Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021188.1 Corchorus olitorius cultivar O-4 contig21221, 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: 13859
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1373 original size:18 final size:19
Alignment explanation
Indices: 1342--1387 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1332 GCCTTAGTCC
*
1342 CAAAAAGAAGAAGGAAAGA
1 CAAAAAGAAGAAGGAAACA
1361 CAAAAAGAA-AAGGAAACA
1 CAAAAAGAAGAAGGAAACA
*
1379 GAAAAAGAA
1 CAAAAAGAA
1388 CAATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.72, C:0.07, G:0.22, T:0.00
Consensus pattern (19 bp):
CAAAAAGAAGAAGGAAACA
Found at i:2378 original size:2 final size:2
Alignment explanation
Indices: 2371--2396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2361 ATTTGAATGT
2371 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2397 AAAGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8558 original size:16 final size:17
Alignment explanation
Indices: 8532--8567 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
8522 ACTTAGACCC
*
8532 AAAAAGAAGAAGGGAAG
1 AAAAAGAAGAAGGAAAG
8549 AAAAAG-AGAAGGAAAG
1 AAAAAGAAGAAGGAAAG
8565 AAA
1 AAA
8568 GGACAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAGGAAAG
Found at i:8587 original size:19 final size:20
Alignment explanation
Indices: 8549--8597 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
8539 AGAAGGGAAG
*
8549 AAAAAGAGAAGGAAAGAAAGG
1 AAAAAGA-AAGGAAAGAAAGA
* *
8570 ACAAAGAAAGGGAA-AAAGA
1 AAAAAGAAAGGAAAGAAAGA
8589 AAAAAGAAA
1 AAAAAGAAA
8598 AATAATTACC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.50
20 6 0.25
21 6 0.25
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAGGAAAGAAAGA
Found at i:10160 original size:179 final size:178
Alignment explanation
Indices: 9860--10251 Score: 518
Period size: 179 Copynumber: 2.2 Consensus size: 178
9850 TTTGCTGATT
* * * * * *
9860 ATGGAACGACCTTTTAACAGACACTTGAATAATCTTAATCAGACATATGGAGCAAAAATTATGTA
1 ATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAAACATACGGAGCAAAAATTATGTA
* * * *
9925 ATATTAAGTAGACCTTACATTCCCGCTAACCGAAGCAACTAATTCTTTGTAAGTATTTTCTTATA
66 ATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAATTCTTTGGAAGTATTTT-TGATA
*
9990 CATT-AAACATTAAATTTAACTTTCGAGTCCTTCATAAAAGTTGTAGATC
130 C-TTGAAACATTAAATTTAACTTTCGAGTCCTTCATAAAACTTGTAGATC
* * *
10039 ATGGAACAACCTTTTAAGAGACACTTGAATCACCTCAATCAAACATCCGGAGCAAAAGTTATGTA
1 ATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAAACATACGGAGCAAAAATTATGTA
* * * *
10104 ATATTAAGTGGACCGTCCATTCTCGTTAACCGAAACAACTAATT-TTTCGGAAGTATTTTTGATA
66 ATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAATTCTTT-GGAAGTATTTTTGATA
** *
10168 CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAACTTGTAGATC
130 CTTGAAACATTAAATTTAACTTTCGAGTCCTTCATAAAACTTGTAGATC
* * * *
10217 ATGGAACAATCTTTGAATAGACACTTAAATCACCT
1 ATGGAACAACCTTTTAACAGACACTTGAATCACCT
10252 TGATCGGATA
Statistics
Matches: 186, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
177 2 0.01
178 80 0.43
179 104 0.56
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (178 bp):
ATGGAACAACCTTTTAACAGACACTTGAATCACCTCAATCAAACATACGGAGCAAAAATTATGTA
ATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAATTCTTTGGAAGTATTTTTGATAC
TTGAAACATTAAATTTAACTTTCGAGTCCTTCATAAAACTTGTAGATC
Found at i:11751 original size:13 final size:13
Alignment explanation
Indices: 11733--11758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11723 GAACACTGGC
11733 CTTTTGAAAAATG
1 CTTTTGAAAAATG
11746 CTTTTGAAAAATG
1 CTTTTGAAAAATG
11759 ATCTTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAATG
Found at i:13429 original size:21 final size:21
Alignment explanation
Indices: 13405--13483 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
13395 AAGTAACGTG
13405 TCTTTTTTTCTTTTTTCTTAT
1 TCTTTTTTTCTTTTTTCTTAT
*
13426 TCTTTTATTCTTTTTTCTTTAT
1 TCTTTTTTTCTTTTTTC-TTAT
** *
13448 AGTTTTTTCTCTTCTTTT-TTCT
1 TCTTTTTT-TCTT-TTTTCTTAT
13470 TCTTTTCTTTCTTT
1 TCTTTT-TTTCTTT
13484 CTTCCTCCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 17 0.36
22 20 0.43
23 6 0.13
24 4 0.09
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (21 bp):
TCTTTTTTTCTTTTTTCTTAT
Found at i:13486 original size:26 final size:25
Alignment explanation
Indices: 13408--13487 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
13398 TAACGTGTCT
*
13408 TTTTTTCTTTTTTCTTATTCTTTTATTC
1 TTTTTTCTTTTTTC-T-TTC-TTTCTTC
* ** *
13436 TTTTTTCTTTATAGTTTTTTCTCTTC
1 TTTTTTCTTTTTTCTTTCTT-TCTTC
13462 TTTTTTCTTCTTTTCTTTCTTTCTTC
1 TTTTTTCTT-TTTTCTTTCTTTCTTC
13488 CTCCTACACG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 2 0.05
26 20 0.49
27 8 0.20
28 11 0.27
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTTTCTTTTTTCTTTCTTTCTTC
Done.