Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01005934.1 Corchorus olitorius cultivar O-4 contig05959, 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, 676
Length: 1127
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Found at i:350 original size:22 final size:22
Alignment explanation
Indices: 294--815 Score: 185
Period size: 22 Copynumber: 23.4 Consensus size: 22
284 CTCTAACATA
* **
294 GAAATATTGATAACCTCATTAT
1 GAAATTTTGATAACCTCCCTAT
***
316 GAAATTCCAATAACCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* *
338 GAAAATTTT-ATAACCACACTAT
1 G-AAATTTTGATAACCTCCCTAT
* * **
360 GAAATTTCGATAATCTCTGTAT
1 GAAATTTTGATAACCTCCCTAT
382 GAAATTTTGATAATCC-CCCTAT
1 GAAATTTTGATAA-CCTCCCTAT
* *
404 GAAATTTTGATAATCAT-ACTAT
1 GAAATTTTGATAA-CCTCCCTAT
* ** * *
426 -AAA-TTTGGTAACAACACAAT
1 GAAATTTTGATAACCTCCCTAT
*
446 GAAAATTTTGATAACCT-CCTCAA
1 G-AAATTTTGATAACCTCCCT-AT
* * * *
469 AAAATTATGATAAACACACC-AT
1 GAAATTTTGATAACCTC-CCTAT
* * *
491 GAAATTTCGATAACCTTCTTAT
1 GAAATTTTGATAACCTCCCTAT
* * *
513 GAGAATAAAACTGTGATATCCTCTCTAT
1 GA-AAT-----TTTGATAACCTCCCTAT
*
541 GTAATTTTGATAACCTCTCC-AT
1 GAAATTTTGATAACCTC-CCTAT
* *
563 -AAATTTTTCATAACCTCCATAT
1 GAAA-TTTTGATAACCTCCCTAT
585 GAAATTTTGTTAATTAACCTCCCTAT
1 GAAATTTTG---A-TAACCTCCCTAT
*
611 GAAATTTTGATAA----GC-A-
1 GAAATTTTGATAACCTCCCTAT
* *
627 CAAATTCTGATAACCTCCCTCCCTAT
1 GAAATTTTGATAA----CCTCCCTAT
* *
653 GAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCTCCCTAT
* ** * * *
675 AAAATTTCAATAACATTCGTAT
1 GAAATTTTGATAACCTCCCTAT
* * *
697 GAGATTTTGTTAACCTCCCTAA
1 GAAATTTTGATAACCTCCCTAT
** ***
719 GAAATTTTGATAAAGTTTTTAT
1 GAAATTTTGATAACCTCCCTAT
**
741 GAAATTTTGATAACCTCTGTAT
1 GAAATTTTGATAACCTCCCTAT
* *
763 GAAATTTTGATAA-CTACACAAT
1 GAAATTTTGATAACCT-CCCTAT
* * *
785 GAAGTGTTGATAACCTCCATAT
1 GAAATTTTGATAACCTCCCTAT
*
807 GAATTTTTG
1 GAAATTTTG
816 GTAGCTATAC
Statistics
Matches: 358, Mismatches: 104, Indels: 76
0.67 0.19 0.14
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
19 2 0.01
20 11 0.03
21 15 0.04
22 241 0.67
23 25 0.07
24 3 0.01
25 2 0.01
26 31 0.09
27 3 0.01
28 12 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:688 original size:112 final size:108
Alignment explanation
Indices: 532--731 Score: 249
Period size: 112 Copynumber: 1.8 Consensus size: 108
522 ACTGTGATAT
* * * * * *
532 CCTCTCTATGTAATTTTGATAACCTCTCCATAAATTTTTCATAACCTCCATATGAAATTTTGTTA
1 CCTCCCTATGAAATTTTGATAACCACACCATAAATATTTCATAACATCCATATGAAATTTTG---
*
597 ATTAACCTCCCTATGAAATTTTGATAAGCACAAATTCTGATAACCTC
63 -TTAACCTCCCTAAGAAATTTTGATAAGCACAAATTCTGATAACCTC
* * * *
644 CCTCCCTATGAAATTTTGATAACCACACTATAAA-ATTTCAATAACATTCGTATGAGATTTTGTT
1 CCTCCCTATGAAATTTTGATAACCACACCATAAATATTTC-ATAACATCCATATGAAATTTTGTT
708 AACCTCCCTAAGAAATTTTGATAA
65 AACCTCCCTAAGAAATTTTGATAA
732 AGTTTTTATG
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 25 0.33
111 4 0.05
112 47 0.62
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (108 bp):
CCTCCCTATGAAATTTTGATAACCACACCATAAATATTTCATAACATCCATATGAAATTTTGTTA
ACCTCCCTAAGAAATTTTGATAAGCACAAATTCTGATAACCTC
Found at i:787 original size:44 final size:44
Alignment explanation
Indices: 739--859 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 44
729 TAAAGTTTTT
* **
739 ATGAAATTTTGATAACCTCTGTATGAAATTTTGATAACTACACA
1 ATGAAATGTTGATAACCTCCATATGAAATTTTGATAACTACACA
* * * * * *
783 ATGAAGTGTTGATAACCTCCATATGAATTTTTGGTAGCTATACT
1 ATGAAATGTTGATAACCTCCATATGAAATTTTGATAACTACACA
* * *
827 ATGAAATGTTAATAATCTTCC-TATGTAATTTTG
1 ATGAAATGTTGATAA-CCTCCATATGAAATTTTG
860 GTTTGATTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 58 0.94
45 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (44 bp):
ATGAAATGTTGATAACCTCCATATGAAATTTTGATAACTACACA
Done.