Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023717.1 Corchorus olitorius cultivar O-4 contig23750, 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: 9378
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:1013 original size:28 final size:28
Alignment explanation
Indices: 973--1027 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
963 TGTATTTAAG
973 CCTTACCATGATAGTATTAGTTTTTTTC
1 CCTTACCATGATAGTATTAGTTTTTTTC
* *
1001 CCTTGCCATGATAGTTTTAGTTTTTTT
1 CCTTACCATGATAGTATTAGTTTTTTT
1028 TTTCCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (28 bp):
CCTTACCATGATAGTATTAGTTTTTTTC
Found at i:2266 original size:13 final size:13
Alignment explanation
Indices: 2237--2266 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2227 CTTAAATTAA
2237 TTTTTGAAAATTG
1 TTTTTGAAAATTG
2250 TTTTT-AAAATTG
1 TTTTTGAAAATTG
2262 TTTTT
1 TTTTT
2267 AGAACTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (13 bp):
TTTTTGAAAATTG
Found at i:6569 original size:35 final size:36
Alignment explanation
Indices: 6527--6604 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 36
6517 AGAAGGAGCT
*
6527 AAAAAAAC-TGGACCTAAAATAGAAAGAGGTCA-AAA
1 AAAAAAACTTGG-CCTAAAACAGAAAGAGGTCAGAAA
*
6562 AAAAAAACTTGGCCTAAAACAGAGAGAGGTCAGAAA
1 AAAAAAACTTGGCCTAAAACAGAAAGAGGTCAGAAA
6598 AAAAAAA
1 AAAAAAA
6605 GAAAATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 26 0.67
36 13 0.33
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (36 bp):
AAAAAAACTTGGCCTAAAACAGAAAGAGGTCAGAAA
Found at i:6652 original size:25 final size:25
Alignment explanation
Indices: 6619--6668 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6609 ATAAATAAAA
6619 AGGAGGGGTTCAGGTTGAAAACCCG
1 AGGAGGGGTTCAGGTTGAAAACCCG
6644 AGGAGGGGTTCAGGTTGAAAACCCG
1 AGGAGGGGTTCAGGTTGAAAACCCG
6669 CAAAGGGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (25 bp):
AGGAGGGGTTCAGGTTGAAAACCCG
Found at i:7560 original size:59 final size:59
Alignment explanation
Indices: 7486--7634 Score: 221
Period size: 58 Copynumber: 2.5 Consensus size: 59
7476 TTAAAAATCC
* *
7486 AAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAGTTTAAAATATCT-TCTTGTTTTA
1 AAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAGTTCAAAATAT-TATCTTGTTTCA
* *
7545 AAATCCTGTTTGAGGTCTCTGTTAGAGAG-TTTTCAGTTCAAAATCTTATCTTGTTTCA
1 AAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAGTTCAAAATATTATCTTGTTTCA
* *
7603 AAATCCTGTTCCAGGTCTTTGTTAGAGAGTTT
1 AAATCCTGTTCGAGGTCTCTGTTAGAGAGTTT
7635 ATATTTCAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 1 0.01
58 50 0.62
59 30 0.37
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (59 bp):
AAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAGTTCAAAATATTATCTTGTTTCA
Found at i:7948 original size:58 final size:59
Alignment explanation
Indices: 7877--8013 Score: 195
Period size: 58 Copynumber: 2.3 Consensus size: 59
7867 TGCAAATCTT
* * * * * *
7877 AGGGGCATCTTGGTCATTTTTACCCATCCAGGGGCGTTTTGGTCATTTTTGCA-TATCC
1 AGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCATTTTTACACAATCC
*
7935 AGGGGTATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCATTTTTACACAATCC
1 AGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCATTTTTACACAATCC
*
7994 GGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
8014 GGTTTTATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
58 47 0.68
59 22 0.32
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (59 bp):
AGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCATTTTAGTCATTTTTACACAATCC
Found at i:8002 original size:30 final size:29
Alignment explanation
Indices: 7877--8013 Score: 175
Period size: 29 Copynumber: 4.7 Consensus size: 29
7867 TGCAAATCTT
*
7877 AGGGGCATCTTGGTCATTTTTACCCATCC
1 AGGGGCATTTTGGTCATTTTTACCCATCC
* * **
7906 AGGGGCGTTTTGGTCATTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTACCCATCC
*
7935 AGGGGTATTTTGGTCATTTTTACCCATCC
1 AGGGGCATTTTGGTCATTTTTACCCATCC
* * *
7964 AAGGGCATTTTAGTCATTTTTACACAATCC
1 AGGGGCATTTTGGTCATTTTTAC-CCATCC
*
7994 GGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
8014 GGTTTTATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 68 0.76
30 22 0.24
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTACCCATCC
Done.