Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012722.1 Corchorus olitorius cultivar O-4 contig12755, 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: 25938
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:987 original size:21 final size:20
Alignment explanation
Indices: 961--999 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
951 AATCCGAGAG
961 TTTTTTGTGTGGTTTTTCTTT
1 TTTTTTGTGT-GTTTTTCTTT
*
982 TTTTTTTTGTGTTTTTCT
1 TTTTTTGTGTGTTTTTCT
1000 GCGTGTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.79
Consensus pattern (20 bp):
TTTTTTGTGTGTTTTTCTTT
Found at i:2957 original size:28 final size:28
Alignment explanation
Indices: 2919--3110 Score: 269
Period size: 28 Copynumber: 6.7 Consensus size: 28
2909 TAAATGTGCA
* *
2919 AAAATGACCAAAACGCCCCCGGATATGC
1 AAAATGACCAAAATGCCCCTGGATATGC
*
2947 AAAATGACCAAAATGTCCCCTGGATGTGC
1 AAAATGACCAAAATG-CCCCTGGATATGC
*
2976 AAAAGTAACCAAAATGCCCCTGGATATGC
1 AAAA-TGACCAAAATGCCCCTGGATATGC
*
3005 AAAATGACCAAAATGTCCCCTGGATGTGC
1 AAAATGACCAAAATG-CCCCTGGATATGC
*
3034 AAAAGTAACCAAAATGCCCCTGGATATGC
1 AAAA-TGACCAAAATGCCCCTGGATATGC
3063 AAAATGACCAAAATGCCCCTGG-TCATGC
1 AAAATGACCAAAATGCCCCTGGAT-ATGC
*
3091 AAAATGATCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
3111 TTAAGTGACC
Statistics
Matches: 148, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
27 1 0.01
28 64 0.43
29 63 0.43
30 20 0.14
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATATGC
Found at i:2995 original size:58 final size:58
Alignment explanation
Indices: 2912--3110 Score: 305
Period size: 58 Copynumber: 3.5 Consensus size: 58
2902 ATACCCCTAA
* * * *
2912 ATGTGCAAAAATGACCAAAACGCCCCCGGATATGCAAAATGACCAAAATGTCCCCTGG
1 ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATGTCCCCTGG
2970 ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATGTCCCCTGG
1 ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATGTCCCCTGG
3028 ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATG-CCCCTGG
1 ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATGTCCCCTGG
* * *
3085 -TCATGCAAAA-TGATCAAAATGCCCCT
1 AT-GTGCAAAAGTAACCAAAATGCCCCT
3111 TTAAGTGACC
Statistics
Matches: 133, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
56 15 0.11
57 14 0.11
58 104 0.78
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (58 bp):
ATGTGCAAAAGTAACCAAAATGCCCCTGGATATGCAAAATGACCAAAATGTCCCCTGG
Found at i:4510 original size:27 final size:27
Alignment explanation
Indices: 4470--4541 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
4460 GTAAAGTGAC
4470 CAAATGACCAAAATG-CCTCTGGATGCA
1 CAAATGACCAAAATGCCCT-TGGATGCA
* *
4497 CAAATGACCGAAATGCCCTTGGGTGCA
1 CAAATGACCAAAATGCCCTTGGATGCA
4524 CAAATGACCAAAATGCCC
1 CAAATGACCAAAATGCCC
4542 CTAGGTGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 38 0.93
28 3 0.07
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCTTGGATGCA
Found at i:5898 original size:17 final size:17
Alignment explanation
Indices: 5868--5901 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5858 GTCAAAGTTG
5868 AAGAAAAAAATGAAAAA
1 AAGAAAAAAATGAAAAA
* *
5885 AAGAAGAAAGTGAAAAA
1 AAGAAAAAAATGAAAAA
5902 TGGAAAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AAGAAAAAAATGAAAAA
Found at i:7839 original size:26 final size:27
Alignment explanation
Indices: 7772--7844 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
7762 GCATTAAAGT
*
7772 CATCCAGGGGCATTTTAGTCATTTTCA
1 CATCCAGGGGCATTTTGGTCATTTTCA
7799 CATCCAGGGGCATTTTGGTCATTTGT-A
1 CATCCAGGGGCATTTTGGTCATTT-TCA
*
7826 C-TTCAGGGGCATTTTGGTC
1 CATCCAGGGGCATTTTGGTC
7845 TTTCTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 17 0.40
27 25 0.58
28 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (27 bp):
CATCCAGGGGCATTTTGGTCATTTTCA
Found at i:14395 original size:14 final size:14
Alignment explanation
Indices: 14376--14405 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14366 AAGGGGAAGA
14376 AGTATTATGAATTG
1 AGTATTATGAATTG
*
14390 AGTATTGTGAATTG
1 AGTATTATGAATTG
14404 AG
1 AG
14406 CTTATTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (14 bp):
AGTATTATGAATTG
Found at i:16014 original size:30 final size:29
Alignment explanation
Indices: 15948--16021 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
15938 GATTTTGTTT
* *
15948 AAGTGCGGGTTGTGCACTTGTGTTGGTTC
1 AAGTGTGGGTTGTGCACTTGGGTTGGTTC
* *
15977 AAGTGTGGGTTGTGCACTTGGGATTGTTTT
1 AAGTGTGGGTTGTGCACTTGGG-TTGGTTC
*
16007 GAGTGTGGGTT-TGCA
1 AAGTGTGGGTTGTGCA
16022 TTCGTGTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.12, C:0.09, G:0.39, T:0.39
Consensus pattern (29 bp):
AAGTGTGGGTTGTGCACTTGGGTTGGTTC
Done.