Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002233.1 Hibiscus syriacus cultivar Beakdansim tig00004543_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: 69052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:282 original size:19 final size:19
Alignment explanation
Indices: 251--287 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
241 GCATGATAGA
251 ATTTTATTTTTTATTTTTC
1 ATTTTATTTTTTATTTTTC
270 ATTTT-TTTATTTATTTTT
1 ATTTTATTT-TTTATTTTT
288 TTGTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTATTTTTTATTTTTC
Found at i:6233 original size:12 final size:12
Alignment explanation
Indices: 6216--6240 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6206 CGACGATTCC
6216 AATGGTAGAGTG
1 AATGGTAGAGTG
6228 AATGGTAGAGTG
1 AATGGTAGAGTG
6240 A
1 A
6241 CTGGAGTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (12 bp):
AATGGTAGAGTG
Found at i:9973 original size:14 final size:14
Alignment explanation
Indices: 9940--9974 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9930 TAGAAATTAG
9940 TAAGTTAAAAGTTA
1 TAAGTTAAAAGTTA
**
9954 GCAGTTAAAAGTTA
1 TAAGTTAAAAGTTA
9968 TAAGTTA
1 TAAGTTA
9975 GTAAAAAATT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (14 bp):
TAAGTTAAAAGTTA
Found at i:12217 original size:2 final size:2
Alignment explanation
Indices: 12210--12240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12200 ATGGATGTAG
12210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12241 GTTAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15582 original size:17 final size:16
Alignment explanation
Indices: 15560--15613 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
15550 TATAGAATTA
15560 TTTCATTTTTTATTTTT
1 TTTCATTTTTT-TTTTT
* *
15577 TTTCATTCTTTTTTTC
1 TTTCATTTTTTTTTTT
15593 TTTC-TTTTCGTTTTTTT
1 TTTCATTTT--TTTTTTT
15610 TTTC
1 TTTC
15614 TTGTGTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.10
16 8 0.26
17 20 0.65
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTCATTTTTTTTTTT
Found at i:15613 original size:21 final size:21
Alignment explanation
Indices: 15565--15615 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
15555 AATTATTTCA
* *
15565 TTTTTTATTTTTTTTCATTCT
1 TTTTTTCTTTCTTTTCATTCT
* *
15586 TTTTTTCTTTCTTTTCGTTTT
1 TTTTTTCTTTCTTTTCATTCT
15607 TTTTTTCTT
1 TTTTTTCTT
15616 GTGTTTCTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTTTCTTTCTTTTCATTCT
Found at i:27581 original size:17 final size:17
Alignment explanation
Indices: 27559--27592 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27549 GATAGAATTA
27559 TTTCATT-TTTTATTTTT
1 TTTCATTCTTTT-TTTTT
27576 TTTCATTCTTTTTTTTT
1 TTTCATTCTTTTTTTTT
27593 ATTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCATTCTTTTTTTTT
Found at i:27592 original size:23 final size:22
Alignment explanation
Indices: 27564--27611 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
27554 AATTATTTCA
27564 TTTTTTATTTTTTTTCATTCTTT
1 TTTTTTATTTTTTTTCATT-TTT
*
27587 TTTTTTATTTTTTTTCGTTTTT
1 TTTTTTATTTTTTTTCATTTTT
27609 TTT
1 TTT
27612 CCTGTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.85
Consensus pattern (22 bp):
TTTTTTATTTTTTTTCATTTTT
Found at i:32092 original size:12 final size:12
Alignment explanation
Indices: 32075--32099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32065 CGACGATTCC
32075 AATGGTAGAGTG
1 AATGGTAGAGTG
32087 AATGGTAGAGTG
1 AATGGTAGAGTG
32099 A
1 A
32100 CCGGAGTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (12 bp):
AATGGTAGAGTG
Found at i:39045 original size:4 final size:4
Alignment explanation
Indices: 39036--39091 Score: 78
Period size: 4 Copynumber: 13.5 Consensus size: 4
39026 TTTTTCATTC
39036 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-T TTCT TTCTT TTCGT TTCTT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTC-T TTC-T
39086 TTCT TT
1 TTCT TT
39092 TTCTCGCTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 3 0.06
4 33 0.69
5 12 0.25
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:49558 original size:17 final size:17
Alignment explanation
Indices: 49515--49561 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
49505 AGCCGAGTCG
49515 TTGATCGTTGACCTCCA
1 TTGATCGTTGACCTCCA
*
49532 TTGACCGTTGACCAT-CA
1 TTGATCGTTGACC-TCCA
*
49549 TTGATTGTTGACC
1 TTGATCGTTGACC
49562 GCACCATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (17 bp):
TTGATCGTTGACCTCCA
Found at i:56348 original size:24 final size:26
Alignment explanation
Indices: 56320--56371 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
56310 TTGTCCGCCA
56320 TTGACCATTGA-CAATCGTTGA-TTT
1 TTGACCATTGATCAATCGTTGACTTT
* *
56344 TTGACCGTTGATCGATCGTTGACTTT
1 TTGACCATTGATCAATCGTTGACTTT
56370 TT
1 TT
56372 TTGGGTACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 9 0.38
26 5 0.21
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (26 bp):
TTGACCATTGATCAATCGTTGACTTT
Found at i:56370 original size:25 final size:24
Alignment explanation
Indices: 56320--56370 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
56310 TTGTCCGCCA
*
56320 TTGACCATTGACAATCGTTGATTT
1 TTGACCATTGACAATCGTTGACTT
* *
56344 TTGACCGTTGATCGATCGTTGACTT
1 TTGACCATTGA-CAATCGTTGACTT
56369 TT
1 TT
56371 TTTGGGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (24 bp):
TTGACCATTGACAATCGTTGACTT
Found at i:62071 original size:48 final size:48
Alignment explanation
Indices: 62018--62109 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
62008 TTCGACCTGA
* *
62018 ATTCTGTTCTGATATATTACCTGAATTCTGTTCTGATTTCTGATCCAG
1 ATTCTGTTCTGATATATGACCTGAATTATGTTCTGATTTCTGATCCAG
* ** *
62066 ATTCTGTTCTGATATCTGATTTGAATTATGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATATGACCTGAATTATGTTCTGATTTCTGAT
62110 ATCTCTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTGATATATGACCTGAATTATGTTCTGATTTCTGATCCAG
Found at i:62083 original size:24 final size:25
Alignment explanation
Indices: 62016--62085 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 25
62006 TTTTCGACCT
* * *
62016 GAATTCTGTTCTGATATATTA-CCT
1 GAATTCTGTTCTGATATCTGATCCA
*
62040 GAATTCTGTTCTGATTTCTGATCCA
1 GAATTCTGTTCTGATATCTGATCCA
62065 G-ATTCTGTTCTGATATCTGAT
1 GAATTCTGTTCTGATATCTGAT
62086 TTGAATTATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 37 0.93
25 3 0.08
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (25 bp):
GAATTCTGTTCTGATATCTGATCCA
Found at i:62097 original size:24 final size:24
Alignment explanation
Indices: 62015--62109 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
62005 ATTTTCGACC
* * **
62015 TGAATTCTGTTCTGATATATTACC
1 TGAATTCTGTTCTGATATCTGATT
*
62039 TGAATTCTGTTCTGATTTCTGA-T
1 TGAATTCTGTTCTGATATCTGATT
**
62062 CCAGATTCTGTTCTGATATCTGATT
1 TGA-ATTCTGTTCTGATATCTGATT
* * *
62087 TGAATTATGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
62110 ATCTCTATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.95
25 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATT
Found at i:62274 original size:2 final size:2
Alignment explanation
Indices: 62267--62343 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
62257 AAGATGGGTG
*
62267 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62309 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
62344 GTTTTAAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:65135 original size:29 final size:28
Alignment explanation
Indices: 65080--65140 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
65070 TAAATAAAGA
*
65080 AAATTAAGTGAATGAATTAAAAGAACAG
1 AAATTAAGTGAATGAATTAAAACAACAG
* *
65108 AAATTGAAGTG-ATGAAATTAAATCAACAT
1 AAATT-AAGTGAATG-AATTAAAACAACAG
65137 AAAT
1 AAAT
65141 ATAAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.25
Consensus pattern (28 bp):
AAATTAAGTGAATGAATTAAAACAACAG
Found at i:65294 original size:14 final size:14
Alignment explanation
Indices: 65269--65307 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
65259 TTTTTAGAAA
65269 TTAGTAAGTTAAAAG
1 TTAG-AAGTTAAAAG
*
65284 TTAGCAGTTAAAAG
1 TTAGAAGTTAAAAG
65298 TTAGAAGTTA
1 TTAGAAGTTA
65308 GTAAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (14 bp):
TTAGAAGTTAAAAG
Done.