Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003078.1 Hibiscus syriacus cultivar Beakdansim tig00006418_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: 46515
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5755 original size:24 final size:25
Alignment explanation
Indices: 5717--5783 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
5707 AAATGTTTGG
* * *
5717 AAAAATCATGGCTTTTGGAA-AACT
1 AAAAATCGTGACTTTTGGAAGAACC
5741 AAAAGAT-GTGACTTTT-GAAGAACC
1 AAAA-ATCGTGACTTTTGGAAGAACC
*
5765 AATAATCGTGACTTTTGGA
1 AAAAATCGTGACTTTTGGA
5784 GATTCACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 5 0.14
24 26 0.74
25 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (25 bp):
AAAAATCGTGACTTTTGGAAGAACC
Found at i:7011 original size:17 final size:17
Alignment explanation
Indices: 6973--7011 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6963 ACCTATAGTT
*
6973 CACATCTTTATAATATG
1 CACATCTTTATAATATA
*
6990 CACATCTTTATATTATA
1 CACATCTTTATAATATA
*
7007 TACAT
1 CACAT
7012 TGTATAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (17 bp):
CACATCTTTATAATATA
Found at i:8956 original size:19 final size:19
Alignment explanation
Indices: 8932--8969 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8922 AATCATGCCC
8932 AATATGATTTTAAGACTAT
1 AATATGATTTTAAGACTAT
8951 AATATGATTTTAAGACTAT
1 AATATGATTTTAAGACTAT
8970 CGTAACTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
AATATGATTTTAAGACTAT
Found at i:11226 original size:20 final size:20
Alignment explanation
Indices: 11186--11224 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11176 CATTGCAGGA
*
11186 ATTTATGGCATCGACAAAAG
1 ATTTATGGCATCCACAAAAG
11206 ATTTCATGGCATCCACAAA
1 ATTT-ATGGCATCCACAAA
11225 GACCTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCATCCACAAAAG
Found at i:22726 original size:29 final size:29
Alignment explanation
Indices: 22677--22769 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
22667 AAATGGATTT
* *
22677 AGTT-AGTGACCAAATTGTAAATTTTGAA
1 AGTTAAGTGACCAAAGTATAAATTTTGAA
*
22705 AGTTAAGTGACCAAAGTATAAACTTTAGAAA
1 AGTTAAGTGACCAAAGTATAAA-TTTTG-AA
* *
22736 AGTTTAAG-GACTAAAGTAT-AATTTTAAA
1 AG-TTAAGTGACCAAAGTATAAATTTTGAA
22764 ACGTTA
1 A-GTTA
22770 TGTAATCCGA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 10 0.19
29 19 0.35
30 6 0.11
31 14 0.26
32 5 0.09
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (29 bp):
AGTTAAGTGACCAAAGTATAAATTTTGAA
Found at i:22922 original size:11 final size:11
Alignment explanation
Indices: 22908--22934 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22898 AATTGAATAG
22908 AAATTTTGGAA
1 AAATTTTGGAA
22919 AAATTTTGGAA
1 AAATTTTGGAA
22930 AAATT
1 AAATT
22935 GAAGGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (11 bp):
AAATTTTGGAA
Found at i:29497 original size:2 final size:2
Alignment explanation
Indices: 29490--29534 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29480 TACACAACAA
29490 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
29532 AT A
1 AT A
29535 CATAACCACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31927 original size:159 final size:159
Alignment explanation
Indices: 31638--31964 Score: 627
Period size: 159 Copynumber: 2.1 Consensus size: 159
31628 AACAATGATC
*
31638 ACATACTTTCATTACATCATAACTCATTTTCAACATGATTTAATACTCATGCTTGCACATATCAC
1 ACATACTTTCATTACATCATAACTCATTTTCAACATGATTTAATACTCATGCTTGCACATATAAC
31703 TTGCTTCCAATGCATCACAAATCATAATTAACACATCACAATTCACATGTTTATCTCAATCATAT
66 TTGCTTCCAATGCATCACAAATCATAATTAACACATCACAATTCACATGTTTATCTCAATCATAT
31768 TCTTTTAATATATTCCTAACACAAAATCA
131 TCTTTTAATATATTCCTAACACAAAATCA
31797 ACATACTTTCATTACATCATAACTCATTTTCAACATGATTTAATACTCATGCTTGCACATATAAC
1 ACATACTTTCATTACATCATAACTCATTTTCAACATGATTTAATACTCATGCTTGCACATATAAC
*
31862 TTGCTTCCAATGCATCACAAATCATAATTAACACATCACAATTCACATGTTTATCTTAATCATAT
66 TTGCTTCCAATGCATCACAAATCATAATTAACACATCACAATTCACATGTTTATCTCAATCATAT
*
31927 TCTTTTAATATATTCCTAACACATAATCA
131 TCTTTTAATATATTCCTAACACAAAATCA
31956 ACATACTTT
1 ACATACTTT
31965 TGTACACATG
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
159 165 1.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (159 bp):
ACATACTTTCATTACATCATAACTCATTTTCAACATGATTTAATACTCATGCTTGCACATATAAC
TTGCTTCCAATGCATCACAAATCATAATTAACACATCACAATTCACATGTTTATCTCAATCATAT
TCTTTTAATATATTCCTAACACAAAATCA
Found at i:34916 original size:19 final size:19
Alignment explanation
Indices: 34879--34918 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34869 CTTTGACTTA
* *
34879 ACTGTTGATCTACCTGTTG
1 ACTGTTGACCTACCCGTTG
*
34898 ACTGTTGACCTGCCCGTTG
1 ACTGTTGACCTACCCGTTG
34917 AC
1 AC
34919 CATTGACCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.35
Consensus pattern (19 bp):
ACTGTTGACCTACCCGTTG
Found at i:39181 original size:18 final size:18
Alignment explanation
Indices: 39155--39189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39145 TGGTCAATTC
*
39155 CCCTGACCTCGTCGTCAT
1 CCCTAACCTCGTCGTCAT
*
39173 CCCTAACCTCGTTGTCA
1 CCCTAACCTCGTCGTCA
39190 CCGCGTGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (18 bp):
CCCTAACCTCGTCGTCAT
Found at i:40241 original size:54 final size:54
Alignment explanation
Indices: 40151--40465 Score: 371
Period size: 54 Copynumber: 5.8 Consensus size: 54
40141 TATAACCTCC
* * * * * *
40151 TTATGAATTACGTGGGGATGCACACCTAGTGCCAATACGAAAATTCATAAATTTA
1 TTATGAATTTCTTAGGG-TGCACACATAGTGCCAATACGGAAATTCATAAACTTA
* * * * *
40206 TTATGAATTTCTTAAGTTACACACACAGTGCCAATACGGAATTTCATAAACTTA
1 TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
* * * * *
40260 TGATGAATTTCTTAGGTTGCACACATAGCGCAAATACGGAAATTCATAAACTCA
1 TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
* ** *
40314 TTATGAA-TTCATTAGGGTGCACACATAGTGGCAATACAAAAATTCATAAACTCA
1 TTATGAATTTC-TTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
40368 TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
1 TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
* * * * * *
40422 CTATGAATTTCTTAGGTTGCCCATATAGTGCCAATTCGGTAATT
1 TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATT
40466 GCAATACATA
Statistics
Matches: 222, Mismatches: 36, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
53 3 0.01
54 204 0.92
55 15 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (54 bp):
TTATGAATTTCTTAGGGTGCACACATAGTGCCAATACGGAAATTCATAAACTTA
Found at i:40437 original size:108 final size:108
Alignment explanation
Indices: 40113--40456 Score: 393
Period size: 108 Copynumber: 3.2 Consensus size: 108
40103 TCCAATATTT
* * * * * * * * * * *
40113 TTGCACCCGTAGTGCCAATTCAACAATTTATAACCTCCTTATGAATTACGTGGGGATGCACACCT
1 TTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGGG-TGCACACAT
* * *
40178 AGTGCCAATACGAAAATTCATAAATTTATTATGAATTTCTTAAG
65 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
* * ** * * * *
40222 TTACACACACAGTGCCAATACGGAATTTCATAAACTTATGATGAATTTCTTAGGTTGCACACATA
1 TTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGGGTGCACACATA
* * *
40287 GCGCAAATACGGAAATTCATAAACTCATTATGAA-TTCATTAGG
66 GTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAGG
* *
40330 GTGCACACATAGTGGCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGGGTGCACACATA
1 TTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGGGTGCACACATA
*
40395 GTGCCAATACGGAAATTCATAAACTTACTATGAATTTCTTAGG
66 GTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
* *
40438 TTGCCCATATAGTGCCAAT
1 TTGCACACATAGTGCCAAT
40457 TCGGTAATTG
Statistics
Matches: 190, Mismatches: 43, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
107 3 0.02
108 147 0.77
109 40 0.21
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (108 bp):
TTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGGGTGCACACATA
GTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
Found at i:45382 original size:25 final size:25
Alignment explanation
Indices: 45353--45402 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45343 GATTAGGGGT
** *
45353 ACTGAAGTGTAAACATGTAGGGATA
1 ACTGAAGCCTAAACAAGTAGGGATA
*
45378 ACTGAAGCCTAAACAAGTAGTGATA
1 ACTGAAGCCTAAACAAGTAGGGATA
45403 TGGTGCTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (25 bp):
ACTGAAGCCTAAACAAGTAGGGATA
Found at i:45906 original size:18 final size:18
Alignment explanation
Indices: 45883--45918 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45873 AGGGTTCTAC
45883 GTGGTCCTACGAGACATA
1 GTGGTCCTACGAGACATA
*
45901 GTGGTCCTACGGGACATA
1 GTGGTCCTACGAGACATA
45919 TGTGCTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (18 bp):
GTGGTCCTACGAGACATA
Found at i:45928 original size:18 final size:18
Alignment explanation
Indices: 45887--45929 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
45877 TTCTACGTGG
*
45887 TCCTACGAGACATAGTGG
1 TCCTACGAGACATAGTGC
*
45905 TCCTACGGGACATATGTGC
1 TCCTACGAGACATA-GTGC
45924 T-CTACG
1 TCCTACG
45930 TGGTCCTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (18 bp):
TCCTACGAGACATAGTGC
Done.