Multiple sequence alignment - TraesCS7A01G532200

Loading Multiple Alignment...

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 TraesCS7A01G532200 chr7A 100.000 2315 0 0 1 2315 710960056 710957742 0.000000e+00 4276.0
1 TraesCS7A01G532200 chr7A 89.470 1472 150 5 737 2204 711172574 711171104 0.000000e+00 1855.0
2 TraesCS7A01G532200 chr7A 89.024 246 24 2 1 243 711173217 711172972 3.740000e-78 302.0
3 TraesCS7A01G532200 chr7A 76.096 251 37 18 372 605 711172815 711172571 2.430000e-20 110.0
4 TraesCS7A01G532200 chr7D 95.579 1606 68 3 713 2315 617197245 617198850 0.000000e+00 2569.0
5 TraesCS7A01G532200 chr7D 89.913 1497 140 9 712 2204 617378196 617376707 0.000000e+00 1917.0
6 TraesCS7A01G532200 chr7D 92.800 125 7 1 368 492 617197082 617197204 1.830000e-41 180.0
7 TraesCS7A01G532200 chr7B 91.489 1504 114 11 712 2211 711489528 711488035 0.000000e+00 2056.0
8 TraesCS7A01G532200 chr7B 91.406 1408 116 5 777 2180 711475569 711476975 0.000000e+00 1925.0
9 TraesCS7A01G532200 chr7B 81.443 97 8 4 385 481 711475373 711475459 1.150000e-08 71.3
10 TraesCS7A01G532200 chr4A 88.078 1275 140 6 895 2160 599612138 599613409 0.000000e+00 1502.0
11 TraesCS7A01G532200 chr4A 83.085 1277 204 10 905 2178 24557430 24556163 0.000000e+00 1151.0
12 TraesCS7A01G532200 chrUn 87.765 1275 144 6 901 2166 241849809 241848538 0.000000e+00 1480.0
13 TraesCS7A01G532200 chr4D 82.707 1278 207 12 905 2178 443206683 443207950 0.000000e+00 1123.0
14 TraesCS7A01G532200 chr1B 90.351 114 11 0 601 714 639906418 639906531 1.430000e-32 150.0
15 TraesCS7A01G532200 chr5B 89.474 114 12 0 601 714 634554196 634554083 6.670000e-31 145.0
16 TraesCS7A01G532200 chr5B 88.596 114 13 0 601 714 634458768 634458655 3.100000e-29 139.0
17 TraesCS7A01G532200 chr5A 89.474 114 12 0 601 714 391770363 391770250 6.670000e-31 145.0
18 TraesCS7A01G532200 chr1D 87.719 114 14 0 601 714 34663038 34663151 1.440000e-27 134.0
19 TraesCS7A01G532200 chr3B 87.387 111 14 0 605 715 582462534 582462644 6.710000e-26 128.0
20 TraesCS7A01G532200 chr4B 85.965 114 16 0 601 714 499289188 499289301 3.120000e-24 122.0


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 TraesCS7A01G532200 chr7A 710957742 710960056 2314 True 4276.000000 4276 100.000000 1 2315 1 chr7A.!!$R1 2314
1 TraesCS7A01G532200 chr7A 711171104 711173217 2113 True 755.666667 1855 84.863333 1 2204 3 chr7A.!!$R2 2203
2 TraesCS7A01G532200 chr7D 617376707 617378196 1489 True 1917.000000 1917 89.913000 712 2204 1 chr7D.!!$R1 1492
3 TraesCS7A01G532200 chr7D 617197082 617198850 1768 False 1374.500000 2569 94.189500 368 2315 2 chr7D.!!$F1 1947
4 TraesCS7A01G532200 chr7B 711488035 711489528 1493 True 2056.000000 2056 91.489000 712 2211 1 chr7B.!!$R1 1499
5 TraesCS7A01G532200 chr7B 711475373 711476975 1602 False 998.150000 1925 86.424500 385 2180 2 chr7B.!!$F1 1795
6 TraesCS7A01G532200 chr4A 599612138 599613409 1271 False 1502.000000 1502 88.078000 895 2160 1 chr4A.!!$F1 1265
7 TraesCS7A01G532200 chr4A 24556163 24557430 1267 True 1151.000000 1151 83.085000 905 2178 1 chr4A.!!$R1 1273
8 TraesCS7A01G532200 chrUn 241848538 241849809 1271 True 1480.000000 1480 87.765000 901 2166 1 chrUn.!!$R1 1265
9 TraesCS7A01G532200 chr4D 443206683 443207950 1267 False 1123.000000 1123 82.707000 905 2178 1 chr4D.!!$F1 1273

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
662 773 0.105964 CACCACCTCAACACCGAGAA 59.894 55.0 0.0 0.0 34.79 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1836 0.594028 GCGCGATCTCGGTGATGTTA 60.594 55.0 12.1 0.0 40.23 2.41 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
39 41 4.510167 ATCCTACCAGGGATGAAACTTG 57.490 45.455 0.00 0.00 43.70 3.16
58 60 4.574828 ACTTGAGGTTTGACACATGTGTAC 59.425 41.667 30.63 23.67 45.05 2.90
122 124 2.787339 TTGCTAGGGAGGTGCCTATA 57.213 50.000 0.00 0.00 36.66 1.31
130 132 4.047883 AGGGAGGTGCCTATAATGACTTT 58.952 43.478 0.00 0.00 36.66 2.66
139 141 7.148086 GGTGCCTATAATGACTTTGTCAATCAA 60.148 37.037 4.46 0.00 45.96 2.57
140 142 8.408601 GTGCCTATAATGACTTTGTCAATCAAT 58.591 33.333 4.46 0.21 45.96 2.57
160 162 5.475909 TCAATATATCCGTCGACTAAGCCTT 59.524 40.000 14.70 0.00 0.00 4.35
162 164 4.667519 ATATCCGTCGACTAAGCCTTTT 57.332 40.909 14.70 0.00 0.00 2.27
163 165 2.074547 TCCGTCGACTAAGCCTTTTG 57.925 50.000 14.70 0.00 0.00 2.44
184 186 5.825593 TGGAGGAGCTTATAAAGGTATGG 57.174 43.478 0.00 0.00 39.77 2.74
190 192 5.924825 GGAGCTTATAAAGGTATGGTGTACG 59.075 44.000 0.00 0.00 39.77 3.67
195 197 3.756933 AAAGGTATGGTGTACGTGTGT 57.243 42.857 0.00 0.00 0.00 3.72
196 198 3.756933 AAGGTATGGTGTACGTGTGTT 57.243 42.857 0.00 0.00 0.00 3.32
197 199 3.756933 AGGTATGGTGTACGTGTGTTT 57.243 42.857 0.00 0.00 0.00 2.83
198 200 4.075963 AGGTATGGTGTACGTGTGTTTT 57.924 40.909 0.00 0.00 0.00 2.43
200 202 5.609423 AGGTATGGTGTACGTGTGTTTTTA 58.391 37.500 0.00 0.00 0.00 1.52
243 247 2.223947 ACATGTGAGCGTCTGTGTTGTA 60.224 45.455 0.00 0.00 0.00 2.41
244 248 2.812358 TGTGAGCGTCTGTGTTGTAT 57.188 45.000 0.00 0.00 0.00 2.29
245 249 3.926821 TGTGAGCGTCTGTGTTGTATA 57.073 42.857 0.00 0.00 0.00 1.47
285 331 5.921962 AAGATCAGGACCAAAAATAAGGC 57.078 39.130 0.00 0.00 0.00 4.35
287 333 5.522641 AGATCAGGACCAAAAATAAGGCAT 58.477 37.500 0.00 0.00 0.00 4.40
288 334 5.960202 AGATCAGGACCAAAAATAAGGCATT 59.040 36.000 0.00 0.00 0.00 3.56
289 335 7.125391 AGATCAGGACCAAAAATAAGGCATTA 58.875 34.615 0.00 0.00 0.00 1.90
290 336 7.619302 AGATCAGGACCAAAAATAAGGCATTAA 59.381 33.333 0.00 0.00 0.00 1.40
291 337 7.169158 TCAGGACCAAAAATAAGGCATTAAG 57.831 36.000 0.00 0.00 0.00 1.85
293 339 7.122650 TCAGGACCAAAAATAAGGCATTAAGAG 59.877 37.037 0.00 0.00 0.00 2.85
294 340 6.954102 AGGACCAAAAATAAGGCATTAAGAGT 59.046 34.615 0.00 0.00 0.00 3.24
295 341 7.454694 AGGACCAAAAATAAGGCATTAAGAGTT 59.545 33.333 0.00 0.00 0.00 3.01
306 352 7.889589 AGGCATTAAGAGTTTAATTTTGTGC 57.110 32.000 0.00 0.00 37.38 4.57
307 353 7.441017 AGGCATTAAGAGTTTAATTTTGTGCA 58.559 30.769 0.00 0.00 37.38 4.57
308 354 7.930865 AGGCATTAAGAGTTTAATTTTGTGCAA 59.069 29.630 0.00 0.00 37.38 4.08
309 355 8.555361 GGCATTAAGAGTTTAATTTTGTGCAAA 58.445 29.630 0.00 0.00 37.38 3.68
310 356 9.928236 GCATTAAGAGTTTAATTTTGTGCAAAA 57.072 25.926 11.77 11.77 43.48 2.44
337 383 7.951530 AGACATTGAAAGCTTAATTTTGTGG 57.048 32.000 0.00 0.00 0.00 4.17
338 384 7.725251 AGACATTGAAAGCTTAATTTTGTGGA 58.275 30.769 0.00 0.00 0.00 4.02
339 385 8.203485 AGACATTGAAAGCTTAATTTTGTGGAA 58.797 29.630 0.00 0.00 0.00 3.53
340 386 8.729805 ACATTGAAAGCTTAATTTTGTGGAAA 57.270 26.923 0.00 0.00 0.00 3.13
341 387 9.171877 ACATTGAAAGCTTAATTTTGTGGAAAA 57.828 25.926 0.00 0.00 35.52 2.29
422 483 1.278337 CGCAAGTGCTACGTTTGCA 59.722 52.632 18.86 15.22 45.58 4.08
428 489 4.030529 GCAAGTGCTACGTTTGCATTAATG 59.969 41.667 15.19 11.27 44.88 1.90
476 569 7.382218 GCTGACTACAATTAATGCTTTGTTTGT 59.618 33.333 14.67 14.67 37.29 2.83
477 570 9.891828 CTGACTACAATTAATGCTTTGTTTGTA 57.108 29.630 15.11 15.11 37.29 2.41
546 649 3.259064 GAAGCACTAGACGCACCAAATA 58.741 45.455 10.72 0.00 0.00 1.40
562 673 4.758165 ACCAAATAAAGACACACTAACCCG 59.242 41.667 0.00 0.00 0.00 5.28
590 701 7.390718 GCTCATAAAGGAAAGAGTACTTCCAAA 59.609 37.037 13.40 0.61 35.05 3.28
603 714 7.227711 AGAGTACTTCCAAAGAAAAGAAAGAGC 59.772 37.037 0.00 0.00 0.00 4.09
604 715 5.175090 ACTTCCAAAGAAAAGAAAGAGCG 57.825 39.130 0.00 0.00 0.00 5.03
605 716 4.640647 ACTTCCAAAGAAAAGAAAGAGCGT 59.359 37.500 0.00 0.00 0.00 5.07
606 717 5.820947 ACTTCCAAAGAAAAGAAAGAGCGTA 59.179 36.000 0.00 0.00 0.00 4.42
607 718 6.486993 ACTTCCAAAGAAAAGAAAGAGCGTAT 59.513 34.615 0.00 0.00 0.00 3.06
608 719 6.877611 TCCAAAGAAAAGAAAGAGCGTATT 57.122 33.333 0.00 0.00 0.00 1.89
609 720 7.272037 TCCAAAGAAAAGAAAGAGCGTATTT 57.728 32.000 0.00 0.00 0.00 1.40
610 721 7.360361 TCCAAAGAAAAGAAAGAGCGTATTTC 58.640 34.615 3.91 3.91 37.00 2.17
611 722 6.582672 CCAAAGAAAAGAAAGAGCGTATTTCC 59.417 38.462 7.45 0.00 37.37 3.13
612 723 5.532025 AGAAAAGAAAGAGCGTATTTCCG 57.468 39.130 7.45 0.00 37.37 4.30
624 735 4.857871 CGTATTTCCGCTGATGAAGAAA 57.142 40.909 0.00 0.00 33.13 2.52
625 736 4.826500 CGTATTTCCGCTGATGAAGAAAG 58.173 43.478 0.00 0.00 32.19 2.62
626 737 4.566759 CGTATTTCCGCTGATGAAGAAAGA 59.433 41.667 0.00 0.00 32.19 2.52
627 738 5.063438 CGTATTTCCGCTGATGAAGAAAGAA 59.937 40.000 0.00 0.00 32.19 2.52
628 739 5.557891 ATTTCCGCTGATGAAGAAAGAAG 57.442 39.130 0.00 0.00 32.19 2.85
629 740 2.350522 TCCGCTGATGAAGAAAGAAGC 58.649 47.619 0.00 0.00 0.00 3.86
630 741 1.399791 CCGCTGATGAAGAAAGAAGCC 59.600 52.381 0.00 0.00 0.00 4.35
631 742 2.079158 CGCTGATGAAGAAAGAAGCCA 58.921 47.619 0.00 0.00 0.00 4.75
632 743 2.681848 CGCTGATGAAGAAAGAAGCCAT 59.318 45.455 0.00 0.00 0.00 4.40
633 744 3.128242 CGCTGATGAAGAAAGAAGCCATT 59.872 43.478 0.00 0.00 0.00 3.16
634 745 4.670347 GCTGATGAAGAAAGAAGCCATTC 58.330 43.478 0.00 0.00 35.52 2.67
635 746 4.730035 GCTGATGAAGAAAGAAGCCATTCG 60.730 45.833 0.00 0.00 40.58 3.34
636 747 3.691118 TGATGAAGAAAGAAGCCATTCGG 59.309 43.478 0.00 0.00 40.58 4.30
637 748 3.417069 TGAAGAAAGAAGCCATTCGGA 57.583 42.857 0.00 0.00 40.58 4.55
638 749 3.074412 TGAAGAAAGAAGCCATTCGGAC 58.926 45.455 0.00 0.00 40.58 4.79
639 750 2.859165 AGAAAGAAGCCATTCGGACA 57.141 45.000 0.00 0.00 40.58 4.02
640 751 3.140325 AGAAAGAAGCCATTCGGACAA 57.860 42.857 0.00 0.00 40.58 3.18
641 752 2.814336 AGAAAGAAGCCATTCGGACAAC 59.186 45.455 0.00 0.00 40.58 3.32
642 753 1.156736 AAGAAGCCATTCGGACAACG 58.843 50.000 0.00 0.00 46.11 4.10
643 754 1.134694 GAAGCCATTCGGACAACGC 59.865 57.895 0.00 0.00 43.86 4.84
644 755 1.573829 GAAGCCATTCGGACAACGCA 61.574 55.000 0.00 0.00 43.86 5.24
645 756 1.852067 AAGCCATTCGGACAACGCAC 61.852 55.000 0.00 0.00 43.86 5.34
646 757 2.867472 CCATTCGGACAACGCACC 59.133 61.111 0.00 0.00 43.86 5.01
647 758 1.963855 CCATTCGGACAACGCACCA 60.964 57.895 0.00 0.00 43.86 4.17
648 759 1.206578 CATTCGGACAACGCACCAC 59.793 57.895 0.00 0.00 43.86 4.16
649 760 1.964373 ATTCGGACAACGCACCACC 60.964 57.895 0.00 0.00 43.86 4.61
650 761 2.391724 ATTCGGACAACGCACCACCT 62.392 55.000 0.00 0.00 43.86 4.00
651 762 2.981977 TTCGGACAACGCACCACCTC 62.982 60.000 0.00 0.00 43.86 3.85
652 763 2.110213 GGACAACGCACCACCTCA 59.890 61.111 0.00 0.00 0.00 3.86
653 764 1.525077 GGACAACGCACCACCTCAA 60.525 57.895 0.00 0.00 0.00 3.02
654 765 1.647084 GACAACGCACCACCTCAAC 59.353 57.895 0.00 0.00 0.00 3.18
655 766 1.078072 ACAACGCACCACCTCAACA 60.078 52.632 0.00 0.00 0.00 3.33
656 767 1.355210 CAACGCACCACCTCAACAC 59.645 57.895 0.00 0.00 0.00 3.32
657 768 1.822186 AACGCACCACCTCAACACC 60.822 57.895 0.00 0.00 0.00 4.16
658 769 3.345808 CGCACCACCTCAACACCG 61.346 66.667 0.00 0.00 0.00 4.94
659 770 2.110213 GCACCACCTCAACACCGA 59.890 61.111 0.00 0.00 0.00 4.69
660 771 1.961277 GCACCACCTCAACACCGAG 60.961 63.158 0.00 0.00 0.00 4.63
661 772 1.745890 CACCACCTCAACACCGAGA 59.254 57.895 0.00 0.00 34.79 4.04
662 773 0.105964 CACCACCTCAACACCGAGAA 59.894 55.000 0.00 0.00 34.79 2.87
663 774 0.834612 ACCACCTCAACACCGAGAAA 59.165 50.000 0.00 0.00 34.79 2.52
664 775 1.210967 ACCACCTCAACACCGAGAAAA 59.789 47.619 0.00 0.00 34.79 2.29
665 776 2.158667 ACCACCTCAACACCGAGAAAAT 60.159 45.455 0.00 0.00 34.79 1.82
666 777 3.071892 ACCACCTCAACACCGAGAAAATA 59.928 43.478 0.00 0.00 34.79 1.40
667 778 4.069304 CCACCTCAACACCGAGAAAATAA 58.931 43.478 0.00 0.00 34.79 1.40
668 779 4.700213 CCACCTCAACACCGAGAAAATAAT 59.300 41.667 0.00 0.00 34.79 1.28
669 780 5.391950 CCACCTCAACACCGAGAAAATAATG 60.392 44.000 0.00 0.00 34.79 1.90
670 781 4.156008 ACCTCAACACCGAGAAAATAATGC 59.844 41.667 0.00 0.00 34.79 3.56
671 782 4.155826 CCTCAACACCGAGAAAATAATGCA 59.844 41.667 0.00 0.00 34.79 3.96
672 783 5.335583 CCTCAACACCGAGAAAATAATGCAA 60.336 40.000 0.00 0.00 34.79 4.08
673 784 6.078202 TCAACACCGAGAAAATAATGCAAA 57.922 33.333 0.00 0.00 0.00 3.68
674 785 6.507900 TCAACACCGAGAAAATAATGCAAAA 58.492 32.000 0.00 0.00 0.00 2.44
675 786 6.640499 TCAACACCGAGAAAATAATGCAAAAG 59.360 34.615 0.00 0.00 0.00 2.27
676 787 6.325919 ACACCGAGAAAATAATGCAAAAGA 57.674 33.333 0.00 0.00 0.00 2.52
677 788 6.149633 ACACCGAGAAAATAATGCAAAAGAC 58.850 36.000 0.00 0.00 0.00 3.01
678 789 5.572896 CACCGAGAAAATAATGCAAAAGACC 59.427 40.000 0.00 0.00 0.00 3.85
679 790 5.102313 CCGAGAAAATAATGCAAAAGACCC 58.898 41.667 0.00 0.00 0.00 4.46
680 791 5.336372 CCGAGAAAATAATGCAAAAGACCCA 60.336 40.000 0.00 0.00 0.00 4.51
681 792 6.155827 CGAGAAAATAATGCAAAAGACCCAA 58.844 36.000 0.00 0.00 0.00 4.12
682 793 6.308766 CGAGAAAATAATGCAAAAGACCCAAG 59.691 38.462 0.00 0.00 0.00 3.61
683 794 7.066307 AGAAAATAATGCAAAAGACCCAAGT 57.934 32.000 0.00 0.00 0.00 3.16
684 795 7.154656 AGAAAATAATGCAAAAGACCCAAGTC 58.845 34.615 0.00 0.00 43.89 3.01
695 806 3.040147 GACCCAAGTCTTTGATGACGA 57.960 47.619 0.00 0.00 41.47 4.20
696 807 3.399330 GACCCAAGTCTTTGATGACGAA 58.601 45.455 0.00 0.00 41.47 3.85
697 808 3.139077 ACCCAAGTCTTTGATGACGAAC 58.861 45.455 0.00 0.00 41.47 3.95
698 809 3.181454 ACCCAAGTCTTTGATGACGAACT 60.181 43.478 0.00 0.00 41.47 3.01
699 810 3.433615 CCCAAGTCTTTGATGACGAACTC 59.566 47.826 0.00 0.00 41.47 3.01
700 811 3.433615 CCAAGTCTTTGATGACGAACTCC 59.566 47.826 0.00 0.00 41.47 3.85
701 812 2.947852 AGTCTTTGATGACGAACTCCG 58.052 47.619 0.00 0.00 41.47 4.63
702 813 5.322038 CAAGTCTTTGATGACGAACTCCGT 61.322 45.833 0.00 0.00 45.01 4.69
703 814 7.290726 CAAGTCTTTGATGACGAACTCCGTG 62.291 48.000 0.00 0.00 43.50 4.94
710 821 3.449042 CGAACTCCGTGCGAAGAC 58.551 61.111 0.00 0.00 36.57 3.01
718 829 0.520827 CCGTGCGAAGACGAGTACTC 60.521 60.000 13.18 13.18 42.10 2.59
719 830 0.443088 CGTGCGAAGACGAGTACTCT 59.557 55.000 20.34 7.83 42.10 3.24
720 831 1.657594 CGTGCGAAGACGAGTACTCTA 59.342 52.381 20.34 0.00 42.10 2.43
723 834 4.090034 GTGCGAAGACGAGTACTCTAAAG 58.910 47.826 20.34 7.56 42.66 1.85
727 838 5.561993 CGAAGACGAGTACTCTAAAGGAAG 58.438 45.833 20.34 5.09 42.66 3.46
733 844 7.447853 AGACGAGTACTCTAAAGGAAGAGAAAA 59.552 37.037 20.34 0.00 44.93 2.29
734 845 7.369607 ACGAGTACTCTAAAGGAAGAGAAAAC 58.630 38.462 20.34 3.61 44.93 2.43
735 846 7.014038 ACGAGTACTCTAAAGGAAGAGAAAACA 59.986 37.037 20.34 0.00 44.93 2.83
825 936 2.357034 GACAACTTCCTCGCCGCA 60.357 61.111 0.00 0.00 0.00 5.69
838 949 1.811266 GCCGCATCATGTGTCGTCT 60.811 57.895 0.00 0.00 0.00 4.18
841 952 1.349234 CGCATCATGTGTCGTCTTCA 58.651 50.000 0.00 0.00 0.00 3.02
876 990 1.744639 GGCGGAGATCATCAGCTGA 59.255 57.895 20.79 20.79 46.97 4.26
928 1042 4.233635 CGGCCGTCGTCTACCTCG 62.234 72.222 19.50 0.00 0.00 4.63
1314 1437 4.745170 CGACATCATCGTGAACAAGTAG 57.255 45.455 0.00 0.00 46.25 2.57
1712 1835 1.991230 CCGGGAATTCACTCCAGGT 59.009 57.895 6.07 0.00 43.68 4.00
1713 1836 0.328258 CCGGGAATTCACTCCAGGTT 59.672 55.000 6.07 0.00 43.68 3.50
1824 1950 1.492176 CATGTCAAGCCCTACATCCCT 59.508 52.381 0.00 0.00 34.12 4.20
1849 1975 1.228094 TCCATGGCGTTCAAGCACA 60.228 52.632 6.96 0.00 39.27 4.57
1899 2025 0.249280 TCGACGAGCTGCAGACAAAA 60.249 50.000 20.43 0.00 0.00 2.44
1905 2031 0.179045 AGCTGCAGACAAAACTCCGT 60.179 50.000 20.43 0.00 0.00 4.69
1941 2067 4.492160 GAGGCGTCGCGGATGACA 62.492 66.667 11.75 0.00 38.84 3.58
2204 2334 9.833917 GCTTACTATCTTTACAGAATAAACCCT 57.166 33.333 0.00 0.00 30.76 4.34
2211 2341 5.703730 TTACAGAATAAACCCTACCCAGG 57.296 43.478 0.00 0.00 42.22 4.45
2213 2343 4.380791 ACAGAATAAACCCTACCCAGGAT 58.619 43.478 0.00 0.00 45.91 3.24
2292 2422 1.669115 TCGCTGCTGCTTTGAGACC 60.669 57.895 14.03 0.00 36.97 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.028638 TCCCTGGTAGGATGGGGTAA 58.971 55.000 0.00 0.00 37.67 2.85
19 20 3.519510 CTCAAGTTTCATCCCTGGTAGGA 59.480 47.826 0.00 0.00 37.67 2.94
39 41 3.740115 AGGTACACATGTGTCAAACCTC 58.260 45.455 32.56 17.39 43.06 3.85
58 60 6.655003 TGAAAGAATAGTCTGCCTTTACAAGG 59.345 38.462 0.00 0.00 41.96 3.61
70 72 4.621747 CGCCTTCCACTGAAAGAATAGTCT 60.622 45.833 0.00 0.00 37.43 3.24
110 112 4.781934 ACAAAGTCATTATAGGCACCTCC 58.218 43.478 0.00 0.00 0.00 4.30
122 124 9.342308 ACGGATATATTGATTGACAAAGTCATT 57.658 29.630 0.12 0.00 42.40 2.57
130 132 6.327279 AGTCGACGGATATATTGATTGACA 57.673 37.500 10.46 0.00 0.00 3.58
139 141 5.979288 AAAGGCTTAGTCGACGGATATAT 57.021 39.130 10.46 0.00 0.00 0.86
140 142 5.508489 CCAAAAGGCTTAGTCGACGGATATA 60.508 44.000 10.46 0.00 0.00 0.86
144 146 1.337447 CCAAAAGGCTTAGTCGACGGA 60.337 52.381 10.46 0.00 0.00 4.69
147 149 2.028385 TCCTCCAAAAGGCTTAGTCGAC 60.028 50.000 7.70 7.70 45.78 4.20
160 162 6.159751 ACCATACCTTTATAAGCTCCTCCAAA 59.840 38.462 0.00 0.00 0.00 3.28
162 164 5.071788 CACCATACCTTTATAAGCTCCTCCA 59.928 44.000 0.00 0.00 0.00 3.86
163 165 5.071923 ACACCATACCTTTATAAGCTCCTCC 59.928 44.000 0.00 0.00 0.00 4.30
177 179 3.756933 AAACACACGTACACCATACCT 57.243 42.857 0.00 0.00 0.00 3.08
184 186 9.525007 CTCAATCTTATAAAAACACACGTACAC 57.475 33.333 0.00 0.00 0.00 2.90
212 216 3.581755 ACGCTCACATGTAAACACGTAT 58.418 40.909 0.00 0.00 0.00 3.06
215 219 2.058798 AGACGCTCACATGTAAACACG 58.941 47.619 0.00 1.08 0.00 4.49
220 224 2.799978 CAACACAGACGCTCACATGTAA 59.200 45.455 0.00 0.00 0.00 2.41
265 311 5.859205 ATGCCTTATTTTTGGTCCTGATC 57.141 39.130 0.00 0.00 0.00 2.92
280 326 9.418045 GCACAAAATTAAACTCTTAATGCCTTA 57.582 29.630 0.00 0.00 37.70 2.69
281 327 7.930865 TGCACAAAATTAAACTCTTAATGCCTT 59.069 29.630 0.00 0.00 37.70 4.35
282 328 7.441017 TGCACAAAATTAAACTCTTAATGCCT 58.559 30.769 0.00 0.00 37.70 4.75
284 330 9.928236 TTTTGCACAAAATTAAACTCTTAATGC 57.072 25.926 4.47 0.00 37.70 3.56
311 357 8.829612 CCACAAAATTAAGCTTTCAATGTCTTT 58.170 29.630 3.20 0.00 0.00 2.52
312 358 8.203485 TCCACAAAATTAAGCTTTCAATGTCTT 58.797 29.630 3.20 0.00 0.00 3.01
313 359 7.725251 TCCACAAAATTAAGCTTTCAATGTCT 58.275 30.769 3.20 0.00 0.00 3.41
315 361 8.729805 TTTCCACAAAATTAAGCTTTCAATGT 57.270 26.923 3.20 1.44 0.00 2.71
346 392 8.239998 GCTGCTTTAATTAAACTCTCAATGTCT 58.760 33.333 6.54 0.00 0.00 3.41
347 393 8.023128 TGCTGCTTTAATTAAACTCTCAATGTC 58.977 33.333 6.54 0.00 0.00 3.06
422 483 4.156455 AGCGAACTGATGGGTCATTAAT 57.844 40.909 0.00 0.00 32.98 1.40
534 637 3.250040 AGTGTGTCTTTATTTGGTGCGTC 59.750 43.478 0.00 0.00 0.00 5.19
546 649 1.692519 AGCTCGGGTTAGTGTGTCTTT 59.307 47.619 0.00 0.00 0.00 2.52
562 673 6.759356 GGAAGTACTCTTTCCTTTATGAGCTC 59.241 42.308 6.82 6.82 33.64 4.09
590 701 5.532025 CGGAAATACGCTCTTTCTTTTCT 57.468 39.130 5.33 0.00 33.93 2.52
603 714 4.566759 TCTTTCTTCATCAGCGGAAATACG 59.433 41.667 0.00 0.00 0.00 3.06
604 715 6.422776 TTCTTTCTTCATCAGCGGAAATAC 57.577 37.500 0.00 0.00 0.00 1.89
605 716 5.065218 GCTTCTTTCTTCATCAGCGGAAATA 59.935 40.000 0.00 0.00 0.00 1.40
606 717 4.142513 GCTTCTTTCTTCATCAGCGGAAAT 60.143 41.667 0.00 0.00 0.00 2.17
607 718 3.189287 GCTTCTTTCTTCATCAGCGGAAA 59.811 43.478 0.00 0.00 0.00 3.13
608 719 2.744202 GCTTCTTTCTTCATCAGCGGAA 59.256 45.455 0.00 0.00 0.00 4.30
609 720 2.350522 GCTTCTTTCTTCATCAGCGGA 58.649 47.619 0.00 0.00 0.00 5.54
610 721 1.399791 GGCTTCTTTCTTCATCAGCGG 59.600 52.381 0.00 0.00 0.00 5.52
611 722 2.079158 TGGCTTCTTTCTTCATCAGCG 58.921 47.619 0.00 0.00 0.00 5.18
612 723 4.670347 GAATGGCTTCTTTCTTCATCAGC 58.330 43.478 0.00 0.00 0.00 4.26
613 724 4.201891 CCGAATGGCTTCTTTCTTCATCAG 60.202 45.833 0.00 0.00 0.00 2.90
614 725 3.691118 CCGAATGGCTTCTTTCTTCATCA 59.309 43.478 0.00 0.00 0.00 3.07
615 726 3.941483 TCCGAATGGCTTCTTTCTTCATC 59.059 43.478 0.00 0.00 34.14 2.92
616 727 3.691609 GTCCGAATGGCTTCTTTCTTCAT 59.308 43.478 0.00 0.00 34.14 2.57
617 728 3.074412 GTCCGAATGGCTTCTTTCTTCA 58.926 45.455 0.00 0.00 34.14 3.02
618 729 3.074412 TGTCCGAATGGCTTCTTTCTTC 58.926 45.455 0.00 0.00 34.14 2.87
619 730 3.140325 TGTCCGAATGGCTTCTTTCTT 57.860 42.857 0.00 0.00 34.14 2.52
620 731 2.814336 GTTGTCCGAATGGCTTCTTTCT 59.186 45.455 0.00 0.00 34.14 2.52
621 732 2.412847 CGTTGTCCGAATGGCTTCTTTC 60.413 50.000 0.00 0.00 39.56 2.62
622 733 1.535462 CGTTGTCCGAATGGCTTCTTT 59.465 47.619 0.00 0.00 39.56 2.52
623 734 1.156736 CGTTGTCCGAATGGCTTCTT 58.843 50.000 0.00 0.00 39.56 2.52
624 735 1.298859 GCGTTGTCCGAATGGCTTCT 61.299 55.000 0.00 0.00 39.56 2.85
625 736 1.134694 GCGTTGTCCGAATGGCTTC 59.865 57.895 0.00 0.00 39.56 3.86
626 737 1.599518 TGCGTTGTCCGAATGGCTT 60.600 52.632 0.00 0.00 39.56 4.35
627 738 2.031919 TGCGTTGTCCGAATGGCT 59.968 55.556 0.00 0.00 39.56 4.75
628 739 2.175811 GTGCGTTGTCCGAATGGC 59.824 61.111 0.00 0.00 39.56 4.40
629 740 1.963855 TGGTGCGTTGTCCGAATGG 60.964 57.895 0.00 0.00 39.56 3.16
630 741 1.206578 GTGGTGCGTTGTCCGAATG 59.793 57.895 0.00 0.00 39.56 2.67
631 742 1.964373 GGTGGTGCGTTGTCCGAAT 60.964 57.895 0.00 0.00 39.56 3.34
632 743 2.589442 GGTGGTGCGTTGTCCGAA 60.589 61.111 0.00 0.00 39.56 4.30
633 744 3.509137 GAGGTGGTGCGTTGTCCGA 62.509 63.158 0.00 0.00 39.56 4.55
634 745 3.041940 GAGGTGGTGCGTTGTCCG 61.042 66.667 0.00 0.00 40.40 4.79
635 746 1.525077 TTGAGGTGGTGCGTTGTCC 60.525 57.895 0.00 0.00 0.00 4.02
636 747 1.092921 TGTTGAGGTGGTGCGTTGTC 61.093 55.000 0.00 0.00 0.00 3.18
637 748 1.078072 TGTTGAGGTGGTGCGTTGT 60.078 52.632 0.00 0.00 0.00 3.32
638 749 1.355210 GTGTTGAGGTGGTGCGTTG 59.645 57.895 0.00 0.00 0.00 4.10
639 750 1.822186 GGTGTTGAGGTGGTGCGTT 60.822 57.895 0.00 0.00 0.00 4.84
640 751 2.203153 GGTGTTGAGGTGGTGCGT 60.203 61.111 0.00 0.00 0.00 5.24
641 752 3.345808 CGGTGTTGAGGTGGTGCG 61.346 66.667 0.00 0.00 0.00 5.34
642 753 1.961277 CTCGGTGTTGAGGTGGTGC 60.961 63.158 0.00 0.00 32.18 5.01
643 754 0.105964 TTCTCGGTGTTGAGGTGGTG 59.894 55.000 0.00 0.00 36.61 4.17
644 755 0.834612 TTTCTCGGTGTTGAGGTGGT 59.165 50.000 0.00 0.00 36.61 4.16
645 756 1.961793 TTTTCTCGGTGTTGAGGTGG 58.038 50.000 0.00 0.00 36.61 4.61
646 757 5.631026 CATTATTTTCTCGGTGTTGAGGTG 58.369 41.667 0.00 0.00 36.61 4.00
647 758 4.156008 GCATTATTTTCTCGGTGTTGAGGT 59.844 41.667 0.00 0.00 36.61 3.85
648 759 4.155826 TGCATTATTTTCTCGGTGTTGAGG 59.844 41.667 0.00 0.00 36.61 3.86
649 760 5.295431 TGCATTATTTTCTCGGTGTTGAG 57.705 39.130 0.00 0.00 37.33 3.02
650 761 5.697473 TTGCATTATTTTCTCGGTGTTGA 57.303 34.783 0.00 0.00 0.00 3.18
651 762 6.640499 TCTTTTGCATTATTTTCTCGGTGTTG 59.360 34.615 0.00 0.00 0.00 3.33
652 763 6.640907 GTCTTTTGCATTATTTTCTCGGTGTT 59.359 34.615 0.00 0.00 0.00 3.32
653 764 6.149633 GTCTTTTGCATTATTTTCTCGGTGT 58.850 36.000 0.00 0.00 0.00 4.16
654 765 5.572896 GGTCTTTTGCATTATTTTCTCGGTG 59.427 40.000 0.00 0.00 0.00 4.94
655 766 5.336451 GGGTCTTTTGCATTATTTTCTCGGT 60.336 40.000 0.00 0.00 0.00 4.69
656 767 5.102313 GGGTCTTTTGCATTATTTTCTCGG 58.898 41.667 0.00 0.00 0.00 4.63
657 768 5.708948 TGGGTCTTTTGCATTATTTTCTCG 58.291 37.500 0.00 0.00 0.00 4.04
658 769 7.154656 ACTTGGGTCTTTTGCATTATTTTCTC 58.845 34.615 0.00 0.00 0.00 2.87
659 770 7.066307 ACTTGGGTCTTTTGCATTATTTTCT 57.934 32.000 0.00 0.00 0.00 2.52
660 771 7.351414 GACTTGGGTCTTTTGCATTATTTTC 57.649 36.000 0.00 0.00 39.24 2.29
675 786 3.040147 TCGTCATCAAAGACTTGGGTC 57.960 47.619 0.00 0.00 42.41 4.46
676 787 3.139077 GTTCGTCATCAAAGACTTGGGT 58.861 45.455 0.00 0.00 36.38 4.51
677 788 3.403038 AGTTCGTCATCAAAGACTTGGG 58.597 45.455 0.00 0.00 36.38 4.12
678 789 3.433615 GGAGTTCGTCATCAAAGACTTGG 59.566 47.826 0.00 0.00 36.38 3.61
679 790 3.121944 CGGAGTTCGTCATCAAAGACTTG 59.878 47.826 0.00 0.00 36.38 3.16
680 791 3.318017 CGGAGTTCGTCATCAAAGACTT 58.682 45.455 0.00 0.00 36.38 3.01
681 792 2.947852 CGGAGTTCGTCATCAAAGACT 58.052 47.619 0.00 0.00 36.38 3.24
694 805 1.066114 CTCGTCTTCGCACGGAGTTC 61.066 60.000 0.00 0.00 40.35 3.01
695 806 1.081376 CTCGTCTTCGCACGGAGTT 60.081 57.895 0.00 0.00 40.35 3.01
696 807 0.952497 TACTCGTCTTCGCACGGAGT 60.952 55.000 0.00 1.63 40.35 3.85
697 808 0.520827 GTACTCGTCTTCGCACGGAG 60.521 60.000 0.00 0.00 40.35 4.63
698 809 0.952497 AGTACTCGTCTTCGCACGGA 60.952 55.000 0.00 0.00 40.35 4.69
699 810 0.520827 GAGTACTCGTCTTCGCACGG 60.521 60.000 7.22 0.00 40.35 4.94
700 811 0.443088 AGAGTACTCGTCTTCGCACG 59.557 55.000 17.07 0.00 41.36 5.34
701 812 3.736530 TTAGAGTACTCGTCTTCGCAC 57.263 47.619 17.07 0.00 36.96 5.34
702 813 3.126514 CCTTTAGAGTACTCGTCTTCGCA 59.873 47.826 17.07 0.00 36.96 5.10
703 814 3.373439 TCCTTTAGAGTACTCGTCTTCGC 59.627 47.826 17.07 0.00 36.96 4.70
704 815 5.350914 TCTTCCTTTAGAGTACTCGTCTTCG 59.649 44.000 17.07 5.11 38.55 3.79
705 816 6.594937 TCTCTTCCTTTAGAGTACTCGTCTTC 59.405 42.308 17.07 0.00 41.91 2.87
706 817 6.474630 TCTCTTCCTTTAGAGTACTCGTCTT 58.525 40.000 17.07 2.42 41.91 3.01
707 818 6.052405 TCTCTTCCTTTAGAGTACTCGTCT 57.948 41.667 17.07 2.80 41.91 4.18
708 819 6.740411 TTCTCTTCCTTTAGAGTACTCGTC 57.260 41.667 17.07 0.00 41.91 4.20
709 820 7.014038 TGTTTTCTCTTCCTTTAGAGTACTCGT 59.986 37.037 17.07 8.42 41.91 4.18
710 821 7.368833 TGTTTTCTCTTCCTTTAGAGTACTCG 58.631 38.462 17.07 2.89 41.91 4.18
718 829 5.009010 TGCTGCTTGTTTTCTCTTCCTTTAG 59.991 40.000 0.00 0.00 0.00 1.85
719 830 4.887071 TGCTGCTTGTTTTCTCTTCCTTTA 59.113 37.500 0.00 0.00 0.00 1.85
720 831 3.701040 TGCTGCTTGTTTTCTCTTCCTTT 59.299 39.130 0.00 0.00 0.00 3.11
723 834 3.572584 CATGCTGCTTGTTTTCTCTTCC 58.427 45.455 7.32 0.00 0.00 3.46
727 838 1.334054 CGCATGCTGCTTGTTTTCTC 58.666 50.000 17.13 0.00 42.25 2.87
733 844 3.425713 CGACCGCATGCTGCTTGT 61.426 61.111 17.13 4.80 42.25 3.16
734 845 3.372676 GACGACCGCATGCTGCTTG 62.373 63.158 17.13 10.85 42.25 4.01
735 846 3.121030 GACGACCGCATGCTGCTT 61.121 61.111 17.13 0.00 42.25 3.91
825 936 3.264947 CACCATGAAGACGACACATGAT 58.735 45.455 19.42 6.44 42.41 2.45
1314 1437 3.088500 GATGTCGCAGCGCAGGTTC 62.089 63.158 10.87 2.98 33.74 3.62
1485 1608 2.042831 GTTTGGCAGGAGCATCGCT 61.043 57.895 0.00 0.00 44.61 4.93
1712 1835 1.835121 CGCGATCTCGGTGATGTTAA 58.165 50.000 0.00 0.00 40.23 2.01
1713 1836 0.594028 GCGCGATCTCGGTGATGTTA 60.594 55.000 12.10 0.00 40.23 2.41
1805 1928 1.898863 AGGGATGTAGGGCTTGACAT 58.101 50.000 0.21 0.21 38.99 3.06
1824 1950 3.334691 CTTGAACGCCATGGAGAAGTTA 58.665 45.455 23.45 0.90 0.00 2.24
1849 1975 3.814268 GCCCGCGTGAATGCACAT 61.814 61.111 4.92 0.00 45.41 3.21
1905 2031 2.041115 CACCTGCTCGTCCGAGAGA 61.041 63.158 20.07 4.98 44.53 3.10
2028 2154 1.669760 GCCGACCATCCAAACACGA 60.670 57.895 0.00 0.00 0.00 4.35
2041 2167 4.821589 CCCTGAGCCGAAGCCGAC 62.822 72.222 0.00 0.00 41.25 4.79
2204 2334 3.009695 ACGAAAACCATTCATCCTGGGTA 59.990 43.478 0.00 0.00 38.14 3.69
2211 2341 5.006358 ACGCATAGTACGAAAACCATTCATC 59.994 40.000 0.00 0.00 0.00 2.92
2213 2343 4.092237 CACGCATAGTACGAAAACCATTCA 59.908 41.667 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.