Multiple sequence alignment - TraesCS3B01G516700

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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 TraesCS3B01G516700 chr3B 100.000 2312 0 0 1 2312 759092384 759094695 0.000000e+00 4270.0
1 TraesCS3B01G516700 chr3B 88.491 530 53 5 1778 2305 758852128 758852651 3.240000e-178 634.0
2 TraesCS3B01G516700 chr3B 85.141 498 46 7 1778 2275 758828887 758829356 3.450000e-133 484.0
3 TraesCS3B01G516700 chr3B 84.739 498 47 9 1778 2275 758748645 758749113 2.690000e-129 472.0
4 TraesCS3B01G516700 chr3B 86.331 417 37 12 1778 2190 759098968 759099368 9.810000e-119 436.0
5 TraesCS3B01G516700 chr3B 78.959 442 72 11 851 1290 328623834 328624256 4.860000e-72 281.0
6 TraesCS3B01G516700 chr3B 78.224 473 75 14 1282 1727 762409775 762409304 6.290000e-71 278.0
7 TraesCS3B01G516700 chr3B 80.935 278 27 6 1819 2096 758968943 758969194 1.810000e-46 196.0
8 TraesCS3B01G516700 chr3B 83.007 153 12 6 1778 1916 758641970 758642122 2.410000e-25 126.0
9 TraesCS3B01G516700 chr3A 91.733 1500 95 18 818 2312 704353454 704354929 0.000000e+00 2056.0
10 TraesCS3B01G516700 chr3A 92.375 341 22 2 1931 2271 704458614 704458950 1.240000e-132 483.0
11 TraesCS3B01G516700 chr3A 79.050 463 83 5 829 1290 715642999 715642550 2.890000e-79 305.0
12 TraesCS3B01G516700 chr3A 78.879 464 74 6 1282 1722 399702548 399702086 2.250000e-75 292.0
13 TraesCS3B01G516700 chr5D 89.210 658 39 13 132 764 56584905 56584255 0.000000e+00 793.0
14 TraesCS3B01G516700 chr5D 86.309 745 70 22 1 727 532839398 532840128 0.000000e+00 782.0
15 TraesCS3B01G516700 chr5D 88.045 619 55 14 1 607 121971157 121970546 0.000000e+00 715.0
16 TraesCS3B01G516700 chr5D 82.684 462 71 2 829 1290 425017523 425017975 3.580000e-108 401.0
17 TraesCS3B01G516700 chr5D 80.705 482 74 7 810 1290 482894591 482894128 7.860000e-95 357.0
18 TraesCS3B01G516700 chr5D 83.204 387 54 6 1346 1723 503829375 503828991 6.120000e-91 344.0
19 TraesCS3B01G516700 chr5D 79.083 349 51 15 1282 1608 230041591 230041939 1.080000e-53 220.0
20 TraesCS3B01G516700 chrUn 90.099 606 34 14 167 751 190469609 190469009 0.000000e+00 763.0
21 TraesCS3B01G516700 chr4D 87.408 683 63 14 1 668 222660355 222659681 0.000000e+00 763.0
22 TraesCS3B01G516700 chr4D 86.080 625 68 14 134 750 262514758 262515371 0.000000e+00 654.0
23 TraesCS3B01G516700 chr4D 83.108 296 40 2 1282 1567 39976993 39977288 6.340000e-66 261.0
24 TraesCS3B01G516700 chr4D 76.947 321 61 9 1284 1601 29796769 29797079 1.100000e-38 171.0
25 TraesCS3B01G516700 chr2D 88.468 633 54 14 1 619 120385996 120386623 0.000000e+00 747.0
26 TraesCS3B01G516700 chr2D 82.573 482 65 7 810 1290 600136759 600136296 7.690000e-110 407.0
27 TraesCS3B01G516700 chr2D 80.529 416 64 9 1283 1686 535282612 535283022 1.040000e-78 303.0
28 TraesCS3B01G516700 chr2D 83.513 279 45 1 1012 1290 469184579 469184856 2.280000e-65 259.0
29 TraesCS3B01G516700 chr2D 80.451 266 52 0 1025 1290 536391883 536391618 1.080000e-48 204.0
30 TraesCS3B01G516700 chr1D 87.500 648 47 11 132 751 232862824 232863465 0.000000e+00 717.0
31 TraesCS3B01G516700 chr1D 78.744 414 60 15 1282 1668 247872228 247872640 3.810000e-63 252.0
32 TraesCS3B01G516700 chr1D 79.420 345 59 11 1420 1758 350301395 350301733 1.380000e-57 233.0
33 TraesCS3B01G516700 chr1D 76.224 429 74 12 1282 1682 38363338 38363766 3.900000e-48 202.0
34 TraesCS3B01G516700 chr1B 88.006 617 56 16 1 606 50842748 50842139 0.000000e+00 713.0
35 TraesCS3B01G516700 chr1B 89.076 238 20 4 1 237 147596122 147596354 8.080000e-75 291.0
36 TraesCS3B01G516700 chr5B 88.403 595 51 10 1 579 175151859 175152451 0.000000e+00 701.0
37 TraesCS3B01G516700 chr5B 80.556 468 67 13 825 1290 514072102 514072547 2.850000e-89 339.0
38 TraesCS3B01G516700 chr5B 79.787 282 36 16 1421 1691 682120164 682119893 3.920000e-43 185.0
39 TraesCS3B01G516700 chr3D 87.622 614 60 9 1 607 535034536 535033932 0.000000e+00 699.0
40 TraesCS3B01G516700 chr3D 87.698 252 22 6 505 751 596227521 596227274 3.760000e-73 285.0
41 TraesCS3B01G516700 chr3D 86.765 204 21 4 551 751 594398970 594399170 2.990000e-54 222.0
42 TraesCS3B01G516700 chr3D 82.937 252 37 5 499 750 607257102 607257347 2.990000e-54 222.0
43 TraesCS3B01G516700 chr3D 88.272 162 18 1 1778 1938 571853392 571853553 2.340000e-45 193.0
44 TraesCS3B01G516700 chr1A 86.392 632 69 12 134 756 161510603 161509980 0.000000e+00 675.0
45 TraesCS3B01G516700 chr1A 75.934 482 85 12 810 1290 547421428 547421879 3.870000e-53 219.0
46 TraesCS3B01G516700 chr2A 84.783 598 62 18 1 590 689961142 689961718 7.170000e-160 573.0
47 TraesCS3B01G516700 chr2A 82.324 413 63 8 1282 1687 678451831 678452240 1.310000e-92 350.0
48 TraesCS3B01G516700 chr4B 82.919 644 66 14 132 764 289271690 289272300 7.270000e-150 540.0
49 TraesCS3B01G516700 chr4B 78.348 351 64 7 816 1164 520843490 520843830 1.390000e-52 217.0
50 TraesCS3B01G516700 chr4B 83.784 185 28 2 1420 1602 122314668 122314484 8.490000e-40 174.0
51 TraesCS3B01G516700 chr7D 83.649 422 59 3 869 1290 454069524 454069113 2.790000e-104 388.0
52 TraesCS3B01G516700 chr7D 80.687 466 73 8 825 1290 575755257 575754809 1.700000e-91 346.0
53 TraesCS3B01G516700 chr7D 79.874 318 54 2 847 1164 203168266 203167959 8.310000e-55 224.0
54 TraesCS3B01G516700 chr7D 91.228 57 4 1 753 809 482053219 482053164 2.460000e-10 76.8
55 TraesCS3B01G516700 chr7B 81.289 481 55 14 810 1288 337157675 337157228 7.860000e-95 357.0
56 TraesCS3B01G516700 chr7B 79.012 243 48 3 1429 1668 451169351 451169593 1.840000e-36 163.0
57 TraesCS3B01G516700 chr2B 84.400 250 39 0 1043 1292 21846198 21845949 1.770000e-61 246.0
58 TraesCS3B01G516700 chr2B 85.646 209 30 0 1082 1290 636561544 636561752 1.080000e-53 220.0
59 TraesCS3B01G516700 chr6B 76.333 469 95 11 825 1290 240838482 240838937 1.070000e-58 237.0
60 TraesCS3B01G516700 chr4A 78.820 373 59 10 1282 1637 519176450 519176819 1.380000e-57 233.0
61 TraesCS3B01G516700 chr7A 81.116 233 38 5 1420 1649 162599562 162599333 5.070000e-42 182.0


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 TraesCS3B01G516700 chr3B 759092384 759094695 2311 False 4270 4270 100.000 1 2312 1 chr3B.!!$F7 2311
1 TraesCS3B01G516700 chr3B 758852128 758852651 523 False 634 634 88.491 1778 2305 1 chr3B.!!$F5 527
2 TraesCS3B01G516700 chr3A 704353454 704354929 1475 False 2056 2056 91.733 818 2312 1 chr3A.!!$F1 1494
3 TraesCS3B01G516700 chr5D 56584255 56584905 650 True 793 793 89.210 132 764 1 chr5D.!!$R1 632
4 TraesCS3B01G516700 chr5D 532839398 532840128 730 False 782 782 86.309 1 727 1 chr5D.!!$F3 726
5 TraesCS3B01G516700 chr5D 121970546 121971157 611 True 715 715 88.045 1 607 1 chr5D.!!$R2 606
6 TraesCS3B01G516700 chrUn 190469009 190469609 600 True 763 763 90.099 167 751 1 chrUn.!!$R1 584
7 TraesCS3B01G516700 chr4D 222659681 222660355 674 True 763 763 87.408 1 668 1 chr4D.!!$R1 667
8 TraesCS3B01G516700 chr4D 262514758 262515371 613 False 654 654 86.080 134 750 1 chr4D.!!$F3 616
9 TraesCS3B01G516700 chr2D 120385996 120386623 627 False 747 747 88.468 1 619 1 chr2D.!!$F1 618
10 TraesCS3B01G516700 chr1D 232862824 232863465 641 False 717 717 87.500 132 751 1 chr1D.!!$F2 619
11 TraesCS3B01G516700 chr1B 50842139 50842748 609 True 713 713 88.006 1 606 1 chr1B.!!$R1 605
12 TraesCS3B01G516700 chr5B 175151859 175152451 592 False 701 701 88.403 1 579 1 chr5B.!!$F1 578
13 TraesCS3B01G516700 chr3D 535033932 535034536 604 True 699 699 87.622 1 607 1 chr3D.!!$R1 606
14 TraesCS3B01G516700 chr1A 161509980 161510603 623 True 675 675 86.392 134 756 1 chr1A.!!$R1 622
15 TraesCS3B01G516700 chr2A 689961142 689961718 576 False 573 573 84.783 1 590 1 chr2A.!!$F2 589
16 TraesCS3B01G516700 chr4B 289271690 289272300 610 False 540 540 82.919 132 764 1 chr4B.!!$F1 632

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
819 903 0.106619 CTAGTAGTGTCTCCGCCCCT 60.107 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1804 0.177141 TTCCGTTCCGCAGATAAGGG 59.823 55.0 0.0 0.0 32.27 3.95 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
45 46 8.352942 ACTTCGACTTTATTTGCAAAATCTCTT 58.647 29.630 17.19 0.49 0.00 2.85
198 219 3.717392 GGCTTTTAAGATCTAGAGGGGGT 59.283 47.826 0.00 0.00 0.00 4.95
262 286 0.819582 TAGGTGCGCCACTAGTAACC 59.180 55.000 20.59 2.44 37.19 2.85
383 421 4.988540 TGAACATGAACAAAGTCCTAGACG 59.011 41.667 0.00 0.00 37.67 4.18
461 499 0.394352 GGTGGTGCTGGGGTTAGATG 60.394 60.000 0.00 0.00 0.00 2.90
476 514 5.116882 GGTTAGATGGAACTGCGAAGTTAT 58.883 41.667 9.31 0.00 31.35 1.89
507 545 2.103373 GCTGGAGTAGTGTGAGGATGA 58.897 52.381 0.00 0.00 0.00 2.92
509 547 2.100584 CTGGAGTAGTGTGAGGATGAGC 59.899 54.545 0.00 0.00 0.00 4.26
537 575 1.804748 CGGGAAGTTTGACCACTTAGC 59.195 52.381 0.00 0.00 37.11 3.09
593 631 5.279206 CGAGATTAAGCCATAGTGACCTGAT 60.279 44.000 0.00 0.00 0.00 2.90
594 632 6.506538 AGATTAAGCCATAGTGACCTGATT 57.493 37.500 0.00 0.00 0.00 2.57
599 637 8.871629 TTAAGCCATAGTGACCTGATTTTAAA 57.128 30.769 0.00 0.00 0.00 1.52
651 733 9.811995 AAATGTTAGTAATGACGCACTTCTATA 57.188 29.630 0.00 0.00 0.00 1.31
680 762 6.087522 GCGCCATTACTAAGTCAGATAGTAG 58.912 44.000 0.00 0.00 37.22 2.57
681 763 6.294065 GCGCCATTACTAAGTCAGATAGTAGT 60.294 42.308 0.00 0.00 37.22 2.73
682 764 7.094890 GCGCCATTACTAAGTCAGATAGTAGTA 60.095 40.741 0.00 0.00 37.22 1.82
704 787 1.219522 GGCGCACCGTGTGATATACC 61.220 60.000 16.31 3.27 35.23 2.73
744 827 5.395324 GGTGCGCCATTAGTATCTGGTATAT 60.395 44.000 12.58 0.00 34.86 0.86
764 848 3.513225 ATGGTGTGCGCCATTAGC 58.487 55.556 11.14 0.00 46.33 3.09
776 860 1.994916 CCATTAGCGGCCAAAAACAG 58.005 50.000 2.24 0.00 0.00 3.16
777 861 1.404047 CCATTAGCGGCCAAAAACAGG 60.404 52.381 2.24 0.00 0.00 4.00
778 862 1.272212 CATTAGCGGCCAAAAACAGGT 59.728 47.619 2.24 0.00 0.00 4.00
779 863 0.671251 TTAGCGGCCAAAAACAGGTG 59.329 50.000 2.24 0.00 0.00 4.00
780 864 0.466555 TAGCGGCCAAAAACAGGTGT 60.467 50.000 2.24 0.00 0.00 4.16
781 865 1.591327 GCGGCCAAAAACAGGTGTG 60.591 57.895 2.24 0.00 0.00 3.82
782 866 1.591327 CGGCCAAAAACAGGTGTGC 60.591 57.895 2.24 0.00 0.00 4.57
783 867 1.227527 GGCCAAAAACAGGTGTGCC 60.228 57.895 0.00 0.00 0.00 5.01
784 868 1.519719 GCCAAAAACAGGTGTGCCA 59.480 52.632 0.00 0.00 37.19 4.92
785 869 0.809636 GCCAAAAACAGGTGTGCCAC 60.810 55.000 0.00 0.00 37.19 5.01
786 870 0.823460 CCAAAAACAGGTGTGCCACT 59.177 50.000 0.00 0.00 37.19 4.00
787 871 2.028130 CCAAAAACAGGTGTGCCACTA 58.972 47.619 0.00 0.00 37.19 2.74
788 872 2.034558 CCAAAAACAGGTGTGCCACTAG 59.965 50.000 0.00 0.00 37.19 2.57
789 873 1.318576 AAAACAGGTGTGCCACTAGC 58.681 50.000 0.00 0.00 44.14 3.42
802 886 2.618045 GCCACTAGCAAGGCTTTTCCTA 60.618 50.000 12.74 0.00 46.94 2.94
803 887 3.274288 CCACTAGCAAGGCTTTTCCTAG 58.726 50.000 17.91 17.91 46.94 3.02
804 888 3.307762 CCACTAGCAAGGCTTTTCCTAGT 60.308 47.826 18.82 18.82 46.94 2.57
805 889 4.081087 CCACTAGCAAGGCTTTTCCTAGTA 60.081 45.833 21.79 0.23 46.94 1.82
806 890 5.112686 CACTAGCAAGGCTTTTCCTAGTAG 58.887 45.833 21.79 15.73 46.94 2.57
807 891 4.778427 ACTAGCAAGGCTTTTCCTAGTAGT 59.222 41.667 21.28 9.28 46.94 2.73
808 892 3.944087 AGCAAGGCTTTTCCTAGTAGTG 58.056 45.455 0.00 0.00 46.94 2.74
809 893 3.328050 AGCAAGGCTTTTCCTAGTAGTGT 59.672 43.478 0.00 0.00 46.94 3.55
810 894 3.685272 GCAAGGCTTTTCCTAGTAGTGTC 59.315 47.826 0.00 0.00 46.94 3.67
811 895 4.563786 GCAAGGCTTTTCCTAGTAGTGTCT 60.564 45.833 0.00 0.00 46.94 3.41
812 896 5.172205 CAAGGCTTTTCCTAGTAGTGTCTC 58.828 45.833 0.00 0.00 46.94 3.36
813 897 3.770388 AGGCTTTTCCTAGTAGTGTCTCC 59.230 47.826 0.00 0.00 45.41 3.71
814 898 3.429135 GGCTTTTCCTAGTAGTGTCTCCG 60.429 52.174 0.00 0.00 0.00 4.63
815 899 3.771798 CTTTTCCTAGTAGTGTCTCCGC 58.228 50.000 0.00 0.00 0.00 5.54
816 900 1.760192 TTCCTAGTAGTGTCTCCGCC 58.240 55.000 0.00 0.00 0.00 6.13
817 901 0.106819 TCCTAGTAGTGTCTCCGCCC 60.107 60.000 0.00 0.00 0.00 6.13
818 902 1.108132 CCTAGTAGTGTCTCCGCCCC 61.108 65.000 0.00 0.00 0.00 5.80
819 903 0.106619 CTAGTAGTGTCTCCGCCCCT 60.107 60.000 0.00 0.00 0.00 4.79
820 904 1.142465 CTAGTAGTGTCTCCGCCCCTA 59.858 57.143 0.00 0.00 0.00 3.53
821 905 0.106619 AGTAGTGTCTCCGCCCCTAG 60.107 60.000 0.00 0.00 0.00 3.02
822 906 0.106819 GTAGTGTCTCCGCCCCTAGA 60.107 60.000 0.00 0.00 0.00 2.43
823 907 0.851469 TAGTGTCTCCGCCCCTAGAT 59.149 55.000 0.00 0.00 0.00 1.98
834 918 2.743183 CGCCCCTAGATCACTCAAAAGG 60.743 54.545 0.00 0.00 0.00 3.11
845 929 0.327591 CTCAAAAGGAGGGCTGAGCT 59.672 55.000 3.72 0.00 40.13 4.09
847 931 1.023513 CAAAAGGAGGGCTGAGCTCG 61.024 60.000 9.64 5.21 32.17 5.03
848 932 1.484444 AAAAGGAGGGCTGAGCTCGT 61.484 55.000 9.64 0.00 32.17 4.18
930 1014 2.897350 CGCTCTCCGCCCAATTCC 60.897 66.667 0.00 0.00 34.21 3.01
957 1041 0.614979 TTCTCCCACCCTCTCCTTCG 60.615 60.000 0.00 0.00 0.00 3.79
962 1046 2.756283 ACCCTCTCCTTCGCTCCG 60.756 66.667 0.00 0.00 0.00 4.63
963 1047 2.756283 CCCTCTCCTTCGCTCCGT 60.756 66.667 0.00 0.00 0.00 4.69
985 1069 2.050714 GACGCACAGAACCGTCGA 60.051 61.111 0.00 0.00 43.37 4.20
987 1071 1.006571 ACGCACAGAACCGTCGAAT 60.007 52.632 0.00 0.00 31.00 3.34
1055 1139 0.392863 CCGACCATCATGCTTGTCCA 60.393 55.000 0.00 0.00 0.00 4.02
1067 1151 2.278854 GCTTGTCCAGAAGATCAGCTC 58.721 52.381 0.00 0.00 0.00 4.09
1068 1152 2.354503 GCTTGTCCAGAAGATCAGCTCA 60.355 50.000 0.00 0.00 0.00 4.26
1079 1163 0.969917 ATCAGCTCAGAGACGTGGCT 60.970 55.000 0.00 0.00 0.00 4.75
1167 1251 4.796495 GGTGGTGGCGATGGTCCC 62.796 72.222 0.00 0.00 0.00 4.46
1367 1451 7.328493 CGCTAGAATTATCATACAATCCGTTCA 59.672 37.037 0.00 0.00 0.00 3.18
1384 1468 4.382040 CCGTTCACTATCAGATGTTGGAGT 60.382 45.833 0.00 0.00 0.00 3.85
1430 1514 3.665675 AAGATGAGGACGCGGTGGC 62.666 63.158 12.47 0.00 0.00 5.01
1469 1553 0.462759 GCACCTCCTTGATCGGGAAG 60.463 60.000 8.31 5.44 31.92 3.46
1496 1580 2.766651 GGGATGGCTGGTCCGGTA 60.767 66.667 0.00 0.00 36.58 4.02
1529 1614 0.721718 GCACTGCCGTACTGATGTTC 59.278 55.000 0.00 0.00 0.00 3.18
1531 1616 2.688507 CACTGCCGTACTGATGTTCTT 58.311 47.619 0.00 0.00 0.00 2.52
1539 1624 5.335661 GCCGTACTGATGTTCTTTTGGATTT 60.336 40.000 0.00 0.00 0.00 2.17
1624 1709 1.532505 GGTGCAATCTAGCGCATTGTG 60.533 52.381 11.47 1.53 46.43 3.33
1640 1725 3.520290 TTGTGTGGGTCATCGTAGATC 57.480 47.619 0.00 0.00 45.12 2.75
1646 1731 4.038042 TGTGGGTCATCGTAGATCTGAATC 59.962 45.833 5.18 0.00 45.12 2.52
1649 1734 4.279671 GGGTCATCGTAGATCTGAATCTGT 59.720 45.833 5.18 0.00 45.12 3.41
1654 1739 8.910666 GTCATCGTAGATCTGAATCTGTATTTG 58.089 37.037 5.18 0.00 45.12 2.32
1657 1742 7.142021 TCGTAGATCTGAATCTGTATTTGCTC 58.858 38.462 5.18 0.00 42.36 4.26
1686 1771 4.481112 GCGGCTTGCGTTGGATGG 62.481 66.667 0.00 0.00 0.00 3.51
1687 1772 2.745884 CGGCTTGCGTTGGATGGA 60.746 61.111 0.00 0.00 0.00 3.41
1693 1778 0.611618 TTGCGTTGGATGGATGCCTT 60.612 50.000 0.00 0.00 0.00 4.35
1694 1779 0.611618 TGCGTTGGATGGATGCCTTT 60.612 50.000 0.00 0.00 0.00 3.11
1696 1781 1.462616 CGTTGGATGGATGCCTTTCA 58.537 50.000 0.00 0.00 0.00 2.69
1700 1785 3.104519 TGGATGGATGCCTTTCACATT 57.895 42.857 0.00 0.00 0.00 2.71
1702 1787 3.025978 GGATGGATGCCTTTCACATTCA 58.974 45.455 0.00 0.00 37.43 2.57
1705 1790 3.433343 TGGATGCCTTTCACATTCATGT 58.567 40.909 0.00 0.00 42.84 3.21
1706 1791 3.444742 TGGATGCCTTTCACATTCATGTC 59.555 43.478 0.00 0.00 39.39 3.06
1707 1792 3.698040 GGATGCCTTTCACATTCATGTCT 59.302 43.478 0.00 0.00 39.39 3.41
1708 1793 4.439700 GGATGCCTTTCACATTCATGTCTG 60.440 45.833 0.00 0.00 39.39 3.51
1709 1794 2.229543 TGCCTTTCACATTCATGTCTGC 59.770 45.455 0.00 0.00 39.39 4.26
1710 1795 2.730090 GCCTTTCACATTCATGTCTGCG 60.730 50.000 0.00 0.00 39.39 5.18
1711 1796 2.159476 CCTTTCACATTCATGTCTGCGG 60.159 50.000 0.00 0.00 39.39 5.69
1712 1797 2.470983 TTCACATTCATGTCTGCGGA 57.529 45.000 0.00 0.00 39.39 5.54
1713 1798 1.725641 TCACATTCATGTCTGCGGAC 58.274 50.000 19.20 19.20 39.39 4.79
1714 1799 1.276138 TCACATTCATGTCTGCGGACT 59.724 47.619 25.54 9.30 42.54 3.85
1715 1800 1.395954 CACATTCATGTCTGCGGACTG 59.604 52.381 25.54 19.64 42.54 3.51
1716 1801 1.276138 ACATTCATGTCTGCGGACTGA 59.724 47.619 25.54 21.35 42.54 3.41
1717 1802 2.093288 ACATTCATGTCTGCGGACTGAT 60.093 45.455 25.54 9.83 42.54 2.90
1718 1803 3.132824 ACATTCATGTCTGCGGACTGATA 59.867 43.478 25.54 15.65 42.54 2.15
1719 1804 2.871182 TCATGTCTGCGGACTGATAC 57.129 50.000 25.54 0.00 42.54 2.24
1720 1805 1.409064 TCATGTCTGCGGACTGATACC 59.591 52.381 25.54 0.00 42.54 2.73
1721 1806 0.753262 ATGTCTGCGGACTGATACCC 59.247 55.000 25.54 0.00 42.54 3.69
1722 1807 0.324368 TGTCTGCGGACTGATACCCT 60.324 55.000 25.54 0.00 42.54 4.34
1723 1808 0.824759 GTCTGCGGACTGATACCCTT 59.175 55.000 18.76 0.00 39.24 3.95
1724 1809 2.029623 GTCTGCGGACTGATACCCTTA 58.970 52.381 18.76 0.00 39.24 2.69
1770 1855 1.138266 GAGGTTGCTATGCCCTAACGA 59.862 52.381 0.00 0.00 0.00 3.85
1841 1930 1.889545 GCCTTTGCTATCAGCCTAGG 58.110 55.000 3.67 3.67 41.51 3.02
1865 1954 2.280797 TTCACCTGCAGCGTCCAC 60.281 61.111 8.66 0.00 0.00 4.02
1903 1992 6.932960 AGTGTTACCTTGGTAAATGTAGTGTC 59.067 38.462 13.17 0.22 0.00 3.67
1959 2048 6.390721 AGTGAGATCCATCGGTTTATATTCG 58.609 40.000 0.00 0.00 0.00 3.34
1977 2066 5.796350 ATTCGATCTCCGTTAGTTTTTGG 57.204 39.130 0.00 0.00 39.75 3.28
2030 2119 4.345257 TCCTCTAGACAGAACACAAAGCTT 59.655 41.667 0.00 0.00 0.00 3.74
2044 2133 3.157087 CAAAGCTTAGTGACCACCCATT 58.843 45.455 0.00 0.00 0.00 3.16
2116 2205 0.583438 GTGGTGATTCATCCGATGCG 59.417 55.000 3.25 0.00 0.00 4.73
2240 2329 0.165944 CGCCTCATTTTGGACGTGTC 59.834 55.000 0.00 0.00 0.00 3.67
2241 2330 1.234821 GCCTCATTTTGGACGTGTCA 58.765 50.000 0.00 0.00 0.00 3.58
2258 2347 2.103432 TGTCACGGGAAGAAAAGCTACA 59.897 45.455 0.00 0.00 0.00 2.74
2286 2375 3.904339 TGGATTAAGGAGCTAGCCTAAGG 59.096 47.826 12.13 0.00 37.26 2.69
2305 2394 2.199117 CCGCTTAGGTAGGCAGTCA 58.801 57.895 0.00 0.00 34.51 3.41
2306 2395 0.103208 CCGCTTAGGTAGGCAGTCAG 59.897 60.000 0.00 0.00 34.51 3.51
2307 2396 1.103803 CGCTTAGGTAGGCAGTCAGA 58.896 55.000 0.00 0.00 0.00 3.27
2309 2398 1.137282 GCTTAGGTAGGCAGTCAGACC 59.863 57.143 0.00 0.00 0.00 3.85
2310 2399 2.457598 CTTAGGTAGGCAGTCAGACCA 58.542 52.381 0.00 0.00 34.18 4.02
2311 2400 2.848678 TAGGTAGGCAGTCAGACCAT 57.151 50.000 0.00 0.00 34.18 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.733857 AAGAGATTTTGCAAATAAAGTCGAAG 57.266 30.769 13.65 0.00 33.20 3.79
45 46 7.684529 AGTTATGCCCATTTTACAAATTCCAA 58.315 30.769 0.00 0.00 0.00 3.53
217 241 3.663995 TTGTGCGCCACTAGTAAGTTA 57.336 42.857 4.18 0.00 35.11 2.24
305 342 8.855110 TCAAACTTCCCGGTAATATTACGTATA 58.145 33.333 17.33 3.15 34.50 1.47
461 499 1.076332 ACGCATAACTTCGCAGTTCC 58.924 50.000 3.03 0.00 42.66 3.62
537 575 5.265477 TGCTTAATCTCAATTCAAATCGCG 58.735 37.500 0.00 0.00 0.00 5.87
680 762 1.366111 ATCACACGGTGCGCCATTAC 61.366 55.000 18.18 0.00 32.98 1.89
681 763 0.175989 TATCACACGGTGCGCCATTA 59.824 50.000 18.18 0.00 32.98 1.90
682 764 0.463654 ATATCACACGGTGCGCCATT 60.464 50.000 18.18 0.00 32.98 3.16
704 787 3.136123 CCAGGGAGTGCGCCATTG 61.136 66.667 4.18 0.00 0.00 2.82
764 848 1.591327 GCACACCTGTTTTTGGCCG 60.591 57.895 0.00 0.00 0.00 6.13
765 849 1.227527 GGCACACCTGTTTTTGGCC 60.228 57.895 0.00 0.00 0.00 5.36
766 850 1.519719 TGGCACACCTGTTTTTGGC 59.480 52.632 0.00 0.00 36.63 4.52
792 876 3.429135 CGGAGACACTACTAGGAAAAGCC 60.429 52.174 0.00 0.00 0.00 4.35
793 877 3.771798 CGGAGACACTACTAGGAAAAGC 58.228 50.000 0.00 0.00 0.00 3.51
794 878 3.429135 GGCGGAGACACTACTAGGAAAAG 60.429 52.174 0.00 0.00 31.66 2.27
795 879 2.494870 GGCGGAGACACTACTAGGAAAA 59.505 50.000 0.00 0.00 31.66 2.29
796 880 2.097825 GGCGGAGACACTACTAGGAAA 58.902 52.381 0.00 0.00 31.66 3.13
797 881 1.684248 GGGCGGAGACACTACTAGGAA 60.684 57.143 0.00 0.00 37.00 3.36
798 882 0.106819 GGGCGGAGACACTACTAGGA 60.107 60.000 0.00 0.00 37.00 2.94
799 883 1.108132 GGGGCGGAGACACTACTAGG 61.108 65.000 0.00 0.00 32.83 3.02
800 884 2.416901 GGGGCGGAGACACTACTAG 58.583 63.158 0.00 0.00 32.83 2.57
801 885 4.672251 GGGGCGGAGACACTACTA 57.328 61.111 0.00 0.00 32.83 1.82
806 890 0.755698 TGATCTAGGGGCGGAGACAC 60.756 60.000 0.00 0.00 45.23 3.67
807 891 0.755698 GTGATCTAGGGGCGGAGACA 60.756 60.000 0.00 0.00 37.00 3.41
808 892 0.468400 AGTGATCTAGGGGCGGAGAC 60.468 60.000 0.00 0.00 0.00 3.36
809 893 0.178987 GAGTGATCTAGGGGCGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
810 894 0.468214 TGAGTGATCTAGGGGCGGAG 60.468 60.000 0.00 0.00 0.00 4.63
811 895 0.032515 TTGAGTGATCTAGGGGCGGA 60.033 55.000 0.00 0.00 0.00 5.54
812 896 0.830648 TTTGAGTGATCTAGGGGCGG 59.169 55.000 0.00 0.00 0.00 6.13
813 897 2.555199 CTTTTGAGTGATCTAGGGGCG 58.445 52.381 0.00 0.00 0.00 6.13
814 898 2.505819 TCCTTTTGAGTGATCTAGGGGC 59.494 50.000 0.00 0.00 0.00 5.80
815 899 3.135530 CCTCCTTTTGAGTGATCTAGGGG 59.864 52.174 0.00 0.00 39.65 4.79
816 900 3.135530 CCCTCCTTTTGAGTGATCTAGGG 59.864 52.174 0.00 0.00 39.65 3.53
817 901 3.432890 GCCCTCCTTTTGAGTGATCTAGG 60.433 52.174 0.00 0.00 39.65 3.02
818 902 3.454082 AGCCCTCCTTTTGAGTGATCTAG 59.546 47.826 0.00 0.00 39.65 2.43
819 903 3.198635 CAGCCCTCCTTTTGAGTGATCTA 59.801 47.826 0.00 0.00 39.65 1.98
820 904 2.026449 CAGCCCTCCTTTTGAGTGATCT 60.026 50.000 0.00 0.00 39.65 2.75
821 905 2.026822 TCAGCCCTCCTTTTGAGTGATC 60.027 50.000 0.00 0.00 39.65 2.92
822 906 1.988107 TCAGCCCTCCTTTTGAGTGAT 59.012 47.619 0.00 0.00 39.65 3.06
823 907 1.349026 CTCAGCCCTCCTTTTGAGTGA 59.651 52.381 0.00 0.00 39.65 3.41
862 946 2.202349 GCGCGGAAACAGTGCATC 60.202 61.111 8.83 0.00 43.84 3.91
922 1006 2.623416 GGAGAAAATAGCGGGAATTGGG 59.377 50.000 0.00 0.00 0.00 4.12
930 1014 0.546598 AGGGTGGGAGAAAATAGCGG 59.453 55.000 0.00 0.00 0.00 5.52
974 1058 3.059044 CGACAAGTTATTCGACGGTTCTG 59.941 47.826 0.00 0.00 37.43 3.02
983 1067 4.041740 TCCATCTCCGACAAGTTATTCG 57.958 45.455 0.10 0.10 34.93 3.34
985 1069 3.432326 GCCTCCATCTCCGACAAGTTATT 60.432 47.826 0.00 0.00 0.00 1.40
987 1071 1.480954 GCCTCCATCTCCGACAAGTTA 59.519 52.381 0.00 0.00 0.00 2.24
1046 1130 1.627329 AGCTGATCTTCTGGACAAGCA 59.373 47.619 0.00 0.00 37.87 3.91
1055 1139 2.423185 CACGTCTCTGAGCTGATCTTCT 59.577 50.000 0.00 0.00 0.00 2.85
1067 1151 1.416813 GCGATTCAGCCACGTCTCTG 61.417 60.000 7.14 7.14 0.00 3.35
1068 1152 1.153745 GCGATTCAGCCACGTCTCT 60.154 57.895 0.00 0.00 0.00 3.10
1079 1163 1.866237 GCTTTGACGTGGCGATTCA 59.134 52.632 0.00 0.00 0.00 2.57
1098 1182 4.388499 TCCTCCTTTGCGGCCGTC 62.388 66.667 28.70 19.46 0.00 4.79
1100 1184 3.605749 TTCTCCTCCTTTGCGGCCG 62.606 63.158 24.05 24.05 0.00 6.13
1103 1187 1.208052 TCATCTTCTCCTCCTTTGCGG 59.792 52.381 0.00 0.00 0.00 5.69
1266 1350 1.605710 GCGGCGTAGTAGTATGGAGAA 59.394 52.381 9.37 0.00 0.00 2.87
1268 1352 0.240411 GGCGGCGTAGTAGTATGGAG 59.760 60.000 9.37 0.00 0.00 3.86
1298 1382 0.109597 CAAGGTTCACATCTTGGCGC 60.110 55.000 0.00 0.00 37.35 6.53
1367 1451 2.840038 TGCCACTCCAACATCTGATAGT 59.160 45.455 0.00 0.00 0.00 2.12
1384 1468 1.538047 GCCAACTGATCTTTCTGCCA 58.462 50.000 0.00 0.00 0.00 4.92
1469 1553 1.455217 AGCCATCCCAGCAAGATGC 60.455 57.895 5.39 0.00 45.46 3.91
1496 1580 1.076192 AGTGCTTGCATTCTGCCCT 59.924 52.632 0.00 0.00 44.23 5.19
1509 1594 0.321671 AACATCAGTACGGCAGTGCT 59.678 50.000 16.11 1.02 44.20 4.40
1529 1614 6.486320 ACTTTTTACATGCCCAAATCCAAAAG 59.514 34.615 0.00 0.00 35.67 2.27
1531 1616 5.934781 ACTTTTTACATGCCCAAATCCAAA 58.065 33.333 0.00 0.00 0.00 3.28
1601 1686 1.097547 ATGCGCTAGATTGCACCCAC 61.098 55.000 9.73 0.00 45.07 4.61
1608 1693 1.064505 CCCACACAATGCGCTAGATTG 59.935 52.381 15.20 15.20 36.94 2.67
1609 1694 1.340017 ACCCACACAATGCGCTAGATT 60.340 47.619 9.73 0.00 0.00 2.40
1624 1709 4.279671 AGATTCAGATCTACGATGACCCAC 59.720 45.833 0.00 0.00 40.84 4.61
1646 1731 6.197276 GCATATTGTCTGTGAGCAAATACAG 58.803 40.000 0.00 0.00 44.31 2.74
1649 1734 4.273235 CCGCATATTGTCTGTGAGCAAATA 59.727 41.667 0.00 0.00 0.00 1.40
1654 1739 0.305922 GCCGCATATTGTCTGTGAGC 59.694 55.000 0.00 0.00 0.00 4.26
1657 1742 1.532505 GCAAGCCGCATATTGTCTGTG 60.533 52.381 0.00 0.00 41.79 3.66
1686 1771 4.669318 CAGACATGAATGTGAAAGGCATC 58.331 43.478 0.00 0.00 41.95 3.91
1687 1772 3.119245 GCAGACATGAATGTGAAAGGCAT 60.119 43.478 0.00 0.00 41.95 4.40
1693 1778 2.076100 GTCCGCAGACATGAATGTGAA 58.924 47.619 14.30 0.00 41.95 3.18
1694 1779 1.276138 AGTCCGCAGACATGAATGTGA 59.724 47.619 14.30 5.19 46.15 3.58
1696 1781 1.276138 TCAGTCCGCAGACATGAATGT 59.724 47.619 0.00 0.00 46.15 2.71
1700 1785 1.409064 GGTATCAGTCCGCAGACATGA 59.591 52.381 0.00 4.05 46.15 3.07
1702 1787 0.753262 GGGTATCAGTCCGCAGACAT 59.247 55.000 2.32 0.00 46.15 3.06
1705 1790 2.447408 TAAGGGTATCAGTCCGCAGA 57.553 50.000 0.00 0.00 0.00 4.26
1706 1791 2.894126 AGATAAGGGTATCAGTCCGCAG 59.106 50.000 0.00 0.00 38.95 5.18
1707 1792 2.628178 CAGATAAGGGTATCAGTCCGCA 59.372 50.000 0.00 0.00 38.95 5.69
1708 1793 2.610727 GCAGATAAGGGTATCAGTCCGC 60.611 54.545 0.00 0.00 38.95 5.54
1709 1794 2.351835 CGCAGATAAGGGTATCAGTCCG 60.352 54.545 0.00 0.00 38.95 4.79
1710 1795 2.028930 CCGCAGATAAGGGTATCAGTCC 60.029 54.545 0.00 0.00 38.95 3.85
1711 1796 2.891580 TCCGCAGATAAGGGTATCAGTC 59.108 50.000 0.00 0.00 38.95 3.51
1712 1797 2.958818 TCCGCAGATAAGGGTATCAGT 58.041 47.619 0.00 0.00 38.95 3.41
1713 1798 3.654414 GTTCCGCAGATAAGGGTATCAG 58.346 50.000 0.00 0.00 38.95 2.90
1714 1799 2.035449 CGTTCCGCAGATAAGGGTATCA 59.965 50.000 0.00 0.00 38.95 2.15
1715 1800 2.609737 CCGTTCCGCAGATAAGGGTATC 60.610 54.545 0.00 0.00 37.04 2.24
1716 1801 1.343465 CCGTTCCGCAGATAAGGGTAT 59.657 52.381 0.00 0.00 0.00 2.73
1717 1802 0.748450 CCGTTCCGCAGATAAGGGTA 59.252 55.000 0.00 0.00 0.00 3.69
1718 1803 0.974010 TCCGTTCCGCAGATAAGGGT 60.974 55.000 0.00 0.00 32.65 4.34
1719 1804 0.177141 TTCCGTTCCGCAGATAAGGG 59.823 55.000 0.00 0.00 32.27 3.95
1720 1805 1.134788 ACTTCCGTTCCGCAGATAAGG 60.135 52.381 0.00 0.00 0.00 2.69
1721 1806 2.295253 ACTTCCGTTCCGCAGATAAG 57.705 50.000 0.00 0.00 0.00 1.73
1722 1807 2.754946 AACTTCCGTTCCGCAGATAA 57.245 45.000 0.00 0.00 0.00 1.75
1723 1808 4.395959 AATAACTTCCGTTCCGCAGATA 57.604 40.909 0.00 0.00 34.59 1.98
1724 1809 2.981859 ATAACTTCCGTTCCGCAGAT 57.018 45.000 0.00 0.00 34.59 2.90
1750 1835 1.138266 TCGTTAGGGCATAGCAACCTC 59.862 52.381 0.00 0.00 35.84 3.85
1770 1855 2.185350 CGGCGATGCTCTTCCTGT 59.815 61.111 0.00 0.00 0.00 4.00
1841 1930 1.080995 CGCTGCAGGTGAAGAGCTAC 61.081 60.000 17.12 0.00 0.00 3.58
1903 1992 7.381408 TCACCGTAATCTCGCTAAATTATCTTG 59.619 37.037 0.00 0.00 0.00 3.02
1923 2012 5.160607 TGGATCTCACTAAATTTCACCGT 57.839 39.130 0.00 0.00 0.00 4.83
1959 2048 3.181523 GCGTCCAAAAACTAACGGAGATC 60.182 47.826 0.00 0.00 35.74 2.75
1977 2066 1.623973 GCTGAACTTACACCCGCGTC 61.624 60.000 4.92 0.00 0.00 5.19
2030 2119 2.633692 TGGGTTAATGGGTGGTCACTA 58.366 47.619 0.93 0.00 0.00 2.74
2044 2133 4.894252 ACCTACTCCTACAGATGGGTTA 57.106 45.455 0.00 0.00 0.00 2.85
2240 2329 2.480419 CTGTGTAGCTTTTCTTCCCGTG 59.520 50.000 0.00 0.00 0.00 4.94
2241 2330 2.104281 ACTGTGTAGCTTTTCTTCCCGT 59.896 45.455 0.00 0.00 0.00 5.28
2258 2347 3.118592 GCTAGCTCCTTAATCCACACTGT 60.119 47.826 7.70 0.00 0.00 3.55
2286 2375 1.227292 GACTGCCTACCTAAGCGGC 60.227 63.158 0.00 0.00 44.02 6.53


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

AutoCloner maintained by Alex Coulton.