Multiple sequence alignment - TraesCS2A01G439700

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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 TraesCS2A01G439700 chr2A 100.000 2546 0 0 1 2546 690804435 690806980 0.000000e+00 4702.0
1 TraesCS2A01G439700 chr2A 83.045 1097 137 26 825 1894 690747324 690748398 0.000000e+00 950.0
2 TraesCS2A01G439700 chr2A 91.787 621 30 8 78 694 690794589 690795192 0.000000e+00 845.0
3 TraesCS2A01G439700 chr2A 82.759 783 110 15 912 1682 691392078 691391309 0.000000e+00 675.0
4 TraesCS2A01G439700 chr2A 93.878 147 9 0 638 784 691392185 691392039 3.300000e-54 222.0
5 TraesCS2A01G439700 chr2A 76.010 396 84 6 1139 1527 632390833 632391224 7.190000e-46 195.0
6 TraesCS2A01G439700 chr2A 98.750 80 1 0 1 80 256121355 256121276 2.640000e-30 143.0
7 TraesCS2A01G439700 chr2A 86.667 120 9 4 633 748 690747279 690747395 2.660000e-25 126.0
8 TraesCS2A01G439700 chr2D 93.028 1090 60 7 912 1992 547489170 547490252 0.000000e+00 1578.0
9 TraesCS2A01G439700 chr2D 93.567 1057 62 4 912 1965 547450719 547451772 0.000000e+00 1570.0
10 TraesCS2A01G439700 chr2D 81.785 1109 138 29 824 1894 547286335 547287417 0.000000e+00 870.0
11 TraesCS2A01G439700 chr2D 88.435 735 46 16 78 781 547450029 547450755 0.000000e+00 850.0
12 TraesCS2A01G439700 chr2D 94.107 560 29 2 1991 2546 174243496 174242937 0.000000e+00 848.0
13 TraesCS2A01G439700 chr2D 81.084 1015 124 31 912 1894 547427084 547428062 0.000000e+00 749.0
14 TraesCS2A01G439700 chr2D 83.605 799 98 15 841 1620 547574459 547575243 0.000000e+00 719.0
15 TraesCS2A01G439700 chr2D 82.234 788 119 9 912 1679 547559400 547560186 0.000000e+00 660.0
16 TraesCS2A01G439700 chr2D 84.513 452 38 18 345 781 547488772 547489206 3.920000e-113 418.0
17 TraesCS2A01G439700 chr2D 83.491 424 54 13 78 492 640367313 640367729 5.140000e-102 381.0
18 TraesCS2A01G439700 chr2D 82.506 423 57 14 69 484 10300159 10300571 3.120000e-94 355.0
19 TraesCS2A01G439700 chr2D 82.297 418 55 16 78 484 10488297 10487888 6.740000e-91 344.0
20 TraesCS2A01G439700 chr2D 82.297 418 55 16 78 484 10505418 10505009 6.740000e-91 344.0
21 TraesCS2A01G439700 chr2D 86.869 297 19 9 455 748 547286128 547286407 5.290000e-82 315.0
22 TraesCS2A01G439700 chr2D 92.105 152 9 3 630 781 547559286 547559434 7.140000e-51 211.0
23 TraesCS2A01G439700 chr2D 86.364 154 9 3 633 781 547426978 547427124 9.430000e-35 158.0
24 TraesCS2A01G439700 chr2D 79.343 213 16 14 537 746 547278057 547278244 9.560000e-25 124.0
25 TraesCS2A01G439700 chr2D 97.297 37 1 0 745 781 547574530 547574566 2.110000e-06 63.9
26 TraesCS2A01G439700 chr2D 100.000 30 0 0 752 781 547286426 547286455 3.540000e-04 56.5
27 TraesCS2A01G439700 chr2B 94.080 777 42 3 912 1684 653796192 653796968 0.000000e+00 1177.0
28 TraesCS2A01G439700 chr2B 85.480 854 107 9 841 1679 653808192 653809043 0.000000e+00 874.0
29 TraesCS2A01G439700 chr2B 82.565 998 134 17 912 1886 653788317 653789297 0.000000e+00 843.0
30 TraesCS2A01G439700 chr2B 90.796 402 22 8 78 474 653795598 653795989 8.070000e-145 523.0
31 TraesCS2A01G439700 chr2B 83.415 410 55 7 78 484 780869646 780870045 4.000000e-98 368.0
32 TraesCS2A01G439700 chr2B 91.339 254 9 3 528 781 653795988 653796228 4.060000e-88 335.0
33 TraesCS2A01G439700 chr2B 97.561 82 1 1 1 82 684813460 684813380 3.420000e-29 139.0
34 TraesCS2A01G439700 chr2B 90.426 94 8 1 688 781 653788261 653788353 3.440000e-24 122.0
35 TraesCS2A01G439700 chr6D 94.794 557 27 2 1991 2546 363871211 363871766 0.000000e+00 867.0
36 TraesCS2A01G439700 chr4D 94.434 557 30 1 1991 2546 670902 670346 0.000000e+00 856.0
37 TraesCS2A01G439700 chr4D 94.107 560 29 2 1991 2546 473744470 473743911 0.000000e+00 848.0
38 TraesCS2A01G439700 chr7D 94.107 560 29 2 1991 2546 376940177 376940736 0.000000e+00 848.0
39 TraesCS2A01G439700 chr1D 94.107 560 29 2 1991 2546 80655496 80654937 0.000000e+00 848.0
40 TraesCS2A01G439700 chr1D 93.929 560 30 2 1991 2546 244555677 244556236 0.000000e+00 843.0
41 TraesCS2A01G439700 chr5D 93.961 563 27 3 1991 2546 503688307 503688869 0.000000e+00 845.0
42 TraesCS2A01G439700 chr5D 93.929 560 30 2 1991 2546 469725886 469726445 0.000000e+00 843.0
43 TraesCS2A01G439700 chr5D 82.692 416 52 17 79 484 22789713 22789308 4.030000e-93 351.0
44 TraesCS2A01G439700 chr4A 81.882 425 58 14 70 484 139718067 139717652 8.720000e-90 340.0
45 TraesCS2A01G439700 chr4A 98.734 79 1 0 1 79 14748463 14748541 9.500000e-30 141.0
46 TraesCS2A01G439700 chr5A 81.164 292 40 6 1425 1706 602413162 602413448 1.190000e-53 220.0
47 TraesCS2A01G439700 chr5B 98.750 80 1 0 1 80 322875136 322875215 2.640000e-30 143.0
48 TraesCS2A01G439700 chr5B 98.734 79 0 1 1 79 158793580 158793657 3.420000e-29 139.0
49 TraesCS2A01G439700 chr4B 98.750 80 0 1 1 80 251699161 251699083 9.500000e-30 141.0
50 TraesCS2A01G439700 chr4B 97.531 81 1 1 1 81 482112346 482112267 1.230000e-28 137.0
51 TraesCS2A01G439700 chr7A 96.429 84 1 2 1 83 285423147 285423229 1.230000e-28 137.0
52 TraesCS2A01G439700 chr3B 93.548 93 2 4 1 91 394943989 394944079 4.420000e-28 135.0


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 TraesCS2A01G439700 chr2A 690804435 690806980 2545 False 4702.000000 4702 100.000000 1 2546 1 chr2A.!!$F3 2545
1 TraesCS2A01G439700 chr2A 690794589 690795192 603 False 845.000000 845 91.787000 78 694 1 chr2A.!!$F2 616
2 TraesCS2A01G439700 chr2A 690747279 690748398 1119 False 538.000000 950 84.856000 633 1894 2 chr2A.!!$F4 1261
3 TraesCS2A01G439700 chr2A 691391309 691392185 876 True 448.500000 675 88.318500 638 1682 2 chr2A.!!$R2 1044
4 TraesCS2A01G439700 chr2D 547450029 547451772 1743 False 1210.000000 1570 91.001000 78 1965 2 chr2D.!!$F6 1887
5 TraesCS2A01G439700 chr2D 547488772 547490252 1480 False 998.000000 1578 88.770500 345 1992 2 chr2D.!!$F7 1647
6 TraesCS2A01G439700 chr2D 174242937 174243496 559 True 848.000000 848 94.107000 1991 2546 1 chr2D.!!$R3 555
7 TraesCS2A01G439700 chr2D 547426978 547428062 1084 False 453.500000 749 83.724000 633 1894 2 chr2D.!!$F5 1261
8 TraesCS2A01G439700 chr2D 547559286 547560186 900 False 435.500000 660 87.169500 630 1679 2 chr2D.!!$F8 1049
9 TraesCS2A01G439700 chr2D 547286128 547287417 1289 False 413.833333 870 89.551333 455 1894 3 chr2D.!!$F4 1439
10 TraesCS2A01G439700 chr2D 547574459 547575243 784 False 391.450000 719 90.451000 745 1620 2 chr2D.!!$F9 875
11 TraesCS2A01G439700 chr2B 653808192 653809043 851 False 874.000000 874 85.480000 841 1679 1 chr2B.!!$F1 838
12 TraesCS2A01G439700 chr2B 653795598 653796968 1370 False 678.333333 1177 92.071667 78 1684 3 chr2B.!!$F4 1606
13 TraesCS2A01G439700 chr2B 653788261 653789297 1036 False 482.500000 843 86.495500 688 1886 2 chr2B.!!$F3 1198
14 TraesCS2A01G439700 chr6D 363871211 363871766 555 False 867.000000 867 94.794000 1991 2546 1 chr6D.!!$F1 555
15 TraesCS2A01G439700 chr4D 670346 670902 556 True 856.000000 856 94.434000 1991 2546 1 chr4D.!!$R1 555
16 TraesCS2A01G439700 chr4D 473743911 473744470 559 True 848.000000 848 94.107000 1991 2546 1 chr4D.!!$R2 555
17 TraesCS2A01G439700 chr7D 376940177 376940736 559 False 848.000000 848 94.107000 1991 2546 1 chr7D.!!$F1 555
18 TraesCS2A01G439700 chr1D 80654937 80655496 559 True 848.000000 848 94.107000 1991 2546 1 chr1D.!!$R1 555
19 TraesCS2A01G439700 chr1D 244555677 244556236 559 False 843.000000 843 93.929000 1991 2546 1 chr1D.!!$F1 555
20 TraesCS2A01G439700 chr5D 503688307 503688869 562 False 845.000000 845 93.961000 1991 2546 1 chr5D.!!$F2 555
21 TraesCS2A01G439700 chr5D 469725886 469726445 559 False 843.000000 843 93.929000 1991 2546 1 chr5D.!!$F1 555

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
24 25 0.108329 CCTTGGGTATTCGTGACGCT 60.108 55.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1698 0.743097 GGCCACATCTTTCCTGATGC 59.257 55.0 0.0 0.0 45.51 3.91 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
20 21 3.048337 GTGAACCTTGGGTATTCGTGA 57.952 47.619 0.00 0.00 33.12 4.35
21 22 2.740447 GTGAACCTTGGGTATTCGTGAC 59.260 50.000 0.00 0.00 33.12 3.67
22 23 1.997606 GAACCTTGGGTATTCGTGACG 59.002 52.381 0.00 0.00 33.12 4.35
23 24 0.390735 ACCTTGGGTATTCGTGACGC 60.391 55.000 0.00 0.00 32.11 5.19
24 25 0.108329 CCTTGGGTATTCGTGACGCT 60.108 55.000 0.00 0.00 0.00 5.07
25 26 0.999406 CTTGGGTATTCGTGACGCTG 59.001 55.000 0.00 0.00 0.00 5.18
26 27 1.017177 TTGGGTATTCGTGACGCTGC 61.017 55.000 0.00 0.00 0.00 5.25
27 28 2.171725 GGGTATTCGTGACGCTGCC 61.172 63.158 0.00 2.92 0.00 4.85
28 29 1.447140 GGTATTCGTGACGCTGCCA 60.447 57.895 0.00 0.00 0.00 4.92
29 30 0.810031 GGTATTCGTGACGCTGCCAT 60.810 55.000 0.00 0.00 0.00 4.40
30 31 0.301687 GTATTCGTGACGCTGCCATG 59.698 55.000 0.00 0.00 0.00 3.66
31 32 0.108377 TATTCGTGACGCTGCCATGT 60.108 50.000 0.00 0.00 0.00 3.21
32 33 1.638388 ATTCGTGACGCTGCCATGTG 61.638 55.000 0.00 0.00 0.00 3.21
33 34 3.792047 CGTGACGCTGCCATGTGG 61.792 66.667 0.00 0.00 38.53 4.17
55 56 6.387041 GGCTTTATTTATAAAGTCGGGCTT 57.613 37.500 18.51 0.00 46.78 4.35
56 57 6.802608 GGCTTTATTTATAAAGTCGGGCTTT 58.197 36.000 12.74 12.74 46.78 3.51
57 58 6.695713 GGCTTTATTTATAAAGTCGGGCTTTG 59.304 38.462 17.37 0.00 46.78 2.77
58 59 6.695713 GCTTTATTTATAAAGTCGGGCTTTGG 59.304 38.462 17.37 0.00 46.78 3.28
59 60 4.649088 ATTTATAAAGTCGGGCTTTGGC 57.351 40.909 17.37 0.00 46.07 4.52
125 126 4.340381 CCATGGAGGCCTTAATCTGAAAAG 59.660 45.833 6.77 0.00 0.00 2.27
262 270 3.643159 AAAACAAATCGGTGGCTCTTC 57.357 42.857 0.00 0.00 0.00 2.87
278 286 7.042335 GTGGCTCTTCTAACATATGTGTACTT 58.958 38.462 9.63 0.00 37.67 2.24
370 378 5.682943 ATTTTGCACACGTACACATTACT 57.317 34.783 0.00 0.00 0.00 2.24
429 438 9.890352 TTTGAAACTGAAAAGTTTGAAATTTGG 57.110 25.926 8.49 0.00 38.96 3.28
431 440 8.934825 TGAAACTGAAAAGTTTGAAATTTGGAG 58.065 29.630 8.49 0.00 41.49 3.86
434 443 8.479313 ACTGAAAAGTTTGAAATTTGGAGTTC 57.521 30.769 0.00 0.00 0.00 3.01
452 461 7.287061 TGGAGTTCTCAAAATTAAGTCCTTCA 58.713 34.615 11.37 0.14 41.42 3.02
453 462 7.944554 TGGAGTTCTCAAAATTAAGTCCTTCAT 59.055 33.333 11.37 0.00 41.42 2.57
626 678 7.327214 CAAGTATATATCAGGGAGAAGGAAGC 58.673 42.308 0.00 0.00 0.00 3.86
682 737 3.984508 TTATCGGTACTAGCAGTGAGC 57.015 47.619 0.00 0.00 46.19 4.26
696 752 3.546815 GCAGTGAGCGCCATTAATTACTG 60.547 47.826 2.29 8.23 37.82 2.74
781 880 2.963782 ACCCCTCGTGTTGTCCTATATC 59.036 50.000 0.00 0.00 0.00 1.63
782 881 2.963101 CCCCTCGTGTTGTCCTATATCA 59.037 50.000 0.00 0.00 0.00 2.15
783 882 3.005897 CCCCTCGTGTTGTCCTATATCAG 59.994 52.174 0.00 0.00 0.00 2.90
784 883 3.637229 CCCTCGTGTTGTCCTATATCAGT 59.363 47.826 0.00 0.00 0.00 3.41
785 884 4.825634 CCCTCGTGTTGTCCTATATCAGTA 59.174 45.833 0.00 0.00 0.00 2.74
786 885 5.278364 CCCTCGTGTTGTCCTATATCAGTAC 60.278 48.000 0.00 0.00 0.00 2.73
787 886 5.531659 CCTCGTGTTGTCCTATATCAGTACT 59.468 44.000 0.00 0.00 0.00 2.73
788 887 6.293516 CCTCGTGTTGTCCTATATCAGTACTC 60.294 46.154 0.00 0.00 0.00 2.59
789 888 5.530171 TCGTGTTGTCCTATATCAGTACTCC 59.470 44.000 0.00 0.00 0.00 3.85
790 889 5.531659 CGTGTTGTCCTATATCAGTACTCCT 59.468 44.000 0.00 0.00 0.00 3.69
791 890 6.039493 CGTGTTGTCCTATATCAGTACTCCTT 59.961 42.308 0.00 0.00 0.00 3.36
792 891 7.416438 CGTGTTGTCCTATATCAGTACTCCTTT 60.416 40.741 0.00 0.00 0.00 3.11
793 892 8.258708 GTGTTGTCCTATATCAGTACTCCTTTT 58.741 37.037 0.00 0.00 0.00 2.27
794 893 8.258007 TGTTGTCCTATATCAGTACTCCTTTTG 58.742 37.037 0.00 0.00 0.00 2.44
795 894 8.475639 GTTGTCCTATATCAGTACTCCTTTTGA 58.524 37.037 0.00 0.00 0.00 2.69
797 896 8.059461 TGTCCTATATCAGTACTCCTTTTGAGA 58.941 37.037 0.00 0.00 44.42 3.27
798 897 8.915036 GTCCTATATCAGTACTCCTTTTGAGAA 58.085 37.037 0.00 0.00 44.42 2.87
799 898 9.137459 TCCTATATCAGTACTCCTTTTGAGAAG 57.863 37.037 0.00 0.00 44.42 2.85
800 899 8.364142 CCTATATCAGTACTCCTTTTGAGAAGG 58.636 40.741 0.00 0.00 44.42 3.46
801 900 7.979786 ATATCAGTACTCCTTTTGAGAAGGA 57.020 36.000 4.27 4.27 44.42 3.36
802 901 6.688073 ATCAGTACTCCTTTTGAGAAGGAA 57.312 37.500 5.92 0.00 45.10 3.36
803 902 6.102897 TCAGTACTCCTTTTGAGAAGGAAG 57.897 41.667 5.92 3.40 45.10 3.46
804 903 5.602978 TCAGTACTCCTTTTGAGAAGGAAGT 59.397 40.000 5.92 8.50 45.10 3.01
805 904 6.781014 TCAGTACTCCTTTTGAGAAGGAAGTA 59.219 38.462 5.92 7.66 45.10 2.24
806 905 7.455008 TCAGTACTCCTTTTGAGAAGGAAGTAT 59.545 37.037 5.92 0.00 45.10 2.12
807 906 7.547370 CAGTACTCCTTTTGAGAAGGAAGTATG 59.453 40.741 5.92 0.25 45.10 2.39
808 907 6.441088 ACTCCTTTTGAGAAGGAAGTATGT 57.559 37.500 5.92 0.00 45.10 2.29
809 908 6.234177 ACTCCTTTTGAGAAGGAAGTATGTG 58.766 40.000 5.92 0.00 45.10 3.21
810 909 6.043243 ACTCCTTTTGAGAAGGAAGTATGTGA 59.957 38.462 5.92 0.00 45.10 3.58
811 910 7.020827 TCCTTTTGAGAAGGAAGTATGTGAT 57.979 36.000 1.42 0.00 43.05 3.06
812 911 6.881065 TCCTTTTGAGAAGGAAGTATGTGATG 59.119 38.462 1.42 0.00 43.05 3.07
813 912 6.656693 CCTTTTGAGAAGGAAGTATGTGATGT 59.343 38.462 0.00 0.00 39.81 3.06
814 913 7.175641 CCTTTTGAGAAGGAAGTATGTGATGTT 59.824 37.037 0.00 0.00 39.81 2.71
815 914 7.439157 TTTGAGAAGGAAGTATGTGATGTTG 57.561 36.000 0.00 0.00 0.00 3.33
816 915 5.491070 TGAGAAGGAAGTATGTGATGTTGG 58.509 41.667 0.00 0.00 0.00 3.77
817 916 5.013079 TGAGAAGGAAGTATGTGATGTTGGT 59.987 40.000 0.00 0.00 0.00 3.67
818 917 6.212589 TGAGAAGGAAGTATGTGATGTTGGTA 59.787 38.462 0.00 0.00 0.00 3.25
819 918 6.407202 AGAAGGAAGTATGTGATGTTGGTAC 58.593 40.000 0.00 0.00 0.00 3.34
820 919 6.213600 AGAAGGAAGTATGTGATGTTGGTACT 59.786 38.462 0.00 0.00 0.00 2.73
821 920 7.399191 AGAAGGAAGTATGTGATGTTGGTACTA 59.601 37.037 0.00 0.00 0.00 1.82
822 921 7.490657 AGGAAGTATGTGATGTTGGTACTAA 57.509 36.000 0.00 0.00 0.00 2.24
823 922 8.090788 AGGAAGTATGTGATGTTGGTACTAAT 57.909 34.615 0.00 0.00 0.00 1.73
824 923 7.987458 AGGAAGTATGTGATGTTGGTACTAATG 59.013 37.037 0.00 0.00 0.00 1.90
825 924 7.985184 GGAAGTATGTGATGTTGGTACTAATGA 59.015 37.037 0.00 0.00 0.00 2.57
826 925 9.378551 GAAGTATGTGATGTTGGTACTAATGAA 57.621 33.333 0.00 0.00 0.00 2.57
827 926 9.905713 AAGTATGTGATGTTGGTACTAATGAAT 57.094 29.630 0.00 0.00 0.00 2.57
828 927 9.330063 AGTATGTGATGTTGGTACTAATGAATG 57.670 33.333 0.00 0.00 0.00 2.67
829 928 6.435430 TGTGATGTTGGTACTAATGAATGC 57.565 37.500 0.00 0.00 0.00 3.56
830 929 5.356751 TGTGATGTTGGTACTAATGAATGCC 59.643 40.000 0.00 0.00 0.00 4.40
831 930 5.356751 GTGATGTTGGTACTAATGAATGCCA 59.643 40.000 0.00 0.00 0.00 4.92
832 931 6.039717 GTGATGTTGGTACTAATGAATGCCAT 59.960 38.462 0.00 0.00 36.99 4.40
833 932 6.606796 TGATGTTGGTACTAATGAATGCCATT 59.393 34.615 0.00 0.00 46.52 3.16
834 933 6.206395 TGTTGGTACTAATGAATGCCATTG 57.794 37.500 0.00 0.00 44.67 2.82
835 934 5.948758 TGTTGGTACTAATGAATGCCATTGA 59.051 36.000 0.00 0.00 44.67 2.57
836 935 6.127758 TGTTGGTACTAATGAATGCCATTGAC 60.128 38.462 0.00 0.00 44.67 3.18
837 936 5.754782 TGGTACTAATGAATGCCATTGACT 58.245 37.500 0.00 0.00 44.67 3.41
838 937 6.894682 TGGTACTAATGAATGCCATTGACTA 58.105 36.000 0.00 0.00 44.67 2.59
839 938 6.765989 TGGTACTAATGAATGCCATTGACTAC 59.234 38.462 0.00 0.00 44.67 2.73
869 968 5.545658 TGAACGCTTCATGTAAATTCTCC 57.454 39.130 0.00 0.00 34.08 3.71
889 988 2.333926 CGAAGTCCAAACTGACGCATA 58.666 47.619 0.00 0.00 40.26 3.14
917 1016 0.668535 ACTTGCCTCCAAAACGCTTC 59.331 50.000 0.00 0.00 0.00 3.86
929 1028 2.663279 AACGCTTCTGCAAGTTAACG 57.337 45.000 0.00 0.00 39.64 3.18
932 1031 0.452784 GCTTCTGCAAGTTAACGCCG 60.453 55.000 0.00 0.00 39.41 6.46
933 1032 0.865769 CTTCTGCAAGTTAACGCCGT 59.134 50.000 0.00 0.00 33.76 5.68
935 1034 1.440353 CTGCAAGTTAACGCCGTGC 60.440 57.895 15.34 15.34 35.75 5.34
938 1039 1.206578 CAAGTTAACGCCGTGCTGG 59.793 57.895 0.00 0.00 42.50 4.85
964 1066 7.489757 GCCTATATAATCACGTCAATTCCTCTC 59.510 40.741 0.00 0.00 0.00 3.20
983 1086 5.507985 CCTCTCAAACTTCACCAAATCAACC 60.508 44.000 0.00 0.00 0.00 3.77
1010 1113 2.735663 CAGAGTCACAGATGCAACAGAC 59.264 50.000 0.00 0.00 0.00 3.51
1326 1441 2.335712 GGGCAGCGGGAAACAAGAG 61.336 63.158 0.00 0.00 0.00 2.85
1587 1727 2.205022 TCAGGAAAGATGTGGCCAAG 57.795 50.000 7.24 0.00 0.00 3.61
1658 1811 5.175859 AGTGATGTGAAATTCGGATTACGT 58.824 37.500 0.00 0.00 44.69 3.57
1664 1817 5.236695 TGTGAAATTCGGATTACGTTGTGAA 59.763 36.000 0.00 0.00 44.69 3.18
1717 1873 1.005156 GCCCGTACCGTAAACCACA 60.005 57.895 0.00 0.00 0.00 4.17
1781 1945 3.897325 TGATAGTGCTATCGCCTAAACG 58.103 45.455 12.79 0.00 43.64 3.60
1783 1947 2.953466 AGTGCTATCGCCTAAACGAA 57.047 45.000 0.00 0.00 46.59 3.85
1784 1948 2.810650 AGTGCTATCGCCTAAACGAAG 58.189 47.619 0.00 0.00 46.59 3.79
1785 1949 2.165845 AGTGCTATCGCCTAAACGAAGT 59.834 45.455 0.00 0.00 46.59 3.01
1819 1987 5.272283 AGTGACTAGTTTTCGACTTTCCA 57.728 39.130 0.00 0.00 39.86 3.53
1876 2047 1.340017 CCTTTCTCCCCGCAATCTGAA 60.340 52.381 0.00 0.00 0.00 3.02
1897 2068 2.440253 ACTGCTCGACCCTACTCTATCT 59.560 50.000 0.00 0.00 0.00 1.98
1910 2081 7.824779 ACCCTACTCTATCTTGATTTGTGTTTC 59.175 37.037 0.00 0.00 0.00 2.78
1915 2086 7.118390 ACTCTATCTTGATTTGTGTTTCTTCCG 59.882 37.037 0.00 0.00 0.00 4.30
1916 2087 6.934645 TCTATCTTGATTTGTGTTTCTTCCGT 59.065 34.615 0.00 0.00 0.00 4.69
2063 2235 2.649034 GCGTCGTCACCCTCTTGA 59.351 61.111 0.00 0.00 0.00 3.02
2075 2247 0.679505 CCTCTTGAGGGTGTCGTTCA 59.320 55.000 8.74 0.00 0.00 3.18
2088 2260 0.684535 TCGTTCATGGTGAGCTTGGA 59.315 50.000 0.00 0.00 0.00 3.53
2099 2271 1.002430 TGAGCTTGGAGTGGATGTGAC 59.998 52.381 0.00 0.00 0.00 3.67
2266 2441 5.363101 GTGCTTCATCCTACTCATTGATGA 58.637 41.667 0.00 0.00 42.20 2.92
2350 2525 1.464734 CAGGAGGACGAAGCTGTCTA 58.535 55.000 4.38 0.00 38.91 2.59
2381 2556 2.581354 GTCGATGGCTGAGTGGCT 59.419 61.111 0.00 0.00 42.34 4.75
2408 2583 6.485171 ACAAGGTAGAAGCCTCAATATTTGT 58.515 36.000 0.00 0.00 38.03 2.83
2410 2585 7.451566 ACAAGGTAGAAGCCTCAATATTTGTTT 59.548 33.333 0.00 0.00 38.03 2.83
2471 2649 1.446618 GCGTCGGACCGGTTTGTAT 60.447 57.895 15.25 0.00 0.00 2.29
2499 2677 2.584608 GTATGTGGCTCGGCTGGT 59.415 61.111 0.00 0.00 0.00 4.00
2501 2679 2.290287 TATGTGGCTCGGCTGGTGT 61.290 57.895 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.740447 GTCACGAATACCCAAGGTTCAC 59.260 50.000 0.00 0.00 37.09 3.18
2 3 1.997606 CGTCACGAATACCCAAGGTTC 59.002 52.381 0.00 0.00 37.09 3.62
5 6 0.108329 AGCGTCACGAATACCCAAGG 60.108 55.000 0.00 0.00 0.00 3.61
6 7 0.999406 CAGCGTCACGAATACCCAAG 59.001 55.000 0.00 0.00 0.00 3.61
7 8 1.017177 GCAGCGTCACGAATACCCAA 61.017 55.000 0.00 0.00 0.00 4.12
8 9 1.447140 GCAGCGTCACGAATACCCA 60.447 57.895 0.00 0.00 0.00 4.51
9 10 2.171725 GGCAGCGTCACGAATACCC 61.172 63.158 0.00 0.00 0.00 3.69
10 11 0.810031 ATGGCAGCGTCACGAATACC 60.810 55.000 0.00 0.00 0.00 2.73
11 12 0.301687 CATGGCAGCGTCACGAATAC 59.698 55.000 0.00 0.00 0.00 1.89
12 13 0.108377 ACATGGCAGCGTCACGAATA 60.108 50.000 0.00 0.00 0.00 1.75
13 14 1.375908 ACATGGCAGCGTCACGAAT 60.376 52.632 0.00 0.00 0.00 3.34
14 15 2.030412 ACATGGCAGCGTCACGAA 59.970 55.556 0.00 0.00 0.00 3.85
15 16 2.738139 CACATGGCAGCGTCACGA 60.738 61.111 0.00 0.00 0.00 4.35
16 17 3.792047 CCACATGGCAGCGTCACG 61.792 66.667 0.00 0.00 0.00 4.35
52 53 8.088365 TCTTTTATTTAGAGAAAAGGCCAAAGC 58.912 33.333 5.01 0.00 41.89 3.51
53 54 9.981114 TTCTTTTATTTAGAGAAAAGGCCAAAG 57.019 29.630 5.01 0.42 41.89 2.77
69 70 9.681692 GCTTTCATTTGGCATTTTCTTTTATTT 57.318 25.926 0.00 0.00 0.00 1.40
70 71 8.298854 GGCTTTCATTTGGCATTTTCTTTTATT 58.701 29.630 0.00 0.00 0.00 1.40
71 72 7.361116 CGGCTTTCATTTGGCATTTTCTTTTAT 60.361 33.333 0.00 0.00 0.00 1.40
72 73 6.073331 CGGCTTTCATTTGGCATTTTCTTTTA 60.073 34.615 0.00 0.00 0.00 1.52
73 74 5.277925 CGGCTTTCATTTGGCATTTTCTTTT 60.278 36.000 0.00 0.00 0.00 2.27
74 75 4.213906 CGGCTTTCATTTGGCATTTTCTTT 59.786 37.500 0.00 0.00 0.00 2.52
75 76 3.747529 CGGCTTTCATTTGGCATTTTCTT 59.252 39.130 0.00 0.00 0.00 2.52
76 77 3.006752 TCGGCTTTCATTTGGCATTTTCT 59.993 39.130 0.00 0.00 0.00 2.52
91 92 1.222936 CTCCATGGAGCTCGGCTTT 59.777 57.895 28.45 0.00 39.88 3.51
193 194 7.915293 TCGACCTGAAATTTTACACATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
244 252 2.568623 AGAAGAGCCACCGATTTGTT 57.431 45.000 0.00 0.00 0.00 2.83
434 443 8.348507 GCTCCATATGAAGGACTTAATTTTGAG 58.651 37.037 3.65 0.00 0.00 3.02
446 455 1.964223 GACCGAGCTCCATATGAAGGA 59.036 52.381 8.47 0.00 0.00 3.36
626 678 3.241426 CGTTTTGCATGTACTACGTACGG 60.241 47.826 21.06 5.00 41.41 4.02
682 737 4.641396 TCATCTCCCAGTAATTAATGGCG 58.359 43.478 23.54 17.07 39.95 5.69
696 752 0.179062 ACATGAAGCGCTCATCTCCC 60.179 55.000 12.06 0.00 43.28 4.30
781 880 5.859495 ACTTCCTTCTCAAAAGGAGTACTG 58.141 41.667 0.00 0.00 46.21 2.74
782 881 7.235812 ACATACTTCCTTCTCAAAAGGAGTACT 59.764 37.037 0.00 0.00 46.21 2.73
783 882 7.332182 CACATACTTCCTTCTCAAAAGGAGTAC 59.668 40.741 6.62 0.00 46.21 2.73
784 883 7.234782 TCACATACTTCCTTCTCAAAAGGAGTA 59.765 37.037 6.62 10.83 46.21 2.59
785 884 6.043243 TCACATACTTCCTTCTCAAAAGGAGT 59.957 38.462 6.62 9.35 46.21 3.85
786 885 6.467677 TCACATACTTCCTTCTCAAAAGGAG 58.532 40.000 6.62 4.74 46.21 3.69
787 886 6.433847 TCACATACTTCCTTCTCAAAAGGA 57.566 37.500 2.40 2.40 44.23 3.36
788 887 6.656693 ACATCACATACTTCCTTCTCAAAAGG 59.343 38.462 0.00 0.00 38.78 3.11
789 888 7.678947 ACATCACATACTTCCTTCTCAAAAG 57.321 36.000 0.00 0.00 0.00 2.27
790 889 7.040478 CCAACATCACATACTTCCTTCTCAAAA 60.040 37.037 0.00 0.00 0.00 2.44
791 890 6.430925 CCAACATCACATACTTCCTTCTCAAA 59.569 38.462 0.00 0.00 0.00 2.69
792 891 5.939883 CCAACATCACATACTTCCTTCTCAA 59.060 40.000 0.00 0.00 0.00 3.02
793 892 5.013079 ACCAACATCACATACTTCCTTCTCA 59.987 40.000 0.00 0.00 0.00 3.27
794 893 5.491982 ACCAACATCACATACTTCCTTCTC 58.508 41.667 0.00 0.00 0.00 2.87
795 894 5.505181 ACCAACATCACATACTTCCTTCT 57.495 39.130 0.00 0.00 0.00 2.85
796 895 6.407202 AGTACCAACATCACATACTTCCTTC 58.593 40.000 0.00 0.00 0.00 3.46
797 896 6.374417 AGTACCAACATCACATACTTCCTT 57.626 37.500 0.00 0.00 0.00 3.36
798 897 7.490657 TTAGTACCAACATCACATACTTCCT 57.509 36.000 0.00 0.00 0.00 3.36
799 898 7.985184 TCATTAGTACCAACATCACATACTTCC 59.015 37.037 0.00 0.00 0.00 3.46
800 899 8.942338 TCATTAGTACCAACATCACATACTTC 57.058 34.615 0.00 0.00 0.00 3.01
801 900 9.905713 ATTCATTAGTACCAACATCACATACTT 57.094 29.630 0.00 0.00 0.00 2.24
802 901 9.330063 CATTCATTAGTACCAACATCACATACT 57.670 33.333 0.00 0.00 0.00 2.12
803 902 8.070171 GCATTCATTAGTACCAACATCACATAC 58.930 37.037 0.00 0.00 0.00 2.39
804 903 7.228507 GGCATTCATTAGTACCAACATCACATA 59.771 37.037 0.00 0.00 0.00 2.29
805 904 6.039717 GGCATTCATTAGTACCAACATCACAT 59.960 38.462 0.00 0.00 0.00 3.21
806 905 5.356751 GGCATTCATTAGTACCAACATCACA 59.643 40.000 0.00 0.00 0.00 3.58
807 906 5.356751 TGGCATTCATTAGTACCAACATCAC 59.643 40.000 0.00 0.00 0.00 3.06
808 907 5.504853 TGGCATTCATTAGTACCAACATCA 58.495 37.500 0.00 0.00 0.00 3.07
809 908 6.639632 ATGGCATTCATTAGTACCAACATC 57.360 37.500 0.00 0.00 30.55 3.06
810 909 6.606796 TCAATGGCATTCATTAGTACCAACAT 59.393 34.615 10.36 0.00 43.70 2.71
811 910 5.948758 TCAATGGCATTCATTAGTACCAACA 59.051 36.000 10.36 0.00 43.70 3.33
812 911 6.095440 AGTCAATGGCATTCATTAGTACCAAC 59.905 38.462 10.36 0.00 43.70 3.77
813 912 6.186957 AGTCAATGGCATTCATTAGTACCAA 58.813 36.000 10.36 0.00 43.70 3.67
814 913 5.754782 AGTCAATGGCATTCATTAGTACCA 58.245 37.500 10.36 0.00 43.70 3.25
815 914 6.992715 AGTAGTCAATGGCATTCATTAGTACC 59.007 38.462 10.36 0.00 43.70 3.34
816 915 7.096023 CGAGTAGTCAATGGCATTCATTAGTAC 60.096 40.741 10.36 12.40 43.70 2.73
817 916 6.923508 CGAGTAGTCAATGGCATTCATTAGTA 59.076 38.462 10.36 1.37 43.70 1.82
818 917 5.755375 CGAGTAGTCAATGGCATTCATTAGT 59.245 40.000 10.36 1.24 43.70 2.24
819 918 5.178252 CCGAGTAGTCAATGGCATTCATTAG 59.822 44.000 10.36 0.00 43.70 1.73
820 919 5.056480 CCGAGTAGTCAATGGCATTCATTA 58.944 41.667 10.36 0.00 43.70 1.90
821 920 3.879295 CCGAGTAGTCAATGGCATTCATT 59.121 43.478 10.36 0.00 46.24 2.57
822 921 3.134623 TCCGAGTAGTCAATGGCATTCAT 59.865 43.478 10.36 1.70 37.79 2.57
823 922 2.499693 TCCGAGTAGTCAATGGCATTCA 59.500 45.455 10.36 0.00 0.00 2.57
824 923 3.126831 CTCCGAGTAGTCAATGGCATTC 58.873 50.000 10.36 0.00 0.00 2.67
825 924 2.766263 TCTCCGAGTAGTCAATGGCATT 59.234 45.455 6.96 6.96 0.00 3.56
826 925 2.388735 TCTCCGAGTAGTCAATGGCAT 58.611 47.619 0.00 0.00 0.00 4.40
827 926 1.847328 TCTCCGAGTAGTCAATGGCA 58.153 50.000 0.00 0.00 0.00 4.92
828 927 2.362397 TCATCTCCGAGTAGTCAATGGC 59.638 50.000 0.00 0.00 0.00 4.40
829 928 4.363999 GTTCATCTCCGAGTAGTCAATGG 58.636 47.826 0.00 0.00 0.00 3.16
830 929 4.038361 CGTTCATCTCCGAGTAGTCAATG 58.962 47.826 0.00 0.00 0.00 2.82
831 930 3.489398 GCGTTCATCTCCGAGTAGTCAAT 60.489 47.826 0.00 0.00 0.00 2.57
832 931 2.159421 GCGTTCATCTCCGAGTAGTCAA 60.159 50.000 0.00 0.00 0.00 3.18
833 932 1.400846 GCGTTCATCTCCGAGTAGTCA 59.599 52.381 0.00 0.00 0.00 3.41
834 933 1.671845 AGCGTTCATCTCCGAGTAGTC 59.328 52.381 0.00 0.00 0.00 2.59
835 934 1.752683 AGCGTTCATCTCCGAGTAGT 58.247 50.000 0.00 0.00 0.00 2.73
836 935 2.097629 TGAAGCGTTCATCTCCGAGTAG 59.902 50.000 0.00 0.00 34.08 2.57
837 936 2.089201 TGAAGCGTTCATCTCCGAGTA 58.911 47.619 0.00 0.00 34.08 2.59
838 937 0.888619 TGAAGCGTTCATCTCCGAGT 59.111 50.000 0.00 0.00 34.08 4.18
839 938 3.721625 TGAAGCGTTCATCTCCGAG 57.278 52.632 0.00 0.00 34.08 4.63
861 960 4.515567 GTCAGTTTGGACTTCGGAGAATTT 59.484 41.667 0.00 0.00 45.90 1.82
867 966 0.599204 GCGTCAGTTTGGACTTCGGA 60.599 55.000 0.00 0.00 35.63 4.55
869 968 1.148310 ATGCGTCAGTTTGGACTTCG 58.852 50.000 0.00 0.00 35.63 3.79
904 1003 1.334869 ACTTGCAGAAGCGTTTTGGAG 59.665 47.619 0.00 0.00 46.23 3.86
910 1009 1.333791 GCGTTAACTTGCAGAAGCGTT 60.334 47.619 3.71 0.00 46.23 4.84
917 1016 1.440353 GCACGGCGTTAACTTGCAG 60.440 57.895 11.19 4.21 33.24 4.41
932 1031 3.926616 ACGTGATTATATAGGCCAGCAC 58.073 45.455 5.01 0.25 0.00 4.40
933 1032 3.576550 TGACGTGATTATATAGGCCAGCA 59.423 43.478 5.01 0.00 0.00 4.41
935 1034 6.313905 GGAATTGACGTGATTATATAGGCCAG 59.686 42.308 5.01 0.00 0.00 4.85
938 1039 7.324178 AGAGGAATTGACGTGATTATATAGGC 58.676 38.462 0.00 0.00 0.00 3.93
964 1066 4.290155 CTCGGTTGATTTGGTGAAGTTTG 58.710 43.478 0.00 0.00 0.00 2.93
983 1086 1.798446 GCATCTGTGACTCTGAGCTCG 60.798 57.143 9.64 4.19 0.00 5.03
1010 1113 1.759445 AGATGGAAGGAGACATGGTCG 59.241 52.381 0.00 0.00 37.67 4.79
1565 1698 0.743097 GGCCACATCTTTCCTGATGC 59.257 55.000 0.00 0.00 45.51 3.91
1587 1727 7.906160 ACGCCTTATTTCGCATCATATATTAC 58.094 34.615 0.00 0.00 0.00 1.89
1638 1787 5.732647 CACAACGTAATCCGAATTTCACATC 59.267 40.000 0.00 0.00 40.70 3.06
1642 1791 5.926214 TTCACAACGTAATCCGAATTTCA 57.074 34.783 0.00 0.00 40.70 2.69
1658 1811 3.243168 GCAACAGACAGCTTCATTCACAA 60.243 43.478 0.00 0.00 0.00 3.33
1717 1873 8.651389 ACATTGCAGTATATATAGCGGGATAAT 58.349 33.333 0.00 0.00 0.00 1.28
1781 1945 4.266714 AGTCACTCCTCTGCTACTACTTC 58.733 47.826 0.00 0.00 0.00 3.01
1783 1947 4.472108 ACTAGTCACTCCTCTGCTACTACT 59.528 45.833 0.00 0.00 0.00 2.57
1784 1948 4.773013 ACTAGTCACTCCTCTGCTACTAC 58.227 47.826 0.00 0.00 0.00 2.73
1785 1949 5.438698 AACTAGTCACTCCTCTGCTACTA 57.561 43.478 0.00 0.00 0.00 1.82
1819 1987 3.504520 GGTGGGAAAATAATCGTGTGTGT 59.495 43.478 0.00 0.00 0.00 3.72
1851 2020 3.431725 GCGGGGAGAAAGGCGTTG 61.432 66.667 0.00 0.00 0.00 4.10
1876 2047 2.440253 AGATAGAGTAGGGTCGAGCAGT 59.560 50.000 17.59 5.43 0.00 4.40
1897 2068 5.568685 TTCACGGAAGAAACACAAATCAA 57.431 34.783 0.00 0.00 0.00 2.57
1935 2106 5.642491 TCTGATCTGTGAAAATGAGCTTCTG 59.358 40.000 0.00 0.00 0.00 3.02
1969 2140 4.216042 CGATGCCATGGCTATTTGAATACA 59.784 41.667 35.53 12.79 42.51 2.29
2038 2210 4.357947 GTGACGACGCCTGGAGCA 62.358 66.667 0.00 0.00 44.04 4.26
2044 2216 2.600769 AAGAGGGTGACGACGCCT 60.601 61.111 16.73 3.55 45.13 5.52
2063 2235 0.321671 CTCACCATGAACGACACCCT 59.678 55.000 0.00 0.00 0.00 4.34
2075 2247 1.064906 CATCCACTCCAAGCTCACCAT 60.065 52.381 0.00 0.00 0.00 3.55
2088 2260 0.108585 ACCAAAGCGTCACATCCACT 59.891 50.000 0.00 0.00 0.00 4.00
2099 2271 2.730604 CGCCAAGCAACCAAAGCG 60.731 61.111 0.00 0.00 37.01 4.68
2133 2305 1.966451 GCCACCAGACAAACTCCGG 60.966 63.158 0.00 0.00 0.00 5.14
2266 2441 2.335369 GCCGCCGAGATACATCGT 59.665 61.111 0.00 0.00 41.12 3.73
2381 2556 7.676683 AATATTGAGGCTTCTACCTTGTCTA 57.323 36.000 0.00 0.00 41.32 2.59
2408 2583 1.487142 TCCACAGGTCCGTCTTCAAAA 59.513 47.619 0.00 0.00 0.00 2.44
2410 2585 1.070134 CTTCCACAGGTCCGTCTTCAA 59.930 52.381 0.00 0.00 0.00 2.69
2471 2649 1.687840 CCACATACCGGGTCTGGGA 60.688 63.158 15.76 0.00 0.00 4.37
2499 2677 3.254657 CCTAACATCAAAAGCCGGAAACA 59.745 43.478 5.05 0.00 0.00 2.83
2501 2679 2.230266 GCCTAACATCAAAAGCCGGAAA 59.770 45.455 5.05 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.