Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001958.1 Hibiscus syriacus cultivar Beakdansim tig00003962_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: 49963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:262 original size:2 final size:2
Alignment explanation
Indices: 255--284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
245 TAGCAGCTTA
255 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
285 TGGCTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4443 original size:15 final size:15
Alignment explanation
Indices: 4423--4494 Score: 90
Period size: 15 Copynumber: 4.7 Consensus size: 15
4413 CCGGATGTTA
4423 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
4438 CGGGTATCCGGATTTT
1 CGGGTACCCGG-TAAT
4454 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
*
4470 CGGGTACCCGATAAT
1 CGGGTACCCGGTAAT
4485 CGGGTACCCG
1 CGGGTACCCG
4495 ATACCCGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
15 34 0.71
16 4 0.08
17 10 0.21
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.22
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:4447 original size:32 final size:32
Alignment explanation
Indices: 4411--4475 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
4401 CCGTGTCCCG
4411 ATCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ATCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
4443 ATCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ATCCGGATGTTACGGGTACCCGGTAATCGGGT
4475 A
1 A
4476 CCCGATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.18, C:0.22, G:0.34, T:0.26
Consensus pattern (32 bp):
ATCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:6460 original size:21 final size:23
Alignment explanation
Indices: 6429--6470 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6419 AAATAAAATA
*
6429 TAAAAATTTTATTAAT-AAAGAG
1 TAAAAATTTTAATAATGAAAGAG
6451 TAAAAA-TTTAATAATGAAAG
1 TAAAAATTTTAATAATGAAAG
6471 TTTATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (23 bp):
TAAAAATTTTAATAATGAAAGAG
Found at i:7932 original size:18 final size:18
Alignment explanation
Indices: 7909--8001 Score: 114
Period size: 18 Copynumber: 4.9 Consensus size: 18
7899 ACTAAATATT
7909 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
7927 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
7946 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* *
7965 TGTCCCGAAGGACCATTGTT
1 TGTCCCGAAGGACCA--CTA
7985 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
8002 GATAATCCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
18 31 0.48
19 2 0.03
20 31 0.48
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:7956 original size:20 final size:20
Alignment explanation
Indices: 7908--8004 Score: 130
Period size: 20 Copynumber: 5.0 Consensus size: 20
7898 CACTAAATAT
7908 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
7927 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
7946 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
7965 -TGTCCCGAAGGACCATTGT
1 TTGTCCCGAAGGACCACTGA
7984 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
8004 T
1 T
8005 AATCCCTCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
18 31 0.47
19 2 0.03
20 33 0.50
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:7964 original size:38 final size:38
Alignment explanation
Indices: 7908--8001 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
7898 CACTAAATAT
7908 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
* * * *
7946 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCATTGT
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
7984 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
8002 GATAATCCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
Found at i:12417 original size:18 final size:18
Alignment explanation
Indices: 12394--12466 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
12384 ACTGAATATT
12394 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
12412 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
12431 TTGTTCCGAAGAACCAATA
1 -TGTCCCGAAGGACCACTA
12450 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
12467 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:12441 original size:38 final size:38
Alignment explanation
Indices: 12393--12469 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
12383 CACTGAATAT
* *
12393 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCAATATGTCCCGAAGGACCACTGA
*
12431 TTGTTCCGAAGAACCAATATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCAATATGTCCCGAAGGACCACTGA
12469 T
1 T
12470 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCAATATGTCCCGAAGGACCACTGA
Found at i:13809 original size:13 final size:13
Alignment explanation
Indices: 13791--13815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13781 ACGGGAGGAG
13791 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
13804 AGGAAGAAGAAG
1 AGGAAGAAGAAG
13816 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:20500 original size:28 final size:28
Alignment explanation
Indices: 20447--20501 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
20437 CGCTTGTATA
* **
20447 ATATATGATCGATTTTACCTTTTAAATC
1 ATATATGATCGATTCTACCTCCTAAATC
*
20475 ATATATGATCGATTCTATCTCCTAAAT
1 ATATATGATCGATTCTACCTCCTAAAT
20502 AATAAATGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (28 bp):
ATATATGATCGATTCTACCTCCTAAATC
Found at i:26001 original size:96 final size:96
Alignment explanation
Indices: 25837--26023 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
25827 TTTCCGTGAT
** * * *
25837 AAATCTGCATTTGAGTGTGATTTTCATTCGCTTGGTGCTGAAGAAAGACTGGTAGGGTCTGAAAT
1 AAATCTGCATTTGAACGTGATTTTCATTCACTGGGTGCTGAAGAAAGACAGGTAGGGTCTGAAAT
*
25902 AGGAAGGGTTTCATCTCCTGGCTTGATTAAC
66 AGGAAGAGTTTCATCTCCTGGCTTGATTAAC
* * * *
25933 AAATCTGCTTTTGAACGTGATTTTCCTTCACTGGGTGCTGAAGAAAGACAGTTTA-GGTCTGAAT
1 AAATCTGCATTTGAACGTGATTTTCATTCACTGGGTGCTGAAGAAAGACAG-GTAGGGTCTGAAA
25997 TAGGAAGAGTTTCATCTCCTGGCTTGA
65 TAGGAAGAGTTTCATCTCCTGGCTTGA
26024 ATAATCTTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 78 0.98
97 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (96 bp):
AAATCTGCATTTGAACGTGATTTTCATTCACTGGGTGCTGAAGAAAGACAGGTAGGGTCTGAAAT
AGGAAGAGTTTCATCTCCTGGCTTGATTAAC
Found at i:32128 original size:2 final size:2
Alignment explanation
Indices: 32121--32151 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32111 TGAAGAGCAA
32121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32152 GTGGCAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.