Multiple sequence alignment - TraesCS2A01G316000

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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 TraesCS2A01G316000 chr2A 100.000 3488 0 0 1 3488 541840400 541843887 0.000000e+00 6442
1 TraesCS2A01G316000 chr2D 93.354 2227 73 32 352 2552 403500598 403502775 0.000000e+00 3223
2 TraesCS2A01G316000 chr2D 94.757 801 20 4 2689 3488 403504544 403505323 0.000000e+00 1227
3 TraesCS2A01G316000 chr2B 89.949 2567 113 61 34 2552 477604490 477606959 0.000000e+00 3177
4 TraesCS2A01G316000 chr2B 92.894 957 44 10 2554 3488 477606994 477607948 0.000000e+00 1369
5 TraesCS2A01G316000 chr7A 86.117 461 37 12 1054 1514 704049700 704049267 4.080000e-129 472
6 TraesCS2A01G316000 chr3A 94.444 198 11 0 1056 1253 611206628 611206431 4.370000e-79 305
7 TraesCS2A01G316000 chr1A 84.967 153 23 0 1956 2108 73352585 73352433 4.660000e-34 156


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 TraesCS2A01G316000 chr2A 541840400 541843887 3487 False 6442 6442 100.0000 1 3488 1 chr2A.!!$F1 3487
1 TraesCS2A01G316000 chr2D 403500598 403505323 4725 False 2225 3223 94.0555 352 3488 2 chr2D.!!$F1 3136
2 TraesCS2A01G316000 chr2B 477604490 477607948 3458 False 2273 3177 91.4215 34 3488 2 chr2B.!!$F1 3454

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
157 169 0.109179 GCAGCAATGCATCAAACGGA 60.109 50.0 8.35 0.0 34.41 4.69 F
1773 1826 0.243907 TGTACTGCCTCTTGCTCGTC 59.756 55.0 0.00 0.0 42.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1978 0.111089 CAGACGCGCAAGAACAAGTC 60.111 55.0 5.73 3.73 43.02 3.01 R
2753 4458 1.338890 TTCCCGTCTGGTGTTGTCCA 61.339 55.0 0.00 0.00 36.00 4.02 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
21 22 4.385358 TTCAGAAAGAAAACCAAGGCAC 57.615 40.909 0.00 0.00 32.05 5.01
22 23 2.693074 TCAGAAAGAAAACCAAGGCACC 59.307 45.455 0.00 0.00 0.00 5.01
23 24 1.681264 AGAAAGAAAACCAAGGCACCG 59.319 47.619 0.00 0.00 0.00 4.94
24 25 0.750249 AAAGAAAACCAAGGCACCGG 59.250 50.000 0.00 0.00 0.00 5.28
25 26 1.744320 AAGAAAACCAAGGCACCGGC 61.744 55.000 0.00 0.00 40.13 6.13
26 27 2.443016 AAAACCAAGGCACCGGCA 60.443 55.556 0.00 0.00 43.71 5.69
27 28 2.693250 GAAAACCAAGGCACCGGCAC 62.693 60.000 0.00 0.00 43.71 5.01
45 46 0.763035 ACGGGGCAACTTCTACTTGT 59.237 50.000 0.00 0.00 0.00 3.16
50 51 1.798813 GGCAACTTCTACTTGTGGTCG 59.201 52.381 0.00 0.00 0.00 4.79
66 67 2.208619 TCGGTGGTTAAGGCACGGA 61.209 57.895 0.00 0.00 0.00 4.69
98 99 3.371102 TCACACTGTGCAGTTACTCTC 57.629 47.619 7.90 0.00 40.20 3.20
117 129 3.785859 CTCCCGCCAGCCAAGCTA 61.786 66.667 0.00 0.00 36.40 3.32
137 149 1.583054 AACACTTTGCTCCGTGACTC 58.417 50.000 6.80 0.00 35.23 3.36
144 156 2.049156 CTCCGTGACTCGCAGCAA 60.049 61.111 0.00 0.00 38.35 3.91
145 157 1.446792 CTCCGTGACTCGCAGCAAT 60.447 57.895 0.00 0.00 38.35 3.56
146 158 1.690283 CTCCGTGACTCGCAGCAATG 61.690 60.000 0.00 0.00 38.35 2.82
147 159 2.097160 CGTGACTCGCAGCAATGC 59.903 61.111 0.00 0.00 0.00 3.56
148 160 2.670210 CGTGACTCGCAGCAATGCA 61.670 57.895 8.35 0.00 34.41 3.96
149 161 1.798735 GTGACTCGCAGCAATGCAT 59.201 52.632 8.35 0.00 34.41 3.96
150 162 0.247974 GTGACTCGCAGCAATGCATC 60.248 55.000 8.35 0.00 34.41 3.91
151 163 0.674269 TGACTCGCAGCAATGCATCA 60.674 50.000 8.35 0.00 34.41 3.07
152 164 0.448990 GACTCGCAGCAATGCATCAA 59.551 50.000 8.35 0.00 34.41 2.57
153 165 0.883153 ACTCGCAGCAATGCATCAAA 59.117 45.000 8.35 0.00 34.41 2.69
154 166 1.265568 CTCGCAGCAATGCATCAAAC 58.734 50.000 8.35 0.00 34.41 2.93
155 167 0.454789 TCGCAGCAATGCATCAAACG 60.455 50.000 8.35 0.97 34.41 3.60
156 168 1.407721 CGCAGCAATGCATCAAACGG 61.408 55.000 8.35 0.00 34.41 4.44
157 169 0.109179 GCAGCAATGCATCAAACGGA 60.109 50.000 8.35 0.00 34.41 4.69
158 170 1.669502 GCAGCAATGCATCAAACGGAA 60.670 47.619 8.35 0.00 34.41 4.30
159 171 2.256174 CAGCAATGCATCAAACGGAAG 58.744 47.619 8.35 0.00 0.00 3.46
208 220 4.459089 GAGTCGGGGCACAGGAGC 62.459 72.222 0.00 0.00 0.00 4.70
210 222 4.021925 GTCGGGGCACAGGAGCTT 62.022 66.667 0.00 0.00 34.17 3.74
211 223 3.706373 TCGGGGCACAGGAGCTTC 61.706 66.667 0.00 0.00 34.17 3.86
212 224 4.020617 CGGGGCACAGGAGCTTCA 62.021 66.667 0.00 0.00 34.17 3.02
213 225 2.045536 GGGGCACAGGAGCTTCAG 60.046 66.667 0.00 0.00 34.17 3.02
214 226 2.596851 GGGGCACAGGAGCTTCAGA 61.597 63.158 0.00 0.00 34.17 3.27
215 227 1.376553 GGGCACAGGAGCTTCAGAC 60.377 63.158 0.00 0.00 34.17 3.51
220 232 1.345741 CACAGGAGCTTCAGACCTTCA 59.654 52.381 0.00 0.00 31.06 3.02
246 258 2.279784 GCCCGTGCTAGCTGCTAG 60.280 66.667 28.07 28.07 43.37 3.42
256 268 0.755079 TAGCTGCTAGCCCAGTGATG 59.245 55.000 13.29 0.00 43.77 3.07
257 269 1.525535 GCTGCTAGCCCAGTGATGG 60.526 63.158 13.29 0.00 34.48 3.51
258 270 1.976132 GCTGCTAGCCCAGTGATGGA 61.976 60.000 13.29 0.00 34.48 3.41
259 271 0.763652 CTGCTAGCCCAGTGATGGAT 59.236 55.000 13.29 0.00 0.00 3.41
260 272 0.471191 TGCTAGCCCAGTGATGGATG 59.529 55.000 13.29 0.00 0.00 3.51
261 273 0.250640 GCTAGCCCAGTGATGGATGG 60.251 60.000 2.29 0.00 36.27 3.51
262 274 1.427809 CTAGCCCAGTGATGGATGGA 58.572 55.000 0.00 0.00 39.02 3.41
263 275 1.983691 CTAGCCCAGTGATGGATGGAT 59.016 52.381 0.00 0.00 39.02 3.41
264 276 0.477204 AGCCCAGTGATGGATGGATG 59.523 55.000 0.00 0.00 39.02 3.51
268 280 2.554564 CCCAGTGATGGATGGATGGATG 60.555 54.545 0.00 0.00 39.02 3.51
281 293 0.979665 ATGGATGGATCGATCGGCTT 59.020 50.000 18.81 4.71 0.00 4.35
282 294 0.758734 TGGATGGATCGATCGGCTTT 59.241 50.000 18.81 1.96 0.00 3.51
283 295 1.270305 TGGATGGATCGATCGGCTTTC 60.270 52.381 18.81 10.33 0.00 2.62
293 305 2.427506 GATCGGCTTTCTGGTTTCTGT 58.572 47.619 0.00 0.00 0.00 3.41
294 306 1.593196 TCGGCTTTCTGGTTTCTGTG 58.407 50.000 0.00 0.00 0.00 3.66
297 309 1.609072 GGCTTTCTGGTTTCTGTGGTC 59.391 52.381 0.00 0.00 0.00 4.02
299 311 2.687935 GCTTTCTGGTTTCTGTGGTCAA 59.312 45.455 0.00 0.00 0.00 3.18
306 318 5.306937 TCTGGTTTCTGTGGTCAAGATCTTA 59.693 40.000 7.86 0.00 0.00 2.10
313 325 5.480422 TCTGTGGTCAAGATCTTAAGCTGTA 59.520 40.000 7.86 0.00 0.00 2.74
325 342 7.718753 AGATCTTAAGCTGTAGGGATTCATTTG 59.281 37.037 0.00 0.00 0.00 2.32
328 345 4.851639 AGCTGTAGGGATTCATTTGACT 57.148 40.909 0.00 0.00 0.00 3.41
330 347 3.557595 GCTGTAGGGATTCATTTGACTCG 59.442 47.826 0.00 0.00 0.00 4.18
332 349 2.787473 AGGGATTCATTTGACTCGCA 57.213 45.000 14.45 0.00 38.53 5.10
333 350 2.636830 AGGGATTCATTTGACTCGCAG 58.363 47.619 14.45 0.00 38.53 5.18
346 363 4.992688 TGACTCGCAGAACAAAACAAAAT 58.007 34.783 0.00 0.00 34.09 1.82
356 384 4.863152 ACAAAACAAAATCTGCACTTGC 57.137 36.364 0.00 0.00 42.50 4.01
424 453 1.668151 GTTCGCTGTCCACCTCCAC 60.668 63.158 0.00 0.00 0.00 4.02
434 463 1.028905 CCACCTCCACGCAAAAGAAA 58.971 50.000 0.00 0.00 0.00 2.52
435 464 1.001378 CCACCTCCACGCAAAAGAAAG 60.001 52.381 0.00 0.00 0.00 2.62
436 465 1.946768 CACCTCCACGCAAAAGAAAGA 59.053 47.619 0.00 0.00 0.00 2.52
437 466 2.357637 CACCTCCACGCAAAAGAAAGAA 59.642 45.455 0.00 0.00 0.00 2.52
524 553 9.872684 AATGATAATCCCATGAGTAAAAGATGT 57.127 29.630 0.00 0.00 0.00 3.06
525 554 8.681486 TGATAATCCCATGAGTAAAAGATGTG 57.319 34.615 0.00 0.00 0.00 3.21
526 555 5.841957 AATCCCATGAGTAAAAGATGTGC 57.158 39.130 0.00 0.00 0.00 4.57
527 556 4.574674 TCCCATGAGTAAAAGATGTGCT 57.425 40.909 0.00 0.00 0.00 4.40
528 557 5.692115 TCCCATGAGTAAAAGATGTGCTA 57.308 39.130 0.00 0.00 0.00 3.49
529 558 5.674525 TCCCATGAGTAAAAGATGTGCTAG 58.325 41.667 0.00 0.00 0.00 3.42
530 559 4.274459 CCCATGAGTAAAAGATGTGCTAGC 59.726 45.833 8.10 8.10 0.00 3.42
533 570 6.707608 CCATGAGTAAAAGATGTGCTAGCATA 59.292 38.462 22.51 19.66 0.00 3.14
569 606 1.135053 GGCCGTGAAACCTCTAGTCTC 60.135 57.143 0.00 0.00 0.00 3.36
613 651 4.201901 CCATGTGCTGTTTTTGTTTTTCCC 60.202 41.667 0.00 0.00 0.00 3.97
658 697 8.162085 ACGCCGGAGATTATATATAGGAGAATA 58.838 37.037 13.83 0.00 0.00 1.75
659 698 9.179909 CGCCGGAGATTATATATAGGAGAATAT 57.820 37.037 5.05 0.00 0.00 1.28
757 796 0.604578 CACCCACAAGCATTTCCCAG 59.395 55.000 0.00 0.00 0.00 4.45
769 808 6.949352 AGCATTTCCCAGTTTGACATATAG 57.051 37.500 0.00 0.00 0.00 1.31
770 809 6.662755 AGCATTTCCCAGTTTGACATATAGA 58.337 36.000 0.00 0.00 0.00 1.98
780 819 2.682594 TGACATATAGAGGCCACAGCT 58.317 47.619 5.01 0.00 39.73 4.24
784 823 2.685106 TATAGAGGCCACAGCTAGCT 57.315 50.000 12.68 12.68 39.73 3.32
833 879 0.849417 AGCATTTCCATCTCTCCCCC 59.151 55.000 0.00 0.00 0.00 5.40
843 894 2.770827 TCTCCCCCGAGAGCAAGA 59.229 61.111 0.00 0.00 40.34 3.02
864 915 6.251655 AGAAAAGTTCTTGCTAGCTCAATG 57.748 37.500 17.23 0.00 36.36 2.82
866 917 2.363683 AGTTCTTGCTAGCTCAATGCC 58.636 47.619 17.23 0.00 44.23 4.40
867 918 2.026449 AGTTCTTGCTAGCTCAATGCCT 60.026 45.455 17.23 0.41 44.23 4.75
868 919 2.322355 TCTTGCTAGCTCAATGCCTC 57.678 50.000 17.23 0.00 44.23 4.70
869 920 0.935898 CTTGCTAGCTCAATGCCTCG 59.064 55.000 17.23 0.00 44.23 4.63
870 921 0.536724 TTGCTAGCTCAATGCCTCGA 59.463 50.000 17.23 0.00 44.23 4.04
1205 1258 1.587054 CCTCGTGGCTCGTCTTCTT 59.413 57.895 8.94 0.00 40.80 2.52
1215 1268 1.514443 CGTCTTCTTCGTCCTCGCC 60.514 63.158 0.00 0.00 36.96 5.54
1284 1337 4.385405 ACGCAGGTGCAGCTCTCC 62.385 66.667 17.16 6.56 42.21 3.71
1765 1818 4.878397 GCAAGTTCATAATGTACTGCCTCT 59.122 41.667 0.00 0.00 28.28 3.69
1773 1826 0.243907 TGTACTGCCTCTTGCTCGTC 59.756 55.000 0.00 0.00 42.00 4.20
1898 1951 1.519234 TGTGCATGCTCGATCGTCC 60.519 57.895 20.33 7.86 0.00 4.79
1913 1966 2.789208 TCGTCCGTTCATTCGACATAC 58.211 47.619 0.00 0.00 0.00 2.39
1914 1967 2.162008 TCGTCCGTTCATTCGACATACA 59.838 45.455 0.00 0.00 0.00 2.29
1919 1972 5.173312 GTCCGTTCATTCGACATACAGTATG 59.827 44.000 17.70 17.70 46.00 2.39
1938 1991 6.738200 CAGTATGTAAATGACTTGTTCTTGCG 59.262 38.462 0.00 0.00 0.00 4.85
1967 2020 1.800805 TTTTCTTCAGCTCTGCTCCG 58.199 50.000 0.00 0.00 36.40 4.63
2251 2313 0.606401 CCTTCCACGCCACTCACATT 60.606 55.000 0.00 0.00 0.00 2.71
2376 2446 2.664851 CTGGAGAACAACCGCGCA 60.665 61.111 8.75 0.00 0.00 6.09
2475 2545 1.452833 GCTGCTGGGGAAGACCATC 60.453 63.158 0.00 0.00 42.91 3.51
2498 2568 4.641094 CGGTATATCTTAGAGAAGGGCGAT 59.359 45.833 0.00 0.00 33.09 4.58
2525 2595 2.146342 GATCCCTGTCAACTGTGTGTG 58.854 52.381 0.00 0.00 0.00 3.82
2552 2622 3.326006 TGATGAACCATCCAGCTCCTATC 59.674 47.826 4.69 0.00 39.87 2.08
2677 4363 4.067896 CTGCTTACCTGATGACAAACTGT 58.932 43.478 0.00 0.00 0.00 3.55
2683 4369 5.947228 ACCTGATGACAAACTGTAACATG 57.053 39.130 0.00 0.00 0.00 3.21
2684 4370 5.376625 ACCTGATGACAAACTGTAACATGT 58.623 37.500 0.00 0.00 0.00 3.21
2686 4372 6.321181 ACCTGATGACAAACTGTAACATGTTT 59.679 34.615 17.78 0.95 36.91 2.83
2687 4373 7.500892 ACCTGATGACAAACTGTAACATGTTTA 59.499 33.333 17.78 5.75 35.01 2.01
2753 4458 4.525487 ACCACAATTCAGCACATTGAGATT 59.475 37.500 8.93 0.00 35.51 2.40
2764 4469 3.569277 CACATTGAGATTGGACAACACCA 59.431 43.478 0.00 0.00 38.24 4.17
2768 4473 2.069273 GAGATTGGACAACACCAGACG 58.931 52.381 0.00 0.00 41.19 4.18
2812 4517 7.750458 GTCGAGCAATATGTCAAAAGAAATTCA 59.250 33.333 0.00 0.00 0.00 2.57
3051 4759 4.749245 ATCTTTTAAACCGCACACTCTG 57.251 40.909 0.00 0.00 0.00 3.35
3080 4788 5.125097 CAGACCAGAAAGAAGCATGCTAAAT 59.875 40.000 23.00 5.09 0.00 1.40
3200 4908 0.620556 GGATCTTGCTTGTCTCCCCA 59.379 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.132111 GGTGCCTTGGTTTTCTTTCTGAA 59.868 43.478 0.00 0.00 0.00 3.02
1 2 2.693074 GGTGCCTTGGTTTTCTTTCTGA 59.307 45.455 0.00 0.00 0.00 3.27
2 3 2.543653 CGGTGCCTTGGTTTTCTTTCTG 60.544 50.000 0.00 0.00 0.00 3.02
3 4 1.681264 CGGTGCCTTGGTTTTCTTTCT 59.319 47.619 0.00 0.00 0.00 2.52
4 5 1.269569 CCGGTGCCTTGGTTTTCTTTC 60.270 52.381 0.00 0.00 0.00 2.62
5 6 0.750249 CCGGTGCCTTGGTTTTCTTT 59.250 50.000 0.00 0.00 0.00 2.52
6 7 1.744320 GCCGGTGCCTTGGTTTTCTT 61.744 55.000 1.90 0.00 0.00 2.52
7 8 2.200337 GCCGGTGCCTTGGTTTTCT 61.200 57.895 1.90 0.00 0.00 2.52
8 9 2.338620 GCCGGTGCCTTGGTTTTC 59.661 61.111 1.90 0.00 0.00 2.29
9 10 2.443016 TGCCGGTGCCTTGGTTTT 60.443 55.556 1.90 0.00 36.33 2.43
10 11 3.223589 GTGCCGGTGCCTTGGTTT 61.224 61.111 1.90 0.00 36.33 3.27
22 23 3.599285 TAGAAGTTGCCCCGTGCCG 62.599 63.158 0.00 0.00 40.16 5.69
23 24 2.038837 GTAGAAGTTGCCCCGTGCC 61.039 63.158 0.00 0.00 40.16 5.01
24 25 0.605589 AAGTAGAAGTTGCCCCGTGC 60.606 55.000 0.00 0.00 41.77 5.34
25 26 1.156736 CAAGTAGAAGTTGCCCCGTG 58.843 55.000 0.00 0.00 0.00 4.94
26 27 0.763035 ACAAGTAGAAGTTGCCCCGT 59.237 50.000 0.00 0.00 31.85 5.28
27 28 1.156736 CACAAGTAGAAGTTGCCCCG 58.843 55.000 0.00 0.00 31.85 5.73
28 29 1.202891 ACCACAAGTAGAAGTTGCCCC 60.203 52.381 0.00 0.00 31.85 5.80
29 30 2.152016 GACCACAAGTAGAAGTTGCCC 58.848 52.381 0.00 0.00 31.85 5.36
30 31 1.798813 CGACCACAAGTAGAAGTTGCC 59.201 52.381 0.00 0.00 31.85 4.52
31 32 1.798813 CCGACCACAAGTAGAAGTTGC 59.201 52.381 0.00 0.00 31.85 4.17
32 33 2.800544 CACCGACCACAAGTAGAAGTTG 59.199 50.000 0.00 0.00 34.77 3.16
39 40 2.037511 CCTTAACCACCGACCACAAGTA 59.962 50.000 0.00 0.00 0.00 2.24
45 46 1.071814 GTGCCTTAACCACCGACCA 59.928 57.895 0.00 0.00 0.00 4.02
50 51 1.471287 GAATTCCGTGCCTTAACCACC 59.529 52.381 0.00 0.00 0.00 4.61
66 67 3.304659 GCACAGTGTGAATGAACGGAATT 60.305 43.478 27.37 0.00 35.23 2.17
72 73 3.698029 AACTGCACAGTGTGAATGAAC 57.302 42.857 27.37 8.34 41.58 3.18
75 76 4.060900 AGAGTAACTGCACAGTGTGAATG 58.939 43.478 27.37 16.47 41.58 2.67
79 80 2.797156 GTGAGAGTAACTGCACAGTGTG 59.203 50.000 19.27 19.27 41.58 3.82
80 81 2.695666 AGTGAGAGTAACTGCACAGTGT 59.304 45.455 3.64 0.00 41.58 3.55
116 128 3.128349 GAGTCACGGAGCAAAGTGTTTA 58.872 45.455 5.58 0.00 39.25 2.01
117 129 1.940613 GAGTCACGGAGCAAAGTGTTT 59.059 47.619 5.58 0.00 39.25 2.83
144 156 1.549203 AAGGCTTCCGTTTGATGCAT 58.451 45.000 0.00 0.00 43.95 3.96
145 157 1.000385 CAAAGGCTTCCGTTTGATGCA 60.000 47.619 0.00 0.00 45.11 3.96
146 158 1.669795 CCAAAGGCTTCCGTTTGATGC 60.670 52.381 0.00 0.00 45.11 3.91
147 159 1.669795 GCCAAAGGCTTCCGTTTGATG 60.670 52.381 0.00 0.00 46.69 3.07
148 160 0.603065 GCCAAAGGCTTCCGTTTGAT 59.397 50.000 0.00 0.00 46.69 2.57
149 161 2.037871 GCCAAAGGCTTCCGTTTGA 58.962 52.632 0.00 0.00 46.69 2.69
150 162 4.653555 GCCAAAGGCTTCCGTTTG 57.346 55.556 0.00 0.00 46.69 2.93
159 171 1.003718 AGGTACAGTCGCCAAAGGC 60.004 57.895 0.00 0.00 46.75 4.35
208 220 1.467734 GCATGCACTGAAGGTCTGAAG 59.532 52.381 14.21 0.00 0.00 3.02
209 221 1.527034 GCATGCACTGAAGGTCTGAA 58.473 50.000 14.21 0.00 0.00 3.02
210 222 0.671472 CGCATGCACTGAAGGTCTGA 60.671 55.000 19.57 0.00 0.00 3.27
211 223 1.792301 CGCATGCACTGAAGGTCTG 59.208 57.895 19.57 0.00 0.00 3.51
212 224 2.037136 GCGCATGCACTGAAGGTCT 61.037 57.895 19.57 0.00 42.15 3.85
213 225 2.482374 GCGCATGCACTGAAGGTC 59.518 61.111 19.57 0.00 42.15 3.85
214 226 3.058160 GGCGCATGCACTGAAGGT 61.058 61.111 19.57 0.00 45.35 3.50
215 227 3.818787 GGGCGCATGCACTGAAGG 61.819 66.667 19.57 0.00 42.93 3.46
246 258 0.538977 CCATCCATCCATCACTGGGC 60.539 60.000 0.00 0.00 43.34 5.36
256 268 2.482664 CGATCGATCCATCCATCCATCC 60.483 54.545 19.51 0.00 0.00 3.51
257 269 2.482664 CCGATCGATCCATCCATCCATC 60.483 54.545 18.66 0.00 0.00 3.51
258 270 1.483827 CCGATCGATCCATCCATCCAT 59.516 52.381 18.66 0.00 0.00 3.41
259 271 0.897621 CCGATCGATCCATCCATCCA 59.102 55.000 18.66 0.00 0.00 3.41
260 272 0.460987 GCCGATCGATCCATCCATCC 60.461 60.000 18.66 0.00 0.00 3.51
261 273 0.534412 AGCCGATCGATCCATCCATC 59.466 55.000 18.66 1.70 0.00 3.51
262 274 0.979665 AAGCCGATCGATCCATCCAT 59.020 50.000 18.66 0.00 0.00 3.41
263 275 0.758734 AAAGCCGATCGATCCATCCA 59.241 50.000 18.66 0.00 0.00 3.41
264 276 1.001406 AGAAAGCCGATCGATCCATCC 59.999 52.381 18.66 5.61 0.00 3.51
268 280 0.105039 ACCAGAAAGCCGATCGATCC 59.895 55.000 18.66 6.69 0.00 3.36
281 293 3.924114 TCTTGACCACAGAAACCAGAA 57.076 42.857 0.00 0.00 0.00 3.02
282 294 3.648067 AGATCTTGACCACAGAAACCAGA 59.352 43.478 0.00 0.00 0.00 3.86
283 295 4.013267 AGATCTTGACCACAGAAACCAG 57.987 45.455 0.00 0.00 0.00 4.00
293 305 4.162320 CCCTACAGCTTAAGATCTTGACCA 59.838 45.833 18.47 0.00 0.00 4.02
294 306 4.406003 TCCCTACAGCTTAAGATCTTGACC 59.594 45.833 18.47 1.15 0.00 4.02
297 309 6.586344 TGAATCCCTACAGCTTAAGATCTTG 58.414 40.000 18.47 3.94 0.00 3.02
299 311 7.385894 AATGAATCCCTACAGCTTAAGATCT 57.614 36.000 6.67 0.00 0.00 2.75
306 318 5.184892 AGTCAAATGAATCCCTACAGCTT 57.815 39.130 0.00 0.00 0.00 3.74
313 325 2.237143 TCTGCGAGTCAAATGAATCCCT 59.763 45.455 5.39 0.00 35.92 4.20
325 342 5.172053 CAGATTTTGTTTTGTTCTGCGAGTC 59.828 40.000 0.00 0.00 0.00 3.36
328 345 3.796178 GCAGATTTTGTTTTGTTCTGCGA 59.204 39.130 7.38 0.00 46.67 5.10
332 349 5.063817 GCAAGTGCAGATTTTGTTTTGTTCT 59.936 36.000 0.00 0.00 41.59 3.01
333 350 5.257864 GCAAGTGCAGATTTTGTTTTGTTC 58.742 37.500 0.00 0.00 41.59 3.18
346 363 2.645838 AAAGAGAAGGCAAGTGCAGA 57.354 45.000 5.52 0.00 44.36 4.26
356 384 4.044426 CGTGGAAAAGCAAAAAGAGAAGG 58.956 43.478 0.00 0.00 0.00 3.46
424 453 5.003778 CACAGAAACACTTCTTTCTTTTGCG 59.996 40.000 0.00 0.00 40.05 4.85
434 463 1.871080 CGAGGCACAGAAACACTTCT 58.129 50.000 0.00 0.00 42.96 2.85
435 464 0.235926 GCGAGGCACAGAAACACTTC 59.764 55.000 0.00 0.00 0.00 3.01
436 465 0.463654 TGCGAGGCACAGAAACACTT 60.464 50.000 0.00 0.00 31.71 3.16
437 466 1.146041 TGCGAGGCACAGAAACACT 59.854 52.632 0.00 0.00 31.71 3.55
508 537 4.877823 TGCTAGCACATCTTTTACTCATGG 59.122 41.667 14.93 0.00 0.00 3.66
541 578 1.353022 AGGTTTCACGGCCCTTATCAA 59.647 47.619 0.00 0.00 0.00 2.57
569 606 6.083098 TGGTAGCTAGTAGAGTAGAGTACG 57.917 45.833 0.00 0.00 0.00 3.67
613 651 6.293244 CCGGCGTAATTCCTTATAAAAAGGAG 60.293 42.308 6.01 0.00 46.21 3.69
757 796 3.561725 GCTGTGGCCTCTATATGTCAAAC 59.438 47.826 3.32 0.00 0.00 2.93
769 808 0.103937 CTGTAGCTAGCTGTGGCCTC 59.896 60.000 27.68 0.00 39.73 4.70
770 809 1.333636 CCTGTAGCTAGCTGTGGCCT 61.334 60.000 27.68 1.05 39.73 5.19
780 819 6.070136 ACGGAGAGACATATATCCTGTAGCTA 60.070 42.308 0.00 0.00 0.00 3.32
784 823 7.232188 AGAAACGGAGAGACATATATCCTGTA 58.768 38.462 0.00 0.00 0.00 2.74
843 894 4.321527 GGCATTGAGCTAGCAAGAACTTTT 60.322 41.667 18.83 0.00 44.79 2.27
864 915 6.258068 GGGTAATAATAATGCTGTATCGAGGC 59.742 42.308 0.00 0.00 0.00 4.70
866 917 7.556844 AGGGGTAATAATAATGCTGTATCGAG 58.443 38.462 0.00 0.00 0.00 4.04
867 918 7.364408 GGAGGGGTAATAATAATGCTGTATCGA 60.364 40.741 0.00 0.00 0.00 3.59
868 919 6.761714 GGAGGGGTAATAATAATGCTGTATCG 59.238 42.308 0.00 0.00 0.00 2.92
869 920 7.862675 AGGAGGGGTAATAATAATGCTGTATC 58.137 38.462 0.00 0.00 0.00 2.24
870 921 7.830848 AGGAGGGGTAATAATAATGCTGTAT 57.169 36.000 0.00 0.00 0.00 2.29
932 983 2.223735 TGTCTTGGCGATCGTATCCTTC 60.224 50.000 17.81 0.00 0.00 3.46
946 997 2.045926 CTCGGCCCCTTGTCTTGG 60.046 66.667 0.00 0.00 0.00 3.61
1422 1475 1.996187 GAGGAGGTGGAAGGACCCC 60.996 68.421 0.00 0.00 36.56 4.95
1545 1598 1.884464 CCACGACGCCATCTCCATG 60.884 63.158 0.00 0.00 0.00 3.66
1593 1646 2.434884 ATCCGGAACAGCACGCAG 60.435 61.111 9.01 0.00 0.00 5.18
1704 1757 2.579201 CGGAGCTGGTCACGGATT 59.421 61.111 9.30 0.00 0.00 3.01
1773 1826 3.357079 GTGAACTGGCTGGCCGTG 61.357 66.667 7.14 5.17 39.42 4.94
1879 1932 1.633171 GACGATCGAGCATGCACAC 59.367 57.895 24.34 9.84 0.00 3.82
1898 1951 7.673810 TTACATACTGTATGTCGAATGAACG 57.326 36.000 30.65 4.61 45.83 3.95
1913 1966 6.738200 CGCAAGAACAAGTCATTTACATACTG 59.262 38.462 0.00 0.00 43.02 2.74
1914 1967 6.620733 GCGCAAGAACAAGTCATTTACATACT 60.621 38.462 0.30 0.00 43.02 2.12
1919 1972 2.902484 CGCGCAAGAACAAGTCATTTAC 59.098 45.455 8.75 0.00 43.02 2.01
1920 1973 2.546368 ACGCGCAAGAACAAGTCATTTA 59.454 40.909 5.73 0.00 43.02 1.40
1921 1974 1.333619 ACGCGCAAGAACAAGTCATTT 59.666 42.857 5.73 0.00 43.02 2.32
1922 1975 0.944386 ACGCGCAAGAACAAGTCATT 59.056 45.000 5.73 0.00 43.02 2.57
1924 1977 0.529773 AGACGCGCAAGAACAAGTCA 60.530 50.000 5.73 0.00 43.02 3.41
1925 1978 0.111089 CAGACGCGCAAGAACAAGTC 60.111 55.000 5.73 3.73 43.02 3.01
1926 1979 1.498865 CCAGACGCGCAAGAACAAGT 61.499 55.000 5.73 0.00 43.02 3.16
1927 1980 1.205064 CCAGACGCGCAAGAACAAG 59.795 57.895 5.73 0.00 43.02 3.16
1928 1981 0.812014 TTCCAGACGCGCAAGAACAA 60.812 50.000 5.73 0.00 43.02 2.83
1929 1982 0.602638 ATTCCAGACGCGCAAGAACA 60.603 50.000 5.73 0.00 43.02 3.18
1930 1983 0.517316 AATTCCAGACGCGCAAGAAC 59.483 50.000 5.73 0.00 43.02 3.01
1931 1984 1.234821 AAATTCCAGACGCGCAAGAA 58.765 45.000 5.73 4.82 43.02 2.52
1932 1985 1.196808 GAAAATTCCAGACGCGCAAGA 59.803 47.619 5.73 0.00 43.02 3.02
1933 1986 1.197721 AGAAAATTCCAGACGCGCAAG 59.802 47.619 5.73 0.00 43.44 4.01
1934 1987 1.234821 AGAAAATTCCAGACGCGCAA 58.765 45.000 5.73 0.00 0.00 4.85
1935 1988 1.196808 GAAGAAAATTCCAGACGCGCA 59.803 47.619 5.73 0.00 0.00 6.09
1936 1989 1.196808 TGAAGAAAATTCCAGACGCGC 59.803 47.619 5.73 0.00 0.00 6.86
1937 1990 2.726066 GCTGAAGAAAATTCCAGACGCG 60.726 50.000 3.53 3.53 0.00 6.01
1938 1991 2.485814 AGCTGAAGAAAATTCCAGACGC 59.514 45.455 0.00 0.00 0.00 5.19
2251 2313 1.210478 GCCTGCCTCTTCTGGTATGAA 59.790 52.381 0.00 0.00 0.00 2.57
2376 2446 2.047274 CCGAACACCGTGATGCCT 60.047 61.111 5.28 0.00 36.31 4.75
2475 2545 4.008330 TCGCCCTTCTCTAAGATATACCG 58.992 47.826 0.00 0.00 34.37 4.02
2498 2568 2.428530 CAGTTGACAGGGATCGAGATGA 59.571 50.000 0.00 0.00 0.00 2.92
2516 2586 6.048732 TGGTTCATCATATACACACACAGT 57.951 37.500 0.00 0.00 0.00 3.55
2525 2595 5.046014 AGGAGCTGGATGGTTCATCATATAC 60.046 44.000 9.68 0.00 42.13 1.47
2552 2622 2.061773 GGTGGCGATCTACATGATTCG 58.938 52.381 0.00 3.42 35.14 3.34
2631 2736 1.522668 CAAGGAGGCAATGAACACGA 58.477 50.000 0.00 0.00 0.00 4.35
2733 4438 4.768448 TCCAATCTCAATGTGCTGAATTGT 59.232 37.500 6.51 0.00 36.58 2.71
2737 4442 3.753815 TGTCCAATCTCAATGTGCTGAA 58.246 40.909 0.00 0.00 0.00 3.02
2746 4451 3.476552 GTCTGGTGTTGTCCAATCTCAA 58.523 45.455 0.00 0.00 37.01 3.02
2753 4458 1.338890 TTCCCGTCTGGTGTTGTCCA 61.339 55.000 0.00 0.00 36.00 4.02
2764 4469 1.619827 TGTATTTCGTGGTTCCCGTCT 59.380 47.619 0.00 0.00 0.00 4.18
2768 4473 2.414138 CGACTTGTATTTCGTGGTTCCC 59.586 50.000 0.00 0.00 0.00 3.97
2775 4480 5.810587 ACATATTGCTCGACTTGTATTTCGT 59.189 36.000 0.00 0.00 36.60 3.85
2777 4482 7.234187 TGACATATTGCTCGACTTGTATTTC 57.766 36.000 0.00 0.00 0.00 2.17
2812 4517 9.520515 AGTCAGACCATTTTGTTATATGTTTCT 57.479 29.630 0.00 0.00 0.00 2.52
3051 4759 2.147150 GCTTCTTTCTGGTCTGGTCAC 58.853 52.381 0.00 0.00 0.00 3.67
3080 4788 3.876914 GCGGAACCACTATTCATGAATCA 59.123 43.478 23.95 10.13 32.50 2.57


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

AutoCloner maintained by Alex Coulton.