Multiple sequence alignment - TraesCS2B01G029100

Loading Multiple Alignment...

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 TraesCS2B01G029100 chr2B 100.000 3674 0 0 1 3674 13390962 13394635 0.000000e+00 6785.0
1 TraesCS2B01G029100 chr2B 98.697 1535 10 1 1 1535 13340278 13341802 0.000000e+00 2715.0
2 TraesCS2B01G029100 chr2B 93.883 1553 82 9 1102 2644 13154044 13155593 0.000000e+00 2329.0
3 TraesCS2B01G029100 chr2B 93.043 1308 71 11 1354 2644 13219742 13221046 0.000000e+00 1893.0
4 TraesCS2B01G029100 chr2B 98.311 592 8 1 3085 3674 431166818 431167409 0.000000e+00 1037.0
5 TraesCS2B01G029100 chr2B 93.165 556 33 3 2 556 13145363 13145914 0.000000e+00 811.0
6 TraesCS2B01G029100 chr2B 92.540 563 33 6 1 560 13204055 13204611 0.000000e+00 798.0
7 TraesCS2B01G029100 chr2B 75.000 1464 276 65 1158 2572 682258552 682259974 8.780000e-166 593.0
8 TraesCS2B01G029100 chr2B 91.014 434 39 0 1668 2101 13179196 13179629 1.470000e-163 586.0
9 TraesCS2B01G029100 chr2B 98.328 299 4 1 2793 3091 431166426 431166723 1.170000e-144 523.0
10 TraesCS2B01G029100 chr2B 91.233 365 31 1 1737 2101 13313481 13313844 2.550000e-136 496.0
11 TraesCS2B01G029100 chr2B 96.139 259 10 0 1102 1360 13207507 13207765 1.220000e-114 424.0
12 TraesCS2B01G029100 chr2B 92.481 133 10 0 906 1038 13152611 13152743 1.350000e-44 191.0
13 TraesCS2B01G029100 chr2B 94.382 89 4 1 752 839 798809089 798809001 6.400000e-28 135.0
14 TraesCS2B01G029100 chr2B 100.000 44 0 0 555 598 13146043 13146086 8.460000e-12 82.4
15 TraesCS2B01G029100 chr2D 90.076 1572 115 11 1102 2643 9873263 9874823 0.000000e+00 2001.0
16 TraesCS2B01G029100 chr2D 94.324 599 25 5 3085 3674 99203322 99202724 0.000000e+00 909.0
17 TraesCS2B01G029100 chr2D 91.815 562 39 4 1 560 9858911 9859467 0.000000e+00 776.0
18 TraesCS2B01G029100 chr2D 94.649 299 15 1 2793 3091 99203714 99203417 2.580000e-126 462.0
19 TraesCS2B01G029100 chr2D 77.278 823 161 15 1763 2572 10980423 10979614 9.300000e-126 460.0
20 TraesCS2B01G029100 chr2D 90.977 133 12 0 906 1038 9872716 9872848 2.910000e-41 180.0
21 TraesCS2B01G029100 chr2A 89.346 1070 87 15 1599 2644 9124539 9125605 0.000000e+00 1319.0
22 TraesCS2B01G029100 chr2A 92.692 561 32 5 2 560 9937054 9936501 0.000000e+00 800.0
23 TraesCS2B01G029100 chr2A 88.084 428 35 6 1102 1526 9904925 9904511 9.170000e-136 494.0
24 TraesCS2B01G029100 chr2A 95.652 299 12 1 2793 3091 30855621 30855324 2.570000e-131 479.0
25 TraesCS2B01G029100 chr2A 86.103 331 45 1 1458 1787 9126995 9127325 4.510000e-94 355.0
26 TraesCS2B01G029100 chr2A 81.525 341 55 6 2049 2382 24149606 24149267 1.300000e-69 274.0
27 TraesCS2B01G029100 chr3D 81.639 1525 232 25 1125 2608 464333736 464332219 0.000000e+00 1221.0
28 TraesCS2B01G029100 chr3D 80.206 778 137 11 1130 1891 464720997 464720221 5.320000e-158 568.0
29 TraesCS2B01G029100 chr3D 81.510 649 98 10 1944 2572 464720205 464719559 7.040000e-142 514.0
30 TraesCS2B01G029100 chr3D 82.353 85 11 3 2232 2314 387354336 387354254 1.830000e-08 71.3
31 TraesCS2B01G029100 chr3A 81.217 1528 221 47 1125 2608 607509625 607508120 0.000000e+00 1171.0
32 TraesCS2B01G029100 chr3A 82.966 681 113 2 1434 2111 608113463 608112783 2.430000e-171 612.0
33 TraesCS2B01G029100 chr4D 94.658 599 23 3 3085 3674 30390185 30389587 0.000000e+00 920.0
34 TraesCS2B01G029100 chr4D 93.990 599 27 5 3085 3674 470264437 470265035 0.000000e+00 898.0
35 TraesCS2B01G029100 chr4D 92.230 296 13 3 2796 3091 30390565 30390280 9.500000e-111 411.0
36 TraesCS2B01G029100 chrUn 94.983 578 23 2 3103 3674 95427278 95426701 0.000000e+00 902.0
37 TraesCS2B01G029100 chrUn 100.000 414 0 0 909 1322 477356242 477355829 0.000000e+00 765.0
38 TraesCS2B01G029100 chrUn 89.649 599 32 6 3085 3674 284412211 284411634 0.000000e+00 736.0
39 TraesCS2B01G029100 chrUn 89.482 599 33 6 3085 3674 284405677 284405100 0.000000e+00 730.0
40 TraesCS2B01G029100 chrUn 96.990 299 8 1 2793 3091 284406069 284405772 5.480000e-138 501.0
41 TraesCS2B01G029100 chrUn 96.990 299 8 1 2793 3091 284412603 284412306 5.480000e-138 501.0
42 TraesCS2B01G029100 chrUn 96.990 299 8 1 2793 3091 376833948 376833651 5.480000e-138 501.0
43 TraesCS2B01G029100 chrUn 95.294 85 3 1 761 844 62663480 62663396 2.300000e-27 134.0
44 TraesCS2B01G029100 chr1D 93.132 597 30 7 3085 3672 1441913 1441319 0.000000e+00 865.0
45 TraesCS2B01G029100 chr1D 94.314 299 16 1 2793 3091 1442305 1442008 1.200000e-124 457.0
46 TraesCS2B01G029100 chr6A 92.333 600 36 5 3085 3674 337207949 337208548 0.000000e+00 845.0
47 TraesCS2B01G029100 chr6B 92.346 601 33 6 3085 3674 29312210 29311612 0.000000e+00 843.0
48 TraesCS2B01G029100 chr6B 95.623 297 11 2 2796 3091 29312600 29312305 3.320000e-130 475.0
49 TraesCS2B01G029100 chr7B 92.114 596 37 6 3088 3674 57869915 57869321 0.000000e+00 832.0
50 TraesCS2B01G029100 chr3B 80.454 926 151 14 1712 2608 618008461 618007537 0.000000e+00 680.0
51 TraesCS2B01G029100 chr3B 92.473 93 7 0 748 840 807080270 807080178 2.300000e-27 134.0
52 TraesCS2B01G029100 chr5D 75.051 1459 277 58 1167 2577 493912464 493913883 6.790000e-167 597.0
53 TraesCS2B01G029100 chr5D 74.266 1465 280 66 1166 2577 494079146 494077726 9.040000e-146 527.0
54 TraesCS2B01G029100 chr5D 72.753 1046 209 53 1570 2577 494060018 494059011 2.160000e-72 283.0
55 TraesCS2B01G029100 chr5B 75.017 1461 276 60 1166 2577 610282404 610280984 8.780000e-166 593.0
56 TraesCS2B01G029100 chr5B 74.880 1457 285 50 1166 2577 610107916 610106496 4.090000e-164 588.0
57 TraesCS2B01G029100 chr5B 93.478 92 5 1 759 849 380317958 380317867 6.400000e-28 135.0
58 TraesCS2B01G029100 chr5A 74.483 1450 295 50 1170 2577 617097301 617095885 3.200000e-155 558.0
59 TraesCS2B01G029100 chr5A 96.471 85 3 0 761 845 207681836 207681920 1.380000e-29 141.0
60 TraesCS2B01G029100 chr5A 97.531 81 2 0 761 841 564177716 564177636 4.950000e-29 139.0
61 TraesCS2B01G029100 chr4A 75.665 1278 226 53 1158 2382 626954581 626953336 3.200000e-155 558.0
62 TraesCS2B01G029100 chr7D 93.333 90 4 2 758 845 47416146 47416057 8.280000e-27 132.0
63 TraesCS2B01G029100 chr6D 94.186 86 5 0 761 846 427966119 427966204 8.280000e-27 132.0


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 TraesCS2B01G029100 chr2B 13390962 13394635 3673 False 6785.0 6785 100.0000 1 3674 1 chr2B.!!$F5 3673
1 TraesCS2B01G029100 chr2B 13340278 13341802 1524 False 2715.0 2715 98.6970 1 1535 1 chr2B.!!$F4 1534
2 TraesCS2B01G029100 chr2B 13219742 13221046 1304 False 1893.0 1893 93.0430 1354 2644 1 chr2B.!!$F2 1290
3 TraesCS2B01G029100 chr2B 13152611 13155593 2982 False 1260.0 2329 93.1820 906 2644 2 chr2B.!!$F8 1738
4 TraesCS2B01G029100 chr2B 431166426 431167409 983 False 780.0 1037 98.3195 2793 3674 2 chr2B.!!$F10 881
5 TraesCS2B01G029100 chr2B 13204055 13207765 3710 False 611.0 798 94.3395 1 1360 2 chr2B.!!$F9 1359
6 TraesCS2B01G029100 chr2B 682258552 682259974 1422 False 593.0 593 75.0000 1158 2572 1 chr2B.!!$F6 1414
7 TraesCS2B01G029100 chr2B 13145363 13146086 723 False 446.7 811 96.5825 2 598 2 chr2B.!!$F7 596
8 TraesCS2B01G029100 chr2D 9872716 9874823 2107 False 1090.5 2001 90.5265 906 2643 2 chr2D.!!$F2 1737
9 TraesCS2B01G029100 chr2D 9858911 9859467 556 False 776.0 776 91.8150 1 560 1 chr2D.!!$F1 559
10 TraesCS2B01G029100 chr2D 99202724 99203714 990 True 685.5 909 94.4865 2793 3674 2 chr2D.!!$R2 881
11 TraesCS2B01G029100 chr2D 10979614 10980423 809 True 460.0 460 77.2780 1763 2572 1 chr2D.!!$R1 809
12 TraesCS2B01G029100 chr2A 9124539 9127325 2786 False 837.0 1319 87.7245 1458 2644 2 chr2A.!!$F1 1186
13 TraesCS2B01G029100 chr2A 9936501 9937054 553 True 800.0 800 92.6920 2 560 1 chr2A.!!$R2 558
14 TraesCS2B01G029100 chr3D 464332219 464333736 1517 True 1221.0 1221 81.6390 1125 2608 1 chr3D.!!$R2 1483
15 TraesCS2B01G029100 chr3D 464719559 464720997 1438 True 541.0 568 80.8580 1130 2572 2 chr3D.!!$R3 1442
16 TraesCS2B01G029100 chr3A 607508120 607509625 1505 True 1171.0 1171 81.2170 1125 2608 1 chr3A.!!$R1 1483
17 TraesCS2B01G029100 chr3A 608112783 608113463 680 True 612.0 612 82.9660 1434 2111 1 chr3A.!!$R2 677
18 TraesCS2B01G029100 chr4D 470264437 470265035 598 False 898.0 898 93.9900 3085 3674 1 chr4D.!!$F1 589
19 TraesCS2B01G029100 chr4D 30389587 30390565 978 True 665.5 920 93.4440 2796 3674 2 chr4D.!!$R1 878
20 TraesCS2B01G029100 chrUn 95426701 95427278 577 True 902.0 902 94.9830 3103 3674 1 chrUn.!!$R2 571
21 TraesCS2B01G029100 chrUn 284411634 284412603 969 True 618.5 736 93.3195 2793 3674 2 chrUn.!!$R6 881
22 TraesCS2B01G029100 chrUn 284405100 284406069 969 True 615.5 730 93.2360 2793 3674 2 chrUn.!!$R5 881
23 TraesCS2B01G029100 chr1D 1441319 1442305 986 True 661.0 865 93.7230 2793 3672 2 chr1D.!!$R1 879
24 TraesCS2B01G029100 chr6A 337207949 337208548 599 False 845.0 845 92.3330 3085 3674 1 chr6A.!!$F1 589
25 TraesCS2B01G029100 chr6B 29311612 29312600 988 True 659.0 843 93.9845 2796 3674 2 chr6B.!!$R1 878
26 TraesCS2B01G029100 chr7B 57869321 57869915 594 True 832.0 832 92.1140 3088 3674 1 chr7B.!!$R1 586
27 TraesCS2B01G029100 chr3B 618007537 618008461 924 True 680.0 680 80.4540 1712 2608 1 chr3B.!!$R1 896
28 TraesCS2B01G029100 chr5D 493912464 493913883 1419 False 597.0 597 75.0510 1167 2577 1 chr5D.!!$F1 1410
29 TraesCS2B01G029100 chr5D 494077726 494079146 1420 True 527.0 527 74.2660 1166 2577 1 chr5D.!!$R2 1411
30 TraesCS2B01G029100 chr5D 494059011 494060018 1007 True 283.0 283 72.7530 1570 2577 1 chr5D.!!$R1 1007
31 TraesCS2B01G029100 chr5B 610280984 610282404 1420 True 593.0 593 75.0170 1166 2577 1 chr5B.!!$R3 1411
32 TraesCS2B01G029100 chr5B 610106496 610107916 1420 True 588.0 588 74.8800 1166 2577 1 chr5B.!!$R2 1411
33 TraesCS2B01G029100 chr5A 617095885 617097301 1416 True 558.0 558 74.4830 1170 2577 1 chr5A.!!$R2 1407
34 TraesCS2B01G029100 chr4A 626953336 626954581 1245 True 558.0 558 75.6650 1158 2382 1 chr4A.!!$R1 1224

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
459 465 3.634568 TGTAGCCAAAACACATTTCCG 57.365 42.857 0.0 0.0 0.00 4.30 F
1761 5426 0.698238 AGTGGGCATTGTTCCAGCTA 59.302 50.000 0.0 0.0 33.13 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 5810 1.410517 CCGTCTGGCATACACAGATCT 59.589 52.381 3.83 0.00 45.72 2.75 R
2751 6488 0.322008 AGTGTAGCAAAGCTCCTGCC 60.322 55.000 15.24 4.19 40.86 4.85 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
459 465 3.634568 TGTAGCCAAAACACATTTCCG 57.365 42.857 0.00 0.00 0.00 4.30
1640 5298 2.030562 CAGCAACCCGTTCGAGGT 59.969 61.111 0.00 0.00 40.14 3.85
1665 5323 4.309950 GACGACCCAGCCACCGTT 62.310 66.667 0.00 0.00 35.22 4.44
1666 5324 2.918802 ACGACCCAGCCACCGTTA 60.919 61.111 0.00 0.00 30.41 3.18
1761 5426 0.698238 AGTGGGCATTGTTCCAGCTA 59.302 50.000 0.00 0.00 33.13 3.32
2124 5810 0.604073 CCAATGGCAGTGCATCAACA 59.396 50.000 18.61 5.38 0.00 3.33
2553 6278 1.141657 GATGTAGGGCAGCTCATGGAA 59.858 52.381 0.00 0.00 0.00 3.53
2652 6389 1.413445 TGCACTGTACCGTGTACCTTT 59.587 47.619 17.31 0.00 37.24 3.11
2653 6390 1.796459 GCACTGTACCGTGTACCTTTG 59.204 52.381 17.31 6.92 37.24 2.77
2664 6401 3.219281 GTGTACCTTTGTCCACCACATT 58.781 45.455 0.00 0.00 33.90 2.71
2666 6403 4.098807 GTGTACCTTTGTCCACCACATTTT 59.901 41.667 0.00 0.00 33.90 1.82
2667 6404 5.299782 GTGTACCTTTGTCCACCACATTTTA 59.700 40.000 0.00 0.00 33.90 1.52
2670 6407 7.724506 TGTACCTTTGTCCACCACATTTTATTA 59.275 33.333 0.00 0.00 33.90 0.98
2671 6408 7.227049 ACCTTTGTCCACCACATTTTATTAG 57.773 36.000 0.00 0.00 33.90 1.73
2672 6409 6.780522 ACCTTTGTCCACCACATTTTATTAGT 59.219 34.615 0.00 0.00 33.90 2.24
2673 6410 7.945664 ACCTTTGTCCACCACATTTTATTAGTA 59.054 33.333 0.00 0.00 33.90 1.82
2674 6411 8.798402 CCTTTGTCCACCACATTTTATTAGTAA 58.202 33.333 0.00 0.00 33.90 2.24
2712 6449 9.472361 AATTCATTTCATGTTCTTCTGAAACTG 57.528 29.630 0.26 2.12 42.38 3.16
2713 6450 6.441274 TCATTTCATGTTCTTCTGAAACTGC 58.559 36.000 0.26 0.00 42.38 4.40
2714 6451 6.263842 TCATTTCATGTTCTTCTGAAACTGCT 59.736 34.615 0.26 0.00 42.38 4.24
2715 6452 5.428496 TTCATGTTCTTCTGAAACTGCTG 57.572 39.130 0.00 0.00 33.52 4.41
2716 6453 3.817084 TCATGTTCTTCTGAAACTGCTGG 59.183 43.478 0.00 0.00 33.52 4.85
2717 6454 1.949525 TGTTCTTCTGAAACTGCTGGC 59.050 47.619 0.00 0.00 33.52 4.85
2718 6455 2.225467 GTTCTTCTGAAACTGCTGGCT 58.775 47.619 0.00 0.00 33.52 4.75
2719 6456 2.620585 GTTCTTCTGAAACTGCTGGCTT 59.379 45.455 0.00 0.00 33.52 4.35
2720 6457 2.498167 TCTTCTGAAACTGCTGGCTTC 58.502 47.619 0.00 0.00 0.00 3.86
2721 6458 2.158769 TCTTCTGAAACTGCTGGCTTCA 60.159 45.455 9.14 9.14 0.00 3.02
2722 6459 1.597742 TCTGAAACTGCTGGCTTCAC 58.402 50.000 6.36 0.00 0.00 3.18
2723 6460 1.141657 TCTGAAACTGCTGGCTTCACT 59.858 47.619 6.36 0.00 0.00 3.41
2724 6461 1.952296 CTGAAACTGCTGGCTTCACTT 59.048 47.619 6.36 0.00 0.00 3.16
2725 6462 2.360165 CTGAAACTGCTGGCTTCACTTT 59.640 45.455 6.36 0.00 0.00 2.66
2726 6463 3.550820 TGAAACTGCTGGCTTCACTTTA 58.449 40.909 6.36 0.00 0.00 1.85
2727 6464 4.144297 TGAAACTGCTGGCTTCACTTTAT 58.856 39.130 6.36 0.00 0.00 1.40
2728 6465 5.312895 TGAAACTGCTGGCTTCACTTTATA 58.687 37.500 6.36 0.00 0.00 0.98
2729 6466 5.412594 TGAAACTGCTGGCTTCACTTTATAG 59.587 40.000 6.36 0.00 0.00 1.31
2730 6467 4.826274 ACTGCTGGCTTCACTTTATAGA 57.174 40.909 0.00 0.00 0.00 1.98
2731 6468 5.365021 ACTGCTGGCTTCACTTTATAGAT 57.635 39.130 0.00 0.00 0.00 1.98
2732 6469 6.485830 ACTGCTGGCTTCACTTTATAGATA 57.514 37.500 0.00 0.00 0.00 1.98
2733 6470 6.889198 ACTGCTGGCTTCACTTTATAGATAA 58.111 36.000 0.00 0.00 0.00 1.75
2734 6471 7.338710 ACTGCTGGCTTCACTTTATAGATAAA 58.661 34.615 0.00 0.00 0.00 1.40
2735 6472 7.995488 ACTGCTGGCTTCACTTTATAGATAAAT 59.005 33.333 0.00 0.00 32.36 1.40
2736 6473 8.383318 TGCTGGCTTCACTTTATAGATAAATC 57.617 34.615 0.00 0.00 32.36 2.17
2737 6474 7.992608 TGCTGGCTTCACTTTATAGATAAATCA 59.007 33.333 0.00 0.00 32.36 2.57
2738 6475 9.007901 GCTGGCTTCACTTTATAGATAAATCAT 57.992 33.333 0.00 0.00 32.36 2.45
2754 6491 9.420118 AGATAAATCATTTTGTATAGTTGGGCA 57.580 29.630 0.00 0.00 0.00 5.36
2755 6492 9.683069 GATAAATCATTTTGTATAGTTGGGCAG 57.317 33.333 0.00 0.00 0.00 4.85
2756 6493 6.469782 AATCATTTTGTATAGTTGGGCAGG 57.530 37.500 0.00 0.00 0.00 4.85
2757 6494 5.186256 TCATTTTGTATAGTTGGGCAGGA 57.814 39.130 0.00 0.00 0.00 3.86
2758 6495 5.192927 TCATTTTGTATAGTTGGGCAGGAG 58.807 41.667 0.00 0.00 0.00 3.69
2759 6496 2.710096 TTGTATAGTTGGGCAGGAGC 57.290 50.000 0.00 0.00 41.10 4.70
2760 6497 1.879575 TGTATAGTTGGGCAGGAGCT 58.120 50.000 0.00 0.00 41.70 4.09
2761 6498 2.196595 TGTATAGTTGGGCAGGAGCTT 58.803 47.619 0.00 0.00 41.70 3.74
2762 6499 2.576191 TGTATAGTTGGGCAGGAGCTTT 59.424 45.455 0.00 0.00 41.70 3.51
2763 6500 2.134789 ATAGTTGGGCAGGAGCTTTG 57.865 50.000 0.00 0.00 41.70 2.77
2764 6501 0.609131 TAGTTGGGCAGGAGCTTTGC 60.609 55.000 13.94 13.94 41.70 3.68
2765 6502 1.905354 GTTGGGCAGGAGCTTTGCT 60.905 57.895 19.53 0.00 43.88 3.91
2766 6503 0.609131 GTTGGGCAGGAGCTTTGCTA 60.609 55.000 19.53 9.65 39.88 3.49
2767 6504 0.609131 TTGGGCAGGAGCTTTGCTAC 60.609 55.000 19.53 14.48 39.88 3.58
2768 6505 1.002134 GGGCAGGAGCTTTGCTACA 60.002 57.895 19.53 0.00 42.99 2.74
2769 6506 1.308783 GGGCAGGAGCTTTGCTACAC 61.309 60.000 19.53 6.79 42.99 2.90
2770 6507 0.322008 GGCAGGAGCTTTGCTACACT 60.322 55.000 19.53 0.00 42.99 3.55
2771 6508 1.528129 GCAGGAGCTTTGCTACACTT 58.472 50.000 14.76 0.00 42.99 3.16
2772 6509 1.198637 GCAGGAGCTTTGCTACACTTG 59.801 52.381 14.76 0.00 42.99 3.16
2773 6510 2.498167 CAGGAGCTTTGCTACACTTGT 58.502 47.619 4.51 0.00 42.99 3.16
2774 6511 3.664107 CAGGAGCTTTGCTACACTTGTA 58.336 45.455 4.51 0.00 42.99 2.41
2775 6512 4.065088 CAGGAGCTTTGCTACACTTGTAA 58.935 43.478 4.51 0.00 42.99 2.41
2776 6513 4.515191 CAGGAGCTTTGCTACACTTGTAAA 59.485 41.667 4.51 0.00 42.99 2.01
2777 6514 5.182001 CAGGAGCTTTGCTACACTTGTAAAT 59.818 40.000 4.51 0.00 42.99 1.40
2778 6515 5.770162 AGGAGCTTTGCTACACTTGTAAATT 59.230 36.000 4.51 0.00 42.99 1.82
2779 6516 6.940298 AGGAGCTTTGCTACACTTGTAAATTA 59.060 34.615 4.51 0.00 42.99 1.40
2780 6517 7.447238 AGGAGCTTTGCTACACTTGTAAATTAA 59.553 33.333 4.51 0.00 42.99 1.40
2781 6518 7.750903 GGAGCTTTGCTACACTTGTAAATTAAG 59.249 37.037 0.00 0.00 39.71 1.85
2782 6519 7.084486 AGCTTTGCTACACTTGTAAATTAAGC 58.916 34.615 12.60 12.60 36.99 3.09
2783 6520 7.040409 AGCTTTGCTACACTTGTAAATTAAGCT 60.040 33.333 15.16 15.16 36.99 3.74
2784 6521 8.234546 GCTTTGCTACACTTGTAAATTAAGCTA 58.765 33.333 12.94 1.20 33.23 3.32
2787 6524 9.496873 TTGCTACACTTGTAAATTAAGCTAAGA 57.503 29.630 0.00 0.00 0.00 2.10
2788 6525 9.496873 TGCTACACTTGTAAATTAAGCTAAGAA 57.503 29.630 0.00 0.00 0.00 2.52
3356 7586 1.375908 TCTCCACAACAGCGATGGC 60.376 57.895 5.32 0.00 40.37 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
459 465 2.000447 GCAGTGAAGAATACCCGTCAC 59.000 52.381 0.00 0.00 42.93 3.67
745 3099 6.662663 ATGGGACGGAGTACTATATAGGAAAC 59.337 42.308 14.25 8.89 42.21 2.78
833 3187 8.580720 TGCAAAGTTTGGCTAAATTTATACTCA 58.419 29.630 17.11 0.00 0.00 3.41
839 3193 5.918608 TGGTGCAAAGTTTGGCTAAATTTA 58.081 33.333 17.11 0.00 0.00 1.40
1640 5298 3.680786 CTGGGTCGTCGGAGCACA 61.681 66.667 0.00 0.00 42.46 4.57
1665 5323 1.834378 CAGCCCCGGCAGAGAGATA 60.834 63.158 8.74 0.00 44.88 1.98
1666 5324 3.160047 CAGCCCCGGCAGAGAGAT 61.160 66.667 8.74 0.00 44.88 2.75
2124 5810 1.410517 CCGTCTGGCATACACAGATCT 59.589 52.381 3.83 0.00 45.72 2.75
2336 6034 2.046892 CCACCTCAAGCACCTCCG 60.047 66.667 0.00 0.00 0.00 4.63
2505 6230 4.452733 GACCCGCCCTTCTCCACG 62.453 72.222 0.00 0.00 0.00 4.94
2553 6278 4.473520 CGGCGGGCCATCAACTCT 62.474 66.667 4.39 0.00 35.37 3.24
2617 6347 1.732917 TGCAAAAGGGAAGCACACG 59.267 52.632 0.00 0.00 32.55 4.49
2622 6352 1.269723 GGTACAGTGCAAAAGGGAAGC 59.730 52.381 0.00 0.00 0.00 3.86
2624 6354 1.134037 ACGGTACAGTGCAAAAGGGAA 60.134 47.619 0.00 0.00 0.00 3.97
2625 6355 0.470766 ACGGTACAGTGCAAAAGGGA 59.529 50.000 0.00 0.00 0.00 4.20
2628 6358 2.222445 GGTACACGGTACAGTGCAAAAG 59.778 50.000 23.64 2.00 45.45 2.27
2691 6428 6.444633 CAGCAGTTTCAGAAGAACATGAAAT 58.555 36.000 0.00 0.00 44.65 2.17
2692 6429 5.221106 CCAGCAGTTTCAGAAGAACATGAAA 60.221 40.000 0.00 0.00 41.76 2.69
2693 6430 4.276678 CCAGCAGTTTCAGAAGAACATGAA 59.723 41.667 0.00 0.00 32.39 2.57
2694 6431 3.817084 CCAGCAGTTTCAGAAGAACATGA 59.183 43.478 0.00 0.00 32.39 3.07
2695 6432 3.611057 GCCAGCAGTTTCAGAAGAACATG 60.611 47.826 0.00 0.00 32.39 3.21
2696 6433 2.555757 GCCAGCAGTTTCAGAAGAACAT 59.444 45.455 0.00 0.00 32.39 2.71
2697 6434 1.949525 GCCAGCAGTTTCAGAAGAACA 59.050 47.619 0.00 0.00 32.39 3.18
2698 6435 2.225467 AGCCAGCAGTTTCAGAAGAAC 58.775 47.619 0.00 0.00 32.39 3.01
2699 6436 2.645838 AGCCAGCAGTTTCAGAAGAA 57.354 45.000 0.00 0.00 0.00 2.52
2700 6437 2.158769 TGAAGCCAGCAGTTTCAGAAGA 60.159 45.455 2.57 0.00 40.37 2.87
2701 6438 2.031333 GTGAAGCCAGCAGTTTCAGAAG 60.031 50.000 6.33 0.00 45.12 2.85
2702 6439 1.949525 GTGAAGCCAGCAGTTTCAGAA 59.050 47.619 6.33 0.00 45.12 3.02
2703 6440 1.141657 AGTGAAGCCAGCAGTTTCAGA 59.858 47.619 6.33 0.00 45.12 3.27
2704 6441 1.602311 AGTGAAGCCAGCAGTTTCAG 58.398 50.000 6.33 0.00 45.12 3.02
2705 6442 2.057137 AAGTGAAGCCAGCAGTTTCA 57.943 45.000 2.57 2.57 42.69 2.69
2706 6443 4.773323 ATAAAGTGAAGCCAGCAGTTTC 57.227 40.909 7.02 0.00 39.10 2.78
2707 6444 5.560724 TCTATAAAGTGAAGCCAGCAGTTT 58.439 37.500 0.00 0.00 40.75 2.66
2708 6445 5.165961 TCTATAAAGTGAAGCCAGCAGTT 57.834 39.130 0.00 0.00 0.00 3.16
2709 6446 4.826274 TCTATAAAGTGAAGCCAGCAGT 57.174 40.909 0.00 0.00 0.00 4.40
2710 6447 7.792374 TTTATCTATAAAGTGAAGCCAGCAG 57.208 36.000 0.00 0.00 0.00 4.24
2711 6448 7.992608 TGATTTATCTATAAAGTGAAGCCAGCA 59.007 33.333 2.00 0.00 35.88 4.41
2712 6449 8.383318 TGATTTATCTATAAAGTGAAGCCAGC 57.617 34.615 2.00 0.00 35.88 4.85
2728 6465 9.420118 TGCCCAACTATACAAAATGATTTATCT 57.580 29.630 0.00 0.00 0.00 1.98
2729 6466 9.683069 CTGCCCAACTATACAAAATGATTTATC 57.317 33.333 0.00 0.00 0.00 1.75
2730 6467 8.641541 CCTGCCCAACTATACAAAATGATTTAT 58.358 33.333 0.00 0.00 0.00 1.40
2731 6468 7.836685 TCCTGCCCAACTATACAAAATGATTTA 59.163 33.333 0.00 0.00 0.00 1.40
2732 6469 6.667414 TCCTGCCCAACTATACAAAATGATTT 59.333 34.615 0.00 0.00 0.00 2.17
2733 6470 6.194235 TCCTGCCCAACTATACAAAATGATT 58.806 36.000 0.00 0.00 0.00 2.57
2734 6471 5.765510 TCCTGCCCAACTATACAAAATGAT 58.234 37.500 0.00 0.00 0.00 2.45
2735 6472 5.186256 TCCTGCCCAACTATACAAAATGA 57.814 39.130 0.00 0.00 0.00 2.57
2736 6473 4.202050 GCTCCTGCCCAACTATACAAAATG 60.202 45.833 0.00 0.00 0.00 2.32
2737 6474 3.954258 GCTCCTGCCCAACTATACAAAAT 59.046 43.478 0.00 0.00 0.00 1.82
2738 6475 3.010138 AGCTCCTGCCCAACTATACAAAA 59.990 43.478 0.00 0.00 40.80 2.44
2739 6476 2.576191 AGCTCCTGCCCAACTATACAAA 59.424 45.455 0.00 0.00 40.80 2.83
2740 6477 2.196595 AGCTCCTGCCCAACTATACAA 58.803 47.619 0.00 0.00 40.80 2.41
2741 6478 1.879575 AGCTCCTGCCCAACTATACA 58.120 50.000 0.00 0.00 40.80 2.29
2742 6479 2.945668 CAAAGCTCCTGCCCAACTATAC 59.054 50.000 0.00 0.00 40.80 1.47
2743 6480 2.683742 GCAAAGCTCCTGCCCAACTATA 60.684 50.000 9.14 0.00 40.80 1.31
2744 6481 1.957113 GCAAAGCTCCTGCCCAACTAT 60.957 52.381 9.14 0.00 40.80 2.12
2745 6482 0.609131 GCAAAGCTCCTGCCCAACTA 60.609 55.000 9.14 0.00 40.80 2.24
2746 6483 1.905354 GCAAAGCTCCTGCCCAACT 60.905 57.895 9.14 0.00 40.80 3.16
2747 6484 0.609131 TAGCAAAGCTCCTGCCCAAC 60.609 55.000 15.24 0.00 40.86 3.77
2748 6485 0.609131 GTAGCAAAGCTCCTGCCCAA 60.609 55.000 15.24 1.67 40.86 4.12
2749 6486 1.002134 GTAGCAAAGCTCCTGCCCA 60.002 57.895 15.24 3.52 40.86 5.36
2750 6487 1.002134 TGTAGCAAAGCTCCTGCCC 60.002 57.895 15.24 8.51 40.86 5.36
2751 6488 0.322008 AGTGTAGCAAAGCTCCTGCC 60.322 55.000 15.24 4.19 40.86 4.85
2752 6489 1.198637 CAAGTGTAGCAAAGCTCCTGC 59.801 52.381 11.82 11.82 40.44 4.85
2753 6490 2.498167 ACAAGTGTAGCAAAGCTCCTG 58.502 47.619 0.00 0.00 40.44 3.86
2754 6491 2.938956 ACAAGTGTAGCAAAGCTCCT 57.061 45.000 0.00 0.00 40.44 3.69
2755 6492 5.629079 ATTTACAAGTGTAGCAAAGCTCC 57.371 39.130 0.00 0.00 40.44 4.70
2756 6493 7.271438 GCTTAATTTACAAGTGTAGCAAAGCTC 59.729 37.037 15.38 0.00 40.44 4.09
2757 6494 7.040409 AGCTTAATTTACAAGTGTAGCAAAGCT 60.040 33.333 17.55 17.55 43.41 3.74
2758 6495 7.084486 AGCTTAATTTACAAGTGTAGCAAAGC 58.916 34.615 15.11 15.11 35.92 3.51
2761 6498 9.496873 TCTTAGCTTAATTTACAAGTGTAGCAA 57.503 29.630 0.00 0.00 0.00 3.91
2762 6499 9.496873 TTCTTAGCTTAATTTACAAGTGTAGCA 57.503 29.630 0.00 0.00 0.00 3.49
2766 6503 8.287503 CCGTTTCTTAGCTTAATTTACAAGTGT 58.712 33.333 0.00 0.00 0.00 3.55
2767 6504 7.270579 GCCGTTTCTTAGCTTAATTTACAAGTG 59.729 37.037 0.00 0.00 0.00 3.16
2768 6505 7.303261 GCCGTTTCTTAGCTTAATTTACAAGT 58.697 34.615 0.00 0.00 0.00 3.16
2769 6506 6.464834 CGCCGTTTCTTAGCTTAATTTACAAG 59.535 38.462 0.00 0.00 0.00 3.16
2770 6507 6.308675 CGCCGTTTCTTAGCTTAATTTACAA 58.691 36.000 0.00 0.00 0.00 2.41
2771 6508 5.163834 CCGCCGTTTCTTAGCTTAATTTACA 60.164 40.000 0.00 0.00 0.00 2.41
2772 6509 5.260900 CCGCCGTTTCTTAGCTTAATTTAC 58.739 41.667 0.00 0.00 0.00 2.01
2773 6510 4.201841 GCCGCCGTTTCTTAGCTTAATTTA 60.202 41.667 0.00 0.00 0.00 1.40
2774 6511 3.427098 GCCGCCGTTTCTTAGCTTAATTT 60.427 43.478 0.00 0.00 0.00 1.82
2775 6512 2.096980 GCCGCCGTTTCTTAGCTTAATT 59.903 45.455 0.00 0.00 0.00 1.40
2776 6513 1.669265 GCCGCCGTTTCTTAGCTTAAT 59.331 47.619 0.00 0.00 0.00 1.40
2777 6514 1.081094 GCCGCCGTTTCTTAGCTTAA 58.919 50.000 0.00 0.00 0.00 1.85
2778 6515 0.741927 GGCCGCCGTTTCTTAGCTTA 60.742 55.000 0.00 0.00 0.00 3.09
2779 6516 2.038837 GGCCGCCGTTTCTTAGCTT 61.039 57.895 0.00 0.00 0.00 3.74
2780 6517 2.436115 GGCCGCCGTTTCTTAGCT 60.436 61.111 0.00 0.00 0.00 3.32
2781 6518 3.861263 CGGCCGCCGTTTCTTAGC 61.861 66.667 24.08 0.00 42.73 3.09
3356 7586 2.484417 CCTGAGATGGACCGAAGAATGG 60.484 54.545 0.00 0.00 0.00 3.16
3401 7638 2.349817 GGTCGCTCATAATTTGCATCCG 60.350 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.