Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold212
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: 1080337
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 10
Found at i:145642 original size:17 final size:17
Alignment explanation
Indices: 145620--145654 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
145610 TATTAATTTA
*
145620 ATTAAAAATAAATTAAT
1 ATTAAAAATAAAATAAT
*
145637 ATTAAAATTAAAATAAT
1 ATTAAAAATAAAATAAT
145654 A
1 A
145655 AAAATTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAAATAAAATAAT
Found at i:147987 original size:2 final size:2
Alignment explanation
Indices: 147982--148025 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
147972 CTCTCTCTCT
* *
147982 CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA TA 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
148024 CA
1 CA
148026 AATGTGATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:149468 original size:8 final size:8
Alignment explanation
Indices: 149451--149481 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
149441 CTTATACAGG
*
149451 TCTCTCTC
1 TCTCTTTC
149459 TCTCTTTC
1 TCTCTTTC
149467 TCTCTTTC
1 TCTCTTTC
149475 TCTCTTT
1 TCTCTTT
149482 GTCTGGTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (8 bp):
TCTCTTTC
Found at i:149954 original size:4 final size:4
Alignment explanation
Indices: 149938--149968 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
149928 CGTTGTTACT
*
149938 TTTA TTTA CTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
149969 TTGATGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:151022 original size:33 final size:31
Alignment explanation
Indices: 150974--151038 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
150964 AATCAAAGTT
**
150974 TTTTTTTTTTTTTTAATACTATCTTTCAGTTGA
1 TTTTTTTTTGGTTTAA-A-TATCTTTCAGTTGA
*
151007 TTTTTTTTTGGTTTAAATATCTTTTAGTTGA
1 TTTTTTTTTGGTTTAAATATCTTTCAGTTGA
151038 T
1 T
151039 GTCTAACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.48
32 1 0.03
33 14 0.48
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.66
Consensus pattern (31 bp):
TTTTTTTTTGGTTTAAATATCTTTCAGTTGA
Found at i:152239 original size:27 final size:27
Alignment explanation
Indices: 152202--152280 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
152192 ATAGTTAGTG
*
152202 TTTTCTATTTTCTCTTTAGTTTTTTTTC
1 TTTTC-ATTTTCTCTTTAGTTTTTTATC
*
152230 TTTTCATTTTTATCTTTAGCTTTTTTATC
1 TTTTCA-TTTTCTCTTTAG-TTTTTTATC
*
152259 --TTCA-TTTCATCTTTAATTTTTT
1 TTTTCATTTTC-TCTTTAGTTTTTT
152281 CTCTACAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 9 0.20
26 6 0.14
27 5 0.11
28 16 0.36
29 8 0.18
ACGTcount: A:0.13, C:0.14, G:0.03, T:0.71
Consensus pattern (27 bp):
TTTTCATTTTCTCTTTAGTTTTTTATC
Found at i:152254 original size:15 final size:15
Alignment explanation
Indices: 152209--152260 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
152199 GTGTTTTCTA
*
152209 TTTTCTCTTTAG-TT
1 TTTTATCTTTAGCTT
* * *
152223 TTTTTTCTTT-TCAT
1 TTTTATCTTTAGCTT
152237 TTTTATCTTTAGCTT
1 TTTTATCTTTAGCTT
152252 TTTTATCTT
1 TTTTATCTT
152261 CATTTCATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.10, C:0.13, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTTATCTTTAGCTT
Found at i:160526 original size:21 final size:21
Alignment explanation
Indices: 160505--160584 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 21
160495 TTAATAAGAT
*
160505 TTTAAA-TTAAGATAATTTGA
1 TTTAAATTTAAAATAATTTGA
160525 TTTAAATTTAAAATAA-TT-A
1 TTTAAATTTAAAATAATTTGA
*
160544 ---AAATTTAAAAAATACATTTTA
1 TTTAAATTT--AAAATA-ATTTGA
160565 TTTAAACTTTAAAATAATTT
1 TTTAAA-TTTAAAATAATTT
160585 AAAATCAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
16 6 0.12
18 6 0.12
19 2 0.04
20 10 0.20
21 9 0.18
22 4 0.08
23 6 0.12
24 3 0.06
25 3 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTAAATTTAAAATAATTTGA
Found at i:160616 original size:16 final size:16
Alignment explanation
Indices: 160583--160645 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
160573 TTAAAATAAT
*
160583 TTAAAATCAATCTAAAC
1 TTAAAAT-AATTTAAAC
160600 TTAAAATAATTTAAAC
1 TTAAAATAATTTAAAC
* *
160616 TTTAAAT-GTATTAAAC
1 TTAAAATAAT-TTAAAC
160632 TT-AAATAATTTAAA
1 TTAAAATAATTTAAA
160646 TCAATAATCG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 10 0.25
16 23 0.57
17 7 0.17
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (16 bp):
TTAAAATAATTTAAAC
Found at i:161410 original size:22 final size:22
Alignment explanation
Indices: 161379--161421 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
161369 TTTTTCGTAT
*
161379 AAAAATGTAAAAAAGTAAATAC
1 AAAAAGGTAAAAAAGTAAATAC
*
161401 AAAAAGGTAAAAAAGTTAATA
1 AAAAAGGTAAAAAAGTAAATA
161422 TAAGCCCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (22 bp):
AAAAAGGTAAAAAAGTAAATAC
Found at i:163060 original size:29 final size:29
Alignment explanation
Indices: 163020--163083 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
163010 ACATGAATTT
163020 AAAT-TAAAAATTT-ATTTAGAAACAA-TAA
1 AAATATAAAAATTTAATTTA-AAA-AATTAA
163048 AAATATAAAAATTTAATTTAAAAAATTAA
1 AAATATAAAAATTTAATTTAAAAAATTAA
163077 AAATATA
1 AAATATA
163084 TATTATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AAATATAAAAATTTAATTTAAAAAATTAA
Found at i:163290 original size:2 final size:2
Alignment explanation
Indices: 163283--163321 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
163273 CAAATTTGGT
163283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
163322 CATTTCTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:164716 original size:28 final size:29
Alignment explanation
Indices: 164655--164716 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
164645 TTATTTTTAA
*
164655 AAATATTTTTAATTTAATTTTTAATAATT
1 AAATATTTTTAATTTAAATTTTAATAATT
* *
164684 TAATATTTTTTA-TTAAATTTTAA-AATAT
1 AAATATTTTTAATTTAAATTTTAATAAT-T
164712 AAATA
1 AAATA
164717 ACTTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.11
28 15 0.54
29 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATATTTTTAATTTAAATTTTAATAATT
Found at i:165120 original size:5 final size:5
Alignment explanation
Indices: 165110--165161 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
165100 TAACAGGTAA
* * *
165110 AATTT AATTT AAATT AATTT AATTT TATAT AATATT ATATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AAT-TT A-ATTT AATTT AATTT
165162 TAAAAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 32 0.82
6 5 0.13
7 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:165789 original size:57 final size:57
Alignment explanation
Indices: 165697--165811 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
165687 ACGAAGCTCT
* *
165697 TAACTTTGGTTGGTCTCCGTCGGATTCTACAGTGTCAGCGGCAGTTAAAGAGGAGCC
1 TAACTTGGGTTGGTCTCCGTCGGATTCTACAGTGTCAGAGGCAGTTAAAGAGGAGCC
* * *
165754 TAACTTGGGTTGGTCTCCGTCGGATTCTACGGTGTCAGATGCCGTTAAAGAGGAGCC
1 TAACTTGGGTTGGTCTCCGTCGGATTCTACAGTGTCAGAGGCAGTTAAAGAGGAGCC
165811 T
1 T
165812 GAGATGATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (57 bp):
TAACTTGGGTTGGTCTCCGTCGGATTCTACAGTGTCAGAGGCAGTTAAAGAGGAGCC
Found at i:168026 original size:23 final size:23
Alignment explanation
Indices: 167964--168062 Score: 69
Period size: 24 Copynumber: 4.3 Consensus size: 23
167954 ATAATTGCAT
* * *
167964 TATTTTAATAACTATAAATGTTAA
1 TATTTTAATAATTATTAAT-ATAA
* * *
167988 CATTTTAATAATTATTCATTTAA
1 TATTTTAATAATTATTAATATAA
*
168011 TAATTTTAATCA-TATTAATATAA
1 T-ATTTTAATAATTATTAATATAA
*
168034 TATTTTAAATTATT-TTAA-ATAA
1 TATTTT-AATAATTATTAATATAA
*
168056 TTTTTTA
1 TATTTTA
168063 TAAAATTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.02
22 14 0.23
23 22 0.35
24 25 0.40
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (23 bp):
TATTTTAATAATTATTAATATAA
Found at i:168055 original size:22 final size:22
Alignment explanation
Indices: 168008--168088 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
167998 ATTATTCATT
* *
168008 TAATAATTTT-AATCATATTAATA
1 TAAT-ATTTTAAATAATTTTAA-A
*
168031 TAATATTTTAAATTATTTTAAA
1 TAATATTTTAAATAATTTTAAA
*
168053 TAATTTTTTATAA-AATTTTTAAA
1 TAATATTTTA-AATAA-TTTTAAA
*
168076 -AATAATTTAAATA
1 TAATATTTTAAATA
168089 TCTCATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.04
22 24 0.50
23 22 0.46
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTTTAAATAATTTTAAA
Found at i:169264 original size:22 final size:22
Alignment explanation
Indices: 169222--169264 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
169212 TTTTTAAATG
* *
169222 AATTTAATTTTTTTACTTAATA
1 AATTTAATTTTTTAAATTAATA
169244 AATTT-ATTTTTTAAATATAAT
1 AATTTAATTTTTTAAAT-TAAT
169265 CTTTTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTAATTTTTTAAATTAATA
Found at i:170037 original size:2 final size:2
Alignment explanation
Indices: 170030--170056 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
170020 GTCCTTTACG
170030 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
170057 TGGCCTCTCA
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:170541 original size:2 final size:2
Alignment explanation
Indices: 170534--170573 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
170524 GCCCTTTACT
170534 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
170574 AATTGGCCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:170819 original size:521 final size:499
Alignment explanation
Indices: 169858--170872 Score: 1634
Period size: 521 Copynumber: 2.0 Consensus size: 499
169848 ATGATCATAA
169858 ATAAATAAATAAATAAAGTTAAAGAATATATAATATATACATATACATACTTTTACAAGTGAAAA
1 ATAAATAAATAAATAAAGTTAAAGAATATATAATATATACATATACATACTTTTACAAGTGAAAA
169923 GGCTGGAACTGGTAAGCAAATATGAAAGGAATAAAATAAGACCTACCACGTTTTCACAGAGCCCA
66 GGCTGGAACTGGTAAGCAAATATGAAAGGAATAAAATAAGACCTACCACGTTTTCACAGAGCCCA
* *
169988 AGCTCAAAGCCTCATACCAATAACTTTATTTTGTCCTTTACGTATATATATATATATATATATAT
131 AGCTCAAAGCCTCATACCAATAACTTTATTTTGCCCTTTACATATATATATATATATATATATAT
* * *
170053 ATATTGGCCTCTCATCATCACGAAATAATGATTGACATCAAACAGCAATTTGGCTACGATTCAAA
196 ATATTGGCCTCTCATAATCACGAAATAATGATTGACATCAAAAAGCAATTTCGCTACGATTCAAA
170118 TTCCACAATCCATCAGCCATTTACTCATCATGACATCGACAAAATTACATTATAAATTTTTCGAT
261 TTCCACAATCCATCAGCCATTTACTCATCATGACATCGACAAAATTACATTATAAATTTTTCGAT
*
170183 TTTTACTAGGAATGAAAATGCTAAAAGATATTTATAATTTAAATAATATTAAAATATTTATAAAT
326 TTTTACTAGGAATGAAAATGCTAAAAGATATTTATAATTTAAATAATATTAAAATATTTAAAAAT
*
170248 TATTTTTATATTAATATTTTTATAATAAAATTTAAATATATTTTTATTATTAAATAATAATTCAA
391 TATTTTTATATTAATATTTTAATAATAAAATTTAAATATATTTTTATTATTAAATAATAATTCAA
*
170313 ATCAAATTAATTTGAATTATTAAAATTTTCATCCTAATCTAATC
456 ATCAAATTAATCTGAATTATTAAAATTTTCATCCTAATCTAATC
*
170357 ATAAATAAATAAATAAAGTTAAAGAATCTATATATATATATATATATATACATACTTTTACAAGT
1 ATAAATAAATAAATAAAGTTAAAG-A---ATATATA-ATATATACATATACATACTTTTACAAGT
* * *
170422 GAAAAGGCTGGAACTGGTAAGCAAATATGAATGGAATAAACTAAGACCTACCATGTTTTCACAGA
61 GAAAAGGCTGGAACTGGTAAGCAAATATGAAAGGAATAAAATAAGACCTACCACGTTTTCACAGA
*
170487 GCCCAAGCTCGAAGCCTCATACCAATAACTTTATTTTGCCCTTTACTTATATATATATATATATA
126 GCCCAAGCTCAAAGCCTCATACCAATAACTTTATTTTGCCCTTTAC--------------ATATA
170552 TATATATATATATATATATATAAATTGGCCTCTCATAATCACGAAATAATGATTGACATCAAAAA
177 TATATATATATATATATATAT--ATTGGCCTCTCATAATCACGAAATAATGATTGACATCAAAAA
*
170617 GCAATTTCGCTATGATTCAAAATTCCACAATCCATCAGCCATTTACTCATCATGACATCGACAAA
240 GCAATTTCGCTACGATTC-AAATTCCACAATCCATCAGCCATTTACTCATCATGACATCGACAAA
* ** * * **
170682 ATTTCATTATAAATTTTTTTATTTTTATTAGGAATGAAAATGTTAAGGGATATTTATAATTTAAA
304 ATTACATTATAAATTTTTCGATTTTTACTAGGAATGAAAATGCTAAAAGATATTTATAATTTAAA
170747 TAATATTAAAATATTTAAAAATTATTTTTATATTAATATTTTAATAATAAAATTTAAATATATTT
369 TAATATTAAAATATTTAAAAATTATTTTTATATTAATATTTTAATAATAAAATTTAAATATATTT
*
170812 TTATTATTAAATAATAATTCAAATCGAATTAATCTGAATTATTAAAATTTTCATCCTAATC
434 TTATTATTAAATAATAATTCAAATCAAATTAATCTGAATTATTAAAATTTTCATCCTAATC
170873 CGATCATGAA
Statistics
Matches: 472, Mismatches: 22, Indels: 22
0.91 0.04 0.04
Matches are distributed among these distances:
499 24 0.05
500 1 0.00
503 7 0.01
504 133 0.28
518 25 0.05
520 56 0.12
521 226 0.48
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (499 bp):
ATAAATAAATAAATAAAGTTAAAGAATATATAATATATACATATACATACTTTTACAAGTGAAAA
GGCTGGAACTGGTAAGCAAATATGAAAGGAATAAAATAAGACCTACCACGTTTTCACAGAGCCCA
AGCTCAAAGCCTCATACCAATAACTTTATTTTGCCCTTTACATATATATATATATATATATATAT
ATATTGGCCTCTCATAATCACGAAATAATGATTGACATCAAAAAGCAATTTCGCTACGATTCAAA
TTCCACAATCCATCAGCCATTTACTCATCATGACATCGACAAAATTACATTATAAATTTTTCGAT
TTTTACTAGGAATGAAAATGCTAAAAGATATTTATAATTTAAATAATATTAAAATATTTAAAAAT
TATTTTTATATTAATATTTTAATAATAAAATTTAAATATATTTTTATTATTAAATAATAATTCAA
ATCAAATTAATCTGAATTATTAAAATTTTCATCCTAATCTAATC
Found at i:176701 original size:8 final size:9
Alignment explanation
Indices: 176684--176712 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
176674 GTACTTTTCA
176684 TAATTTTTT
1 TAATTTTTT
176693 TAATTTTTT
1 TAATTTTTT
176702 TAATTTTTT
1 TAATTTTTT
176711 TA
1 TA
176713 TAAAGAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TAATTTTTT
Found at i:181261 original size:32 final size:33
Alignment explanation
Indices: 181224--181301 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 33
181214 TTTTTAATAA
**
181224 TTTAAAATAAT-TTAATTTAATTTAAA-TT-ATT
1 TTTAAAATAATAAAAATTT-ATTTAAATTTAATT
*
181255 TTTTAAATAATAAAAATTTATTTAAATTTAATT
1 TTTAAAATAATAAAAATTTATTTAAATTTAATT
181288 TTTAAAAT-ATAAAA
1 TTTAAAATAATAAAA
181302 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 17 0.43
32 13 0.32
33 10 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TTTAAAATAATAAAAATTTATTTAAATTTAATT
Found at i:181264 original size:31 final size:32
Alignment explanation
Indices: 181237--181301 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
181227 AAAATAATTT
*
181237 AATTTAATTTAAA-TTATTTTTTAAATAATAAA
1 AATTT-ATTTAAATTTAATTTTTAAATAATAAA
181269 AATTTATTTAAATTTAATTTTTAAA-ATATAAA
1 AATTTATTTAAATTTAATTTTTAAATA-ATAAA
181301 A
1 A
181302 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AATTTATTTAAATTTAATTTTTAAATAATAAA
Found at i:181311 original size:32 final size:31
Alignment explanation
Indices: 181224--181331 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 31
181214 TTTTTAATAA
**
181224 TTTAAAATAAT-TTAATTTAATTTAAATTATT
1 TTTAAAATAATAAAAATTT-ATTTAAATTATT
*
181255 TTTTAAATAATAAAAATTTATTTAAATTTAATT
1 TTTAAAATAATAAAAATTTATTTAAA-TT-ATT
*
181288 TTTAAAAT-AT-AAAA-TTATTTTTAATATATT
1 TTTAAAATAATAAAAATTTA-TTTAAAT-TATT
*
181318 TTAAATAATAATAA
1 TTTAA-AATAATAA
181332 CAAGGTTTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
30 11 0.17
31 30 0.48
32 11 0.17
33 11 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTAAAATAATAAAAATTTATTTAAATTATT
Found at i:181528 original size:19 final size:18
Alignment explanation
Indices: 181479--181530 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
181469 TAATAAAAAA
*
181479 TTTAATTAA-AATTTAAT
1 TTTAAATAATAATTTAAT
* *
181496 TGTAAAATATTAATATTAAT
1 T-TTAAATAATAAT-TTAAT
181516 TTTAAATAATAATTT
1 TTTAAATAATAATTT
181531 GAGTTTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.26
19 13 0.48
20 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTAAATAATAATTTAAT
Found at i:184481 original size:2 final size:2
Alignment explanation
Indices: 184474--184503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
184464 GAACCAACTC
184474 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
184504 GCTGACTTTA
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:185427 original size:3 final size:3
Alignment explanation
Indices: 185414--185449 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
185404 TCAAAAACAC
*
185414 CCA CTA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
185450 ATAGTATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.64, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:186120 original size:159 final size:159
Alignment explanation
Indices: 185831--186148 Score: 537
Period size: 159 Copynumber: 2.0 Consensus size: 159
185821 TAGTTTCAGT
* * * * *
185831 TGTTGGCTTATGTGCAGCTCTGTTGTTTGCTCTGATTATTCATTGATATTTACAGTTGGAAGGAA
1 TGTTGGCTTATGTGCAGCTATGTTGTTTGCTCTGATCATTCATTGATATGTACAGTTGAAAGAAA
* * * *
185896 GCATGTGAGCTATTGGAAGACACATTCTTTTACTTTCGATTCTGAGCTATGTAGACAAACAAATG
66 GCATATGAGCTATTGGAAGACACATTCTTTTACTTTCAATTCTAAGCTATATAGACAAACAAATG
*
185961 AGAATTGACTATCTCTTTTCTCTTTGGAC
131 AGAATTGACTATCTCTGTTCTCTTTGGAC
*
185990 TGTTGGCTTATGTGCAGCTATGTTGTTTGCTCTGATCATTCATTGATATGTATAGTTGAAAGAAA
1 TGTTGGCTTATGTGCAGCTATGTTGTTTGCTCTGATCATTCATTGATATGTACAGTTGAAAGAAA
186055 GCATATGAGCTATTGGAAGACACATTCTTTTACTTTCAATTCTAAGCTATATAGACAAACAAATG
66 GCATATGAGCTATTGGAAGACACATTCTTTTACTTTCAATTCTAAGCTATATAGACAAACAAATG
186120 AGAATTGACTATCTCTGTTCTCTTTGGAC
131 AGAATTGACTATCTCTGTTCTCTTTGGAC
186149 CTTTTGACCA
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
159 148 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (159 bp):
TGTTGGCTTATGTGCAGCTATGTTGTTTGCTCTGATCATTCATTGATATGTACAGTTGAAAGAAA
GCATATGAGCTATTGGAAGACACATTCTTTTACTTTCAATTCTAAGCTATATAGACAAACAAATG
AGAATTGACTATCTCTGTTCTCTTTGGAC
Found at i:187113 original size:2 final size:2
Alignment explanation
Indices: 187106--187137 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
187096 AATATGGATA
187106 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
187138 CTTTCTTCAG
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:190216 original size:23 final size:23
Alignment explanation
Indices: 190189--190262 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
190179 TTTTTTCTTT
190189 GTTTGTTTTAATTCACCATATGA
1 GTTTGTTTTAATTCACCATATGA
* * * **
190212 GTTTGTCTT--TTGA-AATATTTTT
1 GTTTGTTTTAATTCACCATA--TGA
190234 GTTTGTTTTAATTCACCATATGA
1 GTTTGTTTTAATTCACCATATGA
190257 GTTTGT
1 GTTTGT
190263 CTTTTGAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 9 0.25
23 15 0.42
24 3 0.08
25 3 0.08
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (23 bp):
GTTTGTTTTAATTCACCATATGA
Found at i:190236 original size:45 final size:45
Alignment explanation
Indices: 190186--190276 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
190176 GACTTTTTTC
190186 TTTGTTTGTTTTAATTCACCATATGAGTTTGTCTTTTGAAATATT
1 TTTGTTTGTTTTAATTCACCATATGAGTTTGTCTTTTGAAATATT
190231 TTTGTTTGTTTTAATTCACCATATGAGTTTGTCTTTTGAAATATT
1 TTTGTTTGTTTTAATTCACCATATGAGTTTGTCTTTTGAAATATT
190276 T
1 T
190277 ATAATTTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (45 bp):
TTTGTTTGTTTTAATTCACCATATGAGTTTGTCTTTTGAAATATT
Found at i:202615 original size:9 final size:9
Alignment explanation
Indices: 202589--202631 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
202579 GATATAAATA
202589 AAATATA-T
1 AAATATATT
*
202597 AAAT-TTTT
1 AAATATATT
202605 AAATATATT
1 AAATATATT
*
202614 AAAAATATT
1 AAATATATT
202623 AAATATATT
1 AAATATATT
202632 CATATTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 1 0.03
8 9 0.31
9 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATATATT
Found at i:203267 original size:19 final size:20
Alignment explanation
Indices: 203245--203291 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
203235 ATAACGTTGT
203245 ATTATTTAATT-CAAAAAAA
1 ATTATTTAATTGCAAAAAAA
* *
203264 ATTATTT-ATTGTAAAAAAT
1 ATTATTTAATTGCAAAAAAA
203283 ATTATTTAA
1 ATTATTTAA
203292 AATTTTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 20 0.83
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTATTTAATTGCAAAAAAA
Found at i:207484 original size:17 final size:18
Alignment explanation
Indices: 207457--207494 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
207447 AAAAAGTAAT
*
207457 TAGTATTTTTTTATTAGA
1 TAGTATTTTTTTAATAGA
207475 TAGT-TTTTTTTAATAGA
1 TAGTATTTTTTTAATAGA
207492 TAG
1 TAG
207495 CTCTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TAGTATTTTTTTAATAGA
Found at i:207501 original size:18 final size:17
Alignment explanation
Indices: 207463--207501 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
207453 TAATTAGTAT
* *
207463 TTTTTTATTAGATAGTT
1 TTTTTTAATAGATAGTC
207480 TTTTTTAATAGATAGCTC
1 TTTTTTAATAGATAG-TC
207498 TTTT
1 TTTT
207502 ATTTAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (17 bp):
TTTTTTAATAGATAGTC
Found at i:210743 original size:26 final size:25
Alignment explanation
Indices: 210705--210768 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
210695 TAAAATTTGA
* * *
210705 TCAAATTCAAATTGAA-TTTTGGGTC
1 TCAAATTTAAATT-AAGCTTTGAGTC
210730 TCAAAGTTTAAATTAAGCTTTGAGTC
1 TCAAA-TTTAAATTAAGCTTTGAGTC
210756 TCAAATTTTAAAT
1 TCAAA-TTTAAAT
210769 AAAGTTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (25 bp):
TCAAATTTAAATTAAGCTTTGAGTC
Found at i:210954 original size:2 final size:2
Alignment explanation
Indices: 210947--210979 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
210937 TCCTCAAATG
210947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
210980 TTTGGTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212532 original size:21 final size:21
Alignment explanation
Indices: 212507--212546 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
212497 GGTGTTTCAT
* *
212507 TTTTAAATTTTTTTTTTTAGA
1 TTTTAAAATTTTATTTTTAGA
212528 TTTTAAAATTTTATTTTTA
1 TTTTAAAATTTTATTTTTA
212547 TTTCATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTAAAATTTTATTTTTAGA
Found at i:214897 original size:2 final size:2
Alignment explanation
Indices: 214890--214956 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
214880 GGGACACGTG
* * * * * * * *
214890 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
214932 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
214957 GTAAATAGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (2 bp):
TA
Found at i:219045 original size:25 final size:27
Alignment explanation
Indices: 218989--219042 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
218979 ATATTTTAAA
* ** *
218989 AATGTATATATTTTAGTAACTTACACT
1 AATGTATATACTTTAGTAACAGAAACT
219016 AATGTATATACTTTAGT-ACAGAAACT
1 AATGTATATACTTTAGTAACAGAAACT
219042 A
1 A
219043 TGTTTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (27 bp):
AATGTATATACTTTAGTAACAGAAACT
Found at i:226777 original size:13 final size:13
Alignment explanation
Indices: 226754--226791 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
226744 TTTATTTTAA
226754 TATTT-ATAATAT
1 TATTTAATAATAT
*
226766 TATTTAATAATAA
1 TATTTAATAATAT
*
226779 TCTTTAATAATAT
1 TATTTAATAATAT
226792 AAAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTAATAATAT
Found at i:228135 original size:3 final size:3
Alignment explanation
Indices: 228127--228156 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
228117 TAGGAAAACT
228127 TAA TAA TAA TTAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA
228157 TAACAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:229541 original size:2 final size:2
Alignment explanation
Indices: 229534--229564 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
229524 TTTAAGAAAA
229534 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 A
229565 AACTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:231103 original size:21 final size:21
Alignment explanation
Indices: 231079--231123 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
231069 ATTATATAAA
*
231079 ATATTATTTTTATTTTTAT-AT
1 ATATTA-TTTAATTTTTATCAT
231100 ATATTATTTAATTTTTATCAT
1 ATATTATTTAATTTTTATCAT
231121 ATA
1 ATA
231124 AAGATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTATTTAATTTTTATCAT
Found at i:231107 original size:24 final size:26
Alignment explanation
Indices: 231070--231117 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
231060 CAATTTTTAA
231070 TTATATAAAATA-TT-ATTTTTATTT
1 TTATATAAAATATTTAATTTTTATTT
* *
231094 TTATATATATTATTTAATTTTTAT
1 TTATATAAAATATTTAATTTTTAT
231118 CATATAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 2 0.10
26 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATATAAAATATTTAATTTTTATTT
Found at i:232660 original size:2 final size:2
Alignment explanation
Indices: 232647--232681 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
232637 GTCCATTTAC
*
232647 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
232682 TAGGCTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:235239 original size:2 final size:2
Alignment explanation
Indices: 235232--235265 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
235222 CAAAAGCAAG
235232 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
235266 TGTGGAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:236625 original size:2 final size:2
Alignment explanation
Indices: 236618--236660 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
236608 TCGTCCAATC
236618 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
236660 T
1 T
236661 GGAAGAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:236900 original size:23 final size:24
Alignment explanation
Indices: 236865--236913 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
236855 ATCTTTTATA
*
236865 TATATATATATAATGATAGATTTT
1 TATATATAAATAATGATAGATTTT
* *
236889 TATA-ATAAATAATTATATATTTT
1 TATATATAAATAATGATAGATTTT
236912 TA
1 TA
236914 ATTTACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATATAAATAATGATAGATTTT
Found at i:237052 original size:2 final size:2
Alignment explanation
Indices: 237040--237076 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
237030 AAGTGAAATC
* *
237040 AT AT TT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
237077 GATTTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:237081 original size:12 final size:12
Alignment explanation
Indices: 237040--237081 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
237030 AAGTGAAATC
237040 ATATTTATATAT
1 ATATTTATATAT
*
237052 ATATATATATAT
1 ATATTTATATAT
237064 ATATTTATATAT
1 ATATTTATATAT
*
237076 AGATTT
1 ATATTT
237082 GATTTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:242386 original size:12 final size:12
Alignment explanation
Indices: 242365--242399 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
242355 CTTATAAGAA
*
242365 AAAGAAAGAGAG
1 AAAGAGAGAGAG
242377 AAAGAGAGAGAG
1 AAAGAGAGAGAG
*
242389 AGAGAGAGAGA
1 AAAGAGAGAGA
242400 CTTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:243041 original size:2 final size:2
Alignment explanation
Indices: 243022--243061 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
243012 ATGTTATTCG
* *
243022 TA TA TA TT TA TT TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
243062 GTACAGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.97
3 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:244314 original size:2 final size:2
Alignment explanation
Indices: 244307--244336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
244297 ACATACATAC
244307 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
244337 TAGGAGTATG
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:246238 original size:3 final size:3
Alignment explanation
Indices: 246230--246261 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
246220 CCTTTCTCAT
246230 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
246262 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:246701 original size:15 final size:16
Alignment explanation
Indices: 246675--246704 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
246665 TTAATTTTTT
246675 TAAAAAATTTTAAATC
1 TAAAAAATTTTAAATC
246691 TAAAAAA-TTTAAAT
1 TAAAAAATTTTAAAT
246705 AAGAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATTTTAAATC
Found at i:249058 original size:2 final size:2
Alignment explanation
Indices: 249051--249082 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
249041 CAAAAGCAAG
249051 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
249083 TGTGGAACTT
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:250442 original size:2 final size:2
Alignment explanation
Indices: 250435--250461 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
250425 TCGTCCAATC
250435 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
250462 GGAAGAGAAA
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:250701 original size:23 final size:24
Alignment explanation
Indices: 250666--250714 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
250656 ATCTTTTATA
*
250666 TATATATATATAATGATAGATTTT
1 TATATATAAATAATGATAGATTTT
* *
250690 TATA-ATAAATAATTATATATTTT
1 TATATATAAATAATGATAGATTTT
250713 TA
1 TA
250715 ATTTACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATATAAATAATGATAGATTTT
Found at i:250853 original size:2 final size:2
Alignment explanation
Indices: 250841--250877 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
250831 AAGTGAAATC
* *
250841 AT AT TT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250878 GATTTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:250882 original size:12 final size:12
Alignment explanation
Indices: 250841--250882 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
250831 AAGTGAAATC
250841 ATATTTATATAT
1 ATATTTATATAT
*
250853 ATATATATATAT
1 ATATTTATATAT
250865 ATATTTATATAT
1 ATATTTATATAT
*
250877 AGATTT
1 ATATTT
250883 GATTTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:256188 original size:12 final size:12
Alignment explanation
Indices: 256167--256201 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
256157 CTTATAAGAA
*
256167 AAAGAAAGAGAG
1 AAAGAGAGAGAG
256179 AAAGAGAGAGAG
1 AAAGAGAGAGAG
*
256191 AGAGAGAGAGA
1 AAAGAGAGAGA
256202 CTTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:258118 original size:2 final size:2
Alignment explanation
Indices: 258111--258136 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
258101 ACATACATAC
258111 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
258137 TAGGAGTATG
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:260028 original size:3 final size:3
Alignment explanation
Indices: 260020--260051 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
260010 CCTTTCTCAT
260020 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
260052 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:260491 original size:15 final size:16
Alignment explanation
Indices: 260465--260494 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
260455 TTAATTTTTT
260465 TAAAAAATTTTAAATC
1 TAAAAAATTTTAAATC
260481 TAAAAAA-TTTAAAT
1 TAAAAAATTTTAAAT
260495 AAGAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATTTTAAATC
Found at i:262858 original size:2 final size:2
Alignment explanation
Indices: 262851--262894 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
262841 AAAGCAAGAA
262851 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
262893 AT
1 AT
262895 TGTGGAACTT
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:263525 original size:2 final size:2
Alignment explanation
Indices: 263512--263544 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
263502 AAGCAAAGAT
263512 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
263545 GAGTTTTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:264268 original size:2 final size:2
Alignment explanation
Indices: 264261--264285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
264251 CAGTCCAACC
264261 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
264286 GGAAGAAAAA
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:264681 original size:2 final size:2
Alignment explanation
Indices: 264676--264716 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
264666 ATATATTTAT
264676 AG 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 AG A
264717 ATTGGTTTAG
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:265233 original size:11 final size:11
Alignment explanation
Indices: 265201--265239 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
265191 TAGATAACTT
*
265201 TAAATACAATA
1 TAAATATAATA
265212 TAATCATATAATA
1 TAA--ATATAATA
265225 TAAATATAATA
1 TAAATATAATA
265236 TAAA
1 TAAA
265240 AAAATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:266834 original size:19 final size:21
Alignment explanation
Indices: 266801--266842 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
266791 AATAAAAGAA
266801 AAATAATTCATTTT-AAATAC
1 AAATAATTCATTTTAAAATAC
266821 AAATAATT-ATTTTAAAATAC
1 AAATAATTCATTTTAAAATAC
266841 AA
1 AA
266843 GAAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATTCATTTTAAAATAC
Found at i:266869 original size:44 final size:45
Alignment explanation
Indices: 266785--266873 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
266775 CAAATGCCCT
266785 TTTTAAAATAAAAGAAAAATAATTCATTTTAAATACAAATAATTA
1 TTTTAAAATAAAAGAAAAATAATTCATTTTAAATACAAATAATTA
* * **
266830 TTTTAAAATACAAG-AAAATAATTCATTTTAGATGGAAATAATTA
1 TTTTAAAATAAAAGAAAAATAATTCATTTTAAATACAAATAATTA
266874 GAGATATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 27 0.68
45 13 0.32
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (45 bp):
TTTTAAAATAAAAGAAAAATAATTCATTTTAAATACAAATAATTA
Found at i:274418 original size:18 final size:17
Alignment explanation
Indices: 274371--274428 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
274361 AATATTAAAA
274371 TTATATTTA-A-AACATT
1 TTATATTTATATAA-ATT
274387 TTATATTTATATAAATT
1 TTATATTTATATAAATT
*
274404 TTAATATATTA-ATAATTT
1 TT-ATAT-TTATATAAATT
274422 ATTATAT
1 -TTATAT
274429 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 9 0.25
17 6 0.17
18 16 0.44
19 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:274668 original size:19 final size:19
Alignment explanation
Indices: 274644--274696 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
274634 TTTTATTATT
274644 TTTAAAAAT-TTATAATAAA
1 TTTAAAAATATTAT-ATAAA
274663 TTT-AAAATATTATATAAA
1 TTTAAAAATATTATATAAA
274681 TTTAAAAA-ATTA-ATAA
1 TTTAAAAATATTATATAA
274697 TTCAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.12
18 17 0.53
19 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAAAAATATTATATAAA
Found at i:275089 original size:2 final size:2
Alignment explanation
Indices: 275082--275115 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
275072 TTTCCAAACA
275082 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
275116 GAAGTGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276018 original size:13 final size:13
Alignment explanation
Indices: 276000--276028 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
275990 AAAATTTAAT
276000 TAAAATATAAATA
1 TAAAATATAAATA
276013 TAAAATATAAATA
1 TAAAATATAAATA
276026 TAA
1 TAA
276029 CATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAATATAAATA
Found at i:276053 original size:25 final size:25
Alignment explanation
Indices: 276009--276067 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
275999 TTAAAATATA
276009 AATAT-AAAATATAAATATAACA-T
1 AATATAAAAATATAAATATAACATT
*
276032 AATATAAAAATA-ATAATAATAATATT
1 AATATAAAAATATA-AAT-ATAACATT
*
276058 AACATAAAAA
1 AATATAAAAA
276068 AAATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 6 0.20
24 9 0.30
25 5 0.17
26 10 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (25 bp):
AATATAAAAATATAAATATAACATT
Found at i:276055 original size:20 final size:20
Alignment explanation
Indices: 276009--276086 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
275999 TTAAAATATA
*
276009 AATATAAAATATAAATATAACAT
1 AATATAAAA-AT-AATA-AAAAT
*
276032 AATATAAAAATAATAATAAT
1 AATATAAAAATAATAAAAAT
* * *
276052 AATATTAACATAAAAAAAAT
1 AATATAAAAATAATAAAAAT
*
276072 TATATAAAAAATAAT
1 AATAT-AAAAATAAT
276087 TAAGGTGTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 23 0.52
21 10 0.23
22 2 0.05
23 9 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AATATAAAAATAATAAAAAT
Found at i:276061 original size:31 final size:29
Alignment explanation
Indices: 276003--276071 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
275993 ATTTAATTAA
*
276003 AATATAAATATAAAATATAAATATAACAT
1 AATATAAAAATAAAATATAAATATAACAT
276032 AATATAAAAATAATAATA-ATAATATTAACAT
1 AATATAAAAATAA-AATATA-AATA-TAACAT
276063 AA-A-AAAAAT
1 AATATAAAAAT
276072 TATATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 19 0.53
30 9 0.25
31 8 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (29 bp):
AATATAAAAATAAAATATAAATATAACAT
Found at i:279606 original size:16 final size:16
Alignment explanation
Indices: 279585--279647 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
279575 TTTTATAAAT
279585 TTTAATTAATTATTTA
1 TTTAATTAATTATTTA
279601 TTTAA-T-ATATATTT-
1 TTTAATTAAT-TATTTA
*
279615 TATTAAATAATTATTTA
1 T-TTAATTAATTATTTA
279632 TTT-ATTAATTCATTTA
1 TTTAATTAATT-ATTTA
279648 GTGGTCCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 3 0.08
15 16 0.40
16 18 0.45
17 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATTAATTATTTA
Found at i:279614 original size:28 final size:27
Alignment explanation
Indices: 279578--279631 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
279568 CTTTTTTTTT
* *
279578 TATAAATTTTAATTAATTATTTATTTAA
1 TATAAATTTT-ATTAAATAATTATTTAA
*
279606 TATATATTTTATTAAATAATTATTTA
1 TATAAATTTTATTAAATAATTATTTA
279632 TTTATTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATAAATTTTATTAAATAATTATTTAA
Found at i:279792 original size:32 final size:34
Alignment explanation
Indices: 279756--279819 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 34
279746 AATATTAATA
279756 TATTTTTATAAT-TAAATTTAAA-TAAA-TAATTT
1 TATTTTTA-AATATAAATTTAAATTAAACTAATTT
*
279788 TATTTTTAAATATTAATTTAAATTAAACTAAT
1 TATTTTTAAATATAAATTTAAATTAAACTAAT
279820 CTAAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 17 0.61
33 4 0.14
34 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (34 bp):
TATTTTTAAATATAAATTTAAATTAAACTAATTT
Found at i:281515 original size:2 final size:2
Alignment explanation
Indices: 281510--281547 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
281500 TATATGTGTG
281510 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
281548 ACATAATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:283651 original size:12 final size:12
Alignment explanation
Indices: 283634--283664 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
283624 TAAATAGCTT
283634 TACATATATATA
1 TACATATATATA
283646 TACATATATATA
1 TACATATATATA
*
283658 TATATAT
1 TACATAT
283665 GTTTGGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
TACATATATATA
Found at i:284518 original size:2 final size:2
Alignment explanation
Indices: 284511--284555 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
284501 ATGCATTAGT
*
284511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
284553 TA T
1 TA T
284556 CACCTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:286716 original size:2 final size:2
Alignment explanation
Indices: 286709--286735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
286699 ATCTTTTAAT
286709 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
286736 GTAATTAAAC
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:287092 original size:20 final size:20
Alignment explanation
Indices: 287064--287118 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
287054 ATAATATTTT
*
287064 ATATGATATTTAAAAAATAA
1 ATATAATATTTAAAAAATAA
* *
287084 ATATAATATTTTAATACATAA
1 ATATAATA-TTTAAAAAATAA
287105 ATA-AATATATTAAA
1 ATATAATAT-TTAAA
287119 TTGTTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 15 0.52
21 13 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATAATATTTAAAAAATAA
Found at i:287135 original size:15 final size:15
Alignment explanation
Indices: 287110--287196 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 15
287100 CATAAATAAA
*
287110 TATATTAAATTGTTAT
1 TATA-TAAATTATTAT
*
287126 TATATAAATTATTTT
1 TATATAAATTATTAT
287141 TATATATAA-TATT-T
1 TATATA-AATTATTAT
*
287155 TA-A-AAATAATTAT
1 TATATAAATTATTAT
*
287168 AATATATAAA--AATAT
1 --TATATAAATTATTAT
*
287183 AATATAAATTATTA
1 TATATAAATTATTA
287197 AATTATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 19
0.69 0.07 0.23
Matches are distributed among these distances:
11 2 0.04
12 4 0.07
13 9 0.16
14 3 0.05
15 28 0.50
16 7 0.12
17 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (15 bp):
TATATAAATTATTAT
Found at i:287188 original size:20 final size:20
Alignment explanation
Indices: 287144--287194 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
287134 TTATTTTTAT
*
287144 ATATAATATTTTAAAAATAA
1 ATATAATATTATAAAAATAA
*
287164 TTATAATA-TATAAAAATATA
1 ATATAATATTATAAAAATA-A
287184 ATATAA-ATTAT
1 ATATAATATTAT
287195 TAAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATATTATAAAAATAA
Found at i:287544 original size:19 final size:21
Alignment explanation
Indices: 287520--287561 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
287510 AAATTTTTTA
287520 AATTTTATA-AA-AAATAATT
1 AATTTTATATAATAAATAATT
*
287539 AATTTTATATAATAAATATTT
1 AATTTTATATAATAAATAATT
287560 AA
1 AA
287562 ATAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTTATATAATAAATAATT
Found at i:287549 original size:21 final size:20
Alignment explanation
Indices: 287517--287563 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
287507 ATTAAATTTT
287517 TTAAATTTTATAAAAAATAA
1 TTAAATTTTATAAAAAATAA
*
287537 TT-AATTTTATATAATAAATAT
1 TTAAATTTTATA-AA-AAATAA
287558 TTAAAT
1 TTAAAT
287564 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 4 0.17
21 7 0.30
22 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATTTTATAAAAAATAA
Found at i:289608 original size:21 final size:21
Alignment explanation
Indices: 289567--289628 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
289557 TAAAAATTTA
*
289567 TTAAAATATTAAT-TAATATAT
1 TTAAAATATTAATATTA-ATAT
*
289588 TTAACATATTAATATTAATA-
1 TTAAAATATTAATATTAATAT
* *
289608 TTAATATATTTATA-TAATAT
1 TTAAAATATTAATATTAATAT
289628 T
1 T
289629 ACTTATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 15 0.43
22 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATATTAATATTAATAT
Found at i:289844 original size:6 final size:6
Alignment explanation
Indices: 289833--289866 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
289823 TTTTTTATAA
289833 TTTTAT TTTTAT TTTTAT TTATATAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TT-T-TAT TTTTAT TT
289867 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.73
7 2 0.08
8 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:289867 original size:14 final size:14
Alignment explanation
Indices: 289810--289868 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
289800 TTAATTCCTC
289810 ATTTATATTATATTTT
1 ATTTATA-TAT-TTTT
289826 -TTTATA-A-TTTT
1 ATTTATATATTTTT
289837 ATTT-T-TATTTTT
1 ATTTATATATTTTT
289849 ATTTATATATTTTT
1 ATTTATATATTTTT
289863 ATTTAT
1 ATTTAT
289869 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
11 6 0.16
12 11 0.29
13 2 0.05
14 13 0.34
15 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTATATATTTTT
Found at i:289867 original size:24 final size:22
Alignment explanation
Indices: 289811--289870 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
289801 TAATTCCTCA
289811 TTTATATTATATTTTTTTATAATT
1 TTTAT-TTAT-TTTTTTTATAATT
*
289835 TTATTTTTATTTTTATTTATATATT
1 TT-TATTTATTTTT-TTTATA-ATT
289860 TTTATTTATTT
1 TTTATTTATTT
289871 AAAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 4 0.13
24 20 0.65
25 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTATTTTTTTTATAATT
Found at i:289869 original size:18 final size:17
Alignment explanation
Indices: 289810--289871 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
289800 TTAATTCCTC
289810 ATTTATATTATATTTTTT
1 ATTTAT-TTATATTTTTT
*
289828 -TATAATTT-TATTTTTAT
1 AT-TTATTTATATTTTT-T
*
289845 TTTTATTTATATATTTTT
1 ATTTATTTATAT-TTTTT
289863 ATTTATTTA
1 ATTTATTTA
289872 AAAAATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 7 0.19
17 9 0.25
18 16 0.44
19 4 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTATTTATATTTTTT
Found at i:290199 original size:14 final size:13
Alignment explanation
Indices: 290174--290203 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
290164 CTTAATAAAA
290174 AATATTAAAATAT
1 AATATTAAAATAT
290187 AATATTAAAA-AT
1 AATATTAAAATAT
290199 AATAT
1 AATAT
290204 AAATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATTAAAATAT
Found at i:290214 original size:10 final size:11
Alignment explanation
Indices: 290181--290241 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
290171 AAAAATATTA
290181 AAATATAATATT
1 AAATATAATA-T
*
290193 AAAAATAATAT
1 AAATATAATAT
290204 AAATA-AATAT
1 AAATATAATAT
290214 --AT-TAATAT
1 AAATATAATAT
**
290222 TTATATAATAT
1 AAATATAATAT
290233 AAAT-TAATA
1 AAATATAATA
290242 ATATTATGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.17
10 12 0.29
11 13 0.32
12 9 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATATAATAT
Found at i:290215 original size:24 final size:24
Alignment explanation
Indices: 290171--290236 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
290161 TTTCTTAATA
* *
290171 AAAAATATTA-AAATATA-ATATT
1 AAAAATAATATAAATAAATATATT
290193 AAAAATAATATAAATAAATATATT
1 AAAAATAATATAAATAAATATATT
* * *
290217 AATATTTATATAATATAAAT
1 AAAAATAATATAA-ATAAAT
290237 TAATAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.25
23 6 0.17
24 15 0.42
25 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAATAATATAAATAAATATATT
Found at i:290215 original size:29 final size:29
Alignment explanation
Indices: 290179--290247 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
290169 TAAAAAATAT
290179 TAAA-ATA-TAATATTAAAAATAATATAAA
1 TAAATATATTAATATT-AAAATAATATAAA
* *
290207 TAAATATATTAATATTTATATAATATAAA
1 TAAATATATTAATATTAAAATAATATAAA
*
290236 TTAATAATATTA
1 TAAAT-ATATTA
290248 TGGATTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.11
29 18 0.51
30 13 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATATATTAATATTAAAATAATATAAA
Found at i:290220 original size:12 final size:13
Alignment explanation
Indices: 290165--290220 Score: 64
Period size: 12 Copynumber: 4.5 Consensus size: 13
290155 TTACCGTTTC
*
290165 TTAATAAAAAATA
1 TTAATAAATAATA
290178 TTAA-AATATAATA
1 TTAATAA-ATAATA
290191 TTAA-AAATAATA
1 TTAATAAATAATA
*
290203 TAAATAAAT-ATA
1 TTAATAAATAATA
290215 TTAATA
1 TTAATA
290221 TTTATATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
12 19 0.50
13 19 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAATAAATAATA
Found at i:290243 original size:24 final size:24
Alignment explanation
Indices: 290200--290246 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
290190 ATTAAAAATA
*
290200 ATATAAATAAATATATTAATATTT
1 ATATAAATAAATATAATAATATTT
290224 ATATAATATAAAT-TAATAATATT
1 ATATAA-ATAAATATAATAATATT
290247 ATGGATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAAATAAATATAATAATATTT
Found at i:290295 original size:20 final size:21
Alignment explanation
Indices: 290272--290312 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
290262 ATATATTTTT
290272 AAATATAA-TTATA-ATATAAA
1 AAAT-TAATTTATATATATAAA
290292 AAATTAATTTATATATATAAA
1 AAATTAATTTATATATATAAA
290313 TTATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 9 0.47
21 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTAATTTATATATATAAA
Found at i:291076 original size:23 final size:20
Alignment explanation
Indices: 291050--291091 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
291040 GATAGAAGAA
* *
291050 TTTTATAAAAATTATCATAAT
1 TTTTTTAAAAAATAT-ATAAT
291071 TTTTTTAAAAAATATATAAT
1 TTTTTTAAAAAATATATAAT
291091 T
1 T
291092 ATCATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAAAATATATAAT
Found at i:291099 original size:23 final size:24
Alignment explanation
Indices: 291049--291101 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
291039 TGATAGAAGA
291049 ATTTTATAAAAATTATCATAATTT
1 ATTTTATAAAAATTATCATAATTT
291073 -TTTTA-AAAAA-TAT-ATAATTAT
1 ATTTTATAAAAATTATCATAATT-T
291094 CATTTTAT
1 -ATTTTAT
291102 CATAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 5 0.20
23 10 0.40
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTATAAAAATTATCATAATTT
Found at i:292305 original size:12 final size:12
Alignment explanation
Indices: 292288--292315 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
292278 CAATTAAAAA
292288 TTTTTTAATTAT
1 TTTTTTAATTAT
292300 TTTTTTAATTAT
1 TTTTTTAATTAT
292312 TTTT
1 TTTT
292316 ACATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTAATTAT
Found at i:292571 original size:17 final size:17
Alignment explanation
Indices: 292551--292598 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
292541 AAATAAATAT
*
292551 TAAATATAAATATTTTA
1 TAAATATAAATAATTTA
*
292568 TAAAAATAAA-AATTTA
1 TAAATATAAATAATTTA
292584 TATAATATAAATAAT
1 TA-AATATAAATAAT
292599 ATGATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 16 0.62
18 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATAAATAATTTA
Found at i:299358 original size:30 final size:30
Alignment explanation
Indices: 299322--299380 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
299312 CCCAGTTTAA
299322 TCAACAAACCCAGGATATTACCAACCGACT
1 TCAACAAACCCAGGATATTACCAACCGACT
299352 TCAACAAACCCAGGATATTACCAACCGAC
1 TCAACAAACCCAGGATATTACCAACCGAC
299381 CAAATCTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (30 bp):
TCAACAAACCCAGGATATTACCAACCGACT
Found at i:304102 original size:2 final size:2
Alignment explanation
Indices: 304097--304127 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
304087 CAGCTTTGAA
304097 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 A
304128 AGAAGACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:304852 original size:19 final size:20
Alignment explanation
Indices: 304805--304855 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
304795 AATTTAATAT
*
304805 TAAATATAATTAATAATTAA
1 TAAATATAATTTATAATTAA
*
304825 TAAAAATAATTTA-AATTCAA
1 TAAATATAATTTATAATT-AA
304845 -AAATATAATTT
1 TAAATATAATTT
304856 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATAATTTATAATTAA
Found at i:305899 original size:9 final size:9
Alignment explanation
Indices: 305882--305916 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
305872 TTATTTCGCT
305882 AAGAAAAAA
1 AAGAAAAAA
*
305891 AAAAAAAAA
1 AAGAAAAAA
*
305900 AAGGAAAAA
1 AAGAAAAAA
305909 AAGAAAAA
1 AAGAAAAA
305917 CTTTGACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:306345 original size:15 final size:16
Alignment explanation
Indices: 306327--306358 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
306317 TCAAATATAA
306327 ATTTT-AAAAATAAAG
1 ATTTTAAAAAATAAAG
306342 ATTTTAAAAAATAAAG
1 ATTTTAAAAAATAAAG
306358 A
1 A
306359 GTCAGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
ATTTTAAAAAATAAAG
Found at i:311756 original size:16 final size:16
Alignment explanation
Indices: 311735--311768 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
311725 ATCTACGAAT
311735 ATAAGTAATGATTTTA
1 ATAAGTAATGATTTTA
311751 ATAAGTAATGATTTTA
1 ATAAGTAATGATTTTA
311767 AT
1 AT
311769 GTAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
ATAAGTAATGATTTTA
Found at i:312129 original size:2 final size:2
Alignment explanation
Indices: 312122--312158 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
312112 CATTATAAAT
312122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
312159 TATTACATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:312967 original size:33 final size:35
Alignment explanation
Indices: 312929--313003 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
312919 ATAATTTTCA
312929 AAAAAACT-AATATATAAT-AAAAAGTATTTTTATT
1 AAAAAA-TAAATATATAATAAAAAAGTATTTTTATT
* * *
312963 AAAAAATAAAATATATATTAAAAAATTATTTTT-TA
1 AAAAAAT-AAATATATAATAAAAAAGTATTTTTATT
312998 AAAAAA
1 AAAAAA
313004 CTGATTTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.03
34 6 0.17
35 16 0.46
36 12 0.34
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (35 bp):
AAAAAATAAATATATAATAAAAAAGTATTTTTATT
Found at i:312976 original size:35 final size:35
Alignment explanation
Indices: 312937--313003 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
312927 CAAAAAAACT
*
312937 AATATATAAT-AAAAAGTATTTTTATTAAAAAATAA
1 AATATATAATAAAAAAGTATTTTT-TAAAAAAATAA
* *
312972 AATATATATTAAAAAATTATTTTTTAAAAAAA
1 AATATATAATAAAAAAGTATTTTTTAAAAAAA
313004 CTGATTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.57
36 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (35 bp):
AATATATAATAAAAAAGTATTTTTTAAAAAAATAA
Found at i:313240 original size:2 final size:2
Alignment explanation
Indices: 313233--313269 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
313223 TTGTACCCCT
313233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
313270 GAAGGAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:318602 original size:2 final size:2
Alignment explanation
Indices: 318595--318632 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
318585 ACGAAGGGAG
318595 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
318633 TAAATGCTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:319999 original size:394 final size:392
Alignment explanation
Indices: 319297--320011 Score: 934
Period size: 394 Copynumber: 1.8 Consensus size: 392
319287 CAATATGATC
* ** * *
319297 AATTTAACCTAATGCATAATGCTGAGCCCTTCAACCAATAAGCAGCACTAGAAGCTACAGGATAT
1 AATTTAACCTAATACATAATGCCAAGCCCTTCAACAAATAAGCAGCAATAGAAGCTACAGGATAT
* * * * *
319362 GTAATACTTCAAAGAAAGACATCTAAAGTGCTACCCATATGCATTTAGGAAATGTTGTGTCATCA
66 ATAATACTTCAAAGAAAGACAGCTAAAGTACTACCCATATGCATTTAGAAAATGTTGCGTCATCA
* *
319427 TGTTTAAATTACATAAGGCCCCAAATCAACAACAATGCTTCATAGACTAGAAATATTTGGGCAGA
131 TGATTAAATTACATAAGGCCCCAAATCAACAACAATGCTTCATAGACTAGAAACATTTGGGCAGA
* * * *
319492 AACAACTCAGACGATCTCTATATTTTAATAGCATTAGCCATCCAAACCGTACCAAGCAGGGAGAG
196 AACAACTCAGACGATCTCTACATTTTAATAGCATAAGCCATCCAAACAGTAACAAGCA-GGAGAG
*
319557 AAGATCTTGCAACCAAAGAAAGAAGACCAATGAACCTGTTGCTCAAGCTCCCTAGCTCTTGAAAG
260 AAGATCCTGCAACCAAAGAAAGAAGACCAATGAACCTGTTGCTCAAGCTCCCTAGCTCTTGAAAG
319622 TTGAGGTGAATAAACAACTAGAAGTCGGAGATACTAAGCTATGTAAGTGCACAATGAACTACATG
325 TTGAGGTGAATAAACAACTAGAAGTCGGAGATACTAAGCTATGTAAGTGCACAATGAACTACATG
319687 AGT
390 AGT
* * * *
319690 AATTTCACCTAATACATAATGCCAATCCCTTCAACAAATAAGCAGTAATAGAATGCTGCAGGATA
1 AATTTAACCTAATACATAATGCCAAGCCCTTCAACAAATAAGCAGCAATAGAA-GCTACAGGATA
* * * * * *
319755 TATGATACTTCGAGGAAAGATAGCTAAATTATTACCCATTATGCATTTAGAAAATGTTGCGTCAT
65 TATAATACTTCAAAGAAAGACAGCTAAAGTACTACCCA-TATGCATTTAGAAAATGTTGCGTCAT
* * * *
319820 CATGATTAAATTACATAAGTGCCCCACATTAACAACAATG-TTCATAGATTTGAAACATTTGAGG
129 CATGATTAAATTACATAAG-GCCCCAAATCAACAACAATGCTTCATAGACTAGAAACATTTG-GG
* ** * * ** * *
319884 -TGAAACAACTCAGGTGATGCTAC-ACATTTTAATTGGATAAGCCATTGACATAGTAACAAGCA-
192 CAGAAACAACTCAGACGAT-CT-CTACATTTTAATAGCATAAGCCATCCAAACAGTAACAAGCAG
* ** * *
319946 GAGAGAAGATCCTGCAGCCAAAGAAAGAAGAGTAATGGACCTGTTTCTCAAGCTCCCTAGCTCTT
255 GAGAGAAGATCCTGCAACCAAAGAAAGAAGACCAATGAACCTGTTGCTCAAGCTCCCTAGCTCTT
320011 G
320 G
320012 CTTCTGCTTC
Statistics
Matches: 271, Mismatches: 45, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
393 45 0.17
394 99 0.37
395 75 0.28
396 51 0.19
397 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (392 bp):
AATTTAACCTAATACATAATGCCAAGCCCTTCAACAAATAAGCAGCAATAGAAGCTACAGGATAT
ATAATACTTCAAAGAAAGACAGCTAAAGTACTACCCATATGCATTTAGAAAATGTTGCGTCATCA
TGATTAAATTACATAAGGCCCCAAATCAACAACAATGCTTCATAGACTAGAAACATTTGGGCAGA
AACAACTCAGACGATCTCTACATTTTAATAGCATAAGCCATCCAAACAGTAACAAGCAGGAGAGA
AGATCCTGCAACCAAAGAAAGAAGACCAATGAACCTGTTGCTCAAGCTCCCTAGCTCTTGAAAGT
TGAGGTGAATAAACAACTAGAAGTCGGAGATACTAAGCTATGTAAGTGCACAATGAACTACATGA
GT
Done.