Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 105 of 332
Found at i:33839702 original size:30 final size:30
Alignment explanation
Indices: 33839617--33839713 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33839607 TAAACTAAAA
* *
33839617 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
33839647 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33839677 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33839706 ATGAGCTA
1 -TGAGCTA
33839714 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:33840392 original size:22 final size:23
Alignment explanation
Indices: 33840367--33840415 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
33840357 ATGTTTTAAC
33840367 TTTTATTCTAT-TTTAAGAC-TATT
1 TTTTATT-TATCTTTAAG-CTTATT
*
33840390 TTTTATTTTTCTTTAAGCTTATT
1 TTTTATTTATCTTTAAGCTTATT
33840413 TTT
1 TTT
33840416 ATTAGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTATCTTTAAGCTTATT
Found at i:33846005 original size:17 final size:18
Alignment explanation
Indices: 33845968--33846005 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33845958 GATTGAGAGT
* *
33845968 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
33845986 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
33846003 GAA
1 GAA
33846006 GTTGAGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:33848457 original size:30 final size:31
Alignment explanation
Indices: 33848423--33848519 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
33848413 AGCTCACTCC
*
33848423 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
33848453 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
33848483 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
33848513 TAGCTCA
1 TAGCTCA
33848520 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33849493 original size:45 final size:45
Alignment explanation
Indices: 33849442--33849703 Score: 393
Period size: 45 Copynumber: 5.9 Consensus size: 45
33849432 TCGGCCATGG
* * * * * *
33849442 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTTGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33849487 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33849532 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33849577 TGCTTCCTC-AATTCTTCCATGAA-TATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33849620 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
33849665 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
33849704 TCCACCTCTT
Statistics
Matches: 200, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
43 28 0.14
44 28 0.14
45 144 0.72
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33849620 original size:133 final size:135
Alignment explanation
Indices: 33849442--33849703 Score: 411
Period size: 133 Copynumber: 2.0 Consensus size: 135
33849432 TCGGCCATGG
* * * *
33849442 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTTGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAATTTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
**
33849507 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTGG
33849572 CCAAA
131 CCAAA
* *
33849577 TGCTTCCTCAA-TTCTTCCATGAA-TATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAATTTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
* * *
33849640 TGAATTATGCATGATGTTGGTCAAATGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTG
33849704 TCCACCTCTT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
133 96 0.83
134 9 0.08
135 11 0.09
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (135 bp):
TGCTTCCTCAATTTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTGG
CCAAA
Found at i:33849632 original size:88 final size:89
Alignment explanation
Indices: 33849442--33849703 Score: 400
Period size: 88 Copynumber: 2.9 Consensus size: 89
33849432 TCGGCCATGG
* * * * *
33849442 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTTGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCC-TAAATTCTTCCA
33849507 TGAATTATGCATGATGTTGGTCAAA
65 TGAATTATGCATGATGTTGGTCAAA
*
33849532 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTCAATTCTTCCAT
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTAAATTCTTCCAT
33849597 GAA-TATGCATGATGTTGGTCAAA
66 GAATTATGCATGATGTTGGTCAAA
* * *
33849620 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTTAATTTGTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCC-TAAATTCTTCCA
**
33849685 CAAATTATGCATGATGTTG
65 TGAATTATGCATGATGTTG
33849704 TCCACCTCTT
Statistics
Matches: 158, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
88 71 0.45
89 26 0.16
90 61 0.39
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (89 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTAAATTCTTCCAT
GAATTATGCATGATGTTGGTCAAA
Found at i:33849838 original size:16 final size:16
Alignment explanation
Indices: 33849817--33849848 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33849807 CATTCTGCAT
33849817 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
33849833 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
33849849 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:33852230 original size:23 final size:22
Alignment explanation
Indices: 33852178--33852230 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33852168 TCCACGTCTT
*
33852178 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33852200 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33852223 TTTCTTTT
1 TTTCTTTT
33852231 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33858075 original size:45 final size:45
Alignment explanation
Indices: 33858026--33858289 Score: 429
Period size: 45 Copynumber: 5.9 Consensus size: 45
33858016 TCGGCCATGG
* * * * *
33858026 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33858071 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33858116 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33858161 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33858206 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
33858251 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
33858290 TCCACCTCTT
Statistics
Matches: 207, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 207 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33858424 original size:16 final size:16
Alignment explanation
Indices: 33858403--33858434 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33858393 CATTCTGCAT
33858403 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
33858419 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
33858435 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:33860479 original size:30 final size:30
Alignment explanation
Indices: 33860445--33860541 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33860435 TAAACTAAAA
33860445 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33860475 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
33860505 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
33860535 TGAGCTA
1 TGAGCTA
33860542 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33862606 original size:11 final size:10
Alignment explanation
Indices: 33862581--33862641 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
33862571 ACCAATAAAA
33862581 TAAA-TGAGC
1 TAAATTGAGC
*
33862590 TGAATTGTAGC
1 TAAATTG-AGC
33862601 TAAATTGAGC
1 TAAATTGAGC
**
33862611 TCGATTGAGC
1 TAAATTGAGC
33862621 TGAAA-TGAGC
1 T-AAATTGAGC
*
33862631 TCAATTGAGC
1 TAAATTGAGC
33862641 T
1 T
33862642 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:33862642 original size:20 final size:20
Alignment explanation
Indices: 33862582--33862642 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33862572 CCAATAAAAT
*
33862582 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
33862602 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
33862623 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
33862643 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:33864734 original size:18 final size:18
Alignment explanation
Indices: 33864713--33864747 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33864703 TTTTTCTTTT
33864713 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
33864731 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
33864748 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:33865697 original size:30 final size:28
Alignment explanation
Indices: 33865618--33865702 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 28
33865608 GCAAGACTTT
*
33865618 TCACTTTTTTTTAAACTTGATTTTTTTTTGC
1 TCACTTTTTTTT--ACTT-TTTTTTTTTTGC
*
33865649 TCACCTTTTTTTTTCTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTACTTTT-TTTTTTTTGC
33865679 TCGA-TTTTTTTTCACTTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTTT
33865703 GAATTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 14 0.30
30 20 0.43
31 4 0.09
32 9 0.19
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:33865711 original size:14 final size:14
Alignment explanation
Indices: 33865694--33865744 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
33865684 TTTTTTTCAC
33865694 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
* *
33865707 TTTTTTTCAATCAAAT
1 TTTTTTT--TTCGAAT
33865723 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
33865737 TTTTTTTT
1 TTTTTTTT
33865745 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 7 0.23
14 13 0.42
15 1 0.03
16 10 0.32
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:33865749 original size:11 final size:13
Alignment explanation
Indices: 33865683--33865754 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 13
33865673 TTTTGCTCGA
*
33865683 TTTTTTTTC-ACT
1 TTTTTTTTCGAAT
33865695 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
33865707 TTTTTTTCAATCAAATT
1 TTTTTTT---TCGAA-T
33865724 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
33865737 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
33865748 TTTTTTT
1 TTTTTTT
33865755 ACTCCAATAC
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 9 0.18
12 18 0.35
13 9 0.18
14 4 0.08
15 1 0.02
16 2 0.04
17 8 0.16
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:33867109 original size:11 final size:10
Alignment explanation
Indices: 33867084--33867144 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
33867074 ACCAATAAAA
33867084 TAAA-TGAGC
1 TAAATTGAGC
*
33867093 TGAATTGTAGC
1 TAAATTG-AGC
33867104 TAAATTGAGC
1 TAAATTGAGC
**
33867114 TCGATTGAGC
1 TAAATTGAGC
33867124 TGAAA-TGAGC
1 T-AAATTGAGC
*
33867134 TCAATTGAGC
1 TAAATTGAGC
33867144 T
1 T
33867145 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:33867145 original size:20 final size:20
Alignment explanation
Indices: 33867085--33867145 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33867075 CCAATAAAAT
*
33867085 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
33867105 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
33867126 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
33867146 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:33868695 original size:30 final size:30
Alignment explanation
Indices: 33868625--33868706 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
33868615 TTTTGTTTCA
* *
33868625 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
33868656 ATTTC-TTTTCGTTCTCTTTTTCAATCTCA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
33868685 TTTTCTTTTTCATTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
33868707 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.75
31 7 0.16
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:33868706 original size:18 final size:18
Alignment explanation
Indices: 33868657--33868712 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
33868647 CACTCTCAGA
* *
33868657 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
33868674 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
33868692 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
33868711 TT
1 TT
33868713 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:33868713 original size:12 final size:12
Alignment explanation
Indices: 33868682--33868706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33868672 TTTTTCAATC
33868682 TCATTTTCTTTT
1 TCATTTTCTTTT
33868694 TCATTTTCTTTT
1 TCATTTTCTTTT
33868706 T
1 T
33868707 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:33868724 original size:12 final size:12
Alignment explanation
Indices: 33868709--33868739 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33868699 TTCTTTTTGC
33868709 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
33868721 TTTTCGAAGGCT
1 TTTTCAAAGGCT
33868733 TTTTCAA
1 TTTTCAA
33868740 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:33868807 original size:6 final size:6
Alignment explanation
Indices: 33868789--33868834 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
33868779 CTTGCCTCTC
33868789 TTTTC- TTTT-T TTTTCT TTTTCT TTTTC- -TTT-T TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
33868832 TTT
1 TTT
33868835 GTTTTCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
4 3 0.08
5 11 0.31
6 22 0.61
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTCT
Found at i:33868807 original size:15 final size:16
Alignment explanation
Indices: 33868787--33868843 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
33868777 CTCTTGCCTC
33868787 TCTTTTCTTTTT-TTT
1 TCTTTTCTTTTTCTTT
33868802 TCTTTTTCTTTTTCTTT
1 TC-TTTTCTTTTTCTTT
33868819 T-TTTTCTTTTTCTTT
1 TCTTTTCTTTTTCTTT
*
33868834 TGTTTTCTTT
1 TCTTTTCTTT
33868844 ATTTTCTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
15 17 0.44
16 18 0.46
17 4 0.10
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (16 bp):
TCTTTTCTTTTTCTTT
Found at i:33868811 original size:21 final size:20
Alignment explanation
Indices: 33868787--33868854 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
33868777 CTCTTGCCTC
33868787 TCTTTTCTTTTTTTTTCTTTT
1 TCTTTT-TTTTTTTTTCTTTT
33868808 TCTTTTTCTTTTTTTTCTTTT
1 TCTTTTT-TTTTTTTTCTTTT
* * *
33868829 TCTTTTGTTTTCTTTATTTT
1 TCTTTTTTTTTTTTTCTTTT
33868849 CTCTTT
1 -TCTTT
33868855 ATAAGAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 12 0.29
21 30 0.71
ACGTcount: A:0.01, C:0.15, G:0.01, T:0.82
Consensus pattern (20 bp):
TCTTTTTTTTTTTTTCTTTT
Found at i:33871378 original size:30 final size:30
Alignment explanation
Indices: 33871344--33871440 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
33871334 TAAACTAAAA
33871344 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33871374 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
33871404 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
33871434 TGAGCTA
1 TGAGCTA
33871441 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33875263 original size:22 final size:22
Alignment explanation
Indices: 33875235--33875278 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33875225 TTTTGAACCA
33875235 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33875257 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33875279 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33875607 original size:13 final size:13
Alignment explanation
Indices: 33875576--33875627 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
33875566 AATAGGTACG
* *
33875576 TAAAAAAAAGAGT
1 TAAAAAAAAAATT
*
33875589 TCAAAAAAAAATT
1 TAAAAAAAAAATT
*
33875602 TGAAAAAAAAATT
1 TAAAAAAAAAATT
33875615 TAAAAAAAAAATT
1 TAAAAAAAAAATT
33875628 GCATACGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (13 bp):
TAAAAAAAAAATT
Found at i:33877881 original size:19 final size:19
Alignment explanation
Indices: 33877820--33877883 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
33877810 CAAATGAGAG
33877820 AAAAAGAAAAGAGCGAAAAT-A
1 AAAAAGAAAAGA---AAAATCA
* *
33877841 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAATCA
*
33877860 AAAAAGAAAAGAAAATTCA
1 AAAAAGAAAAGAAAAATCA
33877879 AAAAA
1 AAAAA
33877884 AGAGAATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 5 0.13
19 22 0.58
21 11 0.29
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAATCA
Found at i:33882187 original size:22 final size:22
Alignment explanation
Indices: 33882159--33882202 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33882149 TTTTGAACCA
33882159 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33882181 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33882203 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33898267 original size:31 final size:32
Alignment explanation
Indices: 33898227--33898286 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
33898217 AACTGAATGT
33898227 TGAAGAGTCTT-CCAATGTGAACA-AGGTGAAC
1 TGAAGAGTCTTGCC-ATGTGAACATAGGTGAAC
*
33898258 TGAATAGTCTTGCCATGTGAACATAGGTG
1 TGAAGAGTCTTGCCATGTGAACATAGGTG
33898287 TGAAACGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (32 bp):
TGAAGAGTCTTGCCATGTGAACATAGGTGAAC
Found at i:33900923 original size:21 final size:21
Alignment explanation
Indices: 33900874--33900940 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
33900864 CCTCTTTGAA
* * *
33900874 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
33900897 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
33900918 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
33900939 CC
1 CC
33900941 CAAATATCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:33903616 original size:22 final size:22
Alignment explanation
Indices: 33903586--33903629 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33903576 TTTGGTATTT
33903586 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33903608 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33903630 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:33907194 original size:9 final size:10
Alignment explanation
Indices: 33907187--33907249 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
33907177 AAGAGAAAAC
33907187 AAAGAAAAGA
1 AAAGAAAAGA
33907197 AAAGAAAAAGAA
1 AAAG-AAAAG-A
33907209 AAAGCAAAAGA
1 AAAG-AAAAGA
*
33907220 AGA-AAAAGA
1 AAAGAAAAGA
33907229 AAATGAAATA-A
1 AAA-GAAA-AGA
33907240 AAAGAAAAGA
1 AAAGAAAAGA
33907250 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:33907197 original size:5 final size:5
Alignment explanation
Indices: 33907187--33907249 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
33907177 AAGAGAAAAC
*
33907187 AAAGA AAAGA AAAGAA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
33907235 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
33907250 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:33907217 original size:12 final size:11
Alignment explanation
Indices: 33907187--33907247 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 11
33907177 AAGAGAAAAC
33907187 AAAG-AAAAGA
1 AAAGAAAAAGA
33907197 AAAGAAAAAGAA
1 AAAGAAAAAG-A
*
33907209 AAAGCAAAAG-
1 AAAGAAAAAGA
33907219 -AAGAAAAAGA
1 AAAGAAAAAGA
*
33907229 AAATGAAATA-A
1 AAA-GAAAAAGA
33907240 AAAGAAAA
1 AAAGAAAA
33907248 GAGAGGCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.19
10 8 0.19
11 11 0.26
12 15 0.36
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:33907224 original size:15 final size:14
Alignment explanation
Indices: 33907196--33907249 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 14
33907186 CAAAGAAAAG
33907196 AAAAG-AAA-AAGA
1 AAAAGAAAAGAAGA
33907208 AAAAGCAAAAGAAGA
1 AAAAG-AAAAGAAGA
*
33907223 AAAAGAAAATGAAATA
1 AAAAGAAAA-G-AAGA
33907239 AAAAGAAAAGA
1 AAAAGAAAAGA
33907250 GAGGCAAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 5 0.14
14 8 0.22
15 11 0.31
16 12 0.33
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAGAAGA
Found at i:33907247 original size:6 final size:6
Alignment explanation
Indices: 33907187--33907236 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33907177 AAGAGAAAAC
*
33907187 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAAA AGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG--AA A-AAGAA AAAGAA AAAGAA
33907236 A
1 A
33907237 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:33907249 original size:21 final size:21
Alignment explanation
Indices: 33907187--33907247 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
33907177 AAGAGAAAAC
33907187 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
* *
33907209 AAAGCAAAAGAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
*
33907230 AATGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
33907248 GAGAGGCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:33907382 original size:30 final size:31
Alignment explanation
Indices: 33907319--33907389 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
33907309 TTTGAAAAGA
* *
33907319 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
33907349 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
33907379 AAAAAGAAATT
1 AAAAAGAAATT
33907390 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:33909531 original size:30 final size:31
Alignment explanation
Indices: 33909497--33909593 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
33909487 AGCTCACTCC
*
33909497 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
33909527 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
33909557 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
33909587 TAGCTCA
1 TAGCTCA
33909594 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33915478 original size:29 final size:29
Alignment explanation
Indices: 33915445--33915501 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33915435 ATAACCAAAC
*
33915445 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
33915474 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
33915502 TCTTTGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:33920475 original size:5 final size:5
Alignment explanation
Indices: 33920465--33920489 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33920455 TGGCTCATTT
33920465 CTGTC CTGTC CTGTC CTGTC CTGTC
1 CTGTC CTGTC CTGTC CTGTC CTGTC
33920490 AACCCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGTC
Found at i:33923494 original size:46 final size:45
Alignment explanation
Indices: 33923427--33923598 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 45
33923417 AACCCGCCCC
*
33923427 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCA
* * *
33923473 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGC-TACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCATCCA
* ** * * *
33923519 TTTCA-CAAACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCA
33923566 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
33923599 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
45 3 0.03
46 63 0.62
47 31 0.31
48 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCATCCA
Found at i:33923541 original size:93 final size:93
Alignment explanation
Indices: 33923433--33923602 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
33923423 CCCCTAAGTG
* * * *
33923433 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
33923498 GAGTTCGGATGCCTAGCTACATTTCACA
66 GAGTTCGGATGCCTAGCTACATTTCACA
*
33923526 AACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
33923591 GAGTTCGGATGC
66 GAGTTCGGATGC
33923603 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGCTACATTTCACA
Found at i:33928727 original size:11 final size:11
Alignment explanation
Indices: 33928711--33928735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33928701 AGTTGCCGAT
33928711 AATCTATGCAC
1 AATCTATGCAC
33928722 AATCTATGCAC
1 AATCTATGCAC
33928733 AAT
1 AAT
33928736 ACTTGTTTTT
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:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (11 bp):
AATCTATGCAC
Found at i:33929171 original size:14 final size:14
Alignment explanation
Indices: 33929146--33929184 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
33929136 AAAGTAGAAG
* *
33929146 AAGGGTACGAATGG
1 AAGGGTAGGAATGA
*
33929160 AATGGTAGGAATGA
1 AAGGGTAGGAATGA
33929174 AAGGGTAGGAA
1 AAGGGTAGGAA
33929185 CAAAAGGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.41, T:0.15
Consensus pattern (14 bp):
AAGGGTAGGAATGA
Found at i:33933679 original size:15 final size:15
Alignment explanation
Indices: 33933655--33933702 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
33933645 AGGAAACCGA
33933655 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
33933670 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
*
33933684 AATAAAGAAACCCAAG
1 -ATAAAGAAATCCAAG
33933700 ATA
1 ATA
33933703 CGATACTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:33936726 original size:46 final size:46
Alignment explanation
Indices: 33936659--33936827 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
33936649 AACCCGCCCC
*
33936659 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTGTTCACATCCA
*
33936705 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G--T-GTTCACATCCA
* * *** *
33936753 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTGTTCACATCCA
*
33936798 TAAGTGAACTCAGACTCAACTCAACGAGTT
1 TAAGTGAACTCGGACTCAACTCAACGAGTT
33936828 TGGATGCTCA
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
45 2 0.02
46 56 0.55
47 28 0.27
48 3 0.03
50 5 0.05
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTGTTCACATCCA
Found at i:33936776 original size:93 final size:93
Alignment explanation
Indices: 33936664--33936834 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
33936654 GCCCCTAAGT
*** *
33936664 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
33936729 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
33936757 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
*
33936822 CGAGTTTGGATGC
66 CGAGTTCGGATGC
33936835 TCAACCTTCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:33940850 original size:10 final size:10
Alignment explanation
Indices: 33940836--33940893 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
33940826 CAGCTCCGAC
33940836 CAGCTCAATT
1 CAGCTCAATT
* *
33940846 GAGCTCATTT
1 CAGCTCAATT
33940856 CAGCTCAA-T
1 CAGCTCAATT
33940865 CAAGCTCAATT
1 C-AGCTCAATT
*
33940876 TAGCTACAATT
1 CAGCT-CAATT
33940887 CAGCTCA
1 CAGCTCA
33940894 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:33942361 original size:23 final size:22
Alignment explanation
Indices: 33942309--33942361 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33942299 TCCACGTCTT
*
33942309 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33942331 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33942354 TTTCTTTT
1 TTTCTTTT
33942362 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33951297 original size:14 final size:14
Alignment explanation
Indices: 33951250--33951297 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
33951240 ATACGAATGG
* *
33951250 AATGGCAGGAACGA
1 AATGGTAGGAACAA
*
33951264 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
33951278 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
33951292 ATTGGT
1 AATGGT
33951298 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.17
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:33953530 original size:45 final size:45
Alignment explanation
Indices: 33953481--33953744 Score: 420
Period size: 45 Copynumber: 5.9 Consensus size: 45
33953471 TCGGCCATGG
* * * * *
33953481 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33953526 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33953571 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33953616 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33953661 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
33953706 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
33953745 TCCACCTCTT
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 205 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33959937 original size:45 final size:45
Alignment explanation
Indices: 33959886--33960149 Score: 438
Period size: 45 Copynumber: 5.9 Consensus size: 45
33959876 TCGGCCATGG
* * * *
33959886 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33959931 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
33959976 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33960021 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
33960066 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
33960111 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
33960150 TCCACCTCTT
Statistics
Matches: 208, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 208 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33965863 original size:14 final size:14
Alignment explanation
Indices: 33965829--33965876 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
33965819 GTACGAATGG
**
33965829 AATGGTAGGAATGA
1 AATGGTAGGAACAA
*
33965843 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
33965857 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
33965871 ATTGGT
1 AATGGT
33965877 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:33970390 original size:18 final size:19
Alignment explanation
Indices: 33970367--33970405 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33970357 TTTATCTCAA
*
33970367 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
33970385 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
33970404 TT
1 TT
33970406 CTGATACGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:33971424 original size:18 final size:18
Alignment explanation
Indices: 33971403--33971448 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
33971393 TCTCTCAAAC
33971403 TCTTTTTCAATCTCATTT
1 TCTTTTTCAATCTCATTT
* * *
33971421 TCTTTTTCATTTTCTTTT
1 TCTTTTTCAATCTCATTT
*
33971439 TGTTTTTCAA
1 TCTTTTTCAA
33971449 AGGCTTTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.02, T:0.67
Consensus pattern (18 bp):
TCTTTTTCAATCTCATTT
Found at i:33971446 original size:12 final size:12
Alignment explanation
Indices: 33971415--33971439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33971405 TTTTTCAATC
33971415 TCATTTTCTTTT
1 TCATTTTCTTTT
33971427 TCATTTTCTTTT
1 TCATTTTCTTTT
33971439 T
1 T
33971440 GTTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:33971457 original size:13 final size:12
Alignment explanation
Indices: 33971441--33971472 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
33971431 TTTCTTTTTG
33971441 TTTTTCAAAGGC
1 TTTTTCAAAGGC
33971453 TTTTTCAAAGGC
1 TTTTTCAAAGGC
33971465 TTTTTCAA
1 TTTTTCAA
33971473 GTTCTCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTTTCAAAGGC
Found at i:33971531 original size:5 final size:5
Alignment explanation
Indices: 33971521--33971577 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33971511 TTTTTGCCTC
*
33971521 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
33971568 TCTTT TCTTT
1 TCTTT TCTTT
33971578 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:33971561 original size:15 final size:14
Alignment explanation
Indices: 33971521--33971577 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
33971511 TTTTTGCCTC
*
33971521 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
33971536 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
33971551 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
33971568 TCTTTTCTTT
1 TCTTTTCTTT
33971578 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:33971578 original size:21 final size:21
Alignment explanation
Indices: 33971521--33971582 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
33971511 TTTTTGCCTC
* *
33971521 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
33971542 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
33971563 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
33971583 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:33972527 original size:22 final size:22
Alignment explanation
Indices: 33972502--33972543 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
33972492 TTTTCACTTC
*
33972502 AATTTTTTTCGGATTTTTTTTT
1 AATTTTTTTCGAATTTTTTTTT
33972524 AATTTTTTTCGAATTTTTTT
1 AATTTTTTTCGAATTTTTTT
33972544 AACTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (22 bp):
AATTTTTTTCGAATTTTTTTTT
Found at i:33972529 original size:10 final size:11
Alignment explanation
Indices: 33972502--33972543 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
33972492 TTTTCACTTC
33972502 AATTTTTTTCG
1 AATTTTTTTCG
* **
33972513 GATTTTTTTTT
1 AATTTTTTTCG
33972524 AATTTTTTTCG
1 AATTTTTTTCG
33972535 AATTTTTTT
1 AATTTTTTT
33972544 AACTTGTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (11 bp):
AATTTTTTTCG
Found at i:33975019 original size:10 final size:10
Alignment explanation
Indices: 33975004--33975042 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33974994 TAAAAGAAAT
33975004 GAGCTAAAAC
1 GAGCTAAAAC
*
33975014 GAGCTAAATTC
1 GAGCTAAA-AC
*
33975025 GAGCTCAAAC
1 GAGCTAAAAC
33975035 GAGCTAAA
1 GAGCTAAA
33975043 TCAAGCTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:33975049 original size:10 final size:10
Alignment explanation
Indices: 33975000--33975049 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
33974990 AATGTAAAAG
33975000 AAAT-GAGCT
1 AAATCGAGCT
*
33975009 AAAACGAGCT
1 AAATCGAGCT
33975019 AAATTCGAGCT
1 AAA-TCGAGCT
33975030 CAAA-CGAGCT
1 -AAATCGAGCT
*
33975040 AAATCAAGCT
1 AAATCGAGCT
33975050 CAAGTGAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 6 0.18
10 19 0.56
11 6 0.18
12 3 0.09
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (10 bp):
AAATCGAGCT
Found at i:33975059 original size:20 final size:21
Alignment explanation
Indices: 33975005--33975052 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
33974995 AAAAGAAATG
* *
33975005 AGCTAAAACGAGCTAAATTCG
1 AGCTCAAACGAGCTAAATTCA
33975026 AGCTCAAACGAGCTAAA-TCA
1 AGCTCAAACGAGCTAAATTCA
33975046 AGCTCAA
1 AGCTCAA
33975053 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAATTCA
Found at i:33977686 original size:20 final size:20
Alignment explanation
Indices: 33977661--33977698 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
33977651 CTTGAAGTCG
33977661 GCACAAATGTGAACAAACTT
1 GCACAAATGTGAACAAACTT
33977681 GCACAAATGTGAACAAAC
1 GCACAAATGTGAACAAAC
33977699 ATTCCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
GCACAAATGTGAACAAACTT
Found at i:33985177 original size:56 final size:56
Alignment explanation
Indices: 33985072--33985178 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
33985062 ATTAATACCG
* * * * *
33985072 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
33985128 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
33985179 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:33985825 original size:20 final size:20
Alignment explanation
Indices: 33985800--33985854 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
33985790 AACGAGTTAA
* *
33985800 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
33985820 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
33985840 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
33985855 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:33986323 original size:13 final size:13
Alignment explanation
Indices: 33986305--33986339 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
33986295 ATTATATGAA
*
33986305 TAATTATTTTATT
1 TAATTATGTTATT
33986318 TAATTATGTTATT
1 TAATTATGTTATT
33986331 TAATTATGT
1 TAATTATGT
33986340 AGGTTAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:33987528 original size:13 final size:12
Alignment explanation
Indices: 33987510--33987582 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 12
33987500 TTGAAGTATT
33987510 AAAAAAAGAAAA
1 AAAAAAAGAAAA
33987522 CAAAAAAAGGAGGAAA
1 -AAAAAAA-GA--AAA
33987538 AAAAAAAGAAAA
1 AAAAAAAGAAAA
* *
33987550 AAAATACGAAATTA
1 AAAAAAAGAAA--A
*
33987564 AAAAAAA-AAGA
1 AAAAAAAGAAAA
33987575 AAAAAAAG
1 AAAAAAAG
33987583 TGAAGATCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
11 8 0.16
12 12 0.24
13 9 0.18
14 10 0.20
15 7 0.14
16 3 0.06
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:33987560 original size:23 final size:23
Alignment explanation
Indices: 33987510--33987579 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 23
33987500 TTGAAGTATT
* *
33987510 AAAAAAAGAAAACAAAAAAAGGAGG
1 AAAAAAA-AAAA-AAAAAAAAGACG
* *
33987535 AAAAAAAAAAGAAAAAAAATACG
1 AAAAAAAAAAAAAAAAAAAGACG
33987558 AAATTAAAAAAAAAAGAAAAAA
1 AAA--AAAAAAAAAA-AAAAAA
33987580 AAGTGAAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
23 12 0.32
24 3 0.08
25 16 0.43
26 6 0.16
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAAGACG
Found at i:33989662 original size:21 final size:21
Alignment explanation
Indices: 33989636--33989676 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33989626 AGAAAGTGAA
*
33989636 AATGAAAATGAAAGAAAAGAG
1 AATGAAAAAGAAAGAAAAGAG
33989657 AATGAAAAAGAAAGAAAAGA
1 AATGAAAAAGAAAGAAAAGA
33989677 ACATGGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
AATGAAAAAGAAAGAAAAGAG
Found at i:33991038 original size:13 final size:13
Alignment explanation
Indices: 33991020--33991054 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
33991010 ATTATATGAA
*
33991020 TAATTATTTTATT
1 TAATTATGTTATT
33991033 TAATTATGTTATT
1 TAATTATGTTATT
33991046 TAATTATGT
1 TAATTATGT
33991055 AGGTTAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:33994027 original size:46 final size:46
Alignment explanation
Indices: 33993959--33994129 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
33993949 AACCCGCCCC
*
33993959 TAAGTGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
33994004 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACATCCA
* * * * * *
33994052 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
33994097 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
33994130 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 12 0.11
46 47 0.45
47 27 0.26
48 3 0.03
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
Found at i:33994075 original size:93 final size:92
Alignment explanation
Indices: 33993964--33994133 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
33993954 GCCCCTAAGT
* *
33993964 GAACTCGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
33994029 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* * *
33994056 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTC-GACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
33994121 CGAGTTCGGATGC
65 CGAGTTCGGATGC
33994134 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 6 0.08
93 66 0.92
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:33997550 original size:15 final size:15
Alignment explanation
Indices: 33997530--33997577 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
33997520 TCAAAGATGG
33997530 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
33997545 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
33997559 GTTTATGGATATAAA
1 GTTTATGGATATGAA
33997574 GTTT
1 GTTT
33997578 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:33997564 original size:14 final size:14
Alignment explanation
Indices: 33997524--33997567 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33997514 AAGGATTCAA
33997524 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
33997538 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
33997553 AGATGGGTTTATGG
1 AGATGGGTTTATGG
33997567 A
1 A
33997568 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:33997593 original size:29 final size:29
Alignment explanation
Indices: 33997524--33997583 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
33997514 AAGGATTCAA
*
33997524 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
33997553 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
33997582 AG
1 AG
33997584 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:34001649 original size:6 final size:5
Alignment explanation
Indices: 34001625--34001687 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
34001615 AAGAGAAAAC
*
34001625 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
34001673 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
34001688 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:34001655 original size:12 final size:10
Alignment explanation
Indices: 34001625--34001687 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
34001615 AAGAGAAAAC
34001625 AAAGAAAAGA
1 AAAGAAAAGA
34001635 AAAGAAAAAGCA
1 AAAG-AAAAG-A
34001647 AAAGCAAAAGA
1 AAAG-AAAAGA
*
34001658 AGA-AAAAGA
1 AAAGAAAAGA
34001667 AAATGAAATA-A
1 AAA-GAAA-AGA
34001678 AAAGAAAAGA
1 AAAGAAAAGA
34001688 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:34001767 original size:11 final size:12
Alignment explanation
Indices: 34001735--34001765 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
34001725 TTGAGAGAAC
34001735 TTGAAAAAGCCT
1 TTGAAAAAGCCT
34001747 TTGAAAAAGCCT
1 TTGAAAAAGCCT
34001759 TTGAAAA
1 TTGAAAA
34001766 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:34001776 original size:12 final size:12
Alignment explanation
Indices: 34001768--34001792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34001758 TTTGAAAAGC
34001768 AAAAAGAAAATG
1 AAAAAGAAAATG
34001780 AAAAAGAAAATG
1 AAAAAGAAAATG
34001792 A
1 A
34001793 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:34001789 original size:18 final size:18
Alignment explanation
Indices: 34001762--34001817 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
34001752 AAAGCCTTTG
*
34001762 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
34001781 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
34001799 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
34001816 AA
1 AA
34001818 TTTGAGAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:34001802 original size:30 final size:31
Alignment explanation
Indices: 34001768--34001849 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
34001758 TTTGAAAAGC
**
34001768 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGAG
* *
34001798 AAAAAGAGAATG-AAAAGAAATTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGAG
**
34001828 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
34001850 TGAAAAAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGAG
Found at i:34001844 original size:12 final size:12
Alignment explanation
Indices: 34001827--34001881 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
34001817 ATTTGAGAGA
*
34001827 GAAAAAGAAGTT
1 GAAAAAGAAATT
34001839 GAAAAAGAAATT
1 GAAAAAGAAATT
*
34001851 GAAAAAGAGATT
1 GAAAAAGAAATT
*
34001863 ACAGAGAAAGAAATT
1 ---GAAAAAGAAATT
34001878 GAAA
1 GAAA
34001882 TAAAAGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 25 0.71
15 10 0.29
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.15
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:34004017 original size:30 final size:30
Alignment explanation
Indices: 34003981--34004077 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
34003971 AGCTCACTCC
*
34003981 TAGCTCATA-TTCAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
34004011 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
34004041 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
34004071 TAGCTCA
1 TAGCTCA
34004078 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:34004694 original size:10 final size:10
Alignment explanation
Indices: 34004678--34004735 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
34004668 CAACTCCGAC
34004678 CAGCTCAATT
1 CAGCTCAATT
* *
34004688 GAGCTCATTT
1 CAGCTCAATT
34004698 CAGCTCAA-T
1 CAGCTCAATT
34004707 CGAGCTCAATT
1 C-AGCTCAATT
*
34004718 TAGCTACAATT
1 CAGCT-CAATT
34004729 CAGCTCA
1 CAGCTCA
34004736 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:34004701 original size:20 final size:20
Alignment explanation
Indices: 34004678--34004738 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
34004668 CAACTCCGAC
34004678 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
34004698 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
34004719 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
34004739 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:34007098 original size:13 final size:15
Alignment explanation
Indices: 34007080--34007112 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34007070 TTGGAGTAAC
34007080 AAAAAAA-TC-AAAA
1 AAAAAAATTCGAAAA
34007093 AAAAAAATTCGAAAA
1 AAAAAAATTCGAAAA
34007108 AAAAA
1 AAAAA
34007113 TTGATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAAAATTCGAAAA
Found at i:34007113 original size:13 final size:13
Alignment explanation
Indices: 34007091--34007139 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
34007081 AAAAAATCAA
34007091 AAAAAAAAATTCG
1 AAAAAAAAATTCG
34007104 AAAAAAAAATT-G
1 AAAAAAAAATTCG
34007116 ATTGAAAAAAAATTC-
1 A---AAAAAAAATTCG
34007131 AAAAAAAAA
1 AAAAAAAAA
34007140 GTGAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.31
13 11 0.34
15 11 0.34
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:34007146 original size:12 final size:12
Alignment explanation
Indices: 34007091--34007147 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 12
34007081 AAAAAATCAA
34007091 AAAAAAAAATTCG
1 AAAAAAAAATT-G
34007104 AAAAAAAAATTG
1 AAAAAAAAATTG
*
34007116 ATTGAAAAAAAATTC
1 A---AAAAAAAATTG
*
34007131 AAAAAAAAAGTG
1 AAAAAAAAATTG
34007143 AAAAA
1 AAAAA
34007148 GAATCGAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 16 0.42
13 11 0.29
15 11 0.29
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:34008096 original size:18 final size:18
Alignment explanation
Indices: 34008075--34008109 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34008065 AGAAAAGAAA
34008075 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
34008093 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
34008110 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:34010191 original size:10 final size:10
Alignment explanation
Indices: 34010175--34010232 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
34010165 CAACTCCGAC
34010175 CAGCTCAATT
1 CAGCTCAATT
* *
34010185 GAGCTCATTT
1 CAGCTCAATT
34010195 CAGCTCAA-T
1 CAGCTCAATT
34010204 CGAGCTCAATT
1 C-AGCTCAATT
*
34010215 TAGCTACAATT
1 CAGCT-CAATT
34010226 CAGCTCA
1 CAGCTCA
34010233 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:34010198 original size:20 final size:20
Alignment explanation
Indices: 34010175--34010235 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
34010165 CAACTCCGAC
34010175 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
34010195 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
34010216 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
34010236 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:34014795 original size:19 final size:18
Alignment explanation
Indices: 34014773--34014810 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
34014763 GCTATATTCA
34014773 AGCT-AAGTCTGAGCTCGAG
1 AGCTGAAGT-TGAGCT-GAG
34014792 AGCTGAAGTTGAGCTGAG
1 AGCTGAAGTTGAGCTGAG
34014810 A
1 A
34014811 ATAAGCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (18 bp):
AGCTGAAGTTGAGCTGAG
Found at i:34014854 original size:20 final size:20
Alignment explanation
Indices: 34014829--34014878 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
34014819 ATGAGCTAGA
**
34014829 GTTGAGCTGGAGTTGAGCTC
1 GTTGAGCTGGAACTGAGCTC
*
34014849 GTTGAGCTGGAACTGAGCTT
1 GTTGAGCTGGAACTGAGCTC
*
34014869 GCTGAGCTGG
1 GTTGAGCTGG
34014879 TTGCGAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.28
Consensus pattern (20 bp):
GTTGAGCTGGAACTGAGCTC
Found at i:34016742 original size:17 final size:17
Alignment explanation
Indices: 34016709--34016752 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
34016699 GCAAGCGAGA
34016709 AAAAAAGAAGACAAAAAG
1 AAAAAAG-AGACAAAAAG
34016727 AAAAAAGAGATC-AAAAG
1 AAAAAAGAGA-CAAAAAG
*
34016744 AAAAGAGAG
1 AAAAAAGAG
34016753 GCAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAAGAGACAAAAAG
Found at i:34016817 original size:21 final size:21
Alignment explanation
Indices: 34016793--34016860 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
34016783 GATTTTGAAT
34016793 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
34016814 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
34016835 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
34016856 GAAAT
1 GAAAT
34016861 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:34016818 original size:42 final size:42
Alignment explanation
Indices: 34016771--34016867 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
34016761 AGATTATGAG
* * *
34016771 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
34016813 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
34016855 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
34016868 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:34016894 original size:18 final size:18
Alignment explanation
Indices: 34016871--34016932 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
34016861 GAAAGAAAAA
*
34016871 GAAAAAGAGAGTGAGAGT
1 GAAAAAGAGAATGAGAGT
* * *
34016889 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAGAATGAGAGT
** *
34016907 GAAAAAGAGTTTGAGAGA
1 GAAAAAGAGAATGAGAGT
34016925 GAAAAAGA
1 GAAAAAGA
34016933 ATGTGAACAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.31, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:34016911 original size:36 final size:36
Alignment explanation
Indices: 34016862--34016933 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
34016852 CAAAGAAATG
*
34016862 AAAGAAAAAGAAAAAGAGAGTGAGAGTGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
* * **
34016898 AAAGAGAATGAAAAAGAGTTTGAGAGAGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
34016934 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (36 bp):
AAAGAAAAAGAAAAAGAGAGTGAGAGAGAAAAAGAA
Found at i:34018576 original size:20 final size:20
Alignment explanation
Indices: 34018553--34018600 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
34018543 AGCTCCGTCC
34018553 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
34018573 AGCTCGTTTTAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
34018593 AGCTCAAC
1 AGCTCAAC
34018601 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:34027997 original size:13 final size:13
Alignment explanation
Indices: 34027979--34028007 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34027969 GATCACCTTT
34027979 TCGAGATTGATTC
1 TCGAGATTGATTC
34027992 TCGAGATTGATTC
1 TCGAGATTGATTC
34028005 TCG
1 TCG
34028008 GTGGACTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (13 bp):
TCGAGATTGATTC
Found at i:34028212 original size:20 final size:20
Alignment explanation
Indices: 34028181--34028235 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
34028171 AGCTCTGTCC
34028181 AGCTCAAATCCAGCTTATTCG
1 AGCTC-AATCCAGCTTATTCG
* * *
34028202 AGCTCAATCCAACTTGTTTG
1 AGCTCAATCCAGCTTATTCG
* *
34028222 AGCTAAATCGAGCT
1 AGCTCAATCCAGCT
34028236 CACTCCTATC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (20 bp):
AGCTCAATCCAGCTTATTCG
Found at i:34030817 original size:22 final size:22
Alignment explanation
Indices: 34030789--34030832 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34030779 TTTTGAACCA
34030789 TTACCATTTCGTAACAAATCCC
1 TTACCATTTCGTAACAAATCCC
* *
34030811 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTAACAAATCCC
34030833 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTAACAAATCCC
Found at i:34031161 original size:13 final size:13
Alignment explanation
Indices: 34031131--34031171 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
34031121 ATAGGTACGT
*
34031131 AAAAAAAAGAGTTCG
1 AAAAAAAA-AATT-G
34031146 AAAAAAAAAATTG
1 AAAAAAAAAATTG
34031159 AAAAAAAAAATTG
1 AAAAAAAAAATTG
34031172 CATACGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 14 0.56
14 3 0.12
15 8 0.32
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:34033451 original size:20 final size:20
Alignment explanation
Indices: 34033426--34033468 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34033416 AAAAGAAAAG
34033426 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
34033446 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
34033466 AAA
1 AAA
34033469 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:34035796 original size:22 final size:22
Alignment explanation
Indices: 34035768--34035811 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34035758 TTTTGAACCA
34035768 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
34035790 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
34035812 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:34039187 original size:22 final size:21
Alignment explanation
Indices: 34039144--34039187 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
34039134 AGAAAGTTGT
* * *
34039144 AAAAAAATAAAAGAAGAGAAA
1 AAAAAAAAAAAAGAAAACAAA
34039165 AAAAAAGAAAAAAGAAAACAAA
1 AAAAAA-AAAAAAGAAAACAAA
34039187 A
1 A
34039188 GAGAGTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAAGAAAACAAA
Found at i:34042645 original size:30 final size:30
Alignment explanation
Indices: 34042611--34042707 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
34042601 AGCTCACTCC
34042611 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
34042641 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
34042671 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
34042701 TAGCTCA
1 TAGCTCA
34042708 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:34048075 original size:28 final size:28
Alignment explanation
Indices: 34048042--34048124 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
34048032 GATAACAAGA
*
34048042 AAACCGAATAAAGAAATCCAAGATAGAG
1 AAACCGAATAAAGAAATCCAAGATAAAG
34048070 AAACCGAATAAAGAAATCC-AGAATAAAG
1 AAACCGAATAAAGAAATCCAAG-ATAAAG
* * *
34048098 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACC-GAATAAAGAAATCCAAGATA
34048125 CGATACTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.04
28 25 0.53
29 3 0.06
30 15 0.32
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.11
Consensus pattern (28 bp):
AAACCGAATAAAGAAATCCAAGATAAAG
Found at i:34048095 original size:15 final size:15
Alignment explanation
Indices: 34048038--34048115 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
34048028 CAAAGATAAC
*
34048038 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
34048052 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
34048067 GAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
34048080 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
34048095 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
34048110 AAGAAA
1 AAGAAA
34048116 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 8 0.15
14 14 0.26
15 31 0.58
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:34048124 original size:15 final size:15
Alignment explanation
Indices: 34048049--34048124 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
34048039 AGAAAACCGA
34048049 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
34048064 ATAGAGAAA-CCGA-
1 ATAAAGAAATCCAAG
34048077 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
34048091 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
34048107 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
34048122 ATA
1 ATA
34048125 CGATACTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
13 9 0.18
14 5 0.10
15 34 0.69
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:34052498 original size:12 final size:12
Alignment explanation
Indices: 34052481--34052522 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
34052471 ATACAAGTAT
34052481 AAAAAAATTCAA
1 AAAAAAATTCAA
*
34052493 AAAAAAATTCGGA
1 AAAAAAATTC-AA
*
34052506 AAAAAAATTTAA
1 AAAAAAATTCAA
34052518 AAAAA
1 AAAAA
34052523 TGATTTGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:34060649 original size:30 final size:30
Alignment explanation
Indices: 34060615--34060711 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
34060605 TAAACTAAAA
34060615 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * **
34060645 TGAGCTGAGGC-TAAACTCCTAAGCCGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
34060675 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
34060705 TGAGCTA
1 TGAGCTA
34060712 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Done.