Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 143 of 199
Found at i:41727748 original size:13 final size:14
Alignment explanation
Indices: 41727729--41727770 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
41727719 ACTAGCTCTC
41727729 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
41727743 TTTTTTTTTTCA-AA
1 -TTTTTTTTTCACAA
*
41727757 ATTTTTTTTCACAA
1 TTTTTTTTTCACAA
41727771 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
14 4 0.16
15 11 0.44
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:41727749 original size:15 final size:15
Alignment explanation
Indices: 41727729--41727765 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
41727719 ACTAGCTCTC
*
41727729 TTTTTTTTTCACAAT
1 TTTTTTTTTCAAAAT
41727744 TTTTTTTTTCAAAAT
1 TTTTTTTTTCAAAAT
41727759 TTTTTTT
1 TTTTTTT
41727766 CACAACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTTTCAAAAT
Found at i:41727827 original size:11 final size:11
Alignment explanation
Indices: 41727811--41727840 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
41727801 AAACCAAAAT
41727811 TTTTTTTTGAA
1 TTTTTTTTGAA
41727822 TTTTTTTTGAA
1 TTTTTTTTGAA
41727833 TTTTTTTT
1 TTTTTTTT
41727841 CGAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41728554 original size:19 final size:19
Alignment explanation
Indices: 41728530--41728567 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41728520 TGGCTTAGAA
41728530 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
41728549 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
41728568 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:41737649 original size:47 final size:46
Alignment explanation
Indices: 41737592--41737736 Score: 120
Period size: 47 Copynumber: 3.2 Consensus size: 46
41737582 ATAATACCAT
*
41737592 TTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATCA-TATTAAATTATA
** * * *
41737639 TTTAATATTAATTATTTTA--AATTGTATAAATTCATA-TAAGA--AAA
1 TTTAATATTAAGAATTTTATGAAAT-TATATA-TCATATTAA-ATTATA
* * *
41737683 TTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATCA-TATTAAATTATA
*
41737730 TGTAATA
1 TTTAATA
41737737 ATTATTATTT
Statistics
Matches: 73, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
44 19 0.26
45 14 0.19
46 14 0.19
47 26 0.36
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (46 bp):
TTTAATATTAAGAATTTTATGAAATTATATATCATATTAAATTATA
Found at i:41737696 original size:91 final size:91
Alignment explanation
Indices: 41737573--41737780 Score: 292
Period size: 91 Copynumber: 2.3 Consensus size: 91
41737563 TTGATTTTAG
* * *
41737573 TAAATTCATATAATACCATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAATA-AAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
41737638 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* * *
41737665 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
41737730 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * *
41737756 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAATAAAATTTATTA
41737781 GTTATAATTA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 86 0.83
92 17 0.17
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:41737954 original size:15 final size:15
Alignment explanation
Indices: 41737919--41737970 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41737909 TTAAGAATTT
*
41737919 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41737933 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41737947 TATTTAATAATAAT-
1 TATTTAATTATAATA
41737961 TATGTTAATT
1 TAT-TTAATT
41737971 TTTATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41738034 original size:120 final size:119
Alignment explanation
Indices: 41737796--41738087 Score: 461
Period size: 118 Copynumber: 2.5 Consensus size: 119
41737786 AATTATTTTA
* * *
41737796 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTATTTT
*
41737860 ATAGTATATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41737914 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTTTATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAA-ATTTATTT
*
41737978 TACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTAT-ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41738034 AA---T-TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
41738088 ATGATTAAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
116 47 0.29
117 3 0.02
118 49 0.30
119 16 0.10
120 48 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTATTTT
ACAGTATATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41738035 original size:16 final size:16
Alignment explanation
Indices: 41738004--41738045 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
41737994 ATGGTTTGAG
41738004 TAAATTCATATAAGAATAT
1 TAAATT-AT-TAAGAAT-T
41738023 T-AATTATTAAGAATT
1 TAAATTATTAAGAATT
41738038 TAAATTAT
1 TAAATTAT
41738046 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 2 0.09
18 4 0.18
19 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
TAAATTATTAAGAATT
Found at i:41738048 original size:57 final size:57
Alignment explanation
Indices: 41737866--41738050 Score: 146
Period size: 59 Copynumber: 3.1 Consensus size: 57
41737856 TTTTATAGTA
41737866 TATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA---T-TTAAAT
* * * * * * * *
41737927 TATATATTTTAATTAT-AATATATTTA-ATAATAATTATGTTAATT-TT--TATTTTACAGTAT
1 TATATATTATGATT-TGAGTAAATTCATATAAGAA-TA--TTAATTATTAAGAATTTA-A--AT
* *
41737986 CATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTAAAT
1 TATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTAAAT
41738043 TATATATT
1 TATATATT
41738051 TTAATTATAA
Statistics
Matches: 93, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
56 3 0.03
57 17 0.18
58 3 0.03
59 22 0.24
60 18 0.19
61 21 0.23
62 3 0.03
63 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (57 bp):
TATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTAAAT
Found at i:41738063 original size:16 final size:16
Alignment explanation
Indices: 41738044--41738085 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41738034 AATTTAAATT
*
41738044 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41738060 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41738075 AT-TATGTTTAA
1 ATATAT-TTTAA
41738086 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41738070 original size:15 final size:15
Alignment explanation
Indices: 41738022--41738076 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
41738012 TATAAGAATA
*
41738022 TTAATTATTAAGA-AT
1 TTAATTA-TAATATAT
41738037 TTAAATTAT-ATAT-T
1 TT-AATTATAATATAT
41738051 TTAATTATAATATAT
1 TTAATTATAATATAT
*
41738066 TTAATAATAAT
1 TTAATTATAAT
41738077 TATGTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 14 0.41
16 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATTATAATATAT
Found at i:41738190 original size:147 final size:143
Alignment explanation
Indices: 41738023--41738291 Score: 468
Period size: 147 Copynumber: 1.9 Consensus size: 143
41738013 ATAAGAATAT
* *
41738023 TAATTATTAAGAATTTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TAATTATTAAGAATTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAAT
41738088 ATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAA-AATAATTTACCA
66 ATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTT-AATAACAATAATTTACCA
41738152 AAACAAAATTCTGC
130 AAACAAAATTCTGC
41738166 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
1 TAATTATTAAGAA---T-TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
41738231 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
62 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
41738292 CAATAATCAT
Statistics
Matches: 119, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 13 0.11
146 6 0.05
147 100 0.84
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (143 bp):
TAATTATTAAGAATTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAAT
ATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAATTTACCAA
AACAAAATTCTGC
Found at i:41738206 original size:18 final size:17
Alignment explanation
Indices: 41738178--41738212 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41738168 ATTATTAAGA
*
41738178 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41738195 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41738213 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41738460 original size:45 final size:44
Alignment explanation
Indices: 41738371--41738465 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 44
41738361 TTACACCTCT
*
41738371 ATTACATTCAACCAAACATAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACATAGGATTACTATTACACCTCTATTCC
* *
41738415 ATTACATTCAACCAAACAGT-TGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACA-TAGGA-TTACTATTACACCTCTATTCC
41738460 ATTACA
1 ATTACA
41738466 CCTCTAATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (44 bp):
ATTACATTCAACCAAACATAGGATTACTATTACACCTCTATTCC
Found at i:41738495 original size:16 final size:16
Alignment explanation
Indices: 41738446--41738495 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
41738436 GATTTGCTAT
* *
41738446 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
41738462 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
41738478 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41738494 TA
1 TA
41738496 TGCCCTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41742273 original size:10 final size:10
Alignment explanation
Indices: 41742258--41742294 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
41742248 CTTCGGAATT
41742258 TTTTTTTCAA
1 TTTTTTTCAA
41742268 TTTTTTTCAA
1 TTTTTTTCAA
**
41742278 TTTTTTTTTA
1 TTTTTTTCAA
41742288 TTTTTTT
1 TTTTTTT
41742295 TCGAATTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:41742279 original size:22 final size:22
Alignment explanation
Indices: 41742253--41742302 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
41742243 TAATACTTCG
41742253 GAATTTTTTTTTCAATTTTTTTC
1 GAATTTTTTTTT-AATTTTTTTC
*
41742276 -AATTTTTTTTTATTTTTTTTC
1 GAATTTTTTTTTAATTTTTTTC
41742297 GAATTT
1 GAATTT
41742303 CCTCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (22 bp):
GAATTTTTTTTTAATTTTTTTC
Found at i:41755359 original size:37 final size:38
Alignment explanation
Indices: 41755316--41755427 Score: 156
Period size: 40 Copynumber: 2.9 Consensus size: 38
41755306 GCTACTCGTT
* *
41755316 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACT-A
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCA
41755353 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACT--CA
*
41755393 CAAATGCCTTCGGGACTTAACCCGGATTTTGTAAC
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
41755428 ACCCCGAACC
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
37 31 0.46
38 2 0.03
40 35 0.51
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCA
Found at i:41757020 original size:55 final size:55
Alignment explanation
Indices: 41756959--41757135 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
41756949 ATATTAAGTC
* * *
41756959 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
41757014 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
41757069 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
41757125 CGCACACTTAG
1 CGCACACTTAG
41757136 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:41757023 original size:28 final size:27
Alignment explanation
Indices: 41756959--41757110 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
41756949 ATATTAAGTC
* *
41756959 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
41756986 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
41757014 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
41757041 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
41757069 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
41757096 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41757111 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41758824 original size:39 final size:39
Alignment explanation
Indices: 41758781--41758898 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 39
41758771 TGTTACAGAT
41758781 TTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAA
1 TTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAA
* * * *
41758820 TTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG-A
1 TTAGTAACTCGCACCAATGCCTTCGG-GCTTAGCCCGGAA
* * * *
41758859 TATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCGGA
1 T-TAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCCCGGA
41758899 CATCATTCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
39 26 0.42
40 32 0.52
41 4 0.06
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
TTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAA
Found at i:41760092 original size:56 final size:56
Alignment explanation
Indices: 41760025--41760144 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41760015 TATTAGTTTA
41760025 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41760081 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41760137 TTGCCCAT
1 TTGCCCAT
41760145 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41766776 original size:39 final size:39
Alignment explanation
Indices: 41766619--41766843 Score: 202
Period size: 40 Copynumber: 5.6 Consensus size: 39
41766609 GCTACTCATT
* * * *
41766619 CAAATGCCTTCAGGATATAGCCCGG-TTATAGTATCTCGCA
1 CAAATGCCTTCGGGCT-TAACCCGGATT-TAGTAACTCGCA
* *
41766659 CAAATGCCTTCGGAACTTAACCCGGATTTAGTAACTCCCA
1 CAAATGCCTTCGG-GCTTAACCCGGATTTAGTAACTCGCA
41766699 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCA
* * * * *
41766739 CCAATGCCTCCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
41766778 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAACCCGGATTTAGTAAC-TCGCA
*
41766819 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAACCCGGA
41766844 CATCATTCGA
Statistics
Matches: 154, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 33 0.21
40 110 0.71
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
Found at i:41766803 original size:79 final size:82
Alignment explanation
Indices: 41766619--41766843 Score: 223
Period size: 80 Copynumber: 2.8 Consensus size: 82
41766609 GCTACTCATT
* * *
41766619 CAAATGCCTTCAGGAT-ATAGCCCGG-TTATAGTATCTCGCACAAATGCCTTCGGAACTTAACCC
1 CAAATGCCTTCAGGATCTTAGCCCGGATTATAGTAACTCGCACAAATGCCTCCGGAACTTAACCC
*
41766682 GGATTTAGTAACTCCCA
66 GGAATTAGTAACTCCCA
* * * * *
41766699 CAAATGCCTTCGGGA-CTTAACCCGGATT-TAGTAACTCGCACCAATGCCTCCGG-GCTTAGCCC
1 CAAATGCCTTCAGGATCTTAGCCCGGATTATAGTAACTCGCACAAATGCCTCCGGAACTTAACCC
* *
41766761 GGAATTAGTATCTCGCA
66 GGAATTAGTAACTCCCA
* * * * * * *
41766778 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCAGGATCTTAGCCCGGATTATAGTAAC-TCGCACAAATGCCTCCGGAACTTAACC
41766840 CGGA
65 CGGA
41766844 CATCATTCGA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
78 4 0.03
79 53 0.44
80 61 0.51
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCAGGATCTTAGCCCGGATTATAGTAACTCGCACAAATGCCTCCGGAACTTAACCC
GGAATTAGTAACTCCCA
Found at i:41768040 original size:56 final size:56
Alignment explanation
Indices: 41767973--41768092 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41767963 TATTAGTTTA
41767973 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41768029 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41768085 TTGCCCAT
1 TTGCCCAT
41768093 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41776366 original size:16 final size:16
Alignment explanation
Indices: 41776341--41776371 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41776331 TTAGGAGCTG
*
41776341 CTAATTAATTTGTCTC
1 CTAATAAATTTGTCTC
41776357 CTAATAAATTTGTCT
1 CTAATAAATTTGTCT
41776372 TAGCCGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (16 bp):
CTAATAAATTTGTCTC
Found at i:41779658 original size:14 final size:14
Alignment explanation
Indices: 41779639--41779693 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
41779629 TCCATTGAGC
41779639 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
**
41779653 GAGAAAACCAAAAA
1 GAGAAAAAGAAAAA
*
41779667 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
41779682 GAAAGAAAAGAA
1 GAGA-AAAAGAA
41779694 TGACGAAAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 15 0.47
15 17 0.53
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:41780915 original size:46 final size:46
Alignment explanation
Indices: 41780862--41780955 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
41780852 CAAAGAAAAG
*
41780862 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
41780908 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
41780954 AC
1 AC
41780956 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:41796372 original size:26 final size:25
Alignment explanation
Indices: 41796357--41796411 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
41796347 GAGAGAAAAC
41796357 GAAA-AAGAAAATAAAAATGAGAAA
1 GAAAGAAGAAAATAAAAATGAGAAA
* *
41796381 GAAAGAAGAAAAGAAAGATCGAGAGAA
1 GAAAGAAGAAAATAAAAAT-GAGA-AA
41796408 GAAA
1 GAAA
41796412 AATTGAGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 12 0.46
26 4 0.15
27 6 0.23
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (25 bp):
GAAAGAAGAAAATAAAAATGAGAAA
Found at i:41796397 original size:12 final size:12
Alignment explanation
Indices: 41796344--41796398 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
41796334 CTATGTAACA
41796344 AAAGAGAGAAAACG
1 AAAGA-AGAAAA-G
*
41796358 AAA-AAGAAAAT
1 AAAGAAGAAAAG
41796369 AAA-AATGAGAAAG
1 AAAGAA-GA-AAAG
41796382 AAAGAAGAAAAG
1 AAAGAAGAAAAG
41796394 AAAGA
1 AAAGA
41796399 TCGAGAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 9 0.25
14 5 0.14
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:41800373 original size:679 final size:673
Alignment explanation
Indices: 41799070--41800419 Score: 2070
Period size: 679 Copynumber: 2.0 Consensus size: 673
41799060 AGGGTGGCTG
* * *
41799070 GCCAAGCCATACATATAGGCTTCTAACTATTTTCCTAGTCCTAATAGGAAAACTAAAAAAAACCT
1 GCCAAGCCATACATAGAGGCTCCTAACTACTTTCCTAGTCCTAATAGGAAAACTAAAAAAAACCT
* *
41799135 AATTTTTTTTACTTTCAAGGGGAAATTCAGCCAAGGACTTTAAATGGGCCTCTTGCACTGAATTT
66 AAATTTTTTGACTTTCAAGGGGAAATTCAGCCAAGGACTTTAAATGGGCCTCTTGCACTGAATTT
41799200 TAACATAGAAATTTATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAGAATTAAAGCTTAA
131 TAACATAGAAATTTATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAGAATTAAAGCTTAA
** *
41799265 CAAATTGGGCCTGTTTGACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCTTGATTG
196 CAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAACTTCTTGATTG
* * * * *
41799330 GGCTTGGAACATCTTATTGGGCCGTTTCATCAAGCATTTGGGCTTGTAATCCGTTCTCTCCCGAA
261 GGCTTGGAACATCTTATTGGGCCGTATCATCAAGAACTTGGGCTTGTAATCCATTCTCTCCCAAA
* * * *
41799395 ATTGGTTCGTTGATGCTCGCAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGCTTCTTGGA
326 ATTGGCTCGTTGATGCTCGCAACTGAGATCCAATCCACCTTAGCTGCAAGATTCAGCTTCTTGGA
41799460 CCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAAT
391 CCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAAT
*
41799525 TGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCCTTTTCC
456 TGGACCAAGATTCGGTTTCTTGATTTTCTTAAAAACAAGAAAGTGAATCTTGATTTTCCTTTTCC
* * *
41799590 TTCGTGTACGCATCTAAGGCCTTGCTAATAAATTCTTAAATGGTTCCATTTAGTTTTGAACGCAT
521 TTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTAAATGGTTCCATTTAGTTTTCAACGCAT
* *
41799655 TTGTCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTTGAGCTT
586 TTGTCTGGCCTTTGACCTCGTGATTGGGCCTTATGGTAATTTGAGCCCATCACGTCCTTGAG-TT
41799720 GAATTGGGCCTTTGTGACTCGTATCATCT
650 G---T--GCCTTTGTGACTCGTATCATCT
* * *
41799749 GCCAAGCCATATATAGAGGCCTCCTAACTACTTTCCTA-TCCCTACTAGGAAAACTAAAAAAACC
1 GCCAAGCCATACATAGAGG-CTCCTAACTACTTTCCTAGT-CCTAATAGGAAAACTAAAAAAAAC
* * ** * *
41799813 CTAAATTTTTTGCCTTTCAA-TGG-AATTTTGTCCAAGGCCTTTAAATGGGCCTCTTGGACTGAA
64 CTAAATTTTTTGACTTTCAAGGGGAAATTCAG-CCAAGGACTTTAAATGGGCCTCTTGCACTGAA
41799876 TTCTT-ACATAGAAATTTATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAGAATTAAAGC
128 TT-TTAACATAGAAATTTATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAGAATTAAAGC
41799940 TTAACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAA-TGAAGTCTAATTTAAACTTCTT
192 TTAACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAACT-AAGTCTAATTTAAACTTCTT
* * * *
41800004 GGTTGGGCTTGGAACATCTTATTGGGTCGTATCCTTAAGAACTTGGGCTTGTAATCCATTCTCTC
256 GATTGGGCTTGGAACATCTTATTGGGCCGTATCATCAAGAACTTGGGCTTGTAATCCATTCTCTC
* *
41800069 CCAAAATTGGCTCGTTGATGC-CAGTAACTGAGATCCAATCCACCTTAGCTGCAAGATTCAGTTT
321 CCAAAATTGGCTCGTTGATGCTC-GCAACTGAGATCCAATCCACCTTAGCTGCAAGATTCAGCTT
41800133 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAA-AA
385 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAA
* *
41800197 CCAAAATTGGGCCAAGATTCGGTTTCTTGATTTTCTTAAAAACTAGAAAGTGAATCTTGATTTTC
450 -CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTAAAAACAAGAAAGTGAATCTTGATTTTC
* * * *
41800262 TTTTTCCTTTGTATACGCATCTAAGGCCTTGCTAATGAAGTCTTGAATGGTTCCATTTAG-TTTC
514 CTTTTCCTTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTAAATGGTTCCATTTAGTTTTC
* * * *
41800326 ATACGCATTTG-CGTGGCCTTTGACCTTGTGATTGTGTCTTATGGTAATTTGAGCCCATCACGTT
579 A-ACGCATTTGTC-TGGCCTTTGACCTCGTGATTGGGCCTTATGGTAATTTGAGCCCATCACGTC
41800390 CTTGAGTTGTGCCTTTGTGACTCGTATCAT
642 CTTGAGTTGTGCCTTTGTGACTCGTATCAT
41800420 GATTTTAGCT
Statistics
Matches: 614, Mismatches: 48, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
673 20 0.03
675 1 0.00
678 17 0.03
679 519 0.85
680 57 0.09
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (673 bp):
GCCAAGCCATACATAGAGGCTCCTAACTACTTTCCTAGTCCTAATAGGAAAACTAAAAAAAACCT
AAATTTTTTGACTTTCAAGGGGAAATTCAGCCAAGGACTTTAAATGGGCCTCTTGCACTGAATTT
TAACATAGAAATTTATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAGAATTAAAGCTTAA
CAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAACTTCTTGATTG
GGCTTGGAACATCTTATTGGGCCGTATCATCAAGAACTTGGGCTTGTAATCCATTCTCTCCCAAA
ATTGGCTCGTTGATGCTCGCAACTGAGATCCAATCCACCTTAGCTGCAAGATTCAGCTTCTTGGA
CCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAAT
TGGACCAAGATTCGGTTTCTTGATTTTCTTAAAAACAAGAAAGTGAATCTTGATTTTCCTTTTCC
TTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTAAATGGTTCCATTTAGTTTTCAACGCAT
TTGTCTGGCCTTTGACCTCGTGATTGGGCCTTATGGTAATTTGAGCCCATCACGTCCTTGAGTTG
TGCCTTTGTGACTCGTATCATCT
Found at i:41804216 original size:22 final size:22
Alignment explanation
Indices: 41804175--41804217 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41804165 ACTTCCATAT
*
41804175 AGCTTCCTAGAACGTCCCTAGA
1 AGCTTCCTAGAACATCCCTAGA
* *
41804197 AGCTTCCTTGAACATTCCTAG
1 AGCTTCCTAGAACATCCCTAG
41804218 CTTTGGAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (22 bp):
AGCTTCCTAGAACATCCCTAGA
Found at i:41814276 original size:18 final size:18
Alignment explanation
Indices: 41814255--41814298 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
41814245 AAAGGAACAT
41814255 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
41814273 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41814291 AGAGAAAA
1 AGA-AAAA
41814299 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:41816099 original size:33 final size:34
Alignment explanation
Indices: 41816035--41816109 Score: 134
Period size: 33 Copynumber: 2.2 Consensus size: 34
41816025 GAGTTAGTTT
*
41816035 ATTAAATTTAGTTCAGCTTAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
41816068 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
41816102 ATTAATTT
1 ATTAATTT
41816110 GTTTAAATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
Found at i:41826166 original size:18 final size:18
Alignment explanation
Indices: 41826145--41826183 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41826135 AAAGGAAGAC
41826145 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
41826163 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41826181 AGA
1 AGA
41826184 TCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:41827913 original size:33 final size:34
Alignment explanation
Indices: 41827876--41827947 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
41827866 GAGTTAGTTT
41827876 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
41827909 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
41827943 ATTAA
1 ATTAA
41827948 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:41832542 original size:18 final size:18
Alignment explanation
Indices: 41832521--41832559 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41832511 AAAGGAAGAC
41832521 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
41832539 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41832557 AGA
1 AGA
41832560 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:41835673 original size:40 final size:40
Alignment explanation
Indices: 41835575--41835784 Score: 269
Period size: 40 Copynumber: 5.3 Consensus size: 40
41835565 TCCTCGTTCA
* * * * *
41835575 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41835614 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41835654 AATGCCTTCAGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41835694 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
41835734 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41835774 AAGGCCTTCGG
1 AATGCCTTCGG
41835785 ATCTTAGTCC
Statistics
Matches: 150, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 32 0.21
40 118 0.79
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41835821 original size:120 final size:118
Alignment explanation
Indices: 41835573--41835836 Score: 278
Period size: 120 Copynumber: 2.2 Consensus size: 118
41835563 GCTCCTCGTT
* * * * *
41835573 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACGTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
* * * * *
41835638 TTTAACAACTCGCACGAATGCCTTCAGGACTTAACCCGGCTTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCAGGACTTAACCCGGATATAATAACTAGCA
* * * *
41835692 CGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGCTTTAATAACTCACAC-AATGCCCTCGGGACGTAACCCGG
** * ** * **
41835757 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCAGGA-CTTAACCCGGATATAATAAC-TAGCA
41835813 CAAAGCCTTCGGGACTTAGCCCGG
1 CAAAGCCTTCGGGACTTAGCCCGG
41835837 ACAGCATTCA
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
119 35 0.30
120 77 0.66
121 5 0.04
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCAGGACTTAACCCGGATATAATAACTAGCA
Found at i:41843616 original size:40 final size:40
Alignment explanation
Indices: 41843525--41843734 Score: 260
Period size: 40 Copynumber: 5.3 Consensus size: 40
41843515 TCCTCGTTCA
* * * * *
41843525 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41843564 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41843604 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41843644 AATGCCTTCGGGACTTAACCCAGCTTTAATAACTCTCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
41843684 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41843724 AAGGCCTTCGG
1 AATGCCTTCGG
41843735 ATCTTAGTCC
Statistics
Matches: 148, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
39 32 0.22
40 116 0.78
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41845389 original size:33 final size:34
Alignment explanation
Indices: 41845352--41845423 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
41845342 GAGTTAGTTT
41845352 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
41845385 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
41845419 ATTAA
1 ATTAA
41845424 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:41848044 original size:24 final size:24
Alignment explanation
Indices: 41848017--41848062 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41848007 TTGAGTGAAA
41848017 AATTCTCT-TTGAGTTTTCTTTAAG
1 AATTCTCTCTTGAGTTTT-TTTAAG
*
41848041 AATTTTCTCTTGAGTTTTTTTA
1 AATTCTCTCTTGAGTTTTTTTA
41848063 GAAGCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.59
Consensus pattern (24 bp):
AATTCTCTCTTGAGTTTTTTTAAG
Found at i:41849650 original size:16 final size:19
Alignment explanation
Indices: 41849613--41849659 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 19
41849603 CAAGTGAGAG
41849613 AAAAAGAAAAGAGAGTGAA
1 AAAAAGAAAAGAGAGTGAA
41849632 AAAAAGAAAAGA-A-TG-A
1 AAAAAGAAAAGAGAGTGAA
41849648 AAAAAGAAAAGA
1 AAAAAGAAAAGA
41849660 CTGTGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.46
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAGAGAGTGAA
Found at i:41859195 original size:12 final size:12
Alignment explanation
Indices: 41859178--41859211 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
41859168 TCGTGAATTG
41859178 AAAAAAAAGTT-
1 AAAAAAAAGTTC
*
41859189 TAAAAAAAGTTC
1 AAAAAAAAGTTC
41859201 AAAAAAAAGTT
1 AAAAAAAAGTT
41859212 GTATTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (12 bp):
AAAAAAAAGTTC
Found at i:41860254 original size:12 final size:12
Alignment explanation
Indices: 41860225--41860299 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
41860215 AAACAGCATG
41860225 TGAAAAAGAAAA
1 TGAAAAAGAAAA
** *
41860237 ACAAAAAGAAAT
1 TGAAAAAGAAAA
41860249 TGAAAAAGAAAA
1 TGAAAAAGAAAA
* *
41860261 TGAACATG-AAA
1 TGAAAAAGAAAA
*
41860272 -GAAAACAAGAAAT
1 TG-AAA-AAGAAAA
41860285 TGAAAAAGAAAA
1 TGAAAAAGAAAA
41860297 TGA
1 TGA
41860300 GAATGAGAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
10 1 0.02
11 5 0.11
12 35 0.74
13 5 0.11
14 1 0.02
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.11
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:41860331 original size:25 final size:26
Alignment explanation
Indices: 41860286--41860340 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
41860276 ACAAGAAATT
*
41860286 GAAAAAGAAAATGAGAATGAGAGTGA
1 GAAAAAGAAAAAGAGAATGAGAGTGA
*
41860312 GAAAAA-AAAAAGA-AATTGAGATTGA
1 GAAAAAGAAAAAGAGAA-TGAGAGTGA
41860337 -AAAA
1 GAAAA
41860341 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 6 0.23
25 14 0.54
26 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (26 bp):
GAAAAAGAAAAAGAGAATGAGAGTGA
Found at i:41866922 original size:52 final size:52
Alignment explanation
Indices: 41866865--41866965 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
41866855 CATGCACATA
* *
41866865 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
41866917 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
41866966 CGTTGCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:41873512 original size:52 final size:52
Alignment explanation
Indices: 41873455--41873555 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
41873445 CATGCACATA
* *
41873455 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCGTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCGTAAGCTGCTGTCCATTATTG
* *
41873507 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGTTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCGTAAGCTGCTGTCCATTA
41873556 CGTTGCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCGTAAGCTGCTGTCCATTATTG
Found at i:41873855 original size:79 final size:79
Alignment explanation
Indices: 41873759--41873917 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
41873749 CTTATTCATT
41873759 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
1 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
41873824 CCTAAATACGTCAC
66 CCTAAATACGTCAC
*
41873838 AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
1 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
41873903 CCTAAATACGTCAC
66 CCTAAATACGTCAC
41873917 A
1 A
41873918 TATCAGCATG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.55, C:0.23, G:0.04, T:0.18
Consensus pattern (79 bp):
AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
CCTAAATACGTCAC
Found at i:41875731 original size:12 final size:12
Alignment explanation
Indices: 41875714--41875758 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
41875704 GTAGTTTCTC
*
41875714 AAAAAAAACTCG
1 AAAAAAAATTCG
*
41875726 AAAAAAAATTCAA
1 AAAAAAAATTC-G
41875739 AAAAAAAATTCG
1 AAAAAAAATTCG
41875751 AAAAAAAA
1 AAAAAAAA
41875759 ACTAGTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.76, C:0.09, G:0.04, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:41875732 original size:13 final size:13
Alignment explanation
Indices: 41875714--41875761 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
41875704 GTAGTTTCTC
41875714 AAAAAAAACTCG-
1 AAAAAAAACTCGA
* *
41875726 AAAAAAAATTCAA
1 AAAAAAAACTCGA
*
41875739 AAAAAAAATTCGA
1 AAAAAAAACTCGA
41875752 AAAAAAAACT
1 AAAAAAAACT
41875762 AGTTTCCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.73, C:0.10, G:0.04, T:0.12
Consensus pattern (13 bp):
AAAAAAAACTCGA
Found at i:41875817 original size:12 final size:13
Alignment explanation
Indices: 41875797--41875848 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
41875787 GGATATCAAG
41875797 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41875810 TT-TGAAAAAAAAA
1 TTGTG-AAAAAAAA
41875823 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41875836 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
41875849 AGCTAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.05
13 33 0.89
14 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:41875826 original size:26 final size:27
Alignment explanation
Indices: 41875797--41875849 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
41875787 GGATATCAAG
41875797 TTGTGAAAAAAAATT-TGAAAAAAAAA
1 TTGTGAAAAAAAATTGTGAAAAAAAAA
41875823 TTGTGAAAAAAAATTGTGAAAAAAAAA
1 TTGTGAAAAAAAATTGTGAAAAAAAAA
41875850 GCTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (27 bp):
TTGTGAAAAAAAATTGTGAAAAAAAAA
Found at i:41880018 original size:22 final size:22
Alignment explanation
Indices: 41879993--41880041 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
41879983 TTTGGCACGT
41879993 AATGTTTTAAGTTTAAGTACGA
1 AATGTTTTAAGTTTAAGTACGA
** *
41880015 AATGGTTTTTGGTTTAGGTACGA
1 AAT-GTTTTAAGTTTAAGTACGA
41880038 AATG
1 AATG
41880042 GTATGGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (22 bp):
AATGTTTTAAGTTTAAGTACGA
Found at i:41888990 original size:47 final size:47
Alignment explanation
Indices: 41888817--41889350 Score: 807
Period size: 47 Copynumber: 11.1 Consensus size: 47
41888807 CAGCCAAGAG
* * *
41888817 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
41888864 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
41888915 AGTGTATGTATATATGTAATAAGGCCTAATAGCTGACGTGATGAATGTGAA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
*
41888966 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
*
41889013 AGTGTATATGTGTGATAAGGCCTAATAGCCAACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
41889060 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* *
41889107 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
41889154 AGTGTATGTATATATGTAATAAGGCCTAATACCCGACGTGATGAATGTGAA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
*
41889205 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
41889252 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
41889299 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
41889346 AGTGT
1 AGTGT
41889351 GACAAGGCCG
Statistics
Matches: 456, Mismatches: 23, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
47 318 0.70
49 4 0.01
51 134 0.29
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
Found at i:41889240 original size:239 final size:239
Alignment explanation
Indices: 41888817--41889350 Score: 969
Period size: 239 Copynumber: 2.2 Consensus size: 239
41888807 CAGCCAAGAG
* * *
41888817 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTG
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAA--G--TGTATATATGTG
*
41888882 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTAATAAGGCCTAATAG
62 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTAATAAGGCCTAATAC
*
41888947 CTGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
127 CCGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
41889012 AAGTGTATATGTGTGATAAGGCCTAATAGCCAACGTGATGAATGTGAA
192 AAGTGTATATGTGTGATAAGGCCTAATAGCCAACGTGATGAATGTGAA
*
41889060 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGATAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAA
41889125 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTAATAAGGCCTAATACCCGA
66 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTAATAAGGCCTAATACCCGA
41889190 CGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
131 CGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
*
41889255 GTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
196 GTATATGTGTGATAAGGCCTAATAGCCAACGTGATGAATGTGAA
41889299 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGT
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGT
41889351 GACAAGGCCG
Statistics
Matches: 284, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
239 238 0.84
241 1 0.00
243 45 0.16
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (239 bp):
AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTAATAAGGCCTAATACCCGA
CGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
GTATATGTGTGATAAGGCCTAATAGCCAACGTGATGAATGTGAA
Found at i:41889578 original size:37 final size:37
Alignment explanation
Indices: 41889522--41889600 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41889512 CCGAGCTCTA
* * *
41889522 AAGACCAGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCAGATAACTACGTGTGGAGATTATGTCCGGGT
* *
41889559 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCAGATAACTACGTGTGGAGATTATGTCCGGGT
41889596 AAGAC
1 AAGAC
41889601 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCAGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41891155 original size:16 final size:16
Alignment explanation
Indices: 41891101--41891158 Score: 82
Period size: 15 Copynumber: 3.6 Consensus size: 16
41891091 CTTCTTCTTC
41891101 TTTTTTTCACGAAAATTT
1 TTTTTTTCAC--AAATTT
*
41891119 TTTTTTTCACGAA-TT
1 TTTTTTTCACAAATTT
41891134 TTTTTTTCACAAATTT
1 TTTTTTTCACAAATTT
41891150 TTTTTTTCA
1 TTTTTTTCA
41891159 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.38
16 13 0.35
18 10 0.27
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTTTCACAAATTT
Found at i:41891210 original size:11 final size:11
Alignment explanation
Indices: 41891194--41891239 Score: 74
Period size: 11 Copynumber: 4.0 Consensus size: 11
41891184 GAATGGAAAC
41891194 CAATTTTTTTT
1 CAATTTTTTTT
41891205 CAATTTTTTTT
1 CAATTTTTTTT
41891216 CAATTTTTGTTTT
1 CAA-TTTT-TTTT
41891229 CAATTTTTTTT
1 CAATTTTTTTT
41891240 TCGAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 18 0.55
12 8 0.24
13 7 0.21
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:41891249 original size:13 final size:12
Alignment explanation
Indices: 41891195--41891251 Score: 71
Period size: 13 Copynumber: 4.7 Consensus size: 12
41891185 AATGGAAACC
41891195 AATTTTTTTTC-
1 AATTTTTTTTCA
41891206 AATTTTTTTTCA
1 AATTTTTTTTCA
*
41891218 ATTTTTGTTTTCA
1 AATTTT-TTTTCA
*
41891231 ATTTTTTTTTCGA
1 AATTTTTTTTC-A
41891244 AATTTTTT
1 AATTTTTT
41891252 GAAGAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.27
12 10 0.24
13 20 0.49
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTCA
Found at i:41892283 original size:21 final size:23
Alignment explanation
Indices: 41892239--41892284 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
41892229 CACTTGTAAG
* *
41892239 AAACACATTAAAATGAGTTTATT
1 AAACACATTAAAATCAGCTTATT
41892262 AAACACATTAAAA-CA-CTTATT
1 AAACACATTAAAATCAGCTTATT
41892283 AA
1 AA
41892285 TCATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (23 bp):
AAACACATTAAAATCAGCTTATT
Found at i:41894925 original size:11 final size:11
Alignment explanation
Indices: 41894909--41894941 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41894899 GGCATAAAGT
41894909 TGTTCACACCA
1 TGTTCACACCA
*
41894920 TGTTCA-GCCA
1 TGTTCACACCA
41894930 TGTTCACACCA
1 TGTTCACACCA
41894941 T
1 T
41894942 ATGGCTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.30
Consensus pattern (11 bp):
TGTTCACACCA
Found at i:41895746 original size:11 final size:11
Alignment explanation
Indices: 41895730--41895756 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41895720 GTAGTTTCGA
41895730 AAAAAAAATTC
1 AAAAAAAATTC
41895741 AAAAAAAATTC
1 AAAAAAAATTC
41895752 AAAAA
1 AAAAA
41895757 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:41895746 original size:12 final size:12
Alignment explanation
Indices: 41895729--41895761 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41895719 TGTAGTTTCG
41895729 AAAAAAAAATTC
1 AAAAAAAAATTC
41895741 -AAAAAAAATTC
1 AAAAAAAAATTC
41895752 AAAAACAAAA
1 AAAAA-AAAA
41895762 AAAAATCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:41902469 original size:20 final size:20
Alignment explanation
Indices: 41902444--41902483 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41902434 GAATCTATTC
41902444 GGCACCATCCTTGGACAACA
1 GGCACCATCCTTGGACAACA
41902464 GGCACCATCCTTGGACAACA
1 GGCACCATCCTTGGACAACA
41902484 AGAATCGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.20, T:0.15
Consensus pattern (20 bp):
GGCACCATCCTTGGACAACA
Found at i:41905085 original size:55 final size:54
Alignment explanation
Indices: 41904990--41905139 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
41904980 CTACTTTGTT
* ** * *
41904990 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
41905044 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
41905099 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
41905140 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:41905102 original size:27 final size:27
Alignment explanation
Indices: 41904962--41905139 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
41904952 TAAATTGTAC
41904962 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
41904989 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
41905015 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
41905043 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
41905071 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
41905098 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
41905125 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41905140 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:41905103 original size:82 final size:81
Alignment explanation
Indices: 41904963--41905118 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
41904953 AAATTGTACA
* * * *
41904963 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
41905028 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
41905044 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
41905107 TGTGCGAGTTGA
63 TGTGCGAATTGA
41905119 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:41926072 original size:40 final size:40
Alignment explanation
Indices: 41925974--41926276 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
41925964 TCCTCGTTCA
* * * * *
41925974 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41926013 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41926053 AATGCCTTCGGGACTTAACCCGGATTTAACAACCCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41926093 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41926133 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41926173 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41926213 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41926253 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41926277 CAGCATTCAA
Statistics
Matches: 238, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.16
40 193 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41928572 original size:47 final size:47
Alignment explanation
Indices: 41928503--41929198 Score: 1086
Period size: 47 Copynumber: 14.6 Consensus size: 47
41928493 AGTATATGTG
* * *
41928503 GAATGTGAAAGTATATATATATGTGGTAAGGCCTAATGGCTGATGTGAT
1 GAATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928552 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928599 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41928646 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928695 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41928742 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928791 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41928838 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41928885 GAATGTGAAAATGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928932 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41928981 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41929028 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41929077 GAATGTGAAGGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * * * * * *
41929124 GAATGTGAAAGTGTATATATGTGACAGGGTCGAGTGGCCAACGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
41929171 GGACGTGAAAGTGTATAAATGTGATAAG
1 GAATGTGAAAGTGTATATATGTGATAAG
41929199 TCCCGAATGG
Statistics
Matches: 603, Mismatches: 36, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
47 411 0.68
49 192 0.32
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:41928616 original size:96 final size:95
Alignment explanation
Indices: 41928503--41929198 Score: 1101
Period size: 96 Copynumber: 7.3 Consensus size: 95
41928493 AGTATATGTG
* * * *
41928503 GAATGTGAAAGTATATATATATGTGGTAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTG-TA
1 GAATGTGAAAG--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATA
*
41928567 TATATGTGATAAGGCCTAATAGCCGATGTGAT
64 TATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928599 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATAT
41928664 ATATGTGATAAGGCCTAATGGCCGATGTGAT
65 ATATGTGATAAGGCCTAATGGCCGATGTGAT
41928695 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATAT
41928760 ATATGTGATAAGGCCTAATGGCCGATGTGAT
65 ATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41928791 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTG-TATA
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATA
41928855 TATGTGATAAGGCCTAATGGCCGATGTGAT
66 TATGTGATAAGGCCTAATGGCCGATGTGAT
*
41928885 GAATGTGAAAATGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATAT
*
41928950 ATATGTGATAAGGCCTAATGGACGATGTGAT
65 ATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
41928981 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATAT
41929046 ATATGTGATAAGGCCTAATGGCCGATGTGAT
65 ATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41929077 GAATGTGAAGGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATA
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATA
* * * * * * *
41929141 TATGTGACAGGGTCGAGTGGCCAACGTGAT
66 TATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
41929171 GGACGTGAAAGTGTATAAATGTGATAAG
1 GAATGTGAAAGTGTATATATGTGATAAG
41929199 TCCCGAATGG
Statistics
Matches: 564, Mismatches: 32, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
94 187 0.33
96 377 0.67
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (95 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATA
TATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:41928664 original size:143 final size:143
Alignment explanation
Indices: 41928503--41929198 Score: 1112
Period size: 143 Copynumber: 4.9 Consensus size: 143
41928493 AGTATATGTG
* * *
41928503 GAATGTGAAAGTATATATATATGTGGTAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
41928568 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
*
41928633 TCGCCGATGTGAT
131 TGGCCGATGTGAT
41928646 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
41928711 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
41928776 AATGGCCGATGTGAT
129 AATGGCCGATGTGAT
*
41928791 GAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
41928854 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATGTGATAAGGCCTAA
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
*
41928919 TAGCCGATGTGAT
131 TGGCCGATGTGAT
*
41928932 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
41928997 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
41929062 AATGGCCGATGTGAT
129 AATGGCCGATGTGAT
* *
41929077 GAATGTG-AAG-GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * * * * *
41929140 ATATGTGACAGGGTCGAGTGGCCAACGTGATGGACGTGAAAGTGTATAAATGTGATAAG
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41929199 TCCCGAATGG
Statistics
Matches: 522, Mismatches: 25, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
141 60 0.11
143 373 0.71
144 3 0.01
145 86 0.16
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
TGGCCGATGTGAT
Found at i:41937469 original size:20 final size:20
Alignment explanation
Indices: 41937421--41937461 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41937411 AAGAAAGCGA
* *
41937421 AATTGAGCTCGAATTAGCTG
1 AATTGAGCTCAAATGAGCTG
41937441 AATTGAGCTCAAATGAGCTG
1 AATTGAGCTCAAATGAGCTG
41937461 A
1 A
41937462 TTGGAGCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (20 bp):
AATTGAGCTCAAATGAGCTG
Found at i:41938055 original size:20 final size:20
Alignment explanation
Indices: 41938030--41938097 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
41938020 TCCAGGCGGT
41938030 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
41938050 TCAGCTCATTCGGGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* * *
41938070 TCAGTTCACACGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
41938090 TCAGCTCA
1 TCAGCTCA
41938098 TTGAGCTCGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:41945911 original size:11 final size:11
Alignment explanation
Indices: 41945880--41945913 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41945870 GCATAAAGAC
41945880 GTTCACACCAT
1 GTTCACACCAT
*
41945891 GTTCA-GCCAT
1 GTTCACACCAT
41945901 GTTCACACCAT
1 GTTCACACCAT
41945912 GT
1 GT
41945914 GTCTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:41946739 original size:12 final size:12
Alignment explanation
Indices: 41946718--41946754 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
41946708 CGTAAATTGT
41946718 AAATTCAAAAAA
1 AAATTCAAAAAA
*
41946730 AAATT-GAAAAA
1 AAATTCAAAAAA
41946741 AAA-TCAAAAAA
1 AAATTCAAAAAA
41946752 AAA
1 AAA
41946755 GAAGAGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:41948967 original size:15 final size:16
Alignment explanation
Indices: 41948949--41948978 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41948939 AAGAAAAGCA
41948949 AAAAAAAT-GAGTGAT
1 AAAAAAATAGAGTGAT
41948964 AAAAAAATAGAGTGA
1 AAAAAAATAGAGTGA
41948979 AACAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (16 bp):
AAAAAAATAGAGTGAT
Found at i:41952414 original size:11 final size:11
Alignment explanation
Indices: 41952383--41952416 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41952373 GCATAAAGAC
41952383 GTTCACACCAT
1 GTTCACACCAT
*
41952394 GTTCA-GCCAT
1 GTTCACACCAT
41952404 GTTCACACCAT
1 GTTCACACCAT
41952415 GT
1 GT
41952417 GGATCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:41960899 original size:23 final size:22
Alignment explanation
Indices: 41960847--41960899 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
41960837 TCCTCATCTT
*
41960847 TTTCTTTTGTTTCTTTCTCTAA
1 TTTCTTTTCTTTCTTTCTCTAA
* *
41960869 CTTATTTTCTCTTCTTTCT-TCAA
1 TTTCTTTTCT-TTCTTTCTCT-AA
41960892 TTTCTTTT
1 TTTCTTTT
41960900 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTCTCTAA
Found at i:41960974 original size:18 final size:18
Alignment explanation
Indices: 41960951--41960989 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41960941 CTCTTTTTGC
41960951 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
41960969 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
41960987 TCT
1 TCT
41960990 GTCTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:41966789 original size:11 final size:11
Alignment explanation
Indices: 41966773--41966805 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41966763 TTCAGCTTGT
41966773 TAGGAAACTTC
1 TAGGAAACTTC
41966784 TAGGAAA-TTAC
1 TAGGAAACTT-C
41966795 TAGGAAACTTC
1 TAGGAAACTTC
41966806 ATAAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (11 bp):
TAGGAAACTTC
Found at i:41974433 original size:19 final size:19
Alignment explanation
Indices: 41974405--41974443 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41974395 AATAAATTAC
*
41974405 TCATCATAGTTAATTGAGT
1 TCATCATAGTTAATTAAGT
*
41974424 TCATCTTAGTTAATTAAGT
1 TCATCATAGTTAATTAAGT
41974443 T
1 T
41974444 GCTGGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (19 bp):
TCATCATAGTTAATTAAGT
Found at i:41978282 original size:20 final size:20
Alignment explanation
Indices: 41978220--41978286 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
41978210 AGCTAATAAC
*
41978220 GAGCTGAATTGAGCTCGAAT
1 GAGCTGACTTGAGCTCGAAT
*
41978240 AAGCTGACTTGAGCTCGAAT
1 GAGCTGACTTGAGCTCGAAT
41978260 GAGCTGACTTGAGCTC-AAGT
1 GAGCTGACTTGAGCTCGAA-T
41978280 GAGCTGA
1 GAGCTGA
41978287 ACCACATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.05
20 41 0.95
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (20 bp):
GAGCTGACTTGAGCTCGAAT
Found at i:41980828 original size:20 final size:20
Alignment explanation
Indices: 41980800--41980863 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
41980790 GCTGATAGAA
* *
41980800 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCAAATG
41980820 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
41980840 AGCTG-ATTGGAGCTAAAACG
1 AGCTGAATT-GAGCTCAAATG
41980860 AGCT
1 AGCT
41980864 AAAGGAGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:41983700 original size:40 final size:41
Alignment explanation
Indices: 41983656--41983739 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 41
41983646 TAAATAAAAG
41983656 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA-AT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
* * * *
41983696 AAAGTCCAGCAACTCATTTATTAAGTAAGATGAGTTTATAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
41983737 AAA
1 AAA
41983740 TTGCAAGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (41 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
Found at i:41990691 original size:12 final size:12
Alignment explanation
Indices: 41990674--41990717 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
41990664 TGAAAATATT
41990674 AAAAAAATTTGAA
1 AAAAAAATTTG-A
41990687 AAAAAAATTTGA
1 AAAAAAATTTGA
* *
41990699 AAAAAAACTTCA
1 AAAAAAATTTGA
41990711 AAAAAAA
1 AAAAAAA
41990718 AGTGAGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:41990692 original size:13 final size:13
Alignment explanation
Indices: 41990674--41990718 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
41990664 TGAAAATATT
41990674 AAAAAAATTTGAA
1 AAAAAAATTTGAA
41990687 AAAAAAATTTG-A
1 AAAAAAATTTGAA
* *
41990699 AAAAAAACTTCAA
1 AAAAAAATTTGAA
41990712 AAAAAAA
1 AAAAAAA
41990719 GTGAGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:41999389 original size:21 final size:21
Alignment explanation
Indices: 41999365--41999409 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41999355 AAATTCACAT
41999365 ATTTAAAACAAGACAC-AATTA
1 ATTTAAAACAAGAC-CTAATTA
**
41999386 ATTTAAATTAAGACCTAATTA
1 ATTTAAAACAAGACCTAATTA
41999407 ATT
1 ATT
41999410 CGGTTAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
ATTTAAAACAAGACCTAATTA
Found at i:42010879 original size:28 final size:27
Alignment explanation
Indices: 42010815--42010964 Score: 223
Period size: 28 Copynumber: 5.6 Consensus size: 27
42010805 TTATTAAGTC
* *
42010815 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
42010842 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
42010870 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
42010897 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
42010925 CGCACACTTAGTGCTACAT-A-CAATT
1 CGCACACTTAGTGCTACATAATCAACT
42010950 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42010965 GCACAATTTA
Statistics
Matches: 116, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
25 18 0.16
26 1 0.01
27 48 0.41
28 49 0.42
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42010899 original size:55 final size:54
Alignment explanation
Indices: 42010815--42010989 Score: 235
Period size: 55 Copynumber: 3.2 Consensus size: 54
42010805 TTATTAAGTC
* * *
42010815 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACAT-ATCAACTCGCACACTTAGTGCTACATAATCAAACT
*
42010870 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATA-TCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
42010925 CGCACACTTAGTGCTACATA-CAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
42010979 CGCACACTTAG
1 CGCACACTTAG
42010990 CGCCAATCTC
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
53 22 0.20
54 17 0.16
55 69 0.64
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:42018863 original size:28 final size:27
Alignment explanation
Indices: 42018800--42018924 Score: 187
Period size: 27 Copynumber: 4.6 Consensus size: 27
42018790 TTATTAAGTC
* *
42018800 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
42018827 CGCACACTTAGTGCTACATAATTATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
42018855 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
42018882 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
42018910 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42018925 GCACAATTTA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
27 47 0.52
28 44 0.48
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42018884 original size:55 final size:55
Alignment explanation
Indices: 42018800--42018924 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 55
42018790 TTATTAAGTC
* * * *
42018800 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATTATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
42018855 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
42018910 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42018925 GCACAATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:42024700 original size:162 final size:162
Alignment explanation
Indices: 42024417--42024740 Score: 506
Period size: 162 Copynumber: 2.0 Consensus size: 162
42024407 TTGATTTTCT
* * * * *
42024417 TTTTCCATCGTATACACATCTAATGCCTTGCTAATAAATTCTTGAATGGTTCGATTTAGTTTTGA
1 TTTTCCATCGTATACACATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
*
42024482 ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTT
66 ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCTT
42024547 GAGCTTGAATTGGGCCTGTGTGACTCATATCA
131 GAGCTTGAATTGGGCCTGTGTGACTCATATCA
* * * * *
42024579 TTTTCCTTTGTATACGCATCTAAGGCGTTGCTAATGAAGTCTTGAATGATTCCATTTAG-TTTCA
1 TTTTCCATCGTATACACATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
*
42024643 TACGCATTTGCCTTGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCT
66 -ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCT
* *
42024708 TGAGCTTGAATTGGGCCTTTGTGACTCGTATCA
130 TGAGCTTGAATTGGGCCTGTGTGACTCATATCA
42024741 GTGAGGTATC
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 4 0.03
162 143 0.97
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (162 bp):
TTTTCCATCGTATACACATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCTT
GAGCTTGAATTGGGCCTGTGTGACTCATATCA
Found at i:42025269 original size:5 final size:6
Alignment explanation
Indices: 42025235--42025319 Score: 71
Period size: 6 Copynumber: 13.8 Consensus size: 6
42025225 ACGTTGTAAT
* ** **
42025235 GAAAAT GAAAAA GAAAAA GAAATT GAAAAA GAAAAA GAAAAA GAAATC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * *
42025283 GAAAAA GTGAGA GAAAAA GAAAAC GAAGAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA
42025320 TTGAAAAATA
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
6 54 0.90
7 2 0.03
8 4 0.07
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:42025309 original size:24 final size:24
Alignment explanation
Indices: 42025235--42025319 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
42025225 ACGTTGTAAT
* *
42025235 GAAAATGAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAAAAGAAATC
42025259 GAAAAAGAAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAAAAGAAATC
** * *
42025283 GAAAAAGTGAGAGAAAAAGAAAAC
1 GAAAAAGAAAAAGAAAAAGAAATC
42025307 GAAGAAAAGAAAA
1 G-A-AAAAGAAAA
42025320 TTGAAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 43 0.86
25 1 0.02
26 6 0.12
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAAATC
Found at i:42025350 original size:18 final size:18
Alignment explanation
Indices: 42025319--42025353 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42025309 AGAAAAGAAA
42025319 ATTGAAAAATAAATTGAG
1 ATTGAAAAATAAATTGAG
42025337 ATTGAGAAAA-AAATTGA
1 ATTGA-AAAATAAATTGA
42025354 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (18 bp):
ATTGAAAAATAAATTGAG
Found at i:42031020 original size:30 final size:30
Alignment explanation
Indices: 42030986--42031057 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
42030976 TCTAGCATCC
* *
42030986 CCATTCAGCTCCCTAAATACATGCATGCCT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
* * *
42031016 CCATTCATCTCCTTAAACACATTCATGCAT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
**
42031046 TAATTCAGCTCC
1 CCATTCAGCTCC
42031058 ATATGCACAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.35, G:0.07, T:0.31
Consensus pattern (30 bp):
CCATTCAGCTCCCTAAACACATGCATGCAT
Found at i:42035465 original size:20 final size:18
Alignment explanation
Indices: 42035440--42035478 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42035430 AAAGGAAGAC
42035440 AAAAAGAGAAATCGAAAAAG
1 AAAAAGAG-AAT-GAAAAAG
42035460 AAAAAGAGAATGAAAAAG
1 AAAAAGAGAATGAAAAAG
42035478 A
1 A
42035479 GCAAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAATGAAAAAG
Found at i:42035484 original size:20 final size:20
Alignment explanation
Indices: 42035435--42035489 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
42035425 TAATGAAAGG
42035435 AAGACAAAAAGAGAAATCGAAA
1 AAGA-AAAAAGAG-AATCGAAA
42035457 AAG-AAAAAGAGAAT-GAAA
1 AAGAAAAAAGAGAATCGAAA
42035475 AAGAGCAAAAAGAGA
1 AAGA--AAAAAGAGA
42035490 TTGAGAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 8 0.27
21 9 0.30
22 3 0.10
ACGTcount: A:0.69, C:0.05, G:0.22, T:0.04
Consensus pattern (20 bp):
AAGAAAAAAGAGAATCGAAA
Found at i:42035485 original size:27 final size:27
Alignment explanation
Indices: 42035454--42035505 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
42035444 AGAGAAATCG
42035454 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
42035481 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
42035506 ATGTGAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:42035572 original size:18 final size:19
Alignment explanation
Indices: 42035528--42035573 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
42035518 CAAGAAAAGT
*
42035528 GAAAAAGAAATTGAAGGTA
1 GAAAAAGAAAATGAAGGTA
* *
42035547 G-AAGAGAAAATG-AGTTA
1 GAAAAAGAAAATGAAGGTA
42035564 GAAAAAGAAA
1 GAAAAAGAAA
42035574 CAAAAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (19 bp):
GAAAAAGAAAATGAAGGTA
Found at i:42037269 original size:33 final size:33
Alignment explanation
Indices: 42037232--42037295 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
42037222 GAGTTAGTTT
*
42037232 ATTAAATTTAGTTCAGCTCAAATAAGTGTTACA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTACA
* *
42037265 ATTAATTTTAGTTCAACTTAAATAAGTGTTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTA
42037296 GTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (33 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTACA
Found at i:42050716 original size:46 final size:46
Alignment explanation
Indices: 42050663--42050756 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
42050653 CAAAGAAAAG
42050663 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGAATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGAATATGATGA
* * *
42050709 ACCTCGACCCAGTATCAATGATGATAGGAGCCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGAATATGATGA
42050755 AC
1 AC
42050757 GCCACACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGAATATGATGA
Found at i:42053486 original size:19 final size:18
Alignment explanation
Indices: 42053450--42053489 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42053440 TTTCCACTCG
*
42053450 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
42053468 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
42053487 TTT
1 TTT
42053490 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:42055017 original size:46 final size:46
Alignment explanation
Indices: 42054964--42055057 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
42054954 CAAAGAAAAG
* *
42054964 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTTGTCTATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
*
42055010 ACCTCGACCCAGTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
42055056 AC
1 AC
42055058 GCCACACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:42064207 original size:40 final size:40
Alignment explanation
Indices: 42064109--42064411 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
42064099 TCCTCGTTCA
* * * * *
42064109 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42064148 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42064188 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42064228 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42064268 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42064308 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
42064348 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42064388 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42064412 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42072184 original size:40 final size:40
Alignment explanation
Indices: 42072086--42072388 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
42072076 TCCTCGTTCA
* * * * *
42072086 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42072125 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42072165 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42072205 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42072245 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42072285 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
42072325 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42072365 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42072389 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42090412 original size:39 final size:39
Alignment explanation
Indices: 42090358--42090435 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
42090348 TGTTTCTATC
*
42090358 CTTAGCCGAGCCATCACCTATCCTATCCCTAAAACACTT
1 CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
* * *
42090397 CTTAGTCGAACCATCACCTATCCTATTCTTAAAACACTT
1 CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
42090436 TTGATAAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (39 bp):
CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
Found at i:42091703 original size:27 final size:28
Alignment explanation
Indices: 42091668--42091721 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
42091658 GCTGGACTTG
*
42091668 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* *
42091696 GACA-CATTAATAACATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
42091722 AAAACACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:42092942 original size:14 final size:14
Alignment explanation
Indices: 42092923--42092949 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42092913 TGCATCTCCC
42092923 CATGCATGAATCTA
1 CATGCATGAATCTA
42092937 CATGCATGAATCT
1 CATGCATGAATCT
42092950 GCCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:42095237 original size:12 final size:12
Alignment explanation
Indices: 42095204--42095248 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
42095194 TTTTCACTCG
42095204 ATTTC-TTTTCA
1 ATTTCTTTTTCA
* *
42095215 ACTTCTCTTTCA
1 ATTTCTTTTTCA
42095227 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
42095239 ATCTCTTTTT
1 ATTTCTTTTT
42095249 GTTTTTCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:42095270 original size:16 final size:18
Alignment explanation
Indices: 42095232--42095271 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42095222 TTTCAATTTC
42095232 TTTTTCAATCTCTTTTTG
1 TTTTTCAATCTCTTTTTG
*
42095250 TTTTTCACTCTC-TTTTG
1 TTTTTCAATCTCTTTTTG
42095267 TTTTT
1 TTTTT
42095272 GAAATCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTCAATCTCTTTTTG
Found at i:42095279 original size:18 final size:18
Alignment explanation
Indices: 42095232--42095284 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
42095222 TTTCAATTTC
* *
42095232 TTTTTCAATCTCTTTTTG
1 TTTTTAAATCTCATTTTG
* *
42095250 TTTTTCACTCTC-TTTTG
1 TTTTTAAATCTCATTTTG
42095267 TTTTTGAAATCTCATTTT
1 TTTTT-AAATCTCATTTT
42095285 CATATTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.33
18 16 0.53
19 4 0.13
ACGTcount: A:0.13, C:0.17, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTTAAATCTCATTTTG
Found at i:42114320 original size:25 final size:25
Alignment explanation
Indices: 42114299--42114382 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 25
42114289 GCGAAAATAC
42114299 AAAAGAAAA-G-AAAAATGAAAAAA
1 AAAAGAAAATGAAAAAATGAAAAAA
*
42114322 GAAAGAAAATGAAAAAATGAAATGAAAA
1 AAAAGAAAATGAAAAAATG-AA--AAAA
* *
42114350 AAAACGAGAAAAGAAAAAGATGAAAAGA
1 AAAA-GA-AAATGAAAAA-ATGAAAAAA
42114378 AAAAG
1 AAAAG
42114383 TGAGTGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
23 8 0.16
24 1 0.02
25 7 0.14
26 2 0.04
27 1 0.02
28 14 0.29
29 2 0.04
30 11 0.22
31 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (25 bp):
AAAAGAAAATGAAAAAATGAAAAAA
Found at i:42114348 original size:23 final size:22
Alignment explanation
Indices: 42114300--42114381 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 22
42114290 CGAAAATACA
42114300 AAAGAAAAGAAAAATGAAAAAAG
1 AAAGAAAAGAAAAATG-AAAAAG
*
42114323 AAAGAAAATGAAAAAATG-AAATG
1 AAAGAAAA-G-AAAAATGAAAAAG
*
42114346 AAAAAAAACGAGAAAA-GAAAAAG
1 AAAGAAAA-GA-AAAATGAAAAAG
*
42114369 -ATGAAAAGAAAAA
1 AAAGAAAAGAAAAA
42114382 GTGAGTGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.08
21 2 0.04
22 7 0.14
23 28 0.57
24 1 0.02
25 7 0.14
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAGAAAAGAAAAATGAAAAAG
Found at i:42114360 original size:31 final size:30
Alignment explanation
Indices: 42114299--42114381 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
42114289 GCGAAAATAC
*
42114299 AAAAG-AAAAGA-AAAATGAAAAAAGAAAG
1 AAAAGAAAAAGATGAAATGAAAAAAGAAAG
42114327 AAAATGAAAAA-ATGAAATGAAAAAA-AACGAG
1 AAAA-GAAAAAGATGAAATGAAAAAAGAA--AG
*
42114358 AAAAGAAAAAGATGAAAAGAAAAA
1 AAAAGAAAAAGATGAAATGAAAAA
42114382 GTGAGTGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.09
29 4 0.09
30 21 0.45
31 18 0.38
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (30 bp):
AAAAGAAAAAGATGAAATGAAAAAAGAAAG
Found at i:42114393 original size:17 final size:14
Alignment explanation
Indices: 42114303--42114382 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
42114293 AAATACAAAA
42114303 GAAAAGAAAAATGA-
1 GAAAAGAAAAA-GAT
* *
42114317 AAAAAGAAAGAAAAT
1 GAAAAGAAA-AAGAT
*
42114332 GAAAA-AATGAA-AT
1 GAAAAGAA-AAAGAT
*
42114345 GAAAA-AAAACGA-
1 GAAAAGAAAAAGAT
42114357 GAAAAGAAAAAGAT
1 GAAAAGAAAAAGAT
42114371 GAAAAGAAAAAG
1 GAAAAGAAAAAG
42114383 TGAGTGAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
12 6 0.11
13 16 0.30
14 25 0.47
15 6 0.11
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (14 bp):
GAAAAGAAAAAGAT
Found at i:42118178 original size:23 final size:23
Alignment explanation
Indices: 42118148--42118210 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
42118138 TTTGAACCAT
**
42118148 TACCATTTCGTACCAAATCGTAA
1 TACCATTTCGTACCAAATCACAA
*
42118171 TACCATTTC-TAACCAAATCACAT
1 TACCATTTCGT-ACCAAATCACAA
*
42118194 TACCATTTCGTAACAAA
1 TACCATTTCGTACCAAA
42118211 CCTAAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (23 bp):
TACCATTTCGTACCAAATCACAA
Found at i:42121939 original size:17 final size:18
Alignment explanation
Indices: 42121919--42121954 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42121909 CACATTCATT
42121919 TTCTCAATGTTTTT-TTC
1 TTCTCAATGTTTTTCTTC
*
42121936 TTCTCCATGTTTTTCTTC
1 TTCTCAATGTTTTTCTTC
42121954 T
1 T
42121955 ATTGTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (18 bp):
TTCTCAATGTTTTTCTTC
Done.