Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001321.1 Hibiscus syriacus cultivar Beakdansim tig00002575_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: 59754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8643 original size:45 final size:46
Alignment explanation
Indices: 8580--8734 Score: 186
Period size: 53 Copynumber: 3.2 Consensus size: 46
8570 TGTTATCCAC
* *
8580 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTC-A
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTTCAA
*
8626 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCAAAAAAA
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC--TTGTTC-----AA
*
8679 AAAAATAAACCTAACCACATGATATCTAGTTCGCATGCTTGTTCGAA
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTC-AA
8726 AAAAATAAA
1 AAAAATAAA
8735 TGAATCAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
45 28 0.29
46 8 0.08
47 16 0.17
51 5 0.05
53 38 0.40
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (46 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCAA
Found at i:17707 original size:21 final size:21
Alignment explanation
Indices: 17681--17720 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17671 CCCCCTTTGA
*
17681 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
17702 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
17721 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:24425 original size:35 final size:35
Alignment explanation
Indices: 24319--24427 Score: 91
Period size: 35 Copynumber: 3.1 Consensus size: 35
24309 TTTAGGGACA
* * *
24319 AAATATGGAATTCCCATGTTCAAAGTTTGGTCACC
1 AAATATGAAATTTCCATGTTCAAAGTTTGGCCACC
* *
24354 TACCAA-A-GAATTTTCCAATGTGT-ACAAG-TTAGCCACC
1 -A--AATATGAAATTTCC-ATGT-TCA-AAGTTTGGCCACC
24391 AAATATGAAATTTCCATGTTCAAAGTTTGGCCACC
1 AAATATGAAATTTCCATGTTCAAAGTTTGGCCACC
24426 AA
1 AA
24428 CCAAGATGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
34 6 0.11
35 16 0.28
36 16 0.28
37 13 0.23
38 6 0.11
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (35 bp):
AAATATGAAATTTCCATGTTCAAAGTTTGGCCACC
Found at i:24440 original size:38 final size:36
Alignment explanation
Indices: 24327--24444 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 36
24317 CAAAATATGG
* *
24327 AATTCCCATGTTCAAAGTTTGGTCACCTACCAAA-GA
1 AATTTCCATGTTCAAAGTTTGGCCACC-ACCAAATGA
* *
24363 ATTTTCCAATGTGT-ACAAG-TTAGCCACCA--AATATGA
1 AATTTCC-ATGT-TCA-AAGTTTGGCCACCACCAA-ATGA
24399 AATTTCCATGTTCAAAGTTTGGCCACCAACCAAGATGA
1 AATTTCCATGTTCAAAGTTTGGCCACC-ACCAA-ATGA
24437 AATTTCCA
1 AATTTCCA
24445 ACTTGCCAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
34 6 0.09
35 14 0.22
36 15 0.23
37 12 0.18
38 18 0.28
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (36 bp):
AATTTCCATGTTCAAAGTTTGGCCACCACCAAATGA
Found at i:32700 original size:32 final size:32
Alignment explanation
Indices: 32659--32745 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
32649 AGTTGAGGGT
32659 TTACCTATGTTCTACGGAACATATAGACAGAA
1 TTACCTATGTTCTACGGAACATATAGACAGAA
* * * *
32691 TTACCTATG-TCTTTC-GAGACATATGGATAGTA
1 TTACCTATGTTC-TACGGA-ACATATAGACAGAA
*
32723 -TACCTATGTTCTAAGGAACATAT
1 TTACCTATGTTCTACGGAACATAT
32746 GGATAGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATAGACAGAA
Found at i:32730 original size:31 final size:31
Alignment explanation
Indices: 32660--32765 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
32650 GTTGAGGGTT
* * *
32660 TACCTATGTTCT-ACGGAACATATAGACAGAA
1 TACCTATGTTCTAAC-GAACATATGGATAGTA
**
32691 TTACCTATG-TCTTTCGAGACATATGGATAGTA
1 -TACCTATGTTCTAACGA-ACATATGGATAGTA
* *
32723 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAACGAACATATGGATAGTA
*
32754 TACCTAGGTTCT
1 TACCTATGTTCT
32766 TCGGGACCTG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
31 37 0.60
32 25 0.40
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGATAGTA
Found at i:35098 original size:35 final size:35
Alignment explanation
Indices: 34989--35100 Score: 88
Period size: 35 Copynumber: 3.1 Consensus size: 35
34979 TATTTTAGGG
34989 ACCAAATATGAAATTCCCATGTTCAAAGTTTGGCC
1 ACCAAATATGAAATTCCCATGTTCAAAGTTTGGCC
* *** * *
35024 ACCTACCAA-A-GAATTTTTTAAT-TTGTACAAG-TTAGCC
1 ACC-A--AATATGAA-ATTCCCATGTT-CA-AAGTTTGGCC
35061 ACCAAATATGAAATTCCCATGTTCAAAGTTTGGCC
1 ACCAAATATGAAATTCCCATGTTCAAAGTTTGGCC
35096 ACCAA
1 ACCAA
35101 CCAAGATGAA
Statistics
Matches: 55, Mismatches: 12, Indels: 20
0.63 0.14 0.23
Matches are distributed among these distances:
34 5 0.09
35 19 0.35
36 12 0.22
37 14 0.25
38 5 0.09
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (35 bp):
ACCAAATATGAAATTCCCATGTTCAAAGTTTGGCC
Found at i:35141 original size:33 final size:34
Alignment explanation
Indices: 35086--35151 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
35076 CCCATGTTCA
35086 AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
* *
35120 AAGTTT-GCCATCAACCGAGATGAAATTTCCAA
1 AAGTTTGGCCACCAACCAAGATGAAATTTCCAA
35152 CTTGCTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (34 bp):
AAGTTTGGCCACCAACCAAGATGAAATTTCCAAT
Found at i:37479 original size:20 final size:20
Alignment explanation
Indices: 37454--37491 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37444 GACTGCCAAT
*
37454 GAACCGGCTGAAAACCGGTA
1 GAACCGACTGAAAACCGGTA
37474 GAACCGACTGAAAACCGG
1 GAACCGACTGAAAACCGG
37492 CAAAACCGGT
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:0.37, C:0.26, G:0.29, T:0.08
Consensus pattern (20 bp):
GAACCGACTGAAAACCGGTA
Found at i:37498 original size:20 final size:20
Alignment explanation
Indices: 37455--37499 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
37445 ACTGCCAATG
* * *
37455 AACCGGCTGAAAACCGGTAG
1 AACCGACTGAAAACCGGCAA
37475 AACCGACTGAAAACCGGCAA
1 AACCGACTGAAAACCGGCAA
37495 AACCG
1 AACCG
37500 GTTTGAACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.24, T:0.07
Consensus pattern (20 bp):
AACCGACTGAAAACCGGCAA
Found at i:44588 original size:72 final size:72
Alignment explanation
Indices: 44471--44621 Score: 284
Period size: 72 Copynumber: 2.1 Consensus size: 72
44461 GATATTAACC
44471 CTTGGGAAATCTTAGAGAGATTCTTGATTATTCATGACATTGGAGTCACATCCCCACCCTAACAC
1 CTTGGGAAATCTTAGAGAGATTCTTGATTATTCATGACATTGGAGTCACATCCCCACCCTAACAC
*
44536 ATCAACT
66 ACCAACT
*
44543 CTTGGGAAATCTTAGAGAGATTCTTGATTATTCATGACATTGGAGTCGCATCCCCACCCTAACAC
1 CTTGGGAAATCTTAGAGAGATTCTTGATTATTCATGACATTGGAGTCACATCCCCACCCTAACAC
44608 ACCAACT
66 ACCAACT
44615 CTTGGGA
1 CTTGGGA
44622 TAATTCATGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (72 bp):
CTTGGGAAATCTTAGAGAGATTCTTGATTATTCATGACATTGGAGTCACATCCCCACCCTAACAC
ACCAACT
Done.