Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009993.1 Corchorus capsularis cultivar CVL-1 contig10014, 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: 50114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2928 original size:42 final size:42
Alignment explanation
Indices: 2845--2928 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
2835 TATTTAATAG
* *
2845 TACATAATTAATTACAAAATAGGTATAGTTTTAAATATTTAA
1 TACATAATTAATTACAAAATAGGTATAGTATCAAATATTTAA
* *
2887 TACATAATTAATTACAAAATATGTCAT-GTATCAAATTTTTAA
1 TACATAATTAATTACAAAATAGGT-ATAGTATCAAATATTTAA
2929 CCCGTTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (42 bp):
TACATAATTAATTACAAAATAGGTATAGTATCAAATATTTAA
Found at i:6054 original size:12 final size:13
Alignment explanation
Indices: 6037--6065 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6027 AATCTTATTC
6037 TTTCTTTTTCT-T
1 TTTCTTTTTCTAT
6049 TTTCTTTTTCTAT
1 TTTCTTTTTCTAT
6062 TTTC
1 TTTC
6066 ACTCAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTTCTAT
Found at i:45654 original size:22 final size:22
Alignment explanation
Indices: 45601--45704 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
45591 TCATATGAGA
* * *
45601 ATAAAATTGTGATATCCTCTCT
1 ATAAAATTTTGATAACCTCTCC
** * *
45623 ATGTATTTTTGATAGCCTCTCC
1 ATAAAATTTTGATAACCTCTCC
*
45645 ATAAAATTTTCATAACCTC-CC
1 ATAAAATTTTGATAACCTCTCC
* *
45666 TATAAAATTTTGTTAAAC-CTCC
1 -ATAAAATTTTGATAACCTCTCC
45688 ATAGGAAATTTTGATAA
1 ATA--AAATTTTGATAA
45705 GTATAAATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
21 6 0.10
22 46 0.73
23 11 0.17
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAAAATTTTGATAACCTCTCC
Found at i:45826 original size:44 final size:45
Alignment explanation
Indices: 45725--45835 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 45
45715 TGGTAACCTC
* *
45725 CCTCTCTATGAAATTTTGTTAA-CTTTCGTATGAAATTTTATTAA
1 CCTCTCTATGAAATTTTGATAACCTTTCGTATGAAATTTTAGTAA
* * * * * *
45769 CATCCCTAAGAAATTTTGGTAACCTTT-TTATGAAATTTTGGTAA
1 CCTCTCTATGAAATTTTGATAACCTTTCGTATGAAATTTTAGTAA
*
45813 CCTCTGTATGAAATTTTGATAAC
1 CCTCTCTATGAAATTTTGATAAC
45836 TACACTATGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 50 0.93
45 4 0.07
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (45 bp):
CCTCTCTATGAAATTTTGATAACCTTTCGTATGAAATTTTAGTAA
Found at i:45867 original size:66 final size:66
Alignment explanation
Indices: 45731--45872 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 66
45721 CCTCCCTCTC
* * * *
45731 TATGAAATTTTGTTAACTTTCGTATGAAATTTTATTAACATCCCTAAGAAATTTTGGTAACCTTT
1 TATGAAATTTTGGTAACTCTCGTATGAAATTTTATTAACATCACTAAGAAATTTTGATAACCTTT
*
45796 T
66 A
* *
45797 TATGAAATTTTGGTAAC-CTCTGTATGAAATTTTGA-TAAC-TACACTATGAAATTTTGATGA-C
1 TATGAAATTTTGGTAACTCTC-GTATGAAATTTT-ATTAACAT-CACTAAGAAATTTTGATAACC
45858 TTCTA
63 TT-TA
45863 TATGAAATTT
1 TATGAAATTT
45873 GATAATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
65 6 0.09
66 58 0.89
67 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (66 bp):
TATGAAATTTTGGTAACTCTCGTATGAAATTTTATTAACATCACTAAGAAATTTTGATAACCTTT
A
Found at i:45887 original size:21 final size:21
Alignment explanation
Indices: 45727--45893 Score: 95
Period size: 22 Copynumber: 7.7 Consensus size: 21
45717 GTAACCTCCC
*
45727 TCTCTATGAAATTTTGTTAACT
1 TCTCTATGAAA-TTTGATAACT
* *
45749 T-TCGTATGAAATTTTATTAACA
1 TCTC-TATGAAATTTGA-TAACT
* * *
45771 TCCCTAAGAAATTTTGGTAACCT
1 TCTCTATGAAA-TTTGATAA-CT
* * *
45794 T-TTTATGAAATTTTGGTAACC
1 TCTCTATGAAA-TTTGATAACT
*
45815 TCTGTATGAAATTTTGATAACT
1 TCTCTATGAAA-TTTGATAACT
* * *
45837 ACACTATGAAATTTTGATGACT
1 TCTCTATGAAA-TTTGATAACT
* *
45859 TCTATATGAAATTTGATAATT
1 TCTCTATGAAATTTGATAACT
* *
45880 TTTCTATGTAATTT
1 TCTCTATGAAATTT
45894 TGGTTTGATT
Statistics
Matches: 112, Mismatches: 27, Indels: 13
0.74 0.18 0.09
Matches are distributed among these distances:
21 26 0.23
22 80 0.71
23 6 0.05
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (21 bp):
TCTCTATGAAATTTGATAACT
Found at i:48891 original size:35 final size:35
Alignment explanation
Indices: 48852--49467 Score: 909
Period size: 35 Copynumber: 17.7 Consensus size: 35
48842 TTCTTACTAA
*
48852 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTC
*
48887 ACTTAATTACCCTGAATTAAGTT-ACT-C-GACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
48919 ACTTAATTACCCCGAATTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTC
* *
48955 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
48990 AATTAATTGCCCTGAATTAAGTTGATCACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
49025 ACTCAATTAACCTGAATTAAGTTGATTACTGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
49060 ACTTAATTACGCTGAATTAAGTTGATCACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
49095 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * * *
49130 ACTTAATTACCCTGAATTAAGTTGATTATTTAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
49165 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
49200 ACTTAATTACCCTGAATTAAGTTGACTACTGATTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
49235 ACTTAATTACCCTGAATTAAGTTGATTATTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
49270 ACTTAATAACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
49305 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
49340 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
49375 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
49410 ACTTAATTACCCTGAATTAAGTTGATCACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
49445 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
49468 ACTTATTACT
Statistics
Matches: 527, Mismatches: 49, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
31 3 0.01
32 18 0.03
33 5 0.01
34 3 0.01
35 476 0.90
36 22 0.04
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:50052 original size:32 final size:31
Alignment explanation
Indices: 49996--50080 Score: 109
Period size: 30 Copynumber: 2.7 Consensus size: 31
49986 GTTTCATCTT
*
49996 TTACTTAAAAGATTTAATCTTTATTTACAAAAA
1 TTACTTAAAAGATTCAATCTTTA-TT-CAAAAA
50029 TTACTTAAAAG-TTCAATCTTTATTCAAAAA
1 TTACTTAAAAGATTCAATCTTTATTCAAAAA
** *
50059 TTACTCCAAAGATTTAATCTTT
1 TTACTTAAAAGATTCAATCTTT
50081 CAACACAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 15 0.32
31 11 0.23
32 10 0.21
33 11 0.23
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (31 bp):
TTACTTAAAAGATTCAATCTTTATTCAAAAA
Done.