Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005823.1 Hibiscus syriacus cultivar Beakdansim tig00013643_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: 58723
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:336 original size:18 final size:20
Alignment explanation
Indices: 313--359 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
303 AAAAATCCAG
313 CAAAGAAAA-T-AAAGCACT
1 CAAAGAAAATTGAAAGCACT
331 CAAAGAAAAATTGAAAGCACT
1 CAAAG-AAAATTGAAAGCACT
352 CAAA-AAAA
1 CAAAGAAAA
360 GAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 1 0.04
21 12 0.46
ACGTcount: A:0.64, C:0.15, G:0.11, T:0.11
Consensus pattern (20 bp):
CAAAGAAAATTGAAAGCACT
Found at i:7161 original size:20 final size:21
Alignment explanation
Indices: 7133--7179 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7123 GGATTATGAG
*
7133 AAATTATTTTT-AAAATAT-AA
1 AAATGATTTTTCAAAAT-TGAA
7153 AAATGATTTTTCAAAATTGAA
1 AAATGATTTTTCAAAATTGAA
7174 AAATGA
1 AAATGA
7180 AAACAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (21 bp):
AAATGATTTTTCAAAATTGAA
Found at i:31613 original size:33 final size:33
Alignment explanation
Indices: 31576--31645 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
31566 AAATGTAGGC
* *
31576 TGATTTAATGGTGAAGAGATGATAAGGGAATGA
1 TGATTTAATGGTAAAGAGATGATAAGGGAAGGA
31609 TGATTTAATGGTAAAGAGATGATAAGGGAAGGA
1 TGATTTAATGGTAAAGAGATGATAAGGGAAGGA
31642 TGAT
1 TGAT
31646 GATATAAGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (33 bp):
TGATTTAATGGTAAAGAGATGATAAGGGAAGGA
Found at i:31648 original size:17 final size:17
Alignment explanation
Indices: 31589--31649 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
31579 TTTAATGGTG
31589 AAGA-GATGATAAGGGA
1 AAGATGATGATAAGGGA
* * *
31605 ATGATGAT-TTAATGGTA
1 AAGATGATGATAA-GGGA
31622 AAGA-GATGATAAGGGA
1 AAGATGATGATAAGGGA
*
31638 AGGATGATGATA
1 AAGATGATGATA
31650 TAAGCGTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
16 15 0.44
17 19 0.56
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (17 bp):
AAGATGATGATAAGGGA
Found at i:36189 original size:14 final size:14
Alignment explanation
Indices: 36170--36197 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36160 TAAGATACTA
36170 TTTCCATCACCATC
1 TTTCCATCACCATC
36184 TTTCCATCACCATC
1 TTTCCATCACCATC
36198 CTCCATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:36701 original size:30 final size:30
Alignment explanation
Indices: 36659--36726 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
36649 AAATTTGGAG
*
36659 TGCAAAA-GAAAGAAAAGAAAAGAAGAAAAT
1 TGCAAAACAAAAGAAAAGAAAAGAA-AAAAT
* *
36689 T-CAAAACAAAAGAAAAGAGAAGAAAAAGT
1 TGCAAAACAAAAGAAAAGAAAAGAAAAAAT
36718 TGCAAAACA
1 TGCAAAACA
36727 CACTAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (30 bp):
TGCAAAACAAAAGAAAAGAAAAGAAAAAAT
Found at i:41442 original size:33 final size:33
Alignment explanation
Indices: 41400--41467 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
41390 TTGATGAATA
**
41400 AATGATGATTTAATGGTGAAGATATGTTAAGGG
1 AATGATGATTTAATGGTGAAGATATGAGAAGGG
41433 AATGATGATTTAATGGTGAAGATATGAGAAGGG
1 AATGATGATTTAATGGTGAAGATATGAGAAGGG
41466 AA
1 AA
41468 AAATGATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (33 bp):
AATGATGATTTAATGGTGAAGATATGAGAAGGG
Found at i:41506 original size:13 final size:14
Alignment explanation
Indices: 41488--41523 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41478 ATGGGCGTGA
*
41488 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
41501 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
41515 ATGGTGATG
1 ATGGTGATG
41524 AAAATAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:41526 original size:13 final size:13
Alignment explanation
Indices: 41488--41526 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41478 ATGGGCGTGA
* *
41488 ATGGTGATGGAGG
1 ATGGTGATGAAAG
41501 ATGGTGATGGAAAG
1 ATGGTGAT-GAAAG
41515 ATGGTGATGAAA
1 ATGGTGATGAAA
41527 ATAGTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:47570 original size:34 final size:35
Alignment explanation
Indices: 47527--47598 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
47517 AATTAAGAGT
* * *
47527 TAGTTTAATAGATGAAC-AAGTTTAATGAATGAAC
1 TAGTTTAATAAATGAACTAACTTTAATAAATGAAC
*
47561 TAGTTTAATAAATGAACTAACTTTATTAAATGAAC
1 TAGTTTAATAAATGAACTAACTTTAATAAATGAAC
47596 TAG
1 TAG
47599 ATGCATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 16 0.48
35 17 0.52
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAACTTTAATAAATGAAC
Found at i:47578 original size:17 final size:17
Alignment explanation
Indices: 47527--47598 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
47517 AATTAAGAGT
*
47527 TAGTTTAATAGATGAAC
1 TAGTTTAATAAATGAAC
* *
47544 AAGTTTAATGAATGAAC
1 TAGTTTAATAAATGAAC
47561 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
47578 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
47596 TAG
1 TAG
47599 ATGCATGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 31 0.67
18 15 0.33
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:48439 original size:14 final size:14
Alignment explanation
Indices: 48411--48447 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
48401 TGGCATGAAA
*
48411 GTGATGG-AGGATG
1 GTGATGGAAAGATG
48424 GTGATGGAAAGATG
1 GTGATGGAAAGATG
48438 GTGATGGAAA
1 GTGATGGAAA
48448 TAATATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:52236 original size:4 final size:5
Alignment explanation
Indices: 52188--52238 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
52178 TTTTGCAACT
52188 TTTTC TTTTC TTTTC TTTTGC TTTGAAT- TTTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTT-C TTT---TC TTTTC TTTTC TTTTC TTTTC
52235 TTTT
1 TTTT
52239 GCACTCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 5 0.12
5 27 0.68
6 4 0.10
7 3 0.08
9 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:55285 original size:16 final size:15
Alignment explanation
Indices: 55262--55310 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
55252 AGTTATCTTA
55262 ATTTCTTATTATTTC
1 ATTTCTTATTATTTC
*
55277 ATTTCCTTATTCTTTC
1 ATTT-CTTATTATTTC
*
55293 ATCTT-TTCTTATTTC
1 AT-TTCTTATTATTTC
55308 ATT
1 ATT
55311 ACCTTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 14 0.48
16 12 0.41
17 2 0.07
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTCTTATTATTTC
Done.