Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 23 of 24
Found at i:4347742 original size:2 final size:2
Alignment explanation
Indices: 4347735--4347766 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4347725 GTTAGCTAGC
4347735 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
4347767 TAAAAAAGAA
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:4348592 original size:2 final size:2
Alignment explanation
Indices: 4348580--4348611 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4348570 CACTTTTTGA
*
4348580 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4348612 TGCTACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4354659 original size:7 final size:7
Alignment explanation
Indices: 4354647--4354686 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
4354637 AAATATATTA
4354647 TTTTAAT
1 TTTTAAT
4354654 TTTTAAT
1 TTTTAAT
*
4354661 TTTTAAA
1 TTTTAAT
*
4354668 TTTTAAA
1 TTTTAAT
4354675 TTTTAAT
1 TTTTAAT
*
4354682 ATTTA
1 TTTTA
4354687 TATTCTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTTAAT
Found at i:4354671 original size:21 final size:21
Alignment explanation
Indices: 4354646--4354686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4354636 AAAATATATT
* *
4354646 ATTTTAATTTTTAATTTTTAA
1 ATTTTAAATTTTAATATTTAA
4354667 ATTTTAAATTTTAATATTTA
1 ATTTTAAATTTTAATATTTA
4354687 TATTCTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAAATTTTAATATTTAA
Found at i:4354755 original size:24 final size:25
Alignment explanation
Indices: 4354728--4354792 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
4354718 ATATAATTTT
4354728 TTAAAAATTATTTAA-ATATATAAA
1 TTAAAAATTATTTAATATATATAAA
* * *
4354752 TTAAAAAAATATTTAATATATTTATA
1 TT-AAAAATTATTTAATATATATAAA
*
4354778 TTAAATATATATTTA
1 TTAAAAAT-TATTTA
4354793 GATTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 16 0.48
26 15 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAAAATTATTTAATATATATAAA
Found at i:4354759 original size:26 final size:26
Alignment explanation
Indices: 4354730--4354792 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
4354720 ATAATTTTTT
*
4354730 AAAAATTATTTAA-ATATATAAATTA
1 AAAAAATATTTAATATATATAAATTA
* *
4354755 AAAAAATATTTAATATATTTATATTA
1 AAAAAATATTTAATATATATAAATTA
* *
4354781 AATATATATTTA
1 AAAAAATATTTA
4354793 GATTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAAAATATTTAATATATATAAATTA
Found at i:4355029 original size:3 final size:3
Alignment explanation
Indices: 4355021--4355054 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4355011 TTTTTCTAAG
*
4355021 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4355055 ATATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4355552 original size:2 final size:2
Alignment explanation
Indices: 4355545--4355569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4355535 TCAGCTTCAA
4355545 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
4355570 CTGTTTGTGA
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:4356031 original size:11 final size:11
Alignment explanation
Indices: 4356015--4356049 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4356005 TTATTTTATT
4356015 TATTTAAATAA
1 TATTTAAATAA
*
4356026 TATTTAAATAT
1 TATTTAAATAA
*
4356037 TTTTTAAATAA
1 TATTTAAATAA
4356048 TA
1 TA
4356050 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTTAAATAA
Found at i:4359828 original size:2 final size:2
Alignment explanation
Indices: 4359815--4359845 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4359805 AATTGCATCA
*
4359815 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4359846 AAATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4370141 original size:12 final size:12
Alignment explanation
Indices: 4370124--4370148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4370114 GGCTTTGTGG
4370124 TTTGCCATTATA
1 TTTGCCATTATA
4370136 TTTGCCATTATA
1 TTTGCCATTATA
4370148 T
1 T
4370149 GTATCTGGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTGCCATTATA
Found at i:4372011 original size:30 final size:30
Alignment explanation
Indices: 4371923--4372012 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
4371913 AAATAGGAAT
* *
4371923 TTTAATTTAATAAAAATAATATTTTAAGAG
1 TTTAATTAAATAAAAATAATATTTTAATAG
* ** *
4371953 GTTAATTACTTGGAAAATAATATTTTAATAG
1 TTTAATTAAAT-AAAAATAATATTTTAATAG
*
4371984 TTTAATTAAATAAAAATAATACTTTAATA
1 TTTAATTAAATAAAAATAATATTTTAATA
4372013 TTAAAATTGA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 23 0.48
31 25 0.52
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTAATTAAATAAAAATAATATTTTAATAG
Found at i:4372026 original size:29 final size:30
Alignment explanation
Indices: 4371926--4372017 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 30
4371916 TAGGAATTTT
* * *
4371926 AATTTAATAAAAATAATATTTTAAGAGGTT-
1 AATTAAATAAAAATAATACTTTAATA-GTTA
** * * *
4371956 AATTACTTGGAAAATAATATTTTAATAGTTT
1 AATTAAAT-AAAAATAATACTTTAATAGTTA
4371987 AATTAAATAAAAATAATACTTTAATA-TTA
1 AATTAAATAAAAATAATACTTTAATAGTTA
4372016 AA
1 AA
4372018 ATTGATAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.08
30 24 0.48
31 22 0.44
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTAAATAAAAATAATACTTTAATAGTTA
Found at i:4373236 original size:29 final size:29
Alignment explanation
Indices: 4373203--4373259 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4373193 CACTGAATAA
* *
4373203 AATATTTTAATTTTTATGTTATTAAATTT
1 AATATTTTAATATTTATATTATTAAATTT
*
4373232 AATATTTTAATATTTATATTTTTAAATT
1 AATATTTTAATATTTATATTATTAAATT
4373260 ATTATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
AATATTTTAATATTTATATTATTAAATTT
Found at i:4373254 original size:15 final size:15
Alignment explanation
Indices: 4373207--4373256 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
4373197 GAATAAAATA
* *
4373207 TTTTAATTTTTATGT
1 TTTTAATATTTATAT
*
4373222 TATTAA-ATTTA-AT
1 TTTTAATATTTATAT
4373235 ATTTTAATATTTATAT
1 -TTTTAATATTTATAT
4373251 TTTTAA
1 TTTTAA
4373257 ATTATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.32
15 16 0.57
16 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTAATATTTATAT
Found at i:4373382 original size:25 final size:25
Alignment explanation
Indices: 4373327--4373383 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
4373317 TATATATATG
*
4373327 TAAAATAAAATTTTAAATTTAAAGT
1 TAAAATTAAATTTTAAATTTAAAGT
* * *
4373352 TGAAATTAAATTTT-TATTTAAAATT
1 TAAAATTAAATTTTAAATTT-AAAGT
4373377 TAAAATT
1 TAAAATT
4373384 TTATAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TAAAATTAAATTTTAAATTTAAAGT
Found at i:4373385 original size:19 final size:20
Alignment explanation
Indices: 4373357--4373397 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4373347 AAAGTTGAAA
* *
4373357 TTAAATTTTTAT-TTAAAAT
1 TTAAAATTTTATAATAAAAT
4373376 TTAAAATTTTATAATAAAAT
1 TTAAAATTTTATAATAAAAT
4373396 TT
1 TT
4373398 TATTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAAATTTTATAATAAAAT
Found at i:4373393 original size:13 final size:14
Alignment explanation
Indices: 4373377--4373405 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4373367 ATTTAAAATT
4373377 TAAAATTTTA-TAA
1 TAAAATTTTATTAA
4373390 TAAAATTTTATTAA
1 TAAAATTTTATTAA
4373404 TA
1 TA
4373406 TTTTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATTTTATTAA
Found at i:4373436 original size:42 final size:39
Alignment explanation
Indices: 4373380--4373467 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 39
4373370 TAAAATTTAA
4373380 AATTTTATAATAAAATTTTATTAA-TATTTTAATAATTATTTT
1 AATTTTATAATAAAA--TTATTAATTATTTT--TAATTATTTT
** *
4373422 AATTTTATGTTAAAATTATTAATTATTTTTATTTATTTT
1 AATTTTATAATAAAATTATTAATTATTTTTAATTATTTT
4373461 AATTTTA
1 AATTTTA
4373468 AAAATATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 16 0.38
40 7 0.17
41 6 0.14
42 13 0.31
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (39 bp):
AATTTTATAATAAAATTATTAATTATTTTTAATTATTTT
Found at i:4373487 original size:14 final size:13
Alignment explanation
Indices: 4373468--4373517 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
4373458 TTTAATTTTA
4373468 AAAATATAAATATT
1 AAAATATAAA-ATT
4373482 AAAATATTAAAATT
1 AAAATA-TAAAATT
*
4373496 AATAATAAAAAAATT
1 AA-AAT-ATAAAATT
4373511 AAAATAT
1 AAAATAT
4373518 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 1 0.03
14 14 0.45
15 15 0.48
16 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:4378157 original size:17 final size:19
Alignment explanation
Indices: 4378126--4378176 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
4378116 TATAAGTAAA
4378126 TATATAAATATTAAAATAT
1 TATATAAATATTAAAATAT
*
4378145 TATATAAA-A-TAAATTAT
1 TATATAAATATTAAAATAT
*
4378162 TA-ATATAT-TTAAAAT
1 TATATAAATATTAAAAT
4378177 TAACATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.15
17 14 0.52
18 1 0.04
19 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATATAAATATTAAAATAT
Found at i:4378822 original size:13 final size:13
Alignment explanation
Indices: 4378799--4378833 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
4378789 TATTCCGTCT
4378799 GAAAGAAAAAAAA
1 GAAAGAAAAAAAA
*
4378812 -AAGGAAAAAAAA
1 GAAAGAAAAAAAA
4378824 GAAAGAAAAA
1 GAAAGAAAAA
4378834 GCTAAAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAAAA
Found at i:4381882 original size:1 final size:1
Alignment explanation
Indices: 4381876--4381901 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4381866 ACAATACCAG
4381876 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
4381902 CCAACATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4388852 original size:22 final size:22
Alignment explanation
Indices: 4388826--4388867 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4388816 TATTTTTATT
4388826 TAAAT-TTAATTATAAAAATATG
1 TAAATATTAA-TATAAAAATATG
4388848 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
4388868 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATG
Found at i:4389469 original size:2 final size:2
Alignment explanation
Indices: 4389456--4389495 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4389446 TGGTTTAAAA
* * *
4389456 AT AT AT AA AT AT AT AT AT AC AT AC 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
4389496 TGATAGATAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:4389868 original size:21 final size:19
Alignment explanation
Indices: 4389843--4389895 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
4389833 TTACAATTTA
4389843 TTATAAAATAATTACTTTGT
1 TTATAAAATAATTACTTT-T
*
4389863 TATATAGAATAA-TACTTTT
1 T-TATAAAATAATTACTTTT
*
4389882 TTTTAAAATAATTA
1 TTATAAAATAATTA
4389896 TTATATGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 7 0.25
21 9 0.32
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (19 bp):
TTATAAAATAATTACTTTT
Found at i:4390291 original size:13 final size:14
Alignment explanation
Indices: 4390265--4390292 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4390255 TTAAAAAATA
4390265 TAAAAATTATTTTT
1 TAAAAATTATTTTT
4390279 TAAAAATTATTTTT
1 TAAAAATTATTTTT
4390293 CATGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAAAATTATTTTT
Found at i:4390924 original size:30 final size:31
Alignment explanation
Indices: 4390880--4390947 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
4390870 TAAATTCAAG
4390880 ATTATTTTATATATAAATTAAAAATTAAAAA
1 ATTATTTTATATATAAATTAAAAATTAAAAA
**
4390911 ATTATTTTA-ATATAAATTAAATGTTAAAAA
1 ATTATTTTATATATAAATTAAAAATTAAAAA
*
4390941 TTTATTT
1 ATTATTT
4390948 ACATTCAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
ATTATTTTATATATAAATTAAAAATTAAAAA
Found at i:4391537 original size:17 final size:16
Alignment explanation
Indices: 4391503--4391550 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
4391493 TAGTTAATTC
**
4391503 AATTAATAAATTAAAAT
1 AATTAA-AAATTTTAAT
4391520 AATTAAAATATTTTAAT
1 AATTAAAA-ATTTTAAT
*
4391537 AATTTAAAATTTTA
1 AATTAAAAATTTTA
4391551 TTTTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAAATTTTAAT
Found at i:4392352 original size:2 final size:2
Alignment explanation
Indices: 4392294--4392334 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4392284 TTTACTCGTA
4392294 AT AT AT 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 AT AT AT A
4392335 AAGGAACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4392792 original size:22 final size:21
Alignment explanation
Indices: 4392742--4392794 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
4392732 ATAATTTTAA
4392742 ATTATGAAAATTCATAAAAATG
1 ATTAT-AAAATTCATAAAAATG
*
4392764 -TTATATAAAATCATAAATGAATG
1 ATTATA-AAATTCATAAA--AATG
4392787 ATTATAAA
1 ATTATAAA
4392795 TAATTTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
23 6 0.23
24 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.34
Consensus pattern (21 bp):
ATTATAAAATTCATAAAAATG
Found at i:4399317 original size:20 final size:20
Alignment explanation
Indices: 4399294--4399345 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
4399284 ATTTTTTATC
*
4399294 ATTTTAAAAATATTTTAAGT
1 ATTTTAAAAATATTTTAACT
** *
4399314 ATTTTAAAGTTTTTTTAACT
1 ATTTTAAAAATATTTTAACT
*
4399334 AATTTAAAAATA
1 ATTTTAAAAATA
4399346 AAACATTTAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTTTAAAAATATTTTAACT
Found at i:4400186 original size:20 final size:19
Alignment explanation
Indices: 4400144--4400191 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
4400134 GATCACATAT
* *
4400144 AAAAATTGAATTATTGTCAA
1 AAAAATTAAATTATTATC-A
**
4400164 AAAAATTAAATTATTATTT
1 AAAAATTAAATTATTATCA
4400183 AAAAATTAA
1 AAAAATTAA
4400192 TTAACCGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAAATTAAATTATTATCA
Found at i:4400511 original size:2 final size:2
Alignment explanation
Indices: 4400504--4400550 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4400494 GGGTAATGTG
4400504 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
4400546 TA TA T
1 TA TA T
4400551 TTCAACTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4401279 original size:19 final size:20
Alignment explanation
Indices: 4401246--4401288 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4401236 TTTTAAAATA
* *
4401246 TTAATTATATAAAAATTTAT
1 TTAAATATATAAAAATTAAT
4401266 TTAAATATAT-AAAATTAAT
1 TTAAATATATAAAAATTAAT
4401285 TTAA
1 TTAA
4401289 TTTCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATATATAAAAATTAAT
Found at i:4401474 original size:2 final size:2
Alignment explanation
Indices: 4401467--4401502 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4401457 GTGGTTTGAC
4401467 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
4401503 GTGGCATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4403186 original size:10 final size:10
Alignment explanation
Indices: 4403132--4403195 Score: 55
Period size: 9 Copynumber: 6.5 Consensus size: 10
4403122 AATATAATAC
4403132 ATTTAATATAT
1 ATTTAAT-TAT
4403143 ATTATATATTAT
1 ATT-TA-ATTAT
*
4403155 ATTTAA-AAT
1 ATTTAATTAT
4403164 -TTTAA-TAT
1 ATTTAATTAT
4403172 ATTTAATTAT
1 ATTTAATTAT
*
4403182 -TTTTATTAT
1 ATTTAATTAT
4403191 ATTTA
1 ATTTA
4403196 TATTTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
8 7 0.16
9 15 0.34
10 7 0.16
11 5 0.11
12 8 0.18
13 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:4403191 original size:19 final size:17
Alignment explanation
Indices: 4403149--4403195 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
4403139 ATATATTATA
4403149 TATTATATTTAAAATTT
1 TATTATATTTAAAATTT
* *
4403166 TAATATATTTAATTATTTT
1 TATTATATTTAA--AATTT
4403185 TATTATATTTA
1 TATTATATTTA
4403196 TATTTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATATTTAAAATTT
Found at i:4403501 original size:2 final size:2
Alignment explanation
Indices: 4403494--4403542 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
4403484 TTAAACCTTG
* *
4403494 AT AT AT AT A- AT A- AT CT AT AA 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
*
4403534 AT AA AT AT A
1 AT AT AT AT A
4403543 ATTCTCGATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4404711 original size:2 final size:2
Alignment explanation
Indices: 4404685--4404729 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4404675 AATTTCTTTA
4404685 AT AT -T AT AT -T AT AT -T AT AT -T 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
4404723 AT AT AT A
1 AT AT AT A
4404730 AACTCCAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4406826 original size:27 final size:30
Alignment explanation
Indices: 4406788--4406845 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
4406778 TTTTATATTT
*
4406788 TAAATATATTTT-ATAATT-A-AAAATAAA
1 TAAAAATATTTTAATAATTAATAAAATAAA
4406815 TAAAAATATTTTAATAATTAATAAAATAAA
1 TAAAAATATTTTAATAATTAATAAAATAAA
4406845 T
1 T
4406846 TCTGTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.41
28 6 0.22
29 1 0.04
30 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAAAATATTTTAATAATTAATAAAATAAA
Found at i:4407359 original size:2 final size:2
Alignment explanation
Indices: 4407352--4407376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4407342 CCAAATTAAT
4407352 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 T
4407377 TATGATATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4412369 original size:15 final size:16
Alignment explanation
Indices: 4412349--4412380 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4412339 AAATATGTTC
4412349 AGAATCA-AAACAACA
1 AGAATCACAAACAACA
4412364 AGAATCACAAACAACA
1 AGAATCACAAACAACA
4412380 A
1 A
4412381 TCATCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (16 bp):
AGAATCACAAACAACA
Found at i:4413214 original size:102 final size:102
Alignment explanation
Indices: 4413038--4413243 Score: 385
Period size: 102 Copynumber: 2.0 Consensus size: 102
4413028 GATCGCTAAT
* *
4413038 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAATTACCCGATTGAGTGAACT
1 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT
4413103 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
66 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
*
4413140 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTATCCGATCGAGTGAACT
1 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT
4413205 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
66 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
4413242 GA
1 GA
4413244 CGTAGTTCTT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (102 bp):
GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT
TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
Found at i:4416705 original size:2 final size:2
Alignment explanation
Indices: 4416698--4416727 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4416688 AATGCTTTTG
4416698 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
4416728 GTGTGTGTGT
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:4424574 original size:15 final size:14
Alignment explanation
Indices: 4424554--4424589 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4424544 TCAAATCAAA
4424554 TTAATTAATTTTAAT
1 TTAATT-ATTTTAAT
4424569 TTAATTATTTTAAT
1 TTAATTATTTTAAT
4424583 TT-ATTAT
1 TTAATTAT
4424590 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 10 0.48
15 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTAATTATTTTAAT
Found at i:4426563 original size:27 final size:26
Alignment explanation
Indices: 4426520--4426573 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
4426510 GACTAATTTC
*
4426520 AAAATTATTATGGATTAAATTTTTTTTA
1 AAAATTATTAT-GATT-AATTTATTTTA
4426548 AAAATTATTTAT-ATTAATTTATTTTA
1 AAAATTA-TTATGATTAATTTATTTTA
4426574 TATTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 7 0.29
29 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
AAAATTATTATGATTAATTTATTTTA
Found at i:4428453 original size:32 final size:31
Alignment explanation
Indices: 4428417--4428503 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
4428407 TAAAATATAT
*
4428417 TATAATATAAAAAATAAATATTTTAAATTTTA
1 TATAATATAAAAAATAAATA-TATAAATTTTA
4428449 TATAAATATAAAATAATTAAA-A-ATAAATTTTA
1 TAT-AATATAAAA-AA-TAAATATATAAATTTTA
* *
4428481 AATAATATAAATATATAAATATA
1 TATAATATAAA-AAATAAATATA
4428504 AAAAAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
30 4 0.09
31 10 0.22
32 16 0.35
33 9 0.20
34 3 0.07
35 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TATAATATAAAAAATAAATATATAAATTTTA
Found at i:4428498 original size:8 final size:8
Alignment explanation
Indices: 4428447--4428518 Score: 55
Period size: 8 Copynumber: 9.1 Consensus size: 8
4428437 TTTTAAATTT
4428447 TATATAAA
1 TATATAAA
4428455 TATA-AAA
1 TATATAAA
4428462 TA-ATTAAA
1 TATA-TAAA
4428470 -A-ATAAA
1 TATATAAA
*
4428476 T-TTTAAA
1 TATATAAA
4428483 TAATATAAA
1 T-ATATAAA
4428492 TATATAAA
1 TATATAAA
*
4428500 TATAAAAAAA
1 TAT--ATAAA
4428510 TATATAAA
1 TATATAAA
4428518 T
1 T
4428519 TATCATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
6 5 0.10
7 12 0.23
8 22 0.42
9 6 0.12
10 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TATATAAA
Found at i:4428508 original size:37 final size:39
Alignment explanation
Indices: 4428400--4428508 Score: 118
Period size: 37 Copynumber: 2.7 Consensus size: 39
4428390 TATGTAATAA
4428400 AAATAAT-TAAAATATATTATAATATAAAAAATAAATATTTT
1 AAATAATAT-AAATATA-TA-AATATAAAAAATAAATATTTT
* *
4428441 AAATTTTATATAAATATA-AAATAATTAAAAAT-AA-ATTTT
1 AAA--TAATATAAATATATAAAT-ATAAAAAATAAATATTTT
4428480 AAATAATATAAATATATAAATATAAAAAA
1 AAATAATATAAATATATAAATATAAAAAA
4428509 ATATATAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
37 19 0.32
38 4 0.07
39 8 0.14
40 5 0.08
41 12 0.20
43 10 0.17
44 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (39 bp):
AAATAATATAAATATATAAATATAAAAAATAAATATTTT
Found at i:4430190 original size:48 final size:50
Alignment explanation
Indices: 4430096--4430190 Score: 124
Period size: 48 Copynumber: 1.9 Consensus size: 50
4430086 AATTACAAAT
* *
4430096 ATTTGAAAATTAATAAAATGAAAATAAATAAATATTAATTATATTTACAC
1 ATTTGAAAAATAATAAAATGAAAATAAATAAATATTAAATATATTTACAC
* *
4430146 ATTT-AAAAATAA-AAAATTAAATTAAATAAATATATAAATA-ATTTA
1 ATTTGAAAAATAATAAAATGAAAATAAATAAATAT-TAAATATATTTA
4430191 TTTAAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 24 0.60
49 12 0.30
50 4 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (50 bp):
ATTTGAAAAATAATAAAATGAAAATAAATAAATATTAAATATATTTACAC
Found at i:4430208 original size:29 final size:30
Alignment explanation
Indices: 4430162--4430218 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
4430152 AAATAAAAAA
*
4430162 TTAAATTAAATAAATATATAAATAATTTAT
1 TTAAAATAAATAAATATATAAATAATTTAT
* *
4430192 TTAAAATAAA-AATTATATGAATAATTT
1 TTAAAATAAATAAATATATAAATAATTT
4430219 GTTAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAAATAAATAAATATATAAATAATTTAT
Found at i:4435897 original size:2 final size:2
Alignment explanation
Indices: 4435892--4435916 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4435882 ATATATATAT
4435892 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 A
4435917 AAGGAAGAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4436444 original size:23 final size:23
Alignment explanation
Indices: 4436414--4436459 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4436404 ATAATTATTA
**
4436414 ATTATTATATTTAATATAATAAT
1 ATTATTATAAATAATATAATAAT
*
4436437 ATTATTATAAATAATATATTAAT
1 ATTATTATAAATAATATAATAAT
4436460 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTATAAATAATATAATAAT
Found at i:4438084 original size:2 final size:2
Alignment explanation
Indices: 4438077--4438105 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4438067 CTTCTTTTAT
4438077 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 T
4438106 CTATTTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4439783 original size:30 final size:31
Alignment explanation
Indices: 4439738--4439808 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
4439728 ATTTTTTATA
* *
4439738 TTTT-AAAAGTAATTATTAATTA-ATTATTT
1 TTTTAAAAAATAATTATTAATTATATTAATT
*
4439767 TTTTAAAAAATAATTATTAATTATTTTAATT
1 TTTTAAAAAATAATTATTAATTATATTAATT
4439798 TTTTAAAAAAT
1 TTTTAAAAAAT
4439809 TTCGTAGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 4 0.11
30 17 0.46
31 16 0.43
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTTAAAAAATAATTATTAATTATATTAATT
Found at i:4439785 original size:26 final size:28
Alignment explanation
Indices: 4439738--4439793 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 28
4439728 ATTTTTTATA
*
4439738 TTTTAAAAGTAATTATTAATTAATTATTT
1 TTTTAAAAG-AATAATTAATTAATTATTT
4439767 TTTTAAAA-AATAATT-ATTAATTATTT
1 TTTTAAAAGAATAATTAATTAATTATTT
4439793 T
1 T
4439794 AATTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
27 6 0.23
29 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTAAAAGAATAATTAATTAATTATTT
Found at i:4442053 original size:2 final size:2
Alignment explanation
Indices: 4442048--4442083 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4442038 TTTTTTGTTT
4442048 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
4442084 CACGCAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4444108 original size:25 final size:25
Alignment explanation
Indices: 4444079--4444129 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4444069 AAATTTGATG
4444079 AATTA-TTTTATTATTTAAAAATTAA
1 AATTATTTTTA-TATTTAAAAATTAA
* *
4444104 AATTATTTTTATATTTTATAATTAA
1 AATTATTTTTATATTTAAAAATTAA
4444129 A
1 A
4444130 TTTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTATTTTTATATTTAAAAATTAA
Found at i:4444143 original size:23 final size:24
Alignment explanation
Indices: 4444113--4444157 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4444103 AAATTATTTT
4444113 TATATTTTATAAT-TAAATTTAAA
1 TATATTTTATAATATAAATTTAAA
* *
4444136 TATATTTTTTATTATAAATTTA
1 TATATTTTATAATATAAATTTA
4444158 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTTTATAATATAAATTTAAA
Found at i:4444165 original size:23 final size:23
Alignment explanation
Indices: 4444113--4444184 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
4444103 AAATTATTTT
*
4444113 TATA-TTTTATAATTAAATTTAAA
1 TATATTTTTATTA-TAAATTTAAA
4444136 TATATTTTTTATTATAAATTTATAA
1 TATA-TTTTTATTATAAATTTA-AA
4444161 -A-ATTTTTATT-TAAAATTT-AA
1 TATATTTTTATTAT-AAATTTAAA
4444181 TATA
1 TATA
4444185 CGTAGATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 15 0.36
23 5 0.12
24 9 0.21
25 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATTTTTATTATAAATTTAAA
Found at i:4444674 original size:15 final size:16
Alignment explanation
Indices: 4444654--4444684 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4444644 TAATATAAAA
4444654 TTAATTTAATT-TTAT
1 TTAATTTAATTGTTAT
4444669 TTAATTTAATTGTTAT
1 TTAATTTAATTGTTAT
4444685 AAATTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATTTAATTGTTAT
Found at i:4444763 original size:22 final size:25
Alignment explanation
Indices: 4444737--4444783 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
4444727 AATTATTTAT
*
4444737 TTAATACAAA-AA-ATTT-TAATTA
1 TTAATAAAAATAATATTTATAATTA
4444759 TTAATAAAAATAATATTTATAATTA
1 TTAATAAAAATAATATTTATAATTA
4444784 ATTTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 4 0.19
25 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAATAAAAATAATATTTATAATTA
Found at i:4444784 original size:22 final size:22
Alignment explanation
Indices: 4444725--4444785 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
4444715 TTTAAAATAT
4444725 ATAATTATTTAT-TTAATACAAA
1 ATAA-TATTTATATTAATACAAA
4444747 A-AAT-TTTAATTATTAATA-AAA
1 ATAATATTT-A-TATTAATACAAA
4444768 ATAATATTTATAATTAAT
1 ATAATATTTAT-ATTAAT
4444786 TTGATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 8 0.24
22 17 0.52
23 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAATATTTATATTAATACAAA
Found at i:4444851 original size:31 final size:32
Alignment explanation
Indices: 4444766--4444857 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 32
4444756 TTATTAATAA
*
4444766 AAATAATATTTATAATT-AATTTGATAAATTAT
1 AAATAA-ATTTATTATTAAATTTGATAAATTAT
* * *
4444798 AAATATTAATTTAATT-TAAAATTTTATATA-TAT
1 AAATA--AATTT-ATTATTAAATTTGATAAATTAT
4444831 AAATAAATTTATTATTAAATTTGATAA
1 AAATAAATTTATTATTAAATTTGATAA
4444858 TTAATTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
30 3 0.06
31 15 0.31
32 5 0.10
33 13 0.27
34 12 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
AAATAAATTTATTATTAAATTTGATAAATTAT
Found at i:4444876 original size:16 final size:16
Alignment explanation
Indices: 4444857--4444890 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4444847 AAATTTGATA
4444857 ATTAATTTATTAA-AAT
1 ATTAA-TTATTAATAAT
4444873 ATTAATTATTAATAAT
1 ATTAATTATTAATAAT
4444889 AT
1 AT
4444891 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTATTAATAAT
Found at i:4444900 original size:65 final size:63
Alignment explanation
Indices: 4444748--4444917 Score: 152
Period size: 65 Copynumber: 2.7 Consensus size: 63
4444738 TAATACAAAA
4444748 AATTTTAATTAT-TAATAAAAATAATATTTATAATTAATTTGATAAATTATAAATATTAATTT
1 AATTTTAATTATATAATAAAAATAATATTTATAATTAATTTGATAAATTATAAATATTAATTT
* * * * **
4444810 AATTTAAAATTTTATATATATAAATAA-ATTTATTATTAAATTTGAT-AATTA-ATTTATTAAAA
1 AATTT-TAATTATATA-ATAAAAATAATATTTATAATT-AATTTGATAAATTATAAATATT--AA
4444872 TATT
61 T-TT
* **
4444876 AATTATTAATAATATAATAAAAAT-ATATAAATTAATTAATTT
1 AATT-TTAATTATATAATAAAAATAATATTTA-TAATTAATTT
4444918 TATGTCAATA
Statistics
Matches: 85, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
62 5 0.06
63 10 0.12
64 17 0.20
65 35 0.41
66 17 0.20
67 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (63 bp):
AATTTTAATTATATAATAAAAATAATATTTATAATTAATTTGATAAATTATAAATATTAATTT
Found at i:4445289 original size:12 final size:12
Alignment explanation
Indices: 4445240--4445313 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
4445230 TATGTTGTTA
*
4445240 ATTTTTTATATAA
1 ATTTTTTATAT-T
*
4445253 ATTTTGATATATTT
1 ATTTT-TTATA-TT
*
4445267 ATATATTTATATT
1 AT-TTTTTATATT
*
4445280 ATTTTTTATATC
1 ATTTTTTATATT
*
4445292 ATATTTTATA-T
1 ATTTTTTATATT
4445303 ATTTTTTATAT
1 ATTTTTTATAT
4445314 CATATTTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
11 9 0.19
12 17 0.35
13 9 0.19
14 10 0.21
15 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:4445305 original size:23 final size:24
Alignment explanation
Indices: 4445267--4445320 Score: 92
Period size: 23 Copynumber: 2.2 Consensus size: 24
4445257 TGATATATTT
4445267 ATATATTTATATTATTTTTTATATC
1 ATAT-TTTATATTATTTTTTATATC
4445292 ATATTTTATA-TATTTTTTATATC
1 ATATTTTATATTATTTTTTATATC
4445315 ATATTT
1 ATATTT
4445321 AAAATTGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 19 0.66
24 6 0.21
25 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATTTTATATTATTTTTTATATC
Found at i:4445319 original size:40 final size:40
Alignment explanation
Indices: 4445240--4445319 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
4445230 TATGTTGTTA
*
4445240 ATTTTTTATATAAATTTTGATATATTTATATATTTATATT
1 ATTTTTTATATAAATTTTGATATATTTATATATTCATATT
* *
4445280 ATTTTTTATATCATATTTT-ATATATTT-TTTATATCATATT
1 ATTTTTTATAT-AAATTTTGATATATTTATATAT-TCATATT
4445320 TAAAATTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.11
40 25 0.71
41 6 0.17
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
ATTTTTTATATAAATTTTGATATATTTATATATTCATATT
Found at i:4447528 original size:23 final size:23
Alignment explanation
Indices: 4447496--4447539 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4447486 AAATCTGATG
4447496 TGACAAAACACATAATAAAAACA
1 TGACAAAACACATAATAAAAACA
* *
4447519 TGACATAACACATTATAAAAA
1 TGACAAAACACATAATAAAAA
4447540 AATCCAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (23 bp):
TGACAAAACACATAATAAAAACA
Found at i:4448443 original size:9 final size:9
Alignment explanation
Indices: 4448431--4448457 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4448421 AAATTATTTA
4448431 AATTTTATT
1 AATTTTATT
4448440 AATTTTATT
1 AATTTTATT
4448449 AATTTTATT
1 AATTTTATT
4448458 TTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
AATTTTATT
Found at i:4450018 original size:31 final size:31
Alignment explanation
Indices: 4449964--4450047 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 31
4449954 CAATATTCTA
* * **
4449964 TTGATGTATAAGTTAAAGTTTAAACAATTTAT
1 TTGAAGTATAAATTAAAAATTAAA-AATTTAT
*
4449996 TT-AAGTATAAATTAAAAATTAAAATTTTAT
1 TTGAAGTATAAATTAAAAATTAAAAATTTAT
4450026 TTGAA-TAT-AA-TAAAAATATAAA
1 TTGAAGTATAAATTAAAAAT-TAAA
4450048 GATATAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.16
29 6 0.13
30 11 0.24
31 19 0.42
32 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (31 bp):
TTGAAGTATAAATTAAAAATTAAAAATTTAT
Found at i:4450027 original size:30 final size:29
Alignment explanation
Indices: 4449991--4450047 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
4449981 GTTTAAACAA
4449991 TTTATTT-AAGTATAAATTAAAAAT-TAAAAT
1 TTTATTTGAA-TAT-AA-TAAAAATATAAAAT
4450021 TTTATTTGAATATAATAAAAATATAAA
1 TTTATTTGAATATAATAAAAATATAAA
4450048 GATATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.28
29 6 0.24
30 10 0.40
31 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTATTTGAATATAATAAAAATATAAAAT
Found at i:4450245 original size:21 final size:20
Alignment explanation
Indices: 4450200--4450259 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
4450190 AATTAAATAA
* *
4450200 TAATTAAATTATTTAAAAAT
1 TAATTAAATTAATAAAAAAT
* * *
4450220 TAATTTATTTGATAAAAAAT
1 TAATTAAATTAATAAAAAAT
4450240 TAAATTAAATTAATAAAAAA
1 T-AATTAAATTAATAAAAAA
4450260 AATCATATGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATTAAATTAATAAAAAAT
Found at i:4451147 original size:26 final size:27
Alignment explanation
Indices: 4451106--4451156 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
4451096 AAAACTAAAC
* *
4451106 TTAAATTTATATATTAATT-TTAATTA
1 TTAAATTTAAAAATTAATTATTAATTA
*
4451132 TTAAATTTAAAAATTATTTATTAAT
1 TTAAATTTAAAAATTAATTATTAAT
4451157 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAAATTTAAAAATTAATTATTAATTA
Found at i:4451227 original size:28 final size:27
Alignment explanation
Indices: 4451173--4451228 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
4451163 TTATTAAAAT
* *
4451173 TTTTAATAATAAATATTAATGATTTTA
1 TTTTAATAAAAAATATTAATGAATTTA
*
4451200 TTTTAATAAAATAATATTAATTAATTTA
1 TTTTAATAAAA-AATATTAATGAATTTA
4451228 T
1 T
4451229 AAATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTAATAAAAAATATTAATGAATTTA
Found at i:4451554 original size:17 final size:19
Alignment explanation
Indices: 4451525--4451564 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
4451515 TATTTGATCA
4451525 TTAT-TTTAGAAAA-ACTT
1 TTATATTTAGAAAATACTT
*
4451542 TTATATTTA-AAAATATTT
1 TTATATTTAGAAAATACTT
4451560 TTATA
1 TTATA
4451565 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTATATTTAGAAAATACTT
Found at i:4453138 original size:2 final size:2
Alignment explanation
Indices: 4453127--4453167 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
4453117 AAGCATGGTC
*
4453127 TA TA -A TA TA TA TA TA TA TA TA TA TA TG 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
4453168 GTGAGAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4453489 original size:69 final size:69
Alignment explanation
Indices: 4453378--4453517 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 69
4453368 TTAGCTATAT
* * * *
4453378 ATTGAAAATATTAATTTTCTTAATAGATATGATTGAGATATCGGATGTATTCAAAACTTTACACG
1 ATTGAAAATATCAATATTCTCAATAGATATGATTGAGATATCGGATGTATTCAAAACTTTACAAG
4453443 CATG
66 CATG
* *
4453447 ATTGAAAATATCAATATTCTCGATCA-ATATGATT-AGGATATCGGATGTATTCGAAACTTTACA
1 ATTGAAAATATCAATATTCTCAAT-AGATATGATTGA-GATATCGGATGTATTCAAAACTTTACA
4453510 AGCATG
64 AGCATG
4453516 AT
1 AT
4453518 GAATACAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
68 1 0.02
69 61 0.97
70 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (69 bp):
ATTGAAAATATCAATATTCTCAATAGATATGATTGAGATATCGGATGTATTCAAAACTTTACAAG
CATG
Found at i:4454552 original size:2 final size:2
Alignment explanation
Indices: 4454547--4454573 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4454537 TTTTGGGCAG
4454547 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4454574 CTTAGAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4456128 original size:9 final size:9
Alignment explanation
Indices: 4456110--4456185 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
4456100 TTTATATGAT
*
4456110 ATAAATATA
1 ATAAAAATA
4456119 ATAAAAATA
1 ATAAAAATA
4456128 ATTAAAATATA
1 A-TAAAA-ATA
* *
4456139 ATATAAATT
1 ATAAAAATA
4456148 ATATAAAAT-
1 ATA-AAAATA
4456157 ATAAAAAATA
1 AT-AAAAATA
4456167 ATATAAATATA
1 ATA-AAA-ATA
*
4456178 TTAAAAAT
1 ATAAAAAT
4456186 TATATAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
9 24 0.44
10 22 0.40
11 9 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATA
Found at i:4456167 original size:39 final size:41
Alignment explanation
Indices: 4456108--4456192 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 41
4456098 TTTTTATATG
*
4456108 ATAT-AAATATAATAAAAATAAT-TAAAATATAATATAAATT
1 ATATAAAATATAATAAAAATAATAT-AAATATAATAAAAATT
*
4456148 ATATAAAATAT-A-AAAAATAATATAAATATATTAAAAATT
1 ATATAAAATATAATAAAAATAATATAAATATAATAAAAATT
4456187 ATATAA
1 ATATAA
4456193 TATAAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
39 29 0.71
40 6 0.15
41 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (41 bp):
ATATAAAATATAATAAAAATAATATAAATATAATAAAAATT
Found at i:4456190 original size:20 final size:20
Alignment explanation
Indices: 4456108--4456197 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
4456098 TTTTTATATG
4456108 ATATAAATATAATAAAAATA
1 ATATAAATATAATAAAAATA
* *
4456128 AT-TAAAATATAATATAAATT
1 ATAT-AAATATAATAAAAATA
4456148 ATATAAA-AT-ATAAAAAATA
1 ATATAAATATAAT-AAAAATA
* *
4456167 ATATAAATATATTAAAAATT
1 ATATAAATATAATAAAAATA
4456187 ATAT-AATATAA
1 ATATAAATATAA
4456198 ATTTTTAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 21 0.36
20 33 0.57
21 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATAAATATAATAAAAATA
Found at i:4456208 original size:32 final size:32
Alignment explanation
Indices: 4456155--4456241 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
4456145 ATTATATAAA
* * *
4456155 ATATAAAAAATAATATAAATATATTAAAAATT
1 ATATAAATAATATTTTAAATATATTAAAAATT
* * *
4456187 ATATAATATAA-ATTTTTAATATATTTAAATTT
1 ATATAA-ATAATATTTTAAATATATTAAAAATT
4456219 ATATAAATAATATTTTAAATATA
1 ATATAAATAATATTTTAAATATA
4456242 ATTATAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.09
32 39 0.85
33 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAAATAATATTTTAAATATATTAAAAATT
Found at i:4456233 original size:21 final size:21
Alignment explanation
Indices: 4456111--4456280 Score: 85
Period size: 20 Copynumber: 8.4 Consensus size: 21
4456101 TTATATGATA
4456111 TAAATATA-ATAAA-AATAATT
1 TAAATATATATAAATAAT-ATT
* *
4456131 AAAATATAATATAAATTATA-T
1 TAAATAT-ATATAAATAATATT
* *
4456152 AAAATATA-AAAAATAATA--
1 TAAATATATATAAATAATATT
*
4456170 TAAATATAT-TAAA-AATTATA
1 TAAATATATATAAATAA-TATT
* * *
4456190 TAATATAAATTTTTAAT-ATATT
1 TAA-ATATA-TATAAATAATATT
*
4456212 TAAATTTATATAAATAATATTT
1 TAAATATATATAAATAATA-TT
*
4456234 TAAATATA-AT-TATAATATT
1 TAAATATATATAAATAATATT
* * *
4456253 TAAAAATATAT-AATACTATA
1 TAAATATATATAAATAATATT
4456273 TAAATATA
1 TAAATATA
4456281 AAAACAGATG
Statistics
Matches: 116, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.02
18 12 0.10
19 17 0.15
20 36 0.31
21 21 0.18
22 22 0.19
23 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATATATAAATAATATT
Found at i:4456250 original size:23 final size:23
Alignment explanation
Indices: 4456203--4456248 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4456193 TATAAATTTT
*
4456203 TAATATATTTAAATTTATATAAA
1 TAATATATTTAAATTAATATAAA
4456226 TAATAT-TTTAAATATAATTATAA
1 TAATATATTTAAAT-TAA-TATAA
4456249 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATATTTAAATTAATATAAA
Found at i:4456274 original size:103 final size:101
Alignment explanation
Indices: 4456097--4456280 Score: 232
Period size: 103 Copynumber: 1.8 Consensus size: 101
4456087 ATGTAATTAT
4456097 ATTTTTATATGATATAAATATAATAAAAATAATTAAAATATAATATAAATTATATAAAATATAAA
1 ATTTTTATATGATATAAATATAATAAAAATAATTAAAATATAATATAAATTATATAAAATATAAA
4456162 AAATAATATAAATATATTAAAAATTATATAATATAA
66 AAATAATATAAATATATTAAAAATTATATAATATAA
* * * *
4456198 ATTTTTAATAT-ATTTAAATTTATATAAATAATATTTTAAATATAATTATAATATT-TA-AAAAT
1 ATTTTT-ATATGATATAAATATA-ATAAA-AATAATTAAAATATAA-TATAA-ATTATATAAAAT
* *
4456260 ATATAATACT-ATATAAATATA
61 ATA-AAAAATAATATAAATATA
4456281 AAAACAGATG
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
101 15 0.21
102 9 0.13
103 33 0.46
104 11 0.15
105 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (101 bp):
ATTTTTATATGATATAAATATAATAAAAATAATTAAAATATAATATAAATTATATAAAATATAAA
AAATAATATAAATATATTAAAAATTATATAATATAA
Found at i:4459028 original size:2 final size:2
Alignment explanation
Indices: 4459021--4459061 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4459011 AATGTGTAGA
4459021 AT AT AT 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 AT AT AT A
4459062 ATCTTTTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4459123 original size:22 final size:22
Alignment explanation
Indices: 4459098--4459142 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4459088 AAAATTCTAA
4459098 ACATGAATATTTCACTTTTCTG
1 ACATGAATATTTCACTTTTCTG
*
4459120 ACATGAATATTTCGCTTTTCTG
1 ACATGAATATTTCACTTTTCTG
4459142 A
1 A
4459143 TATAGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (22 bp):
ACATGAATATTTCACTTTTCTG
Found at i:4459237 original size:29 final size:29
Alignment explanation
Indices: 4459195--4459253 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4459185 TCCCACGTTG
*
4459195 AATAGGAAAGTTAAGATTAAATAATTTAT
1 AATAGGAAAGTTAAAATTAAATAATTTAT
4459224 AATAGGAAAGTTAAAATTAAATAATTTAT
1 AATAGGAAAGTTAAAATTAAATAATTTAT
4459253 A
1 A
4459254 TTATGTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (29 bp):
AATAGGAAAGTTAAAATTAAATAATTTAT
Found at i:4460615 original size:33 final size:33
Alignment explanation
Indices: 4460534--4460615 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
4460524 AAAGATATTC
*
4460534 ATTACTTATAATAATAGGTTTATAAAATATTTTA
1 ATTAATTATAAT-ATAGGTTTATAAAATATTTTA
* * * *
4460568 ATAAATTTTTATATA-GTTT-TTAAATATTAATTA
1 ATTAATTATAATATAGGTTTATAAAATATT--TTA
4460601 ATTAATTATAATATA
1 ATTAATTATAATATA
4460616 ATTATTATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
31 8 0.21
32 4 0.11
33 18 0.47
34 8 0.21
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (33 bp):
ATTAATTATAATATAGGTTTATAAAATATTTTA
Found at i:4460855 original size:25 final size:25
Alignment explanation
Indices: 4460800--4460862 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
4460790 TTTAAAAAAT
*
4460800 TATATTTA-ATATATTGATAGTGTA
1 TATATTTATATATATTGATAGTATA
* *
4460824 AAAATTTATATATATT-ATTAGTATA
1 TATATTTATATATATTGA-TAGTATA
*
4460849 TATATTTTTATATA
1 TATATTTATATATA
4460863 ATTAAAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
TATATTTATATATATTGATAGTATA
Found at i:4463819 original size:19 final size:18
Alignment explanation
Indices: 4463773--4463821 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
4463763 TTTGTTTTTG
**
4463773 ATTTTAAACTTAAATAATT
1 ATTTTAAA-TTAAATAAAA
4463792 ATTTATAAATTAATATAAAA
1 ATTT-TAAATTAA-ATAAAA
4463812 ATTTTAAATT
1 ATTTTAAATT
4463822 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTAAATAAAA
Found at i:4463862 original size:33 final size:33
Alignment explanation
Indices: 4463793--4463862 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
4463783 TAAATAATTA
* *
4463793 TTTATAAATTAATATAAAAATTTTAAATTTTTT
1 TTTATAAATTAATATAAAAATTTTAAATATTCT
*
4463826 TTTAT-AATTAA-ATATATAATTTTAAAATATTCT
1 TTTATAAATTAATATA-AAAATTTT-AAATATTCT
4463859 TTTA
1 TTTA
4463863 ATCATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 13 0.41
33 16 0.50
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTATAAATTAATATAAAAATTTTAAATATTCT
Found at i:4464850 original size:21 final size:21
Alignment explanation
Indices: 4464810--4464851 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4464800 ATTAAATGGG
* *
4464810 TGAAAAAAGTTATGTGAAAAA
1 TGAAAAAAGTTATATAAAAAA
*
4464831 TGAAAAAAGTTTTATAAAAAA
1 TGAAAAAAGTTATATAAAAAA
4464852 AAGGAGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (21 bp):
TGAAAAAAGTTATATAAAAAA
Found at i:4467164 original size:12 final size:12
Alignment explanation
Indices: 4467132--4467164 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4467122 ATTTTGAGCT
*
4467132 GAGTTGACAAGC
1 GAGTTGACTAGC
4467144 GAGTTGACTAGC
1 GAGTTGACTAGC
4467156 GAGTTGACT
1 GAGTTGACT
4467165 TGTTGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (12 bp):
GAGTTGACTAGC
Found at i:4471660 original size:22 final size:22
Alignment explanation
Indices: 4471634--4471698 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
4471624 ACACATTTGA
4471634 TTTATTAAAATAAAATAATTAT
1 TTTATTAAAATAAAATAATTAT
*
4471656 TTTATAAAAATAAAATAA--AT
1 TTTATTAAAATAAAATAATTAT
* *
4471676 TTAAAATAAAATAAAATAATTAT
1 TT-TATTAAAATAAAATAATTAT
4471699 AACAGTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 17 0.47
23 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTATTAAAATAAAATAATTAT
Found at i:4473555 original size:2 final size:2
Alignment explanation
Indices: 4473548--4473583 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4473538 AGCTTAAAAT
4473548 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
4473584 ACTTTCACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4482261 original size:3 final size:3
Alignment explanation
Indices: 4482255--4482290 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
4482245 GATGATGATG
**
4482255 ATA ATA ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4482291 GTTAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4485406 original size:3 final size:3
Alignment explanation
Indices: 4485398--4485440 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
4485388 AATTTCAACC
4485398 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4485441 TCTTCTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4486074 original size:11 final size:11
Alignment explanation
Indices: 4486047--4486080 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
4486037 AATTTCGAAC
4486047 ACAATATAATTAT
1 ACAATATAA--AT
4486060 ACAATATAAAT
1 ACAATATAAAT
4486071 ACAATATAAA
1 ACAATATAAA
4486081 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
13 9 0.43
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
ACAATATAAAT
Found at i:4486121 original size:24 final size:24
Alignment explanation
Indices: 4486075--4486121 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4486065 ATAAATACAA
*
4486075 TATAAAAAAATTAAAATATGCAAC
1 TATAAAAAAATTAAAATAAGCAAC
*
4486099 TATACAAAAAA-TAATATAAGCAA
1 TATA-AAAAAATTAAAATAAGCAA
4486122 AATATGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (24 bp):
TATAAAAAAATTAAAATAAGCAAC
Found at i:4486227 original size:17 final size:18
Alignment explanation
Indices: 4486191--4486239 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
4486181 TTATATAAAT
4486191 ATATAATATATTAAATATTA
1 ATATAATATA--AAATATTA
*
4486211 TTATAATATAAAA-ATTA
1 ATATAATATAAAATATTA
4486228 ATATAAATATAA
1 ATAT-AATATAA
4486240 TATAAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
20 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATATAAAATATTA
Found at i:4486247 original size:17 final size:17
Alignment explanation
Indices: 4486183--4486247 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
4486173 ATCAAAACTT
4486183 ATATAAATATATAATAT-
1 ATATAAATATA-AATATA
* *
4486200 AT-TAAATATTATTATA
1 ATATAAATATAAATATA
* *
4486216 ATATAAAAATTAATATA
1 ATATAAATATAAATATA
4486233 A-ATATAATATAAATA
1 ATATA-AATATAAATA
4486248 CATATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 4 0.10
16 12 0.31
17 23 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAATATAAATATA
Found at i:4487634 original size:16 final size:16
Alignment explanation
Indices: 4487601--4487655 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
4487591 TTATATTAAA
*
4487601 TTATTTAAATAAAATTT
1 TTATTTAAAT-TAATTT
*
4487618 TTATTTGAATTAATTT
1 TTATTTAAATTAATTT
4487634 TTAATTTAAATT-ATTAT
1 TT-ATTTAAATTAATT-T
4487651 TTATT
1 TTATT
4487656 CATAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATTTAAATTAATTT
Found at i:4487653 original size:17 final size:17
Alignment explanation
Indices: 4487573--4487653 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
4487563 GATTTAAAAA
4487573 TTAAATTATTTATTTAAT
1 TTAAATTA-TTATTTAAT
*
4487591 TTATATTAAATTATTTAA-
1 TTAAATT--ATTATTTAAT
*
4487609 ATAAA--ATT-TTT-AT
1 TTAAATTATTATTTAAT
*
4487622 TTGAATTAATT-TTTAAT
1 TTAAATT-ATTATTTAAT
4487639 TTAAATTATTATTTA
1 TTAAATTATTATTTA
4487654 TTCATAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 3 0.06
16 9 0.18
17 12 0.24
18 9 0.18
19 8 0.16
20 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TTAAATTATTATTTAAT
Found at i:4488070 original size:11 final size:11
Alignment explanation
Indices: 4488056--4488137 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
4488046 TATTTTTTAA
*
4488056 AAAATATATAT
1 AAAATAAATAT
4488067 AAAATAAATAT
1 AAAATAAATAT
4488078 -AAA-AAATA-
1 AAAATAAATAT
4488086 AAAA-AAA-AT
1 AAAATAAATAT
*
4488095 AAAA-AAATAAA
1 AAAATAAAT-AT
4488106 AAAATTAAAT-T
1 AAAA-TAAATAT
*
4488117 AAATTAAAT-T
1 AAAATAAATAT
*
4488127 AAACTAAATAT
1 AAAATAAATAT
4488138 GATCCAACTG
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.02
9 18 0.31
10 17 0.29
11 19 0.32
13 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:4488077 original size:13 final size:13
Alignment explanation
Indices: 4488053--4488119 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
4488043 TTATATTTTT
4488053 TAAAAAAT--ATA
1 TAAAAAATAAATA
*
4488064 TATAAAATAAATA
1 TAAAAAATAAATA
*
4488077 TAAAAAATAAAAA
1 TAAAAAATAAATA
* *
4488090 AAAATAAAAAAATA
1 TAAA-AAATAAATA
4488104 -AAAAAATTAAAT-
1 TAAAAAA-TAAATA
4488116 TAAA
1 TAAA
4488120 TTAAATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
11 7 0.16
12 3 0.07
13 27 0.61
14 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAAAAATAAATA
Found at i:4488090 original size:9 final size:9
Alignment explanation
Indices: 4488065--4488114 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
4488055 AAAAATATAT
*
4488065 ATAAAATAA
1 ATAAAAAAA
*
4488074 ATATAAAAA
1 ATAAAAAAA
4488083 ATAAAAAAA
1 ATAAAAAAA
4488092 A-ATAAAAAA
1 ATA-AAAAAA
4488101 ATAAAAAAA
1 ATAAAAAAA
*
4488110 TTAAA
1 ATAAA
4488115 TTAAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 1 0.03
9 33 0.94
10 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:4488091 original size:8 final size:8
Alignment explanation
Indices: 4488065--4488110 Score: 56
Period size: 8 Copynumber: 5.2 Consensus size: 8
4488055 AAAAATATAT
4488065 ATAAAATAA
1 ATAAAA-AA
4488074 ATATAAAAA
1 ATA-AAAAA
4488083 ATAAAAAAAA
1 AT--AAAAAA
4488093 ATAAAAAA
1 ATAAAAAA
4488101 ATAAAAAA
1 ATAAAAAA
4488109 AT
1 AT
4488111 TAAATTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 16 0.47
9 7 0.21
10 10 0.29
11 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:4488093 original size:10 final size:10
Alignment explanation
Indices: 4488078--4488109 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4488068 AAATAAATAT
4488078 AAAAAATAAA
1 AAAAAATAAA
4488088 AAAAAAT--A
1 AAAAAATAAA
4488096 AAAAAATAAA
1 AAAAAATAAA
4488106 AAAA
1 AAAA
4488110 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:4488120 original size:18 final size:18
Alignment explanation
Indices: 4488053--4488109 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 18
4488043 TTATATTTTT
4488053 TAAAAAATATATATAAAATAAA
1 TAAAAAA-ATA-A-AAAA-AAA
4488075 TATAAAAAATAAAAAAAAA
1 TA-AAAAAATAAAAAAAAA
4488094 TAAAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
4488110 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 14 0.41
19 5 0.15
20 4 0.12
21 1 0.03
22 5 0.15
23 5 0.15
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAAA
Found at i:4488371 original size:14 final size:15
Alignment explanation
Indices: 4488352--4488382 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4488342 TATTTTAGTT
4488352 TTAAATATATTT-TA
1 TTAAATATATTTATA
4488366 TTAAATATATTTATA
1 TTAAATATATTTATA
4488381 TT
1 TT
4488383 TTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATATATTTATA
Found at i:4488385 original size:31 final size:30
Alignment explanation
Indices: 4488342--4488404 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 30
4488332 TTCGATCGAT
4488342 TATTTTAGTTTTA-AATATATTTTATTAAATA
1 TATTTTAGTTTTATAA-ATATTTT-TTAAATA
4488373 TATTTATA-TTTTATTAAATATTTTTTAAATA
1 TATTT-TAGTTTTA-TAAATATTTTTTAAATA
4488404 T
1 T
4488405 TAATTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
31 18 0.62
32 9 0.31
33 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TATTTTAGTTTTATAAATATTTTTTAAATA
Found at i:4488400 original size:11 final size:12
Alignment explanation
Indices: 4488358--4488405 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
4488348 AGTTTTAAAT
4488358 ATATTTTATTAA
1 ATATTTTATTAA
*
4488370 ATA---TATT-T
1 ATATTTTATTAA
4488378 ATATTTTATTAA
1 ATATTTTATTAA
4488390 ATATTTT-TTAA
1 ATATTTTATTAA
4488401 ATATT
1 ATATT
4488406 AATTTGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
11 13 0.43
12 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:4489278 original size:3 final size:3
Alignment explanation
Indices: 4489270--4489296 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4489260 ACTATTGCTC
4489270 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4489297 ATTTTTTTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4490446 original size:28 final size:27
Alignment explanation
Indices: 4490385--4490478 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
4490375 AAACCACCCA
*
4490385 TATATTTGTCAAAAATAGTGGTTATTT
1 TATATTTGTCAAAAATGGTGGTTATTT
*
4490412 TATATTTGTCAAAAATGGTGGTTTTCTT
1 TATATTTGTCAAAAATGGTGGTTAT-TT
* * * * *
4490440 TGTATTTGTCAAATATGGAGGCT-TGT
1 TATATTTGTCAAAAATGGTGGTTATTT
4490466 T-TATTTGTCAAAA
1 TATATTTGTCAAAA
4490479 TTTGTGACTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
25 11 0.19
26 2 0.03
27 24 0.41
28 21 0.36
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (27 bp):
TATATTTGTCAAAAATGGTGGTTATTT
Found at i:4490590 original size:21 final size:20
Alignment explanation
Indices: 4490550--4490590 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4490540 CTCATTCTCA
*
4490550 TGTATCCCTCATCCTTCTTT
1 TGTATCCCTCATCATTCTTT
*
4490570 TGTATCCCTCTTCAATTCTTT
1 TGTATCCCTCATC-ATTCTTT
4490591 CTCATAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.12, C:0.32, G:0.05, T:0.51
Consensus pattern (20 bp):
TGTATCCCTCATCATTCTTT
Found at i:4493060 original size:21 final size:22
Alignment explanation
Indices: 4493031--4493076 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
4493021 TGTTCAGACA
**
4493031 AGTAGTACTCCACGACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4493053 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4493074 AGT
1 AGT
4493077 TTCAACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Done.