Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017563.1 Corchorus olitorius cultivar O-4 contig17596, 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: 5136
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Found at i:678 original size:332 final size:335
Alignment explanation
Indices: 236--840 Score: 808
Period size: 332 Copynumber: 1.8 Consensus size: 335
226 GGCCCCAGAT
* * * ** * * *
236 AAGTTTTGCATGTTTTTTGGCGCTAAGACTTCTTGAAATATTTATATTCATCTAACCAAATCTCA
1 AAGTTTTGCATGTTTTTTGGCACCAAGACTCCTTGAAATACCTATAATAATCTAACAAAATCTCA
* * *
301 GCAACATTTGATTTAAGGATTTGTATTTACGAGAATCTGAATATTGTTTCGATTTTATTATAAAT
66 ACAACATTTGATTTAAGGAATTGTATTTACGAGAATCTGAATATTGTTTCGATTTTATTAGAAAT
* * * * *
366 TAATTCAGAAAAAAAT-GTAAAACTATATTAGAAGCGCGAAAAGCCCTTAAATC-TTTATGGCTT
131 TAATTCAGAAAAAAATGGAAAAACGATACTAGAAGCGCGAAAAGCCCTCAAATCGTTT-TGGCGT
** * *
429 TCAGTTAAAT-ATTTTCCATGATTATTGTGGC-AAAAAATTGAGGAAAAATCTTTCAGGTAAATT
195 TCAAATAAATAATTTTCCATGAGTATTGTGACTAAAAAATTGAGGAAAAATCTTTCAGGTAAATT
*
492 TTCGCAAAATTTTACCCGAAATCATGTACTTAACCCTCACGGTTTTTTGCTAAAAATGCGTTCCA
260 TTCACAAAATTTTACCCGAAATCATGTACTTAACCCTCACGGTTTTTTGCTAAAAATGCGTTCCA
557 GGGCCCCGCCA
325 GGGCCCCGCCA
*
568 AAGTTTTGCATGATTTTTT-GCACCAAGACTCCTTTAAATACCTATAATAATCTAACAAAATCTC
1 AAGTTTTGCATG-TTTTTTGGCACCAAGACTCCTTGAAATACCTATAATAATCTAACAAAATCTC
* **
632 AACAA-ATTTTGATTTAAGGAATTGTTTTTACGATCATCTGAATATTGTTTCGATTTTATTAGAA
65 AACAACA-TTTGATTTAAGGAATTGTATTTACGAGAATCTGAATATTGTTTCGATTTTATTAGAA
* * * * *
696 ATTAATTCGGAAAAAAATGGAAAAACGATACTAGAAGTGTGAAACGCCCTCCAATCGTTTTGGCG
129 ATTAATTCAGAAAAAAATGGAAAAACGATACTAGAAGCGCGAAAAGCCCTCAAATCGTTTTGGCG
* * ** * *
761 TTGAAATATATAATTTTTTATGAGTGTTGTGACTAAAAAATTGAGGAAAAATCTTTCAGGTCAAT
194 TTCAAATAAATAATTTTCCATGAGTATTGTGACTAAAAAATTGAGGAAAAATCTTTCAGGTAAAT
*
826 TTTTACAAAATTTTA
259 TTTCACAAAATTTTA
841 GCATAAATCG
Statistics
Matches: 230, Mismatches: 37, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
331 1 0.00
332 121 0.53
333 46 0.20
334 19 0.08
335 43 0.19
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (335 bp):
AAGTTTTGCATGTTTTTTGGCACCAAGACTCCTTGAAATACCTATAATAATCTAACAAAATCTCA
ACAACATTTGATTTAAGGAATTGTATTTACGAGAATCTGAATATTGTTTCGATTTTATTAGAAAT
TAATTCAGAAAAAAATGGAAAAACGATACTAGAAGCGCGAAAAGCCCTCAAATCGTTTTGGCGTT
CAAATAAATAATTTTCCATGAGTATTGTGACTAAAAAATTGAGGAAAAATCTTTCAGGTAAATTT
TCACAAAATTTTACCCGAAATCATGTACTTAACCCTCACGGTTTTTTGCTAAAAATGCGTTCCAG
GGCCCCGCCA
Found at i:1775 original size:25 final size:25
Alignment explanation
Indices: 1741--1803 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
1731 TATTTTCTAG
1741 CAAGAGCACCATTTTTGATACATAA
1 CAAGAGCACCATTTTTGATACATAA
1766 CAAGAGCACCATTTTTGATACATAA
1 CAAGAGCACCATTTTTGATACATAA
1791 CAAGAGCACCATT
1 CAAGAGCACCATT
1804 GACAACCTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (25 bp):
CAAGAGCACCATTTTTGATACATAA
Found at i:3483 original size:31 final size:31
Alignment explanation
Indices: 3384--4149 Score: 1005
Period size: 31 Copynumber: 25.6 Consensus size: 31
3374 GGAGAAAACA
* *
3384 AAAAGTGAACTATATGCTATAACGATAAACCT
1 AAAA-TGAACTATATGCAATAACGATAGACCT
3416 --AA--AACTATATGCAATAACGATAGACC-
1 AAAATGAACTATATGCAATAACGATAGACCT
3442 -AAA--AACTATATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
3470 AAAATGAACTATATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3501 AAAATGAACTATATGCAATAACGATAAACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
3532 --AA--AACTATATGTAATAACGATAGAACT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3559 AAAATGAACTATATGCAATAACGATAGATCT
1 AAAATGAACTATATGCAATAACGATAGACCT
3590 AAAATGAACTATATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3621 ---A-GAACTATATGCAATAACGATAAACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3648 --AA--AACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
3675 AGAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
3706 AGAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
3737 AGAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3768 AGAATGAACTATATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
3799 ---A-GAACTATATGCAATAACGATA-ACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3825 AAAATGAACTACATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
3856 ---A-GAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
3883 AGAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* * *
3914 AGAACGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* * *
3945 AGAACGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* * *
3976 AGAACGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* *
4007 AGAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
*
4038 AAAATGAACTATATGCAATAACGATGGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
4069 AAAATGAACTATATGCAATAACGATAGACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
* * *
4100 AAAATGAACTATATGCTATGACGATAAACCT
1 AAAATGAACTATATGCAATAACGATAGACCT
4131 AAAAATGAACTATATGCAA
1 -AAAATGAACTATATGCAA
4150 CAGCCACACT
Statistics
Matches: 686, Mismatches: 24, Indels: 48
0.91 0.03 0.06
Matches are distributed among these distances:
26 4 0.01
27 163 0.24
28 4 0.01
29 10 0.01
30 23 0.03
31 465 0.68
32 17 0.02
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (31 bp):
AAAATGAACTATATGCAATAACGATAGACCT
Done.