Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:988372 original size:16 final size:17
Alignment explanation
Indices: 988351--988385 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
988341 AATAATTCAC
988351 TTAATTT-TTTAAAATT
1 TTAATTTATTTAAAATT
*
988367 TTAATTTATTTATAATT
1 TTAATTTATTTAAAATT
988384 TT
1 TT
988386 TTTCTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTATTTAAAATT
Found at i:989743 original size:17 final size:17
Alignment explanation
Indices: 989723--989779 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
989713 TGAATTCATC
989723 TAAAATTATTTTATTAT
1 TAAAATTATTTTATTAT
* *
989740 TAAAATTATATTAATAT
1 TAAAATTATTTTATTAT
* *
989757 TAATATTAATATTTATAAT
1 TAAAATT-AT-TTTATTAT
989776 TAAA
1 TAAA
989780 GTTAAATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 21 0.68
18 2 0.06
19 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATTATTTTATTAT
Found at i:989756 original size:6 final size:6
Alignment explanation
Indices: 989737--989769 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
989727 ATTATTTTAT
*
989737 TATTAA AATT-A TATTAA TATTAA TATTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATT
989770 TATAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:990924 original size:22 final size:23
Alignment explanation
Indices: 990894--990948 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
990884 TATTTTACCA
*
990894 AAAAAAAAAAAATCATA-ATATG
1 AAAATAAAAAAATCATAGATATG
* *
990916 AAAATAAAAAAATTATAGATATT
1 AAAATAAAAAAATCATAGATATG
*
990939 AAAATTAAAA
1 AAAATAAAAA
990949 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAATAAAAAAATCATAGATATG
Found at i:990993 original size:21 final size:21
Alignment explanation
Indices: 990967--991019 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
990957 ATATTAAATA
*
990967 ATAAATTTAAAAAATAATTTT
1 ATAAATTTAAAAAATAAATTT
*
990988 ATAAA-TTAATTAAATTAAATTT
1 ATAAATTTAA--AAAATAAATTT
991010 -TAAATTTAAA
1 ATAAATTTAAA
991020 TCATTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTTAAAAAATAAATTT
Found at i:991017 original size:29 final size:28
Alignment explanation
Indices: 990940--991017 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 28
990930 ATAGATATTA
*
990940 AAATTAAAATTTTAAATATATTAAATAAT
1 AAATT-AAATTTTAAATTTATTAAATAAT
*** *
990969 AAATTTAAAAAATAATTTTA-TAAATTAATT
1 AAA-TTAAATTTTAAATTTATTAAA-TAA-T
990999 AAATTAAATTTTAAATTTA
1 AAATTAAATTTTAAATTTA
991018 AATCATTCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
28 4 0.11
29 27 0.73
30 6 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATTAAATTTTAAATTTATTAAATAAT
Found at i:991253 original size:9 final size:9
Alignment explanation
Indices: 991239--991263 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
991229 TTAACATTTA
991239 TTTTTATAT
1 TTTTTATAT
991248 TTTTTATAT
1 TTTTTATAT
991257 TTTTTAT
1 TTTTTAT
991264 TAAATACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTATAT
Found at i:993081 original size:2 final size:2
Alignment explanation
Indices: 993074--993110 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
993064 TGAGTTTATA
* *
993074 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TC TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
993111 ATTTATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.03, G:0.43, T:0.51
Consensus pattern (2 bp):
TG
Found at i:997261 original size:22 final size:22
Alignment explanation
Indices: 997236--997284 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
997226 TATTATATAC
997236 ATATTATATTTTATCTTGTATT
1 ATATTATATTTTATCTTGTATT
*
997258 ATATTATATTTTATTTTGTATT
1 ATATTATATTTTATCTTGTATT
*
997280 GTATT
1 ATATT
997285 TTAATTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (22 bp):
ATATTATATTTTATCTTGTATT
Found at i:997317 original size:28 final size:28
Alignment explanation
Indices: 997236--997317 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 28
997226 TATTATATAC
* * * *
997236 ATATTATATTTTATCTTGTATTAT-ATT
1 ATATTTTATATTATATTGTATTCTAATT
* * *
997263 ATATTTTATTTTGTATTGTATTTTAATT
1 ATATTTTATATTATATTGTATTCTAATT
*
997291 ATCTTTTATATTATA-TGTATGTCTAAT
1 ATATTTTATATTATATTGTAT-TCTAAT
997318 AAACATATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (28 bp):
ATATTTTATATTATATTGTATTCTAATT
Found at i:997914 original size:14 final size:13
Alignment explanation
Indices: 997898--997939 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
997888 TTTTTTTACT
997898 TTTTTATT-TGTTA
1 TTTTTATTAT-TTA
997911 TTTTTATTATTTAA
1 TTTTTATTATTT-A
997925 TTTTTATTA-TTA
1 TTTTTATTATTTA
997937 TTT
1 TTT
997940 ATAATAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
14 11 0.41
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:997916 original size:13 final size:14
Alignment explanation
Indices: 997898--997935 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
997888 TTTTTTTACT
997898 TTTTTATT-TGTT-A
1 TTTTTATTAT-TTAA
997911 TTTTTATTATTTAA
1 TTTTTATTATTTAA
997925 TTTTTATTATT
1 TTTTTATTATT
997936 ATTTATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTATTATTTAA
Found at i:997923 original size:20 final size:20
Alignment explanation
Indices: 997890--997938 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
997880 TTCTTTTCTT
*
997890 TTTTTACTT-TTTTATTTGTTA
1 TTTTTA-TTATTTAATTT-TTA
997911 TTTTTATTATTTAATTTTTA
1 TTTTTATTATTTAATTTTTA
*
997931 TTATTATT
1 TTTTTATT
997939 TATAATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTATTATTTAATTTTTA
Found at i:998464 original size:21 final size:20
Alignment explanation
Indices: 998440--998483 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
998430 ATTAAATTCA
*
998440 TAAATTACTTAAATTTAATAT
1 TAAATTACTTAAACTTAAT-T
*
998461 TAAATTATTTAAACTTAATT
1 TAAATTACTTAAACTTAATT
998481 TAA
1 TAA
998484 TAATTTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATTACTTAAACTTAATT
Found at i:998476 original size:27 final size:28
Alignment explanation
Indices: 998446--998500 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
998436 TTCATAAATT
*
998446 ACTTAAATTTAAT-A-TTAAATTATTTAA
1 ACTT-AATTTAATAATTTAAACTATTTAA
998473 ACTTAATTTAATAATTTAAACTATTTAA
1 ACTTAATTTAATAATTTAAACTATTTAA
998501 TATAAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 5 0.20
28 12 0.48
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (28 bp):
ACTTAATTTAATAATTTAAACTATTTAA
Found at i:998491 original size:19 final size:19
Alignment explanation
Indices: 998448--998502 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
998438 CATAAATTAC
* *
998448 TTAAATTTAATATTAAATTAT
1 TTAAACTTAAT-TT-AATAAT
998469 TTAAACTTAATTTAATAAT
1 TTAAACTTAATTTAATAAT
998488 TTAAAC-T-ATTTAATA
1 TTAAACTTAATTTAATA
998503 TAAATCTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
19 11 0.34
20 2 0.06
21 10 0.31
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAACTTAATTTAATAAT
Found at i:999340 original size:13 final size:14
Alignment explanation
Indices: 999312--999344 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
999302 ATTAAATTAT
999312 TTAAATTTATTTTA
1 TTAAATTTATTTTA
999326 TTAAATTTA-TTTA
1 TTAAATTTATTTTA
999339 TTAAAT
1 TTAAAT
999345 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAAATTTATTTTA
Found at i:999466 original size:18 final size:18
Alignment explanation
Indices: 999407--999467 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
999397 AATTAAATTC
**
999407 AAATTTAAATTAAAATTTTT
1 AAATTT-AATTAAAA-TAAT
* *
999427 AATTTTAATTAAAATAAA
1 AAATTTAATTAAAATAAT
*
999445 AAATTTAATTAAAATCAT
1 AAATTTAATTAAAATAAT
999463 AAATT
1 AAATT
999468 ATTTAAACCA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 21 0.62
19 8 0.24
20 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAATTAAAATAAT
Found at i:1001117 original size:3 final size:3
Alignment explanation
Indices: 1001109--1001143 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1001099 CTTTTCTTTT
1001109 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1001144 TTCTTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1002426 original size:14 final size:14
Alignment explanation
Indices: 1002404--1002433 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1002394 TATATTAAAA
*
1002404 AATTTAAAAAAATT
1 AATTAAAAAAAATT
1002418 AATTAAAAAAAATT
1 AATTAAAAAAAATT
1002432 AA
1 AA
1002434 ATTTATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAAAAAAAATT
Found at i:1003025 original size:30 final size:30
Alignment explanation
Indices: 1002977--1003075 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
1002967 TAAAATTAAG
* *
1002977 TTTA-TTAGATAT-AATTAAAGATTAAAAG
1 TTTATTTAAATATAAATTAAAGATTAAAAA
*
1003005 TTTATTTAAATATAAATTAAAAATTAAAAA
1 TTTATTTAAATATAAATTAAAGATTAAAAA
1003035 TTTATTTAAATATAAATTTAAAG-TTAAAAA
1 TTTATTTAAATATAAA-TTAAAGATTAAAAA
1003065 TTTATTTAAAT
1 TTTATTTAAAT
1003076 TTAATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 4 0.06
29 7 0.11
30 48 0.75
31 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (30 bp):
TTTATTTAAATATAAATTAAAGATTAAAAA
Found at i:1004126 original size:17 final size:17
Alignment explanation
Indices: 1004104--1004140 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1004094 GATAGATCGA
1004104 TAATAAAATTATTTATT
1 TAATAAAATTATTTATT
1004121 TAATAAAATTATTTATT
1 TAATAAAATTATTTATT
1004138 TAA
1 TAA
1004141 GGCAGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATAAAATTATTTATT
Found at i:1004458 original size:13 final size:14
Alignment explanation
Indices: 1004438--1004478 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1004428 TAATATTTAT
1004438 ATATTTTATAATTA
1 ATATTTTATAATTA
*
1004452 A-ATTTTAATAA-AA
1 ATATTTT-ATAATTA
1004465 ATATTTTATAATTA
1 ATATTTTATAATTA
1004479 TTAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTTTATAATTA
Found at i:1004820 original size:8 final size:9
Alignment explanation
Indices: 1004788--1004844 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 9
1004778 ATATGATTAT
*
1004788 ATATTTAAA
1 ATATTTTAA
*
1004797 ATATATTAAA
1 ATAT-TTTAA
1004807 ATATTTTTAA
1 ATA-TTTTAA
*
1004817 AT-TTATAA
1 ATATTTTAA
1004825 ATATTTATAA
1 ATATTT-TAA
1004835 ATATTTTAA
1 ATATTTTAA
1004844 A
1 A
1004845 ATTACCATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.17
9 10 0.24
10 23 0.56
11 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATTTTAA
Found at i:1004821 original size:27 final size:28
Alignment explanation
Indices: 1004790--1004847 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1004780 ATGATTATAT
*
1004790 ATTTA-AAATATATTA-AAATATTTTTAA
1 ATTTATAAATAT-TTATAAATATTTTAAA
1004817 ATTTATAAATATTTATAAATATTTTAAA
1 ATTTATAAATATTTATAAATATTTTAAA
1004845 ATT
1 ATT
1004848 ACCATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTATAAATATTTATAAATATTTTAAA
Found at i:1006048 original size:2 final size:2
Alignment explanation
Indices: 1006043--1006082 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1006033 CTTTTGTAAA
1006043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
1006083 AAATATCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1006622 original size:21 final size:22
Alignment explanation
Indices: 1006593--1006639 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1006583 AATGATTTCA
1006593 TTTATTTTATTAA-AAAAAATAT
1 TTTATTTTATTAATAAAAAA-AT
*
1006615 TTTA-TTTATTAATAATAAAAT
1 TTTATTTTATTAATAAAAAAAT
1006636 TTTA
1 TTTA
1006640 AAATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATTTTATTAATAAAAAAAT
Found at i:1008134 original size:12 final size:13
Alignment explanation
Indices: 1008103--1008138 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1008093 TTTAATTTTT
1008103 TTAAATAT--ATA
1 TTAAATATAAATA
1008114 TTAAATATAAATA
1 TTAAATATAAATA
1008127 TT-AATATAAATA
1 TTAAATATAAATA
1008139 AAAATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 10 0.43
13 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:1013095 original size:17 final size:18
Alignment explanation
Indices: 1013070--1013124 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
1013060 CAAATTTGTG
*
1013070 TAAAATATTTTATA-ATT
1 TAAATTATTTTATATATT
1013087 TAAATTATTATTATATATT
1 TAAATTATT-TTATATATT
1013106 TAAAATTA-TTTATAT-TT
1 T-AAATTATTTTATATATT
1013123 TA
1 TA
1013125 TTCTAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 1 0.03
17 11 0.32
18 11 0.32
19 5 0.15
20 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTATTTTATATATT
Found at i:1013103 original size:20 final size:20
Alignment explanation
Indices: 1013070--1013115 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1013060 CAAATTTGTG
1013070 TAAAA-TATT-TTATA-ATT
1 TAAAATTATTATTATATATT
1013087 T-AAATTATTATTATATATT
1 TAAAATTATTATTATATATT
1013106 TAAAATTATT
1 TAAAATTATT
1013116 TATATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 5 0.20
18 5 0.20
19 4 0.16
20 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATTATTATTATATATT
Found at i:1018522 original size:13 final size:14
Alignment explanation
Indices: 1018491--1018532 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1018481 TATCATATTT
1018491 TAATAAT-TTTATA
1 TAATAATATTTATA
1018504 TATATATTATATTTATA
1 TA-ATA--ATATTTATA
1018521 TAATAATATTTA
1 TAATAATATTTA
1018533 AAATTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
16 5 0.20
17 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATAATATTTATA
Found at i:1019740 original size:27 final size:26
Alignment explanation
Indices: 1019705--1019760 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
1019695 ATATGGATAA
*
1019705 ATATGTATTTTACATATACAT-AGATGT
1 ATATATATTTTACATA-A-ATAAGATGT
1019732 ATATATATTTTACATAAATAAGATGT
1 ATATATATTTTACATAAATAAGATGT
1019758 ATA
1 ATA
1019761 AATTCTAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.07
26 10 0.37
27 15 0.56
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (26 bp):
ATATATATTTTACATAAATAAGATGT
Found at i:1026267 original size:20 final size:20
Alignment explanation
Indices: 1026208--1026277 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 20
1026198 TTATTAGAAA
*
1026208 TTATTTTATTTAATCAAATAT
1 TTATTATATTTAAT-AAATAT
* *
1026229 ATATTAT-TTT-TTAAATAT
1 TTATTATATTTAATAAATAT
*
1026247 TTATTATATTTAATAATTAT
1 TTATTATATTTAATAAATAT
1026267 TTA--ATATTTAA
1 TTATTATATTTAA
1026278 ATTATATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 20 0.49
19 4 0.10
20 12 0.29
21 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTATATTTAATAAATAT
Found at i:1026298 original size:27 final size:27
Alignment explanation
Indices: 1026242--1026302 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
1026232 TTATTTTTTA
**
1026242 AATATTT-ATTATATTTAATAATTATTT
1 AATATTTAATTATATTT-ATAATTAAAT
1026269 AATATTTAAATTATATTT-TAATTAAAT
1 AATATTT-AATTATATTTATAATTAAAT
1026296 AAT-TTTA
1 AATATTTA
1026303 TCCAACCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
27 17 0.57
29 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AATATTTAATTATATTTATAATTAAAT
Found at i:1028896 original size:34 final size:33
Alignment explanation
Indices: 1028852--1029069 Score: 251
Period size: 34 Copynumber: 6.4 Consensus size: 33
1028842 AAAAACCACA
*
1028852 ATTTAATCAACAATGGCAACCTACCAAATCTACC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
*
1028886 ATTTAGTCAACAATGGTAAAGCC-ACCAAATCACCC
1 ATTTAATCAACAATGGT-AA-CCTACCAAATCA-CC
* * **
1028921 ATTTAATCAATAATGGTAAGCTACCAAATTTCTC
1 ATTTAATCAACAATGGTAACCTACCAAATCAC-C
* *
1028955 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
* *
1028989 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-TAACCTACCAAATCA-CC
*
1029023 ATTTAATCAACAATGGTAAACTACCAAATCACC
1 ATTTAATCAACAATGGTAACCTACCAAATCACC
1029056 ATTTAATCAACAAT
1 ATTTAATCAACAAT
1029070 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
33 21 0.13
34 104 0.66
35 31 0.20
36 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
ATTTAATCAACAATGGTAACCTACCAAATCACC
Found at i:1028996 original size:103 final size:101
Alignment explanation
Indices: 1028852--1029069 Score: 346
Period size: 103 Copynumber: 2.1 Consensus size: 101
1028842 AAAAACCACA
*
1028852 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAAGCCACCAAATC
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAA-CCACCAAATC
* * **
1028917 ACCCATTTAATCAATAATGGTAAGCTACCAAATTTCTC
65 ACCCATTTAATCAACAATGGTAAACTACCAAATCAC-C
* * *
1028955 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
1029020 CCCATTTAATCAACAATGGTAAACTACCAAATCACC
66 CCCATTTAATCAACAATGGTAAACTACCAAATCACC
1029056 ATTTAATCAACAAT
1 ATTTAATCAACAAT
1029070 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 15 0.14
102 42 0.39
103 50 0.47
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
CCCATTTAATCAACAATGGTAAACTACCAAATCACC
Found at i:1033473 original size:34 final size:33
Alignment explanation
Indices: 1033425--1033642 Score: 260
Period size: 34 Copynumber: 6.5 Consensus size: 33
1033415 TGGTAAAAAC
*
1033425 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1033458 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1033492 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1033526 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1033560 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
1033594 CACCATTTAATCAACAATGGTAAACTATCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
1033627 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1033643 TTTTATAACT
Statistics
Matches: 159, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
32 3 0.02
33 43 0.27
34 107 0.67
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1033541 original size:68 final size:67
Alignment explanation
Indices: 1033427--1033642 Score: 290
Period size: 68 Copynumber: 3.2 Consensus size: 67
1033417 GTAAAAACCA
* * *
1033427 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1033492 CAC
65 CAC
* * * *
1033495 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1033560 CTC
65 CAC
* * * * *
1033563 CCATTTAGTCAACAATGGCAAACCACCAAATCACCATTTAATCAACAATGGTAAACTATCAAATC
1 CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
1033628 A-
66 AC
1033629 CCATTTAATCAACA
1 CCATTTAATCAACA
1033643 TTTTATAACT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
66 13 0.10
67 31 0.24
68 85 0.66
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1033569 original size:102 final size:100
Alignment explanation
Indices: 1033425--1033642 Score: 328
Period size: 102 Copynumber: 2.2 Consensus size: 100
1033415 TGGTAAAAAC
* *
1033425 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1033490 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCA-CCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
1033526 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
1033591 AATCACCATTTAATCAACAATGGTAAACTATCAAAT
65 AATCACCATTTAATCAACAATGGTAAACTACCAAAT
1033627 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1033643 TTTTATAACT
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 13 0.12
101 30 0.29
102 61 0.59
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (100 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1034829 original size:32 final size:33
Alignment explanation
Indices: 1034793--1034863 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
1034783 TTATGTGTTT
1034793 TAAAAATATCATAT-TCATAT-T-TATATCATATA
1 TAAAAATATCATATAT-ATATATATATAT-ATATA
*
1034825 TAAAATTATCATATATATATATATATATATATA
1 TAAAAATATCATATATATATATATATATATATA
1034858 TAAAAA
1 TAAAAA
1034864 AAAAATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 17 0.50
33 12 0.35
34 5 0.15
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAAAATATCATATATATATATATATATATATA
Found at i:1034840 original size:2 final size:2
Alignment explanation
Indices: 1034809--1034859 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
1034799 TATCATATTC
* *
1034809 AT AT TT AT AT CAT AT AT A- AA AT -T AT CAT 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
1034851 AT AT AT AT A
1 AT AT AT AT A
1034860 AAAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 2 0.05
2 36 0.86
3 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1035718 original size:21 final size:21
Alignment explanation
Indices: 1035694--1035749 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1035684 ATTTAAATCG
*
1035694 ATTTAATTTAAATTATTATAT
1 ATTTAATTTAAATTATTATAA
1035715 ATTTAA---AAATTATT-TAA
1 ATTTAATTTAAATTATTATAA
1035732 ATTTAATTATAAA-TATTA
1 ATTTAATT-TAAATTATTA
1035750 ATCTAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
20 4 0.14
21 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATTTAAATTATTATAA
Found at i:1035737 original size:17 final size:18
Alignment explanation
Indices: 1035703--1035737 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1035693 GATTTAATTT
*
1035703 AAATTATTATATATTTAA
1 AAATTATTATAAATTTAA
1035721 AAATTATT-TAAATTTAA
1 AAATTATTATAAATTTAA
1035738 TTATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTATTATAAATTTAA
Found at i:1036388 original size:4 final size:4
Alignment explanation
Indices: 1036379--1036404 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1036369 TGCAGCCGTA
1036379 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1036405 TTATTGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1040438 original size:14 final size:16
Alignment explanation
Indices: 1040419--1040455 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1040409 TGAATTTTAA
1040419 TTTATTTTT-AA-TAT
1 TTTATTTTTAAATTAT
1040433 TTTATTTTTAAATTAT
1 TTTATTTTTAAATTAT
1040449 TTTATTT
1 TTTATTT
1040456 AATGGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTTTAAATTAT
Found at i:1041797 original size:11 final size:11
Alignment explanation
Indices: 1041769--1041885 Score: 50
Period size: 12 Copynumber: 10.6 Consensus size: 11
1041759 AATTATTTTG
*
1041769 AATATAAAATA
1 AATATAATATA
1041780 ATTATATAATATA
1 A--ATATAATATA
*
1041793 AATATGATATAA
1 AATATAATAT-A
*
1041805 AAAATAAT-TA
1 AATATAATATA
*
1041815 AA-ATAAAATAA
1 AATATAATAT-A
* *
1041826 AATATGATAAAA
1 AATATAAT-ATA
*
1041838 AAGATAATA-A
1 AATATAATATA
1041848 AATA-AATATAAA
1 AATATAATAT--A
1041860 AATATAATA-A
1 AATATAATATA
*
1041870 AAT-TTATAT-
1 AATATAATATA
1041879 AATATAA
1 AATATAA
1041886 ATTATGAATA
Statistics
Matches: 80, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
9 15 0.19
10 14 0.17
11 14 0.17
12 22 0.28
13 15 0.19
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AATATAATATA
Found at i:1041834 original size:33 final size:32
Alignment explanation
Indices: 1041774--1041871 Score: 112
Period size: 32 Copynumber: 3.0 Consensus size: 32
1041764 TTTTGAATAT
* *
1041774 AAAATAATT-ATATAATAT-AAATATGATATAA
1 AAAATAATTAAAATAAAATAAAATATGATA-AA
1041805 AAAATAATTAAAATAAAATAAAATATGATAAA
1 AAAATAATTAAAATAAAATAAAATATGATAAA
*
1041837 AAAGATAA-TAAAATAAATATAAAAATATAATAAA
1 AAA-ATAATTAAAATAAA-AT-AAAATATGATAAA
1041871 A
1 A
1041872 TTTATATAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
31 9 0.15
32 21 0.36
33 16 0.27
34 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAATAATTAAAATAAAATAAAATATGATAAA
Found at i:1041877 original size:12 final size:12
Alignment explanation
Indices: 1041769--1041887 Score: 62
Period size: 11 Copynumber: 10.2 Consensus size: 12
1041759 AATTATTTTG
*
1041769 AATATAAAAT-A
1 AATATATAATAA
*
1041780 ATTATATAATATA
1 AATATATAATA-A
1041793 AATATGAT-ATAA
1 AATAT-ATAATAA
1041805 AA-A-ATAATTAA
1 AATATATAA-TAA
1041816 AATA-A-AATAA
1 AATATATAATAA
1041826 AATATGAT-A-AA
1 AATAT-ATAATAA
*
1041837 AA-AGATAATAA
1 AATATATAATAA
*
1041848 AATAAAT-ATAA
1 AATATATAATAA
1041859 AA-ATATAATAA
1 AATATATAATAA
1041870 AATTTATATAATATA
1 AA--TATATAATA-A
1041885 AAT
1 AAT
1041888 TATGAATATA
Statistics
Matches: 85, Mismatches: 6, Indels: 32
0.69 0.05 0.26
Matches are distributed among these distances:
9 4 0.05
10 13 0.15
11 36 0.42
12 10 0.12
13 9 0.11
14 10 0.12
15 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AATATATAATAA
Found at i:1041878 original size:14 final size:14
Alignment explanation
Indices: 1041861--1041912 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
1041851 AAATATAAAA
1041861 ATATAATAAAATTT
1 ATATAATAAAATTT
1041875 ATATAATATAAA-TT
1 ATATAATA-AAATTT
1041889 ATGAATATATCAAAATTT
1 AT--ATA-AT-AAAATTT
1041907 ATATAA
1 ATATAA
1041913 AAATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 12 0.38
15 4 0.12
16 6 0.19
17 5 0.16
18 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:1041878 original size:22 final size:22
Alignment explanation
Indices: 1041799--1041880 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
1041789 TATAAATATG
1041799 ATATAA-AAAA-TAAT-T-AAA
1 ATATAATAAAATTAATATAAAA
* *
1041817 ATAAAATAAAATATGATA-AAAA
1 ATATAATAAAAT-TAATATAAAA
* *
1041839 AGATAATAAAATAAATATAAAA
1 ATATAATAAAATTAATATAAAA
*
1041861 ATATAATAAAATTTATATAA
1 ATATAATAAAATTAATATAA
1041881 TATAAATTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
21 6 0.12
22 34 0.69
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
ATATAATAAAATTAATATAAAA
Found at i:1043456 original size:17 final size:16
Alignment explanation
Indices: 1043411--1043478 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
1043401 CATATTATAA
*
1043411 TAATATTTAAAGTATTT
1 TAATATTTAAA-AATTT
1043428 T-ATATTTCAAAAATTT
1 TAATATTT-AAAAATTT
1043444 TAATATATT-AAAA-TT
1 TAATAT-TTAAAAATTT
* *
1043459 TCATATTTTATAAATTT
1 TAATA-TTTAAAAATTT
1043476 TAA
1 TAA
1043479 ATCAGATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 8 0.20
16 19 0.46
17 12 0.29
18 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (16 bp):
TAATATTTAAAAATTT
Found at i:1043466 original size:32 final size:32
Alignment explanation
Indices: 1043411--1043478 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1043401 CATATTATAA
*
1043411 TAATATTTAAAGTATTTTATATTTCAAAAATTT
1 TAATATTTAAAG-ATTTCATATTTCAAAAATTT
* *
1043444 TAATATATTAAA-ATTTCATATTTTATAAATTT
1 TAATAT-TTAAAGATTTCATATTTCAAAAATTT
1043476 TAA
1 TAA
1043479 ATCAGATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 20 0.65
33 6 0.19
34 5 0.16
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (32 bp):
TAATATTTAAAGATTTCATATTTCAAAAATTT
Found at i:1043841 original size:24 final size:23
Alignment explanation
Indices: 1043796--1043841 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1043786 TATCGATTAA
* * *
1043796 ATTTTTTTATATTTTAATATATT
1 ATTTTTTTAAATTTAAAAATATT
1043819 ATTTATTTTAAATTTAAAAATAT
1 ATTT-TTTTAAATTTAAAAATAT
1043842 GATAAAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTTAAATTTAAAAATATT
Found at i:1044001 original size:17 final size:17
Alignment explanation
Indices: 1043971--1044004 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1043961 ATATTTTATT
* *
1043971 TATATTTTATTATAAAA
1 TATATATTAATATAAAA
1043988 TATATATTAATATAAAA
1 TATATATTAATATAAAA
1044005 ATAATTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATTAATATAAAA
Found at i:1044668 original size:27 final size:29
Alignment explanation
Indices: 1044615--1044673 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1044605 GTAGATATAG
* * *
1044615 ATATATATTTTTTATATATATATAGATGT
1 ATATATATTTTTTACACAAATATAGATGT
1044644 ATATATA-TTTTTACACAAATA-AGATGT
1 ATATATATTTTTTACACAAATATAGATGT
1044671 ATA
1 ATA
1044674 AATACCAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 9 0.33
28 11 0.41
29 7 0.26
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (29 bp):
ATATATATTTTTTACACAAATATAGATGT
Found at i:1044901 original size:17 final size:16
Alignment explanation
Indices: 1044858--1044903 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1044848 CACCTTATTC
*
1044858 TTTATTT-TTTTAATA
1 TTTATTTATTTAAATA
1044873 TTTATTTATTTAAATA
1 TTTATTTATTTAAATA
*
1044889 TTTTTTATATTTAAA
1 TTTATT-TATTTAAA
1044904 ATTCGACATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAAATA
Found at i:1047427 original size:20 final size:20
Alignment explanation
Indices: 1047388--1047427 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1047378 TTATTTTTAT
*
1047388 GTATTATAATTATATTTAAA
1 GTATTATAATTATATATAAA
1047408 GTATTATATATT-TATATAAA
1 GTATTATA-ATTATATATAAA
1047428 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
GTATTATAATTATATATAAA
Found at i:1047460 original size:21 final size:20
Alignment explanation
Indices: 1047435--1047496 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1047425 AAATTTTAAA
1047435 ATATTTTTATGTATTTATATT
1 ATATTTTTAT-TATTTATATT
1047456 ATATTATTT-TTATATTATATT
1 ATATT-TTTATTAT-TTATATT
* *
1047477 ATATTTTAATTATTTTTATT
1 ATATTTTTATTATTTATATT
1047497 TTATAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 11 0.31
21 22 0.61
22 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATATTTTTATTATTTATATT
Found at i:1047467 original size:16 final size:17
Alignment explanation
Indices: 1047448--1047515 Score: 81
Period size: 16 Copynumber: 4.1 Consensus size: 17
1047438 TTTTTATGTA
1047448 TTTATATTATATTAT-T
1 TTTATATTATATTATAT
1047464 TTTATATTATATTATAT
1 TTTATATTATATTATAT
*
1047481 TTTA-ATTAT-TTTTAT
1 TTTATATTATATTATAT
1047496 TTTATAATTA-AGTTATAT
1 TTTAT-ATTATA-TTATAT
1047514 TT
1 TT
1047516 AAATTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
15 9 0.20
16 20 0.44
17 9 0.20
18 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (17 bp):
TTTATATTATATTATAT
Found at i:1047476 original size:37 final size:37
Alignment explanation
Indices: 1047359--1047476 Score: 84
Period size: 37 Copynumber: 3.2 Consensus size: 37
1047349 TTATAATTTA
* *
1047359 TATATTTTTAT-TATATT-TATTATTTTTATGTATTATAAT
1 TATATTTTTATGTAT-TTATATTA-TATTAT-TTTTAT-AT
* * * *
1047398 TATA-TTTAAAGTATTATATATTTATATAAATTTTA-A-
1 TATATTTTTATGTATT-TATA-TTATATTATTTTTATAT
*
1047434 AATATTTTTATGTATTTATATTATATTATTTTTATAT
1 TATATTTTTATGTATTTATATTATATTATTTTTATAT
1047471 TATATT
1 TATATT
1047477 ATATTTTAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
35 12 0.20
36 8 0.13
37 15 0.25
38 5 0.08
39 12 0.20
40 5 0.08
41 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (37 bp):
TATATTTTTATGTATTTATATTATATTATTTTTATAT
Found at i:1048252 original size:20 final size:20
Alignment explanation
Indices: 1048213--1048252 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1048203 TATAAATAAT
**
1048213 TTAAATAAAAATTTTTATTA
1 TTAAATAAAAATTTAAATTA
*
1048233 TTAAATAATAATTTAAATTA
1 TTAAATAAAAATTTAAATTA
1048253 AATTATACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATAAAAATTTAAATTA
Found at i:1048896 original size:24 final size:26
Alignment explanation
Indices: 1048858--1048921 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
1048848 TTTTTTTAAA
1048858 AATAAATATAAATAATTT-ATTT-TT
1 AATAAATATAAATAATTTAATTTATT
1048882 AATAAA-ATAACATAATTTAATTTATT
1 AATAAATATAA-ATAATTTAATTTATT
*
1048908 AATAATACATAAAT
1 AATAA-ATATAAAT
1048922 TTATACACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.11
24 13 0.37
25 4 0.11
26 7 0.20
27 3 0.09
28 4 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAATATAAATAATTTAATTTATT
Found at i:1049272 original size:21 final size:20
Alignment explanation
Indices: 1049229--1049273 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1049219 TTTTAAAAAA
* * *
1049229 TAATTTTTAAAGATGATTTT
1 TAATTTTTAAAAATAATTAT
1049249 TAATTTTTAAAAAATAATTAT
1 TAATTTTT-AAAAATAATTAT
1049270 TAAT
1 TAAT
1049274 AGTCTTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TAATTTTTAAAAATAATTAT
Found at i:1051108 original size:29 final size:27
Alignment explanation
Indices: 1051050--1051104 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1051040 TCGTGTTCAT
1051050 ATTTTTTTAATATAATTTCATATTTTA
1 ATTTTTTTAATATAATTTCATATTTTA
1051077 ATTTTTTT-ATATCATATTT-ATATTTTA
1 ATTTTTTTAATAT-A-ATTTCATATTTTA
1051104 A
1 A
1051105 AATTATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.15
27 18 0.69
28 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
ATTTTTTTAATATAATTTCATATTTTA
Found at i:1052221 original size:22 final size:21
Alignment explanation
Indices: 1052187--1052229 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1052177 TTTATTAATA
1052187 AATTTTGAGTTTAAAGTTTTT
1 AATTTTGAGTTTAAAGTTTTT
*
1052208 AATTATTGATTTTAAAGTTTTT
1 AATT-TTGAGTTTAAAGTTTTT
1052230 TCTTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (21 bp):
AATTTTGAGTTTAAAGTTTTT
Found at i:1052238 original size:22 final size:22
Alignment explanation
Indices: 1052189--1052239 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1052179 TATTAATAAA
*
1052189 TTTTGAGTTTAAAGTTTTTAAT
1 TTTTGATTTTAAAGTTTTTAAT
* **
1052211 TATTGATTTTAAAGTTTTTTCT
1 TTTTGATTTTAAAGTTTTTAAT
1052233 TTTTGAT
1 TTTTGAT
1052240 CTAAATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTGATTTTAAAGTTTTTAAT
Found at i:1053853 original size:10 final size:10
Alignment explanation
Indices: 1053838--1053875 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
1053828 ATTAATCATG
1053838 TATAAAATTA
1 TATAAAATTA
1053848 TATAAAATTA
1 TATAAAATTA
1053858 TA-AAAA-TA
1 TATAAAATTA
1053866 TATAAAATTA
1 TATAAAATTA
1053876 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 4 0.15
9 8 0.31
10 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TATAAAATTA
Found at i:1053861 original size:18 final size:18
Alignment explanation
Indices: 1053838--1053875 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1053828 ATTAATCATG
*
1053838 TATAAAATTATATAAAAT
1 TATAAAAATATATAAAAT
1053856 TATAAAAATATATAAAAT
1 TATAAAAATATATAAAAT
1053874 TA
1 TA
1053876 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAAATATATAAAAT
Found at i:1062194 original size:2 final size:2
Alignment explanation
Indices: 1062182--1062210 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1062172 TACGATAAAC
1062182 AT AT A- 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
1062211 TCCTGTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1069331 original size:17 final size:18
Alignment explanation
Indices: 1069291--1069333 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1069281 TTTTAGTTAA
* *
1069291 TTTATATTTAATATATTT
1 TTTATTTTTAAAATATTT
1069309 TATTATTTTTAAAATA-TT
1 T-TTATTTTTAAAATATTT
1069327 TTTATTT
1 TTTATTT
1069334 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 4 0.18
19 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTTTAAAATATTT
Found at i:1069338 original size:23 final size:24
Alignment explanation
Indices: 1069307--1069351 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1069297 TTTAATATAT
1069307 TTTATTATT-TTTAAAATATTTTTA
1 TTTATTATTATTT-AAATATTTTTA
*
1069331 TTTA-TATTATTTTAATATTTT
1 TTTATTATTATTTAAATATTTT
1069352 AATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTATTATTATTTAAATATTTTTA
Found at i:1069359 original size:26 final size:26
Alignment explanation
Indices: 1069297--1069372 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
1069287 TTAATTTATA
1069297 TTTAATATATTT-TATTATTTTTAAAATAT
1 TTTAATA-ATTTATATTA-TTTT--AATAT
1069326 TTT--T-ATTTATATTATTTTAATAT
1 TTTAATAATTTATATTATTTTAATAT
* *
1069349 TTTAATAATTTAAATTATATTAAT
1 TTTAATAATTTATATTATTTTAAT
1069373 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 8 0.20
25 9 0.22
26 20 0.49
27 1 0.02
29 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTAATAATTTATATTATTTTAATAT
Found at i:1069407 original size:21 final size:22
Alignment explanation
Indices: 1069379--1069428 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1069369 TAATTTAAAA
*
1069379 ATATATTTTTA-TATT-TTTAT
1 ATATATTTTTATTATTATATAT
1069399 ATCATATTTTTATTATTATATAT
1 AT-ATATTTTTATTATTATATAT
1069422 ATATATT
1 ATATATT
1069429 ATATTAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 9 0.35
23 6 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATATTTTTATTATTATATAT
Found at i:1069417 original size:19 final size:19
Alignment explanation
Indices: 1069379--1069434 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1069369 TAATTTAAAA
*
1069379 ATATAT-TTTTATATTTTT
1 ATATATATTTTATATTATT
1069397 ATATCATATTTT-TATTATT
1 ATAT-ATATTTTATATTATT
1069416 ATATATATATATTATATTA
1 ATATATAT-T-TTATATTA
1069435 GCATAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.25
19 13 0.41
20 6 0.19
21 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATATATTTTATATTATT
Found at i:1069433 original size:21 final size:19
Alignment explanation
Indices: 1069379--1069434 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
1069369 TAATTTAAAA
*
1069379 ATATATTTTTATATT-TTT
1 ATATATATTTATATTATTT
*
1069397 ATATCATATTTTTATTATTAT
1 ATAT-ATATTTATATTATT-T
1069418 ATATATATATTATATTA
1 ATATATAT-TTATATTA
1069435 GCATAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 6 0.19
21 12 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATATATTTATATTATTT
Found at i:1071769 original size:17 final size:18
Alignment explanation
Indices: 1071742--1071778 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1071732 ATCGTGTTTA
1071742 AAATATTTTATATTAAAT
1 AAATATTTTATATTAAAT
*
1071760 AAAT-TTTTATATTTAAT
1 AAATATTTTATATTAAAT
1071777 AA
1 AA
1071779 TTTATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATTTTATATTAAAT
Found at i:1071780 original size:16 final size:16
Alignment explanation
Indices: 1071738--1071781 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1071728 TATAATCGTG
1071738 TTTAA-AATATTTTATA
1 TTTAATAAT-TTTTATA
*
1071754 TTAAATAAATTTTTATA
1 TTTAAT-AATTTTTATA
1071771 TTTAATAATTT
1 TTTAATAATTT
1071782 ATATTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 9 0.38
17 12 0.50
18 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATAATTTTTATA
Found at i:1071865 original size:19 final size:19
Alignment explanation
Indices: 1071841--1071878 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1071831 TTCACGTAAT
1071841 TGAGTTTAATATCAGATAC
1 TGAGTTTAATATCAGATAC
1071860 TGAGTTTAATATCAGATAC
1 TGAGTTTAATATCAGATAC
1071879 GCTGTACTCT
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:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
TGAGTTTAATATCAGATAC
Found at i:1072267 original size:26 final size:26
Alignment explanation
Indices: 1072238--1072291 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1072228 ATTAGTGTAT
*
1072238 TTAA-ATTTAAATTTTAATGATTTAAA
1 TTAATATTT-AATTTTAATAATTTAAA
*
1072264 TTAATATTTAATTTTAATAATTTGAA
1 TTAATATTTAATTTTAATAATTTAAA
1072290 TT
1 TT
1072292 GATTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTAATATTTAATTTTAATAATTTAAA
Found at i:1072273 original size:20 final size:22
Alignment explanation
Indices: 1072216--1072275 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1072206 GTTTCGAGTG
* *
1072216 TAAATTTTAATAATTAGTGTATT
1 TAAA-TTTAATATTTAATGTATT
1072239 TAAATTTAA-ATTTTAATG-ATT
1 TAAATTTAATA-TTTAATGTATT
1072260 TAAA-TTAATATTTAAT
1 TAAATTTAATATTTAAT
1072276 TTTAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 10 0.30
21 9 0.27
22 10 0.30
23 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TAAATTTAATATTTAATGTATT
Found at i:1072280 original size:13 final size:13
Alignment explanation
Indices: 1072237--1072282 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1072227 AATTAGTGTA
1072237 TTTAA-ATTTAAAT
1 TTTAATATTT-AAT
1072250 TTTAATGATTTAA-
1 TTTAAT-ATTTAAT
*
1072263 ATTAATATTTAAT
1 TTTAATATTTAAT
1072276 TTTAATA
1 TTTAATA
1072283 ATTTGAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 6 0.21
13 16 0.57
14 2 0.07
15 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTTAATATTTAAT
Found at i:1076319 original size:3 final size:3
Alignment explanation
Indices: 1076311--1076345 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1076301 ATAGAAAAGC
1076311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1076346 GCCCTTTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1078149 original size:88 final size:88
Alignment explanation
Indices: 1078000--1078287 Score: 319
Period size: 88 Copynumber: 3.3 Consensus size: 88
1077990 ATCGATCATC
* * * ** *
1078000 GCAAGACCTTCCTGCATCAACCAACATGGATTTTGCAAAACCCTATGAATCTAAA-GTCACAGTA
1 GCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAACCCTATAAATCTAAATGTCACAGT-
*
1078064 AAGATGATAAACATGCCGGCTGTT
65 AAGATGATAAACATGCCGGTTGTT
* **
1078088 GCAAGAACTTACTGCATCAACCAACAGGGATTTTG-GAATCCCTATAAATCTGCATGTCACAGTA
1 GCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAACCCTATAAATCTAAATGTCACAGTA
*
1078152 ACGATGATAAACATGCCAGTTGTT
66 A-GATGATAAACATGCCGGTTGTT
* * * * * * *
1078176 GCAAGAACTTGCGGCATCAACAAACAGGGTTTTTGTGAAACCCTATAAATCTCACTGTGACAGTA
1 GCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAACCCTATAAATCTAAATGTCACAGTA
* ** **
1078241 AGATAATAAACATGCCAATCATT
66 AGATGATAAACATGCCGGTTGTT
* *
1078264 GCAAGATCTTACCGCATCAACCAA
1 GCAAGAACTTACTGCATCAACCAA
1078288 AATGCTATAA
Statistics
Matches: 170, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
87 16 0.09
88 129 0.76
89 25 0.15
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (88 bp):
GCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAACCCTATAAATCTAAATGTCACAGTA
AGATGATAAACATGCCGGTTGTT
Found at i:1078432 original size:164 final size:164
Alignment explanation
Indices: 1078129--1078456 Score: 408
Period size: 164 Copynumber: 2.0 Consensus size: 164
1078119 TTTGGAATCC
* * * * *
1078129 CTATAAATCTGCATGTCACAGTAACGATGATAAACATGCCAGTTGTTGCAAGAACTTGCGGCATC
1 CTATAAATCTGAATGTCACAGTAAAGATGATAAAAAAGCCAGCTGTTGCAAGAACTTGCGGCATC
* * * * *
1078194 AACAAACAGGGTTTTTGTGAAACCCTATAAATCTCACTGTGACAGTAAGATAATAAACATGCCAA
66 AACAAACAGCGCTTTTGTGAAACCCTATAAATCTAAATGTCACAGTAAGATAATAAACATGCCAA
* * *
1078259 TCATTGCAAGATCTTACCGCATCAACCAA-AATG
131 TCATTGCAAGAACTGAACGCATCAACCAACAATG
* ** * *
1078292 CTATAAATCTTAATGTCATGGTAAAGATGATAAAAAAGCCAGCTGTTGCAAGACCTTGCCTGCAT
1 CTATAAATCTGAATGTCACAGTAAAGATGATAAAAAAGCCAGCTGTTGCAAGAACTTG-CGGCAT
*
1078357 CAA-ACAACAGCGCTTTTGTGAAACCCTATAAATCTAAATGTCACAGTAAGATGATAAACATGCC
65 CAACA-AACAGCGCTTTTGTGAAACCCTATAAATCTAAATGTCACAGTAAGATAATAAACATGCC
** ** *
1078421 GGTTGTTGCAAGAACTGAATGCATCAACCAACAATG
129 AATCATTGCAAGAACTGAACGCATCAACCAACAATG
1078457 ATTTTGTGAA
Statistics
Matches: 138, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
163 50 0.36
164 84 0.61
165 4 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (164 bp):
CTATAAATCTGAATGTCACAGTAAAGATGATAAAAAAGCCAGCTGTTGCAAGAACTTGCGGCATC
AACAAACAGCGCTTTTGTGAAACCCTATAAATCTAAATGTCACAGTAAGATAATAAACATGCCAA
TCATTGCAAGAACTGAACGCATCAACCAACAATG
Found at i:1078519 original size:89 final size:88
Alignment explanation
Indices: 1078314--1078705 Score: 464
Period size: 89 Copynumber: 4.4 Consensus size: 88
1078304 ATGTCATGGT
* * * * * * * * *
1078314 AAAGATGATAAAAAAGCCAGCTGTTGCAAGACCTTGCCTGCATCAAACAACAGCGCTTTTGTGAA
1 AAAGATGATAAACATGCCGGTTGTTGCAAGAACTT-ACTGCATCAACCAACAGGGATTTTGTGAA
*
1078379 ACCCTATAAATCTAAATGTCACAG
65 ACCCTATAAATCTAAACGTCACAG
* * * **
1078403 TAAGATGATAAACATGCCGGTTGTTGCAAGAACTGAATGCATCAACCAACAATGATTTTGTGAAA
1 AAAGATGATAAACATGCCGGTTGTTGCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAA
* *
1078468 CCCTACAAATCTAAACGTCGCAG
66 CCCTATAAATCTAAACGTCACAG
* *
1078491 CAAAGATGATACACATGCCGGTCT-TTGCAAGAACTTACTGCATCAACCAGCAGGGATTTTGTGA
1 -AAAGATGATAAACATGCCGGT-TGTTGCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGA
*
1078555 AACCCTATAAATCTAAACTTCACAG
64 AACCCTATAAATCTAAACGTCACAG
* ** * *
1078580 TAAAGATGACATGCATGCTGGTTGTTGCAAGAACTTACTGCATCAACCAATAGGGATTTTGTGAA
1 -AAAGATGATAAACATGCCGGTTGTTGCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAA
* *
1078645 ACCCTATAAAGCTAAATGTCACAG
65 ACCCTATAAATCTAAACGTCACAG
* *
1078669 TAAGATGA-AAATCATGCCGGTTGTTACAAGAACTTAC
1 AAAGATGATAAA-CATGCCGGTTGTTGCAAGAACTTAC
1078706 GTCTAATAAA
Statistics
Matches: 258, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.00
88 75 0.29
89 181 0.70
90 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (88 bp):
AAAGATGATAAACATGCCGGTTGTTGCAAGAACTTACTGCATCAACCAACAGGGATTTTGTGAAA
CCCTATAAATCTAAACGTCACAG
Found at i:1080167 original size:13 final size:13
Alignment explanation
Indices: 1080144--1080168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1080134 GAAATTAAAA
1080144 AAAAAAATTACAC
1 AAAAAAATTACAC
1080157 AAAAAAATTACA
1 AAAAAAATTACA
1080169 GGTAGATTTT
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:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAATTACAC
Found at i:1089398 original size:6 final size:6
Alignment explanation
Indices: 1089387--1089422 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1089377 TAGTTATATG
1089387 ATATAA ATAT-- A-ATAA ATATAA ATATAA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATA
1089423 AAAAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.07
4 1 0.04
5 1 0.04
6 23 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:1090043 original size:33 final size:32
Alignment explanation
Indices: 1090004--1090069 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
1089994 CTTCATATCA
1090004 ATTTTTAAATTAATA-TTAAAATTTTAAAAATTT
1 ATTTTTAAATTAATATTTAAAA--TTAAAAATTT
*
1090037 ATTTTTATATTAATATTTAAAATTAAAAATTT
1 ATTTTTAAATTAATATTTAAAATTAAAAATTT
1090069 A
1 A
1090070 AATAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 11 0.35
33 14 0.45
34 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTTAAATTAATATTTAAAATTAAAAATTT
Found at i:1090217 original size:25 final size:26
Alignment explanation
Indices: 1090184--1090244 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
1090174 CTATTAATAG
1090184 ATATGTATTTATTAAAAA-TTATTTAAT
1 ATAT-TATTT-TTAAAAATTTATTTAAT
1090211 -TATTA-TTTTAAAAATTTATTTAAT
1 ATATTATTTTTAAAAATTTATTTAAT
1090235 ATATTATTTT
1 ATATTATTTT
1090245 AACTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.23
24 11 0.35
25 7 0.23
26 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
ATATTATTTTTAAAAATTTATTTAAT
Found at i:1090229 original size:24 final size:25
Alignment explanation
Indices: 1090195--1090255 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 25
1090185 TATGTATTTA
1090195 TTAAAAA-TTATTTAAT-TATTATT
1 TTAAAAATTTATTTAATATATTATT
1090218 TTAAAAATTTATTTAATATATTATT
1 TTAAAAATTTATTTAATATATTATT
1090243 TTAACTAAATTTA
1 TTAA--AAATTTA
1090256 AAAAATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.21
24 9 0.26
25 11 0.32
27 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAAAATTTATTTAATATATTATT
Found at i:1090262 original size:27 final size:25
Alignment explanation
Indices: 1090211--1090262 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1090201 ATTATTTAAT
***
1090211 TATTATTTTAAAAATTTATTTAATA
1 TATTATTTTAAAAATTTAAAAAATA
1090236 TATTATTTTAACTAAATTTAAAAAATA
1 TATTATTTTAA--AAATTTAAAAAATA
1090263 ATTCATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 11 0.50
27 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTATTTTAAAAATTTAAAAAATA
Found at i:1091001 original size:24 final size:24
Alignment explanation
Indices: 1090907--1091001 Score: 68
Period size: 23 Copynumber: 3.9 Consensus size: 24
1090897 AATTTAAAAC
* *
1090907 ATAAATTATTTATATTATTATATAAT
1 ATAATTTAATTATATTA-TATA-AAT
* * *
1090933 ATAATATAAATGATATTATATTTAAT
1 ATAAT-TTAATTATATTATA-TAAAT
* *
1090959 AT-TTTTAAAT-TATTATATAAAT
1 ATAATTTAATTATATTATATAAAT
*
1090981 ATAATTTATTTATATTATATA
1 ATAATTTAATTATATTATATA
1091002 TAAAAAAATA
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
22 6 0.12
23 12 0.23
24 12 0.23
25 1 0.02
26 11 0.21
27 10 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
ATAATTTAATTATATTATATAAAT
Found at i:1091021 original size:11 final size:11
Alignment explanation
Indices: 1091005--1091032 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1090995 TTATATATAA
1091005 AAAAATAAAAT
1 AAAAATAAAAT
1091016 AAAAATAAAAT
1 AAAAATAAAAT
1091027 AAAAAT
1 AAAAAT
1091033 TAATTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1091700 original size:29 final size:29
Alignment explanation
Indices: 1091669--1091759 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
1091659 ATGTTAAGAG
*
1091669 TTTATTTAAGTATAAATTAAAAATTAAAG
1 TTTATTTAAGTATAAATTAAAAATTAAAA
1091698 TTTATTTAA--AT--A-TAAAAATTAAAA
1 TTTATTTAAGTATAAATTAAAAATTAAAA
* *
1091722 TCTTAATTAGGTATAAATTAAAAATTAAAAA
1 T-TTATTTAAGTATAAATTAAAAATT-AAAA
1091753 TTTATTT
1 TTTATTT
1091760 GAATGTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
24 12 0.24
25 7 0.14
27 4 0.08
29 10 0.20
30 13 0.25
31 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTATTTAAGTATAAATTAAAAATTAAAA
Found at i:1091701 original size:25 final size:25
Alignment explanation
Indices: 1091672--1091756 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 25
1091662 TTAAGAGTTT
1091672 ATTTAAGTATAAATTAAAAATTAAA
1 ATTTAAGTATAAATTAAAAATTAAA
* *
1091697 GTTT-A-TTTAAATATAAAAATTAAA
1 ATTTAAGTATAAAT-TAAAAATTAAA
1091721 ATCTTAATTAGGTATAAATTAAAAATTAAAA
1 AT-TT-A--A-GTATAAATTAAAAATT-AAA
1091752 ATTTA
1 ATTTA
1091757 TTTGAATGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
23 6 0.13
24 13 0.28
25 5 0.11
29 2 0.04
30 10 0.21
31 11 0.23
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (25 bp):
ATTTAAGTATAAATTAAAAATTAAA
Found at i:1091831 original size:22 final size:23
Alignment explanation
Indices: 1091805--1091852 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1091795 AGTAGTATAA
1091805 TTTAAGATTT-TTTAATTATTAT
1 TTTAAGATTTATTTAATTATTAT
* * *
1091827 TTTAAGTTTTATTTATTTATTTT
1 TTTAAGATTTATTTAATTATTAT
1091850 TTT
1 TTT
1091853 GCCCATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTAAGATTTATTTAATTATTAT
Found at i:1095769 original size:22 final size:22
Alignment explanation
Indices: 1095743--1095787 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1095733 TATTATTATG
1095743 ATAATATAAATTATTTTAATTA
1 ATAATATAAATTATTTTAATTA
1095765 ATAATATAAATTATTTTAATTA
1 ATAATATAAATTATTTTAATTA
1095787 A
1 A
1095788 AATTTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATAAATTATTTTAATTA
Found at i:1096131 original size:14 final size:14
Alignment explanation
Indices: 1096084--1096160 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
1096074 ATAAAATTAT
1096084 TTTAT-TATTTAAA
1 TTTATATATTTAAA
* * *
1096097 TTAAAATATTAAAA
1 TTTATATATTTAAA
**
1096111 AAT-TATATTTAAA
1 TTTATATATTTAAA
1096124 TTTATATATTTATAA
1 TTTATATATTTA-AA
1096139 --TA-A-ATTTAAA
1 TTTATATATTTAAA
1096149 TTTATATATTTA
1 TTTATATATTTA
1096161 TAACTAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
10 2 0.04
11 5 0.11
12 3 0.06
13 15 0.32
14 20 0.43
15 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATATATTTAAA
Found at i:1096132 original size:27 final size:25
Alignment explanation
Indices: 1096089--1096176 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 25
1096079 ATTATTTTAT
* *
1096089 TATTTAAATTAAAATATTAAAAAATTA
1 TATTTAAATTTATATATT-AAAAA-TA
* *
1096116 TATTTAAATTTATATATTTATAATA
1 TATTTAAATTTATATATTAAAAATA
* * *
1096141 AATTTAAATTTATATATTTATAACTA
1 TATTTAAATTTATATA-TTAAAAATA
*
1096167 AATTTAAATT
1 TATTTAAATT
1096177 AAAAATATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 17 0.33
26 18 0.35
27 16 0.31
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTTAAATTTATATATTAAAAATA
Found at i:1096144 original size:19 final size:17
Alignment explanation
Indices: 1096120--1096154 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1096110 AAATTATATT
1096120 TAAATTTATATATTTATAA
1 TAAATTTA-A-ATTTATAA
1096139 TAAATTTAAATTTATA
1 TAAATTTAAATTTATA
1096155 TATTTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:1096145 original size:25 final size:26
Alignment explanation
Indices: 1096117--1096176 Score: 113
Period size: 25 Copynumber: 2.3 Consensus size: 26
1096107 AAAAAATTAT
1096117 ATTTAAATTTATATATTTATAA-TAA
1 ATTTAAATTTATATATTTATAACTAA
1096142 ATTTAAATTTATATATTTATAACTAA
1 ATTTAAATTTATATATTTATAACTAA
1096168 ATTTAAATT
1 ATTTAAATT
1096177 AAAAATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.65
26 12 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTAAATTTATATATTTATAACTAA
Found at i:1096211 original size:16 final size:16
Alignment explanation
Indices: 1096170--1096217 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1096160 ATAACTAAAT
*
1096170 TTAAATTAAAAATATTAA
1 TTAAA-TAAAAAT-TTGA
*
1096188 TTAAATAATAATTTGA
1 TTAAATAAAAATTTGA
*
1096204 TTAGATAAAAATTT
1 TTAAATAAAAATTT
1096218 AATCTCGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 15 0.58
17 6 0.23
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TTAAATAAAAATTTGA
Found at i:1096418 original size:12 final size:11
Alignment explanation
Indices: 1096405--1096453 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
1096395 AAATTATATA
1096405 AATTTAAAATT
1 AATTTAAAATT
1096416 AAATTTAAAATT
1 -AATTTAAAATT
*
1096428 TA-TTAAATATT
1 AATTTAAA-ATT
*
1096439 AATTTAAAAAT
1 AATTTAAAATT
1096450 AATT
1 AATT
1096454 ACATAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 5 0.16
11 11 0.34
12 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:1103222 original size:23 final size:23
Alignment explanation
Indices: 1103183--1103233 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1103173 ACATTATTTA
*
1103183 AAAATAATAAAACTTAA-AATAAT
1 AAAATAATAAAAATTAATAA-AAT
1103206 AAAATAA-AAATAATTAATAAAAT
1 AAAATAATAAA-AATTAATAAAAT
1103229 AAAAT
1 AAAAT
1103234 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 20 0.80
24 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATAATAAAAATTAATAAAAT
Found at i:1103227 original size:13 final size:14
Alignment explanation
Indices: 1103181--1103219 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
1103171 ATACATTATT
1103181 TAAAAATAATAAAA
1 TAAAAATAATAAAA
*
1103195 CTTAAAATAATAAAA
1 -TAAAAATAATAAAA
1103210 TAAAAATAAT
1 TAAAAATAAT
1103220 TAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:1103343 original size:15 final size:16
Alignment explanation
Indices: 1103307--1103344 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1103297 AATTAATATT
1103307 TTTAAATATATTTAAA
1 TTTAAATATATTTAAA
**
1103323 AATAAA-ATATTTAAA
1 TTTAAATATATTTAAA
1103338 TTTAAAT
1 TTTAAAT
1103345 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 4, Indels: 2
0.74 0.17 0.09
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATATATTTAAA
Found at i:1103388 original size:11 final size:11
Alignment explanation
Indices: 1103374--1103424 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1103364 AAATAACATA
1103374 AAATATAAAAT
1 AAATATAAAAT
*
1103385 AAATTTATAAAT
1 AAATATA-AAAT
*
1103397 ATAT-TAAAAT
1 AAATATAAAAT
* *
1103407 ATACATAAAAT
1 AAATATAAAAT
1103418 AAATATA
1 AAATATA
1103425 TATTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:1103943 original size:28 final size:29
Alignment explanation
Indices: 1103892--1103958 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 29
1103882 TCGAAATTAA
1103892 ATTTTTAATTAAATATAAAATTAA-ATTT
1 ATTTTTAATTAAATATAAAATTAATATTT
*
1103920 ATTTTT-ATTAAATA-AATAACTTAATTTTT
1 ATTTTTAATTAAATATAA-AA-TTAATATTT
*
1103949 ATTTTAAATT
1 ATTTTTAATT
1103959 TCAATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 10 0.30
29 8 0.24
30 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTTAATTAAATATAAAATTAATATTT
Found at i:1108139 original size:17 final size:18
Alignment explanation
Indices: 1108102--1108154 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
1108092 TGTAATATTA
* *
1108102 AAAATATAAAAATAAAAT
1 AAAATATATAAATATAAT
*
1108120 -AAATATATAAATATATT
1 AAAATATATAAATATAAT
*
1108137 AAAATTTATATAATATAA
1 AAAATATATA-AATATAA
1108155 ATGGTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 14 0.50
18 8 0.29
19 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATATAAATATAAT
Found at i:1112748 original size:14 final size:14
Alignment explanation
Indices: 1112729--1112755 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1112719 TGTAGATCAA
1112729 ACCAAACTCTTCGG
1 ACCAAACTCTTCGG
1112743 ACCAAACTCTTCG
1 ACCAAACTCTTCG
1112756 CTTTGTTTCA
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:0.30, C:0.37, G:0.11, T:0.22
Consensus pattern (14 bp):
ACCAAACTCTTCGG
Found at i:1112978 original size:20 final size:19
Alignment explanation
Indices: 1112955--1112992 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1112945 TTAATTTTAT
1112955 AAATTAAAATTATTTAAATA
1 AAATTAAAATT-TTTAAATA
1112975 AAATTAAAATTTTTAAAT
1 AAATTAAAATTTTTAAAT
1112993 TTTTATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTAAAATTTTTAAATA
Found at i:1112990 original size:29 final size:32
Alignment explanation
Indices: 1112958--1113020 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
1112948 ATTTTATAAA
1112958 TTAAAATTATT-TAA-ATAAAATTAAA-ATTT
1 TTAAAATTATTATAATATAAAATTAAATATTT
*
1112987 TT-AAATTTTTATAATATAAAATTAAATATTT
1 TTAAAATTATTATAATATAAAATTAAATATTT
1113018 TTA
1 TTA
1113021 CTTTAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.24
29 5 0.17
30 11 0.38
31 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAAAATTATTATAATATAAAATTAAATATTT
Found at i:1113580 original size:16 final size:17
Alignment explanation
Indices: 1113540--1113580 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1113530 TTTTATAAGT
1113540 TTTAT-ATATTATTATA
1 TTTATAATATTATTATA
*
1113556 TTTAAAATATTA-TATA
1 TTTATAATATTATTATA
1113572 TTTATAATA
1 TTTATAATA
1113581 AATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATAATATTATTATA
Found at i:1113582 original size:21 final size:21
Alignment explanation
Indices: 1113560--1113600 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1113550 ATTATATTTA
*
1113560 AAATATT-ATATATTTATAAT
1 AAATATTAATATATTAATAAT
*
1113580 AAATTTTAATATATTAATAAT
1 AAATATTAATATATTAATAAT
1113601 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTAATATATTAATAAT
Found at i:1113610 original size:28 final size:28
Alignment explanation
Indices: 1113548--1113611 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1113538 GTTTTATATA
*
1113548 TTATTATA-TTTAAAATATTATATATTT
1 TTATTAAATTTTAAAATATTATATATTT
* * *
1113575 ATAATAAATTTTAATATATTA-ATAATTT
1 TTATTAAATTTTAAAATATTATAT-ATTT
1113603 TTATTAAAT
1 TTATTAAAT
1113612 AAAATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTATTAAATTTTAAAATATTATATATTT
Found at i:1117529 original size:2 final size:2
Alignment explanation
Indices: 1117517--1117548 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1117507 CAAAGACAAA
*
1117517 AT AT GT 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
1117549 TTGCCAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1121324 original size:40 final size:40
Alignment explanation
Indices: 1121238--1121324 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
1121228 AATTATTGTT
*
1121238 TAAATATAAAAATATTTTTATTTAAAATTAATTATAAATA
1 TAAATATAAAAATATTTTTATTTAAAATTAATAATAAATA
* *
1121278 TTAATATAAAACTATTTTT-TTTAAAAATTAAATAATAAA-A
1 TAAATATAAAAATATTTTTATTT-AAAATT-AATAATAAATA
1121318 TAAATAT
1 TAAATAT
1121325 TTAAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 3 0.07
40 30 0.73
41 8 0.20
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (40 bp):
TAAATATAAAAATATTTTTATTTAAAATTAATAATAAATA
Found at i:1121699 original size:2 final size:2
Alignment explanation
Indices: 1121690--1121721 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1121680 TTTTTCTCTC
1121690 TA TA -A 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 TA T
1121722 TTGCAGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1122640 original size:36 final size:32
Alignment explanation
Indices: 1122563--1122640 Score: 77
Period size: 36 Copynumber: 2.3 Consensus size: 32
1122553 AAATTTTTAA
*
1122563 AAATATAAATTAATTTAATTTAAATTATTATT
1 AAATATAAATTAATTTAATTTAAATTATTAGT
*
1122595 AAATAATAAATTAATATTTTTATTTAAATTTCATT-GT
1 AAAT-ATAAATT-A-A-TTTAATTTAAA-TT-ATTAGT
1122632 AAATATAAA
1 AAATATAAA
1122641 CTATTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 4 0.11
33 7 0.18
34 1 0.03
35 1 0.03
36 15 0.39
37 7 0.18
38 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
AAATATAAATTAATTTAATTTAAATTATTAGT
Found at i:1122663 original size:27 final size:28
Alignment explanation
Indices: 1122633--1122695 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
1122623 TTTCATTGTA
*
1122633 AATATAAACTATTAATATAA-AAATAAT
1 AATATAAACTAATAATATAATAAATAAT
**
1122660 AATA-ATATTTAATAATATAATAAATAAT
1 AATATA-AACTAATAATATAATAAATAAT
*
1122688 AAAATAAA
1 AATATAAA
1122696 TTTTTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.04
27 15 0.54
28 11 0.39
29 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AATATAAACTAATAATATAATAAATAAT
Done.