Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004741.1 Hibiscus syriacus cultivar Beakdansim tig00010701_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: 38815
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2198 original size:2 final size:2
Alignment explanation
Indices: 2191--2218 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2181 AAACAATTAT
2191 TA 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 TA
2219 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2273 original size:22 final size:23
Alignment explanation
Indices: 2235--2292 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
2225 AAAAATTTAA
* *
2235 ATTAAATTAAA-AATATTTATAT
1 ATTAATTTAAATATTATTTATAT
*
2257 ATT-ATTTATATATTATTTATAT
1 ATTAATTTAAATATTATTTATAT
2279 ATTAATTTAAATAT
1 ATTAATTTAAATAT
2293 ATACCAGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 16 0.53
23 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTAATTTAAATATTATTTATAT
Found at i:2277 original size:9 final size:11
Alignment explanation
Indices: 2248--2292 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
2238 AAATTAAAAA
2248 TATTTATATAT
1 TATTTATATAT
2259 TATTTATATAT
1 TATTTATATAT
2270 TATTTATATAT
1 TATTTATATAT
*
2281 TAATTTAAATAT
1 T-ATTTATATAT
2293 ATACCAGACC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTATATAT
Found at i:5940 original size:7 final size:7
Alignment explanation
Indices: 5928--5957 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5918 TTGGTTATTT
5928 TTTTTCC
1 TTTTTCC
5935 TTTTTCC
1 TTTTTCC
5942 TTTTTCC
1 TTTTTCC
5949 TTTTTCC
1 TTTTTCC
5956 TT
1 TT
5958 ATATGATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCC
Found at i:6796 original size:24 final size:24
Alignment explanation
Indices: 6743--6818 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
6733 AATAATAATA
* *
6743 TATATTTTAAAATTTTTAGTA-TTT
1 TATATTTT-AAATTTTAAATATTTT
* *
6767 TATTATATTTAACTTTTTGAATATTTT
1 TA-TAT-TTTAA-ATTTTAAATATTTT
6794 TATATTTTAAATTTTAAATATTTT
1 TATATTTTAAATTTTAAATATTTT
6818 T
1 T
6819 TTTATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.35
25 10 0.23
26 13 0.30
27 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (24 bp):
TATATTTTAAATTTTAAATATTTT
Found at i:6801 original size:17 final size:16
Alignment explanation
Indices: 6743--6808 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 16
6733 AATAATAATA
*
6743 TATATTTTAAAATTTT
1 TATATTTTAATATTTT
* *
6759 TAGTATTTTATTATATT
1 TA-TATTTTAATATTTT
6776 TA-ACTTTTTGAATATTTT
1 TATA--TTTT-AATATTTT
6794 TATATTTTAA-ATTTT
1 TATATTTTAATATTTT
6809 AAATATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
15 6 0.15
16 4 0.10
17 21 0.52
18 8 0.20
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (16 bp):
TATATTTTAATATTTT
Found at i:10657 original size:3 final size:3
Alignment explanation
Indices: 10649--10702 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
10639 ATCAATTGGG
10649 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10697 -TA TTA T
1 TTA TTA T
10703 GGTAAATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17173 original size:35 final size:35
Alignment explanation
Indices: 17133--17250 Score: 121
Period size: 36 Copynumber: 3.6 Consensus size: 35
17123 ATTGGACAGT
17133 ACTCGACTC-TTGCTCGTTAGAAAAATTGTTGCTCG
1 ACTCGACTCGTTGCTCGTTA-AAAAATTGTTGCTCG
*
17168 ACTCGATTCGTTGCTCGTT--AAAATT-TTGCT--
1 ACTCGACTCGTTGCTCGTTAAAAAATTGTTGCTCG
* *
17198 --T-GACTCATT-CTCGTTAAAAAACTTGTTGCTCA
1 ACTCGACTCGTTGCTCGTTAAAAAA-TTGTTGCTCG
17230 ACTCGACTCGTTGCTCGTTAA
1 ACTCGACTCGTTGCTCGTTAA
17251 GCTCACATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
26 6 0.09
27 6 0.09
28 5 0.07
29 2 0.03
30 5 0.07
32 5 0.07
33 6 0.09
34 1 0.01
35 15 0.22
36 17 0.25
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTCGACTCGTTGCTCGTTAAAAAATTGTTGCTCG
Found at i:17913 original size:29 final size:30
Alignment explanation
Indices: 17835--17923 Score: 135
Period size: 30 Copynumber: 2.9 Consensus size: 30
17825 AAACCCAAAC
*
17835 TAAATTGATGTCATTACTTACATCATTTAAT
1 TAAA-TGATGTCATTGCTTACATCATTTAAT
*
17866 TAAAAGATGTCATTGCTTACATCATTTAAT
1 TAAATGATGTCATTGCTTACATCATTTAAT
17896 T-AATGATGTCATTGCTTACATCAATTTA
1 TAAATGATGTCATTGCTTACATC-ATTTA
17924 GTTAGGTGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
29 20 0.37
30 30 0.56
31 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (30 bp):
TAAATGATGTCATTGCTTACATCATTTAAT
Found at i:22642 original size:29 final size:29
Alignment explanation
Indices: 22607--22688 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
22597 AAACTAAATT
*
22607 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
22636 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
22665 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
22689 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:27834 original size:29 final size:29
Alignment explanation
Indices: 27799--27880 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
27789 AAACTAAATT
*
27799 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
27828 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
27857 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
27881 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:32590 original size:29 final size:29
Alignment explanation
Indices: 32554--32665 Score: 197
Period size: 29 Copynumber: 3.8 Consensus size: 29
32544 CAAACTAAAT
*
32554 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
32583 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
32612 TGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
32641 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
32666 GTTAGGTGAG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 74 0.94
30 5 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Done.