Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005284.1 Hibiscus syriacus cultivar Beakdansim tig00011956_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: 46432
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:14326 original size:17 final size:17
Alignment explanation
Indices: 14304--14340 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14294 TAGTTCAGGC
14304 ATCGACCCAAGTTAGGG
1 ATCGACCCAAGTTAGGG
14321 ATCGACCCAAGTTAGGG
1 ATCGACCCAAGTTAGGG
14338 ATC
1 ATC
14341 AGAGTAGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (17 bp):
ATCGACCCAAGTTAGGG
Found at i:18015 original size:6 final size:6
Alignment explanation
Indices: 18004--18037 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
17994 CAGATCACTT
18004 GTAGCA GTAGCA GTAGCA GTAGCA GTAGCA GTAG
1 GTAGCA GTAGCA GTAGCA GTAGCA GTAGCA GTAG
18038 GTAAAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.35, T:0.18
Consensus pattern (6 bp):
GTAGCA
Found at i:19903 original size:21 final size:21
Alignment explanation
Indices: 19873--19920 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
19863 TAATTTTCAA
*
19873 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
19894 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
19915 ACATTG
1 ACATTG
19921 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:24554 original size:21 final size:21
Alignment explanation
Indices: 24524--24571 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
24514 TAATTTTCAA
24524 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
24545 ACATTGTTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
24566 ACATTA
1 ACATTA
24572 CAATATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:26008 original size:22 final size:22
Alignment explanation
Indices: 25983--26032 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
25973 GATTAATTAA
25983 GATGATGTTTATTTGTTATCAT
1 GATGATGTTTATTTGTTATCAT
26005 GATGATGTTTATTTGTTATCAT
1 GATGATGTTTATTTGTTATCAT
26027 GATGAT
1 GATGAT
26033 TTTCTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (22 bp):
GATGATGTTTATTTGTTATCAT
Found at i:32606 original size:83 final size:84
Alignment explanation
Indices: 32509--32663 Score: 285
Period size: 83 Copynumber: 1.9 Consensus size: 84
32499 GTCATTGCCA
*
32509 TCTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCTGTTCCCTCTTCT-CAGCCAAGTCAGTGGC
1 TCTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCTATTCCCTCTTCTCCAGCCAAGTCAGTGGC
32573 GACTACTGCCTCTGTTCCC
66 GACTACTGCCTCTGTTCCC
*
32592 TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTATTCCCTCTTCTCCAGCCAAGTCAGTGGC
1 TCTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCTATTCCCTCTTCTCCAGCCAAGTCAGTGGC
32657 GACTACT
66 GACTACT
32664 ACTTCCTCGG
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 46 0.67
84 23 0.33
ACGTcount: A:0.16, C:0.37, G:0.19, T:0.28
Consensus pattern (84 bp):
TCTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCTATTCCCTCTTCTCCAGCCAAGTCAGTGGC
GACTACTGCCTCTGTTCCC
Found at i:32616 original size:42 final size:42
Alignment explanation
Indices: 32509--32663 Score: 285
Period size: 42 Copynumber: 3.7 Consensus size: 42
32499 GTCATTGCCA
*
32509 TCTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCTGTTCCC
1 TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTGTTCCC
32551 TCTTCT-CAGCCAAGTCAGTGGCGACTACTGCCTCTGTTCCC
1 TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTGTTCCC
*
32592 TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTATTCCC
1 TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTGTTCCC
32634 TCTTCTCCAGCCAAGTCAGTGGCGACTACT
1 TCTTCTCCAGCCAAGTCAGTGGCGACTACT
32664 ACTTCCTCGG
Statistics
Matches: 110, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
41 40 0.36
42 70 0.64
ACGTcount: A:0.16, C:0.37, G:0.19, T:0.28
Consensus pattern (42 bp):
TCTTCTCCAGCCAAGTCAGTGGCGACTACTGCCTCTGTTCCC
Found at i:39949 original size:15 final size:15
Alignment explanation
Indices: 39925--39954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39915 AACCATCAAT
*
39925 AAAAATTTAAAAAAA
1 AAAAAGTTAAAAAAA
39940 AAAAAGTTAAAAAAA
1 AAAAAGTTAAAAAAA
39955 CTGCTTTTCG
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:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAAGTTAAAAAAA
Found at i:40175 original size:21 final size:22
Alignment explanation
Indices: 40150--40200 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40140 AGTTGTGGGG
40150 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
40171 ATGTTTTTTGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
40193 AT-TTTTTA
1 ATGTTTTTA
40201 AATAATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.71
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:41964 original size:12 final size:12
Alignment explanation
Indices: 41944--41973 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41934 GCTTTAATTA
*
41944 GGGGTGACAAAG
1 GGGGCGACAAAG
41956 GGGGCGACAAAG
1 GGGGCGACAAAG
41968 GGGGCG
1 GGGGCG
41974 GGACGGGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.57, T:0.03
Consensus pattern (12 bp):
GGGGCGACAAAG
Found at i:44564 original size:16 final size:16
Alignment explanation
Indices: 44543--44580 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44533 TTACCCGACT
44543 TGTTTTCCACCTGACA
1 TGTTTTCCACCTGACA
* *
44559 TGTTTTCTACCTGACC
1 TGTTTTCCACCTGACA
44575 TGTTTT
1 TGTTTT
44581 TAATCTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.47
Consensus pattern (16 bp):
TGTTTTCCACCTGACA
Found at i:45127 original size:25 final size:25
Alignment explanation
Indices: 45093--45180 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
45083 GAAAATATTA
*
45093 TATATATAATTAATATGAAAAATAC
1 TATATATAATTAATATAAAAAATAC
45118 TATATATAATTAATATAAAAAATA-
1 TATATATAATTAATATAAAAAATAC
* *
45142 TA-A-ATAA-TATATATATATATATA-
1 TATATATAATTA-ATATA-AAAAATAC
45165 TATATATAA-TAATATA
1 TATATATAATTAATATA
45181 TATATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
21 2 0.04
22 9 0.16
23 8 0.14
24 8 0.14
25 29 0.52
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (25 bp):
TATATATAATTAATATAAAAAATAC
Found at i:45133 original size:9 final size:9
Alignment explanation
Indices: 45121--45190 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
45111 AAAATACTAT
*
45121 ATATAATTA
1 ATATAAATA
*
45130 ATATAAAAA
1 ATATAAATA
45139 ATATAAATA
1 ATATAAATA
*
45148 ATATATAT-
1 ATATAAATA
*
45156 ATATATATA
1 ATATAAATA
45165 TATATATAATA
1 -ATATA-AATA
*
45176 ATATATATA
1 ATATAAATA
45185 TATATA
1 -ATATA
45191 TATATATCGG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
8 8 0.16
9 25 0.49
10 15 0.29
11 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATAAATA
Found at i:45153 original size:2 final size:2
Alignment explanation
Indices: 45139--45197 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
45129 AATATAAAAA
*
45139 AT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45178 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
45198 CGGGCGGGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:45446 original size:7 final size:7
Alignment explanation
Indices: 45434--45474 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
45424 TTTATATTAG
45434 GGTTTAT
1 GGTTTAT
45441 GGTTTAT
1 GGTTTAT
*
45448 GATTTA-
1 GGTTTAT
45454 GTGTTTAT
1 G-GTTTAT
45462 GGTTTAT
1 GGTTTAT
45469 GGTTTA
1 GGTTTA
45475 AAATTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (7 bp):
GGTTTAT
Found at i:45459 original size:21 final size:21
Alignment explanation
Indices: 45430--45474 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
45420 TCCATTTATA
45430 TTAGGGTTTATGGTTTATGAT
1 TTAGGGTTTATGGTTTATGAT
* *
45451 TTAGTGTTTATGGTTTATGGT
1 TTAGGGTTTATGGTTTATGAT
45472 TTA
1 TTA
45475 AAATTTAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.56
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTATGAT
Found at i:45481 original size:14 final size:14
Alignment explanation
Indices: 45464--45497 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45454 GTGTTTATGG
45464 TTTATGGTTTAAAA
1 TTTATGGTTTAAAA
* *
45478 TTTAGGGTTTAGAA
1 TTTATGGTTTAAAA
45492 TTTATG
1 TTTATG
45498 ATTAGGGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTATGGTTTAAAA
Found at i:45481 original size:21 final size:21
Alignment explanation
Indices: 45436--45488 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
45426 TATATTAGGG
***
45436 TTTATGGTTTATGATTTAGTG
1 TTTATGGTTTATGATTTAAAA
*
45457 TTTATGGTTTATGGTTTAAAA
1 TTTATGGTTTATGATTTAAAA
*
45478 TTTAGGGTTTA
1 TTTATGGTTTA
45489 GAATTTATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTATGGTTTATGATTTAAAA
Found at i:45605 original size:26 final size:27
Alignment explanation
Indices: 45576--45633 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
45566 TTCTATAAAC
*
45576 TATATAATA-ATT-TACTTTATATAGTT
1 TATATAATAGATTATA-TATATATAGTT
*
45602 TATAT-ATAGGTTATATATATATAGTT
1 TATATAATAGATTATATATATATAGTT
45628 TATATA
1 TATATA
45634 TACTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.11
26 22 0.81
27 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (27 bp):
TATATAATAGATTATATATATATAGTT
Found at i:45609 original size:11 final size:11
Alignment explanation
Indices: 45593--45635 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
45583 TAATTTACTT
45593 TATATAGTTTA
1 TATATAGTTTA
45604 TATATAGGTTATATA
1 TATATA-G-T-T-TA
45619 TATATAGTTTA
1 TATATAGTTTA
45630 TATATA
1 TATATA
45636 CTATACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 14 0.50
12 2 0.07
13 2 0.07
14 2 0.07
15 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:45622 original size:15 final size:15
Alignment explanation
Indices: 45602--45640 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
45592 TTATATAGTT
45602 TATATATAGGTTATA
1 TATATATAGGTTATA
*
45617 TATATATAGTTTATA
1 TATATATAGGTTATA
45632 TATACTATA
1 TATA-TATA
45641 CATTGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (15 bp):
TATATATAGGTTATA
Done.