Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002521.1 Hibiscus syriacus cultivar Beakdansim tig00005132_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: 64228
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3418 original size:18 final size:18
Alignment explanation
Indices: 3395--3430 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3385 TCCTAACTTA
3395 TAGAGATTCCTAATGTGG
1 TAGAGATTCCTAATGTGG
* *
3413 TAGAGATTTCTGATGTGG
1 TAGAGATTCCTAATGTGG
3431 AAGCACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.31, T:0.36
Consensus pattern (18 bp):
TAGAGATTCCTAATGTGG
Found at i:4514 original size:22 final size:22
Alignment explanation
Indices: 4486--4532 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
4476 AAATACATCA
4486 GCGACAAAACCTTTCGTTGGTG
1 GCGACAAAACCTTTCGTTGGTG
4508 GCGACAAAACCTTTCGTTGGTG
1 GCGACAAAACCTTTCGTTGGTG
4530 GCG
1 GCG
4533 CCATATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (22 bp):
GCGACAAAACCTTTCGTTGGTG
Found at i:6305 original size:4 final size:4
Alignment explanation
Indices: 6298--6390 Score: 89
Period size: 4 Copynumber: 22.5 Consensus size: 4
6288 AATAAGTTAG
* *
6298 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAC AAAT ACATTT GAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT -AAAT
* * * *
6349 AAAT GAAT AAAT AGAAA AAAT -ATT AAAG AAAT AAAT AAAT AA
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AA
6391 TTCAAAATGA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
3 2 0.03
4 62 0.86
5 5 0.07
6 2 0.03
7 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:6385 original size:47 final size:47
Alignment explanation
Indices: 6283--6386 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 47
6273 ATTTCAAAAC
* *
6283 AAATAAATAAGTTAGAAATAAATAAATAAATAAATAAATAAATAAAT
1 AAATAAATAAGTTAGAAATAAATAAATAAATAAAAAAATAAATAAAG
* * * *
6330 AAACAAATACA-TTTGAAATAAATGAATAAATAGAAAAAAT-ATTAAAG
1 AAATAAATA-AGTTAGAAATAAATAAATAAATA-AAAAAATAAATAAAG
6377 AAATAAATAA
1 AAATAAATAA
6387 ATAATTCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
46 1 0.02
47 40 0.83
48 7 0.15
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (47 bp):
AAATAAATAAGTTAGAAATAAATAAATAAATAAAAAAATAAATAAAG
Found at i:7682 original size:24 final size:24
Alignment explanation
Indices: 7654--7715 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
7644 CGTTCGTGAA
*
7654 CGTTCAGTTATGTTCGTTTCTGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* * *
7678 TGTTCGGTTATGTTTGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
7702 CATTCATTTATGTT
1 CGTTCAGTTATGTT
7716 TAAGTCAATC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:8383 original size:10 final size:10
Alignment explanation
Indices: 8368--8425 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
8358 GGTCTCCAAT
8368 GTTTATGTTC
1 GTTTATGTTC
8378 GTTTATGTTC
1 GTTTATGTTC
*
8388 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
8400 GTTCGTGTTC
1 GTTTATGTTC
8410 GTTTATGTTC
1 GTTTATGTTC
8420 GTTTAT
1 GTTTAT
8426 TTATTAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 27 0.71
11 7 0.18
12 4 0.11
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:8392 original size:16 final size:16
Alignment explanation
Indices: 8373--8421 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
8363 CCAATGTTTA
8373 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
8389 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
8405 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
8421 T
1 T
8422 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:8516 original size:16 final size:16
Alignment explanation
Indices: 8491--8531 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
8481 AAAAACATTT
8491 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
8507 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
8523 T-TT-ATTTAT
1 TGTTCATTTAT
8532 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:8682 original size:18 final size:19
Alignment explanation
Indices: 8640--8682 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
8630 ATTGGTTTAC
* *
8640 GGAATGTAAGATTACCAGT
1 GGAATATAAAATTACCAGT
8659 GGAATATAAAATTACCAG-
1 GGAATATAAAATTACCAGT
8677 GGAATA
1 GGAATA
8683 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATATAAAATTACCAGT
Found at i:12224 original size:31 final size:30
Alignment explanation
Indices: 12176--12251 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
12166 AGAAATTGTT
* *
12176 AAATTGTTA-AAAAAATAATTTAGA-TTATC
1 AAATTATTACAAAAAATAA-TTAAATTTATC
12205 AAATTATTACAAAATAATAATTAAATTTATC
1 AAATTATTACAAAA-AATAATTAAATTTATC
*
12236 AAATTATTGCAAAAAA
1 AAATTATTACAAAAAA
12252 ATCTTTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.20
30 10 0.24
31 23 0.56
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTATTACAAAAAATAATTAAATTTATC
Found at i:15693 original size:14 final size:15
Alignment explanation
Indices: 15670--15709 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
15660 AACTTAAAAA
15670 AGTAATAATAAAA-TT
1 AGTAA-AATAAAATTT
15685 AGTAAAATAAAATTT
1 AGTAAAATAAAATTT
*
15700 AATAAAATAA
1 AGTAAAATAA
15710 CAAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
AGTAAAATAAAATTT
Found at i:15705 original size:15 final size:14
Alignment explanation
Indices: 15676--15724 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
15666 AAAAAGTAAT
*
15676 AATAAAATTAGTAA
1 AATAAAATTAATAA
15690 AATAAAATTTAATAA
1 AATAAAA-TTAATAA
* *
15705 AATAACAAATAATTA
1 AATAA-AATTAATAA
15720 AATAA
1 AATAA
15725 TTATAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 7 0.23
15 21 0.70
16 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAAAATTAATAA
Found at i:23458 original size:46 final size:46
Alignment explanation
Indices: 23391--23485 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 46
23381 ATTTAATTAA
* *
23391 TTTTTAATAGTATGTGATAATTACAATGTAATATATGTTTACAATT
1 TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
* * *
23437 TTTTTAATAGCATATGGTAATTATAATGTAATATATGTTTATAATT
1 TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
23483 TTT
1 TTT
23486 AATCAATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.51
Consensus pattern (46 bp):
TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
Found at i:23871 original size:13 final size:13
Alignment explanation
Indices: 23853--23877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23843 TTTTCGATTC
23853 TCTTTTATTTTTT
1 TCTTTTATTTTTT
23866 TCTTTTATTTTT
1 TCTTTTATTTTT
23878 AATAAGAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TCTTTTATTTTTT
Found at i:25705 original size:36 final size:36
Alignment explanation
Indices: 25664--25736 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
25654 GTTAGTAAAC
* *
25664 ATTATTCTATTAAATTCTCTTTGTACTGTAAACTTA
1 ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
*
25700 ATTATTCCATTAAATTCTCCTTGTACTGTAAATTTA
1 ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
25736 A
1 A
25737 ATCCAACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (36 bp):
ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
Found at i:32890 original size:21 final size:21
Alignment explanation
Indices: 32860--32914 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
32850 GACACGATGC
*
32860 TTATACGATAATTTACAAAGT
1 TTATATGATAATTTACAAAGT
* *
32881 TTATATGATAATCTACAATGT
1 TTATATGATAATTTACAAAGT
*
32902 TTATGTGATAATT
1 TTATATGATAATT
32915 CATGATGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (21 bp):
TTATATGATAATTTACAAAGT
Found at i:33847 original size:33 final size:33
Alignment explanation
Indices: 33805--33868 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
33795 ATAAATTATT
33805 ATTATTATTCAAAAAGTTTATCTGAATATTTCC
1 ATTATTATTCAAAAAGTTTATCTGAATATTTCC
* * *
33838 ATTATTATTCATAAATTTTATTTGAATATTT
1 ATTATTATTCAAAAAGTTTATCTGAATATTT
33869 TCTTTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (33 bp):
ATTATTATTCAAAAAGTTTATCTGAATATTTCC
Found at i:35976 original size:31 final size:31
Alignment explanation
Indices: 35930--36004 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
35920 AAGGCACCAC
* *
35930 AGGATATAACATATACAGTTTCGAAATTTTA
1 AGGATAAAACATATACAGTTTCAAAATTTTA
*
35961 AGGATAAAACGTATACAGTTTCAAAATTTTA
1 AGGATAAAACATATACAGTTTCAAAATTTTA
35992 AGGATAAAACATA
1 AGGATAAAACATA
36005 GATATTACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (31 bp):
AGGATAAAACATATACAGTTTCAAAATTTTA
Found at i:37372 original size:18 final size:18
Alignment explanation
Indices: 37346--37387 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
37336 TAAAACGATT
*
37346 AAAAAAAACACTTATAA-C
1 AAAAAAAAC-CCTATAACC
*
37364 AAAAGAAACCCTATAACC
1 AAAAAAAACCCTATAACC
37382 AAAAAA
1 AAAAAA
37388 GAAAACAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAAAACCCTATAACC
Done.