Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013561.1 Corchorus olitorius cultivar O-4 contig13594, 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: 3811
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:195 original size:18 final size:17
Alignment explanation
Indices: 168--204 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
158 TTTCAAGTGC
*
168 AAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAATG
185 AAAAAATAAAAAAAAATG
1 AAAAAA-AAAAAAAAATG
203 AA
1 AA
205 GAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAAAAAATG
Found at i:1611 original size:69 final size:69
Alignment explanation
Indices: 1515--1753 Score: 415
Period size: 69 Copynumber: 3.5 Consensus size: 69
1505 GAATGCTTTG
1515 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
1580 TATA
66 TATA
1584 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
1649 TATA
66 TATA
* * * *
1653 GGCTTTTCTAGAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
1718 TATA
66 TATA
* * *
1722 GGTTTTTCCACAAGCCGAATTCGTTTCCATAC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATAC
1754 AAATCAAGCC
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 161 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTTCATCCAAGCCA
TATA
Found at i:2041 original size:104 final size:104
Alignment explanation
Indices: 1797--2110 Score: 535
Period size: 104 Copynumber: 3.0 Consensus size: 104
1787 AAGCTTATTC
* * *
1797 CATTTGATAAAACCTCCAGGTACCATTTCATTTCATTAAGTTTTTCATCAAAAATTCATGTTTAA
1 CATTTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTAA
**
1862 G-TTTAAAATTTTTGTTCAAGGTCTCTATTCAGAGTTT-
66 GATTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTG
*
1899 CGA-TTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTATTTCATCAAAGATTCATGTTTA
1 C-ATTTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTA
*
1963 AGATTTAAAATCCTTGTTCAAGGTCTCTATTTAGAGTTTG
65 AGATTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTG
2003 CATTTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTAA
1 CATTTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTAA
2068 GATTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTG
66 GATTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTG
2107 CATT
1 CATT
2111 GGTAAGTCCT
Statistics
Matches: 199, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
102 60 0.30
103 35 0.18
104 104 0.52
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (104 bp):
CATTTGTTAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTAA
GATTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTG
Found at i:2299 original size:169 final size:169
Alignment explanation
Indices: 2010--2460 Score: 660
Period size: 169 Copynumber: 2.7 Consensus size: 169
2000 TTGCATTTGT
*
2010 TAAAACCTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAAGATTCATGTTTAAGATTTAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAG-TTTAA
* * * *
2075 AATCCTTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCTGGCACAAATTAAGAAA
65 AATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAATTAAGAAA
2140 CCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGA
130 CCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGA
* * * *
2180 TAAAACCTCCGGGTATCATTCCATTACATCAAGTTTTCCATCAAAGATTCATGTTTAAGTTTAAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTTTAAA
* * *
2245 ATCCTTGTTTAAGGT-TCCTTTTCAGAGTTTCCATTGGTAAGTCCTCCGGGCACAAGTTCAGAAA
66 ATCCTTGTTTAAGGTCT-CTTTTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAATTAAGAAA
* *
2309 CCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGG
130 CCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGA
*
2349 TAAAGCCTCCGGGTACCATTTCATTTCATCAAGTTTTTCA--AAAG-TTCATGTTTAAG-TTAAA
1 TAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTTTAAA
* * * * *
2410 ATCTTTGTTTAAGGTCTCATTTCAGAGCTTACATTTGATAAGACCTCCGGG
66 ATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACA-TTGGTAAGTCCTCCGGG
2461 ATTCTCATGT
Statistics
Matches: 254, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
165 32 0.13
166 28 0.11
167 4 0.02
168 1 0.00
169 135 0.53
170 54 0.21
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (169 bp):
TAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAGATTCATGTTTAAGTTTAAA
ATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAATTAAGAAAC
CTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGA
Found at i:2568 original size:30 final size:30
Alignment explanation
Indices: 2529--2774 Score: 339
Period size: 30 Copynumber: 8.2 Consensus size: 30
2519 GATTATTGCT
* * *
2529 TCATTGCTTTATGTTAATCCTGTTTGAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
* * *
2559 TCCTTGCTTTGTTTTAATCCTGTTTAAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
*
2589 TCCTTGCTTTGTTTTAATCCTGGTTGAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
* *
2619 TCCTTGCTTTGTTTTAAACCTGGTTGAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
* *
2649 TCATTGCTTTGTTATAGTCCTGGTTGAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
*
2679 TCATTGCTTTGTTTTAATCCTGGTTGGGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
* *
2709 TCATTTCTTTGTTTTAATCCTGTTTGAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
* * *
2739 TCGTTGCTTTATTTTAATCCTGGTTTAGGA
1 TCATTGCTTTGTTTTAATCCTGGTTGAGGA
2769 TCATTG
1 TCATTG
2775 TTTCATCAGT
Statistics
Matches: 193, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 193 1.00
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.48
Consensus pattern (30 bp):
TCATTGCTTTGTTTTAATCCTGGTTGAGGA
Done.