Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023192.1 Corchorus olitorius cultivar O-4 contig23225, 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: 10693
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4821 original size:21 final size:22
Alignment explanation
Indices: 4797--4838 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4787 TTCGCCTCAT
4797 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
4818 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
4839 AAAACCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:8016 original size:51 final size:52
Alignment explanation
Indices: 7949--8098 Score: 182
Period size: 51 Copynumber: 2.9 Consensus size: 52
7939 GAAGCTTTAT
7949 AATAAGATTGCATTCCATTTGTGAGGTCAAGATCAAAATTTCGCTTTTC-AA
1 AATAAGATTGCATTCCATTTGTGAGGTCAAGATCAAAATTTCGCTTTTCAAA
* *
8000 ATTGAA-ATTGCATTCCATTTGTGA-GTCCAAGATCAAAATTT-GCTTGTCAAA
1 AAT-AAGATTGCATTCCATTTGTGAGGT-CAAGATCAAAATTTCGCTTTTCAAA
* ** * **
8051 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCTCGCTTTT
1 AATAAGATTGCATTCCATTTGTGAGGTCAAGATCAAAATTTCGCTTTT
8099 TCGAAAGGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
50 10 0.12
51 66 0.80
52 7 0.08
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (52 bp):
AATAAGATTGCATTCCATTTGTGAGGTCAAGATCAAAATTTCGCTTTTCAAA
Found at i:8779 original size:69 final size:69
Alignment explanation
Indices: 8687--9473 Score: 1173
Period size: 69 Copynumber: 11.3 Consensus size: 69
8677 CGAATGACAC
*
8687 AGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
8752 ACAT
66 ACAT
*
8756 AGGCTTTTCCACAAGCCAAACTCGTTTCCAAACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
8821 ACAT
66 ACAT
* * *
8825 AGGCTTTTCCACAAGCCAAACTCGTTTCCAGACGAGTCAGTTGAAGCCTCGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
8890 ACAT
66 ACAT
8894 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
*
8959 ATAT
66 ACAT
* * *
8963 AGGCTTTTCCACAAGCCAAACTCGTTTCCAAATGAGGCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
9028 ACAT
66 ACAT
*
9032 AGGCTTTTCCACAAGCCAAACTCGTTTCCAGACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCAT-----CC
9097 AAGCCACAT
61 AAGCCACAT
* *
9106 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTCAAGCCTAGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
*
9171 ATAT
66 ACAT
*
9175 AGGCTTTTCCACAAGCCAAACTCGTTTCCAAACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCAT-----CC
9240 AAGCCACAT
61 AAGCCACAT
* *
9249 AGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGGCTTGGTTCCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
*
9314 ATAT
66 ACAT
* * *
9318 AGGCTTTTACACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTCATCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
*
9383 ATAT
66 ACAT
* * * * * * * * *
9387 AGACTTTTCCATAAGTCAAACTCGCTTCCATACGAGTCATTTTAAACATTGGGTCCATCCATA--
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA-AGC
*
9450 CACAG
65 CACAT
*
9455 AGGCTTTTCCATAAGCCAA
1 AGGCTTTTCCACAAGCCAA
9474 GTTTAATGAG
Statistics
Matches: 661, Mismatches: 46, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
68 20 0.03
69 509 0.77
70 1 0.00
74 131 0.20
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (69 bp):
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCC
ACAT
Found at i:9737 original size:102 final size:102
Alignment explanation
Indices: 9561--9796 Score: 366
Period size: 102 Copynumber: 2.3 Consensus size: 102
9551 TATATCCATG
* * *
9561 TAAGTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTGGATTAATAAAATCTCCGGGTATCAT
1 TAAGTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTCTGCATTAATAAAACCTCCGGGTATCAT
9626 GTCATTTCATCAAAG-TTTTCTATCAAAGATTCATGTT
66 GTCATTTCATCAAAGTTTTTC-ATCAAAGATTCATGTT
* **
9663 TAAGTTAAAATCCTTGTTCTAGGTCTCTATTCAGAGTCTGCATTGTTAAAACCTCCGGGTATCAT
1 TAAGTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTCTGCATTAATAAAACCTCCGGGTATCAT
9728 GTCATTTCATCAAAGTTTTTCATCAAAGATTCATGTT
66 GTCATTTCATCAAAGTTTTTCATCAAAGATTCATGTT
* * *
9765 TAAGTTTAATACCCTTGGTCAAGGTCTCTATT
1 TAAG-TTAAAATCCTTGTTCAAGGTCTCTATT
9797 TTAAAGTTTG
Statistics
Matches: 122, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
102 94 0.77
103 28 0.23
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (102 bp):
TAAGTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTCTGCATTAATAAAACCTCCGGGTATCAT
GTCATTTCATCAAAGTTTTTCATCAAAGATTCATGTT
Done.