Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009148.1 Corchorus capsularis cultivar CVL-1 contig09169, 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: 28471
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:986 original size:13 final size:13
Alignment explanation
Indices: 968--992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
958 GATGAAGAGA
968 ATATTTATAATTG
1 ATATTTATAATTG
981 ATATTTATAATT
1 ATATTTATAATT
993 TATACAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATTTATAATTG
Found at i:3030 original size:32 final size:34
Alignment explanation
Indices: 2982--3046 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
2972 TACTTTTACT
*
2982 TTTTTCTTGTCCATTCAAGAACCCATTTCTTTTA
1 TTTTTCTTGTCCATTCAACAACCCATTTCTTTTA
*
3016 TTTTTC-T-TCCATTCAACAACCCATTTTTTTT
1 TTTTTCTTGTCCATTCAACAACCCATTTCTTTT
3047 CTTGTCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
33 1 0.03
34 6 0.21
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.52
Consensus pattern (34 bp):
TTTTTCTTGTCCATTCAACAACCCATTTCTTTTA
Found at i:3057 original size:28 final size:28
Alignment explanation
Indices: 2981--3059 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 28
2971 TTACTTTTAC
* *
2981 TTTTTTCTTGTCCATTCAAGAACCCATT
1 TTTTTTCTTGTCTATTCAACAACCCATT
*
3009 TCTTTTAT-TTTTCTTCCATTCAACAACCCATT
1 T-TTTT-TCTTGTC-T--ATTCAACAACCCATT
3041 TTTTTTCTTGTCTATTCAA
1 TTTTTTCTTGTCTATTCAA
3060 GAACTAGAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
28 7 0.17
29 8 0.20
30 3 0.07
31 8 0.20
32 15 0.37
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (28 bp):
TTTTTTCTTGTCTATTCAACAACCCATT
Found at i:7215 original size:6 final size:6
Alignment explanation
Indices: 7204--7234 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
7194 ATAATTGTTA
7204 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
7235 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:9855 original size:21 final size:21
Alignment explanation
Indices: 9831--9879 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
9821 CAAAAGATGG
*
9831 AAGCCAACGCACCAAAGGAGT
1 AAGCCAACACACCAAAGGAGT
9852 AAGCCAACACACCAAAGGAGT
1 AAGCCAACACACCAAAGGAGT
9873 AAGCCAA
1 AAGCCAA
9880 AGGCCATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.29, G:0.20, T:0.04
Consensus pattern (21 bp):
AAGCCAACACACCAAAGGAGT
Found at i:13501 original size:6 final size:6
Alignment explanation
Indices: 13490--13518 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
13480 TAATTGCTAT
13490 GATTTA GATTTA GATTTA GATTTA -ATTTA
1 GATTTA GATTTA GATTTA GATTTA GATTTA
13519 CTTTGCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
GATTTA
Found at i:15105 original size:3 final size:3
Alignment explanation
Indices: 15097--15154 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
15087 CTGTGTAATT
15097 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15145 TTA TTA TTA T
1 TTA TTA TTA T
15155 AATATATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20083 original size:3 final size:3
Alignment explanation
Indices: 20075--20138 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
20065 GAAAATTAAC
20075 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20123 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
20139 CACGTGGATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20368 original size:12 final size:12
Alignment explanation
Indices: 20351--20375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20341 GGGATACAAT
20351 AATAATAAAAAA
1 AATAATAAAAAA
20363 AATAATAAAAAA
1 AATAATAAAAAA
20375 A
1 A
20376 TTTAACAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AATAATAAAAAA
Found at i:28307 original size:2 final size:2
Alignment explanation
Indices: 28300--28334 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28290 AAAAGAAATC
* *
28300 AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28335 CACACACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:28324 original size:20 final size:20
Alignment explanation
Indices: 28299--28336 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28289 TAAAAGAAAT
28299 CATATATATATATATACATA
1 CATATATATATATATACATA
28319 CATATATATATATATACA
1 CATATATATATATATACA
28337 CACACACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
CATATATATATATATACATA
Done.