Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001124.1 Hibiscus syriacus cultivar Beakdansim tig00002224_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: 82546
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5126 original size:19 final size:19
Alignment explanation
Indices: 5102--5185 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 19
5092 TGCATCGTGT
* *
5102 TTGTATACTTATGCCGTTG
1 TTGTATACTTACGCCCTTG
5121 TTGTATACTTACGCCCTTG
1 TTGTATACTTACGCCCTTG
* * *
5140 TTGATCAACACACTTATGCCGTTG
1 TTG-T----ATACTTACGCCCTTG
5164 TTGTATACTTACGCCCTTG
1 TTGTATACTTACGCCCTTG
5183 TTG
1 TTG
5186 ATCAACGGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 35 0.67
20 1 0.02
23 1 0.02
24 15 0.29
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (19 bp):
TTGTATACTTACGCCCTTG
Found at i:5169 original size:43 final size:43
Alignment explanation
Indices: 5108--5191 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
5098 GTGTTTGTAT
5108 ACTTATGCCGTTGTTGTATACTTACGCCCTTGTTGATCAACAC
1 ACTTATGCCGTTGTTGTATACTTACGCCCTTGTTGATCAACAC
5151 ACTTATGCCGTTGTTGTATACTTACGCCCTTGTTGATCAAC
1 ACTTATGCCGTTGTTGTATACTTACGCCCTTGTTGATCAAC
5192 GGTTACAGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (43 bp):
ACTTATGCCGTTGTTGTATACTTACGCCCTTGTTGATCAACAC
Found at i:9689 original size:3 final size:3
Alignment explanation
Indices: 9681--9707 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9671 CATAGAACCT
9681 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
9708 AATGAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17296 original size:22 final size:22
Alignment explanation
Indices: 17268--17312 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17258 TCTAATCATT
*
17268 TGACATTAAACGCTCATTTCCC
1 TGACATTAAACGCTCATTCCCC
*
17290 TGACATTTAACGCTCATTCCCC
1 TGACATTAAACGCTCATTCCCC
17312 T
1 T
17313 AATATTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (22 bp):
TGACATTAAACGCTCATTCCCC
Found at i:23117 original size:41 final size:41
Alignment explanation
Indices: 23060--23142 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
23050 TTGGAAGGAT
23060 TTATGGTGAACGATAAGAAAAGGGTTTTCGCTGTTGAGATG
1 TTATGGTGAACGATAAGAAAAGGGTTTTCGCTGTTGAGATG
23101 TTATGGTGAACGATAAGAAAAGGGTTTTCGCTGTTGAGATG
1 TTATGGTGAACGATAAGAAAAGGGTTTTCGCTGTTGAGATG
23142 T
1 T
23143 GACGACCTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (41 bp):
TTATGGTGAACGATAAGAAAAGGGTTTTCGCTGTTGAGATG
Found at i:32103 original size:74 final size:74
Alignment explanation
Indices: 31993--32176 Score: 244
Period size: 74 Copynumber: 2.5 Consensus size: 74
31983 TATCAATATG
* * * * * *
31993 AAAAAGGATCTAAAATGCTATTATACCAAAAAGTTTGAGAGGGAAAAAGACCCTATTT-GATTAA
1 AAAAAAGAACTAAAATGCTATTATACCAAAATGTTTGAGAGGAAAAAAAACCCTATTTAG-CTAA
32057 TAATTAAACT
65 TAATTAAACT
* * * * *
32067 AATAAAGACCTAAAATGTTATTATACCAAAATGTTTGAGAGGAAAAAAAATCTTATTTAGCTAAT
1 AAAAAAGAACTAAAATGCTATTATACCAAAATGTTTGAGAGGAAAAAAAACCCTATTTAGCTAAT
*
32132 ATTTAAACT
66 AATTAAACT
32141 AAAAAAGAACTAAAATGCTATTATACCAAAATGTTT
1 AAAAAAGAACTAAAATGCTATTATACCAAAATGTTT
32177 AAGAATCGAC
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
74 94 0.99
75 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (74 bp):
AAAAAAGAACTAAAATGCTATTATACCAAAATGTTTGAGAGGAAAAAAAACCCTATTTAGCTAAT
AATTAAACT
Found at i:36291 original size:50 final size:51
Alignment explanation
Indices: 36236--36350 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 51
36226 GTGTCTCTAC
* * * *
36236 ACCGCGCTATACGTTGATTTGATTCCACGTGGAGTATAGCGC-CCCCCTGA
1 ACCGCGCTATACGCTGACTAGATTACACGTGGAGTATAGCGCACCCCCTGA
* * * *
36286 ACCGCGCTATATGCTGACTAGGTTACACGTGGGGTATAGTGCACCCCCTGA
1 ACCGCGCTATACGCTGACTAGATTACACGTGGAGTATAGCGCACCCCCTGA
* *
36337 TCCACGCTATACGC
1 ACCGCGCTATACGC
36351 CACGTAGGGA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
50 34 0.64
51 19 0.36
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.24
Consensus pattern (51 bp):
ACCGCGCTATACGCTGACTAGATTACACGTGGAGTATAGCGCACCCCCTGA
Found at i:37426 original size:35 final size:34
Alignment explanation
Indices: 37341--37427 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
37331 ATTTGATATT
*
37341 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
37375 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
37413 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
37428 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:37657 original size:9 final size:9
Alignment explanation
Indices: 37639--37686 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
37629 ACTCCTTGCT
37639 GTCATCGTC
1 GTCATCGTC
*
37648 GTCGTCGTC
1 GTCATCGTC
* *
37657 GTCACCATC
1 GTCATCGTC
* *
37666 GTCGTCATC
1 GTCATCGTC
37675 GTCATCGTC
1 GTCATCGTC
37684 GTC
1 GTC
37687 CTGAGAAGGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.23, T:0.31
Consensus pattern (9 bp):
GTCATCGTC
Found at i:38072 original size:18 final size:17
Alignment explanation
Indices: 38021--38074 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
38011 GGCGATGGTG
*
38021 GCATCATATATGGCTAC
1 GCATCATATATGGCTGC
*
38038 GACATTATATATGGCTGC
1 G-CATCATATATGGCTGC
38056 AGCATCATATATGGCTGC
1 -GCATCATATATGGCTGC
38074 G
1 G
38075 GTGGCTGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 2 0.06
18 29 0.91
19 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (17 bp):
GCATCATATATGGCTGC
Found at i:39722 original size:111 final size:111
Alignment explanation
Indices: 39583--39804 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
39573 ATTACAAAAA
* *
39583 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
39648 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
39694 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
39759 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
39805 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:43667 original size:8 final size:8
Alignment explanation
Indices: 43656--43684 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
43646 GTCAACGGGT
43656 CGGGTAAA
1 CGGGTAAA
43664 CGGGTAAA
1 CGGGTAAA
43672 CGGGTAAA
1 CGGGTAAA
43680 CGGGT
1 CGGGT
43685 CATGACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.41, T:0.14
Consensus pattern (8 bp):
CGGGTAAA
Found at i:52475 original size:13 final size:13
Alignment explanation
Indices: 52457--52486 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52447 AGATCTTCCC
52457 AAAACCCGAATAG
1 AAAACCCGAATAG
52470 AAAACCCGAATAG
1 AAAACCCGAATAG
52483 AAAA
1 AAAA
52487 TCTGAGCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAACCCGAATAG
Found at i:54908 original size:2 final size:2
Alignment explanation
Indices: 54901--54935 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54891 CCCATCAATG
54901 TA TA TA TA TA 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 TA TA T
54936 TAATTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56037 original size:13 final size:13
Alignment explanation
Indices: 56019--56044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56009 CATAAGGAGT
56019 GCATCGATGCACC
1 GCATCGATGCACC
56032 GCATCGATGCACC
1 GCATCGATGCACC
56045 TGTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
GCATCGATGCACC
Found at i:62376 original size:2 final size:2
Alignment explanation
Indices: 62369--62397 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62359 CACCTTTATT
62369 TA TA 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 T
62398 GAAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67351 original size:18 final size:17
Alignment explanation
Indices: 67324--67357 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
67314 CACAGTTGTT
67324 TAAATAATTTTAATTTA
1 TAAATAATTTTAATTTA
67341 TAAATTAATTTTAATTT
1 TAAA-TAATTTTAATTT
67358 TTAGCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATAATTTTAATTTA
Found at i:68792 original size:23 final size:23
Alignment explanation
Indices: 68766--68821 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
68756 GTTCATTATG
68766 TATTCGTTTAAAGATTGGGTACA
1 TATTCGTTTAAAGATTGGGTACA
*
68789 TATTCGTTTAATGATTGGGTACA
1 TATTCGTTTAAAGATTGGGTACA
68812 TATTCGTTTA
1 TATTCGTTTA
68822 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (23 bp):
TATTCGTTTAAAGATTGGGTACA
Found at i:70753 original size:28 final size:29
Alignment explanation
Indices: 70682--70754 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
70672 GCAAGGTAAT
*
70682 TATTTTTTTATGATTTT-TTAATTTCATAA
1 TATTTTTTTA-AATTTTATTAATTTCATAA
* ** *
70711 -ATTTATTTATTTTTTATTTATTT-ATAA
1 TATTTTTTTAAATTTTATTAATTTCATAA
70738 TATTTTTTTAAATTTTA
1 TATTTTTTTAAATTTTA
70755 GATGATGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (29 bp):
TATTTTTTTAAATTTTATTAATTTCATAA
Found at i:71802 original size:15 final size:15
Alignment explanation
Indices: 71784--71813 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
71774 TTTAAATACT
*
71784 TTTTATTTTTTTTAA
1 TTTTATTTCTTTTAA
71799 TTTTATTTCTTTTAA
1 TTTTATTTCTTTTAA
71814 AATTTTATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTCTTTTAA
Found at i:73915 original size:34 final size:36
Alignment explanation
Indices: 73849--73928 Score: 137
Period size: 34 Copynumber: 2.2 Consensus size: 36
73839 AACATTTCTC
73849 TTATTAATTTCTTATTTTTTAAATAAATATTTTCTTA
1 TTATTAA-TTCTTATTTTTTAAATAAATATTTTCTTA
73886 TTATTAATTCTTATTTTTTAAAT-AA-ATTTTCTTA
1 TTATTAATTCTTATTTTTTAAATAAATATTTTCTTA
73920 TTATTAATT
1 TTATTAATT
73929 TAATAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 18 0.42
35 2 0.05
36 16 0.37
37 7 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (36 bp):
TTATTAATTCTTATTTTTTAAATAAATATTTTCTTA
Done.