Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 13 of 21
Found at i:1409813 original size:37 final size:38
Alignment explanation
Indices: 1409766--1409839 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1409756 TTTAAAAAAT
*
1409766 ATAATTTAATA-ATTTTTATTTATTAT-TTAAAATATAA
1 ATAATTTAATATATTTTTATAT-TTATATTAAAATATAA
*
1409803 ATAATTTAATATATTTTTATATTTATATTATAATATA
1 ATAATTTAATATATTTTTATATTTATATTAAAATATA
1409840 TATTTAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (38 bp):
ATAATTTAATATATTTTTATATTTATATTAAAATATAA
Found at i:1409917 original size:25 final size:27
Alignment explanation
Indices: 1409889--1409940 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
1409879 TATTATATAA
1409889 TTAAAAAATAAAA-T-AAATTTTAATT
1 TTAAAAAATAAAATTAAAATTTTAATT
*
1409914 TTAAAAATTAAAATTAAAATTTTAATT
1 TTAAAAAATAAAATTAAAATTTTAATT
1409941 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
26 1 0.04
27 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TTAAAAAATAAAATTAAAATTTTAATT
Found at i:1414698 original size:25 final size:24
Alignment explanation
Indices: 1414652--1414699 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1414642 AAAATTTAAC
*
1414652 ATTTTAATAATTCATATTATATTA
1 ATTTTAATAATTCATATCATATTA
* *
1414676 ATTTTATTATATTTATATCATATT
1 ATTTTAATA-ATTCATATCATATT
1414700 TTTATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTAATAATTCATATCATATTA
Found at i:1415567 original size:19 final size:18
Alignment explanation
Indices: 1415543--1415591 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1415533 TTTTATATAG
*
1415543 TATTAAAATATTATTTTTA
1 TATTAAAAT-TTATATTTA
*
1415562 TATTAATATTTATATTTA
1 TATTAAAATTTATATTTA
1415580 TAATT-AAATTTA
1 T-ATTAAAATTTA
1415592 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTAAAATTTATATTTA
Found at i:1416144 original size:65 final size:67
Alignment explanation
Indices: 1416057--1416203 Score: 244
Period size: 65 Copynumber: 2.2 Consensus size: 67
1416047 ATATAAATAT
* *
1416057 ATATATATATATATATATACCAGTCCCTTCACATTCTTTCATAATTGAAT-TTTTTC-TTTTTTT
1 ATATATATATATATACACACCAGTCCCTTCACATTCTTTCATAATTGAATATTTTTCTTTTTTTT
1416120 AA
66 AA
* *
1416122 ATATATATATATATGCACACCAGTTCCTTCACATTCTTTCATAATTGAATATTTTTCTTTTTTTT
1 ATATATATATATATACACACCAGTCCCTTCACATTCTTTCATAATTGAATATTTTTCTTTTTTTT
1416187 AA
66 AA
1416189 ATATATATATATATA
1 ATATATATATATATA
1416204 TATATATATA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
65 46 0.61
66 6 0.08
67 23 0.31
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (67 bp):
ATATATATATATATACACACCAGTCCCTTCACATTCTTTCATAATTGAATATTTTTCTTTTTTTT
AA
Found at i:1416194 original size:2 final size:2
Alignment explanation
Indices: 1416189--1416214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1416179 TTTTTTTTAA
1416189 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
1416215 GACAGAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1416316 original size:16 final size:17
Alignment explanation
Indices: 1416297--1416334 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1416287 TTAAATTAAT
1416297 TTAAAAT-TTTATTTTA
1 TTAAAATATTTATTTTA
*
1416313 TTAAAATATTTTTTTTA
1 TTAAAATATTTATTTTA
1416330 TTAAA
1 TTAAA
1416335 TAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAAAATATTTATTTTA
Found at i:1416459 original size:12 final size:12
Alignment explanation
Indices: 1416442--1416492 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1416432 TAAAATTATT
1416442 TATATTTAAATA
1 TATATTTAAATA
1416454 TATATTTAAATA
1 TATATTTAAATA
* *
1416466 TTAAATATAAA-A
1 -TATATTTAAATA
*
1416478 T-TTTTTAAATA
1 TATATTTAAATA
1416489 TATA
1 TATA
1416493 AAAATATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
10 5 0.17
11 3 0.10
12 14 0.47
13 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:1416471 original size:19 final size:18
Alignment explanation
Indices: 1416430--1416474 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1416420 ATTTAATTTT
*
1416430 TTTAAA-AT-TATTTATA
1 TTTAAATATATATTTAAA
1416446 TTTAAATATATATTTAAA
1 TTTAAATATATATTTAAA
1416464 TATTAAATATA
1 T-TTAAATATA
1416475 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 2 0.08
18 8 0.32
19 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATATATATTTAAA
Found at i:1416493 original size:18 final size:19
Alignment explanation
Indices: 1416470--1416519 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1416460 TAAATATTAA
*
1416470 ATAT-AAAATTTTTTAAAT
1 ATATAAAAATATTTTAAAT
1416488 ATATAAAAATATTTTAAA-
1 ATATAAAAATATTTTAAAT
*
1416506 AAATAAAAATATTT
1 ATATAAAAATATTT
1416520 ATATTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAAAAATATTTTAAAT
Found at i:1416906 original size:31 final size:31
Alignment explanation
Indices: 1416869--1416935 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1416859 TCAAGTCGAT
* *
1416869 TTAAAATTTTATTTT-ATTATT-TATTATATTA
1 TTAAAATATTATTTTGA-TATTATATT-TATGA
1416900 TTAAAATATTATTTTGATATTATATTTATGA
1 TTAAAATATTATTTTGATATTATATTTATGA
1416931 TTAAA
1 TTAAA
1416936 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
TTAAAATATTATTTTGATATTATATTTATGA
Found at i:1416951 original size:25 final size:23
Alignment explanation
Indices: 1416923--1416993 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
1416913 TTGATATTAT
*
1416923 ATTTATGATTAAATTTAAATAATAA
1 ATTTATAATTAAA-TTAAATAAT-A
**
1416948 ATTTATTTTTATAATTAAATAATA
1 ATTTATAATTA-AATTAAATAATA
1416972 ATTTA-AATTAAATTAAACTAAT
1 ATTTATAATTAAATTAAA-TAAT
1416994 CTAAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 7 0.17
23 7 0.17
24 6 0.15
25 18 0.45
26 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTATAATTAAATTAAATAATA
Found at i:1417013 original size:12 final size:13
Alignment explanation
Indices: 1416996--1417042 Score: 59
Period size: 12 Copynumber: 4.0 Consensus size: 13
1416986 AAACTAATCT
1416996 AAATTTT-TTAAA
1 AAATTTTATTAAA
1417008 AAATTTTATT---
1 AAATTTTATTAAA
1417018 AAATTTT-TTAAA
1 AAATTTTATTAAA
1417030 AAATTTTATTAAA
1 AAATTTTATTAAA
1417043 TTTTTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.07
10 7 0.23
12 14 0.47
13 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAATTTTATTAAA
Found at i:1417021 original size:22 final size:22
Alignment explanation
Indices: 1416995--1417047 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1416985 TAAACTAATC
1416995 TAAATTTTTTAAAAAATTTTAT
1 TAAATTTTTTAAAAAATTTTAT
1417017 TAAATTTTTTAAAAAATTTTAT
1 TAAATTTTTTAAAAAATTTTAT
1417039 TAAATTTTT
1 TAAATTTTT
1417048 ATTCAAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAAATTTTTTAAAAAATTTTAT
Found at i:1419028 original size:3 final size:3
Alignment explanation
Indices: 1419020--1419045 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1419010 AATATAACAA
1419020 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1419046 CTACTATGAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1419441 original size:17 final size:17
Alignment explanation
Indices: 1419392--1419442 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
1419382 ATTATAAAAA
*
1419392 AATAATTAAAATATAAAT
1 AATAA-TAAAATATTAAT
1419410 -ATGATATAAATATATTAAT
1 AAT-A-ATAAA-ATATTAAT
1419429 AATAATAAAATATT
1 AATAATAAAATATT
1419443 TATATGACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 7 0.25
18 10 0.36
19 9 0.32
20 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAATAAAATATTAAT
Found at i:1426392 original size:17 final size:17
Alignment explanation
Indices: 1426352--1426393 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1426342 ATTTATAAAA
1426352 ATTTAAATTAAAATAATT
1 ATTT-AATTAAAATAATT
*
1426370 AATTAATTAAAA-ATATT
1 ATTTAATTAAAATA-ATT
1426387 ATTTAAT
1 ATTTAAT
1426394 AATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.81
18 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAATTAAAATAATT
Found at i:1426420 original size:29 final size:27
Alignment explanation
Indices: 1426380--1426434 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
1426370 AATTAATTAA
*
1426380 AAATATTATTTAATAATAAATAAAATATT
1 AAATATAATTTAA-AAT-AATAAAATATT
*
1426409 AAATATAATTTAAAATTATAAAATAT
1 AAATATAATTTAAAATAATAAAATAT
1426435 ATCCATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATATAATTTAAAATAATAAAATATT
Found at i:1426547 original size:30 final size:33
Alignment explanation
Indices: 1426513--1426583 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 33
1426503 ACGTTAATAA
*
1426513 TTATTTAATAATAA-TA-A-TATAAATATTTA-T
1 TTATTTAATAA-AATTATATTACAAATATTTATT
1426543 TTATTTAATAAAATTATATTACAAATATTTATT
1 TTATTTAATAAAATTATATTACAAATATTTATT
1426576 TTATTTAA
1 TTATTTAA
1426584 ATTATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 2 0.06
30 13 0.36
31 1 0.03
32 11 0.31
33 9 0.25
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TTATTTAATAAAATTATATTACAAATATTTATT
Found at i:1429529 original size:20 final size:20
Alignment explanation
Indices: 1429506--1429555 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1429496 ATTTAATATT
*
1429506 TATTTATTATTAAAATTATA
1 TATTTAATATTAAAATTATA
* * *
1429526 TATTTAATATTTATATTTTA
1 TATTTAATATTAAAATTATA
1429546 TATTTTAATA
1 TA-TTTAATA
1429556 CAATTGATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAATATTAAAATTATA
Found at i:1431012 original size:17 final size:19
Alignment explanation
Indices: 1430986--1431023 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1430976 TTATGGTTTT
1430986 TTAATCAAA-TT-ATCTTA
1 TTAATCAAATTTCATCTTA
*
1431003 TTAATTAAATTTCATCTTA
1 TTAATCAAATTTCATCTTA
1431022 TT
1 TT
1431024 TTTATTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATCAAATTTCATCTTA
Found at i:1431745 original size:3 final size:3
Alignment explanation
Indices: 1431733--1431766 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1431723 GACGACGACG
*
1431733 ACA ACG ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1431767 GCCAACCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1432496 original size:18 final size:19
Alignment explanation
Indices: 1432473--1432519 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1432463 TAATAATGTC
1432473 AATTTATAAATTAAAT-CA
1 AATTTATAAATTAAATACA
* *
1432491 AATTTA-AATTTAAATATA
1 AATTTATAAATTAAATACA
1432509 AATTT-TAAATT
1 AATTTATAAATT
1432520 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTATAAATTAAATACA
Found at i:1432517 original size:19 final size:18
Alignment explanation
Indices: 1432473--1432520 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1432463 TAATAATGTC
1432473 AATTTATAAA-TTAAATCA
1 AATTT-TAAATTTAAATCA
*
1432491 AA-TTTAAATTTAAATATA
1 AATTTTAAATTTAAAT-CA
1432509 AATTTTAAATTT
1 AATTTTAAATTT
1432521 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 8 0.31
18 5 0.19
19 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTAAATTTAAATCA
Found at i:1432812 original size:14 final size:14
Alignment explanation
Indices: 1432795--1432834 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1432785 TAATTTCGAT
1432795 TATTTATATAAAT-A
1 TATTTA-ATAAATAA
*
1432809 TATTTAAAAAATAA
1 TATTTAATAAATAA
1432823 TATTTAATAAAT
1 TATTTAATAAAT
1432835 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATTTAATAAATAA
Found at i:1433147 original size:13 final size:14
Alignment explanation
Indices: 1433119--1433156 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1433109 ATATTTTATT
1433119 AATTTAAATAAAAA
1 AATTTAAATAAAAA
*
1433133 AATTTAATTAAAAA
1 AATTTAAATAAAAA
*
1433147 ATTTTAAATA
1 AATTTAAATA
1433157 TGATAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTAAATAAAAA
Found at i:1434228 original size:5 final size:5
Alignment explanation
Indices: 1434207--1434275 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
1434197 AAAAATATAT
* * *
1434207 TTTAA TTTTAA TATAA TTTAA TTTAA ATTAA TTTGA TTATAAA TATT-A
1 TTTAA -TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT-T-AA T-TTAA
*
1434255 TTTAA TTATAA TTTTA TTTAA
1 TTTAA TT-TAA TTTAA TTTAA
1434276 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 33 0.66
6 11 0.22
7 3 0.06
8 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (5 bp):
TTTAA
Found at i:1434275 original size:16 final size:16
Alignment explanation
Indices: 1434200--1434266 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
1434190 AAGTTTAAAA
* *
1434200 AATATATTTTAATTTT
1 AATATAATTTAATTAT
1434216 AATATAATTTAATT-T
1 AATATAATTTAATTAT
*
1434231 AA-ATTAATTTGATTAT
1 AATA-TAATTTAATTAT
*
1434247 AAATATTATTTAATTAT
1 -AATATAATTTAATTAT
1434264 AAT
1 AAT
1434267 TTTATTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.28
16 17 0.40
17 12 0.28
18 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
AATATAATTTAATTAT
Found at i:1443178 original size:30 final size:29
Alignment explanation
Indices: 1443142--1443217 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
1443132 ATTAAATTGA
*
1443142 TTAAATTGATTAAAAATTAGTGAAGAT-TAT
1 TTAAATTGATAAAAAATTAGTGAA-ATAT-T
* *
1443172 TTAAATTGATAAAAAAATTATTTAAATATT
1 TTAAATTGAT-AAAAAATTAGTGAAATATT
1443202 TTAAATTGATAAAAAA
1 TTAAATTGATAAAAAA
1443218 AAAGTAATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.15
30 23 0.56
31 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (29 bp):
TTAAATTGATAAAAAATTAGTGAAATATT
Found at i:1443398 original size:36 final size:33
Alignment explanation
Indices: 1443326--1443400 Score: 80
Period size: 36 Copynumber: 2.2 Consensus size: 33
1443316 TTTATAAATT
*
1443326 TTTAATTTATATTTTATATTAACATTAATATTA
1 TTTAATTTATATTTTATATTAACATTAATATAA
* *
1443359 TTTAATTATATATATTTTTATTAAATATTTAATA-AA
1 TTTAATT-TATAT-TTTATATT-AACA-TTAATATAA
1443395 TTTAAT
1 TTTAAT
1443401 AAAATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 7 0.20
34 5 0.14
35 7 0.20
36 10 0.29
37 6 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTAATTTATATTTTATATTAACATTAATATAA
Found at i:1448112 original size:11 final size:11
Alignment explanation
Indices: 1448096--1448190 Score: 56
Period size: 11 Copynumber: 8.6 Consensus size: 11
1448086 AAAAAAAATT
1448096 TAAATATAATA
1 TAAATATAATA
*
1448107 TAAATACAATA
1 TAAATATAATA
* *
1448118 TAAAAAAAAT-
1 TAAATATAATA
*
1448128 TAAAATATGATA
1 T-AAATATAATA
1448140 TGAAAATATAA-A
1 T--AAATATAATA
1448152 -AAA-ATAATA
1 TAAATATAATA
* *
1448161 CAATTATAA-A
1 TAAATATAATA
1448171 TATAATATGAATA
1 TA-AATAT-AATA
1448184 TAAATAT
1 TAAATAT
1448191 CATAAAATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 4 0.06
9 4 0.06
10 5 0.08
11 32 0.49
12 9 0.14
13 11 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1448123 original size:33 final size:30
Alignment explanation
Indices: 1448086--1448155 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
1448076 TCATATATTA
*
1448086 AAAAAAAATTTAAATATAATATAAATACAATAT
1 AAAAAAAATTAAAATATAATAT-AA-A-AATAT
* *
1448119 AAAAAAAATTAAAATATGATATGAAAATAT
1 AAAAAAAATTAAAATATAATATAAAAATAT
1448149 AAAAAAA
1 AAAAAAA
1448156 TAATACAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 12 0.35
31 1 0.03
32 1 0.03
33 20 0.59
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (30 bp):
AAAAAAAATTAAAATATAATATAAAAATAT
Found at i:1448177 original size:17 final size:17
Alignment explanation
Indices: 1448090--1448205 Score: 62
Period size: 17 Copynumber: 6.6 Consensus size: 17
1448080 ATATTAAAAA
1448090 AAAATT-TAAATATAAT
1 AAAATTATAAATATAAT
* *
1448106 ATAAA-TA-CAATATAAAA
1 A-AAATTATAAATAT-AAT
1448123 AAAATTA-AAATATGATAT
1 AAAATTATAAATAT-A-AT
* *
1448141 GAAAATATAAAAAAATAAT
1 -AAAAT-TATAAATATAAT
*
1448160 ACAATTATAAATATAAT
1 AAAATTATAAATATAAT
* *
1448177 ATGAA-TATAAATATCAT
1 A-AAATTATAAATATAAT
1448194 AAAATTTATAAA
1 AAAA-TTATAAA
1448206 AAATATAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
16 12 0.16
17 37 0.48
18 13 0.17
19 7 0.09
20 3 0.04
21 5 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAATTATAAATATAAT
Found at i:1454087 original size:18 final size:20
Alignment explanation
Indices: 1454066--1454113 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
1454056 AATATTTTAT
1454066 AATTAAAT-TTAAATAA-AA
1 AATTAAATATTAAATAATAA
*
1454084 AATT-ATTATTAAATAATAA
1 AATTAAATATTAAATAATAA
*
1454103 AATAAAATATT
1 AATTAAATATT
1454114 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 5 0.21
20 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAATATTAAATAATAA
Found at i:1454094 original size:24 final size:23
Alignment explanation
Indices: 1454047--1454122 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
1454037 CTTAAATTAA
* ** *
1454047 AAATTTAAAAATATTTTATAATT
1 AAATTTAAAAAAAAATTATTATT
1454070 AAATTTAAATAAAAAATTATTATT
1 AAATTTAAA-AAAAAATTATTATT
* * *
1454094 AAATAATAAAATAAAA-TATTTTT
1 AAAT-TTAAAAAAAAATTATTATT
1454117 AAATTT
1 AAATTT
1454123 TTAATTAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 19 0.44
24 19 0.44
25 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTTAAAAAAAAATTATTATT
Found at i:1454236 original size:20 final size:19
Alignment explanation
Indices: 1454207--1454257 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
1454197 TATATAAAGG
1454207 TTTGAAAAAAAGATAATAT
1 TTTGAAAAAAAGATAATAT
1454226 TTTGAAAAAAAGATAATAT
1 TTTGAAAAAAAGATAATAT
*
1454245 TTTTACAAAAAAG
1 TTTGA-AAAAAAG
1454258 TCCATACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (19 bp):
TTTGAAAAAAAGATAATAT
Found at i:1454370 original size:20 final size:20
Alignment explanation
Indices: 1454319--1454378 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
1454309 AATTAATTTG
*
1454319 ATAAATAAAATTATTAATTATT
1 ATAAATAAAA-TATT-ATAATT
1454341 ATATTTAATAAAATATTATAATT
1 ATA---AATAAAATATTATAATT
*
1454364 ATAAATAATATATTA
1 ATAAATAAAATATTA
1454379 ATTAATCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 11 0.33
22 3 0.09
23 8 0.24
24 4 0.12
25 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAATAAAATATTATAATT
Found at i:1458952 original size:2 final size:2
Alignment explanation
Indices: 1458919--1458943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1458909 TCTAATAATC
1458919 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1458944 ACTTATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1459139 original size:25 final size:25
Alignment explanation
Indices: 1459090--1459148 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1459080 CATACTATAA
*
1459090 TTGTAAAAAAAAAAAATCATGATTT
1 TTGTAAAAAAAAAAAATCATAATTT
*
1459115 TTGTCAAAAAAAATAAAT-ATAATTT
1 TTGT-AAAAAAAAAAAATCATAATTT
*
1459140 GTG-AAAAAA
1 TTGTAAAAAA
1459149 GATTTAGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.20
25 12 0.40
26 12 0.40
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (25 bp):
TTGTAAAAAAAAAAAATCATAATTT
Found at i:1459223 original size:2 final size:2
Alignment explanation
Indices: 1459216--1459262 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1459206 TTCATAGCTT
*
1459216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1459256 TA TA TA T
1 TA TA TA T
1459263 GGAGTTTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1459599 original size:21 final size:21
Alignment explanation
Indices: 1459570--1459609 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1459560 AATTTTGATC
*
1459570 TGTTTAAA-TTATTATTTTAAG
1 TGTTAAAATTTATT-TTTTAAG
1459591 TGTTAAAATTTATTTTTTA
1 TGTTAAAATTTATTTTTTA
1459610 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TGTTAAAATTTATTTTTTAAG
Found at i:1460461 original size:14 final size:14
Alignment explanation
Indices: 1460444--1460476 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1460434 TATTTTATTT
1460444 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
1460458 AAATATTAATATAA
1 AAATATTAATATAA
1460472 AAATA
1 AAATA
1460477 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:1460688 original size:3 final size:3
Alignment explanation
Indices: 1460680--1460721 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1460670 AATGAAAATA
1460680 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1460722 GTGCATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1461226 original size:2 final size:2
Alignment explanation
Indices: 1461219--1461246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1461209 TCTACTTTGA
1461219 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
1461247 GTAGTTGATC
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:1465553 original size:2 final size:2
Alignment explanation
Indices: 1465546--1465579 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1465536 TCATTCTAGT
1465546 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1465580 ACACACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1468292 original size:25 final size:27
Alignment explanation
Indices: 1468245--1468303 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
1468235 TATTTATTAA
1468245 ATTTTAAAATATAAATAATTAATATAT
1 ATTTTAAAATATAAATAATTAATATAT
* * *
1468272 ATTTTAATAT-TAAATTA-TAATTTAT
1 ATTTTAAAATATAAATAATTAATATAT
1468297 ATATTTA
1 AT-TTTA
1468304 TTTTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.32
26 10 0.36
27 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTAAAATATAAATAATTAATATAT
Found at i:1468474 original size:107 final size:109
Alignment explanation
Indices: 1468300--1468574 Score: 346
Period size: 113 Copynumber: 2.5 Consensus size: 109
1468290 AATTTATATA
* * * * *
1468300 TTTATT-TTTATATAATATTTATACTTATTATTTTAATATTTT-TTATTGAATTTAATATTATGA
1 TTTATTATTTAAAAAATATTTATA-ATA-TATTTT-ATATTTTATTATTAAATTTAATATCATGA
*
1468363 TTCAAATTTTTTAAA-A-ATAAAGATTTGAAA-TGATTTAAAAATTTAT
63 TTCAAATTTTTTAAATATATAAA-ATTT-AAATTGATTAAAAAATTTAT
1468409 TTTATTA-TTAAAAAATATTTATAATATATTTTATATTTTATTATTAAATTTAATATCATGATTC
1 TTTATTATTTAAAAAATATTTATAATATATTTTATATTTTATTATTAAATTTAATATCATGATTC
*
1468473 AAATTTTTTAAATTTTTATTTAAAATTTAAATTGATTAAAAAATTTAT
66 AAATTTTTTAAA----TATATAAAATTTAAATTGATTAAAAAATTTAT
* *
1468521 TTTATTATTTAAAAAATATTTATAATATATTTTATATTTTATAATTAAAATTAA
1 TTTATTATTTAAAAAATATTTATAATATATTTTATATTTTATTATTAAATTTAA
1468575 ATAAAAATAT
Statistics
Matches: 147, Mismatches: 9, Indels: 16
0.85 0.05 0.09
Matches are distributed among these distances:
106 7 0.05
107 40 0.27
108 2 0.01
109 20 0.14
111 3 0.02
112 27 0.18
113 48 0.33
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (109 bp):
TTTATTATTTAAAAAATATTTATAATATATTTTATATTTTATTATTAAATTTAATATCATGATTC
AAATTTTTTAAATATATAAAATTTAAATTGATTAAAAAATTTAT
Found at i:1468618 original size:113 final size:112
Alignment explanation
Indices: 1468380--1468603 Score: 278
Period size: 113 Copynumber: 2.0 Consensus size: 112
1468370 TTTTTAAAAA
*
1468380 TAAAGATTTGAAA-TGATTTAAAAATTTATTTTATTATTAAAAAATATTTATAATATATTTTATA
1 TAAA-ATTT-AAATTGATTAAAAAATTTATTTTATTATTAAAAAATATTTATAATATATTTTATA
* * ** * ***
1468444 TTTTATTATTAAATTTAATATCATGATTCAAATTTTTTAAATTTTTATT
64 TTTTATAATTAAAATTAATATCAAAAATCAAATTTTTTAAATAAATATT
1468493 TAAAATTTAAATTGATTAAAAAATTTATTTTATTATTTAAAAAATATTTATAATATATTTTATAT
1 TAAAATTTAAATTGATTAAAAAATTTATTTTATTA-TTAAAAAATATTTATAATATATTTTATAT
*
1468558 TTTATAATTAAAATTAA-AT-AAAAAT-ATATTTTAATT-AATAAATATT
65 TTTATAATTAAAATTAATATCAAAAATCAAATTTT--TTAAATAAATATT
1468604 AATATATATT
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
110 6 0.06
111 13 0.13
112 30 0.31
113 48 0.49
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (112 bp):
TAAAATTTAAATTGATTAAAAAATTTATTTTATTATTAAAAAATATTTATAATATATTTTATATT
TTATAATTAAAATTAATATCAAAAATCAAATTTTTTAAATAAATATT
Found at i:1474134 original size:19 final size:19
Alignment explanation
Indices: 1474097--1474133 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1474087 TGCTTTTTAA
*
1474097 ATAAATTTTATTTTATTTT
1 ATAAATTTTATTATATTTT
1474116 ATAAATTTTATTA-ATTTT
1 ATAAATTTTATTATATTTT
1474134 TTATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATAAATTTTATTATATTTT
Found at i:1474203 original size:17 final size:17
Alignment explanation
Indices: 1474175--1474220 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1474165 TTAAATTTAA
**
1474175 ATAAAT-AATTTAATTT
1 ATAAATAAATTTAATAC
1474191 ATAAATAAATTTAATAC
1 ATAAATAAATTTAATAC
*
1474208 GTAAATAAATTTA
1 ATAAATAAATTTA
1474221 TCGATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
ATAAATAAATTTAATAC
Found at i:1475085 original size:13 final size:13
Alignment explanation
Indices: 1475067--1475091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1475057 AAAATTTATG
1475067 ATTTTATTAAAAT
1 ATTTTATTAAAAT
1475080 ATTTTATTAAAA
1 ATTTTATTAAAA
1475092 ATGATGTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATTAAAAT
Found at i:1475445 original size:21 final size:20
Alignment explanation
Indices: 1475411--1475450 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1475401 CGTAAATAAT
*
1475411 TTTATTATTTTTTAATTATG
1 TTTATAATTTTTTAATTATG
*
1475431 TTTATAATATTTTTAGTTAT
1 TTTATAAT-TTTTTAATTAT
1475451 CATATGTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTATAATTTTTTAATTATG
Found at i:1481846 original size:42 final size:40
Alignment explanation
Indices: 1481774--1481853 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 40
1481764 CTTCGAAAAC
*
1481774 TTATATTATTATTTAAAATAATATTTAATAATTAAAAATATT
1 TTATATTAATATTTAAAATAATATTTAATAA--AAAAATATT
* *
1481816 TTATGTTAATATTTATAATAA-ATTTAAATAAAAAAATA
1 TTATATTAATATTTAAAATAATATTT-AATAAAAAAATA
1481854 ACTCGAGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 7 0.21
41 4 0.12
42 23 0.68
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (40 bp):
TTATATTAATATTTAAAATAATATTTAATAAAAAAATATT
Found at i:1486761 original size:25 final size:25
Alignment explanation
Indices: 1486732--1486782 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1486722 CTTAAAGCAT
*
1486732 TTTTAAAAAATTTAGTTTTCTAAAG
1 TTTTAAAAAATTTAGTTTACTAAAG
*
1486757 TTTTATAAAATTTAGTTTACTAAAG
1 TTTTAAAAAATTTAGTTTACTAAAG
1486782 T
1 T
1486783 CTCACAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (25 bp):
TTTTAAAAAATTTAGTTTACTAAAG
Found at i:1488682 original size:19 final size:21
Alignment explanation
Indices: 1488638--1488684 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
1488628 AATGTTAAAA
1488638 ATAAATTTTATATATTAAATT
1 ATAAATTTTATATATTAAATT
1488659 ATAAATTTT-T-TATTAAATGT
1 ATAAATTTTATATATTAAAT-T
1488679 -TAAATT
1 ATAAATT
1488685 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.56
20 2 0.08
21 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATAAATTTTATATATTAAATT
Found at i:1489145 original size:17 final size:19
Alignment explanation
Indices: 1489112--1489163 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 19
1489102 AATTTTATAT
1489112 ATATTAAAAATTATATTATTA
1 ATATT-AAAA-TATATTATTA
1489133 A-ATT-AAATATA-T-TTA
1 ATATTAAAATATATTATTA
1489148 ATATTAAAATATATTA
1 ATATTAAAATATATTA
1489164 AAAAAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 11 0.41
18 4 0.15
20 3 0.11
21 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTAAAATATATTATTA
Found at i:1489302 original size:29 final size:30
Alignment explanation
Indices: 1489270--1489338 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1489260 GATTAAATTT
1489270 AAATTTTATATTATTAT-TTAAAATTAATA
1 AAATTTTATATTATTATATTAAAATTAATA
* * * *
1489299 AAATTTTTTATTTTTATATTAATATTTATA
1 AAATTTTATATTATTATATTAAAATTAATA
* *
1489329 TATTTTTATA
1 AAATTTTATA
1489339 ATTAAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AAATTTTATATTATTATATTAAAATTAATA
Found at i:1489335 original size:22 final size:22
Alignment explanation
Indices: 1489294--1489348 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1489284 TATTTAAAAT
* *
1489294 TAATAAAATTT-TTTATTTTTA
1 TAATTAAATTTATATATTTTTA
1489315 T-ATTAATATTTATATATTTTTA
1 TAATTAA-ATTTATATATTTTTA
1489337 TAATTAAATTTA
1 TAATTAAATTTA
1489349 AATAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 15 0.52
23 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATTAAATTTATATATTTTTA
Found at i:1489942 original size:37 final size:37
Alignment explanation
Indices: 1489890--1489962 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
1489880 TAGATGGCTC
*
1489890 GTTCTAGGCTGTGTCTTTTCGATTCTTCATTTTGCTT
1 GTTCTAGGCTATGTCTTTTCGATTCTTCATTTTGCTT
1489927 GTTCTAGGCTATGTCTTTTCGATTCTTCATTTTGCT
1 GTTCTAGGCTATGTCTTTTCGATTCTTCATTTTGCT
1489963 AATTCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.10, C:0.19, G:0.18, T:0.53
Consensus pattern (37 bp):
GTTCTAGGCTATGTCTTTTCGATTCTTCATTTTGCTT
Found at i:1491261 original size:16 final size:16
Alignment explanation
Indices: 1491240--1491270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1491230 AGTGACAAAA
1491240 TTTAATAAAAAAATTG
1 TTTAATAAAAAAATTG
*
1491256 TTTAATAATAAAATT
1 TTTAATAAAAAAATT
1491271 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTAATAAAAAAATTG
Found at i:1491883 original size:14 final size:13
Alignment explanation
Indices: 1491856--1491903 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
1491846 TTCAAATTTA
1491856 ATAATTTATTTTT
1 ATAATTTATTTTT
1491869 ATAATTTATTATTT
1 ATAATTTATT-TTT
*
1491883 ATTATTTTATTTTT
1 A-TAATTTATTTTT
*
1491897 AAAATTT
1 ATAATTT
1491904 TGAAGCACCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 14 0.47
14 8 0.27
15 8 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATAATTTATTTTT
Found at i:1491904 original size:14 final size:14
Alignment explanation
Indices: 1491856--1491904 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1491846 TTCAAATTTA
1491856 ATAA-TTTATTTTT
1 ATAATTTTATTTTT
1491869 ATAA-TTTATTATTT
1 ATAATTTTATT-TTT
*
1491883 ATTATTTTATTTTT
1 ATAATTTTATTTTT
*
1491897 AAAATTTT
1 ATAATTTT
1491905 GAAGCACCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.32
14 15 0.48
15 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATAATTTTATTTTT
Found at i:1492238 original size:4 final size:4
Alignment explanation
Indices: 1492229--1492254 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1492219 CGCCAAAAAC
1492229 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1492255 CTACGAAAAA
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):
AATA
Found at i:1492291 original size:12 final size:12
Alignment explanation
Indices: 1492271--1492306 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1492261 AAAAAAGAGA
1492271 TCGCTCTCTCTC
1 TCGCTCTCTCTC
**
1492283 TTTCTCTCTCTC
1 TCGCTCTCTCTC
1492295 TCGCTCTCTCTC
1 TCGCTCTCTCTC
1492307 ACTTTGTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (12 bp):
TCGCTCTCTCTC
Found at i:1498665 original size:176 final size:176
Alignment explanation
Indices: 1498337--1498667 Score: 389
Period size: 177 Copynumber: 1.9 Consensus size: 176
1498327 AATATTACAA
* * * *
1498337 ATATTGATATTTTAATTTTGAATTAACTAAATGTCACATTTTAAAAATATCTCTATAAAACAATT
1 ATATTGAGATTTTAATTTTGAATTAACTAAATATCACATTTTAAAAATAACACTATAAAACAATT
* * * *
1498402 AAGCTAAATCTCGAGTTTAATATAAAATATTAATTAAGGAACATAAAACATAGGTCTCATAAAAA
66 AAGCTAAATCTCGAATTTAATATAAAATATAAATTAAAGAACATAAAACATAGATCTCATAAAAA
*
1498467 TTTAAGCTGTTAAATCTAAGATTTAGTCTGGTTAATTCACTTGTAG
131 TTTAAACTGTTAAATCTAAGATTTAGTCTGGTTAATTCACTTGTAG
* * * * **
1498513 ATATTGAGATTTTAATTTTGAACCTT-ATTAAATATTACTTTTTAAAAATAACAGTATAAATTAA
1 ATATTGAGATTTTAATTTTGAA--TTAACTAAATATCACATTTTAAAAATAACACTATAAAACAA
* * * * ** * *
1498577 TTAAGTTAAATTTCGAATTTAATGTAAAATGTAAATTAAAGAGTA-AGAAACATTGATCTCGTAA
64 TTAAGCTAAATCTCGAATTTAATATAAAATATAAATTAAAGAACATA-AAACATAGATCTCATAA
* *
1498641 AATTTTAAACT-TTAAATTTAAGATTTA
128 AAATTTAAACTGTTAAATCTAAGATTTA
1498668 ATCTCATTAA
Statistics
Matches: 127, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
176 37 0.29
177 88 0.69
178 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (176 bp):
ATATTGAGATTTTAATTTTGAATTAACTAAATATCACATTTTAAAAATAACACTATAAAACAATT
AAGCTAAATCTCGAATTTAATATAAAATATAAATTAAAGAACATAAAACATAGATCTCATAAAAA
TTTAAACTGTTAAATCTAAGATTTAGTCTGGTTAATTCACTTGTAG
Found at i:1498884 original size:2 final size:2
Alignment explanation
Indices: 1498877--1498966 Score: 94
Period size: 2 Copynumber: 44.5 Consensus size: 2
1498867 AAACTTCCCC
* *
1498877 AT AT AT AT AC AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
** *
1498919 ACT -T CCC AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1498962 AT AT A
1 AT AT A
1498967 CCAATTCTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
1 2 0.03
2 71 0.96
3 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1499253 original size:24 final size:24
Alignment explanation
Indices: 1499217--1499262 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1499207 TATATATTTT
1499217 AAAAAATATTATAGTA-AAAAATAA
1 AAAAAATATTATA-TATAAAAATAA
1499241 AAAAAAT-TATATATATAAAAAT
1 AAAAAATAT-TATATATAAAAAT
1499263 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAAATATTATATATAAAAATAA
Found at i:1500282 original size:20 final size:19
Alignment explanation
Indices: 1500259--1500310 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
1500249 TATTGCACTG
*
1500259 TAATTATATTTAAAATATTT
1 TAATTATATATAAAATA-TT
1500279 TAATTA-A-ATAAAA-ATT
1 TAATTATATATAAAATATT
1500295 TAATTATATATAAAAT
1 TAATTATATATAAAAT
1500311 TATAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.29
17 2 0.07
18 11 0.39
19 1 0.04
20 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTATATATAAAATATT
Found at i:1500298 original size:16 final size:17
Alignment explanation
Indices: 1500277--1500311 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1500267 TTTAAAATAT
1500277 TTTAATTAAATA-AAAA
1 TTTAATTAAATATAAAA
*
1500293 TTTAATTATATATAAAA
1 TTTAATTAAATATAAAA
1500310 TT
1 TT
1500312 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAATTAAATATAAAA
Found at i:1500369 original size:20 final size:19
Alignment explanation
Indices: 1500318--1500372 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1500308 AATTATAAAA
1500318 ATTATAAA-ATAAATTAAT
1 ATTATAAATATAAATTAAT
* *
1500336 TTTATATTAATATAAATTTAT
1 ATTATA--AATATAAATTAAT
1500357 CATTATAAATATAAAT
1 -ATTATAAATATAAAT
1500373 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.17
20 11 0.37
21 9 0.30
22 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATAAATATAAATTAAT
Found at i:1500876 original size:14 final size:14
Alignment explanation
Indices: 1500859--1500889 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1500849 AAATTTAATT
1500859 ATAAAAATATAAAA
1 ATAAAAATATAAAA
*
1500873 ATAATAATATAAAA
1 ATAAAAATATAAAA
1500887 ATA
1 ATA
1500890 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAATATAAAA
Found at i:1503773 original size:28 final size:28
Alignment explanation
Indices: 1503742--1503888 Score: 70
Period size: 28 Copynumber: 5.5 Consensus size: 28
1503732 GTGTACGTTA
1503742 AATTTTATTATATTATAATTATAATTAT
1 AATTTTATTATATTATAATTATAATTAT
* * * *
1503770 AATTATAATATTTTATATTTAT-A-TA-
1 AATTTTATTATATTATAATTATAATTAT
*
1503795 AATTTT-TATATATTAT-A-TA-AATTTAA
1 AATTTTAT-TATATTATAATTATAA-TTAT
* *
1503821 AATATTTA-TATATT-TATTTTATATTTAT
1 AAT-TTTATTATATTATA-ATTATAATTAT
1503849 ATTATTTT-TTATATTAT-ATTAT-ATT-T
1 A--ATTTTATTATATTATAATTATAATTAT
1503875 -ATTTATATTATATT
1 AATTT-TATTATATT
1503889 CATCTTATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 37
0.64 0.09 0.27
Matches are distributed among these distances:
23 7 0.08
24 1 0.01
25 22 0.25
26 12 0.13
27 6 0.07
28 28 0.31
29 10 0.11
30 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
AATTTTATTATATTATAATTATAATTAT
Found at i:1503790 original size:6 final size:6
Alignment explanation
Indices: 1503749--1503888 Score: 56
Period size: 6 Copynumber: 25.2 Consensus size: 6
1503739 TTAAATTTTA
* * * *
1503749 TTATA- TTATAA TTATAA TTATAA TTATA- ATAT-T TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
** * * * *
1503794 AAATTT TTATAT ATTATA- -TAAAT TTA-AA ATAT-T TATATAT TTAT-T
1 TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT T-TATAT TTATAT
*
1503839 TTATAT TTATA- TTAT-T TTTTAT ATTATA- TTATA- TT-TAT TTATA-
1 TTATAT TTATAT TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT
1503882 TTATAT T
1 TTATAT T
1503889 CATCTTATAT
Statistics
Matches: 104, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
4 5 0.05
5 40 0.38
6 48 0.46
7 11 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
TTATAT
Found at i:1503812 original size:19 final size:19
Alignment explanation
Indices: 1503744--1503887 Score: 101
Period size: 18 Copynumber: 7.8 Consensus size: 19
1503734 GTACGTTAAA
1503744 TTTTATTATATTATA-ATTAT
1 TTTTA-TATATTATATA-TAT
**
1503764 AATTATA-ATTATA-ATA-
1 TTTTATATATTATATATAT
*
1503780 TTTTATAT-TTATATAAAT
1 TTTTATATATTATATATAT
*
1503798 TTTTATATATTATATA-AA
1 TTTTATATATTATATATAT
* *
1503816 TTTAAAATATT-TATATAT
1 TTTTATATATTATATATAT
*
1503834 TTATTTTATATT-TATATTAT
1 TT-TTATATATTATATA-TAT
1503854 TTTT-TATATTATATTATAT
1 TTTTATATATTATA-TATAT
1503873 TTATT-TATATTATAT
1 TT-TTATATATTATAT
1503888 TCATCTTATA
Statistics
Matches: 102, Mismatches: 12, Indels: 21
0.76 0.09 0.16
Matches are distributed among these distances:
16 10 0.10
17 8 0.08
18 34 0.33
19 29 0.28
20 21 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATATATTATATATAT
Found at i:1503860 original size:23 final size:23
Alignment explanation
Indices: 1503822--1503898 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
1503812 TAAATTTAAA
* *
1503822 ATATTTATATATTTATTTTATATT
1 ATATTTAT-TTTTTATATTATATT
1503846 -TATATTATTTTTTATATTATATT
1 ATAT-TTATTTTTTATATTATATT
*
1503869 ATATTTATTTATATTATATTCATCTT
1 ATATTTATTT-T-TTATATT-ATATT
1503895 ATAT
1 ATAT
1503899 AATAACGTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 22 0.49
24 8 0.18
25 7 0.16
26 8 0.18
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (23 bp):
ATATTTATTTTTTATATTATATT
Found at i:1503896 original size:20 final size:18
Alignment explanation
Indices: 1503826--1503888 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 18
1503816 TTTAAAATAT
1503826 TTATA-TATTTATTTTATA
1 TTATATTATTTA-TTTATA
1503844 TTTATATTATTT-TTTATA
1 -TTATATTATTTATTTATA
1503862 TTATATTATATTTATTTATA
1 TTATA-T-TATTTATTTATA
1503882 TTATATT
1 TTATATT
1503889 CATCTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.12
18 8 0.20
19 11 0.28
20 16 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATATTATTTATTTATA
Found at i:1505026 original size:23 final size:23
Alignment explanation
Indices: 1505000--1505060 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
1504990 TAGCATCTAA
*
1505000 TAATAAAATAATTTATTTAAAT-T
1 TAATAAAA-AATTTATATAAATAT
*
1505023 TAATTATAAAA-TTATATAAATAT
1 TAA-TAAAAAATTTATATAAATAT
1505046 TAATATAAAAATTTA
1 TAATA-AAAAATTTA
1505061 AATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 11 0.35
23 13 0.42
24 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAAAAATTTATATAAATAT
Found at i:1505042 original size:22 final size:22
Alignment explanation
Indices: 1505012--1505055 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1505002 ATAAAATAAT
*
1505012 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATTAA-TATAAAA
1505034 TTATATAAATATTAATATAAAA
1 TTATATAAATATTAATATAAAA
1505056 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATAAATATTAATATAAAA
Found at i:1507883 original size:21 final size:21
Alignment explanation
Indices: 1507857--1507899 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1507847 TTTGATGCCT
1507857 ATATTAAAATAATTAAGATAA
1 ATATTAAAATAATTAAGATAA
1507878 ATATTAAAATAATTAAGATAA
1 ATATTAAAATAATTAAGATAA
1507899 A
1 A
1507900 AGTAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
ATATTAAAATAATTAAGATAA
Found at i:1507917 original size:21 final size:21
Alignment explanation
Indices: 1507857--1507914 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1507847 TTTGATGCCT
*
1507857 ATATTAAAATAATTAAGATAA
1 ATATAAAAATAATTAAGATAA
*
1507878 ATATTAAAATAATTAAGATAA
1 ATATAAAAATAATTAAGATAA
1507899 A-AGTAAAAATGAATTA
1 ATA-TAAAAAT-AATTA
1507915 GATTGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.82
22 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
ATATAAAAATAATTAAGATAA
Found at i:1508667 original size:24 final size:24
Alignment explanation
Indices: 1508634--1508689 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1508624 ATTATTTATA
* *
1508634 AAATATTAAAAATATTTT-ATAATT
1 AAATAATAAAAAT-TTTTAATAAAT
*
1508658 AAATAATAAATATTTTTAATAAAT
1 AAATAATAAAAATTTTTAATAAAT
1508682 AAATAATA
1 AAATAATA
1508690 TTTAAATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATAATAAAAATTTTTAATAAAT
Found at i:1508676 original size:17 final size:19
Alignment explanation
Indices: 1508656--1508696 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1508646 TATTTTATAA
1508656 TTAAAT-AATAAAT-AT-T
1 TTAAATAAATAAATAATAT
*
1508672 TTTAATAAATAAATAATAT
1 TTAAATAAATAAATAATAT
1508691 TTAAAT
1 TTAAAT
1508697 CGAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 2 0.10
19 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATAAATAAATAATAT
Found at i:1508682 original size:20 final size:21
Alignment explanation
Indices: 1508640--1508692 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 21
1508630 TATAAAATAT
1508640 TAAAAATATTTTATAATTAAA
1 TAAAAATATTTTATAATTAAA
1508661 TAATAAATATTTT-TAA-TAAA
1 TAA-AAATATTTTATAATTAAA
1508681 TAAATAATATTT
1 TAAA-AATATTT
1508693 AAATCGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 6 0.20
22 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAATATTTTATAATTAAA
Found at i:1512329 original size:20 final size:20
Alignment explanation
Indices: 1512271--1512330 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1512261 AATCAATCTG
1512271 ATATAAATATTTAAATAGTAAA
1 ATATAAATA-TTAAATA-TAAA
*
1512293 ATAT--ATATTCAATTATAAA
1 ATATAAATATT-AAATATAAA
1512312 TATATAAATATT-AATATAA
1 -ATATAAATATTAAATATAA
1512331 TTTTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
19 6 0.19
20 17 0.53
22 9 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAAATATTAAATATAAA
Found at i:1513851 original size:2 final size:2
Alignment explanation
Indices: 1513844--1513870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1513834 ACAAAATTCT
1513844 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 T
1513871 GCTATGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1515239 original size:19 final size:19
Alignment explanation
Indices: 1515198--1515240 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1515188 AAATTCGTAT
**
1515198 TTTTATATTTTAATTATTT
1 TTTTATATTTTAATTATAA
1515217 TTTTATATTTATAATT-TAA
1 TTTTATATTT-TAATTATAA
1515236 TTTTA
1 TTTTA
1515241 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATATTTTAATTATAA
Found at i:1515602 original size:29 final size:28
Alignment explanation
Indices: 1515548--1515603 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1515538 ATTCACGATT
**
1515548 ACATGATATAAAAAATAATTTAAATATG
1 ACATGATATAAAAAATAATACAAATATG
*
1515576 ACATGATATTAAAAAATAATACGAATAT
1 ACATGATA-TAAAAAATAATACAAATAT
1515604 ATGAATATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (28 bp):
ACATGATATAAAAAATAATACAAATATG
Found at i:1515628 original size:32 final size:32
Alignment explanation
Indices: 1515591--1515658 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
1515581 ATATTAAAAA
*
1515591 ATAATACGAATATATGAAT--ATCACAAATTTAT
1 ATAATACAAAT-TATGAATACATCA-AAATTTAT
*
1515623 ATAATACAAATTATTAATACATCAAAATTTAT
1 ATAATACAAATTATGAATACATCAAAATTTAT
1515655 ATAA
1 ATAA
1515659 AATATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.19
32 22 0.69
33 4 0.12
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (32 bp):
ATAATACAAATTATGAATACATCAAAATTTAT
Found at i:1517022 original size:25 final size:23
Alignment explanation
Indices: 1516976--1517026 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1516966 CTTTTGAAAT
*
1516976 TTTAAATATATATTTTAATATTTA
1 TTTAAATATATAATTTAATA-TTA
**
1517000 TTTAAATAATATAATTTGGTATTA
1 TTTAAAT-ATATAATTTAATATTA
1517024 TTT
1 TTT
1517027 TATCCACCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAAATATATAATTTAATATTA
Found at i:1517028 original size:25 final size:24
Alignment explanation
Indices: 1516974--1517028 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1516964 TTCTTTTGAA
*
1516974 ATTTTAAATATATATTTTAATATT
1 ATTTTAAATATATAATTTAATATT
**
1516998 -TATTTAAATAATATAATTTGGTATT
1 AT-TTTAAAT-ATATAATTTAATATT
1517023 ATTTTA
1 ATTTTA
1517029 TCCACCTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 7 0.28
25 16 0.64
26 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTTAAATATATAATTTAATATT
Found at i:1517252 original size:17 final size:19
Alignment explanation
Indices: 1517222--1517256 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1517212 GTTTAATATA
1517222 TAAATTTAATTAAAAATTT
1 TAAATTTAATTAAAAATTT
1517241 TAAATTT-A-TAAAAATT
1 TAAATTTAATTAAAAATT
1517257 ATATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTTAATTAAAAATTT
Found at i:1518653 original size:28 final size:28
Alignment explanation
Indices: 1518622--1518678 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1518612 TTTTTAAATT
*
1518622 TTTTTACATAATA-TAAAAATAATATTTA
1 TTTTTA-ATAATATTAAAAATAACATTTA
* *
1518650 TTTTTAATACTATTAAAAATTACATTTA
1 TTTTTAATAATATTAAAAATAACATTTA
1518678 T
1 T
1518679 ATTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTTTAATAATATTAAAAATAACATTTA
Found at i:1520662 original size:32 final size:32
Alignment explanation
Indices: 1520625--1520690 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
1520615 TAAAAAAATT
*
1520625 TTAAAAATATAC-TAATTTTTAATATTATTAAA
1 TTAAAAATA-ACATAATTTTTAATATTACTAAA
*
1520657 TTAAAAATAACATTTATTTTTAATATTACTAAA
1 TTAAAAATAACA-TAATTTTTAATATTACTAAA
1520690 T
1 T
1520691 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 2 0.07
32 9 0.30
33 19 0.63
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (32 bp):
TTAAAAATAACATAATTTTTAATATTACTAAA
Found at i:1521995 original size:8 final size:8
Alignment explanation
Indices: 1521982--1522010 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1521972 TTGAGAACCT
1521982 TGTGTCTA
1 TGTGTCTA
1521990 TGTGTCTA
1 TGTGTCTA
1521998 TGTGTCTA
1 TGTGTCTA
1522006 TGTGT
1 TGTGT
1522011 GTGCTGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.28, T:0.52
Consensus pattern (8 bp):
TGTGTCTA
Found at i:1522599 original size:16 final size:15
Alignment explanation
Indices: 1522565--1522611 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1522555 ATATATATTG
*
1522565 AATTAAAAATATTAAA
1 AATTAAAAAT-TAAAA
1522581 AA-TAAATAATTTAAAA
1 AATTAAA-AA-TTAAAA
1522597 AATTAAAAATTAAAA
1 AATTAAAAATTAAAA
1522612 TAAAATAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 10 0.37
16 12 0.44
17 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAAATTAAAA
Found at i:1522787 original size:11 final size:11
Alignment explanation
Indices: 1522771--1522814 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1522761 ATATTATGTG
1522771 TATTTATATTT
1 TATTTATATTT
1522782 TATTTATATATT
1 TATTTATAT-TT
*
1522794 T-TTTATATTA
1 TATTTATATTT
*
1522804 TAATTATATTT
1 TATTTATATTT
1522815 AAAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.07
11 23 0.82
12 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTATATTT
Found at i:1522828 original size:16 final size:16
Alignment explanation
Indices: 1522807--1522841 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1522797 TATATTATAA
1522807 TTATATTTAAAATATT
1 TTATATTTAAAATATT
* *
1522823 TTATATTTATATTATT
1 TTATATTTAAAATATT
1522839 TTA
1 TTA
1522842 ATATATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:1522854 original size:16 final size:16
Alignment explanation
Indices: 1522817--1522945 Score: 57
Period size: 16 Copynumber: 8.4 Consensus size: 16
1522807 TTATATTTAA
1522817 AATATTTT-ATAT-TT
1 AATATTTTAATATATT
1522831 ATATTATTTTAATATATT
1 A-A-TATTTTAATATATT
*
1522849 AATATTTT-GTATTATAT
1 AATATTTTAATA-TAT-T
* *
1522866 AA-ATTTTAA-AAAAT
1 AATATTTTAATATATT
*
1522880 -ATATTTTATTATATT
1 AATATTTTAATATATT
1522895 -ATATTTTAAT-TATT
1 AATATTTTAATATATT
* *
1522909 -TTATTTATATTATATT
1 AATATTT-TAATATATT
1522925 --TA-TTTAATCATAATT
1 AATATTTTAAT-AT-ATT
1522940 AATATT
1 AATATT
1522946 ATCAAATTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.05
14 21 0.24
15 24 0.27
16 25 0.28
17 10 0.11
18 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (16 bp):
AATATTTTAATATATT
Found at i:1522861 original size:26 final size:27
Alignment explanation
Indices: 1522771--1522926 Score: 88
Period size: 28 Copynumber: 5.6 Consensus size: 27
1522761 ATATTATGTG
* * * *
1522771 TATTTATATTTTATTT-ATATATTTTT
1 TATTTATATTATATTTAAAATATTATA
*
1522797 TATATTATAATTATATTTAAAATATTTTA
1 TAT-TTAT-ATTATATTTAAAATATTATA
*
1522826 TATTTATATTAT-TTTAATATATTAATA
1 TATTTATATTATATTTAAAATATT-ATA
* * *
1522853 TTTTGTATTATATAAATTTTAAAA-AATATA
1 TATT-TA-TAT-TATA-TTTAAAATATTATA
* * *
1522883 TTTTATTATATTATATTTTAATTATT-T-
1 -TAT-TTATATTATATTTAAAATATTATA
1522910 TATTTATATTATATTTA
1 TATTTATATTATATTTA
1522927 TTTAATCATA
Statistics
Matches: 103, Mismatches: 15, Indels: 25
0.72 0.10 0.17
Matches are distributed among these distances:
25 13 0.13
26 15 0.15
27 14 0.14
28 20 0.19
29 19 0.18
30 8 0.08
31 7 0.07
32 7 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.62
Consensus pattern (27 bp):
TATTTATATTATATTTAAAATATTATA
Found at i:1522889 original size:28 final size:29
Alignment explanation
Indices: 1522815--1522903 Score: 78
Period size: 32 Copynumber: 3.0 Consensus size: 29
1522805 AATTATATTT
*
1522815 AAAATATTTTATATTTATATT--ATTTTAA
1 AAAATATTTTGTA-TTATATTAAATTTTAA
1522843 TATATTAATATTTTGTATTATA-TAAATTTTAA
1 -A-A--AATATTTTGTATTATATTAAATTTTAA
*
1522875 AAAATATATTT-TATTATATTATATTTTAA
1 AAAATAT-TTTGTATTATATTAAATTTTAA
1522904 TTATTTTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
28 12 0.24
29 13 0.25
30 3 0.06
31 6 0.12
32 17 0.33
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
AAAATATTTTGTATTATATTAAATTTTAA
Found at i:1522918 original size:20 final size:21
Alignment explanation
Indices: 1522888--1522929 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1522878 ATATATTTTA
*
1522888 TTATATTATATTTTAATTATT
1 TTATATTATATTATAATTATT
*
1522909 TTAT-TTATATTATATTTATT
1 TTATATTATATTATAATTATT
1522929 T
1 T
1522930 AATCATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATATTATATTATAATTATT
Found at i:1523322 original size:22 final size:22
Alignment explanation
Indices: 1523277--1523321 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1523267 TTCCAATATG
*
1523277 AATATAAGAATGATATTTTAAA
1 AATATAAGAATAATATTTTAAA
*
1523299 AATATAA-AATAATCTTTTAAA
1 AATATAAGAATAATATTTTAAA
1523320 AA
1 AA
1523322 AATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
AATATAAGAATAATATTTTAAA
Found at i:1525458 original size:44 final size:44
Alignment explanation
Indices: 1525395--1525481 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
1525385 AAAATAGGAC
1525395 TTAAGAACAAGAAGATTCATCAGCATGACCCTATAATCTAGACA
1 TTAAGAACAAGAAGATTCATCAGCATGACCCTATAATCTAGACA
* *
1525439 TTAAGAACAATAAGATTCATCAGTATGACCCTATAATCTAGAC
1 TTAAGAACAAGAAGATTCATCAGCATGACCCTATAATCTAGAC
1525482 CATGTCAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.25
Consensus pattern (44 bp):
TTAAGAACAAGAAGATTCATCAGCATGACCCTATAATCTAGACA
Found at i:1528185 original size:23 final size:22
Alignment explanation
Indices: 1528145--1528187 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1528135 TGCATTATCT
*
1528145 TTTTTTATTTATATTATTTAAA
1 TTTTTTATTTATAATATTTAAA
*
1528167 TTTTTTATTTTTAAATATTTA
1 TTTTTTATTTAT-AATATTTA
1528188 TATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTTATTTATAATATTTAAA
Found at i:1528227 original size:16 final size:16
Alignment explanation
Indices: 1528208--1528245 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1528198 GATATAAGTA
1528208 TAAAAATATAATACTT
1 TAAAAATATAATACTT
* *
1528224 TAAATATATAATATTT
1 TAAAAATATAATACTT
1528240 TAAAAA
1 TAAAAA
1528246 ATTAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAATATAATACTT
Found at i:1528256 original size:19 final size:21
Alignment explanation
Indices: 1528225--1528285 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 21
1528215 ATAATACTTT
1528225 AAATATAT-A-ATATTTTAAA
1 AAATATATAATATATTTTAAA
*
1528244 AAAT-TA-AATATATTTATATA
1 AAATATATAATATATTT-TAAA
1528264 AAATATATAAT-TATATTTAAA
1 AAATATATAATATAT-TTTAAA
1528285 A
1 A
1528286 CTTATTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 7 0.21
21 9 0.26
22 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATATATAATATATTTTAAA
Found at i:1528525 original size:25 final size:24
Alignment explanation
Indices: 1528469--1528534 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 24
1528459 GTATAACTTT
1528469 TAAATATATATA-ATTT-T-TTAA
1 TAAATATATATATATTTATATTAA
*
1528490 -AAAT-TAAATATATTTATATTAAA
1 TAAATATATATATATTTATATT-AA
*
1528513 TAAATATATATATTTTTATATT
1 TAAATATATATATATTTATATT
1528535 TTATTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 1 0.03
22 2 0.06
23 2 0.06
24 4 0.11
25 14 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATATATATATATTTATATTAA
Found at i:1528764 original size:3 final size:3
Alignment explanation
Indices: 1528688--1528752 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
1528678 AAAAGACCAC
* * * * * *
1528688 ATA ATA ACA ATA ACA ACA ATA ATA ACA ATA ATA ATG ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1528736 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1528753 TAGGTAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:1529020 original size:11 final size:12
Alignment explanation
Indices: 1528949--1529039 Score: 55
Period size: 12 Copynumber: 7.6 Consensus size: 12
1528939 TGTCATACTA
1528949 TATTTATTATAT
1 TATTTATTATAT
*
1528961 TATTT-TCATAGT
1 TATTTATTATA-T
* * *
1528973 TATTAAATATAC
1 TATTTATTATAT
* *
1528985 TATACTCTTATCA-
1 TAT-TTATTAT-AT
1528998 TATTTATTATAT
1 TATTTATTATAT
1529010 TATTT-TTATATT
1 TATTTATTATA-T
*
1529022 TATGTATTATA-
1 TATTTATTATAT
1529033 TATTTAT
1 TATTTAT
1529040 ATCGTATTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
11 16 0.27
12 28 0.47
13 14 0.24
14 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.59
Consensus pattern (12 bp):
TATTTATTATAT
Found at i:1529020 original size:20 final size:20
Alignment explanation
Indices: 1528947--1529024 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
1528937 CTTGTCATAC
1528947 TATATTTATTATATTATTTT
1 TATATTTATTATATTATTTT
* *
1528967 CATAGTTATTAAATATACTATACTCTT
1 TATATTTATT--ATAT--TAT--T-TT
1528994 ATCATATTTATTATATTATTTT
1 -T-ATATTTATTATATTATTTT
1529016 TATATTTAT
1 TATATTTAT
1529025 GTATTATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
20 16 0.36
21 1 0.02
22 6 0.13
23 1 0.02
24 3 0.07
25 3 0.07
26 1 0.02
27 6 0.13
29 8 0.18
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.59
Consensus pattern (20 bp):
TATATTTATTATATTATTTT
Found at i:1529040 original size:21 final size:20
Alignment explanation
Indices: 1528997--1529041 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1528987 TACTCTTATC
*
1528997 ATATTTATTATATTATTTTT
1 ATATTTATTATATTATATTT
1529017 ATATTTATGTAT-TATATATTT
1 ATATTTAT-TATAT-TATATTT
1529038 ATAT
1 ATAT
1529042 CGTATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATTTATTATATTATATTT
Found at i:1532457 original size:17 final size:17
Alignment explanation
Indices: 1532431--1532463 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1532421 TTAAAATAAA
1532431 ATATTAAATATAAATAC
1 ATATTAAATATAAATAC
*
1532448 ATATTTAATATAAATA
1 ATATTAAATATAAATA
1532464 TAATAAATAA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTAAATATAAATAC
Found at i:1532494 original size:23 final size:23
Alignment explanation
Indices: 1532462--1532513 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1532452 TTAATATAAA
*
1532462 TATAATAAATAAATTTTTATATATT
1 TATAA-AATTAAATTTTT-TATATT
*
1532487 TATAAAATTATATTTTTTATATT
1 TATAAAATTAAATTTTTTATATT
1532510 TATA
1 TATA
1532514 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 10 0.40
25 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATAAAATTAAATTTTTTATATT
Found at i:1534331 original size:2 final size:2
Alignment explanation
Indices: 1534324--1534354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1534314 TCCAGTTACC
1534324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1534355 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1540026 original size:19 final size:20
Alignment explanation
Indices: 1539993--1540030 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1539983 TATATGTTAT
*
1539993 TATATTATAATTTTTAAAAA
1 TATATTATAAATTTTAAAAA
1540013 TATA-TATAAATTTTAAAA
1 TATATTATAAATTTTAAAA
1540031 TATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATTATAAATTTTAAAAA
Found at i:1540030 original size:18 final size:18
Alignment explanation
Indices: 1539993--1540065 Score: 66
Period size: 15 Copynumber: 4.2 Consensus size: 18
1539983 TATATGTTAT
*
1539993 TATATTATAATTTTTAAAAA
1 TATA-TATAAATTTT-AAAA
1540013 TATATATAAATTTTAAAA
1 TATATATAAATTTTAAAA
*
1540031 TAT-TA-ATAA--TTAATA
1 TATATATA-AATTTTAAAA
1540046 T-TATATAAATTTTAAAA
1 TATATATAAATTTTAAAA
1540063 TAT
1 TAT
1540066 TAACACATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
16 2 0.05
17 10 0.23
18 8 0.18
19 9 0.20
20 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATATAAATTTTAAAA
Found at i:1540066 original size:19 final size:19
Alignment explanation
Indices: 1539998--1540067 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 19
1539988 GTTATTATAT
*
1539998 TATAATTTTTAAAA-ATATA
1 TATAAATTTTAAAATAT-TA
1540017 TATAAATTTTAAAATATTA
1 TATAAATTTTAAAATATTA
1540036 -AT-AA--TT--AATATTA
1 TATAAATTTTAAAATATTA
1540049 TATAAATTTTAAAATATTA
1 TATAAATTTTAAAATATTA
1540068 ACACATTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
13 7 0.16
14 2 0.05
15 4 0.09
17 4 0.09
18 2 0.05
19 22 0.51
20 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAATTTTAAAATATTA
Found at i:1540081 original size:34 final size:32
Alignment explanation
Indices: 1540011--1540085 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
1540001 AATTTTTAAA
*
1540011 AATA-TATATAAATTTTAAAATATTAATAATT
1 AATATTATATAAATTTTAAAATATTAACAATT
1540042 AATATTATATAAATTTTAAAATATTAACACATTT
1 AATATTATATAAATTTTAAAATATTAACA-A-TT
*
1540076 TATATTATAT
1 AATATTATAT
1540086 TATATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
31 4 0.10
32 23 0.59
33 1 0.03
34 11 0.28
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
AATATTATATAAATTTTAAAATATTAACAATT
Found at i:1540357 original size:3 final size:3
Alignment explanation
Indices: 1540349--1540402 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
1540339 AGAAAGTGAA
* *
1540349 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATTT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
1540395 ATTT ATT A
1 A-TT ATT A
1540403 ATTAATTGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 41 0.91
4 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1540408 original size:22 final size:22
Alignment explanation
Indices: 1540351--1540409 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1540341 AAAGTGAAAT
* * *
1540351 TATTATTATTATTA-TTATTAT
1 TATTATTAATATAATTTATTAA
*
1540372 TATTATTATTATAATTTATTAA
1 TATTATTAATATAATTTATTAA
1540394 TATTTATTAAT-TAATT
1 TA-TTATTAATATAATT
1540410 GACTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.39
22 13 0.39
23 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTAATATAATTTATTAA
Done.