Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001801.1 Hibiscus syriacus cultivar Beakdansim tig00003641_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: 91028
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:9627 original size:12 final size:12
Alignment explanation
Indices: 9610--9634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9600 ACTATTAAGA
9610 AAAAATATTATT
1 AAAAATATTATT
9622 AAAAATATTATT
1 AAAAATATTATT
9634 A
1 A
9635 TTTTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:9790 original size:18 final size:19
Alignment explanation
Indices: 9769--9804 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9759 AATAAAACGT
*
9769 TTAATAATAAT-ATTTTTA
1 TTAAAAATAATAATTTTTA
9787 TTAAAAATAATAATTTTT
1 TTAAAAATAATAATTTTT
9805 TACCAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAAATAATAATTTTTA
Found at i:9812 original size:20 final size:21
Alignment explanation
Indices: 9771--9815 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
9761 TAAAACGTTT
**
9771 AATAATAATATTTTTATTAAA
1 AATAATAATATTTTTACCAAA
9792 AATAATAAT-TTTTTACCAAA
1 AATAATAATATTTTTACCAAA
9812 AATA
1 AATA
9816 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAATAATATTTTTACCAAA
Found at i:9841 original size:26 final size:28
Alignment explanation
Indices: 9785--9843 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
9775 ATAATATTTT
*
9785 TATTAAAAATAATAATTTTTTACCAAAAA
1 TATTAAAAATAATAATATTTTA-CAAAAA
*
9814 TATTAAAAAT-ATAATATTTT-CAATAA
1 TATTAAAAATAATAATATTTTACAAAAA
9840 TATT
1 TATT
9844 TATATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
28 9 0.32
29 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (28 bp):
TATTAAAAATAATAATATTTTACAAAAA
Found at i:12020 original size:39 final size:39
Alignment explanation
Indices: 11977--12063 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 39
11967 TAAATTTTGA
*
11977 TATTTTATAAATATTTTATTTTTAT-TTTTAATAATTCAT
1 TATTTTATAAATATTGT-TTTTTATATTTTAATAATTCAT
* *
12016 TA-TTTA-ATA-ATTGTTTTTTATATTTTAATAATTTAT
1 TATTTTATAAATATTGTTTTTTATATTTTAATAATTCAT
12052 TATATTT-TAAAT
1 TAT-TTTATAAAT
12064 TTTAAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
35 7 0.18
36 19 0.49
37 2 0.05
38 9 0.23
39 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (39 bp):
TATTTTATAAATATTGTTTTTTATATTTTAATAATTCAT
Found at i:20996 original size:21 final size:21
Alignment explanation
Indices: 20966--21015 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
20956 ATCGAAAACA
20966 TTATTATTTCTACTGATTTTG
1 TTATTATTTCTACTGATTTTG
* *
20987 TTATTTTTTCTATTGATTTTG
1 TTATTATTTCTACTGATTTTG
21008 TTATTATT
1 TTATTATT
21016 GATCACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.68
Consensus pattern (21 bp):
TTATTATTTCTACTGATTTTG
Found at i:27228 original size:31 final size:31
Alignment explanation
Indices: 27193--27254 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
27183 AAAAGTTCTC
27193 GCTCTTGATTTGCATGAAACGTCAAAATAAA
1 GCTCTTGATTTGCATGAAACGTCAAAATAAA
27224 GCTCTTGATTTGCATGAAACGTCAAAATAAA
1 GCTCTTGATTTGCATGAAACGTCAAAATAAA
27255 TGGAGCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
GCTCTTGATTTGCATGAAACGTCAAAATAAA
Found at i:35343 original size:80 final size:80
Alignment explanation
Indices: 35210--35364 Score: 292
Period size: 80 Copynumber: 1.9 Consensus size: 80
35200 CATGGGATGA
*
35210 GAATCCCACATTCTCATGTTTGGTTGGCCGGGAGTCTCATTCCCGGTAATGTTTTATTACCAATA
1 GAATCCCACATTCTCATGTTTGGTTGGCCGGGAGTCTCATTCCCGGTAATGTTTTATTACAAATA
35275 GTAGATTTTTTGTGG
66 GTAGATTTTTTGTGG
*
35290 GAATCCCACATTCTCATGTTTGGTTGGCCTGGAGTCTCATTCCCGGTAATGTTTTATTACAAATA
1 GAATCCCACATTCTCATGTTTGGTTGGCCGGGAGTCTCATTCCCGGTAATGTTTTATTACAAATA
35355 GTAGATTTTT
66 GTAGATTTTT
35365 GGGGGTATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (80 bp):
GAATCCCACATTCTCATGTTTGGTTGGCCGGGAGTCTCATTCCCGGTAATGTTTTATTACAAATA
GTAGATTTTTTGTGG
Found at i:35686 original size:37 final size:37
Alignment explanation
Indices: 35610--35686 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
35600 TTTTTATATT
*
35610 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
35647 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
35684 TTT
1 TTT
35687 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:37643 original size:2 final size:2
Alignment explanation
Indices: 37638--37670 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
37628 TATTTTCTTC
37638 AT AT AT 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 AT AT AT A
37671 CTTACCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49012 original size:15 final size:17
Alignment explanation
Indices: 48992--49040 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
48982 GGCAATTTGA
48992 GATATAACA-A-CAAGT
1 GATATAACACAGCAAGT
49007 GATATAACAGCAGCAAGT
1 GATATAACA-CAGCAAGT
49025 GATATAACAGCAGCAA
1 GATATAACA-CAGCAA
49041 CTCAGACTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.29
17 1 0.03
18 21 0.68
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.16
Consensus pattern (17 bp):
GATATAACACAGCAAGT
Found at i:49025 original size:18 final size:18
Alignment explanation
Indices: 49002--49040 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
48992 GATATAACAA
49002 CAAGTGATATAACAGCAG
1 CAAGTGATATAACAGCAG
49020 CAAGTGATATAACAGCAG
1 CAAGTGATATAACAGCAG
49038 CAA
1 CAA
49041 CTCAGACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (18 bp):
CAAGTGATATAACAGCAG
Found at i:56732 original size:23 final size:23
Alignment explanation
Indices: 56674--56734 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
56664 TGTAAATGTT
*
56674 CCGAAGGACCACATAGAATTGTC
1 CCGAAAGACCACATAGAATTGTC
* * *
56697 CCTAATGAGCACATAGAATTGTC
1 CCGAAAGACCACATAGAATTGTC
56720 CCGAAAGACCACATA
1 CCGAAAGACCACATA
56735 TATGTTCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (23 bp):
CCGAAAGACCACATAGAATTGTC
Found at i:59559 original size:22 final size:24
Alignment explanation
Indices: 59509--59560 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
59499 TTTTTTAAAG
59509 ATTAAGTGATTATGTATGTCTATT
1 ATTAAGTGATTATGTATGTCTATT
*
59533 ATTAAGTG-TT-TGTCTGT-TACTT
1 ATTAAGTGATTATGTATGTCTA-TT
59555 ATTAAG
1 ATTAAG
59561 ACCAAATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 14 0.54
23 2 0.08
24 8 0.31
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (24 bp):
ATTAAGTGATTATGTATGTCTATT
Found at i:59626 original size:2 final size:2
Alignment explanation
Indices: 59619--59719 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
59609 TATTTTCTTC
59619 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
59661 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
59703 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
59720 CTTACCTTCA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69898 original size:11 final size:11
Alignment explanation
Indices: 69882--69906 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69872 AAGATGAAAC
69882 ATGCAACAAAA
1 ATGCAACAAAA
69893 ATGCAACAAAA
1 ATGCAACAAAA
69904 ATG
1 ATG
69907 TGGGAGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (11 bp):
ATGCAACAAAA
Found at i:70578 original size:31 final size:31
Alignment explanation
Indices: 70536--70599 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
70526 TGATATTTAG
70536 CTTCAACTGAATGTTTTCATGGTAAATATTA
1 CTTCAACTGAATGTTTTCATGGTAAATATTA
*
70567 CTTCAATTGAATGTTTTCATGGTAAATATTA
1 CTTCAACTGAATGTTTTCATGGTAAATATTA
70598 CT
1 CT
70600 ACTTCCGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (31 bp):
CTTCAACTGAATGTTTTCATGGTAAATATTA
Found at i:72056 original size:2 final size:2
Alignment explanation
Indices: 72049--72086 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
72039 TAGATGCTAT
72049 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
72087 AAGGGAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:74840 original size:22 final size:22
Alignment explanation
Indices: 74800--74843 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
74790 CTACAATAGC
74800 AGGAAAAAAAAGCCAGTCATAAG
1 AGGAAAAAAAA-CCAGTCATAAG
74823 AGGAAAAAAAA-CATGTCATAA
1 AGGAAAAAAAACCA-GTCATAA
74844 TGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 7 0.35
23 11 0.55
ACGTcount: A:0.59, C:0.11, G:0.18, T:0.11
Consensus pattern (22 bp):
AGGAAAAAAAACCAGTCATAAG
Found at i:75277 original size:59 final size:58
Alignment explanation
Indices: 75200--75347 Score: 151
Period size: 58 Copynumber: 2.5 Consensus size: 58
75190 TACGTTTTTT
* *
75200 TCTT-AAACTTTTAAATATTTTAATTTCATCCT-TAAATTATAATTCTCACTCTAAA-TAA
1 TCTTCAAA-TTTTAAATATTTTAATTTCATCCTCCAAA-T-TAACTCTCACTCTAAATTAA
* * * *
75258 TCTTCAAATTTTAAAATATTTTAACTGCAT-CTCCAAATTAACTCTCATTCTAAATTAG
1 TCTTCAAATTTT-AAATATTTTAATTTCATCCTCCAAATTAACTCTCACTCTAAATTAA
* *
75316 TCTTCAAATTTTTAAATGTTCTAATTTCATCC
1 TCTTCAAA-TTTTAAATATTTTAATTTCATCC
75348 CTAATCTTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
57 14 0.19
58 34 0.46
59 26 0.35
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (58 bp):
TCTTCAAATTTTAAATATTTTAATTTCATCCTCCAAATTAACTCTCACTCTAAATTAA
Found at i:86449 original size:32 final size:32
Alignment explanation
Indices: 86413--86509 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
86403 ACTAACAGTT
*
86413 TGTTGAACTGATTATTAGCCAACAGCTTCGAG
1 TGTTGTACTGATTATTAGCCAACAGCTTCGAG
86445 TGTTGTACTGATTATTAGCCAACAGCTTCGAG
1 TGTTGTACTGATTATTAGCCAACAGCTTCGAG
86477 TGTTGTACTGATTATTAGCCAACAGCTTCGAG
1 TGTTGTACTGATTATTAGCCAACAGCTTCGAG
86509 T
1 T
86510 TTCAAGTGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (32 bp):
TGTTGTACTGATTATTAGCCAACAGCTTCGAG
Done.