Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016237.1 Corchorus olitorius cultivar O-4 contig16270, 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: 25414
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:342 original size:19 final size:19
Alignment explanation
Indices: 301--342 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
291 GCTAAGTAAA
*
301 TGATTGATGATATTGATGG
1 TGATTGATGATATTGATAG
*
320 TGATTGATGA-ATCTGATAT
1 TGATTGATGATAT-TGATAG
339 TGAT
1 TGAT
343 GAATGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (19 bp):
TGATTGATGATATTGATAG
Found at i:768 original size:6 final size:6
Alignment explanation
Indices: 757--781 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
747 TAGCTTCAAA
757 TGCAAC TGCAAC TGCAAC TGCAAC T
1 TGCAAC TGCAAC TGCAAC TGCAAC T
782 ACTAGACAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (6 bp):
TGCAAC
Found at i:4029 original size:8 final size:8
Alignment explanation
Indices: 4018--4042 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4008 AAATAGATAA
4018 ATAAAAAT
1 ATAAAAAT
4026 ATAAAAAT
1 ATAAAAAT
4034 ATAAAAAT
1 ATAAAAAT
4042 A
1 A
4043 AATCGTCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:4070 original size:7 final size:7
Alignment explanation
Indices: 4051--4091 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
4041 TAAATCGTCC
*
4051 ACTCCTT
1 ACTCATT
4058 ACTCATT
1 ACTCATT
*
4065 AGTCATT
1 ACTCATT
4072 ACTCATT
1 ACTCATT
4079 ACTCATT
1 ACTCATT
4086 ACTCAT
1 ACTCAT
4092 CGAAGGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.41
Consensus pattern (7 bp):
ACTCATT
Found at i:7639 original size:6 final size:6
Alignment explanation
Indices: 7628--7654 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7618 TCTGTATCTA
7628 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
7655 GAAAGAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:12023 original size:2 final size:2
Alignment explanation
Indices: 12016--12045 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12006 TTATTTGATA
12016 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
12046 TGTCACAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16778 original size:43 final size:41
Alignment explanation
Indices: 16683--16779 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
16673 GGCTGCGTTG
* **
16683 ACCTGCTTAAGCTGGAACTAATGGACGCGATGCCTGCGTTG
1 ACCTGCTTAAGCTGGAACTAATGGACACGATGCCTGCGTCA
* * *
16724 ACCTGTTTAAGCTGGAACTAATGGACACGTTTGCATTGCGTCA
1 ACCTGCTTAAGCTGGAACTAATGGACACG-ATGC-CTGCGTCA
16767 ACCTGCTTAAGCT
1 ACCTGCTTAAGCT
16780 ACTAGTGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 27 0.57
42 3 0.06
43 17 0.36
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (41 bp):
ACCTGCTTAAGCTGGAACTAATGGACACGATGCCTGCGTCA
Found at i:16899 original size:17 final size:17
Alignment explanation
Indices: 16877--16911 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16867 TCTGCATCGC
16877 GTCGACCTGCTTAAGCT
1 GTCGACCTGCTTAAGCT
16894 GTCGACCTGCTTAAGCT
1 GTCGACCTGCTTAAGCT
16911 G
1 G
16912 GAACTAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (17 bp):
GTCGACCTGCTTAAGCT
Found at i:24238 original size:75 final size:75
Alignment explanation
Indices: 24110--24271 Score: 252
Period size: 75 Copynumber: 2.2 Consensus size: 75
24100 AAGATGGTGG
* * * *
24110 TGGGCTGGGTTTGGAAGGGTGTTTCCGGCGAGGGCTATGACCAACGGAATCAAAATGGTGATCTT
1 TGGGTTGGGTTTGGAAGGGTATTTCCGGCGAGGGCTATGACCAACGGAATCAAAAAGGTGATCCT
24175 CGTCAGGTTT
66 CGTCAGGTTT
*
24185 TGGGTTGGGTTTGGAAGGGTATTTCCGGCGAGGGCTATGACCAATGGAATCAAAAAGGTGATCCT
1 TGGGTTGGGTTTGGAAGGGTATTTCCGGCGAGGGCTATGACCAACGGAATCAAAAAGGTGATCCT
*
24250 CGTCTGGTTT
66 CGTCAGGTTT
* *
24260 TGGTTTTGGTTT
1 TGGGTTGGGTTT
24272 TGGGTAAGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.31
Consensus pattern (75 bp):
TGGGTTGGGTTTGGAAGGGTATTTCCGGCGAGGGCTATGACCAACGGAATCAAAAAGGTGATCCT
CGTCAGGTTT
Done.