Multiple sequence alignment - TraesCS2A01G134700

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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 TraesCS2A01G134700 chr2A 100.000 2565 0 0 1 2565 81042905 81045469 0.000000e+00 4737.0
1 TraesCS2A01G134700 chr2D 88.957 1965 154 31 1 1930 80315472 80317408 0.000000e+00 2368.0
2 TraesCS2A01G134700 chr2D 92.642 897 44 6 1479 2359 80326195 80327085 0.000000e+00 1271.0
3 TraesCS2A01G134700 chr2D 97.826 184 4 0 2360 2543 80327198 80327381 4.120000e-83 318.0
4 TraesCS2A01G134700 chr2D 80.965 373 50 15 57 423 552101241 552101598 2.510000e-70 276.0
5 TraesCS2A01G134700 chr2D 73.856 306 76 4 1973 2275 538069383 538069687 4.480000e-23 119.0
6 TraesCS2A01G134700 chr2B 87.833 1315 103 32 422 1705 132040907 132042195 0.000000e+00 1489.0
7 TraesCS2A01G134700 chr2B 92.879 323 20 3 803 1123 129199835 129200156 1.390000e-127 466.0
8 TraesCS2A01G134700 chr2B 86.780 295 35 4 422 715 129199543 129199834 2.460000e-85 326.0
9 TraesCS2A01G134700 chr2B 82.645 242 32 5 1691 1930 132042371 132042604 3.350000e-49 206.0
10 TraesCS2A01G134700 chr2B 95.690 116 5 0 1121 1236 129205617 129205732 1.210000e-43 187.0
11 TraesCS2A01G134700 chr2B 82.051 117 17 4 2233 2347 698031830 698031716 2.100000e-16 97.1
12 TraesCS2A01G134700 chr4D 83.182 440 59 10 1 429 275767832 275767397 3.090000e-104 388.0
13 TraesCS2A01G134700 chr4D 77.567 263 59 0 1884 2146 95500181 95500443 2.640000e-35 159.0
14 TraesCS2A01G134700 chr7B 81.818 374 57 10 59 426 555314311 555313943 1.150000e-78 303.0
15 TraesCS2A01G134700 chr7B 78.814 354 57 12 1 342 379224297 379224644 3.320000e-54 222.0
16 TraesCS2A01G134700 chr7D 79.458 443 69 13 1 426 521686440 521686003 6.940000e-76 294.0
17 TraesCS2A01G134700 chr7D 77.577 388 61 16 21 395 392170501 392170875 7.190000e-51 211.0
18 TraesCS2A01G134700 chr7D 93.103 58 4 0 423 480 390898407 390898464 4.550000e-13 86.1
19 TraesCS2A01G134700 chr7A 77.829 433 64 13 1 426 393342740 393343147 3.300000e-59 239.0
20 TraesCS2A01G134700 chr5B 82.824 262 40 4 166 426 421193056 421192799 1.990000e-56 230.0
21 TraesCS2A01G134700 chr1A 76.659 437 86 15 1904 2335 94459374 94459799 7.140000e-56 228.0
22 TraesCS2A01G134700 chr4B 76.500 400 87 7 1877 2272 575652414 575652810 7.190000e-51 211.0
23 TraesCS2A01G134700 chr4B 75.689 399 93 4 1877 2272 575046347 575045950 2.010000e-46 196.0
24 TraesCS2A01G134700 chr4B 80.423 189 32 5 1877 2065 630584990 630584807 3.440000e-29 139.0
25 TraesCS2A01G134700 chr4B 94.828 58 3 0 423 480 534285349 534285292 9.770000e-15 91.6
26 TraesCS2A01G134700 chr4B 91.525 59 3 2 423 480 480017896 480017953 2.120000e-11 80.5
27 TraesCS2A01G134700 chr4B 89.655 58 6 0 423 480 440058143 440058200 9.840000e-10 75.0
28 TraesCS2A01G134700 chr4B 78.351 97 18 3 2178 2273 64093990 64094084 2.760000e-05 60.2
29 TraesCS2A01G134700 chr5A 76.190 399 91 4 1877 2272 288257818 288258215 9.300000e-50 207.0
30 TraesCS2A01G134700 chr5A 74.179 457 104 12 1890 2339 672346520 672346969 7.290000e-41 178.0
31 TraesCS2A01G134700 chr5D 75.377 398 75 13 1892 2287 25303631 25304007 1.220000e-38 171.0
32 TraesCS2A01G134700 chr5D 87.931 58 7 0 423 480 407022551 407022494 4.580000e-08 69.4
33 TraesCS2A01G134700 chr3A 74.528 424 89 14 1936 2353 487441067 487440657 1.580000e-37 167.0
34 TraesCS2A01G134700 chr3D 93.878 49 3 0 1 49 460512629 460512581 9.840000e-10 75.0


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 TraesCS2A01G134700 chr2A 81042905 81045469 2564 False 4737.0 4737 100.0000 1 2565 1 chr2A.!!$F1 2564
1 TraesCS2A01G134700 chr2D 80315472 80317408 1936 False 2368.0 2368 88.9570 1 1930 1 chr2D.!!$F1 1929
2 TraesCS2A01G134700 chr2D 80326195 80327381 1186 False 794.5 1271 95.2340 1479 2543 2 chr2D.!!$F4 1064
3 TraesCS2A01G134700 chr2B 132040907 132042604 1697 False 847.5 1489 85.2390 422 1930 2 chr2B.!!$F3 1508
4 TraesCS2A01G134700 chr2B 129199543 129200156 613 False 396.0 466 89.8295 422 1123 2 chr2B.!!$F2 701

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
731 737 0.171455 ACACGGATGAAGCGAGACTC 59.829 55.0 0.0 0.0 0.00 3.36 F
951 975 0.940126 CCACTCATAGATGCCGTTGC 59.060 55.0 0.0 0.0 38.26 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1604 0.030235 GGCAGAACCAAACGGAACAC 59.970 55.0 0.0 0.0 38.86 3.32 R
2174 2413 0.247736 CTCGCTGCCTAGTTCCTGTT 59.752 55.0 0.0 0.0 0.00 3.16 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
40 41 7.067372 CCACAAGAAATGAGCTATTTATGGACA 59.933 37.037 0.00 0.00 39.06 4.02
49 50 7.999679 TGAGCTATTTATGGACAAAATCAAGG 58.000 34.615 0.00 0.00 0.00 3.61
50 51 7.833682 TGAGCTATTTATGGACAAAATCAAGGA 59.166 33.333 0.00 0.00 0.00 3.36
64 69 7.175641 ACAAAATCAAGGACATGAGAGTAAAGG 59.824 37.037 0.00 0.00 31.76 3.11
71 76 4.898861 GGACATGAGAGTAAAGGAGGAGAT 59.101 45.833 0.00 0.00 0.00 2.75
76 81 7.841729 ACATGAGAGTAAAGGAGGAGATAGAAA 59.158 37.037 0.00 0.00 0.00 2.52
77 82 8.700051 CATGAGAGTAAAGGAGGAGATAGAAAA 58.300 37.037 0.00 0.00 0.00 2.29
135 140 1.103803 AGACGGTGTATCATGCGACT 58.896 50.000 0.00 0.00 0.00 4.18
148 153 2.577112 CGACTGCGACCACTAGCG 60.577 66.667 0.00 0.00 40.82 4.26
170 175 3.493213 CCGTATGGCGTGGAAACC 58.507 61.111 0.00 0.00 39.32 3.27
183 188 0.806492 GGAAACCGATGCCTCTCGTC 60.806 60.000 0.00 0.00 36.93 4.20
188 193 2.501610 GATGCCTCTCGTCCACCC 59.498 66.667 0.00 0.00 0.00 4.61
189 194 2.284625 ATGCCTCTCGTCCACCCA 60.285 61.111 0.00 0.00 0.00 4.51
195 200 1.271379 CCTCTCGTCCACCCAAACAAT 60.271 52.381 0.00 0.00 0.00 2.71
205 210 7.868415 TCGTCCACCCAAACAATTTTTATAAAG 59.132 33.333 0.00 0.00 0.00 1.85
206 211 7.654116 CGTCCACCCAAACAATTTTTATAAAGT 59.346 33.333 0.00 0.00 0.00 2.66
252 257 1.064906 CAACCATGAGAGGAGCCACAT 60.065 52.381 0.00 0.00 0.00 3.21
256 261 2.486191 CCATGAGAGGAGCCACATAACC 60.486 54.545 0.00 0.00 0.00 2.85
264 269 2.474816 GAGCCACATAACCGAGTCATC 58.525 52.381 0.00 0.00 0.00 2.92
265 270 2.101582 GAGCCACATAACCGAGTCATCT 59.898 50.000 0.00 0.00 0.00 2.90
266 271 2.501723 AGCCACATAACCGAGTCATCTT 59.498 45.455 0.00 0.00 0.00 2.40
267 272 2.866762 GCCACATAACCGAGTCATCTTC 59.133 50.000 0.00 0.00 0.00 2.87
268 273 3.678806 GCCACATAACCGAGTCATCTTCA 60.679 47.826 0.00 0.00 0.00 3.02
269 274 4.697514 CCACATAACCGAGTCATCTTCAT 58.302 43.478 0.00 0.00 0.00 2.57
270 275 4.747108 CCACATAACCGAGTCATCTTCATC 59.253 45.833 0.00 0.00 0.00 2.92
271 276 4.747108 CACATAACCGAGTCATCTTCATCC 59.253 45.833 0.00 0.00 0.00 3.51
272 277 2.990066 AACCGAGTCATCTTCATCCC 57.010 50.000 0.00 0.00 0.00 3.85
273 278 1.866015 ACCGAGTCATCTTCATCCCA 58.134 50.000 0.00 0.00 0.00 4.37
274 279 2.402564 ACCGAGTCATCTTCATCCCAT 58.597 47.619 0.00 0.00 0.00 4.00
275 280 2.366916 ACCGAGTCATCTTCATCCCATC 59.633 50.000 0.00 0.00 0.00 3.51
296 301 2.124860 ATCAACCCTAACCGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
317 322 4.013050 GCCATTTTCTATCTCCATAGCCC 58.987 47.826 0.00 0.00 33.10 5.19
343 348 5.344743 TCTCCATCTTCACCATAGTTCAC 57.655 43.478 0.00 0.00 0.00 3.18
351 356 1.486726 CACCATAGTTCACCCTCCTCC 59.513 57.143 0.00 0.00 0.00 4.30
367 372 5.221541 CCCTCCTCCAGTCATACTTGTAATC 60.222 48.000 0.00 0.00 0.00 1.75
373 378 7.342769 TCCAGTCATACTTGTAATCGTGTAT 57.657 36.000 0.00 0.00 0.00 2.29
396 401 1.401552 CACACGGCATCCATTGTAAGG 59.598 52.381 0.00 0.00 0.00 2.69
400 405 2.158682 ACGGCATCCATTGTAAGGCATA 60.159 45.455 0.00 0.00 0.00 3.14
456 461 7.327975 TGTGTGAGTAGTTTGATAAGGTATGG 58.672 38.462 0.00 0.00 0.00 2.74
494 500 5.068198 CCTTGCAACCAATAGATGTATTGCT 59.932 40.000 15.44 1.30 44.02 3.91
496 502 6.528537 TGCAACCAATAGATGTATTGCTTT 57.471 33.333 15.44 8.81 44.02 3.51
625 631 6.820656 TGTGATTTAAACTTGTGGCAATGTTT 59.179 30.769 14.81 14.81 36.69 2.83
641 647 7.331440 TGGCAATGTTTAGATTTGTATGCAAAG 59.669 33.333 14.39 0.00 46.30 2.77
667 673 6.478512 AATTTTCAAATATGGCATACCGGT 57.521 33.333 13.98 13.98 39.70 5.28
669 675 2.761559 TCAAATATGGCATACCGGTCG 58.238 47.619 12.40 4.61 39.70 4.79
714 720 2.289547 GAGCGAACTGGTTAGCAAAACA 59.710 45.455 17.72 0.00 42.45 2.83
719 725 2.858745 ACTGGTTAGCAAAACACGGAT 58.141 42.857 4.59 0.00 0.00 4.18
721 727 2.811431 CTGGTTAGCAAAACACGGATGA 59.189 45.455 4.59 0.00 0.00 2.92
725 731 0.238289 AGCAAAACACGGATGAAGCG 59.762 50.000 0.00 0.00 0.00 4.68
726 732 0.237235 GCAAAACACGGATGAAGCGA 59.763 50.000 0.00 0.00 0.00 4.93
731 737 0.171455 ACACGGATGAAGCGAGACTC 59.829 55.000 0.00 0.00 0.00 3.36
742 748 1.226717 CGAGACTCCGCCTTACAGC 60.227 63.158 0.00 0.00 0.00 4.40
745 751 3.718210 GACTCCGCCTTACAGCCCG 62.718 68.421 0.00 0.00 0.00 6.13
774 788 4.310022 AAACAGATTAAATCCGGGTCCA 57.690 40.909 0.00 0.00 0.00 4.02
800 814 2.172717 AGCGTTGGAGTTGCCCTAATAT 59.827 45.455 0.00 0.00 34.97 1.28
829 849 2.536673 GGCACATCGCATGCATCGA 61.537 57.895 19.57 18.83 45.27 3.59
944 968 5.105957 CGTCCTATCTTCCCACTCATAGATG 60.106 48.000 0.00 0.00 0.00 2.90
951 975 0.940126 CCACTCATAGATGCCGTTGC 59.060 55.000 0.00 0.00 38.26 4.17
990 1014 0.968393 ACCAACAACCACACACCACC 60.968 55.000 0.00 0.00 0.00 4.61
1046 1070 4.803426 CGTCCTCACGCAGAGCCC 62.803 72.222 0.16 0.00 43.31 5.19
1258 1283 2.025584 CGCGACGCCTACAGCATA 59.974 61.111 15.34 0.00 44.04 3.14
1456 1481 1.660575 CGTGGATTAGCTACCGCCG 60.661 63.158 8.04 3.89 36.60 6.46
1459 1484 2.205152 GGATTAGCTACCGCCGGGA 61.205 63.158 8.57 0.00 36.60 5.14
1517 1553 1.437160 GTGTGTGTGGTTTGGCTGG 59.563 57.895 0.00 0.00 0.00 4.85
1534 1576 2.485122 GTTTGGGCTGCCGATTCG 59.515 61.111 13.40 0.00 0.00 3.34
1562 1604 4.253685 AGATTCTACGGTGAAACATGTGG 58.746 43.478 0.00 0.00 39.98 4.17
1575 1617 1.028905 CATGTGGTGTTCCGTTTGGT 58.971 50.000 0.00 0.00 36.30 3.67
1581 1623 0.030235 GTGTTCCGTTTGGTTCTGCC 59.970 55.000 0.00 0.00 36.30 4.85
1598 1640 0.804989 GCCCACATGTGTTCTAGTGC 59.195 55.000 23.79 10.67 0.00 4.40
1611 1653 3.334583 TCTAGTGCTTGTGTCCCAATC 57.665 47.619 0.00 0.00 31.20 2.67
1623 1665 5.136828 TGTGTCCCAATCTGTATTGTGTTT 58.863 37.500 0.00 0.00 40.84 2.83
1665 1712 2.877154 TCTCCTCCCAGCCTCTAAAT 57.123 50.000 0.00 0.00 0.00 1.40
1701 1938 2.929398 CCAAACAATTTTATGAGCCGGC 59.071 45.455 21.89 21.89 0.00 6.13
1762 1999 1.763545 GACTAAGTCACCATCCTCCCC 59.236 57.143 0.00 0.00 32.09 4.81
1845 2084 9.724839 GTACAAGAACACTAAAAGCAACATAAA 57.275 29.630 0.00 0.00 0.00 1.40
1924 2163 1.492133 CCTCCCTCACCAAAGCCAGA 61.492 60.000 0.00 0.00 0.00 3.86
1933 2172 2.955660 CACCAAAGCCAGACAAACCTTA 59.044 45.455 0.00 0.00 0.00 2.69
1934 2173 2.956333 ACCAAAGCCAGACAAACCTTAC 59.044 45.455 0.00 0.00 0.00 2.34
1948 2187 9.176460 AGACAAACCTTACTGTAGTAGATAGTC 57.824 37.037 0.00 0.00 31.01 2.59
2018 2257 4.260538 GCAACCATCGCTGATAAAGAGAAG 60.261 45.833 0.00 0.00 38.30 2.85
2020 2259 3.118629 ACCATCGCTGATAAAGAGAAGCA 60.119 43.478 0.00 0.00 38.30 3.91
2026 2265 6.385843 TCGCTGATAAAGAGAAGCATAGATC 58.614 40.000 0.00 0.00 35.33 2.75
2073 2312 6.013085 CACAAATGTAGACGAACAAATACCG 58.987 40.000 0.00 0.00 32.02 4.02
2103 2342 9.347240 CCATATAGATCCACTGAAGAAAAACAT 57.653 33.333 0.00 0.00 0.00 2.71
2174 2413 0.826256 ACACTAGACGCACCACCAGA 60.826 55.000 0.00 0.00 0.00 3.86
2177 2416 0.317160 CTAGACGCACCACCAGAACA 59.683 55.000 0.00 0.00 0.00 3.18
2220 2459 2.569853 TGTTTCATCTTAAGGGAGCCGA 59.430 45.455 1.85 0.00 0.00 5.54
2242 2481 3.011517 GCCTCCCCTTCCTGAGCA 61.012 66.667 0.00 0.00 0.00 4.26
2285 2524 8.943925 CAAACTCAAAAGAACACGTAAATACAG 58.056 33.333 0.00 0.00 0.00 2.74
2294 2533 6.979238 AGAACACGTAAATACAGAATAGGAGC 59.021 38.462 0.00 0.00 0.00 4.70
2378 2729 3.850173 AGGATGTTTTAAGTGCCTCCCTA 59.150 43.478 0.00 0.00 0.00 3.53
2466 2817 6.443792 AGTTAAAAGAATGCAAACCTAACCG 58.556 36.000 0.00 0.00 0.00 4.44
2477 2828 2.556144 ACCTAACCGAACTCCCAAAC 57.444 50.000 0.00 0.00 0.00 2.93
2543 2894 6.081356 TCCCTCTTCTTCTTCTTCTTCTTCT 58.919 40.000 0.00 0.00 0.00 2.85
2544 2895 6.556874 TCCCTCTTCTTCTTCTTCTTCTTCTT 59.443 38.462 0.00 0.00 0.00 2.52
2545 2896 6.873605 CCCTCTTCTTCTTCTTCTTCTTCTTC 59.126 42.308 0.00 0.00 0.00 2.87
2546 2897 7.256296 CCCTCTTCTTCTTCTTCTTCTTCTTCT 60.256 40.741 0.00 0.00 0.00 2.85
2547 2898 8.150296 CCTCTTCTTCTTCTTCTTCTTCTTCTT 58.850 37.037 0.00 0.00 0.00 2.52
2548 2899 9.196552 CTCTTCTTCTTCTTCTTCTTCTTCTTC 57.803 37.037 0.00 0.00 0.00 2.87
2549 2900 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2550 2901 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2551 2902 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2552 2903 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2553 2904 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2554 2905 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2555 2906 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2556 2907 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2557 2908 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2558 2909 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2559 2910 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2560 2911 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2561 2912 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2562 2913 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2563 2914 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2564 2915 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.067372 TGTCCATAAATAGCTCATTTCTTGTGG 59.933 37.037 0.00 3.52 37.93 4.17
26 27 7.615365 TGTCCTTGATTTTGTCCATAAATAGCT 59.385 33.333 0.00 0.00 0.00 3.32
40 41 7.461749 TCCTTTACTCTCATGTCCTTGATTTT 58.538 34.615 0.00 0.00 0.00 1.82
49 50 7.001674 TCTATCTCCTCCTTTACTCTCATGTC 58.998 42.308 0.00 0.00 0.00 3.06
50 51 6.916909 TCTATCTCCTCCTTTACTCTCATGT 58.083 40.000 0.00 0.00 0.00 3.21
76 81 1.327303 TGCGCCTCCACTTGATTTTT 58.673 45.000 4.18 0.00 0.00 1.94
77 82 1.000274 GTTGCGCCTCCACTTGATTTT 60.000 47.619 4.18 0.00 0.00 1.82
161 166 1.079127 AGAGGCATCGGTTTCCACG 60.079 57.895 0.00 0.00 0.00 4.94
170 175 2.105128 GGTGGACGAGAGGCATCG 59.895 66.667 10.13 10.13 45.40 3.84
183 188 7.717436 ACCACTTTATAAAAATTGTTTGGGTGG 59.283 33.333 17.60 17.60 42.21 4.61
188 193 8.911662 CCTCGACCACTTTATAAAAATTGTTTG 58.088 33.333 0.00 0.00 0.00 2.93
189 194 7.597369 GCCTCGACCACTTTATAAAAATTGTTT 59.403 33.333 0.00 0.00 0.00 2.83
195 200 3.685756 CGGCCTCGACCACTTTATAAAAA 59.314 43.478 0.00 0.00 39.00 1.94
205 210 0.953960 AACATTTCGGCCTCGACCAC 60.954 55.000 0.00 0.00 45.92 4.16
206 211 0.609151 TAACATTTCGGCCTCGACCA 59.391 50.000 0.00 0.00 45.92 4.02
221 226 5.063204 CCTCTCATGGTTGTTCTGTTAACA 58.937 41.667 8.28 8.28 0.00 2.41
222 227 5.305585 TCCTCTCATGGTTGTTCTGTTAAC 58.694 41.667 0.00 0.00 0.00 2.01
252 257 3.371034 TGGGATGAAGATGACTCGGTTA 58.629 45.455 0.00 0.00 0.00 2.85
256 261 4.202192 TGAAGATGGGATGAAGATGACTCG 60.202 45.833 0.00 0.00 0.00 4.18
264 269 3.887716 GGGTTGATGAAGATGGGATGAAG 59.112 47.826 0.00 0.00 0.00 3.02
265 270 3.528905 AGGGTTGATGAAGATGGGATGAA 59.471 43.478 0.00 0.00 0.00 2.57
266 271 3.125656 AGGGTTGATGAAGATGGGATGA 58.874 45.455 0.00 0.00 0.00 2.92
267 272 3.589951 AGGGTTGATGAAGATGGGATG 57.410 47.619 0.00 0.00 0.00 3.51
268 273 4.141158 GGTTAGGGTTGATGAAGATGGGAT 60.141 45.833 0.00 0.00 0.00 3.85
269 274 3.202151 GGTTAGGGTTGATGAAGATGGGA 59.798 47.826 0.00 0.00 0.00 4.37
270 275 3.555966 GGTTAGGGTTGATGAAGATGGG 58.444 50.000 0.00 0.00 0.00 4.00
271 276 3.206150 CGGTTAGGGTTGATGAAGATGG 58.794 50.000 0.00 0.00 0.00 3.51
272 277 2.614057 GCGGTTAGGGTTGATGAAGATG 59.386 50.000 0.00 0.00 0.00 2.90
273 278 2.421529 GGCGGTTAGGGTTGATGAAGAT 60.422 50.000 0.00 0.00 0.00 2.40
274 279 1.065709 GGCGGTTAGGGTTGATGAAGA 60.066 52.381 0.00 0.00 0.00 2.87
275 280 1.379527 GGCGGTTAGGGTTGATGAAG 58.620 55.000 0.00 0.00 0.00 3.02
296 301 4.568592 GGGGGCTATGGAGATAGAAAATGG 60.569 50.000 0.00 0.00 34.44 3.16
317 322 3.649981 ACTATGGTGAAGATGGAGATGGG 59.350 47.826 0.00 0.00 0.00 4.00
343 348 2.472029 ACAAGTATGACTGGAGGAGGG 58.528 52.381 0.00 0.00 0.00 4.30
351 356 9.511144 TGTTATACACGATTACAAGTATGACTG 57.489 33.333 0.00 0.00 35.63 3.51
373 378 2.192664 ACAATGGATGCCGTGTGTTA 57.807 45.000 0.00 0.00 0.00 2.41
382 387 7.395190 TGATAATATGCCTTACAATGGATGC 57.605 36.000 0.00 0.00 0.00 3.91
614 620 6.098679 TGCATACAAATCTAAACATTGCCAC 58.901 36.000 0.00 0.00 0.00 5.01
615 621 6.278172 TGCATACAAATCTAAACATTGCCA 57.722 33.333 0.00 0.00 0.00 4.92
641 647 8.303876 ACCGGTATGCCATATTTGAAAATTATC 58.696 33.333 4.49 0.00 34.09 1.75
644 650 6.478512 ACCGGTATGCCATATTTGAAAATT 57.521 33.333 4.49 0.00 34.09 1.82
647 653 3.562141 CGACCGGTATGCCATATTTGAAA 59.438 43.478 7.34 0.00 34.09 2.69
649 655 2.761559 CGACCGGTATGCCATATTTGA 58.238 47.619 7.34 0.00 34.09 2.69
669 675 2.202298 CCGACGCATTTTGTCCGC 60.202 61.111 0.00 0.00 32.68 5.54
714 720 1.810532 GGAGTCTCGCTTCATCCGT 59.189 57.895 0.00 0.00 0.00 4.69
719 725 0.963856 TAAGGCGGAGTCTCGCTTCA 60.964 55.000 20.37 2.22 40.46 3.02
721 727 1.248785 TGTAAGGCGGAGTCTCGCTT 61.249 55.000 20.37 13.36 40.46 4.68
725 731 1.142097 GGCTGTAAGGCGGAGTCTC 59.858 63.158 0.00 0.00 40.46 3.36
756 770 4.887071 TCAAATGGACCCGGATTTAATCTG 59.113 41.667 0.73 6.79 35.39 2.90
757 771 5.124036 TCAAATGGACCCGGATTTAATCT 57.876 39.130 0.73 0.00 0.00 2.40
761 775 2.650322 GCTCAAATGGACCCGGATTTA 58.350 47.619 0.73 0.00 0.00 1.40
768 782 0.608035 TCCAACGCTCAAATGGACCC 60.608 55.000 0.00 0.00 38.30 4.46
774 788 0.598065 GGCAACTCCAACGCTCAAAT 59.402 50.000 0.00 0.00 34.01 2.32
800 814 0.744057 CGATGTGCCATGTGCCTACA 60.744 55.000 4.07 3.56 41.89 2.74
829 849 1.669265 CTGCTTGCATGACGATGTGAT 59.331 47.619 3.33 0.00 31.50 3.06
882 903 1.500396 GCCGATGGTCGTTTTCACC 59.500 57.895 0.00 0.00 38.40 4.02
951 975 1.576421 GCGTTGTGAGCTTTGGGAG 59.424 57.895 0.00 0.00 0.00 4.30
966 990 2.044848 TGTGGTTGTTGGTGGCGT 60.045 55.556 0.00 0.00 0.00 5.68
990 1014 1.219935 GGCAACGGGTGTAGTAGGG 59.780 63.158 0.00 0.00 0.00 3.53
1045 1069 2.685380 AGGAAGAGGAGCCGGTGG 60.685 66.667 1.90 0.00 0.00 4.61
1046 1070 2.726351 GGAGGAAGAGGAGCCGGTG 61.726 68.421 1.90 0.00 0.00 4.94
1258 1283 3.841758 GCGTTCGGGTACGGGGAT 61.842 66.667 7.53 0.00 41.65 3.85
1443 1468 2.853290 CGTCCCGGCGGTAGCTAAT 61.853 63.158 26.32 0.00 44.37 1.73
1517 1553 2.485122 CGAATCGGCAGCCCAAAC 59.515 61.111 5.63 0.00 0.00 2.93
1534 1576 6.790285 TGTTTCACCGTAGAATCTTAAACC 57.210 37.500 0.00 0.00 0.00 3.27
1562 1604 0.030235 GGCAGAACCAAACGGAACAC 59.970 55.000 0.00 0.00 38.86 3.32
1573 1615 0.598065 GAACACATGTGGGCAGAACC 59.402 55.000 28.64 5.70 37.93 3.62
1575 1617 2.371841 ACTAGAACACATGTGGGCAGAA 59.628 45.455 28.64 8.89 34.19 3.02
1581 1623 3.058708 CACAAGCACTAGAACACATGTGG 60.059 47.826 28.64 13.47 34.73 4.17
1685 1732 3.627577 AGTGTAGCCGGCTCATAAAATTG 59.372 43.478 36.73 0.00 0.00 2.32
1686 1733 3.886123 AGTGTAGCCGGCTCATAAAATT 58.114 40.909 36.73 8.54 0.00 1.82
1701 1938 6.149474 CCATCTTTGTTGGTCCTTTAGTGTAG 59.851 42.308 0.00 0.00 0.00 2.74
1792 2031 8.585471 ACCATGTTGTTTGATGAATAGATCTT 57.415 30.769 0.00 0.00 0.00 2.40
1845 2084 8.102484 AGGTGGTCTATGAACCTAAATGTAAT 57.898 34.615 0.00 0.00 42.59 1.89
1852 2091 5.655532 GTCACTAGGTGGTCTATGAACCTAA 59.344 44.000 2.68 0.00 44.06 2.69
1896 2135 1.649271 GGTGAGGGAGGGGCAATGAT 61.649 60.000 0.00 0.00 0.00 2.45
1924 2163 8.874744 TGACTATCTACTACAGTAAGGTTTGT 57.125 34.615 0.00 0.00 0.00 2.83
1933 2172 8.596781 ACAAATTCCTGACTATCTACTACAGT 57.403 34.615 0.00 0.00 0.00 3.55
1934 2173 8.687242 TGACAAATTCCTGACTATCTACTACAG 58.313 37.037 0.00 0.00 0.00 2.74
1948 2187 4.096984 GGGTCTTAGCATGACAAATTCCTG 59.903 45.833 0.00 0.00 36.26 3.86
2026 2265 4.872691 GTGTCTACATGTTGGATCCTTCTG 59.127 45.833 14.23 7.85 0.00 3.02
2040 2279 6.020971 TCGTCTACATTTGTGTGTCTACAT 57.979 37.500 0.00 0.00 39.39 2.29
2073 2312 9.784531 TTTTCTTCAGTGGATCTATATGGATTC 57.215 33.333 2.77 1.52 0.00 2.52
2103 2342 3.384668 GGATCTTGCGAGATTTGATCGA 58.615 45.455 17.76 0.00 42.66 3.59
2174 2413 0.247736 CTCGCTGCCTAGTTCCTGTT 59.752 55.000 0.00 0.00 0.00 3.16
2177 2416 0.533032 GTTCTCGCTGCCTAGTTCCT 59.467 55.000 0.00 0.00 0.00 3.36
2220 2459 2.041265 AGGAAGGGGAGGCGATGT 59.959 61.111 0.00 0.00 0.00 3.06
2242 2481 6.607019 TGAGTTTGTTTAGGGTTTATGTCCT 58.393 36.000 0.00 0.00 37.18 3.85
2294 2533 2.935481 TCCTTGCCTGTGGGAGGG 60.935 66.667 0.00 0.00 43.07 4.30
2378 2729 8.870075 AGGAGTTAAATTTTATGAGTTCAGCT 57.130 30.769 0.00 0.00 0.00 4.24
2440 2791 7.521585 CGGTTAGGTTTGCATTCTTTTAACTCT 60.522 37.037 0.00 0.00 0.00 3.24
2466 2817 4.969484 TGAGGAGTTAAGTTTGGGAGTTC 58.031 43.478 0.00 0.00 0.00 3.01
2477 2828 4.448060 GTCTGGTTCGTTTGAGGAGTTAAG 59.552 45.833 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.