Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007786.1 Hibiscus syriacus cultivar Beakdansim tig00110071_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: 95711
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3229 original size:14 final size:14
Alignment explanation
Indices: 3210--3252 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3200 ATAAGATACT
* *
3210 ATCTATTCATCATC
1 ATCTATCCATCACC
3224 ATCTATCCATCACC
1 ATCTATCCATCACC
*
3238 ATC-CTCCATCACC
1 ATCTATCCATCACC
3251 AT
1 AT
3253 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:7546 original size:19 final size:20
Alignment explanation
Indices: 7522--7569 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
7512 TCGGCCAGAG
7522 CATGTATCTTCA-TT-AAAAT
1 CATGTAT-TTCATTTAAAAAT
7541 CATGTATTTCATTTAAAAAT
1 CATGTATTTCATTTAAAAAT
7561 CATGTATTT
1 CATGTATTT
7570 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 9 0.33
20 14 0.52
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAAT
Found at i:14079 original size:14 final size:13
Alignment explanation
Indices: 14062--14111 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
14052 GTGCAAAAAG
14062 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
14076 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
14089 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
14100 AAAGAAAAAGAA
1 AAAGAAAAAGAA
14112 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:14108 original size:19 final size:18
Alignment explanation
Indices: 14056--14111 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
14046 ATTGGAGTGC
14056 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
14073 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
14092 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
14111 A
1 A
14112 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:14109 original size:11 final size:11
Alignment explanation
Indices: 14056--14111 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
14046 ATTGGAGTGC
14056 AAAAAG-AAAG
1 AAAAAGAAAAG
14066 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
14080 AAGAAGAAAAG
1 AAAAAGAAAAG
14091 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
14104 AAAAAGAA
1 AAAAAGAA
14112 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:21929 original size:5 final size:5
Alignment explanation
Indices: 21915--21944 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
21905 GTGCTTCAAC
21915 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
21945 CTTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:21951 original size:15 final size:15
Alignment explanation
Indices: 21914--21951 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
21904 AGTGCTTCAA
21914 CTTTCTTTCTTTTCTT
1 CTTT-TTTCTTTTCTT
21930 -TTCTTTTCTTTTCTT
1 CTT-TTTTCTTTTCTT
21945 CTTTTTT
1 CTTTTTT
21952 TAAGTGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTCTTTTCTT
Found at i:31060 original size:24 final size:25
Alignment explanation
Indices: 31025--31079 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
31015 ACTTGGAGCC
*
31025 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
31049 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
31073 TCAAGTG
1 TCAAGTG
31080 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:37577 original size:22 final size:20
Alignment explanation
Indices: 37552--37591 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
37542 ATGTTTGTTT
37552 ATGGTAATGTGAGCTAAGTATG
1 ATGGTAAT-T-AGCTAAGTATG
*
37574 ATGGTCATTAGCTAAGTA
1 ATGGTAATTAGCTAAGTA
37592 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (20 bp):
ATGGTAATTAGCTAAGTATG
Found at i:42661 original size:21 final size:20
Alignment explanation
Indices: 42635--42679 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
42625 TTGCTATTTT
*
42635 AAAAAAAAAACAAAAATGCAA
1 AAAAAAAAAACAAAAA-ACAA
*
42656 AAAAAAAACACAAAAAACAA
1 AAAAAAAAAACAAAAAACAA
42676 AAAA
1 AAAA
42680 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAACAAAAAACAA
Found at i:42677 original size:19 final size:20
Alignment explanation
Indices: 42635--42679 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
42625 TTGCTATTTT
*
42635 AAAAAAAAAACAAAAATGCA
1 AAAAAAAAAACAAAAATACA
42655 AAAAAAAAACACAAAAA-ACA
1 AAAAAAAAA-ACAAAAATACA
42675 AAAAA
1 AAAAA
42680 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAACAAAAATACA
Found at i:48113 original size:14 final size:13
Alignment explanation
Indices: 48096--48145 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
48086 GTGCAAAAAG
48096 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
48110 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
48123 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
48134 AAAGAAAAAGAA
1 AAAGAAAAAGAA
48146 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:48142 original size:19 final size:18
Alignment explanation
Indices: 48090--48145 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
48080 ATTGGAGTGC
48090 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
48107 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
48126 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
48145 A
1 A
48146 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:48143 original size:11 final size:11
Alignment explanation
Indices: 48090--48145 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
48080 ATTGGAGTGC
48090 AAAAAG-AAAG
1 AAAAAGAAAAG
48100 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
48114 AAGAAGAAAAG
1 AAAAAGAAAAG
48125 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
48138 AAAAAGAA
1 AAAAAGAA
48146 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:50581 original size:33 final size:33
Alignment explanation
Indices: 50539--50607 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
50529 GTTGATGAAT
*
50539 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
50572 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
50605 GAA
1 GAA
50608 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:52443 original size:17 final size:17
Alignment explanation
Indices: 52421--52453 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52411 ACCTATAGTT
*
52421 CACATCTTTATAATATG
1 CACATCATTATAATATG
52438 CACATCATTATAATAT
1 CACATCATTATAATAT
52454 ATTACATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:54542 original size:10 final size:10
Alignment explanation
Indices: 54527--54570 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
54517 ATTGGCGTGC
54527 AAAAAGAAAG
1 AAAAAGAAAG
54537 AAAAAG-AAG
1 AAAAAGAAAG
54546 -AAAA-AAAG
1 AAAAAGAAAG
*
54554 AAAAGGAAAG
1 AAAAAGAAAG
54564 AAAAAGA
1 AAAAAGA
54571 GAAGTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 7 0.24
9 6 0.21
10 16 0.55
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:54564 original size:18 final size:17
Alignment explanation
Indices: 54528--54573 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
54518 TTGGCGTGCA
54528 AAAAGAAAGAAAAAGAAG
1 AAAA-AAAGAAAAAGAAG
*
54546 AAAAAAAGAAAAGGAAAG
1 AAAAAAAGAAAAAG-AAG
*
54564 AAAAAGAGAA
1 AAAAAAAGAA
54574 GTTCAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAG
Found at i:59405 original size:27 final size:27
Alignment explanation
Indices: 59375--59440 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
59365 CTACTCTTTC
*
59375 ATGAATGTGCATGACTATTCGGTTGAA
1 ATGAAGGTGCATGACTATTCGGTTGAA
59402 ATGAAGGTGCATGACTATTCGGTTGAA
1 ATGAAGGTGCATGACTATTCGGTTGAA
59429 ATGAAGGTGCAT
1 ATGAAGGTGCAT
59441 CTCCTTGGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (27 bp):
ATGAAGGTGCATGACTATTCGGTTGAA
Found at i:63967 original size:35 final size:37
Alignment explanation
Indices: 63921--64001 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 37
63911 TTTAAGAATT
* *
63921 TGGTGATGATATAGACTTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
* *
63956 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
63993 TGGTGATGA
1 TGGTGATGA
64002 AAATATTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.47
36 4 0.10
37 17 0.43
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
Found at i:67512 original size:14 final size:14
Alignment explanation
Indices: 67495--67533 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
67485 TTGCTTTTGA
67495 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
67509 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
67523 TTTTCTTCTTT
1 TTTTCTTCTTT
67534 CTTGTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:67531 original size:28 final size:29
Alignment explanation
Indices: 67477--67551 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
67467 ACTTGCTTCA
67477 CTTTTCTTTTGCTTTTGATTTTCTTCTTT-TT
1 CTTTTC-TTT-CTTTTG-TTTTCTTCTTTCTT
67508 CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
1 CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
* *
67537 -GTTTCTTTTTTTTGT
1 CTTTTCTTTCTTTTGT
67552 AGCACTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
28 24 0.59
29 8 0.20
30 3 0.07
31 6 0.15
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.76
Consensus pattern (29 bp):
CTTTTCTTTCTTTTGTTTTCTTCTTTCTT
Found at i:71491 original size:22 final size:19
Alignment explanation
Indices: 71479--71515 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
71469 TTATATAATG
71479 TATTATGATAAC-TATAGTA
1 TATTATGATAACTTATA-TA
71498 TATTATGATAACTTATAT
1 TATTATGATAACTTATAT
71516 TTCACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (19 bp):
TATTATGATAACTTATATA
Found at i:73973 original size:15 final size:16
Alignment explanation
Indices: 73953--73994 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
73943 GATAACATTC
73953 CTTTCCATTTCAATT-
1 CTTTCCATTTCAATTA
*
73968 CTTTCCATTTCCATTA
1 CTTTCCATTTCAATTA
*
73984 CTTTTCATTTC
1 CTTTCCATTTC
73995 TTAATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.55
Consensus pattern (16 bp):
CTTTCCATTTCAATTA
Found at i:73987 original size:16 final size:15
Alignment explanation
Indices: 73948--73994 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
73938 ATCTTGATAA
73948 CATTCCTTTCCATTTC
1 CATT-CTTTCCATTTC
*
73964 AATTCTTTCCATTTC
1 CATTCTTTCCATTTC
*
73979 CATTACTTTTCATTTC
1 CATT-CTTTCCATTTC
73995 TTAATTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (15 bp):
CATTCTTTCCATTTC
Found at i:85721 original size:18 final size:18
Alignment explanation
Indices: 85695--85738 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
85685 GTGAAGTATG
* *
85695 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGGCGTGGCA
*
85713 AATGTTGTTGGCGTGGTA
1 AATGTTGTTGGCGTGGCA
*
85731 AGTGTTGT
1 AATGTTGT
85739 AATATTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.39, T:0.39
Consensus pattern (18 bp):
AATGTTGTTGGCGTGGCA
Found at i:90324 original size:14 final size:14
Alignment explanation
Indices: 90305--90334 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
90295 GGTGATGAAC
90305 TATGGTAATGGAAA
1 TATGGTAATGGAAA
*
90319 TATGGTGATGGAAA
1 TATGGTAATGGAAA
90333 TA
1 TA
90335 GTATCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
TATGGTAATGGAAA
Done.