Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022937.1 Corchorus olitorius cultivar O-4 contig22970, 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: 19909
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:8917 original size:7 final size:7
Alignment explanation
Indices: 8901--8966 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
8891 CGGAAAAAGA
*
8901 ACAACAG
1 ACAACGG
8908 ACAACGG
1 ACAACGG
*
8915 ACAGCGG
1 ACAACGG
* *
8922 A-ATCAG
1 ACAACGG
8928 ACAACGG
1 ACAACGG
*
8935 ACAGCGG
1 ACAACGG
8942 ACAACGG
1 ACAACGG
8949 A-ATCACGG
1 ACA--ACGG
8957 ACAACGG
1 ACAACGG
8964 ACA
1 ACA
8967 GCAGAATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
6 5 0.11
7 36 0.77
8 5 0.11
9 1 0.02
ACGTcount: A:0.42, C:0.27, G:0.27, T:0.03
Consensus pattern (7 bp):
ACAACGG
Found at i:8930 original size:20 final size:20
Alignment explanation
Indices: 8905--8942 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
8895 AAAAGAACAA
8905 CAGACAACGGACAGCGGAAT
1 CAGACAACGGACAGCGGAAT
8925 CAGACAACGGACAGCGGA
1 CAGACAACGGACAGCGGA
8943 CAACGGAATC
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:0.39, C:0.26, G:0.32, T:0.03
Consensus pattern (20 bp):
CAGACAACGGACAGCGGAAT
Found at i:8937 original size:27 final size:28
Alignment explanation
Indices: 8901--8966 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
8891 CGGAAAAAGA
* *
8901 ACAACAGACAACGGACAGCGGAATCA-G
1 ACAACGGACAACGGACAACGGAATCACG
*
8928 ACAACGGACAGCGGACAACGGAATCACGG
1 ACAACGGACAACGGACAACGGAATCAC-G
8957 ACAACGGACA
1 ACAACGGACA
8967 GCAGAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 23 0.68
29 11 0.32
ACGTcount: A:0.42, C:0.27, G:0.27, T:0.03
Consensus pattern (28 bp):
ACAACGGACAACGGACAACGGAATCACG
Found at i:8959 original size:22 final size:22
Alignment explanation
Indices: 8931--8975 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8921 GAATCAGACA
* *
8931 ACGGACAGCGGACAACGGAATC
1 ACGGACAACGGACAACAGAATC
*
8953 ACGGACAACGGACAGCAGAATC
1 ACGGACAACGGACAACAGAATC
8975 A
1 A
8976 TCAAGAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.27, G:0.29, T:0.04
Consensus pattern (22 bp):
ACGGACAACGGACAACAGAATC
Found at i:9325 original size:19 final size:20
Alignment explanation
Indices: 9301--9354 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
9291 TCTAGCAGAT
9301 GGATGACGTGGCAGTCAAC-
1 GGATGACGTGGCAGTCAACG
*
9320 GGATGACATGGCAGGTCAACG
1 GGATGACGTGGCA-GTCAACG
9341 GGATGACGTGGCAG
1 GGATGACGTGGCAG
9355 AATCTTACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 12 0.39
20 7 0.23
21 12 0.39
ACGTcount: A:0.26, C:0.19, G:0.41, T:0.15
Consensus pattern (20 bp):
GGATGACGTGGCAGTCAACG
Found at i:9346 original size:21 final size:20
Alignment explanation
Indices: 9301--9354 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 20
9291 TCTAGCAGAT
9301 GGATGACGTGGCA-GTCAAC
1 GGATGACGTGGCAGGTCAAC
*
9320 GGATGACATGGCAGGTCAAC
1 GGATGACGTGGCAGGTCAAC
9340 GGGATGACGTGGCAG
1 -GGATGACGTGGCAG
9355 AATCTTACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.39
20 6 0.19
21 13 0.42
ACGTcount: A:0.26, C:0.19, G:0.41, T:0.15
Consensus pattern (20 bp):
GGATGACGTGGCAGGTCAAC
Found at i:10452 original size:226 final size:219
Alignment explanation
Indices: 10033--10463 Score: 526
Period size: 226 Copynumber: 1.9 Consensus size: 219
10023 GATTAACCAA
* * * *
10033 TACATTTCTTTTTATACCACAATTAATGAGCTTTACCTAACATATAATGTTTTTGTGGTAGGCAG
1 TACATTTCTTTTTATAACACAATTAATGAGCTTTACCTAACATATAATGCTTTTGTAGTACGCAG
* *
10098 GGATGAAGTTAGGAATGAATTAATAAAAAGTTCAAACTTCAAATGTAAAAAGCATCATTTTTTTA
66 GGATGAAGCTAGAAATGAATTAATAAAAAG-----A-TTCAAATGTAAAAAGCATCATTTTTTTA
* * *
10163 AAAATATAAAGTATTATTAAAGTTAAATATTGAAATTAATAATCTGGCAAAAAAAACAAAAAGAA
125 AAAATATAAAGTATTATTAAAGTTAAATATTAAAACTAACAATCTGGCAAAAAAAACAAAAAGAA
10228 AGAAATTAACTATAAATATAGCACCTGGGC
190 AGAAATTAACTATAAATATAGCACCTGGGC
* * * **
10258 TACATTTCTTTTTATAATACAATTAATGAGTTTTGCCTAATTTATTAATGCTTTTGTAGTACGC-
1 TACATTTCTTTTTATAACACAATTAATGAGCTTTACCTAACATA-TAATGCTTTTGTAGTACGCA
*
10322 GGAGATGAAGCTAGAAATGAATTAATAAAAAG-TTCAAATGTGAAAAGCATCATTTTTTTCAAAG
65 GG-GATGAAGCTAGAAATGAATTAATAAAAAGATTCAAATGTAAAAAGCATCATTTTTTT-----
10386 AAGAAAATATAAAGTATTATTAAAGTTAAATATATTAAAACTAACAATCTGGCCAAAAAAAA-AA
124 -A-AAAATATAAAGTATTATTAAAGTT-AA-ATATTAAAACTAACAATCTGG-CAAAAAAAACAA
*
10450 AGAAGAATGAAATT
184 A-AAGAAAGAAATT
10464 CACCACAATA
Statistics
Matches: 177, Mismatches: 16, Indels: 22
0.82 0.07 0.10
Matches are distributed among these distances:
219 26 0.15
225 41 0.23
226 67 0.38
227 2 0.01
228 21 0.12
229 20 0.11
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (219 bp):
TACATTTCTTTTTATAACACAATTAATGAGCTTTACCTAACATATAATGCTTTTGTAGTACGCAG
GGATGAAGCTAGAAATGAATTAATAAAAAGATTCAAATGTAAAAAGCATCATTTTTTTAAAAATA
TAAAGTATTATTAAAGTTAAATATTAAAACTAACAATCTGGCAAAAAAAACAAAAAGAAAGAAAT
TAACTATAAATATAGCACCTGGGC
Found at i:11821 original size:2 final size:2
Alignment explanation
Indices: 11814--11842 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11804 TATTTTCTTA
11814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11843 AGATTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.