Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 10 of 11
Found at i:1069120 original size:114 final size:113
Alignment explanation
Indices: 1068999--1069448 Score: 570
Period size: 113 Copynumber: 3.9 Consensus size: 113
1068989 ATAAAAAAAT
* * *
1068999 TTAAATAAAAATAA-AAAGGGTTTATTAA-TTATTTTTA-TAAAAACATAATAATTAATATTTTA
1 TTAAAAAAAAATAATAAAGGCTTT-TTAATTTATTTTTATTTAAAA-A-AATAATTAATATTTTA
* * *
1069061 ATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTAATTTTA
63 ATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTTTA
* * ** *
1069112 TTAAAATAATATAATAAACCCTTTTTAATTTTATTTTTATTTTTAAAAAATAATTAAT-TTTTAA
1 TTAAAAAAAAATAATAAAGGCTTTTTAA-TTTATTTTTA-TTTAAAAAAATAATTAATATTTTAA
1069176 TTTATTAATATAA-TTTTTTAAAGTTAATTAAATATTATTTTTAATTTTA
64 TTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTTTA
* * * *
1069225 TTAAAAAATAATAATAAAGGCTTTTTAATTTAATATTTATTTTAAAAAATAATTAATTTTTTAAT
1 TTAAAAAAAAATAATAAAGGCTTTTTAATTT-ATTTTTATTTAAAAAAATAATTAATATTTTAAT
* * * *
1069290 TTTTTAATGTAAGTTTTTTAAAGTTAATTAAATATTATTTTTTATTTTA
65 TTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTTTA
* * *
1069339 TT-AAAAAGAATAATAAATGCTTTTTATTTTAATTTTTTATTTTAAAAAAATAATTAATATTTTA
1 TTAAAAAAAAATAATAAAGGCTTTTTAATTT-A-TTTTTA-TTTAAAAAAATAATTAATATTTTA
1069403 ATTTATTAATATAAATTTTTTTAAAGTTAATTAAATATTATTTTTA
63 ATTTATTAATAT-AATTTTTTTAAAGTTAATTAAATATTATTTTTA
1069449 TTAAAAATAA
Statistics
Matches: 296, Mismatches: 30, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
112 21 0.07
113 123 0.42
114 65 0.22
115 51 0.17
116 32 0.11
117 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (113 bp):
TTAAAAAAAAATAATAAAGGCTTTTTAATTTATTTTTATTTAAAAAAATAATTAATATTTTAATT
TATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTTTA
Found at i:1069188 original size:24 final size:23
Alignment explanation
Indices: 1069159--1069229 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
1069149 TATTTTTAAA
1069159 AAATAATTAATTTTTAA-TTTATT
1 AAATAATT-ATTTTTAAGTTTATT
* *
1069182 AATATAATT-TTTTAAAGTTAATT
1 AA-ATAATTATTTTTAAGTTTATT
*
1069205 AAAT-ATTATTTTTAATTTTATT
1 AAATAATTATTTTTAAGTTTATT
1069227 AAA
1 AAA
1069230 AAATAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.08
22 22 0.55
23 9 0.22
24 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
AAATAATTATTTTTAAGTTTATT
Found at i:1069203 original size:113 final size:114
Alignment explanation
Indices: 1069045--1069448 Score: 593
Period size: 113 Copynumber: 3.5 Consensus size: 114
1069035 ATAAAAACAT
* * *
1069045 AATAATTAATATTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTAATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
*
1069110 TATTAAAATAATATAATAAACCCTTTTTAATTTTATTTTTATTTTTAAAA
66 TATTAAAA-AATATAATAAACGCTTTTTAATTTTATTTTTATTTTTAAAA
1069160 AATAATTAAT-TTTTAATTTATTAATATAA-TTTTTTAAAGTTAATTAAATATTATTTTTAATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
* * *
1069223 TATTAAAAAATAATAATAAAGGCTTTTTAATTTAATATTTA-TTTTAAAA
66 TATTAAAAAAT-ATAATAAACGCTTTTTAATTTTATTTTTATTTTTAAAA
* * * * *
1069272 AATAATTAATTTTTTAATTTTTTAATGTAAGTTTTTTAAAGTTAATTAAATATTATTTTTTATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
* *
1069337 TATTAAAAAGA-ATAATAAATGCTTTTT-ATTTTAATTTTTTATTTTAAAAA
66 TATTAAAAA-ATATAATAAACGCTTTTTAATTTT-A-TTTTTATTTTTAAAA
1069387 AATAATTAATATTTTAATTTATTAATATAAATTTTTTTAAAGTTAATTAAATATTATTTTTA
1 AATAATTAATATTTTAATTTATTAATAT-AATTTTTTTAAAGTTAATTAAATATTATTTTTA
1069449 TTAAAAATAA
Statistics
Matches: 262, Mismatches: 19, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
112 25 0.10
113 99 0.38
114 64 0.24
115 43 0.16
116 31 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (114 bp):
AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
TATTAAAAAATATAATAAACGCTTTTTAATTTTATTTTTATTTTTAAAA
Found at i:1069377 original size:13 final size:13
Alignment explanation
Indices: 1069359--1069383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1069349 TAATAAATGC
1069359 TTTTTATTTTAAT
1 TTTTTATTTTAAT
1069372 TTTTTATTTTAA
1 TTTTTATTTTAA
1069384 AAAAATAATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:1069496 original size:18 final size:18
Alignment explanation
Indices: 1069459--1069511 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1069449 TTAAAAATAA
* *
1069459 TAATTAATATATTATTATT
1 TAATTAATTTATTA-AATT
*
1069478 T-ATTAAATTTTTTAAATT
1 TAATT-AATTTATTAAATT
1069496 TAATTAATTTATTAAA
1 TAATTAATTTATTAAA
1069512 AAATTACGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTAATTTATTAAATT
Found at i:1069685 original size:16 final size:15
Alignment explanation
Indices: 1069638--1069686 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
1069628 TTTCTTAACA
*
1069638 TATTTATAAAAAAAC
1 TATTTTTAAAAAAAC
1069653 T-TATTTT-AAAAAA-
1 TAT-TTTTAAAAAAAC
1069666 TATTTTTAAAAAAATC
1 TATTTTTAAAAAAA-C
1069682 TATTT
1 TATTT
1069687 ACGAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 5 0.18
14 14 0.50
15 4 0.14
16 5 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTTTAAAAAAAC
Found at i:1069974 original size:19 final size:19
Alignment explanation
Indices: 1069947--1069984 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
1069937 TTATATCTTA
1069947 AAAATATTATTAAATTTTTT
1 AAAATATTATT-AATTTTTT
1069967 AAAA-ATTATTAATTTTTT
1 AAAATATTATTAATTTTTT
1069985 CATAACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAAATATTATTAATTTTTT
Found at i:1070103 original size:19 final size:19
Alignment explanation
Indices: 1070079--1070118 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1070069 ATTTTTATTT
1070079 TTTATAATTTT-TTAAAATA
1 TTTATAATTTTGTT-AAATA
1070098 TTTATAATTTTGTTAAATA
1 TTTATAATTTTGTTAAATA
1070117 TT
1 TT
1070119 AAAACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTATAATTTTGTTAAATA
Found at i:1070412 original size:19 final size:19
Alignment explanation
Indices: 1070400--1070445 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1070390 ATAATTATGT
1070400 AAATAAAATATAATAATTA
1 AAATAAAATATAATAATTA
*
1070419 AAATATAATATAA-AA-TA
1 AAATAAAATATAATAATTA
*
1070436 AGATAAAATA
1 AAATAAAATA
1070446 ATATAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 2 0.08
19 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATAAAATATAATAATTA
Found at i:1070441 original size:10 final size:10
Alignment explanation
Indices: 1070382--1070452 Score: 63
Period size: 10 Copynumber: 6.8 Consensus size: 10
1070372 AATAATATCA
1070382 AATATAAAAT
1 AATATAAAAT
*
1070392 AATTATGTAAAT
1 AA-TAT-AAAAT
* *
1070404 AAAATATAAT
1 AATATAAAAT
1070414 AAT-TAAAATAT
1 AATAT-AAA-AT
1070425 AATATAAAAT
1 AATATAAAAT
*
1070435 AAGATAAAAT
1 AATATAAAAT
1070445 AATATAAA
1 AATATAAA
1070453 TATTATATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 1 0.02
10 27 0.56
11 13 0.27
12 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
AATATAAAAT
Found at i:1070554 original size:30 final size:30
Alignment explanation
Indices: 1070513--1070594 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
1070503 TATATTAAAT
1070513 TATATATAAAATATTTTAAATAAAATTATAA
1 TATA-ATAAAATATTTTAAATAAAATTATAA
*
1070544 TATAATAAAATATTTTAAATATAATTATAA
1 TATAATAAAATATTTTAAATAAAATTATAA
** *
1070574 TACGATAAAAT-TTATAAATAA
1 TATAATAAAATATTTTAAATAA
1070595 TATAAATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 8 0.17
30 34 0.74
31 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
TATAATAAAATATTTTAAATAAAATTATAA
Found at i:1070878 original size:6 final size:6
Alignment explanation
Indices: 1070869--1070902 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1070859 ATTATAAATT
*
1070869 TTATGA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
1070903 TATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:1070882 original size:21 final size:20
Alignment explanation
Indices: 1070856--1070920 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1070846 TATTTTTTAA
1070856 ATAATTATAAATTTTATGATT
1 ATAATTATAAATTTTAT-ATT
*
1070877 ATAATTAT-AATTATA-ATT
1 ATAATTATAAATTTTATATT
*
1070895 ATAATTATTATATTTTATATT
1 ATAATTA-TAAATTTTATATT
1070916 A-AATT
1 ATAATT
1070921 TCATAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 10 0.26
19 1 0.03
20 15 0.39
21 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATAATTATAAATTTTATATT
Found at i:1079298 original size:31 final size:31
Alignment explanation
Indices: 1079263--1079336 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
1079253 TAAGAAATTT
1079263 GATCAAAGTTACCAAAAGTATATAATAT-TAA
1 GATCAAAGTTACCAAAAGTATATAA-ATCTAA
* * **
1079294 GATCAAAGTAAATCAAAAGTATATAAATCTGT
1 GATCAAAGT-TACCAAAAGTATATAAATCTAA
1079326 GATCAAAGTTA
1 GATCAAAGTTA
1079337 ACAACTTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (31 bp):
GATCAAAGTTACCAAAAGTATATAAATCTAA
Found at i:1081206 original size:16 final size:16
Alignment explanation
Indices: 1081185--1081222 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1081175 AAAAATCTGC
1081185 TTGAATCT-ATCTGAAA
1 TTGAATCTAATCT-AAA
*
1081201 TTGAATCTAATCTAAT
1 TTGAATCTAATCTAAA
1081217 TTGAAT
1 TTGAAT
1081223 TGATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (16 bp):
TTGAATCTAATCTAAA
Found at i:1082476 original size:25 final size:23
Alignment explanation
Indices: 1082432--1082478 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1082422 AATTTTTCTT
**
1082432 ATTTATTTAAAATATTTATTTAC
1 ATTTATTTAAAATAAATATTTAC
1082455 ATTTAATTTATAAATAAATATTTA
1 ATTT-ATTTA-AAATAAATATTTA
1082479 AACAAGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATTTAAAATAAATATTTAC
Found at i:1082647 original size:17 final size:17
Alignment explanation
Indices: 1082603--1082647 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1082593 TTTATTTCTG
*
1082603 TCTTAAATAAATATTTA
1 TCTTAAATAAATATATA
*
1082620 -CTCAAATTAAATATATA
1 TCTTAAA-TAAATATATA
1082637 TCTTAAATAAA
1 TCTTAAATAAA
1082648 CAATGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
TCTTAAATAAATATATA
Found at i:1085097 original size:3 final size:3
Alignment explanation
Indices: 1085089--1085114 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1085079 TCAGCCAAAA
1085089 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1085115 ATAAGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1085717 original size:23 final size:23
Alignment explanation
Indices: 1085691--1085748 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
1085681 AAAGGCAAAG
*
1085691 TAAAAACAAAGATAAGAAAAA-TA
1 TAAAAAAAAAGATAA-AAAAATTA
*
1085714 TAAAATATAAAGATAAAAAAATTA
1 TAAAA-AAAAAGATAAAAAAATTA
1085738 TAAAAAAAAAG
1 TAAAAAAAAAG
1085749 TAATAACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (23 bp):
TAAAAAAAAAGATAAAAAAATTA
Found at i:1086707 original size:13 final size:14
Alignment explanation
Indices: 1086689--1086722 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1086679 ATTATTAATT
1086689 TTATTAAA-TTATA
1 TTATTAAATTTATA
1086702 TTATTAAATTTATA
1 TTATTAAATTTATA
1086716 TTATTAA
1 TTATTAA
1086723 TAAACTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:1086718 original size:24 final size:24
Alignment explanation
Indices: 1086669--1086714 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1086659 AATATTTACA
1086669 TAAATTATTAATTATTAATTTTAT
1 TAAATTATTAATTATTAATTTTAT
*
1086693 TAAATTA-T-ATTATTAAATTTAT
1 TAAATTATTAATTATTAATTTTAT
1086715 ATTATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATTATTAATTATTAATTTTAT
Found at i:1086721 original size:22 final size:19
Alignment explanation
Indices: 1086672--1086723 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 19
1086662 ATTTACATAA
1086672 ATTATTAATTATTAATTTT
1 ATTATTAATTATTAATTTT
1086691 ATTAAATTATATTATTAAATTTAT
1 ATT--ATTA-ATTATT-AATTT-T
1086715 ATTATTAAT
1 ATTATTAAT
1086724 AAACTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.11
21 6 0.21
22 10 0.36
23 5 0.18
24 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTAATTATTAATTTT
Found at i:1087562 original size:39 final size:39
Alignment explanation
Indices: 1087443--1087537 Score: 119
Period size: 34 Copynumber: 2.5 Consensus size: 39
1087433 TACAGATATA
*
1087443 AAAATAATTAAAAATTATATTTATATTCAAT--A-ATAA-T
1 AAAAT-ATT-AAAATTATATTTATATTGAATAAATATAATT
*
1087480 -CAATATTAAAATTATATTTATATTGAATAAATATAATT
1 AAAATATTAAAATTATATTTATATTGAATAAATATAATT
1087518 AAAATATTAAAATTATATTT
1 AAAATATTAAAATTATATTT
1087538 GTTTAAGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
34 20 0.40
35 3 0.06
36 4 0.08
37 4 0.08
38 1 0.02
39 18 0.36
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (39 bp):
AAAATATTAAAATTATATTTATATTGAATAAATATAATT
Found at i:1087563 original size:13 final size:15
Alignment explanation
Indices: 1087540--1087600 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
1087530 TTATATTTGT
1087540 TTAAGAAATAAATTAA
1 TTAA-AAATAAATTAA
1087556 -T-AAAATAAA-TAA
1 TTAAAAATAAATTAA
**
1087568 TTAAAAATAAATTTT
1 TTAAAAATAAATTAA
* *
1087583 TTATAAATAATTTAA
1 TTAAAAATAAATTAA
1087598 TTA
1 TTA
1087601 TGTATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 9 0.25
15 16 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TTAAAAATAAATTAA
Found at i:1088154 original size:15 final size:15
Alignment explanation
Indices: 1088116--1088158 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1088106 TTTATTTACG
*
1088116 TAAATTATTTAA-AA
1 TAAATTTTTTAATAA
*
1088130 TAAATATTTTTAATAT
1 TAAAT-TTTTTAATAA
1088146 TAAATTTTTTAAT
1 TAAATTTTTTAAT
1088159 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 14 0.56
16 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTTTTTAATAA
Found at i:1088165 original size:11 final size:11
Alignment explanation
Indices: 1088149--1088187 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1088139 TTAATATTAA
1088149 ATTTTTTAATT
1 ATTTTTTAATT
*
1088160 A-TTTTTAAAT
1 ATTTTTTAATT
*
1088170 ATTTTTTATTT
1 ATTTTTTAATT
1088181 ATTTTTT
1 ATTTTTT
1088188 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTTAATT
Found at i:1088173 original size:35 final size:35
Alignment explanation
Indices: 1088130--1088209 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
1088120 TTATTTAAAA
1088130 TAAATATTTTTAATATTAAATTTTTT-AATTATTTT
1 TAAATATTTTTAAT-TTAAATTTTTTAAATTATTTT
* **
1088165 TAAATATTTTTTATTTATTTTTTTTAAAATTATTTT
1 TAAATATTTTTAATTTAAATTTTTT-AAATTATTTT
1088201 T-AATATTTT
1 TAAATATTTT
1088210 AGTGATTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.22
35 21 0.52
36 10 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (35 bp):
TAAATATTTTTAATTTAAATTTTTTAAATTATTTT
Found at i:1088459 original size:25 final size:26
Alignment explanation
Indices: 1088430--1088478 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
1088420 TGATGATAAA
1088430 TATAATAAATATTATT-ATAATTAAT
1 TATAATAAATATTATTAATAATTAAT
1088455 TATAATAAATATTATTAATAATTA
1 TATAATAAATATTATTAATAATTA
1088479 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATAATAAATATTATTAATAATTAAT
Found at i:1088462 original size:13 final size:13
Alignment explanation
Indices: 1088430--1088529 Score: 57
Period size: 13 Copynumber: 7.5 Consensus size: 13
1088420 TGATGATAAA
*
1088430 TATAATAAAT-AT
1 TATAATAATTAAT
*
1088442 TATTATAATTAAT
1 TATAATAATTAAT
*
1088455 TATAATAAAT-AT
1 TATAATAATTAAT
1088467 TATTAATAATT-AT
1 TA-TAATAATTAAT
*
1088480 TAATAAAAAATTAAAAT
1 T-AT-AATAATT--AAT
1088497 TATAA-AATAATAAT
1 TATAATAAT--TAAT
1088511 TATAAT-ATTATAT
1 TATAATAATTA-AT
1088524 TATAAT
1 TATAAT
1088530 TACCCTTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
12 14 0.20
13 29 0.41
14 20 0.28
15 2 0.03
16 3 0.04
17 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAATAATTAAT
Found at i:1088828 original size:20 final size:22
Alignment explanation
Indices: 1088785--1088837 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
1088775 TTAAATTTTT
1088785 ATTTTATTATTTATTTTTAATA
1 ATTTTATTATTTATTTTTAATA
*
1088807 ATTTTA-TATTTA-TTTTATTA
1 ATTTTATTATTTATTTTTAATA
1088827 A-TTTATT-TTTA
1 ATTTTATTATTTA
1088838 ATATAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.28
20 9 0.31
21 6 0.21
22 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTATTATTTATTTTTAATA
Found at i:1088837 original size:19 final size:19
Alignment explanation
Indices: 1088779--1088837 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
1088769 TCCCTTTTAA
1088779 ATTTTTATTTTATT-ATTT
1 ATTTTTATTTTATTAATTT
1088797 ATTTTTA----A-TAATTTT
1 ATTTTTATTTTATTAA-TTT
*
1088812 ATATTTATTTTATTAATTT
1 ATTTTTATTTTATTAATTT
1088831 ATTTTTA
1 ATTTTTA
1088838 ATATAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 13
0.68 0.04 0.28
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 9 0.28
18 7 0.22
19 10 0.31
20 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTATTTTATTAATTT
Found at i:1088906 original size:25 final size:24
Alignment explanation
Indices: 1088828--1088907 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
1088818 ATTTTATTAA
1088828 TTTATTT-TTAATATAAATATAATT
1 TTTATTTATTAATATAAATATAA-T
* *
1088852 TTTAATTATTATTTAAGAT-AATATATT
1 TTT-A-T-TTA-TTAATATAAATATAAT
1088879 TTTATTTAGTTAATATAAATATAAT
1 TTTATTTA-TTAATATAAATATAAT
1088904 TTTA
1 TTTA
1088908 ATAACTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
24 12 0.27
25 13 0.29
26 2 0.04
27 6 0.13
28 6 0.13
29 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TTTATTTATTAATATAAATATAAT
Found at i:1088948 original size:27 final size:30
Alignment explanation
Indices: 1088890--1088948 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
1088880 TTATTTAGTT
1088890 AATATAAATATAATTTTAATAACTTATTTTTTA
1 AATATAAATATAATTTTAATAA--TA-TTTTTA
1088923 AATATAAATATAATTTTAA-AA-ATTTT
1 AATATAAATATAATTTTAATAATATTTT
1088949 CAATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 4 0.15
29 1 0.04
32 2 0.08
33 19 0.73
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AATATAAATATAATTTTAATAATATTTTTA
Found at i:1089022 original size:95 final size:94
Alignment explanation
Indices: 1088848--1089035 Score: 238
Period size: 95 Copynumber: 2.0 Consensus size: 94
1088838 ATATAAATAT
* * * * *
1088848 AATTTTTAATTATTATTTAAGATAATATATTTTTATTTAGTTAATATAAATATAATTTTAATAAC
1 AATTTTCAATTATTATTTAACATAATATAATTTTATTTAGTTAATATAAATAAAAATTTAAT-AC
1088913 TTATTTTTTAAATATAAATATAATTTTAAA
65 TTATTTTTTAAATATAAATATAATTTTAAA
* * *
1088943 AATTTTCAATTATTATTTAACATAAATATAATTTTA-TTATTTAATATAAATAAAAATTTGAT-T
1 AATTTTCAATTATTATTTAACAT-AATATAATTTTATTTAGTTAATATAAATAAAAATTTAATAC
1089006 TTATTACTGTTT-AATATAAATATAATTTTA
65 TTATT--T-TTTAAATATAAATATAATTTTA
1089036 TTTATATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
93 5 0.06
95 62 0.77
96 14 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (94 bp):
AATTTTCAATTATTATTTAACATAATATAATTTTATTTAGTTAATATAAATAAAAATTTAATACT
TATTTTTTAAATATAAATATAATTTTAAA
Found at i:1089050 original size:95 final size:93
Alignment explanation
Indices: 1088851--1089083 Score: 235
Period size: 95 Copynumber: 2.5 Consensus size: 93
1088841 TAAATATAAT
* * * * *
1088851 TTTTAATTATTATTTAAGAT-AATATATTTTTATTTAGTTAATATAAATATAATTTTAATAACTT
1 TTTTAATTATTATTTAACATAAATATAATTTTA-TTATTTAATATAAATAAAAATTTAAT-ACTT
1088915 ATTTTTTAAATATAAATATAATTTTAAAAA
64 ATTTTTTAAATATAAATATAATTTTAAAAA
* *
1088945 TTTTCAATTATTATTTAACATAAATATAATTTTATTATTTAATATAAATAAAAATTTGAT-TTTA
1 TTTT-AATTATTATTTAACATAAATATAATTTTATTATTTAATATAAATAAAAATTTAATACTTA
***
1089009 TTACTGTTT-AATATAAATATAATTTTATTTA
65 TT--T-TTTAAATATAAATATAATTTTAAAAA
* * *
1089040 TATT--TTATTATTTAATATAAATA-AATTTTTAATTATTTATTATA
1 TTTTAATTATTATTTAACATAAATATAA-TTTT-ATTATTTAATATA
1089084 TATGCATTTT
Statistics
Matches: 119, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
91 2 0.02
92 22 0.18
93 17 0.14
94 4 0.03
95 60 0.50
96 14 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (93 bp):
TTTTAATTATTATTTAACATAAATATAATTTTATTATTTAATATAAATAAAAATTTAATACTTAT
TTTTTAAATATAAATATAATTTTAAAAA
Found at i:1089070 original size:35 final size:34
Alignment explanation
Indices: 1088973--1089068 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 34
1088963 CATAAATATA
*
1088973 ATTTTATTATTTAATATAAATAAAAATTTGATTT-T
1 ATTTTATTATTTAATATAAAT--AAATTTTATTTAT
* *
1089008 A--TTACTGTTTAATATAAATATAATTTTATTTAT
1 ATTTTATTATTTAATATAAATA-AATTTTATTTAT
1089041 ATTTTATTATTTAATATAAATAAATTTT
1 ATTTTATTATTTAATATAAATAAATTTT
1089069 TAATTATTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
31 1 0.02
32 9 0.17
33 18 0.35
34 6 0.12
35 18 0.35
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTTTATTATTTAATATAAATAAATTTTATTTAT
Found at i:1089182 original size:18 final size:20
Alignment explanation
Indices: 1089159--1089200 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
1089149 TTAAACATAT
*
1089159 ATCTTATTATTAA-T-TTTA
1 ATCTTATTACTAAGTATTTA
1089177 ATCTTATTACTAAGTATTTA
1 ATCTTATTACTAAGTATTTA
1089197 ATCT
1 ATCT
1089201 CATTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (20 bp):
ATCTTATTACTAAGTATTTA
Found at i:1090401 original size:136 final size:136
Alignment explanation
Indices: 1090156--1090421 Score: 478
Period size: 136 Copynumber: 2.0 Consensus size: 136
1090146 TCATCACTTT
*
1090156 TACTACATGATCATGAAACTAACATTATTCACCTACATCCAATTTGATGTACTTTGACTTCTAAT
1 TACTACATGATCATGAAACTAACATTATACACCTACATCCAATTTGATGTACTTTGACTTCTAAT
* * *
1090221 GTTCTTCTACTACATGATTTAAATTTGCTATACTATTATGTACAAAAATTTAAATTATGTTCATG
66 GTTCTTCTACTACATAATTTAAATTTGCTATACTATTATATACAAAAATTTAAATTATGATCATG
1090286 TTCTTC
131 TTCTTC
1090292 TACTACATGATCATGAAACTAACATTATACACCTACATCCAATTTGATGTACTTTGACTTCTAAT
1 TACTACATGATCATGAAACTAACATTATACACCTACATCCAATTTGATGTACTTTGACTTCTAAT
* *
1090357 GTTCTTCTGCTACATAATTTAAATTTGTTATACTATTATATACAAAAATTTAAATTATGATCATG
66 GTTCTTCTACTACATAATTTAAATTTGCTATACTATTATATACAAAAATTTAAATTATGATCATG
1090422 AACATGATTT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 124 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (136 bp):
TACTACATGATCATGAAACTAACATTATACACCTACATCCAATTTGATGTACTTTGACTTCTAAT
GTTCTTCTACTACATAATTTAAATTTGCTATACTATTATATACAAAAATTTAAATTATGATCATG
TTCTTC
Found at i:1091883 original size:21 final size:20
Alignment explanation
Indices: 1091836--1091883 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1091826 TATTATATTT
*
1091836 ATTATTTATTTAATATTACA
1 ATTATTTATTTAAAATTACA
*
1091856 ATGATTTATTTTAAAATTTA-A
1 ATTATTTA-TTTAAAA-TTACA
1091877 ATTATTT
1 ATTATTT
1091884 TTAGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
21 13 0.57
22 3 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTATTTATTTAAAATTACA
Found at i:1096972 original size:23 final size:24
Alignment explanation
Indices: 1096918--1096972 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1096908 ATTAGCATCA
* **
1096918 ATATATTTTAATATTTTATTTTTT
1 ATATATATTAATATTTTATTACTT
*
1096942 A-ATTTATTAATATTTT-TTACTT
1 ATATATATTAATATTTTATTACTT
1096964 ATATATATT
1 ATATATATT
1096973 TATAGGTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.20
23 19 0.76
24 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATATATTAATATTTTATTACTT
Found at i:1097125 original size:21 final size:23
Alignment explanation
Indices: 1097092--1097133 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1097082 TCACATAAGT
1097092 AAAATAAATATAAAA-TATTAAA
1 AAAATAAATATAAAATTATTAAA
*
1097114 AAAATATA-ATAAAATTATTA
1 AAAATAAATATAAAATTATTA
1097134 TTAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAAATATAAAATTATTAAA
Found at i:1097164 original size:17 final size:18
Alignment explanation
Indices: 1097134--1097174 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1097124 AAAATTATTA
*
1097134 TTAA-TTAATTAATA-AT
1 TTAATTTAATGAATATAT
1097150 TTAATTTAATGAATATAT
1 TTAATTTAATGAATATAT
*
1097168 TTTATTT
1 TTAATTT
1097175 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 9 0.43
18 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAATTTAATGAATATAT
Found at i:1102216 original size:13 final size:13
Alignment explanation
Indices: 1102198--1102222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102188 CATAAAGTGT
1102198 TGTATCGATACAA
1 TGTATCGATACAA
1102211 TGTATCGATACA
1 TGTATCGATACA
1102223 TGTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1102303 original size:13 final size:13
Alignment explanation
Indices: 1102285--1102309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102275 ATCACTTAAA
1102285 TGTATCGATACAT
1 TGTATCGATACAT
1102298 TGTATCGATACA
1 TGTATCGATACA
1102310 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1102362 original size:52 final size:52
Alignment explanation
Indices: 1102318--1102498 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
1102308 CACTGATCTT
1102318 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1102370 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1102422 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1102474 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1102499 TCATATTTCG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1106641 original size:10 final size:10
Alignment explanation
Indices: 1106626--1106652 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1106616 TGCTAACTAA
1106626 GTTTTTGTTT
1 GTTTTTGTTT
1106636 GTTTTTGTTT
1 GTTTTTGTTT
1106646 GTTTTTG
1 GTTTTTG
1106653 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:1115943 original size:22 final size:22
Alignment explanation
Indices: 1115890--1115933 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1115880 CAAAGCTCAT
1115890 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
*
1115912 GATATAATTTATTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
1115934 ATTATTATTT
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:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
GATATAATTTACTTTTTGATAA
Found at i:1117006 original size:21 final size:22
Alignment explanation
Indices: 1116963--1117008 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1116953 TTTAAGTTAA
* *
1116963 TTTAAATCGAATCAGATTCAAT
1 TTTAAATCGAATCAGAATAAAT
*
1116985 TTTAAATCGACTCA-AATAAAT
1 TTTAAATCGAATCAGAATAAAT
1117006 TTT
1 TTT
1117009 TGGATTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (22 bp):
TTTAAATCGAATCAGAATAAAT
Found at i:1118013 original size:15 final size:16
Alignment explanation
Indices: 1117993--1118035 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1117983 CGGGTTTAAC
1117993 ATTCGGGTTAATC-AG
1 ATTCGGGTTAATCTAG
* * *
1118008 ATTCGGGTCATTCTGG
1 ATTCGGGTTAATCTAG
1118024 ATTCGGGTTAAT
1 ATTCGGGTTAAT
1118036 TGGGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (16 bp):
ATTCGGGTTAATCTAG
Found at i:1118555 original size:17 final size:17
Alignment explanation
Indices: 1118533--1118565 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1118523 ATAACAATTT
*
1118533 TAAAAAATTTAAATTAA
1 TAAAAAATTAAAATTAA
1118550 TAAAAAATTAAAATTA
1 TAAAAAATTAAAATTA
1118566 TTATAATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATTAAAATTAA
Found at i:1119043 original size:16 final size:16
Alignment explanation
Indices: 1119017--1119077 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
1119007 TGAGTTAATT
*
1119017 ATTCGGGTCATTTCGG
1 ATTCGGATCATTTCGG
* *
1119033 ATTCGAATCATCTCGG
1 ATTCGGATCATTTCGG
*
1119049 ATTCGGGTCATTTC-G
1 ATTCGGATCATTTCGG
1119064 AGTTCGGATCATTT
1 A-TTCGGATCATTT
1119078 TATATTCGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 2 0.05
16 35 0.95
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (16 bp):
ATTCGGATCATTTCGG
Found at i:1119085 original size:32 final size:32
Alignment explanation
Indices: 1119016--1119085 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1119006 TTGAGTTAAT
*
1119016 TATTCGGGTCATTTCGGATTCGAATCATCTCG
1 TATTCGGGTCATTTCGGATTCGAATCATCTCA
* * * *
1119048 GATTCGGGTCATTTC-GAGTTCGGATCATTTTA
1 TATTCGGGTCATTTCGGA-TTCGAATCATCTCA
1119080 TATTCG
1 TATTCG
1119086 TATTATTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (32 bp):
TATTCGGGTCATTTCGGATTCGAATCATCTCA
Found at i:1119315 original size:14 final size:14
Alignment explanation
Indices: 1119281--1119318 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
1119271 ATCGTACTCG
1119281 TATAAA-ATATAAA
1 TATAAAGATATAAA
1119294 T-T-AAGATATAAA
1 TATAAAGATATAAA
1119306 TATAAAGATATAA
1 TATAAAGATATAA
1119319 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.09
12 9 0.41
13 2 0.09
14 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (14 bp):
TATAAAGATATAAA
Found at i:1120742 original size:21 final size:21
Alignment explanation
Indices: 1120686--1120742 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1120676 TATTTTATAT
*
1120686 AATTATCATAA-AA-TATAAA
1 AATTATAATAATAATTATAAA
*
1120705 AATTATAATTATAATTATAAA
1 AATTATAATAATAATTATAAA
* * *
1120726 ATTTTTAATAATGATTA
1 AATTATAATAATAATTA
1120743 AAGAAGTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 9 0.30
20 2 0.07
21 19 0.63
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTATAATAATAATTATAAA
Found at i:1124518 original size:13 final size:14
Alignment explanation
Indices: 1124500--1124533 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1124490 AATTTTAATT
1124500 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
1124513 TTATTAAATTTTTA
1 TTATTAAATTTATA
1124527 TTATTAA
1 TTATTAA
1124534 TAAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:1124996 original size:23 final size:22
Alignment explanation
Indices: 1124965--1125017 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
1124955 AAATATAATA
*
1124965 ATATAAATACATATTTTAAAAT
1 ATATAAATACAAATTTTAAAAT
* *
1124987 ATATATAATATAAATTTTAATAT
1 ATATA-AATACAAATTTTAAAAT
*
1125010 ATTTAAAT
1 ATATAAAT
1125018 TTAGATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAAATACAAATTTTAAAAT
Found at i:1125095 original size:20 final size:18
Alignment explanation
Indices: 1125052--1125105 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1125042 ATACGATTAT
*
1125052 AATATAATAAAATATATA
1 AATATAATAAAATACATA
1125070 AATATAATATAAATACACTA
1 AATATAATA-AAATACA-TA
* *
1125090 ATTATAA-AATATACAT
1 AATATAATAAAATACAT
1125106 TTGGGTTGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 1 0.03
18 15 0.48
19 7 0.23
20 8 0.26
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATAAAATACATA
Found at i:1125630 original size:18 final size:16
Alignment explanation
Indices: 1125591--1125668 Score: 54
Period size: 14 Copynumber: 4.8 Consensus size: 16
1125581 TCCAGGCATC
*
1125591 TAAA-TTAAATAAAAA
1 TAAATTTAATTAAAAA
*
1125606 TTTAATTTAATTAATAAA
1 -TAAATTTAATTAA-AAA
*
1125624 TACAATTATATTTAAAAA
1 TA-AATT-TAATTAAAAA
*
1125642 TAAATTT--TAAAAAA
1 TAAATTTAATTAAAAA
*
1125656 TTAATTTAATTAA
1 TAAATTTAATTAA
1125669 TTCATATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
14 12 0.24
16 7 0.14
17 12 0.24
18 12 0.24
19 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATTTAATTAAAAA
Found at i:1125884 original size:19 final size:19
Alignment explanation
Indices: 1125849--1125892 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1125839 ATGAAATAAA
*
1125849 ATTAAAATAATATAAATAT
1 ATTAAAATAACATAAATAT
1125868 ATTATAAATAACA-AAATAT
1 ATTA-AAATAACATAAATAT
1125887 ATTAAA
1 ATTAAA
1125893 TTTATGTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTAAAATAACATAAATAT
Found at i:1126832 original size:2 final size:2
Alignment explanation
Indices: 1126825--1126853 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1126815 CTGAAGTTGA
1126825 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1126854 CCTGGAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1127075 original size:3 final size:3
Alignment explanation
Indices: 1127067--1127102 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1127057 ACAAAGAGCA
* *
1127067 AAG AAG AAG AAG GAG AAG ATG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1127103 CAGGAGGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1127359 original size:18 final size:19
Alignment explanation
Indices: 1127336--1127382 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
1127326 TAATTAATTG
1127336 TTATTTATTAAAAT-TAAA
1 TTATTTATTAAAATATAAA
*
1127354 TTATTT-TAAAAATATAAA
1 TTATTTATTAAAATATAAA
1127372 TT-TTTA-TAAAA
1 TTATTTATTAAAA
1127383 AATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTTATTAAAATATAAA
Found at i:1127383 original size:18 final size:18
Alignment explanation
Indices: 1127336--1127383 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1127326 TAATTAATTG
*
1127336 TTATTTATTAAAATTAAA
1 TTATTTATAAAAATTAAA
1127354 TTATTT-TAAAAATATAAA
1 TTATTTATAAAAAT-TAAA
1127372 TT-TTTATAAAAA
1 TTATTTATAAAAA
1127384 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTTATAAAAATTAAA
Found at i:1127470 original size:25 final size:27
Alignment explanation
Indices: 1127436--1127500 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 27
1127426 TAAGAAAACG
*
1127436 ATATATAAAATTA-AAAT-TTTAAAAA
1 ATATATAAAATAATAAATATTTAAAAA
*
1127461 ATATTTAAAATAATAAATATTT-AAAA
1 ATATATAAAATAATAAATATTTAAAAA
*
1127487 ATTTA-AAAATAATA
1 ATATATAAAATAATA
1127501 TTATTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 20 0.59
26 11 0.32
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATATAAAATAATAAATATTTAAAAA
Found at i:1127584 original size:19 final size:18
Alignment explanation
Indices: 1127560--1127599 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1127550 TTTAATATTT
*
1127560 TAATTTAAATTGATAAATA
1 TAATTTAAATT-ATAAAAA
*
1127579 TAATTTTAATTATAAAAA
1 TAATTTAAATTATAAAAA
1127597 TAA
1 TAA
1127600 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATTTAAATTATAAAAA
Found at i:1128287 original size:30 final size:30
Alignment explanation
Indices: 1128220--1128287 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
1128210 TAAGCTTGAT
* *
1128220 TTATTT-AAAATATAAAATTCAAGTTTAGC
1 TTATTTAAAAATATAAAATTCAAATTGAGC
*
1128249 TTATTTTAAAAATATAAAATTTAAATTCGA-C
1 TTA-TTTAAAAATATAAAATTCAAATT-GAGC
1128280 TTATTTAA
1 TTATTTAA
1128288 TTCGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 8 0.24
31 21 0.64
32 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (30 bp):
TTATTTAAAAATATAAAATTCAAATTGAGC
Found at i:1129089 original size:22 final size:22
Alignment explanation
Indices: 1129054--1129095 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1129044 TATTTTTATT
1129054 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1129076 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
1129096 ATTTTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1129178 original size:23 final size:23
Alignment explanation
Indices: 1129148--1129193 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1129138 GAAATATGAA
1129148 AATTCTCAAGCTACTACCAAAGC
1 AATTCTCAAGCTACTACCAAAGC
*
1129171 AATTCTCAAGCTACTACCTAAGC
1 AATTCTCAAGCTACTACCAAAGC
1129194 TCTATACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (23 bp):
AATTCTCAAGCTACTACCAAAGC
Found at i:1129298 original size:22 final size:21
Alignment explanation
Indices: 1129273--1129331 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
1129263 TATTAAAAAT
1129273 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTA-A
1129295 TATTTTTATAATTAAATTTAA
1 TATTTTTATAATTAAATTTAA
*
1129316 AATTTTTATTAATTAA
1 TATTTTTA-TAATTAA
1129332 CTAATAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.24
22 21 0.62
23 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTTATAATTAAATTTAA
Found at i:1130170 original size:23 final size:23
Alignment explanation
Indices: 1130143--1130206 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1130133 ATTTAATAAT
**
1130143 TAAAATATATTTAAATTTATTTA
1 TAAAATATATTTAAATTTATGAA
1130166 TAAAATATA--TAAATATTATGAA
1 TAAAATATATTTAAAT-TTATGAA
*
1130188 TAAAAATATATTTTAATTT
1 T-AAAATATATTTAAATTT
1130207 TTATTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 17 0.50
24 2 0.06
25 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAATATATTTAAATTTATGAA
Found at i:1131601 original size:24 final size:26
Alignment explanation
Indices: 1131565--1131612 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1131555 ATTTAAATTA
1131565 TTATTTAATAAATA-A-AAATATTTT
1 TTATTTAATAAATATATAAATATTTT
1131589 TTATTATAA-AAATATATAAATATT
1 TTATT-TAATAAATATATAAATATT
1131613 AATATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 4 0.19
26 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATTTAATAAATATATAAATATTTT
Found at i:1132347 original size:22 final size:24
Alignment explanation
Indices: 1132307--1132351 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1132297 TGATTCAATC
*
1132307 TTAAGTTTTAAAAATATATTTAAT
1 TTAAGTTTTAAAAACATATTTAAT
1132331 TTAA-TTTT-AAAACATATTTAA
1 TTAAGTTTTAAAAACATATTTAA
1132352 AAATAGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAGTTTTAAAAACATATTTAAT
Found at i:1132520 original size:27 final size:26
Alignment explanation
Indices: 1132477--1132529 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1132467 TACAAATACT
*
1132477 TTTGAAAACTAAAAAAATAAATAAAAA
1 TTTGAAAACTAAAAAAAGAAA-AAAAA
1132504 TTTGAAAA-TAAAAAAAAGAAAAAAAA
1 TTTGAAAACT-AAAAAAAGAAAAAAAA
1132530 GGAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (26 bp):
TTTGAAAACTAAAAAAAGAAAAAAAA
Found at i:1132528 original size:26 final size:27
Alignment explanation
Indices: 1132477--1132529 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1132467 TACAAATACT
*
1132477 TTTGAAAACTAAAAAAATAAATAAAAA
1 TTTGAAAACTAAAAAAATAAAAAAAAA
1132504 TTTGAAAA-TAAAAAAA-AGAAAAAAAA
1 TTTGAAAACTAAAAAAATA-AAAAAAAA
1132530 GGAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.62
27 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (27 bp):
TTTGAAAACTAAAAAAATAAAAAAAAA
Found at i:1137957 original size:18 final size:18
Alignment explanation
Indices: 1137907--1137962 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
1137897 TACGAATATC
1137907 TCAAAATTTATAT-AATA
1 TCAAAATTTATATAAATA
1137924 -C-AAA-TTAT-TAACATA
1 TCAAAATTTATATAA-ATA
1137939 TCAAAATTTATATAAATA
1 TCAAAATTTATATAAATA
1137957 T-AAAAT
1 TCAAAAT
1137963 ATCTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 8 0.24
18 8 0.24
19 3 0.09
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAAAATTTATATAAATA
Found at i:1139000 original size:11 final size:10
Alignment explanation
Indices: 1138974--1139006 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1138964 AAATTTAAAA
1138974 TAATTTTTTT
1 TAATTTTTTT
1138984 T-ATTTTTTT
1 TAATTTTTTT
1138993 TAATTTTTTGT
1 TAATTTTTT-T
1139004 TAA
1 TAA
1139007 AAATCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 8 0.38
11 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:1139787 original size:19 final size:18
Alignment explanation
Indices: 1139758--1139793 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1139748 TAAAAAAATT
1139758 AAAATTAAAAAATTAAAA
1 AAAATTAAAAAATTAAAA
*
1139776 AAAATATAAAAATTTAAA
1 AAAAT-TAAAAAATTAAA
1139794 TCTCACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTAAAAAATTAAAA
Found at i:1139840 original size:13 final size:13
Alignment explanation
Indices: 1139822--1139847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1139812 TTATATTTTA
1139822 AAAATAATTAAAT
1 AAAATAATTAAAT
1139835 AAAATAATTAAAT
1 AAAATAATTAAAT
1139848 TATACTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATAATTAAAT
Found at i:1140035 original size:2 final size:2
Alignment explanation
Indices: 1140028--1140069 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1140018 TTTCTTTGAG
1140028 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
1140070 TTTAATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1140368 original size:19 final size:19
Alignment explanation
Indices: 1140336--1140387 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1140326 ATAAATTAAA
1140336 AATATATATTATATAATTT-T
1 AATATAT-TTATAT-ATTTAT
1140356 AATATATTTATATATTTAT
1 AATATATTTATATATTTAT
* *
1140375 ATTAAATTTATAT
1 AATATATTTATAT
1140388 TATCTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 18 0.62
20 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATATTTATATATTTAT
Found at i:1142830 original size:10 final size:11
Alignment explanation
Indices: 1142810--1142850 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1142800 GGAAAAGGAG
1142810 AAAGAGAAAAA
1 AAAGAGAAAAA
1142821 AAAG-GAAAAA
1 AAAGAGAAAAA
* *
1142831 AAAAAGAAAGA
1 AAAGAGAAAAA
1142842 AAAGA-AAAA
1 AAAGAGAAAA
1142851 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 12 0.48
11 13 0.52
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAGAAAAA
Found at i:1149270 original size:14 final size:15
Alignment explanation
Indices: 1149243--1149279 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1149233 ATTAGTATAT
*
1149243 TAAATATTTTAATAA
1 TAAATATTTAAATAA
1149258 TAAA-ATTTAAATAA
1 TAAATATTTAAATAA
1149272 -AAATATTT
1 TAAATATTT
1149280 TATTGATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 13 0.65
15 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATATTTAAATAA
Found at i:1153811 original size:27 final size:28
Alignment explanation
Indices: 1153728--1153811 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
1153718 AAATTTGATA
*
1153728 TATTTTTATATTA-ATAACATGATCATGT
1 TATTTTTATATTATATAACATTAT-ATGT
* * * *
1153756 TATTTTTATATCATATCATATTTTA-GT
1 TATTTTTATATTATATAACATTATATGT
1153783 TATTTTTTATATTATAT-A-ATTATATGT
1 TA-TTTTTATATTATATAACATTATATGT
1153810 TA
1 TA
1153812 CCCAATACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
26 5 0.11
27 9 0.20
28 26 0.57
29 6 0.13
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (28 bp):
TATTTTTATATTATATAACATTATATGT
Found at i:1156061 original size:22 final size:22
Alignment explanation
Indices: 1156035--1156142 Score: 144
Period size: 22 Copynumber: 4.8 Consensus size: 22
1156025 TTAATATCTT
1156035 TATTAAGTGTGTTAGGTAAACA
1 TATTAAGTGTGTTAGGTAAACA
*
1156057 TATTAAGTGTGTTAGGTGAGTAATA
1 TATTAAGTGTGTTAGGT-A--AACA
*
1156082 TATTAAGTGTGTTAAGTAAACA
1 TATTAAGTGTGTTAGGTAAACA
* *
1156104 TATTAGGTGTATTAGGTAAACA
1 TATTAAGTGTGTTAGGTAAACA
*
1156126 TATTAGGTGTGTTAGGT
1 TATTAAGTGTGTTAGGT
1156143 GAACTTATCT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
22 55 0.72
23 1 0.01
24 1 0.01
25 19 0.25
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (22 bp):
TATTAAGTGTGTTAGGTAAACA
Found at i:1156089 original size:47 final size:44
Alignment explanation
Indices: 1156035--1156142 Score: 144
Period size: 47 Copynumber: 2.4 Consensus size: 44
1156025 TTAATATCTT
* *
1156035 TATTAAGTGTGTTAGGTAAACATATTAAGTGTGTTAGGTGAGTAATA
1 TATTAAGTGTGTTAGGTAAACATATTAAGTGTATTAGGT-A--AACA
* *
1156082 TATTAAGTGTGTTAAGTAAACATATTAGGTGTATTAGGTAAACA
1 TATTAAGTGTGTTAGGTAAACATATTAAGTGTATTAGGTAAACA
*
1156126 TATTAGGTGTGTTAGGT
1 TATTAAGTGTGTTAGGT
1156143 GAACTTATCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 18 0.33
46 1 0.02
47 36 0.65
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (44 bp):
TATTAAGTGTGTTAGGTAAACATATTAAGTGTATTAGGTAAACA
Found at i:1159793 original size:20 final size:20
Alignment explanation
Indices: 1159765--1159839 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1159755 TCATACCCTG
1159765 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1159785 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1159805 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1159825 ATGTATCGATACATT
1 ATGTATCGATACATT
1159840 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1159832 original size:40 final size:39
Alignment explanation
Indices: 1159765--1159842 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1159755 TCATACCCTG
* *
1159765 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1159805 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1159843 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1160781 original size:23 final size:23
Alignment explanation
Indices: 1160754--1160809 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
1160744 AGCCTTTGAC
1160754 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1160777 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1160799 CATGCATTTTT
1 CATGCATTTTT
1160810 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1160816 original size:20 final size:21
Alignment explanation
Indices: 1160762--1160816 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1160752 ACCATGCATT
**
1160762 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
1160783 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
1160805 -TTTTTAACATGT
1 TTTTTTAACATGT
1160817 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:1164336 original size:25 final size:22
Alignment explanation
Indices: 1164320--1164369 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1164310 AGGTGATGTA
1164320 TTAAGTAAACATATTAGGTGTG
1 TTAAGTAAACATATTAGGTGTG
* *
1164342 TTAGGTAAACATATTAAGTGTG
1 TTAAGTAAACATATTAGGTGTG
1164364 TTAAGT
1 TTAAGT
1164370 GAACTTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (22 bp):
TTAAGTAAACATATTAGGTGTG
Found at i:1164341 original size:34 final size:38
Alignment explanation
Indices: 1164248--1164347 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 38
1164238 TATTAAGTAT
* *
1164248 GTTAAATAAACATATTAGGTGTGTTAAGTGGTATGGTA
1 GTTAAGTAAACATATTAGGTGTGTTAGGTGGTATGGTA
* * * *
1164286 GGTGAGT-AATATATTAAGTGTGTTAGGT-G-AT-GTA
1 GTTAAGTAAACATATTAGGTGTGTTAGGTGGTATGGTA
1164320 -TTAAGTAAACATATTAGGTGTGTTAGGT
1 GTTAAGTAAACATATTAGGTGTGTTAGGT
1164348 AAACATATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
33 4 0.08
34 22 0.43
35 2 0.04
36 1 0.02
37 18 0.35
38 4 0.08
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (38 bp):
GTTAAGTAAACATATTAGGTGTGTTAGGTGGTATGGTA
Found at i:1165684 original size:30 final size:30
Alignment explanation
Indices: 1165665--1165729 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1165655 ATTTAAAGTC
1165665 TTATTTGAATATAATTTAAAAATTAAAAAT
1 TTATTTGAATATAATTTAAAAATTAAAAAT
1165695 TTATTTGAATATAA--TAAAAATATAAAAAT
1 TTATTTGAATATAATTTAAAAAT-TAAAAAT
1165724 TTATTT
1 TTATTT
1165730 AAAAAAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 7 0.21
29 13 0.38
30 14 0.41
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
TTATTTGAATATAATTTAAAAATTAAAAAT
Found at i:1167929 original size:20 final size:21
Alignment explanation
Indices: 1167875--1167934 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1167865 TATCGCCTAT
*
1167875 AACTTTTCTATCAACTTCTTTT
1 AACTTTT-TATCAACTTCTTTC
**
1167897 AGTTTTTTATCAACTTCTTTC
1 AACTTTTTATCAACTTCTTTC
*
1167918 AACTTTTT-TCAATTTCT
1 AACTTTTTATCAACTTCT
1167935 ATCAGCTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 8 0.25
21 19 0.59
22 5 0.16
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.57
Consensus pattern (21 bp):
AACTTTTTATCAACTTCTTTC
Found at i:1167949 original size:10 final size:10
Alignment explanation
Indices: 1167906--1167948 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1167896 TAGTTTTTTA
1167906 TCAACTTCTT
1 TCAACTTCTT
*
1167916 TCAACTTTTT
1 TCAACTTCTT
* *
1167926 TCAATTTCTA
1 TCAACTTCTT
*
1167936 TCAGCTTCTT
1 TCAACTTCTT
1167946 TCA
1 TCA
1167949 GTTTTCTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (10 bp):
TCAACTTCTT
Found at i:1170798 original size:23 final size:23
Alignment explanation
Indices: 1170768--1170812 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1170758 TCTTATTCGC
1170768 ATTATAAATGATAT-TTTTTTTAG
1 ATTATAAAT-ATATATTTTTTTAG
1170791 ATTATAAATATATATTTTTTTA
1 ATTATAAATATATATTTTTTTA
1170813 TTCGAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTATAAATATATATTTTTTTAG
Found at i:1171161 original size:13 final size:13
Alignment explanation
Indices: 1171143--1171168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1171133 ATAATTGTGC
1171143 ATGTATCGATACA
1 ATGTATCGATACA
1171156 ATGTATCGATACA
1 ATGTATCGATACA
1171169 TCTCGATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1174102 original size:11 final size:11
Alignment explanation
Indices: 1174086--1174128 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1174076 GACATAAACA
1174086 TGAGAGATATT
1 TGAGAGATATT
1174097 TGAGAGATATT
1 TGAGAGATATT
1174108 TGAGA-AGTA--
1 TGAGAGA-TATT
1174117 TGAGAGATATT
1 TGAGAGATATT
1174128 T
1 T
1174129 AAAAACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 19 0.68
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (11 bp):
TGAGAGATATT
Found at i:1174120 original size:20 final size:20
Alignment explanation
Indices: 1174097--1174162 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 20
1174087 GAGAGATATT
1174097 TGAGAGATATTTGAGAAGTA
1 TGAGAGATATTTGAGAAGTA
* *
1174117 TGAGAGATATTTAAAAACACAAGTA
1 TGAGAGATATTT-----GAGAAGTA
1174142 TGAGAGATATTTGAGAAGTA
1 TGAGAGATATTTGAGAAGTA
1174162 T
1 T
1174163 TAACACTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
20 19 0.51
25 18 0.49
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (20 bp):
TGAGAGATATTTGAGAAGTA
Found at i:1174180 original size:45 final size:45
Alignment explanation
Indices: 1174036--1174180 Score: 159
Period size: 45 Copynumber: 3.1 Consensus size: 45
1174026 AAACATTTAA
1174036 AAACACAAGTATGAGAGATATTTGAGAAGTATTAACACTCGACAT
1 AAACACAAGTATGAGAGATATTTGAGAAGTATTAACACTCGACAT
* * * * **
1174081 AAACATGAGAGATATTTGAGAGATATTTGAGAAGTATGAGAGATATTTA-A-
1 AAACA-CA-AG-TA--TGAGAGATATTTGAGAAGTATTA-ACA-CTCGACAT
1174131 AAACACAAGTATGAGAGATATTTGAGAAGTATTAACACTCGACAT
1 AAACACAAGTATGAGAGATATTTGAGAAGTATTAACACTCGACAT
1174176 AAACA
1 AAACA
1174181 TGAGATTAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
43 2 0.03
44 3 0.04
45 32 0.41
46 1 0.01
47 4 0.05
48 4 0.05
49 1 0.01
50 27 0.34
51 3 0.04
52 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.26
Consensus pattern (45 bp):
AAACACAAGTATGAGAGATATTTGAGAAGTATTAACACTCGACAT
Found at i:1177221 original size:319 final size:318
Alignment explanation
Indices: 1176638--1177276 Score: 1188
Period size: 319 Copynumber: 2.0 Consensus size: 318
1176628 AGTCGATGTG
* *
1176638 AACTAGTTGCAATACTCTAGATGTCGTGACAATGTTTATGGGTTTAAAAGAATTTCTTTTATGCT
1 AACTAGTTGCAATACTCTAGATATCGTGACAATATTTATGGGTTTAAAAGAATTTCTTTTATGCT
*
1176703 TTCCCTTAATACATGCATCACATACTTTATTGCAATCAAATTTAACCTTAGGTAATTCAATAACA
66 TTCCCTTAATACATGCATCACATACTTTATCGCAATCAAATTTAACCTTAGGTAATTCAATAACA
* *
1176768 AGGTCTTTCCTAGATAATTTTGAAAGTACGCTCATACTTGCGTGTCCTAATTTTGGGTGTCATAG
131 AGGTCTTTCCTAGATAACTTTGAAAGTACGCTCATACTTGCGTGTCCTAATTTTGGGTGCCATAG
*
1176833 CCAAGGTATGTCATTGTTGTCCGTAACAAAACATACGTTTTGGGAACTTAAAACATCTAAATGCA
196 CCAAGGTATGTCATTGTTGTCCGTAACAAAACATACGTTTTGGGAACTTAAAACATCTAAATACA
*
1176898 CAACATAAATGTTCCTTTCTCTATGTCCTAGGAATATTATTTTTTTTACTACTAGTATC
261 CAACATAAATGTTCCTTTCTCTATGGCCTAGGAATATTA-TTTTTTTACTACTAGTATC
*
1176957 AACTAGTTGCAATACTCTAGATATCGTGATAATATTTATGGGTTTAAAAGAATTTCTTTTATGCT
1 AACTAGTTGCAATACTCTAGATATCGTGACAATATTTATGGGTTTAAAAGAATTTCTTTTATGCT
1177022 TTCCCTTAATACATGCATCACATACTTTATCGCAATCAAATTTAACCTTAGGTAATTCAATAACA
66 TTCCCTTAATACATGCATCACATACTTTATCGCAATCAAATTTAACCTTAGGTAATTCAATAACA
1177087 AGGTCTTTCCTAGATAACTTTGAAAGTACGCTCATACTTGCGTGTCCTAATTTTGGGTGCCATAG
131 AGGTCTTTCCTAGATAACTTTGAAAGTACGCTCATACTTGCGTGTCCTAATTTTGGGTGCCATAG
*
1177152 CCAAGGTATGTCATTGTTGTCCGTAACAAAACATACGTTTTGGGAACTTAAAATATCTAAATACA
196 CCAAGGTATGTCATTGTTGTCCGTAACAAAACATACGTTTTGGGAACTTAAAACATCTAAATACA
1177217 CAACATAAATGTTCCTTTCTCTATGGCCTAGGAATATTATTTTTTTACTACTAGTATC
261 CAACATAAATGTTCCTTTCTCTATGGCCTAGGAATATTATTTTTTTACTACTAGTATC
1177275 AA
1 AA
1177277 TTACATGACA
Statistics
Matches: 311, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
318 21 0.07
319 290 0.93
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (318 bp):
AACTAGTTGCAATACTCTAGATATCGTGACAATATTTATGGGTTTAAAAGAATTTCTTTTATGCT
TTCCCTTAATACATGCATCACATACTTTATCGCAATCAAATTTAACCTTAGGTAATTCAATAACA
AGGTCTTTCCTAGATAACTTTGAAAGTACGCTCATACTTGCGTGTCCTAATTTTGGGTGCCATAG
CCAAGGTATGTCATTGTTGTCCGTAACAAAACATACGTTTTGGGAACTTAAAACATCTAAATACA
CAACATAAATGTTCCTTTCTCTATGGCCTAGGAATATTATTTTTTTACTACTAGTATC
Found at i:1180378 original size:13 final size:13
Alignment explanation
Indices: 1180360--1180386 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1180350 TAATTTGTGC
1180360 ATGTATCGATACA
1 ATGTATCGATACA
1180373 ATGTATCGATACA
1 ATGTATCGATACA
1180386 A
1 A
1180387 AGCGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1182569 original size:19 final size:21
Alignment explanation
Indices: 1182545--1182601 Score: 82
Period size: 19 Copynumber: 2.8 Consensus size: 21
1182535 TCAAAAACCC
*
1182545 AGAATGCATCGATACAA-TG-
1 AGAATGTATCGATACAATTGA
1182564 AGAATGTATCGATACAATTGTA
1 AGAATGTATCGATACAATTG-A
1182586 AGAATGTATCGATACA
1 AGAATGTATCGATACA
1182602 TTTAATTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
22 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (21 bp):
AGAATGTATCGATACAATTGA
Found at i:1182592 original size:22 final size:21
Alignment explanation
Indices: 1182545--1182626 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 21
1182535 TCAAAAACCC
* *
1182545 AGAATGCATCGATACAATG--
1 AGAATGTATCGATACATTGTA
1182564 AGAATGTATCGATACAATTGTA
1 AGAATGTATCGATAC-ATTGTA
1182586 AGAATGTATCGATACATT-TA
1 AGAATGTATCGATACATTGTA
***
1182606 ATTCTGTATCGATACATTGTA
1 AGAATGTATCGATACATTGTA
1182627 TTAATACAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
19 14 0.26
20 20 0.37
21 5 0.09
22 15 0.28
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (21 bp):
AGAATGTATCGATACATTGTA
Found at i:1183513 original size:13 final size:13
Alignment explanation
Indices: 1183495--1183519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1183485 TATATTATTC
1183495 ATATAATATAATG
1 ATATAATATAATG
1183508 ATATAATATAAT
1 ATATAATATAAT
1183520 ATTCAAATTA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATAATATAATG
Found at i:1183738 original size:50 final size:50
Alignment explanation
Indices: 1183675--1183775 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1183665 ATGCTTAAGA
1183675 TAGTTTTTATATATTAAATAGGTTTTATAACTAAAAATTTAAAATAATGC
1 TAGTTTTTATATATTAAATAGGTTTTATAACTAAAAATTTAAAATAATGC
*
1183725 TAGTTTTTATATATTAAATAGGTTTTATAACTAAAAGTTTAAAATAATGC
1 TAGTTTTTATATATTAAATAGGTTTTATAACTAAAAATTTAAAATAATGC
1183775 T
1 T
1183776 TCTTGTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (50 bp):
TAGTTTTTATATATTAAATAGGTTTTATAACTAAAAATTTAAAATAATGC
Found at i:1183964 original size:23 final size:23
Alignment explanation
Indices: 1183921--1183964 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1183911 TACGATTAGG
*
1183921 CGTTAATGACACGATCGATTACA
1 CGTTAATGACACGATCAATTACA
* *
1183944 CGTTAATGACATGATTAATTA
1 CGTTAATGACACGATCAATTA
1183965 ATCGTGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (23 bp):
CGTTAATGACACGATCAATTACA
Found at i:1187329 original size:23 final size:23
Alignment explanation
Indices: 1187296--1187340 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1187286 ATCTTGTTCA
* *
1187296 AAAATTAATAATTTATTATTTAC
1 AAAATTAATAATTAATAATTTAC
*
1187319 AAAATTTATAATTAATAATTTA
1 AAAATTAATAATTAATAATTTA
1187341 AATATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATTAATAATTAATAATTTAC
Found at i:1187597 original size:71 final size:69
Alignment explanation
Indices: 1187510--1187674 Score: 172
Period size: 71 Copynumber: 2.3 Consensus size: 69
1187500 TTTTAAATAA
* * ** * *
1187510 AAATTTAAAATTCTACAAATAAAGTAAATAATA-CTTTCAAAATTTAAATTCATGTAATCATACC
1 AAATTTAAATTTCTACAAATAAA-TAAATAATACCATAAAAAATATAAATTCATATAATCAT--C
*
1187574 AATAAAC
63 AAAAAAC
*
1187581 AAATTTAAATTTCTACAAATGCAAATAAATTATACCATAAAAAATATAAATTCATATAATCATCA
1 AAATTTAAATTTCTACAAAT--AAATAAATAATACCATAAAAAATATAAATTCATATAATCATCA
*
1187646 AAAAAT
64 AAAAAC
*
1187652 ACATTTAAACTTT-TACAAATAAA
1 AAATTTAAA-TTTCTACAAATAAA
1187675 AATAAATTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
69 3 0.04
71 40 0.50
72 11 0.14
73 26 0.32
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (69 bp):
AAATTTAAATTTCTACAAATAAATAAATAATACCATAAAAAATATAAATTCATATAATCATCAAA
AAAC
Found at i:1187833 original size:84 final size:84
Alignment explanation
Indices: 1187692--1187850 Score: 309
Period size: 84 Copynumber: 1.9 Consensus size: 84
1187682 TATATCATAT
*
1187692 TTAAACTCGTATAAGCATACTCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATATCC
1 TTAAACTCGTATAAGCATACTCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATACCC
1187757 AAAAATTTTTTAAGTATGA
66 AAAAATTTTTTAAGTATGA
1187776 TTAAACTCGTATAAGCATACTCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATACCC
1 TTAAACTCGTATAAGCATACTCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATACCC
1187841 AAAAATTTTT
66 AAAAATTTTT
1187851 AACTCGTATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (84 bp):
TTAAACTCGTATAAGCATACTCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATACCC
AAAAATTTTTTAAGTATGA
Found at i:1187874 original size:72 final size:73
Alignment explanation
Indices: 1187510--1187950 Score: 195
Period size: 73 Copynumber: 6.0 Consensus size: 73
1187500 TTTTAAATAA
* * * * * *
1187510 AAATTTAAAATTCTACAAAT-AAAGTAAATAATACTTTC-AAAATTTAAATTCATGTAATCATAC
1 AAATTTAAAATTTTACAAATAAAAATAAATAATAC-TCCAAAAATTTAAACTCGTATAATCATAC
* *
1187573 -CAATAAAC
65 TCAAAAAAT
** * * * * *
1187581 AAATTT-AAATTTCTACAAATGCAAATAAATTATAC-CATAAAAAATATAAATTCATATAATC--
1 AAATTTAAAATTT-TACAAATAAAAATAAATAATACTC--CAAAAATTTAAACTCGTATAATCAT
1187642 A-TCAAAAAAT
63 ACTCAAAAAAT
* * * * *
1187652 ACATTTAAACTTTTACAAATAAAAATAAATTATA-T-C--ATATTTAAACTCGTATAAGCATACT
1 AAATTTAAAATTTTACAAATAAAAATAAATAATACTCCAAAAATTTAAACTCGTATAATCATACT
1187713 C-AAAAAT
66 CAAAAAAT
* * * * * * *
1187720 ACATTTAAACTTTTACAAATAAAAATAAATTATA-TCCAAAAATTTTTTAA---GTATGATTAAA
1 AAATTTAAAATTTTACAAATAAAAATAAATAATACTCCAAAAA--TTTAAACTCGTATAATCATA
*
1187781 CTCGTATAAGCATACTCAA
64 CTC--A-AA--A-A---AT
* * * * *
1187800 AAATACATTTAAACTTT-TACAA-ATAAAAATAAATTATAC-CCAAAAATTTTTAACTCGTATAA
1 AAAT---TTAAAATTTTACA-AATA-AAA-ATAAATAATACTCCAAAAA-TTTAAACTCGTATAA
*
1187862 TCATACTTAAAAAAT
59 TCATACTCAAAAAAT
** * *
1187877 AAATTTAAAATTTTACAAATAAAAATAAATAATACTTTAAAAATTTAAACTCATATAATCA-AAT
1 AAATTTAAAATTTTACAAATAAAAATAAATAATACTCCAAAAATTTAAACTCGTATAATCATACT
1187941 CAAAAAAT
66 CAAAAAAT
1187949 AA
1 AA
1187951 TAATTAAATA
Statistics
Matches: 284, Mismatches: 47, Indels: 77
0.70 0.12 0.19
Matches are distributed among these distances:
66 15 0.05
68 42 0.15
69 3 0.01
70 15 0.05
71 46 0.16
72 27 0.10
73 50 0.18
74 20 0.07
75 2 0.01
76 1 0.00
77 6 0.02
80 5 0.02
81 1 0.00
82 2 0.01
83 21 0.07
84 18 0.06
86 10 0.04
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (73 bp):
AAATTTAAAATTTTACAAATAAAAATAAATAATACTCCAAAAATTTAAACTCGTATAATCATACT
CAAAAAAT
Found at i:1187894 original size:73 final size:73
Alignment explanation
Indices: 1187776--1187950 Score: 221
Period size: 73 Copynumber: 2.4 Consensus size: 73
1187766 TTAAGTATGA
* * * * *
1187776 TTAAACTCGTATAAGCATAC-TCAAAAATACATTTAAACTTTTACAAATAAAAATAAATTATAC-
1 TTAAACTCGTATAATCATACTTAAAAAATAAATTTAAAATTTTACAAATAAAAATAAATAATACT
1187839 CCAAAAATT
66 CCAAAAA-T
*
1187848 TTTAACTCGTATAATCATACTTAAAAAATAAATTTAAAATTTTACAAATAAAAATAAATAATACT
1 TTAAACTCGTATAATCATACTTAAAAAATAAATTTAAAATTTTACAAATAAAAATAAATAATACT
**
1187913 TTAAAAAT
66 CCAAAAAT
* * *
1187921 TTAAACTCATATAATCA-AATCAAAAAATAA
1 TTAAACTCGTATAATCATACTTAAAAAATAA
1187951 TAATTAAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 29 0.33
73 55 0.62
74 5 0.06
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (73 bp):
TTAAACTCGTATAATCATACTTAAAAAATAAATTTAAAATTTTACAAATAAAAATAAATAATACT
CCAAAAAT
Found at i:1188067 original size:54 final size:52
Alignment explanation
Indices: 1187943--1188067 Score: 137
Period size: 54 Copynumber: 2.3 Consensus size: 52
1187933 AATCAAATCA
** *
1187943 AAAAATA-ATAATTAAATAAATTTATTTTAAAATATAAACAAATTTGAAATT
1 AAAAATATATAATTTTATAAATATATTTTAAAATATAAACAAATTTGAAATT
* * *
1187994 AAAAATATAAATAAATTTATAAATATATTTTACAAATAT-AACTTATATTTGAATTT
1 AAAAATAT--ATAATTTTATAAATATATTTTA-AAATATAAAC--AAATTTGAAATT
1188050 AAAAATATATAATTTTAT
1 AAAAATATATAATTTTAT
1188068 GACACATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
51 7 0.11
54 30 0.49
55 6 0.10
56 18 0.30
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (52 bp):
AAAAATATATAATTTTATAAATATATTTTAAAATATAAACAAATTTGAAATT
Found at i:1188466 original size:11 final size:11
Alignment explanation
Indices: 1188436--1188466 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1188426 TTTTCTTGTC
*
1188436 TTTTTTTTGCT
1 TTTTTTTTTCT
1188447 TTTTTTTTTCT
1 TTTTTTTTTCT
1188458 TTTTTTTTT
1 TTTTTTTTT
1188467 TAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:1188467 original size:12 final size:12
Alignment explanation
Indices: 1188426--1188467 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
1188416 CGACAACATC
1188426 TTTTCTTGTCTTTT
1 TTTTCTT-T-TTTT
1188440 TTTTGC-TTTTTT
1 TTTT-CTTTTTTT
1188452 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1188464 TTTT
1 TTTT
1188468 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 18 0.69
13 1 0.04
14 5 0.19
15 1 0.04
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1188484 original size:2 final size:2
Alignment explanation
Indices: 1188479--1188506 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1188469 AATTTTAATA
1188479 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
1188507 TTCTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1188716 original size:10 final size:10
Alignment explanation
Indices: 1188701--1188730 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1188691 TTAAATAATT
1188701 AATTAATAAA
1 AATTAATAAA
1188711 AATTAATAAA
1 AATTAATAAA
1188721 AATATAATAA
1 AAT-TAATAA
1188731 TAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTAATAAA
Found at i:1188728 original size:11 final size:11
Alignment explanation
Indices: 1188704--1188736 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1188694 AATAATTAAT
1188704 TAATAAAAAT-
1 TAATAAAAATA
1188714 TAATAAAAATA
1 TAATAAAAATA
*
1188725 TAATAATAATA
1 TAATAAAAATA
1188736 T
1 T
1188737 TTTTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAAATA
Found at i:1188933 original size:11 final size:10
Alignment explanation
Indices: 1188918--1188966 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
1188908 ATATAATTTT
1188918 ATAATATAAA
1 ATAATATAAA
1188928 TATAAT-TAAA
1 -ATAATATAAA
1188938 A-AATAATAAA
1 ATAAT-ATAAA
1188948 ATAATATAAA
1 ATAATATAAA
1188958 A-AATATAAA
1 ATAATATAAA
1188967 CAATACAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.09
9 9 0.26
10 15 0.43
11 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATATAAA
Found at i:1188950 original size:8 final size:9
Alignment explanation
Indices: 1188926--1188983 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
1188916 TTATAATATA
*
1188926 AATATAATT
1 AATATAAAT
1188935 AA-A-AAAT
1 AATATAAAT
1188942 AATA-AAAT
1 AATATAAAT
*
1188950 AATATAAAA
1 AATATAAAT
*
1188959 AATATAAAC
1 AATATAAAT
*
1188968 AATACAAAT
1 AATATAAAT
1188977 -ATATAAA
1 AATATAAA
1188984 AATTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
7 5 0.12
8 16 0.39
9 20 0.49
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AATATAAAT
Found at i:1188957 original size:20 final size:19
Alignment explanation
Indices: 1188920--1188966 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
1188910 ATAATTTTAT
1188920 AATATAAATATAATTAAAA
1 AATATAAATATAATTAAAA
1188939 AATAATAAA-ATAATATAAAA
1 AAT-ATAAATATAAT-TAAAA
1188959 AATATAAA
1 AATATAAA
1188967 CAATACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATAAATATAATTAAAA
Done.