Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014326.1 Corchorus olitorius cultivar O-4 contig14359, 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: 17244
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:73 original size:33 final size:33
Alignment explanation
Indices: 1--63 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
* *
1 GAGGGCGCCATGGCCAAGTCCATGCCGCCCACC
1 GAGGGCGCCATGGACAAGTCCACGCCGCCCACC
34 GAGGGCGCCATGGACATAG-CCACGCCGCCC
1 GAGGGCGCCATGGACA-AGTCCACGCCGCCC
64 TAGCAGGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.19, C:0.41, G:0.32, T:0.08
Consensus pattern (33 bp):
GAGGGCGCCATGGACAAGTCCACGCCGCCCACC
Found at i:1315 original size:21 final size:22
Alignment explanation
Indices: 1290--1333 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1280 CACAACAATA
1290 ATTTAGTT-AAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
1311 ATTTAGTTAAAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
1333 A
1 A
1334 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTG
Found at i:6334 original size:40 final size:40
Alignment explanation
Indices: 6218--6319 Score: 195
Period size: 40 Copynumber: 2.5 Consensus size: 40
6208 TGTTACATGA
*
6218 GTGGGTTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
1 GTGGATTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
6258 GTGGATTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
1 GTGGATTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
6298 GTGGATTAGAACAAATTGTTTT
1 GTGGATTAGAACAAATTGTTTT
6320 GGATTATATT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (40 bp):
GTGGATTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
Found at i:6630 original size:89 final size:89
Alignment explanation
Indices: 6479--6766 Score: 504
Period size: 89 Copynumber: 3.2 Consensus size: 89
6469 AACGGCGTGT
* * *
6479 GGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTATGGCTTACGTTGCT
1 GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
6544 ATAGAATGTATACCAACAGCGGGG
66 ATAGAATGTATACCAACAGCGGGG
6568 GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
1 GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
* **
6633 ATAGAATGTATACCAACAGTGGAT
66 ATAGAATGTATACCAACAGCGGGG
6657 GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
1 GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
* *
6722 ATAGCATGTATACCAACAGCGTGG
66 ATAGAATGTATACCAACAGCGGGG
6746 GGCGTTGGTATAGCCATAAAC
1 GGCGTTGGTATAGCCATAAAC
6767 AGCCAACAGG
Statistics
Matches: 188, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 188 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (89 bp):
GGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCT
ATAGAATGTATACCAACAGCGGGG
Found at i:6793 original size:178 final size:178
Alignment explanation
Indices: 6478--6800 Score: 522
Period size: 178 Copynumber: 1.8 Consensus size: 178
6468 AAACGGCGTG
* *
6478 TGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCTATGGCTTACGTTGC
1 TGGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTACGTTGC
* *
6543 TATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGG
66 TATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAAACAGTATGATGGG
6608 AGATATACCTACGGCTTCCGTTGCTATAGAATGTATACCAACAGTGGA
131 AGATATACCTACGGCTTCCGTTGCTATAGAATGTATACCAACAGTGGA
*
6656 TGGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGC
1 TGGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTACGTTGC
* * *** *
6721 TATAGCATGTATACCAACAGCGTGGGGCGTTGGTATAGCCATAAA-CAGCCAACAGGTTTGATGG
66 TATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAAACA-GTATGATGG
*
6785 GGGATATACCTACGGC
130 GAGATATACCTACGGC
6801 GAAGAAACTA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
177 5 0.04
178 127 0.96
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (178 bp):
TGGCGTTGGTATAGCCATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTACGTTGC
TATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAAACAGTATGATGGG
AGATATACCTACGGCTTCCGTTGCTATAGAATGTATACCAACAGTGGA
Found at i:10946 original size:37 final size:37
Alignment explanation
Indices: 10902--10972 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
10892 CTTGATCAAC
* *
10902 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
10939 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
10973 ATAATTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:12109 original size:20 final size:20
Alignment explanation
Indices: 12084--12124 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12074 GACTTTCCAA
12084 TGACTTCCATCAATAAATTG
1 TGACTTCCATCAATAAATTG
*
12104 TGACTTTCATCAATAAATTG
1 TGACTTCCATCAATAAATTG
12124 T
1 T
12125 ACTACACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (20 bp):
TGACTTCCATCAATAAATTG
Done.