Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016065.1 Corchorus olitorius cultivar O-4 contig16098, 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: 11720
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8874 original size:46 final size:46
Alignment explanation
Indices: 8821--8910 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
8811 CGAGCCTTAT
8821 CTAGGTTTTTCTTATCATTTTAATGAATCTAAAAGATCAACCATAC
1 CTAGGTTTTTCTTATCATTTTAATGAATCTAAAAGATCAACCATAC
8867 CTAGGTTTTTCTTATCATTTTAATGAATCTAAAAGATCAACCAT
1 CTAGGTTTTTCTTATCATTTTAATGAATCTAAAAGATCAACCAT
8911 TAATAACGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (46 bp):
CTAGGTTTTTCTTATCATTTTAATGAATCTAAAAGATCAACCATAC
Found at i:9837 original size:261 final size:263
Alignment explanation
Indices: 9348--9911 Score: 780
Period size: 261 Copynumber: 2.1 Consensus size: 263
9338 TCAAATTTCG
* * * *
9348 AAAAGAAAAAGCCTTGATGTAAGTATGGAATGTTATTTAGGTTTTGTACCATCATTTAATTAATG
1 AAAA-AAAAAACCTTGACGTAGGTATGGAATCTTATTTAGGTTTTGTACCATCATTT-ATTAATG
* *
9413 TGATATAGTCAAAAAGATTCAACGGTTATACATAACGAACCTTATCTAGGTTTGTCCTATTATTT
64 TAATATAGTCAAAAAGATTCAACGGTTATACATAACGAACCTTATCTAGGTTTGTCCTATCATTT
* *
9478 TAATGAATCTAAAAGATCAATTATTAATAACGATATAAACGGTTTGACAATTTATACTATTTAGC
129 TAATGAATCTAAAAGATCAACTATTAATAACGATATAAACGGTTTCACAATTTATACTATTTAGC
* * *
9543 ATGTTTTGTCTCAATGATTGAAGTTTTTTTTTTTTGCCTTTTT-GTCAAGATTATTTGTGTGA-C
194 ATGTTTTGTCTC-A-GATGGAAGTTTTTTTTTTTGGCCTTTTTGGTCAAGATTATTTATGTGATC
9606 AAGTGTC
257 AAGTGTC
* * *
9613 AAAAAAAAATCCTTGACGTAGGTATGGATTCTTATTTAGGGTTTT-TACCATCA-TT-TTAATTT
1 AAAAAAAAAACCTTGACGTAGGTATGGAATCTTATTTA-GGTTTTGTACCATCATTTATTAATGT
* *
9675 AATGTAGTCAAAAAGATTTAACGGTTATACATAACGAACCTTATCTAGGTTTGTCCTATCATTTT
65 AATATAGTCAAAAAGATTCAACGGTTATACATAACGAACCTTATCTAGGTTTGTCCTATCATTTT
* * * * *
9740 AATGATTCTAAAAGATCAACTGTTAATAACGGTATAAACGGTTTCACAGTTTATACTGTTTAGCA
130 AATGAATCTAAAAGATCAACTATTAATAACGATATAAACGGTTTCACAATTTATACTATTTAGCA
9805 TGTTTTGTCGTC-GATGGAAGCTTTTTTTTTTTTGGCCTTTTTGGTCAAGATTATTTATGTGATC
195 TGTTTTGTC-TCAGATGGAAG--TTTTTTTTTTTGGCCTTTTTGGTCAAGATTATTTATGTGATC
*
9869 AAGTTTC
257 AAGTGTC
* * *
9876 AAAAATAAAAAACTTGACTTAGGTATGCAATCTTAT
1 AAAAA-AAAAACCTTGACGTAGGTATGGAATCTTAT
9912 CTAGATTTAT
Statistics
Matches: 266, Mismatches: 26, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
259 7 0.03
261 153 0.58
262 20 0.08
263 14 0.05
264 62 0.23
265 10 0.04
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (263 bp):
AAAAAAAAAACCTTGACGTAGGTATGGAATCTTATTTAGGTTTTGTACCATCATTTATTAATGTA
ATATAGTCAAAAAGATTCAACGGTTATACATAACGAACCTTATCTAGGTTTGTCCTATCATTTTA
ATGAATCTAAAAGATCAACTATTAATAACGATATAAACGGTTTCACAATTTATACTATTTAGCAT
GTTTTGTCTCAGATGGAAGTTTTTTTTTTTGGCCTTTTTGGTCAAGATTATTTATGTGATCAAGT
GTC
Found at i:10194 original size:118 final size:115
Alignment explanation
Indices: 9987--10201 Score: 335
Period size: 118 Copynumber: 1.8 Consensus size: 115
9977 CAGTTTATAC
* *
9987 TGTTTAGCACGTTTTGTTGTCAATGATGGAAGTTTTTTATGGCTTTTTTGGTTAAGATTAGAATT
1 TGTTTAGCACGTTTTGTTATCAATGATGGAAGTTTTTTATGACTTTTTTGGTTAAGATT--AATT
10052 AATTTATCCTATCATTTTCATGCAACGTAGTTTTTTTTTTTTCACTCAACGT
64 AATTTATCCTATCATTTTCATGCAACGTAGTTTTTTTTTTTTCACTCAACGT
10104 TGTTTAGCACGTTTTGTTATCAATGATTGCGAAGTCTGTTTTTATGAC-TTTTTGGTTAAGATT-
1 TGTTTAGCACGTTTTGTTATCAATGA-TG-GAAG--T-TTTTTATGACTTTTTTGGTTAAGATTA
10167 ATTAATTTATCCTATCATTTTCATGCAACGTAGTT
61 ATTAATTTATCCTATCATTTTCATGCAACGTAGTT
10202 AAAAATATAA
Statistics
Matches: 91, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
117 25 0.27
118 37 0.41
119 4 0.04
121 16 0.18
122 9 0.10
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (115 bp):
TGTTTAGCACGTTTTGTTATCAATGATGGAAGTTTTTTATGACTTTTTTGGTTAAGATTAATTAA
TTTATCCTATCATTTTCATGCAACGTAGTTTTTTTTTTTTCACTCAACGT
Done.