Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003494.1 Hibiscus syriacus cultivar Beakdansim tig00007390_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: 53917
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:4005 original size:7 final size:7
Alignment explanation
Indices: 3990--4019 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3980 CTTTGTAATG
3990 AACCCTA
1 AACCCTA
*
3997 AATCCTA
1 AACCCTA
4004 AACCCTA
1 AACCCTA
4011 AACCCTA
1 AACCCTA
4018 AA
1 AA
4020 TATTAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:4016 original size:21 final size:21
Alignment explanation
Indices: 3990--4043 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3980 CTTTGTAATG
*
3990 AACCCTAAATCCTAAACCCTA
1 AACCCTAAATCCTAAACACTA
** *
4011 AACCCTAAATATTAAACATTA
1 AACCCTAAATCCTAAACACTA
4032 AACCCTAAATCC
1 AACCCTAAATCC
4044 GATTATGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAAATCCTAAACACTA
Found at i:5046 original size:35 final size:34
Alignment explanation
Indices: 5007--5078 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 34
4997 CGTCCCCGTC
*
5007 CCCGTCCCTGTTTAACATAAACGGTTTTTCCCCAT
1 CCCGTCCCCGTTTAACATAAACGG-TTTTCCCCAT
*
5042 CCCGTCCCCGTTTAACATAAACGGTTTTCCCCGT
1 CCCGTCCCCGTTTAACATAAACGGTTTTCCCCAT
5076 CCC
1 CCC
5079 TGTTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.31
Consensus pattern (34 bp):
CCCGTCCCCGTTTAACATAAACGGTTTTCCCCAT
Found at i:7711 original size:17 final size:17
Alignment explanation
Indices: 7689--7721 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7679 TTTGAGTTTG
7689 AGTTCGAGCTTGAATCA
1 AGTTCGAGCTTGAATCA
7706 AGTTCGAGCTTGAATC
1 AGTTCGAGCTTGAATC
7722 GAGCTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCA
Found at i:20211 original size:54 final size:51
Alignment explanation
Indices: 20119--20218 Score: 130
Period size: 54 Copynumber: 1.9 Consensus size: 51
20109 TTTTATGTAA
* * *
20119 TTAACAACAACCATACATTTTAATTAAGACATAAGTTATGCATAAAACTAC
1 TTAACAACAACAATACATTATAATTAAAACATAAGTTATGCATAAAACTAC
20170 TTAACAACAA-AATACATTATAATTTAGAAACATTAAAGTTATGCATAAA
1 TTAACAACAACAATACATTATAA-TTA-AAACA-T-AAGTTATGCATAAA
20219 TAATTTTCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
50 10 0.24
51 13 0.31
52 4 0.10
53 1 0.02
54 14 0.33
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (51 bp):
TTAACAACAACAATACATTATAATTAAAACATAAGTTATGCATAAAACTAC
Found at i:21736 original size:248 final size:247
Alignment explanation
Indices: 21349--21931 Score: 774
Period size: 248 Copynumber: 2.4 Consensus size: 247
21339 AAGCGATGCT
* * * * * *
21349 AAAGTATTCTTCATTACGGCGTTTGTTGGAAAAACGCCACTATAAACCACCATATTGTGGCGTTT
1 AAAGTATTCTTCATTGCGACGTTTGTTGGAAAAATGCCACTATAAACCACCATATTATGACATTT
* * * * *
21414 TAGGTATAAACGCCGCTAATTTACCACTCTATTGCGGCATTTGTGGTATAATCGCCGCTGAATTA
66 TAGGTATAAACGCCGCTAATTTACCAATCTATTGCGGCATTTATGGTACAAACGCCGCTAAATTA
* ** * * *
21479 CCACTCTATTGCGGTGTTTGGGCTAAAACGCCGTTAAATGTCTACTCTATTACGATGT-TTTTAC
131 CCACTCTATTACGACGTTCGGGCTAAAACGCCGCTAAATGTCTACTATATTACG--GTATTTTAC
* * * *
21543 TATAAACGCCGCTATTGATTAACCCTTTTGTGGCATTTATCTAAAAACGACACA
194 TATAAACGCCGCTATTGATTAACCCTTATGTGACATTTATCAAAAAACAACACA
* * *
21597 AACGTATTCTTCATTGCGACGTTCGTTGGAAAAATGCCACTATAAACCACCCTATTATGACATTT
1 AAAGTATTCTTCATTGCGACGTTTGTTGGAAAAATGCCACTATAAACCACCATATTATGACATTT
* * *
21662 TAGGTATAAACACCGCTAATTTACCAATCTATTGCGGCGTTTATGGTACAAACGCTGCTAAATTA
66 TAGGTATAAACGCCGCTAATTTACCAATCTATTGCGGCATTTATGGTACAAACGCCGCTAAATTA
*
21727 CCACTCTATTACGACGTTCGGGCTAAAACGCTGCTAAATGTCTACTATATTACGGTATTTTACTA
131 CCACTCTATTACGACGTTCGGGCTAAAACGCCGCTAAATGTCTACTATATTACGGTATTTTACTA
* * *
21792 TAAACGCCGCTATTGATTAACCCTTATGTGACGTTTGTCAAAAAACAACGCA
196 TAAACGCCGCTATTGATTAACCCTTATGTGACATTTATCAAAAAACAACACA
* * * * * *
21844 AAAGTGTTCATCATTGCAATGTTTGTTGGAAAAATGCCTCTATAAACCACCATATTACGACATTT
1 AAAGTATTCTTCATTGCGACGTTTGTTGGAAAAATGCCACTATAAACCACCATATTATGACA-TT
*
21909 TTA-GTAAAAACGCCGCTATATTT
65 TTAGGTATAAACGCCGCTA-ATTT
21932 CTACTCTATT
Statistics
Matches: 290, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
246 2 0.01
247 119 0.41
248 169 0.58
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (247 bp):
AAAGTATTCTTCATTGCGACGTTTGTTGGAAAAATGCCACTATAAACCACCATATTATGACATTT
TAGGTATAAACGCCGCTAATTTACCAATCTATTGCGGCATTTATGGTACAAACGCCGCTAAATTA
CCACTCTATTACGACGTTCGGGCTAAAACGCCGCTAAATGTCTACTATATTACGGTATTTTACTA
TAAACGCCGCTATTGATTAACCCTTATGTGACATTTATCAAAAAACAACACA
Found at i:28163 original size:30 final size:27
Alignment explanation
Indices: 28106--28163 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
28096 TTCAAAGTAT
**
28106 TATTATTTTATATATTTAATATGAATA
1 TATTATTTTATATATTTAATAAAAATA
28133 TATTATTTTAATATCATTTTAATAAAAATA
1 TATTATTTT-ATAT-A-TTTAATAAAAATA
28163 T
1 T
28164 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 4 0.15
29 1 0.04
30 12 0.46
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:28164 original size:28 final size:26
Alignment explanation
Indices: 28106--28165 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
28096 TTCAAAGTAT
*
28106 TATTATTTTATATATTTAATATGAATA
1 TATTATTTTATATATTTAATA-GAAAA
28133 TATTATTTTAATATCATTTTAATA-AAAA
1 TATTATTTT-ATAT-A-TTTAATAGAAAA
28161 TATTA
1 TATTA
28166 ATTATTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.31
28 12 0.41
29 1 0.03
30 7 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTATTTTATATATTTAATAGAAAA
Found at i:33408 original size:16 final size:16
Alignment explanation
Indices: 33370--33408 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
33360 ATTGGTTTTT
33370 AGATCGGGTCAATATC
1 AGATCGGGTCAATATC
* * *
33386 GGGTCGGGTCATTATC
1 AGATCGGGTCAATATC
33402 AGATCGG
1 AGATCGG
33409 TTGATTTTTG
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (16 bp):
AGATCGGGTCAATATC
Found at i:33422 original size:32 final size:32
Alignment explanation
Indices: 33386--33483 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
33376 GGTCAATATC
* *
33386 GGGTCGGGTCATTATCAGATCGGTTGATTTTT
1 GGGTCGGGTCAATATCAGATCAGTTGATTTTT
* *
33418 GGGTCGGGTTAATA-CTAGATCAGTTAGA-TTTC
1 GGGTCGGGTCAATATC-AGATCAGTT-GATTTTT
* **
33450 AGGTTTGGTCAATATCAGATCAGTTGATTTTT
1 GGGTCGGGTCAATATCAGATCAGTTGATTTTT
33482 GG
1 GG
33484 TTTAGGTCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
31 3 0.06
32 46 0.88
33 3 0.06
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (32 bp):
GGGTCGGGTCAATATCAGATCAGTTGATTTTT
Found at i:33750 original size:30 final size:30
Alignment explanation
Indices: 33716--33772 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
33706 ATAATACATG
33716 TTAGAATTTGTTATCAAAATTTTATATGTT
1 TTAGAATTTGTTATCAAAATTTTATATGTT
*
33746 TTAGAATTTGTTATCAAATTTTTATAT
1 TTAGAATTTGTTATCAAAATTTTATAT
33773 TAATCTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (30 bp):
TTAGAATTTGTTATCAAAATTTTATATGTT
Found at i:34194 original size:19 final size:18
Alignment explanation
Indices: 34147--34194 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
34137 TATCAATTTT
*
34147 ATTTAAATT-AATTTATT
1 ATTTAAATTAAATTTATC
* *
34164 ATTCAAAATAAATTTTATC
1 ATTTAAATTAAA-TTTATC
34183 ATTTAAATTAAA
1 ATTTAAATTAAA
34195 ATAAACTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 7 0.29
18 2 0.08
19 15 0.62
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAATTAAATTTATC
Found at i:43552 original size:28 final size:28
Alignment explanation
Indices: 43512--43584 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
43502 ATATATATAT
43512 ATATATATATATATATAT-CTTTAT-TAAC
1 ATATATATATATATAT-TGCTTTATCT-AC
*
43540 ATATATATGTATATATTGCTTTATCTAC
1 ATATATATATATATATTGCTTTATCTAC
*
43568 TTATATATATATATATT
1 ATATATATATATATATT
43585 TGTTTCCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 38 0.95
29 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (28 bp):
ATATATATATATATATTGCTTTATCTAC
Found at i:43574 original size:2 final size:2
Alignment explanation
Indices: 43501--43555 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
43491 TTTCACTAAT
* * *
43501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TT TA T- TA -A CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
43541 TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA T
43556 TGCTTTATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.