Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006511.1 Hibiscus syriacus cultivar Beakdansim tig00015856_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: 46752
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:8706 original size:23 final size:23
Alignment explanation
Indices: 8661--8715 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
8651 TGCTCGTGTT
* *
8661 TATTCGTTTAGCGTTCACAAACA
1 TATTCATTTAACGTTCACAAACA
**
8684 TATTCATTTAACGTTCATGAACA
1 TATTCATTTAACGTTCACAAACA
*
8707 TACTCATTT
1 TATTCATTT
8716 TTTTAAATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (23 bp):
TATTCATTTAACGTTCACAAACA
Found at i:15470 original size:31 final size:32
Alignment explanation
Indices: 15426--15487 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 32
15416 AATTGTTATG
15426 AAAGTCTTATCATTTTAAAAGTCCATGGATCA
1 AAAGTCTTATCATTTTAAAAGTCCATGGATCA
15458 AAAGTC-TATCATTTTAAAAGTCCATGGATC
1 AAAGTCTTATCATTTTAAAAGTCCATGGATC
15488 CTTGGAGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
AAAGTCTTATCATTTTAAAAGTCCATGGATCA
Found at i:16474 original size:2 final size:2
Alignment explanation
Indices: 16467--16496 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16457 TGATATGTAA
16467 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
16497 TGTAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35159 original size:24 final size:24
Alignment explanation
Indices: 35127--35185 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
35117 CGTAAAAGTA
35127 ATCGAGACAGAAGATATTCACGCT
1 ATCGAGACAGAAGATATTCACGCT
35151 ATCGAGACAGAAGATATTCACGCT
1 ATCGAGACAGAAGATATTCACGCT
35175 ATCGAGACAGA
1 ATCGAGACAGA
35186 TAAATCAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (24 bp):
ATCGAGACAGAAGATATTCACGCT
Found at i:38135 original size:15 final size:16
Alignment explanation
Indices: 38115--38166 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38105 ATATTACTTA
38115 TTCAAGTCATTT-AAG
1 TTCAAGTCATTTCAAG
*
38130 TTCAAGTCAATTTGAA-
1 TTCAAGTC-ATTTCAAG
* *
38146 TTCAGGTCTTTTCAAG
1 TTCAAGTCATTTCAAG
38162 TTCAA
1 TTCAA
38167 ATTGAATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 13 0.43
16 15 0.50
17 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (16 bp):
TTCAAGTCATTTCAAG
Found at i:39484 original size:60 final size:59
Alignment explanation
Indices: 39375--39506 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
39365 TTGAATGAAT
* * * * **
39375 ATTTTGTAATTTTTAATAGTTAGGAGACTCAACAAAACATTGTTTTATAGTCTAACAACC
1 ATTTTGTAACTTTTAATAGTCAGGAGACTCAACAAAACAATATCCTATAGT-TAACAACC
* * *
39435 ATTTTGTAACTTTTAATAGTCAGTG-GACTCGACAAAACAATATCCTATAGTTGAGAACC
1 ATTTTGTAACTTTTAATAGTCAG-GAGACTCAACAAAACAATATCCTATAGTTAACAACC
39494 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
39507 ACCCTATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 15 0.25
60 45 0.74
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAGGAGACTCAACAAAACAATATCCTATAGTTAACAACC
Found at i:40375 original size:21 final size:21
Alignment explanation
Indices: 40349--40391 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40339 AATATAATTA
40349 TTTTTATATTATATTATATTT
1 TTTTTATATTATATTATATTT
40370 TTTTTATATTATATTATATTT
1 TTTTTATATTATATTATATTT
40391 T
1 T
40392 ATATAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATATTATATTATATTT
Found at i:40871 original size:27 final size:27
Alignment explanation
Indices: 40841--40909 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
40831 AAAATACAAA
*
40841 TTATTATAAAATCAAAATCGAAATAAT
1 TTATTAAAAAATCAAAATCGAAATAAT
*
40868 TTATTAAAAAATCTAAATCGAAATAAT
1 TTATTAAAAAATCAAAATCGAAATAAT
40895 TTATTAAAAAATCAA
1 TTATTAAAAAATCAA
40910 CCGAATTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (27 bp):
TTATTAAAAAATCAAAATCGAAATAAT
Found at i:41275 original size:29 final size:29
Alignment explanation
Indices: 41243--41303 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
41233 GGTGACCAAT
41243 TTTTA-AGAATTTAAATATGCAAATATTTA
1 TTTTACAGAATTTAAA-ATGCAAATATTTA
** **
41272 TTTTACATCATTTAAAATTTAAATATTTA
1 TTTTACAGAATTTAAAATGCAAATATTTA
41301 TTT
1 TTT
41304 GACAACTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTACAGAATTTAAAATGCAAATATTTA
Done.