Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006375.1 Hibiscus syriacus cultivar Beakdansim tig00015338_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: 45355
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:2144 original size:16 final size:15
Alignment explanation
Indices: 2123--2165 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2113 TTATTTTTTT
2123 ATTTAATTTTATGCAC
1 ATTTAATTTTATGC-C
*
2139 ATTTAAATTTATGCC
1 ATTTAATTTTATGCC
* *
2154 CTTTACTTTTAT
1 ATTTAATTTTAT
2166 TTATTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (15 bp):
ATTTAATTTTATGCC
Found at i:6635 original size:54 final size:54
Alignment explanation
Indices: 6549--6990 Score: 613
Period size: 54 Copynumber: 8.3 Consensus size: 54
6539 TTAGGTACTC
* * **
6549 TATGTGCAACCCACATAATTCATCATAAGTTGATAAACAACCATTTTGTAACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* * *
6603 TATCTGCAACCCACAGAATTAATCATAAGTTGATGAACAACCGTTTTGGCACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* *
6657 TAAGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* * *
6711 TATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTG
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* * *
6765 TTTGTGC--CCCACAGAATTCATCATAAGTTAATGAACAACCGTTTTGGCACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* *
6817 TA--TGAAACCCACAAAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
* * * *
6869 TATATGCAACCTAGAGAATTCATCATAAGTTGATGAACAACCATTTTGACACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
** * * *
6923 TATGTGCAACCCATGGAATTCATCATAATTTGATGAACAACCGTTTAGGCACTA
1 TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
*
6977 TGTGTGCAACCCAC
1 TATGTGCAACCCAC
6991 GTAATTCTTA
Statistics
Matches: 345, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
50 2 0.01
52 87 0.25
54 256 0.74
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (54 bp):
TATGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTA
Found at i:6934 original size:212 final size:213
Alignment explanation
Indices: 6558--6975 Score: 653
Period size: 212 Copynumber: 2.0 Consensus size: 213
6548 CTATGTGCAA
* * * * *
6558 CCCACATAATTCATCATAAGTTGATAAACAACCATTTTGTAACTATATCTGCAACCCACAGAATT
1 CCCACAGAATTCATCATAAGTTAATAAACAACCATTTTGGAACTATA-CTGAAACCCACAAAATT
*
6623 AATCATAAGTTGATGAACAACCGTTTTGGCACTATAAGTGCAACCCACGGAATTCATCATAAGTT
65 AATCATAAGTTGATGAACAACCATTTTGGCACTATAAGTGCAACCCACGGAATTCATCATAAGTT
*
6688 GATGAACAACCATTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACC
130 GATGAACAACCATTTTGACACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACC
*
6753 GTTTTGGCACTGTTTGTGC
195 GTTTAGGCACTGTTTGTGC
* * * *
6772 CCCACAGAATTCATCATAAGTTAATGAACAACCGTTTTGGCACTATA-TGAAACCCACAAAATTC
1 CCCACAGAATTCATCATAAGTTAATAAACAACCATTTTGGAACTATACTGAAACCCACAAAATTA
*
6836 ATCATAAGTTGATGAACAACCATTTTGGCACTATATA-TGCAACCTA-GAGAATTCATCATAAGT
66 ATCATAAGTTGATGAACAACCATTTTGGCACTATA-AGTGCAACCCACG-GAATTCATCATAAGT
* *
6899 TGATGAACAACCATTTTGACACTATATGTGCAACCCATGGAATTCATCATAATTTGATGAACAAC
129 TGATGAACAACCATTTTGACACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAAC
6964 CGTTTAGGCACT
194 CGTTTAGGCACT
6976 ATGTGTGCAA
Statistics
Matches: 187, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 1 0.01
212 144 0.77
213 1 0.01
214 41 0.22
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (213 bp):
CCCACAGAATTCATCATAAGTTAATAAACAACCATTTTGGAACTATACTGAAACCCACAAAATTA
ATCATAAGTTGATGAACAACCATTTTGGCACTATAAGTGCAACCCACGGAATTCATCATAAGTTG
ATGAACAACCATTTTGACACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCG
TTTAGGCACTGTTTGTGC
Found at i:12386 original size:54 final size:54
Alignment explanation
Indices: 12321--12940 Score: 936
Period size: 54 Copynumber: 11.5 Consensus size: 54
12311 TGTACTTTAC
12321 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* *
12375 GAACTATATGTGCAACCCACGAAATTCATCATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* ** * *
12429 GCACTATATGTTCAACCCACAAAATTCATTATATGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
*
12483 GCACTTTATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* *
12537 GCACTATATGTGCAACCCACGAAATTCATTATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* * * * *
12591 GCACTATATGTTCAACCTATGGAATTCACCATAAGTTGATGAACAACCATTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* * * *
12645 GCACTATATGTTCAACCCACAGAATTCATTATATGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
*
12699 GCACTTTATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* * *
12753 GCACTATATGTGCAACCCACGAAATTCATTATAAGTTG-TGAACAGCCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* * * *
12806 GCACTATATGTTCAACCTATGGAATTCACCATAAGTTGATGAACAACCGTTTTG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* * * *
12860 GCACTATATGTGCAATCCACTGAATTCATCATAAGTTAATGAACAACCGTTTAG
1 GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
* *
12914 GCACTATGTGTGCAACCCACGTAATTC
1 GCACTATATGTGCAACCCACGGAATTC
12941 TTAATGAGGT
Statistics
Matches: 507, Mismatches: 58, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
53 46 0.09
54 461 0.91
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
GCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTTTG
Found at i:20863 original size:11 final size:12
Alignment explanation
Indices: 20837--20867 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
20827 ACATCAATTT
20837 AGTTAGGTGAAG
1 AGTTAGGTGAAG
20849 AGTTAGGTG-AG
1 AGTTAGGTGAAG
20860 AGTTAGGT
1 AGTTAGGT
20868 ATTTGTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:29487 original size:21 final size:21
Alignment explanation
Indices: 29463--29552 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
29453 CGAAGTGCCT
*
29463 CATAATTATCCCGAAGGACCA
1 CATAATTGTCCCGAAGGACCA
* * **
29484 CATAGGTT-TGCACTGAAGTTCCA
1 CATA-ATTGT-C-CCGAAGGACCA
*
29507 CATAATTGTCCCAAAGGACCA
1 CATAATTGTCCCGAAGGACCA
* *
29528 CATAGTTGTCTCGAAGGACCA
1 CATAATTGTCCCGAAGGACCA
29549 CATA
1 CATA
29553 GAACCCTTGA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
21 34 0.64
22 6 0.11
23 13 0.25
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
CATAATTGTCCCGAAGGACCA
Found at i:29511 original size:44 final size:44
Alignment explanation
Indices: 29446--29532 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
29436 TAGCTCGTAA
* *
29446 TTTGCACCGAAGTGCCTCATAATTATCCCGAAGGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTATCCCAAAGGACCACATAGG
* * *
29490 TTTGCACTGAAGTTCCACATAATTGTCCCAAAGGACCACATAG
1 TTTGCACCGAAGTGCCACATAATTATCCCAAAGGACCACATAG
29533 TTGTCTCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTATCCCAAAGGACCACATAGG
Found at i:34542 original size:21 final size:21
Alignment explanation
Indices: 34518--34558 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34508 GAAGTGCCGC
34518 ATAATTATCCCGAAA-GACCAA
1 ATAATTATCCC-AAAGGACCAA
*
34539 ATAATTGTCCCAAAGGACCA
1 ATAATTATCCCAAAGGACCA
34559 CATAGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.20
Consensus pattern (21 bp):
ATAATTATCCCAAAGGACCAA
Found at i:35033 original size:2 final size:2
Alignment explanation
Indices: 35026--35060 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35016 TGTCATAAAT
35026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35061 TGTAGATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44180 original size:23 final size:22
Alignment explanation
Indices: 44112--44204 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 22
44102 CCACAGCTCG
*
44112 TAATTTGCACAGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
*
44134 TAATTAT-C-CCGAAG-ACCACA
1 TAATT-TGCACCGAAGTGCCACA
*
44154 TAGATTTGCACCGAAGTGCCACG
1 TA-ATTTGCACCGAAGTGCCACA
*
44177 TAGATTTGCACCGAAGTGCCTCA
1 TA-ATTTGCACCGAAGTGCCACA
44200 TAATT
1 TAATT
44205 GTCCCGAATG
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
20 8 0.13
21 9 0.15
22 15 0.25
23 28 0.47
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (22 bp):
TAATTTGCACCGAAGTGCCACA
Found at i:44223 original size:21 final size:21
Alignment explanation
Indices: 44199--44239 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44189 GAAGTGCCTC
* *
44199 ATAATTGTCCCGAATGACCAA
1 ATAATTGTCCCAAAGGACCAA
44220 ATAATTGTCCCAAAGGACCA
1 ATAATTGTCCCAAAGGACCA
44240 CATAGAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
ATAATTGTCCCAAAGGACCAA
Done.