Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009304.1 Corchorus capsularis cultivar CVL-1 contig09325, 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: 10987
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:7882 original size:17 final size:17
Alignment explanation
Indices: 7860--7913 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 17
7850 TATTTTACTC
7860 TTTTTACTTAATCACCA
1 TTTTTACTTAATCACCA
* *
7877 TTTTTAC----TCTCCT
1 TTTTTACTTAATCACCA
7890 TTTTTACTTAAT-ACCA
1 TTTTTACTTAATCACCA
7906 TTTTTACT
1 TTTTTACT
7914 CTTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
13 11 0.38
16 10 0.34
17 8 0.28
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTACTTAATCACCA
Found at i:7895 original size:30 final size:28
Alignment explanation
Indices: 7845--7923 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 28
7835 TTGTACTGAT
7845 TACCATATTTTA--CTC-TTTTTACTTAA
1 TACCAT-TTTTACTCTCTTTTTTACTTAA
7871 TCACCATTTTTACTCTCCTTTTTTACTTAA
1 T-ACCATTTTTACTCT-CTTTTTTACTTAA
*
7901 TACCATTTTTACTCTTTTTTTTA
1 TACCATTTTTACTCTCTTTTTTA
7924 TCATTTTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
26 6 0.13
27 5 0.11
28 9 0.19
29 15 0.32
30 12 0.26
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (28 bp):
TACCATTTTTACTCTCTTTTTTACTTAA
Found at i:7905 original size:29 final size:29
Alignment explanation
Indices: 7860--7923 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
7850 TATTTTACTC
7860 TTTTTACTTAATCACCATTTTTACTCTCCT
1 TTTTTACTTAATCACCATTTTTACTCT-CT
*
7890 TTTTTACTTAAT-ACCATTTTTACTCTTT
1 TTTTTACTTAATCACCATTTTTACTCTCT
7918 TTTTTA
1 TTTTTA
7924 TCATTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 7 0.21
29 14 0.42
30 12 0.36
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTACTTAATCACCATTTTTACTCTCT
Found at i:7969 original size:27 final size:26
Alignment explanation
Indices: 7811--7992 Score: 123
Period size: 26 Copynumber: 7.0 Consensus size: 26
7801 TATTTTTTGA
*
7811 TTACT-AATTACCAATTTGTACTC-TTT
1 TTACTGAA-TACC-ATTTTTACTCTTTT
* *
7837 GTACTGATTACCATATTTTACTC-TTT
1 TTACTGAATACCAT-TTTTACTCTTTT
*
7863 TTACTTAATCACCATTTTTACTCTCCTTTT
1 TTACTGAAT-ACCATTTTTA--CT-CTTTT
*
7893 TTACTTAATACCATTTTTACTCTTTT
1 TTACTGAATACCATTTTTACTCTTTT
* * *
7919 TT--T---TATCATTTTTA-TCCCTCT
1 TTACTGAATACCATTTTTACT-CTTTT
7940 TTACTGAATACCACTTTTTACTCTTTT
1 TTACTGAATACCA-TTTTTACTCTTTT
7967 TTACTG-ATCACCATTTCTTACTCTTT
1 TTACTGAAT-ACCATTT-TTACTCTTT
7993 ACTACTAATT
Statistics
Matches: 127, Mismatches: 12, Indels: 33
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.01
21 15 0.12
23 1 0.01
24 1 0.01
25 2 0.02
26 45 0.35
27 36 0.28
28 3 0.02
29 11 0.09
30 12 0.09
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (26 bp):
TTACTGAATACCATTTTTACTCTTTT
Found at i:7998 original size:27 final size:27
Alignment explanation
Indices: 7941--8019 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
7931 TATCCCTCTT
**
7941 TACTGAATACCACTTTTTACTCTTTTT
1 TACTGAATACCACTTTTTACTCTTTAC
7968 TACTG-ATCACCA-TTTCTTACTCTTTAC
1 TACTGAAT-ACCACTTT-TTACTCTTTAC
*
7995 TACT-AATTA-CTCTCTTTTACTCTTT
1 TACTGAA-TACCACT-TTTTACTCTTT
8020 TTATCTTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
26 6 0.14
27 34 0.79
28 3 0.07
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.51
Consensus pattern (27 bp):
TACTGAATACCACTTTTTACTCTTTAC
Found at i:8204 original size:24 final size:24
Alignment explanation
Indices: 8177--8223 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
8167 TCTCTTACTT
8177 TGAATCTCAATTACCACTTTAATA
1 TGAATCTCAATTACCACTTTAATA
* *
8201 TGAATCTTAATTACTACTTTAAT
1 TGAATCTCAATTACCACTTTAAT
8224 TACCAATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (24 bp):
TGAATCTCAATTACCACTTTAATA
Found at i:8592 original size:29 final size:29
Alignment explanation
Indices: 8559--8648 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
8549 TACTTAATTA
*
8559 CTGATTTACTAACTCCTATTACCTTGACT
1 CTGATTTACTAACTCCTATTACCTTAACT
* ** * *
8588 CTGA-TTA--ATCTGTTTTTA-CTTAATT
1 CTGATTTACTAACTCCTATTACCTTAACT
* *
8613 ACTGATTTACTGACTCCTATTACCTTTACT
1 -CTGATTTACTAACTCCTATTACCTTAACT
8643 CTGATT
1 CTGATT
8649 AATCTCTTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 5 0.12
26 11 0.26
27 3 0.07
28 3 0.07
29 16 0.37
30 5 0.12
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.47
Consensus pattern (29 bp):
CTGATTTACTAACTCCTATTACCTTAACT
Found at i:8629 original size:55 final size:55
Alignment explanation
Indices: 8509--8784 Score: 428
Period size: 55 Copynumber: 5.0 Consensus size: 55
8499 CTACTATCTT
*
8509 TTTACTGATTACTATTACTTTGACTCTGATTAATCTC-TTTTACTTAATTACTGA
1 TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
* * * *
8563 TTTACTAACTCCTATTACCTTGACTCTGATTAATCTGTTTTTACTTAATTACTGA
1 TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
* * *
8618 TTTACTGACTCCTATTACCTTTACTCTGATTAATCTCTTTTTACTTAATTACTGA
1 TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
* * * *
8673 TTTAATGGTTATTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTGA
1 TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
*
8728 TTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTGA
1 TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
8783 TT
1 TT
8785 ACCCCTTTTT
Statistics
Matches: 203, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
54 32 0.16
55 171 0.84
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGA
Found at i:9705 original size:50 final size:49
Alignment explanation
Indices: 9574--9900 Score: 319
Period size: 49 Copynumber: 6.7 Consensus size: 49
9564 AACTAATCAA
** * * * *
9574 TTTATTTACTAATGGCCTAAAAGTTCAAACTTTTATTCAAAGATGACA-T
1 TTTATTTACTAAT-TACTAAAAATTCAATCTTTTACTCAAAGGTGACATT
* * * * * * *
9623 TTTATTCACGAATTACTTTTTAAAAATTCAATCTTTTATTCGAAGGTTACGTC
1 TTTATTTACTAATTAC----TAAAAATTCAATCTTTTACTCAAAGGTGACATT
* *
9676 CTTATTTACTAATTACTTAAAAATTCAATCTTTTGCTCAAAGGTGACATT
1 TTTATTTACTAATTAC-TAAAAATTCAATCTTTTACTCAAAGGTGACATT
* * *
9726 TTTACTTACTAATTACTTAGAAATTCAATCTTTTTCTCAAAGGTGACA--
1 TTTATTTACTAATTAC-TAAAAATTCAATCTTTTACTCAAAGGTGACATT
* *
9774 -TT-TTTAC---TTACTAAAAATTCAATCTTTTACCCAAAGATGACATT
1 TTTATTTACTAATTACTAAAAATTCAATCTTTTACTCAAAGGTGACATT
* * *
9818 TTTATTTACTAATTACTAAAAATTCAACCTTTTACCCAAAGATGACATT
1 TTTATTTACTAATTACTAAAAATTCAATCTTTTACTCAAAGGTGACATT
*
9867 TTTATTTACTAATTACTAAAAATTAAATCTTTTA
1 TTTATTTACTAATTACTAAAAATTCAATCTTTTA
9901 TTTTCAAATT
Statistics
Matches: 234, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
42 27 0.12
43 4 0.02
45 2 0.01
46 9 0.04
47 2 0.01
48 1 0.00
49 79 0.34
50 72 0.31
52 25 0.11
53 13 0.06
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (49 bp):
TTTATTTACTAATTACTAAAAATTCAATCTTTTACTCAAAGGTGACATT
Found at i:9791 original size:92 final size:91
Alignment explanation
Indices: 9688--9878 Score: 274
Period size: 92 Copynumber: 2.1 Consensus size: 91
9678 TATTTACTAA
* * * *
9688 TTACTTAAAAATTCAATCTTTTGCTCAAAGGTGACATTTTTACTTACTAATTACTTAGAAATTCA
1 TTAC-TAAAAATTCAATCTTTTACCCAAAGATGACATTTTTACTTACTAATTAC-TAAAAATTCA
* * * *
9753 ATCTTTTTCTCAAAGGTGACATTTTTAC
64 ACCTTTTACCCAAAGATGACATTTTTAC
*
9781 TTACTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTACTAAAAATTCAAC
1 TTACTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAAC
*
9846 CTTTTACCCAAAGATGACATTTTTAT
66 CTTTTACCCAAAGATGACATTTTTAC
9872 TTACTAA
1 TTACTAA
9879 TTACTAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 39 0.44
92 45 0.51
93 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (91 bp):
TTACTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTACTTACTAATTACTAAAAATTCAAC
CTTTTACCCAAAGATGACATTTTTAC
Found at i:9930 original size:30 final size:29
Alignment explanation
Indices: 9864--9932 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
9854 CAAAGATGAC
*
9864 ATTTTTATTTACTAATTACTAAAAATTAA
1 ATTTTTATTTACAAATTACTAAAAATTAA
* * * *
9893 ATCTTTTATTTTCAAATTACTTGAAATTTCA
1 AT-TTTTATTTACAAATTAC-TAAAAATTAA
9924 ATTTTTATT
1 ATTTTTATT
9933 CCAAGGTGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 22 0.67
31 9 0.27
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (29 bp):
ATTTTTATTTACAAATTACTAAAAATTAA
Done.