Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007747.1 Corchorus olitorius cultivar O-4 contig07773, 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: 2085
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Found at i:300 original size:168 final size:166
Alignment explanation
Indices: 20--573 Score: 735
Period size: 168 Copynumber: 3.3 Consensus size: 166
10 AAGTTTTTTT
* *
20 ATTCATGTGTAAGTTTAAAATCCTTGTTCAAGGTCTCAATTCAAAGTTTGCATTGGTAACTCCTC
1 ATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTC-ATTCAAAGTTTGCATTGGTAA-GCCTC
* *
85 CGGGCACAAATTCGGAAACCTCCGGGTATTAATTCTGCTAAGTCCTTCGGGAAATTGATAAAACC
64 CGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGAAATTGATAAAACC
* * *
150 TCCGGGTATCATTTCATTTCATCAAGTTTGTCATTAAA
129 TCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAA
* * **
188 AGTTCATGTTTAAGTTTAAAATCCTTAG-TCATGGTCTCTATTCAGAGTTTGCGCTGGTAAGCCT
1 A-TTCATGTTTAAGTTTAAAATCCTT-GTTCAAGGTCTC-ATTCAAAGTTTGCATTGGTAAGCCT
* *
252 CCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGAAATCGGTAAAAC
63 CCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGAAATTGATAAAAC
*
317 CTCCGGGTACCATTTCATTTCATTAAGTTTTTCATCAAA
128 CTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAA
* * * *
356 ATTCATGTTAAAGTTTAAAATCCTTGTTTAAGGTCTCATTTCAAAGTTCGCATTGGTAAGTCATC
1 ATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCA-TTCAAAGTTTGCATTGGTAAG-CCTC
* * ***
421 CGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAATTTC
64 CGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGAAATTGATAAAACC
* *
486 TCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAA
129 TCCGGGTACCATTTCATTTCATCAAGTTTTTCATC-AAA
* *
525 ATTCATGTTTAAG------ATCCTTGTTTAAGGTCTCAATTTAAAGTTTGCATTG
1 ATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTC-ATTCAAAGTTTGCATTG
574 ATATGACCTC
Statistics
Matches: 343, Mismatches: 36, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
163 32 0.09
164 1 0.00
166 2 0.01
167 48 0.14
168 194 0.57
169 65 0.19
170 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (166 bp):
ATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCATTCAAAGTTTGCATTGGTAAGCCTCCG
GGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTTCGGGAAATTGATAAAACCTC
CGGGTACCATTTCATTTCATCAAGTTTTTCATCAAA
Found at i:718 original size:39 final size:39
Alignment explanation
Indices: 616--731 Score: 164
Period size: 38 Copynumber: 3.0 Consensus size: 39
606 TGAACTATTC
*
616 TACTTTATCAG-TTTATTTCGATCCTGGTTTAGGATCAT
1 TACTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCAT
* * * *
654 TACGTGATTA-TTTTATTTTAATCCTGGTTTAGGATCAT
1 TACTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCAT
*
692 TACTTTATCAGTTTTATTTCAATCCTGGTTGAGGATCAT
1 TACTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCAT
731 T
1 T
732 GCTTCATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
38 39 0.59
39 27 0.41
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (39 bp):
TACTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCAT
Found at i:1369 original size:30 final size:30
Alignment explanation
Indices: 704--1362 Score: 853
Period size: 30 Copynumber: 21.9 Consensus size: 30
694 CTTTATCAGT
* *
704 TTTATTTCAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
734 TTCATTTTTAATCCTGGTTTAGGATCATTGT
1 TTTA-TTTTAATCCTGGTTTAGGATCATTGC
*
765 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
795 TTCATTTTTAATCCTGGTTTAGGATCATTGC
1 TTTA-TTTTAATCCTGGTTTAGGATCATTGC
* *
826 TTTATTTTAATCATGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
856 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
**
886 TTTATTTTAATCCT-GTTTGAGGATTGTTGC
1 TTTATTTTAATCCTGGTTT-AGGATCATTGC
* * *
916 TAT-TTTTAATCCTGTTTTAGGATCAATGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
945 TTTATTTTCATCCT-GTTTGAGGATCATTAC
1 TTTATTTTAATCCTGGTTT-AGGATCATTGC
*
975 TTTATTTTAATCCTGTTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* **
1005 TTTATTTTAAT-CTTGTTTGAGGATTGTTGC
1 TTTATTTTAATCCTGGTTT-AGGATCATTGC
* *
1035 TTTATTTTAATCCTGTTTTAGGATCATTAC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
1065 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
1095 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* ** *
1125 TTCATTTTAATCCTGGTCGAGGATCATTGT
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* **
1155 TTTATTTTAATCAT-GTTTGAGGATTGTTGC
1 TTTATTTTAATCCTGGTTT-AGGATCATTGC
* *
1185 TTTATTTTTAATCCTGTTTTAGGATCAATGC
1 TTTA-TTTTAATCCTGGTTTAGGATCATTGC
*
1216 TTTATTTTCATCCT-GTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTT-AGGATCATTGC
* *
1246 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
1276 TTTATTTTAATCCTGGTTGAGGATCATTCC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
1306 GTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
1336 TTTATTTTAATCCTGGTTTAGGATCAT
1 TTTATTTTAATCCTGGTTTAGGATCAT
1363 CACTTTAGTT
Statistics
Matches: 545, Mismatches: 70, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
29 36 0.07
30 420 0.77
31 86 0.16
32 3 0.01
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:1847 original size:16 final size:15
Alignment explanation
Indices: 1809--1850 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
1799 ACAGAGGTTG
1809 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
1824 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
1839 ACTAGAAAACAA
1 AC-AGAAAACAA
1851 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.