Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002154.1 Hibiscus syriacus cultivar Beakdansim tig00004401_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: 73334
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:13748 original size:29 final size:29
Alignment explanation
Indices: 13716--13787 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
13706 GTCACTTGTC
* *
13716 AACTTGAATTCTTGGTGGTAGCAAAATCA
1 AACTTGAATTCTTAGTGGTAACAAAATCA
* * **
13745 AACTTGAATTTTTTAGTGGTAACAAATTTG
1 AACTTGAA-TTCTTAGTGGTAACAAAATCA
13775 AACTTGAATTCTT
1 AACTTGAATTCTT
13788 TGATGACTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (29 bp):
AACTTGAATTCTTAGTGGTAACAAAATCA
Found at i:24194 original size:7 final size:7
Alignment explanation
Indices: 24182--24216 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
24172 CGTTTAACCA
24182 GAAAAAG
1 GAAAAAG
24189 GAAAAAG
1 GAAAAAG
24196 GAAAAAAG
1 G-AAAAAG
24204 GAAAAA-
1 GAAAAAG
24210 GAAAAAG
1 GAAAAAG
24217 AAACATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:24203 original size:15 final size:14
Alignment explanation
Indices: 24183--24215 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
24173 GTTTAACCAG
24183 AAAAAGGAAAAAGGA
1 AAAAAGGAAAAA-GA
24198 AAAAAGGAAAAAGA
1 AAAAAGGAAAAAGA
24212 AAAA
1 AAAA
24216 GAAACATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAGA
Found at i:29929 original size:9 final size:10
Alignment explanation
Indices: 29916--29942 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29906 AAAAAACAAA
29916 AAAAAAAGGC
1 AAAAAAAGGC
29926 AAAAAAAGGC
1 AAAAAAAGGC
29936 AAAAAAA
1 AAAAAAA
29943 AAAACAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:29942 original size:13 final size:13
Alignment explanation
Indices: 29899--29945 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
29889 CTATTTTTTT
**
29899 CAAAAAAAAAAAA
1 CAAAAAAAAAAGG
29912 CAAAAAAAAAAGG
1 CAAAAAAAAAAGG
29925 C---AAAAAAAGG
1 CAAAAAAAAAAGG
29935 CAAAAAAAAAA
1 CAAAAAAAAAA
29946 ACAAAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 10 0.34
13 19 0.66
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGG
Found at i:33123 original size:21 final size:21
Alignment explanation
Indices: 33097--33141 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33087 GATTTCTGGG
* *
33097 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33118 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33139 CAA
1 CAA
33142 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34708 original size:149 final size:150
Alignment explanation
Indices: 34530--34846 Score: 575
Period size: 151 Copynumber: 2.1 Consensus size: 150
34520 GAATCGAGGG
* *
34530 TCTACGCGGTCCTTCGGG-ATATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACA
1 TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA
34594 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
*
34659 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACAGTGCAAT
34679 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAC
1 TCTACGCGGTCCTTCGGGA-ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAC
34744 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
65 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
34809 TATATGGCACTACAGTGCAAT
130 TATATGGCACTACAGTGCAAT
34830 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
34847 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
149 18 0.11
150 1 0.01
151 143 0.88
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACAGTGCAAT
Found at i:34849 original size:23 final size:23
Alignment explanation
Indices: 34814--34858 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34804 ATTATTATAT
*
34814 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTATACGC
* *
34837 GGCACTTCGGTGCAATTATACG
1 GGCACTACAGTGCAATTATACG
34859 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGC
Found at i:38167 original size:21 final size:21
Alignment explanation
Indices: 38141--38185 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38131 GATTTCTGGG
* *
38141 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
38162 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
38183 CAA
1 CAA
38186 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:39974 original size:149 final size:149
Alignment explanation
Indices: 39649--39963 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
39639 GAGTCGAGGG
* * * *
39649 TCTACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
*
39714 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCACTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
39779 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
39798 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
39863 ACTTGATCACTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCACTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
39928 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
39947 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
39964 TGTAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCACTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:43686 original size:15 final size:16
Alignment explanation
Indices: 43666--43699 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43656 CAAAATACAA
43666 TATTCTC-AGTAATCT
1 TATTCTCTAGTAATCT
*
43681 TATTCTCTGGTAATCT
1 TATTCTCTAGTAATCT
43697 TAT
1 TAT
43700 ATTCCCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (16 bp):
TATTCTCTAGTAATCT
Found at i:54889 original size:31 final size:31
Alignment explanation
Indices: 54867--55068 Score: 377
Period size: 31 Copynumber: 6.5 Consensus size: 31
54857 ATAGATTCCA
* *
54867 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
54898 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
54929 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
54960 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
54991 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
55022 AAGAACATAGGTAAACAATCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
55053 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
55069 CCTCGACCCT
Statistics
Matches: 168, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 168 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:55982 original size:21 final size:21
Alignment explanation
Indices: 55958--56002 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55948 TTTTGTTCGT
* *
55958 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
55979 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
56000 TTG
1 TTG
56003 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:59812 original size:31 final size:31
Alignment explanation
Indices: 59774--59991 Score: 366
Period size: 31 Copynumber: 7.0 Consensus size: 31
59764 CCCGAAGGAC
* * *
59774 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
59805 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59836 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
59867 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
59898 CAGTCCGTATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59929 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59960 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59991 C
1 C
59992 CCTCGACCCT
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 176 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:60904 original size:21 final size:21
Alignment explanation
Indices: 60880--60924 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60870 TTTTGTTCGT
* *
60880 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
60901 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
60922 TTG
1 TTG
60925 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:60955 original size:20 final size:22
Alignment explanation
Indices: 60930--60970 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
60920 CCTTGCCCAG
60930 AAATCA-T-ATTTTTAGCTCGA
1 AAATCACTCATTTTTAGCTCGA
60950 AAATCACTTCATTTTTAGCTC
1 AAATCAC-TCATTTTTAGCTC
60971 AACACTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATCACTCATTTTTAGCTCGA
Found at i:62871 original size:25 final size:25
Alignment explanation
Indices: 62800--62876 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
62790 CAACTCATAT
*
62800 AAATTTGCACCGAAGTGCCACGTAG
1 AAATTTGCACCGAAGTGCCGCGTAG
* * *
62825 AATTTTGTC-TCGAA-TGATCGCGTAG
1 AAATTTG-CACCGAAGTG-CCGCGTAG
*
62850 AAATTTGCACCAAAGTGCCGCGTAG
1 AAATTTGCACCGAAGTGCCGCGTAG
62875 AA
1 AA
62877 TTGTACATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
24 3 0.08
25 34 0.85
26 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (25 bp):
AAATTTGCACCGAAGTGCCGCGTAG
Found at i:63252 original size:25 final size:25
Alignment explanation
Indices: 63207--63256 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
63197 ACATAATGCA
* *
63207 TATAATATGAATTTATGTCATGTAT
1 TATAATATGAATATATATCATGTAT
63232 TATAATATGGAATATA-ATCATGTAT
1 TATAATAT-GAATATATATCATGTAT
63257 CAAGATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
TATAATATGAATATATATCATGTAT
Found at i:67734 original size:15 final size:14
Alignment explanation
Indices: 67714--67743 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
67704 ACGTTGGGGA
67714 ATATATATTATTTGC
1 ATATATATT-TTTGC
67729 ATATATATTTTTGC
1 ATATATATTTTTGC
67743 A
1 A
67744 CTTAATCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (14 bp):
ATATATATTTTTGC
Done.