Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006788.1 Hibiscus syriacus cultivar Beakdansim tig00017204_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: 80974
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2242 original size:13 final size:12
Alignment explanation
Indices: 2213--2257 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
2203 TTTGAAATCT
2213 TTTTC-TTTTTC
1 TTTTCTTTTTTC
*
2224 TCTTCTTTTCTTC
1 TTTTCTTTT-TTC
2237 TTTTCTTTTTGTC
1 TTTTCTTTTT-TC
2250 TTTTCTTT
1 TTTTCTTT
2258 CTTTTTGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 4 0.14
12 4 0.14
13 21 0.72
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:2251 original size:8 final size:7
Alignment explanation
Indices: 2212--2263 Score: 50
Period size: 8 Copynumber: 6.6 Consensus size: 7
2202 TTTTGAAATC
2212 TTTTTCT
1 TTTTTCT
2219 TTTTCTCT
1 TTTT-TCT
2227 TCTTTTCT
1 T-TTTTCT
2235 TCTTTTCT
1 T-TTTTCT
2243 TTTTGTCTT
1 TTTT-TC-T
2252 TTCTTTCT
1 TT-TTTCT
2260 TTTT
1 TTTT
2264 GTACTCCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 9 0.22
8 21 0.52
9 8 0.20
10 2 0.05
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:21694 original size:18 final size:18
Alignment explanation
Indices: 21673--21714 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21663 CCTTTCTGAA
*
21673 TTTTTTTCTTCTTT-TTTC
1 TTTTTGTCTT-TTTCTTTC
21691 TTTTTGTCTTTTTCTTTC
1 TTTTTGTCTTTTTCTTTC
21709 TTTTTG
1 TTTTTG
21715 CACTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTGTCTTTTTCTTTC
Found at i:21998 original size:20 final size:20
Alignment explanation
Indices: 21968--22025 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
21958 AAGATTAATG
21968 AAATG-AAAAAAAAGGAATC
1 AAATGAAAAAAAAAGGAATC
*
21987 AAATGAAAAAAAAAGGAATG
1 AAATGAAAAAAAAAGGAATC
22007 AAATGAAATAAATAAAGGA
1 AAATGAAA-AAA-AAAGGA
22026 TATAGATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 5 0.14
20 21 0.60
21 3 0.09
22 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATGAAAAAAAAAGGAATC
Found at i:22078 original size:22 final size:21
Alignment explanation
Indices: 22044--22084 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22034 GTTGCAGAAT
22044 TGATGGTCCTGATGGATGAAGA
1 TGATGGTCCTGAT-GATGAAGA
**
22066 TGATGGTGTTGATGATGAA
1 TGATGGTCCTGATGATGAA
22085 ATGGAGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.32
Consensus pattern (21 bp):
TGATGGTCCTGATGATGAAGA
Found at i:23972 original size:35 final size:37
Alignment explanation
Indices: 23904--23983 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
23894 ATACTATTTC
* *
23904 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
23941 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
23976 CATCACCA
1 CATCACCA
23984 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:29218 original size:35 final size:37
Alignment explanation
Indices: 29147--29226 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
29137 ATACTATTAC
* *
29147 CATCCCCATAATCCATCTTCCATTATCACGCATATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
* *
29184 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
29219 CATCACCA
1 CATCACCA
29227 AATTCACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCATATAT
Found at i:34842 original size:19 final size:20
Alignment explanation
Indices: 34795--34845 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
34785 GAAACCCTTT
**
34795 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
34815 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
34834 TGAAGATACATG
1 TGAAAATACATG
34846 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:36776 original size:35 final size:35
Alignment explanation
Indices: 36665--36776 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 35
36655 ATACAATCTG
*
36665 TCCATCACCATCATCACGCCTATATCATCACCATCT
1 TCCATCACCAT-ATCACGCCTATATCATCACCATAT
*
36701 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
*
36737 TCCATCACCATATCACGCCTATATCATCACCAAAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
36772 TCCAT
1 TCCAT
36777 TTTTCATTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 28 0.39
36 42 0.59
37 1 0.01
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.28
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:36935 original size:15 final size:16
Alignment explanation
Indices: 36910--36939 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36900 CTTTGATAAC
36910 ATTCTTTTCCATTTCA
1 ATTCTTTTCCATTTCA
36926 ATTC-TTTCCATTTC
1 ATTCTTTTCCATTTC
36940 CATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTCTTTTCCATTTCA
Found at i:37188 original size:24 final size:24
Alignment explanation
Indices: 37148--37194 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
37138 AAAGTGCTAC
37148 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
37173 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
37195 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:40817 original size:35 final size:35
Alignment explanation
Indices: 40706--40817 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 35
40696 ATACAATCTG
*
40706 TCCATCACCATCATCACGCCTATATCATCACCATCT
1 TCCATCACCAT-ATCACGCCTATATCATCACCATAT
*
40742 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
*
40778 TCCATCACCATATCACGCCTATATCATCACCAAAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
40813 TCCAT
1 TCCAT
40818 TTTTCATTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 28 0.39
36 42 0.59
37 1 0.01
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.28
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:40976 original size:15 final size:16
Alignment explanation
Indices: 40951--40980 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40941 CTTTGATAAC
40951 ATTCTTTTCCATTTCA
1 ATTCTTTTCCATTTCA
40967 ATTC-TTTCCATTTC
1 ATTCTTTTCCATTTC
40981 CATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTCTTTTCCATTTCA
Found at i:41229 original size:24 final size:24
Alignment explanation
Indices: 41189--41235 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
41179 AAAGTGCTAC
41189 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
41214 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
41236 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:41885 original size:19 final size:20
Alignment explanation
Indices: 41847--41887 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41837 GAAACCCCTT
*
41847 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
41867 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
41886 TG
1 TG
41888 GAGATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:42822 original size:30 final size:31
Alignment explanation
Indices: 42783--42842 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
42773 ACATGCTGCC
**
42783 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
42814 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
42843 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:45600 original size:19 final size:20
Alignment explanation
Indices: 45572--45611 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
45562 GGATAATAAT
45572 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
45592 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
45611 A
1 A
45612 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:46062 original size:19 final size:20
Alignment explanation
Indices: 46024--46066 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
46014 GAAACCCCTT
*
46024 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
46044 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
46063 TGAA
1 TGAA
46067 GATAAATGCT
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:58385 original size:23 final size:24
Alignment explanation
Indices: 58357--58409 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
58347 AAAATCAGCA
58357 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
* *
58380 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
58404 AAGAAA
1 AAGAAA
58410 GGAAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.64, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCAAAAAG
Found at i:58414 original size:23 final size:23
Alignment explanation
Indices: 58366--58414 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
58356 AAAGAAAATA
*
58366 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAATGG
58389 AAAGCACTCAAAAAGAAGAAA-GG
1 AAAGCACTC-AAAAGAAGAAATGG
58412 AAA
1 AAA
58415 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAATGG
Found at i:64642 original size:24 final size:22
Alignment explanation
Indices: 64582--64644 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 22
64572 AAATCCAGCA
* *
64582 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAA-AAAAGAACTCAAAAG
64605 AAGAAATTAAAAAGAACTCGAAAAG
1 AAGAAA--AAAAAGAACTC-AAAAG
64630 AAGAAAAAGAAAGAA
1 AAGAAAAA-AAAGAA
64645 AGAAAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 8 0.24
24 14 0.41
25 12 0.35
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.08
Consensus pattern (22 bp):
AAGAAAAAAAAGAACTCAAAAG
Done.