Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 10 of 167
Found at i:3165440 original size:33 final size:33
Alignment explanation
Indices: 3165398--3165464 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3165388 ATTGGTTTTA
3165398 GATTAGATCAAATCGGGTTTTAAAATTTTCTAT
1 GATTAGATCAAATCGGGTTTTAAAATTTTCTAT
3165431 GATTAGATCAAATCGGGTTTTAAAATTTTCTAT
1 GATTAGATCAAATCGGGTTTTAAAATTTTCTAT
3165464 G
1 G
3165465 TCATTTCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (33 bp):
GATTAGATCAAATCGGGTTTTAAAATTTTCTAT
Found at i:3165596 original size:23 final size:23
Alignment explanation
Indices: 3165570--3165615 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3165560 GTTTAAATAC
3165570 TAAAAAGCTTAAAGCTCAGCTTA
1 TAAAAAGCTTAAAGCTCAGCTTA
3165593 TAAAAAGCTTAAAGCTCAGCTTA
1 TAAAAAGCTTAAAGCTCAGCTTA
3165616 AAATTTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (23 bp):
TAAAAAGCTTAAAGCTCAGCTTA
Found at i:3181381 original size:57 final size:56
Alignment explanation
Indices: 3181257--3181401 Score: 152
Period size: 57 Copynumber: 2.6 Consensus size: 56
3181247 NNNNNNNNNC
* * * * *
3181257 AAAAAAAAACCTTAGGTATCAAATTAGGAAAAATGTCAAATTCATATATTAAATTGG
1 AAAAAAAAAACTTAGATACCAAATTA-GAAAAATGTCAAATTCATATACTAAATTGA
* *
3181314 ACAAAGAAAACTTAGATACCAAATTAGAAAAATGTATCAAATTCA-AGTACTAAATT-A
1 AAAAAAAAAACTTAGATACCAAATTAGAAAAATG--TCAAATTCATA-TACTAAATTGA
*
3181371 AAAAAAAAAAC-TAAATACCAAATTAAGAAAA
1 AAAAAAAAAACTTAGATACCAAATT-AGAAAA
3181402 GTGTGAAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
56 20 0.27
57 37 0.50
58 17 0.23
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.23
Consensus pattern (56 bp):
AAAAAAAAAACTTAGATACCAAATTAGAAAAATGTCAAATTCATATACTAAATTGA
Found at i:3191533 original size:48 final size:48
Alignment explanation
Indices: 3191459--3191582 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 48
3191449 CTTTAAGTTT
* * * * *
3191459 CGATAACATGGCCCAAAACCAAATCAATATAACTCGCATCC-GAAGTGC
1 CGATATCATGTCCCGAAGCCAAATCAATATAACTAGCA-CCTGAAGTGC
*
3191507 CGATATCATG-CTCCGAAGCCAAATCAATGTAACTAGCACCTGAAGTGC
1 CGATATCATGTC-CCGAAGCCAAATCAATATAACTAGCACCTGAAGTGC
* * *
3191555 TGATATCATGTCCCGGAGCAAAATCAAT
1 CGATATCATGTCCCGAAGCCAAATCAAT
3191583 GAATTCCCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 3 0.05
48 61 0.94
49 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (48 bp):
CGATATCATGTCCCGAAGCCAAATCAATATAACTAGCACCTGAAGTGC
Found at i:3196080 original size:35 final size:35
Alignment explanation
Indices: 3196034--3196104 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
3196024 CATCTCTAGA
* * *
3196034 GCTTGGTAAATATGAAAAGTGATCTTCAAATATAT
1 GCTTGGCAAATATGAAAAGGGATCTTCAAAGATAT
* *
3196069 GCTTGGCAAATATGGAAGGGGATCTTCAAAGATAT
1 GCTTGGCAAATATGAAAAGGGATCTTCAAAGATAT
3196104 G
1 G
3196105 TGATCCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (35 bp):
GCTTGGCAAATATGAAAAGGGATCTTCAAAGATAT
Found at i:3198979 original size:29 final size:28
Alignment explanation
Indices: 3198935--3199002 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
3198925 AATAATTGAA
*
3198935 TTTAAAATTTAAAAAATAAAATAAATTAATT
1 TTTAAAA-TT-AAAAGTAAAA-AAATTAATT
* *
3198966 TCTTAAAATTAAAAGTATAAAGATTAATT
1 T-TTAAAATTAAAAGTAAAAAAATTAATT
3198995 TTTAAAAT
1 TTTAAAAT
3199003 ATACACATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 7 0.21
29 9 0.27
30 8 0.24
31 3 0.09
32 6 0.18
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAAAATTAAAAGTAAAAAAATTAATT
Found at i:3213672 original size:27 final size:27
Alignment explanation
Indices: 3213642--3213699 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3213632 CCCGGTGCAG
* *
3213642 CAGCAGCAGCCACTCCAGGGTTAAACC
1 CAGCAGCAGCAACACCAGGGTTAAACC
* * *
3213669 CAGCAGGAGCAACACCATGGTTGAACC
1 CAGCAGCAGCAACACCAGGGTTAAACC
3213696 CAGC
1 CAGC
3213700 TCCAGCAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.10
Consensus pattern (27 bp):
CAGCAGCAGCAACACCAGGGTTAAACC
Found at i:3214683 original size:30 final size:30
Alignment explanation
Indices: 3214649--3214706 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3214639 CTCCTCCTCC
*
3214649 TCTTCTTCAAATTCCTCTTCTACTTCTACT
1 TCTTCTTCAAATTCCTCTTCCACTTCTACT
* *
3214679 TCTTCTTCGATTTCCTCTTCCACTTCTA
1 TCTTCTTCAAATTCCTCTTCCACTTCTA
3214707 GTACTTGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.02, T:0.50
Consensus pattern (30 bp):
TCTTCTTCAAATTCCTCTTCCACTTCTACT
Found at i:3219680 original size:35 final size:34
Alignment explanation
Indices: 3219634--3219702 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 34
3219624 AACGGTGTTT
3219634 CACTTCCTCAGTGGGTTCTTCAATCTAGGGAAAG
1 CACTTCCTCAGTGGGTTCTTCAATCTAGGGAAAG
*
3219668 NCACTTCCTCAGTGGGTTCTTCAGTCTAGGGAAAG
1 -CACTTCCTCAGTGGGTTCTTCAATCTAGGGAAAG
3219703 AGGTATGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.29
Consensus pattern (34 bp):
CACTTCCTCAGTGGGTTCTTCAATCTAGGGAAAG
Found at i:3225343 original size:8 final size:8
Alignment explanation
Indices: 3225323--3225352 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3225313 TTATAGTTGT
3225323 ATTTTGCAA
1 ATTTTG-AA
3225332 ATTTTGAA
1 ATTTTGAA
3225340 ATTTTGAA
1 ATTTTGAA
3225348 ATTTT
1 ATTTT
3225353 AATAACGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (8 bp):
ATTTTGAA
Found at i:3233044 original size:30 final size:30
Alignment explanation
Indices: 3232998--3233112 Score: 167
Period size: 30 Copynumber: 3.8 Consensus size: 30
3232988 ACTTTTCTCA
* *
3232998 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACATTTTCCACCACCAACTCC
*
3233028 ACTAGGCACACATTTTCCACCACCAACTCC
1 ACTAGCCACACATTTTCCACCACCAACTCC
* *
3233058 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACATTTTCCACCACCAACTCC
* *
3233088 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACATTTTCCACCACCA
3233113 CTTGTACCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACATTTTCCACCACCAACTCC
Found at i:3233091 original size:60 final size:60
Alignment explanation
Indices: 3232998--3233112 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
3232988 ACTTTTCTCA
* *
3232998 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGGCACACATTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACATTCTCCACCACCAACTCC
* *
3233058 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACATTCTCCACCACCA
3233113 CTTGTACCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACATTCTCCACCACCAACTCC
Found at i:3233701 original size:25 final size:25
Alignment explanation
Indices: 3233673--3233831 Score: 99
Period size: 25 Copynumber: 6.1 Consensus size: 25
3233663 ATATTACGTA
*
3233673 TATATATATTTTATACTATTTTATT
1 TATATATATTTTATACTATATTATT
* * *
3233698 TATATATCTTTAATATTATATTATT
1 TATATATATTTTATACTATATTATT
* * *
3233723 TATATATATTTTTTTCTACATGTTATCT
1 TATATATATTTTATACT--ATATTAT-T
* *
3233751 TATGTATATATCTTA-ACTATATTATG
1 TA--TATATATTTTATACTATATTATT
* *
3233777 TATATAT-TTTTAACACTATATTATG
1 TATATATATTTT-ATACTATATTATT
* *
3233802 TACATAT-TTTTAATATTATCATGTATT
1 TATATATATTTT-ATACTAT-AT-TATT
3233829 TAT
1 TAT
3233832 TTTTTATATA
Statistics
Matches: 104, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.03
24 6 0.06
25 60 0.58
26 4 0.04
27 17 0.16
28 3 0.03
29 2 0.02
30 9 0.09
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (25 bp):
TATATATATTTTATACTATATTATT
Found at i:3233832 original size:23 final size:24
Alignment explanation
Indices: 3233752--3233842 Score: 82
Period size: 23 Copynumber: 3.9 Consensus size: 24
3233742 ATGTTATCTT
*
3233752 ATGTATATA-TCTTAACTATAT-T-
1 ATGTATATATTTTTAA-TATATATC
* *
3233774 ATGTATATATTTTTAACACTATATT
1 ATGTATATATTTTTAATA-TATATC
*
3233799 ATGTACATATTTTTAATAT-TATC
1 ATGTATATATTTTTAATATATATC
* *
3233822 ATGTATTTATTTTTTATATAT
1 ATGTATATATTTTTAATATAT
3233843 GTACATATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
22 10 0.18
23 27 0.48
24 3 0.05
25 16 0.29
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (24 bp):
ATGTATATATTTTTAATATATATC
Found at i:3233983 original size:8 final size:8
Alignment explanation
Indices: 3233965--3234016 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
3233955 TAATTATTAT
*
3233965 TATTCTAA
1 TATTTTAA
*
3233973 TATTTTGA
1 TATTTTAA
3233981 TATTTTAA
1 TATTTTAA
*
3233989 TATTTT-T
1 TATTTTAA
3233996 TATTTTATA
1 TATTTTA-A
*
3234005 TATTTTAT
1 TATTTTAA
3234013 TATT
1 TATT
3234017 CCCATCATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 6 0.17
8 23 0.64
9 7 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:3233989 original size:16 final size:15
Alignment explanation
Indices: 3233965--3234012 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3233955 TAATTATTAT
*
3233965 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
*
3233981 TATTTTAATATTTTT
1 TATTTTAATATTTTA
3233996 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3234012 T
1 T
3234013 TATTCCCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3234010 original size:14 final size:15
Alignment explanation
Indices: 3233954--3234013 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 15
3233944 ATCGTTGCGC
3233954 TTAAT-TATTATTATT
1 TTAATATATT-TTATT
*
3233969 CTAATAT-TTTGATATT
1 TTAATATATTT--TATT
*
3233985 TTAATATTTTTTATT
1 TTAATATATTTTATT
3234000 TT-ATATATTTTATT
1 TTAATATATTTTATT
3234014 ATTCCCATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.32
15 12 0.32
16 11 0.29
17 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTAATATATTTTATT
Found at i:3240841 original size:100 final size:100
Alignment explanation
Indices: 3240668--3240867 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
3240658 TGGTCATCGA
3240668 TTACTTCACAAAATGGATAGAAGCCGATTCGTTTGCCAATGTGACGAAGACTGTAGTTTGCAGGT
1 TTACTTCACAAAATGGATAGAAGCCGATTCGTTTGCCAATGTGACGAAGACTGTAGTTTGCAGGT
3240733 TTTTGAAAAAGGAAATCATTTGCCGATATGGTTTG
66 TTTTGAAAAAGGAAATCATTTGCCGATATGGTTTG
3240768 TTACTTCACAAAATGGATAGAAGCCGATTCGTTTGCCAATGTGACGAAGACTGTAGTTTGCAGGT
1 TTACTTCACAAAATGGATAGAAGCCGATTCGTTTGCCAATGTGACGAAGACTGTAGTTTGCAGGT
3240833 TTTTGAAAAAGGAAATCATTTGCCGATATGGTTTG
66 TTTTGAAAAAGGAAATCATTTGCCGATATGGTTTG
3240868 CCTGAAAGAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (100 bp):
TTACTTCACAAAATGGATAGAAGCCGATTCGTTTGCCAATGTGACGAAGACTGTAGTTTGCAGGT
TTTTGAAAAAGGAAATCATTTGCCGATATGGTTTG
Found at i:3243782 original size:7 final size:8
Alignment explanation
Indices: 3243747--3243786 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
3243737 TAATTATTAT
*
3243747 TATTCTAA
1 TATTTTAA
*
3243755 TATTTTGA
1 TATTTTAA
3243763 TATTTTAA
1 TATTTTAA
3243771 TATTTT-A
1 TATTTTAA
3243778 TATTTTAA
1 TATTTTAA
3243786 T
1 T
3243787 TCACATCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:3243782 original size:15 final size:16
Alignment explanation
Indices: 3243747--3243786 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3243737 TAATTATTAT
*
3243747 TATTCTAATATTTTGA
1 TATTTTAATATTTTGA
3243763 TATTTTAATATTTT-A
1 TATTTTAATATTTTGA
3243778 TATTTTAAT
1 TATTTTAAT
3243787 TCACATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTTAATATTTTGA
Found at i:3245476 original size:6 final size:6
Alignment explanation
Indices: 3245465--3245499 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3245455 TCTGTGTATC
* *
3245465 GTTACT GTTACT GTTACT GTTATT GTTACT ATTAC
1 GTTACT GTTACT GTTACT GTTACT GTTACT GTTAC
3245500 GGTGTATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (6 bp):
GTTACT
Found at i:3246294 original size:41 final size:42
Alignment explanation
Indices: 3246220--3246299 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
3246210 ATTTTGAGTC
* *
3246220 CACACGGCATGTCACACGGGCGTGTGATCAGACCGTGTGAGA
1 CACACGGCATGTCACACAGGCATGTGATCAGACCGTGTGAGA
*
3246262 CACACGGCTTG-CACACAGGCATGTTGAT-AGACCGTGTG
1 CACACGGCATGTCACACAGGCATG-TGATCAGACCGTGTG
3246300 TCCCCAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 20 0.59
42 14 0.41
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (42 bp):
CACACGGCATGTCACACAGGCATGTGATCAGACCGTGTGAGA
Found at i:3249262 original size:2 final size:2
Alignment explanation
Indices: 3249255--3249279 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3249245 GCTGTACTTT
3249255 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3249280 ATGCATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3256963 original size:32 final size:32
Alignment explanation
Indices: 3256915--3256977 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3256905 AAGTTTGATG
*
3256915 ATTTGGGTTTAAATTGTTTTGAGTTCAAATTA
1 ATTTAGGTTTAAATTGTTTTGAGTTCAAATTA
* * *
3256947 ATTTAGGTTTATATTGTTTTGTGTTTAAATT
1 ATTTAGGTTTAAATTGTTTTGAGTTCAAATT
3256978 TGTCTGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (32 bp):
ATTTAGGTTTAAATTGTTTTGAGTTCAAATTA
Found at i:3257378 original size:25 final size:25
Alignment explanation
Indices: 3257311--3257380 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
3257301 ATTTAAATTT
* * *
3257311 TAAATTATTTAATATAATGATAAATA
1 TAAATTATTT-TTAAAATAATAAATA
*
3257337 -AAACATATATTTT-AAATAATAAATA
1 TAAA-TTAT-TTTTAAAATAATAAATA
3257362 TAAATTATTTTTAAAATAA
1 TAAATTATTTTTAAAATAA
3257381 ATGGTAATGC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
24 4 0.11
25 22 0.63
26 7 0.20
27 2 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (25 bp):
TAAATTATTTTTAAAATAATAAATA
Found at i:3257382 original size:22 final size:25
Alignment explanation
Indices: 3257330--3257382 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3257320 TAATATAATG
3257330 ATAAATAAAACATATATTTTAAATA
1 ATAAATAAAACATATATTTTAAATA
* *
3257355 ATAAATATAA-AT-TATTTTTAA-A
1 ATAAATAAAACATATATTTTAAATA
3257377 ATAAAT
1 ATAAAT
3257383 GGTAATGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.27
23 8 0.31
24 2 0.08
25 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAATAAAACATATATTTTAAATA
Found at i:3257422 original size:18 final size:17
Alignment explanation
Indices: 3257375--3257423 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
3257365 ATTATTTTTA
*
3257375 AAATAAATGGTAATGCACC
1 AAATAAAT--TAATGCAAC
*
3257394 AAATAATTTAATGCAAC
1 AAATAAATTAATGCAAC
3257411 AATATAAATTAAT
1 AA-ATAAATTAAT
3257424 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.38
18 9 0.35
19 7 0.27
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (17 bp):
AAATAAATTAATGCAAC
Found at i:3262566 original size:13 final size:13
Alignment explanation
Indices: 3262548--3262572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3262538 TAAAAGAGTT
3262548 ATTAATTAAAAAG
1 ATTAATTAAAAAG
3262561 ATTAATTAAAAA
1 ATTAATTAAAAA
3262573 TAAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:3264906 original size:29 final size:27
Alignment explanation
Indices: 3264864--3264918 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3264854 CGTTCTATAT
*
3264864 TTTATAAGCATTTTACTTTTAAAAAAAAG
1 TTTATAAGAATTTT--TTTTAAAAAAAAG
*
3264893 TTTATATGAATTTTTTTTAAAAAAAA
1 TTTATAAGAATTTTTTTTAAAAAAAA
3264919 TTGGTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
29 12 0.50
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (27 bp):
TTTATAAGAATTTTTTTTAAAAAAAAG
Found at i:3272309 original size:17 final size:16
Alignment explanation
Indices: 3272283--3272317 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3272273 GTTAAATCAG
*
3272283 TTAAGGTTTAAGTTTGA
1 TTAAGATTTAAG-TTGA
3272300 TTAAGATTTAAGTTGA
1 TTAAGATTTAAGTTGA
3272316 TT
1 TT
3272318 GGTTAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (16 bp):
TTAAGATTTAAGTTGA
Found at i:3276366 original size:16 final size:16
Alignment explanation
Indices: 3276323--3276374 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
3276313 AAATTAGAAA
3276323 AAAATTA-TAAAAATCAT
1 AAAATTATTAAAAAT--T
3276340 AAAATATTATTAAAAATT
1 -AAA-ATTATTAAAAATT
3276358 AAAATTATTAAAAATT
1 AAAATTATTAAAAATT
3276374 A
1 A
3276375 TTAGAATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 14 0.44
17 3 0.09
18 4 0.12
19 4 0.12
20 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATTAAAAATT
Found at i:3276371 original size:10 final size:10
Alignment explanation
Indices: 3276322--3276377 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
3276312 AAAATTAGAA
3276322 AAAAATTA-T
1 AAAAATTATT
*
3276331 AAAAATCA-T
1 AAAAATTATT
3276340 AAAATATTATT
1 AAAA-ATTATT
3276351 -AAAA--ATT
1 AAAAATTATT
3276358 -AAAATTATT
1 AAAAATTATT
3276367 AAAAATTATT
1 AAAAATTATT
3276377 A
1 A
3276378 GAATTGATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 7 0.17
9 16 0.40
10 16 0.40
11 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTATT
Found at i:3276377 original size:19 final size:18
Alignment explanation
Indices: 3276323--3276382 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
3276313 AAATTAGAAA
*
3276323 AAAATTA-TAAAAATCATA
1 AAAATTATTAAAAAT-ATT
3276341 AAATATTATT-AAAA-ATT
1 AAA-ATTATTAAAAATATT
3276358 AAAATTATTAAAAATTATT
1 AAAATTATTAAAAA-TATT
*
3276377 AGAATT
1 AAAATT
3276383 GATATAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.17
17 9 0.26
18 3 0.09
19 16 0.46
20 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAATTATTAAAAATATT
Found at i:3281852 original size:6 final size:6
Alignment explanation
Indices: 3281841--3281879 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3281831 GAAGAGTGGT
3281841 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAG
3281880 TGTATATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:3290676 original size:52 final size:48
Alignment explanation
Indices: 3290657--3290859 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
3290647 TGACAAGTGG
* *
3290657 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
3290703 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
3290755 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
3290801 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
3290847 AAAGTGATAAGTG
1 AAAGTGATAAGTG
3290860 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:3290711 original size:98 final size:98
Alignment explanation
Indices: 3290591--3290859 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
3290581 TTTGAGTACT
*
3290591 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
3290656 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
3290689 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
3290754 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
3290787 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
3290852 GATAAGTG
65 GAAAAGTG
3290860 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:3290867 original size:37 final size:37
Alignment explanation
Indices: 3290823--3290968 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
3290813 GATAGCTTTA
*
3290823 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3290860 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
3290897 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
3290934 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3290969 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:3295270 original size:16 final size:16
Alignment explanation
Indices: 3295246--3295326 Score: 81
Period size: 16 Copynumber: 5.1 Consensus size: 16
3295236 TTGTGTTAGC
3295246 TTTAAATTTTAATTAT
1 TTTAAATTTTAATTAT
* **
3295262 TTTAGATTTTGGTTAT
1 TTTAAATTTTAATTAT
* *
3295278 TTTAAGTTTAAATTAT
1 TTTAAATTTTAATTAT
* * *
3295294 TTTAAATTTGATTTAA
1 TTTAAATTTTAATTAT
*
3295310 TTTAAATTATAATTAT
1 TTTAAATTTTAATTAT
3295326 T
1 T
3295327 AGTAATTTTT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTAAATTTTAATTAT
Found at i:3295314 original size:32 final size:31
Alignment explanation
Indices: 3295192--3295326 Score: 103
Period size: 32 Copynumber: 4.2 Consensus size: 31
3295182 AGATGGATTG
** * *
3295192 AATTATTTTGTATTTGATTAATTTGAATTTTA
1 AATTATTTTAAATTTGTTTAATTT-AAATTTA
* * *
3295224 AA-AATTTTAAATTTGTGTTAGCTTTAAATTTT
1 AATTATTTTAAATTTGT-TTA-ATTTAAATTTA
* * * *
3295256 AATTATTTTAGATTTTGGTTATTTTAAGTTTA
1 AATTATTTTA-AATTTGTTTAATTTAAATTTA
3295288 AATTATTTTAAATTTGATTTAATTTAAA-TTA
1 AATTATTTTAAATTTG-TTTAATTTAAATTTA
3295319 TAATTATT
1 -AATTATT
3295327 AGTAATTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
31 18 0.22
32 45 0.56
33 12 0.15
34 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.57
Consensus pattern (31 bp):
AATTATTTTAAATTTGTTTAATTTAAATTTA
Found at i:3295407 original size:17 final size:17
Alignment explanation
Indices: 3295387--3295422 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3295377 TTATTTAATT
*
3295387 AAATAATTTCAAATTTA
1 AAATAATTTAAAATTTA
*
3295404 AAATATTTTAAAATTTA
1 AAATAATTTAAAATTTA
3295421 AA
1 AA
3295423 TTATTAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAATTTAAAATTTA
Found at i:3298356 original size:17 final size:17
Alignment explanation
Indices: 3298331--3298366 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3298321 AGTTAATATT
*
3298331 AATATAATAAAACATAA
1 AATAAAATAAAACATAA
3298348 AATAAAATAAAACATAA
1 AATAAAATAAAACATAA
3298365 AA
1 AA
3298367 AGAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAAAATAAAACATAA
Found at i:3298376 original size:17 final size:17
Alignment explanation
Indices: 3298339--3298376 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3298329 TTAATATAAT
*
3298339 AAAACATAAAATAAAAT
1 AAAACATAAAATAAAAC
3298356 AAAACATAAAA-AGAAAC
1 AAAACATAAAATA-AAAC
3298373 AAAA
1 AAAA
3298377 GAAACAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAACATAAAATAAAAC
Found at i:3301118 original size:3 final size:3
Alignment explanation
Indices: 3301110--3301135 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3301100 CTTCTTGCAA
3301110 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
3301136 TATAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3304034 original size:53 final size:52
Alignment explanation
Indices: 3303888--3304036 Score: 183
Period size: 52 Copynumber: 2.8 Consensus size: 52
3303878 CCTTGGCAAT
* * * * *
3303888 ATGTGACATGTGTTTCCGTATAAGACCATAGCT-AGACTATGGAATCGGTGTG
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGA-TATGGCATCGGTGAG
* *
3303940 ATGTGATATGTGCTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGAG
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTGAG
* * *
3303992 ATGTGATTATGTGCTTCCGTATGAGACTATATCTGGGATATGGCA
1 ATGTGA-TATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCA
3304037 AATAAATGAA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 49 0.59
53 34 0.41
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (52 bp):
ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTGAG
Found at i:3308955 original size:38 final size:38
Alignment explanation
Indices: 3308904--3308980 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
3308894 GAATTTTTGA
3308904 TCTACAGTAATGCATCGTTGATCGATCTGGGATGTGTT
1 TCTACAGTAATGCATCGTTGATCGATCTGGGATGTGTT
* * *
3308942 TCTACAGTGATGCATCGTTGATCGGTTTGGGATGTGTT
1 TCTACAGTAATGCATCGTTGATCGATCTGGGATGTGTT
3308980 T
1 T
3308981 TGATGCAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (38 bp):
TCTACAGTAATGCATCGTTGATCGATCTGGGATGTGTT
Found at i:3312012 original size:40 final size:40
Alignment explanation
Indices: 3311968--3312062 Score: 181
Period size: 40 Copynumber: 2.4 Consensus size: 40
3311958 GCGGTTCAAA
3311968 ATAGCTTCGGCTGTAAATAGCACTAAGTGTGCGAAATGGT
1 ATAGCTTCGGCTGTAAATAGCACTAAGTGTGCGAAATGGT
*
3312008 ATAGCTTCGGCTATAAATAGCACTAAGTGTGCGAAATGGT
1 ATAGCTTCGGCTGTAAATAGCACTAAGTGTGCGAAATGGT
3312048 ATAGCTTCGGCTGTA
1 ATAGCTTCGGCTGTA
3312063 TGAGGCACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (40 bp):
ATAGCTTCGGCTGTAAATAGCACTAAGTGTGCGAAATGGT
Found at i:3312094 original size:40 final size:39
Alignment explanation
Indices: 3311968--3312082 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 39
3311958 GCGGTTCAAA
3311968 ATAGCTTCGGCTGTAAATAGCACTAAGTGTGCGAAATGGT
1 ATAGCTTCGGCTGT-AATAGCACTAAGTGTGCGAAATGGT
*
3312008 ATAGCTTCGGCTATAAATAGCACTAAGTGTGCGAAATGGT
1 ATAGCTTCGGCTGT-AATAGCACTAAGTGTGCGAAATGGT
*
3312048 ATAGCTTCGGCTGT-ATGAGGCACTAAGTGTACGAA
1 ATAGCTTCGGCTGTAAT-A-GCACTAAGTGTGCGAA
3312083 CCGAGATAGC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 67 0.96
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (39 bp):
ATAGCTTCGGCTGTAATAGCACTAAGTGTGCGAAATGGT
Found at i:3316794 original size:29 final size:31
Alignment explanation
Indices: 3316745--3316810 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
3316735 TTTTCATGTT
*
3316745 TCAATTTGATAGATTTATTAAGTTCAATTAA
1 TCAATTTGATAGAGTTATTAAGTTCAATTAA
3316776 TCAATTT-ATA-AGTTATTAAGTTCAATTAA
1 TCAATTTGATAGAGTTATTAAGTTCAATTAA
*
3316805 TTAATT
1 TCAATT
3316811 AACATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 23 0.70
30 3 0.09
31 7 0.21
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (31 bp):
TCAATTTGATAGAGTTATTAAGTTCAATTAA
Found at i:3331297 original size:29 final size:28
Alignment explanation
Indices: 3331254--3331331 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
3331244 TCATGAGATT
3331254 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
3331284 -GCACTAAGTGTGCGAGTTTACAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
3331311 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
3331332 GATTATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.12
29 34 0.81
30 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:3331585 original size:174 final size:174
Alignment explanation
Indices: 3331286--3331611 Score: 510
Period size: 174 Copynumber: 1.9 Consensus size: 174
3331276 ATTGTACAGC
* * * *
3331286 ACTAAGTGTGCGAGTTTACAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
* ** *
3331351 TGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATT
66 TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
3331416 TTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
131 TTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
* * * * *
3331461 ACTAAGTGTGTGAGTTTAAAGTGCATGGCACTGAGTGTGCGTGGGTGATTACTAAACATTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
*
3331526 TGC-AACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGGCTTTACCGAGTCAATT
66 TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
3331590 TTGGACAGCGGAAAAGGTAAGT
131 TTGGACAGCGGAAAAGGTAAGT
3331612 ACCTTGAACT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
173 11 0.08
174 67 0.49
175 59 0.43
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
Found at i:3338944 original size:29 final size:28
Alignment explanation
Indices: 3338908--3338985 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
3338898 TCATGAGATT
3338908 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
3338938 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
3338965 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
3338986 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:3339203 original size:174 final size:174
Alignment explanation
Indices: 3338938--3339265 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
3338928 AAATTGTACA
3338938 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
3339003 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
3339068 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
3339112 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
3339177 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
3339242 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
3339266 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:3341140 original size:93 final size:86
Alignment explanation
Indices: 3341067--3341230 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 86
3341057 GGGCGACTCG
* *
3341067 TTTCACAAGC-AGCTAAGGCCTCGTGAAATGCCTCACCACCTTGTGAAGTGACATGCCTCACCAC
1 TTTCACAAGCAATC-AAGGCCTCGTGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCAC
*
3341131 TTCACGGGATCAC-TTGTTCCA
65 TTCACGGGATCACTTTGTACCA
* * * * *
3341152 TTTCGCGAGCAATCAAGGCCTCGTGAAATGCCTCACCAGCTTGCGAAGTGTCATGCCTCATCACT
1 TTTCACAAGCAATCAAGGCCTCGTGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCACT
*
3341217 TCACAGGATCACTT
66 TCACGGGATCACTT
3341231 CGCCCGACTC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
85 66 0.96
86 3 0.04
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (86 bp):
TTTCACAAGCAATCAAGGCCTCGTGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCACT
TCACGGGATCACTTTGTACCA
Found at i:3341582 original size:27 final size:25
Alignment explanation
Indices: 3341552--3341612 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
3341542 ATATTGCTTT
*
3341552 TTAAAATATTAAATATAATACATATTA
1 TTAAAATATTAAA-AT-ATACATATAA
* * *
3341579 TTAAAATTTTAAAATATATATCTAA
1 TTAAAATATTAAAATATACATATAA
3341604 TTAAAATAT
1 TTAAAATAT
3341613 GAGAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 15 0.52
26 2 0.07
27 12 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAATATTAAAATATACATATAA
Found at i:3341808 original size:10 final size:10
Alignment explanation
Indices: 3341793--3341818 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3341783 ACCCAAAATT
3341793 TTAAAATAAA
1 TTAAAATAAA
3341803 TTAAAATAAA
1 TTAAAATAAA
3341813 TTAAAA
1 TTAAAA
3341819 GAGTTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:3345933 original size:34 final size:34
Alignment explanation
Indices: 3345895--3345963 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
3345885 AGAAATTTAT
3345895 TTCTTTTCCCCCATATAAGTTTTTTTTTCCACTG
1 TTCTTTTCCCCCATATAAGTTTTTTTTTCCACTG
3345929 TTCTTTTCCCCCATATAAGTTTTTTTTTCCACTG
1 TTCTTTTCCCCCATATAAGTTTTTTTTTCCACTG
3345963 T
1 T
3345964 GATATGATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.54
Consensus pattern (34 bp):
TTCTTTTCCCCCATATAAGTTTTTTTTTCCACTG
Found at i:3346112 original size:94 final size:91
Alignment explanation
Indices: 3346005--3346190 Score: 327
Period size: 94 Copynumber: 2.0 Consensus size: 91
3345995 CAATCGTGTA
3346005 ATCTAACTTGGAGATTTTTATGAAATTTTCCAGAGAAATTTTCGATTTTTTTTCAATTTCAATTT
1 ATCTAACTTGGAGATTTTTATGAAATTTTCCAGAGAAATTTTCGATTTTTTTTCAATTTCAATTT
3346070 TAGAATTCGAAAGAAAAGAATGTGGTTGG
66 TAGAATTCG-AA-AAAA-AATGTGGTTGG
* *
3346099 ATCTAACTTGGAGATTTTTATGAAATTTTCCAGAGAAATTTTCGATTTTTTTTCAGTTTTAATTT
1 ATCTAACTTGGAGATTTTTATGAAATTTTCCAGAGAAATTTTCGATTTTTTTTCAATTTCAATTT
3346164 TAGAATTCGAAAAAAAATGTGGTTGG
66 TAGAATTCGAAAAAAAATGTGGTTGG
3346190 A
1 A
3346191 AGGCTTTGAG
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
91 12 0.13
92 4 0.04
93 2 0.02
94 72 0.80
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (91 bp):
ATCTAACTTGGAGATTTTTATGAAATTTTCCAGAGAAATTTTCGATTTTTTTTCAATTTCAATTT
TAGAATTCGAAAAAAAATGTGGTTGG
Found at i:3346433 original size:24 final size:25
Alignment explanation
Indices: 3346401--3346465 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
3346391 ATAAGTCGAG
*
3346401 AATTATATATATTTTTA-GAGTAAA
1 AATTATATATATTTTTATCAGTAAA
* * *
3346425 AATTCTATATA-TTTGATCATTAAA
1 AATTATATATATTTTTATCAGTAAA
3346449 AATTATATATATTTTTA
1 AATTATATATATTTTTA
3346466 AATGTAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.12
24 25 0.76
25 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (25 bp):
AATTATATATATTTTTATCAGTAAA
Found at i:3350382 original size:21 final size:20
Alignment explanation
Indices: 3350356--3350410 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 20
3350346 AAAAAATTGT
3350356 TGTTTTTTTTACTATTCTTTC
1 TGTTTTTTTTACTATT-TTTC
3350377 TG-TTTTTTT-CTA-TTTTC
1 TGTTTTTTTTACTATTTTTC
3350394 T-TTTTTTTTACTATTTT
1 TGTTTTTTTTACTATTTT
3350411 GCTATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.39
18 4 0.13
19 6 0.19
20 7 0.23
21 2 0.06
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76
Consensus pattern (20 bp):
TGTTTTTTTTACTATTTTTC
Found at i:3350492 original size:17 final size:19
Alignment explanation
Indices: 3350459--3350493 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3350449 ATTATTTGGA
3350459 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
3350478 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
3350494 AATATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:3356518 original size:40 final size:40
Alignment explanation
Indices: 3356455--3356546 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
3356445 AACTCCGTCC
* * *
3356455 AACCCAACACACC--ATGTGGGGATAAAATCGACCCACCT
1 AACCCTACACACCAAATATGGGGATAAAATCAACCCACCT
* *
3356493 ATCCCTACACACCAAATATGGGGATAAAATCAACCCATCT
1 AACCCTACACACCAAATATGGGGATAAAATCAACCCACCT
*
3356533 AACCCTACGCACCA
1 AACCCTACACACCA
3356547 TAAAGTACCG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 11 0.24
40 34 0.76
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (40 bp):
AACCCTACACACCAAATATGGGGATAAAATCAACCCACCT
Found at i:3364836 original size:33 final size:33
Alignment explanation
Indices: 3364799--3364865 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3364789 ATTCCACTAT
3364799 TATTTATAGTTCATTCAAAGATATCTACTTGAG
1 TATTTATAGTTCATTCAAAGATATCTACTTGAG
*
3364832 TATTTATAGTTCATTCAAAGATGTCTACTTGAG
1 TATTTATAGTTCATTCAAAGATATCTACTTGAG
3364865 T
1 T
3364866 CATAGTCACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (33 bp):
TATTTATAGTTCATTCAAAGATATCTACTTGAG
Found at i:3371772 original size:60 final size:60
Alignment explanation
Indices: 3371588--3371773 Score: 166
Period size: 60 Copynumber: 3.1 Consensus size: 60
3371578 ATCAATGACG
* * * * *
3371588 AATGAAAAGGGATAACTTCCG-CTATC-AATCATGAAAAGAGATGGTGATGACCATC-ATAT
1 AATGAAAAGGGATGACTT-CGACTATCAAATTATGAAAAGGGATGGTGACGACCATCGA-AC
* * * * * *** *
3371647 TATGAAAAGGGATG-GTGACGACTATTAAATTATGAAAAGGGATGGCT-TCGGTTATCGCAC
1 AATGAAAAGGGATGACT-TCGACTATCAAATTATGAAAAGGGATGG-TGACGACCATCGAAC
*
3371707 TATGAAAAGGGATGACTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC
1 AATGAAAAGGGATGACTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC
3371767 AATGAAA
1 AATGAAA
3371774 TGGATAGTTT
Statistics
Matches: 97, Mismatches: 23, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
58 3 0.03
59 17 0.18
60 75 0.77
61 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (60 bp):
AATGAAAAGGGATGACTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC
Found at i:3371773 original size:30 final size:30
Alignment explanation
Indices: 3371609--3371758 Score: 135
Period size: 30 Copynumber: 5.0 Consensus size: 30
3371599 ATAACTTCCG
* * *
3371609 CTATC-AATCATGAAAAGAGATGGTGATGA
1 CTATCAAATTATGAAAAGGGATGGTGACGA
* *
3371638 CCATCATATTATGAAAAGGGATGGTGACGA
1 CTATCAAATTATGAAAAGGGATGGTGACGA
* * *
3371668 CTATTAAATTATGAAAAGGGATGGCT-TCGG
1 CTATCAAATTATGAAAAGGGATGG-TGACGA
* ** * * *
3371698 TTATCGCACTATGAAAAGGGATGACT-TCGA
1 CTATCAAATTATGAAAAGGGATG-GTGACGA
3371728 CTATCAAATTATGAAAAGGGATGGTGACGA
1 CTATCAAATTATGAAAAGGGATGGTGACGA
3371758 C
1 C
3371759 CATCGAACAA
Statistics
Matches: 94, Mismatches: 23, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
29 5 0.05
30 88 0.94
31 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (30 bp):
CTATCAAATTATGAAAAGGGATGGTGACGA
Found at i:3371805 original size:90 final size:90
Alignment explanation
Indices: 3371640--3371813 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 90
3371630 GGTGATGACC
* * * ** * ** *
3371640 ATCATATTATGAAAAGGGATGGTGACGACTATTAAATTATGAAAAGGGATGGCTTCGGTTATCGC
1 ATCAAATTATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCGACTATCGA
3371705 ACTATGAAAAGGGATGACTTCGACT
66 ACTATGAAAAGGGATGACTTCGACT
* * * *
3371730 ATCAAATTATGAAAAGGGATGGTGACGACCATCGAACAATG-AAATGGATAGTTTCGACTGTCGA
1 ATCAAATTATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCGACTATCGA
* *
3371794 ACTATGAAAAAGGATAACTT
66 ACTATGAAAAGGGATGACTT
3371814 TGGTTACCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
89 34 0.49
90 35 0.51
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (90 bp):
ATCAAATTATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATAGCTTCGACTATCGA
ACTATGAAAAGGGATGACTTCGACT
Found at i:3374730 original size:12 final size:13
Alignment explanation
Indices: 3374712--3374766 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
3374702 TAAAAATATG
3374712 ATATTTAATAATA
1 ATATTTAATAATA
3374725 AT-TTTAA-AATA
1 ATATTTAATAATA
* *
3374736 GTATTTAATATACA
1 ATATTTAATA-ATA
*
3374750 ATATATAATATATA
1 ATATTTAATA-ATA
3374764 ATA
1 ATA
3374767 ACAAAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 5 0.15
12 10 0.29
13 3 0.09
14 16 0.47
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:3375132 original size:32 final size:32
Alignment explanation
Indices: 3375086--3375156 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
3375076 TATAGAATAA
*
3375086 AAAATAATATAATAAGTAATATATAATAAAAAT
1 AAAATAATATAATAAATAATATATAAT-AAAAT
**
3375119 AAAA-AATATAATAAATTTTATATAATAAAAT
1 AAAATAATATAATAAATAATATATAATAAAAT
3375150 AAAATAA
1 AAAATAA
3375157 AAATATATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 9 0.26
32 21 0.62
33 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (32 bp):
AAAATAATATAATAAATAATATATAATAAAAT
Found at i:3375154 original size:29 final size:29
Alignment explanation
Indices: 3375072--3375155 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 29
3375062 TATGATATAC
*
3375072 ATAATATAGAATAAAA-AATAATATAATAA
1 ATAATATATAATAAAATAA-AATATAATAA
*
3375101 GTAATATATAATAAAAATAAAAAATATAATAA
1 ATAATATATAAT-AAAAT--AAAATATAATAA
**
3375133 ATTTTATATAATAAAATAAAATA
1 ATAATATATAATAAAATAAAATA
3375156 AAAATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
29 16 0.35
30 4 0.09
31 5 0.11
32 19 0.41
33 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAATATATAATAAAATAAAATATAATAA
Found at i:3375211 original size:27 final size:26
Alignment explanation
Indices: 3375171--3375235 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
3375161 ATATAGGAAA
3375171 ATAATATATGATAAATAAAAATTTTTAAT
1 ATAA-ATAT-ATAAAT-AAAATTTTTAAT
**
3375200 ATAAATATATAAATAGTATTTTTAAT
1 ATAAATATATAAATAAAATTTTTAAT
3375226 A-ATAATATAT
1 ATA-AATATAT
3375236 GTATAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 18 0.55
27 6 0.18
28 4 0.12
29 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATAAATATATAAATAAAATTTTTAAT
Found at i:3375266 original size:26 final size:26
Alignment explanation
Indices: 3375191--3375266 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
3375181 ATAAATAAAA
* *
3375191 ATTTTTAATATAAATATATAAATAGT
1 ATTTTTAAAATAAATATATATATAGT
*
3375217 ATTTTTAATAAT-AATATATGTATAGT
1 ATTTTTAA-AATAAATATATATATAGT
*
3375243 -TTTTTAAAATAAATAAATTATATA
1 ATTTTTAAAATAAATATA-TATATA
3375267 AAAAAATAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 3 0.07
25 12 0.29
26 25 0.60
27 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTTTTAAAATAAATATATATATAGT
Found at i:3377025 original size:20 final size:19
Alignment explanation
Indices: 3377002--3377049 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
3376992 TTTGTCCAAT
3377002 TTTTTATTTAATTAGT-TTA
1 TTTTTATTTAATTA-TATTA
3377021 TTTTTATTCTAATTATATTA
1 TTTTTATT-TAATTATATTA
3377041 TTTTTATTT
1 TTTTTATTT
3377050 TTAAGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTATTTAATTATATTA
Found at i:3403519 original size:6 final size:6
Alignment explanation
Indices: 3403517--3403590 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
3403507 TTAAAAATAA
* * * * *
3403517 AAAAAG AAAAAG AAAAAT AATAAT AATAAT -AAAAT AATAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
3403563 AATAAT -AAAAT AATAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
3403591 GATAGGAGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
5 12 0.21
6 44 0.79
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:3403538 original size:3 final size:3
Alignment explanation
Indices: 3403532--3403587 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
3403522 GAAAAAGAAA
3403532 AAT AAT AAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3403577 AAT AAA AAT AA
1 AAT AAT AAT AA
3403588 AAAGATAGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:3403554 original size:11 final size:11
Alignment explanation
Indices: 3403532--3403583 Score: 95
Period size: 11 Copynumber: 4.6 Consensus size: 11
3403522 GAAAAAGAAA
3403532 AATAATAATAAT
1 AATAA-AATAAT
3403544 AATAAAATAAT
1 AATAAAATAAT
3403555 AATAAAATAAT
1 AATAAAATAAT
3403566 AATAAAATAAT
1 AATAAAATAAT
3403577 AATAAAA
1 AATAAAA
3403584 ATAAAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
11 35 0.88
12 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:3411813 original size:13 final size:13
Alignment explanation
Indices: 3411791--3411823 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3411781 TGGGGTTTGT
3411791 TTAT-TAAACTAA
1 TTATCTAAACTAA
3411803 TTATCTAAACTAA
1 TTATCTAAACTAA
*
3411816 TTAACTAA
1 TTATCTAA
3411824 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:3412879 original size:11 final size:11
Alignment explanation
Indices: 3412855--3412888 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3412845 ATTTGGTCTA
3412855 TTTTGC-CCTT
1 TTTTGCTCCTT
*
3412865 TTTTGCTCGTT
1 TTTTGCTCCTT
3412876 TTTTGCTCCTT
1 TTTTGCTCCTT
3412887 TT
1 TT
3412889 GACTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTTGCTCCTT
Found at i:3414186 original size:53 final size:51
Alignment explanation
Indices: 3414036--3414194 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 51
3414026 TGACGAAAAA
* * *
3414036 GATGAGATATGTGA-TCCGTATAAGACCATAGCCGGGCTATGGCATCGGTAC
1 GATGTGATATGTGATTCCGTATAAGACCATAG-CTGGCTATGGCATCGGTAT
* * *
3414087 AATGTGATTTGTG-TTCCCGTATAAGACCATAGCTGAGCTATGGCATCGGTGT
1 GATGTGATATGTGATT-CCGTATAAGACCATAGCTG-GCTATGGCATCGGTAT
* * *
3414139 GATGTGATAATGTGATTCCGTATAAGACCATATCTAGGATATTGCATCGGTAT
1 GATGTGAT-ATGTGATTCCGTATAAGACCATAGCT-GGCTATGGCATCGGTAT
3414192 GAT
1 GAT
3414195 ATGTGATCTG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
51 13 0.14
52 37 0.41
53 37 0.41
54 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (51 bp):
GATGTGATATGTGATTCCGTATAAGACCATAGCTGGCTATGGCATCGGTAT
Found at i:3415014 original size:20 final size:20
Alignment explanation
Indices: 3414988--3415042 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3414978 ACATGGGCAG
*
3414988 GCCACACGGGCATGTTCC-A
1 GCCACACGGGCATGTCCCAA
*
3415007 GACCACACGGGCGTGTCCCAA
1 G-CCACACGGGCATGTCCCAA
3415028 GCCACACGGGCATGT
1 GCCACACGGGCATGT
3415043 GCCCCTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.90
21 2 0.06
ACGTcount: A:0.22, C:0.36, G:0.29, T:0.13
Consensus pattern (20 bp):
GCCACACGGGCATGTCCCAA
Found at i:3421865 original size:25 final size:25
Alignment explanation
Indices: 3421837--3421897 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
3421827 GATTGCAGAA
*
3421837 AAGAATAAAAAAATAAAAA-AAAAGG
1 AAGAATAAAAAAATAAAAAGAAAA-C
*
3421862 AAGAAT-AGAAAATAAAAAGAAAAC
1 AAGAATAAAAAAATAAAAAGAAAAC
3421886 AAGAAATAAAAA
1 AAG-AATAAAAA
3421898 TGTGAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 14 0.47
25 13 0.43
26 3 0.10
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.08
Consensus pattern (25 bp):
AAGAATAAAAAAATAAAAAGAAAAC
Found at i:3424016 original size:15 final size:16
Alignment explanation
Indices: 3423998--3424035 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
3423988 ATTAAAACAT
*
3423998 AATAGAAATAAAAGA-
1 AATAGAAATAAAAAAC
3424013 AATA-AAATAAAAAAC
1 AATAGAAATAAAAAAC
3424028 AATAGAAA
1 AATAGAAA
3424036 AAAGAACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 8 0.40
16 3 0.15
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (16 bp):
AATAGAAATAAAAAAC
Found at i:3445193 original size:24 final size:24
Alignment explanation
Indices: 3445157--3445205 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3445147 CCAGCAAAGA
* *
3445157 CTTCCAACTGATTCGCCTGAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
*
3445181 CTTCCAACAGATTCTCCTAAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
3445205 C
1 C
3445206 CGAGGGAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (24 bp):
CTTCCAACAGATTCGCCTAAGAGG
Found at i:3447881 original size:15 final size:15
Alignment explanation
Indices: 3447843--3447887 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
3447833 TTTTATTACT
3447843 ATTTTAAAATATATTTTA
1 ATTTT-AAAT-TA-TTTA
*
3447861 AATTTAAATTATTTA
1 ATTTTAAATTATTTA
3447876 ATTTTAAATTAT
1 ATTTTAAATTAT
3447888 GGATTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 15 0.60
16 2 0.08
17 4 0.16
18 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTAAATTATTTA
Found at i:3449616 original size:9 final size:9
Alignment explanation
Indices: 3449539--3449768 Score: 62
Period size: 10 Copynumber: 24.3 Consensus size: 9
3449529 TAATCTATTT
3449539 TTATAAAAA
1 TTATAAAAA
*
3449548 CGTATAAAAAA
1 -TTAT-AAAAA
*
3449559 TTTTAAAAA
1 TTATAAAAA
*
3449568 CTTATAAAAG
1 -TTATAAAAA
*
3449578 TCATTAAAAA
1 TTA-TAAAAA
*
3449588 -TAAAAAAA
1 TTATAAAAA
* * *
3449596 ATAT-ACAC
1 TTATAAAAA
3449604 TTATAAAAA
1 TTATAAAAA
*
3449613 TTATAATAA
1 TTATAAAAA
*
3449622 -TATAATAA
1 TTATAAAAA
*
3449630 TATGTAAAAA
1 T-TATAAAAA
*
3449640 --ATATAAA
1 TTATAAAAA
3449647 TT-TAATGAAA
1 TTATAA--AAA
*
3449657 TGTATTTAAAATT
1 T-TA--TAAAA-A
3449670 TTATAAAAA
1 TTATAAAAA
3449679 CTTATAAAAAA
1 -TTAT-AAAAA
* *
3449690 TTCCTAAAAT
1 TT-ATAAAAA
3449700 TTATAAATAA
1 TTATAAA-AA
3449710 -TATAAAAAA
1 TTAT-AAAAA
* *
3449719 TTCTAATAAG
1 TTATAA-AAA
3449729 TTATATACAAA
1 TTATA-A-AAA
*
3449740 TTATAAAAG
1 TTATAAAAA
3449749 TTATAAAAA
1 TTATAAAAA
*
3449758 AT-TAAAAA
1 TTATAAAAA
3449766 TTA
1 TTA
3449769 AAATTTTTTA
Statistics
Matches: 159, Mismatches: 36, Indels: 51
0.65 0.15 0.21
Matches are distributed among these distances:
7 5 0.03
8 27 0.17
9 42 0.26
10 57 0.36
11 20 0.13
12 4 0.03
13 1 0.01
14 3 0.02
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:3449699 original size:31 final size:29
Alignment explanation
Indices: 3449663--3449747 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 29
3449653 GAAATGTATT
3449663 TAAAATTTTATAAAAACTTATAAAAAATTCC
1 TAAAATTTTATAAAAA-TTATAAAAAATT-C
3449694 TAAAA-TTTATAAATAA-TATAAAAAATTC
1 TAAAATTTTATAAA-AATTATAAAAAATTC
* *
3449722 TAATAAGTTATATACAAATTATAAAA
1 TAA-AA-TTTTATAAAAATTATAAAA
3449748 GTTATAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 4 0.09
29 13 0.28
30 10 0.21
31 20 0.43
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (29 bp):
TAAAATTTTATAAAAATTATAAAAAATTC
Found at i:3449733 original size:20 final size:19
Alignment explanation
Indices: 3449710--3449765 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
3449700 TTATAAATAA
*
3449710 TATAAAAAATTCTAATAAGT
1 TATAAAAAATTATAA-AAGT
*
3449730 TATATACAAATTATAAAAGT
1 TATA-AAAAATTATAAAAGT
3449750 TATAAAAAATTA-AAAA
1 TATAAAAAATTATAAAA
3449766 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.12
19 7 0.22
20 12 0.38
21 9 0.28
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (19 bp):
TATAAAAAATTATAAAAGT
Found at i:3450499 original size:19 final size:18
Alignment explanation
Indices: 3450477--3450547 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
3450467 AATTTACTAG
3450477 ATTTTTATATTTTTATA-
1 ATTTTTATATTTTTATAT
* *
3450494 ATATTTATAAGTTTTAT-T
1 ATTTTTAT-ATTTTTATAT
**
3450512 ATTTTTTATAAAGTTTATAT
1 A-TTTTTAT-ATTTTTATAT
3450532 ATTTTTAATATTTTTA
1 ATTTTT-ATATTTTTA
3450548 GAATTTAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 7 0.17
18 8 0.19
19 23 0.55
20 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTTATATTTTTATAT
Found at i:3450499 original size:28 final size:25
Alignment explanation
Indices: 3450467--3450547 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 25
3450457 AATTTATTAG
3450467 AATTTACTAGATTTTTATATTTTTATA
1 AATTTA-TA-ATTTTTATATTTTTATA
*
3450494 ATATTTATAAGTTTTATTATTTTTTATA
1 A-ATTTATAATTTTTA-TA-TTTTTATA
3450522 AAGTTTATATATTTTTAATATTTTTA
1 AA-TTTATA-ATTTTT-ATATTTTTA
3450548 GAATTTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 6 0.13
27 6 0.13
28 26 0.57
29 7 0.15
30 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (25 bp):
AATTTATAATTTTTATATTTTTATA
Found at i:3450527 original size:20 final size:19
Alignment explanation
Indices: 3450497--3450537 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
3450487 TTTTATAATA
3450497 TTTATAAGTTT-TATTATTT
1 TTTATAAGTTTATA-TATTT
3450516 TTTATAAAGTTTATATATTT
1 TTTAT-AAGTTTATATATTT
3450536 TT
1 TT
3450538 AATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 13 0.65
21 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATAAGTTTATATATTT
Found at i:3451570 original size:24 final size:24
Alignment explanation
Indices: 3451538--3451585 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3451528 GGGAACAAGT
3451538 CATTCCTTTAAGATTAATGCATCG
1 CATTCCTTTAAGATTAATGCATCG
3451562 CATTCCTTTAAGATTAATGCATCG
1 CATTCCTTTAAGATTAATGCATCG
3451586 TTTCTTCTCT
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:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
CATTCCTTTAAGATTAATGCATCG
Found at i:3453243 original size:19 final size:20
Alignment explanation
Indices: 3453198--3453252 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
3453188 TAATTTAAAC
3453198 TAAAAAATAACATTAGTAATGA
1 TAAAAAATAA-ATTAG-AATGA
*
3453220 TAAAAAATAAATTA-AATTA
1 TAAAAAATAAATTAGAATGA
3453239 TAAAAAACTAAATT
1 TAAAAAA-TAAATT
3453253 CTTAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.35
20 6 0.19
21 4 0.13
22 10 0.32
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAAAATAAATTAGAATGA
Found at i:3466296 original size:50 final size:50
Alignment explanation
Indices: 3466221--3466318 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
3466211 TTAAACTAAT
*
3466221 AAATATTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGACTTGC
1 AAATACTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGACTTGC
3466271 AAATACTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGACTT
1 AAATACTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGACTT
3466319 ACAAGTAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (50 bp):
AAATACTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGACTTGC
Found at i:3466954 original size:8 final size:8
Alignment explanation
Indices: 3466909--3466944 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
3466899 AATTTTTTTC
*
3466909 TTTTATTT
1 TTTTATAT
3466917 TTTTATAT
1 TTTTATAT
3466925 TTTTATAT
1 TTTTATAT
*
3466933 TTTTATCT
1 TTTTATAT
3466941 TTTT
1 TTTT
3466945 TTTCTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTATAT
Found at i:3467519 original size:17 final size:18
Alignment explanation
Indices: 3467494--3467533 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3467484 CTAAGAAGCT
3467494 TTAGATTAATTTTATT-G
1 TTAGATTAATTTTATTCG
*
3467511 TTAGCTTAATTTTATTCG
1 TTAGATTAATTTTATTCG
3467529 TTAGA
1 TTAGA
3467534 AAATAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (18 bp):
TTAGATTAATTTTATTCG
Found at i:3469806 original size:23 final size:23
Alignment explanation
Indices: 3469780--3469828 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3469770 GCTCCAATAT
* *
3469780 TAACAATAATGAC-AATAATAGAA
1 TAACAACAATAACAAATAA-AGAA
3469803 TAACAACAATAACAAATAAAGAA
1 TAACAACAATAACAAATAAAGAA
3469826 TAA
1 TAA
3469829 TAATGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.18
Consensus pattern (23 bp):
TAACAACAATAACAAATAAAGAA
Found at i:3470632 original size:18 final size:19
Alignment explanation
Indices: 3470604--3470640 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3470594 AAAAAAAATA
*
3470604 AAATAAAATAAGATAAAAC
1 AAATAAAATAAGAGAAAAC
3470623 AAAT-AAATAAGAGAAAAC
1 AAATAAAATAAGAGAAAAC
3470641 GAAGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (19 bp):
AAATAAAATAAGAGAAAAC
Found at i:3470859 original size:21 final size:21
Alignment explanation
Indices: 3470820--3470859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3470810 CAAGTGGGCA
**
3470820 TGGGCGGTGGTGGCAGGTGCT
1 TGGGCGGTGGCAGCAGGTGCT
*
3470841 TGGGCGGTGGCAGCTGGTG
1 TGGGCGGTGGCAGCAGGTG
3470860 TCAGACGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.57, T:0.23
Consensus pattern (21 bp):
TGGGCGGTGGCAGCAGGTGCT
Found at i:3474627 original size:15 final size:16
Alignment explanation
Indices: 3474601--3474630 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3474591 TGAGGAACCT
3474601 ATTTTAATGTAAATTC
1 ATTTTAATGTAAATTC
3474617 ATTTT-ATGTAAATT
1 ATTTTAATGTAAATT
3474631 GTTCTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTTAATGTAAATTC
Found at i:3476773 original size:18 final size:19
Alignment explanation
Indices: 3476736--3476774 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3476726 CTACACTATT
*
3476736 TTTTAATAAAAAGAATTTA
1 TTTTAATAAAAAGAAATTA
*
3476755 TTTTCATAAAAA-AAATTA
1 TTTTAATAAAAAGAAATTA
3476773 TT
1 TT
3476775 AATAAGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTTAATAAAAAGAAATTA
Found at i:3481320 original size:16 final size:16
Alignment explanation
Indices: 3481301--3481338 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3481291 AAAATTTTCA
3481301 AAATTTAAAATAAT-TT
1 AAATTTAAAAT-ATCTT
*
3481317 AAATTCAAAATATCTT
1 AAATTTAAAATATCTT
3481333 AAATTT
1 AAATTT
3481339 CAACCAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAAAATATCTT
Found at i:3486887 original size:18 final size:17
Alignment explanation
Indices: 3486864--3486906 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3486854 TTAAAACTGT
3486864 TATAAAAATATTAATTAA
1 TATAAAAATATT-ATTAA
* *
3486882 TATAAATATTATTGTTAA
1 TATAAA-AATATTATTAA
3486900 TATAAAA
1 TATAAAA
3486907 TAACATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TATAAAAATATTATTAA
Found at i:3501950 original size:35 final size:35
Alignment explanation
Indices: 3501911--3501980 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3501901 GAAAGATATT
3501911 TGGCATAACAAAACAATTCATACGGCATTTTAGAA
1 TGGCATAACAAAACAATTCATACGGCATTTTAGAA
** *
3501946 TGGCATAACAAAATGATTCATACGGTATTTTAGAA
1 TGGCATAACAAAACAATTCATACGGCATTTTAGAA
3501981 ACAGCCCCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (35 bp):
TGGCATAACAAAACAATTCATACGGCATTTTAGAA
Found at i:3510263 original size:26 final size:26
Alignment explanation
Indices: 3510227--3510278 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3510217 TTGCACCGAG
3510227 GTAAGTTTGTATGTAAATAATACATT
1 GTAAGTTTGTATGTAAATAATACATT
3510253 GTAAGTTTGTATGTAAATAATACATT
1 GTAAGTTTGTATGTAAATAATACATT
3510279 ATCTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (26 bp):
GTAAGTTTGTATGTAAATAATACATT
Found at i:3512968 original size:26 final size:26
Alignment explanation
Indices: 3512932--3512981 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3512922 TTTCACCTAG
3512932 GTAAGTTTGTATGTAAATAATACATT
1 GTAAGTTTGTATGTAAATAATACATT
*
3512958 GTAAGTTTGTATGTAGATAATACA
1 GTAAGTTTGTATGTAAATAATACA
3512982 GTATCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (26 bp):
GTAAGTTTGTATGTAAATAATACATT
Found at i:3515369 original size:20 final size:18
Alignment explanation
Indices: 3515346--3515392 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
3515336 TTATTTTGTT
3515346 TTATTTAGTTTTATTATTTA
1 TTATTTAGTTTTA-T-TTTA
*
3515366 TTATTTATTTTTATTTTA
1 TTATTTAGTTTTATTTTA
3515384 TTAATTTAG
1 TT-ATTTAG
3515393 AATAGGCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 12 0.50
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTTAGTTTTATTTTA
Found at i:3522011 original size:17 final size:16
Alignment explanation
Indices: 3521989--3522056 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
3521979 AACCAACCAC
3521989 ACCCAACACCCACATAA
1 ACCCAA-ACCCACATAA
* *
3522006 ACCCAATACCCATATGA
1 ACCCAA-ACCCACATAA
* *
3522023 ACCCAAACCCAAAATTA
1 ACCCAAACCC-ACATAA
*
3522040 ACCCAAAACCACATAA
1 ACCCAAACCCACATAA
3522056 A
1 A
3522057 ATACCAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 9 0.21
17 33 0.79
ACGTcount: A:0.50, C:0.38, G:0.01, T:0.10
Consensus pattern (16 bp):
ACCCAAACCCACATAA
Found at i:3529957 original size:70 final size:69
Alignment explanation
Indices: 3529823--3529961 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 69
3529813 CTCGAGTGTG
3529823 AGTATCTGACATGGATATGCTTAGATTTTTTAAGTTTTTTCCATAGATTTGAGAATAATGTCATA
1 AGTATCTGACATGGATATGCTTAGATTTTTTAAGTTTTTTCCATAGATTTGAGAATAATGTCATA
3529888 TCTA
66 TCTA
3529892 AGTATCTGACATGGATATGCTTAGATTTTTCTAAGTTTTTTCCATAGATTTGAGAATAATGTCAT
1 AGTATCTGACATGGATATGCTTAGATTTTT-TAAGTTTTTTCCATAGATTTGAGAATAATGTCAT
3529957 ATCTA
65 ATCTA
3529962 CACATCCATG
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 30 0.43
70 39 0.57
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (69 bp):
AGTATCTGACATGGATATGCTTAGATTTTTTAAGTTTTTTCCATAGATTTGAGAATAATGTCATA
TCTA
Found at i:3532776 original size:24 final size:24
Alignment explanation
Indices: 3532749--3532794 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3532739 TTTAATAAAA
*
3532749 ATTAAATTAAAATTTTATAAATTT
1 ATTAAATTAAAATTTTAAAAATTT
* *
3532773 ATTAATTTAAAGTTTTAAAAAT
1 ATTAAATTAAAATTTTAAAAAT
3532795 ATAAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTAAATTAAAATTTTAAAAATTT
Found at i:3536384 original size:21 final size:22
Alignment explanation
Indices: 3536360--3536400 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3536350 GACTTAAATG
*
3536360 AATTTTTTTG-AATATTTTAGT
1 AATTATTTTGTAATATTTTAGT
*
3536381 AATTATTTTGTAATTTTTTA
1 AATTATTTTGTAATATTTTA
3536401 AAGTTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
AATTATTTTGTAATATTTTAGT
Found at i:3537917 original size:24 final size:24
Alignment explanation
Indices: 3537871--3537918 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3537861 ACACCAAATC
* *
3537871 CAATTTTAAAAAGTTATTTTTATA
1 CAATTTTAAAAAGTTAATATTATA
3537895 CAATTTATAAAAA-TTAATATTATA
1 CAATTT-TAAAAAGTTAATATTATA
3537919 AACATGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
CAATTTTAAAAAGTTAATATTATA
Found at i:3538004 original size:27 final size:27
Alignment explanation
Indices: 3537943--3538004 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3537933 AGTGTTTGAG
* *
3537943 ATAATTATAACAAAAAAATATTATATT
1 ATAATTTTAACAAAAAAATATTATAAT
*
3537970 ATAAATTTTAA-AAAAATATATTATAAAT
1 AT-AATTTTAACAAAAAAATATTAT-AAT
3537998 ATAATTT
1 ATAATTT
3538005 GTGTGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAATTTTAACAAAAAAATATTATAAT
Found at i:3548101 original size:995 final size:995
Alignment explanation
Indices: 3546171--3548163 Score: 3977
Period size: 995 Copynumber: 2.0 Consensus size: 995
3546161 GAAAACGAAG
3546171 ACTTATTTGGAGATGGGCCTTTGCCCGAGTGGGTGGGGTGGGGAGAATCATCAGATTTGAAACTA
1 ACTTATTTGGAGATGGGCCTTTGCCCGAGTGGGTGGGGTGGGGAGAATCATCAGATTTGAAACTA
3546236 GGTGGTTCAAGCAAAAACCCATTTCTAGATGATGACAGCTCAGATGTCAATCAGCCAAGTCATAT
66 GGTGGTTCAAGCAAAAACCCATTTCTAGATGATGACAGCTCAGATGTCAATCAGCCAAGTCATAT
3546301 CGAGACGACGGTCACTTATGTCTTTCCCCTGTCGAATGGAGACCCCATACTTCCAAATGTTTCCC
131 CGAGACGACGGTCACTTATGTCTTTCCCCTGTCGAATGGAGACCCCATACTTCCAAATGTTTCCC
3546366 TGGACTCCATGGATCTGAGTGACGGATCAGTGAGCAGTGATACAAGTCAGAAATCTCCACCAGCA
196 TGGACTCCATGGATCTGAGTGACGGATCAGTGAGCAGTGATACAAGTCAGAAATCTCCACCAGCA
*
3546431 GTGCCCTCTTTGTTCGGAGAGGATGTCGAATTCGTAGGGGTGGAATTAGAAGGTACAGAGAAGGC
261 GTGCCCTCTTTGTTCGAAGAGGATGTCGAATTCGTAGGGGTGGAATTAGAAGGTACAGAGAAGGC
3546496 AATGGAACAAGCTTTAAAAGAAGGAATAGTTGGGGAAGCTGGACCGTTAAAGAGGAACATTATTC
326 AATGGAACAAGCTTTAAAAGAAGGAATAGTTGGGGAAGCTGGACCGTTAAAGAGGAACATTATTC
3546561 CAAAGGTACCACAGAAGGAGAATTCGGACGACGATGGGGCTGGAATGAAGGAGTTCAATGATGCA
391 CAAAGGTACCACAGAAGGAGAATTCGGACGACGATGGGGCTGGAATGAAGGAGTTCAATGATGCA
3546626 AACTATTGGAAGGTTGATCAAGAGGTCGCTGTTTTAGAGTAATGGTGGTTGAGTCGAAAGTAAGA
456 AACTATTGGAAGGTTGATCAAGAGGTCGCTGTTTTAGAGTAATGGTGGTTGAGTCGAAAGTAAGA
3546691 TCGACATCACAGTTTTGTTCGCTCTGAGGGCTGAAGCAGCAAAACTCACATGTATATTATAATTT
521 TCGACATCACAGTTTTGTTCGCTCTGAGGGCTGAAGCAGCAAAACTCACATGTATATTATAATTT
3546756 TTTTTTCTTTCCACTGTTATTTACTGTTTTATGTTCCTTTAATTGTTAGCGTTAACTCCTCTTTA
586 TTTTTTCTTTCCACTGTTATTTACTGTTTTATGTTCCTTTAATTGTTAGCGTTAACTCCTCTTTA
3546821 TTGTTGTTTTAATGTTTTCATTATTTGAAGGTATTTGGTTCTTCTCGTTGCCCTGATTTAAGGTA
651 TTGTTGTTTTAATGTTTTCATTATTTGAAGGTATTTGGTTCTTCTCGTTGCCCTGATTTAAGGTA
3546886 AGGGCTTCTCAATATTATTTATGTTAGTCTTTATGGAATTTTAATGCAATCATATTTGGTTGTAT
716 AGGGCTTCTCAATATTATTTATGTTAGTCTTTATGGAATTTTAATGCAATCATATTTGGTTGTAT
3546951 TTTCAATCTTTATATTAAATTGGTAATAATAATCTCTTATATATATGCAACTGACTTGGGCCTCG
781 TTTCAATCTTTATATTAAATTGGTAATAATAATCTCTTATATATATGCAACTGACTTGGGCCTCG
3547016 AAATTGAAGCCAATATTATTACAATATTGTGACTTGAATTGTGGTTACGTTAGGCATATCAGCGG
846 AAATTGAAGCCAATATTATTACAATATTGTGACTTGAATTGTGGTTACGTTAGGCATATCAGCGG
3547081 AAGATTTTATGCTAAATCTTTTTCCAGAAGCTGAATAATTACTAATTAGGTAAAGTAGCCTTTGG
911 AAGATTTTATGCTAAATCTTTTTCCAGAAGCTGAATAATTACTAATTAGGTAAAGTAGCCTTTGG
3547146 TGGGGTGGGTTGGCTTGGTT
976 TGGGGTGGGTTGGCTTGGTT
3547166 ACTTATTTGGAGATGGGCCTTTGCCCGAGTGGGTGGGGTGGGGAGAATCATCAGATTTGAAACTA
1 ACTTATTTGGAGATGGGCCTTTGCCCGAGTGGGTGGGGTGGGGAGAATCATCAGATTTGAAACTA
3547231 GGTGGTTCAAGCAAAAACCCATTTCTAGATGATGACAGCTCAGATGTCAATCAGCCAAGTCATAT
66 GGTGGTTCAAGCAAAAACCCATTTCTAGATGATGACAGCTCAGATGTCAATCAGCCAAGTCATAT
3547296 CGAGACGACGGTCACTTATGTCTTTCCCCTGTCGAATGGAGACCCCATACTTCCAAATGTTTCCC
131 CGAGACGACGGTCACTTATGTCTTTCCCCTGTCGAATGGAGACCCCATACTTCCAAATGTTTCCC
3547361 TGGACTCCATGGATCTGAGTGACGGATCAGTGAGCAGTGATACAAGTCAGAAATCTCCACCAGCA
196 TGGACTCCATGGATCTGAGTGACGGATCAGTGAGCAGTGATACAAGTCAGAAATCTCCACCAGCA
3547426 GTGCCCTCTTTGTTCGAAGAGGATGTCGAATTCGTAGGGGTGGAATTAGAAGGTACAGAGAAGGC
261 GTGCCCTCTTTGTTCGAAGAGGATGTCGAATTCGTAGGGGTGGAATTAGAAGGTACAGAGAAGGC
3547491 AATGGAACAAGCTTTAAAAGAAGGAATAGTTGGGGAAGCTGGACCGTTAAAGAGGAACATTATTC
326 AATGGAACAAGCTTTAAAAGAAGGAATAGTTGGGGAAGCTGGACCGTTAAAGAGGAACATTATTC
3547556 CAAAGGTACCACAGAAGGAGAATTCGGACGACGATGGGGCTGGAATGAAGGAGTTCAATGATGCA
391 CAAAGGTACCACAGAAGGAGAATTCGGACGACGATGGGGCTGGAATGAAGGAGTTCAATGATGCA
3547621 AACTATTGGAAGGTTGATCAAGAGGTCGCTGTTTTAGAGTAATGGTGGTTGAGTCGAAAGTAAGA
456 AACTATTGGAAGGTTGATCAAGAGGTCGCTGTTTTAGAGTAATGGTGGTTGAGTCGAAAGTAAGA
3547686 TCGACATCACAGTTTTGTTCGCTCTGAGGGCTGAAGCAGCAAAACTCACATGTATATTATAATTT
521 TCGACATCACAGTTTTGTTCGCTCTGAGGGCTGAAGCAGCAAAACTCACATGTATATTATAATTT
3547751 TTTTTTCTTTCCACTGTTATTTACTGTTTTATGTTCCTTTAATTGTTAGCGTTAACTCCTCTTTA
586 TTTTTTCTTTCCACTGTTATTTACTGTTTTATGTTCCTTTAATTGTTAGCGTTAACTCCTCTTTA
3547816 TTGTTGTTTTAATGTTTTCATTATTTGAAGGTATTTGGTTCTTCTCGTTGCCCTGATTTAAGGTA
651 TTGTTGTTTTAATGTTTTCATTATTTGAAGGTATTTGGTTCTTCTCGTTGCCCTGATTTAAGGTA
3547881 AGGGCTTCTCAATATTATTTATGTTAGTCTTTATGGAATTTTAATGCAATCATATTTGGTTGTAT
716 AGGGCTTCTCAATATTATTTATGTTAGTCTTTATGGAATTTTAATGCAATCATATTTGGTTGTAT
3547946 TTTCAATCTTTATATTAAATTGGTAATAATAATCTCTTATATATATGCAACTGACTTGGGCCTCG
781 TTTCAATCTTTATATTAAATTGGTAATAATAATCTCTTATATATATGCAACTGACTTGGGCCTCG
3548011 AAATTGAAGCCAATATTATTACAATATTGTGACTTGAATTGTGGTTACGTTAGGCATATCAGCGG
846 AAATTGAAGCCAATATTATTACAATATTGTGACTTGAATTGTGGTTACGTTAGGCATATCAGCGG
3548076 AAGATTTTATGCTAAATCTTTTTCCAGAAGCTGAATAATTACTAATTAGGTAAAGTAGCCTTTGG
911 AAGATTTTATGCTAAATCTTTTTCCAGAAGCTGAATAATTACTAATTAGGTAAAGTAGCCTTTGG
3548141 TGGGGTGGGTTGGCTTGGTT
976 TGGGGTGGGTTGGCTTGGTT
3548161 ACT
1 ACT
3548164 CTGGGGGGTT
Statistics
Matches: 997, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
995 997 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (995 bp):
ACTTATTTGGAGATGGGCCTTTGCCCGAGTGGGTGGGGTGGGGAGAATCATCAGATTTGAAACTA
GGTGGTTCAAGCAAAAACCCATTTCTAGATGATGACAGCTCAGATGTCAATCAGCCAAGTCATAT
CGAGACGACGGTCACTTATGTCTTTCCCCTGTCGAATGGAGACCCCATACTTCCAAATGTTTCCC
TGGACTCCATGGATCTGAGTGACGGATCAGTGAGCAGTGATACAAGTCAGAAATCTCCACCAGCA
GTGCCCTCTTTGTTCGAAGAGGATGTCGAATTCGTAGGGGTGGAATTAGAAGGTACAGAGAAGGC
AATGGAACAAGCTTTAAAAGAAGGAATAGTTGGGGAAGCTGGACCGTTAAAGAGGAACATTATTC
CAAAGGTACCACAGAAGGAGAATTCGGACGACGATGGGGCTGGAATGAAGGAGTTCAATGATGCA
AACTATTGGAAGGTTGATCAAGAGGTCGCTGTTTTAGAGTAATGGTGGTTGAGTCGAAAGTAAGA
TCGACATCACAGTTTTGTTCGCTCTGAGGGCTGAAGCAGCAAAACTCACATGTATATTATAATTT
TTTTTTCTTTCCACTGTTATTTACTGTTTTATGTTCCTTTAATTGTTAGCGTTAACTCCTCTTTA
TTGTTGTTTTAATGTTTTCATTATTTGAAGGTATTTGGTTCTTCTCGTTGCCCTGATTTAAGGTA
AGGGCTTCTCAATATTATTTATGTTAGTCTTTATGGAATTTTAATGCAATCATATTTGGTTGTAT
TTTCAATCTTTATATTAAATTGGTAATAATAATCTCTTATATATATGCAACTGACTTGGGCCTCG
AAATTGAAGCCAATATTATTACAATATTGTGACTTGAATTGTGGTTACGTTAGGCATATCAGCGG
AAGATTTTATGCTAAATCTTTTTCCAGAAGCTGAATAATTACTAATTAGGTAAAGTAGCCTTTGG
TGGGGTGGGTTGGCTTGGTT
Found at i:3559448 original size:25 final size:25
Alignment explanation
Indices: 3559420--3559471 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3559410 CTTTTTTAAA
3559420 TAATTTCGACTTAAGCCCATAATTT
1 TAATTTCGACTTAAGCCCATAATTT
3559445 TAATTTCGACTTAAGCCCATAATTT
1 TAATTTCGACTTAAGCCCATAATTT
3559470 TA
1 TA
3559472 CTTTGGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (25 bp):
TAATTTCGACTTAAGCCCATAATTT
Found at i:3561407 original size:10 final size:10
Alignment explanation
Indices: 3561392--3561416 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3561382 GATTGAAAGC
3561392 AAATGGAAGA
1 AAATGGAAGA
3561402 AAATGGAAGA
1 AAATGGAAGA
3561412 AAATG
1 AAATG
3561417 CCCTAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (10 bp):
AAATGGAAGA
Found at i:3564450 original size:43 final size:43
Alignment explanation
Indices: 3564371--3564452 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
3564361 TTCAAACAAA
* *
3564371 TTAAACATAATAATTTTGCAACAATTTAAATATACATAATAAC
1 TTAAACATAAGAATTTTGCAACAAATTAAATATACATAATAAC
*
3564414 TTAAACATAAGAA-TTT-CAAACAAATTAAATGTTACATAA
1 TTAAACATAAGAATTTTGC-AACAAATTAAAT-ATACATAA
3564453 CAATTGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.03
42 14 0.41
43 19 0.56
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (43 bp):
TTAAACATAAGAATTTTGCAACAAATTAAATATACATAATAAC
Found at i:3565023 original size:147 final size:147
Alignment explanation
Indices: 3564720--3565027 Score: 345
Period size: 147 Copynumber: 2.1 Consensus size: 147
3564710 TAACTCATGT
* **
3564720 TAATTGTATATATTATAATCTACCATAAAGTTAGCTACACATTTAAGGTTTAAGATTATGTATCA
1 TAATTGTATATATTATAATCTACCATAAAGTTAACTACACATTTAAGGTTTAAGATTACATATCA
* **
3564785 TTAATATAAAAAATGTACATTATAATGTCATAATTGTAGATAAGGTGACATATAATTAATAATCT
66 TTAATATAAAAAATATACATTATAATAACATAATTGTAGATAAGGTGACATATAATTAATAATCT
* *
3564850 ATCTTAACTATATAATGG
131 ACCTAAACTATATAAT-G
* * * * ** * * *
3564868 TAACTGTATGTATTATAATTTGA-CATAAAGTTAATTACATGTTTAGGGTTTAAGCTTGCATATC
1 TAATTGTATATATTATAATCT-ACCATAAAGTTAACTACACATTTAAGGTTTAAGATTACATATC
* * * *
3564932 ATTAATAT-AAAAATATACATTATAATAACATAGTTGTATAT-A-GTGATACATATCATTAATTA
65 ATTAATATAAAAAATATACATTATAATAACATAATTGTAGATAAGGTG--ACATATAATTAATAA
*
3564994 TCTACCTAAATTATATAATG
128 TCTACCTAAACTATATAATG
3565014 TCAATTGTATATAT
1 T-AATTGTATATAT
3565028 ATTTTATAAA
Statistics
Matches: 132, Mismatches: 24, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
145 3 0.02
146 3 0.02
147 67 0.51
148 58 0.44
149 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (147 bp):
TAATTGTATATATTATAATCTACCATAAAGTTAACTACACATTTAAGGTTTAAGATTACATATCA
TTAATATAAAAAATATACATTATAATAACATAATTGTAGATAAGGTGACATATAATTAATAATCT
ACCTAAACTATATAATG
Found at i:3570647 original size:46 final size:44
Alignment explanation
Indices: 3570543--3570650 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3570533 TGTCTTTGAC
** * * *
3570543 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3570587 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3570633 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3570651 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3572939 original size:15 final size:16
Alignment explanation
Indices: 3572919--3572952 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3572909 AATTATTTTT
3572919 TAAATAAATTTTTA-A
1 TAAATAAATTTTTACA
*
3572934 TAAATATATTTTTACA
1 TAAATAAATTTTTACA
3572950 TAA
1 TAA
3572953 TTTTTTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAAATTTTTACA
Found at i:3574262 original size:16 final size:16
Alignment explanation
Indices: 3574243--3574286 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3574233 TTATAAATTT
3574243 TTTGAATTATTTTGAA
1 TTTGAATTATTTTGAA
* *
3574259 TTTGAATAATTTTGAT
1 TTTGAATTATTTTGAA
*
3574275 TTTGAGTTATTT
1 TTTGAATTATTT
3574287 CAAACTCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (16 bp):
TTTGAATTATTTTGAA
Found at i:3579672 original size:14 final size:14
Alignment explanation
Indices: 3579650--3579679 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3579640 TCTCTACCGG
*
3579650 AAAATTTTGTACCC
1 AAAACTTTGTACCC
3579664 AAAACTTTGTACCC
1 AAAACTTTGTACCC
3579678 AA
1 AA
3579680 CGGTTGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAACTTTGTACCC
Found at i:3585502 original size:18 final size:17
Alignment explanation
Indices: 3585470--3585510 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
3585460 TGCATGATAA
3585470 ATTT-ATTTTTAAATTT
1 ATTTAATTTTTAAATTT
*
3585486 TTTTAATTTTATAAATTT
1 ATTTAATTTT-TAAATTT
3585504 ATTTAAT
1 ATTTAAT
3585511 ATCGGGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 5 0.24
18 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTAATTTTTAAATTT
Done.