Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013654.1 Corchorus capsularis cultivar CVL-1 contig13675, 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: 30527
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:1984 original size:14 final size:15
Alignment explanation
Indices: 1967--1996 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1957 ACGTCTAGCC
1967 AAAAAGAAAAA-AAA
1 AAAAAGAAAAAGAAA
1981 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
1996 A
1 A
1997 GATCAAACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:3171 original size:13 final size:13
Alignment explanation
Indices: 3153--3178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3143 AAACCCTATA
3153 ATATATATGTGAT
1 ATATATATGTGAT
3166 ATATATATGTGAT
1 ATATATATGTGAT
3179 TAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATATATATGTGAT
Found at i:5273 original size:6 final size:6
Alignment explanation
Indices: 5262--5288 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5252 CATGTTATGG
5262 TCAGAA TCAGAA TCAGAA TCAGAA TCA
1 TCAGAA TCAGAA TCAGAA TCAGAA TCA
5289 TCATGATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (6 bp):
TCAGAA
Found at i:17086 original size:3 final size:3
Alignment explanation
Indices: 17078--17119 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17068 ATGTAGGAAT
17078 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17120 CTAGCTCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20101 original size:152 final size:152
Alignment explanation
Indices: 19825--20125 Score: 541
Period size: 152 Copynumber: 2.0 Consensus size: 152
19815 ACGGACCTGT
19825 CACCATACTGTACACTGCAACATCATAAACCGAAAATTTTTAAGCCACAACCGGCATGATTTTTG
1 CACCATACTGTACACTGCAACATCATAAACCGAAAATTTTTAAGCCACAACCGGCATGATTTTTG
*
19890 TCCAAAAGCTGGATAATGGAACATGTTTTCAAATTAGGGATCGAAATTAAATGGGGAAATAGCTA
66 TCCAAAAGCTGGATAATGGAACAGGTTTTCAAATTAGGGATCGAAATTAAATGGGGAAATAGCTA
19955 AAGATAATAACAGCACACAAAA
131 AAGATAATAACAGCACACAAAA
*
19977 CACCATACTGTACACTGCAACATCATAAATCGAAAATTTTTAAGCCACAACCGGCATGATTTTTG
1 CACCATACTGTACACTGCAACATCATAAACCGAAAATTTTTAAGCCACAACCGGCATGATTTTTG
* * *
20042 TCTGAAAA-CTGGATAATGGAACGGGTTTTCAAATTGGGGATCGAAATTAAATGGGGAAATAGCT
66 TC-CAAAAGCTGGATAATGGAACAGGTTTTCAAATTAGGGATCGAAATTAAATGGGGAAATAGCT
20106 AAAGATAATAACAGCACACA
130 AAAGATAATAACAGCACACA
20126 GAATAACATA
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
152 139 0.97
153 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (152 bp):
CACCATACTGTACACTGCAACATCATAAACCGAAAATTTTTAAGCCACAACCGGCATGATTTTTG
TCCAAAAGCTGGATAATGGAACAGGTTTTCAAATTAGGGATCGAAATTAAATGGGGAAATAGCTA
AAGATAATAACAGCACACAAAA
Found at i:20736 original size:80 final size:80
Alignment explanation
Indices: 20598--20745 Score: 251
Period size: 80 Copynumber: 1.9 Consensus size: 80
20588 CCAATCTGAC
* * *
20598 CATACTGTGCCCAAAGGATGACAGCATTAGCACATATTTTCCTAATTGTTCCACTTCTATGTAAG
1 CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTATGTAAG
20663 AAAGCAATTCTAGAG
66 AAAGCAATTCTAGAG
* *
20678 CATATTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTATGTGAG
1 CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTATGTAAG
20743 AAA
66 AAA
20746 ACATTTCTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (80 bp):
CATACTGTGCCCAAAGGATGACAACATTAGCACATATTCTCCCAATTGTTCCACTTCTATGTAAG
AAAGCAATTCTAGAG
Found at i:23920 original size:15 final size:16
Alignment explanation
Indices: 23900--23930 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
23890 AATTTAATTG
23900 AAAACAAAAA-AAACA
1 AAAACAAAAACAAACA
23915 AAAACAAAAACAAACA
1 AAAACAAAAACAAACA
23931 CACACACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAAAACAAACA
Found at i:29619 original size:193 final size:195
Alignment explanation
Indices: 29241--29628 Score: 512
Period size: 193 Copynumber: 2.0 Consensus size: 195
29231 CTCAATGCTA
* *
29241 CATGATTTTTGGCGCAAAAACTCTTTGAAATATCTACATTCATCGAAAAAAAAATTCAGCCACAT
1 CATGATTTTTGGCGCAAAAACTCCTTGAAATATATACATTCATCG-AAAAAAAATTCAGCCACAT
* * * *
29306 TGGATATAAGGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCG
65 TGAATAGAAGGACTTATTTTTACGAGCATCTCAATATTGTTTCGATTTAATTAGAAATTAATTCG
* * * *
29371 GAAAAAAAAAAGGAAAAACAATGTTAGAAGTGTGAAAAGTCTGTCAATCTTTTTGGAGTTGAATT
130 G--AAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGAGTTGAATT
29436 TTG
193 TTG
* * * ** *
29439 CATGATTTTTGGCGCAAAGAGTCCTTGAAATATATATATTCATCG-AACCAAATCTCAGCCATAT
1 CATGATTTTTGGCGCAAAAACTCCTTGAAATATATACATTCATCGAAAAAAAAT-TCAGCCACAT
* * * *
29503 TGAATAGAATGACTTATTTTTTCTAGCATCTCAATCTT-TTTCGATTTAATTAGAAATTAATTCG
65 TGAATAGAAGGACTTATTTTTACGAGCATCTCAATATTGTTTCGATTTAATTAGAAATTAATTCG
* * *
29567 G-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATT
130 GAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGAGTTGAATT
29629 ATATATTGTT
Statistics
Matches: 166, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
193 54 0.33
196 33 0.20
197 39 0.23
198 40 0.24
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (195 bp):
CATGATTTTTGGCGCAAAAACTCCTTGAAATATATACATTCATCGAAAAAAAATTCAGCCACATT
GAATAGAAGGACTTATTTTTACGAGCATCTCAATATTGTTTCGATTTAATTAGAAATTAATTCGG
AAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGAGTTGAATTTTG
Done.