Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004917.1 Hibiscus syriacus cultivar Beakdansim tig00011072_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: 109818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:79345 original size:3 final size:3
Alignment explanation
Indices: 79337--79435 Score: 189
Period size: 3 Copynumber: 33.0 Consensus size: 3
79327 TAATTATTTG
79337 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
79385 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
79433 TAA
1 TAA
79436 ACGGGAAAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:81049 original size:2 final size:2
Alignment explanation
Indices: 81038--81117 Score: 71
Period size: 2 Copynumber: 42.5 Consensus size: 2
81028 TTCTATTATT
* * *
81038 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA AA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
81077 TT TA TA CA AA TA -A T- 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
81117 T
1 T
81118 CATTTTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
1 5 0.08
2 60 0.92
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98501 original size:7 final size:7
Alignment explanation
Indices: 98489--98564 Score: 67
Period size: 7 Copynumber: 11.6 Consensus size: 7
98479 TAAACAAACA
98489 AATAAAT
1 AATAAAT
98496 AATAAAT
1 AATAAAT
98503 --TAATAT
1 AATAA-AT
98509 AATAAAT
1 AATAAAT
98516 -ATAAAAT
1 AAT-AAAT
98523 AATAAAT
1 AATAAAT
*
98530 AAT-ACT
1 AATAAAT
98536 -ATAAAT
1 AATAAAT
*
98542 AATATAT
1 AATAAAT
98549 AAT--AT
1 AATAAAT
98554 AATAAAT
1 AATAAAT
98561 AATA
1 AATA
98565 TGTACACTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
5 10 0.18
6 8 0.14
7 34 0.60
8 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (7 bp):
AATAAAT
Found at i:98519 original size:19 final size:20
Alignment explanation
Indices: 98489--98565 Score: 85
Period size: 19 Copynumber: 4.0 Consensus size: 20
98479 TAAACAAACA
98489 AATAA-ATAATAAATTAATAT
1 AATAATATAATAAA-TAATAT
98509 AATAA-AT-ATAAAATAATA-
1 AATAATATAAT-AAATAATAT
98527 AATAATACT-ATAAATAATAT
1 AATAATA-TAATAAATAATAT
98547 -ATAATATAATAAATAATAT
1 AATAATATAATAAATAATAT
98566 GTACACTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.12
19 33 0.63
20 13 0.25
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAATATAATAAATAATAT
Found at i:98523 original size:31 final size:34
Alignment explanation
Indices: 98488--98564 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
98478 TTAAACAAAC
98488 AAATAAATAATAA-A-T-TAATATAATAAAT-ATA
1 AAATAAATAATAATACTATAA-ATAATAAATAATA
*
98519 AAAT-AATAAATAATACTATAAATAATATATAATA
1 AAATAAAT-AATAATACTATAAATAATAAATAATA
*
98553 TAATAAATAATA
1 AAATAAATAATA
98565 TGTACACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
30 3 0.08
31 9 0.24
32 1 0.03
33 9 0.24
34 13 0.34
35 3 0.08
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (34 bp):
AAATAAATAATAATACTATAAATAATAAATAATA
Found at i:98539 original size:12 final size:11
Alignment explanation
Indices: 98490--98565 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 11
98480 AAACAAACAA
*
98490 ATAAATAATAA
1 ATAAATAATAT
*
98501 ATTAATATAATAA
1 A-TAA-ATAATAT
98514 ATATAA-AATA-
1 ATA-AATAATAT
98524 ATAAATAATACT
1 ATAAATAATA-T
98536 ATAAATAATAT
1 ATAAATAATAT
98547 AT-AAT-ATA-
1 ATAAATAATAT
98555 ATAAATAATAT
1 ATAAATAATAT
98566 GTACACTATA
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.04
9 8 0.14
10 13 0.23
11 8 0.14
12 16 0.29
13 9 0.16
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:98616 original size:22 final size:22
Alignment explanation
Indices: 98591--98639 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
98581 TTAAAAACTA
*
98591 TATATATTATATTTTGAAAAAC
1 TATATATTATATTTTCAAAAAC
* *
98613 TATA-A-TATGTTTTCAAAAAT
1 TATATATTATATTTTCAAAAAC
98633 TATATAT
1 TATATAT
98640 ATTATATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 16 0.73
21 2 0.09
22 4 0.18
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATATTATATTTTCAAAAAC
Found at i:98689 original size:36 final size:38
Alignment explanation
Indices: 98616--98727 Score: 122
Period size: 38 Copynumber: 2.9 Consensus size: 38
98606 GAAAAACTAT
*
98616 AATATGTTTTCAAAAATTATATATATTATATACGTTTTCAAA
1 AATATGTTTTCAAAAACTATAT-TA-TATAT--GTTTTCAAA
* *
98658 AA-ATCGTTTT-AAAGACTATA-TATATATGTTTTTAAA
1 AATAT-GTTTTCAAAAACTATATTATATATGTTTTCAAA
*
98694 AATATGTTTTCAAAAAGTATATTATATATGTTTT
1 AATATGTTTTCAAAAACTATATTATATATGTTTT
98728 GAAAGAAAGC
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
36 15 0.25
37 10 0.16
38 17 0.28
39 2 0.03
41 10 0.16
42 7 0.11
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (38 bp):
AATATGTTTTCAAAAACTATATTATATATGTTTTCAAA
Found at i:98798 original size:28 final size:28
Alignment explanation
Indices: 98758--98823 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
98748 AACTATATAT
*
98758 TATATATTTTATATGTTTTCAAA-AACTA
1 TATATATTATATAT-TTTTCAAATAACTA
* * *
98786 TATATATTATATATTTTTGAAATTATTA
1 TATATATTATATATTTTTCAAATAACTA
98814 TATATATTAT
1 TATATATTAT
98824 CACATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (28 bp):
TATATATTATATATTTTTCAAATAACTA
Found at i:98833 original size:21 final size:20
Alignment explanation
Indices: 98787--98838 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
98777 CAAAAACTAT
* *
98787 ATATATTATATATTTTTGAA
1 ATATATTATATATTTATCAA
*
98807 AT-TATTATATATATTATCAC
1 ATATATTATATAT-TTATCAA
98827 ATATATTATATA
1 ATATATTATATA
98839 ACGTAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 8 0.30
21 9 0.33
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATTATATATTTATCAA
Found at i:105855 original size:27 final size:26
Alignment explanation
Indices: 105817--105873 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
105807 GAATGCTCTT
* *
105817 GATGTACCATGCACATACCATTCATC
1 GATGTACCATGCACAGACCATGCATC
105843 GATGTACCGATGCACAGACCATGCATC
1 GATGTACC-ATGCACAGACCATGCATC
105870 GATG
1 GATG
105874 CACTCATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (26 bp):
GATGTACCATGCACAGACCATGCATC
Done.