Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019866.1 Corchorus olitorius cultivar O-4 contig19899, 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: 7421
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1161 original size:68 final size:68
Alignment explanation
Indices: 985--1221 Score: 291
Period size: 68 Copynumber: 3.5 Consensus size: 68
975 CCCTGAATGC
* * ***
985 TCGGATGGAACCAAAGCTTGACCT-GCTTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTT
1 TCGGATGGAACCAAAGCTTGAACTGGC-TCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAA
*
1049 G-AT
65 GCAA
* ** *
1052 TGCTTGGGTGGAACCAAAGCTTGAACTGGCTTGTATGGAAACGACTTTGGCTTGTGGAAAAGCCA
1 T-C--GGATGGAACCAAAGCTTGAACTGGCTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCA
1117 AAGCAA
63 AAGCAA
* *
1123 TCAGATGGAACCGAAGCTTGAACTGGCTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAAG
1 TCGGATGGAACCAAAGCTTGAACTGGCTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAAG
1188 CAA
66 CAA
*
1191 TCGGATGGAACCGAAA-CTTGAACTGCCTCAT
1 TCGGATGGAACC-AAAGCTTGAACTGGCTCAT
1222 GTTTGACTTA
Statistics
Matches: 147, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
67 1 0.01
68 86 0.59
69 2 0.01
70 54 0.37
71 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (68 bp):
TCGGATGGAACCAAAGCTTGAACTGGCTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCAAAG
CAA
Found at i:5850 original size:81 final size:81
Alignment explanation
Indices: 5738--6416 Score: 782
Period size: 81 Copynumber: 8.4 Consensus size: 81
5728 GGGAATAAGA
* *
5738 ACAACACCTTCTGATGAGGAAGGGCACACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
* *
5803 TAATTTAGGAATGCTG
66 CAAATTAGGAATGCTG
* * * * **
5819 ACAACACCTTCCGATGAGGAAGGGTAAACTGGAGAAAGACAACAACACCTTCCGATGAGGAAGAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
5884 CAAATT-GGTAAATGCTG
66 CAAATTAGG--AATGCTG
* * * *** * *
5901 ACAACACCTCCCGATGA-GAAGGGCAAATTGGGA-AATGTTGACAACAACTTCCGATGAGGAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACT-GGACAAAGGCAACAACACCTCCCGATGAGGAAGG
* *
5964 GCAAATTGGGAATACTG
65 GCAAATTAGGAATGCTG
5981 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
* *
6046 CAAATTGGGAATACTG
66 CAAATTAGGAATGCTG
* *
6062 ACAACACCTTCCAATGAGGACA-AGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 ACAACACCTTCCGATGAGGA-AGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
* * * *
6126 GTAAATTGGGAAT-TTAA
65 GCAAATTAGGAATGCT-G
*
6143 ACAACACCTTCCGATGAGGAAGTGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
*
6208 TAAATTAGGAATGCTG
66 CAAATTAGGAATGCTG
* * * * **
6224 ACAACACCTTCCGATGAGGAAGGGCAAACTAGAGAAAGACAACAACACCTTCCGATGAGGAAGAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
6289 CAAATT-GGTAAATGCTG
66 CAAATTAGG--AATGCTG
* ** * ** *
6306 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-CAAATACTGACAACACCTTTCGATGAGGAATG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGG
* * *
6370 GCAAGTTAGGAAT-TTAA
65 GCAAATTAGGAATGCT-G
*
6387 ACAACACCTTCCGGTG-GGTAAGGGCAAACT
1 ACAACACCTTCCGATGAGG-AAGGGCAAACT
6417 AGGTATTGTT
Statistics
Matches: 521, Mismatches: 61, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
80 34 0.07
81 393 0.75
82 92 0.18
83 2 0.00
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (81 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
CAAATTAGGAATGCTG
Found at i:6334 original size:41 final size:40
Alignment explanation
Indices: 5738--6373 Score: 567
Period size: 41 Copynumber: 15.7 Consensus size: 40
5728 GGGAATAAGA
* * * * *
5738 ACAACACCTTCTGATGAGGAAGGGCACACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG--AAATGCTG
* * *
5779 ACAACACCTCCCGATGAGGAAGGGTAATTTAGG-AATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATT-GGAAATGCTG
* * * *
5819 ACAACACCTTCCGATGAGGAAGGGTAAACTGGAGAAAGAC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGA-AATG-CTG
**
5860 ACAACACCTTCCGATGAGGAAGAACAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
* *
5901 ACAACACCTCCCGATGA-GAAGGGCAAATTGGGAAATGTTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATT-GGAAATGCTG
* * *
5941 ACAACAACTTCCGATGAGGAAGGGCAAATTGGGAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCTG
* * *
5981 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG--AAATGCTG
* * *
6022 ACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCTG
* * * * *
6062 ACAACACCTTCCAATGAGGACA-AGCAAACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGA-AGGGCAAATTGG--AAATGCTG
* * * * *
6103 ACAACACCTCCCGATGAGGAAGGGTAAATTGGGAAT-TTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCT-G
* * * *
6143 ACAACACCTTCCGATGAGGAAGTGCAAACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG--AAATGCTG
* *
6184 ACAACACCTCCCGATGAGGAAGGGTAAATTAGG-AATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATT-GGAAATGCTG
* *
6224 ACAACACCTTCCGATGAGGAAGGGCAAACTAGAGAAA-GAC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAA-TTG-GAAATG-CTG
**
6265 ACAACACCTTCCGATGAGGAAGAACAAATTGGTAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
*
6306 ACAACACCTTCCGATGAGGAAGGGCAAATTGGCAAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AAATGCTG
* *
6347 ACAACACCTTTCGATGAGGAATGGCAA
1 ACAACACCTTCCGATGAGGAAGGGCAA
6374 GTTAGGAATT
Statistics
Matches: 482, Mismatches: 83, Indels: 60
0.77 0.13 0.10
Matches are distributed among these distances:
39 16 0.03
40 186 0.39
41 263 0.55
42 17 0.04
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAATTGGAAATGCTG
Done.