Multiple sequence alignment - TraesCS1B01G346600

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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 TraesCS1B01G346600 chr1B 100.000 5776 0 0 1 5776 575723427 575729202 0.000000e+00 10667
1 TraesCS1B01G346600 chr1B 93.882 425 25 1 4816 5240 673569993 673569570 1.750000e-179 640
2 TraesCS1B01G346600 chr1A 91.659 4136 205 63 735 4790 521275554 521279629 0.000000e+00 5598
3 TraesCS1B01G346600 chr1A 86.977 622 74 5 79 694 28649925 28649305 0.000000e+00 693
4 TraesCS1B01G346600 chr1D 95.383 3097 99 22 1722 4790 426168668 426171748 0.000000e+00 4887
5 TraesCS1B01G346600 chr1D 92.892 830 44 8 907 1722 426167674 426168502 0.000000e+00 1192
6 TraesCS1B01G346600 chr1D 85.892 964 127 8 4815 5774 480817695 480818653 0.000000e+00 1018
7 TraesCS1B01G346600 chr1D 87.466 726 80 8 1 718 466117696 466118418 0.000000e+00 826
8 TraesCS1B01G346600 chr1D 85.963 748 95 7 1 739 451247730 451246984 0.000000e+00 791
9 TraesCS1B01G346600 chr3B 94.167 960 56 0 4817 5776 63444697 63443738 0.000000e+00 1463
10 TraesCS1B01G346600 chr3B 86.544 758 86 13 1 747 809135747 809134995 0.000000e+00 821
11 TraesCS1B01G346600 chr2B 95.556 900 40 0 4877 5776 624366703 624367602 0.000000e+00 1441
12 TraesCS1B01G346600 chr2B 80.658 972 174 13 4814 5776 185773970 185774936 0.000000e+00 741
13 TraesCS1B01G346600 chr7A 90.739 961 84 5 4818 5776 32688171 32689128 0.000000e+00 1277
14 TraesCS1B01G346600 chr7A 84.969 958 130 8 4819 5774 183321436 183320491 0.000000e+00 959
15 TraesCS1B01G346600 chr7B 90.126 952 92 2 4827 5776 542902565 542903516 0.000000e+00 1236
16 TraesCS1B01G346600 chr5A 89.128 975 90 7 4817 5776 644805318 644804345 0.000000e+00 1199
17 TraesCS1B01G346600 chr2D 88.100 958 109 3 4818 5774 32411570 32412523 0.000000e+00 1133
18 TraesCS1B01G346600 chr4D 85.544 754 91 10 1 741 12191726 12192474 0.000000e+00 773
19 TraesCS1B01G346600 chr7D 85.422 734 96 7 1 725 472926763 472926032 0.000000e+00 752
20 TraesCS1B01G346600 chr7D 85.754 723 87 11 13 725 105927887 105927171 0.000000e+00 750
21 TraesCS1B01G346600 chr3A 83.696 736 107 10 12 738 521574284 521575015 0.000000e+00 682
22 TraesCS1B01G346600 chr5D 85.842 558 65 11 166 720 188388575 188388029 1.080000e-161 580


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 TraesCS1B01G346600 chr1B 575723427 575729202 5775 False 10667.0 10667 100.0000 1 5776 1 chr1B.!!$F1 5775
1 TraesCS1B01G346600 chr1A 521275554 521279629 4075 False 5598.0 5598 91.6590 735 4790 1 chr1A.!!$F1 4055
2 TraesCS1B01G346600 chr1A 28649305 28649925 620 True 693.0 693 86.9770 79 694 1 chr1A.!!$R1 615
3 TraesCS1B01G346600 chr1D 426167674 426171748 4074 False 3039.5 4887 94.1375 907 4790 2 chr1D.!!$F3 3883
4 TraesCS1B01G346600 chr1D 480817695 480818653 958 False 1018.0 1018 85.8920 4815 5774 1 chr1D.!!$F2 959
5 TraesCS1B01G346600 chr1D 466117696 466118418 722 False 826.0 826 87.4660 1 718 1 chr1D.!!$F1 717
6 TraesCS1B01G346600 chr1D 451246984 451247730 746 True 791.0 791 85.9630 1 739 1 chr1D.!!$R1 738
7 TraesCS1B01G346600 chr3B 63443738 63444697 959 True 1463.0 1463 94.1670 4817 5776 1 chr3B.!!$R1 959
8 TraesCS1B01G346600 chr3B 809134995 809135747 752 True 821.0 821 86.5440 1 747 1 chr3B.!!$R2 746
9 TraesCS1B01G346600 chr2B 624366703 624367602 899 False 1441.0 1441 95.5560 4877 5776 1 chr2B.!!$F2 899
10 TraesCS1B01G346600 chr2B 185773970 185774936 966 False 741.0 741 80.6580 4814 5776 1 chr2B.!!$F1 962
11 TraesCS1B01G346600 chr7A 32688171 32689128 957 False 1277.0 1277 90.7390 4818 5776 1 chr7A.!!$F1 958
12 TraesCS1B01G346600 chr7A 183320491 183321436 945 True 959.0 959 84.9690 4819 5774 1 chr7A.!!$R1 955
13 TraesCS1B01G346600 chr7B 542902565 542903516 951 False 1236.0 1236 90.1260 4827 5776 1 chr7B.!!$F1 949
14 TraesCS1B01G346600 chr5A 644804345 644805318 973 True 1199.0 1199 89.1280 4817 5776 1 chr5A.!!$R1 959
15 TraesCS1B01G346600 chr2D 32411570 32412523 953 False 1133.0 1133 88.1000 4818 5774 1 chr2D.!!$F1 956
16 TraesCS1B01G346600 chr4D 12191726 12192474 748 False 773.0 773 85.5440 1 741 1 chr4D.!!$F1 740
17 TraesCS1B01G346600 chr7D 472926032 472926763 731 True 752.0 752 85.4220 1 725 1 chr7D.!!$R2 724
18 TraesCS1B01G346600 chr7D 105927171 105927887 716 True 750.0 750 85.7540 13 725 1 chr7D.!!$R1 712
19 TraesCS1B01G346600 chr3A 521574284 521575015 731 False 682.0 682 83.6960 12 738 1 chr3A.!!$F1 726
20 TraesCS1B01G346600 chr5D 188388029 188388575 546 True 580.0 580 85.8420 166 720 1 chr5D.!!$R1 554

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
242 254 0.109132 GCTGAAGGATGGGCAAAACG 60.109 55.000 0.00 0.0 0.00 3.60 F
1233 1266 0.032017 ACCCTACGAGCCTGATTCCT 60.032 55.000 0.00 0.0 0.00 3.36 F
1498 1538 0.254747 GTACATTGCTGGCTACCCCA 59.745 55.000 0.00 0.0 42.79 4.96 F
1695 1737 1.534729 ATGGAAAGAAAGTGGACGGC 58.465 50.000 0.00 0.0 0.00 5.68 F
2325 2565 1.524621 CCTTCCACCTATGCCAGCG 60.525 63.158 0.00 0.0 0.00 5.18 F
3639 3886 2.005451 CTCTGAAAGCTGGTCATTCCG 58.995 52.381 1.05 0.0 39.52 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1522 0.323725 AACTGGGGTAGCCAGCAATG 60.324 55.000 14.06 0.00 38.72 2.82 R
2147 2387 0.820891 CTGAGCAACTGTTGGCTGGT 60.821 55.000 21.01 2.08 41.22 4.00 R
2325 2565 2.161855 TGTGCTGATTGTGGTGGATTC 58.838 47.619 0.00 0.00 0.00 2.52 R
3529 3776 3.006752 GCCCTCAATTTTTGTGATGTCCA 59.993 43.478 0.00 0.00 0.00 4.02 R
3850 4104 2.027192 GTGGGACTGTTAGAATCTGGCA 60.027 50.000 0.00 0.00 0.00 4.92 R
4799 5071 0.036732 AAAGAGCTCGTCCATGCCAA 59.963 50.000 8.37 0.00 0.00 4.52 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
36 38 2.415168 CGTCCGCAACAAGATAACACAT 59.585 45.455 0.00 0.00 0.00 3.21
90 97 7.068839 CCAAGAGGTATCTTCTAAGCTAAGTGA 59.931 40.741 0.00 0.00 44.15 3.41
102 113 5.629079 AAGCTAAGTGAACTAATTGGTGC 57.371 39.130 0.00 0.00 0.00 5.01
114 125 0.823356 ATTGGTGCGCAGAACAACCT 60.823 50.000 12.22 0.00 0.00 3.50
149 161 5.049828 CAGTTAAAGGAAAGCAAGTTTGGG 58.950 41.667 0.00 0.00 0.00 4.12
159 171 1.468985 CAAGTTTGGGTGTGGTGACA 58.531 50.000 0.00 0.00 38.70 3.58
195 207 1.734137 GCATGCTCAGCCCATCAAG 59.266 57.895 11.37 0.00 0.00 3.02
205 217 2.194056 CCATCAAGGGCGCCTCAT 59.806 61.111 28.56 10.23 30.89 2.90
221 233 0.413434 TCATCCAGGTGGTCTCCTCA 59.587 55.000 0.00 0.00 35.37 3.86
241 253 0.247460 GGCTGAAGGATGGGCAAAAC 59.753 55.000 0.00 0.00 0.00 2.43
242 254 0.109132 GCTGAAGGATGGGCAAAACG 60.109 55.000 0.00 0.00 0.00 3.60
243 255 0.527565 CTGAAGGATGGGCAAAACGG 59.472 55.000 0.00 0.00 0.00 4.44
263 275 3.242739 CGGAAATGTTGATGGATCGTTCC 60.243 47.826 5.52 5.52 42.94 3.62
302 314 2.124151 GGGCGGGCATGATTCTGT 60.124 61.111 3.27 0.00 0.00 3.41
313 325 1.375908 GATTCTGTGCGGCTCCACA 60.376 57.895 0.00 9.11 42.99 4.17
337 350 5.248640 ACGACATCATTTTCTCATCCTGTT 58.751 37.500 0.00 0.00 0.00 3.16
356 369 4.388485 TGTTGAGAGTTGCATACATGTGT 58.612 39.130 9.11 0.00 0.00 3.72
382 395 1.065636 CATTGGAGGCTGAGCTCTCAA 60.066 52.381 16.19 14.25 39.39 3.02
417 430 0.250684 TCAACCTCGCCTTGCAATGA 60.251 50.000 5.85 0.00 0.00 2.57
428 441 2.163010 CCTTGCAATGAACGAAGATGCT 59.837 45.455 0.00 0.00 37.86 3.79
436 449 6.293298 GCAATGAACGAAGATGCTGATAGAAT 60.293 38.462 0.00 0.00 34.29 2.40
438 451 6.594284 TGAACGAAGATGCTGATAGAATTG 57.406 37.500 0.00 0.00 0.00 2.32
439 452 6.340522 TGAACGAAGATGCTGATAGAATTGA 58.659 36.000 0.00 0.00 0.00 2.57
460 473 3.151906 AGGACTGCCTTGTCGCTT 58.848 55.556 0.00 0.00 43.90 4.68
471 484 4.098416 GCCTTGTCGCTTTTAACATGATC 58.902 43.478 0.00 0.00 0.00 2.92
477 490 5.182950 TGTCGCTTTTAACATGATCAATGGT 59.817 36.000 0.00 0.00 40.94 3.55
494 507 2.440147 TCCGAACAGGGACCGGTA 59.560 61.111 7.34 0.00 43.40 4.02
496 509 0.615544 TCCGAACAGGGACCGGTATT 60.616 55.000 7.34 0.00 43.40 1.89
502 515 1.416401 ACAGGGACCGGTATTGCTATG 59.584 52.381 7.34 2.29 0.00 2.23
522 535 4.191033 TGCCATGTTGGTTGATCAAATC 57.809 40.909 10.35 6.42 40.46 2.17
526 539 5.736813 CCATGTTGGTTGATCAAATCCAAT 58.263 37.500 25.16 13.24 41.11 3.16
533 546 4.872124 GGTTGATCAAATCCAATGGCTTTC 59.128 41.667 10.35 0.00 0.00 2.62
546 559 1.265454 GGCTTTCGAGGGAAGGGAGA 61.265 60.000 0.00 0.00 32.80 3.71
551 564 1.486211 TCGAGGGAAGGGAGAATGTC 58.514 55.000 0.00 0.00 0.00 3.06
587 600 2.253610 TCGTAGGGAACAGAATGGTGT 58.746 47.619 0.00 0.00 33.00 4.16
619 632 2.677228 CCTCCTTTGGCCGGACAT 59.323 61.111 13.08 0.00 0.00 3.06
652 665 2.876368 GATGTGGCTGGGTTCGGGAG 62.876 65.000 0.00 0.00 0.00 4.30
657 670 2.581354 CTGGGTTCGGGAGCAGAG 59.419 66.667 0.00 0.00 0.00 3.35
660 673 2.066999 GGGTTCGGGAGCAGAGGAT 61.067 63.158 0.00 0.00 0.00 3.24
720 735 9.874205 GATTGATGAAATAAATTCCCTTTCACA 57.126 29.630 10.45 8.83 40.54 3.58
725 740 5.659440 AATAAATTCCCTTTCACACGCAT 57.341 34.783 0.00 0.00 0.00 4.73
726 741 5.659440 ATAAATTCCCTTTCACACGCATT 57.341 34.783 0.00 0.00 0.00 3.56
727 742 4.335400 AAATTCCCTTTCACACGCATTT 57.665 36.364 0.00 0.00 0.00 2.32
761 776 7.937394 AGAATACCCTAATAAATCGAACCCAAG 59.063 37.037 0.00 0.00 0.00 3.61
787 802 3.909364 TGCCATTGGAAGGGAAAGAAAAT 59.091 39.130 6.95 0.00 29.54 1.82
788 803 4.350520 TGCCATTGGAAGGGAAAGAAAATT 59.649 37.500 6.95 0.00 29.54 1.82
790 805 6.043706 TGCCATTGGAAGGGAAAGAAAATTAA 59.956 34.615 6.95 0.00 29.54 1.40
862 885 6.813293 ATATTTTTCAATAAAGCAGGCCCT 57.187 33.333 0.00 0.00 0.00 5.19
953 978 1.746991 GCCCCTTTTCTCCGCAGAG 60.747 63.158 0.00 0.00 41.93 3.35
989 1015 2.616960 CACATCAAGGAATCGACCGAA 58.383 47.619 0.00 0.00 34.73 4.30
990 1016 3.000041 CACATCAAGGAATCGACCGAAA 59.000 45.455 0.00 0.00 34.73 3.46
1226 1259 2.298661 CCCCAAACCCTACGAGCCT 61.299 63.158 0.00 0.00 0.00 4.58
1228 1261 1.550130 CCCAAACCCTACGAGCCTGA 61.550 60.000 0.00 0.00 0.00 3.86
1233 1266 0.032017 ACCCTACGAGCCTGATTCCT 60.032 55.000 0.00 0.00 0.00 3.36
1425 1465 3.410631 TCCGTGTTTCTATGCAGGAAA 57.589 42.857 11.88 11.88 0.00 3.13
1440 1480 4.291249 TGCAGGAAAGGGTAGGATAAAACT 59.709 41.667 0.00 0.00 0.00 2.66
1445 1485 6.912561 AGGAAAGGGTAGGATAAAACTCCATA 59.087 38.462 0.00 0.00 37.81 2.74
1481 1521 1.893137 AGTCGCTGAACATCTGGTGTA 59.107 47.619 0.00 0.00 41.14 2.90
1482 1522 1.993370 GTCGCTGAACATCTGGTGTAC 59.007 52.381 0.00 0.00 41.14 2.90
1498 1538 0.254747 GTACATTGCTGGCTACCCCA 59.745 55.000 0.00 0.00 42.79 4.96
1555 1596 6.540914 GGAATCGAGGGTCATTTATGTTGTAA 59.459 38.462 0.00 0.00 0.00 2.41
1649 1691 6.599437 GTGTTAATGTTGATAGTGTCACCAC 58.401 40.000 0.00 0.00 42.17 4.16
1687 1729 9.014297 ACCTGTTGTTTCTATATGGAAAGAAAG 57.986 33.333 20.79 18.44 41.18 2.62
1694 1736 5.914033 TCTATATGGAAAGAAAGTGGACGG 58.086 41.667 0.00 0.00 0.00 4.79
1695 1737 1.534729 ATGGAAAGAAAGTGGACGGC 58.465 50.000 0.00 0.00 0.00 5.68
1758 1985 5.069501 ACCGAATCCACTACTTGTTCTAC 57.930 43.478 0.00 0.00 0.00 2.59
1778 2008 1.889829 CGCCTGTTTCCCAATGGTTTA 59.110 47.619 0.00 0.00 0.00 2.01
1837 2067 5.398603 TGTTTTTGCTTTTGTTCTCCTGA 57.601 34.783 0.00 0.00 0.00 3.86
1856 2086 4.278170 CCTGACAAACTTGCCTTGTTATCA 59.722 41.667 0.00 0.00 37.14 2.15
1879 2117 3.206150 GCAGTCAATATAGGGTGTGGTG 58.794 50.000 0.00 0.00 0.00 4.17
1883 2121 5.362717 CAGTCAATATAGGGTGTGGTGTCTA 59.637 44.000 0.00 0.00 0.00 2.59
1885 2123 4.340097 TCAATATAGGGTGTGGTGTCTACG 59.660 45.833 0.00 0.00 0.00 3.51
1966 2204 2.875087 TATGCATTTGTGCTGGATGC 57.125 45.000 3.54 0.88 44.81 3.91
2147 2387 1.565156 GCACAATCTTCCGACACGCA 61.565 55.000 0.00 0.00 0.00 5.24
2274 2514 2.250924 CAACCTTCTGGCCAATTTCCT 58.749 47.619 7.01 0.00 36.63 3.36
2296 2536 1.732259 CGGGCACTTCTAATGTGACAC 59.268 52.381 0.00 0.00 44.73 3.67
2325 2565 1.524621 CCTTCCACCTATGCCAGCG 60.525 63.158 0.00 0.00 0.00 5.18
2655 2895 6.512297 ACAACCAATGTTTCATGTAAGGTTC 58.488 36.000 4.20 0.00 40.06 3.62
2656 2896 6.323739 ACAACCAATGTTTCATGTAAGGTTCT 59.676 34.615 4.20 0.00 40.06 3.01
2657 2897 7.504238 ACAACCAATGTTTCATGTAAGGTTCTA 59.496 33.333 4.20 0.00 40.06 2.10
2658 2898 8.522830 CAACCAATGTTTCATGTAAGGTTCTAT 58.477 33.333 4.20 0.00 36.07 1.98
2659 2899 9.747898 AACCAATGTTTCATGTAAGGTTCTATA 57.252 29.630 0.00 0.00 33.10 1.31
2660 2900 9.396022 ACCAATGTTTCATGTAAGGTTCTATAG 57.604 33.333 0.00 0.00 0.00 1.31
2661 2901 9.396022 CCAATGTTTCATGTAAGGTTCTATAGT 57.604 33.333 0.00 0.00 0.00 2.12
2901 3141 8.561738 TTGATTATCCTGTCTTAAAGTTGACC 57.438 34.615 0.00 0.00 32.67 4.02
2909 3149 6.321435 CCTGTCTTAAAGTTGACCTTTTCCTT 59.679 38.462 0.00 0.00 40.55 3.36
2922 3162 7.897864 TGACCTTTTCCTTGTGTAAAGAAAAA 58.102 30.769 0.00 0.00 36.38 1.94
3003 3245 6.718454 AGCTTTAGGATGTATGAAATGATGGG 59.282 38.462 0.00 0.00 0.00 4.00
3229 3471 3.990959 TCACACATGTTGGCCTACATA 57.009 42.857 28.67 13.16 36.64 2.29
3236 3478 4.700213 ACATGTTGGCCTACATAACAGTTC 59.300 41.667 28.67 0.00 36.64 3.01
3237 3479 4.359434 TGTTGGCCTACATAACAGTTCA 57.641 40.909 16.47 0.00 31.34 3.18
3529 3776 9.614792 GACCACATATCCTAGTTATTCTTGTTT 57.385 33.333 0.00 0.00 0.00 2.83
3597 3844 5.702670 TGGACAGTTTTAAGCATCTCTTCAG 59.297 40.000 0.00 0.00 36.25 3.02
3639 3886 2.005451 CTCTGAAAGCTGGTCATTCCG 58.995 52.381 1.05 0.00 39.52 4.30
3649 3896 4.649674 AGCTGGTCATTCCGTATTCTCTTA 59.350 41.667 0.00 0.00 39.52 2.10
3707 3954 7.287696 AGTTTCAGGTTTAATTCATGTCTTGGT 59.712 33.333 0.00 0.00 0.00 3.67
3783 4033 9.004231 AGGACACCTGAAATTTAGTATAAGGAT 57.996 33.333 0.00 0.00 29.57 3.24
3833 4084 4.642437 TGCAAACCACACATCACTTCTTAA 59.358 37.500 0.00 0.00 0.00 1.85
3887 4141 2.092968 TCCCACCTTATCTGTGATGTGC 60.093 50.000 0.00 0.00 35.74 4.57
3888 4142 1.935873 CCACCTTATCTGTGATGTGCG 59.064 52.381 0.00 0.00 35.74 5.34
4055 4309 2.442830 GGCTCCCATTTCCCTGGC 60.443 66.667 0.00 0.00 34.77 4.85
4100 4354 2.938798 ACCCAAGGGATTGGCGGA 60.939 61.111 13.15 0.00 40.74 5.54
4142 4396 0.687354 CACCTGTAAGTGTCCCTGCT 59.313 55.000 0.00 0.00 32.89 4.24
4193 4447 1.339342 TGCTACGCTTTACCCCCTTTC 60.339 52.381 0.00 0.00 0.00 2.62
4391 4645 1.142748 CAGCTGCCCGAGTAGAAGG 59.857 63.158 0.00 0.00 0.00 3.46
4420 4674 1.799519 GATAGAGCCGCGCAGATCG 60.800 63.158 8.75 0.00 42.12 3.69
4437 4691 1.215382 CGGATCAAGTGCTCCGTGA 59.785 57.895 14.00 0.00 45.63 4.35
4448 4702 0.098376 GCTCCGTGATCGACTTACGT 59.902 55.000 14.26 0.00 43.13 3.57
4454 4708 2.975193 CGTGATCGACTTACGTTGTCAA 59.025 45.455 17.43 3.94 43.13 3.18
4455 4709 3.422876 CGTGATCGACTTACGTTGTCAAA 59.577 43.478 17.43 8.33 43.13 2.69
4478 4732 4.083643 AGTGACATCTTCATTGTTCAAGCG 60.084 41.667 0.00 0.00 36.32 4.68
4580 4834 5.312079 AGGCAGCTCTTTGGATATACATTC 58.688 41.667 0.00 0.00 0.00 2.67
4581 4835 4.153117 GGCAGCTCTTTGGATATACATTCG 59.847 45.833 0.00 0.00 0.00 3.34
4591 4851 7.728847 TTGGATATACATTCGGATTGACAAG 57.271 36.000 6.87 0.00 0.00 3.16
4594 4854 6.929049 GGATATACATTCGGATTGACAAGTGA 59.071 38.462 6.87 0.00 0.00 3.41
4595 4855 7.441157 GGATATACATTCGGATTGACAAGTGAA 59.559 37.037 6.87 0.00 0.00 3.18
4615 4875 1.160329 GCGGCATGATGTGGTACTCC 61.160 60.000 0.00 0.00 0.00 3.85
4638 4901 1.372128 CTGCTGCCGCCAAGTTTTC 60.372 57.895 0.00 0.00 34.43 2.29
4678 4941 2.894731 TCTGGTCCTTGTCTGATGACT 58.105 47.619 0.00 0.00 43.29 3.41
4790 5062 3.788434 ATTTTGTCTTGTCTACGTGCG 57.212 42.857 0.00 0.00 0.00 5.34
4791 5063 2.495409 TTTGTCTTGTCTACGTGCGA 57.505 45.000 0.00 0.00 0.00 5.10
4792 5064 2.495409 TTGTCTTGTCTACGTGCGAA 57.505 45.000 0.00 0.00 0.00 4.70
4793 5065 2.495409 TGTCTTGTCTACGTGCGAAA 57.505 45.000 0.00 0.00 0.00 3.46
4794 5066 2.811855 TGTCTTGTCTACGTGCGAAAA 58.188 42.857 0.00 0.00 0.00 2.29
4795 5067 3.386486 TGTCTTGTCTACGTGCGAAAAT 58.614 40.909 0.00 0.00 0.00 1.82
4796 5068 3.427528 TGTCTTGTCTACGTGCGAAAATC 59.572 43.478 0.00 0.00 0.00 2.17
4797 5069 3.673809 GTCTTGTCTACGTGCGAAAATCT 59.326 43.478 0.00 0.00 0.00 2.40
4798 5070 3.673338 TCTTGTCTACGTGCGAAAATCTG 59.327 43.478 0.00 0.00 0.00 2.90
4799 5071 3.021269 TGTCTACGTGCGAAAATCTGT 57.979 42.857 0.00 0.00 0.00 3.41
4800 5072 3.386486 TGTCTACGTGCGAAAATCTGTT 58.614 40.909 0.00 0.00 0.00 3.16
4801 5073 3.183574 TGTCTACGTGCGAAAATCTGTTG 59.816 43.478 0.00 0.00 0.00 3.33
4802 5074 2.734606 TCTACGTGCGAAAATCTGTTGG 59.265 45.455 0.00 0.00 0.00 3.77
4803 5075 0.040425 ACGTGCGAAAATCTGTTGGC 60.040 50.000 0.00 0.00 33.28 4.52
4804 5076 0.040514 CGTGCGAAAATCTGTTGGCA 60.041 50.000 0.00 0.00 39.53 4.92
4805 5077 1.401409 CGTGCGAAAATCTGTTGGCAT 60.401 47.619 0.00 0.00 42.94 4.40
4806 5078 1.987770 GTGCGAAAATCTGTTGGCATG 59.012 47.619 0.00 0.00 42.94 4.06
4807 5079 1.067706 TGCGAAAATCTGTTGGCATGG 60.068 47.619 0.00 0.00 37.31 3.66
4808 5080 1.202114 GCGAAAATCTGTTGGCATGGA 59.798 47.619 0.00 0.00 32.95 3.41
4809 5081 2.867429 CGAAAATCTGTTGGCATGGAC 58.133 47.619 0.00 0.00 0.00 4.02
4810 5082 2.728846 CGAAAATCTGTTGGCATGGACG 60.729 50.000 0.00 0.00 0.00 4.79
4811 5083 2.198827 AAATCTGTTGGCATGGACGA 57.801 45.000 0.00 0.00 0.00 4.20
4812 5084 1.742761 AATCTGTTGGCATGGACGAG 58.257 50.000 0.00 0.00 0.00 4.18
4813 5085 0.745845 ATCTGTTGGCATGGACGAGC 60.746 55.000 0.00 0.00 0.00 5.03
4869 5154 3.499338 TCAACATCAAAACCTCCAGCAT 58.501 40.909 0.00 0.00 0.00 3.79
4979 5266 2.803155 GATGAGCAGGGACGTTGGCA 62.803 60.000 0.00 0.00 0.00 4.92
5002 5289 3.243569 GCTCTACCGACATGCTGAACTAT 60.244 47.826 0.00 0.00 0.00 2.12
5243 5533 1.614903 CATGCTGCAAGAAGGGTTGAA 59.385 47.619 6.36 0.00 34.07 2.69
5254 5544 1.358152 AGGGTTGAATTGGACCGAGA 58.642 50.000 0.00 0.00 36.78 4.04
5364 5655 0.550914 ATGGCCGGGCAGAATTCTAA 59.449 50.000 35.19 9.28 0.00 2.10
5391 5682 0.681733 TCGAGGCAGCTCAAGAACTT 59.318 50.000 0.00 0.00 0.00 2.66
5490 5781 3.754323 GGTCCAAATCGTCCACATAACAA 59.246 43.478 0.00 0.00 0.00 2.83
5606 5898 2.194056 CATTCGGGGGCTGCATCT 59.806 61.111 0.50 0.00 0.00 2.90
5633 5925 0.248565 GTCTGGCATGAGAGCAGTCA 59.751 55.000 0.00 0.00 35.83 3.41
5750 6042 4.102681 GGTAGAATGCCATGTAGTACCCTT 59.897 45.833 0.00 0.00 42.29 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.621068 ATGATGTGTTATCTTGTTGCGG 57.379 40.909 0.00 0.00 0.00 5.69
25 26 4.512944 CGGCTGCTTATGATGTGTTATCTT 59.487 41.667 0.00 0.00 0.00 2.40
36 38 3.405093 CTGGGGCGGCTGCTTATGA 62.405 63.158 18.85 0.00 42.25 2.15
57 64 5.707066 AGAAGATACCTCTTGGATGCTTT 57.293 39.130 0.00 0.00 41.87 3.51
90 97 2.226330 TGTTCTGCGCACCAATTAGTT 58.774 42.857 5.66 0.00 0.00 2.24
102 113 0.320771 AGCACCTAGGTTGTTCTGCG 60.321 55.000 13.15 0.00 0.00 5.18
114 125 4.101114 TCCTTTAACTGGATCAGCACCTA 58.899 43.478 0.00 0.00 34.37 3.08
159 171 1.378514 CGGTAATGGCTTGCTGGGT 60.379 57.895 0.00 0.00 0.00 4.51
202 214 0.413434 TGAGGAGACCACCTGGATGA 59.587 55.000 0.00 0.00 40.73 2.92
205 217 1.079256 CCTGAGGAGACCACCTGGA 59.921 63.158 0.00 0.00 40.73 3.86
221 233 0.114954 TTTTGCCCATCCTTCAGCCT 59.885 50.000 0.00 0.00 0.00 4.58
241 253 3.242739 GGAACGATCCATCAACATTTCCG 60.243 47.826 6.88 0.00 45.79 4.30
242 254 4.292977 GGAACGATCCATCAACATTTCC 57.707 45.455 6.88 0.00 45.79 3.13
302 314 3.529341 ATGTCGTTGTGGAGCCGCA 62.529 57.895 0.00 0.00 34.35 5.69
313 325 5.248640 ACAGGATGAGAAAATGATGTCGTT 58.751 37.500 0.00 0.00 39.69 3.85
337 350 5.659440 TCTACACATGTATGCAACTCTCA 57.341 39.130 0.00 0.00 0.00 3.27
356 369 1.210478 GCTCAGCCTCCAATGGTTCTA 59.790 52.381 0.00 0.00 0.00 2.10
382 395 0.040058 TTGATGCCCTCCATGCAAGT 59.960 50.000 0.00 0.00 42.92 3.16
417 430 7.044181 TCTTCAATTCTATCAGCATCTTCGTT 58.956 34.615 0.00 0.00 0.00 3.85
428 441 5.190528 AGGCAGTCCTTCTTCAATTCTATCA 59.809 40.000 0.00 0.00 40.66 2.15
460 473 5.707764 TGTTCGGACCATTGATCATGTTAAA 59.292 36.000 0.00 0.00 0.00 1.52
471 484 2.854522 GTCCCTGTTCGGACCATTG 58.145 57.895 0.00 0.00 45.72 2.82
477 490 0.615544 AATACCGGTCCCTGTTCGGA 60.616 55.000 12.40 0.00 45.96 4.55
494 507 3.098377 TCAACCAACATGGCATAGCAAT 58.902 40.909 0.00 0.00 42.67 3.56
496 509 2.212812 TCAACCAACATGGCATAGCA 57.787 45.000 0.00 0.00 42.67 3.49
502 515 3.055963 TGGATTTGATCAACCAACATGGC 60.056 43.478 13.86 0.00 42.67 4.40
522 535 1.098050 CTTCCCTCGAAAGCCATTGG 58.902 55.000 0.00 0.00 0.00 3.16
526 539 1.537889 TCCCTTCCCTCGAAAGCCA 60.538 57.895 0.00 0.00 0.00 4.75
533 546 0.466124 GGACATTCTCCCTTCCCTCG 59.534 60.000 0.00 0.00 31.83 4.63
546 559 4.813161 CGAACATGAGATAGCTTGGACATT 59.187 41.667 0.00 0.00 0.00 2.71
551 564 4.302455 CCTACGAACATGAGATAGCTTGG 58.698 47.826 0.00 0.00 0.00 3.61
612 625 1.275291 ACAGTGTGACCTTATGTCCGG 59.725 52.381 0.00 0.00 43.78 5.14
634 647 2.933287 TCCCGAACCCAGCCACAT 60.933 61.111 0.00 0.00 0.00 3.21
640 653 2.581354 CTCTGCTCCCGAACCCAG 59.419 66.667 0.00 0.00 0.00 4.45
652 665 4.363991 AAATATCAGGGACATCCTCTGC 57.636 45.455 10.10 0.00 46.12 4.26
657 670 9.354673 TCATTCTTAAAAATATCAGGGACATCC 57.645 33.333 0.00 0.00 0.00 3.51
660 673 9.753674 AAGTCATTCTTAAAAATATCAGGGACA 57.246 29.630 0.00 0.00 34.23 4.02
709 722 4.920640 TTTAAATGCGTGTGAAAGGGAA 57.079 36.364 0.00 0.00 0.00 3.97
739 754 6.612456 TCTCTTGGGTTCGATTTATTAGGGTA 59.388 38.462 0.00 0.00 0.00 3.69
761 776 2.442236 TTCCCTTCCAATGGCATCTC 57.558 50.000 0.00 0.00 0.00 2.75
787 802 9.731819 TGAAAAACTTATATGCGTGTTGTTTAA 57.268 25.926 6.82 0.00 0.00 1.52
788 803 9.731819 TTGAAAAACTTATATGCGTGTTGTTTA 57.268 25.926 6.82 0.00 0.00 2.01
790 805 7.702772 TGTTGAAAAACTTATATGCGTGTTGTT 59.297 29.630 0.00 0.00 0.00 2.83
837 860 8.496534 AGGGCCTGCTTTATTGAAAAATATAT 57.503 30.769 4.50 0.00 0.00 0.86
839 862 6.813293 AGGGCCTGCTTTATTGAAAAATAT 57.187 33.333 4.50 0.00 0.00 1.28
840 863 6.212388 TGAAGGGCCTGCTTTATTGAAAAATA 59.788 34.615 14.07 0.00 0.00 1.40
841 864 5.012975 TGAAGGGCCTGCTTTATTGAAAAAT 59.987 36.000 14.07 0.00 0.00 1.82
847 870 2.165030 CTGTGAAGGGCCTGCTTTATTG 59.835 50.000 14.07 0.00 0.00 1.90
989 1015 1.392589 CTGTGTTTGTCTGTGGCCTT 58.607 50.000 3.32 0.00 0.00 4.35
990 1016 0.466189 CCTGTGTTTGTCTGTGGCCT 60.466 55.000 3.32 0.00 0.00 5.19
1163 1196 3.357166 GACATGAGGTCGTACATCTCC 57.643 52.381 0.00 0.00 36.65 3.71
1412 1452 3.731431 TCCTACCCTTTCCTGCATAGAA 58.269 45.455 0.00 0.00 0.00 2.10
1425 1465 5.607171 CAGGTATGGAGTTTTATCCTACCCT 59.393 44.000 13.32 5.40 40.44 4.34
1440 1480 4.534500 ACTACCATTTGTGACAGGTATGGA 59.466 41.667 22.08 10.49 38.39 3.41
1445 1485 2.870435 GCGACTACCATTTGTGACAGGT 60.870 50.000 0.56 0.56 38.14 4.00
1481 1521 1.304282 CTGGGGTAGCCAGCAATGT 59.696 57.895 14.06 0.00 0.00 2.71
1482 1522 0.323725 AACTGGGGTAGCCAGCAATG 60.324 55.000 14.06 0.00 38.72 2.82
1498 1538 4.404073 TGCAAACATGAACCAGGTTTAACT 59.596 37.500 6.21 0.00 44.59 2.24
1601 1642 6.127925 ACGACTATACACCACGTTCTTATGAA 60.128 38.462 0.00 0.00 33.48 2.57
1612 1653 6.587226 TCAACATTAACACGACTATACACCAC 59.413 38.462 0.00 0.00 0.00 4.16
1687 1729 0.721718 CATTCTTCTTCGCCGTCCAC 59.278 55.000 0.00 0.00 0.00 4.02
1694 1736 2.543848 TGTGACACACATTCTTCTTCGC 59.456 45.455 3.56 0.00 39.62 4.70
1726 1953 6.396450 AGTAGTGGATTCGGTTTTAGTCTTC 58.604 40.000 0.00 0.00 0.00 2.87
1758 1985 0.678950 AAACCATTGGGAAACAGGCG 59.321 50.000 7.78 0.00 38.05 5.52
1837 2067 4.039004 TGCATGATAACAAGGCAAGTTTGT 59.961 37.500 0.00 0.00 40.30 2.83
1856 2086 3.459598 ACCACACCCTATATTGACTGCAT 59.540 43.478 0.00 0.00 0.00 3.96
1879 2117 8.456904 TTGAAAGTTCACATATGTACGTAGAC 57.543 34.615 8.32 1.80 36.83 2.59
1883 2121 7.724305 AACTTGAAAGTTCACATATGTACGT 57.276 32.000 8.32 0.00 45.65 3.57
1911 2149 7.766219 ATCATTGTGAGCAAAATAATCAAGC 57.234 32.000 0.00 0.00 38.21 4.01
2147 2387 0.820891 CTGAGCAACTGTTGGCTGGT 60.821 55.000 21.01 2.08 41.22 4.00
2274 2514 2.037902 TGTCACATTAGAAGTGCCCGAA 59.962 45.455 0.00 0.00 36.93 4.30
2325 2565 2.161855 TGTGCTGATTGTGGTGGATTC 58.838 47.619 0.00 0.00 0.00 2.52
2874 3114 9.827411 GTCAACTTTAAGACAGGATAATCAAAC 57.173 33.333 0.00 0.00 34.93 2.93
2901 3141 8.195617 TGCATTTTTCTTTACACAAGGAAAAG 57.804 30.769 6.86 0.00 45.12 2.27
2922 3162 8.627403 CAGAAACATTCAGGAATATACTTGCAT 58.373 33.333 0.00 0.00 0.00 3.96
2980 3220 7.006509 ACCCCATCATTTCATACATCCTAAAG 58.993 38.462 0.00 0.00 0.00 1.85
3003 3245 9.149225 CTGAGATAATAGCAGATCAACAATACC 57.851 37.037 0.00 0.00 0.00 2.73
3229 3471 4.460263 TGTAGAAGGCAATGTGAACTGTT 58.540 39.130 0.00 0.00 0.00 3.16
3236 3478 6.913170 AGTAAAACATGTAGAAGGCAATGTG 58.087 36.000 0.00 0.00 0.00 3.21
3237 3479 7.370383 CAAGTAAAACATGTAGAAGGCAATGT 58.630 34.615 0.00 0.00 0.00 2.71
3529 3776 3.006752 GCCCTCAATTTTTGTGATGTCCA 59.993 43.478 0.00 0.00 0.00 4.02
3649 3896 8.803235 GTTAAGGGTTTCCTATTCAATCTTTGT 58.197 33.333 0.00 0.00 44.07 2.83
3707 3954 6.149142 GCTGGCAATCCATAAATCAACAAAAA 59.851 34.615 0.00 0.00 42.51 1.94
3833 4084 9.807649 GAATCTGGCAAACAACAATAATCTATT 57.192 29.630 0.00 0.00 0.00 1.73
3850 4104 2.027192 GTGGGACTGTTAGAATCTGGCA 60.027 50.000 0.00 0.00 0.00 4.92
3887 4141 5.106197 TGTTGATTTTTGAGTCCATGATCCG 60.106 40.000 0.00 0.00 0.00 4.18
3888 4142 6.071728 ACTGTTGATTTTTGAGTCCATGATCC 60.072 38.462 0.00 0.00 0.00 3.36
4055 4309 4.010349 GTCCAGGTAGACCTTGAAATTGG 58.990 47.826 4.14 0.00 46.09 3.16
4142 4396 5.825679 ACCACTTGTGTTCTAAAATGCAGTA 59.174 36.000 0.00 0.00 0.00 2.74
4391 4645 2.656085 CGGCTCTATCGAACTGTCATC 58.344 52.381 0.00 0.00 0.00 2.92
4420 4674 1.576356 GATCACGGAGCACTTGATCC 58.424 55.000 13.50 3.27 46.58 3.36
4454 4708 5.561532 CGCTTGAACAATGAAGATGTCACTT 60.562 40.000 0.00 0.00 39.72 3.16
4455 4709 4.083643 CGCTTGAACAATGAAGATGTCACT 60.084 41.667 0.00 0.00 39.72 3.41
4580 4834 0.443869 CCGCTTCACTTGTCAATCCG 59.556 55.000 0.00 0.00 0.00 4.18
4581 4835 0.169009 GCCGCTTCACTTGTCAATCC 59.831 55.000 0.00 0.00 0.00 3.01
4591 4851 1.308069 ACCACATCATGCCGCTTCAC 61.308 55.000 0.00 0.00 0.00 3.18
4594 4854 0.253044 AGTACCACATCATGCCGCTT 59.747 50.000 0.00 0.00 0.00 4.68
4595 4855 0.179073 GAGTACCACATCATGCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
4631 4891 2.088423 TCACAACACGGCAGAAAACTT 58.912 42.857 0.00 0.00 0.00 2.66
4638 4901 2.995466 ATTCAATCACAACACGGCAG 57.005 45.000 0.00 0.00 0.00 4.85
4678 4941 3.698539 CAGTCATCTCAAGAGCTAGACCA 59.301 47.826 0.00 0.00 0.00 4.02
4754 5020 7.693969 AGACAAAATTGAGAAAAGATCCGAT 57.306 32.000 0.00 0.00 0.00 4.18
4756 5022 7.141363 ACAAGACAAAATTGAGAAAAGATCCG 58.859 34.615 0.00 0.00 0.00 4.18
4757 5023 8.355913 AGACAAGACAAAATTGAGAAAAGATCC 58.644 33.333 0.00 0.00 0.00 3.36
4790 5062 2.487762 TCGTCCATGCCAACAGATTTTC 59.512 45.455 0.00 0.00 0.00 2.29
4791 5063 2.489329 CTCGTCCATGCCAACAGATTTT 59.511 45.455 0.00 0.00 0.00 1.82
4792 5064 2.086869 CTCGTCCATGCCAACAGATTT 58.913 47.619 0.00 0.00 0.00 2.17
4793 5065 1.742761 CTCGTCCATGCCAACAGATT 58.257 50.000 0.00 0.00 0.00 2.40
4794 5066 0.745845 GCTCGTCCATGCCAACAGAT 60.746 55.000 0.00 0.00 0.00 2.90
4795 5067 1.375908 GCTCGTCCATGCCAACAGA 60.376 57.895 0.00 0.00 0.00 3.41
4796 5068 1.364626 GAGCTCGTCCATGCCAACAG 61.365 60.000 0.00 0.00 0.00 3.16
4797 5069 1.375908 GAGCTCGTCCATGCCAACA 60.376 57.895 0.00 0.00 0.00 3.33
4798 5070 0.674895 AAGAGCTCGTCCATGCCAAC 60.675 55.000 8.37 0.00 0.00 3.77
4799 5071 0.036732 AAAGAGCTCGTCCATGCCAA 59.963 50.000 8.37 0.00 0.00 4.52
4800 5072 0.036732 AAAAGAGCTCGTCCATGCCA 59.963 50.000 8.37 0.00 0.00 4.92
4801 5073 1.168714 AAAAAGAGCTCGTCCATGCC 58.831 50.000 8.37 0.00 0.00 4.40
4869 5154 5.201243 TGTAACTAGCCTCTCAGCAGATTA 58.799 41.667 0.00 0.00 34.23 1.75
4979 5266 1.134965 GTTCAGCATGTCGGTAGAGCT 60.135 52.381 0.00 0.00 37.40 4.09
4982 5269 6.459670 TTTATAGTTCAGCATGTCGGTAGA 57.540 37.500 0.00 0.00 37.40 2.59
5002 5289 9.077885 AGCATGTTCCTTCATTTAAGTCTTTTA 57.922 29.630 0.00 0.00 32.89 1.52
5015 5302 1.198094 TCGGGGAGCATGTTCCTTCA 61.198 55.000 25.62 8.82 37.40 3.02
5101 5388 6.013379 AGTGGTTCTGGAGTCTGATAATTTGA 60.013 38.462 0.00 0.00 0.00 2.69
5144 5431 2.285834 CGATGGAGTTATCTTTGCGCAC 60.286 50.000 11.12 0.00 0.00 5.34
5243 5533 0.037734 GGGGTGTTTCTCGGTCCAAT 59.962 55.000 0.00 0.00 0.00 3.16
5254 5544 2.160853 GGAGGGACAGGGGGTGTTT 61.161 63.158 0.00 0.00 40.56 2.83
5297 5588 5.964758 TGGATCAAAATTAACACTGATGGC 58.035 37.500 0.00 0.00 0.00 4.40
5309 5600 4.202441 CTGAGTCGGGATGGATCAAAATT 58.798 43.478 0.00 0.00 0.00 1.82
5364 5655 1.999071 GAGCTGCCTCGAGATCACGT 61.999 60.000 15.71 0.00 34.70 4.49
5391 5682 2.654877 GGTTCGGGAGTCGCTTGA 59.345 61.111 5.58 0.00 39.05 3.02
5427 5718 4.634004 CCACGACAAGAATGCTTATAACCA 59.366 41.667 0.00 0.00 31.81 3.67
5490 5781 2.485426 CACAAAGAGCGACAATGGTGAT 59.515 45.455 0.00 0.00 0.00 3.06
5606 5898 3.405831 CTCTCATGCCAGACAGTTTTGA 58.594 45.455 0.00 0.00 0.00 2.69
5633 5925 2.029623 GACATGATGCATGCCCTTCTT 58.970 47.619 16.68 5.20 44.80 2.52


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

AutoCloner maintained by Alex Coulton.