Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004024.1 Hibiscus syriacus cultivar Beakdansim tig00008788_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: 49818
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2813 original size:16 final size:16
Alignment explanation
Indices: 2792--2823 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2782 GATAGAAAAT
2792 ATATAAAAAAATTTAA
1 ATATAAAAAAATTTAA
*
2808 ATATAAAAGAATTTAA
1 ATATAAAAAAATTTAA
2824 TTTTAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATAAAAAAATTTAA
Found at i:7380 original size:15 final size:15
Alignment explanation
Indices: 7360--7401 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7350 TTGTAGGAGT
*
7360 TTTTGGTTTGTTTTA
1 TTTTGGCTTGTTTTA
7375 TTTTGGCTTGTTTTA
1 TTTTGGCTTGTTTTA
7390 TTTTGGCGTTGT
1 TTTTGGC-TTGT
7402 CATGTGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.67
Consensus pattern (15 bp):
TTTTGGCTTGTTTTA
Found at i:7522 original size:2 final size:2
Alignment explanation
Indices: 7515--7591 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
7505 GATGTTTCCT
7515 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
7557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7592 GTGAGTGCTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13358 original size:14 final size:14
Alignment explanation
Indices: 13339--13366 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13329 ATTTGAAGTA
13339 TTGTGGAAGGGTTG
1 TTGTGGAAGGGTTG
13353 TTGTGGAAGGGTTG
1 TTGTGGAAGGGTTG
13367 ATGTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (14 bp):
TTGTGGAAGGGTTG
Found at i:23426 original size:2 final size:2
Alignment explanation
Indices: 23419--23456 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23409 GTAGGTATTA
23419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23457 GCAAACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36929 original size:8 final size:8
Alignment explanation
Indices: 36912--36953 Score: 68
Period size: 8 Copynumber: 5.2 Consensus size: 8
36902 AAAATGAGTG
36912 AAAA-AAA
1 AAAATAAA
36919 AAAATAAA
1 AAAATAAA
36927 AAAATAAA
1 AAAATAAA
36935 AAAATAAA
1 AAAATAAA
36943 AAAATGAAA
1 AAAAT-AAA
36952 AA
1 AA
36954 TGGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 4 0.12
8 24 0.73
9 5 0.15
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (8 bp):
AAAATAAA
Found at i:38045 original size:55 final size:55
Alignment explanation
Indices: 37962--38442 Score: 603
Period size: 55 Copynumber: 8.8 Consensus size: 55
37952 CAACGATAAT
* * *
37962 TGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
*
38017 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * *
38072 TGAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
38127 TGAAGATTGTTCGAGTCTTGTACTCTCTGAAGGAATAGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * *
38182 TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * *
38237 TGAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAGGATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGA
* * *
38293 TGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * ** * * * *
38348 TGAAGATTCTTCAAGT-TCCTACTCCCT-AAGAAAGAGGGAAC-GAACCCG-TTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGA
* * * *
38400 CAGAAGATTGTTCGAGT-TCTATACTCCCCGAAGAAAGAGGGAG
1 -TGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
38443 TGAACTCGTT
Statistics
Matches: 377, Mismatches: 44, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
52 5 0.01
53 29 0.08
54 15 0.04
55 276 0.73
56 52 0.14
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
Found at i:38459 original size:55 final size:54
Alignment explanation
Indices: 38349--38506 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 54
38339 CACGATTGAT
* * * * *
38349 GAAGATTCTTCAAGTTC-CTACTCCCTAAGAAAGAGGGAACGAACCCGTTGACA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACTCGTTGACA
* *
38402 GAAGATTGTTCGAGTTCTATACTCCCCGAAGAAAGAGGGAGTGAACTCGTTCG-CA
1 GAAGATTGTTCGAGTTCTATACT-CCCTAAGAAAGAGGGAGCGAACTCGTT-GACA
*
38457 GAAAATTGTTCGAGTTCTATACTCCCTAA-AAATGAGGGAGCGAACTCGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAA-GAGGGAGCGAACTCGTT
38507 TTCCGAATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
53 18 0.20
54 25 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACTCGTTGACA
Found at i:41511 original size:16 final size:17
Alignment explanation
Indices: 41480--41514 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41470 CTTTAGGTTA
41480 ATCATGGATTATTCCTCG
1 ATCATGGA-TATTCCTCG
41498 ATCATGGA-ATTCCTCG
1 ATCATGGATATTCCTCG
41514 A
1 A
41515 GACCCCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (17 bp):
ATCATGGATATTCCTCG
Found at i:43993 original size:2 final size:2
Alignment explanation
Indices: 43986--44048 Score: 85
Period size: 2 Copynumber: 32.0 Consensus size: 2
43976 TACCTTACCA
* *
43986 AT AT AT AT AT TT GAG AT AT AT AT AT AT -T AT AT AT AT AT -T AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44027 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
44049 TCTCAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:44006 original size:15 final size:15
Alignment explanation
Indices: 43986--44044 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
43976 TACCTTACCA
43986 ATATATATAT-TTGAG
1 ATATATATATATT-AG
*
44001 ATATATATATATTAT
1 ATATATATATATTAG
*
44016 ATATATATTATATATAT
1 ATATATA-TATAT-TAG
44033 ATATATATATAT
1 ATATATATATAT
44045 ATATTCTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
15 18 0.45
16 12 0.30
17 10 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATATATATATATTAG
Found at i:46157 original size:21 final size:19
Alignment explanation
Indices: 46132--46179 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
46122 TGGTAATTTT
*
46132 AAAAATTTTATTTTTTTAAAA
1 AAAAATTTTA--TATTTAAAA
*
46153 AAAAATATTATATTTAAAA
1 AAAAATTTTATATTTAAAA
46172 AAAAATTT
1 AAAAATTT
46180 AAATTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.62
21 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATTTTATATTTAAAA
Found at i:48885 original size:21 final size:20
Alignment explanation
Indices: 48837--48888 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
48827 GATAATTCAG
*
48837 TTTTTTTAAAATATTGATAA
1 TTTTTTTAAAATATTGAAAA
48857 TTTATTTTAAAAT-TTGAAAAA
1 TTT-TTTTAAAATATTG-AAAA
48878 TATTTTTTAAA
1 T-TTTTTTAAA
48889 TTATAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.21
21 20 0.71
22 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTTTTAAAATATTGAAAA
Done.