Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008874.1 Hibiscus syriacus cultivar Beakdansim tig00112111_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: 58649
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1444 original size:12 final size:12
Alignment explanation
Indices: 1427--1451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1417 TCTTCGGGGA
1427 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1439 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1451 C
1 C
1452 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1660 original size:24 final size:24
Alignment explanation
Indices: 1626--1672 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1616 CTGAAACATC
1626 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1650 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1673 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2370 original size:20 final size:20
Alignment explanation
Indices: 2342--2710 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2332 AAATTTCAGT
* * * *
2342 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2362 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2382 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2402 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2422 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2442 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2462 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2482 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2502 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2522 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2542 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2562 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2582 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2602 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2622 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2642 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2662 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2682 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2702 GTTGCGATT
1 GTTGCGATT
2711 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:11026 original size:108 final size:107
Alignment explanation
Indices: 10890--11103 Score: 347
Period size: 108 Copynumber: 2.0 Consensus size: 107
10880 TAAAACATAT
10890 ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATCAATGAGAAAGCAAATGCACCCACC
1 ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATCAATGAGAAAGCAAATGCACCCACC
* *
10955 CTGGTAAATTTAGGAACTAAATGAATATTTACTTTCAATCAA
66 CTGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCAA
* ** *
10997 ACAGTTTTCAGTGCCAATAAGCAACCAATTATCAGAATGGTCTATGAGAAAGCAAATGCACCCAC
1 ACAGTTTT-AATGCCAATAAGCAACCAATTATCAGAATCATCAATGAGAAAGCAAATGCACCCAC
* *
11062 CCTGGCAAATTTGGGAACTAAATAAATATTTCCTTTCAATCA
65 CCTGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCA
11104 TCTATATAGA
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
107 8 0.08
108 90 0.92
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (107 bp):
ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATCAATGAGAAAGCAAATGCACCCACC
CTGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCAA
Found at i:13194 original size:41 final size:41
Alignment explanation
Indices: 13118--13203 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
13108 CTTGAGATTT
*
13118 TTTTGACTAAGAATTCGATCTGGGTATCTGAGTATTT-CCTA
1 TTTTGACTAAGAATTCGATCTCGGTATCTGAGTATTTGCC-A
* * *
13159 TTTTGACTAAGAACTT-GATCTCGGTGTTTGGGTATTTGCCA
1 TTTTGACTAAGAA-TTCGATCTCGGTATCTGAGTATTTGCCA
13200 TTTT
1 TTTT
13204 CTTCATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (41 bp):
TTTTGACTAAGAATTCGATCTCGGTATCTGAGTATTTGCCA
Found at i:20952 original size:69 final size:69
Alignment explanation
Indices: 20835--20975 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
20825 CTGTCATGTC
* * * ***
20835 TCAGGAAGTTCTTGGTGATCTGCAAGAGGAACTTCTATTGATTATTGAGAATAAGGCTGAAACTA
1 TCAGGAAGCTCTTGATGATCTGCAAGAGAAACTTCTACCAATTATTGAGAATAAGGCTGAAACTA
20900 GTGT
66 GTGT
* *
20904 TCAGGAAGCTCTTGATGATCTGCAAGAGAAACTTCTACCAATTGTTGAGAATGAGGCTGAAACTA
1 TCAGGAAGCTCTTGATGATCTGCAAGAGAAACTTCTACCAATTATTGAGAATAAGGCTGAAACTA
20969 GTGT
66 GTGT
20973 TCA
1 TCA
20976 AATAGGTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (69 bp):
TCAGGAAGCTCTTGATGATCTGCAAGAGAAACTTCTACCAATTATTGAGAATAAGGCTGAAACTA
GTGT
Found at i:23465 original size:18 final size:18
Alignment explanation
Indices: 23442--23480 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23432 ATGAATTGTA
23442 TCATTTTATTTCTATATT
1 TCATTTTATTTCTATATT
23460 TCATTTTATTTCTATATT
1 TCATTTTATTTCTATATT
23478 TCA
1 TCA
23481 AAGAAGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (18 bp):
TCATTTTATTTCTATATT
Found at i:26464 original size:2 final size:2
Alignment explanation
Indices: 26457--26574 Score: 197
Period size: 2 Copynumber: 60.5 Consensus size: 2
26447 AAAATATTAT
* *
26457 TA TA TA TA TA -A T- TA TT TA T- TA GA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26575 TCAATTATTT
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
1 3 0.03
2 106 0.97
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31920 original size:17 final size:17
Alignment explanation
Indices: 31898--31955 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
31888 TCTGAACCGG
31898 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
31915 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
31932 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
31949 GTTGACC
1 GTTGACC
31956 GTTGACTGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:31970 original size:20 final size:20
Alignment explanation
Indices: 31945--31982 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31935 GACCCGACCC
*
31945 GACCGTTGACCGTTGACTGT
1 GACCGTTAACCGTTGACTGT
31965 GACCGTTAACCGTTGACT
1 GACCGTTAACCGTTGACT
31983 TTCTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (20 bp):
GACCGTTAACCGTTGACTGT
Found at i:53054 original size:31 final size:31
Alignment explanation
Indices: 52985--53087 Score: 190
Period size: 31 Copynumber: 3.4 Consensus size: 31
52975 GAAACTTTCT
52985 TTTTTATTTAACTAAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
53016 -TTTTATTTAACTAAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
*
53046 TTTTTATTTAACTGAGATATGATTATATTCA
1 TTTTTATTTAACTAAGATATGATTATATTCA
53077 TTTTTATTTAA
1 TTTTTATTTAA
53088 TTAATATGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 30 0.43
31 40 0.57
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTTTATTTAACTAAGATATGATTATATTCA
Done.