Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021802.1 Corchorus olitorius cultivar O-4 contig21835, 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: 15019
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:163 original size:27 final size:26
Alignment explanation
Indices: 114--169 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
104 TTTCCACTAT
114 TTTAATAATGAAATATTTAAAATATTA
1 TTTAATAATGAAATATTTAAAATA-TA
**
141 TTTAATAATGGCA-ATTTAGAAATATA
1 TTTAATAATGAAATATTTA-AAATATA
167 TTT
1 TTT
170 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (26 bp):
TTTAATAATGAAATATTTAAAATATA
Found at i:226 original size:2 final size:2
Alignment explanation
Indices: 219--259 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
209 TATTCGTACT
219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
260 CTGTATTGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1839 original size:17 final size:16
Alignment explanation
Indices: 1817--1850 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1807 TAGTAGTTTT
1817 TTTTTTTTAAATGGATA
1 TTTTTTTTAAAT-GATA
1834 TTTTTTTTAAATGATA
1 TTTTTTTTAAATGATA
1850 T
1 T
1851 AAATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
TTTTTTTTAAATGATA
Found at i:2103 original size:22 final size:22
Alignment explanation
Indices: 2077--2122 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2067 AGTTATAACT
* *
2077 TATAAGAGTTAAGTAAGCATTA
1 TATAAGAATTAAGTAAGCAATA
2099 TATAAGAATTAAGTAAGCAATA
1 TATAAGAATTAAGTAAGCAATA
2121 TA
1 TA
2123 GAAACACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
TATAAGAATTAAGTAAGCAATA
Found at i:5557 original size:22 final size:22
Alignment explanation
Indices: 5522--5648 Score: 98
Period size: 22 Copynumber: 5.7 Consensus size: 22
5512 TGATAGAAGG
* *
5522 TTATC-AAATCTCATAGAGTGG
1 TTATCAAAATTTCATAGAGTGA
5543 TTATCAAAATTTCATAGAGTTCAGA
1 TTATCAAAATTTCATAGAG-T--GA
*
5568 TTATCAAAATTT-ATA-AGAAGA
1 TTATCAAAATTTCATAGAG-TGA
* * *
5589 TTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAGAGTGA
* * * *
5611 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGTGA
*
5633 TTATCAAAATTACATA
1 TTATCAAAATTTCATA
5649 ATGTTTCGAT
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
21 19 0.22
22 46 0.54
23 4 0.05
24 3 0.04
25 13 0.15
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:5705 original size:22 final size:22
Alignment explanation
Indices: 5673--5748 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
5663 TATTTTTATG
5673 AAATTTT-ATAACTATCCTATT
1 AAATTTTGATAACTATCCTATT
* *
5694 GAATTTTGATAACTATCATATT
1 AAATTTTGATAACTATCCTATT
* *
5716 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAACTATCCTATT
*
5737 AAATTGTGATAA
1 AAATTTTGATAA
5749 ACTCCATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 21 0.45
22 26 0.55
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAACTATCCTATT
Found at i:8006 original size:27 final size:26
Alignment explanation
Indices: 7951--8012 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
7941 TCTAAATTTC
*
7951 TATTATTTTAATAATGGAATAATTAAAA
1 TATTA-TTTAATAATGCAAT-ATTAAAA
7979 TATTATTTAATAATAGCAAT-TTAGAAA
1 TATTATTTAATAAT-GCAATATTA-AAA
8006 TA-TATTT
1 TATTATTT
8013 GAAAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 8 0.26
27 14 0.45
28 9 0.29
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (26 bp):
TATTATTTAATAATGCAATATTAAAA
Found at i:8654 original size:11 final size:11
Alignment explanation
Indices: 8640--8672 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
8630 ATTCATAACA
8640 AATTTATAATT
1 AATTTATAATT
8651 AATTTATAATT
1 AATTTATAATT
8662 -ATTTGATAATT
1 AATTT-ATAATT
8673 TATATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:9700 original size:178 final size:178
Alignment explanation
Indices: 9335--9706 Score: 480
Period size: 178 Copynumber: 2.1 Consensus size: 178
9325 CCATAAGCAC
* ** * * *
9335 AAATTATGTAATATTAAGTAGACCGTCTATTTTCGTTAACTGAAACAACTAATTCTTTGGAATCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAAGCA
* * *
9400 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
* * * *
9465 AGCCTTTCAAGAGACACATGAATCATCTCAATCAGACATCTGGAGTAA
131 AACCTTTCAAGAGACACATAAATCACCTCAATCAGACAACTGGAGTAA
* *
9513 AAGTTATATAATATTAAGTTGACCGTCTATTCCCGTTAACCGAAACAAC-AAATCTTTCGGAAGC
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTT-GGAAGC
* *
9577 ATTTTTGATA-CTTAAAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCATTAA
65 ATTTTTGATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAA
* * * * * * *
9641 ACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAACTGGAG-AGA
129 ACAACCTTTCAAGAGACACATAAATCACCTCAATCAGACAACTGGAGTA-A
9691 AAATTATATAATATTA
1 AAATTATATAATATTA
9707 GATAGATCGT
Statistics
Matches: 166, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
177 11 0.07
178 155 0.93
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (178 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAAGCA
TTTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
AACCTTTCAAGAGACACATAAATCACCTCAATCAGACAACTGGAGTAA
Done.