Multiple sequence alignment - TraesCS3A01G324300

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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 TraesCS3A01G324300 chr3A 100.000 3365 0 0 1 3365 569166597 569169961 0.000000e+00 6215.0
1 TraesCS3A01G324300 chr3A 94.682 1918 67 11 669 2554 568971613 568973527 0.000000e+00 2944.0
2 TraesCS3A01G324300 chr3A 88.722 1667 166 13 1022 2679 569230146 569231799 0.000000e+00 2017.0
3 TraesCS3A01G324300 chr3A 84.594 1428 169 18 904 2300 576270146 576268739 0.000000e+00 1371.0
4 TraesCS3A01G324300 chr3A 89.149 470 43 6 2680 3144 569231634 569232100 2.250000e-161 579.0
5 TraesCS3A01G324300 chr3A 87.915 331 34 3 2355 2679 576268711 576268381 5.270000e-103 385.0
6 TraesCS3A01G324300 chr3A 98.802 167 2 0 2680 2846 569169109 569169275 7.060000e-77 298.0
7 TraesCS3A01G324300 chr3A 98.802 167 2 0 2513 2679 569169276 569169442 7.060000e-77 298.0
8 TraesCS3A01G324300 chr3A 91.748 206 13 2 3142 3346 569232241 569232443 1.980000e-72 283.0
9 TraesCS3A01G324300 chr3A 93.333 180 12 0 2719 2898 568973580 568973759 1.990000e-67 267.0
10 TraesCS3A01G324300 chr3A 91.071 168 15 0 2683 2850 576268544 576268377 9.390000e-56 228.0
11 TraesCS3A01G324300 chr3A 91.406 128 11 0 2552 2679 568973580 568973707 3.450000e-40 176.0
12 TraesCS3A01G324300 chr3A 96.296 81 3 0 3261 3341 569232600 569232680 2.110000e-27 134.0
13 TraesCS3A01G324300 chr3A 79.032 186 23 7 669 838 685766746 685766931 2.740000e-21 113.0
14 TraesCS3A01G324300 chr3D 94.011 2037 83 7 669 2679 431627555 431629578 0.000000e+00 3049.0
15 TraesCS3A01G324300 chr3D 92.072 2056 85 25 669 2679 431447909 431449931 0.000000e+00 2822.0
16 TraesCS3A01G324300 chr3D 88.636 1672 163 12 1022 2679 431832004 431833662 0.000000e+00 2010.0
17 TraesCS3A01G324300 chr3D 85.127 1533 193 15 1159 2679 438047162 438048671 0.000000e+00 1535.0
18 TraesCS3A01G324300 chr3D 96.934 685 20 1 2680 3364 431629412 431630095 0.000000e+00 1147.0
19 TraesCS3A01G324300 chr3D 96.788 685 21 1 2680 3364 431449765 431450448 0.000000e+00 1142.0
20 TraesCS3A01G324300 chr3D 91.864 676 46 9 1 670 554410103 554410775 0.000000e+00 935.0
21 TraesCS3A01G324300 chr3D 89.650 686 60 9 1 678 577794717 577794035 0.000000e+00 863.0
22 TraesCS3A01G324300 chr3D 88.841 466 47 4 2680 3144 431833497 431833958 4.870000e-158 568.0
23 TraesCS3A01G324300 chr3D 93.301 209 12 1 3142 3348 431834107 431834315 1.170000e-79 307.0
24 TraesCS3A01G324300 chr3D 93.182 88 6 0 3217 3304 431834313 431834400 2.720000e-26 130.0
25 TraesCS3A01G324300 chr3B 92.342 1815 91 20 879 2671 564023125 564024913 0.000000e+00 2538.0
26 TraesCS3A01G324300 chr3B 89.587 1671 154 11 1023 2679 564038190 564039854 0.000000e+00 2104.0
27 TraesCS3A01G324300 chr3B 96.204 685 22 3 2680 3364 564024755 564025435 0.000000e+00 1118.0
28 TraesCS3A01G324300 chr3B 88.889 207 18 2 3142 3348 564040292 564040493 2.000000e-62 250.0
29 TraesCS3A01G324300 chr3B 91.129 124 9 1 3222 3343 564040496 564040619 2.080000e-37 167.0
30 TraesCS3A01G324300 chr3B 80.488 123 18 5 671 788 753210228 753210349 4.620000e-14 89.8
31 TraesCS3A01G324300 chr4B 90.653 674 56 5 1 670 587158938 587159608 0.000000e+00 889.0
32 TraesCS3A01G324300 chr7D 89.676 678 59 6 1 668 351834234 351834910 0.000000e+00 854.0
33 TraesCS3A01G324300 chr7D 79.310 145 25 4 669 812 602686235 602686375 2.760000e-16 97.1
34 TraesCS3A01G324300 chr1B 88.987 681 61 10 1 673 375985715 375985041 0.000000e+00 830.0
35 TraesCS3A01G324300 chr1B 88.399 681 66 10 1 673 376021304 376020629 0.000000e+00 808.0
36 TraesCS3A01G324300 chr2D 88.416 682 59 11 1 668 512422005 512422680 0.000000e+00 804.0
37 TraesCS3A01G324300 chr2D 85.345 116 10 6 669 781 38438336 38438225 2.740000e-21 113.0
38 TraesCS3A01G324300 chr2D 76.301 173 29 11 671 837 107908705 107908539 7.740000e-12 82.4
39 TraesCS3A01G324300 chr6B 89.065 631 61 8 55 678 353948435 353949064 0.000000e+00 776.0
40 TraesCS3A01G324300 chr6B 82.400 125 19 3 669 793 214092211 214092332 4.590000e-19 106.0
41 TraesCS3A01G324300 chr6B 95.082 61 3 0 1 61 353935341 353935401 2.760000e-16 97.1
42 TraesCS3A01G324300 chr1D 87.612 670 66 14 1 660 374737856 374738518 0.000000e+00 761.0
43 TraesCS3A01G324300 chr5A 77.515 169 28 10 673 837 111905246 111905084 3.570000e-15 93.5
44 TraesCS3A01G324300 chr5D 82.500 80 9 5 756 833 557601191 557601267 7.790000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G324300 chr3A 569166597 569169961 3364 False 2270.333333 6215 99.201333 1 3365 3 chr3A.!!$F3 3364
1 TraesCS3A01G324300 chr3A 568971613 568973759 2146 False 1129.000000 2944 93.140333 669 2898 3 chr3A.!!$F2 2229
2 TraesCS3A01G324300 chr3A 569230146 569232680 2534 False 753.250000 2017 91.478750 1022 3346 4 chr3A.!!$F4 2324
3 TraesCS3A01G324300 chr3A 576268377 576270146 1769 True 661.333333 1371 87.860000 904 2850 3 chr3A.!!$R1 1946
4 TraesCS3A01G324300 chr3D 431627555 431630095 2540 False 2098.000000 3049 95.472500 669 3364 2 chr3D.!!$F4 2695
5 TraesCS3A01G324300 chr3D 431447909 431450448 2539 False 1982.000000 2822 94.430000 669 3364 2 chr3D.!!$F3 2695
6 TraesCS3A01G324300 chr3D 438047162 438048671 1509 False 1535.000000 1535 85.127000 1159 2679 1 chr3D.!!$F1 1520
7 TraesCS3A01G324300 chr3D 554410103 554410775 672 False 935.000000 935 91.864000 1 670 1 chr3D.!!$F2 669
8 TraesCS3A01G324300 chr3D 577794035 577794717 682 True 863.000000 863 89.650000 1 678 1 chr3D.!!$R1 677
9 TraesCS3A01G324300 chr3D 431832004 431834400 2396 False 753.750000 2010 90.990000 1022 3348 4 chr3D.!!$F5 2326
10 TraesCS3A01G324300 chr3B 564023125 564025435 2310 False 1828.000000 2538 94.273000 879 3364 2 chr3B.!!$F2 2485
11 TraesCS3A01G324300 chr3B 564038190 564040619 2429 False 840.333333 2104 89.868333 1023 3348 3 chr3B.!!$F3 2325
12 TraesCS3A01G324300 chr4B 587158938 587159608 670 False 889.000000 889 90.653000 1 670 1 chr4B.!!$F1 669
13 TraesCS3A01G324300 chr7D 351834234 351834910 676 False 854.000000 854 89.676000 1 668 1 chr7D.!!$F1 667
14 TraesCS3A01G324300 chr1B 375985041 375985715 674 True 830.000000 830 88.987000 1 673 1 chr1B.!!$R1 672
15 TraesCS3A01G324300 chr1B 376020629 376021304 675 True 808.000000 808 88.399000 1 673 1 chr1B.!!$R2 672
16 TraesCS3A01G324300 chr2D 512422005 512422680 675 False 804.000000 804 88.416000 1 668 1 chr2D.!!$F1 667
17 TraesCS3A01G324300 chr6B 353948435 353949064 629 False 776.000000 776 89.065000 55 678 1 chr6B.!!$F3 623
18 TraesCS3A01G324300 chr1D 374737856 374738518 662 False 761.000000 761 87.612000 1 660 1 chr1D.!!$F1 659

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
368 384 1.37419 GATCAGATCTGGGGCGCAT 59.626 57.895 22.42 7.44 0.0 4.73 F
1240 1357 1.44854 CGCCAAAGCTGAGTCCGAT 60.449 57.895 0.00 0.00 36.6 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1649 0.110486 AGTTCATGGAAGGTTGCGGT 59.890 50.0 0.0 0.0 0.0 5.68 R
2722 2910 0.476338 TCACAGGGCAAGCTAAACCA 59.524 50.0 0.0 0.0 0.0 3.67 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
61 63 3.695830 ACGGAGGAATTACACACATGT 57.304 42.857 0.00 0.00 43.30 3.21
78 82 6.092259 CACACATGTAGTAAAAGGCTACCTTC 59.908 42.308 0.00 0.00 43.92 3.46
81 85 8.038944 CACATGTAGTAAAAGGCTACCTTCTTA 58.961 37.037 0.00 0.00 43.92 2.10
90 94 4.712476 AGGCTACCTTCTTATGCATCTTG 58.288 43.478 0.19 0.00 0.00 3.02
292 303 4.156556 CCCTTGTGATGTTGATGTGGTAAG 59.843 45.833 0.00 0.00 0.00 2.34
297 308 5.046663 TGTGATGTTGATGTGGTAAGCTAGA 60.047 40.000 0.00 0.00 0.00 2.43
307 318 2.315155 TGGTAAGCTAGACCCCTCTCTT 59.685 50.000 13.76 0.00 35.99 2.85
368 384 1.374190 GATCAGATCTGGGGCGCAT 59.626 57.895 22.42 7.44 0.00 4.73
459 479 7.325694 CGATGGAGGTAAGAAACTAGGTTTTA 58.674 38.462 0.00 0.00 35.77 1.52
502 530 3.394836 GGTGAGCGAGAGGGGCTT 61.395 66.667 0.00 0.00 41.72 4.35
660 691 3.123674 CAGTCGACTGGTGGTTAGC 57.876 57.895 33.36 0.00 40.20 3.09
818 849 7.630689 GTTCGAACAATATTGAACGTGTATG 57.369 36.000 23.12 1.89 34.82 2.39
1099 1164 3.358076 CTCCTCCTCGCCAACCGTC 62.358 68.421 0.00 0.00 38.35 4.79
1186 1303 3.838271 GCTGACTCCATCGCGGGA 61.838 66.667 6.13 4.03 34.36 5.14
1240 1357 1.448540 CGCCAAAGCTGAGTCCGAT 60.449 57.895 0.00 0.00 36.60 4.18
1532 1649 2.043604 CTCCATGCCATCCCACGCTA 62.044 60.000 0.00 0.00 0.00 4.26
1624 1741 1.227556 CGAAGCCGGGGATTTCGAT 60.228 57.895 15.36 0.00 44.64 3.59
1709 1826 4.402793 ACTCTTACAACATACTCATCCGCT 59.597 41.667 0.00 0.00 0.00 5.52
2002 2119 1.650314 GGCCAAAACCCGATACGGTG 61.650 60.000 0.00 3.75 46.80 4.94
2079 2196 5.279384 CAAGAAGCTGTATGATGATTTGGC 58.721 41.667 0.00 0.00 0.00 4.52
2189 2306 7.549134 TGAGGTACTGCTATGAAATGTTTAGTG 59.451 37.037 0.00 0.00 41.55 2.74
2201 2318 5.622770 AATGTTTAGTGGTAAAAGGAGCG 57.377 39.130 0.00 0.00 29.74 5.03
2274 2391 3.086600 GAGGGTGGAGGAGGCTGG 61.087 72.222 0.00 0.00 0.00 4.85
2302 2419 2.093394 TGTTGATATCGGGCGGAAGAAA 60.093 45.455 0.00 0.00 0.00 2.52
2400 2528 7.066766 GCAATATCAGAAGAAAAGGAGTGTGAT 59.933 37.037 0.00 0.00 0.00 3.06
2575 2763 1.075374 TGGTTTAGCTTGCCCTGTGAT 59.925 47.619 0.00 0.00 0.00 3.06
2576 2764 2.171003 GGTTTAGCTTGCCCTGTGATT 58.829 47.619 0.00 0.00 0.00 2.57
2577 2765 2.562738 GGTTTAGCTTGCCCTGTGATTT 59.437 45.455 0.00 0.00 0.00 2.17
2578 2766 3.761752 GGTTTAGCTTGCCCTGTGATTTA 59.238 43.478 0.00 0.00 0.00 1.40
2579 2767 4.219725 GGTTTAGCTTGCCCTGTGATTTAA 59.780 41.667 0.00 0.00 0.00 1.52
2580 2768 5.105351 GGTTTAGCTTGCCCTGTGATTTAAT 60.105 40.000 0.00 0.00 0.00 1.40
2581 2769 6.096282 GGTTTAGCTTGCCCTGTGATTTAATA 59.904 38.462 0.00 0.00 0.00 0.98
2582 2770 6.693315 TTAGCTTGCCCTGTGATTTAATAC 57.307 37.500 0.00 0.00 0.00 1.89
2583 2771 4.860022 AGCTTGCCCTGTGATTTAATACT 58.140 39.130 0.00 0.00 0.00 2.12
2584 2772 5.264395 AGCTTGCCCTGTGATTTAATACTT 58.736 37.500 0.00 0.00 0.00 2.24
2585 2773 6.423182 AGCTTGCCCTGTGATTTAATACTTA 58.577 36.000 0.00 0.00 0.00 2.24
2586 2774 7.062957 AGCTTGCCCTGTGATTTAATACTTAT 58.937 34.615 0.00 0.00 0.00 1.73
2587 2775 7.561356 AGCTTGCCCTGTGATTTAATACTTATT 59.439 33.333 0.00 0.00 0.00 1.40
2588 2776 7.649306 GCTTGCCCTGTGATTTAATACTTATTG 59.351 37.037 0.00 0.00 0.00 1.90
2589 2777 8.815565 TTGCCCTGTGATTTAATACTTATTGA 57.184 30.769 0.00 0.00 0.00 2.57
2590 2778 8.815565 TGCCCTGTGATTTAATACTTATTGAA 57.184 30.769 0.00 0.00 0.00 2.69
2591 2779 9.249053 TGCCCTGTGATTTAATACTTATTGAAA 57.751 29.630 0.00 0.00 0.00 2.69
2622 2810 8.704849 TTTTTCCATTTTAGAAGAGATCCACA 57.295 30.769 0.00 0.00 0.00 4.17
2623 2811 7.928307 TTTCCATTTTAGAAGAGATCCACAG 57.072 36.000 0.00 0.00 0.00 3.66
2624 2812 5.994250 TCCATTTTAGAAGAGATCCACAGG 58.006 41.667 0.00 0.00 0.00 4.00
2625 2813 5.726308 TCCATTTTAGAAGAGATCCACAGGA 59.274 40.000 0.00 0.00 35.55 3.86
2626 2814 6.215431 TCCATTTTAGAAGAGATCCACAGGAA 59.785 38.462 0.00 0.00 34.34 3.36
2627 2815 6.541641 CCATTTTAGAAGAGATCCACAGGAAG 59.458 42.308 0.00 0.00 34.34 3.46
2628 2816 6.688073 TTTTAGAAGAGATCCACAGGAAGT 57.312 37.500 0.00 0.00 34.34 3.01
2629 2817 5.923733 TTAGAAGAGATCCACAGGAAGTC 57.076 43.478 0.00 0.00 34.34 3.01
2630 2818 4.059773 AGAAGAGATCCACAGGAAGTCT 57.940 45.455 0.00 0.00 34.34 3.24
2631 2819 4.424842 AGAAGAGATCCACAGGAAGTCTT 58.575 43.478 11.11 11.11 39.20 3.01
2632 2820 4.843516 AGAAGAGATCCACAGGAAGTCTTT 59.156 41.667 12.08 0.00 37.70 2.52
2633 2821 6.019748 AGAAGAGATCCACAGGAAGTCTTTA 58.980 40.000 12.08 0.00 37.70 1.85
2634 2822 6.671779 AGAAGAGATCCACAGGAAGTCTTTAT 59.328 38.462 12.08 5.04 37.70 1.40
2635 2823 6.882768 AGAGATCCACAGGAAGTCTTTATT 57.117 37.500 0.00 0.00 34.34 1.40
2636 2824 6.883744 AGAGATCCACAGGAAGTCTTTATTC 58.116 40.000 0.00 0.00 34.34 1.75
2637 2825 6.671779 AGAGATCCACAGGAAGTCTTTATTCT 59.328 38.462 0.00 0.00 34.34 2.40
2638 2826 7.181845 AGAGATCCACAGGAAGTCTTTATTCTT 59.818 37.037 0.00 0.00 34.34 2.52
2639 2827 8.380742 AGATCCACAGGAAGTCTTTATTCTTA 57.619 34.615 0.00 0.00 34.34 2.10
2640 2828 8.261522 AGATCCACAGGAAGTCTTTATTCTTAC 58.738 37.037 0.00 0.00 34.34 2.34
2641 2829 6.708285 TCCACAGGAAGTCTTTATTCTTACC 58.292 40.000 0.00 0.00 0.00 2.85
2642 2830 6.500751 TCCACAGGAAGTCTTTATTCTTACCT 59.499 38.462 0.00 0.00 0.00 3.08
2643 2831 6.595716 CCACAGGAAGTCTTTATTCTTACCTG 59.404 42.308 0.00 0.00 40.46 4.00
2644 2832 6.092807 CACAGGAAGTCTTTATTCTTACCTGC 59.907 42.308 0.00 0.00 39.54 4.85
2645 2833 6.173339 CAGGAAGTCTTTATTCTTACCTGCA 58.827 40.000 0.00 0.00 35.06 4.41
2646 2834 6.655003 CAGGAAGTCTTTATTCTTACCTGCAA 59.345 38.462 0.00 0.00 35.06 4.08
2647 2835 7.337942 CAGGAAGTCTTTATTCTTACCTGCAAT 59.662 37.037 0.00 0.00 35.06 3.56
2648 2836 7.337942 AGGAAGTCTTTATTCTTACCTGCAATG 59.662 37.037 0.00 0.00 0.00 2.82
2649 2837 7.121315 GGAAGTCTTTATTCTTACCTGCAATGT 59.879 37.037 0.00 0.00 0.00 2.71
2650 2838 7.617041 AGTCTTTATTCTTACCTGCAATGTC 57.383 36.000 0.00 0.00 0.00 3.06
2651 2839 7.398024 AGTCTTTATTCTTACCTGCAATGTCT 58.602 34.615 0.00 0.00 0.00 3.41
2652 2840 7.885399 AGTCTTTATTCTTACCTGCAATGTCTT 59.115 33.333 0.00 0.00 0.00 3.01
2653 2841 7.965107 GTCTTTATTCTTACCTGCAATGTCTTG 59.035 37.037 0.00 0.00 35.36 3.02
2664 2852 3.570926 CAATGTCTTGCTTGTGCTGAT 57.429 42.857 0.00 0.00 40.48 2.90
2665 2853 3.909430 CAATGTCTTGCTTGTGCTGATT 58.091 40.909 0.00 0.00 40.48 2.57
2666 2854 4.304110 CAATGTCTTGCTTGTGCTGATTT 58.696 39.130 0.00 0.00 40.48 2.17
2667 2855 4.595762 ATGTCTTGCTTGTGCTGATTTT 57.404 36.364 0.00 0.00 40.48 1.82
2668 2856 4.389890 TGTCTTGCTTGTGCTGATTTTT 57.610 36.364 0.00 0.00 40.48 1.94
2669 2857 4.362279 TGTCTTGCTTGTGCTGATTTTTC 58.638 39.130 0.00 0.00 40.48 2.29
2670 2858 4.098349 TGTCTTGCTTGTGCTGATTTTTCT 59.902 37.500 0.00 0.00 40.48 2.52
2671 2859 5.045872 GTCTTGCTTGTGCTGATTTTTCTT 58.954 37.500 0.00 0.00 40.48 2.52
2672 2860 5.174579 GTCTTGCTTGTGCTGATTTTTCTTC 59.825 40.000 0.00 0.00 40.48 2.87
2673 2861 4.924305 TGCTTGTGCTGATTTTTCTTCT 57.076 36.364 0.00 0.00 40.48 2.85
2674 2862 5.266733 TGCTTGTGCTGATTTTTCTTCTT 57.733 34.783 0.00 0.00 40.48 2.52
2675 2863 5.045215 TGCTTGTGCTGATTTTTCTTCTTG 58.955 37.500 0.00 0.00 40.48 3.02
2676 2864 4.084693 GCTTGTGCTGATTTTTCTTCTTGC 60.085 41.667 0.00 0.00 36.03 4.01
2677 2865 4.652421 TGTGCTGATTTTTCTTCTTGCA 57.348 36.364 0.00 0.00 0.00 4.08
2678 2866 5.204409 TGTGCTGATTTTTCTTCTTGCAT 57.796 34.783 0.00 0.00 0.00 3.96
2679 2867 6.330004 TGTGCTGATTTTTCTTCTTGCATA 57.670 33.333 0.00 0.00 0.00 3.14
2680 2868 6.747125 TGTGCTGATTTTTCTTCTTGCATAA 58.253 32.000 0.00 0.00 0.00 1.90
2681 2869 6.864685 TGTGCTGATTTTTCTTCTTGCATAAG 59.135 34.615 3.48 3.48 35.16 1.73
2682 2870 6.865205 GTGCTGATTTTTCTTCTTGCATAAGT 59.135 34.615 8.65 0.00 35.38 2.24
2683 2871 6.864685 TGCTGATTTTTCTTCTTGCATAAGTG 59.135 34.615 8.65 0.00 35.38 3.16
2699 2887 3.715628 AAGTGCAAGTTAAAGCAGTGG 57.284 42.857 6.84 0.00 43.18 4.00
2700 2888 2.654863 AGTGCAAGTTAAAGCAGTGGT 58.345 42.857 5.60 0.00 42.44 4.16
2701 2889 3.023832 AGTGCAAGTTAAAGCAGTGGTT 58.976 40.909 0.63 0.63 42.44 3.67
2702 2890 3.447229 AGTGCAAGTTAAAGCAGTGGTTT 59.553 39.130 22.69 22.69 42.44 3.27
2703 2891 4.642885 AGTGCAAGTTAAAGCAGTGGTTTA 59.357 37.500 20.69 20.69 42.44 2.01
2704 2892 5.126384 AGTGCAAGTTAAAGCAGTGGTTTAA 59.874 36.000 27.90 27.90 42.44 1.52
2718 2906 9.227777 AGCAGTGGTTTAACTAGTTTAATAAGG 57.772 33.333 14.49 3.16 29.47 2.69
2719 2907 9.006839 GCAGTGGTTTAACTAGTTTAATAAGGT 57.993 33.333 14.49 0.00 29.47 3.50
2734 2922 9.297586 GTTTAATAAGGTATTGGTTTAGCTTGC 57.702 33.333 0.00 0.00 39.53 4.01
2735 2923 6.465439 AATAAGGTATTGGTTTAGCTTGCC 57.535 37.500 0.00 0.00 39.53 4.52
2736 2924 2.735151 AGGTATTGGTTTAGCTTGCCC 58.265 47.619 0.00 0.00 0.00 5.36
2737 2925 2.311841 AGGTATTGGTTTAGCTTGCCCT 59.688 45.455 0.00 0.00 0.00 5.19
2738 2926 2.427095 GGTATTGGTTTAGCTTGCCCTG 59.573 50.000 0.00 0.00 0.00 4.45
2739 2927 2.309136 ATTGGTTTAGCTTGCCCTGT 57.691 45.000 0.00 0.00 0.00 4.00
2740 2928 1.327303 TTGGTTTAGCTTGCCCTGTG 58.673 50.000 0.00 0.00 0.00 3.66
2741 2929 0.476338 TGGTTTAGCTTGCCCTGTGA 59.524 50.000 0.00 0.00 0.00 3.58
2807 2995 8.261522 AGATCCACAGGAAGTCTTTATTCTTAC 58.738 37.037 0.00 0.00 34.34 2.34
2839 3027 5.174579 GTCTTGCTTGTGCTGATTTTTCTTC 59.825 40.000 0.00 0.00 40.48 2.87
2999 3191 5.892348 ACCTCCCACTTTGTTGATTCTTAT 58.108 37.500 0.00 0.00 0.00 1.73
3103 3298 9.464714 TCAATGATTAGCTTCGATAGTAGTTTC 57.535 33.333 0.00 0.00 35.72 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 7.190335 TGCATAAGAAGGTAGCCTTTTACTA 57.810 36.000 1.64 0.00 44.82 1.82
78 82 4.813027 ACAAAGCCAACAAGATGCATAAG 58.187 39.130 0.00 0.00 0.00 1.73
81 85 3.322828 AGAACAAAGCCAACAAGATGCAT 59.677 39.130 0.00 0.00 0.00 3.96
90 94 6.330278 ACAAGAACTAAAGAACAAAGCCAAC 58.670 36.000 0.00 0.00 0.00 3.77
164 170 5.070313 TCAACCTCTATACACATGCTGCATA 59.930 40.000 15.78 0.00 0.00 3.14
292 303 4.228010 AGGATTTAAGAGAGGGGTCTAGC 58.772 47.826 0.00 0.00 0.00 3.42
297 308 3.916989 ACACAAGGATTTAAGAGAGGGGT 59.083 43.478 0.00 0.00 0.00 4.95
307 318 7.648039 AAACACTACCAAACACAAGGATTTA 57.352 32.000 0.00 0.00 0.00 1.40
401 417 1.227089 CTGCCCCGATCTGTTCTCG 60.227 63.158 0.00 0.00 35.92 4.04
459 479 0.108804 CGCACGTGACTTACCATCCT 60.109 55.000 22.23 0.00 0.00 3.24
489 516 0.402121 AAAAGAAAGCCCCTCTCGCT 59.598 50.000 0.00 0.00 38.53 4.93
514 542 2.360350 ACAACGCATGAGGCCCAG 60.360 61.111 0.00 0.00 40.31 4.45
534 562 4.408821 TTTCGCGAGGCCCAGCAT 62.409 61.111 18.51 0.00 0.00 3.79
660 691 6.114221 TCTTCAATATTTTTAAGGACGCGG 57.886 37.500 12.47 0.00 0.00 6.46
854 885 3.003689 AGCCACAAAGAAAGTGATCAACG 59.996 43.478 0.00 0.00 39.30 4.10
898 929 1.835494 TCTGACCGTCTCCCAAGTAG 58.165 55.000 0.00 0.00 0.00 2.57
1003 1037 4.096003 ATGGGAAGACGGCGGGTG 62.096 66.667 13.24 0.00 0.00 4.61
1005 1039 4.856801 CCATGGGAAGACGGCGGG 62.857 72.222 13.24 0.00 0.00 6.13
1011 1045 2.190578 CGGAGGCCATGGGAAGAC 59.809 66.667 15.13 0.00 0.00 3.01
1012 1046 3.797353 GCGGAGGCCATGGGAAGA 61.797 66.667 15.13 0.00 0.00 2.87
1099 1164 1.135402 GGATTGCGCTTGGGTAGTTTG 60.135 52.381 9.73 0.00 0.00 2.93
1212 1329 2.124901 CTTTGGCGGCGGGATGTA 60.125 61.111 9.78 0.00 0.00 2.29
1532 1649 0.110486 AGTTCATGGAAGGTTGCGGT 59.890 50.000 0.00 0.00 0.00 5.68
1670 1787 3.521947 AGAGTATACGCTGGGAACAAC 57.478 47.619 8.46 0.00 42.06 3.32
1709 1826 0.401356 TCAGGCTTCTGGCACAATGA 59.599 50.000 0.00 0.00 44.01 2.57
2002 2119 4.806247 CCTCGAATCAACTCATTGTAGGAC 59.194 45.833 0.00 0.00 37.11 3.85
2189 2306 2.418334 CCACTCTACCGCTCCTTTTACC 60.418 54.545 0.00 0.00 0.00 2.85
2201 2318 1.000955 CACACCACACTCCACTCTACC 59.999 57.143 0.00 0.00 0.00 3.18
2274 2391 1.268743 GCCCGATATCAACAAGCTTGC 60.269 52.381 26.27 7.12 0.00 4.01
2302 2419 2.504367 CATCCTCAAACCCTTTCGTGT 58.496 47.619 0.00 0.00 0.00 4.49
2400 2528 4.331968 ACTTTTCAGTCTTGTGTTCCACA 58.668 39.130 0.00 0.00 43.02 4.17
2597 2785 8.704849 TGTGGATCTCTTCTAAAATGGAAAAA 57.295 30.769 0.00 0.00 0.00 1.94
2598 2786 7.394359 CCTGTGGATCTCTTCTAAAATGGAAAA 59.606 37.037 0.00 0.00 0.00 2.29
2599 2787 6.886459 CCTGTGGATCTCTTCTAAAATGGAAA 59.114 38.462 0.00 0.00 0.00 3.13
2600 2788 6.215431 TCCTGTGGATCTCTTCTAAAATGGAA 59.785 38.462 0.00 0.00 0.00 3.53
2601 2789 5.726308 TCCTGTGGATCTCTTCTAAAATGGA 59.274 40.000 0.00 0.00 0.00 3.41
2602 2790 5.994250 TCCTGTGGATCTCTTCTAAAATGG 58.006 41.667 0.00 0.00 0.00 3.16
2603 2791 7.108847 ACTTCCTGTGGATCTCTTCTAAAATG 58.891 38.462 0.00 0.00 0.00 2.32
2604 2792 7.181845 AGACTTCCTGTGGATCTCTTCTAAAAT 59.818 37.037 0.00 0.00 0.00 1.82
2605 2793 6.498651 AGACTTCCTGTGGATCTCTTCTAAAA 59.501 38.462 0.00 0.00 0.00 1.52
2606 2794 6.019748 AGACTTCCTGTGGATCTCTTCTAAA 58.980 40.000 0.00 0.00 0.00 1.85
2607 2795 5.584913 AGACTTCCTGTGGATCTCTTCTAA 58.415 41.667 0.00 0.00 0.00 2.10
2608 2796 5.199982 AGACTTCCTGTGGATCTCTTCTA 57.800 43.478 0.00 0.00 0.00 2.10
2609 2797 4.059773 AGACTTCCTGTGGATCTCTTCT 57.940 45.455 0.00 0.00 0.00 2.85
2610 2798 4.817318 AAGACTTCCTGTGGATCTCTTC 57.183 45.455 0.00 0.00 27.92 2.87
2611 2799 6.882768 ATAAAGACTTCCTGTGGATCTCTT 57.117 37.500 0.00 0.00 32.53 2.85
2612 2800 6.671779 AGAATAAAGACTTCCTGTGGATCTCT 59.328 38.462 0.00 0.00 0.00 3.10
2613 2801 6.883744 AGAATAAAGACTTCCTGTGGATCTC 58.116 40.000 0.00 0.00 0.00 2.75
2614 2802 6.882768 AGAATAAAGACTTCCTGTGGATCT 57.117 37.500 0.00 0.00 0.00 2.75
2615 2803 7.496263 GGTAAGAATAAAGACTTCCTGTGGATC 59.504 40.741 0.00 0.00 0.00 3.36
2616 2804 7.182930 AGGTAAGAATAAAGACTTCCTGTGGAT 59.817 37.037 0.00 0.00 0.00 3.41
2617 2805 6.500751 AGGTAAGAATAAAGACTTCCTGTGGA 59.499 38.462 0.00 0.00 0.00 4.02
2618 2806 6.595716 CAGGTAAGAATAAAGACTTCCTGTGG 59.404 42.308 0.91 0.00 37.07 4.17
2619 2807 6.092807 GCAGGTAAGAATAAAGACTTCCTGTG 59.907 42.308 13.75 0.00 39.94 3.66
2620 2808 6.174049 GCAGGTAAGAATAAAGACTTCCTGT 58.826 40.000 13.75 0.00 39.94 4.00
2621 2809 6.173339 TGCAGGTAAGAATAAAGACTTCCTG 58.827 40.000 9.77 9.77 40.28 3.86
2622 2810 6.374417 TGCAGGTAAGAATAAAGACTTCCT 57.626 37.500 0.00 0.00 0.00 3.36
2623 2811 7.121315 ACATTGCAGGTAAGAATAAAGACTTCC 59.879 37.037 0.00 0.00 0.00 3.46
2624 2812 8.045176 ACATTGCAGGTAAGAATAAAGACTTC 57.955 34.615 0.00 0.00 0.00 3.01
2625 2813 7.885399 AGACATTGCAGGTAAGAATAAAGACTT 59.115 33.333 0.00 0.00 0.00 3.01
2626 2814 7.398024 AGACATTGCAGGTAAGAATAAAGACT 58.602 34.615 0.00 0.00 0.00 3.24
2627 2815 7.617041 AGACATTGCAGGTAAGAATAAAGAC 57.383 36.000 0.00 0.00 0.00 3.01
2628 2816 8.044060 CAAGACATTGCAGGTAAGAATAAAGA 57.956 34.615 0.00 0.00 0.00 2.52
2644 2832 3.570926 ATCAGCACAAGCAAGACATTG 57.429 42.857 0.00 0.00 45.49 2.82
2645 2833 4.595762 AAATCAGCACAAGCAAGACATT 57.404 36.364 0.00 0.00 45.49 2.71
2646 2834 4.595762 AAAATCAGCACAAGCAAGACAT 57.404 36.364 0.00 0.00 45.49 3.06
2647 2835 4.098349 AGAAAAATCAGCACAAGCAAGACA 59.902 37.500 0.00 0.00 45.49 3.41
2648 2836 4.614946 AGAAAAATCAGCACAAGCAAGAC 58.385 39.130 0.00 0.00 45.49 3.01
2649 2837 4.924305 AGAAAAATCAGCACAAGCAAGA 57.076 36.364 0.00 0.00 45.49 3.02
2650 2838 5.287226 AGAAGAAAAATCAGCACAAGCAAG 58.713 37.500 0.00 0.00 45.49 4.01
2651 2839 5.266733 AGAAGAAAAATCAGCACAAGCAA 57.733 34.783 0.00 0.00 45.49 3.91
2652 2840 4.924305 AGAAGAAAAATCAGCACAAGCA 57.076 36.364 0.00 0.00 45.49 3.91
2653 2841 4.084693 GCAAGAAGAAAAATCAGCACAAGC 60.085 41.667 0.00 0.00 42.56 4.01
2654 2842 5.045215 TGCAAGAAGAAAAATCAGCACAAG 58.955 37.500 0.00 0.00 0.00 3.16
2655 2843 5.008619 TGCAAGAAGAAAAATCAGCACAA 57.991 34.783 0.00 0.00 0.00 3.33
2656 2844 4.652421 TGCAAGAAGAAAAATCAGCACA 57.348 36.364 0.00 0.00 0.00 4.57
2657 2845 6.865205 ACTTATGCAAGAAGAAAAATCAGCAC 59.135 34.615 16.35 0.00 34.47 4.40
2658 2846 6.864685 CACTTATGCAAGAAGAAAAATCAGCA 59.135 34.615 16.35 0.00 35.60 4.41
2659 2847 7.274442 CACTTATGCAAGAAGAAAAATCAGC 57.726 36.000 16.35 0.00 35.60 4.26
2676 2864 5.156355 CCACTGCTTTAACTTGCACTTATG 58.844 41.667 0.00 0.00 35.20 1.90
2677 2865 4.827284 ACCACTGCTTTAACTTGCACTTAT 59.173 37.500 0.00 0.00 35.20 1.73
2678 2866 4.204012 ACCACTGCTTTAACTTGCACTTA 58.796 39.130 0.00 0.00 35.20 2.24
2679 2867 3.023832 ACCACTGCTTTAACTTGCACTT 58.976 40.909 0.00 0.00 35.20 3.16
2680 2868 2.654863 ACCACTGCTTTAACTTGCACT 58.345 42.857 0.00 0.00 35.20 4.40
2681 2869 3.436700 AACCACTGCTTTAACTTGCAC 57.563 42.857 0.00 0.00 35.20 4.57
2682 2870 5.126384 AGTTAAACCACTGCTTTAACTTGCA 59.874 36.000 13.27 0.00 45.71 4.08
2683 2871 5.588240 AGTTAAACCACTGCTTTAACTTGC 58.412 37.500 13.27 0.00 45.71 4.01
2684 2872 7.927048 ACTAGTTAAACCACTGCTTTAACTTG 58.073 34.615 20.10 19.62 45.71 3.16
2685 2873 8.515695 AACTAGTTAAACCACTGCTTTAACTT 57.484 30.769 20.10 7.42 45.71 2.66
2692 2880 9.227777 CCTTATTAAACTAGTTAAACCACTGCT 57.772 33.333 8.92 0.00 35.33 4.24
2693 2881 9.006839 ACCTTATTAAACTAGTTAAACCACTGC 57.993 33.333 8.92 0.00 35.33 4.40
2708 2896 9.297586 GCAAGCTAAACCAATACCTTATTAAAC 57.702 33.333 0.00 0.00 0.00 2.01
2709 2897 8.471609 GGCAAGCTAAACCAATACCTTATTAAA 58.528 33.333 0.00 0.00 0.00 1.52
2710 2898 7.068962 GGGCAAGCTAAACCAATACCTTATTAA 59.931 37.037 0.00 0.00 0.00 1.40
2711 2899 6.548251 GGGCAAGCTAAACCAATACCTTATTA 59.452 38.462 0.00 0.00 0.00 0.98
2712 2900 5.362717 GGGCAAGCTAAACCAATACCTTATT 59.637 40.000 0.00 0.00 0.00 1.40
2713 2901 4.893524 GGGCAAGCTAAACCAATACCTTAT 59.106 41.667 0.00 0.00 0.00 1.73
2714 2902 4.017867 AGGGCAAGCTAAACCAATACCTTA 60.018 41.667 0.00 0.00 0.00 2.69
2715 2903 3.096852 GGGCAAGCTAAACCAATACCTT 58.903 45.455 0.00 0.00 0.00 3.50
2716 2904 2.311841 AGGGCAAGCTAAACCAATACCT 59.688 45.455 0.00 0.00 0.00 3.08
2717 2905 2.427095 CAGGGCAAGCTAAACCAATACC 59.573 50.000 0.00 0.00 0.00 2.73
2718 2906 3.089284 ACAGGGCAAGCTAAACCAATAC 58.911 45.455 0.00 0.00 0.00 1.89
2719 2907 3.088532 CACAGGGCAAGCTAAACCAATA 58.911 45.455 0.00 0.00 0.00 1.90
2720 2908 1.895131 CACAGGGCAAGCTAAACCAAT 59.105 47.619 0.00 0.00 0.00 3.16
2721 2909 1.133637 TCACAGGGCAAGCTAAACCAA 60.134 47.619 0.00 0.00 0.00 3.67
2722 2910 0.476338 TCACAGGGCAAGCTAAACCA 59.524 50.000 0.00 0.00 0.00 3.67
2723 2911 1.474077 CATCACAGGGCAAGCTAAACC 59.526 52.381 0.00 0.00 0.00 3.27
2724 2912 2.162681 ACATCACAGGGCAAGCTAAAC 58.837 47.619 0.00 0.00 0.00 2.01
2725 2913 2.584835 ACATCACAGGGCAAGCTAAA 57.415 45.000 0.00 0.00 0.00 1.85
2726 2914 3.712016 TTACATCACAGGGCAAGCTAA 57.288 42.857 0.00 0.00 0.00 3.09
2727 2915 3.931907 ATTACATCACAGGGCAAGCTA 57.068 42.857 0.00 0.00 0.00 3.32
2728 2916 2.814805 ATTACATCACAGGGCAAGCT 57.185 45.000 0.00 0.00 0.00 3.74
2729 2917 3.545703 AGTATTACATCACAGGGCAAGC 58.454 45.455 0.00 0.00 0.00 4.01
2730 2918 7.498900 TCAATAAGTATTACATCACAGGGCAAG 59.501 37.037 0.00 0.00 30.46 4.01
2731 2919 7.342581 TCAATAAGTATTACATCACAGGGCAA 58.657 34.615 0.00 0.00 30.46 4.52
2732 2920 6.894682 TCAATAAGTATTACATCACAGGGCA 58.105 36.000 0.00 0.00 30.46 5.36
2733 2921 7.801716 TTCAATAAGTATTACATCACAGGGC 57.198 36.000 0.00 0.00 30.46 5.19
2767 2955 6.215431 TCCTGTGGATCTCTTCTAAAATGGAA 59.785 38.462 0.00 0.00 0.00 3.53
2839 3027 9.158233 ACATTCATAAAAGGAATTTGATGCAAG 57.842 29.630 0.00 0.00 32.86 4.01
3103 3298 5.358298 GTTTGGCAAACTAGTAACCTGAG 57.642 43.478 30.54 0.00 38.35 3.35


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

AutoCloner maintained by Alex Coulton.