Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 14 of 28
Found at i:2177264 original size:15 final size:15
Alignment explanation
Indices: 2177244--2177273 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2177234 ACACATCATC
2177244 ATTGTCTTCATTATT
1 ATTGTCTTCATTATT
2177259 ATTGTCTTCATTATT
1 ATTGTCTTCATTATT
2177274 CCCTTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
ATTGTCTTCATTATT
Found at i:2178678 original size:18 final size:18
Alignment explanation
Indices: 2178657--2178694 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2178647 ATAAAAATTA
2178657 AATT-ATTTAAATTTATTT
1 AATTAATTT-AATTTATTT
*
2178675 AATTAATTTTATTTATTT
1 AATTAATTTAATTTATTT
2178693 AA
1 AA
2178695 CAAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTAATTTAATTTATTT
Found at i:2178760 original size:27 final size:27
Alignment explanation
Indices: 2178731--2178798 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
2178721 TTTAAATTTA
*
2178731 ATTATTTATATTTAAATTAAAAT-TAAA
1 ATTATTTA-ATTTAAATTAAAATAAAAA
*
2178758 ATTTTTTAATATT-AATTAAAATAAAAA
1 ATTATTTAAT-TTAAATTAAAATAAAAA
2178785 ATTATTTAAATTTA
1 ATTATTT-AATTTA
2178799 TAAATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 11 0.32
27 20 0.59
28 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTATTTAATTTAAATTAAAATAAAAA
Found at i:2178793 original size:17 final size:17
Alignment explanation
Indices: 2178768--2178816 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2178758 ATTTTTTAAT
*
2178768 ATTAATTAAAATAAAAA
1 ATTATTTAAAATAAAAA
* * *
2178785 ATTATTTAAATTTATAA
1 ATTATTTAAAATAAAAA
2178802 ATTATTTAAAATAAA
1 ATTATTTAAAATAAA
2178817 TATAAAAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTTAAAATAAAAA
Found at i:2178801 original size:20 final size:20
Alignment explanation
Indices: 2178778--2178836 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 20
2178768 ATTAATTAAA
2178778 ATAAAAAATTATTTAAATTT
1 ATAAAAAATTATTTAAATTT
**
2178798 AT---AAATTATTTAAAATAA
1 ATAAAAAATTATTT-AAATTT
2178816 ATATAAAAA-TATTTAAATTT
1 ATA-AAAAATTATTTAAATTT
2178836 A
1 A
2178837 ATTCATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
20 7 0.23
21 5 0.17
22 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAATTATTTAAATTT
Found at i:2179664 original size:2 final size:2
Alignment explanation
Indices: 2179657--2179689 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2179647 GTCTTCCTTT
2179657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2179690 CACATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2180033 original size:22 final size:23
Alignment explanation
Indices: 2179984--2180050 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 23
2179974 AATATTAATT
2179984 ATATGATATAATAAAAAA-ATTA
1 ATATGATATAATAAAAAATATTA
2180006 A-A--ATATAATAAAAAATA-TA
1 ATATGATATAATAAAAAATATTA
*
2180025 ATATGATATAA-AAATAATATTA
1 ATATGATATAATAAAAAATATTA
2180047 ATAT
1 ATAT
2180051 AAGATAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 16 0.41
20 2 0.05
21 8 0.21
22 13 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
ATATGATATAATAAAAAATATTA
Found at i:2180057 original size:22 final size:22
Alignment explanation
Indices: 2179971--2180058 Score: 58
Period size: 22 Copynumber: 4.0 Consensus size: 22
2179961 AATTATACAC
*
2179971 AATAATATTAATTATATGATATAA
1 AATAATATTAA-TATAAGATA-AA
* * *
2179995 TAAAAAAATTAAAATATA-AT-AA
1 -AATAATATTAATATA-AGATAAA
* *
2180017 AA-AATA-TAATATGATATAAA
1 AATAATATTAATATAAGATAAA
2180037 AATAATATTAATATAAGATAAA
1 AATAATATTAATATAAGATAAA
2180059 TATATAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
18 1 0.02
19 7 0.14
20 7 0.14
21 6 0.12
22 14 0.29
24 5 0.10
25 9 0.18
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (22 bp):
AATAATATTAATATAAGATAAA
Found at i:2180166 original size:41 final size:42
Alignment explanation
Indices: 2180115--2180213 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
2180105 AATTTATAAT
*
2180115 TATAAATATAAAATATC-TAAACATAAATTTATTA-A-ACAAGA
1 TATAATTATAAAATATCTTAAACATAAATTTATTATATAC-A-A
* *
2180156 TATAATTATAAAATATCTTAAATATAATTTTATTATATACAA
1 TATAATTATAAAATATCTTAAACATAAATTTATTATATACAA
*
2180198 TATAATTATATAATAT
1 TATAATTATAAAATAT
2180214 AAAAAATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
41 16 0.31
42 31 0.61
43 2 0.04
44 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (42 bp):
TATAATTATAAAATATCTTAAACATAAATTTATTATATACAA
Found at i:2180201 original size:20 final size:20
Alignment explanation
Indices: 2180155--2180233 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
2180145 ATTAAACAAG
* *
2180155 ATATAATTATAAAATATCTTAA
1 ATATAATTATATAATA--TAAA
* * *
2180177 ATATAATTTTATTATATACA
1 ATATAATTATATAATATAAA
2180197 ATATAATTATATAATATAAA
1 ATATAATTATATAATATAAA
*
2180217 AAATAATTA-A-AATATAA
1 ATATAATTATATAATATAA
2180234 TATAATACAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 7 0.15
19 1 0.02
20 27 0.56
22 13 0.27
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATTATATAATATAAA
Found at i:2180275 original size:19 final size:18
Alignment explanation
Indices: 2180225--2180276 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
2180215 AAAAATAATT
2180225 AAAATATAATATAATACAAA
1 AAAATAT-AT-TAATACAAA
*
2180245 AAAATAACATTAATACAATA
1 AAAAT-ATATTAATACAA-A
*
2180265 TAAATATATTAA
1 AAAATATATTAA
2180277 AATTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 14 0.52
20 12 0.44
21 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATATTAATACAAA
Found at i:2181510 original size:13 final size:13
Alignment explanation
Indices: 2181492--2181522 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2181482 ATAATTACCC
*
2181492 TTATTTTATAATT
1 TTATTTTATAATA
2181505 TTATTTTATAATA
1 TTATTTTATAATA
2181518 TTATT
1 TTATT
2181523 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTTATAATA
Found at i:2181532 original size:19 final size:19
Alignment explanation
Indices: 2181508--2181545 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2181498 TATAATTTTA
2181508 TTTTATAATATTATTAATT
1 TTTTATAATATTATTAATT
* *
2181527 TTTTATATTTTTATTAATT
1 TTTTATAATATTATTAATT
2181546 GAGTTGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATAATATTATTAATT
Found at i:2189422 original size:8 final size:8
Alignment explanation
Indices: 2189409--2189439 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
2189399 AAAGGAAATA
2189409 TAAATATT
1 TAAATATT
2189417 TAAATATT
1 TAAATATT
2189425 TAAATA-T
1 TAAATATT
2189432 TAAATATT
1 TAAATATT
2189440 AAAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAATATT
Found at i:2189436 original size:7 final size:7
Alignment explanation
Indices: 2189404--2189442 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 7
2189394 AAATGAAAGG
2189404 AAATA-T
1 AAATATT
2189410 AAATATTT
1 AAATA-TT
2189418 AAATATTT
1 AAATA-TT
2189426 AAATATT
1 AAATATT
2189433 AAATATT
1 AAATATT
2189440 AAA
1 AAA
2189443 ACAAAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 5 0.16
7 12 0.39
8 14 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:2189503 original size:34 final size:35
Alignment explanation
Indices: 2189453--2189518 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
2189443 ACAAAAACAA
*
2189453 AAAATAATTTTATATTTTAAT-ATATTTTAAATAAT
1 AAAATAATTTTATATTTAAATCA-ATTTTAAATAAT
*
2189488 AAAAT-ATTTTTTATTTAAATCAATTTTAAAT
1 AAAATAATTTTATATTTAAATCAATTTTAAAT
2189519 TAACAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (35 bp):
AAAATAATTTTATATTTAAATCAATTTTAAATAAT
Found at i:2189652 original size:21 final size:22
Alignment explanation
Indices: 2189610--2189660 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2189600 TTTAATTATA
* *
2189610 AAAATAATATTTTAATATTTTT
1 AAAATAATACTATAATATTTTT
2189632 AAAATAATACTATAA-ATTTTT
1 AAAATAATACTATAATATTTTT
*
2189653 AAATTAAT
1 AAAATAAT
2189661 TTTAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATAATACTATAATATTTTT
Found at i:2190204 original size:17 final size:17
Alignment explanation
Indices: 2190184--2190231 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
2190174 TTAAATATTA
2190184 AAATTTTATATTTAAAT
1 AAATTTTATATTTAAAT
*
2190201 AAATTATTTAATTTTTAAAT
1 AAA-T-TTT-ATATTTAAAT
*
2190221 AAATTTAATAT
1 AAATTTTATAT
2190232 AATTAATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 6 0.24
18 3 0.12
19 4 0.16
20 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTTTATATTTAAAT
Found at i:2191510 original size:26 final size:26
Alignment explanation
Indices: 2191481--2191554 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 26
2191471 TAATTACTTT
2191481 TAATTTAATATTATAAAAATATATTA
1 TAATTTAATATTATAAAAATATATTA
*
2191507 TAATTT-AT-TTAT-AAAATATTATTT
1 TAATTTAATATTATAAAAATA-TATTA
* * *
2191531 TAATATATATAATATAAATATATA
1 TAATTTA-ATATTATAAAAATATA
2191555 CTAAAAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 6 0.15
24 13 0.33
25 2 0.05
26 8 0.21
27 5 0.13
28 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATTTAATATTATAAAAATATATTA
Found at i:2191540 original size:15 final size:15
Alignment explanation
Indices: 2191532--2191587 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
2191522 ATATTATTTT
2191532 AATATATATAATATA
1 AATATATATAATATA
*
2191547 AATATATACTAAAAGTA
1 AATATATA-TAATA-TA
* * *
2191564 TATATATAAAATATT
1 AATATATATAATATA
2191579 AATATATAT
1 AATATATAT
2191588 GACTTTAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 16 0.50
16 7 0.22
17 9 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
AATATATATAATATA
Found at i:2191818 original size:14 final size:13
Alignment explanation
Indices: 2191787--2191822 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2191777 AAAAATTTAA
*
2191787 TTTATTTTAATTT
1 TTTAATTTAATTT
2191800 TTTAATTTAATTT
1 TTTAATTTAATTT
2191813 TATTAATTTA
1 T-TTAATTTA
2191823 TCCGCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTAATTTAATTT
Found at i:2192137 original size:3 final size:3
Alignment explanation
Indices: 2192129--2192162 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2192119 CCGCTCTGCT
2192129 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC A
2192163 TCGCCACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:2207395 original size:11 final size:11
Alignment explanation
Indices: 2207381--2207418 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2207371 CTCGATTTGA
2207381 ATAATATTTTT
1 ATAATATTTTT
**
2207392 ATAATATAATT
1 ATAATATTTTT
2207403 AT-ATATTTTT
1 ATAATATTTTT
2207413 ATAATA
1 ATAATA
2207419 ATACTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATATTTTT
Found at i:2207408 original size:21 final size:22
Alignment explanation
Indices: 2207384--2207432 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
2207374 GATTTGAATA
2207384 ATATTTTTATAAT-ATAATTAT
1 ATATTTTTATAATAATAATTAT
*
2207405 ATATTTTTATAATAATACTTAT
1 ATATTTTTATAATAATAATTAT
2207427 A-ATTTT
1 ATATTTT
2207433 GTTTTACTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTTTATAATAATAATTAT
Found at i:2208689 original size:22 final size:22
Alignment explanation
Indices: 2208652--2208709 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2208642 TTTTATATTG
* *
2208652 ATATAAATTTTTATAAATTAATA
1 ATATATATTTATATAAATT-ATA
* *
2208675 ATTTATA-TTATATAAATTTTA
1 ATATATATTTATATAAATTATA
2208696 ATATATATTTATAT
1 ATATATATTTATAT
2208710 TATATTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 8 0.28
22 16 0.55
23 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATATATTTATATAAATTATA
Found at i:2209012 original size:40 final size:40
Alignment explanation
Indices: 2208968--2209060 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 40
2208958 TTTAAAATAA
*
2208968 TATATATTTATATAA-ATTATGATAAATTAATAATTTATAT
1 TATATATTTATATAACATAATGATAAATTAATAATTTAT-T
* * * *
2209008 TATATAATTT-T-TAACATAATTATATATTTATATTTTATT
1 TATAT-ATTTATATAACATAATGATAAATTAATAATTTATT
2209047 TATATATATTATAT
1 TATATAT-TTATAT
2209061 TATATTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
38 2 0.05
39 11 0.26
40 25 0.58
41 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (40 bp):
TATATATTTATATAACATAATGATAAATTAATAATTTATT
Found at i:2209397 original size:15 final size:15
Alignment explanation
Indices: 2209377--2209423 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2209367 ACTTGTTAAT
2209377 TTTTTATTATAAATA
1 TTTTTATTATAAATA
2209392 TTTTTATGTA-AAATA
1 TTTTTAT-TATAAATA
2209407 ---TTATTAT-AATA
1 TTTTTATTATAAATA
2209418 TTTTTA
1 TTTTTA
2209424 AATTCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
11 6 0.22
12 4 0.15
14 3 0.11
15 12 0.44
16 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTTATTATAAATA
Found at i:2209621 original size:22 final size:22
Alignment explanation
Indices: 2209583--2209627 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2209573 TTTTAAAAAA
* *
2209583 TTTAAATTATTATAATAATATT
1 TTTAAATTATTAAAATAAAATT
2209605 TTTAAATT-TTAAAAATAAAATT
1 TTTAAATTATT-AAAATAAAATT
2209627 T
1 T
2209628 AATTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAATTATTAAAATAAAATT
Found at i:2211249 original size:22 final size:21
Alignment explanation
Indices: 2211208--2211259 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
2211198 TTTGATTTGT
2211208 TTTAAATTATTATTTATT-AA
1 TTTAAATTATTATTTATTAAA
2211228 TTTAAATAGTATTA-TTATTTAAA
1 TTTAAAT--TATTATTTA-TTAAA
2211251 TTT-AATTAT
1 TTTAAATTAT
2211260 AAAAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 10 0.36
23 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTAAATTATTATTTATTAAA
Found at i:2211851 original size:19 final size:21
Alignment explanation
Indices: 2211821--2211859 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2211811 AGAGGCTGAC
2211821 ATTTGTTATATTAA-TATAAT
1 ATTTGTTATATTAATTATAAT
2211841 ATTTG-TATATTAATTATAA
1 ATTTGTTATATTAATTATAA
2211860 AAACGGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
ATTTGTTATATTAATTATAAT
Found at i:2217818 original size:25 final size:24
Alignment explanation
Indices: 2217783--2217835 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
2217773 ATATAAATTT
*
2217783 AATAAATTTTAATTATTTAATATA
1 AATAAATTTTAATGATTTAATATA
*
2217807 AATATAATTTTAATGATTTGATATA
1 AATA-AATTTTAATGATTTAATATA
2217832 AATA
1 AATA
2217836 CACTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AATAAATTTTAATGATTTAATATA
Found at i:2217850 original size:25 final size:25
Alignment explanation
Indices: 2217783--2217850 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 25
2217773 ATATAAATTT
* *
2217783 AATA-AATTTTAATTATTTAATATA
1 AATACAATTTGAATAATTTAATATA
* * * *
2217807 AATATAATTTTAATGATTTGATATA
1 AATACAATTTGAATAATTTAATATA
*
2217832 AATACACTTTGAATAATTT
1 AATACAATTTGAATAATTT
2217851 TTATCTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 4 0.11
25 33 0.89
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (25 bp):
AATACAATTTGAATAATTTAATATA
Found at i:2225111 original size:302 final size:300
Alignment explanation
Indices: 2224554--2225158 Score: 994
Period size: 302 Copynumber: 2.0 Consensus size: 300
2224544 TCATTTTATA
* * *
2224554 TTTATCAGATAAGCTTAAAAAGCAAGTTGCTCCAACCTGTTGTTGCTTCAAATTAGGGAAACTTT
1 TTTATCAGATAAGCTTAAAAAGCAAGCTGCTCCAACCTGTTGCTGCTTCAAATTAGGGAAACTAT
2224619 CCTGTATAAGACTAACGTGATAACCACTACACCACAGCGATTTTATTAAAAATTACAAGGAAACT
66 CCTGTATAAGACTAACGTGATAACCACTACACCACAGCGATTTTATTAAAAATTACAAGGAAACT
* * * * *
2224684 TAACAATTTTAAAGTATTGTATCTAAGATATGATAATAATTGTTTTTTGAAGTCATTGTCATCCA
131 TAACAATTTTAAAGTACTGTATCTAAGATATGAAAAAAATTGTCTTTTGAAGTCATTGCCATCCA
* *
2224749 CATGGTTGTACCTTGACTAGGTGTTTAAGGCTCAAGTTACTTGCTTAATTAAGCCCATAAATGAG
196 CATGGTTGTACCTTGACTAGGTGTTTAAGGCTCAAGTAACTTGCTTAATAAAGCCCATAAATGAG
* ** *
2224814 GTTTAACTTGAGTGGGATTTGGTGTAAATTGTTAGATCTATG
261 ATTTAACTTG-GTGGGATTTGGAATAAA-TCTTAGATCTATG
*
2224856 TTTATCAGATAAGCTTAAAAATCAAGCTGCTCCAACCTGTTGCTGCTTCAAATTAGGGAAACTAT
1 TTTATCAGATAAGCTTAAAAAGCAAGCTGCTCCAACCTGTTGCTGCTTCAAATTAGGGAAACTAT
* * * *
2224921 CCTGTATAAGACTAACGTGATAACCACTACATCACAGGGATTTTATTAAGAATTACAGGGAAACT
66 CCTGTATAAGACTAACGTGATAACCACTACACCACAGCGATTTTATTAAAAATTACAAGGAAACT
*
2224986 TAACAATTTTAAAGTACTGTATCTAAGATTTGAAAAAAATTGTCTTTTGAAGTCATTGCCATCCA
131 TAACAATTTTAAAGTACTGTATCTAAGATATGAAAAAAATTGTCTTTTGAAGTCATTGCCATCCA
* *
2225051 CATGGTTGTACCTTGACTAGGTGTTTAAGGCTTAAGTAACTTGCTTAATAAAGTCCATAAATGAG
196 CATGGTTGTACCTTGACTAGGTGTTTAAGGCTCAAGTAACTTGCTTAATAAAGCCCATAAATGAG
2225116 ATTTAACTTGGTGGGATTTGGAATAAATCTTAGATCTATG
261 ATTTAACTTGGTGGGATTTGGAATAAATCTTAGATCTATG
2225156 TTT
1 TTT
2225159 GGCTGATTAC
Statistics
Matches: 281, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
300 15 0.05
301 15 0.05
302 251 0.89
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (300 bp):
TTTATCAGATAAGCTTAAAAAGCAAGCTGCTCCAACCTGTTGCTGCTTCAAATTAGGGAAACTAT
CCTGTATAAGACTAACGTGATAACCACTACACCACAGCGATTTTATTAAAAATTACAAGGAAACT
TAACAATTTTAAAGTACTGTATCTAAGATATGAAAAAAATTGTCTTTTGAAGTCATTGCCATCCA
CATGGTTGTACCTTGACTAGGTGTTTAAGGCTCAAGTAACTTGCTTAATAAAGCCCATAAATGAG
ATTTAACTTGGTGGGATTTGGAATAAATCTTAGATCTATG
Found at i:2225278 original size:3 final size:3
Alignment explanation
Indices: 2225270--2225309 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2225260 TACTTTAAGA
2225270 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2225310 GTAGCAGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2226377 original size:22 final size:21
Alignment explanation
Indices: 2226335--2226378 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2226325 TATTTAAAAG
*
2226335 ATATTTTTTATTTTAATATTT
1 ATATTTTTTATATTAATATTT
2226356 ATATATTTTTATAATTAA-ATTT
1 ATAT-TTTTTAT-ATTAATATTT
2226378 A
1 A
2226379 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTTTTATATTAATATTT
Found at i:2227501 original size:18 final size:18
Alignment explanation
Indices: 2227455--2227502 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2227445 TTATTTATAT
2227455 AATA-AAAATTAAATTAA
1 AATATAAAATTAAATTAA
* ** *
2227472 AAAATATTATTAAATTTA
1 AATATAAAATTAAATTAA
2227490 AATATAAAATTAA
1 AATATAAAATTAA
2227503 TATAAAAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAAAATTAAATTAA
Found at i:2227514 original size:24 final size:24
Alignment explanation
Indices: 2227456--2227514 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2227446 TATTTATATA
*
2227456 ATAAAAATTAAATTAAAAAATATT
1 ATAAAAATTAAATTAAAAAATAAT
* * *
2227480 ATTAAATTTAAA-TATAAAATTAAT
1 ATAAAAATTAAATTA-AAAAATAAT
2227504 ATAAAAATTAA
1 ATAAAAATTAA
2227515 TTTTTAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAAAATTAAATTAAAAAATAAT
Found at i:2227515 original size:12 final size:12
Alignment explanation
Indices: 2227456--2227515 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
2227446 TATTTATATA
2227456 ATAAAAATTAA-
1 ATAAAAATTAAT
* *
2227467 ATTAAAAAATATT
1 A-TAAAAATTAAT
* *
2227480 ATTAAATTTAA-
1 ATAAAAATTAAT
2227491 ATATAAAATTAAT
1 ATA-AAAATTAAT
2227504 ATAAAAATTAAT
1 ATAAAAATTAAT
2227516 TTTTAATATT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
11 3 0.08
12 30 0.81
13 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAAAATTAAT
Found at i:2228123 original size:15 final size:16
Alignment explanation
Indices: 2228105--2228146 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2228095 AAGATTAATA
*
2228105 TTTTAAAAAATATATTT
1 TTTTAAAAAATA-AATT
2228122 TTTTAAAAAATAAATT
1 TTTTAAAAAATAAATT
2228138 TTTTAAAAA
1 TTTTAAAAA
2228147 TAATATGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAAATAAATT
Found at i:2228127 original size:17 final size:17
Alignment explanation
Indices: 2228105--2228152 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2228095 AAGATTAATA
2228105 TTTTAAAAAATATATTT
1 TTTTAAAAAATATATTT
*
2228122 TTTTAAAAAATAAATTT
1 TTTTAAAAAATATATTT
*
2228139 TTTAAAAATAATAT
1 TTTTAAAA-AATAT
2228153 GAACATACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAAATATATTT
Found at i:2228571 original size:16 final size:16
Alignment explanation
Indices: 2228549--2228590 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2228539 GATTTTCGAT
*
2228549 TTAAAAATGGTATAAAA
1 TTAAAAATAGTA-AAAA
*
2228566 TAAAAAATAGTAAAAA
1 TTAAAAATAGTAAAAA
2228582 TTAAAAATA
1 TTAAAAATA
2228591 ATTAAGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (16 bp):
TTAAAAATAGTAAAAA
Found at i:2241758 original size:16 final size:18
Alignment explanation
Indices: 2241721--2241767 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2241711 AAACATTGAA
2241721 TAAAT-AATTTT-AATAT
1 TAAATAAATTTTAAATAT
2241737 TAAATAAATTTTAAATA-
1 TAAATAAATTTTAAATAT
2241754 T-AATAAATATTTAA
1 TAAATAAAT-TTTAA
2241768 TAAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.43
17 12 0.43
18 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATAAATTTTAAATAT
Found at i:2241784 original size:18 final size:19
Alignment explanation
Indices: 2241763--2241810 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2241753 ATAATAAATA
2241763 TTTAATAAA-AATA-TATAT
1 TTTAATAAATAATATTAT-T
*
2241781 TTTATTAAATAATATTATT
1 TTTAATAAATAATATTATT
2241800 TTTAATAAATA
1 TTTAATAAATA
2241811 TCTAAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATAAATAATATTATT
Found at i:2241802 original size:19 final size:19
Alignment explanation
Indices: 2241719--2241810 Score: 74
Period size: 17 Copynumber: 5.2 Consensus size: 19
2241709 TAAAACATTG
2241719 AATAA-ATA-ATTTTAAT-
1 AATAATATATATTTTAATA
* *
2241735 ATTAA-ATAAATTTTAA-A
1 AATAATATATATTTTAATA
* *
2241752 TATAATAAATA-TTTAATA
1 AATAATATATATTTTAATA
*
2241770 AA-AATATATATTTTATTA
1 AATAATATATATTTTAATA
2241788 AATAATAT-TATTTTTAATA
1 AATAATATATA-TTTTAATA
2241807 AATA
1 AATA
2241811 TCTAAAAAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.12
17 22 0.37
18 15 0.25
19 16 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATATATATTTTAATA
Found at i:2244299 original size:11 final size:11
Alignment explanation
Indices: 2244285--2244327 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2244275 ATAAATGAGT
*
2244285 TTTAAATAAAC
1 TTTAAACAAAC
**
2244296 TTTAAACAATT
1 TTTAAACAAAC
2244307 TATTAAACAAAC
1 T-TTAAACAAAC
2244319 TTTAAACAA
1 TTTAAACAA
2244328 TTTATAAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
TTTAAACAAAC
Found at i:2244312 original size:23 final size:23
Alignment explanation
Indices: 2244286--2244336 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2244276 TAAATGAGTT
*
2244286 TTAAATAAACTTTAAACAATTTA
1 TTAAACAAACTTTAAACAATTTA
2244309 TTAAACAAACTTTAAACAATTTA
1 TTAAACAAACTTTAAACAATTTA
2244332 -TAAAC
1 TTAAAC
2244337 GAATAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
TTAAACAAACTTTAAACAATTTA
Found at i:2245333 original size:34 final size:32
Alignment explanation
Indices: 2245269--2245333 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
2245259 ATAATAAAAA
* * *
2245269 TATATTAAATTTTATATAATATAAATTATTTT
1 TATATTAAATTTTATAAAAAATAAAATATTTT
2245301 TATATTAAAATTTATATAAAAAATAAAATATTT
1 TATATT-AAATTT-TATAAAAAATAAAATATTT
2245334 CTCATAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 6 0.21
34 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TATATTAAATTTTATAAAAAATAAAATATTTT
Found at i:2248658 original size:30 final size:32
Alignment explanation
Indices: 2248585--2248658 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
2248575 ACTACCTTTG
*
2248585 GTGTCTTCAACACAGGACTCATATTACTTCATTG
1 GTGTCTTCAACACAGGACTCATATTA--TCATTC
* *
2248619 GTTTCTTCAACACAGGACTCTTATTA-CA-TC
1 GTGTCTTCAACACAGGACTCATATTATCATTC
2248649 GTGTCTTCAA
1 GTGTCTTCAA
2248659 TAATTTCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.28
31 2 0.06
34 24 0.67
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (32 bp):
GTGTCTTCAACACAGGACTCATATTATCATTC
Found at i:2250688 original size:25 final size:27
Alignment explanation
Indices: 2250660--2250722 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
2250650 TTGATATGAT
*
2250660 AAATATAT-AATATAATA-TAGTATAA
1 AAATATATAAATATAATATTAATATAA
*
2250685 AAATCATATAAATATTATATTAATATAA
1 AAAT-ATATAAATATAATATTAATATAA
*
2250713 ACATAT-TAAA
1 AAATATATAAA
2250723 AATGTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 10 0.31
28 10 0.31
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATATATAAATATAATATTAATATAA
Found at i:2250777 original size:31 final size:32
Alignment explanation
Indices: 2250718--2250778 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2250708 TATAAACATA
*
2250718 TTAAAAATGTATATAACATAAATTATATTTAT
1 TTAAAAATGTATATAACATAAATAATATTTAT
* * *
2250750 TTAAAATTTTATATAA-ATATATAATATTT
1 TTAAAAATGTATATAACATAAATAATATTT
2250779 TAAATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
TTAAAAATGTATATAACATAAATAATATTTAT
Found at i:2250778 original size:20 final size:20
Alignment explanation
Indices: 2250755--2250796 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2250745 TTTATTTAAA
*
2250755 ATTTTATATA-AATATATAAT
1 ATTTTAAATATAAT-TATAAT
2250775 ATTTTAAATATAATTATAAT
1 ATTTTAAATATAATTATAAT
2250795 AT
1 AT
2250797 AAAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAATATAATTATAAT
Found at i:2251247 original size:25 final size:25
Alignment explanation
Indices: 2251218--2251272 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2251208 TTGTTCTAAA
2251218 TATAATAAATATT-ATTATAATTAAT
1 TATAATAAATATTAATTAT-ATTAAT
* *
2251243 TATAATTAATATTAATTATATTATT
1 TATAATAAATATTAATTATATTAAT
2251268 TATAA
1 TATAA
2251273 AAACAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATAATAAATATTAATTATATTAAT
Found at i:2255697 original size:2 final size:2
Alignment explanation
Indices: 2255690--2255714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2255680 GTGTTACCTT
2255690 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2255715 TTTCTAAGCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2256105 original size:2 final size:2
Alignment explanation
Indices: 2256100--2256135 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2256090 TAGAAAAAGA
* *
2256100 AT AT AT AC AT AC 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
2256136 GGGATTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2257018 original size:16 final size:17
Alignment explanation
Indices: 2257009--2257083 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 17
2256999 ATTAATTTTT
2257009 ATAAAAATTAAATTTAA
1 ATAAAAATTAAATTTAA
2257026 ATAAAAA-T--ATTTGAA
1 ATAAAAATTAAATTT-AA
* *
2257041 TTAATAAATAATAATTTAA
1 ATAA-AAATTA-AATTTAA
*
2257060 AT-TAAATT-AATTTAA
1 ATAAAAATTAAATTTAA
2257075 ATTAAAAAT
1 A-TAAAAAT
2257084 ATTATTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
14 4 0.09
15 13 0.30
16 5 0.11
17 15 0.34
19 3 0.07
20 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
ATAAAAATTAAATTTAA
Found at i:2257057 original size:20 final size:18
Alignment explanation
Indices: 2257025--2257064 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
2257015 ATTAAATTTA
*
2257025 AATAAAAATATTTGAATT
1 AATAAAAATATTTAAATT
2257043 AATAAATAATAATTTAAATT
1 AATAAA-AAT-ATTTAAATT
2257063 AA
1 AA
2257065 ATTAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATAAAAATATTTAAATT
Found at i:2257070 original size:15 final size:15
Alignment explanation
Indices: 2257052--2257080 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2257042 TAATAAATAA
2257052 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
2257067 TAATTTAAATTAAA
1 TAATTTAAATTAAA
2257081 AATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:2257084 original size:34 final size:32
Alignment explanation
Indices: 2257010--2257100 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
2257000 TTAATTTTTA
* * *
2257010 TAAAAAT-TAAATTTAAATAAAAATATTTGAAT
1 TAAAAATAT-AATTTAAATTAAATTATTTAAAT
2257042 TAATAAATAATAATTTAAATTAAATTAATTTAAAT
1 TAA-AAAT-ATAATTTAAATTAAATT-ATTTAAAT
* *
2257077 TAAAAATATTATTTAAATTCAATT
1 TAAAAATATAATTTAAATTAAATT
2257101 TAATACCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.06
33 19 0.38
34 17 0.34
35 11 0.22
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
TAAAAATATAATTTAAATTAAATTATTTAAAT
Found at i:2257095 original size:33 final size:34
Alignment explanation
Indices: 2257019--2257100 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
2257009 ATAAAAATTA
* * *
2257019 AATTTAAATAAAAATATTTGAATTAATAAATAAT
1 AATTTAAATTAAATTATTTAAATTAATAAATAAT
2257053 AATTTAAATTAAATTAATTTAAATTAA-AAAT-AT
1 AATTTAAATTAAATT-ATTTAAATTAATAAATAAT
* *
2257086 TATTTAAATTCAATT
1 AATTTAAATTAAATT
2257101 TAATACCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 15 0.36
34 17 0.40
35 10 0.24
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (34 bp):
AATTTAAATTAAATTATTTAAATTAATAAATAAT
Found at i:2257370 original size:2 final size:2
Alignment explanation
Indices: 2257363--2257401 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2257353 TGATAATGAT
2257363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2257402 TTCTCTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2257777 original size:19 final size:17
Alignment explanation
Indices: 2257736--2257780 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2257726 TCATAGATAT
2257736 TTATATTTAAAATTTTA
1 TTATATTTAAAATTTTA
**
2257753 AAATATTTAATAATTTTTA
1 TTATATTTAA-AA-TTTTA
2257772 TTATATTTA
1 TTATATTTA
2257781 TATTAAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 2 0.09
19 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTAAAATTTTA
Found at i:2259995 original size:170 final size:170
Alignment explanation
Indices: 2259713--2260051 Score: 669
Period size: 170 Copynumber: 2.0 Consensus size: 170
2259703 TTGGTCCCAG
*
2259713 CTTGCATGGAGTTCTTCATTGATTATCATCTTGCTAACTATGCAATGAGTTTGGGTATCTGAAAG
1 CTTGCATGGAGTTCTTCATCGATTATCATCTTGCTAACTATGCAATGAGTTTGGGTATCTGAAAG
2259778 GTCAAACATTTTATTGAGCCGTTCCAGGCTTAGCGAATCATAGGATGAGCTGTAAGTAAAGAGGT
66 GTCAAACATTTTATTGAGCCGTTCCAGGCTTAGCGAATCATAGGATGAGCTGTAAGTAAAGAGGT
2259843 AAGTCCTCAAAGCCTCTTCCTTGATCTTGGCTTTCAGCAA
131 AAGTCCTCAAAGCCTCTTCCTTGATCTTGGCTTTCAGCAA
2259883 CTTGCATGGAGTTCTTCATCGATTATCATCTTGCTAACTATGCAATGAGTTTGGGTATCTGAAAG
1 CTTGCATGGAGTTCTTCATCGATTATCATCTTGCTAACTATGCAATGAGTTTGGGTATCTGAAAG
2259948 GTCAAACATTTTATTGAGCCGTTCCAGGCTTAGCGAATCATAGGATGAGCTGTAAGTAAAGAGGT
66 GTCAAACATTTTATTGAGCCGTTCCAGGCTTAGCGAATCATAGGATGAGCTGTAAGTAAAGAGGT
2260013 AAGTCCTCAAAGCCTCTTCCTTGATCTTGGCTTTCAGCA
131 AAGTCCTCAAAGCCTCTTCCTTGATCTTGGCTTTCAGCA
2260052 TTGCAAGCAC
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 168 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (170 bp):
CTTGCATGGAGTTCTTCATCGATTATCATCTTGCTAACTATGCAATGAGTTTGGGTATCTGAAAG
GTCAAACATTTTATTGAGCCGTTCCAGGCTTAGCGAATCATAGGATGAGCTGTAAGTAAAGAGGT
AAGTCCTCAAAGCCTCTTCCTTGATCTTGGCTTTCAGCAA
Found at i:2267299 original size:2 final size:2
Alignment explanation
Indices: 2267237--2267285 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2267227 ACGATTTTGG
* *
2267237 AT AT -T AT AT AT AT AT AT AT AT AT GT AT GT 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
2267278 AT AT AT AT
1 AT AT AT AT
2267286 GCATATGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2268803 original size:35 final size:35
Alignment explanation
Indices: 2268762--2268830 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2268752 TAAATTTTTT
* * *
2268762 TAAATTTTTTA-TAGATTTAAATTATTATTTAATAA
1 TAAATTTTTTATTAAATTT-AATTATAATATAATAA
2268797 TAAATTTTTTATTAAATTTAATTATAATATAATA
1 TAAATTTTTTATTAAATTTAATTATAATATAATA
2268831 TTTAAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (35 bp):
TAAATTTTTTATTAAATTTAATTATAATATAATAA
Found at i:2270053 original size:20 final size:19
Alignment explanation
Indices: 2270033--2270098 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 19
2270023 TTTTATTATA
2270033 TTATAATTATATTTAAAAT
1 TTATAATTATATTTAAAAT
* *
2270052 ATTTTATATT-TATAT-AAAT
1 -TTATA-ATTATATTTAAAAT
*
2270071 TT-TAA-TATATTAAAAAT
1 TTATAATTATATTTAAAAT
2270088 TTAT-ATTATAT
1 TTATAATTATAT
2270099 AAATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 1 0.03
16 4 0.11
17 9 0.24
18 8 0.22
19 4 0.11
20 8 0.22
21 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATAATTATATTTAAAAT
Found at i:2270058 original size:16 final size:15
Alignment explanation
Indices: 2270039--2270106 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 15
2270029 TATATTATAA
2270039 TTATATTTAAAATATT
1 TTATATTTAAAA-ATT
2270055 TTATATTTATATAAATT
1 TTATATTTA-A-AAATT
2270072 TTAATATATTAAAAA-T
1 TT-ATAT-TTAAAAATT
*
2270088 TTATATTATATAAATT
1 TTATATT-TAAAAATT
2270104 TTA
1 TTA
2270107 ATATATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
16 16 0.36
17 9 0.20
18 7 0.16
19 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:2270074 original size:27 final size:26
Alignment explanation
Indices: 2270017--2270120 Score: 82
Period size: 32 Copynumber: 3.5 Consensus size: 26
2270007 GTATTGTATT
2270017 TATATTTTTTATTATATTATAATTATATTTAA
1 TATA-TTTTTATT-TA-TATAA--AT-TTTAA
*
2270049 AATATTTTATATTTATATAAATTTTAA
1 TATATTTT-TATTTATATAAATTTTAA
2270076 TATATTAAAAATTTATATTATATAAATTTTAA
1 TATATT-----TTTAT-TTATATAAATTTTAA
2270108 TATATTTTTATTT
1 TATATTTTTATTT
2270121 TAATTATTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
26 2 0.03
27 15 0.24
28 2 0.03
30 5 0.08
31 9 0.14
32 30 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATATTTTTATTTATATAAATTTTAA
Found at i:2270077 original size:25 final size:26
Alignment explanation
Indices: 2270049--2270148 Score: 68
Period size: 32 Copynumber: 3.8 Consensus size: 26
2270039 TTATATTTAA
2270049 AATAT-TTTATATTTATATAAATTTT
1 AATATATTTATATTTATATAAATTTT
*
2270074 AATATATTAAAAATTTATATTATATAAATTTT
1 AATATATT-----TATAT-TTATATAAATTTT
* *
2270106 AATATATTTTTATTT-TA-ATTATTTT
1 AATATATTTATATTTATATA-AATTTT
2270131 -A-ATA-TTATATTTATATAA
1 AATATATTTATATTTATATAA
2270149 TCATATATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
22 7 0.11
23 5 0.08
24 3 0.05
25 12 0.20
26 4 0.07
27 5 0.08
31 4 0.07
32 21 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATATTTATATTTATATAAATTTT
Found at i:2270102 original size:15 final size:15
Alignment explanation
Indices: 2270054--2270104 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2270044 TTTAAAATAT
2270054 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
*
2270070 TTT-TAATATATTAAAAA
1 TTTAT-AT-TA-TATAAA
2270087 TTTATATTATATAAA
1 TTTATATTATATAAA
2270102 TTT
1 TTT
2270105 TAATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 10 0.34
16 8 0.28
17 10 0.34
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:2270102 original size:32 final size:35
Alignment explanation
Indices: 2270040--2270113 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 35
2270030 ATATTATAAT
2270040 TATATTTAAAATATTTTATATTTATATAAATTTTAA
1 TATA-TTAAAATATTTTATATTTATATAAATTTTAA
2270076 TATATTAAAA-A-TTTATA-TTATATAAATTTTAA
1 TATATTAAAATATTTTATATTTATATAAATTTTAA
2270108 TATATT
1 TATATT
2270114 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 21 0.55
33 6 0.16
34 1 0.03
35 6 0.16
36 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TATATTAAAATATTTTATATTTATATAAATTTTAA
Found at i:2270130 original size:15 final size:16
Alignment explanation
Indices: 2270101--2270130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2270091 TATTATATAA
2270101 ATTTTAATATATTTTT
1 ATTTTAATATATTTTT
2270117 ATTTTAAT-TATTTT
1 ATTTTAATATATTTT
2270131 AATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTAATATATTTTT
Found at i:2270149 original size:25 final size:24
Alignment explanation
Indices: 2270088--2270164 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 24
2270078 TATTAAAAAT
2270088 TTATA-TTATATAA-ATTTTAATA
1 TTATATTTATATAATATTTTAATA
* *
2270110 -TATTTTTATTTTAATTATTTTAATA
1 TTATATTTA-TATAA-TATTTTAATA
*
2270135 TTATATTTATATAATCATATATAATA
1 TTATATTTATATAAT-AT-TTTAATA
2270161 TTAT
1 TTAT
2270165 TAAATTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.07
22 3 0.07
23 4 0.09
24 1 0.02
25 15 0.35
26 17 0.40
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATATTTATATAATATTTTAATA
Found at i:2274773 original size:16 final size:16
Alignment explanation
Indices: 2274752--2274788 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2274742 TTGTAAGTTC
2274752 TTTTTT-CACTATATAT
1 TTTTTTACA-TATATAT
2274768 TTTTTTACATATATAT
1 TTTTTTACATATATAT
2274784 TTTTT
1 TTTTT
2274789 ATTTAAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTACATATATAT
Found at i:2278741 original size:3 final size:3
Alignment explanation
Indices: 2278733--2278764 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2278723 AATGATTGCC
2278733 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2278765 GGGGCAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2279118 original size:15 final size:15
Alignment explanation
Indices: 2279080--2279150 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
2279070 GTTTTTTTTT
2279080 TATAATATAAATTT-AA
1 TATAATAT--ATTTAAA
2279096 TATAATATATTTAAA
1 TATAATATATTTAAA
**
2279111 TAT--TATATAAAAA
1 TATAATATATTTAAA
2279124 TATAATATATATTAAA
1 TATAATATAT-TTAAA
*
2279140 TATATTATATT
1 TATAATATATT
2279151 AATCATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.24
14 4 0.09
15 11 0.24
16 20 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATATATTTAAA
Found at i:2279130 original size:18 final size:19
Alignment explanation
Indices: 2279109--2279151 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2279099 AATATATTTA
2279109 AATATTATA-TAAAAATAT
1 AATATTATATTAAAAATAT
*
2279127 AATA-TATATTAAATATAT
1 AATATTATATTAAAAATAT
*
2279145 TATATTA
1 AATATTA
2279152 ATCATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 15 0.71
19 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTATATTAAAAATAT
Found at i:2279153 original size:24 final size:24
Alignment explanation
Indices: 2279126--2279183 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
2279116 TATAAAAATA
2279126 TAATATATATTAAATATATTATAT
1 TAATATATATTAAATATATTATAT
2279150 TAATCATAT-TTAAATATATTATAT
1 TAAT-ATATATTAAATATATTATAT
2279174 TAATTATATA
1 TAA-TATATA
2279184 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATATATATTAAATATATTATAT
Found at i:2279190 original size:29 final size:29
Alignment explanation
Indices: 2279140--2279199 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2279130 ATATATTAAA
*
2279140 TATATTATATTAATCATATTTAAATATAT
1 TATATTATATTAATAATATTTAAATATAT
* * *
2279169 TATATTA-ATTATATAATTTTTATATTTAT
1 TATATTATATTA-ATAATATTTAAATATAT
2279198 TA
1 TA
2279200 AATGTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TATATTATATTAATAATATTTAAATATAT
Found at i:2283442 original size:21 final size:21
Alignment explanation
Indices: 2283417--2283466 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2283407 CTCTTTTTTC
*
2283417 ATATACTG-AATTTTTTATTTG
1 ATATA-TGTAATTTTTTATTGG
2283438 ATATATGTTAAATTTTTTATTGG
1 ATATATG-T-AATTTTTTATTGG
2283461 ATATAT
1 ATATAT
2283467 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.20
23 18 0.72
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (21 bp):
ATATATGTAATTTTTTATTGG
Found at i:2284732 original size:25 final size:24
Alignment explanation
Indices: 2284688--2284736 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2284678 TAAAATTTAT
2284688 ATTTAACTTTAAATAATTATCGTAA
1 ATTTAACTTTAAATAATTAT-GTAA
*
2284713 ATTTAA-TTTTAATAATTTATGTAA
1 ATTTAACTTTAAATAA-TTATGTAA
2284737 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTAACTTTAAATAATTATGTAA
Found at i:2284844 original size:36 final size:33
Alignment explanation
Indices: 2284776--2284852 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 33
2284766 ATTTAAAAAT
2284776 AAAAAATATTTATAATTTAATAAAAAATTTATA
1 AAAAAATATTTATAATTTAATAAAAAATTTATA
* *
2284809 TTAAAAATATTTATTATTATTAATTAAAAAA-TTATA
1 -AAAAAATATTTA-TAAT-TTAA-TAAAAAATTTATA
2284845 AAAAAATA
1 AAAAAATA
2284853 AAAACACTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 11 0.30
35 10 0.27
36 9 0.24
37 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAAAATATTTATAATTTAATAAAAAATTTATA
Found at i:2285137 original size:18 final size:18
Alignment explanation
Indices: 2285098--2285216 Score: 55
Period size: 18 Copynumber: 6.2 Consensus size: 18
2285088 TCTGCAATAT
* *
2285098 TATTTTTAATAATATAAT-
1 TATTTTTAA-ATTATTATA
2285116 TATTTTTAAATTATTATA
1 TATTTTTAAATTATTATA
2285134 TATTTATATAAATT-TTATTA
1 TATTT-T-TAAATTATTA-TA
**
2285154 TATTCATAAATTTAATTAT-
1 TATTTTTAAA-TT-ATTATA
*
2285173 TATTATTATAATTATAATTATA
1 TATT-TT-TAA--ATTATTATA
* *
2285195 TAATATTTAAATTATCATA
1 T-ATTTTTAAATTATTATA
2285214 TAT
1 TAT
2285217 AAACTATGAC
Statistics
Matches: 78, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
17 6 0.08
18 20 0.26
19 18 0.23
20 13 0.17
21 14 0.18
22 4 0.05
23 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTTAAATTATTATA
Found at i:2285174 original size:21 final size:21
Alignment explanation
Indices: 2285148--2285193 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2285138 TATATAAATT
2285148 TTATTA-TATTCATAAATT-TAA
1 TTATTATTATT-AT-AATTATAA
2285169 TTATTATTATTATAATTATAA
1 TTATTATTATTATAATTATAA
2285190 TTAT
1 TTAT
2285194 ATAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATTATAATTATAA
Found at i:2285575 original size:30 final size:29
Alignment explanation
Indices: 2285541--2285609 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2285531 TAAAAATATT
2285541 TAATT-AAAA-TATATGAATATATTAAATAAA
1 TAATTAAAAATTATAT--ATATATTAAAT-AA
* *
2285571 TAATTAAAAATTATATTTATATTGAATAA
1 TAATTAAAAATTATATATATATTAAATAA
2285600 TAATTAAAAA
1 TAATTAAAAA
2285610 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 12 0.34
30 14 0.40
31 4 0.11
32 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
TAATTAAAAATTATATATATATTAAATAA
Found at i:2285656 original size:37 final size:36
Alignment explanation
Indices: 2285572--2285687 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 36
2285562 TTAAATAAAT
*
2285572 AATTAAAAATTATATTTATATTGAATAATAATTAA-A-A
1 AATTAAAAATTATATTTATATT-TATAATAA--AATATA
**
2285609 AATTTTAAATTATATTTATATTTCATAATAAAATATA
1 AATTAAAAATTATATTTATATTT-ATAATAAAATATA
* * * *
2285646 TATTAAAAATTAAAAATTATATTTATATTAAAAT-TA
1 AATTAAAAATT-ATATTTATATTTATAATAAAATATA
2285682 AATTAA
1 AATTAA
2285688 TAAAATAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
35 2 0.03
36 8 0.12
37 45 0.69
38 10 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTAAAAATTATATTTATATTTATAATAAAATATA
Found at i:2285666 original size:19 final size:19
Alignment explanation
Indices: 2285638--2285698 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 19
2285628 ATTTCATAAT
2285638 AAAATATATATTAAAAATTA
1 AAAAT-TATATTAAAAATTA
* *
2285658 AAAATTATATT-TATATT-
1 AAAATTATATTAAAAATTA
* *
2285675 AAAATTAAATTAATAAAATA
1 AAAATTATATTAA-AAATTA
2285695 AAAA
1 AAAA
2285699 AAAGAGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 10 0.31
18 4 0.12
19 9 0.28
20 9 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATATTAAAAATTA
Found at i:2285693 original size:38 final size:38
Alignment explanation
Indices: 2285624--2285699 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
2285614 TAAATTATAT
* *
2285624 TTATATTTCATAATAAAATATATATTAAAAATTAAAAA
1 TTATATTTCATAATAAAATATAAATTAAAAATAAAAAA
*
2285662 TTATATTT-ATATTAAAAT-TAAATTAATAAAATAAAAAA
1 TTATATTTCATAATAAAATATAAATT-A-AAAATAAAAAA
2285700 AAGAGGCCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.15
37 10 0.30
38 18 0.55
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (38 bp):
TTATATTTCATAATAAAATATAAATTAAAAATAAAAAA
Found at i:2285697 original size:44 final size:44
Alignment explanation
Indices: 2285606--2285698 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
2285596 ATAATAATTA
** * * *
2285606 AAAAATTTTAAATTATATTTATATTTCATAATAAAATATATATT
1 AAAAATTAAAAATTATATTTATATTTCAAAATAAAATATAAAAT
*
2285650 AAAAATTAAAAATTATATTTATA-TT-AAAATTAAATTAATAAAAT
1 AAAAATTAAAAATTATATTTATATTTCAAAA-TAAAAT-ATAAAAT
2285694 AAAAA
1 AAAAA
2285699 AAAGAGGCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.07
43 7 0.17
44 31 0.76
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (44 bp):
AAAAATTAAAAATTATATTTATATTTCAAAATAAAATATAAAAT
Found at i:2287831 original size:4 final size:4
Alignment explanation
Indices: 2287822--2287848 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2287812 GTTTCATCTG
2287822 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2287849 CACTTGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2296119 original size:2 final size:2
Alignment explanation
Indices: 2296112--2296146 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2296102 TTATAAATAA
* *
2296112 AT AT AT AT AT TT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2296147 AAGAATGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2297790 original size:2 final size:2
Alignment explanation
Indices: 2297783--2297820 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2297773 TTATTTAGGG
*
2297783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2297821 GTGGATGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2299003 original size:20 final size:19
Alignment explanation
Indices: 2298975--2299013 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2298965 AGTAGCAAAA
*
2298975 TTAATTTTATATACTTTTTT
1 TTAAATTTATATA-TTTTTT
*
2298995 TTAAATTTATTTATTTTTT
1 TTAAATTTATATATTTTTT
2299014 AATGAGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTAAATTTATATATTTTTT
Found at i:2299087 original size:22 final size:21
Alignment explanation
Indices: 2299062--2299104 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2299052 ATATTATATC
2299062 ATTAA-ATTAGATATATATTTTT
1 ATTAATATTA-AT-TATATTTTT
2299084 ATTAATTATTAATTATATTTT
1 ATTAA-TATTAATTATATTTT
2299105 ATAGTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.68
23 2 0.11
24 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTAATATTAATTATATTTTT
Found at i:2299773 original size:10 final size:10
Alignment explanation
Indices: 2299758--2299787 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2299748 TAATTCTTTA
2299758 AATATATAAT
1 AATATATAAT
2299768 AATATATAAT
1 AATATATAAT
2299778 AATAT-TAAT
1 AATATATAAT
2299787 A
1 A
2299788 TTCAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATATAAT
Found at i:2302371 original size:2 final size:2
Alignment explanation
Indices: 2302364--2302400 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2302354 AATAATTAAA
*
2302364 AG AG AG AG AG AG AC 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 AG AG AG AG A
2302401 AGTTGAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2302870 original size:14 final size:13
Alignment explanation
Indices: 2302806--2302893 Score: 51
Period size: 13 Copynumber: 6.7 Consensus size: 13
2302796 ACATAATTAA
2302806 AAAATTAT-ATA-
1 AAAATTATAATAT
2302817 AAAATTA-AATAAT
1 AAAATTATAAT-AT
2302830 AAAA-TATAATAT
1 AAAATTATAATAT
* *
2302842 ATAA-TATATTTAT
1 AAAATTATA-ATAT
2302855 AAAATTATAATGAT
1 AAAATTATAAT-AT
* *
2302869 AATTAACTTTTAAAAT
1 AA--AA-TTATAATAT
2302885 AAAATTATA
1 AAAATTATA
2302894 CTCATTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
11 9 0.15
12 12 0.20
13 18 0.30
14 10 0.17
16 6 0.10
17 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (13 bp):
AAAATTATAATAT
Found at i:2303689 original size:28 final size:28
Alignment explanation
Indices: 2303650--2303738 Score: 107
Period size: 27 Copynumber: 3.3 Consensus size: 28
2303640 TTTATTAAAT
*
2303650 TAATT-ATCAAAATATTATTATTTTATA
1 TAATTAATCAAAATATTAATATTTTATA
*
2303677 TATATTAAT-AAAATAATAATATTTT-TA
1 TA-ATTAATCAAAATATTAATATTTTATA
2303704 TAA-TAATTCAAAATATTAATATTTTA-A
1 TAATTAA-TCAAAATATTAATATTTTATA
2303731 TAATTAAT
1 TAATTAAT
2303739 TTAATAAACG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 26 0.49
28 20 0.38
29 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATTAATCAAAATATTAATATTTTATA
Found at i:2303992 original size:2 final size:2
Alignment explanation
Indices: 2303985--2304024 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2303975 ATCTGATACA
* *
2303985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2304025 TTTGATTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2310677 original size:15 final size:15
Alignment explanation
Indices: 2310659--2310719 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 15
2310649 AATATGTTTT
2310659 TAATTTATTTTTTAA
1 TAATTTATTTTTTAA
*
2310674 TAATTAATCATATTTTCAA
1 TAATT--T-AT-TTTTTAA
*
2310693 TAA-GTATTTTTTAA
1 TAATTTATTTTTTAA
2310707 TAATATTATTTTT
1 TAAT-TTATTTTT
2310720 AAAATATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
14 9 0.25
15 7 0.19
16 8 0.22
17 1 0.03
18 2 0.06
19 9 0.25
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (15 bp):
TAATTTATTTTTTAA
Found at i:2310713 original size:13 final size:13
Alignment explanation
Indices: 2310641--2310718 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
2310631 TTCTTATTAT
2310641 TTTTTTAA-AATA
1 TTTTTTAATAATA
*
2310653 TGTTTTTAAT-TTA
1 T-TTTTTAATAATA
2310666 TTTTTTAATAATTAA
1 TTTTTTAATAA-T-A
2310681 TCATATTTTCAATAAGTA
1 T--T-TTTT-AATAA-TA
2310699 TTTTTTAATAATA
1 TTTTTTAATAATA
2310712 TTATTTT
1 TT-TTTT
2310719 TAAAATATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
12 9 0.17
13 14 0.26
14 10 0.19
15 6 0.11
16 1 0.02
17 1 0.02
18 6 0.11
19 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTTTAATAATA
Found at i:2311237 original size:15 final size:15
Alignment explanation
Indices: 2311215--2311248 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2311205 TCTGTATTAT
2311215 ATTT-ATATAATCAA
1 ATTTAATATAATCAA
*
2311229 ATTTAATATTATCAA
1 ATTTAATATAATCAA
2311244 ATTTA
1 ATTTA
2311249 TTTAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAATATAATCAA
Found at i:2311272 original size:20 final size:20
Alignment explanation
Indices: 2311247--2311289 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2311237 TTATCAAATT
*
2311247 TATTTAAATTTGAT-TAAAAA
1 TATTT-AATTTAATATAAAAA
2311267 TATTTAATTTAATATAAAAA
1 TATTTAATTTAATATAAAAA
2311287 TAT
1 TAT
2311290 AATTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTTAATTTAATATAAAAA
Found at i:2315757 original size:25 final size:26
Alignment explanation
Indices: 2315712--2315763 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2315702 TCAAGTATAT
2315712 TCACATAAAATATAAAAATAAAAATA
1 TCACATAAAATATAAAAATAAAAATA
*
2315738 TCAC-TAAAA-ATAAGAGATAAAAATA
1 TCACATAAAATATAA-AAATAAAAATA
2315763 T
1 T
2315764 AAAAATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (26 bp):
TCACATAAAATATAAAAATAAAAATA
Found at i:2316685 original size:3 final size:3
Alignment explanation
Indices: 2316679--2316705 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2316669 CAACAACAAC
2316679 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2316706 TCTTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2318582 original size:17 final size:18
Alignment explanation
Indices: 2318552--2318586 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2318542 CAATTTAGTT
2318552 TAATGAATTATTATTTAA
1 TAATGAATTATTATTTAA
*
2318570 TAAT-AATTTTTATTTAA
1 TAATGAATTATTATTTAA
2318587 ATTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAATGAATTATTATTTAA
Found at i:2318614 original size:28 final size:26
Alignment explanation
Indices: 2318589--2318660 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 26
2318579 TTATTTAAAT
*
2318589 TTAATTATAAAATATATAAATATTAATA
1 TTAA-TATAAAA-ATAAAAATATTAATA
*
2318617 TTAATATAAAAATAAAAATA--AAAA
1 TTAATATAAAAATAAAAATATTAATA
* *
2318641 TAAAAATAAAAATAAAAATA
1 TTAATATAAAAATAAAAATA
2318661 AATTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 21 0.52
26 8 0.20
27 7 0.17
28 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TTAATATAAAAATAAAAATATTAATA
Found at i:2318631 original size:6 final size:6
Alignment explanation
Indices: 2318622--2318662 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
2318612 TAATATTAAT
2318622 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
2318663 TTTTTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:2320387 original size:2 final size:2
Alignment explanation
Indices: 2320380--2320411 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2320370 GTCTTAACAA
2320380 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
2320412 TTGCCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2322544 original size:29 final size:29
Alignment explanation
Indices: 2322476--2322536 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2322466 TTTGTCTATT
*
2322476 AAAATATATAAAATTATTTCATATTATAAA
1 AAAAT-TATAAAATTATATCATATTATAAA
* *
2322506 AAAATCATAAGATTATAT-ATATT-TAAA
1 AAAATTATAAAATTATATCATATTATAAA
2322533 AAAA
1 AAAA
2322537 ATGTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 10 0.36
30 5 0.18
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTATAAAATTATATCATATTATAAA
Found at i:2323578 original size:2 final size:2
Alignment explanation
Indices: 2323571--2323600 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2323561 CAAGATTTTC
2323571 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
2323601 CATCAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2325471 original size:30 final size:29
Alignment explanation
Indices: 2325424--2325482 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
2325414 GTAAAGATTG
2325424 CATTTGAAAAATATTGAATCAAAAGAAAAT
1 CATTTGAAAAATATTGAATCAAAA-AAAAT
* *
2325454 CATTTG-AAACTATTTGAATCTAAAAAAAT
1 CATTTGAAAAATA-TTGAATCAAAAAAAAT
2325483 TTGAGTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (29 bp):
CATTTGAAAAATATTGAATCAAAAAAAAT
Found at i:2325865 original size:22 final size:22
Alignment explanation
Indices: 2325835--2325879 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2325825 TTAATATAAT
*
2325835 TATATATTTAAAAGATTTAAAA
1 TATAAATTTAAAAGATTTAAAA
* * *
2325857 TATAAATTTTAAATATTTTAAA
1 TATAAATTTAAAAGATTTAAAA
2325879 T
1 T
2325880 TTATTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATAAATTTAAAAGATTTAAAA
Found at i:2326728 original size:2 final size:2
Alignment explanation
Indices: 2326715--2326748 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2326705 CCTATATGCA
*
2326715 TC TC TC TG 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
2326749 CACTGTTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2331274 original size:12 final size:12
Alignment explanation
Indices: 2331257--2331287 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2331247 AAAATATTAA
2331257 TATAATAAAATT
1 TATAATAAAATT
2331269 TATAATAAAATT
1 TATAATAAAATT
*
2331281 AATAATA
1 TATAATA
2331288 TATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TATAATAAAATT
Found at i:2331289 original size:17 final size:17
Alignment explanation
Indices: 2331269--2331302 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2331259 TAATAAAATT
2331269 TATAATAAAATTAATAA
1 TATAATAAAATTAATAA
* *
2331286 TATATTAAAATTTATAA
1 TATAATAAAATTAATAA
2331303 AAAAATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATAAAATTAATAA
Found at i:2331315 original size:29 final size:29
Alignment explanation
Indices: 2331247--2331329 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
2331237 ATATGATGTG
*
2331247 AAAATA-TTAATATAATAAAATTTATAAT
1 AAAATATTTAATATAATAAAATTTATAAA
* *
2331275 AAAAT-TAATAATATATTAAAATTTATAAA
1 AAAATAT-TTAATATAATAAAATTTATAAA
*
2331304 AAAATATTTAATTTTAAATAAAATTT
1 AAAATATTTAA-TAT-AATAAAATTT
2331330 TGATGAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 5 0.11
29 27 0.61
30 3 0.07
31 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATATTTAATATAATAAAATTTATAAA
Found at i:2333502 original size:23 final size:23
Alignment explanation
Indices: 2333466--2333524 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2333456 AATTACATTT
* *
2333466 TATAT-ATAGAATAA-ATAAAAC
1 TATATAATATAATAATATAAAAA
*
2333487 TATATTAATATAATAATTTAAAAA
1 TATA-TAATATAATAATATAAAAA
2333511 TATATAATATAATA
1 TATATAATATAATA
2333525 TATTATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 1 0.03
23 18 0.56
24 9 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TATATAATATAATAATATAAAAA
Found at i:2333602 original size:24 final size:24
Alignment explanation
Indices: 2333555--2333599 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2333545 ATATAACATG
* *
2333555 TAATATACAATTATTTTTATTTAA
1 TAATATACAATAATTTATATTTAA
2333579 TAATATA-AATAATTTATATTT
1 TAATATACAATAATTTATATTT
2333600 TAAAACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATATACAATAATTTATATTTAA
Found at i:2334290 original size:2 final size:2
Alignment explanation
Indices: 2334283--2334326 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2334273 AATAAGAGTT
2334283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2334325 TA
1 TA
2334327 ATTGTCAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2335258 original size:15 final size:17
Alignment explanation
Indices: 2335220--2335258 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2335210 ATATAAATAT
2335220 AATATATAAAAATTTTA
1 AATATATAAAAATTTTA
2335237 AATATATAAAAATTTTA
1 AATATATAAAAATTTTA
2335254 AATAT
1 AATAT
2335259 GAATTCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATAAAAATTTTA
Done.