Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 134 of 438
Found at i:39873542 original size:23 final size:24
Alignment explanation
Indices: 39873504--39873548 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
39873494 TTTGCTCTTC
*
39873504 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTAGTCTTACCTTTT
39873528 TAGCAT-AACTAGTCTTACCTT
1 TAGCATGAACTAGTCTTACCTT
39873549 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTAGTCTTACCTTTT
Found at i:39873803 original size:55 final size:54
Alignment explanation
Indices: 39873674--39873871 Score: 210
Period size: 55 Copynumber: 3.7 Consensus size: 54
39873664 AACTTACTAT
*
39873674 TGCCATGTCTTGACATTGTCTTACATG-GTATCCTTGCCTTATGAACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGAGTATCCTTGCCTTATGAACTCACCAA
* * * *
39873727 TGCCATGCCTTGGCATGGTCTTACATGAG-A-CCTTTGCCTTATAGTAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGAGTATCC-TTGCCTTAT-G-AACTCACCAA
* * *
39873782 TGCCATGTCTTGACATGGTCTTACATGA-TTTCCTTGCCTTA-GAAACCTTACGAA
1 TGCCATGTCTTGACATGGTCTTACATGAGTATCCTTGCCTTATG-AA-CTCACCAA
* *
39873836 TTGCCATGCCTTGGCATGGTCTTACATG-GTATCCTT
1 -TGCCATGTCTTGACATGGTCTTACATGAGTATCCTT
39873872 AAACCCTAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
52 2 0.02
53 37 0.30
54 8 0.07
55 73 0.60
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGTCTTGACATGGTCTTACATGAGTATCCTTGCCTTATGAACTCACCAA
Found at i:39888008 original size:33 final size:34
Alignment explanation
Indices: 39887966--39888071 Score: 142
Period size: 40 Copynumber: 3.0 Consensus size: 34
39887956 GTGGAATTGT
*
39887966 ATCCGGGCTTAAAGACCCGCAAGCTTCGTGCTG-
1 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGA
39887999 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTA
1 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCT-G----A
39888038 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTG
1 -ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTG
39888072 GAATGACATC
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
33 31 0.48
34 1 0.02
39 1 0.02
40 32 0.49
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (34 bp):
ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGA
Found at i:39888101 original size:39 final size:40
Alignment explanation
Indices: 39887999--39888102 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
39887989 CTTCGTGCTG
* *
39887999 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTAT
1 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATGAC
39888039 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATGAC
1 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATGAC
* *
39888079 ATCCGGG-TTAAAAACCTGCAGGCT
1 ATCCGGGCTTAAAGACCCGCAGGCT
39888103 GTGCTAGATA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATGAC
Found at i:39895074 original size:29 final size:28
Alignment explanation
Indices: 39895020--39895074 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
39895010 ACGGGCAACC
*
39895020 ACACGGGTGTGTCTAGGCCGTGTGAAGG
1 ACACGGGCGTGTCTAGGCCGTGTGAAGG
*
39895048 ACACGGGCGTGTGCTTGGCCGTGTGAA
1 ACACGGGCGTGT-CTAGGCCGTGTGAA
39895075 AACCCCTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (28 bp):
ACACGGGCGTGTCTAGGCCGTGTGAAGG
Found at i:39904139 original size:29 final size:29
Alignment explanation
Indices: 39904068--39904163 Score: 142
Period size: 29 Copynumber: 3.3 Consensus size: 29
39904058 AAGTCCACAA
* *
39904068 ACATACATATGGCCCACTAGGCCC-AAT-
1 ACATTCATATGGCCCATTAGGCCCAAATC
39904095 ATCATTCATATGGCCCATTAGGCCCAAATC
1 A-CATTCATATGGCCCATTAGGCCCAAATC
*
39904125 ACATTCATACGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
39904154 ACATTCATAT
1 ACATTCATAT
39904164 ACATACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.02
28 21 0.34
29 39 0.63
30 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.24
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:39904823 original size:29 final size:29
Alignment explanation
Indices: 39904781--39904876 Score: 133
Period size: 29 Copynumber: 3.3 Consensus size: 29
39904771 GAAAGCATGT
39904781 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39904810 ATATGAATGTGATTTGGGACTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
39904839 ATATGAA--TAATATTGGGCCTAGTGGGCC
1 ATATGAATGTGAT-TTGGGCCTAATGGGCC
*
39904867 ATATGCATGT
1 ATATGAATGT
39904877 TTGTAGACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 20 0.34
29 35 0.59
30 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:39909087 original size:16 final size:16
Alignment explanation
Indices: 39909068--39909098 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39909058 CGAAATGCCG
39909068 AAATGCTAAAAAGCTT
1 AAATGCTAAAAAGCTT
*
39909084 AAATGCTGAAAAGCT
1 AAATGCTAAAAAGCT
39909099 GAAAGCTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (16 bp):
AAATGCTAAAAAGCTT
Found at i:39909355 original size:29 final size:29
Alignment explanation
Indices: 39909312--39909407 Score: 165
Period size: 29 Copynumber: 3.3 Consensus size: 29
39909302 GAAAGCATGT
*
39909312 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
* *
39909341 GTATGAATGTGATTTGGGCCTAATAGGTC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
39909370 ATATGAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATAGGCC
39909399 ATATGAATG
1 ATATGAATG
39909408 ATATTGGGCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.32
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATAGGCC
Found at i:39916082 original size:48 final size:47
Alignment explanation
Indices: 39916007--39916109 Score: 116
Period size: 48 Copynumber: 2.2 Consensus size: 47
39915997 TGTGTGTTAA
* * * * *
39916007 TGTAAGACCGTGTTAGAATATGGCATCGGCCACATTATGAGAGCTAG
1 TGTAAGACCATGTTAGAACATGGCATCGACAACATTATGAGAGCCAG
* **
39916054 TGTAAGACCATGTTTGAAACATGGCATCGACAATGTTATGAGAGCCAG
1 TGTAAGACCATGTTAG-AACATGGCATCGACAACATTATGAGAGCCAG
*
39916102 GGTAAGAC
1 TGTAAGAC
39916110 TCCGTCTGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 14 0.30
48 32 0.70
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (47 bp):
TGTAAGACCATGTTAGAACATGGCATCGACAACATTATGAGAGCCAG
Found at i:39916200 original size:48 final size:48
Alignment explanation
Indices: 39916093--39916227 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 48
39916083 ACAATGTTAT
* * * *
39916093 GAGAGCCAGGGTAAGACTC-CGTCTGGGACATGGTATCGGCATTGAGAC
1 GAGAGCCAGTGTAAGAC-CATGTCTGGGACATGGTATCGGCATCGACAC
* * * *
39916141 GAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGCCTCGACAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGGCATCGACAC
*
39916189 GTA-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 G-AGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGG
39916228 TAATTTACCC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
47 1 0.01
48 72 0.97
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.21
Consensus pattern (48 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGGCATCGACAC
Found at i:39928749 original size:40 final size:40
Alignment explanation
Indices: 39928704--39928871 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
39928694 CGGAATATAA
39928704 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
39928744 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
39928784 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
39928824 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
39928864 CCGGATAT
1 CCGGATAT
39928872 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:39931168 original size:31 final size:33
Alignment explanation
Indices: 39931133--39931196 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
39931123 AGCAGCGGGT
39931133 ACTGGGCC-AAG-CCCTTTTCAGA-ATACAGTAA
1 ACTGGGCCTAAGCCCCTTTTCAGATA-ACAGTAA
*
39931164 ACTGGGCCTCAGCCCCTTTTCAGATAACAGTAA
1 ACTGGGCCTAAGCCCCTTTTCAGATAACAGTAA
39931197 GGCCCATAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.28
32 2 0.07
33 18 0.62
34 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (33 bp):
ACTGGGCCTAAGCCCCTTTTCAGATAACAGTAA
Found at i:39934404 original size:48 final size:48
Alignment explanation
Indices: 39934270--39934542 Score: 277
Period size: 48 Copynumber: 5.7 Consensus size: 48
39934260 TATGTGTGCT
* * *
39934270 AGTGTAAAACCATGT-TGGAACATGGCATCGGTC-ACATTATAAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CAACATTATGAGAGCC
* *
39934317 AGTGT-AGACCATGTCTGGGACAAGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACATTATGAGAGCC
* * * * * *
39934364 AGTGTAAGACCATATTTGGAACATGGCATCAGTAATATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACATTATGAGAGCC
* ** * * *
39934412 AGAGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-ACATTATGAGAGCC
* ** * *
39934460 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAC-ATTATGAGAGCC
*
39934508 AGTGTAAGACCATGTCTGGGACATGGAATCGGCAA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAA
39934543 TTTACCATTT
Statistics
Matches: 186, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
46 9 0.05
47 38 0.20
48 138 0.74
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACATTATGAGAGCC
Found at i:39936352 original size:40 final size:39
Alignment explanation
Indices: 39936261--39936412 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 39
39936251 ATAAGCATGT
* * * *
39936261 GCACAAATGCCTTTGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATG-CTA
**
39936301 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCGCTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATA-ATGCTA
* * *
39936341 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAA-TGCTA
* * *
39936381 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
39936413 CATTCAATTT
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.02
40 89 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.27
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATGCTA
Found at i:39944325 original size:9 final size:9
Alignment explanation
Indices: 39944313--39944396 Score: 73
Period size: 9 Copynumber: 9.6 Consensus size: 9
39944303 TTTTGGTTAA
39944313 GAATTAACC
1 GAATTAACC
*
39944322 GAATTAAAC
1 GAATTAACC
* *
39944331 AAATTACCC
1 GAATTAACC
39944340 GAATTAACC
1 GAATTAACC
39944349 GAATTAACC
1 GAATTAACC
*
39944358 G-ATTACCC
1 GAATTAACC
* *
39944366 AAATTAACT
1 GAATTAACC
* *
39944375 G-ATTATCT
1 GAATTAACC
*
39944383 GAATTACCC
1 GAATTAACC
39944392 GAATT
1 GAATT
39944397 GAATCGCTAC
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
8 13 0.22
9 46 0.78
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (9 bp):
GAATTAACC
Found at i:39944388 original size:26 final size:27
Alignment explanation
Indices: 39944313--39944396 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 27
39944303 TTTTGGTTAA
* *
39944313 GAATTAACCGAATTAAACAAATTACCC
1 GAATTAACCGAATTAACCGAATTACCC
39944340 GAATTAACCGAATTAACCG-ATTACCC
1 GAATTAACCGAATTAACCGAATTACCC
* * * *
39944366 AAATTAACTG-ATTATCTGAATTACCC
1 GAATTAACCGAATTAACCGAATTACCC
39944392 GAATT
1 GAATT
39944397 GAATCGCTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
25 6 0.12
26 26 0.53
27 17 0.35
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (27 bp):
GAATTAACCGAATTAACCGAATTACCC
Found at i:39944426 original size:17 final size:17
Alignment explanation
Indices: 39944404--39944501 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
39944394 ATTGAATCGC
39944404 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
39944421 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
* * *
39944441 TGCATAACTAAAAATAT
1 TACATAATTAAAAACAT
* * *
39944458 TACATAAGTTTATGAATCAC
1 TACATAA--TTA-AAAACAT
39944478 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
39944495 TACATAA
1 TACATAA
39944502 GTCTTGAAAT
Statistics
Matches: 55, Mismatches: 20, Indels: 12
0.63 0.23 0.14
Matches are distributed among these distances:
17 28 0.51
18 3 0.05
19 2 0.04
20 22 0.40
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:39944436 original size:37 final size:37
Alignment explanation
Indices: 39944395--39944506 Score: 172
Period size: 37 Copynumber: 3.0 Consensus size: 37
39944385 ATTACCCGAA
*
39944395 TTGAATCGCTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* * *
39944432 TTGAATCACTGCATAACTAAAAATATTACATAAGT-T
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
39944468 TATGAATCACTACATAATTAAAAACATTACATAAGTCT
1 T-TGAATCACTACATAATTAAAAACATTACATAAGTCT
39944506 T
1 T
39944507 GAAATTAACA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 2 0.03
37 62 0.94
38 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:39946953 original size:21 final size:21
Alignment explanation
Indices: 39946924--39946982 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
39946914 GCAAGAAAAA
39946924 AATTATATAATAAATTAAAATAC
1 AATT-TATAAT-AATTAAAATAC
39946947 -ATTTATAAT-ATTAAAATAC
1 AATTTATAATAATTAAAATAC
39946966 ATATTTATAAT-ATTAAA
1 A-ATTTATAATAATTAAA
39946983 CAATTTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.29
21 21 0.62
22 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTATAATAATTAAAATAC
Found at i:39946959 original size:19 final size:20
Alignment explanation
Indices: 39946933--39946982 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
39946923 AAATTATATA
39946933 ATAA-ATTAAAATAC-ATTT
1 ATAATATTAAAATACAATTT
39946951 ATAATATTAAAATACATATTT
1 ATAATATTAAAATACA-ATTT
39946972 ATAATATTAAA
1 ATAATATTAAA
39946983 CAATTTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.14
19 10 0.34
21 15 0.52
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATATTAAAATACAATTT
Found at i:39947050 original size:12 final size:11
Alignment explanation
Indices: 39947030--39947063 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39947020 AGAATACTTG
39947030 TTAAATAAAAT
1 TTAAATAAAAT
*
39947041 TTATAATAAAAA
1 TTA-AATAAAAT
39947053 TTAAATAAAAT
1 TTAAATAAAAT
39947064 ATTGGTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TTAAATAAAAT
Found at i:39947646 original size:14 final size:14
Alignment explanation
Indices: 39947627--39947656 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39947617 TTAGTTTTAG
39947627 TAGATTTTTACTTT
1 TAGATTTTTACTTT
*
39947641 TAGATTTTTATTTT
1 TAGATTTTTACTTT
39947655 TA
1 TA
39947657 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (14 bp):
TAGATTTTTACTTT
Found at i:39951322 original size:30 final size:30
Alignment explanation
Indices: 39951286--39951361 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
39951276 TTTCTATTAG
*
39951286 GAAGAGAGAATTTTTATTTTCACCCCAAAA
1 GAAGAGAGAATTTTTATTTTCAACCCAAAA
*
39951316 GAAGAGAGAATTTTTGTTTTCAACCCAAAA
1 GAAGAGAGAATTTTTATTTTCAACCCAAAA
* *
39951346 GGAGAGAAAACTTTTT
1 GAAGAGAGAA-TTTTT
39951362 TCTAGTTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (30 bp):
GAAGAGAGAATTTTTATTTTCAACCCAAAA
Found at i:39970925 original size:49 final size:50
Alignment explanation
Indices: 39970853--39971044 Score: 172
Period size: 50 Copynumber: 3.8 Consensus size: 50
39970843 CGAAGCTATT
* * *
39970853 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATAGTC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCACAATA-TC
* * * * **
39970902 TGGTATATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCACAATATC
** * * * * *
39970952 TAATACACGTATTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCACA-ATATC
* * * *
39971003 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
39971045 TCACAATAGA
Statistics
Matches: 113, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
49 34 0.30
50 41 0.36
51 38 0.34
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCACAATATC
Found at i:39975657 original size:23 final size:22
Alignment explanation
Indices: 39975604--39975659 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
39975594 ATATATGCTC
* * *
39975604 ATAAGAGCTTACTATTCAGCTCG
1 ATAA-AGCTTACCATTCAACTCA
*
39975627 ATAGAGCTTACCATTTCAACTCA
1 ATAAAGCTTACCA-TTCAACTCA
39975650 ATAAAGCTTA
1 ATAAAGCTTA
39975660 TTGTTCATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (22 bp):
ATAAAGCTTACCATTCAACTCA
Found at i:39981117 original size:17 final size:17
Alignment explanation
Indices: 39981095--39981129 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39981085 ATTATGTTTG
39981095 ATAGAAGACTTGATGAA
1 ATAGAAGACTTGATGAA
*
39981112 ATAGAAGGCTTGATGAA
1 ATAGAAGACTTGATGAA
39981129 A
1 A
39981130 AGATTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (17 bp):
ATAGAAGACTTGATGAA
Found at i:39982159 original size:32 final size:32
Alignment explanation
Indices: 39982122--39982182 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
39982112 TTGATAATTG
*
39982122 ATTTTCATTTGGGAAAAGCAAGTGTAATTATA
1 ATTTTCATTTGGGAAAAGCAAATGTAATTATA
39982154 ATTTTCATTTGGGAAAAGCAAATGTAATT
1 ATTTTCATTTGGGAAAAGCAAATGTAATT
39982183 GCTGACACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (32 bp):
ATTTTCATTTGGGAAAAGCAAATGTAATTATA
Found at i:39986184 original size:26 final size:26
Alignment explanation
Indices: 39986134--39986184 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
39986124 TATTTTTGTT
*
39986134 TTAATTATATATTATATTATGTTATG
1 TTAATTATATATTATATAATGTTATG
39986160 TTAATTTATAGTATTAT-TAAT-TTAT
1 TTAA-TTATA-TATTATATAATGTTAT
39986185 AACTTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (26 bp):
TTAATTATATATTATATAATGTTATG
Found at i:39986822 original size:26 final size:27
Alignment explanation
Indices: 39986793--39986844 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
39986783 CTATATTAGT
* *
39986793 TAAATAATAAAA-TAATACAAAGAAAA
1 TAAATAATAAAAGAAAAACAAAGAAAA
*
39986819 TAAATTATAAAAGAAAAACAAAGAAA
1 TAAATAATAAAAGAAAAACAAAGAAA
39986845 CCAAGGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (27 bp):
TAAATAATAAAAGAAAAACAAAGAAAA
Found at i:39987903 original size:12 final size:12
Alignment explanation
Indices: 39987886--39987910 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39987876 GTCGACTACT
39987886 GTTACTGTTACC
1 GTTACTGTTACC
39987898 GTTACTGTTACC
1 GTTACTGTTACC
39987910 G
1 G
39987911 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:39987938 original size:45 final size:45
Alignment explanation
Indices: 39987888--39988000 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
39987878 CGACTACTGT
* *
39987888 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTG-TCGAA
1 TACTGTTACCGTTACTGTTACCAATTCAG-CACTTTGTGTGCT-AAA
* * *
39987933 TACTGTTATCGTTACTATTACAAATTCAGCACTTTGTGTGCTAAA
1 TACTGTTACCGTTACTGTTACCAATTCAGCACTTTGTGTGCTAAA
* *
39987978 TACTATTACTGTTACTGTTACCA
1 TACTGTTACCGTTACTGTTACCA
39988001 TTTCTGATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
45 54 0.96
46 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACCAATTCAGCACTTTGTGTGCTAAA
Found at i:39989263 original size:34 final size:34
Alignment explanation
Indices: 39989220--39989286 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
39989210 CCACACAGGT
39989220 AGAAACACGGGCGTGTGTCTCAACCATGTGTGAC
1 AGAAACACGGGCGTGTGTCTCAACCATGTGTGAC
*
39989254 AGAAACACGGGCGTGTGTCTCAACCGTGTGTGA
1 AGAAACACGGGCGTGTGTCTCAACCATGTGTGA
39989287 TAGATAGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (34 bp):
AGAAACACGGGCGTGTGTCTCAACCATGTGTGAC
Found at i:39993822 original size:40 final size:40
Alignment explanation
Indices: 39993792--39994023 Score: 365
Period size: 40 Copynumber: 5.8 Consensus size: 40
39993782 CCAGCATGAT
* * *
39993792 TGCTCTTCGGGACCTAGCCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
39993832 TGCTCTTCGGAACTTAGCCCGAATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
39993872 TGCTTTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* * *
39993912 TGCTCTTCGAAACTTAGCCCGGATACGTCTCTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
39993952 TGCTCTTCGGAACTTAGCCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
39993992 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGAACTTAGCCCGGATACATCACT
39994024 CTCAATTCTC
Statistics
Matches: 174, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 174 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:39993881 original size:80 final size:80
Alignment explanation
Indices: 39993766--39994023 Score: 372
Period size: 80 Copynumber: 3.2 Consensus size: 80
39993756 AGGCACGAAG
* * * * *
39993766 GCCCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATACGTCACTAGCACGA
1 GCCCGAATACA--TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGA
39993831 ATGCTCTTCGGAACTTA
64 ATGCTCTTCGGAACTTA
*
39993848 GCCCGAATACATCACTAGCATGAATGCTTTTCGGAACTTAGCCCGGATACATCACTAGCACGAAT
1 GCCCGAATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAAT
*
39993913 GCTCTTCGAAACTTA
66 GCTCTTCGGAACTTA
* * * * *
39993928 GCCCGGATACGTCTCTAGCACGAATGCTCTTCGGAACTTAGCCCAGATACATCACTAGCACGAAT
1 GCCCGAATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAAT
*
39993993 GCTCTTCGGGACTTA
66 GCTCTTCGGAACTTA
*
39994008 GCCCGGATACATCACT
1 GCCCGAATACATCACT
39994024 CTCAATTCTC
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 148 0.93
82 11 0.07
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (80 bp):
GCCCGAATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAAT
GCTCTTCGGAACTTA
Found at i:40002223 original size:24 final size:24
Alignment explanation
Indices: 40002196--40002241 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
40002186 ACTTCAGTCT
40002196 TTGAAAGTTTGTACTCAGGATTCC
1 TTGAAAGTTTGTACTCAGGATTCC
40002220 TTGAAAGTTTGTACTCAGGATT
1 TTGAAAGTTTGTACTCAGGATT
40002242 GCTTACTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (24 bp):
TTGAAAGTTTGTACTCAGGATTCC
Found at i:40002296 original size:14 final size:13
Alignment explanation
Indices: 40002263--40002297 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
40002253 CTGAAAAAAG
40002263 ATGTTTTTGAAAT
1 ATGTTTTTGAAAT
40002276 ATGTTTTTGAAAT
1 ATGTTTTTGAAAT
*
40002289 ATCTTTTTG
1 ATGTTTTTG
40002298 CCACTTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (13 bp):
ATGTTTTTGAAAT
Found at i:40004940 original size:11 final size:11
Alignment explanation
Indices: 40004907--40004946 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
40004897 ATGAATATAT
40004907 TTATAAAATTA
1 TTATAAAATTA
*
40004918 TAATATAAATTA
1 TTATA-AAATTA
40004930 TTATAAAATTA
1 TTATAAAATTA
*
40004941 ATATAA
1 TTATAA
40004947 GAATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATAAAATTA
Found at i:40005539 original size:14 final size:14
Alignment explanation
Indices: 40005516--40005547 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40005506 GACGATTTTC
*
40005516 AAAAGTAAAAGAAA
1 AAAAGAAAAAGAAA
40005530 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
40005544 AAAA
1 AAAA
40005548 CTTGTTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:40023361 original size:21 final size:21
Alignment explanation
Indices: 40023337--40023380 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
40023327 GGTGTTACAT
40023337 TTAGTGGTATTAGAGCCTAAG
1 TTAGTGGTATTAGAGCCTAAG
*
40023358 TTAGTGGTGTTAGAGCCTAAG
1 TTAGTGGTATTAGAGCCTAAG
40023379 TT
1 TT
40023381 CTCTAACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.09, G:0.30, T:0.36
Consensus pattern (21 bp):
TTAGTGGTATTAGAGCCTAAG
Found at i:40030568 original size:46 final size:47
Alignment explanation
Indices: 40030415--40030683 Score: 239
Period size: 46 Copynumber: 5.7 Consensus size: 47
40030405 ATTCGTGTGT
* * *
40030415 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGA
* * * *
40030461 GAGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* * *
40030509 GGGCCAGTATAAGA-CATGTTTGGGACATGCATCGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATG-A
40030556 -AGCCAGTGTAAGA-CATGTCTGGGACATGCATCGG-CTACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGA
* * * * * ** *
40030601 TAGTCAGTGTAATACCATGTTTGGAACATGGCATC-AACTTGAGAT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGA
**
40030647 TGAGCCAGTGTAAGACCATGTCCAGGACATGGCATCG
1 -GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCG
40030684 ACACCTTACC
Statistics
Matches: 182, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
45 3 0.02
46 76 0.42
47 73 0.40
48 29 0.16
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:40030645 original size:93 final size:94
Alignment explanation
Indices: 40030462--40030686 Score: 242
Period size: 93 Copynumber: 2.4 Consensus size: 94
40030452 ACATTATGAG
* *
40030462 AGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACATTGAGACGAGGGCCAGTATAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACATCGAGACGAGAGCCAGTATAAGACATG
* ** *
40030527 TTTGGGACATGCATCGGCCTCGAGATGTA
66 TTTGGAACATGCATCGAACTCGAGATATA
* * * * * *
40030556 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGATGATAGTCAGTGTAATACCA
1 AGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACAT-CGAGACGAGAGCCAGTATAAGA-CA
* *
40030618 TGTTTGGAACATGGCATC-AACTTGAGATATG
64 TGTTTGGAACAT-GCATCGAACTCGAGATATA
** *
40030649 AGCCAGTGTAAGACCATGTCCAGGACATGGCATCGACA
1 AGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACA
40030687 CCTTACCCTA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
91 1 0.01
92 22 0.20
93 48 0.44
94 30 0.28
95 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACATCGAGACGAGAGCCAGTATAAGACATG
TTTGGAACATGCATCGAACTCGAGATATA
Found at i:40030675 original size:140 final size:141
Alignment explanation
Indices: 40030420--40030683 Score: 338
Period size: 140 Copynumber: 1.9 Consensus size: 141
40030410 TGTGTGAGCT
*
40030420 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
* * * ***
40030485 GACATAGCATCGACATTGAGACGAGGGCCAGTATAAGACATGTTTGGGACAT-GCATCGGCCTCG
66 AACATAGCATCAACATTGAGACGAGAGCCAGTATAAGACATGTCCAGGACATGGCATCGGCCTCG
40030549 AGATGTAAGCC
131 AGATGTAAGCC
* * * * *
40030560 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATAGTCAGTGTAATACCATGTTTG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAGCCAGTGTAAGACCATGTCTG
* * *
40030624 GAACATGGCATCAAC-TTGAGA-TATGAGCCAGTGTAAGACCATGTCCAGGACATGGCATCG
65 GAACATAGCATCAACATTGAGACGA-GAGCCAGTATAAGA-CATGTCCAGGACATGGCATCG
40030684 ACACCTTACC
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
138 1 0.01
139 18 0.17
140 79 0.75
141 7 0.07
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
AACATAGCATCAACATTGAGACGAGAGCCAGTATAAGACATGTCCAGGACATGGCATCGGCCTCG
AGATGTAAGCC
Found at i:40030677 original size:47 final size:46
Alignment explanation
Indices: 40030414--40030685 Score: 216
Period size: 47 Copynumber: 5.8 Consensus size: 46
40030404 CATTCGTGTG
* * *
40030414 TGAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGC-C-ACATTA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTCGAGA-TA
* *
40030458 TGAGAGCCAGTGTAAGACCATGTCTGGGACATAGCATCGACATTGAGACGA
1 T--GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGAC-TCGAGA-TA
* * * * *
40030509 -GGGCCAGTATAAGA-CATGTTTGGGACATGCATCGGCCTCGAGATG
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATC-GACTCGAGATA
* *
40030554 TAAGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCTACGAGATGA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACT-CGAGAT-A
* * * * * *
40030601 T-AGTCAGTGTAATACCATGTTTGGAACATGGCATCAACTTGAGATA
1 TGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGACTCGAGATA
**
40030647 TGAGCCAGTGTAAGACCATGTCCAGGACATGGCATCGAC
1 TGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGAC
40030686 ACCTTACCCT
Statistics
Matches: 181, Mismatches: 33, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
44 1 0.01
45 3 0.02
46 71 0.39
47 77 0.43
48 26 0.14
51 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTCGAGATA
Found at i:40039286 original size:42 final size:42
Alignment explanation
Indices: 40039239--40039324 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
40039229 CCCGAGAGGG
40039239 TATAAGAAATAAAATATATTATTTGGCTTGCCCCTTGGTGCT
1 TATAAGAAATAAAATATATTATTTGGCTTGCCCCTTGGTGCT
40039281 TATAAGAAATAAAATATATTATTTGGCTTGCCCCTTGGTGCT
1 TATAAGAAATAAAATATATTATTTGGCTTGCCCCTTGGTGCT
40039323 TA
1 TA
40039325 GGCACCCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (42 bp):
TATAAGAAATAAAATATATTATTTGGCTTGCCCCTTGGTGCT
Found at i:40039612 original size:10 final size:10
Alignment explanation
Indices: 40039597--40039639 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
40039587 ATATAAATAG
*
40039597 ATACATGTAT
1 ATACATATAT
40039607 ATACATATAT
1 ATACATATAT
*
40039617 ATATATATAT
1 ATACATATAT
*
40039627 ATATATATAT
1 ATACATATAT
40039637 ATA
1 ATA
40039640 TTTGGACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (10 bp):
ATACATATAT
Found at i:40039616 original size:2 final size:2
Alignment explanation
Indices: 40039604--40039640 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40039594 TAGATACATG
*
40039604 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40039641 TTGGACAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40041084 original size:20 final size:21
Alignment explanation
Indices: 40041036--40041084 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
40041026 AAAAGTAGAT
40041036 GTACTAAATTCCTGAAAAAAG
1 GTACTAAATTCCTGAAAAAAG
40041057 GTACTAAATTCCTGAAAAAAG
1 GTACTAAATTCCTGAAAAAAG
40041078 GTA-TAAA
1 GTACTAAA
40041085 GAATAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.24
Consensus pattern (21 bp):
GTACTAAATTCCTGAAAAAAG
Found at i:40046529 original size:154 final size:154
Alignment explanation
Indices: 40046248--40046542 Score: 484
Period size: 154 Copynumber: 1.9 Consensus size: 154
40046238 GGACATAGTT
*
40046248 CTCAGCGCGTGTAACTCTCTGTTTATGACGTCATCAACACAATTAGGGTCACATGGCCAAGTCAC
1 CTCAGCGCGTGTAACTCTCTATTTATGACGTCATCAACACAATTAGGGTCACATGGCCAAGTCAC
* *
40046313 ACATCCATGTGCTTAGGCCGTATGGCGAATTAAATTCCAAAAATCAAGTGCAGACTTTACACGGC
66 ACATCCATGTGCTTAGGCCGTATGGCGAATTAAATTCCAAAAATCAAGTGCAGACTTCACAC-GA
40046378 CT-AGACACACGTCCATGTGGCTTC
130 CTGAGACACACGTCCATGTGGCTTC
* * *
40046402 CTCAGCGCGTGTAACTCTCTATTTGTGACGTCATCAACATAATTAGGGTCATATGGCCAAGTCAC
1 CTCAGCGCGTGTAACTCTCTATTTATGACGTCATCAACACAATTAGGGTCACATGGCCAAGTCAC
* * * *
40046467 ACGTCTATGTGCTTAGGCCGTGTGGTGAATTAAATTCCAAAAATCAAGTGCAGACTTCACACGAC
66 ACATCCATGTGCTTAGGCCGTATGGCGAATTAAATTCCAAAAATCAAGTGCAGACTTCACACGAC
40046532 TGAGACACACG
131 TGAGACACACG
40046543 GCCGTGTCTC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 3 0.02
154 127 0.98
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (154 bp):
CTCAGCGCGTGTAACTCTCTATTTATGACGTCATCAACACAATTAGGGTCACATGGCCAAGTCAC
ACATCCATGTGCTTAGGCCGTATGGCGAATTAAATTCCAAAAATCAAGTGCAGACTTCACACGAC
TGAGACACACGTCCATGTGGCTTC
Found at i:40047140 original size:48 final size:48
Alignment explanation
Indices: 40047082--40047284 Score: 145
Period size: 48 Copynumber: 4.4 Consensus size: 48
40047072 TATCCCGGAT
* * *
40047082 ATGGTCTTACATGGGATCACTTATCGATGCCAATGCCATGTCGC-AGAC
1 ATGGTCTTACATGGGATCACATATCAATGCCAATGCCATGTC-CTAGAA
* ** **
40047130 ATGGTATTACAT-GG-TCGTAGGTCAATGCCAATGCCATGTCCTAGAA
1 ATGGTCTTACATGGGATCACATATCAATGCCAATGCCATGTCCTAGAA
* **
40047176 ATGGTCTTACATGGGATCACATATCAATGTCAAT---A-G-CCTAGCT
1 ATGGTCTTACATGGGATCACATATCAATGCCAATGCCATGTCCTAGAA
* * ** * ** * *
40047219 ATGGTCTTATACGAAATTACATATTGATGCCAAAGCCATGTTCC-AGAC
1 ATGGTCTTACATGGGATCACATATCAATGCCAATGCCATG-TCCTAGAA
40047267 ATGGTCTTACATGGGATC
1 ATGGTCTTACATGGGATC
40047285 TTCCATAACC
Statistics
Matches: 114, Mismatches: 32, Indels: 18
0.70 0.20 0.11
Matches are distributed among these distances:
43 30 0.26
44 1 0.01
45 2 0.02
46 35 0.31
47 5 0.04
48 39 0.34
49 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATATCAATGCCAATGCCATGTCCTAGAA
Found at i:40052603 original size:42 final size:42
Alignment explanation
Indices: 40052557--40052637 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
40052547 GAATTTTTTA
40052557 TTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTCTC
1 TTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTCTC
*
40052599 TTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATT
1 TTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATT
40052638 TTCCCAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTCTC
Found at i:40057392 original size:20 final size:20
Alignment explanation
Indices: 40057367--40057404 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40057357 GTTTATTCGC
*
40057367 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
40057387 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
40057405 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:40059050 original size:28 final size:28
Alignment explanation
Indices: 40059018--40059086 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
40059008 GCGTAGATCA
40059018 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
40059046 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
40059074 CGATA-TACCCCTA
1 CGAAATTACCCCTA
40059087 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:40065339 original size:20 final size:20
Alignment explanation
Indices: 40065314--40065351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40065304 GTTTATTCGC
*
40065314 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
40065334 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
40065352 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:40067014 original size:27 final size:28
Alignment explanation
Indices: 40066968--40067035 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
40066958 GCGTAGATCA
40066968 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
40066996 CGAAATTA-CCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
40067023 CGATA-TACCCCTA
1 CGAAATTACCCCTA
40067036 GGTTTTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 2 0.05
27 28 0.74
28 8 0.21
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:40068250 original size:19 final size:19
Alignment explanation
Indices: 40068207--40068250 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40068197 ATATTTTAAA
40068207 TTTATTTAGGTAGACAAAT
1 TTTATTTAGGTAGACAAAT
** * *
40068226 CATATTTAGGTAGATAAGT
1 TTTATTTAGGTAGACAAAT
40068245 TTTATT
1 TTTATT
40068251 CATATTCTAG
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (19 bp):
TTTATTTAGGTAGACAAAT
Found at i:40068306 original size:42 final size:42
Alignment explanation
Indices: 40068267--40068351 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
40068257 CTAGGAACAT
40068267 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
* *
40068309 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
40068351 T
1 T
40068352 ATTTCCAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:40069688 original size:28 final size:28
Alignment explanation
Indices: 40069656--40069709 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40069646 GTAACAGCAT
* *
40069656 AGTGTGGGCCTTAGCCCAATATAGTAAC
1 AGTGTGGGCCTAAGCCCAATACAGTAAC
40069684 AGTGTGGGCCTAAGCCCAATACAGTA
1 AGTGTGGGCCTAAGCCCAATACAGTA
40069710 TCAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (28 bp):
AGTGTGGGCCTAAGCCCAATACAGTAAC
Found at i:40070128 original size:22 final size:22
Alignment explanation
Indices: 40070103--40070150 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40070093 ATGAACAAGA
40070103 TGGCACAAAGCCATATTTAGGT
1 TGGCACAAAGCCATATTTAGGT
40070125 TGGCACAAAGCCATATTTAGGT
1 TGGCACAAAGCCATATTTAGGT
40070147 TGGC
1 TGGC
40070151 CATAATCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (22 bp):
TGGCACAAAGCCATATTTAGGT
Found at i:40070555 original size:27 final size:26
Alignment explanation
Indices: 40070519--40071159 Score: 506
Period size: 27 Copynumber: 23.9 Consensus size: 26
40070509 TACCCTACAG
* *
40070519 GGGTA-TTCGATAATTTTACACTACAA
1 GGGTATTTCGATAATTTTACA-AACGA
40070545 GGGTATTTCGATAATTTTACAAACCGA
1 GGGTATTTCGATAATTTTACAAA-CGA
* * * *
40070572 GGGTATTTCGGTAATTTTATAAATTGG
1 GGGTATTTCGATAATTTTACAAA-CGA
* *
40070599 GGGTATTTCGATAATTTTATAATCTGA
1 GGGTATTTCGATAATTTTACAAAC-GA
* *
40070626 GGGTATTT-TAGTAATTTTACAAATTGA
1 GGGTATTTCGA-TAATTTTACAAA-CGA
* * * *
40070653 GGGTATTTTGGTACTTTTACAAACTA
1 GGGTATTTCGATAATTTTACAAACGA
**
40070679 GGGGTATTTCGATAATTTTACAAATTA
1 -GGGTATTTCGATAATTTTACAAACGA
* *
40070706 GGGGTATTTCGGTAATTTTACAAACTA
1 -GGGTATTTCGATAATTTTACAAACGA
* ** *
40070733 GGGGTTTTTTAATAATTTTATAAATCGA
1 -GGGTATTTCGATAATTTTACAAA-CGA
* * *
40070761 GGGTATTTTGGTAATTTTACAAACTGG
1 GGGTATTTCGATAATTTTACAAAC-GA
*
40070788 GGGTATTTCGGTAATTTTACAAATC-A
1 GGGTATTTCGATAATTTTACAAA-CGA
* * *
40070814 GAGGTATTTTGCTAATTTTATAAACTGA
1 G-GGTATTTCGATAATTTTACAAAC-GA
* * *
40070842 GGGTATTTCGGTAGTTTTACAAATCAA
1 GGGTATTTCGATAATTTTACAAA-CGA
* *
40070869 GGGTATTTCGATAATTTTATAAATTG-
1 GGGTATTTCGATAATTTTACAAA-CGA
*
40070895 GGGTATTTCCG-TAATTTTACAAACTA
1 GGGTATTT-CGATAATTTTACAAACGA
* *
40070921 GGGGTATTTCGATAATTTTACAATCTAA
1 -GGGTATTTCGATAATTTTACAAAC-GA
* * *
40070949 GGGTATTTTGGTAATTTTACAAATCGG
1 GGGTATTTCGATAATTTTACAAA-CGA
*
40070976 GGGTATTTC-ATTAATTTTACAAGCCGA
1 GGGTATTTCGA-TAATTTTACAA-ACGA
* * *
40071003 GGGTATTTCTATAATTCTACAAACTGG
1 GGGTATTTCGATAATTTTACAAAC-GA
* *
40071030 GGGTATTTCGATAATTTTACAATCTAA
1 GGGTATTTCGATAATTTTACAAAC-GA
*
40071057 GGGTATTTCGATAATTTTACAATC-A
1 GGGTATTTCGATAATTTTACAAACGA
* *
40071082 GGGGTATTTCGGTAATTTTACAATCTGA
1 -GGGTATTTCGATAATTTTACAAAC-GA
** *
40071110 GTATATTTCGATAATTGTACAAACCG-
1 GGGTATTTCGATAATTTTACAAA-CGA
40071136 GTGGTATTTCGATAATTTTACAAA
1 G-GGTATTTCGATAATTTTACAAA
40071160 TCGGGCATGT
Statistics
Matches: 503, Mismatches: 83, Indels: 57
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.00
26 57 0.11
27 434 0.86
28 11 0.02
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (26 bp):
GGGTATTTCGATAATTTTACAAACGA
Found at i:40070604 original size:54 final size:54
Alignment explanation
Indices: 40070545--40071159 Score: 623
Period size: 54 Copynumber: 11.4 Consensus size: 54
40070535 TACACTACAA
* * *
40070545 GGGTATTTCGATAATTTTACAAACCGAGGGTATTTCGGTAATTTTATAAATTGG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * ** * *
40070599 GGGTATTTCGATAATTTTATAATCTGAGGGTATTTTAGTAATTTTACAAATTGA
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * * * **
40070653 GGGTATTTTGGTACTTTTACAAACT-AGGGGTATTTCGATAATTTTACAAATTAG
1 GGGTATTTCGATAATTTTACAAACTGA-GGGTATTTCGGTAATTTTACAAATCGG
* * *** * *
40070707 GGGTATTTCGGTAATTTTACAAACT-AGGGGTTTTTTAATAATTTTATAAATCGA
1 GGGTATTTCGATAATTTTACAAACTGA-GGGTATTTCGGTAATTTTACAAATCGG
* * * *
40070761 GGGTATTTTGGTAATTTTACAAACTGGGGGTATTTCGGTAATTTTACAAATCAG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * * * * **
40070815 AGGTATTTTGCTAATTTTATAAACTGAGGGTATTTCGGTAGTTTTACAAATCAA
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * * *
40070869 GGGTATTTCGATAATTTTATAAATTG-GGGTATTTCCGTAATTTTACAAA-CTAG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATC-GG
* * *
40070922 GGGTATTTCGATAATTTTACAATCTAAGGGTATTTTGGTAATTTTACAAATCGG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * ** *
40070976 GGGTATTTC-ATTAATTTTACAAGCCGAGGGTATTTCTATAATTCTACAAA-CTGG
1 GGGTATTTCGA-TAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATC-GG
* * * *
40071030 GGGTATTTCGATAATTTTACAATCTAAGGGTATTTCGATAATTTTAC-AATCAG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
* * ** * * *
40071083 GGGTATTTCGGTAATTTTACAATCTGAGTATATTTCGATAATTGTACAAACCGG
1 GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
*
40071137 TGGTATTTCGATAATTTTACAAA
1 GGGTATTTCGATAATTTTACAAA
40071160 TCGGGCATGT
Statistics
Matches: 473, Mismatches: 78, Indels: 20
0.83 0.14 0.04
Matches are distributed among these distances:
52 1 0.00
53 92 0.19
54 378 0.80
55 2 0.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGTATTTCGATAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATCGG
Found at i:40074281 original size:30 final size:30
Alignment explanation
Indices: 40074245--40074304 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40074235 TTCCCGAGCC
40074245 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
40074275 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
40074305 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:40081527 original size:30 final size:30
Alignment explanation
Indices: 40081491--40081550 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40081481 TTCCCGAGCC
40081491 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
40081521 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
40081551 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:40085155 original size:129 final size:129
Alignment explanation
Indices: 40084925--40085183 Score: 299
Period size: 129 Copynumber: 2.0 Consensus size: 129
40084915 ACGCCTTTAT
* * * * * *
40084925 AGAACATGACCTTTAGCAACGCTTTTCCCACAAACACTGTTATAGAACATGAGCTTTAGCGGCGC
1 AGAACATGACATTTAGCAACGCTTCTCCCACAAACACCGCTAAAGAACATGACCTTTAGCGGCGC
* *
40084990 CTTTCCCAAAAACGCCACTATAGAACAACACCTTTAGT-AGCGCTTTTCCCACAAATGCCGCTAA
66 CTTTCCCAAAAACGCCACTATAGAACAACACCTTTAGTGA-CGCTTTTACCAAAAATGCCGCTAA
** ** *
40085054 AGAACATGACATTTAGCGGCGCTTCTCCCACAAATGCCGCTAAAGAACATGACCTTTAGTGGCG-
1 AGAACATGACATTTAGCAACGCTTCTCCCACAAACACCGCTAAAGAACATGACCTTTAGCGGCGC
* * ** * *
40085118 CTTGT-CCAACAAACGTCGCTATAGAACATGACCTTTAGTGATGCTTTTACTAAAAATGCCGCTA
66 CTT-TCCCAA-AAACGCCACTATAGAACAACACCTTTAGTGACGCTTTTACCAAAAATGCCGCTA
40085182 A
129 A
40085183 A
1 A
40085184 TGTTGTGTTC
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
128 7 0.06
129 100 0.93
130 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (129 bp):
AGAACATGACATTTAGCAACGCTTCTCCCACAAACACCGCTAAAGAACATGACCTTTAGCGGCGC
CTTTCCCAAAAACGCCACTATAGAACAACACCTTTAGTGACGCTTTTACCAAAAATGCCGCTAA
Found at i:40085157 original size:43 final size:43
Alignment explanation
Indices: 40084913--40085155 Score: 261
Period size: 43 Copynumber: 5.7 Consensus size: 43
40084903 TTATTTGAAA
** **
40084913 AAACGCCTTTATAGAACATGACCTTTAGCAACGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
40084956 AAACACTGTTATAGAACATGAGCTTTAGCGGCGCCTTTCCCAA
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* ** **
40084999 AAACGCCACTATAGAACAACACCTTTAGTAGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
40085042 AAATGCCGCTAAAGAACATGACATTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
40085085 AAATGCCGCTAAAGAACATGACCTTTAGTGGCGCTTGTCCAAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
40085128 AAACGTCGCTATAGAACATGACCTTTAG
1 AAACGCCGCTATAGAACATGACCTTTAG
40085156 TGATGCTTTT
Statistics
Matches: 165, Mismatches: 35, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 165 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:40085175 original size:86 final size:86
Alignment explanation
Indices: 40084925--40085183 Score: 277
Period size: 86 Copynumber: 3.0 Consensus size: 86
40084915 ACGCCTTTAT
* * * *
40084925 AGAACATGACCTTTAGCAACGCTTTTCCCACAAAC-ACTGTTATAGAACATGAGCTTTAGCGGCG
1 AGAACATGACCTTTAGTAGCGCTTTTCCCACAAACGAC-GCTATAGAACATGACCTTTAGCGGCG
* * * *
40084989 CCTTTCCCAAAAACGCCACTAT
65 CTTTTCCCAAAAATGCCGCTAA
** * * * *
40085011 AGAACAACACCTTTAGTAGCGCTTTTCCCACAAATGCCGCTAAAGAACATGACATTTAGCGGCGC
1 AGAACATGACCTTTAGTAGCGCTTTTCCCACAAACGACGCTATAGAACATGACCTTTAGCGGCGC
* *
40085076 TTCTCCCACAAATGCCGCTAA
66 TTTTCCCAAAAATGCCGCTAA
* * * * * **
40085097 AGAACATGACCTTTAGTGGCGCTTGTCCAACAAACGTCGCTATAGAACATGACCTTTAGTGATGC
1 AGAACATGACCTTTAGTAGCGCTTTTCCCACAAACGACGCTATAGAACATGACCTTTAGCGGCGC
* *
40085162 TTTTACTAAAAATGCCGCTAA
66 TTTTCCCAAAAATGCCGCTAA
40085183 A
1 A
40085184 TGTTGTGTTC
Statistics
Matches: 140, Mismatches: 32, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
86 139 0.99
87 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (86 bp):
AGAACATGACCTTTAGTAGCGCTTTTCCCACAAACGACGCTATAGAACATGACCTTTAGCGGCGC
TTTTCCCAAAAATGCCGCTAA
Found at i:40089153 original size:42 final size:41
Alignment explanation
Indices: 40089073--40089222 Score: 162
Period size: 41 Copynumber: 3.6 Consensus size: 41
40089063 GAGCTTGGTC
40089073 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* *
40089114 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
40089156 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
*
40089197 TCGAAGGGCTTTTGAGCCGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
40089223 GAGTCGGACT
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.04
40 9 0.10
41 37 0.41
42 28 0.31
43 12 0.13
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:40089205 original size:41 final size:40
Alignment explanation
Indices: 40089053--40089222 Score: 161
Period size: 41 Copynumber: 4.2 Consensus size: 40
40089043 GCTAATCGGG
*
40089053 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* *
40089094 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* *
40089137 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT
* *
40089177 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
40089218 G-CTAA
1 GTCTAA
40089223 GAGTCGGACT
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
39 7 0.07
40 14 0.13
41 50 0.47
42 23 0.21
43 9 0.08
44 1 0.01
45 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:40095059 original size:43 final size:43
Alignment explanation
Indices: 40095012--40095109 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 43
40095002 CTTACATGTT
* * *
40095012 ATCACATATCGATGCCACTGTCCCACACAGGGTCTTACACAAA
1 ATCACATATCGATGCCAATATCCCACACAGGGTATTACACAAA
* * * ***
40095055 ATCACA-ATACAATGCCAATATCCCAGACATGGTATTACATTTA
1 ATCACATAT-CGATGCCAATATCCCACACAGGGTATTACACAAA
40095098 ATCACATATCGA
1 ATCACATATCGA
40095110 GTCGATGCCA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
42 2 0.05
43 39 0.91
44 2 0.05
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (43 bp):
ATCACATATCGATGCCAATATCCCACACAGGGTATTACACAAA
Found at i:40095226 original size:50 final size:50
Alignment explanation
Indices: 40095103--40095247 Score: 152
Period size: 50 Copynumber: 2.9 Consensus size: 50
40095093 ATTTAATCAC
* *
40095103 ATATCGA-GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCTT
1 ATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTT
* * * *
40095152 ATATCGAGGCCGACGTCATATCCCAAACATGGTCTTACACTGGCTCTCCTCT
1 ATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CT-T
* * * * *
40095204 -TTTTG-TGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
1 ATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
40095248 ACATGTATTG
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
49 7 0.09
50 65 0.83
51 5 0.06
52 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (50 bp):
ATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTT
Found at i:40095595 original size:46 final size:46
Alignment explanation
Indices: 40095528--40095619 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
40095518 CTTATCATAT
40095528 TCACTTAATTAAATAGATTGGACACATAACATCATACGAATACCAA
1 TCACTTAATTAAATAGATTGGACACATAACATCATACGAATACCAA
40095574 TCACTTAATTAAATAGATTGGACACATAACATCATACGAATACCAA
1 TCACTTAATTAAATAGATTGGACACATAACATCATACGAATACCAA
40095620 CACACATAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (46 bp):
TCACTTAATTAAATAGATTGGACACATAACATCATACGAATACCAA
Found at i:40097633 original size:40 final size:38
Alignment explanation
Indices: 40097534--40097682 Score: 142
Period size: 40 Copynumber: 3.8 Consensus size: 38
40097524 ATTGAATGAT
* * *
40097534 ATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT-TAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCT---AGTCTAC
*
40097573 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGT--CTAC
* *
40097613 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 ATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTC-TAC
*
40097652 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 -ATCCGGGCTAAGACCCGAAGGCAATTGTGC
40097683 ACATGGTTAT
Statistics
Matches: 94, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 16 0.17
40 73 0.78
41 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (38 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTCTAC
Found at i:40097696 original size:40 final size:40
Alignment explanation
Indices: 40097573--40097698 Score: 146
Period size: 40 Copynumber: 3.1 Consensus size: 40
40097563 TGGAAATTAC
* * * * *
40097573 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTAT
* ** *
40097613 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTAT
*
40097653 ATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGGTTAT
40097693 ATCCGG
1 ATCCGG
40097699 TTATATTCCG
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 70 0.99
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTAT
Found at i:40105577 original size:40 final size:40
Alignment explanation
Indices: 40105511--40105661 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
40105501 AAATTGAATG
* * *
40105511 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
40105550 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
40105590 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
40105630 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
40105662 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40105675 original size:40 final size:40
Alignment explanation
Indices: 40105548--40105677 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
40105538 ATGCTGGAAA
* * *
40105548 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
40105588 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
40105628 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
40105668 TTATATCCGG
1 TTATATCCGG
40105678 TTATATTCCG
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:40109292 original size:40 final size:39
Alignment explanation
Indices: 40109234--40109319 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 39
40109224 TATATATATA
**
40109234 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCA-TTT
* *
40109274 TAGCCGAAGCTATTTCAAACCGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
40109313 TAGCCGA
1 TAGCCGA
40109320 TAAGTCGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
Found at i:40112565 original size:30 final size:30
Alignment explanation
Indices: 40112531--40112594 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
40112521 CTAACATTAT
40112531 AAAATATTTTGAGATGGGTGGATTTTTTTA
1 AAAATATTTTGAGATGGGTGGATTTTTTTA
40112561 AAAATATTTTGAGATGGGTGGATTTTTTTA
1 AAAATATTTTGAGATGGGTGGATTTTTTTA
40112591 AAAA
1 AAAA
40112595 GTAGAATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (30 bp):
AAAATATTTTGAGATGGGTGGATTTTTTTA
Found at i:40116777 original size:118 final size:118
Alignment explanation
Indices: 40116364--40116750 Score: 472
Period size: 118 Copynumber: 3.3 Consensus size: 118
40116354 TTTTGTTGTG
* * * *
40116364 TTTTTTAAAAAGCGCCGCTAATGTTGATCTATTGCGGCATTTATAAGCTAGCGCCGCTAATTTCA
1 TTTTTTAAAAAGCGCCGCTAATGCTGATCTATTGCGGCGTTTATAATCTAGCACCGCTAATTTCA
* **
40116429 CTAAAGCATTAAAACGAAGTCATTTTCATTCAATT-AAA-TTTTTTTGCGGCA
66 CTAAAGCATTAAAACAAAAACATTTTCATTCAATTAAAATTTTTTTTGCGGCA
** * * * * * *
40116480 TTTTACAAAAAACGTCGCTAATGCTAATCTATTGCGGCGTTTATAGTTTAGCACCGCTAATTCCA
1 TTTTTTAAAAAGCGCCGCTAATGCTGATCTATTGCGGCGTTTATAATCTAGCACCGCTAATTTCA
* * ** * *
40116545 CTAAACCACTAAAACAACTACATTTTCATACAATTAAAATTTCTTTTGCGGCA
66 CTAAAGCATTAAAACAAAAACATTTTCATTCAATTAAAATTTTTTTTGCGGCA
* * * * * *
40116598 TTTTTTGAAAAGCGCCGCTAATTCTGATATTTTGCGGCGTTTATAACCTAGCACTGCTAATTTCA
1 TTTTTTAAAAAGCGCCGCTAATGCTGATCTATTGCGGCGTTTATAATCTAGCACCGCTAATTTCA
* *
40116663 CTAAAGCATTAAAACAAAAACATTTTCATTCAATTAAAATTTTTTTTGCCGCG
66 CTAAAGCATTAAAACAAAAACATTTTCATTCAATTAAAATTTTTTTTGCGGCA
* * *
40116716 TTTTTTAAAAGGCTCCGCTAATGCTGAGCTATTGC
1 TTTTTTAAAAAGCGCCGCTAATGCTGATCTATTGC
40116751 ATTGTTTAAA
Statistics
Matches: 220, Mismatches: 49, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
116 81 0.37
117 3 0.01
118 136 0.62
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (118 bp):
TTTTTTAAAAAGCGCCGCTAATGCTGATCTATTGCGGCGTTTATAATCTAGCACCGCTAATTTCA
CTAAAGCATTAAAACAAAAACATTTTCATTCAATTAAAATTTTTTTTGCGGCA
Found at i:40126622 original size:7 final size:7
Alignment explanation
Indices: 40126606--40126684 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
40126596 CACCCCTAAA
*
40126606 CTAAAGC
1 CTAAACC
40126613 CTAAACC
1 CTAAACC
*
40126620 CTAGACC
1 CTAAACC
*
40126627 CTAAATC
1 CTAAACC
*
40126634 ATAAACC
1 CTAAACC
*
40126641 CTAAACT
1 CTAAACC
*
40126648 CTAAATC
1 CTAAACC
* *
40126655 ATAAATC
1 CTAAACC
*
40126662 TTAAACC
1 CTAAACC
*
40126669 CTAAACG
1 CTAAACC
40126676 CTAAACC
1 CTAAACC
40126683 CT
1 CT
40126685 TACTTCTTAA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:40126631 original size:21 final size:21
Alignment explanation
Indices: 40126614--40126673 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
40126604 AACTAAAGCC
*
40126614 TAAACCCTAGACCCTAAATCA
1 TAAACCCTAAACCCTAAATCA
*
40126635 TAAACCCTAAACTCTAAATCA
1 TAAACCCTAAACCCTAAATCA
* *
40126656 TAAATCTTAAACCCTAAA
1 TAAACCCTAAACCCTAAA
40126674 CGCTAAACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATCA
Found at i:40126849 original size:15 final size:14
Alignment explanation
Indices: 40126822--40126889 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
40126812 CTTACCTTTA
*
40126822 AACCCTAATACCCT
1 AACCCTAAAACCCT
40126836 AACCTCTAAAACCCT
1 AACC-CTAAAACCCT
*
40126851 AAACACTAAAACCCT
1 -AACCCTAAAACCCT
** *
40126866 AACTATAAAACACTT
1 AACCCTAAAAC-CCT
40126881 AACCCTAAA
1 AACCCTAAA
40126890 CCATAAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 13 0.30
15 28 0.64
16 3 0.07
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCTAAAACCCT
Found at i:40126865 original size:30 final size:29
Alignment explanation
Indices: 40126820--40126876 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
40126810 CCCTTACCTT
* * *
40126820 TAAACCCTAATACCCTAACCTCTAAAACCC
1 TAAACACTAAAACCCTAA-CTATAAAACCC
40126850 TAAACACTAAAACCCTAACTATAAAAC
1 TAAACACTAAAACCCTAACTATAAAAC
40126877 ACTTAACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (29 bp):
TAAACACTAAAACCCTAACTATAAAACCC
Found at i:40126888 original size:29 final size:29
Alignment explanation
Indices: 40126820--40126953 Score: 94
Period size: 29 Copynumber: 4.6 Consensus size: 29
40126810 CCCTTACCTT
* * *
40126820 TAAACCCTAATACCCTAACCTCTAAAACCC
1 TAAACCCTAAAACCCTAA-CTATAAAACAC
*
40126850 TAAACACTAAAACCCTAACTATAAAACAC
1 TAAACCCTAAAACCCTAACTATAAAACAC
* * *
40126879 TTAACCCT-AAACCATAAACTTTAAAACAC
1 TAAACCCTAAAACCCT-AACTATAAAACAC
* * ** * *
40126908 AAAACCAT-AAACCAAAAATAATAAACCA-
1 TAAACCCTAAAACCCTAACT-ATAAAACAC
*
40126936 TAAACCATAAAACCCTAA
1 TAAACCCTAAAACCCTAA
40126954 ACCATATACT
Statistics
Matches: 83, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
28 16 0.19
29 51 0.61
30 16 0.19
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (29 bp):
TAAACCCTAAAACCCTAACTATAAAACAC
Found at i:40126895 original size:22 final size:22
Alignment explanation
Indices: 40126851--40126896 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40126841 CTAAAACCCT
*
40126851 AAACACTAAAACCCTAACTATA
1 AAACACTAAAACCCTAACCATA
*
40126873 AAACACT-TAACCCTAAACCATA
1 AAACACTAAAACCCT-AACCATA
40126895 AA
1 AA
40126897 CTTTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.17
Consensus pattern (22 bp):
AAACACTAAAACCCTAACCATA
Found at i:40126896 original size:7 final size:7
Alignment explanation
Indices: 40126881--40126959 Score: 61
Period size: 7 Copynumber: 11.0 Consensus size: 7
40126871 TAAAACACTT
*
40126881 AACCCTA
1 AACCATA
40126888 AACCATA
1 AACCATA
**
40126895 AACTTTAA
1 AACCAT-A
40126903 AACACA-A
1 AAC-CATA
40126910 AACCATA
1 AACCATA
*
40126917 AACCAAA
1 AACCATA
**
40126924 AATAATA
1 AACCATA
40126931 AACCATA
1 AACCATA
40126938 AACCATAA
1 AACCAT-A
*
40126946 AACCCTA
1 AACCATA
40126953 AACCATA
1 AACCATA
40126960 TACTTTAAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
6 2 0.04
7 43 0.78
8 10 0.18
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCATA
Found at i:40126912 original size:22 final size:22
Alignment explanation
Indices: 40126887--40126968 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
40126877 ACTTAACCCT
40126887 AAACCATAAACTTTAAAACACA
1 AAACCATAAACTTTAAAACACA
** *
40126909 AAACCATAAAC-CAAAAATA-A
1 AAACCATAAACTTTAAAACACA
** * *
40126929 TAAACCATAAACCATAAAACCCT
1 -AAACCATAAACTTTAAAACACA
*
40126952 AAACCATATACTTTAAA
1 AAACCATAAACTTTAAA
40126969 CATTAAATTC
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.02
21 16 0.35
22 29 0.63
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (22 bp):
AAACCATAAACTTTAAAACACA
Found at i:40127073 original size:41 final size:40
Alignment explanation
Indices: 40127027--40127144 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 40
40127017 TTAAACTGCT
* *
40127027 TGACCTTTTGTAGTATTTTTATCATAAACGTCGCTAATGCC
1 TGACCTTTTGTGGTGTTTTTATCATAAACGTCGCTAATG-C
* *
40127068 TGACCTTTTGTGGCGTTTTTCTCATAAACG-CTGCTAATGC
1 TGACCTTTTGTGGTGTTTTTATCATAAACGTC-GCTAATGC
** *
40127108 TCGACCTTTTACGGTGTTTTTATCATAATCGTCGCTA
1 T-GACCTTTTGTGGTGTTTTTATCATAAACGTCGCTA
40127145 TAGCTCTAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 3 0.05
41 61 0.94
42 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (40 bp):
TGACCTTTTGTGGTGTTTTTATCATAAACGTCGCTAATGC
Found at i:40127871 original size:27 final size:27
Alignment explanation
Indices: 40127841--40127892 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40127831 AGTGTGCCAC
40127841 AAAGGCTTCT-TTATCATAGATCACTAT
1 AAAGG-TTCTCTTATCATAGATCACTAT
* *
40127868 AAAGGTTTTCTTGTCATAGATCACT
1 AAAGGTTCTCTTATCATAGATCACT
40127893 GCTGATGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (27 bp):
AAAGGTTCTCTTATCATAGATCACTAT
Found at i:40134480 original size:61 final size:60
Alignment explanation
Indices: 40134411--40134587 Score: 241
Period size: 61 Copynumber: 2.9 Consensus size: 60
40134401 AATTAATCAC
*
40134411 ATTAATATTAAATTAATAAAATATTATCAAGATAAATACTT-AATTTATTTTAATATCTCA
1 ATTAATATTAAATTAATAAAATATTATCAAGATAAATA-TTAAATTTAATTTAATATCTCA
* * *
40134471 TATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTTAATTTAAAATTTCA
1 -ATTAATATTAAATTAATAAAATATTATCAAGATAAATATTAAATTTAATTTAATATCTCA
* * * *
40134532 AGTAATGTTAATTTAATAAAATACTAT-ATAGATAAATATTAAATTTAATTTAATAT
1 ATTAATATTAAATTAATAAAATATTATCA-AGATAAATATTAAATTTAATTTAATAT
40134588 TAAATTTGTT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
60 51 0.49
61 53 0.51
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (60 bp):
ATTAATATTAAATTAATAAAATATTATCAAGATAAATATTAAATTTAATTTAATATCTCA
Found at i:40134568 original size:60 final size:61
Alignment explanation
Indices: 40134413--40134584 Score: 233
Period size: 60 Copynumber: 2.8 Consensus size: 61
40134403 TTAATCACAT
* * *
40134413 TAATATTAAATTAATAAAATATTATCA-AGATAAATACTT-AATTTATTTTAATATCTCATAT
1 TAATATTAAATTAATAAAATATTAT-ATAGATAAATA-TTAAATTTAATTTAAAATCTCATAG
* *
40134474 TAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTTAATTTAAAATTTCA-AG
1 TAATATTAAATTAATAAAATATTATATAGATAAATATTAAATTTAATTTAAAATCTCATAG
* * *
40134534 TAATGTTAATTTAATAAAATACTATATAGATAAATATTAAATTTAATTTAA
1 TAATATTAAATTAATAAAATATTATATAGATAAATATTAAATTTAATTTAA
40134585 TATTAAATTT
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
60 50 0.50
61 50 0.50
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (61 bp):
TAATATTAAATTAATAAAATATTATATAGATAAATATTAAATTTAATTTAAAATCTCATAG
Found at i:40137273 original size:212 final size:212
Alignment explanation
Indices: 40136903--40137315 Score: 754
Period size: 212 Copynumber: 1.9 Consensus size: 212
40136893 GTTCTATTAG
*
40136903 TTGGAGGTCCCTGAGTTGATAATATACCTTAATTAATGTTAGTGGAAATTTATGTCCATAATTAG
1 TTGGAGGTCCCTAAGTTGATAATATACCTTAATTAATGTTAGTGGAAATTTATGTCCATAATTAG
40136968 CATGGTTATTATATGTTTAAATAAAGGTTATTTTTGCAAATGGCTTATTAAGTTAATAATAATAA
66 CATGGTTATTATATGTTTAAATAAAGGTTATTTTTGCAAATGGCTTATTAAGTTAATAATAATAA
* *
40137033 AAACAAAATCAAAATCACATTATTCAATCCATCTCTTGCCGAAATTGAGAAATAAAAATCAGCCA
131 AAACAAAATCAAAATCACATTATTCAATCCATCTCTTGCCGAAATTGAGAAAGAAAAATCAACCA
40137098 TAGCTATGAAATTTATA
196 TAGCTATGAAATTTATA
* *
40137115 TTGGAGGTCCCTAAGTTGATAATATACCTTAATTAATGTTAGTGGACATTTATGTTCATAATTAG
1 TTGGAGGTCCCTAAGTTGATAATATACCTTAATTAATGTTAGTGGAAATTTATGTCCATAATTAG
* *
40137180 CATGGTTATTATATGTTTAAATAAATGTTATTTTTGTAAATGGCTTATTAAGTTAATAATAATAA
66 CATGGTTATTATATGTTTAAATAAAGGTTATTTTTGCAAATGGCTTATTAAGTTAATAATAATAA
*
40137245 AAACAAAATCAAAATCACATTTTTCAATCCATCTCTTGCCGAAATTGAGAAAGAAAAATCAACCA
131 AAACAAAATCAAAATCACATTATTCAATCCATCTCTTGCCGAAATTGAGAAAGAAAAATCAACCA
40137310 TAGCTA
196 TAGCTA
40137316 GGTTTTACAT
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
212 193 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (212 bp):
TTGGAGGTCCCTAAGTTGATAATATACCTTAATTAATGTTAGTGGAAATTTATGTCCATAATTAG
CATGGTTATTATATGTTTAAATAAAGGTTATTTTTGCAAATGGCTTATTAAGTTAATAATAATAA
AAACAAAATCAAAATCACATTATTCAATCCATCTCTTGCCGAAATTGAGAAAGAAAAATCAACCA
TAGCTATGAAATTTATA
Found at i:40139342 original size:55 final size:54
Alignment explanation
Indices: 40139201--40139344 Score: 137
Period size: 55 Copynumber: 2.6 Consensus size: 54
40139191 ATTAGGGTTT
* * * * ***
40139201 AAAGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTTACAAGGC
1 AAAGATACCATGTAAGACCATGCCAAGGCATGGCATTGATAACTACGACAAGGC
* * * ** *
40139255 AAGGAAATCATGTAAGACCATG-TGAGGACATGGCATTGATAAACTACGATAAGGC
1 AAAGATACCATGTAAGACCATGCCAAGG-CATGGCATTGAT-AACTACGACAAGGC
*
40139310 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCA
1 AAAGATACCATGTAAGACCATGCCAAGGCATGGCA
40139345 ATGGTGAGTT
Statistics
Matches: 68, Mismatches: 19, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
53 3 0.04
54 28 0.41
55 34 0.50
56 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (54 bp):
AAAGATACCATGTAAGACCATGCCAAGGCATGGCATTGATAACTACGACAAGGC
Found at i:40148213 original size:53 final size:53
Alignment explanation
Indices: 40148013--40148219 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
40148003 ATTAGGGTTT
* * * * *
40148013 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * *** * * * * *
40148067 AAGGAAATCATGTAAGACCATATGAAGACATGGCATTGATAAACTACGATAAAGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * *
40148122 AAAGATCCCATGTAAGACCATGCCAAGGCATGACAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
40148175 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
40148220 TAAAAAGGAA
Statistics
Matches: 116, Mismatches: 35, Indels: 5
0.74 0.22 0.03
Matches are distributed among these distances:
53 44 0.38
54 36 0.31
55 36 0.31
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:40149678 original size:22 final size:22
Alignment explanation
Indices: 40149648--40149755 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
40149638 AGCTTATTGT
* *
40149648 TTCAACTCATTGGAGCTTACCG
1 TTCAGCTCAATGGAGCTTACCG
*
40149670 TTCAGCTCATTGGAG---ACCG
1 TTCAGCTCAATGGAGCTTACCG
* * **
40149689 TTCAGCTCAATAGAGGTTACTAT
1 TTCAGCTCAATGGAGCTTAC-CG
* *
40149712 TTCAGCTCAATAGAGCTTACTG
1 TTCAGCTCAATGGAGCTTACCG
40149734 TTCAGCTCGAA-GGAGCTTACCG
1 TTCAGCTC-AATGGAGCTTACCG
40149756 ACCATGACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
19 17 0.24
22 33 0.46
23 21 0.30
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (22 bp):
TTCAGCTCAATGGAGCTTACCG
Found at i:40149719 original size:23 final size:22
Alignment explanation
Indices: 40149628--40149741 Score: 83
Period size: 23 Copynumber: 5.2 Consensus size: 22
40149618 GACTCATCGT
*
40149628 AGCTC-ATAAGAGCTTATTGTTTC
1 AGCTCAAT-AGAGCTTACTG-TTC
* * * *
40149651 AACTCATTGGAGCTTACCGTTC
1 AGCTCAATAGAGCTTACTGTTC
* * *
40149673 AGCTCATTGGAG---ACCGTTC
1 AGCTCAATAGAGCTTACTGTTC
* *
40149692 AGCTCAATAGAGGTTACTATTTC
1 AGCTCAATAGAGCTTACT-GTTC
40149715 AGCTCAATAGAGCTTACTGTTC
1 AGCTCAATAGAGCTTACTGTTC
40149737 AGCTC
1 AGCTC
40149742 GAAGGAGCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
19 17 0.23
22 24 0.32
23 32 0.43
24 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (22 bp):
AGCTCAATAGAGCTTACTGTTC
Found at i:40152474 original size:56 final size:56
Alignment explanation
Indices: 40152398--40152766 Score: 594
Period size: 56 Copynumber: 6.6 Consensus size: 56
40152388 GTGATTTCGT
* *
40152398 GTAAGATCACGTTTAATACGTTGGCATTGATATGTGATTCCGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
* * * * *
40152454 GTAAGACAACATTTAATACGTTGGTATCGATATGTGATTCTGATATATGTATGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
* *
40152510 GTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
* *
40152566 GTAAGACCATGTTTAATAGGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
* *
40152622 GTAAGACCACGTTTAATATGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
* *
40152678 GTAAGACCACGTTTAATACGTTGGCTTCGATATGTGATTCCGATATATGTGTGCGT
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
*
40152734 GTAAGACCACGTCTAATACGTTGGCATCGATAT
1 GTAAGACCACGTTTAATACGTTGGCATCGATAT
40152767 ATGTGGTCAC
Statistics
Matches: 290, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 290 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (56 bp):
GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATATGTGTGCGA
Found at i:40153326 original size:26 final size:27
Alignment explanation
Indices: 40153297--40153352 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
40153287 TAAGAATATT
40153297 TATGGA-ATGATCCATGAATATATGTA
1 TATGGAGATGATCCATGAATATATGTA
* *
40153323 TAT-GAGTTTATCCATGAATATATGTA
1 TATGGAGATGATCCATGAATATATGTA
40153349 TATG
1 TATG
40153353 AGTTTATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (27 bp):
TATGGAGATGATCCATGAATATATGTA
Found at i:40153353 original size:26 final size:26
Alignment explanation
Indices: 40153306--40153359 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40153296 TTATGGAATG
40153306 ATCCATGAATATATGTATATGAGTTT
1 ATCCATGAATATATGTATATGAGTTT
40153332 ATCCATGAATATATGTATATGAGTTT
1 ATCCATGAATATATGTATATGAGTTT
40153358 AT
1 AT
40153360 GTATATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (26 bp):
ATCCATGAATATATGTATATGAGTTT
Found at i:40154344 original size:14 final size:14
Alignment explanation
Indices: 40154325--40154354 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40154315 ATGTCGCAAC
40154325 TAAACTCAATGTAT
1 TAAACTCAATGTAT
40154339 TAAACTCAATGTAT
1 TAAACTCAATGTAT
40154353 TA
1 TA
40154355 CTTACAGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (14 bp):
TAAACTCAATGTAT
Found at i:40160351 original size:19 final size:18
Alignment explanation
Indices: 40160329--40160400 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
40160319 TGTGTAAAAA
40160329 TTATTATATATTATATCTT
1 TTATTAT-TATTATATCTT
*
40160348 TTATTATTCATTATATTATTT
1 TTATTATT-ATTATA-T-CTT
*
40160369 TTATT-TTACTATATCATT
1 TTATTATTATTATATC-TT
40160387 TTATTATTAATTAT
1 TTATTATT-ATTAT
40160401 TTATTATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 9 0.21
19 20 0.47
20 7 0.16
21 7 0.16
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATTATTATATCTT
Found at i:40160403 original size:27 final size:26
Alignment explanation
Indices: 40160331--40160402 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
40160321 TGTAAAAATT
* *
40160331 ATTATA-TATTATATCTTTTATTATTC
1 ATTATATTATTAT-TATTTTACTATTC
*
40160357 ATTATATTATTTTTATTTTACTATATC
1 ATTATATTATTATTATTTTACTAT-TC
*
40160384 ATTTTATTATTAATTATTT
1 ATTATATTATT-ATTATTT
40160403 ATTATGTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 15 0.39
27 17 0.45
28 6 0.16
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTATATTATTATTATTTTACTATTC
Found at i:40161689 original size:25 final size:25
Alignment explanation
Indices: 40161651--40161756 Score: 83
Period size: 25 Copynumber: 4.3 Consensus size: 25
40161641 CTTTCTCGAG
* *
40161651 CATATAACATGAAGCTTATGT-GAGC
1 CATATAACAGGAAGCTCAT-TAGAGC
* * *
40161676 CATATAACGGGAAGCTTATTCGAGC
1 CATATAACAGGAAGCTCATTAGAGC
** *
40161701 GGTATAACAAGAAGCTCATTAGAGC
1 CATATAACAGGAAGCTCATTAGAGC
* **
40161726 CATA-ATCAGGAAGCTCATGCGAGC
1 CATATAACAGGAAGCTCATTAGAGC
40161750 CA-ATAAC
1 CATATAAC
40161757 GGGTAACTTC
Statistics
Matches: 64, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 21 0.33
25 42 0.66
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (25 bp):
CATATAACAGGAAGCTCATTAGAGC
Found at i:40168450 original size:27 final size:27
Alignment explanation
Indices: 40168420--40168522 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 27
40168410 ATTATCAAAG
* *
40168420 TACCCCCAATTTACAGAATTACCGTTC
1 TACCCTCAATTTACAGAATTACCGTTT
* * *
40168447 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCGTTT
** *
40168474 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCGTTT
*
40168501 TACCCTCAATTTACAAAATTAC
1 TACCCTCAATTTACAGAATTAC
40168523 TAAAATACCC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCAATTTACAGAATTACCGTTT
Found at i:40168548 original size:54 final size:54
Alignment explanation
Indices: 40168402--40168548 Score: 123
Period size: 54 Copynumber: 2.7 Consensus size: 54
40168392 AATACTTTAG
* * * ** * * *
40168402 TTTACCAAATTATCAAAGTACCCCCAATTTACAGAATTACCGTTCTACCCTCGA
1 TTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACCGTTCTACCCTCAA
* * *** * * *
40168456 TTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCGTTTTACCCTCAA
1 TTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACCGTTCTACCCTCAA
* * *
40168510 TTTACAAAATTACTAAAATACCCCTGGTTTGTAAAATTA
1 TTTACAAAATTACCAAAATACCCCTGATTTATAAAATTA
40168549 GTAAAATACC
Statistics
Matches: 70, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.36
Consensus pattern (54 bp):
TTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACCGTTCTACCCTCAA
Found at i:40168572 original size:28 final size:27
Alignment explanation
Indices: 40168515--40168867 Score: 166
Period size: 27 Copynumber: 13.0 Consensus size: 27
40168505 CTCAATTTAC
*
40168515 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACTAAAATACCCCTGATTTGT
*
40168542 AAAATTAGTAAAATACCTCCTGATTTGT
1 AAAATTACTAAAATACC-CCTGATTTGT
* *
40168570 AAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACTAAAATACCCCT-GATTTGT
* * *
40168597 AAAAATTACCAAAGTA-CCCTCGATTTAT
1 -AAAATTACTAAAATACCCCT-GATTTGT
* **** **
40168625 AGAATTACTGTTTTA-CCCTCGATTTAC
1 AAAATTACTAAAATACCCCT-GATTTGT
* **** **
40168652 AGAATTACTGTTTTACCCCTGATTTAC
1 AAAATTACTAAAATACCCCTGATTTGT
* *** *
40168679 AAAATTACCATTTTACCCTTGATTATG-
1 AAAATTACTAAAATACCCCTGATT-TGT
* **
40168706 -AAATTACTGAAATACCCCT-ATAGGGT
1 AAAATTACTAAAATACCCCTGAT-TTGT
* * *
40168732 AGAATTACCAAAACACCCCT-AGTTTGT
1 AAAATTACTAAAATACCCCTGA-TTTGT
* * *
40168759 AAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACTAAAATACCCCTGATTTGT
* * *
40168786 GAAATTACCAAAATA-CCCTCAATTTGT
1 AAAATTACTAAAATACCCCT-GATTTGT
* **
40168813 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTAAAATACCCCTGATTTGT
* *
40168840 AAAATTAC-AGAAATACCCTTAATTTGT
1 AAAATTACTA-AAATACCCCTGATTTGT
40168867 A
1 A
40168868 GATTTACCAA
Statistics
Matches: 261, Mismatches: 52, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.01
26 20 0.08
27 184 0.70
28 54 0.21
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGATTTGT
Found at i:40168845 original size:54 final size:54
Alignment explanation
Indices: 40168509--40168884 Score: 199
Period size: 54 Copynumber: 6.9 Consensus size: 54
40168499 TTTACCCTCA
* * * **
40168509 ATTTACAAAATTACTAAAATACCC-CTGGTTTGTAAAATTAGTAAAATACCTCCTG
1 ATTTATAAAATTACCAAAATACCCTC-GATTTGTAAAATTACCAAAATACC-CCTG
* ** * *
40168564 ATTTGTAAAATTACTGAAATACCCTCGACTTGTAAAAATTACCAAAGTA-CCCTCG
1 ATTTATAAAATTACCAAAATACCCTCGATTTGT-AAAATTACCAAAATACCCCT-G
* ***** ** * *****
40168619 ATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCCTG
1 ATTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTG
* *** * **
40168673 ATTTACAAAATTACCATTTTACCCTTGATTATG--AAATTACTGAAATACCCCT-
1 ATTTATAAAATTACCAAAATACCCTCGATT-TGTAAAATTACCAAAATACCCCTG
*** * * * *
40168725 ATAGGGTAGAATTACCAAAACACCC-CTAGTTTGTAAAATTACCAAAATACCACTG
1 AT-TTATAAAATTACCAAAATACCCTCGA-TTTGTAAAATTACCAAAATACCCCTG
* * * *
40168780 GTTTGTGAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTG
1 ATTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTG
* ** * * *
40168834 ATTTACAAAATTA-CAGAAATACCCTTAATTTGTAGATTTACCAAAACACCC
1 ATTTATAAAATTACCA-AAATACCCTCGATTTGTAAAATTACCAAAATACCC
40168885 TTATAGGATG
Statistics
Matches: 247, Mismatches: 62, Indels: 25
0.74 0.19 0.07
Matches are distributed among these distances:
52 5 0.02
53 32 0.13
54 136 0.55
55 61 0.25
56 13 0.05
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
ATTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTG
Found at i:40168864 original size:27 final size:27
Alignment explanation
Indices: 40168734--40168887 Score: 96
Period size: 27 Copynumber: 5.7 Consensus size: 27
40168724 TATAGGGTAG
* * * **
40168734 AATTACCAAAACACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTAATTTACAA
** ***
40168761 AATTACCAAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTAATTTACAA
* **
40168788 AATTACCAAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTAATTTACAA
* *
40168815 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCTTAATTTACAA
** *
40168842 AATTA-CAGAAATACCCTTAATTTGTAG
1 AATTACCA-AAATACCCTTAATTTACAA
* *
40168869 ATTTACCAAAACACCCTTA
1 AATTACCAAAATACCCTTA
40168888 TAGGATGAAA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.03
27 98 0.94
28 3 0.03
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAATTTACAA
Found at i:40168866 original size:81 final size:82
Alignment explanation
Indices: 40168665--40168913 Score: 208
Period size: 81 Copynumber: 3.1 Consensus size: 82
40168655 ATTACTGTTT
*** * ** *
40168665 TACCCCTGATTTACAAAATTACCATTTTACCCTTGA-TTATGAAATTACTGAAATACCC-CTATA
1 TACCCCTGATTTACAAAATTACCAAAATACCCTTGATTTGTGAAATTACCAAAATACCCTCAATA
*
40168728 GGGTAGAATTACCAAAA
66 GGGTAAAATTACCAAAA
* ** *
40168745 CACCCCT-AGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCAAAATACCCTCAA
1 TACCCCTGA-TTTACAAAATTACCAAAATACC-CTTGATTTGTGAAATTACCAAAATACCCTCAA
**
40168808 T-TTGTAAAATTACCAAAA
64 TAGGGTAAAATTACCAAAA
* * * *
40168826 TACCCCTGATTTACAAAATTA-CAGAAATACCCTTAATTTGT-AGATTTACCAAAACACCCT-TA
1 TACCCCTGATTTACAAAATTACCA-AAATACCCTTGATTTGTGA-AATTACCAAAATACCCTCAA
* * * *
40168888 TAGGATGAAATGACTAAAA
64 TAGGGTAAAATTACCAAAA
40168907 TACCCCT
1 TACCCCT
40168914 AATAGGTAAA
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
79 1 0.01
80 31 0.23
81 96 0.73
82 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (82 bp):
TACCCCTGATTTACAAAATTACCAAAATACCCTTGATTTGTGAAATTACCAAAATACCCTCAATA
GGGTAAAATTACCAAAA
Found at i:40168948 original size:27 final size:27
Alignment explanation
Indices: 40168905--40168978 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
40168895 AAATGACTAA
*
40168905 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
40168932 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
40168959 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
40168979 TGATGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:40169717 original size:20 final size:21
Alignment explanation
Indices: 40169682--40169738 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
40169672 TGATACGTGG
40169682 GATATGATAT--ACATGAT-T
1 GATATGATATGCACATGATAT
40169700 GATATGATATGCACATGATAT
1 GATATGATATGCACATGATAT
*
40169721 G-TATGAAATGCACATGAT
1 GATATGATATGCACATGAT
40169739 GTAATCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 23 0.66
21 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (21 bp):
GATATGATATGCACATGATAT
Found at i:40169833 original size:26 final size:26
Alignment explanation
Indices: 40169788--40169871 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
40169778 GAGGAAGTGC
*
40169788 AAAAGGGC-TATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40169813 AAAAGGGCTTATGCCCCAGTTTACAG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40169839 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
40169862 AAAAGAGGCT
1 AAAAG-GGCT
40169872 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 7 0.13
25 16 0.31
26 24 0.46
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40170063 original size:42 final size:42
Alignment explanation
Indices: 40170004--40170095 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
40169994 TAGTCTCCCC
* * *
40170004 AAATGGGCTTGCATACATTCATT-AGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGA-CATTACATGTGATATTG
40170046 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40170088 AAATGGGC
1 AAATGGGC
40170096 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:40172106 original size:44 final size:44
Alignment explanation
Indices: 40172045--40172132 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
40172035 TGGACCAATG
* * * *
40172045 TAATAAATAGTCTTTAGTATTGACATTGAACGTCATTATGTATT
1 TAATAAATAGCCCTTAGTATTGACATTGAACGACACTATGTATT
40172089 TAATAAATAGCCCTTAGTATTGACATTGAACGACACTATGTATT
1 TAATAAATAGCCCTTAGTATTGACATTGAACGACACTATGTATT
40172133 AAAATTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (44 bp):
TAATAAATAGCCCTTAGTATTGACATTGAACGACACTATGTATT
Found at i:40173031 original size:37 final size:37
Alignment explanation
Indices: 40172976--40173473 Score: 597
Period size: 37 Copynumber: 13.3 Consensus size: 37
40172966 AAATGCAGTA
*
40172976 ATTTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* *
40173013 ATTTTGGGCTATGTGCCTAGTAGGCTTTGTGCAGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* *
40173050 -TTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
1 ATT-TT-GGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*
40173088 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
40173125 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* *
40173162 -TTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
1 ATT-TT-GGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*
40173200 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
40173237 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* *
40173274 -TTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
1 ATT-TT-GGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*
40173312 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTG
1 ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*** ** ***
40173349 ATATTCAAGCTCCGTGCCTAGCAGGCTTTGTGTTAGTG
1 AT-TTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* * * ** *
40173387 ATATTCGGGCTCTGTGCCTAGCAGGCTCTGTGCTAGAG
1 AT-TTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
* * * **
40173425 ATATTTGGGCTCTGTGTCTAGTAGGCTTTGCACCGGTG
1 AT-TTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
*
40173463 ATATTCGGGCT
1 AT-TTTGGGCT
40173474 CTATACCTAT
Statistics
Matches: 405, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
36 6 0.01
37 201 0.50
38 192 0.47
39 6 0.01
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (37 bp):
ATTTTGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
Found at i:40173072 original size:75 final size:75
Alignment explanation
Indices: 40172978--40173473 Score: 606
Period size: 75 Copynumber: 6.6 Consensus size: 75
40172968 ATGCAGTAAT
*
40172978 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGTAGGCTTTGT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
*
40173043 GCAGGTGTTA
66 GCCGGTGTTA
* * *
40173053 TTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTGATTTTGGGCCATGTGCCTAGCAGGCTTTGT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
40173118 GCCGGTGATT-
66 GCCGGTG-TTA
*
40173128 TT-GGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG-TTATTCGGGCTATGTGCTTAGCAGGCTTT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATT-TT-GGGCTATGTGCCTAGCAGGCTTT
*
40173191 GTGCTGGTGATT-
64 GTGCCGGTG-TTA
*
40173203 TT-GGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
40173267 GCCGGTGTTA
66 GCCGGTGTTA
* * *
40173277 TTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTGATTTTGGGCCATGTGCCTAGCAGGCTTTGT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
*
40173342 GCCGGTGATA
66 GCCGGTGTTA
** ** *** * * *
40173352 TTCAAGCTCCGTGCCTAGCAGGCTTTGTGTTAGTGATATTCGGGCTCTGTGCCTAGCAGGCTCTG
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGAT-TTTGGGCTATGTGCCTAGCAGGCTTTG
** * *
40173417 TGCTAGAGATA
65 TGCCGGTGTTA
* * * * ** *
40173428 TTTGGGCTCTGTGTCTAGTAGGCTTTGCACCGGTGATATTCGGGCT
1 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGAT-TTTGGGCT
40173474 CTATACCTAT
Statistics
Matches: 371, Mismatches: 43, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
73 4 0.01
74 64 0.17
75 233 0.63
76 70 0.19
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (75 bp):
TTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
GCCGGTGTTA
Found at i:40173183 original size:112 final size:112
Alignment explanation
Indices: 40172976--40173473 Score: 746
Period size: 112 Copynumber: 4.4 Consensus size: 112
40172966 AAATGCAGTA
* * *
40172976 ATTTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGTAGGCTTT
1 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
*
40173041 GTGCAGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
66 GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
40173088 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
1 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
40173153 GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
66 GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
40173200 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
1 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
40173265 GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
66 GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
*** **
40173312 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATATTCAAGCTCCGTGCCTAGCAGGCTT
1 ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGAT-TTTGGGCTATGTGCCTAGCAGGCTT
*** * * * * * *
40173377 TGTGTTAGTGATATTCGGGCTCTGTGCCTAGCAGGCTCTGTGCTAGAG
65 TGTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
* * ** *
40173425 ATATTTGGGCTC-TGTGTCTAGTAGGCTTTGCACCGGTGATATTCGGGCT
1 AT-TTTGGGC-CATGTGCCTAGCAGGCTTTGTGCCGGTGAT-TTTGGGCT
40173474 CTATACCTAT
Statistics
Matches: 359, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
112 259 0.72
113 61 0.17
114 38 0.11
115 1 0.00
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (112 bp):
ATTTTGGGCCATGTGCCTAGCAGGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTT
GTGCCGGTGTTATTCGGGCTATGTGCTTAGCAGGCTTTGTGCTGGTG
Found at i:40182423 original size:29 final size:28
Alignment explanation
Indices: 40182365--40182444 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
40182355 GTATCTAGCT
* *
40182365 CATTAAGCCCAATCATATTCAT-TGGCC
1 CATTAGGCCCAATCACATTCATATGGCC
*
40182392 CATTAGGCCCAAATCACATTTATATGGCC
1 CATTAGGCCC-AATCACATTCATATGGCC
* *
40182421 CATTAGGACCAGTCACATTCATAT
1 CATTAGGCCCAATCACATTCATAT
40182445 TCATGCTTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 9 0.20
28 22 0.49
29 14 0.31
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (28 bp):
CATTAGGCCCAATCACATTCATATGGCC
Found at i:40182790 original size:21 final size:21
Alignment explanation
Indices: 40182766--40182807 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40182756 CTACAATCGA
40182766 TATCACTCAAAGATTAATCTT
1 TATCACTCAAAGATTAATCTT
40182787 TATCACTCAAAGATTAATCTT
1 TATCACTCAAAGATTAATCTT
40182808 ACATACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (21 bp):
TATCACTCAAAGATTAATCTT
Found at i:40185213 original size:13 final size:14
Alignment explanation
Indices: 40185192--40185237 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
40185182 AGTCCTTTAC
40185192 AAATGCAGATA-ACA
1 AAAT-CAGATATACA
40185206 AAATCAGATATACA
1 AAATCAGATATACA
*
40185220 GAAT-AGATATACA
1 AAATCAGATATACA
40185233 AAATC
1 AAATC
40185238 CTACTCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (14 bp):
AAATCAGATATACA
Found at i:40186379 original size:11 final size:10
Alignment explanation
Indices: 40186354--40186381 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40186344 TTAACATCAG
40186354 ATTTTTGGGA
1 ATTTTTGGGA
40186364 ATTTTTGGGA
1 ATTTTTGGGA
40186374 ATTTTTGG
1 ATTTTTGG
40186382 AATAGAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (10 bp):
ATTTTTGGGA
Done.