Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000086.1 Hibiscus syriacus cultivar Beakdansim tig00000157_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: 60985
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3565 original size:6 final size:6
Alignment explanation
Indices: 3536--3564 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3526 TCATTTCATC
3536 CATTTT CATTTT CATTTT CATTTT -ATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
3565 TTTATGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
CATTTT
Found at i:5571 original size:14 final size:14
Alignment explanation
Indices: 5537--5578 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5527 GAGGGAAGAA
5537 GAAGATGAAAGAAGGT
1 GAAG-TGAAA-AAGGT
*
5553 AAAGTGAAAAAGGT
1 GAAGTGAAAAAGGT
5567 GAAGTGAAAAAG
1 GAAGTGAAAAAG
5579 TAAAGTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.67
15 5 0.21
16 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (14 bp):
GAAGTGAAAAAGGT
Found at i:15964 original size:22 final size:22
Alignment explanation
Indices: 15922--15970 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
15912 ATTTTTAATA
* *
15922 ATTTAAATTTCAGTATTTTTAT
1 ATTTAAATTTCAGAATATTTAT
15944 ATTTAAATTT-ATGAATATTTAT
1 ATTTAAATTTCA-GAATATTTAT
*
15966 TTTTA
1 ATTTA
15971 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTAAATTTCAGAATATTTAT
Found at i:15997 original size:28 final size:28
Alignment explanation
Indices: 15935--15995 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
15925 TAAATTTCAG
* *
15935 TATTTTTATATTTAAATTTATGAATATT
1 TATTTTTATATTTAAATTTATAAAAATT
15963 TATTTTTAT-TTTAAATTT-TAAAAATT
1 TATTTTTATATTTAAATTTATAAAAATT
15989 TATTTTT
1 TATTTTT
15996 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.42
27 9 0.29
28 9 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTTTTATATTTAAATTTATAAAAATT
Found at i:16822 original size:13 final size:13
Alignment explanation
Indices: 16804--16833 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16794 ACCACTTTTA
*
16804 ATATCATTTTGAT
1 ATATCATTTTCAT
16817 ATATCATTTTCAT
1 ATATCATTTTCAT
16830 ATAT
1 ATAT
16834 GTTCATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (13 bp):
ATATCATTTTCAT
Found at i:47140 original size:61 final size:64
Alignment explanation
Indices: 47023--47161 Score: 176
Period size: 61 Copynumber: 2.2 Consensus size: 64
47013 GCAGGTTTAT
* * * * **
47023 ATTAGCACTAGTGTGTAAGGACACTAAGTGTAGGTGGTGGGAACAACCTTATGTGTCATATACGG
1 ATTAGCACTAGAGTGTAA-GACACTAAGTGTAGGTGATGGGAACAACCCTACGTGTCATATACAA
* *
47088 ATTAGCACTAGAGTGTAA-AC-CT-AGTGTAGGTGATGGGCACAACCCTACGTGTCATATCCAA
1 ATTAGCACTAGAGTGTAAGACACTAAGTGTAGGTGATGGGAACAACCCTACGTGTCATATACAA
47149 ATTAGCACTAGAG
1 ATTAGCACTAGAG
47162 CGTATGCATA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 45 0.68
62 2 0.03
63 2 0.03
65 17 0.26
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (64 bp):
ATTAGCACTAGAGTGTAAGACACTAAGTGTAGGTGATGGGAACAACCCTACGTGTCATATACAA
Found at i:49416 original size:87 final size:87
Alignment explanation
Indices: 49264--49470 Score: 204
Period size: 87 Copynumber: 2.4 Consensus size: 87
49254 GGTATGACAA
* * *
49264 CACCCAAATCCTAGGCTATGAACTCATTAAGAGTATAAAATTCAACATCTAGAGTCAGTGAATTC
1 CACCCAAATCCTGGGCTATGAATTCATTAAGAGTATAAAAGTCAACATCTAGAGTCAGTGAATTC
* *
49329 ATTAAGTCCTTCTCAC-AAAGAC
66 ATCAAGTCCTCCTCACTAAA-AC
* * * * * * * *
49351 CACCCAAATCCTGGGCTATGAATTCATTAAGAGTGTAAAGGTCATCCTTTCA-CGTTAGTGGATT
1 CACCCAAATCCTGGGCTATGAATTCATTAAGAGTATAAAAGTCAACATCT-AGAGTCAGTGAATT
* *
49415 CATCAAGTCCTCCTCACTATAAT
65 CATCAAGTCCTCCTCACTAAAAC
* * *
49438 CACCAAAAAT-CTGGGCTATGAATCCTTTAAGAG
1 CACC-CAAATCCTGGGCTATGAATTCATTAAGAG
49471 CTAAAACTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
87 92 0.93
88 7 0.07
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (87 bp):
CACCCAAATCCTGGGCTATGAATTCATTAAGAGTATAAAAGTCAACATCTAGAGTCAGTGAATTC
ATCAAGTCCTCCTCACTAAAAC
Found at i:50176 original size:41 final size:41
Alignment explanation
Indices: 50131--50255 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
50121 GAGAGTTATT
*
50131 TTAGGAATCATCTTAACTAAAATTTTTCTATGTAAAAAGAC
1 TTAGGAATCATCTTAACTAAAATATTTCTATGTAAAAAGAC
*
50172 TTAGGAATCATCTTAACTAAAATATTTCTACGTAAAAAGAC
1 TTAGGAATCATCTTAACTAAAATATTTCTATGTAAAAAGAC
*
50213 TTAGGAATCATCTTAACTAAAAAATTTCTATGTAAAAAGAC
1 TTAGGAATCATCTTAACTAAAATATTTCTATGTAAAAAGAC
50254 TT
1 TT
50256 TTTTTAAATA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (41 bp):
TTAGGAATCATCTTAACTAAAATATTTCTATGTAAAAAGAC
Found at i:51549 original size:12 final size:12
Alignment explanation
Indices: 51532--51566 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
51522 ACAATCGCAT
51532 ATATAATATAAA
1 ATATAATATAAA
51544 ATATAATATAAA
1 ATATAATATAAA
51556 ATATAA-ATAAA
1 ATATAATATAAA
51567 GTAGAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:52919 original size:6 final size:5
Alignment explanation
Indices: 52890--52923 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
52880 TTGTAATATG
52890 TAAAA TAAAA TAAAA TAAAA TAATAA TAATAA TA
1 TAAAA TAAAA TAAAA TAAAA TAA-AA TAA-AA TA
52924 TGGTTTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:53622 original size:31 final size:32
Alignment explanation
Indices: 53587--53655 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
53577 CTACCCAAGG
*
53587 AGGTAAAAGTATGAATTTGGTGTCTCAAA-AA
1 AGGTAAAAGTATGAATTTGGAGTCTCAAATAA
** *
53618 AGGTAAGGGTATGAATTTGGAGTCTCAAATAG
1 AGGTAAAAGTATGAATTTGGAGTCTCAAATAA
53650 AGGTAA
1 AGGTAA
53656 TGTCAAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (32 bp):
AGGTAAAAGTATGAATTTGGAGTCTCAAATAA
Found at i:59654 original size:2 final size:2
Alignment explanation
Indices: 59647--59703 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
59637 CAAGGTCCAC
59647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
59688 AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT A
59704 AGATTAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.