Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 170 of 218
Found at i:51585072 original size:23 final size:24
Alignment explanation
Indices: 51585038--51585111 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 24
51585028 AGCTCAAATA
51585038 AGCTTC-CTGATA-GACTCTTTGTG
1 AGCTTCTCTGATATG-CTCTTTGTG
*
51585061 AGCTTCTC-GATATGCTTTTTGTG
1 AGCTTCTCTGATATGCTCTTTGTG
51585084 AGCTTCT-TGATTAATGGCTCTTTGTG
1 AGCTTCTCTGA-T-AT-GCTCTTTGTG
51585110 AG
1 AG
51585112 TTTCCTGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
23 27 0.63
24 3 0.07
25 2 0.05
26 11 0.26
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (24 bp):
AGCTTCTCTGATATGCTCTTTGTG
Found at i:51585126 original size:26 final size:27
Alignment explanation
Indices: 51585070--51585129 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
51585060 GAGCTTCTCG
* *
51585070 ATAT-GCTTTTTGTGAGCTTCTTGATT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
*
51585096 A-ATGGCTCTTTGTGAGTTTCCTG-TT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
51585121 ATATGGCTC
1 ATATGGCTC
51585130 GAGAGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (27 bp):
ATATGGCTCTTTGTGAGCTTCCTGATT
Found at i:51589567 original size:9 final size:9
Alignment explanation
Indices: 51589553--51589589 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51589543 TATAGTTTGA
51589553 TATTCGAAT
1 TATTCGAAT
51589562 TATTCGAAT
1 TATTCGAAT
*
51589571 TATTCGAGT
1 TATTCGAAT
51589580 TATTCGAAT
1 TATTCGAAT
51589589 T
1 T
51589590 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:51589659 original size:9 final size:9
Alignment explanation
Indices: 51589642--51589672 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
51589632 TCGAGTTGAT
51589642 TCGAATAAC
1 TCGAATAAC
*
51589651 TCGATTAAC
1 TCGAATAAC
51589660 TCGAATAAC
1 TCGAATAAC
51589669 TCGA
1 TCGA
51589673 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:51589757 original size:16 final size:16
Alignment explanation
Indices: 51589736--51589767 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51589726 CCCCTACGCT
51589736 AAACAGCTGTCGTGCC
1 AAACAGCTGTCGTGCC
*
51589752 AAACAGTTGTCGTGCC
1 AAACAGCTGTCGTGCC
51589768 CACGATGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (16 bp):
AAACAGCTGTCGTGCC
Found at i:51595316 original size:24 final size:23
Alignment explanation
Indices: 51595283--51595330 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
51595273 AGATTGAAAG
* *
51595283 CCAAAACGTGTTAGGTTAGCAGA
1 CCAAAACGTGCTAGGGTAGCAGA
*
51595306 CCAAAGACGTGCTAGGGTAGTAGA
1 CCAAA-ACGTGCTAGGGTAGCAGA
51595330 C
1 C
51595331 TTTTAGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (23 bp):
CCAAAACGTGCTAGGGTAGCAGA
Found at i:51597539 original size:22 final size:21
Alignment explanation
Indices: 51597501--51597560 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
51597491 TAATATTATA
*
51597501 TTTATATTTTAAGTTTATTTC
1 TTTATATTTTAAATTTATTTC
51597522 TTTATATTTTAAAATTTATTTC
1 TTTATATTTT-AAATTTATTTC
51597544 TTT-TAGTATTTAAATTT
1 TTTATA-T-TTTAAATTT
51597561 CATGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 12 0.34
22 20 0.57
23 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATATTTTAAATTTATTTC
Found at i:51601085 original size:29 final size:29
Alignment explanation
Indices: 51601052--51601110 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
51601042 TTCGATCTCT
*
51601052 ATATTTTTAAAATATTTTTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
*
51601081 ATATTTTTATAATATTATTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
51601110 A
1 A
51601111 ATGGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTTTTAAAATATTATTAATTAGTTCA
Found at i:51603351 original size:31 final size:28
Alignment explanation
Indices: 51603296--51603395 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
51603286 GGTTTAGGGA
* *
51603296 TTTTAAA-AATTAAATCAAGATTTAGCATTT
1 TTTTAAATAATTAAAT-TAGTTTTAG--TTT
***
51603326 TTTTAAATAATTAAATTAGGTTTTAGGGGG
1 TTTTAAATAATTAAATTA-GTTTTA-GTTT
51603356 TTTTAAATAAATTAAATTAGTGTTTAGTTT
1 TTTTAAAT-AATTAAATTAGT-TTTAGTTT
51603386 TTTTAAATAA
1 TTTTAAATAA
51603396 CTTTGTGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.04
30 27 0.47
31 27 0.47
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (28 bp):
TTTTAAATAATTAAATTAGTTTTAGTTT
Found at i:51603390 original size:30 final size:31
Alignment explanation
Indices: 51603323--51603395 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
51603313 AGATTTAGCA
51603323 TTTTTTTAAAT-AATTAAATTAGGTTTTAGG
1 TTTTTTTAAATAAATTAAATTAGGTTTTAGG
***
51603353 GGGTTTTAAATAAATTAAATTA-GTGTTTA-G
1 TTTTTTTAAATAAATTAAATTAGGT-TTTAGG
51603383 TTTTTTTAAATAA
1 TTTTTTTAAATAA
51603396 CTTTGTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTTTTTAAATAAATTAAATTAGGTTTTAGG
Found at i:51603608 original size:126 final size:126
Alignment explanation
Indices: 51603447--51603718 Score: 463
Period size: 126 Copynumber: 2.2 Consensus size: 126
51603437 AATAAGGATT
* *
51603447 TTTTTCTACAGTAATTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* * *
51603512 ACGCTTCAAGCACGATGCACTGTCAGCAAAATTGATGAAAAAGGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
*
51603573 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* * *
51603638 ACGCTTTAAGCAGGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTGGACACTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
51603699 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
51603719 TTTGGCCTTA
Statistics
Matches: 136, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 136 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
Found at i:51607165 original size:18 final size:18
Alignment explanation
Indices: 51607139--51607181 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
51607129 GATTGGGAAA
* *
51607139 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
51607157 AGGATACATATCAGGGCT
1 AGGATACATATAAGGGCT
51607175 AGGATAC
1 AGGATAC
51607182 GCATTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:51608815 original size:26 final size:24
Alignment explanation
Indices: 51608779--51608831 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
51608769 ACTGTTATAA
*
51608779 AAAATTATAAAATAAAAAT-TAATT
1 AAAATTATAAAAGAAAAATAT-ATT
51608803 AAAATTAATTAAAAGAAAAATATATT
1 AAAATT-A-TAAAAGAAAAATATATT
51608829 AAA
1 AAA
51608832 TAATATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 17 0.68
27 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATTATAAAAGAAAAATATATT
Found at i:51609035 original size:30 final size:30
Alignment explanation
Indices: 51609001--51609065 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
51608991 ATTAATTAAA
51609001 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
* *
51609031 GAGAGCTTTGATAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
51609061 GAGAG
1 GAGAG
51609066 TTTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAAAAATTTAAGGAGAAATTT
Found at i:51612590 original size:8 final size:8
Alignment explanation
Indices: 51612573--51612603 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
51612563 CCTTTTACTA
*
51612573 TATATTTG
1 TATATATG
51612581 TATATATG
1 TATATATG
51612589 TATATATG
1 TATATATG
51612597 TATATAT
1 TATATAT
51612604 AGCAAACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATATATG
Found at i:51617429 original size:41 final size:41
Alignment explanation
Indices: 51617377--51617458 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
51617367 ATATTTTATT
* * *
51617377 TTATGTTTTAGTAGTTTATTAGAATAAGTGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
51617418 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
51617459 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
Found at i:51625914 original size:3 final size:3
Alignment explanation
Indices: 51625906--51625962 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
51625896 GGACTCGTAT
* *
51625906 TCA TCA TCA TCA TCA TCA T-A ACAA TAA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA
51625951 TCA TCA TCA TCA
1 TCA TCA TCA TCA
51625963 AAAGAAGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:51627149 original size:10 final size:10
Alignment explanation
Indices: 51627134--51627192 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
51627124 TTTTTTAAAA
*
51627134 ATTAAAAATC
1 ATTAAAAATT
51627144 ATT-AAAATT
1 ATTAAAAATT
51627153 ATTAAAAATT
1 ATTAAAAATT
51627163 A-TAAAAATAT
1 ATTAAAAAT-T
* *
51627173 TTTTAAAATT
1 ATTAAAAATT
*
51627183 -TAAAAAATT
1 ATTAAAAATT
51627192 A
1 A
51627193 AATAACTGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 22 0.55
10 12 0.30
11 6 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:51627169 original size:19 final size:20
Alignment explanation
Indices: 51627134--51627188 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
51627124 TTTTTTAAAA
* *
51627134 ATTAAAAATCATTAAAAT-T
1 ATTAAAAATTATAAAAATAT
51627153 ATTAAAAATTATAAAAATAT
1 ATTAAAAATTATAAAAATAT
* *
51627173 TTTTAAAATT-TAAAAA
1 ATTAAAAATTATAAAAA
51627189 ATTAAATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAAAAATTATAAAAATAT
Found at i:51627190 original size:48 final size:48
Alignment explanation
Indices: 51627097--51627188 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
51627087 TTTTAAAATT
* *
51627097 TTAAAATTTTTAAAAATATAAGAACTATTTTTTAAAAATTAAAAATCA
1 TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
*
51627145 TTAAAATTATTAAAAATTATAA-AAATA-TTTTTAAAATTTAAAAA
1 TTAAAATTATTAAAAA-TATAAGAAATATTTTTTAAAAATTAAAAA
51627189 ATTAAATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 16 0.40
48 19 0.47
49 5 0.12
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (48 bp):
TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
Found at i:51641438 original size:16 final size:16
Alignment explanation
Indices: 51641417--51641447 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51641407 CAAAATTCTT
51641417 GGACAATCTTCTCATG
1 GGACAATCTTCTCATG
*
51641433 GGACAATCTTTTCAT
1 GGACAATCTTCTCAT
51641448 TCCATATGTG
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:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
GGACAATCTTCTCATG
Found at i:51642081 original size:31 final size:31
Alignment explanation
Indices: 51642043--51642106 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
51642033 GCCAAACAAT
51642043 TTAGTGTAATTACTACTACCATACGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
* *
51642074 TTAGTGTAATTACTACTAGCATATGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
51642105 TT
1 TT
51642107 TCTCTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (31 bp):
TTAGTGTAATTACTACTACCATACGCAAATA
Found at i:51648076 original size:7 final size:7
Alignment explanation
Indices: 51648064--51648097 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
51648054 TCCCTCTCCT
51648064 ATATTTA
1 ATATTTA
51648071 ATATTTA
1 ATATTTA
51648078 ATATTTA
1 ATATTTA
51648085 ATATTTA
1 ATATTTA
51648092 ATATTT
1 ATATTT
51648098 GACTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:51650014 original size:21 final size:23
Alignment explanation
Indices: 51649988--51650031 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
51649978 TTTCTCATAA
51649988 AAAATTATAAAAAA-A-TAAAAT
1 AAAATTATAAAAAATATTAAAAT
51650009 AAAATTATAAAAAATATTAAAAT
1 AAAATTATAAAAAATATTAAAAT
51650032 TGATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
22 1 0.05
23 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATTATAAAAAATATTAAAAT
Found at i:51650069 original size:16 final size:16
Alignment explanation
Indices: 51650044--51650079 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
51650034 ATATAAAATT
51650044 ATTA-AAATTATTATA
1 ATTATAAATTATTATA
51650059 ATTATAAATTATTATA
1 ATTATAAATTATTATA
51650075 ATTAT
1 ATTAT
51650080 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAAATTATTATA
Found at i:51650117 original size:75 final size:71
Alignment explanation
Indices: 51650026--51650215 Score: 174
Period size: 75 Copynumber: 2.6 Consensus size: 71
51650016 TAAAAAATAT
* * * *
51650026 TAAAATTGATATAAAATTATTAAAATTATTATAATTATAAATTATTATAATTATTATAAAAAATC
1 TAAAATT-ATAAAAAATTATTAAAATTATTATAATTATAAAGTATTA-AAATACT-TAAAAAA-C
51650091 TAAT-AAATTA
62 -AATAAAATTA
* *
51650101 TAAAATTAATAAAAAATTATTTAAAA-TATTTTGAATTAAAAAAGTATTAAAATACTTAAAAAAC
1 TAAAATT-ATAAAAAATTA-TTAAAATTATTAT-AATT-ATAAAGTATTAAAATACTTAAAAAAC
51650165 AATAAAAATTA
62 AAT-AAAATTA
51650176 TAAAAATTAT-AAAAA-TATTAAAATTGATTA-AATTTATAAA
1 T-AAAATTATAAAAAATTATTAAAATT-ATTATAA-TTATAAA
51650216 AATTTATAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
72 12 0.12
73 8 0.08
74 9 0.09
75 38 0.39
76 21 0.22
77 9 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (71 bp):
TAAAATTATAAAAAATTATTAAAATTATTATAATTATAAAGTATTAAAATACTTAAAAAACAATA
AAATTA
Found at i:51650190 original size:19 final size:19
Alignment explanation
Indices: 51649987--51650224 Score: 87
Period size: 19 Copynumber: 12.1 Consensus size: 19
51649977 TTTTCTCATA
* *
51649987 AAAAATTATAAAAAAATAAA
1 AAAAATTAT-AAAAAATTAT
51650007 ATAAAATTATAAAAAA-TAT
1 A-AAAATTATAAAAAATTAT
* *
51650026 TAAAATTGATATAAAATTAT
1 AAAAATT-ATAAAAAATTAT
* * *
51650046 TAAAATTAT-TATAATTAT
1 AAAAATTATAAAAAATTAT
* **
51650064 AAATTATTAT-AATTATTAT
1 AAA-AATTATAAAAAATTAT
* * *
51650083 AAAAAATCTAATAAATTAT
1 AAAAATTATAAAAAATTAT
51650102 -AAAATTAATAAAAAATTATTT
1 AAAAATT-ATAAAAAATTA--T
*
51650123 AAAATATTTTGAATTAAAAAAGTAT
1 AAAA-A--TT--A-TAAAAAATTAT
* **
51650148 TAAAA-TACTTAAAAAACAAT
1 AAAAATTA--TAAAAAATTAT
51650168 AAAAATTAT-AAAAATTAT
1 AAAAATTATAAAAAATTAT
*
51650186 AAAAA-TAT-TAAAATTGAT
1 AAAAATTATAAAAAATT-AT
* * *
51650204 TAAATTTATAAAAATTTAT
1 AAAAATTATAAAAAATTAT
51650223 AA
1 AA
51650225 TAAAAAAAAA
Statistics
Matches: 168, Mismatches: 31, Indels: 39
0.71 0.13 0.16
Matches are distributed among these distances:
17 9 0.05
18 41 0.24
19 48 0.29
20 36 0.21
21 12 0.07
22 3 0.02
23 1 0.01
24 1 0.01
25 6 0.04
26 2 0.01
27 9 0.05
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATTATAAAAAATTAT
Found at i:51650218 original size:10 final size:9
Alignment explanation
Indices: 51650009--51650224 Score: 102
Period size: 9 Copynumber: 23.1 Consensus size: 9
51649999 AAAATAAAAT
51650009 AAAATTATA
1 AAAATTATA
* *
51650018 AAAAATATT
1 AAAATTATA
51650027 AAAATTGATA
1 AAAATT-ATA
*
51650037 TAAAATTATT
1 -AAAATTATA
*
51650047 AAAATTATT
1 AAAATTATA
*
51650056 ATAATTATA
1 AAAATTATA
*
51650065 AATTATTATA
1 AA-AATTATA
**
51650075 ATTATTATA
1 AAAATTATA
* *
51650084 AAAAATCTA
1 AAAATTATA
51650093 ATAAATTAT-
1 A-AAATTATA
51650102 AAAATTAATAA
1 AAAATT-AT-A
51650113 AAAATTATTTA
1 AAAATTA--TA
51650124 AAATATT-T-
1 AAA-ATTATA
**
51650132 TGAATTA-A
1 AAAATTATA
*
51650140 AAAAGTATTA
1 AAAATTA-TA
51650150 AAATACTTA-A
1 AAA-A-TTATA
**
51650160 AAAACAATA
1 AAAATTATA
51650169 AAAATTATA
1 AAAATTATA
51650178 AAAATTATA
1 AAAATTATA
*
51650187 AAAA-TATT
1 AAAATTATA
*
51650195 AAAATTGATT
1 AAAATT-ATA
*
51650205 AAATTTATA
1 AAAATTATA
51650214 AAAATTTATA
1 AAAA-TTATA
51650224 A
1 A
51650225 TAAAAAAAAA
Statistics
Matches: 157, Mismatches: 30, Indels: 39
0.69 0.13 0.17
Matches are distributed among these distances:
7 3 0.02
8 18 0.11
9 74 0.47
10 39 0.25
11 17 0.11
12 6 0.04
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
AAAATTATA
Found at i:51650648 original size:9 final size:9
Alignment explanation
Indices: 51650636--51650826 Score: 64
Period size: 9 Copynumber: 20.0 Consensus size: 9
51650626 TTTTATGATT
51650636 TTTTTATAA
1 TTTTTATAA
51650645 TTTTTATAA
1 TTTTTATAA
**
51650654 GTTCATATCAA
1 -TTTTTAT-AA
* *
51650665 TTTTAATAC
1 TTTTTATAA
* *
51650674 TATTTATGA
1 TTTTTATAA
*
51650683 TTTTAATAGAA
1 TTTT--TATAA
* *
51650694 TTTTAATACG
1 TTTTTATA-A
51650704 TTTTTATAAA
1 TTTTTAT-AA
*
51650714 TTTTTAAATA
1 TTTTTATA-A
*
51650724 TGTTTTATTA
1 T-TTTTATAA
*
51650734 CTTTTATAAA
1 TTTTTAT-AA
*
51650744 TTTTATAGAA
1 TTTT-TATAA
*
51650754 TTTTTAT-G
1 TTTTTATAA
51650762 TTTTTGATAA
1 TTTTT-ATAA
*
51650772 TATTTATAA
1 TTTTTATAA
*
51650781 GTTTATATCAA
1 -TTTTTAT-AA
*
51650792 TTTTCAT-A
1 TTTTTATAA
51650800 TATTTT-TAA
1 T-TTTTATAA
* *
51650809 TATTTATAT
1 TTTTTATAA
51650818 TTTTTATAA
1 TTTTTATAA
51650827 ATATTTTCTG
Statistics
Matches: 127, Mismatches: 38, Indels: 34
0.64 0.19 0.17
Matches are distributed among these distances:
8 11 0.09
9 49 0.39
10 48 0.38
11 19 0.15
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:51654182 original size:96 final size:94
Alignment explanation
Indices: 51654051--51654371 Score: 479
Period size: 96 Copynumber: 3.4 Consensus size: 94
51654041 ACACTATCAG
51654051 GTATATTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTAT
1 GTAT-TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTAT
51654115 TTAGTACACTATCGGGTATGTAATATTATC
65 TTAGTACACTATCGGGTATGTAATATTATC
51654145 AGGTATATTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATT
1 --GTAT-TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATT
*
51654209 ATTTAGTACACTATTGGGTATGTAATATTATC
63 ATTTAGTACACTATCGGGTATGTAATATTATC
* *
51654241 TTATTTGAT-TCATTTAGTTGGAGGGTAAAATTTTACTATTTGATTGATGGAATGTAAGATTATT
1 GTATTTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAA-A--A-T
*
51654305 TATTTAGTACACCATCGGGTATGTAATATTATC
62 TATTTAGTACACTATCGGGTATGTAATATTATC
* * *
51654338 TTATTTG-TTTCATTTAGCTGGAGGGTAAAATTTT
1 GTATTTGATCTCATTTAGTTGGAGGGTAAAATTTT
51654372 TGATAAAATG
Statistics
Matches: 213, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
92 1 0.00
93 50 0.23
94 4 0.02
96 95 0.45
97 63 0.30
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (94 bp):
GTATTTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATT
TAGTACACTATCGGGTATGTAATATTATC
Found at i:51669437 original size:113 final size:113
Alignment explanation
Indices: 51669250--51669541 Score: 313
Period size: 113 Copynumber: 2.6 Consensus size: 113
51669240 GAGCCTTAAA
* * * *
51669250 CGCCGCAAGATATCTTAATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGCGT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGT-TTGGTCTTGATGTATAATAGAATTAGTGGCGC
*
51669315 TTAAGGAAAACAC-CAG-TAAAGGATAGTTA-TAGCAGCGTTTGGTGGTAA-G
65 TTAAGGAAAA-ACGCAGCTAAAGGATA-TCATTAGCAGCGTTT-GTGG-AACG
* * * * * *
51669364 CGCCTCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTGTATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATAATAGAATTAGTGGCGCT
* * * * *
51669429 TGATGAAAAACGCCGCTAAAGTATATCATTAGCGGCGTTTGTGGAACG
66 TAAGGAAAAACGCAGCTAAAGGATATCATTAGCAGCGTTTGTGGAACG
* * * * *
51669477 CGCCGCAAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTT-GGTCTTGATGTATAATAGAATTAGTGGCGC
51669542 AAATGGGAAA
Statistics
Matches: 147, Mismatches: 26, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
112 4 0.03
113 73 0.50
114 70 0.48
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (113 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATAATAGAATTAGTGGCGCT
TAAGGAAAAACGCAGCTAAAGGATATCATTAGCAGCGTTTGTGGAACG
Found at i:51669449 original size:114 final size:114
Alignment explanation
Indices: 51669019--51669579 Score: 399
Period size: 114 Copynumber: 4.9 Consensus size: 114
51669009 TTTACCACAC
* * * * * * * *
51669019 AGCGCCGCAAAATCTC-AAGACCAACACACAGCGTTCTGGTGTTGATGTATATTGGCATTAGTGG
1 AGCGCCGCAAAATATCTTA-ACCAAAACGCAGAGTT-TGGTCTTGATGTATATTAGAATTAGTGG
* * * *
51669083 CGCTTACGAACAAACGCCGGC-AATGTATAG-TATTAGCGGCGCTTAGTGG-A
64 CGCTTATGAA-AAACGCC-GCTAAAGTATAGTTATTAGCGGCGTTTGGTGGTA
** * * * * * **
51669133 AGTACTGCAAAAGATGTTAGCCAAAATGCAGAGTTTGGTCTTGATGTATATTTCAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
* * * ** ***
51669198 CTTATAAAAAAAACGCCGCTAATGTATAG-TATTAGTGGCG-CAGAGCCTTA
66 CTTAT--GAAAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTG-GTGGTA
* * * * * *
51669248 AACGCCGCAAGATATCTTAATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGT-TTGGTCTTGATGTATATTAGAATTAGTGGC
* * * * * *
51669313 GTTTAAGGAAAACACCAG-TAAAGGATAGTTA-TAGCAGCGTTTGGTGGTA
65 GCTTATGAAAAACGCC-GCTAAAGTATAGTTATTAGCGGCGTTTGGTGGTA
* * * *
51669362 AGCGCCTCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTGTATTAGAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
*
51669427 CTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCGTTT-GTGG-A
66 CTT-ATGAAAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTGGTGGTA
* * * * * *
51669474 ACGCGCCGCAAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGG
1 A-GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGG
** * * * *
51669539 CGCAAATGGGAAAACGCCACTGAAGCATAG-TATTAGCGGCG
64 CGCTTAT-GAAAAACGCCGCTAAAGTATAGTTATTAGCGGCG
51669580 CTTTTACCGA
Statistics
Matches: 343, Mismatches: 87, Indels: 34
0.74 0.19 0.07
Matches are distributed among these distances:
112 2 0.01
113 100 0.29
114 179 0.52
115 31 0.09
116 31 0.09
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (114 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
CTTATGAAAAACGCCGCTAAAGTATAGTTATTAGCGGCGTTTGGTGGTA
Found at i:51669706 original size:18 final size:18
Alignment explanation
Indices: 51669685--51669720 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
51669675 TCATTTTATA
51669685 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
51669703 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
51669721 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:51670075 original size:29 final size:29
Alignment explanation
Indices: 51670042--51670098 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
51670032 AAGGGTTGTA
*
51670042 ATTTAGGGGTTATAGATTAAGAGTCAGGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGGG
* * * *
51670071 ATTTAAGGTTTATGGATTCAGTGTCAGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGG
51670099 TTAGGCTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.32, T:0.35
Consensus pattern (29 bp):
ATTTAAGGGTTATAGATTAAGAGTCAGGG
Found at i:51670676 original size:7 final size:7
Alignment explanation
Indices: 51670666--51670740 Score: 60
Period size: 7 Copynumber: 10.6 Consensus size: 7
51670656 GACTTTTACT
51670666 GTTTGGG
1 GTTTGGG
**
51670673 GTTTTAAG
1 G-TTTGGG
*
51670681 GTTTAGG
1 GTTTGGG
**
51670688 GTTTAAG
1 GTTTGGG
51670695 GTTTGGG
1 GTTTGGG
51670702 GTTTGGG
1 GTTTGGG
**
51670709 GTTTAAG
1 GTTTGGG
51670716 GTTTGGG
1 GTTTGGG
51670723 GTTTGGG
1 GTTTGGG
* *
51670730 ATTTGAG
1 GTTTGGG
51670737 GTTT
1 GTTT
51670741 AAGGTTTACA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 49 0.91
8 5 0.09
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (7 bp):
GTTTGGG
Found at i:51670694 original size:14 final size:14
Alignment explanation
Indices: 51670675--51670748 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
51670665 TGTTTGGGGT
51670675 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
51670689 TTTAAGGTTTGGGG
1 TTTAAGGTTTAGGG
** *
51670703 TTTGGGGTTTAAGG
1 TTTAAGGTTTAGGG
**
51670717 TTTGGGGTTT-GGG
1 TTTAAGGTTTAGGG
* *
51670730 ATTTGAGGTTTAAGG
1 -TTTAAGGTTTAGGG
51670745 TTTA
1 TTTA
51670749 CAAATTATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
13 2 0.04
14 45 0.92
15 2 0.04
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:51670710 original size:21 final size:21
Alignment explanation
Indices: 51670680--51670740 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
51670670 GGGGTTTTAA
*
51670680 GGTTTAGGGTTTAAGGTTTGG
1 GGTTTGGGGTTTAAGGTTTGG
51670701 GGTTTGGGGTTTAAGGTTTGG
1 GGTTTGGGGTTTAAGGTTTGG
* *
51670722 GGTTTGGGATTTGAGGTTT
1 GGTTTGGGGTTTAAGGTTT
51670741 AAGGTTTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.11, C:0.00, G:0.44, T:0.44
Consensus pattern (21 bp):
GGTTTGGGGTTTAAGGTTTGG
Found at i:51670746 original size:21 final size:20
Alignment explanation
Indices: 51670675--51670747 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
51670665 TGTTTGGGGT
51670675 TTTAAGGTTTAGGGTTTAAGG
1 TTTAAGGTTT-GGGTTTAAGG
**
51670696 TTTGGGGTTTGGGGTTTAAGG
1 TTTAAGGTTT-GGGTTTAAGG
** *
51670717 TTTGGGGTTTGGGATTTGAGG
1 TTTAAGGTTTGGG-TTTAAGG
51670738 TTTAAGGTTT
1 TTTAAGGTTT
51670748 ACAAATTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 3 0.07
21 42 0.93
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (20 bp):
TTTAAGGTTTGGGTTTAAGG
Found at i:51671326 original size:74 final size:74
Alignment explanation
Indices: 51671248--51671475 Score: 220
Period size: 74 Copynumber: 3.1 Consensus size: 74
51671238 TGAAATGTTG
51671248 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
51671313 GAAACGGCT
66 GAAACGGCT
* * * * ** * * *
51671322 TCGTTTTGAGT-TATAG--TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGT
1 TCGTTTT-TGTCTATTGTATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-
*** *
51671381 TTATTGAAATGTTG-T
61 TTGGGGAAACG--GCT
51671396 T-GTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
51671460 GAAACGGCT
66 GAAACGGCT
51671469 TCGTTTT
1 TCGTTTT
51671476 GAGTTATAGT
Statistics
Matches: 113, Mismatches: 26, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
71 3 0.03
72 18 0.16
73 32 0.28
74 39 0.35
75 18 0.16
76 3 0.03
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (74 bp):
TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
GAAACGGCT
Found at i:51671351 original size:147 final size:147
Alignment explanation
Indices: 51671191--51671517 Score: 600
Period size: 147 Copynumber: 2.2 Consensus size: 147
51671181 TACGTTGCTA
*
51671191 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
51671256 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671321 TTCGTTTTGAGTTATAG
131 TTCGTTTTGAGTTATAG
*
51671338 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
51671403 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671468 TTCGTTTTGAGTTATAG
131 TTCGTTTTGAGTTATAG
* * * *
51671485 TTAGTGCCGCTTTACTTGAAACGCCGCAAAATT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT
51671518 GTTCAAACAT
Statistics
Matches: 174, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 174 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (147 bp):
TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
TTCGTTTTGAGTTATAG
Found at i:51671401 original size:73 final size:74
Alignment explanation
Indices: 51671190--51671421 Score: 183
Period size: 73 Copynumber: 3.1 Consensus size: 74
51671180 TTACGTTGCT
* *
51671190 ATTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
51671255 TGTCTATTG
66 AGTCTATAG
* * ** * * * *** *
51671264 TATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-TTGGGGAAACG--GCTT
1 -ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTG-TT
51671323 CGTTTTGAGT-TATAG
61 -GTTTT-AGTCTATAG
51671338 -TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
51671402 TGTCTATTG
66 AGTCTATAG
51671411 TATTAGTGGCG
1 -ATTAGTGGCG
51671422 TTTTTCGGAA
Statistics
Matches: 114, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
71 3 0.03
72 18 0.16
73 31 0.27
74 31 0.27
75 28 0.25
76 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (74 bp):
ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
AGTCTATAG
Found at i:51671508 original size:73 final size:72
Alignment explanation
Indices: 51671266--51671518 Score: 194
Period size: 73 Copynumber: 3.5 Consensus size: 72
51671256 GTCTATTGTA
* * * *
51671266 TTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTTGA
1 TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTTGA
51671331 GTTATAG
66 GTTATAG
* * * * *** *
51671338 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTG-TT-G
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTGGGTAA--ACTG-TTGGGGAAACG--GCTTCG
* *
51671398 TTTT-TGTCTATTG
60 TTTTGAGT-TATAG
* * * *
51671411 TATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTT
1 --TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTT
51671476 GAGTTATAG
64 GAGTTATAG
* *
51671485 TTAGTGCCGCTTTACTTGAAACGCCGCAAAATTG
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTG
51671519 TTCAAACATT
Statistics
Matches: 133, Mismatches: 32, Indels: 31
0.68 0.16 0.16
Matches are distributed among these distances:
71 3 0.02
72 30 0.23
73 47 0.35
74 32 0.24
75 18 0.14
76 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (72 bp):
TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTTGA
GTTATAG
Found at i:51671535 original size:147 final size:146
Alignment explanation
Indices: 51671191--51671585 Score: 544
Period size: 147 Copynumber: 2.7 Consensus size: 146
51671181 TACGTTGCTA
* * * **
51671191 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGCCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
51671256 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671321 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* * ** *
51671338 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGCCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
51671403 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671468 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* * * * *
51671485 TTAGTGCCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGCCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAATGTTGTCGTTTT
* * * *
51671548 TGT-AAATGTTATTAGTGGCGTTTTACCGAAAACGCCAC
64 TGTCTATTG-TATTAGTGGCGTTTT-TCGGAAACGCCAC
51671586 GGGTTTGAGG
Statistics
Matches: 228, Mismatches: 16, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
145 3 0.01
146 21 0.09
147 200 0.88
148 2 0.01
149 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (146 bp):
TTAGTGCCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAATGTTGTCGTTTTTG
TCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCT
TCGTTTTGAGTTATAG
Found at i:51671604 original size:147 final size:146
Alignment explanation
Indices: 51671191--51671643 Score: 500
Period size: 147 Copynumber: 3.1 Consensus size: 146
51671181 TACGTTGCTA
* * ** * *
51671191 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * *
51671256 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671321 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* ** * **
51671338 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * *
51671403 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
51671468 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* * * *
51671485 TTAGTGCCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAACGTTGCCGTTTT
**** * ** *
51671548 TGTAAA-TGTTATTAGTGGCGTTTTACCGAAAACGCCACGGGTTTGAGGT-AAGTGTTGATGAAG
64 TGTAAATTG-TATTAGTGGCGTTTT-CCGAAAACGCCACAACATTG-GGTAAACTGTTGGGGAAA
* **
51671611 CGACCGCGTTTTGAGTTATAG
126 CGGCTTCGTTTTGAGTTATAG
51671632 TTAGTGGCGCTT
1 TTAGTGGCGCTT
51671644 AGTTTAAAAC
Statistics
Matches: 273, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
145 2 0.01
146 22 0.08
147 242 0.89
148 5 0.02
149 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (146 bp):
TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAACGTTGCCGTTTTTG
TAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCT
TCGTTTTGAGTTATAG
Found at i:51673153 original size:16 final size:16
Alignment explanation
Indices: 51673132--51673167 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
51673122 ATATTTATAA
*
51673132 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
51673148 TTATCGATTTACAATT
1 TTATCGATTTACAATT
51673164 TTAT
1 TTAT
51673168 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:51673572 original size:13 final size:13
Alignment explanation
Indices: 51673556--51673614 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
51673546 TTACTAAAAT
*
51673556 TTACTTTAATATA
1 TTACTTAAATATA
*
51673569 TTACTTGAATATA
1 TTACTTAAATATA
51673582 TTACTTAAATA-A
1 TTACTTAAATATA
*
51673594 TTTACTTAAATACA
1 -TTACTTAAATATA
51673608 TTACTTA
1 TTACTTA
51673615 CTAAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:51673883 original size:16 final size:16
Alignment explanation
Indices: 51673862--51674186 Score: 90
Period size: 16 Copynumber: 19.8 Consensus size: 16
51673852 ACACTTATTA
51673862 AACTTACATAATACAT
1 AACTTACATAATACAT
*
51673878 AACTTACAT-GT---T
1 AACTTACATAATACAT
51673890 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
51673906 GACTTATATAAAATTCTCAAAT
1 AACTTACAT--AA---T-ACAT
51673928 AAACTTACATAATACAT
1 -AACTTACATAATACAT
* *
51673945 TAGTTACATAATAACTTATAT
1 AACTTACATAAT-AC----AT
51673966 AAACTTACATAATACA-
1 -AACTTACATAATACAT
*
51673982 CA-TTAC-T--TACAT
1 AACTTACATAATACAT
* * *
51673994 AGCATACATAACTTACAC
1 AACTTACATAA--TACAT
* *
51674012 AACTTAAATAATACAA
1 AACTTACATAATACAT
51674028 AACTTACATAACCTACAT
1 AACTTACATAA--TACAT
*
51674046 AACCTACATAATACAT
1 AACTTACATAATACAT
*
51674062 AA-TAAC-T--TAC--
1 AACTTACATAATACAT
51674072 AACTTACATAACATACAT
1 AACTTACAT-A-ATACAT
* **
51674090 TACTTTGATAACTCACAT
1 AACTTACATAA-T-ACAT
51674108 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
51674124 AACTTAAATAGCTTACTT
1 AACTTACATA--ATACAT
51674142 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
* * *
51674158 AACTTATACACGTACAT
1 AACTTACATA-ATACAT
51674175 AACTTACATAAT
1 AACTTACATAAT
51674187 TGACTTAATA
Statistics
Matches: 221, Mismatches: 45, Indels: 86
0.63 0.13 0.24
Matches are distributed among these distances:
10 2 0.01
11 7 0.03
12 14 0.06
13 5 0.02
14 6 0.03
15 4 0.02
16 77 0.35
17 22 0.10
18 57 0.26
21 7 0.03
22 13 0.06
23 7 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:51673967 original size:9 final size:9
Alignment explanation
Indices: 51673955--51674185 Score: 153
Period size: 9 Copynumber: 26.4 Consensus size: 9
51673945 TAGTTACATA
*
51673955 ATAACTTAT
1 ATAACTTAC
51673964 ATAAACTTAC
1 AT-AACTTAC
*
51673974 ATAA-TACAC
1 ATAACT-TAC
*
51673983 ATTACTTAC
1 ATAACTTAC
* *
51673992 ATAGCATAC
1 ATAACTTAC
51674001 ATAACTTAC
1 ATAACTTAC
* *
51674010 ACAACTTAA
1 ATAACTTAC
51674019 ATAA--TAC
1 ATAACTTAC
*
51674026 AAAACTTAC
1 ATAACTTAC
*
51674035 ATAACCTAC
1 ATAACTTAC
*
51674044 ATAACCTAC
1 ATAACTTAC
*
51674053 ATAATACATA-
1 AT-A-ACTTAC
51674063 ATAACTTAC
1 ATAACTTAC
51674072 --AACTTAC
1 ATAACTTAC
*
51674079 ATAACATAC
1 ATAACTTAC
* **
51674088 ATTACTTTG
1 ATAACTTAC
*
51674097 ATAACTCAC
1 ATAACTTAC
51674106 ATAACTTAC
1 ATAACTTAC
51674115 ATAA--TAC
1 ATAACTTAC
*
51674122 ATAACTTAA
1 ATAACTTAC
*
51674131 ATAGCTTAC
1 ATAACTTAC
*
51674140 TTAA--TAC
1 ATAACTTAC
51674147 ATAACTTAC
1 ATAACTTAC
51674156 ATAACTT--
1 ATAACTTAC
*
51674163 ATACACGTAC
1 ATA-ACTTAC
51674173 ATAACTTAC
1 ATAACTTAC
51674182 ATAA
1 ATAA
51674186 TTGACTTAAT
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 28 0.17
8 8 0.05
9 114 0.67
10 15 0.09
11 4 0.02
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:51673977 original size:38 final size:38
Alignment explanation
Indices: 51673890--51673981 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 38
51673880 CTTACATGTT
*
51673890 AACTTACATAATACATGACTTATATAAAATTCTCAAATA
1 AACTTACATAATACATGACTTACATAAAA-TCTCAAATA
* * * *
51673929 AACTTACATAATACATTAGTTACATAATAA-CTTATATA
1 AACTTACATAATACATGACTTACATAA-AATCTCAAATA
51673967 AACTTACATAATACA
1 AACTTACATAATACA
51673982 CATTACTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 21 0.45
39 24 0.51
40 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (38 bp):
AACTTACATAATACATGACTTACATAAAATCTCAAATA
Found at i:51674045 original size:43 final size:45
Alignment explanation
Indices: 51673967--51674089 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 45
51673957 AACTTATATA
* * * *
51673967 AACTTACATAATACACATTACTTACATAGCATACATAACTTACAC
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
51674012 AACTTAAATAATACA-A-AACTTACATAACCTACATAACCTACAT
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
51674055 AA--TACATAATA-ACTTACAACTTACATAACATACAT
1 AACTTAAATAATACAC--ATAACTTACATAACATACAT
51674090 TACTTTGATA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 8 0.12
43 25 0.38
44 18 0.27
45 14 0.21
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.28
Consensus pattern (45 bp):
AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
Found at i:51674047 original size:25 final size:25
Alignment explanation
Indices: 51673997--51674047 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
51673987 CTTACATAGC
* *
51673997 ATACATAACTTACACAACTTAAATA
1 ATACAAAACTTACACAACCTAAATA
* *
51674022 ATACAAAACTTACATAACCTACATA
1 ATACAAAACTTACACAACCTAAATA
51674047 A
1 A
51674048 CCTACATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (25 bp):
ATACAAAACTTACACAACCTAAATA
Found at i:51674138 original size:25 final size:25
Alignment explanation
Indices: 51674097--51674201 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
51674087 CATTACTTTG
* *
51674097 ATAACTCACATAACTTACATAATAC
1 ATAACTTAAATAACTTACATAATAC
* *
51674122 ATAACTTAAATAGCTTACTTAATAC
1 ATAACTTAAATAACTTACATAATAC
* * * *
51674147 ATAACTTACATAACTTATACACGTAC
1 ATAACTTAAATAACTTACATA-ATAC
* *
51674173 ATAACTTACATAA-TTGACTTAATAC
1 ATAACTTAAATAACTT-ACATAATAC
51674198 ATAA
1 ATAA
51674202 ATATATATCA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
25 46 0.72
26 18 0.28
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAACTTAAATAACTTACATAATAC
Found at i:51674193 original size:51 final size:50
Alignment explanation
Indices: 51674097--51674201 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 50
51674087 CATTACTTTG
* *
51674097 ATAACTCACATAACTTACATAATACATAACTTAAATAGCTTACTTAATAC
1 ATAACTCACATAACTTACACAATACATAACTTAAATAGATTACTTAATAC
* * * *
51674147 ATAACTTACATAACTTATACACGTACATAACTTACATA-ATTGACTTAATAC
1 ATAACTCACATAACTTACACA-ATACATAACTTAAATAGATT-ACTTAATAC
51674198 ATAA
1 ATAA
51674202 ATATATATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 20 0.43
51 27 0.57
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (50 bp):
ATAACTCACATAACTTACACAATACATAACTTAAATAGATTACTTAATAC
Found at i:51678459 original size:6 final size:6
Alignment explanation
Indices: 51678448--51678477 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
51678438 GAGAAAGAAA
51678448 AAAAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA
51678478 ACGAATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:51678470 original size:13 final size:12
Alignment explanation
Indices: 51678448--51678477 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
51678438 GAGAAAGAAA
51678448 AAAAATAAAAAT
1 AAAAATAAAAAT
51678460 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
51678473 AAAAA
1 AAAAA
51678478 ACGAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:51682653 original size:21 final size:21
Alignment explanation
Indices: 51682627--51682676 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
51682617 CTACAACTTA
*
51682627 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
51682648 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
51682669 AAGCAGAG
1 AAGCAGAG
51682677 CAAGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:51683104 original size:42 final size:41
Alignment explanation
Indices: 51682994--51683109 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 41
51682984 GTTTTTGTAT
* * * *
51682994 AAAAGCGCCGCTAAAGAACATGTTCTTTAGTGGGGTTTAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
* *****
51683035 AAAAACGCCACTATTTTTCATGTTCTTTAGCGGCGCTTAAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA-A
* *
51683077 ATAAACGCCGCTAAAGAACATGATCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG
51683110 TGTTTTTTTC
Statistics
Matches: 56, Mismatches: 18, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
41 30 0.54
42 26 0.46
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
Found at i:51683201 original size:43 final size:42
Alignment explanation
Indices: 51683082--51683264 Score: 285
Period size: 42 Copynumber: 4.3 Consensus size: 42
51683072 TAAGAATAAA
* *
51683082 CGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
51683124 CGCCGCTAAAGTACATGGTCTTTAGCAGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
51683166 CGCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* **
51683208 CGCCGCTAAAGAACATGGTTTTTAGATGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCTAAG
51683251 CGCCGCTAAAGAAC
1 CGCCGCTAAAGAAC
51683265 TCAAAGCGCC
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 103 0.80
43 26 0.20
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:51684224 original size:14 final size:15
Alignment explanation
Indices: 51684185--51684226 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
51684175 TTTTAACATA
*
51684185 ATTATTATTAAATAT
1 ATTATAATTAAATAT
51684200 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
51684214 A-TATAATTTAATA
1 ATTATAATTAAATA
51684227 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:51684337 original size:18 final size:17
Alignment explanation
Indices: 51684316--51684350 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
51684306 TTATTATTAA
*
51684316 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
51684334 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
51684351 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:51684577 original size:18 final size:17
Alignment explanation
Indices: 51684554--51684590 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
51684544 AATTATTATT
51684554 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
51684570 AAATATATGATTTAATA
1 AAATATATGATTTAATA
51684587 AAAT
1 AAAT
51684591 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:51684600 original size:120 final size:120
Alignment explanation
Indices: 51684182--51684591 Score: 741
Period size: 120 Copynumber: 3.4 Consensus size: 120
51684172 ATATTTTAAC
*
51684182 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
51684247 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
51684301 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
51684366 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
51684422 ATAATTATTATTAAATAAAATTTAATTAAAATATATGATTTAATAAAATTTTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
51684487 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
51684542 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
51684592 TAAAATAATT
Statistics
Matches: 281, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
120 279 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:51684675 original size:15 final size:15
Alignment explanation
Indices: 51684632--51684685 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
51684622 TATGAATTTG
51684632 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
51684646 -ATTA-TTATTAA-A
1 TATAATTTAATAATA
51684658 TATAATTTAATAATA
1 TATAATTTAATAATA
*
51684673 TATAATTTCATAA
1 TATAATTTAATAA
51684686 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 6 0.19
15 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:51684718 original size:71 final size:73
Alignment explanation
Indices: 51684637--51684772 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 73
51684627 ATTTGTATAA
*
51684637 TTTAAAATAATTATTATTAAATATAATTTAAT-A-ATATATAATTTCATAAAATTCTTGATAATA
1 TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
51684700 AATTTTCT
66 AATTTTCT
*
51684708 TTTAGAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAAT
1 TTTAAAATAATTAATATTAAATATAATTTAATAA-GATATATAATTTCATAAAATTCTTGATAAT
51684773 TTAATCATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 30 0.50
72 1 0.02
74 29 0.48
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (73 bp):
TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
AATTTTCT
Found at i:51691917 original size:6 final size:6
Alignment explanation
Indices: 51691894--51691935 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
51691884 ATATACATAG
* *
51691894 TCAGAT TTAGAA TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT
51691936 AACAGAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (6 bp):
TCAGAT
Found at i:51693526 original size:29 final size:32
Alignment explanation
Indices: 51693493--51693551 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
51693483 TGCATCTTGT
51693493 AAAAA-TTGAAAAA-ATA-AAATAAAAAAAGA
1 AAAAATTTGAAAAATATATAAATAAAAAAAGA
* *
51693522 AAAAATTTTAAAAATATATAACTAAAAAAA
1 AAAAATTTGAAAAATATATAAATAAAAAAA
51693552 TTAATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 7 0.28
31 3 0.12
32 10 0.40
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (32 bp):
AAAAATTTGAAAAATATATAAATAAAAAAAGA
Found at i:51699675 original size:46 final size:46
Alignment explanation
Indices: 51699603--51699713 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 46
51699593 GTAAAAGTAT
* *
51699603 ATTT-ATAATATTTT-ATAAATATCGTAAATAACAGATA-TCAACTTG
1 ATTTAATAAT-TTTTAATGAATATCGTAAAAAACAGATACT-AACTTG
* *
51699648 ATTTAATACTTTTTAATGAATATCGTAAAAAACAGATACTAGCTTG
1 ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
51699694 ATTTAATAATTTTTAATGAA
1 ATTTAATAATTTTTAATGAA
51699714 AATATTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
45 8 0.14
46 49 0.84
47 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (46 bp):
ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
Found at i:51703575 original size:115 final size:115
Alignment explanation
Indices: 51703371--51703789 Score: 416
Period size: 115 Copynumber: 3.7 Consensus size: 115
51703361 CGGATAGTGA
* *
51703371 AAGCGCCGCAAAATAT-TTGAACCAAAACGCATCGTTTTGGTATTGATGTATACTAGAATTAGTG
1 AAGCGCCGCAAAATATCTT-AACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
* * *
51703435 GCGTTTACGGTAAAACGCCGTTAAAGCATAGTATTAGCGGCGATTCTTTGC
65 GCGCTTACGGGAAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTCTTTGC
* * * *
51703486 TAGCGCCGCAAAATATCCTAACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAGTGG
1 AAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * * *
51703551 CGCTTACGGGAAACCGCCGCTAAAGAATAGTATTAGCGGCCCTTAC--TGAA
66 CGCTTACGGGAAAACGCCGTTAAAGCATAGTATTAGCGGCGCTT-CTTTG-C
* * ***
51703601 AAGCGCCACAAAATATCTTAACCT-AAACGCATAGTTTTAACCTTGATGTATACTAGAATTAGTG
1 AAGCGCCGCAAAATATCTTAA-CTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
** * * *
51703665 GCGCTTACTAGAAAACGCCATTAAATCATAGCATTAGCGGCGCTT-TTT--
65 GCGCTTACGGGAAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTCTTTGC
* ** * **
51703713 ----GCCGCAACATATCTTAAC-AAAACGCAGAG-TTTGGTCTTGAGGTATGTTAG-ATTAGTGG
1 AAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGG
**
51703771 CGCTTATAGGAAAACGCCG
66 CGCTTACGGGAAAACGCCG
51703790 CAACTGGTGA
Statistics
Matches: 252, Mismatches: 45, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
105 23 0.09
106 15 0.06
107 10 0.04
108 15 0.06
114 2 0.01
115 183 0.73
116 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (115 bp):
AAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGG
CGCTTACGGGAAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTCTTTGC
Found at i:51703966 original size:84 final size:84
Alignment explanation
Indices: 51703805--51703967 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 84
51703795 GGTGAAGCGC
* * **
51703805 CGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTTA
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
*
51703870 CGTTGAAACGCCGCCAAAA
66 CGGTGAAACGCCGCCAAAA
*
51703889 CGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCGT-GATGTATACTAAAATTAGTGGCGCTT
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTC-TCGATGTATACTAAAATTAGTGGCGCTT
*
51703953 AGGGT-AAACCGCCGC
65 ACGGTGAAA-CGCCGC
51703968 GAAAGCATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 3 0.04
84 66 0.94
85 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (84 bp):
CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
CGGTGAAACGCCGCCAAAA
Found at i:51705037 original size:114 final size:115
Alignment explanation
Indices: 51704804--51705108 Score: 307
Period size: 114 Copynumber: 2.7 Consensus size: 115
51704794 TTTGTCTGAT
* * ** *
51704804 TTTTTAGTGGCGTTT-TGACTAAAAC-CCGCAAAAGGAGT-TATATTAGTGGCGTTTTTACAAAA
1 TTTTTAGTGGCGTTTGT-ACCAAAACACCGCAAAAGGA-TATGTATTAGTGGCG-TTTTA-TTAT
* * * * * *
51704866 AAACGCCACAATT-TTGTTTTTAGTCACTGT-TAAACGTTGTCGTTTTTATGTACG
62 AAACGCCGCAATTATT-TTATTAG-GATTTTGTAAACGTTGTCGTTTTTATCTACG
* * * * * * *
51704920 TTTTTAGTGGCGTTTTTACTAAACCACCGCAAAATGATTTGTATTAGTGGCGTTTTTTTGT-AAC
1 TTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGTGGCGTTTTATTATAAAC
*
51704984 GCCGCAATTATTTTATTAGGATTTTGTAAACGTTGTCGTTTTTATCTATG
66 GCCGCAATTATTTTATTAGGATTTTGTAAACGTTGTCGTTTTTATCTACG
* ** *
51705034 TTTTTAGTGGCGTTTGTACCAAAACGCCGGTAAAGGATATGTTTTAGTGGCGTTTTATTATAAAC
1 TTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGTGGCGTTTTATTATAAAC
51705099 GCCGCAATTA
66 GCCGCAATTA
51705109 AGTTTTAAGT
Statistics
Matches: 157, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
113 3 0.02
114 89 0.57
115 15 0.10
116 27 0.17
117 23 0.15
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (115 bp):
TTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGTGGCGTTTTATTATAAAC
GCCGCAATTATTTTATTAGGATTTTGTAAACGTTGTCGTTTTTATCTACG
Found at i:51705328 original size:23 final size:21
Alignment explanation
Indices: 51705263--51705328 Score: 51
Period size: 23 Copynumber: 2.9 Consensus size: 21
51705253 CCACTCTGAT
* *
51705263 TTCCCCAATTTCGTTTCCCTAA
1 TTCCCC-ATTTCATTTCCCCAA
* *
51705285 TTTCCCATTTCCTATTCCCCCAA
1 TTCCCCATTT-C-ATTTCCCCAA
51705308 CTTCCCCGATTTCATTTCCCC
1 -TTCCCC-ATTTCATTTCCCC
51705329 CCAATTCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 4 0.12
22 6 0.18
23 14 0.41
24 6 0.18
25 4 0.12
ACGTcount: A:0.15, C:0.42, G:0.03, T:0.39
Consensus pattern (21 bp):
TTCCCCATTTCATTTCCCCAA
Found at i:51705344 original size:40 final size:40
Alignment explanation
Indices: 51705288--51705367 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
51705278 TCCCTAATTT
* *
51705288 CCCATTTCCTATTCCCCCAACTTCCCCGATTTCATTTCCC
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTCCC
* *
51705328 CCCAATTCCTTTTCCCCCAATTTCCCCGATTTAATTTCCC
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTCCC
51705368 TAAATCCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.16, C:0.45, G:0.03, T:0.36
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTCCC
Found at i:51705352 original size:16 final size:16
Alignment explanation
Indices: 51705311--51705352 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
51705301 CCCCCAACTT
* *
51705311 CCCCGATTTCATTTCC
1 CCCCAATTTCCTTTCC
*
51705327 CCCCAA-TTCCTTTTC
1 CCCCAATTTCCTTTCC
51705342 CCCCAATTTCC
1 CCCCAATTTCC
51705353 CCGATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.14, C:0.48, G:0.02, T:0.36
Consensus pattern (16 bp):
CCCCAATTTCCTTTCC
Found at i:51706834 original size:17 final size:17
Alignment explanation
Indices: 51706814--51706874 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
51706804 TTAATATCTA
51706814 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
51706831 TATAAGTTTTCT--A--
1 TATAAGTTTTCTAAATT
* *
51706844 TATTAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
51706859 TATAAGTTTTCTAAAT
1 TATAAGTTTTCTAAAT
51706875 AAGTGTTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
11 1 0.03
12 2 0.06
13 6 0.18
15 6 0.18
16 2 0.06
17 17 0.50
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:51706844 original size:30 final size:30
Alignment explanation
Indices: 51706810--51706891 Score: 114
Period size: 28 Copynumber: 2.8 Consensus size: 30
51706800 TGTTTTAATA
51706810 TCTATATAAGTTTTCTAAATTTATAAGTTT
1 TCTATATAAGTTTTCTAAATTTATAAGTTT
* *
51706840 TCTATATTAG-TAT-TAAATTTATAAGTTT
1 TCTATATAAGTTTTCTAAATTTATAAGTTT
* *
51706868 TCTAAATAAGTGTTCTAAATTTAT
1 TCTATATAAGTTTTCTAAATTTAT
51706892 TAGTAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 23 0.52
29 3 0.07
30 18 0.41
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.51
Consensus pattern (30 bp):
TCTATATAAGTTTTCTAAATTTATAAGTTT
Found at i:51707065 original size:17 final size:17
Alignment explanation
Indices: 51707045--51707128 Score: 122
Period size: 17 Copynumber: 5.2 Consensus size: 17
51707035 TTAATATCTA
51707045 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
51707062 TATAAGTGTTCTAAATT
1 TATAAGTTTTCTAAATT
51707079 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
51707096 TATAAGTTTTCT--A--
1 TATAAGTTTTCTAAATT
*
51707109 TATAAGTGTTCTAAATT
1 TATAAGTTTTCTAAATT
51707126 TAT
1 TAT
51707129 TAGTAATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
13 11 0.18
15 2 0.03
17 47 0.78
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:51707224 original size:24 final size:26
Alignment explanation
Indices: 51707197--51707252 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
51707187 TTATATATCT
* *
51707197 TACATAATACATAAC-TACATAA-CA
1 TACATAATACAGAACTTACATAATAA
*
51707221 TACATAATATAGAACTTACATAATAA
1 TACATAATACAGAACTTACATAATAA
51707247 TACATA
1 TACATA
51707253 CCGTACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 13 0.48
25 7 0.26
26 7 0.26
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.29
Consensus pattern (26 bp):
TACATAATACAGAACTTACATAATAA
Found at i:51707226 original size:9 final size:9
Alignment explanation
Indices: 51707181--51707475 Score: 187
Period size: 9 Copynumber: 34.4 Consensus size: 9
51707171 ATAATTATAT
*
51707181 ATAAGCTTAT
1 ATAA-CTTAC
*
51707191 ATATCTTAC
1 ATAACTTAC
51707200 ATAA--TAC
1 ATAACTTAC
51707207 ATAAC-TAC
1 ATAACTTAC
*
51707215 ATAACATAC
1 ATAACTTAC
*
51707224 ATAA--TAT
1 ATAACTTAC
*
51707231 AGAACTTAC
1 ATAACTTAC
51707240 ATAA-TAATAC
1 ATAACT--TAC
* *
51707250 ATACCGTAC
1 ATAACTTAC
* *
51707259 ATAAATTAA
1 ATAACTTAC
*
51707268 ATAAGTTAC
1 ATAACTTAC
51707277 ATAA--TAC
1 ATAACTTAC
* **
51707284 ACAAAAATA-
1 A-TAACTTAC
*
51707293 AAAACTTAC
1 ATAACTTAC
51707302 ATAACTTAC
1 ATAACTTAC
51707311 ATAA--TAC
1 ATAACTTAC
* *
51707318 ACAACTGAC
1 ATAACTTAC
51707327 ATAACTTAC
1 ATAACTTAC
51707336 ATAA--TAC
1 ATAACTTAC
* *
51707343 ACAACTTAT
1 ATAACTTAC
51707352 ATAACTTAC
1 ATAACTTAC
51707361 ATAA--TAC
1 ATAACTTAC
*
51707368 ATAATTTAC
1 ATAACTTAC
51707377 ATAACTTAC
1 ATAACTTAC
*
51707386 ATAA--GAC
1 ATAACTTAC
51707393 ATAACTTAC
1 ATAACTTAC
* *
51707402 ATAAGTTTC
1 ATAACTTAC
51707411 ATAA--TAC
1 ATAACTTAC
*
51707418 ACAACTTAC
1 ATAACTTAC
*
51707427 ACAACTTAC
1 ATAACTTAC
51707436 ATAACTTAC
1 ATAACTTAC
* *
51707445 ACAACTTAT
1 ATAACTTAC
51707454 ATAACTTAC
1 ATAACTTAC
51707463 ATAACTTAC
1 ATAACTTAC
51707472 ATAA
1 ATAA
51707476 TAAATAACTT
Statistics
Matches: 225, Mismatches: 39, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
7 46 0.20
8 16 0.07
9 152 0.68
10 11 0.05
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:51707323 original size:25 final size:25
Alignment explanation
Indices: 51707295--51707466 Score: 236
Period size: 25 Copynumber: 6.8 Consensus size: 25
51707285 CAAAAATAAA
51707295 AACTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
51707320 AACTGACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
* *
51707345 AACTTATATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
* * *
51707370 AATTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAC
* *
51707395 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAC
*
51707420 AACTTACACAACTTACATAACTTACAC
1 AACTTACATAACTTACATAA--TACAC
*
51707447 AACTTATATAACTTACATAA
1 AACTTACATAACTTACATAA
51707467 CTTACATAAT
Statistics
Matches: 128, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
25 105 0.82
27 23 0.18
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:51709372 original size:21 final size:21
Alignment explanation
Indices: 51709305--51709373 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
51709295 CAACTTAAAA
** *
51709305 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCCTCAGCGAGAGAAG
*
51709326 CAGAAG-CTGCAGCGAGAGAAG
1 CAGAGGCCT-CAGCGAGAGAAG
51709347 CAGAGGCCTCAGCGAGAGAAG
1 CAGAGGCCTCAGCGAGAGAAG
51709368 CAGAGG
1 CAGAGG
51709374 TTCAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.42, T:0.03
Consensus pattern (21 bp):
CAGAGGCCTCAGCGAGAGAAG
Found at i:51709794 original size:43 final size:43
Alignment explanation
Indices: 51709746--51709905 Score: 130
Period size: 42 Copynumber: 3.8 Consensus size: 43
51709736 ATCCCAAAAT
51709746 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAA-AGTCA-TATCATA
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGAG-CACTA-CATA
* * * * * *
51709789 TAGTGGCGTTTGTGAAATAAGCGCCGCGAAAGAGCACTACTTT
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGAGCACTACATA
** * * * * *
51709832 TAGTGGCGTTTTTT-ACCAAGCGCCGCTATAGAACATTACTTT
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGAGCACTACATA
***
51709874 TAGTGGCGTTTTTTTCTAAA-CGCCGCTAAAGA
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGA
51709906 TCATGTTTCT
Statistics
Matches: 96, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 47 0.49
43 45 0.47
44 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGAGCACTACATA
Found at i:51709872 original size:42 final size:42
Alignment explanation
Indices: 51709807--51710017 Score: 201
Period size: 43 Copynumber: 5.0 Consensus size: 42
51709797 TTTGTGAAAT
* * * *
51709807 AAGCGCCGCGAAAGAGCACTACTTTTAGTGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGTGGCGTTTTTTTCC
* *
51709849 AAGCGCCGCTATAGAACATTACTTTTAGTGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATTACTTTTAGTGGCGTTTTTTTCC
* * * * * * * *
51709891 AAACGCCGCTAAAGATCATGTTTCTTTAACT-GTGTTTTCTCCC
1 AAGCGCCGCTAAAGAACA--TTACTTTTAGTGGCGTTTTTTTCC
* * *
51709934 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACT-TTTAGTGGCGTTTTTTTCC
* *
51709976 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTTC
1 -AAGCGCCGCTAAAGAACATTACTTTTAGTGGCGTTTTTTTC
51710018 TGTAAGCGCC
Statistics
Matches: 135, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 60 0.44
43 62 0.46
44 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGTGGCGTTTTTTTCC
Found at i:51710013 original size:85 final size:84
Alignment explanation
Indices: 51709806--51710013 Score: 222
Period size: 85 Copynumber: 2.5 Consensus size: 84
51709796 GTTTGTGAAA
* * * * * *
51709806 TAAGCGCCGCGAAAGAGCACT-ACTTTTAGTGGCGTTTTTTACCAAGCGCCGCTATAGAACATTA
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
* *
51709870 CTTTTAGTGGCGTTTTTTTC
65 CTATTAGCGGCGTTTTTTTC
* * ** * * * *
51709890 TAAACGCCGCTAAAGATCATGTTTCTTTAACTGTGTTTTCTCCCAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
51709955 -TCATTAGCGGCGTTTTTTTCC
65 CT-ATTAGCGGCGTTTTTTT-C
51709976 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT
51710014 TTTCTGTAAG
Statistics
Matches: 98, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
83 1 0.01
84 18 0.18
85 58 0.59
86 21 0.21
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGAC
TATTAGCGGCGTTTTTTTC
Found at i:51710553 original size:24 final size:24
Alignment explanation
Indices: 51710514--51710561 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51710504 AACACGTTAG
51710514 CAAACAAAAATATATAAATATAAA
1 CAAACAAAAATATATAAATATAAA
* * *
51710538 CAAACAAATATTTATATATATAAA
1 CAAACAAAAATATATAAATATAAA
51710562 ATAAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (24 bp):
CAAACAAAAATATATAAATATAAA
Found at i:51714186 original size:42 final size:42
Alignment explanation
Indices: 51714140--51714223 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
51714130 CAAATTGACG
51714140 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
*
51714182 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAGAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
51714224 AATTCCGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (42 bp):
GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
Found at i:51719190 original size:16 final size:16
Alignment explanation
Indices: 51719145--51719179 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
51719135 TAGATAAATA
* *
51719145 CATACATACAGACATG
1 CATACATAAATACATG
51719161 CATACATAAATACATG
1 CATACATAAATACATG
51719177 CAT
1 CAT
51719180 GCATGCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (16 bp):
CATACATAAATACATG
Found at i:51736833 original size:22 final size:21
Alignment explanation
Indices: 51736802--51736843 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
51736792 TTATTTAATT
*
51736802 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
51736824 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
51736844 TACTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:51737565 original size:11 final size:11
Alignment explanation
Indices: 51737549--51737595 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
51737539 CACAAAATTA
51737549 ATATTTTTATC
1 ATATTTTTATC
51737560 ATA--TTTA-C
1 ATATTTTTATC
51737568 -TATTTTTTATC
1 ATA-TTTTTATC
51737579 ATATTTTTATC
1 ATATTTTTATC
51737590 ATATTT
1 ATATTT
51737596 AATGCACTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.06
8 1 0.03
9 4 0.13
10 4 0.13
11 18 0.58
12 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTTTATC
Found at i:51742781 original size:48 final size:48
Alignment explanation
Indices: 51742713--51742920 Score: 355
Period size: 48 Copynumber: 4.3 Consensus size: 48
51742703 AAGGTATATT
* * *
51742713 TGTCTTTCACTATTTGCACTCTTAGAGTTGGTAC-TTTATTGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTA-TGTATGGCA
51742761 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
51742809 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
* *
51742857 TGTCATTCATTATTTTCACTCTTAGATTTTGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
51742905 TGTCATTCATTATTTT
1 TGTCATTCATTATTTT
51742921 TATTGATAAA
Statistics
Matches: 154, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 150 0.97
49 4 0.03
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (48 bp):
TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
Found at i:51747908 original size:3 final size:3
Alignment explanation
Indices: 51747900--51747950 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
51747890 CCAATACACC
51747900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
51747948 AAT
1 AAT
51747951 GGTAAGAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:51753961 original size:13 final size:14
Alignment explanation
Indices: 51753936--51753969 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
51753926 TAAAGGTGTT
51753936 TCTTTATTTTAATA
1 TCTTTATTTTAATA
51753950 TCTTTA-TTTAATA
1 TCTTTATTTTAATA
51753963 TCATTTA
1 TC-TTTA
51753970 GAAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTTATTTTAATA
Found at i:51755494 original size:34 final size:34
Alignment explanation
Indices: 51755419--51755495 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
51755409 GACAAAAAAT
* * * *
51755419 CTACTATTTTCTTGTGTGTTTTTTTACTATTTTG
1 CTACTATTTTATTGTGTGTTTTCTCACTATTTTA
* *
51755453 CTGCTATTTTATTGT-TGTTTTCTCACTTGTTTTA
1 CTACTATTTTATTGTGTGTTTTCTCAC-TATTTTA
51755487 CTACTATTT
1 CTACTATTT
51755496 CACTATTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
33 9 0.26
34 26 0.74
ACGTcount: A:0.13, C:0.14, G:0.10, T:0.62
Consensus pattern (34 bp):
CTACTATTTTATTGTGTGTTTTCTCACTATTTTA
Found at i:51760334 original size:13 final size:13
Alignment explanation
Indices: 51760295--51760345 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
51760285 AGTTCTTCTT
*
51760295 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
51760308 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
51760321 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
51760334 TGTTTTTGAAAA
1 TGCTTTTGAAAA
51760346 ATTTGGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:51768322 original size:3 final size:3
Alignment explanation
Indices: 51768314--51768338 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51768304 CCACGGTTGA
51768314 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
51768339 CTATTCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:51768803 original size:11 final size:11
Alignment explanation
Indices: 51768787--51768813 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
51768777 ATAATAAAAA
51768787 TAAAAGTATTT
1 TAAAAGTATTT
51768798 TAAAAGTATTT
1 TAAAAGTATTT
51768809 TAAAA
1 TAAAA
51768814 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (11 bp):
TAAAAGTATTT
Found at i:51770523 original size:18 final size:18
Alignment explanation
Indices: 51770500--51770542 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51770490 TAATAGATTT
51770500 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
51770518 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
51770536 TTAATTA
1 TTAATTA
51770543 CACTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:51772280 original size:132 final size:131
Alignment explanation
Indices: 51771920--51772351 Score: 441
Period size: 132 Copynumber: 3.3 Consensus size: 131
51771910 GTTAGAAGCT
* * * * *
51771920 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTAATGGTGAAATGCTTGATGAAAA
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
** * * * * * * * *
51771985 TAGATCTACTGGCTCTCATAGTGAGGAGCAAGATCAGCACTTATTGGTTGAAGGGCGACGTAATG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAA-GGCCACGTAATG
*
51772050 GT
130 GA
* * * * * *
51772052 TGCTATGAGAAGGAACAAAATGCATCCAGAGA---T-A--GTGATGGTGATATGCTCGATGAAAA
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
** * * *
51772111 TAGATCTACTGATTCTTTTAGCAAGAAGCACGGTGAGAACTTATCGATAGAAGGCCAACGTAATG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCC-ACGTAATG
51772176 GA
130 GA
* * * *
51772178 CGCTACGAGAAAGATCAAGATACTTCCAGAGATGGTGATGGTGATGGTGATATGGTTGATGAAAG
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
* *
51772243 TAGGTCTATTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCA--TAATGG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG
51772306 TA
131 -A
** * *
51772308 -GCTACGAGGCAGATCAAATTGCATCCAGAGATGGTGATGGTGAT
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGAT
51772352 ATGGTTGATG
Statistics
Matches: 247, Mismatches: 45, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
125 3 0.01
126 94 0.38
128 1 0.00
129 46 0.19
130 2 0.01
131 1 0.00
132 100 0.40
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (131 bp):
CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG
A
Found at i:51780508 original size:28 final size:28
Alignment explanation
Indices: 51780477--51780556 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
51780467 AGATTAATTG
* *
51780477 ACGAGTAGTGATCATTTTTATTACTAAT
1 ACGAGTAATGATCATTTTCATTACTAAT
* *
51780505 ACGAGTAATGATTATTTTCATTACTAGT
1 ACGAGTAATGATCATTTTCATTACTAAT
51780533 ACGAGTAATGATCATTTTCATTAC
1 ACGAGTAATGATCATTTTCATTAC
51780557 AAAAGATACA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
ACGAGTAATGATCATTTTCATTACTAAT
Found at i:51782777 original size:21 final size:21
Alignment explanation
Indices: 51782751--51782814 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
51782741 TTTTGGTGGA
51782751 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* **
51782772 TCAGCTCTCACAAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* *
51782793 TCATCTCGTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
51782814 T
1 T
51782815 AGCGTGTTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.41
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:51789877 original size:17 final size:17
Alignment explanation
Indices: 51789855--51789888 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51789845 AAATATAACA
*
51789855 TTTTTGAATAATACTTG
1 TTTTTGAATAAAACTTG
51789872 TTTTTGAATAAAACTTG
1 TTTTTGAATAAAACTTG
51789889 ATAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTTTGAATAAAACTTG
Found at i:51791060 original size:21 final size:21
Alignment explanation
Indices: 51791014--51791053 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51791004 TTAAATTACA
*
51791014 TTTTGGTCACTAAACTTTATG
1 TTTTGGTCACTAAACATTATG
51791035 TTTTGGTCACT-AACATTAT
1 TTTTGGTCACTAAACATTAT
51791054 TAATTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTTGGTCACTAAACATTATG
Found at i:51792244 original size:19 final size:18
Alignment explanation
Indices: 51792200--51792244 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
51792190 AAGATGAAAG
51792200 AAAGAAAGGAAATAAAAA
1 AAAGAAAGGAAATAAAAA
**
51792218 AAATGAAAGTGAAATAATTA
1 AAA-GAAAG-GAAATAAAAA
51792238 AAAGAAA
1 AAAGAAA
51792245 AAGAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 9 0.39
20 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (18 bp):
AAAGAAAGGAAATAAAAA
Found at i:51792494 original size:53 final size:53
Alignment explanation
Indices: 51792399--51792505 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 53
51792389 GTTATAAATT
* * * * * *
51792399 AATAAAGTTAATAATTAAAATTTGAAAAATTAAATTTTAGTAATTAAAATATA
1 AATAAAATTAATAATTAAAATATGAAAAAATAAAATTGAGTAATCAAAATATA
51792452 AATAAAATTAATAATTAAAATAT-AACAAAATAAAATTGAGTAATCAAAATATA
1 AATAAAATTAATAATTAAAATATGAA-AAAATAAAATTGAGTAATCAAAATATA
51792505 A
1 A
51792506 TTTAGTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.04
53 45 0.96
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (53 bp):
AATAAAATTAATAATTAAAATATGAAAAAATAAAATTGAGTAATCAAAATATA
Found at i:51792499 original size:19 final size:19
Alignment explanation
Indices: 51792477--51792514 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51792467 TAAAATATAA
51792477 CAAAATAAAATTGAGTAAT
1 CAAAATAAAATTGAGTAAT
* *
51792496 CAAAATATAATTTAGTAAT
1 CAAAATAAAATTGAGTAAT
51792515 ATTGTGATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
CAAAATAAAATTGAGTAAT
Found at i:51792502 original size:29 final size:28
Alignment explanation
Indices: 51792451--51792505 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
51792441 ATTAAAATAT
*
51792451 AAATAAAATTAATAATTAAAATATAACA
1 AAATAAAATTAATAATCAAAATATAACA
*
51792479 AAATAAAATTGAGTAATCAAAATATAA
1 AAATAAAATT-AATAATCAAAATATAA
51792506 TTTAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (28 bp):
AAATAAAATTAATAATCAAAATATAACA
Found at i:51799204 original size:31 final size:31
Alignment explanation
Indices: 51799160--51799252 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
51799150 GGGAATTAGT
*
51799160 CATTCATATTTGCATATCCATACCTTGTAATA
1 CATTCATATTTGCATATTCATACCTTGTAA-A
* * *
51799192 -ATTCGTATTTGCAAATTCATACCCTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
* *
51799222 CATTCATATTTACATATTCATATCTTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
51799253 GTCACATATC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (31 bp):
CATTCATATTTGCATATTCATACCTTGTAAA
Found at i:51816783 original size:14 final size:14
Alignment explanation
Indices: 51816766--51816792 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51816756 TATTTTTCAT
51816766 AAATATTTTTTAAA
1 AAATATTTTTTAAA
51816780 AAATATTTTTTAA
1 AAATATTTTTTAA
51816793 GAACTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATATTTTTTAAA
Found at i:51817028 original size:24 final size:24
Alignment explanation
Indices: 51816996--51817042 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
51816986 TTCTAATATC
51816996 AAAATTTAATTTCAGCATATGAAT
1 AAAATTTAATTTCAGCATATGAAT
51817020 AAAATTTAATTTCAGCATATGAA
1 AAAATTTAATTTCAGCATATGAA
51817043 ATTACCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (24 bp):
AAAATTTAATTTCAGCATATGAAT
Found at i:51819880 original size:40 final size:40
Alignment explanation
Indices: 51819835--51819922 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
51819825 GTTTGGTCAA
*
51819835 AAAACGCTGCAAAAAATCGAGCATTAGCGGCGCTTTATGG
1 AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTATGG
* * *
51819875 AAAACGCCGCTAAAGATCGAGCATTTGCGGCGCTTTATGG
1 AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTATGG
51819915 AAAACGCC
1 AAAACGCC
51819923 ACTAAAGATC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTATGG
Found at i:51819928 original size:40 final size:40
Alignment explanation
Indices: 51819850--51819942 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
51819840 GCTGCAAAAA
* *
51819850 ATCGAGCATTAGCGGCGCTTTATGGAAAACGCCGCTAAAG
1 ATCGAGCATTTGCGGCGCTTTATGGAAAACGCCACTAAAG
51819890 ATCGAGCATTTGCGGCGCTTTATGGAAAACGCCACTAAAG
1 ATCGAGCATTTGCGGCGCTTTATGGAAAACGCCACTAAAG
*
51819930 ATCGAACATTTGC
1 ATCGAGCATTTGC
51819943 AGCGTTTTCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (40 bp):
ATCGAGCATTTGCGGCGCTTTATGGAAAACGCCACTAAAG
Found at i:51821145 original size:11 final size:11
Alignment explanation
Indices: 51821129--51821154 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51821119 TAGAAGAGAC
51821129 GAAACAGGGGA
1 GAAACAGGGGA
51821140 GAAACAGGGGA
1 GAAACAGGGGA
51821151 GAAA
1 GAAA
51821155 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:51821918 original size:39 final size:40
Alignment explanation
Indices: 51821875--51821962 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 40
51821865 CGAATTATGG
*
51821875 AATACTGAATATTGTCT-TG-ATTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGT-TATGCA-TAATGCAGTGAATTGTGAA
*
51821914 AATACTGAATATTGTTATGCATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
*
51821954 ATTACTGAA
1 AATACTGAA
51821963 GTAAAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 21 0.49
40 21 0.49
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (40 bp):
AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
Found at i:51822217 original size:39 final size:39
Alignment explanation
Indices: 51822137--51822312 Score: 167
Period size: 45 Copynumber: 4.2 Consensus size: 39
51822127 ATTTGCCGGC
* * *
51822137 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTG
51822175 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
51822214 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
51822259 TTACTGTTACAGGTTCAGCACTTTGTGTGTTGAATACTGTTACTG
1 TTACTG----A--TTCGGCACTTTGTGTGTCGAATACTGTTACTG
51822304 TTACTGATT
1 TTACTGATT
51822313 ACTGTATACT
Statistics
Matches: 117, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
38 12 0.10
39 29 0.25
41 1 0.01
42 2 0.02
43 1 0.01
45 72 0.62
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:51822232 original size:45 final size:45
Alignment explanation
Indices: 51822164--51822314 Score: 239
Period size: 45 Copynumber: 3.3 Consensus size: 45
51822154 ATGTGCCGAC
*
51822164 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* *
51822209 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
51822254 TACTGTTACTGTTACAGGTTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
51822299 TACTGTTACTGATTAC
1 TACTGTTACTG-TTAC
51822315 TGTATACTGG
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 94 0.96
46 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:51825563 original size:9 final size:9
Alignment explanation
Indices: 51825521--51825588 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
51825511 ATAATTTTAA
51825521 AAAAATTAT
1 AAAAATTAT
* *
51825530 AAAATTTGTT
1 AAAAATT-AT
*
51825540 AAAAGTTACT
1 AAAAATTA-T
51825550 AAAAATTAT
1 AAAAATTAT
51825559 AAAAATT-T
1 AAAAATTAT
*
51825567 AAATATGTA-
1 AAAAAT-TAT
51825576 AAAAA-TAT
1 AAAAATTAT
51825584 AAAAA
1 AAAAA
51825589 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
7 2 0.04
8 11 0.23
9 19 0.40
10 15 0.32
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:51828755 original size:25 final size:26
Alignment explanation
Indices: 51828726--51828797 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
51828716 TTTAGGCCAG
*
51828726 TTGGGCTAGGGT-ATTGGGCTTAG-GT
1 TTGGGCTAGGTTAATTGGG-TTAGAGT
*
51828751 TTGGGCTAGGTTAATTGGGTTAGATT
1 TTGGGCTAGGTTAATTGGGTTAGAGT
51828777 TTGGGCTAGGTTAATTGGGTT
1 TTGGGCTAGGTTAATTGGGTT
51828798 TGTAAAAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 15 0.35
26 28 0.65
ACGTcount: A:0.15, C:0.06, G:0.39, T:0.40
Consensus pattern (26 bp):
TTGGGCTAGGTTAATTGGGTTAGAGT
Found at i:51828768 original size:14 final size:13
Alignment explanation
Indices: 51828726--51828795 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 13
51828716 TTTAGGCCAG
*
51828726 TTGGGCTAGGGTA
1 TTGGGCTAGGTTA
51828739 TTGGGCTTAGG-T-
1 TTGGGC-TAGGTTA
51828751 TTGGGCTAGGTTAA
1 TTGGGCTAGGTT-A
* *
51828765 TTGGGTTAGATT-
1 TTGGGCTAGGTTA
51828777 TTGGGCTAGGTTAA
1 TTGGGCTAGGTT-A
51828791 TTGGG
1 TTGGG
51828796 TTTGTAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.09
12 17 0.36
13 7 0.15
14 19 0.40
ACGTcount: A:0.16, C:0.06, G:0.40, T:0.39
Consensus pattern (13 bp):
TTGGGCTAGGTTA
Found at i:51830535 original size:6 final size:6
Alignment explanation
Indices: 51830526--51830554 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
51830516 ACCCGTTTTT
51830526 AATTAA AATTAA AATTAA AATTAA AATTA
1 AATTAA AATTAA AATTAA AATTAA AATTA
51830555 GTTTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:51830608 original size:16 final size:16
Alignment explanation
Indices: 51830571--51830610 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
51830561 TTAATAAAAT
* *
51830571 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
51830587 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
51830603 TAAAATTA
1 TAAAATTA
51830611 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:51830695 original size:9 final size:9
Alignment explanation
Indices: 51830683--51830719 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51830673 TTTATCAAAT
51830683 TATTAATTG
1 TATTAATTG
51830692 TATTAATTG
1 TATTAATTG
51830701 TATTAATTG
1 TATTAATTG
*
51830710 TATTAGTTG
1 TATTAATTG
51830719 T
1 T
51830720 TGTAACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Done.