Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007436.1 Corchorus capsularis cultivar CVL-1 contig07457, 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: 15489
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Found at i:1960 original size:25 final size:26
Alignment explanation
Indices: 1931--2002 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
1921 TAGTGAACTT
1931 AAAATGACCAAAATGCCCCT-GAATG
1 AAAATGACCAAAATGCCCCTAGAATG
* * * *
1956 CAAATGACCAGAATGCCCTTAGTATG
1 AAAATGACCAAAATGCCCCTAGAATG
*
1982 AAAATCACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
2003 TGTGACCCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTAGAATG
Found at i:2819 original size:3 final size:3
Alignment explanation
Indices: 2811--2870 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
2801 CTTCTAAATT
2811 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2858 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
2871 ATTTTTGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4075 original size:106 final size:102
Alignment explanation
Indices: 3901--4162 Score: 321
Period size: 106 Copynumber: 2.5 Consensus size: 102
3891 GAATTCATTT
* * ** * ** *
3901 TTTTTCTTAAAAGCCTATAATACTAAATCTTTAATTCCATGACTTATCCTCAAATTAAATTAATT
1 TTTTTC-TAAAACCCTATAATACTAAATCTTCAATTTAATGACTTACCCTTGAATTAAATAAATT
*
3966 TTTTTATTT-GGGACTAAACTTAGTGAAATTTGTTGAATTTAC
65 TTTTTATTTGGGGA-TAAA-TTAGTGAAATTCGTT--A-TTAC
4008 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTT-CCCTTGAATTAAATAAATAT
1 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTACCCTTGAATTAAATAAAT-T
*
4072 TTTTTATTTGGGGATAAATTAGTGAAATTCGTTATTAT
65 TTTTTATTTGGGGATAAATTAGTGAAATTCGTTATTAC
* * * *
4110 TTTTTCTAAAACTCTATAATACTACATTTTCAATTTTATGACTTACCCTTGAA
1 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTACCCTTGAA
4163 AAGAATTAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
102 43 0.31
103 9 0.07
105 28 0.20
106 48 0.35
107 10 0.07
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (102 bp):
TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTACCCTTGAATTAAATAAATTT
TTTTATTTGGGGATAAATTAGTGAAATTCGTTATTAC
Found at i:4179 original size:102 final size:104
Alignment explanation
Indices: 3901--4182 Score: 297
Period size: 102 Copynumber: 2.7 Consensus size: 104
3891 GAATTCATTT
* * ** * ** * *
3901 TTTTTCTTAAAAGCCTATAATACTAAATCTTTAATTCCATGACTTATCCTCAAATTAAATTAATT
1 TTTTTC-TAAAACCCTATAATACTAAATCTTCAATTTAATGACTT-CCCTTGAATAAAATTAAAT
* *
3966 TTTTTATTTGGGACTAAACTTAGTGAAATTTGTTGAATTTAC
64 ATTTTATTTGGGACTAAACTTAGTGAAATTCGTT-AATTTAC
*
4008 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTCCCTTGAATTAAA-TAAATAT
1 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTCCCTTGAATAAAATTAAATA-
*
4072 TTTTTATTTGGGGA-TAAA-TTAGTGAAATTCGTT-A-TTAT
65 -TTTTATTT-GGGACTAAACTTAGTGAAATTCGTTAATTTAC
* * * *
4110 TTTTTCTAAAACTCTATAATACTACATTTTCAATTTTATGACTTACCCTTGAA-AAGAATTAAAT
1 TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTT-CCCTTGAATAA-AATTAAAT
4174 ATTTTATTT
64 ATTTTATTT
4183 AAGCCTAAAA
Statistics
Matches: 153, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
102 52 0.34
103 11 0.07
104 10 0.07
105 24 0.16
106 46 0.30
107 10 0.07
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (104 bp):
TTTTTCTAAAACCCTATAATACTAAATCTTCAATTTAATGACTTCCCTTGAATAAAATTAAATAT
TTTATTTGGGACTAAACTTAGTGAAATTCGTTAATTTAC
Found at i:4999 original size:24 final size:24
Alignment explanation
Indices: 4972--5035 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
4962 TTTTCAAAAT
* *
4972 ACCACATGCTGGTTGTTAGGAAAG
1 ACCACATACTGGTCGTTAGGAAAG
*
4996 ACCACATACTGGTCGTTAGGAAAT
1 ACCACATACTGGTCGTTAGGAAAG
*
5020 ACCACACACTGGTCGT
1 ACCACATACTGGTCGT
5036 GACCAAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
ACCACATACTGGTCGTTAGGAAAG
Found at i:8028 original size:14 final size:14
Alignment explanation
Indices: 7991--8021 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7981 CAAATTTATT
7991 TTTCTCTTTTTCCC
1 TTTCTCTTTTTCCC
*
8005 TTTCTCTTTTTTCC
1 TTTCTCTTTTTCCC
8019 TTT
1 TTT
8022 TTTTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCTCTTTTTCCC
Found at i:8049 original size:6 final size:6
Alignment explanation
Indices: 8040--8074 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
8030 TTTTGTTTAG
8040 TTTTTC TTTTTC TTTTTC TTTTTC TCTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTT
8075 ATTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:14944 original size:14 final size:14
Alignment explanation
Indices: 14925--14951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14915 CAAATTTATT
14925 TTTCTCTTTTTCCC
1 TTTCTCTTTTTCCC
14939 TTTCTCTTTTTCC
1 TTTCTCTTTTTCC
14952 TTTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCTCTTTTTCCC
Done.