Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009272.1 Hibiscus syriacus cultivar Beakdansim tig00112945_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: 50070
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3045 original size:24 final size:24
Alignment explanation
Indices: 3013--3086 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
3003 TGCCACATAG
*
3013 ATTTTTCCCGAATGACCGCGTAGA
1 ATTTGTCCCGAATGACCGCGTAGA
* *
3037 ATTTGTCCCGAATGACCACATAGAA
1 ATTTGTCCCGAATGACCGCGTAG-A
*
3062 ATTTGTCCCGAAGGACCGCGTAGA
1 ATTTGTCCCGAATGACCGCGTAGA
3086 A
1 A
3087 CCATTGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 22 0.51
25 21 0.49
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCGAATGACCGCGTAGA
Found at i:3070 original size:25 final size:24
Alignment explanation
Indices: 2985--3078 Score: 104
Period size: 23 Copynumber: 4.0 Consensus size: 24
2975 TCACATTGGT
*
2985 CATA-AATTTGTACCGAAGTG-CCA
1 CATAGAATTTGTCCCGAA-TGACCA
* *
3008 CATAG-ATTTTTCCCGAATGACCG
1 CATAGAATTTGTCCCGAATGACCA
*
3031 CGTAGAATTTGTCCCGAATGACCA
1 CATAGAATTTGTCCCGAATGACCA
*
3055 CATAGAAATTTGTCCCGAAGGACC
1 CATAG-AATTTGTCCCGAATGACC
3079 GCGTAGAACC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.03
23 20 0.34
24 20 0.34
25 17 0.29
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (24 bp):
CATAGAATTTGTCCCGAATGACCA
Found at i:3085 original size:25 final size:25
Alignment explanation
Indices: 3013--3086 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
3003 TGCCACATAG
*
3013 ATTTTTCCCGAATGACCGCGTAG-A
1 ATTTGTCCCGAATGACCGCGTAGAA
* *
3037 ATTTGTCCCGAATGACCACATAGAA
1 ATTTGTCCCGAATGACCGCGTAGAA
*
3062 ATTTGTCCCGAAGGACCGCGTAGAA
1 ATTTGTCCCGAATGACCGCGTAGAA
3087 CCATTGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAATGACCGCGTAGAA
Found at i:3230 original size:15 final size:15
Alignment explanation
Indices: 3212--3277 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
3202 CACATAGGGT
*
3212 ATTTTCATGTAAAAC
1 ATTTTCATATAAAAC
**
3227 ATTTTCACT-TAGCAC
1 ATTTTCA-TATAAAAC
* *
3242 ATTTTCACAT-AGAC
1 ATTTTCATATAAAAC
3256 ATTTTCATATAAAAC
1 ATTTTCATATAAAAC
*
3271 ATATTCA
1 ATTTTCA
3278 CTTACCAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.28
15 28 0.70
16 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (15 bp):
ATTTTCATATAAAAC
Found at i:3259 original size:14 final size:15
Alignment explanation
Indices: 3225--3262 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3215 TTCATGTAAA
*
3225 ACATTTTCACTTAGC
1 ACATTTTCACATAGC
3240 ACATTTTCACATAG-
1 ACATTTTCACATAGC
3254 ACATTTTCA
1 ACATTTTCA
3263 TATAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (15 bp):
ACATTTTCACATAGC
Found at i:4895 original size:12 final size:12
Alignment explanation
Indices: 4878--4902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4868 AAGATTTGAA
4878 AATTTAAGATGC
1 AATTTAAGATGC
4890 AATTTAAGATGC
1 AATTTAAGATGC
4902 A
1 A
4903 CTTTGGTCTT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AATTTAAGATGC
Found at i:5585 original size:20 final size:19
Alignment explanation
Indices: 5536--5586 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
5526 TGATTCAATC
5536 AGTATCGATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
*
5555 AGTATCAATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
5574 AGGTATCGATACC
1 A-GTATCGATACC
5587 ATTTTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:6215 original size:77 final size:77
Alignment explanation
Indices: 6086--6233 Score: 226
Period size: 77 Copynumber: 1.9 Consensus size: 77
6076 AAATGAATGA
**
6086 AAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATGTATATGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATACATATGGGTG
6151 CATTATTGACAT
66 CATTATTGACAT
* **
6163 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCCATAGTTGAAATACATATGGGT
1 AAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGT-CATAACTGAAATACATATGGGT
*
6227 GTATTAT
65 GCATTAT
6234 CGGCATAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.02
77 63 0.98
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (77 bp):
AAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATACATATGGGTG
CATTATTGACAT
Found at i:6259 original size:45 final size:45
Alignment explanation
Indices: 6173--6266 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
6163 AAGAATAATG
* * *
6173 CATATGGGTGCATTATTGGCATGAAAGGATTCCATAGTTGAAATA
1 CATATGGGTGCATTATCGGCATAAAAGGATACCATAGTTGAAATA
* * * *
6218 CATATGGGTGTATTATCGGCATAAAAGTATACTC-TATTTGAAATG
1 CATATGGGTGCATTATCGGCATAAAAGGATAC-CATAGTTGAAATA
6263 CATA
1 CATA
6267 ATGGTTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (45 bp):
CATATGGGTGCATTATCGGCATAAAAGGATACCATAGTTGAAATA
Found at i:7783 original size:28 final size:28
Alignment explanation
Indices: 7743--7799 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
7733 CCGCCATCAA
7743 ACTAAGAATAATCCTTCATGCATTCCCC
1 ACTAAGAATAATCCTTCATGCATTCCCC
7771 ACTAAGAATAATCCTTCATGCATTCCCC
1 ACTAAGAATAATCCTTCATGCATTCCCC
7799 A
1 A
7800 TAACACTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.32, G:0.07, T:0.28
Consensus pattern (28 bp):
ACTAAGAATAATCCTTCATGCATTCCCC
Found at i:8813 original size:27 final size:26
Alignment explanation
Indices: 8783--8836 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
8773 ATAGTTTCTA
* *
8783 ATAAAATTATTTATATTTATATTAATT
1 ATAAAATTATTTAAATATA-ATTAATT
*
8810 ATAAAGTTATTTAAATATAATTAATT
1 ATAAAATTATTTAAATATAATTAATT
8836 A
1 A
8837 ATTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATAAAATTATTTAAATATAATTAATT
Found at i:8832 original size:41 final size:40
Alignment explanation
Indices: 8782--8863 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 40
8772 AATAGTTTCT
* *
8782 AATAAAATTATTTATATTT-ATATTAATTATAAAGTTATTTA
1 AATAAAATTAATTA-ATTTAATATGAA-TATAAAGTTATTTA
* *
8823 AATATAATTAATTAATTTAAATATGAATATAAATTTATTTA
1 AATAAAATTAATTAATTT-AATATGAATATAAAGTTATTTA
8864 TTTATTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
40 4 0.11
41 25 0.71
42 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (40 bp):
AATAAAATTAATTAATTTAATATGAATATAAAGTTATTTA
Found at i:14696 original size:60 final size:59
Alignment explanation
Indices: 14571--14697 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 59
14561 TAATGAATAA
* * *
14571 TCGAGTGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAATAAGCTTCCTATGG
1 TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAACAA-CTTCCTATAG
* * *
14631 CCGAGGGGTCATTTTGTAACTTTTAATAGTC-AGTGGACTCGATAAAGCAA-TATCTTATAG
1 TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGT-GACTCAATAAA-CAACT-TCCTATAG
14691 TCGAGGG
1 TCGAGGG
14698 ACCATGTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.07
60 51 0.89
61 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (59 bp):
TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAACAACTTCCTATAG
Found at i:16483 original size:11 final size:11
Alignment explanation
Indices: 16467--16492 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16457 AATCATTATT
16467 TATTTTTAGAA
1 TATTTTTAGAA
16478 TATTTTTAGAA
1 TATTTTTAGAA
16489 TATT
1 TATT
16493 CTGAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TATTTTTAGAA
Found at i:20566 original size:27 final size:27
Alignment explanation
Indices: 20512--20567 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
20502 TTATTATTTC
***
20512 TATCAGTTTTGTTATTATTGGGTGCTT
1 TATCAGTTTTGTTATTATTGGACACTT
*
20539 TATCGGTTTTGTTATTATTGGACACTT
1 TATCAGTTTTGTTATTATTGGACACTT
20566 TA
1 TA
20568 CCGGAAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.54
Consensus pattern (27 bp):
TATCAGTTTTGTTATTATTGGACACTT
Found at i:21340 original size:21 final size:22
Alignment explanation
Indices: 21315--21355 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
21305 TTCAACCACT
21315 CTTAA-AA-TTTGATTTTTTTTA
1 CTTAAGAATTTTG-TTTTTTTTA
21336 CTTAAGAATTTTGTTTTTTT
1 CTTAAGAATTTTGTTTTTTT
21356 GTTGTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (22 bp):
CTTAAGAATTTTGTTTTTTTTA
Found at i:33256 original size:21 final size:21
Alignment explanation
Indices: 33174--33257 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
33164 CAGAACCCCA
*
33174 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
33193 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
33218 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
33239 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
33258 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:37094 original size:22 final size:21
Alignment explanation
Indices: 37052--37091 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37042 GAGTTTGTTT
*
37052 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
37073 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
37092 ACAATTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Done.