Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001795.1 Hibiscus syriacus cultivar Beakdansim tig00003628_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: 54269
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5941 original size:37 final size:36
Alignment explanation
Indices: 5838--5942 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
5828 TTCTCAAGTC
* *
5838 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAGTTCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
*
5874 AATCAAGCCTTCACAAAAGAGTAGTAAAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
*
5910 AATTC-ATCCTTCACAAAAAGAGTAGTGAAGCAA
1 AA-TCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
5943 GATCAGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 43 0.69
37 19 0.31
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:7368 original size:15 final size:15
Alignment explanation
Indices: 7344--7374 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7334 AGTCCCTTAA
*
7344 ATATTGATTATTATT
1 ATATTAATTATTATT
7359 ATATTAATTATTATT
1 ATATTAATTATTATT
7374 A
1 A
7375 ATACTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATTAATTATTATT
Found at i:10689 original size:2 final size:2
Alignment explanation
Indices: 10682--10717 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
10672 AATCTTTAAA
* *
10682 AG AG AG AG AG AG AG AG AG AG AG AC AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10718 TGAAACTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20088 original size:17 final size:17
Alignment explanation
Indices: 20066--20106 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
20056 AAGAACACCT
20066 TCGTCGACAAATTCGTA
1 TCGTCGACAAATTCGTA
20083 TCGTCGACAAATTCGTA
1 TCGTCGACAAATTCGTA
20100 TCGTCGA
1 TCGTCGA
20107 TAAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (17 bp):
TCGTCGACAAATTCGTA
Found at i:24723 original size:16 final size:17
Alignment explanation
Indices: 24702--24736 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
24692 ATACTATTCA
24702 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
24718 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
24735 CG
1 CG
24737 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:33650 original size:24 final size:24
Alignment explanation
Indices: 33589--33651 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
33579 TAGGACACGC
* **
33589 TTTCTCTACTCTTATGTCACGTGT
1 TTTCTCTACTCTTGTCACACGTGT
**
33613 TTTCTCTGTTCTTGTCACACGTGT
1 TTTCTCTACTCTTGTCACACGTGT
33637 TTTCTCTACTCTTGT
1 TTTCTCTACTCTTGT
33652 GGCCCGATCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.10, C:0.25, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTCTCTACTCTTGTCACACGTGT
Found at i:35924 original size:28 final size:27
Alignment explanation
Indices: 35874--35928 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
35864 TAATCAAATT
*
35874 AAAATAAATATACTATCACTATCTAAAA
1 AAAATAAATATACTAACACTATC-AAAA
35902 AAAATAAAATATACTAACA-TATCAAAA
1 AAAAT-AAATATACTAACACTATCAAAA
35929 GTAGTATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 9 0.36
29 12 0.48
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAATAAATATACTAACACTATCAAAA
Found at i:36125 original size:17 final size:17
Alignment explanation
Indices: 36090--36149 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
36080 AACGTGTTGT
*
36090 AAAATAAGAAAGAATAAA
1 AAAATAAG-AAGAACAAA
*
36108 ACAATAAGAAGAACAAAA
1 AAAATAAGAAGAAC-AAA
36126 AAATATATAGAAGAACAAA
1 AAA-ATA-AGAAGAACAAA
36145 GAAAA
1 -AAAA
36150 AAACCTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 5 0.14
18 12 0.34
19 7 0.20
20 11 0.31
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAATAAGAAGAACAAA
Found at i:40710 original size:18 final size:18
Alignment explanation
Indices: 40679--40751 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
40669 ACTGAATATT
* *
40679 TGTCTCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
40697 TGTCCCGGAGGACCACCGA
1 TGTCCCGAAGGACCA-CTA
* *
40716 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
40735 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
40752 GATAATCCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 27 0.63
19 4 0.09
20 12 0.28
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:43087 original size:26 final size:25
Alignment explanation
Indices: 43053--43101 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
43043 GTTTTCGTTT
* *
43053 CCTCTAAAATTTTATAAGTTTATTA
1 CCTCTAAAATATTATAAATTTATTA
43078 CCTCTTAAAATATTATAAATTTAT
1 CCTC-TAAAATATTATAAATTTAT
43102 ATCTCGCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (25 bp):
CCTCTAAAATATTATAAATTTATTA
Found at i:44899 original size:15 final size:16
Alignment explanation
Indices: 44879--44910 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44869 CATACTTAAC
44879 ATTTAAA-AAAATAAA
1 ATTTAAATAAAATAAA
44894 ATTTAAATAAAATAAA
1 ATTTAAATAAAATAAA
44910 A
1 A
44911 AATGAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTTAAATAAAATAAA
Done.