Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010191.1 Corchorus capsularis cultivar CVL-1 contig10212, 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: 10168
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:8178 original size:19 final size:18
Alignment explanation
Indices: 8145--8182 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
8135 TTGAAATAAT
8145 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
8163 TCTTCAAATTATCTTCAAA
1 TCTTC-AATGATCTTCAAA
8182 T
1 T
8183 AAGTCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:8634 original size:15 final size:15
Alignment explanation
Indices: 8614--8643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8604 CATCATTCTT
8614 AAGTAGCCATAATCA
1 AAGTAGCCATAATCA
*
8629 AAGTAGCCCTAATCA
1 AAGTAGCCATAATCA
8644 CTTACTATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.20
Consensus pattern (15 bp):
AAGTAGCCATAATCA
Found at i:9894 original size:8 final size:7
Alignment explanation
Indices: 9872--9919 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
9862 TTTTCTTTTA
*
9872 TTTTCTT
1 TTTTCAT
9879 TTTTCAT
1 TTTTCAT
9886 TTCTTCAT
1 TT-TTCAT
9894 TTTT--T
1 TTTTCAT
9899 TTTTCATT
1 TTTTCA-T
9907 TTTTCAT
1 TTTTCAT
9914 TTTTCA
1 TTTTCA
9920 CTGCACTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.14
7 17 0.47
8 14 0.39
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCAT
Found at i:9896 original size:15 final size:15
Alignment explanation
Indices: 9872--9919 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
9862 TTTTCTTTTA
9872 TTTTC-TTTTTTCAT
1 TTTTCATTTTTTCAT
9886 TTCTTCA-TTTTT--T
1 TT-TTCATTTTTTCAT
9899 TTTTCATTTTTTCAT
1 TTTTCATTTTTTCAT
9914 TTTTCA
1 TTTTCA
9920 CTGCACTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 8 0.28
14 2 0.07
15 15 0.52
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCATTTTTTCAT
Found at i:9902 original size:20 final size:20
Alignment explanation
Indices: 9871--9917 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
9861 CTTTTCTTTT
9871 ATTTTCTTTTTTCATTTCTTC
1 ATTTT-TTTTTTCATTTCTTC
*
9892 ATTTTTTTTTTCATTTTTTC
1 ATTTTTTTTTTCATTTCTTC
9912 ATTTTT
1 ATTTTT
9918 CACTGCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTCATTTCTTC
Found at i:9909 original size:28 final size:26
Alignment explanation
Indices: 9867--9919 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
9857 TATTCTTTTC
9867 TTTTATTTTCTTTTTTCATTTCTTCAT
1 TTTTATTTTCTTTTTTCATTT-TTCAT
*
9894 TTTTTTTTTCATTTTTTCATTTTTCA
1 TTTTATTTTC-TTTTTTCATTTTTCA
9920 CTGCACTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTATTTTCTTTTTTCATTTTTCAT
Found at i:9976 original size:12 final size:13
Alignment explanation
Indices: 9948--9976 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9938 AGTTAACCCG
9948 AAAACTCTTTTCA
1 AAAACTCTTTTCA
9961 AAAACTCTTTTCA
1 AAAACTCTTTTCA
9974 AAA
1 AAA
9977 GTTTTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACTCTTTTCA
Done.