Multiple sequence alignment - TraesCS4A01G452000

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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 TraesCS4A01G452000 chr4A 100.000 4309 0 0 1 4309 717254386 717258694 0.000000e+00 7958.0
1 TraesCS4A01G452000 chr4A 95.750 2094 64 6 1204 3276 717282097 717284186 0.000000e+00 3350.0
2 TraesCS4A01G452000 chr4A 89.457 2485 123 45 969 3382 717808939 717806523 0.000000e+00 3009.0
3 TraesCS4A01G452000 chr4A 95.432 1598 44 7 1722 3291 717220923 717222519 0.000000e+00 2519.0
4 TraesCS4A01G452000 chr4A 94.700 1283 63 4 1739 3020 717757373 717756095 0.000000e+00 1988.0
5 TraesCS4A01G452000 chr4A 93.785 901 34 5 3423 4309 717806516 717805624 0.000000e+00 1334.0
6 TraesCS4A01G452000 chr4A 93.023 645 29 4 3679 4309 717755454 717754812 0.000000e+00 928.0
7 TraesCS4A01G452000 chr4A 90.091 656 38 7 3276 3916 717222533 717223176 0.000000e+00 826.0
8 TraesCS4A01G452000 chr4A 92.292 493 20 3 1 479 717281616 717282104 0.000000e+00 684.0
9 TraesCS4A01G452000 chr4A 95.110 409 19 1 3902 4309 717284656 717285064 1.010000e-180 643.0
10 TraesCS4A01G452000 chr4A 94.866 409 20 1 3902 4309 717223188 717223596 4.700000e-179 638.0
11 TraesCS4A01G452000 chr4A 90.591 457 28 4 3473 3916 717284190 717284644 3.710000e-165 592.0
12 TraesCS4A01G452000 chr4A 93.064 346 23 1 1167 1511 717757866 717757521 4.970000e-139 505.0
13 TraesCS4A01G452000 chr4A 90.444 293 8 4 3019 3291 717756045 717755753 6.810000e-98 368.0
14 TraesCS4A01G452000 chr4A 87.079 178 19 3 1518 1693 717220758 717220933 9.450000e-47 198.0
15 TraesCS4A01G452000 chr4A 91.935 124 10 0 1558 1681 717757516 717757393 1.590000e-39 174.0
16 TraesCS4A01G452000 chr4A 90.476 126 12 0 1320 1445 717818713 717818588 2.670000e-37 167.0
17 TraesCS4A01G452000 chr4A 93.671 79 5 0 1364 1442 717220646 717220724 7.570000e-23 119.0
18 TraesCS4A01G452000 chr4A 80.723 166 16 5 1028 1177 717760712 717760547 9.790000e-22 115.0
19 TraesCS4A01G452000 chr4A 100.000 29 0 0 3040 3068 717756100 717756072 2.000000e-03 54.7
20 TraesCS4A01G452000 chr7D 92.097 2847 125 26 1520 4309 16756103 16758906 0.000000e+00 3919.0
21 TraesCS4A01G452000 chr7D 92.190 1639 93 8 1759 3371 16997780 16996151 0.000000e+00 2285.0
22 TraesCS4A01G452000 chr7D 93.359 1024 51 8 3301 4309 17124735 17123714 0.000000e+00 1498.0
23 TraesCS4A01G452000 chr7D 92.793 777 38 6 1783 2557 17125913 17125153 0.000000e+00 1109.0
24 TraesCS4A01G452000 chr7D 94.985 339 11 4 3401 3737 16996156 16995822 1.060000e-145 527.0
25 TraesCS4A01G452000 chr7D 86.697 436 26 6 2857 3267 17125158 17124730 5.080000e-124 455.0
26 TraesCS4A01G452000 chr7D 87.879 330 16 14 1018 1331 17128451 17128130 2.450000e-97 366.0
27 TraesCS4A01G452000 chr7D 81.586 353 36 11 1326 1678 17126295 17125972 9.190000e-67 265.0
28 TraesCS4A01G452000 chr7D 88.732 71 8 0 675 745 524859802 524859732 2.130000e-13 87.9
29 TraesCS4A01G452000 chr7B 90.084 2844 209 36 1520 4309 655815576 655812752 0.000000e+00 3622.0
30 TraesCS4A01G452000 chr7B 83.972 705 78 8 3 673 643621949 643622652 1.010000e-180 643.0
31 TraesCS4A01G452000 chr7B 83.830 705 79 8 3 673 643564371 643565074 4.700000e-179 638.0
32 TraesCS4A01G452000 chr7B 83.830 705 79 8 3 673 643604762 643605465 4.700000e-179 638.0
33 TraesCS4A01G452000 chr7B 83.546 705 81 8 3 673 643561783 643562486 1.020000e-175 627.0
34 TraesCS4A01G452000 chr7B 85.052 388 41 2 303 673 643586836 643587223 3.140000e-101 379.0
35 TraesCS4A01G452000 chr7A 93.081 1850 88 20 1172 3011 16436873 16435054 0.000000e+00 2671.0
36 TraesCS4A01G452000 chr7A 93.027 1850 89 20 1172 3011 16324737 16322918 0.000000e+00 2665.0
37 TraesCS4A01G452000 chr7A 91.571 1744 83 16 2576 4285 16394809 16393096 0.000000e+00 2348.0
38 TraesCS4A01G452000 chr7A 89.323 1433 94 21 2185 3562 15818716 15820144 0.000000e+00 1744.0
39 TraesCS4A01G452000 chr7A 95.127 903 44 0 1727 2629 16432656 16431754 0.000000e+00 1424.0
40 TraesCS4A01G452000 chr7A 93.158 877 37 7 2614 3469 16430456 16429582 0.000000e+00 1266.0
41 TraesCS4A01G452000 chr7A 94.331 829 35 3 3491 4309 16429591 16428765 0.000000e+00 1260.0
42 TraesCS4A01G452000 chr7A 89.229 752 57 6 3579 4309 15820126 15820874 0.000000e+00 918.0
43 TraesCS4A01G452000 chr7A 89.158 701 52 6 3631 4309 15791605 15792303 0.000000e+00 852.0
44 TraesCS4A01G452000 chr7A 87.826 690 44 13 1441 2130 16395461 16394812 0.000000e+00 773.0
45 TraesCS4A01G452000 chr7A 94.153 496 22 3 1207 1701 16433142 16432653 0.000000e+00 749.0
46 TraesCS4A01G452000 chr7A 96.403 417 15 0 3893 4309 16317076 16316660 0.000000e+00 688.0
47 TraesCS4A01G452000 chr7A 90.000 510 24 6 3005 3494 16317909 16317407 6.080000e-178 634.0
48 TraesCS4A01G452000 chr7A 90.533 338 16 4 3600 3923 16317411 16317076 2.380000e-117 433.0
49 TraesCS4A01G452000 chr7A 93.066 274 18 1 1170 1442 16395816 16395543 2.410000e-107 399.0
50 TraesCS4A01G452000 chr7A 85.581 215 21 7 972 1177 16324975 16324762 2.610000e-52 217.0
51 TraesCS4A01G452000 chr7A 85.581 215 21 7 972 1177 16437111 16436898 2.610000e-52 217.0
52 TraesCS4A01G452000 chr7A 91.667 84 5 2 1249 1330 16395459 16395542 9.790000e-22 115.0
53 TraesCS4A01G452000 chr3D 83.442 924 87 29 3 864 533720651 533719732 0.000000e+00 798.0
54 TraesCS4A01G452000 chr3D 80.577 659 91 10 3 627 546782803 546782148 1.400000e-129 473.0
55 TraesCS4A01G452000 chr5D 83.017 842 102 18 3 809 6931211 6932046 0.000000e+00 725.0
56 TraesCS4A01G452000 chr5D 82.244 704 88 11 3 672 50633075 50633775 1.340000e-159 573.0
57 TraesCS4A01G452000 chr2A 81.320 985 101 34 3 915 187332843 187333816 0.000000e+00 723.0
58 TraesCS4A01G452000 chr2A 79.114 474 46 23 1237 1703 745558823 745559250 1.180000e-70 278.0
59 TraesCS4A01G452000 chr2A 91.525 59 5 0 669 727 515937920 515937978 9.930000e-12 82.4
60 TraesCS4A01G452000 chr2D 85.856 707 63 9 3 673 537509462 537508757 0.000000e+00 717.0
61 TraesCS4A01G452000 chr2D 83.871 713 78 16 3 681 50117055 50116346 0.000000e+00 645.0
62 TraesCS4A01G452000 chr2D 77.430 895 126 39 9 839 434141351 434140469 8.440000e-127 464.0
63 TraesCS4A01G452000 chr1D 85.653 704 65 14 3 672 36559638 36560339 0.000000e+00 708.0
64 TraesCS4A01G452000 chr6A 85.269 706 67 12 3 673 99025035 99024332 0.000000e+00 693.0
65 TraesCS4A01G452000 chr6A 79.741 928 113 33 4 861 591176815 591177737 1.710000e-168 603.0
66 TraesCS4A01G452000 chrUn 85.085 704 70 10 3 673 2234964 2235665 0.000000e+00 686.0
67 TraesCS4A01G452000 chrUn 83.546 705 81 8 3 673 374074673 374073970 1.020000e-175 627.0
68 TraesCS4A01G452000 chr4D 79.498 917 118 35 3 852 85584049 85584962 4.800000e-164 588.0
69 TraesCS4A01G452000 chr4D 82.069 290 35 6 6 279 502753534 502753822 9.320000e-57 231.0
70 TraesCS4A01G452000 chr6B 85.921 554 55 8 135 673 183723022 183722477 1.740000e-158 569.0
71 TraesCS4A01G452000 chr6D 83.494 624 65 17 3 591 17114911 17115531 8.150000e-152 547.0
72 TraesCS4A01G452000 chr6D 82.586 379 30 15 572 918 449287011 449286637 7.000000e-78 302.0
73 TraesCS4A01G452000 chr6D 85.841 226 27 5 669 892 444877778 444878000 7.200000e-58 235.0
74 TraesCS4A01G452000 chr1A 84.528 530 46 14 3 498 35950234 35950761 3.870000e-135 492.0
75 TraesCS4A01G452000 chr1A 87.446 231 22 7 669 896 36100295 36100521 4.270000e-65 259.0
76 TraesCS4A01G452000 chr5B 77.246 690 123 20 3 673 596903120 596902446 1.460000e-99 374.0
77 TraesCS4A01G452000 chr3B 80.000 155 27 3 752 905 722204359 722204510 1.270000e-20 111.0
78 TraesCS4A01G452000 chr3A 78.107 169 20 9 684 838 360168782 360168617 1.650000e-14 91.6


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 TraesCS4A01G452000 chr4A 717254386 717258694 4308 False 7958.000000 7958 100.000000 1 4309 1 chr4A.!!$F1 4308
1 TraesCS4A01G452000 chr4A 717805624 717808939 3315 True 2171.500000 3009 91.621000 969 4309 2 chr4A.!!$R3 3340
2 TraesCS4A01G452000 chr4A 717281616 717285064 3448 False 1317.250000 3350 93.435750 1 4309 4 chr4A.!!$F3 4308
3 TraesCS4A01G452000 chr4A 717220646 717223596 2950 False 860.000000 2519 92.227800 1364 4309 5 chr4A.!!$F2 2945
4 TraesCS4A01G452000 chr4A 717754812 717760712 5900 True 590.385714 1988 91.984143 1028 4309 7 chr4A.!!$R2 3281
5 TraesCS4A01G452000 chr7D 16756103 16758906 2803 False 3919.000000 3919 92.097000 1520 4309 1 chr7D.!!$F1 2789
6 TraesCS4A01G452000 chr7D 16995822 16997780 1958 True 1406.000000 2285 93.587500 1759 3737 2 chr7D.!!$R2 1978
7 TraesCS4A01G452000 chr7D 17123714 17128451 4737 True 738.600000 1498 88.462800 1018 4309 5 chr7D.!!$R3 3291
8 TraesCS4A01G452000 chr7B 655812752 655815576 2824 True 3622.000000 3622 90.084000 1520 4309 1 chr7B.!!$R1 2789
9 TraesCS4A01G452000 chr7B 643621949 643622652 703 False 643.000000 643 83.972000 3 673 1 chr7B.!!$F3 670
10 TraesCS4A01G452000 chr7B 643604762 643605465 703 False 638.000000 638 83.830000 3 673 1 chr7B.!!$F2 670
11 TraesCS4A01G452000 chr7B 643561783 643565074 3291 False 632.500000 638 83.688000 3 673 2 chr7B.!!$F4 670
12 TraesCS4A01G452000 chr7A 16322918 16324975 2057 True 1441.000000 2665 89.304000 972 3011 2 chr7A.!!$R2 2039
13 TraesCS4A01G452000 chr7A 15818716 15820874 2158 False 1331.000000 1744 89.276000 2185 4309 2 chr7A.!!$F3 2124
14 TraesCS4A01G452000 chr7A 16428765 16437111 8346 True 1264.500000 2671 92.571833 972 4309 6 chr7A.!!$R4 3337
15 TraesCS4A01G452000 chr7A 16393096 16395816 2720 True 1173.333333 2348 90.821000 1170 4285 3 chr7A.!!$R3 3115
16 TraesCS4A01G452000 chr7A 15791605 15792303 698 False 852.000000 852 89.158000 3631 4309 1 chr7A.!!$F1 678
17 TraesCS4A01G452000 chr7A 16316660 16317909 1249 True 585.000000 688 92.312000 3005 4309 3 chr7A.!!$R1 1304
18 TraesCS4A01G452000 chr3D 533719732 533720651 919 True 798.000000 798 83.442000 3 864 1 chr3D.!!$R1 861
19 TraesCS4A01G452000 chr3D 546782148 546782803 655 True 473.000000 473 80.577000 3 627 1 chr3D.!!$R2 624
20 TraesCS4A01G452000 chr5D 6931211 6932046 835 False 725.000000 725 83.017000 3 809 1 chr5D.!!$F1 806
21 TraesCS4A01G452000 chr5D 50633075 50633775 700 False 573.000000 573 82.244000 3 672 1 chr5D.!!$F2 669
22 TraesCS4A01G452000 chr2A 187332843 187333816 973 False 723.000000 723 81.320000 3 915 1 chr2A.!!$F1 912
23 TraesCS4A01G452000 chr2D 537508757 537509462 705 True 717.000000 717 85.856000 3 673 1 chr2D.!!$R3 670
24 TraesCS4A01G452000 chr2D 50116346 50117055 709 True 645.000000 645 83.871000 3 681 1 chr2D.!!$R1 678
25 TraesCS4A01G452000 chr2D 434140469 434141351 882 True 464.000000 464 77.430000 9 839 1 chr2D.!!$R2 830
26 TraesCS4A01G452000 chr1D 36559638 36560339 701 False 708.000000 708 85.653000 3 672 1 chr1D.!!$F1 669
27 TraesCS4A01G452000 chr6A 99024332 99025035 703 True 693.000000 693 85.269000 3 673 1 chr6A.!!$R1 670
28 TraesCS4A01G452000 chr6A 591176815 591177737 922 False 603.000000 603 79.741000 4 861 1 chr6A.!!$F1 857
29 TraesCS4A01G452000 chrUn 2234964 2235665 701 False 686.000000 686 85.085000 3 673 1 chrUn.!!$F1 670
30 TraesCS4A01G452000 chrUn 374073970 374074673 703 True 627.000000 627 83.546000 3 673 1 chrUn.!!$R1 670
31 TraesCS4A01G452000 chr4D 85584049 85584962 913 False 588.000000 588 79.498000 3 852 1 chr4D.!!$F1 849
32 TraesCS4A01G452000 chr6B 183722477 183723022 545 True 569.000000 569 85.921000 135 673 1 chr6B.!!$R1 538
33 TraesCS4A01G452000 chr6D 17114911 17115531 620 False 547.000000 547 83.494000 3 591 1 chr6D.!!$F1 588
34 TraesCS4A01G452000 chr1A 35950234 35950761 527 False 492.000000 492 84.528000 3 498 1 chr1A.!!$F1 495
35 TraesCS4A01G452000 chr5B 596902446 596903120 674 True 374.000000 374 77.246000 3 673 1 chr5B.!!$R1 670

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
966 3702 0.030908 CCGGAGATGCTCTTACGGTC 59.969 60.000 0.00 0.0 40.25 4.79 F
967 3703 0.738975 CGGAGATGCTCTTACGGTCA 59.261 55.000 0.00 0.0 0.00 4.02 F
2092 9497 1.743394 GGACCTTATTCCACAAAGGCG 59.257 52.381 1.06 0.0 45.18 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 9497 1.105759 GGGTCAGCCAATCTCCATGC 61.106 60.0 0.00 0.00 36.17 4.06 R
2802 10217 1.238896 TCCTTCCTCCCCATCCCTCT 61.239 60.0 0.00 0.00 0.00 3.69 R
3716 16386 0.181114 TGTCAGATATGTGCCTGGGC 59.819 55.0 4.43 4.43 42.35 5.36 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
23 25 3.869272 CGAGGTACGACCCCGACG 61.869 72.222 2.62 0.00 45.77 5.12
76 78 1.078848 GCCACGAGGAGCAGATTGT 60.079 57.895 1.86 0.00 36.89 2.71
85 2675 1.364626 GAGCAGATTGTCGCCACCAG 61.365 60.000 0.00 0.00 0.00 4.00
216 2829 2.364448 GCCCCCTCCTTCTCTCGT 60.364 66.667 0.00 0.00 0.00 4.18
667 3307 3.640407 GGTCAGGGGTGCAGCAGA 61.640 66.667 19.06 9.45 0.00 4.26
692 3374 0.887836 TGACGACAGCGACTACACCT 60.888 55.000 0.00 0.00 41.64 4.00
720 3402 0.470833 AGGCTCCTCGGCATGTAGAT 60.471 55.000 0.00 0.00 41.46 1.98
823 3557 5.465724 GTCTAGTTTGGACGAAATTGTGTCT 59.534 40.000 9.44 0.00 35.45 3.41
841 3575 7.055667 TGTGTCTTGTTTGGCCAATTTTATA 57.944 32.000 21.26 0.00 0.00 0.98
904 3640 3.128032 AAACCCAGTCACCCCCACG 62.128 63.158 0.00 0.00 0.00 4.94
905 3641 4.567597 ACCCAGTCACCCCCACGA 62.568 66.667 0.00 0.00 0.00 4.35
915 3651 2.027007 TCACCCCCACGACGAAATTATT 60.027 45.455 0.00 0.00 0.00 1.40
916 3652 2.096819 CACCCCCACGACGAAATTATTG 59.903 50.000 0.00 0.00 0.00 1.90
917 3653 1.064952 CCCCCACGACGAAATTATTGC 59.935 52.381 0.00 0.00 0.00 3.56
918 3654 1.267832 CCCCACGACGAAATTATTGCG 60.268 52.381 3.46 3.46 0.00 4.85
919 3655 1.395608 CCCACGACGAAATTATTGCGT 59.604 47.619 11.11 11.11 41.45 5.24
920 3656 2.159626 CCCACGACGAAATTATTGCGTT 60.160 45.455 12.58 0.00 38.51 4.84
921 3657 3.484683 CCACGACGAAATTATTGCGTTT 58.515 40.909 12.58 0.26 38.51 3.60
922 3658 3.909574 CCACGACGAAATTATTGCGTTTT 59.090 39.130 12.58 0.00 38.51 2.43
923 3659 4.380382 CCACGACGAAATTATTGCGTTTTT 59.620 37.500 12.58 0.00 38.51 1.94
944 3680 4.492604 TTTTTGAGTCCTGGGCCG 57.507 55.556 0.00 0.00 0.00 6.13
945 3681 1.840598 TTTTTGAGTCCTGGGCCGA 59.159 52.632 0.00 0.00 0.00 5.54
946 3682 0.183971 TTTTTGAGTCCTGGGCCGAA 59.816 50.000 0.00 0.00 0.00 4.30
947 3683 0.536460 TTTTGAGTCCTGGGCCGAAC 60.536 55.000 0.00 0.00 0.00 3.95
948 3684 2.406002 TTTGAGTCCTGGGCCGAACC 62.406 60.000 0.00 0.00 37.93 3.62
949 3685 4.452733 GAGTCCTGGGCCGAACCG 62.453 72.222 0.00 0.00 40.62 4.44
962 3698 1.841450 CGAACCGGAGATGCTCTTAC 58.159 55.000 9.46 0.00 0.00 2.34
963 3699 1.841450 GAACCGGAGATGCTCTTACG 58.159 55.000 9.46 0.00 0.00 3.18
964 3700 0.460311 AACCGGAGATGCTCTTACGG 59.540 55.000 9.46 18.96 46.07 4.02
965 3701 2.116383 CCGGAGATGCTCTTACGGT 58.884 57.895 0.00 0.00 40.25 4.83
966 3702 0.030908 CCGGAGATGCTCTTACGGTC 59.969 60.000 0.00 0.00 40.25 4.79
967 3703 0.738975 CGGAGATGCTCTTACGGTCA 59.261 55.000 0.00 0.00 0.00 4.02
989 3725 1.777878 ACCCATGTTCGGCCCATTATA 59.222 47.619 0.00 0.00 0.00 0.98
1370 8657 6.194142 CGATTCTCAATTTGCTCTGAAATTCG 59.806 38.462 0.00 0.00 34.05 3.34
1421 8708 3.548770 CATGGACACTTGCCAGATACAT 58.451 45.455 0.00 0.00 39.11 2.29
1428 8715 6.318648 GGACACTTGCCAGATACATTATTTGA 59.681 38.462 0.00 0.00 0.00 2.69
1757 9155 8.774890 TTATACAGTTATACCTTGTTTCGCAA 57.225 30.769 0.00 0.00 35.50 4.85
1783 9182 8.210946 AGCCTAACCTTTTTCTTAAATTTGCTT 58.789 29.630 0.00 0.00 0.00 3.91
1800 9199 2.172505 TGCTTTGTTGAACAGGGAGAGA 59.827 45.455 0.00 0.00 0.00 3.10
1801 9200 2.550180 GCTTTGTTGAACAGGGAGAGAC 59.450 50.000 0.00 0.00 0.00 3.36
1994 9399 2.257894 GTGTGATCTCTTCTCAGCACG 58.742 52.381 0.00 0.00 0.00 5.34
2005 9410 2.125753 CAGCACGCAGGTCCTCTC 60.126 66.667 0.00 0.00 0.00 3.20
2089 9494 4.827284 ACTGTTGGACCTTATTCCACAAAG 59.173 41.667 0.00 0.00 45.80 2.77
2092 9497 1.743394 GGACCTTATTCCACAAAGGCG 59.257 52.381 1.06 0.00 45.18 5.52
2417 9830 6.190954 GACAAAACACAGTCCTAAAGTTGT 57.809 37.500 0.00 0.00 0.00 3.32
2593 10008 3.371898 GGCAAATGAAAAAGCATGGCTAC 59.628 43.478 0.00 0.00 38.25 3.58
2779 10194 3.422303 GCATTGACGAGCGGTGCA 61.422 61.111 0.00 0.00 35.93 4.57
2802 10217 2.203408 TTGCCGTGCATGAACCCA 60.203 55.556 7.72 0.00 38.76 4.51
3191 15669 3.071874 TCTGTGGCAATTACAAGGGAG 57.928 47.619 0.00 0.00 0.00 4.30
3195 15692 3.572255 TGTGGCAATTACAAGGGAGTTTC 59.428 43.478 0.00 0.00 0.00 2.78
3264 15761 3.199289 GCTAGGCCTGTAACTTCCCTTTA 59.801 47.826 17.99 0.00 0.00 1.85
3360 15911 6.378280 AGTCTTATTGGGTGGAAATGTGAATC 59.622 38.462 0.00 0.00 0.00 2.52
3428 15984 0.323725 ACGCATTTTGGGCTGGAGAT 60.324 50.000 0.00 0.00 33.10 2.75
3516 16074 6.089417 GCAAGTTCAGCCAACAAACATATAAC 59.911 38.462 0.00 0.00 37.48 1.89
3594 16152 3.340034 ACAGAGTGTTCGACAACCAAAA 58.660 40.909 0.00 0.00 0.00 2.44
3597 16155 3.105937 GAGTGTTCGACAACCAAAAAGC 58.894 45.455 0.00 0.00 0.00 3.51
3661 16331 9.671279 TGCATTTGATTATCTCTGTTTAGAAGA 57.329 29.630 0.00 0.00 31.21 2.87
3720 16390 7.475137 AAGCACATAACTAAAATAAAGCCCA 57.525 32.000 0.00 0.00 0.00 5.36
3721 16391 7.100458 AGCACATAACTAAAATAAAGCCCAG 57.900 36.000 0.00 0.00 0.00 4.45
3723 16393 6.273071 CACATAACTAAAATAAAGCCCAGGC 58.727 40.000 0.00 0.00 42.33 4.85
3724 16394 5.955355 ACATAACTAAAATAAAGCCCAGGCA 59.045 36.000 12.03 0.00 44.88 4.75
3727 16397 4.352893 ACTAAAATAAAGCCCAGGCACAT 58.647 39.130 12.03 0.00 44.88 3.21
3779 16462 3.995636 AGACCCAAGGAGCTAGTATTGA 58.004 45.455 0.00 0.00 0.00 2.57
3838 16521 9.628500 AAAGAGGAGTAATTAACAAAGTTCAGT 57.372 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
418 3056 2.852075 ACGGGGAGCAAACCTGGA 60.852 61.111 0.00 0.00 38.74 3.86
535 3174 0.179210 GAGCGGCGATCTCTACGATC 60.179 60.000 19.09 0.00 44.16 3.69
667 3307 2.976350 TCGCTGTCGTCACCGTCT 60.976 61.111 0.00 0.00 36.96 4.18
681 3321 1.542915 TGTAGAACCAGGTGTAGTCGC 59.457 52.381 0.00 0.00 0.00 5.19
692 3374 0.970937 CCGAGGAGCCTGTAGAACCA 60.971 60.000 0.00 0.00 0.00 3.67
734 3429 3.760035 CGACTACGCCCAGCCACT 61.760 66.667 0.00 0.00 0.00 4.00
852 3586 3.267233 AGGTTGCCCCAGATGCCA 61.267 61.111 0.00 0.00 34.66 4.92
888 3624 4.567597 TCGTGGGGGTGACTGGGT 62.568 66.667 0.00 0.00 0.00 4.51
890 3626 4.373116 CGTCGTGGGGGTGACTGG 62.373 72.222 0.00 0.00 32.93 4.00
891 3627 2.372040 TTTCGTCGTGGGGGTGACTG 62.372 60.000 0.00 0.00 32.93 3.51
893 3629 0.604511 AATTTCGTCGTGGGGGTGAC 60.605 55.000 0.00 0.00 0.00 3.67
894 3630 0.975135 TAATTTCGTCGTGGGGGTGA 59.025 50.000 0.00 0.00 0.00 4.02
895 3631 2.032680 ATAATTTCGTCGTGGGGGTG 57.967 50.000 0.00 0.00 0.00 4.61
896 3632 2.361789 CAATAATTTCGTCGTGGGGGT 58.638 47.619 0.00 0.00 0.00 4.95
897 3633 1.064952 GCAATAATTTCGTCGTGGGGG 59.935 52.381 0.00 0.00 0.00 5.40
927 3663 0.183971 TTCGGCCCAGGACTCAAAAA 59.816 50.000 0.00 0.00 0.00 1.94
928 3664 0.536460 GTTCGGCCCAGGACTCAAAA 60.536 55.000 0.00 0.00 0.00 2.44
929 3665 1.072505 GTTCGGCCCAGGACTCAAA 59.927 57.895 0.00 0.00 0.00 2.69
930 3666 2.747686 GTTCGGCCCAGGACTCAA 59.252 61.111 0.00 0.00 0.00 3.02
931 3667 3.319198 GGTTCGGCCCAGGACTCA 61.319 66.667 0.00 0.00 0.00 3.41
932 3668 4.452733 CGGTTCGGCCCAGGACTC 62.453 72.222 0.00 0.00 0.00 3.36
949 3685 6.351563 GGGTATGACCGTAAGAGCATCTCC 62.352 54.167 0.00 0.00 42.52 3.71
950 3686 3.305471 GGGTATGACCGTAAGAGCATCTC 60.305 52.174 0.00 0.00 42.52 2.75
951 3687 2.628657 GGGTATGACCGTAAGAGCATCT 59.371 50.000 0.00 0.00 44.68 2.90
952 3688 2.364324 TGGGTATGACCGTAAGAGCATC 59.636 50.000 0.00 0.00 39.83 3.91
953 3689 2.394632 TGGGTATGACCGTAAGAGCAT 58.605 47.619 0.00 0.00 39.83 3.79
954 3690 1.855295 TGGGTATGACCGTAAGAGCA 58.145 50.000 0.00 0.00 39.83 4.26
955 3691 2.102588 ACATGGGTATGACCGTAAGAGC 59.897 50.000 0.00 0.00 39.83 4.09
956 3692 4.369182 GAACATGGGTATGACCGTAAGAG 58.631 47.826 0.00 0.00 39.83 2.85
957 3693 3.181484 CGAACATGGGTATGACCGTAAGA 60.181 47.826 0.00 0.00 39.83 2.10
958 3694 3.120792 CGAACATGGGTATGACCGTAAG 58.879 50.000 0.00 0.00 39.83 2.34
959 3695 2.159071 CCGAACATGGGTATGACCGTAA 60.159 50.000 0.00 0.00 39.83 3.18
960 3696 1.409790 CCGAACATGGGTATGACCGTA 59.590 52.381 0.00 0.00 39.83 4.02
961 3697 0.177141 CCGAACATGGGTATGACCGT 59.823 55.000 0.00 0.00 39.83 4.83
962 3698 1.157870 GCCGAACATGGGTATGACCG 61.158 60.000 0.00 0.00 39.83 4.79
963 3699 0.818040 GGCCGAACATGGGTATGACC 60.818 60.000 0.00 0.00 37.73 4.02
964 3700 0.818040 GGGCCGAACATGGGTATGAC 60.818 60.000 0.00 0.00 37.73 3.06
965 3701 1.275421 TGGGCCGAACATGGGTATGA 61.275 55.000 0.00 0.00 37.73 2.15
966 3702 0.178992 ATGGGCCGAACATGGGTATG 60.179 55.000 0.00 0.00 40.24 2.39
967 3703 0.555769 AATGGGCCGAACATGGGTAT 59.444 50.000 0.00 0.00 0.00 2.73
1115 3870 1.587933 GACGAGGACGAGGAAGCAGT 61.588 60.000 0.00 0.00 42.66 4.40
1154 3909 1.196766 GGACGAGGTAGGGTTTGGGT 61.197 60.000 0.00 0.00 0.00 4.51
1370 8657 7.809806 ACAGAAAAATAAAAGCAGAGCACATAC 59.190 33.333 0.00 0.00 0.00 2.39
1421 8708 9.778741 ATCGCCTAGTATTTCTCAATCAAATAA 57.221 29.630 0.00 0.00 29.51 1.40
1428 8715 5.760253 CCACAATCGCCTAGTATTTCTCAAT 59.240 40.000 0.00 0.00 0.00 2.57
1490 8864 2.810650 CGCTAGATAGACGGCTTGTTT 58.189 47.619 0.00 0.00 0.00 2.83
1651 9029 1.001068 TCGTTAGGACATCAACGCCAA 59.999 47.619 2.19 0.00 45.37 4.52
1757 9155 7.735917 AGCAAATTTAAGAAAAAGGTTAGGCT 58.264 30.769 0.00 0.00 0.00 4.58
1783 9182 2.930826 GGTCTCTCCCTGTTCAACAA 57.069 50.000 0.00 0.00 0.00 2.83
1800 9199 2.369532 GGCCATTATTTGCATGATGGGT 59.630 45.455 11.79 0.00 43.80 4.51
1801 9200 2.369203 TGGCCATTATTTGCATGATGGG 59.631 45.455 0.00 0.83 43.80 4.00
1807 9206 3.106054 TCCTGTTGGCCATTATTTGCAT 58.894 40.909 6.09 0.00 0.00 3.96
1994 9399 2.730524 GGCTGGAGAGAGGACCTGC 61.731 68.421 0.00 0.00 45.75 4.85
2089 9494 2.517875 AGCCAATCTCCATGCGCC 60.518 61.111 4.18 0.00 0.00 6.53
2092 9497 1.105759 GGGTCAGCCAATCTCCATGC 61.106 60.000 0.00 0.00 36.17 4.06
2417 9830 7.413438 CCACATTTTGTTCAATGGAAAAACGAA 60.413 33.333 0.00 0.00 38.32 3.85
2802 10217 1.238896 TCCTTCCTCCCCATCCCTCT 61.239 60.000 0.00 0.00 0.00 3.69
2884 10299 7.070798 TGTGTCGAACGGTAATAACATTTTTC 58.929 34.615 0.00 0.00 0.00 2.29
3166 15644 4.990426 CCCTTGTAATTGCCACAGAAAAAG 59.010 41.667 0.00 0.00 0.00 2.27
3175 15653 4.112634 AGAAACTCCCTTGTAATTGCCA 57.887 40.909 0.00 0.00 0.00 4.92
3195 15692 7.264373 ACAAGAAAACTCCACAATCTGTAAG 57.736 36.000 0.00 0.00 0.00 2.34
3340 15891 6.252233 TCAAGATTCACATTTCCACCCAATA 58.748 36.000 0.00 0.00 0.00 1.90
3360 15911 2.681848 CTGCCCAAGCTATGTTCTCAAG 59.318 50.000 0.00 0.00 40.80 3.02
3428 15984 5.136828 TCTAATTCTTGGTGACCTTGCAAA 58.863 37.500 2.11 0.00 0.00 3.68
3661 16331 9.499479 CCATACATCTATTTGTAGCTTGATCTT 57.501 33.333 0.00 0.00 35.65 2.40
3716 16386 0.181114 TGTCAGATATGTGCCTGGGC 59.819 55.000 4.43 4.43 42.35 5.36
3717 16387 2.501261 CATGTCAGATATGTGCCTGGG 58.499 52.381 0.00 0.00 0.00 4.45
3720 16390 2.747467 GCACCATGTCAGATATGTGCCT 60.747 50.000 16.79 0.00 31.98 4.75
3721 16391 1.605710 GCACCATGTCAGATATGTGCC 59.394 52.381 16.79 0.00 31.98 5.01
3723 16393 3.064408 GTGTGCACCATGTCAGATATGTG 59.936 47.826 15.69 6.05 0.00 3.21
3724 16394 3.273434 GTGTGCACCATGTCAGATATGT 58.727 45.455 15.69 0.00 0.00 2.29
3727 16397 3.415457 TTGTGTGCACCATGTCAGATA 57.585 42.857 15.69 0.00 0.00 1.98
3767 16450 5.545588 TGCATCCTGAATCAATACTAGCTC 58.454 41.667 0.00 0.00 0.00 4.09
3779 16462 5.134725 AGATAAGGGTTTGCATCCTGAAT 57.865 39.130 4.79 2.95 32.95 2.57
3815 16498 8.603242 TCACTGAACTTTGTTAATTACTCCTC 57.397 34.615 0.00 0.00 0.00 3.71
3816 16499 8.974060 TTCACTGAACTTTGTTAATTACTCCT 57.026 30.769 0.00 0.00 0.00 3.69
3831 16514 4.158394 ACATGTTGCTGTTTTCACTGAACT 59.842 37.500 0.00 0.00 0.00 3.01
3838 16521 3.379688 TGTGCTACATGTTGCTGTTTTCA 59.620 39.130 28.07 15.95 32.65 2.69


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

AutoCloner maintained by Alex Coulton.