Multiple sequence alignment - TraesCS2D01G437100

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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 TraesCS2D01G437100 chr2D 100.000 2552 0 0 1 2552 547426179 547428730 0.000000e+00 4713.0
1 TraesCS2D01G437100 chr2D 91.061 1253 49 27 791 1992 547286282 547287522 0.000000e+00 1635.0
2 TraesCS2D01G437100 chr2D 92.703 836 30 12 920 1735 547278276 547279100 0.000000e+00 1177.0
3 TraesCS2D01G437100 chr2D 81.422 1238 136 41 800 1995 547450609 547451794 0.000000e+00 926.0
4 TraesCS2D01G437100 chr2D 81.291 1224 141 40 791 1972 547489048 547490225 0.000000e+00 911.0
5 TraesCS2D01G437100 chr2D 90.227 706 43 12 61 755 547488367 547489057 0.000000e+00 898.0
6 TraesCS2D01G437100 chr2D 94.659 543 28 1 2011 2552 547287815 547288357 0.000000e+00 841.0
7 TraesCS2D01G437100 chr2D 84.099 849 102 14 805 1631 547559292 547560129 0.000000e+00 789.0
8 TraesCS2D01G437100 chr2D 91.344 543 45 2 2011 2552 547279605 547280146 0.000000e+00 741.0
9 TraesCS2D01G437100 chr2D 81.333 750 94 20 906 1636 547574530 547575252 3.680000e-158 568.0
10 TraesCS2D01G437100 chr2D 88.406 414 35 8 355 755 547547695 547548108 1.060000e-133 486.0
11 TraesCS2D01G437100 chr2D 89.825 285 25 3 2011 2293 547490559 547490841 1.870000e-96 363.0
12 TraesCS2D01G437100 chr2D 87.981 208 17 4 1788 1991 547279108 547279311 3.280000e-59 239.0
13 TraesCS2D01G437100 chr2D 98.361 61 1 0 1 61 547488221 547488281 9.650000e-20 108.0
14 TraesCS2D01G437100 chr2D 95.349 43 2 0 755 797 538941086 538941128 4.560000e-08 69.4
15 TraesCS2D01G437100 chr2D 91.667 48 3 1 430 477 382172365 382172319 5.890000e-07 65.8
16 TraesCS2D01G437100 chr2B 88.390 1180 74 21 856 1992 653788261 653789420 0.000000e+00 1362.0
17 TraesCS2D01G437100 chr2B 94.280 542 30 1 2011 2551 653773701 653774242 0.000000e+00 828.0
18 TraesCS2D01G437100 chr2B 82.899 883 112 17 791 1657 653796073 653796932 0.000000e+00 758.0
19 TraesCS2D01G437100 chr2B 84.218 754 91 15 920 1657 653808271 653809012 0.000000e+00 708.0
20 TraesCS2D01G437100 chr2B 87.234 564 33 14 1452 1990 653772858 653773407 7.810000e-170 606.0
21 TraesCS2D01G437100 chr2B 91.558 308 14 3 2246 2552 653792363 653792659 5.080000e-112 414.0
22 TraesCS2D01G437100 chr2B 96.154 156 6 0 2011 2166 653789713 653789868 3.260000e-64 255.0
23 TraesCS2D01G437100 chr2A 87.840 1176 76 37 800 1924 690747279 690748438 0.000000e+00 1317.0
24 TraesCS2D01G437100 chr2A 81.084 1015 124 31 906 1884 690805346 690806328 0.000000e+00 749.0
25 TraesCS2D01G437100 chr2A 82.373 868 112 21 806 1657 691392185 691391343 0.000000e+00 717.0
26 TraesCS2D01G437100 chr2A 96.721 305 9 1 2011 2314 690748554 690748858 8.150000e-140 507.0
27 TraesCS2D01G437100 chr2A 91.743 218 18 0 61 278 691392426 691392209 1.150000e-78 303.0
28 TraesCS2D01G437100 chr2A 79.433 282 45 7 176 449 690796706 690796982 1.210000e-43 187.0
29 TraesCS2D01G437100 chr2A 86.364 154 9 3 800 946 690805067 690805215 9.450000e-35 158.0
30 TraesCS2D01G437100 chr2A 98.333 60 1 0 2395 2454 690772503 690772562 3.470000e-19 106.0
31 TraesCS2D01G437100 chr2A 96.226 53 2 0 2347 2399 690748856 690748908 1.260000e-13 87.9
32 TraesCS2D01G437100 chr5A 85.345 348 29 8 1431 1758 602413162 602413507 8.740000e-90 340.0
33 TraesCS2D01G437100 chr5A 85.714 98 8 2 1760 1853 602413615 602413710 5.810000e-17 99.0
34 TraesCS2D01G437100 chr1A 81.119 143 18 4 473 607 76485605 76485464 3.470000e-19 106.0
35 TraesCS2D01G437100 chr1A 80.597 134 19 5 477 604 49148682 49148550 2.090000e-16 97.1
36 TraesCS2D01G437100 chr1A 95.349 43 2 0 755 797 463032376 463032418 4.560000e-08 69.4
37 TraesCS2D01G437100 chr4D 79.856 139 20 4 473 603 449913691 449913829 7.520000e-16 95.3
38 TraesCS2D01G437100 chr7D 92.453 53 3 1 428 479 165862265 165862317 9.790000e-10 75.0
39 TraesCS2D01G437100 chr7D 95.349 43 2 0 755 797 8593276 8593234 4.560000e-08 69.4
40 TraesCS2D01G437100 chr7D 100.000 30 0 0 548 577 89218110 89218139 3.550000e-04 56.5
41 TraesCS2D01G437100 chr7B 92.453 53 3 1 428 479 129928976 129929028 9.790000e-10 75.0
42 TraesCS2D01G437100 chr5B 95.652 46 2 0 432 477 445553328 445553283 9.790000e-10 75.0
43 TraesCS2D01G437100 chr5B 97.619 42 1 0 758 799 405748061 405748020 3.520000e-09 73.1
44 TraesCS2D01G437100 chr1D 97.674 43 1 0 755 797 465993268 465993226 9.790000e-10 75.0
45 TraesCS2D01G437100 chr6B 95.349 43 2 0 755 797 690826202 690826160 4.560000e-08 69.4
46 TraesCS2D01G437100 chr5D 93.478 46 3 0 432 477 373935815 373935770 4.560000e-08 69.4
47 TraesCS2D01G437100 chr3D 95.349 43 2 0 755 797 9253413 9253371 4.560000e-08 69.4
48 TraesCS2D01G437100 chr3D 95.349 43 2 0 755 797 500408526 500408568 4.560000e-08 69.4
49 TraesCS2D01G437100 chr6A 93.333 45 3 0 433 477 764239 764195 1.640000e-07 67.6
50 TraesCS2D01G437100 chr4A 86.885 61 4 4 739 797 89677960 89677902 5.890000e-07 65.8
51 TraesCS2D01G437100 chr4A 89.362 47 4 1 432 477 271792331 271792285 9.860000e-05 58.4
52 TraesCS2D01G437100 chr6D 100.000 28 0 0 545 572 15661474 15661447 5.000000e-03 52.8


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 TraesCS2D01G437100 chr2D 547426179 547428730 2551 False 4713.00 4713 100.000000 1 2552 1 chr2D.!!$F2 2551
1 TraesCS2D01G437100 chr2D 547286282 547288357 2075 False 1238.00 1635 92.860000 791 2552 2 chr2D.!!$F8 1761
2 TraesCS2D01G437100 chr2D 547450609 547451794 1185 False 926.00 926 81.422000 800 1995 1 chr2D.!!$F3 1195
3 TraesCS2D01G437100 chr2D 547559292 547560129 837 False 789.00 789 84.099000 805 1631 1 chr2D.!!$F5 826
4 TraesCS2D01G437100 chr2D 547278276 547280146 1870 False 719.00 1177 90.676000 920 2552 3 chr2D.!!$F7 1632
5 TraesCS2D01G437100 chr2D 547488221 547490841 2620 False 570.00 911 89.926000 1 2293 4 chr2D.!!$F9 2292
6 TraesCS2D01G437100 chr2D 547574530 547575252 722 False 568.00 568 81.333000 906 1636 1 chr2D.!!$F6 730
7 TraesCS2D01G437100 chr2B 653772858 653774242 1384 False 717.00 828 90.757000 1452 2551 2 chr2B.!!$F2 1099
8 TraesCS2D01G437100 chr2B 653808271 653809012 741 False 708.00 708 84.218000 920 1657 1 chr2B.!!$F1 737
9 TraesCS2D01G437100 chr2B 653788261 653796932 8671 False 697.25 1362 89.750250 791 2552 4 chr2B.!!$F3 1761
10 TraesCS2D01G437100 chr2A 690747279 690748908 1629 False 637.30 1317 93.595667 800 2399 3 chr2A.!!$F3 1599
11 TraesCS2D01G437100 chr2A 691391343 691392426 1083 True 510.00 717 87.058000 61 1657 2 chr2A.!!$R1 1596
12 TraesCS2D01G437100 chr2A 690805067 690806328 1261 False 453.50 749 83.724000 800 1884 2 chr2A.!!$F4 1084
13 TraesCS2D01G437100 chr5A 602413162 602413710 548 False 219.50 340 85.529500 1431 1853 2 chr5A.!!$F1 422


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
345 439 0.030638 AGGCGTGTTTGTGTTGATGC 59.969 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2325 1.213182 AGAGTAGGGTCGAGCAGATCA 59.787 52.381 17.59 0.0 0.0 2.92 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
37 38 0.246635 GCACGGCCTCAAGAGTTCTA 59.753 55.000 0.00 0.00 0.00 2.10
89 176 2.094597 TGCGGCGTTAGCTTAGACTTTA 60.095 45.455 9.37 0.00 44.37 1.85
92 179 4.357142 CGGCGTTAGCTTAGACTTTATGA 58.643 43.478 0.00 0.00 44.37 2.15
98 185 7.010183 GCGTTAGCTTAGACTTTATGAATGACA 59.990 37.037 0.00 0.00 41.01 3.58
127 214 9.784531 CAATAATATAGTGATTGAGTGGGTCTT 57.215 33.333 0.00 0.00 33.28 3.01
189 276 3.133464 TGCAGCATTAGCACCCGC 61.133 61.111 0.00 0.00 45.49 6.13
215 302 3.724508 AGACAGCTAGATCGTGATTGG 57.275 47.619 0.00 0.00 0.00 3.16
247 334 5.820404 ATGATGGATGAGATAACTGCTCA 57.180 39.130 0.00 0.00 45.52 4.26
274 361 3.182590 AACTTGCCTCGCAGCAGGA 62.183 57.895 14.00 0.00 45.13 3.86
290 384 2.574018 GGACCCTTTGGCCACTTGC 61.574 63.158 3.88 0.00 40.16 4.01
299 393 2.954611 GCCACTTGCCGGTCTTTC 59.045 61.111 1.90 0.00 0.00 2.62
309 403 3.204526 TGCCGGTCTTTCTTTCGTTTTA 58.795 40.909 1.90 0.00 0.00 1.52
319 413 9.665264 GTCTTTCTTTCGTTTTACTTTCATGAT 57.335 29.630 0.00 0.00 0.00 2.45
341 435 6.638873 TGATTTTTATAGGCGTGTTTGTGTTG 59.361 34.615 0.00 0.00 0.00 3.33
345 439 0.030638 AGGCGTGTTTGTGTTGATGC 59.969 50.000 0.00 0.00 0.00 3.91
350 444 1.039068 TGTTTGTGTTGATGCCCCAG 58.961 50.000 0.00 0.00 0.00 4.45
389 483 8.903570 TTTACGGCATTTGAACTTATTGTATG 57.096 30.769 0.00 0.00 0.00 2.39
392 486 7.771183 ACGGCATTTGAACTTATTGTATGAAT 58.229 30.769 0.00 0.00 0.00 2.57
394 488 7.701924 CGGCATTTGAACTTATTGTATGAATGT 59.298 33.333 0.00 0.00 0.00 2.71
464 558 2.515071 GGCCGAGCTCCATGGAGAT 61.515 63.158 40.29 36.50 44.17 2.75
492 586 7.475771 AATTTGAAATTTTGCACACGTACAT 57.524 28.000 0.00 0.00 0.00 2.29
497 591 8.888332 TGAAATTTTGCACACGTACATATTAG 57.112 30.769 0.00 0.00 0.00 1.73
580 674 5.332743 TCAAAATTAAGGCCTCCATGAAGT 58.667 37.500 5.23 0.00 0.00 3.01
582 676 4.591321 AATTAAGGCCTCCATGAAGTGA 57.409 40.909 5.23 0.00 0.00 3.41
583 677 3.350219 TTAAGGCCTCCATGAAGTGAC 57.650 47.619 5.23 0.00 0.00 3.67
595 689 4.681025 CCATGAAGTGACGTTTCCAAAATG 59.319 41.667 0.00 0.00 0.00 2.32
618 712 4.385825 CCCTACTCGGCAAAAGCATATTA 58.614 43.478 0.00 0.00 0.00 0.98
628 722 6.494842 GGCAAAAGCATATTACGAGAAATGA 58.505 36.000 0.00 0.00 0.00 2.57
725 822 5.420739 AGAAGGTCTGATAAGAAGTGTCCTC 59.579 44.000 0.00 0.00 0.00 3.71
754 851 5.656213 TTTTAGTAGGGAGAAGGAAGTCG 57.344 43.478 0.00 0.00 0.00 4.18
755 852 1.476477 AGTAGGGAGAAGGAAGTCGC 58.524 55.000 0.00 0.00 0.00 5.19
756 853 0.100861 GTAGGGAGAAGGAAGTCGCG 59.899 60.000 0.00 0.00 0.00 5.87
757 854 1.664321 TAGGGAGAAGGAAGTCGCGC 61.664 60.000 0.00 0.00 0.00 6.86
758 855 2.881352 GGAGAAGGAAGTCGCGCG 60.881 66.667 26.76 26.76 0.00 6.86
759 856 2.126424 GAGAAGGAAGTCGCGCGT 60.126 61.111 30.98 11.13 0.00 6.01
760 857 2.430921 AGAAGGAAGTCGCGCGTG 60.431 61.111 30.98 14.79 0.00 5.34
761 858 2.733593 GAAGGAAGTCGCGCGTGT 60.734 61.111 30.98 15.56 0.00 4.49
762 859 1.443194 GAAGGAAGTCGCGCGTGTA 60.443 57.895 30.98 7.84 0.00 2.90
763 860 0.801067 GAAGGAAGTCGCGCGTGTAT 60.801 55.000 30.98 14.65 0.00 2.29
764 861 0.452987 AAGGAAGTCGCGCGTGTATA 59.547 50.000 30.98 6.92 0.00 1.47
765 862 0.666913 AGGAAGTCGCGCGTGTATAT 59.333 50.000 30.98 11.21 0.00 0.86
766 863 0.776451 GGAAGTCGCGCGTGTATATG 59.224 55.000 30.98 0.00 0.00 1.78
767 864 1.598676 GGAAGTCGCGCGTGTATATGA 60.599 52.381 30.98 4.20 0.00 2.15
768 865 2.114056 GAAGTCGCGCGTGTATATGAA 58.886 47.619 30.98 3.31 0.00 2.57
769 866 1.474017 AGTCGCGCGTGTATATGAAC 58.526 50.000 30.98 16.88 0.00 3.18
770 867 0.156035 GTCGCGCGTGTATATGAACG 59.844 55.000 30.98 4.21 42.61 3.95
776 873 2.264207 CGTGTATATGAACGCTTGCG 57.736 50.000 13.70 13.70 32.40 4.85
777 874 1.586578 CGTGTATATGAACGCTTGCGT 59.413 47.619 15.19 15.19 32.40 5.24
778 875 2.346376 CGTGTATATGAACGCTTGCGTC 60.346 50.000 20.87 14.17 32.40 5.19
779 876 2.858344 GTGTATATGAACGCTTGCGTCT 59.142 45.455 20.87 11.16 0.00 4.18
780 877 2.857748 TGTATATGAACGCTTGCGTCTG 59.142 45.455 20.87 0.00 0.00 3.51
781 878 2.010145 ATATGAACGCTTGCGTCTGT 57.990 45.000 20.87 11.69 0.00 3.41
782 879 2.640346 TATGAACGCTTGCGTCTGTA 57.360 45.000 20.87 10.79 0.00 2.74
783 880 2.010145 ATGAACGCTTGCGTCTGTAT 57.990 45.000 20.87 5.03 0.00 2.29
784 881 1.790755 TGAACGCTTGCGTCTGTATT 58.209 45.000 20.87 4.26 0.00 1.89
785 882 1.459209 TGAACGCTTGCGTCTGTATTG 59.541 47.619 20.87 0.00 0.00 1.90
786 883 1.459592 GAACGCTTGCGTCTGTATTGT 59.540 47.619 20.87 2.73 0.00 2.71
787 884 0.790207 ACGCTTGCGTCTGTATTGTG 59.210 50.000 15.19 0.00 0.00 3.33
788 885 0.790207 CGCTTGCGTCTGTATTGTGT 59.210 50.000 6.86 0.00 0.00 3.72
789 886 1.194547 CGCTTGCGTCTGTATTGTGTT 59.805 47.619 6.86 0.00 0.00 3.32
796 893 6.606234 TGCGTCTGTATTGTGTTAAAGAAA 57.394 33.333 0.00 0.00 0.00 2.52
798 895 7.644490 TGCGTCTGTATTGTGTTAAAGAAATT 58.356 30.769 0.00 0.00 0.00 1.82
836 933 5.014808 ACGGCTAACCTGTTAATTATCGT 57.985 39.130 0.00 0.00 0.00 3.73
838 935 5.876460 ACGGCTAACCTGTTAATTATCGTTT 59.124 36.000 0.00 0.00 0.00 3.60
900 1151 7.542025 GCTTCATGTTAATTCTCCAAACTGAT 58.458 34.615 0.00 0.00 0.00 2.90
919 1194 1.078709 TGCATACGCTTCTGCAAGTC 58.921 50.000 0.49 0.00 44.87 3.01
920 1195 1.078709 GCATACGCTTCTGCAAGTCA 58.921 50.000 0.00 0.00 38.28 3.41
921 1196 1.464608 GCATACGCTTCTGCAAGTCAA 59.535 47.619 0.00 0.00 38.28 3.18
1259 1536 3.838271 GGACCGGCTCAGCATCGA 61.838 66.667 0.00 0.00 0.00 3.59
1550 1836 1.677576 CTACAACGACCGGCCATACTA 59.322 52.381 0.00 0.00 0.00 1.82
1669 2004 1.340017 TGGGCAATACTGAAGCTGTCC 60.340 52.381 0.00 0.00 34.01 4.02
1863 2325 0.681243 GCCTTTCTCCCCGCAATCTT 60.681 55.000 0.00 0.00 0.00 2.40
1906 2375 6.502863 TCTCCATCCATGATATCCTGATTTCA 59.497 38.462 9.36 3.32 34.25 2.69
1911 2380 8.512956 CATCCATGATATCCTGATTTCAGTTTC 58.487 37.037 9.36 0.00 42.27 2.78
1951 2420 5.106555 ACCAAACAGTTTGCATAGAAGATCG 60.107 40.000 19.19 5.03 39.31 3.69
1963 2432 6.595326 TGCATAGAAGATCGTTTTCACTGATT 59.405 34.615 0.00 0.00 0.00 2.57
2042 2820 9.918630 AAATCATGAGAGGAAACATAAACAAAG 57.081 29.630 0.09 0.00 0.00 2.77
2089 2869 7.762615 CCAATAACAAAAGACAATGATCAGCAT 59.237 33.333 0.09 0.00 39.43 3.79
2218 5086 3.004315 GGGAATTCGAGCAGTAGAGAGAG 59.996 52.174 0.00 0.00 0.00 3.20
2336 5531 1.601477 CACTGCACCATGACTGCCA 60.601 57.895 11.51 1.83 33.36 4.92
2354 5549 2.704572 CCATCCTTCGCTTCTTGAGTT 58.295 47.619 0.00 0.00 0.00 3.01
2386 5581 5.489792 TTCTTCAGGCAGTAGATCAAACT 57.510 39.130 0.00 0.00 0.00 2.66
2461 5656 9.643693 CTTATTCTGCCAATACATTGAAGTTTT 57.356 29.630 3.48 0.00 40.14 2.43
2499 5694 5.378230 TCATCTCATAGCCCTCATTGTTT 57.622 39.130 0.00 0.00 0.00 2.83
2510 5705 4.943705 GCCCTCATTGTTTTCTATCTCACA 59.056 41.667 0.00 0.00 0.00 3.58
2523 5718 0.839277 TCTCACATCCATCCGCCAAT 59.161 50.000 0.00 0.00 0.00 3.16
2544 5740 0.313043 CTCAAAGGGTTGTGCAGCTG 59.687 55.000 10.11 10.11 36.07 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.882352 GCCTCACGGACAAAACTCCAT 60.882 52.381 0.00 0.00 0.00 3.41
61 62 0.953471 AGCTAACGCCGCAAACATCA 60.953 50.000 0.00 0.00 36.60 3.07
63 64 1.396996 CTAAGCTAACGCCGCAAACAT 59.603 47.619 0.00 0.00 36.60 2.71
98 185 8.494433 ACCCACTCAATCACTATATTATTGTGT 58.506 33.333 14.94 0.00 37.65 3.72
110 197 3.864789 ACAAAGACCCACTCAATCACT 57.135 42.857 0.00 0.00 0.00 3.41
202 289 1.269257 CGCTCAGCCAATCACGATCTA 60.269 52.381 0.00 0.00 0.00 1.98
209 296 2.689553 TCATAACGCTCAGCCAATCA 57.310 45.000 0.00 0.00 0.00 2.57
215 302 2.735663 CTCATCCATCATAACGCTCAGC 59.264 50.000 0.00 0.00 0.00 4.26
290 384 5.413969 AAGTAAAACGAAAGAAAGACCGG 57.586 39.130 0.00 0.00 0.00 5.28
309 403 7.391148 ACACGCCTATAAAAATCATGAAAGT 57.609 32.000 0.00 0.00 0.00 2.66
319 413 6.132791 TCAACACAAACACGCCTATAAAAA 57.867 33.333 0.00 0.00 0.00 1.94
324 418 2.095263 GCATCAACACAAACACGCCTAT 60.095 45.455 0.00 0.00 0.00 2.57
345 439 5.507315 CGTAAAATAAAATAGCCTGCTGGGG 60.507 44.000 12.06 0.00 35.12 4.96
350 444 4.927422 TGCCGTAAAATAAAATAGCCTGC 58.073 39.130 0.00 0.00 0.00 4.85
392 486 9.820229 CGCTTTAAAGATAAAGTCAACAATACA 57.180 29.630 19.48 0.00 46.42 2.29
397 491 6.348213 GCCTCGCTTTAAAGATAAAGTCAACA 60.348 38.462 19.48 0.00 46.42 3.33
398 492 6.022208 GCCTCGCTTTAAAGATAAAGTCAAC 58.978 40.000 19.48 0.00 46.42 3.18
399 493 5.163893 CGCCTCGCTTTAAAGATAAAGTCAA 60.164 40.000 19.48 0.00 46.42 3.18
401 495 4.565564 TCGCCTCGCTTTAAAGATAAAGTC 59.434 41.667 19.48 0.00 46.42 3.01
405 499 4.201783 GCTTTCGCCTCGCTTTAAAGATAA 60.202 41.667 19.48 2.27 30.44 1.75
406 500 3.308866 GCTTTCGCCTCGCTTTAAAGATA 59.691 43.478 19.48 4.71 30.44 1.98
407 501 2.096013 GCTTTCGCCTCGCTTTAAAGAT 59.904 45.455 19.48 0.00 30.44 2.40
408 502 1.463444 GCTTTCGCCTCGCTTTAAAGA 59.537 47.619 19.48 0.00 30.44 2.52
409 503 1.883476 GCTTTCGCCTCGCTTTAAAG 58.117 50.000 11.02 11.02 0.00 1.85
464 558 7.763172 ACGTGTGCAAAATTTCAAATTAAGA 57.237 28.000 0.00 0.00 0.00 2.10
469 563 8.755696 ATATGTACGTGTGCAAAATTTCAAAT 57.244 26.923 0.00 0.00 0.00 2.32
580 674 1.698506 AGGGCATTTTGGAAACGTCA 58.301 45.000 0.00 0.00 0.00 4.35
582 676 2.817844 GAGTAGGGCATTTTGGAAACGT 59.182 45.455 0.00 0.00 0.00 3.99
583 677 2.159572 CGAGTAGGGCATTTTGGAAACG 60.160 50.000 0.00 0.00 0.00 3.60
744 841 0.801067 ATACACGCGCGACTTCCTTC 60.801 55.000 39.36 0.00 0.00 3.46
745 842 0.452987 TATACACGCGCGACTTCCTT 59.547 50.000 39.36 9.38 0.00 3.36
747 844 0.776451 CATATACACGCGCGACTTCC 59.224 55.000 39.36 0.00 0.00 3.46
749 846 1.850441 GTTCATATACACGCGCGACTT 59.150 47.619 39.36 21.52 0.00 3.01
750 847 1.474017 GTTCATATACACGCGCGACT 58.526 50.000 39.36 22.41 0.00 4.18
751 848 0.156035 CGTTCATATACACGCGCGAC 59.844 55.000 39.36 19.47 0.00 5.19
752 849 2.487006 CGTTCATATACACGCGCGA 58.513 52.632 39.36 15.84 0.00 5.87
757 854 2.264207 CGCAAGCGTTCATATACACG 57.736 50.000 6.25 2.21 39.49 4.49
769 866 0.790207 ACACAATACAGACGCAAGCG 59.210 50.000 13.50 13.50 46.03 4.68
770 867 2.969443 AACACAATACAGACGCAAGC 57.031 45.000 0.00 0.00 45.62 4.01
772 869 6.606234 TTCTTTAACACAATACAGACGCAA 57.394 33.333 0.00 0.00 0.00 4.85
773 870 6.606234 TTTCTTTAACACAATACAGACGCA 57.394 33.333 0.00 0.00 0.00 5.24
774 871 7.589954 ACAATTTCTTTAACACAATACAGACGC 59.410 33.333 0.00 0.00 0.00 5.19
784 881 9.619316 GCATGTACATACAATTTCTTTAACACA 57.381 29.630 8.32 0.00 39.99 3.72
785 882 9.619316 TGCATGTACATACAATTTCTTTAACAC 57.381 29.630 8.32 0.00 39.99 3.32
796 893 4.157656 AGCCGTTTTGCATGTACATACAAT 59.842 37.500 19.71 3.88 39.99 2.71
798 895 3.078097 AGCCGTTTTGCATGTACATACA 58.922 40.909 8.32 6.32 40.98 2.29
838 935 9.547753 GAGTAATTAATGGAATTCACTGCTAGA 57.452 33.333 7.93 0.00 38.70 2.43
851 948 4.991056 GCTCATCTGCGAGTAATTAATGGA 59.009 41.667 0.00 0.00 35.33 3.41
919 1194 2.486592 GGACAACACGAGGGGTTAATTG 59.513 50.000 0.00 0.00 0.00 2.32
920 1195 2.374170 AGGACAACACGAGGGGTTAATT 59.626 45.455 0.00 0.00 0.00 1.40
921 1196 1.982958 AGGACAACACGAGGGGTTAAT 59.017 47.619 0.00 0.00 0.00 1.40
1259 1536 1.483595 TAGTGGCTCCAGCTTGCAGT 61.484 55.000 0.00 0.00 41.70 4.40
1407 1690 3.078196 TAGGCCCCGCATTCGTGA 61.078 61.111 0.00 0.00 0.00 4.35
1550 1836 8.418597 TCCTGATTTAGCTTCCGTATATACTT 57.581 34.615 11.05 0.00 0.00 2.24
1637 1953 4.704540 CAGTATTGCCCATTACTTGACCAA 59.295 41.667 1.29 0.00 0.00 3.67
1638 1954 4.018870 TCAGTATTGCCCATTACTTGACCA 60.019 41.667 1.29 0.00 0.00 4.02
1639 1955 4.523083 TCAGTATTGCCCATTACTTGACC 58.477 43.478 1.29 0.00 0.00 4.02
1640 1956 5.449177 GCTTCAGTATTGCCCATTACTTGAC 60.449 44.000 1.29 0.00 0.00 3.18
1641 1957 4.640201 GCTTCAGTATTGCCCATTACTTGA 59.360 41.667 1.29 1.59 0.00 3.02
1642 1958 4.641989 AGCTTCAGTATTGCCCATTACTTG 59.358 41.667 1.29 0.00 0.00 3.16
1653 1969 4.495422 AGTAACGGACAGCTTCAGTATTG 58.505 43.478 0.00 0.00 31.58 1.90
1669 2004 6.669873 CGAACTGAACAAAACAAAAGTAACG 58.330 36.000 0.00 0.00 0.00 3.18
1863 2325 1.213182 AGAGTAGGGTCGAGCAGATCA 59.787 52.381 17.59 0.00 0.00 2.92
1995 2464 9.358406 TGATTTCCATGATCTGCAGTTATTATT 57.642 29.630 14.67 0.00 0.00 1.40
1997 2466 8.929260 ATGATTTCCATGATCTGCAGTTATTA 57.071 30.769 14.67 0.00 33.39 0.98
1998 2467 7.834881 ATGATTTCCATGATCTGCAGTTATT 57.165 32.000 14.67 0.00 33.39 1.40
2089 2869 5.187186 GTGGAGTATTCTTCACCTTCACCTA 59.813 44.000 0.00 0.00 42.66 3.08
2173 4875 6.294176 CCCTACTCATATTGCCTGCATTTTAC 60.294 42.308 0.00 0.00 0.00 2.01
2336 5531 2.569404 AGGAACTCAAGAAGCGAAGGAT 59.431 45.455 0.00 0.00 0.00 3.24
2354 5549 3.840666 ACTGCCTGAAGAATACTGAAGGA 59.159 43.478 0.00 0.00 33.76 3.36
2386 5581 3.879295 GGATATTAGCTGCAAAGCTGTGA 59.121 43.478 8.49 0.00 45.81 3.58
2435 5630 9.643693 AAAACTTCAATGTATTGGCAGAATAAG 57.356 29.630 4.89 2.64 38.30 1.73
2461 5656 1.745087 GATGAAATTGGCGAGCTTGGA 59.255 47.619 2.37 0.00 0.00 3.53
2499 5694 2.300152 GGCGGATGGATGTGAGATAGAA 59.700 50.000 0.00 0.00 0.00 2.10
2510 5705 0.846015 TTGAGGATTGGCGGATGGAT 59.154 50.000 0.00 0.00 0.00 3.41
2523 5718 0.823356 GCTGCACAACCCTTTGAGGA 60.823 55.000 0.00 0.00 37.67 3.71



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

AutoCloner maintained by Alex Coulton.