Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005640.1 Hibiscus syriacus cultivar Beakdansim tig00013145_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: 72690
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:9105 original size:22 final size:21
Alignment explanation
Indices: 9074--9115 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
9064 CATCTCCATT
9074 TCATCATCAACACCATCAATA
1 TCATCATCAACACCATCAATA
*
9095 TCATCCATCAAGACCATCAAT
1 TCAT-CATCAACACCATCAAT
9116 TCTGTAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATCATCAACACCATCAATA
Found at i:16175 original size:15 final size:15
Alignment explanation
Indices: 16140--16168 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16130 GTGCTTCAAC
16140 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
16154 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
16169 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:18163 original size:54 final size:54
Alignment explanation
Indices: 18096--18225 Score: 179
Period size: 54 Copynumber: 2.4 Consensus size: 54
18086 AAATTCCGGA
* *
18096 GGTTGCACACTTAGTGCCGATATGGTCGTTCATAAACACATTATGAATTTTATG
1 GGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTATG
** * ** * *
18150 GGTTGCACACTTAGTGAAGATACGGTCTTTCATAAACTTATTTTGAATTCTGTG
1 GGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTATG
18204 GGTTGCACACTTAGTGCCGATA
1 GGTTGCACACTTAGTGCCGATA
18226 GTACACATAG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (54 bp):
GGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTATG
Found at i:27885 original size:14 final size:14
Alignment explanation
Indices: 27851--27882 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
27841 TGTGCTTTTA
27851 ACTTTTC-TTTCTT
1 ACTTTTCTTTTCTT
27864 ACTTTTCTTTTCTT
1 ACTTTTCTTTTCTT
27878 -CTTTT
1 ACTTTT
27883 TCTGAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (14 bp):
ACTTTTCTTTTCTT
Found at i:27899 original size:26 final size:27
Alignment explanation
Indices: 27870--27920 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
27860 TCTTACTTTT
27870 CTTTTCTTCTT-TTTCT-GAGTGCTTGA
1 CTTTTCTTCTTCTTT-TGGAGTGCTTGA
27896 CTTTTCTTCTTCTTTTGGAGTGCTT
1 CTTTTCTTCTTCTTTTGGAGTGCTT
27921 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.06, C:0.20, G:0.16, T:0.59
Consensus pattern (27 bp):
CTTTTCTTCTTCTTTTGGAGTGCTTGA
Found at i:27927 original size:26 final size:26
Alignment explanation
Indices: 27872--27929 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
27862 TTACTTTTCT
* *
27872 TTTCTTCTTTTTCTGAGTGCTTGACT
1 TTTCTTCTTTTTCTGAGTGCTTCACA
27898 TTTCTTCTTCTTT-TGGAGTGCTTCA-A
1 TTTCTTCTT-TTTCT-GAGTGCTTCACA
27924 TTTCTT
1 TTTCTT
27930 TTGCTGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.09, C:0.19, G:0.14, T:0.59
Consensus pattern (26 bp):
TTTCTTCTTTTTCTGAGTGCTTCACA
Found at i:32107 original size:26 final size:27
Alignment explanation
Indices: 32078--32128 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
32068 TCTTACTTTT
*
32078 CTTTTTTTCTT-TTTCT-GAGTGCTTGA
1 CTTTTCTTCTTCTTT-TGGAGTGCTTGA
32104 CTTTTCTTCTTCTTTTGGAGTGCTT
1 CTTTTCTTCTTCTTTTGGAGTGCTT
32129 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.06, C:0.18, G:0.16, T:0.61
Consensus pattern (27 bp):
CTTTTCTTCTTCTTTTGGAGTGCTTGA
Found at i:35427 original size:27 final size:26
Alignment explanation
Indices: 35393--35449 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
35383 AAAGAAAAGA
35393 CAAAAAGAAG--AAGAAAAA-AAATT
1 CAAAAAGAAGAAAAGAAAAAGAAATT
*
35416 CAGAAAAGAAGAAAAGAAAAAGAAGTT
1 CA-AAAAGAAGAAAAGAAAAAGAAATT
35443 CAAAAAG
1 CAAAAAG
35450 GGAAAGCGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 8 0.28
26 13 0.45
27 6 0.21
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (26 bp):
CAAAAAGAAGAAAAGAAAAAGAAATT
Found at i:37176 original size:26 final size:26
Alignment explanation
Indices: 37105--37179 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
37095 TGGCTGCAAC
*
37105 AAAGATAAGAAAATGAAGATG-ATTAAT
1 AAAGATAAG-AAATGAA-ATGAAATAAT
*
37132 AAAG-GAAG-AAT-AAATGAAATAAT
1 AAAGATAAGAAATGAAATGAAATAAT
37155 AAAGATAAGAAATGAAATGAAATAA
1 AAAGATAAGAAATGAAATGAAATAA
37180 AGAAGGGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 3 0.07
23 11 0.27
24 6 0.15
25 3 0.07
26 14 0.34
27 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (26 bp):
AAAGATAAGAAATGAAATGAAATAAT
Found at i:37180 original size:23 final size:23
Alignment explanation
Indices: 37105--37182 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 23
37095 TGGCTGCAAC
37105 AAAGATAAGAAAATGAAGATGATTAAT
1 AAAGATAAG-AAATGAA-ATGA--AAT
* *
37132 AAAGGAAGAATAAATGAAAT--AAT
1 AAA-G-ATAAGAAATGAAATGAAAT
37155 AAAGATAAGAAATGAAATGAAAT
1 AAAGATAAGAAATGAAATGAAAT
37178 AAAGA
1 AAAGA
37183 AGGGATAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 12 0.28
22 1 0.02
23 14 0.33
27 5 0.12
28 8 0.19
29 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAGATAAGAAATGAAATGAAAT
Found at i:37627 original size:19 final size:20
Alignment explanation
Indices: 37589--37631 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
37579 GAAACCCCTT
*
37589 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
37609 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
37628 TGAA
1 TGAA
37632 GATAAATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:46763 original size:31 final size:31
Alignment explanation
Indices: 46728--46787 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
46718 GCTTGTTTTC
46728 TCTTTT-TGAATTTCTAT-TTCTTTTCTTTTAT
1 TCTTTTCTGAATTT-T-TCTTCTTTTCTTTTAT
46759 TCTTTTCTGAATTTTTCTTCTTTTCTTTT
1 TCTTTTCTGAATTTTTCTTCTTTTCTTTT
46788 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 19 0.70
32 7 0.26
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (31 bp):
TCTTTTCTGAATTTTTCTTCTTTTCTTTTAT
Found at i:46793 original size:18 final size:18
Alignment explanation
Indices: 46739--46800 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
46729 CTTTTTGAAT
*
46739 TTCTATTTCTTTTCTTTTA
1 TTCT-TTTCTTTTCTTTTC
**
46758 TTCTTTTCTGAAT-TTTTC
1 TTCTTTTCT-TTTCTTTTC
46776 TTCTTTTCTTTTCTTTTC
1 TTCTTTTCTTTTCTTTTC
46794 TT-TTTTC
1 TTCTTTTC
46801 ACTCCAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 6 0.17
18 25 0.69
19 5 0.14
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (18 bp):
TTCTTTTCTTTTCTTTTC
Found at i:48567 original size:20 final size:19
Alignment explanation
Indices: 48529--48567 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
48519 TAAGTAAAGA
**
48529 TGTGAAAACATATGTTATG
1 TGTGAAAACATATAATATG
48548 TGTGAAAATCATATAATATG
1 TGTGAAAA-CATATAATATG
48568 CAAGTGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTGAAAACATATAATATG
Found at i:55219 original size:23 final size:23
Alignment explanation
Indices: 55191--55244 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
55181 AAAAATCAAA
*
55191 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAGTCAAGCACTCAAAAG
* *
55214 AAAGAAACATCCAGCACTCAAAAG
1 AAAGAAA-GTCAAGCACTCAAAAG
55238 -AAGAAAG
1 AAAGAAAG
55245 AAAAAGCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.57, C:0.17, G:0.19, T:0.07
Consensus pattern (23 bp):
AAAGAAAGTCAAGCACTCAAAAG
Found at i:55252 original size:23 final size:24
Alignment explanation
Indices: 55201--55252 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
55191 AAAGAAAGTG
**
55201 AAGCACTCAAAAGAAAGAAACATC
1 AAGCACTCAAAAGAAAGAAACAAA
* *
55225 CAGCACTCAAAAG-AAGAAAGAAA
1 AAGCACTCAAAAGAAAGAAACAAA
55248 AAGCA
1 AAGCA
55253 AAGAAAAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.60, C:0.19, G:0.15, T:0.06
Consensus pattern (24 bp):
AAGCACTCAAAAGAAAGAAACAAA
Found at i:57726 original size:20 final size:22
Alignment explanation
Indices: 57691--57730 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
57681 CATGCTTAAT
57691 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
57713 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
57731 GGTCTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:65369 original size:366 final size:366
Alignment explanation
Indices: 64685--65420 Score: 1312
Period size: 366 Copynumber: 2.0 Consensus size: 366
64675 TCCCTTGTTT
* *
64685 AAGATTTTGTAGCTTATGATAGAGATCTCTATGATAGTGAGTAGGCACGAACCTTTTCCTCATAA
1 AAGATATTGTAACTTATGATAGAGATCTCTATGATAGTGAGTAGGCACGAACCTTTTCCTCATAA
*
64750 TAGCCTTCATTTCTTCCCACGTAGTGATGGGACGTTCACCATTTCGTCTTCTTGAACTCACCAAT
66 TAGCCTTCATTTCTTCCCACGTAGTGATGGGACGTTCACCATTTCATCTTCTTGAACTCACCAAT
* *
64815 TGATCCCACCAATGATGTAAGGCTCTTCTATTACCTTGACAAACTAATTGTGGATCTAGGAAGGA
131 TGATCCCACCAATGATGTAAGGCTCTTCTATTACCTTAACAAAATAATTGTGGATCTAGGAAGGA
64880 AGCCAAAAAACCTGCAAAGTGAATGGCTCAAAACAGAATGGTTAAGGGTGGTAGACGTATGGGTG
196 AGCCAAAAAACCTGCAAAGTGAATGGCTCAAAACAGAATGGTTAAGGGTGGTAGACGTATGGGTG
64945 ATTAGGTGGGCTGTTTAATTGAGAGATAGAAGAGAAAGATGGTTGATATGGCTATGGTTATGGTT
261 ATTAGGTGGGCTGTTTAATTGAGAGATAGAAGAGAAAGATGGTTGATATGGCTATGGTTATGGTT
*
65010 TATGAAACAAAGGGGATGGTTGTGAGGATAGTATCTTAAAG
326 TATAAAACAAAGGGGATGGTTGTGAGGATAGTATCTTAAAG
*
65051 AAGATATTGTAACTTATGATAGAGATCTCTGTGATAGTGAGTAGGCACGAACCTTTTCCTCATAA
1 AAGATATTGTAACTTATGATAGAGATCTCTATGATAGTGAGTAGGCACGAACCTTTTCCTCATAA
*
65116 TAGCCTTCATTTCTTCCCACGTAGTGATGGGACGTTCATCATTTCATCTTCTTGAACTCACCAAT
66 TAGCCTTCATTTCTTCCCACGTAGTGATGGGACGTTCACCATTTCATCTTCTTGAACTCACCAAT
* * * *
65181 TGATCCCACCAGTGATGTAAGGCTCTTTTGTTACCTTAACAAAATAATTGTGGATTTAGGAAGGA
131 TGATCCCACCAATGATGTAAGGCTCTTCTATTACCTTAACAAAATAATTGTGGATCTAGGAAGGA
*
65246 AG-CAAAACAACCTGCAAAGTGAATGGCTCAAAACAGAATGGTTAAGGGTGGTAGACGTGTGGGT
196 AGCCAAAA-AACCTGCAAAGTGAATGGCTCAAAACAGAATGGTTAAGGGTGGTAGACGTATGGGT
* * *
65310 GATTAGGTGGGCTGTTTAATTGAGAGATGGAAGTGGAAGATGGTTGATATGGCTATGGTTATGGT
260 GATTAGGTGGGCTGTTTAATTGAGAGATAGAAGAGAAAGATGGTTGATATGGCTATGGTTATGGT
65375 TTATAAAACAAAGGGGATGGTTGTGAGGATAGTATCTTAAAG
325 TTATAAAACAAAGGGGATGGTTGTGAGGATAGTATCTTAAAG
65417 AAGA
1 AAGA
65421 CTCAAAGAAG
Statistics
Matches: 353, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
365 5 0.01
366 348 0.99
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (366 bp):
AAGATATTGTAACTTATGATAGAGATCTCTATGATAGTGAGTAGGCACGAACCTTTTCCTCATAA
TAGCCTTCATTTCTTCCCACGTAGTGATGGGACGTTCACCATTTCATCTTCTTGAACTCACCAAT
TGATCCCACCAATGATGTAAGGCTCTTCTATTACCTTAACAAAATAATTGTGGATCTAGGAAGGA
AGCCAAAAAACCTGCAAAGTGAATGGCTCAAAACAGAATGGTTAAGGGTGGTAGACGTATGGGTG
ATTAGGTGGGCTGTTTAATTGAGAGATAGAAGAGAAAGATGGTTGATATGGCTATGGTTATGGTT
TATAAAACAAAGGGGATGGTTGTGAGGATAGTATCTTAAAG
Done.