Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005378.1 Hibiscus syriacus cultivar Beakdansim tig00012275_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: 184360
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:175460 original size:99 final size:100
Alignment explanation
Indices: 175235--175674 Score: 344
Period size: 99 Copynumber: 4.3 Consensus size: 100
175225 AGCGATACAA
* * * * * *
175235 TTGTTTAAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA
1 TTGTTTCAAGTGAAACAATTTCAAA-ATTTGTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAA
*** *
175300 TTTGTTTTTAAGAAAAACAATCTCAAATGCTATCAATT
65 TTTG-TTTT-AGAAAAACAATCTCAAATAAGATAAATT
* * **
175338 TTGTTTCAAGTGAAACAACTTCAAAATTTGTGTTTCGAAGAAAAACTGTCTCAAGTGAGATGAAA
1 TTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTC-AAGAGAAACTGTCTCAAGTGAGACAAAA
* *
175403 TTTGTTTT-G-AGAACAATCTCAAGTAAGATAAATT
65 TTTGTTTTAGAAAAACAATCTCAAATAAGATAAATT
* * * *
175437 TTGTTTCAAGTGAAACAATTTCAAAATTTGTATTTCTAGGGAAACTGTCTTAAGTGAGACAAAAT
1 TTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAAT
*
175502 TTGTTTTTAAGAAAAACAATATCAAAT--G-T---TT
66 TTG-TTTT-AGAAAAACAATCTCAAATAAGATAAATT
* * * * * * * *
175533 GTGTCTT-AAG-GAAGACTATCTCAAGTGAGACGAAATTTGT-TTTTAAAATAAATTGACTCAAG
1 TTGT-TTCAAGTGAA-ACAAT-T----T----CAAAATTTGTGTTTCAAGAGAAACTGTCTCAAG
* * *
175595 CGAGACAAAATTTGTTTTTAGAGAAAACAATCTCAAGTAAGATCAATT
55 TGAGACAAAATTTG-TTTTAGA-AAAACAATCTCAAATAAGATAAATT
175643 TTGTTTCAAGTGAAACAATTTCAAAATTTGTG
1 TTGTTTCAAGTGAAACAATTTCAAAATTTGTG
175675 AAATTTGTCT
Statistics
Matches: 267, Mismatches: 44, Indels: 53
0.73 0.12 0.15
Matches are distributed among these distances:
95 3 0.01
96 12 0.04
97 3 0.01
98 26 0.10
99 58 0.22
100 2 0.01
101 11 0.04
102 25 0.09
103 52 0.19
104 45 0.17
105 10 0.04
106 1 0.00
107 1 0.00
109 3 0.01
110 12 0.04
111 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (100 bp):
TTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAAT
TTGTTTTAGAAAAACAATCTCAAATAAGATAAATT
Found at i:175630 original size:37 final size:35
Alignment explanation
Indices: 175550--175631 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 35
175540 AAGGAAGACT
* *
175550 ATCTCAAGTGAGACGAAATTTGTTTTTAAAATAAA
1 ATCTCAAGCGAGACAAAATTTGTTTTTAAAATAAA
*
175585 TTGACTCAAGCGAGACAAAATTTGTTTTTAGAGAA-AACA
1 AT--CTCAAGCGAGACAAAATTTGTTTTTA-A-AATAA-A
175624 ATCTCAAG
1 ATCTCAAG
175632 TAAGATCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
35 1 0.03
37 30 0.79
38 3 0.08
39 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (35 bp):
ATCTCAAGCGAGACAAAATTTGTTTTTAAAATAAA
Found at i:178564 original size:18 final size:17
Alignment explanation
Indices: 178538--178605 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 17
178528 ACTTGATCCA
*
178538 TTTTATTTCTTCTTTTT
1 TTTTCTTTCTTCTTTTT
178555 CTTTTCTTTCTTCTTTTT
1 -TTTTCTTTCTTCTTTTT
*
178573 TTTCTCTTT-GT-TTTTT
1 TTT-TCTTTCTTCTTTTT
178589 TTTTCTTTTCTTCTTTT
1 TTTTC-TTTCTTCTTTT
178606 CTCTTTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
17 5 0.12
18 25 0.58
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (17 bp):
TTTTCTTTCTTCTTTTT
Found at i:178574 original size:15 final size:15
Alignment explanation
Indices: 178547--178605 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
178537 ATTTTATTTC
178547 TTCTTT-TTCTTTTCT
1 TTCTTTCTTCTTTT-T
178562 TTC-TTCTT-TTTTT
1 TTCTTTCTTCTTTTT
* *
178575 TCTCTTTGTTTTTTTT
1 T-TCTTTCTTCTTTTT
178591 TTCTTTTCTTCTTTT
1 TTC-TTTCTTCTTTT
178606 CTCTTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.06
14 8 0.22
15 11 0.31
16 15 0.42
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TTCTTTCTTCTTTTT
Found at i:178577 original size:30 final size:27
Alignment explanation
Indices: 178538--178621 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 27
178528 ACTTGATCCA
*
178538 TTTTATTTCTTCTTTTTCTTTTCTTTCTT
1 TTTTTTTTC-TCTTTTT-TTTTCTTTCTT
*
178567 CTTTTTTTTCTCTTTGTTTTTTTTTTCTT
1 -TTTTTTTTCTCTTT-TTTTTTCTTTCTT
*
178596 TTCTTCTTTTCTCTTTGTTTTTCTTT
1 TT-TT-TTTTCTCTTTTTTTTTCTTT
178622 GCTCTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.04
29 25 0.53
30 20 0.43
ACGTcount: A:0.01, C:0.17, G:0.02, T:0.80
Consensus pattern (27 bp):
TTTTTTTTCTCTTTTTTTTTCTTTCTT
Found at i:178588 original size:17 final size:17
Alignment explanation
Indices: 178550--178639 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 17
178540 TTATTTCTTC
* *
178550 TTTTTCTTT-TCTTTCT
1 TTTTTTTTTCTCTTTGT
178566 TCTTTTTTTTCTCTTTG-
1 T-TTTTTTTTCTCTTTGT
178583 TTTTTTTTT-TC-TT-T
1 TTTTTTTTTCTCTTTGT
* *
178597 TCTTCTTTTCTCTTTGT
1 TTTTTTTTTCTCTTTGT
* * * *
178614 TTTTCTTTGCTCTATAT
1 TTTTTTTTTCTCTTTGT
178631 TTTTTTTTT
1 TTTTTTTTT
178640 GCTTTTTTCT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.16
15 4 0.07
16 11 0.19
17 29 0.50
18 5 0.09
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCTCTTTGT
Found at i:178588 original size:34 final size:30
Alignment explanation
Indices: 178550--178621 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 30
178540 TTATTTCTTC
*
178550 TTTTTCTTTTCTTTCTTCTTTTTTTTCTCTTTG
1 TTTTTCTTTTC-TT-TTC-TTCTTTTCTCTTTG
*
178583 TTTTTTTTTTCTTTTCTTCTTTTCTCTTTG
1 TTTTTCTTTTCTTTTCTTCTTTTCTCTTTG
178613 TTTTTCTTT
1 TTTTTCTTT
178622 GCTCTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.58
31 3 0.08
32 2 0.06
33 10 0.28
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (30 bp):
TTTTTCTTTTCTTTTCTTCTTTTCTCTTTG
Found at i:178610 original size:15 final size:15
Alignment explanation
Indices: 178553--178611 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
178543 TTTCTTCTTT
178553 TTCTTTTCT-TTCTTC
1 TTCTTTTCTCTT-TTC
*
178568 TTTTTTTTCTCTTTGT-
1 -TTCTTTTCTCTTT-TC
* *
178584 TTTTTTTTTCTTTTC
1 TTCTTTTCTCTTTTC
178599 TTCTTTTCTCTTT
1 TTCTTTTCTCTTT
178612 GTTTTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 1 0.03
15 23 0.64
16 9 0.25
17 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (15 bp):
TTCTTTTCTCTTTTC
Found at i:178634 original size:42 final size:40
Alignment explanation
Indices: 178550--178654 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 40
178540 TTATTTCTTC
* * *
178550 TTTTTCTTTTCTTTCTTCT-TTT-TTTTCTCTTTGTTTTT
1 TTTTTCTTTTCTTTTTTCTCTTTGTTTTCTCTTTGTTATA
178588 TTTTTCTTTTCTTCTTTTCTCTTTGTTTT-TCTTTGCTCTATA
1 TTTTTCTTTTCTT-TTTTCTCTTTGTTTTCTCTTTG-T-TATA
*
178630 TTTTTTTTTTGCTTTTTTCTCTTTG
1 TTTTTCTTTT-CTTTTTTCTCTTTG
178655 CTTTGATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
38 13 0.23
39 5 0.09
40 9 0.16
41 5 0.09
42 22 0.39
43 3 0.05
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (40 bp):
TTTTTCTTTTCTTTTTTCTCTTTGTTTTCTCTTTGTTATA
Found at i:181634 original size:24 final size:24
Alignment explanation
Indices: 181602--181648 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
181592 ATATTTAGGG
181602 GTCTCAGAAT-GATGCTGATCAGGT
1 GTCTCAGAATAG-TGCTGATCAGGT
181626 GTCTCAGAATAGTGCTGATCAGG
1 GTCTCAGAATAGTGCTGATCAGG
181649 AGTCGGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (24 bp):
GTCTCAGAATAGTGCTGATCAGGT
Done.