Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004365.1 Hibiscus syriacus cultivar Beakdansim tig00009564_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: 59936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1568 original size:21 final size:21
Alignment explanation
Indices: 1542--1586 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1532 TCAAAGTGAA
1542 GAACTTCGACTATCGCAACGC
1 GAACTTCGACTATCGCAACGC
* * *
1563 GAACTTGGACTATCGTAATGC
1 GAACTTCGACTATCGCAACGC
1584 GAA
1 GAA
1587 TATGTAAATC
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:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
GAACTTCGACTATCGCAACGC
Found at i:2731 original size:40 final size:40
Alignment explanation
Indices: 2680--2762 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
2670 CCACATGCAT
* *
2680 CCCACAGCTCACAGCTCTCACATGCATCACTCCTTGGTCG
1 CCCACAACTCACAGCTCTCACATGCATCACTCATTGGTCG
2720 CCCACAACTCACAGCTCTCACATGCATCACTCATTGGTCG
1 CCCACAACTCACAGCTCTCACATGCATCACTCATTGGTCG
2760 CCC
1 CCC
2763 GGATTGTATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.43, G:0.13, T:0.22
Consensus pattern (40 bp):
CCCACAACTCACAGCTCTCACATGCATCACTCATTGGTCG
Found at i:2793 original size:28 final size:29
Alignment explanation
Indices: 2753--2811 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
2743 GCATCACTCA
*
2753 TTGGTCGCCCGGATTGTATGG-GATCTCC
1 TTGGTCGCCCGGATTATATGGCGATCTCC
*
2781 TTGGTTGCCCGGATTATATGGCGATCTCC
1 TTGGTCGCCCGGATTATATGGCGATCTCC
2810 TT
1 TT
2812 TTATCATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.36
Consensus pattern (29 bp):
TTGGTCGCCCGGATTATATGGCGATCTCC
Found at i:6652 original size:80 final size:80
Alignment explanation
Indices: 6549--6713 Score: 226
Period size: 80 Copynumber: 2.1 Consensus size: 80
6539 AAATTACTAG
* * * *
6549 GAATATTGTATTTTATATTTGGTTGGTTTAATA-TGAATGTAAGATTACCGTATTTGGTTAAAAG
1 GAATGTTGTATTTTATATTTGGTTGGTTTAACAGT-AAGGTAAGATTAACGTATTTGGTTAAAAG
6613 AATAAAAGATTATTGA
65 AATAAAAGATTATTGA
* * * *
6629 GAATGTTGTATTTTGTGTTTGGTTGGTTTAGCAGTAAGGTAAGATTAACGTGTTTGGTTAAAAGA
1 GAATGTTGTATTTTATATTTGGTTGGTTTAACAGTAAGGTAAGATTAACGTATTTGGTTAAAAGA
*
6694 ATAAAATATTATTGA
66 ATAAAAGATTATTGA
6709 -AATGT
1 GAATGT
6714 ATATTTGATC
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
79 5 0.07
80 69 0.92
81 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (80 bp):
GAATGTTGTATTTTATATTTGGTTGGTTTAACAGTAAGGTAAGATTAACGTATTTGGTTAAAAGA
ATAAAAGATTATTGA
Found at i:6847 original size:28 final size:28
Alignment explanation
Indices: 6790--6845 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
6780 ACTATAAGAT
* *
6790 ATTTATATATTTTCTTTAAAAAATTTAA
1 ATTTATAAATTTTCTTTAAAAAATTAAA
*
6818 ATTTATAAATTTT-TTTACAAAATTAAA
1 ATTTATAAATTTTCTTTAAAAAATTAAA
6845 A
1 A
6846 ATATAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTATAAATTTTCTTTAAAAAATTAAA
Found at i:10202 original size:2 final size:2
Alignment explanation
Indices: 10195--10231 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10185 TTTTAAATGT
10195 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10232 AATTGCGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14419 original size:150 final size:148
Alignment explanation
Indices: 14253--14629 Score: 409
Period size: 150 Copynumber: 2.5 Consensus size: 148
14243 TGCAACGAAT
* *
14253 CAATGGAATTGGAACTCTTGTGATCATCAATGGGATGTTTGAATGAAGATTTGTTTCCCACTGTC
1 CAATGGAA-TGGAACTCTTG-GATCATCAATGGGATGTTTGAAGGAAGATTTGTTTGCCACTGTC
* * * *
14318 AAAATCTTCCCCGCTGCTTTGGATTTCCCCTTAT-TCGAATGATAATAATGTGCAC-CATGCACA
64 AAAATCTTCCCCGCTGATTTGGATATCCCCTT-TCTCGAATCATAATAATGTACACAC-TGCACA
* *
14381 GTTG-TTTCATATTCCGGTGAAG
127 GTTGCTCT-ATATTCCGATGAAG
* * * * * * *
14403 CAATGGAACTAGAACTCTTAGGATCATCAATGGGATGCTTGGAGGAAGCTTTGCTTGTCATTGTC
1 CAATGGAA-TGGAACTCTT-GGATCATCAATGGGATGTTTGAAGGAAGATTTGTTTGCCACTGTC
* * * *
14468 AAAATCTTTCCTGCTGATTTGGATATCCCCTTTCTTGAATCATAATAATGTACACACTGCAGAGT
64 AAAATCTTCCCCGCTGATTTGGATATCCCCTTTCTCGAATCATAATAATGTACACACTGCACAGT
14533 TGCTCTATATTCCGATGAAG
129 TGCTCTATATTCCGATGAAG
** * * * ** *
14553 CAATGGAATCGGAACTCTTACAATCATCAACGGGACGTTTGAAGGAAGATTCGTTTGCTGCTGCC
1 CAATGGAAT-GGAACTCTT-GGATCATCAATGGGATGTTTGAAGGAAGATTTGTTTGCCACTGTC
14618 AAAATCTTCCCC
64 AAAATCTTCCCC
14630 ACCAATTCGG
Statistics
Matches: 185, Mismatches: 37, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
149 2 0.01
150 179 0.97
151 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (148 bp):
CAATGGAATGGAACTCTTGGATCATCAATGGGATGTTTGAAGGAAGATTTGTTTGCCACTGTCAA
AATCTTCCCCGCTGATTTGGATATCCCCTTTCTCGAATCATAATAATGTACACACTGCACAGTTG
CTCTATATTCCGATGAAG
Found at i:29667 original size:2 final size:2
Alignment explanation
Indices: 29660--29706 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
29650 TTAACTCTTA
29660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29702 AT AT A
1 AT AT A
29707 ACACAATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31125 original size:157 final size:156
Alignment explanation
Indices: 30897--31423 Score: 735
Period size: 157 Copynumber: 3.4 Consensus size: 156
30887 GATTTCATTT
* * *
30897 TTTCTTCAATTTC-TCCTTCATTTTAAGTC-CATTTTTACCAAATTTTAACCGCATGCTCCTAAA
1 TTTCTTCAA-TTCATCCTTTATTTTAAGTCTC-TTTTTACCAAATTTGAACCACATGCTCCTAAA
* *
30960 CAATCATAGAATACATGTGTACTTTCAATTCATCTTTTTGATAAT-AATTTTATATTTTTCAATT
64 C-ATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATT
31024 TAGTCCCTCAACTTTTCATATCTTCCTTA
128 TAGTCCCTCAACTTTTCATATCTTCCTTA
* * *
31053 TATT-TTCAATTCATCCTTTATCTTAAATCTGTGTTTTACCAAATTTGAACCACATGCTCCTAAA
1 T-TTCTTCAATTCATCCTTTATTTTAAGTCTCT-TTTTACCAAATTTGAACCACATGCTCCTAAA
* *
31117 TCATCATAGAATACATGTGTACTTTCAATTCCTCGTTTTCATAATAAATTTTCTATTTTT-AATT
64 -CATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATT
* *
31181 CAGTCCCTCAACTTTTCATATATTCCTTA
128 TAGTCCCTCAACTTTTCATATCTTCCTTA
* * *
31210 TTTCTTCAATTTATCCTTTATTTTAAGCCTCTTTTTACCAAATTTGAACCGCATGCTCCTAAACC
1 TTTCTTCAATTCATCCTTTATTTTAAGTCTCTTTTTACCAAATTTGAACCACATGCTCCTAAA-C
* *
31275 ATCATAAAATAC--GTGTACTTTCAATTCCTCTTTTTGATAATAAAATTTCTATTTTTCAATTTA
65 ATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATTTA
* * *
31338 ATCCCTCTACTTTTCATATCTTCTTTA
130 GTCCCTCAACTTTTCATATCTTCCTTA
* *
31365 TTTCTTCAATTCATCTTTTATTTTAAGTCCCCTTTTTACCAAATTTGAACCACATGCTC
1 TTTCTTCAATTCATCCTTTATTTTAAGT-CTCTTTTTACCAAATTTGAACCACATGCTC
31424 ATATACTATA
Statistics
Matches: 329, Mismatches: 33, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
154 41 0.12
155 56 0.17
156 92 0.28
157 126 0.38
158 14 0.04
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (156 bp):
TTTCTTCAATTCATCCTTTATTTTAAGTCTCTTTTTACCAAATTTGAACCACATGCTCCTAAACA
TCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATTTAG
TCCCTCAACTTTTCATATCTTCCTTA
Found at i:31709 original size:2 final size:2
Alignment explanation
Indices: 31702--31728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31692 TGTGAAAAGA
31702 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31729 ATGGTTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35442 original size:2 final size:2
Alignment explanation
Indices: 35435--35462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35425 TAAATAAGCA
35435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35463 TGGTGGGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36033 original size:23 final size:23
Alignment explanation
Indices: 35984--36027 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35974 GATGCAACTC
* * *
35984 GTTTAATGTTTGTGAATATGTCT
1 GTTTAACGTTTGTCAACATGTCT
36007 GTTTAACGTTTGTCAACATGT
1 GTTTAACGTTTGTCAACATGT
36028 TGGTTTGCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (23 bp):
GTTTAACGTTTGTCAACATGTCT
Found at i:36531 original size:31 final size:31
Alignment explanation
Indices: 36486--36566 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
36476 AGAAAAAAAA
* *
36486 TAATAGTTGAGTGACCAAAACATAAATTTAG
1 TAATAGATGGGTGACCAAAACATAAATTTAG
36517 TAATAGATGGGTGACCAAAACATAAATTTAG
1 TAATAGATGGGTGACCAAAACATAAATTTAG
**
36548 TAATAGACAGGTGACCAAA
1 TAATAGATGGGTGACCAAA
36567 TAGTTAGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (31 bp):
TAATAGATGGGTGACCAAAACATAAATTTAG
Found at i:44937 original size:19 final size:19
Alignment explanation
Indices: 44906--44970 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
44896 AATACAAAAT
*
44906 ATAATAATATATAATATAA
1 ATAATTATATATAATATAA
* * *
44925 ATAATTCAT-TATATTTTAT
1 ATAATT-ATATATAATATAA
44944 ATAATTATATATATATATAA
1 ATAATTATATATA-ATATAA
*
44964 AAAATTA
1 ATAATTA
44971 ATCGGGTACT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.06
19 22 0.63
20 11 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATTATATATAATATAA
Found at i:48617 original size:96 final size:96
Alignment explanation
Indices: 48448--48634 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 96
48438 CTGCGGCTGC
* * * * *
48448 TGAGCAGGAGGCATTGTGAATTGTTGACTTGGAATCTCCTGAGTTTGGCCAGGAGGTGGGTAGTA
1 TGAGCAGGAGGCATCGGGAATTGCTGACTTGGAATCTCCTGAGGTTGGCCAGGAGGTGGATAGTA
48513 AGCATCTCGCTGAGAGACAGAAGGAACTTGA
66 AGCATCTCGCTGAGAGACAGAAGGAACTTGA
* * * *
48544 TGAGTAGGAGGCATCGGGAATTGCTGACTTGGAGTCTCCTGAGGTTGGTCAGGTGGTGGATAGTA
1 TGAGCAGGAGGCATCGGGAATTGCTGACTTGGAATCTCCTGAGGTTGGCCAGGAGGTGGATAGTA
* *
48609 AGCATCTCGTTGAGGGACAGAAGGAA
66 AGCATCTCGCTGAGAGACAGAAGGAA
48635 TTTCGTTCTG
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25
Consensus pattern (96 bp):
TGAGCAGGAGGCATCGGGAATTGCTGACTTGGAATCTCCTGAGGTTGGCCAGGAGGTGGATAGTA
AGCATCTCGCTGAGAGACAGAAGGAACTTGA
Found at i:53422 original size:21 final size:21
Alignment explanation
Indices: 53381--53422 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53371 TATTCCATTA
* *
53381 AAAAAATACTAATTTATTAAT
1 AAAAAATACTAAATTACTAAT
53402 AAAAAATGA-TAAATTACTAAT
1 AAAAAAT-ACTAAATTACTAAT
53423 CTATATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAAATACTAAATTACTAAT
Done.