Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012709.1 Corchorus olitorius cultivar O-4 contig12742, 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: 4562
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2086 original size:27 final size:27
Alignment explanation
Indices: 2010--2105 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
2000 AAAGTACTTT
* * *
2010 AAATGACTAAAATACCCCTGGACATGC
1 AAATGACCAAAATGCCCCTGGATATGC
* *
2037 AAATGACCAAAATGCGCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATATGC
* * *
2064 AAATGACCATAATGCCCCTGGATTTTGA
1 AAATGACCAAAATGCCCCTGGA-TATGC
2092 AAATGACCCAAAAT
1 AAATGA-CCAAAAT
2106 TCCCTTAGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 42 0.74
28 9 0.16
29 6 0.11
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATATGC
Found at i:2664 original size:69 final size:68
Alignment explanation
Indices: 2591--2790 Score: 274
Period size: 69 Copynumber: 2.9 Consensus size: 68
2581 CTCTGCAGTA
* * * * * * * ** *
2591 TGGATGGAACCAATGTTTGAACTGACTCGCATGGAAACGATTTTGACTTATGGACAATTCTATAT
1 TGGATGGAACCAAGGCTTGAAC-GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACAT
2656 GGCT
65 GGCT
*
2660 TGGATGGAACCAAGGCTTGAACCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACGT
1 TGGATGGAACCAAGGCTTGAA-CGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACAT
2725 GGCT
65 GGCT
2729 TGGATGGAACCAAGGCTTGAAACGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 TGGATGGAACCAAGGCTTG-AACGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
2791 TATTGAAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
69 115 0.97
70 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (68 bp):
TGGATGGAACCAAGGCTTGAACGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACATG
GCT
Found at i:2808 original size:50 final size:50
Alignment explanation
Indices: 2752--2989 Score: 404
Period size: 50 Copynumber: 4.8 Consensus size: 50
2742 GGCTTGAAAC
* *
2752 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATTGAAAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
* *
2802 GACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTGTGTTGATAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
* *
2852 GACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTGTGTTGATAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
*
2902 GACTCGTATGGAAACGAGTTTGGCTTGTGGAGAAGCCTATGTTGATAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
*
2952 GACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
2990 GTGTATTCGG
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 177 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (50 bp):
GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
Found at i:3265 original size:85 final size:87
Alignment explanation
Indices: 3147--3320 Score: 298
Period size: 85 Copynumber: 2.0 Consensus size: 87
3137 TGATGCGGTC
*
3147 AACTTGAAAAATACCTCTGAGTCTGATGTTGTAACTG-AAACTTCTTAATTGATGATG-AAAAGG
1 AACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGG
*
3210 ACCAATTTGCAGTCAACTTGAA
66 ACCAATGTGCAGTCAACTTGAA
*
3232 AACTTGAAGAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGG
1 AACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGG
*
3297 ACCAATGTGCGGTCAACTTGAA
66 ACCAATGTGCAGTCAACTTGAA
3319 AA
1 AA
3321 ATAACTCTAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
85 35 0.42
86 20 0.24
87 28 0.34
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (87 bp):
AACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGG
ACCAATGTGCAGTCAACTTGAA
Found at i:3343 original size:79 final size:79
Alignment explanation
Indices: 3073--3346 Score: 365
Period size: 79 Copynumber: 3.4 Consensus size: 79
3063 ACACCTTTGG
* *
3073 AAAATAACTCTGAA-TCTGATGTTGTAACTGAAAAACTTCTTGATTGATGATGAAAAAGGACCAC
1 AAAATAACTCT-AAGTCTGATGTTGTAACTG-AAAACTTCTTAATTGATGATGAAAAAGGACCAA
3137 TGATGCGGTCAACTTGA
64 TG-TGCGGTCAACTTGA
* * *
3154 AAAATACCTCTGAGTCTGATGTTGTAACTG-AAACTTCTTAATTGATGATG-AAAAGGACCAATT
1 AAAATAACTCTAAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAATG
*
3217 TGCAGTCAACTTGAAAA
66 TGCGGTCAACTTG---A
*
3234 CTTGAAGAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGAC
1 ----AA-AATAACTCTAAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGAC
3299 CAATGTGCGGTCAACTTGA
61 CAATGTGCGGTCAACTTGA
3318 AAAATAACTCTAAGTCTGATGTTGTAACT
1 AAAATAACTCTAAGTCTGATGTTGTAACT
3347 TGAATCTTTG
Statistics
Matches: 172, Mismatches: 10, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
77 12 0.07
78 11 0.06
79 45 0.26
80 4 0.02
81 26 0.15
84 3 0.02
85 27 0.16
86 20 0.12
87 24 0.14
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (79 bp):
AAAATAACTCTAAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAATG
TGCGGTCAACTTGA
Found at i:3803 original size:50 final size:50
Alignment explanation
Indices: 3749--3852 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
3739 TGGTTTTGGT
** *
3749 CTCACAAATGGAGTGCAATCTTATTTTGAAAAGAAAATTTTGATTTTGAA
1 CTCACAAATGGAAAGCAATCTTATTTTGAAAAGAAAATTTTGATCTTGAA
* **
3799 CTCACAAATGGAAAGCAATTTTATTTTGAAAAGCGAATTTTGATCTTGAA
1 CTCACAAATGGAAAGCAATCTTATTTTGAAAAGAAAATTTTGATCTTGAA
3849 CTCA
1 CTCA
3853 TAAGTGATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (50 bp):
CTCACAAATGGAAAGCAATCTTATTTTGAAAAGAAAATTTTGATCTTGAA
Done.