Multiple sequence alignment - TraesCS3A01G219200

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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 TraesCS3A01G219200 chr3A 100.000 4881 0 0 1 4881 402130787 402135667 0.000000e+00 9014.0
1 TraesCS3A01G219200 chr3A 84.367 403 38 11 2188 2588 639230184 639230563 5.970000e-99 372.0
2 TraesCS3A01G219200 chr3D 94.897 2038 57 21 2854 4881 321874469 321872469 0.000000e+00 3144.0
3 TraesCS3A01G219200 chr3D 91.620 1623 66 33 604 2179 321876067 321874468 0.000000e+00 2180.0
4 TraesCS3A01G219200 chr3D 92.023 514 19 7 1 503 321876844 321876342 0.000000e+00 702.0
5 TraesCS3A01G219200 chr3D 88.193 415 28 9 2378 2780 241400597 241401002 4.420000e-130 475.0
6 TraesCS3A01G219200 chr3D 97.487 199 5 0 2189 2387 241400379 241400577 1.680000e-89 340.0
7 TraesCS3A01G219200 chr3D 89.583 144 15 0 3624 3767 508465700 508465557 3.000000e-42 183.0
8 TraesCS3A01G219200 chr3D 81.967 183 14 8 3457 3626 508466646 508466470 2.370000e-28 137.0
9 TraesCS3A01G219200 chr3D 81.188 101 5 2 3829 3929 606777910 606777996 8.770000e-08 69.4
10 TraesCS3A01G219200 chr1B 92.629 1411 51 22 2868 4271 637911538 637912902 0.000000e+00 1980.0
11 TraesCS3A01G219200 chr1B 92.571 673 32 14 2178 2839 72955623 72956288 0.000000e+00 950.0
12 TraesCS3A01G219200 chr1B 84.512 594 52 18 4310 4881 637913009 637913584 7.140000e-153 551.0
13 TraesCS3A01G219200 chr1B 90.909 198 5 3 1982 2179 637911338 637911522 2.250000e-63 254.0
14 TraesCS3A01G219200 chr1B 85.714 70 3 2 435 503 555630532 555630469 3.150000e-07 67.6
15 TraesCS3A01G219200 chr1B 97.059 34 1 0 3896 3929 565340940 565340907 1.900000e-04 58.4
16 TraesCS3A01G219200 chr3B 90.714 1443 63 26 2853 4271 397676091 397677486 0.000000e+00 1857.0
17 TraesCS3A01G219200 chr3B 88.325 1379 72 41 628 1972 397674595 397675918 0.000000e+00 1572.0
18 TraesCS3A01G219200 chr3B 86.195 594 51 13 4313 4881 397677597 397678184 8.980000e-172 614.0
19 TraesCS3A01G219200 chr3B 93.023 430 10 7 83 503 397673999 397674417 1.160000e-170 610.0
20 TraesCS3A01G219200 chr3B 95.082 183 6 1 2000 2179 397675913 397676095 8.000000e-73 285.0
21 TraesCS3A01G219200 chr3B 97.917 48 0 1 1 47 397673947 397673994 1.130000e-11 82.4
22 TraesCS3A01G219200 chr3B 91.304 46 3 1 617 662 254193139 254193183 1.470000e-05 62.1
23 TraesCS3A01G219200 chr2D 90.748 1243 50 22 970 2179 634651745 634650535 0.000000e+00 1598.0
24 TraesCS3A01G219200 chr2D 92.480 1117 25 21 2871 3975 634650517 634649448 0.000000e+00 1543.0
25 TraesCS3A01G219200 chr2D 85.570 596 47 18 4310 4881 634647636 634647056 5.440000e-164 588.0
26 TraesCS3A01G219200 chr2D 93.750 304 16 1 3963 4266 634648048 634647748 2.070000e-123 453.0
27 TraesCS3A01G219200 chr2D 81.657 507 62 13 2179 2660 385144621 385145121 4.580000e-105 392.0
28 TraesCS3A01G219200 chr2D 94.828 58 3 0 848 905 634651854 634651797 1.870000e-14 91.6
29 TraesCS3A01G219200 chr2D 86.567 67 3 2 437 503 347810896 347810836 8.770000e-08 69.4
30 TraesCS3A01G219200 chr2D 86.885 61 2 2 440 500 647812010 647812064 4.080000e-06 63.9
31 TraesCS3A01G219200 chr1D 93.609 845 32 10 3235 4073 462946843 462947671 0.000000e+00 1242.0
32 TraesCS3A01G219200 chr1D 84.848 594 53 15 4310 4881 462965613 462966191 9.170000e-157 564.0
33 TraesCS3A01G219200 chr1D 93.301 209 11 1 4063 4271 462965301 462965506 6.140000e-79 305.0
34 TraesCS3A01G219200 chr1D 93.939 99 4 2 4784 4881 462888697 462888794 1.090000e-31 148.0
35 TraesCS3A01G219200 chr1D 93.939 99 4 2 4784 4881 462904072 462904169 1.090000e-31 148.0
36 TraesCS3A01G219200 chr1D 93.939 99 4 2 4784 4881 462906611 462906708 1.090000e-31 148.0
37 TraesCS3A01G219200 chr1D 92.929 99 5 2 4784 4881 462886130 462886227 5.090000e-30 143.0
38 TraesCS3A01G219200 chr1D 92.929 99 5 2 4784 4881 462914338 462914435 5.090000e-30 143.0
39 TraesCS3A01G219200 chr1D 92.929 99 5 2 4784 4881 462916383 462916480 5.090000e-30 143.0
40 TraesCS3A01G219200 chr1D 87.143 70 2 2 435 503 412080198 412080135 6.780000e-09 73.1
41 TraesCS3A01G219200 chr2A 97.859 654 11 3 2188 2839 35580321 35580973 0.000000e+00 1127.0
42 TraesCS3A01G219200 chr2A 91.988 674 24 10 2175 2839 10744197 10743545 0.000000e+00 918.0
43 TraesCS3A01G219200 chr2A 86.154 65 4 1 439 503 734991239 734991298 1.130000e-06 65.8
44 TraesCS3A01G219200 chr2A 87.097 62 2 2 439 500 769575742 769575797 1.130000e-06 65.8
45 TraesCS3A01G219200 chr4B 93.443 671 29 12 2178 2839 584537568 584538232 0.000000e+00 981.0
46 TraesCS3A01G219200 chr2B 92.388 670 37 9 2178 2839 186119044 186118381 0.000000e+00 942.0
47 TraesCS3A01G219200 chr2B 83.960 399 53 8 2196 2588 456008885 456009278 5.970000e-99 372.0
48 TraesCS3A01G219200 chr6A 89.605 683 42 12 2178 2839 392127344 392128018 0.000000e+00 841.0
49 TraesCS3A01G219200 chr6A 85.062 482 48 10 3321 3790 508249581 508249112 2.060000e-128 470.0
50 TraesCS3A01G219200 chr4A 86.162 383 25 16 2473 2837 406534569 406534941 5.920000e-104 388.0
51 TraesCS3A01G219200 chr4A 90.476 42 4 0 621 662 18300314 18300355 6.830000e-04 56.5
52 TraesCS3A01G219200 chr6D 86.111 324 24 9 3273 3585 367749855 367749542 3.640000e-86 329.0
53 TraesCS3A01G219200 chr7D 85.075 268 24 6 3457 3713 41303535 41303797 4.850000e-65 259.0
54 TraesCS3A01G219200 chr7D 86.758 219 14 4 3711 3929 41306157 41306360 3.800000e-56 230.0
55 TraesCS3A01G219200 chr4D 89.062 64 1 1 437 500 333773309 333773252 1.880000e-09 75.0
56 TraesCS3A01G219200 chr4D 87.302 63 2 2 438 500 301245041 301245097 3.150000e-07 67.6
57 TraesCS3A01G219200 chr1A 87.143 70 2 2 435 503 508634161 508634098 6.780000e-09 73.1


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 TraesCS3A01G219200 chr3A 402130787 402135667 4880 False 9014.000000 9014 100.000000 1 4881 1 chr3A.!!$F1 4880
1 TraesCS3A01G219200 chr3D 321872469 321876844 4375 True 2008.666667 3144 92.846667 1 4881 3 chr3D.!!$R1 4880
2 TraesCS3A01G219200 chr3D 241400379 241401002 623 False 407.500000 475 92.840000 2189 2780 2 chr3D.!!$F2 591
3 TraesCS3A01G219200 chr1B 72955623 72956288 665 False 950.000000 950 92.571000 2178 2839 1 chr1B.!!$F1 661
4 TraesCS3A01G219200 chr1B 637911338 637913584 2246 False 928.333333 1980 89.350000 1982 4881 3 chr1B.!!$F2 2899
5 TraesCS3A01G219200 chr3B 397673947 397678184 4237 False 836.733333 1857 91.876000 1 4881 6 chr3B.!!$F2 4880
6 TraesCS3A01G219200 chr2D 634647056 634651854 4798 True 854.720000 1598 91.475200 848 4881 5 chr2D.!!$R2 4033
7 TraesCS3A01G219200 chr2D 385144621 385145121 500 False 392.000000 392 81.657000 2179 2660 1 chr2D.!!$F1 481
8 TraesCS3A01G219200 chr1D 462946843 462947671 828 False 1242.000000 1242 93.609000 3235 4073 1 chr1D.!!$F1 838
9 TraesCS3A01G219200 chr1D 462965301 462966191 890 False 434.500000 564 89.074500 4063 4881 2 chr1D.!!$F5 818
10 TraesCS3A01G219200 chr2A 35580321 35580973 652 False 1127.000000 1127 97.859000 2188 2839 1 chr2A.!!$F1 651
11 TraesCS3A01G219200 chr2A 10743545 10744197 652 True 918.000000 918 91.988000 2175 2839 1 chr2A.!!$R1 664
12 TraesCS3A01G219200 chr4B 584537568 584538232 664 False 981.000000 981 93.443000 2178 2839 1 chr4B.!!$F1 661
13 TraesCS3A01G219200 chr2B 186118381 186119044 663 True 942.000000 942 92.388000 2178 2839 1 chr2B.!!$R1 661
14 TraesCS3A01G219200 chr6A 392127344 392128018 674 False 841.000000 841 89.605000 2178 2839 1 chr6A.!!$F1 661
15 TraesCS3A01G219200 chr7D 41303535 41306360 2825 False 244.500000 259 85.916500 3457 3929 2 chr7D.!!$F1 472

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
943 1158 0.107312 CCACCAGCAGAGCAGCTTAT 60.107 55.000 0.00 0.0 43.70 1.73 F
1261 1532 0.105964 TACATACTCCATGCGGCACC 59.894 55.000 4.03 0.0 38.29 5.01 F
1389 1665 0.976641 CCTGTTGTCCTCAGTAGCCA 59.023 55.000 0.00 0.0 0.00 4.75 F
2306 2619 1.001597 GGATTCGCCTCTACAGTACCG 60.002 57.143 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2859 3249 0.250209 CTGCAGCCAAGCGATATCCT 60.250 55.000 0.0 0.0 37.31 3.24 R
3161 3570 2.169978 CAAGCCTCACTGGAGATCATGA 59.830 50.000 0.0 0.0 44.26 3.07 R
3268 3677 1.272769 GCGCTGAGGGTAATAGGGTAG 59.727 57.143 0.0 0.0 0.00 3.18 R
3883 6683 0.475906 AGGCACAAGCTTCTCCACTT 59.524 50.000 0.0 0.0 41.70 3.16 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
80 81 4.940654 GGGGTTTCTCTCAGAAGAATCTTG 59.059 45.833 0.00 0.00 35.37 3.02
122 123 7.174253 TGTGAGACATTAATCGCCTTTAGTTTT 59.826 33.333 0.00 0.00 0.00 2.43
174 176 8.951243 AGAAAGAAGTGTTTATGCTTATTCCTC 58.049 33.333 0.00 0.00 0.00 3.71
301 303 4.668138 TGGCAAAAAGGGTCCTAAGTAT 57.332 40.909 0.00 0.00 0.00 2.12
369 378 1.207488 TCTGCTGTAACCTGGGCCAT 61.207 55.000 6.72 0.00 0.00 4.40
471 483 9.578439 CTTTGATTCAAAGGATTTTCATACTCC 57.422 33.333 25.14 0.00 44.75 3.85
472 484 8.884124 TTGATTCAAAGGATTTTCATACTCCT 57.116 30.769 0.00 0.00 41.19 3.69
473 485 9.973661 TTGATTCAAAGGATTTTCATACTCCTA 57.026 29.630 0.00 0.00 38.47 2.94
478 490 8.781951 TCAAAGGATTTTCATACTCCTAGGAAT 58.218 33.333 13.77 5.21 38.47 3.01
526 648 9.520204 TGAGTCAAAACATCTTTGAAAGAATTC 57.480 29.630 12.10 0.00 41.63 2.17
558 681 3.334078 GATGCAATCAAACGGCCAG 57.666 52.632 2.24 0.00 44.70 4.85
559 682 0.179129 GATGCAATCAAACGGCCAGG 60.179 55.000 2.24 0.00 44.70 4.45
560 683 1.606885 ATGCAATCAAACGGCCAGGG 61.607 55.000 2.24 0.00 0.00 4.45
562 685 1.937546 GCAATCAAACGGCCAGGGAG 61.938 60.000 2.24 0.00 0.00 4.30
564 687 0.112412 AATCAAACGGCCAGGGAGTT 59.888 50.000 2.24 0.00 0.00 3.01
566 689 0.536460 TCAAACGGCCAGGGAGTTTC 60.536 55.000 2.24 0.00 36.12 2.78
911 1122 1.803519 CGCGCGCTCTCTTTTCTCT 60.804 57.895 30.48 0.00 0.00 3.10
917 1132 2.163412 GCGCTCTCTTTTCTCTCTCTCA 59.837 50.000 0.00 0.00 0.00 3.27
919 1134 3.190327 CGCTCTCTTTTCTCTCTCTCACA 59.810 47.826 0.00 0.00 0.00 3.58
921 1136 4.022416 GCTCTCTTTTCTCTCTCTCACACA 60.022 45.833 0.00 0.00 0.00 3.72
935 1150 1.146930 ACACACACCACCAGCAGAG 59.853 57.895 0.00 0.00 0.00 3.35
941 1156 2.033757 CCACCAGCAGAGCAGCTT 59.966 61.111 0.00 0.00 43.70 3.74
942 1157 1.297689 CCACCAGCAGAGCAGCTTA 59.702 57.895 0.00 0.00 43.70 3.09
943 1158 0.107312 CCACCAGCAGAGCAGCTTAT 60.107 55.000 0.00 0.00 43.70 1.73
944 1159 1.139654 CCACCAGCAGAGCAGCTTATA 59.860 52.381 0.00 0.00 43.70 0.98
945 1160 2.420547 CCACCAGCAGAGCAGCTTATAA 60.421 50.000 0.00 0.00 43.70 0.98
946 1161 2.611292 CACCAGCAGAGCAGCTTATAAC 59.389 50.000 0.00 0.00 43.70 1.89
947 1162 2.503356 ACCAGCAGAGCAGCTTATAACT 59.497 45.455 0.00 0.00 43.70 2.24
948 1163 2.871022 CCAGCAGAGCAGCTTATAACTG 59.129 50.000 0.00 0.00 43.70 3.16
949 1164 3.431346 CCAGCAGAGCAGCTTATAACTGA 60.431 47.826 11.37 0.00 43.70 3.41
950 1165 4.378774 CAGCAGAGCAGCTTATAACTGAT 58.621 43.478 11.37 10.73 43.70 2.90
951 1166 4.815308 CAGCAGAGCAGCTTATAACTGATT 59.185 41.667 11.37 6.03 43.70 2.57
952 1167 4.815308 AGCAGAGCAGCTTATAACTGATTG 59.185 41.667 11.37 11.55 43.70 2.67
953 1168 4.813161 GCAGAGCAGCTTATAACTGATTGA 59.187 41.667 11.37 0.00 37.32 2.57
954 1169 5.469421 GCAGAGCAGCTTATAACTGATTGAT 59.531 40.000 11.37 2.29 37.32 2.57
955 1170 6.017275 GCAGAGCAGCTTATAACTGATTGATT 60.017 38.462 11.37 0.38 37.32 2.57
956 1171 7.353497 CAGAGCAGCTTATAACTGATTGATTG 58.647 38.462 15.12 6.52 37.32 2.67
957 1172 7.226128 CAGAGCAGCTTATAACTGATTGATTGA 59.774 37.037 15.12 0.00 37.32 2.57
958 1173 7.937942 AGAGCAGCTTATAACTGATTGATTGAT 59.062 33.333 15.12 0.00 37.32 2.57
959 1174 8.097078 AGCAGCTTATAACTGATTGATTGATC 57.903 34.615 15.12 0.00 37.32 2.92
960 1175 7.014115 GCAGCTTATAACTGATTGATTGATCG 58.986 38.462 15.12 0.00 37.32 3.69
961 1176 7.095481 GCAGCTTATAACTGATTGATTGATCGA 60.095 37.037 15.12 0.00 37.32 3.59
962 1177 8.933807 CAGCTTATAACTGATTGATTGATCGAT 58.066 33.333 0.00 0.00 37.32 3.59
963 1178 9.149225 AGCTTATAACTGATTGATTGATCGATC 57.851 33.333 18.72 18.72 44.46 3.69
964 1179 8.386606 GCTTATAACTGATTGATTGATCGATCC 58.613 37.037 22.31 8.00 43.87 3.36
965 1180 9.428097 CTTATAACTGATTGATTGATCGATCCA 57.572 33.333 22.31 12.46 43.87 3.41
966 1181 9.948964 TTATAACTGATTGATTGATCGATCCAT 57.051 29.630 22.31 16.94 43.87 3.41
967 1182 6.798315 AACTGATTGATTGATCGATCCATC 57.202 37.500 25.28 25.28 43.87 3.51
968 1183 5.861727 ACTGATTGATTGATCGATCCATCA 58.138 37.500 28.91 28.91 43.87 3.07
1083 1328 3.007635 GGTTTTCAGTAAGATGGACCGG 58.992 50.000 0.00 0.00 0.00 5.28
1255 1526 7.555965 TGGATACATACATACATACTCCATGC 58.444 38.462 0.00 0.00 46.17 4.06
1256 1527 6.697455 GGATACATACATACATACTCCATGCG 59.303 42.308 0.00 0.00 38.29 4.73
1261 1532 0.105964 TACATACTCCATGCGGCACC 59.894 55.000 4.03 0.00 38.29 5.01
1262 1533 1.146930 CATACTCCATGCGGCACCT 59.853 57.895 4.03 0.00 0.00 4.00
1273 1549 2.125188 GGCACCTCTCTGCTCTGC 60.125 66.667 0.00 0.00 37.33 4.26
1383 1659 2.175202 ACTAGCTCCTGTTGTCCTCAG 58.825 52.381 0.00 0.00 0.00 3.35
1384 1660 2.175202 CTAGCTCCTGTTGTCCTCAGT 58.825 52.381 0.00 0.00 0.00 3.41
1385 1661 2.310779 AGCTCCTGTTGTCCTCAGTA 57.689 50.000 0.00 0.00 0.00 2.74
1386 1662 2.175202 AGCTCCTGTTGTCCTCAGTAG 58.825 52.381 0.00 0.00 0.00 2.57
1387 1663 1.404851 GCTCCTGTTGTCCTCAGTAGC 60.405 57.143 0.00 0.00 37.62 3.58
1388 1664 1.205893 CTCCTGTTGTCCTCAGTAGCC 59.794 57.143 0.00 0.00 0.00 3.93
1389 1665 0.976641 CCTGTTGTCCTCAGTAGCCA 59.023 55.000 0.00 0.00 0.00 4.75
1397 1673 3.301274 GTCCTCAGTAGCCAGTAGGAAT 58.699 50.000 0.00 0.00 38.06 3.01
1495 1783 2.882761 AGCTAGTTAGACACACGACACA 59.117 45.455 0.00 0.00 0.00 3.72
1536 1834 1.225983 CGTATGCATGGGTTGGGGA 59.774 57.895 10.16 0.00 0.00 4.81
1610 1908 3.070159 CCTTCCTCACTTCTCACTTGTCA 59.930 47.826 0.00 0.00 0.00 3.58
1613 1911 3.706594 TCCTCACTTCTCACTTGTCACTT 59.293 43.478 0.00 0.00 0.00 3.16
1614 1912 4.893524 TCCTCACTTCTCACTTGTCACTTA 59.106 41.667 0.00 0.00 0.00 2.24
1615 1913 5.010112 TCCTCACTTCTCACTTGTCACTTAG 59.990 44.000 0.00 0.00 0.00 2.18
1691 1989 6.209361 TCAGTCAGTCGAATATATGCAAGTC 58.791 40.000 0.00 0.00 0.00 3.01
1692 1990 5.979517 CAGTCAGTCGAATATATGCAAGTCA 59.020 40.000 0.00 0.00 0.00 3.41
1693 1991 6.476706 CAGTCAGTCGAATATATGCAAGTCAA 59.523 38.462 0.00 0.00 0.00 3.18
1694 1992 6.699204 AGTCAGTCGAATATATGCAAGTCAAG 59.301 38.462 0.00 0.00 0.00 3.02
1695 1993 6.477033 GTCAGTCGAATATATGCAAGTCAAGT 59.523 38.462 0.00 0.00 0.00 3.16
1756 2060 4.100963 TGTCCACACAAGTTGATGACTAGT 59.899 41.667 10.54 0.00 37.72 2.57
1827 2132 5.134661 ACCTAATTTGTTCCTTTTCCACGA 58.865 37.500 0.00 0.00 0.00 4.35
2171 2484 2.362397 TGTAAGCCTCTCAGCCTAATCG 59.638 50.000 0.00 0.00 0.00 3.34
2179 2492 5.406649 CCTCTCAGCCTAATCGATTACATC 58.593 45.833 13.85 6.19 0.00 3.06
2180 2493 5.184864 CCTCTCAGCCTAATCGATTACATCT 59.815 44.000 13.85 8.19 0.00 2.90
2181 2494 6.295011 CCTCTCAGCCTAATCGATTACATCTT 60.295 42.308 13.85 0.00 0.00 2.40
2182 2495 7.055667 TCTCAGCCTAATCGATTACATCTTT 57.944 36.000 13.85 0.00 0.00 2.52
2183 2496 8.178313 TCTCAGCCTAATCGATTACATCTTTA 57.822 34.615 13.85 0.00 0.00 1.85
2184 2497 8.082852 TCTCAGCCTAATCGATTACATCTTTAC 58.917 37.037 13.85 0.00 0.00 2.01
2185 2498 7.952671 TCAGCCTAATCGATTACATCTTTACT 58.047 34.615 13.85 0.91 0.00 2.24
2186 2499 9.074576 TCAGCCTAATCGATTACATCTTTACTA 57.925 33.333 13.85 0.00 0.00 1.82
2306 2619 1.001597 GGATTCGCCTCTACAGTACCG 60.002 57.143 0.00 0.00 0.00 4.02
2503 2846 3.526534 GCTTCACGAGATTTTCTAGGCT 58.473 45.455 0.00 0.00 0.00 4.58
2833 3223 8.427012 CCATCGAAACACATGAATTAAAACTTG 58.573 33.333 0.00 0.00 0.00 3.16
2834 3224 7.388290 TCGAAACACATGAATTAAAACTTGC 57.612 32.000 0.00 0.00 0.00 4.01
2835 3225 6.975197 TCGAAACACATGAATTAAAACTTGCA 59.025 30.769 0.00 0.00 0.00 4.08
2836 3226 7.043722 TCGAAACACATGAATTAAAACTTGCAC 60.044 33.333 0.00 0.00 0.00 4.57
2837 3227 6.509317 AACACATGAATTAAAACTTGCACG 57.491 33.333 0.00 0.00 0.00 5.34
2838 3228 5.587289 ACACATGAATTAAAACTTGCACGT 58.413 33.333 0.00 0.00 0.00 4.49
2839 3229 6.730175 ACACATGAATTAAAACTTGCACGTA 58.270 32.000 0.00 0.00 0.00 3.57
2840 3230 6.635239 ACACATGAATTAAAACTTGCACGTAC 59.365 34.615 0.00 0.00 0.00 3.67
2841 3231 6.087555 CACATGAATTAAAACTTGCACGTACC 59.912 38.462 0.00 0.00 0.00 3.34
2842 3232 5.752892 TGAATTAAAACTTGCACGTACCA 57.247 34.783 0.00 0.00 0.00 3.25
2843 3233 5.753744 TGAATTAAAACTTGCACGTACCAG 58.246 37.500 0.00 0.00 0.00 4.00
2844 3234 3.612472 TTAAAACTTGCACGTACCAGC 57.388 42.857 0.00 0.00 0.00 4.85
2845 3235 1.675552 AAAACTTGCACGTACCAGCT 58.324 45.000 0.00 0.00 0.00 4.24
2846 3236 1.675552 AAACTTGCACGTACCAGCTT 58.324 45.000 0.00 0.00 0.00 3.74
2847 3237 2.536761 AACTTGCACGTACCAGCTTA 57.463 45.000 0.00 0.00 0.00 3.09
2848 3238 1.792006 ACTTGCACGTACCAGCTTAC 58.208 50.000 0.00 0.00 0.00 2.34
2849 3239 1.343465 ACTTGCACGTACCAGCTTACT 59.657 47.619 0.00 0.00 0.00 2.24
2850 3240 2.559668 ACTTGCACGTACCAGCTTACTA 59.440 45.455 0.00 0.00 0.00 1.82
2851 3241 2.933495 TGCACGTACCAGCTTACTAG 57.067 50.000 5.86 0.00 0.00 2.57
2852 3242 2.165167 TGCACGTACCAGCTTACTAGT 58.835 47.619 0.00 0.00 0.00 2.57
2853 3243 3.346315 TGCACGTACCAGCTTACTAGTA 58.654 45.455 0.00 0.00 0.00 1.82
2854 3244 3.949754 TGCACGTACCAGCTTACTAGTAT 59.050 43.478 2.79 0.00 0.00 2.12
2859 3249 9.102757 GCACGTACCAGCTTACTAGTATATATA 57.897 37.037 2.79 0.00 0.00 0.86
2894 3290 1.290009 CAGCTTTGCTTTTCCCCCG 59.710 57.895 0.00 0.00 36.40 5.73
2934 3330 4.387026 TGGGACAGAAATGACCATCTTT 57.613 40.909 0.00 0.00 0.00 2.52
2935 3331 4.081406 TGGGACAGAAATGACCATCTTTG 58.919 43.478 0.00 0.00 0.00 2.77
2936 3332 3.119352 GGGACAGAAATGACCATCTTTGC 60.119 47.826 0.00 0.00 0.00 3.68
2937 3333 3.507233 GGACAGAAATGACCATCTTTGCA 59.493 43.478 0.00 0.00 0.00 4.08
2938 3334 4.159135 GGACAGAAATGACCATCTTTGCAT 59.841 41.667 0.00 0.00 0.00 3.96
2939 3335 5.337009 GGACAGAAATGACCATCTTTGCATT 60.337 40.000 0.00 0.00 32.75 3.56
2940 3336 5.475719 ACAGAAATGACCATCTTTGCATTG 58.524 37.500 0.00 0.00 31.86 2.82
2941 3337 4.328983 CAGAAATGACCATCTTTGCATTGC 59.671 41.667 0.46 0.46 31.86 3.56
2942 3338 3.965379 AATGACCATCTTTGCATTGCA 57.035 38.095 7.38 7.38 36.47 4.08
2943 3339 4.481368 AATGACCATCTTTGCATTGCAT 57.519 36.364 12.95 0.00 38.76 3.96
2944 3340 3.965379 TGACCATCTTTGCATTGCATT 57.035 38.095 12.95 0.00 38.76 3.56
2945 3341 3.591023 TGACCATCTTTGCATTGCATTG 58.409 40.909 12.95 8.47 38.76 2.82
2946 3342 2.350498 GACCATCTTTGCATTGCATTGC 59.650 45.455 23.33 23.33 38.76 3.56
3101 3507 4.759183 GCCCTCTGATGGTAATCTGATTTC 59.241 45.833 8.38 3.28 39.29 2.17
3133 3542 7.241663 TGTACCACATTCATTTAGCGAATAC 57.758 36.000 0.00 0.00 31.88 1.89
3268 3677 0.030235 GGTTCTCAAACGGTGTTGCC 59.970 55.000 0.00 0.00 36.16 4.52
3338 3752 2.103373 GCTCCAGGTCTGACACTGATA 58.897 52.381 20.70 11.54 36.86 2.15
3731 6528 4.445452 ACAGATGGACATGCACAATTTC 57.555 40.909 0.00 0.00 0.00 2.17
3931 6731 4.634883 GCTGACACATGACATGAGAGAAAT 59.365 41.667 22.19 0.00 0.00 2.17
4017 8229 5.163992 CGACCGGCATGTGTTGATATATAAC 60.164 44.000 0.00 0.00 0.00 1.89
4081 8296 7.415592 ACTAAGAGTTGTACCCCAGTTATAC 57.584 40.000 0.00 0.00 0.00 1.47
4098 8313 9.912634 CCAGTTATACTGTTTGTTTTGATTGAT 57.087 29.630 6.13 0.00 44.50 2.57
4116 8331 8.806429 TGATTGATCACACCAGTAATTTATGT 57.194 30.769 0.00 0.00 0.00 2.29
4126 8341 7.438459 ACACCAGTAATTTATGTCGATAGCTTC 59.562 37.037 0.00 0.00 0.00 3.86
4155 8370 9.973450 ATATATGCTTGTGTTCTACTACTTCTG 57.027 33.333 0.00 0.00 0.00 3.02
4252 8467 7.112779 TCTCAGGGAAAAGATTTGGAAGATAC 58.887 38.462 0.00 0.00 0.00 2.24
4598 8885 6.488006 ACATGATTAGAATGCTAACACATCCC 59.512 38.462 0.00 0.00 39.29 3.85
4599 8886 6.000246 TGATTAGAATGCTAACACATCCCA 58.000 37.500 0.00 0.00 39.29 4.37
4607 8894 7.981789 AGAATGCTAACACATCCCATATATACG 59.018 37.037 0.00 0.00 0.00 3.06
4683 8970 7.530010 CAGGTGTAAATACATCACAAAGAAGG 58.470 38.462 6.61 0.00 39.75 3.46
4779 9087 4.142859 CGATTGGGATTTTTGTTGGCAATG 60.143 41.667 1.92 0.00 34.18 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 3.791953 TTCCCCCAAGAAAATACACGA 57.208 42.857 0.00 0.00 0.00 4.35
205 207 1.002430 GGCATCACAACTCCACAGAGA 59.998 52.381 0.00 0.00 43.39 3.10
206 208 1.271001 TGGCATCACAACTCCACAGAG 60.271 52.381 0.00 0.00 46.36 3.35
210 212 1.000274 GGTTTGGCATCACAACTCCAC 60.000 52.381 0.00 0.00 0.00 4.02
267 269 5.372373 CCTTTTTGCCAATTCCTAACCAAA 58.628 37.500 0.00 0.00 0.00 3.28
369 378 4.700213 GGGCGTACGTAATAGTAATCCCTA 59.300 45.833 17.90 0.00 37.40 3.53
468 480 7.380423 TCTAATCCTCCAAAATTCCTAGGAG 57.620 40.000 12.26 0.00 45.68 3.69
469 481 7.765149 TTCTAATCCTCCAAAATTCCTAGGA 57.235 36.000 7.62 7.62 40.50 2.94
470 482 8.628630 GATTCTAATCCTCCAAAATTCCTAGG 57.371 38.462 0.82 0.82 0.00 3.02
559 682 4.659111 TTTTTCGAAAAGGGGAAACTCC 57.341 40.909 21.53 0.00 32.30 3.85
619 807 6.554334 TTCTGAAAACACGGGAATAGAAAG 57.446 37.500 0.00 0.00 0.00 2.62
625 814 3.758554 CAGGATTCTGAAAACACGGGAAT 59.241 43.478 0.00 0.00 43.49 3.01
632 821 2.223144 CGTTCGCAGGATTCTGAAAACA 59.777 45.455 4.75 0.00 43.49 2.83
906 1117 2.362397 GTGGTGTGTGTGAGAGAGAGAA 59.638 50.000 0.00 0.00 0.00 2.87
911 1122 0.752658 CTGGTGGTGTGTGTGAGAGA 59.247 55.000 0.00 0.00 0.00 3.10
917 1132 1.146930 CTCTGCTGGTGGTGTGTGT 59.853 57.895 0.00 0.00 0.00 3.72
919 1134 2.111878 GCTCTGCTGGTGGTGTGT 59.888 61.111 0.00 0.00 0.00 3.72
921 1136 2.429058 CTGCTCTGCTGGTGGTGT 59.571 61.111 0.00 0.00 0.00 4.16
935 1150 7.014115 CGATCAATCAATCAGTTATAAGCTGC 58.986 38.462 9.08 0.00 34.21 5.25
941 1156 9.591792 GATGGATCGATCAATCAATCAGTTATA 57.408 33.333 30.04 0.00 37.23 0.98
942 1157 8.098912 TGATGGATCGATCAATCAATCAGTTAT 58.901 33.333 33.67 3.62 42.66 1.89
943 1158 7.386025 GTGATGGATCGATCAATCAATCAGTTA 59.614 37.037 36.06 16.32 45.97 2.24
944 1159 6.204301 GTGATGGATCGATCAATCAATCAGTT 59.796 38.462 36.06 6.74 45.97 3.16
945 1160 5.699915 GTGATGGATCGATCAATCAATCAGT 59.300 40.000 36.06 7.45 45.97 3.41
946 1161 5.121925 GGTGATGGATCGATCAATCAATCAG 59.878 44.000 36.06 0.00 45.97 2.90
947 1162 4.999311 GGTGATGGATCGATCAATCAATCA 59.001 41.667 36.06 25.29 45.97 2.57
948 1163 4.092529 CGGTGATGGATCGATCAATCAATC 59.907 45.833 36.06 29.26 45.97 2.67
949 1164 3.999001 CGGTGATGGATCGATCAATCAAT 59.001 43.478 36.06 18.02 45.97 2.57
950 1165 3.181466 ACGGTGATGGATCGATCAATCAA 60.181 43.478 36.06 22.46 45.97 2.57
951 1166 2.365293 ACGGTGATGGATCGATCAATCA 59.635 45.455 32.64 32.64 43.22 2.57
952 1167 2.733552 CACGGTGATGGATCGATCAATC 59.266 50.000 28.87 28.87 37.68 2.67
953 1168 2.759191 CACGGTGATGGATCGATCAAT 58.241 47.619 25.93 21.00 34.11 2.57
954 1169 1.806247 GCACGGTGATGGATCGATCAA 60.806 52.381 25.93 16.73 34.11 2.57
955 1170 0.249447 GCACGGTGATGGATCGATCA 60.249 55.000 25.93 15.62 0.00 2.92
956 1171 1.278172 CGCACGGTGATGGATCGATC 61.278 60.000 17.36 17.36 0.00 3.69
957 1172 1.300156 CGCACGGTGATGGATCGAT 60.300 57.895 13.29 0.00 0.00 3.59
958 1173 2.104132 CGCACGGTGATGGATCGA 59.896 61.111 13.29 0.00 0.00 3.59
959 1174 2.202743 ACGCACGGTGATGGATCG 60.203 61.111 13.29 7.16 0.00 3.69
1083 1328 1.606224 CCTGCAAACCATCAACAAGGC 60.606 52.381 0.00 0.00 0.00 4.35
1255 1526 2.183811 CAGAGCAGAGAGGTGCCG 59.816 66.667 0.00 0.00 45.20 5.69
1256 1527 2.125188 GCAGAGCAGAGAGGTGCC 60.125 66.667 0.00 0.00 45.20 5.01
1261 1532 2.877168 ACAAACAAAGCAGAGCAGAGAG 59.123 45.455 0.00 0.00 0.00 3.20
1262 1533 2.923121 ACAAACAAAGCAGAGCAGAGA 58.077 42.857 0.00 0.00 0.00 3.10
1273 1549 8.125448 TCAAAACCAAGACAAAAACAAACAAAG 58.875 29.630 0.00 0.00 0.00 2.77
1328 1604 2.355132 CTGAGCTTGGAAGATCACATGC 59.645 50.000 3.23 12.12 45.54 4.06
1383 1659 6.322712 AGCTAGCATATATTCCTACTGGCTAC 59.677 42.308 18.83 0.00 39.73 3.58
1384 1660 6.436027 AGCTAGCATATATTCCTACTGGCTA 58.564 40.000 18.83 0.00 39.73 3.93
1385 1661 5.276440 AGCTAGCATATATTCCTACTGGCT 58.724 41.667 18.83 0.00 37.18 4.75
1386 1662 5.606348 AGCTAGCATATATTCCTACTGGC 57.394 43.478 18.83 0.00 32.48 4.85
1387 1663 8.704849 ATCTAGCTAGCATATATTCCTACTGG 57.295 38.462 18.83 0.00 0.00 4.00
1389 1665 9.496873 CGTATCTAGCTAGCATATATTCCTACT 57.503 37.037 18.83 0.00 0.00 2.57
1414 1690 7.866898 TGTGCTTCTATCTCTAGTAGTACTACG 59.133 40.741 23.87 13.15 38.18 3.51
1495 1783 1.663695 CTTCACACTTCCGTGGTGTT 58.336 50.000 0.00 0.00 44.25 3.32
1536 1834 3.569701 GGCATATGACAAAATGGGTCGAT 59.430 43.478 6.97 0.00 38.10 3.59
1610 1908 1.875488 AGCGGTGGGGAATACTAAGT 58.125 50.000 0.00 0.00 0.00 2.24
1613 1911 2.841881 AGAAAAGCGGTGGGGAATACTA 59.158 45.455 0.00 0.00 0.00 1.82
1614 1912 1.633945 AGAAAAGCGGTGGGGAATACT 59.366 47.619 0.00 0.00 0.00 2.12
1615 1913 2.124277 AGAAAAGCGGTGGGGAATAC 57.876 50.000 0.00 0.00 0.00 1.89
1716 2014 9.562408 TGTGTGGACATATAAGTTTTAGTTCAA 57.438 29.630 0.00 0.00 0.00 2.69
1737 2041 5.835911 CAGACTAGTCATCAACTTGTGTG 57.164 43.478 24.44 5.87 44.18 3.82
1827 2132 0.877071 CCAGCTGCACAAGACGAAAT 59.123 50.000 8.66 0.00 0.00 2.17
2056 2369 1.520342 GGAGATGCACGAGGCTGTC 60.520 63.158 0.00 0.00 45.15 3.51
2306 2619 3.309954 GGAACAAAGCGAGATGATACACC 59.690 47.826 0.00 0.00 0.00 4.16
2503 2846 5.612725 TCTGCCATATCATGTACAGTTCA 57.387 39.130 0.33 0.00 35.35 3.18
2833 3223 2.935481 ACTAGTAAGCTGGTACGTGC 57.065 50.000 0.00 0.00 34.53 5.34
2835 3225 9.829507 CCTATATATACTAGTAAGCTGGTACGT 57.170 37.037 6.70 0.00 40.64 3.57
2847 3237 9.233649 GCCAAGCGATATCCTATATATACTAGT 57.766 37.037 0.00 0.00 0.00 2.57
2848 3238 9.456147 AGCCAAGCGATATCCTATATATACTAG 57.544 37.037 0.00 0.00 0.00 2.57
2849 3239 9.232473 CAGCCAAGCGATATCCTATATATACTA 57.768 37.037 0.00 0.00 0.00 1.82
2850 3240 7.309499 GCAGCCAAGCGATATCCTATATATACT 60.309 40.741 0.00 0.00 0.00 2.12
2851 3241 6.809196 GCAGCCAAGCGATATCCTATATATAC 59.191 42.308 0.00 0.00 0.00 1.47
2852 3242 6.493458 TGCAGCCAAGCGATATCCTATATATA 59.507 38.462 0.00 0.00 37.31 0.86
2853 3243 5.305386 TGCAGCCAAGCGATATCCTATATAT 59.695 40.000 0.00 0.00 37.31 0.86
2854 3244 4.649218 TGCAGCCAAGCGATATCCTATATA 59.351 41.667 0.00 0.00 37.31 0.86
2859 3249 0.250209 CTGCAGCCAAGCGATATCCT 60.250 55.000 0.00 0.00 37.31 3.24
2866 3256 2.430244 CAAAGCTGCAGCCAAGCG 60.430 61.111 34.39 15.27 43.38 4.68
2894 3290 5.014202 TCCCAGAAACAGCCTATAAAAACC 58.986 41.667 0.00 0.00 0.00 3.27
3101 3507 8.338259 GCTAAATGAATGTGGTACATGTAGAAG 58.662 37.037 5.62 0.00 44.52 2.85
3161 3570 2.169978 CAAGCCTCACTGGAGATCATGA 59.830 50.000 0.00 0.00 44.26 3.07
3268 3677 1.272769 GCGCTGAGGGTAATAGGGTAG 59.727 57.143 0.00 0.00 0.00 3.18
3595 4028 1.376424 CGCCTGCAGGAACACAGAT 60.376 57.895 37.21 0.00 37.01 2.90
3731 6528 8.689061 TCAGAAGAAAAATAATGATCATGTGGG 58.311 33.333 9.46 0.00 0.00 4.61
3881 6681 2.106511 AGGCACAAGCTTCTCCACTTAA 59.893 45.455 0.00 0.00 41.70 1.85
3882 6682 1.699634 AGGCACAAGCTTCTCCACTTA 59.300 47.619 0.00 0.00 41.70 2.24
3883 6683 0.475906 AGGCACAAGCTTCTCCACTT 59.524 50.000 0.00 0.00 41.70 3.16
3884 6684 0.475906 AAGGCACAAGCTTCTCCACT 59.524 50.000 0.00 0.00 41.70 4.00
3931 6731 7.150447 TCTCCTCCTCTATAGTGTCAATACA 57.850 40.000 0.00 0.00 0.00 2.29
4017 8229 7.819415 TGTAACATGAAATTCAGTAGTGAGGAG 59.181 37.037 0.00 0.00 32.98 3.69
4058 8273 7.490000 CAGTATAACTGGGGTACAACTCTTAG 58.510 42.308 0.00 0.00 42.35 2.18
4081 8296 6.041511 TGGTGTGATCAATCAAAACAAACAG 58.958 36.000 0.00 0.00 38.72 3.16
4098 8313 6.700081 GCTATCGACATAAATTACTGGTGTGA 59.300 38.462 0.00 0.00 0.00 3.58
4116 8331 8.523658 ACACAAGCATATATTAGAAGCTATCGA 58.476 33.333 0.00 0.00 34.66 3.59
4149 8364 2.320781 ACACTGGACTGCTACAGAAGT 58.679 47.619 0.78 0.00 36.39 3.01
4152 8367 3.082548 GTCTACACTGGACTGCTACAGA 58.917 50.000 0.78 0.00 38.09 3.41
4153 8368 3.085533 AGTCTACACTGGACTGCTACAG 58.914 50.000 0.00 0.00 41.76 2.74
4154 8369 3.156288 AGTCTACACTGGACTGCTACA 57.844 47.619 0.00 0.00 41.76 2.74
4155 8370 4.522722 AAAGTCTACACTGGACTGCTAC 57.477 45.455 0.00 0.00 42.39 3.58
4158 8373 3.495001 GTGAAAAGTCTACACTGGACTGC 59.505 47.826 0.00 0.00 42.39 4.40
4252 8467 7.387948 GCCACAGGTTAGAACATATATGGTTAG 59.612 40.741 16.96 0.30 0.00 2.34
4266 8481 4.534500 TCTTCCAAATAGCCACAGGTTAGA 59.466 41.667 0.00 0.00 0.00 2.10
4271 8517 7.502226 TGTTATTATCTTCCAAATAGCCACAGG 59.498 37.037 0.00 0.00 0.00 4.00
4272 8518 8.450578 TGTTATTATCTTCCAAATAGCCACAG 57.549 34.615 0.00 0.00 0.00 3.66
4489 8776 3.069443 ACAATGTTGATCCCCAAACACAC 59.931 43.478 0.00 0.00 36.36 3.82
4598 8885 7.436970 TGCAAGTGACAGTTTACCGTATATATG 59.563 37.037 0.00 0.00 0.00 1.78
4599 8886 7.494211 TGCAAGTGACAGTTTACCGTATATAT 58.506 34.615 0.00 0.00 0.00 0.86
4607 8894 4.290155 CAACATGCAAGTGACAGTTTACC 58.710 43.478 0.00 0.00 0.00 2.85
4683 8970 6.845302 TCATGAACAGTTTGATGTGATAAGC 58.155 36.000 0.00 0.00 32.52 3.09
4779 9087 2.101415 GGAGCAATAAAGATGGGCCAAC 59.899 50.000 11.89 8.41 0.00 3.77
4860 9177 2.261835 GCTACTGCTATGCCGAATCGG 61.262 57.143 18.67 18.67 42.44 4.18


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

AutoCloner maintained by Alex Coulton.