Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006271.1 Hibiscus syriacus cultivar Beakdansim tig00014951_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: 62946
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:7387 original size:13 final size:13
Alignment explanation
Indices: 7369--7393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7359 ATAGTTGAAC
7369 AGTCTTCATATGT
1 AGTCTTCATATGT
7382 AGTCTTCATATG
1 AGTCTTCATATG
7394 GGCGTCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:7926 original size:25 final size:26
Alignment explanation
Indices: 7870--7927 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
7860 ACATGTAACT
7870 TATAAAATAATTTATCAGTATGCAGA
1 TATAAAATAATTTATCAGTATGCAGA
*
7896 AATAAAATAGATTT-TCAG-ACT-CAGA
1 TATAAAATA-ATTTATCAGTA-TGCAGA
7921 TATAAAA
1 TATAAAA
7928 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 11 0.39
26 13 0.46
27 4 0.14
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (26 bp):
TATAAAATAATTTATCAGTATGCAGA
Found at i:20721 original size:19 final size:20
Alignment explanation
Indices: 20683--20723 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
20673 AAATAATTTT
*
20683 AAAATTATAAATAGATGTAA
1 AAAATTATAAATAGAAGTAA
20703 AAAATTATAAATA-AAGTAA
1 AAAATTATAAATAGAAGTAA
20722 AA
1 AA
20724 TATCATGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAATTATAAATAGAAGTAA
Found at i:24088 original size:5 final size:5
Alignment explanation
Indices: 24078--24111 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
24068 ACTTTATTTT
24078 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
24112 TCGGGTGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.59, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:24495 original size:16 final size:18
Alignment explanation
Indices: 24470--24514 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
24460 TCAGATTCAT
24470 ATTCCAATTCC-T-ACAG
1 ATTCCAATTCCTTCACAG
*
24486 ATTTCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAG
24504 ATTCCAATTCC
1 ATTCCAATTCC
24515 CTCATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 1 0.04
18 14 0.56
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAG
Found at i:25513 original size:27 final size:28
Alignment explanation
Indices: 25464--25519 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
25454 AAAAATCCAG
25464 CCACCTCTTATTTTTTCCTCTACTCTTA
1 CCACCTCTTATTTTTTCCTCTACTCTTA
25492 CCACCTCTTA-TTTTTCCTCTACTCTTA
1 CCACCTCTTATTTTTTCCTCTACTCTTA
25519 C
1 C
25520 TTCTCCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.48
Consensus pattern (28 bp):
CCACCTCTTATTTTTTCCTCTACTCTTA
Found at i:25518 original size:17 final size:17
Alignment explanation
Indices: 25496--25529 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25486 CTCTTACCAC
* *
25496 CTCTTATTTTTCCTCTA
1 CTCTTACTTCTCCTCTA
25513 CTCTTACTTCTCCTCTA
1 CTCTTACTTCTCCTCTA
25530 TCCATTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (17 bp):
CTCTTACTTCTCCTCTA
Found at i:31124 original size:29 final size:29
Alignment explanation
Indices: 31092--31181 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
31082 AGTCAATTAT
*
31092 TCTTTTACTCAACAGTGTTTAACCATTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
*
31121 TCTTTTACTCAACAGTGTTTAATCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
31150 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
31179 TCT
1 TCT
31182 AACTTGCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.43
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCGTTCA
Found at i:31293 original size:81 final size:80
Alignment explanation
Indices: 31150--31386 Score: 314
Period size: 81 Copynumber: 2.9 Consensus size: 80
31140 TAATCGTTCA
* * *
31150 TCTTTTACTCAACAGTGTTTAACCGTTCATCTAACTTGCA-AAGTTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAACGGTATTTAACC-TTCATCTAACTAGCATAA-TTGACACCTTTCTGTCAAATG
*
31214 CACATTTAGGCCATTAT
64 CACAATTAGGCCATTAT
* * * * *
31231 TCTTGTACTCAACGGTATTTAACACATCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAAC-CTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGC
* *
31296 ATAGTTAGGCCATTAT
65 ACAATTAGGCCATTAT
* *
31312 TCTTTTACTCAACGGTATTTAACTGTTCATTTAACTAGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAAC-CTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGC
31377 ACAATTAGGC
65 ACAATTAGGC
31387 ATCAAAGGCA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 132 0.98
82 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (80 bp):
TCTTTTACTCAACGGTATTTAACCTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCA
CAATTAGGCCATTAT
Found at i:31451 original size:68 final size:68
Alignment explanation
Indices: 31337--31846 Score: 779
Period size: 68 Copynumber: 7.5 Consensus size: 68
31327 TATTTAACTG
* * * * * *
31337 TTCATTTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAATTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31402 CCT
66 CCT
* * * * *
31405 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCAAAATTAGGCCTCCAATGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31470 CCT
66 CCT
*
31473 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGTCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31538 CCT
66 CCT
* * *
31541 TTCATCTAACTGGCATAAATGACAACTTTCTGTCAAATGCACAGTTAGGCCGCAAAGGCATTTAT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31606 CCT
66 CCT
* *
31609 TTCATCTAACTGGCATAAATGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGACATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31674 CCT
66 CCT
* * * *
31677 TTCATCTAACTAGCATAAATGACACATTTCTCTCAAATGCACAGTTAGGCCTCAAAGGCGTTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31742 CCT
66 CCT
* * *
31745 TTTATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGTCGCAAAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
31810 CCT
66 CCT
* *
31813 TTCATCTAAC-GGCATAAATGAAACTTTTCTGTCA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCA
31847 TAAATGAAAC
Statistics
Matches: 402, Mismatches: 40, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
67 22 0.05
68 380 0.95
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
CCT
Found at i:31850 original size:20 final size:20
Alignment explanation
Indices: 31825--31866 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31815 CATCTAACGG
31825 CATAAATGAAACTTTTCTGT
1 CATAAATGAAACTTTTCTGT
31845 CATAAATGAAACTTTTCTGT
1 CATAAATGAAACTTTTCTGT
31865 CA
1 CA
31867 AATGTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
CATAAATGAAACTTTTCTGT
Found at i:35250 original size:19 final size:19
Alignment explanation
Indices: 35207--35254 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
35197 TGCTCTAAAA
* *
35207 TTTGATATATGTTTTGATC
1 TTTGATATCTGTTATGATC
* *
35226 TCTGATATCTGTTATGATT
1 TTTGATATCTGTTATGATC
35245 TTTGATATCT
1 TTTGATATCT
35255 CTATTTACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (19 bp):
TTTGATATCTGTTATGATC
Found at i:52818 original size:21 final size:21
Alignment explanation
Indices: 52792--52833 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52782 ACGTAGAATT
*
52792 TGTCCCGAAGGACCACGTATA
1 TGTCCCGAAGGACCACATATA
*
52813 TGTCCCGAATGACCACATATA
1 TGTCCCGAAGGACCACATATA
52834 ACATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:52891 original size:18 final size:18
Alignment explanation
Indices: 52843--52892 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
52833 AACATATATA
*
52843 TCCCGAAGGACCACTATG
1 TCCCGAAGAACCACTATG
*
52861 TCCTGAA-AGACCACTATG
1 TCCCGAAGA-ACCACTATG
52879 TCCCGAAGAACCAC
1 TCCCGAAGAACCAC
52893 GTAAACCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (18 bp):
TCCCGAAGAACCACTATG
Done.