Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007620.1 Hibiscus syriacus cultivar Beakdansim tig00023007_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: 28918
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:4432 original size:21 final size:21
Alignment explanation
Indices: 4406--4445 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4396 CCCCCTTTGA
*
4406 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
4427 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
4446 TGGGGTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:7180 original size:74 final size:73
Alignment explanation
Indices: 7013--7190 Score: 239
Period size: 73 Copynumber: 2.4 Consensus size: 73
7003 CCAAAAAATA
* * * **
7013 CAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGTTTGGC
1 CAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGGC
*
7078 TCGAGATTTC
64 TCGAGAATTC
* * *
7088 CAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACATTTTTGTTC
1 CAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGGCTC
7153 TGAGAATTC
66 -GAGAATTC
*
7162 CAGTATGCTCGGAGGGAACCGATTCCCCC
1 CAGAATGCTCGGAGGGAACCGATTCCCCC
7191 CCCAGGGGGT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
73 35 0.38
74 35 0.38
75 22 0.24
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (73 bp):
CAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGGCTC
GAGAATTC
Found at i:10235 original size:2 final size:2
Alignment explanation
Indices: 10228--10279 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
10218 AGAAAACATA
10228 AT AT AT AT AT AT 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 AT AT AT AT AT AT
10270 AT AT AT AT AT
1 AT AT AT AT AT
10280 CAAGAATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13389 original size:18 final size:19
Alignment explanation
Indices: 13359--13399 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
13349 GAGGACTTTT
13359 ATATTATTTATAAAA-ATA
1 ATATTATTTATAAAACATA
13377 ATATT-TTTCATAAAACATA
1 ATATTATTT-ATAAAACATA
13396 ATAT
1 ATAT
13400 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.52
19 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTATTTATAAAACATA
Found at i:23216 original size:29 final size:28
Alignment explanation
Indices: 23164--23234 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
23154 CTCATAATTC
* *
23164 TAATAATATGATATTATATTCTTTAATAT
1 TAATAATAT-ATAATATATACTTTAATAT
* *
23193 TAATAATATATAATATTATACTTTTATTT
1 TAATAATATATAATA-TATACTTTAATAT
*
23222 TAAT-ATATTTAAT
1 TAATAATATATAAT
23235 GATTTTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TAATAATATATAATATATACTTTAATAT
Found at i:27407 original size:2 final size:2
Alignment explanation
Indices: 27400--27424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27390 TATTTCTTGG
27400 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27425 AGATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.