Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 61 of 145
Found at i:20019657 original size:44 final size:45
Alignment explanation
Indices: 20019607--20019697 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
20019597 CAAGAAAACA
20019607 TTTCTGCTAAATT-AAAAAAAAACAATAAGAAGGTAATATTTTTT
1 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
20019651 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
1 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
20019696 TT
1 TT
20019698 CTTTTTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 13 0.28
45 33 0.72
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (45 bp):
TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
Found at i:20024079 original size:16 final size:17
Alignment explanation
Indices: 20024058--20024104 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
20024048 AGTTTAATTC
20024058 ATTTCTTTATTTTT-TT
1 ATTTCTTTATTTTTGTT
20024074 ATTTCTTTATTTTTGTT
1 ATTTCTTTATTTTTGTT
* *
20024091 ATTTATTAATTTTT
1 ATTTCTTTATTTTT
20024105 ATTCCTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTCTTTATTTTTGTT
Found at i:20028483 original size:138 final size:137
Alignment explanation
Indices: 20028228--20028484 Score: 302
Period size: 138 Copynumber: 1.9 Consensus size: 137
20028218 GGTCTGCTCA
* *
20028228 CACAAGCTGACGGTCAAAATGTAGCTACACGATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
1 CACAAGCTGACAGTCAAAATGTAGCTACACAATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
** * * * **
20028293 AAATGTTGGAACTCAGCCATCGGTAGGACATTCAAGACCAGCACCCTCAACATGGTAACCTGGGT
66 AAATGCCGGAACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATGGTAACCTGGGT
20028358 CTACTAT
131 CTACTAT
** * * **
20028365 CACAAGCTGACAGTCGGAATGTAAGCTACACAATG-CTGCTTACACAAGTTGATGAGTATCCGCA
1 CACAAGCTGACAGTCAAAATGT-AGCTACACAATGTC-GCTCACACAAGCTGACAAGTATCCGCA
* * * *
20028429 ACAAATGCC-GAGCCTAAGGCATCGGTAGAACATTCAGGACCGGAACCCAAAACATG
64 ACAAATGCCGGA-ACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATG
20028485 AAAACCCTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
137 22 0.22
138 76 0.78
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (137 bp):
CACAAGCTGACAGTCAAAATGTAGCTACACAATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
AAATGCCGGAACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATGGTAACCTGGGT
CTACTAT
Found at i:20034788 original size:5 final size:5
Alignment explanation
Indices: 20034778--20034813 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
20034768 TTTAACTAAC
20034778 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
20034814 GTACCAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:20036258 original size:11 final size:11
Alignment explanation
Indices: 20036244--20036281 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
20036234 AAAATAAATC
20036244 AAAATTATTAT
1 AAAATTATTAT
20036255 AAAATTATTAT
1 AAAATTATTAT
*
20036266 AAAATTAAT-T
1 AAAATTATTAT
20036276 AAAATT
1 AAAATT
20036282 CTATGTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAAATTATTAT
Found at i:20043691 original size:50 final size:50
Alignment explanation
Indices: 20043580--20043819 Score: 187
Period size: 50 Copynumber: 4.7 Consensus size: 50
20043570 ATTTGGGTAA
* * *
20043580 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA-C--CGAG---ATG
** * *
20043636 AGAGGTTTCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
* *** ** * *
20043686 GGAGGTCCCCCATAAGACCATATCACGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
** * * *
20043736 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTGCAGG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAG-ATG
* ** *
20043785 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGC
20043820 NNNNNNNNNN
Statistics
Matches: 148, Mismatches: 35, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
48 1 0.01
49 32 0.22
50 73 0.49
53 3 0.02
55 1 0.01
56 38 0.26
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
Found at i:20048223 original size:18 final size:18
Alignment explanation
Indices: 20048200--20048236 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20048190 TTGAGTGTTT
20048200 TTTGACAACTCAATCCTA
1 TTTGACAACTCAATCCTA
20048218 TTTGACAACTCAATCCTA
1 TTTGACAACTCAATCCTA
20048236 T
1 T
20048237 CTTCTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (18 bp):
TTTGACAACTCAATCCTA
Found at i:20050846 original size:52 final size:52
Alignment explanation
Indices: 20050763--20050863 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
20050753 GTGTTTTAGC
*
20050763 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATGCCCATGTCAATCAAT
1 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATCAAT
* * * *
20050815 ACACTTGAACTTAGGTTTTTTTACATTGACAACAATACCCATGTCAATC
1 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATC
20050864 GAGCTAAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (52 bp):
ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATCAAT
Found at i:20051653 original size:20 final size:20
Alignment explanation
Indices: 20051628--20051667 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20051618 AATATTTTCC
*
20051628 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
20051648 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
20051668 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:20051682 original size:34 final size:35
Alignment explanation
Indices: 20051616--20051682 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20051606 CAAACACAAG
*
20051616 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
20051651 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
20051683 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20055326 original size:16 final size:16
Alignment explanation
Indices: 20055307--20055339 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20055297 CTTGCAATTC
20055307 GACAGGCTCACACTTT
1 GACAGGCTCACACTTT
*
20055323 GACAGGCTCGCACTTT
1 GACAGGCTCACACTTT
20055339 G
1 G
20055340 CTTACTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.24
Consensus pattern (16 bp):
GACAGGCTCACACTTT
Found at i:20055526 original size:25 final size:25
Alignment explanation
Indices: 20055498--20055584 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
20055488 CTGAGCTCAT
* *
20055498 AGCTCGCACTTCTCGCTAAGCTTGC
1 AGCTTGCACATCTCGCTAAGCTTGC
*
20055523 AGCTTTG-ACATCTTGCTAAGCTTGC
1 AGC-TTGCACATCTCGCTAAGCTTGC
* * *
20055548 AGCTTGCACATTTTTGCTGAGCTTGC
1 AGCTTGCACA-TCTCGCTAAGCTTGC
*
20055574 TGCTTGCACAT
1 AGCTTGCACAT
20055585 TGGAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.06
25 26 0.49
26 24 0.45
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTTGCACATCTCGCTAAGCTTGC
Found at i:20055571 original size:26 final size:26
Alignment explanation
Indices: 20055498--20055585 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 26
20055488 CTGAGCTCAT
* *
20055498 AGCTCGCAC-TTCTCGCTAAGCTTGC
1 AGCTTGCACATTCTTGCTAAGCTTGC
20055523 AGCTTTG-ACA-TCTTGCTAAGCTTGC
1 AGC-TTGCACATTCTTGCTAAGCTTGC
* *
20055548 AGCTTGCACATTTTTGCTGAGCTTGC
1 AGCTTGCACATTCTTGCTAAGCTTGC
*
20055574 TGCTTGCACATT
1 AGCTTGCACATT
20055586 GGAAAGCTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
24 3 0.06
25 25 0.46
26 26 0.48
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
AGCTTGCACATTCTTGCTAAGCTTGC
Found at i:20055738 original size:65 final size:65
Alignment explanation
Indices: 20055668--20055789 Score: 217
Period size: 65 Copynumber: 1.9 Consensus size: 65
20055658 GAGCTGATGC
*
20055668 TGTCTTTTCTACAAGTAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
1 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
**
20055733 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACATTTTCTTTCTT
1 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTT
20055790 TTTAACAAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (65 bp):
TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
Found at i:20056509 original size:4 final size:4
Alignment explanation
Indices: 20056502--20056538 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
20056492 CCTACATATA
20056502 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
20056539 GCGTGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:20058626 original size:34 final size:34
Alignment explanation
Indices: 20058579--20058653 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
20058569 TCGTTTTTAA
* * *
20058579 TAGGGTTAGGGTTTTGTTTATTGAAATTAGGATT
1 TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
* *
20058613 TAGGGTTAAGGTTTTATTTATTTAAAGTAGGGTT
1 TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
20058647 TAGGGTT
1 TAGGGTT
20058654 TTTTTAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (34 bp):
TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
Found at i:20061842 original size:25 final size:25
Alignment explanation
Indices: 20061746--20061871 Score: 64
Period size: 25 Copynumber: 5.1 Consensus size: 25
20061736 CATTAGGGAT
20061746 TACCGATT-ACAGCTCGT-ATGAGCA
1 TACCGATTCACAGCTCGTGA-GAGCA
* * * ***
20061770 TACTGATT-GCAGCTCGTGAAATTT
1 TACCGATTCACAGCTCGTGAGAGCA
* * * * *
20061794 TACAGATTCTCAACTCAT-ATGAGCT
1 TACCGATTCACAGCTCGTGA-GAGCA
*
20061819 TACCGATTTACAGCTCGTGAGAGCA
1 TACCGATTCACAGCTCGTGAGAGCA
* *
20061844 TATCGATTCATAGCTCGT-ATGAGCA
1 TACCGATTCACAGCTCGTGA-GAGCA
20061869 TAC
1 TAC
20061872 ATGTACAGGC
Statistics
Matches: 74, Mismatches: 23, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
24 25 0.34
25 48 0.65
26 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (25 bp):
TACCGATTCACAGCTCGTGAGAGCA
Found at i:20069174 original size:22 final size:22
Alignment explanation
Indices: 20069130--20069174 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20069120 GGTAATTTTT
*
20069130 CCAAAAATATGTTTTTGACTAA
1 CCAAAAATATGTTTTCGACTAA
*
20069152 CCAAAAATATGTTTTCGATTAA
1 CCAAAAATATGTTTTCGACTAA
20069174 C
1 C
20069175 TTGAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
CCAAAAATATGTTTTCGACTAA
Found at i:20069526 original size:25 final size:25
Alignment explanation
Indices: 20069498--20069625 Score: 104
Period size: 25 Copynumber: 5.2 Consensus size: 25
20069488 TAGCTGGTGA
*
20069498 GAGCTTACCGATTCTCAGCTCGTAT
1 GAGCTTATCGATTCTCAGCTCGTAT
* *
20069523 GAGCATATCGATT-GCAGCTCGTGA-
1 GAGCTTATCGATTCTCAGCTCGT-AT
* * *
20069547 GCGCTTATCAATACTCAGCTCGTAT
1 GAGCTTATCGATTCTCAGCTCGTAT
*
20069572 GAGCTTACCGATT-TACAGCTCGTGA-
1 GAGCTTATCGATTCT-CAGCTCGT-AT
* *
20069597 GAGCATATCGATTCAT-AGCTAGTAT
1 GAGCTTATCGATTC-TCAGCTCGTAT
20069622 GAGC
1 GAGC
20069626 ATACATGTAC
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
24 20 0.25
25 58 0.73
26 1 0.01
27 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
GAGCTTATCGATTCTCAGCTCGTAT
Found at i:20069564 original size:49 final size:49
Alignment explanation
Indices: 20069479--20069629 Score: 178
Period size: 49 Copynumber: 3.1 Consensus size: 49
20069469 CGTTAGGGAT
* * *
20069479 TACCGATTGTAGCTGGTGAGAGCTTACCGATTCTCAGCTCGTATGAGCA
1 TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA
* * * * *
20069528 TATCGATTGCAGCTCGTGAGCGCTTATCAATACTCAGCTCGTATGAGCT
1 TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA
* * *
20069577 TACCGATTTACAGCTCGTGAGAGCATATCGATTCAT-AGCTAGTATGAGCA
1 TACCGA-TTGCAGCTCGTGAGAGCTTATCGATTC-TCAGCTCGTATGAGCA
20069627 TAC
1 TAC
20069630 ATGTACAGGA
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
49 46 0.55
50 37 0.44
51 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (49 bp):
TACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCA
Found at i:20072863 original size:12 final size:12
Alignment explanation
Indices: 20072846--20072870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20072836 TATTTTTTGA
20072846 TATAACTGAGTT
1 TATAACTGAGTT
20072858 TATAACTGAGTT
1 TATAACTGAGTT
20072870 T
1 T
20072871 TTTTTAAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TATAACTGAGTT
Found at i:20074551 original size:76 final size:78
Alignment explanation
Indices: 20074397--20074572 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 78
20074387 ATATTATATA
* * * * *
20074397 AATTGAATTAAAGTTATGAATTTTATATATTTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* * *
20074462 GTATAAGTTCTTG
66 ATACAAGTACTTG
* * *
20074475 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
20074538 ATACAAGTACTTG
66 ATACAAGTACTTG
* *
20074551 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
20074573 GTAAATACTT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 44 0.52
77 2 0.02
78 38 0.45
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
ATACAAGTACTTG
Found at i:20076336 original size:22 final size:22
Alignment explanation
Indices: 20076311--20076356 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
20076301 TTCCTCCTCC
20076311 TTTTTTTATTGATTCTCTCCTT
1 TTTTTTTATTGATTCTCTCCTT
20076333 TTTTTTTATTGATTCTCTCCTT
1 TTTTTTTATTGATTCTCTCCTT
20076355 TT
1 TT
20076357 CTACAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTTTTATTGATTCTCTCCTT
Found at i:20076513 original size:21 final size:21
Alignment explanation
Indices: 20076487--20076640 Score: 126
Period size: 21 Copynumber: 7.4 Consensus size: 21
20076477 AATCATATCT
*
20076487 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
20076508 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
**
20076529 TCTAAGATTGCATATTAAAAGGTA
1 TCTAAGATTGCATA-TATCA--TA
*
20076553 TCTACAAATT--A-A-ATC-T-
1 TCTA-AGATTGCATATATCATA
* *
20076569 T-TAAGATTACA-AAATCATA
1 TCTAAGATTGCATATATCATA
*
20076588 TCTTCTAAGATTGTATATATCATA
1 ---TCTAAGATTGCATATATCATA
20076612 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
20076633 TCTAAGAT
1 TCTAAGAT
20076641 CTAAGATTGT
Statistics
Matches: 108, Mismatches: 11, Indels: 28
0.73 0.07 0.19
Matches are distributed among these distances:
14 4 0.04
15 2 0.02
16 3 0.03
17 4 0.04
18 1 0.01
20 1 0.01
21 62 0.57
22 5 0.05
23 9 0.08
24 13 0.12
25 4 0.04
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:20076618 original size:104 final size:104
Alignment explanation
Indices: 20076438--20076640 Score: 388
Period size: 104 Copynumber: 2.0 Consensus size: 104
20076428 AACGGCTAAG
*
20076438 ATTAAAGGGTATCTACAAATTAAATCTCTAAGATTACAAAATCATATCTTCTAAGATTGTATATA
1 ATTAAAAGGTATCTACAAATTAAATCTCTAAGATTACAAAATCATATCTTCTAAGATTGTATATA
20076503 TCATATCTAAGATTGCATATATCATATCTAAGATTGCAT
66 TCATATCTAAGATTGCATATATCATATCTAAGATTGCAT
*
20076542 ATTAAAAGGTATCTACAAATTAAATCTTTAAGATTACAAAATCATATCTTCTAAGATTGTATATA
1 ATTAAAAGGTATCTACAAATTAAATCTCTAAGATTACAAAATCATATCTTCTAAGATTGTATATA
20076607 TCATATCTAAGATTGCATATATCATATCTAAGAT
66 TCATATCTAAGATTGCATATATCATATCTAAGAT
20076641 CTAAGATTGT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (104 bp):
ATTAAAAGGTATCTACAAATTAAATCTCTAAGATTACAAAATCATATCTTCTAAGATTGTATATA
TCATATCTAAGATTGCATATATCATATCTAAGATTGCAT
Found at i:20076918 original size:44 final size:44
Alignment explanation
Indices: 20076859--20076943 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
20076849 AGGAATTCGT
*
20076859 GCTTCAATCTACTCCACTGTAACTTCAGG-GAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAGGAG-GATAAGACTTATA
* * *
20076903 GCTTTAATCTGCTCCACTGCCACTTCAGGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTT
20076944 GCTGGCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTTATA
Found at i:20077091 original size:132 final size:132
Alignment explanation
Indices: 20076941--20077470 Score: 871
Period size: 132 Copynumber: 4.0 Consensus size: 132
20076931 GAGGATAAGA
* * *
20076941 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
20077006 TACTACTGCCTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
*
20077071 TG
131 GG
* *
20077073 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* * *
20077138 CACTATTGCTTAGGGAGATAAGATCTACAATCTTCAAGCTACTCCGCAGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
20077203 GG
131 GG
*
20077205 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTA
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
*
20077270 CACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
20077335 GG
131 GG
*
20077337 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
** * * * * *
20077402 CACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTTAGGGAGATAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
20077467 GG
131 GG
20077469 CT
1 CT
20077471 GGAGTCTTTG
Statistics
Matches: 374, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 374 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:20077421 original size:44 final size:44
Alignment explanation
Indices: 20077109--20077467 Score: 119
Period size: 44 Copynumber: 8.2 Consensus size: 44
20077099 TATCTTGGAA
* * * *
20077109 AGATAAGATTTGTCATCTTTGATCTGCTCCACTATTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
20077153 AGATAAGATCTACAATCTTCAAGCTACTCCGC-AGCTGCTCAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTA-CTGCTTAGGG
* ** * * * *
20077197 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
20077241 AGATAAGATTTGCCGTCTTTGATCTGCTACACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * *
20077285 AGATAAGATCTACAATT-TTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGC-CTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
20077329 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
20077373 AGATAAGATTTGCCTTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
20077417 AGATAAGATCTGTAATT-TTAAACCTACTCCACTGCTGCTTAGGG
1 AGATAAGATTTG-CCTTCTTTAATCTGCTCCACTACTGCTTAGGG
20077461 AGATAAG
1 AGATAAG
20077468 GCTGGAGTCT
Statistics
Matches: 217, Mismatches: 77, Indels: 42
0.65 0.23 0.12
Matches are distributed among these distances:
42 12 0.06
43 9 0.04
44 176 0.81
45 12 0.06
46 7 0.03
47 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:20077513 original size:88 final size:87
Alignment explanation
Indices: 20077421--20077698 Score: 360
Period size: 88 Copynumber: 3.1 Consensus size: 87
20077411 TTAGGGAGAT
* * ** ** ** *
20077421 AAGATCTGTAATTTTAAACCTACTCCACTGCTGCTTAGGGAGATAAGGCTGGA-GTCTTTGATCT
1 AAGATCTGT-ATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCT-GATGTCTTCGATCT
*
20077485 GCTTCGCTGTCGGTGTAGGAAGGC
64 GCTTCGCTGTCGGTGCAGGAAGGC
*
20077509 AAGATCTGCTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTA
1 AAGATCTG-TATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
**
20077574 CTTCGCCATCGGTGCAGGAAGGC
65 CTTCGCTGTCGGTGCAGGAAGGC
* * *
20077597 AAGATCTTCTATTTTTAACCTGCTCCGCTACAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
1 AAGATC-TGTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTG
20077662 CTTCGCTGTCGGTGCAGGAAGGC
65 CTTCGCTGTCGGTGCAGGAAGGC
20077685 AAGATCTGCTATTT
1 AAGATCTG-TATTT
20077699 CACTAATCTG
Statistics
Matches: 166, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
87 3 0.02
88 161 0.97
89 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (87 bp):
AAGATCTGTATTTTTAACCTACTCCGCTGCAACACAGGGAGGCAAGGCTGATGTCTTCGATCTGC
TTCGCTGTCGGTGCAGGAAGGC
Found at i:20077555 original size:44 final size:43
Alignment explanation
Indices: 20077505--20077643 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 43
20077495 CGGTGTAGGA
20077505 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACACAGGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCT-CAACACAGGG
* * * * ** * * * * *
20077549 AGGCAAG-GCTGATGTCTTCGATCTACTTCGC-CATCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTCAAC---ACAGGG
* *
20077593 AGGCAAGATCTTCTATTTTTAACCTGCTCCGCTACAACACAGGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCT-CAACACAGGG
20077637 AGGCAAG
1 AGGCAAG
20077644 GCTGATGTCT
Statistics
Matches: 65, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
41 3 0.05
43 16 0.25
44 29 0.45
45 14 0.22
47 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (43 bp):
AGGCAAGATCTGCTATTTTTAACCTACTCCGCTCAACACAGGG
Found at i:20079420 original size:63 final size:63
Alignment explanation
Indices: 20079321--20079445 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
20079311 TGGTCAAAAT
* *
20079321 TTGAACTGCTCTGATCACCTCTGCCCCATTCTAATCAATATTTGAGCCGCCCTTTTCGGGTTG
1 TTGAACTGCTCTGATCACCTCTACCCCATTCTAATCAATATTTGAGCCGCCCTTTGCGGGTTG
20079384 TTGAACTGCTCTGATCACCTCTACCCCATTCTAATCAATATTTGAGCCGCCCTTTGCGGGTT
1 TTGAACTGCTCTGATCACCTCTACCCCATTCTAATCAATATTTGAGCCGCCCTTTGCGGGTT
20079446 TTCACCTCGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.34
Consensus pattern (63 bp):
TTGAACTGCTCTGATCACCTCTACCCCATTCTAATCAATATTTGAGCCGCCCTTTGCGGGTTG
Found at i:20090826 original size:22 final size:24
Alignment explanation
Indices: 20090804--20090863 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 24
20090794 CAAATCGTTC
20090804 TCTTTT-TT-ATTC-CT-CTTTTT
1 TCTTTTATTGATTCTCTCCTTTTT
20090824 TCTTTTATTGATTCTCTCC---TT
1 TCTTTTATTGATTCTCTCCTTTTT
20090845 T-TTTTATTGATTCTCTCCT
1 TCTTTTATTGATTCTCTCCT
20090864 CTCCTACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 23 0.66
21 5 0.14
22 4 0.11
23 2 0.06
24 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.03, T:0.67
Consensus pattern (24 bp):
TCTTTTATTGATTCTCTCCTTTTT
Found at i:20090851 original size:20 final size:20
Alignment explanation
Indices: 20090826--20090863 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20090816 CTCTTTTTTC
20090826 TTTTATTGATTCTCTCCTTT
1 TTTTATTGATTCTCTCCTTT
20090846 TTTTATTGATTCTCTCCT
1 TTTTATTGATTCTCTCCT
20090864 CTCCTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATTGATTCTCTCCTTT
Found at i:20091023 original size:21 final size:21
Alignment explanation
Indices: 20090997--20091072 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
20090987 AATCATATCT
*
20090997 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
20091018 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
20091039 CCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
20091058 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
20091073 CCTCGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.31
21 35 0.69
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:20091032 original size:19 final size:19
Alignment explanation
Indices: 20091010--20091073 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
20091000 AAGATTGTAT
20091010 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
*
20091029 ATATATCATACCTAAGATTGC
1 --ATATCATATCTAAGATTGC
* *
20091050 ATATAATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
20091069 ATATC
1 ATATC
20091074 CTCGAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
21 18 0.47
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:20091429 original size:66 final size:66
Alignment explanation
Indices: 20091344--20091575 Score: 308
Period size: 66 Copynumber: 3.5 Consensus size: 66
20091334 ATTTATATCT
* * * * * *
20091344 TATTTGATAAGTATTTATATGCATTCAGTTATATACCTTTGAAGTGTATATGCTTTCAATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
20091409 G
66 G
20091410 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
20091475 G
66 G
* * *
20091476 TATTTGATAGG--TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGGTTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
20091539 G
66 G
* * * * *
20091540 TAGTTGAT-GAGTAGATACATACATTTGGTTATATAC
1 TATTTGATAG-GTATATATATGCATTCGGTTATATAC
20091576 ATTCGATGGG
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
63 1 0.01
64 58 0.39
66 89 0.60
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.44
Consensus pattern (66 bp):
TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
G
Found at i:20091547 original size:31 final size:30
Alignment explanation
Indices: 20091359--20091548 Score: 141
Period size: 31 Copynumber: 5.9 Consensus size: 30
20091349 GATAAGTATT
* *
20091359 TATATGCATTCAGTTAT-ATACCTTTGAAGTG
1 TATATGCATTCGGTTATAATA--TTTGATGTG
* ** *
20091390 TATATGCTTTCAATTATAAGTATTTGATAGGTATA
1 TATATGCATTCGGTTATAA-TATTTGAT--G--TG
20091425 TATATGCATTCGGTTAT-ATACCTTTGATGTG
1 TATATGCATTCGGTTATAATA--TTTGATGTG
* *
20091456 TATATGCATTCGATTATAAGTATTTGATAGGTA
1 TATATGCATTCGGTTATAA-TATTTGAT--GTG
* *
20091489 TATATGCATTCGGTTGTATACATTTGATGTG
1 TATATGCATTCGGTTATA-ATATTTGATGTG
*
20091520 TATATGCATTCGGTTATAAGTAGTTGATG
1 TATATGCATTCGGTTATAA-TATTTGATG
20091549 AGTAGATACA
Statistics
Matches: 128, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
30 1 0.01
31 69 0.54
32 2 0.02
33 33 0.26
34 2 0.02
35 21 0.16
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (30 bp):
TATATGCATTCGGTTATAATATTTGATGTG
Found at i:20096978 original size:18 final size:19
Alignment explanation
Indices: 20096941--20096979 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20096931 ATTACAAAAT
*
20096941 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
20096960 AATTCAGAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
20096978 AA
1 AA
20096980 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:20099858 original size:4 final size:4
Alignment explanation
Indices: 20099849--20099889 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
20099839 ACCAAATCTT
20099849 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
20099890 CACCAAGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:20101118 original size:11 final size:11
Alignment explanation
Indices: 20101095--20101124 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
20101085 AACTAATCCT
20101095 CTCTCATATTTC
1 CTCTCA-ATTTC
20101107 CTCTCAATTTC
1 CTCTCAATTTC
20101118 CTCTCAA
1 CTCTCAA
20101125 AATTCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:20102489 original size:7 final size:7
Alignment explanation
Indices: 20102479--20102503 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20102469 ATTCGATTGA
20102479 TATTTAG
1 TATTTAG
20102486 TATTTAG
1 TATTTAG
20102493 TATTTAG
1 TATTTAG
20102500 TATT
1 TATT
20102504 NNNNNNNNNN
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20103172 original size:18 final size:18
Alignment explanation
Indices: 20103145--20103184 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
20103135 CAGGTGCGTT
*
20103145 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
20103163 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
20103181 TCCT
1 TCCT
20103185 TTTCTGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:20103651 original size:28 final size:28
Alignment explanation
Indices: 20103613--20103688 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 28
20103603 TATTTTGATA
20103613 TTATTTGATGTAATAAAATAGAAGTAAGT
1 TTATTTGATGTAATAAAATAGAAG-AAGT
20103642 TTATTT-ATGTAATAAAAT---AGAAGT
1 TTATTTGATGTAATAAAATAGAAGAAGT
*
20103666 TTATTTGATGCAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
20103689 ATTTTTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
24 10 0.24
25 13 0.31
28 13 0.31
29 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.14, T:0.38
Consensus pattern (28 bp):
TTATTTGATGTAATAAAATAGAAGAAGT
Found at i:20103775 original size:23 final size:23
Alignment explanation
Indices: 20103749--20104072 Score: 286
Period size: 23 Copynumber: 14.6 Consensus size: 23
20103739 ATTAATACCC
20103749 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
20103772 TTAAATTAAAAACCCTAACTTAA
1 TTAACTTAAAAACCCTAACCTAA
*
20103795 TTTAA-TTAAAAACCTTAACCTAA
1 -TTAACTTAAAAACCCTAACCTAA
*
20103818 TTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
20103841 TTTAA-TTAAAAACCCTAACC--C
1 -TTAACTTAAAAACCCTAACCTAA
*
20103862 TTAACCCT-AAAACCCTAACCTAA
1 TTAA-CTTAAAAACCCTAACCTAA
* *
20103885 TTAAATTAAAAAACCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
20103908 TTTAA-TTAAAAACCCTAACCCT--
1 -TTAACTTAAAAACCCTAA-CCTAA
* * *
20103930 TCACCCT-AAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* **
20103952 TTAAATTAAAAACCCTAACC-CG
1 TTAACTTAAAAACCCTAACCTAA
* *
20103974 TT-ACTTAAAAACCCT-AGC-AC
1 TTAACTTAAAAACCCTAACCTAA
***
20103994 TTAACTTAAAAACCCTAACCCCC
1 TTAACTTAAAAACCCTAACCTAA
*
20104017 TTAACTTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
20104038 TTAACTTAAAAACCCTAAACC--C
1 TTAACTTAAAAACCCT-AACCTAA
20104060 TTAACTTAAAAAC
1 TTAACTTAAAAAC
20104073 TCTTACCCTT
Statistics
Matches: 256, Mismatches: 27, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
20 11 0.04
21 66 0.26
22 32 0.12
23 132 0.52
24 15 0.06
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (23 bp):
TTAACTTAAAAACCCTAACCTAA
Found at i:20103814 original size:46 final size:46
Alignment explanation
Indices: 20103749--20104055 Score: 280
Period size: 44 Copynumber: 6.9 Consensus size: 46
20103739 ATTAATACCC
*
20103749 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACTTAAT
1 TTAA-TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
*
20103796 TTAATTAAAAACCTTAACCTAATTAAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
* **
20103842 TTAATTAAAAACCCTAACC--CTTAACCCT-AAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAATTAA-ATTAAAAACCCTAACCTAAT
* * * *
20103886 TAAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAACC--CT
1 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
* ** **
20103930 TCACCCT-AAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CG
1 TTA-ATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
* * * * ***
20103974 TTACTTAAAAACCCT-AGC-ACTTAACTTAAAAACCCTAACC-CCC
1 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
* *
20104017 TTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA
1 TTAA-TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
20104056 ACCCTTAACT
Statistics
Matches: 224, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
42 20 0.09
43 8 0.04
44 114 0.51
45 5 0.02
46 73 0.33
47 4 0.02
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (46 bp):
TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
Found at i:20103907 original size:67 final size:68
Alignment explanation
Indices: 20103749--20104072 Score: 346
Period size: 67 Copynumber: 4.9 Consensus size: 68
20103739 ATTAATACCC
* * *** *
20103749 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA--CTTAATTTAATTAAAAACCTTA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAA---CCCTAAAAACCCTA
20103812 ACCTAA
63 ACCTAA
20103818 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACCCT-AAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAAACCCTAACC
20103882 TAA
66 TAA
* *
20103885 TTAAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAACCCTTCACCCT-AAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAAACCCTAACC
20103949 TAA
66 TAA
** * * * *
20103952 TTAAATTAAAAACCCTAACC--CGTTACTTAAAAACCCTAGCACTTAA-CTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAAACCCTAACC
***
20104014 CCC
66 TAA
* * *
20104017 TTAACTTAAAAACCCTAACC---CTTAACTTAAAAACCCTAAACCCTTAA-CTTAAAAAC
1 TTAAATTAAAAACCCTAACCTAATTTAA-TTAAAAACCCT-AACCCTTAACCCTAAAAAC
20104073 TCTTACCCTT
Statistics
Matches: 226, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
64 5 0.02
65 62 0.27
66 16 0.07
67 98 0.43
68 1 0.00
69 39 0.17
71 5 0.02
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (68 bp):
TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAAACCCTAACC
TAA
Found at i:20103964 original size:90 final size:91
Alignment explanation
Indices: 20103755--20104055 Score: 268
Period size: 90 Copynumber: 3.4 Consensus size: 91
20103745 ACCCTTAACT
* *
20103755 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACTTAATTTAATTAAAAACCTTAACCTAATT
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACCTAATT
* *
20103820 AAATTAAAAACCCTAACCTAATTTAAT
66 AAATTAAAAACCCTAACC-AATTCAAC
* **
20103847 TAAAAACCCTAACC--CTTAACCCT-AAAACCCTAACCTAATTAAATTAAAAAACC-TAACCTAA
1 TAAAAACCCTAACCTAATTAA-ATTAAAAACCCTAACCTAATTAAATT-AAAAACCTTAACCTAA
* * *
20103908 TTTAATTAAAAACCCTAACC-CTTCACCC
64 TTAAATTAAAAACCCTAACCAATTCA-AC
** * * * *
20103936 T-AAAACCCTAACCTAATTAAATTAAAAACCCTAACC-CGTT-ACTTAAAAACCCT-AGC-ACTT
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACCTAATT
* **
20103996 AACTTAAAAACCCTAACCCCCTT-AAC
66 AAATTAAAAACCCTAA-CCAATTCAAC
* *
20104022 TTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA
1 -TAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
20104056 ACCCTTAACT
Statistics
Matches: 175, Mismatches: 23, Indels: 28
0.77 0.10 0.12
Matches are distributed among these distances:
86 35 0.20
87 13 0.07
88 34 0.19
89 4 0.02
90 67 0.38
91 8 0.05
92 14 0.08
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (91 bp):
TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACCTAATT
AAATTAAAAACCCTAACCAATTCAAC
Found at i:20104091 original size:44 final size:42
Alignment explanation
Indices: 20103909--20104100 Score: 176
Period size: 43 Copynumber: 4.5 Consensus size: 42
20103899 CTAACCTAAT
* * * * *
20103909 TTAA-TTAAAAACCCT-AACCCTTCACCCTAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAAACCCTT-AACTTAAAAACCTTACC--C
* * *
20103952 TTAAATTAAAAACCCT-AACCCGTT-ACTTAAAAACCCTAGCAC
1 TTAACTTAAAAACCCTAAACCC-TTAACTTAAAAACCTTA-CCC
* *
20103994 TTAACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTAACCC
1 TTAACTTAAAAACCCTAA-ACCCTTAACTTAAAAA-CCTTACCC
20104038 TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACTCTTACCC
1 TTAACTTAAAAACCCTAAACCCTTAACTTAAAAAC-CTTACCC
* *
20104081 TTAACTTTAAAACCTTAAAC
1 TTAACTTAAAAACCCTAAAC
20104101 TAAGTTAATA
Statistics
Matches: 125, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
42 16 0.13
43 55 0.44
44 49 0.39
45 5 0.04
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (42 bp):
TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCTTACCC
Found at i:20104346 original size:115 final size:116
Alignment explanation
Indices: 20104105--20104346 Score: 382
Period size: 115 Copynumber: 2.1 Consensus size: 116
20104095 TTAAACTAAG
**
20104105 TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAATTA
1 TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAATTA
*
20104170 ATAACCCTAACCTAATTTGATAATTTTACTAACCATTAATACAATTTATCAC
66 ATAACCCTAA-CTAATTTGATAATTTTACTAACCATTAATACAATTTATCAA
20104222 TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATG-TTTTGACTGGTACTAACAATTA
1 TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAATTA
***
20104286 ATAATTTTATA-TAATTTGA-AATTTTTACTAACCATTAATACAATTTATCAA
66 ATAACCCTA-ACTAATTTGATAA-TTTTACTAACCATTAATACAATTTATCAA
20104337 TTAATAATTT
1 TTAATAATTT
20104347 CACAAACTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
114 2 0.02
115 46 0.39
116 26 0.22
117 43 0.37
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (116 bp):
TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAATTA
ATAACCCTAACTAATTTGATAATTTTACTAACCATTAATACAATTTATCAA
Found at i:20111883 original size:32 final size:32
Alignment explanation
Indices: 20111847--20111912 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
20111837 GCTTCTAATC
20111847 CACATGTACCAATTTCGTACAAGTATATTCAA
1 CACATGTACCAATTTCGTACAAGTATATTCAA
** *
20111879 CACATGTGTCGATTTCGTACAAGTATATTCAA
1 CACATGTACCAATTTCGTACAAGTATATTCAA
20111911 CA
1 CA
20111913 ATTTTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (32 bp):
CACATGTACCAATTTCGTACAAGTATATTCAA
Found at i:20112140 original size:41 final size:41
Alignment explanation
Indices: 20112079--20112229 Score: 160
Period size: 41 Copynumber: 3.7 Consensus size: 41
20112069 CATAATTTAA
* *
20112079 CATATTCACCGGCACTTAGCCTGCTTGGCTTATAGCCTGATT
1 CATA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
20112121 CATATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
** ** ** **
20112162 CCGATCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAA
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
20112203 AAT-TCACCGGCATTTAGCCTGCTAGGC
1 CATATCACCGGCACTTAGCCTGCTAGGC
20112230 GCTTAGCCTG
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 21 0.23
41 66 0.73
42 4 0.04
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
CATATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:20112241 original size:40 final size:40
Alignment explanation
Indices: 20112082--20112248 Score: 108
Period size: 41 Copynumber: 4.1 Consensus size: 40
20112072 AATTTAACAT
* ***
20112082 ATTCACCGGCACTTAGCCTGCTTG-GCTTATAGCCTGATTC
1 ATTCACCGGCACTTAGCCTGCTAGAGC-TATAGCCTGAAAA
* * * ***
20112122 ATATCACCGGCACGTAGCCTGCTAG-GTTTATAACCTGATTCCG
1 AT-TCACCGGCACTTAGCCTGCTAGAG-CTATAGCCTGA--AAA
** *
20112165 A-TCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
* *
20112204 ATTCACCGGCATTTAGCCTGCTAGGCGCT-TAGCCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTA-GAGCTATAGCCTGAAAA
*
20112244 TTTCA
1 ATTCA
20112249 ATTTCACAGA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
39 1 0.01
40 36 0.36
41 62 0.62
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (40 bp):
ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
Found at i:20118612 original size:22 final size:23
Alignment explanation
Indices: 20118587--20118630 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20118577 CTTAGTTTAG
* *
20118587 TTAAATGATTTCTAA-TATGTTT
1 TTAAATGAATTCAAATTATGTTT
20118609 TTAAATGAATTCAAATTATGTT
1 TTAAATGAATTCAAATTATGTT
20118631 AGCACCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (23 bp):
TTAAATGAATTCAAATTATGTTT
Found at i:20130444 original size:43 final size:43
Alignment explanation
Indices: 20130373--20130464 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
20130363 AAACTTAAAG
*
20130373 TTATACCTTGTCTTATTACTATTATTAATAATTGACATCATCT
1 TTATCCCTTGTCTTATTACTATTATTAATAATTGACATCATCT
*
20130416 TTATCCCTTTTCTTATTACTATTATTAATAATTGACATCATCT
1 TTATCCCTTGTCTTATTACTATTATTAATAATTGACATCATCT
20130459 TTATCC
1 TTATCC
20130465 GGTAGTCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.03, T:0.50
Consensus pattern (43 bp):
TTATCCCTTGTCTTATTACTATTATTAATAATTGACATCATCT
Found at i:20145476 original size:54 final size:55
Alignment explanation
Indices: 20145407--20145786 Score: 371
Period size: 54 Copynumber: 7.0 Consensus size: 55
20145397 TAATAAACGG
* * ** * * *
20145407 TTCTACTTTCAAGATTTTATGAATCTCACGA-TTTGCTAATTTATGATCATGACT
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * * *
20145461 TTCTACTTTCGAGATTTTACGAATCTCGC-AGTTCGTTGATTTACGATCATGACA
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * * * **
20145515 TTC-AGCTTTTGAGATTTTACGAATTTCA-TAGTCCGTTGATTTACGATCACCACC
1 TTCTA-CTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * *
20145569 TTCTACTTTCGAGATTTTACGAATCTTATG-GTCCGCTGATTTATGATCATGACC
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * ** * *
20145623 TTCCACTTTCGAGATTTTACGAATTTCAC-AGTTTGCTGATTTACAATCATGAAC
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * * * * *
20145677 TTCTACTTTCGAGATTTTACGATTCTCATG-GTCTGCTGAATTACTATCACGACC
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
* * * *
20145731 TTCTACTTTCGAGATTTTATGAATCTCACG-GTCCACTGATTGACGATCACGACC
1 TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
20145785 TT
1 TT
20145787 TGTAACAACT
Statistics
Matches: 270, Mismatches: 49, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
53 2 0.01
54 267 0.99
55 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (55 bp):
TTCTACTTTCGAGATTTTACGAATCTCACGAGTCCGCTGATTTACGATCATGACC
Found at i:20145674 original size:162 final size:162
Alignment explanation
Indices: 20145407--20145786 Score: 478
Period size: 162 Copynumber: 2.3 Consensus size: 162
20145397 TAATAAACGG
* * ** * * *
20145407 TTCTACTTTCAAGATTTTATGAATCTCACGATTTGCTAATTTATGATCATGACTTTCTACTTTCG
1 TTCTACTTTCGAGATTTTATGAATCTCACGGTCCGCTGATTTATGATCATGACCTTCCACTTTCG
* * * *
20145472 AGATTTTACGAATCTCGCAGTTCGTTGATTTACGATCATG-ACATTC-AGCTTTTGAGATTTTAC
66 AGATTTTACGAATCTCACAGTTCGCTGATTTACAATCATGAAC-TTCTA-CTTTCGAGATTTTAC
* *
20145535 GAATT-TCATAGTCCGTTGATTTACGATCACCACC
129 G-ATTCTCATAGTCCGCTGAATTACGATCACCACC
* * *
20145569 TTCTACTTTCGAGATTTTACGAATCTTATGGTCCGCTGATTTATGATCATGACCTTCCACTTTCG
1 TTCTACTTTCGAGATTTTATGAATCTCACGGTCCGCTGATTTATGATCATGACCTTCCACTTTCG
* *
20145634 AGATTTTACGAATTTCACAGTTTGCTGATTTACAATCATGAACTTCTACTTTCGAGATTTTACGA
66 AGATTTTACGAATCTCACAGTTCGCTGATTTACAATCATGAACTTCTACTTTCGAGATTTTACGA
* * * *
20145699 TTCTCATGGTCTGCTGAATTACTATCACGACC
131 TTCTCATAGTCCGCTGAATTACGATCACCACC
* * * *
20145731 TTCTACTTTCGAGATTTTATGAATCTCACGGTCCACTGATTGACGATCACGACCTT
1 TTCTACTTTCGAGATTTTATGAATCTCACGGTCCGCTGATTTATGATCATGACCTT
20145787 TGTAACAACT
Statistics
Matches: 186, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
161 3 0.02
162 180 0.97
163 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (162 bp):
TTCTACTTTCGAGATTTTATGAATCTCACGGTCCGCTGATTTATGATCATGACCTTCCACTTTCG
AGATTTTACGAATCTCACAGTTCGCTGATTTACAATCATGAACTTCTACTTTCGAGATTTTACGA
TTCTCATAGTCCGCTGAATTACGATCACCACC
Found at i:20147511 original size:25 final size:25
Alignment explanation
Indices: 20147483--20147532 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20147473 CAGTTAAAGC
*
20147483 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
* * *
20147508 TCCTTTTTCTTCTTTCATTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
20147533 CTTCTCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.06, C:0.34, G:0.02, T:0.58
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCATTCTTCAT
Found at i:20151108 original size:16 final size:16
Alignment explanation
Indices: 20151079--20151130 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 16
20151069 CAATATATGA
*
20151079 AAAAATTTA-AAATAT
1 AAAAATTTATTAATAT
20151094 AAAAATTTATTAATATGT
1 AAAAATTTATTAATA--T
20151112 ATATAAATTTATTAATAT
1 A-A-AAATTTATTAATAT
20151130 A
1 A
20151131 TGTAAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
18 4 0.13
19 1 0.03
20 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AAAAATTTATTAATAT
Found at i:20151134 original size:22 final size:20
Alignment explanation
Indices: 20151091--20151129 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20151081 AAATTTAAAA
20151091 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
20151111 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
20151130 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:20151294 original size:20 final size:20
Alignment explanation
Indices: 20151236--20151287 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
20151226 CAATTTTCAA
20151236 TAAATCATTTTCCAGAAAAG
1 TAAATCATTTTCCAGAAAAG
*
20151256 TAAATCATTTTCCAAAAAAG
1 TAAATCATTTTCCAGAAAAG
*
20151276 TAAATGATTTTC
1 TAAATCATTTTC
20151288 TGGAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAG
Found at i:20151740 original size:21 final size:22
Alignment explanation
Indices: 20151688--20151740 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
20151678 ACAACTGTTT
*
20151688 CTAATCTCA-CTGCTACAGTAT
1 CTAATCTCACCTGCTACAGTAA
*
20151709 CCAATCTCACCT-CTACAGTAA
1 CTAATCTCACCTGCTACAGTAA
20151730 CTAATCTCACC
1 CTAATCTCACC
20151741 GCCACCGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.28
Consensus pattern (22 bp):
CTAATCTCACCTGCTACAGTAA
Found at i:20155955 original size:45 final size:44
Alignment explanation
Indices: 20155904--20156018 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 44
20155894 ATACCAGAAA
* *
20155904 CGAGTAAGACCGTAGCTACAAGACGTTATAGCATTACG-ATTCTAT
1 CGAGTAAGACCATAGCTA-AAGACGTTATAGCA-TAAGAATTCTAT
* * *
20155949 CGAGTAAGACCATAGCTAAAAGACATTATGGCATAAGAATTTTAT
1 CGAGTAAGACCATAGCT-AAAGACGTTATAGCATAAGAATTCTAT
*
20155994 CAAGTAAGACCATAGCTGAAAGACG
1 CGAGTAAGACCATAGCT-AAAGACG
20156019 CTATGACATC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 3 0.05
45 56 0.93
46 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (44 bp):
CGAGTAAGACCATAGCTAAAGACGTTATAGCATAAGAATTCTAT
Found at i:20156098 original size:46 final size:46
Alignment explanation
Indices: 20156040--20156254 Score: 290
Period size: 46 Copynumber: 4.7 Consensus size: 46
20156030 CTAATCAAAC
20156040 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* * *
20156086 GAATAAGACCATATTTGAAAGACACTATGGCAACATGAAGAAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* *
20156132 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGGAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* * * * * *
20156178 GAATAAGGA-TATGGTTGAAAGACACTATGGCATCAAGTCG-AGAAT
1 GAATAA-GACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* *
20156223 GAATAAGACCATGGTTGAAAGACACCATGGCA
1 GAATAAGACCATAGTTGAAAGACACTATGGCA
20156255 CCCTTCGATC
Statistics
Matches: 151, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
44 2 0.01
45 31 0.21
46 116 0.77
47 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (46 bp):
GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
Found at i:20156160 original size:137 final size:136
Alignment explanation
Indices: 20155998--20156254 Score: 320
Period size: 137 Copynumber: 1.9 Consensus size: 136
20155988 TTTTATCAAG
* * *
20155998 TAAGACCATAGCTGAAAGACGCTATGACATCACTAAT-CAAACGAATAA-GACCATAGTTGAAAG
1 TAAGACCATAGCTGAAAGACACTATGACAACAC-AATGAAAACGAATAAGGA-CATAGTTGAAAG
* * *
20156061 ACACTATGGCAACACGACGAAAAATGAATAAGACCATATTTGAAAGACACTATGGCAACATGAAG
64 ACACTATGGCAACAAGACG-AAAATGAATAAGACCATAGTTGAAAGACACCATGGCAACATGAAG
20156126 AAAAATGAA
128 AAAAATGAA
* * * * * *
20156135 TAAGACCATAGTTGAAAGACACTATGGCAACACGATGGAAAATGAATAAGGATATGGTTGAAAGA
1 TAAGACCATAGCTGAAAGACACTATGACAACACAAT-GAAAACGAATAAGGACATAGTTGAAAGA
* * * *
20156200 CACTATGGCATCAAGTCGAGAATGAATAAGACCATGGTTGAAAGACACCATGGCA
65 CACTATGGCAACAAGACGAAAATGAATAAGACCATAGTTGAAAGACACCATGGCA
20156255 CCCTTCGATC
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
136 2 0.02
137 62 0.61
138 35 0.35
139 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (136 bp):
TAAGACCATAGCTGAAAGACACTATGACAACACAATGAAAACGAATAAGGACATAGTTGAAAGAC
ACTATGGCAACAAGACGAAAATGAATAAGACCATAGTTGAAAGACACCATGGCAACATGAAGAAA
AATGAA
Found at i:20159530 original size:20 final size:20
Alignment explanation
Indices: 20159499--20159554 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
20159489 GCATCATAAA
20159499 TGCATAACAGGGGCATCAAA-G
1 TGCA-AACAGGGGCA-CAAATG
* *
20159520 TGTAGACAGGGGCACAAATG
1 TGCAAACAGGGGCACAAATG
20159540 TGCAAACAGGGGCAC
1 TGCAAACAGGGGCAC
20159555 CGTAGTGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (20 bp):
TGCAAACAGGGGCACAAATG
Found at i:20159562 original size:20 final size:20
Alignment explanation
Indices: 20159539--20159626 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
20159529 GGGCACAAAT
* *
20159539 GTGCAAACAGGGGCACCGTA
1 GTGCAAATAGGGGCACCGAA
* * * *
20159559 GTGCGAATAGAGACACTGAA
1 GTGCAAATAGGGGCACCGAA
* * *
20159579 GTGTATATAGGGGCACTGAA
1 GTGCAAATAGGGGCACCGAA
20159599 GTGCAAATAGGGGCACCGAA
1 GTGCAAATAGGGGCACCGAA
20159619 GTGCAAAT
1 GTGCAAAT
20159627 CCTGTACAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (20 bp):
GTGCAAATAGGGGCACCGAA
Found at i:20165536 original size:15 final size:16
Alignment explanation
Indices: 20165516--20165545 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20165506 TAACAACTAG
20165516 TATATAAT-TATATTT
1 TATATAATATATATTT
20165531 TATATAATATATATT
1 TATATAATATATATT
20165546 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:20174004 original size:847 final size:847
Alignment explanation
Indices: 20172370--20174061 Score: 3294
Period size: 847 Copynumber: 2.0 Consensus size: 847
20172360 CGCAAGGAAC
20172370 CTTGCCGAGCGATACTGAGAATCTAAGAAATTTGGGTAAAGAACATATCAAGGTAGTGGCATTAC
1 CTTGCCGAGCGATACTGAGAATCTAAGAAATTTGGGTAAAGAACATATCAAGGTAGTGGCATTAC
20172435 GAGGTGGTAAAATTCTAGAACCCTGATTGATTGATGTCAAAGATAAACCTGTTGAGAAGAATCAA
66 GAGGTGGTAAAATTCTAGAACCCTGATTGATTGATGTCAAAGATAAACCTGTTGAGAAGAATCAA
20172500 CCAGCTGTTGAAGTTTCTACACTAAAGGAATCAAAATCTGCAAAGTCTGACTACGTAAACCCTGA
131 CCAGCTGTTGAAGTTTCTACACTAAAGGAATCAAAATCTGCAAAGTCTGACTACGTAAACCCTGA
20172565 CTTAGTGAATTCAAATATTTTAACATCTTCTTTGAATGTAGATTTACCTACTCAGAAAAGTTATC
196 CTTAGTGAATTCAAATATTTTAACATCTTCTTTGAATGTAGATTTACCTACTCAGAAAAGTTATC
20172630 CGGTTCAACTGAAATTTCCATCACCTCCATATCTGGAAAGATTGCAGCATAACAAGTAGAAACAG
261 CGGTTCAACTGAAATTTCCATCACCTCCATATCTGGAAAGATTGCAGCATAACAAGTAGAAACAG
20172695 GAGGTGCAATTCAAGAATTTTTTGGATGTTTTGAAGCAGTTACACATCAATATTCCATTGGTGGA
326 GAGGTGCAATTCAAGAATTTTTTGGATGTTTTGAAGCAGTTACACATCAATATTCCATTGGTGGA
20172760 GGCTTTAGAAAAATGTCGAATTATGTGAAGTTTATGAAGGATATACTGTCCAATTAAAAACGGCT
391 GGCTTTAGAAAAATGTCGAATTATGTGAAGTTTATGAAGGATATACTGTCCAATTAAAAACGGCT
20172825 AAGTGAGTATGAGACTATTGCCTTGACAAATGAGTGCATTGCGTTTCTGCAGAACAAATTGCCAC
456 AAGTGAGTATGAGACTATTGCCTTGACAAATGAGTGCATTGCGTTTCTGCAGAACAAATTGCCAC
20172890 CGAAATTGAAAGACTCATGAAGCTTTACTATACCTTGTAACATTGGTGAATCTTACTATGGTAAA
521 CGAAATTGAAAGACTCATGAAGCTTTACTATACCTTGTAACATTGGTGAATCTTACTATGGTAAA
20172955 GCTTTGTGTGACTTAGGAACGAGTATCAACTTGATGCCTAAGTCTATTTTGAAGATGTTAGGGAT
586 GCTTTGTGTGACTTAGGAACGAGTATCAACTTGATGCCTAAGTCTATTTTGAAGATGTTAGGGAT
20173020 AGGTGAAGTAAGACCTACTACTGTGACGCTTCGGCTAGCGGATCGATCTTTAGCATATCCCGAAG
651 AGGTGAAGTAAGACCTACTACTGTGACGCTTCGGCTAGCGGATCGATCTTTAGCATATCCCGAAG
* * *
20173085 GAAATATCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCCTACTGATTTCATTGTCTTA
716 GAAATATCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCATACTGATTTCACTATCTTA
* *
20173150 GATTTTGAAGCAGATAAGAAACTGTCGATCATCATTGGGAGACCTTTCTTAGCCATGGGAAGAAC
781 GATTTTGAAGCAGACAAGAAACTGTCGATCATCATTGGGAGACCTTTCTTAGCCACGGGAAGAAC
20173215 GT
846 GT
20173217 CTTGCCGAGCGATACTGAGAATCTAAGAAATTTGGGTAAAGAACATATCAAGGTAGTGGCATTAC
1 CTTGCCGAGCGATACTGAGAATCTAAGAAATTTGGGTAAAGAACATATCAAGGTAGTGGCATTAC
20173282 GAGGTGGTAAAATTCTAGAACCCTGATTGATTGATGTCAAAGATAAACCTGTTGAGAAGAATCAA
66 GAGGTGGTAAAATTCTAGAACCCTGATTGATTGATGTCAAAGATAAACCTGTTGAGAAGAATCAA
20173347 CCAGCTGTTGAAGTTTCTACACTAAAGGAATCAAAATCTGCAAAGTCTGACTACGTAAACCCTGA
131 CCAGCTGTTGAAGTTTCTACACTAAAGGAATCAAAATCTGCAAAGTCTGACTACGTAAACCCTGA
20173412 CTTAGTGAATTCAAATATTTTAACATCTTCTTTGAATGTAGATTTACCTACTCAGAAAAGTTATC
196 CTTAGTGAATTCAAATATTTTAACATCTTCTTTGAATGTAGATTTACCTACTCAGAAAAGTTATC
20173477 CGGTTCAACTGAAATTTCCATCACCTCCATATCTGGAAAGATTGCAGCATAACAAGTAGAAACAG
261 CGGTTCAACTGAAATTTCCATCACCTCCATATCTGGAAAGATTGCAGCATAACAAGTAGAAACAG
20173542 GAGGTGCAATTCAAGAATTTTTTGGATGTTTTGAAGCAGTTACACATCAATATTCCATTGGTGGA
326 GAGGTGCAATTCAAGAATTTTTTGGATGTTTTGAAGCAGTTACACATCAATATTCCATTGGTGGA
20173607 GGCTTTAGAAAAATGTCGAATTATGTGAAGTTTATGAAGGATATACTGTCCAATTAAAAACGGCT
391 GGCTTTAGAAAAATGTCGAATTATGTGAAGTTTATGAAGGATATACTGTCCAATTAAAAACGGCT
20173672 AAGTGAGTATGAGACTATTGCCTTGACAAATGAGTGCATTGCGTTTCTGCAGAACAAATTGCCAC
456 AAGTGAGTATGAGACTATTGCCTTGACAAATGAGTGCATTGCGTTTCTGCAGAACAAATTGCCAC
20173737 CGAAATTGAAAGACTCATGAAGCTTTACTATACCTTGTAACATTGGTGAATCTTACTATGGTAAA
521 CGAAATTGAAAGACTCATGAAGCTTTACTATACCTTGTAACATTGGTGAATCTTACTATGGTAAA
20173802 GCTTTGTGTGACTTAGGAACGAGTATCAACTTGATGCCTAAGTCTATTTTGAAGATGTTAGGGAT
586 GCTTTGTGTGACTTAGGAACGAGTATCAACTTGATGCCTAAGTCTATTTTGAAGATGTTAGGGAT
20173867 AGGTGAAGTAAGACCTACTACTGTGACGCTTCGGCTAGCGGATCGATCTTTAGCATATCCCGAAG
651 AGGTGAAGTAAGACCTACTACTGTGACGCTTCGGCTAGCGGATCGATCTTTAGCATATCCCGAAG
*
20173932 GAAATATCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCATGCTGATTTCACTATCTTA
716 GAAATATCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCATACTGATTTCACTATCTTA
* * * *
20173997 TATTTTGAAGCAGACAAGGAAGTGTCGATCATCCTTGGGAGACCTTTCTTAGCCACGGGAAGAAC
781 GATTTTGAAGCAGACAAGAAACTGTCGATCATCATTGGGAGACCTTTCTTAGCCACGGGAAGAAC
20174062 ATTAATTGAT
Statistics
Matches: 835, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
847 835 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (847 bp):
CTTGCCGAGCGATACTGAGAATCTAAGAAATTTGGGTAAAGAACATATCAAGGTAGTGGCATTAC
GAGGTGGTAAAATTCTAGAACCCTGATTGATTGATGTCAAAGATAAACCTGTTGAGAAGAATCAA
CCAGCTGTTGAAGTTTCTACACTAAAGGAATCAAAATCTGCAAAGTCTGACTACGTAAACCCTGA
CTTAGTGAATTCAAATATTTTAACATCTTCTTTGAATGTAGATTTACCTACTCAGAAAAGTTATC
CGGTTCAACTGAAATTTCCATCACCTCCATATCTGGAAAGATTGCAGCATAACAAGTAGAAACAG
GAGGTGCAATTCAAGAATTTTTTGGATGTTTTGAAGCAGTTACACATCAATATTCCATTGGTGGA
GGCTTTAGAAAAATGTCGAATTATGTGAAGTTTATGAAGGATATACTGTCCAATTAAAAACGGCT
AAGTGAGTATGAGACTATTGCCTTGACAAATGAGTGCATTGCGTTTCTGCAGAACAAATTGCCAC
CGAAATTGAAAGACTCATGAAGCTTTACTATACCTTGTAACATTGGTGAATCTTACTATGGTAAA
GCTTTGTGTGACTTAGGAACGAGTATCAACTTGATGCCTAAGTCTATTTTGAAGATGTTAGGGAT
AGGTGAAGTAAGACCTACTACTGTGACGCTTCGGCTAGCGGATCGATCTTTAGCATATCCCGAAG
GAAATATCGAGGATGTTTTGGTAAGAGTCGATAAATTTATTTTTCATACTGATTTCACTATCTTA
GATTTTGAAGCAGACAAGAAACTGTCGATCATCATTGGGAGACCTTTCTTAGCCACGGGAAGAAC
GT
Found at i:20186044 original size:18 final size:19
Alignment explanation
Indices: 20186018--20186054 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20186008 AATTTTGGAA
20186018 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
20186036 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
20186055 ATCTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:20193274 original size:25 final size:25
Alignment explanation
Indices: 20193237--20193562 Score: 467
Period size: 25 Copynumber: 13.1 Consensus size: 25
20193227 CTAATCGAAT
* * *
20193237 AGCACTAATGTGCTAATAACCAAAG
1 AGCACTAACGTGCTAATAATCAGAG
20193262 AGCACTAACGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
20193287 AGCACTAACGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
20193312 AGCACTAACGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
* * *
20193337 AGCACTGATGTGCTAATAATCAAAG
1 AGCACTAACGTGCTAATAATCAGAG
* *
20193362 AGGACTAATGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
* *
20193387 AGCACTAACATGCTAATAATTAGAG
1 AGCACTAACGTGCTAATAATCAGAG
* * * *
20193412 TGCACTGATGTGCTAATAATCAGAT
1 AGCACTAACGTGCTAATAATCAGAG
20193437 AGCACTAACGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
20193462 AGCACTAACGTGCTAAT--TCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
20193485 AGCACTAACGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
* * *
20193510 AGCATTGAGGTGCTAATAATCAGAG
1 AGCACTAACGTGCTAATAATCAGAG
* *
20193535 AGCACTAATGTGCTAATAATCAAAG
1 AGCACTAACGTGCTAATAATCAGAG
20193560 AGC
1 AGC
20193563 GCGCTAAGGT
Statistics
Matches: 269, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
23 23 0.09
25 246 0.91
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
AGCACTAACGTGCTAATAATCAGAG
Found at i:20199895 original size:23 final size:24
Alignment explanation
Indices: 20199824--20199895 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
20199814 TTTGTTGTAA
* * * *
20199824 TTCTACAAATATAGTTTGCGGCGT
1 TTCTATAAATACAGTTTGCAGCAT
* * ** *
20199848 TTTTGTAAATACAGTTCACAACAT
1 TTCTATAAATACAGTTTGCAGCAT
20199872 TTCTATAAATA-AGTTTGCAGCAT
1 TTCTATAAATACAGTTTGCAGCAT
20199895 T
1 T
20199896 GTTTCAAATA
Statistics
Matches: 34, Mismatches: 14, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (24 bp):
TTCTATAAATACAGTTTGCAGCAT
Found at i:20200932 original size:5 final size:5
Alignment explanation
Indices: 20200922--20200964 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
20200912 TTTATTTGAC
*
20200922 ATTAA ATTAA ATTAA ATTAA ACTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATT
20200965 CTAAAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:20204343 original size:24 final size:24
Alignment explanation
Indices: 20204311--20204356 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20204301 AAATTACTTG
* *
20204311 ATTCTCTCCCCAATCTCC-TCCTTT
1 ATTCGCTCCACAAT-TCCATCCTTT
20204335 ATTCGCTCCACAATTCCATCCT
1 ATTCGCTCCACAATTCCATCCT
20204357 AGACCAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.17, C:0.43, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTCGCTCCACAATTCCATCCTTT
Found at i:20207096 original size:14 final size:13
Alignment explanation
Indices: 20207077--20207118 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
20207067 ATTAGCATGT
20207077 TTAATTTTAATTAA
1 TTAATTTT-ATTAA
20207091 TTAATTTTA-TAA
1 TTAATTTTATTAA
*
20207103 TAAATTTTGATTAA
1 TTAATTTT-ATTAA
20207117 TT
1 TT
20207119 TAGATCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TTAATTTTATTAA
Found at i:20215036 original size:40 final size:40
Alignment explanation
Indices: 20214991--20215190 Score: 127
Period size: 40 Copynumber: 5.0 Consensus size: 40
20214981 ATAATATTTG
* * * * *
20214991 ATTTAGAGTTACCAGAGTATAAATAGGGGCACGAAAGTGC
1 ATTTAGAGGTAACAAAGTACAAACAGGGGCACGAAAGTGC
* * *
20215031 ATTTAGGGGTAACAAAGTACAAACAGGGGCACGTATGTGC
1 ATTTAGAGGTAACAAAGTACAAACAGGGGCACGAAAGTGC
* * * * *
20215071 ATTCA-AGGGT-ACTGAAGTACAAACAAGGGCATGTAAGTGC
1 ATTTAGA-GGTAAC-AAAGTACAAACAGGGGCACGAAAGTGC
* * * * * *
20215111 AATCAGAGGTACCGAAGTACAAATAGGGGCACGTAAGTGC
1 ATTTAGAGGTAACAAAGTACAAACAGGGGCACGAAAGTGC
* * * * * * *
20215151 AATCAGGGGTACCAAAGTACATACA-AGGCACGTAAGTGC
1 ATTTAGAGGTAACAAAGTACAAACAGGGGCACGAAAGTGC
20215190 A
1 A
20215191 ATCATCGATA
Statistics
Matches: 132, Mismatches: 24, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
39 16 0.12
40 114 0.86
41 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (40 bp):
ATTTAGAGGTAACAAAGTACAAACAGGGGCACGAAAGTGC
Found at i:20215151 original size:80 final size:79
Alignment explanation
Indices: 20215018--20215194 Score: 219
Period size: 80 Copynumber: 2.2 Consensus size: 79
20215008 TATAAATAGG
* * * * * * * *
20215018 GGCACGAAAGTGCATTTAGGGGTAACAAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTAC
1 GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
**
20215083 TGAAGTACAAACAA
66 CAAAGTACAAACAA
* * *
20215097 GGGCATGTAAGTGCAATCAGAGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATCAGGGGTA
1 -GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTA
*
20215162 CCAAAGTACATACAA
65 CCAAAGTACAAACAA
20215177 GGCACGTAAGTGCAATCA
1 GGCACGTAAGTGCAATCA
20215195 TCGATAATTA
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 17 0.21
80 65 0.79
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (79 bp):
GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
CAAAGTACAAACAA
Found at i:20215158 original size:20 final size:20
Alignment explanation
Indices: 20215054--20215194 Score: 67
Period size: 20 Copynumber: 7.1 Consensus size: 20
20215044 AAAGTACAAA
* *
20215054 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTAAGTGCAAT
* * * *
20215074 CAAGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-AAGTGCAAT
* *
20215094 CAAGGGCATGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* * *
20215114 CAGAGGTACCG-AAGTACAAAT
1 CAGGGGCA-CGTAAGTGC-AAT
20215135 -AGGGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* ** *
20215154 CAGGGGTACCAAAGTAC-AT
1 CAGGGGCACGTAAGTGCAAT
*
20215173 ACA-AGGCACGTAAGTGCAAT
1 -CAGGGGCACGTAAGTGCAAT
20215193 CA
1 CA
20215195 TCGATAATTA
Statistics
Matches: 86, Mismatches: 27, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
19 19 0.22
20 62 0.72
21 5 0.06
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTAAGTGCAAT
Found at i:20234293 original size:7 final size:7
Alignment explanation
Indices: 20234283--20234327 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
20234273 GATAAAAGAG
20234283 ATGAAAA
1 ATGAAAA
20234290 ATG-AAA
1 ATGAAAA
20234296 ATGAAAA
1 ATGAAAA
20234303 ATGAAAAA
1 ATG-AAAA
20234311 ATGAAAA
1 ATGAAAA
20234318 A-GTAAAA
1 ATG-AAAA
20234325 ATG
1 ATG
20234328 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:20234301 original size:13 final size:13
Alignment explanation
Indices: 20234283--20234309 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20234273 GATAAAAGAG
20234283 ATGAAAAATGAAA
1 ATGAAAAATGAAA
20234296 ATGAAAAATGAAA
1 ATGAAAAATGAAA
20234309 A
1 A
20234310 AATGAAAAAG
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:20234313 original size:15 final size:14
Alignment explanation
Indices: 20234283--20234327 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
20234273 GATAAAAGAG
20234283 ATGAAAAATG-AAA
1 ATGAAAAATGAAAA
20234296 ATGAAAAATGAAAAA
1 ATGAAAAATG-AAAA
20234311 ATGAAAAA-GTAAAA
1 ATGAAAAATG-AAAA
20234325 ATG
1 ATG
20234328 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:20235931 original size:50 final size:50
Alignment explanation
Indices: 20235877--20236342 Score: 341
Period size: 50 Copynumber: 9.4 Consensus size: 50
20235867 GCAGCGGAAC
*
20235877 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *** * * * ** ** *
20235927 AGATTAAAGCTACAACAACGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * *
20235977 AGATTAAAGTCACATCGGTGAATCTTGGTTCCCCGACAATGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *** * * * ** *
20236027 AGATTAAAGCTACAACAACGAATCTTAC-TCCTCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCC-CCGAC-ATTGCAGTTAAAA
*
20236077 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * **** ** *
20236127 AGATTAAAGCTACAACAGCGAATGTTACTTCCCTGGTGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
20236177 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** ** *
20236227 AGATTAAAGCTACAACAGTG-A-CTTACTT-CTCAAGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGA-CATTGCAGTTAAAA
* * * *
20236275 AGATTAACGCCACAACGGCGAA-CTTTGTTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATC-TTGCTTCCCCGACATTGCAGTTAAAA
*
20236325 AGACTAAAGCCACAACGG
1 AGATTAAAGCCACAACGG
20236343 CGGATCTTAC
Statistics
Matches: 303, Mismatches: 105, Indels: 16
0.71 0.25 0.04
Matches are distributed among these distances:
47 3 0.01
48 31 0.10
49 7 0.02
50 254 0.84
51 8 0.03
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:20236022 original size:100 final size:100
Alignment explanation
Indices: 20235849--20236385 Score: 776
Period size: 100 Copynumber: 5.4 Consensus size: 100
20235839 TTGCATCAGG
* * * *
20235849 TCTTATTTCCCTGGTGGTGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
*
20235914 ATTGCAGTTAAAAAGATTAAAGCTACAACAACGAA
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * *
20235949 TCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGGTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
* *
20236014 AATGCAGTTAAAAAGATTAAAGCTACAACAACGAA
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
*
20236049 TCTTAC-TCCTCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
1 TCTTACTTCC-CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
20236113 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
65 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * *
20236149 TGTTACTTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
*
20236214 ATTGCAGTTAAAAAGATTAAAGCTACAACAGTG-A
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * * * * * *
20236248 -CTTACTTCTCAAGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAA-CTTTGTTTCCCCAA
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TTGCTTCCCCGA
* * * *
20236311 CATTGCAGTTAAAAAGACTAAAGCCACAACGGCGGA
65 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
*
20236347 TCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGAAGC
1 TCTTAC-TTCCCAGGCGGTGCAGTGGAACAGATTAAAGC
20236386 TACAACAACA
Statistics
Matches: 396, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
97 1 0.00
98 81 0.20
99 5 0.01
100 278 0.70
101 31 0.08
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (100 bp):
TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
Found at i:20241734 original size:50 final size:50
Alignment explanation
Indices: 20241659--20241811 Score: 207
Period size: 50 Copynumber: 3.1 Consensus size: 50
20241649 NNNNNNNNNN
20241659 CATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGAC
1 CATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGAC
* * **
20241709 CATGTCGGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGAC
1 CATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGAC
* * * * * **
20241759 CATGTCTGGGAGATGGTATGGGCACCTATATGAGAACTCCCATGTAAGAC
1 CATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGAC
20241809 CAT
1 CAT
20241812 ATTTGGGATG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
CATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGAC
Found at i:20250864 original size:24 final size:24
Alignment explanation
Indices: 20250837--20250884 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20250827 AGCCTAAATC
20250837 TCGAAGAATCTCCTCAATATCTTT
1 TCGAAGAATCTCCTCAATATCTTT
20250861 TCGAAGAATCTCCTCAATATCTTT
1 TCGAAGAATCTCCTCAATATCTTT
20250885 CCCTTGTCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (24 bp):
TCGAAGAATCTCCTCAATATCTTT
Found at i:20253745 original size:50 final size:50
Alignment explanation
Indices: 20253625--20253749 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
20253615 TTATTGAGGT
* * * *
20253625 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCAA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCAA
* * * * *
20253675 GACGAGAGGTCCCCTATAAGACCATGTCTGAGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCAA
* *
20253725 TATGAGAGCTGCCATGTAAGACCAT
1 TATGAGAGGTCCCATGTAAGACCAT
20253750 ACCTGGGATA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCAA
Found at i:20254046 original size:20 final size:20
Alignment explanation
Indices: 20254021--20254070 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
20254011 ATGAGTTATT
20254021 CAAGTAAGCAAGAAAGTAAA
1 CAAGTAAGCAAGAAAGTAAA
*
20254041 CAAGTAAG-AGAGTAAGTAAA
1 CAAGTAAGCA-AGAAAGTAAA
*
20254061 GAAG-AAGCAA
1 CAAGTAAGCAA
20254071 AGACCATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.10
Consensus pattern (20 bp):
CAAGTAAGCAAGAAAGTAAA
Found at i:20264639 original size:39 final size:37
Alignment explanation
Indices: 20264572--20264656 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 37
20264562 ACCAGAATGG
* *
20264572 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
20264611 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
*
20264648 TACCCAGTG
1 CACCCAGTG
20264657 AATTTAGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 13 0.32
38 2 0.05
39 22 0.55
40 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:20264841 original size:15 final size:16
Alignment explanation
Indices: 20264818--20264873 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
20264808 TTTTTATGTT
*
20264818 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
20264835 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
20264852 TTATAT-TGTATTATA
1 TTATATATATATTATA
20264867 TTATATA
1 TTATATA
20264874 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:20264857 original size:5 final size:5
Alignment explanation
Indices: 20264818--20264872 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
20264808 TTTTTATGTT
* *
20264818 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
20264867 TTATA T
1 TTATA T
20264873 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:20264858 original size:27 final size:29
Alignment explanation
Indices: 20264819--20264874 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
20264809 TTTTATGTTT
*
20264819 TATATATATTATTTTATTATATAATATAA
1 TATATATATTATTGTATTATATAATATAA
*
20264848 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTGTATTATATAATATAA
20264875 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATATATTATTGTATTATATAATATAA
Found at i:20273576 original size:27 final size:27
Alignment explanation
Indices: 20273527--20273578 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20273517 TAACATAAAG
* *
20273527 AGTCCACCAGGATAATAACCATGGGAA
1 AGTCCACCAGGACAATAAACATGGGAA
* *
20273554 AGTCCACTAGGACATTAAACATGGG
1 AGTCCACCAGGACAATAAACATGGG
20273579 GTTACATGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (27 bp):
AGTCCACCAGGACAATAAACATGGGAA
Found at i:20275419 original size:50 final size:50
Alignment explanation
Indices: 20275364--20275459 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
20275354 AATCTTAAGT
20275364 ATGAAATAATGAAAACATAATATTAAATACTAAATTGCATAGAAAATAAA
1 ATGAAATAATGAAAACATAATATTAAATACTAAATTGCATAGAAAATAAA
*
20275414 ATGAAATACTGAAAACATAATATTAAATACTAAATTGCATAGAAAA
1 ATGAAATAATGAAAACATAATATTAAATACTAAATTGCATAGAAAA
20275460 GAAACTTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.26
Consensus pattern (50 bp):
ATGAAATAATGAAAACATAATATTAAATACTAAATTGCATAGAAAATAAA
Found at i:20275569 original size:11 final size:11
Alignment explanation
Indices: 20275553--20275591 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
20275543 TGTCCTTAAG
20275553 AAAACTAAATA
1 AAAACTAAATA
20275564 AAAACTAAA-A
1 AAAACTAAATA
20275574 ATAAACTAAACTA
1 A-AAACTAAA-TA
20275587 AAAAC
1 AAAAC
20275592 AGAAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 17 0.68
12 4 0.16
13 2 0.08
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAACTAAATA
Found at i:20275597 original size:23 final size:22
Alignment explanation
Indices: 20275554--20275600 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
20275544 GTCCTTAAGA
20275554 AAACTAAATAAAAACTAAAAAT
1 AAACTAAATAAAAACTAAAAAT
20275576 AAACTAAACTAAAAAC-AGAAAAT
1 AAACTAAA-TAAAAACTA-AAAAT
20275599 AA
1 AA
20275601 CATGCAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AAACTAAATAAAAACTAAAAAT
Found at i:20288308 original size:29 final size:29
Alignment explanation
Indices: 20288266--20288323 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20288256 CTTCTAACCT
20288266 TCGACTTCTACACTGCCAAATCAAAACTA
1 TCGACTTCTACACTGCCAAATCAAAACTA
20288295 TCGACTTCTACACTGCCAAATCAAAACTA
1 TCGACTTCTACACTGCCAAATCAAAACTA
20288324 ATCCGGGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.31, G:0.07, T:0.24
Consensus pattern (29 bp):
TCGACTTCTACACTGCCAAATCAAAACTA
Found at i:20309196 original size:504 final size:504
Alignment explanation
Indices: 20308242--20309228 Score: 1794
Period size: 504 Copynumber: 2.0 Consensus size: 504
20308232 CAACCACCTT
20308242 TGCAATATTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCAC
1 TGCAATATTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCAC
* * *
20308307 CTAGTGCCGAACTCTCTAGCCGTAACACCACCCAGCTTCGCACGTCACCTTTACGCCTAGCAACA
66 CTAGTACCGAACTCTCTAGCCGCAACACCACCCAGCTTCGCACATCACCTTTACGCCTAGCAACA
*
20308372 GCCCCATTCGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTACTGCTCGCATCAG
131 GCCCCATTCGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTACCGCTCGCATCAG
* **
20308437 ACCTACTGTCACACACCCGCTCATGTGCACCAATGCACCAGCCCTGCTATTCGCCCGACAGTGCC
196 ACCTACTCTCACACACCCGCTCATGTGCACCAACACACCAGCCCTGCTATTCGCCCGACAGTGCC
20308502 ACCTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGAACCAACACCCTTTCCTATCAC
261 ACCTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGAACCAACACCCTTTCCTATCAC
*
20308567 ACCATACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTC
326 ACCACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTC
20308632 TTTGAGTTCTTACCAAAGTGAGAAACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAA
391 TTTGAGTTCTTACCAAAGTGAGAAACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAA
20308697 GGCTTTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGA
456 GGCTTTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGA
*
20308746 TGCAATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCAC
1 TGCAATATTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCAC
* *
20308811 CTAGTACCGAAGTCTCTAGCCGCAACACCGCCCAGCTTCGCACATCACCTTTACGCCTAGCAACA
66 CTAGTACCGAACTCTCTAGCCGCAACACCACCCAGCTTCGCACATCACCTTTACGCCTAGCAACA
* *
20308876 GCCTCATTCGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTGCCGCTCGCATCAG
131 GCCCCATTCGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTACCGCTCGCATCAG
** * * *
20308941 ACCTACTCTCATGCACCTGCTCATGTGCACCAACACACCAGCCCTGCTATTTGCCTGACAGTGCC
196 ACCTACTCTCACACACCCGCTCATGTGCACCAACACACCAGCCCTGCTATTCGCCCGACAGTGCC
* *
20309006 ACCTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGC
261 ACCTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGAACCAACACCCTTTCCTATCAC
20309071 ACCACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTC
326 ACCACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTC
20309136 TTTGAGTTCTTACCAAAGTGAGAAACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAA
391 TTTGAGTTCTTACCAAAGTGAGAAACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAA
20309201 GGCTTTACGCTGAAAGAAAACAACTATA
456 GGCTTTACGCTGAAAGAAAACAACTATA
20309229 TTGATTTCAT
Statistics
Matches: 463, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
504 463 1.00
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.22
Consensus pattern (504 bp):
TGCAATATTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCAC
CTAGTACCGAACTCTCTAGCCGCAACACCACCCAGCTTCGCACATCACCTTTACGCCTAGCAACA
GCCCCATTCGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTACCGCTCGCATCAG
ACCTACTCTCACACACCCGCTCATGTGCACCAACACACCAGCCCTGCTATTCGCCCGACAGTGCC
ACCTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGAACCAACACCCTTTCCTATCAC
ACCACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTC
TTTGAGTTCTTACCAAAGTGAGAAACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAA
GGCTTTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGA
Found at i:20311216 original size:17 final size:16
Alignment explanation
Indices: 20311196--20311235 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
20311186 AAATGCTCGT
20311196 GAAAAAAAAAGAAAAAA
1 GAAAAAAAAAG-AAAAA
*
20311213 GAAAAGAAAAGAAAAA
1 GAAAAAAAAAGAAAAA
20311229 GAAAAAA
1 GAAAAAA
20311236 TGAAGAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAGAAAAA
Found at i:20311222 original size:11 final size:10
Alignment explanation
Indices: 20311196--20311235 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
20311186 AAATGCTCGT
20311196 GAAAAAAAAA
1 GAAAAAAAAA
20311206 GAAAAAAGAAAA
1 G-AAAAA-AAAA
20311218 GAAAAGAAAAA
1 GAAAA-AAAAA
20311229 GAAAAAA
1 GAAAAAA
20311236 TGAAGAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 18 0.67
12 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:20312835 original size:20 final size:18
Alignment explanation
Indices: 20312802--20312838 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
20312792 TGTGATGCTG
20312802 ATATGCTTAATTTAATTA
1 ATATGCTTAATTTAATTA
20312820 ATATGGCTTAAATTTAATT
1 ATAT-GCTT-AATTTAATT
20312839 TCTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATGCTTAATTTAATTA
Found at i:20319966 original size:51 final size:51
Alignment explanation
Indices: 20319908--20320141 Score: 278
Period size: 51 Copynumber: 4.6 Consensus size: 51
20319898 CCGGTTCACA
*
20319908 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTTTCATCCGATACACG
* *** * *
20319959 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCT-ATCC-AGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATTTTCATCCGA-TACACG
* * * * *
20320010 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTTTCA-TCCGATACACG
* * *
20320060 TATTAGCCTGCAGATAGTACTACACACGTGACCATTTTCATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTTTCATCCGATACACG
20320111 TAGTAGCCTGCACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
20320142 TCTAGCAACT
Statistics
Matches: 150, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 37 0.25
51 104 0.69
52 7 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTTTCATCCGATACACG
Found at i:20320115 original size:101 final size:101
Alignment explanation
Indices: 20319904--20320136 Score: 292
Period size: 101 Copynumber: 2.3 Consensus size: 101
20319894 ATACCCGGTT
* *
20319904 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TATCATCCGATACACGTAGTAGCCTG
*
20319969 CACATAGTACTACACACGTGATCGAAGCTATCCAGTA
65 CACATAGTACTACACACGTGATCCAAGCTATCCAGTA
* * * *
20320006 CGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGGTACACGTATTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCATATCA-TCCGATACACGTAGTAGCCTG
* ***
20320070 CAGATAGTACTACACACGTGA-CCATTTTCATCC-GATA
65 CACATAGTACTACACACGTGATCCAAGCT-ATCCAG-TA
**
20320107 CATGTAGTAGCCTGCACATAGTACTACACA
1 CACATAGTAGCCTGCACATAGTACTACACA
20320137 CGTGATCTAG
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
100 8 0.07
101 71 0.62
102 35 0.31
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATATCATCCGATACACGTAGTAGCCTGC
ACATAGTACTACACACGTGATCCAAGCTATCCAGTA
Found at i:20320481 original size:47 final size:47
Alignment explanation
Indices: 20320412--20320506 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
20320402 GTTTCATAAT
*
20320412 ATGCTGAACATTTTTCCCTTCTATAGCAACATCAAATTCTTGCTCTA
1 ATGCTGAACATTTTTCCCTTCTATAGCAACATCAAATTCTTACTCTA
20320459 ATGCTGAACATTTTTCCCTTCTATAGCAACATCAAATTCTTACTCTA
1 ATGCTGAACATTTTTCCCTTCTATAGCAACATCAAATTCTTACTCTA
20320506 A
1 A
20320507 CATGCACTTA
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:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (47 bp):
ATGCTGAACATTTTTCCCTTCTATAGCAACATCAAATTCTTACTCTA
Found at i:20321117 original size:11 final size:11
Alignment explanation
Indices: 20321089--20321129 Score: 64
Period size: 11 Copynumber: 3.5 Consensus size: 11
20321079 GCCCAAACGT
20321089 CGAAATTTTTGAA
1 CGAAATTTTT--A
20321102 CGAAATTTTTA
1 CGAAATTTTTA
20321113 CGAAATTTTTA
1 CGAAATTTTTA
20321124 CGAAAT
1 CGAAAT
20321130 CATAGACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (11 bp):
CGAAATTTTTA
Found at i:20325699 original size:51 final size:50
Alignment explanation
Indices: 20325638--20325871 Score: 238
Period size: 51 Copynumber: 4.6 Consensus size: 50
20325628 TCGGTTCACA
*
20325638 TAGTAGCCTGCACATAGTACTACACATGTGAGCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CATTTTCATCCGATACACG
* *** * * *
20325689 TAATAGCCTGCACATAGTACTACACACGTGATCGAAGCT-ATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-C-ATTTTCATCCGATACACG
* * * * * * *
20325740 TAGTAACCTGCACATAGTACTACACATGGGAC-CTATCATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACATTTTCA-TCCGATACACG
* *
20325790 TAGTAGACTGTACATAGTACTACACACGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CATTTTCATCCGATACACG
* *
20325841 TATTAGCCTACACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
20325872 TCTAGCAACT
Statistics
Matches: 146, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 35 0.24
51 103 0.71
52 6 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACATTTTCATCCGATACACG
Found at i:20325833 original size:101 final size:102
Alignment explanation
Indices: 20325634--20325866 Score: 265
Period size: 101 Copynumber: 2.3 Consensus size: 102
20325624 ATACTCGGTT
* * * *
20325634 CACATAGTAGCCTGCACATAGTACTACACATGTGAGCATTTTCATCCGATACACGTAATAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGGGAGCACTATCATCCGATACACGTAATAGACTG
* *
20325699 CACATAGTACTACACACGTGATCGAAGCTATCCGGTA
66 CACATAGTACTACACACGTGATCCAAGCTATCCGATA
* * * * *
20325736 CGCATAGTAACCTGCACATAGTACTACACATGGGA-C-CTATCATTTCGGTACACGTAGTAGACT
1 CACATAGTAGCCTGCACATAGTACTACACATGGGAGCACTATCA-TCCGATACACGTAATAGACT
* ***
20325799 GTACATAGTACTACACACGTGA-CCATTTTCATCCGATA
65 GCACATAGTACTACACACGTGATCCAAGCT-ATCCGATA
* * *
20325837 CACGTATTAGCCTACACATAGTACTACACA
1 CACATAGTAGCCTGCACATAGTACTACACA
20325867 CGTGATCTAG
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
100 7 0.06
101 70 0.64
102 32 0.29
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (102 bp):
CACATAGTAGCCTGCACATAGTACTACACATGGGAGCACTATCATCCGATACACGTAATAGACTG
CACATAGTACTACACACGTGATCCAAGCTATCCGATA
Found at i:20332105 original size:28 final size:26
Alignment explanation
Indices: 20332065--20332124 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 26
20332055 ACTGTACTGA
20332065 TACTGTAATGGGCTAAGGCCCACATTG
1 TACTGTAATGGGCTAAGG-CCACATTG
*
20332092 TTACTGTATTGGGCTAAGGCCACATTG
1 -TACTGTAATGGGCTAAGGCCACATTG
20332119 TACTGT
1 TACTGT
20332125 GACTAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.19
27 8 0.26
28 17 0.55
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (26 bp):
TACTGTAATGGGCTAAGGCCACATTG
Found at i:20333596 original size:27 final size:27
Alignment explanation
Indices: 20333541--20333596 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
20333531 ATTTTTCTAT
* *
20333541 TTTATTTATCTTAGTTATTTATTTTAA
1 TTTATTTATCTTAGTTATTTATCTAAA
*
20333568 TTTATTT-TCTTTAGTTTTTTATCTAAA
1 TTTATTTATC-TTAGTTATTTATCTAAA
20333595 TT
1 TT
20333597 GAATTCGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (27 bp):
TTTATTTATCTTAGTTATTTATCTAAA
Found at i:20334325 original size:66 final size:66
Alignment explanation
Indices: 20334193--20334317 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 66
20334183 TTAACAAAAA
*
20334193 TTTTTCTCTCATTTTTTCTCTTGCCAAACACCACTTTTTTCTTCAAAACACATGGTTGCTGCCAT
1 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTTCTTCAAAACACATGGTTGCTGCCAT
20334258 T
66 T
* * *
20334259 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTTTTCAAAACATATGGTTG
1 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTT-TTCTTCAAAACACATGGTTG
20334318 GTTCATTTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
66 36 0.67
67 18 0.33
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.47
Consensus pattern (66 bp):
TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTTCTTCAAAACACATGGTTGCTGCCAT
T
Found at i:20338865 original size:9 final size:9
Alignment explanation
Indices: 20338851--20338889 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
20338841 TTTATTGTTC
20338851 TATTTTATT
1 TATTTTATT
20338860 TATTTTATT
1 TATTTTATT
20338869 TATTTTAATT
1 TATTTT-ATT
*
20338879 AATTTT-TT
1 TATTTTATT
20338887 TAT
1 TAT
20338890 CTGACTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 4 0.15
9 15 0.56
10 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:20339301 original size:14 final size:14
Alignment explanation
Indices: 20339262--20339302 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
20339252 AATTCATGAG
20339262 TATCTCTTTCCTTTA
1 TATCTCTTT-CTTTA
*
20339277 T-TCT-ATTCTTTA
1 TATCTCTTTCTTTA
20339289 TATCTCTTTCTTTA
1 TATCTCTTTCTTTA
20339303 ACATTGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 10 0.45
15 1 0.05
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (14 bp):
TATCTCTTTCTTTA
Found at i:20344013 original size:24 final size:24
Alignment explanation
Indices: 20343986--20344078 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
20343976 ACACACCACG
*
20343986 TTGTGGCCAAGCCACTCCATAGCA
1 TTGTGGCCAAGCCACTCAATAGCA
* *
20344010 TTGTGGCCAAGCAACTCAATAGCG
1 TTGTGGCCAAGCCACTCAATAGCA
* * *
20344034 TTTTGGTCAAGCCACTCAATAACA
1 TTGTGGCCAAGCCACTCAATAGCA
20344058 TTGTGGCCAAGCCACTCAATA
1 TTGTGGCCAAGCCACTCAATA
20344079 TTACAGATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (24 bp):
TTGTGGCCAAGCCACTCAATAGCA
Found at i:20352256 original size:56 final size:50
Alignment explanation
Indices: 20352150--20352286 Score: 148
Period size: 56 Copynumber: 2.6 Consensus size: 50
20352140 GCCCATGTCT
** *
20352150 TGTCCCAGACATGGTCTTACGGGGGACCTCTCATCGCGGTGCCAACGCCA
1 TGTCCCAGACATGGTCTTACATGGGACCTCTCATCGCGATGCCAACGCCA
* *
20352200 TGTCCCAGACATGGTCTTACATGGGACCTCTCATAAACTCAATGATGCCAATGCCA
1 TGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CGC---GATGCCAACGCCA
* * *
20352256 TCTCCCTGACATGGTCTTACATGGGATCTCT
1 TGTCCCAGACATGGTCTTACATGGGACCTCT
20352287 TTACCCAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 32 0.44
53 2 0.03
56 39 0.53
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGTCCCAGACATGGTCTTACATGGGACCTCTCATCGCGATGCCAACGCCA
Found at i:20356476 original size:50 final size:50
Alignment explanation
Indices: 20356361--20356553 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
20356351 GATAATAACA
* * * ** *
20356361 TGCCAAAGCCATGTCCCAGGCATGGTCTTAAATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
20356412 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
20356462 TGCCAACGCCATGTCCCAGACATGGTATTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20356512 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
20356554 TTACCCAAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
50 93 0.75
51 31 0.25
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:20360664 original size:50 final size:50
Alignment explanation
Indices: 20360589--20360786 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 50
20360579 TTTCTTGTAC
* * **
20360589 TGCCAATGTCATATCCCAGATATGGTCCTACATGGGAGTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCCTACATGGGACCTCTCATATCGG
* * * * *
20360639 TGCCCATGTCTTGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCCTACATGGGACCTCTCATATCGG
* * *
20360689 TGCCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCCTACATGGGACCTCTCAT-A--TC---GG
* *
20360745 TGCCAATGCCATGTCCCAGACATGGTCCTACATGGGATCTCT
1 TGCCAATGTCATGTCCCAGACATGGTCCTACATGGGACCTCT
20360787 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 82 0.67
53 2 0.02
56 39 0.32
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCCTACATGGGACCTCTCATATCGG
Found at i:20367634 original size:50 final size:50
Alignment explanation
Indices: 20367499--20367733 Score: 204
Period size: 50 Copynumber: 4.6 Consensus size: 50
20367489 ACATGACAAA
* ** * * *
20367499 GCCATGTCCCGGACATGGTCTTACATGGGATGTTTCTTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * * * ** *
20367548 GTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * *
20367598 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
* * **
20367648 ACCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAAT
20367704 GCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
20367734 TCTTTTTACC
Statistics
Matches: 146, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 30 0.21
50 79 0.54
53 2 0.01
56 34 0.23
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:20391174 original size:19 final size:19
Alignment explanation
Indices: 20391150--20391188 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20391140 AAAGAAATGA
20391150 TAGTAAAATTATTAATTTG
1 TAGTAAAATTATTAATTTG
20391169 TAGTAAAATTATTAATTTG
1 TAGTAAAATTATTAATTTG
20391188 T
1 T
20391189 TACAATTTAG
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:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
TAGTAAAATTATTAATTTG
Found at i:20397379 original size:26 final size:26
Alignment explanation
Indices: 20397317--20397379 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
20397307 TTCAAAACTT
* *
20397317 TTATGATTTTTTATAAATTTTTTGAA
1 TTATAATTTTTTATAAATTTTTTAAA
*
20397343 TTTTAATTTTTTATAAATTTTTATTAAA
1 TTATAATTTTTTATAAA-TTTT-TTAAA
20397371 TTAT-ATTTT
1 TTATAATTTT
20397380 GATATAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 15 0.48
27 9 0.29
28 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (26 bp):
TTATAATTTTTTATAAATTTTTTAAA
Found at i:20402017 original size:113 final size:113
Alignment explanation
Indices: 20401819--20402145 Score: 532
Period size: 113 Copynumber: 2.9 Consensus size: 113
20401809 TGTGATAGCC
* * * *
20401819 AGTGTTATTTTCCTTACGAATGATCAAATGTTTCACTAGAGAACAAATCACATCGATGTTCAATA
1 AGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATCGATGTTCAATG
20401884 TCATTTTATACGTGATATTATTGCTCATGTTGATGTTGTGATAGTCAG
66 TCATTTTATACGTGATATTATTGCTCATGTTGATGTTGTGATAGTCAG
*
20401932 AGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATCGAGGTTCAATG
1 AGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATCGATGTTCAATG
*
20401997 TCATTTTATACGTGATATTATTGCTTATGTTGATGTTGTGATAGTCAG
66 TCATTTTATACGTGATATTATTGCTCATGTTGATGTTGTGATAGTCAG
**
20402045 AGTGTCATCTTCCTTACAAATGATCAAATGTTTCA-TGAGAGAACAAATCACATCGATGTTCGGT
1 AGTGTCATCTTCCTTACAAATGATCAAATGTTTCACT-AGAGAACAAATCACATCGATGTTCAAT
* *
20402109 GTCATTTTATGCATGATATTATTGCTCATAG-TGATGT
65 GTCATTTTATACGTGATATTATTGCTCAT-GTTGATGT
20402146 GAGCAAAGTT
Statistics
Matches: 200, Mismatches: 12, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 198 0.99
114 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (113 bp):
AGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATCGATGTTCAATG
TCATTTTATACGTGATATTATTGCTCATGTTGATGTTGTGATAGTCAG
Found at i:20402598 original size:5 final size:6
Alignment explanation
Indices: 20402581--20402605 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20402571 AAAATCTATG
20402581 TGTTTT TGTTTT TGTTTT TGTTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT T
20402606 TTATTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TGTTTT
Found at i:20409047 original size:115 final size:115
Alignment explanation
Indices: 20408845--20409067 Score: 419
Period size: 115 Copynumber: 1.9 Consensus size: 115
20408835 CTGATTCTTC
** *
20408845 CTTCTACCTTTCTTCTCCACTCTCCTCGCTGTCTTCTCCTTCTCTTTTTTACCTCTCTTTGGCGT
1 CTTCTACCTTTCTTCTCCACTCTCCTCGCCATCTTCTCCTTCTCTTTTTTACCTCTCTTTGGCAT
20408910 CACAACTGGACTTCGAACACCGATCAGAAAGCAGCCTCCATCTATTTTTT
66 CACAACTGGACTTCGAACACCGATCAGAAAGCAGCCTCCATCTATTTTTT
20408960 CTTCTACCTTTCTTCTCCACTCTCCTCGCCATCTTCTCCTTCTCTTTTTTACCTCTCTTTGGCAT
1 CTTCTACCTTTCTTCTCCACTCTCCTCGCCATCTTCTCCTTCTCTTTTTTACCTCTCTTTGGCAT
20409025 CACAACTGGACTTCGAACACCGATCAGAAAGCAGCCTCCATCT
66 CACAACTGGACTTCGAACACCGATCAGAAAGCAGCCTCCATCT
20409068 CACGTTTTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 105 1.00
ACGTcount: A:0.17, C:0.36, G:0.10, T:0.37
Consensus pattern (115 bp):
CTTCTACCTTTCTTCTCCACTCTCCTCGCCATCTTCTCCTTCTCTTTTTTACCTCTCTTTGGCAT
CACAACTGGACTTCGAACACCGATCAGAAAGCAGCCTCCATCTATTTTTT
Done.