Multiple sequence alignment - TraesCS7D01G545200

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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 TraesCS7D01G545200 chr7D 100.000 3044 0 0 1 3044 632407386 632404343 0.000000e+00 5622.0
1 TraesCS7D01G545200 chr7D 93.280 744 50 0 905 1648 632760663 632759920 0.000000e+00 1098.0
2 TraesCS7D01G545200 chr7D 91.667 684 53 3 204 884 632761720 632761038 0.000000e+00 944.0
3 TraesCS7D01G545200 chr7D 90.745 443 37 2 1762 2200 632759922 632759480 3.380000e-164 588.0
4 TraesCS7D01G545200 chr7D 97.500 80 2 0 2177 2256 632744790 632744711 1.470000e-28 137.0
5 TraesCS7D01G545200 chr7D 98.305 59 1 0 2198 2256 632744881 632744823 1.490000e-18 104.0
6 TraesCS7D01G545200 chr7B 92.248 1535 101 7 931 2447 744570684 744569150 0.000000e+00 2159.0
7 TraesCS7D01G545200 chr7B 92.217 591 41 4 336 921 744571253 744570663 0.000000e+00 832.0
8 TraesCS7D01G545200 chr7B 93.878 294 18 0 2751 3044 744567882 744567589 7.740000e-121 444.0
9 TraesCS7D01G545200 chr7B 92.233 309 22 2 1 307 744571557 744571249 1.300000e-118 436.0
10 TraesCS7D01G545200 chr7B 88.547 358 27 1 2455 2812 744568225 744567882 3.630000e-114 422.0
11 TraesCS7D01G545200 chr6D 79.905 1269 232 16 808 2066 20312312 20311057 0.000000e+00 909.0
12 TraesCS7D01G545200 chrUn 79.748 1269 234 16 808 2066 273854720 273855975 0.000000e+00 898.0
13 TraesCS7D01G545200 chr6B 79.622 1271 232 19 808 2066 34341521 34340266 0.000000e+00 887.0
14 TraesCS7D01G545200 chr6B 79.899 1194 223 11 880 2066 27992451 27991268 0.000000e+00 859.0
15 TraesCS7D01G545200 chr6B 79.443 1221 221 17 857 2066 34685387 34684186 0.000000e+00 837.0
16 TraesCS7D01G545200 chr6B 93.878 98 6 0 2695 2792 233032510 233032413 6.800000e-32 148.0
17 TraesCS7D01G545200 chr6B 93.814 97 6 0 2700 2796 458503575 458503479 2.450000e-31 147.0
18 TraesCS7D01G545200 chr6A 77.841 1223 216 29 857 2066 20340011 20338831 0.000000e+00 706.0
19 TraesCS7D01G545200 chr5D 94.000 100 6 0 2700 2799 509426562 509426463 5.260000e-33 152.0
20 TraesCS7D01G545200 chr5D 94.737 95 3 2 2697 2791 481806199 481806107 2.450000e-31 147.0
21 TraesCS7D01G545200 chr5D 90.654 107 8 2 2696 2802 128577682 128577578 1.140000e-29 141.0
22 TraesCS7D01G545200 chr3D 94.792 96 4 1 2702 2796 612889619 612889714 6.800000e-32 148.0
23 TraesCS7D01G545200 chr3D 89.286 112 10 2 2707 2816 302930471 302930360 4.090000e-29 139.0
24 TraesCS7D01G545200 chr5B 90.654 107 8 2 2696 2802 140966024 140965920 1.140000e-29 141.0
25 TraesCS7D01G545200 chr2B 79.612 103 15 5 707 809 794910132 794910228 5.450000e-08 69.4


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 TraesCS7D01G545200 chr7D 632404343 632407386 3043 True 5622.000000 5622 100.000000 1 3044 1 chr7D.!!$R1 3043
1 TraesCS7D01G545200 chr7D 632759480 632761720 2240 True 876.666667 1098 91.897333 204 2200 3 chr7D.!!$R3 1996
2 TraesCS7D01G545200 chr7B 744567589 744571557 3968 True 858.600000 2159 91.824600 1 3044 5 chr7B.!!$R1 3043
3 TraesCS7D01G545200 chr6D 20311057 20312312 1255 True 909.000000 909 79.905000 808 2066 1 chr6D.!!$R1 1258
4 TraesCS7D01G545200 chrUn 273854720 273855975 1255 False 898.000000 898 79.748000 808 2066 1 chrUn.!!$F1 1258
5 TraesCS7D01G545200 chr6B 34340266 34341521 1255 True 887.000000 887 79.622000 808 2066 1 chr6B.!!$R2 1258
6 TraesCS7D01G545200 chr6B 27991268 27992451 1183 True 859.000000 859 79.899000 880 2066 1 chr6B.!!$R1 1186
7 TraesCS7D01G545200 chr6B 34684186 34685387 1201 True 837.000000 837 79.443000 857 2066 1 chr6B.!!$R3 1209
8 TraesCS7D01G545200 chr6A 20338831 20340011 1180 True 706.000000 706 77.841000 857 2066 1 chr6A.!!$R1 1209

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
920 1312 0.173708 CCTAGGACACTCCAAGCGAC 59.826 60.0 1.05 0.0 39.61 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2701 0.252558 TAAGTCCTCACCAGGGGGAC 60.253 60.0 16.37 16.37 46.94 4.46 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
26 27 3.140814 GCCGCCCCAAATCCTGAC 61.141 66.667 0.00 0.00 0.00 3.51
73 74 2.261361 GCCGGTGCCAATTGAACC 59.739 61.111 16.35 16.35 0.00 3.62
74 75 2.569354 GCCGGTGCCAATTGAACCA 61.569 57.895 22.54 9.31 33.30 3.67
105 106 0.179020 CGGCTGCCATCCATAGGAAA 60.179 55.000 20.29 0.00 34.34 3.13
112 113 2.749800 GCCATCCATAGGAAAGGTGGAC 60.750 54.545 7.43 0.00 44.21 4.02
132 133 1.934220 GCACTCCCTCGATGTCGACA 61.934 60.000 22.48 22.48 44.22 4.35
135 136 1.948145 ACTCCCTCGATGTCGACATAC 59.052 52.381 30.04 20.86 44.22 2.39
137 138 0.314302 CCCTCGATGTCGACATACCC 59.686 60.000 30.04 17.10 44.22 3.69
146 147 2.497770 GACATACCCCACGGACCG 59.502 66.667 13.61 13.61 0.00 4.79
169 170 4.521146 AGGGTGAATGATGATGTCTTGTC 58.479 43.478 0.00 0.00 0.00 3.18
174 175 4.393990 TGAATGATGATGTCTTGTCAGTGC 59.606 41.667 0.00 0.00 0.00 4.40
179 180 2.102925 TGATGTCTTGTCAGTGCACAGA 59.897 45.455 21.04 14.56 0.00 3.41
181 182 0.864455 GTCTTGTCAGTGCACAGAGC 59.136 55.000 21.04 11.58 45.96 4.09
256 258 4.808895 CGAGTCATCAAATCCGTTATTGGA 59.191 41.667 0.00 0.00 43.58 3.53
341 344 6.728632 ACTTTCCATATGGTTGGTTTTGGTAT 59.271 34.615 21.28 0.00 38.01 2.73
382 385 8.479280 CAATTGACGACTTTCCAAAAATAGTTG 58.521 33.333 0.00 0.00 0.00 3.16
385 388 5.744490 ACGACTTTCCAAAAATAGTTGACG 58.256 37.500 0.00 0.00 0.00 4.35
518 521 5.163269 GGTAGGGTGGACGTTAAAATAGGAT 60.163 44.000 0.00 0.00 0.00 3.24
522 525 5.416639 GGGTGGACGTTAAAATAGGATGTTT 59.583 40.000 0.00 0.00 0.00 2.83
589 596 6.946229 TCTTTGTATTTCTTACTCGTGAGC 57.054 37.500 0.00 0.00 0.00 4.26
604 611 2.474816 GTGAGCGGATACCTGTGATTC 58.525 52.381 0.00 0.00 0.00 2.52
642 649 8.417273 AATATAAAGGTGGCAAGTTAGTTGTT 57.583 30.769 1.55 0.00 38.55 2.83
686 693 5.375417 TTGAATACATGCTCCACAACTTG 57.625 39.130 0.00 0.00 0.00 3.16
692 699 1.279840 GCTCCACAACTTGTGCGTC 59.720 57.895 15.42 3.72 46.51 5.19
705 712 3.945981 TGTGCGTCTAAAGGTATGACA 57.054 42.857 0.00 0.00 0.00 3.58
794 801 2.809446 CATGGAAAGTCATGCATGCAG 58.191 47.619 26.69 17.32 41.28 4.41
838 845 5.300286 CAGCATTTCCTAGTTAATTCAGGGG 59.700 44.000 0.00 0.00 0.00 4.79
842 849 7.890655 GCATTTCCTAGTTAATTCAGGGGATAT 59.109 37.037 0.00 0.00 0.00 1.63
845 852 5.046591 TCCTAGTTAATTCAGGGGATATGCG 60.047 44.000 0.00 0.00 0.00 4.73
846 853 4.974645 AGTTAATTCAGGGGATATGCGA 57.025 40.909 0.00 0.00 0.00 5.10
912 1304 2.832733 ACCAAAGCTACCTAGGACACTC 59.167 50.000 17.98 0.00 0.00 3.51
913 1305 2.168728 CCAAAGCTACCTAGGACACTCC 59.831 54.545 17.98 0.00 36.58 3.85
914 1306 2.832129 CAAAGCTACCTAGGACACTCCA 59.168 50.000 17.98 0.00 39.61 3.86
915 1307 2.921834 AGCTACCTAGGACACTCCAA 57.078 50.000 17.98 0.00 39.61 3.53
916 1308 2.741145 AGCTACCTAGGACACTCCAAG 58.259 52.381 17.98 0.80 39.61 3.61
917 1309 1.137282 GCTACCTAGGACACTCCAAGC 59.863 57.143 17.98 7.02 39.61 4.01
918 1310 1.405821 CTACCTAGGACACTCCAAGCG 59.594 57.143 17.98 0.00 39.61 4.68
919 1311 0.251653 ACCTAGGACACTCCAAGCGA 60.252 55.000 17.98 0.00 39.61 4.93
920 1312 0.173708 CCTAGGACACTCCAAGCGAC 59.826 60.000 1.05 0.00 39.61 5.19
921 1313 0.179161 CTAGGACACTCCAAGCGACG 60.179 60.000 0.00 0.00 39.61 5.12
922 1314 2.209064 TAGGACACTCCAAGCGACGC 62.209 60.000 13.03 13.03 39.61 5.19
923 1315 3.112709 GACACTCCAAGCGACGCC 61.113 66.667 17.79 0.00 0.00 5.68
925 1317 4.717629 CACTCCAAGCGACGCCGA 62.718 66.667 17.79 8.92 38.22 5.54
926 1318 3.760035 ACTCCAAGCGACGCCGAT 61.760 61.111 17.79 0.00 38.22 4.18
927 1319 2.411701 CTCCAAGCGACGCCGATA 59.588 61.111 17.79 0.00 38.22 2.92
928 1320 1.658717 CTCCAAGCGACGCCGATAG 60.659 63.158 17.79 5.84 38.22 2.08
929 1321 2.060004 CTCCAAGCGACGCCGATAGA 62.060 60.000 17.79 5.87 38.22 1.98
930 1322 1.007271 CCAAGCGACGCCGATAGAT 60.007 57.895 17.79 0.00 38.22 1.98
931 1323 0.240145 CCAAGCGACGCCGATAGATA 59.760 55.000 17.79 0.00 38.22 1.98
932 1324 1.328439 CAAGCGACGCCGATAGATAC 58.672 55.000 17.79 0.00 38.22 2.24
933 1325 0.240411 AAGCGACGCCGATAGATACC 59.760 55.000 17.79 0.00 38.22 2.73
934 1326 0.605860 AGCGACGCCGATAGATACCT 60.606 55.000 17.79 0.00 38.22 3.08
935 1327 1.081892 GCGACGCCGATAGATACCTA 58.918 55.000 9.14 0.00 38.22 3.08
936 1328 1.062294 GCGACGCCGATAGATACCTAG 59.938 57.143 9.14 0.00 38.22 3.02
937 1329 1.664659 CGACGCCGATAGATACCTAGG 59.335 57.143 7.41 7.41 38.22 3.02
938 1330 2.676176 CGACGCCGATAGATACCTAGGA 60.676 54.545 17.98 0.00 38.22 2.94
939 1331 2.677337 GACGCCGATAGATACCTAGGAC 59.323 54.545 17.98 6.53 39.76 3.85
940 1332 2.039480 ACGCCGATAGATACCTAGGACA 59.961 50.000 17.98 2.60 39.76 4.02
941 1333 2.419324 CGCCGATAGATACCTAGGACAC 59.581 54.545 17.98 5.77 39.76 3.67
942 1334 3.688235 GCCGATAGATACCTAGGACACT 58.312 50.000 17.98 12.94 39.76 3.55
993 1419 4.229096 CAAGAGCAATTGCAACGTTATGT 58.771 39.130 30.89 7.98 45.16 2.29
1124 1550 2.616256 GGTGTGAGCATCTCAATGTGGA 60.616 50.000 0.00 0.00 42.46 4.02
1133 1559 3.786368 TCTCAATGTGGATTGTGACCA 57.214 42.857 0.00 0.00 40.09 4.02
1152 1578 4.373116 GGTGACAAGGCTCGGCGA 62.373 66.667 10.14 10.14 0.00 5.54
1302 1728 2.755655 CTCTAACCTCACGTCAGATGGT 59.244 50.000 0.00 0.00 0.00 3.55
1389 1815 2.124570 GACTGGCGCATGATGGGT 60.125 61.111 10.83 0.00 32.36 4.51
1464 1891 2.443577 TGTTGGGCCTTTGCAGCA 60.444 55.556 4.53 0.00 40.13 4.41
1491 1918 1.599047 CGTGGAGGGCATCAACTCT 59.401 57.895 5.01 0.00 34.22 3.24
1533 1960 0.317770 CATTGTCCGCGCAACAACTT 60.318 50.000 22.94 9.50 39.29 2.66
1602 2029 7.151308 CACAATTGGCCTTCAAGTACATAAAA 58.849 34.615 10.83 0.00 38.95 1.52
1611 2038 7.520937 GCCTTCAAGTACATAAAAGAAAACGGA 60.521 37.037 0.00 0.00 0.00 4.69
1623 2050 0.110486 AAAACGGAGGCATCACCAGT 59.890 50.000 0.00 0.00 43.14 4.00
1803 2233 1.557443 CGAATGGCTTCCGGCGATAC 61.557 60.000 9.30 0.00 38.41 2.24
1892 2322 1.267574 ACCACCGATGAGCATGACCT 61.268 55.000 0.00 0.00 0.00 3.85
2075 2512 4.940046 GTGGCAATGATATCGAGATGGATT 59.060 41.667 0.00 0.00 0.00 3.01
2076 2513 4.939439 TGGCAATGATATCGAGATGGATTG 59.061 41.667 13.44 13.44 0.00 2.67
2088 2525 2.774234 AGATGGATTGTTGGGACTCGAT 59.226 45.455 0.00 0.00 0.00 3.59
2110 2547 7.714813 TCGATGCTATATGTTTCTGGAATTTGA 59.285 33.333 0.00 0.00 0.00 2.69
2117 2554 8.827832 ATATGTTTCTGGAATTTGATCCTTCA 57.172 30.769 0.00 0.00 40.35 3.02
2122 2559 5.195940 TCTGGAATTTGATCCTTCATGTCC 58.804 41.667 0.00 0.00 40.35 4.02
2154 2591 2.235016 TCGGGCACAAAGTAGCATTTT 58.765 42.857 0.00 0.00 0.00 1.82
2157 2594 3.727726 GGGCACAAAGTAGCATTTTGTT 58.272 40.909 9.59 0.00 44.04 2.83
2158 2595 4.126437 GGGCACAAAGTAGCATTTTGTTT 58.874 39.130 9.59 0.00 44.04 2.83
2217 2654 9.890629 CTATAAGTATATTGAAATGGCCTAGCA 57.109 33.333 3.32 0.00 0.00 3.49
2266 2714 1.200760 TGATGTGTCCCCCTGGTGAG 61.201 60.000 0.00 0.00 0.00 3.51
2280 2728 4.194640 CCTGGTGAGGACTTATGTGATTG 58.805 47.826 0.00 0.00 42.93 2.67
2281 2729 3.609853 TGGTGAGGACTTATGTGATTGC 58.390 45.455 0.00 0.00 0.00 3.56
2282 2730 3.264193 TGGTGAGGACTTATGTGATTGCT 59.736 43.478 0.00 0.00 0.00 3.91
2283 2731 4.263462 TGGTGAGGACTTATGTGATTGCTT 60.263 41.667 0.00 0.00 0.00 3.91
2284 2732 4.095483 GGTGAGGACTTATGTGATTGCTTG 59.905 45.833 0.00 0.00 0.00 4.01
2286 2734 5.182001 GTGAGGACTTATGTGATTGCTTGTT 59.818 40.000 0.00 0.00 0.00 2.83
2287 2735 5.412594 TGAGGACTTATGTGATTGCTTGTTC 59.587 40.000 0.00 0.00 0.00 3.18
2288 2736 5.316167 AGGACTTATGTGATTGCTTGTTCA 58.684 37.500 0.00 0.00 0.00 3.18
2302 2752 9.362539 GATTGCTTGTTCATAGACATCAAAATT 57.637 29.630 0.00 0.00 31.18 1.82
2306 2756 7.412237 GCTTGTTCATAGACATCAAAATTTGGC 60.412 37.037 5.83 0.00 0.00 4.52
2329 2779 2.173569 AGTCCCAATGCAATACTCCCTC 59.826 50.000 0.00 0.00 0.00 4.30
2362 2812 7.942145 TTTATAAGTCGTATTTGCTTTTCGC 57.058 32.000 0.00 0.00 39.77 4.70
2384 2834 5.594724 CAAAATTGCACAATGTAAGGTGG 57.405 39.130 0.00 0.00 35.58 4.61
2392 2842 6.862209 TGCACAATGTAAGGTGGATTTATTC 58.138 36.000 0.00 0.00 35.58 1.75
2406 2856 9.971922 GGTGGATTTATTCTAATTTCTCATTGG 57.028 33.333 0.00 0.00 0.00 3.16
2420 2870 6.588719 TTCTCATTGGGGACATTAAAACTG 57.411 37.500 0.00 0.00 42.32 3.16
2430 2880 7.827236 TGGGGACATTAAAACTGAGTACTAATG 59.173 37.037 17.98 17.98 36.48 1.90
2434 2884 8.848474 ACATTAAAACTGAGTACTAATGCACT 57.152 30.769 18.87 5.19 34.67 4.40
2437 2887 5.746990 AAACTGAGTACTAATGCACTCCT 57.253 39.130 0.00 0.00 40.41 3.69
2438 2888 4.993029 ACTGAGTACTAATGCACTCCTC 57.007 45.455 0.00 0.00 40.41 3.71
2439 2889 4.605183 ACTGAGTACTAATGCACTCCTCT 58.395 43.478 0.00 0.00 40.41 3.69
2440 2890 4.642885 ACTGAGTACTAATGCACTCCTCTC 59.357 45.833 0.00 0.00 40.41 3.20
2441 2891 4.600062 TGAGTACTAATGCACTCCTCTCA 58.400 43.478 0.00 0.00 40.41 3.27
2442 2892 4.642437 TGAGTACTAATGCACTCCTCTCAG 59.358 45.833 0.00 0.00 40.41 3.35
2444 2894 1.484240 ACTAATGCACTCCTCTCAGGC 59.516 52.381 0.00 0.00 34.61 4.85
2445 2895 1.483827 CTAATGCACTCCTCTCAGGCA 59.516 52.381 0.00 0.00 39.03 4.75
2448 2898 0.473755 TGCACTCCTCTCAGGCAAAA 59.526 50.000 0.00 0.00 34.61 2.44
2449 2899 0.877743 GCACTCCTCTCAGGCAAAAC 59.122 55.000 0.00 0.00 34.61 2.43
2450 2900 1.151668 CACTCCTCTCAGGCAAAACG 58.848 55.000 0.00 0.00 34.61 3.60
2451 2901 0.603975 ACTCCTCTCAGGCAAAACGC 60.604 55.000 0.00 0.00 34.61 4.84
2452 2902 0.321122 CTCCTCTCAGGCAAAACGCT 60.321 55.000 0.00 0.00 41.91 5.07
2453 2903 0.973632 TCCTCTCAGGCAAAACGCTA 59.026 50.000 0.00 0.00 41.91 4.26
2470 3838 1.787155 GCTATGTTGCGACCACTATCG 59.213 52.381 0.45 0.00 45.09 2.92
2493 3861 5.178252 CGGTCACTAGCATTCATAAGGATTG 59.822 44.000 0.00 0.00 0.00 2.67
2537 3905 1.417890 ACACTAGGGCTCATGGCATAC 59.582 52.381 0.00 0.00 44.01 2.39
2580 3948 9.853177 AAATGAGAATTTAATACTAGTGAGGGG 57.147 33.333 5.39 0.00 0.00 4.79
2584 3952 5.568620 ATTTAATACTAGTGAGGGGCCAG 57.431 43.478 4.39 0.00 0.00 4.85
2586 3954 3.700863 AATACTAGTGAGGGGCCAGTA 57.299 47.619 4.39 3.46 0.00 2.74
2598 3966 2.454941 CCAGTACCCCCTCCCTGT 59.545 66.667 0.00 0.00 0.00 4.00
2601 3969 0.978146 CAGTACCCCCTCCCTGTCAG 60.978 65.000 0.00 0.00 0.00 3.51
2664 4032 7.695480 ATGGTATTTTGTACAGTACATTGCA 57.305 32.000 14.34 0.00 38.68 4.08
2665 4033 6.904498 TGGTATTTTGTACAGTACATTGCAC 58.096 36.000 14.34 10.00 38.68 4.57
2693 4061 1.222567 AGGTTTGAACTGGGTGAGGT 58.777 50.000 0.00 0.00 0.00 3.85
2697 4065 3.288092 GTTTGAACTGGGTGAGGTTCTT 58.712 45.455 0.00 0.00 41.42 2.52
2715 4083 6.056236 GGTTCTTGTATTTGATACTCCCTCC 58.944 44.000 0.43 0.00 36.70 4.30
2719 4087 6.608405 TCTTGTATTTGATACTCCCTCCGTAA 59.392 38.462 0.43 0.00 36.70 3.18
2732 4100 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2855 4284 5.683876 ATAGATGGCAGTTGTCTGTAAGT 57.316 39.130 0.00 0.00 43.05 2.24
2870 4299 2.817258 TGTAAGTTGCCCTTTTCCATCG 59.183 45.455 0.00 0.00 34.46 3.84
2915 4344 4.369182 ACTACTGTTTTTGTCGACCTCTG 58.631 43.478 14.12 5.67 0.00 3.35
2941 4370 0.402504 AACCACCCGAGGCACATTAA 59.597 50.000 0.00 0.00 0.00 1.40
2944 4373 0.381801 CACCCGAGGCACATTAATGC 59.618 55.000 15.48 3.82 45.34 3.56
2955 4384 4.423732 GCACATTAATGCCAGTAACCAAG 58.576 43.478 15.48 0.00 39.86 3.61
2972 4401 0.604243 AAGCGTAATGGAACGTGCCA 60.604 50.000 20.16 20.16 44.64 4.92
3009 4438 3.119101 GGATAATACGATCGGACTGCCAT 60.119 47.826 20.98 0.30 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.676782 GTGGACGTCAGGATTTGGGG 60.677 60.000 18.91 0.00 0.00 4.96
14 15 0.676782 GGTGGACGTCAGGATTTGGG 60.677 60.000 18.91 0.00 0.00 4.12
22 23 1.667830 ATGTTGCGGTGGACGTCAG 60.668 57.895 18.91 6.55 46.52 3.51
55 56 2.126502 GTTCAATTGGCACCGGCG 60.127 61.111 0.00 0.00 42.47 6.46
92 93 2.485479 CGTCCACCTTTCCTATGGATGG 60.485 54.545 4.13 0.00 44.21 3.51
112 113 2.278206 CGACATCGAGGGAGTGCG 60.278 66.667 0.69 0.00 43.02 5.34
132 133 2.443390 CCTCGGTCCGTGGGGTAT 60.443 66.667 22.26 0.00 36.95 2.73
137 138 2.656069 ATTCACCCTCGGTCCGTGG 61.656 63.158 22.90 22.90 39.77 4.94
146 147 4.521146 ACAAGACATCATCATTCACCCTC 58.479 43.478 0.00 0.00 0.00 4.30
169 170 0.642291 CGTTATCGCTCTGTGCACTG 59.358 55.000 19.41 18.10 43.06 3.66
174 175 3.003378 TGATAGACCGTTATCGCTCTGTG 59.997 47.826 2.02 0.00 34.45 3.66
179 180 3.821600 AGATGTGATAGACCGTTATCGCT 59.178 43.478 11.29 0.00 39.90 4.93
181 182 5.358298 TCAGATGTGATAGACCGTTATCG 57.642 43.478 0.00 0.00 33.63 2.92
186 187 3.195610 TGCTTTCAGATGTGATAGACCGT 59.804 43.478 13.42 0.00 34.57 4.83
332 335 8.153479 TGACATACATCAGCATATACCAAAAC 57.847 34.615 0.00 0.00 0.00 2.43
341 344 6.200854 GTCGTCAATTGACATACATCAGCATA 59.799 38.462 32.06 1.57 44.99 3.14
581 588 0.248661 CACAGGTATCCGCTCACGAG 60.249 60.000 0.00 0.00 43.93 4.18
589 596 4.697514 AGATGTTGAATCACAGGTATCCG 58.302 43.478 0.00 0.00 0.00 4.18
604 611 7.492344 GCCACCTTTATATTTGGAAAGATGTTG 59.508 37.037 0.00 0.00 35.12 3.33
655 662 7.341512 TGTGGAGCATGTATTCAAAATTATCCA 59.658 33.333 0.00 0.00 0.00 3.41
686 693 4.106029 TCTGTCATACCTTTAGACGCAC 57.894 45.455 0.00 0.00 35.09 5.34
692 699 5.292101 CGCTTTCCTTCTGTCATACCTTTAG 59.708 44.000 0.00 0.00 0.00 1.85
705 712 4.969484 TCTCCTTTTAACGCTTTCCTTCT 58.031 39.130 0.00 0.00 0.00 2.85
755 762 9.904198 TTTCCATGTATGAGATAGAATCAAACA 57.096 29.630 0.00 0.00 0.00 2.83
838 845 3.248363 TGCACATGTAGCTTTCGCATATC 59.752 43.478 17.30 0.00 39.10 1.63
842 849 0.516877 GTGCACATGTAGCTTTCGCA 59.483 50.000 13.17 10.34 39.10 5.10
845 852 1.879380 TGTGGTGCACATGTAGCTTTC 59.121 47.619 20.43 0.00 39.62 2.62
846 853 1.979855 TGTGGTGCACATGTAGCTTT 58.020 45.000 20.43 0.00 39.62 3.51
912 1304 0.240145 TATCTATCGGCGTCGCTTGG 59.760 55.000 18.11 7.14 36.13 3.61
913 1305 1.328439 GTATCTATCGGCGTCGCTTG 58.672 55.000 18.11 10.34 36.13 4.01
914 1306 0.240411 GGTATCTATCGGCGTCGCTT 59.760 55.000 18.11 5.19 36.13 4.68
915 1307 0.605860 AGGTATCTATCGGCGTCGCT 60.606 55.000 18.11 0.00 36.13 4.93
916 1308 1.062294 CTAGGTATCTATCGGCGTCGC 59.938 57.143 9.22 9.22 36.13 5.19
917 1309 1.664659 CCTAGGTATCTATCGGCGTCG 59.335 57.143 1.15 1.15 37.82 5.12
918 1310 2.677337 GTCCTAGGTATCTATCGGCGTC 59.323 54.545 9.08 0.00 0.00 5.19
919 1311 2.039480 TGTCCTAGGTATCTATCGGCGT 59.961 50.000 9.08 0.00 0.00 5.68
920 1312 2.419324 GTGTCCTAGGTATCTATCGGCG 59.581 54.545 9.08 0.00 0.00 6.46
921 1313 3.688235 AGTGTCCTAGGTATCTATCGGC 58.312 50.000 9.08 0.00 0.00 5.54
922 1314 3.933955 CGAGTGTCCTAGGTATCTATCGG 59.066 52.174 9.08 0.00 0.00 4.18
923 1315 4.818642 TCGAGTGTCCTAGGTATCTATCG 58.181 47.826 9.08 12.09 0.00 2.92
924 1316 5.122711 GCTTCGAGTGTCCTAGGTATCTATC 59.877 48.000 9.08 0.46 0.00 2.08
925 1317 5.005094 GCTTCGAGTGTCCTAGGTATCTAT 58.995 45.833 9.08 0.00 0.00 1.98
926 1318 4.141551 TGCTTCGAGTGTCCTAGGTATCTA 60.142 45.833 9.08 0.00 0.00 1.98
927 1319 3.215975 GCTTCGAGTGTCCTAGGTATCT 58.784 50.000 9.08 5.42 0.00 1.98
928 1320 2.950309 TGCTTCGAGTGTCCTAGGTATC 59.050 50.000 9.08 2.22 0.00 2.24
929 1321 3.014304 TGCTTCGAGTGTCCTAGGTAT 57.986 47.619 9.08 0.00 0.00 2.73
930 1322 2.490903 GTTGCTTCGAGTGTCCTAGGTA 59.509 50.000 9.08 0.00 0.00 3.08
931 1323 1.272769 GTTGCTTCGAGTGTCCTAGGT 59.727 52.381 9.08 0.00 0.00 3.08
932 1324 1.404315 GGTTGCTTCGAGTGTCCTAGG 60.404 57.143 0.82 0.82 0.00 3.02
933 1325 1.272490 TGGTTGCTTCGAGTGTCCTAG 59.728 52.381 0.00 0.00 0.00 3.02
934 1326 1.000506 GTGGTTGCTTCGAGTGTCCTA 59.999 52.381 0.00 0.00 0.00 2.94
935 1327 0.249911 GTGGTTGCTTCGAGTGTCCT 60.250 55.000 0.00 0.00 0.00 3.85
936 1328 0.249911 AGTGGTTGCTTCGAGTGTCC 60.250 55.000 0.00 0.00 0.00 4.02
937 1329 1.583054 AAGTGGTTGCTTCGAGTGTC 58.417 50.000 0.00 0.00 0.00 3.67
938 1330 2.102588 ACTAAGTGGTTGCTTCGAGTGT 59.897 45.455 0.00 0.00 0.00 3.55
939 1331 2.476619 CACTAAGTGGTTGCTTCGAGTG 59.523 50.000 0.00 0.00 32.31 3.51
940 1332 2.102588 ACACTAAGTGGTTGCTTCGAGT 59.897 45.455 0.00 0.00 37.94 4.18
941 1333 2.755650 ACACTAAGTGGTTGCTTCGAG 58.244 47.619 0.00 0.00 37.94 4.04
942 1334 2.902705 ACACTAAGTGGTTGCTTCGA 57.097 45.000 0.00 0.00 37.94 3.71
988 1414 5.872617 GCACGATGGCCATAAGTATACATAA 59.127 40.000 20.84 0.00 0.00 1.90
993 1419 4.202315 ACAAGCACGATGGCCATAAGTATA 60.202 41.667 20.84 0.00 0.00 1.47
1124 1550 1.593196 CTTGTCACCGTGGTCACAAT 58.407 50.000 8.98 0.00 38.35 2.71
1133 1559 4.681978 GCCGAGCCTTGTCACCGT 62.682 66.667 0.00 0.00 0.00 4.83
1152 1578 7.096640 CGAGCATTTTCTTTGAACACGTTAAAT 60.097 33.333 0.00 0.00 0.00 1.40
1302 1728 4.278513 CCTTGGTGCCGGTTCCCA 62.279 66.667 1.90 3.78 0.00 4.37
1389 1815 2.221169 GCTGATGGGCGTTGATCATAA 58.779 47.619 0.00 0.00 0.00 1.90
1491 1918 5.552870 GAATCAGCTTCCTGGTCCTAATA 57.447 43.478 0.00 0.00 39.61 0.98
1533 1960 6.371809 AAATTTTTCTTGTCGCAGTCTACA 57.628 33.333 0.00 0.00 0.00 2.74
1602 2029 0.400213 TGGTGATGCCTCCGTTTTCT 59.600 50.000 0.00 0.00 38.35 2.52
1623 2050 4.988540 GCAACATACGGATAGTTAGCATCA 59.011 41.667 0.00 0.00 0.00 3.07
1635 2062 1.271108 TGCTCAAAGGCAACATACGGA 60.271 47.619 0.00 0.00 39.43 4.69
1803 2233 1.817941 CACAAATACGCCTCCCCCG 60.818 63.158 0.00 0.00 0.00 5.73
1892 2322 4.001652 CCAGTAGTCTACACGTCTCTTGA 58.998 47.826 12.54 0.00 0.00 3.02
2075 2512 3.641436 ACATATAGCATCGAGTCCCAACA 59.359 43.478 0.00 0.00 0.00 3.33
2076 2513 4.258702 ACATATAGCATCGAGTCCCAAC 57.741 45.455 0.00 0.00 0.00 3.77
2088 2525 8.000709 AGGATCAAATTCCAGAAACATATAGCA 58.999 33.333 0.00 0.00 38.32 3.49
2110 2547 3.978672 TCATGATGGAGGACATGAAGGAT 59.021 43.478 0.00 0.00 46.10 3.24
2117 2554 2.039480 CCCGAATCATGATGGAGGACAT 59.961 50.000 19.89 0.00 44.18 3.06
2122 2559 1.233019 GTGCCCGAATCATGATGGAG 58.767 55.000 9.46 3.76 0.00 3.86
2154 2591 9.997482 GGAATTTATTGCTCTTCGTATTAAACA 57.003 29.630 0.00 0.00 0.00 2.83
2251 2699 2.203938 TCCTCACCAGGGGGACAC 60.204 66.667 0.00 0.00 40.80 3.67
2253 2701 0.252558 TAAGTCCTCACCAGGGGGAC 60.253 60.000 16.37 16.37 46.94 4.46
2266 2714 5.627499 TGAACAAGCAATCACATAAGTCC 57.373 39.130 0.00 0.00 0.00 3.85
2269 2717 7.977904 TGTCTATGAACAAGCAATCACATAAG 58.022 34.615 0.00 0.00 0.00 1.73
2280 2728 7.412237 GCCAAATTTTGATGTCTATGAACAAGC 60.412 37.037 10.72 0.00 31.81 4.01
2281 2729 7.816031 AGCCAAATTTTGATGTCTATGAACAAG 59.184 33.333 10.72 0.00 31.81 3.16
2282 2730 7.669427 AGCCAAATTTTGATGTCTATGAACAA 58.331 30.769 10.72 0.00 31.81 2.83
2283 2731 7.230849 AGCCAAATTTTGATGTCTATGAACA 57.769 32.000 10.72 0.00 0.00 3.18
2284 2732 8.462016 ACTAGCCAAATTTTGATGTCTATGAAC 58.538 33.333 10.72 0.00 0.00 3.18
2286 2734 7.283127 GGACTAGCCAAATTTTGATGTCTATGA 59.717 37.037 10.72 0.00 36.34 2.15
2287 2735 7.420800 GGACTAGCCAAATTTTGATGTCTATG 58.579 38.462 10.72 0.00 36.34 2.23
2288 2736 6.547510 GGGACTAGCCAAATTTTGATGTCTAT 59.452 38.462 10.72 0.00 38.95 1.98
2302 2752 2.530460 ATTGCATTGGGACTAGCCAA 57.470 45.000 4.52 4.52 38.95 4.52
2306 2756 3.392616 AGGGAGTATTGCATTGGGACTAG 59.607 47.826 0.00 0.00 0.00 2.57
2329 2779 9.233232 GCAAATACGACTTATAAAAAGGAATGG 57.767 33.333 0.00 0.00 0.00 3.16
2362 2812 5.295950 TCCACCTTACATTGTGCAATTTTG 58.704 37.500 0.00 0.00 0.00 2.44
2392 2842 9.586435 GTTTTAATGTCCCCAATGAGAAATTAG 57.414 33.333 0.00 0.00 0.00 1.73
2399 2849 5.711976 ACTCAGTTTTAATGTCCCCAATGAG 59.288 40.000 0.00 0.00 37.16 2.90
2404 2854 5.836024 AGTACTCAGTTTTAATGTCCCCA 57.164 39.130 0.00 0.00 0.00 4.96
2406 2856 7.335924 TGCATTAGTACTCAGTTTTAATGTCCC 59.664 37.037 16.40 6.54 35.31 4.46
2430 2880 0.877743 GTTTTGCCTGAGAGGAGTGC 59.122 55.000 0.00 0.00 37.67 4.40
2434 2884 4.379174 GCGTTTTGCCTGAGAGGA 57.621 55.556 0.00 0.00 37.67 3.71
2450 2900 1.787155 CGATAGTGGTCGCAACATAGC 59.213 52.381 0.00 0.00 34.56 2.97
2451 2901 2.223735 ACCGATAGTGGTCGCAACATAG 60.224 50.000 0.00 0.00 37.91 2.23
2452 2902 1.752498 ACCGATAGTGGTCGCAACATA 59.248 47.619 0.00 0.00 37.91 2.29
2453 2903 0.535335 ACCGATAGTGGTCGCAACAT 59.465 50.000 0.00 0.00 37.91 2.71
2463 3831 4.307443 TGAATGCTAGTGACCGATAGTG 57.693 45.455 0.00 0.00 0.00 2.74
2464 3832 6.294787 CCTTATGAATGCTAGTGACCGATAGT 60.295 42.308 0.00 0.00 0.00 2.12
2470 3838 5.049129 GCAATCCTTATGAATGCTAGTGACC 60.049 44.000 0.00 0.00 44.85 4.02
2523 3891 0.663153 GTTTCGTATGCCATGAGCCC 59.337 55.000 0.00 0.00 42.71 5.19
2525 3893 3.559655 TGTATGTTTCGTATGCCATGAGC 59.440 43.478 0.00 0.00 44.14 4.26
2560 3928 5.937111 TGGCCCCTCACTAGTATTAAATTC 58.063 41.667 0.00 0.00 0.00 2.17
2580 3948 3.090532 CAGGGAGGGGGTACTGGC 61.091 72.222 0.00 0.00 0.00 4.85
2584 3952 1.689582 CCTGACAGGGAGGGGGTAC 60.690 68.421 14.26 0.00 0.00 3.34
2586 3954 2.138236 ATTCCTGACAGGGAGGGGGT 62.138 60.000 21.56 0.00 35.59 4.95
2643 4011 7.533900 CACTGTGCAATGTACTGTACAAAATAC 59.466 37.037 23.03 18.53 40.71 1.89
2652 4020 3.751479 TCTCACTGTGCAATGTACTGT 57.249 42.857 8.04 8.04 0.00 3.55
2653 4021 4.807834 CCTATCTCACTGTGCAATGTACTG 59.192 45.833 2.12 6.79 0.00 2.74
2654 4022 4.467795 ACCTATCTCACTGTGCAATGTACT 59.532 41.667 2.12 0.00 0.00 2.73
2655 4023 4.759782 ACCTATCTCACTGTGCAATGTAC 58.240 43.478 2.12 0.00 0.00 2.90
2656 4024 5.420725 AACCTATCTCACTGTGCAATGTA 57.579 39.130 2.12 0.00 0.00 2.29
2657 4025 3.988976 ACCTATCTCACTGTGCAATGT 57.011 42.857 2.12 0.00 0.00 2.71
2658 4026 4.696877 TCAAACCTATCTCACTGTGCAATG 59.303 41.667 2.12 0.00 0.00 2.82
2659 4027 4.910195 TCAAACCTATCTCACTGTGCAAT 58.090 39.130 2.12 1.68 0.00 3.56
2660 4028 4.350368 TCAAACCTATCTCACTGTGCAA 57.650 40.909 2.12 0.00 0.00 4.08
2661 4029 4.065088 GTTCAAACCTATCTCACTGTGCA 58.935 43.478 2.12 0.00 0.00 4.57
2662 4030 4.153117 CAGTTCAAACCTATCTCACTGTGC 59.847 45.833 2.12 0.00 0.00 4.57
2663 4031 4.692625 CCAGTTCAAACCTATCTCACTGTG 59.307 45.833 0.17 0.17 0.00 3.66
2664 4032 4.263068 CCCAGTTCAAACCTATCTCACTGT 60.263 45.833 0.00 0.00 0.00 3.55
2665 4033 4.256920 CCCAGTTCAAACCTATCTCACTG 58.743 47.826 0.00 0.00 0.00 3.66
2693 4061 5.424252 ACGGAGGGAGTATCAAATACAAGAA 59.576 40.000 0.39 0.00 38.21 2.52
2697 4065 6.608405 TCTTTACGGAGGGAGTATCAAATACA 59.392 38.462 0.39 0.00 38.21 2.29
2855 4284 0.965363 GGAGCGATGGAAAAGGGCAA 60.965 55.000 0.00 0.00 0.00 4.52
2903 4332 3.399330 GTTTTGATCCAGAGGTCGACAA 58.601 45.455 18.91 0.00 0.00 3.18
2915 4344 1.313091 GCCTCGGGTGGTTTTGATCC 61.313 60.000 0.00 0.00 0.00 3.36
2941 4370 2.483014 TTACGCTTGGTTACTGGCAT 57.517 45.000 0.00 0.00 0.00 4.40
2944 4373 2.980568 TCCATTACGCTTGGTTACTGG 58.019 47.619 0.00 0.00 35.64 4.00
2949 4378 1.533731 CACGTTCCATTACGCTTGGTT 59.466 47.619 0.00 0.00 45.06 3.67
2952 4381 0.179200 GGCACGTTCCATTACGCTTG 60.179 55.000 0.00 0.00 45.06 4.01
2955 4384 1.133869 GTGGCACGTTCCATTACGC 59.866 57.895 10.90 0.00 45.06 4.42
3000 4429 0.398318 GGGATAGGTCATGGCAGTCC 59.602 60.000 0.00 2.88 0.00 3.85
3009 4438 0.621571 AAGGCTGCTGGGATAGGTCA 60.622 55.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.