Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004518.1 Hibiscus syriacus cultivar Beakdansim tig00009963_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: 74948
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:400 original size:17 final size:18
Alignment explanation
Indices: 372--414 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
362 ATTTCATTTC
*
372 CTTATTCTTTCATCTATT
1 CTTATTCCTTCATCTATT
390 C-TATTCCTTCATCTATT
1 CTTATTCCTTCATCTATT
407 CTTATTCC
1 CTTATTCC
415 ACTACCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
CTTATTCCTTCATCTATT
Found at i:569 original size:18 final size:18
Alignment explanation
Indices: 546--580 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
536 AAGGGCCTAC
* *
546 AAAAGGTAATTGAGAGGT
1 AAAAGGCAAATGAGAGGT
564 AAAAGGCAAATGAGAGG
1 AAAAGGCAAATGAGAGG
581 GTGAGCTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.34, T:0.14
Consensus pattern (18 bp):
AAAAGGCAAATGAGAGGT
Found at i:6725 original size:133 final size:134
Alignment explanation
Indices: 6485--6753 Score: 522
Period size: 133 Copynumber: 2.0 Consensus size: 134
6475 TTTAAATTAG
6485 ATTCAAATCCTTCTTGTTAGTTTATTGTTTTTTCAAAAAAAAAAATTCAAAAAGGACCAAAAAAT
1 ATTCAAATCCTTCTTGTTAGTTTATTGTTTTTTC-AAAAAAAAAATTCAAAAAGGACCAAAAAAT
6550 CCAAAATTTCAAAAAAATTGCCAACGAAGGAATTTAGGGTTGATTTTCTCATGATCTCATATTCA
65 CCAAAATTTCAAAAAAATTGCCAACGAAGGAATTTAGGGTTGATTTTCTCATGATCTCATATTCA
6615 TCCTC
130 TCCTC
6620 ATTCAAATCCTTCTTGTTAGTTTATTGTTTTTTC-AAAAAAAAATTCAAAAAGGACCAAAAAATC
1 ATTCAAATCCTTCTTGTTAGTTTATTGTTTTTTCAAAAAAAAAATTCAAAAAGGACCAAAAAATC
6684 CAAAATTTCAAAAAAATTGCCAACGAAGGAATTTAGGGTTGATTTTCTCATGATCTCATATTCAT
66 CAAAATTTCAAAAAAATTGCCAACGAAGGAATTTAGGGTTGATTTTCTCATGATCTCATATTCAT
6749 CCTC
131 CCTC
6753 A
1 A
6754 GAGTAATATT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 100 0.75
135 34 0.25
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (134 bp):
ATTCAAATCCTTCTTGTTAGTTTATTGTTTTTTCAAAAAAAAAATTCAAAAAGGACCAAAAAATC
CAAAATTTCAAAAAAATTGCCAACGAAGGAATTTAGGGTTGATTTTCTCATGATCTCATATTCAT
CCTC
Found at i:9773 original size:43 final size:46
Alignment explanation
Indices: 9668--9773 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 46
9658 AGGATTAGAT
9668 TTATTATTTTATTAGGAATTAAGTTTGAGTTAAAACATTATCTTTAGTTA
1 TTATTATTTTATTAGGAATTAA---TGAGTTAAAACATTA-CTTTAGTTA
9718 TTATTATTTTATTAGGAATT-A-GAGTTAAAACA-TA-TTTAGTT-
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACATTACTTTAGTTA
9759 TGCTATTATTTTATT
1 T--TATTATTTTATT
9774 CATTAGTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
41 1 0.02
42 7 0.13
43 12 0.22
44 2 0.04
45 11 0.20
49 1 0.02
50 20 0.37
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATTACTTTAGTTA
Found at i:17673 original size:19 final size:20
Alignment explanation
Indices: 17635--17683 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
17625 GAAACCCCTT
17635 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
17655 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
17674 TGAAAGTACA
1 TGAAAATACA
17684 AGCTTTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:17690 original size:19 final size:19
Alignment explanation
Indices: 17635--17690 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
17625 GAAACCCCTT
*
17635 TGAAAATACATGATTTTTAA
1 TGAAAATACAAGA-TTTTAA
*
17655 TGAAAATACATGATTTTAA
1 TGAAAATACAAGATTTTAA
* *
17674 TGAAAGTACAAGCTTTT
1 TGAAAATACAAGATTTT
17691 GGCCGAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAAAATACAAGATTTTAA
Found at i:19841 original size:21 final size:21
Alignment explanation
Indices: 19802--19842 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19792 AATAGGCATA
* *
19802 TAGTTATTCAGCGAGCCCTTC
1 TAGTTATTCAGCCAACCCTTC
*
19823 TAGTTATTCGGCCAACCCTT
1 TAGTTATTCAGCCAACCCTT
19843 TAAAATCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (21 bp):
TAGTTATTCAGCCAACCCTTC
Found at i:29043 original size:25 final size:25
Alignment explanation
Indices: 29011--29066 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
29001 AAAAATCAGA
*
29011 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
**
29035 AAAGAAAATTTTAGCACTCAAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
29060 -AAGAAAA
1 AAAGAAAA
29067 AAATAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAGAAAATTGAAGCACTCAAAAAG
Found at i:44252 original size:24 final size:23
Alignment explanation
Indices: 44225--44305 Score: 56
Period size: 24 Copynumber: 3.5 Consensus size: 23
44215 ATTTGGAACG
*
44225 TCAAGAGACATAACTATTGGTTCT
1 TCAAAAGACAT-ACTATTGGTTCT
* ** * *
44249 TCAAAATACAT-CTCGTGGATCA
1 TCAAAAGACATACTATTGGTTCT
* * *
44271 CCAAGAGTCATGACTATTGGTTCT
1 TCAAAAGACAT-ACTATTGGTTCT
44295 TCAAAAGACAT
1 TCAAAAGACAT
44306 GTTTCTTGAA
Statistics
Matches: 38, Mismatches: 17, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 14 0.37
24 24 0.63
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (23 bp):
TCAAAAGACATACTATTGGTTCT
Found at i:47407 original size:13 final size:13
Alignment explanation
Indices: 47389--47414 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47379 AACACCTCTC
47389 ACATACCTTTTCA
1 ACATACCTTTTCA
47402 ACATACCTTTTCA
1 ACATACCTTTTCA
47415 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:52970 original size:19 final size:20
Alignment explanation
Indices: 52948--52997 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
52938 CTTATGAGTG
*
52948 TTTTGATTTCTTT-GCTGGA
1 TTTTGATTTCTTTCGATGGA
52967 TTTTGATTT-TTTCGATGGA
1 TTTTGATTTCTTTCGATGGA
52986 TTTTGATTTCTT
1 TTTTGATTTCTT
52998 CACTTGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.11
19 23 0.82
20 2 0.07
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.62
Consensus pattern (20 bp):
TTTTGATTTCTTTCGATGGA
Found at i:61806 original size:28 final size:28
Alignment explanation
Indices: 61766--61832 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
61756 GCATTCTATG
61766 CCACCTATGTGAGTGCCTCATGACCAGC
1 CCACCTATGTGAGTGCCTCATGACCAGC
*
61794 CCACCCATGTGAGTGCCTCATGACCAGC
1 CCACCTATGTGAGTGCCTCATGACCAGC
61822 CCACCTATGTG
1 CCACCTATGTG
61833 CCATTCGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (28 bp):
CCACCTATGTGAGTGCCTCATGACCAGC
Found at i:62708 original size:18 final size:18
Alignment explanation
Indices: 62687--62721 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
62677 AACAAAAATA
62687 AAAAGA-AAGAAGAAAAAC
1 AAAAGAGAA-AAGAAAAAC
62705 AAAAGAGAAAAGAAAAA
1 AAAAGAGAAAAGAAAAA
62722 GAATCCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAAAGAAAAAC
Found at i:66336 original size:27 final size:28
Alignment explanation
Indices: 66275--66336 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
66265 AAAGAAAATC
66275 AGAAAAGAAATTGAAGCACTACAAAAGA
1 AGAAAAGAAATTGAAGCACTACAAAAGA
* *
66303 A-AGAAAGAAATT-CAGCA-TTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTAC-AAAAGA
66330 AGAAAAG
1 AGAAAAG
66337 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 2 0.07
27 16 0.55
28 11 0.38
ACGTcount: A:0.61, C:0.10, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTACAAAAGA
Found at i:66346 original size:5 final size:5
Alignment explanation
Indices: 66329--66359 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
66319 ATTCAAAAAG
*
66329 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
66360 GTTGAAGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Done.