Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005605.1 Hibiscus syriacus cultivar Beakdansim tig00013037_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: 56760
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3918 original size:8 final size:8
Alignment explanation
Indices: 3905--3936 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
3895 AGACACCAGT
3905 AGGGAGAG
1 AGGGAGAG
3913 AGGGAGAG
1 AGGGAGAG
3921 AGGGAGAG
1 AGGGAGAG
3929 A-GGAGAG
1 AGGGAGAG
3936 A
1 A
3937 CAAGTGGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
AGGGAGAG
Found at i:18697 original size:20 final size:21
Alignment explanation
Indices: 18658--18697 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18648 GAAGTTTTAA
* *
18658 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
18679 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
18698 AAGTAGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:18833 original size:21 final size:21
Alignment explanation
Indices: 18807--18848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18797 GAGATTATTT
*
18807 TCATTTTT-TAATTTTGAAATA
1 TCATTTTTGT-ATTTTAAAATA
18828 TCATTTTTGTATTTTAAAATA
1 TCATTTTTGTATTTTAAAATA
18849 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTGTATTTTAAAATA
Found at i:20845 original size:65 final size:64
Alignment explanation
Indices: 20773--20930 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 64
20763 TACACTAGGA
* * *
20773 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-ACAAGCCAGGAGTGCATCGATGCATGGC
1 GTGCATCGGTACA-TAAAATACATTCGATGTATCAATAAAAGCCA-GAGTGCATCGATGCATGGC
20836 AT
64 -T
* * *
20838 GTGCATCGGTGCATAAAATGCATTCGATGTATCAATAAAATCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACATAAAATACATTCGATGTATCAATAAAAGCCAGAGTGCATCGATGCATGGCT
* *
20902 GTGCATCGGTGCATAAAAATGCATTCGAT
1 GTGCATCGGTACAT-AAAATACATTCGAT
20931 ATGAGGTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
64 16 0.19
65 62 0.74
66 6 0.07
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATGTATCAATAAAAGCCAGAGTGCATCGATGCATGGCT
Found at i:27385 original size:15 final size:15
Alignment explanation
Indices: 27365--27400 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
27355 CTGACAGGTC
27365 TGAGTTGACTCAACA
1 TGAGTTGACTCAACA
27380 TGAGTTGACTCAACA
1 TGAGTTGACTCAACA
27395 TGAGTT
1 TGAGTT
27401 AACTTAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (15 bp):
TGAGTTGACTCAACA
Found at i:27956 original size:20 final size:20
Alignment explanation
Indices: 27933--27976 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
27923 AAAAGGTGGG
* *
27933 TATCAATACTCATGGGTCAA
1 TATCAATACTCAAGGGCCAA
* *
27953 TATCGATACTGAAGGGCCAA
1 TATCAATACTCAAGGGCCAA
27973 TATC
1 TATC
27977 GGTACCAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
TATCAATACTCAAGGGCCAA
Found at i:31606 original size:16 final size:16
Alignment explanation
Indices: 31587--31730 Score: 135
Period size: 16 Copynumber: 8.9 Consensus size: 16
31577 CCCGAACTGA
*
31587 AACCGAAATTAACCCG
1 AACCGAAAGTAACCCG
*
31603 AACCAAAAGTAACCCG
1 AACCGAAAGTAACCCG
* *
31619 AATCGAAAGTAACCCA
1 AACCGAAAGTAACCCG
* *
31635 AACCGAAAGTAAACCA
1 AACCGAAAGTAACCCG
* *
31651 AACCGAAATTAACCAG
1 AACCGAAAGTAACCCG
**
31667 AACCGAATTTTAACCCG
1 AACCGAA-AGTAACCCG
* *
31684 ATCCGAAAGTAACCAG
1 AACCGAAAGTAACCCG
**
31700 AACCGAATTTAACCCG
1 AACCGAAAGTAACCCG
* *
31716 ACCCGAAAGCAACCC
1 AACCGAAAGTAACCC
31731 AAACAGGTTG
Statistics
Matches: 102, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
16 89 0.87
17 13 0.13
ACGTcount: A:0.45, C:0.30, G:0.13, T:0.12
Consensus pattern (16 bp):
AACCGAAAGTAACCCG
Found at i:31690 original size:49 final size:49
Alignment explanation
Indices: 31586--31722 Score: 134
Period size: 49 Copynumber: 2.8 Consensus size: 49
31576 ACCCGAACTG
* * * * * * **
31586 AAACCGAAATTAACCCGAACCAAAAGTAACCCGAATCGAA-AGTAACCC
1 AAACCGAAAGTAACCAGAACCGAAATTAACCAGAACCGAATTTTAACCC
31634 AAACCGAAAGTAAACCA-AACCGAAATTAACCAGAACCGAATTTTAACCC
1 AAACCGAAAGT-AACCAGAACCGAAATTAACCAGAACCGAATTTTAACCC
* * * * *
31683 GATCCGAAAGTAACCAGAACCGAATTTAACCCGACCCGAA
1 AAACCGAAAGTAACCAGAACCGAAATTAACCAGAACCGAA
31723 AGCAACCCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
48 34 0.47
49 39 0.53
ACGTcount: A:0.46, C:0.28, G:0.13, T:0.12
Consensus pattern (49 bp):
AAACCGAAAGTAACCAGAACCGAAATTAACCAGAACCGAATTTTAACCC
Found at i:31833 original size:24 final size:25
Alignment explanation
Indices: 31779--31834 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
31769 AGTTATTTTC
*
31779 AATAAAAAATTAATTTAAATAAAAT
1 AATAAAAAATTAAATTAAATAAAAT
31804 --TAAAAATATTAAATT-AATAAAAT
1 AATAAAAA-ATTAAATTAAATAAAAT
31827 AATAAAAA
1 AATAAAAA
31835 GTTTAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 14 0.52
24 7 0.26
25 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
AATAAAAAATTAAATTAAATAAAAT
Found at i:32439 original size:32 final size:34
Alignment explanation
Indices: 32386--32477 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 34
32376 ACCTAAACTG
* **
32386 AAAATCAACTGATATGATATTGACCCGA-C-CCA
1 AAAATCAACCGATCCGATATTGACCCGACCACCA
* *
32418 AAAATCAACCGATCCGGTATTGACCTGACCTAATCCA
1 AAAATCAACCGATCCGATATTGACCCGACC--A-CCA
32455 AAAATCAACCGATCCGATATTGA
1 AAAATCAACCGATCCGATATTGA
32478 TCTGAACTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 23 0.47
33 1 0.02
37 25 0.51
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (34 bp):
AAAATCAACCGATCCGATATTGACCCGACCACCA
Found at i:32496 original size:32 final size:35
Alignment explanation
Indices: 32416--32501 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 35
32406 TGACCCGACC
* *
32416 CAAAAATCAACCGATCCGGTATTGACCTGACCTAAT
1 CAAAAATCAACCGATCCGATATTGACCTGAACT-AT
*
32452 CCAAAAATCAACCGATCCGATATTGATCTGAACT-T
1 -CAAAAATCAACCGATCCGATATTGACCTGAACTAT
32487 -AAAAA-CAACCGATCC
1 CAAAAATCAACCGATCC
32502 AATAATCACC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.22
33 5 0.11
35 1 0.02
37 30 0.65
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.21
Consensus pattern (35 bp):
CAAAAATCAACCGATCCGATATTGACCTGAACTAT
Found at i:35982 original size:19 final size:20
Alignment explanation
Indices: 35939--35982 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35929 ACATTGTTGG
35939 TTAAATTATACTAAACCCAT
1 TTAAATTATACTAAACCCAT
*
35959 ATAAATTACTA-TAAA-CCAT
1 TTAAATTA-TACTAAACCCAT
35978 TTAAA
1 TTAAA
35983 CGTTATAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.38
20 11 0.52
21 2 0.10
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAATTATACTAAACCCAT
Found at i:36440 original size:266 final size:266
Alignment explanation
Indices: 35966--36475 Score: 984
Period size: 266 Copynumber: 1.9 Consensus size: 266
35956 CATATAAATT
*
35966 ACTATAAACCATTTAAACGTTATAGACATATCATAACATTTCTAACCCAATTAAATATAGCCATA
1 ACTATAAACCATTTAAACATTATAGACATATCATAACATTTCTAACCCAATTAAATATAGCCATA
36031 TAAGAACATTACTAACACCTAAACACGTATACATGCTAACTAGAAAATCAAAACAATAGTAGGAT
66 TAAGAACATTACTAACACCTAAACACGTATACATGCTAACTAGAAAATCAAAACAATAGTAGGAT
36096 CTCATTATTGATACCAATAAGTAGTCATCGATGAGTGATGTCAAGCTAAGCTCCTTAATCATTCG
131 CTCATTATTGATACCAATAAGTAGTCATCGATGAGTGATGTCAAGCTAAGCTCCTTAATCATTCG
36161 ATCTTCTTTTTCTAAGCATGAATATTATAACACACTAAGTATACACTTATACATGCTAAACACCT
196 ATCTTCTTTTTCTAAGCATGAATATTATAACACACTAAGTATACACTTATACATGCTAAACACCT
36226 AAACAC
261 AAACAC
*
36232 ACTATAAACCATTTAAACATTATAGACATATCATAACATTTCTGACCCAATTAAATATAGCCATA
1 ACTATAAACCATTTAAACATTATAGACATATCATAACATTTCTAACCCAATTAAATATAGCCATA
36297 TAAGAACATTACTAACACCTAAACACGTATACATGCTAACTAGAAAATCAAAACAATAGTAGGAT
66 TAAGAACATTACTAACACCTAAACACGTATACATGCTAACTAGAAAATCAAAACAATAGTAGGAT
*
36362 CTCATTATTGATACCAATAAGTAGTCATCGTTGAGTGATGTCAAGCTAAGCTCCTTAATCATTCG
131 CTCATTATTGATACCAATAAGTAGTCATCGATGAGTGATGTCAAGCTAAGCTCCTTAATCATTCG
*
36427 ATCTTCTTTTTCTAAGCATGAATATTATAACATACTAAGTATACACTTA
196 ATCTTCTTTTTCTAAGCATGAATATTATAACACACTAAGTATACACTTA
36476 GTGAGGATTA
Statistics
Matches: 240, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 240 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (266 bp):
ACTATAAACCATTTAAACATTATAGACATATCATAACATTTCTAACCCAATTAAATATAGCCATA
TAAGAACATTACTAACACCTAAACACGTATACATGCTAACTAGAAAATCAAAACAATAGTAGGAT
CTCATTATTGATACCAATAAGTAGTCATCGATGAGTGATGTCAAGCTAAGCTCCTTAATCATTCG
ATCTTCTTTTTCTAAGCATGAATATTATAACACACTAAGTATACACTTATACATGCTAAACACCT
AAACAC
Done.