Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004274.1 Hibiscus syriacus cultivar Beakdansim tig00009368_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: 85731
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:929 original size:35 final size:36
Alignment explanation
Indices: 830--948 Score: 174
Period size: 34 Copynumber: 3.4 Consensus size: 36
820 TTATCCCATT
* *
830 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
865 AAC-TTTTTCAAAGAAACA-TTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
899 ATCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
934 ATCAATTTTTCAAAG
1 ATC-ATTTTTCAAAG
949 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
34 37 0.49
35 28 0.37
36 1 0.01
37 9 0.12
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:5443 original size:37 final size:37
Alignment explanation
Indices: 5385--5503 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 37
5375 TCTCATTATC
* * *
5385 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
*
5421 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
**
5458 A--TTTCAAAGAAACATTTACCAAACTTTGAAAGCCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
5493 ATTTTTCAAAG
1 ATTTTTCAAAG
5504 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 7 0.09
37 34 0.45
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
Found at i:9900 original size:2 final size:2
Alignment explanation
Indices: 9854--9882 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9844 ATTTAAAAAA
9854 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
9883 ATTTGCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13541 original size:25 final size:25
Alignment explanation
Indices: 13507--13555 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
13497 CATAGGTGAG
13507 TTTATTTTCTAGTTATACTTTGGAA
1 TTTATTTTCTAGTTATACTTTGGAA
13532 TTTATTTTCTAGTTATACTTTGGA
1 TTTATTTTCTAGTTATACTTTGGA
13556 CTTCACATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.57
Consensus pattern (25 bp):
TTTATTTTCTAGTTATACTTTGGAA
Found at i:17314 original size:13 final size:13
Alignment explanation
Indices: 17296--17326 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
17286 CCAACGGCTG
17296 CATCAAGGCAATA
1 CATCAAGGCAATA
17309 CATCAAGGCAATA
1 CATCAAGGCAATA
17322 CATCA
1 CATCA
17327 GATAAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (13 bp):
CATCAAGGCAATA
Found at i:31384 original size:21 final size:22
Alignment explanation
Indices: 31360--31402 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
31350 GTGATTTTAT
* *
31360 ATTAGGATCAAAATTTA-AGAA
1 ATTAGAATAAAAATTTAGAGAA
*
31381 ATTATAATAAAAATTTAGAGAA
1 ATTAGAATAAAAATTTAGAGAA
31403 TAGAAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (22 bp):
ATTAGAATAAAAATTTAGAGAA
Found at i:31808 original size:14 final size:14
Alignment explanation
Indices: 31789--31827 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
31779 TAATGGGGAG
31789 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
31803 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
31817 GAATCTCTGCA
1 TAATCCCTGCA
31828 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:44518 original size:23 final size:23
Alignment explanation
Indices: 44492--44540 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
44482 AAGAGATAAC
44492 CTTTACAACTCCCTAGTTTTTCA
1 CTTTACAACTCCCTAGTTTTTCA
44515 CTTTACAACTCCCTAGTTTTTCA
1 CTTTACAACTCCCTAGTTTTTCA
44538 CTT
1 CTT
44541 GGATAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.45
Consensus pattern (23 bp):
CTTTACAACTCCCTAGTTTTTCA
Found at i:51748 original size:24 final size:23
Alignment explanation
Indices: 51710--51773 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
51700 TCACTTTAAT
51710 TAAAATATTAATTATTAAATTATTTA
1 TAAAATA-TAATTATT-AA-TATTTA
*
51736 -AAAATATATTTATTAATATTTA
1 TAAAATATAATTATTAATATTTA
51758 TAATAATATAA-TATTA
1 TAA-AATATAATTATTA
51774 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 6 0.18
23 9 0.26
24 13 0.38
25 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAATATAATTATTAATATTTA
Found at i:51789 original size:30 final size:30
Alignment explanation
Indices: 51756--51862 Score: 89
Period size: 30 Copynumber: 3.6 Consensus size: 30
51746 TATTAATATT
*
51756 TATAATAATATAATATTATTTTTTTAATAT
1 TATAATAATATAATATTATTTTTTTAATAA
* *
51786 TATAATAA-ATAATCAATTA-TATTATAATAA
1 TATAATAATATAAT--ATTATTTTTTTAATAA
* * *
51816 TATAA-GATATTATATTTTTTATTTTAATAA
1 TATAATAATATAATATTATTT-TTTTAATAA
51846 TAT-ATAATA-AATTATTA
1 TATAATAATATAA-TATTA
51863 ATAAAATTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
28 3 0.05
29 9 0.15
30 43 0.73
31 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TATAATAATATAATATTATTTTTTTAATAA
Found at i:51816 original size:55 final size:55
Alignment explanation
Indices: 51755--51860 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
51745 TTATTAATAT
*
51755 TTATAATAATAT-A-ATATTAT-TTTTTTAATATT-ATAATAAATAATCAATTATA
1 TTATAATAATATAAGATATTATATTTTTT-ATATTAATAATAAATAATAAATTATA
* *
51807 TTATAATAATATAAGATATTATATTTTTTATTTTAATAATATATAATAAATTAT
1 TTATAATAATATAAGATATTATATTTTTTATATTAATAATAAATAATAAATTAT
51861 TAATAAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
52 12 0.26
53 1 0.02
54 11 0.23
55 23 0.49
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (55 bp):
TTATAATAATATAAGATATTATATTTTTTATATTAATAATAAATAATAAATTATA
Found at i:51933 original size:19 final size:18
Alignment explanation
Indices: 51909--51976 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
51899 ATATTATTAA
51909 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
51928 ATTATTTAT-ATATTAAT
1 ATTATTAATAATAATAAT
51945 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
51967 ATT-TTAATAA
1 ATTATTAATAA
51977 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 17 0.43
20 2 0.05
22 9 0.22
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:52132 original size:27 final size:26
Alignment explanation
Indices: 52082--52132 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
52072 ATTATAAAAA
*
52082 TAATATTTAATAATAAATAAATTATT
1 TAATATTTAAAAATAAATAAATTATT
52108 TAATACTTTAAAAAT-AATAATATTA
1 TAATA-TTTAAAAATAAATAA-ATTA
52133 CGTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATATTTAAAAATAAATAAATTATT
Found at i:55573 original size:44 final size:44
Alignment explanation
Indices: 55505--55617 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
55495 TTTAGATATT
*
55505 TTACAGCGTTTGTATCCAAAAAACG-ACACTATATACCAGACCTT-
1 TTACGGCGTTTGTATCCAAAAAACGTA-ACTATATACCAGA-CTTG
* * * *
55549 TTGCGGCGTTTGTATCTAAAAAACGTAGCTATATACTAGACTTG
1 TTACGGCGTTTGTATCCAAAAAACGTAACTATATACCAGACTTG
*
55593 TTACGGCGTTTGTATCCGAAAAACG
1 TTACGGCGTTTGTATCCAAAAAACG
55618 CCGCTTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 3 0.05
44 55 0.93
45 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (44 bp):
TTACGGCGTTTGTATCCAAAAAACGTAACTATATACCAGACTTG
Found at i:55629 original size:13 final size:13
Alignment explanation
Indices: 55611--55635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55601 TTTGTATCCG
55611 AAAAACGCCGCTT
1 AAAAACGCCGCTT
55624 AAAAACGCCGCT
1 AAAAACGCCGCT
55636 ATTGGTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (13 bp):
AAAAACGCCGCTT
Found at i:65239 original size:24 final size:24
Alignment explanation
Indices: 65211--65260 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
65201 AGGAGATGTT
65211 AGTAATCTGTTAGAGTAGTTACAA
1 AGTAATCTGTTAGAGTAGTTACAA
65235 AGTAATCTGTTAGAGTAGTTACAA
1 AGTAATCTGTTAGAGTAGTTACAA
65259 AG
1 AG
65261 CAGTTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (24 bp):
AGTAATCTGTTAGAGTAGTTACAA
Found at i:68712 original size:15 final size:16
Alignment explanation
Indices: 68671--68704 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
68661 TTCGTTTTTC
*
68671 TTAACAGATGATCGAA
1 TTAACAGATTATCGAA
68687 TTAACAGATTATCGAA
1 TTAACAGATTATCGAA
68703 TT
1 TT
68705 CAAGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (16 bp):
TTAACAGATTATCGAA
Found at i:69219 original size:13 final size:13
Alignment explanation
Indices: 69203--69245 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
69193 AAAAAAGTGA
69203 TAAAAAGTATTTT
1 TAAAAAGTATTTT
69216 TAAAAAGTGATTTT
1 TAAAAAGT-ATTTT
* *
69230 T-AGAATTATTTT
1 TAAAAAGTATTTT
69242 TAAA
1 TAAA
69246 TTATTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (13 bp):
TAAAAAGTATTTT
Found at i:74905 original size:2 final size:2
Alignment explanation
Indices: 74898--74945 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
74888 GCAAAGCAAA
74898 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
74940 AT AT AT
1 AT AT AT
74946 CATTTCTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75309 original size:20 final size:20
Alignment explanation
Indices: 75284--75331 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
75274 GTGGTTTGAT
75284 TGATCAAATTGAAACATCAG
1 TGATCAAATTGAAACATCAG
75304 TGATCAAATTGAAACATCAG
1 TGATCAAATTGAAACATCAG
75324 TGATCAAA
1 TGATCAAA
75332 ATGATTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
TGATCAAATTGAAACATCAG
Done.