Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007151.1 Corchorus olitorius cultivar O-4 contig07176, 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: 2035
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1185 original size:35 final size:35
Alignment explanation
Indices: 1139--1551 Score: 583
Period size: 35 Copynumber: 11.7 Consensus size: 35
1129 CTTAGGAATC
*
1139 CAGATGACTCGGTGTAGCATCTTCCAAGATAAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1174 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1209 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1244 CAGATGACTCGGTGTAGCATCTTCCAAGATAAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1279 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1314 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1349 CAGATGACTCGGTGTAGCATCTTCAAAGATGAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
* * * * * *
1384 CAGGTGACTCGGTATAACATCTTTAAAGATGAATC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1419 CAGATGACTCGGTGTAGCATCTTCAAAGATGAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
* * * * *
1454 CAGGTGACTCAGTGTAGCATCTTAAAAAAAACGAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATA--AATT
* * * **
1491 CAGGTGACTCGGTGAAGCATCTTCAAAAACGAATT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
*
1526 CAGATGACTTGGTGTAGCATCTTCAA
1 CAGATGACTCGGTGTAGCATCTTCAA
1552 CATGAACTCA
Statistics
Matches: 344, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
35 314 0.91
37 30 0.09
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (35 bp):
CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
Found at i:1848 original size:28 final size:28
Alignment explanation
Indices: 1808--1997 Score: 281
Period size: 28 Copynumber: 6.7 Consensus size: 28
1798 GGCCACTTCA
*
1808 AGGGGCATTTTGGTCATTTTGCATATCT
1 AGGGGCATTTTGGTCATTTTGCATATCC
1836 AGGGGCATTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
* *
1864 AGGAGCATTTTGGTCATTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
1892 AAGGGGCATTTTTGGTCATTTTGCATATCC
1 -AGGGGCA-TTTTGGTCATTTTGCATATCC
1922 AGGGGCATTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
* * * *
1950 GGGGGCGTTTTGGTCATTTTTGCACATCT
1 AGGGGCATTTTGGTCA-TTTTGCATATCC
*
1979 AGGGGTATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
1998 CAAGTGCACT
Statistics
Matches: 147, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
28 91 0.62
29 36 0.24
30 20 0.14
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCATATCC
Found at i:1919 original size:58 final size:56
Alignment explanation
Indices: 1808--1997 Score: 281
Period size: 58 Copynumber: 3.3 Consensus size: 56
1798 GGCCACTTCA
*
1808 AGGGGCATTTTGGTCATTTTGCATATCTAGGGGCATTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCC
* *
1864 AGGAGCATTTTGGTCATTTTGCACATCCAAGGGGCATTTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC-AGGGGCA-TTTTGGTCATTTTGCATATCC
* * * *
1922 AGGGGCATTTTGGTCATTTTGCATATCCGGGGGCGTTTTGGTCATTTTTGCACATCT
1 AGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCA-TTTTGCATATCC
*
1979 AGGGGTATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
1998 CAAGTGCACT
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
56 34 0.28
57 40 0.33
58 47 0.39
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (56 bp):
AGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCC
Found at i:1961 original size:86 final size:85
Alignment explanation
Indices: 1805--1997 Score: 307
Period size: 86 Copynumber: 2.3 Consensus size: 85
1795 TAGGGCCACT
*
1805 TCAAGGGGCATTTTGGTCATTTTGCATATCTAGGGGCATTTTGGTCATTTTGCATATCCAGGAGC
1 TCAAGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGAGC
1870 ATTTTGGTCA-TTTTGCACA
66 ATTTTGGTCATTTTTGCACA
* *
1889 TCCAAGGGGCATTTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCGGGG
1 T-CAAGGGGCA-TTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGA
*
1954 GCGTTTTGGTCATTTTTGCACA
64 GCATTTTGGTCATTTTTGCACA
* *
1976 TCTAGGGGTATTTTGGTCATTT
1 TCAAGGGGCATTTTGGTCATTT
1998 CAAGTGCACT
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
84 1 0.01
85 21 0.21
86 68 0.68
87 10 0.10
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (85 bp):
TCAAGGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCATATCCAGGAGC
ATTTTGGTCATTTTTGCACA
Done.