Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003297.1 Hibiscus syriacus cultivar Beakdansim tig00006934_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: 54902
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6046 original size:27 final size:27
Alignment explanation
Indices: 5991--6069 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
5981 AAAATTGCCC
* * *
5991 TAAAATAAATCAAATTAATAATAAACAA
1 TAAAATAAATTAAAATGA-AATAAACAA
6019 TAAAATAAATTAAAATGAAATAAACAA
1 TAAAATAAATTAAAATGAAATAAACAA
*
6046 TATCAAATAAA-TAAAA-GAATTAAA
1 TA--AAATAAATTAAAATGAAATAAA
6070 AGAGAATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
27 18 0.40
28 20 0.44
29 7 0.16
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (27 bp):
TAAAATAAATTAAAATGAAATAAACAA
Found at i:6111 original size:15 final size:15
Alignment explanation
Indices: 6063--6111 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
6053 TAAATAAAAG
6063 AATTAAAAGAGAATTCA
1 AATTAAAA-AGAATT-A
6080 AATTAAAAAGGAA-TA
1 AATTAAAAA-GAATTA
*
6095 AATTGAAAAGAATTA
1 AATTAAAAAGAATTA
6110 AA
1 AA
6112 AATCAAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 3 0.10
15 13 0.45
16 2 0.07
17 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (15 bp):
AATTAAAAAGAATTA
Found at i:7891 original size:37 final size:37
Alignment explanation
Indices: 7841--7915 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
7831 CTGTCACTGA
7841 TCACATGTATTAGATTGTGTGGAAAGTAGTTGGTTGG
1 TCACATGTATTAGATTGTGTGGAAAGTAGTTGGTTGG
7878 TCACATGTATTAGATTGTGTGGAAAGTAGTTGGTTGG
1 TCACATGTATTAGATTGTGTGGAAAGTAGTTGGTTGG
7915 T
1 T
7916 TGCACATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (37 bp):
TCACATGTATTAGATTGTGTGGAAAGTAGTTGGTTGG
Found at i:8709 original size:32 final size:32
Alignment explanation
Indices: 8667--8728 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
8657 GAAACATGGA
*
8667 AGACAAGACTGAATGTTAAAGTAAAGCTAGGG
1 AGACAAGACTGAATGTTAAAATAAAGCTAGGG
*
8699 AGACACGACTGAATGTTAAAATAAAGCTAG
1 AGACAAGACTGAATGTTAAAATAAAGCTAG
8729 AGATTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.19
Consensus pattern (32 bp):
AGACAAGACTGAATGTTAAAATAAAGCTAGGG
Found at i:9891 original size:34 final size:33
Alignment explanation
Indices: 9839--9905 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 33
9829 TTTATTTGTT
9839 ATTAATATAAAAATATAAAATATTATATATATA
1 ATTAATATAAAAATATAAAATATTATATATATA
9872 ATTAATATACAAAATATAAAATATTATATATATA
1 ATTAATATA-AAAATATAAAATATTATATATATA
9906 TATAATCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 9 0.27
34 24 0.73
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATTAATATAAAAATATAAAATATTATATATATA
Found at i:10507 original size:36 final size:36
Alignment explanation
Indices: 10467--10560 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
10457 ACAATAGGTA
*
10467 TGACACATTCAGTGCCATGTGACT-CTACCGTAGATG
1 TGACACATTCAGTGCCCTGTGACTGC-ACCGTAGATG
* * *
10503 TGACACATTCAATGCCCTTTGATTGCACCGTAGATG
1 TGACACATTCAGTGCCCTGTGACTGCACCGTAGATG
* *
10539 CGTCACATTCAGTGCCCTGTGA
1 TGACACATTCAGTGCCCTGTGA
10561 ATGTACATAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 48 0.98
37 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (36 bp):
TGACACATTCAGTGCCCTGTGACTGCACCGTAGATG
Found at i:13974 original size:29 final size:30
Alignment explanation
Indices: 13910--13981 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
13900 TCTACTCATT
*
13910 ATCTTATACAAATTTATGTTTTAGATCCACA
1 ATCTTATAC-AATTTATATTTTAGATCCACA
* **
13941 A-CTTATACAATTTGTATTTTAG-TCCTTA
1 ATCTTATACAATTTATATTTTAGATCCACA
13969 ATCTTA-ACAATTT
1 ATCTTATACAATTT
13982 TACAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 12 0.33
29 16 0.44
30 7 0.19
31 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (30 bp):
ATCTTATACAATTTATATTTTAGATCCACA
Found at i:16818 original size:19 final size:19
Alignment explanation
Indices: 16782--16835 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
16772 CTCAAAATCA
***
16782 TTTTTCAAAATTTCATTTT
1 TTTTTCAAAATCAAATTTT
16801 TTTTTCAAAATCAAATTTT
1 TTTTTCAAAATCAAATTTT
**
16820 GCTTTCAAAATCAAAT
1 TTTTTCAAAATCAAAT
16836 CATTTTCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTTCAAAATCAAATTTT
Found at i:21975 original size:31 final size:30
Alignment explanation
Indices: 21908--21985 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
21898 CAGTTACGTC
* *
21908 GGGGAACATATTGCAAACGGACTAAATGTTA
1 GGGG-ACATATTGCAAACAGACTAAATATTA
* *
21939 GGGGACCATATTGCAAATAGACTAAATATTT
1 GGGGA-CATATTGCAAACAGACTAAATATTA
*
21970 TGGGACATTATTGCAA
1 GGGGACA-TATTGCAA
21986 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 3 0.08
31 37 0.93
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (30 bp):
GGGGACATATTGCAAACAGACTAAATATTA
Found at i:26684 original size:24 final size:23
Alignment explanation
Indices: 26651--26697 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
26641 ATCTCAAGGG
* *
26651 TATCGGTACTACTATATTTAGTAT
1 TATCGATACTACCAT-TTTAGTAT
26675 TATCGATACTACCATTTTAGTAT
1 TATCGATACTACCATTTTAGTAT
26698 ACTGGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (23 bp):
TATCGATACTACCATTTTAGTAT
Found at i:26850 original size:20 final size:20
Alignment explanation
Indices: 26821--26860 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
26811 AGCATTCTGT
* *
26821 CTTAATAGTATCAGTACTAC
1 CTTAACAGTATCAATACTAC
26841 CTTAACAGTATCAATACTAC
1 CTTAACAGTATCAATACTAC
26861 TTCATTATTT
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:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (20 bp):
CTTAACAGTATCAATACTAC
Found at i:34329 original size:36 final size:36
Alignment explanation
Indices: 34278--34361 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
34268 GATACTAATT
* *
34278 GATGAGTCAATAGAAACGATTAAATAGACAAGAGGG
1 GATGAGTTAACAGAAACGATTAAATAGACAAGAGGG
*
34314 GATGAGTTAACAGAAAGGATTAAATAGACAAGAGGG
1 GATGAGTTAACAGAAACGATTAAATAGACAAGAGGG
34350 GATGAGTTAACA
1 GATGAGTTAACA
34362 ATTAAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.46, C:0.07, G:0.29, T:0.18
Consensus pattern (36 bp):
GATGAGTTAACAGAAACGATTAAATAGACAAGAGGG
Found at i:38200 original size:10 final size:10
Alignment explanation
Indices: 38181--38214 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38171 GGCAACCCAC
38181 TTTA-TTTTA
1 TTTATTTTTA
38190 TTTATTTTTA
1 TTTATTTTTA
*
38200 TTTATTTTTC
1 TTTATTTTTA
38210 TTTAT
1 TTTAT
38215 AGTTTTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:45565 original size:24 final size:23
Alignment explanation
Indices: 45532--45578 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
45522 ATCACAAGGG
* *
45532 TATCGGTACTACTATATTTAGTAT
1 TATCGATACTACCAT-TTTAGTAT
45556 TATCGATACTACCATTTTAGTAT
1 TATCGATACTACCATTTTAGTAT
45579 ACTGGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (23 bp):
TATCGATACTACCATTTTAGTAT
Done.