Multiple sequence alignment - TraesCS2B01G485400

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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 TraesCS2B01G485400 chr2B 100.000 3017 0 0 1 3017 682574604 682571588 0.000000e+00 5572.0
1 TraesCS2B01G485400 chr2B 88.316 1087 91 16 903 1978 682227493 682226432 0.000000e+00 1271.0
2 TraesCS2B01G485400 chr2D 90.060 2495 201 26 343 2812 570090597 570088125 0.000000e+00 3190.0
3 TraesCS2B01G485400 chr2D 92.621 1030 53 10 962 1978 570063161 570062142 0.000000e+00 1459.0
4 TraesCS2B01G485400 chr2D 89.260 1108 91 13 893 1978 569854360 569853259 0.000000e+00 1362.0
5 TraesCS2B01G485400 chr2D 88.049 820 85 7 2002 2819 570058647 570057839 0.000000e+00 959.0
6 TraesCS2B01G485400 chr2D 89.381 339 35 1 2 340 570091003 570090666 2.780000e-115 425.0
7 TraesCS2B01G485400 chr2D 88.430 121 14 0 2897 3017 570057468 570057348 2.420000e-31 147.0
8 TraesCS2B01G485400 chr2D 84.337 83 12 1 2496 2578 635746751 635746832 2.490000e-11 80.5
9 TraesCS2B01G485400 chr2A 89.114 2223 184 20 783 2977 709186019 709183827 0.000000e+00 2712.0
10 TraesCS2B01G485400 chr2A 87.583 604 59 5 1227 1818 709126695 709126096 0.000000e+00 686.0
11 TraesCS2B01G485400 chr2A 85.924 341 26 9 903 1237 709153366 709153042 8.010000e-91 344.0
12 TraesCS2B01G485400 chr2A 94.839 155 7 1 579 732 709186192 709186038 1.080000e-59 241.0
13 TraesCS2B01G485400 chr2A 85.644 202 14 8 3 204 709186381 709186195 6.600000e-47 198.0
14 TraesCS2B01G485400 chr2A 85.950 121 13 3 1852 1970 709126095 709125977 3.160000e-25 126.0
15 TraesCS2B01G485400 chr4D 81.220 410 59 10 1402 1802 685261 684861 6.280000e-82 315.0
16 TraesCS2B01G485400 chr4A 84.828 290 38 5 1394 1677 933119 932830 1.370000e-73 287.0
17 TraesCS2B01G485400 chr4A 85.526 76 11 0 2495 2570 641847011 641846936 2.490000e-11 80.5
18 TraesCS2B01G485400 chr4B 83.946 299 42 5 1385 1677 1102327 1102625 6.370000e-72 281.0
19 TraesCS2B01G485400 chr5B 86.765 68 9 0 2506 2573 598981338 598981405 3.230000e-10 76.8
20 TraesCS2B01G485400 chr1B 76.692 133 29 2 2476 2606 317842583 317842451 4.170000e-09 73.1
21 TraesCS2B01G485400 chr7A 93.617 47 3 0 2525 2571 657372952 657372998 1.500000e-08 71.3


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 TraesCS2B01G485400 chr2B 682571588 682574604 3016 True 5572.000000 5572 100.000000 1 3017 1 chr2B.!!$R2 3016
1 TraesCS2B01G485400 chr2B 682226432 682227493 1061 True 1271.000000 1271 88.316000 903 1978 1 chr2B.!!$R1 1075
2 TraesCS2B01G485400 chr2D 570088125 570091003 2878 True 1807.500000 3190 89.720500 2 2812 2 chr2D.!!$R3 2810
3 TraesCS2B01G485400 chr2D 569853259 569854360 1101 True 1362.000000 1362 89.260000 893 1978 1 chr2D.!!$R1 1085
4 TraesCS2B01G485400 chr2D 570057348 570063161 5813 True 855.000000 1459 89.700000 962 3017 3 chr2D.!!$R2 2055
5 TraesCS2B01G485400 chr2A 709183827 709186381 2554 True 1050.333333 2712 89.865667 3 2977 3 chr2A.!!$R3 2974
6 TraesCS2B01G485400 chr2A 709125977 709126695 718 True 406.000000 686 86.766500 1227 1970 2 chr2A.!!$R2 743

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
325 326 0.098200 GTTCGAGCAAAATACCCGGC 59.902 55.0 0.0 0.0 0.0 6.13 F
1112 1198 0.250467 AGCAGCATTTCACCGTCACT 60.250 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1884 0.107116 GAGCTCCTCCAGGTACTCGA 60.107 60.0 0.87 0.0 34.60 4.04 R
2381 6008 0.032515 TCAAGAGGCCGGTCTATCCA 60.033 55.0 9.57 0.0 35.57 3.41 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
46 47 8.504005 GCAACATCTAGTTATACAACAACACTT 58.496 33.333 0.00 0.00 38.74 3.16
176 177 8.906867 AGAGATTATTCAATTATGTGTGTTGGG 58.093 33.333 0.00 0.00 0.00 4.12
200 201 2.335316 TGCAAGTAGAAAACACCGGT 57.665 45.000 0.00 0.00 0.00 5.28
213 214 2.858745 ACACCGGTAACAAGAAATGCT 58.141 42.857 6.87 0.00 0.00 3.79
223 224 7.095355 CGGTAACAAGAAATGCTACTACAACTT 60.095 37.037 0.00 0.00 32.35 2.66
226 227 7.426929 ACAAGAAATGCTACTACAACTTCTG 57.573 36.000 0.00 0.00 30.46 3.02
228 229 7.171678 ACAAGAAATGCTACTACAACTTCTGAC 59.828 37.037 0.00 0.00 30.46 3.51
235 236 7.313646 TGCTACTACAACTTCTGACTACATTC 58.686 38.462 0.00 0.00 0.00 2.67
236 237 6.752815 GCTACTACAACTTCTGACTACATTCC 59.247 42.308 0.00 0.00 0.00 3.01
251 252 7.094075 TGACTACATTCCGAAACACTACTATGT 60.094 37.037 0.00 0.00 0.00 2.29
265 266 7.450074 ACACTACTATGTCCATTTCAACTCAA 58.550 34.615 0.00 0.00 0.00 3.02
281 282 6.841119 TCAACTCAATAATGGTCATTTGACG 58.159 36.000 4.72 0.00 45.65 4.35
284 285 4.980590 TCAATAATGGTCATTTGACGCAC 58.019 39.130 4.72 0.00 45.65 5.34
295 296 5.846994 GTCATTTGACGCACGTATTTGTTTA 59.153 36.000 0.00 0.00 35.12 2.01
303 304 8.016229 TGACGCACGTATTTGTTTACATATTTT 58.984 29.630 0.00 0.00 0.00 1.82
325 326 0.098200 GTTCGAGCAAAATACCCGGC 59.902 55.000 0.00 0.00 0.00 6.13
332 333 1.905637 CAAAATACCCGGCCCCTATC 58.094 55.000 0.00 0.00 0.00 2.08
333 334 0.775542 AAAATACCCGGCCCCTATCC 59.224 55.000 0.00 0.00 0.00 2.59
340 341 1.447643 CGGCCCCTATCCTGTGAAG 59.552 63.158 0.00 0.00 0.00 3.02
341 342 1.839894 GGCCCCTATCCTGTGAAGG 59.160 63.158 0.00 0.00 0.00 3.46
345 412 0.390860 CCCTATCCTGTGAAGGCTCG 59.609 60.000 0.00 0.00 0.00 5.03
351 418 3.137687 TGTGAAGGCTCGCAGACA 58.862 55.556 0.00 0.00 37.15 3.41
366 433 3.494626 CGCAGACAGTTAAGAGCAAAAGA 59.505 43.478 0.00 0.00 0.00 2.52
367 434 4.024893 CGCAGACAGTTAAGAGCAAAAGAA 60.025 41.667 0.00 0.00 0.00 2.52
370 437 6.416161 GCAGACAGTTAAGAGCAAAAGAAAAG 59.584 38.462 0.00 0.00 0.00 2.27
371 438 6.416161 CAGACAGTTAAGAGCAAAAGAAAAGC 59.584 38.462 0.00 0.00 0.00 3.51
378 445 6.639632 AAGAGCAAAAGAAAAGCATAGTGA 57.360 33.333 0.00 0.00 0.00 3.41
396 463 7.414429 GCATAGTGAAAGAAGTATGTTGCATGA 60.414 37.037 0.00 0.00 36.32 3.07
397 464 6.246420 AGTGAAAGAAGTATGTTGCATGAC 57.754 37.500 0.00 0.00 0.00 3.06
398 465 5.764686 AGTGAAAGAAGTATGTTGCATGACA 59.235 36.000 0.00 0.00 0.00 3.58
407 474 6.594744 AGTATGTTGCATGACATTCCATCTA 58.405 36.000 9.22 0.00 40.54 1.98
411 478 7.263100 TGTTGCATGACATTCCATCTATTAC 57.737 36.000 0.00 0.00 0.00 1.89
414 481 5.696270 TGCATGACATTCCATCTATTACGAC 59.304 40.000 0.00 0.00 0.00 4.34
415 482 5.696270 GCATGACATTCCATCTATTACGACA 59.304 40.000 0.00 0.00 0.00 4.35
439 506 8.358148 ACAAGAACGTCATAAGAGAAAAGAGTA 58.642 33.333 0.00 0.00 0.00 2.59
442 509 7.537991 AGAACGTCATAAGAGAAAAGAGTAACG 59.462 37.037 0.00 0.00 0.00 3.18
451 518 4.683832 AGAAAAGAGTAACGATCGATGGG 58.316 43.478 24.34 2.01 0.00 4.00
453 520 2.359981 AGAGTAACGATCGATGGGGA 57.640 50.000 24.34 0.00 0.00 4.81
459 526 1.324740 ACGATCGATGGGGAAACGGA 61.325 55.000 24.34 0.00 0.00 4.69
465 532 0.322546 GATGGGGAAACGGAAGCACT 60.323 55.000 0.00 0.00 0.00 4.40
466 533 0.609131 ATGGGGAAACGGAAGCACTG 60.609 55.000 0.00 0.00 0.00 3.66
500 567 6.183347 AGGATGGAAAAGAGAACAATGGTAG 58.817 40.000 0.00 0.00 0.00 3.18
504 571 9.396022 GATGGAAAAGAGAACAATGGTAGATAA 57.604 33.333 0.00 0.00 0.00 1.75
519 586 5.201243 GGTAGATAAGAAAATGGGGTTGCT 58.799 41.667 0.00 0.00 0.00 3.91
520 587 5.067805 GGTAGATAAGAAAATGGGGTTGCTG 59.932 44.000 0.00 0.00 0.00 4.41
530 597 3.756082 TGGGGTTGCTGGAGATAAAAT 57.244 42.857 0.00 0.00 0.00 1.82
534 601 2.695147 GGTTGCTGGAGATAAAATGGGG 59.305 50.000 0.00 0.00 0.00 4.96
536 603 0.954452 GCTGGAGATAAAATGGGGCG 59.046 55.000 0.00 0.00 0.00 6.13
542 609 3.498661 GGAGATAAAATGGGGCGGAGATT 60.499 47.826 0.00 0.00 0.00 2.40
543 610 3.490348 AGATAAAATGGGGCGGAGATTG 58.510 45.455 0.00 0.00 0.00 2.67
581 648 0.944386 CAATGGCCGTTTAGCGCTAT 59.056 50.000 19.60 0.00 39.71 2.97
606 673 8.492673 TGACACTATGGATGAAATACTTGTTC 57.507 34.615 0.00 0.00 0.00 3.18
607 674 8.100164 TGACACTATGGATGAAATACTTGTTCA 58.900 33.333 0.00 0.00 39.24 3.18
609 676 8.950210 ACACTATGGATGAAATACTTGTTCAAG 58.050 33.333 10.50 10.50 38.44 3.02
610 677 8.950210 CACTATGGATGAAATACTTGTTCAAGT 58.050 33.333 19.64 19.64 38.44 3.16
697 765 6.887002 TGCATACAACATTAGTTTACCATCCA 59.113 34.615 0.00 0.00 35.28 3.41
718 786 9.559958 CATCCAAGAGTTTATTTGTGTTGATAC 57.440 33.333 0.00 0.00 0.00 2.24
745 813 7.914427 TCATAAGGTGATAAGGATGTACTGT 57.086 36.000 0.00 0.00 0.00 3.55
746 814 9.601810 ATCATAAGGTGATAAGGATGTACTGTA 57.398 33.333 0.00 0.00 45.67 2.74
747 815 9.078990 TCATAAGGTGATAAGGATGTACTGTAG 57.921 37.037 0.00 0.00 0.00 2.74
748 816 8.861086 CATAAGGTGATAAGGATGTACTGTAGT 58.139 37.037 0.00 0.00 0.00 2.73
793 866 4.310769 CAATTTTCATGGGCGTGGTTAAA 58.689 39.130 0.00 0.00 0.00 1.52
829 902 1.718757 GATGCCGATGCCTTGGTGTC 61.719 60.000 0.00 0.00 36.33 3.67
839 912 1.798079 GCCTTGGTGTCTCGTCGTATC 60.798 57.143 0.00 0.00 0.00 2.24
912 986 1.588082 GTCGCAGTCCGTTCCCTTA 59.412 57.895 0.00 0.00 38.35 2.69
974 1048 3.062639 CGCAGTGGTGAGCTGTATAAAAG 59.937 47.826 0.00 0.00 36.42 2.27
1112 1198 0.250467 AGCAGCATTTCACCGTCACT 60.250 50.000 0.00 0.00 0.00 3.41
1237 1332 2.660064 CCCTCTTGGAGTCCACGGG 61.660 68.421 20.45 20.45 35.39 5.28
1255 1350 1.153208 GTCATGCCTCCTGCTCTGG 60.153 63.158 0.00 0.00 42.00 3.86
1388 1498 4.001226 GCCGTGCCCATTGCCAAA 62.001 61.111 0.00 0.00 40.16 3.28
1818 1934 2.124570 AGCCGCACATGGGTCATC 60.125 61.111 0.00 0.00 33.58 2.92
2209 5836 7.201902 GCATATGACAAATTTCACCCCTCATAA 60.202 37.037 6.97 0.00 0.00 1.90
2221 5848 1.414181 CCCTCATAAGTCTGCGGATGT 59.586 52.381 0.00 0.00 0.00 3.06
2227 5854 4.408821 GTCTGCGGATGTGGCCCA 62.409 66.667 0.00 0.00 0.00 5.36
2232 5859 2.051518 GCGGATGTGGCCCAATCAA 61.052 57.895 14.78 0.00 0.00 2.57
2243 5870 3.055240 TGGCCCAATCAACCATCATTTTC 60.055 43.478 0.00 0.00 0.00 2.29
2244 5871 3.055240 GGCCCAATCAACCATCATTTTCA 60.055 43.478 0.00 0.00 0.00 2.69
2246 5873 4.081531 GCCCAATCAACCATCATTTTCAGA 60.082 41.667 0.00 0.00 0.00 3.27
2248 5875 5.097529 CCAATCAACCATCATTTTCAGACG 58.902 41.667 0.00 0.00 0.00 4.18
2257 5884 2.228582 TCATTTTCAGACGGGTGCAATG 59.771 45.455 0.00 0.00 0.00 2.82
2327 5954 6.585322 ACTCAAAAGCAACGTACTACTACATC 59.415 38.462 0.00 0.00 0.00 3.06
2342 5969 6.713903 ACTACTACATCGCTATAGCCTAAACA 59.286 38.462 19.00 0.00 37.91 2.83
2359 5986 1.360551 CAGTCGGCGGAGATGTAGG 59.639 63.158 7.21 0.00 0.00 3.18
2381 6008 2.034879 CCTTCGTGTCGGCAATGCT 61.035 57.895 4.82 0.00 0.00 3.79
2397 6024 4.609098 CTGGATAGACCGGCCTCT 57.391 61.111 0.00 0.00 42.61 3.69
2409 6036 0.465097 CGGCCTCTTGATCATTGGCT 60.465 55.000 23.94 0.00 42.84 4.75
2416 6043 1.038681 TTGATCATTGGCTGCCGCAT 61.039 50.000 14.98 5.74 38.10 4.73
2447 6074 0.809385 TCCTCGTCGAACTCCATGTC 59.191 55.000 0.00 0.00 0.00 3.06
2448 6075 0.526211 CCTCGTCGAACTCCATGTCA 59.474 55.000 0.00 0.00 0.00 3.58
2451 6078 1.406219 CGTCGAACTCCATGTCAGCG 61.406 60.000 0.00 0.00 0.00 5.18
2499 6126 4.607293 CTCATGGAGGAATCGATGGTTA 57.393 45.455 0.00 0.00 0.00 2.85
2504 6131 2.548920 GGAGGAATCGATGGTTAGCCTG 60.549 54.545 0.00 0.00 35.27 4.85
2516 6143 1.492133 TTAGCCTGCACCTCTGCCTT 61.492 55.000 0.00 0.00 43.51 4.35
2517 6144 1.492133 TAGCCTGCACCTCTGCCTTT 61.492 55.000 0.00 0.00 43.51 3.11
2522 6149 2.338785 GCACCTCTGCCTTTGAGCC 61.339 63.158 0.00 0.00 37.45 4.70
2541 6168 0.605589 CTATGGAGTCGAGGATGGCC 59.394 60.000 0.00 0.00 0.00 5.36
2551 6178 4.119363 GGATGGCCTGCTGCTCCA 62.119 66.667 3.32 6.27 40.92 3.86
2552 6179 2.195139 GATGGCCTGCTGCTCCAT 59.805 61.111 17.07 17.07 42.83 3.41
2642 6271 2.935481 CACCTTCCTCCCCTGGCA 60.935 66.667 0.00 0.00 0.00 4.92
2665 6294 1.227999 CGCCCGTCATGTCTGTGTTT 61.228 55.000 0.00 0.00 0.00 2.83
2714 6343 1.380112 GAGTCCAGAGGTAGGCCGT 60.380 63.158 0.00 0.00 40.50 5.68
2751 6380 1.000866 GCCTGGCCCAAATCTCCTT 59.999 57.895 7.66 0.00 0.00 3.36
2787 6416 4.872357 CTCCGGAGCAAGCATGAT 57.128 55.556 20.67 0.00 0.00 2.45
2794 6423 2.009774 GGAGCAAGCATGATGTACGTT 58.990 47.619 0.00 0.00 0.00 3.99
2801 6430 3.860641 AGCATGATGTACGTTGTGATCA 58.139 40.909 0.00 0.00 0.00 2.92
2802 6431 4.252878 AGCATGATGTACGTTGTGATCAA 58.747 39.130 0.00 0.00 0.00 2.57
2828 6457 0.969894 GGCCATGACTACTAGCGGAT 59.030 55.000 0.00 0.00 0.00 4.18
2830 6459 1.337260 GCCATGACTACTAGCGGATGG 60.337 57.143 0.00 0.00 34.62 3.51
2851 6480 4.185413 GCTCGAGCGAATTGGACA 57.815 55.556 23.61 0.00 0.00 4.02
2917 6839 0.247185 GTTGGGGTTACGTCATCCGA 59.753 55.000 0.00 0.00 40.70 4.55
2960 6882 4.980805 GGGTGGCACGTCGAAGCA 62.981 66.667 12.17 0.00 0.00 3.91
2963 6885 3.334751 TGGCACGTCGAAGCAACG 61.335 61.111 14.34 0.00 45.37 4.10
2978 6900 0.389391 CAACGACACTCACTGGACCT 59.611 55.000 0.00 0.00 0.00 3.85
2980 6902 1.210413 CGACACTCACTGGACCTCG 59.790 63.158 0.00 0.00 0.00 4.63
2987 6909 2.616969 CACTGGACCTCGGTGTTTG 58.383 57.895 0.00 0.00 45.35 2.93
2990 6912 0.602905 CTGGACCTCGGTGTTTGGAC 60.603 60.000 0.00 0.00 0.00 4.02
2992 6914 1.068585 GACCTCGGTGTTTGGACGT 59.931 57.895 0.00 0.00 0.00 4.34
2993 6915 1.219522 GACCTCGGTGTTTGGACGTG 61.220 60.000 0.00 0.00 0.00 4.49
3005 6927 2.660552 GACGTGTGTCCGTGTGGG 60.661 66.667 0.00 0.00 41.98 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.464865 CTCTTGCCGATCCGTCTTTAG 58.535 52.381 0.00 0.00 0.00 1.85
12 13 2.015736 ACTAGATGTTGCTCTTGCCG 57.984 50.000 0.00 0.00 38.71 5.69
17 18 8.094548 TGTTGTTGTATAACTAGATGTTGCTCT 58.905 33.333 0.00 0.00 39.55 4.09
57 58 7.386573 CCACACTTTGTACACACATATAACTCA 59.613 37.037 0.00 0.00 33.76 3.41
58 59 7.623506 GCCACACTTTGTACACACATATAACTC 60.624 40.741 0.00 0.00 33.76 3.01
81 82 0.596082 GCCTTCAAAAGCTTACGCCA 59.404 50.000 0.00 0.00 36.60 5.69
151 152 8.902806 TCCCAACACACATAATTGAATAATCTC 58.097 33.333 0.00 0.00 0.00 2.75
176 177 4.679654 CCGGTGTTTTCTACTTGCATTTTC 59.320 41.667 0.00 0.00 0.00 2.29
200 201 8.988934 CAGAAGTTGTAGTAGCATTTCTTGTTA 58.011 33.333 0.00 0.00 0.00 2.41
213 214 6.656270 TCGGAATGTAGTCAGAAGTTGTAGTA 59.344 38.462 0.00 0.00 0.00 1.82
223 224 4.866508 AGTGTTTCGGAATGTAGTCAGA 57.133 40.909 0.00 0.00 0.00 3.27
226 227 7.256286 ACATAGTAGTGTTTCGGAATGTAGTC 58.744 38.462 0.00 0.00 0.00 2.59
228 229 6.696148 GGACATAGTAGTGTTTCGGAATGTAG 59.304 42.308 0.00 0.00 31.16 2.74
235 236 5.872617 TGAAATGGACATAGTAGTGTTTCGG 59.127 40.000 0.00 0.00 31.16 4.30
236 237 6.961359 TGAAATGGACATAGTAGTGTTTCG 57.039 37.500 0.00 0.00 31.16 3.46
265 266 3.006940 ACGTGCGTCAAATGACCATTAT 58.993 40.909 7.91 0.00 41.86 1.28
303 304 2.226912 CCGGGTATTTTGCTCGAACAAA 59.773 45.455 9.84 9.84 37.74 2.83
305 306 1.444836 CCGGGTATTTTGCTCGAACA 58.555 50.000 0.00 0.00 30.18 3.18
307 308 1.027792 GGCCGGGTATTTTGCTCGAA 61.028 55.000 2.18 0.00 30.18 3.71
309 310 2.478033 GGGCCGGGTATTTTGCTCG 61.478 63.158 2.18 0.00 0.00 5.03
313 314 1.546998 GGATAGGGGCCGGGTATTTTG 60.547 57.143 2.18 0.00 0.00 2.44
325 326 0.761802 GAGCCTTCACAGGATAGGGG 59.238 60.000 0.00 0.00 39.72 4.79
332 333 1.739562 GTCTGCGAGCCTTCACAGG 60.740 63.158 0.00 0.00 44.28 4.00
333 334 1.005748 TGTCTGCGAGCCTTCACAG 60.006 57.895 0.00 0.00 35.31 3.66
340 341 1.634702 CTCTTAACTGTCTGCGAGCC 58.365 55.000 0.00 0.00 0.00 4.70
341 342 0.995728 GCTCTTAACTGTCTGCGAGC 59.004 55.000 0.00 0.00 37.35 5.03
345 412 5.424121 TTCTTTTGCTCTTAACTGTCTGC 57.576 39.130 0.00 0.00 0.00 4.26
351 418 8.078596 CACTATGCTTTTCTTTTGCTCTTAACT 58.921 33.333 0.00 0.00 0.00 2.24
366 433 7.809806 GCAACATACTTCTTTCACTATGCTTTT 59.190 33.333 0.00 0.00 0.00 2.27
367 434 7.040478 TGCAACATACTTCTTTCACTATGCTTT 60.040 33.333 0.00 0.00 0.00 3.51
370 437 6.182039 TGCAACATACTTCTTTCACTATGC 57.818 37.500 0.00 0.00 0.00 3.14
371 438 7.907045 GTCATGCAACATACTTCTTTCACTATG 59.093 37.037 0.00 0.00 0.00 2.23
378 445 6.209192 TGGAATGTCATGCAACATACTTCTTT 59.791 34.615 4.48 0.00 38.92 2.52
396 463 6.475727 CGTTCTTGTCGTAATAGATGGAATGT 59.524 38.462 0.00 0.00 0.00 2.71
397 464 6.475727 ACGTTCTTGTCGTAATAGATGGAATG 59.524 38.462 0.00 0.00 39.78 2.67
398 465 6.570692 ACGTTCTTGTCGTAATAGATGGAAT 58.429 36.000 0.00 0.00 39.78 3.01
407 474 6.849502 TCTCTTATGACGTTCTTGTCGTAAT 58.150 36.000 8.51 0.00 44.82 1.89
411 478 6.362551 TCTTTTCTCTTATGACGTTCTTGTCG 59.637 38.462 0.00 0.00 41.87 4.35
414 481 7.644986 ACTCTTTTCTCTTATGACGTTCTTG 57.355 36.000 0.00 0.00 0.00 3.02
415 482 9.194271 GTTACTCTTTTCTCTTATGACGTTCTT 57.806 33.333 0.00 0.00 0.00 2.52
439 506 0.461339 CCGTTTCCCCATCGATCGTT 60.461 55.000 15.94 3.47 0.00 3.85
442 509 1.583054 CTTCCGTTTCCCCATCGATC 58.417 55.000 0.00 0.00 0.00 3.69
451 518 1.576421 CTGCAGTGCTTCCGTTTCC 59.424 57.895 17.60 0.00 0.00 3.13
453 520 2.555547 GCCTGCAGTGCTTCCGTTT 61.556 57.895 17.60 0.00 0.00 3.60
466 533 4.802051 TCCATCCTTGCCGCCTGC 62.802 66.667 0.00 0.00 41.77 4.85
477 544 6.180472 TCTACCATTGTTCTCTTTTCCATCC 58.820 40.000 0.00 0.00 0.00 3.51
500 567 4.023291 TCCAGCAACCCCATTTTCTTATC 58.977 43.478 0.00 0.00 0.00 1.75
504 571 1.428912 TCTCCAGCAACCCCATTTTCT 59.571 47.619 0.00 0.00 0.00 2.52
509 576 3.756082 TTTTATCTCCAGCAACCCCAT 57.244 42.857 0.00 0.00 0.00 4.00
519 586 1.142870 CTCCGCCCCATTTTATCTCCA 59.857 52.381 0.00 0.00 0.00 3.86
520 587 1.420138 TCTCCGCCCCATTTTATCTCC 59.580 52.381 0.00 0.00 0.00 3.71
530 597 2.070039 CCCTACAATCTCCGCCCCA 61.070 63.158 0.00 0.00 0.00 4.96
534 601 0.539986 TGTTCCCCTACAATCTCCGC 59.460 55.000 0.00 0.00 0.00 5.54
536 603 3.954258 CCATTTGTTCCCCTACAATCTCC 59.046 47.826 0.00 0.00 37.81 3.71
542 609 1.549037 GCCACCATTTGTTCCCCTACA 60.549 52.381 0.00 0.00 0.00 2.74
543 610 1.182667 GCCACCATTTGTTCCCCTAC 58.817 55.000 0.00 0.00 0.00 3.18
577 644 8.715998 CAAGTATTTCATCCATAGTGTCATAGC 58.284 37.037 0.00 0.00 0.00 2.97
581 648 8.100164 TGAACAAGTATTTCATCCATAGTGTCA 58.900 33.333 0.00 0.00 0.00 3.58
697 765 9.214957 TGATCGTATCAACACAAATAAACTCTT 57.785 29.630 0.00 0.00 36.11 2.85
718 786 7.757173 CAGTACATCCTTATCACCTTATGATCG 59.243 40.741 0.00 0.00 45.52 3.69
759 832 6.164876 CCCATGAAAATTGCAATTGTCACTA 58.835 36.000 36.11 20.86 43.40 2.74
769 842 0.037512 CCACGCCCATGAAAATTGCA 60.038 50.000 0.00 0.00 0.00 4.08
793 866 0.176680 ATCGCGCTTCTTCACATCCT 59.823 50.000 5.56 0.00 0.00 3.24
912 986 7.880195 CCTCCTGATTTGATCCGAGTAATTTAT 59.120 37.037 0.00 0.00 0.00 1.40
960 1034 1.745827 GCGGGGCTTTTATACAGCTCA 60.746 52.381 5.52 0.00 39.81 4.26
1049 1134 4.180946 CGACGGGGAGACAGAGCG 62.181 72.222 0.00 0.00 0.00 5.03
1176 1271 2.530177 CATGTCGCTCATGTCGTAGTT 58.470 47.619 10.71 0.00 46.18 2.24
1255 1350 4.668151 TCGAAGAGAGAGAGGGGC 57.332 61.111 0.00 0.00 0.00 5.80
1352 1459 4.947147 GCGGTGGCTTGGTGACCA 62.947 66.667 0.00 0.00 35.83 4.02
1388 1498 2.579201 CGCACCCCGATGAAGTCT 59.421 61.111 0.00 0.00 40.02 3.24
1768 1884 0.107116 GAGCTCCTCCAGGTACTCGA 60.107 60.000 0.87 0.00 34.60 4.04
1807 1923 1.361204 TGTGTGGAGATGACCCATGT 58.639 50.000 0.00 0.00 35.91 3.21
1813 1929 1.626654 CGCCGTTGTGTGGAGATGAC 61.627 60.000 0.00 0.00 0.00 3.06
1818 1934 3.403057 CGTCGCCGTTGTGTGGAG 61.403 66.667 0.00 0.00 0.00 3.86
2109 5736 0.893727 AGATTTGCCGCCGGTTTTCT 60.894 50.000 4.45 0.00 0.00 2.52
2152 5779 8.718102 AAGATGCACTTATGTTATTCTTACGT 57.282 30.769 0.00 0.00 37.03 3.57
2209 5836 4.101448 GGGCCACATCCGCAGACT 62.101 66.667 4.39 0.00 0.00 3.24
2221 5848 2.250921 AATGATGGTTGATTGGGCCA 57.749 45.000 0.00 0.00 36.64 5.36
2227 5854 4.158394 CCCGTCTGAAAATGATGGTTGATT 59.842 41.667 0.00 0.00 38.57 2.57
2232 5859 2.436417 CACCCGTCTGAAAATGATGGT 58.564 47.619 0.00 0.00 38.57 3.55
2243 5870 2.672651 TGCCATTGCACCCGTCTG 60.673 61.111 0.00 0.00 44.23 3.51
2273 5900 8.733458 CATGGTGTAGTATGGATTTGGATTATG 58.267 37.037 0.00 0.00 0.00 1.90
2277 5904 5.072741 GCATGGTGTAGTATGGATTTGGAT 58.927 41.667 0.00 0.00 0.00 3.41
2278 5905 4.080072 TGCATGGTGTAGTATGGATTTGGA 60.080 41.667 0.00 0.00 0.00 3.53
2279 5906 4.206375 TGCATGGTGTAGTATGGATTTGG 58.794 43.478 0.00 0.00 0.00 3.28
2327 5954 2.662700 CCGACTGTTTAGGCTATAGCG 58.337 52.381 18.30 5.39 43.26 4.26
2342 5969 2.491022 GCCTACATCTCCGCCGACT 61.491 63.158 0.00 0.00 0.00 4.18
2359 5986 1.369091 ATTGCCGACACGAAGGATGC 61.369 55.000 0.00 0.00 0.00 3.91
2381 6008 0.032515 TCAAGAGGCCGGTCTATCCA 60.033 55.000 9.57 0.00 35.57 3.41
2397 6024 1.038681 ATGCGGCAGCCAATGATCAA 61.039 50.000 13.30 0.00 44.33 2.57
2435 6062 0.994995 CTTCGCTGACATGGAGTTCG 59.005 55.000 0.00 0.00 0.00 3.95
2437 6064 1.620819 ACTCTTCGCTGACATGGAGTT 59.379 47.619 0.00 0.00 31.14 3.01
2438 6065 1.261480 ACTCTTCGCTGACATGGAGT 58.739 50.000 0.00 0.00 0.00 3.85
2451 6078 1.697207 GAAGCGCGACGAACTCTTC 59.303 57.895 12.10 7.52 0.00 2.87
2494 6121 1.679311 CAGAGGTGCAGGCTAACCA 59.321 57.895 17.99 0.07 39.05 3.67
2516 6143 1.063942 TCCTCGACTCCATAGGCTCAA 60.064 52.381 0.00 0.00 0.00 3.02
2517 6144 0.551396 TCCTCGACTCCATAGGCTCA 59.449 55.000 0.00 0.00 0.00 4.26
2522 6149 0.605589 GGCCATCCTCGACTCCATAG 59.394 60.000 0.00 0.00 0.00 2.23
2541 6168 2.588314 GAGGCGATGGAGCAGCAG 60.588 66.667 0.00 0.00 39.27 4.24
2551 6178 2.370445 CCCAAGTGGAGGAGGCGAT 61.370 63.158 0.00 0.00 37.39 4.58
2552 6179 3.003173 CCCAAGTGGAGGAGGCGA 61.003 66.667 0.00 0.00 37.39 5.54
2648 6277 1.877637 TCAAACACAGACATGACGGG 58.122 50.000 0.00 0.00 0.00 5.28
2650 6279 2.481568 AGCATCAAACACAGACATGACG 59.518 45.455 0.00 0.00 0.00 4.35
2659 6288 2.608506 GCATGAGCAAGCATCAAACACA 60.609 45.455 0.00 0.00 41.58 3.72
2665 6294 0.255033 AGGAGCATGAGCAAGCATCA 59.745 50.000 0.00 0.00 45.49 3.07
2714 6343 2.125552 CGCCACTCGGATTGCAGA 60.126 61.111 0.00 0.00 33.78 4.26
2751 6380 1.359117 CGGCGATTCGAGCTCCTAA 59.641 57.895 10.88 3.18 34.52 2.69
2779 6408 4.252878 TGATCACAACGTACATCATGCTT 58.747 39.130 0.00 0.00 0.00 3.91
2794 6423 1.003839 GGCCCGACAGTTGATCACA 60.004 57.895 0.00 0.00 0.00 3.58
2801 6430 0.249398 GTAGTCATGGCCCGACAGTT 59.751 55.000 21.00 6.55 35.77 3.16
2802 6431 0.614979 AGTAGTCATGGCCCGACAGT 60.615 55.000 21.00 9.61 35.77 3.55
2828 6457 0.737367 CAATTCGCTCGAGCTCACCA 60.737 55.000 32.88 13.67 39.32 4.17
2830 6459 0.458543 TCCAATTCGCTCGAGCTCAC 60.459 55.000 32.88 6.78 39.32 3.51
2848 6477 1.961277 CCTCCGTGTTGCCACTGTC 60.961 63.158 0.00 0.00 39.55 3.51
2851 6480 3.953775 CCCCTCCGTGTTGCCACT 61.954 66.667 0.00 0.00 39.55 4.00
2871 6500 1.565759 CAGTCCCATTTCCATCCTCCA 59.434 52.381 0.00 0.00 0.00 3.86
2874 6503 0.259938 GCCAGTCCCATTTCCATCCT 59.740 55.000 0.00 0.00 0.00 3.24
2876 6505 2.487986 CCTAGCCAGTCCCATTTCCATC 60.488 54.545 0.00 0.00 0.00 3.51
2877 6506 1.496429 CCTAGCCAGTCCCATTTCCAT 59.504 52.381 0.00 0.00 0.00 3.41
2917 6839 6.415573 AGACTTTCAATCCGGCTATTTAAGT 58.584 36.000 0.00 4.86 29.99 2.24
2960 6882 0.674534 GAGGTCCAGTGAGTGTCGTT 59.325 55.000 0.00 0.00 0.00 3.85
2963 6885 1.179814 ACCGAGGTCCAGTGAGTGTC 61.180 60.000 0.00 0.00 0.00 3.67
2978 6900 0.806884 GACACACGTCCAAACACCGA 60.807 55.000 0.00 0.00 36.02 4.69
2990 6912 2.660552 GACCCACACGGACACACG 60.661 66.667 0.00 0.00 40.31 4.49
2992 6914 3.552384 GGGACCCACACGGACACA 61.552 66.667 5.33 0.00 34.64 3.72


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

AutoCloner maintained by Alex Coulton.