Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011183.1 Corchorus olitorius cultivar O-4 contig11216, 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: 5781
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Found at i:84 original size:27 final size:27
Alignment explanation
Indices: 53--246 Score: 88
Period size: 27 Copynumber: 7.4 Consensus size: 27
43 AAAATAATAA
* *
53 TAATATATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
80 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* * * * *
107 AAATAGATAATAA-TTAAATTAATAAA-
1 TAATAAATAAAAAGATAAA-TAGTAAAT
**
133 TAGATAAATAGTAA-ATAAATAG-AGAA-
1 TA-ATAAATAAAAAGATAAATAGTA-AAT
* *
159 TAGTTAAA-AATAA-ATAAATAGATAAA-
1 TA-ATAAATAAAAAGATAAATAG-TAAAT
* *
185 TAGTAAATAAATAGAT-AATAGTTAAA-
1 TAATAAATAAAAAGATAAATAG-TAAAT
* *
211 A-ATAAATAAATAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
237 AAATAGATAA
1 TAATAAATAA
247 TAGTTAAAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
25 34 0.25
26 38 0.28
27 58 0.43
28 5 0.04
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:90 original size:4 final size:4
Alignment explanation
Indices: 75--246 Score: 90
Period size: 4 Copynumber: 43.8 Consensus size: 4
65 AGATAATAGC
* * * *
75 TAAA TTAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA T-AA TAAT
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * * *
121 TAAA TTAA TAAA TAGA TAAA T-AG TAAA TAAA TAGA GAATA GTTAA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA
* * * *
169 TAAA TAAA TAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA
* * *
217 TAAA TAGA TAAA T-AG TAAA TAAA TAGA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
247 TAGTTAAAAA
Statistics
Matches: 121, Mismatches: 34, Indels: 26
0.67 0.19 0.14
Matches are distributed among these distances:
3 16 0.13
4 96 0.79
5 6 0.05
6 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:190 original size:44 final size:44
Alignment explanation
Indices: 59--283 Score: 334
Period size: 44 Copynumber: 5.2 Consensus size: 44
49 ATAATAATAT
* *
59 ATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAA--AATAAATAAATAGATAAATAGTAA
* *
105 ATAAATAGATAATAATT--AAATTAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
*
147 ATAAATAGAGAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
191 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
*
235 ATAAATAGATAATAGTTAAAAATAAATTAAA-A-A-AAATAGTGA
1 ATAAATAGATAATAGTTAAAAATAAA-TAAATAGATAAATAGTAA
277 ATAAATA
1 ATAAATA
284 AAAAAATCTT
Statistics
Matches: 167, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
42 52 0.31
43 1 0.01
44 95 0.57
45 4 0.02
46 15 0.09
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (44 bp):
ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
Found at i:246 original size:8 final size:8
Alignment explanation
Indices: 1--237 Score: 79
Period size: 8 Copynumber: 29.0 Consensus size: 8
1 GATAAATA
1 GATAAATA
* *
9 GATACAGA
1 GATAAATA
17 GA-ATAATA
1 GATA-AATA
25 GATAAATA
1 GATAAATA
* **
33 GGTAGCTA
1 GATAAATA
* *
41 AAAAAATA
1 GATAAATA
49 -ATAATAATA
1 GAT-A-AATA
*
58 TATAAATA
1 GATAAATA
66 GAT-AATA
1 GATAAATA
*
73 GCTAAATTA
1 GATAAA-TA
82 -ATAAAT-
1 GATAAATA
88 -A-AAA-A
1 GATAAATA
93 GATAAATA
1 GATAAATA
101 GTAAATAAATA
1 G---ATAAATA
112 GAT-AATA
1 GATAAATA
119 -ATTAAATTA
1 GA-TAAA-TA
128 -ATAAATA
1 GATAAATA
135 GATAAATA
1 GATAAATA
143 GTAAATAAATA
1 G---ATAAATA
*
154 GA-GAATA
1 GATAAATA
*
161 GTTAAAAATA
1 G--ATAAATA
*
171 AATAAATA
1 GATAAATA
179 GATAAATA
1 GATAAATA
187 GTAAATAAATA
1 G---ATAAATA
198 GAT-AATA
1 GATAAATA
*
205 GTTAAAAATA
1 G--ATAAATA
*
215 AATAAATA
1 GATAAATA
223 GATAAATA
1 GATAAATA
231 G-TAAATA
1 GATAAATA
238 AATAGATAAT
Statistics
Matches: 174, Mismatches: 25, Indels: 61
0.67 0.10 0.23
Matches are distributed among these distances:
5 3 0.02
6 3 0.02
7 35 0.20
8 86 0.49
9 13 0.07
10 10 0.06
11 24 0.14
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (8 bp):
GATAAATA
Found at i:254 original size:19 final size:19
Alignment explanation
Indices: 69--250 Score: 139
Period size: 19 Copynumber: 9.7 Consensus size: 19
59 ATAAATAGAT
* *
69 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
*
89 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
108 AATAGATAATAATTAAATTAATA
1 AATAGAT-A-AA-T-AGTAAATA
131 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
150 AATAGA-GAATAGTTAA-A
1 AATAGATAAATAGTAAATA
*
167 AATAAATAAATAG---ATA
1 AATAGATAAATAGTAAATA
* *
183 AATAG-TAAATAAATAGAT-
1 AATAGATAAAT-AGTAAATA
* *
201 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
219 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
238 AATAGAT-AATAGT
1 AATAGATAAATAGT
251 TAAAAATAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 28
0.75 0.10 0.16
Matches are distributed among these distances:
15 6 0.05
16 6 0.05
17 12 0.09
18 33 0.25
19 46 0.35
20 10 0.08
21 4 0.03
22 2 0.02
23 13 0.10
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Found at i:3513 original size:46 final size:46
Alignment explanation
Indices: 3443--3560 Score: 191
Period size: 46 Copynumber: 2.6 Consensus size: 46
3433 TCCTGAAGTA
3443 AACCATGCATGAAAAGGCAATAGAAGGATGTAACTTAAAATCAGAC
1 AACCATGCATGAAAAGGCAATAGAAGGATGTAACTTAAAATCAGAC
* *
3489 AACCATGCATGAAAAGGCAGTAGAAGGATGTAATTTAAAATCAGAC
1 AACCATGCATGAAAAGGCAATAGAAGGATGTAACTTAAAATCAGAC
* * *
3535 AACAATGCGTGAAAAGGCAAAAGAAG
1 AACCATGCATGAAAAGGCAATAGAAG
3561 TTTACAACTG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.16
Consensus pattern (46 bp):
AACCATGCATGAAAAGGCAATAGAAGGATGTAACTTAAAATCAGAC
Done.