Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008732.1 Corchorus capsularis cultivar CVL-1 contig08753, 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: 24318
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:250 original size:8 final size:8
Alignment explanation
Indices: 222--258 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
212 GAATTGGCTA
222 TGAATTTT
1 TGAATTTT
*
230 TGAAGTTTC
1 TGAA-TTTT
239 TGAATTTT
1 TGAATTTT
247 TGAATTTT
1 TGAATTTT
255 TGAA
1 TGAA
259 GAAGGTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (8 bp):
TGAATTTT
Found at i:1268 original size:12 final size:12
Alignment explanation
Indices: 1253--1284 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1243 TCGCATGCGA
1253 TGGCCGGTCATG
1 TGGCCGGTCATG
1265 TGGCCGGTCATG
1 TGGCCGGTCATG
1277 TGGCCGGT
1 TGGCCGGT
1285 GTTGCGCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.25, G:0.44, T:0.25
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:6530 original size:33 final size:33
Alignment explanation
Indices: 6487--6573 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
6477 CCGAACCTAG
6487 TTTAGGTGTTGTTTGCGATGACACTAAATCTGTT
1 TTTA-GTGTTGTTTGCGATGACACTAAATCTGTT
6521 TTTAGTGTTGTTTGCGATGACACTAAATCTGTT
1 TTTAGTGTTGTTTGCGATGACACTAAATCTGTT
* *
6554 TTGAGTGTTGTTTGTGATGA
1 TTTAGTGTTGTTTGCGATGA
6574 TAAAACAGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 47 0.92
34 4 0.08
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.46
Consensus pattern (33 bp):
TTTAGTGTTGTTTGCGATGACACTAAATCTGTT
Found at i:9789 original size:22 final size:22
Alignment explanation
Indices: 9757--9836 Score: 99
Period size: 22 Copynumber: 3.5 Consensus size: 22
9747 CAAAGCAAAC
9757 AAAACAATTAAAGAAAATTAAG
1 AAAACAATTAAAGAAAATTAAG
*
9779 AAAGCAATT-AAGAAAATTAAAG
1 AAAACAATTAAAGAAAATT-AAG
* *
9801 AAAAAAATTAATAAGTAAATTAAG
1 AAAACAATT-A-AAGAAAATTAAG
9825 AAAACAATTAAA
1 AAAACAATTAAA
9837 ATTAAGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 9 0.18
22 20 0.41
23 1 0.02
24 11 0.22
25 8 0.16
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAACAATTAAAGAAAATTAAG
Found at i:9821 original size:25 final size:24
Alignment explanation
Indices: 9767--9835 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
9757 AAAACAATTA
**
9767 AAGAAAATTAAGAAAGCAA-T--T
1 AAGAAAATTAAGAAAAAAATTAAT
9788 AAGAAAATTAAAGAAAAAAATTAAT
1 AAGAAAATT-AAGAAAAAAATTAAT
* *
9813 AAGTAAATTAAGAAAACAATTAA
1 AAGAAAATTAAGAAAAAAATTAA
9836 AATTAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.22
22 8 0.20
23 1 0.03
24 13 0.32
25 9 0.22
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.20
Consensus pattern (24 bp):
AAGAAAATTAAGAAAAAAATTAAT
Found at i:9969 original size:17 final size:17
Alignment explanation
Indices: 9947--9980 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
9937 AATTAAATCC
9947 TAAATTA-CCAAATTAGA
1 TAAATTAGCC-AATTAGA
9964 TAAATTAGCCAATTAGA
1 TAAATTAGCCAATTAGA
9981 AACATGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (17 bp):
TAAATTAGCCAATTAGA
Found at i:16986 original size:18 final size:18
Alignment explanation
Indices: 16963--16998 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16953 TACCATGGCA
*
16963 CTCCACATTCACATCCAC
1 CTCCACATCCACATCCAC
*
16981 CTCCACATCCACCTCCAC
1 CTCCACATCCACATCCAC
16999 ATCACCTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.56, G:0.00, T:0.19
Consensus pattern (18 bp):
CTCCACATCCACATCCAC
Found at i:16987 original size:12 final size:12
Alignment explanation
Indices: 16972--17005 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
16962 ACTCCACATT
16972 CACATCCACCTC
1 CACATCCACCTC
16984 CACATCCACCTC
1 CACATCCACCTC
16996 CACAT-CACCT
1 CACATCCACCT
17006 TCATCAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.26, C:0.56, G:0.00, T:0.18
Consensus pattern (12 bp):
CACATCCACCTC
Found at i:17132 original size:18 final size:18
Alignment explanation
Indices: 17084--17126 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
17074 CTCAATATTC
*
17084 TCTTCAGCACCATTCTGT
1 TCTTCAGCACCATTATGT
17102 TCTTCAGCACCATTATGT
1 TCTTCAGCACCATTATGT
17120 TCTTCAG
1 TCTTCAG
17127 GGCCATATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.40
Consensus pattern (18 bp):
TCTTCAGCACCATTATGT
Found at i:20549 original size:14 final size:15
Alignment explanation
Indices: 20530--20558 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20520 ACTTTCCTTA
20530 TAATCTA-TTGCTTT
1 TAATCTATTTGCTTT
20544 TAATCTATTTGCTTT
1 TAATCTATTTGCTTT
20559 CTTAGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
TAATCTATTTGCTTT
Found at i:20910 original size:6 final size:7
Alignment explanation
Indices: 20882--20931 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
20872 ATCAAGTTAG
20882 AAATTAA
1 AAATTAA
20889 AAATTAA
1 AAATTAA
20896 AAATTTAA
1 AAA-TTAA
20904 AAA-TAA
1 AAATTAA
*
20910 AAATTGA
1 AAATTAA
*
20917 AAAGTAA
1 AAATTAA
20924 AAA-TAA
1 AAATTAA
20930 AA
1 AA
20932 TTGGGTTGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
6 11 0.29
7 20 0.53
8 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AAATTAA
Done.