Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006931.1 Hibiscus syriacus cultivar Beakdansim tig00017788_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: 61899
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1086 original size:13 final size:13
Alignment explanation
Indices: 1068--1093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1058 CCAAGGCGTA
1068 TTGGGGATAGTTG
1 TTGGGGATAGTTG
1081 TTGGGGATAGTTG
1 TTGGGGATAGTTG
1094 ACCTAAGAAC
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTGGGGATAGTTG
Found at i:9453 original size:18 final size:16
Alignment explanation
Indices: 9432--9465 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
9422 ATTCGGGATA
9432 ATTAATATATATATATAT
1 ATTAATAT-TAT-TATAT
9450 ATTAATATTATTATAT
1 ATTAATATTATTATAT
9466 TCTTCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATATTATTATAT
Found at i:15718 original size:164 final size:157
Alignment explanation
Indices: 15487--15795 Score: 413
Period size: 164 Copynumber: 1.9 Consensus size: 157
15477 AATAAATCAC
* * * * *
15487 AAATTGAAGAACTAAATTGAAAAATAAAATATTTGTTATCAAAAAGAGAAATTGAAAGTACACAT
1 AAATTGAAAAACTAAATTGAAAAAAAAAACAATTGTTATAAAAAAGAGAAATTGAAAGTACACAT
* * *
15552 GTATTCTAGTATGGTTTAGGAGCATGT-GTCTCAAATTTGGTAAAAAAAAGAACTTAAAATAAAT
66 GTATTCTACTATGGTTTAGG-GCATGTGGT-TCAAATTTGGT-AAAAAAAGAACATAAAATAAAG
15616 GATGAATTGAAGAAATAAAAAGATTATGAA
128 GATGAATTGAAGAAATAAAAAGATTATGAA
*
15646 AAATTGAAAAACTAAATTGAAAATAAAAAACAATTGTTATAAAAAAAAAAGAGGAATTGAAAGTA
1 AAATTGAAAAACTAAATTGAAAA-AAAAAACAATTGTTAT----AAAAAAGAGAAATTGAAAGTA
* * * *
15711 CACATGTATTCTACTATGGTTTAGGGCATGTGGTTCAAATTTGGTGAAAAATGGACATAAAATGA
61 CACATGTATTCTACTATGGTTTAGGGCATGTGGTTCAAATTTGGTAAAAAAAGAACATAAAATAA
*
15776 AGGATGAATTGAGGAAATAA
126 AGGATGAATTGAAGAAATAA
15796 TGAAATTGGG
Statistics
Matches: 130, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
159 22 0.17
160 13 0.10
162 33 0.25
163 17 0.13
164 45 0.35
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (157 bp):
AAATTGAAAAACTAAATTGAAAAAAAAAACAATTGTTATAAAAAAGAGAAATTGAAAGTACACAT
GTATTCTACTATGGTTTAGGGCATGTGGTTCAAATTTGGTAAAAAAAGAACATAAAATAAAGGAT
GAATTGAAGAAATAAAAAGATTATGAA
Found at i:21144 original size:24 final size:24
Alignment explanation
Indices: 21117--21169 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
21107 TAGCGTGGTT
*
21117 GTGTTTGTAAATTAGCCGCATCTA
1 GTGTTTGTAAATTAGCCGCAACTA
21141 GTGTTTGTAAATTAGCCGCAACTA
1 GTGTTTGTAAATTAGCCGCAACTA
21165 GTGTT
1 GTGTT
21170 GTAGTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (24 bp):
GTGTTTGTAAATTAGCCGCAACTA
Found at i:24836 original size:13 final size:13
Alignment explanation
Indices: 24818--24843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24808 CCAAGGCGTA
24818 TTGGGGATAGTTG
1 TTGGGGATAGTTG
24831 TTGGGGATAGTTG
1 TTGGGGATAGTTG
24844 ACCTAAGAAC
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTGGGGATAGTTG
Found at i:40293 original size:159 final size:158
Alignment explanation
Indices: 39991--40295 Score: 418
Period size: 159 Copynumber: 1.9 Consensus size: 158
39981 AATAAATCAC
* * * * *
39991 AAATTGAAGAACTAAATTGAAAAATAAAATATTTGTTATCAAAAAGAGAAATTGAAAGTACACAT
1 AAATTGAAAAACTAAATTGAAAAAAAAAACAATTGTTATAAAAAAGAGAAATTGAAAGTACACAT
* * *
40056 GTATTCTAGTATGATTTAGGAGCATGTGTCTCAAATTTGGTAAAAAAAGAACTTAAAATAAATGA
66 GTATTCTACTATGATTTAGGAGCATGTGTCTCAAATTTGGTAAAAAAAGAACATAAAATAAAGGA
40121 TGAATTGAAGAAATAAAAAGATTATGAA
131 TGAATTGAAGAAATAAAAAGATTATGAA
*
40149 AAATTGAAAAACTAAATTGAAAATAAAAAACAATTGTTATAAAAAAAAGAGGAATTGAAAGTACA
1 AAATTGAAAAACTAAATTGAAAA-AAAAAACAATTGTTAT--AAAAAAGAGAAATTGAAAGTACA
* * * * *
40214 CATGTATTCTACTATGGTTTAGG-GCATGTGGT-TCAAATTTGGT-GAAAATGGACATAAAATGA
63 CATGTATTCTACTATGATTTAGGAGCATGT-GTCTCAAATTTGGTAAAAAAAGAACATAAAATAA
*
40276 AGGATGAATTGAGGAAATAA
127 AGGATGAATTGAAGAAATAA
40296 TGAAATTGGG
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
158 22 0.17
159 45 0.35
160 17 0.13
161 44 0.34
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (158 bp):
AAATTGAAAAACTAAATTGAAAAAAAAAACAATTGTTATAAAAAAGAGAAATTGAAAGTACACAT
GTATTCTACTATGATTTAGGAGCATGTGTCTCAAATTTGGTAAAAAAAGAACATAAAATAAAGGA
TGAATTGAAGAAATAAAAAGATTATGAA
Found at i:45653 original size:24 final size:24
Alignment explanation
Indices: 45626--45678 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
45616 TAGCGTGGTT
*
45626 GTGTTTGTAAATTAGCCGCATCTA
1 GTGTTTGTAAATTAGCCGCAACTA
45650 GTGTTTGTAAATTAGCCGCAACTA
1 GTGTTTGTAAATTAGCCGCAACTA
45674 GTGTT
1 GTGTT
45679 GTAGTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (24 bp):
GTGTTTGTAAATTAGCCGCAACTA
Found at i:49345 original size:13 final size:13
Alignment explanation
Indices: 49327--49352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49317 CCAAGGCGTA
49327 TTGGGGATAGTTG
1 TTGGGGATAGTTG
49340 TTGGGGATAGTTG
1 TTGGGGATAGTTG
49353 ACCTAAGAAC
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:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTGGGGATAGTTG
Done.