Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 62 of 97
Found at i:24970812 original size:26 final size:25
Alignment explanation
Indices: 24970734--24970809 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
24970724 ATGTATTCAT
* *
24970734 TTCTGGTGATAAAATTATTCTTAGA
1 TTCTGGTGGTAAAATTATTCTTAAA
* * *
24970759 TTCTGATGGTAAAATTATCCATTCAA
1 TTCTGGTGGTAAAATTATTC-TTAAA
24970785 TTCTGGTGGTAAAATTATTCTTAAA
1 TTCTGGTGGTAAAATTATTCTTAAA
24970810 ATTAAAATAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (25 bp):
TTCTGGTGGTAAAATTATTCTTAAA
Found at i:24971554 original size:20 final size:20
Alignment explanation
Indices: 24971529--24971566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24971519 GATCACTTGT
24971529 TTTTCTTTAATTTTTCTTTG
1 TTTTCTTTAATTTTTCTTTG
**
24971549 TTTTCTTTTTTTTTTCTT
1 TTTTCTTTAATTTTTCTT
24971567 CTCTTTCATT
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:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTTAATTTTTCTTTG
Found at i:24996304 original size:33 final size:28
Alignment explanation
Indices: 24996239--24996295 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
24996229 GTTTCAGGTA
24996239 ATTTTTGAGTTTTGGTTACTTTAGGTTC
1 ATTTTTGAGTTTTGGTTACTTTAGGTTC
24996267 ATTTTTGAGTTTTGGTTACTTTAGGTTC
1 ATTTTTGAGTTTTGGTTACTTTAGGTTC
24996295 A
1 A
24996296 GATCATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.16, C:0.07, G:0.21, T:0.56
Consensus pattern (28 bp):
ATTTTTGAGTTTTGGTTACTTTAGGTTC
Found at i:24997597 original size:16 final size:16
Alignment explanation
Indices: 24997576--24997627 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
24997566 TAACGATAAT
24997576 AAATAACTT-GTAATAC
1 AAATAA-TTAGTAATAC
*
24997592 AAATAATTAATAATAC
1 AAATAATTAGTAATAC
24997608 AAATAATTAGTAATAC
1 AAATAATTAGTAATAC
24997624 AAAT
1 AAAT
24997628 TTTTGAAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 2 0.06
16 31 0.94
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATAATTAGTAATAC
Found at i:25011567 original size:24 final size:23
Alignment explanation
Indices: 25011522--25011573 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
25011512 AATCATACTA
25011522 AATATTCTAGAATGAGGATATTT
1 AATATTCTAGAATGAGGATATTT
* **
25011545 GAATATTCTAGATTGAGTTTATTT
1 -AATATTCTAGAATGAGGATATTT
25011569 AATAT
1 AATAT
25011574 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (23 bp):
AATATTCTAGAATGAGGATATTT
Found at i:25023077 original size:21 final size:21
Alignment explanation
Indices: 25023053--25023097 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
25023043 CCTATTTATG
* *
25023053 AATAGCGGCATTCATTTTCTA
1 AATAGCAGCATTCAATTTCTA
25023074 AATAGCAGCATTCAATTTCTA
1 AATAGCAGCATTCAATTTCTA
25023095 AAT
1 AAT
25023098 TTTGTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
AATAGCAGCATTCAATTTCTA
Found at i:25028423 original size:13 final size:13
Alignment explanation
Indices: 25028405--25028429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25028395 TTTCAGAAAA
25028405 TTTATAAAATCAT
1 TTTATAAAATCAT
25028418 TTTATAAAATCA
1 TTTATAAAATCA
25028430 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:25046651 original size:26 final size:26
Alignment explanation
Indices: 25046622--25046680 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
25046612 ATTTTCTAGT
* *
25046622 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
25046648 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
25046674 TTTCCTT
1 TTTCCTT
25046681 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:25049486 original size:15 final size:15
Alignment explanation
Indices: 25049468--25049498 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25049458 ATAGATATTT
*
25049468 TCAAACTCATCTCCC
1 TCAAACTCACCTCCC
25049483 TCAAACTCACCTCCC
1 TCAAACTCACCTCCC
25049498 T
1 T
25049499 GATCACTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (15 bp):
TCAAACTCACCTCCC
Found at i:25052921 original size:71 final size:72
Alignment explanation
Indices: 25052753--25052951 Score: 226
Period size: 71 Copynumber: 2.8 Consensus size: 72
25052743 GCAGAGAGCT
* * * *
25052753 CTTAGTCGACTAA-TATA-CTTCTTAGTCGATTAAGTTGGTTCTGTCTTCTGATCCCAGTTTCAG
1 CTTAGTCGACTAACAATATC-TCTTAGTCGATTAAGTTGGTTCTGT-TTTTGAACCCAGCTTCA-
* *
25052816 GCAGTAAGCC
63 GCAATAAGCA
* * *
25052826 CTTAGTCGACTAACGAT-TCCTCTTAGTCGATTAAGTGGGTTCTGTTTTTGAACTCAGCTTC-GC
1 CTTAGTCGACTAACAATAT-CTCTTAGTCGATTAAGTTGGTTCTGTTTTTGAACCCAGCTTCAGC
25052889 AATAAGCA
65 AATAAGCA
* * *
25052897 TTTAGTCGACTAACAATATCTCTTAGTCAATTAAGTTGATTCTGTTTTTGAACCC
1 CTTAGTCGACTAACAATATCTCTTAGTCGATTAAGTTGGTTCTGTTTTTGAACCC
25052952 GCCAACTCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
71 55 0.51
72 1 0.01
73 25 0.23
74 26 0.24
75 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (72 bp):
CTTAGTCGACTAACAATATCTCTTAGTCGATTAAGTTGGTTCTGTTTTTGAACCCAGCTTCAGCA
ATAAGCA
Found at i:25053318 original size:24 final size:25
Alignment explanation
Indices: 25053265--25053317 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
25053255 AGAGTATCGT
25053265 TTTTCAATTAAAAATTTTGAAAGTC
1 TTTTCAATTAAAAATTTTGAAAGTC
25053290 TTTTCAATTAAAAATTTTGAAAGTC
1 TTTTCAATTAAAAATTTTGAAAGTC
25053315 TTT
1 TTT
25053318 CTTACCAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTCAATTAAAAATTTTGAAAGTC
Found at i:25061164 original size:20 final size:20
Alignment explanation
Indices: 25061127--25061165 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25061117 AAAATCTTTT
*
25061127 CTTTTTTCTTTTTATTCTTC
1 CTTTTTTCTTTCTATTCTTC
25061147 CTTTTCTTCTTTCT-TTCTT
1 CTTTT-TTCTTTCTATTCTT
25061166 TCTCTTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (20 bp):
CTTTTTTCTTTCTATTCTTC
Found at i:25069056 original size:47 final size:47
Alignment explanation
Indices: 25068997--25069323 Score: 339
Period size: 47 Copynumber: 7.0 Consensus size: 47
25068987 ACGTCATGTT
* * * * * *
25068997 GGGAATGTGTGACACGCTAGCGTTCACAGTTGGTGAGACGTCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * * * * * * *
25069044 GAGAATCTGTGACACGTCAAAGTTAAAAGTTGGTGACACGTCATAGT
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * * * *
25069091 GGGAATCCGAGACACGCCAGCGTTCAGAGTTAGTGAGACGCCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * * * *
25069138 GGGAATTTATGACACACCAAAGTTCAGAGTTGGTGACACGGCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* ** * *
25069185 GGGAATCTGTGACACGCCAGTGTTCAGAGTTCATGAGAGGCCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * *
25069232 GGGATTCTGTGACATGCCAGAGTTAAGAGTTGGTGACACGCCATGGA
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
* * *
25069279 GGGAAGCTGTGACACTCCAGAGTTCAAAGTTGGTGACACGCCATG
1 GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATG
25069324 TTTAGAGTGT
Statistics
Matches: 222, Mismatches: 58, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 222 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (47 bp):
GGGAATCTGTGACACGCCAGAGTTCAGAGTTGGTGACACGCCATGGA
Found at i:25069403 original size:53 final size:53
Alignment explanation
Indices: 25069323--25069424 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
25069313 GACACGCCAT
*
25069323 GTTTAGAGTGTGTGACACGACATTGCTTGAAAAGCTGACACGCCATGGTCATA
1 GTTTAGAGTGTGTGACAAGACATTGCTTGAAAAGCTGACACGCCATGGTCATA
* * *
25069376 GTTTAGAGTGTGTGACAAGGCATTGCTTGAACAGCTGACACGTCATGGT
1 GTTTAGAGTGTGTGACAAGACATTGCTTGAAAAGCTGACACGCCATGGT
25069425 TTGAAATAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (53 bp):
GTTTAGAGTGTGTGACAAGACATTGCTTGAAAAGCTGACACGCCATGGTCATA
Found at i:25069962 original size:31 final size:31
Alignment explanation
Indices: 25069924--25070186 Score: 325
Period size: 31 Copynumber: 8.5 Consensus size: 31
25069914 GTCAGCGTTA
* *
25069924 GCGTGTGACAACATTTGACTCGATATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
*
25069955 GCGTGTGACAACATTTGACTTGATATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
* *
25069986 GAGTGTCACAACATTTGATTTGATATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
* *
25070017 GCGTGTGACAACATTTTACTTGATATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
* *
25070048 GTGTGTCACAGCATTT-ACTTGATATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
* * * *
25070078 GCATGTCATAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTGACTTGATATGCATG
*
25070109 GCGTGTCACAACATTTTG-CTTGCTATGCATG
1 GCGTGTCACAACA-TTTGACTTGATATGCATG
* *
25070140 GCGTGTCACAATATTTTG-CTTGTTATGCATG
1 GCGTGTCACAACA-TTTGACTTGATATGCATG
* *
25070171 GTGTTTCACAACATTT
1 GCGTGTCACAACATTT
25070187 ATTCCTTATT
Statistics
Matches: 205, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
30 29 0.14
31 173 0.84
32 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (31 bp):
GCGTGTCACAACATTTGACTTGATATGCATG
Found at i:25070105 original size:92 final size:93
Alignment explanation
Indices: 25069924--25070186 Score: 343
Period size: 92 Copynumber: 2.8 Consensus size: 93
25069914 GTCAGCGTTA
* * *
25069924 GCGTGTGACAACATTTGACTCGATATGCATGGCGTGTGACAACATTTGACTTGATATGCATGGAG
1 GCGTGTGACAACATTTTACTTGATATGCATGGCGTGTCACAACATTTGACTTGATATGCATGGAG
*
25069989 TGTCACAACATTTGATTTGATATGCATG
66 TGTCACAACATTTGACTTGATATGCATG
* *
25070017 GCGTGTGACAACATTTTACTTGATATGCATGGTGTGTCACAGCATTT-ACTTGATATGCATGGCA
1 GCGTGTGACAACATTTTACTTGATATGCATGGCGTGTCACAACATTTGACTTGATATGCATGG-A
* * *
25070081 -TGTCATAACATTTTACTTGTTATGCATG
65 GTGTCACAACATTTGACTTGATATGCATG
* * * * * *
25070109 GCGTGTCACAACATTTTGCTTGCTATGCATGGCGTGTCACAATATTTTG-CTTGTTATGCATGGT
1 GCGTGTGACAACATTTTACTTGATATGCATGGCGTGTCACAACA-TTTGACTTGATATGCATGGA
*
25070173 GTTTCACAACATTT
65 GTGTCACAACATTT
25070187 ATTCCTTATT
Statistics
Matches: 147, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
92 77 0.52
93 70 0.48
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (93 bp):
GCGTGTGACAACATTTTACTTGATATGCATGGCGTGTCACAACATTTGACTTGATATGCATGGAG
TGTCACAACATTTGACTTGATATGCATG
Found at i:25070167 original size:123 final size:123
Alignment explanation
Indices: 25069926--25070187 Score: 355
Period size: 123 Copynumber: 2.1 Consensus size: 123
25069916 CAGCGTTAGC
* * *
25069926 GTGTGACAACATTTGACTCGATATGCATGGCGTGTGACAACATTTGACTTGATATGCATGGAGTG
1 GTGTCACAACATTT-ACTCGATATGCATGGCATGTCACAACATTTGACTTGATATGCATGGAGTG
* *
25069991 TCACAACATTTGATTTGATATGCATGGCGTGTGACAACATTTTACTTGATATGCATGGT
65 TCACAACATTTGACTTGATATGCATGGCGTGTCACAACATTTTACTTGATATGCATGGT
* * * * * *
25070050 GTGTCACAGCATTTACTTGATATGCATGGCATGTCATAACATTTTACTTGTTATGCATGGCGTGT
1 GTGTCACAACATTTACTCGATATGCATGGCATGTCACAACATTTGACTTGATATGCATGGAGTGT
* * * *
25070115 CACAACATTTTG-CTTGCTATGCATGGCGTGTCACAATATTTTGCTTGTTATGCATGGT
66 CACAACA-TTTGACTTGATATGCATGGCGTGTCACAACATTTTACTTGATATGCATGGT
*
25070173 GTTTCACAACATTTA
1 GTGTCACAACATTTA
25070188 TTCCTTATTT
Statistics
Matches: 120, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 104 0.87
124 16 0.13
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (123 bp):
GTGTCACAACATTTACTCGATATGCATGGCATGTCACAACATTTGACTTGATATGCATGGAGTGT
CACAACATTTGACTTGATATGCATGGCGTGTCACAACATTTTACTTGATATGCATGGT
Found at i:25072093 original size:156 final size:156
Alignment explanation
Indices: 25071849--25072173 Score: 461
Period size: 156 Copynumber: 2.1 Consensus size: 156
25071839 AGGTAATTTC
* * ** * *
25071849 TGTTATTACAGTTTACGAAAGCGACGATAGGTCCTCAAGCACCTATCGGTCCAATTCCATCACAG
1 TGTTATTGCAGTTTACGAAAGCGACGACAGGTCCTCAAGCACAGATCGGTCCAACTCCACCACAG
* *
25071914 ACTGCTAACGAGCCGCCGATAAGGATATTAAAGTTGTAACAATTAATGTTCAACAATTCCATACA
66 ACTGCTAACAAGCCACCGATAAGGATATTAAAGTTGTAACAATTAATGTTCAACAATTCCATACA
* *
25071979 TGATTATTGAATAACATAGTTATATT
131 TGATTATTGAATAACACAGTTATATA
* * ***
25072005 TGTTATTGCAGTTTACGGAAGCGACGACAGGTCGTCAAGCACAGATCGGTCTGGCTCCACCACAG
1 TGTTATTGCAGTTTACGAAAGCGACGACAGGTCCTCAAGCACAGATCGGTCCAACTCCACCACAG
* * ** *
25072070 ACTGCTAACAAGCCATCGGTAAGGATATTAAAGTTGTAACGGTTAATGTTCAACAATTCCATATA
66 ACTGCTAACAAGCCACCGATAAGGATATTAAAGTTGTAACAATTAATGTTCAACAATTCCATACA
25072135 TGATTATTGAATAACACAGTTATATA
131 TGATTATTGAATAACACAGTTATATA
*
25072161 TGTTATTGTAGTT
1 TGTTATTGCAGTT
25072174 GACCCAGTCG
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
156 148 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (156 bp):
TGTTATTGCAGTTTACGAAAGCGACGACAGGTCCTCAAGCACAGATCGGTCCAACTCCACCACAG
ACTGCTAACAAGCCACCGATAAGGATATTAAAGTTGTAACAATTAATGTTCAACAATTCCATACA
TGATTATTGAATAACACAGTTATATA
Found at i:25072560 original size:31 final size:31
Alignment explanation
Indices: 25072525--25072825 Score: 300
Period size: 31 Copynumber: 9.5 Consensus size: 31
25072515 GTCAACATTA
* * *
25072525 GCGTGTGACAACATTTGACTTGATATGCATG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
*
25072556 GCGTGTCGA-AACATTTTACTTGTTATGCATG
1 GCGTGTC-ACAACATTTAACTTGTTATGCATG
* *
25072587 GCGTGTCATAACGTTTAACTTGTTATGCATG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
* ** * *
25072618 GCGTGTCAGAACATTTTGCTTGTTATTCTTG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
**
25072649 GCGTGTCACAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
* *
25072680 GCGTGTCACAACGTTTAACTTGTTATCCATG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
* * *
25072711 GCGTGTCACAACGTTTAAC-TGTTATCCATA
1 GCGTGTCACAACATTTAACTTGTTATGCATG
* * ** *
25072741 ACGTGCCACAATGTTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTAACTTGTTATGCATG
*
25072772 GTGTGTCACAACATTTTACTTGTTACTTGTTATGCATG
1 GCGTGTCACAACA-TTTA------ACTTGTTATGCATG
25072810 GCGTGTCACAACATTT
1 GCGTGTCACAACATTT
25072826 TACAACATTT
Statistics
Matches: 228, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
30 26 0.11
31 169 0.74
32 4 0.02
37 3 0.01
38 26 0.11
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GCGTGTCACAACATTTAACTTGTTATGCATG
Found at i:25072807 original size:38 final size:38
Alignment explanation
Indices: 25072756--25072828 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
25072746 CCACAATGTT
*
25072756 TTACTTGTTATGCATGGTGTGTCACAACATTTTACTTG
1 TTACTTGTTATGCATGGCGTGTCACAACATTTTACTTG
25072794 TTACTTGTTATGCATGGCGTGTCACAACATTTTAC
1 TTACTTGTTATGCATGGCGTGTCACAACATTTTAC
25072829 AACATTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (38 bp):
TTACTTGTTATGCATGGCGTGTCACAACATTTTACTTG
Found at i:25074411 original size:14 final size:14
Alignment explanation
Indices: 25074384--25074521 Score: 55
Period size: 14 Copynumber: 8.7 Consensus size: 14
25074374 GTACATTTTT
*
25074384 TTTTATATAGAATTA
1 TTTT-TATACAATTA
25074399 TTTTTATACAATTAA
1 TTTTTATACAATT-A
* *
25074414 TTTTATACACAATTT
1 TTTT-TATACAATTA
25074429 TTTTGTATACACAATT-
1 TTTT-TAT--ACAATTA
25074445 TATTTTATACAATTCA
1 T-TTTTATACAATT-A
*
25074461 -TTGTATACAGAATTAA
1 TTTTTATAC--AATT-A
*
25074477 TTCTTTTTGTATACACAATA
1 ----TTTT-TATACA-ATTA
25074497 TATTTTATACAATTA
1 T-TTTTATACAATTA
25074512 TTTTTATACA
1 TTTTTATACA
25074522 CAATTAATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 35
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.31
15 19 0.20
16 24 0.25
17 12 0.12
20 2 0.02
21 4 0.04
22 5 0.05
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (14 bp):
TTTTTATACAATTA
Found at i:25074425 original size:16 final size:16
Alignment explanation
Indices: 25074384--25074536 Score: 86
Period size: 16 Copynumber: 9.5 Consensus size: 16
25074374 GTACATTTTT
* *
25074384 TTTTATATAGAATT-A
1 TTTTATACACAATTAA
*
25074399 TTTT-TATACAATTAA
1 TTTTATACACAATTAA
**
25074414 TTTTATACACAATTTT
1 TTTTATACACAATTAA
*
25074430 TTTGTATACACAATTTA
1 TTT-TATACACAATTAA
*
25074447 TTTTAT--ACAATTCA
1 TTTTATACACAATTAA
* *
25074461 TTGTATACAGAATTAA
1 TTTTATACACAATTAA
25074477 TTCTTTTTGTATACACAA-TATA
1 -----TTT-TATACACAATTA-A
*
25074499 TTTTAT--ACAATTAT
1 TTTTATACACAATTAA
25074513 TTTTATACACAATTAA
1 TTTTATACACAATTAA
*
25074529 TTTGATAC
1 TTTTATAC
25074537 CAAGAATTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
14 30 0.28
15 11 0.10
16 37 0.34
17 18 0.17
21 4 0.04
22 9 0.08
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (16 bp):
TTTTATACACAATTAA
Found at i:25074501 original size:52 final size:51
Alignment explanation
Indices: 25074378--25074531 Score: 169
Period size: 52 Copynumber: 3.1 Consensus size: 51
25074368 TTGTTTGTAC
* * *
25074378 ATTTTTTTTTATATAGAAT-TATTTTTATACAATTAATTT-TATACAC----A
1 ATTTTTTTGTATACACAATATA-TTTTATACAATT-ATTTGTATACACAATTA
* *
25074425 ATTTTTTTGTATACACAATTTATTTTATACAATTCA-TTGTATACAGAATTA
1 ATTTTTTTGTATACACAATATATTTTATACAATT-ATTTGTATACACAATTA
*
25074476 ATTCTTTTTGTATACACAATATATTTTATACAATTATTTTTATACACAATTA
1 ATT-TTTTTGTATACACAATATATTTTATACAATTATTTGTATACACAATTA
25074528 ATTT
1 ATTT
25074532 GATACCAAGA
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
46 2 0.02
47 35 0.38
48 2 0.02
51 6 0.07
52 46 0.51
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (51 bp):
ATTTTTTTGTATACACAATATATTTTATACAATTATTTGTATACACAATTA
Found at i:25075780 original size:31 final size:31
Alignment explanation
Indices: 25075742--25076065 Score: 441
Period size: 31 Copynumber: 10.5 Consensus size: 31
25075732 TGGCGTGTCA
* * * *
25075742 GTGTGACAACATTTCATTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* **
25075773 GTGTGACAACATTTGGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
25075804 GTGTCACAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
25075835 GTGTCACAAAATTTTACTTGTTATTCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
25075866 GTATCACAACATTTGACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
25075897 GTGTCAGAATATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
25075928 GTATCACAACATTTAACTTGTTATGCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * *
25075959 GTGTCAGAACATTTTGCTTGTTATCCTTGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
25075990 GTGTCACAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
25076021 GTGTCACAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
25076052 GTGTCACAACATTT
1 GTGTCACAACATTT
25076066 ATTCTTTATT
Statistics
Matches: 259, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 259 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:25088243 original size:18 final size:20
Alignment explanation
Indices: 25088220--25088258 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25088210 CCACCATTAC
*
25088220 TTTCTT-GGA-TTTCTTATT
1 TTTCTTAGGAGTTTCATATT
25088238 TTTCTTAGGAGTTTCATATT
1 TTTCTTAGGAGTTTCATATT
25088258 T
1 T
25088259 CAGCAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62
Consensus pattern (20 bp):
TTTCTTAGGAGTTTCATATT
Found at i:25090384 original size:23 final size:23
Alignment explanation
Indices: 25090358--25090401 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25090348 CCAACATTAC
25090358 GGACCGAATGCTATGGTATATAT
1 GGACCGAATGCTATGGTATATAT
* *
25090381 GGACTGAATGCTGTGGTATAT
1 GGACCGAATGCTATGGTATAT
25090402 GTGAAGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (23 bp):
GGACCGAATGCTATGGTATATAT
Found at i:25090901 original size:31 final size:31
Alignment explanation
Indices: 25090859--25091098 Score: 318
Period size: 31 Copynumber: 7.6 Consensus size: 31
25090849 TCATGTTGTT
* *
25090859 ACACGCTATGCATATAGCGTAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
*
25090890 ACACGCCATGCATATAACATAACATAAAATGTGGTA
1 ACACGCCATGC--AT---ATAACGTAAAATGTGGTA
*
25090926 ACACGCCATGCATATAACGTAAAATGTCGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
* *
25090957 ACACGCCATGCATTTAACGAAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
* *
25090988 ACACGCCATGCATATAACATAAAATATGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
* *
25091019 ACACGCCATGCATATAACATAAAATATGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
* *
25091050 ACACGCCATGCATATAACGTTAAATGTTGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
*
25091081 ACACGCCATGCATTTAAC
1 ACACGCCATGCATATAAC
25091099 CAATGTCGTG
Statistics
Matches: 187, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
31 156 0.83
33 2 0.01
34 2 0.01
36 27 0.14
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (31 bp):
ACACGCCATGCATATAACGTAAAATGTGGTA
Found at i:25092024 original size:17 final size:17
Alignment explanation
Indices: 25092002--25092044 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
25091992 GAATTAAATC
25092002 ATAAAATTATTTTATTA
1 ATAAAATTATTTTATTA
*
25092019 ATAAAA--AATTTATTA
1 ATAAAATTATTTTATTA
25092034 AGTAAAATTAT
1 A-TAAAATTAT
25092045 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 6 0.29
18 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAAAATTATTTTATTA
Found at i:25092068 original size:18 final size:18
Alignment explanation
Indices: 25092045--25092091 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
25092035 GTAAAATTAT
*
25092045 AAAAATAAATTTTTTTTA
1 AAAAATAAATTTTTTTAA
25092063 AAAAATAAATTTTTTTAA
1 AAAAATAAATTTTTTTAA
25092081 AAAAATAAATT
1 AAAAATAAATT
25092092 GACCCAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATAAATTTTTTTAA
Found at i:25100365 original size:89 final size:89
Alignment explanation
Indices: 25100193--25100372 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 89
25100183 TCAAATATTG
* *
25100193 ATTTTCTTGACATGTTCACCAACCTTACACATTAGGGTGTATATAGCAATATCATAGTGATACTA
1 ATTTGCTTGACATGTTCACCAACCTCACACATTAGGGTGTATATAGCAATATCATAGTGATACTA
* *
25100258 ACGCGGCAGATAAAAAATCAAAGC
66 ACGCAGCAAATAAAAAATCAAAGC
* * * * *
25100282 ATTTGCTTGACATGTTCACCAACCTCACACGTTAGGTTGTGTGTAGCAATATCATAGTGATAGTA
1 ATTTGCTTGACATGTTCACCAACCTCACACATTAGGGTGTATATAGCAATATCATAGTGATACTA
* *
25100347 AGGCAGCAAATAAGAAATCAAAGC
66 ACGCAGCAAATAAAAAATCAAAGC
25100371 AT
1 AT
25100373 GGTTAAAAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (89 bp):
ATTTGCTTGACATGTTCACCAACCTCACACATTAGGGTGTATATAGCAATATCATAGTGATACTA
ACGCAGCAAATAAAAAATCAAAGC
Found at i:25101817 original size:6 final size:7
Alignment explanation
Indices: 25101799--25101825 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25101789 AATGCTTCCG
25101799 ATTTTTA
1 ATTTTTA
25101806 ATTTTTA
1 ATTTTTA
25101813 ATTTTTA
1 ATTTTTA
25101820 ATTTTT
1 ATTTTT
25101826 TTATAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:25103728 original size:24 final size:24
Alignment explanation
Indices: 25103701--25103747 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
25103691 CTATCATGTA
*
25103701 TTCTACCATGTGTTCTGTCACATC
1 TTCTACCATATGTTCTGTCACATC
*
25103725 TTCTATCATATGTTCTGTCACAT
1 TTCTACCATATGTTCTGTCACAT
25103748 TATCTGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.45
Consensus pattern (24 bp):
TTCTACCATATGTTCTGTCACATC
Found at i:25106346 original size:21 final size:19
Alignment explanation
Indices: 25106320--25106360 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
25106310 AATTTAAAAC
25106320 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
25106341 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
25106360 A
1 A
25106361 CTCAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:25106618 original size:12 final size:12
Alignment explanation
Indices: 25106603--25106646 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
25106593 TGCCACGTGT
25106603 TCTGTCACATAA
1 TCTGTCACATAA
* **
25106615 TCTGTCACGTGT
1 TCTGTCACATAA
25106627 TCTGTCACATAA
1 TCTGTCACATAA
*
25106639 TCTATCAC
1 TCTGTCAC
25106647 GTGTTTTGTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.36
Consensus pattern (12 bp):
TCTGTCACATAA
Found at i:25106700 original size:24 final size:24
Alignment explanation
Indices: 25106588--25106736 Score: 154
Period size: 24 Copynumber: 6.2 Consensus size: 24
25106578 TTTTGTTTAG
*
25106588 TATTCTGCCACGTGTTCTGTCACA
1 TATTCTGCCACGTGTTTTGTCACA
* * *
25106612 TAATCTGTCACGTGTTCTGTCACA
1 TATTCTGCCACGTGTTTTGTCACA
* **
25106636 TAATCTATCACGTGTTTTGTCACA
1 TATTCTGCCACGTGTTTTGTCACA
* *
25106660 TATTTTACCACGTGTTTTGTCACA
1 TATTCTGCCACGTGTTTTGTCACA
* **
25106684 TATTCTGCCACGTGTTTTATTCATG
1 TATTCTGCCACGTGTTTT-GTCACA
* * *
25106709 TATTCTGTCACATGTTTTGTTACA
1 TATTCTGCCACGTGTTTTGTCACA
25106733 TATT
1 TATT
25106737 TTATCACGTG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 87 0.82
25 19 0.18
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.44
Consensus pattern (24 bp):
TATTCTGCCACGTGTTTTGTCACA
Found at i:25106743 original size:24 final size:24
Alignment explanation
Indices: 25106569--25106758 Score: 132
Period size: 24 Copynumber: 7.9 Consensus size: 24
25106559 TCAAGTACTA
* *
25106569 TATCATGTGTTTTGTTTA-GTATTC
1 TATCACGTGTTTTG-TTACATATTC
** * * *
25106593 TGCCACGTGTTCTGTCACATAATC
1 TATCACGTGTTTTGTTACATATTC
* * * *
25106617 TGTCACGTGTTCTGTCACATAATC
1 TATCACGTGTTTTGTTACATATTC
* *
25106641 TATCACGTGTTTTGTCACATATTT
1 TATCACGTGTTTTGTTACATATTC
* *
25106665 TACCACGTGTTTTGTCACATATTC
1 TATCACGTGTTTTGTTACATATTC
** *
25106689 TGCCACGTGTTTTATT-CATGTATTC
1 TATCACGTGTTTTGTTACA--TATTC
* * *
25106714 TGTCACATGTTTTGTTACATATTT
1 TATCACGTGTTTTGTTACATATTC
* *
25106738 TATCACGTGTTCTATTACATA
1 TATCACGTGTTTTGTTACATA
25106759 CTGTGTCAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
23 4 0.03
24 113 0.82
25 18 0.13
26 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (24 bp):
TATCACGTGTTTTGTTACATATTC
Found at i:25110348 original size:22 final size:22
Alignment explanation
Indices: 25110323--25110368 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
25110313 TTTTTAATGT
* *
25110323 ATTCATTATACATTAGTTCCAG
1 ATTCATTATACATCAATTCCAG
*
25110345 ATTCATTATGCATCAATTCCAG
1 ATTCATTATACATCAATTCCAG
25110367 AT
1 AT
25110369 GAGTTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTCATTATACATCAATTCCAG
Found at i:25126258 original size:2 final size:2
Alignment explanation
Indices: 25126251--25126313 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
25126241 GGTATATTAT
* *
25126251 AC AC AC AC AT AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
25126293 AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A
25126314 TATATATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.48, G:0.02, T:0.02
Consensus pattern (2 bp):
AC
Found at i:25144064 original size:17 final size:17
Alignment explanation
Indices: 25144042--25144074 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25144032 ATAATAATAA
25144042 AAAATA-AAATGAAAAAC
1 AAAATAGAAA-GAAAAAC
25144059 AAAATAGAAAGAAAAA
1 AAAATAGAAAGAAAAA
25144075 GAAGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAGAAAAAC
Found at i:25144367 original size:22 final size:22
Alignment explanation
Indices: 25144339--25144392 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
25144329 TTTTGTAGAT
*
25144339 TTTTTTTTTAAAAAAAAGCTAC
1 TTTTTTTTAAAAAAAAAGCTAC
*
25144361 TTTTTTTTAAAAAAAAAGTTAC
1 TTTTTTTTAAAAAAAAAGCTAC
25144383 TTTTTTTTAA
1 TTTTTTTTAA
25144393 GAGCTTCTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTTTTTAAAAAAAAAGCTAC
Found at i:25144852 original size:36 final size:36
Alignment explanation
Indices: 25144805--25144880 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
25144795 GATTAACAAC
25144805 AACTCATACCAAGACTCTTGGATTAATTTAAATTCT
1 AACTCATACCAAGACTCTTGGATTAATTTAAATTCT
*
25144841 AACTCATACCAAGACTTTTGGATTAATTTAAATTCT
1 AACTCATACCAAGACTCTTGGATTAATTTAAATTCT
25144877 AACT
1 AACT
25144881 TGAAAATGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (36 bp):
AACTCATACCAAGACTCTTGGATTAATTTAAATTCT
Found at i:25147453 original size:42 final size:42
Alignment explanation
Indices: 25147407--25147498 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
25147397 GTGGACCCGG
* * *
25147407 CTATGTGCGAGTAGAAGTATGCATACGTCGATGATGACCCAA
1 CTATGTGCGAGTAGAAGTACGCATAAGCCGATGATGACCCAA
* * * *
25147449 CTATGTGCGAGTAGGAGTGCGCATAAGCCGATGCTGACCCAG
1 CTATGTGCGAGTAGAAGTACGCATAAGCCGATGATGACCCAA
*
25147491 CCATGTGC
1 CTATGTGC
25147499 TAGTTGGGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (42 bp):
CTATGTGCGAGTAGAAGTACGCATAAGCCGATGATGACCCAA
Found at i:25167310 original size:2 final size:2
Alignment explanation
Indices: 25167303--25167327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25167293 ACTTTCAATT
25167303 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
25167328 TTGAAACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25169771 original size:18 final size:19
Alignment explanation
Indices: 25169750--25169785 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25169740 CAAGAAAGAG
*
25169750 AAGTGG-AGAAGGAAACTC
1 AAGTGGAAGAAGAAAACTC
25169768 AAGTGGAAGAAGAAAACT
1 AAGTGGAAGAAGAAAACT
25169786 TGAATGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.08, G:0.31, T:0.11
Consensus pattern (19 bp):
AAGTGGAAGAAGAAAACTC
Found at i:25173449 original size:30 final size:30
Alignment explanation
Indices: 25173415--25173473 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
25173405 GGAATAGAAG
*
25173415 ATATTCACA-ATGAGTTAATTGAGAAAAAAT
1 ATATTCACAGA-GAGCTAATTGAGAAAAAAT
* *
25173445 ATATTCATAGAGCGCTAATTGAGAAAAAA
1 ATATTCACAGAGAGCTAATTGAGAAAAAA
25173474 AAATTGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.27
Consensus pattern (30 bp):
ATATTCACAGAGAGCTAATTGAGAAAAAAT
Found at i:25176922 original size:20 final size:20
Alignment explanation
Indices: 25176875--25176918 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25176865 GTATTGGTAT
* *
25176875 AATATTTTAAAATATCTTTA
1 AATAATTTAAAAAATCTTTA
*
25176895 AATTATTTAAAAAAT-TTTA
1 AATAATTTAAAAAATCTTTA
25176914 AATAA
1 AATAA
25176919 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATTTAAAAAATCTTTA
Found at i:25178999 original size:15 final size:15
Alignment explanation
Indices: 25178979--25179021 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25178969 ATCGACAAAA
25178979 ATAAATTTTTTATTT
1 ATAAATTTTTTATTT
* *
25178994 ATAAATTATTAATTT
1 ATAAATTTTTTATTT
*
25179009 AAATAATTTTTTA
1 ATA-AATTTTTTA
25179022 ATAGTTATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAAATTTTTTATTT
Found at i:25179969 original size:21 final size:19
Alignment explanation
Indices: 25179945--25179983 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
25179935 TATTTTAAAT
25179945 TGATTAGTATCGTTTCTTAAC
1 TGATTAGTAT--TTTCTTAAC
*
25179966 TGATTATTATTTTCTTAA
1 TGATTAGTATTTTCTTAA
25179984 TTGAAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (19 bp):
TGATTAGTATTTTCTTAAC
Found at i:25180593 original size:21 final size:20
Alignment explanation
Indices: 25180564--25180603 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
25180554 GGTTTTGATT
25180564 AAAAAGATGGTAATCAGTTA
1 AAAAAGATGGTAATCAGTTA
* *
25180584 AAAAACGATGTTACTCAGTT
1 AAAAA-GATGGTAATCAGTT
25180604 TGAAGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (20 bp):
AAAAAGATGGTAATCAGTTA
Found at i:25183600 original size:45 final size:45
Alignment explanation
Indices: 25183531--25183632 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
25183521 AAAAAGAAAA
* *
25183531 TATTTAA-A-TATTATTTAACTATAATAAATATTATTAA-GAATAT
1 TATTTAATATTATTATTTAACTATAATAAAT-GTAATAAGGAATAT
25183574 TATTTAATATTATTATTTGAA-TATAATAAATGTAATAAGGAATAT
1 TATTTAATATTATTATTT-AACTATAATAAATGTAATAAGGAATAT
*
25183619 TATTTAGTATTATT
1 TATTTAATATTATT
25183633 TAAGTTTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
43 7 0.13
44 6 0.12
45 37 0.71
46 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (45 bp):
TATTTAATATTATTATTTAACTATAATAAATGTAATAAGGAATAT
Found at i:25183687 original size:28 final size:28
Alignment explanation
Indices: 25183655--25183714 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
25183645 AGAATATATT
* ** * *
25183655 TTATCTTTTAATATTAAATATTATTTAA
1 TTATCTTCTAATACAAAATATCATTAAA
25183683 TTATCTTCTAATACAAAATATCATTAAA
1 TTATCTTCTAATACAAAATATCATTAAA
25183711 TTAT
1 TTAT
25183715 AATAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATCTTCTAATACAAAATATCATTAAA
Found at i:25184619 original size:17 final size:17
Alignment explanation
Indices: 25184561--25184621 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
25184551 TGTTTAGTCG
25184561 GTTTGGTCTTCCTTTAT
1 GTTTGGTCTTCCTTTAT
* *
25184578 GCTTGGTCAGTT--TTGATT
1 GTTTGGTC--TTCCTTTA-T
25184596 GGTTTGGTCTTCCTTTAT
1 -GTTTGGTCTTCCTTTAT
25184614 GTTTGGTC
1 GTTTGGTC
25184622 AGTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
17 20 0.59
18 2 0.06
19 12 0.35
ACGTcount: A:0.07, C:0.15, G:0.25, T:0.54
Consensus pattern (17 bp):
GTTTGGTCTTCCTTTAT
Found at i:25189222 original size:18 final size:19
Alignment explanation
Indices: 25189201--25189239 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
25189191 AATCCTAACA
*
25189201 TATTTA-TATTTTTTTAAT
1 TATTTATTATTATTTTAAT
25189219 TA-TTATTATTATTTTAAT
1 TATTTATTATTATTTTAAT
25189237 TAT
1 TAT
25189240 AACACCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTATTATTATTTTAAT
Found at i:25198777 original size:21 final size:21
Alignment explanation
Indices: 25198735--25198777 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25198725 CCTGTACCGA
*
25198735 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
25198756 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
25198777 T
1 T
25198778 TGACTAGTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:25211458 original size:20 final size:20
Alignment explanation
Indices: 25211434--25211477 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
25211424 TATATAAATG
25211434 AAAAATATACATTTA-ATATCT
1 AAAAATA-A-ATTTAGATATCT
*
25211455 AAAAATAAATTTAGGTATCT
1 AAAAATAAATTTAGATATCT
25211475 AAA
1 AAA
25211478 TCATCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATAAATTTAGATATCT
Found at i:25220334 original size:16 final size:16
Alignment explanation
Indices: 25220315--25220346 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25220305 AAAAATAAAT
25220315 GCACATAGAAATTTTA
1 GCACATAGAAATTTTA
25220331 GCACATAGAAATTTTA
1 GCACATAGAAATTTTA
25220347 TACATACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
GCACATAGAAATTTTA
Found at i:25224600 original size:29 final size:29
Alignment explanation
Indices: 25224567--25224643 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
25224557 CCATCTTAAA
*
25224567 GATCAGGCGTAACTTTTTACCTTTTCAAG
1 GATCAGGCGTAACCTTTTACCTTTTCAAG
** * * **
25224596 GATCATACATAACCTCTTGTCTTTTCAAG
1 GATCAGGCGTAACCTTTTACCTTTTCAAG
*
25224625 GATTAGGCGTAACCTTTTA
1 GATCAGGCGTAACCTTTTA
25224644 ACAACACTGC
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (29 bp):
GATCAGGCGTAACCTTTTACCTTTTCAAG
Found at i:25227928 original size:68 final size:67
Alignment explanation
Indices: 25227819--25227946 Score: 211
Period size: 68 Copynumber: 1.9 Consensus size: 67
25227809 GGGCAACTCC
*
25227819 TAAGAATAAAACTAAGCTTTGCTTAATTTTGGAGCTAGCCAAACTATTATCGAAGATTTGTGGAA
1 TAAGAATAAAACTAAGCTTTGCTCAATTTTGGAGCTAGCC-AACTATTATCGAAGATTTGTGGAA
25227884 GGA
65 GGA
* * *
25227887 TAAGAATATAACTAAGCTTTGCTCATTTTTGGGGCTAGCCAACTATTATCGAAGATTTGT
1 TAAGAATAAAACTAAGCTTTGCTCAATTTTGGAGCTAGCCAACTATTATCGAAGATTTGT
25227947 ATAAGAGTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
67 20 0.36
68 36 0.64
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (67 bp):
TAAGAATAAAACTAAGCTTTGCTCAATTTTGGAGCTAGCCAACTATTATCGAAGATTTGTGGAAG
GA
Found at i:25230996 original size:60 final size:59
Alignment explanation
Indices: 25230900--25231101 Score: 167
Period size: 61 Copynumber: 3.3 Consensus size: 59
25230890 ATGATTCTCA
* * * *
25230900 CTGCAGCAAAAAAGGAATCTAGCTGCAACGAA-AAACTCTCTGTTTCATCAGCGAAATTTCG
1 CTGCAGCGAAAAA-GAATCTCGCTGCAGC-AAGAAACTCTCTGTTTC-TCAGTGAAATTTCG
* * * * * *
25230961 CTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACTTTTTATTT-TCTAGGTTGCAATTTTG
1 CTGCAGCGAAAAAGAATCTCGCTGCAGCAAGAAACTCTCTGTTTCTC-A-G-TGAAATTTCG
* * ** *
25231022 CTACAGCGAAAAAGAATCTCGCTGCAGCGAGAAAC-CTTCTGTTTCTGGGTTACAATTTCG
1 CTGCAGCGAAAAAGAATCTCGCTGCAGCAAGAAACTC-TCTGTTTCTCAGTGA-AATTTCG
*
25231082 CTGCAGCGAGAAAGAATCTC
1 CTGCAGCGAAAAAGAATCTC
25231102 CCTGAAACAA
Statistics
Matches: 111, Mismatches: 23, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
58 2 0.02
59 4 0.04
60 49 0.44
61 55 0.50
62 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (59 bp):
CTGCAGCGAAAAAGAATCTCGCTGCAGCAAGAAACTCTCTGTTTCTCAGTGAAATTTCG
Found at i:25231117 original size:60 final size:60
Alignment explanation
Indices: 25230954--25231125 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 60
25230944 TCATCAGCGA
* * * *
25230954 AATTTCGCTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACTTTTTATTTTCTAGGTTGC
1 AATTTCGCTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACCTTCT-GTTTCTAGGTTAC
* * * * *
25231015 AATTTTGCTACAGCGAAAAAGAATCTCGCTGCAGCGAGAAACCTTCTGTTTCTGGGTTAC
1 AATTTCGCTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACCTTCTGTTTCTAGGTTAC
* * * *
25231075 AATTTCGCTGCAGCGAGAAAGAATCTCCCTGAAACAAAAAACCTTCTGTTT
1 AATTTCGCTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACCTTCTGTTT
25231126 TGGTCTCCTA
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 53 0.56
61 41 0.44
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (60 bp):
AATTTCGCTGCAGCGAGAAAGAATCTCGCTGCAGCAAGAAACCTTCTGTTTCTAGGTTAC
Found at i:25233626 original size:6 final size:6
Alignment explanation
Indices: 25233617--25233737 Score: 120
Period size: 6 Copynumber: 19.8 Consensus size: 6
25233607 CACATATCTA
* * *
25233617 TATATG TATA-- TATATT TATGTA TATATG TATATG TATATG TATATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG --TATATG
* *
25233665 TATATG TATATG TATATATG TATATG TATATG TATATA TATATG TATATA
1 TATATG TATATG --TATATG TATATG TATATG TATATG TATATG TATATG
* * *
25233715 TATATA TATATA TATATA TATAT
1 TATATG TATATG TATATG TATAT
25233738 CCATCACCAT
Statistics
Matches: 102, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
4 4 0.04
6 86 0.84
8 12 0.12
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:25233636 original size:14 final size:14
Alignment explanation
Indices: 25233610--25233737 Score: 143
Period size: 14 Copynumber: 9.3 Consensus size: 14
25233600 GATAACACAC
*
25233610 ATATCTATATATGT
1 ATATATATATATGT
*
25233624 ATATATATTTATGT
1 ATATATATATATGT
*
25233638 ATATATGTATATGT
1 ATATATATATATGT
*
25233652 ATATGTATATATG-
1 ATATATATATATGT
*
25233665 -TATATGTATATGT
1 ATATATATATATGT
*
25233678 ATATATGTATATGT
1 ATATATATATATGT
* *
25233692 ATATGTATATATAT
1 ATATATATATATGT
* *
25233706 ATGTATATATATAT
1 ATATATATATATGT
*
25233720 ATATATATATATAT
1 ATATATATATATGT
25233734 ATAT
1 ATAT
25233738 CCATCACCAT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
12 10 0.10
14 88 0.90
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:25233648 original size:20 final size:20
Alignment explanation
Indices: 25233610--25233735 Score: 162
Period size: 20 Copynumber: 6.2 Consensus size: 20
25233600 GATAACACAC
*
25233610 ATATCTATATATGTATATAT
1 ATATGTATATATGTATATAT
*
25233630 ATTTATGTATATATGTATATGT
1 A--TATGTATATATGTATATAT
*
25233652 ATATGTATATATGTATATGT
1 ATATGTATATATGTATATAT
*
25233672 ATATGTATATATGTATATGT
1 ATATGTATATATGTATATAT
* *
25233692 ATATGTATATATATATGTAT
1 ATATGTATATATGTATATAT
* *
25233712 ATATATATATATATATATAT
1 ATATGTATATATGTATATAT
25233732 ATAT
1 ATAT
25233736 ATCCATCACC
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
20 79 0.81
22 18 0.19
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.51
Consensus pattern (20 bp):
ATATGTATATATGTATATAT
Found at i:25233821 original size:42 final size:42
Alignment explanation
Indices: 25233774--25233968 Score: 203
Period size: 42 Copynumber: 4.6 Consensus size: 42
25233764 TTGTCATATA
* *
25233774 CACTCCCACTAGCACATGGCTGGGTCAGCATCAGCTTATGCG
1 CACTCCCACTAGCACATAGCCGGGTCAGCATCAGCTTATGCG
* * *
25233816 CACTCCGACTTGCACATAACCGGGTCAGCATCAGCTTATGCG
1 CACTCCCACTAGCACATAGCCGGGTCAGCATCAGCTTATGCG
* * * * *
25233858 CACTCCCCCTCA-CACATAGTCGGGTCAGAATCGGCTTATACG
1 CACTCCCACT-AGCACATAGCCGGGTCAGCATCAGCTTATGCG
* ** * * * *
25233900 CACTCCCCCCCGCACATAACCGGGTCAGTATTAGCTTATGCA
1 CACTCCCACTAGCACATAGCCGGGTCAGCATCAGCTTATGCG
* *
25233942 CACTCCTACTCGCACATAGCCGGGTCA
1 CACTCCCACTAGCACATAGCCGGGTCA
25233969 ATATCATTAC
Statistics
Matches: 125, Mismatches: 26, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (42 bp):
CACTCCCACTAGCACATAGCCGGGTCAGCATCAGCTTATGCG
Found at i:25233915 original size:84 final size:84
Alignment explanation
Indices: 25233773--25233968 Score: 232
Period size: 84 Copynumber: 2.3 Consensus size: 84
25233763 ATTGTCATAT
* * * * * **
25233773 ACACTCCCACT-AGCACATGGCTGGGTCAGCATCAGCTTATGCGCACTCCGACTTGCACATAACC
1 ACACTCCCACTCA-CACATAGCCGGGTCAGAATCAGCTTATACGCACTCCCACCCGCACATAACC
25233837 GGGTCAGCATCAGCTTATGC
65 GGGTCAGCATCAGCTTATGC
* * * * *
25233857 GCACTCCCCCTCACACATAGTCGGGTCAGAATCGGCTTATACGCACTCCCCCCCGCACATAACCG
1 ACACTCCCACTCACACATAGCCGGGTCAGAATCAGCTTATACGCACTCCCACCCGCACATAACCG
* *
25233922 GGTCAGTATTAGCTTATGC
66 GGTCAGCATCAGCTTATGC
* *
25233941 ACACTCCTACTCGCACATAGCCGGGTCA
1 ACACTCCCACTCACACATAGCCGGGTCA
25233969 ATATCATTAC
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 91 0.99
85 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (84 bp):
ACACTCCCACTCACACATAGCCGGGTCAGAATCAGCTTATACGCACTCCCACCCGCACATAACCG
GGTCAGCATCAGCTTATGC
Found at i:25241253 original size:42 final size:41
Alignment explanation
Indices: 25241206--25241332 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 41
25241196 CAATTGGCTA
*
25241206 GGTCAGCATCGGCTTATGCGAACTCGTACTCGCACATAGTCC
1 GGTCAGCATCGGCTTATGCGAACTCCTACTCGCACATAG-CC
* **
25241248 GGTCAGCATCGGCTTATGCGCACTCCCCCTCGCACATAGCC
1 GGTCAGCATCGGCTTATGCGAACTCCTACTCGCACATAGCC
* * *
25241289 GGGTCAACATCGGCTTATGC-ACACTCTTACTTGCACATAGCC
1 -GGTCAGCATCGGCTTATGCGA-ACTCCTACTCGCACATAGCC
25241331 GG
1 GG
25241333 ATCAATATCA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.05
42 69 0.95
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (41 bp):
GGTCAGCATCGGCTTATGCGAACTCCTACTCGCACATAGCC
Found at i:25245082 original size:155 final size:154
Alignment explanation
Indices: 25244799--25245108 Score: 595
Period size: 155 Copynumber: 2.0 Consensus size: 154
25244789 ACTTCCTCAC
25244799 TCTAAGAATACAAAGAGAGAAGTAATGAGAGTGTACCTATGATCACACGGTTGATCTAAATGGTA
1 TCTAAGAATACAAAGAGAGAAGTAATGAGAGTGTACCTATGATCACACGGTTGATCTAAATGGTA
25244864 CAAGTGAAATGTATATCACAATTATAAAGATAGAAGTTGAGTGCAGTAAATGAGCAGTAAGTTTT
66 CAAGTGAAATGTATATCACAATTATAAAGATAGAAGTTGAGTGCAGTAAATGAGCAGTAAGTTTT
25244929 TGTAGGTTTTTCAGCTTTTTTTTT
131 TGTAGGTTTTTCAGCTTTTTTTTT
25244953 TNCTAAGAATACAAAGAGAGAAGTAAT-AGGAGTGTACCTATGATCACACGGTTGATCTAAATGG
1 T-CTAAGAATACAAAGAGAGAAGTAATGA-GAGTGTACCTATGATCACACGGTTGATCTAAATGG
25245017 TACAAGTGAAATGTATATCACAATTATAAAGATAGAAGTTGAGTGCAGTAAATGAGCAGTAAGTT
64 TACAAGTGAAATGTATATCACAATTATAAAGATAGAAGTTGAGTGCAGTAAATGAGCAGTAAGTT
25245082 TTTGTAGGTTTTTCAGCTTTTTTTTT
129 TTTGTAGGTTTTTCAGCTTTTTTTTT
25245108 T
1 T
25245109 TTTTGGAAGC
Statistics
Matches: 154, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
154 2 0.01
155 152 0.99
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (154 bp):
TCTAAGAATACAAAGAGAGAAGTAATGAGAGTGTACCTATGATCACACGGTTGATCTAAATGGTA
CAAGTGAAATGTATATCACAATTATAAAGATAGAAGTTGAGTGCAGTAAATGAGCAGTAAGTTTT
TGTAGGTTTTTCAGCTTTTTTTTT
Found at i:25248930 original size:99 final size:99
Alignment explanation
Indices: 25248767--25248951 Score: 239
Period size: 99 Copynumber: 1.9 Consensus size: 99
25248757 TGAAAAGTTA
* *
25248767 GTGTAAAGGTTACGGTTGATCCCTGAAAAAGTCATTGTATTGGTTTGTGATCAAGCCCATTAAAA
1 GTGTAAAGGTTACGGTTGATCCCTGAAAAAGCCATTGTATGGGTTTGTGATCAAGCCCATTAAAA
*
25248832 ACCATGGGTTATCGCTTGATCGTGTAAAAAGTCG
66 ACCATGAGTTATCGCTTGATCGTGTAAAAAGTCG
* * * * **
25248866 GTGTATAGGTTATGGTTGATCTC-GAAAAAAGCCATTGTATGGGTTTGTGGAT-GAGCCTGTTAA
1 GTGTAAAGGTTACGGTTGATCCCTG-AAAAAGCCATTGTATGGGTTTGT-GATCAAGCCCATTAA
* *
25248929 AAACCATGAGTTATTGTTTGATC
64 AAACCATGAGTTATCGCTTGATC
25248952 TTATGAAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
98 1 0.01
99 69 0.95
100 3 0.04
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (99 bp):
GTGTAAAGGTTACGGTTGATCCCTGAAAAAGCCATTGTATGGGTTTGTGATCAAGCCCATTAAAA
ACCATGAGTTATCGCTTGATCGTGTAAAAAGTCG
Found at i:25250294 original size:32 final size:31
Alignment explanation
Indices: 25250261--25250379 Score: 136
Period size: 32 Copynumber: 3.8 Consensus size: 31
25250251 AGAAGCGGAT
* *
25250261 TTGAAGAAGTTTAATAGAAGGAAAAAAAAGAT
1 TTGAAGAAATTTAATAGAA-GAAAAAAAAGAC
*
25250293 TTGACA-AAATTTAAT--AAGAAAAGAAAAAAC
1 TTGA-AGAAATTTAATAGAAGAAAA-AAAAGAC
*
25250323 TTGAAGAATTTTAATAGAAGAAAGAAAAAGAC
1 TTGAAGAAATTTAATAGAAGAAA-AAAAAGAC
25250355 TTGAAGAAATTTAATAGAAAGAAAA
1 TTGAAGAAATTTAATAG-AAGAAAA
25250380 TTTGAAGAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
29 6 0.08
30 19 0.26
32 41 0.55
33 8 0.11
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.22
Consensus pattern (31 bp):
TTGAAGAAATTTAATAGAAGAAAAAAAAGAC
Found at i:25250327 original size:62 final size:58
Alignment explanation
Indices: 25250261--25250425 Score: 185
Period size: 62 Copynumber: 2.8 Consensus size: 58
25250251 AGAAGCGGAT
*
25250261 TTGAAGAAGTTTAATAGAAGGAAA-AAAAAGATTTGACA-AAATTTAATAAGAAAAGAAAAAAC
1 TTGAAGAAGTTTAATAGAA-GAAAGAAAAAGACTTGA-AGAAATTTAAT-AG-AAAG--AAAAC
* *
25250323 TTGAAGAATTTTAATAGAAGAAAGAAAAAGACTTGAAGAAATTTAATAGAAAGAAAAT
1 TTGAAGAAGTTTAATAGAAGAAAGAAAAAGACTTGAAGAAATTTAATAGAAAGAAAAC
* * *
25250381 TTGAAGAAGTTTAATAGTAA-AAGGAAGAACAC-TGAAGAAATTTAA
1 TTGAAGAAGTTTAATAG-AAGAAAGAAAAAGACTTGAAGAAATTTAA
25250426 AAAAAAAGAA
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
57 13 0.14
58 29 0.31
59 2 0.02
60 4 0.04
61 7 0.08
62 38 0.41
ACGTcount: A:0.56, C:0.03, G:0.18, T:0.23
Consensus pattern (58 bp):
TTGAAGAAGTTTAATAGAAGAAAGAAAAAGACTTGAAGAAATTTAATAGAAAGAAAAC
Found at i:25250332 original size:29 final size:28
Alignment explanation
Indices: 25250261--25250440 Score: 116
Period size: 32 Copynumber: 6.0 Consensus size: 28
25250251 AGAAGCGGAT
* *
25250261 TTGAAGAAGTTTAATAGAAGGAAAAAAAAGAT
1 TTGAAGAA-TTTAATAGAA--AAGAAAAA-AC
*
25250293 TTGACAAAATTTAATAAGAAAAGAAAAAAC
1 TTGA-AGAATTTAAT-AGAAAAGAAAAAAC
25250323 TTGAAGAATTTTAATAGAAGAAAGAAAAAGAC
1 TTGAAGAA-TTTAATAG-A-AAAGAAAAA-AC
*
25250355 TTGAAGAAATTTAATAG-AAAG--AAAAT
1 TTGAAG-AATTTAATAGAAAAGAAAAAAC
*
25250381 TTGAAGAAGTTTAATAGTAAAAGGAAGAACAC
1 TTGAAGAA-TTTAATAG-AAAA-GAA-AAAAC
* *
25250413 -TGAAGAAATTTAAAAAAAAAGAAGAAAA
1 TTGAAG-AATTTAATAGAAAAGAA-AAAA
25250441 AAACTTGAAG
Statistics
Matches: 123, Mismatches: 10, Indels: 33
0.74 0.06 0.20
Matches are distributed among these distances:
25 2 0.02
26 15 0.12
27 3 0.02
28 3 0.02
29 17 0.14
30 16 0.13
31 27 0.22
32 31 0.25
33 9 0.07
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.21
Consensus pattern (28 bp):
TTGAAGAATTTAATAGAAAAGAAAAAAC
Found at i:25250434 original size:58 final size:59
Alignment explanation
Indices: 25250261--25250435 Score: 171
Period size: 58 Copynumber: 2.9 Consensus size: 59
25250251 AGAAGCGGAT
* * *
25250261 TTGAAGAAGTTTAATAGAAGGAAA-AAAAAGATTTGACA-AAATTTAATAAGAAAAGAAAAAAC
1 TTGAAGAAGTTTAATAGAA-GAAAGAAAAACACTTGA-AGAAATTTAA-AA-AAAA-AGAAAAC
* * * * *
25250323 TTGAAGAATTTTAATAGAAGAAAGAAAAAGACTTGAAGAAATTT-AATAGAAAGAAAAT
1 TTGAAGAAGTTTAATAGAAGAAAGAAAAACACTTGAAGAAATTTAAAAAAAAAGAAAAC
* *
25250381 TTGAAGAAGTTTAATAGTAA-AAGGAAGAACAC-TGAAGAAATTTAAAAAAAAAGAA
1 TTGAAGAAGTTTAATAG-AAGAAAGAAAAACACTTGAAGAAATTTAAAAAAAAAGAA
25250436 GAAAAAAACT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
57 11 0.11
58 39 0.40
59 5 0.05
60 1 0.01
61 6 0.06
62 35 0.36
ACGTcount: A:0.58, C:0.03, G:0.17, T:0.22
Consensus pattern (59 bp):
TTGAAGAAGTTTAATAGAAGAAAGAAAAACACTTGAAGAAATTTAAAAAAAAAGAAAAC
Found at i:25252926 original size:345 final size:342
Alignment explanation
Indices: 25252297--25252978 Score: 1046
Period size: 345 Copynumber: 2.0 Consensus size: 342
25252287 GGTTCATAGC
* **
25252297 TTAAAATGAAGAAATAGATGCAATCCTTTATTCAAACCACTAATCATTATGTATGAAAATGTTGT
1 TTAAAATGAAGAAATAGATGCAATCCTTTATTCAAACCACTAATCATTATGTATGAAAATGCTAC
25252362 TGAATAAAAATAAAAAAATGCTAATTTCCTCAAAGAAATCCTTTTCTTCCCTAACGATATTCGCT
66 TGAATAAAAATAAAAAAATGCTAATTTCCTCAAAGAAATCCTTTTCTTCCCTAACGATATTCGCT
*
25252427 CACACCAACCAAAAGAAAAAAGCAAATAAAATCTTAATAAAAGAAAACTCAAATTGGAATTTATA
131 CACACCAACCAAAAGAAAAAAGCAAACAAAATCTTAATAAAAGAAAACTCAAATTGGAATTTATA
* * *
25252492 GCCATGCTTTAAAGGACAAAATATAGACTCAAAAAAACTCCAAACTTATATAACCTACATTCAAA
196 GCCATACTTTAAAGGAAAAAATATAGACTCAAAAAAACTCCAAACTTACATAACCTACATTCAAA
* ** *
25252557 ATTGGTTTAGAGTGCCCAACACTAAAGGCATACAAAAAAGCATCAAATTCCAGAGTTCAGGGAGA
261 ATTGGTTTAGAGTGCCCAACACTAAAGGCATAC-AAAAAGCAGCAAAGCCCAAAGTTCAGGGAGA
*
25252622 TTGTTTTATATAGATGTG
325 TTGTTCTATATAGATGTG
** * * *
25252640 TTAAAATGAAGAAATAGATGCAATGTTTTATTCAAGCCACTAATCATTATGTGTGACAATGCTAC
1 TTAAAATGAAGAAATAGATGCAATCCTTTATTCAAACCACTAATCATTATGTATGAAAATGCTAC
* *
25252705 TGAATGAAAGCAA-AAAAAAATGCTAATTTCCTCAAAGAAATCCTTTTTTTCCCTCACGATATTC
66 TGAAT-AAA--AATAAAAAAATGCTAATTTCCTCAAAGAAATCCTTTTCTTCCCTAACGATATTC
* *
25252769 AG-TTACACCAACCAAAAGAAAAAAGCACACAAAATCTTAATAAAAGAAAAGC-CAAATTGGAAT
128 -GCTCACACCAACCAAAAGAAAAAAGCAAACAAAATCTTAATAAAAGAAAA-CTCAAATTGGAAT
* * *
25252832 TTATAGCCATACTTTAAAGGAAAAAATATAGATTCAAAAAAACTTCAAACTTACGTAACCTACAT
191 TTATAGCCATACTTTAAAGGAAAAAATATAGACTCAAAAAAACTCCAAACTTACATAACCTACAT
* * *
25252897 TCAAAATTGGTTTAGAGTGCCCAACACTAAGGGCATACAAAATGCAGCAAAGCCCAAAGTTCAGT
256 TCAAAATTGGTTTAGAGTGCCCAACACTAAAGGCATACAAAAAGCAGCAAAGCCCAAAGTTCAGG
25252962 GAGATTGTTCTATATAG
321 GAGATTGTTCTATATAG
25252979 GTGTATCAGT
Statistics
Matches: 307, Mismatches: 27, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
343 62 0.20
344 40 0.13
345 201 0.65
346 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (342 bp):
TTAAAATGAAGAAATAGATGCAATCCTTTATTCAAACCACTAATCATTATGTATGAAAATGCTAC
TGAATAAAAATAAAAAAATGCTAATTTCCTCAAAGAAATCCTTTTCTTCCCTAACGATATTCGCT
CACACCAACCAAAAGAAAAAAGCAAACAAAATCTTAATAAAAGAAAACTCAAATTGGAATTTATA
GCCATACTTTAAAGGAAAAAATATAGACTCAAAAAAACTCCAAACTTACATAACCTACATTCAAA
ATTGGTTTAGAGTGCCCAACACTAAAGGCATACAAAAAGCAGCAAAGCCCAAAGTTCAGGGAGAT
TGTTCTATATAGATGTG
Found at i:25255567 original size:16 final size:17
Alignment explanation
Indices: 25255535--25255569 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25255525 GAGAAAAAAG
*
25255535 AAAAAAGAAAGATAAGA
1 AAAAAAGAAAGAGAAGA
25255552 AAAAAAGAAAG-GAAGA
1 AAAAAAGAAAGAGAAGA
25255568 AA
1 AA
25255570 GGAGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAGAGAAGA
Found at i:25259037 original size:23 final size:22
Alignment explanation
Indices: 25259000--25259042 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
25258990 GCTATTAAAA
*
25259000 ATATTTTTAATAACACTTTTTTT
1 ATATTTTTAAGAACA-TTTTTTT
*
25259023 ATATTTTTTAGAACATTTTT
1 ATATTTTTAAGAACATTTTT
25259043 GTAAATCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTTTTAAGAACATTTTTTT
Found at i:25263930 original size:120 final size:123
Alignment explanation
Indices: 25263707--25263940 Score: 377
Period size: 120 Copynumber: 1.9 Consensus size: 123
25263697 CATTTAAAAA
* *
25263707 TATTTATCCTTTTTCAATCTTTTAATTTTTATTTTCATTAAAAATTTAAAATATTAATAATTTAT
1 TATTTATCATTTTTCAATCTTTTAATTTCTATTTTCATTAAAAATTTAAAATATTAATAATTTAT
25263772 TATTAAATTATTAACATAATTTTTTATTTCAATTTCTTTTTA-TTTTTTCTCTATTTG
66 TATTAAATTATTAACATAATTTTTTATTTCAATTTCTTTTTACTTTTTTCTCTATTTG
* * *
25263829 TATTT-TCATTTTTTAATCTTTTAATTTCTATTTTCTTTCAAAATTT-AAATATTAATAATTTAT
1 TATTTATCATTTTTCAATCTTTTAATTTCTATTTTCATTAAAAATTTAAAATATTAATAATTTAT
*
25263892 TATTAAATTATTAATATAATTTTTTATTTTC-ATTTCTTTTTACTTTTTT
66 TATTAAATTATTAACATAATTTTTTA-TTTCAATTTCTTTTTACTTTTTT
25263941 TAATTTTATT
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
120 53 0.51
121 46 0.44
122 5 0.05
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (123 bp):
TATTTATCATTTTTCAATCTTTTAATTTCTATTTTCATTAAAAATTTAAAATATTAATAATTTAT
TATTAAATTATTAACATAATTTTTTATTTCAATTTCTTTTTACTTTTTTCTCTATTTG
Found at i:25265684 original size:29 final size:29
Alignment explanation
Indices: 25265651--25265727 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
25265641 TATTTCAAAA
*
25265651 ATTCAAATAAGTCTTTATATTTTTATTAT
1 ATTCAAATAAATCTTTATATTTTTATTAT
* * *
25265680 ATTCAATTAAATTTTTATATTTTTATTTT
1 ATTCAAATAAATCTTTATATTTTTATTAT
* *
25265709 AAGTCAAATAAATCCTTAT
1 -ATTCAAATAAATCTTTAT
25265728 GATTAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (29 bp):
ATTCAAATAAATCTTTATATTTTTATTAT
Found at i:25271742 original size:49 final size:49
Alignment explanation
Indices: 25271663--25271761 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
25271653 CCATTAAATC
* *
25271663 ATAAGATATTACATCCATGCATCTTATATTAAGTCACTCGATAATTCTA
1 ATAAGATATTACATCCATGCATATAATATTAAGTCACTCGATAATTCTA
* * **
25271712 ATAAGATATTACATTCAT-CTTATAATTATTAAGTTGCTCGATAATTCTA
1 ATAAGATATTACATCCATGCATATAA-TATTAAGTCACTCGATAATTCTA
25271761 A
1 A
25271762 AACTGCCTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.09
49 39 0.91
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (49 bp):
ATAAGATATTACATCCATGCATATAATATTAAGTCACTCGATAATTCTA
Found at i:25274930 original size:52 final size:53
Alignment explanation
Indices: 25274868--25274981 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 53
25274858 AAGATGTGAG
* * ** *
25274868 TTAGTCGACTAAATGCTCTCTGCCCAAATCTG-GACTTCAAGATAGAACCAAC
1 TTAGTCGACTAAATGCTCTCTGCCAAAATCTGCAACCACAAGACAGAACCAAC
* * * *
25274920 TTAGTCGACTAAATGGTCTTTGCCAAAATTTGCAACCAGAAGACAGAACCAAC
1 TTAGTCGACTAAATGCTCTCTGCCAAAATCTGCAACCACAAGACAGAACCAAC
25274973 TTAGTCGAC
1 TTAGTCGAC
25274982 CAAGAAGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
52 28 0.54
53 24 0.46
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (53 bp):
TTAGTCGACTAAATGCTCTCTGCCAAAATCTGCAACCACAAGACAGAACCAAC
Found at i:25284085 original size:73 final size:71
Alignment explanation
Indices: 25283926--25284095 Score: 182
Period size: 73 Copynumber: 2.4 Consensus size: 71
25283916 ACCAAGACGT
* * * * *
25283926 GAGTTAGTCGACTAAATGCTTTCTGCCAAAATCTAGACTTCAAGATAGAACCAACTTAGTCGACT
1 GAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTAGACTACAAGACAAAACCAACTTAGTCGACC
25283991 AAAAAA
66 AAAAAA
* * * * * *
25283997 TGAGTTAGTCTACTAAATGCTCTCTGCTAGAATCTATGACTAGAAGACAAAACCAATTTAGTTGA
1 -GAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTA-GACTACAAGACAAAACCAACTTAGTCGA
25284062 CCAATAAGAA
64 CCAA-AA-AA
25284072 -AGTTAGTCGACTAAGA-GCTCTCTG
1 GAGTTAGTCGACTAA-ATGCTCTCTG
25284096 TCTGCAATTT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
72 31 0.38
73 46 0.56
74 3 0.04
75 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (71 bp):
GAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTAGACTACAAGACAAAACCAACTTAGTCGACC
AAAAAA
Found at i:25287617 original size:102 final size:101
Alignment explanation
Indices: 25287435--25287638 Score: 363
Period size: 102 Copynumber: 2.0 Consensus size: 101
25287425 ACTTCAAAGC
* *
25287435 TTAGGAAATGCCATCCTTCACATTCATCACCTTTGTAAGCAACACGATTGCAAGAGTTTCAGTGG
1 TTAGGAAATGCCATCCTCCACATTCATCACCTCTGTAAGCAACACGATTGCAAGAGTTTCAGTGG
* *
25287500 GAGTTCTTCCTTGCACCTCACCCAAATTAAGCCATA
66 GAGTTCTTCCCTGCACCTAACCCAAATTAAGCCATA
25287536 TTAGCGAAATGCCATCCTCCACATTCATCACCTCTGTAAGCAACACGATTGCAAGAGTTTCAGTG
1 TTAG-GAAATGCCATCCTCCACATTCATCACCTCTGTAAGCAACACGATTGCAAGAGTTTCAGTG
25287601 GGAGTTCTTCCCTGCACCTAACCCAAATTAAGCCATA
65 GGAGTTCTTCCCTGCACCTAACCCAAATTAAGCCATA
25287638 T
1 T
25287639 CAGCTTTTAC
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 4 0.04
102 94 0.96
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (101 bp):
TTAGGAAATGCCATCCTCCACATTCATCACCTCTGTAAGCAACACGATTGCAAGAGTTTCAGTGG
GAGTTCTTCCCTGCACCTAACCCAAATTAAGCCATA
Found at i:25288646 original size:19 final size:20
Alignment explanation
Indices: 25288602--25288648 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
25288592 ATTTATTTTA
*
25288602 ATTTAAA-ATAAATATTAAT
1 ATTTAAATATAAATAATAAT
*
25288621 A-TAAAATATAAA-AATAAT
1 ATTTAAATATAAATAATAAT
25288639 ATTTAAATAT
1 ATTTAAATAT
25288649 TTAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTAAATATAAATAATAAT
Found at i:25289921 original size:164 final size:168
Alignment explanation
Indices: 25289628--25289965 Score: 524
Period size: 164 Copynumber: 2.0 Consensus size: 168
25289618 ACGTTCTTTG
*
25289628 ATTGTTCTCTTCTTTTTTATCGTAACTGGATTATCTTCTTCTCCCCTTCTTCTTCTTCTAGCATT
1 ATTGTTCTCTTCTTTTTTATCCTAACTGGATTATCTTCTTCTCCCCTTCTTCTTCTTCTAGCATT
* * *
25289693 AAAATTACGTTTACAAAATTATTTATCTTCAAGAGATTTCAAGATAATTTTTATATTTTTAAGTG
66 AAAACTAAGTTTACAAAATTATTTATCTTCAAGAGACTTCAAGATAATTTTTATATTTTTAAGTG
* * *
25289758 ATTTTTACATTTGATGTAGGGTTATAATGTGATAATCA
131 ATTTTTACAATTGATGTAAGGTTACAATGTGATAATCA
* *
25289796 ATTGTTCTCTTCTTTTTTATCCTAACTTGATTATCTTCTTCTCCCCTTC-T-TT-TTCTAGCTTT
1 ATTGTTCTCTTCTTTTTTATCCTAACTGGATTATCTTCTTCTCCCCTTCTTCTTCTTCTAGCATT
*
25289858 AAAACTAAGTTT-CAAAATTGTTTAAT-TTCAAGAGACTTCAAGATAATTTTTATATTTTTAAGT
66 AAAACTAAGTTTACAAAATTATTT-ATCTTCAAGAGACTTCAAGATAATTTTTATATTTTTAAGT
* *
25289921 GATTTTTACAATTGATTTAAGGTTACAATGTGATAATTA
130 GATTTTTACAATTGATGTAAGGTTACAATGTGATAATCA
25289960 ATTGTT
1 ATTGTT
25289966 TTTTTTCAAG
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
164 86 0.55
165 21 0.13
166 2 0.01
167 1 0.01
168 47 0.30
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (168 bp):
ATTGTTCTCTTCTTTTTTATCCTAACTGGATTATCTTCTTCTCCCCTTCTTCTTCTTCTAGCATT
AAAACTAAGTTTACAAAATTATTTATCTTCAAGAGACTTCAAGATAATTTTTATATTTTTAAGTG
ATTTTTACAATTGATGTAAGGTTACAATGTGATAATCA
Found at i:25294226 original size:13 final size:13
Alignment explanation
Indices: 25294201--25294234 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
25294191 AAAAATTGCT
25294201 AAATTATTTAAAA
1 AAATTATTTAAAA
25294214 AAATT-TTTAAAA
1 AAATTATTTAAAA
25294226 AAATTATTT
1 AAATTATTT
25294235 TTTATTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTATTTAAAA
Found at i:25294610 original size:17 final size:18
Alignment explanation
Indices: 25294588--25294623 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
25294578 AGTCTTTTGA
25294588 TTGTTCAAA-AATTATGT
1 TTGTTCAAATAATTATGT
25294605 TTGTTCAAATAATTATGT
1 TTGTTCAAATAATTATGT
25294623 T
1 T
25294624 GGAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGTTCAAATAATTATGT
Found at i:25297642 original size:18 final size:17
Alignment explanation
Indices: 25297602--25297645 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
25297592 TCCTTTGAAC
*
25297602 AATTATGATTGTTCAAA
1 AATTATGTTTGTTCAAA
*
25297619 AATTATGTTTGTTTAAA
1 AATTATGTTTGTTCAAA
25297636 TAATTATGTT
1 -AATTATGTT
25297646 GAAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (17 bp):
AATTATGTTTGTTCAAA
Found at i:25305159 original size:2 final size:2
Alignment explanation
Indices: 25305113--25305140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25305103 TGTGTGTGTG
25305113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25305141 AATTTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25308477 original size:29 final size:29
Alignment explanation
Indices: 25308435--25308524 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
25308425 GCAATGTTGT
25308435 CAAGAAGTTATGCCTGATCCTTGAAAAGG
1 CAAGAAGTTATGCCTGATCCTTGAAAAGG
* * *
25308464 CAAGATGTTATGCCTAATCCTTGCAAAGG
1 CAAGAAGTTATGCCTGATCCTTGAAAAGG
** * * *
25308493 CAAGGGGTTATGCTTGCTCTTGTGAAAAGG
1 CAAGAAGTTATGCCTGATCCT-TGAAAAGG
25308523 CA
1 CA
25308525 TTGTTGTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 41 0.82
30 9 0.18
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
CAAGAAGTTATGCCTGATCCTTGAAAAGG
Found at i:25312465 original size:30 final size:30
Alignment explanation
Indices: 25312429--25312488 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
25312419 CATTTGTCTA
25312429 TGCTTGATGTATGATTGATGGTCTTGAATG
1 TGCTTGATGTATGATTGATGGTCTTGAATG
25312459 TGCTTGATGTATGATTGATGGTCTTGAATG
1 TGCTTGATGTATGATTGATGGTCTTGAATG
25312489 GTAATGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (30 bp):
TGCTTGATGTATGATTGATGGTCTTGAATG
Found at i:25313557 original size:35 final size:35
Alignment explanation
Indices: 25313511--25313581 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
25313501 AAACATACAG
25313511 TTCTTGAGTCATTTGAAAGACAACGAACTTGAGAC
1 TTCTTGAGTCATTTGAAAGACAACGAACTTGAGAC
*
25313546 TTCTTTAGTCATTTGAAAGACAACGAACTTGAGAC
1 TTCTTGAGTCATTTGAAAGACAACGAACTTGAGAC
25313581 T
1 T
25313582 ATGGGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (35 bp):
TTCTTGAGTCATTTGAAAGACAACGAACTTGAGAC
Found at i:25327021 original size:19 final size:19
Alignment explanation
Indices: 25326997--25327036 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
25326987 TCTAATAGTC
25326997 ATAATTTCATTTTAAAGAA
1 ATAATTTCATTTTAAAGAA
25327016 ATAATTTCATTTTAAAGAA
1 ATAATTTCATTTTAAAGAA
25327035 AT
1 AT
25327037 GTTTTAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
ATAATTTCATTTTAAAGAA
Found at i:25333157 original size:18 final size:19
Alignment explanation
Indices: 25333118--25333162 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
25333108 TTAATATTTT
*
25333118 AATATTATTTCATTAGTAA
1 AATATTATTTCATTACTAA
*
25333137 AATATTATTTTATT-CTAA
1 AATATTATTTCATTACTAA
*
25333155 AATTTTAT
1 AATATTAT
25333163 CTTGTCTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
AATATTATTTCATTACTAA
Found at i:25339158 original size:18 final size:20
Alignment explanation
Indices: 25339119--25339160 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
25339109 GGGTTTTTTC
*
25339119 ATAATTTGCTACCGAGACTG
1 ATAATTTGCTACCGACACTG
25339139 ATAATTTGC-ACC-ACACTG
1 ATAATTTGCTACCGACACTG
25339157 ATAA
1 ATAA
25339161 ACATTAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 3 0.14
20 9 0.43
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (20 bp):
ATAATTTGCTACCGACACTG
Found at i:25344799 original size:63 final size:63
Alignment explanation
Indices: 25344678--25344813 Score: 175
Period size: 63 Copynumber: 2.2 Consensus size: 63
25344668 GTGGAAAAAT
*
25344678 TGACATCTCATGAAAAAAGAATCAATTCTCCAAAGACAAACAATTCCAAACTTTATGAAGAAC
1 TGACATCTCATGAAAAAAGAATCAATTCTCCAAAGACAAACAATTCCAAACTTCATGAAGAAC
** * * * * *
25344741 TGACATCTCATGAAGGAAGAATCCATTCTCCAAAGATAGAA-AGTTTCAGACTTCATGAAGAAC
1 TGACATCTCATGAAAAAAGAATCAATTCTCCAAAGACA-AACAATTCCAAACTTCATGAAGAAC
*
25344804 TAACATCTCA
1 TGACATCTCA
25344814 AAAAAGAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 61 0.97
64 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (63 bp):
TGACATCTCATGAAAAAAGAATCAATTCTCCAAAGACAAACAATTCCAAACTTCATGAAGAAC
Found at i:25347435 original size:2 final size:2
Alignment explanation
Indices: 25347423--25347505 Score: 87
Period size: 2 Copynumber: 39.5 Consensus size: 2
25347413 ACCATATACC
*
25347423 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT CA- AT CAT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT -AT AT
* *
25347465 ANT ACC AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25347506 AATCATCATG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
1 1 0.01
2 60 0.86
3 9 0.13
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:25347593 original size:42 final size:41
Alignment explanation
Indices: 25347546--25347624 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
25347536 ATCTCATATG
*
25347546 CAATGGCTTATGCGCACTCCCACTCGCACATAGCTCGGTCAA
1 CAATGGCTTATACGCACTCCCACTCGCACATAG-TCGGTCAA
* * *
25347588 CAATGGCTTATATGCACTTCTACTCGCACATAGTCGG
1 CAATGGCTTATACGCACTCCCACTCGCACATAGTCGG
25347625 GTCCACATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (41 bp):
CAATGGCTTATACGCACTCCCACTCGCACATAGTCGGTCAA
Found at i:25354069 original size:17 final size:17
Alignment explanation
Indices: 25354047--25354084 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25354037 TCCAATTACT
25354047 CAATTTCATAATCAACA
1 CAATTTCATAATCAACA
* *
25354064 CAATTTTATAATCAATA
1 CAATTTCATAATCAACA
25354081 CAAT
1 CAAT
25354085 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (17 bp):
CAATTTCATAATCAACA
Found at i:25356748 original size:60 final size:60
Alignment explanation
Indices: 25356647--25356810 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
25356637 TAGGAGACAA
* * * *
25356647 AAACAGAAAGTTTTTCGCTACAGCAAGATTCAATCTCGCTGCAGCGAAATTGTGACCCAG
1 AAACAGAAAGTTTCTCGCTACAGCAAGATTGAATTTCGCTGCAGCGAAATTGTAACCCAG
* * *
25356707 AAACAGAATGTTTCTCGCTACAG-AGAGATTGAATTTTGCTGCAACGAAATTGTAACCCAG
1 AAACAGAAAGTTTCTCGCTACAGCA-AGATTGAATTTCGCTGCAGCGAAATTGTAACCCAG
*
25356767 AAACAGAAAGTTTCTCGCTACAGCAAGAATGAATTTCGCTGCAG
1 AAACAGAAAGTTTCTCGCTACAGCAAGATTGAATTTCGCTGCAG
25356811 TGAGAAACTA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 1 0.01
60 89 0.98
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTACAGCAAGATTGAATTTCGCTGCAGCGAAATTGTAACCCAG
Found at i:25358963 original size:18 final size:18
Alignment explanation
Indices: 25358898--25358963 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
25358888 CTTGGAAAAA
* *
25358898 TATTTTAGCTTGATTCAT
1 TATTTTTGCTTGAATCAT
*
25358916 TATTTTTGCTTAGGAA--AC
1 TATTTTTGCTT--GAATCAT
25358934 TATTTTCT-CTTGAATCAT
1 TATTTT-TGCTTGAATCAT
25358952 TATTTTTGCTTG
1 TATTTTTGCTTG
25358964 TACTTGACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 3 0.08
17 1 0.03
18 31 0.82
19 1 0.03
20 2 0.05
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (18 bp):
TATTTTTGCTTGAATCAT
Found at i:25358991 original size:23 final size:23
Alignment explanation
Indices: 25358964--25359038 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
25358954 TTTTTGCTTG
25358964 TACTTGACTTAGGAATATATTTT
1 TACTTGACTTAGGAATATATTTT
* ** * * *
25358987 TACTTTGATTTA-TTATTTGTTCAT
1 TAC-TTGACTTAGGAATATATT-TT
*
25359011 TACTTGACTTAGGAAAATATTTT
1 TACTTGACTTAGGAATATATTTT
25359034 TACTT
1 TACTT
25359039 TGATTTATTA
Statistics
Matches: 36, Mismatches: 13, Indels: 6
0.65 0.24 0.11
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (23 bp):
TACTTGACTTAGGAATATATTTT
Found at i:25359013 original size:24 final size:24
Alignment explanation
Indices: 25358986--25359058 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
25358976 GAATATATTT
25358986 TTACTTTGATTTATTATTTGTTCA
1 TTACTTTGATTTATTATTTGTTCA
* ** ** * *
25359010 TTAC-TTGACTTAGGAAAATATT-T
1 TTACTTTGATTTA-TTATTTGTTCA
25359033 TTACTTTGATTTATTATTTGTTCA
1 TTACTTTGATTTATTATTTGTTCA
25359057 TT
1 TT
25359059 TCAATTTATT
Statistics
Matches: 32, Mismatches: 14, Indels: 6
0.62 0.27 0.12
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.58
Consensus pattern (24 bp):
TTACTTTGATTTATTATTTGTTCA
Found at i:25359015 original size:47 final size:47
Alignment explanation
Indices: 25358964--25359058 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
25358954 TTTTTGCTTG
*
25358964 TACTTGACTTAGGAATATATTTTTACTTTGATTTATTATTTGTTCAT
1 TACTTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCAT
25359011 TACTTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCAT
1 TACTTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCAT
25359058 T
1 T
25359059 TCAATTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (47 bp):
TACTTGACTTAGGAAAATATTTTTACTTTGATTTATTATTTGTTCAT
Found at i:25367401 original size:42 final size:43
Alignment explanation
Indices: 25367332--25367487 Score: 199
Period size: 42 Copynumber: 3.7 Consensus size: 43
25367322 GTGATGATAT
* * ** *
25367332 TGACCCGGTTATGTGCTAGT-GAAAGTGCGCATAAGCCAATGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGC
* *
25367374 TGACCCGGCTATGTGTGAGT-GGGAGTGCGCATAAGCCGATGT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGC
*
25367416 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGC
** *
25367459 TGACCTAGCTATGTGCGAGTAAGGAGTGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGC
25367488 ACATGAGCTG
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 54 0.54
43 46 0.46
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.23
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGC
Found at i:25367473 original size:85 final size:85
Alignment explanation
Indices: 25367331--25367487 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
25367321 TGTGATGATA
* * * * *
25367331 TTGACCCGGTTATGTGCTAGTGAAAGTGCGCATAAGCCAATGCTGACCCGGCTATGTGTGAGT-G
1 TTGACCCGGCTATGTGCGAGTGAAAGTGCGCATAAGCCAATGCTGACCCAGCTATGTGCGAGTAA
25367395 GGAGTGCGCATAAGCCGATG
66 GGAGTGCGCATAAGCCGATG
** ** *
25367415 TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGTTGCTGACCTAGCTATGTGCGAGTA
1 TTGACCCGGCTATGTGCGAGT-GAAAGTGCGCATAAGCCAATGCTGACCCAGCTATGTGCGAGTA
25367480 AGGAGTGC
65 AGGAGTGC
25367488 ACATGAGCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 19 0.31
85 35 0.57
86 7 0.11
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (85 bp):
TTGACCCGGCTATGTGCGAGTGAAAGTGCGCATAAGCCAATGCTGACCCAGCTATGTGCGAGTAA
GGAGTGCGCATAAGCCGATG
Found at i:25370223 original size:18 final size:18
Alignment explanation
Indices: 25370189--25370223 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25370179 AATTCACAAA
25370189 ATCATATAAGAGCTCATC
1 ATCATATAAGAGCTCATC
25370207 ATCATCATAAGAG-TCAT
1 ATCAT-ATAAGAGCTCAT
25370224 GCTATTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (18 bp):
ATCATATAAGAGCTCATC
Found at i:25375729 original size:25 final size:25
Alignment explanation
Indices: 25375695--25375754 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
25375685 CAGTCTATGA
**
25375695 TTATACGTGGCAA-GCCCACGGGTTG
1 TTATACGTGGCAATG-CCACAAGTTG
25375720 TTATACGTGGCAATGCCACAAGTTG
1 TTATACGTGGCAATGCCACAAGTTG
*
25375745 ATATACGTGG
1 TTATACGTGG
25375755 TTGCGATCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (25 bp):
TTATACGTGGCAATGCCACAAGTTG
Found at i:25394235 original size:31 final size:30
Alignment explanation
Indices: 25394200--25394258 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
25394190 TTTGAAGGAC
* * *
25394200 CAAATTGTAAAGGATGAAAAGTTTAGAGGGT
1 CAAATGGTAAAGAAGGAAAAGTTT-GAGGGT
*
25394231 CAAATGGTAAATAAGGAAAAGTTTGAGG
1 CAAATGGTAAAGAAGGAAAAGTTTGAGG
25394259 ACTTATGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (30 bp):
CAAATGGTAAAGAAGGAAAAGTTTGAGGGT
Found at i:25396330 original size:2 final size:2
Alignment explanation
Indices: 25396323--25396361 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
25396313 TTGTGTTTAC
* *
25396323 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25396362 GTAAAGTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:25396799 original size:25 final size:25
Alignment explanation
Indices: 25396764--25396823 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
25396754 TAGTCTGTGA
* *
25396764 ATATACATGGCAAGGCCACGGGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
*
25396789 TTATACGTGGCAAGGCCACGAGTTG
1 ATATACGTGGCAAGGCCACGAGTTG
25396814 ATATACGTGG
1 ATATACGTGG
25396824 TTGTGACCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACGAGTTG
Found at i:25401491 original size:2 final size:2
Alignment explanation
Indices: 25401484--25401512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25401474 AGTAACCACT
25401484 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25401513 GTGCATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25402593 original size:19 final size:19
Alignment explanation
Indices: 25402569--25402607 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
25402559 AAACAATTAA
25402569 ACAACTTAGAGTGGATTCG
1 ACAACTTAGAGTGGATTCG
25402588 ACAACTTAGAGTGGATTCG
1 ACAACTTAGAGTGGATTCG
25402607 A
1 A
25402608 GTTTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (19 bp):
ACAACTTAGAGTGGATTCG
Found at i:25402941 original size:12 final size:12
Alignment explanation
Indices: 25402924--25402972 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
25402914 AGTCAAAAGA
25402924 TAATTTTTTTAT
1 TAATTTTTTTAT
25402936 TAA--TTTTTA-
1 TAATTTTTTTAT
25402945 TAATTATTTTT-T
1 TAATT-TTTTTAT
25402957 T-ATTTTTTTAT
1 TAATTTTTTTAT
25402968 TAATT
1 TAATT
25402973 AAAAAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
9 3 0.10
10 11 0.35
11 5 0.16
12 12 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:25402949 original size:21 final size:21
Alignment explanation
Indices: 25402923--25402973 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
25402913 AAGTCAAAAG
25402923 ATAATT-TTTTTATTAATTTTT
1 ATAATTATTTTT-TTAATTTTT
*
25402944 ATAATTATTTTTTTATTTTTTT
1 ATAATTATTTTTTTA-ATTTTT
25402966 ATTAATTA
1 A-TAATTA
25402974 AAAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 9 0.35
22 11 0.42
23 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATAATTATTTTTTTAATTTTT
Found at i:25402965 original size:23 final size:24
Alignment explanation
Indices: 25402926--25402973 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25402916 TCAAAAGATA
25402926 ATTTTTTTATTAATTTTTA-TAATT
1 ATTTTTTTA-TAATTTTTATTAATT
*
25402950 ATTTTTTTAT-TTTTTTATTAATT
1 ATTTTTTTATAATTTTTATTAATT
25402973 A
1 A
25402974 AAAAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 7 0.32
24 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
ATTTTTTTATAATTTTTATTAATT
Found at i:25411330 original size:27 final size:27
Alignment explanation
Indices: 25411300--25411387 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
25411290 TTACCTCCAC
*
25411300 GAGAGACTTGAGTGCTCTCTTCTTCTT
1 GAGAGACTTGAGTGCTCTCTTCTTCAT
* * **
25411327 GAGAGACTTGAGTGCTGTCTTCTCCCC
1 GAGAGACTTGAGTGCTCTCTTCTTCAT
25411354 GAGAGACTTGAGTGCTCTCTTCTTCAT
1 GAGAGACTTGAGTGCTCTCTTCTTCAT
25411381 GAGAGAC
1 GAGAGAC
25411388 GTCGGTGACT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (27 bp):
GAGAGACTTGAGTGCTCTCTTCTTCAT
Found at i:25412501 original size:12 final size:12
Alignment explanation
Indices: 25412472--25412517 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
25412462 ACTTTCTTTC
25412472 TTCTCTTTAATTA
1 TTCT-TTTAATTA
25412485 TTCTTTTAAGTTA
1 TTCTTTTAA-TTA
*
25412498 -TC-TTTATTTA
1 TTCTTTTAATTA
25412508 TTCTTTTAAT
1 TTCTTTTAAT
25412518 ATTTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.11
11 6 0.21
12 12 0.43
13 7 0.25
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (12 bp):
TTCTTTTAATTA
Found at i:25413192 original size:26 final size:26
Alignment explanation
Indices: 25413156--25413233 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
25413146 AGGATCTAAA
25413156 GATAATTTTGCCACCAAAAGTGGATG
1 GATAATTTTGCCACCAAAAGTGGATG
* *
25413182 GATAATTTTGCCACCAAGAGTAGATG
1 GATAATTTTGCCACCAAAAGTGGATG
* * * *
25413208 GATAAATTTACCACTAGAAGTGGATG
1 GATAATTTTGCCACCAAAAGTGGATG
25413234 AATACCGTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (26 bp):
GATAATTTTGCCACCAAAAGTGGATG
Found at i:25420515 original size:19 final size:19
Alignment explanation
Indices: 25420491--25420528 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25420481 CCATTTGACT
*
25420491 TATTGGAGTATGGTTTGAG
1 TATTGGAGTATGATTTGAG
25420510 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25420529 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:25423500 original size:24 final size:24
Alignment explanation
Indices: 25423473--25423520 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25423463 GTTTAAAGAC
*
25423473 TAAATACTCAACTTAATTTCCTTT
1 TAAATACTCAACATAATTTCCTTT
* *
25423497 TAAATACTCGAGATAATTTCCTTT
1 TAAATACTCAACATAATTTCCTTT
25423521 AAACTAAATA
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:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (24 bp):
TAAATACTCAACATAATTTCCTTT
Found at i:25424517 original size:20 final size:20
Alignment explanation
Indices: 25424489--25424538 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
25424479 AAGGTTGAAA
* *
25424489 TAAGTGAAGCCTCAACCAGT
1 TAAGGGAAGACTCAACCAGT
* *
25424509 TAAGGGAAGAGTCAACCATT
1 TAAGGGAAGACTCAACCAGT
*
25424529 TAAAGGAAGA
1 TAAGGGAAGA
25424539 TTGTTATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
TAAGGGAAGACTCAACCAGT
Done.