Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 113 of 240
Found at i:35171952 original size:40 final size:37
Alignment explanation
Indices: 35171843--35171954 Score: 115
Period size: 35 Copynumber: 3.0 Consensus size: 37
35171833 ACCGACAATG
35171843 ATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAAC-A
1 ATAA-TTTGAGCCCAGCTCTAGTTGGATAAACCAACGA
* * *
35171880 AT-ATTTGCA-CCCA-ATGCTAGTCGGATATACCAACGATA
1 ATAATTTG-AGCCCAGCT-CTAGTTGGATAAACCAACG--A
35171918 ATAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACG
1 ATAATT-TGAGCCCAGCTCTAGTTGGATAAACCAACG
35171955 GTGATTGCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
34 1 0.02
35 24 0.40
36 2 0.03
37 2 0.03
38 3 0.05
39 4 0.07
40 23 0.38
41 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (37 bp):
ATAATTTGAGCCCAGCTCTAGTTGGATAAACCAACGA
Found at i:35178702 original size:170 final size:170
Alignment explanation
Indices: 35178420--35178760 Score: 673
Period size: 170 Copynumber: 2.0 Consensus size: 170
35178410 TTGCTACTGG
35178420 TTTTAAATATTCTCTTCGACAAGAATGGCTTCTATACTTTCTTATAATCCATTGGGATCCCAGAT
1 TTTTAAATATTCTCTTCGACAAGAATGGCTTCTATACTTTCTTATAATCCATTGGGATCCCAGAT
*
35178485 TTGTCACAACATTAAGCACTTATTGAAGAAAATCTCAATTGATGTTGTTTATCATAGGGTAGTAC
66 TTGTCACAACATCAAGCACTTATTGAAGAAAATCTCAATTGATGTTGTTTATCATAGGGTAGTAC
35178550 TCATCTTCCTCAACATCAAGTAAATTAAACAAATCATTGA
131 TCATCTTCCTCAACATCAAGTAAATTAAACAAATCATTGA
35178590 TTTTAAATATTCTCTTCGACAAGAATGGCTTCTATACTTTCTTATAATCCATTGGGATCCCAGAT
1 TTTTAAATATTCTCTTCGACAAGAATGGCTTCTATACTTTCTTATAATCCATTGGGATCCCAGAT
35178655 TTGTCACAACATCAAGCACTTATTGAAGAAAATCTCAATTGATGTTGTTTATCATAGGGTAGTAC
66 TTGTCACAACATCAAGCACTTATTGAAGAAAATCTCAATTGATGTTGTTTATCATAGGGTAGTAC
35178720 TCATCTTCCTCAACATCAAGTAAATTAAACAAATCATTGA
131 TCATCTTCCTCAACATCAAGTAAATTAAACAAATCATTGA
35178760 T
1 T
35178761 GGACTTAGAA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTTAAATATTCTCTTCGACAAGAATGGCTTCTATACTTTCTTATAATCCATTGGGATCCCAGAT
TTGTCACAACATCAAGCACTTATTGAAGAAAATCTCAATTGATGTTGTTTATCATAGGGTAGTAC
TCATCTTCCTCAACATCAAGTAAATTAAACAAATCATTGA
Found at i:35184266 original size:13 final size:12
Alignment explanation
Indices: 35184248--35184283 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
35184238 AAACCAAAAT
35184248 TTTCAAAAGCAC
1 TTTCAAAAGCAC
35184260 TTCTCAAAAGCAC
1 TT-TCAAAAGCAC
*
35184273 TTTTAAAAGCA
1 TTTCAAAAGCA
35184284 ATGAAGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (12 bp):
TTTCAAAAGCAC
Found at i:35198106 original size:22 final size:21
Alignment explanation
Indices: 35198068--35198108 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
35198058 ATTTGTTATA
**
35198068 AACAAAGAGAATTATAGAATG
1 AACAAAGAGAAGAATAGAATG
35198089 AACAAGAGAGAAGAATAGAA
1 AACAA-AGAGAAGAATAGAA
35198109 AAATGAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.61, C:0.05, G:0.22, T:0.12
Consensus pattern (21 bp):
AACAAAGAGAAGAATAGAATG
Found at i:35199610 original size:17 final size:17
Alignment explanation
Indices: 35199582--35199614 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35199572 ATTATATCAA
35199582 AAAAACAGTATATATGAT
1 AAAAACAGTATA-ATGAT
35199600 AAAAACA-TATAATGA
1 AAAAACAGTATAATGA
35199615 AATTAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAACAGTATAATGAT
Found at i:35200228 original size:32 final size:33
Alignment explanation
Indices: 35200156--35200228 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
35200146 ATTTTTTAAA
* *
35200156 TTAAAATTATTTAAAATATATTTTTTATAATTT
1 TTAAATTTTTTTAAAATATATTTTTTATAATTT
*
35200189 TT-CATTTTTTTAAAA-ATATTTTTT-TGAATTT
1 TTAAATTTTTTTAAAATATATTTTTTAT-AATTT
35200220 TTAAATTTT
1 TTAAATTTT
35200229 AAAAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 1 0.03
31 16 0.47
32 15 0.44
33 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (33 bp):
TTAAATTTTTTTAAAATATATTTTTTATAATTT
Found at i:35203647 original size:18 final size:17
Alignment explanation
Indices: 35203605--35203647 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
35203595 CAACAAATGA
* *
35203605 ATTTAAACTTAAGAAAT
1 ATTTAAAATTAAAAAAT
*
35203622 AATTAAAATTAAAAAAT
1 ATTTAAAATTAAAAAAT
35203639 CATTTAAAA
1 -ATTTAAAA
35203648 CCCGTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTTAAAATTAAAAAAT
Found at i:35205854 original size:78 final size:79
Alignment explanation
Indices: 35205679--35205881 Score: 311
Period size: 82 Copynumber: 2.6 Consensus size: 79
35205669 AATATACATT
* * * *
35205679 TTTCAACAAATCAGTTCAGAAAACAAACAAAATACGTTATACTAACAAAATAATCCTATAGCAGT
1 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATAATCCTATAACAGT
35205744 AAGATGTTAACCAACCA
66 AAGATGTT-A--AACCA
* *
35205761 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATGCTAACAAAATGATCCTATAACAGT
1 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATAATCCTATAACAGT
35205826 AAGATGTT-AACCA
66 AAGATGTTAAACCA
35205839 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTA-ACTA
1 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTA
35205882 TCTCAATCCA
Statistics
Matches: 114, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
77 3 0.03
78 44 0.39
82 67 0.59
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.26
Consensus pattern (79 bp):
TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATAATCCTATAACAGT
AAGATGTTAAACCA
Found at i:35206231 original size:160 final size:157
Alignment explanation
Indices: 35205951--35206380 Score: 496
Period size: 160 Copynumber: 2.7 Consensus size: 157
35205941 TATGCCATCC
* ** * * *
35205951 TTTTTT-GGCTTCTACTTCTCATACTCATACCAGACTGAG---AACAAAAATCAGAACCCTAAAT
1 TTTTTTGGGCTTCTAGTTCTTGTACTCGTACCAGACTAAGCTCAA-AAAAATCAAAACCC-AAAT
* * * * *
35206012 TAGATTTAAATAATTTAGAATTGAGATTAAAAAAGTGTTTGCAATATACCTGTGATCCAGTTGTA
64 TAGATTTAAATATTTTAGAATTGACATTAAAAAA-TGTTTACGATATACCTATGATCCAGTTGTA
* *
35206077 TTAGGCTGAATGCATGGTGTTATGTTGTTC
128 TTAGGCTGAATGCATGGTGTTATATTGTTA
35206107 TCTTTTT-GGCTTCTAGTT-TGTGTACTCGTACCAGACTAAGGCT-AAAAAAAGTCAAAATCCCA
1 T-TTTTTGGGCTTCTAGTTCT-TGTACTCGTACCAGACTAA-GCTCAAAAAAA-TCAAAA-CCCA
* * * *
35206169 AATTAGATTAAAATATTTTTGAATTGACATTAAAATAATGTATACGATATACTTATGATCCAGTT
61 AATTAGATTTAAATATTTTAGAATTGACATTAAAA-AATGTTTACGATATACCTATGATCCAGTT
*
35206234 GTATTATGCTGAATGCATGGTGTTATATTGTTA
125 GTATTAGGCTGAATGCATGGTGTTATATTGTTA
* ** *
35206267 TTTTTTGGGCTTCTAGTTCTTGTACTCGTACTAGACTAATTTCAAAAAAATCAGAACCCAAATTA
1 TTTTTTGGGCTTCTAGTTCTTGTACTCGTACCAGACTAAGCTCAAAAAAATCAAAACCCAAATTA
* * *
35206332 GATTTTAATATTTTGGAATTGACAATGAAAAAATGTTTACGATATACCT
66 GATTTAAATATTTTAGAATTGAC-ATTAAAAAATGTTTACGATATACCT
35206381 GTGTTACGAC
Statistics
Matches: 234, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
156 2 0.01
157 30 0.13
158 46 0.20
159 22 0.09
160 128 0.55
161 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (157 bp):
TTTTTTGGGCTTCTAGTTCTTGTACTCGTACCAGACTAAGCTCAAAAAAATCAAAACCCAAATTA
GATTTAAATATTTTAGAATTGACATTAAAAAATGTTTACGATATACCTATGATCCAGTTGTATTA
GGCTGAATGCATGGTGTTATATTGTTA
Found at i:35207332 original size:54 final size:54
Alignment explanation
Indices: 35207250--35207367 Score: 173
Period size: 54 Copynumber: 2.2 Consensus size: 54
35207240 CCACTTCCCT
* * *
35207250 AACCCCCTCCTTACCACCTCCATCACTCTCACCACCTTCATTGACAGCAACATC
1 AACCCCCTCCTCACCACCTCCATCACTCTCACCACCTTCACTGACAACAACATC
* *
35207304 AACCCCCTCCTCACCGCCTCTATCACTCTCACCACCTTCACTGACAACAACATC
1 AACCCCCTCCTCACCACCTCCATCACTCTCACCACCTTCACTGACAACAACATC
* *
35207358 ATCACCCTCC
1 AACCCCCTCC
35207368 CTACCTAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.21
Consensus pattern (54 bp):
AACCCCCTCCTCACCACCTCCATCACTCTCACCACCTTCACTGACAACAACATC
Found at i:35209595 original size:9 final size:9
Alignment explanation
Indices: 35209574--35209612 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
35209564 CTAGTTAATG
35209574 TTTAACTTGT
1 TTTAA-TTGT
*
35209584 TTTAATTTTT
1 TTTAA-TTGT
35209594 TTTAATTGT
1 TTTAATTGT
35209603 TTTAATTGT
1 TTTAATTGT
35209612 T
1 T
35209613 AGTAAACCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (9 bp):
TTTAATTGT
Found at i:35209674 original size:18 final size:18
Alignment explanation
Indices: 35209641--35209679 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
35209631 TCTAAATGCT
*
35209641 TTTTTTAATTTTAATT-A
1 TTTTTTAATTTAAATTCA
35209658 TTTTTTAAGTTTAAATTCA
1 TTTTTTAA-TTTAAATTCA
35209677 TTT
1 TTT
35209680 GCTGACATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTTAAATTCA
Found at i:35209952 original size:99 final size:100
Alignment explanation
Indices: 35209834--35210036 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 100
35209824 AAAAAAAAGG
35209834 TTATGTATGAAAGTGCTCC-AAAAAAACCTTAAAGGCCAAAGTGACCCAACACCCAAACATTAAG
1 TTATGTATGAAAGTGCTCCAAAAAAAACCTTAAAGGCCAAAGTGACCCAACACCCAAACATTAAG
35209898 GGCTAATTTTGTCATTATGCAAATTTATTTTAAAT
66 GGCTAATTTTGTCATTATGCAAATTTATTTTAAAT
*
35209933 TTATGTATGAAAGTGCTCCAAAAAAAAACCTTAAAGGCCAAAGTGACCCAACACCCAAACGTTAA
1 TTATGTATGAAAGTGCTCC-AAAAAAAACCTTAAAGGCCAAAGTGACCCAACACCCAAACATTAA
35209998 GGGCTAATTTTGTCATTATGCAAATTTATTTTAAAT
65 GGGCTAATTTTGTCATTATGCAAATTTATTTTAAAT
35210034 TTA
1 TTA
35210037 ATAACTTGTA
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 19 0.19
101 82 0.81
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (100 bp):
TTATGTATGAAAGTGCTCCAAAAAAAACCTTAAAGGCCAAAGTGACCCAACACCCAAACATTAAG
GGCTAATTTTGTCATTATGCAAATTTATTTTAAAT
Found at i:35210510 original size:24 final size:25
Alignment explanation
Indices: 35210471--35210525 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 25
35210461 TATTCTGGAC
35210471 TTATTTTTTAATAAATTTTAT-AATTT
1 TTATTTTTTAATAAATTTT-TGAA-TT
35210497 TTATTTTTT-A-AAATTTTTGAATT
1 TTATTTTTTAATAAATTTTTGAATT
35210520 TTATTT
1 TTATTT
35210526 AATATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.32
24 9 0.32
25 1 0.04
26 9 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATTTTTTAATAAATTTTTGAATT
Found at i:35219988 original size:16 final size:16
Alignment explanation
Indices: 35219967--35220000 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
35219957 AAAACAGTAC
35219967 TTATAAAATTTT-TATA
1 TTAT-AAATTTTATATA
35219983 TTATAAATTTTATATA
1 TTATAAATTTTATATA
35219999 TT
1 TT
35220001 TTTACTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAAATTTTATATA
Found at i:35223749 original size:114 final size:113
Alignment explanation
Indices: 35223550--35223775 Score: 407
Period size: 114 Copynumber: 2.0 Consensus size: 113
35223540 TACATGTATT
*
35223550 TGAACTTACTAAGCACAGCGTGCTCATATTATCATATTTTTCTTGTAGATTATGTGAAGCCTAGT
1 TGAACTTACTAAGCACAACGTGCTCATATTATCATATTTTTCTTGTAGATTATGTGAAGCCTAGT
*
35223615 AGATCAAAAATTCAAGTCAGAGCATACAAACTGTAACACCTTGACCCA
66 AGATCAAAAATTCAAGTCAGAGCATACAAACTGTAACACCCTGACCCA
*
35223663 TGAACTTACTAAGCACAACGTGCTCATATTATCATGTTTTTTCTTGTAGATTATGTGAAGCCTAG
1 TGAACTTACTAAGCACAACGTGCTCATATTATCAT-ATTTTTCTTGTAGATTATGTGAAGCCTAG
*
35223728 TAGATCAAAAATTCAATTCAGAGCATACAAACTGTAACACCCTGACCC
65 TAGATCAAAAATTCAAGTCAGAGCATACAAACTGTAACACCCTGACCC
35223776 GTGTCCGTCG
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
113 34 0.31
114 74 0.69
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (113 bp):
TGAACTTACTAAGCACAACGTGCTCATATTATCATATTTTTCTTGTAGATTATGTGAAGCCTAGT
AGATCAAAAATTCAAGTCAGAGCATACAAACTGTAACACCCTGACCCA
Found at i:35225885 original size:106 final size:106
Alignment explanation
Indices: 35225700--35225914 Score: 360
Period size: 106 Copynumber: 2.0 Consensus size: 106
35225690 CTTCAAAAGG
* *
35225700 AAAATTTCAAAGTAAGGCAATATTTTGTGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
*
35225765 GTTTTGATTTCTCGTTTGACCAAATAGCCAAATATCCTTTT
66 GTTTTGATTTCTCGTTTGACCAAATAGCCAAATATCCTCTT
* *
35225806 AAAATTTCAAAATAGGGTAATATTTTGCGTTTGGAAAATCGA-AAAATCGTGCCCTAACGTGCTG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAA-CGTGCCCTAACGTGCTG
*
35225870 GGTTTTGATTTCTCGTTTGATCAAATAGCCAAATATCCTCTT
65 GGTTTTGATTTCTCGTTTGACCAAATAGCCAAATATCCTCTT
35225912 AAA
1 AAA
35225915 TCTCAATCCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 4 0.04
106 98 0.96
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (106 bp):
AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGG
GTTTTGATTTCTCGTTTGACCAAATAGCCAAATATCCTCTT
Found at i:35226646 original size:23 final size:23
Alignment explanation
Indices: 35226620--35227083 Score: 381
Period size: 23 Copynumber: 19.7 Consensus size: 23
35226610 TCTACCCTGT
*
35226620 AACAATTTGGGCAGCATATATAC
1 AACAAATTGGGCAGCATATATAC
*
35226643 AACAAATTGGGCAGCATATATAT
1 AACAAATTGGGCAGCATATATAC
* * * *
35226666 ACCAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* *
35226689 ATCAAAATTGGACAGCATATATAC
1 AAC-AAATTGGGCAGCATATATAC
* *
35226713 AACAATTTGGGCAGCATAAATAC
1 AACAAATTGGGCAGCATATATAC
* * *
35226736 AACAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* * *
35226759 ACCAAAAATTGGACAACATATATAC
1 A--ACAAATTGGGCAGCATATATAC
*
35226784 AACAAATTGGGCAGCATATATAT
1 AACAAATTGGGCAGCATATATAC
* * * *
35226807 ACCAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* *
35226830 ATCAAAATTGGACAGCATATATAC
1 AAC-AAATTGGGCAGCATATATAC
* * *
35226854 AACTATTTGGGCAGCATAAATAC
1 AACAAATTGGGCAGCATATATAC
* * *
35226877 AACAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* *
35226900 ACCAAAAATTGGACAGCATATATAC
1 A--ACAAATTGGGCAGCATATATAC
* *
35226925 AACAATTTGGGCAGCATAAATAC
1 AACAAATTGGGCAGCATATATAC
* * *
35226948 AACAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* *
35226971 ACCAAAAATCGGAG-AGCATATATAC
1 A--ACAAATTGG-GCAGCATATATAC
** *
35226996 AACAAATTGGATAGCATATATAT
1 AACAAATTGGGCAGCATATATAC
* * * *
35227019 ACCAAATTGAGCAGCATTTTTAC
1 AACAAATTGGGCAGCATATATAC
* * *
35227042 ACCAAAATTTGGACAGCATATATAT
1 AAC-AAA-TTGGGCAGCATATATAC
*
35227067 AACAATTTGGGCAGCAT
1 AACAAATTGGGCAGCAT
35227084 TGAAGCATCT
Statistics
Matches: 339, Mismatches: 90, Indels: 24
0.75 0.20 0.05
Matches are distributed among these distances:
23 232 0.68
24 41 0.12
25 65 0.19
26 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (23 bp):
AACAAATTGGGCAGCATATATAC
Found at i:35226800 original size:71 final size:71
Alignment explanation
Indices: 35226626--35227083 Score: 695
Period size: 71 Copynumber: 6.5 Consensus size: 71
35226616 CTGTAACAAT
* * * * * *
35226626 TTGGGCAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
35226691 C-AAAA
66 CAAAAA
35226696 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
35226761 CAAAAA
66 CAAAAA
* * * * * *
35226767 TTGGACAACATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
35226832 C-AAAA
66 CAAAAA
*
35226837 TTGGACAGCATATATACAACTATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
35226902 CAAAAA
66 CAAAAA
35226908 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
35226973 CAAAAA
66 CAAAAA
* * * ** * * *
35226979 TCGGAGAGCATATATACAACAAATTGGATAGCATATATATACCAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
*
35227044 CAAAAT
66 CAAAAA
*
35227050 TTGGACAGCATATATATAACAATTTGGGCAGCAT
1 TTGGACAGCATATATACAACAATTTGGGCAGCAT
35227084 TGAAGCATCT
Statistics
Matches: 351, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
70 123 0.35
71 228 0.65
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (71 bp):
TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
CAAAAA
Found at i:35226888 original size:141 final size:141
Alignment explanation
Indices: 35226626--35227083 Score: 736
Period size: 141 Copynumber: 3.2 Consensus size: 141
35226616 CTGTAACAAT
*
35226626 TTGGGCAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
35226691 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
66 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
35226756 TACACCAAAAA
131 TACACCAAAAA
*
35226767 TTGGACAACATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
*
35226832 CAAAATTGGACAGCATATATACAACTATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
66 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
35226897 TACACCAAAAA
131 TACACCAAAAA
* * * * *
35226908 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
* * * ** * * *
35226973 CAAAAATCGGAGAGCATATATACAACAAATTGGATAGCATATATATACCAAATTGAGCAGCATTT
66 C-AAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTT
*
35227038 TTACACCAAAAT
130 TTACACCAAAAA
* *
35227050 TTGGACAGCATATATATAACAATTTGGGCAGCAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCAT
35227084 TGAAGCATCT
Statistics
Matches: 296, Mismatches: 20, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
141 198 0.67
142 98 0.33
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (141 bp):
TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
TACACCAAAAA
Found at i:35227084 original size:48 final size:47
Alignment explanation
Indices: 35226626--35227083 Score: 360
Period size: 48 Copynumber: 9.7 Consensus size: 47
35226616 CTGTAACAAT
* *
35226626 TTGGGCAGCATATATACAACAAATTGGGCAGCATATATATACC-AAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAA
* * * * * *
35226672 TT-GAGCAGCATTTTTACATCAAAATTGGACAGCATATATACAAC-AAT
1 TTGGA-CAGCATATATACAAC-AAATTGGGCAGCATATATACACCAAAA
* * * * *
35226719 TTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACC-AAAA
* *
35226767 TTGGACAACATATATACAACAAATTGGGCAGCATATATATACC-AAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAA
* * * * * * *
35226813 TT-GAGCAGCATTTTTACATCAAAATTGGACAGCATATATACAAC-TAT
1 TTGGA-CAGCATATATACAAC-AAATTGGGCAGCATATATACACCAAAA
* * * * *
35226860 TTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACC-AAAA
* * *
35226908 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAAC-AAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAA
* * * * *
35226954 TT-GAGCAGCATTTTTACACCAAAAATCGGAG-AGCATATATACAAC-AAA
1 TTGGA-CAGCATATATACA--ACAAATTGG-GCAGCATATATACACCAAAA
* * * * * *
35227002 TTGGATAGCATATATATACCAAATTGAGCAGCATTTTTACACCAAAA
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAA
* *
35227049 TTTGGACAGCATATATATAACAATTTGGGCAGCAT
1 -TTGGACAGCATATATACAACAAATTGGGCAGCAT
35227084 TGAAGCATCT
Statistics
Matches: 318, Mismatches: 76, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
45 6 0.02
46 98 0.31
47 72 0.23
48 139 0.44
49 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (47 bp):
TTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAA
Found at i:35228152 original size:24 final size:24
Alignment explanation
Indices: 35228125--35228205 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 24
35228115 TCGAAAATAT
*
35228125 TTAATAAGTTCGCACACTTAGTGC
1 TTAATAAATTCGCACACTTAGTGC
35228149 TTAATAATCAATCTCGCACACTTAGTGC
1 TTAAT-A--AAT-TCGCACACTTAGTGC
*
35228177 TTTACAATTAAACTCGCACACTTAGTGC
1 -TT--AA-TAAATTCGCACACTTAGTGC
35228205 T
1 T
35228206 AATCTCATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
24 5 0.11
25 1 0.02
27 3 0.06
28 30 0.64
29 4 0.09
31 3 0.06
32 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (24 bp):
TTAATAAATTCGCACACTTAGTGC
Found at i:35228166 original size:28 final size:28
Alignment explanation
Indices: 35228134--35228205 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
35228124 TTTAATAAGT
* *
35228134 TCGCACACTTAGTGCTTAATAATCAATC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
35228162 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
35228190 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
35228206 AATCTCATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:35232321 original size:70 final size:67
Alignment explanation
Indices: 35232236--35232364 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 67
35232226 AATAAGGAAA
** *
35232236 GGCAAAACTAAGTCGTTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATTAAGT
1 GGCAAAACTAAGTCGTTTTGATAAATGTTTA-CTCAT-T-AAGTTAAAAGGCAAAACCATTAAGT
35232301 TAAAG
63 TAAAG
*
35232306 GGCAAAACTATGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
1 GGCAAAACTAAGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
35232365 TATTGTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 3 0.05
70 30 0.55
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (67 bp):
GGCAAAACTAAGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTAAGTTAA
AG
Found at i:35244392 original size:33 final size:33
Alignment explanation
Indices: 35244318--35244410 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
35244308 TATAGCATCC
* *
35244318 ACAGAGATAGTCTGCTGGGACAGTAAACACAGA
1 ACAGAGATAGTCTACTGGGACAGTAAACACAAA
* *
35244351 ACATAGATAGTCTACTGGGACAGTAAACATAAA
1 ACAGAGATAGTCTACTGGGACAGTAAACACAAA
* *
35244384 ATAGAGATAATCTA-TCGGGACAGTAAA
1 ACAGAGATAGTCTACT-GGGACAGTAAA
35244411 TATGAGTAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (33 bp):
ACAGAGATAGTCTACTGGGACAGTAAACACAAA
Found at i:35247933 original size:39 final size:39
Alignment explanation
Indices: 35247845--35247937 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
35247835 AAATAGAACC
** * *
35247845 TTGGCTTTGCAAAGGAATGTATAGGTTTTACTTTTGAAG
1 TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTTAAAG
*
35247884 TTGGCTTTGCGGAGGAATGTATATGCTTTA-TTTTCAAAG
1 TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTT-AAAG
*
35247923 TTGGTTTTGCGGAGG
1 TTGGCTTTGCGGAGG
35247938 GAAGTTGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.41
Consensus pattern (39 bp):
TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTTAAAG
Found at i:35248044 original size:26 final size:26
Alignment explanation
Indices: 35248008--35248624 Score: 490
Period size: 26 Copynumber: 23.6 Consensus size: 26
35247998 AGAGAGGAAG
*
35248008 GTGTGCTAGCTGTTATTACCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
*
35248034 GTGTGCCAGCTAG-TATTACCATGCCAT
1 GTGTGCGAGCT-GTTATTACCATG-CAT
*
35248061 GCATGTATGCGAGCTGTTATTAACATGCAT
1 G--TG--TGCGAGCTGTTATTACCATGCAT
* **
35248091 GTTTGCGATTTGTTATTACCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
35248117 GTGTGCGAGCTGTTATTACC-TAGCAT
1 GTGTGCGAGCTGTTATTACCAT-GCAT
* *
35248143 GTATGTGAGCTGTTATTACCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* * * *
35248169 GCGTGCG-GACTATTGTTACCTTGCAT
1 GTGTGCGAG-CTGTTATTACCATGCAT
* * * *
35248195 GTATGCGAGCTATTATTAACTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* *
35248221 GTATGTGAGCTGTTATTACCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* *
35248247 GTGT-CTGAGTTGTTATTACCTTGCAT
1 GTGTGC-GAGCTGTTATTACCATGCAT
* * * *
35248273 GTGTGCAAGCTATCATTACCTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
** * *
35248299 GAATG-TATGCTATTATTACCATGCAT
1 GTGTGCGA-GCTGTTATTACCATGCAT
* *
35248325 GT-CGCGAGCTGTTATTACCTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* * * * *
35248350 GTATACGAGTTTTTATTACCTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
** * * *
35248376 GAATGTGAGCTATTATTCCCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* *
35248402 GTGTGCGAGCTGTTATTACCTTGTAT
1 GTGTGCGAGCTGTTATTACCATGCAT
** *
35248428 GTGTATGAGCTGTTATTACCATACAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* * *
35248454 GTGTGTGAGCTATTATTGCCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* ** * *
35248480 GTGTGCAAATTTTTATTACCTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* ** * *
35248506 GTATATGAGATTTTATTACCATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* * * *
35248532 GTGTGCAAGTTGTTATTACCTTACAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* *
35248558 GTATGCGAGCTGTTATTACCTTGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
* * * *
35248584 GTATGTGAGTTGTTATTACAATGCAT
1 GTGTGCGAGCTGTTATTACCATGCAT
35248610 GTGTGCGAGCTGTTA
1 GTGTGCGAGCTGTTA
35248625 ATTGAAAGTA
Statistics
Matches: 471, Mismatches: 104, Indels: 32
0.78 0.17 0.05
Matches are distributed among these distances:
25 22 0.05
26 417 0.89
27 8 0.02
28 1 0.00
29 2 0.00
30 5 0.01
31 16 0.03
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (26 bp):
GTGTGCGAGCTGTTATTACCATGCAT
Found at i:35248061 original size:31 final size:31
Alignment explanation
Indices: 35248026--35248088 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
35248016 GCTGTTATTA
* *
35248026 CCATGCATGTGTGCCAGCTAG-TATTACCATG
1 CCATGCATGTATGCCAGCT-GTTATTAACATG
*
35248057 CCATGCATGTATGCGAGCTGTTATTAACATG
1 CCATGCATGTATGCCAGCTGTTATTAACATG
35248088 C
1 C
35248089 ATGTTTGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (31 bp):
CCATGCATGTATGCCAGCTGTTATTAACATG
Found at i:35271113 original size:25 final size:26
Alignment explanation
Indices: 35271085--35271133 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
35271075 TTTCATCCCT
35271085 ATTTTACCC-CAGTAAAATTTTGATG
1 ATTTTACCCTCAGTAAAATTTTGATG
**
35271110 ATTTTACCCTTGGTAAAATTTTGA
1 ATTTTACCCTCAGTAAAATTTTGA
35271134 AAAAGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTCAGTAAAATTTTGATG
Found at i:35272796 original size:27 final size:26
Alignment explanation
Indices: 35272764--35273031 Score: 286
Period size: 27 Copynumber: 9.9 Consensus size: 26
35272754 GAAGATTACC
*
35272764 GAAATACCCTCGAGGGGTAAAATTACT
1 GAAATACCCTCGAAGGGTAAAATTA-T
* * *
35272791 AAAATACCCTCGAATGGTACAATTACT
1 GAAATACCCTCGAAGGGTAAAATTA-T
*
35272818 GAAATACCCTCAAAGGGTAAAATTAT
1 GAAATACCCTCGAAGGGTAAAATTAT
*
35272844 CGAAATAACCCT-AAAGGGTAAAATTAT
1 -GAAAT-ACCCTCGAAGGGTAAAATTAT
35272871 CGAAATACCCTCGAAGGGTAAAATTAT
1 -GAAATACCCTCGAAGGGTAAAATTAT
*
35272898 CGAAATACCCTCGAAGGGTAAAATTACC
1 -GAAATACCCTCGAAGGGTAAAATTA-T
* * *
35272926 GAAATACTCTTGAAGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTA-T
* * * *
35272953 AAAATACCCTTGAATGGTAAAATGATT
1 GAAATACCCTCGAAGGGTAAAATTA-T
*
35272980 GAAATACCCTCGAAGGGGTAAAATGAT
1 GAAATACCCTCGAA-GGGTAAAATTAT
35273007 CGAAATACCCTCGAAAGGGTAAAAT
1 -GAAATACCCTCG-AAGGGTAAAAT
35273032 GACCATTATA
Statistics
Matches: 213, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
26 6 0.03
27 169 0.79
28 36 0.17
29 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (26 bp):
GAAATACCCTCGAAGGGTAAAATTAT
Found at i:35272836 original size:54 final size:54
Alignment explanation
Indices: 35272758--35273031 Score: 329
Period size: 54 Copynumber: 5.0 Consensus size: 54
35272748 TGGACCGAAG
* * * * *
35272758 ATTACCGAAATACCCTCGAGGGGTAAAATTA-CTAAAATACCCTCGAATGGTACA
1 ATTACTGAAATACCCTCGAAGGGTAAAATTATC-GAAATACCCTCGAAGGGTAAA
* *
35272812 ATTACTGAAATACCCTCAAAGGGTAAAATTATCGAAATAACCCT-AAAGGGTAAA
1 ATTACTGAAATACCCTCGAAGGGTAAAATTATCGAAAT-ACCCTCGAAGGGTAAA
35272866 ATTA-TCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAA
1 ATTACT-GAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAA
* * * * * * *
35272920 ATTACCGAAATACTCTTGAAGGGTAAAATTACCAAAATACCCTTGAATGGTAAA
1 ATTACTGAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAA
* * *
35272974 ATGATTGAAATACCCTCGAAGGGGTAAAATGATCGAAATACCCTCGAAAGGGTAAA
1 ATTACTGAAATACCCTCGAA-GGGTAAAATTATCGAAATACCCTCG-AAGGGTAAA
35273030 AT
1 AT
35273032 GACCATTATA
Statistics
Matches: 187, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
53 6 0.03
54 144 0.77
55 27 0.14
56 10 0.05
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (54 bp):
ATTACTGAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAA
Found at i:35272903 original size:81 final size:79
Alignment explanation
Indices: 35272758--35273031 Score: 316
Period size: 81 Copynumber: 3.4 Consensus size: 79
35272748 TGGACCGAAG
* * * *
35272758 ATTACCGAAATACCCTCGAGGGGTAAAATTACTAAAATACCCTCGAATGGTACAATTA-CTGAAA
1 ATTATCGAAATACCCT-AAAGGGTAAAATTAC-AAAATACCCTCGAATGGTAAAATTATC-GAAA
35272822 TACCCTCAAAGGGTAAA
63 TACCCTCAAAGGGTAAA
* *
35272839 ATTATCGAAATAACCCTAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTATCGAAAT
1 ATTATCGAAAT-ACCCTAAAGGGTAAAATTA-CAAAATACCCTCGAATGGTAAAATTATCGAAAT
*
35272904 ACCCTCGAAGGGTAAA
64 ACCCTCAAAGGGTAAA
* * * * * *
35272920 ATTACCGAAATACTCTTGAAGGGTAAAATTACCAAAATACCCTTGAATGGTAAAATGATTGAAAT
1 ATTATCGAAATAC-CCTAAAGGGTAAAATTA-CAAAATACCCTCGAATGGTAAAATTATCGAAAT
*
35272985 ACCCTCGAAGGGGTAAA
64 ACCCTC-AAAGGGTAAA
*
35273002 ATGATCGAAATACCCTCGAAAGGGTAAAAT
1 ATTATCGAAATACCCT--AAAGGGTAAAAT
35273032 GACCATTATA
Statistics
Matches: 164, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
80 2 0.01
81 125 0.76
82 26 0.16
83 11 0.07
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (79 bp):
ATTATCGAAATACCCTAAAGGGTAAAATTACAAAATACCCTCGAATGGTAAAATTATCGAAATAC
CCTCAAAGGGTAAA
Found at i:35273258 original size:26 final size:26
Alignment explanation
Indices: 35273227--35273297 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
35273217 CCACATATAA
* *
35273227 TGTTACTGGCAGCTTTGTTGCGTTAC
1 TGTTACTGGCAGCTTTGCTACGTTAC
*
35273253 TGTTACTGGCAGCTTTGCTACGTTAT
1 TGTTACTGGCAGCTTTGCTACGTTAC
*
35273279 TATTACTGGCAGCTTTGCT
1 TGTTACTGGCAGCTTTGCT
35273298 TCGATATTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTACGTTAC
Found at i:35273305 original size:26 final size:26
Alignment explanation
Indices: 35273229--35273305 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
35273219 ACATATAATG
* *
35273229 TTACTGGCAGCTTTG-TTGCGTTACTG
1 TTACTGGCAGCTTTGCTT-CGTTATTA
*
35273255 TTACTGGCAGCTTTGCTACGTTATTA
1 TTACTGGCAGCTTTGCTTCGTTATTA
*
35273281 TTACTGGCAGCTTTGCTTCGATATT
1 TTACTGGCAGCTTTGCTTCGTTATT
35273306 GGTGTGTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 44 0.98
27 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTTCGTTATTA
Found at i:35273430 original size:28 final size:28
Alignment explanation
Indices: 35273390--35273474 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
35273380 ATTGTACCGA
* * * *
35273390 TTACTGTTTTGGGCTAATGCCCATATTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
35273418 TTACTGTATTGGGCTAAGGCTCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
35273446 TTACTGTAATGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
35273474 T
1 T
35273475 ACTTATACTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:35273493 original size:33 final size:28
Alignment explanation
Indices: 35273390--35273501 Score: 91
Period size: 28 Copynumber: 3.8 Consensus size: 28
35273380 ATTGTACCGA
* * * * *
35273390 TTACTGTTTTGGGCTAATGCCCATATTG
1 TTACTGTATAGGGCTAAGGCCCACACTG
* *
35273418 TTACTGTATTGGGCTAAGGCTCACACTG
1 TTACTGTATAGGGCTAAGGCCCACACTG
35273446 TTACTGTA-ATGGGCTAAGGCCCACACTG
1 TTACTGTATA-GGGCTAAGGCCCACACTG
*
35273474 TACTTATACTGTATAGGGCTCAGGCCCA
1 ----T-TACTGTATAGGGCTAAGGCCCA
35273502 GATTGATTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
28 48 0.70
32 1 0.01
33 19 0.28
34 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (28 bp):
TTACTGTATAGGGCTAAGGCCCACACTG
Found at i:35275404 original size:10 final size:10
Alignment explanation
Indices: 35275372--35275411 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
35275362 TAAAAGAATG
35275372 AATTTTAATT
1 AATTTTAATT
35275382 AATTCTATAATT
1 AATT-T-TAATT
*
35275394 AATTTTGATT
1 AATTTTAATT
35275404 AATTTTAA
1 AATTTTAA
35275412 CTATTTTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (10 bp):
AATTTTAATT
Found at i:35280547 original size:29 final size:29
Alignment explanation
Indices: 35280486--35280547 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
35280476 TGATTATATT
* *
35280486 TTATCAAGTACTATGTACCGGTGACTATA
1 TTATCAAGTACTATGTACCGATGACCATA
* * * *
35280515 TTATCAGGTACTTTGTACCGATGTCCATG
1 TTATCAAGTACTATGTACCGATGACCATA
35280544 TTAT
1 TTAT
35280548 ACTAGGCATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (29 bp):
TTATCAAGTACTATGTACCGATGACCATA
Found at i:35291428 original size:48 final size:48
Alignment explanation
Indices: 35291357--35291450 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
35291347 CTGAGGACCG
35291357 GATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAAACCC
1 GATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAAACCC
*
35291405 GATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGGAAAC
1 GATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAAAC
35291451 TTAATTGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (48 bp):
GATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAAACCC
Found at i:35291822 original size:33 final size:34
Alignment explanation
Indices: 35291728--35291978 Score: 286
Period size: 32 Copynumber: 7.6 Consensus size: 34
35291718 AGAGAATATT
*
35291728 TCCTGTTCACGCATTATTCTGTTGCAGGG-ATCTT
1 TCCTGTTCACGCATTATT-TGTTGCAGGGAATCTC
* *
35291762 TCCTGTTCA--CATCATTTCTTGCA-GGAATCTC
1 TCCTGTTCACGCATTATTTGTTGCAGGGAATCTC
35291793 TCCTGTTCACGCATTATTTGTTGCA-GGAATCTC
1 TCCTGTTCACGCATTATTTGTTGCAGGGAATCTC
* *
35291826 TCCTGTTCACACATTATTTTGTTGCAGGGAATCTT
1 TCCTGTTCACGCATTA-TTTGTTGCAGGGAATCTC
* *
35291861 TCCTGTTCA--CATCATTTCTTGCAGGGAATCTC
1 TCCTGTTCACGCATTATTTGTTGCAGGGAATCTC
35291893 TCCTGTTCACGCATTATTTTGTTGCAGGGAATCTC
1 TCCTGTTCACGCATTA-TTTGTTGCAGGGAATCTC
* ** *
35291928 TCATGTTCA--CATCGTTTCTTGCAGGGAATCTC
1 TCCTGTTCACGCATTATTTGTTGCAGGGAATCTC
* * *
35291960 TCCTATTCATGTATTATTT
1 TCCTGTTCACGCATTATTT
35291979 CTTTTTGGAC
Statistics
Matches: 186, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.01
31 19 0.10
32 55 0.30
33 42 0.23
34 27 0.15
35 41 0.22
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (34 bp):
TCCTGTTCACGCATTATTTGTTGCAGGGAATCTC
Found at i:35291950 original size:99 final size:98
Alignment explanation
Indices: 35291749--35291968 Score: 329
Period size: 99 Copynumber: 2.2 Consensus size: 98
35291739 CATTATTCTG
35291749 TTGCAGGG-ATCTTTCCTGTTCACATCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTATTTG
1 TTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTATTTG
* * *
35291813 TTGCAGGAATCTCTCCTGTTCACACATTATTTTG
66 TTGCAGGAATCTCTCATGTT-ACACATTAGTTTC
35291847 TTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
1 TTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCA-GGAATCTCTCCTGTTCACGCATTA-TT
*
35291912 TGTTGCAGGGAATCTCTCATGTT-CACA-TCGTTTC
64 TGTTGCA-GGAATCTCTCATGTTACACATTAGTTTC
* *
35291946 TTGCAGGGAATCTCTCCTATTCA
1 TTGCAGGGAATCTTTCCTGTTCA
35291969 TGTATTATTT
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
98 8 0.07
99 53 0.47
100 28 0.25
101 9 0.08
102 14 0.12
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.40
Consensus pattern (98 bp):
TTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTATTTG
TTGCAGGAATCTCTCATGTTACACATTAGTTTC
Found at i:35291976 original size:67 final size:67
Alignment explanation
Indices: 35291749--35291978 Score: 292
Period size: 67 Copynumber: 3.5 Consensus size: 67
35291739 CATTATTCTG
* * * *
35291749 TTGCAGGG-ATCTTTCCTGTTCA--CATCA-TTTCTTGCA-GGAATCTCTCCTGTTCACGCATTA
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCA--CATCA
*
35291809 TTTG
64 TTTC
* *
35291813 TTGCA-GGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACATCATT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT
35291877 TC
66 TC
* *
35291879 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACATCGTT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT
35291944 TC
66 TC
* * *
35291946 TTGCAGGGAATCTCTCCTATTCATGTATTATTT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTT
35291979 CTTTTTGGAC
Statistics
Matches: 147, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
63 2 0.01
64 18 0.12
66 16 0.11
67 95 0.65
68 16 0.11
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (67 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT
TC
Found at i:35294797 original size:20 final size:22
Alignment explanation
Indices: 35294760--35294803 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
35294750 GAGCAAATCG
35294760 TTGATTCTATTTCTTTTTG-AT
1 TTGATTCTATTTCTTTTTGTAT
35294781 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTC-TTTTTGTAT
35294802 TT
1 TT
35294804 CTCTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTGATTCTATTTCTTTTTGTAT
Found at i:35302519 original size:23 final size:23
Alignment explanation
Indices: 35302476--35302520 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35302466 GAGAATGCAA
**
35302476 AAAAAAAGAGCATGAGGGAAAAG
1 AAAAAAAGAGCATGAAAGAAAAG
35302499 AAAAAAAGAGCGAT-AAAGAAAA
1 AAAAAAAGAGC-ATGAAAGAAAA
35302521 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (23 bp):
AAAAAAAGAGCATGAAAGAAAAG
Found at i:35302521 original size:24 final size:23
Alignment explanation
Indices: 35302476--35302526 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
35302466 GAGAATGCAA
* * *
35302476 AAAAAAAGAGCATGAGGGAAAAG
1 AAAAAAAGAGCATAAAGAAAAAG
*
35302499 AAAAAAAGAGCGATAAAGAAAAAT
1 AAAAAAAGAGC-ATAAAGAAAAAG
35302523 AAAA
1 AAAA
35302527 GAAAAACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.06
Consensus pattern (23 bp):
AAAAAAAGAGCATAAAGAAAAAG
Found at i:35305671 original size:55 final size:55
Alignment explanation
Indices: 35305596--35305700 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
35305586 TAAAGTTGTG
* **
35305596 TTTATGTTTCATTGAATGTTTTGTTGTATTCATAAATAAAGTTGTGTTTTCTTTA
1 TTTATGTTTCATTGAATGTTTTGTTGCATTCATAAATAAAGCGGTGTTTTCTTTA
*
35305651 TTTATGTTTTATT-AATTGTTTTGTTGCATTCATAAATAAAGCGGTGTTTT
1 TTTATGTTTCATTGAA-TGTTTTGTTGCATTCATAAATAAAGCGGTGTTTT
35305701 TAATTATGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 2 0.04
55 43 0.96
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (55 bp):
TTTATGTTTCATTGAATGTTTTGTTGCATTCATAAATAAAGCGGTGTTTTCTTTA
Found at i:35305718 original size:55 final size:52
Alignment explanation
Indices: 35305612--35305733 Score: 124
Period size: 55 Copynumber: 2.3 Consensus size: 52
35305602 TTTCATTGAA
* * * *
35305612 TGTTTTGTTGTATTCATAAATAAAGTTGTGTTTTCTTTATTTATGTTTTATTAAT
1 TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATGTTTTA-T--T
35305667 TGTTTTGTTGCATTCATAAATAAAG-CG-GTGTT-TTTAATTATGCTTCATTATT
1 TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATG-TT--TTATT
35305719 TGTTTTTGTTGCATT
1 TG-TTTTGTTGCATT
35305734 TATTTTTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
52 12 0.20
53 18 0.31
54 2 0.03
55 27 0.46
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (52 bp):
TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATGTTTTATT
Found at i:35309059 original size:12 final size:12
Alignment explanation
Indices: 35309038--35309071 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35309028 TGGGCTTTCA
35309038 TTTTCCTTTTTTG
1 TTTT-CTTTTTTG
*
35309051 TTTTGTTTTTTG
1 TTTTCTTTTTTG
35309063 TTTTCTTTT
1 TTTTCTTTT
35309072 GTACTAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:35317567 original size:10 final size:11
Alignment explanation
Indices: 35317541--35317573 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
35317531 AGTTAAGATT
35317541 AAAACTTCTGGA
1 AAAACTTCT-GA
35317553 AAAACTTCT-A
1 AAAACTTCTGA
35317563 AAAACTTCTGA
1 AAAACTTCTGA
35317574 TAAATACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 1 0.05
12 9 0.45
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (11 bp):
AAAACTTCTGA
Found at i:35327167 original size:21 final size:22
Alignment explanation
Indices: 35327126--35327169 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
35327116 CTTATTTTGT
*
35327126 GGAGAAATAAGAGGTGAGAGAA
1 GGAGAAATAAGAGGGGAGAGAA
35327148 GGAGAAATAA-AGGGGAGAGAA
1 GGAGAAATAAGAGGGGAGAGAA
35327169 G
1 G
35327170 TATGTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (22 bp):
GGAGAAATAAGAGGGGAGAGAA
Found at i:35330278 original size:39 final size:39
Alignment explanation
Indices: 35330224--35330362 Score: 197
Period size: 39 Copynumber: 3.6 Consensus size: 39
35330214 CATATTCACT
* * * *
35330224 TTTAAGTATATATCACATTACTTATATAGTGACAAAACA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
*
35330263 TTTAAGCATCTATCACAATACTTATATAATCACAAAACA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
* * *
35330302 TTTAAGCATATATCACAATACTCATATAATCACAGAATA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
*
35330341 TTTAAGCATATATCGCAATACT
1 TTTAAGCATATATCACAATACT
35330363 CAAAAACATG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 90 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTTATATAATCACAAAACA
Found at i:35330280 original size:22 final size:21
Alignment explanation
Indices: 35330255--35330319 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
35330245 TTATATAGTG
35330255 ACAAAACATTTAAGCATCTATC
1 ACAAAACATTTAAGCAT-TATC
* * *
35330277 ACAATAC--TT-A-TATAATC
1 ACAAAACATTTAAGCATTATC
35330294 ACAAAACATTTAAGCATATATC
1 ACAAAACATTTAAGCAT-TATC
35330316 ACAA
1 ACAA
35330320 TACTCATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 9 0.28
18 2 0.06
19 3 0.09
20 3 0.09
21 2 0.06
22 13 0.41
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (21 bp):
ACAAAACATTTAAGCATTATC
Found at i:35330296 original size:17 final size:17
Alignment explanation
Indices: 35330274--35330335 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
35330264 TTAAGCATCT
35330274 ATCACAATACTTATATA
1 ATCACAATACTTATATA
* *
35330291 ATCACAAAACATTTAAGCATA
1 ATCACAATAC--TT-A-TATA
*
35330312 TATCACAATACTCATATA
1 -ATCACAATACTTATATA
35330330 ATCACA
1 ATCACA
35330336 GAATATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 15 0.43
18 3 0.09
19 3 0.09
20 2 0.06
21 3 0.09
22 9 0.26
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (17 bp):
ATCACAATACTTATATA
Found at i:35331972 original size:32 final size:32
Alignment explanation
Indices: 35331936--35332028 Score: 177
Period size: 32 Copynumber: 2.9 Consensus size: 32
35331926 TTTTCTAAAA
35331936 AACCATAATCGAAAACATTACCAATAAACCAT
1 AACCATAATCGAAAACATTACCAATAAACCAT
35331968 AACCATAATCGAAAACATTACCAATAAACCAT
1 AACCATAATCGAAAACATTACCAATAAACCAT
*
35332000 GACCATAATCGAAAACATTACCAATAAAC
1 AACCATAATCGAAAACATTACCAATAAAC
35332029 TATGTCACAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.53, C:0.25, G:0.04, T:0.18
Consensus pattern (32 bp):
AACCATAATCGAAAACATTACCAATAAACCAT
Found at i:35332026 original size:19 final size:18
Alignment explanation
Indices: 35331937--35332022 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 18
35331927 TTTCTAAAAA
35331937 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
* *
35331955 ACC--AAT--AAACCATA
1 ACCATAATCGAAAACATT
35331969 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
* *
35331987 ACC--AAT--AAACCATG
1 ACCATAATCGAAAACATT
35332001 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
35332019 ACCA
1 ACCA
35332023 ATAAACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 18 0.35
16 12 0.23
18 22 0.42
ACGTcount: A:0.51, C:0.26, G:0.05, T:0.19
Consensus pattern (18 bp):
ACCATAATCGAAAACATT
Found at i:35343705 original size:125 final size:125
Alignment explanation
Indices: 35343483--35343771 Score: 427
Period size: 125 Copynumber: 2.3 Consensus size: 125
35343473 TTTTTTTAAG
* * * * *
35343483 GAAATCACTCCCATGTGAACACACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTTGAGTAGAC
1 GAAATCACTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGAA
*
35343548 GTTTCTAAGCAAATAATGTCAAAAATGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
66 GTTTCTAAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
* *
35343608 GAAATCGA-TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGA
1 GAAATC-ACTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGA
* * * *
35343672 AGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACT
65 AGTTTCTAAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
* * *
35343733 GAAATCACTTCCATGTGGACGCACTTTTTCTACAGTAGC
1 GAAATCACTCCCACGTGGACGCACTTTTGCTACAGTAGC
35343772 GCATGTTTGG
Statistics
Matches: 146, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.01
125 144 0.99
126 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (125 bp):
GAAATCACTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGAA
GTTTCTAAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
Found at i:35344329 original size:24 final size:24
Alignment explanation
Indices: 35344302--35344347 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35344292 GTAGCGATAT
* *
35344302 GGAATACACATCCTTGACGAAGTA
1 GGAAAACACATCCTTGAAGAAGTA
*
35344326 GGAAAACACTTCCTTGAAGAAG
1 GGAAAACACATCCTTGAAGAAG
35344348 CGTTTTGTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (24 bp):
GGAAAACACATCCTTGAAGAAGTA
Found at i:35344861 original size:123 final size:124
Alignment explanation
Indices: 35344648--35344926 Score: 452
Period size: 123 Copynumber: 2.2 Consensus size: 124
35344638 AGGAAATCGC
* * *
35344648 TCCCACGTAGACGCGTTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACATTTCTGA
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCT-AAAAAATAATTTCGAGTAGACATTTCTGA
35344713 GCAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
65 GCAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
* *
35344773 TCCCACGTGGACGCGCTTTTGCTACAATAGCTCCT-AAAAATAATTTCGAGTAGACGTTTCTGAG
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAATAATTTCGAGTAGACATTTCTGAG
** * * *
35344837 CAAATAGTGTCAAAAATGCTTTAAACAGGATGCATTGTTAGCAAAAGTATTGAAATCGA
66 CAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
35344896 TCCCACGTGGACGCGCTTTTGCTACAGTAGC
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGC
35344927 GCATGTTTGG
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 112 0.78
125 31 0.22
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (124 bp):
TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAATAATTTCGAGTAGACATTTCTGAG
CAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
Found at i:35345532 original size:7 final size:7
Alignment explanation
Indices: 35345520--35345576 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
35345510 TGCCCTGCCG
35345520 TTAGGGT
1 TTAGGGT
35345527 TTAGGGT
1 TTAGGGT
35345534 TTAGGG-
1 TTAGGGT
35345540 TTAGGGT
1 TTAGGGT
* *
35345547 TAAGGTT
1 TTAGGGT
35345554 TTAGGGTT
1 TTAGGG-T
35345562 TTA-GGT
1 TTAGGGT
35345568 TTAGGGT
1 TTAGGGT
35345575 TT
1 TT
35345577 TAGAGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 10 0.23
7 29 0.67
8 4 0.09
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:35345579 original size:14 final size:13
Alignment explanation
Indices: 35345524--35345576 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
35345514 CTGCCGTTAG
35345524 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
* *
35345537 GGGTTAGGGTTAA
1 GGTTTAGGGTTTA
35345550 GGTTTTAGGGTTTTA
1 GG-TTTAGGG-TTTA
35345565 GGTTTAGGGTTT
1 GGTTTAGGGTTT
35345577 TAGAGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 16 0.47
14 13 0.38
15 5 0.15
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:35345964 original size:123 final size:125
Alignment explanation
Indices: 35345750--35346034 Score: 398
Period size: 123 Copynumber: 2.3 Consensus size: 125
35345740 AAGGAAATCG
* * *
35345750 CTCCCACA-TGGACGCGCTTTTTCTACAATAGCTCCTGAAAAAATAATTTCGAATAGACATTTCT
1 CTCCCA-AGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAATAGACATTTCT
*
35345814 AAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
65 AAGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAAT-AA
* * * *
35345876 -TCCCAAGTGGACGCGCTTTTGCTACTGTAGCTCATG-AAAAA-AATTTCGAGTAGACGTTTCTG
1 CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAATAGACATTTCTA
* * * *
35345938 AGCAAATAGTGTAAAAAATGCTTTAAATAGGATGCTTTGTTAGCAAAAGTACTGAAATAA
66 AGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATAA
* *
35345998 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCGCATG
1 CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATG
35346035 TTTGGCCTGA
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
122 2 0.01
123 104 0.73
124 6 0.04
125 30 0.21
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (125 bp):
CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAATAGACATTTCTA
AGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATAA
Found at i:35350384 original size:14 final size:15
Alignment explanation
Indices: 35350367--35350399 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35350357 TTATATACAT
35350367 AATACAT-AATACTA
1 AATACATAAATACTA
35350381 AATA-ATAAATACTA
1 AATACATAAATACTA
35350395 AATAC
1 AATAC
35350400 CAATCGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
AATACATAAATACTA
Found at i:35351532 original size:14 final size:14
Alignment explanation
Indices: 35351503--35351532 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
35351493 TTTACGATTT
35351503 AAAAAAAATTTAAA
1 AAAAAAAATTTAAA
35351517 AAAATAAAATTTAAA
1 AAAA-AAAATTTAAA
35351532 A
1 A
35351533 CTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAAAATTTAAA
Found at i:35351598 original size:22 final size:23
Alignment explanation
Indices: 35351573--35351630 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 23
35351563 TTTTTTAAAT
35351573 AGGAAATTGAGAG-GAA-ATTGAG
1 AGGAAATTGAGAGAGAATATT-AG
35351595 AGG-AATTG-GAGAGAATATTAG
1 AGGAAATTGAGAGAGAATATTAG
*
35351616 AGATAAATTGAGAGA
1 AG-GAAATTGAGAGA
35351631 AAGGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 3 0.10
21 12 0.40
22 6 0.20
23 5 0.17
24 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (23 bp):
AGGAAATTGAGAGAGAATATTAG
Found at i:35351628 original size:10 final size:10
Alignment explanation
Indices: 35351575--35351632 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
35351565 TTTTAAATAG
35351575 GAAATTGAGA
1 GAAATTGAGA
35351585 GGAAATTGAGA
1 -GAAATTGAGA
*
35351596 GGAATTGGAGA
1 GAAATT-GAGA
35351607 GAATATTAGAGA
1 GAA-ATT-GAGA
*
35351619 TAAATTGAGA
1 GAAATTGAGA
35351629 GAAA
1 GAAA
35351633 GGATTAAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 12 0.30
11 19 0.47
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:35352364 original size:18 final size:18
Alignment explanation
Indices: 35352340--35352378 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35352330 AAAATAAAAT
*
35352340 TATATAATTGTAGGATTTAA
1 TATA-AATTG-AGCATTTAA
35352360 TATAAATTGAGCATTTAA
1 TATAAATTGAGCATTTAA
35352378 T
1 T
35352379 CTATTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (18 bp):
TATAAATTGAGCATTTAA
Found at i:35361900 original size:14 final size:15
Alignment explanation
Indices: 35361873--35361907 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
35361863 TTGGGTGAGT
*
35361873 TTTTTATTTATTATA
1 TTTTAATTTATTATA
35361888 TTTTAATTT-TTATA
1 TTTTAATTTATTATA
35361902 TTTTAA
1 TTTTAA
35361908 ATGTGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTATTATA
Found at i:35362722 original size:19 final size:20
Alignment explanation
Indices: 35362698--35362745 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
35362688 TTATAATTTA
*
35362698 AAAATTAAGTAAATT-AATT
1 AAAATTAAGTAAATTAAAGT
*
35362717 AAAATTAA-TTAATTAAAGT
1 AAAATTAAGTAAATTAAAGT
35362736 AAAATTAAGT
1 AAAATTAAGT
35362746 TAGAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 19 0.76
20 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAATTAAGTAAATTAAAGT
Found at i:35364508 original size:38 final size:38
Alignment explanation
Indices: 35364417--35364500 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
35364407 AGAACATGAA
** *
35364417 TACATATTAAACATGTTTACTTTTAATGATGAATTGCG
1 TACATATTAAACATGTTTACGATTAATGATGAATTGAG
* *
35364455 TACATGTTAAACATGTTTACGATTAGTGATGAATTGAG
1 TACATATTAAACATGTTTACGATTAATGATGAATTGAG
35364493 TACATATT
1 TACATATT
35364501 GTACATGTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (38 bp):
TACATATTAAACATGTTTACGATTAATGATGAATTGAG
Found at i:35364520 original size:38 final size:38
Alignment explanation
Indices: 35364417--35364520 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 38
35364407 AGAACATGAA
* *** * *
35364417 TACATATTAAACATGTTTACTTTTAATGATGAATTGCG
1 TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
* * *
35364455 TACATGTTAAACATGTTTACGATTAGTGATGAATTGAG
1 TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
**
35364493 TACATATTGTACATGTCTACTG-CTAGTG
1 TACATATTAAACATGTCTAC-GACTAGTG
35364521 TTGAGTTGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 54 0.98
39 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (38 bp):
TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
Found at i:35364736 original size:43 final size:43
Alignment explanation
Indices: 35364647--35364780 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 43
35364637 GTATTTTTCC
* * * **
35364647 TTTAACTGCAAGTATGTTGTGCATCCAGAACCTAGTGGCAGCT
1 TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
* * *
35364690 TTTACCTGCAATTATGTAGTGCATCCACAGTCTAGTGGCAAAT
1 TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
** * * * *
35364733 TTTATTTGCGAATTTTGTTGTGTACCCATAGCCTAGTGGCAAAT
1 TTTAACTGC-AATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
35364777 TTTA
1 TTTA
35364781 TTTGCGAATT
Statistics
Matches: 74, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 42 0.57
44 32 0.43
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (43 bp):
TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
Found at i:35364866 original size:44 final size:44
Alignment explanation
Indices: 35364712--35364874 Score: 125
Period size: 44 Copynumber: 3.8 Consensus size: 44
35364702 TATGTAGTGC
* * * * * *
35364712 ATCCACAGTCTAGTGGCAAATTTTATTTGCGAATTTTGTTGTGT
1 ATCCACAGCCCAGTGGCAAATTTTATCTGCAAATTTTGCTATGT
* * * * *
35364756 ACCCATAGCCTAGTGGCAAATTTTATTTGCGAATTTT-CTATGT
1 ATCCACAGCCCAGTGGCAAATTTTATCTGCAAATTTTGCTATGT
* * ** ***
35364799 ATTCATAGTTCA-TCGGTTGATTTTATCTGCAAATTTTGCTATGT
1 ATCCACAGCCCAGT-GGCAAATTTTATCTGCAAATTTTGCTATGT
*
35364843 ATCCACAGCCCAGTGGCGAATTTT-TCTGCAAA
1 ATCCACAGCCCAGTGGCAAATTTTATCTGCAAA
35364875 CCAGTGATGG
Statistics
Matches: 94, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
42 1 0.01
43 37 0.39
44 55 0.59
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (44 bp):
ATCCACAGCCCAGTGGCAAATTTTATCTGCAAATTTTGCTATGT
Found at i:35365872 original size:91 final size:90
Alignment explanation
Indices: 35365734--35365960 Score: 257
Period size: 91 Copynumber: 2.5 Consensus size: 90
35365724 TCAGGGTGCA
* * * * ** * *
35365734 AAAAGCCCTCAAA-CTTTT-TCAAAAAAAGCAATTGAGCCTTTGGTTTTTTTTGCACTCATTTGG
1 AAAAGCCCTTAAACCTTTTCTAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTGCACTCAATTCG
35365797 GTACTTGAACTTTCAAAATGCAT-C
66 GTACTTGAACTTTCAAAATGCATCC
*
35365821 AGAAAGGCCCTTAAACCTTTTCTAAAAAAAAGCAATTAATCCCTTACTTTTTTTTGCACTCAATT
1 A-AAA-GCCCTTAAACCTTTTCTAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTGCACTCAATT
*
35365886 CGGTACTTGAACTTTCAAAATGTATCC
64 CGGTACTTGAACTTTCAAAATGCATCC
* * * * *
35365913 AAAAGACCTTCAAACTTTTTC-AGAAAAAA-CAATTAAGCCATTGCTTTT
1 AAAAGCCCTT-AAACCTTTTCTAAAAAAAAGCAATTAAGCCCTTACTTTT
35365961 ATTAAAAATT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
87 1 0.01
88 3 0.03
89 24 0.20
90 17 0.14
91 71 0.60
92 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (90 bp):
AAAAGCCCTTAAACCTTTTCTAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTGCACTCAATTCG
GTACTTGAACTTTCAAAATGCATCC
Found at i:35366110 original size:10 final size:10
Alignment explanation
Indices: 35366093--35366118 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35366083 TCTTAAAAAA
35366093 TATAAAATTT
1 TATAAAATTT
35366103 TATAAAATTT
1 TATAAAATTT
35366113 TATAAA
1 TATAAA
35366119 GTTGTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATAAAATTT
Found at i:35366365 original size:29 final size:28
Alignment explanation
Indices: 35366308--35366362 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
35366298 CCAGGGGTCG
*
35366308 TTATTTTTTTATGATTTTTATAAAAAAT
1 TTATTTATTTATGATTTTTATAAAAAAT
35366336 TTATTTATTTATGATTTTTATAAAAAA
1 TTATTTATTTATGATTTTTATAAAAAA
35366363 ATTCTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
TTATTTATTTATGATTTTTATAAAAAAT
Found at i:35366375 original size:29 final size:27
Alignment explanation
Indices: 35366313--35366375 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 27
35366303 GGTCGTTATT
*
35366313 TTTTTATGATTTTTATAAAAAATTTAT
1 TTTTTATGATTTTTATAAAAAATTTAA
35366340 TTATTTATGATTTTTATAAAAAAATTCTAA
1 TT-TTTATGATTTTTAT-AAAAAATT-TAA
35366370 TTTTTA
1 TTTTTA
35366376 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 2 0.06
28 14 0.44
29 12 0.38
30 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTTATGATTTTTATAAAAAATTTAA
Found at i:35373719 original size:61 final size:61
Alignment explanation
Indices: 35373649--35373772 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
35373639 TTTAATCCTT
35373649 AACACTTTTTTTAATCAATTTGATTCTATTCTTCATCAGTTCTTTTTTTTTGTAACAAGAA
1 AACACTTTTTTTAATCAATTTGATTCTATTCTTCATCAGTTCTTTTTTTTTGTAACAAGAA
35373710 AACACTTTTTTTAATCAATTTGATTCTATTCTTCATCAGTTCTTTTTTTTTGTAACAAGAA
1 AACACTTTTTTTAATCAATTTGATTCTATTCTTCATCAGTTCTTTTTTTTTGTAACAAGAA
35373771 AA
1 AA
35373773 AGTATTAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (61 bp):
AACACTTTTTTTAATCAATTTGATTCTATTCTTCATCAGTTCTTTTTTTTTGTAACAAGAA
Found at i:35383187 original size:4 final size:4
Alignment explanation
Indices: 35383178--35383211 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
35383168 AGTATACATA
35383178 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
35383212 CAGACAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (4 bp):
AGTT
Found at i:35384690 original size:7 final size:7
Alignment explanation
Indices: 35384674--35384708 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
35384664 ATTACGATTT
*
35384674 ATTTTGA
1 ATTTTAA
35384681 ATTTTAA
1 ATTTTAA
35384688 ATTTTAA
1 ATTTTAA
35384695 ATTTTAA
1 ATTTTAA
35384702 ATTTTAA
1 ATTTTAA
35384709 TTGAATTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:35385045 original size:8 final size:8
Alignment explanation
Indices: 35385032--35385095 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
35385022 TAAATATATT
35385032 TAAAAATA
1 TAAAAATA
35385040 TAAAAAT-
1 TAAAAATA
*
35385047 CAAAAATA
1 TAAAAATA
35385055 TAAAAATTA
1 TAAAAA-TA
35385064 TAAAAATAAA
1 TAAAAAT--A
*
35385074 TAAAAGTGA
1 TAAAAAT-A
*
35385083 AAAAAATA
1 TAAAAATA
35385091 TAAAA
1 TAAAA
35385096 CAAATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
7 6 0.13
8 18 0.40
9 14 0.31
10 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (8 bp):
TAAAAATA
Found at i:35385073 original size:15 final size:15
Alignment explanation
Indices: 35385033--35385061 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35385023 AAATATATTT
35385033 AAAAATATAAAAATC
1 AAAAATATAAAAATC
35385048 AAAAATATAAAAAT
1 AAAAATATAAAAAT
35385062 TATAAAAATA
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:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATATAAAAATC
Found at i:35385078 original size:27 final size:28
Alignment explanation
Indices: 35385043--35385095 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
35385033 AAAAATATAA
*
35385043 AAATCAAAAAT-ATAAAAATTATAAAAAT
1 AAATCAAAAATGA-AAAAAATATAAAAAT
*
35385071 AAAT-AAAAGTGAAAAAAATATAAAA
1 AAATCAAAAATGAAAAAAATATAAAA
35385096 CAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (28 bp):
AAATCAAAAATGAAAAAAATATAAAAAT
Found at i:35385396 original size:18 final size:16
Alignment explanation
Indices: 35385375--35385451 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 16
35385365 ATGTATTTTT
35385375 TATTTTTATATTTTTAAA
1 TATTTTTA-ATTTTT-AA
*
35385393 TATTTTCTAATTTTTAT
1 TATTTT-TAATTTTTAA
35385410 TAATTTTTTAATATTTTAA
1 T-A-TTTTTAAT-TTTTAA
35385429 TA-TTTTAATATTTTAA
1 TATTTTTAAT-TTTTAA
35385445 TATTTTT
1 TATTTTT
35385452 CTTAATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
16 16 0.31
17 6 0.12
18 18 0.35
19 12 0.23
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTAATTTTTAA
Found at i:35385397 original size:10 final size:9
Alignment explanation
Indices: 35385375--35385451 Score: 83
Period size: 8 Copynumber: 8.8 Consensus size: 9
35385365 ATGTATTTTT
35385375 TATTTTT-A
1 TATTTTTAA
35385383 TATTTTTAAA
1 TATTTTT-AA
35385393 TATTTTCTAA
1 TATTTT-TAA
*
35385403 TTTTTATTAA
1 TATTT-TTAA
35385413 T-TTTTTAA
1 TATTTTTAA
35385421 TA-TTTTAA
1 TATTTTTAA
35385429 TA-TTTTAA
1 TATTTTTAA
35385437 TA-TTTTAA
1 TATTTTTAA
35385445 TATTTTT
1 TATTTTT
35385452 CTTAATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
8 36 0.58
9 7 0.11
10 17 0.27
11 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTTTAA
Found at i:35385598 original size:28 final size:29
Alignment explanation
Indices: 35385562--35385617 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
35385552 TTGTCATTTA
* * *
35385562 TAATATTTTTATGATTTTTTTCATTTTTC
1 TAATATTTTAATGATTTTCTTAATTTTTC
35385591 TAAT-TTTTAATGATTTTCTTAATTTTT
1 TAATATTTTAATGATTTTCTTAATTTTT
35385618 TATGATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (29 bp):
TAATATTTTAATGATTTTCTTAATTTTTC
Found at i:35385606 original size:19 final size:20
Alignment explanation
Indices: 35385584--35385626 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
35385574 GATTTTTTTC
35385584 ATTTTTC-TAATTTTTAATG
1 ATTTTTCTTAATTTTTAATG
*
35385603 A-TTTTCTTAATTTTTTATG
1 ATTTTTCTTAATTTTTAATG
35385622 ATTTT
1 ATTTT
35385627 AGTGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 13 0.62
20 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTTTTCTTAATTTTTAATG
Found at i:35386440 original size:19 final size:19
Alignment explanation
Indices: 35386416--35386454 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35386406 TGGAAGCTTT
35386416 TCTAAAGATATAAGTTTTA
1 TCTAAAGATATAAGTTTTA
35386435 TCTAAAGATATAAGTTTTA
1 TCTAAAGATATAAGTTTTA
35386454 T
1 T
35386455 GTTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
TCTAAAGATATAAGTTTTA
Found at i:35388353 original size:41 final size:42
Alignment explanation
Indices: 35388285--35388558 Score: 348
Period size: 41 Copynumber: 6.6 Consensus size: 42
35388275 CCATTTGAGG
* * * *
35388285 CTTTAGCGGTGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTGGGAAAGCGCCGCTAATGCTCATGGT
* *
35388328 -TTTAGCGGTGTTTTTGGAAAAGCGCCGCTAATGCTC-TGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCATGGT
* *
35388368 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATACTC-TGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCATGGT
* *
35388409 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATGCT-TTGGT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCATGGT
*
35388450 CTTTAGCGGCGGTTTTGGGAAAGCGCCGCTAATGCTC-TAGG-
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAT-GGT
*
35388491 CTTTAGCGGCGTTTTT-GGAGAAGCGCCGCTAATGCTC-TAGT
1 CTTTAGCGGCGTTTTTGGGA-AAGCGCCGCTAATGCTCATGGT
*
35388532 CTTTAGTGGCGTTTTTGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCC
35388559 ACAAAAACAG
Statistics
Matches: 212, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
40 7 0.03
41 190 0.90
42 15 0.07
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCATGGT
Found at i:35388423 original size:82 final size:82
Alignment explanation
Indices: 35388285--35388558 Score: 390
Period size: 82 Copynumber: 3.3 Consensus size: 82
35388275 CCATTTGAGG
* * * * * *
35388285 CTTTAGCGGTGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT-TTTAGCGGTGTTTTTGGAAAA
1 CTTTAGCGGCG-TTTTTGGGAAAGCGCCGCTAATGCTC-TGGTCTTTAGCGGCGTTTTTGGAGAA
35388349 GCGCCGCTAATGCTCTGGT
64 GCGCCGCTAATGCTCTGGT
* * *
35388368 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATACTCTGGTCTTTAGCGGCGTTTTTGGGGAAGC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAGAAGC
*
35388433 GCCGCTAATGCTTTGGT
66 GCCGCTAATGCTCTGGT
*
35388450 CTTTAGCGGCGGTTTTGGGAAAGCGCCGCTAATGCTCTAGG-CTTTAGCGGCGTTTTTGGAGAAG
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCT-GGTCTTTAGCGGCGTTTTTGGAGAAG
*
35388514 CGCCGCTAATGCTCTAGT
65 CGCCGCTAATGCTCTGGT
*
35388532 CTTTAGTGGCGTTTTTGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCC
35388559 ACAAAAACAG
Statistics
Matches: 171, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
81 3 0.02
82 156 0.91
83 12 0.07
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.32
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAGAAGC
GCCGCTAATGCTCTGGT
Found at i:35388443 original size:123 final size:123
Alignment explanation
Indices: 35388285--35388558 Score: 390
Period size: 123 Copynumber: 2.2 Consensus size: 123
35388275 CCATTTGAGG
* * * * *
35388285 CTTTAGCGGTGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT-TTTAGCGGTGTTTTTGGAAAA
1 CTTTAGCGGCG-TTTTTGGGAAAGCGCCGCTAATGCT-AGGGTCTTTAGCGGCGGTTTTGGAAAA
* *
35388349 GCGCCGCTAATGCTCT-GGTCTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATACTCTGGT
64 GCGCCGCTAATGCTCTAGG-CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATACTCTAGT
* ** *
35388409 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATGCTTTGGTCTTTAGCGGCGGTTTTGGGAAAGC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTAGGGTCTTTAGCGGCGGTTTTGGAAAAGC
*
35388474 GCCGCTAATGCTCTAGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTAGT
66 GCCGCTAATGCTCTAGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATACTCTAGT
*
35388532 CTTTAGTGGCGTTTTTGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCC
35388559 ACAAAAACAG
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
122 3 0.02
123 119 0.89
124 12 0.09
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.32
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTAGGGTCTTTAGCGGCGGTTTTGGAAAAGC
GCCGCTAATGCTCTAGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATACTCTAGT
Found at i:35388982 original size:7 final size:7
Alignment explanation
Indices: 35388929--35389017 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
35388919 GAGTTACTAT
*
35388929 TTTAAGG
1 TTTATGG
35388936 TTTATGG
1 TTTATGG
*
35388943 ATTATGAG
1 TTTATG-G
*
35388951 TTTAGGG
1 TTTATGG
*
35388958 GTTATGG
1 TTTATGG
***
35388965 TTTACAC
1 TTTATGG
35388972 TTTATGG
1 TTTATGG
* *
35388979 TTTAAGA
1 TTTATGG
35388986 TTTATGG
1 TTTATGG
*
35388993 TTTAAGG
1 TTTATGG
* *
35389000 GTTACGG
1 TTTATGG
35389007 TTTATGG
1 TTTATGG
35389014 TTTA
1 TTTA
35389018 AGGGTATAGA
Statistics
Matches: 59, Mismatches: 22, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
7 54 0.92
8 5 0.08
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:35388996 original size:21 final size:21
Alignment explanation
Indices: 35388980--35389022 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
35388970 ACTTTATGGT
35388980 TTAAGATTTATGGTTTAAGGG
1 TTAAGATTTATGGTTTAAGGG
* *
35389001 TTACGGTTTATGGTTTAAGGG
1 TTAAGATTTATGGTTTAAGGG
35389022 T
1 T
35389023 ATAGATTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.44
Consensus pattern (21 bp):
TTAAGATTTATGGTTTAAGGG
Found at i:35389105 original size:14 final size:15
Alignment explanation
Indices: 35389077--35389109 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35389067 GGGTTGATGG
35389077 TTAAGAGTTAGGGGT
1 TTAAGAGTTAGGGGT
*
35389092 TTAAGATTTA-GGGT
1 TTAAGAGTTAGGGGT
35389106 TTAA
1 TTAA
35389110 ATTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (15 bp):
TTAAGAGTTAGGGGT
Found at i:35389457 original size:21 final size:22
Alignment explanation
Indices: 35389433--35389473 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35389423 ATAGTTTATT
35389433 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
35389454 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
35389474 GGATTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:35390629 original size:7 final size:7
Alignment explanation
Indices: 35390617--35390650 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
35390607 TACAACAACA
35390617 TCAAGTT
1 TCAAGTT
35390624 TCAAGTT
1 TCAAGTT
35390631 TCAAGTT
1 TCAAGTT
35390638 TCAAGTT
1 TCAAGTT
35390645 TCAAGT
1 TCAAGT
35390651 ACGGGAGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
TCAAGTT
Found at i:35394286 original size:14 final size:14
Alignment explanation
Indices: 35394246--35394293 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
35394236 GTTGGTGGGT
* *
35394246 CTTTTTTTTTTGTC
1 CTTTTTTTTTTCTG
*
35394260 CTTTTTCATTTTCTG
1 CTTTTT-TTTTTCTG
35394275 CTTTTTTTTTTCTG
1 CTTTTTTTTTTCTG
*
35394289 GTTTT
1 CTTTT
35394294 GTAATGGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (14 bp):
CTTTTTTTTTTCTG
Found at i:35396268 original size:43 final size:42
Alignment explanation
Indices: 35395979--35396291 Score: 265
Period size: 43 Copynumber: 7.4 Consensus size: 42
35395969 ATGTTATGTT
* * * * *
35395979 TTTAGTGGCGTTTTT-CAAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAAAGGTCATGGTC
* * * * * *
35396020 TATAGCGGCGTTTGTGGTAAAAGTGCTGCTAAAGGTCTTTAG-C
1 TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAAAGGTC-ATGGTC
* * * * *
35396063 TATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGATCCTGATC
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
35396106 TATAGCGGCGTTTCTCGTAAAAGCGTCGCTAAAGGCCATGGTC
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
35396149 TTTAGCGGCGTTTGTTGGAGAAGCGCCGTTAAAGATTA-GGATC
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGG-TC
*
35396192 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGCC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
35396234 TTTAGCGGCGTTTTTGGGAAAAGCGCCGTTAAAGGTCATGGCC
1 TTTAGCGGCGTTTTT-GGAAAAGCGCCGCTAAAGGTCATGGTC
*
35396277 TTTAGCGGCATTTTT
1 TTTAGCGGCGTTTTT
35396292 TGCGGCGCTT
Statistics
Matches: 221, Mismatches: 42, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
41 12 0.05
42 52 0.24
43 153 0.69
44 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:35396280 original size:85 final size:84
Alignment explanation
Indices: 35396022--35396291 Score: 283
Period size: 85 Copynumber: 3.2 Consensus size: 84
35396012 GTTTGTTCTA
* * * * * * *
35396022 TAGCGGCGTTTGTGGTAAAAGTGCTGCTAAAGGTCTTTAGCTATAGCGGCGTTTATGGGAAAAGC
1 TAGCGGCGTTTTTGG-AAAAGCGCCGCTAAAGGTC-ATGGCTTTAGCGGCGTTTTTGGGAAAAGC
* * * *
35396087 GCCGCTAAAGATCCTGATCTA
64 GCCGTTAAAGATCATGGTCTT
* * * * *
35396108 TAGCGGCGTTTCTCGTAAAAGCGTCGCTAAAGGCCATGGTCTTTAGCGGCGTTTGTT-GGAGAAG
1 TAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGG-CTTTAGCGGCGTTT-TTGGGAAAAG
*
35396172 CGCCGTTAAAGATTA-GGATCTT
63 CGCCGTTAAAGATCATGG-TCTT
35396194 TAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGCCTTTAGCGGCGTTTTTGGGAAAAGCG
1 TAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGG-CTTTAGCGGCGTTTTTGGGAAAAGCG
* *
35396259 CCGTTAAAGGTCATGGCCTT
65 CCGTTAAAGATCATGGTCTT
*
35396279 TAGCGGCATTTTT
1 TAGCGGCGTTTTT
35396292 TGCGGCGCTT
Statistics
Matches: 151, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
84 2 0.01
85 74 0.49
86 73 0.48
87 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (84 bp):
TAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGCTTTAGCGGCGTTTTTGGGAAAAGCGC
CGTTAAAGATCATGGTCTT
Found at i:35402151 original size:3 final size:3
Alignment explanation
Indices: 35402143--35402168 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35402133 TAAATAGATC
35402143 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
35402169 TAGGTGATCA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:35410677 original size:3 final size:3
Alignment explanation
Indices: 35410669--35410704 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35410659 AATCTGAATT
35410669 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35410705 GGTTATCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35413755 original size:21 final size:20
Alignment explanation
Indices: 35413731--35413826 Score: 54
Period size: 21 Copynumber: 4.6 Consensus size: 20
35413721 AATAGAAACC
35413731 CATAAGGGTTGAACGAAAGCT
1 CATAAGGGTT-AACGAAAGCT
* * *
35413752 CATAAGAGCTTAATGGAAA-CC
1 CATAAG-GGTTAA-CGAAAGCT
35413773 CATAAGGGTTAAAC-AGAAGCT
1 CATAAGGGTT-AACGA-AAGCT
* * *
35413794 CATAAGAGCTAGACGGAAA-CC
1 CATAAGGGTTA-AC-GAAAGCT
35413815 CATAAGGGTTAA
1 CATAAGGGTTAA
35413827 ACAGAAGCTC
Statistics
Matches: 56, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
19 1 0.02
20 7 0.12
21 38 0.68
22 9 0.16
23 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (20 bp):
CATAAGGGTTAACGAAAGCT
Found at i:35413760 original size:42 final size:42
Alignment explanation
Indices: 35413700--35413907 Score: 278
Period size: 42 Copynumber: 5.0 Consensus size: 42
35413690 CCAAAGACTG
* ** *
35413700 AACAGAAGCTCATGAGAGCTAAATAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* *
35413742 AAC-GAAAGCTCATAAGAGCTTAATGGAAACCCATAAGGGTTA
1 AACAG-AAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
*
35413784 AACAGAAGCTCATAAGAGCTAGACGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
*
35413826 AACAGAAGCTCAATAA-AGCTGAACGGAAACCCATAAGGGTTA
1 AACAGAAGCTC-ATAAGAGCTAAACGGAAACCCATAAGGGTTA
* *
35413868 AACAGAAGCTCA-ATAGAGCTAAACGGAAACTCATATGGGT
1 AACAGAAGCTCATA-AGAGCTAAACGGAAACCCATAAGGGT
35413908 AATTTTCCAC
Statistics
Matches: 149, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 140 0.94
43 5 0.03
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
Found at i:35413900 original size:21 final size:22
Alignment explanation
Indices: 35413745--35413900 Score: 83
Period size: 21 Copynumber: 7.4 Consensus size: 22
35413735 AGGGTTGAAC
* *
35413745 GAAAGCTC-ATAAGAGCTTAATG
1 GAAA-CTCAATAAGAGCTAAACG
* * * *
35413767 GAAAC-CCATAAGGGTTAAACA
1 GAAACTCAATAAGAGCTAAACG
* *
35413788 GAAGCTC-ATAAGAGCTAGACG
1 GAAACTCAATAAGAGCTAAACG
* * * *
35413809 GAAAC-CCATAAGGGTTAAACA
1 GAAACTCAATAAGAGCTAAACG
* *
35413830 GAAGCTCAATAA-AGCTGAACG
1 GAAACTCAATAAGAGCTAAACG
* * * *
35413851 GAAAC-CCATAAGGGTTAAACA
1 GAAACTCAATAAGAGCTAAACG
*
35413872 GAAGCTCAAT-AGAGCTAAACG
1 GAAACTCAATAAGAGCTAAACG
35413893 GAAACTCA
1 GAAACTCA
35413901 TATGGGTAAT
Statistics
Matches: 95, Mismatches: 33, Indels: 13
0.67 0.23 0.09
Matches are distributed among these distances:
20 7 0.07
21 75 0.79
22 13 0.14
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (22 bp):
GAAACTCAATAAGAGCTAAACG
Found at i:35416617 original size:15 final size:15
Alignment explanation
Indices: 35416596--35416646 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
35416586 GCATATATAT
35416596 AAAATATAAAATGTA
1 AAAATATAAAATGTA
* *
35416611 TAAATATTAGAAAAGTA
1 AAAATA-TA-AAATGTA
*
35416628 AAAATATAAAATATA
1 AAAATATAAAATGTA
35416643 AAAA
1 AAAA
35416647 AGTATGTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 14 0.48
16 4 0.14
17 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
AAAATATAAAATGTA
Found at i:35416698 original size:3 final size:3
Alignment explanation
Indices: 35416690--35416731 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
35416680 ATATGTACAG
* * *
35416690 TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35416732 AGTCATAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35418541 original size:132 final size:132
Alignment explanation
Indices: 35418315--35419377 Score: 1534
Period size: 132 Copynumber: 8.1 Consensus size: 132
35418305 ATATCTGCTT
* * * * * * * * *
35418315 TCTTCGATCGATTCCACTGCTGACCGGGGAAATAGAATTACTGGCTTCAATATACTCCATTACAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * *
35418380 CCTCAGGGAGGTAAAAGCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTAA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35418445 AA
131 AA
**
35418447 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * *
35418512 CCACAGGGAGGTAAAATCTGCCATATTTGATCTGCCCCACTACTGCTTAGGGAGACAAGATCTGA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35418577 AA
131 AA
* * * *
35418579 TCTTCAATCTATTCTGCTGCTGCCCAAGGAGGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * *
35418644 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35418709 AA
131 AA
* *
35418711 TCTTCAATCTATTCCGCTGCTGCCCAAGGAGGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * *
35418776 CTTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35418841 AA
131 AA
* * *
35418843 TCTTCAATCTATTCCGCTGCTGCCTAGGGAAGTAGAATTACCGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * *
35418908 CCACATGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAAGGAGACAAGATCTGA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35418973 AA
131 AA
* * **
35418975 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAAAATTACTGGCTTTAATGTACTCCACTATAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * * *
35419040 CTTCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGA
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35419105 AA
131 AA
* * * *
35419107 TCTTCAATCTATTCCACTGCTACCTAGGGAAGTAGAAGTACTGGCTTCAATGTACTCCACTGCAA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * * *
35419172 CCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
35419237 AA
131 AA
* *
35419239 TCTTCAATCTATTCCACTGCTGCCCAGAG-AGATAGAATTACTGGCTTCAATGTACTCCACTGCA
1 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGCA
* * * *
35419303 ACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCATTACTGCTTAGGAAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
**
35419368 CTA
130 AAA
35419371 TCTTCAA
1 TCTTCAA
35419378 CCTGCTCCCC
Statistics
Matches: 847, Mismatches: 83, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
131 2 0.00
132 845 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
CCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
AA
Found at i:35418696 original size:44 final size:44
Alignment explanation
Indices: 35418648--35419377 Score: 233
Period size: 44 Copynumber: 16.6 Consensus size: 44
35418638 CTGTAACCAC
** *
35418648 AGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * ** * * * **
35418692 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCC
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * *** * * **
35418736 AAGGAGGTAGAAT-TACTGGCTTCAATGTACTCCACTGCAACTT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * *
35418779 CAGGGAGGTAAAATCCGCCATCTTCGACCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * ** * * * *
35418824 AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * ** * **
35418868 AGGGAAGTAGAAT-TACCGGCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTGCTT
* ** *
35418912 ATGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* ** * ** * * * **
35418956 AAGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCC
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * *
35419000 AGGGAAGTAAAATTACTGGC-T-TT-AATGTACTCCACTA-TAACTT
1 AGGGAGGTAAAA-T-CTGCCATCTTCAATCTACTCCACTACT-GCTT
* * *
35419043 CAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * ** * * * *
35419088 AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTACCT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * * * ** *
35419132 AGGGAAGTAGAAGTACTG---GCTTCAATGTACTCCACTGCAACCTC
1 AGGGAGGTA-AAAT-CTGCCATCTTCAATCTACTCCACTAC-TGCTT
** * * *
35419176 AGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTATTGCTT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * ** * * **
35419220 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * * *** * * ** *
35419264 AGAGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGCAACCTC
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTAC-TGCTT
** ** * *
35419308 AGGGAGGTAAAATCCACCATCTTTGATCTGCTCCATTACTGCTT
1 AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * * *
35419352 AGGAAGATAAGATCTGCTATCTTCAA
1 AGGGAGGTAAAATCTGCCATCTTCAA
35419378 CCTGCTCCCC
Statistics
Matches: 461, Mismatches: 201, Indels: 48
0.65 0.28 0.07
Matches are distributed among these distances:
42 8 0.02
43 84 0.18
44 281 0.61
45 80 0.17
46 8 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
AGGGAGGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
Found at i:35420710 original size:7 final size:7
Alignment explanation
Indices: 35420696--35420742 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
35420686 TCCATTTTAT
35420696 TTTTTCA
1 TTTTTCA
*
35420703 TTTCTCA
1 TTTTTCA
35420710 TTTTTCA
1 TTTTTCA
35420717 TTTTTCA
1 TTTTTCA
35420724 -TTTTCA
1 TTTTTCA
35420730 TCTTTTCA
1 T-TTTTCA
35420738 TTTTT
1 TTTTT
35420743 TCACATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 7 0.19
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:35420714 original size:21 final size:22
Alignment explanation
Indices: 35420690--35420745 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
35420680 AGCCTCTCCA
35420690 TTTT-ATTTTTTCATTTCTCAT-
1 TTTTCATTTTTTCATTT-TCATC
35420711 TTTTCA-TTTTTCATTTTCATC
1 TTTTCATTTTTTCATTTTCATC
35420732 TTTTCATTTTTTCA
1 TTTTCATTTTTTCA
35420746 CATCACTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 8 0.25
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCATTTTTTCATTTTCATC
Found at i:35423668 original size:22 final size:22
Alignment explanation
Indices: 35423640--35423690 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
35423630 TCAGGAGTCC
35423640 CCTAGGGTTTGGTATAGCTCTA
1 CCTAGGGTTTGGTATAGCTCTA
35423662 CCTAGGGTTTGGTATAGCTCTA
1 CCTAGGGTTTGGTATAGCTCTA
35423684 CCTAGGG
1 CCTAGGG
35423691 CAAGTTCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (22 bp):
CCTAGGGTTTGGTATAGCTCTA
Found at i:35425320 original size:15 final size:15
Alignment explanation
Indices: 35425299--35425349 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
35425289 GCATATATAT
35425299 AAAATATAAAATGTA
1 AAAATATAAAATGTA
* *
35425314 TAAATATTAGAAAAGTA
1 AAAATA-TA-AAATGTA
*
35425331 AAAATATAAAATATA
1 AAAATATAAAATGTA
35425346 AAAA
1 AAAA
35425350 AGTATGTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 14 0.48
16 4 0.14
17 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
AAAATATAAAATGTA
Found at i:35426994 original size:24 final size:23
Alignment explanation
Indices: 35426940--35426985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35426930 ATTAGTAACA
35426940 TCATAAAAATATAGGGATAAATT
1 TCATAAAAATATAGGGATAAATT
35426963 TCATAAAAATATAGGGATAAATT
1 TCATAAAAATATAGGGATAAATT
35426986 ATGTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (23 bp):
TCATAAAAATATAGGGATAAATT
Found at i:35438156 original size:18 final size:18
Alignment explanation
Indices: 35438126--35438175 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
35438116 GTATTATAAA
*
35438126 ATTAATTAATAAAATATT
1 ATTACTTAATAAAATATT
*
35438144 ATTACTTATTAAAATATT
1 ATTACTTAATAAAATATT
35438162 ATTACTTAATAAAA
1 ATTACTTAATAAAA
35438176 AATCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTACTTAATAAAATATT
Found at i:35442608 original size:21 final size:20
Alignment explanation
Indices: 35442580--35442618 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
35442570 CGGCATCGAT
35442580 TCTGTAAGTGTTTGAAAAGC
1 TCTGTAAGTGTTTGAAAAGC
*
35442600 TCTGATAAGTTTTTGAAAA
1 TCTG-TAAGTGTTTGAAAA
35442619 TGAGTAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTGTTTGAAAAGC
Found at i:35458114 original size:17 final size:18
Alignment explanation
Indices: 35458072--35458119 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
35458062 TATTTTAAAA
35458072 AAATTAAA-AATAAATCC
1 AAATTAAAGAATAAATCC
35458089 AAA--AAAGAATAAA-CC
1 AAATTAAAGAATAAATCC
*
35458104 AAATTAAAGAAGAAAT
1 AAATTAAAGAATAAAT
35458120 AGAATCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.31
16 6 0.23
17 12 0.46
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATTAAAGAATAAATCC
Found at i:35461114 original size:37 final size:37
Alignment explanation
Indices: 35461064--35461173 Score: 141
Period size: 37 Copynumber: 3.0 Consensus size: 37
35461054 CCTGGAAGAC
35461064 AAAAGAC-AGAGATGAATAGTAATGATTCTCTACAAAG
1 AAAAGACGA-AGATGAATAGTAATGATTCTCTACAAAG
* *
35461101 AAGAGATGAAGATGAATAGTAATGATTCTCTACAAAG
1 AAAAGACGAAGATGAATAGTAATGATTCTCTACAAAG
* * * * *
35461138 AAAAGACGGAGATGAACAATAACGATTCTCTGCAAA
1 AAAAGACGAAGATGAATAGTAATGATTCTCTACAAA
35461174 AATTCTCCCA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 62 0.98
38 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (37 bp):
AAAAGACGAAGATGAATAGTAATGATTCTCTACAAAG
Found at i:35461609 original size:3 final size:3
Alignment explanation
Indices: 35461601--35461654 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
35461591 AAAGTTGTCG
*
35461601 TTA TTA TTA TTA TTA TTA TTA CTA 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
35461649 TTA TTA
1 TTA TTA
35461655 AAACTATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:35463373 original size:19 final size:19
Alignment explanation
Indices: 35463346--35463383 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35463336 ATCGATTTCG
*
35463346 GATATTTCTATATTTATTC
1 GATAATTCTATATTTATTC
35463365 GATAATTCTATATTTATTC
1 GATAATTCTATATTTATTC
35463384 AACATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (19 bp):
GATAATTCTATATTTATTC
Found at i:35476608 original size:20 final size:20
Alignment explanation
Indices: 35476585--35476624 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35476575 TTAATTAACA
*
35476585 TAATTAACCTTACTTTAATT
1 TAATAAACCTTACTTTAATT
* *
35476605 TAATAAACTTTATTTTAATT
1 TAATAAACCTTACTTTAATT
35476625 AAGTTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATAAACCTTACTTTAATT
Found at i:35478838 original size:16 final size:17
Alignment explanation
Indices: 35478807--35478840 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35478797 CTCGTAATAC
*
35478807 AATAACTCATATTACTA
1 AATAACTCACATTACTA
35478824 AATAAC-CACATTACTA
1 AATAACTCACATTACTA
35478840 A
1 A
35478841 CAATTGCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAACTCACATTACTA
Done.