Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002175.1 Corchorus olitorius cultivar O-4 contig02175, 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, 922
Length: 1538
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Found at i:462 original size:2 final size:2
Alignment explanation
Indices: 440--531 Score: 105
Period size: 2 Copynumber: 42.5 Consensus size: 2
430 CATATAGATC
440 AT AT CAT AT CAT AT CAT AT AT AT AT AT A- 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
482 AT AT CAT AT AT CAT AT AT CAT AT AT CAT AT AT CAT 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
527 AT AT A
1 AT AT A
532 ATGATAACAA
Statistics
Matches: 81, Mismatches: 0, Indels: 18
0.82 0.00 0.18
Matches are distributed among these distances:
1 1 0.01
2 64 0.79
3 16 0.20
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:471 original size:7 final size:7
Alignment explanation
Indices: 437--531 Score: 121
Period size: 7 Copynumber: 14.1 Consensus size: 7
427 AATCATATAG
437 ATCATAT
1 ATCATAT
444 CAT-ATCAT
1 -ATCAT-AT
452 ATCATAT
1 ATCATAT
459 AT-ATAT
1 ATCATAT
*
465 ATAATAT
1 ATCATAT
472 AT-ATAT
1 ATCATAT
478 AT-ATAT
1 ATCATAT
484 ATCATAT
1 ATCATAT
491 ATCATAT
1 ATCATAT
498 ATCATAT
1 ATCATAT
505 ATCATAT
1 ATCATAT
512 ATCATAT
1 ATCATAT
519 AT-ATAT
1 ATCATAT
525 AT-ATAT
1 ATCATAT
531 A
1 A
532 ATGATAACAA
Statistics
Matches: 83, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
6 29 0.35
7 48 0.58
8 6 0.07
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (7 bp):
ATCATAT
Found at i:493 original size:49 final size:47
Alignment explanation
Indices: 431--531 Score: 152
Period size: 47 Copynumber: 2.1 Consensus size: 47
421 AATAATAATC
*
431 ATATAGATCATATCAT-ATCATATCATATAT-ATATATAATATATATAT
1 ATATATATCATAT-ATCAT-ATATCATATATCATATATAATATATATAT
*
478 ATATATATCATATATCATATATCATATATCATATATCATATATATAT
1 ATATATATCATATATCATATATCATATATCATATATAATATATATAT
525 ATATATA
1 ATATATA
532 ATGATAACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
46 13 0.26
47 37 0.74
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.44
Consensus pattern (47 bp):
ATATATATCATATATCATATATCATATATCATATATAATATATATAT
Found at i:912 original size:7 final size:7
Alignment explanation
Indices: 880--976 Score: 132
Period size: 7 Copynumber: 14.1 Consensus size: 7
870 AAAAATAATA
880 ATCATAT
1 ATCATAT
887 AT-ATCAT
1 ATCAT-AT
894 ATCATAT
1 ATCATAT
901 CAT-ATAAT
1 -ATCAT-AT
909 AT-ATAT
1 ATCATAT
915 AT-ATAT
1 ATCATAT
921 AT-ATAT
1 ATCATAT
927 ATCATAT
1 ATCATAT
934 ATCATAT
1 ATCATAT
941 ATCATAT
1 ATCATAT
948 ATCATAT
1 ATCATAT
955 ATCATAT
1 ATCATAT
962 ATCATAT
1 ATCATAT
969 ATCATAT
1 ATCATAT
976 A
1 A
977 ATGATAACAA
Statistics
Matches: 85, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.21
7 61 0.72
8 6 0.07
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (7 bp):
ATCATAT
Found at i:1392 original size:82 final size:82
Alignment explanation
Indices: 1288--1446 Score: 300
Period size: 82 Copynumber: 1.9 Consensus size: 82
1278 CTCAAATATT
1288 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
1 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
1353 ATTTCCTTTTATATCTA
66 ATTTCCTTTTATATCTA
* *
1370 CCGATTTGATTTGATTTTAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
1 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
1435 ATTTCCTTTTAT
66 ATTTCCTTTTAT
1447 GATACCTATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (82 bp):
CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
ATTTCCTTTTATATCTA
Done.