Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011124.1 Kokia drynarioides strain JFW-HI SEQ_126097, whole genome shotgun sequence
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: 574181
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 221 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:280295 original size:4 final size:4
Alignment explanation
Indices: 280286--280336 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
280276 TCAGAAATCT
280286 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
280334 ATA
1 ATA
280337 TATGCATGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:289409 original size:21 final size:21
Alignment explanation
Indices: 289385--289429 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
289375 ATACCTTATG
* * *
289385 TAATGGACTTCACGGACCTCA
1 TAATGCACCTCACGAACCTCA
289406 TAATGCACCTCACGAACCTCA
1 TAATGCACCTCACGAACCTCA
289427 TAA
1 TAA
289430 CATGGCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.22
Consensus pattern (21 bp):
TAATGCACCTCACGAACCTCA
Found at i:291326 original size:22 final size:22
Alignment explanation
Indices: 291301--291350 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
291291 TGGTTGAACC
**
291301 TATTTATAATTTTTTAATAATT
1 TATTTATAAAATTTTAATAATT
* *
291323 TATTTTTAAAATTTTAATTATT
1 TATTTATAAAATTTTAATAATT
291345 TATTTA
1 TATTTA
291351 ATTAATTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTATAAAATTTTAATAATT
Found at i:291733 original size:30 final size:30
Alignment explanation
Indices: 291685--291752 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
291675 TTAAAAATCT
* *
291685 TTAAAAATTATAAAAATTTTA-CAAAAAGA
1 TTAAAAATTATAAAAATTTTATAAAAAAAA
291714 TTAAAAGATT-TAAATAATTTTATAAAAAAAA
1 TTAAAA-ATTATAAA-AATTTTATAAAAAAAA
291745 TTAAAAAT
1 TTAAAAAT
291753 ATGTTAGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 12 0.35
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
TTAAAAATTATAAAAATTTTATAAAAAAAA
Found at i:296900 original size:20 final size:17
Alignment explanation
Indices: 296858--296901 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
296848 AAAAATAATA
296858 AATAATAAATCCATGTT
1 AATAATAAATCCATGTT
*
296875 ACTAATAAATCACTATGTT
1 AATAATAAATC-C-ATGTT
296894 AGATAATA
1 A-ATAATA
296902 TATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 10 0.45
18 1 0.05
19 6 0.27
20 5 0.23
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (17 bp):
AATAATAAATCCATGTT
Found at i:302681 original size:15 final size:15
Alignment explanation
Indices: 302661--302694 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
302651 ATACGATTGG
302661 TGTAAATATAATTTT
1 TGTAAATATAATTTT
**
302676 TGTAAATATCCTTTT
1 TGTAAATATAATTTT
302691 TGTA
1 TGTA
302695 CCTATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (15 bp):
TGTAAATATAATTTT
Found at i:303411 original size:18 final size:18
Alignment explanation
Indices: 303385--303439 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
303375 TTTATAATTC
303385 AAAAAATTATAAAAAAAT
1 AAAAAATTATAAAAAAAT
* *
303403 AAAATATTATATAAAAATTTT
1 AAAAAATTATA-AAAAA--AT
303424 AAAAAATATATAAAAA
1 AAAAAAT-TATAAAAA
303440 TGCTAAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
21 11 0.37
22 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATTATAAAAAAAT
Found at i:304571 original size:2 final size:2
Alignment explanation
Indices: 304564--304588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
304554 TCTTTTGGAT
304564 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
304589 TTCAATGTCT
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:313225 original size:29 final size:29
Alignment explanation
Indices: 313202--313602 Score: 354
Period size: 29 Copynumber: 13.7 Consensus size: 29
313192 TTCGAAGTCG
313202 AAAATGGAGA-TTTTGGAAGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTCGAGGGTA
***
313231 AAAATGGAATTTTTGGAAGTTTTCGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
* *
313261 AAAAT-GACACTTTTGGAAGTTCGAGGGTG
1 AAAATGGA-ATTTTTGGAAGTTCGAGGGTA
*
313290 AAAATGGAATTTTTGGAAGTTTTG-GGGTAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* * *
313320 AAAATGGGATTTTTGAAAGTT-TAGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTA
*
313349 AAAATGGAA-TTTTGGAAGTTTTGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
313378 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
313407 AAAATAGAAGTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
313437 AAAATGGGATTTTTGGAAGTTTG-GGGATA
1 AAAATGGAATTTTTGGAAGTTCGAGGG-TA
* * *
313466 AAAATGAAATTTTTGGAAGTTTTG-GTGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAG-GGTA
* *
313496 AAAATGGGATTTTTGGAAGTTAGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
313525 AAAACGTAATTTTTGGAAGTTTCG-GGATCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
313555 AAAATGGGATTTTTGGAAGTTCGAGAGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
313584 AAAATGGGATTTTTGGAAG
1 AAAATGGAATTTTTGGAAG
313603 GTTTAGAGAC
Statistics
Matches: 306, Mismatches: 44, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
28 12 0.04
29 163 0.53
30 130 0.42
31 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:313231 original size:59 final size:59
Alignment explanation
Indices: 313179--313602 Score: 518
Period size: 59 Copynumber: 7.2 Consensus size: 59
313169 GTAAAAAGAT
** *
313179 AATTTTT-GAGAGTTTCGAAGTCGAAAATGGAGA-TTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGA-AGTTTCGGGGTCAAAAATGG-GATTTTTGGAAGTTCGAGGGTAAAAATGG
** * *
313238 AATTTTTGGAAGTTTTC-GGGTCAAAAATGACACTTTTGGAAGTTCGAGGGTGAAAATGG
1 AATTTTTGGAAG-TTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * * *
313297 AATTTTTGGAAGTTTTGGGGTAAAAAATGGGATTTTTGAAAGTT-TAGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGG
* * * *
313356 AA-TTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * *
313414 AAGTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTG-GGGATAAAAATGA
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAAATGG
* * * * * *
313473 AATTTTTGGAAGTTTTGGTGTTAAAAATGGGATTTTTGGAAGTTAGAGGGTAAAAACGT
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* *
313532 AATTTTTGGAAGTTTCGGGATCAAAAATGGGATTTTTGGAAGTTCGAGAGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
*
313591 GATTTTTGGAAG
1 AATTTTTGGAAG
313603 GTTTAGAGAC
Statistics
Matches: 315, Mismatches: 41, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
58 59 0.19
59 247 0.78
60 9 0.03
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:313284 original size:88 final size:87
Alignment explanation
Indices: 313141--313602 Score: 398
Period size: 88 Copynumber: 5.2 Consensus size: 87
313131 ATTTGGGGTT
* * * *
313141 TAAAAATGGAATTTTTAGACA-TTTGGGGGTAAAAA-GATAATTTTT-GAGAGTTTCGAAGTCGA
1 TAAAAATGGAATTTTTGGA-AGTTTGCGGGTAAAAATG--AATTTTTGGA-AGTTTCGAGGTCAA
313203 AAATGGAGA-TTTTGGAAGTTCGAGGG
62 AAATGGAGATTTTTGGAAGTTCG-GGG
* * *
313229 TAAAAATGGAATTTTTGGAAGTTTTCGGGTCAAAAATGACACTTTTGGAAG-TTCGAGGGT-GAA
1 TAAAAATGGAATTTTTGGAAGTTTGCGGGT-AAAAATGA-ATTTTTGGAAGTTTCGA-GGTCAAA
*
313292 AATGGA-ATTTTTGGAAGTTTTGGGG
63 AATGGAGATTTTTGGAAG-TTCGGGG
* * *
313317 TAAAAAATGGGATTTTTGAAAGTTTAG-GGGTAAAAATGGAA-TTTTGGAAGTTTTGAGGTCAAA
1 T-AAAAATGGAATTTTTGGAAGTTT-GCGGGTAAAAAT-GAATTTTTGGAAGTTTCGAGGTCAAA
313380 AATGG-GATTTTTGGAAGTTCGGGGG
63 AATGGAGATTTTTGGAAGTTC-GGGG
* * * *
313405 TAAAAATAGAAGTTTTGGAAGTTT-CGGGGTCAAAAATGGGATTTTTGGAAGTTT-GGGGAT-AA
1 TAAAAATGGAATTTTTGGAAGTTTGC-GGGT-AAAAAT-GAATTTTTGGAAGTTTCGAGG-TCAA
* * *
313467 AAAT-GAAATTTTTGGAAGTTTTGGTGT
62 AAATGGAGATTTTTGGAAG-TTCGG-GG
* * * *
313494 TAAAAATGGGATTTTTGGAAGTTAGAGGGTAAAAACGTAATTTTTGGAAGTTTCG-GGATCAAAA
1 TAAAAATGGAATTTTTGGAAGTTTGCGGGTAAAAATG-AATTTTTGGAAGTTTCGAGG-TCAAAA
*
313558 ATGG-GATTTTTGGAAGTTCGAGAG
64 ATGGAGATTTTTGGAAGTTCG-GGG
*
313582 TAAAAATGGGATTTTTGGAAG
1 TAAAAATGGAATTTTTGGAAG
313603 GTTTAGAGAC
Statistics
Matches: 313, Mismatches: 32, Indels: 58
0.78 0.08 0.14
Matches are distributed among these distances:
87 41 0.13
88 165 0.53
89 103 0.33
90 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (87 bp):
TAAAAATGGAATTTTTGGAAGTTTGCGGGTAAAAATGAATTTTTGGAAGTTTCGAGGTCAAAAAT
GGAGATTTTTGGAAGTTCGGGG
Found at i:314593 original size:33 final size:32
Alignment explanation
Indices: 314554--314644 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
314544 ATGGGGCAGT
314554 TATTATTATTAATACATTATTATTATTACCACTG-
1 TATTATTATTAATACATTATTATTATTA-CA--GA
*
314588 T-TTATTATTAATACCATTGA-TATTATTATAGA
1 TATTATTATTAATA-CATT-ATTATTATTACAGA
*
314620 TATTATTATTAATCCATTATTATTA
1 TATTATTATTAATACATTATTATTA
314645 ATGTCATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
31 2 0.04
32 10 0.20
33 24 0.48
34 13 0.26
35 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (32 bp):
TATTATTATTAATACATTATTATTATTACAGA
Found at i:314594 original size:19 final size:18
Alignment explanation
Indices: 314552--314616 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
314542 TAATGGGGCA
**
314552 GTTATTATTATTAATAC-
1 GTTATTATTATTACCACT
*
314569 ATTATTATTATTACCACT
1 GTTATTATTATTACCACT
* *
314587 GTTTATTATTAATACCATT
1 G-TTATTATTATTACCACT
*
314606 GATATTATTAT
1 GTTATTATTAT
314617 AGATATTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 14 0.37
18 8 0.21
19 16 0.42
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (18 bp):
GTTATTATTATTACCACT
Found at i:315300 original size:17 final size:17
Alignment explanation
Indices: 315280--315388 Score: 130
Period size: 17 Copynumber: 6.3 Consensus size: 17
315270 CTTTATTTAT
* *
315280 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
315297 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
315315 TTTAAACTTGAAATAAA
1 TTTAAATTTAAAATAAA
315332 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
315349 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
315367 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
315384 TTTAA
1 TTTAA
315389 GATGAGTTTG
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 50 0.64
18 27 0.35
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:315330 original size:35 final size:35
Alignment explanation
Indices: 315291--315388 Score: 128
Period size: 35 Copynumber: 2.8 Consensus size: 35
315281 TTAAATTTAT
*
315291 AATAATTTTAAATTTGAAAATAAATTTAAA-CTTGA
1 AATAAATTTAAATTT-AAAATAAATTTAAATCTTGA
* *
315326 AATAAATTTAAATTTAAAATAAATTTAAATTTTTA
1 AATAAATTTAAATTTAAAATAAATTTAAATCTTGA
*
315361 AACAAATTT-AATCTTAAAATAAATTTAA
1 AATAAATTTAAAT-TTAAAATAAATTTAA
315389 GATGAGTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 17 0.30
35 40 0.70
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (35 bp):
AATAAATTTAAATTTAAAATAAATTTAAATCTTGA
Found at i:315337 original size:6 final size:6
Alignment explanation
Indices: 315280--315357 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
315270 CTTTATTTAT
* * *
315280 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTGAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA -TTTAAA
*
315328 --TAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
315358 TTAAACAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 32 0.58
7 10 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:315347 original size:52 final size:52
Alignment explanation
Indices: 315280--315388 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
315270 CTTTATTTAT
* * * *
315280 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTGAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
** *
315332 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
315384 TTTAA
1 TTTAA
315389 GATGAGTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:316212 original size:31 final size:31
Alignment explanation
Indices: 316166--316251 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
316156 ACCCAATGAT
* *
316166 TTAAATAAAAACTTTTGAATAGTTCAGTAAC
1 TTAAATGAAATCTTTTGAATAGTTCAGTAAC
*
316197 TTAAATGAAATCTTTTGAATAGTTCAGTGAC
1 TTAAATGAAATCTTTTGAATAGTTCAGTAAC
316228 TTAAATGAAATCTTTTGAATAGTT
1 TTAAATGAAATCTTTTGAATAGTT
316252 TAATAACCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (31 bp):
TTAAATGAAATCTTTTGAATAGTTCAGTAAC
Found at i:319278 original size:24 final size:25
Alignment explanation
Indices: 319232--319291 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
319222 TTAAAATACA
* * * *
319232 TATTTTTTGTTTGTTTTTTTTC-TC
1 TATTTTTTTTTTCTCTTTCTTCTTC
319256 TATTTTTTTTTTCTCTTTCTTCTTC
1 TATTTTTTTTTTCTCTTTCTTCTTC
*
319281 T-TTTGTTTTTT
1 TATTTTTTTTTT
319292 GCAGGTAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (25 bp):
TATTTTTTTTTTCTCTTTCTTCTTC
Found at i:319495 original size:13 final size:13
Alignment explanation
Indices: 319477--319501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319467 TTTGTAATAA
319477 ATTTAAAAATTTT
1 ATTTAAAAATTTT
319490 ATTTAAAAATTT
1 ATTTAAAAATTT
319502 GGAACAAGAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAAAATTTT
Found at i:320491 original size:31 final size:31
Alignment explanation
Indices: 320456--320518 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
320446 AACAGTCCGG
320456 TGATTTAAATAAAAACTTTCGAATAATTTAA
1 TGATTTAAATAAAAACTTTCGAATAATTTAA
* * * *
320487 TGATTTAAATGAAATCTTTTGAATAGTTTAA
1 TGATTTAAATAAAAACTTTCGAATAATTTAA
320518 T
1 T
320519 AATCATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (31 bp):
TGATTTAAATAAAAACTTTCGAATAATTTAA
Found at i:323723 original size:2 final size:2
Alignment explanation
Indices: 323718--323756 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
323708 TTGAAAAATA
*
323718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
323757 AAATAATCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 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):
AT
Found at i:325220 original size:29 final size:29
Alignment explanation
Indices: 325161--325227 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
325151 TGGGGGTGTT
* *
325161 ATGTCTGCATTTGTAACGGTATCTGTATC
1 ATGTCTGCATCTGTAACGGTATCTATATC
* * *
325190 ATGTCTGCATCTGTAACTGTTTCTATGTC
1 ATGTCTGCATCTGTAACGGTATCTATATC
325219 ATGCTCTGC
1 ATG-TCTGC
325228 TCCACTCTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (29 bp):
ATGTCTGCATCTGTAACGGTATCTATATC
Found at i:326151 original size:15 final size:15
Alignment explanation
Indices: 326133--326166 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
326123 TTAAATTATA
*
326133 ATATATTTTATTAAT
1 ATATATTTAATTAAT
*
326148 ATATATTTAATTTAT
1 ATATATTTAATTAAT
326163 ATAT
1 ATAT
326167 CACATCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATATTTAATTAAT
Found at i:331748 original size:23 final size:23
Alignment explanation
Indices: 331718--331761 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
331708 CTAAGCATTA
331718 GTGGCACATTCTATATTGCCTTT
1 GTGGCACATTCTATATTGCCTTT
*
331741 GTGGCACATTCTGTATTGCCT
1 GTGGCACATTCTATATTGCCT
331762 ATGTTGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (23 bp):
GTGGCACATTCTATATTGCCTTT
Found at i:334475 original size:6 final size:6
Alignment explanation
Indices: 334451--334517 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
334441 CCGGATCGCT
* *
334451 TTTAAA TTT-AT TTTAAA TTTGAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
334497 TTT-AA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTA
334518 TTTTCAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 2 0.04
5 11 0.21
6 36 0.69
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:334477 original size:17 final size:17
Alignment explanation
Indices: 334450--334531 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
334440 ACCGGATCGC
*
334450 TTTTAAATTT-ATTTTAA
1 TTTTAAATTTAAATTT-A
* * *
334467 ATTTGAATTTAAATTAA
1 TTTTAAATTTAAATTTA
*
334484 TCTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
334501 ATTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
334518 TTTTCAAAATTAAA
1 TTTT-AAATTTAAA
334532 AGTCTAAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 40 0.78
18 11 0.22
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:334478 original size:23 final size:23
Alignment explanation
Indices: 334451--334517 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
334441 CCGGATCGCT
*
334451 TTTAAATTTATTTTAAATTTGAA
1 TTTAAATTTATTTTAAATTTAAA
* *
334474 TTTAAATTAATCTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
*
334497 TTT-AATTTAAATTTAAATTTA
1 TTTAAATTT-ATTTTAAATTTA
334518 TTTTCAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:335216 original size:3 final size:3
Alignment explanation
Indices: 335208--335313 Score: 88
Period size: 3 Copynumber: 34.0 Consensus size: 3
335198 AATAAGGCTT
* **
335208 TAA TAA TAA TAG TGG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** *
335256 TAT TAA TGA CGA CAA TAA TAA TAA TAA -ACA TTAA TAA TTAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA -TAA TAA -TAA
335304 TAAA TAA TAA
1 T-AA TAA TAA
335314 AAAAGGGGGA
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
2 1 0.01
3 75 0.86
4 10 0.11
5 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:335297 original size:7 final size:7
Alignment explanation
Indices: 335269--335313 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
335259 TAATGACGAC
335269 AATAA-T
1 AATAATT
335275 AATAA-T
1 AATAATT
335281 AA-ACATT
1 AATA-ATT
335288 AATAATT
1 AATAATT
335295 AATAATT
1 AATAATT
*
335302 AATAAAT
1 AATAATT
335309 AATAA
1 AATAA
335314 AAAAGGGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
5 1 0.03
6 9 0.26
7 24 0.69
8 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (7 bp):
AATAATT
Found at i:336307 original size:29 final size:28
Alignment explanation
Indices: 336268--336516 Score: 264
Period size: 29 Copynumber: 8.5 Consensus size: 28
336258 TAATTGTCTG
*
336268 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCC-CGAACTTCCA
* *
336297 AAAATTCCATTTTCGACCCCAAAACTTCCA
1 AAAATTCCATTTT-TACCCC-GAACTTCCA
*
336327 AAAATTCCATTTTTACTCTCGAACTTCCA
1 AAAATTCCATTTTTAC-CCCGAACTTCCA
*
336356 AAAATTCCATTTTTGACCCTGAAGCTTCCA
1 AAAATTCCATTTTT-ACCCCGAA-CTTCCA
*
336386 AAAATTCCATTTTTACCCTCAAACTTCCA
1 AAAATTCCATTTTTACCC-CGAACTTCCA
*
336415 AAAATTCCATTTTTAACCCGAAACTTCCA
1 AAAATTCCATTTTTACCCCG-AACTTCCA
* * *
336444 AATATTCAATTTTTACGCCCGAACTTCTA
1 AAAATTCCATTTTTAC-CCCGAACTTCCA
* * * *
336473 AAATTTCCATATTTGACCCCAAAACTTTCA
1 AAAATTCCAT-TTTTACCCC-GAACTTCCA
336503 AAAATTACCATTTT
1 AAAATT-CCATTTT
336517 GTCGCCAGAT
Statistics
Matches: 185, Mismatches: 24, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
28 1 0.01
29 106 0.57
30 74 0.40
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGAACTTCCA
Found at i:336325 original size:30 final size:28
Alignment explanation
Indices: 336268--336549 Score: 233
Period size: 29 Copynumber: 9.6 Consensus size: 28
336258 TAATTGTCTG
* * *
336268 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTGACCC-CAAACTTCCA
336297 AAAATTCCATTTTCGACCCCAAAACTTCCA
1 AAAATTCCATTTT-GACCCC-AAACTTCCA
* * *
336327 AAAATTCCATTTTTACTCTCGAACTTCCA
1 AAAATTCCATTTTGAC-CCCAAACTTCCA
* *
336356 AAAATTCCATTTTTGACCCTGAAGCTTCCA
1 AAAATTCCA-TTTTGACCC-CAAACTTCCA
*
336386 AAAATTCCATTTTTACCCTCAAACTTCCA
1 AAAATTCCATTTTGACCC-CAAACTTCCA
* *
336415 AAAATTCCATTTTTAACCCGAAACTTCCA
1 AAAATTCCA-TTTTGACCCCAAACTTCCA
* * * * *
336444 AATATTCAATTTTTACGCCCGAACTTCTA
1 AAAATTCCATTTTGAC-CCCAAACTTCCA
* *
336473 AAATTTCCATATTTGACCCCAAAACTTTCA
1 AAAATTCCAT-TTTGACCCC-AAACTTCCA
* * *
336503 AAAATTACCATTTTGTCGCCAGA-TGTCCA
1 AAAATT-CCATTTTGACCCCAAACT-TCCA
*
336532 AAAACTCCATTTTCGACC
1 AAAATTCCATTTT-GACC
336550 TCGAAACTCT
Statistics
Matches: 204, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
28 14 0.07
29 106 0.52
30 80 0.39
31 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTGACCCCAAACTTCCA
Found at i:336360 original size:59 final size:58
Alignment explanation
Indices: 336268--336516 Score: 320
Period size: 59 Copynumber: 4.2 Consensus size: 58
336258 TAATTGTCTG
*
336268 AAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTT-GACCCCAAAACTTCCA
* ** *
336327 AAAATTCCATTTTTACTCTCGAACTTCCAAAAATTCCATTTTTGACCCTGAAGCTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCCCAAAACTTCCA
* * * *
336386 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCA
* * * * *
336444 AATATTCAATTTTTACGCC-CGAACTTCTAAAATTTCCATATTTGACCCCAAAACTTTCA
1 AAAATTCCATTTTTAC-CCTCGAACTTCCAAAAATTCCAT-TTTGACCCCAAAACTTCCA
336503 AAAATTACCATTTT
1 AAAATT-CCATTTT
336517 GTCGCCAGAT
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
58 47 0.29
59 107 0.65
60 10 0.06
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCA
Found at i:349307 original size:6 final size:6
Alignment explanation
Indices: 349287--349359 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
349277 TCGAGCCCCT
* * * *
349287 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
349333 -TT-AA TCTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTTA
349360 TTTTCAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 40 0.74
7 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:349312 original size:17 final size:17
Alignment explanation
Indices: 349287--349359 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
349277 TCGAGCCCCT
349287 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
349304 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* **
349321 TTTGAATTTAAATT-AA
1 TTTAAATTTATTTTAAA
*
349337 TCTTAAATTTAAATTTAAA
1 T-TTAAATTT-ATTTTAAA
349356 TTTA
1 TTTA
349360 TTTTCAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.07
17 33 0.72
18 7 0.15
19 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:349328 original size:23 final size:23
Alignment explanation
Indices: 349298--349373 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
349288 TTAAATTTAT
*
349298 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
* * *
349321 TTTGAATTTAAATTAATCTTAAA
1 TTTAAATTTAAATTTATTTTAAA
349344 TTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTAAATTTATTTT-AAA
*
349368 ATTAAA
1 TTTAAA
349374 AGTCCAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 36 0.82
24 8 0.18
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:350154 original size:3 final size:3
Alignment explanation
Indices: 350060--350143 Score: 98
Period size: 3 Copynumber: 28.0 Consensus size: 3
350050 AATAAGACTT
* **
350060 TAA TAA TAA TAG TGG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
350108 TAA TAA TAA TAT TAA TGAC T-G TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
350144 ACATTAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.01
3 67 0.96
4 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:351125 original size:29 final size:30
Alignment explanation
Indices: 351092--351196 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
351082 CTAAACTATT
* *
351092 CAAAAATTATATTTT-TACCCTCGAACTTC
1 CAAAAATTACATTTTCGACCCTCGAACTTC
* * *
351121 CAAAAATTCCATTTTCGACCTTGGAACTTC
1 CAAAAATTACATTTTCGACCCTCGAACTTC
* * * * *
351151 CAAAAATTCCTTTTTTGA-CCTTGAAACTTT
1 CAAAAATTACATTTTCGACCCTCG-AACTTC
351181 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
351197 GTTGCCGGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 16 0.26
30 40 0.66
31 5 0.08
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (30 bp):
CAAAAATTACATTTTCGACCCTCGAACTTC
Found at i:351150 original size:30 final size:30
Alignment explanation
Indices: 351114--351196 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 30
351104 TTTTACCCTC
351114 GAACTTCCAAAAATTCCATTTTCGACCTTG
1 GAACTTCCAAAAATTCCATTTTCGACCTTG
* *
351144 GAACTTCCAAAAATTCCTTTTTTGACCTTG
1 GAACTTCCAAAAATTCCATTTTCGACCTTG
* *
351174 AAACTTTCAAAAATTACCATTTT
1 GAACTTCCAAAAATT-CCATTTT
351197 GTTGCCGGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 41 0.87
31 6 0.13
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (30 bp):
GAACTTCCAAAAATTCCATTTTCGACCTTG
Found at i:351765 original size:96 final size:96
Alignment explanation
Indices: 351574--351765 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
351564 AAAACTTTAA
** * * * *
351574 AATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGTCTTAACTTATTAGGTGTAATT
1 AATCGAGGCAATATTTCCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAATC
* *
351639 TTTCTGCAAATCGAAATAATCGAATACCCTT
66 GTTCTGCAAATCGAAATAATCGAACACCCTT
*
351670 AATCGAGGCAATGTTTCCTTATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTTCCTTAT-TTCGAGTTTC-GAAAATTTGCGCCTTAACTTACTAGGTGCAA
* *
351733 -CGTTCTTCAAATCGAGATAATCGAACATCCCTT
64 TCGTTCTGCAAATCGAAATAATCGAACA-CCCTT
351766 TTCCCAAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 25 0.30
96 52 0.63
97 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAATC
GTTCTGCAAATCGAAATAATCGAACACCCTT
Found at i:354273 original size:26 final size:27
Alignment explanation
Indices: 354221--354274 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
354211 TGAAGAAAGA
*
354221 TTAAGTGGTGACACCAATGGAGGGTTT
1 TTAAGTGGGGACACCAATGGAGGGTTT
* * *
354248 TTAAGTGGGGGCACTAA-GGAGTGTTT
1 TTAAGTGGGGACACCAATGGAGGGTTT
354274 T
1 T
354275 GTCACTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.31
Consensus pattern (27 bp):
TTAAGTGGGGACACCAATGGAGGGTTT
Found at i:355687 original size:22 final size:22
Alignment explanation
Indices: 355657--355699 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
355647 TTAGAAACCC
* *
355657 AAAACAAAAAGAGAGAGAAAGT
1 AAAAAAAAAAAAGAGAGAAAGT
*
355679 AAAAAAAAAAAAGAGGGAAAG
1 AAAAAAAAAAAAGAGAGAAAG
355700 AAGAATTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAGAGAGAAAGT
Found at i:360632 original size:15 final size:17
Alignment explanation
Indices: 360608--360641 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
360598 CACCATTTAC
360608 AAAAACCAAATAA-AAT
1 AAAAACCAAATAATAAT
360624 AAAAA-CAAATAATAAT
1 AAAAACCAAATAATAAT
360640 AA
1 AA
360642 TGAAAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAACCAAATAATAAT
Found at i:362998 original size:20 final size:20
Alignment explanation
Indices: 362961--362998 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
362951 AGAAGAAAGC
*
362961 TGAAGAAGACTTAGAAGACT
1 TGAAGAAGACTTACAAGACT
362981 TGAAGAAG-CATTACAAGA
1 TGAAGAAGAC-TTACAAGA
362999 AACTTCGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (20 bp):
TGAAGAAGACTTACAAGACT
Found at i:367700 original size:18 final size:18
Alignment explanation
Indices: 367679--367729 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
367669 ATTTGCTCAC
367679 ACGAGCCAGTATGCTCGA
1 ACGAGCCAGTATGCTCGA
*
367697 ACGAGCCAATATGCTCGA
1 ACGAGCCAGTATGCTCGA
* *
367715 ATGAGCTAGTATGCT
1 ACGAGCCAGTATGCT
367730 ATTCCTTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (18 bp):
ACGAGCCAGTATGCTCGA
Found at i:373621 original size:19 final size:19
Alignment explanation
Indices: 373563--373641 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 19
373553 CTTGTTGAGT
*
373563 AATACTGGCTTGTAAGAG-
1 AATACTGGCTCGTAAGAGC
* *
373581 ATATATTGGCTCGTTA-AGC
1 A-ATACTGGCTCGTAAGAGC
373600 AATACTGGCTCGTAAGAGC
1 AATACTGGCTCGTAAGAGC
* *
373619 AATACTAGCTTGTAAGAGC
1 AATACTGGCTCGTAAGAGC
373638 AATA
1 AATA
373642 TTAGATAGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
18 15 0.29
19 36 0.71
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (19 bp):
AATACTGGCTCGTAAGAGC
Found at i:373652 original size:19 final size:19
Alignment explanation
Indices: 373597--373653 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
373587 TGGCTCGTTA
* * *
373597 AGCAATACTGGCTCGTAAG
1 AGCAATACTAGATAGTAAG
* *
373616 AGCAATACTAGCTTGTAAG
1 AGCAATACTAGATAGTAAG
*
373635 AGCAATATTAGATAGTAAG
1 AGCAATACTAGATAGTAAG
373654 GAGTTATTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.25
Consensus pattern (19 bp):
AGCAATACTAGATAGTAAG
Found at i:374373 original size:21 final size:21
Alignment explanation
Indices: 374349--374406 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
374339 GTGAAGTAAG
* *
374349 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
374370 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
374391 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
374407 ATCTGTACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:380745 original size:19 final size:19
Alignment explanation
Indices: 380721--380757 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
380711 CTTGCGGTTC
380721 AATATTGCTCATACGAGCT
1 AATATTGCTCATACGAGCT
*
380740 AATATTGCTCTTACGAGC
1 AATATTGCTCATACGAGC
380758 CAGTAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (19 bp):
AATATTGCTCATACGAGCT
Found at i:383213 original size:80 final size:79
Alignment explanation
Indices: 383069--383232 Score: 258
Period size: 80 Copynumber: 2.1 Consensus size: 79
383059 TACACGCATT
* *
383069 AATTTCATTTTAACTCTTATAAGTAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGT
1 AATTTCATTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTCTTAATTAGGATCTGATGTAGT
383134 TGAAAAGGCATGGC
66 TGAAAAGGCATGGC
* * * *
383148 AATTTCGTTTTCAACTCTTGTAGGGAAGCTAATGAGTCATGTCTCTTAATTAGGATCTGATGTAG
1 AATTTCATTTT-AACTCTTATAAGGAAGCCAATGAGTCATGTCTCTTAATTAGGATCTGATGTAG
383213 TTGAAAAGGCATGGC
65 TTGAAAAGGCATGGC
383228 -ATTTC
1 AATTTC
383233 TCCTTAATGA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 15 0.19
80 63 0.81
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (79 bp):
AATTTCATTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTCTTAATTAGGATCTGATGTAGT
TGAAAAGGCATGGC
Found at i:383702 original size:48 final size:47
Alignment explanation
Indices: 383649--383792 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 47
383639 GTTGATGCAT
* * *
383649 TAATGCAAGGTATTTAACAAAGATGCATTTAACAAACAAAACATTTAA
1 TAATGC-AGATATTAAACAAAGATGCATTTAACAAACAAAACACTTAA
* **
383697 TAATGCAGATTACTAAACAAAGATGCATTTAACAAACGGAACACTTAA
1 TAATGCAGA-TATTAAACAAAGATGCATTTAACAAACAAAACACTTAA
* * *
383745 TGATGCAGATCATTAAACAAAAATGTATTTAACAAACAAAACACTTAA
1 TAATGCAGAT-ATTAAACAAAGATGCATTTAACAAACAAAACACTTAA
383793 CGAAGCATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 3 0.04
48 79 0.96
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (47 bp):
TAATGCAGATATTAAACAAAGATGCATTTAACAAACAAAACACTTAA
Found at i:401901 original size:48 final size:47
Alignment explanation
Indices: 401778--402088 Score: 212
Period size: 48 Copynumber: 6.6 Consensus size: 47
401768 TCTATAGGTT
* *
401778 TGAAGGGAAAGGTTGAAGCCGCAACGGCAAACCTTATACCTTAGAGACA
1 TGAAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAG--A
* * *
401827 TGATA-GGAAAGATTGAAGCCGTAACGGCGAATCTTGTACCGTT-GAGA
1 TGA-AGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACC-TTAGAGA
*
401874 TGCAAGGGAAAGGTTGAAGCTGCAACGGCGAACCTTGTACCTTAGAGA
1 TG-AAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGA
* * ** ** * *
401922 CGTGATGGAAAATATTGAAGCCGCAACGATGAATCTTGTACCAT-GAAGA
1 --TGAAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAG-AGA
* *
401971 TGTCAGGGAAAGGTTGAAGCCGCAACGGC-AA------ACCTTAGAAA
1 TG-AAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGA
* ** * * * *
402012 CGTGATGGGAAAGACTGAAGCCACAATGGCGAATCTTGTACCAT-GAAGA
1 --TGAAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAG-AGA
*
402061 TGCAAGGGAAAGGTTGAAGCCACAACGG
1 TG-AAGGGAAAGGTTGAAGCCGCAACGG
402089 TGATGTAACA
Statistics
Matches: 202, Mismatches: 39, Indels: 43
0.71 0.14 0.15
Matches are distributed among these distances:
41 6 0.03
42 21 0.10
43 4 0.02
47 12 0.06
48 78 0.39
49 76 0.38
50 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (47 bp):
TGAAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGA
Found at i:401956 original size:97 final size:94
Alignment explanation
Indices: 401780--402088 Score: 380
Period size: 97 Copynumber: 3.3 Consensus size: 94
401770 TATAGGTTTG
*
401780 AAGGGAAAGGTTGAAGCCGCAACGGCAAACCTTATACCTTAGAGACATGATAGGAAAGATTGAAG
1 AAGGGAAAGGTTGAAGCCGCAACGGC-AACCTT-TACCTTAGAGACGTGAT-GGAAAGATTGAAG
* *
401845 CCGTAACGGCGAATCTTGTACCGTTG-AGATGC
63 CCGCAACGGCGAATCTTGTACC-ATGAAGATGC
* *
401877 AAGGGAAAGGTTGAAGCTGCAACGGCGAACCTTGTACCTTAGAGACGTGATGGAAAATATTGAAG
1 AAGGGAAAGGTTGAAGCCGCAACGGC-AACCTT-TACCTTAGAGACGTGATGG-AAAGATTGAAG
**
401942 CCGCAACGATGAATCTTGTACCATGAAGATGTC
63 CCGCAACGGCGAATCTTGTACCATGAAGATG-C
* *
401975 -AGGGAAAGGTTGAAGCCGCAACGGCAA-----ACCTTAGAAACGTGATGGGAAAGACTGAAGCC
1 AAGGGAAAGGTTGAAGCCGCAACGGCAACCTTTACCTTAGAGACGTGAT-GGAAAGATTGAAGCC
* *
402034 ACAATGGCGAATCTTGTACCATGAAGATGC
65 GCAACGGCGAATCTTGTACCATGAAGATGC
*
402064 AAGGGAAAGGTTGAAGCCACAACGG
1 AAGGGAAAGGTTGAAGCCGCAACGG
402089 TGATGTAACA
Statistics
Matches: 189, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
89 1 0.01
90 74 0.39
91 2 0.01
96 6 0.03
97 105 0.56
98 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (94 bp):
AAGGGAAAGGTTGAAGCCGCAACGGCAACCTTTACCTTAGAGACGTGATGGAAAGATTGAAGCCG
CAACGGCGAATCTTGTACCATGAAGATGC
Found at i:401960 original size:49 final size:47
Alignment explanation
Indices: 401783--402006 Score: 186
Period size: 49 Copynumber: 4.6 Consensus size: 47
401773 AGGTTTGAAG
* * *
401783 GGAAAGGTTGAAGCCGCAACGGCAAACCTTATACCTTAGAGACATGAT
1 GGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGAC-TGAT
* * *
401831 AGGAAAGATTGAAGCCGTAACGGCGAATCTTGTACCGTT-GAGA-TGCAAG
1 -GGAAAGATTGAAGCCGCAACGGCGAACCTTGTACC-TTAGAGACTG--AT
* *
401880 GGAAAGGTTGAAGCTGCAACGGCGAACCTTGTACCTTAGAGACGTGAT
1 GGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGAC-TGAT
* ** * * *
401928 GGAAAATATTGAAGCCGCAACGATGAATCTTGTACCAT-GAAGA-TGTCAG
1 GG-AAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAG-AGACTG--AT
* *
401977 GGAAAGGTTGAAGCCGCAACGGCAAACCTT
1 GGAAAGATTGAAGCCGCAACGGCGAACCTT
402007 AGAAACGTGA
Statistics
Matches: 140, Mismatches: 25, Indels: 21
0.75 0.13 0.11
Matches are distributed among these distances:
47 6 0.04
48 61 0.44
49 69 0.49
50 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (47 bp):
GGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACTGAT
Found at i:402069 original size:90 final size:90
Alignment explanation
Indices: 401912--402088 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 90
401902 CGAACCTTGT
* * * * *
401912 ACCTTAGAGACGTGATGGAAAATATTGAAGCCGCAACGATGAATCTTGTACCATGAAGATGTCAG
1 ACCTTAGAAACGTGATGGAAAAGACTGAAGCCACAACGACGAATCTTGTACCATGAAGATGTCAG
*
401977 GGAAAGGTTGAAGCCGCAACGGCAA
66 GGAAAGGTTGAAGCCACAACGGCAA
* * *
402002 ACCTTAGAAACGTGATGGGAAAGACTGAAGCCACAATGGCGAATCTTGTACCATGAAGATG-CAA
1 ACCTTAGAAACGTGATGGAAAAGACTGAAGCCACAACGACGAATCTTGTACCATGAAGATGTC-A
402066 GGGAAAGGTTGAAGCCACAACGG
65 GGGAAAGGTTGAAGCCACAACGG
402089 TGATGTAACA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 1 0.01
90 76 0.99
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (90 bp):
ACCTTAGAAACGTGATGGAAAAGACTGAAGCCACAACGACGAATCTTGTACCATGAAGATGTCAG
GGAAAGGTTGAAGCCACAACGGCAA
Found at i:402712 original size:23 final size:23
Alignment explanation
Indices: 402678--402811 Score: 171
Period size: 23 Copynumber: 5.8 Consensus size: 23
402668 GCTAGGGAAA
*
402678 CAGTCAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
402701 TAGTAGGCACACACAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
*
402724 CAATAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
402747 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
*
402770 CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTGC-AAAT
402793 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
402812 TGAACAGTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 93 0.97
24 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:402812 original size:23 final size:22
Alignment explanation
Indices: 402675--402823 Score: 163
Period size: 23 Copynumber: 6.5 Consensus size: 22
402665 AGTGCTAGGG
*
402675 AAACAGTCAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* *
402697 AAATTAGTAGGCACACACAGTGC
1 AAA-CAGTAAGCACACACAGTGC
*
402720 AAAACAATAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
* *
402743 AAATCAGTAAGCACATATAGTGC
1 AAA-CAGTAAGCACACACAGTGC
*
402766 GAATCAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
402789 TGAACAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
402812 TGAACAGTAAGC
1 -AAACAGTAAGC
402824 GCGCTAATGT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
22 6 0.06
23 97 0.90
24 5 0.05
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.14
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:402820 original size:69 final size:68
Alignment explanation
Indices: 402675--402823 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 68
402665 AGTGCTAGGG
* * *
402675 AAACAGTCAGCACACACAGTGCAAATTAGTAGGCACACACAGTGCAAAACAATAAGCACACACAG
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAACAATAAGCACACACAG
402740 TGC
66 TGC
* * * ** *
402743 AAATCAGTAAGCACATATAGTGCGAATCAGTAAGCACACACAGTGCTGAACAGTAAGCACACACA
1 AAA-CAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAACAATAAGCACACACA
402808 GTGC
65 GTGC
*
402812 TGAACAGTAAGC
1 -AAACAGTAAGC
402824 GCGCTAATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 3 0.04
69 64 0.93
70 2 0.03
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.14
Consensus pattern (68 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCAAAACAATAAGCACACACAG
TGC
Found at i:404622 original size:49 final size:49
Alignment explanation
Indices: 404543--404680 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 49
404533 TGTTACAGGC
* * *
404543 GAACCTTGTACCTTAGAGATGT-AATTGGAAAGATTGAAGCCGCAACAGT
1 GAACCTTGTACCATAGAGATATGAA-GGGAAAGATTGAAGCCGCAACAGT
* * * * **
404592 GAATCTTGTACCATGGAGATATGGAGGGAAATG-TTGAAGCCGTAATGGT
1 GAACCTTGTACCATAGAGATATGAAGGGAAA-GATTGAAGCCGCAACAGT
*
404641 GAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
1 GAACCTTGTACCATAGAGATATGAAGGGAAAGATTGAAGC
404681 TACAACGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 70 0.96
50 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (49 bp):
GAACCTTGTACCATAGAGATATGAAGGGAAAGATTGAAGCCGCAACAGT
Found at i:405049 original size:15 final size:17
Alignment explanation
Indices: 405025--405058 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
405015 CACCAAGTAC
405025 AAAAACCAAATAA-AAT
1 AAAAACCAAATAATAAT
405041 AAAAA-CAAATAATAAT
1 AAAAACCAAATAATAAT
405057 AA
1 AA
405059 TAATAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAACCAAATAATAAT
Found at i:405309 original size:11 final size:11
Alignment explanation
Indices: 405293--405322 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
405283 CCCCTCTCCT
405293 GCCACGTCAGC
1 GCCACGTCAGC
405304 GCCACGTCAGC
1 GCCACGTCAGC
405315 GCCACGTC
1 GCCACGTC
405323 GTTAGGGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.47, G:0.27, T:0.10
Consensus pattern (11 bp):
GCCACGTCAGC
Found at i:406829 original size:22 final size:23
Alignment explanation
Indices: 406785--406830 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
406775 TTTAACCATG
*
406785 AATTTTTTTAAATTAATACATATT
1 AATTCTTTTAAA-TAATACATATT
*
406809 AATTCTTTTAAA-AATATATATT
1 AATTCTTTTAAATAATACATATT
406831 TTAACGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTCTTTTAAATAATACATATT
Found at i:407106 original size:110 final size:108
Alignment explanation
Indices: 406893--407107 Score: 272
Period size: 110 Copynumber: 2.0 Consensus size: 108
406883 GAGGGAGACA
* * *
406893 ATGTTATTTTATTTAGAGAATTCGAAAAATTGTGTTCAAACGTATTGAGTGTGATTTTTCTTTGA
1 ATGTTATTTTATTTAGAGAATTCGAAAAATTGTGATCAAACGTACTGAGTATGATTTTTCTTTGA
* *
406958 ACTTAAATAATCGAGTATCCTATTTAAAATCAACAAATGTTCG
66 ACCTAAATAATCGAATATCCTATTTAAAATCAACAAATGTTCG
* * *
407001 ATGTTCTTTTGTTTAG-GAAATTC-AAGAAATTGTGATCAAACGTACTGGGTATGATTTTTTTCT
1 ATGTTATTTTATTTAGAG-AATTCGAA-AAATTGTGATCAAACGTACTGAGTATGA--TTTTTCT
* * * *
407064 TTGAACCTAAATAGTTGAATATCCTATTTAAAATCGATAAATGT
62 TTGAACCTAAATAATCGAATATCCTATTTAAAATCAACAAATGT
407108 CTTTGATCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 3 0.03
108 43 0.47
110 45 0.49
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (108 bp):
ATGTTATTTTATTTAGAGAATTCGAAAAATTGTGATCAAACGTACTGAGTATGATTTTTCTTTGA
ACCTAAATAATCGAATATCCTATTTAAAATCAACAAATGTTCG
Found at i:410930 original size:57 final size:57
Alignment explanation
Indices: 410842--410957 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
410832 TGACATGTAG
410842 AAATAATATTACATGACATTATATAAATGGATGGAACCATTACTTATATGATGAGAA
1 AAATAATATTACATGACATTATATAAATGGATGGAACCATTACTTATATGATGAGAA
*
410899 AAATAATCTTACATGACATTATATAAATGGATGGAACCATTACTTATATGATGAGAA
1 AAATAATATTACATGACATTATATAAATGGATGGAACCATTACTTATATGATGAGAA
410956 AA
1 AA
410958 GTTCACCTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (57 bp):
AAATAATATTACATGACATTATATAAATGGATGGAACCATTACTTATATGATGAGAA
Found at i:412089 original size:26 final size:27
Alignment explanation
Indices: 412036--412091 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
412026 TTCGAAAATG
412036 TATATGTAACAAATACAATTATATAAA
1 TATATGTAACAAATACAATTATATAAA
* *
412063 TATATTTAACAATTA-AATTAT-TAAA
1 TATATGTAACAAATACAATTATATAAA
412088 -ATAT
1 TATAT
412092 TAATCATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 4 0.15
26 6 0.22
27 13 0.48
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
TATATGTAACAAATACAATTATATAAA
Found at i:419839 original size:5 final size:5
Alignment explanation
Indices: 419829--419871 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
419819 GCCATAAACT
*
419829 CAACC CAACC CAACC CAACC CAACC CAACC CAATC CAACC CAA
1 CAACC CAACC CAACC CAACC CAACC CAACC CAACC CAACC CAA
419872 TTTCACATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.42, C:0.56, G:0.00, T:0.02
Consensus pattern (5 bp):
CAACC
Found at i:420070 original size:21 final size:21
Alignment explanation
Indices: 420044--420094 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
420034 ATAATTACGT
420044 TTATTTTTTTAAAATT-AAT-AA
1 TTATTTTTTT--AATTAAATGAA
420065 TTATTTTTTTAATTAAATGAA
1 TTATTTTTTTAATTAAATGAA
420086 TTATTTTTT
1 TTATTTTTT
420095 ACATGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTTTTTTAATTAAATGAA
Found at i:422107 original size:43 final size:42
Alignment explanation
Indices: 422049--422185 Score: 143
Period size: 40 Copynumber: 3.3 Consensus size: 42
422039 TTTTGGGGAA
* *
422049 AAACGCCGGTAAAGAACATGATCTTTAGCGGCGCTTTTCACAC
1 AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTTTC-CAC
* * **
422092 AAACACTGCTAAAGAACATGGTCTTTAGC-G-GCTTCCCCAC
1 AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAC
* * * * * *
422132 AAACGCCGCTAAAAAACATGTTCTATAGCGGCGTTTTTCTAC
1 AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAC
422174 AAACGCTGCTAA
1 AAACGCTGCTAA
422186 CAGTAACAGA
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 27 0.36
41 6 0.08
42 18 0.24
43 25 0.33
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (42 bp):
AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAC
Found at i:424393 original size:33 final size:33
Alignment explanation
Indices: 424351--424415 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
424341 AAGAAGTCCG
424351 TAATACTCCACATTTCCCTCAACAGGATTACTA
1 TAATACTCCACATTTCCCTCAACAGGATTACTA
424384 TAATACTCCACATTTCCCTCAACAGGATTACT
1 TAATACTCCACATTTCCCTCAACAGGATTACT
424416 GTCTCTAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (33 bp):
TAATACTCCACATTTCCCTCAACAGGATTACTA
Found at i:429891 original size:58 final size:58
Alignment explanation
Indices: 429805--429924 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
429795 AAAAGAAGTT
* *
429805 GTTTGTGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTT-GAGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGA-TTTA
* * * *
429863 GTTTATGAGTGTTTTTTAAGAATGAAATTCTATTTGGGTTTAAAAATATTTGGATTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
429921 GTTT
1 GTTT
429925 GTTGATGGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 53 0.96
59 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
Found at i:429938 original size:58 final size:58
Alignment explanation
Indices: 429819--429939 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 58
429809 GTGAGTGTTA
* **
429819 TTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGTTTATGAGTGTTT
1 TTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGTTTATGAGTGGGT
* * * *
429877 TTTAAGAATGAAATTCTATTTGGGTTTAAAAATATTTG-GATTTAGTTTGTTGA-TGGGT
1 TTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAG-TTTAGTTT-ATGAGTGGGT
429935 TTTAA
1 TTTAA
429940 ATATTAGGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.02
58 50 0.93
59 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (58 bp):
TTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTAGTTTATGAGTGGGT
Found at i:431844 original size:59 final size:59
Alignment explanation
Indices: 431750--431921 Score: 215
Period size: 59 Copynumber: 2.9 Consensus size: 59
431740 TTTTGACGGT
* * * * * *
431750 AAAAATGGCAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGGATTTTTGAAAGTTC-GGAGG
1 AAAAATGGTAATTTTTGGA-AGGTTCAAGGTCAAAAATGAGATTTTTGGAAGTTCGGGA-G
431808 AAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGAGATTTTTGGAAGTTCGGGAG
1 AAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGAGATTTTTGGAAGTTCGGGAG
* * *
431867 TAAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGAGATTTTTTGGAAGTTC
1 AAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGAGA-TTTTTGGAAGTTC
431922 AAGGGTAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
58 10 0.10
59 73 0.72
60 18 0.18
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
AAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGAGATTTTTGGAAGTTCGGGAG
Found at i:431854 original size:30 final size:29
Alignment explanation
Indices: 431781--432394 Score: 412
Period size: 30 Copynumber: 20.8 Consensus size: 29
431771 TTCGAGGTCG
* *
431781 AAAATGGGATTTTT-GAAAGTTCGGAGG-A
1 AAAATGAGATTTTTGGAAGGTTCGG-GGTA
**
431809 AAAATG-GTAATTTTTGGAAGGTTCAAGGTCA
1 AAAATGAG--ATTTTTGGAAGGTTCGGGGT-A
431840 AAAATGAGATTTTTGGAA-GTTCGGGAGT-
1 AAAATGAGATTTTTGGAAGGTTCGGG-GTA
*
431868 AAAATG-GTAATTTTTGGAAGGTTCAGGGTTA
1 AAAATGAG--ATTTTTGGAAGGTTC-GGGGTA
*
431899 AAAATGAGATTTTTTGGAA-GTTCAAGGGT-
1 AAAATGAGA-TTTTTGGAAGGTTC-GGGGTA
* * *
431928 AAAATGGGATTTTTGG-AGTTTTGGGGGT-
1 AAAATGAGATTTTTGGAAG-GTTCGGGGTA
*
431956 AAAATG-GTATTTTTTGGAAGGTTTGGGGTTA
1 AAAATGAG-A-TTTTTGGAAGGTTCGGGG-TA
*
431987 AAAATGGGATTTTTGGAA-GTTCGAGGGT-
1 AAAATGAGATTTTTGGAAGGTTCG-GGGTA
*
432015 AAAATGATAATTTTTGGAAGGTTCGGGGTTA
1 AAAATGA-GATTTTTGGAAGGTTCGGGG-TA
* * *
432046 AAAATGGGATTTTTGGAAGTTTGGGGGT-
1 AAAATGAGATTTTTGGAAGGTTCGGGGTA
* *
432074 AAAATGGTGATTTTTGGAAGGTTCGAGGTTA
1 AAAAT-GAGATTTTTGGAAGGTTCG-GGGTA
*
432105 AAAATGGGATTTTTGGAA-GTTCGGGGGT-
1 AAAATGAGATTTTTGGAAGGTTC-GGGGTA
* ** * **
432133 AAAATGGTGATTTTTTAAAGGTTTGAGTTTA
1 AAAAT-GAGATTTTTGGAAGGTTCG-GGGTA
*
432164 AAAATGCGATTTTTGGAA-GTTCGGGGGT-
1 AAAATGAGATTTTTGGAAGGTTC-GGGGTA
*
432192 AAAATGGTGATTTTTGGAAGGTTCGGGGTTA
1 AAAAT-GAGATTTTTGGAAGGTTCGGGG-TA
432223 AAAATG-GAATTTTTGGAA-GTTCGGGGGGT-
1 AAAATGAG-ATTTTTGGAAGGTTC--GGGGTA
*
432252 AAAATGGTGATTTTTGGAAGGTTCGGGGTTA
1 AAAAT-GAGATTTTTGGAAGGTTCGGGG-TA
* *
432283 AAAATGGGATTTTTGGAA-GTTCGGGGGA
1 AAAATGAGATTTTTGGAAGGTTCGGGGTA
* * * * *
432311 TAAATTGGTGATTTTTGAAAGGTTAAGGGTTA
1 -AAAAT-GAGATTTTTGGAAGGTT-CGGGGTA
* *
432343 AAAATGAAATTTTTTGAA-GTTCGAGGGT-
1 AAAATGAGATTTTTGGAAGGTTCG-GGGTA
*
432371 AAAATGATGATTTTTAGAAGGTTC
1 AAAATGA-GATTTTTGGAAGGTTC
432395 AGGGACCTTC
Statistics
Matches: 474, Mismatches: 57, Indels: 108
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.01
28 60 0.13
29 161 0.34
30 168 0.35
31 74 0.16
32 7 0.01
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
AAAATGAGATTTTTGGAAGGTTCGGGGTA
Found at i:431940 original size:59 final size:59
Alignment explanation
Indices: 431781--432394 Score: 682
Period size: 59 Copynumber: 10.4 Consensus size: 59
431771 TTCGAGGTCG
* * **
431781 AAAATGG-GATTTTT-GAAAGTTCGGAGG--AAAAATGGTAATTTTTGGAAGGTTC-AAGGT
1 AAAATGGTGATTTTTGGAAGGTTCGG-GGTTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT
* * * *
431838 CAAAAAT-GAGATTTTTGGAA-GTTCGGGAG-T-AAAATGGTAATTTTTGGAAGGTTCAGGGTT
1 --AAAATGGTGATTTTTGGAAGGTTCGGG-GTTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT
* * *
431898 AAAAAT-GAGATTTTTTGGAA-GTTCAAGGG-T-AAAATGGGATTTTTGG-AGTTTTGGGGGT
1 -AAAATGGTGA-TTTTTGGAAGGTTC-GGGGTTAAAAATGGGATTTTTGGAAG-TTCGGGGGT
* *
431956 AAAATGGT-ATTTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTGA-TTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
432015 AAAATGATAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
432074 AAAATGGTGATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
** * * * *
432133 AAAATGGTGATTTTTTAAAGGTTTGAGTTTAAAAATGCGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
432192 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC-GGGGGT
432252 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGAT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGG-T
* * ** ** * *
432312 AAATTGGTGATTTTTGAAAGGTTAAGGGTTAAAAATGAAATTTTTTGAAGTTCGAGGGT
1 AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
432371 AAAATGATGATTTTTAGAAGGTTC
1 AAAATGGTGATTTTTGGAAGGTTC
432395 AGGGACCTTC
Statistics
Matches: 492, Mismatches: 47, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
57 20 0.04
58 14 0.03
59 317 0.64
60 139 0.28
61 2 0.00
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (59 bp):
AAAATGGTGATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:434179 original size:17 final size:17
Alignment explanation
Indices: 434152--434229 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
434142 GGACATTTTT
434152 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
* *
434170 TAAATTTAAATTTCTAC
1 TAAATTTAAATTTATAA
* *
434187 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
434204 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
434221 TAAATTTAA
1 TAAATTTAA
434230 GCTAATTGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 45 0.92
18 4 0.08
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:434306 original size:18 final size:19
Alignment explanation
Indices: 434276--434314 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
434266 ATATTAAGTG
434276 TTAAAGTTTTTTTATCCAT
1 TTAAAGTTTTTTTATCCAT
434295 TTAAAGTTTTTTTATCCAT
1 TTAAAGTTTTTTTATCCAT
434314 T
1 T
434315 GGGTATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAAGTTTTTTTATCCAT
Found at i:442958 original size:19 final size:17
Alignment explanation
Indices: 442922--442993 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
442912 TTAAATTGAT
442922 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
442939 TTTAAATTTATTTTTTAAA
1 TTTAAATTTA--TCTTAAA
*
442958 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATC-TTAAA
* *
442975 TTTGAATTTA-ATTAAA
1 TTTAAATTTATCTTAAA
442991 TTT
1 TTT
442994 GAGACAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 8 0.17
17 23 0.50
19 15 0.33
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:443814 original size:12 final size:12
Alignment explanation
Indices: 443797--443907 Score: 73
Period size: 12 Copynumber: 8.9 Consensus size: 12
443787 AACTATTCAA
*
443797 ATTAATAATGAT
1 ATTAATAATAAT
443809 ATTAATAATAAT
1 ATTAATAATAAT
*
443821 ATTGATAATAAT
1 ATTAATAATAAT
*
443833 GTTAATAATAAAT
1 ATTAATAAT-AAT
* * *
443846 AGAGGTAATAAATGAC
1 --A-TTAAT-AATAAT
*
443862 ATTAATAACTATT
1 ATTAATAA-TAAT
*
443875 AATAATAATAAT
1 ATTAATAATAAT
*
443887 TTTAATAATAA-
1 ATTAATAATAAT
443898 A-TAATAATAA
1 ATTAATAATAA
443908 AATTGAAAAG
Statistics
Matches: 76, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
10 9 0.12
12 43 0.57
13 15 0.20
14 1 0.01
16 5 0.07
17 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:443838 original size:9 final size:9
Alignment explanation
Indices: 443799--443841 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
443789 CTATTCAAAT
443799 TAATAATGA
1 TAATAATGA
* *
443808 TATTAATAA
1 TAATAATGA
*
443817 TAATATTGA
1 TAATAATGA
*
443826 TAATAATGT
1 TAATAATGA
443835 TAATAAT
1 TAATAAT
443842 AAATAGAGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (9 bp):
TAATAATGA
Found at i:443893 original size:15 final size:16
Alignment explanation
Indices: 443873--443902 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
443863 TTAATAACTA
443873 TTAATAAT-AATAATT
1 TTAATAATAAATAATT
443888 TTAATAATAAATAAT
1 TTAATAATAAATAAT
443903 AATAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATAATAAATAATT
Found at i:445024 original size:60 final size:58
Alignment explanation
Indices: 444916--445254 Score: 280
Period size: 60 Copynumber: 5.8 Consensus size: 58
444906 CTAAACTGTC
* *
444916 CAAAAATTACATTTTTCCCT-AAACTTTCC-AAAATTCCATTTTTGACCTTGATTTTTT
1 CAAAAATTACATTTTACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTT-ATTTTTT
* *
444973 CAAAAATTACATTTTCACCCTCGAACTTTCCAAAAATTCCATTTTTAACCTTGATTTTTC
1 CAAAAATTACATTTT-ACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTT-ATTTTTT
* * ** * *
445033 CAAAAATTACATTTTTACCC-CTGAACTTT-CTAAAATTTTA-TTTTAACCCTATTCTTT
1 CAAAAATTACA-TTTTACCCTC-AAACTTTCCAAAAATTCCATTTTTAACCTTATTTTTT
* * * * * * *
445090 CTAAAATTACATTTTTGCCTTTAAACTTTCC-AAAATTCTATTTTTAACCTCAATTTTT
1 CAAAAATTACA-TTTTACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTTATTTTTT
* * *
445148 CTAAAAATTACCATTTTACCCTTAAAC-TTCCAAAAATTCCATTTTTTTACCTTAGTTTTTCC
1 C-AAAAATTA-CATTTTACCCTCAAACTTTCCAAAAATTCCA-TTTTTAACCTTA-TTTTT-T
* * * * * *
445210 CAAAAAGTACCGTTTTACCCTCGAA-TATCTAAAAATTCCTTTTTT
1 CAAAAATTA-CATTTTACCCTCAAACTTTCCAAAAATTCCATTTTT
445255 GACCCTCGAC
Statistics
Matches: 232, Mismatches: 35, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
57 51 0.22
58 32 0.14
59 44 0.19
60 65 0.28
61 39 0.17
62 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (58 bp):
CAAAAATTACATTTTACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTTATTTTTT
Found at i:445068 original size:29 final size:28
Alignment explanation
Indices: 444916--445193 Score: 159
Period size: 30 Copynumber: 9.6 Consensus size: 28
444906 CTAAACTGTC
*
444916 CAAAAATTACATTTTT-CCCTAAACTTT
1 CAAAAATTACATTTTTACCCTGAACTTT
* * * **
444943 CCAAAATTCCATTTTTGACCTTGATTTTTT
1 CAAAAATTACATTTTT-ACCCTGA-ACTTT
*
444973 CAAAAATTACATTTTCACCCTCGAACTTT
1 CAAAAATTACATTTTTACCCT-GAACTTT
* * **
445002 CCAAAAATTCCATTTTTAACCTTGATTTTT
1 -CAAAAATTACATTTTT-ACCCTGAACTTT
445032 CCAAAAATTACATTTTTACCCCTGAACTTT
1 -CAAAAATTACATTTTTA-CCCTGAACTTT
* ** * *
445062 CTAAAATTTTATTTTAACCCT-ATTCTTT
1 CAAAAATTACATTTTTACCCTGA-ACTTT
* * * *
445090 CTAAAATTACATTTTTGCCTTTAAACTTT
1 CAAAAATTACATTTTTACC-CTGAACTTT
* * * *
445119 CCAAAATT-CTATTTTTAACCTCAATTTTT
1 CAAAAATTAC-ATTTTTACCCTGAA-CTTT
* *
445148 CTAAAAATTACCA-TTTTACCCTTAAACTTC
1 C-AAAAATTA-CATTTTTACCC-TGAACTTT
*
445178 CAAAAATTCCATTTTT
1 CAAAAATTACATTTTT
445194 TTACCTTAGT
Statistics
Matches: 190, Mismatches: 44, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
27 15 0.08
28 29 0.15
29 59 0.31
30 78 0.41
31 8 0.04
32 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCTGAACTTT
Found at i:445117 original size:57 final size:59
Alignment explanation
Indices: 444917--445193 Score: 266
Period size: 59 Copynumber: 4.7 Consensus size: 59
444907 TAAACTGTCC
* * **
444917 AAAAATTACATTTTT--CCCTAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTT-T
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCAATTTTTCT
* * * ** *
444973 CAAAAATTACATTTTCA-CCCTCGAACTTTCCAAAAATTCCATTTTTAACCTTGATTTTTCC
1 -AAAAATTACATTTTTACCCCT-AAACTTTCC-AAAATTCTATTTTTAACCTCAATTTTTCT
* * * *
445034 AAAAATTACATTTTTACCCCTGAACTTTCTAAAATTTTA-TTTTAACC-CTATTCTTTCT
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCAATT-TTTCT
* **
445092 -AAAATTACATTTTTGCCTTTAAACTTTCCAAAATTCTATTTTTAACCTCAATTTTTCT
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCAATTTTTCT
* *
445150 AAAAATTACCA-TTTTACCCTTAAAC-TTCCAAAAATTCCATTTTT
1 AAAAATTA-CATTTTTACCCCTAAACTTTCC-AAAATTCTATTTTT
445194 TTACCTTAGT
Statistics
Matches: 188, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
57 49 0.26
58 33 0.18
59 51 0.27
60 51 0.27
61 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCAATTTTTCT
Found at i:445120 original size:117 final size:118
Alignment explanation
Indices: 444914--445193 Score: 329
Period size: 117 Copynumber: 2.4 Consensus size: 118
444904 CTCTAAACTG
* * *
444914 TCCAAAAATTACATTTTT--CCCTAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTTTCAAA
1 TCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTCTTTCAAA
* **
444977 AATTACATTTTCACCCTCGAACTTTCCAAAAATTCCATTTTTAACCTTGATTTT
66 AATTACATTTTCACCCTCAAACTTTCC-AAAATTCCATTTTTAACCTCAATTTT
* * ** *
445031 TCCAAAAATTACATTTTTACCCCTGAACTTTCTAAAATTTTA-TTTTAACCCT-ATTCTTTCTAA
1 TCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTCTTTCAAA
** * * *
445094 AATTACATTTTTGCCTTTAAACTTTCCAAAATTCTATTTTTAACCTCAATTTT
66 AATTACATTTTCACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTT
* *
445147 TCTAAAAATTACCA-TTTTACCCTTAAAC-TTCCAAAAATTCCATTTTT
1 TCCAAAAATTA-CATTTTTACCCCTAAACTTTCC-AAAATTCCATTTTT
445194 TTACCTTAGT
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
115 3 0.02
116 52 0.38
117 55 0.40
118 8 0.06
119 18 0.13
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (118 bp):
TCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTCTTTCAAA
AATTACATTTTCACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTT
Found at i:445243 original size:176 final size:174
Alignment explanation
Indices: 444918--445243 Score: 430
Period size: 176 Copynumber: 1.9 Consensus size: 174
444908 AAACTGTCCA
* **
444918 AAAATTACATTTTTCCCTAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTTTCAAAAATTAC
1 AAAATTACATTTTTCCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTCAAAAATTAC
* * *
444983 ATTTTCACCCTCGAACTTTCCAAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACATTTT
66 ATTTTCACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTTGATTTTTCCAAAAAGTACAGTTT
*
445048 TACCCCTGAACTTTCTAAAATTTTATTTTAACCCTATTCTTTCT
131 TACCCCTGAACTATCTAAAATTTTATTTTAACCCTATTCTTTCT
* *
445092 AAAATTACATTTTTGCCTTTAAACTTTCCAAAATTCTATTTTTAACCTCAA-TTTTTCTAAAAAT
1 AAAATTACATTTTT-CC-CTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTC-AAAAAT
* *
445156 TACCATTTT-ACCCTTAAAC-TTCCAAAAATTCCATTTTTTTACCTT-AGTTTTTCCCAAAAAGT
63 TA-CATTTTCACCCTCAAACTTTCCAAAAATTCCA-TTTTTAACCTTGA-TTTTT-CCAAAAAGT
*
445218 ACCGTTTTA-CCCTCGAA-TATCTAAAA
124 ACAGTTTTACCCCT-GAACTATCTAAAA
445244 ATTCCTTTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
174 14 0.11
175 23 0.17
176 71 0.54
177 24 0.18
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (174 bp):
AAAATTACATTTTTCCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTCAAAAATTAC
ATTTTCACCCTCAAACTTTCCAAAAATTCCATTTTTAACCTTGATTTTTCCAAAAAGTACAGTTT
TACCCCTGAACTATCTAAAATTTTATTTTAACCCTATTCTTTCT
Found at i:452107 original size:19 final size:18
Alignment explanation
Indices: 452049--452099 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
452039 GTGAAGGAAG
*
452049 AAAAGAAG-GAAATA-AA
1 AAAAGAAGCGAAAGATAA
452065 AAAAGGAAGCGAAAGATAA
1 AAAA-GAAGCGAAAGATAA
*
452084 AAAAGAAGCGAGAGAT
1 AAAAGAAGCGAAAGAT
452100 GAGAAAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 16 0.53
19 6 0.20
ACGTcount: A:0.65, C:0.04, G:0.25, T:0.06
Consensus pattern (18 bp):
AAAAGAAGCGAAAGATAA
Found at i:456697 original size:48 final size:49
Alignment explanation
Indices: 456626--456952 Score: 277
Period size: 48 Copynumber: 6.7 Consensus size: 49
456616 AGTACCGCAA
* * * * * *
456626 AAGGGAAAGGTTTAAGTCGCAACGGCAAACCCAATACCACGAAGACA-C
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGAAGACATG
* * * *
456674 AAGGGAAATATCTAAGCCGCAACGGCGGATCCAATACCACTAAGACA-C
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGAAGACATG
* * * * *
456722 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCAC-AGAGGCATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGA-AGACATG
* * * * * *
456771 AAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTATCGCAAAGATACA-A
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGAAG--ACATG
* * * * ** *
456821 AAGGGAAAGGTTTAAGTCGCAACGGCGGA-CCGTGTACCTCAGAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCC-AATACCAC-GAAGACATG
* * *
456871 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCACGAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGAAGACATG
* *
456920 AAGGGAAAGATCTAAGCCGCAACGACGGATCCA
1 AAGGGAAAGATCTAAGCCGCAACGGCGAATCCA
456953 GTATCGCAAG
Statistics
Matches: 227, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
47 1 0.00
48 80 0.35
49 78 0.34
50 61 0.27
51 7 0.03
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGCCGCAACGGCGAATCCAATACCACGAAGACATG
Found at i:456794 original size:49 final size:49
Alignment explanation
Indices: 456626--457056 Score: 279
Period size: 49 Copynumber: 8.8 Consensus size: 49
456616 AGTACCGCAA
* * * ** * * *
456626 AAGGGAAAGGTTTAAGTCGCAACGGCAAACCCAATACCAC-GAAGACA-C
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAG-AGACATG
* * *
456674 AAGGGAAATATCTAAGCCGCAACGGCGGATCCAATACCACTA-AGACA-C
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC-AGAGACATG
* * *
456722 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACAGAGGCATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAGAGACATG
* * * * *
456771 AAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTATCGCAAAGATACA-A
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTA-C-CACAGAGACATG
* * * * *
456821 AAGGGAAAGGTTTAAGTCGCAACGGCGGA-CCGTGTACCTCAGAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACCACAG-AGACATG
* * * * *
456871 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCAC-GAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAG-AGACATG
* * *
456920 AAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTATCGCA-AGGATACA-A
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTA-C-CACA-GAGACATG
* * * * ** * * *
456970 AAGGGAAAGGTTTAAGTCGCAA-TGATGAACCTAGTACCTCAAAGACATG
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACCACAGAGACATG
* * * **
457019 AAGGGAAAGATTTAAGCCACAATGGCAAATCCAGTACC
1 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
457057 GCGAAAATAC
Statistics
Matches: 300, Mismatches: 65, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
47 1 0.00
48 87 0.29
49 109 0.36
50 87 0.29
51 15 0.05
52 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAGAGACATG
Found at i:456910 original size:149 final size:147
Alignment explanation
Indices: 456722--457061 Score: 459
Period size: 149 Copynumber: 2.3 Consensus size: 147
456712 ACTAAGACAC
* * * * *
456722 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCAC-AGAGGCATGAAGGGAAAGATCTAA
1 AAGGGAAAGATTTAAGC-GCAATGGCGAATCCAGTACCACGA-AGACATGAAGGGAAAGATCTAA
* * *
456786 GCCACAACGGCGAATCCAGTATCGCAAAGATACAAAAGGGAAAGGTTTAAGTCGCAACGGCGGAC
64 GCCACAACGACGAATCCAGTATCGCAAAGATACAAAAGGGAAAGGTTTAAGTCGCAACGACGAAC
456851 CGT-GTACCTCAGAAGACATG
129 C-TAGTACCTCA-AAGACATG
*
456871 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCACGAAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGATTTAAG-CGCAATGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAG
* * * * *
456936 CCGCAACGACGGATCCAGTATCGCAAGGATACAAAAGGGAAAGGTTTAAGTCGCAATGATGAACC
65 CCACAACGACGAATCCAGTATCGCAAAGATACAAAAGGGAAAGGTTTAAGTCGCAACGACGAACC
457001 TAGTACCTCAAAGACATG
130 TAGTACCTCAAAGACATG
* * *
457019 AAGGGAAAGATTTAAGCCACAATGGCAAATCCAGTACCGCGAA
1 AAGGGAAAGATTTAAG-CGCAATGGCGAATCCAGTACCACGAA
457062 AATACGAGGG
Statistics
Matches: 169, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
148 47 0.28
149 120 0.71
150 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (147 bp):
AAGGGAAAGATTTAAGCGCAATGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGC
CACAACGACGAATCCAGTATCGCAAAGATACAAAAGGGAAAGGTTTAAGTCGCAACGACGAACCT
AGTACCTCAAAGACATG
Found at i:456924 original size:99 final size:97
Alignment explanation
Indices: 456626--457034 Score: 326
Period size: 99 Copynumber: 4.2 Consensus size: 97
456616 AGTACCGCAA
* ** * * * *
456626 AAGGGAAAGGTTTAAGTCGCAACGGCAAACCCAATACCAC-GAAGACACAAGGGAAATATCTAAG
1 AAGGGAAAGATTTAAGTCGCAACGGCGGATCCAGTACCACAGAAGACAGAAGGGAAAGATCTAAG
* * *
456690 CCGCAACGGCGGATCCAATACCACTAAGACAC
66 CCGCAACGGCGAATCCAATACCACAAAGACAG
* * *
456722 AAGGGAAAGATCTAAG-CTGCAACGGTGGATCCAGTACCACAG-AGGCATGAAGGGAAAGATCTA
1 AAGGGAAAGATTTAAGTC-GCAACGGCGGATCCAGTACCACAGAAGACA-GAAGGGAAAGATCTA
* * * * *
456785 AGCCACAACGGCGAATCCAGTATCGCAAAGATACAA
64 AGCCGCAACGGCGAATCCAATACCACAAAG--ACAG
* * * *
456821 AAGGGAAAGGTTTAAGTCGCAACGGCGGA-CCGTGTACCTCAGAAGACATGAAGGGAAAGATTTA
1 AAGGGAAAGATTTAAGTCGCAACGGCGGATCC-AGTACCACAGAAGACA-GAAGGGAAAGATCTA
* * *
456885 AGTCGCAATGGCGAATCCAATACCACGAAGACATG
64 AGCCGCAACGGCGAATCCAATACCACAAAGACA-G
* * * * * * * *
456920 AAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTATCGCA-AGGATACAAAAGGGAAAGGTTTA
1 AAGGGAAAGATTTAAGTCGCAACGGCGGATCCAGTA-C-CACAGAAGACAGAAGGGAAAGATCTA
* * ** * *
456984 AGTCGCAATGATGAA-CCTAGTACCTCAAAGACATG
64 AGCCGCAACGGCGAATCC-AATACCACAAAGACA-G
457019 AAGGGAAAGATTTAAG
1 AAGGGAAAGATTTAAG
457035 CCACAATGGC
Statistics
Matches: 252, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
95 1 0.00
96 35 0.14
97 38 0.15
98 7 0.03
99 118 0.47
100 52 0.21
101 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (97 bp):
AAGGGAAAGATTTAAGTCGCAACGGCGGATCCAGTACCACAGAAGACAGAAGGGAAAGATCTAAG
CCGCAACGGCGAATCCAATACCACAAAGACAG
Found at i:457051 original size:99 final size:97
Alignment explanation
Indices: 456871--457083 Score: 241
Period size: 99 Copynumber: 2.2 Consensus size: 97
456861 AGAAGACATG
* * *
456871 AAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCACGAAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCGCAATGACGAATCCAATACCACAAAGACATGAAGGGAAAGATCTAAG
* ** * *
456936 CCGCAACGACGGATCCAGTATCGC-AAGGATAC
66 CCACAACGACAAATCCAGTACCGCGAA-AATAC
* * * *
456968 AAAAGGGAAAGGTTTAAGTCGCAATGATGAA-CCTAGTACCTCAAAGACATGAAGGGAAAGATTT
1 --AAGGGAAAGGTTTAAGTCGCAATGACGAATCC-AATACCACAAAGACATGAAGGGAAAGATCT
* *
457032 AAGCCACAATGGCAAATCCAGTACCGCGAAAATAC
63 AAGCCACAACGACAAATCCAGTACCGCGAAAATAC
*
457067 GAGGGAAAGGTTTAAGT
1 AAGGGAAAGGTTTAAGT
457084 TACGATGGCA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
97 16 0.16
98 2 0.02
99 77 0.79
100 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGTCGCAATGACGAATCCAATACCACAAAGACATGAAGGGAAAGATCTAAG
CCACAACGACAAATCCAGTACCGCGAAAATAC
Found at i:457614 original size:18 final size:19
Alignment explanation
Indices: 457591--457671 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 19
457581 TTAAATTGAT
*
457591 TTTAAATTT-TTTTTTCAA
1 TTTAAATTTATTTTTTAAA
*
457609 TTTAAATTTA--TCTTAAA
1 TTTAAATTTATTTTTTAAA
*
457626 TTTAAATTTATTCTTTAAA
1 TTTAAATTTATTTTTTAAA
*
457645 TTTAAA-TT-TGTTTTAAA
1 TTTAAATTTATTTTTTAAA
*
457662 TTTGAATTTA
1 TTTAAATTTA
457672 ATTAAATTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
17 27 0.53
18 13 0.25
19 11 0.22
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAAATTTATTTTTTAAA
Found at i:457618 original size:6 final size:6
Alignment explanation
Indices: 457607--457680 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
457597 TTTTTTTTTC
**
457607 AATTTA AATTT- -ATCTTA AATTTA AATTTA TTCTTTA AATTTA AATTT-
1 AATTTA AATTTA AAT-TTA AATTTA AATTTA -AATTTA AATTTA AATTTA
** *
457654 GTTTTA AATTTG AATTT- AA-TTA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTT
457681 GAGATAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
4 4 0.08
5 9 0.17
6 33 0.63
7 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:457629 original size:17 final size:17
Alignment explanation
Indices: 457607--457680 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
457597 TTTTTTTTTC
457607 AATTTAAATTTATCTTA
1 AATTTAAATTTATCTTA
457624 AATTTAAATTTATTCTTTA
1 AATTTAAATTTA-TC-TTA
* *
457643 AATTTAAATTTGTTTTA
1 AATTTAAATTTATCTTA
* *
457660 AATTTGAATTTA-ATTA
1 AATTTAAATTTATCTTA
457676 AATTT
1 AATTT
457681 GAGATAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.16
17 25 0.50
18 3 0.06
19 14 0.28
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATCTTA
Found at i:457651 original size:36 final size:36
Alignment explanation
Indices: 457591--457671 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
457581 TTAAATTGAT
* *
457591 TTTAAATTT-TTTTTTCAATTTAAATTTATCTTAAA
1 TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
* *
457626 TTTAAATTTATTCTTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
*
457662 TTTGAATTTA
1 TTTAAATTTA
457672 ATTAAATTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 9 0.22
36 31 0.77
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (36 bp):
TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
Found at i:457810 original size:11 final size:11
Alignment explanation
Indices: 457794--457826 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
457784 TCTTTAATTG
*
457794 ACCCAATACCA
1 ACCCAATACAA
457805 ACCCAATACAA
1 ACCCAATACAA
457816 ACCCAATACAA
1 ACCCAATACAA
457827 GCCTAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.09
Consensus pattern (11 bp):
ACCCAATACAA
Found at i:458498 original size:12 final size:12
Alignment explanation
Indices: 458472--458581 Score: 68
Period size: 12 Copynumber: 9.1 Consensus size: 12
458462 AACTATTCAA
**
458472 ATTAATAATGCT
1 ATTAATAATAAT
458484 ATTAATAATAAT
1 ATTAATAATAAT
*
458496 ATTGATAATAAT
1 ATTAATAATAAT
*
458508 GTTAATAATAA-
1 ATTAATAATAAT
*
458519 ATAAAGGTAATAA-
1 ATTAA--TAATAAT
*
458532 ATGACATTAATAAAT
1 ATTA-A-TAAT-AAT
458547 ATTAATAATAAT
1 ATTAATAATAAT
*
458559 AATT-TTAATAAT
1 -ATTAATAATAAT
458571 A--AATAATAAT
1 ATTAATAATAAT
458581 A
1 A
458582 AAATTGAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
10 8 0.10
11 4 0.05
12 40 0.51
13 20 0.25
14 4 0.05
15 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.37
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:458568 original size:15 final size:16
Alignment explanation
Indices: 458548--458577 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
458538 TTAATAAATA
458548 TTAATAAT-AATAATT
1 TTAATAATAAATAATT
458563 TTAATAATAAATAAT
1 TTAATAATAAATAAT
458578 AATAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATAATAAATAATT
Found at i:458579 original size:10 final size:10
Alignment explanation
Indices: 458510--458583 Score: 53
Period size: 13 Copynumber: 7.0 Consensus size: 10
458500 ATAATAATGT
458510 TAATAATAAA
1 TAATAATAAA
458520 TAAAGGTAATAAA
1 T-AA--TAATAAA
458533 TGACATTAATAAA
1 T-A-A-TAATAAA
*
458546 TATTAAT-AA
1 TAATAATAAA
**
458555 TAATAAT-TT
1 TAATAATAAA
458564 TAATAATAAA
1 TAATAATAAA
458574 TAATAATAAA
1 TAATAATAAA
458584 ATTGAAAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 15 0.29
10 15 0.29
11 2 0.04
12 1 0.02
13 17 0.33
14 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
TAATAATAAA
Found at i:459648 original size:30 final size:30
Alignment explanation
Indices: 459612--459842 Score: 210
Period size: 30 Copynumber: 7.8 Consensus size: 30
459602 TTTACATTAT
*
459612 TTTCCAAAAATTACATTTTCACCCTCGAAC
1 TTTCCAAAAATTACATTTTTACCCTCGAAC
* * * **
459642 ATTCCAAAAATTCCATTTTTGATCC-CGATT
1 TTTCCAAAAATTACATTTTT-ACCCTCGAAC
459672 TTTCCAAAAATTACATTTTTACCCTCGAAC
1 TTTCCAAAAATTACATTTTTACCCTCGAAC
* *
459702 TTTCC-AAAATT-CTATTTTTGACCCT-TATC
1 TTTCCAAAAATTAC-ATTTTT-ACCCTCGAAC
**
459731 TTTTTAAAAATTACATTTTTACCC-CTGAAC
1 TTTCCAAAAATTACATTTTTACCCTC-GAAC
* * *
459761 TTTCC-AAAATTCCA-TTTTAACCTCG-AT
1 TTTCCAAAAATTACATTTTTACCCTCGAAC
*
459788 TTTCCAAAAATTACATTTTTACCCTCAAAAC
1 TTTCCAAAAATTACATTTTTACCCTC-GAAC
*
459819 TTTCC-AAAATTCCATTTTTTACCC
1 TTTCCAAAAATTACA-TTTTTACCC
459843 CGATTATTTT
Statistics
Matches: 160, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
27 6 0.04
28 17 0.11
29 42 0.26
30 76 0.47
31 19 0.12
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTCCAAAAATTACATTTTTACCCTCGAAC
Found at i:459679 original size:60 final size:60
Alignment explanation
Indices: 459611--460052 Score: 369
Period size: 59 Copynumber: 7.4 Consensus size: 60
459601 TTTTACATTA
* * *
459611 TTTTCCAAAAATTACATTTTCACCCTCGAACATTCCAAAAATTCCATTTTTGATCCCGAT
1 TTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCCCGAT
* **
459671 TTTTCCAAAAATTACATTTTTACCCTCGAACTTTCC-AAAATTCTATTTTTGACCCTTAT
1 TTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCCCGAT
* * *
459730 CTTTT-TAAAAATTACATTTTTACCC-CTGAACTTTCC-AAAATTCCA-TTTTAACCTCGA-
1 -TTTTCCAAAAATTACATTTTTACCCTC-GAACTTTCCAAAAATTCCATTTTTGACCCCGAT
* *
459787 TTTTCCAAAAATTACATTTTTACCCTCAAAACTTTCC-AAAATTCCATTTTTTACCCCGAT
1 TTTTCCAAAAATTACATTTTTACCCTC-GAACTTTCCAAAAATTCCATTTTTGACCCCGAT
** * * * * *
459847 TATTT-TGAAAATTACCATTTTAACCC-CAAAC-TTCTAGAAATTCCATTTTTTGACCCCAATT
1 T-TTTCCAAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTCCA-TTTTTGACCCCGA-T
* * * * * * * *
459908 TTTTCCAACAATTTCCA-TTTTACCCCCAAAC-TTCCAAAAGTTCCATTTTTTATCTCGAT
1 TTTTCCAA-AAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCCCGAT
* * *
459967 TTTTCCAAAAAAGTACCA-TTTAACCCTCGAA--TTCTAAAAATTCCATTTTTTTGACCCCGA-
1 TTTTCC-AAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTCCA--TTTTTGACCCCGAT
* *
460027 CTTTCCTAAAATTACCA-TTTTACCCT
1 TTTTCCAAAAATTA-CATTTTTACCCT
460053 TGAGTGAGCA
Statistics
Matches: 313, Mismatches: 51, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
56 4 0.01
57 19 0.06
58 30 0.10
59 116 0.37
60 96 0.31
61 44 0.14
62 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.40
Consensus pattern (60 bp):
TTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCCCGAT
Found at i:459836 original size:117 final size:116
Alignment explanation
Indices: 459607--459957 Score: 356
Period size: 117 Copynumber: 2.9 Consensus size: 116
459597 AAAATTTTAC
* *
459607 ATTATTTTCCAAAAATTACATTTTCA-CCCTCGAACATTCCAAAAATTCCATTTTTGATCCCGAT
1 ATTATTTT--AAAAATTACATTTTAACCCCT-GAAC-TTCC-AAAATTCCA-TTTTGAACCCGAT
* * **
459671 TTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCCTT
60 TTTTCCAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCCG
*
459728 ATCT-TTTTAAAAATTACATTTTTACCCCTGAACTTTCCAAAATTCCATTTT-AACCTCGA-TTT
1 AT-TATTTTAAAAATTACATTTTAACCCCTGAAC-TTCCAAAATTCCATTTTGAACC-CGATTTT
*
459790 TCCAAAAATTACATTTTTACCCTCAAAACTTTCCAAAATTCCATTTTTTACCCCG
63 TCCAAAAATTACATTTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCCCG
* * * * *
459845 ATTATTTTGAAAATTACCATTTTAACCCC-AAACTTCTAGAAATTCCATTTTTTGACCCCAATTT
1 ATTATTTTAAAAATTA-CATTTTAACCCCTGAACTTCCA-AAATTCCA--TTTTGAACCCGA-TT
* * *
459909 TTTCCAACAATTTCCA-TTTTACCCCCAAAC-TTCCAAAAGTTCCATTTTT
61 TTTCCAA-AAATTACATTTTTACCCTCAAACTTTCCAAAA-TTCCATTTTT
459958 TATCTCGATT
Statistics
Matches: 199, Mismatches: 17, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
116 35 0.18
117 56 0.28
118 20 0.10
119 37 0.19
120 21 0.11
121 23 0.12
122 7 0.04
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.40
Consensus pattern (116 bp):
ATTATTTTAAAAATTACATTTTAACCCCTGAACTTCCAAAATTCCATTTTGAACCCGATTTTTCC
AAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCCG
Found at i:459959 original size:30 final size:28
Alignment explanation
Indices: 459737--459957 Score: 108
Period size: 29 Copynumber: 7.5 Consensus size: 28
459727 TATCTTTTTA
* **
459737 AAAATTACATTTTTACCCCTGAACTTTCC
1 AAAATTCCATTTTTACCCCCAAAC-TTCC
* * * **
459766 AAAATTCCA-TTTTAACCTCGATTTTCC
1 AAAATTCCATTTTTACCCCCAAACTTCC
* *
459793 AAAAATTACATTTTTACCCTCAAAACTTTCC
1 -AAAATTCCATTTTTACCC-CCAAAC-TTCC
* * * **
459824 AAAATTCCATTTTTTACCCCGATTATTTTG
1 AAAATTCCA-TTTTTACCCCCA-AACTTCC
* *
459854 AAAATTACCA-TTTTAACCCCAAACTTCT
1 AAAATT-CCATTTTTACCCCCAAACTTCC
**
459882 AGAAATTCCATTTTTTGA-CCCCAATTTTTTCC
1 A-AAATTCCA-TTTTT-ACCCCCAA--ACTTCC
459914 AACAATTTCCA-TTTTACCCCCAAACTTCC
1 AA-AA-TTCCATTTTTACCCCCAAACTTCC
459943 AAAAGTTCCATTTTT
1 AAAA-TTCCATTTTT
459958 TATCTCGATT
Statistics
Matches: 144, Mismatches: 31, Indels: 34
0.69 0.15 0.16
Matches are distributed among these distances:
27 4 0.03
28 31 0.22
29 39 0.27
30 30 0.21
31 29 0.20
32 6 0.04
33 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCCAAACTTCC
Found at i:459990 original size:120 final size:122
Alignment explanation
Indices: 459617--460024 Score: 325
Period size: 117 Copynumber: 3.4 Consensus size: 122
459607 ATTATTTTCC
* * * * *
459617 AAAAATTA-CATTTTCACCCTCGAACATTCCAAAAATTCCA--TTTTTGATCCCGA-TTTTTCCA
1 AAAAAGTACCATTTTAACCCTC-AA-ATTCTAAAAATTCCATTTTTTTGACCCCAATTTTTTCCA
* * * ** *
459678 AAAATTACATTTTTACCCTC-GAACTTTCCAAAATTCTATTTTTGACCCTTATCT-TTTT
64 AAAATTACATTTTTACCCTCAAAACTTTCCAAAATTCCATTTTTTACCCCGAT-TATTTA
* * * * * * * *
459736 AAAAATTA-CATTTTTACCCCTGAACTT-TCCAAAATTCCA---TTTTAACCTCGA--TTTTCCA
1 AAAAAGTACCA-TTTTAACCCTCAAATTCT-AAAAATTCCATTTTTTTGACCCCAATTTTTTCCA
*
459794 AAAATTACATTTTTACCCTCAAAACTTTCCAAAATTCCATTTTTTACCCCGATTATTTT
64 AAAATTACATTTTTACCCTCAAAACTTTCCAAAATTCCATTTTTTACCCCGATTATTTA
* * *
459853 GAAAATTACCATTTTAACCC-CAAACTTCTAGAAATTCCA-TTTTTTGACCCCAATTTTTTCCAA
1 AAAAAGTACCATTTTAACCCTCAAA-TTCTAAAAATTCCATTTTTTTGACCCCAATTTTTTCCAA
* * * * *
459916 CAATTTCCA-TTTTACCC-CCAAAC-TTCCAAAAGTTCCATTTTTTATCTCGATT-TTTCCA
65 -AAATTACATTTTTACCCTCAAAACTTTCCAAAA-TTCCATTTTTTACCCCGATTATTT--A
*
459974 AAAAAGTACCA-TTTAACCCTCGAATTCTAAAAATTCCATTTTTTTGACCCC
1 AAAAAGTACCATTTTAACCCTCAAATTCTAAAAATTCCATTTTTTTGACCCC
460025 GACTTTCCTA
Statistics
Matches: 239, Mismatches: 33, Indels: 32
0.79 0.11 0.11
Matches are distributed among these distances:
116 30 0.13
117 65 0.27
118 14 0.06
119 32 0.13
120 52 0.22
121 40 0.17
122 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (122 bp):
AAAAAGTACCATTTTAACCCTCAAATTCTAAAAATTCCATTTTTTTGACCCCAATTTTTTCCAAA
AATTACATTTTTACCCTCAAAACTTTCCAAAATTCCATTTTTTACCCCGATTATTTA
Found at i:460992 original size:30 final size:28
Alignment explanation
Indices: 460949--461025 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
460939 GTCACATTTT
460949 AAAATTA-CATTTTGACCCCAAAGTCATCC-
1 AAAATTACCATTTTG-CCCCAAA--CATCCA
*
460978 AAAATTACCATTTTGCCCTCGAACATCCA
1 AAAATTACCATTTTGCCC-CAAACATCCA
*
461007 AAAATCACCATTTTGCCCC
1 AAAATTACCATTTTGCCCC
461026 TAAAATTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 6 0.14
29 27 0.63
30 10 0.23
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.27
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCAAACATCCA
Found at i:470949 original size:3 final size:3
Alignment explanation
Indices: 470943--470975 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
470933 TTATGATATT
470943 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
470976 AGGGATGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:473201 original size:48 final size:48
Alignment explanation
Indices: 473142--473317 Score: 172
Period size: 48 Copynumber: 3.6 Consensus size: 48
473132 ACCTCAAAAG
*
473142 ATGTGAAGGGAAAGATTGAGGCCGTAACGGTGAATCCGATACCATGAA
1 ATGTGAAGGGAAAGATTGAGGCCGTAACGGCGAATCCGATACCATGAA
* * * * * *
473190 ATGTGATGGGAAAGGTTGAGGCCGAAACGGCAAATCTGGTACCATGAA
1 ATGTGAAGGGAAAGATTGAGGCCGTAACGGCGAATCCGATACCATGAA
* * * * * * *
473238 GATTTGAAGGAAAAGATTGAGGTCGTAAAGGCGAACCCGACACCTTAGAAA
1 -ATGTGAAGGGAAAGATTGAGGCCGTAACGGCGAATCCGATACCAT-G-AA
** *
473289 ACATGACGGGAAAGATTGAGGCCGTAACG
1 ATGTGAAGGGAAAGATTGAGGCCGTAACG
473318 ACGAGTCTTA
Statistics
Matches: 99, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
48 41 0.41
49 32 0.32
50 24 0.24
51 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.18
Consensus pattern (48 bp):
ATGTGAAGGGAAAGATTGAGGCCGTAACGGCGAATCCGATACCATGAA
Found at i:473615 original size:72 final size:72
Alignment explanation
Indices: 473498--473641 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
473488 TTGCAGTGGA
*
473498 GTTGGATTCAAACTATATCTTTTCAATTTTTTACCCTTAAACAAGAAGGACAGATGGAAGATTCT
1 GTTGGATTCAAACTATATCTTTCCAATTTTTTACCCTTAAACAAGAAGGACAGATGGAAGATTCT
473563 GATCTCT
66 GATCTCT
*
473570 GTTGGATTCAAACTATAT-TATTCCAATTTTTTACCCTTAAACAAGAAGGGCAGATGGAAGATTC
1 GTTGGATTCAAACTATATCT-TTCCAATTTTTTACCCTTAAACAAGAAGGACAGATGGAAGATTC
473634 TGATCTCT
65 TGATCTCT
473642 TACACTGATC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 1 0.01
72 68 0.99
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (72 bp):
GTTGGATTCAAACTATATCTTTCCAATTTTTTACCCTTAAACAAGAAGGACAGATGGAAGATTCT
GATCTCT
Found at i:473742 original size:78 final size:78
Alignment explanation
Indices: 473636--474035 Score: 421
Period size: 78 Copynumber: 5.1 Consensus size: 78
473626 GAAGATTCTG
* * * * * *
473636 ATCTCTTACACTGATCATGGGGCAAATTGAAGCCATCTGATCATTTACCCCGAGTCTGGGGTAGA
1 ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCATCTGATCTTTTACCCCGAGCCTGGGGCAGA
* *
473701 TCACAATCAACCA
66 TCACCATCAGCCA
* * * *
473714 ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCAT-TCGATCCTTTACCTCGAGCTTGGGGTAG
1 ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCATCT-GATCTTTTACCCCGAGCCTGGGGCAG
*
473778 ATCACCATTAGCCA
65 ATCACCATCAGCCA
* * * * * * * *
473792 ATCTCTTACCCCGAGCTTGGGGCAGATTGAAGTCATCCGATCTTTTATCCCGAGCCTGAGACAAA
1 ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCATCTGATCTTTTACCCCGAGCCTGGGGCAGA
*
473857 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * *
473870 ATCTCTTA-CCTCGAGCTTGGGGTAGATTGAAGTCATCTGATCTTTTACCCCGAGCCTAGGGCAG
1 ATCTCTTACCCT-GAGCTTGGGGCAAATTGAAGCCATCTGATCTTTTACCCCGAGCCTGGGGCAG
* *
473934 ATCAGCATCAACCA
65 ATCACCATCAGCCA
* * * * * * *
473948 GTCTCTTACCCCGAGCCTAGAG-TAATTGAAGCCAT-TCGATCTTTTACCCCGAGCCTGAGGCAG
1 ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCATCT-GATCTTTTACCCCGAGCCTGGGGCAG
*
474011 ATCACCGTCAGCCA
65 ATCACCATCAGCCA
474025 ATCTCTTACCC
1 ATCTCTTACCC
474036 CACGATAGGG
Statistics
Matches: 268, Mismatches: 49, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
76 1 0.00
77 58 0.22
78 207 0.77
79 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCTGAGCTTGGGGCAAATTGAAGCCATCTGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:473844 original size:39 final size:38
Alignment explanation
Indices: 473653--473935 Score: 110
Period size: 39 Copynumber: 7.3 Consensus size: 38
473643 ACACTGATCA
* * * *
473653 TGGGGCAAATTGAAGCCATCTGATCATTTACCCCGAG-T
1 TGGGGCAGATTGAAGTCATCCGATCTTTTA-CCCGAGCT
* * * * * *
473691 CTGGGGTAGA-TCACAATCAACCAATCTCTTACCCTGAGCT
1 -TGGGGCAGATTGA-AGTCATCCGATCTTTTACCC-GAGCT
* * * *
473731 TGGGGCAAATTGAAGCCATTCGATCCTTTACCTCGAGCT
1 TGGGGCAGATTGAAGTCATCCGATCTTTTACC-CGAGCT
* * * * * *
473770 TGGGGTAGA-TCACCA-TTAGCCAATCTCTTACCCCGAGCT
1 TGGGGCAGATTGA--AGTCATCCGATCTTTTA-CCCGAGCT
*
473809 TGGGGCAGATTGAAGTCATCCGATCTTTTATCCCGAGCC
1 TGGGGCAGATTGAAGTCATCCGATCTTTTA-CCCGAGCT
* * * * * ** *
473848 TGAGACA-AATCACCA-TCAGCTAATCTCTTACCTCGAGCT
1 TGGGGCAGATTGA--AGTCATCCGATCTTTTACC-CGAGCT
* * *
473887 TGGGGTAGATTGAAGTCATCTGATCTTTTACCCCGAGCC
1 TGGGGCAGATTGAAGTCATCCGATCTTTTA-CCCGAGCT
*
473926 TAGGGCAGAT
1 TGGGGCAGAT
473936 CAGCATCAAC
Statistics
Matches: 170, Mismatches: 58, Indels: 32
0.65 0.22 0.12
Matches are distributed among these distances:
38 14 0.08
39 141 0.83
40 15 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (38 bp):
TGGGGCAGATTGAAGTCATCCGATCTTTTACCCGAGCT
Found at i:476371 original size:30 final size:30
Alignment explanation
Indices: 476337--476687 Score: 290
Period size: 30 Copynumber: 11.9 Consensus size: 30
476327 AAAACTTCAT
476337 AAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
* *
476367 AAAAATCACATTTT-ACCCTTAAAC-TTTC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
* * * * *
476395 TAGAAATCATATTTTGACACCTAAACTTCTC
1 -AAAAATTACATTTTGACCCCTAAACTTTTC
* * *
476426 TAAAATTACATTTTAACCCTTAAACTTTTC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
*
476456 CAAAATTACATTTTGA--CCTAAACTTTTC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
* **
476484 CAAAATTACATTTTGACCCCTAATTTTTTTC
1 AAAAATTACATTTTGACCCCTAA-ACTTTTC
* * * * *
476515 CAAAATTACATGTTAACCCTTAAACTTCT-
1 AAAAATTACATTTTGACCCCTAAACTTTTC
* *
476544 ATAAAATTACATTTT-ATCCCTTAAACTTTCC
1 A-AAAATTACATTTTGA-CCCCTAAACTTTTC
* ** *
476575 AAAAATCACATTTAAACCTCTAAACTTTTGC
1 AAAAATTACATTTTGACCCCTAAACTTTT-C
* * *
476606 -AAAATCACATTTTAACCCC-AAACATTTC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
* * * *
476634 CAAAATTACAATTTGA-CCCTGAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTTTC
*
476663 TAAAATTACATTTTGACCCC-AAACT
1 AAAAATTACATTTTGACCCCTAAACT
476688 CATCCAAAAT
Statistics
Matches: 260, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
28 35 0.13
29 65 0.25
30 129 0.50
31 31 0.12
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:476432 original size:89 final size:86
Alignment explanation
Indices: 476338--476700 Score: 338
Period size: 89 Copynumber: 4.1 Consensus size: 86
476328 AAACTTCATA
* * *
476338 AAAATTACATTTTGACCCCTAAACTTTTCAAAAATCACATTTTACCCTTAAACTTTCTAGAAATC
1 AAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTACCC-TAAACTTTCCA-AAATC
* *
476403 ATATTTTGACACCTAAACTTCTCT
64 ACATTTTGAC-CCTAAACTTCTCC
* * *
476427 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGA-CCTAAACTTTTCCAAAATT
1 AAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTT-ACCCTAAAC-TTTCCAAAATC
** *
476491 ACATTTTGACCCCTAATTTTTTTCC
64 ACATTTTGA-CCCTAA-ACTTCTCC
* * *
476516 AAAATTACATGTTAACCCTTAAACTTCT-ATAAAATTACATTTTATCCCTTAAACTTTCCAAAAA
1 AAAATTACATTTTAACCCCTAAACTTTTCA-AAAATTACATTTTA-CCC-TAAACTTTCC-AAAA
** * *
476580 TCACATTTAAACCTCTAAACTTTTGC
62 TCACATTTTGACC-CTAAACTTCTCC
* * * * * *
476606 AAAATCACATTTTAACCCC-AAACATTTCCAAAATTACAATTTGACCCTGAACTTTCCTAAAATT
1 AAAATTACATTTTAACCCCTAAACTTTTCAAAAATTAC-ATTTTACCCTAAACTTTCC-AAAATC
*
476670 ACATTTTGACCCCAAAC-TCATCC
64 ACATTTTGACCCTAAACTTC-TCC
476693 AAAATTAC
1 AAAATTAC
476701 CATGCTACCC
Statistics
Matches: 225, Mismatches: 36, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
86 1 0.00
87 14 0.06
88 46 0.20
89 107 0.48
90 36 0.16
91 21 0.09
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (86 bp):
AAAATTACATTTTAACCCCTAAACTTTTCAAAAATTACATTTTACCCTAAACTTTCCAAAATCAC
ATTTTGACCCTAAACTTCTCC
Found at i:476539 original size:119 final size:115
Alignment explanation
Indices: 476338--476700 Score: 367
Period size: 119 Copynumber: 3.1 Consensus size: 115
476328 AAACTTCATA
* * * * *
476338 AAAATTACATTTTGACCCCTAAACTTTTCAAAAATCACATTTTACCCTTAAACTTTCTAGAAATC
1 AAAATTACATTTTGA-CCCTAAACTTTTCCAAAATCACATTTTACCCCTAAAATTTCCA-AAATT
*
476403 ATATTTTGACACCTAAACTTCTCTAAAATTACATTTTAACCCTTAAACTTTTCC
64 ACA-TTTGAC-CCTAAACTTCTCTAAAATTACATTTTAACCCTTAAACTTTTCC
* **
476457 AAAATTACATTTTGA-CCTAAACTTTTCCAAAATTACATTTTGACCCCTAATTTTTTTCCAAAAT
1 AAAATTACATTTTGACCCTAAACTTTTCCAAAATCACATTTT-ACCCCTAA--AATTTCCAAAAT
* * *
476521 TACATGTTAACCCTTAAACTTCTATAAAATTACATTTTATCCCTTAAAC-TTTCC
63 TACAT-TTGACCC-TAAACTTCTCTAAAATTACATTTTAACCCTTAAACTTTTCC
* ** *
476575 AAAAATCACATTTAAACCTCTAAACTTTTGCAAAATCACATTTTAACCCC-AAACATTTCCAAAA
1 -AAAATTACATTTTGACC-CTAAACTTTTCCAAAATCACATTTT-ACCCCTAAA-ATTTCCAAAA
* * * **
476639 TTACAATTTGACCCTGAACTT-TCCTAAAATTACATTTTGACCC-CAAACTCATCC
62 TTAC-ATTTGACCCTAAACTTCT-CTAAAATTACATTTTAACCCTTAAACTTTTCC
476693 AAAATTAC
1 AAAATTAC
476701 CATGCTACCC
Statistics
Matches: 204, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
117 36 0.18
118 41 0.20
119 89 0.44
120 10 0.05
121 28 0.14
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (115 bp):
AAAATTACATTTTGACCCTAAACTTTTCCAAAATCACATTTTACCCCTAAAATTTCCAAAATTAC
ATTTGACCCTAAACTTCTCTAAAATTACATTTTAACCCTTAAACTTTTCC
Found at i:476711 original size:58 final size:59
Alignment explanation
Indices: 476606--476716 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 59
476596 AAACTTTTGC
* *
476606 AAAATCACATTTTAACCCCAAACATTTCCAAAATTACAATTTGACCCT-GAACTTTCCT
1 AAAATCACATTTTAACCCCAAACATATCCAAAATTACAATCTGACCCTCGAACTTTCCT
* * *
476664 AAAATTACATTTTGACCCCAAAC-TCATCCAAAATTACCATGCT-ACCCTCGAAC
1 AAAATCACATTTTAACCCCAAACAT-ATCCAAAATTACAAT-CTGACCCTCGAAC
476717 ATCCAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.02
58 39 0.87
59 5 0.11
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.28
Consensus pattern (59 bp):
AAAATCACATTTTAACCCCAAACATATCCAAAATTACAATCTGACCCTCGAACTTTCCT
Found at i:478160 original size:24 final size:24
Alignment explanation
Indices: 478116--478161 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
478106 TTTCTAAAAG
**
478116 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGTATTTATTAACATAATAT
*
478140 ATTTTGTATTTATTAACATAAT
1 ATTTAGTATTTATTAACATAAT
478162 TTACTTGACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Found at i:478814 original size:3 final size:3
Alignment explanation
Indices: 478806--478836 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
478796 TAAATTTTAA
478806 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
478837 ATGTTTATAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:485790 original size:9 final size:9
Alignment explanation
Indices: 485776--485802 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
485766 TGATTCATTG
485776 AACAACATC
1 AACAACATC
485785 AACAACATC
1 AACAACATC
485794 AACAACATC
1 AACAACATC
485803 CCCATCCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.11
Consensus pattern (9 bp):
AACAACATC
Found at i:490821 original size:21 final size:19
Alignment explanation
Indices: 490787--490828 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
490777 GAATCACTTG
490787 TTTTGCTGTTATTTTCTACTA
1 TTTTGCTGTTA-TTTC-ACTA
490808 TTTTGCT-TTCATTTCACTA
1 TTTTGCTGTT-ATTTCACTA
490827 TT
1 TT
490829 ATATTGCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 8 0.40
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTGCTGTTATTTCACTA
Found at i:500161 original size:36 final size:36
Alignment explanation
Indices: 500113--500186 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
500103 ATAGACTAAC
500113 TAGGGGGACTTTGATAGTAAATAATTTGAGTAATTT
1 TAGGGGGACTTTGATAGTAAATAATTTGAGTAATTT
*
500149 TAGGGGGCCTTTGATAGTAAATAATTTGAGTAATTT
1 TAGGGGGACTTTGATAGTAAATAATTTGAGTAATTT
500185 TA
1 TA
500187 TTTGCGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.39
Consensus pattern (36 bp):
TAGGGGGACTTTGATAGTAAATAATTTGAGTAATTT
Found at i:502088 original size:16 final size:16
Alignment explanation
Indices: 502067--502097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
502057 TTGTGGATCC
502067 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
502083 CATTTTATCTTTATT
1 CATTTTACCTTTATT
502098 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Done.