Multiple sequence alignment - TraesCS4A01G429900

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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 TraesCS4A01G429900 chr4A 100.000 2715 0 0 1 2715 701292297 701295011 0.000000e+00 5014
1 TraesCS4A01G429900 chr4A 85.327 627 82 2 1019 1639 701282940 701283562 8.200000e-180 640
2 TraesCS4A01G429900 chr4A 84.191 272 39 2 2228 2496 702515858 702515588 7.460000e-66 261
3 TraesCS4A01G429900 chr4A 80.565 283 42 9 1023 1300 705546370 705546096 3.540000e-49 206
4 TraesCS4A01G429900 chr4A 92.683 123 9 0 688 810 702517879 702517757 7.720000e-41 178
5 TraesCS4A01G429900 chr7A 92.360 733 50 4 1984 2711 29155945 29155214 0.000000e+00 1038
6 TraesCS4A01G429900 chr7A 84.606 851 101 10 837 1680 29161073 29160246 0.000000e+00 819
7 TraesCS4A01G429900 chr7A 83.767 653 93 4 996 1639 29165588 29164940 8.310000e-170 606
8 TraesCS4A01G429900 chr7A 92.593 189 11 1 634 822 29161342 29161157 4.460000e-68 268
9 TraesCS4A01G429900 chr7A 92.969 128 8 1 1857 1984 29160000 29159874 4.620000e-43 185
10 TraesCS4A01G429900 chr7A 84.865 185 22 5 640 822 29166176 29165996 5.970000e-42 182
11 TraesCS4A01G429900 chr7A 82.979 188 28 3 1452 1639 83526677 83526494 1.670000e-37 167
12 TraesCS4A01G429900 chr7A 84.659 176 7 9 1683 1858 29160207 29160052 1.010000e-34 158
13 TraesCS4A01G429900 chr3D 96.491 627 21 1 1 627 463224942 463225567 0.000000e+00 1035
14 TraesCS4A01G429900 chr4B 96.209 633 19 2 1 628 16080230 16079598 0.000000e+00 1031
15 TraesCS4A01G429900 chr6D 95.840 625 23 1 3 627 444671782 444671161 0.000000e+00 1007
16 TraesCS4A01G429900 chr2D 95.534 627 25 1 1 627 172412823 172413446 0.000000e+00 1000
17 TraesCS4A01G429900 chr1A 94.560 625 32 2 1 625 302880457 302879835 0.000000e+00 965
18 TraesCS4A01G429900 chr7D 94.737 589 30 1 2128 2715 28705716 28705128 0.000000e+00 915
19 TraesCS4A01G429900 chr7D 83.710 620 97 2 1020 1639 29057363 29056748 1.400000e-162 582
20 TraesCS4A01G429900 chr7D 81.447 318 43 12 1023 1329 22624652 22624340 2.090000e-61 246
21 TraesCS4A01G429900 chr7D 96.000 100 3 1 1984 2082 28705813 28705714 7.780000e-36 161
22 TraesCS4A01G429900 chr5D 85.962 634 75 9 1 630 410244348 410244971 0.000000e+00 665
23 TraesCS4A01G429900 chr1B 96.440 309 10 1 322 630 529948595 529948288 2.410000e-140 508
24 TraesCS4A01G429900 chr5A 94.606 241 11 1 1 239 32761147 32760907 3.300000e-99 372
25 TraesCS4A01G429900 chr5A 89.862 217 22 0 1 217 521745293 521745509 2.060000e-71 279
26 TraesCS4A01G429900 chr6B 98.450 129 2 0 499 627 625384296 625384168 7.560000e-56 228


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 TraesCS4A01G429900 chr4A 701292297 701295011 2714 False 5014.000000 5014 100.000000 1 2715 1 chr4A.!!$F2 2714
1 TraesCS4A01G429900 chr4A 701282940 701283562 622 False 640.000000 640 85.327000 1019 1639 1 chr4A.!!$F1 620
2 TraesCS4A01G429900 chr4A 702515588 702517879 2291 True 219.500000 261 88.437000 688 2496 2 chr4A.!!$R2 1808
3 TraesCS4A01G429900 chr7A 29155214 29166176 10962 True 465.142857 1038 87.974143 634 2711 7 chr7A.!!$R2 2077
4 TraesCS4A01G429900 chr3D 463224942 463225567 625 False 1035.000000 1035 96.491000 1 627 1 chr3D.!!$F1 626
5 TraesCS4A01G429900 chr4B 16079598 16080230 632 True 1031.000000 1031 96.209000 1 628 1 chr4B.!!$R1 627
6 TraesCS4A01G429900 chr6D 444671161 444671782 621 True 1007.000000 1007 95.840000 3 627 1 chr6D.!!$R1 624
7 TraesCS4A01G429900 chr2D 172412823 172413446 623 False 1000.000000 1000 95.534000 1 627 1 chr2D.!!$F1 626
8 TraesCS4A01G429900 chr1A 302879835 302880457 622 True 965.000000 965 94.560000 1 625 1 chr1A.!!$R1 624
9 TraesCS4A01G429900 chr7D 29056748 29057363 615 True 582.000000 582 83.710000 1020 1639 1 chr7D.!!$R2 619
10 TraesCS4A01G429900 chr7D 28705128 28705813 685 True 538.000000 915 95.368500 1984 2715 2 chr7D.!!$R3 731
11 TraesCS4A01G429900 chr5D 410244348 410244971 623 False 665.000000 665 85.962000 1 630 1 chr5D.!!$F1 629

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
936 1197 0.036732 TAGCTTTCCACACCAGCTGG 59.963 55.0 31.6 31.6 43.85 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 6699 2.100418 GAGTATCCACACGGTAGTTCCC 59.9 54.545 0.0 0.0 0.0 3.97 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
74 75 7.913674 TTTGGTGTCAAATTTTGTTAAAGCT 57.086 28.000 8.89 0.00 37.89 3.74
434 448 5.279006 CGAGGACATATGTATACAGGCAAGT 60.279 44.000 8.71 5.47 0.00 3.16
539 557 3.960102 AGAAGTGTTTTTGGGCAGATGAA 59.040 39.130 0.00 0.00 0.00 2.57
542 560 2.102252 GTGTTTTTGGGCAGATGAACCA 59.898 45.455 0.00 0.00 0.00 3.67
657 676 6.767456 AGATAGCTCATCATTAACTCCTTGG 58.233 40.000 0.00 0.00 35.96 3.61
658 677 3.549794 AGCTCATCATTAACTCCTTGGC 58.450 45.455 0.00 0.00 0.00 4.52
660 679 3.314635 GCTCATCATTAACTCCTTGGCTG 59.685 47.826 0.00 0.00 0.00 4.85
662 681 2.128771 TCATTAACTCCTTGGCTGCC 57.871 50.000 12.87 12.87 0.00 4.85
664 683 2.041620 TCATTAACTCCTTGGCTGCCTT 59.958 45.455 21.03 7.03 0.00 4.35
665 684 2.200373 TTAACTCCTTGGCTGCCTTC 57.800 50.000 21.03 0.00 0.00 3.46
667 686 1.768684 AACTCCTTGGCTGCCTTCGA 61.769 55.000 21.03 10.69 0.00 3.71
668 687 1.222936 CTCCTTGGCTGCCTTCGAT 59.777 57.895 21.03 0.00 0.00 3.59
669 688 1.078214 TCCTTGGCTGCCTTCGATG 60.078 57.895 21.03 1.49 0.00 3.84
670 689 2.117156 CCTTGGCTGCCTTCGATGG 61.117 63.158 21.03 12.90 0.00 3.51
671 690 1.377725 CTTGGCTGCCTTCGATGGT 60.378 57.895 21.03 0.00 0.00 3.55
673 692 0.107703 TTGGCTGCCTTCGATGGTAG 60.108 55.000 25.13 25.13 41.78 3.18
675 694 0.750850 GGCTGCCTTCGATGGTAGTA 59.249 55.000 28.05 10.13 41.09 1.82
676 695 1.138266 GGCTGCCTTCGATGGTAGTAA 59.862 52.381 28.05 7.61 41.09 2.24
677 696 2.224305 GGCTGCCTTCGATGGTAGTAAT 60.224 50.000 28.05 0.00 41.09 1.89
678 697 3.060602 GCTGCCTTCGATGGTAGTAATC 58.939 50.000 28.05 13.62 41.09 1.75
679 698 3.492656 GCTGCCTTCGATGGTAGTAATCA 60.493 47.826 28.05 12.38 41.09 2.57
692 711 7.592885 TGGTAGTAATCACCTTGGATAGTAC 57.407 40.000 0.00 0.00 36.96 2.73
696 715 4.423625 AATCACCTTGGATAGTACAGGC 57.576 45.455 0.00 0.00 0.00 4.85
697 716 2.116238 TCACCTTGGATAGTACAGGCC 58.884 52.381 0.00 0.00 0.00 5.19
757 776 4.012374 CTCATTAATGGAGCAAGTGGTGT 58.988 43.478 15.36 0.00 0.00 4.16
763 782 0.953960 GGAGCAAGTGGTGTTACGGG 60.954 60.000 0.00 0.00 0.00 5.28
779 798 5.067413 TGTTACGGGCATTTGAAACAAGTTA 59.933 36.000 0.00 0.00 0.00 2.24
793 812 7.051623 TGAAACAAGTTAAGGTACAGTCACAT 58.948 34.615 0.00 0.00 0.00 3.21
814 834 3.633361 CTTGGAAGCTTCTTCCGGT 57.367 52.632 25.05 0.00 41.43 5.28
819 839 2.771943 TGGAAGCTTCTTCCGGTGATAT 59.228 45.455 25.05 0.00 41.43 1.63
836 870 5.477291 GGTGATATATCTTGGAGAGACCGAA 59.523 44.000 13.79 0.00 42.61 4.30
839 873 4.927978 ATATCTTGGAGAGACCGAAGTG 57.072 45.455 0.00 0.00 42.61 3.16
841 875 1.613925 TCTTGGAGAGACCGAAGTGTG 59.386 52.381 0.00 0.00 42.61 3.82
842 876 0.679505 TTGGAGAGACCGAAGTGTGG 59.320 55.000 0.00 0.00 42.61 4.17
843 877 1.185618 TGGAGAGACCGAAGTGTGGG 61.186 60.000 0.00 0.00 42.61 4.61
847 881 2.737376 GACCGAAGTGTGGGTCGC 60.737 66.667 0.00 0.00 42.05 5.19
848 882 4.309950 ACCGAAGTGTGGGTCGCC 62.310 66.667 0.00 0.00 35.93 5.54
858 892 4.089105 GGGTCGCCCATGAAAACA 57.911 55.556 9.72 0.00 44.65 2.83
859 893 2.346597 GGGTCGCCCATGAAAACAA 58.653 52.632 9.72 0.00 44.65 2.83
860 894 0.676736 GGGTCGCCCATGAAAACAAA 59.323 50.000 9.72 0.00 44.65 2.83
861 895 1.604438 GGGTCGCCCATGAAAACAAAC 60.604 52.381 9.72 0.00 44.65 2.93
862 896 1.067821 GGTCGCCCATGAAAACAAACA 59.932 47.619 0.00 0.00 0.00 2.83
863 897 2.124122 GTCGCCCATGAAAACAAACAC 58.876 47.619 0.00 0.00 0.00 3.32
864 898 1.127701 CGCCCATGAAAACAAACACG 58.872 50.000 0.00 0.00 0.00 4.49
865 899 1.496934 GCCCATGAAAACAAACACGG 58.503 50.000 0.00 0.00 0.00 4.94
867 901 1.127701 CCATGAAAACAAACACGGCG 58.872 50.000 4.80 4.80 0.00 6.46
869 903 2.455032 CATGAAAACAAACACGGCGAA 58.545 42.857 16.62 0.00 0.00 4.70
870 904 2.631418 TGAAAACAAACACGGCGAAA 57.369 40.000 16.62 0.00 0.00 3.46
871 905 3.152261 TGAAAACAAACACGGCGAAAT 57.848 38.095 16.62 0.00 0.00 2.17
873 907 4.669318 TGAAAACAAACACGGCGAAATAA 58.331 34.783 16.62 0.00 0.00 1.40
874 908 5.282510 TGAAAACAAACACGGCGAAATAAT 58.717 33.333 16.62 0.00 0.00 1.28
875 909 6.436261 TGAAAACAAACACGGCGAAATAATA 58.564 32.000 16.62 0.00 0.00 0.98
879 1134 2.941891 ACACGGCGAAATAATATGCG 57.058 45.000 16.62 0.00 0.00 4.73
880 1135 2.206750 ACACGGCGAAATAATATGCGT 58.793 42.857 16.62 0.00 0.00 5.24
897 1152 2.389386 GTGAGCACGTGTTGGTTCA 58.611 52.632 18.38 10.48 35.52 3.18
899 1154 1.069906 GTGAGCACGTGTTGGTTCATC 60.070 52.381 18.38 0.00 35.52 2.92
900 1155 0.163788 GAGCACGTGTTGGTTCATCG 59.836 55.000 18.38 0.00 35.52 3.84
901 1156 0.249699 AGCACGTGTTGGTTCATCGA 60.250 50.000 18.38 0.00 28.85 3.59
902 1157 0.796312 GCACGTGTTGGTTCATCGAT 59.204 50.000 18.38 0.00 0.00 3.59
903 1158 1.201921 GCACGTGTTGGTTCATCGATC 60.202 52.381 18.38 0.00 0.00 3.69
904 1159 2.065512 CACGTGTTGGTTCATCGATCA 58.934 47.619 7.58 0.00 0.00 2.92
910 1171 2.932614 GTTGGTTCATCGATCACCTCTG 59.067 50.000 19.60 0.00 0.00 3.35
911 1172 2.179427 TGGTTCATCGATCACCTCTGT 58.821 47.619 19.60 0.00 0.00 3.41
920 1181 5.881777 TCGATCACCTCTGTACATATAGC 57.118 43.478 0.00 0.00 0.00 2.97
921 1182 5.561679 TCGATCACCTCTGTACATATAGCT 58.438 41.667 0.00 0.00 0.00 3.32
923 1184 6.490381 TCGATCACCTCTGTACATATAGCTTT 59.510 38.462 0.00 0.00 0.00 3.51
926 1187 5.897250 TCACCTCTGTACATATAGCTTTCCA 59.103 40.000 0.00 0.00 0.00 3.53
935 1196 2.119801 ATAGCTTTCCACACCAGCTG 57.880 50.000 6.78 6.78 43.85 4.24
936 1197 0.036732 TAGCTTTCCACACCAGCTGG 59.963 55.000 31.60 31.60 43.85 4.85
950 1211 1.325640 CAGCTGGTTCATCGTTCATCG 59.674 52.381 5.57 0.00 41.41 3.84
964 1225 0.830648 TCATCGATCACCTCCCAACC 59.169 55.000 0.00 0.00 0.00 3.77
970 1231 3.458118 TCGATCACCTCCCAACCAATTAT 59.542 43.478 0.00 0.00 0.00 1.28
972 1233 3.662759 TCACCTCCCAACCAATTATCC 57.337 47.619 0.00 0.00 0.00 2.59
973 1234 2.922955 TCACCTCCCAACCAATTATCCA 59.077 45.455 0.00 0.00 0.00 3.41
974 1235 3.531397 TCACCTCCCAACCAATTATCCAT 59.469 43.478 0.00 0.00 0.00 3.41
976 1237 3.149196 CCTCCCAACCAATTATCCATCG 58.851 50.000 0.00 0.00 0.00 3.84
980 1241 4.350816 TCCCAACCAATTATCCATCGATCT 59.649 41.667 0.00 0.00 0.00 2.75
983 1244 7.401782 TCCCAACCAATTATCCATCGATCTATA 59.598 37.037 0.00 0.00 0.00 1.31
984 1245 8.213679 CCCAACCAATTATCCATCGATCTATAT 58.786 37.037 0.00 0.00 0.00 0.86
1010 1271 1.146774 TGAAACTGAAATGGCTGGGGA 59.853 47.619 0.00 0.00 0.00 4.81
1011 1272 2.247358 GAAACTGAAATGGCTGGGGAA 58.753 47.619 0.00 0.00 0.00 3.97
1013 1274 2.629017 ACTGAAATGGCTGGGGAAAT 57.371 45.000 0.00 0.00 0.00 2.17
1014 1275 3.756082 ACTGAAATGGCTGGGGAAATA 57.244 42.857 0.00 0.00 0.00 1.40
1015 1276 4.059773 ACTGAAATGGCTGGGGAAATAA 57.940 40.909 0.00 0.00 0.00 1.40
1016 1277 4.424842 ACTGAAATGGCTGGGGAAATAAA 58.575 39.130 0.00 0.00 0.00 1.40
1017 1278 4.222810 ACTGAAATGGCTGGGGAAATAAAC 59.777 41.667 0.00 0.00 0.00 2.01
1030 1294 3.426292 GGAAATAAACGAGGTGAAGCTGC 60.426 47.826 0.00 0.00 0.00 5.25
1036 1300 2.530151 AGGTGAAGCTGCTGGGGA 60.530 61.111 1.35 0.00 0.00 4.81
1037 1301 1.919600 GAGGTGAAGCTGCTGGGGAT 61.920 60.000 1.35 0.00 0.00 3.85
1088 1352 0.674581 CTGGCGCTTCACATCAAGGA 60.675 55.000 7.64 0.00 0.00 3.36
1164 1428 4.629523 TCCAACCCCGTCCGCAAC 62.630 66.667 0.00 0.00 0.00 4.17
1191 1455 2.509336 GTGCTCATCCACGACGGG 60.509 66.667 0.00 0.00 34.36 5.28
1194 1458 1.519455 GCTCATCCACGACGGGAAG 60.519 63.158 0.00 0.00 41.12 3.46
1207 1471 2.899339 GGAAGCCCATCTGCGAGC 60.899 66.667 0.00 0.00 36.02 5.03
1230 1494 3.742327 CGCAGGTCATCATCCAGTACATT 60.742 47.826 0.00 0.00 0.00 2.71
1233 1497 5.618236 CAGGTCATCATCCAGTACATTGAT 58.382 41.667 0.00 0.00 0.00 2.57
1315 1579 4.096003 GCTTCTGGGCCGCCTACA 62.096 66.667 9.86 0.00 0.00 2.74
1348 1612 4.337177 TGCCGCCGTGGGAAATGA 62.337 61.111 0.00 0.00 38.63 2.57
1355 1619 2.091541 GCCGTGGGAAATGATCTTGAA 58.908 47.619 0.00 0.00 0.00 2.69
1387 1657 4.787280 AGGAGAGGGCGGAGTGGG 62.787 72.222 0.00 0.00 0.00 4.61
1399 1669 1.371558 GAGTGGGCGAAACAGACCT 59.628 57.895 0.00 0.00 40.90 3.85
1401 1671 0.182775 AGTGGGCGAAACAGACCTTT 59.817 50.000 0.00 0.00 40.90 3.11
1403 1673 0.821711 TGGGCGAAACAGACCTTTGG 60.822 55.000 0.00 0.00 40.90 3.28
1408 1678 1.872237 CGAAACAGACCTTTGGAGCGA 60.872 52.381 0.00 0.00 0.00 4.93
1425 1695 1.596477 GATGGATGCGCTGGAGGAC 60.596 63.158 9.73 0.00 0.00 3.85
1429 1699 3.157217 GATGCGCTGGAGGACGGAT 62.157 63.158 9.73 0.00 43.29 4.18
1431 1701 2.586357 GCGCTGGAGGACGGATTC 60.586 66.667 0.00 0.00 0.00 2.52
1435 1705 1.330655 GCTGGAGGACGGATTCAGGA 61.331 60.000 0.00 0.00 0.00 3.86
1443 1713 0.250513 ACGGATTCAGGAAGTGCTCC 59.749 55.000 0.00 0.00 45.81 4.70
1461 1731 0.972471 CCATGGGCAAGGGGTTCTTC 60.972 60.000 2.85 0.00 32.41 2.87
1464 1734 2.434774 GGCAAGGGGTTCTTCGGT 59.565 61.111 0.00 0.00 32.41 4.69
1467 1737 1.971695 CAAGGGGTTCTTCGGTGGC 60.972 63.158 0.00 0.00 32.41 5.01
1494 6417 2.404995 CGGCTACCTCGACGTCCTT 61.405 63.158 10.58 0.00 0.00 3.36
1529 6452 4.409218 GTGGCTGTACGCGACCGA 62.409 66.667 15.93 0.00 40.97 4.69
1530 6453 3.445687 TGGCTGTACGCGACCGAT 61.446 61.111 15.93 0.00 40.44 4.18
1531 6454 2.654404 GGCTGTACGCGACCGATC 60.654 66.667 15.93 0.00 40.44 3.69
1558 6481 3.073650 AGATCTCTGGCCACAACTTCTTT 59.926 43.478 0.00 0.00 0.00 2.52
1561 6484 3.152341 CTCTGGCCACAACTTCTTTGAT 58.848 45.455 0.00 0.00 38.73 2.57
1573 6496 1.250328 TCTTTGATGCCAGCAAGGTG 58.750 50.000 4.69 0.00 40.61 4.00
1582 6505 4.020617 AGCAAGGTGCCGCTGCTA 62.021 61.111 15.85 0.00 46.52 3.49
1607 6530 1.234615 ATGGGTGGAGCGTTTTGTCG 61.235 55.000 0.00 0.00 0.00 4.35
1648 6571 1.374758 GTTCCAGGAGCAGGACGTG 60.375 63.158 0.00 0.00 34.19 4.49
1673 6596 0.391130 CCTGGTTGAATTCGCTCGGA 60.391 55.000 0.04 0.00 0.00 4.55
1674 6597 1.656652 CTGGTTGAATTCGCTCGGAT 58.343 50.000 0.04 0.00 0.00 4.18
1714 6673 2.847234 ACCTGCTCCGTTGGGTGA 60.847 61.111 0.00 0.00 33.83 4.02
1728 6687 2.658285 TGGGTGATTGATGCAAGGATC 58.342 47.619 0.00 0.00 0.00 3.36
1730 6689 2.621998 GGGTGATTGATGCAAGGATCAG 59.378 50.000 4.48 0.00 33.86 2.90
1732 6691 4.454678 GGTGATTGATGCAAGGATCAGTA 58.545 43.478 4.48 0.00 33.86 2.74
1740 6699 1.669779 GCAAGGATCAGTAAGCTGCAG 59.330 52.381 10.11 10.11 42.29 4.41
1756 6715 2.358039 CAGGGAACTACCGTGTGGA 58.642 57.895 0.00 0.00 45.95 4.02
1757 6716 0.902531 CAGGGAACTACCGTGTGGAT 59.097 55.000 0.00 0.00 45.95 3.41
1758 6717 2.104967 CAGGGAACTACCGTGTGGATA 58.895 52.381 0.00 0.00 45.95 2.59
1759 6718 2.105766 AGGGAACTACCGTGTGGATAC 58.894 52.381 0.00 0.00 40.61 2.24
1760 6719 2.105766 GGGAACTACCGTGTGGATACT 58.894 52.381 0.00 0.00 40.11 2.12
1761 6720 2.100418 GGGAACTACCGTGTGGATACTC 59.900 54.545 0.00 0.00 40.11 2.59
1762 6721 2.223433 GGAACTACCGTGTGGATACTCG 60.223 54.545 0.00 0.00 41.89 4.18
1763 6722 2.119801 ACTACCGTGTGGATACTCGT 57.880 50.000 0.00 0.00 40.96 4.18
1764 6723 1.741706 ACTACCGTGTGGATACTCGTG 59.258 52.381 0.00 0.00 40.96 4.35
1765 6724 0.452987 TACCGTGTGGATACTCGTGC 59.547 55.000 0.00 0.00 40.96 5.34
1766 6725 1.214325 CCGTGTGGATACTCGTGCA 59.786 57.895 0.00 0.00 40.96 4.57
1767 6726 0.179111 CCGTGTGGATACTCGTGCAT 60.179 55.000 0.00 0.00 40.96 3.96
1768 6727 1.640428 CGTGTGGATACTCGTGCATT 58.360 50.000 0.00 0.00 38.57 3.56
1769 6728 1.999735 CGTGTGGATACTCGTGCATTT 59.000 47.619 0.00 0.00 38.57 2.32
1770 6729 2.415168 CGTGTGGATACTCGTGCATTTT 59.585 45.455 0.00 0.00 38.57 1.82
1771 6730 3.615056 CGTGTGGATACTCGTGCATTTTA 59.385 43.478 0.00 0.00 38.57 1.52
1772 6731 4.270084 CGTGTGGATACTCGTGCATTTTAT 59.730 41.667 0.00 0.00 38.57 1.40
1935 6947 6.267471 TCTTGTTTCATAGCATTGGGTTTTCT 59.733 34.615 0.00 0.00 0.00 2.52
1980 7288 9.225201 CTTAATTTTTCATGGTGTATCATCACG 57.775 33.333 0.00 0.00 39.00 4.35
2047 11405 3.909574 GCATTGCATTGCACAAAATGAAC 59.090 39.130 24.71 4.72 42.31 3.18
2088 11447 5.241403 AGGTTTGTGTCAATATCTCCACA 57.759 39.130 0.00 0.00 36.12 4.17
2092 11451 6.317088 GTTTGTGTCAATATCTCCACATGTG 58.683 40.000 19.31 19.31 37.63 3.21
2097 11456 6.036517 GTGTCAATATCTCCACATGTGAAGAC 59.963 42.308 27.46 19.00 0.00 3.01
2123 11482 7.093988 CCACAAGTGGGTATGAAATGAATTGTA 60.094 37.037 11.43 0.00 46.81 2.41
2299 11763 2.200923 TAAAGGTAACCAGGGCCGCC 62.201 60.000 0.00 0.00 37.17 6.13
2304 11768 2.913117 TAACCAGGGCCGCCACAAT 61.913 57.895 12.58 0.00 0.00 2.71
2351 11815 4.136796 CAGGTTTCATCAGGACTTGTTCA 58.863 43.478 0.00 0.00 0.00 3.18
2462 11926 6.152323 GGTATGAGGTGTGACAAGTAGACTAA 59.848 42.308 0.00 0.00 0.00 2.24
2465 11929 5.106277 TGAGGTGTGACAAGTAGACTAATCG 60.106 44.000 0.00 0.00 0.00 3.34
2545 12009 7.043458 GGATATAAACAACGTAAAATCGGTCGA 60.043 37.037 0.00 0.00 34.94 4.20
2610 12074 9.371136 GATGAATGAGAATATTTATGCCTCGTA 57.629 33.333 0.00 0.00 0.00 3.43
2655 12119 6.709397 TCTGGCATTTGAATTGCAACAAAATA 59.291 30.769 16.36 5.69 39.01 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 2.510382 TGGTTGGGACACTTTACCTGAA 59.490 45.455 0.00 0.00 39.29 3.02
539 557 6.882678 ACAACGATAAAATAAAGCTAGGTGGT 59.117 34.615 0.00 0.00 0.00 4.16
630 649 9.941325 CAAGGAGTTAATGATGAGCTATCTTAT 57.059 33.333 0.00 0.00 36.71 1.73
631 650 8.370940 CCAAGGAGTTAATGATGAGCTATCTTA 58.629 37.037 0.00 0.00 36.71 2.10
632 651 7.222872 CCAAGGAGTTAATGATGAGCTATCTT 58.777 38.462 0.00 0.00 36.71 2.40
633 652 6.743773 GCCAAGGAGTTAATGATGAGCTATCT 60.744 42.308 0.00 0.00 36.71 1.98
634 653 5.411053 GCCAAGGAGTTAATGATGAGCTATC 59.589 44.000 0.00 0.00 36.29 2.08
635 654 5.072872 AGCCAAGGAGTTAATGATGAGCTAT 59.927 40.000 0.00 0.00 0.00 2.97
636 655 4.410228 AGCCAAGGAGTTAATGATGAGCTA 59.590 41.667 0.00 0.00 0.00 3.32
637 656 3.201708 AGCCAAGGAGTTAATGATGAGCT 59.798 43.478 0.00 0.00 0.00 4.09
638 657 3.314635 CAGCCAAGGAGTTAATGATGAGC 59.685 47.826 0.00 0.00 0.00 4.26
639 658 3.314635 GCAGCCAAGGAGTTAATGATGAG 59.685 47.826 0.00 0.00 0.00 2.90
640 659 3.282021 GCAGCCAAGGAGTTAATGATGA 58.718 45.455 0.00 0.00 0.00 2.92
641 660 2.360165 GGCAGCCAAGGAGTTAATGATG 59.640 50.000 6.55 0.00 0.00 3.07
642 661 2.243221 AGGCAGCCAAGGAGTTAATGAT 59.757 45.455 15.80 0.00 0.00 2.45
643 662 1.635487 AGGCAGCCAAGGAGTTAATGA 59.365 47.619 15.80 0.00 0.00 2.57
644 663 2.134789 AGGCAGCCAAGGAGTTAATG 57.865 50.000 15.80 0.00 0.00 1.90
645 664 2.728007 GAAGGCAGCCAAGGAGTTAAT 58.272 47.619 15.80 0.00 0.00 1.40
657 676 2.596904 TTACTACCATCGAAGGCAGC 57.403 50.000 6.60 0.00 0.00 5.25
658 677 4.051922 GTGATTACTACCATCGAAGGCAG 58.948 47.826 6.60 5.93 0.00 4.85
660 679 3.069729 AGGTGATTACTACCATCGAAGGC 59.930 47.826 6.60 0.00 40.74 4.35
662 681 5.050490 CCAAGGTGATTACTACCATCGAAG 58.950 45.833 0.00 0.00 40.74 3.79
664 683 4.283337 TCCAAGGTGATTACTACCATCGA 58.717 43.478 0.00 0.00 40.74 3.59
665 684 4.665833 TCCAAGGTGATTACTACCATCG 57.334 45.455 0.00 0.00 40.74 3.84
667 686 7.787904 TGTACTATCCAAGGTGATTACTACCAT 59.212 37.037 0.00 0.00 40.74 3.55
668 687 7.127405 TGTACTATCCAAGGTGATTACTACCA 58.873 38.462 0.00 0.00 40.74 3.25
669 688 7.255871 CCTGTACTATCCAAGGTGATTACTACC 60.256 44.444 0.00 0.00 38.52 3.18
670 689 7.659186 CCTGTACTATCCAAGGTGATTACTAC 58.341 42.308 0.00 0.00 0.00 2.73
671 690 6.267014 GCCTGTACTATCCAAGGTGATTACTA 59.733 42.308 0.00 0.00 0.00 1.82
673 692 5.298347 GCCTGTACTATCCAAGGTGATTAC 58.702 45.833 0.00 0.00 0.00 1.89
675 694 3.136626 GGCCTGTACTATCCAAGGTGATT 59.863 47.826 0.00 0.00 0.00 2.57
676 695 2.706190 GGCCTGTACTATCCAAGGTGAT 59.294 50.000 0.00 0.00 0.00 3.06
677 696 2.116238 GGCCTGTACTATCCAAGGTGA 58.884 52.381 0.00 0.00 0.00 4.02
678 697 1.202533 CGGCCTGTACTATCCAAGGTG 60.203 57.143 0.00 0.00 0.00 4.00
679 698 1.120530 CGGCCTGTACTATCCAAGGT 58.879 55.000 0.00 0.00 0.00 3.50
692 711 1.533625 TTGATGTTCCTTTCGGCCTG 58.466 50.000 0.00 0.00 0.00 4.85
696 715 9.931210 GTAGTTAATTATTGATGTTCCTTTCGG 57.069 33.333 0.00 0.00 0.00 4.30
724 743 8.662781 TGCTCCATTAATGAGATGTTAGTTAC 57.337 34.615 17.23 0.00 0.00 2.50
757 776 4.657436 AACTTGTTTCAAATGCCCGTAA 57.343 36.364 0.00 0.00 0.00 3.18
763 782 7.200455 ACTGTACCTTAACTTGTTTCAAATGC 58.800 34.615 0.00 0.00 0.00 3.56
779 798 3.838317 TCCAAGCTATGTGACTGTACCTT 59.162 43.478 0.00 0.00 0.00 3.50
804 824 6.209589 TCTCCAAGATATATCACCGGAAGAAG 59.790 42.308 9.46 5.85 0.00 2.85
810 830 4.158764 GGTCTCTCCAAGATATATCACCGG 59.841 50.000 15.08 0.00 36.11 5.28
811 831 4.142578 CGGTCTCTCCAAGATATATCACCG 60.143 50.000 17.39 17.39 36.11 4.94
814 834 6.207614 CACTTCGGTCTCTCCAAGATATATCA 59.792 42.308 15.08 0.00 36.11 2.15
819 839 3.444034 CACACTTCGGTCTCTCCAAGATA 59.556 47.826 0.00 0.00 36.11 1.98
843 877 2.124122 GTGTTTGTTTTCATGGGCGAC 58.876 47.619 0.00 0.00 0.00 5.19
845 879 1.127701 CGTGTTTGTTTTCATGGGCG 58.872 50.000 0.00 0.00 0.00 6.13
847 881 1.496934 GCCGTGTTTGTTTTCATGGG 58.503 50.000 0.00 0.00 40.07 4.00
848 882 1.127701 CGCCGTGTTTGTTTTCATGG 58.872 50.000 0.00 0.00 41.92 3.66
850 884 2.853731 TTCGCCGTGTTTGTTTTCAT 57.146 40.000 0.00 0.00 0.00 2.57
852 886 5.815964 ATTATTTCGCCGTGTTTGTTTTC 57.184 34.783 0.00 0.00 0.00 2.29
853 887 6.183360 GCATATTATTTCGCCGTGTTTGTTTT 60.183 34.615 0.00 0.00 0.00 2.43
854 888 5.287513 GCATATTATTTCGCCGTGTTTGTTT 59.712 36.000 0.00 0.00 0.00 2.83
855 889 4.796312 GCATATTATTTCGCCGTGTTTGTT 59.204 37.500 0.00 0.00 0.00 2.83
857 891 3.417321 CGCATATTATTTCGCCGTGTTTG 59.583 43.478 0.00 0.00 0.00 2.93
858 892 3.064271 ACGCATATTATTTCGCCGTGTTT 59.936 39.130 0.00 0.00 0.00 2.83
859 893 2.610374 ACGCATATTATTTCGCCGTGTT 59.390 40.909 0.00 0.00 0.00 3.32
860 894 2.033236 CACGCATATTATTTCGCCGTGT 60.033 45.455 0.00 0.00 0.00 4.49
861 895 2.219903 TCACGCATATTATTTCGCCGTG 59.780 45.455 0.00 0.00 33.38 4.94
862 896 2.475111 CTCACGCATATTATTTCGCCGT 59.525 45.455 0.00 0.00 0.00 5.68
863 897 2.721797 GCTCACGCATATTATTTCGCCG 60.722 50.000 0.00 0.00 35.78 6.46
864 898 2.223144 TGCTCACGCATATTATTTCGCC 59.777 45.455 0.00 0.00 42.25 5.54
865 899 3.519908 TGCTCACGCATATTATTTCGC 57.480 42.857 0.00 0.00 42.25 4.70
879 1134 0.944386 ATGAACCAACACGTGCTCAC 59.056 50.000 17.22 3.36 0.00 3.51
880 1135 1.225855 GATGAACCAACACGTGCTCA 58.774 50.000 17.22 11.02 0.00 4.26
886 1141 1.393539 GGTGATCGATGAACCAACACG 59.606 52.381 18.00 0.00 33.94 4.49
895 1150 6.094186 GCTATATGTACAGAGGTGATCGATGA 59.906 42.308 0.54 0.00 0.00 2.92
896 1151 6.094742 AGCTATATGTACAGAGGTGATCGATG 59.905 42.308 0.54 0.00 0.00 3.84
897 1152 6.184068 AGCTATATGTACAGAGGTGATCGAT 58.816 40.000 0.00 0.00 0.00 3.59
899 1154 5.888691 AGCTATATGTACAGAGGTGATCG 57.111 43.478 0.33 0.00 0.00 3.69
900 1155 7.093992 GGAAAGCTATATGTACAGAGGTGATC 58.906 42.308 0.33 6.77 0.00 2.92
901 1156 6.554982 TGGAAAGCTATATGTACAGAGGTGAT 59.445 38.462 0.33 0.00 0.00 3.06
902 1157 5.897250 TGGAAAGCTATATGTACAGAGGTGA 59.103 40.000 0.33 0.00 0.00 4.02
903 1158 5.986135 GTGGAAAGCTATATGTACAGAGGTG 59.014 44.000 0.33 0.00 0.00 4.00
904 1159 5.661312 TGTGGAAAGCTATATGTACAGAGGT 59.339 40.000 0.33 1.40 0.00 3.85
910 1171 4.511826 GCTGGTGTGGAAAGCTATATGTAC 59.488 45.833 0.00 0.00 34.05 2.90
911 1172 4.408921 AGCTGGTGTGGAAAGCTATATGTA 59.591 41.667 0.00 0.00 45.26 2.29
942 1203 0.459899 TGGGAGGTGATCGATGAACG 59.540 55.000 0.54 0.00 44.09 3.95
943 1204 2.280628 GTTGGGAGGTGATCGATGAAC 58.719 52.381 0.54 0.00 0.00 3.18
950 1211 4.145052 GGATAATTGGTTGGGAGGTGATC 58.855 47.826 0.00 0.00 0.00 2.92
957 1218 4.350816 AGATCGATGGATAATTGGTTGGGA 59.649 41.667 0.54 0.00 31.51 4.37
958 1219 4.655963 AGATCGATGGATAATTGGTTGGG 58.344 43.478 0.54 0.00 31.51 4.12
970 1231 9.035890 AGTTTCACCAATATATAGATCGATGGA 57.964 33.333 0.54 0.00 0.00 3.41
972 1233 9.860898 TCAGTTTCACCAATATATAGATCGATG 57.139 33.333 0.54 0.00 0.00 3.84
980 1241 8.849168 CAGCCATTTCAGTTTCACCAATATATA 58.151 33.333 0.00 0.00 0.00 0.86
983 1244 5.105228 CCAGCCATTTCAGTTTCACCAATAT 60.105 40.000 0.00 0.00 0.00 1.28
984 1245 4.220382 CCAGCCATTTCAGTTTCACCAATA 59.780 41.667 0.00 0.00 0.00 1.90
986 1247 2.364970 CCAGCCATTTCAGTTTCACCAA 59.635 45.455 0.00 0.00 0.00 3.67
987 1248 1.962807 CCAGCCATTTCAGTTTCACCA 59.037 47.619 0.00 0.00 0.00 4.17
988 1249 1.273327 CCCAGCCATTTCAGTTTCACC 59.727 52.381 0.00 0.00 0.00 4.02
989 1250 1.273327 CCCCAGCCATTTCAGTTTCAC 59.727 52.381 0.00 0.00 0.00 3.18
991 1252 1.923356 TCCCCAGCCATTTCAGTTTC 58.077 50.000 0.00 0.00 0.00 2.78
992 1253 2.397044 TTCCCCAGCCATTTCAGTTT 57.603 45.000 0.00 0.00 0.00 2.66
993 1254 2.397044 TTTCCCCAGCCATTTCAGTT 57.603 45.000 0.00 0.00 0.00 3.16
994 1255 2.629017 ATTTCCCCAGCCATTTCAGT 57.371 45.000 0.00 0.00 0.00 3.41
1010 1271 3.189287 CAGCAGCTTCACCTCGTTTATTT 59.811 43.478 0.00 0.00 0.00 1.40
1011 1272 2.744202 CAGCAGCTTCACCTCGTTTATT 59.256 45.455 0.00 0.00 0.00 1.40
1013 1274 1.608025 CCAGCAGCTTCACCTCGTTTA 60.608 52.381 0.00 0.00 0.00 2.01
1014 1275 0.886490 CCAGCAGCTTCACCTCGTTT 60.886 55.000 0.00 0.00 0.00 3.60
1015 1276 1.302033 CCAGCAGCTTCACCTCGTT 60.302 57.895 0.00 0.00 0.00 3.85
1016 1277 2.345244 CCAGCAGCTTCACCTCGT 59.655 61.111 0.00 0.00 0.00 4.18
1017 1278 2.435586 CCCAGCAGCTTCACCTCG 60.436 66.667 0.00 0.00 0.00 4.63
1030 1294 4.864334 GCTCGCCCACATCCCCAG 62.864 72.222 0.00 0.00 0.00 4.45
1054 1318 1.220206 CCAGCTTCACTCTCGCCAT 59.780 57.895 0.00 0.00 0.00 4.40
1191 1455 2.899339 GGCTCGCAGATGGGCTTC 60.899 66.667 0.00 0.00 33.89 3.86
1207 1471 0.752658 TACTGGATGATGACCTGCGG 59.247 55.000 0.00 0.00 0.00 5.69
1219 1483 3.051581 AGGCCTCATCAATGTACTGGAT 58.948 45.455 0.00 0.00 0.00 3.41
1315 1579 1.738099 GCAGCACCTTGTCGTCGAT 60.738 57.895 0.00 0.00 0.00 3.59
1343 1607 4.082571 CCGTCTTTGCCTTCAAGATCATTT 60.083 41.667 0.00 0.00 33.12 2.32
1348 1612 2.427506 GTCCGTCTTTGCCTTCAAGAT 58.572 47.619 0.00 0.00 33.12 2.40
1355 1619 1.878656 CTCCTCGTCCGTCTTTGCCT 61.879 60.000 0.00 0.00 0.00 4.75
1387 1657 0.238553 GCTCCAAAGGTCTGTTTCGC 59.761 55.000 0.00 0.00 0.00 4.70
1391 1661 1.611673 CCATCGCTCCAAAGGTCTGTT 60.612 52.381 0.00 0.00 0.00 3.16
1392 1662 0.036010 CCATCGCTCCAAAGGTCTGT 60.036 55.000 0.00 0.00 0.00 3.41
1399 1669 3.812203 CGCATCCATCGCTCCAAA 58.188 55.556 0.00 0.00 0.00 3.28
1408 1678 2.507944 GTCCTCCAGCGCATCCAT 59.492 61.111 11.47 0.00 0.00 3.41
1425 1695 0.250234 TGGAGCACTTCCTGAATCCG 59.750 55.000 0.00 0.00 46.92 4.18
1429 1699 0.329261 CCCATGGAGCACTTCCTGAA 59.671 55.000 15.22 0.00 46.92 3.02
1431 1701 1.751927 GCCCATGGAGCACTTCCTG 60.752 63.158 15.22 0.00 46.92 3.86
1435 1705 1.304713 CCTTGCCCATGGAGCACTT 60.305 57.895 22.74 0.00 40.69 3.16
1443 1713 1.315257 CGAAGAACCCCTTGCCCATG 61.315 60.000 0.00 0.00 34.68 3.66
1445 1715 2.434331 CGAAGAACCCCTTGCCCA 59.566 61.111 0.00 0.00 34.68 5.36
1532 6455 2.235898 AGTTGTGGCCAGAGATCTTCTC 59.764 50.000 5.11 0.00 43.70 2.87
1546 6469 2.608752 GCTGGCATCAAAGAAGTTGTGG 60.609 50.000 0.00 0.00 38.47 4.17
1558 6481 2.677524 GGCACCTTGCTGGCATCA 60.678 61.111 0.00 0.00 44.28 3.07
1586 6509 1.080569 CAAAACGCTCCACCCATGC 60.081 57.895 0.00 0.00 0.00 4.06
1592 6515 1.429463 AGATCGACAAAACGCTCCAC 58.571 50.000 0.00 0.00 0.00 4.02
1607 6530 2.464459 CCTTGGCGGCGTCAAGATC 61.464 63.158 44.84 12.73 46.78 2.75
1648 6571 0.804989 CGAATTCAACCAGGCTGTCC 59.195 55.000 14.43 0.00 0.00 4.02
1673 6596 1.134220 CATGCCTACCGGTTGTACCAT 60.134 52.381 15.04 10.16 38.47 3.55
1674 6597 0.250793 CATGCCTACCGGTTGTACCA 59.749 55.000 15.04 8.09 38.47 3.25
1714 6673 4.789807 AGCTTACTGATCCTTGCATCAAT 58.210 39.130 0.00 0.00 32.24 2.57
1730 6689 1.739371 CGGTAGTTCCCTGCAGCTTAC 60.739 57.143 8.66 5.21 0.00 2.34
1732 6691 1.296715 CGGTAGTTCCCTGCAGCTT 59.703 57.895 8.66 0.00 0.00 3.74
1740 6699 2.100418 GAGTATCCACACGGTAGTTCCC 59.900 54.545 0.00 0.00 0.00 3.97
1787 6746 9.197306 GGTACTTGATATTTATCCACCCTTTTT 57.803 33.333 0.00 0.00 31.71 1.94
1789 6748 7.998964 CAGGTACTTGATATTTATCCACCCTTT 59.001 37.037 0.00 0.00 34.60 3.11
1892 6904 7.639113 AACAAGACAAATTCCAAGAACTGTA 57.361 32.000 0.00 0.00 0.00 2.74
1900 6912 7.048629 TGCTATGAAACAAGACAAATTCCAA 57.951 32.000 0.00 0.00 0.00 3.53
1935 6947 8.842358 AATTAAGATACACTTTGGAACGAGAA 57.158 30.769 0.00 0.00 39.72 2.87
1970 7278 6.143919 TCAAATGCGAGAATACGTGATGATAC 59.856 38.462 0.00 0.00 35.59 2.24
2092 11451 3.695830 TCATACCCACTTGTGGTCTTC 57.304 47.619 17.35 0.00 37.31 2.87
2097 11456 5.920193 ATTCATTTCATACCCACTTGTGG 57.080 39.130 12.54 12.54 0.00 4.17
2101 11460 8.650143 ACTTACAATTCATTTCATACCCACTT 57.350 30.769 0.00 0.00 0.00 3.16
2123 11482 2.302157 GGACCTATGCGGCCTATAACTT 59.698 50.000 0.00 0.00 35.61 2.66
2272 11733 4.850680 CCCTGGTTACCTTTAGTGCAATA 58.149 43.478 2.07 0.00 0.00 1.90
2285 11749 3.853698 TTGTGGCGGCCCTGGTTAC 62.854 63.158 17.97 7.29 0.00 2.50
2351 11815 6.232692 CAACTTTCCAATCCAATCACCAATT 58.767 36.000 0.00 0.00 0.00 2.32
2531 11995 9.088059 CATTAAAATATGTCGACCGATTTTACG 57.912 33.333 27.53 21.65 34.89 3.18
2572 12036 6.653273 TTCTCATTCATCGCAGAAGTAAAG 57.347 37.500 0.00 0.00 43.58 1.85
2610 12074 6.094603 GCCAGAAAAGATCACATGTACATCTT 59.905 38.462 19.68 19.68 38.30 2.40


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

AutoCloner maintained by Alex Coulton.