Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000943.1 Hibiscus syriacus cultivar Beakdansim tig00001883_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: 108082
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4697 original size:29 final size:30
Alignment explanation
Indices: 4655--4713 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
4645 AAAGTTATCA
* *
4655 TTTTTGTCAAAAATAGGTACTTAAAGTATT
1 TTTTTGTCAAAAATAGGTACATAAAATATT
*
4685 TTTTTGT-TAAAATAGGTACATAAAATATT
1 TTTTTGTCAAAAATAGGTACATAAAATATT
4714 ATATAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTTTGTCAAAAATAGGTACATAAAATATT
Found at i:4723 original size:29 final size:29
Alignment explanation
Indices: 4664--4723 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
4654 ATTTTTGTCA
* * * * **
4664 AAAATAGGTACTTAAAGTATTTTTTTGTT
1 AAAATAGGTACATAAAATATTATATAATT
4693 AAAATAGGTACATAAAATATTATATAATT
1 AAAATAGGTACATAAAATATTATATAATT
4722 AA
1 AA
4724 TGCAAGACGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (29 bp):
AAAATAGGTACATAAAATATTATATAATT
Found at i:9289 original size:95 final size:95
Alignment explanation
Indices: 9126--9317 Score: 348
Period size: 95 Copynumber: 2.0 Consensus size: 95
9116 AGAACAACAG
*
9126 AATAACTCCAACTTATTGAATCACACAAACAAGTGAAGATCTAAATCGATCTTACATTTATTTGA
1 AATAACTCCAACTTATTGAATCACACAAACAAGTGAAGATCTAAATCGACCTTACATTTATTTGA
*
9191 CACCCCAAACGGAAAGGCACTTATCGGAGC
66 CACCCCAAAAGGAAAGGCACTTATCGGAGC
*
9221 AATAACTCCAACTTATTGAATCACACATACAAGTGAAGATCTAAATCGACCTTACATTTATTTGA
1 AATAACTCCAACTTATTGAATCACACAAACAAGTGAAGATCTAAATCGACCTTACATTTATTTGA
*
9286 CACCCCAAAAGGAAAGGCACTTGTCGGAGC
66 CACCCCAAAAGGAAAGGCACTTATCGGAGC
9316 AA
1 AA
9318 AGCATTACAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (95 bp):
AATAACTCCAACTTATTGAATCACACAAACAAGTGAAGATCTAAATCGACCTTACATTTATTTGA
CACCCCAAAAGGAAAGGCACTTATCGGAGC
Found at i:11994 original size:22 final size:22
Alignment explanation
Indices: 11966--12013 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
11956 TCTAATTTTT
*
11966 TATAATTTCTTAATCATTAATA
1 TATAATTTCTTAATAATTAATA
* *
11988 TATAATTTTTTAATAATTAATT
1 TATAATTTCTTAATAATTAATA
12010 TATA
1 TATA
12014 TCAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TATAATTTCTTAATAATTAATA
Found at i:12020 original size:32 final size:32
Alignment explanation
Indices: 11958--12020 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
11948 TAAAAAAATC
** *
11958 TAATTTTTTATAATTTCTTAATCATTAATATA
1 TAATTTTTTATAATTAATTAATCATCAATATA
*
11990 TAATTTTTTAATAATTAATTTAT-ATCAATAT
1 TAATTTTTT-ATAATTAATTAATCATCAATAT
12021 TTTAAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (32 bp):
TAATTTTTTATAATTAATTAATCATCAATATA
Found at i:12023 original size:26 final size:23
Alignment explanation
Indices: 11966--12037 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 23
11956 TCTAATTTTT
* *
11966 TATAAT-TTCTTAATCATTAATA
1 TATAATATTTTTAATAATTAATA
11988 TATAAT-TTTTTAATAATTAATTTA
1 TATAATATTTTTAATAATTAA--TA
* * *
12012 TATCAATATTTTAAATATTTATTA
1 TAT-AATATTTTTAATAATTAATA
12036 TA
1 TA
12038 ACATAATCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 18 0.44
24 9 0.22
25 3 0.07
26 11 0.27
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TATAATATTTTTAATAATTAATA
Found at i:17298 original size:6 final size:6
Alignment explanation
Indices: 17287--17315 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17277 ACACCAGACA
17287 CGGTGC CGGTGC CGGTGC CGGTGC CGGTG
1 CGGTGC CGGTGC CGGTGC CGGTGC CGGTG
17316 TCATGTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.52, T:0.17
Consensus pattern (6 bp):
CGGTGC
Found at i:18727 original size:21 final size:21
Alignment explanation
Indices: 18702--18749 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
18692 CATAATATTG
18702 CAATGTCAAAATTAAGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
18723 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAAGTGCAA
*
18744 TAATGT
1 CAATGT
18750 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAAGTGCAA
Found at i:23374 original size:21 final size:21
Alignment explanation
Indices: 23349--23396 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
23339 CCTAATATTG
23349 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
23370 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
23391 TAATGT
1 CAATGT
23397 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:27161 original size:25 final size:26
Alignment explanation
Indices: 27109--27161 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
27099 AAAATTTACA
* * *
27109 TTGATTAAAAAATATTTTAATTATAT
1 TTGAATAAAAAATAGTTTAAATATAT
*
27135 TTGAATAAAAATTAGTTTAAATA-AT
1 TTGAATAAAAAATAGTTTAAATATAT
27160 TT
1 TT
27162 TATAAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (26 bp):
TTGAATAAAAAATAGTTTAAATATAT
Found at i:29476 original size:45 final size:45
Alignment explanation
Indices: 29421--29513 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
29411 CTTCGCCTTA
*
29421 TCTAATAACCGACAACTGCTCTCTCATTGCCATTTTTCTTCTTTT
1 TCTAATAACCGACAACCGCTCTCTCATTGCCATTTTTCTTCTTTT
29466 TCTAATAACCGACAACCGCTCTCTCATTGCCATTTTTCTTCTTTT
1 TCTAATAACCGACAACCGCTCTCTCATTGCCATTTTTCTTCTTTT
29511 TCT
1 TCT
29514 CCTACGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.44
Consensus pattern (45 bp):
TCTAATAACCGACAACCGCTCTCTCATTGCCATTTTTCTTCTTTT
Found at i:33990 original size:3 final size:3
Alignment explanation
Indices: 33984--34010 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33974 GACGATGGTG
33984 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
34011 TCCCATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51836 original size:14 final size:13
Alignment explanation
Indices: 51817--51847 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
51807 TACTTACCTC
51817 ATATTAATAATAAA
1 ATATTAATAA-AAA
51831 ATATTAATAAAAA
1 ATATTAATAAAAA
51844 ATAT
1 ATAT
51848 AAGTTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATTAATAAAAA
Found at i:56213 original size:28 final size:30
Alignment explanation
Indices: 56175--56230 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
56165 AAAGTACATG
56175 AATGATCCCT-CGACTATTA-AACGTTACAA
1 AATGATCCCTCCGACTA-TAGAACGTTACAA
56204 AATGAT-CCTCCGACTATAGAACGTTAC
1 AATGATCCCTCCGACTATAGAACGTTAC
56231 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (30 bp):
AATGATCCCTCCGACTATAGAACGTTACAA
Found at i:62236 original size:61 final size:61
Alignment explanation
Indices: 62170--62286 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
62160 TCGGTTTGTC
* * *
62170 TTATTTTATTTTTTAGTCTCTTAAATCTCGTTAGTTTAATGATGTGACACATTAGTCTATT
1 TTATTTTATTCTTTAGTATCTTAAATCTCGTTAATTTAATGATGTGACACATTAGTCTATT
* * * * *
62231 TTATTTTGTTCTTTAGTATGTTAACTCTCGTTAATTTAATGATGTGATATATTAGT
1 TTATTTTATTCTTTAGTATCTTAAATCTCGTTAATTTAATGATGTGACACATTAGT
62287 AAACAAACCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (61 bp):
TTATTTTATTCTTTAGTATCTTAAATCTCGTTAATTTAATGATGTGACACATTAGTCTATT
Found at i:66010 original size:31 final size:31
Alignment explanation
Indices: 65972--66030 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
65962 ATATTCAGCA
* *
65972 CGTATTTCTTAATCATTAACATCACACAAAT
1 CGTATTTCTTAATAATTAACAACACACAAAT
*
66003 CGTATTTCTTAATAATTGACAACACACA
1 CGTATTTCTTAATAATTAACAACACACA
66031 CCATATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (31 bp):
CGTATTTCTTAATAATTAACAACACACAAAT
Found at i:69884 original size:21 final size:23
Alignment explanation
Indices: 69859--69900 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
69849 TGAACACATG
69859 ATAAAAGTTAAA-A-TTTAAACT
1 ATAAAAGTTAAAGAGTTTAAACT
*
69880 ATAAAATTTAAAGAGTTTAAA
1 ATAAAAGTTAAAGAGTTTAAA
69901 AACTAATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
ATAAAAGTTAAAGAGTTTAAACT
Found at i:82939 original size:18 final size:18
Alignment explanation
Indices: 82916--82950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
82906 TTCCATCCGG
*
82916 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
82934 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
82951 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:87158 original size:23 final size:23
Alignment explanation
Indices: 87132--87192 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
87122 TTGATGACAT
* *
87132 GTTTATCTCTGTCTTTTTGGTAC
1 GTTTATCTCTATCTTTGTGGTAC
*
87155 GTTTATCTCTATCTTTGTGGTAT
1 GTTTATCTCTATCTTTGTGGTAC
*
87178 ATTTATCTCTA-CTTT
1 GTTTATCTCTATCTTT
87193 TCTGTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.57
Consensus pattern (23 bp):
GTTTATCTCTATCTTTGTGGTAC
Found at i:103053 original size:10 final size:10
Alignment explanation
Indices: 103038--103064 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
103028 CCAAGCAGAG
103038 CTTCCTCTCA
1 CTTCCTCTCA
103048 CTTCCTCTCA
1 CTTCCTCTCA
103058 CTTCCTC
1 CTTCCTC
103065 CATAGCCGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (10 bp):
CTTCCTCTCA
Done.