** **
29561060 AGTACCTTAGAAGACGTGATGGG-AAGGATTGATGTCGCAACGGTAAATAC
1 GGTACCAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCC
* * * * * *
29561110 GGCACCATAAAG-TGTGATGGGAAAGGTTGAGGTCACAACGGTGAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * *
29561158 GATTCCATAAAGATTTGAAGGGAAAGGTTGAGGCCAG-AACGGTGAACCA
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCC-GCAACGGCGAACCC
* * * * * **
29561207 AGTACCATAAAGATATGAAGGGAAAGGTTGAGGTCGTAACGGTAAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * **
29561256 AGTACCTTAGAAGACGTG-ATGG-AAGGATTAAGGCCGCAATGATGAACCC
1 GGTACCAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCC
* * * * *
29561305 GATACCATGAATATATAAAGGGAAAGGTTGAGGCCGTAACGGCGAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * *
29561354 GATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCACAATGGCGAACCC
1 GGTACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
** * * * *
29561404 TATACCATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGACAAACCC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * *** *
29561453 AGTACCTTAGAAGACGTGATGGG-AAGGATTAAGGCCGTAACAATGAATCC
1 GGTACCAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCC
* * ** *
29561503 GGTACCATGAAG-TATGATGGGAAAGGTTGAGGCCGCAACGATGAACTC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
* ** * * * * *
29561551 AGTACTTTAGAAGATGTGATGGG-AAGGATTGAGTCTGCAACGGTGAATCC
1 GGTACCAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCC
* * * *
29561601 GGCACCATGAAGATATAAAGAGAAAGGTTGAGGCCGCAACGGCGAACC
1 GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
29561649 AAGTACCTTA
Statistics
Matches: 712, Mismatches: 198, Indels: 48
0.74 0.21 0.05
Matches are distributed among these distances:
48 106 0.15
49 351 0.49
50 255 0.36
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (49 bp):
GGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCC
Found at i:29561435 original size:99 final size:99
Alignment explanation
Indices: 29560685--29561648 Score: 652
Period size: 99 Copynumber: 9.8 Consensus size: 99
29560675 AAGATATAAA
* * * ** * * * *
29560685 GGGAAAGGTTGAGGCCGTAATGGCGAACCCATTACCTTAGAAGATGTGATGGGAAAAGTTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCAT-GAAGATATGAAGGGAAAGGTTGAGGC
* * * * * *
29560750 CGCAACGGTGAACCCGGTACCAT-GAAGATATAAA
65 CGCAACGGCGAACCCGATACCTTAGAAGATGTGAT
* * * ** * * * *
29560784 GGGAAAGATTGAGGTCGCAAGGGCAAACTCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCAT-GAAGATATGAAGGGAAAGGTTGAGGC
* * * * * *
29560849 CGTAACGGCGAACTCGGTA-C-TATGAATATTTGAA
65 CGCAACGGCGAACCCGATACCTTA-GAAGATGTGAT
* *** * ** * *
29560883 GGGAAAGGTTGAGGCCTCAACGACAAACCCGGTACCTTAGAAGACGTGATGGG-AAGGATTAAGG
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCAT-GAAGATATGAAGGGAAAGG-TTGAGG
* ** * * * * *
29560947 TCGCAACAACGAATCTGACACCAT-GAAG-TATGAT
64 CCGCAACGGCGAACCCGATACCTTAGAAGATGTGAT
* * ** **
29560981 GGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCATGAAGATTTGAAGGGAAATATTGAGGTT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
* * *
29561046 GCAACGACAAACCC-AGTACCTTAGAAGACGTGAT
66 GCAACGGCGAACCCGA-TACCTTAGAAGATGTGAT
* * * ** * * * * *
29561080 GGG-AAGGATTGATGTCGCAACGGTAAATACGGCACCATAAAG-TGTGATGGGAAAGGTTGAGGT
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGC
* * * * * *
29561143 CACAACGGTGAACCCGATTCCATA-AAGATTTGAA
65 CGCAACGGCGAACCCGATACCTTAGAAGATGTGAT
** * *
29561177 GGGAAAGGTTGAGGCCAG-AACGGTGAACCAAGTACCATAAAGATATGAAGGGAAAGGTTGAGGT
1 GGGAAAGGTTGAGGCC-GCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGC
* ** *
29561241 CGTAACGGTAAACCC-AGTACCTTAGAAGACGTGAT
65 CGCAACGGCGAACCCGA-TACCTTAGAAGATGTGAT
* * * * * *
29561276 -GG-AAGGATTAAGGCCGCAATGATGAACCCGATACCATGAATATATAAAGGGAAAGGTTGAGGC
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGC
*
29561339 CGTAACGGCGAACCCGATACCTTAGAAGATGTGAT
65 CGCAACGGCGAACCCGATACCTTAGAAGATGTGAT
* * * ** * *
29561374 GGGAAAGGTTGAGGCCACAATGGCGAACCCTATACCATGAAGATTTGAAGGGAAAGGTTGAGGTC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
* * *
29561439 GCAACGACAAACCC-AGTACCTTAGAAGACGTGAT
66 GCAACGGCGAACCCGA-TACCTTAGAAGATGTGAT
* * ** * *
29561473 GGG-AAGGATTAAGGCCGTAACAATGAATCCGGTACCATGAAG-TATGATGGGAAAGGTTGAGGC
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGC
** * *
29561536 CGCAACGATGAACTC-AGTACTTTAGAAGATGTGAT
65 CGCAACGGCGAACCCGA-TACCTTAGAAGATGTGAT
* * * * * *
29561571 GGG-AAGGATTGAGTCTGCAACGGTGAATCCGGCACCATGAAGATATAAAGAGAAAGGTTGAGGC
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGC
29561635 CGCAACGGCGAACC
65 CGCAACGGCGAACC
29561649 AAGTACCTTA
Statistics
Matches: 690, Mismatches: 151, Indels: 48
0.78 0.17 0.05
Matches are distributed among these distances:
96 1 0.00
97 72 0.10
98 288 0.42
99 323 0.47
100 5 0.01
101 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (99 bp):
GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCC
GCAACGGCGAACCCGATACCTTAGAAGATGTGAT
Found at i:29561459 original size:197 final size:197
Alignment explanation
Indices: 29560977--29561658 Score: 773
Period size: 197 Copynumber: 3.5 Consensus size: 197
29560967 CCATGAAGTA
* * * * **
29560977 TGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCATGAAGATTTGAAGGGAAATATTGA
1 TGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGA
* * * * * *
29561042 GGTTGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTGATGTCGCAACGGTAAA
66 GGTCGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTAAGGCCGCAACGATGAA
* * * * * * *
29561107 TACGGCACCAT-AAAGTGTGATGGGAAAGGTTGAGGTCACAACGGTGAACCCGATTCCATA-AAG
131 TCCGGTACCATGAAA-TATGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTTAGAAG
*
29561170 ATT
195 ATG
* * * *
29561173 TGAAGGGAAAGGTTGAGGCCAGAACGGTGAA-CCAAGTACCATAAAGATATGAAGGGAAAGGTTG
1 TGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGA-TACCATGAAGATATGAAGGGAAAGGTTG
* ** *
29561237 AGGTCGTAACGGTAAACCCAGTACCTTAGAAGACGTGAT-GGAAGGATTAAGGCCGCAATGATGA
65 AGGTCGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTAAGGCCGCAACGATGA
* * * * * *
29561301 ACCCGATACCATGAATATATAAAGGGAAAGGTTGAGGCCGTAACGGCGAACCCGATACCTTAGAA
130 ATCCGGTACCATGAA-ATATGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTTAGAA
29561366 GATG
194 GATG
* * * *
29561370 TGATGGGAAAGGTTGAGGCCACAATGGCGAACCCTATACCATGAAGATTTGAAGGGAAAGGTTGA
1 TGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGA
* *
29561435 GGTCGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTAAGGCCGTAACAATGAA
66 GGTCGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTAAGGCCGCAACGATGAA
* * * *
29561500 TCCGGTACCATGAAGTATGATGGGAAAGGTTGAGGCCGCAACGATGAACTC-AGTACTTTAGAAG
131 TCCGGTACCATGAAATATGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGA-TACCTTAGAAG
29561564 ATG
195 ATG
* ** * ** * *
29561567 TGATGGG-AAGGATTGAGTCTGCAACGGTGAATCCGGCACCATGAAGATATAAAGAGAAAGGTTG
1 TGATGGGAAAGG-TTGAGGCCACAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTG
* * * *
29561631 AGGCCGCAACGGCGAACCAAGTACCTTA
65 AGGTCGCAACGACAAACCCAGTACCTTA
29561659 AGAAAACATG
Statistics
Matches: 405, Mismatches: 73, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
195 29 0.07
196 129 0.32
197 209 0.52
198 38 0.09
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (197 bp):
TGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGA
GGTCGCAACGACAAACCCAGTACCTTAGAAGACGTGATGGGAAGGATTAAGGCCGCAACGATGAA
TCCGGTACCATGAAATATGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGA
TG
Found at i:29561729 original size:39 final size:39
Alignment explanation
Indices: 29561685--29561767 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
29561675 AAGATTGAAG
* *
29561685 CATCCAATCTCTTACCTCGATCATGGGGCAGATTACAGC
1 CATCCAATCTCTTACCCCGATCATAGGGCAGATTACAGC
* *
29561724 CATCCAATCTCTTACCCCGATCATAGGGCAGATTGCAGT
1 CATCCAATCTCTTACCCCGATCATAGGGCAGATTACAGC
29561763 CATCC
1 CATCC
29561768 GAAGCAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (39 bp):
CATCCAATCTCTTACCCCGATCATAGGGCAGATTACAGC
Found at i:29563581 original size:30 final size:30
Alignment explanation
Indices: 29563545--29563792 Score: 290
Period size: 30 Copynumber: 8.3 Consensus size: 30
29563535 TAAAAACTAT
29563545 ATTTTGACCCCCAAATCTTTCCAAAATCAC
1 ATTTTGACCCCCAAATCTTTCCAAAATCAC
29563575 ATTTTGACCCCCAAATCTTTCCAAAATCAC
1 ATTTTGACCCCCAAATCTTTCCAAAATCAC
*
29563605 ATTTTGACCCCCAAATATTTCCAAAATCAC
1 ATTTTGACCCCCAAATCTTTCCAAAATCAC
* *
29563635 ATTTTGACCTCCAAATCTTTCCAAAATTAC
1 ATTTTGACCCCCAAATCTTTCCAAAATCAC
*
29563665 ATTTTGACCCTCAAAT-TTTCCCAAAATCAC
1 ATTTTGACCCCCAAATCTTT-CCAAAATCAC
* * *
29563695 ATTTTGA-CCACAAACCTTCCCAAAATCAC
1 ATTTTGACCCCCAAATCTTTCCAAAATCAC
* * * *
29563724 ATTTT-AACCCTAAA-CTTTCATAAAATTAC
1 ATTTTGACCCCCAAATCTTTC-CAAAATCAC
* * * *
29563753 CTTTTGACCCTCGAATTCTTT-CAAAATTAC
1 ATTTTGACCC-CCAAATCTTTCCAAAATCAC
*
29563783 ATTTTAACCC
1 ATTTTGACCC
29563793 TAAATTCTTT
Statistics
Matches: 189, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.03
29 40 0.21
30 137 0.72
31 3 0.02
32 4 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
ATTTTGACCCCCAAATCTTTCCAAAATCAC
Found at i:29563793 original size:30 final size:30
Alignment explanation
Indices: 29563545--29563821 Score: 229
Period size: 30 Copynumber: 9.4 Consensus size: 30
29563535 TAAAAACTAT
*
29563545 ATTTTGACCCCCAAA-TCTTTCCAAAATCAC
1 ATTTTGACCCTCAAATTCTTT-CAAAATCAC
*
29563575 ATTTTGACCCCCAAA-TCTTTCCAAAATCAC
1 ATTTTGACCCTCAAATTCTTT-CAAAATCAC
* *
29563605 ATTTTGACCCCCAAATAT-TTCCAAAATCAC
1 ATTTTGACCCTCAAAT-TCTTTCAAAATCAC
*
29563635 ATTTTGA-CCTCCAAA-TCTTTCCAAAATTAC
1 ATTTTGACCCT-CAAATTCTTT-CAAAATCAC
*
29563665 ATTTTGACCCTCAAATT-TTCCCAAAATCAC
1 ATTTTGACCCTCAAATTCTT-TCAAAATCAC
* * *
29563695 ATTTTGA-CCACAAA-CCTTCCCAAAATCAC
1 ATTTTGACCCTCAAATTCTT-TCAAAATCAC
* *
29563724 ATTTTAACCCT-AAA--CTTTCATAAAATTAC
1 ATTTTGACCCTCAAATTCTTTC--AAAATCAC
* * *
29563753 CTTTTGACCCTCGAATTCTTTCAAAATTAC
1 ATTTTGACCCTCAAATTCTTTCAAAATCAC
* **
29563783 ATTTTAACCCT-AAATTCTTT-AAAATTTC
1 ATTTTGACCCTCAAATTCTTTCAAAATCAC
29563811 ATTTTGACCCT
1 ATTTTGACCCT
29563822 ATTTTTTATT
Statistics
Matches: 212, Mismatches: 20, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.00
28 21 0.10
29 56 0.26
30 122 0.58
31 6 0.03
32 6 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCTCAAATTCTTTCAAAATCAC
Found at i:29563813 original size:28 final size:28
Alignment explanation
Indices: 29563716--29563822 Score: 108
Period size: 29 Copynumber: 3.7 Consensus size: 28
29563706 AAACCTTCCC
* *
29563716 AAAATCACATTTTAACCCTAAACTT-TCAT
1 AAAATTACATTTTAACCCTAAA-TTCT-TT
* * *
29563745 AAAATTACCTTTTGACCCTCGAATTCTTT
1 AAAATTACATTTTAACCCT-AAATTCTTT
29563774 CAAAATTACATTTTAACCCTAAATTCTTT
1 -AAAATTACATTTTAACCCTAAATTCTTT
* *
29563803 AAAATTTCATTTTGACCCTA
1 AAAATTACATTTTAACCCTA
29563823 TTTTTTATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 18 0.28
29 27 0.42
30 20 0.31
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTAAATTCTTT
Found at i:29565109 original size:3 final size:3
Alignment explanation
Indices: 29565101--29565145 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
29565091 TTTATAAAGG
29565101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29565146 AATATATGTA
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):
TTA
Found at i:29566158 original size:37 final size:37
Alignment explanation
Indices: 29566080--29566160 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
29566070 TTAGGCTTTG
* * * * *
29566080 TGCCTAGTAGGCTTTATGCTGGTGTTTTCAGACTTTG
1 TGCCTAGTAGGCCTTATGCCGGTGTATTCAGACTATA
* * *
29566117 TGCCTAGTAGGCCTTGTGCCGGTGTATTCGGGCTATA
1 TGCCTAGTAGGCCTTATGCCGGTGTATTCAGACTATA
29566154 TGCCTAG
1 TGCCTAG
29566161 CAAGCTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.37
Consensus pattern (37 bp):
TGCCTAGTAGGCCTTATGCCGGTGTATTCAGACTATA
Found at i:29569703 original size:2 final size:2
Alignment explanation
Indices: 29569696--29569738 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
29569686 ACATATTTTT
* * *
29569696 CA CA CA CA CA -A CA CG CA CA CG CA CA CT CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29569737 CA
1 CA
29569739 TATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.49, G:0.05, T:0.02
Consensus pattern (2 bp):
CA
Found at i:29569743 original size:2 final size:2
Alignment explanation
Indices: 29569738--29569763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29569728 ACACACACAC
29569738 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
29569764 TTCATTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29573177 original size:20 final size:20
Alignment explanation
Indices: 29573135--29573178 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29573125 ACTTTTATTA
* *
29573135 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
29573155 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
29573175 TTAA
1 TTAA
29573179 AAGTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:29573688 original size:12 final size:12
Alignment explanation
Indices: 29573671--29573727 Score: 87
Period size: 12 Copynumber: 4.7 Consensus size: 12
29573661 GCTAATGGAT
29573671 TTAGGGTTGATG
1 TTAGGGTTGATG
29573683 TTAGGGTTGATG
1 TTAGGGTTGATG
*
29573695 TTAAGGTTGATG
1 TTAGGGTTGATG
29573707 TTTAGGGTTGATG
1 -TTAGGGTTGATG
*
29573720 TTAAGGTT
1 TTAGGGTT
29573728 AATTAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 30 0.73
13 11 0.27
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (12 bp):
TTAGGGTTGATG
Found at i:29573717 original size:25 final size:24
Alignment explanation
Indices: 29573675--29573727 Score: 97
Period size: 25 Copynumber: 2.2 Consensus size: 24
29573665 ATGGATTTAG
29573675 GGTTGATGTTAGGGTTGATGTTAA
1 GGTTGATGTTAGGGTTGATGTTAA
29573699 GGTTGATGTTTAGGGTTGATGTTAA
1 GGTTGATG-TTAGGGTTGATGTTAA
29573724 GGTT
1 GGTT
29573728 AATTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (24 bp):
GGTTGATGTTAGGGTTGATGTTAA
Found at i:29573740 original size:29 final size:28
Alignment explanation
Indices: 29573707--29573784 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 28
29573697 AAGGTTGATG
*
29573707 TTTAGGGTTGATGTTAAGGTTAATTAATA
1 TTTAGGGTTAATGTT-AGGTTAATTAATA
29573736 TTTAGGGTTAATGTTAGAGTTAATTAATA
1 TTTAGGGTTAATGTTAG-GTTAATTAATA
*
29573765 TTTAAGGTTAATGTTAGGTT
1 TTTAGGGTTAATGTTAGGTT
29573785 TTAGGGTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 5 0.11
29 41 0.89
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (28 bp):
TTTAGGGTTAATGTTAGGTTAATTAATA
Found at i:29573792 original size:19 final size:19
Alignment explanation
Indices: 29573765--29573811 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29573755 TTAATTAATA
* *
29573765 TTTAAGGTTAATGTTAG-G
1 TTTAGGGTTAATGGTAGAG
29573783 TTTTAGGGTTAATGGTAGAG
1 -TTTAGGGTTAATGGTAGAG
29573803 TTTAGGGTT
1 TTTAGGGTT
29573812 TAGGGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (19 bp):
TTTAGGGTTAATGGTAGAG
Found at i:29573813 original size:26 final size:26
Alignment explanation
Indices: 29573778--29573841 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
29573768 AAGGTTAATG
* *
29573778 TTAGGTTTTAGGGTTAATGGTAGAGT
1 TTAGGGTTTAGGGTTAATGGTAGAGA
* *
29573804 TTAGGGTTTAGGGTTAATGTTAGTGA
1 TTAGGGTTTAGGGTTAATGGTAGAGA
29573830 TTAGGGTTTAGG
1 TTAGGGTTTAGG
29573842 ATTTAGGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (26 bp):
TTAGGGTTTAGGGTTAATGGTAGAGA
Found at i:29573814 original size:7 final size:7
Alignment explanation
Indices: 29573802--29573964 Score: 67
Period size: 7 Copynumber: 24.7 Consensus size: 7
29573792 TAATGGTAGA
29573802 GTTTAGG
1 GTTTAGG
29573809 GTTTAGG
1 GTTTAGG
**
29573816 G-TTAAT
1 GTTTAGG
*
29573822 G-TTAGT
1 GTTTAGG
*
29573828 GATTAGG
1 GTTTAGG
29573835 GTTTAGG
1 GTTTAGG
*
29573842 ATTTAGG
1 GTTTAGG
* *
29573849 G-TCAGT
1 GTTTAGG
29573855 G-TTAGG
1 GTTTAGG
* *
29573861 TTTTAAG
1 GTTTAGG
*
29573868 G-TTATG
1 GTTTAGG
*
29573874 G-TTATG
1 GTTTAGG
29573880 G-TTAGG
1 GTTTAGG
*
29573886 GTTAAGG
1 GTTTAGG
*
29573893 GTTAAGG
1 GTTTAGG
*
29573900 GTTAAGG
1 GTTTAGG
*
29573907 GTTAAGG
1 GTTTAGG
29573914 G-TTAGG
1 GTTTAGG
*
29573920 G-TTAAG
1 GTTTAGG
**
29573926 GTTTAAT
1 GTTTAGG
*
29573933 G-TTATG
1 GTTTAGG
29573939 GTTTAGG
1 GTTTAGG
*
29573946 GTTTAAG
1 GTTTAGG
*
29573953 GTTTAAG
1 GTTTAGG
29573960 GTTTA
1 GTTTA
29573965 TGTGTATTTT
Statistics
Matches: 127, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
6 46 0.36
7 81 0.64
ACGTcount: A:0.23, C:0.01, G:0.36, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:29573902 original size:14 final size:14
Alignment explanation
Indices: 29573879--29573931 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
29573869 TTATGGTTAT
29573879 GGTT-AGGGTTAAG
1 GGTTAAGGGTTAAG
29573892 GGTTAAGGGTTAAG
1 GGTTAAGGGTTAAG
29573906 GGTTAAGGGTT-AG
1 GGTTAAGGGTTAAG
*
29573919 GGTTAAGGTTTAA
1 GGTTAAGGGTTAA
29573932 TGTTATGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 16 0.43
14 21 0.57
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.32
Consensus pattern (14 bp):
GGTTAAGGGTTAAG
Found at i:29573920 original size:20 final size:20
Alignment explanation
Indices: 29573873--29573953 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
29573863 TTAAGGTTAT
*
29573873 GGTTATGGTT-AGGGTTAAG
1 GGTTAGGGTTAAGGGTTAAG
29573892 GGTTAAGGGTTAAGGGTTAAG
1 GGTT-AGGGTTAAGGGTTAAG
*
29573913 GGTTAGGGTTAAGGTTTAA-
1 GGTTAGGGTTAAGGGTTAAG
* * *
29573932 TGTTATGGTTTAGGGTTTAAG
1 GGTTAGGGTTAAGGG-TTAAG
29573953 G
1 G
29573954 TTTAAGGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 15 0.29
20 23 0.45
21 13 0.25
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (20 bp):
GGTTAGGGTTAAGGGTTAAG
Found at i:29573922 original size:6 final size:6
Alignment explanation
Indices: 29573804--29573928 Score: 70
Period size: 7 Copynumber: 19.3 Consensus size: 6
29573794 ATGGTAGAGT
** * * * *
29573804 TTAGGG TTTAGGG TTAATG TTAGTGA TTAGGG TTTAGGAT TTAGGG TCAGTG
1 TTAGGG -TTAGGG TTAGGG TTAG-GG TTAGGG -TTAGG-G TTAGGG TTAGGG
* * * *
29573856 TTAGGTT TTAAGG TTATGG TTATGG TTAGGG TTAAGGG TTAAGGG TTAAGGG
1 TTAGG-G TTAGGG TTAGGG TTAGGG TTAGGG TT-AGGG TT-AGGG TT-AGGG
*
29573908 TTAAGGG TTAGGG TTAAGG TT
1 TT-AGGG TTAGGG TTAGGG TT
29573929 TAATGTTATG
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
6 44 0.46
7 51 0.54
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:29573936 original size:13 final size:13
Alignment explanation
Indices: 29573862--29573962 Score: 80
Period size: 14 Copynumber: 7.7 Consensus size: 13
29573852 AGTGTTAGGT
*
29573862 TTTAAGGTTATGG
1 TTTAAGGTTAAGG
*
29573875 -TTATGGTT-AGG
1 TTTAAGGTTAAGG
*
29573886 GTTAAGGGTTAAGG
1 TTTAA-GGTTAAGG
*
29573900 GTTAAGGGTTAAGG
1 TTTAA-GGTTAAGG
* *
29573914 GTTAGGGTTAAGG
1 TTTAAGGTTAAGG
* *
29573927 TTTAATGTTATGG
1 TTTAAGGTTAAGG
*
29573940 TTTAGGGTTTAAGG
1 TTTAAGG-TTAAGG
29573954 TTTAAGGTT
1 TTTAAGGTT
29573963 TATGTGTATT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
11 2 0.03
12 10 0.14
13 28 0.39
14 32 0.44
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.41
Consensus pattern (13 bp):
TTTAAGGTTAAGG
Found at i:29573957 original size:14 final size:13
Alignment explanation
Indices: 29573808--29573962 Score: 82
Period size: 13 Copynumber: 11.8 Consensus size: 13
29573798 TAGAGTTTAG
29573808 GGTTTAGGGTTAA
1 GGTTTAGGGTTAA
* * *
29573821 TG-TTAGTGATTAG
1 GGTTTAG-GGTTAA
* *
29573834 GGTTTAGGATTTA
1 GGTTTAGGGTTAA
* * *
29573847 GGGTCAGTGTT-A
1 GGTTTAGGGTTAA
* *
29573859 GGTTTTAAGGTTAT
1 GG-TTTAGGGTTAA
* *
29573873 GG-TTATGGTTAG
1 GGTTTAGGGTTAA
*
29573885 GGTTAAGGGTTAA
1 GGTTTAGGGTTAA
*
29573898 GGGTTAAGGGTTAA
1 -GGTTTAGGGTTAA
*
29573912 GGGTTAGGGTTAA
1 GGTTTAGGGTTAA
** *
29573925 GGTTTAATGTTAT
1 GGTTTAGGGTTAA
29573938 GGTTTAGGGTTTAA
1 GGTTTAGGG-TTAA
*
29573952 GGTTTAAGGTT
1 GGTTTAGGGTT
29573963 TATGTGTATT
Statistics
Matches: 105, Mismatches: 30, Indels: 14
0.70 0.20 0.09
Matches are distributed among these distances:
12 17 0.16
13 58 0.55
14 30 0.29
ACGTcount: A:0.23, C:0.01, G:0.36, T:0.41
Consensus pattern (13 bp):
GGTTTAGGGTTAA
Found at i:29573964 original size:14 final size:14
Alignment explanation
Indices: 29573887--29573960 Score: 82
Period size: 14 Copynumber: 5.4 Consensus size: 14
29573877 ATGGTTAGGG
*
29573887 TTAAGGGTTAAGGG
1 TTAAGGGTTAAGGT
*
29573901 TTAAGGGTTAAGGG
1 TTAAGGGTTAAGGT
29573915 TT-AGGGTTAAGGT
1 TTAAGGGTTAAGGT
* *
29573928 TTAA-TGTTATGGT
1 TTAAGGGTTAAGGT
29573941 TT-AGGGTTTAAGGT
1 TTAAGGG-TTAAGGT
29573955 TTAAGG
1 TTAAGG
29573961 TTTATGTGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.02
13 22 0.43
14 25 0.49
15 3 0.06
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (14 bp):
TTAAGGGTTAAGGT
Found at i:29576841 original size:20 final size:21
Alignment explanation
Indices: 29576818--29576865 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
29576808 TTACATTTAT
29576818 TTTATTTAAATTAA-G-AGTTA
1 TTTATTTAAATTAATGTA-TTA
*
29576838 TTTATTTAATTTAATGTATTA
1 TTTATTTAAATTAATGTATTA
29576859 TTTATTT
1 TTTATTT
29576866 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 11 0.44
22 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTATTTAAATTAATGTATTA
Found at i:29577273 original size:33 final size:32
Alignment explanation
Indices: 29577231--29577299 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
29577221 CTTAATTTGA
29577231 AATTCAAATTAATCATTTTAAAATCCTAACTAG
1 AATTCAAATTAATCATTTTAAAATCCTAA-TAG
* * *
29577264 AATTCAAATTATTCCTTTTCAAATCCTAATAG
1 AATTCAAATTAATCATTTTAAAATCCTAATAG
29577296 AATT
1 AATT
29577300 TATCTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (32 bp):
AATTCAAATTAATCATTTTAAAATCCTAATAG
Found at i:29577738 original size:29 final size:29
Alignment explanation
Indices: 29577677--29577875 Score: 151
Period size: 29 Copynumber: 7.0 Consensus size: 29
29577667 GACCATGCAC
*
29577677 CACTG-TTTTACAGATTTTTATA-TTTCT-T
1 CACTGATTTTTCAGA-TTTTATAGTTT-TGT
* * * *
29577705 CCACTGTTTTTTTAGATTTTACAATTTTGT
1 -CACTGATTTTTCAGATTTTATAGTTTTGT
* * *
29577735 CACTGATTTTCCAAATTTTATAGTTCTGT
1 CACTGATTTTTCAGATTTTATAGTTTTGT
* * *
29577764 CACT-ATTTTTCATA-TTTACAGTTTTTT
1 CACTGATTTTTCAGATTTTATAGTTTTGT
* * *
29577791 CATTG-GTTTTCAGATTTTATAGTTTTGC
1 CACTGATTTTTCAGATTTTATAGTTTTGT
* *
29577819 CATTGGTTTTTCAGATTTTATAGTTTTGT
1 CACTGATTTTTCAGATTTTATAGTTTTGT
* *
29577848 CACT-ATTTTTTCAAATTTTATAATTTTG
1 CACTGA-TTTTTCAGATTTTATAGTTTTG
29577876 CCAATATTCT
Statistics
Matches: 136, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
27 20 0.15
28 23 0.17
29 82 0.60
30 11 0.08
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.56
Consensus pattern (29 bp):
CACTGATTTTTCAGATTTTATAGTTTTGT
Found at i:29578550 original size:110 final size:110
Alignment explanation
Indices: 29578348--29578672 Score: 348
Period size: 110 Copynumber: 3.0 Consensus size: 110
29578338 TGTTTGTTCG
* * * * *
29578348 ATGTGTACTCACAGATTAGCAGATTCCAATTGCGACTATATGAATGGAGCATCCACAATTTCCTC
1 ATGTGTACTCATAGATTAGCAGATTCCAACTGTGACTATATGAATAGAGCATCCACGATTTCCTC
* * * * * * ***
29578413 TGACAGCTCTTATATACGAGAGATTGTGGATCCTCGACCATTTTG
66 TGACGGCTTTTATATGCGAGGGGTTGTGGATCCTCAACCATTCCA
* * * * *
29578458 TTGTGTATTCATAGATTAGCAAATTCCAACTGTGACTATATAAACT-GAGCATCCATGATTTCCT
1 ATGTGTACTCATAGATTAGCAGATTCCAACTGTGACTATATGAA-TAGAGCATCCACGATTTCCT
* * *
29578522 CTAACGGCTTTTATGTGCGAGGGGTTGTGGATCCTTAACCATTCCA
65 CTGACGGCTTTTATATGCGAGGGGTTGTGGATCCTCAACCATTCCA
* * * * * * *
29578568 ATGTGTACTCATAAATTAACAGATTCCAGCTGTGACTATATGAATAGAGTATCTACGATTTTCTT
1 ATGTGTACTCATAGATTAGCAGATTCCAACTGTGACTATATGAATAGAGCATCCACGATTTCCTC
*
29578633 TGACAGG-TTTTATTTGCGAGGGGTTGTGGATCCTCAACCA
66 TGAC-GGCTTTTATATGCGAGGGGTTGTGGATCCTCAACCA
29578673 ATCGGCAACT
Statistics
Matches: 176, Mismatches: 36, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
109 1 0.01
110 172 0.98
111 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (110 bp):
ATGTGTACTCATAGATTAGCAGATTCCAACTGTGACTATATGAATAGAGCATCCACGATTTCCTC
TGACGGCTTTTATATGCGAGGGGTTGTGGATCCTCAACCATTCCA
Found at i:29580417 original size:12 final size:12
Alignment explanation
Indices: 29580400--29580432 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
29580390 AACTAAGCCC
29580400 ATTTTAAAATTT
1 ATTTTAAAATTT
29580412 ATTTTAAAATTT
1 ATTTTAAAATTT
*
29580424 ATTATAAAA
1 ATTTTAAAA
29580433 ATTAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTT
Found at i:29582107 original size:29 final size:28
Alignment explanation
Indices: 29582074--29582389 Score: 179
Period size: 29 Copynumber: 10.8 Consensus size: 28
29582064 CCCTAAATTA
*
29582074 TCCAAAATTATATTTTTACCCTCAAACTT
1 TCCAAAATTACATTTTTACCC-CAAACTT
** * * **
29582103 TCCAAAATCCCATTTTAACCCCGATTTT
1 TCCAAAATTACATTTTTACCCCAAACTT
29582131 TCCAAAAATTACATTTTTACCCCCAAACTT
1 TCC-AAAATTACATTTTTA-CCCCAAACTT
* * * **
29582161 TCTAAAATTCCATTTTTAACCCTAATTTTT
1 TCCAAAATTACATTTTT-ACCCCAA-ACTT
* * *
29582191 TCCAAAAAGTATATTTTTACCCCTGAACTT
1 TCC-AAAATTACATTTTTACCCC-AAACTT
*
29582221 TCCAAAATTCCATTTTTGACCCCAAAACTT
1 TCCAAAATTACATTTTT-ACCCC-AAACTT
* * *
29582251 TCAAAAATTACCA-TTTTACCCCAGAAATG
1 TCCAAAATTA-CATTTTTACCCCA-AACTT
* **
29582280 TCCAAAAATTCCATTTTTGACCTTGAAACTT
1 TCC-AAAATTACATTTTT-ACC-CCAAACTT
** * *
29582311 TTGAAAATTACCA-TTTTACCCTCGAA-TG
1 TCCAAAATTA-CATTTTTACCC-CAAACTT
* * *
29582339 TCCAAAAATTCCATTTTTGATCCCAAACCT
1 TCC-AAAATTACATTTTT-ACCCCAAACTT
*
29582369 TCCAAAATTACCTTTTTACCC
1 TCCAAAATTACATTTTTACCC
29582390 TCGAATGCCC
Statistics
Matches: 210, Mismatches: 58, Indels: 39
0.68 0.19 0.13
Matches are distributed among these distances:
28 15 0.07
29 100 0.48
30 71 0.34
31 23 0.11
32 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (28 bp):
TCCAAAATTACATTTTTACCCCAAACTT
Found at i:29582211 original size:60 final size:59
Alignment explanation
Indices: 29582077--29582297 Score: 234
Period size: 60 Copynumber: 3.7 Consensus size: 59
29582067 TAAATTATCC
* * *
29582077 AAAATTATATTTTTACCCTCAAACTTTCCAAAATCCCA-TTTTAACCCCGATTTTTCCA
1 AAAATTATATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTTTCCA
* * *
29582135 AAAATTACATTTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCTAATTTTTTCCA
1 AAAATTATATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAA-TTTTTCCA
* ** * **
29582195 AAAAGTATATTTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCCCAAAACTTT-CA
1 AAAATTATATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC-AATTTTTCCA
* * *
29582254 AAAATTACCA-TTTTA-CCCCAGAAATGTCCAAAAATTCCATTTTT
1 AAAATTA-TATTTTTACCCCCA-AACTTTCC-AAAATTCCATTTTT
29582298 GACCTTGAAA
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
58 37 0.27
59 29 0.21
60 68 0.50
61 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTATATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTTTCCA
Found at i:29582284 original size:59 final size:56
Alignment explanation
Indices: 29582205--29582581 Score: 351
Period size: 59 Copynumber: 6.4 Consensus size: 56
29582195 AAAAGTATAT
*
29582205 TTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCA
1 TTTTACCCC-GAA-TGTCCAAAATTCCATTTTTGACCCC-AAACTTTCAAAAATTACCA
** **
29582264 TTTTACCCCAGAAATGTCCAAAAATTCCATTTTTGACCTTGAAACTTTTGAAAATTACCA
1 TTTTACCCC-G-AATGTCC-AAAATTCCATTTTTGACC-CCAAACTTTCAAAAATTACCA
* * * *
29582324 TTTTACCCTCGAATGTCCAAAAATTCCATTTTTGATCCCAAACCTTCCAAAATTACCT
1 TTTTACCC-CGAATGTCC-AAAATTCCATTTTTGACCCCAAACTTTCAAAAATTACCA
* * * * *
29582382 TTTTACCCTCGAATGCCCAAAAACTCCATTTTTGATCCCGAACCTTCTAAAAATTACCA
1 TTTTACCC-CGAATGTCC-AAAATTCCATTTTTGACCCCAAACTTTC-AAAAATTACCA
* * * * * *
29582441 TTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCCCGAACCTTCCAAAAATTACCA
1 TTTTACCC-CGAATGTC-CAAAATTCCATTTTTGA-CCCCAAACTTTCAAAAATTACCA
* * * *
29582500 TTTTACCCCAAGATGTCTAAAAATTCCATTTTTGACCCCAAACCTTT-TAAAATTATCA
1 TTTTACCCCGA-ATGTC-CAAAATTCCATTTTTGACCCCAAA-CTTTCAAAAATTACCA
*
29582558 TTTTACCCCTGAGTGTCCAAAATT
1 TTTTACCCC-GAATGTCCAAAATT
29582582 ATCGTTTTTC
Statistics
Matches: 270, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
57 6 0.02
58 88 0.33
59 123 0.46
60 52 0.19
61 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (56 bp):
TTTTACCCCGAATGTCCAAAATTCCATTTTTGACCCCAAACTTTCAAAAATTACCA
Found at i:29582447 original size:117 final size:114
Alignment explanation
Indices: 29582224--29582579 Score: 426
Period size: 117 Copynumber: 3.0 Consensus size: 114
29582214 TGAACTTTCC
* * *
29582224 AAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAAATGTCCAAAAAT
1 AAAATTCCATTTTTGATCCC-AAACCTTCCAAAATTACCATTTTACCCC-G-AATGTCCAAAAAT
* * *
29582289 TCCATTTTTGACCTTGAAACTTTTGAAAATTACCATTTTACCCTCGAATGTCCA
63 TCCATTTTTGACC-CG-AACCTTTAAAAATTACCATTTTACCCTCGAATGTCCA
* * *
29582343 AAAATTCCATTTTTGATCCCAAACCTTCCAAAATTACCTTTTTACCCTCGAATGCCCAAAAACTC
1 AAAATTCCATTTTTGATCCCAAACCTTCCAAAATTACCATTTTACCC-CGAATGTCCAAAAATTC
*
29582408 CATTTTTGATCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAATGTCTA
65 CATTTTTGA-CCCGAACCTT-TAAAAATTACCATTTTACCCTCGAATGTCCA
* * * * *
29582460 AAAACTCCATTTTTTATCCCGAACCTTCCAAAAATTACCATTTTACCCCAAGATGTCTAAAAATT
1 AAAATTCCATTTTTGATCCCAAACCTTCC-AAAATTACCATTTTACCCCGA-ATGTCCAAAAATT
* * * *
29582525 CCATTTTTGACCCCAAACCTTTTAAAATTATCATTTTACCC-CTGAGTGTCCA
64 CCATTTTTGA-CCCGAACCTTTAAAAATTACCATTTTACCCTC-GAATGTCCA
29582577 AAA
1 AAA
29582580 TTATCGTTTT
Statistics
Matches: 207, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
116 6 0.03
117 108 0.52
118 73 0.35
119 20 0.10
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (114 bp):
AAAATTCCATTTTTGATCCCAAACCTTCCAAAATTACCATTTTACCCCGAATGTCCAAAAATTCC
ATTTTTGACCCGAACCTTTAAAAATTACCATTTTACCCTCGAATGTCCA
Found at i:29582473 original size:29 final size:28
Alignment explanation
Indices: 29582224--29582538 Score: 139
Period size: 29 Copynumber: 10.7 Consensus size: 28
29582214 TGAACTTTCC
* *
29582224 AAAATTCCATTTTTGACCCCAAAACTTTC-A
1 AAAATTCCATTTTT-ACCCC-GAA-TGTCTA
*
29582254 AAAATTACCA-TTTTACCCCAGAAATGTCCA
1 AAAATT-CCATTTTTACCCC-G-AATGTCTA
** * *
29582284 AAAATTCCATTTTTGACCTTGAAACT-TTTG
1 AAAATTCCATTTTT-ACCCCG-AA-TGTCTA
*
29582314 AAAATTACCA-TTTTACCCTCGAATGTCCA
1 AAAATT-CCATTTTTACCC-CGAATGTCTA
* * *
29582343 AAAATTCCATTTTTGATCCCAAACCT-TC-C
1 AAAATTCCATTTTT-ACCCCGAA--TGTCTA
* *
29582372 AAAATTACC-TTTTTACCCTCGAATGCCCA
1 AAAATT-CCATTTTTACCC-CGAATGTCTA
* *
29582401 AAAACTCCATTTTTGATCCCGAACCT-TCTA
1 AAAATTCCATTTTT-ACCCCGAA--TGTCTA
29582431 AAAATTACCA-TTTTACCCTCGAATGTCTA
1 AAAATT-CCATTTTTACCC-CGAATGTCTA
* * *
29582460 AAAACTCCATTTTTTATCCCGAACCT-TCCA
1 AAAATTCCA-TTTTTACCCCGAA--TGTCTA
*
29582490 AAAATTACCA-TTTTACCCCAAGATGTCTA
1 AAAATT-CCATTTTTACCCCGA-ATGTCTA
29582519 AAAATTCCATTTTTGACCCC
1 AAAATTCCATTTTT-ACCCC
29582539 AAACCTTTTA
Statistics
Matches: 220, Mismatches: 32, Indels: 66
0.69 0.10 0.21
Matches are distributed among these distances:
27 1 0.00
28 18 0.08
29 97 0.44
30 85 0.39
31 19 0.09
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGAATGTCTA
Found at i:29582529 original size:176 final size:177
Alignment explanation
Indices: 29582224--29582565 Score: 442
Period size: 176 Copynumber: 1.9 Consensus size: 177
29582214 TGAACTTTCC
* *
29582224 AAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAAATGTCCAAAAAT
1 AAAACTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAAATGTCCAAAAAC
* *** *
29582289 TCCATTTTTGACCTTGAAACTTTTGAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATT
66 TCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATT
* *
29582354 TTTGATCCCAAACCTTCCAAAATTACCTTTTTACCCTCGAATGCCCA
131 TTTGACCCCAAACCTTCCAAAATTACCATTTTACCCTCGAATGCCCA
* * * *
29582401 AAAACTCCATTTTTGATCCC-GAACCTTCTAAAAATTACCATTTTACCCTC-G-AATGTCTAAAA
1 AAAACTCCATTTTTGACCCCAAAACTTTC-AAAAATTACCATTTTACCC-CAGAAATGTCCAAAA
* * *
29582463 ACTCCATTTTTTATCC-CGAACCTTCCAAAAATTACCATTTTACCC-CAAGATGTCTAAAAATTC
64 ACTCCATTTTTGA-CCTCGAAACTTCCAAAAATTACCATTTTACCCTCAA-ATGTCCAAAAATTC
** *
29582526 CATTTTTGACCCCAAACCTTTTAAAATTATCATTTTACCC
127 CATTTTTGACCCCAAACCTTCCAAAATTACCATTTTACCC
29582566 CTGAGTGTCC
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
175 2 0.01
176 99 0.70
177 40 0.28
178 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34
Consensus pattern (177 bp):
AAAACTCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCCAGAAATGTCCAAAAAC
TCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATT
TTTGACCCCAAACCTTCCAAAATTACCATTTTACCCTCGAATGCCCA
Found at i:29586989 original size:20 final size:19
Alignment explanation
Indices: 29586945--29586991 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
29586935 TATCTATTTA
*
29586945 TTATTTATATGTAAGTTTT
1 TTATTTTTATGTAAGTTTT
* *
29586964 TT-TTTTTATTTAATTTTGT
1 TTATTTTTATGTAAGTTT-T
29586983 TTATTTTTA
1 TTATTTTTA
29586992 GGTATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 12 0.52
19 5 0.22
20 6 0.26
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
TTATTTTTATGTAAGTTTT
Found at i:29593679 original size:191 final size:193
Alignment explanation
Indices: 29593344--29593734 Score: 653
Period size: 191 Copynumber: 2.0 Consensus size: 193
29593334 CATTATCGTC
* *
29593344 TTTTCATTTCAAGACTTGCTCTTTATAGGCTTTGTTTATTGTAAAATTAGAATGAAAGAAGATTT
1 TTTTCAGTTCAAGACTTGCTCTTTATAGGCTTTGTTTATTGTAAAATTAGAATCAAAGAAGATTT
* *
29593409 TTCAGAAAGGTCTTAAAGTGAAAAGAGATTTGAAATAACATATTTTATAATTTAAACAATTTTCT
66 TTCAGAAAGGTCTTAAAGTGAAAAGAGATTTGAAATAAAATACTTTATAATTTAAACAATTTTCT
*
29593474 TTGATGCCAAAGAATTGTTAAAATGCTA-TTCAAAATTTCCATGAACC-AATCATAGTTTCAAT
131 TAGATGCCAAAGAATTGTTAAAATGCTATTTCAAAATTTCCATGAACCAAAT-ATAGTTTCAAT
29593536 TTTTCAGTTCAAGACTTGCTCTTTATAGGC-TTGTTTATTGTAAAATTAGAATCAAAGAAGATTT
1 TTTTCAGTTCAAGACTTGCTCTTTATAGGCTTTGTTTATTGTAAAATTAGAATCAAAGAAGATTT
*
29593600 TTCAGGAAGGTCTTAAAGTGAAAAGAGATTTGAAATAAAATACTTTATAATTTAAACAATTTTCT
66 TTCAGAAAGGTCTTAAAGTGAAAAGAGATTTGAAATAAAATACTTTATAATTTAAACAATTTTCT
* * *
29593665 TAGATGCTAAAGAATTGTTAAAATGCTATTCTTCAAATTTTCCTTGAACCAAATATAGTTTCAAT
131 TAGATGCCAAAGAATTGTTAAAATGCTA-T-TTCAAAATTTCCATGAACCAAATATAGTTTCAAT
29593730 TTTTC
1 TTTTC
29593735 TGGGTTCATC
Statistics
Matches: 186, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
191 121 0.65
192 29 0.16
194 33 0.18
195 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (193 bp):
TTTTCAGTTCAAGACTTGCTCTTTATAGGCTTTGTTTATTGTAAAATTAGAATCAAAGAAGATTT
TTCAGAAAGGTCTTAAAGTGAAAAGAGATTTGAAATAAAATACTTTATAATTTAAACAATTTTCT
TAGATGCCAAAGAATTGTTAAAATGCTATTTCAAAATTTCCATGAACCAAATATAGTTTCAAT
Found at i:29600062 original size:52 final size:52
Alignment explanation
Indices: 29600003--29600107 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
29599993 TGGCATCAAA
*
29600003 ATGAAAACTAGAACATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGT
1 ATGAAAACTAGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGT
* * *
29600055 ATGAAAACTAGAAAATTTCGAACTCCTTTGCTATCAAGTTTATAGGATGTGT
1 ATGAAAACTAGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGT
29600107 A
1 A
29600108 CCTCAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (52 bp):
ATGAAAACTAGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGT
Found at i:29600120 original size:52 final size:51
Alignment explanation
Indices: 29600006--29600120 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 51
29599996 CATCAAAATG
* *
29600006 AAAACTAGAACATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGTATG
1 AAAAC-AGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGTATC
* * *
29600058 AAAACTAGAAAATTTCGAACTCCTTTGCTATCAAGTTTATAGGATGTGTACCTC
1 AAAAC-AGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGTA--TC
29600112 AAAA-AGAAA
1 AAAACAGAAA
29600121 TCATTCATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 51 0.91
54 5 0.09
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (51 bp):
AAAACAGAAAATTTCAAACTCCTTTGCAATCAAGCTTATAGGATGTGTATC
Found at i:29601116 original size:2 final size:2
Alignment explanation
Indices: 29601109--29601136 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29601099 TATAATTGAT
29601109 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
29601137 GTTTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29613366 original size:37 final size:37
Alignment explanation
Indices: 29613277--29613429 Score: 182
Period size: 37 Copynumber: 4.1 Consensus size: 37
29613267 AATTTTGGTT
* * *
29613277 CAATCTTA-AAGTGCTCATGTGGTGACAGTTTTTGGGCG
1 CAATC-TAGAAGTGCTCATGCGGCGACA-TGTTTGGGCG
* *
29613315 CAATTTAGAGGTGCTCATGCGGCGACATGTTTGGGCG
1 CAATCTAGAAGTGCTCATGCGGCGACATGTTTGGGCG
* **
29613352 TAATCTAGAAGTGCTCATGCGATGACATGTTTGGGCG
1 CAATCTAGAAGTGCTCATGCGGCGACATGTTTGGGCG
* * *
29613389 CAATCTAAAAATGCTCATGCAGCGACATGTTTGGGCG
1 CAATCTAGAAGTGCTCATGCGGCGACATGTTTGGGCG
29613426 CAAT
1 CAAT
29613430 TCTGGATTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
37 78 0.80
38 20 0.20
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (37 bp):
CAATCTAGAAGTGCTCATGCGGCGACATGTTTGGGCG
Found at i:29613367 original size:75 final size:74
Alignment explanation
Indices: 29613285--29613425 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 74
29613275 TTCAATCTTA
* * * * * ** *
29613285 AAGTGCTCATGTGGTGACAGTTTTTGGGCGCAATTTAGAGGTGCTCATGCGGCGACATGTTTGGG
1 AAGTGCTCATGCGATGACA-TGTTTGGGCGCAATCTAAAAATGCTCATGCAGCGACATGTTTGGG
29613350 CGTAATCTAG
65 CGTAATCTAG
29613360 AAGTGCTCATGCGATGACATGTTTGGGCGCAATCTAAAAATGCTCATGCAGCGACATGTTTGGGC
1 AAGTGCTCATGCGATGACATGTTTGGGCGCAATCTAAAAATGCTCATGCAGCGACATGTTTGGGC
29613425 G
66 G
29613426 CAATTCTGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 41 0.71
75 17 0.29
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (74 bp):
AAGTGCTCATGCGATGACATGTTTGGGCGCAATCTAAAAATGCTCATGCAGCGACATGTTTGGGC
GTAATCTAG
Found at i:29615546 original size:18 final size:18
Alignment explanation
Indices: 29615500--29615548 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
29615490 AATCTTATTT
29615500 TATATTTAT-AA-AAAAA
1 TATATTTATAAATAAAAA
*
29615516 TAATCTTTAATAAATAAAAA
1 T-ATATTT-ATAAATAAAAA
29615536 TATATTTATAAAT
1 TATATTTATAAAT
29615549 TTTATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 8 0.30
19 7 0.26
20 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATTTATAAATAAAAA
Found at i:29618925 original size:6 final size:6
Alignment explanation
Indices: 29618899--29618943 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
29618889 TTACATCTGG
*
29618899 AAAAT- AAATTA AAACATA AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAA-ATA AAAATA AAAATA AAAATA AAAATA AAA
29618944 GTGACATGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:29619807 original size:28 final size:28
Alignment explanation
Indices: 29619754--29619807 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
29619744 TAGATTACTT
* *
29619754 TTTTTTATGTTTTATTAATTTGATTCAA
1 TTTTTTAAGTTTTATTAATTTAATTCAA
*
29619782 TTTTTTAAGTTTT-TTATTTTCAATTC
1 TTTTTTAAGTTTTATTAATTT-AATTC
29619808 CGTGTCACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (28 bp):
TTTTTTAAGTTTTATTAATTTAATTCAA
Found at i:29620968 original size:18 final size:17
Alignment explanation
Indices: 29620941--29620984 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
29620931 ATTACTTTTC
*
29620941 AAAAGCATTTTTGGGATA-
1 AAAAGTATTTTT--GATAT
29620959 AAAAGTATTTTTGATAT
1 AAAAGTATTTTTGATAT
29620976 AAAAGTATT
1 AAAAGTATT
29620985 ATTAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 9 0.38
18 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (17 bp):
AAAAGTATTTTTGATAT
Found at i:29622569 original size:12 final size:12
Alignment explanation
Indices: 29622554--29622578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29622544 TAACCATTTA
29622554 ACTAAGGAAGCT
1 ACTAAGGAAGCT
29622566 ACTAAGGAAGCT
1 ACTAAGGAAGCT
29622578 A
1 A
29622579 ATGTGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
ACTAAGGAAGCT
Found at i:29633328 original size:241 final size:241
Alignment explanation
Indices: 29632905--29633634 Score: 1415
Period size: 241 Copynumber: 3.0 Consensus size: 241
29632895 TCAACAAGAT
*
29632905 AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTATAACATCCTAAACAAGTAATCGT
1 AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
29632970 CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
66 CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
29633035 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
131 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
29633100 CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
196 CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
*
29633146 AAATTACTGGCATTATGGTTATTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
1 AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
29633211 CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
66 CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
29633276 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
131 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
*
29633341 CAGTTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
196 CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
29633387 AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
1 AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
*
29633452 CACCGATTTAGGGTCCCAAAGTGTTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
66 CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
29633517 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
131 TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
29633582 CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
196 CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
29633628 AACATTA
1 AA-ATTA
29633635 GCTTTATCGG
Statistics
Matches: 482, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
241 478 0.99
242 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (241 bp):
AAATTACTGGCATTATGGTTGTTATCCACGATTAGCAGCCTGTAACATCCTAAACAAGTAATCGT
CACCGATTTAGGGTCCCAAAGTATTACAAGACATTTTACAATCATTAATAAACTTCTAGCCATTA
TTCAAATATGTATAGGCTATTCACAAGTACATATAAAATCATGCTAATAATCACGTATATTAACT
CAATTTAAGCATACATGGTCATATACAAGCATCACGAACAATATAC
Found at i:29640328 original size:20 final size:19
Alignment explanation
Indices: 29640303--29640413 Score: 107
Period size: 18 Copynumber: 5.5 Consensus size: 19
29640293 TTTATATTGT
29640303 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTAC
* *
29640323 TGTTTTGGTTATTGTTTTTTAT
1 TGTTTTGG-T-GT-TTTTTTAC
29640345 TGTTTTGGTGTTGTTTTTTTTAC
1 TGTTTT-G-G-TG-TTTTTTTAC
*
29640368 TGTTTTGGT-TTTTTTTGC
1 TGTTTTGGTGTTTTTTTAC
*
29640386 TATTTTGGTGTTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
29640405 TGTTTTGGT
1 TGTTTTGGT
29640414 TGCTATTTTG
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
18 16 0.21
19 16 0.21
20 9 0.12
21 3 0.04
22 14 0.18
23 14 0.18
24 4 0.05
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.69
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:29640343 original size:22 final size:22
Alignment explanation
Indices: 29640315--29640414 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
29640305 TTTTGGTGCT
29640315 TTTTTTACTGTTTTGGTTAT-TG
1 TTTTTTACTGTTTTGGTT-TGTG
* *
29640337 TTTTTTATTGTTTTGGTGTTGTT
1 TTTTTTACTGTTTTGGT-TTGTG
29640360 TTTTTTACTGTTTTGG--T-T-
1 TTTTTTACTGTTTTGGTTTGTG
* *
29640378 TTTTTTGCTATTTTGG--TGT-
1 TTTTTTACTGTTTTGGTTTGTG
29640397 TTTTTTACTGTTTTGGTT
1 TTTTTTACTGTTTTGGTT
29640415 GCTATTTTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.23
19 16 0.24
20 1 0.02
22 17 0.26
23 17 0.26
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (22 bp):
TTTTTTACTGTTTTGGTTTGTG
Found at i:29640417 original size:31 final size:31
Alignment explanation
Indices: 29640382--29640442 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
29640372 TTGGTTTTTT
*
29640382 TTGCTATTTTGGTGTTTTTTTACTGTTTTGG
1 TTGCTATTTTGGTGCTTTTTTACTGTTTTGG
29640413 TTGCTATTTTGGTGCTTTTTTACTGTTTTG
1 TTGCTATTTTGGTGCTTTTTTACTGTTTTG
29640443 ATGCTGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.07, C:0.08, G:0.21, T:0.64
Consensus pattern (31 bp):
TTGCTATTTTGGTGCTTTTTTACTGTTTTGG
Found at i:29640422 original size:23 final size:21
Alignment explanation
Indices: 29640303--29640415 Score: 112
Period size: 19 Copynumber: 5.5 Consensus size: 21
29640293 TTTATATTGT
*
29640303 TGTTTTGG-TGCTTTTTTTAC
1 TGTTTTGGTTGTTTTTTTTAC
* *
29640323 TGTTTTGGTTATTGTTTTTTAT
1 TGTTTTGGTTGTT-TTTTTTAC
29640345 TGTTTTGGTGTTGTTTTTTTTAC
1 TGTTTT-G-GTTGTTTTTTTTAC
*
29640368 TGTTTT-G--GTTTTTTTTGC
1 TGTTTTGGTTGTTTTTTTTAC
*
29640386 TATTTTGG-TG-TTTTTTTAC
1 TGTTTTGGTTGTTTTTTTTAC
29640405 TGTTTTGGTTG
1 TGTTTTGGTTG
29640416 CTATTTTGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.19
19 16 0.21
20 12 0.16
21 2 0.03
22 13 0.17
23 14 0.18
24 5 0.06
ACGTcount: A:0.05, C:0.04, G:0.21, T:0.69
Consensus pattern (21 bp):
TGTTTTGGTTGTTTTTTTTAC
Found at i:29640471 original size:24 final size:24
Alignment explanation
Indices: 29640444--29640503 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
29640434 ACTGTTTTGA
*
29640444 TGCTGTTATTTTTGTTGCTATTTT
1 TGCTATTATTTTTGTTGCTATTTT
29640468 TGCTATTATTTTTGTTGCTATTTT
1 TGCTATTATTTTTGTTGCTATTTT
*
29640492 TGTTATTATTTT
1 TGCTATTATTTT
29640504 GCTGTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.12, C:0.07, G:0.13, T:0.68
Consensus pattern (24 bp):
TGCTATTATTTTTGTTGCTATTTT
Found at i:29640501 original size:12 final size:12
Alignment explanation
Indices: 29640449--29640503 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
29640439 TTTGATGCTG
*
29640449 TTATTTTTGTTG
1 TTATTTTTGTTA
* *
29640461 CTATTTTTGCTA
1 TTATTTTTGTTA
*
29640473 TTATTTTTGTTG
1 TTATTTTTGTTA
*
29640485 CTATTTTTGTTA
1 TTATTTTTGTTA
29640497 TTATTTT
1 TTATTTT
29640504 GCTGTTTTGG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (12 bp):
TTATTTTTGTTA
Found at i:29653178 original size:27 final size:27
Alignment explanation
Indices: 29653113--29653178 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
29653103 ATACTCGTTG
*
29653113 ACTCGAGTTGACCAACAAAACTTGTTC
1 ACTCGAGTTGATCAACAAAACTTGTTC
29653140 ACTCGAGTTGATCAACAAAACTTGTTC
1 ACTCGAGTTGATCAACAAAACTTGTTC
29653167 ACTCGAGTTGAT
1 ACTCGAGTTGAT
29653179 TGACCCGACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (27 bp):
ACTCGAGTTGATCAACAAAACTTGTTC
Found at i:29653243 original size:20 final size:19
Alignment explanation
Indices: 29653214--29653289 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
29653204 ACTCGACCCA
* *
29653214 TTGACTTTGATCGTTAGTCG
1 TTGACCTTGATCGTT-GACG
*
29653234 TTGACCTTGATCGTTGACT
1 TTGACCTTGATCGTTGACG
* * *
29653253 TTGACCTTGACCATTGACT
1 TTGACCTTGATCGTTGACG
* *
29653272 TTGACTTTGACCGTTGAC
1 TTGACCTTGATCGTTGAC
29653290 TTTTTTGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 35 0.71
20 14 0.29
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
TTGACCTTGATCGTTGACG
Found at i:29653258 original size:19 final size:19
Alignment explanation
Indices: 29653234--29653292 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
29653224 TCGTTAGTCG
*
29653234 TTGACCTTGATCGTTGACT
1 TTGACCTTGACCGTTGACT
*
29653253 TTGACCTTGACCATTGACT
1 TTGACCTTGACCGTTGACT
*
29653272 TTGACTTTGACCGTTGACT
1 TTGACCTTGACCGTTGACT
29653291 TT
1 TT
29653293 TTTGACCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (19 bp):
TTGACCTTGACCGTTGACT
Found at i:29653290 original size:13 final size:13
Alignment explanation
Indices: 29653232--29653292 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
29653222 GATCGTTAGT
* *
29653232 CGTTGACCTTGAT
1 CGTTGACTTTGAC
29653245 CGTTGACTTTGAC
1 CGTTGACTTTGAC
*
29653258 C-TTGACCATTGA-
1 CGTTGA-CTTTGAC
*
29653270 CTTTGACTTTGAC
1 CGTTGACTTTGAC
29653283 CGTTGACTTT
1 CGTTGACTTT
29653293 TTTGACCAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.25
13 30 0.75
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (13 bp):
CGTTGACTTTGAC
Found at i:29657716 original size:27 final size:27
Alignment explanation
Indices: 29657686--29657781 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 27
29657676 CCAATACTCG
* *
29657686 TTGACCCGAGTTGACCAACACGACCCA
1 TTGACCCAAGTTGACCAACCCGACCCA
* * * *
29657713 TTGACTCGATTTGACCCACCCGACCCA
1 TTGACCCAAGTTGACCAACCCGACCCA
* ***
29657740 TTGACCCAAGTTGACTAACCCGACTTG
1 TTGACCCAAGTTGACCAACCCGACCCA
29657767 TTGACCCAAGTTGAC
1 TTGACCCAAGTTGAC
29657782 TTGACCCATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (27 bp):
TTGACCCAAGTTGACCAACCCGACCCA
Found at i:29657796 original size:13 final size:15
Alignment explanation
Indices: 29657740--29657789 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
29657730 ACCCGACCCA
29657740 TTGACCCAAGTTGAC
1 TTGACCCAAGTTGAC
* * *
29657755 -TAACCCGACTTG--
1 TTGACCCAAGTTGAC
29657767 TTGACCCAAGTTGAC
1 TTGACCCAAGTTGAC
29657782 TTGACCCA
1 TTGACCCA
29657790 TTGACTTTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 9 0.35
14 9 0.35
15 8 0.31
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (15 bp):
TTGACCCAAGTTGAC
Found at i:29660155 original size:55 final size:55
Alignment explanation
Indices: 29660090--29660196 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
29660080 TATACGAGTC
29660090 ACTAATGAAACTAGCATGTTTGTGTTAGTCTATGTTGATGATATTATCATTACAG
1 ACTAATGAAACTAGCATGTTTGTGTTAGTCTATGTTGATGATATTATCATTACAG
* * *
29660145 ACTAATGAAACTAGCATGTTTTTGTTAGTTTATGTTGTTGATATTATCATTA
1 ACTAATGAAACTAGCATGTTTGTGTTAGTCTATGTTGATGATATTATCATTA
29660197 TAGGGAATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (55 bp):
ACTAATGAAACTAGCATGTTTGTGTTAGTCTATGTTGATGATATTATCATTACAG
Found at i:29664397 original size:19 final size:19
Alignment explanation
Indices: 29664375--29664423 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
29664365 TAGAACACAT
29664375 TAAATAAATAA-ACATATGC
1 TAAATAAATAATAC-TATGC
* *
29664394 TAAATATATAATACTATTC
1 TAAATAAATAATACTATGC
29664413 TAATATAAATA
1 TAA-ATAAATA
29664424 TTAATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAATAAATAATACTATGC
Found at i:29664898 original size:18 final size:19
Alignment explanation
Indices: 29664877--29664914 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29664867 GTAAATAATA
29664877 ATATGTAATTATT-ATTAT
1 ATATGTAATTATTAATTAT
*
29664895 ATATGTAATTTTTAATTAT
1 ATATGTAATTATTAATTAT
29664914 A
1 A
29664915 GAAAAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATATGTAATTATTAATTAT
Found at i:29672759 original size:52 final size:52
Alignment explanation
Indices: 29672675--29672912 Score: 343
Period size: 52 Copynumber: 4.6 Consensus size: 52
29672665 TAAATGAAAT
* * *
29672675 AGGTTCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
29672727 AGGTCTGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
29672779 AGGTCCGACGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * *
29672831 AGGTCCAATGACTATGTGTCATCGTAAGTATATGAATTCTTTATGGGTTA-A
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
29672882 AGGTCCGATGACTCTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
29672913 TAAATACACA
Statistics
Matches: 166, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
51 28 0.17
52 138 0.83
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:29675021 original size:28 final size:28
Alignment explanation
Indices: 29674985--29675047 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
29674975 CGTCGAAAAC
*
29674985 ACTAGTTTT-TGAAATGTCAGCCTTTGTG
1 ACTAATTTTGTGAAA-GTCAGCCTTTGTG
* *
29675013 ACTAATTTTGTTAAAGTGAGCCTTTGTG
1 ACTAATTTTGTGAAAGTCAGCCTTTGTG
*
29675041 GCTAATT
1 ACTAATT
29675048 CTATTAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (28 bp):
ACTAATTTTGTGAAAGTCAGCCTTTGTG
Found at i:29675054 original size:28 final size:29
Alignment explanation
Indices: 29675003--29675107 Score: 113
Period size: 29 Copynumber: 3.7 Consensus size: 29
29674993 TTGAAATGTC
* * *
29675003 AGCCTTTGTGACTAATTTTGTT-AAAGTG
1 AGCCTTTGTGGCTAATTCTATTAAAAGTG
*
29675031 AGCCTTTGTGGCTAATTCTATTAAAAGTT
1 AGCCTTTGTGGCTAATTCTATTAAAAGTG
* * * *
29675060 AGCCATTGTGACTGATTCTGTTAAAAGTG
1 AGCCTTTGTGGCTAATTCTATTAAAAGTG
* *
29675089 AGCATTTGTCGCTAATTCT
1 AGCCTTTGTGGCTAATTCT
29675108 GATAATGGAG
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 19 0.31
29 43 0.69
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (29 bp):
AGCCTTTGTGGCTAATTCTATTAAAAGTG
Found at i:29675269 original size:31 final size:31
Alignment explanation
Indices: 29675226--29675300 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 31
29675216 TGGAAAATCT
** *
29675226 TTTGTGGCTATCTTTTTTTTATAAGGAGGCC
1 TTTGTGGCTATCTTTTCGTTATAAGGACGCC
*
29675257 TTTGTGGGTATC--TTCGTTATAAGGACGCC
1 TTTGTGGCTATCTTTTCGTTATAAGGACGCC
29675286 TTTGTGGCTATCTTT
1 TTTGTGGCTATCTTT
29675301 GTTTGAGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 25 0.68
31 12 0.32
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.47
Consensus pattern (31 bp):
TTTGTGGCTATCTTTTCGTTATAAGGACGCC
Found at i:29678242 original size:233 final size:231
Alignment explanation
Indices: 29677821--29678276 Score: 795
Period size: 233 Copynumber: 2.0 Consensus size: 231
29677811 AATATTGAAC
* *
29677821 AGAAAGATAAATAATATTTAGTTGAGAAGGGTTAGAATTGCCTAACAACAAAACATGGGAAGATT
1 AGAAAGATAAATAATATTTAGTGGAGAAGGGTAAGAATTGCCTAACAACAAAACATGGGAAGATT
29677886 TGAAGAAAACTGGTATTAATATAATTTGAACTAAATTTTGAAATTTTTATGGTAAAAAAATTCAT
66 TGAAGAAAACTGGTATTAATATAATTTGAACTAAATTTTGAAATTTTTATGGTAAAAAAATTCAT
*
29677951 TAAGCCTAGTTTCAAAAACAATAAGCAGATCTTTATTTCAATTTCTGTAGGTCAAGATAAAAATA
131 TAAGCCTAGTTTCAAAAACAATAAGCAGATCTTTATTTCAATTTCTGTAGGCCAAGATAAAAATA
29678016 ATTTAGTGATTGCTACTCAAGTAGACAATCTTGTAT
196 ATTTAGTGATTGCTACTCAAGTAGACAATCTTGTAT
* **
29678052 AGAAAGATAAATAATATTTTGTGGAGAAGGGTAAGAATTGCCTAACAGGAAAACATGGGAAGATT
1 AGAAAGATAAATAATATTTAGTGGAGAAGGGTAAGAATTGCCTAACAACAAAACATGGGAAGATT
* *
29678117 TGAAGAAAAACTGGTATTAATCTAATTTGAACTAAATTTTGAAATTTTTTATGGTAAAAAATTTC
66 TGAAG-AAAACTGGTATTAATATAATTTGAACTAAATTTTGAAA-TTTTTATGGTAAAAAAATTC
* * *
29678182 ATTAAGCCTAGTTTCAAAAACAATAAGTAGCTTTTTATTTCAATTTCTGTAGGCCAAGATAAAAA
129 ATTAAGCCTAGTTTCAAAAACAATAAGCAGATCTTTATTTCAATTTCTGTAGGCCAAGATAAAAA
29678247 TAATTTAGTGATTGCTACTCAAGTAGACAA
194 TAATTTAGTGATTGCTACTCAAGTAGACAA
29678277 CCTTATTAAT
Statistics
Matches: 212, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
231 65 0.31
232 37 0.17
233 110 0.52
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (231 bp):
AGAAAGATAAATAATATTTAGTGGAGAAGGGTAAGAATTGCCTAACAACAAAACATGGGAAGATT
TGAAGAAAACTGGTATTAATATAATTTGAACTAAATTTTGAAATTTTTATGGTAAAAAAATTCAT
TAAGCCTAGTTTCAAAAACAATAAGCAGATCTTTATTTCAATTTCTGTAGGCCAAGATAAAAATA
ATTTAGTGATTGCTACTCAAGTAGACAATCTTGTAT
Found at i:29685526 original size:18 final size:18
Alignment explanation
Indices: 29685494--29685545 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
29685484 CTGGGATGAG
29685494 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
29685510 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
29685528 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
29685546 TAACTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:29685697 original size:15 final size:15
Alignment explanation
Indices: 29685677--29685722 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29685667 ACAAAACGAT
29685677 AACATAAATGACTAA
1 AACATAAATGACTAA
* *
29685692 AACATAACAT--TTCA
1 AACATAA-ATGACTAA
29685706 AACATAAATGACTAA
1 AACATAAATGACTAA
29685721 AA
1 AA
29685723 TGCAATCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.22
Consensus pattern (15 bp):
AACATAAATGACTAA
Found at i:29687129 original size:16 final size:17
Alignment explanation
Indices: 29687098--29687131 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29687088 ATATTTTTTT
29687098 AAATAAAAATATTTAAA
1 AAATAAAAATATTTAAA
*
29687115 AAATTAAAA-ATTTAAA
1 AAATAAAAATATTTAAA
29687131 A
1 A
29687132 CAACCCAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAATATTTAAA
Found at i:29690157 original size:22 final size:22
Alignment explanation
Indices: 29690132--29690176 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29690122 TTTATTGTAC
* *
29690132 TTAAG-TATGTTTAGTTGCATTT
1 TTAAGATAT-TTTAATTACATTT
29690154 TTAAGATATTTTAATTACATTT
1 TTAAGATATTTTAATTACATTT
29690176 T
1 T
29690177 GCACATTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (22 bp):
TTAAGATATTTTAATTACATTT
Found at i:29691398 original size:28 final size:28
Alignment explanation
Indices: 29691299--29691400 Score: 120
Period size: 28 Copynumber: 3.7 Consensus size: 28
29691289 TATTCGTAAA
* *
29691299 TTTT-CCATCACA-TTATTTGTTTATTT
1 TTTTGCCATAACATTTATTTCTTTATTT
* *
29691325 GTTTGCCATAACATTTACTTCTTTATTT
1 TTTTGCCATAACATTTATTTCTTTATTT
29691353 GTTTT-CCATAACATTTATTTCTTTATTT
1 -TTTTGCCATAACATTTATTTCTTTATTT
* *
29691381 TTTTGCCGTAATATTTATTT
1 TTTTGCCATAACATTTATTT
29691401 GTTAATAACA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.05
27 11 0.17
28 47 0.73
29 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTTGCCATAACATTTATTTCTTTATTT
Found at i:29697155 original size:38 final size:38
Alignment explanation
Indices: 29697104--29697182 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
29697094 TTTAATAGAG
29697104 TCCATTTTAGATCCGGATTAGGGTATGACTTCGATATA
1 TCCATTTTAGATCCGGATTAGGGTATGACTTCGATATA
29697142 TCCATTTTAGATCCGGATTAGGGTATGACTTCGATATA
1 TCCATTTTAGATCCGGATTAGGGTATGACTTCGATATA
29697180 TCC
1 TCC
29697183 CAATGTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (38 bp):
TCCATTTTAGATCCGGATTAGGGTATGACTTCGATATA
Done.