Multiple sequence alignment - TraesCS1B01G141100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G141100 chr1B 100.000 3425 0 0 1 3425 188259734 188263158 0.000000e+00 6325
1 TraesCS1B01G141100 chr1D 95.874 3078 81 12 372 3425 123698301 123701356 0.000000e+00 4939
2 TraesCS1B01G141100 chr1A 95.603 3070 92 11 372 3425 135966450 135969492 0.000000e+00 4881
3 TraesCS1B01G141100 chr2D 85.064 1011 129 5 1324 2325 43284097 43285094 0.000000e+00 1011
4 TraesCS1B01G141100 chr2B 80.750 987 147 28 1362 2334 68149781 68150738 0.000000e+00 730
5 TraesCS1B01G141100 chr2B 94.681 376 17 3 1 373 36839006 36838631 6.370000e-162 580
6 TraesCS1B01G141100 chr3B 96.247 373 11 2 1 371 141865249 141865620 2.920000e-170 608
7 TraesCS1B01G141100 chr7B 95.710 373 13 2 1 371 351929755 351929384 6.330000e-167 597
8 TraesCS1B01G141100 chr7B 95.187 374 16 2 1 373 246018821 246018449 1.060000e-164 590
9 TraesCS1B01G141100 chr4B 95.664 369 14 2 1 367 671836965 671837333 2.940000e-165 592
10 TraesCS1B01G141100 chr4A 95.174 373 15 2 1 371 637414250 637413879 1.370000e-163 586
11 TraesCS1B01G141100 chr6B 94.086 372 21 1 3 373 569047738 569048109 6.420000e-157 564
12 TraesCS1B01G141100 chr5B 93.834 373 20 2 1 371 384739591 384739962 2.990000e-155 558
13 TraesCS1B01G141100 chr5B 93.122 378 18 4 1 371 679824126 679824502 6.460000e-152 547
14 TraesCS1B01G141100 chr3A 74.058 902 189 34 1391 2265 77411061 77410178 9.160000e-86 327
15 TraesCS1B01G141100 chr2A 82.770 296 41 6 1548 1834 44849736 44850030 4.390000e-64 255
16 TraesCS1B01G141100 chr3D 72.512 844 189 32 1448 2265 66310396 66311222 2.060000e-57 233


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G141100 chr1B 188259734 188263158 3424 False 6325 6325 100.000 1 3425 1 chr1B.!!$F1 3424
1 TraesCS1B01G141100 chr1D 123698301 123701356 3055 False 4939 4939 95.874 372 3425 1 chr1D.!!$F1 3053
2 TraesCS1B01G141100 chr1A 135966450 135969492 3042 False 4881 4881 95.603 372 3425 1 chr1A.!!$F1 3053
3 TraesCS1B01G141100 chr2D 43284097 43285094 997 False 1011 1011 85.064 1324 2325 1 chr2D.!!$F1 1001
4 TraesCS1B01G141100 chr2B 68149781 68150738 957 False 730 730 80.750 1362 2334 1 chr2B.!!$F1 972
5 TraesCS1B01G141100 chr3A 77410178 77411061 883 True 327 327 74.058 1391 2265 1 chr3A.!!$R1 874
6 TraesCS1B01G141100 chr3D 66310396 66311222 826 False 233 233 72.512 1448 2265 1 chr3D.!!$F1 817

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
25 26 0.034896 CCCGCCTAGGCACGATTATT 59.965 55.0 32.47 0.00 42.06 1.40 F
224 225 0.524414 AAAAGTTAATCGGGCCGTGC 59.476 50.0 27.32 12.25 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1949 3.882326 CCAGGGAGGCCGATGCAT 61.882 66.667 0.00 0.0 40.13 3.96 R
2428 2475 0.316689 GTTTTGACACGGCGAACAGG 60.317 55.000 16.62 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.134879 CCCGCCTAGGCACGATTA 58.865 61.111 32.47 0.00 42.06 1.75
24 25 1.671742 CCCGCCTAGGCACGATTAT 59.328 57.895 32.47 0.00 42.06 1.28
25 26 0.034896 CCCGCCTAGGCACGATTATT 59.965 55.000 32.47 0.00 42.06 1.40
26 27 1.274167 CCCGCCTAGGCACGATTATTA 59.726 52.381 32.47 0.00 42.06 0.98
27 28 2.093658 CCCGCCTAGGCACGATTATTAT 60.094 50.000 32.47 0.00 42.06 1.28
28 29 3.131577 CCCGCCTAGGCACGATTATTATA 59.868 47.826 32.47 0.00 42.06 0.98
29 30 4.110482 CCGCCTAGGCACGATTATTATAC 58.890 47.826 32.47 0.00 42.06 1.47
30 31 3.789756 CGCCTAGGCACGATTATTATACG 59.210 47.826 32.47 7.82 42.06 3.06
31 32 4.110482 GCCTAGGCACGATTATTATACGG 58.890 47.826 29.33 0.00 41.49 4.02
32 33 4.679662 CCTAGGCACGATTATTATACGGG 58.320 47.826 0.00 0.00 0.00 5.28
36 37 2.950433 CACGATTATTATACGGGCCGT 58.050 47.619 35.91 35.91 44.35 5.68
37 38 2.664568 CACGATTATTATACGGGCCGTG 59.335 50.000 39.80 22.32 41.39 4.94
38 39 1.657094 CGATTATTATACGGGCCGTGC 59.343 52.381 39.80 16.99 41.39 5.34
89 90 4.230002 GGCACGGCCCGTATGCTA 62.230 66.667 9.25 0.00 44.06 3.49
90 91 2.202960 GCACGGCCCGTATGCTAA 60.203 61.111 9.25 0.00 38.32 3.09
91 92 1.597027 GCACGGCCCGTATGCTAAT 60.597 57.895 9.25 0.00 38.32 1.73
92 93 1.566018 GCACGGCCCGTATGCTAATC 61.566 60.000 9.25 0.00 38.32 1.75
93 94 1.006571 ACGGCCCGTATGCTAATCG 60.007 57.895 7.20 0.00 38.73 3.34
94 95 1.736645 CGGCCCGTATGCTAATCGG 60.737 63.158 0.00 0.00 43.30 4.18
97 98 4.278956 CCGTATGCTAATCGGGCC 57.721 61.111 0.00 0.00 40.49 5.80
98 99 1.736645 CCGTATGCTAATCGGGCCG 60.737 63.158 22.51 22.51 40.49 6.13
99 100 1.736645 CGTATGCTAATCGGGCCGG 60.737 63.158 27.98 11.17 0.00 6.13
100 101 2.033194 GTATGCTAATCGGGCCGGC 61.033 63.158 27.98 21.18 0.00 6.13
101 102 3.248446 TATGCTAATCGGGCCGGCC 62.248 63.158 38.57 38.57 0.00 6.13
123 124 2.345991 GGCACGTCAAGCCCACTA 59.654 61.111 4.06 0.00 46.50 2.74
124 125 1.302192 GGCACGTCAAGCCCACTAA 60.302 57.895 4.06 0.00 46.50 2.24
125 126 0.676782 GGCACGTCAAGCCCACTAAT 60.677 55.000 4.06 0.00 46.50 1.73
126 127 0.727398 GCACGTCAAGCCCACTAATC 59.273 55.000 0.00 0.00 0.00 1.75
127 128 1.676014 GCACGTCAAGCCCACTAATCT 60.676 52.381 0.00 0.00 0.00 2.40
128 129 2.418197 GCACGTCAAGCCCACTAATCTA 60.418 50.000 0.00 0.00 0.00 1.98
129 130 3.187700 CACGTCAAGCCCACTAATCTAC 58.812 50.000 0.00 0.00 0.00 2.59
130 131 2.167900 ACGTCAAGCCCACTAATCTACC 59.832 50.000 0.00 0.00 0.00 3.18
131 132 2.431057 CGTCAAGCCCACTAATCTACCT 59.569 50.000 0.00 0.00 0.00 3.08
132 133 3.491104 CGTCAAGCCCACTAATCTACCTC 60.491 52.174 0.00 0.00 0.00 3.85
133 134 3.039011 TCAAGCCCACTAATCTACCTCC 58.961 50.000 0.00 0.00 0.00 4.30
134 135 3.041946 CAAGCCCACTAATCTACCTCCT 58.958 50.000 0.00 0.00 0.00 3.69
135 136 4.078805 TCAAGCCCACTAATCTACCTCCTA 60.079 45.833 0.00 0.00 0.00 2.94
136 137 4.768807 AGCCCACTAATCTACCTCCTAT 57.231 45.455 0.00 0.00 0.00 2.57
137 138 5.094569 AGCCCACTAATCTACCTCCTATT 57.905 43.478 0.00 0.00 0.00 1.73
138 139 5.477913 AGCCCACTAATCTACCTCCTATTT 58.522 41.667 0.00 0.00 0.00 1.40
139 140 5.544562 AGCCCACTAATCTACCTCCTATTTC 59.455 44.000 0.00 0.00 0.00 2.17
140 141 5.567025 GCCCACTAATCTACCTCCTATTTCG 60.567 48.000 0.00 0.00 0.00 3.46
141 142 5.471257 CCACTAATCTACCTCCTATTTCGC 58.529 45.833 0.00 0.00 0.00 4.70
142 143 5.154932 CACTAATCTACCTCCTATTTCGCG 58.845 45.833 0.00 0.00 0.00 5.87
143 144 2.726832 ATCTACCTCCTATTTCGCGC 57.273 50.000 0.00 0.00 0.00 6.86
144 145 1.395635 TCTACCTCCTATTTCGCGCA 58.604 50.000 8.75 0.00 0.00 6.09
145 146 1.961394 TCTACCTCCTATTTCGCGCAT 59.039 47.619 8.75 0.00 0.00 4.73
146 147 2.364324 TCTACCTCCTATTTCGCGCATT 59.636 45.455 8.75 0.00 0.00 3.56
147 148 2.038387 ACCTCCTATTTCGCGCATTT 57.962 45.000 8.75 0.00 0.00 2.32
148 149 3.188159 ACCTCCTATTTCGCGCATTTA 57.812 42.857 8.75 0.00 0.00 1.40
149 150 3.131396 ACCTCCTATTTCGCGCATTTAG 58.869 45.455 8.75 2.40 0.00 1.85
150 151 2.096218 CCTCCTATTTCGCGCATTTAGC 60.096 50.000 8.75 0.00 40.87 3.09
162 163 3.487563 GCATTTAGCGTTTTGTAGCCT 57.512 42.857 0.00 0.00 0.00 4.58
163 164 4.609691 GCATTTAGCGTTTTGTAGCCTA 57.390 40.909 0.00 0.00 0.00 3.93
164 165 5.169836 GCATTTAGCGTTTTGTAGCCTAT 57.830 39.130 0.00 0.00 0.00 2.57
165 166 5.578776 GCATTTAGCGTTTTGTAGCCTATT 58.421 37.500 0.00 0.00 0.00 1.73
166 167 6.033966 GCATTTAGCGTTTTGTAGCCTATTT 58.966 36.000 0.00 0.00 0.00 1.40
167 168 6.530181 GCATTTAGCGTTTTGTAGCCTATTTT 59.470 34.615 0.00 0.00 0.00 1.82
168 169 7.062956 GCATTTAGCGTTTTGTAGCCTATTTTT 59.937 33.333 0.00 0.00 0.00 1.94
169 170 9.562583 CATTTAGCGTTTTGTAGCCTATTTTTA 57.437 29.630 0.00 0.00 0.00 1.52
171 172 9.777575 TTTAGCGTTTTGTAGCCTATTTTTATC 57.222 29.630 0.00 0.00 0.00 1.75
172 173 7.625828 AGCGTTTTGTAGCCTATTTTTATCT 57.374 32.000 0.00 0.00 0.00 1.98
173 174 7.472543 AGCGTTTTGTAGCCTATTTTTATCTG 58.527 34.615 0.00 0.00 0.00 2.90
174 175 7.120726 AGCGTTTTGTAGCCTATTTTTATCTGT 59.879 33.333 0.00 0.00 0.00 3.41
175 176 7.753580 GCGTTTTGTAGCCTATTTTTATCTGTT 59.246 33.333 0.00 0.00 0.00 3.16
176 177 9.061610 CGTTTTGTAGCCTATTTTTATCTGTTG 57.938 33.333 0.00 0.00 0.00 3.33
177 178 9.353999 GTTTTGTAGCCTATTTTTATCTGTTGG 57.646 33.333 0.00 0.00 0.00 3.77
178 179 6.693315 TGTAGCCTATTTTTATCTGTTGGC 57.307 37.500 0.00 0.00 39.40 4.52
179 180 5.592688 TGTAGCCTATTTTTATCTGTTGGCC 59.407 40.000 0.00 0.00 39.90 5.36
180 181 3.960755 AGCCTATTTTTATCTGTTGGCCC 59.039 43.478 0.00 0.00 39.90 5.80
181 182 3.704061 GCCTATTTTTATCTGTTGGCCCA 59.296 43.478 0.00 0.00 33.66 5.36
182 183 4.344968 GCCTATTTTTATCTGTTGGCCCAT 59.655 41.667 0.00 0.00 33.66 4.00
183 184 5.538433 GCCTATTTTTATCTGTTGGCCCATA 59.462 40.000 0.00 0.00 33.66 2.74
184 185 6.211384 GCCTATTTTTATCTGTTGGCCCATAT 59.789 38.462 0.00 0.00 33.66 1.78
185 186 7.256296 GCCTATTTTTATCTGTTGGCCCATATT 60.256 37.037 0.00 0.00 33.66 1.28
186 187 9.308000 CCTATTTTTATCTGTTGGCCCATATTA 57.692 33.333 0.00 0.00 0.00 0.98
188 189 7.595819 TTTTTATCTGTTGGCCCATATTAGG 57.404 36.000 0.00 0.00 0.00 2.69
189 190 6.523035 TTTATCTGTTGGCCCATATTAGGA 57.477 37.500 0.00 0.00 0.00 2.94
190 191 6.718593 TTATCTGTTGGCCCATATTAGGAT 57.281 37.500 0.00 0.00 0.00 3.24
191 192 7.822749 TTATCTGTTGGCCCATATTAGGATA 57.177 36.000 0.00 0.00 0.00 2.59
192 193 5.499004 TCTGTTGGCCCATATTAGGATAC 57.501 43.478 0.00 0.00 0.00 2.24
193 194 4.910913 TCTGTTGGCCCATATTAGGATACA 59.089 41.667 0.00 0.00 41.41 2.29
194 195 5.551583 TCTGTTGGCCCATATTAGGATACAT 59.448 40.000 0.00 0.00 41.41 2.29
195 196 6.733334 TCTGTTGGCCCATATTAGGATACATA 59.267 38.462 0.00 0.00 41.41 2.29
196 197 7.238723 TCTGTTGGCCCATATTAGGATACATAA 59.761 37.037 0.00 0.00 41.41 1.90
197 198 7.760607 TGTTGGCCCATATTAGGATACATAAA 58.239 34.615 0.00 0.00 41.41 1.40
198 199 8.228206 TGTTGGCCCATATTAGGATACATAAAA 58.772 33.333 0.00 0.00 41.41 1.52
199 200 9.084533 GTTGGCCCATATTAGGATACATAAAAA 57.915 33.333 0.00 0.00 41.41 1.94
224 225 0.524414 AAAAGTTAATCGGGCCGTGC 59.476 50.000 27.32 12.25 0.00 5.34
262 263 2.592308 CCCTTCAGGCCTAGGCAC 59.408 66.667 34.09 22.83 44.11 5.01
263 264 2.187946 CCTTCAGGCCTAGGCACG 59.812 66.667 34.09 23.65 44.11 5.34
264 265 2.187946 CTTCAGGCCTAGGCACGG 59.812 66.667 34.09 22.65 44.11 4.94
265 266 4.096003 TTCAGGCCTAGGCACGGC 62.096 66.667 34.09 17.37 46.83 5.68
309 310 4.097863 GCCCGTTTAGCACGTGCC 62.098 66.667 35.51 19.74 45.60 5.01
350 351 4.581093 GGCCGGCCCAACTATCCC 62.581 72.222 36.64 5.01 0.00 3.85
351 352 4.929707 GCCGGCCCAACTATCCCG 62.930 72.222 18.11 0.00 40.39 5.14
353 354 4.929707 CGGCCCAACTATCCCGGC 62.930 72.222 0.00 0.00 40.85 6.13
355 356 4.581093 GCCCAACTATCCCGGCCC 62.581 72.222 0.00 0.00 35.23 5.80
356 357 4.250305 CCCAACTATCCCGGCCCG 62.250 72.222 0.00 0.00 0.00 6.13
357 358 3.476419 CCAACTATCCCGGCCCGT 61.476 66.667 0.85 0.00 0.00 5.28
358 359 2.587889 CAACTATCCCGGCCCGTT 59.412 61.111 0.85 0.00 0.00 4.44
359 360 1.078001 CAACTATCCCGGCCCGTTT 60.078 57.895 0.85 0.00 0.00 3.60
360 361 1.078001 AACTATCCCGGCCCGTTTG 60.078 57.895 0.85 0.00 0.00 2.93
361 362 2.203153 CTATCCCGGCCCGTTTGG 60.203 66.667 0.85 0.00 37.09 3.28
405 406 1.299926 CGCGTAGGCACCCATAGAC 60.300 63.158 8.32 0.00 39.92 2.59
542 543 0.874390 CCAAATCAGTCCACCACACG 59.126 55.000 0.00 0.00 0.00 4.49
576 577 3.913370 TCCTTTTCCATTTTCCCCTCA 57.087 42.857 0.00 0.00 0.00 3.86
577 578 4.206244 TCCTTTTCCATTTTCCCCTCAA 57.794 40.909 0.00 0.00 0.00 3.02
671 672 2.294078 CCACTCGCTTTCCTCCCCT 61.294 63.158 0.00 0.00 0.00 4.79
673 674 1.229209 ACTCGCTTTCCTCCCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
674 675 1.219393 CTCGCTTTCCTCCCCTCAC 59.781 63.158 0.00 0.00 0.00 3.51
675 676 2.245438 CTCGCTTTCCTCCCCTCACC 62.245 65.000 0.00 0.00 0.00 4.02
676 677 2.677848 GCTTTCCTCCCCTCACCC 59.322 66.667 0.00 0.00 0.00 4.61
677 678 2.990479 CTTTCCTCCCCTCACCCG 59.010 66.667 0.00 0.00 0.00 5.28
783 785 3.947910 AATTTTAGTCTCCCGTCACGA 57.052 42.857 0.00 0.00 0.00 4.35
794 796 2.219562 CGTCACGAATACCGCGTCC 61.220 63.158 4.92 0.00 40.44 4.79
795 797 2.100797 TCACGAATACCGCGTCCG 59.899 61.111 4.92 3.29 40.44 4.79
796 798 2.202518 CACGAATACCGCGTCCGT 60.203 61.111 4.92 3.97 40.44 4.69
797 799 2.100991 ACGAATACCGCGTCCGTC 59.899 61.111 4.92 0.00 43.32 4.79
879 883 1.169661 CCATCTCCTCCTCCTCGTCG 61.170 65.000 0.00 0.00 0.00 5.12
882 886 2.125229 TCCTCCTCCTCGTCGTCG 60.125 66.667 0.00 0.00 38.55 5.12
886 900 1.500512 CTCCTCCTCGTCGTCGATCC 61.501 65.000 5.00 0.00 45.21 3.36
939 953 2.415625 CGACTGCCAGTACTGTACTTCC 60.416 54.545 21.18 11.65 36.76 3.46
942 956 1.542915 TGCCAGTACTGTACTTCCGAC 59.457 52.381 21.18 6.62 36.76 4.79
990 1004 0.606944 AGCCAAGACTCGACGAGACT 60.607 55.000 30.56 25.76 36.37 3.24
1142 1156 1.227176 CCTTCCCTTACTACGGCGC 60.227 63.158 6.90 0.00 0.00 6.53
1227 1253 4.453480 AATGACTGGTCAAGGAAGGAAA 57.547 40.909 7.53 0.00 43.58 3.13
1735 1773 2.935481 CCTCCAGGTTCCAGGCCA 60.935 66.667 5.01 0.00 0.00 5.36
1746 1784 2.597340 CAGGCCATGTCCGGGATT 59.403 61.111 5.01 0.00 0.00 3.01
1911 1949 4.424566 GGCGCCTTCACGGACGTA 62.425 66.667 22.15 0.00 35.59 3.57
2428 2475 1.540580 GCGTTACATTCCTCTAGGGGC 60.541 57.143 2.72 0.00 35.41 5.80
2435 2482 0.976073 TTCCTCTAGGGGCCTGTTCG 60.976 60.000 2.72 0.00 35.41 3.95
2528 2575 4.686091 CAGTTCAGAACATACAGCTTTCGA 59.314 41.667 15.85 0.00 0.00 3.71
2621 2669 1.665679 ACGTAGCGCATTCAAATCTGG 59.334 47.619 11.47 0.00 0.00 3.86
2657 2705 9.903682 CATAATGTGGAAGGAATTCACAATATC 57.096 33.333 7.93 0.00 43.38 1.63
2886 2934 2.371841 ACAAGCACCATTCTGTGAGGTA 59.628 45.455 0.00 0.00 38.55 3.08
2920 2968 5.188555 TGGAAATCTGACTCTCACTTGCTAT 59.811 40.000 0.00 0.00 0.00 2.97
2959 3007 1.146263 ATTTCCATCCGGGTCTCGC 59.854 57.895 0.00 0.00 38.11 5.03
2980 3028 2.954684 AAAGATCGCTGGTCGCCCA 61.955 57.895 0.00 0.00 38.87 5.36
3080 3128 7.064728 ACGATAGAGAAATTTTGTGAGGCTAAC 59.935 37.037 0.00 0.00 41.38 2.34
3108 3156 6.913873 ATCCAGCATAATGAATTGCAAAAC 57.086 33.333 1.71 0.80 41.35 2.43
3225 3273 6.034363 CAGTGAGTCTTTATGTTCTCATGTCG 59.966 42.308 0.00 0.00 38.80 4.35
3246 3294 1.971149 AGAGATGGGAATGTGGGTGA 58.029 50.000 0.00 0.00 0.00 4.02
3275 3323 3.074504 TGTGGACGTAATATGCTCGAC 57.925 47.619 0.00 0.00 0.00 4.20
3310 3358 8.593492 AATCAATTGACCAGTCTTTTAAAAGC 57.407 30.769 20.93 15.92 35.99 3.51
3322 3370 9.985318 CAGTCTTTTAAAAGCTTATCTGATCAG 57.015 33.333 20.93 17.07 35.99 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.034896 AATAATCGTGCCTAGGCGGG 59.965 55.000 28.28 21.60 45.51 6.13
7 8 2.736144 TAATAATCGTGCCTAGGCGG 57.264 50.000 28.28 21.97 45.51 6.13
8 9 3.789756 CGTATAATAATCGTGCCTAGGCG 59.210 47.826 28.28 15.51 45.51 5.52
9 10 4.110482 CCGTATAATAATCGTGCCTAGGC 58.890 47.826 27.71 27.71 42.35 3.93
10 11 4.679662 CCCGTATAATAATCGTGCCTAGG 58.320 47.826 3.67 3.67 0.00 3.02
11 12 4.110482 GCCCGTATAATAATCGTGCCTAG 58.890 47.826 0.00 0.00 0.00 3.02
12 13 3.119029 GGCCCGTATAATAATCGTGCCTA 60.119 47.826 0.00 0.00 42.74 3.93
13 14 2.354403 GGCCCGTATAATAATCGTGCCT 60.354 50.000 0.00 0.00 42.74 4.75
14 15 2.004733 GGCCCGTATAATAATCGTGCC 58.995 52.381 0.00 0.00 40.23 5.01
15 16 1.657094 CGGCCCGTATAATAATCGTGC 59.343 52.381 0.00 0.00 0.00 5.34
16 17 2.664568 CACGGCCCGTATAATAATCGTG 59.335 50.000 9.25 0.00 38.32 4.35
17 18 2.927871 GCACGGCCCGTATAATAATCGT 60.928 50.000 9.25 0.00 38.32 3.73
18 19 1.657094 GCACGGCCCGTATAATAATCG 59.343 52.381 9.25 0.00 38.32 3.34
19 20 2.004733 GGCACGGCCCGTATAATAATC 58.995 52.381 9.25 0.00 44.06 1.75
20 21 2.103537 GGCACGGCCCGTATAATAAT 57.896 50.000 9.25 0.00 44.06 1.28
21 22 3.610637 GGCACGGCCCGTATAATAA 57.389 52.632 9.25 0.00 44.06 1.40
73 74 1.566018 GATTAGCATACGGGCCGTGC 61.566 60.000 39.80 33.49 41.39 5.34
74 75 1.282248 CGATTAGCATACGGGCCGTG 61.282 60.000 39.80 25.77 41.39 4.94
75 76 1.006571 CGATTAGCATACGGGCCGT 60.007 57.895 35.91 35.91 44.35 5.68
76 77 1.736645 CCGATTAGCATACGGGCCG 60.737 63.158 27.06 27.06 42.48 6.13
77 78 4.278956 CCGATTAGCATACGGGCC 57.721 61.111 0.00 0.00 42.48 5.80
80 81 1.736645 CGGCCCGATTAGCATACGG 60.737 63.158 0.00 0.00 45.24 4.02
81 82 1.736645 CCGGCCCGATTAGCATACG 60.737 63.158 3.71 0.00 0.00 3.06
82 83 2.033194 GCCGGCCCGATTAGCATAC 61.033 63.158 18.11 0.00 0.00 2.39
83 84 2.345991 GCCGGCCCGATTAGCATA 59.654 61.111 18.11 0.00 0.00 3.14
84 85 4.643387 GGCCGGCCCGATTAGCAT 62.643 66.667 36.64 0.00 0.00 3.79
107 108 0.727398 GATTAGTGGGCTTGACGTGC 59.273 55.000 0.00 0.00 0.00 5.34
108 109 2.386661 AGATTAGTGGGCTTGACGTG 57.613 50.000 0.00 0.00 0.00 4.49
109 110 2.167900 GGTAGATTAGTGGGCTTGACGT 59.832 50.000 0.00 0.00 0.00 4.34
110 111 2.431057 AGGTAGATTAGTGGGCTTGACG 59.569 50.000 0.00 0.00 0.00 4.35
111 112 3.181464 GGAGGTAGATTAGTGGGCTTGAC 60.181 52.174 0.00 0.00 0.00 3.18
112 113 3.039011 GGAGGTAGATTAGTGGGCTTGA 58.961 50.000 0.00 0.00 0.00 3.02
113 114 3.041946 AGGAGGTAGATTAGTGGGCTTG 58.958 50.000 0.00 0.00 0.00 4.01
114 115 3.423058 AGGAGGTAGATTAGTGGGCTT 57.577 47.619 0.00 0.00 0.00 4.35
115 116 4.768807 ATAGGAGGTAGATTAGTGGGCT 57.231 45.455 0.00 0.00 0.00 5.19
116 117 5.567025 CGAAATAGGAGGTAGATTAGTGGGC 60.567 48.000 0.00 0.00 0.00 5.36
117 118 5.567025 GCGAAATAGGAGGTAGATTAGTGGG 60.567 48.000 0.00 0.00 0.00 4.61
118 119 5.471257 GCGAAATAGGAGGTAGATTAGTGG 58.529 45.833 0.00 0.00 0.00 4.00
119 120 5.154932 CGCGAAATAGGAGGTAGATTAGTG 58.845 45.833 0.00 0.00 0.00 2.74
120 121 4.321082 GCGCGAAATAGGAGGTAGATTAGT 60.321 45.833 12.10 0.00 0.00 2.24
121 122 4.167268 GCGCGAAATAGGAGGTAGATTAG 58.833 47.826 12.10 0.00 0.00 1.73
122 123 3.570975 TGCGCGAAATAGGAGGTAGATTA 59.429 43.478 12.10 0.00 0.00 1.75
123 124 2.364324 TGCGCGAAATAGGAGGTAGATT 59.636 45.455 12.10 0.00 0.00 2.40
124 125 1.961394 TGCGCGAAATAGGAGGTAGAT 59.039 47.619 12.10 0.00 0.00 1.98
125 126 1.395635 TGCGCGAAATAGGAGGTAGA 58.604 50.000 12.10 0.00 0.00 2.59
126 127 2.440539 ATGCGCGAAATAGGAGGTAG 57.559 50.000 12.10 0.00 0.00 3.18
127 128 2.902705 AATGCGCGAAATAGGAGGTA 57.097 45.000 12.10 0.00 0.00 3.08
128 129 2.038387 AAATGCGCGAAATAGGAGGT 57.962 45.000 12.10 0.00 0.00 3.85
129 130 2.096218 GCTAAATGCGCGAAATAGGAGG 60.096 50.000 12.10 0.00 0.00 4.30
130 131 3.174799 GCTAAATGCGCGAAATAGGAG 57.825 47.619 12.10 2.23 0.00 3.69
142 143 3.487563 AGGCTACAAAACGCTAAATGC 57.512 42.857 0.00 0.00 38.57 3.56
143 144 8.460831 AAAAATAGGCTACAAAACGCTAAATG 57.539 30.769 0.00 0.00 0.00 2.32
145 146 9.777575 GATAAAAATAGGCTACAAAACGCTAAA 57.222 29.630 0.00 0.00 0.00 1.85
146 147 9.169592 AGATAAAAATAGGCTACAAAACGCTAA 57.830 29.630 0.00 0.00 0.00 3.09
147 148 8.609176 CAGATAAAAATAGGCTACAAAACGCTA 58.391 33.333 0.00 0.00 0.00 4.26
148 149 7.120726 ACAGATAAAAATAGGCTACAAAACGCT 59.879 33.333 0.00 0.00 0.00 5.07
149 150 7.248437 ACAGATAAAAATAGGCTACAAAACGC 58.752 34.615 0.00 0.00 0.00 4.84
150 151 9.061610 CAACAGATAAAAATAGGCTACAAAACG 57.938 33.333 0.00 0.00 0.00 3.60
151 152 9.353999 CCAACAGATAAAAATAGGCTACAAAAC 57.646 33.333 0.00 0.00 0.00 2.43
152 153 8.032451 GCCAACAGATAAAAATAGGCTACAAAA 58.968 33.333 0.00 0.00 37.89 2.44
153 154 7.363443 GGCCAACAGATAAAAATAGGCTACAAA 60.363 37.037 0.00 0.00 40.61 2.83
154 155 6.096282 GGCCAACAGATAAAAATAGGCTACAA 59.904 38.462 0.00 0.00 40.61 2.41
155 156 5.592688 GGCCAACAGATAAAAATAGGCTACA 59.407 40.000 0.00 0.00 40.61 2.74
156 157 5.009710 GGGCCAACAGATAAAAATAGGCTAC 59.990 44.000 4.39 0.00 40.61 3.58
157 158 5.137551 GGGCCAACAGATAAAAATAGGCTA 58.862 41.667 4.39 0.00 40.61 3.93
158 159 3.960755 GGGCCAACAGATAAAAATAGGCT 59.039 43.478 4.39 0.00 40.61 4.58
159 160 3.704061 TGGGCCAACAGATAAAAATAGGC 59.296 43.478 2.13 0.00 40.08 3.93
160 161 7.781324 ATATGGGCCAACAGATAAAAATAGG 57.219 36.000 11.89 0.00 0.00 2.57
162 163 9.308000 CCTAATATGGGCCAACAGATAAAAATA 57.692 33.333 11.89 0.00 0.00 1.40
163 164 8.010105 TCCTAATATGGGCCAACAGATAAAAAT 58.990 33.333 11.89 0.00 0.00 1.82
164 165 7.358263 TCCTAATATGGGCCAACAGATAAAAA 58.642 34.615 11.89 0.00 0.00 1.94
165 166 6.916909 TCCTAATATGGGCCAACAGATAAAA 58.083 36.000 11.89 0.00 0.00 1.52
166 167 6.523035 TCCTAATATGGGCCAACAGATAAA 57.477 37.500 11.89 0.00 0.00 1.40
167 168 6.718593 ATCCTAATATGGGCCAACAGATAA 57.281 37.500 11.89 0.00 0.00 1.75
168 169 6.733334 TGTATCCTAATATGGGCCAACAGATA 59.267 38.462 11.89 8.94 0.00 1.98
169 170 5.551583 TGTATCCTAATATGGGCCAACAGAT 59.448 40.000 11.89 9.94 0.00 2.90
170 171 4.910913 TGTATCCTAATATGGGCCAACAGA 59.089 41.667 11.89 2.12 0.00 3.41
171 172 5.241403 TGTATCCTAATATGGGCCAACAG 57.759 43.478 11.89 5.14 0.00 3.16
172 173 5.858876 ATGTATCCTAATATGGGCCAACA 57.141 39.130 11.89 7.42 0.00 3.33
173 174 8.644374 TTTTATGTATCCTAATATGGGCCAAC 57.356 34.615 11.89 0.35 0.00 3.77
204 205 1.068125 GCACGGCCCGATTAACTTTTT 60.068 47.619 11.71 0.00 0.00 1.94
205 206 0.524414 GCACGGCCCGATTAACTTTT 59.476 50.000 11.71 0.00 0.00 2.27
206 207 1.310216 GGCACGGCCCGATTAACTTT 61.310 55.000 11.71 0.00 44.06 2.66
207 208 1.747745 GGCACGGCCCGATTAACTT 60.748 57.895 11.71 0.00 44.06 2.66
208 209 2.124860 GGCACGGCCCGATTAACT 60.125 61.111 11.71 0.00 44.06 2.24
245 246 2.592308 GTGCCTAGGCCTGAAGGG 59.408 66.667 30.81 15.41 41.09 3.95
246 247 2.187946 CGTGCCTAGGCCTGAAGG 59.812 66.667 30.81 17.05 41.09 3.46
247 248 2.187946 CCGTGCCTAGGCCTGAAG 59.812 66.667 30.81 14.39 41.09 3.02
333 334 4.581093 GGGATAGTTGGGCCGGCC 62.581 72.222 38.57 38.57 0.00 6.13
334 335 4.929707 CGGGATAGTTGGGCCGGC 62.930 72.222 21.18 21.18 0.00 6.13
335 336 4.250305 CCGGGATAGTTGGGCCGG 62.250 72.222 0.00 0.00 34.60 6.13
336 337 4.929707 GCCGGGATAGTTGGGCCG 62.930 72.222 2.18 0.00 39.67 6.13
338 339 4.581093 GGGCCGGGATAGTTGGGC 62.581 72.222 2.18 0.00 46.84 5.36
339 340 4.250305 CGGGCCGGGATAGTTGGG 62.250 72.222 20.56 0.00 0.00 4.12
340 341 2.546114 AAACGGGCCGGGATAGTTGG 62.546 60.000 31.78 0.00 0.00 3.77
341 342 1.078001 AAACGGGCCGGGATAGTTG 60.078 57.895 31.78 0.00 0.00 3.16
342 343 1.078001 CAAACGGGCCGGGATAGTT 60.078 57.895 31.78 11.46 0.00 2.24
343 344 2.587889 CAAACGGGCCGGGATAGT 59.412 61.111 31.78 4.41 0.00 2.12
344 345 2.203153 CCAAACGGGCCGGGATAG 60.203 66.667 31.78 14.48 0.00 2.08
353 354 0.180406 ACTATAGCTGGCCAAACGGG 59.820 55.000 7.01 0.00 40.85 5.28
354 355 1.299541 CACTATAGCTGGCCAAACGG 58.700 55.000 7.01 0.00 0.00 4.44
355 356 1.299541 CCACTATAGCTGGCCAAACG 58.700 55.000 7.01 0.00 0.00 3.60
362 363 0.109086 CGGATCGCCACTATAGCTGG 60.109 60.000 13.86 13.86 0.00 4.85
363 364 0.109086 CCGGATCGCCACTATAGCTG 60.109 60.000 0.00 0.00 0.00 4.24
364 365 0.539901 ACCGGATCGCCACTATAGCT 60.540 55.000 9.46 0.00 0.00 3.32
365 366 0.317479 AACCGGATCGCCACTATAGC 59.683 55.000 9.46 0.00 0.00 2.97
366 367 1.611977 TCAACCGGATCGCCACTATAG 59.388 52.381 9.46 0.00 0.00 1.31
367 368 1.338973 GTCAACCGGATCGCCACTATA 59.661 52.381 9.46 0.00 0.00 1.31
368 369 0.104304 GTCAACCGGATCGCCACTAT 59.896 55.000 9.46 0.00 0.00 2.12
369 370 1.514087 GTCAACCGGATCGCCACTA 59.486 57.895 9.46 0.00 0.00 2.74
370 371 2.264794 GTCAACCGGATCGCCACT 59.735 61.111 9.46 0.00 0.00 4.00
405 406 1.134521 TGTATGGCCGGCTAGTCTTTG 60.135 52.381 28.56 0.00 0.00 2.77
479 480 1.906824 GGAGTGGTGGACTGACCGA 60.907 63.158 0.00 0.00 42.61 4.69
542 543 6.737254 TGGAAAAGGAAAATATCGTCTGTC 57.263 37.500 0.00 0.00 0.00 3.51
576 577 4.320870 CCGCAACGGGGTTCTATTATATT 58.679 43.478 0.00 0.00 44.15 1.28
577 578 3.934068 CCGCAACGGGGTTCTATTATAT 58.066 45.455 0.00 0.00 44.15 0.86
671 672 2.993264 GGGAGAACGGACGGGTGA 60.993 66.667 0.00 0.00 0.00 4.02
673 674 4.626402 TGGGGAGAACGGACGGGT 62.626 66.667 0.00 0.00 0.00 5.28
674 675 4.078516 GTGGGGAGAACGGACGGG 62.079 72.222 0.00 0.00 0.00 5.28
675 676 4.078516 GGTGGGGAGAACGGACGG 62.079 72.222 0.00 0.00 0.00 4.79
676 677 4.078516 GGGTGGGGAGAACGGACG 62.079 72.222 0.00 0.00 0.00 4.79
677 678 4.078516 CGGGTGGGGAGAACGGAC 62.079 72.222 0.00 0.00 0.00 4.79
783 785 3.841758 GGGGACGGACGCGGTATT 61.842 66.667 12.47 0.00 0.00 1.89
879 883 1.253100 GGATGAGGAGGAGGATCGAC 58.747 60.000 0.00 0.00 34.37 4.20
882 886 1.540435 GCGGGATGAGGAGGAGGATC 61.540 65.000 0.00 0.00 0.00 3.36
886 900 2.835431 ACGCGGGATGAGGAGGAG 60.835 66.667 12.47 0.00 0.00 3.69
990 1004 1.417288 AGGTGCTCATGATCCGATCA 58.583 50.000 13.46 13.46 44.55 2.92
1911 1949 3.882326 CCAGGGAGGCCGATGCAT 61.882 66.667 0.00 0.00 40.13 3.96
2428 2475 0.316689 GTTTTGACACGGCGAACAGG 60.317 55.000 16.62 0.00 0.00 4.00
2435 2482 4.676586 CCCGCGTTTTGACACGGC 62.677 66.667 4.92 0.00 44.29 5.68
2438 2485 1.370051 GAAGCCCGCGTTTTGACAC 60.370 57.895 4.92 0.00 0.00 3.67
2621 2669 8.958119 TTCCTTCCACATTATGATACTTACAC 57.042 34.615 0.00 0.00 0.00 2.90
2649 2697 5.832595 TGGGTATGGACAAATGGATATTGTG 59.167 40.000 0.00 0.00 40.90 3.33
2657 2705 3.630168 TGACATGGGTATGGACAAATGG 58.370 45.455 0.00 0.00 38.66 3.16
2703 2751 8.428852 ACTTAAAATGTTAGCCAATTTGGTCTT 58.571 29.630 16.62 5.99 40.46 3.01
2886 2934 7.038729 TGAGAGTCAGATTTCCAACTAGAACAT 60.039 37.037 0.00 0.00 0.00 2.71
2920 2968 5.950758 ATGCGTTGGAATTTACACAAGTA 57.049 34.783 0.00 0.00 0.00 2.24
2959 3007 2.697425 CGACCAGCGATCTTTGCG 59.303 61.111 0.00 0.00 44.57 4.85
2980 3028 1.363744 GCTACACGCTCAGCAAATCT 58.636 50.000 0.00 0.00 37.73 2.40
3080 3128 7.210718 TGCAATTCATTATGCTGGATTCTAG 57.789 36.000 0.00 0.00 42.97 2.43
3108 3156 9.740239 ATTAATGTTAATTAGACTGCATTGCAG 57.260 29.630 31.84 31.84 44.56 4.41
3132 3180 5.279384 CGCGTCACCTACTATGACTTTATT 58.721 41.667 0.00 0.00 43.60 1.40
3212 3260 4.442612 CCCATCTCTTCGACATGAGAACAT 60.443 45.833 13.59 0.00 41.82 2.71
3225 3273 2.239654 TCACCCACATTCCCATCTCTTC 59.760 50.000 0.00 0.00 0.00 2.87
3246 3294 7.217200 AGCATATTACGTCCACATGACTTTAT 58.783 34.615 0.00 0.00 42.13 1.40
3275 3323 8.954350 AGACTGGTCAATTGATTTCTAAGAATG 58.046 33.333 12.12 0.00 0.00 2.67


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.