Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011654.1 Corchorus capsularis cultivar CVL-1 contig11675, 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: 33851
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2270 original size:6 final size:6
Alignment explanation
Indices: 2259--2288 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2249 GAGGCAACCC
2259 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
2289 TGTTTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:3877 original size:21 final size:21
Alignment explanation
Indices: 3852--3901 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
3842 TCCAGCTGGG
3852 CACCCAGGCCAAAAGCCTGAA
1 CACCCAGGCCAAAAGCCTGAA
** * * *
3873 CACCCAACCCATAGGCCTGAG
1 CACCCAGGCCAAAAGCCTGAA
3894 CACCCAGG
1 CACCCAGG
3902 TACCAAGCAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.42, G:0.20, T:0.06
Consensus pattern (21 bp):
CACCCAGGCCAAAAGCCTGAA
Found at i:14190 original size:11 final size:11
Alignment explanation
Indices: 14174--14205 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
14164 GAAGTTCGTG
14174 TTTGAAGATTA
1 TTTGAAGATTA
*
14185 TTTGAAGATAA
1 TTTGAAGATTA
14196 TTTGAAGATT
1 TTTGAAGATT
14206 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:14201 original size:22 final size:22
Alignment explanation
Indices: 14174--14233 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
14164 GAAGTTCGTG
*
14174 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
14196 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
14215 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
14234 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:14208 original size:19 final size:18
Alignment explanation
Indices: 14184--14221 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
14174 TTTGAAGATT
*
14184 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
14203 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
14221 A
1 A
14222 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:15578 original size:6 final size:6
Alignment explanation
Indices: 15567--15603 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
15557 ATAATTGTCA
15567 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
15604 TTTTGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:15943 original size:21 final size:21
Alignment explanation
Indices: 15917--15962 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
15907 CGTTTTTTCT
15917 AAAAAAAAAAAATTTGCGTCG
1 AAAAAAAAAAAATTTGCGTCG
*
15938 AAAAAAAAAAAATTTGTGTCG
1 AAAAAAAAAAAATTTGCGTCG
15959 AAAA
1 AAAA
15963 TAAATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.20
Consensus pattern (21 bp):
AAAAAAAAAAAATTTGCGTCG
Found at i:17043 original size:15 final size:15
Alignment explanation
Indices: 17023--17063 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
17013 TCTTGCTAAG
17023 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
17038 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
17053 CAAGAAGATGA
1 CCAGAAGATGA
17064 ACAACTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:18749 original size:12 final size:12
Alignment explanation
Indices: 18732--18761 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18722 TGGGGGAGAG
18732 AGTCTAATAGAA
1 AGTCTAATAGAA
*
18744 AGTCTAATAGAG
1 AGTCTAATAGAA
18756 AGTCTA
1 AGTCTA
18762 CATGAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (12 bp):
AGTCTAATAGAA
Found at i:18798 original size:9 final size:9
Alignment explanation
Indices: 18786--18810 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18776 CATGAAATTT
18786 TTTTGAAAA
1 TTTTGAAAA
18795 TTTTGAAAA
1 TTTTGAAAA
18804 TTTTGAA
1 TTTTGAA
18811 TTTTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (9 bp):
TTTTGAAAA
Found at i:19945 original size:8 final size:8
Alignment explanation
Indices: 19932--19972 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
19922 CTATTCGGAA
19932 TGAAGATT
1 TGAAGATT
19940 TGAAGATT
1 TGAAGATT
19948 TGAAGATAATT
1 TGAAG---ATT
19959 TGAAGATT
1 TGAAGATT
19967 TGAAGA
1 TGAAGA
19973 CAATTGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 22 0.73
11 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (8 bp):
TGAAGATT
Found at i:19961 original size:19 final size:19
Alignment explanation
Indices: 19937--19982 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
19927 CGGAATGAAG
*
19937 ATTTGAAGATTTGAAGATA
1 ATTTGAAGATTTGAAGACA
19956 ATTTGAAGATTTGAAGACA
1 ATTTGAAGATTTGAAGACA
19975 A-TTGAAGA
1 ATTTGAAGA
19983 ATTATTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (19 bp):
ATTTGAAGATTTGAAGACA
Found at i:21337 original size:6 final size:6
Alignment explanation
Indices: 21326--21362 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
21316 ATAATTGCCA
21326 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
21363 TTTTGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:27145 original size:10 final size:10
Alignment explanation
Indices: 27130--27154 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27120 GAGGACTCTA
27130 GAATTTTCTG
1 GAATTTTCTG
27140 GAATTTTCTG
1 GAATTTTCTG
27150 GAATT
1 GAATT
27155 AAGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Done.