Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015366.1 Corchorus olitorius cultivar O-4 contig15399, 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: 3680
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Found at i:2667 original size:62 final size:57
Alignment explanation
Indices: 2620--2916 Score: 271
Period size: 62 Copynumber: 4.9 Consensus size: 57
2610 GTTTCCTCAG
2620 CATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTT
1 CATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTT
* * *
2677 CATGATAACTTCTGGTGTTAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTT
1 CATGACAACTTCTGGTGTCAAGATAATAA--T--T-TGACAACTTCTGGTGTCAATAATTTT
2739 CATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAAGATAATAATT
1 CATGACAACTTCTGGTGTCAAGATAATAA--T--T-TGACAACTTCTGGTGTC-A-ATAAT--TT
2804 T
57 T
*
2805 GCTATGACAACTTCTGGTGTC-A-ATAAT-TTTCATGACAACTTCTGGTGTCAAGATAATAATTT
1 -C-ATGACAACTTCTGGTGTCAAGATAATAATT--TGACAACTTCTGGTGTC-A-ATAAT--TTT
* **
2867 GATATGACAACTTCTGGTGTCAA-A-AATTTTTATGACAACTTCTGGTGTCA
1 --CATGACAACTTCTGGTGTCAAGATAATAATT-TGACAACTTCTGGTGTCA
2917 TTTGTAAGAC
Statistics
Matches: 215, Mismatches: 10, Indels: 26
0.86 0.04 0.10
Matches are distributed among these distances:
57 27 0.13
59 1 0.00
61 3 0.01
62 145 0.67
63 7 0.03
64 4 0.02
66 8 0.04
67 2 0.01
68 18 0.08
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (57 bp):
CATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTT
Found at i:2799 original size:96 final size:95
Alignment explanation
Indices: 2621--2916 Score: 411
Period size: 96 Copynumber: 3.2 Consensus size: 95
2611 TTTCCTCAGC
*
2621 ATGACAACTTCTGGTGTCAAGATAATAATT--TGACAACTTCTGGTGTC-A-ATAAT--TTT-C-
1 ATGACAACTTCTGGTGTCAA-A-AAT-TTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCT
* *
2678 ATGATAACTTCTGGTGTTAAGATAATAATTTGAT
63 ATGACAACTTCTGGTGTCAAGATAATAATTTG-T
2712 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCTATG
1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCTATG
2777 ACAACTTCTGGTGTCAAGATAATAATTTGCT
66 ACAACTTCTGGTGTCAAGATAATAATTTG-T
* *
2808 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGATATG
1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCTATG
2873 ACAACTTCTGGTGTCAA-A-AAT--TTT-T
66 ACAACTTCTGGTGTCAAGATAATAATTTGT
2898 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
2917 TTTGTAAGAC
Statistics
Matches: 191, Mismatches: 6, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
88 2 0.01
89 3 0.02
90 38 0.20
91 21 0.11
92 8 0.04
94 6 0.03
95 2 0.01
96 111 0.58
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (95 bp):
ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCTATG
ACAACTTCTGGTGTCAAGATAATAATTTGT
Found at i:2904 original size:158 final size:153
Alignment explanation
Indices: 2621--2916 Score: 520
Period size: 158 Copynumber: 1.9 Consensus size: 153
2611 TTTCCTCAGC
*
2621 ATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTTCATGATAAC
1 ATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTTCATGACAAC
*
2686 TTCTGGTGTTAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTC
66 TTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTC
2751 TGGTGTCAAGATAATAATTTGCT
131 TGGTGTCAAGATAATAATTTGCT
2774 ATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAATAATTTTCATG
1 ATGACAACTTCTGGTGTCAAGATAATAA--T--T-TGACAACTTCTGGTGTCAATAATTTTCATG
*
2839 ACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTTATGACA
61 ACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCATGACA
2904 ACTTCTGGTGTCA
126 ACTTCTGGTGTCA
2917 TTTGTAAGAC
Statistics
Matches: 135, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
153 28 0.21
155 1 0.01
157 1 0.01
158 105 0.78
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (153 bp):
ATGACAACTTCTGGTGTCAAGATAATAATTTGACAACTTCTGGTGTCAATAATTTTCATGACAAC
TTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTC
TGGTGTCAAGATAATAATTTGCT
Found at i:2934 original size:30 final size:30
Alignment explanation
Indices: 2898--2984 Score: 174
Period size: 30 Copynumber: 2.9 Consensus size: 30
2888 AAAAATTTTT
2898 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCATTTGTAAGACC
2928 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCATTTGTAAGACC
2958 ATGACAACTTCTGGTGTCATTTGTAAG
1 ATGACAACTTCTGGTGTCATTTGTAAG
2985 TAGAATAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCATTTGTAAGACC
Done.