Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:2802390 original size:2 final size:2
Alignment explanation
Indices: 2802383--2802426 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2802373 AAGTTTCATC
* *
2802383 AT AT AT AT AT AT A- AG AT AT AT AT AT AT GT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2802423 AT AT
1 AT AT
2802427 TTTCGAGTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2803913 original size:5 final size:5
Alignment explanation
Indices: 2803891--2803946 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
2803881 AAAAATTTTA
* **
2803891 TAATT TAAATT T-ATT TAATT TAATT TAATT TAAAT CGATT TAAATT TAATT
1 TAATT T-AATT TAATT TAATT TAATT TAATT TAATT TAATT T-AATT TAATT
2803942 TAATT
1 TAATT
2803947 ATAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 4 0.10
5 29 0.69
6 9 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (5 bp):
TAATT
Found at i:2803957 original size:26 final size:25
Alignment explanation
Indices: 2803891--2803962 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
2803881 AAAAATTTTA
**
2803891 TAATTTAAATTTATTTAATTTAATT
1 TAATTTAAATCAATTTAATTTAATT
*
2803916 TAATTTAAATCGATTTAAATTTAATT
1 TAATTTAAATCAATTT-AATTTAATT
*
2803942 TAATTATAAAT-AATTTTATTT
1 TAATT-TAAATCAATTTAATTT
2803963 TTTTAACTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.44
26 18 0.44
27 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (25 bp):
TAATTTAAATCAATTTAATTTAATT
Found at i:2805377 original size:2 final size:2
Alignment explanation
Indices: 2805370--2805409 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2805360 TAAAATCAAT
2805370 TA TA TA TA TA TA TA TA TA TA T- 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 TA T
2805410 CTCAGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2805394 original size:21 final size:21
Alignment explanation
Indices: 2805368--2805409 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2805358 CATAAAATCA
2805368 ATTATATATATATATATATAT
1 ATTATATATATATATATATAT
2805389 ATTATATATATATATATATAT
1 ATTATATATATATATATATAT
2805410 CTCAGGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATATATATATATATATAT
Found at i:2809276 original size:20 final size:18
Alignment explanation
Indices: 2809243--2809287 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
2809233 AAATAAAAAT
*
2809243 TATAAAATAAAACATAACA
1 TATATAATAAAACATAA-A
*
2809262 TAATATAATATAACATAAA
1 T-ATATAATAAAACATAAA
2809281 TATATAA
1 TATATAA
2809288 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 14 0.61
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (18 bp):
TATATAATAAAACATAAA
Found at i:2809287 original size:13 final size:13
Alignment explanation
Indices: 2809202--2809287 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
2809192 ATAATTTTAA
*
2809202 ATATAACATAATT
1 ATATAACATAAAT
* * *
2809215 ATATGATATAATAA
1 ATATAACATAA-AT
* *
2809229 AAATAA-ATAAAA
1 ATATAACATAAAT
*
2809241 ATTATAAAATAAA-
1 A-TATAACATAAAT
*
2809254 ACATAACATAATAT
1 ATATAACATAA-AT
2809268 AATATAACATAAAT
1 -ATATAACATAAAT
2809282 ATATAA
1 ATATAA
2809288 ATTTATTAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
12 11 0.19
13 25 0.44
14 11 0.19
15 10 0.18
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (13 bp):
ATATAACATAAAT
Found at i:2812342 original size:26 final size:26
Alignment explanation
Indices: 2812311--2812365 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2812301 GTTACTTAAT
2812311 ATTAAAAAAATTTAAATAAATAA-AAA
1 ATTAAAAAAATTTAAA-AAATAATAAA
***
2812337 ATTAAATTTATTTAAAAAATAATAAA
1 ATTAAAAAAATTTAAAAAATAATAAA
2812363 ATT
1 ATT
2812366 TTAATTCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTAAAAAAATTTAAAAAATAATAAA
Found at i:2812352 original size:22 final size:21
Alignment explanation
Indices: 2812317--2812366 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2812307 TAATATTAAA
2812317 AAAATTTAAATAAATAAAAAAT
1 AAAATTTAAATAAA-AAAAAAT
* ** *
2812339 TAAATTTATTTAAAAAATAAT
1 AAAATTTAAATAAAAAAAAAT
2812360 AAAATTT
1 AAAATTT
2812367 TAATTCTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTTAAATAAAAAAAAAT
Found at i:2812438 original size:26 final size:24
Alignment explanation
Indices: 2812399--2812462 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
2812389 AGTTATTTAT
*
2812399 TTTATAATTATATAATA-TATATTAAA
1 TTTAT-ATTTTATAATATTA-ATT-AA
2812425 TTTATATTTT-TATATATTAATTAA
1 TTTATATTTTATA-ATATTAATTAA
*
2812449 TTTTTATTTTATAA
1 TTTATATTTTATAA
2812463 AAATTACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 14 0.42
25 12 0.36
26 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATATTTTATAATATTAATTAA
Found at i:2812440 original size:21 final size:18
Alignment explanation
Indices: 2812414--2812455 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
2812404 AATTATATAA
2812414 TATATATTAAATTTATATTTT
1 TATATATT-AA-TTA-ATTTT
2812435 TATATATTAATTAATTTT
1 TATATATTAATTAATTTT
2812453 TAT
1 TAT
2812456 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
20 2 0.10
21 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATTAATTAATTTT
Found at i:2812559 original size:33 final size:32
Alignment explanation
Indices: 2812495--2812563 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
2812485 ATATAAATAT
**
2812495 TAAAAATATATTATTTAAAATTTAAAATTTAA
1 TAAAAATATATTATTTAAAAAATAAAATTTAA
*
2812527 TAAAAATAT-TATATTATAAAAAATAAATTTTAA
1 TAAAAATATAT-TATT-TAAAAAATAAAATTTAA
2812560 -AAAA
1 TAAAA
2812564 TAATTCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.03
32 17 0.53
33 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAATATATTATTTAAAAAATAAAATTTAA
Found at i:2812625 original size:31 final size:31
Alignment explanation
Indices: 2812583--2812666 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
2812573 AATAATATAA
* *
2812583 ATAAATGTAAATAAATTTAAATTATA-TATTT
1 ATAAATTTAAATAAATTTAAATTATATTA-AT
**
2812614 ATAAATTTAAATAAATAAAAATTATATTAAT
1 ATAAATTTAAATAAATTTAAATTATATTAAT
*
2812645 ATTAAATTTAAATTTAATTTAA
1 A-TAAATTTAAA-TAAATTTAA
2812667 TTTGAGAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 25 0.58
32 12 0.28
33 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
ATAAATTTAAATAAATTTAAATTATATTAAT
Found at i:2812629 original size:10 final size:10
Alignment explanation
Indices: 2812580--2812629 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2812570 AATAATAATA
*
2812580 TAAATAAATG
1 TAAATAAATT
2812590 TAAATAAATT
1 TAAATAAATT
2812600 TAAATTATATATT
1 TAAA-TA-A-ATT
2812613 T--ATAAATT
1 TAAATAAATT
2812621 TAAATAAAT
1 TAAATAAAT
2812630 AAAAATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 4 0.12
9 1 0.03
10 21 0.62
11 3 0.09
12 1 0.03
13 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TAAATAAATT
Found at i:2819292 original size:20 final size:20
Alignment explanation
Indices: 2819264--2819303 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2819254 AATTAAATGT
*
2819264 TTATTTTTATTCAT-TATTTA
1 TTATATTTATT-ATGTATTTA
2819284 TTATATTTATTATGTATTTA
1 TTATATTTATTATGTATTTA
2819304 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATATTTATTATGTATTTA
Found at i:2819676 original size:14 final size:14
Alignment explanation
Indices: 2819657--2819690 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2819647 CAGAAAGTCT
2819657 GAAAAAAAAAAAAG
1 GAAAAAAAAAAAAG
*
2819671 GAAAAAAAAAAGAG
1 GAAAAAAAAAAAAG
2819685 GAAAAA
1 GAAAAA
2819691 CAATTAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAAG
Found at i:2819689 original size:12 final size:13
Alignment explanation
Indices: 2819659--2819690 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
2819649 GAAAGTCTGA
2819659 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
2819672 AAAAAAAAAAGAGG
1 AAAAAAAAAA-AGG
2819686 AAAAA
1 AAAAA
2819691 CAATTAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:2820130 original size:20 final size:20
Alignment explanation
Indices: 2820093--2820130 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2820083 GTTAATAAAT
*
2820093 ATATATTTTTATTTTTATTC
1 ATATATTTTTATTCTTATTC
2820113 ATAT-TTTTTATATCTTAT
1 ATATATTTTTAT-TCTTAT
2820131 CAATTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATATTTTTATTCTTATTC
Found at i:2821485 original size:18 final size:19
Alignment explanation
Indices: 2821462--2821499 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2821452 AATTACATAT
2821462 AATTTTATATTTA-AATCA
1 AATTTTATATTTATAATCA
*
2821480 AATTTTTTATTTATAATCA
1 AATTTTATATTTATAATCA
2821499 A
1 A
2821500 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTTATATTTATAATCA
Found at i:2821802 original size:2 final size:2
Alignment explanation
Indices: 2821789--2821822 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2821779 CCAACTCTTA
*
2821789 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2821823 GTAACATATG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2822480 original size:36 final size:36
Alignment explanation
Indices: 2822401--2822480 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
2822391 TTTTTACCTA
*
2822401 TTAATA-TTAATCAATATTACAGTTATTACAAATGT
1 TTAATATTTAATCAACATTACAGTTATTACAAATGT
**
2822436 TTTTTATTTAATCAACA-TAGCAGTTATTACAAATGT
1 TTAATATTTAATCAACATTA-CAGTTATTACAAATGT
2822472 TTAATATTT
1 TTAATATTT
2822481 TAAAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
35 6 0.16
36 32 0.84
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (36 bp):
TTAATATTTAATCAACATTACAGTTATTACAAATGT
Found at i:2822662 original size:31 final size:31
Alignment explanation
Indices: 2822582--2822663 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
2822572 TAATAATAAG
* *
2822582 TTATTAT-ATTTTAAAATATTTGTATATTTAT
1 TTATTATAATTTTAAAAT-TTTGGATATTAAT
**
2822613 TTATTATAATTAAAAAATTTTGGATATTAAAT
1 TTATTATAATTTTAAAATTTTGGATATT-AAT
2822645 TT-TTATAATTTTAAAATTT
1 TTATTATAATTTTAAAATTT
2822664 ATATTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
31 31 0.72
32 12 0.28
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (31 bp):
TTATTATAATTTTAAAATTTTGGATATTAAT
Found at i:2823577 original size:21 final size:22
Alignment explanation
Indices: 2823553--2823607 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2823543 AATATATAAA
2823553 TATATATATA-TTATATGA-AT
1 TATATATATACTTATATGACAT
* *
2823573 GTATATGTATACGTTATATTACAT
1 -TATATATATAC-TTATATGACAT
2823597 TATATATATAC
1 TATATATATAC
2823608 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.32
23 17 0.61
24 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (22 bp):
TATATATATACTTATATGACAT
Found at i:2827246 original size:19 final size:18
Alignment explanation
Indices: 2827214--2827270 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
2827204 ATATAATATA
2827214 ATGTAAAAAAAATTTAAT
1 ATGTAAAAAAAATTTAAT
2827232 ATGTAAAATAAAATTTAAT
1 ATGTAAAA-AAAATTTAAT
*
2827251 ATGATATAAAAAA-TTAAT
1 ATG-TAAAAAAAATTTAAT
2827269 AT
1 AT
2827271 TTTATACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 15 0.42
19 17 0.47
20 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
ATGTAAAAAAAATTTAAT
Found at i:2828780 original size:8 final size:8
Alignment explanation
Indices: 2828767--2828855 Score: 67
Period size: 8 Copynumber: 10.5 Consensus size: 8
2828757 TTAAAATATA
2828767 ATATAAAT
1 ATATAAAT
2828775 ATATAAAT
1 ATATAAAT
2828783 ATATTATTAAT
1 ATA-TA--AAT
2828794 ATAATAAATTT
1 AT-ATAAA--T
2828805 ATATAAAT
1 ATATAAAT
2828813 ATA-AAAT
1 ATATAAAT
*
2828820 ATATTAA-
1 ATATAAAT
*
2828827 ATATGAAT
1 ATATAAAT
2828835 ATAATAAA-
1 AT-ATAAAT
2828843 ATAATAAAT
1 AT-ATAAAT
2828852 ATAT
1 ATAT
2828856 GGAATCAAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
7 13 0.19
8 29 0.43
9 10 0.15
10 5 0.07
11 10 0.15
12 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:2828797 original size:17 final size:18
Alignment explanation
Indices: 2828760--2828855 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 18
2828750 AAATTAATTA
* *
2828760 AAATATAATATAAATATAT
1 AAATATATTATTAA-ATAT
2828779 AAATATATTATT-AATAT
1 AAATATATTATTAAATAT
*
2828796 -AATAAATTTATATAAATAT
1 AAATATA-TTAT-TAAATAT
2828815 AAA-ATA-TATTAAATAT
1 AAATATATTATTAAATAT
* *
2828831 GAATATA--ATAAAATAAT
1 AAATATATTATTAAAT-AT
2828848 AAATATAT
1 AAATATAT
2828856 GGAATCAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
16 20 0.32
17 22 0.35
18 2 0.03
19 17 0.27
20 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
AAATATATTATTAAATAT
Found at i:2830210 original size:2 final size:2
Alignment explanation
Indices: 2830199--2830228 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2830189 TCATCATGGT
2830199 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2830229 GAAGAATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2830422 original size:27 final size:27
Alignment explanation
Indices: 2830313--2830427 Score: 83
Period size: 28 Copynumber: 4.2 Consensus size: 27
2830303 TGTAATTTAA
* * *
2830313 ATAATAT-AATTTATTAATATATTAAAT
1 ATAATATAAATATATAAAT-TAATAAAT
* *
2830340 ATTATATAAATATATAATATT-TTAAAT
1 ATAATATAAATATATAA-ATTAATAAAT
* * *
2830367 AAAATTATAAAAAGTA-AAAATATATAAAT
1 ATAA-TATAAATA-TATAAATTA-ATAAAT
2830396 ATAATATAAATATATAAATTAATAAAT
1 ATAATATAAATATATAAATTAATAAAT
*
2830423 TTAAT
1 ATAAT
2830428 TATTAATCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
27 28 0.41
28 29 0.42
29 12 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAATATAAATATATAAATTAATAAAT
Found at i:2830689 original size:35 final size:32
Alignment explanation
Indices: 2830621--2830691 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 32
2830611 TTTTAGTTTT
* *
2830621 TAAAATTAAAAATAAAATATATTTTTATATTA
1 TAAAAATAAAAATAAAATAGATTTTTATATTA
2830653 TAAAAATAAAAATTTAATAATAGATTTTTA-ACTTA
1 TAAAAATAAAAA--TAA-AATAGATTTTTATA-TTA
2830688 TAAA
1 TAAA
2830692 TTAAAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 11 0.33
34 4 0.12
35 18 0.55
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
TAAAAATAAAAATAAAATAGATTTTTATATTA
Found at i:2831898 original size:33 final size:36
Alignment explanation
Indices: 2831838--2831908 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 36
2831828 TTAAATTACT
2831838 ATTTAATAATAAAAATATATATTTTTAAA-AATTAAA
1 ATTTAATAATAAAAATATATATTTTTAAATAA-TAAA
*
2831874 ATTTAA-AATATAAA-A-ATATTTTTAAATAATAAA
1 ATTTAATAATAAAAATATATATTTTTAAATAATAAA
2831907 AT
1 AT
2831909 AAGTCATGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 17 0.52
34 3 0.09
35 7 0.21
36 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
ATTTAATAATAAAAATATATATTTTTAAATAATAAA
Found at i:2834250 original size:11 final size:11
Alignment explanation
Indices: 2834234--2834310 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
2834224 ATATATTAAA
2834234 TTTATTATATT
1 TTTATTATATT
2834245 TTTATTATATT
1 TTTATTATATT
*
2834256 ATTA-TA-ATT
1 TTTATTATATT
2834265 TTTATT-TATT
1 TTTATTATATT
* *
2834275 AAATATATAATATT
1 ---TTTATTATATT
*
2834289 TATATTATATT
1 TTTATTATATT
*
2834300 TTAATTA-ATT
1 TTTATTATATT
2834310 T
1 T
2834311 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
9 6 0.11
10 10 0.19
11 29 0.55
13 4 0.08
14 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATTATATT
Found at i:2834259 original size:19 final size:19
Alignment explanation
Indices: 2834235--2834275 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2834225 TATATTAAAT
2834235 TTATTAT-ATTTTTATTATA
1 TTATTATAATTTTTATT-TA
2834254 TTATTATAATTTTTATTTA
1 TTATTATAATTTTTATTTA
2834273 TTA
1 TTA
2834276 AATATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATAATTTTTATTTA
Found at i:2839463 original size:60 final size:60
Alignment explanation
Indices: 2839389--2839513 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
2839379 TTTTATGTAT
* * *
2839389 TAATAATTATTATTATATAAATTTTACAATTTATATATTTATCATTCA-TATAATTTTATC
1 TAATAATTATTATTATATAAATTTTAAAATTTATACATTTATCATT-AGTATAATCTTATC
*
2839449 TAATAATT-TATATTATATAAATTTTAAAATTTATGCATTTATCATTAGTATAATCTTATC
1 TAATAATTAT-TATTATATAAATTTTAAAATTTATACATTTATCATTAGTATAATCTTATC
2839509 TAATA
1 TAATA
2839514 TTCTCAAAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
59 2 0.03
60 57 0.97
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (60 bp):
TAATAATTATTATTATATAAATTTTAAAATTTATACATTTATCATTAGTATAATCTTATC
Found at i:2841653 original size:2 final size:2
Alignment explanation
Indices: 2841648--2841673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2841638 CCCCCCCCCC
2841648 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2841674 TAGCTTATTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2841814 original size:11 final size:11
Alignment explanation
Indices: 2841798--2841823 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2841788 ATAAACTAAC
2841798 AAGTTCTGCAA
1 AAGTTCTGCAA
2841809 AAGTTCTGCAA
1 AAGTTCTGCAA
2841820 AAGT
1 AAGT
2841824 CATGAACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (11 bp):
AAGTTCTGCAA
Found at i:2846419 original size:2 final size:2
Alignment explanation
Indices: 2846412--2846448 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2846402 AAGACCGGAT
*
2846412 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2846449 ACCCGACTTA
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2846748 original size:21 final size:21
Alignment explanation
Indices: 2846705--2846757 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2846695 TTGGTTTGAT
* *
2846705 TTTAAAATAATTATATATAATA
1 TTTAAAA-AATAAAATATAATA
*
2846727 TTTAAAAAATAAAATATTATA
1 TTTAAAAAATAAAATATAATA
* *
2846748 TATAATAAAT
1 TTTAAAAAAT
2846758 TTATTTGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAAAATAAAATATAATA
Found at i:2853389 original size:13 final size:13
Alignment explanation
Indices: 2853371--2853400 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2853361 GCTTAAAGGC
2853371 TTTTTTTTTTAAT
1 TTTTTTTTTTAAT
2853384 TTTTTTTTTTAAT
1 TTTTTTTTTTAAT
2853397 TTTT
1 TTTT
2853401 AAACATCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTAAT
Found at i:2854081 original size:16 final size:15
Alignment explanation
Indices: 2854035--2854088 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
2854025 ACCAACAGTC
2854035 AATATATAAATTTT-
1 AATATATAAATTTTA
*
2854049 AATATATTAATAATTTA
1 AATATA-TAA-ATTTTA
2854066 AATTATATAAATTTTA
1 AA-TATATAAATTTTA
2854082 AA-ATATA
1 AATATATA
2854089 TTTATATCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 11 0.32
15 3 0.09
16 11 0.32
17 5 0.15
18 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATAAATTTTA
Found at i:2854089 original size:16 final size:16
Alignment explanation
Indices: 2854035--2854089 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
2854025 ACCAACAGTC
2854035 AATATATAAATTTTAA
1 AATATATAAATTTTAA
* *
2854051 TATAT-TAATAATTTAA
1 AATATATAA-ATTTTAA
*
2854067 ATTATATAAATTTTAA
1 AATATATAAATTTTAA
2854083 AATATAT
1 AATATAT
2854090 TTATATCGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATAAATTTTAA
Found at i:2854980 original size:19 final size:21
Alignment explanation
Indices: 2854958--2855003 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2854948 AATTTATGTG
2854958 AAATATAT-TAATTTTTTTA-
1 AAATATATCTAATTTTTTTAT
*
2854977 AAATAATATCTTATTTTTTTAT
1 AAAT-ATATCTAATTTTTTTAT
2854999 AAATA
1 AAATA
2855004 AGATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 11 0.48
22 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATATCTAATTTTTTTAT
Found at i:2854994 original size:22 final size:23
Alignment explanation
Indices: 2854959--2855019 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2854949 ATTTATGTGA
2854959 AATATATTAATTTTTT-TAAAAT
1 AATATATTAATTTTTTATAAAAT
* *
2854981 AATATCTTATTTTTTTAT-AAAT
1 AATATATTAATTTTTTATAAAAT
*
2855003 AAGATAAATTAATTTTT
1 -A-ATATATTAATTTTT
2855020 ATCTCTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 18 0.58
23 2 0.06
24 11 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATATTAATTTTTTATAAAAT
Found at i:2855652 original size:16 final size:16
Alignment explanation
Indices: 2855631--2855665 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2855621 TTAGTCCTCG
2855631 ACATGTTTGGTGTCGT
1 ACATGTTTGGTGTCGT
2855647 ACATGTTTGGTGTCGT
1 ACATGTTTGGTGTCGT
2855663 ACA
1 ACA
2855666 AAATACATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (16 bp):
ACATGTTTGGTGTCGT
Found at i:2857698 original size:13 final size:13
Alignment explanation
Indices: 2857669--2857715 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
2857659 GAAAGAATTG
*
2857669 GAGAGGGATA-TAA
1 GAGAGGGATACT-T
*
2857682 GAGAGGGATGCTT
1 GAGAGGGATACTT
2857695 GAGAGGGATACTT
1 GAGAGGGATACTT
2857708 GAGAGGGA
1 GAGAGGGA
2857716 GGAGGGAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 29 0.97
14 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.45, T:0.17
Consensus pattern (13 bp):
GAGAGGGATACTT
Found at i:2864941 original size:13 final size:13
Alignment explanation
Indices: 2864907--2864945 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2864897 TAATAGTACT
*
2864907 AAAAATAACTTTTT
1 AAAAATAA-TTTTA
*
2864921 AAAGATAATTTTA
1 AAAAATAATTTTA
2864934 AAAAATAATTTT
1 AAAAATAATTTT
2864946 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:2864969 original size:29 final size:30
Alignment explanation
Indices: 2864927--2864987 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
2864917 TTTTAAAGAT
2864927 AATTTTAAAAAATAATTTTTT-ATTTTTAA
1 AATTTTAAAAAATAATTTTTTAATTTTTAA
* *
2864956 AATTTTTAATAATAATTTTTTAATTTTTAA
1 AATTTTAAAAAATAATTTTTTAATTTTTAA
2864986 AA
1 AA
2864988 ATAATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTTTAAAAAATAATTTTTTAATTTTTAA
Found at i:2864974 original size:21 final size:21
Alignment explanation
Indices: 2864950--2864998 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2864940 AATTTTTTAT
*
2864950 TTTTAAAATTTTTAATAATAA
1 TTTTAAAATTTTTAAAAATAA
**
2864971 TTTTTTAATTTTTAAAAATAA
1 TTTTAAAATTTTTAAAAATAA
2864992 TTATTAA
1 TT-TTAA
2864999 TTACCTCCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAATTTTTAAAAATAA
Found at i:2864976 original size:30 final size:29
Alignment explanation
Indices: 2864927--2864987 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
2864917 TTTTAAAGAT
*
2864927 AATTTTAAAAAATAATTTTTTATTTTTAA
1 AATTTTAAAAAATAATTTTTAATTTTTAA
* *
2864956 AATTTTTAATAATAATTTTTTAATTTTTAA
1 AATTTTAAAAAATAA-TTTTTAATTTTTAA
2864986 AA
1 AA
2864988 ATAATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTTAAAAAATAATTTTTAATTTTTAA
Found at i:2866979 original size:17 final size:17
Alignment explanation
Indices: 2866947--2866980 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2866937 TAAAAATAAT
* *
2866947 TAAAATATTATCTAAAA
1 TAAAATATAATATAAAA
2866964 TAAAATATAATATAAAA
1 TAAAATATAATATAAAA
2866981 AATTACATAA
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:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAATATAAAA
Found at i:2866991 original size:29 final size:30
Alignment explanation
Indices: 2866931--2867006 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 30
2866921 ATTACACTAT
* *
2866931 ATAATATAAAA-ATAAT-TAAAATATTATC
1 ATAAAATAAAATATAATATAAAAAATTATC
2866959 -TAAAATAAAATATAATATAAAAAATTA-C
1 ATAAAATAAAATATAATATAAAAAATTATC
2866987 AT-AAATAAAATATGAATATA
1 ATAAAATAAAATAT-AATATA
2867007 TTAAAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 9 0.21
28 17 0.40
29 16 0.38
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (30 bp):
ATAAAATAAAATATAATATAAAAAATTATC
Found at i:2867025 original size:30 final size:28
Alignment explanation
Indices: 2866961--2867048 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 28
2866951 ATATTATCTA
*
2866961 AAATAAAATATAATATA-AAAAATTACAT
1 AAATAAAATATAATATATAAAAATT-TAT
*
2866989 AAATAAAATATGAATATATTAAAATTTAT
1 AAATAAAATAT-AATATATAAAAATTTAT
* *
2867018 AATATAAATTATTAACATATAAAAATTTAT
1 AA-ATAAAATA-TAATATATAAAAATTTAT
2867048 A
1 A
2867049 TCAATACATA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.22
29 10 0.20
30 29 0.57
31 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (28 bp):
AAATAAAATATAATATATAAAAATTTAT
Found at i:2867635 original size:26 final size:26
Alignment explanation
Indices: 2867606--2867661 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2867596 ATATTAATTG
* *
2867606 TATAAACAT-TAATAAAAATTATTCAA
1 TATAAAAATATAATAAAAA-TATTAAA
*
2867632 TATAAAAATATAATATAAATATTAAA
1 TATAAAAATATAATAAAAATATTAAA
2867658 TATA
1 TATA
2867662 TCATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
TATAAAAATATAATAAAAATATTAAA
Found at i:2867669 original size:14 final size:13
Alignment explanation
Indices: 2867643--2867691 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2867633 ATAAAAATAT
*
2867643 AATATAAATATTA
1 AATATATATATTA
2867656 AATATATCATATT-
1 AATATAT-ATATTA
2867669 AAT-TATAT-TTA
1 AATATATATATTA
2867680 AATATATATATT
1 AATATATATATT
2867692 TTTTATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 8 0.26
13 11 0.35
14 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATATATTA
Found at i:2871506 original size:2 final size:2
Alignment explanation
Indices: 2871493--2871535 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2871483 CAAATGAAAA
* *
2871493 AT AT AT AC AT AT AT 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 AT AT AT
2871535 A
1 A
2871536 AAAGAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2873653 original size:27 final size:27
Alignment explanation
Indices: 2873589--2873663 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
2873579 AATAACATGT
*
2873589 CACCATTTTTGACAAATAAAAAGAAAC
1 CACCATTTTTGACAAACAAAAAGAAAC
* * * *
2873616 TACTATATTTGACAAACACAAAA-TAAC
1 CACCATTTTTGACAAACA-AAAAGAAAC
*
2873643 CACCATTTTTGACAAATAAAA
1 CACCATTTTTGACAAACAAAA
2873664 GGTGATTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 3 0.08
27 31 0.82
28 4 0.11
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.25
Consensus pattern (27 bp):
CACCATTTTTGACAAACAAAAAGAAAC
Found at i:2876539 original size:27 final size:27
Alignment explanation
Indices: 2876505--2876578 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
2876495 ATAACATACC
*
2876505 ATCATTTTTGATAAATAAAAAAAAACT
1 ATCATTTTTAATAAATAAAAAAAAACT
* * * *
2876532 ATCATTTTTTATAAACACAAAATAACT
1 ATCATTTTTAATAAATAAAAAAAAACT
*
2876559 A-CTATTTTTAACAAATAAAA
1 ATC-ATTTTTAATAAATAAAA
2876579 GGTGATTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (27 bp):
ATCATTTTTAATAAATAAAAAAAAACT
Found at i:2877401 original size:16 final size:15
Alignment explanation
Indices: 2877360--2877405 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2877350 TTAATTCAAA
2877360 TAAA-AAAATTTAAT
1 TAAATAAAATTTAAT
*
2877374 TAAATTATAATTTAAAT
1 TAAA-TAAAATTT-AAT
2877391 TAAATAAAA-TTAAT
1 TAAATAAAATTTAAT
2877405 T
1 T
2877406 TAAAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 10 0.37
17 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATAAAATTTAAT
Found at i:2877424 original size:21 final size:20
Alignment explanation
Indices: 2877369--2877424 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
2877359 ATAAAAAAAT
*
2877369 TTAATTAAATTATAATTTAAA
1 TTAAATAAATT-TAATTTAAA
*
2877390 TTAAATAAAATTAATTTAAAA
1 TTAAATAAATTTAATTT-AAA
* *
2877411 TTGAATCAATTTAA
1 TTAAATAAATTTAA
2877425 ATCAAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAATAAATTTAATTTAAA
Found at i:2878910 original size:75 final size:75
Alignment explanation
Indices: 2878787--2878938 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
2878777 AAGAGTAAGA
2878787 AAAAGGCAGCGAAGATTGTTCTAAGACTTTTAACTTTATCCCACAGTCACACCTTTTACACCAGA
1 AAAAGGCAGCGAAGATTGTTCTAAGACTTTTAACTTTATCCCACAGTCACACCTTTTACACCAGA
*
2878852 ATGCGTGGAG
66 ATGCATGGAG
* * * * * *
2878862 AAAAGGTAGCGAGGATTGTTCTAGGACTTTTAACTTTATCTCACAGTCATACCTTTTACACCTGA
1 AAAAGGCAGCGAAGATTGTTCTAAGACTTTTAACTTTATCCCACAGTCACACCTTTTACACCAGA
2878927 ATGCATGGAG
66 ATGCATGGAG
2878937 AA
1 AA
2878939 TCTAAGGCAC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (75 bp):
AAAAGGCAGCGAAGATTGTTCTAAGACTTTTAACTTTATCCCACAGTCACACCTTTTACACCAGA
ATGCATGGAG
Found at i:2888190 original size:20 final size:21
Alignment explanation
Indices: 2888169--2888227 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
2888159 GATAATTTTA
* *
2888169 AATATAATATAATAAAT-ATA
1 AATATAAAATAAAAAATAATA
2888189 AATATAAAATAAAAAATAATAA
1 AATATAAAATAAAAAATAAT-A
*
2888211 AATATAAAA-AAATAATA
1 AATATAAAATAAAAAATA
2888228 TGATTTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.44
21 9 0.26
22 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATATAAAATAAAAAATAATA
Found at i:2888219 original size:15 final size:15
Alignment explanation
Indices: 2888168--2888225 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
2888158 TGATAATTTT
*
2888168 AAATATAATATAAT-
1 AAATATAAAATAATA
2888182 AAATAT-AAAT-ATA
1 AAATATAAAATAATA
*
2888195 AAATAAAAAATAATA
1 AAATATAAAATAATA
*
2888210 AAATATAAAAAAATA
1 AAATATAAAATAATA
2888225 A
1 A
2888226 TATGATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 2 0.05
13 8 0.22
14 10 0.27
15 17 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATAAAATAATA
Found at i:2889213 original size:2 final size:2
Alignment explanation
Indices: 2889206--2889250 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2889196 AGGAAGATGC
2889206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2889248 AT A
1 AT A
2889251 GCAAAAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2893841 original size:16 final size:17
Alignment explanation
Indices: 2893822--2893854 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2893812 TTAACAGAAA
2893822 TACAATTTT-TTTAATT
1 TACAATTTTATTTAATT
2893838 TACAATTTTATTTAATT
1 TACAATTTTATTTAATT
2893855 AATTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TACAATTTTATTTAATT
Found at i:2895510 original size:2 final size:2
Alignment explanation
Indices: 2895505--2895548 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
2895495 ATTTTGTGTG
* *
2895505 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TG TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
2895548 T
1 T
2895549 CGTAAAGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2895873 original size:21 final size:19
Alignment explanation
Indices: 2895825--2895874 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
2895815 AAATGTCATT
*
2895825 TAAATATAATTAAAAATTAA
1 TAAATA-AATTAAAAATAAA
2895845 TAAA-AAATTAAAAATAAGA
1 TAAATAAATTAAAAATAA-A
2895864 TATAATAAATT
1 TA-AATAAATT
2895875 TTTAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.42
19 4 0.15
20 6 0.23
21 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAATAAATTAAAAATAAA
Found at i:2897600 original size:3 final size:3
Alignment explanation
Indices: 2897592--2897632 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2897582 GACAATCCCT
2897592 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2897633 TCTATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2898930 original size:20 final size:21
Alignment explanation
Indices: 2898892--2898933 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2898882 ATATTTTTAA
2898892 TCTTCTATTATTTTAAACATT
1 TCTTCTATTATTTTAAACATT
* *
2898913 TCTTCT-TTTTTTTTAACATT
1 TCTTCTATTATTTTAAACATT
2898933 T
1 T
2898934 AAACTCGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTTCTATTATTTTAAACATT
Found at i:2900804 original size:38 final size:36
Alignment explanation
Indices: 2900761--2900842 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 36
2900751 ATTTTTTATC
*
2900761 ATATTTATATATTT-TATTATATTATAATTATATTTAAT
1 ATATTTATATATTTATATTAAATTA-AA-TATA-TTAAT
*
2900799 ATATTT-TAAATTTATATTAAATTAAATATATTAAT
1 ATATTTATATATTTATATTAAATTAAATATATTAAT
*
2900834 A-ATTAATAT
1 ATATTTATAT
2900843 TAAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
34 3 0.08
35 8 0.21
36 4 0.11
37 8 0.21
38 15 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
ATATTTATATATTTATATTAAATTAAATATATTAAT
Found at i:2900823 original size:16 final size:16
Alignment explanation
Indices: 2900777--2900854 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 16
2900767 ATATATTTTA
*
2900777 TTATATTATAATTATAT
1 TTATATTA-AATTAAAT
**
2900794 TTA-ATATATTTTAAAT
1 TTATAT-TAAATTAAAT
2900810 TTATATTAAATTAAA-
1 TTATATTAAATTAAAT
2900825 -TATATT-AA-T-AAT
1 TTATATTAAATTAAAT
* *
2900837 TAATATTAAATAAAAT
1 TTATATTAAATTAAAT
2900853 TT
1 TT
2900855 TAAAATTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 7 0.15
14 8 0.17
16 21 0.46
17 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATTAAATTAAAT
Found at i:2900826 original size:27 final size:28
Alignment explanation
Indices: 2900767--2900864 Score: 82
Period size: 27 Copynumber: 3.6 Consensus size: 28
2900757 TATCATATTT
* * * *
2900767 ATATATTTTATTATATTATAATTATATTTA
1 ATATATTTAATAAT-TTAT-ATTAAATTAA
*
2900797 ATATATTTTA-AATTTATATTAAATTAA
1 ATATATTTAATAATTTATATTAAATTAA
*
2900824 ATATA-TTAATAATTAATATTAAA-TAA
1 ATATATTTAATAATTTATATTAAATTAA
2900850 A-AT-TTTAA-AATTTAT
1 ATATATTTAATAATTTAT
2900865 TTTTACATCA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.10
25 6 0.10
26 7 0.12
27 25 0.42
28 4 0.07
29 2 0.03
30 10 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATATTTAATAATTTATATTAAATTAA
Found at i:2900848 original size:14 final size:13
Alignment explanation
Indices: 2900776--2900849 Score: 54
Period size: 11 Copynumber: 6.1 Consensus size: 13
2900766 TATATATTTT
2900776 ATTATATT--ATA
1 ATTATATTAAATA
*
2900787 ATTATATTTAAT-
1 ATTATATTAAATA
*
2900799 A-TATTTTAAAT-
1 ATTATATTAAATA
2900810 -TTATATTAAATTA
1 ATTATATTAAA-TA
*
2900823 AATATATT-AATA
1 ATTATATTAAATA
2900835 ATTAATATTAAATA
1 ATT-ATATTAAATA
2900849 A
1 A
2900850 AATTTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 24 0.48
12 6 0.12
13 9 0.18
14 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATATTAAATA
Found at i:2903504 original size:16 final size:16
Alignment explanation
Indices: 2903463--2903504 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2903453 AAATAAAATT
2903463 TTATAT-AATA-TAAA
1 TTATATAAATATTAAA
2903477 TTAT-TAACATATTAAA
1 TTATATAA-ATATTAAA
2903493 TTATATAAATAT
1 TTATATAAATAT
2903505 ATATCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.04
14 5 0.21
15 3 0.12
16 12 0.50
17 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATATAAATATTAAA
Found at i:2903877 original size:24 final size:25
Alignment explanation
Indices: 2903850--2903908 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
2903840 TAAAATAGCC
* *
2903850 TTAATTTATTAG-GTAATTTATATT
1 TTAAATTATTAGAATAATTTATATT
2903874 TTAAATTATT-GAATAATTTATATT
1 TTAAATTATTAGAATAATTTATATT
2903898 TTAAATTATTA
1 TTAAATTATTA
2903909 AATTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (25 bp):
TTAAATTATTAGAATAATTTATATT
Found at i:2907912 original size:17 final size:17
Alignment explanation
Indices: 2907892--2907925 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2907882 TTTTTTTAAG
*
2907892 TATTCTTATTTTATATT
1 TATTCTTAATTTATATT
*
2907909 TATTTTTAATTTATATT
1 TATTCTTAATTTATATT
2907926 AATTATTAAA
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:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTCTTAATTTATATT
Found at i:2907934 original size:17 final size:17
Alignment explanation
Indices: 2907901--2907934 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2907891 GTATTCTTAT
* *
2907901 TTTATATTTATTTTTAA
1 TTTATATTAATTATTAA
2907918 TTTATATTAATTATTAA
1 TTTATATTAATTATTAA
2907935 AATATAAATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATATTAATTATTAA
Found at i:2908000 original size:31 final size:31
Alignment explanation
Indices: 2907920--2908001 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
2907910 ATTTTTAATT
* *
2907920 TATATTAATTATTAAA-ATATAAATATACAAA
1 TATATTTATTA-TAAATATATAAATAAACAAA
*
2907951 TATAATTT-TTA-AAATATATAAA-AAATAAA
1 TAT-ATTTATTATAAATATATAAATAAACAAA
2907980 TATATTTATTATCAAATATATA
1 TATATTTATTAT-AAATATATA
2908002 TTTAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
28 4 0.09
29 14 0.33
30 7 0.16
31 15 0.35
32 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TATATTTATTATAAATATATAAATAAACAAA
Found at i:2913143 original size:62 final size:63
Alignment explanation
Indices: 2913053--2913173 Score: 190
Period size: 62 Copynumber: 1.9 Consensus size: 63
2913043 ATAGTGATCT
* * * * *
2913053 AGTGACATTTAAAAATAACTTATTAAAAAA-TTAAAATTTAATTCAGTTGATTTATATAGTGA
1 AGTGACATGTAAAAATAAATTATAAAAAAATTTAAAATTTAATTCAATTGATTCATATAGTGA
2913115 AGTGACATGTAAAAATAAATTATAAAAAAATTTAAAATTTAATTCAATTGATTCATATA
1 AGTGACATGTAAAAATAAATTATAAAAAAATTTAAAATTTAATTCAATTGATTCATATA
2913174 ATTAATTGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 27 0.51
63 26 0.49
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (63 bp):
AGTGACATGTAAAAATAAATTATAAAAAAATTTAAAATTTAATTCAATTGATTCATATAGTGA
Found at i:2913349 original size:20 final size:20
Alignment explanation
Indices: 2913324--2913365 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2913314 TATATTGTAA
2913324 TTATAACTTTTCTCAAATAT
1 TTATAACTTTTCTCAAATAT
2913344 TTATAACTTTTCTCAAATAT
1 TTATAACTTTTCTCAAATAT
2913364 TT
1 TT
2913366 GAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATAACTTTTCTCAAATAT
Found at i:2913713 original size:14 final size:14
Alignment explanation
Indices: 2913696--2913730 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2913686 AATATTAATA
*
2913696 ATATTTTTTATTTT
1 ATATTTTTTATATT
*
2913710 ATATCTTTTATATT
1 ATATTTTTTATATT
2913724 ATATTTT
1 ATATTTT
2913731 AAGTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
ATATTTTTTATATT
Found at i:2914552 original size:7 final size:7
Alignment explanation
Indices: 2914540--2914570 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2914530 TACAATTATG
2914540 ATTGGCA
1 ATTGGCA
2914547 ATTGGCA
1 ATTGGCA
2914554 ATTGGCA
1 ATTGGCA
2914561 ATTGGCA
1 ATTGGCA
2914568 ATT
1 ATT
2914571 TAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (7 bp):
ATTGGCA
Found at i:2915037 original size:17 final size:18
Alignment explanation
Indices: 2915003--2915040 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2914993 AATGATTTTA
2915003 TATTTGATATATTAATAT
1 TATTTGATATATTAATAT
* *
2915021 TATTT-ATATTTTTATAT
1 TATTTGATATATTAATAT
2915038 TAT
1 TAT
2915041 AATGAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTTGATATATTAATAT
Found at i:2917344 original size:2 final size:2
Alignment explanation
Indices: 2917337--2917361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2917327 TGCATTAACA
2917337 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
2917362 AATGAAAATT
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:2918621 original size:2 final size:2
Alignment explanation
Indices: 2918614--2918647 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2918604 CGGTTTTGAT
*
2918614 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2918648 GATTTTTTGT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2919316 original size:15 final size:15
Alignment explanation
Indices: 2919296--2919334 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
2919286 TTTTGCCCAA
2919296 AAAAATAATAATAAT
1 AAAAATAATAATAAT
2919311 AAAAATAATAATAAT
1 AAAAATAATAATAAT
2919326 AACAAATAA
1 AA-AAATAA
2919335 AAAAATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:2919501 original size:23 final size:23
Alignment explanation
Indices: 2919475--2919521 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2919465 AATTTAATAG
2919475 AAATAATATATTAAATAAATTTA
1 AAATAATATATTAAATAAATTTA
* * *
2919498 AAATAATATTTTAACTATATTTA
1 AAATAATATATTAAATAAATTTA
2919521 A
1 A
2919522 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATAATATATTAAATAAATTTA
Found at i:2920014 original size:2 final size:2
Alignment explanation
Indices: 2920007--2920038 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2919997 ATCGAATGTA
2920007 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
2920039 TCCTACTTAT
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:2920123 original size:2 final size:2
Alignment explanation
Indices: 2920116--2920159 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2920106 TTATTTAACG
*
2920116 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2920158 AT
1 AT
2920160 TTGCAACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2927990 original size:2 final size:2
Alignment explanation
Indices: 2927983--2928010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2927973 CTTTCTTAAC
2927983 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
2928011 GACAATTATG
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:2929563 original size:13 final size:13
Alignment explanation
Indices: 2929545--2929571 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2929535 GGCTCCCTCC
2929545 TCCCTCTCTTGTA
1 TCCCTCTCTTGTA
2929558 TCCCTCTCTTGTA
1 TCCCTCTCTTGTA
2929571 T
1 T
2929572 ACTTCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.37, G:0.07, T:0.48
Consensus pattern (13 bp):
TCCCTCTCTTGTA
Found at i:2930013 original size:24 final size:24
Alignment explanation
Indices: 2929981--2930038 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
2929971 TGGCAGAGTG
2929981 AAGTTCTAGATGCACTATTTCAGC
1 AAGTTCTAGATGCACTATTTCAGC
* *
2930005 AAGTTCTAGATGCGCTATTTCAGT
1 AAGTTCTAGATGCACTATTTCAGC
*
2930029 AAGGTCTAGA
1 AAGTTCTAGA
2930039 CACTGCTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (24 bp):
AAGTTCTAGATGCACTATTTCAGC
Found at i:2934991 original size:2 final size:2
Alignment explanation
Indices: 2934984--2935013 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2934974 TTCAGTCGCC
2934984 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
2935014 TCAGATAGTC
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:2936675 original size:12 final size:12
Alignment explanation
Indices: 2936658--2936701 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
2936648 TATCGTGTAC
2936658 ATATTATTTTTT
1 ATATTATTTTTT
*
2936670 ATATTATATTTT
1 ATATTATTTTTT
2936682 A-ATTATTTTTT
1 ATATTATTTTTT
2936693 AT-TTATTTT
1 ATATTATTTT
2936702 ATGTTCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:2937383 original size:17 final size:18
Alignment explanation
Indices: 2937342--2937384 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2937332 TTTTTTTATA
*
2937342 TTATATTTATATTGTGTT
1 TTATATTTATATTATGTT
*
2937360 TTA-ATTTATCTTAT-TT
1 TTATATTTATATTATGTT
2937376 TTATATTTA
1 TTATATTTA
2937385 ATAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATATTTATATTATGTT
Found at i:2937456 original size:18 final size:19
Alignment explanation
Indices: 2937422--2937472 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
2937412 TTAATTACAT
*
2937422 AATATTTTAAAT-TATAA-A
1 AATA-TTTAAATAAATAATA
2937440 AATATTTAAATAAATAATA
1 AATATTTAAATAAATAATA
*
2937459 ATTATTTAATATAA
1 AATATTTAA-ATAA
2937473 TTTATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 9 0.32
20 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTTAAATAAATAATA
Found at i:2943033 original size:2 final size:2
Alignment explanation
Indices: 2943028--2943055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2943018 TACTACTTTC
2943028 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2943056 TTATATTTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3026788 original size:2 final size:2
Alignment explanation
Indices: 3026783--3026814 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3026773 TACTACTTTC
3026783 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3026815 TTTATTTTGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3028975 original size:17 final size:18
Alignment explanation
Indices: 3028955--3028993 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3028945 TATCGATTTG
*
3028955 ATTTTTAA-CGATTTTTA
1 ATTTTTAATCGATTATTA
*
3028972 ATTTTTAATTGATTATTA
1 ATTTTTAATCGATTATTA
3028990 ATTT
1 ATTT
3028994 CAGTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTTTAATCGATTATTA
Found at i:3035009 original size:15 final size:17
Alignment explanation
Indices: 3034989--3035030 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3034979 ATTATTTCAT
3034989 AAATTTTATTT-A-TAA
1 AAATTTTATTTCATTAA
3035004 AAATTTTAATTTCATTAA
1 AAATTTT-ATTTCATTAA
3035022 AAATGTTTA
1 AAAT-TTTA
3035031 AATAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 1 0.04
18 8 0.35
19 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTTATTTCATTAA
Found at i:3035878 original size:6 final size:6
Alignment explanation
Indices: 3035861--3035909 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
3035851 AGTTTTGAAA
* *
3035861 AAATTT -AATTT AAATTT AAATTT AAAATT AAATAT AAATAATT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT--TT AAATTT
3035910 GAAGTTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 5 0.14
6 26 0.72
8 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:3046414 original size:2 final size:2
Alignment explanation
Indices: 3046409--3046443 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3046399 ACACACCCCA
3046409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3046444 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3046448 original size:2 final size:2
Alignment explanation
Indices: 3046443--3046481 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3046433 ATATATATAT
3046443 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3046482 ACAGAAGCAC
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3049331 original size:2 final size:2
Alignment explanation
Indices: 3049324--3049363 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
3049314 TTTAATTATT
3049324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
3049364 TAAAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3049813 original size:16 final size:15
Alignment explanation
Indices: 3049787--3049816 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3049777 CATAATCTAA
3049787 AAATAAAATATTTAT
1 AAATAAAATATTTAT
3049802 AAATATAAATATTTA
1 AAATA-AAATATTTA
3049817 AATTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAAAATATTTAT
Found at i:3050132 original size:3 final size:3
Alignment explanation
Indices: 3050124--3050156 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3050114 TTGAATTAGT
3050124 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3050157 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3050161 original size:3 final size:3
Alignment explanation
Indices: 3050155--3050182 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3050145 ATAATAATAA
3050155 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3050183 TGCATGTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3054552 original size:2 final size:2
Alignment explanation
Indices: 3054545--3054571 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3054535 TTTGAGATGC
3054545 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
3054572 CTCTGAGGAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3054852 original size:28 final size:28
Alignment explanation
Indices: 3054821--3054881 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
3054811 GAAAAATAAA
* *
3054821 TAAATAAATATATAAACAAAGAAATTAG
1 TAAATAAATAAAGAAACAAAGAAATTAG
3054849 TAAATAAATAAAGAAACAAAGAAATTAG
1 TAAATAAATAAAGAAACAAAGAAATTAG
3054877 TAAAT
1 TAAAT
3054882 TACCAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (28 bp):
TAAATAAATAAAGAAACAAAGAAATTAG
Found at i:3056144 original size:20 final size:20
Alignment explanation
Indices: 3056107--3056158 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3056097 CTCTCCAAAG
3056107 AAGAAAATGAAA-TTTTTTAA
1 AAGAAAAT-AAATTTTTTTAA
3056127 AAGAAAATAAATTTTTTTTAA
1 AAGAAAATAAA-TTTTTTTAA
*
3056148 AA-AAAAGAAAT
1 AAGAAAATAAAT
3056159 ATTGGTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.14
20 15 0.52
21 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AAGAAAATAAATTTTTTTAA
Found at i:3056152 original size:19 final size:20
Alignment explanation
Indices: 3056107--3056143 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
3056097 CTCTCCAAAG
3056107 AAGAAAATGAAATTTTTTAA
1 AAGAAAATGAAATTTTTTAA
3056127 AAGAAAAT-AAATTTTTT
1 AAGAAAATGAAATTTTTT
3056144 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
AAGAAAATGAAATTTTTTAA
Found at i:3056557 original size:20 final size:21
Alignment explanation
Indices: 3056521--3056591 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 21
3056511 CATAAATTAT
* *
3056521 TAATATATAAAAATTTACATA
1 TAATATATAATAATTTAAATA
*
3056542 -AATATATAATATTTTAAATA
1 TAATATATAATAATTTAAATA
*
3056562 T-A-AT-T-ATAATTTAAAAA
1 TAATATATAATAATTTAAATA
3056579 TATATATATAATA
1 TA-ATATATAATA
3056592 TCAATATACG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 11 0.28
18 1 0.03
19 3 0.08
20 20 0.51
21 1 0.03
22 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATATATAATAATTTAAATA
Found at i:3056588 original size:19 final size:18
Alignment explanation
Indices: 3056522--3056590 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 18
3056512 ATAAATTATT
*
3056522 AATATATAAAAATTTACATA
1 AATATATAATAATTTA-A-A
*
3056542 AATATATAATATTTTAAA
1 AATATATAATAATTTAAA
* *
3056560 TATA-ATTATAATTTAAA
1 AATATATAATAATTTAAA
3056577 AATATATATATAAT
1 AATATATA-ATAAT
3056591 ATCAATATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 14 0.35
18 6 0.15
19 6 0.15
20 14 0.35
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATATAATAATTTAAA
Found at i:3056970 original size:56 final size:55
Alignment explanation
Indices: 3056894--3057018 Score: 130
Period size: 56 Copynumber: 2.2 Consensus size: 55
3056884 AAATCTATTA
* * *
3056894 ATTTTAAATATGACATATATATA-TATATAATAT-TTAATATTTCGTATAAATATAT
1 ATTTTAAATATGACATATATAAATTAT-TAATATATTAAAATTT-ATATAAATATAT
*
3056949 ATTTTAAAATAT-ATATAATATAAATTATTAATATATTAAAATTTATATAAATATAAAAT
1 ATTTT-AAATATGACAT-ATATAAATTATTAATATATTAAAATTTATATAAATAT---AT
3057008 ATTTTAAATAT
1 ATTTTAAATAT
3057019 AATTAATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
55 8 0.14
56 27 0.46
57 11 0.19
58 6 0.10
59 7 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (55 bp):
ATTTTAAATATGACATATATAAATTATTAATATATTAAAATTTATATAAATATAT
Found at i:3056994 original size:18 final size:17
Alignment explanation
Indices: 3056953--3057020 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
3056943 ATATATATTT
*
3056953 TAAAATATATAT-AATA
1 TAAAATTTATATAAATA
3056969 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
3056984 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
3057002 TAAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
3057018 TAA
1 TAA
3057021 TTAATAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.14
16 11 0.25
17 10 0.23
18 9 0.20
19 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3056996 original size:32 final size:33
Alignment explanation
Indices: 3056947--3057010 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3056937 GTATAAATAT
* *
3056947 ATATTTTAAAATATATAT-AATATAAATTATTA
1 ATATATTAAAATATATATAAATATAAAATATTA
*
3056979 ATATATTAAAATTTATATAAATATAAAATATT
1 ATATATTAAAATATATATAAATATAAAATATT
3057011 TTAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATATTAAAATATATATAAATATAAAATATTA
Found at i:3058605 original size:3 final size:3
Alignment explanation
Indices: 3058597--3058629 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3058587 CTTGTCGGTC
*
3058597 TTG TTG TTG TTG TTG TTG CTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
3058630 CCGCTGCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.33, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:3062471 original size:15 final size:15
Alignment explanation
Indices: 3062428--3062471 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3062418 TAAAACGTAT
*
3062428 TACATAAATTTAAAA
1 TACATAAAATTAAAA
3062443 TA-ATAATAATTAAAA
1 TACATAA-AATTAAAA
*
3062458 TACATAAAAATAAA
1 TACATAAAATTAAA
3062472 TAAATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
TACATAAAATTAAAA
Found at i:3062542 original size:25 final size:25
Alignment explanation
Indices: 3062491--3062559 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
3062481 TATAAGATTG
* *
3062491 ATAAATTTTTTAAAAT-TTATATATT
1 ATAAA-TTATTAAAATATTAAATATT
*
3062516 ATAAATTATTAAAATATTAAATTTT
1 ATAAATTATTAAAATATTAAATATT
* *
3062541 ATATAAATATCAAAATATT
1 ATA-AATTATTAAAATATT
3062560 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.24
25 15 0.41
26 13 0.35
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAAATTATTAAAATATTAAATATT
Found at i:3069212 original size:28 final size:26
Alignment explanation
Indices: 3069169--3069226 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
3069159 TTTTATTAAA
**
3069169 TTAAAAAATATATTAATTATATATATT
1 TTAAAAAATATATTAAAAATATA-ATT
3069196 TTAAAAAATCA-ACTTAAAAATATAATT
1 TTAAAAAAT-ATA-TTAAAAATATAATT
3069223 TTAA
1 TTAA
3069227 TATTATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAAAATATATTAAAAATATAATT
Found at i:3069398 original size:20 final size:21
Alignment explanation
Indices: 3069357--3069399 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3069347 ATTTTTTCAA
3069357 AATTGATAAAGAAATTAAATT
1 AATTGATAAAGAAATTAAATT
*
3069378 AATT-ATAAA-AAACTTATATT
1 AATTGATAAAGAAA-TTAAATT
3069398 AA
1 AA
3069400 GTAATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (21 bp):
AATTGATAAAGAAATTAAATT
Found at i:3071446 original size:11 final size:11
Alignment explanation
Indices: 3071430--3071494 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
3071420 TGATAATTTT
3071430 AATAAAATATA
1 AATAAAATATA
3071441 AATAAAATAT-
1 AATAAAATATA
* *
3071451 -GTAAAAAATA
1 AATAAAATATA
*
3071461 ATTAAAATAT-
1 AATAAAATATA
* *
3071471 AACAATATATA
1 AATAAAATATA
3071482 AAT--AATATA
1 AATAAAATATA
3071491 AATA
1 AATA
3071495 TATTAATTCA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
9 15 0.37
10 7 0.17
11 19 0.46
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (11 bp):
AATAAAATATA
Done.