Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007927.1 Hibiscus syriacus cultivar Beakdansim tig00110333_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: 706544
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:692082 original size:50 final size:50
Alignment explanation
Indices: 692009--692149 Score: 282
Period size: 50 Copynumber: 2.8 Consensus size: 50
691999 CTTACCAAAA
692009 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
692059 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
692109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
692150 GGCAAATTCA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:692286 original size:133 final size:133
Alignment explanation
Indices: 692059--692299 Score: 473
Period size: 133 Copynumber: 1.8 Consensus size: 133
692049 TCTGTCTAAT
*
692059 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTATGTCTAATCAGATCAGATAACTC
692124 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
692189 AAC
131 AAC
692192 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTATGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTATGTCTAATCAGATCAGATAACTC
692257 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
692300 TTTAATGTTT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 107 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (133 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTATGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
AAC
Found at i:693083 original size:16 final size:17
Alignment explanation
Indices: 693042--693084 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
693032 AATAGAAAAG
*
693042 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
*
693060 AATGAATTGAATCTC-A
1 AATAAATTGAATCTCAA
693076 AATAAATTG
1 AATAAATTG
693085 CACTTGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
18 13 0.59
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:693423 original size:7 final size:7
Alignment explanation
Indices: 693411--693491 Score: 109
Period size: 7 Copynumber: 12.1 Consensus size: 7
693401 CCTTGACCCC
693411 TCTTTTT
1 TCTTTTT
693418 TCTTTTT
1 TCTTTTT
693425 T-TTTTT
1 TCTTTTT
693431 T-TTTTT
1 TCTTTTT
693437 T-TTTTT
1 TCTTTTT
*
693443 TTTTTTT
1 TCTTTTT
693450 TCTTTTT
1 TCTTTTT
693457 T-TTTTT
1 TCTTTTT
693463 TCTTTTT
1 TCTTTTT
693470 TC-TTTT
1 TCTTTTT
693476 TCTTTTT
1 TCTTTTT
693483 TCTCTTTT
1 TCT-TTTT
693491 T
1 T
693492 TTCTTCTTCA
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
6 30 0.43
7 34 0.49
8 5 0.07
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TCTTTTT
Found at i:693424 original size:1 final size:1
Alignment explanation
Indices: 693413--693493 Score: 99
Period size: 1 Copynumber: 81.0 Consensus size: 1
693403 TTGACCCCTC
* * * * *
693413 TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTCTTTTTTCTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
693478 TTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTT
693494 CTTCTTCAAG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:693431 original size:13 final size:13
Alignment explanation
Indices: 693411--693483 Score: 112
Period size: 13 Copynumber: 5.6 Consensus size: 13
693401 CCTTGACCCC
693411 TCTTTTTTCTTTTT
1 TCTTTTTT-TTTTT
693425 T-TTTTTTTTTTT
1 TCTTTTTTTTTTT
*
693437 TTTTTTTTTTTTT
1 TCTTTTTTTTTTT
693450 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
*
693463 TCTTTTTTCTTTT
1 TCTTTTTTTTTTT
693476 TCTTTTTT
1 TCTTTTTT
693484 CTCTTTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
12 6 0.11
13 49 0.88
14 1 0.02
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:693436 original size:20 final size:20
Alignment explanation
Indices: 693411--693496 Score: 120
Period size: 20 Copynumber: 4.2 Consensus size: 20
693401 CCTTGACCCC
*
693411 TCTTTTTTCTTTTTTTTTTT
1 TCTTTTTTTTTTTTTTTTTT
693431 T-TTTTTTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTTTTTTT
*
693450 TCTTTTTTTTTTTTCTTTTT
1 TCTTTTTTTTTTTTTTTTTT
693470 TCTTTTTCTTTTTTCTCTTTTTT
1 TCTTTTT-TTTTTT-T-TTTTTT
693493 TCTT
1 TCTT
693497 CTTCAAGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
19 18 0.31
20 25 0.42
21 6 0.10
22 1 0.02
23 9 0.15
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (20 bp):
TCTTTTTTTTTTTTTTTTTT
Found at i:704847 original size:19 final size:20
Alignment explanation
Indices: 704811--704849 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
704801 AAATAAAGAC
*
704811 TATAAAATTAATAACTAATT
1 TATAAAAATAATAACTAATT
704831 TATAAAAATAA-AACTAATT
1 TATAAAAATAATAACTAATT
704850 ACTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAAAATAATAACTAATT
Found at i:706145 original size:3 final size:3
Alignment explanation
Indices: 706137--706259 Score: 162
Period size: 3 Copynumber: 41.7 Consensus size: 3
706127 TTTAATATTT
*
706137 ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
706185 ATA A-A AAA ATA ATA A-A ATA ATA ATG ATA ATA ATA TTA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
706231 AT- ATA ATA TTA ATA ATA ATGA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT
706260 GGATAAAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
2 6 0.06
3 96 0.91
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Done.