Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 13 of 24
Found at i:1725275 original size:28 final size:27
Alignment explanation
Indices: 1725238--1725336 Score: 72
Period size: 27 Copynumber: 3.4 Consensus size: 27
1725228 TATAACTTTC
1725238 AAATTTCAATGGCTTTTTTCAAACATT
1 AAATTTCAATGGCTTTTTTCAAACATT
*** * *
1725265 AAATTTACAATTATATAATTTTTATATAACTTT
1 AAATTT-CAA-TGGCT--TTTTT-CA-AACATT
*
1725298 CAAATTTCAATGGCTTTTTTCGAACATT
1 -AAATTTCAATGGCTTTTTTCAAACATT
1725326 AAATTTACAAT
1 AAATTT-CAAT
1725337 TATATAATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 15
0.67 0.14 0.19
Matches are distributed among these distances:
27 12 0.23
28 12 0.23
29 2 0.04
30 5 0.09
31 5 0.09
32 3 0.06
33 8 0.15
34 6 0.11
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (27 bp):
AAATTTCAATGGCTTTTTTCAAACATT
Found at i:1725691 original size:22 final size:22
Alignment explanation
Indices: 1725663--1725706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1725653 AGATATAGAG
*
1725663 TTTTTTATTTGAATAATAATAA
1 TTTTTTAATTGAATAATAATAA
1725685 TTTTTTAATTGAATAATAATAA
1 TTTTTTAATTGAATAATAATAA
1725707 AAACCCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTTTAATTGAATAATAATAA
Found at i:1725826 original size:32 final size:32
Alignment explanation
Indices: 1725790--1725859 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1725780 AATTAAATAT
*
1725790 TATTTTTTATTTTATTAAAAA-ATAATAAAAAA
1 TATTTTTTATTTT-TAAAAAATATAATAAAAAA
**
1725822 TATTTTTTATTTTTAAAAAATATAATAATTAA
1 TATTTTTTATTTTTAAAAAATATAATAAAAAA
1725854 TATTTT
1 TATTTT
1725860 AATTTGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 6 0.18
32 28 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTTTTTATTTTTAAAAAATATAATAAAAAA
Found at i:1725860 original size:30 final size:31
Alignment explanation
Indices: 1725794--1725869 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 31
1725784 AAATATTATT
*
1725794 TTTTATTTTATTAAAAAATAATAAAAAATATT
1 TTTTA-TTTATTAAAAAATAATAAAAAATATA
* *
1725826 TTTTATTT-TTAAAAAAT-ATAATAATTAATA
1 TTTTATTTATTAAAAAATAATAAAAAAT-ATA
*
1725856 TTTTAATTTGTTAA
1 TTTT-ATTTATTAA
1725870 TATAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 7 0.18
30 15 0.39
31 7 0.18
32 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TTTTATTTATTAAAAAATAATAAAAAATATA
Found at i:1725863 original size:108 final size:108
Alignment explanation
Indices: 1725748--1725944 Score: 306
Period size: 108 Copynumber: 1.8 Consensus size: 108
1725738 TATCATTATT
* * * *
1725748 TTTTAATTTGTTAATGTAAATTTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAA-AA
1 TTTTAATTTGTTAATATAAAATTTTTAAACTAAATTAAATATTA-TTTTTATTTTATTAAAAGAA
*
1725812 TAATAAAAAATATTTTTTATTTTTAAAAAATATAATAATTAATA
65 TAATAAAAAACATTTTTTATTTTTAAAAAATATAATAATTAATA
*
1725856 TTTTAATTTGTTAATATAAAATTTTTAAACTAAATTAAATATTATTTTTATTTTATTAAAAGTTA
1 TTTTAATTTGTTAATATAAAATTTTTAAACTAAATTAAATATTATTTTTATTTTATTAAAAG-AA
*
1725921 TAATAAAAAACCTTTTTTATTTTT
65 TAATAAAAAACATTTTTTATTTTT
1725945 TATTGTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
107 17 0.21
108 40 0.50
109 23 0.29
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (108 bp):
TTTTAATTTGTTAATATAAAATTTTTAAACTAAATTAAATATTATTTTTATTTTATTAAAAGAAT
AATAAAAAACATTTTTTATTTTTAAAAAATATAATAATTAATA
Found at i:1725995 original size:132 final size:129
Alignment explanation
Indices: 1725827--1726176 Score: 434
Period size: 132 Copynumber: 2.8 Consensus size: 129
1725817 AAAAATATTT
* * * * *
1725827 TTTATTTTTAAAAAATATAATAATTAATATTTTAATTTGTTAATATAAAATTTTTAAACTAAATT
1 TTTATTTTTATAAAATATAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAACTTAATT
*** * * *
1725892 AAATATTATTTTTATTTTATTAAAAGTTATAATAAAAAACCTTTTTTATTTTTTATTGTAAAATT
66 AAATATTATTTTTATAAAATTAAAAATAATAATAAAAAACCCTTTTTATTTTTTATT-T-AAATT
*
1725957 G
129 A
* *
1725958 TTTATTTTTATAAAATCATAATAATTAATATTTTAATTTTTTAATGT-AATTTTTTGAACTTAAT
1 TTTATTTTTATAAAAT-ATAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAACTTAAT
*
1726022 TAAATATTATTTTTAATAAAATTAAAAATAATAATAATAAACCCTTTTTATTTTTTATTTAAATT
65 TAAATATTATTTTT-ATAAAATTAAAAATAATAATAAAAAACCCTTTTTATTTTTTATTTAAATT
1726087 A
129 A
*
1726088 TTT-TATTT-T--AA-A-AATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAAACTTAAT
1 TTTATTTTTATAAAATATAATAATTAATATTTTAATTTATTAATGTAAATTTTTT-AAACTTAAT
1726147 TAAATATTA-TTTT-T--AATTAAAAATAATAAT
65 TAAATATTATTTTTATAAAATTAAAAATAATAAT
1726177 TAATACATTA
Statistics
Matches: 198, Mismatches: 17, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
120 16 0.08
122 1 0.01
123 27 0.14
124 13 0.07
125 17 0.09
126 2 0.01
128 1 0.01
129 4 0.02
130 8 0.04
131 44 0.22
132 65 0.33
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (129 bp):
TTTATTTTTATAAAATATAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAACTTAATT
AAATATTATTTTTATAAAATTAAAAATAATAATAAAAAACCCTTTTTATTTTTTATTTAAATTA
Found at i:1727319 original size:22 final size:23
Alignment explanation
Indices: 1727289--1727331 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1727279 AATTATAATT
1727289 ATAAATTAT-AAATTTTTTAAAA
1 ATAAATTATGAAATTTTTTAAAA
* *
1727311 ATAATTTATGATATTTTTTAA
1 ATAAATTATGAAATTTTTTAA
1727332 TTTTTTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATAAATTATGAAATTTTTTAAAA
Found at i:1727398 original size:34 final size:33
Alignment explanation
Indices: 1727360--1727424 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
1727350 ATTATTCAAG
*
1727360 AATTATAAATTTAA-AATATATACATATAATTAAT
1 AATTATAAATTTAATAAT-TATAAATA-AATTAAT
1727394 AATTATAAATTTAATAATTATAAATAAATTA
1 AATTATAAATTTAATAATTATAAATAAATTA
1727425 TTTATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 21 0.72
35 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTATAAATTTAATAATTATAAATAAATTAAT
Found at i:1727409 original size:15 final size:15
Alignment explanation
Indices: 1727360--1727418 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 15
1727350 ATTATTCAAG
1727360 AATTATAAATTTAA-
1 AATTATAAATTTAAT
1727374 AATATATACATATAATTAAT
1 AAT-TATA-A-AT--TTAAT
1727394 AATTATAAATTTAAT
1 AATTATAAATTTAAT
1727409 AATTATAAAT
1 AATTATAAAT
1727419 AAATTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.08
15 19 0.49
16 1 0.03
17 4 0.10
18 1 0.03
19 8 0.21
20 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATAAATTTAAT
Found at i:1727461 original size:17 final size:17
Alignment explanation
Indices: 1727430--1727480 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1727420 AATTATTTAT
*
1727430 ATATTAAT-TAAAATAA
1 ATATTAATAAAAAATAA
1727446 ATATTAATAAAAAATAA
1 ATATTAATAAAAAATAA
*
1727463 AT-TATAAAAAAAAATAA
1 ATAT-TAATAAAAAATAA
1727480 A
1 A
1727481 AAAATTGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 9 0.29
17 22 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATTAATAAAAAATAA
Found at i:1728695 original size:58 final size:58
Alignment explanation
Indices: 1728625--1728739 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
1728615 TTATTTGGTT
*
1728625 TGCTTTCATGCAGACACCAAAATGCTTCTAGTGTTCATTCAAACCACATTTCAAGATA
1 TGCTTTCATGCAGACACCAAAATGCTTCTAGTGTCCATTCAAACCACATTTCAAGATA
** *
1728683 TGCTTTCATGCAGACACTGAAATGCTTCTAGTGTCCATTTAAACCACATTTCAAGAT
1 TGCTTTCATGCAGACACCAAAATGCTTCTAGTGTCCATTCAAACCACATTTCAAGAT
1728740 GACATCCTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (58 bp):
TGCTTTCATGCAGACACCAAAATGCTTCTAGTGTCCATTCAAACCACATTTCAAGATA
Found at i:1728989 original size:2 final size:2
Alignment explanation
Indices: 1728982--1729031 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1728972 CTTACTTATC
1728982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1729024 AT AT AT AT
1 AT AT AT AT
1729032 TTCTTGAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1732045 original size:5 final size:5
Alignment explanation
Indices: 1732037--1732093 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
1732027 TGATTAAAAG
* *
1732037 TATTA TATTA TATT- TATTA TATTA TATT- TATTA -AATA TATTA TTTTTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA
*
1732085 TATAA TATT
1 TATTA TATT
1732094 TAAAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 11 0.26
5 27 0.64
6 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:1732054 original size:14 final size:14
Alignment explanation
Indices: 1732037--1732095 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
1732027 TGATTAAAAG
1732037 TATTATATTATATT
1 TATTATATTATATT
1732051 TATTATATTATATT
1 TATTATATTATATT
*
1732065 TATTAAATATATTATT
1 TATTATAT-TA-TATT
*
1732081 T-TTATATAATATT
1 TATTATATTATATT
1732094 TA
1 TA
1732096 AAATTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
13 5 0.13
14 22 0.56
15 7 0.18
16 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:1732092 original size:18 final size:18
Alignment explanation
Indices: 1732019--1732085 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
1732009 TATAATGTAA
*
1732019 ATATTATA-TGATTAAA-
1 ATATTATATTTATTAAAT
* *
1732035 AGTATTATATTATATTTATT
1 A-TATTATATT-TATTAAAT
1732055 ATATTATATTTATTAAAT
1 ATATTATATTTATTAAAT
*
1732073 ATATTATTTTTAT
1 ATATTATATTTAT
1732086 ATAATATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 7 0.17
18 19 0.46
19 13 0.32
20 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTATATTTATTAAAT
Found at i:1732110 original size:26 final size:28
Alignment explanation
Indices: 1732053--1732110 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
1732043 ATTATATTTA
* **
1732053 TTATATTATATTTATTAAATATATTATTT
1 TTATATAATATTTA-TAAATATATTAAGT
1732082 TTATATAATATTTA-AAAT-TATTAAGT
1 TTATATAATATTTATAAATATATTAAGT
1732108 TTA
1 TTA
1732111 CTATTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 4 0.15
29 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TTATATAATATTTATAAATATATTAAGT
Found at i:1733061 original size:22 final size:22
Alignment explanation
Indices: 1733011--1733061 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1733001 TTAAAATATT
1733011 AATATAAAAATATTTTTTAAATA
1 AATA-AAAAATATTTTTTAAATA
**
1733034 TTTAAAAAATATTTTTTTAAA-A
1 AATAAAAAATA-TTTTTTAAATA
1733056 AATAAA
1 AATAAA
1733062 TATATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAAAAATATTTTTTAAATA
Found at i:1734289 original size:32 final size:32
Alignment explanation
Indices: 1734253--1734322 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1734243 AATAATAAAA
*
1734253 ATATAATAC-AAATATAAAAATATTTTAAATTT
1 ATATAATACTAAATATAAAAATA-TTAAAATTT
* * *
1734285 ATATAATACTAACTATTAATATATTAAAATTT
1 ATATAATACTAAATATAAAAATATTAAAATTT
1734317 ATATAA
1 ATATAA
1734323 ATATAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATACTAAATATAAAAATATTAAAATTT
Found at i:1734358 original size:29 final size:27
Alignment explanation
Indices: 1734302--1734363 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
1734292 ACTAACTATT
* *
1734302 AATATATTAAAATTTATATAAATATAA
1 AATATATTAAAAATAATATAAATATAA
*
1734329 AATATTTTAAAAATAATATAAAATAATAA
1 AATATATTAAAAATAATAT-AAAT-ATAA
1734358 AATATA
1 AATATA
1734364 CGAATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 16 0.55
28 4 0.14
29 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATATATTAAAAATAATATAAATATAA
Found at i:1734469 original size:19 final size:17
Alignment explanation
Indices: 1734445--1734487 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1734435 TGTGCATACA
1734445 TAAATATAATATAAATTAT
1 TAAATATAATA-AAATT-T
* *
1734464 TAAATAGACTAAAATTT
1 TAAATATAATAAAATTT
1734481 TAAATAT
1 TAAATAT
1734488 CAATGTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATATAATAAAATTT
Found at i:1736017 original size:16 final size:16
Alignment explanation
Indices: 1735928--1736019 Score: 53
Period size: 16 Copynumber: 5.4 Consensus size: 16
1735918 ATAATACAAA
* *
1735928 AAATATATAAAAATAT
1 AAATATATAATAATTT
1735944 AAATATATTAA-AATTT
1 AAATATA-TAATAATTT
*
1735960 ATTAA-ATATGAATAGTTT
1 A--AATATAT-AATAATTT
* * *
1735978 AACATATCAAAATTTATAT
1 AA-ATAT-ATAA-TAATTT
1735997 AAATATATAATAATTT
1 AAATATATAATAATTT
1736013 AAATATA
1 AAATATA
1736020 ATTATTACAT
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
16 25 0.43
17 12 0.21
18 15 0.26
19 6 0.10
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATATATAATAATTT
Found at i:1736536 original size:31 final size:30
Alignment explanation
Indices: 1736473--1736546 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
1736463 ATTTTACTTT
*
1736473 TAAATTTTT-TTGTTTGTATTTTATGTAAA
1 TAAATTTTTATTTTTTGTATTTTATGTAAA
*
1736502 TAAATTTTTTATTTTTTG-ATTTATATTTAAA
1 TAAA-TTTTTATTTTTTGTATTT-TATGTAAA
*
1736533 TAAAATTTTATTTT
1 TAAATTTTTATTTT
1736547 AAATAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.10
30 18 0.46
31 17 0.44
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (30 bp):
TAAATTTTTATTTTTTGTATTTTATGTAAA
Found at i:1736544 original size:30 final size:30
Alignment explanation
Indices: 1736474--1736546 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1736464 TTTTACTTTT
1736474 AAATTTT-TTTGTTTGTATTTTATGTAAATA
1 AAATTTTATTT-TTTGTATTTTATGTAAATA
* *
1736504 AATTTTTTATTTTTTG-ATTTATATTTAAATA
1 AA-ATTTTATTTTTTGTATTT-TATGTAAATA
1736535 AAATTTTATTTT
1 AAATTTTATTTT
1736547 AAATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 15 0.41
31 19 0.51
32 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (30 bp):
AAATTTTATTTTTTGTATTTTATGTAAATA
Found at i:1736547 original size:17 final size:18
Alignment explanation
Indices: 1736521--1736564 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1736511 TATTTTTTGA
1736521 TTTATATTTAAATAAAAT
1 TTTATATTTAAATAAAAT
1736539 TTTAT-TTTAAATAAAAT
1 TTTATATTTAAATAAAAT
*
1736556 ATTA-ATTTA
1 TTTATATTTA
1736565 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATATTTAAATAAAAT
Found at i:1736555 original size:22 final size:22
Alignment explanation
Indices: 1736530--1736571 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1736520 ATTTATATTT
1736530 AAATA-AAATTTTATTTTAAATA
1 AAATATAAA-TTTATTTTAAATA
*
1736552 AAATATTAATTTATTTTAAA
1 AAATATAAATTTATTTTAAA
1736572 AATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATAAATTTATTTTAAATA
Found at i:1736797 original size:16 final size:17
Alignment explanation
Indices: 1736778--1736810 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1736768 AATATGATAT
1736778 TAAAAAAATAAT-TAAA
1 TAAAAAAATAATATAAA
*
1736794 TAAAAATATAATATAAA
1 TAAAAAAATAATATAAA
1736811 ATAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAAATAATATAAA
Found at i:1738901 original size:6 final size:6
Alignment explanation
Indices: 1738885--1739005 Score: 57
Period size: 6 Copynumber: 21.2 Consensus size: 6
1738875 TCAAAAGTAG
* * * *
1738885 ATTAGTA ATTATA ATTATG A-TATA ATTATA TAATATA AATATA ATATAAA
1 ATTA-TA ATTATA ATTATA ATTATA ATTATA -ATTATA ATTATA AT-TATA
* * *
1738935 ATATATA AGTAAA ATTATA A-TATGA A-TAT- ATTA-A AAT-TA A-TATA
1 AT-TATA ATTATA ATTATA ATTAT-A ATTATA ATTATA ATTATA ATTATA
1738979 ATTAT- -TT-TA ATTATA ATTATA A-TATA A
1 ATTATA ATTATA ATTATA ATTATA ATTATA A
1739006 AAATAATAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
3 1 0.01
4 4 0.04
5 23 0.25
6 44 0.48
7 19 0.21
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTATA
Found at i:1738920 original size:13 final size:13
Alignment explanation
Indices: 1738904--1738953 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1738894 TATAATTATG
1738904 ATATAATTATATA
1 ATATAATTATATA
1738917 ATATAA--ATATA
1 ATATAATTATATA
*
1738928 ATATAAAATATATA
1 ATAT-AATTATATA
*
1738942 AGTAAAATTATA
1 A-TATAATTATA
1738954 ATATGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 6 0.19
14 12 0.39
15 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
ATATAATTATATA
Found at i:1739763 original size:14 final size:15
Alignment explanation
Indices: 1739744--1739778 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1739734 TTAAGTGATA
1739744 AATAAAAT-AATTTG
1 AATAAAATAAATTTG
1739758 AATAAAATAAAATTTG
1 AATAAAAT-AAATTTG
1739774 AATAA
1 AATAA
1739779 TTATTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AATAAAATAAATTTG
Found at i:1740399 original size:11 final size:11
Alignment explanation
Indices: 1740380--1740463 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
1740370 AAATATGATT
* *
1740380 ATATGATATGA
1 ATATAATATAA
1740391 ATATAATATAA
1 ATATAATATAA
*
1740402 AAATAAT-TAA
1 ATATAATATAA
* *
1740412 TTATGATATAA
1 ATATAATATAA
1740423 ATTATAATATAAAA
1 A-TATAATAT--AA
* *
1740437 AAATAATATGA
1 ATATAATATAA
*
1740448 ATATGATATAA
1 ATATAATATAA
1740459 ATATA
1 ATATA
1740464 TTAATATTAA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
10 7 0.13
11 31 0.56
12 7 0.13
13 7 0.13
14 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1740427 original size:12 final size:12
Alignment explanation
Indices: 1740392--1740492 Score: 57
Period size: 13 Copynumber: 8.2 Consensus size: 12
1740382 ATGATATGAA
1740392 TATAATATAAA-
1 TATAATATAAAT
*
1740403 AATAAT-T-AAT
1 TATAATATAAAT
*
1740413 TATGATATAAAT
1 TATAATATAAAT
*
1740425 TATAATATAAAAA
1 TATAATAT-AAAT
* *
1740438 AATAATATGAA-
1 TATAATATAAAT
*
1740449 TATGATATAAAT
1 TATAATATAAAT
1740461 ATATTAATATTAAAAT
1 -TA-TAATA-T-AAAT
*
1740477 ATATAACATAAAT
1 -TATAATATAAAT
1740490 TAT
1 TAT
1740493 TATTATATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
9 2 0.03
10 5 0.07
11 14 0.20
12 15 0.22
13 16 0.23
14 5 0.07
15 5 0.07
16 7 0.10
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (12 bp):
TATAATATAAAT
Found at i:1740464 original size:19 final size:19
Alignment explanation
Indices: 1740371--1740470 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 19
1740361 TTTTAGATAA
*
1740371 AATATGAT-TATATGATATG
1 AATATGATATAAAT-ATATG
* * *
1740390 AATATAATATAAAAATAATT
1 AATATGATATAAATAT-ATG
1740410 AATTATGATATAAAT-TAT-
1 AA-TATGATATAAATATATG
* *
1740428 AATAT-AAAAAAATAATATG
1 AATATGATATAAAT-ATATG
*
1740447 AATATGATATAAATATATT
1 AATATGATATAAATATATG
1740466 AATAT
1 AATAT
1740471 TAAAATATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 6 0.10
17 3 0.05
18 5 0.08
19 25 0.40
20 14 0.22
21 10 0.16
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
AATATGATATAAATATATG
Found at i:1740476 original size:36 final size:33
Alignment explanation
Indices: 1740381--1740477 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 33
1740371 AATATGATTA
*
1740381 TATGATATGAA-TATAATATAAAAATAATTAAT
1 TATGATATAAATTATAATATAAAAATAATTAAT
1740413 TATGATATAAATTATAATATAAAAAAATAATATGAA-
1 TATGATATAAATTATAATAT--AAAAATAAT-T-AAT
*
1740449 TATGATATAAATATATTAATATTAAAATA
1 TATGATATAAAT-TA-TAATATAAAAATA
1740478 TATAACATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
32 10 0.18
33 8 0.14
35 9 0.16
36 19 0.34
37 4 0.07
38 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (33 bp):
TATGATATAAATTATAATATAAAAATAATTAAT
Found at i:1740503 original size:30 final size:29
Alignment explanation
Indices: 1740455--1740511 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1740445 TGAATATGAT
1740455 ATAAATATATTAATATTAAAATATATAAC
1 ATAAATATATTAATATTAAAATATATAAC
*
1740484 ATAAAT-TATTATTATATTAAAATTTATA
1 ATAAATATATTA--ATATTAAAATATATA
1740512 TTAATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 6 0.24
30 14 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAAATATATTAATATTAAAATATATAAC
Found at i:1740894 original size:7 final size:7
Alignment explanation
Indices: 1740882--1740916 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1740872 ATTTAAGTTT
1740882 AATTAAA
1 AATTAAA
1740889 AATTAAA
1 AATTAAA
1740896 AATTAAA
1 AATTAAA
1740903 AATTAAA
1 AATTAAA
1740910 AATTAAA
1 AATTAAA
1740917 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:1740919 original size:5 final size:5
Alignment explanation
Indices: 1740909--1740933 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1740899 TAAAAATTAA
1740909 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
1740934 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:1740965 original size:20 final size:20
Alignment explanation
Indices: 1740927--1740965 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1740917 TTAAATTAAA
* **
1740927 TTAAATTTTATTTTTAATAT
1 TTAAATTTAATTTAAAATAT
1740947 TTAAATTTAATTTAAAATA
1 TTAAATTTAATTTAAAATA
1740966 AAAATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTTAATTTAAAATAT
Found at i:1741071 original size:6 final size:6
Alignment explanation
Indices: 1741052--1741085 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1741042 AAACTTAATT
* *
1741052 ATTTAT ATTCAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1741086 TTAATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:1741150 original size:22 final size:22
Alignment explanation
Indices: 1741115--1741157 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1741105 ATAAAATTAA
1741115 TTAAATTTATAAATTATTTAAAC
1 TTAAATTTATAAA-TATTTAAAC
*
1741138 TTAATTTTA-AAATATTTAAA
1 TTAAATTTATAAATATTTAAA
1741158 TTTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAATTTATAAATATTTAAAC
Found at i:1741210 original size:21 final size:21
Alignment explanation
Indices: 1741170--1741210 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1741160 TTATTAATTT
* *
1741170 AATAATTAAATTTAACTTAAC
1 AATAATAAAATTAAACTTAAC
*
1741191 AATAATAAAATTAAATTTAA
1 AATAATAAAATTAAACTTAA
1741211 ATATTTTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAATAAAATTAAACTTAAC
Found at i:1744769 original size:12 final size:12
Alignment explanation
Indices: 1744752--1744776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1744742 CACTCCAATT
1744752 GAAAGATAAAGA
1 GAAAGATAAAGA
1744764 GAAAGATAAAGA
1 GAAAGATAAAGA
1744776 G
1 G
1744777 TGGGGAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAAGATAAAGA
Found at i:1745531 original size:141 final size:141
Alignment explanation
Indices: 1745277--1745533 Score: 505
Period size: 141 Copynumber: 1.8 Consensus size: 141
1745267 GCCAAGTGAG
1745277 TAATGAAATGAAGCTAAAAGTGGTGGACACCATAATAATTTGGTTCCTTGTTTTTCTCTTCCCTG
1 TAATGAAATGAAGCTAAAAGTGGTGGACACCATAATAATTTGGTTCCTTGTTTTTCTCTTCCCTG
*
1745342 TTCTTTTGGTCAGTTTCGTTGACAATTAATTGAAAGCAGGCTTTTGGTATTCATACTATCAGGTT
66 TCCTTTTGGTCAGTTTCGTTGACAATTAATTGAAAGCAGGCTTTTGGTATTCATACTATCAGGTT
1745407 AGGTCCCATTA
131 AGGTCCCATTA
1745418 TAATGAAATGAAGCTAAAAGTGGTGGACACCATAATAATTTGGTTCCTTGTTTTTCTCTTCCCTG
1 TAATGAAATGAAGCTAAAAGTGGTGGACACCATAATAATTTGGTTCCTTGTTTTTCTCTTCCCTG
1745483 TCCTTTTGGTCAGTTTCGTTGACAATTAATTGAAAGCAGGCTTTTGGTATT
66 TCCTTTTGGTCAGTTTCGTTGACAATTAATTGAAAGCAGGCTTTTGGTATT
1745534 TTAATTTGCT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 115 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (141 bp):
TAATGAAATGAAGCTAAAAGTGGTGGACACCATAATAATTTGGTTCCTTGTTTTTCTCTTCCCTG
TCCTTTTGGTCAGTTTCGTTGACAATTAATTGAAAGCAGGCTTTTGGTATTCATACTATCAGGTT
AGGTCCCATTA
Found at i:1746320 original size:12 final size:12
Alignment explanation
Indices: 1746303--1746330 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1746293 TTCTAACCTC
1746303 ACAATTTTTAAT
1 ACAATTTTTAAT
1746315 ACAATTTTTAAT
1 ACAATTTTTAAT
1746327 ACAA
1 ACAA
1746331 GTACGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (12 bp):
ACAATTTTTAAT
Found at i:1747291 original size:28 final size:28
Alignment explanation
Indices: 1747238--1747296 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1747228 AAAATATTTA
* * *
1747238 TATATTTAAAAAATTATATTTTTATATT
1 TATATTTAAAAAATTATATATATATAAT
*
1747266 TATATTT-AAACATGTATATATATATAAT
1 TATATTTAAAAAAT-TATATATATATAAT
1747294 TAT
1 TAT
1747297 TGGATAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TATATTTAAAAAATTATATATATATAAT
Found at i:1749195 original size:20 final size:20
Alignment explanation
Indices: 1749153--1749192 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1749143 AACTGATATA
1749153 TTCTCTACCTTTCCTTTCTT
1 TTCTCTACCTTTCCTTTCTT
*
1749173 TTCTC-ACCTTTTCTTT-TT
1 TTCTCTACCTTTCCTTTCTT
1749191 TT
1 TT
1749193 TTCCCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCTCTACCTTTCCTTTCTT
Found at i:1749690 original size:14 final size:14
Alignment explanation
Indices: 1749673--1749702 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1749663 CATTCTTGTA
1749673 TATTGAAACTTGAT
1 TATTGAAACTTGAT
1749687 TATTGAAACTTGAT
1 TATTGAAACTTGAT
1749701 TA
1 TA
1749703 AAGTATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (14 bp):
TATTGAAACTTGAT
Found at i:1750785 original size:2 final size:2
Alignment explanation
Indices: 1750778--1750817 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1750768 AAAGCAACAC
1750778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1750818 TTATCTACGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1752304 original size:2 final size:2
Alignment explanation
Indices: 1752297--1752336 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1752287 CATGTGGAGA
1752297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1752337 CCTAATTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1753518 original size:3 final size:3
Alignment explanation
Indices: 1753510--1753550 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1753500 TGAAAAGCTT
1753510 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1753551 GTGACTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1754164 original size:25 final size:26
Alignment explanation
Indices: 1754136--1754186 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1754126 ATATGACACG
* *
1754136 TATTTATAAAA-TACTATAATAAAAA
1 TATTTAAAAAATTAATATAATAAAAA
*
1754161 TATTTAAAAAATTAATTTAATAAAAA
1 TATTTAAAAAATTAATATAATAAAAA
1754187 ATATAATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTAAAAAATTAATATAATAAAAA
Found at i:1754279 original size:2 final size:2
Alignment explanation
Indices: 1754239--1754263 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1754229 ATGTGTTGAT
1754239 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1754264 TTGTAGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1755677 original size:33 final size:32
Alignment explanation
Indices: 1755640--1755715 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
1755630 AATAAAATAA
* *
1755640 ATATAATAT-AATTATATAAATATGTCAAAATTT
1 ATATAAAATAAATTAT-T-AATATATCAAAATTT
1755673 ATATAAAAATAAATTATTAATATATCAAAATTT
1 ATAT-AAAATAAATTATTAATATATCAAAATTT
1755706 ATATAAAATA
1 ATATAAAATA
1755716 TATAATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 6 0.15
33 22 0.56
34 5 0.13
35 6 0.15
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (32 bp):
ATATAAAATAAATTATTAATATATCAAAATTT
Found at i:1755821 original size:18 final size:17
Alignment explanation
Indices: 1755790--1755824 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1755780 ATCAAATTAA
*
1755790 TTTTTTTCATATTTTAT
1 TTTTTTTCAAATTTTAT
1755807 TTTTTTTCACAATTTTAT
1 TTTTTTTCA-AATTTTAT
1755825 GGATCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTTCAAATTTTAT
Found at i:1756435 original size:19 final size:20
Alignment explanation
Indices: 1756382--1756440 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
1756372 AAAAATGAAT
* *
1756382 TTTATATTAAAAATCATATTA
1 TTTAAATTAAATAT-ATATTA
*
1756403 TTTAAATTATATAT-TATTA
1 TTTAAATTAAATATATATTA
1756422 -TTAAATATAAATATATATT
1 TTTAAAT-TAAATATATATT
1756441 TGATATAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 4 0.12
21 11 0.34
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAATTAAATATATATTA
Found at i:1756449 original size:23 final size:24
Alignment explanation
Indices: 1756405--1756449 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1756395 TCATATTATT
*
1756405 TAAATTATATATTATTATTAAATA
1 TAAATTATATATTATGATTAAATA
1756429 TAAA-TATATATT-TGATATAAA
1 TAAATTATATATTATGAT-TAAA
1756450 CGATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 12 0.63
24 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAAATTATATATTATGATTAAATA
Found at i:1757163 original size:12 final size:12
Alignment explanation
Indices: 1757126--1757167 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1757116 TTAATTTTTT
*
1757126 TAAAATTTAATTA
1 TAAAAATTAA-TA
1757139 TAAAAA-T-ATA
1 TAAAAATTAATA
1757149 TAAAAATTAATA
1 TAAAAATTAATA
1757161 TAAAAAT
1 TAAAAAT
1757168 AACTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 11 0.42
13 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:1757165 original size:22 final size:23
Alignment explanation
Indices: 1757126--1757168 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1757116 TTAATTTTTT
*
1757126 TAAAATTTAATTATAAAAATATA
1 TAAAAATTAATTATAAAAATATA
1757149 TAAAAATTAA-TATAAAAATA
1 TAAAAATTAATTATAAAAATA
1757169 ACTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAATTAATTATAAAAATATA
Found at i:1757719 original size:2 final size:2
Alignment explanation
Indices: 1757712--1757744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1757702 TCTTAACGCC
1757712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1757745 AAAGTGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1760376 original size:17 final size:17
Alignment explanation
Indices: 1760335--1760381 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
1760325 AAATAAAAAA
*
1760335 TTAA-ATATATTCGTAT
1 TTAATATATATTCATAT
1760351 TATATATATATATTCATAT
1 T-TA-ATATATATTCATAT
*
1760370 TTAATATTTATT
1 TTAATATATATT
1760382 TTTAATTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 3 0.12
19 12 0.46
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATATATATTCATAT
Found at i:1761840 original size:12 final size:12
Alignment explanation
Indices: 1761807--1761844 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1761797 TTAATTATTA
1761807 ATTATATTTAAT
1 ATTATATTTAAT
1761819 ATT-TATTTAAT
1 ATTATATTTAAT
*
1761830 ATTAAATTTAAT
1 ATTATATTTAAT
1761842 ATT
1 ATT
1761845 GAGATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATATTTAAT
Found at i:1763765 original size:13 final size:13
Alignment explanation
Indices: 1763749--1763782 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1763739 ATTTTATTTT
1763749 TTTATTATCAATA
1 TTTATTATCAATA
* *
1763762 TTTATTATTAATT
1 TTTATTATCAATA
1763775 TTTATTAT
1 TTTATTAT
1763783 AATTAATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATTATCAATA
Found at i:1764944 original size:18 final size:18
Alignment explanation
Indices: 1764921--1764956 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1764911 ATACTATACA
1764921 TATGGATATAAAAATATG
1 TATGGATATAAAAATATG
1764939 TATGGATATAAAAATATG
1 TATGGATATAAAAATATG
1764957 ATCGATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
TATGGATATAAAAATATG
Found at i:1764963 original size:17 final size:18
Alignment explanation
Indices: 1764925--1764963 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1764915 TATACATATG
*
1764925 GATATAAAAATATGTATG
1 GATATAAAAATATGTATC
1764943 GATATAAAAATATG-ATC
1 GATATAAAAATATGTATC
1764960 GATA
1 GATA
1764964 ATTAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (18 bp):
GATATAAAAATATGTATC
Found at i:1766004 original size:17 final size:17
Alignment explanation
Indices: 1765982--1766036 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
1765972 TTTTTAAGAG
1765982 ATTTTAAATTTATATAA
1 ATTTTAAATTTATATAA
*
1765999 ATTTTAATATGT-TA-AA
1 ATTTTAA-ATTTATATAA
**
1766015 ATTTT-TTTTTATATAA
1 ATTTTAAATTTATATAA
1766031 ATTTTA
1 ATTTTA
1766037 TAATATGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 14 0.47
17 9 0.30
18 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTATATAA
Found at i:1766069 original size:11 final size:11
Alignment explanation
Indices: 1766055--1766092 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1766045 ATGTATTTGA
1766055 ATTATATTTAT
1 ATTATATTTAT
*
1766066 ATTATTTTTAT
1 ATTATATTTAT
1766077 ATTATATTTTAT
1 ATTATA-TTTAT
1766089 ATTA
1 ATTA
1766093 CGTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:1766355 original size:23 final size:24
Alignment explanation
Indices: 1766328--1766378 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
1766318 TGGTCGAATT
1766328 ATTATTTAAATATTAATA-ATATA
1 ATTATTTAAATATTAATATATATA
**
1766351 ATTATTTTTATATTAATATATATA
1 ATTATTTAAATATTAATATATATA
1766375 ATTA
1 ATTA
1766379 AATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATTTAAATATTAATATATATA
Found at i:1771845 original size:26 final size:25
Alignment explanation
Indices: 1771787--1771845 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
1771777 TTTATACAGA
* *
1771787 TAGGATTGATAAAGTTTAACTTTAT
1 TAGGATTAATAAAGTCTAACTTTAT
*
1771812 TTGTGATTAATAAAGTCTAACTTTAT
1 TAG-GATTAATAAAGTCTAACTTTAT
1771838 CTAGGATT
1 -TAGGATT
1771846 TTAGATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.07
26 24 0.86
27 2 0.07
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (25 bp):
TAGGATTAATAAAGTCTAACTTTAT
Found at i:1772123 original size:3 final size:3
Alignment explanation
Indices: 1772115--1772146 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1772105 AGATTAATTG
1772115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1772147 TATGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1773473 original size:6 final size:6
Alignment explanation
Indices: 1773453--1773522 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1773443 CGATAGTTCG
* * * * *
1773453 TATATT TAT-TT TATATT TATATAT TTTATGT CATAAT CATATT TA-AAT
1 TATATT TATATT TATATT TATAT-T TATAT-T TATATT TATATT TATATT
1773501 TA-ATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATAT
1773523 AGATTTTAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 13 0.25
6 31 0.60
7 8 0.15
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:1773611 original size:24 final size:21
Alignment explanation
Indices: 1773571--1773615 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 21
1773561 GAGGCAACTA
1773571 TATTTTAGTGTCATATTCATAT
1 TATTTTAGTGTCATATT-ATAT
*
1773593 TATTTTATCGTGTCCTATTATAT
1 TATTTTA--GTGTCATATTATAT
1773616 CTGAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (21 bp):
TATTTTAGTGTCATATTATAT
Found at i:1774017 original size:25 final size:25
Alignment explanation
Indices: 1773983--1774033 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1773973 ATGGGTTAGT
1773983 GGGTTTTGGATAAGGCATTTAAATA
1 GGGTTTTGGATAAGGCATTTAAATA
1774008 GGGTTTTGGATAAGGCATTTAAATA
1 GGGTTTTGGATAAGGCATTTAAATA
1774033 G
1 G
1774034 AAAATACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (25 bp):
GGGTTTTGGATAAGGCATTTAAATA
Found at i:1775048 original size:3 final size:3
Alignment explanation
Indices: 1775042--1775083 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1775032 TTTCAAATTA
1775042 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1775084 TTTCAGTGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1780545 original size:22 final size:23
Alignment explanation
Indices: 1780520--1780566 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1780510 GGTATTACGG
*
1780520 TCAAATATAATT-TTATTTTTTT
1 TCAAATATAATTATTATTATTTT
*
1780542 TC-AATTTAATTATTATTATTTT
1 TCAAATATAATTATTATTATTTT
1780564 TCA
1 TCA
1780567 GTACCGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TCAAATATAATTATTATTATTTT
Found at i:1780813 original size:18 final size:18
Alignment explanation
Indices: 1780786--1780839 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
1780776 ATAATACGAA
1780786 AAAAATTAAAATATAATAT
1 AAAAA-TAAAATATAATAT
*
1780805 AAAAATAAAATAAAATAT
1 AAAAATAAAATATAATAT
*
1780823 AAAAATAATAT-TAATAT
1 AAAAATAAAATATAATAT
1780840 GATATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 5 0.16
18 22 0.69
19 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATAAAATATAATAT
Found at i:1780822 original size:23 final size:22
Alignment explanation
Indices: 1780774--1780824 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1780764 TAGATGATAT
* *
1780774 ATATAATACGAAAAAAATTAAA
1 ATATAATACAAAAAAAAATAAA
*
1780796 ATATAATATAAAAATAAAATAAA
1 ATATAATACAAAAA-AAAATAAA
1780819 ATATAA
1 ATATAA
1780825 AAATAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
ATATAATACAAAAAAAAATAAA
Found at i:1780830 original size:13 final size:12
Alignment explanation
Indices: 1780787--1780826 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1780777 TAATACGAAA
1780787 AAAATTAAAATAT
1 AAAA-TAAAATAT
*
1780800 AATATAAAA-AT
1 AAAATAAAATAT
1780811 AAAATAAAATAT
1 AAAATAAAATAT
1780823 AAAA
1 AAAA
1780827 ATAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 11 0.46
13 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:1781189 original size:2 final size:2
Alignment explanation
Indices: 1781182--1781258 Score: 113
Period size: 2 Copynumber: 39.0 Consensus size: 2
1781172 GATAATTTAA
* *
1781182 AT AT AT AT AT AT AT AT -T AC ACT -T TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1781223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1781259 CACCTTAGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1782216 original size:11 final size:12
Alignment explanation
Indices: 1782178--1782223 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
1782168 TTTAAATATT
*
1782178 TTAAAAATAAAA
1 TTAAAAATTAAA
1782190 TT-AAAATTAAA
1 TTAAAAATTAAA
*
1782201 TTAAAAATTATA
1 TTAAAAATTAAA
1782213 -T-AAAATTAAA
1 TTAAAAATTAAA
1782223 T
1 T
1782224 ATATGTCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
12 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:1785734 original size:2 final size:2
Alignment explanation
Indices: 1785727--1785757 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1785717 AATTTAAACT
1785727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1785758 TAGATAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1786150 original size:2 final size:2
Alignment explanation
Indices: 1786143--1786172 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1786133 AAGAGCATAC
*
1786143 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1786173 TTTCTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1788794 original size:17 final size:16
Alignment explanation
Indices: 1788764--1788804 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
1788754 TATTTATGTA
1788764 ATTATATTATTTTTAT
1 ATTATATTATTTTTAT
1788780 ATTATATTATATTTTAT
1 ATTATATTAT-TTTTAT
*
1788797 ATTTTATT
1 ATTATATT
1788805 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTATATTATTTTTAT
Found at i:1788805 original size:12 final size:12
Alignment explanation
Indices: 1788765--1788803 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1788755 ATTTATGTAA
1788765 TTATATTAT-TT
1 TTATATTATATT
1788776 TTATATTATATT
1 TTATATTATATT
* *
1788788 ATATTTTATATT
1 TTATATTATATT
1788800 TTAT
1 TTAT
1788804 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1791758 original size:92 final size:92
Alignment explanation
Indices: 1791648--1791911 Score: 316
Period size: 96 Copynumber: 2.8 Consensus size: 92
1791638 TTGCAACTTT
* * *
1791648 TCAAATAAACCCATTTGAATTGGCTTAAAACAAGCAAAGAAGTGGCTAGAGTTACAGGAAGAAAC
1 TCAAATAAACCCTTTTGAATTGGCTTAAAACAAGCAAAGAAGTGGCTAGAGTTAAAGGAAAAAAC
* *
1791713 TTAGGGCAAAAAG-GAGGGGGTTTGAGC
66 TTAGGGC-AAAAGTGAGAGGGATTGAGC
* * **
1791740 TCAAATAAACCCTTTTGAATTGGCTAAAAACAAGCAAAAAAGTGGCTAGAGATAATAGAAAAAAA
1 TCAAATAAACCCTTTTGAATTGGCTTAAAACAAGCAAAGAAGTGGCTAGAG-T--TA-AAGGAAA
*
1791805 AAACTTAGGGCAAAAGTTAGAGGGATTGAGC
62 AAACTTAGGGCAAAAGTGAGAGGGATTGAGC
* * * *
1791836 TCATATAAACCCTTTTGAATTGGCATGAAACAAGCAAAGAAGTGGCTTAGAGTTATAGGAATAAA
1 TCAAATAAACCCTTTTGAATTGGCTTAAAACAAGCAAAGAAGTGGC-TAGAGTTAAAGGAA-AAA
*
1791901 ACTCA-GGCAAA
64 ACTTAGGGCAAA
1791912 GATTAGAAGA
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
92 48 0.33
93 10 0.07
94 9 0.06
95 7 0.05
96 67 0.46
97 5 0.03
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (92 bp):
TCAAATAAACCCTTTTGAATTGGCTTAAAACAAGCAAAGAAGTGGCTAGAGTTAAAGGAAAAAAC
TTAGGGCAAAAGTGAGAGGGATTGAGC
Found at i:1792140 original size:94 final size:93
Alignment explanation
Indices: 1791945--1792147 Score: 259
Period size: 94 Copynumber: 2.2 Consensus size: 93
1791935 TTTGAGGCGC
* * *
1791945 TTGAGCTC-AAATAAA-CCCTTTTGAATTGGCAAAAAACAAGCAAAGACGTGGCCAGAGTTATAG
1 TTGAGCTCAAAATAAACCCCTTTTGAATTGGCAAAAAACAAGCAAAAAAGTAGCCAGAGTTATAG
* * * *
1792008 AAAAAACTTAGGGCAAAGAGTAGAGGGG
66 AAAAAACTTAAGGCAAAAAATAGAGGGA
* * **
1792036 CTGAGCTCAAAATAAACCCCTTTTGAATTGGCAAAAAACAAGCAAAAAATTAGCTGGAGTTA-AG
1 TTGAGCTCAAAATAAACCCCTTTTGAATTGGCAAAAAACAAGCAAAAAAGTAGCCAGAGTTATA-
*
1792100 GGAAGAAACTTAAGGCAAAAAATAGAGGGA
65 -GAAAAAACTTAAGGCAAAAAATAGAGGGA
1792130 TTGAGCTCAAAATAAACC
1 TTGAGCTCAAAATAAACC
1792148 TTTTTTTTGT
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
91 7 0.07
92 8 0.08
93 39 0.41
94 41 0.43
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (93 bp):
TTGAGCTCAAAATAAACCCCTTTTGAATTGGCAAAAAACAAGCAAAAAAGTAGCCAGAGTTATAG
AAAAAACTTAAGGCAAAAAATAGAGGGA
Found at i:1793775 original size:32 final size:31
Alignment explanation
Indices: 1793724--1793806 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 31
1793714 AATATAACAA
* *
1793724 ATATGATATAGTATTTTTAA-ACATGAAT-AT
1 ATAT-ATATAATATATTTAACACATGAATCAT
*
1793754 ATAATTAATATAATATATTTAACACATGTATCAT
1 AT-A-T-ATATAATATATTTAACACATGAATCAT
1793788 ATATATATATATATATTTA
1 ATATATATA-ATATATTTA
1793807 GAATTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 2 0.05
31 6 0.14
32 24 0.55
33 8 0.18
34 4 0.09
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATATATAATATATTTAACACATGAATCAT
Found at i:1794343 original size:13 final size:13
Alignment explanation
Indices: 1794310--1794353 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1794300 TAAAAATAAA
1794310 AAAATTAT-TTTT
1 AAAATTATATTTT
*
1794322 AACAGTTATATTTT
1 AA-AATTATATTTT
1794336 AAAATTATATTTT
1 AAAATTATATTTT
1794349 CAAAA
1 -AAAA
1794354 AGTTTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 15 0.56
14 10 0.37
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (13 bp):
AAAATTATATTTT
Found at i:1794952 original size:23 final size:23
Alignment explanation
Indices: 1794900--1794952 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1794890 CCGTTCAGTT
1794900 ATTTTTAAAAGTTAACATTTAAA
1 ATTTTTAAAAGTTAACATTTAAA
** * *
1794923 AGATTTAAAATTTAA-ATTTTAAC
1 ATTTTTAAAAGTTAACA-TTTAAA
1794946 ATTTTTA
1 ATTTTTA
1794953 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTTTAAAAGTTAACATTTAAA
Found at i:1796781 original size:2 final size:2
Alignment explanation
Indices: 1796770--1796800 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1796760 TTAATCAATC
1796770 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1796801 CAAATTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1797240 original size:14 final size:14
Alignment explanation
Indices: 1797203--1797241 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1797193 TATTAACTAT
1797203 TAATATTTTTAAAA
1 TAATATTTTTAAAA
*
1797217 TAAAATTTTTAAAA
1 TAATATTTTTAAAA
1797231 -AATATCTTTTA
1 TAATAT-TTTTA
1797242 TTGATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATATTTTTAAAA
Found at i:1797619 original size:2 final size:2
Alignment explanation
Indices: 1797614--1797643 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1797604 TCCATATAGC
1797614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1797644 CAATCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1797954 original size:30 final size:30
Alignment explanation
Indices: 1797928--1797989 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1797918 TATATTATTT
1797928 TTAT-TAA-ATTTAAAAAATAATTTATTAA
1 TTATATAATATTTAAAAAATAATTTATTAA
* *
1797956 TTATATAATTTTTAAAAAATTATTTTAATTAA
1 TTATATAATATTTAAAAAA-TAATTT-ATTAA
1797988 TT
1 TT
1797990 TCATTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.14
29 3 0.11
30 9 0.32
31 5 0.18
32 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATATAATATTTAAAAAATAATTTATTAA
Found at i:1797976 original size:39 final size:39
Alignment explanation
Indices: 1797897--1797976 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
1797887 TAATTATCAT
* **
1797897 TTTAAAAAAAAAATTATTTAATATATTATTTTTATTAAA
1 TTTAAAAAAAAAATTATTTAATATATAATTTTTAAAAAA
* *
1797936 TTTAAAAAATAATTTA-TTAATTATATAATTTTTAAAAAA
1 TTTAAAAAAAAAATTATTTAA-TATATAATTTTTAAAAAA
1797975 TT
1 TT
1797977 ATTTTAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 4 0.11
39 31 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TTTAAAAAAAAAATTATTTAATATATAATTTTTAAAAAA
Found at i:1799209 original size:2 final size:2
Alignment explanation
Indices: 1799202--1799241 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1799192 CCTTTTGTAA
1799202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1799242 TTAAATGTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1800260 original size:3 final size:3
Alignment explanation
Indices: 1800252--1800310 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1800242 TTCAATTTTA
1800252 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1800300 AAT AAT AAT AA
1 AAT AAT AAT AA
1800311 AGCAGCAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1800646 original size:23 final size:20
Alignment explanation
Indices: 1800617--1800670 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
1800607 ATCTGTTTAT
*
1800617 TAATATTATATTTATGTATTTT
1 TAATATTATATTTATG-A-TTG
*
1800639 TATATATTATAATTATGATTG
1 TA-ATATTATATTTATGATTG
1800660 TAATATTATAT
1 TAATATTATAT
1800671 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 3 0.11
23 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TAATATTATATTTATGATTG
Found at i:1800746 original size:72 final size:68
Alignment explanation
Indices: 1800665--1800827 Score: 154
Period size: 72 Copynumber: 2.3 Consensus size: 68
1800655 GATTGTAATA
* * *
1800665 TTATA-TATTTTTATAAATTTTAATATGT-TAATA-ATTTATGTTGTATATAA-TTTAAAATATT
1 TTATATTATTTTTATAAATTTT-ATAT-TATAATATATTTA-ATTATATA-AATTTTAAAATAAT
1800726 TATATTAT
62 TATA-TAT
* * *
1800734 CTTCATATTATTTTTTATATATATTATATTATATTATATTTAATTATATAAATTTTAAAATAATT
1 -TT-ATATTA-TTTTTATAAATTTTATATTATAATATATTTAATTATATAAATTTTAAAATAATT
1800799 ATATAT
63 ATATAT
*
1800805 TTATATTATATTTATATAATTTT
1 TTATATTATTTTTATA-AATTTT
1800828 TATAATGTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
68 7 0.09
69 10 0.13
70 4 0.05
71 9 0.12
72 30 0.39
73 17 0.22
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (68 bp):
TTATATTATTTTTATAAATTTTATATTATAATATATTTAATTATATAAATTTTAAAATAATTATA
TAT
Found at i:1800763 original size:5 final size:5
Alignment explanation
Indices: 1800725--1800821 Score: 58
Period size: 5 Copynumber: 19.2 Consensus size: 5
1800715 TTTAAAATAT
* * *
1800725 TTATA TTATC TTCATA TTATT TTTTA TATATA TTATA TTATA TTATA TT-TAA
1 TTATA TTATA TT-ATA TTATA TTATA T-TATA TTATA TTATA TTATA TTAT-A
* * **
1800777 TTATA -TAAA TTTTA AAATAA TTATA -TAT- TTATA TTATA TTTATA T
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA -TTATA T
1800822 AATTTTTATA
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
4 10 0.14
5 42 0.61
6 17 0.25
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1800781 original size:27 final size:27
Alignment explanation
Indices: 1800726--1800783 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1800716 TTAAAATATT
* * *
1800726 TATATTATCTTCATATTATTTTTTATA
1 TATATTATATTCATATTATATTTAATA
1800753 TATATTATATT-ATATTATATTTAATTA
1 TATATTATATTCATATTATATTTAA-TA
1800780 TATA
1 TATA
1800784 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATTATATTCATATTATATTTAATA
Found at i:1801625 original size:20 final size:19
Alignment explanation
Indices: 1801579--1801643 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 19
1801569 ATATATTATA
*
1801579 TAATCATATTT-A-AAATAT
1 TAAT-ATATTTAATAAATTT
1801597 TATATATATTTATATAAATTT
1 TA-ATATATTTA-ATAAATTT
1801618 TAATATA-TTAATAAATTT
1 TAATATATTTAATAAATTT
*
1801636 TATTATAT
1 TAATATAT
1801644 ATTCACATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 22 0.55
19 5 0.12
20 6 0.15
21 7 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATTTAATAAATTT
Found at i:1801644 original size:20 final size:20
Alignment explanation
Indices: 1801591--1801646 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1801581 ATCATATTTA
*
1801591 AAATATTATATATATTTATAT
1 AAATTTTATATATA-TTATAT
1801612 AAATTTTA-ATATATTA-AT
1 AAATTTTATATATATTATAT
1801630 AAATTTTATTATATATT
1 AAATTTTA-TATATATT
1801647 CACATATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.31
19 3 0.09
20 12 0.38
21 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTATATATATTATAT
Found at i:1802010 original size:17 final size:17
Alignment explanation
Indices: 1801971--1802017 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1801961 GATATATATC
* * *
1801971 TAATATTTATTTTTTAT
1 TAATATTTATATATTAA
*
1801988 TTATATTTATATATTAA
1 TAATATTTATATATTAA
1802005 TAATATTTA-ATAT
1 TAATATTTATATAT
1802018 AAAATTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATATTTATATATTAA
Found at i:1802040 original size:19 final size:20
Alignment explanation
Indices: 1802008--1802052 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1801998 ATATTAATAA
* *
1802008 TATTTAATATAAAAT-TAAT
1 TATTTAATAAAAAATAAAAT
*
1802027 TATTTTATAAAAAATAAAAT
1 TATTTAATAAAAAATAAAAT
1802047 TATTTA
1 TATTTA
1802053 TATTTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTAATAAAAAATAAAAT
Found at i:1803239 original size:2 final size:2
Alignment explanation
Indices: 1803232--1803264 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1803222 AAATAGAATG
1803232 AT AT AT AT AT AT AT AT AT AT AT AT -T AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
1803265 ATAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1804579 original size:11 final size:11
Alignment explanation
Indices: 1804554--1804628 Score: 52
Period size: 11 Copynumber: 7.2 Consensus size: 11
1804544 TATATACACG
**
1804554 AATATAATAAA
1 AATATAATATT
1804565 AATA-AATATAT
1 AATATAATAT-T
1804576 AATATAATATT
1 AATATAATATT
* *
1804587 AATATATTA-A
1 AATATAATATT
*
1804597 AAT-TTATA-T
1 AATATAATATT
1804606 AATATAA-ATT
1 AATATAATATT
*
1804616 ATTATAATATT
1 AATATAATATT
1804627 AA
1 AA
1804629 AAATTATATA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
9 7 0.14
10 16 0.33
11 21 0.43
12 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAATATT
Found at i:1804599 original size:32 final size:32
Alignment explanation
Indices: 1804554--1804681 Score: 92
Period size: 30 Copynumber: 4.1 Consensus size: 32
1804544 TATATACACG
*
1804554 AATATAATAAAAATAAATATATAATATAATATT
1 AATATAATTAAAATAAATATATAATATAA-ATT
*
1804587 AATAT-ATTAAAAT--TTATATAATATAAATT
1 AATATAATTAAAATAAATATATAATATAAATT
* * *
1804616 ATTATAATATTAAA-AATTATATAA-A-AAA-T
1 AATATAAT-TAAAATAAATATATAATATAAATT
* * *
1804645 AATTATGATTAAAAAATAATATA-AATATAATTT
1 AA-TATAATTAAAATA-AATATATAATATAAATT
1804678 AATA
1 AATA
1804682 CATGAATTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
29 13 0.17
30 25 0.33
31 11 0.14
32 19 0.25
33 8 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
AATATAATTAAAATAAATATATAATATAAATT
Found at i:1804607 original size:30 final size:31
Alignment explanation
Indices: 1804571--1804639 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
1804561 TAAAAATAAA
*
1804571 TATATAATATAATATTA-AT-ATATTAAAATT
1 TATATAATATAA-ATTATATAATATTAAAAAT
1804601 TATATAATATAAATTATTATAATATTAAAAAT
1 TATATAATATAAATTA-TATAATATTAAAAAT
1804633 TATATAA
1 TATATAA
1804640 AAAATAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 4 0.11
30 12 0.34
31 2 0.06
32 17 0.49
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TATATAATATAAATTATATAATATTAAAAAT
Found at i:1804621 original size:15 final size:15
Alignment explanation
Indices: 1804573--1804625 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1804563 AAAATAAATA
*
1804573 TATAATATAATATTAA
1 TATAATATAA-ATTAT
*
1804589 TATATTA-AAATT-T
1 TATAATATAAATTAT
1804602 ATATAATATAAATTAT
1 -TATAATATAAATTAT
1804618 TATAATAT
1 TATAATAT
1804626 TAAAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.29
15 15 0.48
16 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATATAAATTAT
Found at i:1804634 original size:15 final size:15
Alignment explanation
Indices: 1804556--1804671 Score: 52
Period size: 15 Copynumber: 7.9 Consensus size: 15
1804546 TATACACGAA
*
1804556 TATAATAAAAATAAAT
1 TATAATATAAAT-AAT
1804572 ATATAATATAATATTAA-
1 -TATAATATAA-A-TAAT
* *
1804589 TATATTA-AAAT-TT
1 TATAATATAAATAAT
*
1804602 ATATAATATAAATTAT
1 -TATAATATAAATAAT
1804618 TATAATATTAAA-AAT
1 TATAATA-TAAATAAT
*
1804633 TAT-ATAAAAAATAAT
1 TATAAT-ATAAATAAT
*
1804648 TATGAT-TAAA-AA-
1 TATAATATAAATAAT
1804660 -ATAATATAAATA
1 TATAATATAAATA
1804672 TAATTTAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
11 4 0.05
12 4 0.05
13 4 0.05
14 15 0.19
15 25 0.32
16 13 0.17
17 9 0.12
18 3 0.04
19 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
TATAATATAAATAAT
Found at i:1804674 original size:28 final size:29
Alignment explanation
Indices: 1804604--1804681 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
1804594 TAAAATTTAT
*
1804604 ATAATATAAAT-T-ATTATAATATTAAAA
1 ATAATATAAATATAATTATAATATAAAAA
* * *
1804631 ATTATATAAAAAATAATTATGAT-TAAAAA
1 ATAATAT-AAATATAATTATAATATAAAAA
1804660 ATAATATAAATATAATT-TAATA
1 ATAATATAAATATAATTATAATA
1804682 CATGAATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 9 0.22
28 12 0.30
29 12 0.30
30 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
ATAATATAAATATAATTATAATATAAAAA
Found at i:1804714 original size:21 final size:22
Alignment explanation
Indices: 1804664--1804715 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
1804654 TAAAAAATAA
*
1804664 TATAAATATAATTTAATACATG
1 TATAAATAAAATTTAATACATG
* * *
1804686 AAT-TATAAAATTTAAT-CATT
1 TATAAATAAAATTTAATACATG
1804706 TATAAATAAA
1 TATAAATAAA
1804716 TAGTATCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TATAAATAAAATTTAATACATG
Found at i:1804948 original size:13 final size:13
Alignment explanation
Indices: 1804930--1804954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1804920 ATGTTCCTGT
1804930 CTTTTTTTTTTTC
1 CTTTTTTTTTTTC
1804943 CTTTTTTTTTTT
1 CTTTTTTTTTTT
1804955 TTAAATTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTTTTTC
Found at i:1805525 original size:3 final size:3
Alignment explanation
Indices: 1805511--1805565 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
1805501 TCTGAATTTT
* * *
1805511 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA AT- ATA TTA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1805558 ATG ATA AT
1 ATA ATA AT
1805566 TTATATACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1807331 original size:23 final size:24
Alignment explanation
Indices: 1807271--1807331 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
1807261 TAAAAGTTAT
* *
1807271 TTTATATTAATATTTATGATTTAA
1 TTTATATAAATATATATGATTTAA
* * *
1807295 TTTAAATAAA-ATATATTATTTTA
1 TTTATATAAATATATATGATTTAA
1807318 -TTATATAAATATAT
1 TTTATATAAATATAT
1807332 TAATTATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 8 0.27
23 14 0.47
24 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTATATAAATATATATGATTTAA
Found at i:1811858 original size:13 final size:13
Alignment explanation
Indices: 1811822--1811855 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1811812 AATATTAAAA
*
1811822 AATATTTTATATT
1 AATATTTAATATT
1811835 AATATTTAATATT
1 AATATTTAATATT
1811848 AA-ATTTAA
1 AATATTTAA
1811856 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTAATATT
Found at i:1815688 original size:20 final size:20
Alignment explanation
Indices: 1815663--1815733 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
1815653 AAATACTCAG
1815663 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1815683 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1815703 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1815723 ATGTATCGATA
1 ATGTATCGATA
1815734 TATTCTGTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1817919 original size:24 final size:24
Alignment explanation
Indices: 1817880--1817955 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
1817870 ATCAAAATTT
* *
1817880 TTATTCCTTGGGGATACTCCAACC
1 TTATTCCTCGGAGATACTCCAACC
1817904 TTATTCCTCGGAGATACTCCAACC
1 TTATTCCTCGGAGATACTCCAACC
** *
1817928 CCATTCCTCCGAGGAGATATTCCAACC
1 TTATTCCT-C--GGAGATACTCCAACC
1817955 T
1 T
1817956 CGCTTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
24 28 0.65
25 1 0.02
27 14 0.33
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (24 bp):
TTATTCCTCGGAGATACTCCAACC
Found at i:1818085 original size:97 final size:97
Alignment explanation
Indices: 1817911--1818156 Score: 379
Period size: 97 Copynumber: 2.5 Consensus size: 97
1817901 ACCTTATTCC
* * * *
1817911 TCGGAGATACTCCAACCCCATTCCTCCGAGGAGATATTCCAACCTCGCTTTTAAACTTGTCAAGA
1 TCGGAGACACTCCAACCCCATTCCTCCGAGGGGATATTCCAACCCCACTTTTAAACTTGTCAAGA
1817976 TTCAAATCTTATTCTTC-CTTAAATTGTCATCA
66 TTCAAATCTTATTC-TCGCTTAAATTGTCATCA
*
1818008 TC-GAGGACACTCCAACCCCATTTCTCCGAGGGGATATTCCAACCCCACTTTTAAACTTGTCAAG
1 TCGGA-GACACTCCAACCCCATTCCTCCGAGGGGATATTCCAACCCCACTTTTAAACTTGTCAAG
*
1818072 ATTCAAATCTTATTCTCGTTTAAATTGTCATCA
65 ATTCAAATCTTATTCTCGCTTAAATTGTCATCA
* * *
1818105 TCGGAGACACTCCAACCCCATTCCTCCGAGGGGATACTCTAACCCCATTTTT
1 TCGGAGACACTCCAACCCCATTCCTCCGAGGGGATATTCCAACCCCACTTTT
1818157 TTCAATAAAA
Statistics
Matches: 136, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
96 4 0.03
97 130 0.96
98 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.31
Consensus pattern (97 bp):
TCGGAGACACTCCAACCCCATTCCTCCGAGGGGATATTCCAACCCCACTTTTAAACTTGTCAAGA
TTCAAATCTTATTCTCGCTTAAATTGTCATCA
Found at i:1820133 original size:48 final size:47
Alignment explanation
Indices: 1820066--1820172 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 47
1820056 TGATAATAAA
*
1820066 AAAATAAGTCACCAATTTTGACA-CTAATAAGGGTGGCTTTTGTTGACT
1 AAAA-AAGCCACCAATTTTGACATC-AATAAGGGTGGCTTTTGTTGACT
*
1820114 AAAGAAAGCCACCATTTTTGACATCAATAAGGGTGGCTTTTGTTGACT
1 AAA-AAAGCCACCAATTTTGACATCAATAAGGGTGGCTTTTGTTGACT
*
1820162 AAATAAGCCAC
1 AAAAAAGCCAC
1820173 TCACCACAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
47 7 0.13
48 45 0.83
49 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (47 bp):
AAAAAAGCCACCAATTTTGACATCAATAAGGGTGGCTTTTGTTGACT
Found at i:1820167 original size:24 final size:24
Alignment explanation
Indices: 1820091--1820168 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
1820081 TTTTGACACT
1820091 AATAAGGGTGGCTTTTGTTGACTA
1 AATAAGGGTGGCTTTTGTTGACTA
* * **** * *
1820115 AAGAAAGCCACCATTT-TTGACATC
1 AATAAGGGTGGCTTTTGTTGAC-TA
1820139 AATAAGGGTGGCTTTTGTTGACTA
1 AATAAGGGTGGCTTTTGTTGACTA
1820163 AATAAG
1 AATAAG
1820169 CCACTCACCA
Statistics
Matches: 36, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
23 5 0.14
24 26 0.72
25 5 0.14
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (24 bp):
AATAAGGGTGGCTTTTGTTGACTA
Found at i:1826542 original size:2 final size:2
Alignment explanation
Indices: 1826530--1826565 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1826520 CTTCTTCTTT
*
1826530 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1826566 GCTACTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.