Multiple sequence alignment - TraesCS4A01G457100

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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 TraesCS4A01G457100 chr4A 100.000 4642 0 0 665 5306 722409811 722414452 0.000000e+00 8573.0
1 TraesCS4A01G457100 chr4A 100.000 284 0 0 1 284 722409147 722409430 4.710000e-145 525.0
2 TraesCS4A01G457100 chr4A 77.054 353 51 20 3557 3888 2154727 2155070 5.460000e-40 176.0
3 TraesCS4A01G457100 chr7A 93.613 2192 106 14 687 2867 13801068 13798900 0.000000e+00 3241.0
4 TraesCS4A01G457100 chr7A 92.440 754 41 9 4041 4793 13798317 13797579 0.000000e+00 1062.0
5 TraesCS4A01G457100 chr7A 89.910 446 33 6 4330 4765 13776920 13776477 9.980000e-157 564.0
6 TraesCS4A01G457100 chr7A 84.000 225 17 10 57 279 13801688 13801481 1.170000e-46 198.0
7 TraesCS4A01G457100 chr7A 97.101 69 2 0 1 69 13801776 13801708 3.360000e-22 117.0
8 TraesCS4A01G457100 chr1B 88.530 2232 165 34 667 2860 45201116 45198938 0.000000e+00 2619.0
9 TraesCS4A01G457100 chr1B 89.085 1191 73 24 3581 4752 45198903 45197751 0.000000e+00 1426.0
10 TraesCS4A01G457100 chr1B 85.095 738 94 11 4057 4780 45032448 45031713 0.000000e+00 739.0
11 TraesCS4A01G457100 chr1B 84.959 738 95 11 4057 4780 44989359 44988624 0.000000e+00 734.0
12 TraesCS4A01G457100 chr1B 87.654 243 29 1 706 947 297183951 297183709 1.130000e-71 281.0
13 TraesCS4A01G457100 chr1B 85.185 243 16 14 58 284 297184294 297184056 1.150000e-56 231.0
14 TraesCS4A01G457100 chr7D 93.629 1758 77 14 3554 5306 14548609 14546882 0.000000e+00 2593.0
15 TraesCS4A01G457100 chr7D 92.004 1013 55 10 1857 2867 14549590 14548602 0.000000e+00 1399.0
16 TraesCS4A01G457100 chr7D 95.362 733 30 2 4574 5306 14167507 14166779 0.000000e+00 1162.0
17 TraesCS4A01G457100 chr7D 90.059 845 62 7 665 1508 14551711 14550888 0.000000e+00 1075.0
18 TraesCS4A01G457100 chr7D 88.244 689 57 5 2886 3550 580806019 580806707 0.000000e+00 802.0
19 TraesCS4A01G457100 chr7D 90.588 595 53 3 2956 3549 621777661 621778253 0.000000e+00 785.0
20 TraesCS4A01G457100 chr7D 89.000 600 62 4 2956 3555 45736401 45736996 0.000000e+00 739.0
21 TraesCS4A01G457100 chr7D 94.915 354 16 1 1507 1858 14550689 14550336 2.160000e-153 553.0
22 TraesCS4A01G457100 chr7D 84.817 191 16 7 11 189 14552108 14551919 4.220000e-41 180.0
23 TraesCS4A01G457100 chr7D 75.519 241 38 11 4496 4720 194693284 194693049 1.220000e-16 99.0
24 TraesCS4A01G457100 chr2D 89.879 662 42 3 2886 3523 57326117 57325457 0.000000e+00 828.0
25 TraesCS4A01G457100 chr2D 87.931 696 59 7 2886 3557 432877034 432876340 0.000000e+00 797.0
26 TraesCS4A01G457100 chr2D 100.000 29 0 0 4884 4912 519340803 519340831 3.000000e-03 54.7
27 TraesCS4A01G457100 chr1A 88.571 700 45 11 2886 3550 500556909 500557608 0.000000e+00 817.0
28 TraesCS4A01G457100 chr1A 84.886 483 41 16 4429 4887 29010972 29010498 4.840000e-125 459.0
29 TraesCS4A01G457100 chr1A 98.701 77 1 0 2886 2962 191861145 191861221 2.580000e-28 137.0
30 TraesCS4A01G457100 chr3D 90.484 599 56 1 2956 3554 557873015 557873612 0.000000e+00 789.0
31 TraesCS4A01G457100 chr3D 89.482 599 61 2 2956 3553 604827264 604826667 0.000000e+00 756.0
32 TraesCS4A01G457100 chr5B 87.663 689 61 9 2886 3550 704162847 704163535 0.000000e+00 780.0
33 TraesCS4A01G457100 chr5B 100.000 29 0 0 4859 4887 511619643 511619671 3.000000e-03 54.7
34 TraesCS4A01G457100 chr1D 89.833 600 60 1 2956 3554 13854755 13855354 0.000000e+00 769.0
35 TraesCS4A01G457100 chr1D 93.421 76 5 0 2886 2961 405000885 405000960 4.340000e-21 113.0
36 TraesCS4A01G457100 chrUn 85.306 735 92 11 4057 4777 249818043 249818775 0.000000e+00 745.0
37 TraesCS4A01G457100 chr7B 84.965 705 68 14 2886 3553 609011671 609010968 0.000000e+00 680.0
38 TraesCS4A01G457100 chr6D 82.319 690 70 15 2886 3550 7109274 7109936 7.770000e-153 551.0
39 TraesCS4A01G457100 chr5A 88.477 243 27 1 706 947 150806587 150806345 5.200000e-75 292.0
40 TraesCS4A01G457100 chr5A 85.324 293 16 12 16 284 150806982 150806693 1.460000e-70 278.0
41 TraesCS4A01G457100 chr3B 78.378 296 40 15 1348 1624 727476560 727476270 2.540000e-38 171.0
42 TraesCS4A01G457100 chr2A 94.805 77 4 0 2886 2962 198755204 198755128 2.600000e-23 121.0
43 TraesCS4A01G457100 chr2B 100.000 29 0 0 4884 4912 611313143 611313171 3.000000e-03 54.7


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 TraesCS4A01G457100 chr4A 722409147 722414452 5305 False 4549.0 8573 100.0000 1 5306 2 chr4A.!!$F2 5305
1 TraesCS4A01G457100 chr7A 13797579 13801776 4197 True 1154.5 3241 91.7885 1 4793 4 chr7A.!!$R2 4792
2 TraesCS4A01G457100 chr1B 45197751 45201116 3365 True 2022.5 2619 88.8075 667 4752 2 chr1B.!!$R3 4085
3 TraesCS4A01G457100 chr1B 45031713 45032448 735 True 739.0 739 85.0950 4057 4780 1 chr1B.!!$R2 723
4 TraesCS4A01G457100 chr1B 44988624 44989359 735 True 734.0 734 84.9590 4057 4780 1 chr1B.!!$R1 723
5 TraesCS4A01G457100 chr1B 297183709 297184294 585 True 256.0 281 86.4195 58 947 2 chr1B.!!$R4 889
6 TraesCS4A01G457100 chr7D 14166779 14167507 728 True 1162.0 1162 95.3620 4574 5306 1 chr7D.!!$R1 732
7 TraesCS4A01G457100 chr7D 14546882 14552108 5226 True 1160.0 2593 91.0848 11 5306 5 chr7D.!!$R3 5295
8 TraesCS4A01G457100 chr7D 580806019 580806707 688 False 802.0 802 88.2440 2886 3550 1 chr7D.!!$F2 664
9 TraesCS4A01G457100 chr7D 621777661 621778253 592 False 785.0 785 90.5880 2956 3549 1 chr7D.!!$F3 593
10 TraesCS4A01G457100 chr7D 45736401 45736996 595 False 739.0 739 89.0000 2956 3555 1 chr7D.!!$F1 599
11 TraesCS4A01G457100 chr2D 57325457 57326117 660 True 828.0 828 89.8790 2886 3523 1 chr2D.!!$R1 637
12 TraesCS4A01G457100 chr2D 432876340 432877034 694 True 797.0 797 87.9310 2886 3557 1 chr2D.!!$R2 671
13 TraesCS4A01G457100 chr1A 500556909 500557608 699 False 817.0 817 88.5710 2886 3550 1 chr1A.!!$F2 664
14 TraesCS4A01G457100 chr3D 557873015 557873612 597 False 789.0 789 90.4840 2956 3554 1 chr3D.!!$F1 598
15 TraesCS4A01G457100 chr3D 604826667 604827264 597 True 756.0 756 89.4820 2956 3553 1 chr3D.!!$R1 597
16 TraesCS4A01G457100 chr5B 704162847 704163535 688 False 780.0 780 87.6630 2886 3550 1 chr5B.!!$F2 664
17 TraesCS4A01G457100 chr1D 13854755 13855354 599 False 769.0 769 89.8330 2956 3554 1 chr1D.!!$F1 598
18 TraesCS4A01G457100 chrUn 249818043 249818775 732 False 745.0 745 85.3060 4057 4777 1 chrUn.!!$F1 720
19 TraesCS4A01G457100 chr7B 609010968 609011671 703 True 680.0 680 84.9650 2886 3553 1 chr7B.!!$R1 667
20 TraesCS4A01G457100 chr6D 7109274 7109936 662 False 551.0 551 82.3190 2886 3550 1 chr6D.!!$F1 664
21 TraesCS4A01G457100 chr5A 150806345 150806982 637 True 285.0 292 86.9005 16 947 2 chr5A.!!$R1 931

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
859 929 0.249155 CTGTGTTGTTGCTGCAAGGG 60.249 55.0 16.53 0.00 0.00 3.95 F
1251 1338 0.320683 TGTGGATCAGTGGCAGTTCG 60.321 55.0 0.00 0.00 0.00 3.95 F
2869 3925 0.036164 CTCCACCCGGTTGTGAATCA 59.964 55.0 11.95 0.00 38.55 2.57 F
3283 4380 0.103208 AGGCTGCTAGCACGTGATAC 59.897 55.0 22.23 12.59 44.75 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 3235 0.179111 CCACAAGATAAGCGGCGAGA 60.179 55.0 12.98 0.0 0.0 4.04 R
2974 4054 0.178975 ATGGCGGGTTTCAGGTTCAA 60.179 50.0 0.00 0.0 0.0 2.69 R
3988 5118 0.323360 GAGTTGCCAGCCATAACCCA 60.323 55.0 0.00 0.0 0.0 4.51 R
5251 6512 1.830279 ATCACACACATTGGCTCCAG 58.170 50.0 0.00 0.0 0.0 3.86 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
185 236 1.939785 CTCGTCGTCATAGGTGCGC 60.940 63.158 0.00 0.00 0.00 6.09
235 287 4.227134 CGCCCCTCGTGCTATGCT 62.227 66.667 0.00 0.00 0.00 3.79
727 792 2.232208 CTGGTCGATATGGCATGCTAGA 59.768 50.000 18.92 9.73 0.00 2.43
729 798 3.261643 TGGTCGATATGGCATGCTAGATT 59.738 43.478 18.92 0.00 0.00 2.40
759 828 1.081242 GGCATGTTGTTCTGCGGTG 60.081 57.895 0.00 0.00 39.30 4.94
814 884 3.433615 GCACAACACAGTGGAGATTAGAC 59.566 47.826 5.31 0.00 39.87 2.59
837 907 4.561105 GCAAGTGTATGCCTAGGTAGATC 58.439 47.826 11.31 1.29 40.49 2.75
859 929 0.249155 CTGTGTTGTTGCTGCAAGGG 60.249 55.000 16.53 0.00 0.00 3.95
907 980 4.091549 AGATTTGTTGCTGGAATGGATGT 58.908 39.130 0.00 0.00 0.00 3.06
908 981 4.529377 AGATTTGTTGCTGGAATGGATGTT 59.471 37.500 0.00 0.00 0.00 2.71
1008 1082 7.880195 ACCCAAGATGCTCTATACATGAATTAC 59.120 37.037 0.00 0.00 0.00 1.89
1104 1191 2.000048 AGATTTCCTAAAGGTGCCCCA 59.000 47.619 0.00 0.00 36.34 4.96
1110 1197 0.748005 CTAAAGGTGCCCCATGGACG 60.748 60.000 15.22 3.56 0.00 4.79
1244 1331 3.268330 CATGTTCTCTGTGGATCAGTGG 58.732 50.000 0.00 0.00 43.97 4.00
1245 1332 1.002430 TGTTCTCTGTGGATCAGTGGC 59.998 52.381 0.00 0.00 43.97 5.01
1251 1338 0.320683 TGTGGATCAGTGGCAGTTCG 60.321 55.000 0.00 0.00 0.00 3.95
1276 1363 7.358830 GGTTTTTCTGATCAACTTCTCTGAAG 58.641 38.462 0.00 5.85 32.98 3.02
1293 1380 2.354510 TGAAGAAGTGTCGTTTGCTTGG 59.645 45.455 0.00 0.00 0.00 3.61
1322 1409 6.817765 TTGTCCATAGATCAACTTTGTTCC 57.182 37.500 0.00 0.00 0.00 3.62
1323 1410 6.126863 TGTCCATAGATCAACTTTGTTCCT 57.873 37.500 0.00 0.00 0.00 3.36
1324 1411 6.542821 TGTCCATAGATCAACTTTGTTCCTT 58.457 36.000 0.00 0.00 0.00 3.36
1325 1412 7.685481 TGTCCATAGATCAACTTTGTTCCTTA 58.315 34.615 0.00 0.00 0.00 2.69
1326 1413 7.606456 TGTCCATAGATCAACTTTGTTCCTTAC 59.394 37.037 0.00 0.00 0.00 2.34
1327 1414 7.065923 GTCCATAGATCAACTTTGTTCCTTACC 59.934 40.741 0.00 0.00 0.00 2.85
1328 1415 6.037172 CCATAGATCAACTTTGTTCCTTACCG 59.963 42.308 0.00 0.00 0.00 4.02
1329 1416 5.223449 AGATCAACTTTGTTCCTTACCGA 57.777 39.130 0.00 0.00 0.00 4.69
1482 1569 9.796120 TTTAAGGTAGTGTTTTCATTGTTTCAG 57.204 29.630 0.00 0.00 0.00 3.02
1489 1576 8.188531 AGTGTTTTCATTGTTTCAGATGTTTG 57.811 30.769 0.00 0.00 0.00 2.93
1502 1589 3.190327 CAGATGTTTGATGCCACCGTTTA 59.810 43.478 0.00 0.00 0.00 2.01
1511 1798 1.398739 TGCCACCGTTTATGCATTACG 59.601 47.619 20.71 20.71 35.20 3.18
1532 1821 3.610114 CGGTTTTGCTGATTCTGTCTTGG 60.610 47.826 0.00 0.00 0.00 3.61
1534 1823 4.540824 GTTTTGCTGATTCTGTCTTGGTC 58.459 43.478 0.00 0.00 0.00 4.02
1655 1944 4.569943 TGTTTCTTCTCTATCCACAGTGC 58.430 43.478 0.00 0.00 0.00 4.40
2067 3103 6.819397 ACTCAATTTGAAGGTAAGTTAGGC 57.181 37.500 0.01 0.00 0.00 3.93
2082 3118 5.134725 AGTTAGGCCATCTTCATTGGAAT 57.865 39.130 5.01 0.00 36.26 3.01
2160 3196 2.472695 AGCGCCTCTTGTTACAATGA 57.527 45.000 2.29 0.00 0.00 2.57
2245 3283 2.487274 AAATCCCAAGCGCCCGGTTA 62.487 55.000 2.29 0.00 34.20 2.85
2256 3294 1.465200 GCCCGGTTACCCTTTTTGCA 61.465 55.000 0.00 0.00 0.00 4.08
2472 3510 6.790285 ATGCCTTGCTGTTTATTTCAAAAG 57.210 33.333 0.00 0.00 0.00 2.27
2680 3718 6.763715 AGGATATGGAGGTACATGCTTTTA 57.236 37.500 0.00 0.00 32.39 1.52
2750 3788 4.724279 ATGGAGTTTGTTCACCCTACTT 57.276 40.909 0.00 0.00 0.00 2.24
2755 3793 3.974642 AGTTTGTTCACCCTACTTCTCCT 59.025 43.478 0.00 0.00 0.00 3.69
2778 3816 9.807921 TCCTGGACAACTTTAAGAAATCTAAAT 57.192 29.630 0.00 0.00 0.00 1.40
2852 3891 5.776173 TTAAGTAGGATGCTGCTAGTCTC 57.224 43.478 5.05 0.00 0.00 3.36
2861 3917 1.229082 TGCTAGTCTCCACCCGGTT 60.229 57.895 0.00 0.00 0.00 4.44
2862 3918 1.218316 GCTAGTCTCCACCCGGTTG 59.782 63.158 0.00 0.00 0.00 3.77
2863 3919 1.542187 GCTAGTCTCCACCCGGTTGT 61.542 60.000 0.00 0.00 0.00 3.32
2864 3920 0.246635 CTAGTCTCCACCCGGTTGTG 59.753 60.000 0.00 1.65 35.98 3.33
2865 3921 0.178955 TAGTCTCCACCCGGTTGTGA 60.179 55.000 11.95 0.41 38.55 3.58
2866 3922 1.052124 AGTCTCCACCCGGTTGTGAA 61.052 55.000 11.95 0.00 38.55 3.18
2867 3923 0.036306 GTCTCCACCCGGTTGTGAAT 59.964 55.000 11.95 0.00 38.55 2.57
2868 3924 0.323629 TCTCCACCCGGTTGTGAATC 59.676 55.000 11.95 0.00 38.55 2.52
2869 3925 0.036164 CTCCACCCGGTTGTGAATCA 59.964 55.000 11.95 0.00 38.55 2.57
2870 3926 0.474614 TCCACCCGGTTGTGAATCAA 59.525 50.000 11.95 0.00 38.55 2.57
2871 3927 0.881118 CCACCCGGTTGTGAATCAAG 59.119 55.000 11.95 0.00 38.55 3.02
2872 3928 1.544537 CCACCCGGTTGTGAATCAAGA 60.545 52.381 11.95 0.00 38.55 3.02
2873 3929 2.436417 CACCCGGTTGTGAATCAAGAT 58.564 47.619 4.97 0.00 38.55 2.40
2874 3930 2.162208 CACCCGGTTGTGAATCAAGATG 59.838 50.000 4.97 0.00 38.55 2.90
2875 3931 1.745087 CCCGGTTGTGAATCAAGATGG 59.255 52.381 0.00 0.00 36.66 3.51
2876 3932 1.133025 CCGGTTGTGAATCAAGATGGC 59.867 52.381 0.00 0.00 36.66 4.40
2877 3933 1.811965 CGGTTGTGAATCAAGATGGCA 59.188 47.619 0.00 0.00 36.66 4.92
2878 3934 2.228582 CGGTTGTGAATCAAGATGGCAA 59.771 45.455 0.00 0.00 36.66 4.52
2879 3935 3.119388 CGGTTGTGAATCAAGATGGCAAT 60.119 43.478 0.00 0.00 36.66 3.56
2880 3936 4.178540 GGTTGTGAATCAAGATGGCAATG 58.821 43.478 0.00 0.00 36.66 2.82
2881 3937 4.322198 GGTTGTGAATCAAGATGGCAATGT 60.322 41.667 0.00 0.00 36.66 2.71
2882 3938 5.232463 GTTGTGAATCAAGATGGCAATGTT 58.768 37.500 0.00 0.00 36.66 2.71
2883 3939 5.471556 TGTGAATCAAGATGGCAATGTTT 57.528 34.783 0.00 0.00 0.00 2.83
2884 3940 5.856156 TGTGAATCAAGATGGCAATGTTTT 58.144 33.333 0.00 0.00 0.00 2.43
2954 4010 3.429684 GGGCCGTTGTTGGGTAAAATATG 60.430 47.826 0.00 0.00 0.00 1.78
2981 4061 4.277423 CCCGTTTCAACAATACTTGAACCT 59.723 41.667 0.00 0.00 39.37 3.50
3283 4380 0.103208 AGGCTGCTAGCACGTGATAC 59.897 55.000 22.23 12.59 44.75 2.24
3294 4391 2.973224 GCACGTGATACTTTTGCAACTG 59.027 45.455 22.23 0.00 33.24 3.16
3356 4453 9.310449 ACAAGTAGTGGAATTCTAGTTCTAAGA 57.690 33.333 4.31 0.00 31.27 2.10
3373 4470 1.003646 AGAGGTAGAGCTCCAGTCCA 58.996 55.000 10.93 0.00 0.00 4.02
3425 4534 2.933495 GGTTTAGAAAACCCGATGGC 57.067 50.000 9.92 0.00 34.26 4.40
3505 4614 1.406887 CGATTTTCTCGTGGGGATGGT 60.407 52.381 0.00 0.00 42.56 3.55
3511 4620 0.251165 CTCGTGGGGATGGTTTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
3512 4621 0.186386 TCGTGGGGATGGTTTTGGTT 59.814 50.000 0.00 0.00 0.00 3.67
3550 4659 0.975556 TTCGTCCCTGCTGCCATCTA 60.976 55.000 0.00 0.00 0.00 1.98
3561 4670 3.054875 TGCTGCCATCTAGAGTTGTGAAT 60.055 43.478 0.00 0.00 0.00 2.57
3666 4786 0.615331 GCTTGGACATCTGAGGACCA 59.385 55.000 9.32 9.32 0.00 4.02
3667 4787 1.003580 GCTTGGACATCTGAGGACCAA 59.996 52.381 21.12 21.12 38.12 3.67
3790 4918 1.129251 CGCACGTGAGCATCTTCAATT 59.871 47.619 22.23 0.00 34.92 2.32
3793 4921 2.743664 CACGTGAGCATCTTCAATTCCA 59.256 45.455 10.90 0.00 34.92 3.53
3868 4998 0.541863 CACCGGGTTTAGATGAGCCT 59.458 55.000 6.32 0.00 32.55 4.58
3916 5046 8.818141 TTTGAGTAGTTCTTTACTGATCTGTG 57.182 34.615 14.91 0.00 37.73 3.66
3947 5077 4.635765 TGCTGGTTGATGCTATAGTTGAAC 59.364 41.667 0.84 0.76 0.00 3.18
4054 5297 5.483685 TCTCTTGTGTACCTGCTAACAAT 57.516 39.130 0.00 0.00 32.47 2.71
4164 5409 2.673368 GACACCCGCTATCTTTGTCAAG 59.327 50.000 0.00 0.00 37.20 3.02
4258 5503 3.699894 CGCTGGACCAGGCAGTCT 61.700 66.667 23.09 0.00 36.95 3.24
4437 5685 9.856162 ACATTATCGTAACCCCTATGTAAAAAT 57.144 29.630 0.00 0.00 0.00 1.82
4531 5779 4.699637 TCGGCTTAATAAGGTGGTGTATG 58.300 43.478 1.88 0.00 0.00 2.39
4817 6076 9.061435 ACCTACTATAATTTGTAGACCTCGTAC 57.939 37.037 7.13 0.00 38.62 3.67
4818 6077 8.226448 CCTACTATAATTTGTAGACCTCGTACG 58.774 40.741 9.53 9.53 38.62 3.67
4824 6083 1.276138 TGTAGACCTCGTACGGAGACA 59.724 52.381 16.52 8.58 46.23 3.41
4825 6084 2.289631 TGTAGACCTCGTACGGAGACAA 60.290 50.000 16.52 0.00 46.23 3.18
5001 6260 2.522185 ACTCTTGCGTTCCACCTAGTA 58.478 47.619 0.00 0.00 0.00 1.82
5088 6347 9.850198 TTTTCCAATTTCTCATTTGAATTTCCT 57.150 25.926 0.00 0.00 0.00 3.36
5233 6494 5.782893 TTGTGCTTACCTTGCAAGTAAAT 57.217 34.783 24.35 9.88 42.41 1.40
5298 6559 7.684670 TGTAGAATATTTAGCAAAACTGAGCG 58.315 34.615 0.00 0.00 35.48 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 250 1.153086 CGGGGAGGGAATCTTGCAG 60.153 63.158 0.00 0.00 0.00 4.41
230 282 2.494471 AGCAAGCAAGCAATCAAGCATA 59.506 40.909 3.19 0.00 36.85 3.14
231 283 1.275291 AGCAAGCAAGCAATCAAGCAT 59.725 42.857 3.19 0.00 36.85 3.79
232 284 0.677288 AGCAAGCAAGCAATCAAGCA 59.323 45.000 3.19 0.00 36.85 3.91
234 286 2.030185 AGTGAGCAAGCAAGCAATCAAG 60.030 45.455 3.19 0.00 36.85 3.02
235 287 1.958579 AGTGAGCAAGCAAGCAATCAA 59.041 42.857 3.19 0.00 36.85 2.57
727 792 6.648879 ACAACATGCCAAGTAACTAACAAT 57.351 33.333 0.00 0.00 0.00 2.71
729 798 5.825679 AGAACAACATGCCAAGTAACTAACA 59.174 36.000 0.00 0.00 0.00 2.41
759 828 1.546476 AGCTAGTGGGCTATGCGTATC 59.454 52.381 0.00 0.00 41.16 2.24
766 835 1.749334 GCACCGAGCTAGTGGGCTAT 61.749 60.000 16.00 0.00 43.20 2.97
798 868 2.654749 TGCGTCTAATCTCCACTGTG 57.345 50.000 0.00 0.00 0.00 3.66
814 884 2.361119 TCTACCTAGGCATACACTTGCG 59.639 50.000 9.30 0.00 43.71 4.85
831 901 3.681897 CAGCAACAACACAGGAGATCTAC 59.318 47.826 0.00 0.00 0.00 2.59
837 907 0.740149 TTGCAGCAACAACACAGGAG 59.260 50.000 2.83 0.00 0.00 3.69
907 980 3.056607 GCTGCTAAATTTTCCCAGCTCAA 60.057 43.478 20.77 1.54 44.00 3.02
908 981 2.493278 GCTGCTAAATTTTCCCAGCTCA 59.507 45.455 20.77 2.08 44.00 4.26
1104 1191 2.504032 CCATGGTACCGCGTCCAT 59.496 61.111 17.70 17.70 44.15 3.41
1110 1197 1.590792 GTAGTCGCCATGGTACCGC 60.591 63.158 14.67 3.64 0.00 5.68
1244 1331 3.896648 TGATCAGAAAAACCGAACTGC 57.103 42.857 0.00 0.00 0.00 4.40
1245 1332 5.424121 AGTTGATCAGAAAAACCGAACTG 57.576 39.130 0.00 0.00 0.00 3.16
1251 1338 6.867662 TCAGAGAAGTTGATCAGAAAAACC 57.132 37.500 0.00 0.00 0.00 3.27
1276 1363 5.600908 TTATACCAAGCAAACGACACTTC 57.399 39.130 0.00 0.00 0.00 3.01
1322 1409 2.015587 AGCTCTCGGTAAGTCGGTAAG 58.984 52.381 0.00 0.00 0.00 2.34
1323 1410 2.119801 AGCTCTCGGTAAGTCGGTAA 57.880 50.000 0.00 0.00 0.00 2.85
1324 1411 2.988010 TAGCTCTCGGTAAGTCGGTA 57.012 50.000 0.00 0.00 0.00 4.02
1325 1412 2.119801 TTAGCTCTCGGTAAGTCGGT 57.880 50.000 0.00 0.00 0.00 4.69
1326 1413 2.879646 AGATTAGCTCTCGGTAAGTCGG 59.120 50.000 0.00 0.00 36.63 4.79
1327 1414 4.136517 GAGATTAGCTCTCGGTAAGTCG 57.863 50.000 0.00 0.00 41.07 4.18
1482 1569 2.723124 AAACGGTGGCATCAAACATC 57.277 45.000 0.00 0.00 0.00 3.06
1489 1576 2.869233 AATGCATAAACGGTGGCATC 57.131 45.000 0.00 0.00 45.52 3.91
1502 1589 4.158394 AGAATCAGCAAAACCGTAATGCAT 59.842 37.500 10.18 0.00 42.45 3.96
1511 1798 3.319122 ACCAAGACAGAATCAGCAAAACC 59.681 43.478 0.00 0.00 0.00 3.27
1512 1799 4.540824 GACCAAGACAGAATCAGCAAAAC 58.459 43.478 0.00 0.00 0.00 2.43
1532 1821 0.611714 TCCTCTGGCCTAAAACGGAC 59.388 55.000 3.32 0.00 0.00 4.79
1534 1823 0.744771 GCTCCTCTGGCCTAAAACGG 60.745 60.000 3.32 0.00 0.00 4.44
1655 1944 5.870433 TGCTACAAGAAAATGGATGCAATTG 59.130 36.000 0.00 0.00 0.00 2.32
1791 2080 6.460953 CCAGAGCAGAGAACTCCTACTTATTC 60.461 46.154 0.00 0.00 34.56 1.75
2067 3103 1.679680 AGCGCATTCCAATGAAGATGG 59.320 47.619 11.47 0.00 38.70 3.51
2199 3235 0.179111 CCACAAGATAAGCGGCGAGA 60.179 55.000 12.98 0.00 0.00 4.04
2540 3578 2.006169 GCAGAGCAACTTTAGAGAGGC 58.994 52.381 0.00 0.00 0.00 4.70
2680 3718 8.097038 TGTAATTCATAAGCTGAACTCTCAAGT 58.903 33.333 0.00 0.00 46.37 3.16
2750 3788 7.079451 AGATTTCTTAAAGTTGTCCAGGAGA 57.921 36.000 0.00 0.00 0.00 3.71
2778 3816 7.559897 ACAGAAGAACAAATACCCTCTGAAAAA 59.440 33.333 3.35 0.00 0.00 1.94
2783 3821 6.109359 CCTACAGAAGAACAAATACCCTCTG 58.891 44.000 0.00 0.00 0.00 3.35
2792 3830 3.857157 AGGTGCCTACAGAAGAACAAA 57.143 42.857 0.00 0.00 0.00 2.83
2832 3871 2.962421 GGAGACTAGCAGCATCCTACTT 59.038 50.000 0.00 0.00 0.00 2.24
2852 3891 0.881118 CTTGATTCACAACCGGGTGG 59.119 55.000 26.30 13.21 39.27 4.61
2861 3917 5.471556 AAACATTGCCATCTTGATTCACA 57.528 34.783 0.00 0.00 0.00 3.58
2862 3918 6.790285 AAAAACATTGCCATCTTGATTCAC 57.210 33.333 0.00 0.00 0.00 3.18
2974 4054 0.178975 ATGGCGGGTTTCAGGTTCAA 60.179 50.000 0.00 0.00 0.00 2.69
2975 4055 0.608035 GATGGCGGGTTTCAGGTTCA 60.608 55.000 0.00 0.00 0.00 3.18
2981 4061 2.566111 GATGGGGATGGCGGGTTTCA 62.566 60.000 0.00 0.00 0.00 2.69
3256 4353 2.699954 GTGCTAGCAGCCTCAAAGTTA 58.300 47.619 20.03 0.00 41.51 2.24
3283 4380 0.936297 GCTGACCGCAGTTGCAAAAG 60.936 55.000 0.00 0.00 44.17 2.27
3311 4408 3.342719 TGTGCTAAATGCTGATTCCGAA 58.657 40.909 0.00 0.00 43.37 4.30
3336 4433 8.337739 TCTACCTCTTAGAACTAGAATTCCACT 58.662 37.037 0.65 0.00 33.54 4.00
3356 4453 3.116939 ACATATGGACTGGAGCTCTACCT 60.117 47.826 14.64 0.00 0.00 3.08
3425 4534 1.623163 TTTTTGCCCGTCCCCTAAAG 58.377 50.000 0.00 0.00 0.00 1.85
3476 4585 1.429423 GAGAAAATCGCAAGCCCGG 59.571 57.895 0.00 0.00 37.18 5.73
3541 4650 5.911752 ACTATTCACAACTCTAGATGGCAG 58.088 41.667 0.00 0.00 0.00 4.85
3687 4811 7.371159 TCGGCTATGAATAGTGTTCTTCTATG 58.629 38.462 1.08 0.00 32.96 2.23
3688 4812 7.526142 TCGGCTATGAATAGTGTTCTTCTAT 57.474 36.000 1.08 0.00 32.96 1.98
3690 4814 5.854010 TCGGCTATGAATAGTGTTCTTCT 57.146 39.130 1.08 0.00 32.96 2.85
3733 4861 3.913548 TTTCATGGTGTTTGGACATCG 57.086 42.857 0.00 0.00 39.86 3.84
3868 4998 3.430098 GCGATAATTCAAAATGGTGCCCA 60.430 43.478 0.00 0.00 38.19 5.36
3916 5046 3.077359 AGCATCAACCAGCAAGAACTAC 58.923 45.455 0.00 0.00 0.00 2.73
3980 5110 5.211973 TGCCAGCCATAACCCATAATTAAA 58.788 37.500 0.00 0.00 0.00 1.52
3985 5115 2.024464 AGTTGCCAGCCATAACCCATAA 60.024 45.455 0.00 0.00 0.00 1.90
3986 5116 1.568597 AGTTGCCAGCCATAACCCATA 59.431 47.619 0.00 0.00 0.00 2.74
3987 5117 0.336048 AGTTGCCAGCCATAACCCAT 59.664 50.000 0.00 0.00 0.00 4.00
3988 5118 0.323360 GAGTTGCCAGCCATAACCCA 60.323 55.000 0.00 0.00 0.00 4.51
3989 5119 0.323360 TGAGTTGCCAGCCATAACCC 60.323 55.000 0.00 0.00 0.00 4.11
3990 5120 1.098050 CTGAGTTGCCAGCCATAACC 58.902 55.000 0.00 0.00 0.00 2.85
4122 5367 3.987868 TCGAGAACAAGTCAGCAACATAC 59.012 43.478 0.00 0.00 0.00 2.39
4164 5409 2.221169 TCAACAATGTCAGTCACAGCC 58.779 47.619 0.00 0.00 38.85 4.85
4258 5503 4.318332 CTGATGAAGTCTACCACTTGCAA 58.682 43.478 0.00 0.00 46.10 4.08
4437 5685 2.888594 CTCCGAGTAATCGCCAAGAAA 58.111 47.619 7.14 0.00 0.00 2.52
4531 5779 5.221244 GCCCATCATTTATTCCAGTGTAACC 60.221 44.000 0.00 0.00 37.80 2.85
4960 6219 7.442656 AGAGTAACTGCTACAAGTGTACAAAT 58.557 34.615 0.00 0.00 32.37 2.32
5001 6260 8.125978 TCATGTAAAAGAAAAGGATGCAGAAT 57.874 30.769 0.00 0.00 0.00 2.40
5233 6494 6.169800 GCTCCAGGTAATTGCCAAATAAAAA 58.830 36.000 15.49 0.00 0.00 1.94
5251 6512 1.830279 ATCACACACATTGGCTCCAG 58.170 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.