Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002420.1 Hibiscus syriacus cultivar Beakdansim tig00004948_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: 97714
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3330 original size:14 final size:14
Alignment explanation
Indices: 3311--3355 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3301 GAATTAAATA
*
3311 ATATTTTATTTTTT
1 ATATTTTAATTTTT
* *
3325 ATA-TTTAAGTTTA
1 ATATTTTAATTTTT
3338 ATATTTTAATTTTT
1 ATATTTTAATTTTT
3352 ATAT
1 ATAT
3356 GAATTTGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:4696 original size:97 final size:99
Alignment explanation
Indices: 4516--4703 Score: 283
Period size: 97 Copynumber: 1.9 Consensus size: 99
4506 CTTTGCAAGT
4516 AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCCTTCTTTATTACTGTTAATCCATTTCAGAAG
1 AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCCTTC-----TACTGTTAATCCATTTCAGAAG
4581 GGAGCGTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
61 GGAGCGTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
*
4620 AAACCTCGCTCAATAAGCAAACCTTGTTGCCCCCGC-TC-A-TGTTAATCCATTTCAGAAGGGAG
1 AAACCTCGCTCAATAAGCAAACCTTGTT-CCCCCCCTTCTACTGTTAATCCATTTCAGAAGGGAG
*
4682 CGTACAAAAGCTGTGGCGTAAA
65 CGTACAAAAACTGTGGCGTAAA
4704 CCAGGAAAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
97 44 0.54
98 1 0.01
104 30 0.37
105 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (99 bp):
AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCCTTCTACTGTTAATCCATTTCAGAAGGGAGC
GTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
Found at i:14416 original size:2 final size:2
Alignment explanation
Indices: 14409--14434 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14399 CGTCTTCTTT
14409 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
14435 CAGGACAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17357 original size:45 final size:45
Alignment explanation
Indices: 17289--17374 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
17279 TTATGGGCGG
*
17289 CAAGGTCCATAACTTAAAAAAATATAAACGATAAACAAAAAATTA
1 CAAGGTCCATAACTTAAAAAAATAGAAACGATAAACAAAAAATTA
* * *
17334 CAAGGTGCATAACTTAAATAAATAGAAACGATAAACTAAAA
1 CAAGGTCCATAACTTAAAAAAATAGAAACGATAAACAAAAA
17375 TGACGCTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.58, C:0.13, G:0.09, T:0.20
Consensus pattern (45 bp):
CAAGGTCCATAACTTAAAAAAATAGAAACGATAAACAAAAAATTA
Found at i:21204 original size:12 final size:14
Alignment explanation
Indices: 21179--21207 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21169 GGTTACATTT
21179 ATATATTTTAAAAA
1 ATATATTTTAAAAA
21193 ATATA-TTTAAAAA
1 ATATATTTTAAAAA
21206 AT
1 AT
21208 TAAAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATTTTAAAAA
Found at i:21978 original size:20 final size:19
Alignment explanation
Indices: 21952--21993 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
21942 ACGAGAATTC
*
21952 ATAAAAAAAAATTATAATAAA
1 ATAAAAAGAAATT-TAA-AAA
21973 ATAAAAAGAAATTTAAAAA
1 ATAAAAAGAAATTTAAAAA
21992 AT
1 AT
21994 TAAGATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAAAAAGAAATTTAAAAA
Found at i:28306 original size:50 final size:50
Alignment explanation
Indices: 28248--28347 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
28238 GGAAGCCCTT
28248 CCCATTCTCTTTTATTTGAGTATTTATTTATTTCTCTATGTGGTAGAGCA
1 CCCATTCTCTTTTATTTGAGTATTTATTTATTTCTCTATGTGGTAGAGCA
28298 CCCATTCTCTTTTATTTGAGTATTTATTTATTTCTCTATGTGGTAGAGCA
1 CCCATTCTCTTTTATTTGAGTATTTATTTATTTCTCTATGTGGTAGAGCA
28348 TAATATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (50 bp):
CCCATTCTCTTTTATTTGAGTATTTATTTATTTCTCTATGTGGTAGAGCA
Found at i:33976 original size:20 final size:20
Alignment explanation
Indices: 33951--34063 Score: 145
Period size: 20 Copynumber: 5.5 Consensus size: 20
33941 TTTTCCCAAT
33951 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
33971 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
** *
33991 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
34012 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
34032 TCGCAACGCGAAATGGGAAAA
1 TCGCAATGCG-AATAAGTAAA
34053 TCGCAATGCGA
1 TCGCAATGCGA
34064 TACTGACTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
20 47 0.59
21 33 0.41
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:34013 original size:41 final size:40
Alignment explanation
Indices: 33951--34063 Score: 172
Period size: 41 Copynumber: 2.8 Consensus size: 40
33941 TTTTCCCAAT
** *
33951 TCGCAATGCGAATAAGTAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATGGGAAAATCGCAATGCGAATAAGTAAA
33991 TCGCAATGCGAATTGGGAAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAA-TGGGAAAATCGCAATGCGAATAAGTAAA
*
34032 TCGCAACGCGAAATGGGAAAATCGCAATGCGA
1 TCGCAATGCG-AATGGGAAAATCGCAATGCGA
34064 TACTGACTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
40 12 0.18
41 53 0.79
42 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (40 bp):
TCGCAATGCGAATGGGAAAATCGCAATGCGAATAAGTAAA
Found at i:34077 original size:20 final size:20
Alignment explanation
Indices: 34052--34125 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
34042 AAATGGGAAA
*
34052 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
34072 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
34092 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
34112 TTCGCAACGCGATA
1 ATCGCAACGCGATA
34126 ATACATAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:34078 original size:61 final size:60
Alignment explanation
Indices: 33951--34068 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
33941 TTTTCCCAAT
* * *
33951 TCGCAATGCGAATAAGTAAATCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGAAAATCGCAATGCGAACT-GGAAAA
**
34012 TCGCAATGCGAATAAGTAAATCGCAACGCGAAATGGGAAAATCGCAATGCGATACTG
1 TCGCAATGCGAATAAGTAAATCGCAACGCG-AATAAGAAAATCGCAATGCGA-ACTG
34069 ACTATCGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 29 0.58
62 19 0.38
63 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.19
Consensus pattern (60 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGAAAATCGCAATGCGAACTGGAAAA
Found at i:34083 original size:41 final size:41
Alignment explanation
Indices: 33968--34063 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
33958 GCGAATAAGT
* *
33968 AAATCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGA
1 AAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGGGA
34009 AAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGGGA
1 AAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGGGA
34050 AAATCGCAATGCGA
1 AAATCGCAATGCGA
34064 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (41 bp):
AAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGGGA
Found at i:34341 original size:22 final size:22
Alignment explanation
Indices: 34313--34356 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34303 CACTCTCTCA
34313 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
34335 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
34357 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:34629 original size:20 final size:20
Alignment explanation
Indices: 34600--34643 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34590 GAGATTTTAG
34600 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
34620 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
34640 TTTC
1 TTTC
34644 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:34834 original size:25 final size:24
Alignment explanation
Indices: 34780--34834 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
34770 TGTTTATTAT
* *
34780 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
34804 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
34830 TGTTT
1 TGTTT
34835 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:35984 original size:18 final size:18
Alignment explanation
Indices: 35963--36007 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
35953 TCCACTTTGG
*
35963 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
35981 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
35999 GAGCCATCA
1 GAGCCATCA
36008 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:36511 original size:14 final size:14
Alignment explanation
Indices: 36492--36549 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
36482 TTGTGTTTCG
36492 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
36506 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
36522 CGCGTTGCGGTTTTGT
1 --CGTTGCGATTTTGT
36538 CGTTGCGATTTT
1 CGTTGCGATTTT
36550 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:36526 original size:32 final size:33
Alignment explanation
Indices: 36487--36565 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
36477 GCGATTTGTG
36487 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
36519 TTTCGCGTTGCGGTTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
36552 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
36566 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:36584 original size:20 final size:19
Alignment explanation
Indices: 36550--36605 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
36540 TTGCGATTTT
*
36550 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
36569 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
36589 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
36606 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:38493 original size:14 final size:14
Alignment explanation
Indices: 38474--38509 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38464 ATTGTTTAAT
38474 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
38488 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
38502 TGATTTGT
1 TGATTTGT
38510 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:38629 original size:19 final size:19
Alignment explanation
Indices: 38593--38629 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38583 AGGCAAAACA
**
38593 GACTATCGCAACGCGAAAT
1 GACTATCGCAACAAGAAAT
38612 GACTATCGCAACAAGAAA
1 GACTATCGCAACAAGAAA
38630 ATCGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (19 bp):
GACTATCGCAACAAGAAAT
Found at i:38635 original size:14 final size:17
Alignment explanation
Indices: 38597--38674 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 17
38587 AAAACAGACT
**
38597 ATCGCAACGCGAAATGACT
1 ATCGCAA-GC-AAATGAAA
38616 ATCGCAA-C-AA-GAAA
1 ATCGCAAGCAAATGAAA
38630 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GC-AAATGAAA
38649 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GC-AAATGAAA
38668 ATCGCAA
1 ATCGCAA
38675 CGAGAAAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 1 0.02
17 1 0.02
18 2 0.04
19 37 0.71
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (17 bp):
ATCGCAAGCAAATGAAA
Found at i:38648 original size:19 final size:19
Alignment explanation
Indices: 38626--38693 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
38616 ATCGCAACAA
38626 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
38645 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
38664 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
38678 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
38694 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:38737 original size:20 final size:20
Alignment explanation
Indices: 38712--38769 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
38702 TCGCATTGCG
*
38712 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
38732 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
38752 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
38770 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:39827 original size:24 final size:24
Alignment explanation
Indices: 39800--39853 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
39790 GTATTCGAAA
* *
39800 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
39824 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
39848 TTTGAT
1 TTTGAT
39854 GATGTTTCAG
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:42369 original size:33 final size:33
Alignment explanation
Indices: 42332--42458 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
42322 GAAAATTACT
*
42332 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
42365 ATCGCAATGCGAAGTGAAAATCGAAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
42397 TTTCGCAATGCGAAATGGAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
42431 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
42459 CGAATTTAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.01
33 76 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:42423 original size:19 final size:19
Alignment explanation
Indices: 42399--42462 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
42389 AACGCTAATT
42399 TCGCAATGCGAAATGGAAA
1 TCGCAATGCGAAATGGAAA
*
42418 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGGAAA
*
42432 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGGAAA
*
42451 TCGCAACGCGAA
1 TCGCAATGCGAA
42463 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (19 bp):
TCGCAATGCGAAATGGAAA
Found at i:42439 original size:66 final size:66
Alignment explanation
Indices: 42333--42465 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
42323 AAAATTACTA
* * *
42333 TCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAGTGAAAATCGAAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGAAACGCGAAT
42398 T
66 T
* * *
42399 TCGCAATGCGAAATGGAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGAAACGCGAAT
42464 T
66 T
42465 T
1 T
42466 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGAAACGCGAAT
T
Found at i:42480 original size:19 final size:20
Alignment explanation
Indices: 42458--42500 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
42448 AAATCGCAAC
42458 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
42477 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
42497 GCGA
1 GCGA
42501 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:42660 original size:14 final size:14
Alignment explanation
Indices: 42641--42677 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42631 CATCAATTAA
42641 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
42655 ACAAATCACCTTTT
1 ACAAATCAACTTTT
42669 ACAAATCAA
1 ACAAATCAA
42678 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:44099 original size:21 final size:21
Alignment explanation
Indices: 44033--44099 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
44023 GTGAATCGGG
*
44033 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
44053 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
44075 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
44096 CTCT
1 CTCT
44100 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:44118 original size:42 final size:41
Alignment explanation
Indices: 44033--44155 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
44023 GTGAATCGGG
* * * *
44033 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
44075 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
44117 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
44156 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:46239 original size:33 final size:33
Alignment explanation
Indices: 46182--46280 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
46172 ACGAGATAAT
46182 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* *
46216 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
46249 GACAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
46281 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:46274 original size:19 final size:19
Alignment explanation
Indices: 46157--46302 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
46147 TCTTTTGGTT
*
46157 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
46176 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
46196 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
46214 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
46230 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
46248 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
46263 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
46282 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
46301 GA
1 GA
46303 TTTTTGTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.04
19 44 0.43
20 27 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:46334 original size:19 final size:19
Alignment explanation
Indices: 46298--46342 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
46288 AAAATCGCAA
*
46298 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
46317 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
46336 TACGATT
1 TGCGATT
46343 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:46916 original size:20 final size:20
Alignment explanation
Indices: 46868--46907 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46858 GCGCTATGTA
46868 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
46888 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
46908 TATCTCGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:46954 original size:20 final size:20
Alignment explanation
Indices: 46929--46982 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
46919 GATTTTGTAT
*
46929 TATCGCATTGCGATAGTAAG
1 TATCGCATTACGATAGTAAG
*
46949 TATCGCATTACGATAGTCAG
1 TATCGCATTACGATAGTAAG
46969 TATCGCATTACGAT
1 TATCGCATTACGAT
46983 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (20 bp):
TATCGCATTACGATAGTAAG
Found at i:46954 original size:61 final size:61
Alignment explanation
Indices: 46869--46985 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
46859 CGCTATGTAA
* * * * * *
46869 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTACGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTTGTATT
* * *
46930 ATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTACGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTT
46986 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTTGTATT
Found at i:47001 original size:61 final size:61
Alignment explanation
Indices: 46869--47003 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
46859 CGCTATGTAA
* * * * * * ** *
46869 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTACGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTTCCAAT
* * *
46930 ATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCAGTATCGCATTACGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTT-CCAAT
46992 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
47004 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGTATCGCATTACGATTTTCCAAT
Found at i:48279 original size:16 final size:16
Alignment explanation
Indices: 48258--48290 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48248 AATACCAAAA
48258 TATTATAAAAAATAAT
1 TATTATAAAAAATAAT
48274 TATTATAAAAAATAAT
1 TATTATAAAAAATAAT
48290 T
1 T
48291 TAAATGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATTATAAAAAATAAT
Found at i:48408 original size:26 final size:24
Alignment explanation
Indices: 48347--48409 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
48337 TTGGCCAGCT
48347 ATTAATTCAAAATCTATTGATTATA
1 ATTAATT-AAAATCTATTGATTATA
*
48372 ATTACTTAAAATCATTATCTGATTA-A
1 ATTAATTAAAATC--TAT-TGATTATA
*
48398 TTTAATTAAAAT
1 ATTAATTAAAAT
48410 TAAATGAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.19
25 6 0.19
26 14 0.44
27 6 0.19
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTAATTAAAATCTATTGATTATA
Found at i:48583 original size:19 final size:20
Alignment explanation
Indices: 48524--48583 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
48514 GATATCATTT
*
48524 AAATAATTTATAA-CAATTA
1 AAATAATTTATAATCAAATA
*
48543 AAATTAATTTAACTAATAAAATA
1 AAA-TAATTT-A-TAATCAAATA
48566 AAATAA-TTATAATCAAAT
1 AAATAATTTATAATCAAAT
48584 TTAAAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 11 0.32
20 7 0.21
21 3 0.09
22 6 0.18
23 7 0.21
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAATTTATAATCAAATA
Found at i:65398 original size:91 final size:91
Alignment explanation
Indices: 65287--65456 Score: 306
Period size: 91 Copynumber: 1.9 Consensus size: 91
65277 AGGATTTTTT
*
65287 TAATCCATTAACAACACACATGCATCCTGCTGACGTAACTATTTAAACTAAAAAAA-CCTTATTC
1 TAATCCATTAACAACACACATGCATCCTGCTGACATAACTATTTAAACTAAAAAAATCC-TATTC
65351 GAACTCAATTTTTTTAATCACTAAAAC
65 GAACTCAATTTTTTTAATCACTAAAAC
*
65378 TAATCCATTAACAACACACATGCATCCTGCTGACATAACTATTTAAACTAAAAAAATCCTATTTG
1 TAATCCATTAACAACACACATGCATCCTGCTGACATAACTATTTAAACTAAAAAAATCCTATTCG
65443 AACTCAATTTTTTT
66 AACTCAATTTTTTT
65457 TTAAAGAGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 74 0.97
92 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.32
Consensus pattern (91 bp):
TAATCCATTAACAACACACATGCATCCTGCTGACATAACTATTTAAACTAAAAAAATCCTATTCG
AACTCAATTTTTTTAATCACTAAAAC
Found at i:83809 original size:5 final size:5
Alignment explanation
Indices: 83799--83823 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
83789 GATATCGATC
83799 TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG
83824 GATATTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:84499 original size:22 final size:22
Alignment explanation
Indices: 84473--84517 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
84463 CTAAATTACG
84473 TAGAACTTAATATAAATATAAA
1 TAGAACTTAATATAAATATAAA
*
84495 TAGAATTTAATATAAATATAAA
1 TAGAACTTAATATAAATATAAA
84517 T
1 T
84518 TAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
TAGAACTTAATATAAATATAAA
Found at i:84508 original size:16 final size:16
Alignment explanation
Indices: 84487--84522 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
84477 ACTTAATATA
*
84487 AATATAAATAGAATTT
1 AATATAAATAGAAATT
*
84503 AATATAAATATAAATT
1 AATATAAATAGAAATT
84519 AATA
1 AATA
84523 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAAATAGAAATT
Found at i:88060 original size:2 final size:2
Alignment explanation
Indices: 88053--88125 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
88043 ATCTTATCGC
88053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88095 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88126 TAAAGTATGA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:91230 original size:82 final size:82
Alignment explanation
Indices: 91119--91420 Score: 498
Period size: 82 Copynumber: 3.7 Consensus size: 82
91109 GAATTATCAG
* *
91119 TTGAAATCAGTA-CTTGCTTACTGATTCGTACATGTTAGCATGGTTTGGCATGACATGGTCTACC
1 TTGAAATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACATGGTCTACC
91183 ATACTAATTGGATTATC
66 ATACTAATTGGATTATC
* * * * * *
91200 TTGAAATCAATAGCTTGCTTACTGACTCGTATATGTTAGCAAGGTTTGGCTTGAAATGGTCTACC
1 TTGAAATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACATGGTCTACC
91265 ATACTAATTGGATTATC
66 ATACTAATTGGATTATC
* *
91282 CTGAAATCAGTAGCTTGCTTACTGATTCGTATATGTCAGCAAGGTTTGGCATGACATGGTCTACC
1 TTGAAATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACATGGTCTACC
91347 ATACTAATTGGATTATC
66 ATACTAATTGGATTATC
*
91364 TTGAGATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACAT
1 TTGAAATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACAT
91421 TAGTCCATAA
Statistics
Matches: 205, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
81 11 0.05
82 194 0.95
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (82 bp):
TTGAAATCAGTAGCTTGCTTACTGATTCGTACATGTCAGCAAGGTTTGGCATGACATGGTCTACC
ATACTAATTGGATTATC
Done.