Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007209.1 Hibiscus syriacus cultivar Beakdansim tig00019052_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: 77104
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4513 original size:26 final size:26
Alignment explanation
Indices: 4470--4519 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4460 TACTCCATGA
* *
4470 AAAAAATAGCAGCAGTTCGAAAAAAG
1 AAAAAAGAGAAGCAGTTCGAAAAAAG
*
4496 AAAAAAGAGAAGCTGTTCGAAAAA
1 AAAAAAGAGAAGCAGTTCGAAAAA
4520 TGGAGACATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.58, C:0.10, G:0.20, T:0.12
Consensus pattern (26 bp):
AAAAAAGAGAAGCAGTTCGAAAAAAG
Found at i:5371 original size:26 final size:26
Alignment explanation
Indices: 5317--5373 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5307 TTGACGTGGT
* ** *
5317 AGTTTCTAGAAGGTGTAGTCAGCGGC
1 AGTTTCTAAAAGGTCCAGTCAGCAGC
*
5343 AGTTTCTAAAAGGTCCAGTCAGCATC
1 AGTTTCTAAAAGGTCCAGTCAGCAGC
5369 AGTTT
1 AGTTT
5374 TTTAGAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (26 bp):
AGTTTCTAAAAGGTCCAGTCAGCAGC
Found at i:5648 original size:32 final size:29
Alignment explanation
Indices: 5606--5665 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 29
5596 TTTTATAAAA
5606 GTTTCTCTTTTACTTTTCAAGTTTTCGTTTTC
1 GTTTCTCTTTTAC-TTT-AAGTTTT-GTTTTC
*
5638 GTTTTTCTTTTACTTTAAGTTTTGTTTT
1 GTTTCTCTTTTACTTTAAGTTTTGTTTT
5666 TAAATGTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 7 0.26
31 3 0.11
32 12 0.44
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (29 bp):
GTTTCTCTTTTACTTTAAGTTTTGTTTTC
Found at i:6592 original size:29 final size:28
Alignment explanation
Indices: 6558--6623 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
6548 AATATTTAAT
* *
6558 AAATAATTTTATAACTAAATAATCAAATA
1 AAATAATTCTA-AAATAAATAATCAAATA
* * *
6587 AAATAAATACTAAAATAAATAATTACATA
1 AAAT-AATTCTAAAATAAATAATCAAATA
6616 AAATAATT
1 AAATAATT
6624 AATTACACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.10
29 22 0.73
30 5 0.17
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (28 bp):
AAATAATTCTAAAATAAATAATCAAATA
Found at i:6595 original size:17 final size:17
Alignment explanation
Indices: 6573--6621 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
6563 ATTTTATAAC
*
6573 TAAATAATCAAATAAAA
1 TAAATAATAAAATAAAA
*
6590 TAAATACTAAAAT-AAA
1 TAAATAATAAAATAAAA
*
6606 TAATTACATAAAATAA
1 TAAATA-ATAAAATAA
6622 TTAATTACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.31
17 17 0.65
18 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAATAAAATAAAA
Found at i:6616 original size:12 final size:11
Alignment explanation
Indices: 6539--6626 Score: 63
Period size: 12 Copynumber: 7.7 Consensus size: 11
6529 TTTTTATCTG
6539 TAATTAATAAA
1 TAATTAATAAA
*
6550 TATTTAATAAA
1 TAATTAATAAA
* *
6561 TAATTTTATAAC
1 TAA-TTAATAAA
*
6573 TAAATAATCAAA
1 TAATTAAT-AAA
6585 TAA--AATAAA
1 TAATTAATAAA
* *
6594 TACTAAAATAAA
1 TAAT-TAATAAA
6606 TAATTACATAAAA
1 TAATTA-AT-AAA
6619 TAATTAAT
1 TAATTAAT
6627 TACACAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
9 5 0.08
10 3 0.05
11 16 0.27
12 27 0.45
13 9 0.15
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATTAATAAA
Found at i:6626 original size:17 final size:17
Alignment explanation
Indices: 6582--6641 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
6572 CTAAATAATC
*
6582 AAATAAAATAAATAC-TA
1 AAAT-AAATAATTACATA
6599 AAATAAATAATTACATA
1 AAATAAATAATTACATA
* *
6616 AAATAATTAATTACACA
1 AAATAAATAATTACATA
6633 ATAATAAAT
1 A-AATAAAT
6642 TTTAATGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 9 0.24
17 22 0.59
18 6 0.16
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAATAATTACATA
Found at i:12964 original size:2 final size:2
Alignment explanation
Indices: 12957--12989 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12947 AGATTTATCA
12957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12990 ATTTAAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17312 original size:17 final size:17
Alignment explanation
Indices: 17290--17330 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17280 CTTTAAATTA
17290 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTAT-T
*
17307 TTTATTTAATTCTTATT
1 TTTATTTAATTATTATT
17324 TTTATTT
1 TTTATTT
17331 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTAATTATTATT
Found at i:18225 original size:13 final size:13
Alignment explanation
Indices: 18204--18247 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
18194 AAGCGAGCGA
*
18204 ATTACGAAGGAGC
1 ATTATGAAGGAGC
18217 ATTATGAAGGAGC
1 ATTATGAAGGAGC
18230 ATTATGAAGGAGC
1 ATTATGAAGGAGC
18243 ATTAT
1 ATTAT
18248 TTCCATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (13 bp):
ATTATGAAGGAGC
Found at i:22314 original size:5 final size:5
Alignment explanation
Indices: 22286--22341 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
22276 TTTGTTATAT
* * *
22286 TTTTG TTTTA TTCTA TTTTCA TTTTA TTTTA TTTTG TTTTA TTTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
22338 TTTT
1 TTTT
22342 TAGCAAACCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
5 34 0.77
6 10 0.23
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:22315 original size:21 final size:21
Alignment explanation
Indices: 22283--22339 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
22273 CATTTTGTTA
*
22283 TATTTTTGTTTTATTCTATTT
1 TATTTTTATTTTATTCTATTT
* *
22304 TCA-TTTTATTTTATTTTGTTT
1 T-ATTTTTATTTTATTCTATTT
22325 TATTTTTATTTTATT
1 TATTTTTATTTTATT
22340 TTTAGCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (21 bp):
TATTTTTATTTTATTCTATTT
Found at i:22331 original size:16 final size:15
Alignment explanation
Indices: 22286--22341 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
22276 TTTGTTATAT
* *
22286 TTTTGTTTTATTCTA
1 TTTTATTTTATTTTA
22301 TTTTCATTTTATTTTA
1 TTTT-ATTTTATTTTA
*
22317 TTTTGTTTTATTTTTA
1 TTTTATTTTA-TTTTA
22333 TTTTATTTT
1 TTTTATTTT
22342 TAGCAAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:25328 original size:17 final size:18
Alignment explanation
Indices: 25306--25347 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
25296 CTTTAAATTA
25306 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
25323 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
25341 TTTATTT
1 TTTATTT
25348 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:27423 original size:21 final size:21
Alignment explanation
Indices: 27376--27424 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
27366 TTATTATCGA
27376 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCGC
**
27397 GTTGCGATTTTCCCAA-TTCGC
1 AATGCGATTTT-CCAATTTCGC
27418 AATGCGA
1 AATGCGA
27425 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCGC
Found at i:27439 original size:20 final size:21
Alignment explanation
Indices: 27414--27465 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
27404 TTTTCCCAAT
*
27414 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
27434 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
27455 TCGCAATGCGA
1 TCGCAATGCGA
27466 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:27444 original size:41 final size:41
Alignment explanation
Indices: 27399--27630 Score: 150
Period size: 41 Copynumber: 5.7 Consensus size: 41
27389 AATTTCGCGT
* *
27399 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAAATCGCAATGCGAATAAGTAAATCGCAA
* *** * *
27440 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAAATCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * * **
27481 CGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAAATCGCAATGCGA-ATAAGTAAATCGCAA
* *
27522 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAAATCGCAATGCGAATAAGTAAATCGCAA
*** * *
27563 TGCGA-TTAAGTAAATCGCAATGCGAATTATGAAAATCGCAA
1 TGCGATTTTCCTAAATCGCAATGCGAA-TAAGTAAATCGCAA
* * *
27604 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAAATCGCAATGCGAAT
27631 CTGACTATCG
Statistics
Matches: 146, Mismatches: 38, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
39 2 0.01
40 27 0.18
41 115 0.79
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAAATCGCAATGCGAATAAGTAAATCGCAA
Found at i:27509 original size:21 final size:21
Alignment explanation
Indices: 27485--27547 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
27475 TCGCAACGCA
*
27485 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
27506 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
* *
27526 ATTTTCATAAATCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
27547 A
1 A
27548 ATACGTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:27558 original size:20 final size:20
Alignment explanation
Indices: 27533--27630 Score: 151
Period size: 20 Copynumber: 4.8 Consensus size: 20
27523 GCGATTTTCA
27533 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
27553 TAAATCGCAATGCGATTAAG
1 TAAATCGCAATGCGAATACG
*
27573 TAAATCGCAATGCGAATTATG
1 TAAATCGCAATGCGAA-TACG
*
27594 AAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
27614 TAAATCGCAATGCGAAT
1 TAAATCGCAATGCGAAT
27631 CTGACTATCG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 52 0.74
21 18 0.26
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:27646 original size:61 final size:59
Alignment explanation
Indices: 27534--27650 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 59
27524 CGATTTTCAT
*
27534 AAATCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAATGCGAATTATGA
1 AAATCGCAATGCGAATACGTAAATCGCAATGCGATTAACT-AATCGCAATGC-AATTATGA
* *
27595 AAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACT-ATCGTAATGCAATT
1 AAATCGCAATGCGAATACGTAAATCGCAATGCG-AT-TAACTAATCGCAATGCAATT
27651 TACATAGCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
60 4 0.08
61 42 0.82
62 2 0.04
63 3 0.06
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (59 bp):
AAATCGCAATGCGAATACGTAAATCGCAATGCGATTAACTAATCGCAATGCAATTATGA
Found at i:28307 original size:20 final size:19
Alignment explanation
Indices: 28237--28310 Score: 68
Period size: 20 Copynumber: 4.1 Consensus size: 19
28227 GAAACCAAAA
*
28237 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28256 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28270 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
28289 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
28309 TC
1 TC
28311 AACCAAAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 10 0.23
16 2 0.05
17 3 0.07
19 12 0.28
20 16 0.37
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30224 original size:94 final size:94
Alignment explanation
Indices: 30003--30306 Score: 503
Period size: 94 Copynumber: 3.3 Consensus size: 94
29993 TAGATTGCTT
* *
30003 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
30064 ATTT-TCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
30092 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
30157 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
30186 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
30251 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
30280 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
30307 GAAACTATTC
Statistics
Matches: 203, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
89 35 0.17
91 3 0.01
92 2 0.01
93 42 0.21
94 121 0.60
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32187 original size:14 final size:14
Alignment explanation
Indices: 32168--32203 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32158 ATTGTTTAAT
32168 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
32182 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
32196 TGATTTGT
1 TGATTTGT
32204 TTAATTGATG
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:32392 original size:19 final size:19
Alignment explanation
Indices: 32342--32380 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
32332 GCAATGAGAG
*
32342 AATTGCAACGCGAAACTAA
1 AATTGCAATGCGAAACTAA
32361 AATTGCAATGCGAAACTAA
1 AATTGCAATGCGAAACTAA
32380 A
1 A
32381 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (19 bp):
AATTGCAATGCGAAACTAA
Found at i:32403 original size:19 final size:19
Alignment explanation
Indices: 32381--32531 Score: 107
Period size: 19 Copynumber: 8.7 Consensus size: 19
32371 CGAAACTAAA
32381 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32400 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
32415 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32433 TTCGCGTTGCGATTCTC--
1 TTCGCGTTGCGATTTTCAT
32450 TT---GTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32466 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
32481 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
32499 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
32518 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
32532 AGACATTAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 28 0.28
16 8 0.08
17 8 0.08
19 46 0.46
20 10 0.10
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:32427 original size:33 final size:33
Alignment explanation
Indices: 32385--32511 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
32375 ACTAAATTCG
* *
32385 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
32418 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
32451 TGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
32484 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
32512 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:32530 original size:20 final size:19
Alignment explanation
Indices: 32484--32538 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
32474 GCGATTCTCT
**
32484 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
32503 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
32523 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
32539 AGAATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:32577 original size:20 final size:20
Alignment explanation
Indices: 32505--32577 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
32495 TCATTTCGCA
*
32505 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* ****
32525 TTGCGATAGACATTAGAATG
1 TTGCGATAGTCATTTCCGTG
*
32545 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTCCGTG
32566 TTGCGATAGTCA
1 TTGCGATAGTCA
32578 AATGATTGCC
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:35075 original size:24 final size:24
Alignment explanation
Indices: 35041--35094 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35031 CTGAAACATC
*
35041 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
35065 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
35089 ATCAAA
1 ATCAAA
35095 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:35864 original size:20 final size:20
Alignment explanation
Indices: 35834--35947 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
35824 GATTCTGTAT
*
35834 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
35854 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
35874 TATCACGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
35894 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
35915 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
35935 TATCGCATTGCGA
1 TATCGCGTTGCGA
35948 TTTTCCAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.76
21 14 0.17
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:35920 original size:21 final size:21
Alignment explanation
Indices: 35894--36013 Score: 88
Period size: 21 Copynumber: 5.8 Consensus size: 21
35884 CGAAAGTCAG
*
35894 TATCGCGTTGCGATTTTGTAT
1 TATCGCATTGCGATTTTGTAT
* * *
35915 TATCGCGTTGCGA--TAGTCAG
1 TATCGCATTGCGATTTTGT-AT
**
35935 TATCGCATTGCGATTTTCCA-
1 TATCGCATTGCGATTTTGTAT
* *
35955 AATTCGCATTGTGATTTTGTAT
1 TA-TCGCATTGCGATTTTGTAT
* *
35977 TATCGCATTGCGA--TAGTCAG
1 TATCGCATTGCGATTTTGT-AT
35997 TATCGCATTGCGATTTT
1 TATCGCATTGCGATTTT
36014 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
19 6 0.08
20 28 0.37
21 39 0.51
22 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (21 bp):
TATCGCATTGCGATTTTGTAT
Found at i:35948 original size:20 final size:20
Alignment explanation
Indices: 35841--36010 Score: 112
Period size: 20 Copynumber: 8.3 Consensus size: 20
35831 TATTATCTCG
* * *
35841 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
* * *
35861 TTGCGAAAGTCAGTATCACG
1 TTGCGATAGTCAGTATCGCA
* *
35881 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCA
* * *
35901 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGTATCGCA
35922 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
** *
35942 TTGCGATTTTCCA-AATTCGCA
1 TTGCGATAGT-CAGTA-TCGCA
* * *
35963 TTGTGATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCAGTATCGCA
35984 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
36004 TTGCGAT
1 TTGCGAT
36011 TTTCCAAATT
Statistics
Matches: 123, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.05
20 74 0.60
21 37 0.30
22 3 0.02
23 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:35950 original size:41 final size:41
Alignment explanation
Indices: 35814--35951 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
35804 AACTTTGAAA
* * *
35814 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCACGTTGCGAAAGTCAGT
* ** *
35855 ATCGCGTTGCGA--AAGTCAGTATCACGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCACGTTGCGAAAGTCAGT
* * *
35895 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACGTTGCGAAAGTCAGT
35936 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
35952 CCAAATTCGC
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 46 0.56
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCACGTTGCGAAAGTCAGT
Found at i:35988 original size:62 final size:62
Alignment explanation
Indices: 35896--36033 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
35886 AAAGTCAGTA
* *
35896 TCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
*
35958 TCGCATTGTGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
36020 TCGCATTGCGATTT
1 TCGCATTGCGATTT
36034 ACTTATTCGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:36025 original size:21 final size:20
Alignment explanation
Indices: 35937--36050 Score: 95
Period size: 21 Copynumber: 5.5 Consensus size: 20
35927 ATAGTCAGTA
35937 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTT-CAAAT
* ** *
35958 TCGCATTGTGATTTTGTATT
1 TCGCATTGCGATTTTCAAAT
** *
35978 ATCGCATTGCGATAGTC-AGT
1 -TCGCATTGCGATTTTCAAAT
35998 ATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATTTT-CAAAT
* **
36020 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCAAAT
36040 TCGCATTGCGA
1 TCGCATTGCGA
36051 ATTGGGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
20 32 0.43
21 41 0.55
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAT
Found at i:36092 original size:21 final size:20
Alignment explanation
Indices: 36040--36101 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
36030 ATTTACTTAT
36040 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
36061 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
36082 TCGCATTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
36102 CTGATTTACG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.09
21 28 0.80
22 4 0.11
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:36639 original size:14 final size:14
Alignment explanation
Indices: 36614--36647 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36604 TTGGTGATGG
36614 TGTGATGGCAATGA
1 TGTGATGGCAATGA
* *
36628 TTTGATGTCAATGA
1 TGTGATGGCAATGA
36642 TGTGAT
1 TGTGAT
36648 CAACATCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (14 bp):
TGTGATGGCAATGA
Found at i:39988 original size:15 final size:16
Alignment explanation
Indices: 39970--40003 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39960 AAAATAAAAT
39970 AAATA-AACAAAATAA
1 AAATAGAACAAAATAA
39985 AAATAGAACAAAATAA
1 AAATAGAACAAAATAA
40001 AAA
1 AAA
40004 ATAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (16 bp):
AAATAGAACAAAATAA
Found at i:39989 original size:24 final size:23
Alignment explanation
Indices: 39957--40020 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
39947 TATATCAACG
39957 ATAAAAATAAAATAAATAAACAAA
1 ATAAAAATAAAA-AAATAAACAAA
39981 ATAAAAATAGAACAAAAT-AA-AAA
1 ATAAAAATA-AA-AAAATAAACAAA
40004 ATAATAAGATAAAAAAA
1 ATAA-AA-ATAAAAAAA
40021 AGTAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 11 0.31
24 15 0.42
25 9 0.25
26 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (23 bp):
ATAAAAATAAAAAAATAAACAAA
Found at i:40030 original size:35 final size:34
Alignment explanation
Indices: 39960--40031 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
39950 ATCAACGATA
* *
39960 AAAATAAAATAAATAAACAAAATAAAAATAGAAC
1 AAAATAAAAAAAATAAACAAAATAAAAATAAAAC
* *
39994 AAAATAAAAAATAATAAGATAAAA-AAAAGTAAAAC
1 AAAATAAAAAA-AATAA-ACAAAATAAAAATAAAAC
40029 AAA
1 AAA
40032 GAAGACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 10 0.31
35 17 0.53
36 5 0.16
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (34 bp):
AAAATAAAAAAAATAAACAAAATAAAAATAAAAC
Found at i:40707 original size:35 final size:35
Alignment explanation
Indices: 40646--40801 Score: 149
Period size: 35 Copynumber: 4.3 Consensus size: 35
40636 TTAGTTTGTG
*
40646 CAATAAAAT--AAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
* *
40679 C-ATAAAAATAAAAAAAGTTAGTATGTTAGTATGAA
1 CAAT-AAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
*
40714 CAATAAAATAAAAGCTAGAATGTTTGTAAGTTAGTAAGAA
1 CAATAAAATAAAA---A-AA-GTTAGTAAGTTAGTAAGAA
* * *
40754 CAATAAAAAAATAAAAAGTTAG-AATGCTAGTATGAA
1 CAATAAAATAA-AAAAAGTTAGTAA-GTTAGTAAGAA
40790 CAATAAAATAAA
1 CAATAAAATAAA
40802 CGTTAGAATG
Statistics
Matches: 101, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
32 2 0.02
33 6 0.06
35 34 0.34
36 25 0.25
37 2 0.02
38 2 0.02
39 2 0.02
40 26 0.26
41 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (35 bp):
CAATAAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:40737 original size:32 final size:32
Alignment explanation
Indices: 40646--40817 Score: 123
Period size: 32 Copynumber: 4.9 Consensus size: 32
40636 TTAGTTTGTG
*
40646 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTATGAA
*
40679 C-ATAAAAATAAAAAAAGTTAGTATGTTAGTATGAA
1 CAAT-AAAAT---AAAAGTTAGAATGTTAGTATGAA
*
40714 CAATAAAATAAAAGCTAGAATGTTTGTAAGTTAGTAAGAA
1 CAATAAAATAAAAGTTAGAATG--T-T-AG-TA-T--GAA
*
40754 CAATAAAAAAATAAAAAGTTAGAATGCTAGTATGAA
1 CAAT--A-AAAT-AAAAGTTAGAATGTTAGTATGAA
*
40790 CAATAAAATAAACGTTAGAATGTTAGTA
1 CAATAAAATAAAAGTTAGAATGTTAGTA
40818 AGTTAGAAAA
Statistics
Matches: 113, Mismatches: 8, Indels: 37
0.72 0.05 0.23
Matches are distributed among these distances:
32 30 0.27
33 10 0.09
34 3 0.03
35 22 0.19
36 15 0.13
37 2 0.02
38 2 0.02
39 2 0.02
40 9 0.08
41 1 0.01
42 1 0.01
43 4 0.04
44 12 0.11
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTATGAA
Found at i:40755 original size:40 final size:38
Alignment explanation
Indices: 40647--40823 Score: 170
Period size: 40 Copynumber: 4.7 Consensus size: 38
40637 TAGTTTGTGC
*
40647 AATAAAATAAAATGTTAGTAAGTTAGTAAGAAC-ATAAA
1 AATAAAATAGAATGTTAGTAAGTTAGTAAGAACAAT-AA
* *
40685 AATAAAA-A-AA-GTTAGTATGTTAGTATGAACAATAA
1 AATAAAATAGAATGTTAGTAAGTTAGTAAGAACAATAA
*
40720 AATAAAAGCTAGAATGTTTGTAAGTTAGTAAGAACAAT-A
1 AATAAAA--TAGAATGTTAGTAAGTTAGTAAGAACAATAA
* * * *
40759 AA-AAAATAAAAAGTTAG-AATGCTAGTATGAACAATAA
1 AATAAAATAGAATGTTAGTAA-GTTAGTAAGAACAATAA
*
40796 AATAAACGTTAGAATGTTAGTAAGTTAG
1 AATAAA--ATAGAATGTTAGTAAGTTAG
40824 AAAAGTTAGC
Statistics
Matches: 113, Mismatches: 14, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
35 29 0.26
36 25 0.22
37 4 0.04
38 15 0.13
39 5 0.04
40 33 0.29
41 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (38 bp):
AATAAAATAGAATGTTAGTAAGTTAGTAAGAACAATAA
Found at i:40786 original size:76 final size:75
Alignment explanation
Indices: 40657--40823 Score: 264
Period size: 76 Copynumber: 2.2 Consensus size: 75
40647 AATAAAATAA
* *
40657 AATGTTAGTAAGTTAGTAAGAACATAAAAATAAAAAAAGTTAGTATGTTAGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACATAAAAATAAAAAAAGTTAGAATGCTAGTATGAACAATAAAA
40722 TAAAAGCTAG
66 TAAAAGCTAG
*
40732 AATGTTTGTAAGTTAGTAAGAACAATAAAAA-AATAAAAAGTTAGAATGCTAGTATGAACAATAA
1 AATGTTAGTAAGTTAGTAAGAAC-ATAAAAATAA-AAAAAGTTAGAATGCTAGTATGAACAATAA
* *
40796 AATAAACGTTAG
64 AATAAAAGCTAG
40808 AATGTTAGTAAGTTAG
1 AATGTTAGTAAGTTAG
40824 AAAAGTTAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
75 24 0.29
76 60 0.71
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACATAAAAATAAAAAAAGTTAGAATGCTAGTATGAACAATAAAA
TAAAAGCTAG
Found at i:40950 original size:14 final size:14
Alignment explanation
Indices: 40931--40957 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40921 AAACATATAA
40931 AAATAAAATAAAAT
1 AAATAAAATAAAAT
40945 AAATAAAATAAAA
1 AAATAAAATAAAA
40958 AAGGTTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:41066 original size:11 final size:11
Alignment explanation
Indices: 41050--41074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41040 TAGAAACAAT
41050 AAATAAAAATA
1 AAATAAAAATA
41061 AAATAAAAATA
1 AAATAAAAATA
41072 AAA
1 AAA
41075 AAAGGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:41104 original size:118 final size:120
Alignment explanation
Indices: 40860--41173 Score: 418
Period size: 118 Copynumber: 2.6 Consensus size: 120
40850 GGTTCAAATA
* * * * *
40860 ATAATAATGTGAATTATATCCCAGATTTGGTCACCACAAGGTCAAATCAAATAATTCAAACAAAC
1 ATAATAATGTGAATCATACCCCAGATATGGTCACCACAAGGTCAAATCGAAT-ATT---AGAAAC
*
40925 ATATAAAAATAAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAACC
62 A-ATAAATA-AAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAACC
* * * **
40986 ATAATAATGTGGATCTTACCCCGGATATGGTCACCACAAGGTTGAATCGAATATTAGAAACAATA
1 ATAATAATGTGAATCATACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAATA
* *
41051 AATAAAAATAAAATAAA-AATA-AAAAAAGGTTAGTGGTTAGCATAGTCCGAACC
66 AATAAAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAACC
*
41104 ATAATAATGTGAATCATACCCCAGATCTGGTCACCACAAGGTCAAATCGAATATTAG-AACAATA
1 ATAATAATGTGAATCATACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAATA
*
41168 GATAAA
66 AATAAA
41174 CAAATAACAA
Statistics
Matches: 168, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
117 12 0.07
118 82 0.49
119 3 0.02
120 13 0.08
121 6 0.04
122 6 0.04
125 3 0.02
126 43 0.26
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (120 bp):
ATAATAATGTGAATCATACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAATA
AATAAAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAACC
Found at i:42544 original size:122 final size:122
Alignment explanation
Indices: 42312--42610 Score: 345
Period size: 122 Copynumber: 2.5 Consensus size: 122
42302 GAGGATTCAG
** * * * *
42312 AGATGACACTGTTCCTTCAT-GTTGAGGACTTCGGGTCAATGTGGATATAACTTGGTGTTGAAGA
1 AGATGACACTGTTCCTTC-TCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
* *
42376 CGACATTGCTCAGTCACGTTAAAGAGATCTGGCTGCTTTCAAATAAATTGTTTGTTGA
65 AGACATTGCTCAGTCACGTTAAAGAGATCTGGCTGCTTTCAAATAAATTATTTGTTGA
* *
42434 ATATGACACTGTTCCTTCTCGTTGAGAAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
1 AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
* * * * * *
42499 GA-TTCTGCTCA-TCCATGTTGAAGAGATCT-GCTCGTTTTTAGATAAATTATTTGTTGA
66 GACAT-TGCTCAGT-CACGTTAAAGAGATCTGGCT-GCTTTCAAATAAATTATTTGTTGA
* * * * *
42556 AGATGACAATGTTTCTTTTCGTTGAGGAAGTTGGGTCAATCTGGAGATAATTTGG
1 AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGG
42611 AGACAACACG
Statistics
Matches: 150, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
121 6 0.04
122 144 0.96
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (122 bp):
AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
GACATTGCTCAGTCACGTTAAAGAGATCTGGCTGCTTTCAAATAAATTATTTGTTGA
Found at i:42864 original size:220 final size:219
Alignment explanation
Indices: 42436--43572 Score: 1495
Period size: 220 Copynumber: 5.2 Consensus size: 219
42426 TTTGTTGAAT
* * * * * *
42436 ATGACACTGTTCCTTCTCGTTGAGAAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * * * *
42501 TTCTGCTCATCCATGTTGAAGAGATCTGCTCGTTTTTAGATAAATTATTTGTTGAAGATGACAAT
66 CTCTGCTCATCCGTGTTGAAGAGATCTG-TAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
* * *
42566 GTTTCTTTTCGTTGAGGAAGTTGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
130 GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
*
42631 GGTGAGGAAGTCTGATTGTCTGAGG
195 GTTGAGGAAGTCTGATTGTCTGAGG
* * * * *
42656 ATAACACTGCTCCTTCGGGTTGAGGAGATCGAGTTAATCTGGAGATAATTTGGTGTTGAAGATGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* *
42721 CTCTGCACATCCGTGTTGAGGAGATCATGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
66 CTCTGCTCATCCGTGTTGAAGAGATC-TGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
* * * * *
42786 ATTCCTTCTTGTTGAGGAAGTCGGGTCAATCTAGAGATAATTTGGAGACAACACGGTTTCTTCGC
130 GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
**
42851 GTTGAATAAGTCTGATTGTCTGAGG
195 GTTGAGGAAGTCTGATTGTCTGAGG
* * *
42876 ATGACACTGCTCCTTCACGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTATTTGAATAGG
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGT-GTTGAAGAGG
* * * *
42941 ACTCTACTCATTCGTGTTGAAGAGATCTGGTA-TTTTTCAGATAAATTGTTTGTTGAAGATGACG
65 ACTCTGCTCATCCGTGTTGAAGAGATCT-GTAGCTTTT-AGATAAATTGTTTGTTGAAGATGACA
* * * * *
43005 TTGTTCCTTCTCGTTGAAGAAGTCAGGTCAATCTGGAGATAATTTGGGGACAACACGGTTCCTGC
128 CTGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTC
* * *
43070 GCATTGAGGAAGCCTGATTGTCTGAGG
193 ACGTTGAGGAAGTCTGATTGTCTGAGG
* * *
43097 ATGACACTGCTCATTCGCGTTGAGGAGATCGGGTTAATCTAGAGATAATTTGGTGTTGAAGAGGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * *
43162 CTCTGCTCATCCGTGTTGAAGAGATATGATCA-CTTTCAGATAAATTGTTTTTTTGAAGATGACA
66 CTCTGCTCATCCGTGTTGAAGAGATCTG-T-AGCTTTTAGATAAATTG-TTTGTTGAAGATGACA
* * *
43226 CTGTTCCTTCTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGAGACAACACGGTTCCTTC
128 CTGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTC
43291 ACGTTGAGGAAGTCTGATTGTCTGAGG
193 ACGTTGAGGAAGTCTGATTGTCTGAGG
* * * *
43318 ATGACAATGCTTCTTCGCGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * * * * * **
43383 CTCTACTCATCTGTTTTGAAGAGATCTAGTCGCTTTCAGATAAATTATTTGCTGAAGATGATGCT
66 CTCTGCTCATCCGTGTTGAAGAGATCT-GTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
* * * *
43448 GTTCCTTCTCGTTCAGGAAGTCGGGTCAATTTGGAGATAATTTGGAGACAACATGGTTCATTCAC
130 GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
* *
43513 ATTGAGGAAATCTGATTGTCTGAGG
195 GTTGAGGAAGTCTGATTGTCTGAGG
* * *
43538 ATGACACTGCTCCTTCACATTGAGGAGATCTGGTC
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTC
43573 GGTGGATGAC
Statistics
Matches: 798, Mismatches: 110, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
219 1 0.00
220 410 0.51
221 386 0.48
222 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (219 bp):
ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
CTCTGCTCATCCGTGTTGAAGAGATCTGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACTG
TTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCACG
TTGAGGAAGTCTGATTGTCTGAGG
Found at i:43387 original size:441 final size:440
Alignment explanation
Indices: 42436--43567 Score: 1570
Period size: 441 Copynumber: 2.6 Consensus size: 440
42426 TTTGTTGAAT
* * * * *
42436 ATGACACTGTTCCTTCTCGTTGAGAAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
1 ATGACAATGCTCCTTCACGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
* * * * * * *
42501 TTCTGCTCATCCATGTTGAAGAGATCTGCTCGTTTTT-AGATAAATTATTTGTTGAAGATGACAA
66 CTCTACTCATTCGTGTTGAAGAGATCTGGT-ATTTTTCAGATAAATTATTTGTTGAAGATGACGA
* * *
42565 TGTTTCTTTTCGTTGAGGAAGTTGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCA
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCA
** * *
42630 CGGTGAGGAAGTCTGATTGTCTGAGGATAACACTGCTCCTTCGGGTTGAGGAGATCGAGTTAATC
195 CATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCGAGTTAATC
* * * *
42695 TGGAGATAATTTGGTGTTGAAGATGACTCTGCACATCCGTGTTGAGGAGATCATGTAGCTTTTAG
260 TAGAGATAATTTGGTGTTGAAGAGGACTCTGCACATCCGTGTTGAAGAGATCATGTAGCTTTCAG
** *
42760 ATAAATTGTTTGTTGAAGATGACACTATTCCTTCTTGTTGAGGAAGTCGGGTCAATCTAGAGATA
325 ATAAATTGTTTGTTGAAGATGACACTATTCCTTCTCATTGAGGAAGTCAGGTCAATCTAGAGATA
* * * *
42825 ATTTGGAGACAACACGGTTTCTTCGCGTTGAATAAGTCTGATTGTCTGAGG
390 ATTTAGAGACAACACGGTTCCTTCACGTTGAAGAAGTCTGATTGTCTGAGG
* * * * *
42876 ATGACACTGCTCCTTCACGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTATTTGAATAGG
1 ATGACAATGCTCCTTCACGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGT-GTTGAAGAAG
* *
42941 ACTCTACTCATTCGTGTTGAAGAGATCTGGTATTTTTCAGATAAATTGTTTGTTGAAGATGACGT
65 ACTCTACTCATTCGTGTTGAAGAGATCTGGTATTTTTCAGATAAATTATTTGTTGAAGATGACGA
* * * * *
43006 TGTTCCTTCTCGTTGAAGAAGTCAGGTCAATCTGGAGATAATTTGGGGACAACACGGTTCCTGCG
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCA
* * *
43071 CATTGAGGAAGCCTGATTGTCTGAGGATGACACTGCTCATTCGCGTTGAGGAGATCGGGTTAATC
195 CATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCGAGTTAATC
*
43136 TAGAGATAATTTGGTGTTGAAGAGGACTCTGCTCATCCGTGTTGAAGAGAT-ATGATCA-CTTTC
260 TAGAGATAATTTGGTGTTGAAGAGGACTCTGCACATCCGTGTTGAAGAGATCATG-T-AGCTTTC
* * *
43199 AGATAAATTGTTTTTTTGAAGATGACACTGTTCCTTCTCATTGAGGAAGTCAGGTCAATCTGGAG
323 AGATAAATTG-TTTGTTGAAGATGACACTATTCCTTCTCATTGAGGAAGTCAGGTCAATCTAGAG
*
43264 ATAATTTAGAGACAACACGGTTCCTTCACGTTGAGGAAGTCTGATTGTCTGAGG
387 ATAATTTAGAGACAACACGGTTCCTTCACGTTGAAGAAGTCTGATTGTCTGAGG
* * *
43318 ATGACAATGCTTCTTCGCGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGA
1 ATGACAATGCTCCTTCACGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
* * *** * * *
43383 CTCTACTCA-TCTGTTTTGAAGAGATCTAGTCGCTTTCAGATAAATTATTTGCTGAAGATGATGC
66 CTCTACTCATTC-GTGTTGAAGAGATCTGGTATTTTTCAGATAAATTATTTGTTGAAGATGACGA
* * * *
43447 TGTTCCTTCTCGTTCAGGAAGTCGGGTCAATTTGGAGATAATTTGGAGACAACATGGTTCATTCA
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCA
* * *
43512 CATTGAGGAAATCTGATTGTCTGAGGATGACACTGCTCCTTCACATTGAGGAGATC
195 CATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATC
43568 TGGTCGGTGG
Statistics
Matches: 608, Mismatches: 78, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
440 59 0.10
441 401 0.66
442 148 0.24
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (440 bp):
ATGACAATGCTCCTTCACGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
CTCTACTCATTCGTGTTGAAGAGATCTGGTATTTTTCAGATAAATTATTTGTTGAAGATGACGAT
GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
ATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCGAGTTAATCT
AGAGATAATTTGGTGTTGAAGAGGACTCTGCACATCCGTGTTGAAGAGATCATGTAGCTTTCAGA
TAAATTGTTTGTTGAAGATGACACTATTCCTTCTCATTGAGGAAGTCAGGTCAATCTAGAGATAA
TTTAGAGACAACACGGTTCCTTCACGTTGAAGAAGTCTGATTGTCTGAGG
Found at i:43592 original size:40 final size:41
Alignment explanation
Indices: 43498--43593 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 41
43488 TTTGGAGACA
* * *
43498 ACATGGTTCATTCACATTGAGGAAATCTGATTGTCTGAGGATG
1 ACATTGTTCCTTCACATTGAGGAAATCTG--TGTCGGAGGATG
* * * *
43541 ACACTGCTCCTTCACATTGAGGAGATCTG-GTCGGTGGATG
1 ACATTGTTCCTTCACATTGAGGAAATCTGTGTCGGAGGATG
43581 ACATTGTTCCTTC
1 ACATTGTTCCTTC
43594 GTGATGAGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 20 0.45
43 24 0.55
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
ACATTGTTCCTTCACATTGAGGAAATCTGTGTCGGAGGATG
Found at i:43749 original size:140 final size:139
Alignment explanation
Indices: 43483--43760 Score: 351
Period size: 140 Copynumber: 2.0 Consensus size: 139
43473 TCAATTTGGA
* * *
43483 GATAATTTGGAGACAACATGGTTCATTCACATTGAGGAAATCTGATTGTCTGAGGATGACACTGC
1 GATAAGTTGGAGACAACATGGTTCATTCACATTGAGGAAATATGATTGTCTGAGGATGACACTAC
* * * * * * *
43548 TCCTTCACATTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTAGCC
66 TCATTCACATTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAGCC
43613 ATGTTTAGGG
131 AT-TTTAGGG
* * * * * *
43623 GATAAGTTGGAGACAACATGGTTCTTTCGCACTT-AGGAAGTATGGTTTTCTGAGGATGACTCTA
1 GATAAGTTGGAGACAACATGGTTCATTCACA-TTGAGGAAATATGATTGTCTGAGGATGACACTA
* * *
43687 CTCATTCACGTTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTTGTGTTGAAGAAGTCTAGC
65 CTCATTCACATTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAGC
*
43752 CGTTTTAGG
130 CATTTTAGG
43761 AAATAATTTT
Statistics
Matches: 117, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
139 6 0.05
140 109 0.93
141 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (139 bp):
GATAAGTTGGAGACAACATGGTTCATTCACATTGAGGAAATATGATTGTCTGAGGATGACACTAC
TCATTCACATTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAGCC
ATTTTAGGG
Found at i:43793 original size:17 final size:16
Alignment explanation
Indices: 43771--43805 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
43761 AAATAATTTT
43771 TTTCTTTGGAAATGACA
1 TTTCTTTGGAAATG-CA
*
43788 TTTCTTTGTAAATGCA
1 TTTCTTTGGAAATGCA
43804 TT
1 TT
43806 ACTCCTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCTTTGGAAATGCA
Found at i:47297 original size:11 final size:11
Alignment explanation
Indices: 47244--47308 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
47234 TTTCTTCTTC
47244 TTTCTTTGCTTT
1 TTTCTTTG-TTT
* *
47256 TTTCATTGGTT
1 TTTCTTTGTTT
*
47267 TTTCATTGTTT
1 TTTCTTTGTTT
47278 TTTCCCTTT-TTT
1 TTT--CTTTGTTT
47290 TTTGCTTTGTTT
1 TTT-CTTTGTTT
47302 TTTCTTT
1 TTTCTTT
47309 ACTTTGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 23 0.51
12 19 0.42
13 3 0.07
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTCTTTGTTT
Found at i:48719 original size:21 final size:23
Alignment explanation
Indices: 48676--48719 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
48666 CTTTATTGAA
*
48676 TTTTCCATGAATTGATCCCTGTG
1 TTTTCCATGAATTGATCCATGTG
*
48699 TTTT-CATGAA-TGATGCATGTG
1 TTTTCCATGAATTGATCCATGTG
48720 AAAATGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (23 bp):
TTTTCCATGAATTGATCCATGTG
Found at i:51500 original size:15 final size:15
Alignment explanation
Indices: 51443--51501 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
51433 ATCAACGATA
51443 AAAATAAAATAAATAAAC
1 AAAAT-AAA-AAAT-AAC
*
51461 AAAATAAAATATAAC
1 AAAATAAAAAATAAC
*
51476 AAAATAAAAAATAAT
1 AAAATAAAAAATAAC
*
51491 AAGATAAAAAA
1 AAAATAAAAAA
51502 ATATAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 26 0.70
16 3 0.08
17 3 0.08
18 5 0.14
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAAAAATAAC
Found at i:51502 original size:18 final size:18
Alignment explanation
Indices: 51439--51507 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
51429 TTATATCAAC
51439 GATAAAAATAAAATAAATAA
1 GATAAAAA-AAAAT-AATAA
* *
51459 -ACAAAATAAAAT-ATAA
1 GATAAAAAAAAATAATAA
*
51475 CA-AAATAAAAAATAATAA
1 GATAAA-AAAAAATAATAA
*
51493 GATAAAAAAATATAA
1 GATAAAAAAAAATAA
51508 CAAAGAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 18 0.45
19 8 0.20
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (18 bp):
GATAAAAAAAAATAATAA
Found at i:51915 original size:15 final size:15
Alignment explanation
Indices: 51895--51926 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51885 TATTAGATGT
*
51895 AAATATACCACATGC
1 AAATATACCACAAGC
51910 AAATATACCACAAGC
1 AAATATACCACAAGC
51925 AA
1 AA
51927 GATCAGTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATATACCACAAGC
Found at i:52221 original size:40 final size:40
Alignment explanation
Indices: 52120--52244 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
52110 AATAAAATAA
*
52120 AATGTTACTAAGTTAGTAAGAACAATAAAAATAAA---A-
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAGTTAG
* * * * *
52156 AAAGTCAGTATGTTTGTATGAACAAT-AAAATAAATGTTAG
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAA-GTTAG
52196 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAGTTAG
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAAT--AAAGTTAG
52238 AATGTTA
1 AATGTTA
52245 ATATGAATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
35 8 0.11
36 20 0.29
39 1 0.01
40 21 0.30
41 5 0.07
42 12 0.17
43 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (40 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAGTTAG
Found at i:52257 original size:74 final size:75
Alignment explanation
Indices: 52120--52285 Score: 244
Period size: 74 Copynumber: 2.2 Consensus size: 75
52110 AATAAAATAA
* * **
52120 AATGTTACTAAGTTAGTAAGAACAATAAAAATAAAAAAAGTCAGTATGTTTGTATGAACAATAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAAT-AAAAAAGTCAGAATGTTAATATGAACAATAAA
*
52185 ATAAATGTTAG
65 ATAAAAGTTAG
* *
52196 AATGTTAGTAAGTTAGTAAGAACAATAAAAAT-AAAAAGTTAGAATGTTAATATGAATAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAATATGAACAATAAAA
52260 TAAAAGTTAG
66 TAAAAGTTAG
*
52270 AATGTTAGTAAATTAG
1 AATGTTAGTAAGTTAG
52286 AAAAATTAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 51 0.62
76 31 0.38
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAATATGAACAATAAAA
TAAAAGTTAG
Found at i:52682 original size:29 final size:29
Alignment explanation
Indices: 52650--52706 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
52640 TAAATAACAA
*
52650 TGGTTAAAGTGTAATAAAATAAAAGTTAG
1 TGGTTAAAGTGCAATAAAATAAAAGTTAG
*
52679 TGGTTAATGTGCAATAAAATAAAAGTTA
1 TGGTTAAAGTGCAATAAAATAAAAGTTA
52707 TCAGTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (29 bp):
TGGTTAAAGTGCAATAAAATAAAAGTTAG
Found at i:52713 original size:29 final size:29
Alignment explanation
Indices: 52652--52715 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
52642 AATAACAATG
* * *
52652 GTTAAAGTGTAATAAAATAAAAGTTAGTG
1 GTTAATGTGCAATAAAATAAAAGTTAGTA
52681 GTTAATGTGCAATAAAATAAAAGTTA-TCA
1 GTTAATGTGCAATAAAATAAAAGTTAGT-A
52710 GTTAAT
1 GTTAAT
52716 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (29 bp):
GTTAATGTGCAATAAAATAAAAGTTAGTA
Found at i:52723 original size:29 final size:29
Alignment explanation
Indices: 52662--52724 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
52652 GTTAAAGTGT
* **
52662 AATAAAATAAAAGTTAGTGGTTAATGTGC
1 AATAAAATAAAAGTTAGTAGTTAATGTAA
*
52691 AATAAAATAAAAGTTA-TCAGTTAATTTAA
1 AATAAAATAAAAGTTAGT-AGTTAATGTAA
52720 AATAA
1 AATAA
52725 TAAAAATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGTAGTTAATGTAA
Found at i:53509 original size:32 final size:33
Alignment explanation
Indices: 53473--53550 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
53463 TTTAAATAGT
* *
53473 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
53505 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
53538 TATTATTTATTTA
1 TATTATTT-TTTA
53551 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:55301 original size:21 final size:21
Alignment explanation
Indices: 55271--55318 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
55261 GCAGGGGTAC
* *
55271 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
55292 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
55313 ATGCCA
1 ATGCCA
55319 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:55348 original size:21 final size:21
Alignment explanation
Indices: 55322--55415 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
55312 TATGCCATCT
* *
55322 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
* *
55343 CCGCAGGGTTACATTCTTAGC
1 CCGCAGGGTTACATGCCTAGC
55364 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
55385 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
55406 CCGCAGGGTT
1 CCGCAGGGTT
55416 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:55997 original size:33 final size:34
Alignment explanation
Indices: 55938--56034 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
55928 AAATGTTTTT
*
55938 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
55972 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
56005 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
56035 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:56041 original size:34 final size:33
Alignment explanation
Indices: 55936--56041 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
55926 ATAAATGTTT
*
55936 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
55970 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
56002 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
56037 TTAAA
1 TTAAA
56042 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:71129 original size:21 final size:20
Alignment explanation
Indices: 71075--71130 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 20
71065 CTTATAATAT
71075 TTTTTATATTTTTAATATGAA
1 TTTTTAT-TTTTTAATATGAA
71096 TTATTTACTTTTTTTAAACTAT-AA
1 TT-TTTA--TTTTTT-AA-TATGAA
71120 TTTTTATTTTT
1 TTTTTATTTTT
71131 AGTGTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
21 7 0.23
22 4 0.13
23 9 0.30
24 7 0.23
25 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTATTTTTTAATATGAA
Found at i:76279 original size:19 final size:20
Alignment explanation
Indices: 76255--76294 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
76245 GTTGTGGCAA
*
76255 ACAATCTACGCAAGT-ATAC
1 ACAATCGACGCAAGTAATAC
*
76274 ACAATCGATGCAAGTAATAC
1 ACAATCGACGCAAGTAATAC
76294 A
1 A
76295 GTAGTGAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (20 bp):
ACAATCGACGCAAGTAATAC
Done.