Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004831.1 Hibiscus syriacus cultivar Beakdansim tig00010883_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: 186144
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:180920 original size:10 final size:10
Alignment explanation
Indices: 180902--180976 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
180892 GGGTCTCCAA
*
180902 CGTTGATGTT
1 CGTTTATGTT
180912 CGTTTATGTT
1 CGTTTATGTT
180922 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
180933 ATGTTCATGTT
1 -CGTTTATGTT
180944 CGTTTATGTT
1 CGTTTATGTT
180954 CG----TGTT
1 CGTTTATGTT
*
180960 CATTTATGTT
1 CGTTTATGTT
180970 CGTTTAT
1 CGTTTAT
180977 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 7 0.14
12 4 0.08
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:180933 original size:16 final size:16
Alignment explanation
Indices: 180908--180980 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
180898 CCAACGTTGA
*
180908 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
180924 TGTTCATTTATGTTCA
1 TGTTCATTTATGTTCG
*
180940 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
180956 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
180972 T-TT-ATTTAT
1 TGTTCATTTAT
180981 TAAATGAACG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 44 0.85
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:180948 original size:32 final size:32
Alignment explanation
Indices: 180907--180970 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
180897 TCCAACGTTG
180907 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
180939 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
180971 GTTTATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (32 bp):
ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
Found at i:181063 original size:16 final size:16
Alignment explanation
Indices: 181042--181074 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
181032 AAAAACATTT
181042 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
181058 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
181074 T
1 T
181075 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:181450 original size:8 final size:8
Alignment explanation
Indices: 181437--181463 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
181427 GCATGTATAA
181437 ATAAATAC
1 ATAAATAC
181445 ATAAATAC
1 ATAAATAC
181453 ATAAATAC
1 ATAAATAC
181461 ATA
1 ATA
181464 GTTGAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAAATAC
Found at i:184596 original size:18 final size:18
Alignment explanation
Indices: 184573--184608 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
184563 CAAGGATGTT
184573 ATCCCTTGAGGTTTTGTC
1 ATCCCTTGAGGTTTTGTC
184591 ATCCCTTGAGGTTTTGTC
1 ATCCCTTGAGGTTTTGTC
184609 GCCTTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
ATCCCTTGAGGTTTTGTC
Done.