Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018966.1 Corchorus olitorius cultivar O-4 contig18999, 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: 1832
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Found at i:173 original size:12 final size:12
Alignment explanation
Indices: 156--189 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
146 CTCCATCAAG
156 AAATTCAAAAAA
1 AAATTCAAAAAA
168 AAATTC-AAAAA
1 AAATTCAAAAAA
179 AAA-TCAAAAAA
1 AAATTCAAAAAA
190 TCAAATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 13 0.62
12 6 0.29
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:179 original size:11 final size:11
Alignment explanation
Indices: 156--189 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
146 CTCCATCAAG
156 AAATTCAAAAAA
1 AAATTC-AAAAA
168 AAATTCAAAAA
1 AAATTCAAAAA
179 AAA-TCAAAAA
1 AAATTCAAAAA
189 A
1 A
190 TCAAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 8 0.36
12 6 0.27
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:217 original size:13 final size:14
Alignment explanation
Indices: 179--253 Score: 72
Period size: 13 Copynumber: 5.6 Consensus size: 14
169 AATTCAAAAA
179 AAATCAAAA--AAT
1 AAATCAAAATCAAT
*
191 CAAATCAAAGTCAAT
1 -AAATCAAAATCAAT
*
206 AAA-AAAAATCAAT
1 AAATCAAAATCAAT
219 CAAATCAAAATCAA-
1 -AAATCAAAATCAAT
233 AAATCAAAATC-A-
1 AAATCAAAATCAAT
245 AAATCAAAA
1 AAATCAAAA
254 GAGAATGGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.19
13 27 0.50
14 6 0.11
15 11 0.20
ACGTcount: A:0.68, C:0.15, G:0.01, T:0.16
Consensus pattern (14 bp):
AAATCAAAATCAAT
Found at i:220 original size:28 final size:28
Alignment explanation
Indices: 188--245 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
178 AAAATCAAAA
*
188 AATCAAATCAAAGTCAATAAA-AAAAATC
1 AATCAAATCAAAATCAA-AAATAAAAATC
*
216 AATCAAATCAAAATCAAAAATCAAAATC
1 AATCAAATCAAAATCAAAAATAAAAATC
244 AA
1 AA
246 AATCAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.17
Consensus pattern (28 bp):
AATCAAATCAAAATCAAAAATAAAAATC
Found at i:242 original size:19 final size:18
Alignment explanation
Indices: 216--253 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
206 AAAAAAAATC
216 AATCAAATCAAAATCAAA
1 AATCAAATCAAAATCAAA
234 AATCAAAATCAAAATCAAA
1 AATC-AAATCAAAATCAAA
253 A
1 A
254 GAGAATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (18 bp):
AATCAAATCAAAATCAAA
Found at i:253 original size:6 final size:6
Alignment explanation
Indices: 186--253 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
176 AAAAAATCAA
* **
186 AAAATC -AAATC AAAGTC AATAAAA AAAATC --AATC -AAATC AAAATC
1 AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC AAAATC
231 AAAAATC AAAATC AAAATC AAAA
1 -AAAATC AAAATC AAAATC AAAA
254 GAGAATGGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.08
5 9 0.18
6 29 0.57
7 9 0.18
ACGTcount: A:0.68, C:0.15, G:0.01, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:1079 original size:50 final size:50
Alignment explanation
Indices: 832--1063 Score: 340
Period size: 50 Copynumber: 4.6 Consensus size: 50
822 GAATATTTAC
*
832 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * * *
882 AGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * *
932 AATGAGATTGCATTTCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
**
982 AACGAGATTGCATTCCATTTGTGAG-CCTAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCC-AAGATCAAAATTCGCTTTTCAA
* *
1032 AATAAGATTGCACTCCATTTGTGAGACCAAGA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGA
1064 CCAACGGTCG
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
49 1 0.01
50 161 0.98
51 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:1741 original size:50 final size:50
Alignment explanation
Indices: 1680--1828 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
1670 TGCTTTGGCT
*
1680 TTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCC
1 TTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGCC
* * *
1730 TTTCCACAAGTCGAACTCGTTTCCATACGAGTCAATTATCAACACAGG-T
1 TTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGCC
*
1779 TTTCCATAAGCCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGC
1 TTTCCATAAG-TCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGC
1829 TTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 9 0.10
50 81 0.90
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
TTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGCC
Done.