Multiple sequence alignment - TraesCS3A01G446800

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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 TraesCS3A01G446800 chr3A 100.000 2636 0 0 664 3299 686862898 686865533 0.000000e+00 4868.0
1 TraesCS3A01G446800 chr3A 100.000 356 0 0 1 356 686862235 686862590 0.000000e+00 658.0
2 TraesCS3A01G446800 chr3A 81.116 233 38 6 1421 1650 542203149 542203378 7.270000e-42 182.0
3 TraesCS3A01G446800 chr3A 86.466 133 17 1 664 796 483151969 483152100 9.540000e-31 145.0
4 TraesCS3A01G446800 chr3A 100.000 29 0 0 3040 3068 13085207 13085235 2.000000e-03 54.7
5 TraesCS3A01G446800 chr3D 96.612 1948 51 3 730 2662 549704733 549706680 0.000000e+00 3217.0
6 TraesCS3A01G446800 chr3D 90.223 358 33 1 1 356 549704063 549704420 1.790000e-127 466.0
7 TraesCS3A01G446800 chr3D 90.391 281 8 3 3038 3299 549706993 549707273 5.240000e-93 351.0
8 TraesCS3A01G446800 chr3D 87.218 133 16 1 664 796 362727806 362727937 2.050000e-32 150.0
9 TraesCS3A01G446800 chr3B 95.696 1603 44 6 840 2429 729414512 729416102 0.000000e+00 2555.0
10 TraesCS3A01G446800 chr3B 89.855 276 14 2 3038 3299 729416829 729417104 3.150000e-90 342.0
11 TraesCS3A01G446800 chr3B 95.266 169 8 0 181 349 729412642 729412810 5.430000e-68 268.0
12 TraesCS3A01G446800 chr3B 86.813 182 17 3 664 844 729413172 729413347 2.600000e-46 196.0
13 TraesCS3A01G446800 chr5D 88.115 1464 140 17 997 2443 65753735 65755181 0.000000e+00 1709.0
14 TraesCS3A01G446800 chr5D 89.655 377 38 1 2656 3032 170282436 170282811 2.300000e-131 479.0
15 TraesCS3A01G446800 chr5A 85.655 1680 174 36 797 2439 55018252 55019901 0.000000e+00 1705.0
16 TraesCS3A01G446800 chr5B 87.586 1458 154 13 998 2439 65279535 65278089 0.000000e+00 1664.0
17 TraesCS3A01G446800 chr1D 90.155 386 35 3 2654 3037 174199216 174199600 1.770000e-137 499.0
18 TraesCS3A01G446800 chr1D 81.203 266 45 5 1399 1662 426587341 426587603 3.340000e-50 209.0
19 TraesCS3A01G446800 chr1D 84.874 119 17 1 677 795 346018976 346018859 5.780000e-23 119.0
20 TraesCS3A01G446800 chr4A 90.667 375 33 2 2663 3036 510712701 510712328 6.360000e-137 497.0
21 TraesCS3A01G446800 chr6D 89.867 375 37 1 2663 3037 208851845 208851472 6.400000e-132 481.0
22 TraesCS3A01G446800 chr6D 83.200 125 18 2 674 796 10712231 10712354 9.680000e-21 111.0
23 TraesCS3A01G446800 chr4D 88.974 390 39 4 2651 3037 212073282 212072894 2.300000e-131 479.0
24 TraesCS3A01G446800 chr4D 88.802 384 43 0 2654 3037 286963434 286963817 3.850000e-129 472.0
25 TraesCS3A01G446800 chr4D 83.333 132 19 3 666 797 508989512 508989384 5.780000e-23 119.0
26 TraesCS3A01G446800 chr2D 88.889 387 39 3 2654 3037 341646562 341646947 1.070000e-129 473.0
27 TraesCS3A01G446800 chr2D 88.630 387 44 0 2651 3037 632374980 632375366 3.850000e-129 472.0
28 TraesCS3A01G446800 chr1A 88.802 384 43 0 2654 3037 291683303 291682920 3.850000e-129 472.0
29 TraesCS3A01G446800 chr1A 80.827 266 46 5 1399 1662 521629506 521629768 1.550000e-48 204.0
30 TraesCS3A01G446800 chr1B 80.827 266 46 5 1399 1662 576205888 576206150 1.550000e-48 204.0
31 TraesCS3A01G446800 chr2A 85.714 133 18 1 665 797 497445564 497445433 4.440000e-29 139.0
32 TraesCS3A01G446800 chr4B 83.582 134 19 3 664 797 658581021 658581151 4.470000e-24 122.0
33 TraesCS3A01G446800 chr7A 83.333 96 15 1 2522 2616 66224005 66223910 1.630000e-13 87.9


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 TraesCS3A01G446800 chr3A 686862235 686865533 3298 False 2763.000000 4868 100.000000 1 3299 2 chr3A.!!$F4 3298
1 TraesCS3A01G446800 chr3D 549704063 549707273 3210 False 1344.666667 3217 92.408667 1 3299 3 chr3D.!!$F2 3298
2 TraesCS3A01G446800 chr3B 729412642 729417104 4462 False 840.250000 2555 91.907500 181 3299 4 chr3B.!!$F1 3118
3 TraesCS3A01G446800 chr5D 65753735 65755181 1446 False 1709.000000 1709 88.115000 997 2443 1 chr5D.!!$F1 1446
4 TraesCS3A01G446800 chr5A 55018252 55019901 1649 False 1705.000000 1705 85.655000 797 2439 1 chr5A.!!$F1 1642
5 TraesCS3A01G446800 chr5B 65278089 65279535 1446 True 1664.000000 1664 87.586000 998 2439 1 chr5B.!!$R1 1441

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
174 175 0.319555 CTTCTTCCACCTCGACGCAA 60.320 55.000 0.0 0.0 0.0 4.85 F
177 178 1.156736 CTTCCACCTCGACGCAAAAT 58.843 50.000 0.0 0.0 0.0 1.82 F
302 305 1.377856 GGTGGAGAGGAAGGCAAGC 60.378 63.158 0.0 0.0 0.0 4.01 F
1863 3270 1.289066 CCTCGACTCGCACCTTGAA 59.711 57.895 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3222 0.889186 GCTTGACGAACCATGGGTGT 60.889 55.000 18.09 10.69 35.34 4.16 R
1863 3270 4.704103 TGGCTGTCGAGGAGGCCT 62.704 66.667 3.86 3.86 44.36 5.19 R
2257 3673 1.771255 ACTGCTATCCCAAGCCCTAAG 59.229 52.381 0.00 0.00 42.05 2.18 R
2666 4529 2.036604 CCACCGGTGGTAGCAAAAATTT 59.963 45.455 40.44 0.00 45.53 1.82 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
27 28 1.220206 CAGCCGATTGTGCTCTCCT 59.780 57.895 0.00 0.00 36.81 3.69
31 32 1.202580 GCCGATTGTGCTCTCCTACAT 60.203 52.381 0.00 0.00 0.00 2.29
36 37 0.817654 TGTGCTCTCCTACATGACGG 59.182 55.000 0.00 0.00 0.00 4.79
38 39 1.068250 GCTCTCCTACATGACGGCC 59.932 63.158 0.00 0.00 0.00 6.13
80 81 1.005394 GCGACTGTCTTCCCCGAAA 60.005 57.895 6.21 0.00 0.00 3.46
85 86 2.346365 GTCTTCCCCGAAAGCCGT 59.654 61.111 0.00 0.00 36.31 5.68
172 173 1.446272 CCTTCTTCCACCTCGACGC 60.446 63.158 0.00 0.00 0.00 5.19
174 175 0.319555 CTTCTTCCACCTCGACGCAA 60.320 55.000 0.00 0.00 0.00 4.85
177 178 1.156736 CTTCCACCTCGACGCAAAAT 58.843 50.000 0.00 0.00 0.00 1.82
179 180 1.600023 TCCACCTCGACGCAAAATTT 58.400 45.000 0.00 0.00 0.00 1.82
226 227 3.075005 TCCTACCTGGGCAGCGAC 61.075 66.667 0.00 0.00 36.20 5.19
259 260 2.235016 GATGGTTACAACACTTGGGCA 58.765 47.619 0.00 0.00 34.12 5.36
302 305 1.377856 GGTGGAGAGGAAGGCAAGC 60.378 63.158 0.00 0.00 0.00 4.01
689 739 1.402968 GCAACACGGATAGGACTACGA 59.597 52.381 0.00 0.00 0.00 3.43
691 741 2.941064 CAACACGGATAGGACTACGAGA 59.059 50.000 0.00 0.00 0.00 4.04
703 753 5.194432 AGGACTACGAGATGACACACTTAT 58.806 41.667 0.00 0.00 0.00 1.73
720 770 7.173735 ACACACTTATAAAACTTTTAGGACCCG 59.826 37.037 0.72 0.00 0.00 5.28
761 977 8.653036 AGTATTAGGACTAACTTGACAGTCTT 57.347 34.615 1.31 0.00 40.83 3.01
763 979 6.971726 TTAGGACTAACTTGACAGTCTTCA 57.028 37.500 1.31 0.00 40.83 3.02
911 2300 3.958798 ACCGTCACCTAATGCTACTACAT 59.041 43.478 0.00 0.00 0.00 2.29
945 2334 8.677300 CATACATTTGTTACTCCATAGCAAACT 58.323 33.333 0.00 0.00 43.97 2.66
1815 3222 1.642513 TAGAGGCTCTAGCGGGGACA 61.643 60.000 20.11 0.00 43.26 4.02
1863 3270 1.289066 CCTCGACTCGCACCTTGAA 59.711 57.895 0.00 0.00 0.00 2.69
2257 3673 2.089600 AGAGCTAGGGGATGGTGTAC 57.910 55.000 0.00 0.00 0.00 2.90
2275 3691 1.893315 ACTTAGGGCTTGGGATAGCA 58.107 50.000 0.00 0.00 43.02 3.49
2531 4394 1.849977 ACGAAGTTCTACTCCCTCCC 58.150 55.000 0.56 0.00 37.78 4.30
2616 4479 8.946085 AGTTCGCAGAAAAGTATATCAAAATCA 58.054 29.630 0.00 0.00 45.90 2.57
2681 4544 6.670077 TTTTGGACAAATTTTTGCTACCAC 57.330 33.333 13.04 0.00 41.79 4.16
2682 4545 4.329462 TGGACAAATTTTTGCTACCACC 57.671 40.909 3.00 0.00 41.79 4.61
2683 4546 3.243569 TGGACAAATTTTTGCTACCACCG 60.244 43.478 3.00 0.00 41.79 4.94
2684 4547 3.313690 GACAAATTTTTGCTACCACCGG 58.686 45.455 0.00 0.00 41.79 5.28
2685 4548 2.696187 ACAAATTTTTGCTACCACCGGT 59.304 40.909 0.00 0.00 41.79 5.28
2686 4549 3.056304 CAAATTTTTGCTACCACCGGTG 58.944 45.455 28.26 28.26 36.19 4.94
2709 4572 5.128205 GGTAGTTACCACCACTTGAGTTTT 58.872 41.667 3.45 0.00 45.73 2.43
2710 4573 5.008316 GGTAGTTACCACCACTTGAGTTTTG 59.992 44.000 3.45 0.00 45.73 2.44
2711 4574 4.595986 AGTTACCACCACTTGAGTTTTGT 58.404 39.130 0.00 0.00 0.00 2.83
2712 4575 5.747342 AGTTACCACCACTTGAGTTTTGTA 58.253 37.500 0.00 0.00 0.00 2.41
2713 4576 5.587443 AGTTACCACCACTTGAGTTTTGTAC 59.413 40.000 0.00 0.00 0.00 2.90
2714 4577 2.940410 ACCACCACTTGAGTTTTGTACG 59.060 45.455 0.00 0.00 0.00 3.67
2715 4578 2.940410 CCACCACTTGAGTTTTGTACGT 59.060 45.455 0.00 0.00 0.00 3.57
2716 4579 3.375922 CCACCACTTGAGTTTTGTACGTT 59.624 43.478 0.00 0.00 0.00 3.99
2717 4580 4.339429 CACCACTTGAGTTTTGTACGTTG 58.661 43.478 0.00 0.00 0.00 4.10
2718 4581 4.004982 ACCACTTGAGTTTTGTACGTTGT 58.995 39.130 0.00 0.00 0.00 3.32
2719 4582 5.063691 CACCACTTGAGTTTTGTACGTTGTA 59.936 40.000 0.00 0.00 0.00 2.41
2720 4583 5.818857 ACCACTTGAGTTTTGTACGTTGTAT 59.181 36.000 0.00 0.00 0.00 2.29
2721 4584 6.133392 CCACTTGAGTTTTGTACGTTGTATG 58.867 40.000 0.00 0.00 0.00 2.39
2722 4585 6.238266 CCACTTGAGTTTTGTACGTTGTATGT 60.238 38.462 0.00 0.00 0.00 2.29
2723 4586 7.042590 CCACTTGAGTTTTGTACGTTGTATGTA 60.043 37.037 0.00 0.00 0.00 2.29
2724 4587 8.002107 CACTTGAGTTTTGTACGTTGTATGTAG 58.998 37.037 0.00 0.00 0.00 2.74
2725 4588 7.707893 ACTTGAGTTTTGTACGTTGTATGTAGT 59.292 33.333 0.00 0.00 0.00 2.73
2726 4589 9.184062 CTTGAGTTTTGTACGTTGTATGTAGTA 57.816 33.333 0.00 0.00 0.00 1.82
2727 4590 9.695526 TTGAGTTTTGTACGTTGTATGTAGTAT 57.304 29.630 0.00 0.00 0.00 2.12
2728 4591 9.345517 TGAGTTTTGTACGTTGTATGTAGTATC 57.654 33.333 0.00 0.00 0.00 2.24
2729 4592 9.565213 GAGTTTTGTACGTTGTATGTAGTATCT 57.435 33.333 0.00 0.00 0.00 1.98
2738 4601 9.608617 ACGTTGTATGTAGTATCTATCAAATCG 57.391 33.333 0.00 0.00 0.00 3.34
2739 4602 9.062674 CGTTGTATGTAGTATCTATCAAATCGG 57.937 37.037 0.00 0.00 0.00 4.18
2742 4605 9.734984 TGTATGTAGTATCTATCAAATCGGAGA 57.265 33.333 0.00 0.00 45.75 3.71
2744 4607 8.871629 ATGTAGTATCTATCAAATCGGAGAGT 57.128 34.615 0.00 0.00 43.63 3.24
2745 4608 9.961264 ATGTAGTATCTATCAAATCGGAGAGTA 57.039 33.333 0.00 0.00 43.63 2.59
2746 4609 9.961264 TGTAGTATCTATCAAATCGGAGAGTAT 57.039 33.333 0.00 0.00 43.63 2.12
2752 4615 7.917597 TCTATCAAATCGGAGAGTATATACGC 58.082 38.462 8.43 8.43 43.63 4.42
2753 4616 4.966249 TCAAATCGGAGAGTATATACGCG 58.034 43.478 3.53 3.53 43.63 6.01
2754 4617 4.453478 TCAAATCGGAGAGTATATACGCGT 59.547 41.667 19.17 19.17 43.63 6.01
2755 4618 5.639082 TCAAATCGGAGAGTATATACGCGTA 59.361 40.000 22.94 22.94 43.63 4.42
2756 4619 5.715429 AATCGGAGAGTATATACGCGTAG 57.285 43.478 24.78 6.80 43.63 3.51
2757 4620 4.179926 TCGGAGAGTATATACGCGTAGT 57.820 45.455 24.78 17.26 0.00 2.73
2758 4621 5.310720 TCGGAGAGTATATACGCGTAGTA 57.689 43.478 24.78 16.25 40.03 1.82
2759 4622 5.895928 TCGGAGAGTATATACGCGTAGTAT 58.104 41.667 24.78 20.90 46.90 2.12
2760 4623 5.745769 TCGGAGAGTATATACGCGTAGTATG 59.254 44.000 24.78 8.64 45.10 2.39
2761 4624 5.518128 CGGAGAGTATATACGCGTAGTATGT 59.482 44.000 24.78 9.82 45.10 2.29
2762 4625 6.693113 CGGAGAGTATATACGCGTAGTATGTA 59.307 42.308 24.78 11.82 45.10 2.29
2763 4626 7.096681 CGGAGAGTATATACGCGTAGTATGTAG 60.097 44.444 24.78 5.92 45.10 2.74
2764 4627 7.704472 GGAGAGTATATACGCGTAGTATGTAGT 59.296 40.741 24.78 13.70 45.10 2.73
2765 4628 9.723447 GAGAGTATATACGCGTAGTATGTAGTA 57.277 37.037 24.78 9.61 45.10 1.82
2832 4695 9.472361 AGTATGTATCGTATTTTTCGTATGCTT 57.528 29.630 0.00 0.00 0.00 3.91
2833 4696 9.723299 GTATGTATCGTATTTTTCGTATGCTTC 57.277 33.333 0.00 0.00 0.00 3.86
2834 4697 7.997107 TGTATCGTATTTTTCGTATGCTTCT 57.003 32.000 0.00 0.00 0.00 2.85
2835 4698 8.415192 TGTATCGTATTTTTCGTATGCTTCTT 57.585 30.769 0.00 0.00 0.00 2.52
2836 4699 8.875803 TGTATCGTATTTTTCGTATGCTTCTTT 58.124 29.630 0.00 0.00 0.00 2.52
2837 4700 9.698617 GTATCGTATTTTTCGTATGCTTCTTTT 57.301 29.630 0.00 0.00 0.00 2.27
2840 4703 9.532697 TCGTATTTTTCGTATGCTTCTTTTTAC 57.467 29.630 0.00 0.00 0.00 2.01
2841 4704 8.502058 CGTATTTTTCGTATGCTTCTTTTTACG 58.498 33.333 0.00 0.00 38.93 3.18
2842 4705 9.321590 GTATTTTTCGTATGCTTCTTTTTACGT 57.678 29.630 0.00 0.00 38.74 3.57
2844 4707 8.698172 TTTTTCGTATGCTTCTTTTTACGTAC 57.302 30.769 0.00 0.00 38.74 3.67
2845 4708 7.405469 TTTCGTATGCTTCTTTTTACGTACA 57.595 32.000 0.00 0.00 38.74 2.90
2846 4709 7.405469 TTCGTATGCTTCTTTTTACGTACAA 57.595 32.000 0.00 0.00 38.74 2.41
2847 4710 7.405469 TCGTATGCTTCTTTTTACGTACAAA 57.595 32.000 6.71 6.71 38.74 2.83
2848 4711 8.020861 TCGTATGCTTCTTTTTACGTACAAAT 57.979 30.769 7.32 0.00 38.74 2.32
2849 4712 9.138062 TCGTATGCTTCTTTTTACGTACAAATA 57.862 29.630 7.32 0.00 38.74 1.40
2850 4713 9.910511 CGTATGCTTCTTTTTACGTACAAATAT 57.089 29.630 7.32 1.97 34.32 1.28
2887 4750 9.814899 CATAAATGTAATAAAAATCACTGGCCA 57.185 29.630 4.71 4.71 0.00 5.36
2889 4752 8.546597 AAATGTAATAAAAATCACTGGCCAAC 57.453 30.769 7.01 0.00 0.00 3.77
2890 4753 6.909550 TGTAATAAAAATCACTGGCCAACT 57.090 33.333 7.01 0.00 0.00 3.16
2891 4754 7.296628 TGTAATAAAAATCACTGGCCAACTT 57.703 32.000 7.01 0.00 0.00 2.66
2892 4755 7.151308 TGTAATAAAAATCACTGGCCAACTTG 58.849 34.615 7.01 4.43 0.00 3.16
2893 4756 5.806654 ATAAAAATCACTGGCCAACTTGT 57.193 34.783 7.01 0.00 0.00 3.16
2894 4757 6.909550 ATAAAAATCACTGGCCAACTTGTA 57.090 33.333 7.01 0.00 0.00 2.41
2895 4758 5.606348 AAAAATCACTGGCCAACTTGTAA 57.394 34.783 7.01 0.00 0.00 2.41
2896 4759 5.806654 AAAATCACTGGCCAACTTGTAAT 57.193 34.783 7.01 0.00 0.00 1.89
2897 4760 5.806654 AAATCACTGGCCAACTTGTAATT 57.193 34.783 7.01 0.00 0.00 1.40
2898 4761 5.806654 AATCACTGGCCAACTTGTAATTT 57.193 34.783 7.01 0.00 0.00 1.82
2899 4762 4.846779 TCACTGGCCAACTTGTAATTTC 57.153 40.909 7.01 0.00 0.00 2.17
2900 4763 4.469657 TCACTGGCCAACTTGTAATTTCT 58.530 39.130 7.01 0.00 0.00 2.52
2901 4764 4.892934 TCACTGGCCAACTTGTAATTTCTT 59.107 37.500 7.01 0.00 0.00 2.52
2902 4765 5.009610 TCACTGGCCAACTTGTAATTTCTTC 59.990 40.000 7.01 0.00 0.00 2.87
2903 4766 4.892934 ACTGGCCAACTTGTAATTTCTTCA 59.107 37.500 7.01 0.00 0.00 3.02
2904 4767 5.539955 ACTGGCCAACTTGTAATTTCTTCAT 59.460 36.000 7.01 0.00 0.00 2.57
2905 4768 6.041979 ACTGGCCAACTTGTAATTTCTTCATT 59.958 34.615 7.01 0.00 0.00 2.57
2906 4769 6.825610 TGGCCAACTTGTAATTTCTTCATTT 58.174 32.000 0.61 0.00 0.00 2.32
2907 4770 7.957002 TGGCCAACTTGTAATTTCTTCATTTA 58.043 30.769 0.61 0.00 0.00 1.40
2908 4771 8.424918 TGGCCAACTTGTAATTTCTTCATTTAA 58.575 29.630 0.61 0.00 0.00 1.52
2909 4772 8.708742 GGCCAACTTGTAATTTCTTCATTTAAC 58.291 33.333 0.00 0.00 0.00 2.01
2910 4773 9.476202 GCCAACTTGTAATTTCTTCATTTAACT 57.524 29.630 0.00 0.00 0.00 2.24
2998 4861 5.707242 CCACGTGGTAGTATATGAGACAT 57.293 43.478 26.95 0.00 0.00 3.06
2999 4862 5.461526 CCACGTGGTAGTATATGAGACATG 58.538 45.833 26.95 0.00 0.00 3.21
3001 4864 5.915196 CACGTGGTAGTATATGAGACATGTG 59.085 44.000 7.95 0.00 37.82 3.21
3002 4865 5.009710 ACGTGGTAGTATATGAGACATGTGG 59.990 44.000 1.15 0.00 0.00 4.17
3003 4866 5.564848 CGTGGTAGTATATGAGACATGTGGG 60.565 48.000 1.15 0.00 0.00 4.61
3004 4867 4.838423 TGGTAGTATATGAGACATGTGGGG 59.162 45.833 1.15 0.00 0.00 4.96
3005 4868 4.838986 GGTAGTATATGAGACATGTGGGGT 59.161 45.833 1.15 0.00 0.00 4.95
3006 4869 6.014647 GGTAGTATATGAGACATGTGGGGTA 58.985 44.000 1.15 0.00 0.00 3.69
3007 4870 6.495872 GGTAGTATATGAGACATGTGGGGTAA 59.504 42.308 1.15 0.00 0.00 2.85
3008 4871 6.420913 AGTATATGAGACATGTGGGGTAAC 57.579 41.667 1.15 0.00 0.00 2.50
3010 4873 7.302948 AGTATATGAGACATGTGGGGTAACTA 58.697 38.462 1.15 0.00 0.00 2.24
3011 4874 4.755266 ATGAGACATGTGGGGTAACTAC 57.245 45.455 1.15 0.00 0.00 2.73
3012 4875 2.835764 TGAGACATGTGGGGTAACTACC 59.164 50.000 1.15 0.00 45.71 3.18
3096 5152 5.533482 CAAGTATGTATGTCCAGCTCTACC 58.467 45.833 0.00 0.00 0.00 3.18
3097 5153 4.153411 AGTATGTATGTCCAGCTCTACCC 58.847 47.826 0.00 0.00 0.00 3.69
3237 5312 7.615582 TTTAGAGTTGCATAAGATTGACCTG 57.384 36.000 0.00 0.00 0.00 4.00
3269 5344 7.345422 TGAGGTTCACTTTTCAAATGATCAA 57.655 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.124983 AGCACAATCGGCTGCGAT 60.125 55.556 0.00 0.00 40.80 4.58
14 15 3.119291 CGTCATGTAGGAGAGCACAATC 58.881 50.000 0.00 0.00 0.00 2.67
18 19 0.528684 GCCGTCATGTAGGAGAGCAC 60.529 60.000 12.24 0.00 0.00 4.40
27 28 2.363975 GGTCTGGGGCCGTCATGTA 61.364 63.158 0.00 0.00 0.00 2.29
36 37 4.062032 GGGAAAGGGGTCTGGGGC 62.062 72.222 0.00 0.00 0.00 5.80
38 39 2.763902 GTGGGAAAGGGGTCTGGG 59.236 66.667 0.00 0.00 0.00 4.45
68 69 2.033194 CACGGCTTTCGGGGAAGAC 61.033 63.158 0.00 0.00 44.45 3.01
96 97 3.058160 CCGTCCTCCCACGTACGT 61.058 66.667 16.72 16.72 38.14 3.57
98 99 4.487412 CGCCGTCCTCCCACGTAC 62.487 72.222 0.00 0.00 38.14 3.67
116 117 0.953727 TGTCTGCTGATTGTTGCCAC 59.046 50.000 0.00 0.00 0.00 5.01
135 136 1.704070 GGAGGAATGAGGATGGAGCAT 59.296 52.381 0.00 0.00 0.00 3.79
172 173 5.034852 AGAAAGTGGGGTCCAAAATTTTG 57.965 39.130 21.65 21.65 34.18 2.44
174 175 3.646162 GGAGAAAGTGGGGTCCAAAATTT 59.354 43.478 0.00 0.00 34.18 1.82
177 178 1.133294 GGGAGAAAGTGGGGTCCAAAA 60.133 52.381 0.00 0.00 34.18 2.44
179 180 0.402861 AGGGAGAAAGTGGGGTCCAA 60.403 55.000 0.00 0.00 34.18 3.53
226 227 0.815734 AACCATCCTGACGTCTACCG 59.184 55.000 17.92 2.62 44.03 4.02
259 260 3.626924 GCCACTGTCCACCTCGGT 61.627 66.667 0.00 0.00 35.57 4.69
271 274 2.113139 CCACCTTTGACGGCCACT 59.887 61.111 2.24 0.00 0.00 4.00
302 305 1.081892 CCCTTGCACACATCTTCTCG 58.918 55.000 0.00 0.00 0.00 4.04
703 753 6.885376 TGCATATTCGGGTCCTAAAAGTTTTA 59.115 34.615 7.80 7.80 0.00 1.52
763 979 4.959839 ACACCACAAGTCCCAAAACTATTT 59.040 37.500 0.00 0.00 0.00 1.40
773 989 5.557866 AGAGTAAAATACACCACAAGTCCC 58.442 41.667 0.00 0.00 0.00 4.46
811 1027 7.868974 ACTACTAGGGTTTATGGCTTTGTTAT 58.131 34.615 0.00 0.00 0.00 1.89
911 2300 6.170506 GGAGTAACAAATGTATGTCTGTGGA 58.829 40.000 0.00 0.00 31.81 4.02
945 2334 5.763204 AGCTCGAAATTAAGAACACCTCAAA 59.237 36.000 0.00 0.00 0.00 2.69
1010 2417 1.153469 CCGCTGCTCTTCTTCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
1041 2448 2.579787 CCGAGCTCGTACTTGCCG 60.580 66.667 32.41 12.50 37.74 5.69
1140 2547 1.811266 CACCTCCGCCTTGTCGATG 60.811 63.158 0.00 0.00 0.00 3.84
1257 2664 1.519455 GTAGATGCTGGCGCGAGTT 60.519 57.895 20.92 8.92 39.65 3.01
1710 3117 4.137872 CACGGCGGGACCACGTAT 62.138 66.667 13.24 0.00 39.02 3.06
1815 3222 0.889186 GCTTGACGAACCATGGGTGT 60.889 55.000 18.09 10.69 35.34 4.16
1863 3270 4.704103 TGGCTGTCGAGGAGGCCT 62.704 66.667 3.86 3.86 44.36 5.19
2257 3673 1.771255 ACTGCTATCCCAAGCCCTAAG 59.229 52.381 0.00 0.00 42.05 2.18
2275 3691 5.594317 ACTAAACTTGTTGCAAATCCTCACT 59.406 36.000 0.00 0.00 0.00 3.41
2317 3740 7.795734 GTCCGTTAACTAGTTAAGCTTTCAAAC 59.204 37.037 24.97 13.42 35.90 2.93
2624 4487 8.937835 TCTGATGAATCTAATGAGGGTAATTCA 58.062 33.333 0.00 0.00 37.48 2.57
2662 4525 3.313690 CGGTGGTAGCAAAAATTTGTCC 58.686 45.455 0.00 8.26 40.24 4.02
2663 4526 3.243602 ACCGGTGGTAGCAAAAATTTGTC 60.244 43.478 6.12 1.08 35.81 3.18
2664 4527 2.696187 ACCGGTGGTAGCAAAAATTTGT 59.304 40.909 6.12 0.00 35.81 2.83
2665 4528 3.056304 CACCGGTGGTAGCAAAAATTTG 58.944 45.455 27.57 1.52 36.21 2.32
2666 4529 2.036604 CCACCGGTGGTAGCAAAAATTT 59.963 45.455 40.44 0.00 45.53 1.82
2670 4533 4.484987 CCACCGGTGGTAGCAAAA 57.515 55.556 40.44 0.00 45.53 2.44
2686 4549 4.347360 AACTCAAGTGGTGGTAACTACC 57.653 45.455 0.00 0.00 46.62 3.18
2687 4550 5.587443 ACAAAACTCAAGTGGTGGTAACTAC 59.413 40.000 0.00 0.00 38.03 2.73
2689 4552 4.595986 ACAAAACTCAAGTGGTGGTAACT 58.404 39.130 0.00 0.00 37.61 2.24
2690 4553 4.976224 ACAAAACTCAAGTGGTGGTAAC 57.024 40.909 0.00 0.00 0.00 2.50
2692 4555 4.121317 CGTACAAAACTCAAGTGGTGGTA 58.879 43.478 0.00 0.00 0.00 3.25
2693 4556 2.940410 CGTACAAAACTCAAGTGGTGGT 59.060 45.455 0.00 0.00 0.00 4.16
2694 4557 2.940410 ACGTACAAAACTCAAGTGGTGG 59.060 45.455 0.00 0.00 0.00 4.61
2695 4558 4.142773 ACAACGTACAAAACTCAAGTGGTG 60.143 41.667 0.00 0.00 0.00 4.17
2696 4559 4.004982 ACAACGTACAAAACTCAAGTGGT 58.995 39.130 0.00 0.00 0.00 4.16
2698 4561 6.711579 ACATACAACGTACAAAACTCAAGTG 58.288 36.000 0.00 0.00 0.00 3.16
2699 4562 6.913873 ACATACAACGTACAAAACTCAAGT 57.086 33.333 0.00 0.00 0.00 3.16
2701 4564 9.695526 ATACTACATACAACGTACAAAACTCAA 57.304 29.630 0.00 0.00 0.00 3.02
2702 4565 9.345517 GATACTACATACAACGTACAAAACTCA 57.654 33.333 0.00 0.00 0.00 3.41
2703 4566 9.565213 AGATACTACATACAACGTACAAAACTC 57.435 33.333 0.00 0.00 0.00 3.01
2712 4575 9.608617 CGATTTGATAGATACTACATACAACGT 57.391 33.333 0.00 0.00 0.00 3.99
2713 4576 9.062674 CCGATTTGATAGATACTACATACAACG 57.937 37.037 0.00 0.00 0.00 4.10
2716 4579 9.734984 TCTCCGATTTGATAGATACTACATACA 57.265 33.333 0.00 0.00 0.00 2.29
2718 4581 9.961264 ACTCTCCGATTTGATAGATACTACATA 57.039 33.333 0.00 0.00 0.00 2.29
2719 4582 8.871629 ACTCTCCGATTTGATAGATACTACAT 57.128 34.615 0.00 0.00 0.00 2.29
2720 4583 9.961264 ATACTCTCCGATTTGATAGATACTACA 57.039 33.333 0.00 0.00 0.00 2.74
2726 4589 8.561212 GCGTATATACTCTCCGATTTGATAGAT 58.439 37.037 11.05 0.00 0.00 1.98
2727 4590 7.254353 CGCGTATATACTCTCCGATTTGATAGA 60.254 40.741 11.05 0.00 0.00 1.98
2728 4591 6.846786 CGCGTATATACTCTCCGATTTGATAG 59.153 42.308 11.05 0.00 0.00 2.08
2729 4592 6.314648 ACGCGTATATACTCTCCGATTTGATA 59.685 38.462 11.67 0.00 0.00 2.15
2730 4593 5.123502 ACGCGTATATACTCTCCGATTTGAT 59.876 40.000 11.67 0.00 0.00 2.57
2731 4594 4.453478 ACGCGTATATACTCTCCGATTTGA 59.547 41.667 11.67 0.00 0.00 2.69
2732 4595 4.720090 ACGCGTATATACTCTCCGATTTG 58.280 43.478 11.67 0.00 0.00 2.32
2733 4596 5.641209 ACTACGCGTATATACTCTCCGATTT 59.359 40.000 20.91 0.00 0.00 2.17
2734 4597 5.174395 ACTACGCGTATATACTCTCCGATT 58.826 41.667 20.91 0.00 0.00 3.34
2735 4598 4.753233 ACTACGCGTATATACTCTCCGAT 58.247 43.478 20.91 0.00 0.00 4.18
2736 4599 4.179926 ACTACGCGTATATACTCTCCGA 57.820 45.455 20.91 0.00 0.00 4.55
2737 4600 5.518128 ACATACTACGCGTATATACTCTCCG 59.482 44.000 20.91 6.35 36.69 4.63
2738 4601 6.900568 ACATACTACGCGTATATACTCTCC 57.099 41.667 20.91 0.00 36.69 3.71
2739 4602 8.627487 ACTACATACTACGCGTATATACTCTC 57.373 38.462 20.91 0.00 36.69 3.20
2806 4669 9.472361 AAGCATACGAAAAATACGATACATACT 57.528 29.630 0.00 0.00 34.70 2.12
2807 4670 9.723299 GAAGCATACGAAAAATACGATACATAC 57.277 33.333 0.00 0.00 34.70 2.39
2808 4671 9.687210 AGAAGCATACGAAAAATACGATACATA 57.313 29.630 0.00 0.00 34.70 2.29
2809 4672 8.589335 AGAAGCATACGAAAAATACGATACAT 57.411 30.769 0.00 0.00 34.70 2.29
2810 4673 7.997107 AGAAGCATACGAAAAATACGATACA 57.003 32.000 0.00 0.00 34.70 2.29
2811 4674 9.698617 AAAAGAAGCATACGAAAAATACGATAC 57.301 29.630 0.00 0.00 34.70 2.24
2814 4677 9.532697 GTAAAAAGAAGCATACGAAAAATACGA 57.467 29.630 0.00 0.00 34.70 3.43
2815 4678 8.502058 CGTAAAAAGAAGCATACGAAAAATACG 58.498 33.333 0.00 0.00 42.66 3.06
2816 4679 9.321590 ACGTAAAAAGAAGCATACGAAAAATAC 57.678 29.630 10.69 0.00 42.66 1.89
2818 4681 9.321590 GTACGTAAAAAGAAGCATACGAAAAAT 57.678 29.630 10.69 0.00 42.66 1.82
2819 4682 8.333908 TGTACGTAAAAAGAAGCATACGAAAAA 58.666 29.630 10.69 0.00 42.66 1.94
2820 4683 7.849496 TGTACGTAAAAAGAAGCATACGAAAA 58.151 30.769 10.69 0.00 42.66 2.29
2821 4684 7.405469 TGTACGTAAAAAGAAGCATACGAAA 57.595 32.000 10.69 0.00 42.66 3.46
2822 4685 7.405469 TTGTACGTAAAAAGAAGCATACGAA 57.595 32.000 10.69 0.00 42.66 3.85
2823 4686 7.405469 TTTGTACGTAAAAAGAAGCATACGA 57.595 32.000 6.83 0.00 42.66 3.43
2824 4687 9.910511 ATATTTGTACGTAAAAAGAAGCATACG 57.089 29.630 15.76 2.96 44.82 3.06
2861 4724 9.814899 TGGCCAGTGATTTTTATTACATTTATG 57.185 29.630 0.00 0.00 0.00 1.90
2863 4726 9.646427 GTTGGCCAGTGATTTTTATTACATTTA 57.354 29.630 5.11 0.00 0.00 1.40
2864 4727 8.374743 AGTTGGCCAGTGATTTTTATTACATTT 58.625 29.630 5.11 0.00 0.00 2.32
2865 4728 7.906327 AGTTGGCCAGTGATTTTTATTACATT 58.094 30.769 5.11 0.00 0.00 2.71
2866 4729 7.480760 AGTTGGCCAGTGATTTTTATTACAT 57.519 32.000 5.11 0.00 0.00 2.29
2867 4730 6.909550 AGTTGGCCAGTGATTTTTATTACA 57.090 33.333 5.11 0.00 0.00 2.41
2868 4731 7.151976 ACAAGTTGGCCAGTGATTTTTATTAC 58.848 34.615 17.33 3.98 0.00 1.89
2869 4732 7.296628 ACAAGTTGGCCAGTGATTTTTATTA 57.703 32.000 17.33 0.00 0.00 0.98
2870 4733 6.173427 ACAAGTTGGCCAGTGATTTTTATT 57.827 33.333 17.33 0.00 0.00 1.40
2871 4734 5.806654 ACAAGTTGGCCAGTGATTTTTAT 57.193 34.783 17.33 0.00 0.00 1.40
2872 4735 6.716934 TTACAAGTTGGCCAGTGATTTTTA 57.283 33.333 17.33 0.00 0.00 1.52
2873 4736 5.606348 TTACAAGTTGGCCAGTGATTTTT 57.394 34.783 17.33 0.00 0.00 1.94
2874 4737 5.806654 ATTACAAGTTGGCCAGTGATTTT 57.193 34.783 17.33 3.45 0.00 1.82
2875 4738 5.806654 AATTACAAGTTGGCCAGTGATTT 57.193 34.783 17.33 0.00 0.00 2.17
2876 4739 5.539955 AGAAATTACAAGTTGGCCAGTGATT 59.460 36.000 17.33 12.14 0.00 2.57
2877 4740 5.079643 AGAAATTACAAGTTGGCCAGTGAT 58.920 37.500 17.33 7.14 0.00 3.06
2878 4741 4.469657 AGAAATTACAAGTTGGCCAGTGA 58.530 39.130 17.33 5.13 0.00 3.41
2879 4742 4.853924 AGAAATTACAAGTTGGCCAGTG 57.146 40.909 5.11 8.63 0.00 3.66
2880 4743 4.892934 TGAAGAAATTACAAGTTGGCCAGT 59.107 37.500 5.11 2.46 0.00 4.00
2881 4744 5.452078 TGAAGAAATTACAAGTTGGCCAG 57.548 39.130 5.11 0.00 0.00 4.85
2882 4745 6.418057 AATGAAGAAATTACAAGTTGGCCA 57.582 33.333 0.00 0.00 0.00 5.36
2883 4746 8.708742 GTTAAATGAAGAAATTACAAGTTGGCC 58.291 33.333 7.96 0.00 0.00 5.36
2884 4747 9.476202 AGTTAAATGAAGAAATTACAAGTTGGC 57.524 29.630 7.96 0.00 0.00 4.52
2979 4842 5.461526 CCACATGTCTCATATACTACCACG 58.538 45.833 0.00 0.00 0.00 4.94
2992 4855 3.538634 GGTAGTTACCCCACATGTCTC 57.461 52.381 0.00 0.00 40.53 3.36
3003 4866 2.557555 ACCACCTAGGGGTAGTTACC 57.442 55.000 17.62 0.00 45.41 2.85
3011 4874 3.562108 ATACATCCTACCACCTAGGGG 57.438 52.381 14.81 9.46 42.51 4.79
3012 4875 5.221864 GGAAAATACATCCTACCACCTAGGG 60.222 48.000 14.81 1.73 42.51 3.53
3013 4876 5.510861 CGGAAAATACATCCTACCACCTAGG 60.511 48.000 7.41 7.41 43.54 3.02
3014 4877 5.510861 CCGGAAAATACATCCTACCACCTAG 60.511 48.000 0.00 0.00 34.66 3.02
3016 4879 3.135895 CCGGAAAATACATCCTACCACCT 59.864 47.826 0.00 0.00 34.66 4.00
3017 4880 3.135167 TCCGGAAAATACATCCTACCACC 59.865 47.826 0.00 0.00 34.66 4.61
3018 4881 4.411256 TCCGGAAAATACATCCTACCAC 57.589 45.455 0.00 0.00 34.66 4.16
3019 4882 6.750660 TTATCCGGAAAATACATCCTACCA 57.249 37.500 9.01 0.00 34.66 3.25
3020 4883 7.222161 AGTTTATCCGGAAAATACATCCTACC 58.778 38.462 9.01 0.00 34.66 3.18
3021 4884 8.672823 AAGTTTATCCGGAAAATACATCCTAC 57.327 34.615 9.01 0.00 34.66 3.18
3022 4885 9.991906 CTAAGTTTATCCGGAAAATACATCCTA 57.008 33.333 9.01 0.00 34.66 2.94
3023 4886 8.711170 TCTAAGTTTATCCGGAAAATACATCCT 58.289 33.333 9.01 0.64 34.66 3.24
3024 4887 8.897872 TCTAAGTTTATCCGGAAAATACATCC 57.102 34.615 9.01 0.00 0.00 3.51
3026 4889 9.901172 AGTTCTAAGTTTATCCGGAAAATACAT 57.099 29.630 9.01 1.00 0.00 2.29
3027 4890 9.729281 AAGTTCTAAGTTTATCCGGAAAATACA 57.271 29.630 9.01 0.00 0.00 2.29
3029 4892 9.947433 TGAAGTTCTAAGTTTATCCGGAAAATA 57.053 29.630 9.01 0.00 0.00 1.40
3030 4893 8.857694 TGAAGTTCTAAGTTTATCCGGAAAAT 57.142 30.769 9.01 0.00 0.00 1.82
3031 4894 8.680039 TTGAAGTTCTAAGTTTATCCGGAAAA 57.320 30.769 9.01 7.99 0.00 2.29
3033 4896 8.857694 ATTTGAAGTTCTAAGTTTATCCGGAA 57.142 30.769 9.01 0.00 0.00 4.30
3068 5124 3.432186 GCTGGACATACATACTTGCTCCA 60.432 47.826 0.00 0.00 0.00 3.86
3096 5152 5.105917 GGATAAACACAACCATTACACAGGG 60.106 44.000 0.00 0.00 0.00 4.45
3097 5153 5.475220 TGGATAAACACAACCATTACACAGG 59.525 40.000 0.00 0.00 0.00 4.00
3237 5312 5.890334 TGAAAAGTGAACCTCATGTTTGAC 58.110 37.500 0.00 0.00 37.29 3.18
3269 5344 3.384789 GCTTTTGAAAAAGGGTGTCCTCT 59.615 43.478 15.40 0.00 44.07 3.69


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

AutoCloner maintained by Alex Coulton.