Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017832.1 Corchorus olitorius cultivar O-4 contig17865, 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: 14274
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:2865 original size:3 final size:3
Alignment explanation
Indices: 2857--2939 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
2847 CCTGAAATTA
2857 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2940 AGCAAGGGTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6951 original size:59 final size:56
Alignment explanation
Indices: 6859--7025 Score: 223
Period size: 59 Copynumber: 3.0 Consensus size: 56
6849 TCTTTCAAAC
*
6859 TACTATCAAGCCCTAATCATTAACTGCGTCTTGCATTGATGAATTTGAAATTAATGAAG
1 TACTAACAAGCCCTAATCATTAACTGCGTCTTGCATTGATGAATTTGAAATTAAT---G
6918 TACTAACAAGCCCTAATCATTAACTGCGTCTTGCATTGATGAATTTGAAATTAATG
1 TACTAACAAGCCCTAATCATTAACTGCGTCTTGCATTGATGAATTTGAAATTAATG
* ** * *
6974 CACTAA-AA--TTTAATAGATTAACTGCGTCTTGCACTGATGAATTTGAAATTAA
1 TACTAACAAGCCCTAAT-CATTAACTGCGTCTTGCATTGATGAATTTGAAATTAA
7026 CGCATTGAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
53 4 0.04
54 35 0.35
55 2 0.02
56 6 0.06
59 54 0.53
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (56 bp):
TACTAACAAGCCCTAATCATTAACTGCGTCTTGCATTGATGAATTTGAAATTAATG
Found at i:8182 original size:18 final size:18
Alignment explanation
Indices: 8159--8197 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
8149 ATAATAGAAG
8159 TTATCAAATTTACAGTAA
1 TTATCAAATTTACAGTAA
*
8177 TTATCAAATTTACAGTGA
1 TTATCAAATTTACAGTAA
8195 TTA
1 TTA
8198 CTGAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (18 bp):
TTATCAAATTTACAGTAA
Found at i:8847 original size:246 final size:244
Alignment explanation
Indices: 8414--8905 Score: 806
Period size: 246 Copynumber: 2.0 Consensus size: 244
8404 CCAGGAAATT
* * * *
8414 TACCAAAGGCCCCTTTTGAGGATGGATGAGGAGGCTTCATTTGAACTTTTTTTGTCCTTTTCTGT
1 TACCAAAGACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTTGTCATTTTCTGT
* *
8479 CTTTTCTCACTTGCCAAATTACTAAGAAGACCATAGGTTTATTTCTAGCCAGTTCTTGCCCTTGA
66 CTTTTCTCACTTGCCAAATTACTAAGAAGACCATAGGTTTATTTCTAGCAAGTTCTTACCCTTGA
* * *
8544 ACCGTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTACAATAAATTATATCCCCCTTAATT
131 ACCCTTTTTTGTAATTATCCCTTCCTTTCACATAAATGTTACAATAAATCATATCCCCCTTAATT
*
8609 ATCTAGAATTGTAAGCTATTTTCAGGCCTTTCATGTCCATATGAAGAAG
196 ATCTAGAATTGTAACCTATTTTCAGGCCTTTCATGTCCATATGAAGAAG
8658 TACCAAAGACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTTTTGTCATTTTCT
1 TACCAAAGACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAAC--TTTTTTTGTCATTTTCT
* *
8723 GTCTTTTCTCACTTGTCAAATTACTAAGAAGACCCTAGG-TTAGTTTCTAGCAAGTTCTTACCCT
64 GTCTTTTCTCACTTGCCAAATTACTAAGAAGACCATAGGTTTA-TTTCTAGCAAGTTCTTACCCT
* * * *
8787 TGAGCCCTTTTTTGTAATTATCCCTTCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTA
128 TGAACCCTTTTTTGTAATTATCCCTTCCTTTCACATAAATGTTACAATAAATCATATCCCCCTTA
8852 ATTATCTAGAATTGTAACCTATTTTCAGGCCTTTCATGTCCATATGAAGAAG
193 ATTATCTAGAATTGTAACCTATTTTCAGGCCTTTCATGTCCATATGAAGAAG
8904 TA
1 TA
8906 GGGGTGATAC
Statistics
Matches: 229, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
244 43 0.19
245 3 0.01
246 183 0.80
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (244 bp):
TACCAAAGACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTTGTCATTTTCTGT
CTTTTCTCACTTGCCAAATTACTAAGAAGACCATAGGTTTATTTCTAGCAAGTTCTTACCCTTGA
ACCCTTTTTTGTAATTATCCCTTCCTTTCACATAAATGTTACAATAAATCATATCCCCCTTAATT
ATCTAGAATTGTAACCTATTTTCAGGCCTTTCATGTCCATATGAAGAAG
Found at i:9084 original size:11 final size:11
Alignment explanation
Indices: 9068--9172 Score: 54
Period size: 11 Copynumber: 9.8 Consensus size: 11
9058 AAAAAAATTG
9068 TTATATATATT
1 TTATATATATT
*
9079 TTATATATATC
1 TTATATATATT
* * *
9090 ATAAATATAAT
1 TTATATATATT
* *
9101 ATATATATATG
1 TTATATATATT
*
9112 TTACATATA-T
1 TTATATATATT
* * **
9122 TCA-A-AAAAA
1 TTATATATATT
*
9131 TTAAATATATT
1 TTATATATATT
*
9142 TTATATATATC
1 TTATATATATT
* *
9153 ATAAATATATT
1 TTATATATATT
9164 TTATATATA
1 TTATATATA
9173 ATAGCGTAAT
Statistics
Matches: 66, Mismatches: 25, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
8 2 0.03
9 3 0.05
10 3 0.05
11 58 0.88
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (11 bp):
TTATATATATT
Done.