Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008591.1 Corchorus capsularis cultivar CVL-1 contig08612, 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: 11117
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1610 original size:10 final size:10
Alignment explanation
Indices: 1595--1621 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1585 AAAATTCTTT
1595 CAATTAATGG
1 CAATTAATGG
1605 CAATTAATGG
1 CAATTAATGG
1615 CAATTAA
1 CAATTAA
1622 CAGAGCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (10 bp):
CAATTAATGG
Found at i:5426 original size:22 final size:22
Alignment explanation
Indices: 5401--5443 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5391 ATCAGATAAT
5401 CACAATCTCCATA-CAAAGAATA
1 CACAATCTCCATATC-AAGAATA
*
5423 CACAATCTTCATATCAAGAAT
1 CACAATCTCCATATCAAGAAT
5444 CACCATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (22 bp):
CACAATCTCCATATCAAGAATA
Found at i:8501 original size:36 final size:35
Alignment explanation
Indices: 8403--8501 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 35
8393 ATTTCATCAG
* *
8403 ATTCAACACTTGGGGGC-CGCAGCAACCCCTTCATC
1 ATTCAACACTTGGGGACTC-CAGCAACCCCCTCATC
* **
8438 TTTCAAACACTTGAAAGACTCCAGCAACCCCCTCAATC
1 ATTC-AACACTTG-GGGACTCCAGCAACCCCCTC-ATC
8476 ATTCAACACTTGGGGACTCCAGCAAC
1 ATTCAACACTTGGGGACTCCAGCAAC
8502 TCCTTCGTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.06
36 20 0.38
37 22 0.42
38 7 0.13
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.20
Consensus pattern (35 bp):
ATTCAACACTTGGGGACTCCAGCAACCCCCTCATC
Found at i:9019 original size:72 final size:72
Alignment explanation
Indices: 8905--9172 Score: 362
Period size: 72 Copynumber: 3.8 Consensus size: 72
8895 CCCATGGTCC
* * *
8905 TCTTCTTCATCGCGATTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCTTTCGCACAATCCTTAC
1 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
8970 ATGATCC
66 ATGATCA
*
8977 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTTAC
1 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
9042 ATGATAA
66 ATGATCA
* *
9049 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
1 TCTT-CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
* * *
9113 TACGATTA
65 CATGATCA
* * * * *
9121 TCTTC-ACACTGCGGTTGTAGCCGAGACAGTTTCCACA-TTGGCAGTCCTTCGC
1 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGC
9173 CAGTTCCCAC
Statistics
Matches: 178, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
70 15 0.08
71 28 0.16
72 133 0.75
73 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.31
Consensus pattern (72 bp):
TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATCA
Found at i:9176 original size:26 final size:27
Alignment explanation
Indices: 9147--9199 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
9137 GTAGCCGAGA
*
9147 CAGTTTCCACA-TTGGCAGTCCTTCGC
1 CAGTTCCCACATTTGGCAGTCCTTCGC
9173 CAGTTCCCACATTTGGCAGTCCTTCGC
1 CAGTTCCCACATTTGGCAGTCCTTCGC
9200 ACAATCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.15, C:0.36, G:0.19, T:0.30
Consensus pattern (27 bp):
CAGTTCCCACATTTGGCAGTCCTTCGC
Found at i:9293 original size:72 final size:72
Alignment explanation
Indices: 9173--9425 Score: 323
Period size: 72 Copynumber: 3.5 Consensus size: 72
9163 AGTCCTTCGC
* * * * *
9173 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATAATCATCTTCCATATTGTGATTGTA
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACTTGATAATCTTCCATATTGCGGTTGTA
9238 GCCGAGG
66 GCCGAGG
* * *
9245 TAATTCCCACATTTGGCAGCCCTTCGCACAATCCTTACTTGATAATCTTCCATATTGCGGTTGTA
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACTTGATAATCTTCCATATTGCGGTTGTA
*
9310 GCCAAGG
66 GCCGAGG
* * * * *
9317 CAGTTCCGACATTTGGCAGTCCTTCGCACAATCCTTA-TACGATTATCTT-CACACTGCGGTTGT
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACT-TGATAATCTTCCATATTGCGGTTGT
9380 AGCCGAGG
65 AGCCGAGG
* * *
9388 CCGTTTCCACA-TTGGCAGTCCTTCGCAAAATCCTTACT
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACT
9426 ATTACCTTCA
Statistics
Matches: 157, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
70 24 0.15
71 29 0.18
72 104 0.66
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (72 bp):
CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACTTGATAATCTTCCATATTGCGGTTGTA
GCCGAGG
Found at i:9355 original size:241 final size:241
Alignment explanation
Indices: 8932--9413 Score: 831
Period size: 241 Copynumber: 2.0 Consensus size: 241
8922 GTAGCCGAGG
* * * * *
8932 CAGTTCCCACATTTGGTAGTCTTTCGCACAATCCTTACATGATCCTCTTCTTCATTGCGATTGTA
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATAATCATCTTCATCATTGCGATTGTA
*
8997 GCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGATAATCTTCCATATTGC
66 GCCGAGGCAATTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGATAATCTTCCATATTGC
*
9062 GGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATACGATTATCTTCA
131 GGTTGTAGCCAAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATACGATTATCTTCA
9127 CACTGCGGTTGTAGCCGAGACAGTTTCCACATTGGCAGTCCTTCGC
196 CACTGCGGTTGTAGCCGAGACAGTTTCCACATTGGCAGTCCTTCGC
*
9173 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATAATCATCTTCCAT-ATTGTGATTGT
1 CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATAATCATCTT-CATCATTGCGATTGT
* *
9237 AGCCGAGGTAATTCCCACATTTGGCAGCCCTTCGCACAATCCTTACTTGATAATCTTCCATATTG
65 AGCCGAGGCAATTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGATAATCTTCCATATTG
*
9302 CGGTTGTAGCCAAGGCAGTTCCGACATTTGGCAGTCCTTCGCACAATCCTTATACGATTATCTTC
130 CGGTTGTAGCCAAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATACGATTATCTTC
* *
9367 ACACTGCGGTTGTAGCCGAGGCCGTTTCCACATTGGCAGTCCTTCGC
195 ACACTGCGGTTGTAGCCGAGACAGTTTCCACATTGGCAGTCCTTCGC
9414 AAAATCCTTA
Statistics
Matches: 227, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
241 225 0.99
242 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.31
Consensus pattern (241 bp):
CAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATAATCATCTTCATCATTGCGATTGTA
GCCGAGGCAATTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGATAATCTTCCATATTGC
GGTTGTAGCCAAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATACGATTATCTTCA
CACTGCGGTTGTAGCCGAGACAGTTTCCACATTGGCAGTCCTTCGC
Done.