Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 195 of 210
Found at i:57389691 original size:13 final size:13
Alignment explanation
Indices: 57389675--57389699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57389665 TTAAATATAT
57389675 TTTTTTAAAATTA
1 TTTTTTAAAATTA
57389688 TTTTTTAAAATT
1 TTTTTTAAAATT
57389700 TAAATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAAATTA
Found at i:57389707 original size:34 final size:35
Alignment explanation
Indices: 57389640--57389716 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
57389630 ATTTGAAATG
* * *
57389640 TTTTATAATATTATCTTTTACAATTTTAAATATAT
1 TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
*
57389675 TTTTTTAAAATTATTTTTTA-AAATTTAAATATAT
1 TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
57389709 TTTTTTAA
1 TTTTTTAA
57389717 TAAATAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
34 21 0.55
35 17 0.45
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (35 bp):
TTTTTTAAAATTATCTTTTACAAATTTAAATATAT
Found at i:57389796 original size:22 final size:21
Alignment explanation
Indices: 57389770--57389836 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
57389760 TTATTATTTG
57389770 TTTTATAATATTTAAATGTAT
1 TTTTATAATATTTAAATGTAT
* *
57389791 ATTTTA-AATATTTTAAATTTGT
1 -TTTTATAATA-TTTAAATGTAT
*
57389813 TTTTATAATTTTTAAA--TAT
1 TTTTATAATATTTAAATGTAT
57389832 TTTTA
1 TTTTA
57389837 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.18
21 15 0.38
22 17 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTTATAATATTTAAATGTAT
Found at i:57389816 original size:21 final size:22
Alignment explanation
Indices: 57389765--57389829 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
57389755 CAAATTTATT
57389765 ATTTG-TTTTATAATA-TTTAA
1 ATTTGTTTTTATAATATTTTAA
* *
57389785 ATGTATATTTTA-AATATTTTAA
1 ATTTGT-TTTTATAATATTTTAA
57389807 ATTTGTTTTTATAAT-TTTTAA
1 ATTTGTTTTTATAATATTTTAA
57389828 AT
1 AT
57389830 ATTTTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.08
21 17 0.46
22 17 0.46
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTGTTTTTATAATATTTTAA
Found at i:57389832 original size:123 final size:123
Alignment explanation
Indices: 57389710--57389934 Score: 300
Period size: 121 Copynumber: 1.8 Consensus size: 123
57389700 TAAATATATT
57389710 TTTTTAA-TAAATAAAACAT-TTAAATATTTTAAAGATATGACCTTTCAAATT-TATTATTTG-T
1 TTTTTAATTAAATAAAACATATT--AT-TTTTAAAGATATGACCTTTC-AATTATATTATTTGTT
*
57389771 TTTATAATA-TTTAAATGTATATTTTAAATATT-TTAAATTTGTTTTTATAATTTTTAAATA
62 TTTACAATATTTTAAATGTATATTTTAAATATTCTTAAATTTGTTTTTATAATTTTTAAATA
*** * *
57389831 TTTTTAATTTTTTTAAAATATATTATTTTTAAAGATATGATCTTTCAATTATATTATTTGTTTTT
1 TTTTTAA-TTAAATAAAACATATTATTTTTAAAGATATGACCTTTCAATTATATTATTTGTTTTT
*
57389896 ACAATATTTTAAATGTATATTTTAAATATTCTTTAATTT
65 ACAATATTTTAAATGTATATTTTAAATATTCTTAAATTT
57389935 TAAATATAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
120 4 0.04
121 35 0.39
122 11 0.12
123 31 0.34
124 9 0.10
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (123 bp):
TTTTTAATTAAATAAAACATATTATTTTTAAAGATATGACCTTTCAATTATATTATTTGTTTTTA
CAATATTTTAAATGTATATTTTAAATATTCTTAAATTTGTTTTTATAATTTTTAAATA
Found at i:57389949 original size:30 final size:28
Alignment explanation
Indices: 57389901--57389979 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
57389891 TTTTTACAAT
* * *
57389901 ATTTTAAATGTATATTTTAAATATTCTTTA
1 ATTTTAAATATAT-TTTTAAA-ATTATTAA
57389931 ATTTTAAATATAATTTTTATAAATTATTAA
1 ATTTTAAATAT-ATTTTTA-AAATTATTAA
57389961 ATTTTAAA-ATATTTTTAAA
1 ATTTTAAATATATTTTTAAA
57389980 GATATTCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 2 0.05
30 29 0.66
31 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATATTTTTAAAATTATTAA
Found at i:57389966 original size:121 final size:120
Alignment explanation
Indices: 57389736--57389972 Score: 320
Period size: 123 Copynumber: 2.0 Consensus size: 120
57389726 CATTTAAATA
*
57389736 TTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTAAATGTATATTTTAAATA
1 TTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTACAATATTTAAATGTATATTTTAAATA
*** * *
57389801 TTTTAAATTTGTTTTTATAATTTTTAAATATTTTTAATTTTTTTAAAATATATTAT
66 TTTTAAATTTGTAAATATAATTTTTAAATATTATTAA-TATTTTAAAATATATTAT
*
57389857 TTTTAAAGATATGATCTTTC-AATTATATTATTTGTTTTTACAATATTTTAAATGTATATTTTAA
1 TTTTAAAGATATGACCTTTCAAATT-TATTATTTG-TTTTACAATA-TTTAAATGTATATTTTAA
*
57389921 ATATTCTTTAATTT-TAAATATAATTTTTATAA-ATTATTAA-ATTTTAAAATAT
63 ATATT-TTAAATTTGTAAATATAATTTTTA-AATATTATTAATATTTTAAAATAT
57389973 TTTTAAAGAT
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
120 4 0.04
121 39 0.38
122 9 0.09
123 42 0.41
124 9 0.09
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (120 bp):
TTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTACAATATTTAAATGTATATTTTAAATA
TTTTAAATTTGTAAATATAATTTTTAAATATTATTAATATTTTAAAATATATTAT
Found at i:57390014 original size:19 final size:21
Alignment explanation
Indices: 57389990--57390029 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
57389980 GATATTCAAA
57389990 AAAATTTT-AAATT-ATATTT
1 AAAATTTTAAAATTAATATTT
57390009 AAAATTTTAAAATTAATATTT
1 AAAATTTTAAAATTAATATTT
57390030 TATTTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTTTAAAATTAATATTT
Found at i:57394716 original size:25 final size:25
Alignment explanation
Indices: 57394688--57394750 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
57394678 TACCGATTCG
57394688 CAGCTCATATGAGCTTACCG-TTATT
1 CAGCTCATATGAGCTTACCGTTTA-T
* * *
57394713 CAGCTCAAAAGAGTTTACCGTTTAT
1 CAGCTCATATGAGCTTACCGTTTAT
*
57394738 C-GCTCGTATGAGC
1 CAGCTCATATGAGC
57394751 ATACATGTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 3 0.10
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (25 bp):
CAGCTCATATGAGCTTACCGTTTAT
Found at i:57399045 original size:21 final size:21
Alignment explanation
Indices: 57398998--57399046 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
57398988 GTTATAGTAT
**
57398998 ATATTTTTAATTTTTTAATTT
1 ATATTTTTAATTTTTTAATAC
* *
57399019 AAATTTTTACTTTTTTAATAC
1 ATATTTTTAATTTTTTAATAC
57399040 ATATTTT
1 ATATTTT
57399047 AAAAAAGTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
ATATTTTTAATTTTTTAATAC
Found at i:57399219 original size:9 final size:10
Alignment explanation
Indices: 57399179--57399252 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 10
57399169 TTTGAATATC
57399179 TTTAAAAATAA
1 TTTAAAAAT-A
57399190 TTTAAAAAATCA
1 TTT-AAAAAT-A
57399202 TAATTAAAAA-A
1 T--TTAAAAATA
57399213 TTTAAAAATA
1 TTTAAAAATA
57399223 TTTAAAATATACA
1 TTTAAAA-AT--A
57399236 TTT-AAAATA
1 TTTAAAAATA
57399245 TTATAAAA
1 TT-TAAAA
57399253 CAAGTAATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
9 10 0.19
10 9 0.17
11 12 0.23
12 11 0.21
13 9 0.17
14 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:57399252 original size:33 final size:33
Alignment explanation
Indices: 57399179--57399252 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
57399169 TTTGAATATC
57399179 TTTAAAAATAATTTAAAAAATCATAATTAAAAAA
1 TTTAAAAATAATTTAAAAAATCAT-ATTAAAAAA
* *
57399213 TTTAAAAAT-ATTTAAAATATACAT-TTAAAATA
1 TTTAAAAATAATTTAAAAAAT-CATATTAAAAAA
57399245 TTATAAAA
1 TT-TAAAA
57399253 CAAGTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 9 0.25
33 15 0.42
34 12 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (33 bp):
TTTAAAAATAATTTAAAAAATCATATTAAAAAA
Found at i:57399364 original size:22 final size:21
Alignment explanation
Indices: 57399339--57399405 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
57399329 AAAAACAATC
57399339 TAAAAGATATATATTTAAAATT
1 TAAAA-ATATATATTTAAAATT
57399361 TAAAAA-ATTATATTATAAAATAT
1 TAAAAATA-TATATT-TAAAAT-T
** *
57399384 TTCAAATATACATTTAAAATT
1 TAAAAATATATATTTAAAATT
57399405 T
1 T
57399406 TATAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.03
21 9 0.24
22 17 0.45
23 10 0.26
24 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
TAAAAATATATATTTAAAATT
Found at i:57409234 original size:10 final size:9
Alignment explanation
Indices: 57409205--57409234 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
57409195 TGTATATGCT
57409205 AAATAAGAA
1 AAATAAGAA
57409214 AAATAAGAA
1 AAATAAGAA
*
57409223 AAATATGAA
1 AAATAAGAA
57409232 AAA
1 AAA
57409235 CAGTACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (9 bp):
AAATAAGAA
Found at i:57410811 original size:44 final size:44
Alignment explanation
Indices: 57410748--57410957 Score: 267
Period size: 44 Copynumber: 4.8 Consensus size: 44
57410738 TCATCTTCAA
* * * * *
57410748 CCTATTCCACTGCTAGTCAGGGAGCTAGGATTTACAGTCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCT
* * * * *
57410792 CCTATTCCATTGTTGGTCAGGGAGCTAGGACTTATAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCT
* *
57410836 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCCG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCT
* *
57410880 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCCA
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCT
* * *
57410924 CCTATTCCACTGTTGGTCAGAGAACTAGGGCTTA
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
57410958 TAGTTTTACC
Statistics
Matches: 148, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 148 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (44 bp):
CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCT
Found at i:57421621 original size:8 final size:9
Alignment explanation
Indices: 57421602--57421662 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
57421592 AAAATATTTT
57421602 AAAAATTAA
1 AAAAATTAA
57421611 AAAAATTAAA
1 AAAAATT-AA
**
57421621 AAAAGTATTTT
1 AAAA--ATTAA
*
57421632 AAAAATT-T
1 AAAAATTAA
*
57421640 TAAAATTAA
1 AAAAATTAA
57421649 AAAAATTAA
1 AAAAATTAA
57421658 AAAAA
1 AAAAA
57421663 GTATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.16
9 23 0.53
10 6 0.14
11 4 0.09
12 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTAA
Found at i:57421630 original size:30 final size:28
Alignment explanation
Indices: 57421591--57421654 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
57421581 AAAGTATTTT
57421591 AAAAATATTTTAAAAATTAAAAAAATTAA
1 AAAAATATTTTAAAAATT-AAAAAATTAA
**
57421620 AAAAAGTATTTTAAAAATTTTAAAATTAA
1 AAAAA-TATTTTAAAAATTAAAAAATTAA
57421649 AAAAAT
1 AAAAAT
57421655 TAAAAAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 18 0.56
30 13 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAATATTTTAAAAATTAAAAAATTAA
Found at i:57421673 original size:11 final size:11
Alignment explanation
Indices: 57421659--57421683 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57421649 AAAAATTAAA
57421659 AAAAGTATTTT
1 AAAAGTATTTT
57421670 AAAAGTATTTT
1 AAAAGTATTTT
57421681 AAA
1 AAA
57421684 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:57421698 original size:38 final size:39
Alignment explanation
Indices: 57421552--57421692 Score: 203
Period size: 38 Copynumber: 3.5 Consensus size: 39
57421542 ACCAAAAATT
57421552 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTT-AAAA
57421596 TATTTTAAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
1 TATTTT-AAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
57421636 -ATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
*
57421674 GTATTTTAAAGTTAAAAAA
1 -TATTTTAAAATTAAAAAA
57421693 TAAAAATATT
Statistics
Matches: 94, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
38 33 0.35
39 5 0.05
40 20 0.21
41 21 0.22
42 2 0.02
44 13 0.14
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
Found at i:57430886 original size:15 final size:15
Alignment explanation
Indices: 57430862--57430897 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
57430852 TGTAAGGAGG
57430862 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
*
57430877 AAGAAGTACAGTGTA
1 AAGAAATACAGTGTA
*
57430892 AGGAAA
1 AAGAAA
57430898 GGAATAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.17
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:57431155 original size:22 final size:20
Alignment explanation
Indices: 57431107--57431149 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
57431097 AAATGTAATG
*
57431107 TATTTTAAAAATAAAAAATA
1 TATTTTAAAAATAAAAAAAA
57431127 TATTTTAAAAATAAAAAAAA
1 TATTTTAAAAATAAAAAAAA
57431147 TAT
1 TAT
57431150 GGTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAA
Found at i:57454923 original size:42 final size:42
Alignment explanation
Indices: 57454767--57454925 Score: 237
Period size: 42 Copynumber: 3.8 Consensus size: 42
57454757 CAAACAAAAA
* * * *
57454767 CGCCGCTAAAGACCATGATCTTTAGCAGTGTTTCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
* * *
57454809 CGCCGCTAAAGAACATGGTCTTTAACGACGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
*
57454851 CGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
*
57454893 CGCCGCTAAAGAACATAGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
57454926 TATACAAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
Found at i:57455268 original size:21 final size:21
Alignment explanation
Indices: 57455242--57455291 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
57455232 TTTTGCTCTG
*
57455242 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
57455263 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
57455284 CTCTGCTT
1 CTCTGCTT
57455292 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.46, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:57457477 original size:21 final size:22
Alignment explanation
Indices: 57457436--57457487 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
57457426 TCATATGTAT
57457436 GTTATGTATAACTTGTAATTAA
1 GTTATGTATAACTTGTAATTAA
57457458 GTTATGTATAA-TAT-TAATTAA
1 GTTATGTATAACT-TGTAATTAA
*
57457479 GTTGTGTAT
1 GTTATGTAT
57457488 TATGTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
GTTATGTATAACTTGTAATTAA
Found at i:57457495 original size:16 final size:16
Alignment explanation
Indices: 57457476--57457565 Score: 121
Period size: 16 Copynumber: 5.8 Consensus size: 16
57457466 TAATATTAAT
*
57457476 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
57457492 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
57457508 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
* *
57457524 TAATTTATGTATCATG
1 TAAGTTATGTATTATG
57457540 T-A-TTATGTATTATG
1 TAAGTTATGTATTATG
*
57457554 TATGTTATGTAT
1 TAAGTTATGTAT
57457566 AATATTAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
14 12 0.18
15 1 0.01
16 54 0.81
ACGTcount: A:0.28, C:0.01, G:0.19, T:0.52
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:57457509 original size:7 final size:7
Alignment explanation
Indices: 57457483--57457556 Score: 76
Period size: 7 Copynumber: 9.7 Consensus size: 7
57457473 AATTAAGTTG
57457483 TGTATTA
1 TGTATTA
*
57457490 TGTAAGTTG
1 TGT-A-TTA
57457499 TGTATTA
1 TGTATTA
57457506 TGTAAGTTA
1 TGT-A-TTA
57457515 TGTATTA
1 TGTATTA
57457522 TGTAATTTA
1 TGT-A-TTA
*
57457531 TGTATCA
1 TGTATTA
57457538 TGTATTA
1 TGTATTA
57457545 TGTATTA
1 TGTATTA
57457552 TGTAT
1 TGTAT
57457557 GTTATGTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
7 34 0.60
8 6 0.11
9 17 0.30
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.53
Consensus pattern (7 bp):
TGTATTA
Found at i:57457581 original size:21 final size:21
Alignment explanation
Indices: 57457557--57457626 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
57457547 TATTATGTAT
57457557 GTTATGTATAATATTAATTAA
1 GTTATGTATAATATTAATTAA
*
57457578 GTTATGTAT--TATT-ATGTAT
1 GTTATGTATAATATTAAT-TAA
57457597 GTTATGTATAATATTAATTAA
1 GTTATGTATAATATTAATTAA
*
57457618 GTTGTGTAT
1 GTTATGTAT
57457627 TATGTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.05
19 15 0.36
21 23 0.55
22 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
GTTATGTATAATATTAATTAA
Found at i:57457593 original size:40 final size:40
Alignment explanation
Indices: 57457547--57457637 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
57457537 ATGTATTATG
57457547 TATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
1 TATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
*
57457587 TATTATGTATGTTATGTATAATATTAATTAAGTTGTGTAT
1 TATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
57457627 TATGTAT-TATG
1 TAT-TATGTATG
57457638 CAAGTTTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (40 bp):
TATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
Found at i:57460716 original size:14 final size:14
Alignment explanation
Indices: 57460694--57460789 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 14
57460684 CTTATCCGAC
57460694 CCCTGAAATCCTAAA
1 CCCT-AAATCCTAAA
57460709 CCCTAAATCCTAAA
1 CCCTAAATCCTAAA
* *
57460723 CCACT-AACCCTTAA
1 CC-CTAAATCCTAAA
* * *
57460737 CCCGTAACTCGTAAC
1 CCC-TAAATCCTAAA
*
57460752 CCCTAAACCCCTAAA
1 CCCTAAA-TCCTAAA
* * *
57460767 CCTTATATCCCAAA
1 CCCTAAATCCTAAA
*
57460781 CCTTAAATC
1 CCCTAAATC
57460790 AATACCCCCT
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
13 1 0.02
14 38 0.62
15 22 0.36
ACGTcount: A:0.36, C:0.39, G:0.03, T:0.22
Consensus pattern (14 bp):
CCCTAAATCCTAAA
Found at i:57461182 original size:23 final size:23
Alignment explanation
Indices: 57461116--57461182 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
57461106 ACCGTTGAAA
*
57461116 CCCTAAACCCC-AAATCCAT-AACC
1 CCCT-AACCCCTAAA-CCATAAATC
* * *
57461139 CCCTAACCCCTTACCCCTAAATC
1 CCCTAACCCCTAAACCATAAATC
*
57461162 CCCTAACCCCTAAAGCATAAA
1 CCCTAACCCCTAAACCATAAA
57461183 GCATNNNNNN
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 9 0.26
23 25 0.74
ACGTcount: A:0.36, C:0.46, G:0.01, T:0.16
Consensus pattern (23 bp):
CCCTAACCCCTAAACCATAAATC
Found at i:57461648 original size:114 final size:114
Alignment explanation
Indices: 57461441--57461760 Score: 516
Period size: 114 Copynumber: 2.8 Consensus size: 114
57461431 TTTAAATCCT
* * * *
57461441 TGAGCATTAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
*
57461506 TGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
66 TGGTCTTAGGTATTTTTGCGGCGTTTTCCCAAAAACGCCGCTAAAGCCC
*
57461555 TGAGCGTTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
*
57461620 TGGTCTTAGGTATTTTTGCGGTGTTTTCCCAAAAACGCCGCTAAAGCCC
66 TGGTCTTAGGTATTTTTGCGGCGTTTTCCCAAAAACGCCGCTAAAGCCC
* * * * *
57461669 TGAGCATTAGTGGCGCTTACTTAGAAACGCTACTAAATCCCCGAAAGCTCCGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
*
57461734 TGGGCTTAGGTA-TTTTGCGGCGTTTTC
66 TGGTCTTAGGTATTTTTGCGGCGTTTTC
57461761 TGGAAACGCC
Statistics
Matches: 191, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
113 14 0.07
114 177 0.93
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (114 bp):
TGAGCATTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAACGGCGTCGT
TGGTCTTAGGTATTTTTGCGGCGTTTTCCCAAAAACGCCGCTAAAGCCC
Found at i:57461836 original size:40 final size:38
Alignment explanation
Indices: 57461750--57461836 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 38
57461740 TAGGTATTTT
* *
57461750 GCGGCGTTTTCTGGAAACGCCGCTAATGTTTATTTTCA
1 GCGGCGTTTTCTGGAAACGCCACTAATGTCTATTTTCA
*
57461788 GCGGCGTTTTCCAT-GAAGCGCCACTAATGATCTATCTTT-A
1 GCGGCGTTTT-C-TGGAAACGCCACTAATG-TCTAT-TTTCA
57461828 GCGGCGTTT
1 GCGGCGTTT
57461837 GTTATCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 10 0.24
39 14 0.33
40 15 0.36
41 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (38 bp):
GCGGCGTTTTCTGGAAACGCCACTAATGTCTATTTTCA
Found at i:57466027 original size:60 final size:60
Alignment explanation
Indices: 57465929--57466056 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
57465919 TTTATGCATT
*
57465929 TATGATTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
1 TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
*
57465989 TATGGTTGTATTTTTCTTCAAGGTTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
1 TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
57466049 TATGGTTG
1 TATGGTTG
57466057 ATACAAGCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (60 bp):
TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
Found at i:57467726 original size:12 final size:12
Alignment explanation
Indices: 57467693--57467732 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
57467683 TGTTCATTCA
*
57467693 TTCATCAAGTGTT
1 TTCATCAAG-CTT
57467706 TTCCATCAAGCTT
1 TT-CATCAAGCTT
57467719 TTCATCAAGCTT
1 TTCATCAAGCTT
57467731 TT
1 TT
57467733 ATGTCCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (12 bp):
TTCATCAAGCTT
Found at i:57470296 original size:109 final size:109
Alignment explanation
Indices: 57470105--57470433 Score: 640
Period size: 109 Copynumber: 3.0 Consensus size: 109
57470095 TACCAGTGTA
57470105 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
1 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
*
57470170 GTCCTGGCTGTTTTTTATTCTTACAAGTAAAGAAATGTTTTCTG
66 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
57470214 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
1 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
57470279 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
66 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
*
57470323 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTACTGCT
1 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
57470388 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
66 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
57470432 TT
1 TT
57470434 GGCTGGTCCA
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 218 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (109 bp):
TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
Found at i:57472424 original size:41 final size:41
Alignment explanation
Indices: 57472351--57472671 Score: 201
Period size: 41 Copynumber: 7.8 Consensus size: 41
57472341 ATTTTTAAAC
* * * * *
57472351 CTTTAGCGGCGTTTTTATTTGTGCACCACTAATGCTCGCAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGCAT
* * * *
57472392 CTATAGTAGCGTTTTTATCTGAGCGCCGCTAATTC-CCCGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGC-AT
* * * * *
57472433 CTTTAGGGGCGTTTTTATATGAACGCCGC-AATATCTCTG-GT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAAT-GCTC-GCAT
* * * * * *
57472474 CTTTAGCGGCGATTTTATTTCAGCGCCGCTAATGCTTGTAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGCAT
*
57472515 CTTTAGTGGCG-TTTTATTCTGAGCGCCACTAATGCTCTTTGCA-
1 CTTTAGTGGCGTTTTTA-TCTGAGCGCCGCTAATGCTC---GCAT
* * * * * *
57472558 -TTTAGCGGCGATTTTGTATAAGCGCCGCTAATGCTCGGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGCAT
* * *
57472598 CTTTAGTGACGTTTTTATCTGAGCCCCAG-TAATCCTCCGGC-T
1 CTTTAGTGGCGTTTTTATCTGAGCGCC-GCTAATGCT-C-GCAT
* *
57472640 -TTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAAT
57472672 TTATTACCTT
Statistics
Matches: 214, Mismatches: 49, Indels: 34
0.72 0.16 0.11
Matches are distributed among these distances:
39 2 0.01
40 12 0.06
41 160 0.75
42 33 0.15
43 5 0.02
44 2 0.01
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGCAT
Found at i:57472588 original size:83 final size:82
Alignment explanation
Indices: 57472475--57472671 Score: 243
Period size: 83 Copynumber: 2.4 Consensus size: 82
57472465 ATCTCTGGTC
* * * * *
57472475 TTTAGCGGCGATTTTATTTCAGCGCCGCTAATGCTTGTATCTTTAGTGGCG-TTTTATTCTGAGC
1 TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGGATCTTTAGTGACGTTTTTA-TCTGAGC
* * **
57472539 GCCACTAATGCTCTTTGCA
65 CCCACTAATCCTC-CGGCA
*
57472558 TTTAGCGGCGATTTTGTATAAGCGCCGCTAATGCTCGGATCTTTAGTGACGTTTTTATCTGAGCC
1 TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGGATCTTTAGTGACGTTTTTATCTGAGCC
* *
57472623 CCAGTAATCCTCCGGCT
66 CCACTAATCCTCCGGCA
* *
57472640 TTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
1 TTTAGCGGCGATTTTATATAAGCGCCGCTAAT
57472672 TTATTACCTT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
82 31 0.32
83 62 0.63
84 5 0.05
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (82 bp):
TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGGATCTTTAGTGACGTTTTTATCTGAGCC
CCACTAATCCTCCGGCA
Found at i:57473214 original size:14 final size:14
Alignment explanation
Indices: 57473194--57473232 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
57473184 TTTAAGGTTA
57473194 ATTTAGGGTTAGAG
1 ATTTAGGGTTAGAG
* *
57473208 GTTTAGGGGTTTGAG
1 ATTTA-GGGTTAGAG
57473223 ATTTAGGGTT
1 ATTTAGGGTT
57473233 TCAACGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
ATTTAGGGTTAGAG
Found at i:57473233 original size:14 final size:14
Alignment explanation
Indices: 57473167--57473233 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
57473157 TACGGGGTAT
* *
57473167 AGATTTAAGGTTTA
1 AGATTTAGGGTTTG
*
57473181 AGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
57473193 A-ATTTAGGGTTAG
1 AGATTTAGGGTTTG
*
57473206 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
57473221 AGATTTAGGGTTT
1 AGATTTAGGGTTT
57473234 CAACGGTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.16
12 2 0.05
13 3 0.07
14 20 0.45
15 12 0.27
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:57474631 original size:27 final size:27
Alignment explanation
Indices: 57474601--57474652 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
57474591 AATAAACAAA
* *
57474601 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTAATTATTTGT
**
57474628 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATAAGTAATTAATTATTT
57474653 AAATGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (27 bp):
TAAATAAATAAGTAATTAATTATTTGT
Found at i:57477350 original size:21 final size:22
Alignment explanation
Indices: 57477301--57477351 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
57477291 NNNNNNNNNG
*
57477301 ATATATATATTTATATAAAGTT
1 ATATATATATTTATATAAAATT
*
57477323 TTA-ATATATTTAT-TAAAATT
1 ATATATATATTTATATAAAATT
57477343 ATATATATA
1 ATATATATA
57477352 CTTGAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATATATATTTATATAAAATT
Found at i:57477463 original size:16 final size:16
Alignment explanation
Indices: 57477402--57477480 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
57477392 ACACATAGCC
* *
57477402 TACATGACTTACTTAA
1 TACATAACTTACATAA
* *
57477418 TACACAACTTAAATAA
1 TACATAACTTACATAA
*
57477434 TTTAAATAACTTACATAA
1 --TACATAACTTACATAA
57477452 TACATAACTTACAT--
1 TACATAACTTACATAA
57477466 T-CATAACTTACATAA
1 TACATAACTTACATAA
57477481 ACTTATATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:57477472 original size:13 final size:15
Alignment explanation
Indices: 57477439--57477479 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
57477429 AATAATTTAA
57477439 ATAACTTACATAATAC
1 ATAACTTACAT-ATAC
57477455 ATAACTTACAT-T-C
1 ATAACTTACATATAC
57477468 ATAACTTACATA
1 ATAACTTACATA
57477480 AACTTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAACTTACATATAC
Found at i:57477605 original size:27 final size:24
Alignment explanation
Indices: 57477551--57477609 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 24
57477541 ATACATAGCA
57477551 TACATAACAAATATAAACAAAACT
1 TACATAACAAATATAAACAAAACT
* *
57477575 TACATAACTTAAATATATTACACAACT
1 TACATAAC--AAATATA-AACAAAACT
57477602 TACATAAC
1 TACATAAC
57477610 CTGGAATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 8 0.27
26 7 0.23
27 15 0.50
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (24 bp):
TACATAACAAATATAAACAAAACT
Found at i:57480001 original size:21 final size:21
Alignment explanation
Indices: 57479976--57480027 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
57479966 GCTACAACTT
* *
57479976 AAAGCAGATGCGGCAACGAGA
1 AAAGCAGAGGCAGCAACGAGA
* *
57479997 GAAGCAGAGGCAGCAGCGAGA
1 AAAGCAGAGGCAGCAACGAGA
*
57480018 AAAGCTGAGG
1 AAAGCAGAGG
57480028 TTCAACGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.38, T:0.04
Consensus pattern (21 bp):
AAAGCAGAGGCAGCAACGAGA
Found at i:57480029 original size:87 final size:87
Alignment explanation
Indices: 57479927--57480103 Score: 268
Period size: 87 Copynumber: 2.0 Consensus size: 87
57479917 AGGCAACATT
* *
57479927 GAGAGAAGCTGAGGTTCAA-AAAATATATGAAGAACTCCAGCTA-CAACTTAAAGCAGATGCGGC
1 GAGAAAAGCTGAGGTTCAACAAAA-ATATGAAGAACTCCAGC-AGCAACTTAAAGCAGATGCAGC
57479990 AACGAGAGAAGCAGAGGCAGCAGC
64 AACGAGAGAAGCAGAGGCAGCAGC
* * *
57480014 GAGAAAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCAGCAA
1 GAGAAAAGCTGAGGTTCAACAAAAATATGAAGAACTCCAGCAGCAACTTAAAGCAGATGCAGCAA
*
57480079 CGAGAGAAGCAGAGGCTGCAGC
66 CGAGAGAAGCAGAGGCAGCAGC
57480101 GAG
1 GAG
57480104 GGAATTAGAG
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
86 1 0.01
87 78 0.95
88 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.12
Consensus pattern (87 bp):
GAGAAAAGCTGAGGTTCAACAAAAATATGAAGAACTCCAGCAGCAACTTAAAGCAGATGCAGCAA
CGAGAGAAGCAGAGGCAGCAGC
Found at i:57480103 original size:21 final size:21
Alignment explanation
Indices: 57480064--57480103 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
57480054 CAGCAGCTTA
*
57480064 AAGCAGATGCAGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
* *
57480085 AAGCAGAGGCTGCAGCGAG
1 AAGCAGAGGCAGCAACGAG
57480104 GGAATTAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.20, G:0.38, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:57480511 original size:43 final size:43
Alignment explanation
Indices: 57480464--57480893 Score: 221
Period size: 43 Copynumber: 10.0 Consensus size: 43
57480454 ATTGTGGCGT
* * *
57480464 TTTTTTGCATAAGCGCCGCGAAAGATCCCCGTCTGTAGTGGCA
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * * *
57480507 TTTTTAG-ACTAAGCGCCGCAAAAGAACCCTATCTATCGTGGCA
1 TTTTTTGCA-TAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * * *
57480550 TTTCTTGCATAAGCGCCG-GAAAAGAACCTCATCTATCGTGGCG
1 TTTTTTGCATAAGCGCCGCG-AAAGAACCCCATCTATAGTGGCA
** ** * * *
57480593 TTTCCTATAGAAGCGCCG-GAGAAGAACCCTATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGA-AAGAACCCCATCTATAGTGGCA
* * * *
57480636 TTTCTTGTATAAGCGCCG-GAAAAGAACCCTC-TCTCTAGTGGCG
1 TTTTTTGCATAAGCGCCGCG-AAAGAACCC-CATCTATAGTGGCA
* * * * * * * *
57480679 TTTGTTGTACAAGCGCCGCTATAGAACCCAAGCTATAGTGGCGT
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGC-A
* * * * * *
57480723 TTTTTTGTATAAGCGCCGCTATAG-ATCACATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
** * * * * * *
57480765 TTTTGAGTATAATCGCC-AGAATAGACCCACCCTCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAA-AGAACC-CCATCTATAGTGGCA
* * * ** * *
57480809 TTTTTTGGATAAGCGCCGCTAGAGAGGCCGATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * *
57480852 TTTTGTATG--TAAGCGCCGCTAAAGAGCCACATCTATAGTGGC
1 TTTT-T-TGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGC
57480894 GCGGCAAAAG
Statistics
Matches: 307, Mismatches: 65, Indels: 30
0.76 0.16 0.07
Matches are distributed among these distances:
41 1 0.00
42 18 0.06
43 230 0.75
44 55 0.18
45 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (43 bp):
TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
Found at i:57480761 original size:86 final size:84
Alignment explanation
Indices: 57480452--57480894 Score: 302
Period size: 86 Copynumber: 5.1 Consensus size: 84
57480442 AAAACACAGC
* * * * *
57480452 CTATTGTGGCGTTTTTTTGCATAAGCGCCGCGAAAGATCCCCGTCTGTAGTGGCATTTTTAG-AC
1 CTATAGTGGCG-TTTTTTGCATAAGCGCCGCAAAAGAT-CCCATCTATAGTGGCGTTTTT-GTAC
*
57480516 TAAGCGCCGCAAAAGAACCCTAT
63 -AAGCGCCGCAAAAGAACCCAAT
* * * * * * * * *
57480539 CTATCGTGGCATTTCTTGCATAAGCGCCGGAAAAGAACCTCATCTATCGTGGCGTTTCCTATAGA
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCC-CATCTATAGTGGCGTTT-TTGTACA
* * *
57480604 AGCGCCGGAGAAGAACCCTAT
64 AGCGCCGCAAAAGAACCCAAT
* * * * * *
57480625 CTATAGTGGCGTTTCTTGTATAAGCGCCGGAAAAGAACCCTCTCTCTAGTGGCGTTTGTTGTACA
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCCC-ATCTATAGTGGCGTTT-TTGTACA
* * *
57480690 AGCGCCGCTATAGAACCCAAG
64 AGCGCCGCAAAAGAACCCAAT
* * * * * *
57480711 CTATAGTGGCGTTTTTTTGTATAAGCGCCGCTATAGATCACATCTATAGTGGCGTTTTGAGTATA
1 CTATAGTGGCG-TTTTTTGCATAAGCGCCGCAAAAGATCCCATCTATAGTGGCGTTTT-TGTACA
* * *
57480776 ATCGCCAG-AATAG-ACCCACCCT
64 AGCGCC-GCAAAAGAACCCA--AT
* * * * * *
57480798 CTATAGTGGCGTTTTTTGGATAAGCGCCGCTAGAGAGGCCGATCTATAGTGGCG-TTTTGTATGT
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGA-TCCCATCTATAGTGGCGTTTTTGTA--C
* *
57480862 AAGCGCCGCTAAAG-AGCCACAT
63 AAGCGCCGCAAAAGAACCCA-AT
57480884 CTATAGTGGCG
1 CTATAGTGGCG
57480895 CGGCAAAAGA
Statistics
Matches: 287, Mismatches: 56, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
85 12 0.04
86 201 0.70
87 74 0.26
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (84 bp):
CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCCCATCTATAGTGGCGTTTTTGTACAAG
CGCCGCAAAAGAACCCAAT
Found at i:57486027 original size:21 final size:21
Alignment explanation
Indices: 57486002--57486057 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
57485992 AAACGATATA
*
57486002 GTTTTGTCTTTTAATATAATG
1 GTTTTGACTTTTAATATAATG
57486023 GTTTTGACTTTTAATATAATG
1 GTTTTGACTTTTAATATAATG
57486044 GTTTTGACTTTTAA
1 GTTTTGACTTTTAA
57486058 CTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.55
Consensus pattern (21 bp):
GTTTTGACTTTTAATATAATG
Found at i:57491929 original size:87 final size:87
Alignment explanation
Indices: 57491783--57491958 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
57491773 AAGTACTAGT
57491783 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
* *
57491848 ATGTTTTTAATGGCTCCTTGAG
66 ATGTTCTTAACGGCTCCTTGAG
57491870 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
57491935 ATGTTCTTAACGGCTCCTTGAG
66 ATGTTCTTAACGGCTCCTTGAG
57491957 TC
1 TC
57491959 CCACCACTGT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (87 bp):
TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
ATGTTCTTAACGGCTCCTTGAG
Found at i:57493646 original size:33 final size:33
Alignment explanation
Indices: 57493604--57493673 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
57493594 GAAAGACATT
57493604 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
1 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
57493637 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
1 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
57493670 TCTG
1 TCTG
57493674 CCACATCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.49
Consensus pattern (33 bp):
TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
Found at i:57505214 original size:16 final size:17
Alignment explanation
Indices: 57505193--57505227 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
57505183 GACATGAAAT
57505193 TAATAAAATAAATA-AA
1 TAATAAAATAAATATAA
*
57505209 TAATAATATAAATATAA
1 TAATAAAATAAATATAA
57505226 TA
1 TA
57505228 GCATTCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAATAAATATAA
Found at i:57505697 original size:21 final size:22
Alignment explanation
Indices: 57505671--57505715 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
57505661 ATCATAGTAG
*
57505671 AATAATAAT-TTTATTATTTTT
1 AATAATAATATTAATTATTTTT
*
57505692 AATAATACTATTAATTATTTTT
1 AATAATAATATTAATTATTTTT
57505714 AA
1 AA
57505716 GTACAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATAATAATATTAATTATTTTT
Found at i:57513914 original size:47 final size:48
Alignment explanation
Indices: 57513789--57514173 Score: 160
Period size: 49 Copynumber: 8.1 Consensus size: 48
57513779 AAAAAAAAAC
* * * *
57513789 AAAAAAAATTTTTAGTGCTGGCCTGTCAATGGTCGGCACTAGTATATGA
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
* * * * *
57513838 AAAAAAAAATTTAGGCGCT-GCCTTATCAATTGTCAGCACCAATATACG-
1 AAAAAAAAATTT-TGTGCTGGCC-TGTCAATGGTCGGCACCAATATACGA
**
57513886 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTAC--
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
** * * **
57513933 --AAAAAAA-TTTGTTTTGG-GTG-C--TGGCCGGCACCAGCAGTACG-
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
* * * * ** *
57513974 AAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATGA
1 AAAAAAAAATTT-TGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
** * * ** *
57514024 AAAAAAATTTTTTGGTGCTGCCCTGTCAAT-GTCCGGTACCAGCAGTATG-
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGT-CGGCACCAATA-TACGA
** * * *
57514073 AAAAAAAAATTTTGGGTGCTAACCTGTGAATGGCCGGCACCAAT-T--TA
1 AAAAAAAAATTTT--GTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
* * **
57514120 AAAAAAAAA-TTGGTGTTGGCCTGTCAATGACCGAG-ACCAATATACGA
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCG-GCACCAATATACGA
57514167 AAAAAAA
1 AAAAAAA
57514174 TTTAGGTGCT
Statistics
Matches: 261, Mismatches: 52, Indels: 48
0.72 0.14 0.13
Matches are distributed among these distances:
40 17 0.07
42 1 0.00
43 8 0.03
44 32 0.12
45 15 0.06
46 3 0.01
47 38 0.15
48 22 0.08
49 65 0.25
50 59 0.23
51 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (48 bp):
AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
Found at i:57513939 original size:49 final size:48
Alignment explanation
Indices: 57513789--57514114 Score: 208
Period size: 49 Copynumber: 6.8 Consensus size: 48
57513779 AAAAAAAAAC
* * * *
57513789 AAAAAAAATTTTTAGTGCTGGCCTGTCAATGGTCGGCACTAGTA-TATG
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * * * **
57513837 AAAAAAAAAATTTAGGCGCT-GCCTTATCAATTGTCAGCACCAATA-TACG
1 -AAAAAAAAATTT-TGTGCTGGCC-TGTCAATGGTCGGCACCAGCAGTACG
*
57513886 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTAC-
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
** * *
57513933 --AAAAAAA-TTTGTTTTGG-GTG-C--TGGCCGGCACCAGCAGTACG
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * * * *
57513974 AAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATG
1 AAAAAAAAATTT-TGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * *
57514023 AAAAAAAATTTTTTGGTGCTGCCCTGTCAAT-GTCCGGTACCAGCAGTATG
1 AAAAAAAA-ATTTT-GTGCTGGCCTGTCAATGGT-CGGCACCAGCAGTACG
** * *
57514073 AAAAAAAAATTTTGGGTGCTAACCTGTGAATGGCCGGCACCA
1 AAAAAAAAATTTT--GTGCTGGCCTGTCAATGGTCGGCACCA
57514115 ATTTAAAAAA
Statistics
Matches: 219, Mismatches: 40, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
40 17 0.08
42 1 0.00
43 8 0.04
44 10 0.05
45 13 0.06
46 1 0.00
47 21 0.10
48 21 0.10
49 66 0.30
50 60 0.27
51 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (48 bp):
AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
Found at i:57514003 original size:89 final size:87
Alignment explanation
Indices: 57513882--57514043 Score: 236
Period size: 89 Copynumber: 1.8 Consensus size: 87
57513872 AGCACCAATA
* * *
57513882 TACGAAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTA-CAAAAAAATTTGTT
1 TACGAAAAAAAAATTTTGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATT-TT
57513946 TTGGGTGCTGGCCGGCACCAGCAG
65 TT-GGTGCTGGCCGGCACCAGCAG
* * *
57513970 TACGAAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATGAAAAAAAATTTT
1 TACGAAAAAAAAATTT-TGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATTTT
57514035 TTGGTGCTG
65 TTGGTGCTG
57514044 CCCTGTCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 22 0.33
89 35 0.53
90 9 0.14
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
TACGAAAAAAAAATTTTGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATTTTT
TGGTGCTGGCCGGCACCAGCAG
Found at i:57514053 original size:50 final size:50
Alignment explanation
Indices: 57513954--57514114 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
57513944 TTTTGGGTGC
* * ** *
57513954 TGGCCGGCACCAGCAGTACGAAAAAAAATTTTAT-GTGCTGGTCTATCAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
* *
57514003 TGGCCGGCACCACCAGTATGAAAAAAAATTTTTTGGTGCTGCCCTGTCAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
* * * * * *
57514053 TGTCCGGTACCAGCAGTATGAAAAAAAAATTTTGGGTGCTAACCTGTGAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
57514103 TGGCCGGCACCA
1 TGGCCGGCACCA
57514115 ATTTAAAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 31 0.33
50 64 0.67
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (50 bp):
TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
Found at i:57518126 original size:20 final size:21
Alignment explanation
Indices: 57518088--57518150 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
57518078 TTAAAATATA
57518088 TTTTTTTCAATTTCAATTTAT
1 TTTTTTTCAATTTCAATTTAT
57518109 TTTTTTCTCAA-TTC-ATTTAT
1 TTTTTT-TCAATTTCAATTTAT
* *
57518129 ATTATTTTTTAATTTAAATTTA
1 -TT-TTTTTCAATTTCAATTTA
57518151 AATTTTTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 6 0.17
21 14 0.40
22 10 0.29
23 5 0.14
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTCAATTTCAATTTAT
Found at i:57518143 original size:43 final size:43
Alignment explanation
Indices: 57518084--57518177 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
57518074 TCATTTAAAA
* **
57518084 TATATTTTTTTCAATTTCAATTTATTTTTTTCT-CAATTCATT
1 TATATTTTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
* *
57518126 TATATTATTTTTTAATTTAAATTTAAATTTTTCTGCACTTCATT
1 TATATT-TTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
*
57518170 TAAATTTT
1 TATATTTT
57518178 CTATTTTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 6 0.14
43 25 0.57
44 13 0.30
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.62
Consensus pattern (43 bp):
TATATTTTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
Found at i:57518263 original size:91 final size:90
Alignment explanation
Indices: 57518102--57518266 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
57518092 TTTCAATTTC
* * *
57518102 AATTTATTTTTTTCTCAATTCATTTATATTATTTTTTAATTTAAATTTAAATTTTTCTGCACTTC
1 AATTTATTTTTATCTCAATTCATTTATATTATTTTCTAATTTAAATTCAAATTTTTCTGCACTTC
57518167 ATTTAAATTTTCTATTTTCAATGCA
66 ATTTAAATTTTCTATTTTCAATGCA
* * * *
57518192 AATTTATTTTTATCTTATTTCATTTTATATTGAATTTTCTATTTTCAATTCAAATTTTTTCT-C-
1 AATTTATTTTTATCTCAATTCA-TTTATATT--ATTTTCTAATTTAAATTCAAA-TTTTTCTGCA
57518255 C-TCATTTAAATT
62 CTTCATTTAAATT
57518267 AAAATTTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
90 19 0.30
91 19 0.30
92 1 0.02
93 18 0.28
94 7 0.11
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.59
Consensus pattern (90 bp):
AATTTATTTTTATCTCAATTCATTTATATTATTTTCTAATTTAAATTCAAATTTTTCTGCACTTC
ATTTAAATTTTCTATTTTCAATGCA
Found at i:57519005 original size:13 final size:13
Alignment explanation
Indices: 57518987--57519011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57518977 TATTTTAATA
57518987 TTATTTTGTGTGT
1 TTATTTTGTGTGT
57519000 TTATTTTGTGTG
1 TTATTTTGTGTG
57519012 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:57520186 original size:2 final size:2
Alignment explanation
Indices: 57520179--57520249 Score: 90
Period size: 2 Copynumber: 35.0 Consensus size: 2
57520169 AATAAGCATG
* * *
57520179 TA TA TA TA TA TA TA TA TG TA TA TA TA TA -A TGC TA GA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA
57520222 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
57520250 AAAGTTATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:57520572 original size:2 final size:2
Alignment explanation
Indices: 57520565--57520595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57520555 GAATATGTAC
57520565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57520596 AATGTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57521087 original size:41 final size:41
Alignment explanation
Indices: 57521038--57521168 Score: 199
Period size: 41 Copynumber: 3.2 Consensus size: 41
57521028 GACTTTAAGT
**
57521038 CTAGCAGGCTAATTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
57521079 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * **
57521120 CTAGTAGGCTACGTGCCGGTGATCTGACTCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
57521161 CTAGCAGG
1 CTAGCAGG
57521169 TTATGTGTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:57524754 original size:49 final size:48
Alignment explanation
Indices: 57524352--57524755 Score: 375
Period size: 49 Copynumber: 8.2 Consensus size: 48
57524342 CGGCCTAAAA
*** * * * *
57524352 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGTCTAACACTC
1 AAAATTT-TTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* ** * *
57524402 -AAATTTTTTTTCGTATACT-GTGTAGGCCATTGACAGGACAACACCC
1 AAAATTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* *
57524448 AAAATTCTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCC
1 AAAATTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCA-CCC
* * *
57524497 AAAAATTTTTTTCGTACTGTTGGTGCCGGCCATTAACAGGCCAGCACCC
1 AAAATTTTTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* *
57524546 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGCCAGCACCTAT
1 AAAATTTTTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCCAGCACC--C
* ** * **
57524597 AAAATTTTTTTTTTCATACTGCTGGTGTGGGCCATTGACAAGCCAGCATGC
1 AAAA--TTTTTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* * *
57524648 AAAATTTTTTTTTCGTCTGGTGGTGCCGACCATTGACAGGCCAGCACCC
1 AAAA-TTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* * * * *
57524697 AAAATTTTTTTTCGTATACTGATGCAGGCCATTAACAAGGCCAACACCC
1 AAAATTTTTTTTCGTATGCTGGTGCCGGCCATTGAC-AGGCCAGCACCC
57524746 --AATTTTTTTT
1 AAAATTTTTTTT
57524756 GTTTTTTTTA
Statistics
Matches: 298, Mismatches: 47, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
46 19 0.06
47 31 0.10
48 54 0.18
49 112 0.38
50 37 0.12
51 8 0.03
53 37 0.12
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (48 bp):
AAAATTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCACCC
Found at i:57524762 original size:102 final size:97
Alignment explanation
Indices: 57524352--57524755 Score: 388
Period size: 102 Copynumber: 4.1 Consensus size: 97
57524342 CGGCCTAAAA
*** * * * *
57524352 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGTCTAACACTC-AAATTTTTTTTCGT
1 AAAATTT-TTTTTCGT-CTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
* * *
57524416 A-TACT-GTGTAGGCCATTGACAGGACAACACCC
64 ACTACTGGTGCAGGCCATTAACAGGCCAACACCC
* * * *
57524448 AAAATTCTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCCAAAAATTTTTTTCGTA
1 AAAATTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTTCGTA
** * *
57524513 CTGTTGGTGCCGGCCATTAACAGGCCAGCACCC
65 CTACTGGTGCAGGCCATTAACAGGCCAACACCC
* *
57524546 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGCCAGCACCTATAAAATTTTTTTTTT
1 AAAATTTTTTTTCGT-CTGCTGGTGCCGGCCATTGACAGGCCAGCACC--CAAAA--TTTTTTTT
* * ** * * * **
57524611 CATACTGCTGGTGTGGGCCATTGACAAGCCAGCATGC
61 CGTACTACTGGTGCAGGCCATTAACAGGCCAACACCC
* *
57524648 AAAATTTTTTTTTCGTCTGGTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTA
1 AAAA-TTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTA
*
57524713 -TACTGATGCAGGCCATTAACAAGGCCAACACCC
65 CTACTGGTGCAGGCCATTAAC-AGGCCAACACCC
57524746 --AATTTTTTTT
1 AAAATTTTTTTT
57524756 GTTTTTTTTA
Statistics
Matches: 252, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
94 22 0.09
95 18 0.07
96 22 0.09
97 17 0.07
98 57 0.23
99 27 0.11
100 8 0.03
102 70 0.28
103 11 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (97 bp):
AAAATTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTAC
TACTGGTGCAGGCCATTAACAGGCCAACACCC
Found at i:57526262 original size:12 final size:12
Alignment explanation
Indices: 57526247--57526275 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
57526237 AAAACAAAAA
57526247 TTAAAAAAAATT
1 TTAAAAAAAATT
57526259 TT-AAAAAAATT
1 TTAAAAAAAATT
57526270 TTAAAA
1 TTAAAA
57526276 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:57526281 original size:17 final size:17
Alignment explanation
Indices: 57526259--57526362 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
57526249 AAAAAAAATT
*
57526259 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAA
*
57526276 TTAAAAAAAATTAAAAAAGTA
1 TT-AAAAAAATT-TAAAA--A
*
57526297 TTTTAAAAAATTTAAAAA
1 -TTAAAAAAATTTAAAAA
* *
57526315 TTTAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAA
*
57526332 TTAAAAAAATTAAAAAAA
1 TTAAAAAAATT-TAAAAA
* *
57526350 ATAAAAATATTTA
1 TTAAAAAAATTTA
57526363 TTATATTCGG
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
17 29 0.41
18 23 0.33
19 3 0.04
20 4 0.06
21 9 0.13
22 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:57526281 original size:29 final size:28
Alignment explanation
Indices: 57526243--57526351 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 28
57526233 AATAAAAACA
57526243 AAAATTAAAAAAAATTTTAAAAAAATTTT
1 AAAATTAAAAAAAA-TTTAAAAAAATTTT
57526272 AAAATTAAAAAAAA-TTAAAAAAGTATTTT
1 AAAATTAAAAAAAATTTAAAAAA--ATTTT
*
57526301 AAAA--AATTTAAAAATTT-AAAAAATTTT
1 AAAATTAA--AAAAAATTTAAAAAAATTTT
*
57526328 AAAATT-AAAAAAATTAAAAAAAAT
1 AAAATTAAAAAAAATTTAAAAAAAT
57526352 AAAAATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
26 7 0.10
27 26 0.38
28 1 0.01
29 33 0.48
30 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAATTAAAAAAAATTTAAAAAAATTTT
Found at i:57526305 original size:39 final size:39
Alignment explanation
Indices: 57526227--57526323 Score: 124
Period size: 39 Copynumber: 2.4 Consensus size: 39
57526217 AAAAATTTAT
*
57526227 TTTAAAAATAAAAACAAAAATTAAAAAAAATTTTAAAAAAA
1 TTTAAAAAT-TAAA-AAAAATTAAAAAAAATTTTAAAAAAA
* *
57526268 TTTTAAAATTAAAAAAAATTAAAAAAGTATTTT-AAAAAA
1 TTTAAAAATTAAAAAAAATTAAAAAA-AATTTTAAAAAAA
*
57526307 TTTAAAAATTTAAAAAA
1 TTTAAAAATTAAAAAAA
57526324 TTTTAAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 34 0.68
40 8 0.16
41 8 0.16
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (39 bp):
TTTAAAAATTAAAAAAAATTAAAAAAAATTTTAAAAAAA
Found at i:57526321 original size:7 final size:8
Alignment explanation
Indices: 57526302--57526347 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
57526292 AAGTATTTTA
57526302 AAAAATTT
1 AAAAATTT
57526310 AAAAATTT
1 AAAAATTT
57526318 AAAAAATTT
1 -AAAAATTT
* *
57526327 TAAAATTA
1 AAAAATTT
*
57526335 AAAAAATT
1 AAAAATTT
57526343 AAAAA
1 AAAAA
57526348 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAAATTT
Found at i:57526340 original size:9 final size:9
Alignment explanation
Indices: 57526242--57526356 Score: 74
Period size: 9 Copynumber: 12.3 Consensus size: 9
57526232 AAATAAAAAC
57526242 AAAAATTAAA
1 AAAAATT-AA
57526252 AAAAATTTTAA
1 AAAAA--TTAA
*
57526263 AAAAATT-T
1 AAAAATTAA
*
57526271 TAAAATTAAA
1 AAAAATT-AA
57526281 AAAAATTAA
1 AAAAATTAA
*
57526290 AAAAGTATTTTA
1 AAAA--A-TTAA
*
57526302 AAAAATT-T
1 AAAAATTAA
*
57526310 AAAAATTTA
1 AAAAATTAA
*
57526319 AAAAATT-T
1 AAAAATTAA
*
57526327 TAAAATTAA
1 AAAAATTAA
57526336 AAAAATTAA
1 AAAAATTAA
*
57526345 AAAAAATAA
1 AAAAATTAA
57526354 AAA
1 AAA
57526357 TATTTATTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
8 19 0.23
9 36 0.43
10 12 0.14
11 8 0.10
12 9 0.11
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAAATTAA
Found at i:57526497 original size:5 final size:5
Alignment explanation
Indices: 57526487--57526516 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
57526477 CCCATATTTC
57526487 GGCCG GGCCG GGCCG GGCCG GGCCG GGCCG
1 GGCCG GGCCG GGCCG GGCCG GGCCG GGCCG
57526517 CCCGGCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
GGCCG
Found at i:57527714 original size:18 final size:19
Alignment explanation
Indices: 57527668--57527718 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
57527658 TTTCTCATAC
* * *
57527668 AAAATGATTAAAAAATCAT
1 AAAATCATTAAAAAAACAG
*
57527687 AAAATCATTAAAAAAAGAG
1 AAAATCATTAAAAAAACAG
57527706 AAAAT-ATTAAAAA
1 AAAATCATTAAAAA
57527719 TATTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAATCATTAAAAAAACAG
Found at i:57527735 original size:23 final size:23
Alignment explanation
Indices: 57527709--57527757 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
57527699 AAAAGAGAAA
57527709 ATATTAAAAATATTAAAATTGAT
1 ATATTAAAAATATTAAAATTGAT
57527732 ATATTAAAAATATTAAAATTGAT
1 ATATTAAAAATATTAAAATTGAT
57527755 ATA
1 ATA
57527758 AACTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
ATATTAAAAATATTAAAATTGAT
Found at i:57527765 original size:20 final size:22
Alignment explanation
Indices: 57527708--57527771 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 22
57527698 AAAAAGAGAA
57527708 AATATTAAAAATATTAAAATTG
1 AATATTAAAAATATTAAAATTG
57527730 ATATATTAAAAATATTAAAATTG
1 A-ATATTAAAAATATTAAAATTG
**
57527753 -ATA-TAAACTTATTAAAATT
1 AATATTAAAAATATTAAAATT
57527772 ATAAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.36
21 3 0.08
22 1 0.03
23 21 0.54
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (22 bp):
AATATTAAAAATATTAAAATTG
Found at i:57527799 original size:27 final size:26
Alignment explanation
Indices: 57527767--57527829 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 26
57527757 AAACTTATTA
57527767 AAATTATAAAAATATAA-AAACTAAT
1 AAATTATAAAAATATAACAAACTAAT
57527792 GAATATTAT-AAAATATAACAAACTAAT
1 -AA-ATTATAAAAATATAACAAACTAAT
57527819 AAATTATAAAA
1 AAATTATAAAA
57527830 GGAAATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.15
26 16 0.47
27 13 0.38
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATTATAAAAATATAACAAACTAAT
Found at i:57528103 original size:21 final size:19
Alignment explanation
Indices: 57528052--57528103 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
57528042 GAATCCTTTA
57528052 AAAATA-ATAAAAAATGTT
1 AAAATATATAAAAAATGTT
* *
57528070 AAAATTTATTAAAAAATATTT
1 AAAATATA-TAAAAAAT-GTT
57528091 AAAATGATATAAA
1 AAAAT-ATATAAA
57528104 GTTATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 8 0.30
21 11 0.41
22 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATATATAAAAAATGTT
Found at i:57528621 original size:22 final size:23
Alignment explanation
Indices: 57528591--57528643 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
57528581 TAATACTTTT
*
57528591 TATGATTTTTAT-AGAATTAT-AA
1 TATG-TTTTTATAAAAATTATAAA
*
57528613 TATGTTTTTATAAAAATTTTAAA
1 TATGTTTTTATAAAAATTATAAA
57528636 TATGTTTT
1 TATGTTTT
57528644 ATTAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (23 bp):
TATGTTTTTATAAAAATTATAAA
Found at i:57528735 original size:12 final size:12
Alignment explanation
Indices: 57528718--57528770 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
57528708 TTATATCTCT
57528718 TGATTATTTTTA
1 TGATTATTTTTA
57528730 TGATTATTTTTA
1 TGATTATTTTTA
57528742 T-A--ATTTTTA
1 TGATTATTTTTA
*
57528751 TGA-TAATTTTA
1 TGATTATTTTTA
57528762 TGATT-TTTT
1 TGATTATTTT
57528771 AATTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 13 0.36
12 14 0.39
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (12 bp):
TGATTATTTTTA
Found at i:57528749 original size:21 final size:21
Alignment explanation
Indices: 57528723--57528779 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
57528713 TCTCTTGATT
57528723 ATTTTTATGATTATTTTTATA
1 ATTTTTATGATTATTTTTATA
* *
57528744 ATTTTTATGA-TAATTTTATG
1 ATTTTTATGATTATTTTTATA
*
57528764 ATTTTT-TAATTATTTT
1 ATTTTTATGATTATTTT
57528780 ATGGAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 19 0.61
21 10 0.32
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTATGATTATTTTTATA
Found at i:57528762 original size:11 final size:11
Alignment explanation
Indices: 57528725--57528765 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
57528715 TCTTGATTAT
*
57528725 TTTTATGATTA
1 TTTTATGATAA
57528736 TTTT-T-ATAA
1 TTTTATGATAA
57528745 TTTTTATGATAA
1 -TTTTATGATAA
57528757 TTTTATGAT
1 TTTTATGAT
57528766 TTTTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.12
10 5 0.19
11 14 0.54
12 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTTATGATAA
Found at i:57535840 original size:2 final size:2
Alignment explanation
Indices: 57535835--57535869 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
57535825 TGAGAATGTT
57535835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57535870 GCCACCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57537786 original size:16 final size:17
Alignment explanation
Indices: 57537754--57537786 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57537744 TAGTATTTCT
*
57537754 TTCTTTTTTTCTTGTTC
1 TTCTTTTTTTCTAGTTC
57537771 TTCTTTTTTT-TAGTTC
1 TTCTTTTTTTCTAGTTC
57537787 ATTTTTGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTCTAGTTC
Found at i:57558797 original size:29 final size:29
Alignment explanation
Indices: 57558746--57558804 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
57558736 TTTTTTTGTA
*
57558746 TTTCCTTTTGAAGAATTCATGGAAAGCTT
1 TTTCCTTTTGAAGAATGCATGGAAAGCTT
* **
57558775 TTTCCTTTTGAAGGATGGTTGGAAAGCTT
1 TTTCCTTTTGAAGAATGCATGGAAAGCTT
57558804 T
1 T
57558805 ATTATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (29 bp):
TTTCCTTTTGAAGAATGCATGGAAAGCTT
Found at i:57559347 original size:12 final size:12
Alignment explanation
Indices: 57559312--57559370 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
57559302 GTTCACGAAC
* *
57559312 AAGCTTATTTAA
1 AAGCTTGTTTAT
*
57559324 AAGCTCGTTTAT
1 AAGCTTGTTTAT
57559336 AAGCTTGTTTAT
1 AAGCTTGTTTAT
*
57559348 -TGACTTGTTTAT
1 AAG-CTTGTTTAT
*
57559360 AA-CTTATTTAT
1 AAGCTTGTTTAT
57559371 TTATTAATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (12 bp):
AAGCTTGTTTAT
Found at i:57559590 original size:23 final size:23
Alignment explanation
Indices: 57559542--57559596 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
57559532 ATTATTTATT
**
57559542 AACATTGTTCGTTTAATGTTCGTG
1 AACA-TGTTCGTTTAATGTTAATG
57559566 AACATGTTCGTTTAA-GTTAAATG
1 AACATGTTCGTTTAATGTT-AATG
*
57559589 AACGTGTT
1 AACATGTT
57559597 TGTGAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (23 bp):
AACATGTTCGTTTAATGTTAATG
Found at i:57572201 original size:35 final size:36
Alignment explanation
Indices: 57572155--57572231 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 36
57572145 TATGATGAAA
57572155 AAAAAATTATAAATGTAATTTATTTAATTTTAA-TT
1 AAAAAATTATAAATGTAATTTATTTAATTTTAATTT
* *
57572190 AAAATATTATAAATGTACTTTATTTAATTTTAATTT
1 AAAAAATTATAAATGTAATTTATTTAATTTTAATTT
57572226 AAAAAA
1 AAAAAA
57572232 AAATTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 31 0.82
36 7 0.18
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
AAAAAATTATAAATGTAATTTATTTAATTTTAATTT
Found at i:57584395 original size:18 final size:18
Alignment explanation
Indices: 57584352--57584396 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
57584342 TTTGAAAAAA
**
57584352 AAATATAAATATGTACAT
1 AAATATAAATATACACAT
*
57584370 AAAAATAAATATACACAT
1 AAATATAAATATACACAT
*
57584388 ATATATAAA
1 AAATATAAA
57584397 GATAAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATATAAATATACACAT
Found at i:57584415 original size:28 final size:29
Alignment explanation
Indices: 57584384--57584450 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
57584374 ATAAATATAC
57584384 ACATATATATAAAGAT-AAAATAATAATT
1 ACATATATATAAAGATAAAAATAATAATT
**
57584412 ACATATGA-A-AATTATAAAAATAATAATT
1 ACATAT-ATATAAAGATAAAAATAATAATT
57584440 ACAT-TAT-TAAA
1 ACATATATATAAA
57584451 ATTAAGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.03
27 7 0.22
28 23 0.72
29 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (29 bp):
ACATATATATAAAGATAAAAATAATAATT
Found at i:57591758 original size:19 final size:19
Alignment explanation
Indices: 57591734--57591795 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
57591724 TTTGGTTCAG
57591734 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
* *
57591753 ACTTTCAA-TGGCTTTGGTTGAC
1 ACTTTCAATTGG--TTGCTT--T
57591775 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
57591794 AC
1 AC
57591796 ATTTAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 5 0.15
21 5 0.15
22 8 0.24
23 3 0.09
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (19 bp):
ACTTTCAATTGGTTGCTTT
Found at i:57591763 original size:41 final size:41
Alignment explanation
Indices: 57591718--57591795 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
57591708 TGGCAATTCT
*
57591718 AATGGCTTTGGTTCAGACTTTCAATTGGTTGCTTTACTTTC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
*
57591759 AATGGCTTTGGTTGACACTTTCAATTGGTTGCTTTAC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTAC
57591796 ATTTAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.45
Consensus pattern (41 bp):
AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
Found at i:57598155 original size:18 final size:16
Alignment explanation
Indices: 57598118--57598152 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
57598108 TATAATTTTT
57598118 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
57598134 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
57598150 TAT
1 TAT
57598153 ATTAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTTAATCAAATA
Found at i:57598572 original size:2 final size:2
Alignment explanation
Indices: 57598561--57598591 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
57598551 CTTATTCATC
57598561 TA TA -A 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
57598592 AACATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:57601650 original size:13 final size:13
Alignment explanation
Indices: 57601632--57601661 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57601622 TCTTAATGTT
57601632 ATTTGAATTTTTC
1 ATTTGAATTTTTC
*
57601645 ATTTGAATTTTTT
1 ATTTGAATTTTTC
57601658 ATTT
1 ATTT
57601662 TTCTGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (13 bp):
ATTTGAATTTTTC
Found at i:57602392 original size:5 final size:5
Alignment explanation
Indices: 57602382--57602423 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
57602372 TTACATGTTG
57602382 TTTTC TTTTC TTTTC TTTTC TTTTC TGTTT- TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTT
57602424 GAGAAATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 11 0.31
5 22 0.61
6 3 0.08
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:57604525 original size:16 final size:16
Alignment explanation
Indices: 57604504--57604552 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
57604494 TTCGCTATAT
57604504 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
57604520 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
57604536 CGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
57604552 T
1 T
57604553 AGCAATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.37, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:57604807 original size:18 final size:17
Alignment explanation
Indices: 57604786--57604820 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57604776 TTATTATTAA
*
57604786 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
57604804 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
57604821 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:57604869 original size:61 final size:61
Alignment explanation
Indices: 57604801--57604991 Score: 221
Period size: 61 Copynumber: 3.2 Consensus size: 61
57604791 TTTTAATTAA
57604801 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * ** * * *
57604862 AATATATAATACT-ATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTATTAAA
1 AATATATAAT-TTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
57604921 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
57604982 AATATATAAT
1 AATATATAAT
57604992 ACTATAAAAT
Statistics
Matches: 100, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 3 0.03
59 34 0.34
60 16 0.16
61 44 0.44
62 3 0.03
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:57604900 original size:120 final size:120
Alignment explanation
Indices: 57604766--57605054 Score: 508
Period size: 120 Copynumber: 2.4 Consensus size: 120
57604756 ATAATCATAT
* *
57604766 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
57604831 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
57604886 TTTAAAATAATTATTATTAAATATAATTT-ATTAAAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATTATTATTAAATATAATTTAATT-AAAATATATAATTTAATAAAATTCTTAATAT
57604950 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
57605006 TTTAAAATAATTATTATTATTAAATATAATTTAATAAAAATATATAATT
1 TTTAAAAT-A--ATTATTATTAAATATAATTTAATTAAAATATATAATT
57605055 CCCCTCACTT
Statistics
Matches: 161, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
119 3 0.02
120 122 0.76
121 1 0.01
123 33 0.20
124 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:57612928 original size:30 final size:30
Alignment explanation
Indices: 57612876--57612938 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
57612866 TATCAGTATT
*
57612876 AGAATGCATAATGATTATTTTAATTGTAGA
1 AGAATGCATAATGATCATTTTAATTGTAGA
*
57612906 AGAATGCATAATGATCATTTTAATTGTGGA
1 AGAATGCATAATGATCATTTTAATTGTAGA
57612936 AGA
1 AGA
57612939 TATAACGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (30 bp):
AGAATGCATAATGATCATTTTAATTGTAGA
Found at i:57615429 original size:16 final size:16
Alignment explanation
Indices: 57615408--57615438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57615398 GTTTTGCAGC
57615408 TATGGTTCACTTTTAG
1 TATGGTTCACTTTTAG
*
57615424 TATGGTTCGCTTTTA
1 TATGGTTCACTTTTA
57615439 CCGTGGAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (16 bp):
TATGGTTCACTTTTAG
Found at i:57616499 original size:26 final size:26
Alignment explanation
Indices: 57616452--57616508 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
57616442 TTCCGACTTC
57616452 CTTTTTTTTCTATTTTTGTTCTATATCT
1 CTTTTTTTTCTATTTTTGTTCT-T-TCT
57616480 CTTTTTTTTAC-A-TTTT-TTCTTTCT
1 CTTTTTTTT-CTATTTTTGTTCTTTCT
57616504 CTTTT
1 CTTTT
57616509 CATTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 4 0.14
27 4 0.14
28 10 0.36
29 1 0.04
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.74
Consensus pattern (26 bp):
CTTTTTTTTCTATTTTTGTTCTTTCT
Found at i:57617085 original size:3 final size:3
Alignment explanation
Indices: 57617077--57617122 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
57617067 AATCTAATAC
*
57617077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
57617123 CACTCATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57622199 original size:9 final size:9
Alignment explanation
Indices: 57622185--57622214 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
57622175 CATAAGACTT
57622185 TTGCTTAAA
1 TTGCTTAAA
57622194 TTGCTTAAA
1 TTGCTTAAA
57622203 TTGCTTAAA
1 TTGCTTAAA
57622212 TTG
1 TTG
57622215 AAGGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
TTGCTTAAA
Found at i:57622575 original size:41 final size:40
Alignment explanation
Indices: 57622530--57622656 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
57622520 AAACAGGCTT
57622530 TTAGCGGCG-TTTAGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCCACTAAAAATCAAGCA
* * **
57622571 TTAGCGGCGCTTTTATAAAAACGCCACTAAAGGTCAAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
*
57622611 TTAGCGGCGACTCTTCG---AAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCG-CT-TT-GAAAAAAACGCCACTAAAAATCAAGCA
57622650 TTAGCGG
1 TTAGCGG
57622657 TGTTTTTTGG
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
39 12 0.16
40 45 0.61
41 12 0.16
42 5 0.07
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
Found at i:57622600 original size:40 final size:40
Alignment explanation
Indices: 57622547--57622656 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
57622537 CGTTTAGACA
* *
57622547 AAAAACGCCACTAAAAATCAAGCATTAGCGGCG-CTTTTAT
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGACTCTT-C
**
57622587 AAAAACGCCACTAAAGGTCAAGCATTAGCGGCGACTCTTC
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGACTCTTC
* *
57622627 GAAAACGCCGCTAAAAAT-AAGCATTAGCGG
1 AAAAACGCCACTAAAAATCAAGCATTAGCGG
57622657 TGTTTTTTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 12 0.20
40 45 0.74
41 4 0.07
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATCAAGCATTAGCGGCGACTCTTC
Found at i:57622777 original size:41 final size:41
Alignment explanation
Indices: 57622720--57623119 Score: 550
Period size: 41 Copynumber: 9.7 Consensus size: 41
57622710 GTTTTTGAGG
* **
57622720 CCTTTAGCGGCGTTTTTTATGAAGCGCCGCTAATGCTCGGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
57622761 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
* *
57622802 CCTTTAGTGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
57622843 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
57622884 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
* * * *
57622925 CCTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATTCTCTGT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
* *** *
57622966 CCTTTAGCGGCGTTTTTGAGAAAGCGTAACTAATGCTCGAT
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
* * *
57623007 CCTTTAGCGGCGTTTTTTGAAAAAGCGCTGCTAATTCTCTGT
1 CCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGCTCGGT
* * *
57623049 CCTTTAGCGGCGGTTCTTCAAAAA-CGCCGCTAATGCTCGGG
1 CCTTTAGCGGC-GTTTTTGAAAAAGCGCCGCTAATGCTCGGT
* * * * *
57623090 GCTGTAGTGGCGTTTTTGAAGATGCGCCGC
1 CCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
57623120 AAAAACATTT
Statistics
Matches: 316, Mismatches: 40, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
40 8 0.03
41 265 0.84
42 42 0.13
43 1 0.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGT
Found at i:57623510 original size:14 final size:15
Alignment explanation
Indices: 57623478--57623510 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
57623468 AAGGTTTATA
57623478 GATTATGGAATTAGG
1 GATTATGGAATTAGG
*
57623493 GATTATGG-ATTTGG
1 GATTATGGAATTAGG
57623507 GATT
1 GATT
57623511 CTGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:57623599 original size:15 final size:15
Alignment explanation
Indices: 57623545--57623613 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
57623535 GTTTAATATT
*
57623545 GGTTA-TGGGTTAAG
1 GGTTAGTGGTTTAAG
* *
57623559 GGTTAGAGG-TTAAA
1 GGTTAGTGGTTTAAG
*
57623573 AGTTAG-GAGTTTAAG
1 GGTTAGTG-GTTTAAG
* *
57623588 GTTTATTGGTTTAAG
1 GGTTAGTGGTTTAAG
57623603 GGTTAGTGGTT
1 GGTTAGTGGTT
57623614 AGGGATTTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
13 1 0.02
14 15 0.36
15 25 0.60
16 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (15 bp):
GGTTAGTGGTTTAAG
Found at i:57623623 original size:8 final size:8
Alignment explanation
Indices: 57623612--57623665 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
57623602 GGGTTAGTGG
57623612 TTAGGGAT
1 TTAGGGAT
*
57623620 TTAGGGGT
1 TTAGGGAT
*
57623628 TT-GGGGT
1 TTAGGGAT
57623635 TTAGGGAT
1 TTAGGGAT
*
57623643 TTAGGG-G
1 TTAGGGAT
57623650 TTA-GGAT
1 TTAGGGAT
*
57623657 ATAGGGAT
1 TTAGGGAT
57623665 T
1 T
57623666 ATCACATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.05
7 12 0.32
8 23 0.62
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (8 bp):
TTAGGGAT
Found at i:57623633 original size:7 final size:8
Alignment explanation
Indices: 57623595--57623651 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
57623585 AAGGTTTATT
*
57623595 GGTTTAAG
1 GGTTTAGG
*
57623603 GG-TTAGT
1 GGTTTAGG
57623610 GG-TTAGG
1 GGTTTAGG
*
57623617 GATTTAGG
1 GGTTTAGG
57623625 GGTTT-GG
1 GGTTTAGG
57623632 GGTTTAGG
1 GGTTTAGG
*
57623640 GATTTAGG
1 GGTTTAGG
57623648 GGTT
1 GGTT
57623652 AGGATATAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 17 0.43
8 23 0.57
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.39
Consensus pattern (8 bp):
GGTTTAGG
Found at i:57624380 original size:16 final size:16
Alignment explanation
Indices: 57624359--57624414 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
57624349 ACTTAGTAAT
57624359 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
57624375 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
* * *
57624391 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
57624407 TAAAAGAT
1 TAAAAGAT
57624415 GTGAGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:57625060 original size:14 final size:14
Alignment explanation
Indices: 57625041--57625068 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57625031 GAATGCGCAA
57625041 ATTGTTGATGGGTT
1 ATTGTTGATGGGTT
57625055 ATTGTTGATGGGTT
1 ATTGTTGATGGGTT
57625069 TTAGACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (14 bp):
ATTGTTGATGGGTT
Found at i:57625248 original size:27 final size:27
Alignment explanation
Indices: 57625217--57625274 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
57625207 TTCATGACTA
*
57625217 TCCTGTTTGTTCATAATTTTGTTTATT
1 TCCTGTTTGTTAATAATTTTGTTTATT
57625244 TCCTGTTTGTTAATAATTTTGTTTATT
1 TCCTGTTTGTTAATAATTTTGTTTATT
57625271 TCCT
1 TCCT
57625275 CATTATTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.62
Consensus pattern (27 bp):
TCCTGTTTGTTAATAATTTTGTTTATT
Found at i:57625351 original size:12 final size:12
Alignment explanation
Indices: 57625336--57625375 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
57625326 TGTAATACTG
*
57625336 TTTGTTCATATT
1 TTTGTTCATAAT
*
57625348 TTTGTTAATAAT
1 TTTGTTCATAAT
*
57625360 TTTGTTCATAAG
1 TTTGTTCATAAT
57625372 TTTG
1 TTTG
57625376 AAACTGTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (12 bp):
TTTGTTCATAAT
Found at i:57625352 original size:24 final size:24
Alignment explanation
Indices: 57625325--57625386 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
57625315 ATTTGCAGGC
**
57625325 TTGTAATACTGTTTGTTCATATTT
1 TTGTAATACTGTTTGTTCATAAGT
*
57625349 TTGTTAATAAT-TTTGTTCATAAGT
1 TTG-TAATACTGTTTGTTCATAAGT
57625373 TTG-AA-ACTGTTTGT
1 TTGTAATACTGTTTGT
57625387 ATTACAGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.22
24 17 0.53
25 6 0.19
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (24 bp):
TTGTAATACTGTTTGTTCATAAGT
Found at i:57626348 original size:23 final size:26
Alignment explanation
Indices: 57626314--57626376 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
57626304 AATTTTCATT
*
57626314 CTTA-CATAACTTAC-TTATA-ATAA
1 CTTATCATAACTTACATTATACACAA
57626337 CTT-TCATAACTTACATTATACACAA
1 CTTATCATAACTTACATTATACACAA
57626362 CTTAT-ATAACTTACA
1 CTTATCATAACTTACA
57626377 CAAATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 13 0.37
24 5 0.14
25 16 0.46
26 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (26 bp):
CTTATCATAACTTACATTATACACAA
Found at i:57630553 original size:21 final size:21
Alignment explanation
Indices: 57630529--57630573 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57630519 CAGCTTAAAT
*
57630529 AGAGGCGGCAGCGAGAGAAGC
1 AGAGGCGGCAGCAAGAGAAGC
* *
57630550 AGAGGCTGCAGCAAGGGAAGC
1 AGAGGCGGCAGCAAGAGAAGC
57630571 AGA
1 AGA
57630574 CCAGCGTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AGAGGCGGCAGCAAGAGAAGC
Done.