Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021235.1 Corchorus olitorius cultivar O-4 contig21268, 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: 33154
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:8915 original size:45 final size:45
Alignment explanation
Indices: 8864--8950 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
8854 GGAGAACGTG
* **
8864 TTCCAGCCAGAATCTATTTGAGCCTGTAAATGAAAAGCTCATCAA
1 TTCCAGCCAGAATCTAATTGAGCCACTAAATGAAAAGCTCATCAA
* *
8909 TTCCAGCCAGAATCTAATTGAGCCACTTAGTGAAAAGCTCAT
1 TTCCAGCCAGAATCTAATTGAGCCACTAAATGAAAAGCTCAT
8951 TTCCAGCAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
TTCCAGCCAGAATCTAATTGAGCCACTAAATGAAAAGCTCATCAA
Found at i:14838 original size:11 final size:11
Alignment explanation
Indices: 14822--14851 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
14812 TTACAAGGTG
14822 TTATTTTTTTT
1 TTATTTTTTTT
14833 TTA-TTTTTTT
1 TTATTTTTTTT
14843 TTATTTTTT
1 TTATTTTTT
14852 GGCTAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:15013 original size:83 final size:83
Alignment explanation
Indices: 14874--15037 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 83
14864 ATAAGGTAAA
* ** * *
14874 ATACAAATTAGATAAGTTAACGTCAAAAGGTAGAATTTGTGTTTGACAATTTTAGCCAAGTAAGT
1 ATACAAATTAGATAAATTAACCCCAAAAGGTAGAATTTGTGTTTAACAATTTTAGCCAAGCAAGT
*
14939 TATAAGGTAAAATACATT
66 TACAAGGTAAAATACATT
* *
14957 ATACAAATTGGATAAATTAACCCCAAAAGGTAGAATTTGTGTTTAACGATTTTAGCCAAGCAAGT
1 ATACAAATTAGATAAATTAACCCCAAAAGGTAGAATTTGTGTTTAACAATTTTAGCCAAGCAAGT
15022 TACAAGGTAAAATACA
66 TACAAGGTAAAATACA
15038 AACTGGATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (83 bp):
ATACAAATTAGATAAATTAACCCCAAAAGGTAGAATTTGTGTTTAACAATTTTAGCCAAGCAAGT
TACAAGGTAAAATACATT
Found at i:20329 original size:15 final size:15
Alignment explanation
Indices: 20301--20333 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
20291 AATTTGTTTC
20301 AAAATTGATAAAAAA
1 AAAATTGATAAAAAA
20316 AAAATATGATAAAAAA
1 AAAAT-TGATAAAAAA
20332 AA
1 AA
20334 CATGATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATTGATAAAAAA
Found at i:27132 original size:12 final size:12
Alignment explanation
Indices: 27115--27139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27105 GTAAACTTTG
27115 ATTTGATTTAAA
1 ATTTGATTTAAA
27127 ATTTGATTTAAA
1 ATTTGATTTAAA
27139 A
1 A
27140 CTTAGTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTTGATTTAAA
Found at i:28764 original size:189 final size:189
Alignment explanation
Indices: 28444--28813 Score: 697
Period size: 189 Copynumber: 2.0 Consensus size: 189
28434 TTGCTAATTG
*
28444 AAGTTTAAGGTTATTGGTAAAAACTTGATGAGCCCTTCTTGTAGTTTAGTTTGAACAACATGACA
1 AAGTTTAAGGTTATTGGTAAAAACTTGATGAGCCCTTCTTGTAGTTTAGTTCGAACAACATGACA
*
28509 ATCAATGTCAAGATGCTTGGTCCTCTCATGAAAGACTGAATTATGTCCAATGTGTATTGCTGAGA
66 ATCAATGTCAAGATGCTTGGTCCTCTCATGAAAGACTGAATTATATCCAATGTGTATTGCTGAGA
28574 GATTATCACAAAACAGTGGTTGGG-AAAAAAGATATTTTTTTTTGCTACTTAGTAAAACA
131 GATTATCACAAAACAGTGGTTGGGAAAAAAAGATA-TTTTTTTTGCTACTTAGTAAAACA
28633 AAGTTTAAGGTTATTGGTAAAAACTTGATGAGCCCTTCTTGTAGTTTAGTTCGAACAACATGACA
1 AAGTTTAAGGTTATTGGTAAAAACTTGATGAGCCCTTCTTGTAGTTTAGTTCGAACAACATGACA
*
28698 ATCAATGTCAAGATGCTTGGTCCTCTCATGAAAGACTGAATTCTATCCAATGTGTATTGCTGAGA
66 ATCAATGTCAAGATGCTTGGTCCTCTCATGAAAGACTGAATTATATCCAATGTGTATTGCTGAGA
28763 GATTATCACAAAACAGTGGTTGGGAAAAAAAGATATTTTTTTTGCTACTTA
131 GATTATCACAAAACAGTGGTTGGGAAAAAAAGATATTTTTTTTGCTACTTA
28814 TGAATATGAT
Statistics
Matches: 177, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
189 167 0.94
190 10 0.06
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (189 bp):
AAGTTTAAGGTTATTGGTAAAAACTTGATGAGCCCTTCTTGTAGTTTAGTTCGAACAACATGACA
ATCAATGTCAAGATGCTTGGTCCTCTCATGAAAGACTGAATTATATCCAATGTGTATTGCTGAGA
GATTATCACAAAACAGTGGTTGGGAAAAAAAGATATTTTTTTTGCTACTTAGTAAAACA
Done.