Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004510.1 Hibiscus syriacus cultivar Beakdansim tig00009948_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: 44435
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:6942 original size:13 final size:13
Alignment explanation
Indices: 6924--6986 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
6914 AGGTAATGGT
6924 ATAATTTTATTAA
1 ATAATTTTATTAA
*
6937 ATAATTTTA-TGA
1 ATAATTTTATTAA
6949 ATAA--TTATTATA
1 ATAATTTTATTA-A
*
6961 ATACATTTTTTTAA
1 ATA-ATTTTATTAA
*
6975 TTAAATTTTATT
1 AT-AATTTTATT
6987 TTATATCAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
10 3 0.08
11 1 0.03
12 10 0.26
13 10 0.26
14 9 0.23
15 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:8874 original size:24 final size:23
Alignment explanation
Indices: 8846--8900 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
8836 ATTAAAACAA
*
8846 TTTAATAAATATAATATTTCATAT
1 TTTAATAAATATAA-ATTTAATAT
* * *
8870 TTTAAAAAATATTAATTTAATTT
1 TTTAATAAATATAAATTTAATAT
8893 TTTAATAA
1 TTTAATAA
8901 CCTTGTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAATAAATATAAATTTAATAT
Found at i:27202 original size:21 final size:20
Alignment explanation
Indices: 27177--27217 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
27167 TAAAGTAAAA
27177 TTATTTTTGA-TTATATTATTT
1 TTATTTTT-ATTTA-ATTATTT
27198 TTATTTTTATTTAATTATTT
1 TTATTTTTATTTAATTATTT
27218 GAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTTTTATTTAATTATTT
Found at i:27214 original size:20 final size:21
Alignment explanation
Indices: 27177--27217 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27167 TAAAGTAAAA
27177 TTATTTTTGATTATATTATTT
1 TTATTTTTGATTATATTATTT
27198 TTATTTTT-ATT-TAATTATTT
1 TTATTTTTGATTAT-ATTATTT
27218 GAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 10 0.53
21 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATTTTTGATTATATTATTT
Found at i:28712 original size:21 final size:21
Alignment explanation
Indices: 28686--28730 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28676 GATTTCTGGG
* *
28686 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
28707 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
28728 CAA
1 CAA
28731 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:30498 original size:103 final size:103
Alignment explanation
Indices: 30314--30531 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
30304 GTCGAGGGTC
* *
30314 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
30379 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
30417 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
*
30482 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
30520 TATGTGGTCCTT
1 TATGTGGTCCTT
30532 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:30615 original size:23 final size:23
Alignment explanation
Indices: 30547--30607 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
30537 CATTATTATA
*
30547 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
30570 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
30593 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
30608 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:33838 original size:21 final size:21
Alignment explanation
Indices: 33812--33856 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33802 GATTTCTGGG
* *
33812 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33833 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33854 CAA
1 CAA
33857 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35664 original size:103 final size:103
Alignment explanation
Indices: 35439--35656 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
35429 GTCGAGGGTC
35439 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
35504 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
35542 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
35607 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
35645 TATGTGGTCCTT
1 TATGTGGTCCTT
35657 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:35703 original size:23 final size:23
Alignment explanation
Indices: 35673--35732 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
35663 ATTATTATAT
*
35673 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
35696 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
35719 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
35733 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:35740 original size:23 final size:23
Alignment explanation
Indices: 35663--35740 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
35653 CCTTATGGAC
* *
35663 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
35687 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
35710 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
35733 TTTATATG
1 ATTATATG
35741 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:43416 original size:20 final size:20
Alignment explanation
Indices: 43391--43759 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
43381 GATTTTCCAT
* ** *
43391 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
43411 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
43431 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43451 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
43471 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
* *
43491 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43511 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
43531 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43551 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
43571 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43591 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
43611 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43631 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
43651 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43671 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
43691 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43711 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
43731 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
43751 AATCACAAC
1 AATCGCAAC
43760 ACTAAATTTT
Statistics
Matches: 304, Mismatches: 35, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 296 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Done.