Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 59 of 195
Found at i:12076576 original size:231 final size:231
Alignment explanation
Indices: 12075991--12076608 Score: 696
Period size: 231 Copynumber: 2.6 Consensus size: 231
12075981 TTTTCAGTAT
*
12075991 AAAATGCCTTTAATATTATA-TAACTAAAATTTTAAAGGATTATTGAAGGCGTTTGTT-CAAGAA
1 AAAATGCCTTTAATATTCTACT-ACTAAAATTTTAAAGGATTATTGAAGGCGTTTGTTCCAA-AA
* * * *
12076054 AAACACCTTCATTAATTCATTCTAATTTTTGAAAGAATTTATTAAATGCATTTTTTGCATTATAT
64 AAACGCCTTCACTAATTCATTCTAA-TTTTGAAAGAATTTATTAAAGGCATTTTTTGCATTATAC
* * * *
12076119 GCCTTTAATAATTTTTGTATAAAATTATTGAAGGCATTTTTTGAGAAAAAATACCTTCAATAATT
128 GCCTTCAATAATTTTTG--TAAAATTATTAAAGGC--TGTTT--GAAAAAATACCTTCAAAAATT
* *
12076184 TTCTATTAAAAATTGTTTGAGATTATTAAAGGTATCTTGTAGCAA
187 TTCTATTAAAAATTGTTTGAGATTATTAAAGGCATCTTCTAGCAA
* *
12076229 AAAATGCCTTTAATATTCTACTACTAAAATTTTAAGAAGG-TTATTGAAAGTGTTTGTTCCAAAA
1 AAAATGCCTTTAATATTCTACTACTAAAATTTT-A-AAGGATTATTGAAGGCGTTTGTTCC-AAA
* *
12076293 AAAATGCCTTCACTAATTCATTCAAATCTTTGAACA-AATTTATTAAAGGCATTTTTTGCATTAT
63 AAAACGCCTTCACTAATTCATTCTAAT-TTTGAA-AGAATTTATTAAAGGCATTTTTTGCATTAT
* * **
12076357 A-GACCTTCAATAATTTTTGTAGAGTTATTAAAGGC-GTTT-AAAAAATGTCTTCAAAAATTTTC
126 ACG-CCTTCAATAATTTTTGTAAAATTATTAAAGGCTGTTTGAAAAAATACCTTCAAAAATTTTC
* * *
12076419 TTTTAAAAATTGTTTGGGATTATTAAAGGCATCTTCTAG-TA
190 TATTAAAAATTGTTTGAGATTATTAAAGGCATCTTCTAGCAA
* * ** *
12076460 GAAATG-CTTTCAATATTCTTCTACTAAAATTTTAAAGGGATTATTGAAGGCGTTCATTCCATAA
1 AAAATGCCTTT-AATATTCTACTACTAAAATTTTAAA-GGATTATTGAAGGCGTTTGTTCCAAAA
* ** * * *
12076524 AAACGCCTTCAGTAATTTGTTCTAGTTTTGAAGGAATTTGGTGTAAAGGCATTTTTTGCATTATA
64 AAACGCCTTCACTAATTCATTCTAATTTTGAAAGAATTT-AT-TAAAGGCATTTTTTGCATTATA
*
12076589 CGCCTTGAATAATTTTTGTA
127 CGCCTTCAATAATTTTTGTA
12076609 CATTTATTTG
Statistics
Matches: 328, Mismatches: 37, Indels: 37
0.82 0.09 0.09
Matches are distributed among these distances:
229 13 0.04
230 31 0.09
231 82 0.25
232 56 0.17
235 3 0.01
238 43 0.13
239 20 0.06
240 77 0.23
241 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (231 bp):
AAAATGCCTTTAATATTCTACTACTAAAATTTTAAAGGATTATTGAAGGCGTTTGTTCCAAAAAA
ACGCCTTCACTAATTCATTCTAATTTTGAAAGAATTTATTAAAGGCATTTTTTGCATTATACGCC
TTCAATAATTTTTGTAAAATTATTAAAGGCTGTTTGAAAAAATACCTTCAAAAATTTTCTATTAA
AAATTGTTTGAGATTATTAAAGGCATCTTCTAGCAA
Found at i:12076773 original size:184 final size:184
Alignment explanation
Indices: 12076431--12076792 Score: 471
Period size: 185 Copynumber: 2.0 Consensus size: 184
12076421 TTAAAAATTG
* * *
12076431 TTTGGGATTATTAAAGGCATCTTCTAGTAGAAATGCTTTCAATATTCTTCTACTAAAATTTTAAA
1 TTTGAGATTATTAAAAGCATCTTCTAGTAGAAATGCTTTCAATATTCTTCTAATAAAATTTTAAA
* * *
12076496 GGGATTATTGAAGGCGTTCATTCCATAAAAACGCCTTCAGTAATTTGTTCTAGTTTTGAAGGAAT
66 GGGATTATTGAAGGCGTTCATTCCATAAAAACGCCTCCACTAATTCGTTCTAGTTTTGAAGGAAT
* * * *
12076561 TTGGTGTAAAGGCATTTTTTGCATTATACGCCTTGAATAATTTTTGTACATTTA
131 TTGATGTAAAGGCATTTTTTACATTATACACCTTCAATAATTTTTGTACATTTA
*
12076615 TTTGAGATTATTAAAAGTATCTTCTAGTAGAAAATGCCTTT-AATATT-TTCCTAATAAAATTTT
1 TTTGAGATTATTAAAAGCATCTTCTAGTAG-AAATG-CTTTCAATATTCTT-CTAATAAAATTTT
* * * * * * *
12076678 AAGGGGGTTATTGAAGGCGTTTATTCTATAAAAATGCCTCCACTAATTCGTTCTATTTTTTTAAG
63 AAAGGGATTATTGAAGGCGTTCATTCCATAAAAACGCCTCCACTAATTCGTTCTA-GTTTTGAAG
* * *
12076743 GAATTT-AT-TGAAGGCGTTTTTTATATTATACACCTTCAATAATTTTTGTA
127 GAATTTGATGTAAAGGCATTTTTTACATTATACACCTTCAATAATTTTTGTA
12076793 TACAATTATT
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
184 65 0.42
185 71 0.46
186 17 0.11
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (184 bp):
TTTGAGATTATTAAAAGCATCTTCTAGTAGAAATGCTTTCAATATTCTTCTAATAAAATTTTAAA
GGGATTATTGAAGGCGTTCATTCCATAAAAACGCCTCCACTAATTCGTTCTAGTTTTGAAGGAAT
TTGATGTAAAGGCATTTTTTACATTATACACCTTCAATAATTTTTGTACATTTA
Found at i:12077684 original size:28 final size:28
Alignment explanation
Indices: 12077627--12077687 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
12077617 ATGGTTTGTC
* * * *
12077627 GAATGGTATTGTGTGATATTATTTTACT
1 GAATGATATTGTATGATATTAGTATACT
*
12077655 GAATGATATTGTATGATATTAGTATGCT
1 GAATGATATTGTATGATATTAGTATACT
12077683 GAATG
1 GAATG
12077688 GTTTGCTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.44
Consensus pattern (28 bp):
GAATGATATTGTATGATATTAGTATACT
Found at i:12077696 original size:12 final size:12
Alignment explanation
Indices: 12077679--12077738 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
12077669 GATATTAGTA
12077679 TGCTGAATGGTT
1 TGCTGAATGGTT
12077691 TGCTGAATGGTT
1 TGCTGAATGGTT
* * *
12077703 TACTAAATAGTACT
1 TGCTGAATGGT--T
12077717 T-CTGAATGGTT
1 TGCTGAATGGTT
12077728 TGCTGAATGGT
1 TGCTGAATGGT
12077739 GTTTTTGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 2 0.05
12 29 0.73
13 7 0.17
14 2 0.05
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (12 bp):
TGCTGAATGGTT
Found at i:12077747 original size:25 final size:24
Alignment explanation
Indices: 12077679--12077748 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
12077669 GATATTAGTA
*
12077679 TGCTGAATGGTTTGCTGAATGGTT
1 TGCTGAATGGTTTTCTGAATGGTT
* * * *
12077703 TACTAAATAGTACTTCTGAATGGTT
1 TGCTGAATGGT-TTTCTGAATGGTT
*
12077728 TGCTGAATGGTGTTTTTGAAT
1 TGCTGAATGGT-TTTCTGAAT
12077749 ACATTGTTGA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
24 8 0.24
25 26 0.76
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (24 bp):
TGCTGAATGGTTTTCTGAATGGTT
Found at i:12080965 original size:34 final size:35
Alignment explanation
Indices: 12080919--12080986 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
12080909 TATAAACTAA
12080919 ATGTTTTCTGGGCATAAACCTAC-ACTGACTTCAG
1 ATGTTTTCTGGGCATAAACCTACAACTGACTTCAG
*
12080953 ATGTTTTTTGGGCATAAACCTACAACTGACTTCA
1 ATGTTTTCTGGGCATAAACCTACAACTGACTTCA
12080987 CATATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 22 0.69
35 10 0.31
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (35 bp):
ATGTTTTCTGGGCATAAACCTACAACTGACTTCAG
Found at i:12081695 original size:63 final size:63
Alignment explanation
Indices: 12081615--12081750 Score: 170
Period size: 63 Copynumber: 2.2 Consensus size: 63
12081605 TTTCTTGTAG
* * *
12081615 AAAATGCCTTCAATAATCCCATA-CATTTTTTTATAAGGGGATTATTTAATG-CAT-TGTCTACC
1 AAAATGCCTTCAATAATCCCATATCAATTTTTT-TAACGGGATTATTCAA-GCCATAT-TCTACC
12081677 A
63 A
* * *
12081678 AAAATGCCTTCAGTAATCCCTTATCAATTTTTTTAACTGGATTATTCAAGCCATATTCTACCA
1 AAAATGCCTTCAATAATCCCATATCAATTTTTTTAACGGGATTATTCAAGCCATATTCTACCA
12081741 AAAATGCCTT
1 AAAATGCCTT
12081751 TACTATTCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 1 0.02
63 54 0.84
64 9 0.14
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (63 bp):
AAAATGCCTTCAATAATCCCATATCAATTTTTTTAACGGGATTATTCAAGCCATATTCTACCA
Found at i:12082070 original size:18 final size:19
Alignment explanation
Indices: 12082033--12082069 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12082023 CTATGTGGCA
*
12082033 CCCCAAATTGCCTTTTTTT
1 CCCCAAATTACCTTTTTTT
12082052 CCCCAAATTACCTTTTTT
1 CCCCAAATTACCTTTTTT
12082070 CTTTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.32, G:0.03, T:0.46
Consensus pattern (19 bp):
CCCCAAATTACCTTTTTTT
Found at i:12082219 original size:7 final size:7
Alignment explanation
Indices: 12082217--12082258 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
12082207 TTTTTTTAAT
12082217 TTTTTC-
1 TTTTTCA
12082223 TTTTTC-
1 TTTTTCA
12082229 TTTTT--
1 TTTTTCA
12082234 TTTTTCA
1 TTTTTCA
12082241 TTTTTCA
1 TTTTTCA
12082248 TTTTTCA
1 TTTTTCA
12082255 TTTT
1 TTTT
12082259 ACTTTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 11 0.32
7 18 0.53
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCA
Found at i:12082243 original size:25 final size:25
Alignment explanation
Indices: 12082197--12082258 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
12082187 CTTCACTGAG
12082197 TTTTCTTTTCTTTTTTTAATTTTTTC-T
1 TTTTC-TTT-TTTTTTTAA-TTTTTCAT
*
12082224 TTTTCTTTTTTTTTTCATTTTTCAT
1 TTTTCTTTTTTTTTTAATTTTTCAT
*
12082249 TTTTCATTTT
1 TTTTCTTTTT
12082259 ACTTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 18 0.56
26 3 0.09
27 5 0.16
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTCTTTTTTTTTTAATTTTTCAT
Found at i:12082244 original size:18 final size:18
Alignment explanation
Indices: 12082216--12082252 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
12082206 CTTTTTTTAA
12082216 TTTTTTCTTTTTC-TTTT
1 TTTTTTCTTTTTCATTTT
12082233 TTTTTTCATTTTTCATTTT
1 TTTTTTC-TTTTTCATTTT
12082252 T
1 T
12082253 CATTTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTTTTTCATTTT
Found at i:12082251 original size:14 final size:13
Alignment explanation
Indices: 12082217--12082265 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
12082207 TTTTTTTAAT
12082217 TTTTTCTTTTTC-
1 TTTTTCTTTTTCA
12082229 TTTTT-TTTTTCA
1 TTTTTCTTTTTCA
12082241 TTTTTCATTTTTCA
1 TTTTTC-TTTTTCA
*
12082255 TTTTACTTTTT
1 TTTTTCTTTTT
12082266 TTGTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 6 0.18
12 10 0.30
13 5 0.15
14 12 0.36
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCA
Found at i:12082265 original size:7 final size:6
Alignment explanation
Indices: 12082197--12082265 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
12082187 CTTCACTGAG
**
12082197 TTTTC- TTTTCT TTTT-T TAAT-T TTTTCT TTTTCT TTTT-T TTTTCAT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T
*
12082242 TTTTCAT TTTTCAT TTTACT TTTT
1 TTTTC-T TTTTC-T TTTTCT TTTT
12082266 TTGTTTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
5 16 0.30
6 19 0.35
7 19 0.35
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:12082760 original size:18 final size:18
Alignment explanation
Indices: 12082710--12082779 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
12082700 TGTGAACAAT
*
12082710 TTTTTTTTTCATTTTTCTCC
1 TTTTTTTTT-ATTTTTC-AC
* *
12082730 TTTTTCTCT-TTTTTCAC
1 TTTTTTTTTATTTTTCAC
**
12082747 TTTTTTTTTATTTTT-GT
1 TTTTTTTTTATTTTTCAC
12082764 TTATTTTTTTATTTTT
1 TT-TTTTTTTATTTTT
12082780 ATTAGATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 10 0.24
18 24 0.59
20 7 0.17
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTATTTTTCAC
Found at i:12083633 original size:12 final size:12
Alignment explanation
Indices: 12083607--12083640 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12083597 TAAATTTTAA
12083607 ATTTT-ATAT-T
1 ATTTTAATATAT
12083617 ATTTTAATATAT
1 ATTTTAATATAT
12083629 ATTTTAATATAT
1 ATTTTAATATAT
12083641 TTAAACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 4 0.18
12 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTAATATAT
Found at i:12083650 original size:22 final size:22
Alignment explanation
Indices: 12083607--12083650 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12083597 TAAATTTTAA
* *
12083607 ATTTTATATTATTTTAATATAT
1 ATTTTATATTATTTAAACATAT
12083629 ATTTTA-ATATATTTAAACATAT
1 ATTTTATAT-TATTTAAACATAT
12083651 TTAGATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATATTATTTAAACATAT
Found at i:12087581 original size:2 final size:2
Alignment explanation
Indices: 12087574--12087605 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12087564 TTAATAAGTA
12087574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12087606 GTGTGTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12095750 original size:27 final size:26
Alignment explanation
Indices: 12095706--12095778 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 26
12095696 TTTTTTTTTA
12095706 AATAATATATTGTATTTATATATGAAGAGC
1 AATAATAT-TT-T-TTT-TATATGAAGAGC
*
12095736 AATAATA-TTTTTTTATATGAAGAGT
1 AATAATATTTTTTTTATATGAAGAGC
*
12095761 AGTAATATTTTTTTTATA
1 AATAATATTTTTTTTATA
12095779 GTTTTATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 17 0.43
26 13 0.32
27 1 0.03
28 2 0.05
30 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (26 bp):
AATAATATTTTTTTTATATGAAGAGC
Found at i:12102713 original size:69 final size:69
Alignment explanation
Indices: 12102609--12102783 Score: 253
Period size: 69 Copynumber: 2.5 Consensus size: 69
12102599 CTTAAAGATT
* *
12102609 AAATCTCAAAAACTTTTGAATGCTCATCCAATCAAAAGCCATGAAACTTTAAAAATTAAAAATAT
1 AAATCTC-AAAACTTTTGAATGCTCCTCCATTCAAAAGCCATGAAACTTTAAAAATTAAAAATAT
*
12102674 TTTTC
65 TTTAC
* * *
12102679 AAATCTCAAAA-TCTTTGAATGCTCCTCCATTCAAAAGTCGTGAAACTTTAAAAATTAAAAATGT
1 AAATCTCAAAACT-TTTGAATGCTCCTCCATTCAAAAGCCATGAAACTTTAAAAATTAAAAATAT
12102743 TTTAC
65 TTTAC
**
12102748 AAATCTCAAAACTTTTGAATGCTCCTCTGTTCAAAA
1 AAATCTCAAAACTTTTGAATGCTCCTCCATTCAAAA
12102784 TGCTCCTTCA
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
68 1 0.01
69 86 0.91
70 8 0.08
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (69 bp):
AAATCTCAAAACTTTTGAATGCTCCTCCATTCAAAAGCCATGAAACTTTAAAAATTAAAAATATT
TTAC
Found at i:12102903 original size:35 final size:35
Alignment explanation
Indices: 12102844--12102915 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
12102834 GCAAATTTCT
* * *
12102844 AAACCTTTGAATGCTTCTCCGATTAAAGGCTATGA
1 AAACCTTTAAATGCTCCTCCGATTAAAGGCCATGA
* *
12102879 AAACTTTTAAATGCTCCTCTGATTAAAGGCCATGA
1 AAACCTTTAAATGCTCCTCCGATTAAAGGCCATGA
12102914 AA
1 AA
12102916 TGTTAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (35 bp):
AAACCTTTAAATGCTCCTCCGATTAAAGGCCATGA
Found at i:12103084 original size:69 final size:69
Alignment explanation
Indices: 12102878--12103204 Score: 358
Period size: 67 Copynumber: 4.8 Consensus size: 69
12102868 AAAGGCTATG
* * ** * *
12102878 AAAACTTTTAAATGCTCCTCTGATTAAAGGCCATGAAA-TGTTAAAAATTTAAAAATATTTTACA
1 AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACT-TTAAAAATTT-AAAATATTTTGCA
12102942 AATCTC
64 AATCTC
* * * * * * *
12102948 TAAACCTTTGACTACTCCTCCAATCAGAGGCTATGAAAC--TCAAAATTTAAAATGTTTTGCAAA
1 AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAA
12103011 TCTC
66 TCTC
* *
12103015 AAAACTTTTGAGTACTCTTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAA
1 AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAA
12103080 TCTC
66 TCTC
* * * * * * *
12103084 AAAACTTTTGAATGCTCCTCTAATGAGAGGCCATAAAACTTT--AAATTTAAAATGTTTTTCAAA
1 AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAA
*
12103147 TATC
66 TCTC
* * * *
12103151 AAAACTTTTAAATGCTCTTCCAACCAAAGGCCATGAAACTTTAAAAATTTAAAA
1 AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAA
12103205 ATATATTTTT
Statistics
Matches: 214, Mismatches: 38, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
67 107 0.50
68 8 0.04
69 71 0.33
70 28 0.13
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (69 bp):
AAAACTTTTGAATACTCCTCCAATCAAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAA
TCTC
Found at i:12103123 original size:136 final size:136
Alignment explanation
Indices: 12102903--12103204 Score: 426
Period size: 136 Copynumber: 2.2 Consensus size: 136
12102893 TCCTCTGATT
* *
12102903 AAAGGCCATGAAA-TGTTAAAAATTTAAAAATATTTTACAAATCTCTAAACCTTTGACTACTCCT
1 AAAGGCCATGAAACT-TTAAAAATTT-AAAATATTTTACAAATCTCAAAACCTTTGAATACTCCT
* * * * *
12102967 CCAATCAGAGGCTATGAAACTCAAAATTTAAAATGTTTTGCAAATCTCAAAACTTTTGAGTACTC
64 CCAATCAGAGGCCATAAAACTCAAAATTTAAAATGTTTTGCAAATATCAAAACTTTTAAATACTC
*
12103032 TTCCAATC
129 TTCCAACC
* * * *
12103040 AAAGGCCATGAAACTTTAAAAATTTAAAATATTTTGCAAATCTCAAAACTTTTGAATGCTCCTCT
1 AAAGGCCATGAAACTTTAAAAATTTAAAATATTTTACAAATCTCAAAACCTTTGAATACTCCTCC
* ** * *
12103105 AATGAGAGGCCATAAAACTTTAAATTTAAAATGTTTTTCAAATATCAAAACTTTTAAATGCTCTT
66 AATCAGAGGCCATAAAACTCAAAATTTAAAATGTTTTGCAAATATCAAAACTTTTAAATACTCTT
12103170 CCAACC
131 CCAACC
12103176 AAAGGCCATGAAACTTTAAAAATTTAAAA
1 AAAGGCCATGAAACTTTAAAAATTTAAAA
12103205 ATATATTTTT
Statistics
Matches: 147, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
136 123 0.84
137 23 0.16
138 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.32
Consensus pattern (136 bp):
AAAGGCCATGAAACTTTAAAAATTTAAAATATTTTACAAATCTCAAAACCTTTGAATACTCCTCC
AATCAGAGGCCATAAAACTCAAAATTTAAAATGTTTTGCAAATATCAAAACTTTTAAATACTCTT
CCAACC
Found at i:12103808 original size:12 final size:12
Alignment explanation
Indices: 12103788--12103831 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
12103778 TTATCAAATG
*
12103788 ATGTGAATACAA
1 ATGTCAATACAA
12103800 ATGTCAATACAA
1 ATGTCAATACAA
*
12103812 ATGTCAATGCAA
1 ATGTCAATACAA
*
12103824 ATGCCAAT
1 ATGTCAAT
12103832 GCCAATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (12 bp):
ATGTCAATACAA
Found at i:12103824 original size:24 final size:24
Alignment explanation
Indices: 12103788--12103845 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
12103778 TTATCAAATG
* *
12103788 ATGTGAATACAAATGTCAATACAA
1 ATGTGAATGCAAATGCCAATACAA
* * *
12103812 ATGTCAATGCAAATGCCAATGCCA
1 ATGTGAATGCAAATGCCAATACAA
12103836 ATGTGAATGC
1 ATGTGAATGC
12103846 TTGATGTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
ATGTGAATGCAAATGCCAATACAA
Found at i:12103832 original size:12 final size:12
Alignment explanation
Indices: 12103797--12103845 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
12103787 GATGTGAATA
*
12103797 CAAATGTCAATA
1 CAAATGTCAATG
12103809 CAAATGTCAATG
1 CAAATGTCAATG
*
12103821 CAAATGCCAATG
1 CAAATGTCAATG
* *
12103833 CCAATGTGAATG
1 CAAATGTCAATG
12103845 C
1 C
12103846 TTGATGTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (12 bp):
CAAATGTCAATG
Found at i:12104065 original size:41 final size:41
Alignment explanation
Indices: 12104010--12104094 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
12104000 TAGATACAAG
12104010 TGCAAATACAAATGTCTTTCTTATAATGCAGATGCAAGCGA
1 TGCAAATACAAATGTCTTTCTTATAATGCAGATGCAAGCGA
* * * * *
12104051 TGCAAATACGAATGTCTTTTTTGTGATGCAGATGCAAGTGA
1 TGCAAATACAAATGTCTTTCTTATAATGCAGATGCAAGCGA
12104092 TGC
1 TGC
12104095 GTATGCAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (41 bp):
TGCAAATACAAATGTCTTTCTTATAATGCAGATGCAAGCGA
Found at i:12104112 original size:41 final size:41
Alignment explanation
Indices: 12104010--12104112 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
12104000 TAGATACAAG
* * * *
12104010 TGCAAATACAAATGTCTTTCTTATAATGCAGATGCAAGCGA
1 TGCAAATACAAATATCTTTTTTGTGATGCAGATGCAAGCGA
* * *
12104051 TGCAAATACGAATGTCTTTTTTGTGATGCAGATGCAAGTGA
1 TGCAAATACAAATATCTTTTTTGTGATGCAGATGCAAGCGA
** *
12104092 TGCGTATGCAAATAT-TTTTTT
1 TGCAAATACAAATATCTTTTTT
12104113 CTTATATCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (41 bp):
TGCAAATACAAATATCTTTTTTGTGATGCAGATGCAAGCGA
Found at i:12106739 original size:18 final size:19
Alignment explanation
Indices: 12106716--12106755 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
12106706 AGATACTGCA
12106716 TTTAATTTTACTGCATT-G
1 TTTAATTTTACTGCATTAG
*
12106734 TTTAATTTTTCTGCATTAG
1 TTTAATTTTACTGCATTAG
12106753 TTT
1 TTT
12106756 TAGGTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTAATTTTACTGCATTAG
Found at i:12109302 original size:117 final size:117
Alignment explanation
Indices: 12109092--12109316 Score: 339
Period size: 117 Copynumber: 1.9 Consensus size: 117
12109082 TTGATTTTCC
*
12109092 CTCTAGATTTCTATTTTCTATCTATTTCCTTACTTATTCTACACCCTTTACTTTCACAGCCACTA
1 CTCTAGATTTCTATTTTCTATCTATTTCCTTACTTATTCTACACCATTTACTTTCACAGCCACTA
*
12109157 TATCAAACTAAATAACTAAATTATCAAGGAAATGTAGCACATGCAGGCCTAT
66 TATCAAACTAAATAACTAAATTACCAAGGAAATGTAGCACATGCAGGCCTAT
* * * *
12109209 CTCT-GATTTCTATTTTCTATCTCTTTCCTTTACTTGGTT-TACATCATTTACTTTCACAGTCAC
1 CTCTAGATTTCTATTTTCTATCTATTTCC-TTACTT-ATTCTACACCATTTACTTTCACAGCCAC
*
12109272 TATATCAAACCTAAA-AACTAAATTACCAAGGATATGTAGCACATG
64 TATATCAAA-CTAAATAACTAAATTACCAAGGAAATGTAGCACATG
12109317 TAAGAAATAA
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
116 23 0.23
117 68 0.69
118 7 0.07
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (117 bp):
CTCTAGATTTCTATTTTCTATCTATTTCCTTACTTATTCTACACCATTTACTTTCACAGCCACTA
TATCAAACTAAATAACTAAATTACCAAGGAAATGTAGCACATGCAGGCCTAT
Found at i:12113380 original size:26 final size:26
Alignment explanation
Indices: 12113351--12113410 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
12113341 TATAAGTAGT
* *
12113351 ATTAAAATCTTTAAAAATATTTTTAC
1 ATTAAAATCTTTAAAAACATTTTTAA
*
12113377 ATTAAAATCTTTAAATACATTTTTAA
1 ATTAAAATCTTTAAAAACATTTTTAA
12113403 ATTAAAAT
1 ATTAAAAT
12113411 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTAAAATCTTTAAAAACATTTTTAA
Found at i:12114908 original size:16 final size:15
Alignment explanation
Indices: 12114866--12114926 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
12114856 TATTCTAATT
*
12114866 AAAAAAACAAAAAAG
1 AAAAAAAAAAAAAAG
**
12114881 TAAAAAGTAAAAAAAG
1 -AAAAAAAAAAAAAAG
12114897 ACAAAAAAAAAAGAAGAG
1 A-AAAAAAAAAA-AA-AG
12114915 AAAAAAAAAAAA
1 AAAAAAAAAAAA
12114927 CACCCCATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 1 0.03
16 21 0.57
17 12 0.32
18 3 0.08
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:12114918 original size:25 final size:24
Alignment explanation
Indices: 12114866--12114926 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
12114856 TATTCTAATT
*
12114866 AAAAAAACAAAAAAGTAAAAAGTA
1 AAAAAAACAAAAAAGAAAAAAGTA
12114890 AAAAAAGACAAAAAA-AAAAGAAG-A
1 AAAAAA-ACAAAAAAGAAAA-AAGTA
*
12114914 GAAAAAA-AAAAAA
1 AAAAAAACAAAAAA
12114927 CACCCCATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 15 0.45
25 11 0.33
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (24 bp):
AAAAAAACAAAAAAGAAAAAAGTA
Found at i:12115440 original size:17 final size:17
Alignment explanation
Indices: 12115418--12115451 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12115408 AAATGTGTAA
12115418 AATTTATAATATGGATG
1 AATTTATAATATGGATG
*
12115435 AATTTATTATATGGATG
1 AATTTATAATATGGATG
12115452 GATGCGCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
AATTTATAATATGGATG
Found at i:12119278 original size:16 final size:15
Alignment explanation
Indices: 12119257--12119357 Score: 58
Period size: 16 Copynumber: 6.2 Consensus size: 15
12119247 TGGAGTTTGG
12119257 AAAAAGAATAAGAAAA
1 AAAAAGAA-AAGAAAA
12119273 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
***** *
12119288 TTTGTGAAAAAGGAAA
1 AAAAAG-AAAAGAAAA
*
12119304 AAAAAGAAAAAAAGAA
1 AAAAAGAAAAGAA-AA
*
12119320 AGAAAACTAAAAGAAAA
1 A-AAAA-GAAAAGAAAA
12119337 AGAAAAGAAAGAGCAAAA
1 A-AAAAGAAA-AG-AAAA
12119355 AAA
1 AAA
12119358 TAAAGTGGTG
Statistics
Matches: 63, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
15 13 0.21
16 23 0.37
17 16 0.25
18 11 0.17
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:12119287 original size:11 final size:11
Alignment explanation
Indices: 12119258--12119396 Score: 57
Period size: 11 Copynumber: 11.9 Consensus size: 11
12119248 GGAGTTTGGA
*
12119258 AAAAGAATAAG
1 AAAAGAAAAAG
12119269 AAAA-AAAAAG
1 AAAAGAAAAAG
*
12119279 AAAAGAAAATTTGTG
1 AAAAGAAAA----AG
*
12119294 AAAAAGGAAAA-
1 -AAAAGAAAAAG
*
12119305 AAAAGAAAAAA
1 AAAAGAAAAAG
**
12119316 AGAAAGAAAACT
1 A-AAAGAAAAAG
12119328 AAAAGAAAAAG
1 AAAAGAAAAAG
*
12119339 AAAAGAAAGAG
1 AAAAGAAAAAG
*
12119350 CAAAAAAATAAAG
1 -AAAAGAA-AAAG
****
12119363 TGGTGAAAAAG
1 AAAAGAAAAAG
*
12119374 TAAAGAAAAGAAG
1 AAAAG-AAA-AAG
12119387 AAAAGAAAAA
1 AAAAGAAAAA
12119397 AAAGGGGGGG
Statistics
Matches: 95, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
10 18 0.19
11 35 0.37
12 23 0.24
13 10 0.11
15 1 0.01
16 8 0.08
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:12122293 original size:18 final size:19
Alignment explanation
Indices: 12122267--12122302 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12122257 GAAAACAGAA
12122267 AAAGAAAAAAAT-AAAAAT
1 AAAGAAAAAAATGAAAAAT
*
12122285 AAAGGAAAAAATGAAAAA
1 AAAGAAAAAAATGAAAAA
12122303 GAGCTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAGAAAAAAATGAAAAAT
Found at i:12122773 original size:14 final size:14
Alignment explanation
Indices: 12122751--12122783 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12122741 TAACTTTATT
*
12122751 AAAAAAAAAAAAAG
1 AAAATAAAAAAAAG
12122765 AAAATAAAAAAAAG
1 AAAATAAAAAAAAG
12122779 AAAAT
1 AAAAT
12122784 TAAGATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (14 bp):
AAAATAAAAAAAAG
Found at i:12123011 original size:5 final size:5
Alignment explanation
Indices: 12122996--12123033 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
12122986 TTTAAAAAAA
*
12122996 CAACT CCACT CAACT CAACT CAACT CAACT CAACT CAA
1 CAACT CAACT CAACT CAACT CAACT CAACT CAACT CAA
12123034 TTCGATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.18
Consensus pattern (5 bp):
CAACT
Found at i:12123276 original size:18 final size:18
Alignment explanation
Indices: 12123262--12123299 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12123252 AGTAAAAAGT
12123262 AAAAAA-AAGACAAAAAA
1 AAAAAAGAAGACAAAAAA
*
12123279 AAAAAAGAAGAGAAAAAA
1 AAAAAAGAAGACAAAAAA
12123297 AAA
1 AAA
12123300 CACCCCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAGACAAAAAA
Found at i:12123280 original size:15 final size:14
Alignment explanation
Indices: 12123239--12123299 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 14
12123229 TATTCTAATT
12123239 AAAAAAACAAAAAAG
1 AAAAAAA-AAAAAAG
12123254 TAAAAAGTAAAAAAAAG
1 -AAAAA--AAAAAAAAG
12123271 ACAAAAAAAAAAAAG
1 A-AAAAAAAAAAAAG
12123286 AAGAGAAAAAAAAA
1 AA-A-AAAAAAAAA
12123300 CACCCCATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 15 0.38
17 11 0.28
18 2 0.05
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:12127646 original size:16 final size:17
Alignment explanation
Indices: 12127618--12127702 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 17
12127608 TGGAGTTTGG
12127618 AAAAAGAATAAGAAAA-A
1 AAAAAGAA-AAGAAAATA
*
12127635 AAAAAGAAAAGAAAATTTGTG
1 AAAAAGAAAAGAAAA----TA
* *
12127656 AAAAAGGAAA-AAAAGA
1 AAAAAGAAAAGAAAATA
12127672 AAAAAG-AAAGAAAACT-
1 AAAAAGAAAAGAAAA-TA
12127688 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
12127703 GAAAGAGCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
15 3 0.05
16 23 0.42
17 16 0.29
20 4 0.07
21 9 0.16
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAAGAAAATA
Found at i:12127770 original size:39 final size:39
Alignment explanation
Indices: 12127688--12127770 Score: 89
Period size: 39 Copynumber: 2.1 Consensus size: 39
12127678 AAAGAAAACT
* * * *
12127688 AAAAAGAAAAGAAAAGAAAGAGCAAAAAATAAAGTGGTG
1 AAAAAGAAAAGAAAAGAAAGAGAAAAAAAAAAAGGGGGG
*
12127727 AAAAAGTAAAGAAAAG-AAGA-AAAGAAAAAAAAGGGGGG
1 AAAAAGAAAAGAAAAGAAAGAGAAA-AAAAAAAAGGGGGG
12127765 CAAAAA
1 -AAAAA
12127771 CAAAGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
37 2 0.05
38 15 0.41
39 20 0.54
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (39 bp):
AAAAAGAAAAGAAAAGAAAGAGAAAAAAAAAAAGGGGGG
Found at i:12132634 original size:19 final size:18
Alignment explanation
Indices: 12132605--12132647 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
12132595 ATCATACAAA
*
12132605 ATAATATCATGGAATAAT
1 ATAATACCATGGAATAAT
*
12132623 ATGAATACCATGTAATAAT
1 AT-AATACCATGGAATAAT
12132642 ATAATA
1 ATAATA
12132648 TATCATCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (18 bp):
ATAATACCATGGAATAAT
Found at i:12132660 original size:20 final size:20
Alignment explanation
Indices: 12132617--12132673 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
12132607 AATATCATGG
* * *
12132617 AATAATATGA-ATACCATGT
1 AATAATATAATATATCATCT
12132636 AATAATATAATATATCATCT
1 AATAATATAATATATCATCT
12132656 AATAATATAATATATCAT
1 AATAATATAATATATCAT
12132674 GCAATTAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 9 0.26
20 25 0.74
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (20 bp):
AATAATATAATATATCATCT
Found at i:12135367 original size:16 final size:16
Alignment explanation
Indices: 12135334--12135367 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12135324 TAATGCTTAT
* *
12135334 AATACAAAAATAAGAA
1 AATACAAAAACAAAAA
12135350 AATACAAAAACAAAAA
1 AATACAAAAACAAAAA
12135366 AA
1 AA
12135368 AAGCCTTTTA
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:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (16 bp):
AATACAAAAACAAAAA
Found at i:12136070 original size:151 final size:148
Alignment explanation
Indices: 12135855--12136310 Score: 358
Period size: 149 Copynumber: 3.1 Consensus size: 148
12135845 CAAATGTTCC
* *
12135855 AAAAAAAAGC-AAAGAAAGAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
1 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
* * *
12135919 AAGTTTCAATTAGAATCTCAAAGAA-AAAAAAGAAGATAGAATTCAAGAAAGTAGAATGCTAAAA
66 AAGCTTCAATTAGAAT-TCAAA-AAGAAAAAA-AAGATAGAATTCAAAAAAGTAGAATACTAAAA
* *
12135983 TTGAAGT-ATGATGTTTTTAGAA
128 TTGAAGTCA-AATGTTTCTA-AA
** * ** *
12136005 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTTGAAGATGAGAGT-CTGGAGTGAAA-AATGAA
1 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAG-GT-AAATAATAAA
* * * * *
12136068 TAATGCTTCATTTAGAATTCAAAAAGGAAAAAAAGATAGAATTCAAAAAATTAGAATACTAAAGT
64 TAAAGCTTCAATTAGAATTCAAAAAGAAAAAAAAGATAGAATTCAAAAAAGTAGAATACTAAAAT
12136133 TGAAGTCAAATGTTTCTAAA
129 TGAAGTCAAATGTTTCTAAA
* * * * * ** * ** * *
12136153 AAAGAAAAAGCAAATAAAGAAAA-ACATGTACTTCGGAGATGAGAA-TCCTAGACAAAAAATGAA
1 AAA-AAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGA-AAGTCCAAGGTAAATAATAAA
* * * * * * * *
12136216 TAAAGCTTTAGTTAGAATTTAAAAAGTAAAAAGGGAA-ATAGAAATCAAGAAAGCA-AATGC-AA
64 TAAAGCTTCAATTAGAATTCAAAAAG-AAAAA--AAAGATAGAATTCAAAAAAGTAGAATACTAA
*
12136278 AAGTCGAAGTCAAATGTTTC-AAA
126 AA-TTGAAGTCAAATGTTTCTAAA
12136301 AAAAATAAAG
1 AAAAA-AAAG
12136311 AAAGAAAGAA
Statistics
Matches: 250, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
147 5 0.02
148 61 0.24
149 90 0.36
150 37 0.15
151 54 0.22
152 3 0.01
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.21
Consensus pattern (148 bp):
AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
AAGCTTCAATTAGAATTCAAAAAGAAAAAAAAGATAGAATTCAAAAAAGTAGAATACTAAAATTG
AAGTCAAATGTTTCTAAA
Found at i:12136147 original size:149 final size:150
Alignment explanation
Indices: 12135855--12136176 Score: 361
Period size: 149 Copynumber: 2.1 Consensus size: 150
12135845 CAAATGTTCC
* *
12135855 AAAAAAAAGC-AAAGAAAGAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
1 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
* * *
12135919 AAGTTTCAATTAGAATCTCAAAGAAAAAAAAGAAGATAGAATTCAAGAAAGTAGAATGCTAAAAT
66 AAGCTTCAATTAGAATCTCAAAGAAAAAAAAGAAGATAGAATTCAAAAAAGTAGAATACTAAAAT
* *
12135984 TGAAGTATGATGTTTTTAGAA
131 TGAAGTATAATGTTTCTA-AA
** * ** *
12136005 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTTGAAGATGAGAGT-CTGGAGTGAAA-AATGAA
1 AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAG-GT-AAATAATAAA
* * * *
12136068 TAATGCTTCATTTAGAAT-TCAAA-AAGGAAAAA-AAGATAGAATTCAAAAAATTAGAATACTAA
64 TAAAGCTTCAATTAGAATCTCAAAGAA-AAAAAAGAAGATAGAATTCAAAAAAGTAGAATACTAA
*
12136130 AGTTGAAGTCA-AATGTTTCTAAA
128 AATTGAAGT-ATAATGTTTCTAAA
*
12136153 AAAGAAAAAGCAAATAAAGAAAAA
1 AAA-AAAAAGCAAA-AAAAAAAAA
12136177 CATGTACTTC
Statistics
Matches: 146, Mismatches: 19, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
148 5 0.03
149 55 0.38
150 31 0.21
151 52 0.36
152 3 0.02
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.20
Consensus pattern (150 bp):
AAAAAAAAGCAAAAAAAAAAAAGATATGCACCTCCAAGATGAAAGTCCAAGGTAAATAATAAATA
AAGCTTCAATTAGAATCTCAAAGAAAAAAAAGAAGATAGAATTCAAAAAAGTAGAATACTAAAAT
TGAAGTATAATGTTTCTAAA
Found at i:12138031 original size:23 final size:22
Alignment explanation
Indices: 12137952--12138035 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 22
12137942 GCATCTATGC
* **
12137952 CCAGATTAATTGGCAC-CCAAG
1 CCAGATTAGTTGGCACTTTAAG
* *
12137973 CCCAGATTAGCTGGCACTTTAAA
1 -CCAGATTAGTTGGCACTTTAAG
*
12137996 CGCATATTAGTTGGCACTTTAAG
1 C-CAGATTAGTTGGCACTTTAAG
*
12138019 CCAAGATTCGTTGGCAC
1 CC-AGATTAGTTGGCAC
12138036 CTAAGCCCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (22 bp):
CCAGATTAGTTGGCACTTTAAG
Found at i:12138131 original size:22 final size:22
Alignment explanation
Indices: 12138091--12138132 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12138081 CAAATCAAAT
*
12138091 TAAGCCTAGTGTAGTTGGCACC
1 TAAGCCTAGTGTAGCTGGCACC
12138113 TAAGCCTAGAT-TAGCTGGCA
1 TAAGCCTAG-TGTAGCTGGCA
12138133 TTCAAGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
TAAGCCTAGTGTAGCTGGCACC
Found at i:12138249 original size:32 final size:33
Alignment explanation
Indices: 12138205--12138269 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
12138195 TGGTATCCAA
12138205 GCCCAGTCTAGTTGGCATCC-AAA-TCAAACTAG
1 GCCCAGTCTAGTTGGCA-CCAAAACTCAAACTAG
*
12138237 GCCCAGTTTAGTTGGCACCAAAACTCAAACTAG
1 GCCCAGTCTAGTTGGCACCAAAACTCAAACTAG
12138270 CTAGAGCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 19 0.63
33 9 0.30
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (33 bp):
GCCCAGTCTAGTTGGCACCAAAACTCAAACTAG
Found at i:12138433 original size:22 final size:22
Alignment explanation
Indices: 12138394--12138454 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
12138384 GGTATTTATG
* * *
12138394 CCCAAAGTAGTTGGCACCTAAG
1 CCCAAATTAGCTGGCACCTAAA
* * *
12138416 CTCAGATTGGCTGGCACCTAAA
1 CCCAAATTAGCTGGCACCTAAA
12138438 CCCAAATTAGCTGGCAC
1 CCCAAATTAGCTGGCAC
12138455 TTTAAGCCTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (22 bp):
CCCAAATTAGCTGGCACCTAAA
Found at i:12138958 original size:104 final size:103
Alignment explanation
Indices: 12138775--12139080 Score: 400
Period size: 104 Copynumber: 3.0 Consensus size: 103
12138765 TAAACCTTTA
* * *
12138775 GGCATAATTTCTAAGA-CTTTCGGATAAAATATTTTAAATCTTCAAAGTTTCAATGCCTCTGATA
1 GGCATAATTTCTAAGACCTTT-GGGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATA
* *
12138839 CGAGAAGCATTCAAAGATGTTGAAATTTGTAAGACC-TC
65 CGAGGAGCATTCAAAGATGTTGAGATTTGTAAGACCTTC
* * *
12138877 TGAGTATAATTTCTAAGACCTTTGGGTAAAACATTTTGAATTTTCAAAGTTTCAATGCCTTTGAT
1 -G-GCATAATTTCTAAGACCTTTGGGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGAT
12138942 ACGAGGAGCATTCAAAGATGTTGAGATTTGTAAGACCTTC
64 ACGAGGAGCATTCAAAGATGTTGAGATTTGTAAGACCTTC
* * *** * * *
12138982 GGCATAATCTCTATGACCTCCAGGTAAAACATTTTAAATTTTCAAAGTTTTAATGCCTCTAATAT
1 GGCATAATTTCTAAGACCTTTGGGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATAC
* * *
12139047 GATGAGCATTAAAAAATGTTGAGATTTGTAAGAC
66 GAGGAGCATTCAAAGATGTTGAGATTTGTAAGAC
12139081 TTCTAGGCAA
Statistics
Matches: 178, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
103 85 0.48
104 87 0.49
105 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (103 bp):
GGCATAATTTCTAAGACCTTTGGGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATAC
GAGGAGCATTCAAAGATGTTGAGATTTGTAAGACCTTC
Found at i:12139153 original size:82 final size:82
Alignment explanation
Indices: 12139007--12139162 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 82
12138997 ACCTCCAGGT
* * * *
12139007 AAAACATTTTAAATTTTCAAAGTTTTAATGCCTCTAATATGATGAGCATTAAAAAATGTTGAGAT
1 AAAACATTTTAAATTTTCAAAATTTCAATGCCTCTAATATAATGAGCATTAAAAAATGTCGAGAT
12139072 TTGTAAGACTTCTAGGC
66 TTGTAAGACTTCTAGGC
* * * *
12139089 AAAACATTTTAAATTTTCAAAATTTCAATGCCTTTGATATAA-GTAGCATTCAAAGATGTCGAGA
1 AAAACATTTTAAATTTTCAAAATTTCAATGCCTCTAATATAATG-AGCATTAAAAAATGTCGAGA
12139153 TTTGTAAGAC
65 TTTGTAAGAC
12139163 CTTTGGGCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
81 1 0.02
82 64 0.98
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (82 bp):
AAAACATTTTAAATTTTCAAAATTTCAATGCCTCTAATATAATGAGCATTAAAAAATGTCGAGAT
TTGTAAGACTTCTAGGC
Found at i:12139503 original size:13 final size:13
Alignment explanation
Indices: 12139485--12139511 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12139475 TAATCAAGAC
12139485 AAAACAAATAAAA
1 AAAACAAATAAAA
12139498 AAAACAAATAAAA
1 AAAACAAATAAAA
12139511 A
1 A
12139512 CAAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACAAATAAAA
Found at i:12141136 original size:2 final size:2
Alignment explanation
Indices: 12141131--12141166 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12141121 AAAAATCAGT
12141131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12141167 AAAGGCCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12149529 original size:2 final size:2
Alignment explanation
Indices: 12149522--12149565 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12149512 GTAGCCCTCC
*
12149522 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12149564 AT
1 AT
12149566 TTTTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12152149 original size:28 final size:26
Alignment explanation
Indices: 12152086--12152150 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 26
12152076 TTCTCAACTT
**
12152086 TTTGTTTTT-TTTTTTTTTTTATCAA
1 TTTGTTTTTCTTTAATTTTTTATCAA
* *
12152111 TTTGATCTTCTTTAATTTTTTACTTCAA
1 TTTGTTTTTCTTTAATTTTTTA--TCAA
12152139 TTTGTTTTTCTT
1 TTTGTTTTTCTT
12152151 GAATCTGCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 7 0.23
26 10 0.32
28 14 0.45
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTGTTTTTCTTTAATTTTTTATCAA
Found at i:12153566 original size:52 final size:52
Alignment explanation
Indices: 12153462--12153567 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
12153452 GATCTCAAGG
* **
12153462 TTCGTAAAAATTAAAGGTTTGCAAGATATTTATATTCATAAGAATTGGAAGA
1 TTCGTAAAAATTAAAGGTTTGCAAGATATTTAGATTCATAAGAATTCAAAGA
* * * *
12153514 TTCGTAAGAATTGAAGGTTTGCTAGATTTTTAGATTCATAAGAATTCAAAGA
1 TTCGTAAAAATTAAAGGTTTGCAAGATATTTAGATTCATAAGAATTCAAAGA
12153566 TT
1 TT
12153568 TAAAAGATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (52 bp):
TTCGTAAAAATTAAAGGTTTGCAAGATATTTAGATTCATAAGAATTCAAAGA
Found at i:12153586 original size:18 final size:18
Alignment explanation
Indices: 12153565--12153608 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12153555 GAATTCAAAG
12153565 ATTTAAAAGATTCA-AAAA
1 ATTT-AAAGATTCATAAAA
*
12153583 ATTTTAAGATTCATAAAA
1 ATTTAAAGATTCATAAAA
*
12153601 ATTCAAAG
1 ATTTAAAG
12153609 GTTTGCAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (18 bp):
ATTTAAAGATTCATAAAA
Found at i:12153604 original size:44 final size:45
Alignment explanation
Indices: 12153539--12153626 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
12153529 GGTTTGCTAG
* *
12153539 ATTTTTAGATTCATAAGAATTCAAAGATTTAAAAGA-TTCAAAAA
1 ATTTTAAGATTCATAAAAATTCAAAGATTTAAAAGATTTCAAAAA
* **
12153583 ATTTTAAGATTCATAAAAATTCAAAGGTTTGCAAGATTTCAAAA
1 ATTTTAAGATTCATAAAAATTCAAAGATTTAAAAGATTTCAAAA
12153627 TTCACAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 31 0.82
45 7 0.18
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (45 bp):
ATTTTAAGATTCATAAAAATTCAAAGATTTAAAAGATTTCAAAAA
Found at i:12153643 original size:25 final size:25
Alignment explanation
Indices: 12153547--12153646 Score: 69
Period size: 27 Copynumber: 3.8 Consensus size: 25
12153537 AGATTTTTAG
*
12153547 ATTCATAAGAATT-CAAAGATTTAAAA
1 ATTCA-AAGAATTGC-AAGATTTCAAA
* ** *
12153573 GATTCAAAAAATTTTAAGATTCATAAAA
1 -ATTCAAAGAATTGCAAGATT--TCAAA
**
12153601 ATTCAAAGGTTTGCAAGATTTCAAA
1 ATTCAAAGAATTGCAAGATTTCAAA
12153626 ATTCACAAGAATTG-AAGATTT
1 ATTCA-AAGAATTGCAAGATTT
12153647 TCAAGATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
25 16 0.27
26 18 0.31
27 20 0.34
28 5 0.08
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (25 bp):
ATTCAAAGAATTGCAAGATTTCAAA
Found at i:12153680 original size:18 final size:18
Alignment explanation
Indices: 12153659--12153700 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12153649 AAGATTTTTC
12153659 AGATTCGTAAGAA-TTCAA
1 AGATTCGTAA-AATTTCAA
*
12153677 AGATTCTTAAAATTTCAA
1 AGATTCGTAAAATTTCAA
*
12153695 GGATTC
1 AGATTC
12153701 ACAAGAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (18 bp):
AGATTCGTAAAATTTCAA
Found at i:12153978 original size:43 final size:42
Alignment explanation
Indices: 12153907--12153988 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
12153897 TTTAGAGGTT
*
12153907 CACACCCAAAATTCAAATATTTTCATTTGAAAAACTTTAGAC
1 CACACCCAAAATTCAAAGATTTTCATTTGAAAAACTTTAGAC
* * *
12153949 CACATCCAAAATTTCAAAGATTCTT-ATTTGCAAAATTTTA
1 CACACCCAAAA-TTCAAAGATT-TTCATTTGAAAAACTTTA
12153989 AGATTTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 10 0.29
43 22 0.65
44 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (42 bp):
CACACCCAAAATTCAAAGATTTTCATTTGAAAAACTTTAGAC
Found at i:12157224 original size:12 final size:12
Alignment explanation
Indices: 12157187--12157230 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
12157177 AAATTATTTG
12157187 TTCATTTAGATC
1 TTCATTTAGATC
* *
12157199 TTTAATT-GATTC
1 TTCATTTAGA-TC
12157211 TTCATTTAGATC
1 TTCATTTAGATC
12157223 TTCATTTA
1 TTCATTTA
12157231 ATTTAGGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.55
Consensus pattern (12 bp):
TTCATTTAGATC
Found at i:12160017 original size:23 final size:21
Alignment explanation
Indices: 12159968--12160012 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
12159958 TTGGGGAAGG
12159968 AAAATAAAAATTTTGATTGAAA
1 AAAATAAAAATTTTGA-TGAAA
12159990 AAAATAAACAATTTTGA-GAAA
1 AAAATAAA-AATTTTGATGAAA
12160011 AA
1 AA
12160013 TAAATGGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATAAAAATTTTGATGAAA
Found at i:12160417 original size:54 final size:53
Alignment explanation
Indices: 12160308--12160418 Score: 123
Period size: 54 Copynumber: 2.1 Consensus size: 53
12160298 GGGAAATAAC
* * *
12160308 TTTGAAACTTTAAGAAAAGAAGATTCTGAACATTTGTACATTTTGACTAGGCT
1 TTTGAAACTTTAAGAAAAGAAGATTCTGAACATTTGCACATTTTAACTAGACT
* * * * * **
12160361 TTTGAAAATTTTAAGAAAGGAAGATTTTGAGCATTTGCATATTTTAACTTTACT
1 TTTG-AAACTTTAAGAAAAGAAGATTCTGAACATTTGCACATTTTAACTAGACT
12160415 TTTG
1 TTTG
12160419 CATCATTAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (53 bp):
TTTGAAACTTTAAGAAAAGAAGATTCTGAACATTTGCACATTTTAACTAGACT
Found at i:12161043 original size:128 final size:127
Alignment explanation
Indices: 12160900--12161237 Score: 351
Period size: 129 Copynumber: 2.6 Consensus size: 127
12160890 GCAATCTTTG
* * * * *
12160900 AATTTTT-TCAAATCTTTGGTGGTGACATCCAAACTATTTTCAAAGTCTTCAATGGAGATCTTTG
1 AATTTTTCTAAAATCTTTGGTGGTGATATCCAAACTATTTTCAAA-TATTCAATGGTGATATTTG
* * * *
12160964 AATTTTCTCAAATCTTTGGTGGTGACATCCAAATTGTTTTTAAAGTCTTCGATGGCGATAT-T
65 AATTTTCTCAAATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATATCC
* * * * * *
12161026 ATATTTTTCTTAAATCTTTAGTGGTTATATCCAAACTGTTTTCAAAATATTCAGTGGTGATATCT
1 A-ATTTTTCTAAAATCTTTGGTGGTGATATCCAAACTATTTTC-AAATATTCAATGGTGATATTT
* * * **
12161091 GAATTTTCTCTAAGTCTTTGGTGTTAACTTCCAAATTGTTTTCAATTTCTTCGATGGCAATATCC
64 GAATTTTCTC-AAATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATATCC
** * * * *
12161156 AAAATTTCGAAAATCTTTGGTGGTGATATACAAA-TCATTTTCAAATTTTCAATGGTGAAATTTG
1 AATTTTTCTAAAATCTTTGGTGGTGATATCCAAACT-ATTTTCAAATATTCAATGGTGATATTTG
*
12161220 AATTTGTC-AAAATCTTTG
65 AATTT-TCTCAAATCTTTG
12161238 ATAGCTATAT
Statistics
Matches: 172, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
126 1 0.01
127 14 0.08
128 76 0.44
129 80 0.47
130 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.43
Consensus pattern (127 bp):
AATTTTTCTAAAATCTTTGGTGGTGATATCCAAACTATTTTCAAATATTCAATGGTGATATTTGA
ATTTTCTCAAATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATATCC
Found at i:12161088 original size:64 final size:64
Alignment explanation
Indices: 12160844--12161109 Score: 259
Period size: 64 Copynumber: 4.1 Consensus size: 64
12160834 ATTTTTTTTG
* * * * *
12160844 CAAATCTTTAATGGTGATATCCAAACTATTTTCAAAGTTTTCAGTGGCAATCTTTGAATTTTT-T
1 CAAATCTTTAGTGGTGACATCCAAACTATTTTCAAAGTCTTCAGTGGCGATATTTG-ATTTTTCT
* * * * *
12160908 CAAATCTTTGGTGGTGACATCCAAACTATTTTCAAAGTCTTCAATGGAGATCTTTGAATTTTCT
1 CAAATCTTTAGTGGTGACATCCAAACTATTTTCAAAGTCTTCAGTGGCGATATTTGATTTTTCT
* * * *
12160972 CAAATCTTTGGTGGTGACATCCAAATTGTTTTTAAAGTCTTC-GATGGCGATATTAT-ATTTTTC
1 CAAATCTTTAGTGGTGACATCCAAACTATTTTCAAAGTCTTCAG-TGGCGATATT-TGATTTTTC
12161035 T
64 T
* * * * * * * * *
12161036 TAAATCTTTAGTGGTTATATCCAAACTGTTTTCAAAATATTCAGTGGTGATATCTGAATTTTCT
1 CAAATCTTTAGTGGTGACATCCAAACTATTTTCAAAGTCTTCAGTGGCGATATTTGATTTTTCT
*
12161100 CTAAGTCTTT
1 C-AAATCTTT
12161110 GGTGTTAACT
Statistics
Matches: 168, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
63 6 0.04
64 153 0.91
65 9 0.05
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (64 bp):
CAAATCTTTAGTGGTGACATCCAAACTATTTTCAAAGTCTTCAGTGGCGATATTTGATTTTTCT
Found at i:12161154 original size:65 final size:64
Alignment explanation
Indices: 12160898--12161154 Score: 195
Period size: 64 Copynumber: 4.0 Consensus size: 64
12160888 TGGCAATCTT
* * * * * * * * * *
12160898 TGAATTTTTTC-AAATCTTTGGTGGTGACATCCAAACTATTTTCAAAGTCTTCAATGGAGATCTT
1 TGAATTTTCTCTAAATCTTTGGT-GTTACTTCCAAATTGTTTTCAAAATCTTCGATGGCGATATC
* * * *
12160962 TGAATTTTCTC-AAATCTTTGGTGGTGACATCCAAATTGTTTTTAAAGTCTTCGATGGCGATAT-
1 TGAATTTTCTCTAAATCTTTGGT-GTTACTTCCAAATTGTTTTCAAAATCTTCGATGGCGATATC
* * * *
12161025 T-ATATTTT-TCTTAAATCTTTAGTGGTTA-TATCCAAACTGTTTTCAAAATATTC-AGTGGTGA
1 TGA-ATTTTCTC-TAAATCTTTGGT-GTTACT-TCCAAATTGTTTTCAAAATCTTCGA-TGGCGA
12161086 TATC
61 TATC
* ** *
12161090 TGAATTTTCTCTAAGTCTTTGGTGTTAACTTCCAAATTGTTTTCAATTTCTTCGATGGCAATATC
1 TGAATTTTCTCTAAATCTTTGGTGTT-ACTTCCAAATTGTTTTCAAAATCTTCGATGGCGATATC
12161155 CAAAATTTCG
Statistics
Matches: 159, Mismatches: 23, Indels: 21
0.78 0.11 0.10
Matches are distributed among these distances:
62 3 0.02
63 7 0.04
64 100 0.63
65 44 0.28
66 5 0.03
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (64 bp):
TGAATTTTCTCTAAATCTTTGGTGTTACTTCCAAATTGTTTTCAAAATCTTCGATGGCGATATC
Found at i:12161172 original size:129 final size:128
Alignment explanation
Indices: 12160909--12161237 Score: 351
Period size: 128 Copynumber: 2.6 Consensus size: 128
12160899 GAATTTTTTC
* * * * *
12160909 AAATCTTTGGTGGTGACATCCAAACTATTTTCAAAGTCTTCAATGGAGATCTTTGAATTTTCTCA
1 AAATCTTTGGTGGTGATATCCAAACTATTTTCAAAATATTCAATGGTGATATTTGAATTTTCTCA
* * * * ** **
12160974 AATCTTTGGTGGTGACATCCAAATTGTTTTTAAAGTCTTCGATGGCGATATTATATTTTTCTT
66 AATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATATCATAAATTTCGA
* * * * *
12161037 AAATCTTTAGTGGTTATATCCAAACTGTTTTCAAAATATTCAGTGGTGATATCTGAATTTTCTCT
1 AAATCTTTGGTGGTGATATCCAAACTATTTTCAAAATATTCAATGGTGATATTTGAATTTTCTC-
* * * **
12161102 AAGTCTTTGGTGTTAACTTCCAAATTGTTTTCAATTTCTTCGATGGCAATATCCA-AAATTTCGA
65 AAATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATAT-CATAAATTTCGA
* * *
12161166 AAATCTTTGGTGGTGATATACAAA-TCATTTTC-AAATTTTCAATGGTGAAATTTGAATTTGTC-
1 AAATCTTTGGTGGTGATATCCAAACT-ATTTTCAAAATATTCAATGGTGATATTTGAATTT-TCT
*
12161228 AAAATCTTTG
64 CAAATCTTTG
12161238 ATAGCTATAT
Statistics
Matches: 164, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
127 8 0.05
128 78 0.48
129 77 0.47
130 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (128 bp):
AAATCTTTGGTGGTGATATCCAAACTATTTTCAAAATATTCAATGGTGATATTTGAATTTTCTCA
AATCTTTGGTGGTAACATCCAAATTGTTTTCAAAGTCTTCGATGGCAATATCATAAATTTCGA
Found at i:12161482 original size:57 final size:57
Alignment explanation
Indices: 12161391--12161531 Score: 153
Period size: 57 Copynumber: 2.5 Consensus size: 57
12161381 CTCAGTGCTG
* * * *
12161391 ATATCAGAAGTCATTTGCGTT-ATCTCGATGGTGAT-TCTTGAG-TCCTTTATAGTGGCA
1 ATATCAGAAGTCATTTGCATTCA-CTCGATAGTGATAT-TCGAGTTCCCTT-TAGTGGCA
* **
12161448 ATATCTGAAGTCATTTGCATTCACTCGATAGTGATATTCGAGTTCCCTTTAGTGGTG
1 ATATCAGAAGTCATTTGCATTCACTCGATAGTGATATTCGAGTTCCCTTTAGTGGCA
* *
12161505 ACATCCGAAGTCATTTGCATTCACTCG
1 ATATCAGAAGTCATTTGCATTCACTCG
12161532 TCACCCAATG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 65 0.90
58 7 0.10
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (57 bp):
ATATCAGAAGTCATTTGCATTCACTCGATAGTGATATTCGAGTTCCCTTTAGTGGCA
Found at i:12161697 original size:58 final size:58
Alignment explanation
Indices: 12161540--12161851 Score: 226
Period size: 57 Copynumber: 5.4 Consensus size: 58
12161530 CGTCACCCAA
* * * ** * *
12161540 TGGCGATATCTGAG--TTCCTTTCAGTGACAATATATGAAGTCATTCACATTTACTTGA
1 TGGCGATATCTAAGTTTTCCTTT-AGTGGCAATATTTGAAGTCATTTGCATTTTCTTGG
* * * * *
12161597 TGGTGATATCTAAG--TTCCTTTCGATGGCGATATTTAAAGTCATTTGCATTGTCTTGG
1 TGGCGATATCTAAGTTTTCCTTTAG-TGGCAATATTTGAAGTCATTTGCATTTTCTTGG
* **
12161654 TGGCGATATCTAAGTTTTCTTTTAGTGGTGATATTTGAAGTCATTTGCATTTTCTTGG
1 TGGCGATATCTAAGTTTTCCTTTAGTGGCAATATTTGAAGTCATTTGCATTTTCTTGG
* * * * * * *
12161712 TGGCAATATCTTTA-TTTTCCTTTAGTGGCAATATCTGTAGTCATTTGTATTTTCTCGA
1 TGGCGATATC-TAAGTTTTCCTTTAGTGGCAATATTTGAAGTCATTTGCATTTTCTTGG
* ** * * ** *
12161770 TGGCAATATCCGAGTTTT-C-TTCGATGGTAATATTCAAAGTCATTTGCATTTTCTCGG
1 TGGCGATATCTAAGTTTTCCTTTAG-TGGCAATATTTGAAGTCATTTGCATTTTCTTGG
** * *
12161827 TACCGATATCTGAG-TTCCCTTTAGT
1 TGGCGATATCTAAGTTTTCCTTTAGT
12161852 AAGTCATCTC
Statistics
Matches: 203, Mismatches: 44, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
56 6 0.03
57 96 0.47
58 92 0.45
59 9 0.04
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (58 bp):
TGGCGATATCTAAGTTTTCCTTTAGTGGCAATATTTGAAGTCATTTGCATTTTCTTGG
Found at i:12163513 original size:17 final size:16
Alignment explanation
Indices: 12163487--12163524 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
12163477 AAAAATTTAT
12163487 TAAATAAT-AAAATAAA
1 TAAATAATAAAAAT-AA
12163503 TAAATAGATAAAAATAA
1 TAAATA-ATAAAAATAA
12163520 TAAAT
1 TAAAT
12163525 GAGAGATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAATAATAAAAATAA
Found at i:12166309 original size:18 final size:17
Alignment explanation
Indices: 12166283--12166316 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12166273 ACATTGATAA
12166283 CATCAAAAGTATTTTTTT
1 CATCAAAAGT-TTTTTTT
*
12166301 CATCTAAAGTTTTTTT
1 CATCAAAAGTTTTTTT
12166317 AGGTATCGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
CATCAAAAGTTTTTTTT
Found at i:12168280 original size:26 final size:26
Alignment explanation
Indices: 12168220--12168284 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
12168210 ACTAATGCCT
*
12168220 ATTTAGGGTTTCGAGTTTTGGATTTC
1 ATTTAGGGTTTTGAGTTTTGGATTTC
* * *
12168246 -CTTAAGGTTTTGATTTTATGG-TTTC
1 ATTTAGGGTTTTGAGTTT-TGGATTTC
12168271 ATTTAGGGTTTTGA
1 ATTTAGGGTTTTGA
12168285 CTTTGACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.52
Consensus pattern (26 bp):
ATTTAGGGTTTTGAGTTTTGGATTTC
Found at i:12168363 original size:26 final size:26
Alignment explanation
Indices: 12168314--12168364 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12168304 GGTTTCGATC
* *
12168314 TAGGGTTTCAACCTTAGGATTTTATT
1 TAGGGTTTCAACCTTAGAAATTTATT
12168340 TAGGGCTTT-AACCTTAGAAATTTAT
1 TAGGG-TTTCAACCTTAGAAATTTAT
12168365 GAACTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TAGGGTTTCAACCTTAGAAATTTATT
Found at i:12168569 original size:18 final size:18
Alignment explanation
Indices: 12168546--12168584 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12168536 AAATTTATTA
12168546 TTATTATAATTTATAA-AT
1 TTATTATAATTT-TAATAT
*
12168564 TTATTATTATTTTAATAT
1 TTATTATAATTTTAATAT
12168582 TTA
1 TTA
12168585 ATAATTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAATTTTAATAT
Found at i:12169363 original size:207 final size:207
Alignment explanation
Indices: 12169008--12169384 Score: 657
Period size: 207 Copynumber: 1.8 Consensus size: 207
12168998 GAACCAATGG
*
12169008 ACCATAAACATAAGCAGTACCTCAAGCTCTTATGACGGTAGAAAGACCAAAACCTGGTTTGAATA
1 ACCATAAACATAAGCAGTACCTCAAGCTCTTATGACGGTAGAAAGACCAAAACCTGGTTTGAAAA
* *
12169073 CACATTTTAACAAAATATAATCACAAAACCTCCATGAACCCTTTCTGATTTCTCTTCTACATAAG
66 CACATTTTAACAAAATATAATCACAAAACCTCCATGAACCCTTTCTGATTTCTATTCTACATAAC
* *
12169138 TATCAAGTCTTCCTTCCCATTTTTATTGCAGAGAAAAAAAAAAAATCCTTTTTGCAAGCAAAGAA
131 TATCAAGTATTCCTTCCCAATTTTATTGCAGAGAAAAAAAAAAAATCCTTTTTGCAAGCAAAGAA
12169203 TGATATTTTGCA
196 TGATATTTTGCA
*
12169215 ACCATAAACATAAGCAGTACCTCAAGCTCTTATGATGGTAGAAAGACCAAAACCTGGTTTGAAAA
1 ACCATAAACATAAGCAGTACCTCAAGCTCTTATGACGGTAGAAAGACCAAAACCTGGTTTGAAAA
*
12169280 CACATTTTAACAAAATATAATCACAAAACCTCTATGAACCCTTTCTGATTAT-TATTCTACATAA
66 CACATTTTAACAAAATATAATCACAAAACCTCCATGAACCCTTTCTGATT-TCTATTCTACATAA
* *
12169344 CTTTCAAGTATTCCTTCCCAATTTTATTGCTGAGAAAAAAA
130 CTATCAAGTATTCCTTCCCAATTTTATTGCAGAGAAAAAAA
12169385 TTCCTTTTTG
Statistics
Matches: 160, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
207 159 0.99
208 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (207 bp):
ACCATAAACATAAGCAGTACCTCAAGCTCTTATGACGGTAGAAAGACCAAAACCTGGTTTGAAAA
CACATTTTAACAAAATATAATCACAAAACCTCCATGAACCCTTTCTGATTTCTATTCTACATAAC
TATCAAGTATTCCTTCCCAATTTTATTGCAGAGAAAAAAAAAAAATCCTTTTTGCAAGCAAAGAA
TGATATTTTGCA
Found at i:12170624 original size:16 final size:15
Alignment explanation
Indices: 12170563--12170627 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
12170553 CATTTCTTCA
*
12170563 ATTTTTTATTTTTCAA
1 ATTTTTTATTTTT-AT
*
12170579 ATTTTATT-TTATTACT
1 ATTTT-TTATTTTTA-T
*
12170595 ATTTTTTGTATTTTAT
1 ATTTTTTAT-TTTTAT
12170611 ATTTTTATATTTTTAT
1 ATTTTT-TATTTTTAT
12170627 A
1 A
12170628 CATATTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.08
16 29 0.73
17 8 0.20
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTTTATTTTTAT
Found at i:12171099 original size:20 final size:19
Alignment explanation
Indices: 12171065--12171127 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
12171055 TTATATTACA
**
12171065 TTTTTTTAGGCTTTTTATT
1 TTTTTTTAGTTTTTTTATT
12171084 ATTTTTTTAGTTTTTTT-TT
1 -TTTTTTTAGTTTTTTTATT
* * *
12171103 TGTTTTTGGTTTTTTGATT
1 TTTTTTTAGTTTTTTTATT
12171122 TTTTTT
1 TTTTTT
12171128 ATGACTAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.36
19 9 0.25
20 14 0.39
ACGTcount: A:0.08, C:0.02, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTTTTAGTTTTTTTATT
Found at i:12171216 original size:31 final size:31
Alignment explanation
Indices: 12171179--12171416 Score: 137
Period size: 31 Copynumber: 7.7 Consensus size: 31
12171169 GAGACAAGCC
12171179 ACAAGTTGAATGAGGTGACTGAGATTAAACT
1 ACAAGTTGAATGAGGTGACTGAGATTAAACT
* * *
12171210 ACAAGTTGAATGAGGTGACCTG-GACTAAGCC
1 ACAAGTTGAATGAGGTGA-CTGAGATTAAACT
* * * * *
12171241 ATAAGTCGAATGAAGTGA-TCGAGATTGAATT
1 ACAAGTTGAATGAGGTGACT-GAGATTAAACT
* * * * * * *
12171272 GCAAGTCGAATAAGGTGAAC-GATACTAAGCC
1 ACAAGTTGAATGAGGTG-ACTGAGATTAAACT
* * *
12171303 ACAAATTGAATGAAGTGA-TCGACATTAAACT
1 ACAAGTTGAATGAGGTGACT-GAGATTAAACT
* * * *
12171334 ACAAGTTGAATGAGATGACT-AGGACTAAGCC
1 ACAAGTTGAATGAGGTGACTGA-GATTAAACT
* * * *
12171365 ACAAGTTAAATGAAGTGACTAAGATTAAATT
1 ACAAGTTGAATGAGGTGACTGAGATTAAACT
*
12171396 AC-AGGTGAAATGAGGTGACTG
1 ACAAGTTG-AATGAGGTGACTG
12171417 GGACGAAATC
Statistics
Matches: 148, Mismatches: 48, Indels: 22
0.68 0.22 0.10
Matches are distributed among these distances:
29 1 0.01
30 6 0.04
31 135 0.91
32 6 0.04
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (31 bp):
ACAAGTTGAATGAGGTGACTGAGATTAAACT
Found at i:12171265 original size:62 final size:62
Alignment explanation
Indices: 12171174--12171414 Score: 249
Period size: 62 Copynumber: 3.9 Consensus size: 62
12171164 TGATCGAGAC
*
12171174 AAGCCACAAGTTGAATGAGGTGACTGAGATTAAACTACAAGTTGAATGAGGTGACCTGGACT
1 AAGCCACAAGTTGAATGAAGTGACTGAGATTAAACTACAAGTTGAATGAGGTGACCTGGACT
* * * * * * * * *
12171236 AAGCCATAAGTCGAATGAAGTGA-TCGAGATTGAATTGCAAGTCGAATAAGGTGAAC-GATACT
1 AAGCCACAAGTTGAATGAAGTGACT-GAGATTAAACTACAAGTTGAATGAGGTGACCTG-GACT
* * *
12171298 AAGCCACAAATTGAATGAAGTGA-TCGACATTAAACTACAAGTTGAATGAGATGA-CTAGGACT
1 AAGCCACAAGTTGAATGAAGTGACT-GAGATTAAACTACAAGTTGAATGAGGTGACCT-GGACT
* * * *
12171360 AAGCCACAAGTTAAATGAAGTGACTAAGATTAAATTAC-AGGTGAAATGAGGTGAC
1 AAGCCACAAGTTGAATGAAGTGACTGAGATTAAACTACAAGTTG-AATGAGGTGAC
12171415 TGGGACGAAA
Statistics
Matches: 144, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
61 7 0.05
62 135 0.94
63 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (62 bp):
AAGCCACAAGTTGAATGAAGTGACTGAGATTAAACTACAAGTTGAATGAGGTGACCTGGACT
Found at i:12171377 original size:124 final size:124
Alignment explanation
Indices: 12171157--12171382 Score: 323
Period size: 124 Copynumber: 1.8 Consensus size: 124
12171147 GAGTTGAAAG
* * * *
12171157 ATAAGGATGATCGAGACAAGCCACAAGTTGAATGAGGTGACTGAGATTAAACTACAAGTTGAATG
1 ATAAGGATGAACGAGACAAGCCACAAATTGAATGAAGTGACTGACATTAAACTACAAGTTGAATG
* * *
12171222 AGGTGACCTGGACTAAGCCATAAGTCGAATGAAGTGATCGAGATTGAATTGCAAGTCGA
66 AGATGACCTGGACTAAGCCACAAGTCAAATGAAGTGATCGAGATTGAATTGCAAGTCGA
*
12171281 ATAAGG-TGAACGATACTAAGCCACAAATTGAATGAAGTGA-TCGACATTAAACTACAAGTTGAA
1 ATAAGGATGAACGAGAC-AAGCCACAAATTGAATGAAGTGACT-GACATTAAACTACAAGTTGAA
*
12171344 TGAGATGA-CTAGGACTAAGCCACAAGTTAAATGAAGTGA
64 TGAGATGACCT-GGACTAAGCCACAAGTCAAATGAAGTGA
12171383 CTAAGATTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
123 11 0.12
124 79 0.88
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (124 bp):
ATAAGGATGAACGAGACAAGCCACAAATTGAATGAAGTGACTGACATTAAACTACAAGTTGAATG
AGATGACCTGGACTAAGCCACAAGTCAAATGAAGTGATCGAGATTGAATTGCAAGTCGA
Found at i:12171476 original size:35 final size:34
Alignment explanation
Indices: 12171425--12171869 Score: 129
Period size: 35 Copynumber: 12.7 Consensus size: 34
12171415 TGGGACGAAA
* *
12171425 TCACAAGTCAATAAATAAAGATGACCAAGATAAAG
1 TCACAAGTCAAAAAATAAAGATGA-CAGGATAAAG
* * **
12171460 TCACAAGTCAGAAAATAAATATGATTGGGACT-AAG
1 TCACAAGTCAAAAAATAAAGATGA-CAGGA-TAAAG
*
12171495 TCGCAAGTCAAAAAATAAAGATGACAGGGATAAA-
1 TCACAAGTCAAAAAATAAAGATGACA-GGATAAAG
* * *
12171529 ACTACAAGTCAAAAAATAAAGATAATC-GAGACTAAAC
1 TC-ACAAGTCAAAAAATAAAGATGA-CAG-GA-TAAAG
* * ** *
12171566 T-GCAAGTTAAAAAATAAAGATGATTGGGACAAAG
1 TCACAAGTCAAAAAATAAAGATGA-CAGGATAAAG
*** * ** *
12171600 TTGTAAGTTAAAAAATAAAGATGATTGGAATGAAG
1 TCACAAGTCAAAAAATAAAGATGACAGG-ATAAAG
** * *
12171635 -CTGTAAGTCAAAAAATAAATATGACTGGGATGAAA-
1 TC-ACAAGTCAAAAAATAAAGATGAC-AGGAT-AAAG
* * * *
12171670 CCACAATTCAAAAAATAAAGATGATCGGGATTAAG
1 TCACAAGTCAAAAAATAAAGATGA-CAGGATAAAG
* * ** ** * *
12171705 CCATAAGTTGATGAATAAACATGA-AGTGGA-AGAAA
1 TCACAAGTCAAAAAATAAAGATGACA--GGATA-AAG
* * *
12171740 CCACAAGTCAAAAAATAAAGATAAACGGGATGAAA-
1 TCACAAGTCAAAAAATAAAGAT-GACAGGAT-AAAG
** * * * *
12171775 TGGCAAGTCAAAAAACAAAAATGACTATGATGAAAC
1 TCACAAGTCAAAAAATAAAGATGAC-AGGAT-AAAG
* * *
12171811 T-TCAAGTTAAAAAATAAAGATGACTGGGACT-AAG
1 TCACAAGTCAAAAAATAAAGATGAC-AGGA-TAAAG
* * *
12171845 TCGCAAGTCGAAGAATAAAGATGAC
1 TCACAAGTCAAAAAATAAAGATGAC
12171870 CAAGACTAAG
Statistics
Matches: 308, Mismatches: 74, Indels: 56
0.70 0.17 0.13
Matches are distributed among these distances:
34 17 0.06
35 272 0.88
36 18 0.06
37 1 0.00
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (34 bp):
TCACAAGTCAAAAAATAAAGATGACAGGATAAAG
Found at i:12171528 original size:70 final size:69
Alignment explanation
Indices: 12171428--12171869 Score: 265
Period size: 70 Copynumber: 6.3 Consensus size: 69
12171418 GACGAAATCA
* * * * *
12171428 CAAGTCAATAAATAAAGATGACCA-AGATAAAGTCACAAGTCAGAAAATAAATATGATTGGGACT
1 CAAGTCAAAAAATAAAGATGA-CAGGGATAAA-TCACAAGTCAAAAAATAAAGATGATCGGGACT
12171492 AAG-TCG
64 AAGCT-G
* * *
12171498 CAAGTCAAAAAATAAAGATGACAGGGATAAAACTACAAGTCAAAAAATAAAGATAATCGAGACTA
1 CAAGTCAAAAAATAAAGATGACAGGGATAAATC-ACAAGTCAAAAAATAAAGATGATCGGGACTA
*
12171563 AACTG
65 AGCTG
* ** * *** * * *
12171568 CAAGTTAAAAAATAAAGATGATTGGGACAAAGTTGTAAGTTAAAAAATAAAGATGAT-TGGAATG
1 CAAGTCAAAAAATAAAGATGACAGGGATAAA-TCACAAGTCAAAAAATAAAGATGATCGGGACT-
12171632 AAGCTG
64 AAGCTG
* * * * * *
12171638 TAAGTCAAAAAATAAATATGACTGGGATGAAACCACAATTCAAAAAATAAAGATGATCGGGATTA
1 CAAGTCAAAAAATAAAGATGACAGGGAT-AAATCACAAGTCAAAAAATAAAGATGATCGGGACTA
**
12171703 AGCCA
65 AGCTG
* ** ** * * * * *
12171708 TAAGTTGATGAATAAACATGA-AGTGGAAGAAACCACAAGTCAAAAAATAAAGATAAACGGGA-T
1 CAAGTCAAAAAATAAAGATGACAG-GG-ATAAATCACAAGTCAAAAAATAAAGATGATCGGGACT
*
12171771 GAA-ATGG
64 -AAGCT-G
* * * * *
12171778 CAAGTCAAAAAACAAAAATGACTA-TGATGAAA-CTTCAAGTTAAAAAATAAAGATGA-CTGGGA
1 CAAGTCAAAAAATAAAGATGAC-AGGGAT-AAATC-ACAAGTCAAAAAATAAAGATGATC-GGGA
12171840 CTAAG-TCG
62 CTAAGCT-G
* *
12171848 CAAGTCGAAGAATAAAGATGAC
1 CAAGTCAAAAAATAAAGATGAC
12171870 CAAGACTAAG
Statistics
Matches: 286, Mismatches: 68, Indels: 36
0.73 0.17 0.09
Matches are distributed among these distances:
69 11 0.04
70 264 0.92
71 10 0.03
72 1 0.00
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (69 bp):
CAAGTCAAAAAATAAAGATGACAGGGATAAATCACAAGTCAAAAAATAAAGATGATCGGGACTAA
GCTG
Found at i:12171613 original size:105 final size:105
Alignment explanation
Indices: 12171427--12171699 Score: 271
Period size: 105 Copynumber: 2.6 Consensus size: 105
12171417 GGACGAAATC
* * * * * *
12171427 ACAAGTCAATAAATAAAGATGACCAAGATAAAGTCACAAGTCAGAAAATAAATATGATTGGGACT
1 ACAAGTCAAAAAATAAAGATAACCAAGATAAACTCACAAGTCAAAAAATAAAGATGATTGGGACA
12171492 AAGTCGCAAGTCAAAAAATAAAGATGACAGGGATAAAACT
66 AAGTCGCAAGTCAAAAAATAAAGATGACAGGGATAAAACT
* * * *
12171532 ACAAGTCAAAAAATAAAGATAATCGAGACTAAACT-GCAAGTTAAAAAATAAAGATGATTGGGAC
1 ACAAGTCAAAAAATAAAGATAACCAAGA-TAAACTCACAAGTCAAAAAATAAAGATGATTGGGAC
* * * ** * * *
12171596 AAAGTTGTAAGTTAAAAAATAAAGATGATTGGAATGAAGCT
65 AAAGTCGCAAGTCAAAAAATAAAGATGACAGGGATAAAACT
** * * *** * *
12171637 GTAAGTCAAAAAATAAATATGACTGGGATGAAAC-CACAATTCAAAAAATAAAGATGATCGGGA
1 ACAAGTCAAAAAATAAAGATAACCAAGAT-AAACTCACAAGTCAAAAAATAAAGATGATTGGGA
12171700 TTAAGCCATA
Statistics
Matches: 136, Mismatches: 29, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
104 1 0.01
105 130 0.96
106 5 0.04
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (105 bp):
ACAAGTCAAAAAATAAAGATAACCAAGATAAACTCACAAGTCAAAAAATAAAGATGATTGGGACA
AAGTCGCAAGTCAAAAAATAAAGATGACAGGGATAAAACT
Found at i:12171786 original size:105 final size:104
Alignment explanation
Indices: 12171463--12171798 Score: 255
Period size: 105 Copynumber: 3.2 Consensus size: 104
12171453 GATAAAGTCA
* * * * * ** * * ** * *
12171463 CAAGTCAGAAAATAAATATGATTGGGACTAAGTCGCAAGTCAAAAAATAAAGATGACAGGGATAA
1 CAAGTCAAAAAATAAAGATGATCGGGACAAAGCCATAAGTTAAAAAATAAACATGAGTGGAATGA
* *
12171528 AACTACAAGTCAAAAAATAAAGATAATCGAGACT-AAACTG
66 AACTACAAGTCAAAAAATAAAGATAAACGGGA-TGAAA-TG
* * *** * *
12171568 CAAGTTAAAAAATAAAGATGATTGGGACAAAGTTGTAAGTTAAAAAATAAAGATGATTGGAATGA
1 CAAGTCAAAAAATAAAGATGATCGGGACAAAGCCATAAGTTAAAAAATAAACATGAGTGGAATGA
* ** * * **
12171633 AGCTGTAAGTCAAAAAATAAATAT-GACTGGGATGAAACCA
66 AACTACAAGTCAAAAAATAAAGATAAAC-GGGATGAAA-TG
* ** * **
12171673 CAATTCAAAAAATAAAGATGATCGGGATTAAGCCATAAGTTGATGAATAAACATGAAGTGGAA-G
1 CAAGTCAAAAAATAAAGATGATCGGGACAAAGCCATAAGTTAAAAAATAAACATG-AGTGGAATG
*
12171737 AAACCACAAGTCAAAAAATAAAGATAAACGGGATGAAATGG
65 AAACTACAAGTCAAAAAATAAAGATAAACGGGATGAAAT-G
* *
12171778 CAAGTCAAAAAACAAAAATGA
1 CAAGTCAAAAAATAAAGATGA
12171799 CTATGATGAA
Statistics
Matches: 182, Mismatches: 44, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
104 2 0.01
105 172 0.95
106 8 0.04
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.19
Consensus pattern (104 bp):
CAAGTCAAAAAATAAAGATGATCGGGACAAAGCCATAAGTTAAAAAATAAACATGAGTGGAATGA
AACTACAAGTCAAAAAATAAAGATAAACGGGATGAAATG
Found at i:12171923 original size:35 final size:35
Alignment explanation
Indices: 12171813--12171938 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 35
12171803 GATGAAACTT
* ** * *
12171813 CAAGTTAAAAAATAAAGATGACTGGGACTAAGTCG
1 CAAGTTAGAAAATAAAGATGACTAAGACTAAGCCA
* * *
12171848 CAAG-TCGAAGAATAAAGATGACCAAGACTAAGCTA
1 CAAGTTAGAA-AATAAAGATGACTAAGACTAAGCCA
* *
12171883 CAAGTTAGAAAATAAAGATAACTAAGACAAAGCCA
1 CAAGTTAGAAAATAAAGATGACTAAGACTAAGCCA
* * *
12171918 CAAGTTTGGAAATAAGGATGA
1 CAAGTTAGAAAATAAAGATGA
12171939 TTGAGATTGA
Statistics
Matches: 72, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
34 3 0.04
35 65 0.90
36 4 0.06
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (35 bp):
CAAGTTAGAAAATAAAGATGACTAAGACTAAGCCA
Found at i:12172093 original size:23 final size:22
Alignment explanation
Indices: 12172020--12172093 Score: 53
Period size: 23 Copynumber: 3.3 Consensus size: 22
12172010 AATTTGAGCA
*
12172020 TACGTGCAGCTAATC-TAGACT
1 TACGTGCAGCTAATCTTAGGCT
** * *
12172041 TTTGTGCCAGCTAAT-TATGGGTT
1 TACGTG-CAGCTAATCT-TAGGCT
*
12172064 TATGTGCTAGCTAATCTTAGGCT
1 TACGTGC-AGCTAATCTTAGGCT
12172087 TACGTGC
1 TACGTGC
12172094 CAACTAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 4 0.10
22 9 0.23
23 25 0.64
24 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (22 bp):
TACGTGCAGCTAATCTTAGGCT
Found at i:12172220 original size:66 final size:67
Alignment explanation
Indices: 12172140--12172298 Score: 175
Period size: 66 Copynumber: 2.4 Consensus size: 67
12172130 TAAACTGACC
* *
12172140 TTAAAT-TTTCATTGAGTACTAGCTAAACTGAGCTTAAAACTTCTT-TGGGTGCTAGATAATCTG
1 TTAAATATTTCATTGAGTGCTAGCTAAACTGAGCTTAAAACTT-TTATGAGTGCTAGATAATCTG
12172203 GGG
65 GGG
* * * * *
12172206 TTAAATATTT-ATTGA-TGCCAACTAAATTGGGCTTAAATCTTTTCATGAGTGCTAGATAATCTG
1 TTAAATATTTCATTGAGTGCTAGCTAAACTGAGCTTAAAACTTTT-ATGAGTGCTAGATAATCTG
*
12172269 GGT
65 GGG
*
12172272 TTAAAAATTTCATT-AGGTGCTAGCTAA
1 TTAAATATTTCATTGA-GTGCTAGCTAA
12172299 GTTAGGCTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
64 2 0.03
65 20 0.26
66 40 0.53
67 6 0.08
68 8 0.11
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.38
Consensus pattern (67 bp):
TTAAATATTTCATTGAGTGCTAGCTAAACTGAGCTTAAAACTTTTATGAGTGCTAGATAATCTGG
GG
Found at i:12172292 original size:34 final size:34
Alignment explanation
Indices: 12172187--12172342 Score: 94
Period size: 32 Copynumber: 4.7 Consensus size: 34
12172177 AACTTCTTTG
* *
12172187 GGTGCTAGATAATCTGGGGTTAAATATTT-ATT-
1 GGTGCTAGATAATCTGGGCTTAAAAATTTCATTA
* * ** *
12172219 GATGCCA-ACTAAAT-TGGGCTTAAATCTTTTCATGA
1 GGTGCTAGA-T-AATCTGGGCTTAAA-AATTTCATTA
*
12172254 -GTGCTAGATAATCTGGGTTTAAAAATTTCATTA
1 GGTGCTAGATAATCTGGGCTTAAAAATTTCATTA
* * * *
12172287 GGTGCTAGCTAAGT-TAGGCTT--AAATTTTATTG
1 GGTGCTAGATAA-TCTGGGCTTAAAAATTTCATTA
* *
12172319 GGTGCTAGATAAACTAGGCTTAAA
1 GGTGCTAGATAATCTGGGCTTAAA
12172343 TTGAGCTTAA
Statistics
Matches: 93, Mismatches: 19, Indels: 22
0.69 0.14 0.16
Matches are distributed among these distances:
31 1 0.01
32 42 0.45
33 16 0.17
34 32 0.34
35 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.37
Consensus pattern (34 bp):
GGTGCTAGATAATCTGGGCTTAAAAATTTCATTA
Found at i:12172324 original size:66 final size:64
Alignment explanation
Indices: 12172171--12172330 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 64
12172161 GCTAAACTGA
* * *
12172171 GCTTAAAACTTCTTTGGGTGCTAGATAATCTGGGGTTAAATATTTATTGATGCCAACTAAATTGG
1 GCTTAAATCTT-TTTGGGTGCTAGATAATCTGGGGTTAAAAATTTATTGATGCCAACTAAATTAG
* * * * * *
12172236 GCTTAAATCTTTTCATGAGTGCTAGATAATCTGGGTTTAAAAATTTCATTAGGTGCTAGCTAAGT
1 GCTTAAATCTTTT--TGGGTGCTAGATAATCTGGGGTTAAAAATTT-ATT-GATGCCAACTAAAT
12172301 TAG
62 TAG
12172304 GCTTAAAT-TTTATTGGGTGCTAGATAA
1 GCTTAAATCTTT-TTGGGTGCTAGATAA
12172331 ACTAGGCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
64 2 0.03
65 10 0.12
66 41 0.51
67 6 0.08
68 21 0.26
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.38
Consensus pattern (64 bp):
GCTTAAATCTTTTTGGGTGCTAGATAATCTGGGGTTAAAAATTTATTGATGCCAACTAAATTAG
Found at i:12172405 original size:33 final size:34
Alignment explanation
Indices: 12172347--12172465 Score: 113
Period size: 33 Copynumber: 3.6 Consensus size: 34
12172337 CTTAAATTGA
*
12172347 GCTT-AAT-TTTCATTGAGTGTCAGCTAAAATGG
1 GCTTAAATCTTTCATTGGGTGTCAGCTAAAATGG
* *
12172379 GTTTAAATC-TTCATTGGGTG-CTAGCTAAATTGG
1 GCTTAAATCTTTCATTGGGTGTC-AGCTAAAATGG
* * * *
12172412 GCTTAAATCTTTCATTAGGTGTCAACTAAACTAG
1 GCTTAAATCTTTCATTGGGTGTCAGCTAAAATGG
* *
12172446 GCTTTAAT-TTTCATTAGGTG
1 GCTTAAATCTTTCATTGGGTG
12172466 CTATATAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
32 4 0.05
33 43 0.59
34 25 0.34
35 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (34 bp):
GCTTAAATCTTTCATTGGGTGTCAGCTAAAATGG
Found at i:12172417 original size:76 final size:75
Alignment explanation
Indices: 12172306--12172563 Score: 218
Period size: 76 Copynumber: 3.5 Consensus size: 75
12172296 TAAGTTAGGC
* *
12172306 TTAAAT-TTTATTGGGTGCTAGATAAACTAGGCTTAAATTGAGCTTAATTTTCATTGAGTGTCAG
1 TTAAATCTTCATTGGGTGCTAGATAAACTGGGCTTAAATT-AGCTTAATTTTCATTGAGTGTCAG
12172370 CTAAAATGGGT
65 CTAAAATGGGT
* * *
12172381 TTAAATCTTCATTGGGTGCTAGCTAAATTGGGCTTAAA-T--C-----TTTCATT-AGGTGTCAA
1 TTAAATCTTCATTGGGTGCTAGATAAACTGGGCTTAAATTAGCTTAATTTTCATTGA-GTGTCAG
* *
12172437 CTAAACTAGGCT
65 CTAAAAT-GGGT
* * * * * *
12172449 TT-AATTTTCATTAGGTGCTATATAAATTGGGCTTAAACTAGGCTTAATTTCCATTGAGTG-CTA
1 TTAAATCTTCATTGGGTGCTAGATAAACTGGGCTTAAATTA-GCTTAATTTTCATTGAGTGTC-A
* * *
12172512 GCTAAATTAGGC
64 GCTAAAATGGGT
*
12172524 TTAAATCTTCATTGGGTGCCA-ACTAAACTGGGCTTAAATT
1 TTAAATCTTCATTGGGTGCTAGA-TAAACTGGGCTTAAATT
12172564 TTTAAGAATT
Statistics
Matches: 145, Mismatches: 22, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
66 1 0.01
67 50 0.34
68 6 0.04
71 1 0.01
72 1 0.01
75 12 0.08
76 73 0.50
77 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (75 bp):
TTAAATCTTCATTGGGTGCTAGATAAACTGGGCTTAAATTAGCTTAATTTTCATTGAGTGTCAGC
TAAAATGGGT
Found at i:12172459 original size:67 final size:66
Alignment explanation
Indices: 12172339--12172485 Score: 174
Period size: 67 Copynumber: 2.2 Consensus size: 66
12172329 AAACTAGGCT
* * * *
12172339 TAAATTGAGCTT-AATTTTCATTGAGTGTCAGCTAAAATGGGTTTAAATCTTCATTGGGTGCTAG
1 TAAATTGGGCTTAAATTTTCATTGAGTGTCAACTAAAATGGCTTTAAATCTTCATTAGGTGCTAG
*
12172403 C
66 A
* *
12172404 TAAATTGGGCTTAAATCTTTCATT-AGGTGTCAACTAAACTAGGCTTT-AATTTTCATTAGGTGC
1 TAAATTGGGCTTAAAT-TTTCATTGA-GTGTCAACTAAAAT-GGCTTTAAATCTTCATTAGGTGC
*
12172467 TATA
63 TAGA
12172471 TAAATTGGGCTTAAA
1 TAAATTGGGCTTAAA
12172486 CTAGGCTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
65 11 0.16
66 4 0.06
67 50 0.71
68 5 0.07
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (66 bp):
TAAATTGGGCTTAAATTTTCATTGAGTGTCAACTAAAATGGCTTTAAATCTTCATTAGGTGCTAG
A
Found at i:12172482 original size:33 final size:32
Alignment explanation
Indices: 12172371--12172482 Score: 93
Period size: 33 Copynumber: 3.4 Consensus size: 32
12172361 GAGTGTCAGC
* * * *
12172371 TAAAATGGG-TTTAAATCTTCATTGGGTGCTAGC
1 TAAATTGGGCTTT-AATTTTCATTAGGTGCTA-A
*
12172404 TAAATTGGGCTTAAATCTTTCATTAGGTG-TCAA
1 TAAATTGGGCTTTAAT-TTTCATTAGGTGCT-AA
* *
12172437 CTAAACTAGGCTTTAATTTTCATTAGGTGCTATA
1 -TAAATTGGGCTTTAATTTTCATTAGGTGCTA-A
12172471 TAAATTGGGCTT
1 TAAATTGGGCTT
12172483 AAACTAGGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
33 35 0.56
34 28 0.44
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
TAAATTGGGCTTTAATTTTCATTAGGTGCTAA
Found at i:12172497 original size:143 final size:142
Alignment explanation
Indices: 12172227--12172562 Score: 385
Period size: 143 Copynumber: 2.4 Consensus size: 142
12172217 TTGATGCCAA
* * * *
12172227 CTAAATTGGGCTTAAATCTTTTCA-TGAGTGCTAGAT-AATCTGGGTTTAAAAATTTCATTAGGT
1 CTAAATTGGGCTTAAATC--TTCATTGGGTGCTAGCTAAAT-TGGGCTTAAATATTTCATTAGGT
* ** * *
12172290 GCTAGCTAAGTTAGGCTTAAATTTTATTGGGTGCTAGATAAACTAGGCTTAAATTGAGCTTAATT
63 GCTAACTAAACTAGGCTTAAATTTTATTAGGTGCTAGATAAACTAGGCTTAAATAGAGCTTAATT
*
12172355 TTCATTGAGTG-TCAG
128 TCCATTGAGTGCT-AG
* * *
12172370 CTAAAATGGGTTTAAATCTTCATTGGGTGCTAGCTAAATTGGGCTTAAATCTTTCATTAGGTG-T
1 CTAAATTGGGCTTAAATCTTCATTGGGTGCTAGCTAAATTGGGCTTAAATATTTCATTAGGTGCT
* * * *
12172434 CAACTAAACTAGGCTTTAATTTTCATTAGGTGCTATATAAATTGGGCTTAAACTAG-GCTTAATT
66 -AACTAAACTAGGCTTAAATTTT-ATTAGGTGCTAGATAAACTAGGCTTAAA-TAGAGCTTAATT
12172498 TCCATTGAGTGCTAG
128 TCCATTGAGTGCTAG
* * * *
12172513 CTAAATTAGGCTTAAATCTTCATTGGGTGCCAACTAAACTGGGCTTAAAT
1 CTAAATTGGGCTTAAATCTTCATTGGGTGCTAGCTAAATTGGGCTTAAAT
12172563 TTTTAAGAAT
Statistics
Matches: 164, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
141 5 0.03
142 49 0.30
143 107 0.65
144 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (142 bp):
CTAAATTGGGCTTAAATCTTCATTGGGTGCTAGCTAAATTGGGCTTAAATATTTCATTAGGTGCT
AACTAAACTAGGCTTAAATTTTATTAGGTGCTAGATAAACTAGGCTTAAATAGAGCTTAATTTCC
ATTGAGTGCTAG
Found at i:12172510 original size:43 final size:44
Alignment explanation
Indices: 12172438--12172528 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 44
12172428 AGGTGTCAAC
* * *
12172438 TAAACTAGGCTTTAATTTTCATTAGGTGCTATATAAATTGGGCT
1 TAAACTAGGCTTTAATTTCCATTAGGTGCTAGATAAATTAGGCT
*
12172482 TAAACTAGGC-TTAATTTCCATT-GAGTGCTAGCTAAATTAGGCT
1 TAAACTAGGCTTTAATTTCCATTAG-GTGCTAGATAAATTAGGCT
12172525 TAAA
1 TAAA
12172529 TCTTCATTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 31 0.74
44 10 0.24
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (44 bp):
TAAACTAGGCTTTAATTTCCATTAGGTGCTAGATAAATTAGGCT
Found at i:12172550 original size:33 final size:33
Alignment explanation
Indices: 12172482--12172564 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
12172472 AAATTGGGCT
* *
12172482 TAAACTAGGCTT-AATTTCCATTGAGTGCTAGC
1 TAAACTAGGCTTAAATTTCCATTGAGTGCCAAC
* *
12172514 TAAATTAGGCTTAAATCTT-CATTGGGTGCCAAC
1 TAAACTAGGCTTAAAT-TTCCATTGAGTGCCAAC
*
12172547 TAAACTGGGCTTAAATTT
1 TAAACTAGGCTTAAATTT
12172565 TTAAGAATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 13 0.30
33 28 0.65
34 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (33 bp):
TAAACTAGGCTTAAATTTCCATTGAGTGCCAAC
Found at i:12174022 original size:10 final size:10
Alignment explanation
Indices: 12173997--12174047 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
12173987 ATAACCATTA
12173997 TTCTTTTTCCTT
1 TTCTTTTT--TT
12174009 TTCTTTTTTT
1 TTCTTTTTTT
12174019 TTCTTTTTTT
1 TTCTTTTTTT
*
12174029 TCCTTATTTTGT
1 TTCTT-TTTT-T
12174041 TT-TTTTT
1 TTCTTTTT
12174048 ACATGCCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 19 0.54
11 6 0.17
12 10 0.29
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:12174763 original size:23 final size:22
Alignment explanation
Indices: 12174724--12174799 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
12174714 CTTTGATTTT
*
12174724 TTTATTTTTTTATTATTAATTA
1 TTTATTTTTTTACTATTAATTA
*
12174746 TTTATTTTTATTACTATTATTTA
1 TTTATTTTT-TTACTATTAATTA
* *
12174769 TTTTTATTTTTTA-TATT-TTTA
1 TTTAT-TTTTTTACTATTAATTA
*
12174790 TATATTTTTT
1 TTTATTTTTT
12174800 ATTTAGCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
20 5 0.11
21 7 0.15
22 13 0.28
23 18 0.38
24 4 0.09
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTTTTTACTATTAATTA
Found at i:12174764 original size:19 final size:20
Alignment explanation
Indices: 12174730--12174776 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
12174720 TTTTTTTATT
*
12174730 TTTTTATTATTAATTATTTA
1 TTTTTATTACTAATTATTTA
12174750 TTTTTATTACT-ATTATTTA
1 TTTTTATTACTAATTATTTA
12174769 TTTTTATT
1 TTTTTATT
12174777 TTTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTATTACTAATTATTTA
Found at i:12174778 original size:55 final size:55
Alignment explanation
Indices: 12174710--12174843 Score: 141
Period size: 55 Copynumber: 2.4 Consensus size: 55
12174700 GGCCAAGCCC
* * *
12174710 ATTTCTTTGATTTTTTTATTTTTTTAT-TATTAATTATTTA-TTTTTATTACT-ATT
1 ATTTTTTTTATTTTTTTATTTTTTTATATATTAATTATTTACTTTTT-TTA-TAATG
* **
12174764 ATTTATTTTTA-TTTTTTATATTTTTATATATTTTTTATTTAGCTTTTTTTATAATG
1 ATTT-TTTTTATTTTTTTATTTTTTTATATATTAATTATTTA-CTTTTTTTATAATG
12174820 ATTTTTTTTATATTTTTTATTTTT
1 ATTTTTTTTAT-TTTTTTATTTTT
12174844 ATTTGAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
54 19 0.29
55 22 0.33
56 9 0.14
57 16 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (55 bp):
ATTTTTTTTATTTTTTTATTTTTTTATATATTAATTATTTACTTTTTTTATAATG
Found at i:12174785 original size:19 final size:18
Alignment explanation
Indices: 12174719--12174801 Score: 55
Period size: 19 Copynumber: 4.5 Consensus size: 18
12174709 CATTTCTTTG
12174719 ATTTTTT-TA-TTTTTTT
1 ATTTTTTATATTTTTTTT
* *
12174735 ATTATTAATTATTTATTTTT
1 ATTTTTTA-TATTT-TTTTT
* *
12174755 ATTACTATTAT-TTATTTTT
1 ATT--TTTTATATTTTTTTT
*
12174774 ATTTTTTATATTTTTATAT
1 ATTTTTTATATTTTT-TTT
12174793 ATTTTTTAT
1 ATTTTTTAT
12174802 TTAGCTTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
18 6 0.12
19 21 0.42
20 10 0.20
21 1 0.02
22 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTTATATTTTTTTT
Found at i:12174835 original size:25 final size:22
Alignment explanation
Indices: 12174765--12174837 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
12174755 ATTACTATTA
*
12174765 TTTATTTTTATTTTTTATATTTT
1 TTTATATTT-TTTTTTATATTTT
* **
12174788 TATATATTTTTTATTTAGCTTTT
1 TTTATATTTTTT-TTTATATTTT
12174811 TTTATAATGATTTTTTTTATATTTT
1 TTTAT-AT--TTTTTTTTATATTTT
12174836 TT
1 TT
12174838 ATTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
22 3 0.08
23 19 0.49
24 2 0.05
25 10 0.26
26 5 0.13
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTATATTTTTTTTTATATTTT
Found at i:12177174 original size:164 final size:157
Alignment explanation
Indices: 12176859--12177486 Score: 509
Period size: 164 Copynumber: 4.0 Consensus size: 157
12176849 TTGGCATCTA
* * * * * *
12176859 TGAATACTCCTCTAAAAAGAGGTCTTGAAACTTTAAAATTTAAACATTGTGCCCAAAAGACTTAC
1 TGAATGCTCCTCTAAAAAGAGGACTTGAAACTTTAAAATTTAAACATTCT-ACCTAAAGACTTAT
** * * * * * *
12176924 GAATTGTGATACTAGAATAGATTCAGCTTAAAAAATTTATGAATCTTGTTCGAAGGATTTAGAGA
65 GAATCATGACACTAGAATAGATTCAACTTGAAAGACTTATGAATCTTGTT-GAAGGACTTAGAGA
*
12176989 TTAT-ATTAGAAGGTCTTACAAATCTCAACATGT
129 TTATGCTTA-AA-GTCTTACAAAT-T-AACAT-T
* *
12177022 TCGAATGCTCCTCTAAAAAGATGACTTAAAACTTTAAAATTTAAACATTCTACCTGAAAGA-TTG
1 T-GAATGCTCCTCTAAAAAGAGGACTTGAAACTTTAAAATTTAAACATTCTACCT-AAAGACTT-
* *
12177086 ATGAATCATGATACTAGAATAGATTCAACTCGAAAGACTTATGAATCTTGCTTGAAGGACTTAGA
63 ATGAATCATGACACTAGAATAGATTCAACTTGAAAGACTTATGAATCTTG-TTGAAGGACTTAGA
*
12177151 GATTATGCTTAACAGTTTTACAAA-T-AC---
127 GATTATGCTTAA-AGTCTTACAAATTAACATT
* * *
12177178 T---T--T--TCTAAAAAAAGGCCTTGAAACTTTAAAATTTAAACATTCTACCTAGAGGACTTAT
1 TGAATGCTCCTCTAAAAAGAGGACTTGAAACTTTAAAATTTAAACATTCTACCTA-AAGACTTAT
* * *
12177236 GAATCATGACACTAGAATAGATTCAACTTGGAAGACTTAT-AAGTCTTGTTTAGAGGACTTAGAA
65 GAATCATGACACTAGAATAGATTCAACTTGAAAGACTTATGAA-TCTTGTTGA-AGGACTTAGAG
* * *
12177300 ATTATGTCTGAAGGTCTTACAAATTTTAATATTT
128 ATTATG-CTTAAAGTCTTACAAA--TTAACA-TT
* * *
12177334 ATGAATGCTCCTCT-AAAAGAAGG-CATTGAAACTTTAAAATTTAGACATTCTACTTAAAGGATT
1 -TGAATGCTCCTCTAAAAAG-AGGAC-TTGAAACTTTAAAATTTAAACATTCTACCTAAA-GACT
* * * * * * * * *
12177397 TATGAATCGTTACATTAGAACAGA-TCAGCTAGGAAGACTTAAGAATCTTGCTTGAAAGACTTAG
62 TATGAATCATGACACTAGAATAGATTCAACTTGAAAGACTTATGAATCTTG-TTGAAGGACTTAG
* **
12177461 AGATTTTGCCCGAAAGTCTTACAAAT
126 AGATTATG-CTTAAAGTCTTACAAAT
12177487 CTTGATGTCT
Statistics
Matches: 382, Mismatches: 51, Indels: 66
0.77 0.10 0.13
Matches are distributed among these distances:
147 6 0.02
148 112 0.29
149 6 0.02
150 1 0.00
151 1 0.00
152 2 0.01
156 1 0.00
157 1 0.00
160 3 0.01
161 1 0.00
162 2 0.01
163 59 0.15
164 181 0.47
165 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (157 bp):
TGAATGCTCCTCTAAAAAGAGGACTTGAAACTTTAAAATTTAAACATTCTACCTAAAGACTTATG
AATCATGACACTAGAATAGATTCAACTTGAAAGACTTATGAATCTTGTTGAAGGACTTAGAGATT
ATGCTTAAAGTCTTACAAATTAACATT
Found at i:12177320 original size:148 final size:148
Alignment explanation
Indices: 12177050--12177323 Score: 387
Period size: 148 Copynumber: 1.9 Consensus size: 148
12177040 AGATGACTTA
*
12177050 AAACTTTAAAATTTAAACATTCTACCTGAAAGATTGATGAATCATGATACTAGAATAGATTCAAC
1 AAACTTTAAAATTTAAACATTCTACCTGAAAGATTGATGAATCATGACACTAGAATAGATTCAAC
* * *
12177115 TCGAAAGACTTATGAATCTTGCTTGAAGGACTTAGAGATTATGCTTAACAGTTTTACAAATACTT
66 TCGAAAGACTTATGAATCTTGCTTGAAGGACTTAGAAATTATGCTGAACAGTCTTACAAATACTT
12177180 TTCTAAAAAAAGGCCTTG
131 TTCTAAAAAAAGGCCTTG
*
12177198 AAACTTTAAAATTTAAACATTCTACCT-AGAGGACTT-ATGAATCATGACACTAGAATAGATTCA
1 AAACTTTAAAATTTAAACATTCTACCTGA-AAGA-TTGATGAATCATGACACTAGAATAGATTCA
* * * *
12177261 ACTTGGAAGACTTAT-AAGTCTTG-TTTAGAGGACTTAGAAATTATGTCTGAA-GGTCTTACAAA
64 ACTCGAAAGACTTATGAA-TCTTGCTTGA-AGGACTTAGAAATTATG-CTGAACAGTCTTACAAA
12177323 T
126 T
12177324 TTTAATATTT
Statistics
Matches: 112, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
147 6 0.05
148 100 0.89
149 6 0.05
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (148 bp):
AAACTTTAAAATTTAAACATTCTACCTGAAAGATTGATGAATCATGACACTAGAATAGATTCAAC
TCGAAAGACTTATGAATCTTGCTTGAAGGACTTAGAAATTATGCTGAACAGTCTTACAAATACTT
TTCTAAAAAAAGGCCTTG
Found at i:12184182 original size:3 final size:3
Alignment explanation
Indices: 12184174--12184229 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
12184164 TGGCTTTCCT
* * *
12184174 TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12184222 TTA TTA TT
1 TTA TTA TT
12184230 TTGTTTAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12185344 original size:12 final size:11
Alignment explanation
Indices: 12185325--12185358 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
12185315 TCTCATTTCT
12185325 TTTTTTTTTTA
1 TTTTTTTTTTA
12185336 TTATTTTTTTTA
1 TT-TTTTTTTTA
*
12185348 TTTTATTTTTA
1 TTTTTTTTTTA
12185359 GAGAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:12185344 original size:14 final size:14
Alignment explanation
Indices: 12185324--12185357 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
12185314 ATCTCATTTC
*
12185324 TTTTTTTTTTTATTA
1 TTTTTTTTATT-TTA
12185339 TTTTTTTTATTTTA
1 TTTTTTTTATTTTA
12185353 TTTTT
1 TTTTT
12185358 AGAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:12185575 original size:12 final size:12
Alignment explanation
Indices: 12185554--12185588 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12185544 TTGAACAGGG
12185554 TTGGTCAATGGC
1 TTGGTCAATGGC
*
12185566 TTGGTTAATGGC
1 TTGGTCAATGGC
12185578 TTGGTCAATGG
1 TTGGTCAATGG
12185589 TCTGGGCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.37
Consensus pattern (12 bp):
TTGGTCAATGGC
Found at i:12187704 original size:25 final size:25
Alignment explanation
Indices: 12187667--12187720 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12187657 TCCATGTGAC
12187667 TCAAAAAGGTGAATTGAATTAGGCT
1 TCAAAAAGGTGAATTGAATTAGGCT
* *
12187692 TCAAAAAGTTGAATTGAATTGGGCT
1 TCAAAAAGGTGAATTGAATTAGGCT
12187717 TCAA
1 TCAA
12187721 CTCATGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (25 bp):
TCAAAAAGGTGAATTGAATTAGGCT
Found at i:12193295 original size:6 final size:6
Alignment explanation
Indices: 12193269--12193335 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
12193259 TTTTTATTTT
* **
12193269 TTTATTA TTTAT- TTAAT- TTTATA TTTATA CATATA TTTATA TTTAT-
1 TTTA-TA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* *
12193315 TTAAT- TTTGTA TTTATA TTTA
1 TTTATA TTTATA TTTATA TTTA
12193336 AAAAATAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
5 15 0.31
6 29 0.60
7 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:12193352 original size:21 final size:20
Alignment explanation
Indices: 12193334--12193371 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12193324 TATTTATATT
12193334 TAAAAAATAATATTTTATAC
1 TAAAAAATAATATTTTATAC
* *
12193354 TAACAATTAATATTTTAT
1 TAAAAAATAATATTTTAT
12193372 TAATTTCAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAAATAATATTTTATAC
Found at i:12197692 original size:25 final size:25
Alignment explanation
Indices: 12197666--12197716 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 25
12197656 CAACTTTGTT
12197666 TCTCTTTTCTTCTTTTTTT-TTC-CTT
1 TCTC-TTTCTT-TTTTTTTCTTCTCTT
12197691 TCTCTTTCTTTTTTTTTCTTCTCTT
1 TCTCTTTCTTTTTTTTTCTTCTCTT
12197716 T
1 T
12197717 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.29
24 9 0.38
25 8 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (25 bp):
TCTCTTTCTTTTTTTTTCTTCTCTT
Found at i:12197696 original size:20 final size:20
Alignment explanation
Indices: 12197664--12197724 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
12197654 AACAACTTTG
12197664 TTTCTCTTT-TCTTCTTTTTT
1 TTTC-CTTTCTCTTCTTTTTT
12197684 TTTCCTTTCTCTTTCTTTTTT
1 TTTCCTTTCTC-TTCTTTTTT
12197705 TTT-C-TTCTCTT-TTTTTT
1 TTTCCTTTCTCTTCTTTTTT
12197722 TTT
1 TTT
12197725 AAACAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.23
18 2 0.05
19 9 0.23
20 7 0.18
21 12 0.31
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCCTTTCTCTTCTTTTTT
Found at i:12197702 original size:19 final size:18
Alignment explanation
Indices: 12197676--12197723 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
12197666 TCTCTTTTCT
*
12197676 TCTTTTTTTTTCCT-TTC
1 TCTTTTTTTTTTCTCTTC
*
12197693 TCTTTCTTTTTTTTTCTTC
1 TCTTT-TTTTTTTCTCTTC
12197712 TCTTTTTTTTTT
1 TCTTTTTTTTTT
12197724 TAAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTTTTCTCTTC
Found at i:12197717 original size:15 final size:14
Alignment explanation
Indices: 12197664--12197722 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
12197654 AACAACTTTG
* *
12197664 TTTCTCTTTTCTTC
1 TTTCTTTTTTTTTC
*
12197678 TTTTTTTTTCCTTTCTC
1 TTTCTTTTT--TTT-TC
12197695 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
12197709 TTCTCTTTTTTTTT
1 TT-TCTTTTTTTTT
12197723 TTAAACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.30
15 14 0.38
16 2 0.05
17 10 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:12197724 original size:19 final size:19
Alignment explanation
Indices: 12197668--12197724 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
12197658 ACTTTGTTTC
* *
12197668 TCTTTTCTTCTTTTTTTTT
1 TCTTCTCTTTTTTTTTTTT
* *
12197687 CCTTTCTCTTTCTTTTTTTT
1 TC-TTCTCTTTTTTTTTTTT
12197707 TCTTCTCTTTTTTTTTTT
1 TCTTCTCTTTTTTTTTTT
12197725 AAACAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TCTTCTCTTTTTTTTTTTT
Found at i:12199485 original size:5 final size:5
Alignment explanation
Indices: 12199472--12199565 Score: 98
Period size: 5 Copynumber: 18.2 Consensus size: 5
12199462 TAGTTTAGGA
* * *
12199472 TTGGTT TTGGT TTGAT TTGGGT TTGTT TTGGT TTGGC TTGGT TTGGT TTGGT
1 TTGG-T TTGGT TTGGT TT-GGT TTGGT TTGGT TTGGT TTGGT TTGGT TTGGT
* * * *
12199524 TTGGC TTGGT TTGAT TTGGT TTAGCT TGGGT TTGGT TTGGT T
1 TTGGT TTGGT TTGGT TTGGT TT-GGT TTGGT TTGGT TTGGT T
12199566 AGGATCTTTA
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
5 61 0.85
6 11 0.15
ACGTcount: A:0.03, C:0.03, G:0.36, T:0.57
Consensus pattern (5 bp):
TTGGT
Done.