Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002604.1 Hibiscus syriacus cultivar Beakdansim tig00005265_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: 88391
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:373 original size:16 final size:16
Alignment explanation
Indices: 343--383 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
333 ATACAAAAGC
*
343 TATTAAAAA-ATTAAA
1 TATTAAAAATACTAAA
358 TATTAAAAATACTAAA
1 TATTAAAAATACTAAA
*
374 AATTAAAAAT
1 TATTAAAAAT
384 TAAATTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TATTAAAAATACTAAA
Found at i:378 original size:23 final size:22
Alignment explanation
Indices: 348--404 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
338 AAAGCTATTA
*
348 AAAAATTAAATATTAAAAATACT
1 AAAAATTAAAAATT-AAAATACT
*
371 AAAAATTAAAAATTAAATTACT
1 AAAAATTAAAAATTAAAATACT
393 -AAAATTAAAAAT
1 AAAAATTAAAAAT
405 ATATTATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 12 0.38
22 7 0.22
23 13 0.41
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATTAAAAATTAAAATACT
Found at i:397 original size:30 final size:28
Alignment explanation
Indices: 348--404 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
338 AAAGCTATTA
*
348 AAAAATTAAATATTAAAAATACTAAAAATT
1 AAAAATTAAATACTAAAAAT--TAAAAATT
378 AAAAATTAAATTACT-AAAATTAAAAAT
1 AAAAATTAAA-TACTAAAAATTAAAAAT
405 ATATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
30 15 0.60
31 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAATTAAATACTAAAAATTAAAAATT
Found at i:403 original size:7 final size:7
Alignment explanation
Indices: 348--404 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
338 AAAGCTATTA
348 AAAAATT
1 AAAAATT
*
355 AAATATT
1 AAAAATT
362 AAAAATACT
1 AAAAAT--T
371 AAAAATT
1 AAAAATT
378 AAAAATT
1 AAAAATT
385 --AAATT
1 AAAAATT
390 ACTAAAATT
1 A--AAAATT
399 AAAAAT
1 AAAAAT
405 ATATTATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 5 0.12
7 24 0.57
9 13 0.31
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAAATT
Found at i:8399 original size:21 final size:21
Alignment explanation
Indices: 8366--8463 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
8356 TTCATGTCAT
*
8366 AACT-TAAACCCTAACACATA
1 AACTCTAAATCCTAACACATA
8386 AACTCTAAATCCTAACACATA
1 AACTCTAAATCCTAACACATA
* *
8407 AACCCTAAA-CTCTAA-ACTTTA
1 AACTCTAAATC-CTAACAC-ATA
*
8428 AAC-CTTAAATCCTATCACATA
1 AACTC-TAAATCCTAACACATA
8449 AACTCTAAATCCTAA
1 AACTCTAAATCCTAA
8464 ACCCTAAACC
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
20 8 0.12
21 53 0.82
22 4 0.06
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (21 bp):
AACTCTAAATCCTAACACATA
Found at i:8416 original size:42 final size:42
Alignment explanation
Indices: 8370--8476 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
8360 TGTCATAACT
8370 TAAACCCTAACAC-ATAAA-CTCTAAATCCTAACACATAAACCC
1 TAAACCCTAA-ACTATAAACCT-TAAATCCTAACACATAAACCC
* * * *
8412 TAAACTCTAAACTTTAAACCTTAAATCCTATCACATAAACTC
1 TAAACCCTAAACTATAAACCTTAAATCCTAACACATAAACCC
* **
8454 TAAATCCTAAACCCTAAACCTTA
1 TAAACCCTAAACTATAAACCTTA
8477 TCACATAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (42 bp):
TAAACCCTAAACTATAAACCTTAAATCCTAACACATAAACCC
Found at i:8451 original size:35 final size:35
Alignment explanation
Indices: 8412--8484 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
8402 ACATAAACCC
* *
8412 TAAACTCTAAA-CTTTAAACCTTAAATCC-TATCACA
1 TAAACTCTAAATC-CTAAACCCTAAA-CCTTATCACA
8447 TAAACTCTAAATCCTAAACCCTAAACCTTATCACA
1 TAAACTCTAAATCCTAAACCCTAAACCTTATCACA
8482 TAA
1 TAA
8485 TTAGTTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 2 0.06
35 31 0.91
36 1 0.03
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (35 bp):
TAAACTCTAAATCCTAAACCCTAAACCTTATCACA
Found at i:8754 original size:14 final size:14
Alignment explanation
Indices: 8737--8779 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
8727 TATTTATTCA
8737 TTAATAATGTATTT
1 TTAATAATGTATTT
8751 TTAAT-A--TATTT
1 TTAATAATGTATTT
*
8762 TTAATAATGTAATT
1 TTAATAATGTATTT
8776 TTAA
1 TTAA
8780 AAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.40
12 1 0.04
13 1 0.04
14 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTAATAATGTATTT
Found at i:17457 original size:45 final size:45
Alignment explanation
Indices: 17401--17504 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
17391 ATGCACAGGA
* *
17401 AGTGCATCGATGCA-CCCATTAGAAATGGAAACATCAAATGCAATT
1 AGTGCATCGATGCACCCCATTA-AAATGAAAACATCAAAGGCAATT
* **
17446 AGTGCATCGATGCACCCCCTTAAAATGAAAACATCAAAGGTGATT
1 AGTGCATCGATGCACCCCATTAAAATGAAAACATCAAAGGCAATT
*
17491 AGTGTATCGATGCA
1 AGTGCATCGATGCA
17505 TGGGTAGTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 46 0.88
46 6 0.12
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGCATCGATGCACCCCATTAAAATGAAAACATCAAAGGCAATT
Found at i:17557 original size:20 final size:20
Alignment explanation
Indices: 17532--17569 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17522 CACATGTTAA
17532 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
17552 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
17570 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:21807 original size:14 final size:13
Alignment explanation
Indices: 21790--21839 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
21780 GTGCAAAAAG
21790 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
21804 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
21817 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
21828 AAAGAAAAAGAA
1 AAAGAAAAAGAA
21840 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:21836 original size:19 final size:18
Alignment explanation
Indices: 21784--21839 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
21774 ATTGGAGTGC
21784 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
21801 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
21820 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
21839 A
1 A
21840 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:21837 original size:11 final size:11
Alignment explanation
Indices: 21784--21853 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
21774 ATTGGAGTGC
21784 AAAAAG-AAAG
1 AAAAAGAAAAG
21794 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
21808 AAGAAGAAAAG
1 AAAAAGAAAAG
21819 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
***
21832 AAAAAGAATTC
1 AAAAAGAAAAG
21843 AAAAAGAAAAG
1 AAAAAGAAAAG
21854 CAAAGCCAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
10 6 0.13
11 20 0.43
12 2 0.04
13 9 0.20
14 9 0.20
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:30891 original size:21 final size:21
Alignment explanation
Indices: 30865--30911 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
30855 TAATTTTCAA
30865 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
30886 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
30907 ACATT
1 ACATT
30912 GCAATATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:35541 original size:21 final size:21
Alignment explanation
Indices: 35511--35558 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
35501 TAATTTTCAA
*
35511 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
35532 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
35553 ACATTG
1 ACATTG
35559 CAATATTAGG
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:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:55593 original size:11 final size:11
Alignment explanation
Indices: 55579--55604 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55569 AGGATAATTT
55579 GAAGTTAATAG
1 GAAGTTAATAG
55590 GAAGTTAATAG
1 GAAGTTAATAG
55601 GAAG
1 GAAG
55605 AGGGGTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (11 bp):
GAAGTTAATAG
Found at i:62832 original size:6 final size:6
Alignment explanation
Indices: 62821--62850 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
62811 ATTATATTAA
62821 TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT
62851 ATTAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:62930 original size:15 final size:15
Alignment explanation
Indices: 62906--62959 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
62896 TAAATAAGTA
62906 AATA-TTATATTAAT
1 AATATTTATATTAAT
*
62920 TATATTTATATTAAT
1 AATATTTATATTAAT
62935 AATATTTATATATTAAT
1 AATA-TT-TATATTAAT
62952 AATATTTA
1 AATATTTA
62960 ATTCTAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 3 0.09
15 15 0.43
16 4 0.11
17 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTTATATTAAT
Found at i:62948 original size:17 final size:17
Alignment explanation
Indices: 62911--62959 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
62901 AAGTAAATAT
*
62911 TATATTAATTATA-TT-
1 TATATTAATAATATTTA
62926 TATATTAATAATATTTA
1 TATATTAATAATATTTA
62943 TATATTAATAATATTTA
1 TATATTAATAATATTTA
62960 ATTCTAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 12 0.39
16 2 0.06
17 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTAATAATATTTA
Found at i:71437 original size:65 final size:63
Alignment explanation
Indices: 71368--71527 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
71358 AATTAAATTG
* *
71368 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
71432 A
63 A
* * * *
71433 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
71497 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
71528 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:71527 original size:17 final size:19
Alignment explanation
Indices: 71499--71547 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
71489 TATTTTGAAA
71499 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
71517 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
71536 CACCGATGCACT
1 CATCGATGCACT
71548 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:79240 original size:19 final size:19
Alignment explanation
Indices: 79195--79240 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
79185 GAATGCATTT
*
79195 GATGCACCAGCCATGCATC
1 GATGCACTAGCCATGCATC
79214 GATGCACTAGCCATGCATC
1 GATGCACTAGCCATGCATC
79233 GATGCACT
1 GATGCACT
79241 CTGGCTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (19 bp):
GATGCACTAGCCATGCATC
Done.