Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008435.1 Hibiscus syriacus cultivar Beakdansim tig00111233_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: 43738
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11440 original size:16 final size:16
Alignment explanation
Indices: 11419--11476 Score: 116
Period size: 16 Copynumber: 3.6 Consensus size: 16
11409 CGCGATCGTG
11419 GTGACGGGCGGCACGT
1 GTGACGGGCGGCACGT
11435 GTGACGGGCGGCACGT
1 GTGACGGGCGGCACGT
11451 GTGACGGGCGGCACGT
1 GTGACGGGCGGCACGT
11467 GTGACGGGCG
1 GTGACGGGCG
11477 ACAAGGACAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.12, C:0.24, G:0.52, T:0.12
Consensus pattern (16 bp):
GTGACGGGCGGCACGT
Found at i:13540 original size:15 final size:17
Alignment explanation
Indices: 13520--13556 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
13510 TTTTATTAAT
13520 TATTATTTA-AA-TGTA
1 TATTATTTATAATTGTA
13535 TATTATTTATAATTGTA
1 TATTATTTATAATTGTA
13552 -ATTAT
1 TATTAT
13557 AATACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 7 0.35
17 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TATTATTTATAATTGTA
Found at i:15943 original size:20 final size:21
Alignment explanation
Indices: 15893--15943 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
15883 CCGTTTGAGC
*
15893 GATCGATTGACCATTGATTGTT
1 GATCG-TTGACCATTGAATGTT
15915 GA-C-TATGACCATTGAAT-TT
1 GATCGT-TGACCATTGAATGTT
15934 GATCGTTGAC
1 GATCGTTGAC
15944 TTTTTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 2 0.08
22 2 0.08
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (21 bp):
GATCGTTGACCATTGAATGTT
Found at i:16450 original size:2 final size:2
Alignment explanation
Indices: 16443--16501 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
16433 ATGATATGAT
16443 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
16485 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
16502 GTATGTATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16684 original size:29 final size:29
Alignment explanation
Indices: 16617--16719 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
16607 GGCATAATCT
* *
16617 CCGTCCTGATTCTGCATGAGATTTATTCC
1 CCGTACTGATTCTGCATAAGATTTATTCC
*
16646 TCGTACTGATTCTGCATAAGATTTATTCC
1 CCGTACTGATTCTGCATAAGATTTATTCC
* * * ** *
16675 CC-TTCATGATTTTGCAT-GGGCTTAGTCC
1 CCGTAC-TGATTCTGCATAAGATTTATTCC
*
16703 CCGTTCTGATTCTGCAT
1 CCGTACTGATTCTGCAT
16720 GGGACCTCAT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
28 21 0.34
29 40 0.66
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (29 bp):
CCGTACTGATTCTGCATAAGATTTATTCC
Found at i:19808 original size:37 final size:33
Alignment explanation
Indices: 19745--19861 Score: 148
Period size: 32 Copynumber: 3.5 Consensus size: 33
19735 CTTTATTTTG
*
19745 TTCGGGT-GGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGGTCGGTTTTTTTAAGTGTGATA
*
19777 TTCGGGTCGAGTCGGTCTGGTTTTTTTAAGTGTGCTA
1 TTCGGGTCG-G--GGTC-GGTTTTTTTAAGTGTGATA
*
19814 TTCAGGTC-GGGTCGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGGTCGGTTTTTTTAAGTGTGATA
*
19846 TTCGGGTCGGGTTCGG
1 TTCGGGTCGGGGTCGG
19862 GTTTAGGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
32 32 0.44
33 11 0.15
34 1 0.01
35 1 0.01
36 4 0.05
37 24 0.33
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.41
Consensus pattern (33 bp):
TTCGGGTCGGGGTCGGTTTTTTTAAGTGTGATA
Found at i:20429 original size:18 final size:18
Alignment explanation
Indices: 20391--20438 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
20381 ATATAGAGTT
*
20391 AGATTCCAATT-CTTGAC
1 AGATTCCAATTCCTTCAC
20408 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
20426 AGATTTCAATTCC
1 AGATTCCAATTCC
20439 CTCGTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:21446 original size:2 final size:2
Alignment explanation
Indices: 21439--21473 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21429 TATGCTTGTT
21439 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
21474 TTGTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30186 original size:18 final size:18
Alignment explanation
Indices: 30158--30193 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
30148 GCTGAGTATC
30158 AAATTATATTT-AATATT
1 AAATTATATTTAAATATT
30175 AAATTAATATTTAAATATT
1 AAATT-ATATTTAAATATT
30194 TTAAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 6 0.35
19 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTATATTTAAATATT
Found at i:31959 original size:3 final size:3
Alignment explanation
Indices: 31947--32010 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
31937 TTTTTATCCA
31947 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
31994 CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
32011 ATAAATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:32028 original size:11 final size:12
Alignment explanation
Indices: 32011--32044 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
32001 ATTATTATTA
*
32011 ATAAATATATAT
1 ATAAATAAATAT
32023 -TAAATAAATAT
1 ATAAATAAATAT
32034 ATAAATAAATA
1 ATAAATAAATA
32045 ATTACAGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAATAAATAT
Found at i:32030 original size:15 final size:14
Alignment explanation
Indices: 32006--32044 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
31996 TTATTATTAT
32006 TATTAATAAATATA
1 TATTAATAAATATA
32020 TATTAAATAAATATA
1 TATT-AATAAATATA
32035 TA--AATAAATA
1 TATTAATAAATA
32045 ATTACAGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.33
14 4 0.17
15 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:32477 original size:16 final size:16
Alignment explanation
Indices: 32452--32524 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 16
32442 ACCCCAACCT
32452 GAAA-AAAAAAACGGA
1 GAAAGAAAAAAACGGA
* *
32467 GACAGAAAAAAA--AA
1 GAAAGAAAAAAACGGA
* * * *
32481 GAGAGACAGAACCGGA
1 GAAAGAAAAAAACGGA
*
32497 GAAAGAAAAAAACAGA
1 GAAAGAAAAAAACGGA
32513 GAAAGAAAAAAA
1 GAAAGAAAAAAA
32525 AAACTACTAA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
14 9 0.21
15 3 0.07
16 31 0.72
ACGTcount: A:0.70, C:0.08, G:0.22, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAACGGA
Found at i:32477 original size:18 final size:18
Alignment explanation
Indices: 32454--32491 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
32444 CCCAACCTGA
32454 AAAAAAAAACG-GAGACAG
1 AAAAAAAAA-GAGAGACAG
32472 AAAAAAAAAGAGAGACAG
1 AAAAAAAAAGAGAGACAG
32490 AA
1 AA
32492 CCGGAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAGAGACAG
Done.