Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004360.1 Hibiscus syriacus cultivar Beakdansim tig00009551_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: 53046
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2427 original size:27 final size:29
Alignment explanation
Indices: 2352--2424 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
2342 ATATATATAT
*
2352 ATATATTTTAAAATTAATAGAAGAATGAA
1 ATATATTTTAAAGTTAATAGAAGAATGAA
*
2381 ATATATTTTTAAAGTTAATATAAGAAT-AA
1 ATATA-TTTTAAAGTTAATAGAAGAATGAA
2410 A-ATATTTT-AAGTTAA
1 ATATATTTTAAAGTTAA
2425 ATAAATTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 7 0.17
27 4 0.10
28 3 0.07
29 8 0.20
30 19 0.46
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (29 bp):
ATATATTTTAAAGTTAATAGAAGAATGAA
Found at i:12204 original size:18 final size:18
Alignment explanation
Indices: 12181--12217 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12171 ATTAATTGGT
12181 TTGCCTATTCTCGTGCAC
1 TTGCCTATTCTCGTGCAC
* *
12199 TTGCCTGTTCTTGTGCAC
1 TTGCCTATTCTCGTGCAC
12217 T
1 T
12218 CCTTTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.30, G:0.19, T:0.43
Consensus pattern (18 bp):
TTGCCTATTCTCGTGCAC
Found at i:12524 original size:2 final size:2
Alignment explanation
Indices: 12517--12544 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12507 GATAATTTTG
12517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12545 ATTTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17454 original size:19 final size:18
Alignment explanation
Indices: 17426--17461 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17416 AATAAGTAAA
17426 GTAAATATGATAATTGTT
1 GTAAATATGATAATTGTT
*
17444 GTAACATATGATAGTTGT
1 GTAA-ATATGATAATTGT
17462 CACATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (18 bp):
GTAAATATGATAATTGTT
Found at i:19219 original size:18 final size:16
Alignment explanation
Indices: 19189--19222 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
19179 TACATAATTG
19189 AAAAAAAATATTAAAT
1 AAAAAAAATATTAAAT
19205 AAAAAAATATGATTAAAT
1 AAAAAAA-AT-ATTAAAT
19223 TTCAAGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAAAATATTAAAT
Found at i:19310 original size:39 final size:39
Alignment explanation
Indices: 19257--19378 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 39
19247 AATATTTAAA
*
19257 AAAAAATTAGAATGTTGATGTGAAATAATTTAAGAAATT
1 AAAAATTTAGAATGTTGATGTGAAATAATTTAAGAAATT
*
19296 AAAAATTTCA-AATGTT-ATGGTAGCAA-AATTTAAGAAATT
1 AAAAATTT-AGAATGTTGAT-GT-GAAATAATTTAAGAAATT
** *
19335 AGGAATTTAGAATGTTAGA-GTGAAATAATTTGA-AAATT
1 AAAAATTTAGAATGTT-GATGTGAAATAATTTAAGAAATT
*
19373 ATAAAT
1 AAAAAT
19379 AAACATTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
38 15 0.22
39 48 0.71
40 4 0.06
41 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.34
Consensus pattern (39 bp):
AAAAATTTAGAATGTTGATGTGAAATAATTTAAGAAATT
Found at i:19395 original size:2 final size:2
Alignment explanation
Indices: 19388--19414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19378 TAAACATTTA
19388 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 A
19415 AATAAACCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23174 original size:22 final size:21
Alignment explanation
Indices: 23149--23191 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
23139 TTTATAAAAA
23149 ATAAATACTGAAAAAATAAATT
1 ATAAATACT-AAAAAATAAATT
* * *
23171 ATAATTTCTAGAAAATAAATT
1 ATAAATACTAAAAAATAAATT
23192 TTGGAAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAAATACTAAAAAATAAATT
Found at i:23716 original size:24 final size:24
Alignment explanation
Indices: 23653--23716 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
23643 GAATAATTAT
* *
23653 GTTTGTTCTCTACCTTTATGGCAC
1 GTTTTTTCTCTGCCTTTATGGCAC
* * * *
23677 -ATTTATCTCTGTCTTTGTGGCAC
1 GTTTTTTCTCTGCCTTTATGGCAC
23700 GTTTTTTCTCTGCCTTT
1 GTTTTTTCTCTGCCTTT
23717 TTGGTAGCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.09, C:0.23, G:0.16, T:0.52
Consensus pattern (24 bp):
GTTTTTTCTCTGCCTTTATGGCAC
Found at i:25446 original size:17 final size:18
Alignment explanation
Indices: 25421--25454 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25411 GTGGGAGTTG
*
25421 TAACTACTCT-AACAACT
1 TAACGACTCTCAACAACT
25438 TAACGACTCTCAACAAC
1 TAACGACTCTCAACAAC
25455 CCATGCAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.32, G:0.03, T:0.24
Consensus pattern (18 bp):
TAACGACTCTCAACAACT
Found at i:38997 original size:6 final size:6
Alignment explanation
Indices: 38986--39010 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38976 TCGGTTCGGC
38986 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
39011 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:45636 original size:17 final size:18
Alignment explanation
Indices: 45624--45663 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45614 CTAATAATTG
45624 AATATAATAAATAATTAA
1 AATATAATAAATAATTAA
*
45642 AATATAAT-AATAAAT-A
1 AATATAATAAATAATTAA
45658 AATATA
1 AATATA
45664 GTAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATAAATAATTAA
Found at i:45647 original size:18 final size:16
Alignment explanation
Indices: 45573--45679 Score: 63
Period size: 17 Copynumber: 6.4 Consensus size: 16
45563 TTTCAAATTG
*
45573 AAAT-TAATAAAAAAT
1 AAATATAATAATAAAT
* * *
45588 AAGTATAGTAAAAAAAT
1 AAATATAAT-AATAAAT
* *
45605 ATAATAATACTAATAATT
1 A-AAT-ATAATAATAAAT
* *
45623 GAATATAATAAATAATT
1 AAATATAAT-AATAAAT
45640 AAAATATAATAATAAAT
1 -AAATATAATAATAAAT
* *
45657 AAATATAGTAATTAAAA
1 AAATATAATAA-TAAAT
45674 AAATAT
1 AAATAT
45680 TTTATAAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.04
16 17 0.23
17 34 0.47
18 15 0.21
19 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:45662 original size:34 final size:34
Alignment explanation
Indices: 45567--45663 Score: 88
Period size: 35 Copynumber: 2.9 Consensus size: 34
45557 AGGACCTTTC
* * * *
45567 AAATTGAAAT-TAATAAAAAATAAGTATAGTAAA
1 AAATTAAAATATAATAATAAATAAATATAATAAA
* * * * *
45600 AAAATATAATAATACTAATAATTGAATATAATAAA
1 AAATTAAAAT-ATAATAATAAATAAATATAATAAA
*
45635 TAATTAAAATATAATAATAAATAAATATA
1 AAATTAAAATATAATAATAAATAAATATA
45664 GTAATTAAAA
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
33 7 0.15
34 16 0.34
35 24 0.51
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (34 bp):
AAATTAAAATATAATAATAAATAAATATAATAAA
Found at i:49576 original size:12 final size:13
Alignment explanation
Indices: 49548--49618 Score: 51
Period size: 13 Copynumber: 5.4 Consensus size: 13
49538 TATAAATATC
49548 TATTTAATTACTT
1 TATTTAATTACTT
49561 TATTT-ATTA-TT
1 TATTTAATTACTT
49572 ATATTTTAATTA-TT
1 -TA-TTTAATTACTT
* *
49586 TATTATATTTAATAT
1 TATT-TAATTACT-T
49601 TA-TTAATTACTAT
1 TATTTAATTACT-T
49614 TATTT
1 TATTT
49619 TTTATTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.04
12 8 0.17
13 25 0.52
14 10 0.21
15 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTAATTACTT
Found at i:49583 original size:26 final size:26
Alignment explanation
Indices: 49550--49624 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
49540 TAAATATCTA
49550 TTTAATTACTTTATTTATTATTATAT
1 TTTAATTACTTTATTTATTATTATAT
*
49576 TTTAATTA-TTTATTATATT-TAATAT
1 TTTAATTACTTTATT-TATTATTATAT
*
49601 TATTAATTACTATTATTTTTTATT
1 T-TTAATTACT-TTATTTATTATT
49625 TTAATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 12 0.29
26 19 0.46
27 4 0.10
28 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTAATTACTTTATTTATTATTATAT
Found at i:49625 original size:48 final size:52
Alignment explanation
Indices: 49521--49639 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 52
49511 AATTTACAAA
*
49521 ATATTATAATTA-TTATT-TATAAATATCTATTTAATTACTTTATTTATTATT
1 ATATTTTAATTATTTATTATATAAATATCTATTTAATTAC-TTATTTATTATT
*
49572 ATATTTTAATTATTTATTATATTTAATAT-TA-TTAATTAC-TA-TTATT-TT
1 ATATTTTAATTATTTATTATA-TAAATATCTATTTAATTACTTATTTATTATT
* *
49620 TTATTTTAATTATTTGTTAT
1 ATATTTTAATTATTTATTAT
49640 TAATTTCAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
48 20 0.33
49 5 0.08
50 2 0.03
51 11 0.18
52 13 0.21
53 4 0.07
54 6 0.10
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (52 bp):
ATATTTTAATTATTTATTATATAAATATCTATTTAATTACTTATTTATTATT
Found at i:49631 original size:16 final size:16
Alignment explanation
Indices: 49559--49640 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
49549 ATTTAATTAC
* *
49559 TTTATTTATTATTATAT
1 TTTAATTATT-TTTTAT
*
49576 TTTAATTATTTATTAT
1 TTTAATTATTTTTTAT
* *
49592 ATTTAA-TATTATTAAT
1 -TTTAATTATTTTTTAT
*
49608 TACT-ATTATTTTTTAT
1 T-TTAATTATTTTTTAT
*
49624 TTTAATTATTTGTTAT
1 TTTAATTATTTTTTAT
49640 T
1 T
49641 AATTTCAATT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
15 3 0.06
16 33 0.66
17 14 0.28
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTAATTATTTTTTAT
Found at i:50505 original size:46 final size:46
Alignment explanation
Indices: 50396--50554 Score: 115
Period size: 49 Copynumber: 3.3 Consensus size: 46
50386 TAATATTTCT
** *
50396 AATATAATATTATTTTAATATTATAATAA-AATAATTAATTATTTATAAT-
1 AATAT-ATATTATTTTTTTATT-TAATAATAATAATAAATTA--TA-AATA
*
50445 AATATAGATATATTTTTTTATTTAATAATAATAATAAATTATAAATA
1 AATATATAT-TATTTTTTTATTTAATAATAATAATAAATTATAAATA
* * * * * *
50492 AATTTATATTATTTATTAATTTCATAGAAATAATATTAAATTATTAATAA
1 AATATATATTATTTTTTTATTT-A-A-TAATAATAATAAATTATAAAT-A
50542 TAATATATATTAT
1 -AATATATATTAT
50555 ATAGTAATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
46 14 0.16
47 10 0.11
48 10 0.11
49 44 0.49
50 1 0.01
51 11 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (46 bp):
AATATATATTATTTTTTTATTTAATAATAATAATAAATTATAAATA
Found at i:50543 original size:20 final size:18
Alignment explanation
Indices: 50520--50567 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
50510 ATTTCATAGA
50520 AATAATATTAAATTAT-T
1 AATAATATTAAATTATAT
*
50537 AATAATAATATATATTATAT
1 AATAAT-AT-TAAATTATAT
*
50557 AGTAATATTAA
1 AATAATATTAA
50568 TCTAATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 9 0.36
20 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATAATATTAAATTATAT
Found at i:51016 original size:15 final size:15
Alignment explanation
Indices: 50974--51017 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
50964 TTTAATAAAT
50974 GTAATTTATTTTTCA
1 GTAATTTATTTTTCA
* **
50989 G-AATTCAAATTTCA
1 GTAATTTATTTTTCA
51003 GTAATTTATTTTTCA
1 GTAATTTATTTTTCA
51018 AAAAATCAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (15 bp):
GTAATTTATTTTTCA
Done.