Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018585.1 Corchorus olitorius cultivar O-4 contig18618, 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: 8641
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2853 original size:25 final size:25
Alignment explanation
Indices: 2800--2851 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2790 TTAGTTTATT
*
2800 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATA
*
2825 AAATTAGATTTGAGTTACATG-ATA
1 AAATTAGATTTGAGCTACATGAATA
2849 AAA
1 AAA
2852 ATGCAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATA
Found at i:3537 original size:70 final size:70
Alignment explanation
Indices: 3417--3566 Score: 212
Period size: 70 Copynumber: 2.1 Consensus size: 70
3407 ACTTGACTTA
* *
3417 TGGAAAAGCCCCTGAATGCTCGGATGGAACCAAAGCTTGAGCTGCTTCGTATGGAAACAAGTTTG
1 TGGAAAAGCCCCTGAATGCTCGGATGGAACCAAAACTTGAACTGCTTCGTATGGAAACAAGTTTG
3482 GCTTG
66 GCTTG
* * * * * *
3487 TGGAAAAGCCCTTGATTGTTTGGATGGAACCAAAACTTGAATTGGC-TCGTATGGAAACGAGTTT
1 TGGAAAAGCCCCTGAATGCTCGGATGGAACCAAAACTTGAACT-GCTTCGTATGGAAACAAGTTT
3551 GGCTTG
65 GGCTTG
3557 TGGAAAAGCC
1 TGGAAAAGCC
3567 AAAGCAATCG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 69 0.97
71 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (70 bp):
TGGAAAAGCCCCTGAATGCTCGGATGGAACCAAAACTTGAACTGCTTCGTATGGAAACAAGTTTG
GCTTG
Found at i:5519 original size:14 final size:13
Alignment explanation
Indices: 5494--5544 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
5484 AAAAAAACTA
5494 AAAACC-TTTTTG
1 AAAACCATTTTTG
5506 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
* *
5520 GAAACCTTTTCTTG
1 AAAACCATTT-TTG
5534 AAAA-CATTTTT
1 AAAACCATTTTT
5545 CCTGAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 7 0.22
13 9 0.28
14 16 0.50
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:5541 original size:26 final size:25
Alignment explanation
Indices: 5495--5544 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
5485 AAAAAACTAA
5495 AAACCTTTTTGAAAACTCATTTTTGG
1 AAACCTTTTTGAAAAC-CATTTTTGG
5521 AAACCTTTTCTTGAAAA-CATTTTT
1 AAACC-TTT-TTGAAAACCATTTTT
5545 CCTGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (25 bp):
AAACCTTTTTGAAAACCATTTTTGG
Found at i:8374 original size:48 final size:48
Alignment explanation
Indices: 8298--8506 Score: 305
Period size: 48 Copynumber: 4.4 Consensus size: 48
8288 CATTGAAGAA
* * *
8298 AGGAATGAAATATTGAAAACAACGCCTTCCAACCGGGAAGGGCAAAAC
1 AGGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
* *
8346 AGGAATAAAACATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAAC
1 AGGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
*
8394 AGGAATAAAATATTCAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
1 AGGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
*
8442 TA-GAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGG-AAATAC
1 -AGGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAA-AC
* *
8490 GGGAATAAAACATTGAA
1 AGGAATAAAATATTGAA
8507 GACAGGAATG
Statistics
Matches: 146, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
47 3 0.02
48 142 0.97
49 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (48 bp):
AGGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
Found at i:8560 original size:68 final size:68
Alignment explanation
Indices: 8444--8578 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
8434 GGCAAAACTA
8444 GAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGGAAATACGGGAATAAAACATTGAAGA
1 GAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGGAAATACGGGAATAAAACATTGAAGA
8509 CAG
66 CAG
* * *
8512 GAATGAAATATTGAAACCAACACCTTCCGACCGGGAAGGGCAAA-ACGGGAATAAAACATTGAAG
1 GAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGG-AAATACGGGAATAAAACATTGAAG
8576 ACA
65 ACA
8579 ACACCTTCCG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 60 0.95
69 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (68 bp):
GAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGGAAATACGGGAATAAAACATTGAAGA
CAG
Found at i:8582 original size:48 final size:48
Alignment explanation
Indices: 8508--8622 Score: 178
Period size: 48 Copynumber: 2.4 Consensus size: 48
8498 AACATTGAAG
8508 ACAGGAATGAAATATTGAAACCAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATGAAATATTGAAACCAACACCTTCCGACCGGGAAGGGCAAA
* * *
8556 ACGGGAATAAAACATTGAAGA-CAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATGAAATATTGAA-ACCAACACCTTCCGACCGGGAAGGGCAAA
*
8604 ATAGGAATGAAATATTGAA
1 ACAGGAATGAAATATTGAA
8623 CACCTTCCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 58 0.98
49 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (48 bp):
ACAGGAATGAAATATTGAAACCAACACCTTCCGACCGGGAAGGGCAAA
Found at i:8611 original size:116 final size:115
Alignment explanation
Indices: 8392--8622 Score: 338
Period size: 116 Copynumber: 2.0 Consensus size: 115
8382 GAAGGGCAAA
* *
8392 ACAGGAATAAAATATTCAAAACAACACCTTCCGACCGGGAAGGGCAAAACTAGAATAAAATATTG
1 ACAGGAATAAAATATTCAAAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAACATTG
8457 AAAACAACACCTTCCGACCGAGAAGGGAAATACGGGAATAAAACATTGAAG
66 AAAACAACACCTTCCGACCGAGAAGGGAAATAC-GGAATAAAACATTGAAG
* * * *
8508 ACAGGAATGAAATATTGAAACCAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTG
1 ACAGGAATAAAATATTCAAAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAACATTG
* * * *
8573 AAGACAACACCTTCCGACCGGGAAGGGCAAAATA-GGAATGAAATATTGAA
66 AAAACAACACCTTCCGACCGAGAAGGG--AAATACGGAATAAAACATTGAA
8623 CACCTTCCAG
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
116 98 0.95
118 5 0.05
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (115 bp):
ACAGGAATAAAATATTCAAAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAAACATTG
AAAACAACACCTTCCGACCGAGAAGGGAAATACGGAATAAAACATTGAAG
Done.