Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009165.1 Hibiscus syriacus cultivar Beakdansim tig00112700_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: 53121
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:4348 original size:13 final size:13
Alignment explanation
Indices: 4330--4354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4320 TGTATCAAGT
4330 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
4343 TCTTTTCTTCTT
1 TCTTTTCTTCTT
4355 TTCTGACCTC
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TCTTTTCTTCTTC
Found at i:5507 original size:12 final size:13
Alignment explanation
Indices: 5488--5532 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
5478 AGTGGCGAGG
5488 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
*
5501 A-AAGAAAAATGA
1 AGAAGAAAAGTGA
5513 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
5526 AGAAGAA
1 AGAAGAA
5533 GATGGGAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (13 bp):
AGAAGAAAAGTGA
Found at i:11213 original size:82 final size:83
Alignment explanation
Indices: 11033--11241 Score: 271
Period size: 83 Copynumber: 2.5 Consensus size: 83
11023 TTTCTTAAAC
* *
11033 AACGCCGTGATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGCCAAATAGGGATCGTTTAT
1 AACGCCGCGATAGAGTAGTACTTTATC-GCGTTTTTATACAAACTGCCAAATAGGGATCGTTTAT
* *
11097 AGTGGCATTTTTTCTAATA
65 AGTGGCATTTTTTCCAACA
* *
11116 AACGCCGCGATAGAGTAGTACTTTATCGTGTTTTTATACAAACT-CCTCAATAGGGATCGTTTAT
1 AACGCCGCGATAGAGTAGTACTTTATCGCGTTTTTATACAAACTGCC-AAATAGGGATCGTTTAT
*
11180 ATTGGCA-TTTTTCCAACA
65 AGTGGCATTTTTTCCAACA
* * * *
11198 AATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACGCCGCGATAGAGTAGTACTTT-ATCGCGTTTTTATACAAAC
11242 ACTGTAATAG
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
82 47 0.42
83 64 0.58
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (83 bp):
AACGCCGCGATAGAGTAGTACTTTATCGCGTTTTTATACAAACTGCCAAATAGGGATCGTTTATA
GTGGCATTTTTTCCAACA
Found at i:11538 original size:38 final size:38
Alignment explanation
Indices: 11494--11582 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
11484 TTATCTTTTA
*
11494 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGAAG
* *
11532 TGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTGAAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGAAG
*
11570 TGGTGTTTTTAAA
1 TGGCGTTTTTAAA
11583 TACAAACACC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (38 bp):
TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGAAG
Found at i:15820 original size:60 final size:61
Alignment explanation
Indices: 15727--15850 Score: 223
Period size: 60 Copynumber: 2.0 Consensus size: 61
15717 ACCCGTTTTT
*
15727 ATAGTTTACACACTTTTGTATTACCTCTTCTTAAT-TGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATATGTACTTATGTTAATGCATTTCCTA
15787 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTACTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAAT-ATGTACTTATGTTAATGCATTTCCTA
15849 AT
1 AT
15851 GATACGTAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 35 0.57
62 26 0.43
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (61 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATATGTACTTATGTTAATGCATTTCCTA
Found at i:28899 original size:13 final size:14
Alignment explanation
Indices: 28878--28923 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
28868 AGTGGCGAGG
28878 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
*
28891 A-AAGAAAAAATGA
1 AGAAGAAAAAGTGA
28904 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
28917 AGAAGAA
1 AGAAGAA
28924 GATGGGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
14 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (14 bp):
AGAAGAAAAAGTGA
Found at i:34545 original size:83 final size:82
Alignment explanation
Indices: 34446--34659 Score: 277
Period size: 83 Copynumber: 2.6 Consensus size: 82
34436 GAGTTTCTTA
* *
34446 AACAAACGCCGTGATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGCCAGAATAGGGATCG
1 AACAAACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACT-CCACAATAGGGATCG
*
34510 TTTATAGTGGCATTTTTCT
64 TTTATAGTGGCATTTTTCC
* * *
34529 AATAAACGCCGCGATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCGT
1 AACAAACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACTCCACAATAGGGATCGT
* *
34594 TTATATTGGTATTTTTCC
65 TTATAGTGGCATTTTTCC
* * * *
34612 AACAAATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACAAACGCCGCGATAGAGTAGTACTTTACT-GCGTTTTTATACAAAC
34660 ACTGTAATAG
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 113 0.99
84 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (82 bp):
AACAAACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACTCCACAATAGGGATCGTT
TATAGTGGCATTTTTCC
Found at i:34692 original size:83 final size:83
Alignment explanation
Indices: 34458--34684 Score: 221
Period size: 83 Copynumber: 2.7 Consensus size: 83
34448 CAAACGCCGT
* * * * * *
34458 GATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGC-CAGAATAGGGATCGTTTATAGTGGC
1 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTC--AATAGGGATCGTTTACAGCGGT
* * * *
34521 ATTTTTCTAATAAACGCCGC
64 ATTTTTCCAACAAATGTCGC
* * **
34541 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTCCTCAATAGGGATCGTTTATATTGGTAT
1 GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTCAATAGGGATCGTTTACAGCGGTAT
34606 TTTTCCAACAAATGTCGC
66 TTTTCCAACAAATGTCGC
* * *
34624 GATAGAGTAGTACTTTAAT-GGCGTTTTTATATAAAC-ACTGTAATAGGGTTC-TTTAGCAGCG
1 GATAGAGTAGTACTTT-ATCGGCGTTTTTATACAAACTACT-CAATAGGGATCGTTTA-CAGCG
34685 TTTTTTTTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
82 6 0.05
83 112 0.91
84 4 0.03
85 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (83 bp):
GATAGAGTAGTACTTTATCGGCGTTTTTATACAAACTACTCAATAGGGATCGTTTACAGCGGTAT
TTTTCCAACAAATGTCGC
Found at i:35006 original size:39 final size:40
Alignment explanation
Indices: 34914--35006 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 40
34904 TTGTCTTTTA
*
34914 TGGCGTTTTTTAACAAACGCCGCAATAAATCAGTGCAGTAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-AG
* *
34955 TGGCGTTTTTAAACAAAACGCCGCAATAAGTTAGTG-A-AG
1 TGGCGTTTTTAAAC-AAACGCCGCAATAAATCAGTGCAGAG
*
34994 TGGTGTTTTTAAA
1 TGGCGTTTTTAAA
35007 TACAAACACC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 14 0.30
41 14 0.30
42 19 0.40
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
Found at i:36465 original size:22 final size:22
Alignment explanation
Indices: 36440--36494 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
36430 TTTGTAAAGC
36440 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
36462 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
36484 CTTCTTGATCC
1 CTTCTTGATCC
36495 GTCTATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:39249 original size:61 final size:61
Alignment explanation
Indices: 39155--39278 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 61
39145 ACCCGTTTTT
*
39155 ATAGTTTACACACTTTGTATTACCTCTTCTTAATTATGTATTTA-GTTAATGCATTTCCTA
1 ATAGTTTACACACTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
39215 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACAC-TTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
39277 AT
1 AT
39279 GATACGTAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 13 0.21
61 30 0.49
62 18 0.30
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.48
Consensus pattern (61 bp):
ATAGTTTACACACTTTGTATTACCTCTTCTTAATAATGTATTTATGTTAATGCATTTCCTA
Found at i:44337 original size:14 final size:14
Alignment explanation
Indices: 44318--44350 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
44308 AGACCCTTGA
44318 ATCACGGATGCTTC
1 ATCACGGATGCTTC
44332 ATCACGGATGCTTC
1 ATCACGGATGCTTC
44346 ATCAC
1 ATCAC
44351 TATCATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (14 bp):
ATCACGGATGCTTC
Found at i:50417 original size:14 final size:14
Alignment explanation
Indices: 50400--50432 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
50390 AGACCCTTGA
50400 ATCACGGATGCTTC
1 ATCACGGATGCTTC
50414 ATCACGGATGCTTC
1 ATCACGGATGCTTC
50428 ATCAC
1 ATCAC
50433 TATCATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (14 bp):
ATCACGGATGCTTC
Done.