Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020746.1 Corchorus olitorius cultivar O-4 contig20779, 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: 9819
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Found at i:133 original size:7 final size:7
Alignment explanation
Indices: 114--146 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
104 TCTTTTACTA
114 AAATTT-
1 AAATTTC
120 AATATTTC
1 AA-ATTTC
128 AAATTTC
1 AAATTTC
135 AAATTTC
1 AAATTTC
142 AAATT
1 AAATT
147 AGTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 21 0.84
8 2 0.08
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (7 bp):
AAATTTC
Found at i:5607 original size:49 final size:49
Alignment explanation
Indices: 5535--5632 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
5525 TATATCCAGG
5535 CTGAGATCTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTA
1 CTGAGATCTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTA
5584 CTGAGATCTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTA
1 CTGAGATCTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTA
5633 TGCGCCAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (49 bp):
CTGAGATCTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTA
Found at i:6877 original size:645 final size:638
Alignment explanation
Indices: 5591--7130 Score: 1649
Period size: 645 Copynumber: 2.4 Consensus size: 638
5581 CTACTGAGAT
* * *
5591 CTGAGATTTGGTTCAATGAATATGGATATTTCAAGAAGTCTATGCGCCAAAAATCATGTAAAACT
1 CTGAGATTTGGTTCGATGAATATGGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACT
**
5656 GAGAT-AGGGCCCCGAAACACGTTTTTAGCCCAAAAC--------C-A-TACACGATTTCGGCTA
66 GAG-TCAGGG---C--AATGCGTTTTTAGCCCAAAACAGTGATGGCTAGTACACGATTTCGGCTA
** * * * *
5710 AAAACTGACCCGAAACTTATTTTTCTGAATTGTTTGCCACAATACTCAAAATATATATATAATTT
125 AAAACTGACCCGAAAAATATTTTTCTAAATT-TTTGCCACAATACT-AAAAAAAATATATAATTC
* * * * *
5775 AACGCAAAAAAATTGAAAGGTTTTTCACGCGTCTAATATCGTTTTTCCATTTTTTTCCGAATTTA
188 AACCCAAAAAGATTGAGA-GTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAA
* * * * *
5840 TTTTTAATTAAATCGAAACAAGAATCAGATACTTGTACAAACAAATCCTTAAATCCAATGTGGCT
252 TTTCTAATTAAATCGAAACAAGAATAAGATACTCGTAAAAACAAATCCTTAAATCCAATATGGCT
* ** *
5905 GAGATTTTGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCCAAAATCATGCAAAACTGA
317 GAGATTTGGTTAGATGAATATAGATATTTCAAAAAATCATTCTACCCAAAATCATGCAAAACTGA
** * ** *
5970 ACCGGTGCCCCCGAAATGCGTTTTTAGCCCAAAAACCGTGATGTAATATACACGATTACGGCTAA
382 ACCGGTGCCCCCGAAACACATTTTTAGCAAAAAAACCGTGATGT-ATATACACGATTACAGCTAA
* *
6035 AAATTAACCAAAAAAAAATCCTTATCCTGAATTTTTTGCCACAATACTTAGAAAAAAAATATAAT
446 AAATTAA-CAAAAAAAAAT-CTTATCCTGAATTCTTTGCCACAATACTCAGAAAAAAAATATAAT
* * * * *
6100 TTAACACCAAAAATATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATT
509 TCAACACAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTACTATTTTTTCCGAATT
* *
6165 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG
574 AATTTCCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
*
6230 CTGAGATTTGGTTCGATGAATATGGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACT
1 CTGAGATTTGGTTCGATGAATATGGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACT
*
6295 GAGTCAGGGCTATGCGTTTTTAGCCCAAAACAGTGATGGCTAGTACACGATTTCGGCTAAAAACT
66 GAGTCAGGGCAATGCGTTTTTAGCCCAAAACAGTGATGGCTAGTACACGATTTCGGCTAAAAACT
* *
6360 AACCCGAAAAATATTTTTCTAAATTTTGTGCCACAATACTAAAAAAAAACATATAATTCAACACC
131 GACCCGAAAAATATTTTTCTAAATTTT-TGCCACAATACT-AAAAAAAATATATAATTCAAC-CC
* * *
6425 AAAAAGATTGACGAGCTTTTCATGCTTCTAATATCGTTTTTTCATTTTTTT-CGAATTAATTTCT
193 AAAAAGATTGA-GAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCT
* * * * *
6489 AATTAAATTGAAAC-A-ATTAAGATGCTCGTAAAAACAAATCCTTAAATTCAATATGGCTGGGAT
257 AATTAAATCGAAACAAGAATAAGATACTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGAT
* * *
6552 TTGGTTCGATGAATATAGATATTTTAAAAAAT-ATT-TACGCCAAAAAT-ATGCAAAACTGAGCC
322 TTGGTTAGATGAATATAGATATTTCAAAAAATCATTCTAC-CC-AAAATCATGCAAAACTGAACC
* * *
6614 GG-GGCCCCGTAACACATTTTTAGCAAAAATAACCGTGATGGT-TAGTACACGATTTCAGCTAAA
385 GGTGCCCCCGAAACACATTTTTAGCAAAAA-AACCGTGAT-GTATA-TACACGATTACAGCTAAA
** * * * * *
6677 TTTTGTAA-AAATTGACTCGGAAAAT-TTTTCCTTAATTCTTTG-C-CAATACTCAGAATAAATA
447 -AAT-TAACAAA---A----AAAAATCTTATCCTGAATTCTTTGCCACAATACTCAGAAAAAAAA
* * * *
6738 TATAATTCAA-ATAAAAAAAATTTAAGGG-TTTTCACGCTTCTAGTATCGTTTTACATTTTTTTT
503 TATAATTCAACACAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTAC-TATTTTTT
** * *
6801 CCCCGAATTTGTTTCCAATTAAATTGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAAT
567 --CCGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
6866 CCAATGTGG
630 CCAATGTGG
* * * ** * * *
6875 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGTATGTCAAAAACCATGCAAAATT
1 CTGAGATTTGGTTCGATGAATATGGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACT
* * * * *
6940 GAGTCGAGATCCCGAAATGTGTTTTTAG-CTAAAAGCAGTGATGGTTAGTACACGATTTCGGCTA
66 GAGTC-AG----GGCAATGCGTTTTTAGCCCAAAA-CAGTGATGGCTAGTACACGATTTCGGCTA
* * * * *
7004 AAAACTGACACG-AAAATTTTTTTCTCAATTTTTTGCCATAATACTAGAAAAAATATATAATTCA
125 AAAACTGACCCGAAAAATATTTTTCT-AAATTTTTGCCACAATACTAAAAAAAATATATAATTCA
* * * *
7068 ACGCTAAAAAGATTGAAGGGTTTTTCACGCTTCTAATCTCATTTTTCCATTTCTTTTCCGAAT
189 AC-CCAAAAAGATTG-AGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTT-TTTTCCGAAT
7131 CAAAACAACA
Statistics
Matches: 757, Mismatches: 103, Indels: 71
0.81 0.11 0.08
Matches are distributed among these distances:
634 18 0.02
636 1 0.00
638 1 0.00
639 68 0.09
640 25 0.03
641 48 0.06
642 100 0.13
643 27 0.04
644 121 0.16
645 173 0.23
646 17 0.02
648 64 0.08
649 33 0.04
650 61 0.08
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (638 bp):
CTGAGATTTGGTTCGATGAATATGGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACT
GAGTCAGGGCAATGCGTTTTTAGCCCAAAACAGTGATGGCTAGTACACGATTTCGGCTAAAAACT
GACCCGAAAAATATTTTTCTAAATTTTTGCCACAATACTAAAAAAAATATATAATTCAACCCAAA
AAGATTGAGAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATT
AAATCGAAACAAGAATAAGATACTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGG
TTAGATGAATATAGATATTTCAAAAAATCATTCTACCCAAAATCATGCAAAACTGAACCGGTGCC
CCCGAAACACATTTTTAGCAAAAAAACCGTGATGTATATACACGATTACAGCTAAAAATTAACAA
AAAAAAATCTTATCCTGAATTCTTTGCCACAATACTCAGAAAAAAAATATAATTCAACACAAAAA
AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTACTATTTTTTCCGAATTAATTTCCAATTA
AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
Found at i:7938 original size:20 final size:21
Alignment explanation
Indices: 7901--7943 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
7891 AATCCGTTAA
*
7901 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
7922 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
7942 TT
1 TT
7944 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:8001 original size:42 final size:43
Alignment explanation
Indices: 7931--8013 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
7921 CTTAAACGTG
*
7931 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
*
7974 TTAATCGTGTC-CGACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGGACACGAAACACGATAA
8014 GTCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 25 0.68
43 12 0.32
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
Done.