Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004688.1 Hibiscus syriacus cultivar Beakdansim tig00010521_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: 54266
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:651 original size:17 final size:17
Alignment explanation
Indices: 629--661 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
619 TTTCATTTAA
629 AATTT-ATTGTATTTGCT
1 AATTTAATT-TATTTGCT
646 AATTTAATTTATTTGC
1 AATTTAATTTATTTGC
662 AAAAGGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (17 bp):
AATTTAATTTATTTGCT
Found at i:4287 original size:2 final size:2
Alignment explanation
Indices: 4280--4310 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4270 GGAAATCACG
4280 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4311 TGCACAGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4548 original size:90 final size:91
Alignment explanation
Indices: 4394--4575 Score: 357
Period size: 90 Copynumber: 2.0 Consensus size: 91
4384 TGCTCGTACG
4394 GATGAAATGGGAAGAGAGATAAAAAAAATTCTTTAACCGTAGAGACAAGAGAGGGGCAATTGCAA
1 GATGAAATGGGAAGAGAGATAAAAAAAATTCTTTAACCGTAGAGACAAGAGAGGGGCAATTGCAA
4459 AGGACATGGTTATGGATTTTATCACA
66 AGGACATGGTTATGGATTTTATCACA
4485 GATGAAATGGGAAGAGAGAT-AAAAAAATTCTTTAACCGTAGAGACAAGAGAGGGGCAATTGCAA
1 GATGAAATGGGAAGAGAGATAAAAAAAATTCTTTAACCGTAGAGACAAGAGAGGGGCAATTGCAA
4549 AGGACATGGTTATGGATTTTATCACA
66 AGGACATGGTTATGGATTTTATCACA
4575 G
1 G
4576 TGTTGCGGGT
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 71 0.78
91 20 0.22
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (91 bp):
GATGAAATGGGAAGAGAGATAAAAAAAATTCTTTAACCGTAGAGACAAGAGAGGGGCAATTGCAA
AGGACATGGTTATGGATTTTATCACA
Found at i:13354 original size:11 final size:12
Alignment explanation
Indices: 13327--13353 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13317 ACGTCAATAA
13327 TTTTATTAATTT
1 TTTTATTAATTT
13339 TTTTATTAATTT
1 TTTTATTAATTT
13351 TTT
1 TTT
13354 AACGACGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTAATTT
Found at i:19601 original size:7 final size:7
Alignment explanation
Indices: 19583--19617 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
19573 TCTCGTCTCG
19583 TGGTCG-
1 TGGTCGT
19589 TGGTCGT
1 TGGTCGT
19596 TGGTCGT
1 TGGTCGT
19603 TGGTCGT
1 TGGTCGT
19610 TGGTCGT
1 TGGTCGT
19617 T
1 T
19618 TTCGTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.00, C:0.14, G:0.43, T:0.43
Consensus pattern (7 bp):
TGGTCGT
Found at i:21122 original size:28 final size:28
Alignment explanation
Indices: 21086--21148 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
21076 TCCTCGGCTG
21086 ATCACCTAGTAGAATAACCTACCCCTGA
1 ATCACCTAGTAGAATAACCTACCCCTGA
21114 ATCACCTAGTAGAATAACCTACCCCTGA
1 ATCACCTAGTAGAATAACCTACCCCTGA
21142 ATCACCT
1 ATCACCT
21149 GCAGATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (28 bp):
ATCACCTAGTAGAATAACCTACCCCTGA
Found at i:25829 original size:19 final size:19
Alignment explanation
Indices: 25805--25842 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25795 TGTCGCAAGG
*
25805 AGCACTTGGCGACCTATGA
1 AGCACTTGGCGACCAATGA
25824 AGCACTTGGCGACCAATGA
1 AGCACTTGGCGACCAATGA
25843 GGTCACTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (19 bp):
AGCACTTGGCGACCAATGA
Found at i:26209 original size:12 final size:12
Alignment explanation
Indices: 26192--26216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26182 TGTAACAATA
26192 AACTTTAATTTT
1 AACTTTAATTTT
26204 AACTTTAATTTT
1 AACTTTAATTTT
26216 A
1 A
26217 TCACTAGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
AACTTTAATTTT
Found at i:31387 original size:25 final size:23
Alignment explanation
Indices: 31327--31377 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
31317 ATATGAATCA
*
31327 TATTTAACACTAAAAATATTATTT
1 TATTTAA-ATTAAAAATATTATTT
*
31351 TATTTCAATTAAAAATA-TATTT
1 TATTTAAATTAAAAATATTATTT
31373 TATTT
1 TATTT
31378 TAATATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 9 0.36
24 6 0.24
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAAATTAAAAATATTATTT
Found at i:31719 original size:31 final size:32
Alignment explanation
Indices: 31665--31726 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
31655 AAAAAATAAG
* *
31665 ATATTGTCACTTTCATTTTTTATTTAATTAAA
1 ATATGGTCACTTTCAGTTTTTATTTAATTAAA
31697 ATATGGTCACTTTC-GTTTTTATTTAATTAA
1 ATATGGTCACTTTCAGTTTTTATTTAATTAA
31727 GATGTGATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (32 bp):
ATATGGTCACTTTCAGTTTTTATTTAATTAAA
Found at i:31921 original size:27 final size:27
Alignment explanation
Indices: 31891--31978 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 27
31881 AGAAAACAAA
31891 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
31918 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
31943 -ATAAAAATATTTTTAAGTTAA--T-AT
1 AAT-AAAATATTTTTAAATTAAGTTAAT
31967 ATATAAAATATT
1 A-ATAAAATATT
31979 ATGAATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
24 4 0.08
25 28 0.53
26 5 0.09
27 16 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:31988 original size:25 final size:23
Alignment explanation
Indices: 31910--31992 Score: 64
Period size: 25 Copynumber: 3.5 Consensus size: 23
31900 TTTTTAAATT
31910 AAGTT-AATAATAAAATATATTTAAT-
1 AAGTTAAAT-ATAAAA-ATA-TT-ATG
* *
31935 AAGTT-AATATAAAAATATTTTT
1 AAGTTAAATATAAAAATATTATG
31957 AAGTTAATATATATAAAATATTATG
1 AAGTTAA-ATATA-AAAATATTATG
*
31982 AATTTAAATAT
1 AAGTTAAATAT
31993 TTATACACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
21 1 0.02
22 7 0.14
23 4 0.08
24 15 0.30
25 23 0.46
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AAGTTAAATATAAAAATATTATG
Found at i:46208 original size:2 final size:2
Alignment explanation
Indices: 46201--46242 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
46191 AGAATCAATC
*
46201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46243 GCAAAAGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47861 original size:14 final size:16
Alignment explanation
Indices: 47824--47869 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
47814 AAAAAATGAA
47824 AGTTTAAATATTAAAAT
1 AGTTTAAATATT-AAAT
*
47841 AGATTAAA-ATT-AAT
1 AGTTTAAATATTAAAT
47855 AGTTTAAATACTTAA
1 AGTTTAAATA-TTAA
47870 TGTGTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.42
15 1 0.04
16 5 0.21
17 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (16 bp):
AGTTTAAATATTAAAT
Done.