Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001566.1 Hibiscus syriacus cultivar Beakdansim tig00003100_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: 80989
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2439 original size:2 final size:2
Alignment explanation
Indices: 2432--2457 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2422 AAAAGCAACT
2432 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2458 CTGGGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3338 original size:19 final size:19
Alignment explanation
Indices: 3308--3363 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
3298 ATGTATTTAA
*
3308 TAAAATAATATTTTATAAT
1 TAAAAAAATATTTTATAAT
*
3327 TAGAAAAATATTTTATAAT
1 TAAAAAAATATTTTATAAT
3346 TAAAAAAATATTTTATAA
1 TAAAAAAATATTTTATAA
3364 CTTTTAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAAAAATATTTTATAAT
Found at i:5137 original size:69 final size:70
Alignment explanation
Indices: 5017--5152 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 70
5007 GTATTTAAAC
* * * *
5017 AATACAATATCTAAAATTTAATGCTATTTGATATAATTTGTCCATTCCTACATCTATTTCTAATT
1 AATACAATATCTAAAATTTAAT-CTATATGATATAATTTATCCATACCTACACCTATTTCTAATT
5082 ATACCT
65 ATACCT
* * *
5088 AATATAATGTCTAAAATTTAAT-TATAT-ATAATAATTTATCTATACCTACACCTATTTCTAATT
1 AATACAATATCTAAAATTTAATCTATATGAT-ATAATTTATCCATACCTACACCTATTTCTAATT
5151 AT
65 AT
5153 GTTTTAAGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 2 0.04
69 35 0.61
71 20 0.35
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (70 bp):
AATACAATATCTAAAATTTAATCTATATGATATAATTTATCCATACCTACACCTATTTCTAATTA
TACCT
Found at i:14683 original size:22 final size:22
Alignment explanation
Indices: 14655--14705 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
14645 TTTTCTGTAA
14655 TTTATATAAATTATAAGTTC-AG
1 TTTATATAAATTATAA-TTCGAG
*
14677 TTTATAT--ATTCTAATTCGAG
1 TTTATATAAATTATAATTCGAG
14697 TTTATATAA
1 TTTATATAA
14706 TCAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
22 7 0.28
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (22 bp):
TTTATATAAATTATAATTCGAG
Found at i:17575 original size:14 final size:14
Alignment explanation
Indices: 17556--17648 Score: 141
Period size: 14 Copynumber: 6.5 Consensus size: 14
17546 GGGGGTATAA
17556 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
17570 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
* *
17584 CTCGCCATCTGTAT
1 TTCGCCACCTGTAT
*
17598 TTTGCCACCTGTAT
1 TTCGCCACCTGTAT
17612 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
17626 AATTCGCCACCTGTAT
1 --TTCGCCACCTGTAT
17642 TTCGCCA
1 TTCGCCA
17649 TCTAACTCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
14 57 0.80
16 14 0.20
ACGTcount: A:0.16, C:0.34, G:0.14, T:0.35
Consensus pattern (14 bp):
TTCGCCACCTGTAT
Found at i:21595 original size:16 final size:16
Alignment explanation
Indices: 21574--21609 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
21564 TGTGTCATGC
21574 AAGTTAAAAGTGTTGG
1 AAGTTAAAAGTGTTGG
21590 AAGTTAAAAGTGTTGG
1 AAGTTAAAAGTGTTGG
21606 AAGT
1 AAGT
21610 ATACATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (16 bp):
AAGTTAAAAGTGTTGG
Found at i:25498 original size:2 final size:2
Alignment explanation
Indices: 25491--25549 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
25481 GCTTACATAC
25491 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
25533 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
25550 GTTGTATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27305 original size:2 final size:2
Alignment explanation
Indices: 27298--27341 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
27288 TTGCTCTATT
27298 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27340 GA
1 GA
27342 TGGCGCTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27737 original size:2 final size:2
Alignment explanation
Indices: 27726--27755 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27716 GACAAACATT
27726 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27756 TTGATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47940 original size:2 final size:2
Alignment explanation
Indices: 47933--47970 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47923 TTATTTTTAC
47933 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
47971 TAAATAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49597 original size:68 final size:68
Alignment explanation
Indices: 49485--49620 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
49475 CAGAGGAAAG
*
49485 GGGCATTGGTTATGTGAGGGACTGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
1 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
49550 AAC
66 AAC
* * *
49553 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACTCATTTGCAGCCTTTAATGCCAACTT
1 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
49618 AAC
66 AAC
49621 ACGGAAACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (68 bp):
GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
AAC
Found at i:51356 original size:35 final size:35
Alignment explanation
Indices: 51276--51365 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 35
51266 GACGATCATA
* * *
51276 AGCATATTTATC-AATATGTTCGTTTAATGTTTACC
1 AGCATATTTGTCTAA-ATGTTCATTTAATATTTACC
51311 AGCATATTTGTCTAAATGTTCATTTAATATTTACC
1 AGCATATTTGTCTAAATGTTCATTTAATATTTACC
* * * *
51346 GGCATGTTTGTTTATATGTT
1 AGCATATTTGTCTAAATGTT
51366 TAAAAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 45 0.96
36 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (35 bp):
AGCATATTTGTCTAAATGTTCATTTAATATTTACC
Found at i:77811 original size:18 final size:18
Alignment explanation
Indices: 77788--77829 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
77778 TTCAAGCACA
77788 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
77806 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
*
77824 CGACAC
1 AGACAC
77830 TCAATTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (18 bp):
AGACACCACCTAACATGC
Found at i:78054 original size:23 final size:22
Alignment explanation
Indices: 78027--78070 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
78017 TGATTATTTT
78027 ATTATA-ATTTTTAAATATTTATA
1 ATTATATA-TTTTAAA-ATTTATA
*
78050 ATTATTTATTTTAAAATTTAT
1 ATTATATATTTTAAAATTTAT
78071 TAAGCGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATATATTTTAAAATTTATA
Found at i:80084 original size:10 final size:10
Alignment explanation
Indices: 80065--80094 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
80055 TCACCCACAA
80065 CAAATCCTCT
1 CAAATCCTCT
*
80075 CAAATTCTCT
1 CAAATCCTCT
80085 CAAATCCTCT
1 CAAATCCTCT
80095 AAAAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Done.