Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002396.1 Hibiscus syriacus cultivar Beakdansim tig00004899_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: 91769
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:5015 original size:6 final size:6
Alignment explanation
Indices: 5004--5029 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4994 GTATTTAAAA
5004 CAGCTT CAGCTT CAGCTT CAGCTT CA
1 CAGCTT CAGCTT CAGCTT CAGCTT CA
5030 AGTACTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (6 bp):
CAGCTT
Found at i:13269 original size:20 final size:21
Alignment explanation
Indices: 13246--13327 Score: 87
Period size: 20 Copynumber: 4.0 Consensus size: 21
13236 CTTTTGCTAC
13246 ACAAATTCGCGTTGCG-ATTT
1 ACAAATTCGCGTTGCGAATTT
*
13266 ACAAATACGCGTTGCGAATTT
1 ACAAATTCGCGTTGCGAATTT
* *
13287 -CATATTCGCGTTGCGTATTT
1 ACAAATTCGCGTTGCGAATTT
** * *
13307 GGAAAATCGCATTGCGAATTT
1 ACAAATTCGCGTTGCGAATTT
13328 GGAAACTGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 32 0.63
21 19 0.37
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (21 bp):
ACAAATTCGCGTTGCGAATTT
Found at i:13321 original size:21 final size:21
Alignment explanation
Indices: 13292--13332 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13282 AATTTCATAT
* *
13292 TCGCGTTGCGTATTTGGAAAA
1 TCGCATTGCGAATTTGGAAAA
13313 TCGCATTGCGAATTTGGAAA
1 TCGCATTGCGAATTTGGAAA
13333 CTGTGTTGCG
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:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGAATTTGGAAAA
Found at i:13963 original size:111 final size:111
Alignment explanation
Indices: 13769--14101 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
13759 TGGAAATCAT
*
13769 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
13834 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * * *
13880 ATATCTCGAAACTTTGTTGATACAGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
13945 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
13991 ATATATTGGCACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
14056 TAATTATTTGATTTATTTAATGCATGATTATTAGAGTAATAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
14102 TTTTTGTAAT
Statistics
Matches: 206, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 206 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:15989 original size:24 final size:24
Alignment explanation
Indices: 15950--16019 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
15940 GCCTGCTCAG
*
15950 GACGACGACGATGATGGTGACAAC
1 GACGACGACGACGATGGTGACAAC
*
15974 GACGACGATGACGATGGTGACAAC
1 GACGACGACGACGATGGTGACAAC
*
15998 GACGACGACGACGATGATGACA
1 GACGACGACGACGATGGTGACA
16020 GCGAGGAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.11
Consensus pattern (24 bp):
GACGACGACGACGATGGTGACAAC
Found at i:33001 original size:22 final size:22
Alignment explanation
Indices: 32958--33002 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
32948 TAAATATTGT
* *
32958 ATTTTAATTAAATTACATTTAC
1 ATTTTAACTAAATTACAATTAC
* *
32980 ATTTTAACTAATTTATAATTAC
1 ATTTTAACTAAATTACAATTAC
33002 A
1 A
33003 CGTTTATTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTAACTAAATTACAATTAC
Found at i:44086 original size:2 final size:2
Alignment explanation
Indices: 44079--44110 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44069 AAACCTGCTG
44079 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44111 TATTGCAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:45218 original size:15 final size:14
Alignment explanation
Indices: 45194--45223 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
45184 AATCATTTAA
45194 TTATTTAATTATTC
1 TTATTTAATTATTC
45208 TTATCTTAATTATTC
1 TTAT-TTAATTATTC
45223 T
1 T
45224 ACCGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTTAATTATTC
Found at i:45231 original size:15 final size:15
Alignment explanation
Indices: 45198--45235 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
45188 ATTTAATTAT
*
45198 TTAATTATTCTTATC
1 TTAATTATTCTTACC
45213 TTAATTATTC-TACC
1 TTAATTATTCTTACC
45227 GTTAATTAT
1 -TTAATTAT
45236 GAAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAATTATTCTTACC
Found at i:55389 original size:29 final size:29
Alignment explanation
Indices: 55354--55435 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
55344 AAACTAAATT
*
55354 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
55383 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
55412 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
55436 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:60147 original size:29 final size:29
Alignment explanation
Indices: 60112--60193 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
60102 AAACTAAATT
*
60112 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
60141 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
60170 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
60194 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:67470 original size:20 final size:19
Alignment explanation
Indices: 67432--67470 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
67422 TTTTATTACG
*
67432 AAAATTTAAATTTTAAATT
1 AAAATTTAAATATTAAATT
*
67451 AAAATTTAAAATATTCAATT
1 AAAATTT-AAATATTAAATT
67471 TGTGTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTTAAATATTAAATT
Found at i:69096 original size:31 final size:30
Alignment explanation
Indices: 69041--69129 Score: 133
Period size: 30 Copynumber: 2.9 Consensus size: 30
69031 CTATATACTA
**
69041 TATATAAATTTTCAAATTTATTTTAAAAAAC
1 TATAT-AATTTTCAAAAATATTTTAAAAAAC
*
69072 TATATAATTTTCAAAAATATTTTTAAAAAC
1 TATATAATTTTCAAAAATATTTTAAAAAAC
*
69102 TATATAATTTTCAAAAATGTTTTAAAAA
1 TATATAATTTTCAAAAATATTTTAAAAA
69130 TTATATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 48 0.91
31 5 0.09
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTAAAAAAC
Found at i:69145 original size:38 final size:38
Alignment explanation
Indices: 69102--69321 Score: 144
Period size: 37 Copynumber: 5.9 Consensus size: 38
69092 TTTTAAAAAC
69102 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
*
69140 TATATAAGTTTTCAAAAATGTTTTTTTATAAAAAAAACTATATATTA
1 TATATAA-TTTTCAAAAATG----TTT-T---AAAAATTATATATTA
* * **
69187 TATA-AATTTTTTAAAAATGATTTAAAAA--CCATA-TA
1 TATATAA-TTTTCAAAAATGTTTTAAAAATTATATATTA
* *
69222 T-TAT-A---T-AAAAATGATTTAAAAATCATATATTA
1 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
69254 TATAT--TTTTCTAAAAATGTTTTAAAAATTATATA-T-
1 TATATAATTTTC-AAAAATGTTTTAAAAATTATATATTA
* * * *
69289 TATATAGTTTTCGAAAGTGTTTTAAAAACTATA
1 TATATAATTTTCAAAAATGTTTTAAAAATTATA
69322 CACTATATTC
Statistics
Matches: 148, Mismatches: 13, Indels: 44
0.72 0.06 0.21
Matches are distributed among these distances:
29 16 0.11
30 1 0.01
31 3 0.02
32 3 0.02
33 3 0.02
34 3 0.02
35 9 0.06
36 22 0.15
37 26 0.18
38 12 0.08
39 12 0.08
41 1 0.01
42 2 0.01
43 3 0.02
44 1 0.01
46 13 0.09
47 18 0.12
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
Found at i:69230 original size:29 final size:29
Alignment explanation
Indices: 69198--69257 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
69188 ATAAATTTTT
69198 TAAAAATGATTTAAAAACCATATATTATA
1 TAAAAATGATTTAAAAACCATATATTATA
*
69227 TAAAAATGATTTAAAAATCATATATTATA
1 TAAAAATGATTTAAAAACCATATATTATA
69256 TA
1 TA
69258 TTTTTCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAAAATGATTTAAAAACCATATATTATA
Found at i:69899 original size:20 final size:19
Alignment explanation
Indices: 69855--69901 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
69845 CTAGATTTTC
*
69855 TCCAT-TTTTCTCATCAAT
1 TCCATATTTGCTCATCAAT
**
69873 TTTATATTTGCTCACTCAAT
1 TCCATATTTGCTCA-TCAAT
69893 TCCATATTT
1 TCCATATTT
69902 TCTTATCAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 3 0.14
19 7 0.32
20 12 0.55
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (19 bp):
TCCATATTTGCTCATCAAT
Found at i:82941 original size:41 final size:42
Alignment explanation
Indices: 82890--82974 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
82880 TGGAAAGATG
**
82890 AATATAAAGTACGTGGCCATAG-TCAATACCATGATGATGAC
1 AATATAAAGTAAATGGCCATAGTTCAATACCATGATGATGAC
*
82931 AATATAAAGTAAATGGTCATAGTTCAATACCATGATGATGAC
1 AATATAAAGTAAATGGCCATAGTTCAATACCATGATGATGAC
82973 AA
1 AA
82975 CCTATCTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 19 0.47
42 21 0.52
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (42 bp):
AATATAAAGTAAATGGCCATAGTTCAATACCATGATGATGAC
Found at i:86015 original size:23 final size:23
Alignment explanation
Indices: 85964--86016 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
85954 ACCGAAGACT
*
85964 GAGAATGTTGGTCAACCAAATAA
1 GAGAATGTTGGTCAACCAAACAA
*
85987 GAGAATGTTGGTCAACCAAACGA
1 GAGAATGTTGGTCAACCAAACAA
*
86010 GGGAATG
1 GAGAATG
86017 ATGATTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (23 bp):
GAGAATGTTGGTCAACCAAACAA
Done.