Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014440.1 Corchorus olitorius cultivar O-4 contig14473, 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: 18328
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2769 original size:29 final size:29
Alignment explanation
Indices: 2737--3037 Score: 324
Period size: 29 Copynumber: 10.1 Consensus size: 29
2727 TAGAGCATTC
2737 AAAATGACCAAAATGCCCCTGGATGAGCA
1 AAAATGACCAAAATGCCCCTGGATGAGCA
* *
2766 AAAATGACCAAAATGCCCATGGACGTA-CA
1 AAAATGACCAAAATGCCCCTGGATG-AGCA
* *
2795 AAAATGACCAAAATGCCCCTAGATGTGCA
1 AAAATGACCAAAATGCCCCTGGATGAGCA
*
2824 AAAATGACCAAAATG-CTCTAGGATGAGCA
1 AAAATGACCAAAATGCCCCT-GGATGAGCA
*
2853 AAAATGACCAAAATGCCCC-GAGATGTGCA
1 AAAATGACCAAAATGCCCCTG-GATGAGCA
2882 AAAATGAGCAAAATGAGCAAAATGCCCCTGGATGTA-CA
1 AAAATGA-C--------CAAAATGCCCCTGGATG-AGCA
*
2920 AAAATGACCAAAATGCCCCGGGAAT-AGCA
1 AAAATGACCAAAATGCCCCTGG-ATGAGCA
* **
2949 AAAATGACCAAAATGCCCCTGGATTATTA
1 AAAATGACCAAAATGCCCCTGGATGAGCA
* *
2978 AAAATGACCAAAATGCCCCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGGATGAGCA
*
3007 AAAATGACCAAAACGCCCCTGGATGAGCA
1 AAAATGACCAAAATGCCCCTGGATGAGCA
3036 AA
1 AA
3038 TGATCAATTA
Statistics
Matches: 229, Mismatches: 24, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.03
29 190 0.83
30 6 0.03
37 1 0.00
38 24 0.10
39 1 0.00
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATGAGCA
Found at i:2895 original size:38 final size:38
Alignment explanation
Indices: 2846--2934 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
2836 ATGCTCTAGG
*
2846 ATGAGCAAAAATGACCAAAATGCCCC-GAGATGTGCAAAA
1 ATGAGC-AAAATGACCAAAATGCCCCTG-GATGTACAAAA
*
2885 ATGAGCAAAATGAGCAAAATGCCCCTGGATGTACAAAA
1 ATGAGCAAAATGACCAAAATGCCCCTGGATGTACAAAA
*
2923 ATGACCAAAATG
1 ATGAGCAAAATG
2935 CCCCGGGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 39 0.85
39 7 0.15
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (38 bp):
ATGAGCAAAATGACCAAAATGCCCCTGGATGTACAAAA
Found at i:2895 original size:67 final size:67
Alignment explanation
Indices: 2824--2963 Score: 187
Period size: 67 Copynumber: 2.1 Consensus size: 67
2814 TAGATGTGCA
* *
2824 AAAATGACCAAAATG-CTCTAGGATG-AGCAAAAATGACCAAAATGCCCCGAG-ATGTGCAAAAA
1 AAAATGACCAAAATGCCCCT-GGATGTA-CAAAAATGACCAAAATGCCCCGAGAAT-AGCAAAAA
*
2886 TGAGC
63 TGACC
* *
2891 AAAATGAGCAAAATGCCCCTGGATGTACAAAAATGACCAAAATGCCCCGGGAATAGCAAAAATGA
1 AAAATGACCAAAATGCCCCTGGATGTACAAAAATGACCAAAATGCCCCGAGAATAGCAAAAATGA
2956 CC
66 CC
2958 AAAATG
1 AAAATG
2964 CCCCTGGATT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
67 59 0.91
68 6 0.09
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (67 bp):
AAAATGACCAAAATGCCCCTGGATGTACAAAAATGACCAAAATGCCCCGAGAATAGCAAAAATGA
CC
Found at i:2922 original size:154 final size:154
Alignment explanation
Indices: 2736--3025 Score: 417
Period size: 154 Copynumber: 1.9 Consensus size: 154
2726 CTAGAGCATT
* *
2736 CAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCATGGACGTA-CAAAAAT
1 CAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCAGGGA-ATAGCAAAAAT
* *
2800 GACCAAAATGCCCCTAGATGT-GCAAAAATGACCAAAATG-CTCTAGGATGAGCAAAAATGACCA
65 GACCAAAATGCCCCTAGAT-TAGCAAAAATGACCAAAATGCCCCT-GAATGAGCAAAAATGACCA
*
2863 AAATGCCCCGAGATGTGCAAAAATGAG
128 AAACGCCCCGAGATGTGCAAAAATGAG
* *
2890 CAAAATGAGCAAAATGCCCCTGGATGTA-CAAAAATGACCAAAATGCCCCGGGAATAGCAAAAAT
1 CAAAATGACCAAAATGCCCCTGGATG-AGCAAAAATGACCAAAATGCCCAGGGAATAGCAAAAAT
* ** *
2954 GACCAAAATGCCCCTGGATTATTAAAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAA
65 GACCAAAATGCCCCTAGATTAGCAAAAATGACCAAAATGCCCCTGAATGAGCAAAAATGACCAAA
3019 ACGCCCC
130 ACGCCCC
3026 TGGATGAGCA
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
153 3 0.02
154 114 0.94
155 4 0.03
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.15
Consensus pattern (154 bp):
CAAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCAGGGAATAGCAAAAATG
ACCAAAATGCCCCTAGATTAGCAAAAATGACCAAAATGCCCCTGAATGAGCAAAAATGACCAAAA
CGCCCCGAGATGTGCAAAAATGAG
Found at i:2958 original size:125 final size:125
Alignment explanation
Indices: 2759--3019 Score: 366
Period size: 125 Copynumber: 2.1 Consensus size: 125
2749 ATGCCCCTGG
* *
2759 ATGAGCAAAAATGACCAAAATGCCCATGGACGTACAAAAATGACCAAAATGCCCCTAGATGTGCA
1 ATGAGC-AAAATGACCAAAATGCCCATGGACGTACAAAAATGACCAAAATGCCCCGAGATGAGCA
*
2824 AAAATGACCAAAATG-CTCTAGGATGAGCAAAAATGACCAAAATGCCCC-GAGATGTGCAAAA
65 AAAATGACCAAAATGCCCCT-GGATGAGCAAAAATGACCAAAATGCCCCTGA-ATGTGCAAAA
* * * *
2885 ATGAGCAAAATGAGCAAAATGCCCCTGGATGTACAAAAATGACCAAAATGCCCCGGGAAT-AGCA
1 ATGAGCAAAATGACCAAAATGCCCATGGACGTACAAAAATGACCAAAATGCCCCGAG-ATGAGCA
* **
2949 AAAATGACCAAAATGCCCCTGGATTATTAAAAATGACCAAAATGCCCCTGAATGTGCAAAA
65 AAAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCCTGAATGTGCAAAA
*
3010 ATGACCAAAA
1 ATGAGCAAAA
3020 CGCCCCTGGA
Statistics
Matches: 121, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
125 108 0.89
126 13 0.11
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.16
Consensus pattern (125 bp):
ATGAGCAAAATGACCAAAATGCCCATGGACGTACAAAAATGACCAAAATGCCCCGAGATGAGCAA
AAATGACCAAAATGCCCCTGGATGAGCAAAAATGACCAAAATGCCCCTGAATGTGCAAAA
Found at i:2981 original size:96 final size:96
Alignment explanation
Indices: 2795--3037 Score: 276
Period size: 96 Copynumber: 2.6 Consensus size: 96
2785 TGGACGTACA
* * *
2795 AAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCTCTAGGATGAGCAAAAATGA
1 AAAATGACCAAAATGCCCCTAGATGTACAAAAATGACCAAAATGCCCCAGGATGAGCAAAAATGA
*
2860 CCAAAATGCCCCGAGATGTGCAAAAATGAGC
66 CCAAAATGCCCCGAGATGTGCAAAAATGACC
* * *
2891 AAAATGAGCAAAATGCCCCTGGATGTACAAAAATGACCAAAATGCCCCGGGAAT-AGCAAAAATG
1 AAAATGACCAAAATGCCCCTAGATGTACAAAAATGACCAAAATGCCCCAGG-ATGAGCAAAAATG
*
2955 ACCAAAATGCCCCTG-GAT-T------ATTA--
65 ACCAAAATGCCCC-GAGATGTGCAAAAATGACC
* * *
2978 AAAATGACCAAAATGCCCCT-GAATGTGCAAAAATGACCAAAACGCCCCTGGATGAGCAAA
1 AAAATGACCAAAATGCCCCTAG-ATGTACAAAAATGACCAAAATGCCCCAGGATGAGCAAA
3038 TGATCAATTA
Statistics
Matches: 132, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
86 3 0.02
87 51 0.39
89 3 0.02
95 1 0.01
96 71 0.54
97 3 0.02
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (96 bp):
AAAATGACCAAAATGCCCCTAGATGTACAAAAATGACCAAAATGCCCCAGGATGAGCAAAAATGA
CCAAAATGCCCCGAGATGTGCAAAAATGACC
Done.