Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000666.1 Hibiscus syriacus cultivar Beakdansim tig00001296_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: 53363
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:353 original size:12 final size:12
Alignment explanation
Indices: 336--360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
326 ATTCTAATAA
336 TCCTTTTTTTTT
1 TCCTTTTTTTTT
348 TCCTTTTTTTTT
1 TCCTTTTTTTTT
360 T
1 T
361 TGGGTTGGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCCTTTTTTTTT
Found at i:6988 original size:2 final size:2
Alignment explanation
Indices: 6981--7018 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6971 TAAATGCATT
6981 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7019 GCGCGCGCGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7374 original size:14 final size:14
Alignment explanation
Indices: 7355--7385 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
7345 CATTCATGTA
7355 ATTTTAAAAAAAAT
1 ATTTTAAAAAAAAT
7369 ATTTTAAAAAAAAT
1 ATTTTAAAAAAAAT
7383 ATT
1 ATT
7386 ATACTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTTAAAAAAAAT
Found at i:8329 original size:14 final size:14
Alignment explanation
Indices: 8312--8356 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
8302 GTTCAGTTAT
*
8312 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
*
8326 GTTCGGTTATATTC
1 GTTCGGTTATGTTC
8340 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
8354 GTT
1 GTT
8357 TATGTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.53
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:9653 original size:21 final size:21
Alignment explanation
Indices: 9620--9660 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9610 CTCTGGGCAA
* *
9620 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
9641 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
9661 CGAACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:10532 original size:11 final size:11
Alignment explanation
Indices: 10516--10543 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10506 GAGTAAGTTT
10516 ATAGGATATTG
1 ATAGGATATTG
10527 ATAGGATATTG
1 ATAGGATATTG
10538 ATAGGA
1 ATAGGA
10544 CATATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (11 bp):
ATAGGATATTG
Found at i:11335 original size:149 final size:147
Alignment explanation
Indices: 11024--11328 Score: 547
Period size: 149 Copynumber: 2.1 Consensus size: 147
11014 GAGTCGAGGG
* *
11024 TCTACGCGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TCTACGCGGTCCTTCGGGACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
*
11089 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
11154 TGGCACTACGATGCAAT
131 TGGCACTACGATGCAAT
*
11171 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGG--ACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
11236 ACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
64 ACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
11301 TATGGCACTACGGTGCAAT
129 TATGGCACTACGATGCAAT
11320 TCTACGCGG
1 TCTACGCGG
11329 CACTTCGTGC
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 18 0.12
149 133 0.88
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
TGGCACTACGATGCAAT
Found at i:11340 original size:22 final size:23
Alignment explanation
Indices: 11304--11347 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11294 ATTATTATAT
*
11304 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
11327 GGCACTTC-GTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
11348 AGCTGTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:14654 original size:21 final size:21
Alignment explanation
Indices: 14611--14655 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14601 GATTTCTGGG
* * *
14611 CAAGGGGAATCGGTACTCATT
1 CAAGGGGAACCGATACCCATT
*
14632 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
14653 CAA
1 CAA
14656 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:15544 original size:11 final size:11
Alignment explanation
Indices: 15528--15555 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
15518 GAGTAAGTTT
15528 ATAGGATATTG
1 ATAGGATATTG
15539 ATAGGATATTG
1 ATAGGATATTG
15550 ATAGGA
1 ATAGGA
15556 CATATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (11 bp):
ATAGGATATTG
Found at i:16299 original size:30 final size:30
Alignment explanation
Indices: 16243--16396 Score: 274
Period size: 30 Copynumber: 5.1 Consensus size: 30
16233 GAAGGACCTA
* *
16243 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
16272 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
16302 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
16332 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
16362 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
16393 TCCA
1 TCCA
16397 TATGTCTCGA
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
29 16 0.13
30 96 0.79
31 9 0.07
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:17149 original size:22 final size:22
Alignment explanation
Indices: 17105--17146 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17095 TAAATCAATT
*
17105 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
17127 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
17147 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:17624 original size:21 final size:21
Alignment explanation
Indices: 17594--17638 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17584 ATTCTGTCGT
* *
17594 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17615 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17636 TTG
1 TTG
17639 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18894 original size:149 final size:149
Alignment explanation
Indices: 18713--19027 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
18703 GAGTCGAGGG
* **
18713 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGCGGAACATGTGTGAAGTCTTGAAAGACACAT
*
18778 ACTTGATCCCTAGTATATGTATATGATTCTTAAGAAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAATATATGTATATGATTCTTAAGAAATAATATGTGGTCCTTATGGACATTATTA
18843 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
18862 TCTACGCGGTCCTTCGGGATATATATATATTCTGCGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGCGGAACATGTGTGAAGTCTTGAAAGACACAT
*
18927 ACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAATATATGTATATGATTCTTAAGAAATAATATGTGGTCCTTATGGACATTATTA
18992 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
19011 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
19028 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGCGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAATATATGTATATGATTCTTAAGAAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:19028 original size:23 final size:23
Alignment explanation
Indices: 18995--19039 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
18985 ATTATTATAT
*
18995 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
19018 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
19040 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:22351 original size:21 final size:21
Alignment explanation
Indices: 22325--22369 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22315 GATTTCTGGG
* *
22325 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
22346 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
22367 CAA
1 CAA
22370 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:23262 original size:11 final size:11
Alignment explanation
Indices: 23246--23273 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
23236 GAGTAAGTTT
23246 ATAGGATATTG
1 ATAGGATATTG
23257 ATAGGATATTG
1 ATAGGATATTG
23268 ATAGGA
1 ATAGGA
23274 CATATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (11 bp):
ATAGGATATTG
Found at i:24775 original size:16 final size:16
Alignment explanation
Indices: 24754--24820 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
24744 GTCTCCAACG
24754 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
24770 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
24786 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
24802 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
24816 TTTAT
1 TTTAT
24821 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:24793 original size:32 final size:32
Alignment explanation
Indices: 24752--24812 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
24742 GGGTCTCCAA
24752 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
24784 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
24813 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:25273 original size:16 final size:16
Alignment explanation
Indices: 25262--25295 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
25252 TGTTTTCATC
25262 ATATGAAATTTTATAA
1 ATATGAAATTTTATAA
25278 ATATGAAATTTTATAA
1 ATATGAAATTTTATAA
25294 AT
1 AT
25296 TCGTCAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
ATATGAAATTTTATAA
Found at i:49186 original size:2 final size:2
Alignment explanation
Indices: 49175--49204 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49165 AATATAGGAC
49175 TA TA -A 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 T
49205 TGGTTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.