Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 108 of 230
Found at i:31164266 original size:46 final size:46
Alignment explanation
Indices: 31164168--31164288 Score: 127
Period size: 48 Copynumber: 2.6 Consensus size: 46
31164158 TATGTGAAAC
** *
31164168 CTTTGTGTAATATTCTGTAACGCCTTTGTGGCATATTCTACAATGT
1 CTTTGTGGCATATTCTGTAACGCCTTTGTGGCATATTCTACAATGA
* * * *
31164214 CTTTGTGGCATATTTTGTAATGCCTTTGTGTGGCGTATTCTATAAT-A
1 CTTTGTGGCATATTCTGTAACGCC-TT-TGTGGCATATTCTACAATGA
* *
31164261 CTTGTGTGGCGTATTCTTTAACGCCTTT
1 CTT-TGTGGCATATTCTGTAACGCCTTT
31164289 AAGGCAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
46 21 0.34
47 7 0.11
48 33 0.54
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (46 bp):
CTTTGTGGCATATTCTGTAACGCCTTTGTGGCATATTCTACAATGA
Found at i:31169584 original size:33 final size:33
Alignment explanation
Indices: 31169537--31169603 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
31169527 AAGTCGATGA
*
31169537 AAGTTTGAAATGGGATGCTAAAGGAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
**
31169570 AAGTCTGAAATGGGATGCTAAATTAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
31169603 A
1 A
31169604 GGTTTAGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.25
Consensus pattern (33 bp):
AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
Found at i:31183634 original size:25 final size:25
Alignment explanation
Indices: 31183602--31183672 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
31183592 CAAACCCATT
**
31183602 TCACAACTTTTGTAAGCATTTAAAG
1 TCACAACTCGTGTAAGCATTTAAAG
** *
31183627 TCACAACTCGTGTGGGCATTTATAG
1 TCACAACTCGTGTAAGCATTTAAAG
*
31183652 TCACAACTCGTGTGAGCATTT
1 TCACAACTCGTGTAAGCATTT
31183673 TTCCCGCGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (25 bp):
TCACAACTCGTGTAAGCATTTAAAG
Found at i:31191586 original size:40 final size:40
Alignment explanation
Indices: 31191542--31191673 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
31191532 CTATGTTTAA
* * *
31191542 CACTTAGTATGAAATTTGAGATAGTTTCGGCTATTTATGG
1 CACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATGG
* *
31191582 CACTTAGTGTGAGATTTGAAATAGCTTCGGCTATATATGG
1 CACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATGG
* * * * *
31191622 AACTTAGTGTGCGAGA-CTGAGATAGCTTCGGCTATGTAAGG
1 CACTTAGTAT--GAGATTTGAGATAGCTTCGGCTATATATGG
31191663 CACTTAGTATG
1 CACTTAGTATG
31191674 CGAGATTATA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 44 0.56
41 29 0.37
42 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (40 bp):
CACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATGG
Found at i:31191668 original size:41 final size:42
Alignment explanation
Indices: 31191558--31191679 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 42
31191548 GTATGAAATT
* * *
31191558 TGAGATAGTTTCGGCTATTTATGGCACTTAGTGT--GAGATT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* *
31191598 TGAAATAGCTTCGGCTATATATGGAACTTAGTGTGCGAGA-C
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* * *
31191639 TGAGATAGCTTCGGCTATGTAAGGCACTTAGTATGCGAGAT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
31191680 TATAATAGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 30 0.43
41 35 0.51
42 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (42 bp):
TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
Found at i:31192394 original size:23 final size:23
Alignment explanation
Indices: 31192357--31192508 Score: 128
Period size: 23 Copynumber: 6.5 Consensus size: 23
31192347 TGACTGATTG
*
31192357 ATGCTGCCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
**
31192380 ATATTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
31192403 ATGCTGTCCAATTTGATGTATTA
1 ATGCTGTCCAATTTGATGTATAA
* *
31192426 ATGCTGTCCATTTTGA-GCATATTA
1 ATGCTGTCCAATTTGATG--TATAA
* * *
31192450 ATGCTGTCCATTTTG-CGCTTATTA
1 ATGCTGTCCAATTTGATG--TATAA
* * *
31192474 ATGTTGTCTAAGTTTGAGGTATAA
1 ATGCTGTCCAA-TTTGATGTATAA
*
31192498 AGGCTGTCCAA
1 ATGCTGTCCAA
31192509 AATAAGGTAG
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
22 1 0.01
23 55 0.51
24 47 0.44
25 4 0.04
26 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.40
Consensus pattern (23 bp):
ATGCTGTCCAATTTGATGTATAA
Found at i:31192453 original size:24 final size:23
Alignment explanation
Indices: 31192384--31192481 Score: 101
Period size: 24 Copynumber: 4.2 Consensus size: 23
31192374 GTATAAATAT
* *
31192384 TGTCCAATTTGATG-TATAAATGC
1 TGTCCATTTTGA-GCTATTAATGC
*
31192407 TGTCCAATTTGATG-TATTAATGC
1 TGTCCATTTTGA-GCTATTAATGC
31192430 TGTCCATTTTGAGCATATTAATGC
1 TGTCCATTTTGAGC-TATTAATGC
* *
31192454 TGTCCATTTTGCGCTTATTAATGT
1 TGTCCATTTTGAGC-TATTAATGC
31192478 TGTC
1 TGTC
31192482 TAAGTTTGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.01
23 33 0.49
24 34 0.50
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTCCATTTTGAGCTATTAATGC
Found at i:31194901 original size:16 final size:16
Alignment explanation
Indices: 31194848--31194905 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
31194838 AAAAATTCAC
31194848 TTAAAAATAAAAAATA
1 TTAAAAATAAAAAATA
* *
31194864 -GAACAATTAAAAAATA
1 TTAA-AAATAAAAAATA
31194880 GTTAAAAATAAAAAATCA
1 -TTAAAAATAAAAAAT-A
*
31194898 TAAAAAAT
1 TTAAAAAT
31194906 CCAAAAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.06
16 11 0.33
17 17 0.52
18 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (16 bp):
TTAAAAATAAAAAATA
Found at i:31207606 original size:3 final size:3
Alignment explanation
Indices: 31207598--31207622 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31207588 ACCAAATGCA
31207598 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
31207623 ATCAGAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:31210696 original size:11 final size:11
Alignment explanation
Indices: 31210680--31210704 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31210670 AGTTGGTTGG
31210680 TTTTGGTATGT
1 TTTTGGTATGT
31210691 TTTTGGTATGT
1 TTTTGGTATGT
31210702 TTT
1 TTT
31210705 AAAGTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (11 bp):
TTTTGGTATGT
Found at i:31211107 original size:19 final size:19
Alignment explanation
Indices: 31211082--31211124 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
31211072 CATGTTTCCA
31211082 AAATTTTAAATTTT-TTTC
1 AAATTTTAAATTTTCTTTC
*
31211100 ATAATTTTATATTTTCTTTC
1 A-AATTTTAAATTTTCTTTC
31211120 AAATT
1 AAATT
31211125 GGTCCTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATTTTAAATTTTCTTTC
Found at i:31229617 original size:79 final size:81
Alignment explanation
Indices: 31229514--31229698 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
31229504 GCTCCTCGTT
* * *
31229514 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGTCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTT-GGGATCTTAACCC
* *
31229577 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* * **
31229594 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTTGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTGGGATCTTAACCCGG
* *
31229658 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
31229674 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31229699 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTGGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:31229698 original size:40 final size:40
Alignment explanation
Indices: 31229514--31229698 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
31229504 GCTCCTCGTT
* *
31229514 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
31229554 CAAATGTCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
31229594 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
31229633 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
31229674 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31229699 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 77 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:31233925 original size:23 final size:23
Alignment explanation
Indices: 31233907--31233984 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 23
31233897 TAGGCTTCAT
31233907 AGAATACGCCACAAGGGCTCCAC
1 AGAATACGCCACAAGGGCTCCAC
* ** * *
31233930 AGTATATTCCACAAAGGCTTCAC
1 AGAATACGCCACAAGGGCTCCAC
* *
31233953 AGATTATGCCACAAGGGCTCCAC
1 AGAATACGCCACAAGGGCTCCAC
31233976 AGAATACGC
1 AGAATACGC
31233985 TGCAAAGACG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (23 bp):
AGAATACGCCACAAGGGCTCCAC
Found at i:31233991 original size:46 final size:46
Alignment explanation
Indices: 31233898--31234039 Score: 133
Period size: 46 Copynumber: 3.1 Consensus size: 46
31233888 CTAGCCATTT
* * * **
31233898 AGGCTTCATAGAATACGCCACAAGGGCTCCACAGTATATTCCACAA
1 AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
* **
31233944 AGGCTTCACAGATTATGCCACAAGGGCTCCACAGAATACGCTGCAA
1 AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
* * * * * * *
31233990 AGACGTCATATATTATGCCATAAAGGCAT-CACCGAATATGCCACAA
1 AGGCTTCATAGATTATGCCACAAGGGC-TCCACAGAATACGCCACAA
31234036 AGGC
1 AGGC
31234040 ATTACAGGAT
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
46 75 0.99
47 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (46 bp):
AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
Found at i:31234075 original size:24 final size:23
Alignment explanation
Indices: 31234011--31234086 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
31234001 ATTATGCCAT
* * **
31234011 AAAGGCATCACCGAATATGCCAC
1 AAAGGCATTACAGAATACACCAC
*
31234034 AAAGGCATTACAGGATACACCAC
1 AAAGGCATTACAGAATACACCAC
** * *
31234057 AAATGGCATTTTAGAATACGCTAC
1 AAA-GGCATTACAGAATACACCAC
31234081 AAAGGC
1 AAAGGC
31234087 TCTGTTTGGA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
23 24 0.57
24 18 0.43
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (23 bp):
AAAGGCATTACAGAATACACCAC
Found at i:31235745 original size:20 final size:20
Alignment explanation
Indices: 31235643--31235747 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
31235633 GACAAGCGAG
* *
31235643 CAGTAATGCAAATAAACTGT
1 CAGTAATGCAGATAAACTGC
* *
31235663 CAGTATTGCAGATAAACTAC
1 CAGTAATGCAGATAAACTGC
* *
31235683 CAGTAATGCAGATGAGCTGC
1 CAGTAATGCAGATAAACTGC
* * ** * * **
31235703 TAGTATTGTGGACAAGCCAC
1 CAGTAATGCAGATAAACTGC
*
31235723 CAGTAATGTAGATAAACTGC
1 CAGTAATGCAGATAAACTGC
31235743 CAGTA
1 CAGTA
31235748 CTTCTTCCTT
Statistics
Matches: 62, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (20 bp):
CAGTAATGCAGATAAACTGC
Found at i:31238878 original size:25 final size:25
Alignment explanation
Indices: 31238830--31238881 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
31238820 ATCCCGAGAT
* *
31238830 GAAAACCTCAAATTTTAAGTGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
*
31238855 GAAAACCTCAAATTCTACGCGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
31238880 GA
1 GA
31238882 TACATTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (25 bp):
GAAAACCTCAAATTCTAAGCGGGTG
Found at i:31239568 original size:13 final size:13
Alignment explanation
Indices: 31239546--31239581 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31239536 TTTTTAAAAC
31239546 ATCATCACCCTTA
1 ATCATCACCCTTA
*
31239559 ATCTTCACCCTTA
1 ATCATCACCCTTA
31239572 ATCATCACCC
1 ATCATCACCC
31239582 ACAAGTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATCACCCTTA
Found at i:31254838 original size:22 final size:22
Alignment explanation
Indices: 31254799--31254862 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
31254789 TCATAGATAC
31254799 GCCACAAGGGGCTCCACAG-TATAT
1 GCCACAA--GGCTCCACAGAT-TAT
* *
31254823 TCCACAAGGCTTCACAGATTAT
1 GCCACAAGGCTCCACAGATTAT
*
31254845 GCCACAGGGCTCCACAGA
1 GCCACAAGGCTCCACAGA
31254863 ATACGCTGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 27 0.79
23 1 0.03
24 6 0.18
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (22 bp):
GCCACAAGGCTCCACAGATTAT
Found at i:31256494 original size:20 final size:20
Alignment explanation
Indices: 31256445--31256496 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
31256435 GACAAGCGAG
* **
31256445 CAGTAATGCAAATAAACTGT
1 CAGTAATGCAGATAAACTAC
31256465 CAGT-ATGCAGATAAACTAC
1 CAGTAATGCAGATAAACTAC
31256484 CAGTAATGCAGAT
1 CAGTAATGCAGAT
31256497 GAGCTGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
CAGTAATGCAGATAAACTAC
Found at i:31256546 original size:20 final size:20
Alignment explanation
Indices: 31256445--31256548 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
31256435 GACAAGCGAG
* *
31256445 CAGTAATGCAAATAAACTGT
1 CAGTAATGCAGATAAACTGC
*
31256465 CAGT-ATGCAGATAAACTAC
1 CAGTAATGCAGATAAACTGC
* *
31256484 CAGTAATGCAGATGAGCTGC
1 CAGTAATGCAGATAAACTGC
* * ** * * **
31256504 TAGTATTGTGGACAAGCCAC
1 CAGTAATGCAGATAAACTGC
*
31256524 CAGTAATGTAGATAAACTGC
1 CAGTAATGCAGATAAACTGC
31256544 CAGTA
1 CAGTA
31256549 CTTCTTCCTT
Statistics
Matches: 62, Mismatches: 21, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
19 16 0.26
20 46 0.74
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
CAGTAATGCAGATAAACTGC
Found at i:31259676 original size:25 final size:25
Alignment explanation
Indices: 31259628--31259679 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
31259618 ATCCCGAGAT
* *
31259628 GAAAACCTCAAATTTTAAGTGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
*
31259653 GAAAACCTCAAATTCTACGCGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
31259678 GA
1 GA
31259680 TACATTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (25 bp):
GAAAACCTCAAATTCTAAGCGGGTG
Found at i:31260367 original size:13 final size:13
Alignment explanation
Indices: 31260345--31260380 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31260335 TTTTTAAAAC
31260345 ATCATCACCCTTA
1 ATCATCACCCTTA
*
31260358 ATCTTCACCCTTA
1 ATCATCACCCTTA
31260371 ATCATCACCC
1 ATCATCACCC
31260381 ACAAGTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATCACCCTTA
Found at i:31283907 original size:13 final size:13
Alignment explanation
Indices: 31283889--31283914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31283879 AGACTTAGAC
31283889 TCTAAGTCTTGAG
1 TCTAAGTCTTGAG
31283902 TCTAAGTCTTGAG
1 TCTAAGTCTTGAG
31283915 ACTTGCAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TCTAAGTCTTGAG
Found at i:31284649 original size:23 final size:26
Alignment explanation
Indices: 31284623--31284670 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
31284613 AAAAACCTAT
31284623 TTTTTTCAAAA-AA-TAA-AATTTCC
1 TTTTTTCAAAAGAATTAATAATTTCC
*
31284646 TTTTTTTAAAAGAATTAATAATTTC
1 TTTTTTCAAAAGAATTAATAATTTC
31284671 ATCTCTCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 2 0.10
25 3 0.14
26 6 0.29
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTTCAAAAGAATTAATAATTTCC
Found at i:31284649 original size:24 final size:26
Alignment explanation
Indices: 31284622--31284670 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
31284612 AAAAAACCTA
31284622 TTTTTTTCAAAA-AA-TAA-AATTTCC
1 TTTTTTT-AAAAGAATTAATAATTTCC
31284646 TTTTTTTAAAAGAATTAATAATTTC
1 TTTTTTTAAAAGAATTAATAATTTC
31284671 ATCTCTCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 3 0.14
26 6 0.27
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTTTAAAAGAATTAATAATTTCC
Found at i:31296735 original size:17 final size:17
Alignment explanation
Indices: 31296713--31296746 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31296703 CTTGAATATT
*
31296713 CTCTCTTGTTGTTGTAG
1 CTCTCTTGTTGGTGTAG
31296730 CTCTCTTGTTGGTGTAG
1 CTCTCTTGTTGGTGTAG
31296747 GACATTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.26, T:0.50
Consensus pattern (17 bp):
CTCTCTTGTTGGTGTAG
Found at i:31297348 original size:19 final size:21
Alignment explanation
Indices: 31297320--31297359 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
31297310 ATGAATTGTC
*
31297320 CAAAATATTTT-TAAG-TGTT
1 CAAAACATTTTCTAAGATGTT
31297339 CAAAACATTTTCTAAGATGTT
1 CAAAACATTTTCTAAGATGTT
31297360 TGGAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (21 bp):
CAAAACATTTTCTAAGATGTT
Found at i:31298107 original size:44 final size:44
Alignment explanation
Indices: 31298054--31298142 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
31298044 TTGAAACCAA
* * *
31298054 AATATAAGTTGTGATAATTATACATTTAAAAATATTTATAATTT
1 AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
*
31298098 AATAGAAGTTGTGATAATTGCACATTTAAAAATAATTATAATTT
1 AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
31298142 A
1 A
31298143 TTTTACAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (44 bp):
AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
Found at i:31299893 original size:20 final size:20
Alignment explanation
Indices: 31299876--31299924 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 20
31299866 AAAACTTTTG
31299876 AATTATTGATAAATCTTTAGA
1 AATT-TTGATAAATCTTTAGA
31299897 AATTTTGATAAATCATCTTAGA
1 AATTTTGATAAATC-T-TTAGA
31299919 AATTTT
1 AATTTT
31299925 AGTAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.38
21 5 0.19
22 11 0.42
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTTTGATAAATCTTTAGA
Found at i:31299931 original size:22 final size:20
Alignment explanation
Indices: 31299793--31299924 Score: 83
Period size: 20 Copynumber: 6.6 Consensus size: 20
31299783 AGTATTTTCT
* *
31299793 TTTAGGAATTTTGGTAAATC
1 TTTAGAAATTTTGATAAATC
* ** *
31299813 TTTAGATATTTCAATGAATC
1 TTTAGAAATTTTGATAAATC
*
31299833 GTTA-AATATTTTGATAAATC
1 TTTAGAA-ATTTTGATAAATC
**** *
31299853 TTTA-AAAAAAAG-TAAAAC
1 TTTAGAAATTTTGATAAATC
*
31299871 TTTTG-AATTATTGATAAATC
1 TTTAGAAATT-TTGATAAATC
31299891 TTTAGAAATTTTGATAAATC
1 TTTAGAAATTTTGATAAATC
31299911 ATCTTAGAAATTTT
1 -T-TTAGAAATTTT
31299925 AGTAAATGAT
Statistics
Matches: 81, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
18 10 0.12
19 4 0.05
20 51 0.63
21 5 0.06
22 11 0.14
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (20 bp):
TTTAGAAATTTTGATAAATC
Found at i:31301122 original size:22 final size:22
Alignment explanation
Indices: 31301092--31301135 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31301082 TTTGGTATTT
31301092 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31301114 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31301136 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31303089 original size:75 final size:76
Alignment explanation
Indices: 31302906--31303118 Score: 349
Period size: 75 Copynumber: 2.8 Consensus size: 76
31302896 TATCTGTTAT
*
31302906 CGGT-GGATTCAGCACTTAGCAACCACTAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTC
1 CGGTGGGA-TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCC-TTTC
31302970 ACATTCAAAAATA
64 ACATTCAAAAATA
* *
31302983 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
31303048 ATT-TAAGATA
66 ATTCAAAAATA
31303058 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
31303119 GGGGGAATCA
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
75 64 0.50
76 9 0.07
77 53 0.41
78 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (76 bp):
CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAAAATA
Found at i:31303127 original size:27 final size:27
Alignment explanation
Indices: 31303093--31303170 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
31303083 CCAATGATTC
*
31303093 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTA
31303120 GGGGAATCAGCACTTAGCAACCCCTTA
1 GGGGAATCAGCACTTAGCAACCCCTTA
*
31303147 GGGGAATCAACACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
31303171 CTTCACATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTA
Found at i:31307363 original size:30 final size:30
Alignment explanation
Indices: 31307320--31307545 Score: 239
Period size: 30 Copynumber: 7.6 Consensus size: 30
31307310 TTACCACCAT
*
31307320 TTTTCATAGTTTGATAGTCGAAGCTATCCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCC
* * *
31307350 TTTCCATATTTTGATAG-CTGAAGCCATCCC
1 TTTTCATAATTTGATAGTC-GAAGCTATCCC
*
31307380 TTTTCATAATTTGATAGTCGAAGCTATTCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCC
* *
31307410 TTTTCATAATTCGATAG-CTGAAGCCATCCC
1 TTTTCATAATTTGATAGTC-GAAGCTATCCC
*
31307440 TTTTCATGATTTGATAGTCG-AG-TCATCCC
1 TTTTCATAATTTGATAGTCGAAGCT-ATCCC
* * *
31307469 TTTTCATAATTCGATGGTC-ATCA-CCATCCC
1 TTTTCATAATTTGATAGTCGA--AGCTATCCC
*
31307499 TTTTCATAATTTGATAGCCGAAGCTATCCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCC
* *
31307529 TTTCCATATTTTGATAG
1 TTTTCATAATTTGATAG
31307546 CCAAAGCCAC
Statistics
Matches: 162, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
29 26 0.16
30 132 0.81
31 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTCATAATTTGATAGTCGAAGCTATCCC
Found at i:31307500 original size:59 final size:60
Alignment explanation
Indices: 31307320--31307565 Score: 295
Period size: 60 Copynumber: 4.1 Consensus size: 60
31307310 TTACCACCAT
* * * *
31307320 TTTTCATAGTTTGATAGTCGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCCC
*
31307380 TTTTCATAATTTGATAGTCGAAGCTATTCCTTTTCATAATTCGATAGCTGAAGCCATCCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCCC
* * *
31307440 TTTTCATGATTTGATAGTCG-AG-TCATCCCTTTTCATAATTCGATGGTCAT-CA-CCATCCC
1 TTTTCATAATTTGATAGTCGAAGCT-ATCCCTTTTCATAATTCGATAG-C-TGAAGCCATCCC
* * * * **
31307499 TTTTCATAATTTGATAGCCGAAGCTATCCCTTTCCATATTTTGATAGCCAAAGCCA-CTCC
1 TTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATC-CC
31307559 TTTTCAT
1 TTTTCAT
31307566 TGGTTGATAA
Statistics
Matches: 161, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 50 0.31
60 108 0.67
61 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (60 bp):
TTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAGCTGAAGCCATCCC
Found at i:31307507 original size:89 final size:90
Alignment explanation
Indices: 31307320--31307565 Score: 281
Period size: 89 Copynumber: 2.7 Consensus size: 90
31307310 TTACCACCAT
*
31307320 TTTTCATAGTTTGATAG-TCGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTTT
1 TTTTCATAATTTGATAGCT-GAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTTT
* * *
31307384 CATAATTTGATAGTCGAAGCTATTCC
65 CATAATTCGATAGTCGAAGCCATCCC
* * * *
31307410 TTTTCATAATTCGATAGCTGAAGCCATCCCTTTTCATGA-TTTGATAG-TCG-AGTCATCCCTTT
1 TTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCAT-ATTTTGATAGCT-GAAGCCATCCCTTT
*
31307472 TCATAATTCGATGGTC-ATCA-CCATCCC
64 TCATAATTCGATAGTCGA--AGCCATCCC
* **
31307499 TTTTCATAATTTGATAGCCGAAGCTATCCCTTTCCATATTTTGATAGCCAAAGCCA-CTCCTTTT
1 TTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATC-CCTTTT
31307563 CAT
65 CAT
31307566 TGGTTGATAA
Statistics
Matches: 131, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
88 2 0.02
89 73 0.56
90 54 0.41
91 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (90 bp):
TTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATATTTTGATAGCTGAAGCCATCCCTTTTC
ATAATTCGATAGTCGAAGCCATCCC
Found at i:31311567 original size:51 final size:52
Alignment explanation
Indices: 31311472--31311582 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 52
31311462 ATTGAAATGG
*
31311472 TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGGTTTTCTCAAAAA
1 TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGATTTTCTCAAAAA
* * *
31311524 TGAAATTGGAGAAAT-AG-AATAATTTGGAAATGAATG-TGATTTTCTCCAAAA
1 TGAAAATGGAGAAATGAGAAAT-ATTTGAAAATG-ATGATGATTTTCTCAAAAA
31311575 TGAAAATG
1 TGAAAATG
31311583 ACCTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 3 0.06
51 32 0.62
52 17 0.33
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAAATATTTGAAAATGATGATGATTTTCTCAAAAA
Found at i:31313495 original size:7 final size:7
Alignment explanation
Indices: 31313483--31313512 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
31313473 TGATACAAGG
31313483 AAGAAGA
1 AAGAAGA
31313490 AAGAAGA
1 AAGAAGA
*
31313497 GAGAAGA
1 AAGAAGA
31313504 AAGAAGA
1 AAGAAGA
31313511 AA
1 AA
31313513 AATTGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:31322715 original size:42 final size:42
Alignment explanation
Indices: 31322668--31322749 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
31322658 AATATTTTAT
*
31322668 TTTATCTTTTAGTAGTTTATTAGAATAAGTGAATTAATTTCC
1 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTTCC
*
31322710 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTTATTT
1 TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTT
31322750 TCCCAATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.51
Consensus pattern (42 bp):
TTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTAATTTCC
Found at i:31328943 original size:22 final size:22
Alignment explanation
Indices: 31328917--31328961 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31328907 ATTATATGTA
31328917 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
31328939 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
31328961 T
1 T
31328962 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:31337237 original size:25 final size:25
Alignment explanation
Indices: 31337177--31337237 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
31337167 TTCCTAAATT
*
31337177 TTAATTTAATTATCTAATTTTTAAA
1 TTAATTAAATTATCTAATTTTTAAA
* * *
31337202 TTTATTGAATTAT-TAATATTTTATA
1 TTAATTAAATTATCTAAT-TTTTAAA
31337227 TTAATTAAATT
1 TTAATTAAATT
31337238 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTAAA
Found at i:31337536 original size:11 final size:11
Alignment explanation
Indices: 31337520--31337544 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31337510 GAGGAGTTAG
31337520 TACGCGAATTC
1 TACGCGAATTC
31337531 TACGCGAATTC
1 TACGCGAATTC
31337542 TAC
1 TAC
31337545 CTCAAGCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (11 bp):
TACGCGAATTC
Found at i:31342815 original size:26 final size:26
Alignment explanation
Indices: 31342783--31342835 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31342773 TTGTTAGAAG
31342783 ATAAATTTGGTGCATCACATGTAAGA
1 ATAAATTTGGTGCATCACATGTAAGA
31342809 ATAAATTTGGTGCATCACATGTAAGA
1 ATAAATTTGGTGCATCACATGTAAGA
31342835 A
1 A
31342836 GTACTTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (26 bp):
ATAAATTTGGTGCATCACATGTAAGA
Found at i:31343597 original size:21 final size:21
Alignment explanation
Indices: 31343559--31343598 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31343549 CACGTACAGT
**
31343559 GGTATCACGATATTCACTTTG
1 GGTATCACGATACCCACTTTG
*
31343580 GGTATCGCGATACCCACTT
1 GGTATCACGATACCCACTT
31343599 GCCCAAGGAA
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:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (21 bp):
GGTATCACGATACCCACTTTG
Found at i:31358334 original size:47 final size:47
Alignment explanation
Indices: 31358271--31358364 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
31358261 TGGACTTGGT
*
31358271 CAATTGATCCACGATGACCCATATTGAATCCTTTTTAGTGGGTGTTA
1 CAATTGATCCACGATGACCCATATTGAATCCTTGTTAGTGGGTGTTA
*
31358318 CAATTGATCCATGATGACCCATATTGAATCCTTGTTAGTGGGTGTTA
1 CAATTGATCCACGATGACCCATATTGAATCCTTGTTAGTGGGTGTTA
31358365 AAGGCAACCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (47 bp):
CAATTGATCCACGATGACCCATATTGAATCCTTGTTAGTGGGTGTTA
Found at i:31361055 original size:25 final size:25
Alignment explanation
Indices: 31361007--31361061 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
31360997 TCTGTATAGT
*
31361007 CTATCTATAGTAGTCTCAGTATATA
1 CTATCTATAGTAGTCTCAGGATATA
* *
31361032 CTATCTATAGTAGTTTTAGGATATA
1 CTATCTATAGTAGTCTCAGGATATA
31361057 CTATC
1 CTATC
31361062 AATGACAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (25 bp):
CTATCTATAGTAGTCTCAGGATATA
Found at i:31362425 original size:18 final size:19
Alignment explanation
Indices: 31362385--31362425 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
31362375 TATGATGTTC
31362385 ACCCATGTAGGCCCACACG
1 ACCCATGTAGGCCCACACG
*
31362404 -CCCATG-AGGCCCACATG
1 ACCCATGTAGGCCCACACG
31362421 ACCCA
1 ACCCA
31362426 AATTCGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.27, C:0.44, G:0.20, T:0.10
Consensus pattern (19 bp):
ACCCATGTAGGCCCACACG
Found at i:31366052 original size:29 final size:31
Alignment explanation
Indices: 31365994--31366052 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
31365984 TTTCAAATTG
* * *
31365994 TATATATCATTTGTACCATATTGTTTATTTA
1 TATATATCATTTATACCATATTATTGATTTA
31366025 TATATAT-ATTTATA-CATATTATTGATTT
1 TATATATCATTTATACCATATTATTGATTT
31366053 TAATTCTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 6 0.24
31 7 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (31 bp):
TATATATCATTTATACCATATTATTGATTTA
Found at i:31367713 original size:96 final size:96
Alignment explanation
Indices: 31367549--31367732 Score: 228
Period size: 96 Copynumber: 1.9 Consensus size: 96
31367539 ATGTCATTTG
* * * * * *
31367549 GGTTACAATGTTTCGGGTGTTGGTCTTGAATGTCCTACTGGTGGCTGAGTTCTAGCATGTGTTGC
1 GGTTACAATGTTTCGGGTGCTAGTCTGGAATGTCCTACTGATGGCTGAGTCCGAGCATGTGTTGC
* *
31367614 GGATACTTGACAGCTTGTGTGAGCAAACCTA
66 GGATACTAGACAGATTGTGTGAGCAAACCTA
* *
31367645 GGTTACCATGTTTTGGGTGCTAGTCTGGAATGTCCTACTGATGGCTGAGGTCCGA-CAT-TAGTT
1 GGTTACAATGTTTCGGGTGCTAGTCTGGAATGTCCTACTGATGGCTGA-GTCCGAGCATGT-GTT
* *
31367708 GCGGATGCTAGATAGATTGTGTGAG
64 GCGGATACTAGACAGATTGTGTGAG
31367733 TAGTATCATG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
95 1 0.01
96 69 0.93
97 4 0.05
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.34
Consensus pattern (96 bp):
GGTTACAATGTTTCGGGTGCTAGTCTGGAATGTCCTACTGATGGCTGAGTCCGAGCATGTGTTGC
GGATACTAGACAGATTGTGTGAGCAAACCTA
Found at i:31373327 original size:20 final size:20
Alignment explanation
Indices: 31373277--31373335 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
31373267 AGCTCCACTC
* *
31373277 AGCTCAAATCAGCTCACTTG
1 AGCTCAATTTAGCTCACTTG
* * *
31373297 AGCTTATTTTAGCTCGCTTG
1 AGCTCAATTTAGCTCACTTG
*
31373317 AGCTCAATTTAGCTTACTT
1 AGCTCAATTTAGCTCACTT
31373336 TTAGCTCGTC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:31378666 original size:15 final size:15
Alignment explanation
Indices: 31378646--31378676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31378636 CCCCAGTCAT
31378646 AGATACAGAAATATC
1 AGATACAGAAATATC
*
31378661 AGATACAGTAATATC
1 AGATACAGAAATATC
31378676 A
1 A
31378677 TGCATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (15 bp):
AGATACAGAAATATC
Found at i:31395625 original size:75 final size:75
Alignment explanation
Indices: 31395542--31395688 Score: 258
Period size: 75 Copynumber: 2.0 Consensus size: 75
31395532 ATGGAAATTA
*
31395542 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTTCATTTCTCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTCTCTTCTCTATTAATAAGG
31395607 GAATAATCCT
66 GAATAATCCT
* * *
31395617 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGTCTTCTTTTTTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTCTCTTCTCTATTAATAAGG
31395682 GAATAAT
66 GAATAAT
31395689 ATTGGTTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTCTCTTCTCTATTAATAAGG
GAATAATCCT
Found at i:31398995 original size:41 final size:41
Alignment explanation
Indices: 31398915--31398997 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
31398905 GGAGAAATCA
* * *
31398915 AACACTGTTAGACATGGTTTGATCAATGATGAGTCATGTTG
1 AACACTATTAGACATGGTTCGATCAATGATAAGTCATGTTG
**
31398956 AACACTATTAGACATGGTTCGATCCTTGATAAG-CTATGTTG
1 AACACTATTAGACATGGTTCGATCAATGATAAGTC-ATGTTG
31398997 A
1 A
31398998 TCTTCCTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (41 bp):
AACACTATTAGACATGGTTCGATCAATGATAAGTCATGTTG
Found at i:31401082 original size:21 final size:21
Alignment explanation
Indices: 31401056--31401096 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31401046 AACACAACAG
31401056 AAGCATGATCATCTCACTAAA
1 AAGCATGATCATCTCACTAAA
**
31401077 AAGCATGATTTTCTCACTAA
1 AAGCATGATCATCTCACTAA
31401097 GTCACTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
AAGCATGATCATCTCACTAAA
Found at i:31407563 original size:138 final size:138
Alignment explanation
Indices: 31407410--31407693 Score: 444
Period size: 138 Copynumber: 2.1 Consensus size: 138
31407400 GAGAACATAG
** * *
31407410 ATATAATTAATATATGAATTTGA-TTCTTACAAAATATTAATTGTATATATTTTACCGAATTTAT
1 ATATAATTAATATATGAATTT-ACTTAATACAAAATATTAATTGTATAAATTTTACCAAATTTAT
* *
31407474 TAATAAAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTGTT
65 TAACAAAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
31407539 TTAGAAAGA
130 TTAGAAAGA
* *
31407548 ATATAATTAATATATGAATTTACTTAATGCAAAATATTAATTTTATAAATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTACTTAATACAAAATATTAATTGTATAAATTTTACCAAATTTATT
** *
31407613 AACCTAAACAGTTATATTAATTAATTTCGGTTAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AACAAAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
31407678 TGGAAAGA
131 TAGAAAGA
31407686 ATATAATT
1 ATATAATT
31407694 CATTTTTCTA
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
137 1 0.01
138 132 0.99
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTACTTAATACAAAATATTAATTGTATAAATTTTACCAAATTTATT
AACAAAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TAGAAAGA
Found at i:31408498 original size:67 final size:67
Alignment explanation
Indices: 31408406--31408541 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 67
31408396 GTAACTTTTT
31408406 TCATCATGGTTCGTAAACTATTTTTGGTCCACATTAATTCCAAAACTTAACAATTTTC-CTAATT
1 TCATCATGGTTCGTAAACTATTTTTGGTCCACATTAATTCCAAAACTTAACAATTTTCTC-AATT
31408470 TGG
65 TGG
31408473 TCATCATGGTTCGTAAACTATTTTTGGTCCACATTAATTCCAAAACTTAACAATTTTCTCAATTT
1 TCATCATGGTTCGTAAACTATTTTTGGTCCACATTAATTCCAAAACTTAACAATTTTCTCAATTT
31408538 GG
66 GG
31408540 TC
1 TC
31408542 CACGAACTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
67 67 0.99
68 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (67 bp):
TCATCATGGTTCGTAAACTATTTTTGGTCCACATTAATTCCAAAACTTAACAATTTTCTCAATTT
GG
Found at i:31410380 original size:16 final size:16
Alignment explanation
Indices: 31410348--31410377 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31410338 TATTTTGAGA
31410348 TTAAAAATTATATAAT
1 TTAAAAATTATATAAT
31410364 TTAAAAA-TATATAA
1 TTAAAAATTATATAA
31410378 ATTAGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAATTATATAAT
Found at i:31412136 original size:21 final size:21
Alignment explanation
Indices: 31412110--31412151 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31412100 TTAAAATGTG
31412110 TATATAAATACATACATATAAAT
1 TATA-AAATACATA-ATATAAAT
*
31412133 TATAAAATAGATAATATAA
1 TATAAAATACATAATATAA
31412152 TCATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TATAAAATACATAATATAAAT
Found at i:31414045 original size:175 final size:175
Alignment explanation
Indices: 31413817--31414327 Score: 751
Period size: 175 Copynumber: 2.9 Consensus size: 175
31413807 CAGTATACTA
* * * * * *
31413817 CACTGCAACCTCAGTGAGATAAGACTTGATGCGAT-TCACTCTACTGCAACTTCAGAGAGATAAG
1 CACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT-ACTCTGCTGTAACTTCAGAGAGATAAG
* * * * * *
31413881 AT-CTATTACTTTAATCCGCTCCAATATAATCTCAGGAAGATAGGATTACCAGCTTCAATCTGCT
65 ATCCT-TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCT
*
31413945 CCGCTGTAATCTTAGGGAGATAAGATCTGA-AATCTTTCGGTCTGCTC
129 CCGCTGTAATCTCAGGGAGATAAGATCTGACAATC-TTCGGTCTGCTC
* *
31413992 CACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCTGCTGTAACTTCAGAGATATAAGA
1 CACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGA
* *
31414057 TCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAGTCTGCTCC
66 TCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCC
*
31414122 GCTGTAATCTCAGGGAGATAAGATCTGATGCAATCTTCGGTCTGTTC
131 GCTGTAATCTCAGGGAGATAAGATCTGA--CAATCTTCGGTCTGCTC
* *
31414169 CACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGA
1 CACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGA
* *
31414234 TCCTTCATTTTAATCCACTCCACTGTAATCT-AGGGAGATAGGATTACTAACTTCAATCTGCTCC
66 TCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCC
31414298 GCTGTAATCTCAGGGAGATAAGATCTGACA
131 GCTGTAATCTCAGGGAGATAAGATCTGACA
31414328 TGATATGCTC
Statistics
Matches: 306, Mismatches: 25, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
174 2 0.01
175 137 0.45
176 62 0.20
177 101 0.33
178 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (175 bp):
CACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGA
TCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCC
GCTGTAATCTCAGGGAGATAAGATCTGACAATCTTCGGTCTGCTC
Found at i:31414127 original size:44 final size:44
Alignment explanation
Indices: 31413868--31414495 Score: 296
Period size: 44 Copynumber: 14.3 Consensus size: 44
31413858 TACTGCAACT
* * * * * *
31413868 TCAGAGAGATAAGATCTATTA-CTTTAATCCGCTCCAATATAATC
1 TCAGGGAGATAAGAT-TACTATCTTCAATCTGCTCCACTGTAATC
* * * * *
31413912 TCAGGAAGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATC
* * **
31413956 TTAGGGAGATAAGATCTGA-AATCTTTCGGTCTGCTCCACTGTAATC
1 TCAGGGAGATAAGAT-T-ACTATC-TTCAATCTGCTCCACTGTAATC
* * * **
31414002 TCAGGGAGATAAGA--CCTGA--TGCAATCTACTCTGCTGTAA-C
1 TCAGGGAGATAAGATTACT-ATCTTCAATCTGCTCCACTGTAATC
* * * * *
31414042 TTCAGAGATATAAGATCCT-TTAT-TTTAATCCGCTCCACTGTAATC
1 -TCAGGGAGATAAGAT--TACTATCTTCAATCTGCTCCACTGTAATC
* * *
31414087 TCAGGGAGATAGGATTACTATCTTCAGTCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATC
* ** *
31414131 TCAGGGAGATAAGATCTGATGCAATCTTCGGTCTGTTCCACTGTAATC
1 TCAGGGAGATAAGAT-T-A--CTATCTTCAATCTGCTCCACTGTAATC
* * * * * **
31414179 TCAGGGAAATAAGA--CCTGA-C-GCGATCTACTCTGCTGTAA-C
1 TCAGGGAGATAAGATTACT-ATCTTCAATCTGCTCCACTGTAATC
* * * **
31414219 TTCAGAGAGATAAGA-TCCT-TCATTTTAATCCACTCCACTGTAATC
1 -TCAGGGAGATAAGATTACTATC--TTCAATCTGCTCCACTGTAATC
* * *
31414264 T-AGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATC
* * * * *
31414307 TCAGGGAGATAAGA-T-CTGA-CAT-GATATGCTCTACTGTAATT
1 TCAGGGAGATAAGATTACT-ATCTTCAATCTGCTCCACTGTAATC
* * * * * *
31414348 TCAGAGAGGTAAGATCCT-TTAT-TTTAATCCGCTCCACTGCAATC
1 TCAGGGAGATAAGAT--TACTATCTTCAATCTGCTCCACTGTAATC
* *
31414392 TCAGGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATC
* * ** *
31414436 TCAGCGAGATAAGATCTGA-AATTCTTCGGTCTGTTCCACTGTAATC
1 TCAGGGAGATAAGAT-T-ACTA-TCTTCAATCTGCTCCACTGTAATC
*
31414482 TCAGGGAAATAAGA
1 TCAGGGAGATAAGA
31414496 CCTGACGCGA
Statistics
Matches: 437, Mismatches: 106, Indels: 80
0.70 0.17 0.13
Matches are distributed among these distances:
40 2 0.00
41 78 0.18
42 11 0.03
43 44 0.10
44 188 0.43
45 9 0.02
46 69 0.16
48 36 0.08
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATC
Found at i:31414305 original size:305 final size:302
Alignment explanation
Indices: 31413985--31414541 Score: 913
Period size: 305 Copynumber: 1.8 Consensus size: 302
31413975 AATCTTTCGG
* *
31413985 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCA-ATCTACTCTGCTGTAACTTCAGAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGA--CAGATATACTCTACTGTAACTTCAGAG
* *
31414049 ATATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTC-A
64 AGATAAGATCCTTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAGGATTACTATCTTCGA
* *
31414113 GTCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGCAA-TCTTCGGTCTGTTCCACTGTAA
129 -TCTGCTCCACTGTAATCTCAGCGAGATAAGATCTGA---AATTCTTCGGTCTGTTCCACTGTAA
31414177 TCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCAT
190 TCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCAT
31414242 TTTAATCCACTCCACTGTAATCTAGGGAGATAGGATTACTAACTTCAA
255 TTTAATCCACTCCACTGTAATCTAGGGAGATAGGATTACTAACTTCAA
* * * *
31414290 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATGATATGCTCTACTGTAATTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACA-GATATACTCTACTGTAACTTCAGAGA
*
31414355 GGTAAGATCCTTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAGGATTACTATCTTCGAT
65 GATAAGATCCTTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAGGATTACTATCTTCGAT
31414420 CTGCTCCACTGTAATCTCAGCGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCA
130 CTGCTCCACTGTAATCTCAGCGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCA
* *
31414485 GGGAAATAAGACCTGACGCGATCTATTCTGCTGTAACTTCAGAGAGATAATATCCTT
195 GGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTT
31414542 TCTTCAATCA
Statistics
Matches: 235, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
302 2 0.01
303 84 0.36
305 148 0.63
306 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (302 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACAGATATACTCTACTGTAACTTCAGAGAG
ATAAGATCCTTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAGGATTACTATCTTCGATC
TGCTCCACTGTAATCTCAGCGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAG
GGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAAT
CCACTCCACTGTAATCTAGGGAGATAGGATTACTAACTTCAA
Found at i:31414454 original size:129 final size:129
Alignment explanation
Indices: 31414117--31414454 Score: 444
Period size: 128 Copynumber: 2.6 Consensus size: 129
31414107 TCTTCAGTCT
* * * * *
31414117 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGCAATCTTCGGTCTGTTCCACTGTAATCTCA
1 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-A--CTATCTTCGATCTGCTCCACTGTAATCTCA
* * * * *
31414182 GGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAA
62 GGGAGATAAGATCTGACACGATATACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAA
31414247 TCC
127 TCC
* * * *
31414250 ACTCCACTGTAATCT-AGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAATCTCAGGGA
* * * * *
31414314 GATAAGATCTGACATGATATGCTCTACTGTAATTTCAGAGAGGTAAGATCCTTTATTTTAATCC
66 GATAAGATCTGACACGATATACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
* *
31414378 GCTCCACTGCAATCTCAGGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAATCTCAGCGA
1 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAATCTCAGGGA
31414443 GATAAGATCTGA
66 GATAAGATCTGA
31414455 AATTCTTCGG
Statistics
Matches: 179, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
128 95 0.53
129 57 0.32
130 1 0.01
131 1 0.01
132 12 0.07
133 13 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAATCTCAGGGA
GATAAGATCTGACACGATATACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
Found at i:31414479 original size:46 final size:46
Alignment explanation
Indices: 31414412--31414500 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
31414402 AGGATTACTA
* *
31414412 TCTTCGATCTGCTCCACTGTAATCTCAGCGAGATAAGATCTGAAAT
1 TCTTCGATCTGCTCCACTGTAATCTCAGCGAAATAAGACCTGAAAT
* * *
31414458 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGA
1 TCTTCGATCTGCTCCACTGTAATCTCAGCGAAATAAGACCTGA
31414501 CGCGATCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
TCTTCGATCTGCTCCACTGTAATCTCAGCGAAATAAGACCTGAAAT
Found at i:31414692 original size:87 final size:87
Alignment explanation
Indices: 31414542--31414887 Score: 388
Period size: 87 Copynumber: 4.0 Consensus size: 87
31414532 TAATATCCTT
* * * * * * * * * *
31414542 TCTTCAATCAGCTTCATTGCAACCAATAGAGGCAAGGCTTTGTTTTCGATCTGCTTTGTTGTTAA
1 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAA
*
31414607 TGCAGGAAGGCAAGATCTGCTA
66 CGCAGGAAGGCAAGATCTGCTA
*
31414629 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGTTTTGTTTTCAATCTGCTTCGCTGTTAA
1 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAA
* * *
31414694 CGCAAGAATGCCAGATCTGCTA
66 CGCAGGAAGGCAAGATCTGCTA
31414716 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAA
1 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAA
* *
31414781 CGTAGGAAGGCCAGATCTGCTA
66 CGCAGGAAGGCAAGATCTGCTA
* * ** ** * * * * * *
31414803 TCTTTAACCAGTTCCACCGCAACCGATGAAGACAAAGC-TTGTATCTTCGATCTGCTTCACTATC
1 TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGT-T-TTCAATCTGCTTCGCTGTT
* *
31414867 AAGGCAGGACGGCAAGATCTG
64 AACGCAGGAAGGCAAGATCTG
31414888 TTGTCTTTGA
Statistics
Matches: 222, Mismatches: 35, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
86 4 0.02
87 186 0.84
88 32 0.14
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (87 bp):
TCTTCAATCAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAA
CGCAGGAAGGCAAGATCTGCTA
Found at i:31416037 original size:21 final size:21
Alignment explanation
Indices: 31416011--31416057 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31416001 GGTATAGCAA
31416011 GATCACCGCATGCCCCAATCT
1 GATCACCGCATGCCCCAATCT
** *
31416032 GATCACTTCATGCCCCATTCT
1 GATCACCGCATGCCCCAATCT
31416053 GATCA
1 GATCA
31416058 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (21 bp):
GATCACCGCATGCCCCAATCT
Found at i:31416152 original size:7 final size:7
Alignment explanation
Indices: 31416140--31416192 Score: 76
Period size: 7 Copynumber: 8.0 Consensus size: 7
31416130 TTAGCCTCTC
31416140 CATTTTT
1 CATTTTT
31416147 CA-TTTT
1 CATTTTT
31416153 CA-TTTT
1 CATTTTT
31416159 CATTTTT
1 CATTTTT
31416166 CATTTTT
1 CATTTTT
*
31416173 CA-TTCT
1 CATTTTT
31416179 CATTTTT
1 CATTTTT
31416186 CATTTTT
1 CATTTTT
31416193 TTTACTCAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 17 0.40
7 25 0.60
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:31416154 original size:6 final size:6
Alignment explanation
Indices: 31416143--31416191 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
31416133 GCCTCTCCAT
*
31416143 TTTTCA TTTTCA TTTTCA TTTTTCA TTTTTCA TTCTCA TTTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA -TTTTCA -TTTTCA TTTTCA -TTTTCA TTTT
31416192 TTTTACTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 21 0.54
7 18 0.46
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:31416158 original size:13 final size:13
Alignment explanation
Indices: 31416140--31416191 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
31416130 TTAGCCTCTC
31416140 CATTTTTCATTTT
1 CATTTTTCATTTT
31416153 CA-TTTTCATTTTT
1 CATTTTTCA-TTTT
*
31416166 CATTTTTCATTCT
1 CATTTTTCATTTT
31416179 CATTTTTCATTTT
1 CATTTTTCATTTT
31416192 TTTTACTCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 6 0.17
13 23 0.66
14 6 0.17
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:31416172 original size:20 final size:20
Alignment explanation
Indices: 31416140--31416192 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
31416130 TTAGCCTCTC
*
31416140 CATTTTTCA-TTTTCATTTT
1 CATTTTTCATTTTTCATTCT
31416159 CATTTTTCATTTTTCATTCT
1 CATTTTTCATTTTTCATTCT
31416179 CATTTTTCATTTTT
1 CATTTTTCATTTTT
31416193 TTTACTCAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
CATTTTTCATTTTTCATTCT
Found at i:31416200 original size:20 final size:19
Alignment explanation
Indices: 31416140--31416200 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
31416130 TTAGCCTCTC
*
31416140 CATTTTTCATTTTCATTT-T
1 CATTTTTCATTTT-TTTTCT
*
31416159 CATTTTTCATTTTTCATTCT
1 CATTTTTCATTTTT-TTTCT
31416179 CATTTTTCATTTTTTTTACT
1 CATTTTTCATTTTTTTT-CT
31416199 CA
1 CA
31416201 GAGTGCCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (19 bp):
CATTTTTCATTTTTTTTCT
Found at i:31416944 original size:15 final size:16
Alignment explanation
Indices: 31416924--31416954 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31416914 TGGCCTCTCA
31416924 TTTTCTTTTTC-TTTT
1 TTTTCTTTTTCATTTT
31416939 TTTTCTTTTTCATTTT
1 TTTTCTTTTTCATTTT
31416955 GATTTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTCATTTT
Found at i:31420797 original size:21 final size:21
Alignment explanation
Indices: 31420771--31420812 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31420761 TTAAAATGTG
31420771 TATATAAATACATACATATAAAT
1 TATA-AAATACATA-ATATAAAT
*
31420794 TATAAAATAGATAATATAA
1 TATAAAATACATAATATAA
31420813 TCATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TATAAAATACATAATATAAAT
Found at i:31422561 original size:41 final size:44
Alignment explanation
Indices: 31422516--31422599 Score: 138
Period size: 41 Copynumber: 2.0 Consensus size: 44
31422506 CTAGTGTCAT
31422516 ATCATCATATTCTAACAACATTATAAAAA-AAT-T-AAAATGTG
1 ATCATCATATTCTAACAACATTATAAAAAGAATATCAAAATGTG
*
31422557 ATCATCATATTCTAACGACATTATAAAAAGAATATCAAAATGT
1 ATCATCATATTCTAACAACATTATAAAAAGAATATCAAAATGT
31422600 ATTATGGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 28 0.72
42 3 0.08
43 1 0.03
44 7 0.18
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (44 bp):
ATCATCATATTCTAACAACATTATAAAAAGAATATCAAAATGTG
Found at i:31424406 original size:40 final size:41
Alignment explanation
Indices: 31424355--31424453 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
31424345 TTTGAATACT
* *
31424355 TGAAAAGGTTGAAAAGGA-AATAT-CTAAAAAGGATACTGAA
1 TGAAAAGGTTGAAAAGGACAATATCCAAAAAAGGATA-TCAA
* *
31424395 TGAAAATGTTGAAAAGGACATTATCCAAAAAAGGATATCAA
1 TGAAAAGGTTGAAAAGGACAATATCCAAAAAAGGATATCAA
*
31424436 TGAAAAGGTCGAAAAGGA
1 TGAAAAGGTTGAAAAGGA
31424454 TAGCAATGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 17 0.33
41 23 0.45
42 11 0.22
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (41 bp):
TGAAAAGGTTGAAAAGGACAATATCCAAAAAAGGATATCAA
Found at i:31432394 original size:14 final size:16
Alignment explanation
Indices: 31432359--31432396 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31432349 GCTTGATTAA
31432359 ATATATGTGTTACATG
1 ATATATGTGTTACATG
*
31432375 ATATATGT-TTGCATG
1 ATATATGTGTTACATG
31432390 A-ATATGT
1 ATATATGT
31432397 AAAGGCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (16 bp):
ATATATGTGTTACATG
Found at i:31434343 original size:31 final size:34
Alignment explanation
Indices: 31434307--31434388 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
31434297 TTTTGAATAT
31434307 TTTTAC-AACTTTTT-AATTTCT-TAA-ATAATTA
1 TTTTACTAA-TTTTTGAATTTCTATAATATAATTA
*
31434338 TTTTACTAATTTTTGAATTTTTATAATATAATTA
1 TTTTACTAATTTTTGAATTTCTATAATATAATTA
*
31434372 TTATCACT-ATTTTTGAA
1 TT-TTACTAATTTTTGAA
31434389 ATCTTTTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 11 0.25
32 8 0.18
33 3 0.07
34 18 0.41
35 4 0.09
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTTACTAATTTTTGAATTTCTATAATATAATTA
Found at i:31439071 original size:185 final size:185
Alignment explanation
Indices: 31438753--31439122 Score: 578
Period size: 185 Copynumber: 2.0 Consensus size: 185
31438743 ACTTTGGTAA
* * **
31438753 GTTGGCATTTGACAACATACATCGAACCTTCTCCATGATCATTCTGTTCATTCGTTCTGGAATGC
1 GTTGGCATTTGACAACATACATCGAACCTTCTCCATGATCATTCTGTACATTCGTTCTGCAACAC
*
31438818 CATTTTGCTGTGGAGTATGACGAACTATCAAGTGTCTCAAAATCCCTTCTGACTTACACAGATTA
66 CATTTTGCTGTGGAGTATGACGAACTATCAAGTGTCTCAAAATCCCTTCTAACTTACACAGATTA
* * *
31438883 TTAAACTCATTAGAATAGAACTCTAAGCCATTACCTGTGCGGAGGTATTTTATTT
131 TTAAACTCATCAGAACAGAACTCTAAGCCATTACCTATGCGGAGGTATTTTATTT
* *
31438938 GTTGGCATTTGACAACATACATTGAACCTTCTCCATGATCGTTCTGTACATTCGTTCTGCAACAC
1 GTTGGCATTTGACAACATACATCGAACCTTCTCCATGATCATTCTGTACATTCGTTCTGCAACAC
* * ** * *
31439003 CGTTTTGCTGTGGAGTATGACGAACTGTCAAGTGTCTCACGATCCCTTCTAACTTGCACAGTTTA
66 CATTTTGCTGTGGAGTATGACGAACTATCAAGTGTCTCAAAATCCCTTCTAACTTACACAGATTA
**
31439068 TTAAACTCATCAGAACAGAACTCTAAGCCATTGTCTATGCGGAGGTATTTTATTT
131 TTAAACTCATCAGAACAGAACTCTAAGCCATTACCTATGCGGAGGTATTTTATTT
31439123 CTTTTCCCAT
Statistics
Matches: 167, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
185 167 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (185 bp):
GTTGGCATTTGACAACATACATCGAACCTTCTCCATGATCATTCTGTACATTCGTTCTGCAACAC
CATTTTGCTGTGGAGTATGACGAACTATCAAGTGTCTCAAAATCCCTTCTAACTTACACAGATTA
TTAAACTCATCAGAACAGAACTCTAAGCCATTACCTATGCGGAGGTATTTTATTT
Found at i:31441735 original size:18 final size:19
Alignment explanation
Indices: 31441714--31441756 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
31441704 AAATCTTGAA
* *
31441714 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTACTTTG
31441732 AATTTTAAAAATTACTTTG
1 AATTTTAAAAATTACTTTG
31441751 AATTTT
1 AATTTT
31441757 CCCTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTTTAAAAATTACTTTG
Found at i:31442729 original size:11 final size:11
Alignment explanation
Indices: 31442710--31442740 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31442700 AAATTATTAG
*
31442710 AAATCATAAAA
1 AAATTATAAAA
31442721 AAATTATAAAA
1 AAATTATAAAA
31442732 AAATTATAA
1 AAATTATAA
31442741 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:31443288 original size:20 final size:18
Alignment explanation
Indices: 31443239--31443312 Score: 51
Period size: 20 Copynumber: 3.8 Consensus size: 18
31443229 AAGTTTATAA
31443239 TTTTA-AATTTTAAATTT
1 TTTTATAATTTTAAATTT
*
31443256 TTTAACTATATTTATAAACTTT
1 TTTTA-TA-ATTT-TAAA-TTT
* *
31443278 TTTTATAATTTTTATGATCT
1 TTTTATAA-TTTTA-AATTT
*
31443298 TTTAATAATTTTAAA
1 TTTTATAATTTTAAA
31443313 AGTGCTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 6 0.14
20 16 0.36
21 10 0.23
22 7 0.16
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTATAATTTTAAATTT
Found at i:31447616 original size:21 final size:21
Alignment explanation
Indices: 31447592--31447641 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
31447582 CCCAAGCAGA
*
31447592 GGGAGAAGGGATAATAGAAGG
1 GGGAGAAGGGACAATAGAAGG
31447613 GGGAGAAGGGACAATAGAAGG
1 GGGAGAAGGGACAATAGAAGG
31447634 GGGAGAAG
1 GGGAGAAG
31447642 AGAGAGATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.50, T:0.06
Consensus pattern (21 bp):
GGGAGAAGGGACAATAGAAGG
Found at i:31449598 original size:16 final size:17
Alignment explanation
Indices: 31449579--31449619 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
31449569 AGGAGGTATC
31449579 AATTTAATTTAAAT-CA
1 AATTTAATTTAAATACA
*
31449595 AATTTTA-TTAAATACA
1 AATTTAATTTAAATACA
31449611 ATATTTAAT
1 A-ATTTAAT
31449620 AAATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAATTTAAATACA
Found at i:31457592 original size:28 final size:28
Alignment explanation
Indices: 31457489--31457587 Score: 173
Period size: 28 Copynumber: 3.5 Consensus size: 28
31457479 AAAAATAAAA
31457489 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
31457518 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
31457546 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
31457574 ATTTACCAAAATAT
1 ATTTACCAAAATAT
31457588 ATAAAAAAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
28 47 0.68
29 22 0.32
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:31457664 original size:27 final size:27
Alignment explanation
Indices: 31457626--31457736 Score: 188
Period size: 27 Copynumber: 4.1 Consensus size: 27
31457616 CCTGATCACC
31457626 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
31457653 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
31457680 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
31457707 CCAATGCCATTGGCGGCACC-AATGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
31457733 CCAA
1 CCAA
31457737 AGGACTAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
26 8 0.10
27 73 0.90
ACGTcount: A:0.24, C:0.31, G:0.28, T:0.17
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAAAGGTG
Found at i:31458258 original size:19 final size:18
Alignment explanation
Indices: 31458234--31458294 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
31458224 TCTAATTAAG
31458234 TAATAATTCTATTTTAATT
1 TAATAA-TCTATTTTAATT
* * *
31458253 TAATAAACTATTCTCATT
1 TAATAATCTATTTTAATT
* *
31458271 TAATAACTATATTTTAAAT
1 TAATAA-TCTATTTTAATT
31458290 TAATA
1 TAATA
31458295 GAAATATCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATCTATTTTAATT
Found at i:31458263 original size:18 final size:18
Alignment explanation
Indices: 31458242--31458294 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
31458232 AGTAATAATT
31458242 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* *
31458260 CTATTCTCATTTAAT-AA
1 CTATTTTAATTTAATAAA
*
31458277 CTATATTTTAAATTAATA
1 C--TATTTTAATTTAATA
31458295 GAAATATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:31458821 original size:27 final size:27
Alignment explanation
Indices: 31458785--31458868 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
31458775 TTTTAGTCCT
31458785 TTGGCA-CATTGGTGCCGCCAATGGCA
1 TTGGCACCATTGGTGCCGCCAATGGCA
*
31458811 TTGGCACCATTGGTGTCGCCAATGGCA
1 TTGGCACCATTGGTGCCGCCAATGGCA
* *
31458838 CTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCACCATTGGTGCCGCCAATGGCA
31458865 TTGG
1 TTGG
31458869 GGTGATCAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
26 6 0.12
27 46 0.88
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATGGCA
Found at i:31458904 original size:11 final size:10
Alignment explanation
Indices: 31458887--31458914 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
31458877 GGCTGTGTCA
31458887 GTTTTTTTTT
1 GTTTTTTTTT
31458897 GTTTTTTTTT
1 GTTTTTTTTT
31458907 GTTTTTTT
1 GTTTTTTT
31458915 AGATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:31458993 original size:29 final size:28
Alignment explanation
Indices: 31458919--31459017 Score: 164
Period size: 28 Copynumber: 3.5 Consensus size: 28
31458909 TTTTTTAGAT
31458919 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
31458946 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
31458975 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAAT-AAAAAAAAGTTGTA
*
31459004 ATGTTTTGGTAAAT
1 ATATTTTGGTAAAT
31459018 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
28 39 0.57
29 29 0.43
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:31462683 original size:14 final size:14
Alignment explanation
Indices: 31462664--31462704 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
31462654 ATTTGTAAAT
*
31462664 AAAAAAATTCGTCA
1 AAAAAAATTCGTAA
*
31462678 AAAAAAATTTGTAA
1 AAAAAAATTCGTAA
31462692 AAAAAAATT-GTAA
1 AAAAAAATTCGTAA
31462705 TTATTTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (14 bp):
AAAAAAATTCGTAA
Found at i:31462702 original size:13 final size:13
Alignment explanation
Indices: 31462664--31462704 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
31462654 ATTTGTAAAT
31462664 AAAAAAATTCGTCAA
1 AAAAAAATT-GT-AA
*
31462679 AAAAAATTTGTAA
1 AAAAAAATTGTAA
31462692 AAAAAAATTGTAA
1 AAAAAAATTGTAA
31462705 TTATTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.58
14 2 0.08
15 8 0.33
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (13 bp):
AAAAAAATTGTAA
Found at i:31478952 original size:6 final size:6
Alignment explanation
Indices: 31478941--31478969 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31478931 CAATGGTATT
31478941 ATTATG ATTATG ATTATG ATTATG ATTAT
1 ATTATG ATTATG ATTATG ATTATG ATTAT
31478970 TTTCCTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTATG
Found at i:31486041 original size:4 final size:4
Alignment explanation
Indices: 31486014--31486067 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
31486004 TACCAATTTT
* *
31486014 TAAA TATAA TAAA TACAAA GAAA TAAA TAAA TAAA TACA TAAA TAAA TCAAA
1 TAAA TA-AA TAAA T--AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA
31486066 TA
1 TA
31486068 GGAATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 31 0.74
5 8 0.19
6 3 0.07
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:31487083 original size:17 final size:17
Alignment explanation
Indices: 31487061--31487095 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31487051 AATCACCATC
31487061 TTTTTTT-TATTATGATT
1 TTTTTTTGTATT-TGATT
31487078 TTTTTTTGTATTTGATT
1 TTTTTTTGTATTTGATT
31487095 T
1 T
31487096 CTCCCACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTTTTGTATTTGATT
Found at i:31487686 original size:44 final size:44
Alignment explanation
Indices: 31487613--31488206 Score: 297
Period size: 44 Copynumber: 13.0 Consensus size: 44
31487603 GACTTGTAAC
* ** * * *
31487613 TTGTAGCTTCAATCTATTCTACTGGAACTTCAGAGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * *
31487657 TTGTAGCTTTAATCTGCTTCATTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * * * * *
31487701 TTGCTATCTTCAGTCTGCTCCACTACAAATTTAGGGAGATAAGAC
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * * * *
31487746 TTGCAACTTCAACCTGC-CTCACTGCAACTTCGGGGATATAAGGT
1 TTGTAGCTTTAATCTGCTC-CACTGCAACTTCAGGGAAATAAGAT
*
31487790 TTGTGGCTTTAATCTGCTCCACTGCAACTTCA-GGAAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGAT
* * *
31487834 TTGTAGCTTGTAGCTTTAGTCTGTTCCATTGGAACTTCAGGGAAATAAGAT
1 TTGTAGCTT-TA-----A-TCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * *
31487885 TTGTAGCTTTAATCTACTCCACTGCAACTTTAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* ** * *
31487929 TTGCTACCTTATAGCTTTAGTCTATTCCACTGCAACCTC-GAGGAGATAAGACTTGT
1 TTG--------TAGCTTTAATCTGCTCCACTGCAACTTCAG-GGAAATAAGA----T
* * * *
31487985 TATGGTAGATTTAATCTGAC-CTACTGTAACCTT-AGAGG-TAT-AGAAT
1 T-T-GTAGCTTTAATCTG-CTCCACTGCAA-CTTCAG-GGAAATAAG-AT
** * * * * *
31488031 TCATCGTTTTAATCCGCTCCACTGCAACTTCCA-GGAGATAGGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTT-CAGGGAAATAAGAT
* * * *
31488075 TAGTAGCTTCAATCTGCTCCACTGTAACTTC-GGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * * * *
31488118 TGGTATCTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * *
31488162 TAGTAGCTTTAATATGCTCCACTGCAACTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
31488206 T
1 T
31488207 GGTTTATTTG
Statistics
Matches: 424, Mismatches: 88, Indels: 76
0.72 0.15 0.13
Matches are distributed among these distances:
43 48 0.11
44 226 0.53
45 41 0.10
46 2 0.00
49 2 0.00
50 23 0.05
51 40 0.09
52 38 0.09
56 2 0.00
57 1 0.00
58 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
Found at i:31487894 original size:95 final size:96
Alignment explanation
Indices: 31487771--31487957 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 96
31487761 GCCTCACTGC
* * * * *
31487771 AACTTCGGGGATATAAGGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTT
1 AACTTCAGGGAAATAAGATTTGTAGCTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGATTT
* * *
31487836 G-TAGCTTGTAGCTTTAGTCTGTTCCATTGG
66 GCTACCTTATAGCTTTAGTCTATTCCATTGG
* *
31487866 AACTTCAGGGAAATAAGATTTGTAGCTTTAATCTACTCCACTGCAACTTTAGGGAGATAAGATTT
1 AACTTCAGGGAAATAAGATTTGTAGCTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGATTT
31487931 GCTACCTTATAGCTTTAGTCTATTCCA
66 GCTACCTTATAGCTTTAGTCTATTCCA
31487958 CTGCAACCTC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 59 0.73
96 22 0.27
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (96 bp):
AACTTCAGGGAAATAAGATTTGTAGCTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGATTT
GCTACCTTATAGCTTTAGTCTATTCCATTGG
Found at i:31488156 original size:87 final size:88
Alignment explanation
Indices: 31488046--31488659 Score: 253
Period size: 87 Copynumber: 6.8 Consensus size: 88
31488036 GTTTTAATCC
* * *
31488046 GCTCCACTGCAACTTCCAGGAGAT-AGGATTAGTAGCTTCAATCTGCTCCACTGTAACTTC-GGG
1 GCTCCACTGCAACTTCCAGGAGATAAGG-TTAGTAGCTTCAATATGCTCCACTGCAACTTCAGAG
31488109 AGATAAGATTGGTATCTTCAACCT
65 AGATAAGATTGGTATCTTCAACCT
*
31488133 GCTCCACTGCAACTT-CAGAGAGATAAGGTTAGTAGCTTTAATATGCTCCACTGCAACTTCAGAG
1 GCTCCACTGCAACTTCCAG-GAGATAAGGTTAGTAGCTTCAATATGCTCCACTGCAACTTCAGAG
* *
31488197 AGATAAGATTGGTTTAT-TTGTAACCC
65 AGATAAGATTGG--TATCTT-CAACCT
* * * * * * * *
31488223 GTTCCACTACAACTT-CAGGGAGATAAGGTTCGATATG-ATC--TA--CTCTACTACAAATTTAG
1 GCTCCACTGCAACTTCCA-GGAGATAAGGTTAG-TA-GCTTCAATATGCTCCACTGCAACTTCAG
* * *
31488282 AGAGATAAAATTTGCAATTTATAGCTTCAATCT
63 AGAGATAAGA-TTG----GTAT--CTTCAACCT
* * * ** * * * * * * * *
31488315 GTTCCGCTGCAACTT-CAGGGAAATAAAATTCACTATCTTCAGTCTGTTCCACTGTAACTTTAGG
1 GCTCCACTGCAACTTCCA-GGAGATAAGGTT-AGTAGCTTCAATATGCTCCACTGCAACTTCAGA
*
31488379 GAGATAAGACTT-GTAACTTCAACCT
64 GAGATAAGA-TTGGTATCTTCAACCT
* * * * * * *
31488404 ACTCCACTGCAAC-TCTAGGGAGATAAGGTT--T-GCTAT-GATTTGCTCTATTGCAAATTCAGA
1 GCTCCACTGCAACTTCCA-GGAGATAAGGTTAGTAGCT-TCAATATGCTCCACTGCAACTTCAGA
* *
31488464 GAGATAAGATCTGCAATTTATAGATTCAATCCAT
64 GAGATAAGAT-TG----GTAT--CTTCAA-CC-T
* * * * * * * * *
31488498 --TCCACTGCAACTT-CAGGGAAATAAGATTCGCTATCTTCAGTTTGATCCACTACAACTTCAGG
1 GCTCCACTGCAACTTCCA-GGAGATAAGGTTAG-TAGCTTCAATATGCTCCACTGCAACTTCAGA
* **
31488560 GAGATAAGACTTGTTATCTTCAGTCT
64 GAGATAAGA-TTGGTATCTTCAACCT
* * * * ** *
31488586 GCTCCACTGCAACTT-CAGGGAGATAAGGCTAATGGCTTCAATCTATTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCCA-GGAGATAAGGTTAGTAGCTTCAATATGCTCCACTGCAACTTCAGAG
31488650 AGATAAGATT
65 AGATAAGATT
31488660 CACTATGATG
Statistics
Matches: 394, Mismatches: 89, Indels: 87
0.69 0.16 0.15
Matches are distributed among these distances:
84 1 0.00
85 26 0.07
86 5 0.01
87 71 0.18
88 24 0.06
89 67 0.17
90 68 0.17
91 6 0.02
92 65 0.16
93 5 0.01
94 2 0.01
95 2 0.01
96 51 0.13
97 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (88 bp):
GCTCCACTGCAACTTCCAGGAGATAAGGTTAGTAGCTTCAATATGCTCCACTGCAACTTCAGAGA
GATAAGATTGGTATCTTCAACCT
Found at i:31488252 original size:90 final size:87
Alignment explanation
Indices: 31488044--31488252 Score: 262
Period size: 87 Copynumber: 2.4 Consensus size: 87
31488034 TCGTTTTAAT
* *
31488044 CCGCTCCACTGCAACTTCCA-GGAGAT-AGGATTAGTAGCTTCAATCTGCTCCACTGTAACTTCG
1 CCGCTCCACTGCAACTT-CAGGGAGATAAGG-TTAGTAGCTTCAATATGCTCCACTGCAACTTCG
*
31488107 GGAGATAAGATTGGTATCTTCAAC
64 AGAGATAAGATTGGTATCTTCAAC
* * *
31488131 CTGCTCCACTGCAACTTCAGAGAGATAAGGTTAGTAGCTTTAATATGCTCCACTGCAACTTCAGA
1 CCGCTCCACTGCAACTTCAGGGAGATAAGGTTAGTAGCTTCAATATGCTCCACTGCAACTTC-GA
*
31488196 GAGATAAGATTGGTTTAT-TTGTAAC
65 GAGATAAGATTGG--TATCTT-CAAC
* *
31488221 CCGTTCCACTACAACTTCAGGGAGATAAGGTT
1 CCGCTCCACTGCAACTTCAGGGAGATAAGGTT
31488253 CGATATGATC
Statistics
Matches: 105, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
86 2 0.02
87 50 0.48
88 17 0.16
89 2 0.02
90 34 0.32
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (87 bp):
CCGCTCCACTGCAACTTCAGGGAGATAAGGTTAGTAGCTTCAATATGCTCCACTGCAACTTCGAG
AGATAAGATTGGTATCTTCAAC
Found at i:31488467 original size:181 final size:182
Alignment explanation
Indices: 31488225--31488613 Score: 530
Period size: 181 Copynumber: 2.1 Consensus size: 182
31488215 TGTAACCCGT
* *
31488225 TCCACTACAACTTCAGGGAGATAAGGTTCGATATGATCTACTCTACTACAAATTTAGAGAGATAA
1 TCCACTGCAACTTCAGGGAGATAAGGTTCGATATGATCTACTCTACTACAAATTCAGAGAGATAA
* * ** *
31488290 AATTTGCAATTTATAGCTTCAATCTGTTCCGCTGCAACTTCAGGGAAATAAAATTCACTATCTTC
66 AATCTGCAATTTATAGATTCAATCCATTCCACTGCAACTTCAGGGAAATAAAATTCACTATCTTC
* ** *
31488355 AGTCTGTTCCACTGTAACTTTAGGGAGATAAGACTTG-TAACTTCAACCTAC
131 AGTCTGATCCACTACAACTTCAGGGAGATAAGACTTGTTAACTTCAACCTAC
* * * * * *
31488406 TCCACTGCAAC-TCTAGGGAGATAAGGTTTGCTATGATTTGCTCTATTGCAAATTCAGAGAGATA
1 TCCACTGCAACTTC-AGGGAGATAAGGTTCGATATGATCTACTCTACTACAAATTCAGAGAGATA
* * *
31488470 AGATCTGCAATTTATAGATTCAATCCATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTT
65 AAATCTGCAATTTATAGATTCAATCCATTCCACTGCAACTTCAGGGAAATAAAATTCACTATCTT
* * ** *
31488535 CAGTTTGATCCACTACAACTTCAGGGAGATAAGACTTGTTATCTTCAGTCTGC
130 CAGTCTGATCCACTACAACTTCAGGGAGATAAGACTTGTTAACTTCAACCTAC
31488588 TCCACTGCAACTTCAGGGAGATAAGG
1 TCCACTGCAACTTCAGGGAGATAAGG
31488614 CTAATGGCTT
Statistics
Matches: 180, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
180 2 0.01
181 143 0.79
182 33 0.18
183 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (182 bp):
TCCACTGCAACTTCAGGGAGATAAGGTTCGATATGATCTACTCTACTACAAATTCAGAGAGATAA
AATCTGCAATTTATAGATTCAATCCATTCCACTGCAACTTCAGGGAAATAAAATTCACTATCTTC
AGTCTGATCCACTACAACTTCAGGGAGATAAGACTTGTTAACTTCAACCTAC
Found at i:31488567 original size:45 final size:45
Alignment explanation
Indices: 31488498--31488657 Score: 182
Period size: 45 Copynumber: 3.6 Consensus size: 45
31488488 TTCAATCCAT
* *
31488498 TCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTTTGA
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAGTCTGA
* * *
31488543 TCCACTACAACTTCAGGGAGATAAGACTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGA
* ** ** *
31488588 TCCACTGCAACTTCAGGGAGATAAGGC-TAATGGCTTCAATCT-A
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGA
31488631 TTCCACTGCAACTTCAGGGAGATAAGA
1 -TCCACTGCAACTTCAGGGAGATAAGA
31488658 TTCACTATGA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
44 35 0.35
45 62 0.63
46 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGA
Found at i:31490331 original size:20 final size:20
Alignment explanation
Indices: 31490306--31490345 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31490296 ATGGATTCCA
31490306 TTGATTCTTTGTAAGGTAGG
1 TTGATTCTTTGTAAGGTAGG
31490326 TTGATTCTTTGTAAGGTAGG
1 TTGATTCTTTGTAAGGTAGG
31490346 ATCTGTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (20 bp):
TTGATTCTTTGTAAGGTAGG
Found at i:31494053 original size:16 final size:17
Alignment explanation
Indices: 31494029--31494062 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31494019 TTACATTGTT
31494029 TATTATTTCTCT-TTGC
1 TATTATTTCTCTGTTGC
*
31494045 TATTGTTTCTCTGTTGC
1 TATTATTTCTCTGTTGC
31494062 T
1 T
31494063 GCTTTGCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.09, C:0.18, G:0.12, T:0.62
Consensus pattern (17 bp):
TATTATTTCTCTGTTGC
Found at i:31500061 original size:14 final size:15
Alignment explanation
Indices: 31500037--31500074 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
31500027 AAAAAGGCAA
31500037 GAAGAAGGAAAAGAG
1 GAAGAAGGAAAAGAG
31500052 GAAG-AGGAAAAGA-
1 GAAGAAGGAAAAGAG
31500065 GAACGAAGGA
1 GAA-GAAGGA
31500075 GGTGAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 10 0.48
15 8 0.38
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAAAAGAG
Found at i:31501337 original size:20 final size:21
Alignment explanation
Indices: 31501306--31501344 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31501296 TTTATGGTTT
31501306 TAAATAATTTTTGGGTAAAAA
1 TAAATAATTTTTGGGTAAAAA
*
31501327 TAAAT-ATTTTTGGTTAAA
1 TAAATAATTTTTGGGTAAA
31501345 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (21 bp):
TAAATAATTTTTGGGTAAAAA
Found at i:31521585 original size:18 final size:20
Alignment explanation
Indices: 31521545--31521592 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
31521535 AGAGAAGAAA
*
31521545 AGAGGAGAGGATTTTTGGAG
1 AGAGAAGAGGATTTTTGGAG
31521565 AGAGAAGAGGATTTTTGGAG
1 AGAGAAGAGGATTTTTGGAG
31521585 AGAGAAGA
1 AGAGAAGA
31521593 ATTGGAGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.21
Consensus pattern (20 bp):
AGAGAAGAGGATTTTTGGAG
Found at i:31524143 original size:10 final size:10
Alignment explanation
Indices: 31524128--31524158 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31524118 GGTTAGATGG
31524128 GTTAGACTTA
1 GTTAGACTTA
*
31524138 GTTAGACCTA
1 GTTAGACTTA
31524148 GTTAGACTTA
1 GTTAGACTTA
31524158 G
1 G
31524159 ACAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (10 bp):
GTTAGACTTA
Found at i:31527453 original size:22 final size:22
Alignment explanation
Indices: 31527400--31527453 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
31527390 TACAGAAACG
*
31527400 GAAG-AAATAAGAAGGAAGGAA
1 GAAGAAAAAAAGAAGGAAGGAA
* *
31527421 GCAGAAGAAAAGAAGGAAGGAA
1 GAAGAAAAAAAGAAGGAAGGAA
31527443 -AAGAATAAAAA
1 GAAGAA-AAAAA
31527454 AATAAGGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.65, C:0.02, G:0.30, T:0.04
Consensus pattern (22 bp):
GAAGAAAAAAAGAAGGAAGGAA
Found at i:31530792 original size:6 final size:6
Alignment explanation
Indices: 31530781--31530833 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
31530771 AGAATGTAGT
* *
31530781 TCTGTC TCTGTC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
31530829 TCTGG
1 TCTGG
31530834 TGCATGATGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.32, G:0.30, T:0.38
Consensus pattern (6 bp):
TCTGGC
Found at i:31532486 original size:16 final size:15
Alignment explanation
Indices: 31532455--31532488 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31532445 ACAAAATCAA
*
31532455 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
31532470 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
31532486 ATA
1 ATA
31532489 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:31532576 original size:38 final size:38
Alignment explanation
Indices: 31532533--31532614 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
31532523 AAAAAGTCAG
31532533 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
31532571 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
31532609 TTATAA
1 TTATAA
31532615 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:31532798 original size:8 final size:8
Alignment explanation
Indices: 31532785--31532946 Score: 53
Period size: 8 Copynumber: 19.4 Consensus size: 8
31532775 CATACAAAAA
31532785 ATTACAAT
1 ATTACAAT
31532793 ATTACAAT
1 ATTACAAT
* * *
31532801 ATATCCCGAC
1 AT-T-ACAAT
31532811 ATTACAAT
1 ATTACAAT
*
31532819 ATTCATACAAA
1 A-T--TACAAT
31532830 ATTACAAT
1 ATTACAAT
31532838 ATTACAAT
1 ATTACAAT
31532846 ATT-C-AT
1 ATTACAAT
** * *
31532852 ACAAAAAA
1 ATTACAAT
*
31532860 ATTGCAAT
1 ATTACAAT
*
31532868 ATTCATACAAA
1 A-T--TACAAT
*
31532879 ATTAAAAT
1 ATTACAAT
31532887 ATTACAAT
1 ATTACAAT
31532895 ATT-C-AT
1 ATTACAAT
** * *
31532901 ACAAAAAA
1 ATTACAAT
31532909 ATTACAAT
1 ATTACAAT
*
31532917 ATTCATACAAA
1 A-T--TACAAT
31532928 ATTACAAT
1 ATTACAAT
31532936 ATTACAAT
1 ATTACAAT
31532944 ATT
1 ATT
31532947 CATACAAAAA
Statistics
Matches: 107, Mismatches: 32, Indels: 30
0.63 0.19 0.18
Matches are distributed among these distances:
6 6 0.06
7 2 0.02
8 70 0.65
9 5 0.05
10 7 0.07
11 17 0.16
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (8 bp):
ATTACAAT
Found at i:31532835 original size:19 final size:19
Alignment explanation
Indices: 31532811--31533188 Score: 209
Period size: 19 Copynumber: 20.2 Consensus size: 19
31532801 ATATCCCGAC
31532811 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
31532830 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
31532846 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
31532860 ATTGCAATATTCATACAAA
1 ATTACAATATTCATACAAA
* *
31532879 ATTAAAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
31532895 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
31532909 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
31532928 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
31532944 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
31532958 ATTGCAATATTCATACAAAACTATAA
1 ATTACAATATTCAT-----AC-A-AA
31532984 TATTACAATATTCATACAAAAA
1 -ATTACAATATTCATAC--AAA
31533006 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
31533025 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
31533046 ATTACAATATTCATAC-AA
1 ATTACAATATTCATACAAA
* * *
31533064 ATTACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
31533085 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
31533107 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
31533126 ATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAA
31533145 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
31533166 AGTTAGAATATTCATACAAA
1 A-TTACAATATTCATACAAA
31533186 ATT
1 ATT
31533189 CTAATCTAAA
Statistics
Matches: 282, Mismatches: 30, Indels: 94
0.69 0.07 0.23
Matches are distributed among these distances:
14 27 0.10
15 5 0.02
16 33 0.12
17 3 0.01
18 20 0.07
19 89 0.32
20 13 0.05
21 44 0.16
22 23 0.08
23 6 0.02
24 1 0.00
25 3 0.01
26 2 0.01
27 13 0.05
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:31532847 original size:27 final size:26
Alignment explanation
Indices: 31532811--31533035 Score: 259
Period size: 27 Copynumber: 9.1 Consensus size: 26
31532801 ATATCCCGAC
31532811 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
31532838 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
31532860 ATTGCAATATTCATACAAAATTAAAAT
1 ATTACAATATTCATACAAAATT-AAAT
31532887 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
31532909 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
31532936 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
31532958 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
31532985 ATTACAATATTCATAC--AA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
31533006 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
31533033 ATT
1 ATT
31533036 CATACAAAAA
Statistics
Matches: 173, Mismatches: 4, Indels: 42
0.79 0.02 0.19
Matches are distributed among these distances:
21 16 0.09
22 48 0.28
23 19 0.11
24 2 0.01
25 5 0.03
26 18 0.10
27 65 0.38
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:31532888 original size:49 final size:49
Alignment explanation
Indices: 31532758--31533035 Score: 413
Period size: 49 Copynumber: 5.7 Consensus size: 49
31532748 AATTAATTAT
*
31532758 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-AT-C
1 AAAAAAATTACAATATTCATAC--AAAATTACAATATTACAATATTCATAC
*** *
31532806 -CCGACATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
31532854 AAAAAAATTGCAATATTCATACAAAATTAAAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
31532903 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
31532952 AAAAAAATTGCAATATTCATACAAAACTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
31533001 -AAAAAATTACAATATTCATACAAAATTACAATATT
1 AAAAAAATTACAATATTCATACAAAATTACAATATT
31533036 CATACAAAAA
Statistics
Matches: 207, Mismatches: 19, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
45 20 0.10
46 1 0.00
47 18 0.09
48 33 0.16
49 135 0.65
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:31533029 original size:40 final size:40
Alignment explanation
Indices: 31532985--31533188 Score: 222
Period size: 40 Copynumber: 5.1 Consensus size: 40
31532975 AAACTATAAT
31532985 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
1 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
31533025 ATTACAATATTCATACAAAAAATTACAATATTCATAC-AA
1 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
* * * * * *
31533064 ATTACTA-ATCCAAAACTATAAA-TACAAATTTAATT-ATAAAATA
1 ATTACAATATTC-ATACAAAAAATTAC-AA--T-ATTCATACAA-A
* *
31533107 ATTACAATATTCATAC--AACATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
*
31533145 ATTACAATATTCATACAAAAAAGTTAGAATATTCATACAAA
1 ATTACAATATTCATACAAAAAA-TTACAATATTCATACAAA
31533186 ATT
1 ATT
31533189 CTAATCTAAA
Statistics
Matches: 137, Mismatches: 14, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
38 26 0.19
39 24 0.18
40 40 0.29
41 27 0.20
42 7 0.05
43 10 0.07
44 3 0.02
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (40 bp):
ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
Found at i:31533149 original size:120 final size:121
Alignment explanation
Indices: 31532985--31533203 Score: 354
Period size: 120 Copynumber: 1.8 Consensus size: 121
31532975 AAACTATAAT
*
31532985 ATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTACAATATTCATACAAAAAA-TT
1 ATTACAATATTCATAC-AAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAAGTT
31533049 ACAATATTCATAC-AAATTACTAATCCAAAACTATAAATACAAATTTAATTATAAAATA
65 ACAATATTCATACAAAATT-CTAAT-CAAAACTATAAATACAAATTTAATTATAAAATA
*
31533107 ATTACAATATTCATAC-AACATTACAATATTCATAAAAAATTACAATATTCATACAAAAAAGTTA
1 ATTACAATATTCATACAAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAAGTTA
* *
31533171 GAATATTCATACAAAATTCTAATCTAAACTATA
66 CAATATTCATACAAAATTCTAATCAAAACTATA
31533204 TACACTAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
120 51 0.56
121 19 0.21
122 21 0.23
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (121 bp):
ATTACAATATTCATACAAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAAGTTA
CAATATTCATACAAAATTCTAATCAAAACTATAAATACAAATTTAATTATAAAATA
Found at i:31533175 original size:22 final size:21
Alignment explanation
Indices: 31533022--31533186 Score: 134
Period size: 21 Copynumber: 8.1 Consensus size: 21
31533012 ATATTCATAC
31533022 AAAATTACAATATTCATACAA
1 AAAATTACAATATTCATACAA
31533043 AAAATTACAATATTCATAC--
1 AAAATTACAATATTCATACAA
* * * *
31533062 -AAATTACTA-ATCCAAAACTA
1 AAAATTACAATATTC-ATACAA
* * *
31533082 TAAA-TACAA-ATTTAATTATAA
1 AAAATTACAATA-TTCA-TACAA
31533103 AATAATTACAATATTCATAC--
1 AA-AATTACAATATTCATACAA
*
31533123 AACATTACAATATTCAT--AA
1 AAAATTACAATATTCATACAA
31533142 AAAATTACAATATTCATACAA
1 AAAATTACAATATTCATACAA
*
31533163 AAAAGTTAGAATATTCATACAA
1 AAAA-TTACAATATTCATACAA
31533185 AA
1 AA
31533187 TTCTAATCTA
Statistics
Matches: 115, Mismatches: 15, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.03
18 11 0.10
19 30 0.26
20 8 0.07
21 32 0.28
22 22 0.19
23 8 0.07
24 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAATTACAATATTCATACAA
Found at i:31533383 original size:17 final size:17
Alignment explanation
Indices: 31533345--31533385 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
31533335 TTCTTTCTTT
31533345 CTTTCT-TCTTCTTCTC
1 CTTTCTCTCTTCTTCTC
31533361 C--T-TCTCTTCTTCTC
1 CTTTCTCTCTTCTTCTC
31533375 CTTTCTCTCTT
1 CTTTCTCTCTT
31533386 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.05
14 12 0.57
16 2 0.10
17 6 0.29
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (17 bp):
CTTTCTCTCTTCTTCTC
Done.