Multiple sequence alignment - TraesCS3A01G273900

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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 TraesCS3A01G273900 chr3A 100.000 4566 0 0 1 4566 502514651 502510086 0.000000e+00 8432
1 TraesCS3A01G273900 chr3B 91.103 2158 125 22 517 2656 493658420 493656312 0.000000e+00 2859
2 TraesCS3A01G273900 chr3B 89.172 1376 87 25 2691 4028 493656219 493654868 0.000000e+00 1659
3 TraesCS3A01G273900 chr3B 87.861 519 58 5 4 519 371983319 371982803 5.050000e-169 604
4 TraesCS3A01G273900 chr3B 87.179 507 41 13 4064 4566 493654763 493654277 5.160000e-154 555
5 TraesCS3A01G273900 chr3D 90.065 1993 132 25 673 2656 378581451 378579516 0.000000e+00 2523
6 TraesCS3A01G273900 chr3D 90.548 1259 72 18 2691 3920 378579423 378578183 0.000000e+00 1622
7 TraesCS3A01G273900 chr3D 87.850 321 20 7 4252 4566 378577798 378577491 4.340000e-95 359
8 TraesCS3A01G273900 chr3D 89.474 190 10 2 4021 4210 378577981 378577802 9.880000e-57 231
9 TraesCS3A01G273900 chr7D 88.417 518 57 3 4 519 391314465 391313949 5.020000e-174 621
10 TraesCS3A01G273900 chr4D 87.908 521 60 3 2 519 254699529 254699009 1.090000e-170 610
11 TraesCS3A01G273900 chr4D 87.379 515 62 3 8 519 494649379 494648865 5.090000e-164 588
12 TraesCS3A01G273900 chr4B 87.308 520 61 4 2 519 424068206 424067690 1.410000e-164 590
13 TraesCS3A01G273900 chr5D 87.189 523 60 6 3 519 220486359 220486880 5.090000e-164 588
14 TraesCS3A01G273900 chr1D 87.115 520 62 5 3 519 298650424 298649907 6.580000e-163 584
15 TraesCS3A01G273900 chr1D 86.898 519 65 3 4 519 285015236 285014718 3.060000e-161 579
16 TraesCS3A01G273900 chr1B 86.207 522 66 5 4 519 141463343 141462822 1.110000e-155 560


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 TraesCS3A01G273900 chr3A 502510086 502514651 4565 True 8432.00 8432 100.000000 1 4566 1 chr3A.!!$R1 4565
1 TraesCS3A01G273900 chr3B 493654277 493658420 4143 True 1691.00 2859 89.151333 517 4566 3 chr3B.!!$R2 4049
2 TraesCS3A01G273900 chr3B 371982803 371983319 516 True 604.00 604 87.861000 4 519 1 chr3B.!!$R1 515
3 TraesCS3A01G273900 chr3D 378577491 378581451 3960 True 1183.75 2523 89.484250 673 4566 4 chr3D.!!$R1 3893
4 TraesCS3A01G273900 chr7D 391313949 391314465 516 True 621.00 621 88.417000 4 519 1 chr7D.!!$R1 515
5 TraesCS3A01G273900 chr4D 254699009 254699529 520 True 610.00 610 87.908000 2 519 1 chr4D.!!$R1 517
6 TraesCS3A01G273900 chr4D 494648865 494649379 514 True 588.00 588 87.379000 8 519 1 chr4D.!!$R2 511
7 TraesCS3A01G273900 chr4B 424067690 424068206 516 True 590.00 590 87.308000 2 519 1 chr4B.!!$R1 517
8 TraesCS3A01G273900 chr5D 220486359 220486880 521 False 588.00 588 87.189000 3 519 1 chr5D.!!$F1 516
9 TraesCS3A01G273900 chr1D 298649907 298650424 517 True 584.00 584 87.115000 3 519 1 chr1D.!!$R2 516
10 TraesCS3A01G273900 chr1D 285014718 285015236 518 True 579.00 579 86.898000 4 519 1 chr1D.!!$R1 515
11 TraesCS3A01G273900 chr1B 141462822 141463343 521 True 560.00 560 86.207000 4 519 1 chr1B.!!$R1 515

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
694 703 0.040942 TCTCTGCTTCTCTCCAGCCT 59.959 55.0 0.0 0.0 36.33 4.58 F
724 733 0.179045 TAGACCCGTACTCCCGTAGC 60.179 60.0 0.0 0.0 0.00 3.58 F
1306 1333 0.322906 AAGAGCTTAACAGGCAGGGC 60.323 55.0 0.0 0.0 0.00 5.19 F
2642 2679 0.902531 CTCGTGTCCCTAACCCACAT 59.097 55.0 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1831 1.829849 TCATGACTGAAGGAGGAGCAG 59.170 52.381 0.00 0.00 35.81 4.24 R
2602 2639 2.230508 GAGTGACCGGAACATACTGTGA 59.769 50.000 9.46 0.00 0.00 3.58 R
3102 3208 1.074752 GAGAAAGAGCAACAGGAGCG 58.925 55.000 0.00 0.00 37.01 5.03 R
4387 4703 0.099082 GCAGAGAATTCAGCAGCTGC 59.901 55.000 31.53 31.53 41.38 5.25 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
60 61 1.466025 GGATACCGTACCCGCATGGA 61.466 60.000 0.00 0.00 37.49 3.41
61 62 0.606604 GATACCGTACCCGCATGGAT 59.393 55.000 0.00 0.00 37.49 3.41
116 117 6.364945 AGTATTCGTACCCTACTCGTTAAC 57.635 41.667 0.00 0.00 0.00 2.01
129 130 2.764572 CTCGTTAACTCATGGGTAGGGT 59.235 50.000 0.00 0.00 0.00 4.34
140 143 2.143602 TGGGTAGGGTACGGGTATAGT 58.856 52.381 0.00 0.00 0.00 2.12
141 144 2.517980 TGGGTAGGGTACGGGTATAGTT 59.482 50.000 0.00 0.00 0.00 2.24
146 149 4.476628 AGGGTACGGGTATAGTTTTGTG 57.523 45.455 0.00 0.00 0.00 3.33
189 194 5.339200 CCCTGTCCCTTTATACTGACATGTT 60.339 44.000 0.00 0.00 37.14 2.71
194 199 6.541278 GTCCCTTTATACTGACATGTTTACCC 59.459 42.308 0.00 0.00 0.00 3.69
212 217 4.986054 ACCCTACCTGTGAAATGTGTTA 57.014 40.909 0.00 0.00 0.00 2.41
230 235 8.668510 ATGTGTTATGAGATTGTGAACCTATC 57.331 34.615 0.00 0.00 0.00 2.08
298 303 7.914427 ATGTACCCATCTATCTGTTACTGAA 57.086 36.000 0.00 0.00 0.00 3.02
506 515 6.325286 TGGTATGTGTATGGTATTGCTCTACA 59.675 38.462 0.00 0.00 0.00 2.74
509 518 4.158949 TGTGTATGGTATTGCTCTACACGT 59.841 41.667 0.00 0.00 43.11 4.49
632 641 2.588989 CCTCCTTGCTGGCTCCTC 59.411 66.667 0.00 0.00 35.26 3.71
636 645 4.120755 CTTGCTGGCTCCTCCCCC 62.121 72.222 0.00 0.00 0.00 5.40
694 703 0.040942 TCTCTGCTTCTCTCCAGCCT 59.959 55.000 0.00 0.00 36.33 4.58
712 721 3.818787 CCGACCACCGTAGACCCG 61.819 72.222 0.00 0.00 36.31 5.28
713 722 3.058160 CGACCACCGTAGACCCGT 61.058 66.667 0.00 0.00 0.00 5.28
714 723 1.745115 CGACCACCGTAGACCCGTA 60.745 63.158 0.00 0.00 0.00 4.02
715 724 1.803289 GACCACCGTAGACCCGTAC 59.197 63.158 0.00 0.00 0.00 3.67
716 725 0.678048 GACCACCGTAGACCCGTACT 60.678 60.000 0.00 0.00 0.00 2.73
717 726 0.678048 ACCACCGTAGACCCGTACTC 60.678 60.000 0.00 0.00 0.00 2.59
718 727 1.379642 CCACCGTAGACCCGTACTCC 61.380 65.000 0.00 0.00 0.00 3.85
719 728 1.077429 ACCGTAGACCCGTACTCCC 60.077 63.158 0.00 0.00 0.00 4.30
724 733 0.179045 TAGACCCGTACTCCCGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
786 795 1.829096 GAGGAGCTCCCGGGTACTC 60.829 68.421 29.54 27.45 44.77 2.59
797 806 1.446366 GGGTACTCCGGCAGAATCC 59.554 63.158 0.00 1.65 33.83 3.01
798 807 1.335132 GGGTACTCCGGCAGAATCCA 61.335 60.000 0.00 0.00 33.83 3.41
804 813 2.162681 CTCCGGCAGAATCCAAAAACT 58.837 47.619 0.00 0.00 0.00 2.66
821 830 1.981256 ACTGAGCCAAATTGTCGGTT 58.019 45.000 0.00 0.00 0.00 4.44
822 831 2.306847 ACTGAGCCAAATTGTCGGTTT 58.693 42.857 0.00 0.00 0.00 3.27
823 832 2.693074 ACTGAGCCAAATTGTCGGTTTT 59.307 40.909 0.00 0.00 0.00 2.43
824 833 3.132111 ACTGAGCCAAATTGTCGGTTTTT 59.868 39.130 0.00 0.00 0.00 1.94
1243 1266 1.603739 GTGCTCCCCCACAGGTTTC 60.604 63.158 0.00 0.00 35.80 2.78
1306 1333 0.322906 AAGAGCTTAACAGGCAGGGC 60.323 55.000 0.00 0.00 0.00 5.19
1364 1394 2.266554 CACTTTCAGAGAGCCATCGTC 58.733 52.381 0.00 0.00 0.00 4.20
1382 1412 2.037847 ATGCCCAACCTGAAGCCC 59.962 61.111 0.00 0.00 0.00 5.19
1391 1421 2.598787 CCTGAAGCCCCCGGTTACA 61.599 63.158 0.00 0.00 0.00 2.41
1398 1428 1.227913 CCCCCGGTTACAACAACGT 60.228 57.895 0.00 0.00 0.00 3.99
1428 1458 2.561569 TCGCGTACAGAGATGAGATCA 58.438 47.619 5.77 0.00 0.00 2.92
1430 1460 3.058639 TCGCGTACAGAGATGAGATCATG 60.059 47.826 5.77 0.00 36.57 3.07
1502 1532 2.656069 GGACAGCACTAGCCCGGAA 61.656 63.158 0.73 0.00 43.56 4.30
1514 1544 5.823045 CACTAGCCCGGAAGAAATTAAGATT 59.177 40.000 0.73 0.00 0.00 2.40
1538 1568 1.492176 AGTACGGATTCTCCCTACCGA 59.508 52.381 11.27 0.00 46.94 4.69
1556 1586 4.142038 ACCGAAATTGGTTCTTTAGCTGT 58.858 39.130 0.00 0.00 39.99 4.40
1557 1587 4.583073 ACCGAAATTGGTTCTTTAGCTGTT 59.417 37.500 0.00 0.00 39.99 3.16
1558 1588 5.068591 ACCGAAATTGGTTCTTTAGCTGTTT 59.931 36.000 0.00 0.00 39.99 2.83
1559 1589 5.983118 CCGAAATTGGTTCTTTAGCTGTTTT 59.017 36.000 0.00 0.00 33.70 2.43
1560 1590 6.478673 CCGAAATTGGTTCTTTAGCTGTTTTT 59.521 34.615 0.00 0.00 33.70 1.94
1588 1621 5.826601 TTTTTGCTGTGTGTACTTCATGA 57.173 34.783 0.00 0.00 0.00 3.07
1593 1626 3.725895 GCTGTGTGTACTTCATGATTGCG 60.726 47.826 0.00 0.00 0.00 4.85
1598 1631 3.307242 GTGTACTTCATGATTGCGTCTCC 59.693 47.826 0.00 0.00 0.00 3.71
1635 1668 5.953571 TCTATATCTGTCTCCCAACTAGCA 58.046 41.667 0.00 0.00 0.00 3.49
1674 1707 5.631119 AGTCAGCCCTATTGTTTGTTAGTT 58.369 37.500 0.00 0.00 0.00 2.24
1687 1720 7.922505 TGTTTGTTAGTTTTGATGTGCATAC 57.077 32.000 0.00 0.00 0.00 2.39
1688 1721 7.484140 TGTTTGTTAGTTTTGATGTGCATACA 58.516 30.769 0.00 0.00 41.89 2.29
1719 1752 5.827666 AGTTTGTTACCACATTGTTAGTGC 58.172 37.500 0.00 0.00 35.69 4.40
1720 1753 5.358442 AGTTTGTTACCACATTGTTAGTGCA 59.642 36.000 0.00 0.00 35.69 4.57
1740 1773 7.786030 AGTGCATGTTAGAAGCTAGAATAAGA 58.214 34.615 0.00 0.00 0.00 2.10
1780 1813 6.302535 TGGTTATTCCCTTAACGATTCTGA 57.697 37.500 0.00 0.00 33.71 3.27
1781 1814 6.895782 TGGTTATTCCCTTAACGATTCTGAT 58.104 36.000 0.00 0.00 33.71 2.90
1798 1831 9.430838 CGATTCTGATTCATCTTGTAAATGTTC 57.569 33.333 1.09 0.00 0.00 3.18
2003 2039 2.290577 GCCTGTCCTTGAAGAGATGGTT 60.291 50.000 0.00 0.00 0.00 3.67
2058 2094 4.602340 TGTTCTTCTCCCTACACAGAAC 57.398 45.455 3.84 3.84 42.45 3.01
2096 2132 1.276421 TCTGCCAAGTTGGTCTCTAGC 59.724 52.381 22.85 7.36 40.46 3.42
2109 2145 7.616150 AGTTGGTCTCTAGCTTTACTTCAGATA 59.384 37.037 0.00 0.00 0.00 1.98
2123 2159 6.396829 ACTTCAGATATTAAATGGGCTTGC 57.603 37.500 0.00 0.00 0.00 4.01
2141 2177 1.068895 TGCCATTTGTTGCCTTGACAG 59.931 47.619 0.00 0.00 0.00 3.51
2146 2182 2.719531 TTGTTGCCTTGACAGTACCA 57.280 45.000 0.00 0.00 0.00 3.25
2149 2185 3.357203 TGTTGCCTTGACAGTACCAAAA 58.643 40.909 0.00 0.00 0.00 2.44
2212 2248 3.876914 CTGTACGGTCAATGCCAACATAT 59.123 43.478 0.00 0.00 34.62 1.78
2277 2314 3.295093 AGTCACAGATCCTCATGTCGAT 58.705 45.455 0.00 0.00 0.00 3.59
2416 2453 5.511234 AGAATCATGCAAAGAAGGTATGC 57.489 39.130 0.00 0.00 40.45 3.14
2420 2457 1.086696 TGCAAAGAAGGTATGCGCTC 58.913 50.000 9.73 0.00 42.91 5.03
2430 2467 4.342862 AGGTATGCGCTCTTACAATGAT 57.657 40.909 9.73 0.00 0.00 2.45
2432 2469 4.058124 GGTATGCGCTCTTACAATGATCA 58.942 43.478 9.73 0.00 0.00 2.92
2473 2510 6.576185 TCCCTATACGTGGTTCTTACATTTC 58.424 40.000 0.00 0.00 0.00 2.17
2474 2511 6.381994 TCCCTATACGTGGTTCTTACATTTCT 59.618 38.462 0.00 0.00 0.00 2.52
2476 2513 7.551617 CCCTATACGTGGTTCTTACATTTCTTT 59.448 37.037 0.00 0.00 0.00 2.52
2477 2514 8.943002 CCTATACGTGGTTCTTACATTTCTTTT 58.057 33.333 0.00 0.00 0.00 2.27
2478 2515 9.755064 CTATACGTGGTTCTTACATTTCTTTTG 57.245 33.333 0.00 0.00 0.00 2.44
2602 2639 2.549778 GCCAGTGCTGAAGAGAGAAACT 60.550 50.000 0.02 0.00 33.53 2.66
2625 2662 3.152261 CAGTATGTTCCGGTCACTCTC 57.848 52.381 0.00 0.00 0.00 3.20
2636 2673 1.201880 GGTCACTCTCGTGTCCCTAAC 59.798 57.143 0.00 0.00 41.60 2.34
2642 2679 0.902531 CTCGTGTCCCTAACCCACAT 59.097 55.000 0.00 0.00 0.00 3.21
2656 2694 4.021102 ACCCACATAAGTTTCCAGTCTG 57.979 45.455 0.00 0.00 0.00 3.51
2657 2695 2.749621 CCCACATAAGTTTCCAGTCTGC 59.250 50.000 0.00 0.00 0.00 4.26
2668 2763 2.398588 TCCAGTCTGCCCTACCATTAG 58.601 52.381 0.00 0.00 0.00 1.73
2672 2767 4.443034 CCAGTCTGCCCTACCATTAGTTAC 60.443 50.000 0.00 0.00 0.00 2.50
2674 2769 4.650131 AGTCTGCCCTACCATTAGTTACTC 59.350 45.833 0.00 0.00 0.00 2.59
2676 2771 4.894114 TCTGCCCTACCATTAGTTACTCTC 59.106 45.833 0.00 0.00 0.00 3.20
2677 2772 4.616553 TGCCCTACCATTAGTTACTCTCA 58.383 43.478 0.00 0.00 0.00 3.27
2678 2773 4.404715 TGCCCTACCATTAGTTACTCTCAC 59.595 45.833 0.00 0.00 0.00 3.51
2681 2776 5.892119 CCCTACCATTAGTTACTCTCACTGA 59.108 44.000 0.00 0.00 0.00 3.41
2682 2777 6.380274 CCCTACCATTAGTTACTCTCACTGAA 59.620 42.308 0.00 0.00 0.00 3.02
2683 2778 7.093465 CCCTACCATTAGTTACTCTCACTGAAA 60.093 40.741 0.00 0.00 0.00 2.69
2684 2779 8.478877 CCTACCATTAGTTACTCTCACTGAAAT 58.521 37.037 0.00 0.00 0.00 2.17
2712 2808 5.450818 TGGTAGAAAACATAGGCTTGGAT 57.549 39.130 0.00 0.00 0.00 3.41
2757 2853 9.405587 GACTAGATCTACAACATTGCTATTCTC 57.594 37.037 0.00 0.00 0.00 2.87
2765 2861 4.715520 ACATTGCTATTCTCGCATTACG 57.284 40.909 0.00 0.00 45.62 3.18
2768 2864 4.514545 TTGCTATTCTCGCATTACGTTG 57.485 40.909 0.00 0.00 44.19 4.10
2773 2869 5.401376 GCTATTCTCGCATTACGTTGTCATA 59.599 40.000 0.00 0.00 44.19 2.15
2781 2877 5.676744 CGCATTACGTTGTCATATTCCTTTG 59.323 40.000 0.00 0.00 36.87 2.77
2782 2878 6.456315 CGCATTACGTTGTCATATTCCTTTGA 60.456 38.462 0.00 0.00 36.87 2.69
2783 2879 7.417612 GCATTACGTTGTCATATTCCTTTGAT 58.582 34.615 0.00 0.00 0.00 2.57
2784 2880 7.376866 GCATTACGTTGTCATATTCCTTTGATG 59.623 37.037 0.00 0.00 0.00 3.07
2785 2881 5.235305 ACGTTGTCATATTCCTTTGATGC 57.765 39.130 0.00 0.00 0.00 3.91
2786 2882 4.943705 ACGTTGTCATATTCCTTTGATGCT 59.056 37.500 0.00 0.00 0.00 3.79
2789 2885 7.283127 ACGTTGTCATATTCCTTTGATGCTTAT 59.717 33.333 0.00 0.00 0.00 1.73
2813 2919 6.973229 ATTCTTTGCCAGCATTACAATTTC 57.027 33.333 0.00 0.00 0.00 2.17
2819 2925 6.389830 TGCCAGCATTACAATTTCGAATAT 57.610 33.333 0.00 0.00 0.00 1.28
2821 2927 8.109705 TGCCAGCATTACAATTTCGAATATAT 57.890 30.769 0.00 0.00 0.00 0.86
2832 2938 8.632679 ACAATTTCGAATATATGAACATGGCTT 58.367 29.630 0.00 0.00 0.00 4.35
2841 2947 2.942804 TGAACATGGCTTTGGACTTCA 58.057 42.857 0.00 0.00 0.00 3.02
2868 2974 9.486497 TTGCATTCTTTTATTATCAAAAGTGCA 57.514 25.926 16.30 16.30 45.67 4.57
2886 2992 8.644374 AAAGTGCACCTTTATTTGTAGGATAA 57.356 30.769 14.63 0.00 41.63 1.75
2890 2996 7.120726 GTGCACCTTTATTTGTAGGATAACACT 59.879 37.037 5.22 0.00 0.00 3.55
2893 2999 9.886132 CACCTTTATTTGTAGGATAACACTAGT 57.114 33.333 0.00 0.00 0.00 2.57
2899 3005 8.948631 ATTTGTAGGATAACACTAGTGATGTG 57.051 34.615 29.30 3.49 40.87 3.21
2909 3015 4.283467 ACACTAGTGATGTGCTTGGTAGAA 59.717 41.667 29.30 0.00 38.86 2.10
2916 3022 7.112122 AGTGATGTGCTTGGTAGAAAATATGA 58.888 34.615 0.00 0.00 0.00 2.15
2922 3028 8.970020 TGTGCTTGGTAGAAAATATGATCAATT 58.030 29.630 0.00 0.00 0.00 2.32
2943 3049 9.196139 TCAATTTCCCTTTTCTTCTTTCTACAA 57.804 29.630 0.00 0.00 0.00 2.41
2960 3066 9.912634 CTTTCTACAACATCCAATGTGTTTAAT 57.087 29.630 0.00 0.00 44.07 1.40
2980 3086 8.884726 GTTTAATTGTCTCTGAATCTTCTACCC 58.115 37.037 0.00 0.00 0.00 3.69
3102 3208 5.491070 TGTGGATGTGCAGGAATATATAGC 58.509 41.667 0.00 0.00 0.00 2.97
3179 3285 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
3180 3286 4.646945 TGTCTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
3322 3429 6.884295 TCCGACATGAAAATGTTAGGATTTCT 59.116 34.615 0.00 0.00 37.02 2.52
3421 3528 4.618635 TCAATGGGCCAGATTTTTATGGA 58.381 39.130 13.78 0.00 39.02 3.41
3444 3551 4.202609 ACTCCCAAGGAACACATCAAAGAT 60.203 41.667 0.00 0.00 0.00 2.40
3580 3687 7.064609 CCTGAAGAATAAGCAAATTACAGACGA 59.935 37.037 0.00 0.00 0.00 4.20
3626 3733 3.090532 GCCGTTCCATCTCCCCCT 61.091 66.667 0.00 0.00 0.00 4.79
3629 3736 1.209621 CCGTTCCATCTCCCCCTTTA 58.790 55.000 0.00 0.00 0.00 1.85
3630 3737 1.562475 CCGTTCCATCTCCCCCTTTAA 59.438 52.381 0.00 0.00 0.00 1.52
3631 3738 2.025699 CCGTTCCATCTCCCCCTTTAAA 60.026 50.000 0.00 0.00 0.00 1.52
3808 3917 3.820467 CAGTGGATTGCACTAAAACCTCA 59.180 43.478 10.71 0.00 0.00 3.86
3843 3970 4.632153 AGGGTAAGCTGATACTATTTGCG 58.368 43.478 0.00 0.00 0.00 4.85
3912 4095 2.176546 CATGGCGTCAAAGGCGTG 59.823 61.111 0.00 0.00 45.05 5.34
3964 4155 3.531538 ACAGGTTGGTGCTCATATTACG 58.468 45.455 0.00 0.00 0.00 3.18
4000 4244 5.257262 AGAAGAAGAATTTAGCCAGTTCCC 58.743 41.667 0.00 0.00 0.00 3.97
4032 4315 1.278127 TCGTCTCTTTCATTCCACCCC 59.722 52.381 0.00 0.00 0.00 4.95
4040 4323 2.953284 TCATTCCACCCCGTGTTTAA 57.047 45.000 0.00 0.00 0.00 1.52
4083 4396 6.258727 CGTAGTTGCAGGTGATAATTCAAGAT 59.741 38.462 0.00 0.00 32.48 2.40
4203 4516 6.591935 TCCCTCCACACAAATATAAGATGTC 58.408 40.000 0.00 0.00 0.00 3.06
4217 4530 9.884814 AATATAAGATGTCCTACAGTAACCTCT 57.115 33.333 0.00 0.00 0.00 3.69
4218 4531 9.884814 ATATAAGATGTCCTACAGTAACCTCTT 57.115 33.333 7.63 7.63 34.00 2.85
4219 4532 6.936968 AAGATGTCCTACAGTAACCTCTTT 57.063 37.500 0.00 0.00 27.71 2.52
4283 4596 6.987992 AGTGTGCTTGTTCATTCATTTCAATT 59.012 30.769 0.00 0.00 0.00 2.32
4339 4652 7.277981 ACATCTTACATTTGTGAACGGATACTC 59.722 37.037 0.00 0.00 0.00 2.59
4383 4699 8.496707 AAAAATCCAATGCAGATAAAACATCC 57.503 30.769 0.00 0.00 0.00 3.51
4385 4701 6.795144 ATCCAATGCAGATAAAACATCCAA 57.205 33.333 0.00 0.00 0.00 3.53
4386 4702 6.795144 TCCAATGCAGATAAAACATCCAAT 57.205 33.333 0.00 0.00 0.00 3.16
4387 4703 6.575267 TCCAATGCAGATAAAACATCCAATG 58.425 36.000 0.00 0.00 0.00 2.82
4388 4704 5.235616 CCAATGCAGATAAAACATCCAATGC 59.764 40.000 0.00 0.00 0.00 3.56
4389 4705 5.601583 ATGCAGATAAAACATCCAATGCA 57.398 34.783 0.00 0.00 45.42 3.96
4390 4706 5.001237 TGCAGATAAAACATCCAATGCAG 57.999 39.130 0.00 0.00 37.50 4.41
4448 4767 1.228583 ACCACCTCTCGTGCTCTCA 60.229 57.895 0.00 0.00 41.53 3.27
4449 4768 0.827925 ACCACCTCTCGTGCTCTCAA 60.828 55.000 0.00 0.00 41.53 3.02
4450 4769 0.389166 CCACCTCTCGTGCTCTCAAC 60.389 60.000 0.00 0.00 41.53 3.18
4451 4770 0.315251 CACCTCTCGTGCTCTCAACA 59.685 55.000 0.00 0.00 35.18 3.33
4452 4771 0.600557 ACCTCTCGTGCTCTCAACAG 59.399 55.000 0.00 0.00 0.00 3.16
4462 4781 2.017623 GCTCTCAACAGCAGCATCCAT 61.018 52.381 0.00 0.00 39.43 3.41
4493 4812 0.523546 CGTCCTCGTCGTCTTGGATG 60.524 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.279513 TGGGTAAAATTGCCATCTTTAGTG 57.720 37.500 2.69 0.00 34.27 2.74
6 7 3.040477 CCCATGGGTAAAATTGCCATCT 58.960 45.455 23.93 0.00 34.27 2.90
100 101 4.202090 CCCATGAGTTAACGAGTAGGGTAC 60.202 50.000 14.27 0.00 0.00 3.34
109 110 2.823959 ACCCTACCCATGAGTTAACGA 58.176 47.619 0.00 0.00 0.00 3.85
116 117 0.398098 ACCCGTACCCTACCCATGAG 60.398 60.000 0.00 0.00 0.00 2.90
129 130 2.570752 TGGGCACAAAACTATACCCGTA 59.429 45.455 0.00 0.00 40.41 4.02
169 174 6.541278 GGGTAAACATGTCAGTATAAAGGGAC 59.459 42.308 0.00 0.00 0.00 4.46
173 178 8.483758 AGGTAGGGTAAACATGTCAGTATAAAG 58.516 37.037 0.00 0.00 0.00 1.85
189 194 4.986054 ACACATTTCACAGGTAGGGTAA 57.014 40.909 0.00 0.00 0.00 2.85
194 199 8.393366 CAATCTCATAACACATTTCACAGGTAG 58.607 37.037 0.00 0.00 0.00 3.18
212 217 9.965902 AACTTTAAGATAGGTTCACAATCTCAT 57.034 29.630 0.00 0.00 0.00 2.90
488 497 4.202080 GGACGTGTAGAGCAATACCATACA 60.202 45.833 0.00 0.00 0.00 2.29
527 536 4.120331 GCGATGGCCAAGGCACAC 62.120 66.667 22.42 2.30 41.84 3.82
694 703 2.361610 GGGTCTACGGTGGTCGGA 60.362 66.667 0.00 0.00 44.45 4.55
712 721 3.885521 AGCGCGCTACGGGAGTAC 61.886 66.667 35.79 0.00 46.17 2.73
713 722 3.884350 CAGCGCGCTACGGGAGTA 61.884 66.667 36.02 0.00 46.17 2.59
737 746 4.111016 CGTGCAGCGACGTAGGGA 62.111 66.667 8.65 0.00 44.77 4.20
781 790 2.396590 TTTGGATTCTGCCGGAGTAC 57.603 50.000 5.05 0.00 0.00 2.73
786 795 1.885887 TCAGTTTTTGGATTCTGCCGG 59.114 47.619 0.00 0.00 0.00 6.13
797 806 3.490526 CCGACAATTTGGCTCAGTTTTTG 59.509 43.478 0.00 0.00 0.00 2.44
798 807 3.132111 ACCGACAATTTGGCTCAGTTTTT 59.868 39.130 0.00 0.00 0.00 1.94
804 813 3.810310 AAAAACCGACAATTTGGCTCA 57.190 38.095 0.00 0.00 0.00 4.26
824 833 8.747666 CCAAAATGACGAACGAAATTAGAAAAA 58.252 29.630 0.14 0.00 0.00 1.94
825 834 7.380065 CCCAAAATGACGAACGAAATTAGAAAA 59.620 33.333 0.14 0.00 0.00 2.29
1153 1176 2.285773 TGATGGTGAGCTCCTGCGT 61.286 57.895 12.15 0.00 45.42 5.24
1224 1247 2.351924 GAAACCTGTGGGGGAGCACA 62.352 60.000 0.00 0.00 40.03 4.57
1306 1333 2.164219 AGCACACAACAAAACACAGAGG 59.836 45.455 0.00 0.00 0.00 3.69
1307 1334 3.127548 AGAGCACACAACAAAACACAGAG 59.872 43.478 0.00 0.00 0.00 3.35
1308 1335 3.081061 AGAGCACACAACAAAACACAGA 58.919 40.909 0.00 0.00 0.00 3.41
1350 1380 2.602738 GCATGACGATGGCTCTCTG 58.397 57.895 0.00 0.00 0.00 3.35
1364 1394 2.353610 GGGCTTCAGGTTGGGCATG 61.354 63.158 0.00 0.00 0.00 4.06
1382 1412 0.582960 GTGACGTTGTTGTAACCGGG 59.417 55.000 6.32 0.00 0.00 5.73
1391 1421 1.850640 GATCGCACGTGACGTTGTT 59.149 52.632 22.23 9.14 38.32 2.83
1398 1428 2.574999 GTACGCGATCGCACGTGA 60.575 61.111 36.45 15.51 44.86 4.35
1502 1532 7.865706 ATCCGTACTTGCAATCTTAATTTCT 57.134 32.000 0.00 0.00 0.00 2.52
1588 1621 3.627395 TTGATAACCAGGAGACGCAAT 57.373 42.857 0.00 0.00 0.00 3.56
1757 1790 6.302535 TCAGAATCGTTAAGGGAATAACCA 57.697 37.500 0.00 0.00 41.20 3.67
1758 1791 7.497909 TGAATCAGAATCGTTAAGGGAATAACC 59.502 37.037 0.00 0.00 33.19 2.85
1759 1792 8.433421 TGAATCAGAATCGTTAAGGGAATAAC 57.567 34.615 0.00 0.00 33.40 1.89
1780 1813 6.888632 AGGAGCAGAACATTTACAAGATGAAT 59.111 34.615 0.00 0.00 0.00 2.57
1781 1814 6.240894 AGGAGCAGAACATTTACAAGATGAA 58.759 36.000 0.00 0.00 0.00 2.57
1798 1831 1.829849 TCATGACTGAAGGAGGAGCAG 59.170 52.381 0.00 0.00 35.81 4.24
1834 1867 9.531942 TGCAAAATAAACATTATGATCCATCAC 57.468 29.630 0.00 0.00 40.03 3.06
1840 1876 8.367943 TGGCATGCAAAATAAACATTATGATC 57.632 30.769 21.36 0.00 0.00 2.92
1855 1891 3.693085 ACAAAACAAACATGGCATGCAAA 59.307 34.783 26.70 7.48 0.00 3.68
1908 1944 3.306989 CCAGCAGGATACAACTTGACAGA 60.307 47.826 0.00 0.00 41.41 3.41
2096 2132 9.956720 CAAGCCCATTTAATATCTGAAGTAAAG 57.043 33.333 0.00 0.00 0.00 1.85
2123 2159 3.305335 GGTACTGTCAAGGCAACAAATGG 60.305 47.826 0.00 0.00 41.41 3.16
2188 2224 5.701445 ATGTTGGCATTGACCGTACAGGT 62.701 47.826 8.80 8.80 44.54 4.00
2212 2248 9.651913 GAAATGAAAAATAGCCATAAAGGTGAA 57.348 29.630 0.00 0.00 40.61 3.18
2449 2486 6.381994 AGAAATGTAAGAACCACGTATAGGGA 59.618 38.462 0.00 0.00 0.00 4.20
2452 2489 9.755064 CAAAAGAAATGTAAGAACCACGTATAG 57.245 33.333 0.00 0.00 0.00 1.31
2458 2495 7.033185 ACACACAAAAGAAATGTAAGAACCAC 58.967 34.615 0.00 0.00 0.00 4.16
2473 2510 5.410067 ACATGACCTGAAAACACACAAAAG 58.590 37.500 0.00 0.00 0.00 2.27
2474 2511 5.398603 ACATGACCTGAAAACACACAAAA 57.601 34.783 0.00 0.00 0.00 2.44
2476 2513 4.742417 CAACATGACCTGAAAACACACAA 58.258 39.130 0.00 0.00 0.00 3.33
2477 2514 3.428725 GCAACATGACCTGAAAACACACA 60.429 43.478 0.00 0.00 0.00 3.72
2478 2515 3.115554 GCAACATGACCTGAAAACACAC 58.884 45.455 0.00 0.00 0.00 3.82
2602 2639 2.230508 GAGTGACCGGAACATACTGTGA 59.769 50.000 9.46 0.00 0.00 3.58
2625 2662 2.235402 ACTTATGTGGGTTAGGGACACG 59.765 50.000 0.00 0.00 37.92 4.49
2636 2673 2.749621 GCAGACTGGAAACTTATGTGGG 59.250 50.000 4.26 0.00 0.00 4.61
2642 2679 2.570302 GGTAGGGCAGACTGGAAACTTA 59.430 50.000 4.26 0.00 0.00 2.24
2656 2694 4.650131 AGTGAGAGTAACTAATGGTAGGGC 59.350 45.833 0.00 0.00 0.00 5.19
2657 2695 5.892119 TCAGTGAGAGTAACTAATGGTAGGG 59.108 44.000 0.00 0.00 0.00 3.53
2684 2779 9.349713 CCAAGCCTATGTTTTCTACCATAAATA 57.650 33.333 0.00 0.00 0.00 1.40
2685 2780 8.058847 TCCAAGCCTATGTTTTCTACCATAAAT 58.941 33.333 0.00 0.00 0.00 1.40
2686 2781 7.406916 TCCAAGCCTATGTTTTCTACCATAAA 58.593 34.615 0.00 0.00 0.00 1.40
2688 2783 6.569127 TCCAAGCCTATGTTTTCTACCATA 57.431 37.500 0.00 0.00 0.00 2.74
2703 2799 2.511218 TGCTGAAGGAATATCCAAGCCT 59.489 45.455 13.02 0.00 39.61 4.58
2705 2801 3.549794 ACTGCTGAAGGAATATCCAAGC 58.450 45.455 0.00 10.19 39.61 4.01
2712 2808 8.362464 TCTAGTCTTTTACTGCTGAAGGAATA 57.638 34.615 0.00 0.00 39.39 1.75
2773 2869 8.146412 GGCAAAGAATATAAGCATCAAAGGAAT 58.854 33.333 0.00 0.00 0.00 3.01
2781 2877 5.443185 TGCTGGCAAAGAATATAAGCATC 57.557 39.130 0.00 0.00 34.46 3.91
2783 2879 5.857471 AATGCTGGCAAAGAATATAAGCA 57.143 34.783 0.00 0.00 42.76 3.91
2784 2880 6.738114 TGTAATGCTGGCAAAGAATATAAGC 58.262 36.000 0.00 0.00 0.00 3.09
2785 2881 9.754382 AATTGTAATGCTGGCAAAGAATATAAG 57.246 29.630 0.00 0.00 0.00 1.73
2789 2885 6.751425 CGAAATTGTAATGCTGGCAAAGAATA 59.249 34.615 0.00 0.00 0.00 1.75
2796 2902 4.717233 ATTCGAAATTGTAATGCTGGCA 57.283 36.364 0.00 0.00 0.00 4.92
2797 2903 8.236586 TCATATATTCGAAATTGTAATGCTGGC 58.763 33.333 0.00 0.00 0.00 4.85
2813 2919 6.205464 AGTCCAAAGCCATGTTCATATATTCG 59.795 38.462 0.00 0.00 0.00 3.34
2819 2925 4.661222 TGAAGTCCAAAGCCATGTTCATA 58.339 39.130 0.00 0.00 0.00 2.15
2821 2927 2.942804 TGAAGTCCAAAGCCATGTTCA 58.057 42.857 0.00 0.00 0.00 3.18
2862 2968 7.668052 TGTTATCCTACAAATAAAGGTGCACTT 59.332 33.333 17.98 6.12 42.52 3.16
2863 2969 7.120726 GTGTTATCCTACAAATAAAGGTGCACT 59.879 37.037 17.98 0.00 34.30 4.40
2864 2970 7.120726 AGTGTTATCCTACAAATAAAGGTGCAC 59.879 37.037 8.80 8.80 34.30 4.57
2865 2971 7.172342 AGTGTTATCCTACAAATAAAGGTGCA 58.828 34.615 0.00 0.00 34.30 4.57
2866 2972 7.625828 AGTGTTATCCTACAAATAAAGGTGC 57.374 36.000 0.00 0.00 34.30 5.01
2867 2973 9.886132 ACTAGTGTTATCCTACAAATAAAGGTG 57.114 33.333 0.00 0.00 34.30 4.00
2868 2974 9.886132 CACTAGTGTTATCCTACAAATAAAGGT 57.114 33.333 15.06 0.00 34.30 3.50
2886 2992 3.832490 TCTACCAAGCACATCACTAGTGT 59.168 43.478 21.99 7.40 39.17 3.55
2890 2996 8.264347 TCATATTTTCTACCAAGCACATCACTA 58.736 33.333 0.00 0.00 0.00 2.74
2893 2999 7.774625 TGATCATATTTTCTACCAAGCACATCA 59.225 33.333 0.00 0.00 0.00 3.07
2899 3005 9.468532 GGAAATTGATCATATTTTCTACCAAGC 57.531 33.333 18.24 5.83 0.00 4.01
2916 3022 9.367160 TGTAGAAAGAAGAAAAGGGAAATTGAT 57.633 29.630 0.00 0.00 0.00 2.57
2922 3028 7.230712 GGATGTTGTAGAAAGAAGAAAAGGGAA 59.769 37.037 0.00 0.00 0.00 3.97
2943 3049 7.448161 TCAGAGACAATTAAACACATTGGATGT 59.552 33.333 0.00 0.00 46.22 3.06
2960 3066 4.425772 TGGGGTAGAAGATTCAGAGACAA 58.574 43.478 0.00 0.00 0.00 3.18
2980 3086 2.165030 CAGAAACAATAGCTTGCCCTGG 59.835 50.000 0.00 0.00 35.69 4.45
3102 3208 1.074752 GAGAAAGAGCAACAGGAGCG 58.925 55.000 0.00 0.00 37.01 5.03
3158 3264 4.646945 TGAGAGAGAGAGAGAGAGAGAGAC 59.353 50.000 0.00 0.00 0.00 3.36
3179 3285 7.523709 GCCAAAGAAAATACTGAACTCCAATGA 60.524 37.037 0.00 0.00 0.00 2.57
3180 3286 6.587608 GCCAAAGAAAATACTGAACTCCAATG 59.412 38.462 0.00 0.00 0.00 2.82
3263 3370 9.547753 GTTCTTTGCCTATAAGATTGTGATAGA 57.452 33.333 0.00 0.00 32.09 1.98
3278 3385 5.298777 GTCGGATAGAGTAGTTCTTTGCCTA 59.701 44.000 0.00 0.00 37.36 3.93
3363 3470 3.288092 TCTAGCTTATCAAGAGCACCGA 58.712 45.455 0.00 0.00 42.56 4.69
3421 3528 3.138283 TCTTTGATGTGTTCCTTGGGAGT 59.862 43.478 0.00 0.00 31.21 3.85
3444 3551 0.693049 GGGGCTCCTTCTCAGAACAA 59.307 55.000 0.00 0.00 0.00 2.83
3580 3687 3.558608 TTGTTTCTCCCCCAAATGGAT 57.441 42.857 0.00 0.00 37.39 3.41
3626 3733 7.500892 TGTTTGTCAGGCTCATTCTACTTTAAA 59.499 33.333 0.00 0.00 0.00 1.52
3629 3736 5.376625 TGTTTGTCAGGCTCATTCTACTTT 58.623 37.500 0.00 0.00 0.00 2.66
3630 3737 4.973168 TGTTTGTCAGGCTCATTCTACTT 58.027 39.130 0.00 0.00 0.00 2.24
3631 3738 4.623932 TGTTTGTCAGGCTCATTCTACT 57.376 40.909 0.00 0.00 0.00 2.57
3688 3797 7.196331 AGTTGCTCTTACAAAGTTGCTTTTAG 58.804 34.615 0.00 0.00 30.60 1.85
3808 3917 5.190528 TCAGCTTACCCTTTCATCTTCTGAT 59.809 40.000 0.00 0.00 32.72 2.90
3827 3936 1.860950 CGCACGCAAATAGTATCAGCT 59.139 47.619 5.54 0.00 0.00 4.24
3828 3937 1.858458 TCGCACGCAAATAGTATCAGC 59.142 47.619 0.00 0.00 0.00 4.26
3829 3938 3.116300 ACTCGCACGCAAATAGTATCAG 58.884 45.455 0.00 0.00 0.00 2.90
3843 3970 0.778815 CGACTCAACAAGACTCGCAC 59.221 55.000 0.00 0.00 0.00 5.34
3912 4095 0.736325 ATGCCGACACAACTCTACGC 60.736 55.000 0.00 0.00 0.00 4.42
3964 4155 5.591643 TTCTTCTTCTCGTATTGTTGTGC 57.408 39.130 0.00 0.00 0.00 4.57
3969 4160 7.103641 TGGCTAAATTCTTCTTCTCGTATTGT 58.896 34.615 0.00 0.00 0.00 2.71
4000 4244 6.392625 TGAAAGAGACGAGGAATATACCAG 57.607 41.667 0.00 0.00 0.00 4.00
4005 4249 6.284459 GTGGAATGAAAGAGACGAGGAATAT 58.716 40.000 0.00 0.00 0.00 1.28
4011 4255 2.622436 GGGTGGAATGAAAGAGACGAG 58.378 52.381 0.00 0.00 0.00 4.18
4032 4315 4.198787 CGAACAACACGTCTTTTAAACACG 59.801 41.667 14.49 14.49 39.48 4.49
4040 4323 1.011574 GCGCGAACAACACGTCTTT 60.012 52.632 12.10 0.00 0.00 2.52
4237 4550 9.784680 CACACTAAAACTAGAACGTGTCTATAT 57.215 33.333 0.00 0.00 38.20 0.86
4238 4551 7.752239 GCACACTAAAACTAGAACGTGTCTATA 59.248 37.037 0.00 0.00 38.20 1.31
4239 4552 6.585322 GCACACTAAAACTAGAACGTGTCTAT 59.415 38.462 0.00 0.00 38.20 1.98
4247 4560 7.011828 TGAACAAGCACACTAAAACTAGAAC 57.988 36.000 0.00 0.00 0.00 3.01
4250 4563 7.639039 TGAATGAACAAGCACACTAAAACTAG 58.361 34.615 0.00 0.00 0.00 2.57
4307 4620 7.537306 CCGTTCACAAATGTAAGATGTTTTAGG 59.463 37.037 0.00 0.00 0.00 2.69
4310 4623 7.033530 TCCGTTCACAAATGTAAGATGTTTT 57.966 32.000 0.00 0.00 0.00 2.43
4326 4639 4.288670 TGATTCTCGAGTATCCGTTCAC 57.711 45.455 24.09 4.16 0.00 3.18
4366 4682 5.979993 TGCATTGGATGTTTTATCTGCATT 58.020 33.333 0.00 0.00 33.80 3.56
4376 4692 1.067142 CAGCAGCTGCATTGGATGTTT 60.067 47.619 38.24 12.75 45.16 2.83
4378 4694 0.323087 TCAGCAGCTGCATTGGATGT 60.323 50.000 38.24 14.33 45.16 3.06
4379 4695 0.815095 TTCAGCAGCTGCATTGGATG 59.185 50.000 38.24 26.19 45.16 3.51
4380 4696 1.776662 ATTCAGCAGCTGCATTGGAT 58.223 45.000 38.24 25.92 45.16 3.41
4381 4697 1.475280 GAATTCAGCAGCTGCATTGGA 59.525 47.619 38.24 24.86 45.16 3.53
4382 4698 1.476891 AGAATTCAGCAGCTGCATTGG 59.523 47.619 38.24 24.06 45.16 3.16
4383 4699 2.423892 AGAGAATTCAGCAGCTGCATTG 59.576 45.455 38.24 28.32 45.16 2.82
4385 4701 2.017782 CAGAGAATTCAGCAGCTGCAT 58.982 47.619 38.24 21.83 45.16 3.96
4386 4702 1.450025 CAGAGAATTCAGCAGCTGCA 58.550 50.000 38.24 20.45 45.16 4.41
4387 4703 0.099082 GCAGAGAATTCAGCAGCTGC 59.901 55.000 31.53 31.53 41.38 5.25
4388 4704 1.740297 AGCAGAGAATTCAGCAGCTG 58.260 50.000 17.10 17.10 38.22 4.24
4389 4705 3.055240 AGTTAGCAGAGAATTCAGCAGCT 60.055 43.478 17.67 17.67 38.22 4.24
4390 4706 3.269178 AGTTAGCAGAGAATTCAGCAGC 58.731 45.455 8.44 7.80 38.22 5.25


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

AutoCloner maintained by Alex Coulton.