Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 131 of 141
Found at i:42000127 original size:25 final size:25
Alignment explanation
Indices: 42000099--42000146 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42000089 TTTAAAAAAT
42000099 AAAAAATAATAATATTTTATTCAAA
1 AAAAAATAATAATATTTTATTCAAA
** * *
42000124 AAAATTTAATATTTTTTTATTCA
1 AAAAAATAATAATATTTTATTCA
42000147 TTGGCGCCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAAATAATAATATTTTATTCAAA
Found at i:42000435 original size:19 final size:16
Alignment explanation
Indices: 42000411--42000454 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
42000401 CATACAAAGA
42000411 TAATCTTATATTCCACTTG
1 TAATCTTATATTCC-C--G
*
42000430 TAATCTAATATTCCCG
1 TAATCTTATATTCCCG
42000446 TAATCTTAT
1 TAATCTTAT
42000455 TATGAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
18 1 0.04
19 13 0.57
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (16 bp):
TAATCTTATATTCCCG
Found at i:42005612 original size:29 final size:30
Alignment explanation
Indices: 42005566--42005646 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
42005556 AAATTGGATC
*
42005566 AAATCAAAATTTTATGTATAAAATTACACA-
1 AAATCAAAA-TTCATGTATAAAATTACACAT
*
42005596 AAATCAAAATTCATGTATACAATTACACATT
1 AAATCAAAATTCATGTATAAAATTACACA-T
* *
42005627 AAACCATAATTCATGTATAA
1 AAATCAAAATTCATGTATAA
42005647 TTTTGATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 18 0.41
30 9 0.20
31 17 0.39
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTACACAT
Found at i:42007689 original size:23 final size:23
Alignment explanation
Indices: 42007662--42007705 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42007652 ATCTTCCATA
*
42007662 TCTATTTTACGGTCTATATTTGG
1 TCTATTTTACAGTCTATATTTGG
42007685 TCTATTTTACAGTCTATATTT
1 TCTATTTTACAGTCTATATTT
42007706 AGAGTTCGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (23 bp):
TCTATTTTACAGTCTATATTTGG
Found at i:42007701 original size:12 final size:13
Alignment explanation
Indices: 42007662--42007706 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
42007652 ATCTTCCATA
42007662 TCTAT-TTTACGG
1 TCTATATTTACGG
42007674 TCTATATTT--GG
1 TCTATATTTACGG
*
42007685 TCTAT-TTTACAG
1 TCTATATTTACGG
42007697 TCTATATTTA
1 TCTATATTTA
42007707 GAGTTCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 3 0.11
11 7 0.25
12 11 0.39
13 7 0.25
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (13 bp):
TCTATATTTACGG
Found at i:42024733 original size:7 final size:7
Alignment explanation
Indices: 42024721--42024761 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
42024711 GGAAAAAGAA
42024721 TAAAAAT
1 TAAAAAT
42024728 TAAAAAT
1 TAAAAAT
42024735 TAAAAAT
1 TAAAAAT
42024742 TAAAAAT
1 TAAAAAT
42024749 TAAAAAT
1 TAAAAAT
42024756 TAAAAA
1 TAAAAA
42024762 AAATAACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:42035547 original size:22 final size:20
Alignment explanation
Indices: 42035520--42035576 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
42035510 AATATCCAAA
*
42035520 CAATAACAACAAAATAGTAG
1 CAATAACAACAAAATAGCAG
*
42035540 CAACATAACAGCAAAATAGCAG
1 C-A-ATAACAACAAAATAGCAG
42035562 CAATGAACAACAAAA
1 CAAT-AACAACAAAA
42035577 CAACAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 17 0.55
ACGTcount: A:0.60, C:0.19, G:0.11, T:0.11
Consensus pattern (20 bp):
CAATAACAACAAAATAGCAG
Found at i:42037929 original size:2 final size:2
Alignment explanation
Indices: 42037922--42037948 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42037912 AACTAGTACC
42037922 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 T
42037949 TCGAAGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42039320 original size:43 final size:44
Alignment explanation
Indices: 42039259--42039348 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 44
42039249 TTTATTTCAC
*
42039259 TCCCACCAAAGTCTTGAATGCAATCCTT-AATACTTGTGGCATA
1 TCCCACCAAAGTCTTGAATGCAATCCTTGAATACTTGTCGCATA
42039302 TCCCACCAAAGTCTTGAATGCAATCCTTGAATACTTGTCGCATA
1 TCCCACCAAAGTCTTGAATGCAATCCTTGAATACTTGTCGCATA
42039346 TCC
1 TCC
42039349 GGAGGTGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 28 0.62
44 17 0.38
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (44 bp):
TCCCACCAAAGTCTTGAATGCAATCCTTGAATACTTGTCGCATA
Found at i:42040371 original size:21 final size:21
Alignment explanation
Indices: 42040328--42040371 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42040318 GTGTAATAAG
*
42040328 AAATTGAGCAAGATTCGCTAC
1 AAATTGAGCAAGATTCGCAAC
* *
42040349 AAATTGAGCAAGTTTCTCAAC
1 AAATTGAGCAAGATTCGCAAC
42040370 AA
1 AA
42040372 TGTTATATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (21 bp):
AAATTGAGCAAGATTCGCAAC
Found at i:42042131 original size:23 final size:25
Alignment explanation
Indices: 42042105--42042154 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
42042095 TAATCTAAAA
42042105 TAATATAATATT-A-TTAAAAATTT
1 TAATATAATATTAATTTAAAAATTT
*
42042128 TAATATAGTATTAATTTTAAAAATTT
1 TAATATAATATTAA-TTTAAAAATTT
42042154 T
1 T
42042155 GTTTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
26 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATATAATATTAATTTAAAAATTT
Found at i:42042651 original size:25 final size:24
Alignment explanation
Indices: 42042609--42042668 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
42042599 TAGCAAAAGT
* *
42042609 AATAATAA-AACAAGATAGTATATA
1 AATAATAATAACAAAATAGTA-ACA
42042633 AATAATAATAACAAAATAGTAACA
1 AATAATAATAACAAAATAGTAACA
42042657 ACATAATAATAA
1 A-ATAATAATAA
42042669 AATGATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (24 bp):
AATAATAATAACAAAATAGTAACA
Found at i:42054984 original size:17 final size:19
Alignment explanation
Indices: 42054962--42054998 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
42054952 TTAAATTGTG
42054962 TTTATTTT-GA-TAGAAAA
1 TTTATTTTCGATTAGAAAA
42054979 TTTATTTTCGATTAGAAAA
1 TTTATTTTCGATTAGAAAA
42054998 T
1 T
42054999 GAAGAGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (19 bp):
TTTATTTTCGATTAGAAAA
Found at i:42057573 original size:1 final size:1
Alignment explanation
Indices: 42057567--42057597 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
42057557 CCTCCGCTGC
42057567 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42057598 GTTTCGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42063791 original size:22 final size:23
Alignment explanation
Indices: 42063748--42063793 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
42063738 AAATTATAAA
*
42063748 ATATATTAAAATATACTCTTCGT
1 ATATATTAAAATATAATCTTCGT
* *
42063771 ATAT-TTAAAATTTAATTTTCGT
1 ATATATTAAAATATAATCTTCGT
42063793 A
1 A
42063794 CTTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATATTAAAATATAATCTTCGT
Found at i:42064285 original size:99 final size:99
Alignment explanation
Indices: 42063993--42064285 Score: 365
Period size: 99 Copynumber: 3.0 Consensus size: 99
42063983 TAGTGTTTAC
* ** *
42063993 AACTCGTAAAAGTTAAATCAATATTTTAATCAAAATAAAGTATTTGGGCTAATCAATGATATTGT
1 AACTCTTAAAAGTTAAATCAACGTTTTAATCAAAATAAAGTATTTGAGCTAATCAATGATATTGT
*
42064058 AAAAGTCGTGGTACCAAATTTTGTCAAAAATACT
66 AAAAGTCGAGGTACCAAATTTTGTCAAAAATACT
* * *
42064092 -ACTCTTAAAAGTTATATCAACGTTTTAATCAAAATAAAGTATTTGAGCTAATCAATGACACTGT
1 AACTCTTAAAAGTTAAATCAACGTTTTAATCAAAATAAAGTATTTGAGCTAATCAATGATATTGT
** ** ** *
42064156 AAAAGTTAAATTACCAAATCATGTAAAAAAATA-T
66 AAAAGTCGAGGTACCAAATTTTGT-CAAAAATACT
* * * *
42064190 AACTCTTAAAAGTTACATCAACGTCTTAATCAAAATAAAGTATTTGAGTTAATTAATGATATTGT
1 AACTCTTAAAAGTTAAATCAACGTTTTAATCAAAATAAAGTATTTGAGCTAATCAATGATATTGT
**
42064255 AAAAGTCGAGGTACCATTTTTTTGTCAAAAA
66 AAAAGTCGAGGTACCA-AATTTTGTCAAAAA
42064286 GTTAAAGTAT
Statistics
Matches: 161, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
98 75 0.47
99 82 0.51
100 4 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (99 bp):
AACTCTTAAAAGTTAAATCAACGTTTTAATCAAAATAAAGTATTTGAGCTAATCAATGATATTGT
AAAAGTCGAGGTACCAAATTTTGTCAAAAATACT
Found at i:42070577 original size:25 final size:26
Alignment explanation
Indices: 42070540--42070598 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
42070530 AGAGACCAGT
42070540 TTTTAACAATAG-AAATGAATGAAAA
1 TTTTAACAATAGAAAATGAATGAAAA
* * * *
42070565 TTTTAATAGTAGAAAATGGATGAAAT
1 TTTTAACAATAGAAAATGAATGAAAA
42070591 TTTTAACA
1 TTTTAACA
42070599 GAAGGACCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (26 bp):
TTTTAACAATAGAAAATGAATGAAAA
Found at i:42071089 original size:6 final size:6
Alignment explanation
Indices: 42071078--42071104 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42071068 ATTTTATTTG
42071078 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
42071105 TTTGTCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:42078889 original size:23 final size:25
Alignment explanation
Indices: 42078843--42078890 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42078833 TTTTGAGCAA
* *
42078843 TTTAATTTTTTTTATTTTATGTTCT
1 TTTAACTTTTTTTATTTTACGTTCT
42078868 TTTAACTTTTTTT-TTTT-CGTTCT
1 TTTAACTTTTTTTATTTTACGTTCT
42078891 CTTTTGCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 4 0.19
25 12 0.57
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTAACTTTTTTTATTTTACGTTCT
Found at i:42083016 original size:95 final size:96
Alignment explanation
Indices: 42082888--42083079 Score: 377
Period size: 95 Copynumber: 2.0 Consensus size: 96
42082878 TAAAATAGTG
42082888 AAAATAATTTAAAAGTTCTTGAAAATTTATTGTTTTTTAGAAATATTTATGAAAAACTTTTAAAA
1 AAAATAATTTAAAAGTTCTTGAAAATTTATTGTTTTTTAGAAATATTTATGAAAAACTTTTAAAA
42082953 TATTGTCAAATAATATTCAAACGCCAAAAAT
66 TATTGTCAAATAATATTCAAACGCCAAAAAT
42082984 AAAATAATTT-AAAGTTCTTGAAAATTTATTGTTTTTTAGAAATATTTATGAAAAACTTTTAAAA
1 AAAATAATTTAAAAGTTCTTGAAAATTTATTGTTTTTTAGAAATATTTATGAAAAACTTTTAAAA
42083048 TATTGTCAAATAATATTCAAACGCCAAAAAT
66 TATTGTCAAATAATATTCAAACGCCAAAAAT
42083079 A
1 A
42083080 CAAAACTCAT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 86 0.90
96 10 0.10
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (96 bp):
AAAATAATTTAAAAGTTCTTGAAAATTTATTGTTTTTTAGAAATATTTATGAAAAACTTTTAAAA
TATTGTCAAATAATATTCAAACGCCAAAAAT
Found at i:42096905 original size:22 final size:23
Alignment explanation
Indices: 42096849--42096906 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
42096839 CGGCCCGTTT
* * *
42096849 TTAATTAAAATTAAAATTATTTTT
1 TTAA-TAAAATTAAAACTATATTG
42096873 TTAATAAAATTAAAACTA-ATTG
1 TTAATAAAATTAAAACTATATTG
*
42096895 TTAGTAAAATTA
1 TTAATAAAATTA
42096907 TCAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAATAAAATTAAAACTATATTG
Found at i:42098050 original size:51 final size:50
Alignment explanation
Indices: 42097974--42098119 Score: 136
Period size: 51 Copynumber: 2.8 Consensus size: 50
42097964 ATTAGTATAA
*
42097974 TAATAAATTTAG-TCATCAAAGTTTACTCATTCTGTCAAATTTATCTTGATT
1 TAATAAATTTAGCTCA-CAAA-TTTACTCATTCTGTCAAATTTATCCTGATT
* *
42098025 TAATAAATTTAGCTCACAATATTTACAT-ATTCT-ACCAATTTGATCCTGATT
1 TAATAAATTTAGCTCACAA-ATTTAC-TCATTCTGTCAAATTT-ATCCTGATT
* * * * *
42098076 TAACAAAATTAGCCCACAAAATTTACACATTTTGTCAACATTTA
1 TAATAAATTTAGCTCAC-AAATTTACTCATTCTGTCAA-ATTTA
42098120 CATAGAATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
50 6 0.08
51 57 0.74
52 10 0.13
53 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (50 bp):
TAATAAATTTAGCTCACAAATTTACTCATTCTGTCAAATTTATCCTGATT
Found at i:42112923 original size:24 final size:24
Alignment explanation
Indices: 42112878--42112923 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42112868 ATCTAATCCT
*
42112878 TTTTAACTTTGGCCCATTCAAAGC
1 TTTTAACTTTGGCCCATACAAAGC
*
42112902 TTTTAGCTTTGGCCTC-TACAAA
1 TTTTAACTTTGGCC-CATACAAA
42112924 ATTCTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (24 bp):
TTTTAACTTTGGCCCATACAAAGC
Found at i:42122612 original size:26 final size:28
Alignment explanation
Indices: 42122577--42122631 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
42122567 TTAGGGGGGA
42122577 GGGGAG-A-AGCATATAATTCACAGGTG
1 GGGGAGAACAGCATATAATTCACAGGTG
42122603 GGGGAGAAGCTAGCATATAATTCACAGGT
1 GGGGAGAA-C-AGCATATAATTCACAGGT
42122632 CAATTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.24
27 1 0.04
30 18 0.72
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (28 bp):
GGGGAGAACAGCATATAATTCACAGGTG
Found at i:42129560 original size:35 final size:35
Alignment explanation
Indices: 42129502--42129577 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
42129492 TTACAAATGT
* *
42129502 ATATACATTATAATTTAATTATCATAAATTCATATA
1 ATATAAATTATAATTTAAATATCATAAATT-ATATA
*
42129538 ATATAAATTAT-ATTTAAATATCATTAATTATATA
1 ATATAAATTATAATTTAAATATCATAAATTATATA
42129572 AT-TAAA
1 ATATAAA
42129578 ACAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 4 0.11
34 7 0.19
35 16 0.43
36 10 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAAATTATAATTTAAATATCATAAATTATATA
Found at i:42131832 original size:13 final size:13
Alignment explanation
Indices: 42131816--42131840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42131806 AAAATATTTT
42131816 TAAAAATAAAAAA
1 TAAAAATAAAAAA
42131829 TAAAAATAAAAA
1 TAAAAATAAAAA
42131841 TATTTTTAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:42134558 original size:14 final size:14
Alignment explanation
Indices: 42134539--42134594 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
42134529 TTAAACTCAT
42134539 TTATATATTATTTA
1 TTATATATTATTTA
42134553 TTATATATTATTTA
1 TTATATATTATTTA
** * *
42134567 TTCCAAACT-TTT-
1 TTATATATTATTTA
42134579 TTATATATTATTTA
1 TTATATATTATTTA
42134593 TT
1 TT
42134595 CCAAACTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 21 0.66
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATATTATTTA
Found at i:42134584 original size:26 final size:26
Alignment explanation
Indices: 42134553--42134602 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
42134543 ATATTATTTA
42134553 TTATATATTATTTATTCCAAACTTTT
1 TTATATATTATTTATTCCAAACTTTT
42134579 TTATATATTATTTATTCCAAACTT
1 TTATATATTATTTATTCCAAACTT
42134603 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATATTATTTATTCCAAACTTTT
Found at i:42134610 original size:26 final size:26
Alignment explanation
Indices: 42134555--42134614 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
42134545 ATTATTTATT
* **
42134555 ATATATTATTTATTCCAAACTTTTTT
1 ATATATTATTTATTCCAAACTTATAC
42134581 ATATATTATTTATTCCAAACTTATAC
1 ATATATTATTTATTCCAAACTTATAC
42134607 ATATATTA
1 ATATATTA
42134615 CCTACTTTTT
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:0.37, C:0.12, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATATTATTTATTCCAAACTTATAC
Found at i:42138257 original size:14 final size:14
Alignment explanation
Indices: 42138235--42138273 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
42138225 TTTGATCCCG
42138235 CTTTCTACTTTTTA
1 CTTTCTACTTTTTA
* *
42138249 CTTTTTACTTTTTG
1 CTTTCTACTTTTTA
*
42138263 CTTTCTGCTTT
1 CTTTCTACTTT
42138274 CTGGTTTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.21, G:0.05, T:0.67
Consensus pattern (14 bp):
CTTTCTACTTTTTA
Found at i:42140349 original size:14 final size:14
Alignment explanation
Indices: 42140313--42140351 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
42140303 GTTAATAGAT
42140313 AGATTAGATTAACTA
1 AGATTA-ATTAACTA
*
42140328 AG-TTAATTTACTA
1 AGATTAATTAACTA
42140341 AGATTAATTAA
1 AGATTAATTAA
42140352 TAACTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 9 0.43
14 10 0.48
15 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (14 bp):
AGATTAATTAACTA
Found at i:42144370 original size:36 final size:36
Alignment explanation
Indices: 42144320--42144392 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
42144310 CATGTCATAG
42144320 TCATTGATACAATATTTCAAGATCATTAAGAGTATC
1 TCATTGATACAATATTTCAAGATCATTAAGAGTATC
* *
42144356 TCATTGATATAATATTTCAAGATCATTAATAGTATC
1 TCATTGATACAATATTTCAAGATCATTAAGAGTATC
42144392 T
1 T
42144393 TTGTGAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (36 bp):
TCATTGATACAATATTTCAAGATCATTAAGAGTATC
Found at i:42144589 original size:27 final size:27
Alignment explanation
Indices: 42144551--42144602 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
42144541 ATCAAGTTTA
42144551 TCTTTACACCTTCTACAAGAAAATTAG
1 TCTTTACACCTTCTACAAGAAAATTAG
*
42144578 TCTTTACACCTTCTACAAGGAAATT
1 TCTTTACACCTTCTACAAGAAAATT
42144603 TGTTTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (27 bp):
TCTTTACACCTTCTACAAGAAAATTAG
Found at i:42146758 original size:71 final size:72
Alignment explanation
Indices: 42146667--42146812 Score: 285
Period size: 71 Copynumber: 2.0 Consensus size: 72
42146657 AATTATTGAT
42146667 ATATCAAAATGATAATAATTTGTAATAATATAAAAATAAATTAATAAAAATTTAATGAAAGTTCC
1 ATATCAAAATGATAATAATTTGTAATAATATAAAAATAAATTAATAAAAATTTAATGAAAGTTCC
42146732 AAAGTGA
66 AAAGTGA
42146739 ATATCAAAAT-ATAATAATTTGTAATAATATAAAAATAAATTAATAAAAATTTAATGAAAGTTCC
1 ATATCAAAATGATAATAATTTGTAATAATATAAAAATAAATTAATAAAAATTTAATGAAAGTTCC
42146803 AAAGTGA
66 AAAGTGA
42146810 ATA
1 ATA
42146813 AACAGTGCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 64 0.86
72 10 0.14
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (72 bp):
ATATCAAAATGATAATAATTTGTAATAATATAAAAATAAATTAATAAAAATTTAATGAAAGTTCC
AAAGTGA
Found at i:42147066 original size:6 final size:7
Alignment explanation
Indices: 42147025--42147063 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
42147015 TTTTTAAAAT
42147025 TTTTAAAA
1 TTTT-AAA
42147033 TTTTAAA
1 TTTTAAA
42147040 TTTTAAA
1 TTTTAAA
42147047 TTTTAAA
1 TTTTAAA
42147054 TTTTAAA
1 TTTTAAA
42147061 TTT
1 TTT
42147064 AAAGATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:42153043 original size:22 final size:23
Alignment explanation
Indices: 42152999--42153043 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
42152989 AGAGTTGACT
**
42152999 TTTTTTATTTTTTAAATGAGATCA
1 TTTTTTATTTTCCAAAT-AGATCA
42153023 TTTTTTATTTTCCAAAT-GATC
1 TTTTTTATTTTCCAAATAGATC
42153044 CAAAGGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
24 15 0.79
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTTTTATTTTCCAAATAGATCA
Found at i:42164036 original size:80 final size:80
Alignment explanation
Indices: 42163951--42164204 Score: 229
Period size: 80 Copynumber: 3.1 Consensus size: 80
42163941 TTTTATAATT
42163951 ATAATTATAAACATGTATTTTAATATACTAAATTACACATAACTATTGATGCTATATCATTTATT
1 ATAATTATAAACATGTATTTTAATATACTAAATTACACATAACTATTGATGCTATATCATTTATT
42164016 ATAATCTACAATATA
66 ATAATCTACAATATA
* * ** * *
42164031 ATAATTATTATA-TTGTAGATT-ATA-A-TAAATGATATAGCATCAA-TAGTT-ATG-TGTA--A
1 ATAATTA-TAAACATGTATTTTAATATACTAAAT--TACA-CAT-AACTA-TTGATGCTATATCA
** *
42164087 TTTAGTATATTAAAATACATGTTTATAATT
60 TTTA-T-TA-TAATCTACA-----AT-ATA
42164117 ATAATTATAAACATGTATTTTAATATACTAAATTACACATAACTATTGATGCTATATCATTTATT
1 ATAATTATAAACATGTATTTTAATATACTAAATTACACATAACTATTGATGCTATATCATTTATT
42164182 ATAATCTACAATATA
66 ATAATCTACAATATA
42164197 ATAATTAT
1 ATAATTAT
42164205 TATAAAATAT
Statistics
Matches: 132, Mismatches: 18, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
77 10 0.08
78 2 0.02
79 11 0.08
80 38 0.29
81 9 0.07
85 9 0.07
86 30 0.23
87 11 0.08
88 2 0.02
89 10 0.08
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (80 bp):
ATAATTATAAACATGTATTTTAATATACTAAATTACACATAACTATTGATGCTATATCATTTATT
ATAATCTACAATATA
Found at i:42169251 original size:24 final size:24
Alignment explanation
Indices: 42169210--42169280 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
42169200 AATTTAAATT
* *
42169210 AATAAAATCTTAAATTTAT-TATTC
1 AATAAAAT-TTTATTTTATATATTC
*
42169234 AATAAAAATTTTATTTTAATATATTT
1 AAT-AAAATTTTATTTT-ATATATTC
*
42169260 TATAAAATTTTATTTTA-ATAT
1 AATAAAATTTTATTTTATATAT
42169281 GTATAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 4 0.10
24 10 0.25
25 20 0.50
26 6 0.15
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
AATAAAATTTTATTTTATATATTC
Found at i:42170639 original size:113 final size:114
Alignment explanation
Indices: 42170502--42170731 Score: 453
Period size: 113 Copynumber: 2.0 Consensus size: 114
42170492 TATCTTCTTT
42170502 TTTTTTTTGTTGAATTTCATTTATAATATATAACATTATGTAGTTAGATTTATGTTTGCATAATA
1 TTTTTTTTGTTGAATTTCATTTATAATATATAACATTATGTAGTTAGATTTATGTTTGCATAATA
42170567 TTTAAAATATAAAAGGTGTTTATATTTGACATATTTTAATGTTAACAAA
66 TTTAAAATATAAAAGGTGTTTATATTTGACATATTTTAATGTTAACAAA
42170616 TTTTTTTTGTTG-ATTTCATTTATAATATATAACATTATGTAGTTAGATTTATGTTTGCATAATA
1 TTTTTTTTGTTGAATTTCATTTATAATATATAACATTATGTAGTTAGATTTATGTTTGCATAATA
42170680 TTTAAAATATAAAAGGTGTTTATATTTGACATATTTTAATGTTAACAAA
66 TTTAAAATATAAAAGGTGTTTATATTTGACATATTTTAATGTTAACAAA
42170729 TTT
1 TTT
42170732 GTAATAACTT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 104 0.90
114 12 0.10
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.50
Consensus pattern (114 bp):
TTTTTTTTGTTGAATTTCATTTATAATATATAACATTATGTAGTTAGATTTATGTTTGCATAATA
TTTAAAATATAAAAGGTGTTTATATTTGACATATTTTAATGTTAACAAA
Found at i:42178209 original size:29 final size:28
Alignment explanation
Indices: 42178148--42178212 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
42178138 TTAATTTTTG
42178148 AATTTAATTTATATATTTTTATTTTAAC
1 AATTTAATTTATATATTTTTATTTTAAC
*
42178176 GAATTTAATTT-TTTATTTTTTAAATTTTAA-
1 -AATTTAATTTATATA-TTTTT--ATTTTAAC
42178206 AATTTAA
1 AATTTAA
42178213 ATCCAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.09
29 22 0.69
31 7 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
AATTTAATTTATATATTTTTATTTTAAC
Found at i:42179104 original size:10 final size:10
Alignment explanation
Indices: 42179089--42179115 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42179079 CTTATGAATT
42179089 GGATCTGTTC
1 GGATCTGTTC
42179099 GGATCTGTTC
1 GGATCTGTTC
42179109 GGATCTG
1 GGATCTG
42179116 CTCATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.37
Consensus pattern (10 bp):
GGATCTGTTC
Found at i:42179860 original size:141 final size:140
Alignment explanation
Indices: 42179170--42179874 Score: 1031
Period size: 142 Copynumber: 5.0 Consensus size: 140
42179160 GTTTTCTCCT
* *
42179170 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATTATAGTTCTTCAAAATTACGTGG
1 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATCAAAGTTCTTCAAAATTACGTGG
* * * *
42179235 AAATTTGAATTCATGAGTCGGATTCCAATGCGAATGCATTTGTAACTTTAGATTTGAATTTAAAG
66 AAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAA-TTTAGATTTGAATTCAAAA
* *
42179300 TCACGTTCTTG
130 TTACGTTCTTC
* *
42179311 TTTTGATCTGTGTGTAATTTGAGTTCTTTAGCTCATTTTTCATTCCAAGTTCTTCAAAATTACGT
1 TTTTGATCTGTGTGTAA-TTGAGTTCTTTACCTCATTTTTCA-TCAAAGTTCTTCAAAATTACGT
* * * * *
42179376 CGAAATTTGAATTCACGAGTCTGGTTTCAATGCGAATGCTTTTGTAAGTTTAGATTTGAATTCAA
64 GGAAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAA-TTTAGATTTGAATTCAA
42179441 AATTACG---TTC
128 AATTACGTTCTTC
* * * *
42179451 TTTTGATCTGTGTGTAATTGAGTGCTTTACCTCAGTTTTCATCAAAATTCTTCAAATTTACGTGG
1 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATCAAAGTTCTTCAAAATTACGTGG
* * * *
42179516 AAATTTGAATTCATGAGTCCGGTTCCAATGGGAACGCTTTTGTAATTTTAGATTTGAATTCGAAA
66 AAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAA-TTTAGATTTGAATTCAAAA
*
42179581 TTGCGTTCTTC
130 TTACGTTCTTC
* *
42179592 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATTCCAAGTTCTTCAAAATTACGCG
1 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCA-TCAAAGTTCTTCAAAATTACGTG
* *
42179657 GAAATTTGAATTCATGAGTCCGATTTCAATGTGAATGCTTTTGTAATTTTAGATTTGAATTCAAA
65 GAAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAA-TTTAGATTTGAATTCAAA
42179722 ATTACGTTCTTC
129 ATTACGTTCTTC
* *
42179734 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATCAAAGTTCTTCAAATTTACGTTG
1 TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATCAAAGTTCTTCAAAATTACGTGG
42179799 AAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAATTCTAGATTTGAATTC-AAA
66 AAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAATT-TAGATTTGAATTCAAAA
42179863 TTCACGTTCTTC
130 TT-ACGTTCTTC
42179875 GAGACTTTTG
Statistics
Matches: 508, Mismatches: 48, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
138 82 0.16
139 21 0.04
140 26 0.05
141 144 0.28
142 154 0.30
143 81 0.16
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (140 bp):
TTTTGATCTGTGTGTAATTGAGTTCTTTACCTCATTTTTCATCAAAGTTCTTCAAAATTACGTGG
AAATTTGAATTCATGAGTCCGATTCCAATGCGAATGCTTTTGTAATTTAGATTTGAATTCAAAAT
TACGTTCTTC
Found at i:42193294 original size:2 final size:2
Alignment explanation
Indices: 42193287--42193316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42193277 TTTGTGATTC
42193287 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
42193317 TGTAACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42204141 original size:18 final size:18
Alignment explanation
Indices: 42204118--42204160 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42204108 GAATAGATTT
42204118 TTAATTAAATATATTT-AA
1 TTAATTAAATAT-TTTAAA
*
42204136 TTAATTGAATATTTTAAA
1 TTAATTAAATATTTTAAA
42204154 TTAATTA
1 TTAATTA
42204161 CACCTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTAATTAAATATTTTAAA
Found at i:42223445 original size:3 final size:3
Alignment explanation
Indices: 42223437--42223462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42223427 TATGGTAGAA
42223437 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
42223463 GTAAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:42231489 original size:2 final size:2
Alignment explanation
Indices: 42231482--42231506 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42231472 TAGTAGTTAT
42231482 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 T
42231507 GCATTAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42233247 original size:19 final size:19
Alignment explanation
Indices: 42233223--42233261 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42233213 GATCAAGTTT
*
42233223 AAATA-TAATATTGAGCTTC
1 AAATATTAA-ATTAAGCTTC
42233242 AAATATTAAATTAAGCTTC
1 AAATATTAAATTAAGCTTC
42233261 A
1 A
42233262 GCTTATCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (19 bp):
AAATATTAAATTAAGCTTC
Found at i:42237641 original size:6 final size:6
Alignment explanation
Indices: 42237630--42237662 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
42237620 ATGAGAAAAG
*
42237630 TGATCA TGATCA TGATCA GGATCA TGATCA TGA
1 TGATCA TGATCA TGATCA TGATCA TGATCA TGA
42237663 AGAGGAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (6 bp):
TGATCA
Found at i:42237668 original size:18 final size:18
Alignment explanation
Indices: 42237631--42237668 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42237621 TGAGAAAAGT
*
42237631 GATCATGATCATGATCAG
1 GATCATGATCATGAACAG
*
42237649 GATCATGATCATGAAGAG
1 GATCATGATCATGAACAG
42237667 GA
1 GA
42237669 GGAGGAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (18 bp):
GATCATGATCATGAACAG
Found at i:42240394 original size:18 final size:18
Alignment explanation
Indices: 42240372--42240417 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
42240362 ATATATATAA
*
42240372 ATATATATATGTATGTAT
1 ATATATGTATGTATGTAT
*
42240390 GTATATGTATGTATGTAT
1 ATATATGTATGTATGTAT
42240408 ATATATGTAT
1 ATATATGTAT
42240418 ATATATATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (18 bp):
ATATATGTATGTATGTAT
Found at i:42240396 original size:10 final size:10
Alignment explanation
Indices: 42240359--42240423 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
42240349 CACTTTTCTT
*
42240359 TATATATATA
1 TATATATGTA
* *
42240369 TAAATATATA
1 TATATATGTA
*
42240379 TATGTATGTA
1 TATATATGTA
*
42240389 TGTATATG--
1 TATATATGTA
*
42240397 TATGTATGTA
1 TATATATGTA
42240407 TATATATGTA
1 TATATATGTA
42240417 TATATAT
1 TATATAT
42240424 ATGCATGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
8 6 0.14
10 38 0.86
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (10 bp):
TATATATGTA
Found at i:42240424 original size:14 final size:14
Alignment explanation
Indices: 42240359--42240443 Score: 82
Period size: 14 Copynumber: 5.9 Consensus size: 14
42240349 CACTTTTCTT
**
42240359 TATATATATATAAA
1 TATATATATATATG
*
42240373 TATATATATGTATG
1 TATATATATATATG
* *
42240387 TATGTATATGTATG
1 TATATATATATATG
*
42240401 TATGTATATATATG
1 TATATATATATATG
42240415 TATATATATATGCATG
1 TATATATATAT--ATG
42240431 TA-AGTATATATAT
1 TATA-TATATATAT
42240444 TAATGGCATT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
14 49 0.79
15 1 0.02
16 12 0.19
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (14 bp):
TATATATATATATG
Found at i:42240443 original size:4 final size:4
Alignment explanation
Indices: 42240359--42240425 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
42240349 CACTTTTCTT
* * * * * * *
42240359 TATA TATA TATA AATA TATA TATG TATG TATG TATA TGTA TGTA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
42240407 TATA TATG TATA TATA TAT
1 TATA TATA TATA TATA TAT
42240426 GCATGTAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:42242715 original size:30 final size:29
Alignment explanation
Indices: 42242659--42242715 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
42242649 TATTTAATAA
*
42242659 GATATTTTTTAATATATTTTAGTTATTGT
1 GATATTTTTTAATATATTTTAATTATTGT
42242688 GATATATTTTTAATA-ATTTTATATTATT
1 GATAT-TTTTTAATATATTTTA-ATTATT
42242716 AAATTATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (29 bp):
GATATTTTTTAATATATTTTAATTATTGT
Found at i:42244007 original size:16 final size:18
Alignment explanation
Indices: 42243968--42244001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42243958 TAAGTTGATA
42243968 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
42243985 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
42244002 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:42244114 original size:26 final size:27
Alignment explanation
Indices: 42244084--42244166 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
42244074 TAAGATGAAT
*
42244084 ATATAAAAATTTTCAATAAATAAAA-A
1 ATATAAAAATTTTAAATAAATAAAATA
*
42244110 ATATATAAAATTATTAAAT-ATTAAAATA
1 ATATA-AAAATT-TTAAATAAATAAAATA
*
42244138 AAATAAAATATTTTAAAT-AATAATAATA
1 ATATAAAA-ATTTTAAATAAATAA-AATA
42244166 A
1 A
42244167 AGGTGGGCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 5 0.10
27 25 0.52
28 18 0.38
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAAAATTTTAAATAAATAAAATA
Found at i:42244148 original size:18 final size:20
Alignment explanation
Indices: 42244125--42244163 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42244115 TAAAATTATT
42244125 AAATA-TTAAAATAA-AATA
1 AAATATTTAAAATAATAATA
*
42244143 AAATATTTTAAATAATAATA
1 AAATATTTAAAATAATAATA
42244163 A
1 A
42244164 TAAAGGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATTTAAAATAATAATA
Found at i:42254210 original size:22 final size:22
Alignment explanation
Indices: 42254185--42254230 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42254175 GGGTTGGGTA
42254185 AAAATA-TAGTTTAAATTTTTTT
1 AAAATACT-GTTTAAATTTTTTT
* *
42254207 AAAATACTTTTTTAATTTTTTT
1 AAAATACTGTTTAAATTTTTTT
42254229 AA
1 AA
42254231 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AAAATACTGTTTAAATTTTTTT
Found at i:42254247 original size:39 final size:43
Alignment explanation
Indices: 42254197--42254284 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 43
42254187 AATATAGTTT
*
42254197 AAATTTTTTTAAAATAC-TTTTTTAA-TTT-TTTTAA-TTTTA
1 AAATATTTTTAAAATACTTTTTTTAATTTTGTTTTAATTTTTA
42254236 AAATATTTTTAAAATACTTTTTTTAATTTTTGTTTTAATTTTTA
1 AAATATTTTTAAAATACTTTTTTTAA-TTTTGTTTTAATTTTTA
42254280 AAATA
1 AAATA
42254285 AATTTTTGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
39 16 0.37
40 8 0.19
42 3 0.07
43 6 0.14
44 10 0.23
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (43 bp):
AAATATTTTTAAAATACTTTTTTTAATTTTGTTTTAATTTTTA
Found at i:42254256 original size:28 final size:28
Alignment explanation
Indices: 42254203--42254256 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
42254193 GTTTAAATTT
* **
42254203 TTTTAAAATACTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
42254231 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
42254257 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:42261722 original size:14 final size:14
Alignment explanation
Indices: 42261703--42261730 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42261693 CCTCAATATT
42261703 TATAAGGATCAATA
1 TATAAGGATCAATA
42261717 TATAAGGATCAATA
1 TATAAGGATCAATA
42261731 AGGATCAATA
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:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
TATAAGGATCAATA
Found at i:42264585 original size:19 final size:19
Alignment explanation
Indices: 42264544--42264585 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42264534 CCAAGTTCGG
*
42264544 TTTTATATTTAATTTTCAA
1 TTTTATATTTAAGTTTCAA
42264563 -TTTAGTATTTAAGTTT-AA
1 TTTTA-TATTTAAGTTTCAA
42264581 TTTTA
1 TTTTA
42264586 ACATTCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATATTTAAGTTTCAA
Found at i:42264723 original size:31 final size:31
Alignment explanation
Indices: 42264682--42264747 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
42264672 ATCGGGTATT
* * *
42264682 AAATTTAACATTAAAGTTAAATTCAAGTACC
1 AAATTAAACATTAAAGTCAAATGCAAGTACC
42264713 AAATTAAACATTAAAGTCAAATGCAAGTACC
1 AAATTAAACATTAAAGTCAAATGCAAGTACC
42264744 AAAT
1 AAAT
42264748 GGCATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (31 bp):
AAATTAAACATTAAAGTCAAATGCAAGTACC
Found at i:42267800 original size:66 final size:66
Alignment explanation
Indices: 42267694--42267826 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
42267684 AATAATAATC
42267694 CAATGAAAAATAAACATCTTGCCTATGAATGAAATCTACAACATCTTGCAAGTAACCTATAACCA
1 CAATGAAAAATAAACATCTTGCCTATGAATGAAATCTACAACATCTTGCAAGTAACCTATAACCA
42267759 T
66 T
42267760 CAATGAAAAATAAACATCTTGCCTATGAATGAAATCTACAACATCTTGCAAGTAACCTATAACCA
1 CAATGAAAAATAAACATCTTGCCTATGAATGAAATCTACAACATCTTGCAAGTAACCTATAACCA
42267825 T
66 T
42267826 C
1 C
42267827 CTCACATCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.26
Consensus pattern (66 bp):
CAATGAAAAATAAACATCTTGCCTATGAATGAAATCTACAACATCTTGCAAGTAACCTATAACCA
T
Found at i:42274179 original size:245 final size:247
Alignment explanation
Indices: 42273915--42274407 Score: 972
Period size: 245 Copynumber: 2.0 Consensus size: 247
42273905 TATTATTTAA
42273915 AATTGAATAATAGTATTTTTTCCATTTTTATTACTTTTCCTAAATTAAATTTTAGGAACTAAATA
1 AATTGAATAATAGTATTTTTTCCATTTTTATTACTTTTCCTAAATTAAATTTTAGGAACTAAATA
42273980 ATTAGAAACAGGAAAAAAAAAGTAATAGCAAATTTTTGTTATTTTTTTGTTCCATAATGCACTAT
66 ATTAGAAACAGGAAAAAAAAAGTAATAGCAAATTTTTGTTATTTTTTTGTTCCATAATGCACTAT
42274045 TTATGACCATCGCTGTAGTTGTTT-AAAAAAAAAAAAAACTGTCTTTAGCCATGGAACAAAAGTT
131 TTATGACCATCGCTGTAGTTGTTTAAAAAAAAAAAAAAACTGTCTTTAGCCATGGAACAAAAGTT
42274109 GAGCCTTTTGAGGAATATTGTGGCATATGTTCTTTTATTTGGTATATTGGTG
196 GAGCCTTTTGAGGAATATTGTGGCATATGTTCTTTTATTTGGTATATTGGTG
42274161 AATTGAATAAT-GTATTTTTTCCATTTTTATTACTTTTCCTAAATTAAATTTTAGGAACTAAATA
1 AATTGAATAATAGTATTTTTTCCATTTTTATTACTTTTCCTAAATTAAATTTTAGGAACTAAATA
42274225 ATTAGAAACAGGAAAAAAAAAGTAATAGCAAATTTTTGTTATTTTTTTGTTCCATAATGCACTAT
66 ATTAGAAACAGGAAAAAAAAAGTAATAGCAAATTTTTGTTATTTTTTTGTTCCATAATGCACTAT
42274290 TTATGACCATCGCTGTAGTTGTTTAAAAAAAAAAAAAAACTGTCTTTAGCCATGGAACAAAAGTT
131 TTATGACCATCGCTGTAGTTGTTTAAAAAAAAAAAAAAACTGTCTTTAGCCATGGAACAAAAGTT
42274355 GAGCCTTTTGAGGAATATTGTGGCATATGTTCTTTTATTTGGTATATTGGTG
196 GAGCCTTTTGAGGAATATTGTGGCATATGTTCTTTTATTTGGTATATTGGTG
42274407 A
1 A
42274408 CGGTGATCAG
Statistics
Matches: 246, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
245 142 0.58
246 104 0.42
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (247 bp):
AATTGAATAATAGTATTTTTTCCATTTTTATTACTTTTCCTAAATTAAATTTTAGGAACTAAATA
ATTAGAAACAGGAAAAAAAAAGTAATAGCAAATTTTTGTTATTTTTTTGTTCCATAATGCACTAT
TTATGACCATCGCTGTAGTTGTTTAAAAAAAAAAAAAAACTGTCTTTAGCCATGGAACAAAAGTT
GAGCCTTTTGAGGAATATTGTGGCATATGTTCTTTTATTTGGTATATTGGTG
Found at i:42277261 original size:13 final size:13
Alignment explanation
Indices: 42277226--42277254 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42277216 AGTTCTGACA
42277226 CCCCCCCC-CCCC
1 CCCCCCCCTCCCC
42277238 CCCCCCCCTCCCC
1 CCCCCCCCTCCCC
42277251 CCCC
1 CCCC
42277255 TCGCTCCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (13 bp):
CCCCCCCCTCCCC
Found at i:42277906 original size:13 final size:13
Alignment explanation
Indices: 42277888--42277912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42277878 TTTTACATGG
42277888 TTTTAATTTTAAT
1 TTTTAATTTTAAT
42277901 TTTTAATTTTAA
1 TTTTAATTTTAA
42277913 AACCCCTCTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:42285608 original size:21 final size:21
Alignment explanation
Indices: 42285582--42285625 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42285572 CAAAGGTTAA
* *
42285582 ATATTATTTGAGGGTATTTTT
1 ATATTATTTAAAGGTATTTTT
42285603 ATATTATTTAAAGGTATTTTT
1 ATATTATTTAAAGGTATTTTT
42285624 AT
1 AT
42285626 CTTTTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATATTATTTAAAGGTATTTTT
Found at i:42285989 original size:20 final size:20
Alignment explanation
Indices: 42285966--42286003 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42285956 GTCACTGTAT
*
42285966 TTTTATTTTTAGAAATTTAG
1 TTTTATTTTTAAAAATTTAG
42285986 TTTTATTTTTAAAAATTT
1 TTTTATTTTTAAAAATTT
42286004 TGAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATTTTTAAAAATTTAG
Found at i:42288228 original size:27 final size:28
Alignment explanation
Indices: 42288178--42288243 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
42288168 TTTTAGCCAC
*
42288178 AGTTTT-TTTTTTATTTTCAGAAATTT-
1 AGTTTTATTTTTTAATTTCAGAAATTTA
42288204 AGTTTTATTTTTTAAATTTCA-AAATTTA
1 AGTTTTATTTTTT-AATTTCAGAAATTTA
*
42288232 AGTTTAATTTTT
1 AGTTTTATTTTT
42288244 ATCATTACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.17
27 12 0.34
28 17 0.49
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (28 bp):
AGTTTTATTTTTTAATTTCAGAAATTTA
Found at i:42288244 original size:27 final size:28
Alignment explanation
Indices: 42288192--42288244 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
42288182 TTTTTTTTAT
*
42288192 TTTCAGAAATTTAGTTTTATTTTTTAAA
1 TTTCAGAAATTTAGTTTTAATTTTTAAA
42288220 TTTCA-AAATTTAAG-TTTAATTTTTA
1 TTTCAGAAATTT-AGTTTTAATTTTTA
42288245 TCATTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTCAGAAATTTAGTTTTAATTTTTAAA
Found at i:42289215 original size:284 final size:287
Alignment explanation
Indices: 42288691--42289261 Score: 1121
Period size: 284 Copynumber: 2.0 Consensus size: 287
42288681 TAATATATCA
42288691 AAATAAAATTATACTAATTCGAAAACATTATTAATAATTTCTGAAAATTAAATAAAATAAAAATT
1 AAATAAAATTATACTAATTCGAAAACATTATTAATAATTTCTGAAAATTAAATAAAATAAAAATT
42288756 TAAGATGTAAAATCGTAAAAAAATCATAATTTTATGTATACAGTGGGAAGTGAAGAAGAATGTGA
66 TAAGATGTAAAATCGTAAAAAAATCATAATTTTATGTATACAGTGGGAAGTGAAGAAGAATGTGA
42288821 AATGCAAACGCTATAGCACGCGTGGCAATCCGACAACAGTAAGTGCCGATGACTCGGTCCTTATC
131 AATGCAAACGCTATAGCACGCGTGGCAATCCGACAACAGTAAGTGCCGATGACTCGGTCCTTATC
42288886 ACCCCGTATAGCAAAGTGCTAATTAAGTCCAATTCTGTAAATTCAACAAAAAGCAAGGGGTATAA
196 ACCCCGTATAGCAAAGTGCTAATTAAGTCCAATTCTGTAAATTCAACAAAAAGCAAGGGGTATAA
42288951 AAGTCTATATTTTGTTTCCTTAAAATC
261 AAGTCTATATTTTGTTTCCTTAAAATC
42288978 AAATAAAA-TA-A-TAATTCGAAAACATTATTAATAATTTCTGAAAATTAAATAAAATAAAAATT
1 AAATAAAATTATACTAATTCGAAAACATTATTAATAATTTCTGAAAATTAAATAAAATAAAAATT
42289040 TAAGATGTAAAATCGTAAAAAAATCATAATTTTATGTATACAGTGGGAAGTGAAGAAGAATGTGA
66 TAAGATGTAAAATCGTAAAAAAATCATAATTTTATGTATACAGTGGGAAGTGAAGAAGAATGTGA
42289105 AATGCAAACGCTATAGCACGCGTGGCAATCCGACAACAGTAAGTGCCGATGACTCGGTCCTTATC
131 AATGCAAACGCTATAGCACGCGTGGCAATCCGACAACAGTAAGTGCCGATGACTCGGTCCTTATC
42289170 ACCCCGTATAGCAAAGTGCTAATTAAGTCCAATTCTGTAAATTCAACAAAAAGCAAGGGGTATAA
196 ACCCCGTATAGCAAAGTGCTAATTAAGTCCAATTCTGTAAATTCAACAAAAAGCAAGGGGTATAA
42289235 AAGTCTATATTTTGTTTCCTTAAAATC
261 AAGTCTATATTTTGTTTCCTTAAAATC
42289262 TCCTTTAAAG
Statistics
Matches: 284, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
284 273 0.96
285 1 0.00
286 2 0.01
287 8 0.03
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (287 bp):
AAATAAAATTATACTAATTCGAAAACATTATTAATAATTTCTGAAAATTAAATAAAATAAAAATT
TAAGATGTAAAATCGTAAAAAAATCATAATTTTATGTATACAGTGGGAAGTGAAGAAGAATGTGA
AATGCAAACGCTATAGCACGCGTGGCAATCCGACAACAGTAAGTGCCGATGACTCGGTCCTTATC
ACCCCGTATAGCAAAGTGCTAATTAAGTCCAATTCTGTAAATTCAACAAAAAGCAAGGGGTATAA
AAGTCTATATTTTGTTTCCTTAAAATC
Found at i:42289885 original size:14 final size:13
Alignment explanation
Indices: 42289859--42289883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42289849 TGCAAATTTA
42289859 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
42289872 AAAAAAAGAAAA
1 AAAAAAAGAAAA
42289884 AGCCTTGACC
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:42304025 original size:3 final size:3
Alignment explanation
Indices: 42304010--42304055 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
42304000 CGTGGATGCT
* *
42304010 GAG GAG GAA GAG GAG GAG GAG GAG GAG GAG CA- GAG GA- GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
42304056 TGACGGAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.37, C:0.02, G:0.61, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:42309055 original size:24 final size:24
Alignment explanation
Indices: 42309023--42309076 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
42309013 GGGAAAAGTA
* *
42309023 AGTTC-TTTCTGTATGTGTTGAAC
1 AGTTCATTTCTGCATGTATTGAAC
*
42309046 AGTTCATTTCTGCATGTATTTAAC
1 AGTTCATTTCTGCATGTATTGAAC
42309070 AGTTCAT
1 AGTTCAT
42309077 CTTTCTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
AGTTCATTTCTGCATGTATTGAAC
Found at i:42315789 original size:3 final size:3
Alignment explanation
Indices: 42315781--42315814 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
42315771 TTTATATTGT
*
42315781 TTA TTA TTA TAA TTA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42315815 GTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42315811 original size:14 final size:14
Alignment explanation
Indices: 42315781--42315819 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
42315771 TTTATATTGT
42315781 TTATTATTATA--A
1 TTATTATTATATTA
42315793 TTATTATTATATTA
1 TTATTATTATATTA
*
42315807 TTATTATTGTATT
1 TTATTATTATATT
42315820 TATATGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:42315853 original size:16 final size:16
Alignment explanation
Indices: 42315834--42315864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42315824 TGTGTGCGCC
*
42315834 TATATATATATATTAA
1 TATACATATATATTAA
42315850 TATACATATATATTA
1 TATACATATATATTA
42315865 TAAATGTTTT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATACATATATATTAA
Found at i:42320462 original size:24 final size:26
Alignment explanation
Indices: 42320429--42320484 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
42320419 AACATTTATA
*
42320429 TTTTTT-GTTAA-TTTGAT-TTTAAT
1 TTTTTTAGTTAATTTTGATCCTTAAT
42320452 TTTTTTAGTTAATTTTGATCCTTAAT
1 TTTTTTAGTTAATTTTGATCCTTAAT
42320478 TTTTTTA
1 TTTTTTA
42320485 AAAAGTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 6 0.21
24 5 0.17
25 6 0.21
26 12 0.41
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (26 bp):
TTTTTTAGTTAATTTTGATCCTTAAT
Found at i:42323781 original size:9 final size:9
Alignment explanation
Indices: 42323755--42323788 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
42323745 CTCCAACTTA
42323755 AATTAAATT
1 AATTAAATT
42323764 AAATTAAATT
1 -AATTAAATT
*
42323774 ACTTAAATT
1 AATTAAATT
42323783 AATTAA
1 AATTAA
42323789 TTTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTAAATT
Found at i:42323790 original size:4 final size:5
Alignment explanation
Indices: 42323752--42323788 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
42323742 ATTCTCCAAC
*
42323752 TTAAA TTAAA TTAAA TTAAA TT-AC TTAAA TT-AA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
42323789 TTTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 7 0.25
5 21 0.75
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:42325664 original size:25 final size:25
Alignment explanation
Indices: 42325617--42325680 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
42325607 GGCTTCAGCA
*
42325617 TTTATATTTTTTTTGTTAATTTGAT-
1 TTTA-ATTTTTTTAGTTAATTTGATC
42325642 TTTAATTTTTTTAGTTAATTTTGATC
1 TTTAATTTTTTTAGTTAA-TTTGATC
* *
42325668 CTTAACTTTTTTA
1 TTTAATTTTTTTA
42325681 AAAAGTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
25 10 0.29
26 11 0.32
ACGTcount: A:0.22, C:0.05, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTAATTTTTTTAGTTAATTTGATC
Found at i:42335603 original size:109 final size:108
Alignment explanation
Indices: 42335404--42335814 Score: 625
Period size: 108 Copynumber: 3.8 Consensus size: 108
42335394 AAGATTCAAG
* * * * *
42335404 AGGATATTTGGCTATTTGGTTAAACG-AGAAACCGAAACCCAGCACATTAGGGCACG-TTCCTCG
1 AGGATATTTAGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
* * *
42335467 AATTTCTAAACG-TAAAACATTGCCTTATTTTGAAATTTTTTGAA
66 AATTTCCAAACGCT-AAATATTGCCTTATTTTGAAA-TTTTTAAA
*
42335511 AGGATATTTAGCTATTTGGTCAAACGAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCG
1 AGGATATTTAGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
**
42335576 AATTTCCAAACGCTAAATATTGCCTTATTTCAAAATTTTTAAA
66 AATTTCCAAACGCTAAATATTGCCTTATTTTGAAATTTTTAAA
*
42335619 AGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
1 AGGATATTTAGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
42335684 AATTTCCAAACGCTAAATATTGCCTTATTTTTGAAA-TTTTAAA
66 AATTTCCAAACGCTAAATATTGCCTTA-TTTTGAAATTTTTAAA
*
42335727 AGGATATTTAGCTATTTGGT-AGAACGAAAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCT
1 AGGATATTTAGCTATTTGGTCA-AACG-AAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
42335791 CGAATTTCCAAACGCTAAATATTG
64 CGAATTTCCAAACGCTAAATATTG
42335815 TCTCATTTAG
Statistics
Matches: 281, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
107 24 0.09
108 155 0.55
109 101 0.36
110 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
AATTTCCAAACGCTAAATATTGCCTTATTTTGAAATTTTTAAA
Found at i:42335810 original size:217 final size:214
Alignment explanation
Indices: 42335404--42335814 Score: 639
Period size: 217 Copynumber: 1.9 Consensus size: 214
42335394 AAGATTCAAG
* * *
42335404 AGGATATTTGGCTATTTGGTTAAACGAGAAACCGAAACCCAGCACATTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCAAACGAAAAACCGAAACCCAGCACATTAGGGCACGTTCCTCGAA
* *
42335469 TTTCTAAACGTAAAACATTGCCTTATTTTGAAATTTTTTGAAAGGATATTTAGCTATTTGGTCAA
66 TTTCCAAACGTAAAACATTGCCTTATTTTGAAA-TTTTTAAAAGGATATTTAGCTATTTGGTCAA
* *
42335534 ACGAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCTAAATATTGC
130 ACGAAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCGAATTTCCAAACGCTAAATATTGC
42335599 CTTATTTCAAAATTTTTAAA
195 CTTATTTCAAAATTTTTAAA
* * *
42335619 AGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
1 AGGATATTTAGCTATTTGGTCAAACG-AAAAACCGAAACCCAGCACATTAGGGCACG-TTCCTCG
*
42335684 AATTTCCAAACGCT-AAATATTGCCTTATTTTTGAAA-TTTTAAAAGGATATTTAGCTATTTGGT
64 AATTTCCAAACG-TAAAACATTGCCTTA-TTTTGAAATTTTTAAAAGGATATTTAGCTATTTGGT
42335747 -AGAACGAAAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCGAATTTCCAAACGCTAAAT
127 CA-AACG-AAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCGAATTTCCAAACGCTAAAT
42335811 ATTG
190 ATTG
42335815 TCTCATTTAG
Statistics
Matches: 179, Mismatches: 11, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
215 24 0.13
216 58 0.32
217 88 0.49
218 9 0.05
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (214 bp):
AGGATATTTAGCTATTTGGTCAAACGAAAAACCGAAACCCAGCACATTAGGGCACGTTCCTCGAA
TTTCCAAACGTAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATATTTAGCTATTTGGTCAAA
CGAAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCGAATTTCCAAACGCTAAATATTGCC
TTATTTCAAAATTTTTAAA
Found at i:42338226 original size:102 final size:103
Alignment explanation
Indices: 42338097--42338301 Score: 403
Period size: 102 Copynumber: 2.0 Consensus size: 103
42338087 TATAATTCTA
42338097 TAGGGATTTTACTTTTATTTTATTTTACCCCAGTATTTTATTTAAATAAGGATTCGGGTCACTTA
1 TAGGGATTTTACTTTTATTTTATTTTACCCCAGTATTTTATTTAAATAAGGATTCGGGTCACTTA
42338162 ATTCTAACACCAGCCAATTAGATCTTTTCAATGGTTGG
66 ATTCTAACACCAGCCAATTAGATCTTTTCAATGGTTGG
42338200 TAGGGATTTT-CTTTTATTTTATTTTACCCCAGTATTTTATTTAAATAAGGATTCGGGTCACTTA
1 TAGGGATTTTACTTTTATTTTATTTTACCCCAGTATTTTATTTAAATAAGGATTCGGGTCACTTA
42338264 ATTCTAACACCAGCCAATTAGATCTTTTCAATGGTTGG
66 ATTCTAACACCAGCCAATTAGATCTTTTCAATGGTTGG
42338302 CTTAGTTGCT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 92 0.90
103 10 0.10
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (103 bp):
TAGGGATTTTACTTTTATTTTATTTTACCCCAGTATTTTATTTAAATAAGGATTCGGGTCACTTA
ATTCTAACACCAGCCAATTAGATCTTTTCAATGGTTGG
Found at i:42339331 original size:20 final size:20
Alignment explanation
Indices: 42339293--42339337 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42339283 TTTAATAGTT
*
42339293 TATTATTTTAATTATTAAAA
1 TATTATTTTAATTAATAAAA
*
42339313 -ATTATTTTTATTTAATAAAA
1 TATTA-TTTTAATTAATAAAA
42339333 TATTA
1 TATTA
42339338 GTAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTTTAATTAATAAAA
Found at i:42342607 original size:24 final size:24
Alignment explanation
Indices: 42342556--42342607 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42342546 CCTACCCTAG
* ** *
42342556 TAAAGATTAATACTTATAATGAAT
1 TAAAGATTAATACATATAAACAAC
*
42342580 TAAAGATTAGTACATATAAACAAC
1 TAAAGATTAATACATATAAACAAC
42342604 TAAA
1 TAAA
42342608 TATGAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
TAAAGATTAATACATATAAACAAC
Found at i:42344525 original size:3 final size:3
Alignment explanation
Indices: 42344517--42344543 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42344507 AGAGCTCTGC
42344517 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
42344544 ACATACGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:42346291 original size:2 final size:2
Alignment explanation
Indices: 42346284--42346312 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42346274 AATGTAAGTT
42346284 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
42346313 AATATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42365289 original size:20 final size:20
Alignment explanation
Indices: 42365264--42365315 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
42365254 ATGTAATTTT
42365264 GGTATCGATACCACATCCAA
1 GGTATCGATACCACATCCAA
*
42365284 GGTATCGATATCACATCCAA
1 GGTATCGATACCACATCCAA
42365304 GGTATCGATACC
1 GGTATCGATACC
42365316 TTAATCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
GGTATCGATACCACATCCAA
Found at i:42367089 original size:10 final size:10
Alignment explanation
Indices: 42367074--42367156 Score: 112
Period size: 10 Copynumber: 8.3 Consensus size: 10
42367064 CCATGGTCTT
42367074 ATGTTCACTG
1 ATGTTCACTG
42367084 ATGTTCACTG
1 ATGTTCACTG
*
42367094 AAGTTCACTG
1 ATGTTCACTG
*
42367104 ATATTCACTG
1 ATGTTCACTG
*
42367114 ATGATCACTG
1 ATGTTCACTG
* *
42367124 ATGATCATTG
1 ATGTTCACTG
42367134 ATGTTCACTG
1 ATGTTCACTG
*
42367144 ATGATCACTG
1 ATGTTCACTG
42367154 ATG
1 ATG
42367157 ACATAGCCCA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 64 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (10 bp):
ATGTTCACTG
Found at i:42378898 original size:3 final size:3
Alignment explanation
Indices: 42378885--42378932 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
42378875 CCACTCCAGG
* * * *
42378885 TTC TCC TTC TTC TTC CTC TTC TTC TTC TTC CTC CTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
42378933 CGATGATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (3 bp):
TTC
Found at i:42378910 original size:15 final size:15
Alignment explanation
Indices: 42378890--42378929 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
42378880 CCAGGTTCTC
*
42378890 CTTCTTCTTCCTCTT
1 CTTCTTCTTCCTCCT
42378905 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
42378920 CTTCTTCTTC
1 CTTCTTCTTC
42378930 TTCCGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTCTTCTTCCTCCT
Found at i:42378911 original size:18 final size:18
Alignment explanation
Indices: 42378885--42378933 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
42378875 CCACTCCAGG
* *
42378885 TTCTCCTTCTTCTTCCTC
1 TTCTTCTTCTTCCTCCTC
42378903 TTCTTCTTCTTCCTCCTC
1 TTCTTCTTCTTCCTCCTC
42378921 TTCTTCTTCTTCC
1 TTCTTCTTCTTCC
42378934 GATGATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (18 bp):
TTCTTCTTCTTCCTCCTC
Found at i:42390069 original size:17 final size:17
Alignment explanation
Indices: 42390027--42390066 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
42390017 ACGTGATTAG
*
42390027 AATTGAATTGAGAAAAT
1 AATTTAATTGAGAAAAT
*
42390044 TATTTAATTGA-AAAAT
1 AATTTAATTGAGAAAAT
42390060 AATTTAA
1 AATTTAA
42390067 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AATTTAATTGAGAAAAT
Found at i:42392759 original size:13 final size:13
Alignment explanation
Indices: 42392741--42392765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42392731 AAGCTAAATA
42392741 GATATTGTAACGT
1 GATATTGTAACGT
42392754 GATATTGTAACG
1 GATATTGTAACG
42392766 ATCTGCAGTT
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GATATTGTAACGT
Found at i:42398198 original size:45 final size:45
Alignment explanation
Indices: 42398147--42398323 Score: 354
Period size: 45 Copynumber: 3.9 Consensus size: 45
42398137 AAAGAGTTTT
42398147 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
1 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
42398192 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
1 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
42398237 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
1 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
42398282 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGT
1 ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGT
42398324 AAAAAAAAAG
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 132 1.00
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (45 bp):
ATAACAACAAACTTGTTACAACTCAACAACCCCAACTTTAGTTAG
Found at i:42402578 original size:6 final size:6
Alignment explanation
Indices: 42402569--42402593 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42402559 TTAATGTATG
42402569 TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA T
42402594 GTTGTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:42403320 original size:31 final size:32
Alignment explanation
Indices: 42403270--42403329 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
42403260 TCATTCTAGT
42403270 AAAAAAAATTAAATATTTCTTTTATTTTTTAC
1 AAAAAAAATTAAATATTTCTTTTATTTTTTAC
*
42403302 AAAAAAAATTGAAT-TTTCTTTTATTTTT
1 AAAAAAAATTAAATATTTCTTTTATTTTT
42403330 GCTGATGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (32 bp):
AAAAAAAATTAAATATTTCTTTTATTTTTTAC
Found at i:42409624 original size:3 final size:3
Alignment explanation
Indices: 42409616--42409663 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
42409606 ATAATTACCC
42409616 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42409664 ATTACCTACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42412065 original size:3 final size:3
Alignment explanation
Indices: 42412057--42412093 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42412047 AAATAACCCC
42412057 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42412094 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42423328 original size:9 final size:9
Alignment explanation
Indices: 42423314--42423356 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
42423304 ATTGTTGTTG
*
42423314 GTAGTAGAA
1 GTAGTAGGA
42423323 GTAGTAGGA
1 GTAGTAGGA
* *
42423332 GTAGGAGTA
1 GTAGTAGGA
*
42423341 GGAGTAGGA
1 GTAGTAGGA
42423350 GTAGTAG
1 GTAGTAG
42423357 TGGAGAAGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (9 bp):
GTAGTAGGA
Found at i:42423334 original size:6 final size:6
Alignment explanation
Indices: 42423325--42423353 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42423315 TAGTAGAAGT
42423325 AGTAGG AGTAGG AGTAGG AGTAGG AGTAG
1 AGTAGG AGTAGG AGTAGG AGTAGG AGTAG
42423354 TAGTGGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
AGTAGG
Found at i:42423492 original size:3 final size:3
Alignment explanation
Indices: 42423478--42423521 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
42423468 AGGAAACGGA
* *
42423478 GGT GGA GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGC GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
42423522 CGGAGGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.02, G:0.68, T:0.27
Consensus pattern (3 bp):
GGT
Found at i:42435422 original size:2 final size:2
Alignment explanation
Indices: 42435415--42435441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42435405 CCTCCTTCTC
42435415 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 A
42435442 AAGCTTGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42435859 original size:12 final size:12
Alignment explanation
Indices: 42435844--42435870 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42435834 TATTAGGTCC
42435844 TCACCATCATCA
1 TCACCATCATCA
42435856 TCACCATCATCA
1 TCACCATCATCA
42435868 TCA
1 TCA
42435871 TCCTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (12 bp):
TCACCATCATCA
Found at i:42445726 original size:176 final size:177
Alignment explanation
Indices: 42445421--42445774 Score: 701
Period size: 176 Copynumber: 2.0 Consensus size: 177
42445411 TTTTTTAGGG
42445421 TAAACTATACAAATGGTCACCCAACTATACTCGTGTTCCTGTTTTGATCACCCAACTTTAAAATT
1 TAAACTATACAAATGGTCACCCAACTATACTCGTGTTCCTGTTTTGATCACCCAACTTTAAAATT
42445486 TTTCAATTTAGGCACTAACAATTGAATTCATTCCTATTTTGATCAAGCCTTTTTTAATTGGTATA
66 TTTCAATTTAGGCACTAACAATTGAATTCATTCCTATTTTGATCAAGCCTTTTTTAATTGGTATA
42445551 ATAACACATTTAGTCCTTAATATTACATATTCTATCAATTTAATCCT
131 ATAACACATTTAGTCCTTAATATTACATATTCTATCAATTTAATCCT
42445598 TAAACTATAC-AATGGTCACCCAACTATACTCGTGTTCCTGTTTTGATCACCCAACTTTAAAATT
1 TAAACTATACAAATGGTCACCCAACTATACTCGTGTTCCTGTTTTGATCACCCAACTTTAAAATT
42445662 TTTCAATTTAGGCACTAACAATTGAATTCATTCCTATTTTGATCAAGCCTTTTTTAATTGGTATA
66 TTTCAATTTAGGCACTAACAATTGAATTCATTCCTATTTTGATCAAGCCTTTTTTAATTGGTATA
42445727 ATAACACATTTAGTCCTTAATATTACATATTCTATCAATTTAATCCT
131 ATAACACATTTAGTCCTTAATATTACATATTCTATCAATTTAATCCT
42445774 T
1 T
42445775 CACATTTACA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 167 0.94
177 10 0.06
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (177 bp):
TAAACTATACAAATGGTCACCCAACTATACTCGTGTTCCTGTTTTGATCACCCAACTTTAAAATT
TTTCAATTTAGGCACTAACAATTGAATTCATTCCTATTTTGATCAAGCCTTTTTTAATTGGTATA
ATAACACATTTAGTCCTTAATATTACATATTCTATCAATTTAATCCT
Found at i:42445768 original size:30 final size:31
Alignment explanation
Indices: 42445734--42445804 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
42445724 ATAATAACAC
*
42445734 ATTTAGTCCTT-A-ATATTACATATTCTATCA
1 ATTTAGTCCTTCACAT-TTACAAATTCTATCA
*
42445764 ATTTAATCCTTCACATTTACAAATTCTATCA
1 ATTTAGTCCTTCACATTTACAAATTCTATCA
*
42445795 ATTTGGTCCT
1 ATTTAGTCCT
42445805 CAAACTTACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 23 0.66
32 2 0.06
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (31 bp):
ATTTAGTCCTTCACATTTACAAATTCTATCA
Found at i:42447141 original size:21 final size:22
Alignment explanation
Indices: 42447095--42447155 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
42447085 CTCTCGGATT
* * **
42447095 TAGGGGTTAGTGTTTATGATCT
1 TAGGGTTTAGTGTTTAGGATAG
42447117 TA-GGTTTAGTGTTTAGGATAG
1 TAGGGTTTAGTGTTTAGGATAG
* *
42447138 TAGGGTTAAGAGTTTAGG
1 TAGGGTTTAGTGTTTAGG
42447156 GTTTTAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.41
Consensus pattern (22 bp):
TAGGGTTTAGTGTTTAGGATAG
Found at i:42447225 original size:30 final size:27
Alignment explanation
Indices: 42447163--42447221 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
42447153 AGGGTTTTAA
*
42447163 TATT-TATTTACAATTAATTATTATTT
1 TATTATATTTACAATAAATTATTATTT
42447189 TATTATATTTA-AATAAAGTTATTAATATT
1 TATTATATTTACAATAAA-TTATT-AT-TT
42447218 TATT
1 TATT
42447222 TATAAGTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.32
27 11 0.39
28 2 0.07
29 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATTATATTTACAATAAATTATTATTT
Found at i:42447862 original size:8 final size:8
Alignment explanation
Indices: 42447849--42447882 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
42447839 GAAAACTAAC
42447849 ATACATAT
1 ATACATAT
42447857 ATACATAT
1 ATACATAT
*
42447865 ATATATAT
1 ATACATAT
*
42447873 ATATATAT
1 ATACATAT
42447881 AT
1 AT
42447883 GCTTTAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (8 bp):
ATACATAT
Found at i:42447866 original size:2 final size:2
Alignment explanation
Indices: 42447853--42447882 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42447843 ACTAACATAC
*
42447853 AT AT AT AC 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
42447883 GCTTTAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42449782 original size:218 final size:219
Alignment explanation
Indices: 42449392--42449830 Score: 871
Period size: 218 Copynumber: 2.0 Consensus size: 219
42449382 TTTATTTATT
42449392 ATGAATTATATAAAAATAATTTTTTTACTATTTTTTCATTAAATTGGCAACTATTTATAAATAGA
1 ATGAATTATATAAAAATAATTTTTTTACTATTTTTTCATTAAATTGGCAACTATTTATAAATAGA
42449457 AAGGTTCATGGATCGAGTTGGATAGCGATCAAATTACTAAAAAATATTTATATTCAAATTAAAAT
66 AAGGTTCATGGATCGAGTTGGATAGCGATCAAATTACTAAAAAATATTTATATTCAAATTAAAAT
42449522 TAGATTAAACTTGTCAATCATCTACTATTTAAAAATAATAAAATATTTTAAAATTTAAAAGTTGG
131 TAGATTAAACTTGTCAATCATCTACTATTTAAAAATAATAAAATATTTTAAAATTTAAAAGTTGG
42449587 TAATTGAATTATTTGAAAGTTTTC
196 TAATTGAATTATTTGAAAGTTTTC
42449611 ATGAATTATAT-AAAATAATTTTTTTACTATTTTTTCATTAAATTGGCAACTATTTATAAATAGA
1 ATGAATTATATAAAAATAATTTTTTTACTATTTTTTCATTAAATTGGCAACTATTTATAAATAGA
42449675 AAGGTTCATGGATCGAGTTGGATAGCGATCAAATTACTAAAAAATATTTATATTCAAATTAAAAT
66 AAGGTTCATGGATCGAGTTGGATAGCGATCAAATTACTAAAAAATATTTATATTCAAATTAAAAT
42449740 TAGATTAAACTTGTCAATCATCTACTATTTAAAAATAATAAAATATTTTAAAATTTAAAAGTTGG
131 TAGATTAAACTTGTCAATCATCTACTATTTAAAAATAATAAAATATTTTAAAATTTAAAAGTTGG
42449805 TAATTGAATTATTTGAAAGTTTTC
196 TAATTGAATTATTTGAAAGTTTTC
42449829 AT
1 AT
42449831 TTAAGTTACT
Statistics
Matches: 220, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 209 0.95
219 11 0.05
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (219 bp):
ATGAATTATATAAAAATAATTTTTTTACTATTTTTTCATTAAATTGGCAACTATTTATAAATAGA
AAGGTTCATGGATCGAGTTGGATAGCGATCAAATTACTAAAAAATATTTATATTCAAATTAAAAT
TAGATTAAACTTGTCAATCATCTACTATTTAAAAATAATAAAATATTTTAAAATTTAAAAGTTGG
TAATTGAATTATTTGAAAGTTTTC
Found at i:42468431 original size:26 final size:27
Alignment explanation
Indices: 42468402--42468452 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
42468392 ATTCATTGAT
*
42468402 TTTTTTATACTTC-CTTTTTTAATTTC
1 TTTTTTATACTTCAATTTTTTAATTTC
42468428 TTTTTTATACTTCAATTTTTTAATT
1 TTTTTTATACTTCAATTTTTTAATT
42468453 CATTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTTATACTTCAATTTTTTAATTTC
Found at i:42468447 original size:14 final size:13
Alignment explanation
Indices: 42468402--42468440 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
42468392 ATTCATTGAT
42468402 TTTTTTATACTTCC
1 TTTTTTATACTT-C
*
42468416 TTTTTTA-ATTTC
1 TTTTTTATACTTC
42468428 TTTTTTATACTTC
1 TTTTTTATACTTC
42468441 AATTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 8 0.36
13 7 0.32
14 7 0.32
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTATACTTC
Found at i:42468454 original size:13 final size:13
Alignment explanation
Indices: 42468402--42468456 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
42468392 ATTCATTGAT
*
42468402 TTTTTTATACTTCC
1 TTTTTTA-ACTTCA
*
42468416 TTTTTTAATTTC-
1 TTTTTTAACTTCA
42468428 TTTTTTATACTTCAA
1 TTTTTTA-ACTTC-A
42468443 TTTTTTAA-TTCA
1 TTTTTTAACTTCA
42468455 TT
1 TT
42468457 GAAAAAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 10 0.28
13 11 0.31
14 8 0.22
15 7 0.19
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTAACTTCA
Found at i:42474004 original size:5 final size:5
Alignment explanation
Indices: 42473996--42474035 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
42473986 TTTATTACAT
42473996 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
42474036 TGTACGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:42474272 original size:31 final size:30
Alignment explanation
Indices: 42474204--42474277 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
42474194 ATATAATATC
* *
42474204 GTAATTAAATTAAATTAATTATTACGTAAT
1 GTAATTAAATTAAATTAAATATTACATAAT
* * *
42474234 GTGATTAAATTAAATTAAAATGTTATATAAT
1 GTAATTAAATTAAATT-AAATATTACATAAT
42474265 GTAATTAAATTAA
1 GTAATTAAATTAA
42474278 GTTGATAGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (30 bp):
GTAATTAAATTAAATTAAATATTACATAAT
Found at i:42475888 original size:88 final size:89
Alignment explanation
Indices: 42475738--42475914 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 89
42475728 TGAATTTGGA
*
42475738 ATTTACAGGCTGAACAAAAAAAAAAAAAACACTTACGTTTAACCAAAATATGGACAAGCCAAGCT
1 ATTTACAGGCTGAAAAAAAAAAAAAAAAACACTTACGTTTAACCAAAATATGGACAAGCCAAGCT
42475803 TTATATATGTTGGAGCTATGATGT
66 TTATATATGTTGGAGCTATGATGT
*
42475827 ATTTACGGGC-GAAAAAAAAAAAAAAAAACACTTACGTTTAACCAAAATATGGACAAGCCAAGCT
1 ATTTACAGGCTGAAAAAAAAAAAAAAAAACACTTACGTTTAACCAAAATATGGACAAGCCAAGCT
42475891 TTATATATGTTGGAGCTATGATGT
66 TTATATATGTTGGAGCTATGATGT
42475915 TGGGCAACTT
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 77 0.90
89 9 0.10
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (89 bp):
ATTTACAGGCTGAAAAAAAAAAAAAAAAACACTTACGTTTAACCAAAATATGGACAAGCCAAGCT
TTATATATGTTGGAGCTATGATGT
Found at i:42479737 original size:2 final size:2
Alignment explanation
Indices: 42479724--42479758 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
42479714 TTCACGTGAG
*
42479724 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
42479759 GATTTCTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Done.