Multiple sequence alignment - TraesCS3A01G002000

Loading Multiple Alignment...

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 TraesCS3A01G002000 chr3A 100.000 3149 0 0 1 3149 1330822 1327674 0.000000e+00 5816.0
1 TraesCS3A01G002000 chr2D 95.257 759 35 1 1 759 75202798 75202041 0.000000e+00 1201.0
2 TraesCS3A01G002000 chr1D 95.132 760 34 3 1 759 175890942 175890185 0.000000e+00 1195.0
3 TraesCS3A01G002000 chr1D 94.993 759 37 1 1 759 296556946 296557703 0.000000e+00 1190.0
4 TraesCS3A01G002000 chr1D 94.993 759 36 2 1 759 448002857 448002101 0.000000e+00 1190.0
5 TraesCS3A01G002000 chr1D 85.246 61 8 1 2503 2563 363104407 363104466 9.430000e-06 62.1
6 TraesCS3A01G002000 chr6D 94.993 759 37 1 1 759 421629469 421630226 0.000000e+00 1190.0
7 TraesCS3A01G002000 chr6D 75.974 154 30 6 2398 2549 311241838 311241986 4.360000e-09 73.1
8 TraesCS3A01G002000 chr4D 94.993 759 37 1 1 759 32798013 32798770 0.000000e+00 1190.0
9 TraesCS3A01G002000 chr4D 94.993 759 37 1 1 759 252414365 252415122 0.000000e+00 1190.0
10 TraesCS3A01G002000 chr4D 86.766 937 76 23 2208 3138 82268463 82269357 0.000000e+00 1000.0
11 TraesCS3A01G002000 chr3D 94.993 759 37 1 1 759 371829253 371828496 0.000000e+00 1190.0
12 TraesCS3A01G002000 chr3D 94.993 759 37 1 1 759 371834734 371833977 0.000000e+00 1190.0
13 TraesCS3A01G002000 chr3B 84.949 1176 52 43 1052 2136 1481746 1480605 0.000000e+00 1075.0
14 TraesCS3A01G002000 chr3B 82.143 1064 84 52 1156 2136 15865336 15864296 0.000000e+00 815.0
15 TraesCS3A01G002000 chr3B 89.503 181 9 6 758 934 1482103 1481929 1.470000e-53 220.0
16 TraesCS3A01G002000 chr3B 71.786 280 70 7 2315 2591 730663845 730664118 1.570000e-08 71.3
17 TraesCS3A01G002000 chr3B 86.885 61 4 3 973 1029 1481843 1481783 7.290000e-07 65.8
18 TraesCS3A01G002000 chr3B 97.222 36 1 0 2130 2165 1480590 1480555 9.430000e-06 62.1
19 TraesCS3A01G002000 chr4A 87.794 934 88 14 2216 3138 492387388 492388306 0.000000e+00 1070.0
20 TraesCS3A01G002000 chrUn 83.955 1153 61 27 1051 2136 43305682 43306777 0.000000e+00 990.0
21 TraesCS3A01G002000 chrUn 84.000 325 18 11 758 1056 43305340 43305656 6.650000e-72 281.0
22 TraesCS3A01G002000 chr4B 86.681 901 107 9 2245 3138 116168253 116169147 0.000000e+00 987.0
23 TraesCS3A01G002000 chr4B 85.385 910 96 11 2245 3149 71916626 71917503 0.000000e+00 909.0
24 TraesCS3A01G002000 chr1A 78.753 946 171 18 2216 3146 462265019 462265949 9.660000e-170 606.0
25 TraesCS3A01G002000 chr7D 78.594 939 165 22 2216 3138 449518878 449519796 3.500000e-164 588.0
26 TraesCS3A01G002000 chr2A 87.834 337 23 10 1808 2130 752552396 752552064 2.290000e-101 379.0
27 TraesCS3A01G002000 chr2A 90.909 55 5 0 2496 2550 40478459 40478513 1.210000e-09 75.0
28 TraesCS3A01G002000 chr5A 83.193 119 15 4 1452 1570 672412866 672412753 1.540000e-18 104.0
29 TraesCS3A01G002000 chr1B 71.338 314 78 10 2253 2563 486341689 486341993 1.570000e-08 71.3


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 TraesCS3A01G002000 chr3A 1327674 1330822 3148 True 5816.000 5816 100.00000 1 3149 1 chr3A.!!$R1 3148
1 TraesCS3A01G002000 chr2D 75202041 75202798 757 True 1201.000 1201 95.25700 1 759 1 chr2D.!!$R1 758
2 TraesCS3A01G002000 chr1D 175890185 175890942 757 True 1195.000 1195 95.13200 1 759 1 chr1D.!!$R1 758
3 TraesCS3A01G002000 chr1D 296556946 296557703 757 False 1190.000 1190 94.99300 1 759 1 chr1D.!!$F1 758
4 TraesCS3A01G002000 chr1D 448002101 448002857 756 True 1190.000 1190 94.99300 1 759 1 chr1D.!!$R2 758
5 TraesCS3A01G002000 chr6D 421629469 421630226 757 False 1190.000 1190 94.99300 1 759 1 chr6D.!!$F2 758
6 TraesCS3A01G002000 chr4D 32798013 32798770 757 False 1190.000 1190 94.99300 1 759 1 chr4D.!!$F1 758
7 TraesCS3A01G002000 chr4D 252414365 252415122 757 False 1190.000 1190 94.99300 1 759 1 chr4D.!!$F3 758
8 TraesCS3A01G002000 chr4D 82268463 82269357 894 False 1000.000 1000 86.76600 2208 3138 1 chr4D.!!$F2 930
9 TraesCS3A01G002000 chr3D 371828496 371829253 757 True 1190.000 1190 94.99300 1 759 1 chr3D.!!$R1 758
10 TraesCS3A01G002000 chr3D 371833977 371834734 757 True 1190.000 1190 94.99300 1 759 1 chr3D.!!$R2 758
11 TraesCS3A01G002000 chr3B 15864296 15865336 1040 True 815.000 815 82.14300 1156 2136 1 chr3B.!!$R1 980
12 TraesCS3A01G002000 chr3B 1480555 1482103 1548 True 355.725 1075 89.63975 758 2165 4 chr3B.!!$R2 1407
13 TraesCS3A01G002000 chr4A 492387388 492388306 918 False 1070.000 1070 87.79400 2216 3138 1 chr4A.!!$F1 922
14 TraesCS3A01G002000 chrUn 43305340 43306777 1437 False 635.500 990 83.97750 758 2136 2 chrUn.!!$F1 1378
15 TraesCS3A01G002000 chr4B 116168253 116169147 894 False 987.000 987 86.68100 2245 3138 1 chr4B.!!$F2 893
16 TraesCS3A01G002000 chr4B 71916626 71917503 877 False 909.000 909 85.38500 2245 3149 1 chr4B.!!$F1 904
17 TraesCS3A01G002000 chr1A 462265019 462265949 930 False 606.000 606 78.75300 2216 3146 1 chr1A.!!$F1 930
18 TraesCS3A01G002000 chr7D 449518878 449519796 918 False 588.000 588 78.59400 2216 3138 1 chr7D.!!$F1 922

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
859 866 0.251297 TTGCACAAGTCCCTGGATGG 60.251 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2424 0.026933 CTCAGATGAGTCGTCGACGG 59.973 60.0 35.05 17.87 37.67 4.79 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 8.449397 GTTGATTGATGATCTAGATTGGTATGC 58.551 37.037 6.70 0.00 35.69 3.14
105 106 6.589454 GTTGTATGTTTTATTTTGGTGCTGC 58.411 36.000 0.00 0.00 0.00 5.25
216 217 4.453478 TGCTTGAGTGACAGAAGCATAAAG 59.547 41.667 14.80 0.00 37.41 1.85
230 231 2.548480 GCATAAAGACGGATAAGTGGGC 59.452 50.000 0.00 0.00 0.00 5.36
239 240 3.969250 ATAAGTGGGCCACGGCGTG 62.969 63.158 31.78 31.78 43.06 5.34
324 325 0.462581 TTGCGGATGCTTGCTAGAGG 60.463 55.000 0.00 0.00 43.34 3.69
395 396 6.770286 ATGCCTCTCCCTCTTATGAAATTA 57.230 37.500 0.00 0.00 0.00 1.40
471 472 3.199946 ACCCATCATTATTCCACACTCGT 59.800 43.478 0.00 0.00 0.00 4.18
572 573 4.511826 GCAAAGTTATCCTCTTCATACCCG 59.488 45.833 0.00 0.00 0.00 5.28
699 701 1.475280 TCCTTATGGGTTCGACACTCG 59.525 52.381 0.00 0.00 37.53 4.18
713 715 6.432607 TCGACACTCGATACTTATCACTTT 57.567 37.500 0.00 0.00 44.82 2.66
722 724 7.608153 TCGATACTTATCACTTTCACCTTTGA 58.392 34.615 0.00 0.00 32.98 2.69
740 742 9.158233 CACCTTTGAAAATTGCTATGATGATTT 57.842 29.630 0.00 0.00 0.00 2.17
752 754 3.438216 TGATGATTTCCTGCACTTGGA 57.562 42.857 0.00 0.00 0.00 3.53
776 778 9.905171 GGAGATTATTTATTTTTCAGCATCTCC 57.095 33.333 8.28 8.28 44.27 3.71
790 792 2.158784 GCATCTCCTTCTTCCTGCTGAT 60.159 50.000 0.00 0.00 0.00 2.90
825 827 4.158764 ACACTGTCGATCCAAAAACCAAAA 59.841 37.500 0.00 0.00 0.00 2.44
858 865 1.619654 TTTGCACAAGTCCCTGGATG 58.380 50.000 0.00 0.00 0.00 3.51
859 866 0.251297 TTGCACAAGTCCCTGGATGG 60.251 55.000 0.00 0.00 0.00 3.51
860 867 1.133181 TGCACAAGTCCCTGGATGGA 61.133 55.000 0.00 0.00 38.35 3.41
934 952 1.958902 GAGAGACAGGGCAGAGCAGG 61.959 65.000 0.00 0.00 0.00 4.85
936 954 4.792804 GACAGGGCAGAGCAGGGC 62.793 72.222 0.00 0.00 0.00 5.19
938 956 4.798344 CAGGGCAGAGCAGGGCAG 62.798 72.222 0.00 0.00 0.00 4.85
956 974 4.899239 GGCCGCCGGAGAGACATG 62.899 72.222 7.68 0.00 0.00 3.21
971 1054 6.239217 AGAGACATGCATATTCCAAGTGTA 57.761 37.500 0.00 0.00 0.00 2.90
1009 1092 3.903282 CCATTTCCATGCCGCCGG 61.903 66.667 0.00 0.00 0.00 6.13
1033 1122 1.587613 CGTCTGCTAGCTTCGCCTC 60.588 63.158 17.23 0.00 0.00 4.70
1083 1204 1.885887 TGTAATCAACCAGCAGCCAAC 59.114 47.619 0.00 0.00 0.00 3.77
1135 1263 0.472925 TTGCTCCCAGTCCCAGTACA 60.473 55.000 0.00 0.00 0.00 2.90
1136 1264 0.472925 TGCTCCCAGTCCCAGTACAA 60.473 55.000 0.00 0.00 0.00 2.41
1137 1265 0.250513 GCTCCCAGTCCCAGTACAAG 59.749 60.000 0.00 0.00 0.00 3.16
1138 1266 1.645710 CTCCCAGTCCCAGTACAAGT 58.354 55.000 0.00 0.00 0.00 3.16
1139 1267 2.816411 CTCCCAGTCCCAGTACAAGTA 58.184 52.381 0.00 0.00 0.00 2.24
1140 1268 2.496470 CTCCCAGTCCCAGTACAAGTAC 59.504 54.545 2.18 2.18 36.35 2.73
1141 1269 2.158279 TCCCAGTCCCAGTACAAGTACA 60.158 50.000 12.43 0.00 38.48 2.90
1414 1581 4.271816 CGCCCATCCGAGACCGAG 62.272 72.222 0.00 0.00 38.22 4.63
1415 1582 2.833582 GCCCATCCGAGACCGAGA 60.834 66.667 0.00 0.00 38.22 4.04
1416 1583 2.851071 GCCCATCCGAGACCGAGAG 61.851 68.421 0.00 0.00 38.22 3.20
1419 1586 2.902846 ATCCGAGACCGAGAGCCG 60.903 66.667 0.00 0.00 38.22 5.52
1677 1877 2.147150 GACAAGGAGAAGAAGCACCAC 58.853 52.381 0.00 0.00 0.00 4.16
2130 2402 3.243636 CCAACAAAGACAAGCAGAAGCAT 60.244 43.478 0.00 0.00 45.49 3.79
2147 2419 4.970392 TGCCGCTGCAAAGAAATG 57.030 50.000 0.00 0.00 46.66 2.32
2148 2420 2.339403 TGCCGCTGCAAAGAAATGA 58.661 47.368 0.00 0.00 46.66 2.57
2149 2421 0.241749 TGCCGCTGCAAAGAAATGAG 59.758 50.000 0.00 0.00 46.66 2.90
2150 2422 1.074872 GCCGCTGCAAAGAAATGAGC 61.075 55.000 0.00 0.00 37.47 4.26
2151 2423 2.633639 CGCTGCAAAGAAATGAGCG 58.366 52.632 0.00 0.00 45.60 5.03
2152 2424 1.400990 CGCTGCAAAGAAATGAGCGC 61.401 55.000 0.00 0.00 45.13 5.92
2153 2425 1.074872 GCTGCAAAGAAATGAGCGCC 61.075 55.000 2.29 0.00 0.00 6.53
2154 2426 0.795735 CTGCAAAGAAATGAGCGCCG 60.796 55.000 2.29 0.00 0.00 6.46
2155 2427 1.210155 GCAAAGAAATGAGCGCCGT 59.790 52.632 2.29 0.00 0.00 5.68
2156 2428 0.794605 GCAAAGAAATGAGCGCCGTC 60.795 55.000 2.29 0.00 0.00 4.79
2157 2429 0.519175 CAAAGAAATGAGCGCCGTCG 60.519 55.000 2.29 0.00 39.07 5.12
2158 2430 0.669318 AAAGAAATGAGCGCCGTCGA 60.669 50.000 2.29 0.00 38.10 4.20
2159 2431 1.352156 AAGAAATGAGCGCCGTCGAC 61.352 55.000 2.29 5.18 38.10 4.20
2160 2432 3.126722 GAAATGAGCGCCGTCGACG 62.127 63.158 30.33 30.33 38.10 5.12
2161 2433 3.620300 AAATGAGCGCCGTCGACGA 62.620 57.895 37.65 18.21 43.02 4.20
2162 2434 4.831307 ATGAGCGCCGTCGACGAC 62.831 66.667 37.65 26.87 43.02 4.34
2166 2438 4.831307 GCGCCGTCGACGACTCAT 62.831 66.667 37.65 0.00 43.02 2.90
2167 2439 2.648102 CGCCGTCGACGACTCATC 60.648 66.667 37.65 17.28 43.02 2.92
2168 2440 2.792599 GCCGTCGACGACTCATCT 59.207 61.111 37.65 0.00 43.02 2.90
2169 2441 1.583967 GCCGTCGACGACTCATCTG 60.584 63.158 37.65 19.51 43.02 2.90
2170 2442 1.978712 GCCGTCGACGACTCATCTGA 61.979 60.000 37.65 0.00 43.02 3.27
2171 2443 0.026933 CCGTCGACGACTCATCTGAG 59.973 60.000 37.65 13.95 43.02 3.35
2172 2444 0.587737 CGTCGACGACTCATCTGAGC 60.588 60.000 33.35 0.00 45.79 4.26
2173 2445 0.248296 GTCGACGACTCATCTGAGCC 60.248 60.000 20.52 0.00 45.79 4.70
2176 2448 4.700037 CGACTCATCTGAGCCGTC 57.300 61.111 7.62 0.00 45.79 4.79
2177 2449 1.064946 CGACTCATCTGAGCCGTCC 59.935 63.158 7.62 0.00 45.79 4.79
2178 2450 1.657751 CGACTCATCTGAGCCGTCCA 61.658 60.000 7.62 0.00 45.79 4.02
2179 2451 0.102120 GACTCATCTGAGCCGTCCAG 59.898 60.000 7.11 0.00 45.79 3.86
2180 2452 0.613292 ACTCATCTGAGCCGTCCAGT 60.613 55.000 7.11 0.00 45.79 4.00
2181 2453 0.534412 CTCATCTGAGCCGTCCAGTT 59.466 55.000 0.00 0.00 35.13 3.16
2182 2454 0.247460 TCATCTGAGCCGTCCAGTTG 59.753 55.000 0.00 0.00 34.39 3.16
2183 2455 0.036952 CATCTGAGCCGTCCAGTTGT 60.037 55.000 0.00 0.00 33.57 3.32
2184 2456 1.204704 CATCTGAGCCGTCCAGTTGTA 59.795 52.381 0.00 0.00 33.57 2.41
2185 2457 1.334160 TCTGAGCCGTCCAGTTGTAA 58.666 50.000 0.00 0.00 33.57 2.41
2186 2458 1.000506 TCTGAGCCGTCCAGTTGTAAC 59.999 52.381 0.00 0.00 33.57 2.50
2187 2459 1.000955 CTGAGCCGTCCAGTTGTAACT 59.999 52.381 0.00 0.00 40.60 2.24
2188 2460 2.230508 CTGAGCCGTCCAGTTGTAACTA 59.769 50.000 0.00 0.00 37.08 2.24
2189 2461 2.829720 TGAGCCGTCCAGTTGTAACTAT 59.170 45.455 0.00 0.00 37.08 2.12
2190 2462 4.018490 TGAGCCGTCCAGTTGTAACTATA 58.982 43.478 0.00 0.00 37.08 1.31
2191 2463 4.647853 TGAGCCGTCCAGTTGTAACTATAT 59.352 41.667 0.00 0.00 37.08 0.86
2192 2464 5.128171 TGAGCCGTCCAGTTGTAACTATATT 59.872 40.000 0.00 0.00 37.08 1.28
2193 2465 6.321945 TGAGCCGTCCAGTTGTAACTATATTA 59.678 38.462 0.00 0.00 37.08 0.98
2194 2466 7.014905 TGAGCCGTCCAGTTGTAACTATATTAT 59.985 37.037 0.00 0.00 37.08 1.28
2195 2467 7.152645 AGCCGTCCAGTTGTAACTATATTATG 58.847 38.462 0.00 0.00 37.08 1.90
2196 2468 6.128634 GCCGTCCAGTTGTAACTATATTATGC 60.129 42.308 0.00 0.00 37.08 3.14
2197 2469 6.926826 CCGTCCAGTTGTAACTATATTATGCA 59.073 38.462 0.00 0.00 37.08 3.96
2198 2470 7.439955 CCGTCCAGTTGTAACTATATTATGCAA 59.560 37.037 0.00 0.00 37.08 4.08
2199 2471 8.822855 CGTCCAGTTGTAACTATATTATGCAAA 58.177 33.333 0.00 0.00 37.08 3.68
2270 2544 5.111293 CCACAATTGTTATGATTCCCAAGC 58.889 41.667 8.77 0.00 0.00 4.01
2283 2557 2.902608 TCCCAAGCTACTTTCTCCAGA 58.097 47.619 0.00 0.00 0.00 3.86
2293 2567 7.462590 AGCTACTTTCTCCAGAAAAAGGTATT 58.537 34.615 11.39 0.00 42.72 1.89
2302 2576 6.977213 TCCAGAAAAAGGTATTGCAGTTTAC 58.023 36.000 0.00 0.00 0.00 2.01
2378 2652 8.632679 GCCATGAGATTGAAATTATTTCTACCA 58.367 33.333 17.16 9.92 40.32 3.25
2396 2670 9.589461 TTTCTACCAGAAATAATAAACCCAACA 57.411 29.630 0.00 0.00 39.13 3.33
2431 2707 1.142262 CCCTGGGAGGTTAATTACGGG 59.858 57.143 7.01 0.00 31.93 5.28
2436 2712 5.294734 TGGGAGGTTAATTACGGGTAATC 57.705 43.478 4.66 0.00 34.90 1.75
2473 2755 3.731652 AAGCTTGCACACAATTAAGCA 57.268 38.095 0.00 1.13 45.90 3.91
2474 2756 3.731652 AGCTTGCACACAATTAAGCAA 57.268 38.095 10.21 8.03 45.90 3.91
2475 2757 4.057406 AGCTTGCACACAATTAAGCAAA 57.943 36.364 10.21 0.00 45.18 3.68
2552 2834 4.380023 GCATATGATCGAGTAGAGTGGGTC 60.380 50.000 6.97 0.00 0.00 4.46
2609 2891 8.677148 TTAATGCTAACTGGGTAAAGATGATC 57.323 34.615 0.00 0.00 0.00 2.92
2611 2893 5.428253 TGCTAACTGGGTAAAGATGATCAC 58.572 41.667 0.00 0.00 0.00 3.06
2617 2899 4.647611 TGGGTAAAGATGATCACGTTGTT 58.352 39.130 0.00 0.00 0.00 2.83
2660 2942 2.035576 AGTCAGGTACAACTCAACGGAC 59.964 50.000 0.00 0.00 0.00 4.79
2694 2976 6.697641 TTAAACCAACTAGAGGTCTCCATT 57.302 37.500 11.15 5.54 38.76 3.16
2782 3069 1.301401 CCGAACAAGAAGGCGACCA 60.301 57.895 0.00 0.00 0.00 4.02
2788 3075 2.504274 AAGAAGGCGACCACGTGGA 61.504 57.895 40.21 0.00 41.98 4.02
2856 3143 2.097250 GCAAATGAGTCGCTTGTTTTGC 60.097 45.455 0.00 0.00 41.19 3.68
2857 3144 2.422276 AATGAGTCGCTTGTTTTGCC 57.578 45.000 0.00 0.00 0.00 4.52
3045 3353 1.486726 GGTACCTGGGTCTTCCATCTG 59.513 57.143 4.06 0.00 46.01 2.90
3068 3376 6.919721 TGACTTTGGGTATTGATAAAAGTGC 58.080 36.000 3.99 0.00 40.25 4.40
3072 3382 3.692101 TGGGTATTGATAAAAGTGCCGTG 59.308 43.478 0.00 0.00 0.00 4.94
3138 3448 5.664908 TGGAAGGAGAGATGCTTATCTTCTT 59.335 40.000 15.63 15.63 42.83 2.52
3143 3453 5.304101 GGAGAGATGCTTATCTTCTTCTGGA 59.696 44.000 0.00 0.00 30.26 3.86
3144 3454 6.409524 AGAGATGCTTATCTTCTTCTGGAG 57.590 41.667 0.00 0.00 30.26 3.86
3145 3455 5.305128 AGAGATGCTTATCTTCTTCTGGAGG 59.695 44.000 0.00 0.00 30.26 4.30
3146 3456 4.968080 AGATGCTTATCTTCTTCTGGAGGT 59.032 41.667 0.00 0.00 0.00 3.85
3147 3457 6.139671 AGATGCTTATCTTCTTCTGGAGGTA 58.860 40.000 0.00 0.00 0.00 3.08
3148 3458 6.613271 AGATGCTTATCTTCTTCTGGAGGTAA 59.387 38.462 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 6.615418 GCAGCACCAAAATAAAACATACAACG 60.615 38.462 0.00 0.00 0.00 4.10
154 155 3.700538 ACCATGGACATATTGCAACACT 58.299 40.909 21.47 0.00 0.00 3.55
216 217 1.520787 CGTGGCCCACTTATCCGTC 60.521 63.158 12.94 0.00 31.34 4.79
239 240 3.953542 ATCAAGTCCCCTTTATCCCAC 57.046 47.619 0.00 0.00 0.00 4.61
264 265 8.493787 AAGGTAAAACCCAACCATAACATTAA 57.506 30.769 0.00 0.00 39.75 1.40
270 271 8.903059 ATCATTAAGGTAAAACCCAACCATAA 57.097 30.769 0.00 0.00 39.75 1.90
324 325 6.656270 TGGATCATATGCACTTATGATTGGAC 59.344 38.462 19.14 12.60 45.13 4.02
395 396 5.416271 ACAAGACCGGTAATCACTATTGT 57.584 39.130 7.34 0.00 0.00 2.71
572 573 7.067728 AGAAACGAGAAATAAAACTACGTTGC 58.932 34.615 0.00 0.00 41.09 4.17
677 678 1.831736 AGTGTCGAACCCATAAGGAGG 59.168 52.381 0.00 0.00 39.89 4.30
713 715 7.465353 TCATCATAGCAATTTTCAAAGGTGA 57.535 32.000 0.00 0.00 0.00 4.02
722 724 6.759827 GTGCAGGAAATCATCATAGCAATTTT 59.240 34.615 0.00 0.00 31.30 1.82
732 734 3.009363 TCTCCAAGTGCAGGAAATCATCA 59.991 43.478 0.00 0.00 34.08 3.07
740 742 8.593945 AAAATAAATAATCTCCAAGTGCAGGA 57.406 30.769 0.00 0.00 0.00 3.86
776 778 2.996249 TGCCTATCAGCAGGAAGAAG 57.004 50.000 0.00 0.00 38.00 2.85
858 865 1.216990 AGGGAATCCATGTCCTGTCC 58.783 55.000 0.09 0.00 35.33 4.02
859 866 2.422093 GGAAGGGAATCCATGTCCTGTC 60.422 54.545 0.09 0.00 39.42 3.51
860 867 1.566231 GGAAGGGAATCCATGTCCTGT 59.434 52.381 0.09 0.00 39.42 4.00
861 868 1.849039 AGGAAGGGAATCCATGTCCTG 59.151 52.381 14.49 0.00 42.27 3.86
862 869 2.243221 CAAGGAAGGGAATCCATGTCCT 59.757 50.000 10.72 10.72 42.27 3.85
941 959 2.087462 TATGCATGTCTCTCCGGCGG 62.087 60.000 22.51 22.51 0.00 6.13
942 960 0.037882 ATATGCATGTCTCTCCGGCG 60.038 55.000 10.16 0.00 0.00 6.46
943 961 2.072298 GAATATGCATGTCTCTCCGGC 58.928 52.381 10.16 0.00 0.00 6.13
944 962 2.037641 TGGAATATGCATGTCTCTCCGG 59.962 50.000 10.16 0.00 0.00 5.14
945 963 3.391506 TGGAATATGCATGTCTCTCCG 57.608 47.619 10.16 0.00 0.00 4.63
946 964 4.514441 CACTTGGAATATGCATGTCTCTCC 59.486 45.833 10.16 7.57 0.00 3.71
947 965 5.121811 ACACTTGGAATATGCATGTCTCTC 58.878 41.667 10.16 0.00 0.00 3.20
948 966 5.108187 ACACTTGGAATATGCATGTCTCT 57.892 39.130 10.16 0.00 0.00 3.10
949 967 6.540189 ACTTACACTTGGAATATGCATGTCTC 59.460 38.462 10.16 2.69 0.00 3.36
950 968 6.317140 CACTTACACTTGGAATATGCATGTCT 59.683 38.462 10.16 0.00 0.00 3.41
951 969 6.489675 CACTTACACTTGGAATATGCATGTC 58.510 40.000 10.16 6.56 0.00 3.06
952 970 5.163622 GCACTTACACTTGGAATATGCATGT 60.164 40.000 10.16 0.00 0.00 3.21
953 971 5.163632 TGCACTTACACTTGGAATATGCATG 60.164 40.000 10.16 0.00 35.74 4.06
954 972 4.949238 TGCACTTACACTTGGAATATGCAT 59.051 37.500 3.79 3.79 35.74 3.96
955 973 4.155826 GTGCACTTACACTTGGAATATGCA 59.844 41.667 10.32 8.51 38.17 3.96
956 974 4.662145 GTGCACTTACACTTGGAATATGC 58.338 43.478 10.32 4.35 37.58 3.14
957 975 4.727734 GCGTGCACTTACACTTGGAATATG 60.728 45.833 16.19 0.00 38.45 1.78
1009 1092 1.749153 GAAGCTAGCAGACGATCGAC 58.251 55.000 24.34 16.66 0.00 4.20
1043 1132 2.813908 GCGACGGCGGTCTCAATT 60.814 61.111 15.06 0.00 41.16 2.32
1067 1187 0.467844 TGTGTTGGCTGCTGGTTGAT 60.468 50.000 0.00 0.00 0.00 2.57
1083 1204 2.100797 CGGCGATGGCAATGTGTG 59.899 61.111 0.00 0.00 42.47 3.82
1109 1230 0.957888 GGACTGGGAGCAAGCTGAAC 60.958 60.000 0.00 0.00 0.00 3.18
1135 1263 4.062677 TGGCTTTGAACGTACTGTACTT 57.937 40.909 15.35 3.77 0.00 2.24
1136 1264 3.738830 TGGCTTTGAACGTACTGTACT 57.261 42.857 15.35 0.00 0.00 2.73
1137 1265 3.124636 CCATGGCTTTGAACGTACTGTAC 59.875 47.826 7.90 7.90 0.00 2.90
1138 1266 3.331150 CCATGGCTTTGAACGTACTGTA 58.669 45.455 0.00 0.00 0.00 2.74
1139 1267 2.151202 CCATGGCTTTGAACGTACTGT 58.849 47.619 0.00 0.00 0.00 3.55
1140 1268 1.135689 GCCATGGCTTTGAACGTACTG 60.136 52.381 29.98 0.00 38.26 2.74
1141 1269 1.165270 GCCATGGCTTTGAACGTACT 58.835 50.000 29.98 0.00 38.26 2.73
1302 1451 3.637273 GGAGGAGTGGGTTGGCGT 61.637 66.667 0.00 0.00 0.00 5.68
1329 1496 4.767255 GAGGACGCCTGGCTGTGG 62.767 72.222 17.92 3.21 31.76 4.17
1412 1579 3.842925 TTGGTGTTGGGCGGCTCTC 62.843 63.158 9.56 0.00 0.00 3.20
1413 1580 3.884774 TTGGTGTTGGGCGGCTCT 61.885 61.111 9.56 0.00 0.00 4.09
1414 1581 3.670377 GTTGGTGTTGGGCGGCTC 61.670 66.667 9.56 0.00 0.00 4.70
1415 1582 4.204028 AGTTGGTGTTGGGCGGCT 62.204 61.111 9.56 0.00 0.00 5.52
1416 1583 3.670377 GAGTTGGTGTTGGGCGGC 61.670 66.667 0.00 0.00 0.00 6.53
1419 1586 1.739667 GTTGGAGTTGGTGTTGGGC 59.260 57.895 0.00 0.00 0.00 5.36
1645 1842 0.823356 TCCTTGTCCTTGTGCTTGCC 60.823 55.000 0.00 0.00 0.00 4.52
1737 1964 3.058160 CCCTTGTGCTTGCCCTCG 61.058 66.667 0.00 0.00 0.00 4.63
1973 2242 2.437359 CCTGCTTCTTCTGCCCGG 60.437 66.667 0.00 0.00 0.00 5.73
2136 2408 1.209898 CGGCGCTCATTTCTTTGCA 59.790 52.632 7.64 0.00 0.00 4.08
2138 2410 0.519175 CGACGGCGCTCATTTCTTTG 60.519 55.000 6.90 0.00 0.00 2.77
2139 2411 0.669318 TCGACGGCGCTCATTTCTTT 60.669 50.000 5.31 0.00 37.46 2.52
2140 2412 1.080093 TCGACGGCGCTCATTTCTT 60.080 52.632 5.31 0.00 37.46 2.52
2141 2413 1.805945 GTCGACGGCGCTCATTTCT 60.806 57.895 5.31 0.00 37.46 2.52
2142 2414 2.695646 GTCGACGGCGCTCATTTC 59.304 61.111 5.31 0.00 37.46 2.17
2143 2415 3.179265 CGTCGACGGCGCTCATTT 61.179 61.111 29.70 0.00 37.46 2.32
2144 2416 4.111016 TCGTCGACGGCGCTCATT 62.111 61.111 35.05 0.00 40.29 2.57
2145 2417 4.831307 GTCGTCGACGGCGCTCAT 62.831 66.667 35.05 0.00 40.29 2.90
2151 2423 1.583967 CAGATGAGTCGTCGACGGC 60.584 63.158 33.71 33.71 45.56 5.68
2152 2424 0.026933 CTCAGATGAGTCGTCGACGG 59.973 60.000 35.05 17.87 37.67 4.79
2153 2425 0.587737 GCTCAGATGAGTCGTCGACG 60.588 60.000 31.30 31.30 43.85 5.12
2154 2426 0.248296 GGCTCAGATGAGTCGTCGAC 60.248 60.000 17.70 17.70 43.85 4.20
2155 2427 2.099143 GGCTCAGATGAGTCGTCGA 58.901 57.895 11.31 6.70 43.85 4.20
2156 2428 4.700037 GGCTCAGATGAGTCGTCG 57.300 61.111 11.31 2.77 43.85 5.12
2160 2432 0.102120 CTGGACGGCTCAGATGAGTC 59.898 60.000 11.31 8.00 43.85 3.36
2161 2433 0.613292 ACTGGACGGCTCAGATGAGT 60.613 55.000 12.96 0.00 43.85 3.41
2162 2434 0.534412 AACTGGACGGCTCAGATGAG 59.466 55.000 12.96 5.45 44.75 2.90
2163 2435 0.247460 CAACTGGACGGCTCAGATGA 59.753 55.000 12.96 0.00 37.25 2.92
2164 2436 0.036952 ACAACTGGACGGCTCAGATG 60.037 55.000 12.96 13.04 39.76 2.90
2165 2437 1.557099 TACAACTGGACGGCTCAGAT 58.443 50.000 12.96 0.00 36.22 2.90
2166 2438 1.000506 GTTACAACTGGACGGCTCAGA 59.999 52.381 12.96 0.00 36.22 3.27
2167 2439 1.000955 AGTTACAACTGGACGGCTCAG 59.999 52.381 5.32 5.32 37.98 3.35
2168 2440 1.045407 AGTTACAACTGGACGGCTCA 58.955 50.000 0.00 0.00 37.98 4.26
2169 2441 3.521947 ATAGTTACAACTGGACGGCTC 57.478 47.619 4.86 0.00 40.07 4.70
2170 2442 5.609533 AATATAGTTACAACTGGACGGCT 57.390 39.130 4.86 0.00 40.07 5.52
2171 2443 6.128634 GCATAATATAGTTACAACTGGACGGC 60.129 42.308 4.86 0.00 40.07 5.68
2172 2444 6.926826 TGCATAATATAGTTACAACTGGACGG 59.073 38.462 4.86 0.00 40.07 4.79
2173 2445 7.940178 TGCATAATATAGTTACAACTGGACG 57.060 36.000 4.86 0.00 40.07 4.79
2192 2464 9.394767 TCTGTTAGAATTGCTCTTATTTGCATA 57.605 29.630 0.00 0.00 39.07 3.14
2193 2465 8.284945 TCTGTTAGAATTGCTCTTATTTGCAT 57.715 30.769 0.00 0.00 39.07 3.96
2194 2466 7.686438 TCTGTTAGAATTGCTCTTATTTGCA 57.314 32.000 0.00 0.00 35.41 4.08
2195 2467 8.400947 TGATCTGTTAGAATTGCTCTTATTTGC 58.599 33.333 0.00 0.00 35.41 3.68
2198 2470 8.566260 GCATGATCTGTTAGAATTGCTCTTATT 58.434 33.333 0.00 0.00 35.41 1.40
2199 2471 7.174599 GGCATGATCTGTTAGAATTGCTCTTAT 59.825 37.037 0.00 0.00 35.41 1.73
2200 2472 6.484643 GGCATGATCTGTTAGAATTGCTCTTA 59.515 38.462 0.00 0.00 35.41 2.10
2201 2473 5.298777 GGCATGATCTGTTAGAATTGCTCTT 59.701 40.000 0.00 0.00 35.41 2.85
2202 2474 4.820716 GGCATGATCTGTTAGAATTGCTCT 59.179 41.667 0.00 0.00 38.28 4.09
2203 2475 4.023365 GGGCATGATCTGTTAGAATTGCTC 60.023 45.833 0.00 0.00 31.96 4.26
2204 2476 3.887716 GGGCATGATCTGTTAGAATTGCT 59.112 43.478 0.00 0.00 31.96 3.91
2205 2477 3.005155 GGGGCATGATCTGTTAGAATTGC 59.995 47.826 0.00 0.00 31.10 3.56
2206 2478 4.209538 TGGGGCATGATCTGTTAGAATTG 58.790 43.478 0.00 0.00 0.00 2.32
2207 2479 4.524802 TGGGGCATGATCTGTTAGAATT 57.475 40.909 0.00 0.00 0.00 2.17
2208 2480 4.467769 CTTGGGGCATGATCTGTTAGAAT 58.532 43.478 0.00 0.00 0.00 2.40
2209 2481 3.371917 CCTTGGGGCATGATCTGTTAGAA 60.372 47.826 0.00 0.00 0.00 2.10
2210 2482 2.173356 CCTTGGGGCATGATCTGTTAGA 59.827 50.000 0.00 0.00 0.00 2.10
2211 2483 2.579873 CCTTGGGGCATGATCTGTTAG 58.420 52.381 0.00 0.00 0.00 2.34
2212 2484 2.734755 CCTTGGGGCATGATCTGTTA 57.265 50.000 0.00 0.00 0.00 2.41
2213 2485 3.602104 CCTTGGGGCATGATCTGTT 57.398 52.632 0.00 0.00 0.00 3.16
2233 2505 2.166907 TTGTGGTGTGGTTCCCAATT 57.833 45.000 0.00 0.00 34.18 2.32
2234 2506 2.368221 CAATTGTGGTGTGGTTCCCAAT 59.632 45.455 0.00 0.00 34.18 3.16
2235 2507 1.759445 CAATTGTGGTGTGGTTCCCAA 59.241 47.619 0.00 0.00 34.18 4.12
2236 2508 1.342474 ACAATTGTGGTGTGGTTCCCA 60.342 47.619 11.07 0.00 0.00 4.37
2237 2509 1.408969 ACAATTGTGGTGTGGTTCCC 58.591 50.000 11.07 0.00 0.00 3.97
2243 2515 5.047448 TGGGAATCATAACAATTGTGGTGTG 60.047 40.000 12.82 6.27 35.00 3.82
2270 2544 7.174946 TGCAATACCTTTTTCTGGAGAAAGTAG 59.825 37.037 11.04 4.73 43.90 2.57
2283 2557 5.299782 TCGGTGTAAACTGCAATACCTTTTT 59.700 36.000 1.25 0.00 0.00 1.94
2293 2567 2.027561 AGGCTTATCGGTGTAAACTGCA 60.028 45.455 0.00 0.00 0.00 4.41
2302 2576 3.141398 ACATTGCATAGGCTTATCGGTG 58.859 45.455 0.00 0.00 41.91 4.94
2378 2652 7.309194 GCACTCTGTGTTGGGTTTATTATTTCT 60.309 37.037 0.00 0.00 35.75 2.52
2389 2663 1.682854 CAAATGCACTCTGTGTTGGGT 59.317 47.619 0.00 0.00 35.75 4.51
2396 2670 1.546323 CCAGGGACAAATGCACTCTGT 60.546 52.381 0.00 0.00 0.00 3.41
2480 2762 2.038820 CCACCCATCCTTGCATGTTTTT 59.961 45.455 0.00 0.00 0.00 1.94
2552 2834 6.624642 GCTTCAAAAGAATAGCTTCCAGGAAG 60.625 42.308 23.49 23.49 42.03 3.46
2609 2891 5.150683 TCAACTGAAGAAACAAACAACGTG 58.849 37.500 0.00 0.00 0.00 4.49
2611 2893 6.869421 ATTCAACTGAAGAAACAAACAACG 57.131 33.333 0.00 0.00 37.48 4.10
2617 2899 8.735315 TGACTTTGTATTCAACTGAAGAAACAA 58.265 29.630 11.04 11.04 37.48 2.83
2660 2942 7.202016 TCTAGTTGGTTTAAATGCTTCTGTG 57.798 36.000 0.00 0.00 0.00 3.66
2782 3069 2.350498 CGACAAACTTTGACTTCCACGT 59.650 45.455 8.55 0.00 0.00 4.49
2788 3075 3.376859 TGCATCACGACAAACTTTGACTT 59.623 39.130 8.55 0.00 0.00 3.01
2838 3125 1.334960 CGGCAAAACAAGCGACTCATT 60.335 47.619 0.00 0.00 0.00 2.57
2856 3143 4.711949 AGCAGCACTGGCCTTCGG 62.712 66.667 3.32 0.00 42.56 4.30
2857 3144 2.670934 AAGCAGCACTGGCCTTCG 60.671 61.111 3.32 0.00 42.56 3.79
2866 3162 5.179929 AAAATGGATTTTAAGCAAGCAGCAC 59.820 36.000 0.00 0.00 41.01 4.40
2967 3275 1.586422 CATACCTCGGCCTTCACATG 58.414 55.000 0.00 0.00 0.00 3.21
3045 3353 6.330278 GGCACTTTTATCAATACCCAAAGTC 58.670 40.000 0.00 0.00 35.89 3.01
3084 3394 8.704234 CATTAATCTCTAAACTAGGCGATCAAC 58.296 37.037 0.00 0.00 0.00 3.18
3092 3402 8.207350 TCCATCCCATTAATCTCTAAACTAGG 57.793 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.