Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024630.1 Corchorus olitorius cultivar O-4 contig24663, 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: 14709
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:3731 original size:20 final size:21
Alignment explanation
Indices: 3697--3750 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3687 AGCAACTATT
*
3697 TCAAATC-AAGGAATAAGCAA
1 TCAAATCAAAGCAATAAGCAA
*
3717 TC-AATCAAAGCAATAATCAA
1 TCAAATCAAAGCAATAAGCAA
3737 TCAAATCAAAGCAA
1 TCAAATCAAAGCAA
3751 AGGAAGGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 11 0.37
ACGTcount: A:0.56, C:0.19, G:0.09, T:0.17
Consensus pattern (21 bp):
TCAAATCAAAGCAATAAGCAA
Found at i:10833 original size:18 final size:19
Alignment explanation
Indices: 10810--10846 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
10800 GTATCCTAGC
10810 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
10828 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
10847 AGAGATCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:12366 original size:42 final size:42
Alignment explanation
Indices: 12245--12390 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
12235 GGTCGACAAT
* * * * *
12245 GATCTTTTTACAAGCGTTGGTTGTTGCTGCATCCTCAGCAGC
1 GATCTTTCTACAAGCATTGGTTGATGTTGCATCCTCAGCAAC
* ** * * * *
12287 GATTTTTCTACAAGCATCAGCTGCTGTTTCATTCTCAGCAAC
1 GATCTTTCTACAAGCATTGGTTGATGTTGCATCCTCAGCAAC
*
12329 GATCTTTCCACAAGCATTGGTTGATGTTGCATCCTCAGCAAC
1 GATCTTTCTACAAGCATTGGTTGATGTTGCATCCTCAGCAAC
* *
12371 GACCTTTCTAAAAGCATTGG
1 GATCTTTCTACAAGCATTGG
12391 CTGCTGCTAC
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (42 bp):
GATCTTTCTACAAGCATTGGTTGATGTTGCATCCTCAGCAAC
Found at i:12409 original size:42 final size:42
Alignment explanation
Indices: 12320--12410 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
12310 CTGTTTCATT
* * * * *
12320 CTCAGCAACGATCTTTCCACAAGCATTGGTTGATGTTGCATC
1 CTCAGCAACGACCTTTCCAAAAGCATTGGCTGATGCTACATC
* *
12362 CTCAGCAACGACCTTTCTAAAAGCATTGGCTGCTGCTACATC
1 CTCAGCAACGACCTTTCCAAAAGCATTGGCTGATGCTACATC
*
12404 TTCAGCA
1 CTCAGCA
12411 GTGGTCTTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (42 bp):
CTCAGCAACGACCTTTCCAAAAGCATTGGCTGATGCTACATC
Found at i:12409 original size:84 final size:84
Alignment explanation
Indices: 12245--12410 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 84
12235 GGTCGACAAT
** * * * ** *
12245 GATCTTTTTACAAGCGTTGGTTGTTGCTGCATCCTCAGCAGCGATTTTTCTACAAGCATCAGCTG
1 GATCTTTCCACAAGCATTGGTTGATGCTGCATCCTCAGCAACGACCTTTCTAAAAGCATCAGCTG
* *
12310 CTGTTTCATTCTCAGCAAC
66 CTGCTACATTCTCAGCAAC
* **
12329 GATCTTTCCACAAGCATTGGTTGATGTTGCATCCTCAGCAACGACCTTTCTAAAAGCATTGGCTG
1 GATCTTTCCACAAGCATTGGTTGATGCTGCATCCTCAGCAACGACCTTTCTAAAAGCATCAGCTG
12394 CTGCTACA-TCTTCAGCA
66 CTGCTACATTC-TCAGCA
12411 GTGGTCTTGC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 2 0.03
84 66 0.97
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (84 bp):
GATCTTTCCACAAGCATTGGTTGATGCTGCATCCTCAGCAACGACCTTTCTAAAAGCATCAGCTG
CTGCTACATTCTCAGCAAC
Found at i:13825 original size:15 final size:15
Alignment explanation
Indices: 13807--13837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13797 ACAAACTCGC
*
13807 CAGCAGAGAGCTTGT
1 CAGCAGAAAGCTTGT
13822 CAGCAGAAAGCTTGT
1 CAGCAGAAAGCTTGT
13837 C
1 C
13838 GACAACATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (15 bp):
CAGCAGAAAGCTTGT
Found at i:14199 original size:143 final size:142
Alignment explanation
Indices: 13941--14217 Score: 439
Period size: 143 Copynumber: 1.9 Consensus size: 142
13931 AAAAGCTTCA
* *
13941 TTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGATGGTCACCATTTGATTATA
1 TTATTCCTCTTGAAGGCTACCATTGTGGTCGTAACTCCAACAAGGATGGTCACCATTTGATTATA
* * * *
14006 AAGAACCCATATATTAAGAGGTAGCTTGAATCCTGGTGGCCGGCCTAGAATGGTAAATCCCCCAT
66 AAGAACCCATATATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTAGAATGGTAAAT-CCCCAT
14071 GGTTTAAGTGTCT
130 GGTTTAAGTGTCT
*
14084 TTATTCTTCTTGAAGGCTACCATTGTGGTCGTAACTCCAACAATGG-TGGTCACCATTTGATTAT
1 TTATTCCTCTTGAAGGCTACCATTGTGGTCGTAACTCCAACAA-GGATGGTCACCATTTGATTAT
** *
14148 AAAGAACCGGTATATCAAGAGGTAGCTTAAATCATGGTGACTGGCCTAGAATGGTAAATCCCCAT
65 AAAGAACCCATATATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTAGAATGGTAAATCCCCAT
14213 GGTTT
130 GGTTT
14218 CCTTCTCCTT
Statistics
Matches: 123, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
142 11 0.09
143 110 0.89
144 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (142 bp):
TTATTCCTCTTGAAGGCTACCATTGTGGTCGTAACTCCAACAAGGATGGTCACCATTTGATTATA
AAGAACCCATATATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTAGAATGGTAAATCCCCATG
GTTTAAGTGTCT
Found at i:14404 original size:72 final size:72
Alignment explanation
Indices: 14287--14563 Score: 509
Period size: 72 Copynumber: 3.8 Consensus size: 72
14277 GGTTCATCTC
14287 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
14352 ATTTACA
66 ATTTACA
14359 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
14424 ATTTACA
66 ATTTACA
* *
14431 AAGGTCCTCTATGTGGCAAGGCATTGGTGATTGTAGCGATCTATAGCTCTCACCTTGTCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
14496 ATTTACA
66 ATTTACA
* * *
14503 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGTAACCTATAGCTCTCACCTAGTCTT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTT
14564 CATTGTTATG
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 198 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (72 bp):
AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
ATTTACA
Done.