Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006060.1 Hibiscus syriacus cultivar Beakdansim tig00014335_pilon, 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: 128914
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2147 original size:24 final size:23
Alignment explanation
Indices: 2081--2150 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
2071 ATTTTAAAAA
* *
2081 TTTTTGTCTTTGTGATATGTTTTT
1 TTTTTGT-TTTGTGACACGTTTTT
* *
2105 TTTTTGTTTTCTTGGCACGTTTTT
1 TTTTTGTTTT-GTGACACGTTTTT
2129 TTTTTGTTATTGTGACACGTTT
1 TTTTTGTT-TTGTGACACGTTT
2151 CGGTAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 3 0.08
24 33 0.87
25 2 0.05
ACGTcount: A:0.09, C:0.09, G:0.17, T:0.66
Consensus pattern (23 bp):
TTTTTGTTTTGTGACACGTTTTT
Found at i:3688 original size:36 final size:36
Alignment explanation
Indices: 3625--3729 Score: 115
Period size: 35 Copynumber: 2.9 Consensus size: 36
3615 ATCTCATTAT
* * *
3625 CATTTTTCAACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTAAAAAAACATTTACCAAACTTTGAAAAAC
* * * *
3661 TATTTTTCAAAGAAA-TTTTACCCAACTTT-AAAAAC
1 CATTTTT-AAAAAAACATTTACCAAACTTTGAAAAAC
*
3696 CATTTTTAAAAAAACATTTATCAAACTTTGAAAA
1 CATTTTTAAAAAAACATTTACCAAACTTTGAAAA
3730 TCATTTAGGC
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
34 6 0.11
35 23 0.42
36 21 0.38
37 5 0.09
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (36 bp):
CATTTTTAAAAAAACATTTACCAAACTTTGAAAAAC
Found at i:15555 original size:20 final size:19
Alignment explanation
Indices: 15522--15560 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
15512 AATTAGAGTT
15522 TTTTTATAAATATAATAATA
1 TTTTTATAAATATAA-AATA
**
15542 TTTTTATATTTATAAAATA
1 TTTTTATAAATATAAAATA
15561 ACTTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTATAAATATAAAATA
Found at i:16546 original size:274 final size:275
Alignment explanation
Indices: 16166--16717 Score: 1043
Period size: 274 Copynumber: 2.0 Consensus size: 275
16156 TGTTTCAAGT
16166 AAATAACCGGTTATGTTATCTTTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATACACGTC
1 AAATAACCGGTTATGTTATCTTTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATACACGTC
*
16231 TAATGGTTTATTTTTATGTTACGATATATATTATTATTAAATTAAAAATAATAAACATATATATT
66 TAATGGTTTATTTTTATGTTACGATATATATTATTATTAAATTAAAAATAATAAACATAGATATT
* *
16296 ACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAAT
131 ACATATTTATTATTATATTTGGTTAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAAT
16361 ATCAAAACAATCAAATAATTTTTTGTGTAAACGAAATTATTAAATTAATATTGTAGGTGGAAAAC
196 ATCAAAACAATCAAATAATTTTTTGTGTAAACGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
16426 ATGAAACACTATTAA
261 ATGAAACAATATTAA
*
16441 AAATAACTGGTTATGTTAT-TTTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATACACGTC
1 AAATAACCGGTTATGTTATCTTTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATACACGTC
16505 TAATGGTTTATTTTTATGTTACGATATATATTATTATTAAATTAAAAATAATAAACATAGATATT
66 TAATGGTTTATTTTTATGTTACGATATATATTATTATTAAATTAAAAATAATAAACATAGATATT
16570 ACATATTTATTATTATATTTGGTTAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAAT
131 ACATATTTATTATTATATTTGGTTAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAAT
*
16635 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
196 ATCAAAACAATCAAATAATTTTTTGTGTAAACGAAATTATTAAATTAATATTGTAGGTGGAAAAC
16700 ATGAAACAATATTAA
261 ATGAAACAATATTAA
16715 AAA
1 AAA
16718 ATTTTGAAAC
Statistics
Matches: 271, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
274 253 0.93
275 18 0.07
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (275 bp):
AAATAACCGGTTATGTTATCTTTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATACACGTC
TAATGGTTTATTTTTATGTTACGATATATATTATTATTAAATTAAAAATAATAAACATAGATATT
ACATATTTATTATTATATTTGGTTAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAAT
ATCAAAACAATCAAATAATTTTTTGTGTAAACGAAATTATTAAATTAATATTGTAGGTGGAAAAC
ATGAAACAATATTAA
Found at i:16927 original size:23 final size:23
Alignment explanation
Indices: 16900--16989 Score: 153
Period size: 23 Copynumber: 3.9 Consensus size: 23
16890 TAAAACTATG
*
16900 ATGTAATAGGTAGCGATTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
16923 ATGTAATAGGTAACGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
16946 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
16969 ATTTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGCGCTTATA
16990 AAATAGGTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:17151 original size:23 final size:23
Alignment explanation
Indices: 17101--17145 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17091 AACATATTTT
* *
17101 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACATAATAC
*
17124 ATTATATAAGCGGTACATAATA
1 ATTATATAAGCGCTACATAATA
17146 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACATAATAC
Found at i:18547 original size:21 final size:21
Alignment explanation
Indices: 18432--18547 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
18422 GCGAAATAAA
**
18432 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
18452 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
18472 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
18493 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
18513 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
18535 AATCGCAACGCGA
1 AATCGCAACGCGA
18548 ATATGAAAAA
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:18559 original size:21 final size:20
Alignment explanation
Indices: 18535--18587 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
18525 GATTTTCCAG
* *
18535 AATCGCAACGCGAATATGAAA
1 AATCGCAACGCGAACA-CAAA
*
18556 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACAAA
18576 AATCGCAACGCG
1 AATCGCAACGCG
18588 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
AATCGCAACGCGAACACAAA
Found at i:18580 original size:20 final size:20
Alignment explanation
Indices: 18555--18728 Score: 244
Period size: 20 Copynumber: 8.7 Consensus size: 20
18545 CGAATATGAA
* *
18555 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
18575 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
18595 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
18615 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
18635 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
18655 ATATCGCAACACGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
18675 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
18695 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
18716 AAATCGCAACGCG
1 AAATCGCAACGCG
18729 ATTTTTAAAG
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
20 119 0.86
21 19 0.14
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:19148 original size:33 final size:33
Alignment explanation
Indices: 19109--19179 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
19099 TTCACTTAGA
19109 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
19142 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
19175 TTTCA
1 TTTCA
19180 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:19285 original size:21 final size:20
Alignment explanation
Indices: 19259--19364 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
19249 TGCAGAAGAG
19259 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
19280 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
19300 TCTGCAACGAGAAAAATG-AAA
1 TC-GCAACGAG-AAAATGAAAA
19321 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
19335 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
19354 TCGCAACGAGA
1 TCGCAACGAGA
19365 GAATCGCAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.16
15 1 0.01
16 2 0.03
17 1 0.01
19 11 0.16
20 17 0.25
21 20 0.29
22 6 0.09
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:19338 original size:14 final size:14
Alignment explanation
Indices: 19319--19375 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19309 AGAAAAATGA
19319 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
19333 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
19352 AATCGCAACGAGAG
1 AATCGCAACGAGAG
19366 AATCGCAACG
1 AATCGCAACG
19376 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:19358 original size:33 final size:33
Alignment explanation
Indices: 19313--19391 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
19303 GCAACGAGAA
19313 AAATG-AAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
19345 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
19378 AAACCAAAATCGCA
1 AAATGAAAATCGCA
19392 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 5 0.11
33 39 0.89
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:19409 original size:19 final size:19
Alignment explanation
Indices: 19387--19500 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
19377 GAAACCAAAA
*
19387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19406 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19425 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
19439 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
19459 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
19479 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
19499 TC
1 TC
19501 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 31 0.39
20 19 0.24
21 14 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19462 original size:21 final size:21
Alignment explanation
Indices: 19436--19500 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
19426 CGCGTTGCGA
19436 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
19457 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
19477 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
19498 TTC
1 TTC
19501 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:21343 original size:93 final size:92
Alignment explanation
Indices: 21184--21405 Score: 417
Period size: 93 Copynumber: 2.4 Consensus size: 92
21174 TAGATTGCTT
*
21184 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21249 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
*
21277 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21342 TTTGTCTTTGTTTTGTCTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTGGTTGAA
21369 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
21406 AATACCCTGA
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 46 0.37
93 80 0.63
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTGGTTGAA
Found at i:21556 original size:33 final size:33
Alignment explanation
Indices: 21503--21626 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
21493 TAGTTTACTT
* * *
21503 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
21537 TCACAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
21570 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
21603 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
21627 TTGCGAGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:21562 original size:19 final size:18
Alignment explanation
Indices: 21535--21626 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 18
21525 GCAACGAGAG
*
21535 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
21554 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
21568 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
21587 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
21601 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
21620 AATCGCA
1 AATCGCA
21627 TTGCGAGTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 25 0.42
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:21573 original size:14 final size:14
Alignment explanation
Indices: 21552--21610 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
21542 ACGCGAAATG
21552 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
21566 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
21585 AAAATCGCAACGAC
1 AAAATCGCAACGAC
21599 AAAATCGCAACG
1 AAAATCGCAACG
21611 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:21644 original size:19 final size:18
Alignment explanation
Indices: 21622--21758 Score: 74
Period size: 19 Copynumber: 7.8 Consensus size: 18
21612 GAAACCAAAA
21622 TCGCATTGCGAGTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
21641 TCGCGTTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
21657 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
21674 TCGCATTGCGA-TTC-TG
1 TCGCATTGCGATTTCATT
**
21690 TCG--TTGCGATTTTGGTT
1 TCGCATTGCGA-TTTCATT
* **
21707 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGA-TTTCATT
* *
21726 TCTCGTTGCGATTCTCATT
1 TCGCATTGCGATT-TCATT
*
21745 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
21759 TAAGTTTCGT
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
14 12 0.12
16 13 0.13
17 14 0.14
18 3 0.03
19 55 0.57
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:21663 original size:14 final size:14
Alignment explanation
Indices: 21644--21700 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
21634 TTTCATTTCG
21644 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21658 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
21675 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
21691 CGTTGCGATT
1 CGTTGCGATT
21701 TTGGTTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21671 original size:33 final size:33
Alignment explanation
Indices: 21627--21757 Score: 154
Period size: 33 Copynumber: 3.8 Consensus size: 33
21617 CAAAATCGCA
*
21627 TTGCGAGTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
21660 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
21693 TTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
21731 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
21758 TTAAGTTTCG
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
33 53 0.65
35 1 0.01
36 1 0.01
38 27 0.33
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23717 original size:14 final size:14
Alignment explanation
Indices: 23698--23733 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
23688 ATTGTTTAAT
23698 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
23712 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
23726 TGATTTGT
1 TGATTTGT
23734 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:23848 original size:19 final size:19
Alignment explanation
Indices: 23824--23911 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
23814 GCATTATGTT
23824 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
23843 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
23860 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
23876 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
23895 AGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
23912 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:23914 original size:53 final size:52
Alignment explanation
Indices: 23824--23930 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 52
23814 GCATTATGTT
23824 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
23876 GAAATGAAAATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
23929 GA
1 GA
23931 TTTCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:23955 original size:19 final size:19
Alignment explanation
Indices: 23920--24177 Score: 276
Period size: 19 Copynumber: 14.7 Consensus size: 19
23910 AACGAGAGAA
*
23920 TCGCAATGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
23938 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23957 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
23974 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
23990 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
24009 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
24025 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24042 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
24061 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
24078 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24095 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24114 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24133 TCCGCATTGCGA-TTTC--T
1 T-CGCATTGCGATTTTCATT
*
24150 T-G--TTGGGA-TTTCATT
1 TCGCATTGCGATTTTCATT
24165 TCGCATTGCGATT
1 TCGCATTGCGATT
24178 CTCTCGTTGC
Statistics
Matches: 206, Mismatches: 9, Indels: 49
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.04
14 18 0.09
15 6 0.03
16 19 0.09
17 17 0.08
18 27 0.13
19 80 0.39
20 30 0.15
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:23986 original size:52 final size:51
Alignment explanation
Indices: 23926--24191 Score: 385
Period size: 52 Copynumber: 5.1 Consensus size: 51
23916 AGAATCGCAA
23926 TGCGATTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
23978 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
24029 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGA-TTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
24082 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * *** *
24133 TCCGCATTGCGATTTCTTGTTGGGA-TTTCATTTCGCATTGCGATTCTCTCGT
1 TGCG-ATTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
24185 TGCGATT
1 TGCGATT
24192 GTAATTTCCG
Statistics
Matches: 198, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
50 2 0.01
51 55 0.28
52 87 0.44
53 54 0.27
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (51 bp):
TGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:24146 original size:72 final size:70
Alignment explanation
Indices: 24002--24127 Score: 106
Period size: 72 Copynumber: 1.9 Consensus size: 70
23992 GCATTGCGAT
* *
24002 TTTCATTTCGCATTGCGAT--TC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTT-TCAT
1 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCTC-G
*
24060 TTCCGCA
65 TTGCG-A
* * *
24067 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTT
1 TTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
24128 TCATTTCCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
65 3 0.06
66 3 0.06
67 10 0.20
69 2 0.04
70 4 0.08
72 28 0.56
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (70 bp):
TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCTCGT
TGCGA
Found at i:24173 original size:31 final size:33
Alignment explanation
Indices: 23943--24210 Score: 219
Period size: 33 Copynumber: 7.8 Consensus size: 33
23933 TCATTTCGCA
23943 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGA-TTTCATTTCCGCATTGCGATTCTCTCG
*
23977 TTGCGATTTCATTT-CGCATTGCGATT-T-TCA
1 TTGCGATTTCATTTCCGCATTGCGATTCTCTCG
* * *
24007 TTTCGCATTGCGATTCTCTCG--TTGCGATTTTCATTTCG
1 TTGCG-ATTTC-ATT-TC-CGCATTGCGA--TTC-TCTCG
24045 CATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 --TTGCGA-TTTCATTTCCGCATTGCGATTCTCTCG
*
24081 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
1 TTGCGA-TTTCATTTCCGCATTGCGA--TTC-TCTCG
*
24117 CATTGCGATTTTCATTTCCGCATTGCGATT-TCTTG
1 --TTGCGA-TTTCATTTCCGCATTGCGATTCTCTCG
*
24152 TTGGGATTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATTTCATTTCCGCATTGCGATTCTCTCG
* **
24184 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-TCATTTCCGCATTGCGAT
24211 AGTCAAATGC
Statistics
Matches: 194, Mismatches: 16, Indels: 48
0.75 0.06 0.19
Matches are distributed among these distances:
30 6 0.03
31 17 0.09
32 34 0.18
33 35 0.18
34 30 0.15
35 10 0.05
36 8 0.04
37 8 0.04
38 19 0.10
39 20 0.10
40 7 0.04
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTCATTTCCGCATTGCGATTCTCTCG
Found at i:26491 original size:12 final size:12
Alignment explanation
Indices: 26474--26498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26464 TCTTCGAGGA
26474 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26486 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26498 C
1 C
26499 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27440 original size:20 final size:20
Alignment explanation
Indices: 27412--27640 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
27402 AAATTTCAGT
* * *
27412 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27432 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27452 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27472 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
27492 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27512 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27532 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
27552 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
27572 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27592 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27612 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27632 GTTGCGATT
1 GTTGCGATT
27641 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27693 original size:21 final size:20
Alignment explanation
Indices: 27608--27705 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
27598 ATTTATGTGT
* *
27608 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
27628 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
27649 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
27670 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
27691 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
27706 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:27701 original size:42 final size:43
Alignment explanation
Indices: 27608--27706 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
27598 ATTTATGTGT
* *
27608 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
27649 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
27691 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
27707 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:34329 original size:5 final size:5
Alignment explanation
Indices: 34302--34341 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
34292 AGACACGTAT
34302 GACCAC GACCAC GACCAC GACCC GACCC GACCC GACCC GA
1 GACC-C GACC-C GACC-C GACCC GACCC GACCC GACCC GA
34342 GACGGCGGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.53
6 16 0.47
ACGTcount: A:0.28, C:0.53, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:34998 original size:41 final size:41
Alignment explanation
Indices: 34915--35058 Score: 238
Period size: 41 Copynumber: 3.5 Consensus size: 41
34905 TTTTTAATTT
*
34915 ACTGTAGACTATCGCAA--CGAATTTGAAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAA-ATGAAAAATCGCAACGAC
*
34955 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGAC
*
34996 ACTGTAGACTAGCGCAACGCGAAATGAAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGAC
35037 ACTGTAGACTATCGCAACGCGA
1 ACTGTAGACTATCGCAACGCGA
35059 TTTTCAACTA
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
40 17 0.18
41 76 0.78
42 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGAC
Found at i:35087 original size:21 final size:21
Alignment explanation
Indices: 34962--35087 Score: 66
Period size: 21 Copynumber: 6.1 Consensus size: 21
34952 GACACTGTAG
*
34962 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
34983 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
*
35002 GACTAGCGCAACGCGAAATG-A
1 -ACTATCGCAACGCGAAATGCA
** * *
35023 AAAATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
** *
35043 GACTATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGCA
35065 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
35086 AC
1 AC
35088 ATGAATTTGC
Statistics
Matches: 76, Mismatches: 19, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
18 6 0.08
19 7 0.09
20 16 0.21
21 36 0.47
22 5 0.07
23 6 0.08
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:37269 original size:16 final size:16
Alignment explanation
Indices: 37248--37280 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
37238 AGAATTTCTG
*
37248 AATTATTCAATATTTA
1 AATTATTCAACATTTA
37264 AATTATTCAACATTTA
1 AATTATTCAACATTTA
37280 A
1 A
37281 TCATTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATTCAACATTTA
Found at i:37517 original size:22 final size:22
Alignment explanation
Indices: 37492--37546 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
37482 TTATCCTATC
*
37492 ATTTTAATACTCATATTTTAAA-
1 ATTTTAATAATCAT-TTTTAAAT
*
37514 ATTTATAAGAATCATTTTTAAAT
1 ATTT-TAATAATCATTTTTAAAT
*
37537 AATTTAATAA
1 ATTTTAATAA
37547 ATTACTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTTAATAATCATTTTTAAAT
Found at i:41453 original size:15 final size:15
Alignment explanation
Indices: 41433--41473 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
41423 GTTGGTATCT
41433 GCGATTGTTTCACTA
1 GCGATTGTTTCACTA
41448 GCGATTGTTTCACTA
1 GCGATTGTTTCACTA
41463 GCGATTGTTTC
1 GCGATTGTTTC
41474 GTTTCGGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (15 bp):
GCGATTGTTTCACTA
Found at i:42711 original size:18 final size:18
Alignment explanation
Indices: 42685--42758 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
42675 TCAGAACTTC
42685 GGCGGCATGGGCGGTATG
1 GGCGGCATGGGCGGTATG
* *
42703 GGTGGCATGGGCGGAATG
1 GGCGGCATGGGCGGTATG
* * *
42721 GGCGGAATGGGTGGCATG
1 GGCGGCATGGGCGGTATG
* *
42739 GGCGGAATGGGTGGTATG
1 GGCGGCATGGGCGGTATG
42757 GG
1 GG
42759 TGACATGATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.15, C:0.11, G:0.57, T:0.18
Consensus pattern (18 bp):
GGCGGCATGGGCGGTATG
Found at i:42723 original size:27 final size:27
Alignment explanation
Indices: 42685--42765 Score: 126
Period size: 27 Copynumber: 3.0 Consensus size: 27
42675 TCAGAACTTC
*
42685 GGCGGCATGGGCGGTATGGGTGGCATG
1 GGCGGAATGGGCGGTATGGGTGGCATG
*
42712 GGCGGAATGGGCGGAATGGGTGGCATG
1 GGCGGAATGGGCGGTATGGGTGGCATG
* *
42739 GGCGGAATGGGTGGTATGGGTGACATG
1 GGCGGAATGGGCGGTATGGGTGGCATG
42766 ATGGGCGGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.16, C:0.11, G:0.54, T:0.19
Consensus pattern (27 bp):
GGCGGAATGGGCGGTATGGGTGGCATG
Found at i:42760 original size:9 final size:9
Alignment explanation
Indices: 42685--42749 Score: 76
Period size: 9 Copynumber: 7.2 Consensus size: 9
42675 TCAGAACTTC
*
42685 GGCGGCATG
1 GGCGGAATG
*
42694 GGCGGTATG
1 GGCGGAATG
* *
42703 GGTGGCATG
1 GGCGGAATG
42712 GGCGGAATG
1 GGCGGAATG
42721 GGCGGAATG
1 GGCGGAATG
* *
42730 GGTGGCATG
1 GGCGGAATG
42739 GGCGGAATG
1 GGCGGAATG
42748 GG
1 GG
42750 TGGTATGGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.15, C:0.12, G:0.57, T:0.15
Consensus pattern (9 bp):
GGCGGAATG
Found at i:42778 original size:21 final size:21
Alignment explanation
Indices: 42745--42800 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
42735 CATGGGCGGA
* *
42745 ATGGGTGGTATGGGTGACATG
1 ATGGGCGGCATGGGTGACATG
42766 ATGGGCGGCATGGGTGACATG
1 ATGGGCGGCATGGGTGACATG
42787 ATGGGCGGCATGGG
1 ATGGGCGGCATGGG
42801 CGGCATGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.50, T:0.21
Consensus pattern (21 bp):
ATGGGCGGCATGGGTGACATG
Found at i:42807 original size:21 final size:21
Alignment explanation
Indices: 42709--42807 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
42699 TATGGGTGGC
*
42709 ATGGGCGGAATGGGCGG-A--
1 ATGGGCGGCATGGGCGGCATG
*
42727 ATGGGTGGCATGGGCGG-A--
1 ATGGGCGGCATGGGCGGCATG
* * * *
42745 ATGGGTGGTATGGGTGACATG
1 ATGGGCGGCATGGGCGGCATG
* *
42766 ATGGGCGGCATGGGTGACATG
1 ATGGGCGGCATGGGCGGCATG
42787 ATGGGCGGCATGGGCGGCATG
1 ATGGGCGGCATGGGCGGCATG
42808 GGTGAGTTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
18 30 0.43
19 1 0.01
21 38 0.55
ACGTcount: A:0.18, C:0.12, G:0.52, T:0.18
Consensus pattern (21 bp):
ATGGGCGGCATGGGCGGCATG
Found at i:45932 original size:34 final size:34
Alignment explanation
Indices: 45894--45961 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
45884 CTCAAAAAGA
*
45894 GTATCATTCTGATGCTCAATAGTCCAAAATTAAC
1 GTATCATTCTGATGCCCAATAGTCCAAAATTAAC
*
45928 GTATCATTCTGATGCCCAGTAGTCCAAAATTAAC
1 GTATCATTCTGATGCCCAATAGTCCAAAATTAAC
45962 TACTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (34 bp):
GTATCATTCTGATGCCCAATAGTCCAAAATTAAC
Found at i:47614 original size:6 final size:6
Alignment explanation
Indices: 47603--47627 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47593 GGACCATCTT
47603 CTCTAC CTCTAC CTCTAC CTCTAC C
1 CTCTAC CTCTAC CTCTAC CTCTAC C
47628 ACGGCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTAC
Found at i:49521 original size:21 final size:20
Alignment explanation
Indices: 49497--49541 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
49487 TTTAAATAAG
*
49497 CTTTGACTAGAAGTTTCGAAA
1 CTTTGACAAG-AGTTTCGAAA
*
49518 CTTTTACAAGAGTTTCGAAA
1 CTTTGACAAGAGTTTCGAAA
49538 CTTT
1 CTTT
49542 CCAAGACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CTTTGACAAGAGTTTCGAAA
Found at i:49603 original size:20 final size:19
Alignment explanation
Indices: 49561--49616 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
49551 TAGCCCAAAA
*
49561 AGTTTCGATACTTTCATAT
1 AGTTTCGAAACTTTCATAT
49580 AGTTTCGAAACTATCTCA-AT
1 AGTTTCGAAACT-T-TCATAT
*
49600 AGTTTCAAAACTTTCAT
1 AGTTTCGAAACTTTCAT
49617 TAAAGTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.09
19 12 0.38
20 14 0.44
21 3 0.09
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (19 bp):
AGTTTCGAAACTTTCATAT
Found at i:49623 original size:20 final size:20
Alignment explanation
Indices: 49559--49624 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
49549 AGTAGCCCAA
*
49559 AAAGTTTCGATACTTTCA-T
1 AAAGTTTCGAAACTTTCATT
* * *
49578 ATAGTTTCGAAACTATC-TC
1 AAAGTTTCGAAACTTTCATT
*
49597 AATAGTTTCAAAACTTTCATT
1 AA-AGTTTCGAAACTTTCATT
49618 AAAGTTT
1 AAAGTTT
49625 TGATACTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
19 15 0.42
20 18 0.50
21 3 0.08
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
AAAGTTTCGAAACTTTCATT
Found at i:55503 original size:12 final size:12
Alignment explanation
Indices: 55486--55516 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55476 AGATGACACA
55486 GAATAAAAATTC
1 GAATAAAAATTC
55498 GAATAAAAATTC
1 GAATAAAAATTC
*
55510 AAATAAA
1 GAATAAA
55517 CAGGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (12 bp):
GAATAAAAATTC
Found at i:56403 original size:29 final size:29
Alignment explanation
Indices: 56353--56409 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
56343 GGGTTAAAAG
*
56353 CTTGGTCGTCGGACGTGCATGGCAACCTC
1 CTTGGTCGCCGGACGTGCATGGCAACCTC
* *
56382 CTTGGTCGCCCGGA-GTGTATGGCGACCT
1 CTTGGTCG-CCGGACGTGCATGGCAACCT
56410 AGGAGGTCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (29 bp):
CTTGGTCGCCGGACGTGCATGGCAACCTC
Found at i:56799 original size:16 final size:16
Alignment explanation
Indices: 56778--56808 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56768 TAATATTTCA
56778 GGTCGGATCGAGTTCG
1 GGTCGGATCGAGTTCG
*
56794 GGTCGGATTGAGTTC
1 GGTCGGATCGAGTTC
56809 AAATGGAAGA
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:0.13, C:0.16, G:0.42, T:0.29
Consensus pattern (16 bp):
GGTCGGATCGAGTTCG
Found at i:56990 original size:8 final size:8
Alignment explanation
Indices: 56977--57001 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56967 AAGGATAGGA
56977 TTAAGATT
1 TTAAGATT
56985 TTAAGATT
1 TTAAGATT
56993 TTAAGATT
1 TTAAGATT
57001 T
1 T
57002 ACTTCATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTAAGATT
Found at i:57232 original size:4 final size:4
Alignment explanation
Indices: 57215--57245 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
57205 GCCAAATCAA
*
57215 ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
57246 CTTGAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:67792 original size:55 final size:55
Alignment explanation
Indices: 67708--67820 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
67698 CTAATGGATG
*
67708 TAAATCAGTAATCATTTGCTTTGGCTTTGTAATTTCCTTTATTATAAGTGTTTGA
1 TAAATCAGTAATCATTTGATTTGGCTTTGTAATTTCCTTTATTATAAGTGTTTGA
67763 TAAATCAGTAATCATTTGATTTGGCTTTGTAATTTCCTTTATTATAAGTGTTTGA
1 TAAATCAGTAATCATTTGATTTGGCTTTGTAATTTCCTTTATTATAAGTGTTTGA
67818 TAA
1 TAA
67821 CGATTTCTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (55 bp):
TAAATCAGTAATCATTTGATTTGGCTTTGTAATTTCCTTTATTATAAGTGTTTGA
Found at i:69593 original size:31 final size:31
Alignment explanation
Indices: 69555--69628 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
69545 AATTTGCGTC
*
69555 AATATAACCATTGAACTATTTAAAAGGATTT
1 AATATAACCACTGAACTATTTAAAAGGATTT
69586 AATATAACCACTGAACTATTTAAAAGGATTT
1 AATATAACCACTGAACTATTTAAAAGGATTT
69617 AATATAACCACT
1 AATATAACCACT
69629 ATAAGTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (31 bp):
AATATAACCACTGAACTATTTAAAAGGATTT
Found at i:72950 original size:31 final size:29
Alignment explanation
Indices: 72891--72983 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 29
72881 TTTTACATTG
* *
72891 AAGTACTTAAAGTATTTTTTGATAAAAAT
1 AAGTACCTAAAGTATTTTTTGGTAAAAAT
*
72920 AAGTACCTAAAGTTATCTTTTTGGTTAAAAT
1 AAGTACCTAAAG-TAT-TTTTTGGTAAAAAT
* * *
72951 AGGTACCTAAAGTA-TTTTAGGTCAAAAT
1 AAGTACCTAAAGTATTTTTTGGTAAAAAT
72979 AAGTA
1 AAGTA
72984 TTTTAAAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
28 16 0.29
29 11 0.20
30 5 0.09
31 23 0.42
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (29 bp):
AAGTACCTAAAGTATTTTTTGGTAAAAAT
Found at i:72978 original size:28 final size:30
Alignment explanation
Indices: 72915--72983 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
72905 TTTTTTGATA
* *
72915 AAAATAAGTACCTAAAGTTATCTTTTTGGTT
1 AAAATAAGTACCTAAAGTTA-CTTTTAGGTC
*
72946 AAAATAGGTACCTAAAG-TA-TTTTAGGTC
1 AAAATAAGTACCTAAAGTTACTTTTAGGTC
72974 AAAATAAGTA
1 AAAATAAGTA
72984 TTTTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.47
30 2 0.06
31 16 0.47
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (30 bp):
AAAATAAGTACCTAAAGTTACTTTTAGGTC
Found at i:73255 original size:60 final size:59
Alignment explanation
Indices: 73191--73332 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 59
73181 ATCGGTCATT
* * *
73191 AAACTTTTAAATATTTTAATTTCATACAT-AAGCTATTAT-TATCATTCTAAATTAGT-CCTC
1 AAACTTTTAAACATTTTAATTTCAT-CATCAAACTATGATAT-TCATTCT-AATTAGTACC-C
* * *
73251 AAACTTTTGAACATTTTAGTTTCATCCTCAAACTATGATATTCATTCTAATTAGTACCC
1 AAACTTTTAAACATTTTAATTTCATCATCAAACTATGATATTCATTCTAATTAGTACCC
* *
73310 AAACTTTTTGAACATTTCAATTT
1 AAAC-TTTTAAACATTTTAATTT
73333 TATCCCAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
59 14 0.20
60 55 0.79
61 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.44
Consensus pattern (59 bp):
AAACTTTTAAACATTTTAATTTCATCATCAAACTATGATATTCATTCTAATTAGTACCC
Found at i:74241 original size:18 final size:16
Alignment explanation
Indices: 74191--74242 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 16
74181 AATCTTGTTT
74191 ATATATTTTAATTAGTA
1 ATATATTTTAATTA-TA
74208 ATATATTTGTACATTATA
1 ATATATTT-TA-ATTATA
74226 ATGATTATTTTAATTAT
1 AT-A-TATTTTAATTAT
74243 TCAATAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.26
18 11 0.35
19 7 0.23
20 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:77149 original size:33 final size:31
Alignment explanation
Indices: 77082--77149 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
77072 CTTAAAGTAT
* * * *
77082 TTTTTGTCAAAATAAGTATTTAAATTTATCA
1 TTTTGGTCAAAATAAATAGTTAAATTTATAA
77113 TTTTGGTCAAAATAAATAGTTAACTATTTATAA
1 TTTTGGTCAAAATAAATAGTTAA--ATTTATAA
77146 TTTT
1 TTTT
77150 TAATCTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 20 0.65
33 11 0.35
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTTGGTCAAAATAAATAGTTAAATTTATAA
Found at i:78562 original size:14 final size:15
Alignment explanation
Indices: 78543--78581 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
78533 TAATGGTTAG
78543 TAAATCCCTGCG-AA
1 TAAATCCCTGCGTAA
78557 TAAATCCCTGCGTAA
1 TAAATCCCTGCGTAA
*
78572 -AAATCTCTGC
1 TAAATCCCTGC
78582 TTATAGACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (15 bp):
TAAATCCCTGCGTAA
Found at i:79079 original size:14 final size:14
Alignment explanation
Indices: 79060--79089 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
79050 CACCGTAGTC
79060 TTCCCTCTCTCAAT
1 TTCCCTCTCTCAAT
79074 TTCCCTCTCTCAAT
1 TTCCCTCTCTCAAT
79088 TT
1 TT
79090 TTAACAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.40, G:0.00, T:0.47
Consensus pattern (14 bp):
TTCCCTCTCTCAAT
Found at i:80500 original size:21 final size:20
Alignment explanation
Indices: 80463--80506 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
80453 TAAAATATTT
*
80463 TATCTTTATATTGTTAAAATA
1 TATCTTTATATTATTAAAA-A
80484 TATCATTTA-ATTATTAAAAA
1 TATC-TTTATATTATTAAAAA
80504 TAT
1 TAT
80507 TATAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TATCTTTATATTATTAAAAA
Found at i:80513 original size:32 final size:34
Alignment explanation
Indices: 80477--80542 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
80467 TTTATATTGT
80477 TAAAATATATCA-TTTAATTA-TTAAAAATATTA
1 TAAAATATATCATTTTAATTATTTAAAAATATTA
* *
80509 TAAAATATATTATTTTAATTATTTTAAAATATTA
1 TAAAATATATCATTTTAATTATTTAAAAATATTA
80543 ATATATTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.37
33 8 0.27
34 11 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (34 bp):
TAAAATATATCATTTTAATTATTTAAAAATATTA
Found at i:80520 original size:24 final size:24
Alignment explanation
Indices: 80493--80540 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
80483 ATATCATTTA
80493 ATTATTAAAAATATTATAAAATAT
1 ATTATTAAAAATATTATAAAATAT
** * *
80517 ATTATTTTAATTATTTTAAAATAT
1 ATTATTAAAAATATTATAAAATAT
80541 TAATATATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTAAAAATATTATAAAATAT
Found at i:81054 original size:19 final size:19
Alignment explanation
Indices: 81030--81066 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
81020 GAATGCATTT
81030 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
*
81049 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
81067 GGCTATTTTT
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:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
CATGCACCGATGCACTCTC
Found at i:86988 original size:23 final size:24
Alignment explanation
Indices: 86937--86997 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 24
86927 GCACTTAACA
86937 ATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCATCCCTTTGAAT
* *
86961 GTGCATCGATGCATGCC-TTGAAT
1 ATGCATCGATGCATCCCTTTGAAT
86984 ATGCATCGATGCAT
1 ATGCATCGATGCAT
86998 AAGACCATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
ATGCATCGATGCATCCCTTTGAAT
Found at i:88967 original size:16 final size:16
Alignment explanation
Indices: 88946--88978 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
88936 TTGTTGGTTG
*
88946 ATGAATGCTTGGACTT
1 ATGAATGCTTGAACTT
88962 ATGAATGCTTGAACTT
1 ATGAATGCTTGAACTT
88978 A
1 A
88979 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (16 bp):
ATGAATGCTTGAACTT
Found at i:90877 original size:18 final size:19
Alignment explanation
Indices: 90835--90874 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
90825 TTTGGTTCAC
**
90835 GGAATGTAAGATTATTAGTG
1 GGAATGTAAGATTACCAG-G
90855 GGAATGTAAGATTACCAGG
1 GGAATGTAAGATTACCAGG
90874 G
1 G
90875 AATAAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:94404 original size:30 final size:30
Alignment explanation
Indices: 94370--94433 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
94360 CCACCCTGAA
94370 ATTTTATTTGTGCTCAGGTCACACGAAAAT
1 ATTTTATTTGTGCTCAGGTCACACGAAAAT
94400 ATTTTATTTGTGCTCAGGTCACACGAAAAT
1 ATTTTATTTGTGCTCAGGTCACACGAAAAT
94430 ATTT
1 ATTT
94434 GTTGTTCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (30 bp):
ATTTTATTTGTGCTCAGGTCACACGAAAAT
Found at i:97281 original size:15 final size:15
Alignment explanation
Indices: 97261--97318 Score: 116
Period size: 15 Copynumber: 3.9 Consensus size: 15
97251 TTTCTCATCT
97261 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
97276 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
97291 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
97306 CTGAATGATTCAG
1 CTGAATGATTCAG
97319 CATAAAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:97497 original size:357 final size:352
Alignment explanation
Indices: 96788--97497 Score: 1208
Period size: 357 Copynumber: 2.0 Consensus size: 352
96778 GAATAAAATT
96788 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGATGTTTGTTTGGCTCTGAATG
1 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGATGTTTGTTTGGCTCTGAATG
* *
96853 AAACCATTCAACGATGAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTTTCATCTCTGAATG
66 AAACCATTCAACGATGAATGCTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
* *
96918 ATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGACTGATTCAGCATAGAAGTACATTTTGAATG
131 ATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCAGCATAAAAGTACATTTTGAATG
96983 ATTCAGAGTCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCAT
196 ATTCAGAGTCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCAT
97048 TCAACATTTGAATAATTCAGCGCTTAATCATTATGAAATAAATAAACAACCCCTAAGACAAGAAC
261 TCAACATTTGAATAATTCAGCGCTTAATCATTATGAAATAAATAAACAACCCCTAAGACAAGAAC
* *
97113 AACTCTACATCAGTTTACGCCGCGAAA
326 AACTCTACAGCAGTTTACGCAGCGAAA
* *
97140 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAATTAA-GGGTTGTTTGTTTGGCT-TGAATG
1 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGATGTTTGTTTGGCTCTGAATG
* * *
97203 AAATCATTCAGCGCTGAATGCTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
66 AAACCATTCAACGATGAATGCTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
*
97268 ATTCAGTGCTGAATGATTCAGTGCTGAATGATTCAGTGCTGAATGATTCAGCATAAAAGTACATT
131 ATTCAGTGCTGAATGATTCA--GC--AA--A-ACAGTGCTGAATGATTCAGCATAAAAGTACATT
97333 TTGAATGATTCAGAGTCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCT
189 TTGAATGATTCAGAGTCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCT
* * *
97398 GAATCATTCAATATTTGAATAATTCAGCGCTTAATCATTCTGAAATAAATAAACAACCCCTAAGG
254 GAATCATTCAACATTTGAATAATTCAGCGCTTAATCATTATGAAATAAATAAACAACCCCTAAGA
97463 CAAGAACAACTCTACAGCAGTTTACGCAGCGAAA
319 CAAGAACAACTCTACAGCAGTTTACGCAGCGAAA
97497 T
1 T
97498 ACCCACACAA
Statistics
Matches: 336, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
350 86 0.26
351 16 0.05
352 41 0.12
354 2 0.01
356 1 0.00
357 190 0.57
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (352 bp):
TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGATGTTTGTTTGGCTCTGAATG
AAACCATTCAACGATGAATGCTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
ATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCAGCATAAAAGTACATTTTGAATG
ATTCAGAGTCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCAT
TCAACATTTGAATAATTCAGCGCTTAATCATTATGAAATAAATAAACAACCCCTAAGACAAGAAC
AACTCTACAGCAGTTTACGCAGCGAAA
Found at i:98390 original size:19 final size:20
Alignment explanation
Indices: 98366--98404 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
98356 CCGGTTTTAG
98366 TGAATT-ATAATGAACCGTT
1 TGAATTGATAATGAACCGTT
**
98385 TGAATTGATTTTGAACCGTT
1 TGAATTGATAATGAACCGTT
98405 CAAATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
TGAATTGATAATGAACCGTT
Found at i:98483 original size:23 final size:21
Alignment explanation
Indices: 98437--98490 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
98427 CGGTTCAACC
*
98437 TAAATTTTTTTGATTTTTTGT
1 TAAATTTTTTAGATTTTTTGT
98458 TAAATATTTTTAGTATTTTTAT-T
1 TAAAT-TTTTTAG-ATTTTT-TGT
98481 T-AATTTTTTA
1 TAAATTTTTTA
98491 AATAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 11 0.38
22 9 0.31
23 8 0.28
24 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TAAATTTTTTAGATTTTTTGT
Found at i:104043 original size:2 final size:2
Alignment explanation
Indices: 104036--104066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104026 GAAATAACTT
104036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104067 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104901 original size:31 final size:33
Alignment explanation
Indices: 104866--104938 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
104856 GTTTATTTTG
*
104866 ATTTTGTCCCT-TCATTTT-TACGGTTAATTAT
1 ATTTTGTCCCTCTCATTTTCTACGATTAATTAT
* *
104897 ATTTTAT-CCTCTCATTTTCTATGATTAATTAT
1 ATTTTGTCCCTCTCATTTTCTACGATTAATTAT
*
104929 ACTTTGTCCC
1 ATTTTGTCCC
104939 CTTAAGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 3 0.09
31 13 0.38
32 16 0.47
33 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (33 bp):
ATTTTGTCCCTCTCATTTTCTACGATTAATTAT
Found at i:106401 original size:21 final size:21
Alignment explanation
Indices: 106366--106408 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
106356 ATATTTTATC
*
106366 TTTATATTGTTAAAAAATATTA
1 TTTATATTATT-AAAAATATTA
106388 TTTA-ATTATTAAAAATATTA
1 TTTATATTATTAAAAATATTA
106408 T
1 T
106409 AAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTATATTATTAAAAATATTA
Found at i:106412 original size:32 final size:34
Alignment explanation
Indices: 106376--106441 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
106366 TTTATATTGT
106376 TAAAAAATATTA-TTTAATTA-TTAAAAATATTA
1 TAAAAAATATTATTTTAATTATTTAAAAATATTA
* *
106408 TAAAATATATTATTTTAATTATTTTAAAATATTA
1 TAAAAAATATTATTTTAATTATTTAAAAATATTA
106442 ATATATTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.37
33 8 0.27
34 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TAAAAAATATTATTTTAATTATTTAAAAATATTA
Found at i:106419 original size:24 final size:24
Alignment explanation
Indices: 106392--106439 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
106382 ATATTATTTA
106392 ATTATTAAAAATATTATAAAATAT
1 ATTATTAAAAATATTATAAAATAT
** * *
106416 ATTATTTTAATTATTTTAAAATAT
1 ATTATTAAAAATATTATAAAATAT
106440 TAATATATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTAAAAATATTATAAAATAT
Found at i:112899 original size:15 final size:15
Alignment explanation
Indices: 112879--112921 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
112869 TTTCTCATCT
112879 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
112894 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
112909 CTGAATGATTCAG
1 CTGAATGATTCAG
112922 CATAGAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:113080 original size:343 final size:337
Alignment explanation
Indices: 112420--113100 Score: 1184
Period size: 343 Copynumber: 2.0 Consensus size: 337
112410 GAATAAAAAT
112420 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGTTGTTTGTTTGGCTCTGAATG
1 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGTTGTTTGTTTGGCTCTGAATG
*
112485 AAACCATTCAACGCTGAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGACTG
66 AAACCATTCAACGCTGAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
*
112550 ATTCAGCAAAACAGTGCTGACTGATTCAGCATAGAAGTACATTTTGAATGATTCAGAGTCATTAT
131 ATTCAGCAAAACAGTGCTGAATGATTCAGCATAGAAGTACATTTTGAATGATTCAGAGTCATTAT
*
112615 CAAACAACATGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCATTCAACATTTGAATAA
196 CAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCATTCAACATTTGAATAA
* *
112680 TTCAGCGCTTAATCATTATGAAATAAATAAACAACCCCTAAGACAAGAACAACTCTACAGCAGTT
261 TTCAACGCTTAATCATTATGAAATAAACAAACAACCCCTAAGACAAGAACAACTCTACAGCAGTT
112745 TACGCCGCGAAA
326 TACGCCGCGAAA
*
112757 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAATTAA-GGGTTGTTTGTTTGGCTCTGAATG
1 TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGTTGTTTGTTTGGCTCTGAATG
* * *
112821 AAATCATTCAGCGCTTAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
66 AAACCATTCAACGCTGAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
*
112886 ATTCAGTGCTGAATGATTCAGTGCTGAATGATTCAGCATAGAAGTACATTTTGAATGATTCAGAG
131 ATTCA--GC--AA--A-ACAGTGCTGAATGATTCAGCATAGAAGTACATTTTGAATGATTCAGAG
112951 TCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCATTCAACATT
189 TCATTATCAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCATTCAACATT
* *
113016 TGAATAATTCAACGCTTAATCATTCTGAAATAAACAAACAACCCCTAAGACAATAACAACTCTAC
254 TGAATAATTCAACGCTTAATCATTATGAAATAAACAAACAACCCCTAAGACAAGAACAACTCTAC
113081 AGCAGTTTACGCCGCGAAA
319 AGCAGTTTACGCCGCGAAA
113100 T
1 T
113101 ACCCACACAA
Statistics
Matches: 325, Mismatches: 12, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
336 90 0.28
337 39 0.12
338 2 0.01
340 2 0.01
342 1 0.00
343 191 0.59
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (337 bp):
TTCCCTAAATCTAAATAGATAAAAGAGTACTCCTAACTAAGGGGTTGTTTGTTTGGCTCTGAATG
AAACCATTCAACGCTGAATGTTGAACCGTTCAACATTCAGACTGTTTGTTTCTCATCTCTGAATG
ATTCAGCAAAACAGTGCTGAATGATTCAGCATAGAAGTACATTTTGAATGATTCAGAGTCATTAT
CAAACAACACGTCACATTCAGAATTAATTCATACAGAGCCTCTGAATCATTCAACATTTGAATAA
TTCAACGCTTAATCATTATGAAATAAACAAACAACCCCTAAGACAAGAACAACTCTACAGCAGTT
TACGCCGCGAAA
Found at i:115656 original size:13 final size:14
Alignment explanation
Indices: 115633--115661 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
115623 AGAAGAGAAC
115633 AAATGATTTTTAAA
1 AAATGATTTTTAAA
115647 AAAT-ATTTTTAAA
1 AAATGATTTTTAAA
115660 AA
1 AA
115662 TAAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AAATGATTTTTAAA
Found at i:118068 original size:31 final size:31
Alignment explanation
Indices: 118027--118102 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
118017 TTTATTAATT
*
118027 TAGCCCTCGAAGTTGTCTATGATGTTCATCA
1 TAGCCTTCGAAGTTGTCTATGATGTTCATCA
* *
118058 TAGCCTTCGAAATTGTCTATGATGTTCATCC
1 TAGCCTTCGAAGTTGTCTATGATGTTCATCA
118089 TAG-CTCTCGAAGTT
1 TAGCCT-TCGAAGTT
118103 CATTTTGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.05
31 38 0.95
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (31 bp):
TAGCCTTCGAAGTTGTCTATGATGTTCATCA
Found at i:118984 original size:31 final size:31
Alignment explanation
Indices: 118942--119008 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
118932 CATGTTTTTG
*
118942 TAGGGCCTCGATTGCTAAATCCGCGGAAGTT
1 TAGGGCCTCGATTGCTAAATCAGCGGAAGTT
* *
118973 TAGGGCTTCGATTGCTAAATCAGCTGAAGTT
1 TAGGGCCTCGATTGCTAAATCAGCGGAAGTT
119004 TAGGG
1 TAGGG
119009 TTCAATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (31 bp):
TAGGGCCTCGATTGCTAAATCAGCGGAAGTT
Found at i:125637 original size:16 final size:17
Alignment explanation
Indices: 125618--125650 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
125608 ATAATTTACT
125618 TTATTAAAA-TTTTAAA
1 TTATTAAAACTTTTAAA
125634 TTATTAAAACTTTTAAA
1 TTATTAAAACTTTTAAA
125651 ATAATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTAAAACTTTTAAA
Found at i:125656 original size:28 final size:28
Alignment explanation
Indices: 125625--125689 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
125615 ACTTTATTAA
** *
125625 AATTTTAAATTATTAAAACTTTTAAAAT
1 AATTTTAAATTATTAAAAAATATAAAAT
125653 AATTATT-AATTATTAAAAAATATAAAAT
1 AATT-TTAAATTATTAAAAAATATAAAAT
*
125681 TATTTTAAA
1 AATTTTAAA
125690 ACTTTTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 27 0.87
29 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTTTAAATTATTAAAAAATATAAAAT
Found at i:125657 original size:18 final size:16
Alignment explanation
Indices: 125620--125681 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 16
125610 AATTTACTTT
*
125620 ATTAAAATTTTAAATT
1 ATTAAAATTTTAAATA
125636 ATTAAAACTTTTAAAATA
1 ATTAAAA-TTTT-AAATA
* *
125654 ATTATTAATTATTAAAAA
1 ATTA-AAATT-TTAAATA
125672 ATATAAAATT
1 AT-TAAAATT
125682 ATTTTAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 20 0.54
19 6 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAAATTTTAAATA
Done.