Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 124 of 167
Found at i:41405773 original size:37 final size:37
Alignment explanation
Indices: 41405723--41405794 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
41405713 AATGTTGTGC
*
41405723 TTCATGATAATTAGACTCATGCAATTTTAATGATTGT
1 TTCATGATAATTAGACTCATGCAATTTTAACGATTGT
*
41405760 TTCATGATCATTAGACTCATGCAATTTTAACGATT
1 TTCATGATAATTAGACTCATGCAATTTTAACGATT
41405795 CCACCTCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (37 bp):
TTCATGATAATTAGACTCATGCAATTTTAACGATTGT
Found at i:41409370 original size:13 final size:13
Alignment explanation
Indices: 41409354--41409380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41409344 ATATGCATAT
41409354 AATATATATACAC
1 AATATATATACAC
41409367 AATATATATACAC
1 AATATATATACAC
41409380 A
1 A
41409381 CACAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATATATACAC
Found at i:41411752 original size:17 final size:16
Alignment explanation
Indices: 41411741--41411773 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41411731 TATTTTTTAG
41411741 TTTT-TTAAATTTGTTT
1 TTTTATTAAATTT-TTT
41411757 TTTTATTAAATTTTTT
1 TTTTATTAAATTTTTT
41411773 T
1 T
41411774 AAAATAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTATTAAATTTTTT
Found at i:41411901 original size:18 final size:18
Alignment explanation
Indices: 41411871--41411908 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
41411861 TAAATTTTTT
41411871 AAAATTTTAAAAATTCAAA
1 AAAATTTTAAAAATT-AAA
41411890 AAAATTTT-AAAATTAAA
1 AAAATTTTAAAAATTAAA
41411907 AA
1 AA
41411909 TTATTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTTTAAAAATTAAA
Found at i:41411927 original size:20 final size:20
Alignment explanation
Indices: 41411902--41411961 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
41411892 AATTTTAAAA
* * *
41411902 TTAAAAATTATTAAACTTAT
1 TTAAAAAGTATAAAAATTAT
41411922 TTAAAAAGTATAAAAATTAT
1 TTAAAAAGTATAAAAATTAT
**
41411942 TTTTAAA--ATAAAAATTAT
1 TTAAAAAGTATAAAAATTAT
41411960 TT
1 TT
41411962 TTAATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 13 0.37
20 22 0.63
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAAAGTATAAAAATTAT
Found at i:41411954 original size:18 final size:18
Alignment explanation
Indices: 41411931--41411965 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41411921 TTTAAAAAGT
41411931 ATAAAAATTATTTTTAAA
1 ATAAAAATTATTTTTAAA
41411949 ATAAAAATTATTTTTAA
1 ATAAAAATTATTTTTAA
41411966 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAAATTATTTTTAAA
Found at i:41412488 original size:15 final size:15
Alignment explanation
Indices: 41412468--41412503 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41412458 GTTGACCCCA
41412468 TTGACCCACCAGTAT
1 TTGACCCACCAGTAT
41412483 TTGACCCACCAGTAT
1 TTGACCCACCAGTAT
41412498 TTGACC
1 TTGACC
41412504 AAAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (15 bp):
TTGACCCACCAGTAT
Found at i:41419667 original size:21 final size:21
Alignment explanation
Indices: 41419643--41419684 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41419633 CGTCTTGTCA
41419643 ACAACATAAGTGCCGACAATT
1 ACAACATAAGTGCCGACAATT
*
41419664 ACAACATAAGTGCTGACAATT
1 ACAACATAAGTGCCGACAATT
41419685 TCATCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (21 bp):
ACAACATAAGTGCCGACAATT
Found at i:41420868 original size:16 final size:18
Alignment explanation
Indices: 41420849--41420881 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41420839 CATACGAATT
41420849 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
41420865 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
41420882 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:41421510 original size:43 final size:43
Alignment explanation
Indices: 41421442--41421609 Score: 209
Period size: 43 Copynumber: 4.0 Consensus size: 43
41421432 AAGTCTGAAC
* *
41421442 TCAT-TCATCGGCATT-TTGCCTGCTAGGCTCGAAACCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAACCCGATA
* * *
41421483 TCATCTCGCCGGCATTATAGCCTGCTAGG-TCTGAAGCCTGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTC-GAAACCCGATA
* * *
41421526 TCATCTCACCGGTATTATAGCCTCCTAGGCTCGAATCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAACCCGATA
*
41421569 TCATCTCACCGGTATTATAGCCTGCTAGGCTC-AAAGCCCGA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAA-CCCGA
41421610 ATGTCACATT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.04
42 13 0.12
43 91 0.83
44 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (43 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAACCCGATA
Found at i:41440631 original size:26 final size:26
Alignment explanation
Indices: 41440602--41440667 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
41440592 TAAATATTTT
41440602 TATATATATTATTTATTTGAAAT-TCA
1 TATATATATTATTTATTTGAAATAT-A
* * * *
41440628 TATATATTTTATCTATTTTAAATATG
1 TATATATATTATTTATTTGAAATATA
*
41440654 TATATATATAATTT
1 TATATATATTATTT
41440668 GGTTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
TATATATATTATTTATTTGAAATATA
Found at i:41440723 original size:24 final size:23
Alignment explanation
Indices: 41440690--41440741 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
41440680 TTAAAATGTT
* * *
41440690 ATTTTTTTATTTTTTATTTTTAC
1 ATTTTTTTATTATCTATTTTAAC
41440713 ATTTTTGTTATTATCTATTTTAAC
1 ATTTTT-TTATTATCTATTTTAAC
41440737 -TTTTT
1 ATTTTT
41440742 ATATAACGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTTTTATTATCTATTTTAAC
Found at i:41443981 original size:44 final size:44
Alignment explanation
Indices: 41443928--41444160 Score: 140
Period size: 44 Copynumber: 5.3 Consensus size: 44
41443918 ATCCGCTCGA
41443928 CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
* * * * * * *
41443972 CTATTGCTTA-GGAGGATAAGGCTCACCGT--CTTCGATCC-G-CTCC
1 CTACTGCTTAGGGA-GATAA-GAT--CTGTAATTTCCAGCCTGTTTCC
*
41444015 ACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
* * * * *** * * *
41444060 CTACTGCTTAGGGGGTTAAG-GCT-CACCGTCCTCGATCTG-CTCC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTCC-AG-CCTGTTTCC
* ** *
41444103 ACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCCTGTTGCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
41444148 CTACTGCTTAGGG
1 CTACTGCTTAGGG
41444161 GATTAAGGCT
Statistics
Matches: 132, Mismatches: 41, Indels: 32
0.64 0.20 0.16
Matches are distributed among these distances:
41 3 0.02
42 3 0.02
43 19 0.14
44 83 0.63
45 19 0.14
46 2 0.02
47 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
Found at i:41444030 original size:88 final size:87
Alignment explanation
Indices: 41443837--41444172 Score: 462
Period size: 88 Copynumber: 3.9 Consensus size: 87
41443827 GTTTCAATCT
* * * * * ** *
41443837 GCTCCGCTACTGCTTAGAGAGATATGATTTGTAATCTTCAGCCCATTTCCCTACTACTTAAGGGG
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTT-AGGGG
41443902 ATAAGGCT-A--GTCTTCGATCC
65 ATAAGGCTCACCGTCTTCGATCC
* * *
41443922 GCTCGACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCCTATTGCTTAGGAGG
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGG-GG
41443987 ATAAGGCTCACCGTCTTCGATCC
65 ATAAGGCTCACCGTCTTCGATCC
41444010 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGGG
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTA-GGGG
* * *
41444075 TTAAGGCTCACCGTCCTCGATCT
65 ATAAGGCTCACCGTCTTCGATCC
* * *
41444098 GCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCCTGTTGCCCTACTGCTTAGGGGA
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGGA
41444163 TTAAGGCTCA
66 -TAAGGCTCA
41444173 TGAATTTTTT
Statistics
Matches: 224, Mismatches: 21, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
84 3 0.01
85 58 0.26
86 1 0.00
87 4 0.02
88 156 0.70
89 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (87 bp):
GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAGGGGA
TAAGGCTCACCGTCTTCGATCC
Found at i:41448825 original size:19 final size:19
Alignment explanation
Indices: 41448801--41448846 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
41448791 TGTGAAGTTT
*
41448801 AATGCACATG-ATGCAATG
1 AATGCAAATGCATGCAATG
*
41448819 CAATGCAAATGCATGGAATG
1 -AATGCAAATGCATGCAATG
41448839 AATGCAAA
1 AATGCAAA
41448847 AGAAAGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCAAATGCATGCAATG
Found at i:41451172 original size:21 final size:21
Alignment explanation
Indices: 41451125--41451173 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
41451115 GATGGCATAC
41451125 ATATAATGGAAAAAAAATTAAA
1 ATAT-ATGGAAAAAAAATTAAA
*
41451147 A-ATATGTAAAAAAAA-TAATA
1 ATATATGGAAAAAAAATTAA-A
41451167 ATATATG
1 ATATATG
41451174 AAAGGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
21 7 0.29
22 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (21 bp):
ATATATGGAAAAAAAATTAAA
Found at i:41454551 original size:13 final size:13
Alignment explanation
Indices: 41454533--41454575 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
41454523 TTTAATAATA
41454533 AAATAAAGAAATG
1 AAATAAAGAAATG
41454546 AAATAAAGAAAT-
1 AAATAAAGAAATG
* *
41454558 AAATGAAATAAAAG
1 AAAT-AAAGAAATG
41454572 AAAT
1 AAAT
41454576 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:41454563 original size:17 final size:18
Alignment explanation
Indices: 41454529--41454575 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
41454519 ATATTTTAAT
* *
41454529 AATAAAATAAAGAAATGA
1 AATAAAAGAAATAAATGA
41454547 AAT-AAAGAAATAAATGA
1 AATAAAAGAAATAAATGA
41454564 AATAAAAGAAAT
1 AATAAAAGAAAT
41454576 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AATAAAAGAAATAAATGA
Found at i:41454567 original size:9 final size:9
Alignment explanation
Indices: 41454541--41454575 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
41454531 TAAAATAAAG
41454541 AAATGAAAT
1 AAATGAAAT
41454550 AAA-GAAAT
1 AAATGAAAT
41454558 AAATGAAAT
1 AAATGAAAT
*
41454567 AAAAGAAAT
1 AAATGAAAT
41454576 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (9 bp):
AAATGAAAT
Found at i:41455985 original size:45 final size:45
Alignment explanation
Indices: 41455935--41456043 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
41455925 CGACTACTGT
*
41455935 TACTGTTA-TCGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACT-GTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* * *
41455980 TACTGTTACTGTTACCGTTATCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
41456025 TACTGTTACTGTTACTGTT
1 TACTGTTACTGTTACTGTT
41456044 CCGGATTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 57 0.98
46 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:41456040 original size:51 final size:50
Alignment explanation
Indices: 41455920--41456043 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 50
41455910 CAGGCACTTA
* * *
41455920 TGTGCCGACTACTGTTACTGTTA-TCGTTACTGTTACCGATTCGGCACTTTG
1 TGTGTCGA-TACTGTTACTGTTACT-GTTACCGTTACCGATTCAGCACTTTG
*
41455971 TGTGTCGA-A----TACTGTTACTGTTACCGTTATCGATTCAGCACTTTG
1 TGTGTCGATACTGTTACTGTTACTGTTACCGTTACCGATTCAGCACTTTG
*
41456016 TGTGTTGAATACTGTTACTGTTACTGTT
1 TGTGTCG-ATACTGTTACTGTTACTGTT
41456044 CCGGATTTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
45 37 0.61
46 2 0.03
47 1 0.02
49 1 0.02
51 20 0.33
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (50 bp):
TGTGTCGATACTGTTACTGTTACTGTTACCGTTACCGATTCAGCACTTTG
Found at i:41456265 original size:18 final size:18
Alignment explanation
Indices: 41456224--41456258 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41456214 GATTATTTCT
41456224 GAATAATTGACTATTACC
1 GAATAATTGACTATTACC
*
41456242 GAATAATTGACTGTTAC
1 GAATAATTGACTATTAC
41456259 TGGATAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
GAATAATTGACTATTACC
Found at i:41468340 original size:26 final size:26
Alignment explanation
Indices: 41468311--41468523 Score: 372
Period size: 26 Copynumber: 8.2 Consensus size: 26
41468301 TGGTACAAAT
*
41468311 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
41468337 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
41468363 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
41468389 TGATAATGGGTTGGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
41468415 TGATAATAGGTCAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
41468441 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
41468467 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
41468493 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
41468519 TGATA
1 TGATA
41468524 GAATTTCATG
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 177 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:41470038 original size:26 final size:26
Alignment explanation
Indices: 41470009--41470061 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
41469999 TTTACAGTTT
41470009 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
41470035 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
41470061 T
1 T
41470062 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:41473467 original size:62 final size:61
Alignment explanation
Indices: 41473338--41473469 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 61
41473328 ACTAACTTCA
* **
41473338 TTATTTTTACACAAACACCACACTATGCACCACCATACCTGCATCAACACATTCTGTACCTG
1 TTATTTTTACACAAACACCACACTATGAACCACCATACCTGCATCAACACATTCTG-ACAGG
* *** * *
41473400 TTATTTTTACACAAGCACCACACTATGAACCATTGTGCCCTGCATCAACACCTTCTG-CAGG
1 TTATTTTTACACAAACACCACACTATGAACCACCAT-ACCTGCATCAACACATTCTGACAGG
41473461 TATATTTTT
1 T-TATTTTT
41473470 TGTACCACCT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 3 0.05
62 38 0.64
63 18 0.31
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (61 bp):
TTATTTTTACACAAACACCACACTATGAACCACCATACCTGCATCAACACATTCTGACAGG
Found at i:41480054 original size:17 final size:18
Alignment explanation
Indices: 41480028--41480066 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
41480018 TAAATTGTGG
41480028 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
41480044 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
41480062 AAAAT
1 AAAAT
41480067 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:41480243 original size:15 final size:15
Alignment explanation
Indices: 41480223--41480253 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41480213 AAAACAATAT
41480223 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41480238 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41480253 A
1 A
41480254 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:41483602 original size:15 final size:15
Alignment explanation
Indices: 41483592--41483621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41483582 TCCCTTCTTG
41483592 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
41483607 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
41483622 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:41484389 original size:17 final size:18
Alignment explanation
Indices: 41484363--41484401 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
41484353 CAAATTGTGG
41484363 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
41484379 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
41484397 AAAAT
1 AAAAT
41484402 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:41484578 original size:15 final size:15
Alignment explanation
Indices: 41484558--41484588 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41484548 AAAACAATAT
41484558 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41484573 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41484588 A
1 A
41484589 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:41493137 original size:5 final size:5
Alignment explanation
Indices: 41493129--41493175 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
41493119 TTAGTTTATT
*
41493129 TATAA TAT-A -ATAA TATAA TATAA T-TAA TATAA TAAAA TAATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T-ATAA TATA
41493176 CTTTATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 24 0.67
6 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:41493143 original size:8 final size:8
Alignment explanation
Indices: 41493130--41493175 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
41493120 TAGTTTATTT
41493130 ATAATATA
1 ATAATATA
41493138 ATAATATA
1 ATAATATA
41493146 AT-ATA-A
1 ATAATATA
*
41493152 TTAATATA
1 ATAATATA
*
41493160 ATAAAATA
1 ATAATATA
41493168 ATAATATA
1 ATAATATA
41493176 CTTTATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 6 0.19
8 24 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATATA
Found at i:41493183 original size:20 final size:20
Alignment explanation
Indices: 41493160--41493201 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41493150 AATTAATATA
41493160 ATAAAAT-AATAATATACTTT
1 ATAAAATAAATAATATA-TTT
*
41493180 AT-AATTAAATAATATATTT
1 ATAAAATAAATAATATATTT
41493199 ATA
1 ATA
41493202 TATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAATAAATAATATATTT
Found at i:41495637 original size:21 final size:21
Alignment explanation
Indices: 41495609--41495650 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41495599 AAATAATAAA
41495609 ATAGATTATATATTAT-TTTT
1 ATAGATTATATATTATGTTTT
41495629 ATAGTATTATATATTATGTTTT
1 ATAG-ATTATATATTATGTTTT
41495651 TCTAATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATAGATTATATATTATGTTTT
Found at i:41495967 original size:16 final size:16
Alignment explanation
Indices: 41495946--41496000 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
41495936 TGAATTACTG
* *
41495946 ATTACAGCTCTGTTCT
1 ATTACAGCTCTATTCA
41495962 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
* * *
41495978 ATTACAACCCTATTCC
1 ATTACAGCTCTATTCA
41495994 ATTACAG
1 ATTACAG
41496001 TGAACCAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:41507937 original size:25 final size:25
Alignment explanation
Indices: 41507887--41507963 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
41507877 TGCTATACAA
41507887 AGAGCACAAGCATGCT---AAATAG
1 AGAGCACAAGCATGCTAGAAAATAG
*
41507909 AGAGCACAAACATGCTAGAAAATAG
1 AGAGCACAAGCATGCTAGAAAATAG
41507934 AGAGCACAAGCATGCTAGAAAATAG
1 AGAGCACAAGCATGCTAGAAAATAG
41507959 AGAGC
1 AGAGC
41507964 GCGCTAGAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
22 15 0.30
25 35 0.70
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (25 bp):
AGAGCACAAGCATGCTAGAAAATAG
Found at i:41514201 original size:21 final size:22
Alignment explanation
Indices: 41514171--41514211 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
41514161 TTATTTTATT
*
41514171 ATATTGTAAT-TTATATTAATG
1 ATATTATAATATTATATTAATG
*
41514192 ATATTATAATATTATTTTAA
1 ATATTATAATATTATATTAA
41514212 CAATTGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
ATATTATAATATTATATTAATG
Found at i:41514314 original size:5 final size:5
Alignment explanation
Indices: 41514304--41514361 Score: 116
Period size: 5 Copynumber: 11.6 Consensus size: 5
41514294 AAGAAATTGT
41514304 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
41514354 TATTA TAT
1 TATTA TAT
41514362 AAATAAGTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:41515216 original size:22 final size:22
Alignment explanation
Indices: 41515182--41515306 Score: 92
Period size: 23 Copynumber: 5.6 Consensus size: 22
41515172 TCAATGACCC
*
41515182 TAAACCCTAAACCCTAAAACCA
1 TAAACACTAAACCCTAAAACCA
* *
41515204 TAAGCACTAAACCCTAAAACCC
1 TAAACACTAAACCCTAAAACCA
* * *
41515226 TAAACCCTTAAACCCTTAAACCC
1 TAAACAC-TAAACCCTAAAACCA
* * *
41515249 TAAACCCTTAAACCAT-AAACCC
1 TAAACAC-TAAACCCTAAAACCA
* *
41515271 TAAAACCCTAAAACCCT-AAACCC
1 T-AAACACT-AAACCCTAAAACCA
*
41515294 TAAACCCTAAACC
1 TAAACACTAAACC
41515307 AATAATTAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.05
22 39 0.42
23 48 0.52
ACGTcount: A:0.46, C:0.38, G:0.01, T:0.16
Consensus pattern (22 bp):
TAAACACTAAACCCTAAAACCA
Found at i:41515225 original size:8 final size:7
Alignment explanation
Indices: 41515178--41515306 Score: 159
Period size: 7 Copynumber: 17.4 Consensus size: 7
41515168 TAAATCAATG
41515178 ACCCTAA
1 ACCCTAA
41515185 ACCCTAA
1 ACCCTAA
41515192 ACCCTAAA
1 ACCCT-AA
*
41515200 ACCATAA
1 ACCCTAA
* *
41515207 GCACTAA
1 ACCCTAA
41515214 ACCCTAAA
1 ACCCT-AA
41515222 ACCCTAA
1 ACCCTAA
41515229 ACCCTTAA
1 ACCC-TAA
41515237 ACCCTTAA
1 ACCC-TAA
41515245 ACCCTAA
1 ACCCTAA
41515252 ACCCTTAA
1 ACCC-TAA
*
41515260 ACCATAA
1 ACCCTAA
41515267 ACCCTAAA
1 ACCCT-AA
41515275 ACCCTAAA
1 ACCCT-AA
41515283 ACCCTAA
1 ACCCTAA
41515290 ACCCTAA
1 ACCCTAA
41515297 ACCCTAA
1 ACCCTAA
41515304 ACC
1 ACC
41515307 AATAATTAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
7 60 0.55
8 49 0.45
ACGTcount: A:0.45, C:0.39, G:0.01, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:41515228 original size:15 final size:14
Alignment explanation
Indices: 41515178--41515306 Score: 159
Period size: 15 Copynumber: 8.7 Consensus size: 14
41515168 TAAATCAATG
41515178 ACCCTAAACCCTAA
1 ACCCTAAACCCTAA
*
41515192 ACCCTAAAACCATAA
1 ACCCT-AAACCCTAA
* *
41515207 GCACTAAACCCTAAA
1 ACCCTAAACCCT-AA
41515222 ACCCTAAACCCTTAA
1 ACCCTAAACCC-TAA
41515237 ACCCTTAAACCCTAA
1 ACCC-TAAACCCTAA
*
41515252 ACCCTTAAACCATAA
1 ACCC-TAAACCCTAA
41515267 ACCCTAAAACCCTAAA
1 ACCCT-AAACCCT-AA
41515283 ACCCTAAACCCTAA
1 ACCCTAAACCCTAA
41515297 ACCCTAAACC
1 ACCCTAAACC
41515307 AATAATTAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
14 24 0.24
15 62 0.61
16 15 0.15
ACGTcount: A:0.45, C:0.39, G:0.01, T:0.16
Consensus pattern (14 bp):
ACCCTAAACCCTAA
Found at i:41516257 original size:45 final size:44
Alignment explanation
Indices: 41516207--41516322 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 44
41516197 TGACTACTGT
*
41516207 TACTGTTTCTGTTACTGTTACTGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACT-ATTCAG-CACTTTGTGTGTCGAA
* * *
41516252 TACTGTTACTGTTACCGTTATCAATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTA-CTATTCAGCACTTTGTGTGTCGAA
*
41516297 TATTGTTACTGTTACTGTTACTATTC
1 TACTGTTACTGTTACTGTTACTATTC
41516323 CAGATTTGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 5 0.08
45 55 0.89
46 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (44 bp):
TACTGTTACTGTTACTGTTACTATTCAGCACTTTGTGTGTCGAA
Found at i:41516518 original size:18 final size:18
Alignment explanation
Indices: 41516497--41516767 Score: 170
Period size: 18 Copynumber: 14.6 Consensus size: 18
41516487 TAACTGATTA
41516497 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
41516515 TTACCGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
41516533 TTACTGGATAATGGACTG
1 TTACTGAATAATTGACTG
* * *
41516551 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
41516569 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
41516587 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* * *
41516605 TCACTAAATAAATGACTG
1 TTACTGAATAATTGACTG
* *
41516623 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* * *
41516642 CTACTGAATATTTGA-TT
1 TTACTGAATAATTGACTG
* *
41516659 TTACTAAATAATTGAGTG
1 TTACTGAATAATTGACTG
41516677 TTACTAGATAACCGATCAATTGA-TCG
1 TTACT-G---A---AT-AATTGACT-G
* * ** *
41516703 ATACTGAATAACTGGTTA
1 TTACTGAATAATTGACTG
* *
41516721 TTATTGAATAATTGATTG
1 TTACTGAATAATTGACTG
* *
41516739 TTACCGAATAAGTGACTG
1 TTACTGAATAATTGACTG
41516757 TTACTGAATAA
1 TTACTGAATAA
41516768 ATAATTGTTC
Statistics
Matches: 195, Mismatches: 44, Indels: 28
0.73 0.16 0.10
Matches are distributed among these distances:
17 14 0.07
18 147 0.75
19 17 0.09
22 2 0.01
25 4 0.02
26 11 0.06
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:41516537 original size:36 final size:35
Alignment explanation
Indices: 41516485--41516767 Score: 197
Period size: 36 Copynumber: 7.7 Consensus size: 35
41516475 AAAGGTATAA
* *
41516485 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGATTGTTACTGAATAATTGA-TGTTACTG
* * * *
41516521 AATAATTGACTGTTACTGGATAATGGACTGTTACTG
1 AATAACTGATTGTTACTGAATAATTGA-TGTTACTG
* * *
41516557 AATAACTGAATATTACTGAATAATTGATCATTACTG
1 AATAACTGATTGTTACTGAATAATTGAT-GTTACTG
* * *
41516593 AATAACTGATTGTCACTAAATAAATGACTGTTACTG
1 AATAACTGATTGTTACTGAATAATTGA-TGTTACTG
* * * * *
41516629 AATAACTTAATTGCTACTGAATATTTGATTTTACTA
1 AATAAC-TGATTGTTACTGAATAATTGATGTTACTG
* * *
41516665 AATAATTGAGTGTTACTAGATAACCGATCAATTGATCGATACTG
1 AATAACTGATTGTTACT-G---A---AT-AATTGAT-GTTACTG
* * * *
41516709 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGATTGTTACTGAATAATTGA-TGTTACTG
* *
41516745 AATAAGTGACTGTTACTGAATAA
1 AATAACTGATTGTTACTGAATAA
41516768 ATAATTGTTC
Statistics
Matches: 188, Mismatches: 46, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
35 9 0.05
36 133 0.71
37 19 0.10
39 1 0.01
40 1 0.01
42 2 0.01
43 7 0.04
44 16 0.09
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (35 bp):
AATAACTGATTGTTACTGAATAATTGATGTTACTG
Found at i:41526970 original size:61 final size:61
Alignment explanation
Indices: 41526875--41526997 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
41526865 GCACTATAAA
*
41526875 ATAGGAAAAAAATAAAACGGAGTAAGTATTACATGCTTAGTAAGTTCATATAATAGAAACT
1 ATAGGAAAAAAATAAAACGGAGTAAGCATTACATGCTTAGTAAGTTCATATAATAGAAACT
* *
41526936 ATAGGAAAAAAGTAAAGCGGAGTAAGCATTACATGCTTAGTAAGTTCATATAATAGAAACT
1 ATAGGAAAAAAATAAAACGGAGTAAGCATTACATGCTTAGTAAGTTCATATAATAGAAACT
41526997 A
1 A
41526998 AACTTACCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (61 bp):
ATAGGAAAAAAATAAAACGGAGTAAGCATTACATGCTTAGTAAGTTCATATAATAGAAACT
Found at i:41537010 original size:44 final size:44
Alignment explanation
Indices: 41536948--41537032 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
41536938 AAATTAGATA
** *
41536948 CGATGCCAATGTCCAAGACATAGTCTTACATGCAAAACAGAAGT
1 CGATGCCAACATCCAAGACATAGTCTTACACGCAAAACAGAAGT
* * *
41536992 CGATGCCAACATCGAAGACGTGGTCTTACACGCAAAACAGA
1 CGATGCCAACATCCAAGACATAGTCTTACACGCAAAACAGA
41537033 TATCGGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (44 bp):
CGATGCCAACATCCAAGACATAGTCTTACACGCAAAACAGAAGT
Found at i:41540247 original size:13 final size:13
Alignment explanation
Indices: 41540229--41540256 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41540219 CTTTTCAGAC
41540229 CATTCAAACTTCA
1 CATTCAAACTTCA
41540242 CATTCAAACTTCA
1 CATTCAAACTTCA
41540255 CA
1 CA
41540257 AGTTTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (13 bp):
CATTCAAACTTCA
Found at i:41550496 original size:39 final size:39
Alignment explanation
Indices: 41550407--41550622 Score: 371
Period size: 39 Copynumber: 5.5 Consensus size: 39
41550397 ACAAAGCATG
* * *
41550407 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
41550447 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
41550486 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
41550525 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
41550564 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
41550603 CGGGAATTAGCCCGGATATA
1 CGGGACTTAGCCCGGATATA
41550623 TATCTCACAC
Statistics
Matches: 171, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
38 20 0.12
39 145 0.85
40 6 0.04
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:41555567 original size:15 final size:15
Alignment explanation
Indices: 41555547--41555603 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
41555537 CGATGAATTT
41555547 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
41555562 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
41555577 ATTGAATTTATATTG
1 ATTGAATTTATATTG
41555592 ATTGAA-TTATAT
1 ATTGAATTTATAT
41555604 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:41560010 original size:8 final size:8
Alignment explanation
Indices: 41559997--41560025 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41559987 TTATGTTTAG
41559997 TATATTAT
1 TATATTAT
41560005 TATATTAT
1 TATATTAT
41560013 TATATTAT
1 TATATTAT
41560021 TATAT
1 TATAT
41560026 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:41560058 original size:5 final size:5
Alignment explanation
Indices: 41560048--41560108 Score: 115
Period size: 5 Copynumber: 12.4 Consensus size: 5
41560038 TTATGTTTTA
41560048 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
41560098 ATTAT A-TAT AT
1 ATTAT ATTAT AT
41560109 AAACTAAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.07
5 51 0.93
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:41561399 original size:15 final size:15
Alignment explanation
Indices: 41561379--41561435 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
41561369 CGATGAATTT
41561379 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
41561394 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
41561409 ATTGAATTTATATTG
1 ATTGAATTTATATTG
41561424 ATTGAA-TTATAT
1 ATTGAATTTATAT
41561436 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:41561837 original size:23 final size:23
Alignment explanation
Indices: 41561819--41561893 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 23
41561809 AGGCACTTTA
41561819 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
41561842 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
*
41561863 TGTGTCGT-TTT-AGGCACTTTC-
1 TGTGTCGTATTTCAGGCAC-CTCG
41561884 TGTGTCGTAT
1 TGTGTCGTAT
41561894 ACTGATCAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
21 34 0.72
22 4 0.09
23 9 0.19
ACGTcount: A:0.12, C:0.23, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:41570185 original size:23 final size:24
Alignment explanation
Indices: 41570139--41570185 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
41570129 CAGTGATCAC
*
41570139 ACGCCCGTGTAAACAGGTCATGTG
1 ACGCCCGTGTAAACAGGCCATGTG
* *
41570163 ACGCCCGTGT-CACAGGCCGTGTG
1 ACGCCCGTGTAAACAGGCCATGTG
41570186 GAAACAGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (24 bp):
ACGCCCGTGTAAACAGGCCATGTG
Found at i:41574375 original size:16 final size:17
Alignment explanation
Indices: 41574354--41574392 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
41574344 GTAACGCCCT
41574354 AAAAATCT-CGAAACCC
1 AAAAATCTCCGAAACCC
41574370 AAAAAT-TCCGAAACCC
1 AAAAATCTCCGAAACCC
41574386 AAAAATC
1 AAAAATC
41574393 CTGAAATCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.54, C:0.28, G:0.05, T:0.13
Consensus pattern (17 bp):
AAAAATCTCCGAAACCC
Found at i:41574398 original size:16 final size:16
Alignment explanation
Indices: 41574354--41574398 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
41574344 GTAACGCCCT
41574354 AAAAAT-CTCGAAACCC
1 AAAAATCCT-GAAACCC
41574370 AAAAATTCC-GAAACCC
1 AAAAA-TCCTGAAACCC
41574386 AAAAATCCTGAAA
1 AAAAATCCTGAAA
41574399 TCCCGAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
16 21 0.81
17 1 0.04
18 1 0.04
ACGTcount: A:0.53, C:0.27, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAAATCCTGAAACCC
Found at i:41575978 original size:29 final size:29
Alignment explanation
Indices: 41575945--41576046 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
41575935 TGAATATGAC
*
41575945 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * *
41575974 TGGGCCTAATGGGACATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
41576003 TGGGCCTAATGGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
41576031 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
41576047 GATACAGGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 16 0.25
29 47 0.75
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:41576017 original size:58 final size:57
Alignment explanation
Indices: 41575945--41576055 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 57
41575935 TGAATATGAC
* *
41575945 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGACATATACAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGA-TTGGGCCTAATGGGACAGATACAGGTGATT
* * * *
41576003 TGGGCCTAATGGGCCATATGAATATGATTGGGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAATGGGACAGATACAGGT
41576056 ATGTGAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 23 0.49
58 24 0.51
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (57 bp):
TGGGCCTAACGGGCCATATAAATATGATTGGGCCTAATGGGACAGATACAGGTGATT
Found at i:41578751 original size:27 final size:27
Alignment explanation
Indices: 41578720--41578897 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41578710 TAAATTGTAC
41578720 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41578747 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41578773 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41578801 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41578829 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41578856 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41578883 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41578898 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41578834 original size:82 final size:81
Alignment explanation
Indices: 41578721--41578876 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41578711 AAATTGTACA
* *
41578721 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41578785 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41578802 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41578867 TGCGAGTTGA
65 TGCGAATTGA
41578877 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41578888 original size:82 final size:81
Alignment explanation
Indices: 41578717--41578897 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41578707 GATTAAATTG
* *
41578717 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41578782 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41578798 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41578862 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41578880 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41578898 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41589787 original size:5 final size:5
Alignment explanation
Indices: 41589747--41589771 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41589737 ATAATTTTAA
41589747 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
41589772 ATTCCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:41589937 original size:26 final size:26
Alignment explanation
Indices: 41589904--41589963 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
41589894 GTTAATTCAA
41589904 TAATTTTAATACTTTAGAATCATAAT
1 TAATTTTAATACTTTAGAATCATAAT
41589930 TAATTTTAATACTTTAGAATCATAAT
1 TAATTTTAATACTTTAGAATCATAAT
41589956 TAATTTTA
1 TAATTTTA
41589964 TTTATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (26 bp):
TAATTTTAATACTTTAGAATCATAAT
Found at i:41594308 original size:5 final size:6
Alignment explanation
Indices: 41594265--41594316 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
41594255 TGCCAGAAAC
* * * *
41594265 AAATAA AAA-AA AATTAGA AAACAA AAATTA AACTAA AAATAA AAATAA
1 AAATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAATAA
41594313 AAAT
1 AAAT
41594317 GATTAAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:41614601 original size:17 final size:17
Alignment explanation
Indices: 41614570--41614602 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41614560 GTATTGATTT
41614570 TGACATTCTTATGTCAA
1 TGACATTCTTATGTCAA
41614587 TGACAATTCTT-TGTCA
1 TGAC-ATTCTTATGTCA
41614603 TCAATCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACATTCTTATGTCAA
Found at i:41619103 original size:23 final size:22
Alignment explanation
Indices: 41619041--41619126 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 22
41619031 TTTCGAGCTA
**
41619041 TGAACAGTAAGCTCCTCCTGAGC
1 TGAACAGTAAGCT-CTAATGAGC
*
41619064 TGATTGACAGTAAGCTCTATTGAGC
1 TGA---ACAGTAAGCTCTAATGAGC
*
41619089 TGAAACGGTAAGCTCTAATGAGC
1 TG-AACAGTAAGCTCTAATGAGC
41619112 TGAACAGTAAGCTCT
1 TGAACAGTAAGCTCT
41619127 TGCGAGTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
22 12 0.22
23 22 0.41
25 9 0.17
26 11 0.20
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (22 bp):
TGAACAGTAAGCTCTAATGAGC
Found at i:41620506 original size:43 final size:42
Alignment explanation
Indices: 41620410--41620529 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 42
41620400 ATTATAGTAC
* * * * *
41620410 CATACCAATGCTATATCCCAGATATGGTCTTACATGAAATCT
1 CATATCAATGCCATAGCCAAGATATGGTCTTACATCAAATCT
* * * *
41620452 CGTTTCGATGCCAATAGCCAAGCTATGGTCTTACA-CAAAGTCT
1 CATATCAATGCC-ATAGCCAAGATATGGTCTTACATCAAA-TCT
* *
41620495 CATATCAATGCCATATCCCAGATATGGTCTTACAT
1 CATATCAATGCCATAGCCAAGATATGGTCTTACAT
41620530 GTAATCTTAG
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
42 29 0.48
43 31 0.52
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
CATATCAATGCCATAGCCAAGATATGGTCTTACATCAAATCT
Found at i:41628324 original size:19 final size:17
Alignment explanation
Indices: 41628290--41628322 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41628280 TAGCCATGTG
41628290 TGACACACAGCCGTGTA
1 TGACACACAGCCGTGTA
*
41628307 TGACACACAGCTGTGT
1 TGACACACAGCCGTGT
41628323 GTCCCCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (17 bp):
TGACACACAGCCGTGTA
Found at i:41634572 original size:40 final size:40
Alignment explanation
Indices: 41634465--41634648 Score: 250
Period size: 40 Copynumber: 4.6 Consensus size: 40
41634455 CGGATGATAA
* * *
41634465 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATA-T
41634505 CCGGGCTAAG-CCCGAAGGCAATT-GTGCGAGTTA-TAATAT
1 CCGGGCTAAGTCCCGAAGGC-ATTCGTGCGAGTTACT-ATAT
*
41634544 CAGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* *
41634584 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
*
41634624 CCGGGCTATGTCCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCATTCG
41634649 AGCAAGTAGC
Statistics
Matches: 130, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.01
39 31 0.24
40 97 0.75
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:41652016 original size:48 final size:48
Alignment explanation
Indices: 41651956--41652182 Score: 159
Period size: 46 Copynumber: 4.8 Consensus size: 48
41651946 CCACATTATG
* * *
41651956 AGAGCTAGTGTAAAACCATGTTTGGGACATGGCATTGGCATTGAGAT-A
1 AGAGCTAGTGTAAAA-CATGTCTGGGACATGGCATCGGCATCGAGATGA
* * *
41652004 AGAGCTAATGTAAGACATGTCTGGGACAT-GCATCGGCATCGAGATGT
1 AGAGCTAGTGTAAAACATGTCTGGGACATGGCATCGGCATCGAGATGA
* *
41652051 A-AGCCAGTGTAAAACATGTCTGGGACAT-GCATCGACTAT-GA-A--A
1 AGAGCTAGTGTAAAACATGTCTGGGACATGGCATCGGC-ATCGAGATGA
* * * * * * *
41652094 AGTG-TCAGTGTAAGACTATCTCTAGGACATGGCATCGGTA-CGGATATGTG
1 AGAGCT-AGTGTAAAAC-ATGTCTGGGACATGGCATCGGCATC-GAGATG-A
* * *
41652144 AGAGCTAGTGTAAGACCATGCCTGGGACATGACATCGGC
1 AGAGCTAGTGTAA-AACATGTCTGGGACATGGCATCGGC
41652183 CTCAATTTTG
Statistics
Matches: 138, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
43 1 0.01
44 10 0.07
45 13 0.09
46 55 0.40
47 17 0.12
48 13 0.09
50 27 0.20
51 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (48 bp):
AGAGCTAGTGTAAAACATGTCTGGGACATGGCATCGGCATCGAGATGA
Found at i:41655973 original size:37 final size:37
Alignment explanation
Indices: 41655873--41655974 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 37
41655863 TATACTACCC
*
41655873 GAATTTGGCGTGTTATT-GGATGGATTAGCTCTTACGA
1 GAATTTGGCGTGTT-TTCGGTTGGATTAGCTCTTACGA
* ** * * *
41655910 GCATTTGGTATGTTATCGATTGGATTAGCTCTTATGA
1 GAATTTGGCGTGTTTTCGGTTGGATTAGCTCTTACGA
*
41655947 GAATTTGGCGTGTTTTCGGTTAGATTAG
1 GAATTTGGCGTGTTTTCGGTTGGATTAG
41655975 TTCTATACTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
36 1 0.02
37 50 0.98
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (37 bp):
GAATTTGGCGTGTTTTCGGTTGGATTAGCTCTTACGA
Found at i:41658372 original size:30 final size:30
Alignment explanation
Indices: 41658336--41658395 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
41658326 ATTGTGAAGA
41658336 ACAAATATCCATTGCCAAGGATCGATGATT
1 ACAAATATCCATTGCCAAGGATCGATGATT
*
41658366 ACAAATATCCATTGCCAAGGATTGATGATT
1 ACAAATATCCATTGCCAAGGATCGATGATT
41658396 TGTTCAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (30 bp):
ACAAATATCCATTGCCAAGGATCGATGATT
Found at i:41662247 original size:46 final size:46
Alignment explanation
Indices: 41662107--41662457 Score: 198
Period size: 46 Copynumber: 7.4 Consensus size: 46
41662097 TGTGCTACTA
* * *
41662107 TAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCCAGTG
* * * * *
41662153 TAAAACCATGTTTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCCAGTG
*
41662201 TAAGACATGTCTGGGACATACATCGGCCTCGAGATGTA-AGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCCAGTG
* * *
41662247 TAAGACATGTCTGGGACATGCATCAG-CTACGA-AAG-GTGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCCAGTG
* * * * * **
41662291 TAAGACCATGTTTAGGACATGGCATCAGCAC-GGATATGTTAGAGATAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGC-CTCGAGATG--AGAGCCAGTG
* * * * ** * *
41662341 TAGGACCATGTTTGGGACATGGCTTCGGCCTCAATTTTGATAGTCAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-GATGAGAGCCAGTG
* * *
41662390 TAAGACCATGTCTGGGACATGGAATC-GACT--TGATGGATGAGCCAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGAT-GA-GAGCCAGTG
*
41662437 TAAGACCATGTCTAGGACATG
1 TAAGA-CATGTCTGGGACATG
41662458 GGATCGGCAT
Statistics
Matches: 241, Mismatches: 46, Indels: 36
0.75 0.14 0.11
Matches are distributed among these distances:
44 12 0.05
45 17 0.07
46 64 0.27
47 55 0.23
48 27 0.11
49 31 0.13
50 32 0.13
51 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
TAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCCAGTG
Found at i:41667988 original size:21 final size:21
Alignment explanation
Indices: 41667964--41668011 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
41667954 ATGTTTAAGT
41667964 TCCACACGGGCGCGTTGCCCA
1 TCCACACGGGCGCGTTGCCCA
41667985 TCCACACGGGCGCGTTGCCCA
1 TCCACACGGGCGCGTTGCCCA
41668006 TCCACA
1 TCCACA
41668012 TAGGCGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.15
Consensus pattern (21 bp):
TCCACACGGGCGCGTTGCCCA
Found at i:41668017 original size:21 final size:21
Alignment explanation
Indices: 41667964--41668017 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
41667954 ATGTTTAAGT
*
41667964 TCCACACGGGCGCGTTGCCCA
1 TCCACACAGGCGCGTTGCCCA
*
41667985 TCCACACGGGCGCGTTGCCCA
1 TCCACACAGGCGCGTTGCCCA
*
41668006 TCCACATAGGCG
1 TCCACACAGGCG
41668018 TGTGCCCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.41, G:0.28, T:0.15
Consensus pattern (21 bp):
TCCACACAGGCGCGTTGCCCA
Found at i:41672900 original size:21 final size:21
Alignment explanation
Indices: 41672874--41672917 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41672864 TTCACTAACT
41672874 AAATCTTTGTATTACCCATTG
1 AAATCTTTGTATTACCCATTG
41672895 AAATCTTTGTATTACCCATTG
1 AAATCTTTGTATTACCCATTG
41672916 AA
1 AA
41672918 CGCTCGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (21 bp):
AAATCTTTGTATTACCCATTG
Found at i:41674287 original size:62 final size:62
Alignment explanation
Indices: 41674190--41674311 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
41674180 TGCCCTTTAA
*
41674190 AAACCCCCAAATTAAAGTTCATAGCAATTTAACACCTTTAGCTAACAATTCAAGACTTTTTT
1 AAACCCCCAAATTAAAGTTCATAACAATTTAACACCTTTAGCTAACAATTCAAGACTTTTTT
* *
41674252 AAACCCCCAAATTAAAGTTCATAACAATTTAACACCTTTATCTAACAATTTAAGACTTTT
1 AAACCCCCAAATTAAAGTTCATAACAATTTAACACCTTTAGCTAACAATTCAAGACTTTT
41674312 GTACTTTATG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (62 bp):
AAACCCCCAAATTAAAGTTCATAACAATTTAACACCTTTAGCTAACAATTCAAGACTTTTTT
Found at i:41681290 original size:26 final size:26
Alignment explanation
Indices: 41681252--41681301 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41681242 TCTCATCCTT
41681252 ATTTTACCCCTAGTAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGATG
* *
41681278 ATTTTACCTCTAGTAAATTTTTGA
1 ATTTTACCCCTAGTAAAATTTTGA
41681302 GAAAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGATG
Found at i:41690052 original size:40 final size:40
Alignment explanation
Indices: 41689954--41690256 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
41689944 TCCTCGTTCA
* * * ** *
41689954 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41689993 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41690033 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41690073 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41690113 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
41690153 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
41690193 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
41690233 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41690257 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:41698045 original size:40 final size:40
Alignment explanation
Indices: 41697945--41698209 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
41697935 GCTCCTCGTT
* * * *
41697945 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
41697985 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
41698024 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
41698064 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
41698104 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
41698144 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41698185 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41698210 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41698169 original size:80 final size:80
Alignment explanation
Indices: 41697912--41698209 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
41697902 AAATCACGTA
* ** * * *
41697912 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
41697974 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
41697990 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
41698053 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
41698070 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
41698134 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
41698150 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
41698210 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:41698218 original size:41 final size:41
Alignment explanation
Indices: 41698141--41698218 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41698131 TTTGTATCTC
* * *
41698141 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41698182 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41698219 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41701239 original size:15 final size:15
Alignment explanation
Indices: 41701219--41701249 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41701209 GAATTTAATG
41701219 AGACGGCAAGACTAA
1 AGACGGCAAGACTAA
41701234 AGACGGCAAGACTAA
1 AGACGGCAAGACTAA
41701249 A
1 A
41701250 TGCTCCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.06
Consensus pattern (15 bp):
AGACGGCAAGACTAA
Found at i:41712063 original size:44 final size:44
Alignment explanation
Indices: 41712015--41712275 Score: 143
Period size: 44 Copynumber: 5.7 Consensus size: 44
41712005 TTTATATTAC
*
41712015 AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTGAAATGCA
1 AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTTAAATGCA
** * * * *
41712059 AAAGTTTTCGAGTAGGAATTGAGCTAATGTACTCCAATGTATA-TAATTTATATTACA
1 AAAG-TTT-GA-T--CCA---AG-T-TTGT--TCCAATG-AAACTAATTTA-AATGCA
*
41712116 A-AGTTTGATCCAAGTTTGTTCCAATGAAACTAATTGAAATGCA
1 AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTTAAATGCA
* * * * * *
41712159 AAAGTTTGTTTCAAGTTTGTTCTAATTAATCTAATTTAAA-GTA
1 AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTTAAATGCA
* * * * *
41712202 CAAAGTTGGTTCCAAGTTTGTTACAATGAATCTAATTTAAAT-TA
1 -AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTTAAATGCA
* * * *
41712246 CAAAGTTGGTTCCAAGTTTGGTGCAATGAA
1 -AAAGTTTGATCCAAGTTTGTTCCAATGAA
41712276 CACAACTTGT
Statistics
Matches: 171, Mismatches: 28, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
43 9 0.05
44 114 0.67
45 3 0.02
46 5 0.03
47 2 0.01
48 2 0.01
49 1 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 5 0.03
55 3 0.02
56 15 0.09
57 7 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (44 bp):
AAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTTAAATGCA
Found at i:41712139 original size:100 final size:100
Alignment explanation
Indices: 41711966--41712165 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
41711956 CTTATCGCAA
41711966 TCGAGTAGGAATTGAGCTAATGTACTCCAATGTATATAATTTATATTACAAAGTTTGATCCAAGT
1 TCGAGTAGGAATTGAGCTAATGTACTCCAATGTATATAATTTATATTACAAAGTTTGATCCAAGT
41712031 TTGTTCCAATGAAACTAATTGAAATGCAAAAGTTT
66 TTGTTCCAATGAAACTAATTGAAATGCAAAAGTTT
41712066 TCGAGTAGGAATTGAGCTAATGTACTCCAATGTATATAATTTATATTACAAAGTTTGATCCAAGT
1 TCGAGTAGGAATTGAGCTAATGTACTCCAATGTATATAATTTATATTACAAAGTTTGATCCAAGT
41712131 TTGTTCCAATGAAACTAATTGAAATGCAAAAGTTT
66 TTGTTCCAATGAAACTAATTGAAATGCAAAAGTTT
41712166 GTTTCAAGTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (100 bp):
TCGAGTAGGAATTGAGCTAATGTACTCCAATGTATATAATTTATATTACAAAGTTTGATCCAAGT
TTGTTCCAATGAAACTAATTGAAATGCAAAAGTTT
Found at i:41712208 original size:88 final size:88
Alignment explanation
Indices: 41712102--41712265 Score: 222
Period size: 88 Copynumber: 1.9 Consensus size: 88
41712092 CCAATGTATA
* * * * *
41712102 TAATTTATATTACAAAGTTTGATCCAAGTTTGTTCCAATGAAACTAATTGAAATGCA-AAAGTTT
1 TAATTTAAAGTACAAAGTTGGATCCAAGTTTGTTACAATGAAACTAATTGAAAT-CACAAAGTTG
*
41712166 GTTTCAAGTTTGTTCTAATTAATC
65 GTTCCAAGTTTGTTCTAATTAATC
* * * *
41712190 TAATTTAAAGTACAAAGTTGGTTCCAAGTTTGTTACAATGAATCTAATTTAAATTACAAAGTTGG
1 TAATTTAAAGTACAAAGTTGGATCCAAGTTTGTTACAATGAAACTAATTGAAATCACAAAGTTGG
41712255 TTCCAAGTTTG
66 TTCCAAGTTTG
41712266 GTGCAATGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.02
88 64 0.98
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (88 bp):
TAATTTAAAGTACAAAGTTGGATCCAAGTTTGTTACAATGAAACTAATTGAAATCACAAAGTTGG
TTCCAAGTTTGTTCTAATTAATC
Found at i:41713552 original size:40 final size:40
Alignment explanation
Indices: 41713520--41713711 Score: 276
Period size: 40 Copynumber: 4.8 Consensus size: 40
41713510 CCAGCATGAT
* * *
41713520 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
41713560 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
41713600 TGCTCTTCGGAACTTAGTCTGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
41713640 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41713680 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
41713712 CTCAATTCTC
Statistics
Matches: 131, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 131 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:41714976 original size:37 final size:37
Alignment explanation
Indices: 41714926--41715004 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41714916 TTATTACGAA
* * *
41714926 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41714963 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41715000 GTCTT
1 GTCTT
41715005 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41715248 original size:49 final size:47
Alignment explanation
Indices: 41715123--41715300 Score: 241
Period size: 47 Copynumber: 3.7 Consensus size: 47
41715113 CCCTTCGGGA
* * * * *
41715123 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* * *
41715170 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
*
41715217 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATCCATCACATCGGCCATTAGGC
41715266 CTTATCACATATATACA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
41715301 AGAACCCTAA
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
46 1 0.01
47 69 0.59
49 47 0.40
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
Found at i:41715289 original size:96 final size:94
Alignment explanation
Indices: 41715123--41715300 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 94
41715113 CCCTTCGGGA
* * * *
41715123 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
41715188 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATCCATCACATCGGCCATTAGGC
* * *
41715217 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
41715282 A-TGTTCACATCCATCACAT
64 ACT-TTCACATCCATCACAT
41715301 AGAACCCTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 10 0.14
95 2 0.03
96 61 0.84
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (94 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATCCATCACATCGGCCATTAGGC
Found at i:41719560 original size:13 final size:13
Alignment explanation
Indices: 41719542--41719568 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41719532 GCTCGACAGG
41719542 GACATGCCCGTGT
1 GACATGCCCGTGT
41719555 GACATGCCCGTGT
1 GACATGCCCGTGT
41719568 G
1 G
41719569 CGATTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GACATGCCCGTGT
Found at i:41728722 original size:43 final size:43
Alignment explanation
Indices: 41728535--41728728 Score: 219
Period size: 43 Copynumber: 4.5 Consensus size: 43
41728525 GATTACTGAG
* * * *
41728535 ATGTGATTACATGTAAGACAATGTCTGGGGCATTGGCATTGTA
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTA
* * *
41728578 TTGGGATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTA
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTA
* ** *
41728621 ATATGATTTTGTGTAAGAACATGTCTGGGACATTGGCATCGTA
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTA
** **
41728664 ATACGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCG-A
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTA
* *
41728706 TATGTGATAACATGTAAGACCAT
1 -ATGTGATTACGTGTAAGACCAT
41728729 ATCTAGGATA
Statistics
Matches: 128, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
42 1 0.01
43 127 0.99
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTA
Found at i:41735144 original size:43 final size:43
Alignment explanation
Indices: 41735083--41735187 Score: 201
Period size: 43 Copynumber: 2.4 Consensus size: 43
41735073 TAAAGACAAA
*
41735083 ATTTAGCCTGTACTAGTAATTCTGATCTTACATTGAAATTAAG
1 ATTTAGCCTGGACTAGTAATTCTGATCTTACATTGAAATTAAG
41735126 ATTTAGCCTGGACTAGTAATTCTGATCTTACATTGAAATTAAG
1 ATTTAGCCTGGACTAGTAATTCTGATCTTACATTGAAATTAAG
41735169 ATTTAGCCTGGACTAGTAA
1 ATTTAGCCTGGACTAGTAA
41735188 CCTTGATTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (43 bp):
ATTTAGCCTGGACTAGTAATTCTGATCTTACATTGAAATTAAG
Found at i:41737397 original size:42 final size:42
Alignment explanation
Indices: 41737281--41737437 Score: 129
Period size: 43 Copynumber: 3.7 Consensus size: 42
41737271 GATGTGATAC
* * *
41737281 CGTGTAAGACCATGTCCGAGACATTGGCATCAATATGAGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-AGATTA
* * ** *
41737324 CGTGTAAGGCCATGTATGGGACATTAACATCG-TATATGATTT
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATA-GATTA
* * * *
41737366 CGTGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGATAA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATA-TAGATTA
* * * *
41737409 CATGTAAGAGCATGCCTGGGATA-TGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
41737438 TGTACGAGTT
Statistics
Matches: 89, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.01
42 39 0.44
43 48 0.54
44 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATAGATTA
Found at i:41747324 original size:51 final size:51
Alignment explanation
Indices: 41747218--41747325 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
41747208 TTACATAATA
* * * * * ***
41747218 TGTCAATTTGGTCTTGATTTAATAAATTTAGCCCACAACATTTATGTATTG
1 TGTCAACTTGGTCCTAATCTAACAAATTTAGCCCACAACATTTACCCATTG
* *
41747269 TGTCAACTTGGTCCTAATCTAACAAATTTAGCCCATAACATTTACCCATTT
1 TGTCAACTTGGTCCTAATCTAACAAATTTAGCCCACAACATTTACCCATTG
41747320 TGTCAA
1 TGTCAA
41747326 AATTTACACA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (51 bp):
TGTCAACTTGGTCCTAATCTAACAAATTTAGCCCACAACATTTACCCATTG
Found at i:41750199 original size:6 final size:6
Alignment explanation
Indices: 41750188--41750221 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
41750178 CCGAGTAGGC
*
41750188 CAAGCT CAAGCT CAAGCA CAAGCT CAAGCT CAAG
1 CAAGCT CAAGCT CAAGCT CAAGCT CAAGCT CAAG
41750222 GCTAAGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.32, G:0.18, T:0.12
Consensus pattern (6 bp):
CAAGCT
Found at i:41753849 original size:38 final size:38
Alignment explanation
Indices: 41753807--41753883 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
41753797 CTTATGCCTC
41753807 ATGGGTAGAACCATCCTAGTCAGATACTCAGATATAAA
1 ATGGGTAGAACCATCCTAGTCAGATACTCAGATATAAA
41753845 ATGGGTAGAACCATCCTAGTCAGATACTCAGATATAAA
1 ATGGGTAGAACCATCCTAGTCAGATACTCAGATATAAA
41753883 A
1 A
41753884 GCATTTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (38 bp):
ATGGGTAGAACCATCCTAGTCAGATACTCAGATATAAA
Found at i:41761820 original size:80 final size:80
Alignment explanation
Indices: 41761717--41761957 Score: 455
Period size: 80 Copynumber: 3.0 Consensus size: 80
41761707 ATCACAAGGA
* *
41761717 ATTTCAAATAAAACACACACACACAAAATTCCATGAAGATTTTCGTTTAAAAGAAATAAAATATT
1 ATTTCAAATAAAA-AAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATT
41761782 TCAATTTATAATGTTT
65 TCAATTTATAATGTTT
41761798 ATTTCAAATAAAAAAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATTT
1 ATTTCAAATAAAAAAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATTT
41761863 CAATTTATAATGTTT
66 CAATTTATAATGTTT
41761878 ATTTCAAATAAAAAAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATTT
1 ATTTCAAATAAAAAAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATTT
41761943 CAATTTATAATGTTT
66 CAATTTATAATGTTT
41761958 TTAATTAAAA
Statistics
Matches: 158, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 145 0.92
81 13 0.08
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (80 bp):
ATTTCAAATAAAAAAACACACACAAAATTCCATGAAGTTTTTCGTTTAAAAGAAATAAAATATTT
CAATTTATAATGTTT
Found at i:41763687 original size:29 final size:29
Alignment explanation
Indices: 41763635--41763694 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
41763625 TTTAGTTAAT
**
41763635 TTTTTAAAAATTAAAAATTTTTAAAAATA
1 TTTTTAAAAATTAAAAATCATTAAAAATA
*
41763664 TTTTTAAAAATTAAAAATCATTAAAATTA
1 TTTTTAAAAATTAAAAATCATTAAAAATA
41763693 TT
1 TT
41763695 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTTAAAAATTAAAAATCATTAAAAATA
Found at i:41774444 original size:240 final size:240
Alignment explanation
Indices: 41774021--41774500 Score: 906
Period size: 240 Copynumber: 2.0 Consensus size: 240
41774011 ATACTAGTCG
*
41774021 CTTTAAAAATCATATCTTGAGTTTCACAATTCGAAAATCAGTTTCGTGATTTTTCACTGAAACTA
1 CTTTAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTTTCGTGATTTTTCACTGAAACTA
41774086 GACTCATATGCCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGGCCAATTAGTACAGTTTAT
66 GACTCATATGCCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGGCCAATTAGTACAGTTTAT
* *
41774151 TAGTCAAAGTCTCCCATGTTATAGGGATCGACTACCCTGACCTTTGCGCATTACGACTTGGATAT
131 TAGTCAAAGTCTCCCATGTTACAAGGATCGACTACCCTGACCTTTGCGCATTACGACTTGGATAT
*
41774216 CTCCTTGTACAGGGCTCCAATACTGATGCCGTTTGTTTCTATAGA
196 CTCATTGTACAGGGCTCCAATACTGATGCCGTTTGTTTCTATAGA
*
41774261 CTTTAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTTTCGTGATTTTTCCCTGAAACTA
1 CTTTAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTTTCGTGATTTTTCACTGAAACTA
41774326 GACTCATATGCCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGGCCAATTAGTACAGTTTAT
66 GACTCATATGCCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGGCCAATTAGTACAGTTTAT
41774391 TAGTCAAAGTCTCCCATGTTACAAGGATCGACTACCCTGACCTTTGCGCATTACGACTTGGATAT
131 TAGTCAAAGTCTCCCATGTTACAAGGATCGACTACCCTGACCTTTGCGCATTACGACTTGGATAT
*
41774456 CTCATTGTACAGGGCTTCAATACTGATGCCGTTTGTTTCTATAGA
196 CTCATTGTACAGGGCTCCAATACTGATGCCGTTTGTTTCTATAGA
41774501 AACTAGACTC
Statistics
Matches: 234, Mismatches: 6, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
240 234 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (240 bp):
CTTTAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTTTCGTGATTTTTCACTGAAACTA
GACTCATATGCCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGGCCAATTAGTACAGTTTAT
TAGTCAAAGTCTCCCATGTTACAAGGATCGACTACCCTGACCTTTGCGCATTACGACTTGGATAT
CTCATTGTACAGGGCTCCAATACTGATGCCGTTTGTTTCTATAGA
Found at i:41786118 original size:10 final size:10
Alignment explanation
Indices: 41786103--41786127 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41786093 TAAGGTTTGA
41786103 ATTTTGTTCG
1 ATTTTGTTCG
41786113 ATTTTGTTCG
1 ATTTTGTTCG
41786123 ATTTT
1 ATTTT
41786128 TATGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (10 bp):
ATTTTGTTCG
Found at i:41790710 original size:13 final size:13
Alignment explanation
Indices: 41790692--41790716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41790682 TAATGGTATA
41790692 TTGAATCCATGAT
1 TTGAATCCATGAT
41790705 TTGAATCCATGA
1 TTGAATCCATGA
41790717 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:41792619 original size:25 final size:25
Alignment explanation
Indices: 41792591--41792669 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
41792581 CTAATGGCCG
41792591 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * * *
41792616 ATGTGAT-AAGGCCGAATG-GCA-A-
1 ATGTGATGAATG-TGAAAGTGTATAT
41792638 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
41792663 ATGTGAT
1 ATGTGAT
41792670 AAGGCCTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.27
23 6 0.15
24 6 0.15
25 18 0.44
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41792619 original size:47 final size:47
Alignment explanation
Indices: 41792566--41792719 Score: 272
Period size: 47 Copynumber: 3.3 Consensus size: 47
41792556 ACAATATATG
41792566 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
* **
41792613 TATATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
*
41792660 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
41792707 TATATGTGATAAG
1 TATATGTGATAAG
41792720 TCCCGAAGGA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 100 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:41794624 original size:40 final size:40
Alignment explanation
Indices: 41794560--41794797 Score: 246
Period size: 40 Copynumber: 6.0 Consensus size: 40
41794550 AGTTCAGTGA
* * * *
41794560 GTTATATCCGGGCTAAGCCCCGAAGGGCATTTGTGCCGAT
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGAT
* * * * * *
41794600 GCTATATCCGGGTTAAGTCTCGAAGAGCATCCGTGCTGGT
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGAT
* * *
41794640 GTTATACCCAGGTTAAGACCCGAAGAGCATTCGTG-CTAGT
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGA-T
* * *
41794680 GTTATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGAT
* * *
41794720 GTTATACCCGGGTTAAGACCCGAAGAGCATTCATG-CTAGT
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGA-T
* * *
41794760 GTTATATCCGAGCTAAGTCCCGAAGAGCATTCGTGCCG
1 GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCG
41794798 GTGATGTGTA
Statistics
Matches: 158, Mismatches: 36, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
40 157 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GTTATATCCGGGTTAAGACCCGAAGAGCATTCGTGCCGAT
Found at i:41794693 original size:80 final size:80
Alignment explanation
Indices: 41794602--41794800 Score: 335
Period size: 80 Copynumber: 2.5 Consensus size: 80
41794592 GTGCCGATGC
* *
41794602 TATATCCGGGTTAAGTCTCGAAGAGCATCCGTGCTGGTGTTATACCCAGGTTAAGACCCGAAGAG
1 TATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATACCCAGGTTAAGACCCGAAGAG
*
41794667 CATTCGTGCTAGTGT
66 CATTCATGCTAGTGT
*
41794682 TATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATACCCGGGTTAAGACCCGAAGAG
1 TATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATACCCAGGTTAAGACCCGAAGAG
41794747 CATTCATGCTAGTGT
66 CATTCATGCTAGTGT
* * *
41794762 TATATCCGAGCTAAGTCCCGAAGAGCATTCGTGCCGGTG
1 TATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTG
41794801 ATGTGTATTC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 112 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATACCCAGGTTAAGACCCGAAGAG
CATTCATGCTAGTGT
Found at i:41794782 original size:120 final size:120
Alignment explanation
Indices: 41794560--41794795 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 120
41794550 AGTTCAGTGA
* * * * *
41794560 GTTATATCCGGGCTAAGCCCCGAAGGGCATTTGTGCCGATGCTATATCCGGGTTAAGTCTCGAAG
1 GTTATATCCGGGCTAAGCCCCGAAGAGCATTCGTGCCGATGCTATACCCGGGTTAAGACCCGAAG
* * *
41794625 AGCATCCGTGCTGGTGTTATACCCAGGTTAAGACCCGAAGAGCATTCGTGCTAGT
66 AGCATCCATGCTAGTGTTATACCCAGGCTAAGACCCGAAGAGCATTCGTGCTAGT
* * * * *
41794680 GTTATATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATACCCGGGTTAAGACCCGAAG
1 GTTATATCCGGGCTAAGCCCCGAAGAGCATTCGTGCCGATGCTATACCCGGGTTAAGACCCGAAG
* * *
41794745 AGCATTCATGCTAGTGTTATATCC-GAGCTAAGTCCCGAAGAGCATTCGTGC
66 AGCATCCATGCTAGTGTTATACCCAG-GCTAAGACCCGAAGAGCATTCGTGC
41794796 CGGTGATGTG
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
119 1 0.01
120 98 0.99
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (120 bp):
GTTATATCCGGGCTAAGCCCCGAAGAGCATTCGTGCCGATGCTATACCCGGGTTAAGACCCGAAG
AGCATCCATGCTAGTGTTATACCCAGGCTAAGACCCGAAGAGCATTCGTGCTAGT
Found at i:41794867 original size:43 final size:43
Alignment explanation
Indices: 41794788--41794871 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
41794778 CCCGAAGAGC
* * * *
41794788 ATTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGG
1 ATTCATGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCAGG
*
41794831 ATTCATGCCGGTGATATGTATTCAGGCTTTCATGCCTAGCA
1 ATTCATGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCA
41794872 AGCTTAATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.32
Consensus pattern (43 bp):
ATTCATGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCAGG
Found at i:41794887 original size:43 final size:43
Alignment explanation
Indices: 41794793--41794888 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
41794783 AGAGCATTCG
* * * * *
41794793 TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGATTCA
1 TGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCAAGATTAA
* *
41794836 TGCCGGTGATATGTATTCAGGCTTTCATGCCTAGCAAGCTTAA
1 TGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCAAGATTAA
*
41794879 TGCTGGTGAT
1 TGCCGGTGAT
41794889 CTGAGCAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (43 bp):
TGCCGGTGATATGTATTCAGGCCTTCATGCCTAGCAAGATTAA
Found at i:41795079 original size:54 final size:57
Alignment explanation
Indices: 41795020--41795139 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 57
41795010 ATGAATAAGG
* *
41795020 GCACTATGTGTGTGA-A-CGAT-TTGAGGCATTGTGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGGGTGAGATCGATATTGAGGCACTGTGTGTGCAAATTCCTTTAACCGA
* *
41795074 GCACTATGTGGGTGAGATCGATAATTGAGGCACTGTGTGTGCGAATTTCTTTAACCGA
1 GCACTATGTGGGTGAGATCGAT-ATTGAGGCACTGTGTGTGCAAATTCCTTTAACCGA
*
41795132 GTACTATG
1 GCACTATG
41795140 AGTGCAAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 14 0.25
55 1 0.02
56 4 0.07
58 38 0.67
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (57 bp):
GCACTATGTGGGTGAGATCGATATTGAGGCACTGTGTGTGCAAATTCCTTTAACCGA
Found at i:41797318 original size:13 final size:13
Alignment explanation
Indices: 41797300--41797324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41797290 AAATGGTATA
41797300 TTGAATCCATGAT
1 TTGAATCCATGAT
41797313 TTGAATCCATGA
1 TTGAATCCATGA
41797325 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:41816461 original size:11 final size:11
Alignment explanation
Indices: 41816426--41816462 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
41816416 TAGGATAGTT
41816426 TTTTC-TTTAG
1 TTTTCTTTTAG
*
41816436 TTTTCTTAT-G
1 TTTTCTTTTAG
41816446 TTTTCTTTTAG
1 TTTTCTTTTAG
41816457 TTTTCT
1 TTTTCT
41816463 CTTCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTCTTTTAG
Found at i:41816470 original size:21 final size:21
Alignment explanation
Indices: 41816426--41816475 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
41816416 TAGGATAGTT
*
41816426 TTTTC-TTTAGTTTTCTTATG
1 TTTTCTTTTAGTTTTCTTATC
41816446 TTTTCTTTTAGTTTTCTCT-TC
1 TTTTCTTTTAGTTTTCT-TATC
*
41816467 TTTTTTTTT
1 TTTTCTTTT
41816476 TCAGGGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTAGTTTTCTTATC
Found at i:41824181 original size:24 final size:24
Alignment explanation
Indices: 41824154--41824213 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
41824144 GTTTCCTCAT
* *
41824154 ACACATAGTGCTATATAATCTCGC
1 ACACATAGTGCTACATAACCTCGC
**
41824178 ACACATAGTGCCGCATAACCTCGC
1 ACACATAGTGCTACATAACCTCGC
41824202 ACACATAGTGCT
1 ACACATAGTGCT
41824214 GAAATTTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (24 bp):
ACACATAGTGCTACATAACCTCGC
Found at i:41831070 original size:46 final size:46
Alignment explanation
Indices: 41831003--41831224 Score: 308
Period size: 46 Copynumber: 4.8 Consensus size: 46
41830993 TGTAACCCGC
* * *
41831003 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
**
41831049 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTCGCAT
* *
41831099 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
41831142 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
41831188 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41831225 TGCTCAATCA
Statistics
Matches: 157, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
43 6 0.04
44 2 0.01
45 4 0.03
46 107 0.68
47 29 0.18
48 2 0.01
49 2 0.01
50 5 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41831122 original size:93 final size:93
Alignment explanation
Indices: 41831010--41831178 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
41831000 CGCCCATAAG
*
41831010 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
41831074 AACGAGTTCGGATGCCTATTTACATCTCA
65 AACGAGTTCGGATGCCTATTTACATCTCA
*
41831103 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41831168 ACGAGTTCGGA
66 ACGAGTTCGGA
41831179 CATTCGCATC
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTATTTACATCTCA
Found at i:41838981 original size:15 final size:15
Alignment explanation
Indices: 41838961--41838993 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41838951 TGAATAACAA
*
41838961 TAATTAATAAATTAG
1 TAATTAATAAATCAG
41838976 TAATTAATAAATCAG
1 TAATTAATAAATCAG
41838991 TAA
1 TAA
41838994 GAACAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (15 bp):
TAATTAATAAATCAG
Found at i:41839097 original size:16 final size:16
Alignment explanation
Indices: 41839076--41839106 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41839066 AACAAGATTG
41839076 GGATTTAACTAAACTT
1 GGATTTAACTAAACTT
41839092 GGATTTAACTAAACT
1 GGATTTAACTAAACT
41839107 GGAACTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
GGATTTAACTAAACTT
Found at i:41839225 original size:15 final size:15
Alignment explanation
Indices: 41839205--41839236 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41839195 ACATGAATGA
41839205 CAGTAATTAATAAAT
1 CAGTAATTAATAAAT
41839220 CAGTAATTAATAAAT
1 CAGTAATTAATAAAT
41839235 CA
1 CA
41839237 ATAAGAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (15 bp):
CAGTAATTAATAAAT
Found at i:41856423 original size:20 final size:18
Alignment explanation
Indices: 41856398--41856438 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
41856388 TGTATGGTNG
41856398 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAG-AAGAAAGG-GA
41856418 AAAGAAAGAAGAAAGGGA
1 AAAGAAAGAAGAAAGGGA
41856436 AAA
1 AAA
41856439 TTGAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGAAAGGGA
Done.