Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 47 of 213
Found at i:12708806 original size:26 final size:26
Alignment explanation
Indices: 12708777--12708836 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
12708767 TTTACTTTGA
12708777 TTGA-TTTCTCTTTTTTGCTTTTGAC-T
1 TTGATTTTCT-TTTTTTGCTTTTG-CTT
*
12708803 TTGATTTTCTTTTTTTGTTTTTGCTT
1 TTGATTTTCTTTTTTTGCTTTTGCTT
12708829 TTGATTTT
1 TTGATTTT
12708837 GAGTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 1 0.03
26 25 0.81
27 5 0.16
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.72
Consensus pattern (26 bp):
TTGATTTTCTTTTTTTGCTTTTGCTT
Found at i:12708828 original size:32 final size:31
Alignment explanation
Indices: 12708788--12708848 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
12708778 TGATTTCTCT
*
12708788 TTTTTGCTTTTGACTTTGATTTTCTTTTTTTG
1 TTTTTGCTTTTGACTTTGAGTTT-TTTTTTTG
*
12708820 TTTTTGCTTTTGATTTTGAGTTTTTTTTT
1 TTTTTGCTTTTGACTTTGAGTTTTTTTTT
12708849 ACTGAACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.74
Consensus pattern (31 bp):
TTTTTGCTTTTGACTTTGAGTTTTTTTTTTG
Found at i:12708843 original size:26 final size:26
Alignment explanation
Indices: 12708788--12708848 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
12708778 TGATTTCTCT
* **
12708788 TTTTTGCTTTTGACTTTGATTTTCTT
1 TTTTTGTTTTTGACTTTGATTTTCAG
*
12708814 TTTTTGTTTTTG-CTTTTGATTTTGAG
1 TTTTTGTTTTTGAC-TTTGATTTTCAG
12708840 TTTTT-TTTT
1 TTTTTGTTTT
12708849 ACTGAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.74
Consensus pattern (26 bp):
TTTTTGTTTTTGACTTTGATTTTCAG
Found at i:12719773 original size:20 final size:20
Alignment explanation
Indices: 12719736--12719773 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12719726 TCCCCCCAAA
**
12719736 TCTTTTTCTTTTCATTTTTT
1 TCTTTTTCTCCTCATTTTTT
12719756 TCTTTTTCTCCTC-TTTTT
1 TCTTTTTCTCCTCATTTTT
12719774 GCTGTCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTTTCTCCTCATTTTTT
Found at i:12730476 original size:23 final size:25
Alignment explanation
Indices: 12730446--12730497 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
12730436 TATCAGATTT
*
12730446 TATAAAATAT-ATTTGT-CCAAATA
1 TATAAAATATAATTTATACCAAATA
*
12730469 TATAAAATATAATTTATATCAAATA
1 TATAAAATATAATTTATACCAAATA
12730494 TATA
1 TATA
12730498 GAAAAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
TATAAAATATAATTTATACCAAATA
Found at i:12733011 original size:22 final size:22
Alignment explanation
Indices: 12732983--12733025 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12732973 AATATACATT
12732983 CTTAATGATCTAAGAAAGGTTG
1 CTTAATGATCTAAGAAAGGTTG
* *
12733005 CTTAATGATGTAAGAAGGGTT
1 CTTAATGATCTAAGAAAGGTT
12733026 ACTAGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (22 bp):
CTTAATGATCTAAGAAAGGTTG
Found at i:12735620 original size:113 final size:113
Alignment explanation
Indices: 12735492--12735706 Score: 324
Period size: 113 Copynumber: 1.9 Consensus size: 113
12735482 ATTTTTCAGA
* * *
12735492 TCATTTTTATTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTCTCCATTTTCGTTTTC
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTCTCCA-TTTCATTTTC
*
12735557 ATTTTGGAGAAAATCGTAATAATTTCCAAATG-TTTCCACTTGTCCATT
65 ATTTTGGAGAAAATCATAATAATTTCCAAATGATTTCCACTTGTCCATT
* * *
12735605 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTATTTCTCCATTTCATTTTCA
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTCTCCATTTCATTTTCA
* * *
12735670 TTTTGTAGAAAATCATAATCATTTCTAAATGATTTCC
66 TTTTGGAGAAAATCATAATAATTTCCAAATGATTTCC
12735707 TATTTCTCCA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 37 0.41
113 54 0.59
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (113 bp):
TCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTCTCCATTTCATTTTCA
TTTTGGAGAAAATCATAATAATTTCCAAATGATTTCCACTTGTCCATT
Found at i:12735638 original size:56 final size:56
Alignment explanation
Indices: 12735492--12735719 Score: 303
Period size: 56 Copynumber: 4.0 Consensus size: 56
12735482 ATTTTTCAGA
* * * *
12735492 TCATTTTTATTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTCTCCA-TT
* * * * * *
12735549 TCGTTTTCATTTTGGAGAAAATCGTAATAATTTCCAAATGTTTCCACTTGTCCATT
1 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTCTCCATT
*
12735605 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTATTTCTCCATT
1 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTCTCCATT
* * *
12735661 TCATTTTCATTTTGTAGAAAATCATAATCATTTCTAAATGATTTCCTATTTCTCCATT
1 TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATG-TTTCC-ATTTCTCCATT
12735719 T
1 T
12735720 TCACCAATTT
Statistics
Matches: 148, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
56 88 0.59
57 48 0.32
58 12 0.08
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (56 bp):
TCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTCTCCATT
Found at i:12737209 original size:102 final size:103
Alignment explanation
Indices: 12737082--12737287 Score: 333
Period size: 103 Copynumber: 2.0 Consensus size: 103
12737072 TTAGTTACTA
* * * *
12737082 AATCTCTTTAGTTGTTTGAAAGTTAGTTTCTAATGATAATAGC-AAAAAAACTAGCATACATTGG
1 AATCTCTCTAGTTGTTTGAAAGTTAGTTCCTAATGACAATAGCAAAAAAAACTAGCATACATTGA
* *
12737146 ATCTGAAGAAGAGGCTCGGAGACTACCTTTTTCTAGCC
66 ATCTGAAGAAGAGGCTCAGAGACTACATTTTTCTAGCC
* *
12737184 AATCTCTCTAGTTGTTTGAAAGTTAGTTCCTAGTGGCAATAGCAAAAAAAACTAGCATACATTGA
1 AATCTCTCTAGTTGTTTGAAAGTTAGTTCCTAATGACAATAGCAAAAAAAACTAGCATACATTGA
12737249 ATCTGAAGAAGAGGCTCAGAGACTACATTTTTCTAGCC
66 ATCTGAAGAAGAGGCTCAGAGACTACATTTTTCTAGCC
12737287 A
1 A
12737288 GGTTGGATGT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 38 0.40
103 57 0.60
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (103 bp):
AATCTCTCTAGTTGTTTGAAAGTTAGTTCCTAATGACAATAGCAAAAAAAACTAGCATACATTGA
ATCTGAAGAAGAGGCTCAGAGACTACATTTTTCTAGCC
Found at i:12743261 original size:25 final size:25
Alignment explanation
Indices: 12743201--12743271 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
12743191 AGGGTTATCG
* *
12743201 ATTCTAGCTCTTATAAGCTTATCGAT
1 ATTC-AGCTCGTATGAGCTTATCGAT
* * *
12743227 ACTCATCTCGTATGAGCTTATCGTT
1 ATTCAGCTCGTATGAGCTTATCGAT
* *
12743252 ATTCAGCTCGGAGGAGCTTA
1 ATTCAGCTCGTATGAGCTTA
12743272 CATTTTATAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 33 0.92
26 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (25 bp):
ATTCAGCTCGTATGAGCTTATCGAT
Found at i:12743478 original size:28 final size:28
Alignment explanation
Indices: 12743412--12743479 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
12743402 ATATGAATTT
**
12743412 GATACATGGAAATGGTTTATATATATGT
1 GATACATGGAAATGGTTTATATATATAA
12743440 GAATTACATGGAAATGGTTTATATATATAA
1 G-A-TACATGGAAATGGTTTATATATATAA
*
12743470 GATATATGGA
1 GATACATGGA
12743480 TACATGGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.23
29 2 0.06
30 25 0.71
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (28 bp):
GATACATGGAAATGGTTTATATATATAA
Found at i:12743487 original size:30 final size:30
Alignment explanation
Indices: 12743414--12743471 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
12743404 ATGAATTTGA
**
12743414 TACATGGAAATGGTTTATATATATGTGAAT
1 TACATGGAAATGGTTTATATATATAAGAAT
12743444 TACATGGAAATGGTTTATATATATAAGA
1 TACATGGAAATGGTTTATATATATAAGA
12743472 TATATGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (30 bp):
TACATGGAAATGGTTTATATATATAAGAAT
Found at i:12759603 original size:24 final size:25
Alignment explanation
Indices: 12759554--12759604 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
12759544 ACCCTTCTCA
* *
12759554 TTTCTTCACTTCTCTCTCATTTTTC
1 TTTCTTCACTTCCCTCTCATTGTTC
12759579 TTTCTTCA-TTCCCT-TCCATTGTTC
1 TTTCTTCACTTCCCTCT-CATTGTTC
12759603 TT
1 TT
12759605 CATTTTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.61
25 8 0.35
ACGTcount: A:0.08, C:0.31, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTCTTCACTTCCCTCTCATTGTTC
Found at i:12759856 original size:20 final size:18
Alignment explanation
Indices: 12759823--12759859 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
12759813 TGTGATGTTG
12759823 ATATGTTTAATTTAATTA
1 ATATGTTTAATTTAATTA
12759841 ATATGTCTTAAATTTAATT
1 ATATGT-TT-AATTTAATT
12759860 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATGTTTAATTTAATTA
Found at i:12763713 original size:13 final size:12
Alignment explanation
Indices: 12763690--12763727 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
12763680 TTTTAAAAAT
12763690 AAAAA-ATTTTA
1 AAAAATATTTTA
12763701 AAAAAGTATTTT-
1 AAAAA-TATTTTA
12763713 AAAAATATTTTA
1 AAAAATATTTTA
12763725 AAA
1 AAA
12763728 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.46
12 8 0.33
13 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
AAAAATATTTTA
Found at i:12763744 original size:40 final size:41
Alignment explanation
Indices: 12763672--12763753 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 41
12763662 ATAAACACCA
** *
12763672 AAAAATTATTTTAAAAATAAAAAATTTTAAAAAAGTAT-TTT
1 AAAAATTATTTTAAAAATAAAAAA-TAAAAAAAAATATATTT
12763713 AAAAA-TATTTT-AAAATAAAAAATAAAAAAAAAATATATTT
1 AAAAATTATTTTAAAAATAAAAAAT-AAAAAAAAATATATTT
12763753 A
1 A
12763754 TTATATTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.03
39 20 0.56
40 10 0.28
41 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (41 bp):
AAAAATTATTTTAAAAATAAAAAATAAAAAAAAATATATTT
Found at i:12763798 original size:5 final size:6
Alignment explanation
Indices: 12763772--12763797 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12763762 AGGTCGGGTC
12763772 GGGCCG GGGCCG GGGCCG GGGCCG GG
1 GGGCCG GGGCCG GGGCCG GGGCCG GG
12763798 CCAAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.69, T:0.00
Consensus pattern (6 bp):
GGGCCG
Found at i:12764281 original size:17 final size:17
Alignment explanation
Indices: 12764255--12764295 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12764245 ATTATGTGAA
12764255 TTTAAA-ATTTAT-ATAT
1 TTTAAATATTTATAAT-T
*
12764271 TTTAAATATTTTTAATT
1 TTTAAATATTTATAATT
12764288 TTTAAATA
1 TTTAAATA
12764296 CAAGTTGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 14 0.64
18 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATATTTATAATT
Found at i:12769030 original size:12 final size:13
Alignment explanation
Indices: 12769009--12769041 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12768999 AATAAACATC
*
12769009 TACAAATAT-ATA
1 TACAAGTATAATA
12769021 TACAAGTATAATA
1 TACAAGTATAATA
12769034 TACAAGTA
1 TACAAGTA
12769042 AATTTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (13 bp):
TACAAGTATAATA
Found at i:12770529 original size:16 final size:17
Alignment explanation
Indices: 12770508--12770543 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12770498 TTTTTGTTTT
*
12770508 TTTGGGC-TAGGTTTGG
1 TTTGGGCTTAGGTTTAG
12770524 TTTGGGCTTAGGTTTAG
1 TTTGGGCTTAGGTTTAG
12770541 TTT
1 TTT
12770544 ATTGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.08, C:0.06, G:0.36, T:0.50
Consensus pattern (17 bp):
TTTGGGCTTAGGTTTAG
Found at i:12771073 original size:44 final size:44
Alignment explanation
Indices: 12771007--12771367 Score: 187
Period size: 44 Copynumber: 8.2 Consensus size: 44
12770997 CTGTAACCTC
* * ** *
12771007 AGGGAGGTAAAATCTGCCATCTTCAATTTACTCCACTACTGCCT
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * ** *
12771051 AGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * *
12771095 AGGGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTA-TAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACT-GCCT
* * **** ** * *
12771138 CAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * *
12771183 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
* * * * * **
12771227 AGGGAGAT-AGA-AT-TACTGGCTTCAATATACTCCGCTGCAACCT
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTACTGCCT
* * ** * * *
12771270 CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
** * * * *
12771315 AAAGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCAT
1 AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
12771359 AGGGAGATA
1 AGGGAGATA
12771368 GAATTACTGG
Statistics
Matches: 223, Mismatches: 80, Indels: 28
0.67 0.24 0.08
Matches are distributed among these distances:
41 6 0.03
42 3 0.01
43 40 0.18
44 134 0.60
45 36 0.16
46 2 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTACTGCCT
Found at i:12771216 original size:132 final size:132
Alignment explanation
Indices: 12770979--12772144 Score: 1712
Period size: 132 Copynumber: 8.8 Consensus size: 132
12770969 GATATAGGAT
* ** * *
12770979 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCAATTTACTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* * * * *
12771044 ACTGCCTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCCCAGGG-AGATAGAAT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAAT
12771108 TAC
130 TAC
* *
12771111 TGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* *
12771176 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAAT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAAT
12771240 TAC
130 TAC
* * * * *
12771243 TGGCTTCAATATACTCCGCTGCAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
** * * * **
12771308 ACTGCTTAAAGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCATAGGG-AGATAGAAT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAAT
12771372 TAC
130 TAC
*
12771375 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* *
12771440 ACTGCTTAGGGAGACAAGATCTAAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
12771505 AC
131 AC
* * *
12771507 TGGCTTCAATGTACTCCACTGCAACCTCAAGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* * * * *
12771572 ACTGCTTAGGGAGACAAGATCTAAAATCTTTAATTTATTCCACTGCTGCCTAGGGAAATAGAATT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
12771637 AC
131 AC
* * *
12771639 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* *
12771704 ACTGCTTGGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGAGAAGTAGAATT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
12771769 AC
131 AC
* * *
12771771 TGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCCTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* * * *
12771836 ACTGCTTAGGCAGACAAGATCTAAAATCTTTAATCTATTCCACTGCTGCCCAGGAAAGTAGAATT
66 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
12771901 AC
131 AC
* * * *
12771903 TGGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
12771968 ACTGCTT-GGGAAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
66 ACTGCTTAGGG-AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
12772032 TAC
130 TAC
* * * * *
12772035 TGGTTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATTCGACATCCTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
* *
12772100 ACTGGTTAGGGAGACAAGATCTAAAATCTTTC-ATCTATTCCACTG
66 ACTGCTTAGGGAGACAAGATCTGAAATC-TTCAATCTATTCCACTG
12772145 TCTCCGAGGG
Statistics
Matches: 941, Mismatches: 89, Indels: 8
0.91 0.09 0.01
Matches are distributed among these distances:
131 2 0.00
132 931 0.99
133 8 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (132 bp):
TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACT
ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
AC
Found at i:12778159 original size:12 final size:13
Alignment explanation
Indices: 12778138--12778170 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12778128 GATAAACATT
*
12778138 TACAAATAT-ATA
1 TACAAGTATAATA
12778150 TACAAGTATAATA
1 TACAAGTATAATA
12778163 TACAAGTA
1 TACAAGTA
12778171 AATTTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (13 bp):
TACAAGTATAATA
Found at i:12779666 original size:16 final size:17
Alignment explanation
Indices: 12779645--12779680 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12779635 TTTTTGTTTT
*
12779645 TTTGGGC-TAGGTTTGG
1 TTTGGGCTTAGGTTTAG
12779661 TTTGGGCTTAGGTTTAG
1 TTTGGGCTTAGGTTTAG
12779678 TTT
1 TTT
12779681 ATTGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.08, C:0.06, G:0.36, T:0.50
Consensus pattern (17 bp):
TTTGGGCTTAGGTTTAG
Found at i:12780368 original size:42 final size:40
Alignment explanation
Indices: 12780290--12780368 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
12780280 AAAATTTATG
* *
12780290 TTTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAAGTCAT
1 TTTTTAGCGGCGTTTGTGAAAAAGCGCCACTAAAAGTCAT
12780330 TTTTATAGCGGCGTTTGT-AATATAAGCGCCACTAAAAGT
1 TTTT-TAGCGGCGTTTGTGAA-A-AAGCGCCACTAAAAGT
12780369 TATGACCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 6 0.18
41 14 0.41
42 14 0.41
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTGTGAAAAAGCGCCACTAAAAGTCAT
Found at i:12780434 original size:43 final size:42
Alignment explanation
Indices: 12780386--12780642 Score: 266
Period size: 43 Copynumber: 6.0 Consensus size: 42
12780376 TATAGTGGTG
* * *
12780386 TTTGTGGTAGAAGTGCCGCTAAAGGTCATGGTATTTAGCGGCA
1 TTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
* **
12780429 TTTGTGGGAAAAGCGCCGATAAAGGTCATGGTCTTTAGCCGGTG
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAG-CGGCA
* *
12780473 TTTGTCGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCG
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
* * *
12780516 CTAGTGGGAAAAGCGCCGCTAAAGGTCATGGTCGTTAGCGGCA
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
**
12780559 TTTGTAGG-ATTGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
1 TTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
* ** * *
12780601 CTTTTTCCACAAA-CGCCGTTAAAGGTCATGATCTTTAGCGGC
1 -TTTGTGGA-AAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGC
12780643 GTTTTTTGTG
Statistics
Matches: 180, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.17
43 107 0.59
44 42 0.23
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (42 bp):
TTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA
Found at i:12780496 original size:87 final size:86
Alignment explanation
Indices: 12780382--12780639 Score: 281
Period size: 87 Copynumber: 3.0 Consensus size: 86
12780372 GACCTATAGT
* * *
12780382 GGTGTTTGTGGTAGAAGTGCCGCTAAAGGTCATGGTATTTAGCGGCATTTGTGGGAAAAGCGCCG
1 GGTGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGGAAAAGCGCCG
12780447 ATAAAGGTCATGGTCTTTAGCC
65 ATAAAGGTCATGGTCTTTAGCC
* ** *
12780469 GGTGTTTGTCGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGCTAGTGGGAAAAGCGCCG
1 GGTGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGGAAAAGCGCCG
* *
12780534 CTAAAGGTCATGGTCGTTAG-C
65 ATAAAGGTCATGGTCTTTAGCC
** ** ***
12780555 GGCATTTGTAGG-ATTGCGCCGCTAAAGGTCATGGTCTTTAGCGGCACTTT-TTCCACAAA-CGC
1 GGTGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCA-TTTGTGGGA-AAAGCGC
* *
12780617 CGTTAAAGGTCATGATCTTTAGC
63 CGATAAAGGTCATGGTCTTTAGC
12780640 GGCGTTTTTT
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
85 54 0.38
86 14 0.10
87 73 0.51
88 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (86 bp):
GGTGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTGGGAAAAGCGCCGA
TAAAGGTCATGGTCTTTAGCC
Found at i:12780624 original size:85 final size:86
Alignment explanation
Indices: 12780400--12780642 Score: 285
Period size: 85 Copynumber: 2.8 Consensus size: 86
12780390 TGGTAGAAGT
*
12780400 GCCGCTAAAGGTCATGGTATTTAGCGGCA-TTTGTGGGAAAAGCGCCGATAAAGGTCATGGTCTT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCACTTT-TGGGAAAAGCGCCGATAAAGGTCATGGTCTT
** *
12780464 TAGCCGGTGTTTGTCGGAAAAGC
65 TAG-CGGCATTTGTAGGAAAAGC
* * ** * *
12780487 GCCGCTAAAGGTCATGGTCTTTAGTGGCGCTAGTGGGAAAAGCGCCGCTAAAGGTCATGGTCGTT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCACTTTTGGGAAAAGCGCCGATAAAGGTCATGGTCTTT
**
12780552 AGCGGCATTTGTAGG-ATTGC
66 AGCGGCATTTGTAGGAAAAGC
*** * *
12780572 GCCGCTAAAGGTCATGGTCTTTAGCGGCACTTTTTCCACAAA-CGCCGTTAAAGGTCATGATCTT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCACTTTTGGGA-AAAGCGCCGATAAAGGTCATGGTCTT
12780636 TAGCGGC
65 TAGCGGC
12780643 GTTTTTTGTG
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
85 60 0.45
86 13 0.10
87 58 0.44
88 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (86 bp):
GCCGCTAAAGGTCATGGTCTTTAGCGGCACTTTTGGGAAAAGCGCCGATAAAGGTCATGGTCTTT
AGCGGCATTTGTAGGAAAAGC
Found at i:12781804 original size:3 final size:3
Alignment explanation
Indices: 12781796--12781851 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
12781786 ATGAGGTAAG
12781796 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12781844 TAT TAT TA
1 TAT TAT TA
12781852 AGATGAGTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12789606 original size:3 final size:3
Alignment explanation
Indices: 12789598--12789629 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12789588 ATGAGGTAAG
*
12789598 TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12789630 AGATGAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12793561 original size:23 final size:23
Alignment explanation
Indices: 12793535--12793583 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12793525 TATTTATTTT
*
12793535 TTAAAAAATAATTAATTAAAA-TA
1 TTAAAAAAT-ATTAATAAAAACTA
*
12793558 TTAATAAATATTAATAAAAACTA
1 TTAAAAAATATTAATAAAAACTA
12793581 TTA
1 TTA
12793584 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAAAATATTAATAAAAACTA
Found at i:12794553 original size:43 final size:43
Alignment explanation
Indices: 12794505--12794757 Score: 247
Period size: 43 Copynumber: 5.9 Consensus size: 43
12794495 AAGTAATGAT
* * *
12794505 CTTTAGCGGCGC-TTTCCCTACAAATGTCGCTATAGACCATAAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCATAAC
*
12794548 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAAC
** ** * * * ** *
12794591 CTTTAATGGCATTTTTTCCACAAACGCCGGTAAAAACCACGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAAC
* * * * *
12794634 CTTTAACGGCACTATTCCCACAAACGCCGCTAAATACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAAC
* * *
12794677 CTTTAGCAGCGCTTTTTCGCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACCATAAC
** * *
12794721 CTTTAGCAACGCTTTTCGCGCAAACGCCGCTAAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
12794758 ATATCATACA
Statistics
Matches: 179, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
43 134 0.75
44 45 0.25
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATAAC
Found at i:12799325 original size:19 final size:17
Alignment explanation
Indices: 12799271--12799328 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
12799261 TATTAATTTT
*
12799271 AAATAAATAAATTTTGAA
1 AAATTAATAAATTTT-AA
12799289 AAATTAAGTAATATTTTAA
1 AAATTAA-TAA-ATTTTAA
12799308 AGAATTAGATAAATTTTAA
1 A-AATTA-ATAAATTTTAA
12799327 AA
1 AA
12799329 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAATTAATAAATTTTAA
Found at i:12799628 original size:10 final size:10
Alignment explanation
Indices: 12799581--12799640 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
12799571 AAAATAAAAG
12799581 TTTAAAATCTT
1 TTTAAAATC-T
* *
12799592 TTTTAAAT-A
1 TTTAAAATCT
**
12799601 TTTAAAAAAT
1 TTTAAAATCT
12799611 TTTAAAATCT
1 TTTAAAATCT
12799621 TTTAAAATTCAT
1 TTTAAAA-TC-T
12799633 TTTAAAAT
1 TTTAAAAT
12799641 TTTAAATCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 6 0.15
10 15 0.38
11 10 0.26
12 8 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:12799637 original size:12 final size:12
Alignment explanation
Indices: 12799609--12799641 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12799599 TATTTAAAAA
12799609 ATTTTAAAA-TC
1 ATTTTAAAATTC
12799620 -TTTTAAAATTC
1 ATTTTAAAATTC
12799631 ATTTTAAAATT
1 ATTTTAAAATT
12799642 TTAAATCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:12799640 original size:30 final size:30
Alignment explanation
Indices: 12799574--12799646 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
12799564 TATTATAAAA
* *
12799574 ATAAAAGTTTAAAATCTTTTTTAAATATTT
1 ATAAAATTTTAAAATCTTTTTAAAATATTT
*
12799604 AAAAAATTTTAAAATC-TTTTAAAATTCATTT
1 ATAAAATTTTAAAATCTTTTTAAAA-T-ATTT
12799635 -TAAAATTTTAAA
1 ATAAAATTTTAAA
12799647 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.19
30 26 0.70
31 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
ATAAAATTTTAAAATCTTTTTAAAATATTT
Found at i:12799643 original size:20 final size:19
Alignment explanation
Indices: 12799575--12799646 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
12799565 ATTATAAAAA
* *
12799575 TAAAAGTTTAAAATCTTTT
1 TAAAATTTTAAAATCATTT
* *
12799594 TTAAATATTTAAAA-AATTT
1 TAAAAT-TTTAAAATCATTT
12799613 TAAAATCTTTTAAAATTCATTT
1 TAAAA--TTTTAAAA-TCATTT
12799635 TAAAATTTTAAA
1 TAAAATTTTAAA
12799647 TCACGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
19 11 0.26
20 21 0.50
21 1 0.02
22 9 0.21
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (19 bp):
TAAAATTTTAAAATCATTT
Found at i:12800445 original size:21 final size:21
Alignment explanation
Indices: 12800395--12800456 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
12800385 CTAACTCGAC
12800395 CCCAAATCTCTAAACCCTAAAT
1 CCCAAA-CTCTAAACCCTAAAT
* *
12800417 CTCTAACTCTAAACCTCT-AAT
1 CCCAAACTCTAAACC-CTAAAT
12800438 CCCAAACTC-ATAACCCTAA
1 CCCAAACTCTA-AACCCTAA
12800457 TTACCCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.09
21 24 0.73
22 6 0.18
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCAAACTCTAAACCCTAAAT
Found at i:12800576 original size:7 final size:7
Alignment explanation
Indices: 12800565--12800659 Score: 50
Period size: 7 Copynumber: 13.3 Consensus size: 7
12800555 GACCCTTAAC
12800565 CCCTAAA
1 CCCTAAA
*
12800572 TCCTAAA
1 CCCTAAA
12800579 CCCTAAA
1 CCCTAAA
*
12800586 CCCTTAA
1 CCCTAAA
*
12800593 CCCTGAA
1 CCCTAAA
*
12800600 CCTTAAAA
1 CCCT-AAA
12800608 CCC-ATAA
1 CCCTA-AA
12800615 CCC-ATAA
1 CCCTA-AA
* *
12800622 CCCTCAG
1 CCCTAAA
*
12800629 CCCTTAA
1 CCCTAAA
*
12800636 CCTCTAAC
1 CC-CTAAA
*
12800644 CCCTAAC
1 CCCTAAA
*
12800651 CCCTGAA
1 CCCTAAA
12800658 CC
1 CC
12800660 TTATTTAATA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
6 1 0.01
7 59 0.86
8 9 0.13
ACGTcount: A:0.34, C:0.44, G:0.03, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:12801303 original size:41 final size:41
Alignment explanation
Indices: 12801258--12801368 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
12801248 ATATGTTTTT
*
12801258 GCGGCGCTT-TACCAAAAACGTCGCTAAAGGTCTGCGCATTA
1 GCGGCGCTTCT-CCAAAAACGCCGCTAAAGGTCTGCGCATTA
** *
12801299 GCGGCGCTTCTTTACAAACGCCGCTAAAGGTCTGCGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGTCTGCGCATTA
** *
12801340 GCGGCGCTTCTTGAAAAACGCTGCTAAAG
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAG
12801369 ACCCGCAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGGTCTGCGCATTA
Found at i:12801471 original size:40 final size:40
Alignment explanation
Indices: 12801427--12801502 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
12801417 GCTTTCCTAA
*
12801427 AAGCGCCGCTAATACTCGATCTTTAGCGGCGTTTTTGGGG
1 AAGCGCCGCTAATACTCGATCTTTAGCGGCATTTTTGGGG
* * *
12801467 AAGCGCTGCTAATGCTCGATTTTTAGCGGCATTTTT
1 AAGCGCCGCTAATACTCGATCTTTAGCGGCATTTTT
12801503 TCTACAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (40 bp):
AAGCGCCGCTAATACTCGATCTTTAGCGGCATTTTTGGGG
Found at i:12801701 original size:9 final size:9
Alignment explanation
Indices: 12801671--12801717 Score: 69
Period size: 9 Copynumber: 5.2 Consensus size: 9
12801661 AAACCCTTTT
12801671 AAAATT-TA
1 AAAATTATA
*
12801679 ACAATTATTA
1 AAAATTA-TA
12801689 AAAATTATA
1 AAAATTATA
12801698 AAAATTATA
1 AAAATTATA
12801707 AAAATTATA
1 AAAATTATA
12801716 AA
1 AA
12801718 CTAAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
8 5 0.14
9 22 0.63
10 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:12801735 original size:12 final size:11
Alignment explanation
Indices: 12801688--12801742 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 11
12801678 AACAATTATT
12801688 AAAAATTAT--
1 AAAAATTATAA
12801697 AAAAATTAT--
1 AAAAATTATAA
12801706 AAAAATTATAA
1 AAAAATTATAA
*
12801717 ACTAAATTTATAA
1 A--AAAATTATAA
12801730 AAAAATTATAA
1 AAAAATTATAA
12801741 AA
1 AA
12801743 TTTTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 18 0.45
11 12 0.30
13 10 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:12806898 original size:26 final size:25
Alignment explanation
Indices: 12806869--12806949 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 25
12806859 AATTTAATAT
*
12806869 TTGATAAAAAAATTAAAAAAGTTTTG
1 TTGATAAAAAAATTAAAAAA-TTTTA
*
12806895 TTGATAAAAAAGTTTAAAAAATTTTA
1 TTGATAAAAAA-ATTAAAAAATTTTA
12806921 TTGATAAAAAAATTAAAAAAAATTTTA
1 TTGATAAAAAAATT--AAAAAATTTTA
12806948 TT
1 TT
12806950 TTTGAGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
25 2 0.04
26 26 0.53
27 21 0.43
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (25 bp):
TTGATAAAAAAATTAAAAAATTTTA
Found at i:12806912 original size:27 final size:25
Alignment explanation
Indices: 12806869--12806949 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 25
12806859 AATTTAATAT
* *
12806869 TTGATAAAAAAATTAAAAAAGTTTTG
1 TTGATAAAAAATTTAAAAAA-TTTTA
12806895 TTGATAAAAAAGTTTAAAAAATTTTA
1 TTGATAAAAAA-TTTAAAAAATTTTA
*
12806921 TTGATAAAAAAATTAAAAAAAATTTTA
1 TTGAT-AAAAAATT-TAAAAAATTTTA
12806948 TT
1 TT
12806950 TTTGAGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 22 0.45
27 27 0.55
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (25 bp):
TTGATAAAAAATTTAAAAAATTTTA
Found at i:12811213 original size:26 final size:25
Alignment explanation
Indices: 12811184--12811376 Score: 117
Period size: 26 Copynumber: 7.6 Consensus size: 25
12811174 ATCTTCTTTC
12811184 GAGCCATATAACAGGAAGCTCACAAA
1 GAGCCAT-TAACAGGAAGCTCACAAA
*
12811210 GAGCCATTAATCGGGAAGCTCACAAA
1 GAGCCATTAA-CAGGAAGCTCACAAA
* * ***
12811236 GAGCC-TT-TCAGGAAGCTTATTCA
1 GAGCCATTAACAGGAAGCTCACAAA
* * *
12811259 G-GCTATATAACAGGAAGCTAACATA
1 GAGCCAT-TAACAGGAAGCTCACAAA
* *
12811284 GAGCCA-TAATCAGGAAGTTCATAAA
1 GAGCCATTAA-CAGGAAGCTCACAAA
* ** * *
12811309 GAACTTTTAATCAGGAAGATCACGAA
1 GAGCCATTAA-CAGGAAGCTCACAAA
* *
12811335 GAGCCTTTAAACGGGAAGCTCACGAAA
1 GAGCCATT-AACAGGAAGCTCAC-AAA
12811362 -AGCCATTAATCAGGA
1 GAGCCATTAA-CAGGA
12811377 GCTTCGGATA
Statistics
Matches: 126, Mismatches: 31, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.02
23 12 0.10
24 4 0.03
25 33 0.26
26 71 0.56
27 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (25 bp):
GAGCCATTAACAGGAAGCTCACAAA
Found at i:12811531 original size:65 final size:65
Alignment explanation
Indices: 12811451--12811629 Score: 243
Period size: 65 Copynumber: 2.7 Consensus size: 65
12811441 GTTTATGCCT
* * *
12811451 ACAACATATGCAGGATCACAACTGATCATAAAATAGGACGCTCAAAAAGACCTGGGTTTCTGTTC
1 ACAATATATGCAGGATCACAACTGATCATATAATAGGACGCTCAAAAAGACCTGGGTTTCTGTCC
* * * * * *
12811516 GCAATATATGCAGGATCATAA-TAGATCATATAATAGGACGCTCACAAAGAGCTGTGTTTGTGTC
1 ACAATATATGCAGGATCACAACT-GATCATATAATAGGACGCTCAAAAAGACCTGGGTTTCTGTC
12811580 C
65 C
*
12811581 ACAATATATACAGGATCACAACTGATCATATAATAGGACGCTCACAAAA
1 ACAATATATGCAGGATCACAACTGATCATATAATAGGACGCTCA-AAAA
12811630 TGCTACGGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
64 1 0.01
65 93 0.95
66 4 0.04
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (65 bp):
ACAATATATGCAGGATCACAACTGATCATATAATAGGACGCTCAAAAAGACCTGGGTTTCTGTCC
Found at i:12830854 original size:27 final size:27
Alignment explanation
Indices: 12830824--12831031 Score: 186
Period size: 27 Copynumber: 7.8 Consensus size: 27
12830814 TATAACAGTT
12830824 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* ** *
12830851 ATTTTA-CC-ATGAGCTTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
12830876 ATTCTACCTTATGGGGGTATTTCAATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* ** * ** *
12830903 ATTCTATTCTATAGGGGTATTTCAATT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
12830930 ATTTTACCCTATGAGGGTATATCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
12830957 ATTTTACCCTATAGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
12830984 ATTTTACCTTATGGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
12831011 TTTTTATCCTATGAGGGTATT
1 ATTTTACCCTATGGGGGTATT
12831032 GTGGTAATTT
Statistics
Matches: 141, Mismatches: 38, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
25 18 0.13
26 3 0.02
27 120 0.85
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:12830988 original size:54 final size:54
Alignment explanation
Indices: 12830824--12831041 Score: 210
Period size: 54 Copynumber: 4.1 Consensus size: 54
12830814 TATAACAGTT
* **
12830824 ATTTTACCCTATGGGGGTATTTCGGTCATTTTA-CC-ATGAGCTTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCAGTCATTTTATCCTATGAGGGTATTTTGGTC
* * * * * *** *
12830876 ATTCTACCTTATGGGGGTATTTCAATCATTCTATTCTAT-AGGGGTATTTCAATT
1 ATTTTACCCTATGGGGGTATTTCAGTCATTTTATCCTATGA-GGGTATTTTGGTC
* * * *
12830930 ATTTTACCCTATGAGGGTATATCGGTCATTTTACCCTAT-AGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCAGTCATTTTATCCTATGA-GGGTATTTTGGTC
* * * *
12830984 ATTTTACCTTATGGGGGTATTTCAGTCTTTTTATCCTATGAGGGTATTGTGGTA
1 ATTTTACCCTATGGGGGTATTTCAGTCATTTTATCCTATGAGGGTATTTTGGTC
12831038 ATTT
1 ATTT
12831042 ATTGACCCCT
Statistics
Matches: 129, Mismatches: 33, Indels: 6
0.77 0.20 0.04
Matches are distributed among these distances:
52 28 0.22
53 2 0.02
54 98 0.76
55 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (54 bp):
ATTTTACCCTATGGGGGTATTTCAGTCATTTTATCCTATGAGGGTATTTTGGTC
Found at i:12837900 original size:16 final size:16
Alignment explanation
Indices: 12837879--12837909 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12837869 TTGAGTGATT
12837879 TAGCTTGTTAGTAACC
1 TAGCTTGTTAGTAACC
12837895 TAGCTTGTTAGTAAC
1 TAGCTTGTTAGTAAC
12837910 TAACAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (16 bp):
TAGCTTGTTAGTAACC
Found at i:12839400 original size:28 final size:27
Alignment explanation
Indices: 12839368--12839459 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
12839358 AGTTCTTCTA
12839368 GACTCTTGCTTGAAAGATAGTCCATCTG
1 GACTCTTGCTTGAAAGATAGTCCATC-G
* * * *
12839396 GACTCTTGGTCGAAAGATAGTCTAAGCG
1 GACTCTTGCTTGAAAGATAGTC-CATCG
* * *
12839424 GACTCTTCCTTGAAAGAGAGTCCATGCA
1 GACTCTTGCTTGAAAGATAGTCCAT-CG
12839452 GACTCTTG
1 GACTCTTG
12839460 TATGGCGGAG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.02
28 47 0.94
29 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (27 bp):
GACTCTTGCTTGAAAGATAGTCCATCG
Found at i:12848265 original size:12 final size:12
Alignment explanation
Indices: 12848248--12848277 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12848238 GACTAATACG
*
12848248 ATTATGCATGTT
1 ATTATGCATGAT
12848260 ATTATGCATGAT
1 ATTATGCATGAT
12848272 ATTATG
1 ATTATG
12848278 TTTTATCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (12 bp):
ATTATGCATGAT
Found at i:12863811 original size:23 final size:25
Alignment explanation
Indices: 12863776--12863821 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12863766 TTATGGTTTT
12863776 CTTGACTATTGAT-GTAAATTTAAA
1 CTTGACTATTGATGGTAAATTTAAA
*
12863800 CTTGAC-ATTGATGGTTAATTTA
1 CTTGACTATTGATGGTAAATTTA
12863822 CTTAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (25 bp):
CTTGACTATTGATGGTAAATTTAAA
Found at i:12865912 original size:45 final size:44
Alignment explanation
Indices: 12865763--12865974 Score: 226
Period size: 44 Copynumber: 4.8 Consensus size: 44
12865753 TTCTTGCTTC
* * * * * ** *
12865763 AATCTACTTCACTGCAACTTCAGGGAGATGAGGTTTGCAACTTA
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGACTTT
* * * *
12865807 AATCTACTCTATTGCAACTTTAGAGAGATAAGATTTGTGACTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGACTTT
* * ***
12865851 AATATGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTCTTTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG-TGACTTT
* *
12865896 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTC
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGACTTT
* *
12865940 AATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
12865975 CACCACAGTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 104 0.73
45 38 0.27
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTGACTTT
Found at i:12872911 original size:25 final size:25
Alignment explanation
Indices: 12872866--12872928 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
12872856 GCAAACATGT
*
12872866 AAACGGGAAGCTCTTTCGAGCCATA
1 AAACGGGAAGCTCTGTCGAGCCATA
* *
12872891 AAATGGGAAGCTCATGT-GAGCCATG
1 AAACGGGAAGCTC-TGTCGAGCCATA
*
12872916 TAACGGGAAGCTC
1 AAACGGGAAGCTC
12872929 CATAAAGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.19
Consensus pattern (25 bp):
AAACGGGAAGCTCTGTCGAGCCATA
Found at i:12872961 original size:24 final size:23
Alignment explanation
Indices: 12872896--12872972 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 23
12872886 CCATAAAATG
* *
12872896 GGAAGCTCATGTGAGCCATGTAAC
1 GGAAACTCATATGAGCCAT-TAAC
* *
12872920 GGGAAGCTCCATA-AAGCCATTAAC
1 -GGAAACT-CATATGAGCCATTAAC
*
12872944 GAGAAACTCATATGAGCCAATAAC
1 G-GAAACTCATATGAGCCATTAAC
12872968 GGAAA
1 GGAAA
12872973 GGTTCAAGCG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 9 0.20
24 19 0.43
25 13 0.30
26 3 0.07
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (23 bp):
GGAAACTCATATGAGCCATTAAC
Found at i:12873060 original size:27 final size:27
Alignment explanation
Indices: 12873003--12873058 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12872993 GAGAAGCTCC
* *
12873003 AAAGAGCTATTAATTGGGAAGCTTATG
1 AAAGAGCTATTAATCGGGAAGCTCATG
12873030 AAAGAGCCT-TTAATCGGGAAGCTCA-G
1 AAAGAG-CTATTAATCGGGAAGCTCATG
12873056 AAA
1 AAA
12873059 AGCCATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 20 0.77
28 2 0.08
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (27 bp):
AAAGAGCTATTAATCGGGAAGCTCATG
Found at i:12875180 original size:41 final size:39
Alignment explanation
Indices: 12875081--12875187 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 39
12875071 CATTGAATGT
**
12875081 AAGGGGTTGCTAAGTGCAGATTCTCAGAATCACTGATCAA
1 AAGGGGTTGCTAAGTGCAGATTC-CCCAATCACTGATCAA
12875121 AAGGGGTTGCTAAGTGCAGATTCCCCAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAATCACTGATC-AA
12875161 AAGGGGGTTG-TCAAGTGCAGATTCCCC
1 AA-GGGGTTGCT-AAGTGCAGATTCCCC
12875188 GAGGGGTTAC
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
39 12 0.19
40 28 0.45
41 22 0.35
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (39 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCAATCACTGATCAA
Found at i:12875281 original size:43 final size:42
Alignment explanation
Indices: 12875192--12875337 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
12875182 TTCCCCGAGG
* * * * *
12875192 GGTTACTAAGTGCTGATTCCCTGAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGGT
* * *
12875234 GGTTGCTAAGTGCTAATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTAT-AAAGGT
* *
12875277 GGTTGCTATGTGCTGATTCCCCGTATCATTGAATAT-AAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGGT
12875318 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
12875338 ACCAAGTAAC
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 19 0.22
42 31 0.35
43 29 0.33
44 5 0.06
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGGT
Found at i:12884144 original size:22 final size:23
Alignment explanation
Indices: 12884091--12884144 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
12884081 TTAAATATGT
* *
12884091 AAAAAAGTAAAGAAATAACAAAT
1 AAAAAAATAAAGAAATAACAAAG
** *
12884114 AAATGAATAAATAAAT-ACAAAG
1 AAAAAAATAAAGAAATAACAAAG
12884136 AAAAAAATA
1 AAAAAAATA
12884145 GAACAATATA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (23 bp):
AAAAAAATAAAGAAATAACAAAG
Found at i:12889423 original size:21 final size:20
Alignment explanation
Indices: 12889397--12889440 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
12889387 ACATCAACGC
12889397 ATGCTAACTAACTGCTAACTG
1 ATGCTAACTAACTGC-AACTG
*
12889418 ATGCTAACTATCTGCAACTG
1 ATGCTAACTAACTGCAACTG
12889438 ATG
1 ATG
12889441 AATAACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGCTAACTAACTGCAACTG
Found at i:12889446 original size:21 final size:21
Alignment explanation
Indices: 12889401--12889446 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12889391 CAACGCATGC
*
12889401 TAACTAACTGCTAACTGATGC
1 TAACTAACTGCTAACTGATGA
*
12889422 TAACTATCTGC-AACTGATGAA
1 TAACTAACTGCTAACTGATG-A
12889443 TAAC
1 TAAC
12889447 CGTTTTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (21 bp):
TAACTAACTGCTAACTGATGA
Found at i:12915404 original size:21 final size:21
Alignment explanation
Indices: 12915380--12915419 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12915370 TTAGCACACT
12915380 CAGATACATCCACAACAAAGC
1 CAGATACATCCACAACAAAGC
* *
12915401 CAGATGCATCCACACCAAA
1 CAGATACATCCACAACAAA
12915420 ATCAAACGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.35, G:0.10, T:0.10
Consensus pattern (21 bp):
CAGATACATCCACAACAAAGC
Found at i:12917016 original size:17 final size:17
Alignment explanation
Indices: 12916994--12917028 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12916984 GCAAACAATC
12916994 GATTGAGCAATAAAGAA
1 GATTGAGCAATAAAGAA
12917011 GATTGAGCAATAAAGAA
1 GATTGAGCAATAAAGAA
12917028 G
1 G
12917029 GTTAAACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.26, T:0.17
Consensus pattern (17 bp):
GATTGAGCAATAAAGAA
Found at i:12924064 original size:7 final size:7
Alignment explanation
Indices: 12924054--12924132 Score: 56
Period size: 7 Copynumber: 11.3 Consensus size: 7
12924044 TGAGAGCTAA
*
12924054 GAGAGTT
1 GAGAGAT
12924061 GAGAGA-
1 GAGAGAT
12924067 GAG-GAT
1 GAGAGAT
12924073 GAGAGAT
1 GAGAGAT
12924080 GAGAGAT
1 GAGAGAT
*
12924087 GAGAGGGAA
1 GAGA--GAT
*
12924096 GAGTGAT
1 GAGAGAT
12924103 GATG-GAT
1 GA-GAGAT
*
12924110 GAGGGAT
1 GAGAGAT
*
12924117 GAGGGAT
1 GAGAGAT
*
12924124 GAGGGAT
1 GAGAGAT
12924131 GA
1 GA
12924133 TTGAAAAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
5 2 0.03
6 7 0.11
7 47 0.76
8 1 0.02
9 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.49, T:0.15
Consensus pattern (7 bp):
GAGAGAT
Found at i:12937926 original size:102 final size:102
Alignment explanation
Indices: 12937752--12938096 Score: 532
Period size: 102 Copynumber: 3.4 Consensus size: 102
12937742 CCAGTGATTT
*
12937752 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTT-ACATTCAAA-ATACGGTGGAATCAGCACTTAGCAAC
* *
12937816 CACCAATGATTCGGGGAATCAACACATAGCAACCCCTTG
64 CACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
* *
12937855 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
*
12937920 CCAATGAATT-GGGGAATCAGCACTTAGCAACCCCTTA
66 CCAATG-ATTCGGGGAATCAGCACTTAGCAACCCCTTG
* * *
12937957 GGAGAATCAGCACTTAGCAACCCCCTTTATATTCAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
12938022 CCAATGAGTCGGGCAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
* *
12938059 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAA
12938097 ATACTTTTGC
Statistics
Matches: 220, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
101 2 0.01
102 180 0.82
103 31 0.14
104 7 0.03
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:12938066 original size:27 final size:30
Alignment explanation
Indices: 12938001--12938082 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 30
12937991 AAGATACGGT
12938001 GGAATCAGCACTTAGCAACCACCAATGAGTCG
1 GGAATCAGCACTTAGCAACC-CCAATGAG-CG
*
12938033 GGCAATCAGCACTTAGCAACCCC-TTG-G-G
1 GG-AATCAGCACTTAGCAACCCCAATGAGCG
12938061 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
12938083 CTTCACATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
27 20 0.42
28 3 0.06
30 1 0.02
31 2 0.04
32 4 0.08
33 18 0.38
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (30 bp):
GGAATCAGCACTTAGCAACCCCAATGAGCG
Found at i:12942427 original size:16 final size:17
Alignment explanation
Indices: 12942400--12942434 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12942390 AGAGAGCTGA
12942400 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
12942417 GAGAG-GGATGAGTGAT
1 GAGAGAGGATGAGAGAT
12942433 GA
1 GA
12942435 TGGATGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:12943025 original size:32 final size:29
Alignment explanation
Indices: 12942984--12943042 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
12942974 TAAAAAATAA
*
12942984 TATGCTTAAATTAATATAAAATAAGACATTT
1 TATGCTTAAA--AATATAAAATAAAACATTT
*
12943015 TATGCATTAAAAATATATAATAAAACAT
1 TATGC-TTAAAAATATAAAATAAAACAT
12943043 AAAATCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.60
31 5 0.20
32 5 0.20
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (29 bp):
TATGCTTAAAAATATAAAATAAAACATTT
Found at i:12946572 original size:17 final size:17
Alignment explanation
Indices: 12946543--12946575 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12946533 ATAAATATAA
12946543 AAAATATTTATTTTTAT
1 AAAATATTTATTTTTAT
12946560 AAAAT-TTTAATTTTTA
1 AAAATATTT-ATTTTTA
12946576 AATATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAAATATTTATTTTTAT
Found at i:12959737 original size:67 final size:67
Alignment explanation
Indices: 12959661--12959925 Score: 406
Period size: 68 Copynumber: 3.9 Consensus size: 67
12959651 TGTGAGTTGC
* *
12959661 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTTAAAAATTTAAATTTGATATTATTTA-AA
1 TTTATCTATTTATTTATTTGTTATTCTTTTAC-TTTTAAATATTTAAATTTGATATTATTTATAT
12959725 TTT
65 TTT
* *
12959728 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATGTT
1 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATTTATATT
12959793 TGT
66 T-T
* * *
12959796 TTTATCTATTTCTTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTAATATTATGTATATT
1 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATTTATATT
12959861 TT
66 TT
* *
12959863 TTTATCTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATGTAAAATTTGATATTATTTA
1 TTTATCTATTTATTTATTTGTTATTCTTTTAC-TTTTAAATAT-TTAAATTTGATATTATTTA
12959926 GAGCTCTCAC
Statistics
Matches: 181, Mismatches: 13, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
66 27 0.15
67 65 0.36
68 73 0.40
69 16 0.09
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.63
Consensus pattern (67 bp):
TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATTTATATT
TT
Found at i:12959739 original size:17 final size:16
Alignment explanation
Indices: 12959702--12959785 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
12959692 CTTTTTAAAA
12959702 ATTTAAATTTGATATT
1 ATTTAAATTTGATATT
**
12959718 ATTTAAATTTTTTATCT
1 ATTTAAATTTGATAT-T
* *
12959735 ATTTATTTATTTGTTATT
1 ATTTA--AATTTGATATT
* * * * *
12959753 CTTTTACTTTTA-AAT
1 ATTTAAATTTGATATT
12959768 ATTTAAATTTGATATT
1 ATTTAAATTTGATATT
12959784 AT
1 AT
12959786 CTATGTTTGT
Statistics
Matches: 48, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
15 10 0.21
16 20 0.42
17 6 0.12
18 4 0.08
19 8 0.17
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (16 bp):
ATTTAAATTTGATATT
Found at i:12959812 original size:135 final size:137
Alignment explanation
Indices: 12959661--12959922 Score: 431
Period size: 135 Copynumber: 1.9 Consensus size: 137
12959651 TGTGAGTTGC
* *
12959661 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTTAAAAATTTAAATTTGATATTATTTA-AA
1 TTTATCTATTTATTTATTTGTTATTCTTTTAC-TTTTAAAAATTTAAATTTAATATTATGTATAA
* *
12959725 TTTTTTATCTATTTATTTATTTGTTATTCTTTTAC-TTTTAAATAT-TTAAATTTGATATTATCT
65 TTTTTTATCTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATGTAAAATTTGATATTATCT
12959788 ATGTTTGT
130 ATGTTTGT
* * *
12959796 TTTATCTATTTCTTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTAATATTATGTATATT
1 TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAAAATTTAAATTTAATATTATGTATAAT
12959861 TTTTTATCTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATGTAAAATTTGATATTAT
66 TTTTTATCTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATGTAAAATTTGATATTAT
12959923 TTAGAGCTCT
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
134 26 0.22
135 66 0.56
136 10 0.09
137 15 0.13
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (137 bp):
TTTATCTATTTATTTATTTGTTATTCTTTTACTTTTAAAAATTTAAATTTAATATTATGTATAAT
TTTTTATCTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATGTAAAATTTGATATTATCTA
TGTTTGT
Found at i:12962174 original size:44 final size:44
Alignment explanation
Indices: 12962115--12962212 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
12962105 TATCACTTGC
*
12962115 CACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTTAT
1 CACTTGTCACCGATCAGATAAGTGTAACTAAAGCTACCACTTAT
*
12962159 CACTTGTCACCGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACCGATCAGATAAGTGTAACTAAAGCTACCACTTAT
12962203 CACTTGTCAC
1 CACTTGTCAC
12962213 TTGTCACTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (44 bp):
CACTTGTCACCGATCAGATAAGTGTAACTAAAGCTACCACTTAT
Found at i:12962249 original size:47 final size:47
Alignment explanation
Indices: 12962180--12962270 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
12962170 GATCAGATAA
* *
12962180 GTGTAGCTAAAGCTACCACTTATCACTTGT-CACTTGTCACTGATTAG
1 GTGTAGATAAAGCTACCACTTATCACTT-TCCACGTGTCACTGATTAG
*
12962227 GTGTAGATAAAGGTACCACTTATCACTTTCCACGTGTCACTGAT
1 GTGTAGATAAAGCTACCACTTATCACTTTCCACGTGTCACTGAT
12962271 CAGATAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (47 bp):
GTGTAGATAAAGCTACCACTTATCACTTTCCACGTGTCACTGATTAG
Found at i:12966378 original size:68 final size:68
Alignment explanation
Indices: 12966281--12966617 Score: 516
Period size: 68 Copynumber: 4.8 Consensus size: 68
12966271 TTGTTTTATC
* *
12966281 TATCTATTTATTTATTTGTTATCCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
1 TATCCATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
12966346 TTT
66 TTT
12966349 TATCCATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
1 TATCCATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
12966414 TTT
66 TTT
*
12966417 TATCCATTTATTTATTTGTTATTATTTTACTTTTAAATATTTAAATTTGATATTATCTATATTT-
1 TATCCATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
12966481 TTCT
66 TT-T
12966485 TATCTATCTATTTATTTATTTGTTATTC-TTTACTTTTAAATATTTAAATTTGATATTATCTATA
1 TATC---C-ATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATA
12966549 TTTGTTT
62 TTTGTTT
* *
12966556 TATCTATTTATTTATTTATTCGTTATTCTTTTACTTTTTAAATATTTAAAATTTGATGTTAT
1 TATCCATTTATTTA--T-TT-GTTATTCTTTTAC-TTTTAAATATTT-AAATTTGATATTAT
12966618 TTGTATTTCC
Statistics
Matches: 250, Mismatches: 6, Indels: 20
0.91 0.02 0.07
Matches are distributed among these distances:
67 11 0.04
68 134 0.54
69 1 0.00
70 2 0.01
71 52 0.21
72 25 0.10
73 12 0.05
74 13 0.05
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (68 bp):
TATCCATTTATTTATTTGTTATTCTTTTACTTTTAAATATTTAAATTTGATATTATCTATATTTG
TTT
Found at i:12974952 original size:21 final size:21
Alignment explanation
Indices: 12974923--12974984 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
12974913 AGCAGTTACA
* *
12974923 GTTCCCATATAATTTCTATGG
1 GTTCACATATAATTTCTACGG
* *
12974944 GTTCACATATAACTTCTACGT
1 GTTCACATATAATTTCTACGG
*
12974965 GTTCACATTATAATTCCTAC
1 GTTCACA-TATAATTTCTAC
12974985 AGTACTCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 24 0.71
22 10 0.29
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (21 bp):
GTTCACATATAATTTCTACGG
Found at i:12978123 original size:43 final size:43
Alignment explanation
Indices: 12978062--12978329 Score: 330
Period size: 43 Copynumber: 6.2 Consensus size: 43
12978052 CGCTATTGTC
*
12978062 AACGCCGATATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
1 AACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
* *
12978105 AACGCCGCTATAGATCAGGACCTTTAGCAGCGCTGTTTACAAA
1 AACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
*
12978148 AACACCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
1 AACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
* * *
12978191 AATGCCGCTATAGATCAGGACCTTTAGCGACGCATTTTT-CACA
1 AACGCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTTACAAA
* * *
12978234 AACGCCGCTATA-ACTCAAGACCTTTAGCGGCGCTTTTTTCACA
1 AACGCCGCTATAGA-TCAGGACCTTTAGCGGCGCTTTTTACAAA
* * * *
12978277 AACGCCACTATA-ACTCAAGACATTTAGCGACGCTTTGATTAC--A
1 AACGCCGCTATAGA-TCAGGACCTTTAGCGGCGCTTT--TTACAAA
12978320 AACGCCGCTA
1 AACGCCGCTA
12978330 AAAGTACCAT
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
42 6 0.03
43 188 0.93
44 5 0.02
45 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
AACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACAAA
Found at i:12978517 original size:14 final size:14
Alignment explanation
Indices: 12978494--12978523 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12978484 AAATCATGTT
12978494 AAATTACAAGTTCA
1 AAATTACAAGTTCA
*
12978508 AAATTTCAAGTTCA
1 AAATTACAAGTTCA
12978522 AA
1 AA
12978524 TAGTGCAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
AAATTACAAGTTCA
Found at i:12983109 original size:21 final size:22
Alignment explanation
Indices: 12983086--12983136 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
12983076 ACCCTTAAAA
* *
12983086 CCCTAAATCTCTAACTCTTAAC
1 CCCTAAACCCCTAACTCTTAAC
12983108 CCCT-AACCCCTAACTCTTAAC
1 CCCTAAACCCCTAACTCTTAAC
12983129 CCCTAAAC
1 CCCTAAAC
12983137 ATTAAATCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.31, C:0.43, G:0.00, T:0.25
Consensus pattern (22 bp):
CCCTAAACCCCTAACTCTTAAC
Found at i:12983188 original size:15 final size:15
Alignment explanation
Indices: 12983153--12983190 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12983143 TCCCAACACT
12983153 TAAAT-CATAATCCA
1 TAAATCCATAATCCA
*
12983167 T-AATCCATAATCCC
1 TAAATCCATAATCCA
12983181 TAAATCCATA
1 TAAATCCATA
12983191 TATAATCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 10 0.48
15 8 0.38
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCA
Found at i:12983387 original size:29 final size:29
Alignment explanation
Indices: 12983355--12983439 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
12983345 ATCCATGTTT
12983355 CTTAAACCCTAA-ATTACAAACCCCT-AAAC
1 CTTAAACCCTAACA-T-CAAACCCCTAAAAC
*
12983384 CTTAAACCCCAACCATCAAACCCCTAAAAC
1 CTTAAACCCTAA-CATCAAACCCCTAAAAC
*
12983414 C-TAAATCCCTAACTAT-TAACCCCTAA
1 CTTAAA-CCCTAAC-ATCAAACCCCTAA
12983440 CATCTAACAC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 34 0.71
30 13 0.27
31 1 0.02
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (29 bp):
CTTAAACCCTAACATCAAACCCCTAAAAC
Found at i:12983390 original size:15 final size:15
Alignment explanation
Indices: 12983372--12983425 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
12983362 CCTAAATTAC
12983372 AAACCCCTAAACCTT
1 AAACCCCTAAACCTT
*
12983387 AAACCCC--AACCATC
1 AAACCCCTAAACC-TT
12983401 AAACCCCTAAAACC-T
1 AAACCCCT-AAACCTT
*
12983416 AAATCCCTAA
1 AAACCCCTAA
12983426 CTATTAACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.12
14 10 0.31
15 14 0.44
17 4 0.12
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (15 bp):
AAACCCCTAAACCTT
Found at i:12983937 original size:41 final size:40
Alignment explanation
Indices: 12983841--12984073 Score: 252
Period size: 41 Copynumber: 5.7 Consensus size: 40
12983831 AATACATTTT
* * *
12983841 GCGGCGCTTTCCCAAAAACGCCGCTAAAGA-CAAAGTAATA
1 GCGGCGCTTT-CCAAAAACGCCGCTAAAGACCAGAGCATTA
* *
12983881 GCGGCACTTCTACAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTT-TCCAAAAACGCCGCTAAAGACCAGAGCATTA
* * **
12983922 GCGGCGTTTTCACAAAAGCGCCGCTAAAGAATAGAGCATTA
1 GCGGCGCTTTC-CAAAAACGCCGCTAAAGACCAGAGCATTA
* *
12983963 GCGGCGCTGTCCAAAAAATGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTCC-AAAAACGCCGCTAAAGACCAGAGCATTA
*
12984004 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCTTTA
1 GCGGCGC-TTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
* * ** *
12984045 GTGGCACTTTTTGAAAAACGCCACTAAAG
1 GCGGCGC-TTTCCAAAAACGCCGCTAAAG
12984074 CCCCAAAAAC
Statistics
Matches: 163, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
40 28 0.17
41 131 0.80
42 4 0.02
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (40 bp):
GCGGCGCTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
Found at i:12984416 original size:69 final size:70
Alignment explanation
Indices: 12984305--12984447 Score: 173
Period size: 69 Copynumber: 2.0 Consensus size: 70
12984295 ACAATTTTAC
* * * * * *
12984305 TTGTTACCATCTATTAATTTATATTTTTAAGTTGACTTTTATTTTTATAGGTTTCGATAA-TAAC
1 TTGTTACCATCTATTAATTCATATTTTTAAGTGGACTATTATTTTTATAAGTCTCGAAAACTAAC
12984369 AATGA
66 AATGA
* * *
12984374 TTGTTACGATCTATTAATTCATATTTTTAAGTAGGTC-ATTATTTTTGTAAGTCTCGAAAACCTA
1 TTGTTACCATCTATTAATTCATATTTTTAAGT-GGACTATTATTTTTATAAGTCTCGAAAA-CTA
12984438 ACAATGA
64 ACAATGA
12984445 TTG
1 TTG
12984448 ATGAAAAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
69 48 0.77
70 2 0.03
71 12 0.19
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (70 bp):
TTGTTACCATCTATTAATTCATATTTTTAAGTGGACTATTATTTTTATAAGTCTCGAAAACTAAC
AATGA
Found at i:12984888 original size:40 final size:39
Alignment explanation
Indices: 12984806--12984899 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
12984796 TTTGGACGAC
*
12984806 AAACGCTGCTAAAAATCGAGCATTAGCGGCGCACAGCATA
1 AAACGCCGCTAAAAATCGAGCATTAGCGGCGCACAG-ATA
* * *
12984846 AAACGCCGCTAAAGATCTAGCATTAGCGGCGCTATCTG-TA
1 AAACGCCGCTAAAAATCGAGCATTAGCGGCGC-A-CAGATA
12984886 AAACGCCGC-AAAAA
1 AAACGCCGCTAAAAA
12984900 GTCAGACCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 1 0.02
42 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (39 bp):
AAACGCCGCTAAAAATCGAGCATTAGCGGCGCACAGATA
Found at i:12985298 original size:113 final size:114
Alignment explanation
Indices: 12985083--12986047 Score: 1179
Period size: 114 Copynumber: 8.4 Consensus size: 114
12985073 TATTTGCAAG
*
12985083 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTAGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
*
12985148 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTGTAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* * *
12985197 CGCCGCAAAATATCTTGACCAAATCGCAGTGTTTGGTCTTGAGGTATATTA-AATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * **
12985261 TATGCAAAAATGCCACTAAAGCACAGTATTAGTGGCGCATTATAAAAGG
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
** *
12985310 CGCCGCAAAATATCTTAACCAAAATACAGCGTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * *
12985375 TATGGAAAAACGCCGCTAAAGCACAGTATTAGCAGCGCATTATACAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* *
12985424 CACCGTAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
12985489 TATGCAAAAATGCCGCTAAAGCACAGTATTTGCGGCGC-----------
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* * **
12985527 C-CCGCAAAATATCTTAACCAAAACGCAGCGTTTGGACTTGAGGTATAGTAGAATTAGTGGTACT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * *
12985591 TATGCAAAAAACAG-CGCTTATGGAAAAACACCGCTA-AAGCACAGTATTAACGGCGCATTATAA
66 TATGC-AAAAAC-GCCGC---T---AAAGCACAG-TATTAG--C-G----G----CGCATTATAA
*
12985654 AAAG
111 AAAA
* * *
12985658 CTCCGTAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * *
12985723 TATGGAAAAACGCCACTGAAGCACAGTATTAGCGGCGCATTATAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* * *
12985772 CGCCGCAAAATATCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* *
12985837 TATGAAAAAACGCCGCTAAAGCATAGTATTAGCGGCGCATTATAAAAAA
66 TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
* *
12985886 CGCAGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * * * * *
12985951 TATG-AAGAAACGCCGCAAAATCACAGTATTAGCGACGCTTTGTGAAAAG
66 TATGCAA-AAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
*
12986000 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGTTATA
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
12986048 GAGCCAATAG
Statistics
Matches: 734, Mismatches: 81, Indels: 72
0.83 0.09 0.08
Matches are distributed among these distances:
102 63 0.09
103 9 0.01
104 1 0.00
106 1 0.00
109 8 0.01
110 2 0.00
111 1 0.00
112 1 0.00
113 104 0.14
114 455 0.62
120 3 0.00
122 1 0.00
123 1 0.00
124 2 0.00
125 8 0.01
128 1 0.00
130 1 0.00
131 9 0.01
132 63 0.09
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
TATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAA
Found at i:12985729 original size:348 final size:350
Alignment explanation
Indices: 12985256--12985946 Score: 1008
Period size: 348 Copynumber: 2.0 Consensus size: 350
12985246 TAAATTAGTG
** ** *
12985256 GCGCTTATGCAAAAATGCCACTAAAGCACAGTATTAGTGGCGCATTATAAAAGGCGCCGCAAAAT
1 GCGCTTATGCAAAAACACCACTAAAGCACAGTATTAACGGCGCATTATAAAAAGCGCCGCAAAAT
* *
12985321 ATCTTAACCAAAATACAGCGTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTATGGAAAAAC
66 ATCTTAACCAAAACACAGCGTTTGGTCTTGAGGTATATTAAAATTAGTGGCACTTATGGAAAAAC
* * *
12985386 GCCGCTAAAGCACAGTATTAGCAGCGCATTATACAAAACACCGTAAAATATCTTAACCAAAACGC
131 GCCACTAAAGCACAGTATTAGCAGCGCATTATAAAAAACACCGCAAAATATCTTAACCAAAACGC
* * *
12985451 AGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGCAAAAATGCCGCTAAAGCACAGT
196 AGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGCCGCTAAAGCACAGT
* *
12985516 ATTTGCGGCGC-C-CCGCAAAATATCTTAACCAAAACGCAGCGTTTGGACTTGAGGTATAGTAGA
261 ATTAGCGGCGCACGCAGCAAAATATCTTAACCAAAACGCAGCGTTTGGACTTGAGGTATAGTAGA
12985579 ATTAGTGGTACTTATGCAAAAAACA
326 ATTAGTGGTACTTATGCAAAAAACA
* * * *
12985604 GCGCTTATGGAAAAACACCGCTAAAGCACAGTATTAACGGCGCATTATAAAAAGCTCCGTAAAAT
1 GCGCTTATGCAAAAACACCACTAAAGCACAGTATTAACGGCGCATTATAAAAAGCGCCGCAAAAT
* *
12985669 ATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGGAAAAAC
66 ATCTTAACCAAAACACAGCGTTTGGTCTTGAGGTATATTAAAATTAGTGGCACTTATGGAAAAAC
* * * *
12985734 GCCACTGAAGCACAGTATTAGCGGCGCATTATAAAAAACGCCGCAAAATATCTTAACCAAAATGC
131 GCCACTAAAGCACAGTATTAGCAGCGCATTATAAAAAACACCGCAAAATATCTTAACCAAAACGC
* *
12985799 AGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGTTTATGAAAAAACGCCGCTAAAGCATAGT
196 AGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGCCGCTAAAGCACAGT
* *
12985864 ATTAGCGGCGCATTATAAAAAACGCAGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAG
261 ATTAGCGGCGC----------ACGCAGCAAAATATCTTAACCAAAACGCAGCGTTTGGACTTGAG
*
12985929 GTATATTAGAATTAGTGG
316 GTATAGTAGAATTAGTGG
12985947 CGCTTATGAA
Statistics
Matches: 301, Mismatches: 30, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
348 245 0.81
359 1 0.00
360 55 0.18
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (350 bp):
GCGCTTATGCAAAAACACCACTAAAGCACAGTATTAACGGCGCATTATAAAAAGCGCCGCAAAAT
ATCTTAACCAAAACACAGCGTTTGGTCTTGAGGTATATTAAAATTAGTGGCACTTATGGAAAAAC
GCCACTAAAGCACAGTATTAGCAGCGCATTATAAAAAACACCGCAAAATATCTTAACCAAAACGC
AGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGCCGCTAAAGCACAGT
ATTAGCGGCGCACGCAGCAAAATATCTTAACCAAAACGCAGCGTTTGGACTTGAGGTATAGTAGA
ATTAGTGGTACTTATGCAAAAAACA
Found at i:12988613 original size:16 final size:16
Alignment explanation
Indices: 12988592--12988649 Score: 80
Period size: 16 Copynumber: 3.4 Consensus size: 16
12988582 ATGTTAAGCT
12988592 ATGTTAAACATTTTGA
1 ATGTTAAACATTTTGA
*
12988608 ATGTTAAGCATAGTTTTGA
1 ATGTTAA--ACA-TTTTGA
12988627 ATGTTAAACATTTTGA
1 ATGTTAAACATTTTGA
12988643 ATGTTAA
1 ATGTTAA
12988650 GCATATGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 20 0.54
17 2 0.05
18 2 0.05
19 13 0.35
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (16 bp):
ATGTTAAACATTTTGA
Found at i:12988626 original size:19 final size:18
Alignment explanation
Indices: 12988601--12988655 Score: 78
Period size: 16 Copynumber: 3.1 Consensus size: 18
12988591 TATGTTAAAC
12988601 ATTTTGAATGTTAAGCAT
1 ATTTTGAATGTTAAGCAT
*
12988619 AGTTTTGAATGTTAA--AC
1 A-TTTTGAATGTTAAGCAT
12988636 ATTTTGAATGTTAAGCAT
1 ATTTTGAATGTTAAGCAT
12988654 AT
1 AT
12988656 GAGTTTCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 13 0.41
17 2 0.06
18 4 0.12
19 13 0.41
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (18 bp):
ATTTTGAATGTTAAGCAT
Found at i:12988784 original size:29 final size:30
Alignment explanation
Indices: 12988712--12988785 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
12988702 ATAATCTTTG
*
12988712 AAAACTGAACAAAAAAATTATGCACAGTTA
1 AAAACTGAACAAAAAAAATATGCACAGTTA
* * ***
12988742 AACA-TAAACTAAAAAAAATA-GTTTAGTTA
1 AAAACTGAAC-AAAAAAAATATGCACAGTTA
12988771 AAAACTGAACAAAAA
1 AAAACTGAACAAAAA
12988786 TCCAGCAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.20
Consensus pattern (30 bp):
AAAACTGAACAAAAAAAATATGCACAGTTA
Found at i:12989066 original size:21 final size:21
Alignment explanation
Indices: 12989042--12989114 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
12989032 GTTTTGGGAC
*
12989042 TATTTATTTATATTTTCAGCG
1 TATTTATTTATATTTTCAGCA
* *
12989063 TATTTAATATTAT-TTATATTA-TA
1 TATTT-AT-TTATATT-T-TCAGCA
12989086 TTATTTATTTATATTTTCAGCA
1 -TATTTATTTATATTTTCAGCA
12989108 TATTTAT
1 TATTTAT
12989115 ATAAATATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
23 9 0.22
24 7 0.17
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.60
Consensus pattern (21 bp):
TATTTATTTATATTTTCAGCA
Found at i:12989088 original size:14 final size:13
Alignment explanation
Indices: 12989063--12989100 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
12989053 ATTTTCAGCG
12989063 TATTTAATATTATT
1 TATTT-ATATTATT
12989077 TATATTATATTATT
1 TAT-TTATATTATT
12989091 TATTTATATT
1 TATTTATATT
12989101 TTCAGCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 14 0.61
15 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTATATTATT
Found at i:12989818 original size:9 final size:9
Alignment explanation
Indices: 12989804--12990361 Score: 135
Period size: 9 Copynumber: 64.4 Consensus size: 9
12989794 ACTATCACAT
12989804 CTTACATAA
1 CTTACATAA
*
12989813 CTTACATAG
1 CTTACATAA
*
12989822 CTTA-ATTA
1 CTTACATAA
*
12989830 --TACTTAA
1 CTTACATAA
12989837 CTTACATAA
1 CTTACATAA
*
12989846 CTTACATTA
1 CTTACATAA
*
12989855 --TACACAA
1 CTTACATAA
12989862 CTTACATAA
1 CTTACATAA
*
12989871 CTTTCATTATACA
1 C-TT-A-CATA-A
*
12989884 CATACATAA
1 CTTACATAA
*
12989893 ATTACATATA
1 CTTACATA-A
* *
12989903 -ATACACAA
1 CTTACATAA
*
12989911 CATACATAA
1 CTTACATAA
12989920 CTTACATAA
1 CTTACATAA
*
12989929 --TA-TTGAA
1 CTTACAT-AA
12989936 CTTACATAA
1 CTTACATAA
* *
12989945 TTTTCATAA
1 CTTACATAA
12989954 --TACATAA
1 CTTACATAA
* *
12989961 CTTACTTAT
1 CTTACATAA
* *
12989970 TTTTCATAA
1 CTTACATAA
* *
12989979 --AAAATAA
1 CTTACATAA
12989986 CTTACATAA
1 CTTACATAA
12989995 CTTACATAA
1 CTTACATAA
* *
12990004 ATTTCATAA
1 CTTACATAA
*
12990013 CCTACATAA
1 CTTACATAA
*
12990022 CTTACACAA
1 CTTACATAA
*
12990031 --TACACAA
1 CTTACATAA
12990038 CTTACATAA
1 CTTACATAA
* *
12990047 TTTTCATAA
1 CTTACATAA
12990056 C--ACATAA
1 CTTACATAA
12990063 CTTACATAA
1 CTTACATAA
*
12990072 --TA-TTGAA
1 CTTACAT-AA
12990079 CTTACATAA
1 CTTACATAA
* * *
12990088 TTTTCGTAA
1 CTTACATAA
12990097 --TACATAA
1 CTTACATAA
*
12990104 CTTACGTAA
1 CTTACATAA
*
12990113 --TA-TTGAA
1 CTTACAT-AA
*
12990120 CTAACATAA
1 CTTACATAA
* *
12990129 TTTTCATAA
1 CTTACATAA
12990138 --TACATAA
1 CTTACATAA
* *
12990145 GTTACTTAA
1 CTTACATAA
* *
12990154 TTTTCATAA
1 CTTACATAA
12990163 -TATA-A-AA
1 CT-TACATAA
12990170 CTTACATAA
1 CTTACATAA
12990179 CTTATACAGTACA
1 C-T-TACA-TA-A
12990192 CTGCTTACATAA
1 ---CTTACATAA
* *
12990204 TTTTCATAA
1 CTTACATAA
12990213 --TACATAA
1 CTTACATAA
12990220 CTTACA-AA
1 CTTACATAA
*
12990228 ATTGATCATAA
1 CTT-A-CATAA
12990239 --TACA-ACA
1 CTTACATA-A
12990246 CTTACATAA
1 CTTACATAA
* *
12990255 --TCCACAA
1 CTTACATAA
12990262 CTTACATAA
1 CTTACATAA
*
12990271 -TATTCATAA
1 CT-TACATAA
*
12990280 --TACATAG
1 CTTACATAA
12990287 CTTACATAA
1 CTTACATAA
* *
12990296 TTTTCATAA
1 CTTACATAA
*
12990305 --TAAATAA
1 CTTACATAA
12990312 CTTAATACATAA
1 C-T--TACATAA
12990324 CTTACATAA
1 CTTACATAA
12990333 --TACATAA
1 CTTACATAA
12990340 CTTACATAA
1 CTTACATAA
*
12990349 CTTACATAG
1 CTTACATAA
12990358 CTTA
1 CTTA
12990362 ATTATACTTA
Statistics
Matches: 397, Mismatches: 85, Indels: 134
0.64 0.14 0.22
Matches are distributed among these distances:
6 6 0.02
7 88 0.22
8 13 0.03
9 243 0.61
10 13 0.03
11 9 0.02
12 14 0.04
13 5 0.01
14 4 0.01
15 1 0.00
16 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.35
Consensus pattern (9 bp):
CTTACATAA
Found at i:12989863 original size:25 final size:25
Alignment explanation
Indices: 12989806--12990071 Score: 209
Period size: 25 Copynumber: 10.6 Consensus size: 25
12989796 TATCACATCT
* *
12989806 TACATAACTTACATAGCTTA-ATTA
1 TACATAACTTACATAACTTACATAA
* *
12989830 TACTTAACTTACATAACTTACATTA
1 TACATAACTTACATAACTTACATAA
* * *
12989855 TACACAACTTACATAACTTTCATTA
1 TACATAACTTACATAACTTACATAA
* *
12989880 TAC---ACATACATAAATTACATATAA
1 TACATAACTTACATAACTTAC--ATAA
* *
12989904 TACACAACATACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* * *
12989929 TA-TTGAACTTACATAATTTTCATAA
1 TACAT-AACTTACATAACTTACATAA
* ** *
12989954 TACATAACTTACTTATTTTTCATAA
1 TACATAACTTACATAACTTACATAA
* *
12989979 AAAATAACTTACATAACTTACATAAA
1 TACATAACTTACATAACTTACAT-AA
* * *
12990005 TTTCATAACCTACATAACTTACACAA
1 -TACATAACTTACATAACTTACATAA
* * *
12990031 TACACAACTTACATAATTTTCATAA
1 TACATAACTTACATAACTTACATAA
*
12990056 CACATAACTTACATAA
1 TACATAACTTACATAA
12990072 TATTGAACTT
Statistics
Matches: 195, Mismatches: 37, Indels: 19
0.78 0.15 0.08
Matches are distributed among these distances:
22 12 0.06
24 24 0.12
25 122 0.63
26 5 0.03
27 32 0.16
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.35
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:12990081 original size:41 final size:41
Alignment explanation
Indices: 12989993--12990154 Score: 198
Period size: 41 Copynumber: 3.9 Consensus size: 41
12989983 TAACTTACAT
* * ***
12989993 AACTTACATAAATTTCATAACCTACATAACTTACACAATACAC
1 AACTTACATAATTTTCATAA-C-ACATAACTTACATAATATTG
12990036 AACTTACATAATTTTCATAACACATAACTTACATAATATTG
1 AACTTACATAATTTTCATAACACATAACTTACATAATATTG
* * *
12990077 AACTTACATAATTTTCGTAATACATAACTTACGTAATATTG
1 AACTTACATAATTTTCATAACACATAACTTACATAATATTG
* * * *
12990118 AACTAACATAATTTTCATAATACATAAGTTACTTAAT
1 AACTTACATAATTTTCATAACACATAACTTACATAAT
12990155 TTTCATAATA
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 87 0.81
42 1 0.01
43 19 0.18
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (41 bp):
AACTTACATAATTTTCATAACACATAACTTACATAATATTG
Found at i:12990100 original size:16 final size:16
Alignment explanation
Indices: 12990081--12990114 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12990071 ATATTGAACT
* *
12990081 TACATAATTTTCGTAA
1 TACATAACTTACGTAA
12990097 TACATAACTTACGTAA
1 TACATAACTTACGTAA
12990113 TA
1 TA
12990115 TTGAACTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (16 bp):
TACATAACTTACGTAA
Found at i:12990138 original size:25 final size:24
Alignment explanation
Indices: 12990110--12990165 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
12990100 ATAACTTACG
12990110 TAATATTGAACTAACATAATTTTCA
1 TAATATT-AACTAACATAATTTTCA
* * * *
12990135 TAATACATAAGTTACTTAATTTTCA
1 TAATA-TTAACTAACATAATTTTCA
12990160 TAATAT
1 TAATAT
12990166 AAAACTTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (24 bp):
TAATATTAACTAACATAATTTTCA
Found at i:12990174 original size:25 final size:25
Alignment explanation
Indices: 12990126--12990255 Score: 84
Period size: 25 Copynumber: 5.2 Consensus size: 25
12990116 TGAACTAACA
* *
12990126 TAATTTTCATAATACATAAGTTACT
1 TAATTTTCATAATACAAAACTTACT
* *
12990151 TAATTTTCATAATATAAAACTTACA
1 TAATTTTCATAATACAAAACTTACT
* *** *
12990176 TAA-CTT-ATACAGTACACTGCTTACA
1 TAATTTTCATA-A-TACAAAACTTACT
* *
12990201 TAATTTTCATAATACATAACTTACA
1 TAATTTTCATAATACAAAACTTACT
* * * *
12990226 AAATTGATCATAATACAACACTTACA
1 TAATT-TTCATAATACAAAACTTACT
12990252 TAAT
1 TAAT
12990256 CCACAACTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
23 3 0.04
24 3 0.04
25 50 0.61
26 23 0.28
27 3 0.04
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.37
Consensus pattern (25 bp):
TAATTTTCATAATACAAAACTTACT
Found at i:12990321 original size:28 final size:27
Alignment explanation
Indices: 12990264--12990343 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 27
12990254 ATCCACAACT
* *
12990264 TACATAATATTCATAATACATAGC-T-
1 TACATAATTTTCATAATACATAACTTA
*
12990289 TACATAATTTTCATAATAAATAACTTAA
1 TACATAATTTTCATAATACATAACTT-A
* *
12990317 TACATAACTTACATAATACATAACTTA
1 TACATAATTTTCATAATACATAACTTA
12990344 CATAACTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.46
26 1 0.02
27 1 0.02
28 23 0.50
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.36
Consensus pattern (27 bp):
TACATAATTTTCATAATACATAACTTA
Found at i:12990340 original size:16 final size:16
Alignment explanation
Indices: 12990234--12990348 Score: 82
Period size: 16 Copynumber: 7.3 Consensus size: 16
12990224 CAAAATTGAT
12990234 CATAATACA-ACACTTA
1 CATAATACATA-ACTTA
* *
12990250 CATAATCCACAACTTA
1 CATAATACATAACTTA
12990266 CATAATATTCATAA--TA
1 CATAATA--CATAACTTA
* * *
12990282 CATAGCTTACATAATTTT
1 CATA--ATACATAACTTA
*
12990300 CATAATAAATAAC-T-
1 CATAATACATAACTTA
12990314 --TAATACATAACTTA
1 CATAATACATAACTTA
12990328 CATAATACATAACTTA
1 CATAATACATAACTTA
12990344 CATAA
1 CATAA
12990349 CTTACATAGC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
12 10 0.13
13 1 0.01
15 1 0.01
16 55 0.70
17 1 0.01
18 11 0.14
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.32
Consensus pattern (16 bp):
CATAATACATAACTTA
Found at i:12990349 original size:25 final size:25
Alignment explanation
Indices: 12990245--12990356 Score: 118
Period size: 25 Copynumber: 4.4 Consensus size: 25
12990235 ATAATACAAC
* *
12990245 ACTTACATAATCCACAACTTACATA
1 ACTTACATAATACATAACTTACATA
* *
12990270 A-TATTCATAATACATAGCTTACATA
1 ACT-TACATAATACATAACTTACATA
* * *
12990295 ATTTTCATAATAAATAACTTAATACATA
1 ACTTACATAATACATAAC-T--TACATA
12990323 ACTTACATAATACATAACTTACATA
1 ACTTACATAATACATAACTTACATA
12990348 ACTTACATA
1 ACTTACATA
12990357 GCTTAATTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
24 1 0.01
25 48 0.66
26 2 0.03
27 1 0.01
28 21 0.29
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (25 bp):
ACTTACATAATACATAACTTACATA
Found at i:12995299 original size:21 final size:21
Alignment explanation
Indices: 12995249--12995301 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
12995239 CTACAACTTA
** *
12995249 AAGTAGAGGCGGCAGCGAGGG
1 AAGTAGAGGTTGCAGCGAGAG
12995270 AAGTAGAGGTTGCAGCGAGAG
1 AAGTAGAGGTTGCAGCGAGAG
12995291 AAGCT-GAGGTT
1 AAG-TAGAGGTT
12995302 CAAAGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.45, T:0.13
Consensus pattern (21 bp):
AAGTAGAGGTTGCAGCGAGAG
Found at i:12995769 original size:44 final size:43
Alignment explanation
Indices: 12995721--12995852 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 43
12995711 AGAGGCATTT
** *
12995721 GTGGAAAAATCCGCCGCTAAAGAGCATGACCTTTAGCGGCGTTC
1 GTGGAAAAAAACGCCGCTAAAGAACATGA-CTTTAGCGGCGTTC
* * *
12995765 GTGGAAAAAAAACGCCGCTAAAGAACATTACTTGTAGCGGTGTTT
1 GTGG-AAAAAAACGCCGCTAAAGAACATGACTT-TAGCGGCGTTC
**
12995810 GTGG-AAAAGGCGCCGCTAAAAGAACATGAGCTTTAGCGGCGTT
1 GTGGAAAAAAACGCCGCT-AAAGAACATGA-CTTTAGCGGCGTT
12995853 TGTTGGTATG
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 11 0.15
44 26 0.35
45 37 0.50
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (43 bp):
GTGGAAAAAAACGCCGCTAAAGAACATGACTTTAGCGGCGTTC
Found at i:12995854 original size:44 final size:42
Alignment explanation
Indices: 12995683--12995855 Score: 150
Period size: 44 Copynumber: 3.9 Consensus size: 42
12995673 GCATTTTTAT
* * * * *
12995683 AAAAGCGCCGCTAAA-AGTCATGTTCTATAGAGGCATTTGTGGA
1 AAAAGCGCCGCTAAAGA-ACATG-ACTTTAGCGGCGTTTGTGGA
* * *
12995726 AAAATCCGCCGCTAAAGAGCATGACCTTTAGCGGCGTTCGTGGAAA
1 AAAA-GCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTGTGG--A
* * *
12995772 AAAAACGCCGCTAAAGAACATTACTTGTAGCGGTGTTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGACTT-TAGCGGCGTTTGTGGA
*
12995815 AAAGGCGCCGCTAAAAGAACATGAGCTTTAGCGGCGTTTGT
1 AAAAGCGCCGCT-AAAGAACATGA-CTTTAGCGGCGTTTGT
12995856 TGGTATGCGC
Statistics
Matches: 106, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
43 15 0.14
44 53 0.50
45 33 0.31
46 5 0.05
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTGTGGA
Found at i:12999668 original size:17 final size:16
Alignment explanation
Indices: 12999638--12999671 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12999628 GTGATAGATC
*
12999638 TCCGACGAGTTTCCAA
1 TCCGACGAGCTTCCAA
12999654 TCCGATCGAGCTTCCAA
1 TCCGA-CGAGCTTCCAA
12999671 T
1 T
12999672 AACCTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (16 bp):
TCCGACGAGCTTCCAA
Found at i:13002133 original size:29 final size:29
Alignment explanation
Indices: 13002073--13002133 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
13002063 GACTATCGTC
*
13002073 GCCACACGACCGTATGCCAGGCCGGGTGA
1 GCCACACGACCGTATGCCAGGCCGGGTAA
* * * * *
13002102 GCCACGCGAGCGTGTGCTAGGCCGTGTAA
1 GCCACACGACCGTATGCCAGGCCGGGTAA
13002131 GCC
1 GCC
13002134 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.33, G:0.36, T:0.13
Consensus pattern (29 bp):
GCCACACGACCGTATGCCAGGCCGGGTAA
Found at i:13015581 original size:44 final size:44
Alignment explanation
Indices: 13015518--13016059 Score: 293
Period size: 44 Copynumber: 12.4 Consensus size: 44
13015508 CCACTAATCC
* *
13015518 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAGATCT
* * ** * * *
13015562 TATCTCACTGAAGTTGCAGTAGAGTGGA-T--CGCATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAGATCT
* * *
13015603 TATCTCCCTGAAGTTGCAGCGGAGCAGACT-AAGTAACCA-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-CAGA-TCT
* * * * ** * *
13015647 TATCCCCCTAAAGTTGCAATGGGGCAGATCGAAG-ATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA--ACAGATCT
* * * * *
13015692 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAACAGATCT
* ** * * *
13015736 TATCTCCCTGTAGTTGCAACGAAGCAGATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAGATCT
* * * * * * *** *
13015780 TATCCCCCTAAAGTTGTAGTGGGGCAGATCGAAGGTGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGCAACAGATCT
** * * * * * * *
13015825 TATCTTTCTGAGGTTGCAGTGGAACAAATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAACAGATCT
* * * *
13015869 TATCTCCCTGAAGTTGCGGTGGAGCGGATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAGATCT
* * * * *
13015913 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAACAGATCT
** * *
13015957 TATCTCCCTGAAGTTGCAACGGAGC-GAATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCAACAGATCT
* *
13016001 TATCTCTCTGAAGTTGCAGTAGAGCAGATT---GCAACCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-CAGATCT
* *
13016042 CATCTCCCAGAAGTTGCA
1 TATCTCCCTGAAGTTGCA
13016060 ACGGAACGGA
Statistics
Matches: 363, Mismatches: 116, Indels: 41
0.70 0.22 0.08
Matches are distributed among these distances:
41 51 0.14
42 4 0.01
43 10 0.03
44 227 0.63
45 70 0.19
46 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAACAGATCT
Found at i:13015677 original size:85 final size:87
Alignment explanation
Indices: 13015513--13015719 Score: 206
Period size: 85 Copynumber: 2.4 Consensus size: 87
13015503 TGAAGCCACT
* * * * *
13015513 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAACAGATCTTATCTCACTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAACAGATCTTATCCCACTAAAGTTG
* **
13015578 CAGTAGAGTGGATCG-CAT-CA
66 CAATAGAGCAGATCGACATGCA
** * *
13015598 GGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACT-AAGTAACCA-AGTCTTATCCCCCTAAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAA-CAGA-TCTTATCCCACTAAAGT
* * *
13015661 TGCAATGGGGCAGATCGAAGATGGCA
64 TGCAATAGAGCAGATCG-ACAT-GCA
*
13015687 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
13015720 TTGAAGCCGA
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
84 7 0.07
85 57 0.59
87 2 0.02
89 31 0.32
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (87 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGTAACAGATCTTATCCCACTAAAGTTG
CAATAGAGCAGATCGACATGCA
Found at i:13015763 original size:133 final size:132
Alignment explanation
Indices: 13015603--13015946 Score: 422
Period size: 133 Copynumber: 2.6 Consensus size: 132
13015593 CATCAGGTCT
* *
13015603 TATCTCCCTGAAGTTGCAGCGGAGCAGACTAAGTAAC-CA-AGTCTTATCCCCCTAAAGTTGCAA
1 TATCTCCCTGAAGTTGCAACGAAGCAGACTAA--AACACAGA-TCTTATCCCCCTAAAGTTGCAA
* *
13015666 TGGGGCAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
63 TGGGGCAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAAATTGAAGCCGAT
13015731 AATCC
128 AATCC
* * * *
13015736 TATCTCCCTGTAGTTGCAACGAAGCAGATTAAAACATCAGATCTTATCCCCCTAAAGTTGTAGTG
1 TATCTCCCTGAAGTTGCAACGAAGCAGACTAAAACA-CAGATCTTATCCCCCTAAAGTTGCAATG
* **
13015801 GGGCAGATCGAAGGTGGCAAATCTTATCTTTCTGAGGTTGCAGTGGAACAAATTGAAGCCGATAA
65 GGGCAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAAATTGAAGCCGATAA
13015866 TCC
130 TCC
*** * * * * * * *
13015869 TATCTCCCTGAAGTTGCGGTGGAGCGGATTAAAACATCAGATCTTATCTCCCTGAGGTTGCAGTG
1 TATCTCCCTGAAGTTGCAACGAAGCAGACTAAAACA-CAGATCTTATCCCCCTAAAGTTGCAATG
* *
13015934 GAGCAGATTGAAG
65 GGGCAGATCGAAG
13015947 CCGATAATCC
Statistics
Matches: 185, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
131 3 0.02
133 181 0.98
134 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (132 bp):
TATCTCCCTGAAGTTGCAACGAAGCAGACTAAAACACAGATCTTATCCCCCTAAAGTTGCAATGG
GGCAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAACAAATTGAAGCCGATAAT
CC
Found at i:13016026 original size:88 final size:88
Alignment explanation
Indices: 13015821--13016031 Score: 332
Period size: 88 Copynumber: 2.4 Consensus size: 88
13015811 AAGGTGGCAA
* * *
13015821 ATCTTATCTTTCTGAGGTTGCAGTGGAACAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGC
1 ATCTTATCTCTCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGC
*** *
13015886 GGTGGAGCGGATTAAAACATCAG
66 AACGGAGCGAATTAAAACATCAG
*
13015909 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGC
1 ATCTTATCTCTCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGC
13015974 AACGGAGCGAATTAAAACATCAG
66 AACGGAGCGAATTAAAACATCAG
* *
13015997 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTG
1 ATCTTATCTCTCTGAGGTTGCAGTGGAGCAGATTG
13016032 CAACCAGTCT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 112 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCTCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGC
AACGGAGCGAATTAAAACATCAG
Found at i:13019766 original size:18 final size:19
Alignment explanation
Indices: 13019737--13019773 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
13019727 ACTGTAGATT
13019737 GTTTTGGACTTTTTTTTTC
1 GTTTTGGACTTTTTTTTTC
13019756 GTTTT-GACTTTTTTTTTC
1 GTTTTGGACTTTTTTTTTC
13019774 AGATTAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.05, C:0.11, G:0.14, T:0.70
Consensus pattern (19 bp):
GTTTTGGACTTTTTTTTTC
Found at i:13022064 original size:7 final size:7
Alignment explanation
Indices: 13022054--13022079 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13022044 AATCAAAATC
13022054 AAAAAGA
1 AAAAAGA
13022061 AAAAAGA
1 AAAAAGA
13022068 AAAAAGA
1 AAAAAGA
13022075 AAAAA
1 AAAAA
13022080 TCAAAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:13022065 original size:14 final size:14
Alignment explanation
Indices: 13022048--13022084 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13022038 TAAAAAAATC
13022048 AAAATCAAAAAGAA
1 AAAATCAAAAAGAA
**
13022062 AAAAGAAAAAAGAA
1 AAAATCAAAAAGAA
13022076 AAAATCAAA
1 AAAATCAAA
13022085 GTCAAATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAATCAAAAAGAA
Found at i:13023035 original size:14 final size:14
Alignment explanation
Indices: 13023003--13023037 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13022993 AAAAAAGGTG
13023003 AAAAATGAAAAAAT
1 AAAAATGAAAAAAT
* *
13023017 GAAAATGAAAAAGT
1 AAAAATGAAAAAAT
13023031 AAAAATG
1 AAAAATG
13023038 GAAAGGCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAAAAT
Found at i:13024467 original size:131 final size:131
Alignment explanation
Indices: 13024233--13024551 Score: 539
Period size: 131 Copynumber: 2.4 Consensus size: 131
13024223 TCAATGAAAT
* ** *
13024233 CACAAGTCATATGTCCCTGACCAGCAGTGGAATAGGTCAGAAATTGTAGATCTTATCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAAG
* *
13024298 CAATAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
13024363 C
131 C
*
13024364 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAAG
*
13024429 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
13024494 C
131 C
* * *
13024495 CATAAGCCCTATGTCCCTGACCAGCAGTGGAATAGGTTGAAAATTGCAGATCTTATC
1 CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTATC
13024552 GAAGACGACG
Statistics
Matches: 176, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 176 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (131 bp):
CACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAAG
CAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
C
Found at i:13024708 original size:41 final size:42
Alignment explanation
Indices: 13024648--13024760 Score: 124
Period size: 44 Copynumber: 2.7 Consensus size: 42
13024638 AAGTAATAGA
* * *
13024648 TCTTATCTCTCTGAAGTTGCAGTAGAG-TG-GA-TCACATCAAG
1 TCTTATCTCCCTGAGGTTGCAGTAGAGCTGAGAGT-A-AGCAAG
*
13024689 TCTTATCTCCCTGAGGTTGCAGTGGAGCTGACTGAGTAAGCAAG
1 TCTTATCTCCCTGAGGTTGCAGTAGAGCTGA--GAGTAAGCAAG
*
13024733 TCTTATCTCCCTGAGGTTGCAGTGGAGC
1 TCTTATCTCCCTGAGGTTGCAGTAGAGC
13024761 AGATTGAAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
41 24 0.38
42 2 0.03
44 33 0.52
45 3 0.05
46 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (42 bp):
TCTTATCTCCCTGAGGTTGCAGTAGAGCTGAGAGTAAGCAAG
Found at i:13025943 original size:20 final size:21
Alignment explanation
Indices: 13025894--13025952 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
13025884 ATTTTTGCAA
13025894 TGTAT-TTATTTATTTTAAAC
1 TGTATATTATTTATTTTAAAC
*
13025914 TTTATATTATTTATTTTAAA-
1 TGTATATTATTTATTTTAAAC
13025934 TCGT-TATTATTTATTTTAA
1 T-GTATATTATTTATTTTAA
13025953 GTTTTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TGTATATTATTTATTTTAAAC
Found at i:13025982 original size:21 final size:21
Alignment explanation
Indices: 13025899--13026046 Score: 84
Period size: 21 Copynumber: 6.5 Consensus size: 21
13025889 TGCAATGTAT
13025899 TTATTTATTTTAAACTT-TATA
1 TTATTTATTTTAAA-TTATATA
**
13025920 TTATTTATTTTAAATCGT-TA
1 TTATTTATTTTAAATTATATA
*
13025940 TTATTTATTTTAAGTTTTTTATATA
1 TTATTTATTTTAA----ATTATATA
*
13025965 TTATGTATTTTAAATTATGTTAATCAA
1 TTATTTATTTTAAATTA---T-AT--A
*
13025992 TTATTCATTTTAAATATATATA
1 TTATTTATTTTAAAT-TATATA
* * *
13026014 TTATTTATGTTAAACTACATA
1 TTATTTATTTTAAATTATATA
13026035 TTTATATTATTT
1 -TTAT-TTATTT
13026047 ATTTGGAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
20 16 0.16
21 23 0.23
22 17 0.17
23 5 0.05
24 5 0.05
25 17 0.17
27 14 0.14
28 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (21 bp):
TTATTTATTTTAAATTATATA
Found at i:13026039 original size:22 final size:22
Alignment explanation
Indices: 13025991--13026044 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
13025981 ATGTTAATCA
* * *
13025991 ATTATTCATTTTAAATATATAT
1 ATTATTTATGTTAAATACATAT
13026013 ATTATTTATGTTAAACTACATAT
1 ATTATTTATGTTAAA-TACATAT
13026036 -TTATATTAT
1 ATTAT-TTAT
13026045 TTATTTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTATTTATGTTAAATACATAT
Done.