Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022015.1 Corchorus olitorius cultivar O-4 contig22048, 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: 25073
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:768 original size:35 final size:35
Alignment explanation
Indices: 680--780 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 35
670 TCAAGGCAAG
****
680 GCAAAGTTCTTCTCCATCAAGCAAAGCAA-ATCTGCA
1 GCAAAGTTCTTCTCCATCAA-CAAAGCAACA-AAAAA
716 GCAAAGTT-TTCTCCATCAACAAAGCAACAAAAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAAAAAA
*
750 GCAAAGTTCTTCTTCATCAACAAAGCAACAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAA
781 CGAAGCCTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 17 0.29
35 33 0.57
36 8 0.14
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (35 bp):
GCAAAGTTCTTCTCCATCAACAAAGCAACAAAAAA
Found at i:1000 original size:42 final size:42
Alignment explanation
Indices: 941--1021 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
931 AACAAATCCG
* *
941 ACAACGAGGAATAACAAGTCTTCGGCCATTTCTCTCAAAGCC
1 ACAACGAGGAATAACAAGCCTTCGGCCATTCCTCTCAAAGCC
983 ACAACGAGGAATAACAAGCCTTCGGCCATTCCTCTCAAA
1 ACAACGAGGAATAACAAGCCTTCGGCCATTCCTCTCAAA
1022 TCCATTTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.20
Consensus pattern (42 bp):
ACAACGAGGAATAACAAGCCTTCGGCCATTCCTCTCAAAGCC
Found at i:1308 original size:35 final size:35
Alignment explanation
Indices: 1225--1331 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 35
1215 TCAAGGCAAG
****
1225 GCAAAGTTCTTCTCCATCAAGCAAAGCAA-ATCTGCA
1 GCAAAGTTCTTCTCCATCAA-CAAAGCAACA-AAAAA
1261 GCAAAGTT-TTCTCCATCAACAAAGCAACAAAAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAAAAAA
* *
1295 GCAAAGTTCTTCTCCATCAACAATGCAACAACAAA
1 GCAAAGTTCTTCTCCATCAACAAAGCAACAAAAAA
1330 GC
1 GC
1332 TTACGAAAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
34 17 0.27
35 38 0.60
36 8 0.13
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (35 bp):
GCAAAGTTCTTCTCCATCAACAAAGCAACAAAAAA
Found at i:8085 original size:172 final size:172
Alignment explanation
Indices: 7799--8143 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
7789 ATTGCGATAA
7799 TATAATAAGATTTTAGGAAAATTCCTCTTGCCCCGCGAAACTCCTATCGCCAATTCATCCCGCAT
1 TATAATAAGATTTTAGGAAAATTCCTCTTGCCCCGCGAAACTCCTATCGCCAATTCATCCCGCAT
7864 GATGTGTAAATGTGCTGGTGTTTTGTTAATGTGGGTATGTAAAGTAAGTGGAGGGACCAGCCAGA
66 GATGTGTAAATGTGCTGGTGTTTTGTTAATGTGGGTATGTAAAGTAAGTGGAGGGACCAGCCAGA
7929 ATTATTGGCCTAACGGGATTTTTTGCGAAACAATTAACTAGG
131 ATTATTGGCCTAACGGGATTTTTTGCGAAACAATTAACTAGG
7971 TATAATAAGATTTTAGGAAAATTCCTCTTGCCCCGCGAAACTCCTATCGCCAATTCATCCCGCAT
1 TATAATAAGATTTTAGGAAAATTCCTCTTGCCCCGCGAAACTCCTATCGCCAATTCATCCCGCAT
8036 GATGTGTAAATGTGCTGGTGTTTTGTTAATGTGGGTATGTAAAGTAAGTGGAGGGACCAGCCAGA
66 GATGTGTAAATGTGCTGGTGTTTTGTTAATGTGGGTATGTAAAGTAAGTGGAGGGACCAGCCAGA
8101 ATTATTGGCCTAACGGGATTTTTTGCGAAACAATTAACTAGG
131 ATTATTGGCCTAACGGGATTTTTTGCGAAACAATTAACTAGG
8143 T
1 T
8144 GTGTAGCAGA
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (172 bp):
TATAATAAGATTTTAGGAAAATTCCTCTTGCCCCGCGAAACTCCTATCGCCAATTCATCCCGCAT
GATGTGTAAATGTGCTGGTGTTTTGTTAATGTGGGTATGTAAAGTAAGTGGAGGGACCAGCCAGA
ATTATTGGCCTAACGGGATTTTTTGCGAAACAATTAACTAGG
Found at i:9156 original size:109 final size:109
Alignment explanation
Indices: 9025--9238 Score: 383
Period size: 109 Copynumber: 2.0 Consensus size: 109
9015 CTATCATATA
*
9025 TATTATTATTAATTATGGTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATA
1 TATTATTATTAATTATGGTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
9090 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
* * *
9134 TATTATTATTTATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTATGGTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
*
9199 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAG
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAG
9239 TACCAAAATG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (109 bp):
TATTATTATTAATTATGGTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:18787 original size:24 final size:24
Alignment explanation
Indices: 18759--18808 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
18749 GATCTACAGA
18759 TTAATCCAACTTTCACTTGCGATT
1 TTAATCCAACTTTCACTTGCGATT
*
18783 TTAATCCGACTTTCACTTGCGATT
1 TTAATCCAACTTTCACTTGCGATT
18807 TT
1 TT
18809 TTTTTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (24 bp):
TTAATCCAACTTTCACTTGCGATT
Found at i:21738 original size:10 final size:10
Alignment explanation
Indices: 21723--21751 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
21713 GTCTATGTTT
21723 AGGAAAGGGA
1 AGGAAAGGGA
21733 AGGAAAGGGA
1 AGGAAAGGGA
21743 AGGAAAGGG
1 AGGAAAGGG
21752 GAGGGAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (10 bp):
AGGAAAGGGA
Found at i:22035 original size:34 final size:34
Alignment explanation
Indices: 21992--22059 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
21982 AGAAATTTTC
21992 AAAAAAAATAAAATTTTCACAAGAAAAGAGATGA
1 AAAAAAAATAAAATTTTCACAAGAAAAGAGATGA
22026 AAAAAAAATAAAATTTTCACAAGAAAAGAGATGA
1 AAAAAAAATAAAATTTTCACAAGAAAAGAGATGA
22060 GAGAGGCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (34 bp):
AAAAAAAATAAAATTTTCACAAGAAAAGAGATGA
Done.