Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003167.1 Hibiscus syriacus cultivar Beakdansim tig00006662_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: 57600
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1997 original size:16 final size:16
Alignment explanation
Indices: 1973--2007 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1963 CATGCATTCC
* *
1973 TTTATTTCTTTTTTGT
1 TTTAATTCTTTTCTGT
1989 TTTAATTCTTTTCTGT
1 TTTAATTCTTTTCTGT
2005 TTT
1 TTT
2008 CACAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTAATTCTTTTCTGT
Found at i:4045 original size:4 final size:4
Alignment explanation
Indices: 4026--4063 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
4016 TAATATTTTA
4026 TAAT T-AT TAA- TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
4064 ATGACCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:7203 original size:7 final size:7
Alignment explanation
Indices: 7191--7215 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7181 ATACATACAC
7191 GATTCAT
1 GATTCAT
7198 GATTCAT
1 GATTCAT
7205 GATTCAT
1 GATTCAT
7212 GATT
1 GATT
7216 TCAAGCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (7 bp):
GATTCAT
Found at i:7415 original size:32 final size:33
Alignment explanation
Indices: 7373--7440 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
7363 CGAGTCTCAC
7373 GAAAGGCATTTCATAATTTGGAAATTTCCCACG
1 GAAAGGCATTTCATAATTTGGAAATTTCCCACG
7406 GAAA-GCATTTCATAATTTGGAAATTTCCCACG
1 GAAAGGCATTTCATAATTTGGAAATTTCCCACG
7438 GAA
1 GAA
7441 GTTGTTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (33 bp):
GAAAGGCATTTCATAATTTGGAAATTTCCCACG
Found at i:12686 original size:26 final size:27
Alignment explanation
Indices: 12650--12703 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
12640 TTGTTTGAGC
*
12650 TTCATGTTGATTTTTCTGCA-ATATTT
1 TTCATGTTGATTTTGCTGCATATATTT
*
12676 TTCATGTTGATTTTGCTTCATATATTT
1 TTCATGTTGATTTTGCTGCATATATTT
12703 T
1 T
12704 AGATATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (27 bp):
TTCATGTTGATTTTGCTGCATATATTT
Found at i:21766 original size:13 final size:13
Alignment explanation
Indices: 21725--21773 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
21715 ATGTTGTTAT
21725 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
* *
21739 AATTGTAACGTTTG
1 TATT-TAATGTTTG
21753 TATTTAATGTTTG
1 TATTTAATGTTTG
21766 TATTTAAT
1 TATTTAAT
21774 TATTTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 11 0.37
15 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:21780 original size:22 final size:22
Alignment explanation
Indices: 21755--21819 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
21745 AACGTTTGTA
21755 TTTAATGTTTGTATTTAATTA-T
1 TTTAATGTTT-TATTTAATTAGT
* *
21777 TTTAATTGTTTT-TACTATTTAGT
1 TTTAA-TGTTTTAT-TTAATTAGT
21800 TTGTAATGTTTTATTTAATT
1 TT-TAATGTTTTATTTAATT
21820 TTCACTTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.32
23 18 0.53
24 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.65
Consensus pattern (22 bp):
TTTAATGTTTTATTTAATTAGT
Found at i:23753 original size:20 final size:20
Alignment explanation
Indices: 23724--23762 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23714 ATAGCCTATA
*
23724 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
23744 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
23763 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:28674 original size:21 final size:21
Alignment explanation
Indices: 28648--28689 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28638 CCAGAATGGG
*
28648 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
28669 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
28690 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:28895 original size:29 final size:31
Alignment explanation
Indices: 28863--28922 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
28853 AAATTTTGAA
*
28863 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
28892 TAAATTTAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
28923 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:33422 original size:22 final size:21
Alignment explanation
Indices: 33382--33458 Score: 127
Period size: 21 Copynumber: 3.6 Consensus size: 21
33372 TCCAGAGGGA
33382 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAAGGGGGT
*
33403 ACCGATTCCCCCCTAGGGGGT
1 ACCGATTCCCCCCAAGGGGGT
33424 ACCGATTACCCCCCAAGGGGGT
1 ACCGATT-CCCCCCAAGGGGGT
*
33446 ACCAATTCCCCCC
1 ACCGATTCCCCCC
33459 TGAATGGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 33 0.63
22 19 0.37
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (21 bp):
ACCGATTCCCCCCAAGGGGGT
Found at i:39222 original size:23 final size:23
Alignment explanation
Indices: 39179--39267 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
39169 TCAGTTTTGG
* *
39179 TGAAGAGGGAATCGA-TGCCCCTT
1 TGAAG-GGGAACCGATTCCCCCTT
39202 TGAAGGGGAACCGATTCCCCCTT
1 TGAAGGGGAACCGATTCCCCCTT
39225 TGAAGGGGAACCGATTCCCCC--
1 TGAAGGGGAACCGATTCCCCCTT
* * *
39246 TGTAGGGGAATCGATACCCCCT
1 TGAAGGGGAACCGATTCCCCCT
39268 GGATGTTCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.31
22 8 0.14
23 33 0.56
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGAAGGGGAACCGATTCCCCCTT
Found at i:40877 original size:18 final size:18
Alignment explanation
Indices: 40842--40880 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40832 GGAGCAGCAC
*
40842 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
40860 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
40878 GAG
1 GAG
40881 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:42101 original size:10 final size:10
Alignment explanation
Indices: 42088--42151 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
42078 AACAACAAGA
*
42088 AACAAGTATC
1 AACAAGAATC
42098 AACAAGAATC
1 AACAAGAATC
* **
42108 AAACAACAAGA
1 -AACAAGAATC
*
42119 AACAAGTATC
1 AACAAGAATC
42129 AACAAGAATC
1 AACAAGAATC
*
42139 AAGAGAGAATC
1 AACA-AGAATC
42150 AA
1 AA
42152 AGAGAAAGCA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
10 27 0.64
11 15 0.36
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.11
Consensus pattern (10 bp):
AACAAGAATC
Found at i:42102 original size:17 final size:17
Alignment explanation
Indices: 42080--42141 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
42070 CATTGATCAA
42080 CAACAAGAAACAAGTAT
1 CAACAAGAAACAAGTAT
*
42097 CAACAAGAATCAA--A-
1 CAACAAGAAACAAGTAT
42111 CAACAAGAAACAAGTAT
1 CAACAAGAAACAAGTAT
*
42128 CAACAAGAATCAAG
1 CAACAAGAAACAAG
42142 AGAGAATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.31
15 1 0.03
16 1 0.03
17 25 0.64
ACGTcount: A:0.60, C:0.19, G:0.11, T:0.10
Consensus pattern (17 bp):
CAACAAGAAACAAGTAT
Found at i:42115 original size:31 final size:31
Alignment explanation
Indices: 42078--42140 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42068 GCCATTGATC
42078 AACAACAAGAAACAAGTATCAACAAGAATCA
1 AACAACAAGAAACAAGTATCAACAAGAATCA
42109 AACAACAAGAAACAAGTATCAACAAGAATCA
1 AACAACAAGAAACAAGTATCAACAAGAATCA
42140 A
1 A
42141 GAGAGAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.62, C:0.19, G:0.10, T:0.10
Consensus pattern (31 bp):
AACAACAAGAAACAAGTATCAACAAGAATCA
Found at i:52499 original size:15 final size:15
Alignment explanation
Indices: 52479--52508 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52469 TAAATTTATC
52479 ATTATATCAATTTAA
1 ATTATATCAATTTAA
*
52494 ATTATATTAATTTAA
1 ATTATATCAATTTAA
52509 TAAAATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATATCAATTTAA
Done.