Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009196.1 Hibiscus syriacus cultivar Beakdansim tig00112778_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: 45454
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:9851 original size:12 final size:13
Alignment explanation
Indices: 9834--9882 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
9824 AAATTATAAC
9834 TTTAAG-TTAGAG
1 TTTAAGTTTAGAG
9846 TTTAAGTTTAG-G
1 TTTAAGTTTAGAG
9858 TTTATAGTTTAGAG
1 TTTA-AGTTTAGAG
*
9872 ATTATAGTTTA
1 TTTA-AGTTTA
9883 CGATTTAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (13 bp):
TTTAAGTTTAGAG
Found at i:9878 original size:14 final size:14
Alignment explanation
Indices: 9840--9882 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
9830 TAACTTTAAG
9840 TTAGAGTTTA-AGT
1 TTAGAGTTTATAGT
9853 TTAG-GTTTATAGT
1 TTAGAGTTTATAGT
*
9866 TTAGAGATTATAGT
1 TTAGAGTTTATAGT
9880 TTA
1 TTA
9883 CGATTTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 5 0.19
13 11 0.41
14 11 0.41
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (14 bp):
TTAGAGTTTATAGT
Found at i:15278 original size:2 final size:2
Alignment explanation
Indices: 15271--15340 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
15261 ACTTAAATCG
15271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15341 TCGATAAATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15422 original size:14 final size:13
Alignment explanation
Indices: 15403--15440 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
15393 CAAATATTCA
15403 AAAAATTAAATATT
1 AAAAATTAAA-ATT
15417 AAAAATT-AAATT
1 AAAAATTAAAATT
15429 AAAATATTAAAA
1 AAAA-ATTAAAA
15441 AAATATCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 5 0.23
14 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:16851 original size:55 final size:53
Alignment explanation
Indices: 16767--16909 Score: 205
Period size: 55 Copynumber: 2.6 Consensus size: 53
16757 TTGTATGAGA
*
16767 GTGTATCGGTACACTAAGGAGTGTATCGATACGCTCAAAACATCGAATGCCATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATAC-CT-AAAACATCGAATGCCATTT
* * * *
16822 GTGTATCGATACACTGAGGAGTGTATCGATGCACCTAAAACATTGAGTGCTATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGAT--ACCTAAAACATCGAATGCCATTT
16877 GTGTATCGGTACACTGAGGAGTGTATCGATACC
1 GTGTATCGGTACACTGAGGAGTGTATCGATACC
16910 CCCAAGTATG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
53 3 0.04
55 73 0.91
56 2 0.03
57 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (53 bp):
GTGTATCGGTACACTGAGGAGTGTATCGATACCTAAAACATCGAATGCCATTT
Found at i:17484 original size:23 final size:23
Alignment explanation
Indices: 17456--17564 Score: 120
Period size: 23 Copynumber: 4.9 Consensus size: 23
17446 TTCGGGATAA
*
17456 TATGTGACACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
17479 TATGTGGCACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
* *
17502 TATGTGGCACTTTGGTGCAA-TC
1 TATGTGGCACTTCGGTGCAACCC
*
17524 TATGTGGTC-CTTCGG-GACAA--T
1 TATGTGG-CACTTCGGTG-CAACCC
*
17545 TATGTGCCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
17565 ATTACGAGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.21
22 17 0.22
23 42 0.55
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:17562 original size:43 final size:43
Alignment explanation
Indices: 17434--17564 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 43
17424 GAGTCGATGG
* *
17434 TCTATGTGGTTCTTCGGGATAATATGTGACACTTCGGTGCAAC
1 TCTATGTGGTCCTTCGGGACAATATGTGACACTTCGGTGCAAC
* * *
17477 CCTATGTGG-CACTTCGGTG-CAACCCTATGTGGCACTTTGGTGCAA-
1 TCTATGTGGTC-CTTCGG-GACAA---TATGTGACACTTCGGTGCAAC
*
17522 TCTATGTGGTCCTTCGGGACAATTATGTGCCACTTCGGTGCAA
1 TCTATGTGGTCCTTCGGGACAA-TATGTGACACTTCGGTGCAA
17565 ATTACGAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
43 34 0.47
44 2 0.03
45 17 0.24
46 19 0.26
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (43 bp):
TCTATGTGGTCCTTCGGGACAATATGTGACACTTCGGTGCAAC
Found at i:18452 original size:8 final size:8
Alignment explanation
Indices: 18427--18481 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
18417 TAGTTTTTTT
18427 ATATTTAA
1 ATATTTAA
*
18435 TATTTTTAA
1 -ATATTTAA
18444 ATATTTAA
1 ATATTTAA
*
18452 ATAATTT-T
1 AT-ATTTAA
18460 ATATTTATA
1 ATATTTA-A
18469 ATA-TTAA
1 ATATTTAA
18476 ATATTT
1 ATATTT
18482 TTATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
7 8 0.21
8 16 0.42
9 14 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATTTAA
Found at i:18475 original size:24 final size:26
Alignment explanation
Indices: 18429--18489 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
18419 GTTTTTTTAT
* *
18429 ATTTAATATTTTTAAATATTTAAATA
1 ATTTTATATTTATAAATATTTAAATA
18455 ATTTTATATTTAT-AATA-TTAAATA
1 ATTTTATATTTATAAATATTTAAATA
*
18479 TTTTTAT-TTTA
1 ATTTTATATTTA
18490 AAAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.12
24 13 0.41
25 4 0.12
26 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTTTATATTTATAAATATTTAAATA
Found at i:18498 original size:22 final size:24
Alignment explanation
Indices: 18449--18501 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
18439 TTTAAATATT
* *
18449 TAAATAATTTTATATTTATAATAT
1 TAAATAATTTTATATTTATAAAAA
*
18473 TAAATATTTTTAT-TTTA-AAAAA
1 TAAATAATTTTATATTTATAAAAA
18495 TAAATAA
1 TAAATAA
18502 ATCCTTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAAATAATTTTATATTTATAAAAA
Found at i:29362 original size:2 final size:2
Alignment explanation
Indices: 29355--29405 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
29345 AAGTTTTATC
29355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29397 AT AT AT AT A
1 AT AT AT AT A
29406 AAGCACGAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32818 original size:19 final size:19
Alignment explanation
Indices: 32791--32857 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
32781 AATGTTTTTA
* *
32791 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
32810 TGAACAGTAAATTAATATT
1 TGAACAGTAAATTACTATT
* *
32829 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
32848 TGAACAGTAA
1 TGAACAGTAA
32858 CCCGAGGCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:32968 original size:21 final size:21
Alignment explanation
Indices: 32942--32983 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32932 ATTTGAATAT
*
32942 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32963 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32984 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:33045 original size:21 final size:21
Alignment explanation
Indices: 33012--33051 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
33002 TTTTTGTAGA
*
33012 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
33034 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
33052 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:33299 original size:30 final size:32
Alignment explanation
Indices: 33263--33326 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
33253 TTTATCCTTT
33263 TGTAAAAG-GG-AAAGGTTCTAGCTTAGCCCG
1 TGTAAAAGAGGAAAAGGTTCTAGCTTAGCCCG
*
33293 TGTAAAAGCTAGGAAAAGGTTCTAGTTTAGCCCG
1 TGTAAAAG--AGGAAAAGGTTCTAGCTTAGCCCG
33327 GAAAAACTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.28
33 2 0.07
34 19 0.66
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (32 bp):
TGTAAAAGAGGAAAAGGTTCTAGCTTAGCCCG
Done.