Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 126 of 216
Found at i:39872698 original size:23 final size:22
Alignment explanation
Indices: 39872646--39872698 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
39872636 TCCTTGTCTT
*
39872646 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
39872668 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
39872691 TTTCTTTT
1 TTTCTTTT
39872699 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39872712 original size:18 final size:18
Alignment explanation
Indices: 39872691--39872730 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39872681 CTTTCTTCAA
* * *
39872691 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
39872709 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
39872727 TTTC
1 TTTC
39872731 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:39877372 original size:26 final size:27
Alignment explanation
Indices: 39877311--39877386 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
39877301 TGTGTAAATT
*
39877311 AAGATAATTAGAAGTTTAAATTATATT
1 AAGATAATTAGAAGTTTAAATTATATG
* * *
39877338 ATGAAAATTA-AAGTTTTAATT-TAGTG
1 AAGATAATTAGAAGTTTAAATTATA-TG
* *
39877364 AAGATAATTAGAAATATAAATTA
1 AAGATAATTAGAAGTTTAAATTA
39877387 ATAGGTTAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
25 2 0.05
26 19 0.51
27 16 0.43
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (27 bp):
AAGATAATTAGAAGTTTAAATTATATG
Found at i:39877784 original size:13 final size:13
Alignment explanation
Indices: 39877768--39877801 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39877758 ACCTCTGAAG
39877768 GGTTCCTCAAAGA
1 GGTTCCTCAAAGA
*
39877781 GGTTCCTCAGAGA
1 GGTTCCTCAAAGA
39877794 GGTATCCT
1 GGT-TCCT
39877802 TACATGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (13 bp):
GGTTCCTCAAAGA
Found at i:39878430 original size:23 final size:23
Alignment explanation
Indices: 39878404--39878470 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
39878394 TTGCTAGCTT
*
39878404 TATTGTGAAAATATTGTA-AATAG
1 TATTGTAAAAATATTG-AGAATAG
*
39878427 TATTGTAAAAATAATGAGAATAG
1 TATTGTAAAAATATTGAGAATAG
* * *
39878450 TGTTGCAAAAATATTGCGAAT
1 TATTGTAAAAATATTGAGAAT
39878471 TGTACCGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (23 bp):
TATTGTAAAAATATTGAGAATAG
Found at i:39878733 original size:54 final size:54
Alignment explanation
Indices: 39878564--39879022 Score: 377
Period size: 54 Copynumber: 8.4 Consensus size: 54
39878554 ATTGAAAACT
* * *
39878564 GCAAGATTCTAG-AAATCTTGTAAGTATAAGGCTGGGATCTTAAAT-GGCGAGCC
1 GCAAGATTC-AGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * ** *
39878617 ACAAGATTCATAAAATCTTGCAAGTATAAGGCAGGTTGCGATCTTAAATTGGTGAGCA
1 GCAAGATTCAGAAAATCTTGTAAGTAT-A---AGGTTGCGATCTTAAATCGGCAAGCC
* ** * * *
39878675 ACAAGATTTGGAAAATCTTGTAAGTATAAGGTTGAGATCTTAAATCGGTAACCC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * * * * *
39878729 ACAAGATTCAAAAAATCTTATAAGTATAATGTTTCGATCTTAAATCAGCGAGCT
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
** **
39878783 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAATC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* *** * *
39878837 GCAAGATTCAGAAAATCCTGTAAGTATAAGGCAACGATCTTAAATCGGCCAGTC
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * * *
39878891 GCAAGATTTAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCAAACT
1 GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* * * * * ** *
39878945 GTAAGA-TCGGGAAAATCCTGTAAGTATAAGGTTGAGATATTAAATTAGCCAGCC
1 GCAAGATTC-AGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
* *
39878999 GTAAGACT-AGAAAAATCTTGTAAG
1 GCAAGATTCAG-AAAATCTTGTAAG
39879023 CAGCGAATTG
Statistics
Matches: 323, Mismatches: 74, Indels: 17
0.78 0.18 0.04
Matches are distributed among these distances:
52 1 0.00
53 24 0.07
54 252 0.78
55 1 0.00
57 16 0.05
58 29 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (54 bp):
GCAAGATTCAGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCAAGCC
Found at i:39878861 original size:162 final size:162
Alignment explanation
Indices: 39878565--39878989 Score: 435
Period size: 162 Copynumber: 2.6 Consensus size: 162
39878555 TTGAAAACTG
* * * * * * ** *
39878565 CAAGATTCTAGAAATCTTGTAAGTATAAGGCTGGGATCTTAAAT-GGCGAGCCACAAGATTCATA
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCGAGCTGCAAGATTCAGA
* * *** ** *
39878629 AAATCTTGCAAGTATAAGGCAGGTTGCGATCTTAAATTGGTGAGCAACAAGATTTGGAAAATCTT
66 AAATCTTGTAAGTAT-A---AGGTTGCGATCTTAAATCGAAAAGCAACAAGATTCAGAAAATCCT
** *
39878694 GTAAGTATAAGGTTGA-GATCTTAAATCGGTAACCCA
127 GTAAGTATAAGG-CAACGATCTTAAATCGGCAACCCA
* *
39878730 CAAGATTCAAAAAATCTTATAAGTATAATGTTTCGATCTTAAATCAGCGAGCTGCAAGATTCAGA
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCGAGCTGCAAGATTCAGA
* *
39878795 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAATC-GCAAGATTCAGAAAATCCTGTA
66 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCG-AAAAGCAACAAGATTCAGAAAATCCTGTA
* ** *
39878859 AGTATAAGGCAACGATCTTAAATCGGCCAGTCG
130 AGTATAAGGCAACGATCTTAAATCGGCAACCCA
* * * * *
39878892 CAAGATTTAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCAAACTGTAAGA-TCGGG
1 CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCGAGCTGCAAGATTC-AG
* * *
39878956 AAAATCCTGTAAGTATAAGGTTGAGATATTAAAT
65 AAAATCTTGTAAGTATAAGGTTGCGATCTTAAAT
39878990 TAGCCAGCCG
Statistics
Matches: 218, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
161 3 0.01
162 145 0.67
163 2 0.01
165 38 0.17
166 30 0.14
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (162 bp):
CAAGATTCAAAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCAGCGAGCTGCAAGATTCAGA
AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGAAAAGCAACAAGATTCAGAAAATCCTGTAA
GTATAAGGCAACGATCTTAAATCGGCAACCCA
Found at i:39884031 original size:16 final size:17
Alignment explanation
Indices: 39884003--39884034 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39883993 TAAAAATATG
39884003 TATATATGTATATAAAT
1 TATATATGTATATAAAT
39884020 TATATA-GTATATAAA
1 TATATATGTATATAAA
39884035 AATGTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATATGTATATAAAT
Found at i:39884936 original size:16 final size:16
Alignment explanation
Indices: 39884915--39884956 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
39884905 TGAAACAAAC
39884915 AAAAATAAAAGA-AAAG
1 AAAAATAAAA-ATAAAG
39884931 AAAAATAAAAATAAAG
1 AAAAATAAAAATAAAG
39884947 -AAAATAAAAA
1 AAAAATAAAAA
39884957 ACGCAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAAATAAAAATAAAG
Found at i:39884940 original size:21 final size:21
Alignment explanation
Indices: 39884915--39884956 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39884905 TGAAACAAAC
39884915 AAAAATAAAAGAAAAGAAAAAT
1 AAAAAT-AAAGAAAAGAAAAAT
*
39884937 AAAAATAAAGAAAATAAAAA
1 AAAAATAAAGAAAAGAAAAA
39884957 ACGCAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAATAAAGAAAAGAAAAAT
Found at i:39884957 original size:22 final size:22
Alignment explanation
Indices: 39884915--39884957 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39884905 TGAAACAAAC
*
39884915 AAAAATAAAAGAAAAGAAAAAT
1 AAAAATAAAAGAAAAAAAAAAT
39884937 AAAAAT-AAAGAAAATAAAAAA
1 AAAAATAAAAGAAAA-AAAAAA
39884958 CGCAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAAATAAAAGAAAAAAAAAAT
Found at i:39894074 original size:29 final size:29
Alignment explanation
Indices: 39894042--39894119 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
39894032 AAAATATTAG
* *
39894042 TTAAACTAATTAAATTACTTAAACTAAAA
1 TTAACCTAATTAAATTAATTAAACTAAAA
* *
39894071 TTAACCTAATTGAATTAATTAATCTAAAA
1 TTAACCTAATTAAATTAATTAAACTAAAA
*
39894100 -TAACCTAATGAAATTAATTA
1 TTAACCTAATTAAATTAATTA
39894120 GTCTAAGGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 18 0.42
29 25 0.58
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAACCTAATTAAATTAATTAAACTAAAA
Found at i:39894131 original size:28 final size:27
Alignment explanation
Indices: 39894054--39894125 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
39894044 AAACTAATTA
* *
39894054 AATTACTTAAACTAAAATTAACCTAATTG
1 AATTAATTAATCTAAAA-TAACCTAA-TG
39894083 AATTAATTAATCTAAAATAACCTAATG
1 AATTAATTAATCTAAAATAACCTAATG
*
39894110 AAATTAATTAGTCTAA
1 -AATTAATTAATCTAA
39894126 GGTAACTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 22 0.56
29 15 0.38
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (27 bp):
AATTAATTAATCTAAAATAACCTAATG
Found at i:39894758 original size:37 final size:37
Alignment explanation
Indices: 39894708--39894781 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
39894698 AAATTACAAA
39894708 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
1 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
39894745 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
1 GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
39894782 AACAACCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (37 bp):
GAAAAATAAAATAAAACTATTTAATTGTCTAGCTATC
Found at i:39899719 original size:29 final size:29
Alignment explanation
Indices: 39899669--39899746 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
39899659 AAAATATTAG
* * *
39899669 TTAAACTAATTAATTTACTTAACCTAAAA
1 TTAACCTAATTAAATTAATTAACCTAAAA
* *
39899698 TTAACCTAATTAAATCAATTAATCTAAAA
1 TTAACCTAATTAAATTAATTAACCTAAAA
*
39899727 -TAACCTAATGAAATTAATTA
1 TTAACCTAATTAAATTAATTA
39899747 GTCTAAGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (29 bp):
TTAACCTAATTAAATTAATTAACCTAAAA
Found at i:39899740 original size:28 final size:28
Alignment explanation
Indices: 39899687--39899763 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
39899677 ATTAATTTAC
* *
39899687 TTAACCTAAAATTAACCTAATTAAATCAA
1 TTAATCTAAAA-TAACCTAATGAAATCAA
*
39899716 TTAATCTAAAATAACCTAATGAAATTAA
1 TTAATCTAAAATAACCTAATGAAATCAA
* *
39899744 TTAGTCTAAGATAA-CTAATG
1 TTAATCTAAAATAACCTAATG
39899764 GAATTTCCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 6 0.14
28 27 0.63
29 10 0.23
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (28 bp):
TTAATCTAAAATAACCTAATGAAATCAA
Found at i:39901492 original size:33 final size:33
Alignment explanation
Indices: 39901455--39901550 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
39901445 TGAGTTAATG
39901455 CATGACTTAATTTAATAATGCAAACTTAACTAA
1 CATGACTTAATTTAATAATGCAAACTTAACTAA
* *
39901488 CATGA---AAGTTACATAAT------TAAACTAA
1 CATGACTTAATTTA-ATAATGCAAACTTAACTAA
* *
39901513 CATGACTTAGTTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATAATGCAAACTTAACTAA
39901546 CATGA
1 CATGA
39901551 AAGTTACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
25 12 0.26
27 4 0.09
28 4 0.09
30 5 0.11
31 5 0.11
33 17 0.36
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (33 bp):
CATGACTTAATTTAATAATGCAAACTTAACTAA
Found at i:39915196 original size:7 final size:7
Alignment explanation
Indices: 39915107--39915203 Score: 86
Period size: 7 Copynumber: 13.9 Consensus size: 7
39915097 AAATTTCAGA
*
39915107 ATTGAGA
1 ATTGAGG
39915114 ATTGAGG
1 ATTGAGG
39915121 ATTGAGG
1 ATTGAGG
*
39915128 ATTGAGA
1 ATTGAGG
*
39915135 ATTGAGA
1 ATTGAGG
*
39915142 ATTGAGA
1 ATTGAGG
*
39915149 ATTGATG
1 ATTGAGG
* **
39915156 ATTAAAA
1 ATTGAGG
*
39915163 ATTGAAG
1 ATTGAGG
*
39915170 ATTGAAG
1 ATTGAGG
*
39915177 ATTTAGG
1 ATTGAGG
39915184 ATTGAGG
1 ATTGAGG
*
39915191 ATTGAGT
1 ATTGAGG
39915198 ATTGAG
1 ATTGAG
39915204 TTGAAAAGAA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 77 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (7 bp):
ATTGAGG
Found at i:39923844 original size:14 final size:14
Alignment explanation
Indices: 39923825--39923856 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39923815 TCCAATCACC
39923825 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39923839 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39923853 GGGC
1 GGGC
39923857 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:39928966 original size:14 final size:14
Alignment explanation
Indices: 39928947--39928978 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39928937 TCCAATCACC
*
39928947 GGGCCAGTTTGGTT
1 GGGCCAATTTGGTT
39928961 GGGCCAATTTGGTT
1 GGGCCAATTTGGTT
39928975 GGGC
1 GGGC
39928979 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.44, T:0.31
Consensus pattern (14 bp):
GGGCCAATTTGGTT
Found at i:39935090 original size:95 final size:94
Alignment explanation
Indices: 39934926--39935206 Score: 375
Period size: 95 Copynumber: 3.0 Consensus size: 94
39934916 GTACTGGTGG
* * * * * *
39934926 TGGATACCTCACCGATGGCTAAGATCCTGCATATATTACGGATTCTTCACAGCTCGTGTGGGTAA
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTA-AGATTCTTCACAGCTCGTGTGAGCAA
*
39934991 CATCGTGTAATAGTTAATGTCTCGATTTAC
65 CATCGTGTAATGGTTAATGTCTCGATTTAC
*
39935021 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAGAATTCTTCACAGCTCGTGTGAGCAG
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAG-ATTCTTCACAGCTCGTGTGAGCAA
* *
39935086 CATCGTGTAATGGTTAATGTCCCGATTTTC
65 CATCGTGTAATGGTTAATGTCTCGATTTAC
* * * * * *
39935116 TGGATACCTTACTGATGGTTAAGATTCTGCATGTGTTGCAGATTCTTCATAGCTCGTGTGAGGAA
1 TGGATACCTTACTGATGGTTAAGATCCTGCATATATT-AAGATTCTTCACAGCTCGTGTGAGCAA
*
39935181 CATTGTGTAATGGTTAATGTCT-GATT
65 CATCGTGTAATGGTTAATGTCTCGATT
39935207 CACAGCTCAT
Statistics
Matches: 165, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
94 5 0.03
95 158 0.96
96 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (94 bp):
TGGATACCTTACTGATGGTTAAGATCCTGCATATATTAAGATTCTTCACAGCTCGTGTGAGCAAC
ATCGTGTAATGGTTAATGTCTCGATTTAC
Found at i:39938198 original size:27 final size:26
Alignment explanation
Indices: 39938128--39938198 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
39938118 CACGTTGGGG
*
39938128 AAGAAAGCCTTTGTGG-TGTAATATGA
1 AAGAAAGCCTTTGTGGCAG-AATATGA
39938154 AAGAAAGCCTTTGTGGCAGAATATGA
1 AAGAAAGCCTTTGTGGCAGAATATGA
* *
39938180 AAGGTAAGTCTTTGTGGCA
1 AA-GAAAGCCTTTGTGGCA
39938199 AACTCTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.62
27 15 0.38
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (26 bp):
AAGAAAGCCTTTGTGGCAGAATATGA
Found at i:39942339 original size:96 final size:95
Alignment explanation
Indices: 39942167--39942346 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 95
39942157 TATTGTCCCA
* * *
39942167 ACCAACATTTTGTATTAAATGAAGAAGGTTTTTAATGTCATTATTTTAGTAATTGAACTTCCAAG
1 ACCAACATTTTGTATTAAAT--AGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAG
*
39942232 TACATCGATCATGTTTATTTTTGGAAGTATGGCG
64 TACATCAATCAT-TTT-TTTTTGGAAGTATGGCG
* * * *
39942266 ACCAACATTTTGTATTAAAT-GAAGGTTTTTAATGTTATTAATTCAGCGATTGAACTTCCAATTC
1 ACCAACATTTTGTATTAAATAGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAGTA
39942330 CATCAATCATTTTTTTT
66 CATCAATCATTTTTTTT
39942347 AGTATGACGT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
94 4 0.05
95 3 0.04
96 46 0.63
99 20 0.27
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (95 bp):
ACCAACATTTTGTATTAAATAGAAGGTTTTTAATGTCATTAATTCAGCAATTGAACTTCCAAGTA
CATCAATCATTTTTTTTTGGAAGTATGGCG
Found at i:39953509 original size:15 final size:15
Alignment explanation
Indices: 39953489--39953521 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39953479 GTCTTATAAC
*
39953489 AAGTTAAATAACAAT
1 AAGTTAAATAAAAAT
39953504 AAGTTAAATAAAAAT
1 AAGTTAAATAAAAAT
39953519 AAG
1 AAG
39953522 CACATACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (15 bp):
AAGTTAAATAAAAAT
Found at i:39959360 original size:49 final size:49
Alignment explanation
Indices: 39959283--39959416 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 49
39959273 CACCATTTGT
* * * *
39959283 GGACAAGCCACCACTAATTTGTAGATAAACTGCCACTAAAAAACTTTAA
1 GGACAAGCCACCACTGATTTGAAAATAAACTACCACTAAAAAACTTTAA
* * * * **
39959332 GGACAAGCCACTATTGATTTGAAAATAAACAACCACTAAAACACTTTGT
1 GGACAAGCCACCACTGATTTGAAAATAAACTACCACTAAAAAACTTTAA
* *
39959381 GGACAAGCCACCACTGATTTGCAAATAGACTACCAC
1 GGACAAGCCACCACTGATTTGAAAATAAACTACCAC
39959417 ATACATCCAC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (49 bp):
GGACAAGCCACCACTGATTTGAAAATAAACTACCACTAAAAAACTTTAA
Found at i:39961252 original size:26 final size:26
Alignment explanation
Indices: 39961222--39961283 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
39961212 TTCCTCCAAC
* *
39961222 AAAATTTTGATAATTTTACCCTAGGT
1 AAAATTTTGACAATTTTACCCTAAGT
* * * *
39961248 AAAATTTTAACGATTTTGCCTTAAGT
1 AAAATTTTGACAATTTTACCCTAAGT
39961274 AAAATTTTGA
1 AAAATTTTGA
39961284 GAAAATAAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCTAAGT
Found at i:39965013 original size:36 final size:36
Alignment explanation
Indices: 39964971--39965042 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
39964961 TACTTTCACA
*
39964971 CAAAACTCTTTGAATTTGTCAAAGGTTTCACATTTG
1 CAAAACTCTTTGAATTTCTCAAAGGTTTCACATTTG
*
39965007 CAAAACTCTTTGAATTTCTCAAAGGTTTCACTTTTG
1 CAAAACTCTTTGAATTTCTCAAAGGTTTCACATTTG
39965043 TAGGGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
CAAAACTCTTTGAATTTCTCAAAGGTTTCACATTTG
Found at i:39965023 original size:18 final size:19
Alignment explanation
Indices: 39964971--39965029 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
39964961 TACTTTCACA
39964971 CAAAACTCTTTGAATTTGT
1 CAAAACTCTTTGAATTTGT
** *
39964990 C-AAA-GGTTTCACATTTG-
1 CAAAACTCTTTGA-ATTTGT
*
39965007 CAAAACTCTTTGAATTTCT
1 CAAAACTCTTTGAATTTGT
39965026 CAAA
1 CAAA
39965030 GGTTTCACTT
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 9 0.31
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
CAAAACTCTTTGAATTTGT
Found at i:39968536 original size:26 final size:25
Alignment explanation
Indices: 39968487--39968598 Score: 118
Period size: 26 Copynumber: 4.3 Consensus size: 25
39968477 AACACGTTAG
* * *
39968487 GAAAGAAAGTCTTTATGGAGTAATAT
1 GAAAGAAAGCCTTTGTGCA-TAATAT
*
39968513 GAAAGAAAGCTTTTGTGTCATAATAT
1 GAAAGAAAGCCTTTGTG-CATAATAT
* *
39968539 GAAAGAAAACCTTTGTGAAGTAATAT
1 GAAAGAAAGCCTTTGTGCA-TAATAT
39968565 GAAAGAAAGCCTTTGTGGCGA-AATAT
1 GAAAGAAAGCCTTTGT-GC-ATAATAT
39968591 GAAAGAAA
1 GAAAGAAA
39968599 TGTCTTAGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
25 1 0.01
26 69 0.95
27 2 0.03
28 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (25 bp):
GAAAGAAAGCCTTTGTGCATAATAT
Found at i:39968565 original size:52 final size:52
Alignment explanation
Indices: 39968487--39968598 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 52
39968477 AACACGTTAG
** * * *
39968487 GAAAGAAAGTCTTTATGGAGTAATATGAAAGAAAGCTTTTGTGTC-ATAATAT
1 GAAAGAAAACCTTTATGAAGTAATATGAAAGAAAGCCTTTGTGGCGA-AATAT
*
39968539 GAAAGAAAACCTTTGTGAAGTAATATGAAAGAAAGCCTTTGTGGCGAAATAT
1 GAAAGAAAACCTTTATGAAGTAATATGAAAGAAAGCCTTTGTGGCGAAATAT
39968591 GAAAGAAA
1 GAAAGAAA
39968599 TGTCTTAGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 52 0.98
53 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (52 bp):
GAAAGAAAACCTTTATGAAGTAATATGAAAGAAAGCCTTTGTGGCGAAATAT
Found at i:39968664 original size:27 final size:27
Alignment explanation
Indices: 39968606--39968664 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
39968596 AAATGTCTTA
* *
39968606 GTGGCAAACTCCGTCAGGAACGCCTTC
1 GTGGCAAACTCCGTAAAGAACGCCTTC
* *
39968633 ATGGCAAACTCCGTAAAGAACGCCTTT
1 GTGGCAAACTCCGTAAAGAACGCCTTC
39968660 GTGGC
1 GTGGC
39968665 GCACTCTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (27 bp):
GTGGCAAACTCCGTAAAGAACGCCTTC
Found at i:39968670 original size:27 final size:27
Alignment explanation
Indices: 39968607--39968658 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
39968597 AATGTCTTAG
* *
39968607 TGGCAAACTCCGTCAGGAACGCCTTCA
1 TGGCAAACTCCGTAAAGAACGCCTTCA
39968634 TGGCAAACTCCGTAAAGAACGCCTT
1 TGGCAAACTCCGTAAAGAACGCCTT
39968659 TGTGGCGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (27 bp):
TGGCAAACTCCGTAAAGAACGCCTTCA
Found at i:39969126 original size:20 final size:21
Alignment explanation
Indices: 39969090--39969128 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
39969080 AAAAATCAGT
39969090 AAATAATATTTCAAAAAATAA
1 AAATAATATTTCAAAAAATAA
39969111 AAAT-ATATTT-AGAAAAAT
1 AAATAATATTTCA-AAAAAT
39969129 TAATTTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATAATATTTCAAAAAATAA
Found at i:39973584 original size:12 final size:12
Alignment explanation
Indices: 39973567--39973591 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39973557 AATTGAAGAA
39973567 ACTAATAAAATG
1 ACTAATAAAATG
39973579 ACTAATAAAATG
1 ACTAATAAAATG
39973591 A
1 A
39973592 GTGTAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
ACTAATAAAATG
Found at i:39978423 original size:19 final size:19
Alignment explanation
Indices: 39978399--39978438 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39978389 TTTTGATCAA
*
39978399 CTATTTTTCGAATATTTCC
1 CTATTTTTCGAATATTACC
39978418 CTATTTTTCGAATATTACC
1 CTATTTTTCGAATATTACC
39978437 CT
1 CT
39978439 TCTCTCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (19 bp):
CTATTTTTCGAATATTACC
Found at i:39979362 original size:27 final size:27
Alignment explanation
Indices: 39979332--39979466 Score: 164
Period size: 27 Copynumber: 5.0 Consensus size: 27
39979322 AATAAATTAT
*
39979332 CGAAATACCCCCATAGGGTAAAATGAC
1 CGAAATACCCCTATAGGGTAAAATGAC
39979359 CGAAATACCCCTATAGGGTAAAATGAC
1 CGAAATACCCCTATAGGGTAAAATGAC
* *
39979386 CGAAATA-CCCTCATAGAGTAAAATGAT
1 CGAAATACCCCT-ATAGGGTAAAATGAC
** * *
39979413 TTAAATACCACTATAAGGTAAAATGAC
1 CGAAATACCCCTATAGGGTAAAATGAC
** *
39979440 TAAAATACCCCTATAAGGTAAAATGAC
1 CGAAATACCCCTATAGGGTAAAATGAC
39979467 TATTATACCC
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
26 4 0.04
27 88 0.93
28 3 0.03
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (27 bp):
CGAAATACCCCTATAGGGTAAAATGAC
Found at i:39987148 original size:26 final size:26
Alignment explanation
Indices: 39987119--39987172 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
39987109 TTGCCACATT
*
39987119 TACTGTTACTGACAGC-TTCACTGCGA
1 TACTATTACTGACAGCTTTC-CTGCGA
**
39987145 TACTATTACTGGTAGCTTTCCTGCGA
1 TACTATTACTGACAGCTTTCCTGCGA
39987171 TA
1 TA
39987173 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (26 bp):
TACTATTACTGACAGCTTTCCTGCGA
Found at i:39987322 original size:28 final size:27
Alignment explanation
Indices: 39987275--39987340 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
39987265 ATTGCACGGT
39987275 ACTGATACTGTATTGAGCTAAGGCCCAC
1 ACTG-TACTGTATTGAGCTAAGGCCCAC
* *
39987303 ATTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTG-TACTGTATTGAGCTAAGGCCCAC
39987331 ACTGTACTGT
1 ACTGTACTGT
39987341 TACTGAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (27 bp):
ACTGTACTGTATTGAGCTAAGGCCCAC
Found at i:39987342 original size:33 final size:31
Alignment explanation
Indices: 39987273--39987362 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 31
39987263 TCATTGCACG
* *
39987273 GTACTGATACTGTATTGAGCTAAGGCCCACA
1 GTACTGTTACTGTATTGGGCTAAGGCCCACA
39987304 -T--TGTTACTGTATTGGGCTAAGGCCCACA
1 GTACTGTTACTGTATTGGGCTAAGGCCCACA
* *
39987332 CTGTACTGTTACTGAATAGGGCTCAA-GCCCA
1 --GTACTGTTACTGTATTGGGCT-AAGGCCCA
39987363 GAATGTCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
28 25 0.51
30 1 0.02
31 1 0.02
33 20 0.41
34 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (31 bp):
GTACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:40011276 original size:11 final size:11
Alignment explanation
Indices: 40011260--40011338 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
40011250 TATTTTTTAA
40011260 TTTTAAAATAC
1 TTTTAAAATAC
40011271 TTTTAAAATAC
1 TTTTAAAATAC
40011282 TTTTTTTAAAAT--
1 ---TTTTAAAATAC
* *
40011294 TTTT---TTAA
1 TTTTAAAATAC
*
40011302 TTTTAAAATAT
1 TTTTAAAATAC
*
40011313 TTTTAAAATAT
1 TTTTAAAATAC
40011324 TTTTAAAATAC
1 TTTTAAAATAC
40011335 TTTT
1 TTTT
40011339 TTAATTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
6 1 0.02
8 4 0.07
9 4 0.07
11 38 0.68
14 9 0.16
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40011300 original size:42 final size:42
Alignment explanation
Indices: 40011250--40011372 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
40011240 TAAATATTTT
*
40011250 TATTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAAA
1 TATTTTTTAATTTTAAAATAATTTTAAAATA-TTTTTTTAAAA
*
40011293 T-TTTTTTAATTTTAAAATATTTTTAAAATA--TTTTTAAAA
1 TATTTTTTAATTTTAAAATAATTTTAAAATATTTTTTTAAAA
***
40011332 TACTTTTTTAATTTT-TTTTAATTTTAAAATAATTTTTTTAA
1 TA-TTTTTTAATTTTAAAATAATTTTAAAAT-ATTTTTTTAA
40011373 TTTTTAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
39 10 0.14
40 11 0.16
41 13 0.19
42 28 0.40
43 8 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (42 bp):
TATTTTTTAATTTTAAAATAATTTTAAAATATTTTTTTAAAA
Found at i:40011348 original size:22 final size:21
Alignment explanation
Indices: 40011282--40011349 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
40011272 TTTAAAATAC
40011282 TTTTTTTAAAAT-TTTTTTAA
1 TTTTTTTAAAATATTTTTTAA
*
40011302 ---TTTTAAAATATTTTTAAAA
1 TTTTTTTAAAATATTTTT-TAA
*
40011321 TATTTTTAAAATACTTTTTTAA
1 TTTTTTTAAAATA-TTTTTTAA
40011343 TTTTTTT
1 TTTTTTT
40011350 TAATTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 9 0.23
18 5 0.13
19 2 0.05
22 18 0.46
23 5 0.13
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTAAAATATTTTTTAA
Found at i:40011364 original size:21 final size:21
Alignment explanation
Indices: 40011344--40011390 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
40011334 CTTTTTTAAT
40011344 TTTTTTTAA-TTTTAAAATAA
1 TTTTTTTAATTTTTAAAATAA
40011364 TTTTTTTAATTTTTAAAATAA
1 TTTTTTTAATTTTTAAAATAA
*
40011385 ATTTTT
1 TTTTTT
40011391 GGTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATTTTTAAAATAA
Found at i:40011369 original size:20 final size:22
Alignment explanation
Indices: 40011344--40011390 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
40011334 CTTTTTTAAT
40011344 TTTTTTTAA-TTTTAAAAT-AA
1 TTTTTTTAATTTTTAAAATAAA
40011364 TTTTTTTAATTTTTAAAATAAA
1 TTTTTTTAATTTTTAAAATAAA
40011386 TTTTT
1 TTTTT
40011391 GGTATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTTTAATTTTTAAAATAAA
Found at i:40011369 original size:53 final size:53
Alignment explanation
Indices: 40011260--40011368 Score: 177
Period size: 53 Copynumber: 2.1 Consensus size: 53
40011250 TATTTTTTAA
40011260 TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATAT
* *
40011313 TTTTAAAATATTTTTAAAATAC-TTTTTT-AATTTTTTTTAATTTTAAAATAAT
1 TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAAT-AT
40011365 TTTT
1 TTTT
40011369 TTAATTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
51 20 0.38
52 12 0.23
53 21 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (53 bp):
TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATAT
Found at i:40011390 original size:51 final size:53
Alignment explanation
Indices: 40011260--40011390 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 53
40011250 TATTTTTTAA
* **
40011260 TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATAAATTTTTTAAAATTTTTTTAATTTTAAAATAT
* *
40011313 TTTTAAAATATTTTTAAAAT-ACTTTTTT-AATTTTTTTTAATTTTAAAATAAT
1 TTTTAAAATATTTTTAAAATAAATTTTTTAAAATTTTTTTAATTTTAAAAT-AT
**
40011365 TTTT-TTA-ATTTTTAAAATAAATTTTT
1 TTTTAAAATATTTTTAAAATAAATTTTT
40011391 GGTATTTATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 11 0.16
51 27 0.39
52 12 0.17
53 19 0.28
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (53 bp):
TTTTAAAATATTTTTAAAATAAATTTTTTAAAATTTTTTTAATTTTAAAATAT
Found at i:40011397 original size:22 final size:21
Alignment explanation
Indices: 40011344--40011405 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
40011334 CTTTTTTAAT
*
40011344 TTTTTTTAA-TTTTAAAATAA
1 TTTTTGTAATTTTTAAAATAA
*
40011364 TTTTTTTAATTTTTAAAATAAA
1 TTTTTGTAATTTTTAAAAT-AA
*
40011386 TTTTTGGTATTTATTTAAAA
1 TTTTT-GTAATT-TTTAAAA
40011406 AACCGGCCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.25
21 9 0.25
22 7 0.19
23 4 0.11
24 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTGTAATTTTTAAAATAA
Found at i:40011403 original size:51 final size:52
Alignment explanation
Indices: 40011260--40011390 Score: 151
Period size: 53 Copynumber: 2.5 Consensus size: 52
40011250 TATTTTTTAA
* ** *
40011260 TTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATA-AATTTTTAATATTTTTTTAATTTTAAAATAT
**
40011313 TTTTAAAATATTTTTAAAATACTTTTTTAAT-TTTTTTTAATTTTAAAATAAT
1 TTTTAAAATATTTTTAAAATAAATTTTTAATATTTTTTTAATTTTAAAAT-AT
**
40011365 TTTT-TTA-ATTTTTAAAATAAATTTTT
1 TTTTAAAATATTTTTAAAATAAATTTTT
40011391 GGTATTTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 17 0.24
51 19 0.27
52 14 0.20
53 20 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (52 bp):
TTTTAAAATATTTTTAAAATAAATTTTTAATATTTTTTTAATTTTAAAATAT
Found at i:40011607 original size:22 final size:22
Alignment explanation
Indices: 40011557--40011607 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
40011547 TGCAATGTAA
40011557 TATATTTATAAATAATGAAAAT
1 TATATTTATAAATAATGAAAAT
* *
40011579 T-TAATTTAATATATAGT-AAAAT
1 TAT-ATTT-ATAAATAATGAAAAT
40011601 TATATTT
1 TATATTT
40011608 CGGTTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATTTATAAATAATGAAAAT
Found at i:40011889 original size:37 final size:37
Alignment explanation
Indices: 40011829--40011908 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
40011819 CAGCAAAATA
* *
40011829 ATTATTTAATTATTATTTAATAATAATAATAATTATT
1 ATTATTTAATAATAATTTAATAATAATAATAATTATT
* *
40011866 ATTATTTAGATAATAATTT-ATAATTATAATTATTATT
1 ATTATTTA-ATAATAATTTAATAATAATAATAATTATT
40011903 ATTATT
1 ATTATT
40011909 ATCGTCCGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 30 0.79
38 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
ATTATTTAATAATAATTTAATAATAATAATAATTATT
Found at i:40015221 original size:23 final size:23
Alignment explanation
Indices: 40015169--40015223 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
40015159 AATTTTAATA
*
40015169 ATATTATTTATTAATTCAATTTT
1 ATATTATTTATTAACTCAATTTT
*
40015192 ATTTTATTTAATT-ACTCAATATTT
1 ATATTATTT-ATTAACTCAAT-TTT
40015216 -TATTATTT
1 ATATTATTT
40015224 CTTTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTATTTATTAACTCAATTTT
Found at i:40019188 original size:19 final size:17
Alignment explanation
Indices: 40019162--40019205 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
40019152 CACGTTTTAG
*
40019162 TTTTAATTAATCTTAACT
1 TTTTAATTAAGCTTAA-T
40019180 TTCTTAATTAAGCTTAAT
1 TT-TTAATTAAGCTTAAT
40019198 TTTTAATT
1 TTTTAATT
40019206 CCGTACATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 13 0.54
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTAATTAAGCTTAAT
Found at i:40021586 original size:30 final size:31
Alignment explanation
Indices: 40021541--40021603 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
40021531 TACAGGTACT
* *
40021541 CACCTAACTATAAAAAAAATCT-CATTTTAAG
1 CACCTAACAATAAAAAAAAT-TACAATTTAAG
40021572 CACCTAA-AATAAAAAAAATTACAATTTAAG
1 CACCTAACAATAAAAAAAATTACAATTTAAG
40021602 CA
1 CA
40021604 TTCACGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.03
30 21 0.72
31 7 0.24
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.25
Consensus pattern (31 bp):
CACCTAACAATAAAAAAAATTACAATTTAAG
Found at i:40021847 original size:18 final size:18
Alignment explanation
Indices: 40021811--40021849 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40021801 AAGAAATATA
*
40021811 AAAAATACATAATATTTT
1 AAAAATACATAATAATTT
40021829 AAAAATA-ATAATAAATTT
1 AAAAATACATAAT-AATTT
40021847 AAA
1 AAA
40021850 TTTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATACATAATAATTT
Found at i:40022592 original size:27 final size:27
Alignment explanation
Indices: 40022539--40022594 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40022529 AAATTTATGA
*
40022539 TTATATATATTTTAAAAATATTTATTT
1 TTATATATATTTTAAAAATATTCATTT
**
40022566 TTATATAT-TTTTAAATTTATTCCATTT
1 TTATATATATTTTAAAAATATT-CATTT
40022593 TT
1 TT
40022595 TCTTCTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATATATATTTTAAAAATATTCATTT
Found at i:40024129 original size:21 final size:21
Alignment explanation
Indices: 40024090--40024129 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40024080 TGAATAAAAT
**
40024090 AACTAAAAAAGGGCTAAATTG
1 AACTAAAAAAGGGAAAAATTG
*
40024111 AACTTAAAAAGGGAAAAAT
1 AACTAAAAAAGGGAAAAAT
40024130 GGGGCAGATT
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:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (21 bp):
AACTAAAAAAGGGAAAAATTG
Found at i:40025840 original size:132 final size:132
Alignment explanation
Indices: 40025690--40026566 Score: 1450
Period size: 132 Copynumber: 6.6 Consensus size: 132
40025680 AGATCTGCTT
* * * * *
40025690 TCTTCGATCGATTCCACTGCTGACCAGGGAGATAGAATTATTGGCTTCAATATACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
40025755 CCTCAGGGAGGTAAAATCTGCCAT-CTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTG
66 CCTCAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
40025819 TAA
130 TAA
* * *
40025822 TCTTCAATCTATTACACTGCTGCCTAGGGAGATAGAATTGCTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
40025887 CCTCAGGGAGGTAAAATCCGTCATCCTTGATCTACTCCACTACTGTTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40025952 AA
131 AA
40025954 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
*
40026019 CCTCAGGGAGGTAAAATCTGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40026084 AA
131 AA
* *
40026086 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTATAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
40026151 CCTCAGGGAGGTAAAACCCGCCATCCTTGATTTGCTCAACTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40026216 AA
131 AA
**
40026218 TCTTCAATCTATTCCACTATTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
40026283 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTTCGCTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40026348 AA
131 AA
*
40026350 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
*
40026415 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40026480 AA
131 AA
* * * *
40026482 TCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGACTTCAATGTACTCTACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
40026547 CCTTAGGGAGGCAAAATCCG
66 CCTCAGGGAGGTAAAATCCG
40026567 TCATTAACCT
Statistics
Matches: 697, Mismatches: 47, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
132 694 1.00
133 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
AA
Found at i:40026513 original size:44 final size:44
Alignment explanation
Indices: 40025690--40026515 Score: 245
Period size: 44 Copynumber: 18.8 Consensus size: 44
40025680 AGATCTGCTT
* * * * *
40025690 TCTTCGATCGATTCCACTGCTGACCAGGGAGAT-AGA-AT-TAT
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* * * * * **
40025731 TGGCTTCAATATACTCCACTG-TAACCTCAGGGAGGTAAAATCTGCCA
1 T--CTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* * * *
40025778 TCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* * *
40025822 TCTTCAATCTATTACACTGCTGCCTAGGGAGAT-AGAAT-TGCT-G
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAG-ATCTG-TAA
* * * * * * * *
40025865 GCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCGTCA
1 TCTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* * * ***
40025910 TCCTT-GATCTACTCCACTACTGTTTAGGGAGATAAGATCTGTAA
1 T-CTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* *
40025954 TCTTCAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TAC
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* * * * * **
40025995 TGGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCTGCCA
1 T--CTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* ** * **
40026042 TCCTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 T-CTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* *
40026086 TCTTCAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TAT
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* * * * * * * * **
40026127 TGGCTTCAATGTACTCCACT-ATAACCTCAGGGAGGTAAAACCCGCCA
1 T--CTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* * ** * * **
40026174 TCCTT-GATTTGCTCAACTACTGCTTAGGGAGATAAGATCTGTAA
1 T-CTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
** * *
40026218 TCTTCAATCTATTCCACTATTGCCCAGGGAGAT-AGA-AT-TAC
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* * * * * * **
40026259 TGGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCGCCA
1 T--CTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* * * * **
40026306 TCCTT-GATCTGCTT-CGCTACTGCTTAGGGAGATAAGATCTGTAA
1 T-CTTCAATCT-ATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
*
40026350 TCTTCAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TACTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTA--A
* * * * * * * **
40026393 GCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCGCCA
1 TCTTCAATCTATTCCACTGCT-GCC-CAGGGAGATAAGATCTGTAA
* * * **
40026438 TCCTT-GATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 T-CTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
* *
40026482 TCTTCAATCTATTCCACTGTTGCCCATGGAGATA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATA
40026516 GAATTACTGA
Statistics
Matches: 543, Mismatches: 185, Indels: 111
0.65 0.22 0.13
Matches are distributed among these distances:
41 12 0.02
42 10 0.02
43 136 0.25
44 278 0.51
45 79 0.15
46 24 0.04
47 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTAA
Found at i:40028766 original size:20 final size:20
Alignment explanation
Indices: 40028741--40028781 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
40028731 AATTTGGCAG
40028741 AAAAAATC-TAAAAGAATGAA
1 AAAAAATCGT-AAAGAATGAA
40028761 AAAAAATCGTAAAGAATGAA
1 AAAAAATCGTAAAGAATGAA
40028781 A
1 A
40028782 GAACATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAAAATCGTAAAGAATGAA
Found at i:40032694 original size:28 final size:26
Alignment explanation
Indices: 40032650--40032708 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
40032640 AAATTGTTAA
* *
40032650 ATATATAAAAAAATATGAAAATATGT
1 ATATACAAAAAAATATGAAAATAGGT
* *
40032676 ATATACAAAAAAATGTATGTATATAGGT
1 ATATACAAAAAAA--TATGAAAATAGGT
40032704 ATATA
1 ATATA
40032709 TATGTACGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.44
28 15 0.56
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (26 bp):
ATATACAAAAAAATATGAAAATAGGT
Found at i:40035110 original size:576 final size:579
Alignment explanation
Indices: 40033865--40035181 Score: 1653
Period size: 576 Copynumber: 2.3 Consensus size: 579
40033855 CTCTACAACT
* * ** * * * *
40033865 TGAGTGGCT-AAGCCGCTTAAGGGAGATTAACAAATGGATGGGGATGTGATTAATGGAGTATTTA
1 TGAGTGGCTAAATCC-CTTAGGGGAGATTAATGAGTGGATGGGAATGTGATTAATAGAGGATTTA
** *
40033929 GGGTTTCCTGAGTGAGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCC
65 GGGTTT-CTGAAAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCC
* * * * * *
40033994 TAAGAAGTTACCATAAGCAATACGACCACAAAAACAACAACTATCCACTCAAGCACTGAGTAATC
129 TAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAGTAATA
** * * * * *
40034059 TTGATGCTAATCACTTCCATAATACGAAAGTCAAAACTTTTTTTTTTAACAAATGAGTGGACAAC
194 TCAATACCAATCACTTCCATAATAAGAAAGTCAAAACTTTTTTGTTT-A-AAATGAGTAGACAAC
* * * **
40034124 CATTTATATAAGAATATGGGTTTGATCCCACCATGACTTTTTACCATGAAATAGGAGAGTTGGTA
257 CATTTATACAAGAACATGGGTTCGATCCCACCATGACTGCTTACCATGAAATAGGAGAGTTGGTA
* *
40034189 CAGTTCCATTATTGGATCAAATTTTGCGCAACCTCGACTGAACTGGCAGTTGACGTAGTAGTTTA
322 CAGTTCCATCATTGGATCAAATTTT-----ACCTCGACTGAACTGGCAGTTGACCTAGTAGTTTA
* ** * * * * *
40034254 CGAATCCTACGCCTTCTTGAAAGATAAGAAGAATTGCTAGCAACGTGGTGAGATGATCTCTCTTG
382 CGAATCCTACGCCTTCCTGAAAGATAAGAAGAATCACTAGCAACGCGGCGAGACGATCTCTATCG
* * **
40034319 TGGTTGTTAGGGGCAAAGAGGTGTCGATTGCACCTCGCGATCCAATCCATTATTATTCCATTCTC
447 TGGTTGTTAGGGGAAAAGAGGTGTCGATTGCACCTCGCGATCAAATCCACAATTATTCCATTCTC
* * *
40034384 TTTTCTCTTCTGAACCGATTGTTTTCTTCACCTGATTTATTCAATCGAGAAAGAGATCGTGAATA
512 TTTTCTCTTCTGAACCGATCGTTTTCTTCACCTAATTTATTCAATCGAGAAAGAGATCATGAATA
40034449 ACA
577 ACA
* * *
40034452 TGAGTGGCTAAATCCCTTAGAGGAGATTAATGAGTGGATGAGAATGTGATTAACAGAGGATTTAG
1 TGAGTGGCTAAATCCCTTAGGGGAGATTAATGAGTGGATGGGAATGTGATTAATAGAGGATTTAG
** *
40034517 GGTTTCCCAAGAGGGATTAGTTAGTATGAATTACGAATGCTTAAACCACTAAGCTTGACAACCCT
66 GGTTTCTGAA-AGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCCT
* * * * ** *
40034582 AGGAATTTATTATAGGTAAGATGACCATGAAAACAACAACGATCCACTCAAGCATTGAGTAATAT
130 AGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAGTAATAT
* * * *
40034647 CAATACCAATCGCTTCCATAATAAGAAAGTC-GAACGGTTTTTTGTTT-AAATGAGTAGACGATC
195 CAATACCAATCACTTCCATAATAAGAAAGTCAAAAC--TTTTTTGTTTAAAATGAGTAGACAACC
*
40034710 ATTTATACAAGAACATGGGTTCGATCCCACCATGACTGCTTACGATGAAATATGG-GAGTTGGTA
258 ATTTATACAAGAACATGGGTTCGATCCCACCATGACTGCTTACCATGAAATA-GGAGAGTTGGTA
* *
40034774 CAGTTCCATCATTGGATCAAA-TTT-CC-CGA-TCGAACTGGCGGTTGACCTAGTAGTTTATGAA
322 CAGTTCCATCATTGGATCAAATTTTACCTCGACT-GAACTGGCAGTTGACCTAGTAGTTTACGAA
* * * * **
40034835 TCCTATGCCTTCCTGAAAGTTAGGGAGAATCACTAGCAGGGCGGCGAGACGATCTCTATCGTGGT
386 TCCTACGCCTTCCTGAAAGATAAGAAGAATCACTAGCAACGCGGCGAGACGATCTCTATCGTGGT
* *
40034900 TGTTAGGGGAAAAGAGGTGTTGATTGCACTTCGCGATCAAATCCACAATTA-TCCATTCTCTTTT
451 TGTTAGGGGAAAAGAGGTGTCGATTGCACCTCGCGATCAAATCCACAATTATTCCATTCTCTTTT
* ** * *
40034964 CTCTTTTGAATTGATCGTTTTCTTCACCTAATTTATTCAATCGAGAAAGAGATTATGAATAATA
516 CTCTTCTGAACCGATCGTTTTCTTCACCTAATTTATTCAATCGAGAAAGAGATCATGAATAACA
* * *
40035028 TGAGTGGCTAAATCTCTTAGGGGAGATTAATGAGTGGATGGGAATATGATTAATAGAGGATTTAA
1 TGAGTGGCTAAATCCCTTAGGGGAGATTAATGAGTGGATGGGAATGTGATTAATAGAGGATTTAG
* * * * *
40035093 GGTTTCTTGAAAGGGATTTGTTAGTATGCATTATGTATGCTTAAACTACTAGGCTTGACAACCCT
66 GGTTTC-TGAAAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCCT
40035158 AGGAAGTTATCATAGGCAAGACGA
130 AGGAAGTTATCATAGGCAAGACGA
40035182 GGTTGGGAGA
Statistics
Matches: 626, Mismatches: 97, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
576 203 0.32
577 128 0.20
578 2 0.00
584 3 0.00
585 88 0.14
586 7 0.01
587 182 0.29
588 13 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (579 bp):
TGAGTGGCTAAATCCCTTAGGGGAGATTAATGAGTGGATGGGAATGTGATTAATAGAGGATTTAG
GGTTTCTGAAAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCCTA
GGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAGTAATATC
AATACCAATCACTTCCATAATAAGAAAGTCAAAACTTTTTTGTTTAAAATGAGTAGACAACCATT
TATACAAGAACATGGGTTCGATCCCACCATGACTGCTTACCATGAAATAGGAGAGTTGGTACAGT
TCCATCATTGGATCAAATTTTACCTCGACTGAACTGGCAGTTGACCTAGTAGTTTACGAATCCTA
CGCCTTCCTGAAAGATAAGAAGAATCACTAGCAACGCGGCGAGACGATCTCTATCGTGGTTGTTA
GGGGAAAAGAGGTGTCGATTGCACCTCGCGATCAAATCCACAATTATTCCATTCTCTTTTCTCTT
CTGAACCGATCGTTTTCTTCACCTAATTTATTCAATCGAGAAAGAGATCATGAATAACA
Found at i:40037804 original size:13 final size:16
Alignment explanation
Indices: 40037786--40037821 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 16
40037776 AAAAGGTTAC
40037786 AGAAAGAA-AA-AAG-
1 AGAAAGAAGAAGAAGA
40037799 AGAAAGAAGAAGAAGA
1 AGAAAGAAGAAGAAGA
40037815 AGAAAGA
1 AGAAAGA
40037822 GTAACATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.40
14 2 0.10
15 3 0.15
16 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAAGAAGAAGAAGA
Found at i:40043076 original size:25 final size:25
Alignment explanation
Indices: 40043024--40043077 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40043014 CTCAGTACAG
* *
40043024 TTTCAAAAAGTACTAACTACAGTGT
1 TTTCAAAAAGTACTAACTACAATAT
* * *
40043049 TTTCAGAAAGTTCTAACTATAATAT
1 TTTCAAAAAGTACTAACTACAATAT
40043074 TTTC
1 TTTC
40043078 TAAATTCAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (25 bp):
TTTCAAAAAGTACTAACTACAATAT
Found at i:40044926 original size:15 final size:16
Alignment explanation
Indices: 40044906--40044942 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
40044896 AAAAGGTTGC
40044906 AGAAAGAAAAAAAAG-
1 AGAAAGAAAAAAAAGA
*
40044921 AGAAAGAAAAAGAAGA
1 AGAAAGAAAAAAAAGA
40044937 AGAAAG
1 AGAAAG
40044943 CGTAACGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAAAGA
Found at i:40046769 original size:35 final size:36
Alignment explanation
Indices: 40046730--40046798 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
40046720 ATTATAATCA
*
40046730 TTGTCACATGGTATGAA-AACATACCCACATATTTG
1 TTGTCACATGGCATGAATAACATACCCACATATTTG
*
40046765 TTGTCACATGGCATGAATAACATGCCCACATATT
1 TTGTCACATGGCATGAATAACATACCCACATATT
40046799 CTCTTTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (36 bp):
TTGTCACATGGCATGAATAACATACCCACATATTTG
Found at i:40046808 original size:36 final size:35
Alignment explanation
Indices: 40046730--40046808 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 35
40046720 ATTATAATCA
* *
40046730 TTGTCACATGGTATGAAAACATACCCACATATTTG
1 TTGTCACATGGCATGAAAACATACCCACATATTTC
*
40046765 TTGTCACATGGCATGAATAACATGCCCACATATTCTC
1 TTGTCACATGGCATGAA-AACATACCCACATATT-TC
40046802 TT-TCACA
1 TTGTCACA
40046809 ACAGTCATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 16 0.41
36 20 0.51
37 3 0.08
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (35 bp):
TTGTCACATGGCATGAAAACATACCCACATATTTC
Found at i:40051110 original size:13 final size:11
Alignment explanation
Indices: 40051078--40051105 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40051068 GGGGGAGAGC
40051078 TTTTTTGAAGT
1 TTTTTTGAAGT
40051089 TTTTTTGAAGT
1 TTTTTTGAAGT
40051100 TTTTTT
1 TTTTTT
40051106 TTGAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (11 bp):
TTTTTTGAAGT
Found at i:40051615 original size:18 final size:18
Alignment explanation
Indices: 40051578--40051617 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40051568 TATATATATG
** *
40051578 TATATTTATTTTTATGTA
1 TATATTTATTTCCATCTA
40051596 TATATTTATTTCCATCTA
1 TATATTTATTTCCATCTA
40051614 TATA
1 TATA
40051618 CGCATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATTTATTTCCATCTA
Found at i:40052091 original size:15 final size:16
Alignment explanation
Indices: 40052073--40052102 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40052063 TATGTTAATT
40052073 TTGTTTAT-TTATTTA
1 TTGTTTATATTATTTA
40052088 TTGTTTATATTATTT
1 TTGTTTATATTATTT
40052103 CTATACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
TTGTTTATATTATTTA
Found at i:40058182 original size:88 final size:88
Alignment explanation
Indices: 40058029--40058243 Score: 349
Period size: 88 Copynumber: 2.4 Consensus size: 88
40058019 GTGAAGATAA
* * *
40058029 CAGATCTTGCCTTTCTGCACCGACAGCGAAGTAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTAGGTT
*
40058094 GTAGCGGAGCAGGTTAAAAATAG
66 GTAGCGAAGCAGGTTAAAAATAG
* * * *
40058117 CAGATCTTGCCTTCCTGCACCGACAACAAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTAGGTT
40058182 GTAGCGAAGCAGGTTAAAAATAG
66 GTAGCGAAGCAGGTTAAAAATAG
*
40058205 TAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
40058244 TGGCCCTAGC
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 116 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTAGGTT
GTAGCGAAGCAGGTTAAAAATAG
Found at i:40058317 original size:44 final size:44
Alignment explanation
Indices: 40058254--40058353 Score: 159
Period size: 44 Copynumber: 2.3 Consensus size: 44
40058244 TGGCCCTAGC
40058254 CCTATCTCCCTGGATAGCAGTGGAATAGGTTAAAGATTGT-AAGT
1 CCTATCTCCCTGGATAGCAGTGGAATAGGTTAAAGATTGTGAA-T
*
40058298 CCTATCTCCCTGG-TCAGCAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGAT-AGCAGTGGAATAGGTTAAAGATTGTGAAT
40058342 CCTATCTCCCTG
1 CCTATCTCCCTG
40058354 AGCAACAGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
43 1 0.02
44 50 0.94
45 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (44 bp):
CCTATCTCCCTGGATAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:40058363 original size:44 final size:43
Alignment explanation
Indices: 40058254--40058375 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
40058244 TGGCCCTAGC
*
40058254 CCTATCTCCCTGG-ATAGCAGTGGAATAGGTTAAAGATTGTAAGT
1 CCTATCTCCCTGGCA-A-CAGTGGAATAGGTTGAAGATTGTAAGT
*
40058298 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-T
1 CCTATCTCCCTGG-CAACAGTGGAATAGGTTGAAGATTGT-AAGT
**
40058342 CCTATCTCCCTGAGCAACAGTGGGGTAGGTTGAA
1 CCTATCTCCCTG-GCAACAGTGGAATAGGTTGAA
40058376 AATAGCAGAT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 65 0.94
45 3 0.04
46 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
CCTATCTCCCTGGCAACAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:40058785 original size:44 final size:44
Alignment explanation
Indices: 40058688--40058801 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
40058678 GAATATGGCA
* *
40058688 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAC
1 AATCTTATCTCCCTGAAGTTGCAGAGGAGTAGATTAAAGACAAC
* * * **
40058732 AATCCTATCTCCCTAAAGTTGCAGAGGAGTGGATTAAA-ATTAC
1 AATCTTATCTCCCTGAAGTTGCAGAGGAGTAGATTAAAGACAAC
* *
40058775 AGATCTTATCTCTCTGAAGTTGTAGAG
1 A-ATCTTATCTCCCTGAAGTTGCAGAG
40058802 AGCAGGTCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.05
44 55 0.95
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGAGGAGTAGATTAAAGACAAC
Found at i:40060404 original size:18 final size:18
Alignment explanation
Indices: 40060362--40060406 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
40060352 TTTTATATAT
* **
40060362 ATATGTATATTTATTTTT
1 ATATATATATTTATTTCC
*
40060380 ATGTATATATTTATTTCC
1 ATATATATATTTATTTCC
40060398 ATATATATA
1 ATATATATA
40060407 CGCATATTTT
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:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
ATATATATATTTATTTCC
Found at i:40060877 original size:19 final size:20
Alignment explanation
Indices: 40060849--40060894 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40060839 CATGTCCGCG
*
40060849 TTTATCTATTTA-TGTTAAT
1 TTTATTTATTTATTGTTAAT
*
40060868 TTTATTTATTTATTGTTTAT
1 TTTATTTATTTATTGTTAAT
*
40060888 ATTATTT
1 TTTATTT
40060895 CTATACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTATTGTTAAT
Found at i:40090075 original size:16 final size:16
Alignment explanation
Indices: 40090054--40090084 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40090044 TTAATTAAAA
*
40090054 TTAATTAATTAATTTC
1 TTAATTAAATAATTTC
40090070 TTAATTAAATAATTT
1 TTAATTAAATAATTT
40090085 TTTCAACCCT
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:40090323 original size:20 final size:20
Alignment explanation
Indices: 40090298--40090356 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
40090288 ACAATTTTAA
*
40090298 AACCAAGTGCAAATGATTTT
1 AACCAAGTGAAAATGATTTT
* *
40090318 AACCAAGTTAAAATGATTTC
1 AACCAAGTGAAAATGATTTT
* * *
40090338 AATCAAGTTAAAATAATTT
1 AACCAAGTGAAAATGATTT
40090357 ATAAATGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (20 bp):
AACCAAGTGAAAATGATTTT
Found at i:40090408 original size:32 final size:31
Alignment explanation
Indices: 40090328--40090408 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
40090318 AACCAAGTTA
40090328 AAATGATTTCAATCAAGTTAAAATAATTTAT
1 AAATGATTTCAATCAAGTTAAAATAATTTAT
*
40090359 AAATGATTTCAATCAAGTTAAAATCATTTAT
1 AAATGATTTCAATCAAGTTAAAATAATTTAT
*
40090390 AAATGATTTTCAAACAAGT
1 AAATGA-TTTCAATCAAGT
40090409 CAAATTTACT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 36 0.77
32 11 0.23
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (31 bp):
AAATGATTTCAATCAAGTTAAAATAATTTAT
Found at i:40094255 original size:149 final size:149
Alignment explanation
Indices: 40094046--40094338 Score: 523
Period size: 149 Copynumber: 2.0 Consensus size: 149
40094036 TGACTCAAGA
* * * **
40094046 CTCTCTTTATATAGGGAGAGTTTAAAGAGCTCAACTATGATTAAACTTAATTACTTTAATATTAA
1 CTCTATTTATATAGGAAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
40094111 ATTAATATAATATTTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
66 ATTAATATAATATTTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
40094176 AGAATGTTTATCTATAAGG
131 AGAATGTTTATCTATAAGG
*
40094195 CTCTATTTATATAGGAAGAGTTTAGAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
1 CTCTATTTATATAGGAAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
*
40094260 ATTAATATAATATTTATCAAGACAAATATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
66 ATTAATATAATATTTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
40094325 AGAATGTTTATCTA
131 AGAATGTTTATCTA
40094339 CAATATAAAA
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 137 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (149 bp):
CTCTATTTATATAGGAAGAGTTTAAAGAACTCAACTATGATTAAACTTAACCACTTTAATATTAA
ATTAATATAATATTTATCAAGACAAAGATTAGATTAAATTTAATATAAAATCTTATTAAAATAAT
AGAATGTTTATCTATAAGG
Found at i:40094357 original size:5 final size:5
Alignment explanation
Indices: 40094347--40094375 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40094337 TACAATATAA
40094347 AAATT AAATT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAAT
40094376 ATTAAGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:40100051 original size:17 final size:17
Alignment explanation
Indices: 40100031--40100084 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
40100021 GTCTGCAAAG
40100031 AGATACTCCTGTCACAC
1 AGATACTCCTGTCACAC
40100048 AGATACGAT-CTG-CA-AC
1 AGATAC--TCCTGTCACAC
40100064 GAGATACTCCTGTCACAC
1 -AGATACTCCTGTCACAC
40100082 AGA
1 AGA
40100085 CTTCTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
15 1 0.03
16 5 0.16
17 19 0.61
18 5 0.16
19 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (17 bp):
AGATACTCCTGTCACAC
Found at i:40100060 original size:34 final size:34
Alignment explanation
Indices: 40100016--40100084 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
40100006 TAGCTCTCAT
*
40100016 ATACGGTCTGCAAAGAGATACTCCTGTCACACAG
1 ATACGATCTGCAAAGAGATACTCCTGTCACACAG
*
40100050 ATACGATCTGCAACGAGATACTCCTGTCACACAG
1 ATACGATCTGCAAAGAGATACTCCTGTCACACAG
40100084 A
1 A
40100085 CTTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (34 bp):
ATACGATCTGCAAAGAGATACTCCTGTCACACAG
Found at i:40102113 original size:24 final size:24
Alignment explanation
Indices: 40102073--40102128 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
40102063 ATATATCACA
*
40102073 ATTATAAAATTACATAATATAAAT
1 ATTATAAAATTACATAAAATAAAT
* *
40102097 ATTATAAACATT-TATAAAATAGAT
1 ATTATAAA-ATTACATAAAATAAAT
40102121 ATATATAA
1 AT-TATAA
40102129 TGAGATAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTATAAAATTACATAAAATAAAT
Found at i:40103756 original size:318 final size:318
Alignment explanation
Indices: 40103179--40103816 Score: 949
Period size: 318 Copynumber: 2.0 Consensus size: 318
40103169 CAAATTAATA
* *
40103179 AAATTTTCTGTTAAAGTCCCTATGGTAATGTAACTCTTCCACTGCTCAACCACCGAATATCAACC
1 AAATTTTCTGGTAAAGTCCCTATGGTAATGTAACTATTCCACTGCTCAACCACCGAATATCAACC
* * *
40103244 ACTGCCAACCACCGGAACGCCGTCGCCGCAATCGCCGTGTCTAGTGATACAGGTGCAACACTTTT
66 ACCGCCAACCACCGGAACGCCGTCGCCGCAACCGCCGTGTCTAGTGATACAGCTGCAACACTTTT
* * * * * * *
40103309 ACAGTACCTCAAACCAGTTTAGTTACTATCGATTCGGTCCGGGTCAGTGATGACCCAATCGGTCC
131 ACAGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTCC
* * ** *
40103374 AGTCTAGCCACCGGTTGGATTGTCGACTCAATTTCACATACAGGGCCTGATTTAATCAGTTTTTG
196 AGTCTAACCACCGGTTGGATTGTCGACCCAATTTCACATACAGGGCCCAATTTAACCAGTTTTTG
*
40103439 GGTCTTGGTCTCAGTTTTAGGCTCTCGTGCCCAATTTATGATCTCAAGTCCAATTTTC
261 GGTCTTGGTCTCAGTTTTAGGCTCTCGTACCCAATTTATGATCTCAAGTCCAATTTTC
* *
40103497 AAATTTTCTGGTAGAGTCCCTATAGG-AGTGTAACTATTCCACTGCTCAACCACCGAATATCAAC
1 AAATTTTCTGGTAAAGTCCCTAT-GGTAATGTAACTATTCCACTGCTCAACCACCGAATATCAAC
* * * * **
40103561 CACCGCCAGCCACCGGAACGCCGTCGTCGCAGCCGCTGTGTCTAGTGATACAGCTGTGACACTTT
65 CACCGCCAACCACCGGAACGCCGTCGCCGCAACCGCCGTGTCTAGTGATACAGCTGCAACACTTT
* *
40103626 TACGGCACCCCAAACAAGTTCAATTACTATCGATTTGGTACGGGTCAGTGACGACCCAATCGGTC
130 TACAGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTC
**
40103691 TGGTCTAACCACCGGTTGGATTGTCGACCCAATTTCACATACCA-GGCCCAATTCT-ACCAGTTT
195 CAGTCTAACCACCGGTTGGATTGTCGACCCAATTTCACATA-CAGGGCCCAATT-TAACCAGTTT
*
40103754 TTGGGTCTTGGTCTCAGTTTTAGGCTCTCGTACCCAATTTATGATCTCAAGTCTAATTTTC
258 TTGGGTCTTGGTCTCAGTTTTAGGCTCTCGTACCCAATTTATGATCTCAAGTCCAATTTTC
40103815 AA
1 AA
40103817 GTTTAATTAC
Statistics
Matches: 286, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
318 281 0.98
319 5 0.02
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (318 bp):
AAATTTTCTGGTAAAGTCCCTATGGTAATGTAACTATTCCACTGCTCAACCACCGAATATCAACC
ACCGCCAACCACCGGAACGCCGTCGCCGCAACCGCCGTGTCTAGTGATACAGCTGCAACACTTTT
ACAGCACCCCAAACAAGTTCAATTACTATCGATTCGGTACGGGTCAGTGACGACCCAATCGGTCC
AGTCTAACCACCGGTTGGATTGTCGACCCAATTTCACATACAGGGCCCAATTTAACCAGTTTTTG
GGTCTTGGTCTCAGTTTTAGGCTCTCGTACCCAATTTATGATCTCAAGTCCAATTTTC
Found at i:40108837 original size:3 final size:3
Alignment explanation
Indices: 40108829--40108857 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40108819 AAGTTAAAAT
40108829 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40108858 GGAAGAGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40109064 original size:15 final size:15
Alignment explanation
Indices: 40109011--40109073 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
40109001 ACCCTTCTAA
*
40109011 TTTTCTTTAATTTTTC
1 TTTT-TTTATTTTTTC
* *
40109027 TTTCTTTATTTAGTTC
1 TTTTTTTATTT-TTTC
* *
40109043 TTGTTTTCTTTTTTC
1 TTTTTTTATTTTTTC
*
40109058 TTTTTTTTTTTTTTC
1 TTTTTTTATTTTTTC
40109073 T
1 T
40109074 GATCGGTGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
15 23 0.62
16 14 0.38
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTTATTTTTTC
Found at i:40113874 original size:19 final size:20
Alignment explanation
Indices: 40113816--40113869 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
40113806 AAATAGTGAG
40113816 AATT-TATTTTCTGAGTATA
1 AATTCTATTTTCTGAGTATA
40113835 AATTCTATTTT-TCGAGTATA
1 AATTCTATTTTCT-GAGTATA
40113855 AATTCTATTTTCTGA
1 AATTCTATTTTCTGA
40113870 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 26 0.81
21 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
AATTCTATTTTCTGAGTATA
Found at i:40114590 original size:46 final size:46
Alignment explanation
Indices: 40114537--40114627 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
40114527 GATTAAATAA
40114537 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
1 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
*
40114583 TTTATTTAACTTTGATTTAATTTTATTTCAAAATTAAGAAAACTA
1 TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTA
40114628 ACTTTTATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (46 bp):
TTTATTTAAATTTGATTTAATTTTATTTCAAAATTAAGAAAACTAG
Found at i:40114794 original size:23 final size:23
Alignment explanation
Indices: 40114752--40114795 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40114742 CTATATCTCG
*
40114752 AAATGACCTGACCCTCAAATTTA
1 AAATGACCTGAACCTCAAATTTA
* *
40114775 AAATGACCTGAATCTGAAATT
1 AAATGACCTGAACCTCAAATT
40114796 AACTGAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (23 bp):
AAATGACCTGAACCTCAAATTTA
Found at i:40118369 original size:15 final size:15
Alignment explanation
Indices: 40118349--40118377 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40118339 TATATTAGTA
40118349 TTTTCTATTCTATTT
1 TTTTCTATTCTATTT
40118364 TTTTCTATTCTATT
1 TTTTCTATTCTATT
40118378 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCTATTCTATTT
Found at i:40118389 original size:5 final size:6
Alignment explanation
Indices: 40118374--40118444 Score: 68
Period size: 5 Copynumber: 13.2 Consensus size: 6
40118364 TTTTCTATTC
* *
40118374 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
40118418 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
40118445 TAGTGATCCC
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
4 4 0.07
5 28 0.48
6 26 0.45
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:40118389 original size:11 final size:11
Alignment explanation
Indices: 40118375--40118448 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
40118365 TTTCTATTCT
40118375 ATTAGTATTAG
1 ATTAGTATTAG
**
40118386 ATTAGTATTCT
1 ATTAGTATTAG
*
40118397 ATT-CTATTAG
1 ATTAGTATTAG
40118407 --TA-T--TAG
1 ATTAGTATTAG
40118413 ATTAGTATTAG
1 ATTAGTATTAG
40118424 -TTAG-ATTAG
1 ATTAGTATTAG
40118433 ATTAGTATTAG
1 ATTAGTATTAG
40118444 -TTAGT
1 ATTAGT
40118449 GATCCCGGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
6 3 0.06
8 4 0.08
9 6 0.12
10 17 0.34
11 20 0.40
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:40118396 original size:27 final size:27
Alignment explanation
Indices: 40118366--40118421 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
40118356 TTCTATTTTT
40118366 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
40118393 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
40118420 TT
1 TT
40118422 AGTTAGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:40118433 original size:20 final size:21
Alignment explanation
Indices: 40118403--40118448 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
40118393 TTCTATTCTA
40118403 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
40118424 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
40118444 TTAGT
1 TTAGT
40118449 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:40126977 original size:20 final size:20
Alignment explanation
Indices: 40126929--40126977 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40126919 CGGAAAAGTT
*
40126929 ATTTTTATATATATTAATAA
1 ATTTTTATACATATTAATAA
* *
40126949 ATCTATATACATATTAATAA
1 ATTTTTATACATATTAATAA
40126969 ATTTTTATA
1 ATTTTTATA
40126978 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTATACATATTAATAA
Found at i:40128275 original size:32 final size:32
Alignment explanation
Indices: 40128229--40128289 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
40128219 TGTCAATCAT
40128229 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
40128261 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
40128290 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:40128296 original size:27 final size:30
Alignment explanation
Indices: 40128229--40128302 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
40128219 TGTCAATCAT
*
40128229 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
40128261 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
40128289 -TCAATATCTAACAA
1 TTCAATATCTAACAA
40128303 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 14 0.34
28 2 0.05
29 2 0.05
32 23 0.56
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:40128313 original size:27 final size:27
Alignment explanation
Indices: 40128230--40128316 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 27
40128220 GTCAATCATT
* *
40128230 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
40128261 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
40128289 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
40128316 T
1 T
40128317 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:40146860 original size:31 final size:30
Alignment explanation
Indices: 40146825--40146893 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
40146815 ATTGAACAGC
*
40146825 TCAATGACTTAAATAAAAACTTTTGAATATT
1 TCAATGACTTAAATAAAAACTTTCGAATA-T
* *
40146856 TCAATTACTTGAATAAAAACTTTCGAATAT
1 TCAATGACTTAAATAAAAACTTTCGAATAT
40146886 TCAATGAC
1 TCAATGAC
40146894 CATTTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (30 bp):
TCAATGACTTAAATAAAAACTTTCGAATAT
Found at i:40149331 original size:14 final size:14
Alignment explanation
Indices: 40149312--40149357 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
40149302 GTTAATATAC
40149312 GCCAACACTGCTTT
1 GCCAACACTGCTTT
* *
40149326 GCCAACAATAC---
1 GCCAACACTGCTTT
40149337 GCCAACACTGCTTT
1 GCCAACACTGCTTT
40149351 GCCAACA
1 GCCAACA
40149358 ATGCAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
11 9 0.36
14 16 0.64
ACGTcount: A:0.30, C:0.37, G:0.13, T:0.20
Consensus pattern (14 bp):
GCCAACACTGCTTT
Found at i:40149340 original size:25 final size:25
Alignment explanation
Indices: 40149308--40149359 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40149298 CTCGGTTAAT
40149308 ATACGCCAACACTGCTTTGCCAACA
1 ATACGCCAACACTGCTTTGCCAACA
40149333 ATACGCCAACACTGCTTTGCCAACA
1 ATACGCCAACACTGCTTTGCCAACA
40149358 AT
1 AT
40149360 GCAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.21
Consensus pattern (25 bp):
ATACGCCAACACTGCTTTGCCAACA
Found at i:40159878 original size:29 final size:30
Alignment explanation
Indices: 40159839--40159901 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
40159829 GACCAAAAAA
40159839 GGCCGGTTTTTTTCAA-AATTTACCGAAATG
1 GGCCGGTTTTTTT-AATAATTTACCGAAATG
* *
40159869 GGCCGG-TTTTTTAATTATTTACCGGAATG
1 GGCCGGTTTTTTTAATAATTTACCGAAATG
40159898 GGCC
1 GGCC
40159902 ATTTTCCGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 22 0.73
30 6 0.20
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (30 bp):
GGCCGGTTTTTTTAATAATTTACCGAAATG
Found at i:40174463 original size:15 final size:15
Alignment explanation
Indices: 40174445--40174478 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
40174435 ATTTATTTTA
40174445 ATATTATTTTATGGT
1 ATATTATTTTATGGT
40174460 ATATTATTTTATGGT
1 ATATTATTTTATGGT
40174475 ATAT
1 ATAT
40174479 AGTATCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (15 bp):
ATATTATTTTATGGT
Found at i:40178082 original size:25 final size:25
Alignment explanation
Indices: 40178048--40178158 Score: 127
Period size: 25 Copynumber: 4.4 Consensus size: 25
40178038 ACAACTCTCT
40178048 TGAGCTTCCCGATATTTAGCTCATA
1 TGAGCTTCCCGATATTTAGCTCATA
*
40178073 TGAGCTTCCCGAT-TTCTAGCTCGTA
1 TGAGCTTCCCGATATT-TAGCTCATA
* *
40178098 TGAGCTTCCCGATATAT-GACTCGTA
1 TGAGCTTCCCGATATTTAG-CTCATA
* * *
40178123 TGAGCTTCTCGTTACTTAGCTCATA
1 TGAGCTTCCCGATATTTAGCTCATA
*
40178148 TGAGCATCCCG
1 TGAGCTTCCCG
40178159 TTATATGGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
24 3 0.04
25 68 0.93
26 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
TGAGCTTCCCGATATTTAGCTCATA
Found at i:40178125 original size:50 final size:50
Alignment explanation
Indices: 40178048--40178185 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 50
40178038 ACAACTCTCT
* * * *
40178048 TGAGCTTCCCGATAT-TTAGCTCATATGAGCTTCCCGATTTC-TAGCTCGTA
1 TGAGCTTCCCGATATATGA-CTCGTATGAGCTTCCCG-TTACTTAGCTCATA
*
40178098 TGAGCTTCCCGATATATGACTCGTATGAGCTTCTCGTTACTTAGCTCATA
1 TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTTACTTAGCTCATA
* * * * *
40178148 TGAGCATCCCGTTATATGGCTCGGAAGAGCTTCCCGTT
1 TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTT
40178186 TACATGCTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.04
50 70 0.93
51 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (50 bp):
TGAGCTTCCCGATATATGACTCGTATGAGCTTCCCGTTACTTAGCTCATA
Found at i:40178169 original size:25 final size:25
Alignment explanation
Indices: 40178048--40178185 Score: 120
Period size: 25 Copynumber: 5.5 Consensus size: 25
40178038 ACAACTCTCT
* *
40178048 TGAGCTTCCCGATATTTAGCTCATA
1 TGAGCTTCCCGTTATATAGCTCATA
* *
40178073 TGAGCTTCCCGATT-TCTAGCTCGTA
1 TGAGCTTCCCG-TTATATAGCTCATA
* *
40178098 TGAGCTTCCCGATATAT-GACTCGTA
1 TGAGCTTCCCGTTATATAG-CTCATA
*
40178123 TGAGCTTCTCGTTACT-TAGCTCATA
1 TGAGCTTCCCGTTA-TATAGCTCATA
* * **
40178148 TGAGCATCCCGTTATATGGCTCGGA
1 TGAGCTTCCCGTTATATAGCTCATA
*
40178173 AGAGCTTCCCGTT
1 TGAGCTTCCCGTT
40178186 TACATGCTTG
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.03
25 86 0.93
26 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
TGAGCTTCCCGTTATATAGCTCATA
Found at i:40186628 original size:21 final size:21
Alignment explanation
Indices: 40186561--40186629 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
40186551 GCATTAAAGA
* *
40186561 GTGTTGTGGTTGCATCTGATT
1 GTGTTGTGGATGCATCTGAGT
* *
40186582 CTGATGTGGATGCATCT-AGCT
1 GTGTTGTGGATGCATCTGAG-T
* *
40186603 TTGTTGTGGATGAATCTGAGT
1 GTGTTGTGGATGCATCTGAGT
40186624 GTGTTG
1 GTGTTG
40186630 ATTGCAGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.42
Consensus pattern (21 bp):
GTGTTGTGGATGCATCTGAGT
Found at i:40198254 original size:16 final size:16
Alignment explanation
Indices: 40198216--40198247 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40198206 TTATTTTATA
*
40198216 GTTTATTTTTTCTTTT
1 GTTTTTTTTTTCTTTT
40198232 GTTTTTTTTTTCTTTT
1 GTTTTTTTTTTCTTTT
40198248 TCTTTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (16 bp):
GTTTTTTTTTTCTTTT
Found at i:40209072 original size:21 final size:21
Alignment explanation
Indices: 40209035--40209074 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40209025 AATTAAAATG
*
40209035 TTTTAATTTCACTTTAATTTA
1 TTTTAATTTCACGTTAATTTA
40209056 TTTTAATTTC-CAGTTAATT
1 TTTTAATTTCAC-GTTAATT
40209075 ACAAAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTAATTTCACGTTAATTTA
Found at i:40212036 original size:4 final size:4
Alignment explanation
Indices: 40212027--40212084 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
40212017 TATTAAATCA
40212027 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
40212075 GTAT GTAT GT
1 GTAT GTAT GT
40212085 CTATTGTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:40214122 original size:20 final size:20
Alignment explanation
Indices: 40214097--40214138 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40214087 ATGATGCTGA
40214097 TTAATTTATTATATACTTTT
1 TTAATTTATTATATACTTTT
40214117 TTAATTTATTATATACTTTT
1 TTAATTTATTATATACTTTT
40214137 TT
1 TT
40214139 TCTTGCAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAATTTATTATATACTTTT
Found at i:40216593 original size:20 final size:20
Alignment explanation
Indices: 40216568--40216670 Score: 65
Period size: 20 Copynumber: 5.5 Consensus size: 20
40216558 ATGTTTTTAA
*
40216568 TTATGTATTGATTCAAAGAC
1 TTATGTAATGATTCAAAGAC
***
40216588 TTATGTAAT-ATTTTTA-A-
1 TTATGTAATGATTCAAAGAC
*
40216605 TTATGTAGTGATTCAAAGAC
1 TTATGTAATGATTCAAAGAC
* ***
40216625 TTATTTAAT-ATTTTTA-A-
1 TTATGTAATGATTCAAAGAC
* *
40216642 TTATGTAGTGATTCAAAGAT
1 TTATGTAATGATTCAAAGAC
40216662 TTATGTAAT
1 TTATGTAAT
40216671 ATTTTTAATT
Statistics
Matches: 58, Mismatches: 19, Indels: 12
0.65 0.21 0.13
Matches are distributed among these distances:
17 15 0.26
18 10 0.17
19 10 0.17
20 23 0.40
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.48
Consensus pattern (20 bp):
TTATGTAATGATTCAAAGAC
Found at i:40216596 original size:37 final size:37
Alignment explanation
Indices: 40216526--40216691 Score: 264
Period size: 37 Copynumber: 4.5 Consensus size: 37
40216516 AAGACTTATA
* *
40216526 TTTTAATTATGT-GTTAATTC-AAGACTTATGTAATGT
1 TTTTAATTATGTAG-TGATTCAAAGACTTATGTAATAT
*
40216562 TTTTAATTATGTATTGATTCAAAGACTTATGTAATAT
1 TTTTAATTATGTAGTGATTCAAAGACTTATGTAATAT
*
40216599 TTTTAATTATGTAGTGATTCAAAGACTTATTTAATAT
1 TTTTAATTATGTAGTGATTCAAAGACTTATGTAATAT
*
40216636 TTTTAATTATGTAGTGATTCAAAGATTTATGTAATAT
1 TTTTAATTATGTAGTGATTCAAAGACTTATGTAATAT
40216673 TTTTAATTATGTAGTGATT
1 TTTTAATTATGTAGTGATT
40216692 TAATTCGGGT
Statistics
Matches: 121, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
36 17 0.14
37 104 0.86
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (37 bp):
TTTTAATTATGTAGTGATTCAAAGACTTATGTAATAT
Found at i:40216684 original size:17 final size:17
Alignment explanation
Indices: 40216551--40216685 Score: 63
Period size: 17 Copynumber: 7.4 Consensus size: 17
40216541 AATTCAAGAC
*
40216551 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
* ***
40216568 TTATGTATTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
40216587 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ***
40216605 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
*
40216624 CTTATTTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ***
40216642 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
40216661 TTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
40216679 TTATGTA
1 TTATGTA
40216686 GTGATTTAAT
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
17 30 0.37
18 14 0.17
19 15 0.18
20 23 0.28
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:40216706 original size:9 final size:9
Alignment explanation
Indices: 40216692--40216788 Score: 106
Period size: 9 Copynumber: 10.6 Consensus size: 9
40216682 TGTAGTGATT
40216692 TAATTCGGG
1 TAATTCGGG
40216701 TAATTCGGG
1 TAATTCGGG
*
40216710 TAATTTTCAGG
1 TAA--TTCGGG
40216721 TAATTCGGG
1 TAATTCGGG
40216730 TAATTCGGG
1 TAATTCGGG
*
40216739 TAAATCGGG
1 TAATTCGGG
*
40216748 TAATTCTGG
1 TAATTCGGG
40216757 TAATTAC-GG
1 TAATT-CGGG
*
40216766 TATTTCGGG
1 TAATTCGGG
*
40216775 TATTTCGGG
1 TAATTCGGG
*
40216784 CAATT
1 TAATT
40216789 TTTAACCAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
8 1 0.01
9 66 0.87
10 1 0.01
11 8 0.11
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (9 bp):
TAATTCGGG
Found at i:40217782 original size:42 final size:42
Alignment explanation
Indices: 40217734--40217918 Score: 257
Period size: 42 Copynumber: 4.4 Consensus size: 42
40217724 TTAGCGCGTC
* *
40217734 GCAGGCTTATTGCCAGTGAAACAATATCAGACTTTACGTCTA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
* * * *
40217776 ACAGGCTTAATGCCGATGAAATAATTTCAGACTTTACGTCTA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
40217818 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
* * * *
40217860 GCAGGCTTAATGCCGGTGAAAC-ATTTCAAACTATATGTCTA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
40217901 GCAGGC-TAAGTGCCGGTG
1 GCAGGCTTAA-TGCCGGTG
40217919 TACTGAATCA
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 3 0.02
41 29 0.23
42 96 0.75
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (42 bp):
GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTA
Found at i:40217961 original size:82 final size:83
Alignment explanation
Indices: 40217734--40217961 Score: 248
Period size: 84 Copynumber: 2.7 Consensus size: 83
40217724 TTAGCGCGTC
* * * * * * *
40217734 GCAGGCTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAACAGGCTTAATGCCGATGAAATA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTAAGCCTAGCAGGCTTAATGCCGGTGAAA-C
* *
40217799 ATTTCAGACTTTACGTCTA
65 ATTTCAAACTATACGTCTA
* *
40217818 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACA
1 GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTAAGCCTAGCAGGCTTAATGCCGGTGAAACA
*
40217883 TTTCAAACTATATGTCTA
66 TTTCAAACTATACGTCTA
* * * *
40217901 GCAGGC-TAAGTGCCGGTG-TACTGA-ATCAGGCTTTAAGCCTAGCAGGC-TAAGTGCTGGTGAA
1 GCAGGCTTAA-TGCCGGTGAAAC-AATATCAGACTTTAAGCCTAGCAGGCTTAA-TGCCGGTGAA
40217962 TCTGTTTAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
81 3 0.02
82 34 0.27
83 31 0.24
84 59 0.46
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (83 bp):
GCAGGCTTAATGCCGGTGAAACAATATCAGACTTTAAGCCTAGCAGGCTTAATGCCGGTGAAACA
TTTCAAACTATACGTCTA
Found at i:40219920 original size:16 final size:16
Alignment explanation
Indices: 40219896--40219941 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
40219886 TCCAAGTCAA
40219896 ATAA-AATAAATAAAT
1 ATAACAATAAATAAAT
*
40219911 ACTAA-GATAAATAAAT
1 A-TAACAATAAATAAAT
40219927 ATAACAATAAATAAA
1 ATAACAATAAATAAA
40219942 ATATTGGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (16 bp):
ATAACAATAAATAAAT
Found at i:40219940 original size:20 final size:19
Alignment explanation
Indices: 40219894--40219941 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
40219884 AATCCAAGTC
* *
40219894 AAATAAAATAAATAAATACT
1 AAAT-AAATAAATAAACAAT
40219914 AAGATAAATAAATATAACAAT
1 AA-ATAAATAAATA-AACAAT
40219935 AAATAAA
1 AAATAAA
40219942 ATATTGGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAATAAATAAACAAT
Found at i:40220160 original size:25 final size:25
Alignment explanation
Indices: 40220127--40220190 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 25
40220117 TTGTTAAAAC
40220127 TCTTCTAAAAGAAACTCAAGAGAAAT
1 TCTT-TAAAAGAAACTCAAGAGAAAT
40220153 TCTTTAAAAGAAACTCAAGAGAAAT
1 TCTTTAAAAGAAACTCAAGAGAAAT
40220178 TCTTTAAAAGAAA
1 TCTTTAAAAGAAA
40220191 AACTCAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 34 0.89
26 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (25 bp):
TCTTTAAAAGAAACTCAAGAGAAAT
Done.