Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005476.1 Corchorus capsularis cultivar CVL-1 contig05494, 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: 21033
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:762 original size:12 final size:12
Alignment explanation
Indices: 745--772 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
735 TCAAATTCAA
745 AGTTGGACAATC
1 AGTTGGACAATC
757 AGTTGGACAATC
1 AGTTGGACAATC
769 AGTT
1 AGTT
773 TGGTCTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (12 bp):
AGTTGGACAATC
Found at i:6346 original size:22 final size:22
Alignment explanation
Indices: 6316--6360 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6306 TTAATACAAC
*
6316 AACACAATATTATACACTTGAA
1 AACACAATATCATACACTTGAA
*
6338 AACATAATATCATACACTTGAA
1 AACACAATATCATACACTTGAA
6360 A
1 A
6361 CTGCATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (22 bp):
AACACAATATCATACACTTGAA
Found at i:13622 original size:22 final size:21
Alignment explanation
Indices: 13588--13704 Score: 94
Period size: 22 Copynumber: 5.3 Consensus size: 21
13578 CATATCCCTG
*
13588 TGAAACTTTGATACCCACACTA
1 TGAAA-TTTGATAACCACACTA
*
13610 TGAAATTTCGATAATCATC-CTA
1 TGAAATTT-GATAACCA-CACTA
* *
13632 TTAAATTTTGATTACCACACTA
1 TGAAA-TTTGATAACCACACTA
13654 TGAAACTTTGATAACCACACTA
1 TGAAA-TTTGATAACCACACTA
* * *
13676 TAAAATAGTGATAACCTCTAC-A
1 TGAAAT-TTGATAACCAC-ACTA
13698 TGAAATT
1 TGAAATT
13705 AATTTTGCTA
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
21 5 0.07
22 65 0.86
23 6 0.08
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (21 bp):
TGAAATTTGATAACCACACTA
Found at i:13861 original size:22 final size:22
Alignment explanation
Indices: 13836--13883 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
13826 GATAACTTCC
13836 CTATAGAATTTTGTTAATCTCA
1 CTATAGAATTTTGTTAATCTCA
13858 CTAT-GAATTTTGTTAATCTCA
1 CTATAGAATTTTGTTAATCTCA
*
13879 TTATA
1 CTATA
13884 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (22 bp):
CTATAGAATTTTGTTAATCTCA
Found at i:13866 original size:21 final size:21
Alignment explanation
Indices: 13769--13878 Score: 80
Period size: 22 Copynumber: 5.1 Consensus size: 21
13759 TGATTTGGTA
* *
13769 CACTATGAAATTTGGATAACCAT
1 CACTATG-AATTTTGATAATC-T
*
13792 -ACTATGAAATTTTGATAACCT
1 CACTATG-AATTTTGATAATCT
* * *
13813 CCCTAGGAATGTTGATAA-CTT
1 CACTATGAATTTTGATAATC-T
* *
13834 CCCTATAGAATTTTGTTAATCT
1 CACTAT-GAATTTTGATAATCT
*
13856 CACTATGAATTTTGTTAATCT
1 CACTATGAATTTTGATAATCT
13877 CA
1 CA
13879 TTATATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
20 1 0.01
21 34 0.45
22 39 0.52
23 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
CACTATGAATTTTGATAATCT
Found at i:14131 original size:32 final size:34
Alignment explanation
Indices: 14063--14141 Score: 110
Period size: 32 Copynumber: 2.4 Consensus size: 34
14053 TCGTTATATC
* *
14063 AAGTTAATGGTTCTTTTGTTTCACCAAAAAAAAA
1 AAGTTAATGGTTCTTTTGTCTCACAAAAAAAAAA
14097 AAGTTAATGGTTC-TTT-TCTCA-AAAGAAAAAAA
1 AAGTTAATGGTTCTTTTGTCTCACAAA-AAAAAAA
14129 AAGTTAATGGTTC
1 AAGTTAATGGTTC
14142 CTCAAGCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 2 0.05
32 24 0.57
33 3 0.07
34 13 0.31
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (34 bp):
AAGTTAATGGTTCTTTTGTCTCACAAAAAAAAAA
Found at i:14855 original size:16 final size:16
Alignment explanation
Indices: 14808--14856 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
14798 CGTTGTAGGA
14808 TAATATTGACCCAAAC
1 TAATATTGACCCAAAC
* *
14824 TAATACT-A---ATAC
1 TAATATTGACCCAAAC
14836 TAATATTGACCCAAAC
1 TAATATTGACCCAAAC
14852 TAATA
1 TAATA
14857 ATATTTAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
15 1 0.04
16 14 0.56
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (16 bp):
TAATATTGACCCAAAC
Found at i:15693 original size:53 final size:53
Alignment explanation
Indices: 15612--15718 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
15602 CCATCTCAAA
15612 CCACAGCATTGGCTAAAAACTGAGACTCCTCTCGATTGTGAATAACCCCATTT
1 CCACAGCATTGGCTAAAAACTGAGACTCCTCTCGATTGTGAATAACCCCATTT
* * * *
15665 CCACAGCATTGGCT-TAAACTCGATACTCCTCTCGGTTGTGAATAGCCCCATTT
1 CCACAGCATTGGCTAAAAACT-GAGACTCCTCTCGATTGTGAATAACCCCATTT
15718 C
1 C
15719 ACAATCCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 5 0.10
53 44 0.90
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (53 bp):
CCACAGCATTGGCTAAAAACTGAGACTCCTCTCGATTGTGAATAACCCCATTT
Found at i:15998 original size:2 final size:2
Alignment explanation
Indices: 15991--16018 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15981 GAAAAATACG
15991 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
16019 GGATTGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.