Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007433.1 Hibiscus syriacus cultivar Beakdansim tig00020238_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: 68182
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:647 original size:16 final size:16
Alignment explanation
Indices: 626--682 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
616 AATAAATAAT
626 GAACATAAATGAACAC
1 GAACATAAATGAACAC
*
642 GAACATAAACGAACAC
1 GAACATAAATGAACAC
*
658 GAACATAACTGAACAC
1 GAACATAAATGAACAC
674 GAACATAAA
1 GAACATAAA
683 CGTTGGACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (16 bp):
GAACATAAATGAACAC
Found at i:1442 original size:14 final size:14
Alignment explanation
Indices: 1421--1464 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1411 AAGATTGAGT
1421 TAAACATAAATGAA
1 TAAACATAAATGAA
* *
1435 TGAACATAAACGAA
1 TAAACATAAATGAA
*
1449 CAAACATAAATGAA
1 TAAACATAAATGAA
1463 TA
1 TA
1465 TAACCGAACG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.18
Consensus pattern (14 bp):
TAAACATAAATGAA
Found at i:1460 original size:24 final size:24
Alignment explanation
Indices: 1433--1481 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1423 AACATAAATG
1433 AATGAACATAAACGAACAAACATA
1 AATGAACATAAACGAACAAACATA
* * *
1457 AATGAATATAACCGAACGAACATA
1 AATGAACATAAACGAACAAACATA
1481 A
1 A
1482 TCGAACGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.14
Consensus pattern (24 bp):
AATGAACATAAACGAACAAACATA
Found at i:4125 original size:19 final size:20
Alignment explanation
Indices: 4101--4143 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4091 AGCATTTATC
*
4101 TTCATT-AAAATTATGTATT
1 TTCATTGAAAATCATGTATT
*
4120 TTCATTGAAAATCATGTGTT
1 TTCATTGAAAATCATGTATT
4140 TTCA
1 TTCA
4144 AGGGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTGAAAATCATGTATT
Found at i:4701 original size:16 final size:16
Alignment explanation
Indices: 4667--4713 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
4657 ATAACATCTC
*
4667 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
4683 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
4698 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
4711 TAT
1 TAT
4714 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:4715 original size:12 final size:13
Alignment explanation
Indices: 4688--4716 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4678 TTTCTTATCC
4688 TTTCATTTCTTTA
1 TTTCATTTCTTTA
4701 TTTCATTTC-TTA
1 TTTCATTTCTTTA
4713 TTTC
1 TTTC
4717 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:8143 original size:19 final size:20
Alignment explanation
Indices: 8119--8161 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
8109 AGCATTTATC
*
8119 TTCATT-AAAATTATGTATT
1 TTCATTGAAAATCATGTATT
*
8138 TTCATTGAAAATCATGTGTT
1 TTCATTGAAAATCATGTATT
8158 TTCA
1 TTCA
8162 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTGAAAATCATGTATT
Found at i:8735 original size:12 final size:12
Alignment explanation
Indices: 8708--8748 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
8698 TTTCTTATTC
8708 TTTCATTTCTTTA
1 TTTCATTTC-TTA
8721 TTTCATTTCTTA
1 TTTCATTTCTTA
8733 TTTCATTTCTTA
1 TTTCATTTCTTA
8745 TTTC
1 TTTC
8749 CAATATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCATTTCTTA
Found at i:17344 original size:34 final size:35
Alignment explanation
Indices: 17292--17364 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
17282 ATTCATCTTG
*
17292 AAAAAAAAGAATTCTGAAAATTTAAAAAA-AAAAC
1 AAAAAAAAGAATTCTGAAAATTAAAAAAAGAAAAC
* *
17326 AAAAAAACA-AATTTTGAAAATTAAAAAAAGAAAAG
1 AAAAAAA-AGAATTCTGAAAATTAAAAAAAGAAAAC
17361 AAAA
1 AAAA
17365 GTTCTGGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (35 bp):
AAAAAAAAGAATTCTGAAAATTAAAAAAAGAAAAC
Found at i:18692 original size:19 final size:21
Alignment explanation
Indices: 18668--18719 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
18658 CGGCCAGGAG
*
18668 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
18687 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
18708 CATGTATTTTCA
1 CATGTATTTTCA
18720 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:19847 original size:36 final size:35
Alignment explanation
Indices: 19772--19855 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
19762 ATTTATAAGT
* *
19772 TGGTGATGATATAGGCGTGATATAGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAATAGTAATGGAAGA
* * * *
19807 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTG-AAATAGTAATGGAAGA
19843 TGGTGATGA-ATAG
1 TGGTGATGATATAG
19856 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 22 0.54
36 19 0.46
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGAAATAGTAATGGAAGA
Found at i:22969 original size:381 final size:381
Alignment explanation
Indices: 22261--23017 Score: 1487
Period size: 381 Copynumber: 2.0 Consensus size: 381
22251 TACTAAGATG
*
22261 AAATGCAAAACTAATATGATACAATAATATGCTTGACATGAATGATGATTGAACGAAAATGTGAA
1 AAATACAAAACTAATATGATACAATAATATGCTTGACATGAATGATGATTGAACGAAAATGTGAA
*
22326 ACATGATATGTAAAGCTACTCTAACATACTAAACAACTTAATTACTAATATGCAATGTAATGCAT
66 ACATGATATGCAAAGCTACTCTAACATACTAAACAACTTAATTACTAATATGCAATGTAATGCAT
22391 AAATAAGTAAATAAGTAATAAAGTAAGGAATTACTCCCTTAGAGTTAATAAGGTAGAACGTCCTT
131 AAATAAGTAAATAAGTAATAAAGTAAGGAATTACTCCCTTAGAGTTAATAAGGTAGAACGTCCTT
22456 GAGGGGTTTTCATCATGGAGAAAACCGGCCCTAAACGTGCTCACATCATCCTCCCTTTCTTTTTG
196 GAGGGGTTTTCATCATGGAGAAAACCGGCCCTAAACGTGCTCACATCATCCTCCCTTTCTTTTTG
22521 GCGATTTGTCCTCAAATCGAAATGATTTCTCATTGAAGACCTTCTTGATGTAGGATGGATGGAAT
261 GCGATTTGTCCTCAAATCGAAATGATTTCTCATTGAAGACCTTCTTGATGTAGGATGGATGGAAT
22586 CCTCATACCTTTCTCCAATGGTCAACCTCTTGACTTCATATTTGGTAACTTAATGA
326 CCTCATACCTTTCTCCAATGGTCAACCTCTTGACTTCATATTTGGTAACTTAATGA
22642 AAATACAAAACTAATATGATACAATAATATGCTTGACATGAATGATGATTGAACGAAAATGTGAA
1 AAATACAAAACTAATATGATACAATAATATGCTTGACATGAATGATGATTGAACGAAAATGTGAA
22707 ACATGATATGCAAAGCTACTCTAACATACTAAACAACTTAATTACTAATATGCAATGTAATGCAT
66 ACATGATATGCAAAGCTACTCTAACATACTAAACAACTTAATTACTAATATGCAATGTAATGCAT
22772 AAATAAGTAAATAAGTAATAAAGTAAGGAATTACTCCCTTAGAGTTAATAAGGTAGAACGTCCTT
131 AAATAAGTAAATAAGTAATAAAGTAAGGAATTACTCCCTTAGAGTTAATAAGGTAGAACGTCCTT
*
22837 GAGGGGTTTTCGTCATGGAGAAAACCGGCCCTAAACGTGCTCACATCATCCTCCCTTTCTTTTTG
196 GAGGGGTTTTCATCATGGAGAAAACCGGCCCTAAACGTGCTCACATCATCCTCCCTTTCTTTTTG
22902 GCGATTTGTCCTCAAATCGAAATGATTTCTCATTGAAGACCTTCTTGATGTAGGATGGATGGAAT
261 GCGATTTGTCCTCAAATCGAAATGATTTCTCATTGAAGACCTTCTTGATGTAGGATGGATGGAAT
22967 CCTCATACCTTTCTCCAATGGTCAACCTCTTGACTTCATATTTGGTAACTT
326 CCTCATACCTTTCTCCAATGGTCAACCTCTTGACTTCATATTTGGTAACTT
23018 CATATTTCCT
Statistics
Matches: 373, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
381 373 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (381 bp):
AAATACAAAACTAATATGATACAATAATATGCTTGACATGAATGATGATTGAACGAAAATGTGAA
ACATGATATGCAAAGCTACTCTAACATACTAAACAACTTAATTACTAATATGCAATGTAATGCAT
AAATAAGTAAATAAGTAATAAAGTAAGGAATTACTCCCTTAGAGTTAATAAGGTAGAACGTCCTT
GAGGGGTTTTCATCATGGAGAAAACCGGCCCTAAACGTGCTCACATCATCCTCCCTTTCTTTTTG
GCGATTTGTCCTCAAATCGAAATGATTTCTCATTGAAGACCTTCTTGATGTAGGATGGATGGAAT
CCTCATACCTTTCTCCAATGGTCAACCTCTTGACTTCATATTTGGTAACTTAATGA
Found at i:30046 original size:15 final size:15
Alignment explanation
Indices: 30013--30050 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
30003 TTGTTTCACT
30013 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
30028 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
30042 TTTCTTTTG
1 TTTCTTTTG
30051 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:32952 original size:19 final size:20
Alignment explanation
Indices: 32928--32967 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
32918 TATCTTTTAT
32928 TTATTTCAT-TTCATT-CTTA
1 TTATTT-ATATTCATTACTTA
32947 TTATTTATATTCATTACTTA
1 TTATTTATATTCATTACTTA
32967 T
1 T
32968 ATTATTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.63
20 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTATATTCATTACTTA
Found at i:33259 original size:14 final size:13
Alignment explanation
Indices: 33242--33291 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
33232 GTGCAAAAAG
33242 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
33256 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
33269 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
33280 AAAGAAAAAGAA
1 AAAGAAAAAGAA
33292 TTCAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:33288 original size:19 final size:18
Alignment explanation
Indices: 33236--33291 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
33226 ATTGGAGTGC
33236 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
33253 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
33272 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
33291 A
1 A
33292 TTCAAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:37559 original size:19 final size:20
Alignment explanation
Indices: 37535--37574 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
37525 TATCTTTTAT
37535 TTATTTCAT-TTCATT-CTTA
1 TTATTT-ATATTCATTACTTA
37554 TTATTTATATTCATTACTTA
1 TTATTTATATTCATTACTTA
37574 T
1 T
37575 ATTATTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.63
20 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTATATTCATTACTTA
Found at i:41432 original size:19 final size:21
Alignment explanation
Indices: 41408--41459 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
41398 CGGCCAAGAG
*
41408 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
41427 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
41448 CATGTATTTTCA
1 CATGTATTTTCA
41460 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:43958 original size:24 final size:25
Alignment explanation
Indices: 43931--43982 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
43921 AAGAAAAATC
* *
43931 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
*
43955 AG-AAAGAAAAATCCAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
43979 AGAA
1 AGAA
43983 GAAAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:45339 original size:24 final size:25
Alignment explanation
Indices: 45293--45347 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
45283 ATAGTTATGC
*
45293 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
45317 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
45342 CA-TTGA
1 CACTTGA
45348 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:47872 original size:33 final size:33
Alignment explanation
Indices: 47830--47898 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
47820 GTTGATGAAT
*
47830 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
47863 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
47896 GAA
1 GAA
47899 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:52331 original size:33 final size:33
Alignment explanation
Indices: 52289--52357 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
52279 GTTGATGAAT
52289 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGTG-TGAAATGGTAATG
* * *
52322 GAAGGATGATGTTATTGGTGTGATATGGTGATG
1 GAAGGATGATGTTAATGGTGTGAAATGGTAATG
52355 GAA
1 GAA
52358 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGTGTGAAATGGTAATG
Found at i:66237 original size:19 final size:20
Alignment explanation
Indices: 66190--66238 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
66180 TTGAAACCCT
**
66190 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
66210 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
66229 TGAAGATACA
1 TGAAAATACA
66239 CTCTTGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.