Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006649.1 Hibiscus syriacus cultivar Beakdansim tig00016398_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: 30845
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5243 original size:15 final size:14
Alignment explanation
Indices: 5223--5265 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5213 TCCTAAGTTG
* *
5223 AAAAAAAA-AATAT
1 AAAAAAAACAAAAA
5236 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
*
5250 CAAAAAAACAAAAA
1 AAAAAAAACAAAAA
5264 AA
1 AA
5266 CGCTTAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAACAAAAA
Found at i:6816 original size:105 final size:105
Alignment explanation
Indices: 6034--6807 Score: 1478
Period size: 105 Copynumber: 7.4 Consensus size: 105
6024 AGGTTTTACC
6034 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6099 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
6139 CAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6204 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
6244 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6309 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
6349 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6414 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
6454 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
*
6519 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
6559 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6624 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
6664 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
6729 ACGAAGGGACCGCTGGTTGTC-ACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
6768 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
6808 GAAAACAACA
Statistics
Matches: 659, Mismatches: 10, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
104 58 0.09
105 601 0.91
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:8185 original size:2 final size:2
Alignment explanation
Indices: 8178--8202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8168 ATTTACTATT
8178 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 T
8203 TTGAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8256 original size:2 final size:2
Alignment explanation
Indices: 8249--8274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8239 TTCTTATGTT
8249 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
8275 CATTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9677 original size:14 final size:14
Alignment explanation
Indices: 9655--9707 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
9645 GAAAACTGTT
*
9655 TTACGTAAAATGAA
1 TTACCTAAAATGAA
**
9669 TTACCTAAAATTGTT
1 TTACCTAAAA-TGAA
* *
9684 TTACATTAAATGAA
1 TTACCTAAAATGAA
9698 TTACCTAAAA
1 TTACCTAAAA
9708 CCGTTTAACG
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (14 bp):
TTACCTAAAATGAA
Found at i:9694 original size:29 final size:29
Alignment explanation
Indices: 9630--9730 Score: 132
Period size: 29 Copynumber: 3.4 Consensus size: 29
9620 ATAATTTATA
9630 TAAAAT-AGATTACCTGAAAACTGTTTTACG
1 TAAAATGA-ATTACCT-AAAACTGTTTTACG
* *
9660 TAAAATGAATTACCTAAAATTGTTTTACA
1 TAAAATGAATTACCTAAAACTGTTTTACG
* * *
9689 TTAAATGAATTACCTAAAACCGTTTAACG
1 TAAAATGAATTACCTAAAACTGTTTTACG
9718 TAAAATGAATTAC
1 TAAAATGAATTAC
9731 ATTTTTAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
29 48 0.77
30 13 0.21
31 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (29 bp):
TAAAATGAATTACCTAAAACTGTTTTACG
Found at i:10016 original size:30 final size:27
Alignment explanation
Indices: 9980--10080 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 27
9970 GAACACCCTT
9980 AATTATTAGTATT-TTATTAACATAATACTA
1 AATTATTA-TATTATTATTAA-AT-ATA-TA
10010 AATTATTATATTAATT-TTAAATATATA
1 AATTATTATATT-ATTATTAAATATATA
*
10037 AATTATTATTACTTATTATT-AATAATTTA
1 AATTATTA-TA-TTATTATTAAAT-ATATA
*
10066 ATAATATTATATTAT
1 A-ATTATTATATTAT
10081 GAAAACAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
27 10 0.16
28 15 0.24
29 17 0.27
30 18 0.29
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTATTATATTATTATTAAATATATA
Found at i:10199 original size:47 final size:46
Alignment explanation
Indices: 10127--10240 Score: 110
Period size: 47 Copynumber: 2.5 Consensus size: 46
10117 ATTTAATATC
* *
10127 ATAA-ATTATTATAA-TATATGAGTATATATTAATAATATTAA-AATT-
1 ATAATATTATTAAAATTATAT-AGTATAT-TAAAT-ATATTAATAATTG
*
10172 ATAATATTATTAAAATTATATATGTATATTAAATATTTTAATAATTG
1 ATAATATTATTAAAATTATATA-GTATATTAAATATATTAATAATTG
* * *
10219 ATATTTTTATTAAAATGATATA
1 ATAATATTATTAAAATTATATA
10241 AAAATATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
45 10 0.17
46 18 0.31
47 30 0.52
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.47
Consensus pattern (46 bp):
ATAATATTATTAAAATTATATAGTATATTAAATATATTAATAATTG
Found at i:10201 original size:19 final size:18
Alignment explanation
Indices: 10156--10214 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
10146 GAGTATATAT
10156 TAATA-ATATTAAAATTA
1 TAATATATATTAAAATTA
10173 TAATAT-TATTAAAATTA
1 TAATATATATTAAAATTA
* *
10190 TATATGTATATTAAATATTT
1 TA-ATATATATTAAA-ATTA
10210 TAATA
1 TAATA
10215 ATTGATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 18 0.51
18 3 0.09
19 9 0.26
20 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATATATATTAAAATTA
Found at i:10387 original size:18 final size:18
Alignment explanation
Indices: 10360--10394 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10350 ATAAAAAGAA
*
10360 ATTAGGAAAATCAATTAC
1 ATTAGAAAAATCAATTAC
10378 ATTAGAAAAATCAATTA
1 ATTAGAAAAATCAATTA
10395 TAACTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (18 bp):
ATTAGAAAAATCAATTAC
Found at i:12427 original size:20 final size:20
Alignment explanation
Indices: 12389--12428 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12379 TACCATATTG
**
12389 ACCCCTTAAAATTTTTGTTT
1 ACCCCTTAAAATTCCTGTTT
12409 ACCCCTTAAAATTCCTGTTT
1 ACCCCTTAAAATTCCTGTTT
12429 TAATAGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (20 bp):
ACCCCTTAAAATTCCTGTTT
Found at i:14919 original size:10 final size:10
Alignment explanation
Indices: 14875--14902 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
14865 AAATCTCAGT
14875 TTTTTTCCTG
1 TTTTTTCCTG
14885 TTTTTTCCTG
1 TTTTTTCCTG
14895 TTTTTTCC
1 TTTTTTCC
14903 CCTTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTTTTCCTG
Found at i:14951 original size:17 final size:18
Alignment explanation
Indices: 14929--14962 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14919 TCAACCGGTC
14929 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
14946 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
14963 CTAATAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:15291 original size:2 final size:2
Alignment explanation
Indices: 15284--15361 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
15274 GAATTATGTA
15284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
15326 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15362 TGGTCTCGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Done.