Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021756.1 Corchorus olitorius cultivar O-4 contig21789, 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: 27632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4924 original size:21 final size:22
Alignment explanation
Indices: 4900--4941 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4890 ATCTTTAGAC
4900 TAGTTCTGAA-TATCCAATTTA
1 TAGTTCTGAATTATCCAATTTA
*
4921 TAGTTTTGAATTATCCAATTT
1 TAGTTCTGAATTATCCAATTT
4942 CACTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
TAGTTCTGAATTATCCAATTTA
Found at i:6260 original size:39 final size:39
Alignment explanation
Indices: 6206--6285 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
6196 CCATTATGTC
6206 TTCCGTACTCTGAGTTTCAGGAGAATGTTGTTCATCTGG
1 TTCCGTACTCTGAGTTTCAGGAGAATGTTGTTCATCTGG
6245 TTCCGTACTCTGAGTTTCAGGAGAATGTTGTTCATCTGG
1 TTCCGTACTCTGAGTTTCAGGAGAATGTTGTTCATCTGG
6284 TT
1 TT
6286 GTTCTTTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (39 bp):
TTCCGTACTCTGAGTTTCAGGAGAATGTTGTTCATCTGG
Found at i:8870 original size:65 final size:65
Alignment explanation
Indices: 8759--8889 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
8749 TCAGAACAAC
* * *
8759 TAACATAGATGCGAGAACATCCCTTAGATAATTCAAACATCCAGCTTTCCGTTTTGAATGTATAA
1 TAACATAGATGCAAGAACATCCCTTAGACAATTCAAACATCCAGCTTTCCATTTTGAATGTATAA
* * * *
8824 TAACATCA-ATGCAAGAACATCCC-TAGGACAATTCAAAGATCTAGCTTTCCATTTTTAGTGTAT
1 TAACAT-AGATGCAAGAACATCCCTTA-GACAATTCAAACATCCAGCTTTCCATTTTGAATGTAT
8887 AA
64 AA
8889 T
1 T
8890 CTTGAACTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.04
65 54 0.95
66 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (65 bp):
TAACATAGATGCAAGAACATCCCTTAGACAATTCAAACATCCAGCTTTCCATTTTGAATGTATAA
Found at i:11232 original size:30 final size:30
Alignment explanation
Indices: 11196--11255 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
11186 GTAAAATTAG
11196 AAGGGTTGTAGCAGAAGAAAATAGACTATC
1 AAGGGTTGTAGCAGAAGAAAATAGACTATC
**
11226 AAGGGTTGTAGCAGATTAAAATAGACTATC
1 AAGGGTTGTAGCAGAAGAAAATAGACTATC
11256 TGTAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (30 bp):
AAGGGTTGTAGCAGAAGAAAATAGACTATC
Found at i:18209 original size:39 final size:40
Alignment explanation
Indices: 18153--18233 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
18143 TTTAATTCCT
18153 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
18193 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
18232 AT
1 AT
18234 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:18259 original size:24 final size:23
Alignment explanation
Indices: 18224--18269 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
18214 AATACTTACA
18224 TTAATTAAATTCTTAGGTATTTT
1 TTAATTAAATTCTTAGGTATTTT
18247 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
18270 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGGTATTTT
Found at i:18688 original size:204 final size:203
Alignment explanation
Indices: 18339--18944 Score: 1135
Period size: 204 Copynumber: 3.0 Consensus size: 203
18329 TTCCTTAATA
18339 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
18403 AATTTAATAAATCTACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-TATATATATAATAG
18468 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
18533 TCACCATTG
195 TCACCATTG
18542 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
18607 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-TATATATATAATAG
18672 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
*
18737 TTACCATTG
195 TCACCATTG
18746 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * *
18811 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTGTATAGTTT-TATATATAATAAT
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTATATATATAATAGT
18875 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
18940 CACCA
196 CACCA
18945 AAAGTTATTA
Statistics
Matches: 395, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
202 81 0.21
203 17 0.04
204 297 0.75
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTATATATATAATAGT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCATTG
Found at i:27147 original size:6 final size:6
Alignment explanation
Indices: 27136--27193 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
27126 GAGGTACCCG
* * * * *
27136 CGAGTC CGAGTC CGAGTC CGAGCC CGAGCC CGAGTT CAAGTC CAAGTC
1 CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC CGAGTC
*
27184 CAAGTC CGAG
1 CGAGTC CGAG
27194 AAGAATTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.22, C:0.34, G:0.29, T:0.14
Consensus pattern (6 bp):
CGAGTC
Done.