Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005359.1 Hibiscus syriacus cultivar Beakdansim tig00012171_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: 43772
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:284 original size:22 final size:21
Alignment explanation
Indices: 256--331 Score: 86
Period size: 20 Copynumber: 3.7 Consensus size: 21
246 ACACCTAACA
256 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCA-CCTTGAAT
* * *
278 GTGCATCGATACA-CATGAAG
1 GTGCATCGATGCACCTTGAAT
298 GTGCA-CGATGCACCCTTGAAT
1 GTGCATCGATGCA-CCTTGAAT
319 G-GCATCGATGCAC
1 GTGCATCGATGCAC
332 AGGGTCATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.13
20 14 0.31
21 13 0.29
22 12 0.27
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACCTTGAAT
Found at i:301 original size:20 final size:20
Alignment explanation
Indices: 237--306 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
227 TTGTGGTTCA
*
237 TGCATCGATACACCT-AACAG
1 TGCATCGATACACATGAA-AG
* * *
257 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA--CATGAAAG
*
279 TGCATCGATACACATGAAGG
1 TGCATCGATACACATGAAAG
299 TGCA-CGAT
1 TGCATCGAT
307 GCACCCTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 21 0.51
22 14 0.34
23 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (20 bp):
TGCATCGATACACATGAAAG
Found at i:302 original size:42 final size:41
Alignment explanation
Indices: 237--332 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 41
227 TTGTGGTTCA
* *
237 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACATAACAGTGCA-CGATGCACCCTTGAATG
*
279 TGCATCGATACACATGAA-GGTGCACGATGCACCCTTGAATG
1 TGCATCGATACACAT-AACAGTGCACGATGCACCCTTGAATG
*
320 -GCATCGATGCACA
1 TGCATCGATACACA
333 GGGTCATGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 12 0.24
41 16 0.33
42 19 0.39
43 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
TGCATCGATACACATAACAGTGCACGATGCACCCTTGAATG
Found at i:348 original size:41 final size:42
Alignment explanation
Indices: 237--349 Score: 115
Period size: 41 Copynumber: 2.7 Consensus size: 42
227 TTGTGGTTCA
** *
237 TGCATCGATACAC-CTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACAGGAACA-TGCATCGATGCACCCTTGAATG
* **
279 TGCATCGATACACATGAAGGTGCA-CGATGCACCCTTGAATG
1 TGCATCGATACACAGGAACATGCATCGATGCACCCTTGAATG
* **
320 -GCATCGATGCACAGGGTCATGCATCGATGC
1 TGCATCGATACACAGGAACATGCATCGATGC
350 CCCGTCGGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
40 17 0.29
41 22 0.38
42 17 0.29
43 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (42 bp):
TGCATCGATACACAGGAACATGCATCGATGCACCCTTGAATG
Found at i:3144 original size:64 final size:63
Alignment explanation
Indices: 2938--3147 Score: 210
Period size: 65 Copynumber: 3.3 Consensus size: 63
2928 TTTATCAAAG
* * * **
2938 TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCAATGCACC-A-CCATGCATCGATGCACTATGGA-TATTTTGAAACATCGAATGCAT
3002 T
63 T
* * * *
3003 TCATGCATCGATGCACTTACCATGCACCGATGCACTGA-GGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCAATGCAC-CACCATGCATCGATGCACT-ATGGATATTT-TG-AAACATCGAATGCA
3066 TT
62 TT
* * * *
3068 TGATGCATCAATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGAAACACCGAATGCACT
1 TGATGCATCAATGCACCA-CCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCATT
3132 TGATGCATCAATGCAC
1 TGATGCATCAATGCAC
3148 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 48 0.39
65 67 0.55
66 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
TGATGCATCAATGCACCACCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCATT
Found at i:3163 original size:64 final size:63
Alignment explanation
Indices: 2988--3167 Score: 159
Period size: 65 Copynumber: 2.8 Consensus size: 63
2978 AATTAAATTG
* * * * * *
2988 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACACCGAATGCACTTGATGCATCAATGCAC-CAGC-TGCACCGATGCACTGAGGATTTTATGAA
* * * ** *
3053 AACATCGAATGCATTTGATGCATCAATGCACCAGCCATGCATCGATGCACTTTGGCTATTT-TG-
1 AACACCGAATGCACTTGATGCATCAATGCACCAG-C-TGCACCGATGCACTGAGGAT-TTTATGA
3116 A
63 A
3117 AACACCGAATGCACTTGATGCATCAATGCACTCTTAG-TGCACCGATGCACT
1 AACACCGAATGCACTTGATGCATCAATGCAC-C--AGCTGCACCGATGCACT
3168 AAGGGTTCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 44 0.44
65 50 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (63 bp):
AACACCGAATGCACTTGATGCATCAATGCACCAGCTGCACCGATGCACTGAGGATTTTATGAA
Found at i:12097 original size:32 final size:32
Alignment explanation
Indices: 12055--12119 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
12045 TCTAAACCCT
*
12055 AAATTAAATTATTTTAGAATTTAGGATTTAAA
1 AAATTAAATTACTTTAGAATTTAGGATTTAAA
* * *
12087 AAATTGAATTACTTTAGAATTTGGGGTTTAAA
1 AAATTAAATTACTTTAGAATTTAGGATTTAAA
12119 A
1 A
12120 TATAATTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.42
Consensus pattern (32 bp):
AAATTAAATTACTTTAGAATTTAGGATTTAAA
Found at i:12488 original size:7 final size:7
Alignment explanation
Indices: 12476--12529 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
12466 AGGGTTGGTT
12476 GGAATTA
1 GGAATTA
12483 GGAATTA
1 GGAATTA
12490 GGAATTA
1 GGAATTA
12497 GGAATTA
1 GGAATTA
12504 GGAATTA
1 GGAATTA
12511 GGAATTA
1 GGAATTA
12518 GGAATTA
1 GGAATTA
12525 GGAAT
1 GGAAT
12530 ATAAATTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (7 bp):
GGAATTA
Found at i:13683 original size:16 final size:17
Alignment explanation
Indices: 13662--13696 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
13652 TTACTATTCA
13662 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
13678 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
13695 CG
1 CG
13697 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:17769 original size:15 final size:15
Alignment explanation
Indices: 17745--17774 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17735 TGGCAACCAA
*
17745 CTTTGGAAAATGTTT
1 CTTTGAAAAATGTTT
17760 CTTTGAAAAATGTTT
1 CTTTGAAAAATGTTT
17775 TTCAAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
CTTTGAAAAATGTTT
Found at i:19384 original size:14 final size:14
Alignment explanation
Indices: 19365--19423 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
19355 TTTTTAAAAA
19365 ATAATAATAATAAT
1 ATAATAATAATAAT
19379 ATAATAATAATGAAT
1 ATAATAATAAT-AAT
* *
19394 A-AA-AA-AACGAAA
1 ATAATAATAA-TAAT
*
19406 ATAATAAAAATAAT
1 ATAATAATAATAAT
19420 ATAA
1 ATAA
19424 AGTTATAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 21 0.58
15 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:19696 original size:16 final size:17
Alignment explanation
Indices: 19664--19697 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19654 TATATACATA
*
19664 ATAATAATAACATGAAT
1 ATAAAAATAACATGAAT
19681 ATAAAAATAA-ATGAAT
1 ATAAAAATAACATGAAT
19697 A
1 A
19698 AATATCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
ATAAAAATAACATGAAT
Found at i:25680 original size:31 final size:31
Alignment explanation
Indices: 25644--25749 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
25634 CAAATTAAAT
*
25644 GTTTTGATCACTTACGTTATTGTTTTATTAA
1 GTTTTGATCACTTACGTTATCGTTTTATTAA
*
25675 GTTTTGATCACTTACGCTATCGTTTTATTAA
1 GTTTTGATCACTTACGTTATCGTTTTATTAA
* * *
25706 GTTTTGGTCACTTATGTTATCATTTTATTAA
1 GTTTTGATCACTTACGTTATCGTTTTATTAA
*
25737 GTTTTGGTCACTT
1 GTTTTGATCACTT
25750 GAACGTTGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (31 bp):
GTTTTGATCACTTACGTTATCGTTTTATTAA
Found at i:28355 original size:27 final size:27
Alignment explanation
Indices: 28323--28384 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
28313 AAGACGACGA
*
28323 GGTGACGCGTGAGCATCGCGCGTCAAT
1 GGTGACGCGTGAGCATCGCGCGTCAAC
*
28350 GGTGACGCGTGAGTATCGCGCGTCAAC
1 GGTGACGCGTGAGCATCGCGCGTCAAC
28377 GGTGACGC
1 GGTGACGC
28385 CACCATGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.39, T:0.18
Consensus pattern (27 bp):
GGTGACGCGTGAGCATCGCGCGTCAAC
Found at i:30535 original size:24 final size:25
Alignment explanation
Indices: 30501--30547 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
30491 TTTCACCTCT
*
30501 TTTTCTTTTCT-TTTATTTTTCTCC
1 TTTTCTATTCTATTTATTTTTCTCC
*
30525 TTTTCTATTCTATTTCTTTTTCT
1 TTTTCTATTCTATTTATTTTTCT
30548 TTTCTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTCTATTCTATTTATTTTTCTCC
Found at i:30549 original size:36 final size:34
Alignment explanation
Indices: 30502--30572 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 34
30492 TTCACCTCTT
30502 TTTCTTTTCTTTTAT-TTTTCTCCTTTTCTATTCTA
1 TTTCTTTTCTTTTATATTTT-TCCTTTT-TATTCTA
* *
30537 TTTCTTTTTCTTTTCTATTTTTCCTTTTTTTTCTA
1 TTTC-TTTTCTTTTATATTTTTCCTTTTTATTCTA
30572 T
1 T
30573 AAAGATTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 11 0.34
36 17 0.53
37 4 0.12
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTCTTTTCTTTTATATTTTTCCTTTTTATTCTA
Found at i:30559 original size:30 final size:29
Alignment explanation
Indices: 30503--30559 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
30493 TCACCTCTTT
*
30503 TTCTTTTCTTTTATTTTTCTCCTTTTCTA
1 TTCTTTTCTTTTATTTTTCTACTTTTCTA
*
30532 TTCTATTTCTTTT-TCTTTTCTATTTTTC
1 TTCT-TTTCTTTTAT-TTTTCTACTTTTC
30560 CTTTTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (29 bp):
TTCTTTTCTTTTATTTTTCTACTTTTCTA
Found at i:31253 original size:21 final size:19
Alignment explanation
Indices: 31210--31256 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
31200 TGAACCCTTC
* *
31210 TTTTCTTTTTCTATTTTTC
1 TTTTCTTTTTCTAATTTTA
31229 TTTTCTTTTTCCTTAATTTTA
1 TTTTCTTTTT-C-TAATTTTA
31250 TTTTCTT
1 TTTTCTT
31257 CAAGCGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 1 0.04
21 13 0.54
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTCTAATTTTA
Found at i:36545 original size:19 final size:19
Alignment explanation
Indices: 36507--36544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36497 GTCACGTGAG
36507 ATTATTTTCTTCTTATTTT
1 ATTATTTTCTTCTTATTTT
*
36526 ATTATTTATCTTTTTATTT
1 ATTATTT-TCTTCTTATTT
36545 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTATTTTCTTCTTATTTT
Done.