Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007428.1 Hibiscus syriacus cultivar Beakdansim tig00020138_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: 917797
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:868402 original size:10 final size:10
Alignment explanation
Indices: 868384--868418 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
868374 TCAATCATGC
868384 AAAAA-AAAA
1 AAAAAGAAAA
868393 AAAAAGAAAA
1 AAAAAGAAAA
868403 AAAAAGAAAA
1 AAAAAGAAAA
868413 AGAAAA
1 A-AAAA
868419 AGCATGGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 15 0.62
11 4 0.17
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:868405 original size:16 final size:16
Alignment explanation
Indices: 868384--868419 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
868374 TCAATCATGC
868384 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
868400 AAAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAGA
868416 AAAA
1 AAAA
868420 GCATGGTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:872448 original size:6 final size:6
Alignment explanation
Indices: 872437--872466 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
872427 TTAAACGAGA
*
872437 GAAGTG GAAGTG GAAGTG GAAGTA GAAGTG
1 GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG
872467 TTTGGTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.17
Consensus pattern (6 bp):
GAAGTG
Found at i:873164 original size:31 final size:30
Alignment explanation
Indices: 873102--873166 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
873092 CACTAAATTT
* * *
873102 TTTTTTAAGTTTTTATTTAGATTATTGAAC
1 TTTTTTAAATTTTTATTTAGATTACTCAAC
873132 TTTTTTAAATCTTTTATTTAGATCT-CTCAAC
1 TTTTTTAAAT-TTTTATTTAGAT-TACTCAAC
873163 TTTT
1 TTTT
873167 AAAATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
31 20 0.67
32 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTTTTAAATTTTTATTTAGATTACTCAAC
Found at i:881717 original size:30 final size:31
Alignment explanation
Indices: 881683--881801 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 31
881673 CAATAAAAAA
* *
881683 TTTATTTAAA-TTCATGAGTCAAATTAATAT
1 TTTATCTAAAGTTCATGAATCAAATTAATAT
*
881713 TTTATCTAAAGTT--TGAATATCAAATTGATA-
1 TTTATCTAAAGTTCATG-A-ATCAAATTAATAT
* * *
881743 TTTATCTAAATTTTATTG-ATTAAATTAATAT
1 TTTATCTAAAGTTCA-TGAATCAAATTAATAT
881774 TTTATCTAAA-TTCTATGAATCAAATTAA
1 TTTATCTAAAGTTC-ATGAATCAAATTAA
881802 AAATTAAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
29 2 0.03
30 36 0.50
31 32 0.44
33 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTATCTAAAGTTCATGAATCAAATTAATAT
Found at i:881736 original size:31 final size:31
Alignment explanation
Indices: 881696--881801 Score: 112
Period size: 31 Copynumber: 3.4 Consensus size: 31
881686 ATTTAAATTC
881696 ATGAGTCAAATTAATATTTTATCTAAAGTTTGA
1 ATGA-TCAAATTAATATTTTATCTAAA-TTTGA
* *
881729 AT-ATCAAATTGATA-TTTATCTAAATTTTA
1 ATGATCAAATTAATATTTTATCTAAATTTGA
* *
881758 TTGATTAAATTAATATTTTATCTAAATTCT--
1 ATGATCAAATTAATATTTTATCTAAATT-TGA
881788 ATGAATCAAATTAA
1 ATG-ATCAAATTAA
881802 AAATTAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 5 0.08
30 22 0.35
31 31 0.50
32 2 0.03
33 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (31 bp):
ATGATCAAATTAATATTTTATCTAAATTTGA
Found at i:881748 original size:15 final size:15
Alignment explanation
Indices: 881730--881785 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
881720 AAAGTTTGAA
881730 TATC-AAATTGATATT
1 TATCTAAATT-ATATT
*
881745 TATCTAAATTTTATT
1 TATCTAAATTATATT
*
881760 GAT-TAAATTAATATTT
1 TATCTAAATT-ATA-TT
881776 TATCTAAATT
1 TATCTAAATT
881786 CTATGAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.18
15 12 0.36
16 9 0.27
17 6 0.18
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (15 bp):
TATCTAAATTATATT
Found at i:882337 original size:22 final size:22
Alignment explanation
Indices: 882295--882339 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
882285 ATAAATATTA
* *
882295 ATTTAATTATTGTATGTATAAT
1 ATTTAAATATTATATGTATAAT
882317 ATTTAAATATTATAT-TAATAAT
1 ATTTAAATATTATATGT-ATAAT
882339 A
1 A
882340 ATTATTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTAAATATTATATGTATAAT
Found at i:885827 original size:30 final size:31
Alignment explanation
Indices: 885793--885851 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
885783 TAAAAATTTT
885793 GGGACC-ATTCTG-TAATGTTT-GAAAAGTTAG
1 GGGACCAATT-TGATAAT-TTTGGAAAAGTTAG
885823 GGGACCAATTTGATAATTTTGGAAAAGTT
1 GGGACCAATTTGATAATTTTGGAAAAGTT
885852 GTGAATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (31 bp):
GGGACCAATTTGATAATTTTGGAAAAGTTAG
Found at i:893936 original size:31 final size:31
Alignment explanation
Indices: 893890--893982 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
893880 GTGTCCGACC
* *
893890 ATCAAAATGACATTTTATCTAAATTTCAAGG
1 ATCAAATTGATATTTTATCTAAATTTCAAGG
*
893921 ATCAAATTGATATTTTATGTAAAGTTT-AGAGGG
1 ATCAAATTGATATTTTATCTAAA-TTTCA-A-GG
*
893954 A-CAAATTTATATTTTATCATAAA-TTCAAG
1 ATCAAATTGATATTTTATC-TAAATTTCAAG
893983 AGTCAAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
30 1 0.02
31 24 0.46
32 20 0.38
33 7 0.13
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (31 bp):
ATCAAATTGATATTTTATCTAAATTTCAAGG
Found at i:903748 original size:21 final size:21
Alignment explanation
Indices: 903715--903772 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
903705 ATCCCTTTTC
*
903715 AAAAGGATTGATCCCTCGGGG
1 AAAAAGATTGATCCCTCGGGG
*
903736 AAAAAGATCGATCCCTCGGGG
1 AAAAAGATTGATCCCTCGGGG
903757 AAAAAGATTGATCCCT
1 AAAAAGATTGATCCCT
903773 TGAAAGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
AAAAAGATTGATCCCTCGGGG
Found at i:909681 original size:21 final size:21
Alignment explanation
Indices: 909657--909709 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
909647 ATTCCTTTTC
*
909657 AAAAAGATCAATCCCTCCGGA
1 AAAAAGATCAATCCCTCAGGA
* *
909678 AAAAATATCGATCCCTCAGGA
1 AAAAAGATCAATCCCTCAGGA
909699 AAAAAGATCAA
1 AAAAAGATCAA
909710 CCCCCAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAGATCAATCCCTCAGGA
Found at i:912718 original size:90 final size:89
Alignment explanation
Indices: 912603--912779 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
912593 TAATCACGAA
* * *
912603 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
912668 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
912693 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
912758 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
912780 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 34 0.41
90 49 0.59
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Done.