Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007329.1 Corchorus capsularis cultivar CVL-1 contig07350, 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: 25859
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3520 original size:42 final size:42
Alignment explanation
Indices: 3474--3559 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
3464 ACGCATGGGA
3474 CATCGCACGGGCCAACGCATAGGCCATCCGGCCACAACCGGC
1 CATCGCACGGGCCAACGCATAGGCCATCCGGCCACAACCGGC
* * * *
3516 CATCGCACGGGCCATCGCATGGGCCATTCGGTCACAACCGGC
1 CATCGCACGGGCCAACGCATAGGCCATCCGGCCACAACCGGC
3558 CA
1 CA
3560 CTTGACCCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (42 bp):
CATCGCACGGGCCAACGCATAGGCCATCCGGCCACAACCGGC
Found at i:3530 original size:12 final size:12
Alignment explanation
Indices: 3513--3542 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3503 GGCCACAACC
3513 GGCCATCGCACG
1 GGCCATCGCACG
*
3525 GGCCATCGCATG
1 GGCCATCGCACG
3537 GGCCAT
1 GGCCAT
3543 TCGGTCACAA
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:0.17, C:0.37, G:0.33, T:0.13
Consensus pattern (12 bp):
GGCCATCGCACG
Found at i:18799 original size:18 final size:18
Alignment explanation
Indices: 18773--18823 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
18763 CATTTCATCA
*
18773 TTTTATTTTATGCTTCCT
1 TTTTTTTTTATGCTTCCT
18791 TTTTTTTTTATGCTTCCT
1 TTTTTTTTTATGCTTCCT
18809 TTTTTTTTTATGCTT
1 TTTTTTTTTATGCTT
18824 ATGCAAATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTTTTTTTATGCTTCCT
Found at i:20364 original size:14 final size:14
Alignment explanation
Indices: 20345--20372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20335 CAATTATCAA
20345 AAATAAATAAAAAT
1 AAATAAATAAAAAT
20359 AAATAAATAAAAAT
1 AAATAAATAAAAAT
20373 TGGCACATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:21182 original size:2 final size:2
Alignment explanation
Indices: 21172--21210 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
21162 TTATTTGTTG
21172 AT AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
21211 GTACACCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21184 original size:9 final size:9
Alignment explanation
Indices: 21172--21210 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21162 TTATTTGTTG
21172 ATATAATAT
1 ATATAATAT
21181 ATAT-ATAT
1 ATATAATAT
*
21189 ATATATTAT
1 ATATAATAT
*
21198 ATATAGTAT
1 ATATAATAT
21207 ATAT
1 ATAT
21211 GTACACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
ATATAATAT
Found at i:21344 original size:26 final size:27
Alignment explanation
Indices: 21296--21346 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
21286 TTTTAGATTT
* * *
21296 ATAGTTTTATTTTTATAATTAATTAAC
1 ATAGTTTAATTCTTATAAATAATTAAC
21323 ATAGTTTAATTCTTA-AAATAATTA
1 ATAGTTTAATTCTTATAAATAATTA
21347 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ATAGTTTAATTCTTATAAATAATTAAC
Found at i:22120 original size:92 final size:92
Alignment explanation
Indices: 21963--22184 Score: 410
Period size: 92 Copynumber: 2.4 Consensus size: 92
21953 ATTTGCATTA
*
21963 AGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCA
1 AGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAAACCTTCATAATTTGGCTTTCTCTTCA
*
22028 TCCAATGATTCAGCTTTGCATTATTGG
66 TCCAATGAGTCAGCTTTGCATTATTGG
22055 AGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAAACCTTCATAATTTGGCTTTCTCTTCA
1 AGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAAACCTTCATAATTTGGCTTTCTCTTCA
22120 TCCAATGAGTCAGCTTTGCATTATTGG
66 TCCAATGAGTCAGCTTTGCATTATTGG
22147 AGACAATATT-TGCAGAGATTCTTCATGATAACTTTGCA
1 AGACAAT-TTCTGCAGAGATTCTTCATGATAACTTTGCA
22185 GACCATTATT
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
92 125 0.98
93 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (92 bp):
AGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAAACCTTCATAATTTGGCTTTCTCTTCA
TCCAATGAGTCAGCTTTGCATTATTGG
Found at i:22223 original size:21 final size:21
Alignment explanation
Indices: 22178--22217 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22168 TTCATGATAA
22178 CTTTGCAGACCATTATTTTCT
1 CTTTGCAGACCATTATTTTCT
22199 CTTTGCAGACCATTATTTT
1 CTTTGCAGACCATTATTTT
22218 TCCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (21 bp):
CTTTGCAGACCATTATTTTCT
Done.