Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008494.1 Hibiscus syriacus cultivar Beakdansim tig00111337_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: 46708
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2892 original size:22 final size:22
Alignment explanation
Indices: 2851--2893 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2841 TCATTGCATA
2851 AAAATTAAACAGTTATAACTCCT
1 AAAATTAAACAG-TATAACTCCT
2874 AAAATTAAATCA-TATAACTC
1 AAAATTAAA-CAGTATAACTC
2894 ATGTAACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTAAACAGTATAACTCCT
Found at i:5921 original size:12 final size:12
Alignment explanation
Indices: 5904--5935 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5894 AGAAGAGGAG
*
5904 GTGGAGGCTTAC
1 GTGGAGGCTCAC
5916 GTGGAGGCTCAC
1 GTGGAGGCTCAC
5928 GTGGAGGC
1 GTGGAGGC
5936 AGGGTAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.47, T:0.19
Consensus pattern (12 bp):
GTGGAGGCTCAC
Found at i:14021 original size:16 final size:17
Alignment explanation
Indices: 14002--14035 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13992 AATATTACTT
14002 TTATTCAA-TAAAAAAA
1 TTATTCAATTAAAAAAA
*
14018 TTATTTAATTAAAAAAA
1 TTATTCAATTAAAAAAA
14035 T
1 T
14036 AATATAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATTCAATTAAAAAAA
Found at i:17980 original size:17 final size:17
Alignment explanation
Indices: 17955--17989 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17945 TATTCCAAGA
17955 CAAGACGGATCCCGAGG
1 CAAGACGGATCCCGAGG
* *
17972 CAAGTCGGATCTCGAGG
1 CAAGACGGATCCCGAGG
17989 C
1 C
17990 TTGCCTAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (17 bp):
CAAGACGGATCCCGAGG
Found at i:27467 original size:21 final size:20
Alignment explanation
Indices: 27442--27480 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27432 CATCAAGGTC
27442 TTTGTAGACGCCATGAAATCT
1 TTTGTAGACGCCAT-AAATCT
* *
27463 TTTGTCGAGGCCATAAAT
1 TTTGTAGACGCCATAAAT
27481 TTCTGCAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
TTTGTAGACGCCATAAATCT
Found at i:37461 original size:87 final size:87
Alignment explanation
Indices: 37350--37512 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 87
37340 GAAAAATTAT
* *
37350 TTTATAAATTACAATAAAGGACAAAATT-TGTTATAAACTACAATAAAGTACAAAA-CTATTTAT
1 TTTATAAATTACAATAAAAGACAAAATTAT-TTATAAACTACAATAAAGGACAAAACCT-TTTAT
37413 AAATAACAATAAATTAAAAAACAA
64 AAATAACAATAAATTAAAAAACAA
* * *
37437 TTTATAAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGATAAAACCTTTTATAA
1 TTTATAAATTACAATAAAAGACAAAATTATTTATAAACTACAATAAAGGACAAAACCTTTTATAA
* *
37502 ATTATAATAAA
66 ATAACAATAAA
37513 AGGAGACATT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 64 0.96
88 3 0.04
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (87 bp):
TTTATAAATTACAATAAAAGACAAAATTATTTATAAACTACAATAAAGGACAAAACCTTTTATAA
ATAACAATAAATTAAAAAACAA
Found at i:37491 original size:29 final size:28
Alignment explanation
Indices: 37269--37542 Score: 183
Period size: 29 Copynumber: 9.5 Consensus size: 28
37259 AAGAATCATC
* *
37269 AAATTACAATAAAAGACAAAATGTTTTAG
1 AAATTACAATAAAGGACAAAAT-TTTTAT
* * *** * *
37298 AATTTATAATAAAAGTTTAAACTTTTTAG
1 AAATTACAAT-AAAGGACAAAATTTTTAT
*
37327 AATTTACAATAAA-GA-AAAATTATTTTAT
1 AAATTACAATAAAGGACAAAA-T-TTTTAT
37355 AAATTACAATAAAGGACAAAATTTGTTAT
1 AAATTACAATAAAGGACAAAATTT-TTAT
* * *
37384 AAACTACAATAAAGTACAAAACTATTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
* ** * **
37413 AAATAACAATAAATTAAAAAACAATTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
**
37442 AAATTACAATAAAATACAAAATTATTTAT
1 AAATTACAATAAAGGACAAAATT-TTTAT
* *
37471 AAATTACAATAAAGGATAAAACCTTTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
* * **
37500 AAATTATAATAAAAGGAGACATTTTTTTAT
1 AAATTACAAT-AAAGGACA-AAATTTTTAT
*
37530 AAAATACAATAAA
1 AAATTACAATAAA
37543 TTTAGCATAA
Statistics
Matches: 197, Mismatches: 37, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.02
27 1 0.01
28 22 0.11
29 135 0.69
30 35 0.18
31 1 0.01
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATTACAATAAAGGACAAAATTTTTAT
Found at i:37513 original size:58 final size:58
Alignment explanation
Indices: 37269--37513 Score: 219
Period size: 58 Copynumber: 4.2 Consensus size: 58
37259 AAGAATCATC
* * * * * *** * *
37269 AAATTACAATAAAAGACAAAATGT-TTTAGAATTTATAATAAAAGTTTAAACTTTTTAG
1 AAATTACAATAAAATACAAAAT-TATTTATAAATTACAATAAAGGAAAAAACATTTTAT
* * * *
37327 AATTTACAAT-AAAGA-AAAATTATTTTATAAATTACAATAAAGGACAAAA-TTTGTTAT
1 AAATTACAATAAAATACAAAATTA-TTTATAAATTACAATAAAGGAAAAAACATT-TTAT
* * * * ** *
37384 AAACTACAATAAAGTACAAAACTATTTATAAATAACAATAAATTAAAAAACAATTTAT
1 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
* *
37442 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGATAAAACCTTTTAT
1 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
*
37500 AAATTATAATAAAA
1 AAATTACAATAAAA
37514 GGAGACATTT
Statistics
Matches: 151, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
55 1 0.01
56 8 0.05
57 35 0.23
58 100 0.66
59 7 0.05
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (58 bp):
AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
Done.