Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010349.1 Corchorus capsularis cultivar CVL-1 contig10370, 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: 54701
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2087 original size:14 final size:14
Alignment explanation
Indices: 2068--2102 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2058 TACTATGTTC
2068 TTTTTTTGTTTTTG
1 TTTTTTTGTTTTTG
2082 TTTTTTTGTTTTTG
1 TTTTTTTGTTTTTG
2096 TTTTTTT
1 TTTTTTT
2103 TTTCCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTTTGTTTTTG
Found at i:2677 original size:2 final size:2
Alignment explanation
Indices: 2666--2718 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
2656 GGATTCTCAT
2666 TA TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2705 TA -A TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA
2719 GGTATAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2680 original size:9 final size:9
Alignment explanation
Indices: 2666--2716 Score: 86
Period size: 9 Copynumber: 5.7 Consensus size: 9
2656 GGATTCTCAT
2666 TATATAATA
1 TATATAATA
2675 TATAT-ATA
1 TATATAATA
2683 TATATAATA
1 TATATAATA
2692 TATATAATA
1 TATATAATA
2701 TATATAATAA
1 TATATAAT-A
2711 TATATA
1 TATATA
2717 TAGGTATAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.20
9 25 0.62
10 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATAATA
Found at i:2737 original size:6 final size:6
Alignment explanation
Indices: 2666--2718 Score: 71
Period size: 5 Copynumber: 9.7 Consensus size: 6
2656 GGATTCTCAT
2666 TATATA -ATATA TATATA TATATA -ATATA TATA-A TATATA TA-ATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
2710 -ATATA TATA
1 TATATA TATA
2719 GGTATAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.02
5 21 0.50
6 20 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:2970 original size:2 final size:2
Alignment explanation
Indices: 2963--2992 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2953 TCAGTAATCC
2963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2993 TACATATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3802 original size:2 final size:2
Alignment explanation
Indices: 3795--3821 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3785 TTTTCACTGG
3795 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3822 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3826 original size:2 final size:2
Alignment explanation
Indices: 3821--3845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3811 TCTCTCTCTC
3821 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 T
3846 GTCACAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8844 original size:45 final size:45
Alignment explanation
Indices: 8781--8875 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
8771 AGTGTCGCAT
8781 ATATACTTACTTTACTAATTGCTTTATCCTTGATTATTATTAATC
1 ATATACTTACTTTACTAATTGCTTTATCCTTGATTATTATTAATC
8826 ATATACTTACTTTACTAATTGCTTTATCCTTGATTATTATTAATC
1 ATATACTTACTTTACTAATTGCTTTATCCTTGATTATTATTAATC
8871 ATATA
1 ATATA
8876 AAATTAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.51
Consensus pattern (45 bp):
ATATACTTACTTTACTAATTGCTTTATCCTTGATTATTATTAATC
Found at i:20148 original size:2 final size:2
Alignment explanation
Indices: 20141--20173 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20131 ATGTAACACA
20141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20174 AAAAGATGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21494 original size:27 final size:27
Alignment explanation
Indices: 21456--21509 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
21446 TTCTATCTTA
21456 ATAGAAGTGAACAGATAATATGAGACG
1 ATAGAAGTGAACAGATAATATGAGACG
*
21483 ATAGAAGTGAACAGATAATATGGGACG
1 ATAGAAGTGAACAGATAATATGAGACG
21510 GAGGGAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.19
Consensus pattern (27 bp):
ATAGAAGTGAACAGATAATATGAGACG
Found at i:28320 original size:3 final size:3
Alignment explanation
Indices: 28312--28344 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28302 TGAGTAACAA
28312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28345 TCAAACTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39938 original size:2 final size:2
Alignment explanation
Indices: 39933--39961 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39923 TGGCAAATTG
39933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39962 ACTATAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44049 original size:20 final size:21
Alignment explanation
Indices: 44023--44069 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
44013 AGTAGTTAGC
44023 ATTTTTGTTATTAT-ATGCATG
1 ATTTTTGTT-TTATCATGCATG
*
44044 -TTTTTGTTTTATCTTGCATG
1 ATTTTTGTTTTATCATGCATG
44064 ATTTTT
1 ATTTTT
44070 TTTACAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 14 0.61
21 5 0.22
ACGTcount: A:0.17, C:0.06, G:0.13, T:0.64
Consensus pattern (21 bp):
ATTTTTGTTTTATCATGCATG
Found at i:46679 original size:2 final size:2
Alignment explanation
Indices: 46672--46705 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46662 GTTGCATTGC
46672 AT AT AT AT AT AT AT AT AT AT 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
46706 GTAGAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50336 original size:79 final size:79
Alignment explanation
Indices: 50205--50362 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
50195 GACAATATAG
50205 AGTTGGATCAAGCGCTTGTTTCAACTAGGTCTCATGTTCGAGACCTTTCGTATGCAGTAGTCCCC
1 AGTTGGATCAAGCGCTTGTTTCAACTAGGTCTCATGTTCGAGACCTTTCGTATGCAGTAGTCCCC
50270 ATTCATTGGTAGAC
66 ATTCATTGGTAGAC
50284 AGTTGGATCAAGCGCTTGTTTCAACTAGGTCTCATGTTCGAGACCTTTCGTATGCAGTAGTCCCC
1 AGTTGGATCAAGCGCTTGTTTCAACTAGGTCTCATGTTCGAGACCTTTCGTATGCAGTAGTCCCC
50349 ATTCATTGGTAGAC
66 ATTCATTGGTAGAC
50363 TCATCCACGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (79 bp):
AGTTGGATCAAGCGCTTGTTTCAACTAGGTCTCATGTTCGAGACCTTTCGTATGCAGTAGTCCCC
ATTCATTGGTAGAC
Done.