Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019627.1 Corchorus olitorius cultivar O-4 contig19660, 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: 40298
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:1108 original size:30 final size:30
Alignment explanation
Indices: 1068--1129 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
1058 AATATCTTAG
* *
1068 AATATTTATGTGATAAATTTCTTTCTTTAA
1 AATATATATGTGATAAATTTCTTACTTTAA
*
1098 AATATATATGTGATAAATTTCTTAGTTTAA
1 AATATATATGTGATAAATTTCTTACTTTAA
1128 AA
1 AA
1130 GTTTAGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (30 bp):
AATATATATGTGATAAATTTCTTACTTTAA
Found at i:10039 original size:53 final size:53
Alignment explanation
Indices: 9980--10090 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
9970 ACCATAAGGC
9980 AGGTGCTCATGTATGCAAATATGTACATATGCATGTTGTGCATACATACAAGT
1 AGGTGCTCATGTATGCAAATATGTACATATGCATGTTGTGCATACATACAAGT
10033 AGGTGCTCATGTATGCAAATATGTACATATGCATGTTGTGCATACATACAAGT
1 AGGTGCTCATGTATGCAAATATGTACATATGCATGTTGTGCATACATACAAGT
10086 AGGTG
1 AGGTG
10091 ACTGCATACG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (53 bp):
AGGTGCTCATGTATGCAAATATGTACATATGCATGTTGTGCATACATACAAGT
Found at i:13679 original size:71 final size:71
Alignment explanation
Indices: 13548--13680 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
13538 TTAAAAGGAA
** * * * *
13548 CAAATATACTTGATTCAATCATATAGCGATATGTGTCATCTTCCTATTTATATAGGCAAATATAC
1 CAAATATACTCAATTCAACCATATAGCGATATGTGTCATATTCCTATTTAGATAGACAAATATAC
13613 TCGATG
66 TCGATG
* *
13619 CAAATATACTCAATTCAACCATATATCGATATGTGTCATATTCCTATTTAGGTAGACAAATA
1 CAAATATACTCAATTCAACCATATAGCGATATGTGTCATATTCCTATTTAGATAGACAAATA
13681 CACTGGATTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (71 bp):
CAAATATACTCAATTCAACCATATAGCGATATGTGTCATATTCCTATTTAGATAGACAAATATAC
TCGATG
Found at i:13792 original size:56 final size:56
Alignment explanation
Indices: 13619--13806 Score: 218
Period size: 56 Copynumber: 3.4 Consensus size: 56
13609 ATACTCGATG
* * ***
13619 CAAATATACTCAATTCAACCATATATCGATATGTGTCATATTCCTATTTAGGTAGA
1 CAAATATACTCGATTCAACCATATAACGATATGTGTCATATTCCTATTTATAAAGA
* * * * *
13675 CAAATACACTGGATTCAACCATATAACGATATGTGTCATATTTCT-TTTAGTAACGG
1 CAAATATACTCGATTCAACCATATAACGATATGTGTCATATTCCTATTTA-TAAAGA
* *
13731 CAAATATACTCGATTCAACCATATAACGATATGTGTCA-CTTCCTATGTATAAAGA
1 CAAATATACTCGATTCAACCATATAACGATATGTGTCATATTCCTATTTATAAAGA
**
13786 CAAAATATAAACGATTCAACC
1 C-AAATATACTCGATTCAACC
13807 TGTCAATCAT
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
55 13 0.12
56 97 0.88
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (56 bp):
CAAATATACTCGATTCAACCATATAACGATATGTGTCATATTCCTATTTATAAAGA
Found at i:26003 original size:45 final size:45
Alignment explanation
Indices: 25939--26120 Score: 364
Period size: 45 Copynumber: 4.0 Consensus size: 45
25929 TTGTTATATT
25939 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
1 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
25984 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
1 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
26029 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
1 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
26074 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
1 GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
26119 GT
1 GT
26121 TACTAAGCAT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.42
Consensus pattern (45 bp):
GTCAATTGCATTAGGGAAGTTATCATGTGGATTTCTTCTTCTATC
Found at i:34109 original size:87 final size:87
Alignment explanation
Indices: 33966--34126 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
33956 CAGCTTGGAA
* * * **
33966 AAAACATTCTGCAGCTTTCTCCACATAAGATTCCCCACATTTTTCCAAATATATTTGACCTGCCT
1 AAAACATTCTGCAGCTCTCTCCACAGAAGATTCCCCACATTTTTCCAAATAAATTTGACCTGCAA
34031 TTTCAAAACGTCCAGCAAGAAC
66 TTTCAAAACGTCCAGCAAGAAC
** * *
34053 AAAACATTCTGCAGCTCTCTTTACAGCAGATTCCCCACATTTTTCCAGATAAATTTGACCTGCAA
1 AAAACATTCTGCAGCTCTCTCCACAGAAGATTCCCCACATTTTTCCAAATAAATTTGACCTGCAA
34118 TTTCAAAAC
66 TTTCAAAAC
34127 TTAACTTTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (87 bp):
AAAACATTCTGCAGCTCTCTCCACAGAAGATTCCCCACATTTTTCCAAATAAATTTGACCTGCAA
TTTCAAAACGTCCAGCAAGAAC
Done.