Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 180 of 210
Found at i:59946694 original size:22 final size:21
Alignment explanation
Indices: 59946664--59946708 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
59946654 ACACCAAAAC
*
59946664 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
59946686 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
59946707 AG
1 AG
59946709 CGCCACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:59946849 original size:43 final size:43
Alignment explanation
Indices: 59946800--59946898 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
59946790 TTTTTGAAAT
* * * * * *
59946800 AAACGCCGCTAAAGGTCA-GGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGCTCATGAG-CTTTAGCGGCACTTCTCACAA
*
59946843 AAACGCCGCTATAGCTCATGAGCTTTAGCGGCACTTCTCACAA
1 AAACGCCGCTAAAGCTCATGAGCTTTAGCGGCACTTCTCACAA
*
59946886 AAACGCCACTAAA
1 AAACGCCGCTAAA
59946899 AATATAACAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGCTCATGAGCTTTAGCGGCACTTCTCACAA
Found at i:59946943 original size:20 final size:20
Alignment explanation
Indices: 59946917--59946961 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
59946907 ATTTAAAAAA
59946917 ATATTTTAATCAAATAATATT
1 ATATTTTAATCAAA-AATATT
* *
59946938 -TATTTTTATCATAAATATT
1 ATATTTTAATCAAAAATATT
59946957 ATATT
1 ATATT
59946962 ATGTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTTAATCAAAAATATT
Found at i:59952131 original size:19 final size:20
Alignment explanation
Indices: 59952103--59952145 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
59952093 AAATTATAAA
*
59952103 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
59952123 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
59952142 TTTT
1 TTTT
59952146 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:59953055 original size:82 final size:82
Alignment explanation
Indices: 59952968--59953118 Score: 275
Period size: 82 Copynumber: 1.8 Consensus size: 82
59952958 CCCCTGACAA
* *
59952968 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCT
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
59953033 AACCCGACCCCGAATCT
66 AACCCGACCCCGAATCT
*
59953050 CTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAACCCT
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
59953115 AACC
66 AACC
59953119 TGTCACTGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (82 bp):
CTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
AACCCGACCCCGAATCT
Found at i:59953501 original size:41 final size:41
Alignment explanation
Indices: 59953444--59953758 Score: 432
Period size: 41 Copynumber: 7.6 Consensus size: 41
59953434 TGTTTTTGCA
*
59953444 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTAGCG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* * *
59953485 GCGCTGTTACAAAAACGCCGCTAAAGAACTGAACATTAGCG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* * *
59953526 GCGCTTTTACAAAAACGCCGTTAAAGAACTAAGCATTAGCG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
*
59953567 GCGCTTTTACAAAAAACGCCGCTAAAGAACTGAGCATTAGCG
1 GCGCTTTT-CCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* * *
59953609 GCGCTTCTCCAAAAACGCCACTAAAGATCTGAGCATTAGCG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* * * * *
59953650 GCGCTTCTCCATAAACGCCACTAAAGATCTGAGCATTAGTG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* *
59953691 GCGCTTTTCCAAAAAAGCCGCTAAAGATCTGAGCATTAGCG
1 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
**
59953732 GCGCTTTTTTTAAAAACGCCGCTAAAG
1 GCGC-TTTTCCAAAAACGCCGCTAAAG
59953759 CCCTGAAAGT
Statistics
Matches: 246, Mismatches: 26, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
41 191 0.78
42 55 0.22
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTAGCG
Found at i:59953610 original size:124 final size:122
Alignment explanation
Indices: 59953444--59953758 Score: 416
Period size: 124 Copynumber: 2.5 Consensus size: 122
59953434 TGTTTTTGCA
* *
59953444 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTAGCGGCGCTGTTACAAAAACGCCGCTAA
1 GCGCTTTTCAAAAAACGCCGCTAAAGAACTGAGCATTAGCGGCGCT-TTACAAAAACGCCGCTAA
* **
59953509 AGAACTGAACATTAGCGGCGCTTTTACAAAAACGCCGTTAAAGAACTAAGCATTAGCG
65 AGAACTGAACATTAGCGGCGCTTCTACAAAAACGCCACTAAAGAACTAAGCATTAGCG
* *
59953567 GCGCTTTTACAAAAAACGCCGCTAAAGAACTGAGCATTAGCGGCGCTTCTCCAAAAACGCCACTA
1 GCGCTTTT-CAAAAAACGCCGCTAAAGAACTGAGCATTAGCGGCGCTT-TACAAAAACGCCGCTA
* * * * * * *
59953632 AAGATCTGAGCATTAGCGGCGCTTCTCCATAAACGCCACTAAAGATCTGAGCATTAGTG
64 AAGAACTGAACATTAGCGGCGCTTCTACAAAAACGCCACTAAAGAACTAAGCATTAGCG
* **
59953691 GCGCTTTTCCAAAAAA-GCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTTTAAAAACGCCGCT
1 GCGCTTTT-CAAAAAACGCCGCTAAAGAACTGAGCATTAGCGGCGC--TTTACAAAAACGCCGCT
59953755 AAAG
63 AAAG
59953759 CCCTGAAAGT
Statistics
Matches: 169, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
123 37 0.22
124 130 0.77
125 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (122 bp):
GCGCTTTTCAAAAAACGCCGCTAAAGAACTGAGCATTAGCGGCGCTTTACAAAAACGCCGCTAAA
GAACTGAACATTAGCGGCGCTTCTACAAAAACGCCACTAAAGAACTAAGCATTAGCG
Found at i:59953728 original size:165 final size:165
Alignment explanation
Indices: 59953444--59953758 Score: 452
Period size: 165 Copynumber: 1.9 Consensus size: 165
59953434 TGTTTTTGCA
* * * *
59953444 GCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTAGCGGCGCTGTTACAAAAACGCCGCTAA
1 GCGCTTCTCCAAAAACGCCACTAAAGAACTGAGCATTAGCGGCGCTGTTACAAAAACGCCACTAA
* *
59953509 AGAACTGAACATTAGCGGCGCTTTTACAAAAACGCCGTTAAAGAACTAAGCATTAGCGGCGCTTT
66 AGAACTGAACATTAGCGGCGCTTTTACAAAAAAGCCGCTAAAGAACTAAGCATTAGCGGCGCTTT
59953574 TACAAAAAACGCCGCTAAAGAACTGAGCATTAGCG
131 TACAAAAAACGCCGCTAAAGAACTGAGCATTAGCG
* * *
59953609 GCGCTTCTCCAAAAACGCCACTAAAGATCTGAGCATTAGCGGCGCT-TCTCCATAAACGCCACTA
1 GCGCTTCTCCAAAAACGCCACTAAAGAACTGAGCATTAGCGGCGCTGT-TACAAAAACGCCACTA
* * * * * *
59953673 AAGATCTGAGCATTAGTGGCGCTTTTCCAAAAAAGCCGCTAAAGATCTGAGCATTAGCGGCGCTT
65 AAGAACTGAACATTAGCGGCGCTTTTACAAAAAAGCCGCTAAAGAACTAAGCATTAGCGGCGCTT
***
59953738 TTTTTAAAAACGCCGCTAAAG
130 TTACAAAAAACGCCGCTAAAG
59953759 CCCTGAAAGT
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
164 1 0.01
165 130 0.99
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (165 bp):
GCGCTTCTCCAAAAACGCCACTAAAGAACTGAGCATTAGCGGCGCTGTTACAAAAACGCCACTAA
AGAACTGAACATTAGCGGCGCTTTTACAAAAAAGCCGCTAAAGAACTAAGCATTAGCGGCGCTTT
TACAAAAAACGCCGCTAAAGAACTGAGCATTAGCG
Found at i:59953850 original size:40 final size:39
Alignment explanation
Indices: 59953795--59953931 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
59953785 GGGCTTAGGG
* * *
59953795 TTTTTTGCGGCGTTTTTCCAAAAATCGCCGCTAATGCTCC
1 TTTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATGCTCA
* *
59953835 TTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTC-A
* * ** *
59953875 TCTTTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC-TCA
59953915 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
59953932 TATCCAAACG
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 19 0.23
40 61 0.75
41 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
Found at i:59957009 original size:41 final size:41
Alignment explanation
Indices: 59956952--59957033 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
59956942 ACGATAGTTG
59956952 TTGCTACAAGTCCTAATAGTATCATTTCCCTCTTTTTCTAT
1 TTGCTACAAGTCCTAATAGTATCATTTCCCTCTTTTTCTAT
59956993 TTGCTACAAGTCCTAATAGTATCATTTCCCTCTTTTTCTAT
1 TTGCTACAAGTCCTAATAGTATCATTTCCCTCTTTTTCTAT
59957034 CATTACATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.46
Consensus pattern (41 bp):
TTGCTACAAGTCCTAATAGTATCATTTCCCTCTTTTTCTAT
Found at i:59962644 original size:4 final size:4
Alignment explanation
Indices: 59962620--59962743 Score: 221
Period size: 4 Copynumber: 30.8 Consensus size: 4
59962610 GTAAGGGCAG
* *
59962620 CATA CATTA CATG CATG CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
59962669 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
59962717 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
59962744 TCACATATAT
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
4 113 0.97
5 4 0.03
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:59968636 original size:37 final size:38
Alignment explanation
Indices: 59968582--59968654 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
59968572 TTTTCATAAT
* *
59968582 TTCACTTTTCCACTTTCAA-TCACTATTCAATTCAAAA
1 TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAAAA
*
59968619 TTCACTTTGCCATTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAA
59968655 TTCCACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.41
Consensus pattern (38 bp):
TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAAAA
Found at i:59968685 original size:23 final size:22
Alignment explanation
Indices: 59968642--59968685 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
59968632 TTTCAAGTCA
59968642 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
59968665 ATATTCATGATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
59968686 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:59968914 original size:51 final size:51
Alignment explanation
Indices: 59968849--59969049 Score: 221
Period size: 51 Copynumber: 4.0 Consensus size: 51
59968839 ATTAATGATA
* * * *
59968849 CCGATTCACATAGTAGCCTACACATAGTACTACAGATGTGACCATCACTAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
59968900 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * * *
59968951 CAGGTACTCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
* * *
59969001 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
59969050 TTCACTTTCA
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
49 4 0.03
50 42 0.33
51 77 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:59969021 original size:101 final size:102
Alignment explanation
Indices: 59968857--59969041 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
59968847 TACCGATTCA
* *
59968857 CATAGTAGCCTACACATAGTACTACAGATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
59968922 CATAGTACTACACACGTGATCGAAGCTATCAGGTACT
66 CATAGTACTACACACGTGATCGAAGCTATCAGGTACT
* * *
59968959 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
59969022 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
59969042 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 40 0.52
102 33 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCAGGTACT
Found at i:59969306 original size:30 final size:30
Alignment explanation
Indices: 59969272--59969328 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
59969262 CCTTGGCTCG
59969272 AACTTTAGCAAAATTACAATTTTGCCCTTA
1 AACTTTAGCAAAATTACAATTTTGCCCTTA
* * * *
59969302 AACTTTTGCATATTTACACTTTTGCCC
1 AACTTTAGCAAAATTACAATTTTGCCC
59969329 CAAAGCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTAGCAAAATTACAATTTTGCCCTTA
Found at i:59975063 original size:23 final size:22
Alignment explanation
Indices: 59975013--59975063 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
59975003 TCTGCACCAA
* * *
59975013 AGTGCCACTATTACTTGTATGG
1 AGTGCCACTATCACTTGCACGG
59975035 AGGTGCCACTATCACTTGCACGAG
1 A-GTGCCACTATCACTTGCACG-G
59975059 AGTGC
1 AGTGC
59975064 TATTGTCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 21 0.88
24 2 0.08
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
AGTGCCACTATCACTTGCACGG
Found at i:59975994 original size:19 final size:21
Alignment explanation
Indices: 59975953--59975995 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59975943 TTTAACCAAT
*
59975953 TCAAAATATGATCAAATACAA
1 TCAAAACATGATCAAATACAA
59975974 TCAAAACATG-TCAAA-ACAA
1 TCAAAACATGATCAAATACAA
59975993 TCA
1 TCA
59975996 TCCTAGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.21
Consensus pattern (21 bp):
TCAAAACATGATCAAATACAA
Found at i:59977364 original size:15 final size:15
Alignment explanation
Indices: 59977346--59977376 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59977336 TCCTTTTTTC
59977346 TTCTTTCTTTTTCTT
1 TTCTTTCTTTTTCTT
59977361 TTCTTTCTTTTTCTT
1 TTCTTTCTTTTTCTT
59977376 T
1 T
59977377 CAAATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTCTTTTTCTT
Found at i:59994582 original size:21 final size:21
Alignment explanation
Indices: 59994556--59994595 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
59994546 TTTAGTTAGC
59994556 CTTGAAAAGG-TTGCATTTTCA
1 CTTGAAAAGGATTG-ATTTTCA
59994577 CTTGAAAAGGATTGATTTT
1 CTTGAAAAGGATTGATTTT
59994596 GTGATAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
CTTGAAAAGGATTGATTTTCA
Found at i:59997328 original size:100 final size:100
Alignment explanation
Indices: 59997206--59997569 Score: 712
Period size: 100 Copynumber: 3.6 Consensus size: 100
59997196 TTTTATGATT
59997206 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
1 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
59997271 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
66 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
59997306 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
1 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
59997371 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
66 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
59997406 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
1 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
59997471 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
66 AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
*
59997506 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACC-GATTAACCGAA
1 TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
59997570 TTCGGTCGAT
Statistics
Matches: 263, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
99 10 0.04
100 253 0.96
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (100 bp):
TTTCGGTTAACGGTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTAACCGACCTTATTAACCGAA
AAAATTCCGGTTCATTTAATTTAAAAAAAAAATCG
Found at i:59998224 original size:21 final size:21
Alignment explanation
Indices: 59998199--59998241 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
59998189 TAATTTGGTC
59998199 ATTTAACTATT-AATTATTTCG
1 ATTTAACTATTCAATT-TTTCG
*
59998220 ATTTAATTATTCAATTTTTCG
1 ATTTAACTATTCAATTTTTCG
59998241 A
1 A
59998242 AATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTTAACTATTCAATTTTTCG
Found at i:60004410 original size:18 final size:20
Alignment explanation
Indices: 60004370--60004411 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
60004360 TCTCTCAACA
*
60004370 AAAATTTCAAAATAATTTTT
1 AAAATTTCAAAATAATTTAT
*
60004390 AAAA-TTCAAACT-ATTTAT
1 AAAATTTCAAAATAATTTAT
60004408 AAAA
1 AAAA
60004412 AATTATAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTCAAAATAATTTAT
Found at i:60007905 original size:12 final size:12
Alignment explanation
Indices: 60007879--60007919 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
60007869 ATATTTGCAG
*
60007879 CTTTTTCCTTCTT
1 CTTTTTCATT-TT
60007892 CTTTTTCATTTT
1 CTTTTTCATTTT
60007904 CTTTTTCATTTT
1 CTTTTTCATTTT
60007916 -TTTT
1 CTTTT
60007920 CTTTTTCCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 4 0.15
12 14 0.52
13 9 0.33
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (12 bp):
CTTTTTCATTTT
Found at i:60012145 original size:41 final size:40
Alignment explanation
Indices: 60012074--60012175 Score: 150
Period size: 41 Copynumber: 2.5 Consensus size: 40
60012064 GGCTTAGCAC
* * *
60012074 CTAGCAGGCTATTGCCAGTGAAACAATTCAGACTTTATGT
1 CTAGCAGGCTAATGCCGGTGAAACAATTCAGACTATATGT
*
60012114 CTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGT
1 CTAGCAGGC-TAATGCCGGTGAAACAATTCAGACTATATGT
60012155 CTAGCAGGCTAAGTGCCGGTG
1 CTAGCAGGCTAA-TGCCGGTG
60012176 TCCTGAATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 12 0.21
41 44 0.79
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (40 bp):
CTAGCAGGCTAATGCCGGTGAAACAATTCAGACTATATGT
Found at i:60016417 original size:40 final size:41
Alignment explanation
Indices: 60016323--60016420 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
60016313 TGATCTCAGT
* *
60016323 TTCGCACACTTAGTGCTTGTTATTTAACATCATTATTTAAA
1 TTCGCACACTTAGTGCTTGTTATTCAACATCATCATTTAAA
*
60016364 TTCGCACACTTAGTGCTCT-TTATTCAACCTCATCATTT-AA
1 TTCGCACACTTAGTGCT-TGTTATTCAACATCATCATTTAAA
60016404 TTCGCACACTTAGTGCT
1 TTCGCACACTTAGTGCT
60016421 AATCATATAG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 19 0.36
41 33 0.62
42 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (41 bp):
TTCGCACACTTAGTGCTTGTTATTCAACATCATCATTTAAA
Found at i:60020361 original size:16 final size:16
Alignment explanation
Indices: 60020327--60020365 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
60020317 CCATGGAGGG
*
60020327 AGAGAGAGAGAAAACA
1 AGAGAGAGAGAAAAAA
60020343 AGAG-GAGAGAATAAAA
1 AGAGAGAGAGAA-AAAA
60020359 AGAGAGA
1 AGAGAGA
60020366 AAGTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 11 0.55
17 2 0.10
ACGTcount: A:0.62, C:0.03, G:0.33, T:0.03
Consensus pattern (16 bp):
AGAGAGAGAGAAAAAA
Found at i:60020452 original size:19 final size:19
Alignment explanation
Indices: 60020428--60020472 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
60020418 AAAAAAAAAG
60020428 TATTTTTATTAATTTTTAA
1 TATTTTTATTAATTTTTAA
**
60020447 TATTTTTATTGGTTTTTAA
1 TATTTTTATTAATTTTTAA
60020466 TATTTTT
1 TATTTTT
60020473 TAGATTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TATTTTTATTAATTTTTAA
Found at i:60021558 original size:39 final size:39
Alignment explanation
Indices: 60021440--60021590 Score: 185
Period size: 40 Copynumber: 3.8 Consensus size: 39
60021430 CATTTGGATA
* * * *
60021440 AAAAAATGCCGCTAAAAATCAATCATTAGCGGCGCTTTTA
1 AAAAAACGCCGCTAAAAAT-TAGCATTAGCGGCGCTTTTC
* *
60021480 AAAAAACACCGCTAAAAATTGAGTATTAGCGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATT-AGCATTAGCGGCGCTTTTC
* *
60021520 AGAATACGCCGCTAAAAATTAGCATTAGCGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTTC
** *
60021559 AAAAAACGATGCTAAAAATGAGCATTAGCGGC
1 AAAAAACGCCGCTAAAAATTAGCATTAGCGGC
60021591 ATTTTCTGAA
Statistics
Matches: 95, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 45 0.47
40 50 0.53
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTTC
Found at i:60021707 original size:41 final size:41
Alignment explanation
Indices: 60021650--60021843 Score: 225
Period size: 41 Copynumber: 4.7 Consensus size: 41
60021640 TGAGTTTTTT
* * *
60021650 GGGCTTTAGTGGCGTTTTTGAAAAAGAGTCGCTAATGCATG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCATG
* * * *
60021691 GGGCTTTAGCAGCGTTTTCGAAAAGGCGCCGCTAATGCTTG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCATG
* *
60021732 GGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC-TCA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT-G
*
60021773 GGGCTTTAGCAGCGTTTTT-AAATAAGCGCCGCTAATGTTCA--
1 GGGCTTTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATG--CATG
*
60021814 AGGCTTTAGCGGCGTTTTTGAAAAAGCGCC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCC
60021844 ACAAAAAATA
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
40 4 0.03
41 125 0.94
42 3 0.02
43 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCATG
Found at i:60021784 original size:82 final size:82
Alignment explanation
Indices: 60021650--60021843 Score: 259
Period size: 82 Copynumber: 2.4 Consensus size: 82
60021640 TGAGTTTTTT
* * * *
60021650 GGGCTTTAGTGGCGTTTTTGAAAAAGAGTCGCTAATGCATGGGGCTTTAGCAGCGTTTTCGAAA-
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCATAGGGCTTTAGCAGCGTTTT-GAAAT
* *
60021714 AGGCGCCGCTAATGCTT-G
65 AAGCGCCGCTAATG-TTCA
* *
60021732 GGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC-TCAGGGCTTTAGCAGCGTTTTTAAAT
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT-AGGGCTTTAGCAGCGTTTTGAAAT
60021796 AAGCGCCGCTAATGTTCA
65 AAGCGCCGCTAATGTTCA
*
60021814 AGGCTTTAGCGGCGTTTTTGAAAAAGCGCC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCC
60021844 ACAAAAAATA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
81 6 0.06
82 93 0.94
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (82 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCATAGGGCTTTAGCAGCGTTTTGAAATA
AGCGCCGCTAATGTTCA
Found at i:60022291 original size:21 final size:21
Alignment explanation
Indices: 60022264--60022320 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
60022254 TAAAGACTGG
60022264 GGTTTAAGGTTTAGAGGTTAT
1 GGTTTAAGGTTTAGAGGTTAT
*
60022285 -GTGTTAAGGGTTTAG-GTTTAT
1 GGT-TTAA-GGTTTAGAGGTTAT
*
60022306 GGTTTACGGTTTAGA
1 GGTTTAAGGTTTAGA
60022321 TTAACTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 9 0.30
21 12 0.40
22 9 0.30
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (21 bp):
GGTTTAAGGTTTAGAGGTTAT
Found at i:60023041 original size:15 final size:15
Alignment explanation
Indices: 60023021--60023054 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
60023011 CTTGTATTAT
60023021 TATTAATTCA-ATATA
1 TATTAATT-ATATATA
60023036 TATTAATTATATATA
1 TATTAATTATATATA
60023051 TATT
1 TATT
60023055 TCATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAATTATATATA
Found at i:60023711 original size:26 final size:26
Alignment explanation
Indices: 60023670--60023728 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
60023660 GGAGCTCAGA
60023670 ACGGCG-T-GCTGCGATTCGGTCTCC
1 ACGGCGTTAGCTGCGATTCGGTCTCC
*
60023694 ACGGCGTTAGCTGTGATTCGGTCTCC
1 ACGGCGTTAGCTGCGATTCGGTCTCC
*
60023720 ACCGCGTTA
1 ACGGCGTTA
60023729 AGAGCGACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 6 0.19
25 1 0.03
26 24 0.77
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.27
Consensus pattern (26 bp):
ACGGCGTTAGCTGCGATTCGGTCTCC
Found at i:60026300 original size:43 final size:43
Alignment explanation
Indices: 60026235--60026342 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
60026225 AAATATTTTT
* * * *
60026235 TAAAAGTCATG-TTTTTAGCGGCGTTTGTCGTAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTCGGAGAAGCACCGC
* * *
60026277 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGGAGAGGCATCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTCGGAGAAGCACCGC
*
60026320 TAAAGATCATGA-CTTTTAGCGGC
1 TAAAGGTCATGATC-TTTAGCGGC
60026343 TTTTTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 11 0.20
43 45 0.80
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTCGGAGAAGCACCGC
Found at i:60028319 original size:14 final size:14
Alignment explanation
Indices: 60028297--60028348 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
60028287 TCTCCTTCCT
*
60028297 TTTCCTTTTCTTTC
1 TTTCTTTTTCTTTC
60028311 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
* *
60028325 TGTT-TCATTTCTATC
1 T-TTCT-TTTTCTTTC
60028340 TTTCTTTTT
1 TTTCTTTTT
60028349 ATTTATTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:60030406 original size:28 final size:27
Alignment explanation
Indices: 60030347--60030410 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
60030337 AAATAAAAAT
* *
60030347 TTACCAAAATATTATCCCTTTTTTTAT
1 TTACCAAAATATTATCACTTTTTTTAA
* *
60030374 TTACCAAAATATTATTATTATTTTTTAA
1 TTACCAAAATATTATCACT-TTTTTTAA
60030402 TTACCAAAA
1 TTACCAAAA
60030411 AATACCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATTATCACTTTTTTTAA
Found at i:60030555 original size:4 final size:4
Alignment explanation
Indices: 60030546--60030633 Score: 55
Period size: 4 Copynumber: 22.0 Consensus size: 4
60030536 GAAGGAGAGG
*
60030546 GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA GGAAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GAAA GAAA
60030594 -AAA G-AA G-AA GAAGA GGAAA GGAGAA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAA-A -GAAA -GA-AA GAAA GAAA GAAA GAAA
60030634 AGGAAAAGAG
Statistics
Matches: 72, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
3 19 0.26
4 29 0.40
5 18 0.25
6 6 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:60030570 original size:10 final size:10
Alignment explanation
Indices: 60030547--60030639 Score: 53
Period size: 10 Copynumber: 8.7 Consensus size: 10
60030537 AAGGAGAGGG
60030547 AAAGAAAGAAA
1 AAAGAAAG-AA
60030558 GAAAGAAA-AA
1 -AAAGAAAGAA
*
60030568 GAAGGAAAGAA
1 -AAAGAAAGAA
*
60030579 AAGGAAAGGAA
1 AAAGAAA-GAA
*
60030590 AAAAAAAGAA
1 AAAGAAAGAA
* *
60030600 GAAGAAGAGGA
1 AAAGAA-AGAA
*
60030611 AAGGAGAAGAAA
1 AAAGA-AAG-AA
60030623 AAAGAAAGAA
1 AAAGAAAGAA
*
60030633 AAGGAAA
1 AAAGAAA
60030640 AGAGAAGAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
10 31 0.48
11 21 0.32
12 13 0.20
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:60030586 original size:32 final size:32
Alignment explanation
Indices: 60030550--60030691 Score: 116
Period size: 32 Copynumber: 4.3 Consensus size: 32
60030540 GAGAGGGAAA
60030550 GAAAGAAAGAAAGAAA-AAGAAGGAAAGAAAAG
1 GAAAGAAA-AAAGAAAGAAGAAGGAAAGAAAAG
*
60030582 GAAAGGAAAAAA-AAAGAAGAA-GAAGAGGAAAG
1 GAAA-GAAAAAAGAAAGAAGAAGGAA-AGAAAAG
*
60030614 GAGAAGAAAAAAGAAAGAA-AAGGAAAAGAGAAG
1 GA-AAGAAAAAAGAAAGAAGAAGG-AAAGAAAAG
*
60030647 AGAAAAAAAAAAGAAGATGGAAGGAAGGAAA-AAAAG
1 -GAAAGAAAAAAGAA-A--GAA-GAAGGAAAGAAAAG
*
60030683 GGAA-AAAAA
1 GAAAGAAAAA
60030692 GGTAATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
31 6 0.07
32 29 0.32
33 29 0.32
34 10 0.11
35 3 0.03
36 7 0.08
37 3 0.03
38 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (32 bp):
GAAAGAAAAAAGAAAGAAGAAGGAAAGAAAAG
Found at i:60030593 original size:27 final size:26
Alignment explanation
Indices: 60030545--60030639 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 26
60030535 AGAAGGAGAG
*
60030545 GGAAAG-AAA-GAAAGAAAGAAAAAGAA
1 GGAAAGAAAAGGAAAGGAA-AAAAA-AA
60030571 GGAAAGAAAAGGAAAGGAAAAAAAAA
1 GGAAAGAAAAGGAAAGGAAAAAAAAA
* *
60030597 GAAGAAGAAGAGGAAAGGAGAAGAAAAAA
1 GGA-AAGAAAAGGAAAGGA-AA-AAAAAA
60030626 -GAAAGAAAAGGAAA
1 GGAAAGAAAAGGAAA
60030640 AGAGAAGAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.17
27 33 0.56
28 10 0.17
29 6 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (26 bp):
GGAAAGAAAAGGAAAGGAAAAAAAAA
Found at i:60030623 original size:29 final size:28
Alignment explanation
Indices: 60030554--60030680 Score: 108
Period size: 29 Copynumber: 4.6 Consensus size: 28
60030544 GGGAAAGAAA
60030554 GAAA-GAAAG-AAAAAGAAGGAAAGAAAAG
1 GAAAGGAAAGAAAAAAGAA-G-AAGAAAAG
*
60030582 GAAAGGAAA-AAAAAAGAAGAAGAAGAG
1 GAAAGGAAAGAAAAAAGAAGAAGAAAAG
60030609 GAAAGGAGAAGAAAAAAG-A-AAGAAAAG
1 GAAAGGA-AAGAAAAAAGAAGAAGAAAAG
*
60030636 GAAAAGAGAAGAGAAAAAA-AA-AAGAAGATG
1 G-AAAG-GAA-AGAAAAAAGAAGAAGAA-AAG
*
60030666 G-AAGGAAGGAAAAAA
1 GAAAGGAAAGAAAAAA
60030681 AGGGAAAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
26 7 0.08
27 25 0.29
28 16 0.19
29 35 0.41
30 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (28 bp):
GAAAGGAAAGAAAAAAGAAGAAGAAAAG
Found at i:60030644 original size:27 final size:27
Alignment explanation
Indices: 60030555--60030653 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 27
60030545 GGAAAGAAAG
60030555 AAAGA-AAGAAAAAGAAGGAAAGAAAAGG-
1 AAAGAGAAG-AAAA-AA-GAAAGAAAAGGA
* *
60030583 AAAG-GAAAAAAAAAGAAGAAGAAGAGGA
1 AAAGAGAAGAAAAAAG-A-AAGAAAAGGA
*
60030611 AAGGAGAAGAAAAAAGAAAGAAAAGGA
1 AAAGAGAAGAAAAAAGAAAGAAAAGGA
60030638 AAAGAGAAGAGAAAAA
1 AAAGAGAAGA-AAAAA
60030654 AAAAAGAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
25 1 0.02
26 3 0.05
27 30 0.51
28 15 0.25
29 10 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (27 bp):
AAAGAGAAGAAAAAAGAAAGAAAAGGA
Found at i:60030656 original size:22 final size:22
Alignment explanation
Indices: 60030583--60030656 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
60030573 AAAGAAAAGG
*
60030583 AAAGGAAAAAAAAAGAAGAAGAAGA
1 AAAGGAAAAGAAAA-AAGAA-AA-A
* *
60030608 GGAAAGGAGAAGAAAAAAGAAAGA
1 --AAAGGAAAAGAAAAAAGAAAAA
* *
60030632 AAAGGAAAAGAGAAGAGAAAAA
1 AAAGGAAAAGAAAAAAGAAAAA
60030654 AAA
1 AAA
60030657 AAGAAGATGG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 21 0.52
24 1 0.03
25 1 0.03
26 5 0.12
27 12 0.30
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
AAAGGAAAAGAAAAAAGAAAAA
Found at i:60030658 original size:18 final size:17
Alignment explanation
Indices: 60030553--60030660 Score: 51
Period size: 18 Copynumber: 6.1 Consensus size: 17
60030543 AGGGAAAGAA
60030553 AGAAAGAAAGAAAAAGAAG
1 AGAAAGAAA-AAAAA-AAG
** *
60030572 -GAAAGAAAAGGAAAGG
1 AGAAAGAAAAAAAAAAG
*
60030588 A-AAAAAAAAGAAGAAGAAG
1 AGAAAGAAAA-AA-AA-AAG
* *
60030607 AGGAAAGGAGAAGAAAAA-
1 A-GAAA-GAAAAAAAAAAG
**
60030625 AGAAAGAAAAGGAAAAG
1 AGAAAGAAAAAAAAAAG
60030642 AGAAGAGAAAAAAAAAAG
1 AGAA-AGAAAAAAAAAAG
60030660 A
1 A
60030661 AGATGGAAGG
Statistics
Matches: 66, Mismatches: 14, Indels: 19
0.67 0.14 0.19
Matches are distributed among these distances:
16 18 0.27
17 11 0.17
18 23 0.35
19 5 0.08
20 2 0.03
21 4 0.06
22 3 0.05
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAAAG
Found at i:60030662 original size:16 final size:17
Alignment explanation
Indices: 60030617--60030663 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
60030607 AGGAAAGGAG
60030617 AAGAAAAAAGAA-AGAA
1 AAGAAAAAAGAAGAGAA
*
60030633 AAGGAAAAGAGAAGAGAA
1 AA-GAAAAAAGAAGAGAA
60030651 AA-AAAAAAGAAGA
1 AAGAAAAAAGAAGA
60030664 TGGAAGGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 9 0.33
18 6 0.22
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAGAAGAGAA
Found at i:60030673 original size:27 final size:27
Alignment explanation
Indices: 60030573--60030681 Score: 102
Period size: 27 Copynumber: 4.0 Consensus size: 27
60030563 AAAAAGAAGG
*
60030573 AAAGAAAAGGAAAGGAA-A-AAAAAAGA
1 AAAGAAGAGGAAAGGAAGAGAAAAAA-A
*
60030599 AGAAGAAGAGGAAAGG-AGAAGAAAAAAG
1 A-AAGAAGAGGAAAGGAAG-AGAAAAAAA
*
60030627 AAAGAAAAGGAAAAGAGAAGAGAAAAAAA
1 AAAGAAGAGG-AAAG-GAAGAGAAAAAAA
60030656 AAAGAAGATGG-AAGGAAG-GAAAAAAA
1 AAAGAAGA-GGAAAGGAAGAGAAAAAAA
60030682 GGGAAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
26 10 0.14
27 25 0.36
28 9 0.13
29 22 0.31
30 4 0.06
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (27 bp):
AAAGAAGAGGAAAGGAAGAGAAAAAAA
Found at i:60030828 original size:13 final size:13
Alignment explanation
Indices: 60030810--60030850 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
60030800 TTTTTGCAAC
*
60030810 CCAAATTCCCAAA
1 CCAAATACCCAAA
60030823 CCAAATACCCAAA
1 CCAAATACCCAAA
* *
60030836 TCTAATACCCAAA
1 CCAAATACCCAAA
60030849 CC
1 CC
60030851 TAAACCCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
CCAAATACCCAAA
Found at i:60030853 original size:13 final size:13
Alignment explanation
Indices: 60030817--60030858 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
60030807 AACCCAAATT
*
60030817 CCCAAACCAAATA
1 CCCAAACCTAATA
*
60030830 CCCAAATCTAATA
1 CCCAAACCTAATA
60030843 CCCAAACCTAA-A
1 CCCAAACCTAATA
60030855 CCCA
1 CCCA
60030859 CTACCCCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (13 bp):
CCCAAACCTAATA
Found at i:60032032 original size:18 final size:18
Alignment explanation
Indices: 60031950--60032032 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 18
60031940 TAATGTTATC
60031950 ATTATTTTTACTACTATT
1 ATTATTTTTACTACTATT
**
60031968 ATTATGTTTAATACTGTTATCACT
1 ATTAT-TTT--TACTACTAT---T
* *
60031992 ATTATTTTT-TTA-TTTT
1 ATTATTTTTACTACTATT
60032008 ATATATTTTTACTACTATT
1 AT-TATTTTTACTACTATT
60032027 ATTATT
1 ATTATT
60032033 ATTCTTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 11 0.22
19 10 0.20
20 1 0.02
21 8 0.16
23 3 0.06
24 6 0.12
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTATTTTTACTACTATT
Found at i:60034349 original size:275 final size:275
Alignment explanation
Indices: 60034015--60034600 Score: 1104
Period size: 275 Copynumber: 2.1 Consensus size: 275
60034005 ATTTTTAAAA
* * * * *
60034015 AAAATTCAGAAATAATCAATAC-AAATAATTGAAACAAAATGTACTGAAATAATATAAAATAATA
1 AAAATTAAGAAATAATTAATACAAAATATTTCAAAAAAAATGTACTGAAATAATATAAAATAATA
60034079 AAATACGAAAATAATATATTTTTATT-CAAAGTAATAAAAATGGGGAAAACAATAATACGAGCAA
66 AAATACGAAAATAATA-ATTTTTATTGCAAAGTAATAAAAATGGGGAAAACAATAATACGAGCAA
60034143 AGGGTAGGGAAAAAGGTTTTTTTTTTGTTTTTACCAAAATATTACAAAAAAATAAAAAAATACCG
130 AGGGTAGGGAAAAAGGTTTTTTTTTTGTTTTTACCAAAATATTACAAAAAAATAAAAAAATACCG
60034208 AAATATTATAAACTTTTTTTTATTTACCAAAAAATACGACCAAATGGCGGAAGTAAGAGTGTAGT
195 AAATATTATAAACTTTTTTTTATTTACCAAAAAATACGACCAAATGGCGGAAGTAAGAGTGTAGT
60034273 AATACTAACTTTTTTT
260 AATACTAACTTTTTTT
60034289 AAAATTAAGAAATAATTAATACAAAATATTTCAAAAAAAATGTACTGAAATAATATAAAATAATA
1 AAAATTAAGAAATAATTAATACAAAATATTTCAAAAAAAATGTACTGAAATAATATAAAATAATA
60034354 AAATACGAAAATAATAATTTTTATTGCAAAGTAATAAAAATGGGGAAAACAATAATACGAGCAAA
66 AAATACGAAAATAATAATTTTTATTGCAAAGTAATAAAAATGGGGAAAACAATAATACGAGCAAA
60034419 GGGTAGGGAAAAAGGTTTTTTTTTTGTTTTTACCAAAATATTACAAAAAAATAAAAAAATACCGA
131 GGGTAGGGAAAAAGGTTTTTTTTTTGTTTTTACCAAAATATTACAAAAAAATAAAAAAATACCGA
60034484 AATATTATAAACTTTTTTTTATTTACCAAAAAATACGACCAAATGGCGGAAGTAAGAGTGTAGTA
196 AATATTATAAACTTTTTTTTATTTACCAAAAAATACGACCAAATGGCGGAAGTAAGAGTGTAGTA
60034549 ATACTAACTTTTTTT
261 ATACTAACTTTTTTT
60034564 AAAATTAAGAAATAATTAATACAAAATATTTCAAAAA
1 AAAATTAAGAAATAATTAATACAAAATATTTCAAAAA
60034601 TTTTTTTCAA
Statistics
Matches: 305, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
274 29 0.10
275 276 0.90
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (275 bp):
AAAATTAAGAAATAATTAATACAAAATATTTCAAAAAAAATGTACTGAAATAATATAAAATAATA
AAATACGAAAATAATAATTTTTATTGCAAAGTAATAAAAATGGGGAAAACAATAATACGAGCAAA
GGGTAGGGAAAAAGGTTTTTTTTTTGTTTTTACCAAAATATTACAAAAAAATAAAAAAATACCGA
AATATTATAAACTTTTTTTTATTTACCAAAAAATACGACCAAATGGCGGAAGTAAGAGTGTAGTA
ATACTAACTTTTTTT
Found at i:60036769 original size:11 final size:11
Alignment explanation
Indices: 60036753--60036779 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60036743 TTTATAACTT
60036753 AATTTGGATAC
1 AATTTGGATAC
60036764 AATTTGGATAC
1 AATTTGGATAC
60036775 AATTT
1 AATTT
60036780 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:60039053 original size:18 final size:18
Alignment explanation
Indices: 60039030--60039074 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
60039020 ATCCCAATGA
60039030 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
* *
60039048 TCGCCAGCACCTTCTTCT
1 TCGCCACCACATTCTTCT
*
60039066 TCACCACCA
1 TCGCCACCA
60039075 ACCATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:60040394 original size:25 final size:27
Alignment explanation
Indices: 60040358--60040424 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 27
60040348 TTTTTTTGGT
*
60040358 ATATTTTCGTAAAT-AAAAAAAAG-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTA
60040383 ATATTTTGGTAAATAAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAAG-T-TA
60040412 ATATTTTGGTAAA
1 ATATTTTGGTAAA
60040425 CTTTTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 13 0.35
26 9 0.24
29 15 0.41
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAAAGTTA
Found at i:60050761 original size:45 final size:46
Alignment explanation
Indices: 60050668--60050789 Score: 151
Period size: 45 Copynumber: 2.7 Consensus size: 46
60050658 ATTAAAAATA
60050668 TCAAATAATTATTTCAAATATCACTATTATTTATATATATAATATT
1 TCAAATAATTATTTCAAATATCACTATTATTTATATATATAATATT
* * * *
60050714 TCAAAAAATTGTTTCAAATATCATTATT-TTTATATGTGA-AATATT
1 TCAAATAATTATTTCAAATATCACTATTATTTATATAT-ATAATATT
** *
60050759 TCAAATAATTATTAGAAATATCAATA-TATTT
1 TCAAATAATTATTTCAAATATCACTATTATTT
60050790 TCACCTACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 38 0.58
46 26 0.40
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (46 bp):
TCAAATAATTATTTCAAATATCACTATTATTTATATATATAATATT
Found at i:60061252 original size:12 final size:11
Alignment explanation
Indices: 60061224--60061253 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
60061214 CCACTTTTTT
60061224 TATTTTTAAAA
1 TATTTTTAAAA
60061235 TATTTTTAAAA
1 TATTTTTAAAA
60061246 TACTTTTT
1 TA-TTTTT
60061254 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:60061672 original size:30 final size:30
Alignment explanation
Indices: 60061596--60061680 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 30
60061586 TAGAACTCAT
* *
60061596 AAAATTATAAAAAAAACAAATTTATTTTTTA
1 AAAATTATAAAAAAAATAAGTTTA-TTTTTA
60061627 AAAATTAT-AAAAAAATAAGTTTATTTTTA
1 AAAATTATAAAAAAAATAAGTTTATTTTTA
*
60061656 AAAATTATAAAAAAAATAAGATTAT
1 AAAATTATAAAAAAAATAAGTTTAT
60061681 AAGTATGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.28
30 28 0.56
31 8 0.16
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTATAAAAAAAATAAGTTTATTTTTA
Found at i:60061774 original size:21 final size:20
Alignment explanation
Indices: 60061729--60061775 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
60061719 ATTGTATTGT
*
60061729 TTTTA-GAAAACTTTTAGAA
1 TTTTATGAAAAATTTTAGAA
**
60061748 AATTATGAAAAATTTTAAGAA
1 TTTTATGAAAAATTTT-AGAA
60061769 TTTTATG
1 TTTTATG
60061776 GTATTTCTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.14
20 9 0.43
21 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (20 bp):
TTTTATGAAAAATTTTAGAA
Found at i:60061861 original size:19 final size:17
Alignment explanation
Indices: 60061839--60061893 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 17
60061829 AAAAGTGCAA
60061839 AAAATCTAAAATTTTTCAT
1 AAAATCTAAAA-TTTTC-T
60061858 AAAATTCTAAAATTTTCT
1 AAAA-TCTAAAATTTTCT
*
60061876 AAAACCT-AAA-TTTCT
1 AAAATCTAAAATTTTCT
60061891 AAA
1 AAA
60061894 CAAATAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 8 0.24
16 3 0.09
17 2 0.06
18 5 0.15
19 9 0.26
20 7 0.21
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATCTAAAATTTTCT
Found at i:60063070 original size:19 final size:20
Alignment explanation
Indices: 60063030--60063070 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
60063020 ATATAAGCTA
*
60063030 TTATTTTTAATATATTAAAT
1 TTATTCTTAATATATTAAAT
*
60063050 TTATTCTTAAT-TATTACAT
1 TTATTCTTAATATATTAAAT
60063069 TT
1 TT
60063071 TGTATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTCTTAATATATTAAAT
Found at i:60077213 original size:20 final size:20
Alignment explanation
Indices: 60077168--60077214 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
60077158 TTTCAAAATA
60077168 TAATT-ATAATTTTTATTAT
1 TAATTAATAATTTTTATTAT
**
60077187 TTTTTAATAATTTTTA-TAT
1 TAATTAATAATTTTTATTAT
60077206 GTAATTAAT
1 -TAATTAAT
60077215 GTTTTCATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TAATTAATAATTTTTATTAT
Found at i:60077312 original size:28 final size:26
Alignment explanation
Indices: 60077255--60077338 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 26
60077245 AATTTCAATA
*
60077255 ATGTAATTATTATTATTTTTATATAT
1 ATGTAATTATTATTATATTTATATAT
*
60077281 ATGTAATTATTTTTTATAATTTATATAT
1 ATGTAATTA-TTATTAT-ATTTATATAT
*
60077309 ATGT-ATAGATTTATT-T-TTTATATAT
1 ATGTAAT-TA-TTATTATATTTATATAT
60077334 ATGTA
1 ATGTA
60077339 CATGTAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 13 0.26
26 9 0.18
27 9 0.18
28 19 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATGTAATTATTATTATATTTATATAT
Found at i:60077330 original size:32 final size:28
Alignment explanation
Indices: 60077255--60077313 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
60077245 AATTTCAATA
* *
60077255 ATGTAATTA-TTATTAT-TTTTATATAT
1 ATGTAATTATTTTTTATAATTTATATAT
60077281 ATGTAATTATTTTTTATAATTTATATAT
1 ATGTAATTATTTTTTATAATTTATATAT
60077309 ATGTA
1 ATGTA
60077314 TAGATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.31
27 6 0.21
28 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (28 bp):
ATGTAATTATTTTTTATAATTTATATAT
Found at i:60081096 original size:18 final size:18
Alignment explanation
Indices: 60081073--60081108 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60081063 TGATGACTTT
60081073 TTGCATTCATTTCATGTA
1 TTGCATTCATTTCATGTA
**
60081091 TTGCATTTGTTTCATGTA
1 TTGCATTCATTTCATGTA
60081109 CATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (18 bp):
TTGCATTCATTTCATGTA
Found at i:60089501 original size:88 final size:88
Alignment explanation
Indices: 60089392--60089565 Score: 267
Period size: 88 Copynumber: 2.0 Consensus size: 88
60089382 CGGTGATATT
* *
60089392 TCAGCCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
1 TCAGCCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACT
* *
60089457 GGCAGTAAAGTAGATGGAAGATA
66 GACAGTAAAGTAGATCGAAGATA
* * * *
60089480 TCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCTTGTGCT
1 TCAGCCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACT
*
60089545 GACAGTGAAGTAGATCGAAGA
66 GACAGTAAAGTAGATCGAAGA
60089566 CATTAGTCTT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (88 bp):
TCAGCCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACT
GACAGTAAAGTAGATCGAAGATA
Found at i:60089557 original size:45 final size:44
Alignment explanation
Indices: 60089413--60089557 Score: 130
Period size: 45 Copynumber: 3.3 Consensus size: 44
60089403 TCCCTAAGCA
* **
60089413 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATT
1 GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTGCT
* * * * * * * * *
60089457 GGCAGTAAAGTAGATGGAAGATATCAG-CCTTGTCTCCCTGAGCA
1 -GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTGCT
* * *
60089501 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCTTGTGCT
1 GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTGCT
60089545 GACAGTGAAGTAG
1 G-CAGTGAAGTAG
60089558 ATCGAAGACA
Statistics
Matches: 73, Mismatches: 25, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
43 20 0.27
44 23 0.32
45 30 0.41
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (44 bp):
GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTGCT
Found at i:60089959 original size:168 final size:166
Alignment explanation
Indices: 60089589--60089960 Score: 354
Period size: 168 Copynumber: 2.2 Consensus size: 166
60089579 GCCTTGACGT
* * ** * * *
60089589 TGCAATGGAAAAGATTGAAGCCGCGACGTCGAATCTTATCTCCCTGGAGTTAAAGCTTGGATTAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATCTCCCTGGAGTTAAAGCTTGAAATAG
* * * * * * * *
60089654 CTGAAGTGGAGCGGATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTTGAACAG
66 CTAAAGCGAAGCGGATTAAAGCTGTGGACAGCGAATCCTATCTATTTAGCATTATAGTGGAACAG
***** *
60089719 ATTAAAGCTAAAGGTAGCGAATATTGTTTTCCTAGAAT
131 ATTAAAGCTAAAGGTA--GAATATTACACCCCTAGAAG
* * * * * * * *
60089757 TGCAGCGGAGCAGATTAAAGCTAGGGCAGCGAATCTTATCTCCCTGGCGTT-AGGACTTGAAATA
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATCTCCCTGGAGTTAAAG-CTTGAAATA
* *
60089821 GCTAAAGCGAAGCGGATTAAAGCTGTGGACAGCGAATCCTATCTATTTAGCATTTTTAGTGGAAT
65 GCTAAAGCGAAGCGGATTAAAGCTGTGGACAGCGAATCCTATCTATTTAGCA-TTATAGTGGAAC
* *
60089886 AGATTAAAGCCGTAATGGT-GAATCTTACACCCCT-GACAG
129 AGATTAAAG-C-TAAAGGTAGAATATTACACCCCTAGA-AG
*
60089925 TGTAGTGGAACAGATTGAAGCTACGACGGCGAATCT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCT
60089961 CGTTTCCCCA
Statistics
Matches: 159, Mismatches: 40, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
167 4 0.03
168 130 0.82
169 18 0.11
170 1 0.01
171 6 0.04
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (166 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATCTCCCTGGAGTTAAAGCTTGAAATAG
CTAAAGCGAAGCGGATTAAAGCTGTGGACAGCGAATCCTATCTATTTAGCATTATAGTGGAACAG
ATTAAAGCTAAAGGTAGAATATTACACCCCTAGAAG
Found at i:60090058 original size:44 final size:42
Alignment explanation
Indices: 60090000--60090159 Score: 144
Period size: 44 Copynumber: 3.8 Consensus size: 42
60089990 TGAAGATGAC
*
60090000 AAATCTTATTTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCA
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA-CCA
* * *
60090043 ATAATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCA
1 A-AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AAACCA
* * * * * * *
60090087 CAGATCTTATCTCTCTGAAGCTGTAG-AGAGCAGATCATATC-
1 -AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACCA
** *
60090128 AGGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 AAATCTTATCTCCCTGAAGTTGCAGTAGAGCA
60090160 TACCCAAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
40 21 0.22
41 5 0.05
42 3 0.03
43 8 0.09
44 53 0.56
45 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (42 bp):
AAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACCA
Found at i:60092097 original size:27 final size:26
Alignment explanation
Indices: 60092064--60092116 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
60092054 AATTGTCATT
*
60092064 GTTTATTTTTTTATGTATATTAGTTTC
1 GTTTATTTATTTATGTATATTA-TTTC
* *
60092091 GTTTATTTATTTGTTTATATTATTTC
1 GTTTATTTATTTATGTATATTATTTC
60092117 TATGTCATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (26 bp):
GTTTATTTATTTATGTATATTATTTC
Found at i:60092113 original size:13 final size:14
Alignment explanation
Indices: 60092079--60092116 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
60092069 TTTTTTTATG
60092079 TATATTAGTTTCGTT
1 TATATTA-TTTCGTT
60092094 TAT-TTATTT-GTT
1 TATATTATTTCGTT
60092106 TATATTATTTC
1 TATATTATTTC
60092117 TATGTCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:60092154 original size:15 final size:15
Alignment explanation
Indices: 60092123--60092156 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
60092113 TTTCTATGTC
*
60092123 ATTGTTGTATTTATT
1 ATTGTTGTATTCATT
*
60092138 ATTGTTGTATTCGTT
1 ATTGTTGTATTCATT
60092153 ATTG
1 ATTG
60092157 CGACATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.62
Consensus pattern (15 bp):
ATTGTTGTATTCATT
Found at i:60094485 original size:9 final size:9
Alignment explanation
Indices: 60094468--60094504 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
60094458 TAAGTTTTCG
60094468 AATTCGAAT
1 AATTCGAAT
*
60094477 AACTCGAAT
1 AATTCGAAT
60094486 AATTCGAAT
1 AATTCGAAT
60094495 AATTCGAAT
1 AATTCGAAT
60094504 A
1 A
60094505 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:60102451 original size:73 final size:72
Alignment explanation
Indices: 60102351--60102580 Score: 291
Period size: 73 Copynumber: 3.2 Consensus size: 72
60102341 CGTTTCCCAG
* * * * * * *
60102351 AAGCGCCGC-AAAGAACCTAAGCTCAACGACGCCATTTACCGAGCTTTTGGGGATTTAGCGGCAT
1 AAGCGCCGCTAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC-T
60102415 TTTTGAGA
65 TTTTGAGA
* * * *
60102423 AAGCGCCGCTAAAAAACCTAAGCCCAACGGCATCGTTTTCTGAGATTTCGGGGATTTAGCAGCGT
1 AAGCGCCGCTAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC-T
*
60102488 TTTTGGGA
65 TTTTGAGA
* * *
60102496 AAGCGCCGCTAAAAAACCTAAGCCCAACGATGTCGTTTTGTGAGCTTTCGGGGATTTAGCGGCGT
1 AAGCGCCGCTAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGCTT
60102561 TTTGAAGA
66 TTTG-AGA
60102569 AAGCGCCGCTAA
1 AAGCGCCGCTAA
60102581 TGTTCAGGGC
Statistics
Matches: 135, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
72 14 0.10
73 121 0.90
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (72 bp):
AAGCGCCGCTAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGCTT
TTTGAGA
Found at i:60102677 original size:114 final size:114
Alignment explanation
Indices: 60102473--60102939 Score: 574
Period size: 114 Copynumber: 4.1 Consensus size: 114
60102463 TGAGATTTCG
* * ** * *
60102473 GGGATTTAGCAGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCCCAACGATGTCGTTTTGTG
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCACAACGGCGCCGTTTTCTG
* *
60102538 AGCTTTCGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
66 AGATTTTGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
* * *
60102587 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCGAAAAAACCTAAGCACAACGGCGCCGTTTTCTG
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCACAACGGCGCCGTTTTCTG
* * * * *
60102652 AGATTTTGGGGATTGAGCGGCGTTTTTAGGAAAGCGCCACTAATGCTCA
66 AGATTTTGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
* ** * * * * *
60102701 GAGATTTATTGCCATTTTTGGGAAAGCGCTGCTAAAGAACCTAAGCACAACGGTGCCGTTTTCTG
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCACAACGGCGCCGTTTTCTG
* *
60102766 AGATTTTGGGGATTTAGCGGTGTTTTGAAGAAAGCGCTGCTAATGTTCA
66 AGATTTTGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
* * * *
60102815 GGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAAACCTAAACCCAACGGCGCCGTTTTC
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGC--TAAAAAACCTAAGCACAACGGCGCCGTTTTC
* * * * * * *
60102880 GGAGCTTTCAGGGGATTTAGCGGCGTTTTTAATAAAGCGTCGCTAATGGTCA
64 TGAGATTT-TGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
60102932 GGGATTTA
1 GGGATTTA
60102940 AAATAATTTA
Statistics
Matches: 294, Mismatches: 56, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
114 219 0.74
116 32 0.11
117 43 0.15
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (114 bp):
GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCACAACGGCGCCGTTTTCTG
AGATTTTGGGGATTTAGCGGCGTTTTGAAGAAAGCGCCGCTAATGTTCA
Found at i:60103187 original size:7 final size:7
Alignment explanation
Indices: 60103177--60103261 Score: 55
Period size: 7 Copynumber: 11.7 Consensus size: 7
60103167 GATTTAAGAT
60103177 TTAGGGG
1 TTAGGGG
*
60103184 TTAGGTG
1 TTAGGGG
* **
60103191 TTATGCT
1 TTAGGGG
60103198 TTAGGGG
1 TTAGGGG
60103205 TTATGGGG
1 TTA-GGGG
*
60103213 ATTTATGGG
1 --TTAGGGG
60103222 TTAGGGG
1 TTAGGGG
* **
60103229 TTATGCT
1 TTAGGGG
60103236 TTAGGGG
1 TTAGGGG
60103243 TTAGGGGG
1 TTA-GGGG
60103251 TTA-GGG
1 TTAGGGG
60103257 TTAGG
1 TTAGG
60103262 ATTTCAACGC
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
6 6 0.10
7 35 0.60
8 11 0.19
9 3 0.05
10 3 0.05
ACGTcount: A:0.15, C:0.02, G:0.45, T:0.38
Consensus pattern (7 bp):
TTAGGGG
Found at i:60103223 original size:38 final size:36
Alignment explanation
Indices: 60103174--60103261 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 36
60103164 TGGGATTTAA
*
60103174 GATTTAGGGGTTAGGTGTTATGCTTTAGGGGTTATGGG
1 GATTTA-GGGTTAGGGGTTATGCTTTAGGGGTTA-GGG
60103212 GATTTATGGGTTAGGGGTTATGCTTTAGGGGTTAGGG
1 GATTTA-GGGTTAGGGGTTATGCTTTAGGGGTTAGGG
*
60103249 G-GTTAGGGTTAGG
1 GATTTAGGGTTAGG
60103262 ATTTCAACGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
35 8 0.17
36 3 0.06
37 4 0.09
38 32 0.68
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.38
Consensus pattern (36 bp):
GATTTAGGGTTAGGGGTTATGCTTTAGGGGTTAGGG
Found at i:60103424 original size:20 final size:20
Alignment explanation
Indices: 60103401--60103452 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
60103391 ATGTGTTAGA
60103401 GTTTGAGTTTGGGGTTTAAG
1 GTTTGAGTTTGGGGTTTAAG
* *
60103421 GTTTGAGTTTAGGGTTTTAGG
1 GTTTGAGTTT-GGGGTTTAAG
60103442 GTTT-AGTTTGG
1 GTTTGAGTTTGG
60103453 AAATTGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.48
Consensus pattern (20 bp):
GTTTGAGTTTGGGGTTTAAG
Found at i:60103652 original size:28 final size:28
Alignment explanation
Indices: 60103585--60103666 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
60103575 CAAAAAATAT
* **
60103585 GGTTTAGGA-TTACAGTTTGGGGTTTAC
1 GGTTTAGGATTTAGAGTTTAAGGTTTAC
* **
60103612 GGTTTA-GAGTTTAGAGTTTTAGGTTTGG
1 GGTTTAGGA-TTTAGAGTTTAAGGTTTAC
60103640 GGTTTAGGATTTATGA-TTTAAGGTTTA
1 GGTTTAGGATTTA-GAGTTTAAGGTTTA
60103667 TGGTATATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.05
27 6 0.14
28 32 0.73
29 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (28 bp):
GGTTTAGGATTTAGAGTTTAAGGTTTAC
Found at i:60103782 original size:7 final size:7
Alignment explanation
Indices: 60103727--60103786 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 7
60103717 AAGGGTTAAA
60103727 GTTTAGG
1 GTTTAGG
60103734 GTTTAAGG
1 GTTT-AGG
*
60103742 GTTTAATG
1 GTTT-AGG
60103750 GTTTAGG
1 GTTTAGG
*
60103757 ATTTTAGG
1 -GTTTAGG
60103765 GTTTA--
1 GTTTAGG
*
60103770 GATTAGG
1 GTTTAGG
60103777 GTTTAGG
1 GTTTAGG
60103784 GTT
1 GTT
60103787 AGATTTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 4 0.09
7 19 0.44
8 20 0.47
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:60103842 original size:15 final size:16
Alignment explanation
Indices: 60103824--60103856 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60103814 AGATAAATAT
*
60103824 AAAATAT-TATTTCAA
1 AAAATATATATATCAA
60103839 AAAATATATATATCAA
1 AAAATATATATATCAA
60103855 AA
1 AA
60103857 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATATATATCAA
Found at i:60105741 original size:9 final size:9
Alignment explanation
Indices: 60105727--60106008 Score: 183
Period size: 9 Copynumber: 31.8 Consensus size: 9
60105717 TTTAATTTAA
*
60105727 TACATAATT
1 TACATAACT
60105736 TACATAACT
1 TACATAACT
*
60105745 CACATAACT
1 TACATAACT
* *
60105754 TACAAAAGT
1 TACATAACT
* *
60105763 CACAT-ACA
1 TACATAACT
60105771 TACATAACT
1 TACATAACT
*
60105780 TA-ATAAAT
1 TACATAACT
*
60105788 GGTACATAGCT
1 --TACATAACT
*
60105799 TATATAACT
1 TACATAACT
60105808 TACATAA--
1 TACATAACT
60105815 TACATAACT
1 TACATAACT
* *
60105824 TAAATAA-A
1 TACATAACT
60105832 TACATAACT
1 TACATAACT
**
60105841 TATTTAA--
1 TACATAACT
*
60105848 TACATTACT
1 TACATAACT
60105857 TACATAATAACT
1 TAC---ATAACT
*
60105869 TACATAGCT
1 TACATAACT
*
60105878 TATATAACT
1 TACATAACT
60105887 TACATAACT
1 TACATAACT
*
60105896 TATATAACT
1 TACATAACT
60105905 TACATAA--
1 TACATAACT
60105912 TACATAACT
1 TACATAACT
* *
60105921 TAAATAA-A
1 TACATAACT
60105929 TACATAACT
1 TACATAACT
**
60105938 TATTTAA--
1 TACATAACT
*
60105945 TACATTACT
1 TACATAACT
60105954 TACATAATAACT
1 TAC---ATAACT
*
60105966 TACATAGCT
1 TACATAACT
*
60105975 TATATAACT
1 TACATAACT
60105984 TACATAACT
1 TACATAACT
*
60105993 TATATAACT
1 TACATAACT
60106002 TACATAA
1 TACATAA
60106009 TACATATTAT
Statistics
Matches: 204, Mismatches: 49, Indels: 40
0.70 0.17 0.14
Matches are distributed among these distances:
7 22 0.11
8 22 0.11
9 138 0.68
10 2 0.01
11 4 0.02
12 16 0.08
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.35
Consensus pattern (9 bp):
TACATAACT
Found at i:60105901 original size:97 final size:97
Alignment explanation
Indices: 60105790--60106014 Score: 441
Period size: 97 Copynumber: 2.3 Consensus size: 97
60105780 TAATAAATGG
*
60105790 TACATAGCTTATATAACTTACATAATACATAACTTAAATAAATACATAACTTATTTAATACATTA
1 TACATAACTTATATAACTTACATAATACATAACTTAAATAAATACATAACTTATTTAATACATTA
60105855 CTTACATAATAACTTACATAGCTTATATAACT
66 CTTACATAATAACTTACATAGCTTATATAACT
60105887 TACATAACTTATATAACTTACATAATACATAACTTAAATAAATACATAACTTATTTAATACATTA
1 TACATAACTTATATAACTTACATAATACATAACTTAAATAAATACATAACTTATTTAATACATTA
60105952 CTTACATAATAACTTACATAGCTTATATAACT
66 CTTACATAATAACTTACATAGCTTATATAACT
60105984 TACATAACTTATATAACTTACATAATACATA
1 TACATAACTTATATAACTTACATAATACATA
60106015 TTATATGTGC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 127 1.00
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (97 bp):
TACATAACTTATATAACTTACATAATACATAACTTAAATAAATACATAACTTATTTAATACATTA
CTTACATAATAACTTACATAGCTTATATAACT
Found at i:60106772 original size:21 final size:21
Alignment explanation
Indices: 60106746--60106811 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60106736 AACTTAAAGC
* *
60106746 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60106767 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60106788 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60106809 AGA
1 AGA
60106812 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60106878 original size:108 final size:108
Alignment explanation
Indices: 60106705--60107612 Score: 1807
Period size: 108 Copynumber: 8.4 Consensus size: 108
60106695 CACAGTTGAG
*
60106705 GTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60106770 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60106813 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60106878 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60106921 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60106986 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107029 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60107094 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107137 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60107202 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107245 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60107310 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107353 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60107418 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107461 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
60107526 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
66 GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
60107569 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
60107613 TACGGACTCG
Statistics
Matches: 799, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 799 1.00
ACGTcount: A:0.39, C:0.17, G:0.32, T:0.12
Consensus pattern (108 bp):
GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
GGCTGCAGCGAGAGAAGCAGAGGCTGCAGCGAGAGAAATAGAT
Found at i:60106880 original size:21 final size:21
Alignment explanation
Indices: 60106854--60106919 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60106844 AACTTAAAGC
* *
60106854 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60106875 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60106896 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60106917 AGA
1 AGA
60106920 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60106988 original size:21 final size:21
Alignment explanation
Indices: 60106962--60107027 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60106952 AACTTAAAGC
* *
60106962 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60106983 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107004 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107025 AGA
1 AGA
60107028 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60107096 original size:21 final size:21
Alignment explanation
Indices: 60107070--60107135 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60107060 AACTTAAAGC
* *
60107070 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60107091 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107112 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107133 AGA
1 AGA
60107136 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60107204 original size:21 final size:21
Alignment explanation
Indices: 60107178--60107243 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60107168 AACTTAAAGC
* *
60107178 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60107199 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107220 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107241 AGA
1 AGA
60107244 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60107312 original size:21 final size:21
Alignment explanation
Indices: 60107286--60107351 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60107276 AACTTAAAGC
* *
60107286 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60107307 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107328 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107349 AGA
1 AGA
60107352 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60107420 original size:21 final size:21
Alignment explanation
Indices: 60107394--60107459 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60107384 AACTTAAAGC
* *
60107394 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60107415 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107436 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107457 AGA
1 AGA
60107460 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60107528 original size:21 final size:21
Alignment explanation
Indices: 60107502--60107567 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
60107492 AACTTAAAGC
* *
60107502 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCTGCAGCGAGAGAAGT
*
60107523 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGT
*
60107544 AGAGGCTGCAGCGAGAGAAAT
1 AGAGGCTGCAGCGAGAGAAGT
60107565 AGA
1 AGA
60107568 TGTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGT
Found at i:60108066 original size:40 final size:40
Alignment explanation
Indices: 60107939--60108091 Score: 189
Period size: 40 Copynumber: 3.7 Consensus size: 40
60107929 TTTATTTGTT
* *
60107939 GCTAAAGAACATGATCTTTAGCGGCATTTTTCTTCAAGTGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTC-T-AAGCGCC
* * * *
60107981 GCTAAAAAACATGATCTTTAGCGTCGTCTTTTTTTTAAGCACC
1 GCTAAAGAACATGATCTTTAGCG--G-CGTTTTTCTAAGCGCC
60108024 GCTAAAGAACATGATCTTTAGCGGCGTTTTTCTAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTCTAAGCGCC
* *
60108064 GCTAAAGAACATGACCTTTAGCGACGTT
1 GCTAAAGAACATGATCTTTAGCGGCGTT
60108092 GTCGTTAGCG
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
40 39 0.40
41 1 0.01
42 22 0.23
43 27 0.28
44 2 0.02
45 6 0.06
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (40 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTCTAAGCGCC
Found at i:60112786 original size:20 final size:21
Alignment explanation
Indices: 60112754--60112792 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
60112744 TATCTTTACA
60112754 AACTAATAGCTAA-TAATTGC
1 AACTAATAGCTAACTAATTGC
60112774 AACTAATTA-CTAACTAATT
1 AACTAA-TAGCTAACTAATT
60112793 ACATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
AACTAATAGCTAACTAATTGC
Found at i:60113549 original size:19 final size:19
Alignment explanation
Indices: 60113525--60113561 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
60113515 CATTACAAGA
60113525 TCATTTTTTAGAGAAATAC
1 TCATTTTTTAGAGAAATAC
60113544 TCATTTTTTAGAGAAATA
1 TCATTTTTTAGAGAAATA
60113562 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (19 bp):
TCATTTTTTAGAGAAATAC
Found at i:60113564 original size:2 final size:2
Alignment explanation
Indices: 60113559--60113596 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
60113549 TTTTAGAGAA
60113559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60113597 TCAATTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60115714 original size:2 final size:2
Alignment explanation
Indices: 60115707--60115741 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60115697 TCCAATTCTC
60115707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60115742 CATTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60116070 original size:14 final size:15
Alignment explanation
Indices: 60116046--60116078 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
60116036 TCGTGCGTTC
60116046 TTCTTTCTCTTTTCT
1 TTCTTTCTCTTTTCT
60116061 TTCTTT-TCTTTTCT
1 TTCTTTCTCTTTTCT
60116075 TTCT
1 TTCT
60116079 AGTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTCTCTTTTCT
Found at i:60124966 original size:20 final size:20
Alignment explanation
Indices: 60124912--60124976 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
60124902 AATCTATATA
*
60124912 TATATTGATTAATAATACTC
1 TATATAGATTAATAATACTC
60124932 TATATA-ATTAATAATACTC
1 TATATAGATTAATAATACTC
* *
60124951 TATATAGATAAATAATAATC
1 TATATAGATTAATAATACTC
60124971 TATATA
1 TATATA
60124977 AAGTACCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.46
20 22 0.54
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATAGATTAATAATACTC
Found at i:60124966 original size:23 final size:19
Alignment explanation
Indices: 60124919--60124977 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
60124909 ATATATATTG
60124919 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
60124938 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
* *
60124957 GATAAATAATAATCTATATA
1 -ATTAATAATACTCTATATA
60124977 A
1 A
60124978 AGTACCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAATAATACTCTATATA
Found at i:60125096 original size:149 final size:149
Alignment explanation
Indices: 60124826--60125126 Score: 575
Period size: 149 Copynumber: 2.0 Consensus size: 149
60124816 AGAAGAATTT
60124826 TAAAGTACCAATTCACCCTCCTCTTGGTATTTTAGGGTCTAACATACTTTGAAAATGTTTGATAA
1 TAAAGTACCAATTCACCCTCCTCTTGGTATTTTAGGGTCTAACATACTTTGAAAATGTTTGATAA
*
60124891 AATTTTCAATCAATCTATATATATATTGATTAATAATACTCTATATAATTAATAATACTCTATAT
66 AATTTTCAATCAATCTATATATATATGGATTAATAATACTCTATATAATTAATAATACTCTATAT
60124956 AGATAAATAATAATCTATA
131 AGATAAATAATAATCTATA
*
60124975 TAAAGTACCAATTCCCCCTCCTCTTGGTATTTTAGGGTCTAACATACTTTGAAAATGTTTGATAA
1 TAAAGTACCAATTCACCCTCCTCTTGGTATTTTAGGGTCTAACATACTTTGAAAATGTTTGATAA
*
60125040 AATTTTCAATCAATCTATATATCTATGGATTAATAATACTCTATATAATTAATAATACTCTATAT
66 AATTTTCAATCAATCTATATATATATGGATTAATAATACTCTATATAATTAATAATACTCTATAT
60125105 AGATAAATAATAATCTATA
131 AGATAAATAATAATCTATA
60125124 TAA
1 TAA
60125127 CAAAGATTTA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (149 bp):
TAAAGTACCAATTCACCCTCCTCTTGGTATTTTAGGGTCTAACATACTTTGAAAATGTTTGATAA
AATTTTCAATCAATCTATATATATATGGATTAATAATACTCTATATAATTAATAATACTCTATAT
AGATAAATAATAATCTATA
Found at i:60125115 original size:23 final size:19
Alignment explanation
Indices: 60125068--60125126 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
60125058 ATATCTATGG
60125068 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
60125087 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
* *
60125106 GATAAATAATAATCTATATA
1 -ATTAATAATACTCTATATA
60125126 A
1 A
60125127 CAAAGATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAATAATACTCTATATA
Found at i:60126046 original size:29 final size:32
Alignment explanation
Indices: 60125991--60126062 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
60125981 TTTTAATAAA
*
60125991 AAAATTAAAA-GACTTACAATTTGAAATATG-
1 AAAAGTAAAAGGACTTACAATTTGAAATATGT
*
60126021 AAAAGTAAAAGGAC-TA-AATTTTAAATATGT
1 AAAAGTAAAAGGACTTACAATTTGAAATATGT
*
60126051 AAAAGGAAAAGG
1 AAAAGTAAAAGG
60126063 TAGAAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 12 0.32
30 22 0.59
31 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (32 bp):
AAAAGTAAAAGGACTTACAATTTGAAATATGT
Found at i:60127911 original size:23 final size:24
Alignment explanation
Indices: 60127866--60127912 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
60127856 AGACATCCAT
* *
60127866 AAATTGAACCATCTATTACAAATA
1 AAATTGAACCATCCATCACAAATA
60127890 AAATTGAACCATCCATCA-AAATA
1 AAATTGAACCATCCATCACAAATA
60127913 CAACCATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATTGAACCATCCATCACAAATA
Found at i:60129758 original size:4 final size:4
Alignment explanation
Indices: 60129727--60129823 Score: 63
Period size: 4 Copynumber: 22.2 Consensus size: 4
60129717 CCATCTGGAT
* * *
60129727 ATAC ATGAC AGTAC ATAAC ATAAC ATAC ATAC AAAT ATAC AAAC ATAAC
1 ATAC AT-AC A-TAC AT-AC AT-AC ATAC ATAC ATAC ATAC ATAC AT-AC
60129776 AGTA- A-AC ATAAC ATAC ATAC ATAC ATAAC AGTAC ATAAC ATAC ATAC
1 A-TAC ATAC AT-AC ATAC ATAC ATAC AT-AC A-TAC AT-AC ATAC ATAC
60129823 A
1 A
60129824 AATATACAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
2 1 0.01
3 1 0.01
4 38 0.50
5 33 0.43
6 3 0.04
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.21
Consensus pattern (4 bp):
ATAC
Found at i:60129790 original size:17 final size:15
Alignment explanation
Indices: 60129729--60129817 Score: 86
Period size: 12 Copynumber: 6.3 Consensus size: 15
60129719 ATCTGGATAT
*
60129729 ACATGACAGTACATA
1 ACATAACAGTACATA
60129744 ACATAACA-TACAT-
1 ACATAACAGTACATA
*
60129757 ACA-AATA-TACA-A
1 ACATAACAGTACATA
60129769 ACATAACAGTAAACATA
1 ACATAACAGT--ACATA
60129786 ACAT-ACA-TACAT-
1 ACATAACAGTACATA
60129798 ACATAACAGTACATA
1 ACATAACAGTACATA
60129813 ACATA
1 ACATA
60129818 CATACAAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
12 14 0.23
13 13 0.21
14 11 0.18
15 13 0.21
16 6 0.10
17 5 0.08
ACGTcount: A:0.55, C:0.20, G:0.04, T:0.20
Consensus pattern (15 bp):
ACATAACAGTACATA
Found at i:60129801 original size:29 final size:27
Alignment explanation
Indices: 60129729--60129825 Score: 108
Period size: 27 Copynumber: 3.5 Consensus size: 27
60129719 ATCTGGATAT
60129729 ACATGACAGTACATAACATAACA-TACAT-
1 ACAT-ACA-TACA-AACATAACAGTACATA
* *
60129757 ACAAATATACAAACATAACAGTAAACATA
1 ACATACATACAAACATAACAGT--ACATA
*
60129786 ACATACATACATACATAACAGTACATA
1 ACATACATACAAACATAACAGTACATA
60129813 ACATACATACAAA
1 ACATACATACAAA
60129826 TATACAAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.15
26 5 0.08
27 19 0.32
28 7 0.12
29 19 0.32
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.20
Consensus pattern (27 bp):
ACATACATACAAACATAACAGTACATA
Found at i:60129833 original size:64 final size:66
Alignment explanation
Indices: 60129744--60129870 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 66
60129734 ACAGTACATA
60129744 ACATAACATACATACAAATATAC-AAACATAACAGTAAACATAACATACAT-ACATACATAACAG
1 ACATAACATACATACAAATATACAAAACATAACAGTAAACATAACATACATAACATACATAACAG
60129807 T
66 T
* * *
60129808 ACATAACATACATACAAATATACAAAACTTAACATTAAACATAACATACATAATATACATAAC
1 ACATAACATACATACAAATATACAAAACATAACAGTAAACATAACATACATAACATACATAAC
60129871 TGTTTAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 23 0.40
65 25 0.43
66 10 0.17
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (66 bp):
ACATAACATACATACAAATATACAAAACATAACAGTAAACATAACATACATAACATACATAACAG
T
Found at i:60129889 original size:5 final size:5
Alignment explanation
Indices: 60129739--60129870 Score: 75
Period size: 5 Copynumber: 26.4 Consensus size: 5
60129729 ACATGACAGT
*
60129739 ACATA ACATA ACAT- ACATA CAAATA TACA-A ACATA ACAGTAA ACATA
1 ACATA ACATA ACATA ACATA -ACATA -ACATA ACATA ACA-T-A ACATA
* *
60129786 ACAT- ACAT- ACAT- ACATA ACAGT- ACATA ACAT- ACATA CAAATA TACAAA
1 ACATA ACATA ACATA ACATA ACA-TA ACATA ACATA ACATA -ACATA -ACATA
* *
60129834 ACTTA ACATTAA ACATA ACAT- ACATA ATAT- ACATA AC
1 ACATA ACA-T-A ACATA ACATA ACATA ACATA ACATA AC
60129871 TGTTTAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
4 31 0.31
5 44 0.44
6 18 0.18
7 8 0.08
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (5 bp):
ACATA
Found at i:60129893 original size:38 final size:35
Alignment explanation
Indices: 60129808--60129897 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 35
60129798 ACATAACAGT
*
60129808 ACATAACATACATACA-AATATACAAAACTTAACA
1 ACATAACATACATACATAATATACAAAACTTAAAA
** *
60129842 TTA-AACATAACATACATAATATACATAACTGTTTAAAA
1 ACATAACAT-ACATACATAATATACAAAAC---TTAAAA
60129880 ACATAACATACATACATA
1 ACATAACATACATACATA
60129898 CATAAACAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
33 5 0.11
34 8 0.18
35 11 0.25
38 15 0.34
39 5 0.11
ACGTcount: A:0.56, C:0.18, G:0.01, T:0.26
Consensus pattern (35 bp):
ACATAACATACATACATAATATACAAAACTTAAAA
Found at i:60130062 original size:30 final size:29
Alignment explanation
Indices: 60129995--60130062 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
60129985 TACCAACAAT
60129995 AACAAAAAATAAAAGTCAGATATAATACG
1 AACAAAAAATAAAAGTCAGATATAATACG
* * *
60130024 AATTAAAAATTGAAAGTCAGATATAATACG
1 AA-CAAAAAATAAAAGTCAGATATAATACG
*
60130054 TACAAAAAA
1 AACAAAAAA
60130063 AAACAATCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (29 bp):
AACAAAAAATAAAAGTCAGATATAATACG
Found at i:60133834 original size:5 final size:5
Alignment explanation
Indices: 60133824--60133849 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
60133814 GAACAAATAT
60133824 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
60133850 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:60135270 original size:15 final size:15
Alignment explanation
Indices: 60135250--60135279 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60135240 ACGAGTATGT
60135250 GAGTTTAAGACTGTA
1 GAGTTTAAGACTGTA
60135265 GAGTTTAAGACTGTA
1 GAGTTTAAGACTGTA
60135280 AATACTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
GAGTTTAAGACTGTA
Found at i:60136614 original size:76 final size:77
Alignment explanation
Indices: 60136488--60136656 Score: 299
Period size: 76 Copynumber: 2.2 Consensus size: 77
60136478 GACCAATTCG
*
60136488 ATTGGTTC-AACT-GTCGGGCCAACAATAATTAAATAAATAATTAAAATTTATAAAAATCTAAAA
1 ATTGGTTCAAACTATTC-GGCCAACAATAATTAAATAAATAATTAAAATTTATAAAAATCTAAAA
60136551 AAAAAAATATTAA
65 AAAAAAATATTAA
60136564 ATTGG-TCAAACTATTCGGCCAACAATAATTAAATAAATAATTAAAATTTATAAAAATCTAAAAA
1 ATTGGTTCAAACTATTCGGCCAACAATAATTAAATAAATAATTAAAATTTATAAAAATCTAAAAA
60136628 AAAAAATATTAA
66 AAAAAATATTAA
60136640 ATTGGTTCAAACTATTC
1 ATTGGTTCAAACTATTC
60136657 AATTGTCGAT
Statistics
Matches: 89, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
75 2 0.02
76 74 0.83
77 13 0.15
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (77 bp):
ATTGGTTCAAACTATTCGGCCAACAATAATTAAATAAATAATTAAAATTTATAAAAATCTAAAAA
AAAAAATATTAA
Found at i:60146132 original size:19 final size:18
Alignment explanation
Indices: 60146110--60146147 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
60146100 AAATTTTCAA
60146110 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
60146129 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
60146147 A
1 A
60146148 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:60146141 original size:30 final size:30
Alignment explanation
Indices: 60146072--60146141 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
60146062 CTCTCTCAAC
* *
60146072 AATTACAAAATAATTCAAAATAATTTTCAA
1 AATTACAAAAAAATTCAAAATAATTTTAAA
* *
60146102 ATTTTCAAAAAAATTCAAAAT-ATTTATAAA
1 AATTACAAAAAAATTCAAAATAATTT-TAAA
*
60146132 AATTCCAAAA
1 AATTACAAAA
60146142 TTTATATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (30 bp):
AATTACAAAAAAATTCAAAATAATTTTAAA
Found at i:60153086 original size:19 final size:19
Alignment explanation
Indices: 60153049--60153099 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
60153039 GGACTTAGAT
*
60153049 TTAATT-TAAATAATTAAAA
1 TTAATTATAAA-ATTTAAAA
* *
60153068 TTATTTTTAAAATTTAAAA
1 TTAATTATAAAATTTAAAA
60153087 TTAATTATAAAAT
1 TTAATTATAAAAT
60153100 ATATAGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTATAAAATTTAAAA
Found at i:60153128 original size:8 final size:8
Alignment explanation
Indices: 60153115--60153141 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
60153105 GGAAATCAAT
60153115 TAAAATTA
1 TAAAATTA
60153123 TAAAATTA
1 TAAAATTA
60153131 TAAAATTA
1 TAAAATTA
60153139 TAA
1 TAA
60153142 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATTA
Found at i:60155825 original size:29 final size:29
Alignment explanation
Indices: 60155765--60155825 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
60155755 TGGGGAAAAT
* *
60155765 GGCCCATTCCGGTAAATAATAAAATACCG
1 GGCCCATTCCGGTAAATAATAAAAAACAG
* ** *
60155794 GGCCCATTTCGGTAAATTTTAAAAAATAG
1 GGCCCATTCCGGTAAATAATAAAAAACAG
60155823 GGC
1 GGC
60155826 TTTTTTTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATAAAAAACAG
Found at i:60158676 original size:15 final size:15
Alignment explanation
Indices: 60158656--60158696 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
60158646 TGGCAATATT
60158656 AATAATAA-AAACAAC
1 AATAATAATAAA-AAC
*
60158671 AATAATAATAAAAAT
1 AATAATAATAAAAAC
60158686 AATAATAATAA
1 AATAATAATAA
60158697 GAGTACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAATAATAAAAAC
Found at i:60158678 original size:18 final size:18
Alignment explanation
Indices: 60158655--60158696 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
60158645 GTGGCAATAT
60158655 TAATAATAAAAACAACAA
1 TAATAATAAAAACAACAA
* *
60158673 TAATAATAAAAATAATAA
1 TAATAATAAAAACAACAA
60158691 TAATAA
1 TAATAA
60158697 GAGTACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAATAATAAAAACAACAA
Done.