Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004806.1 Hibiscus syriacus cultivar Beakdansim tig00010824_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: 76641
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2481 original size:19 final size:18
Alignment explanation
Indices: 2457--2528 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 18
2447 TAGTATGGTG
2457 ATATTTTAAATGGTGATAT
1 ATATTTTAAATGGT-ATAT
2476 ATATTTTAAAT-GTA-AT
1 ATATTTTAAATGGTATAT
**
2492 A-ATAGT--ATGGT-TAT
1 ATATTTTAAATGGTATAT
2506 ATATTTTAAATGGTGATAT
1 ATATTTTAAATGGT-ATAT
2525 ATAT
1 ATAT
2529 GACATATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 6 0.14
16 3 0.07
17 6 0.14
18 2 0.05
19 18 0.43
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (18 bp):
ATATTTTAAATGGTATAT
Found at i:2494 original size:47 final size:49
Alignment explanation
Indices: 2436--2528 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
2426 TTATATTAAA
2436 AAATGTAATAATAGTATGG-T-GATATTTTAAATGGTGATATATATTTT
1 AAATGTAATAATAGTATGGTTAGATATTTTAAATGGTGATATATATTTT
*
2483 AAATGTAATAATAGTATGGTTATATATTTTAAATGGTGATATATAT
1 AAATGTAATAATAGTATGGTTAGATATTTTAAATGGTGATATATAT
2529 GACATATAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 19 0.44
48 1 0.02
49 23 0.53
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (49 bp):
AAATGTAATAATAGTATGGTTAGATATTTTAAATGGTGATATATATTTT
Found at i:17992 original size:23 final size:23
Alignment explanation
Indices: 17948--17996 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
17938 ATAAAGAACC
*
17948 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
17971 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
17994 AAA
1 AAA
17997 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:18966 original size:26 final size:26
Alignment explanation
Indices: 18937--19004 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
18927 ACTTAGAATT
18937 TGTCCCGAAGAACCACATATCACATA
1 TGTCCCGAAGAACCACATATCACATA
18963 TGTCCCGAA-AGACCACATATCACATA
1 TGTCCCGAAGA-ACCACATATCACATA
*
18989 TGTCCCGAAGGACCAC
1 TGTCCCGAAGAACCAC
19005 TCCTTAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 1 0.03
26 38 0.97
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (26 bp):
TGTCCCGAAGAACCACATATCACATA
Found at i:22915 original size:14 final size:15
Alignment explanation
Indices: 22884--22917 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
22874 AAAAGTTATG
*
22884 ATTTTTAACTTTTTC
1 ATTTTTAACTTTTGC
22899 ATTTTTAAC-TTTGC
1 ATTTTTAACTTTTGC
22913 ATTTT
1 ATTTT
22918 AAAGCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.65
Consensus pattern (15 bp):
ATTTTTAACTTTTGC
Found at i:23130 original size:11 final size:12
Alignment explanation
Indices: 23105--23134 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
23095 GTTATATAAA
23105 TATATTTTTATT
1 TATATTTTTATT
23117 TATATTTTTA-T
1 TATATTTTTATT
23128 TATATTT
1 TATATTT
23135 AAATTGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATATTTTTATT
Found at i:23684 original size:38 final size:36
Alignment explanation
Indices: 23642--23712 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
23632 TCTATTAATG
*
23642 ATTTAATTTATTATTTATA-AAATTTTAAAAATTTAAAA
1 ATTTAATTT-TT-TTAATATAAATTTT-AAAATTTAAAA
*
23680 ATTTAATTTTTTTAATATAAGTTTTAAAATTTA
1 ATTTAATTTTTTTAATATAAATTTTAAAATTTA
23713 CATATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 13 0.43
37 8 0.27
38 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
ATTTAATTTTTTTAATATAAATTTTAAAATTTAAAA
Found at i:33770 original size:53 final size:53
Alignment explanation
Indices: 33701--33808 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
33691 TGGTTGCCAC
* *
33701 CGTACACTGTTGGGAATGTTTCGCTCCATTAAGATGGAATGAGTTGCACCCCT
1 CGTACACTGTTGGGAATGTTTCGCTCCATTAAGATGGAACGAGTTGCAACCCT
33754 CGTACACTGTTGGGAATGTTTCGCTCCATTAAGATGGAACGAGTTGCAACCCT
1 CGTACACTGTTGGGAATGTTTCGCTCCATTAAGATGGAACGAGTTGCAACCCT
33807 CG
1 CG
33809 CTAACGTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (53 bp):
CGTACACTGTTGGGAATGTTTCGCTCCATTAAGATGGAACGAGTTGCAACCCT
Found at i:33858 original size:29 final size:29
Alignment explanation
Indices: 33816--33875 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
33806 TCGCTAACGT
33816 TTTGCTTATTACCTTCGTCCAGTGTCTAC
1 TTTGCTTATTACCTTCGTCCAGTGTCTAC
*
33845 TTTGCTTATTACCTTCGTCCAGTGTTTAC
1 TTTGCTTATTACCTTCGTCCAGTGTCTAC
33874 TT
1 TT
33876 CTTTCCAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.25, G:0.13, T:0.48
Consensus pattern (29 bp):
TTTGCTTATTACCTTCGTCCAGTGTCTAC
Found at i:33995 original size:20 final size:22
Alignment explanation
Indices: 33957--33996 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
33947 TCTTAACTAA
*
33957 GGTTTAGGATTATACATTTTAG
1 GGTTTAGGATTATAAATTTTAG
33979 GGTTTA-GA-TATAAATTTT
1 GGTTTAGGATTATAAATTTT
33997 GAAGTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (22 bp):
GGTTTAGGATTATAAATTTTAG
Found at i:39125 original size:29 final size:29
Alignment explanation
Indices: 39083--39142 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
39073 AAACGACTAT
*
39083 ATATGGTCACTTGTTTTTATTTAATTAAG
1 ATATAGTCACTTGTTTTTATTTAATTAAG
*
39112 ATATAGTCGCTTGTTTTTATTTAATTAAG
1 ATATAGTCACTTGTTTTTATTTAATTAAG
39141 AT
1 AT
39143 GTGATCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (29 bp):
ATATAGTCACTTGTTTTTATTTAATTAAG
Found at i:39367 original size:19 final size:19
Alignment explanation
Indices: 39343--39382 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39333 ATTTTAATTT
*
39343 AATATATTAAATTAAAATA
1 AATATATTAAAATAAAATA
*
39362 AATATATTAAAATAAATTA
1 AATATATTAAAATAAAATA
39381 AA
1 AA
39383 ATCAAGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATATTAAAATAAAATA
Found at i:39956 original size:15 final size:16
Alignment explanation
Indices: 39920--39958 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
39910 AGAGCCTCTG
* *
39920 AATCATTCAGCATTTA
1 AATCATTTAGCACTTA
39936 AATCATTTAGCACTT-
1 AATCATTTAGCACTTA
39951 AATCATTT
1 AATCATTT
39959 TGAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (16 bp):
AATCATTTAGCACTTA
Found at i:44472 original size:23 final size:23
Alignment explanation
Indices: 44446--44492 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44436 AATTTCTCAT
*
44446 AATTTAATCATTTTAATTTTAAA
1 AATTTAATCATTTTAATTATAAA
** *
44469 AATTTTTTTATTTTAATTATAAA
1 AATTTAATCATTTTAATTATAAA
44492 A
1 A
44493 TAATAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTAATCATTTTAATTATAAA
Found at i:50562 original size:78 final size:78
Alignment explanation
Indices: 50414--50564 Score: 214
Period size: 78 Copynumber: 1.9 Consensus size: 78
50404 CCACCTCCAG
*
50414 CGCAGATAATCTTACGTTCCCCACCTCCTCCAGATAATGTACCAACGCCGCCTTCCTCAAAATAT
1 CGCAGATAATCTTACGTTCCCCACCTCCCCCAGATAATGTACCAACGCCGCCTTCCTCAAAATAT
*
50479 CCACCTTCACCGC
66 ACACCTTCACCGC
* * * * * *
50492 CGCAGATAATTTTTA-GTTCCCCACCTCCCCCAGCTAATGTTCCAACGCCGTCTTCCTCAAAGTC
1 CGCAGATAA-TCTTACGTTCCCCACCTCCCCCAGATAATGTACCAACGCCGCCTTCCTCAAAATA
50556 TACACCTTC
65 TACACCTTC
50565 GCCACCACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 60 0.94
79 4 0.06
ACGTcount: A:0.24, C:0.40, G:0.11, T:0.26
Consensus pattern (78 bp):
CGCAGATAATCTTACGTTCCCCACCTCCCCCAGATAATGTACCAACGCCGCCTTCCTCAAAATAT
ACACCTTCACCGC
Found at i:63563 original size:32 final size:32
Alignment explanation
Indices: 63524--63586 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
63514 AGAATCGGTA
63524 AAAATCGCAGGTCTAGAAGACTAGAACCAAGT
1 AAAATCGCAGGTCTAGAAGACTAGAACCAAGT
63556 AAAATCGCAGGTCTAGAAGACTAGAACCAAG
1 AAAATCGCAGGTCTAGAAGACTAGAACCAAG
63587 AAAGCTGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (32 bp):
AAAATCGCAGGTCTAGAAGACTAGAACCAAGT
Found at i:66526 original size:5 final size:5
Alignment explanation
Indices: 66502--66540 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
66492 ATCTGTCCGT
* * *
66502 CTCGT CTCGT CTCGG CTCGG CTCGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
66541 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:66549 original size:6 final size:6
Alignment explanation
Indices: 66538--66616 Score: 70
Period size: 6 Copynumber: 13.2 Consensus size: 6
66528 ACGGCTCGGC
** * * * * * *
66538 TCGTGG TCGTGG TCAAGG TCGAT-G TCGAGG TCGAGG TAGAGG TTGAGG
1 TCGTGG TCGTGG TCGTGG TCG-TGG TCGTGG TCGTGG TCGTGG TCGTGG
66586 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
66617 AATACGTGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.10, C:0.14, G:0.47, T:0.29
Consensus pattern (6 bp):
TCGTGG
Done.