Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold169
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: 2015121
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 45543 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:4506 original size:7 final size:7
Alignment explanation
Indices: 4496--4520 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4486 CTTAAACCCG
4496 AATCTCT
1 AATCTCT
4503 AATCTCT
1 AATCTCT
4510 AATCTCT
1 AATCTCT
4517 AATC
1 AATC
4521 ATTAAACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
AATCTCT
Found at i:9193 original size:11 final size:11
Alignment explanation
Indices: 9177--9201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9167 GTGTGACCTG
9177 TTTCTTTTCTT
1 TTTCTTTTCTT
9188 TTTCTTTTCTT
1 TTTCTTTTCTT
9199 TTT
1 TTT
9202 GGTTCGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:9610 original size:21 final size:21
Alignment explanation
Indices: 9586--9642 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
9576 AAATATTTCT
9586 TTTAAATTAATTAATATATTA
1 TTTAAATTAATTAATATATTA
*
9607 TTTATAA-TAATAATAATATTTTA
1 TTTA-AATTAAT--TAATATATTA
*
9630 TATTAAATAAATT
1 T-TTAAATTAATT
9643 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
21 8 0.28
22 3 0.10
23 12 0.41
24 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAATTAATTAATATATTA
Found at i:9697 original size:35 final size:35
Alignment explanation
Indices: 9614--9697 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
9604 TTATTTATAA
* *
9614 TAATAATAATATTT--TATATTAAATAAATTTTTT
1 TAATAATAATCTTTAATATATTAAATAAATATTTT
* * *
9647 TATTTATAATTTTTAATATATTAAATAAAATATTTT
1 TAATAATAATCTTTAATATATTAAAT-AAATATTTT
9683 TAATAATAA-CTTTAA
1 TAATAATAATCTTTAA
9698 AACACTTGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 11 0.27
35 15 0.37
36 15 0.37
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (35 bp):
TAATAATAATCTTTAATATATTAAATAAATATTTT
Found at i:11376 original size:26 final size:26
Alignment explanation
Indices: 11327--11376 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
11317 TTTTTAAAAC
* *
11327 AAAAAAACAAACAAATGAAAAAAAGT
1 AAAAAAACAAAAAAACGAAAAAAAGT
* *
11353 AAAATAACAAAAAAACGAATAAAA
1 AAAAAAACAAAAAAACGAAAAAAA
11377 CAAATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.78, C:0.08, G:0.06, T:0.08
Consensus pattern (26 bp):
AAAAAAACAAAAAAACGAAAAAAAGT
Found at i:11378 original size:17 final size:17
Alignment explanation
Indices: 11321--11380 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
11311 TGTTTTTTTT
*
11321 TAAAACAAAAAAACAAA
1 TAAAACAAAAAAACGAA
* **
11338 CAAATGAAAAAAA-GTAA
1 TAAAACAAAAAAACG-AA
11355 -AATAACAAAAAAACGAA
1 TAA-AACAAAAAAACGAA
11372 TAAAACAAA
1 TAAAACAAA
11381 TATCAATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 2 0.06
17 28 0.85
18 3 0.09
ACGTcount: A:0.77, C:0.10, G:0.05, T:0.08
Consensus pattern (17 bp):
TAAAACAAAAAAACGAA
Found at i:11904 original size:28 final size:26
Alignment explanation
Indices: 11854--11918 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
11844 ACTTTTTAAA
*
11854 TATATAATAATATTAAATTTTATCATTT
1 TATATAATAATATT-AATTTTAT-AATT
11882 TATATAATATATATT-ATTCTTATAATT
1 TATATAATA-ATATTAATT-TTATAATT
*
11909 TAAATAATAA
1 TATATAATAA
11919 AAAATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 14 0.42
28 13 0.39
29 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATAATAATATTAATTTTATAATT
Found at i:18308 original size:16 final size:15
Alignment explanation
Indices: 18287--18334 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
18277 AATTGGGTAG
18287 GTTAGGTTGGTTTCGA
1 GTTAGGTT-GTTTCGA
18303 GTTAGGTTGTTTCG-
1 GTTAGGTTGTTTCGA
* * *
18317 GGTAGATTATTTCGA
1 GTTAGGTTGTTTCGA
18332 GTT
1 GTT
18335 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.15, C:0.06, G:0.33, T:0.46
Consensus pattern (15 bp):
GTTAGGTTGTTTCGA
Found at i:20792 original size:61 final size:60
Alignment explanation
Indices: 20715--20832 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 60
20705 ACTAAATTTT
* **
20715 ATGTTTTTTTTTAAAGTAG-CATGCAGATGGAAAACTCCAAAATCAACTTTAAAAGTCGAG
1 ATGTTTTTTTTAAAAGT-GTCACACAGATGGAAAACTCCAAAATCAACTTTAAAAGTCGAG
* * *
20775 ATGTTTTTTTTAAAAAGTGTCACATATATGGAAAACTCCAAGATCAACTTTAAAAGTC
1 ATGTTTTTTTT-AAAAGTGTCACACAGATGGAAAACTCCAAAATCAACTTTAAAAGTC
20833 AAGAAGAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 12 0.24
61 38 0.76
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (60 bp):
ATGTTTTTTTTAAAAGTGTCACACAGATGGAAAACTCCAAAATCAACTTTAAAAGTCGAG
Found at i:22143 original size:96 final size:96
Alignment explanation
Indices: 22026--22199 Score: 269
Period size: 96 Copynumber: 1.8 Consensus size: 96
22016 TACCAATTAG
* *
22026 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAA-TAAAAAAATTTATCTTTAATTAAA
1 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATTAAAAAAATTTATATCTAATTAAA
*
22090 ATAAATTAAATTAATTAAGAGATAAATCAATA
66 ATAAACT-AATTAATTAAGAGATAAATCAATA
* **
22122 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATTAAGTAAATTTATATCTAATTAAA
1 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATTAAAAAAATTTATATCTAATTAAA
*
22187 TTAAACTAATTAA
66 ATAAACTAATTAA
22200 GAGATAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
96 45 0.64
97 25 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (96 bp):
AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATTAAAAAAATTTATATCTAATTAAA
ATAAACTAATTAATTAAGAGATAAATCAATA
Found at i:22144 original size:46 final size:46
Alignment explanation
Indices: 22026--22216 Score: 240
Period size: 46 Copynumber: 4.1 Consensus size: 46
22016 TACCAATTAG
* *
22026 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATAAAAA
1 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATAAATA
* * *
22072 AATTTATCTTTAATTAAAATAAATTAAATTAATTAAGAGATAAATCAATA
1 AATTT-TATTT-A-T-AATTAAATTAAATTAATTAAGAGATAAATAAATA
*
22122 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATTAAGTA
1 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAA-TAAATA
* * * *
22169 AA-TTTATATCTAATTAAATTAAACTAATTAAGAGATAAATAAAAA
1 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATAAATA
22214 AAT
1 AAT
22217 AAGTTTTTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
45 6 0.05
46 66 0.53
47 11 0.09
48 2 0.02
49 5 0.04
50 35 0.28
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (46 bp):
AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATAAATA
Found at i:22211 original size:25 final size:24
Alignment explanation
Indices: 22088--22211 Score: 71
Period size: 25 Copynumber: 5.3 Consensus size: 24
22078 TCTTTAATTA
22088 AAATAAATTAAATTAATTAAGAGAT
1 AAATAAATTAAA-TAATTAAGAGAT
* * ***
22113 AAATCAA-TAAAT--TTTATTTAT
1 AAATAAATTAAATAATTAAGAGAT
*
22134 AATTAAATTAAATTAATTAAGAGAT
1 AAATAAATTAAA-TAATTAAGAGAT
* * * **
22159 AAATTAAGTAAAT--TT-ATATCT
1 AAATAAATTAAATAATTAAGAGAT
*
22180 AATTAAATTAAACTAATTAAGAGAT
1 AAATAAATTAAA-TAATTAAGAGAT
22205 AAATAAA
1 AAATAAA
22212 AAAATAAGTT
Statistics
Matches: 67, Mismatches: 24, Indels: 16
0.63 0.22 0.15
Matches are distributed among these distances:
21 22 0.33
22 7 0.10
23 2 0.03
24 7 0.10
25 29 0.43
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AAATAAATTAAATAATTAAGAGAT
Found at i:22218 original size:96 final size:96
Alignment explanation
Indices: 22026--22223 Score: 247
Period size: 96 Copynumber: 2.1 Consensus size: 96
22016 TACCAATTAG
* *
22026 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATAAAAAAATTTATCTTTAATTAAAA
1 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATAAAAAAATTTATATCTAATTAAAA
* * * **
22091 TAAATTAAATTAATTAAGAGATAAATCAATA
66 TAAACTAAATTAATGAAGAAATAAAAAAATA
* **
22122 AATTTTATTTATAATTAAATTAAATTAATTAAGAGATAAATTAAGTAAATTTATATCTAATTAAA
1 AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAA-TAAAAAAATTTATATCTAATTAAA
* *
22187 TTAAACT-AATTAA-GAGATAAATAAAAAAATA
65 ATAAACTAAATTAATGA-AGAAATAAAAAAATA
*
22218 AGTTTT
1 AATTTT
22224 TTTGAAACTT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 1 0.01
96 61 0.70
97 25 0.29
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (96 bp):
AATTTTATTTATAATTAAATTAAATTAAATAAGAGATAAATAAAAAAATTTATATCTAATTAAAA
TAAACTAAATTAATGAAGAAATAAAAAAATA
Found at i:26155 original size:17 final size:16
Alignment explanation
Indices: 26133--26166 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
26123 GAATTGAATT
26133 AAATTATAAAATTAAAA
1 AAATTATAAAA-TAAAA
*
26150 AAATTATACAATAAAA
1 AAATTATAAAATAAAA
26166 A
1 A
26167 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTATAAAATAAAA
Found at i:29695 original size:5 final size:5
Alignment explanation
Indices: 29656--29689 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
29646 CGATCAGAGC
29656 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
29690 ATTATAGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:31162 original size:2 final size:2
Alignment explanation
Indices: 31155--31186 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31145 AGCCCATTAA
31155 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
31187 GCATTCACAA
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:31850 original size:2 final size:2
Alignment explanation
Indices: 31845--31877 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31835 TATATATATA
*
31845 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31878 TTATATATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:32633 original size:3 final size:3
Alignment explanation
Indices: 32625--32663 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
32615 CAGGTCTTTA
32625 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32664 ATAAATGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32861 original size:2 final size:2
Alignment explanation
Indices: 32854--32897 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
32844 GTTAGTCGTA
32854 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
32896 AT
1 AT
32898 GGGAATCTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37294 original size:2 final size:2
Alignment explanation
Indices: 37287--37325 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37277 AATAAATTAA
37287 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
37326 CTCAAGGTTG
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:42306 original size:3 final size:3
Alignment explanation
Indices: 42298--42335 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42288 CGTTTAACAC
42298 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42336 AAAACCAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42954 original size:21 final size:21
Alignment explanation
Indices: 42918--43016 Score: 66
Period size: 21 Copynumber: 4.8 Consensus size: 21
42908 GCTTTTTATT
42918 AAAAATATATAAATT-AGATAA
1 AAAAATATATAAATTAAG-TAA
* **
42939 AATAATATATTTATTAAGTAA
1 AAAAATATATAAATTAAGTAA
**
42960 AAAAATATA-ATTTTTATAGTAA
1 AAAAATATATA-AATTA-AGTAA
*
42982 AAAATTATTATAAATT-A-TAA
1 AAAAATA-TATAAATTAAGTAA
43002 AAAAA-AT-TAAATTAA
1 AAAAATATATAAATTAA
43017 AATATATCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 1 0.02
20 7 0.11
21 28 0.45
22 13 0.21
23 4 0.06
24 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAATATATAAATTAAGTAA
Found at i:43351 original size:27 final size:27
Alignment explanation
Indices: 43283--43359 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
43273 CATCATGCCC
**
43283 AATAAAAACTCTGCA-CTAGCCCAATAA
1 AATAAAAACTCTATATC-AGCCCAATAA
*
43310 AAT-AAAATTCTATATCAGCCCAATAA
1 AATAAAAACTCTATATCAGCCCAATAA
*
43336 AATAAAAACTCTATATCAGACCAA
1 AATAAAAACTCTATATCAGCCCAA
43360 AATAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 21 0.49
27 22 0.51
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (27 bp):
AATAAAAACTCTATATCAGCCCAATAA
Found at i:43377 original size:26 final size:28
Alignment explanation
Indices: 43305--43370 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
43295 GCACTAGCCC
* *
43305 AATAAAATAAAATTCTATATCAGCCCAAT
1 AATAAAA-AAAACTCTATATCAGACCAAT
*
43334 AA-AATAAAAACTCTATATCAGACCAA-
1 AATAAAAAAAACTCTATATCAGACCAAT
43360 AATAAAAAAAA
1 AATAAAAAAAA
43371 GTCATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.06
27 25 0.78
28 3 0.09
29 2 0.06
ACGTcount: A:0.61, C:0.15, G:0.03, T:0.21
Consensus pattern (28 bp):
AATAAAAAAAACTCTATATCAGACCAAT
Found at i:56412 original size:31 final size:32
Alignment explanation
Indices: 56376--56436 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
56366 AGTTTTTAAT
* *
56376 TTTGATCACAGAT-TTATATATTTTTGGTTAC
1 TTTGATCACAGATATTATACACTTTTGGTTAC
**
56407 TTTGATCTTAGATATTATACACTTTTGGTT
1 TTTGATCACAGATATTATACACTTTTGGTT
56437 TAACTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTGATCACAGATATTATACACTTTTGGTTAC
Found at i:65438 original size:40 final size:40
Alignment explanation
Indices: 65362--65439 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
65352 AAAACCCAGA
* * * *
65362 ATGTATCGATACAATGAGAATTGTATCAATAGAATTTCTT
1 ATGTATCGATACAATGAAAAATATATCAATACAATTTCTT
* * *
65402 ATGTATCGATACATTTAAAAATATATCGATACAATTTC
1 ATGTATCGATACAATGAAAAATATATCAATACAATTTC
65440 CTTTCAGTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (40 bp):
ATGTATCGATACAATGAAAAATATATCAATACAATTTCTT
Found at i:69156 original size:23 final size:23
Alignment explanation
Indices: 69129--69185 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
69119 TGAAAGATTG
69129 TTATAATTTTACCAAATGATAGA
1 TTATAATTTTACCAAATGATAGA
* *
69152 TTATAATTCTACCAAATGGTAGA
1 TTATAATTTTACCAAATGATAGA
*
69175 TTATAAATTTA
1 TTATAATTTTA
69186 TAACTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
TTATAATTTTACCAAATGATAGA
Found at i:72631 original size:2 final size:2
Alignment explanation
Indices: 72626--72665 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
72616 TTTACATTCA
*
72626 AT AT AT AT AT AC 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
72666 TTAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:73506 original size:7 final size:7
Alignment explanation
Indices: 73496--73551 Score: 76
Period size: 7 Copynumber: 8.0 Consensus size: 7
73486 CACTGCCAGT
73496 AGCCATG
1 AGCCATG
73503 AGCCATG
1 AGCCATG
73510 AGCCATG
1 AGCCATG
73517 AGCCATG
1 AGCCATG
*
73524 AGCCATA
1 AGCCATG
*
73531 ATCCATG
1 AGCCATG
*
73538 AGTCATG
1 AGCCATG
*
73545 AGTCATG
1 AGCCATG
73552 CAAGTGCGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (7 bp):
AGCCATG
Found at i:77792 original size:150 final size:149
Alignment explanation
Indices: 77522--77820 Score: 483
Period size: 150 Copynumber: 2.0 Consensus size: 149
77512 AACTCAATCT
*
77522 CGAGTTTTGAAGTGCTGTAGTTAAAGAAATCTGCCGTAAACCCATGAATGGCACTGTCAAGAATG
1 CGAGTTTTGAAGTGCTGTAGTAAAAGAAATCTGCCGTAAACCCATGAATGGCACTGTCAAGAATG
* *
77587 AATTTCTATTATAGAACAAACATATTCAAAAAAAGTCAACTGTATCTTAGCCTTCAATGTACTAG
66 AATTTCTATTATAGAACAAACATATTCAAAAAAAGTAAACTGTATCTTAGCCTTCAATGCACTAG
77652 AAGTAATGAAGTCAATGGG
131 AAGTAATGAAGTCAATGGG
* *
77671 CGAGTTTTGAAGTGTTGTAGTAAAAGAAATCTGCCGTAAAACCCATGAATGGCACTGTCAGGAAT
1 CGAGTTTTGAAGTGCTGTAGTAAAAGAAATCTGCCGT-AAACCCATGAATGGCACTGTCAAGAAT
* * * *
77736 GAATTTCTCTTATA-ACACAAACATCTTCAAAAAATGTAAATTGTATCTTAGCCTTCAATGCACT
65 GAATTTCTATTATAGA-ACAAACATATTCAAAAAAAGTAAACTGTATCTTAGCCTTCAATGCACT
*
77800 AGAAGTACTGAAGTCAATGGG
129 AGAAGTAATGAAGTCAATGGG
77821 AAACTTTTCA
Statistics
Matches: 138, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
149 36 0.26
150 102 0.74
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (149 bp):
CGAGTTTTGAAGTGCTGTAGTAAAAGAAATCTGCCGTAAACCCATGAATGGCACTGTCAAGAATG
AATTTCTATTATAGAACAAACATATTCAAAAAAAGTAAACTGTATCTTAGCCTTCAATGCACTAG
AAGTAATGAAGTCAATGGG
Found at i:79459 original size:160 final size:160
Alignment explanation
Indices: 79273--79595 Score: 646
Period size: 160 Copynumber: 2.0 Consensus size: 160
79263 ATAACCTAAG
79273 TTTCATGCCTGGGGCTCCTTGATCACATCACAAAACCAAGAAGAAAGAAAACCTAACCATTACAC
1 TTTCATGCCTGGGGCTCCTTGATCACATCACAAAACCAAGAAGAAAGAAAACCTAACCATTACAC
79338 ATAGGGTTGATTGCATCACATAATCTAGATAGTAATAATGCTAAAAAATTTCTCAAATTCATAAT
66 ATAGGGTTGATTGCATCACATAATCTAGATAGTAATAATGCTAAAAAATTTCTCAAATTCATAAT
79403 ATACCCTTTAAAAGAAAAAGTACATTGTTA
131 ATACCCTTTAAAAGAAAAAGTACATTGTTA
79433 TTTCATGCCTGGGGCTCCTTGATCACATCACAAAACCAAGAAGAAAGAAAACCTAACCATTACAC
1 TTTCATGCCTGGGGCTCCTTGATCACATCACAAAACCAAGAAGAAAGAAAACCTAACCATTACAC
79498 ATAGGGTTGATTGCATCACATAATCTAGATAGTAATAATGCTAAAAAATTTCTCAAATTCATAAT
66 ATAGGGTTGATTGCATCACATAATCTAGATAGTAATAATGCTAAAAAATTTCTCAAATTCATAAT
79563 ATACCCTTTAAAAGAAAAAGTACATTGTTA
131 ATACCCTTTAAAAGAAAAAGTACATTGTTA
79593 TTT
1 TTT
79596 ATATAAAGGA
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (160 bp):
TTTCATGCCTGGGGCTCCTTGATCACATCACAAAACCAAGAAGAAAGAAAACCTAACCATTACAC
ATAGGGTTGATTGCATCACATAATCTAGATAGTAATAATGCTAAAAAATTTCTCAAATTCATAAT
ATACCCTTTAAAAGAAAAAGTACATTGTTA
Found at i:83939 original size:12 final size:12
Alignment explanation
Indices: 83922--83946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83912 CGGGTTTAAT
83922 TTTTGTATCGGG
1 TTTTGTATCGGG
83934 TTTTGTATCGGG
1 TTTTGTATCGGG
83946 T
1 T
83947 GACTTTAATT
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:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TTTTGTATCGGG
Found at i:86964 original size:10 final size:10
Alignment explanation
Indices: 86949--86978 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
86939 TTTCCAAAAG
86949 TCTCCCCTCC
1 TCTCCCCTCC
86959 TCTCCCCTCC
1 TCTCCCCTCC
*
86969 TCTTCCCTCC
1 TCTCCCCTCC
86979 CCACTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (10 bp):
TCTCCCCTCC
Found at i:88728 original size:2 final size:2
Alignment explanation
Indices: 88723--88752 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
88713 ACACACAAAC
88723 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
88753 GAATATTTTT
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:94542 original size:12 final size:12
Alignment explanation
Indices: 94525--94549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94515 TTGTACCAAA
94525 AAAGAGAGAGAG
1 AAAGAGAGAGAG
94537 AAAGAGAGAGAG
1 AAAGAGAGAGAG
94549 A
1 A
94550 GAGAACTTTA
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:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:94874 original size:2 final size:2
Alignment explanation
Indices: 94862--94909 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
94852 GTTTTTCTTT
*
94862 TA TA CA 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
94904 TA TA TA
1 TA TA TA
94910 CATGAGCACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:96060 original size:15 final size:15
Alignment explanation
Indices: 96042--96072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
96032 TTGGCCTGCA
96042 TGTTTTTCTGCTTCT
1 TGTTTTTCTGCTTCT
*
96057 TGTTTTTCTTCTTCT
1 TGTTTTTCTGCTTCT
96072 T
1 T
96073 ATTCTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (15 bp):
TGTTTTTCTGCTTCT
Found at i:96371 original size:10 final size:11
Alignment explanation
Indices: 96351--96396 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
96341 ACATAACATC
*
96351 AATTCAATTAA
1 AATTAAATTAA
96362 AATT-AATTAAA
1 AATTAAATT-AA
96373 ATATTAAA-TAA
1 A-ATTAAATTAA
96384 AATTAAATTAA
1 AATTAAATTAA
96395 AA
1 AA
96397 AATATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.32
11 15 0.48
12 4 0.13
13 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:105344 original size:21 final size:21
Alignment explanation
Indices: 105320--105361 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
105310 GTAACTTATG
*
105320 AATTTTATATGATAGTGATTT
1 AATTTTATACGATAGTGATTT
*
105341 AATTTTATGCGATAGTGATTT
1 AATTTTATACGATAGTGATTT
105362 TAAATCACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (21 bp):
AATTTTATACGATAGTGATTT
Found at i:110605 original size:25 final size:24
Alignment explanation
Indices: 110551--110615 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
110541 TAAATAATTA
**
110551 AAATATAATATTATTTTTAAAAAAT
1 AAATATAAT-TTAAATTTAAAAAAT
* *
110576 TAATATAATTTAAATTTAAATATAT
1 AAATATAATTTAAATTTAAA-AAAT
110601 AAATAT-A-TTAAATTT
1 AAATATAATTTAAATTT
110616 TTATAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.24
24 10 0.29
25 16 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATATAATTTAAATTTAAAAAAT
Found at i:110613 original size:23 final size:23
Alignment explanation
Indices: 110585--110634 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
110575 TTAATATAAT
110585 TTAAATTTAAAT-ATATAAATATA
1 TTAAATTTAAATAATATAAAT-TA
**
110608 TTAAATTTTTATAATATAAATTA
1 TTAAATTTAAATAATATAAATTA
110631 TTAA
1 TTAA
110635 TATAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATTTAAATAATATAAATTA
Found at i:110658 original size:22 final size:23
Alignment explanation
Indices: 110633--110685 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
110623 ATAAATTATT
*
110633 AATATAATAAAA-TCTATATATA
1 AATATAATAAAATTCTATAAATA
*
110655 AATAT-ATAAAATTTTATAAATA
1 AATATAATAAAATTCTATAAATA
*
110677 ATTATAATA
1 AATATAATA
110686 TAAAAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 17 0.65
23 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAATAAAATTCTATAAATA
Found at i:110674 original size:18 final size:18
Alignment explanation
Indices: 110598--110676 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
110588 AATTTAAATA
*
110598 TATAAATATATTAAATTT
1 TATAAATATATAAAATTT
*
110616 T-TATA-ATAT-AAA--T
1 TATAAATATATAAAATTT
*
110629 TATTAATATAATAAAATCTAT
1 TATAAATAT-ATAAAAT-T-T
110650 ATATAAATATATAAAATTT
1 -TATAAATATATAAAATTT
110669 TATAAATA
1 TATAAATA
110677 ATTATAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 5 0.10
16 6 0.12
17 6 0.12
18 9 0.19
19 1 0.02
20 1 0.02
21 8 0.17
22 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAATATATAAAATTT
Found at i:110708 original size:53 final size:53
Alignment explanation
Indices: 110595--110694 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
110585 TTAAATTTAA
* *
110595 ATATATAAATATATTAAATTTTTATAATATAAATTATTAATATAATAAAATCT
1 ATATATAAATATATTAAAATTTTATAATATAAATTATTAATATAATAAAAACT
110648 ATATATAAATATA-TAAAATTTTATAA-AT-AATTA-TAATATAA-AAAAAC
1 ATATATAAATATATTAAAATTTTATAATATAAATTATTAATATAATAAAAAC
110695 ATAAATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
48 5 0.11
49 8 0.18
50 5 0.11
51 2 0.04
52 12 0.27
53 13 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (53 bp):
ATATATAAATATATTAAAATTTTATAATATAAATTATTAATATAATAAAAACT
Found at i:111742 original size:2 final size:2
Alignment explanation
Indices: 111735--111778 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
111725 GAAGCCCACT
111735 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
111777 CA
1 CA
111779 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:111783 original size:2 final size:2
Alignment explanation
Indices: 111778--111826 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
111768 ACACACACAC
111778 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
111820 AT AT AT A
1 AT AT AT A
111827 AGTTGCGGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:117102 original size:17 final size:17
Alignment explanation
Indices: 117080--117114 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
117070 CTGGATTTTA
117080 TTTTGAAAACAGGATAT
1 TTTTGAAAACAGGATAT
117097 TTTTGAAAACAGGATAT
1 TTTTGAAAACAGGATAT
117114 T
1 T
117115 CCGTGTCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TTTTGAAAACAGGATAT
Found at i:119720 original size:13 final size:13
Alignment explanation
Indices: 119702--119726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119692 CAAAGATCAG
119702 TGTATCGATACAA
1 TGTATCGATACAA
119715 TGTATCGATACA
1 TGTATCGATACA
119727 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:119807 original size:13 final size:13
Alignment explanation
Indices: 119789--119813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119779 ACAAAACTTA
119789 TGTATCGATACAT
1 TGTATCGATACAT
119802 TGTATCGATACA
1 TGTATCGATACA
119814 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:119809 original size:32 final size:33
Alignment explanation
Indices: 119768--119833 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
119758 AGTAGCTTAA
119768 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
119800 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
119833 A
1 A
119834 AATCATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:126203 original size:13 final size:12
Alignment explanation
Indices: 126185--126227 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
126175 CATGGAAATG
126185 AAACACACAAAAA
1 AAACACA-AAAAA
126198 AAACACAAAACAA
1 AAACACAAAA-AA
126211 AAA-ACAAAAACA
1 AAACACAAAAA-A
126223 AAACA
1 AAACA
126228 AAACAGCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 13 0.48
13 13 0.48
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACACAAAAAA
Found at i:126205 original size:11 final size:11
Alignment explanation
Indices: 126189--126230 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
126179 GAAATGAAAC
126189 ACACAAAAAAA
1 ACACAAAAAAA
126200 ACACAAAACAAA
1 ACACAAAA-AAA
*
126212 AAACAAAAACAA
1 ACACAAAAA-AA
126224 A-ACAAAA
1 ACACAAAA
126231 CAGCTGCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 15 0.54
12 13 0.46
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (11 bp):
ACACAAAAAAA
Found at i:126223 original size:18 final size:17
Alignment explanation
Indices: 126193--126230 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
126183 TGAAACACAC
*
126193 AAAAAAAACACAAAACA
1 AAAAAAAAAACAAAACA
126210 AAAAACAAAAACAAAACA
1 AAAAA-AAAAACAAAACA
126228 AAA
1 AAA
126231 CAGCTGCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAACA
Found at i:127655 original size:13 final size:13
Alignment explanation
Indices: 127637--127661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127627 AGGAGTTTAG
127637 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
127650 TTTTTTTTTTTT
1 TTTTTTTTTTTT
127662 TTTGAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:128799 original size:285 final size:282
Alignment explanation
Indices: 128282--128843 Score: 835
Period size: 285 Copynumber: 2.0 Consensus size: 282
128272 ACTCCTAATG
* * * * *
128282 CAAGAAGCAAGAAGTAAAGTGCACAACTTTAAAACAATAGTAGAGTTTGTATTTTTTTTTTTTTT
1 CAAGAAACAAGAAGTAAAGAGCACAACTTTAAAACAACAGTAAAGTATGTATTTTTTTTTTTTTT
128347 AATTTCATACACTATTTCTCCTAACTTTCTATTAATCCAATTCTCTATCATTCCTTCTAGTCAGT
66 AATTTCATACACTATTTCTCCTAACTTTCTATTAATCCAATTCTCTATCATTCCTTCTAGTCAG-
* * * ** **
128412 AGTCAAGATCATACCATAACAGGGGCCACCTTTGGTAGAAAGGTAATACATTTTAGTAATACCAT
130 AGTCAAAATCATAACATAACAGGGGCCACCTTTAGTAGAAACATAATACATTCAAGTAATACCAT
* * *
128477 ATTTAGTGATAGAAGCGGTGCAATTTAACTGCTGTCCTATGACTCTAAAATGCAGCA-TTGCCAG
195 ACTTAGTGATAGAAGCGATGCAATTTAACTACTGTCCTATGACTCTAAAATGCAGCATTTG-CAG
*
128541 ATTCTAAATTCTGTATGTGTGATA
259 ATTCCAAATTCTGTATGTGTGATA
*
128565 CAAGAAACAAGAAGTAAAGAGCACAACTTTAAAACAACAGTAAAGTATGTCTTTTTTTTTTATTT
1 CAAGAAACAAGAAGTAAAGAGCACAACTTTAAAACAACAGTAAAGTATGT-ATTTTTTTTT-TTT
*
128630 ATTTATTTCATACACTCTATTTCTCCTAACTTTCTATTAATCCAATTCTCTATCATTCCTTCTAG
64 -TTAATTTCATACA--CTATTTCTCCTAACTTTCTATTAATCCAATTCTCTATCATTCCTTCTAG
*
128695 TCA-A-TCAAAATCATAACATAACAGGGGCCACCTTTAGTAGAAACATAATACATTCAAGTAA-G
126 TCAGAGTCAAAATCATAACATAACAGGGGCCACCTTTAGTAGAAACATAATACATTCAAGTAATA
*
128757 CCTATACTTAGTGCTAGAAGCGATGCAATTTAACTACTGTCCTATGACTCTAAAATGCAGCATTT
191 CC-ATACTTAGTGATAGAAGCGATGCAATTTAACTACTGTCCTATGACTCTAAAATGCAGCATTT
*
128822 GCAGATTCCAAATTGTGTATGT
255 GCAGATTCCAAATTCTGTATGT
128844 TTGAGCATGT
Statistics
Matches: 251, Mismatches: 21, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
283 45 0.18
284 11 0.04
285 127 0.51
286 16 0.06
288 52 0.21
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (282 bp):
CAAGAAACAAGAAGTAAAGAGCACAACTTTAAAACAACAGTAAAGTATGTATTTTTTTTTTTTTT
AATTTCATACACTATTTCTCCTAACTTTCTATTAATCCAATTCTCTATCATTCCTTCTAGTCAGA
GTCAAAATCATAACATAACAGGGGCCACCTTTAGTAGAAACATAATACATTCAAGTAATACCATA
CTTAGTGATAGAAGCGATGCAATTTAACTACTGTCCTATGACTCTAAAATGCAGCATTTGCAGAT
TCCAAATTCTGTATGTGTGATA
Found at i:137739 original size:2 final size:2
Alignment explanation
Indices: 137732--137764 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
137722 TGTGCATTTT
137732 GA GA GA 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 GA GA GA G
137765 GGAGGAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:139727 original size:1 final size:1
Alignment explanation
Indices: 139721--139745 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
139711 AGTCAATATC
139721 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
139746 CACTATCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:148765 original size:3 final size:3
Alignment explanation
Indices: 148757--148787 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
148747 GGCAAAGGAA
148757 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
148788 GAAAGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:150984 original size:22 final size:22
Alignment explanation
Indices: 150956--151011 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
150946 AGATAAGTTC
150956 ACTTAACACACCTAATATATTT
1 ACTTAACACACCTAATATATTT
*
150978 ACTTAACACACCTAATATGTTT
1 ACTTAACACACCTAATATATTT
151000 ACTTAACACACC
1 ACTTAACACACC
151012 ACCTAACACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (22 bp):
ACTTAACACACCTAATATATTT
Found at i:155469 original size:23 final size:22
Alignment explanation
Indices: 155439--155482 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
155429 CACACTTAAT
* *
155439 ATATTATTCAACTAACATATTTG
1 ATATTATT-AACAAAAATATTTG
155462 ATATTATTAACAAAAATATTT
1 ATATTATTAACAAAAATATTT
155483 TAACAGATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATTATTAACAAAAATATTTG
Found at i:158114 original size:20 final size:20
Alignment explanation
Indices: 158089--158137 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
158079 AAATTAATCT
158089 ATAAATAATATTTTAAAAAA
1 ATAAATAATATTTTAAAAAA
* *
158109 ATAAAT-ATA-TTTAAGAGA
1 ATAAATAATATTTTAAAAAA
158127 A-AAATAATATT
1 ATAAATAATATT
158138 ATCTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 4 0.16
20 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAATAATATTTTAAAAAA
Found at i:158131 original size:21 final size:20
Alignment explanation
Indices: 158089--158133 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
158079 AAATTAATCT
*
158089 ATAAATAATATTTTAAAAAA
1 ATAAATAATATTTAAAAAAA
158109 ATAAAT-ATATTTAAGAGAAAA
1 ATAAATAATATTTAA-A-AAAA
158130 ATAA
1 ATAA
158134 TATTATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 7 0.32
21 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
ATAAATAATATTTAAAAAAA
Found at i:158203 original size:26 final size:25
Alignment explanation
Indices: 158155--158203 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
158145 TTTTAAAAGT
*
158155 AAATAAAATTATTTTTAAATTTAAA
1 AAATAAAATAATTTTTAAATTTAAA
*
158180 AAATAATAATAATTTTTAATTTTA
1 AAATAA-AATAATTTTTAAATTTA
158204 TTAGCGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATAAAATAATTTTTAAATTTAAA
Found at i:159468 original size:2 final size:2
Alignment explanation
Indices: 159463--159487 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
159453 GGGTTTTTTA
159463 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
159488 ATTAAGAGAC
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:160653 original size:3 final size:3
Alignment explanation
Indices: 160647--160672 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
160637 CTTCTTCTTC
160647 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
160673 TGTTTTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:163177 original size:14 final size:13
Alignment explanation
Indices: 163158--163207 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
163148 AGGATTATTT
163158 ATTTAATTTGATAA
1 ATTTAATTT-ATAA
163172 ATTTAA-TT-T--
1 ATTTAATTTATAA
163181 ATTTAATTTAATAA
1 ATTTAATTT-ATAA
163195 ATTTAATTTATAA
1 ATTTAATTTATAA
163208 GATAAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 1 0.03
12 1 0.03
13 6 0.19
14 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
ATTTAATTTATAA
Found at i:163182 original size:23 final size:23
Alignment explanation
Indices: 163154--163205 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
163144 TGTTAGGATT
*
163154 ATTTATTTAATTTGATAAATTTA
1 ATTTATTTAATTTAATAAATTTA
163177 ATTTATTTAATTTAATAAATTTA
1 ATTTATTTAATTTAATAAATTTA
163200 ATTTAT
1 ATTTAT
163206 AAGATAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTATTTAATTTAATAAATTTA
Found at i:164095 original size:15 final size:15
Alignment explanation
Indices: 164075--164105 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
164065 ATGTGTGAAC
*
164075 AATAAATACAATATA
1 AATAAATAAAATATA
164090 AATAAATAAAATATA
1 AATAAATAAAATATA
164105 A
1 A
164106 TTATAGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAATAAAATATA
Found at i:164662 original size:3 final size:3
Alignment explanation
Indices: 164654--164690 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
164644 GGACGGGTAT
* *
164654 TAA TAA TAA TAA TAA TAC TGA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
164691 TGCTTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:165044 original size:3 final size:3
Alignment explanation
Indices: 165036--165061 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
165026 GATAAAATCT
165036 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
165062 AATTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:165647 original size:2 final size:2
Alignment explanation
Indices: 165640--165670 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
165630 CTTGCAGATT
165640 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
165671 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:166214 original size:2 final size:2
Alignment explanation
Indices: 166207--166247 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
166197 TGGCTTCTAA
166207 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
166248 AGATTTGGCA
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:169553 original size:41 final size:41
Alignment explanation
Indices: 169496--169577 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
169486 TGTTCTACAT
169496 GCTAGATTGCTTATGTTATACGTACACAGAACAAAGACTAA
1 GCTAGATTGCTTATGTTATACGTACACAGAACAAAGACTAA
169537 GCTAGATTGCTTATGTTATACGTACACAGAACAAAGACTAA
1 GCTAGATTGCTTATGTTATACGTACACAGAACAAAGACTAA
169578 CTCTCTTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (41 bp):
GCTAGATTGCTTATGTTATACGTACACAGAACAAAGACTAA
Found at i:177617 original size:31 final size:30
Alignment explanation
Indices: 177576--177638 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
177566 ATTAATTAAA
*
177576 TATTTATAAAT-TTATTAAAAATAAAAATAAT
1 TATTTATAAATATTA-AAAAAAT-AAAATAAT
*
177607 TATTTTTAAATATTAAAAAAATAAAATAAT
1 TATTTATAAATATTAAAAAAATAAAATAAT
177637 TA
1 TA
177639 CCTATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 16 0.55
32 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTTATAAATATTAAAAAAATAAAATAAT
Found at i:180380 original size:23 final size:23
Alignment explanation
Indices: 180351--180395 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
180341 AAATGATATT
180351 AATTTAATTAAAAATTAATAAAA
1 AATTTAATTAAAAATTAATAAAA
**
180374 AATTTAATTAAATTTTAATAAA
1 AATTTAATTAAAAATTAATAAA
180396 TACTCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTAATTAAAAATTAATAAAA
Found at i:181419 original size:3 final size:3
Alignment explanation
Indices: 181411--181445 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
181401 ATTGATCGGA
181411 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
181446 AAATAGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:181539 original size:5 final size:5
Alignment explanation
Indices: 181531--181555 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
181521 AAGGAAAAGG
181531 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
181556 TTAGTTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:183030 original size:18 final size:18
Alignment explanation
Indices: 183007--183047 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
182997 TTATTAAAAC
*
183007 TAAAA-TTATATATATTTT
1 TAAAATTTATA-ATATTAT
183025 TAAAATTTATAATATTAT
1 TAAAATTTATAATATTAT
183043 TAAAA
1 TAAAA
183048 AAATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATTTATAATATTAT
Found at i:183305 original size:17 final size:18
Alignment explanation
Indices: 183270--183309 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
183260 TTTATAATAA
183270 AAATTATATTATTTAATT
1 AAATTATATTATTTAATT
183288 AAATATATATT-TTT-ATT
1 AAAT-TATATTATTTAATT
183305 AAATT
1 AAATT
183310 TAATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 7 0.33
18 7 0.33
19 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATTATATTATTTAATT
Found at i:183342 original size:5 final size:5
Alignment explanation
Indices: 183323--183364 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
183313 TATTAAAATT
*
183323 ATTTA ATTTA TATTTA ATTTA ATTTA A-CTA ATTTA ATTTA AT
1 ATTTA ATTTA -ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
183365 AATATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 25 0.76
6 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTTA
Found at i:183347 original size:21 final size:21
Alignment explanation
Indices: 183306--183364 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
183296 ATTTTTATTA
* *
183306 AATTTAATATTAAAATT-ATTT
1 AATTT-ATATTTAATTTAATTT
183327 AATTTATATTTAATTTAATTT
1 AATTTATATTTAATTTAATTT
*
183348 AA-CTA-ATTTAATTTAAT
1 AATTTATATTTAATTTAAT
183365 AATATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 11 0.32
21 11 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTATATTTAATTTAATTT
Found at i:183356 original size:14 final size:13
Alignment explanation
Indices: 183323--183367 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
183313 TATTAAAATT
183323 ATTTAATTTATATTTA
1 ATTTAATTTA-A--TA
183339 ATTTAATTTAACTA
1 ATTTAATTTAA-TA
183353 ATTTAATTTAATA
1 ATTTAATTTAATA
183366 AT
1 AT
183368 ATATAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 1 0.04
16 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTAATTTAATA
Found at i:189140 original size:2 final size:2
Alignment explanation
Indices: 189133--189160 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
189123 TGTTGGAACA
189133 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
189161 GTATGTATGG
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:191741 original size:13 final size:13
Alignment explanation
Indices: 191725--191749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
191715 TACTTATAAT
191725 TTAATTTAATTAA
1 TTAATTTAATTAA
191738 TTAATTTAATTA
1 TTAATTTAATTA
191750 TTTTTAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:192709 original size:17 final size:16
Alignment explanation
Indices: 192679--192714 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
192669 AAATTGCAGT
192679 CTCTTCCCCCTCCCCC
1 CTCTTCCCCCTCCCCC
*
192695 CTCTTCCCTCCTCCCTC
1 CTCTTCCC-CCTCCCCC
192712 CTC
1 CTC
192715 CCATCCCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (16 bp):
CTCTTCCCCCTCCCCC
Found at i:193039 original size:3 final size:3
Alignment explanation
Indices: 193031--193064 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
193021 ATTAGTTAAC
193031 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
193065 CATTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:195584 original size:2 final size:2
Alignment explanation
Indices: 195577--195603 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
195567 CCAGCCTAAC
195577 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 A
195604 TTTTAAAAAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:197668 original size:3 final size:3
Alignment explanation
Indices: 197660--197697 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
197650 ACCTTCTTAG
197660 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
197698 GTTACAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:198705 original size:13 final size:12
Alignment explanation
Indices: 198677--198750 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
198667 TCTGTATCTG
*
198677 TATTTGATTTTT
1 TATTTTATTTTT
198689 TATTTTATTTTT
1 TATTTTATTTTT
198701 ATATTTTTGTATTTTT
1 -TA--TTT-TATTTTT
* *
198717 TAATTTTAATTAT
1 T-ATTTTATTTTT
*
198730 TATTATTA-TTAT
1 TATT-TTATTTTT
198742 TATTTTATT
1 TATTTTATT
198751 ATTAAAAACC
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
11 3 0.06
12 23 0.44
13 11 0.21
14 3 0.06
15 4 0.08
16 8 0.15
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:198733 original size:3 final size:3
Alignment explanation
Indices: 198725--198754 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
198715 TTTAATTTTA
198725 ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
198755 AAAACCTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:198733 original size:28 final size:27
Alignment explanation
Indices: 198679--198733 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
198669 TGTATCTGTA
* *
198679 TTTGATTTTTTATTTTATTTTTATATT
1 TTTGATTTTTTATTTTAATTATATATT
198706 TTTGTATTTTTTAATTTTAATTAT-TATT
1 TTTG-ATTTTTT-ATTTTAATTATATATT
198734 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 9 0.38
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTGATTTTTTATTTTAATTATATATT
Found at i:198751 original size:8 final size:8
Alignment explanation
Indices: 198683--198753 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
198673 TCTGTATTTG
198683 ATTTT-TT
1 ATTTTATT
198690 ATTTTA-T
1 ATTTTATT
198697 -TTTTA-T
1 ATTTTATT
198703 ATTTT-TGT
1 ATTTTAT-T
198711 ATTTT-TT
1 ATTTTATT
198718 AATTTTA--
1 -ATTTTATT
198725 ATTATTATT
1 ATT-TTATT
198734 ATTATTATT
1 ATT-TTATT
198743 ATTTTATT
1 ATTTTATT
198751 ATT
1 ATT
198754 AAAAACCTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
6 9 0.16
7 14 0.25
8 20 0.36
9 12 0.22
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.73
Consensus pattern (8 bp):
ATTTTATT
Found at i:202936 original size:2 final size:2
Alignment explanation
Indices: 202931--202980 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
202921 ATCTGTGTGA
202931 TC TC TC TC TC TC TC TC TC T- TC -C TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
202971 TC TC TC TC TC
1 TC TC TC TC TC
202981 ATATTAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:210669 original size:2 final size:2
Alignment explanation
Indices: 210662--210691 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
210652 ACAATCAAGC
210662 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
210692 CTTGCACAAT
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:216864 original size:21 final size:23
Alignment explanation
Indices: 216827--216893 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 23
216817 TGACAAGTAA
*
216827 AATTAATAATTTTTATAT-TT-T
1 AATTAATTATTTTTATATATTAT
*
216848 TATT-A-TATTTTTATATATTAT
1 AATTAATTATTTTTATATATTAT
216869 AATTAATTATTTTTATGATATTAT
1 AATTAATTATTTTTAT-ATATTAT
216893 A
1 A
216894 TTTTTAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.26
20 3 0.08
21 7 0.18
22 1 0.03
23 9 0.24
24 8 0.21
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
AATTAATTATTTTTATATATTAT
Found at i:226800 original size:14 final size:14
Alignment explanation
Indices: 226783--226815 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
226773 TAAATATTAA
226783 AATTTAAAATTATT
1 AATTTAAAATTATT
*
226797 AATTTAAAATTTTT
1 AATTTAAAATTATT
226811 AATTT
1 AATTT
226816 TAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAAAATTATT
Found at i:226805 original size:21 final size:20
Alignment explanation
Indices: 226779--226821 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
226769 ACTGTAAATA
226779 TTAAAATTTAAAATTATTAAT
1 TTAAAATTTAAAATT-TTAAT
**
226800 TTAAAATTTTTAATTTTAAT
1 TTAAAATTTAAAATTTTAAT
226820 TT
1 TT
226822 TATTGACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAAATTTAAAATTTTAAT
Found at i:227126 original size:29 final size:29
Alignment explanation
Indices: 227093--227149 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
227083 TATGCTATCA
227093 AACACAATTACTTTAATGATTATTCATAG
1 AACACAATTACTTTAATGATTATTCATAG
*
227122 AACACAATTAGTTTAATGATTATTCATA
1 AACACAATTACTTTAATGATTATTCATA
227150 CGGATTTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (29 bp):
AACACAATTACTTTAATGATTATTCATAG
Found at i:228478 original size:16 final size:18
Alignment explanation
Indices: 228444--228482 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
228434 GAGTTTTTAA
228444 ATTTTGGAGTAAGTTTTG
1 ATTTTGGAGTAAGTTTTG
228462 ATTTT-GAGTAA-TTTTG
1 ATTTTGGAGTAAGTTTTG
228478 ATTTT
1 ATTTT
228483 AAATTACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 6 0.29
18 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (18 bp):
ATTTTGGAGTAAGTTTTG
Found at i:233911 original size:20 final size:20
Alignment explanation
Indices: 233886--233937 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
233876 TTCTAGCCAA
** *
233886 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
233906 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
233925 TGTATCGATACAA
1 TGTATCGATACAA
233938 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:233943 original size:19 final size:18
Alignment explanation
Indices: 233886--233943 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
233876 TTCTAGCCAA
*
233886 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
233906 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
233925 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
233944 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:234667 original size:21 final size:21
Alignment explanation
Indices: 234626--234669 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
234616 CTCCCATTTA
* *
234626 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
234647 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
234668 TC
1 TC
234670 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:236490 original size:13 final size:13
Alignment explanation
Indices: 236472--236510 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
236462 ATAATCACCC
236472 TGTATCGATACAA
1 TGTATCGATACAA
236485 TGTATCGATACAA
1 TGTATCGATACAA
236498 TGTATCGATACAA
1 TGTATCGATACAA
236511 GGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:238609 original size:15 final size:15
Alignment explanation
Indices: 238589--238619 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
238579 ATTTCGTTTG
*
238589 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
238604 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
238619 G
1 G
238620 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:240452 original size:21 final size:21
Alignment explanation
Indices: 240423--240467 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
240413 AAGTTTTCAT
*
240423 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
240443 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
240465 TTT
1 TTT
240468 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:242700 original size:13 final size:13
Alignment explanation
Indices: 242682--242707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242672 CAATTTTTTG
242682 TGTATCGATACAT
1 TGTATCGATACAT
242695 TGTATCGATACAT
1 TGTATCGATACAT
242708 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:242722 original size:32 final size:33
Alignment explanation
Indices: 242662--242725 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
242652 TCTAAGCCAA
** *
242662 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
242695 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
242726 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:245470 original size:30 final size:27
Alignment explanation
Indices: 245405--245471 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 27
245395 ACATAATCTA
*
245405 AAATTTAAAAAATCGAATCAAAATTTT
1 AAATTTAAAAAATCAAATCAAAATTTT
245432 ---TTTAAAAAAATCAAATCAAATCAATTTT
1 AAATTT-AAAAAATCAAATC-AA--AATTTT
245460 AAATTTAAAAAA
1 AAATTTAAAAAA
245472 CCATAACAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 2 0.06
28 6 0.19
30 6 0.19
31 3 0.09
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.33
Consensus pattern (27 bp):
AAATTTAAAAAATCAAATCAAAATTTT
Found at i:245969 original size:8 final size:8
Alignment explanation
Indices: 245956--245995 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
245946 ATGATCGTGG
245956 AATAAAAA
1 AATAAAAA
245964 AATAAAAA
1 AATAAAAA
245972 AATAAAAA
1 AATAAAAA
**
245980 AATAATTA
1 AATAAAAA
245988 AATAAAAA
1 AATAAAAA
245996 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AATAAAAA
Found at i:246002 original size:16 final size:16
Alignment explanation
Indices: 245961--246002 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
245951 CGTGGAATAA
245961 AAAAATAAAA--AAAT
1 AAAAATAAAATTAAAT
245975 AAAAA-AATAATTAAAT
1 AAAAATAA-AATTAAAT
245991 AAAAATAAAATT
1 AAAAATAAAATT
246003 TAAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 7 0.29
16 13 0.54
17 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATTAAAT
Found at i:246008 original size:27 final size:27
Alignment explanation
Indices: 245977--246070 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 27
245967 AAAAAAATAA
245977 AAAAATAATTAAATAAAAATAAAATTT
1 AAAAATAATTAAATAAAAATAAAATTT
*
246004 AAAAAT-ATTAAAATAATAATATAAATTT
1 AAAAATAATT-AAATAAAAATA-AAATTT
*
246032 AATAAATAA--AAATACTAAATAAAACATTT
1 AA-AAATAATTAAATA-AAAAT-AAA-ATTT
246061 AAAAA-AATTA
1 AAAAATAATTA
246071 TCAAAATTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
26 3 0.05
27 23 0.42
28 16 0.29
29 12 0.22
30 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATAATTAAATAAAAATAAAATTT
Found at i:246445 original size:22 final size:20
Alignment explanation
Indices: 246397--246452 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
246387 AAATTTTTAT
* *
246397 AAAAATTTTAAATATAATTA
1 AAAAATTATAAATATAATAA
*
246417 AATAATTATAATATTATAATAA
1 AAAAATTATAA-A-TATAATAA
*
246439 AAAAATTGTAAATA
1 AAAAATTATAAATA
246453 AAATGGTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATTATAAATATAATAA
Found at i:247174 original size:29 final size:28
Alignment explanation
Indices: 247119--247184 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
247109 ATTAAATATT
247119 TAATTTAAACTTAATTAATAATATATAAA
1 TAATTT-AACTTAATTAATAATATATAAA
247148 TAAGTTTAACTTAAATTAA-AA-ACTATAAA
1 TAA-TTTAACTT-AATTAATAATA-TATAAA
247177 TAATTTAA
1 TAATTTAA
247185 AATTTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 6 0.18
29 19 0.56
30 9 0.26
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (28 bp):
TAATTTAACTTAATTAATAATATATAAA
Found at i:247338 original size:38 final size:36
Alignment explanation
Indices: 247278--247351 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 36
247268 CAAATTCTTT
* *
247278 CATAAAAAATATATTATAATTAAAATAACAAAATAAAA
1 CATAAAAAATATATAATAATT-AAACAA-AAAATAAAA
*
247316 CATAAAAAATA-ATAAATTATTAAACAAAAAATAAAA
1 CATAAAAAATATAT-AATAATTAAACAAAAAATAAAA
247352 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 9 0.28
37 7 0.22
38 16 0.50
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (36 bp):
CATAAAAAATATATAATAATTAAACAAAAAATAAAA
Found at i:247778 original size:2 final size:2
Alignment explanation
Indices: 247771--247796 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
247761 ATAATTGCAC
247771 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
247797 GATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249267 original size:2 final size:2
Alignment explanation
Indices: 249262--249305 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
249252 ATGTGCGTGA
249262 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
249304 AT
1 AT
249306 CACATGTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249606 original size:16 final size:16
Alignment explanation
Indices: 249585--249619 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
249575 ATTTAAAAAG
*
249585 ATTAATCTAACTTTAA
1 ATTAATCTAAATTTAA
*
249601 ATTAATTTAAATTTAA
1 ATTAATCTAAATTTAA
249617 ATT
1 ATT
249620 TTAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAATCTAAATTTAA
Found at i:250211 original size:20 final size:20
Alignment explanation
Indices: 250183--250257 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
250173 TTTTACCTTG
250183 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
250203 ATATATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
250223 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
250243 ATGTATCGATACATT
1 ATGTATCGATACATT
250258 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:251202 original size:23 final size:23
Alignment explanation
Indices: 251165--251220 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
251155 TAGCCTTTGA
251165 CCATGCA--TTTTTTATTATGTT
1 CCATGCATTTTTTTTATTATGTT
251186 CCATGCATTTTTTTTATTATGTT
1 CCATGCATTTTTTTTATTATGTT
*
251209 TCATG--TTTTTTT
1 CCATGCATTTTTTT
251221 AACATGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (23 bp):
CCATGCATTTTTTTTATTATGTT
Found at i:254565 original size:19 final size:20
Alignment explanation
Indices: 254528--254565 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
254518 GGGCCACTTT
*
254528 TTTTTTTTATTGATGTTCAA
1 TTTTTTTTATTGATATTCAA
*
254548 TTTTTTTT-TTGCTATTCA
1 TTTTTTTTATTGATATTCA
254566 TTCCCATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTTTTTATTGATATTCAA
Done.