Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001910.1 Hibiscus syriacus cultivar Beakdansim tig00003866_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: 48339
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:564 original size:25 final size:25
Alignment explanation
Indices: 525--572 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
515 GATCACAAGA
*
525 GAAATGATATGAATACATGACCATAT
1 GAAATGATAAGAATA-ATGACCATAT
*
551 GAAAT-ATAAGAATAATGCCCAT
1 GAAATGATAAGAATAATGACCAT
573 GTTATACGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 8 0.40
26 5 0.25
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (25 bp):
GAAATGATAAGAATAATGACCATAT
Found at i:7638 original size:8 final size:8
Alignment explanation
Indices: 7626--7690 Score: 51
Period size: 9 Copynumber: 7.6 Consensus size: 8
7616 TCAAAATATC
7626 ATTTTATAT
1 ATTTT-TAT
*
7635 TTTTTTAT
1 ATTTTTAT
7643 AGTTTTTAT
1 A-TTTTTAT
7652 ATTTTTTAAT
1 A-TTTTT-AT
7662 AGTTTTTAT
1 A-TTTTTAT
*
7671 ATTTCTAT
1 ATTTTTAT
*
7679 ATTATTAT
1 ATTTTTAT
7687 -TTTT
1 ATTTT
7691 AAATTATGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 3 0.07
8 15 0.33
9 20 0.43
10 8 0.17
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.71
Consensus pattern (8 bp):
ATTTTTAT
Found at i:7640 original size:10 final size:10
Alignment explanation
Indices: 7627--7674 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 10
7617 CAAAATATCA
7627 TTTTATATTT
1 TTTTATATTT
*
7637 TTTTATA-GT
1 TTTTATATTT
7646 TTTTATATTT
1 TTTTATATTT
* *
7656 TTTAATA-GT
1 TTTTATATTT
7665 TTTTATATTT
1 TTTTATATTT
7675 CTATATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (10 bp):
TTTTATATTT
Found at i:7651 original size:19 final size:19
Alignment explanation
Indices: 7627--7674 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
7617 CAAAATATCA
*
7627 TTTTATATTTTTTTATAGT
1 TTTTATATTTTTTAATAGT
7646 TTTTATATTTTTTAATAGT
1 TTTTATATTTTTTAATAGT
7665 TTTTATATTT
1 TTTTATATTT
7675 CTATATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTATATTTTTTAATAGT
Found at i:9451 original size:35 final size:35
Alignment explanation
Indices: 9405--9543 Score: 145
Period size: 35 Copynumber: 3.9 Consensus size: 35
9395 CTTTTTTTTT
9405 TGTAGATATTAGGTTTAGTATTTATTAATAAAAGG
1 TGTAGATATTAGGTTTAGTATTTATTAATAAAAGG
* * * *
9440 TGTAGATATTAGGTATAGTCTTTACTAATAAAAGT
1 TGTAGATATTAGGTTTAGTATTTATTAATAAAAGG
** * * *
9475 TGTAGGCATGA-TTTACTACTATTTATTAATAAAAGG
1 TGTAGATATTAGGTT--TAGTATTTATTAATAAAAGG
* * *
9511 TGTAGATATTGGGTTTAGTAATCATTAATAAAA
1 TGTAGATATTAGGTTTAGTATTTATTAATAAAA
9544 ATATATATTT
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
34 1 0.01
35 54 0.68
36 23 0.29
37 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.40
Consensus pattern (35 bp):
TGTAGATATTAGGTTTAGTATTTATTAATAAAAGG
Found at i:9623 original size:23 final size:23
Alignment explanation
Indices: 9568--9623 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
9558 TAGTTTTAAA
*
9568 AAATTAAATTAAAAAAAGTGATT
1 AAATTAAATTAAAAAAAGTCATT
* * *
9591 AAGTTCAATTAAAACGAA-TCATT
1 AAATTAAATTAAAA-AAAGTCATT
9614 AAATTAAATT
1 AAATTAAATT
9624 TATTAATCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (23 bp):
AAATTAAATTAAAAAAAGTCATT
Found at i:14169 original size:59 final size:59
Alignment explanation
Indices: 14058--14169 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
14048 TCATCTACCG
* *
14058 ATAGTTTAGGATGAAATTGAAATGTTTAGACGTTTAAAGACCAATTTAGAATAAAGGTC
1 ATAGTTTAGGATGAAATTGAAATATTTAGAAGTTTAAAGACCAATTTAGAATAAAGGTC
* * *
14117 ATAGTTTAAGGATGAAATTGAAATATTTAGAAG-TTAAGGGCCAATTTTGAATA
1 ATAGTTT-AGGATGAAATTGAAATATTTAGAAGTTTAAAGACCAATTTAGAATA
14170 TGATTCAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 24 0.51
60 23 0.49
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (59 bp):
ATAGTTTAGGATGAAATTGAAATATTTAGAAGTTTAAAGACCAATTTAGAATAAAGGTC
Found at i:18851 original size:4 final size:4
Alignment explanation
Indices: 18842--18868 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18832 CATTCTTTGT
18842 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
18869 TAAATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:18877 original size:8 final size:8
Alignment explanation
Indices: 18841--18900 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
18831 TCATTCTTTG
18841 TATAAATA
1 TATAAATA
*
18849 AATAAATA
1 TATAAATA
*
18857 AATAAATAAA
1 TATAAAT--A
18867 TATAAATA
1 TATAAATA
*
18875 TATATATA
1 TATAAATA
*
18883 TATATATA
1 TATAAATA
*
18891 TATATATA
1 TATAAATA
18899 TA
1 TA
18901 CTGAGAATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
8 40 0.85
10 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAAATA
Found at i:18879 original size:2 final size:2
Alignment explanation
Indices: 18866--18900 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
18856 AAATAAATAA
*
18866 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18901 CTGAGAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18881 original size:12 final size:12
Alignment explanation
Indices: 18841--18900 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
18831 TCATTCTTTG
*
18841 TATAAATAAATA
1 TATATATAAATA
* *
18853 AATAAATAAATA
1 TATATATAAATA
18865 -A-ATATAAATA
1 TATATATAAATA
*
18875 TATATATATATA
1 TATATATAAATA
*
18887 TATATATATATA
1 TATATATAAATA
18899 TA
1 TA
18901 CTGAGAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 33 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATATAAATA
Found at i:34224 original size:3 final size:3
Alignment explanation
Indices: 34216--34245 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
34206 TACAAGTATT
*
34216 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34246 AAAAGCATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:45120 original size:29 final size:31
Alignment explanation
Indices: 45088--45158 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
45078 AAATAGTTAT
*
45088 TATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTTTTTATATTAAATAATATTTATATAAA
* *
45117 TATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTTTTTATATT-AAATAATATTTATATAAA
*
45149 TATTATTTAT
1 TATTTTTTAT
45159 TTAGAATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 12 0.35
31 3 0.09
32 19 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TATTTTTTATATTAAATAATATTTATATAAA
Found at i:45323 original size:17 final size:17
Alignment explanation
Indices: 45301--45354 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
45291 AATGTTAATA
45301 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * *
45318 TTTAAATTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
45335 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
45352 TTT
1 TTT
45355 TTATAATGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:46967 original size:21 final size:20
Alignment explanation
Indices: 46936--47021 Score: 102
Period size: 21 Copynumber: 4.2 Consensus size: 20
46926 TATGCCATCT
* *
46936 CCGCAGGTTACATTCCGAGC
1 CCGCAGGTTACATGCCTAGC
*
46956 CCGCAGGGTTACATTCCTAG-
1 CCGCA-GGTTACATGCCTAGC
46976 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
*
46997 CCGCCAAGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
47018 CCGC
1 CCGC
47022 CGGGTTTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
20 22 0.37
21 38 0.63
ACGTcount: A:0.20, C:0.37, G:0.23, T:0.20
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:46984 original size:41 final size:42
Alignment explanation
Indices: 46939--47027 Score: 110
Period size: 41 Copynumber: 2.1 Consensus size: 42
46929 GCCATCTCCG
* * *
46939 CAGGTTACATTCCGAGCCCG-CAGGGTTACATTCCTAG-CCGC
1 CAGGTTACATGCCGAGCCCGCCA-AGTTACATGCCTAGCCCGC
*
46980 CAGGTTACATGCCTAGCCCGCCAAGTTACATGCCTAGCCCGC
1 CAGGTTACATGCCGAGCCCGCCAAGTTACATGCCTAGCCCGC
*
47022 CGGGTT
1 CAGGTT
47028 TTATAACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 30 0.73
42 11 0.27
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (42 bp):
CAGGTTACATGCCGAGCCCGCCAAGTTACATGCCTAGCCCGC
Found at i:47648 original size:34 final size:33
Alignment explanation
Indices: 47543--47648 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
47533 ATAAATGTTT
* *
47543 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCCAAATTT-AAA
* *
47577 TAAAAATAAAAATAATATTATT-CAAATTTAAA
1 TTAAAATAAAAATTATATTATTCCAAATTTAAA
* *
47609 TTTAAAATATAAATTATAGTATTCCAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCCAAATTTAA-A
47644 TTAAA
1 TTAAA
47649 TTCAACTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 3 0.05
33 24 0.39
34 33 0.54
35 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCCAAATTTAAA
Done.