Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013986.1 Corchorus olitorius cultivar O-4 contig14019, 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: 44322
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:440 original size:21 final size:21
Alignment explanation
Indices: 416--549 Score: 200
Period size: 21 Copynumber: 6.4 Consensus size: 21
406 CTTAGGCAAT
*
416 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
437 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
458 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
479 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
500 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
521 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
542 TCCAATGA
1 TCCAATGA
550 ACTTCTAGCA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 105 0.97
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:3909 original size:15 final size:16
Alignment explanation
Indices: 3889--3928 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
3879 AGAGGTTGAA
3889 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
3904 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
3920 AGAAAACAA
1 AGAAAACAA
3929 AACAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8583 original size:23 final size:23
Alignment explanation
Indices: 8530--8587 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
8520 TAAATATTAA
* *
8530 ATATCTTATATTATTATATAATTT
1 ATATATTAT-TTATTATATAATCT
*
8554 ATTTATTATTTATTATAT-ATACT
1 ATATATTATTTATTATATAAT-CT
8577 ATATATTATTT
1 ATATATTATTT
8588 TTAGTGACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 20 0.69
24 7 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATATTATTTATTATATAATCT
Found at i:9804 original size:42 final size:42
Alignment explanation
Indices: 9745--9835 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
9735 AACAACAATT
9745 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
*
9787 AATATTAGCTTTATTTTGTTGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
9829 AAT-TTAG
1 AATATTAG
9836 GTAATGTACT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
Found at i:10044 original size:7 final size:7
Alignment explanation
Indices: 10032--10075 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
10022 ACCACTTGTA
10032 TATTATT
1 TATTATT
*
10039 TATTATA
1 TATTATT
*
10046 TATTATA
1 TATTATT
10053 TATTATT
1 TATTATT
10060 TATTATT
1 TATTATT
10067 TA-TATT
1 TATTATT
10073 TAT
1 TAT
10076 ATATCTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TATTATT
Found at i:10055 original size:21 final size:23
Alignment explanation
Indices: 10030--10079 Score: 77
Period size: 21 Copynumber: 2.2 Consensus size: 23
10020 AGACCACTTG
10030 TATATTATTTATTA-TATA-TTA
1 TATATTATTTATTATTATATTTA
10051 TATATTATTTATTATTTATATTTA
1 TATATTATTTATTA-TTATATTTA
10075 TATAT
1 TATAT
10080 CTAATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.54
23 4 0.15
24 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATTATTTATTATTATATTTA
Found at i:26809 original size:2 final size:2
Alignment explanation
Indices: 26802--26846 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
26792 AGGTATAATC
26802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26844 AT A
1 AT A
26847 CCAAATAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42221 original size:65 final size:65
Alignment explanation
Indices: 42112--42241 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
42102 GGAAAAACTG
* *
42112 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAATGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
* *
42177 GTCCAACCCATGCATGGGGTACCCTTGGCCTGCCCACGCCTGGGCTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
42242 AATAGCAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
Found at i:42457 original size:21 final size:21
Alignment explanation
Indices: 42431--42472 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42421 GCATCTTAGG
* *
42431 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTCAAAC
42452 CAACTCCAATGAGCTTCAAAC
1 CAACTCCAATGAGCTTCAAAC
42473 TTCTTTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTCAAAC
Done.