Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005671.1 Hibiscus syriacus cultivar Beakdansim tig00013260_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: 77593
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:13588 original size:21 final size:17
Alignment explanation
Indices: 13544--13585 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
13534 TCTCCTTCCA
13544 AGCTAGCTTGAGTGTGG
1 AGCTAGCTTGAGTGTGG
13561 AGCTAGCTTGAGTGTGG
1 AGCTAGCTTGAGTGTGG
13578 AGCTAGCT
1 AGCTAGCT
13586 AGCAAGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.14, G:0.38, T:0.29
Consensus pattern (17 bp):
AGCTAGCTTGAGTGTGG
Found at i:25129 original size:16 final size:16
Alignment explanation
Indices: 25095--25128 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25085 TTTAACTTTC
*
25095 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
25111 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
25126 TTT
1 TTT
25129 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:30447 original size:20 final size:22
Alignment explanation
Indices: 30412--30451 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
30402 CATGCTTAAT
30412 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
30434 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
30452 GGTCTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:44763 original size:30 final size:31
Alignment explanation
Indices: 44690--44765 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
44680 GTGCTGCAAC
*
44690 AAAAGCAACA-AAAAGAGAAAAAGAATGAATA
1 AAAAGCAAAAGAAAAGAGAAAAAGAA-GAATA
* * *
44721 AAAAGAAAAAGAAAAGAGAAGAAGAA-AATT
1 AAAAGCAAAAGAAAAGAGAAAAAGAAGAATA
*
44751 CAAAGCAAAAGAAAA
1 AAAAGCAAAAGAAAA
44766 AGTGAAGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 16 0.42
31 8 0.21
32 14 0.37
ACGTcount: A:0.72, C:0.05, G:0.17, T:0.05
Consensus pattern (31 bp):
AAAAGCAAAAGAAAAGAGAAAAAGAAGAATA
Found at i:52663 original size:24 final size:23
Alignment explanation
Indices: 52613--52677 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
52603 TTTTCTTTGC
52613 TTTTTCTTCTTTTGAGTGCTGGA
1 TTTTTCTTCTTTTGAGTGCTGGA
*
52636 TTTTTCTTCTTTTGAGTGCTGGT
1 TTTTTCTTCTTTTGAGTGCTGGA
52659 TTTTTCTTTCTTTTGAGTG
1 TTTTTC-TTCTTTTGAGTG
52678 TTTCACTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 28 0.70
24 12 0.30
ACGTcount: A:0.06, C:0.12, G:0.20, T:0.62
Consensus pattern (23 bp):
TTTTTCTTCTTTTGAGTGCTGGA
Found at i:57540 original size:26 final size:25
Alignment explanation
Indices: 57484--57545 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
57474 AGATTAGAAC
**
57484 AAAATAAACAAAAGATAAAGAAATTG
1 AAAATAAA-AAAAGATAAAGAAATAA
57510 AAAATAAAAAAAGAT-AAGATAATAA
1 AAAATAAAAAAAGATAAAGA-AATAA
*
57535 AGAAATCAAAA
1 A-AAATAAAAA
57546 GATCTCCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 11 0.35
26 16 0.52
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.15
Consensus pattern (25 bp):
AAAATAAAAAAAGATAAAGAAATAA
Found at i:67066 original size:43 final size:47
Alignment explanation
Indices: 66964--67069 Score: 141
Period size: 50 Copynumber: 2.3 Consensus size: 47
66954 TGGATTAGAT
66964 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACAATAGTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACAATAGTTTTAGTTA
67014 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-AT-G-TTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTTAG-TTA
67057 TTATTATTTTATT
1 TTATTATTTTATT
67070 CTTTAGTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
42 5 0.09
43 17 0.31
44 2 0.04
45 10 0.18
49 1 0.02
50 20 0.36
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTTAGTTA
Found at i:75078 original size:19 final size:20
Alignment explanation
Indices: 75054--75096 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
75044 AGCATTTATC
*
75054 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
75073 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
75093 TTCA
1 TTCA
75097 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:75534 original size:19 final size:19
Alignment explanation
Indices: 75510--75549 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
75500 TATCCCATCC
75510 TTATTTCATTTCATT-CTTA
1 TTATTTC-TTTCATTACTTA
75529 TTATTTCTTTCATTACTTA
1 TTATTTCTTTCATTACTTA
75548 TT
1 TT
75550 CTATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTCTTTCATTACTTA
Done.