Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006199.1 Hibiscus syriacus cultivar Beakdansim tig00014757_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: 74068
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3690 original size:15 final size:15
Alignment explanation
Indices: 3672--3710 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3662 TAACCGGTTT
3672 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3687 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3702 CGATTTTAA
1 CGGTTTTAA
3711 TATTCCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:4122 original size:13 final size:13
Alignment explanation
Indices: 4101--4155 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4091 AAGTTCGATA
*
4101 AATTCAAATACTT
1 AATTGAAATACTT
4114 AATTGAAATACTT
1 AATTGAAATACTT
* *
4127 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
4141 AATTGAAATACTT
1 AATTGAAATACTT
4154 AA
1 AA
4156 ATACTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:4186 original size:33 final size:33
Alignment explanation
Indices: 4141--4239 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
4131 AACTCAACAT
* * *
4141 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
*
4174 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
4207 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
4239 A
1 A
4240 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 13 0.21
33 48 0.79
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTCGATA
Found at i:4258 original size:21 final size:21
Alignment explanation
Indices: 4234--4273 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4224 ACTTCAAGTT
4234 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
4255 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
4274 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:6581 original size:11 final size:12
Alignment explanation
Indices: 6560--6591 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6550 TCCGGATAAA
6560 AACCGGTTTTTT
1 AACCGGTTTTTT
6572 AACCGGTTTTTT
1 AACCGGTTTTTT
*
6584 ATCCGGTT
1 AACCGGTT
6592 AAAATACCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:15438 original size:14 final size:14
Alignment explanation
Indices: 15419--15449 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15409 AAATGAACAC
15419 AAATGAACGAATAT
1 AAATGAACGAATAT
*
15433 AAATGAACGAATGT
1 AAATGAACGAATAT
15447 AAA
1 AAA
15450 CTAACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (14 bp):
AAATGAACGAATAT
Found at i:15470 original size:20 final size:20
Alignment explanation
Indices: 15445--15484 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15435 ATGAACGAAT
*
15445 GTAAACTAACATAAATGAAC
1 GTAAACAAACATAAATGAAC
*
15465 GTAAACAAACATAAGTGAAC
1 GTAAACAAACATAAATGAAC
15485 ACAAGCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (20 bp):
GTAAACAAACATAAATGAAC
Found at i:26011 original size:3 final size:3
Alignment explanation
Indices: 26003--26070 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
25993 TGACGTCTCA
26003 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26051 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
26071 GGGTAAATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28049 original size:17 final size:17
Alignment explanation
Indices: 28027--28064 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28017 TTTTCATATT
28027 AAAATGAATATTAAATC
1 AAAATGAATATTAAATC
28044 AAAATGAATATTAAATC
1 AAAATGAATATTAAATC
28061 AAAA
1 AAAA
28065 AATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAATGAATATTAAATC
Found at i:28625 original size:2 final size:2
Alignment explanation
Indices: 28620--28645 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28610 AAAAAAATAC
28620 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
28646 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30053 original size:6 final size:6
Alignment explanation
Indices: 30034--30070 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30024 AAAGAAGCAA
*
30034 TTAT-T TTAT-T TTATTT TTATGT TTATGT TTATGT TTA
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTA
30071 CTAGAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (6 bp):
TTATGT
Found at i:33177 original size:2 final size:2
Alignment explanation
Indices: 33170--33198 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33160 GTAGCTCAGA
33170 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 A
33199 AATAGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34759 original size:12 final size:12
Alignment explanation
Indices: 34744--34787 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
34734 GCAGCAGCAG
*
34744 CAACAGCATCAT
1 CAACAGCATCAA
* *
34756 CAACAACAACAA
1 CAACAGCATCAA
34768 CAACAGCATCAA
1 CAACAGCATCAA
34780 CAACAGCA
1 CAACAGCA
34788 ACAGCAGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.52, C:0.34, G:0.07, T:0.07
Consensus pattern (12 bp):
CAACAGCATCAA
Found at i:34780 original size:18 final size:18
Alignment explanation
Indices: 34759--34793 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34749 GCATCATCAA
34759 CAACAACAACAACAGCAT
1 CAACAACAACAACAGCAT
*
34777 CAACAACAGCAACAGCA
1 CAACAACAACAACAGCA
34794 GGAGCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.34, G:0.09, T:0.03
Consensus pattern (18 bp):
CAACAACAACAACAGCAT
Found at i:34791 original size:6 final size:6
Alignment explanation
Indices: 34735--34793 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
34725 AAAAATGCAG
* * * * * * *
34735 CAGCAG CAGCAA CAGCAT CATCAA CAACAA CAACAA CAGCAT CAACAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
34783 CAGCAA CAGCA
1 CAGCAA CAGCA
34794 GGAGCAACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.34, G:0.12, T:0.05
Consensus pattern (6 bp):
CAGCAA
Found at i:36212 original size:14 final size:15
Alignment explanation
Indices: 36185--36217 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
36175 AACAAAAGGA
36185 AAAAGAAGAAGAAAG
1 AAAAGAAGAAGAAAG
36200 AAAAGAA-AAGAAAG
1 AAAAGAAGAAGAAAG
36214 AAAA
1 AAAA
36218 AAACAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAGAAAG
Found at i:38038 original size:15 final size:15
Alignment explanation
Indices: 38015--38048 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
38005 TAACCAAATA
38015 TTTTTTTTT-CTTTT
1 TTTTTTTTTCCTTTT
38029 TTTTTCTTTTCCTTTT
1 TTTTT-TTTTCCTTTT
38045 TTTT
1 TTTT
38049 GCGATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTCCTTTT
Found at i:40150 original size:31 final size:31
Alignment explanation
Indices: 40112--40236 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
40102 AGGGTCAAGG
*
40112 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * *
40143 GTTTACCTATGTTCTTGGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
40174 GTTTACCTATGTTCTTCTGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * *
40205 GATTACCTAGGTTCTTCGGAACCTATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
40236 G
1 G
40237 GTCCTTTGGG
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:40321 original size:31 final size:31
Alignment explanation
Indices: 40286--40499 Score: 313
Period size: 31 Copynumber: 6.9 Consensus size: 31
40276 ATAGTGCACA
*
40286 ACCTATGTTCTTCGGGACATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
*
40317 ACCTATGTTCTTCGTGACATATGGACTGATT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
40348 ACCTATGTTCTTCGGGACATATGGACT-ATTT
1 ACCTATGTTCTTCGGGACATATGGACTGA-TT
*
40379 ACCTATGTTCTTCGGGACATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
* *
40410 ACCCATGTTCTTCGGAACATATGGACTGATT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
* * *
40441 ACCTAGGTTCTTTGGAACATATGGACTGATT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
* * *
40472 ACCTAGGTTCTTCGGAACCTATGGACTG
1 ACCTATGTTCTTCGGGACATATGGACTG
40500 GTGTACATAG
Statistics
Matches: 169, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
30 1 0.01
31 168 0.99
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (31 bp):
ACCTATGTTCTTCGGGACATATGGACTGATT
Found at i:40680 original size:18 final size:17
Alignment explanation
Indices: 40647--40685 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
40637 TAAAAGGTAT
*
40647 TAATGATAATAAGAGGA
1 TAATGATAAGAAGAGGA
40664 TAATGATAAGGAAGAGGA
1 TAATGATAA-GAAGAGGA
40682 TAAT
1 TAAT
40686 CATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (17 bp):
TAATGATAAGAAGAGGA
Found at i:44996 original size:2 final size:2
Alignment explanation
Indices: 44989--45014 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44979 CCCTTTCTTC
44989 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
45015 TCCTCTTTGA
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):
CT
Found at i:46199 original size:15 final size:15
Alignment explanation
Indices: 46170--46286 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
46160 TAATAAGGTT
46170 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
46184 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
46199 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
46214 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
46229 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
46248 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
46266 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
46280 ATTTATT
1 ATTTATT
46287 AGTATTGATT
Statistics
Matches: 89, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
14 21 0.24
15 48 0.54
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:46305 original size:22 final size:22
Alignment explanation
Indices: 46293--46333 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
46283 TATTAGTATT
46293 GATTGATTTATTTTGAAATATG
1 GATTGATTTATTTTGAAATATG
46315 GATTGATTTATTTT-AAATA
1 GATTGATTTATTTTGAAATA
46334 ATTTATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTGAAATATG
Found at i:46324 original size:69 final size:67
Alignment explanation
Indices: 46184--46398 Score: 210
Period size: 69 Copynumber: 3.2 Consensus size: 67
46174 ATTTTAAATA
46184 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
46249 TG
66 TG
* ** * * * * *
46251 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATTGATTGATTTATTTTGAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
46315 GATTG
63 GATTG
* * * * *
46320 ATTTATTTT-AAATAATTTATTAGTATGTATTGATTTATTTT-AAAT-AA-T-TTAT-TAGTATG
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATAAATTATTATAAAATATG
46379 GATTG
63 GATTG
46384 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
46399 TGGATTGATT
Statistics
Matches: 122, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
64 19 0.16
65 8 0.07
66 14 0.11
67 23 0.19
68 15 0.12
69 32 0.26
70 2 0.02
72 9 0.07
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:46354 original size:32 final size:31
Alignment explanation
Indices: 46315--46395 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 31
46305 TTGAAATATG
46315 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
46346 GTATTGATTTATTTTAAATAATTTATTAGTAT
1 G-ATTGATTTATTTTAAATAATTTATTAGTAT
46378 GGATTGATTTATTTTAAA
1 -GATTGATTTATTTTAAA
46396 ATATGGATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 46 0.96
33 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (31 bp):
GATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:46391 original size:22 final size:23
Alignment explanation
Indices: 46366--46439 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
46356 ATTTTAAATA
46366 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
46388 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
46410 ATTATTGTAATTGTATGGATTGATTT
1 A-T-TTAT-ATAGTATGGATTGATTT
46436 ATTT
1 ATTT
46440 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 2 0.05
26 15 0.36
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:46426 original size:26 final size:23
Alignment explanation
Indices: 46373--46440 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 23
46363 ATAATTTATT
46373 AGTATGGATTGATTTA-TTTTAA
1 AGTATGGATTGATTTATTTTTAA
*
46395 AATATGGATTGATTTATTATTGTAA
1 AGTATGGATTGATTTATT-TT-TAA
*
46420 TTGTATGGATTGATTTATTTT
1 -AGTATGGATTGATTTATTTT
46441 AAATAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.38
23 1 0.03
24 2 0.05
25 5 0.13
26 16 0.41
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (23 bp):
AGTATGGATTGATTTATTTTTAA
Found at i:46468 original size:32 final size:31
Alignment explanation
Indices: 46422--46539 Score: 218
Period size: 31 Copynumber: 3.7 Consensus size: 31
46412 TATTGTAATT
46422 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
46454 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
46486 GTATGATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
46517 GTATGATTGATTTATTTTAAATA
1 GTATGATTGATTTATTTTAAATA
46540 TGGATTGATT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
31 50 0.59
32 35 0.41
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:46545 original size:21 final size:21
Alignment explanation
Indices: 46521--46560 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
46511 TTATTAGTAT
46521 GATTGATTTATTTTAAATATG
1 GATTGATTTATTTTAAATATG
46542 GATTGATTTATTTTAAATA
1 GATTGATTTATTTTAAATA
46561 ATTTTTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (21 bp):
GATTGATTTATTTTAAATATG
Found at i:46567 original size:63 final size:62
Alignment explanation
Indices: 46436--46565 Score: 158
Period size: 62 Copynumber: 2.1 Consensus size: 62
46426 GGATTGATTT
* * * *
46436 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTT
1 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTGATTA-TATGATTAAATA
*
46499 ATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAATATGGATTGATT-TAT-TTTAAATA
1 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA---ATTGATTATATGATTAAATA
46561 ATTTT
1 ATTTT
46566 TATTGTAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
62 28 0.47
63 25 0.42
65 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (62 bp):
ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTGATTATATGATTAAATA
Found at i:53293 original size:6 final size:6
Alignment explanation
Indices: 53282--53325 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
53272 TAGCCATACA
53282 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
53326 ATTAGATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:55913 original size:44 final size:44
Alignment explanation
Indices: 55865--55972 Score: 173
Period size: 43 Copynumber: 2.5 Consensus size: 44
55855 TAACTCGTAA
*
55865 TTTGCACCGAAGTGCCACATATTTGTCTCAAATGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCTCAAATGACCACATAGG
* *
55909 TTTGCACCG-AGTGCCACATAATTGTCTCGAATGACCACATATG
1 TTTGCACCGAAGTGCCACATAATTGTCTCAAATGACCACATAGG
*
55952 TTTGCACCAAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
55973 GTTTTACACC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 39 0.66
44 20 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTGTCTCAAATGACCACATAGG
Found at i:55982 original size:23 final size:23
Alignment explanation
Indices: 55943--55995 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
55933 TCTCGAATGA
*
55943 CCACATATGTTTGCACCAAAGTG
1 CCACATATGTTTACACCAAAGTG
*
55966 CCACATA-GTTTTACACCGAAGTG
1 CCACATATG-TTTACACCAAAGTG
55989 CCACATA
1 CCACATA
55996 ATTATCCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (23 bp):
CCACATATGTTTACACCAAAGTG
Found at i:56017 original size:21 final size:21
Alignment explanation
Indices: 55993--56033 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55983 GAAGTGCCAC
* *
55993 ATAATTATCCTGAAGGACCAT
1 ATAATTATCCCGAAGAACCAT
*
56014 ATAATTGTCCCGAAGAACCA
1 ATAATTATCCCGAAGAACCA
56034 CTTAAAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (21 bp):
ATAATTATCCCGAAGAACCAT
Found at i:57314 original size:15 final size:15
Alignment explanation
Indices: 57294--57325 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
57284 TTATCCCTTA
57294 ATAAAGGAGATAATT
1 ATAAAGGAGATAATT
57309 ATAAAGGAGATAATT
1 ATAAAGGAGATAATT
57324 AT
1 AT
57326 CCTTTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (15 bp):
ATAAAGGAGATAATT
Found at i:61076 original size:30 final size:31
Alignment explanation
Indices: 61020--61086 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
61010 GCATTAAGCA
*
61020 TTAATTGAATCAATTTTTTCGATTTGAGAAT
1 TTAATTGAATCAATTTCTTCGATTTGAGAAT
* * *
61051 TTAATTGATTTAATTTCTT-GATTTGAGAGT
1 TTAATTGAATCAATTTCTTCGATTTGAGAAT
61081 TTAATT
1 TTAATT
61087 AGATGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (31 bp):
TTAATTGAATCAATTTCTTCGATTTGAGAAT
Found at i:62368 original size:19 final size:19
Alignment explanation
Indices: 62316--62368 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
62306 TCTAGTTTCC
*
62316 TTTTTCATTTT-ATTACTA
1 TTTTTCATTTTAATTACGA
*
62334 TTTTTTATTTTAAATTA-GA
1 TTTTTCATTTT-AATTACGA
62353 TTTTTCATTTCTAATT
1 TTTTTCATTT-TAATT
62369 TCAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTCATTTTAATTACGA
Found at i:66898 original size:2 final size:2
Alignment explanation
Indices: 66891--66924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
66881 ACACCAACAA
66891 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
66925 CACTTTTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.