Multiple sequence alignment - TraesCS3A01G175500

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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 TraesCS3A01G175500 chr3A 100.000 2345 0 0 1 2345 195455498 195453154 0.000000e+00 4331.0
1 TraesCS3A01G175500 chr3A 89.141 617 56 8 914 1523 743831627 743831015 0.000000e+00 758.0
2 TraesCS3A01G175500 chr3A 89.271 494 42 8 45 531 38273081 38273570 1.990000e-170 608.0
3 TraesCS3A01G175500 chr3A 100.000 34 0 0 2112 2145 265542789 265542756 1.950000e-06 63.9
4 TraesCS3A01G175500 chr3B 94.156 1694 71 8 1 1685 239901144 239899470 0.000000e+00 2555.0
5 TraesCS3A01G175500 chr3B 88.979 617 57 8 914 1525 34707161 34707771 0.000000e+00 752.0
6 TraesCS3A01G175500 chr3B 87.045 494 53 8 46 530 490890715 490891206 4.410000e-152 547.0
7 TraesCS3A01G175500 chr3B 86.942 291 12 9 1671 1946 239899450 239899171 1.050000e-78 303.0
8 TraesCS3A01G175500 chr3B 100.000 34 0 0 2112 2145 284678925 284678892 1.950000e-06 63.9
9 TraesCS3A01G175500 chr3B 82.667 75 4 6 2112 2177 2190864 2190938 9.050000e-05 58.4
10 TraesCS3A01G175500 chr3D 92.177 1828 68 27 329 2121 163118481 163116694 0.000000e+00 2514.0
11 TraesCS3A01G175500 chr3D 89.406 623 57 7 908 1525 465071228 465071846 0.000000e+00 776.0
12 TraesCS3A01G175500 chr3D 96.324 136 5 0 2210 2345 364520567 364520432 8.430000e-55 224.0
13 TraesCS3A01G175500 chr3D 100.000 34 0 0 2112 2145 206978514 206978547 1.950000e-06 63.9
14 TraesCS3A01G175500 chr2B 88.817 617 60 7 914 1525 276492582 276491970 0.000000e+00 749.0
15 TraesCS3A01G175500 chr2A 88.622 624 58 10 908 1523 479846960 479847578 0.000000e+00 747.0
16 TraesCS3A01G175500 chr2A 96.403 139 4 1 2208 2345 224904812 224904674 6.520000e-56 228.0
17 TraesCS3A01G175500 chr2A 94.737 38 2 0 2112 2149 66004853 66004816 2.520000e-05 60.2
18 TraesCS3A01G175500 chr7B 88.655 617 61 7 914 1525 519228804 519228192 0.000000e+00 743.0
19 TraesCS3A01G175500 chr7B 88.816 456 46 5 43 496 612313106 612313558 2.630000e-154 555.0
20 TraesCS3A01G175500 chr7B 88.300 453 49 4 45 496 709247261 709246812 7.370000e-150 540.0
21 TraesCS3A01G175500 chr7B 96.324 136 4 1 2210 2345 744749739 744749605 3.030000e-54 222.0
22 TraesCS3A01G175500 chr5B 88.511 618 58 10 914 1523 248665018 248664406 0.000000e+00 736.0
23 TraesCS3A01G175500 chr5B 89.474 456 40 8 44 496 633310088 633310538 9.400000e-159 569.0
24 TraesCS3A01G175500 chr5B 87.045 494 54 7 44 531 622971070 622970581 1.230000e-152 549.0
25 TraesCS3A01G175500 chr5B 100.000 34 0 0 2112 2145 307412638 307412605 1.950000e-06 63.9
26 TraesCS3A01G175500 chr7A 88.816 456 45 6 43 496 648144750 648145201 2.630000e-154 555.0
27 TraesCS3A01G175500 chr7A 88.742 453 44 5 45 496 498941094 498941540 4.410000e-152 547.0
28 TraesCS3A01G175500 chr7A 97.080 137 3 1 2209 2345 45932744 45932879 1.810000e-56 230.0
29 TraesCS3A01G175500 chr7A 97.059 136 4 0 2210 2345 657727771 657727906 1.810000e-56 230.0
30 TraesCS3A01G175500 chr1A 96.479 142 5 0 2204 2345 570361837 570361978 3.900000e-58 235.0
31 TraesCS3A01G175500 chr1A 96.324 136 4 1 2210 2345 565281040 565280906 3.030000e-54 222.0
32 TraesCS3A01G175500 chr1A 95.620 137 5 1 2210 2345 547924599 547924463 3.920000e-53 219.0
33 TraesCS3A01G175500 chr1B 97.059 136 4 0 2210 2345 582551253 582551388 1.810000e-56 230.0
34 TraesCS3A01G175500 chr6A 100.000 34 0 0 2112 2145 35578020 35578053 1.950000e-06 63.9
35 TraesCS3A01G175500 chr5D 100.000 34 0 0 2112 2145 40719352 40719385 1.950000e-06 63.9
36 TraesCS3A01G175500 chr1D 97.297 37 0 1 2110 2145 299928208 299928244 7.000000e-06 62.1


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 TraesCS3A01G175500 chr3A 195453154 195455498 2344 True 4331 4331 100.000 1 2345 1 chr3A.!!$R1 2344
1 TraesCS3A01G175500 chr3A 743831015 743831627 612 True 758 758 89.141 914 1523 1 chr3A.!!$R3 609
2 TraesCS3A01G175500 chr3B 239899171 239901144 1973 True 1429 2555 90.549 1 1946 2 chr3B.!!$R2 1945
3 TraesCS3A01G175500 chr3B 34707161 34707771 610 False 752 752 88.979 914 1525 1 chr3B.!!$F2 611
4 TraesCS3A01G175500 chr3D 163116694 163118481 1787 True 2514 2514 92.177 329 2121 1 chr3D.!!$R1 1792
5 TraesCS3A01G175500 chr3D 465071228 465071846 618 False 776 776 89.406 908 1525 1 chr3D.!!$F2 617
6 TraesCS3A01G175500 chr2B 276491970 276492582 612 True 749 749 88.817 914 1525 1 chr2B.!!$R1 611
7 TraesCS3A01G175500 chr2A 479846960 479847578 618 False 747 747 88.622 908 1523 1 chr2A.!!$F1 615
8 TraesCS3A01G175500 chr7B 519228192 519228804 612 True 743 743 88.655 914 1525 1 chr7B.!!$R1 611
9 TraesCS3A01G175500 chr5B 248664406 248665018 612 True 736 736 88.511 914 1523 1 chr5B.!!$R1 609

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
803 816 1.251527 CGCTCCCTGTCTACACCAGT 61.252 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1655 0.111061 ATCACAGGCAAGCAAGTCCA 59.889 50.0 0.0 0.0 0.0 4.02 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
25 26 8.042944 CAATATTTTGCCTAGCCAACATTTTT 57.957 30.769 0.00 0.00 0.00 1.94
280 281 5.711506 TGTTGCCTTGATGTTCTAATGATGT 59.288 36.000 0.00 0.00 0.00 3.06
300 301 2.574006 TGCAGCTGATCTGGAAGTTT 57.426 45.000 20.43 0.00 40.35 2.66
314 315 9.178758 GATCTGGAAGTTTATAAACCTGAACAT 57.821 33.333 21.92 9.97 39.71 2.71
338 339 1.987080 AAGTAGGAAGGGAATGGCCT 58.013 50.000 3.32 0.00 36.66 5.19
372 373 9.387257 GGCTAAAAACTGCCTAGTAGTTAATTA 57.613 33.333 9.31 10.33 45.26 1.40
500 507 6.127507 GGGTCCGAATAACAGTTAACTACTCT 60.128 42.308 8.04 0.00 33.85 3.24
516 529 4.699257 ACTACTCTACAGTTAACTGACCGG 59.301 45.833 36.14 24.34 46.59 5.28
525 538 4.630069 CAGTTAACTGACCGGTATTTGGAG 59.370 45.833 28.17 0.00 46.59 3.86
618 631 6.308766 GCTATTGTGTATGAGCAAAAAGGTTG 59.691 38.462 0.00 0.00 34.96 3.77
731 744 5.600696 CAACTTTACTTGGATTTTGCACCT 58.399 37.500 0.00 0.00 0.00 4.00
783 796 4.277257 TCGTCAATTTATCATGCACTGC 57.723 40.909 0.00 0.00 0.00 4.40
797 810 2.352032 ACTGCCGCTCCCTGTCTAC 61.352 63.158 0.00 0.00 0.00 2.59
803 816 1.251527 CGCTCCCTGTCTACACCAGT 61.252 60.000 0.00 0.00 0.00 4.00
869 882 4.588951 ACTGTATTCCTCAGTGTGTTCTGA 59.411 41.667 0.00 0.00 43.32 3.27
915 928 8.113173 ACCGCTGATAATTTAAAACTGGTTTA 57.887 30.769 0.00 0.00 31.63 2.01
1092 1107 6.649141 TGCATTTCTCGAACAAGTATGTAACT 59.351 34.615 0.00 0.00 39.40 2.24
1221 1236 0.040204 AGATTGGGAAGTTGCTGGGG 59.960 55.000 0.00 0.00 0.00 4.96
1402 1417 4.156190 CAGTCTTGAGCTGCATTTCTGATT 59.844 41.667 1.02 0.00 0.00 2.57
1442 1461 5.879223 ACTTTTGTGTTCATGAATTTGGCAA 59.121 32.000 12.12 9.58 0.00 4.52
1444 1463 5.926214 TTGTGTTCATGAATTTGGCAATG 57.074 34.783 12.12 0.00 0.00 2.82
1545 1569 8.337532 GCACTTTTTATTTGAAACAAATCTGCT 58.662 29.630 12.02 0.00 0.00 4.24
1569 1593 3.871485 AGCACTTGATGACTTGAGGATC 58.129 45.455 0.00 0.00 0.00 3.36
1602 1626 2.699954 TGTTTCTCCTCTCCGAAATGC 58.300 47.619 0.00 0.00 32.43 3.56
1631 1655 6.069731 GGAGATTATTGGGCTGGAGATATTCT 60.070 42.308 0.00 0.00 0.00 2.40
1639 1663 3.137533 GCTGGAGATATTCTGGACTTGC 58.862 50.000 0.00 0.00 0.00 4.01
1661 1685 3.235157 TGCCTGTGATGCTAAATTTGC 57.765 42.857 0.00 3.44 0.00 3.68
1677 1701 8.642020 GCTAAATTTGCTATTCAAGACTGTTTG 58.358 33.333 0.00 0.00 35.84 2.93
1896 1969 6.869695 TGCTAAACCTCAAGATCGTATTGTA 58.130 36.000 0.00 0.00 0.00 2.41
1899 1972 9.472361 GCTAAACCTCAAGATCGTATTGTATTA 57.528 33.333 0.00 0.00 0.00 0.98
1975 2048 8.119226 CGTTTCTTTTAGGAGATGCTAATCTTG 58.881 37.037 0.00 0.00 43.48 3.02
1983 2056 5.902431 AGGAGATGCTAATCTTGAAGGTAGT 59.098 40.000 0.00 0.00 43.48 2.73
1984 2057 7.069986 AGGAGATGCTAATCTTGAAGGTAGTA 58.930 38.462 0.00 0.00 43.48 1.82
2042 2122 7.337942 CCTGGCAAGAAACAGTATTAAGAAGAT 59.662 37.037 0.00 0.00 32.90 2.40
2071 2151 2.355756 GTGTGACTTTGTGTGCATGACT 59.644 45.455 0.00 0.00 0.00 3.41
2072 2152 2.613595 TGTGACTTTGTGTGCATGACTC 59.386 45.455 0.00 0.00 0.00 3.36
2101 2181 6.295041 TCCCCCTCCACATCTATATATAGG 57.705 45.833 17.81 7.09 0.00 2.57
2121 2201 2.224719 GGAGTATACTGCTCCCTCCGTA 60.225 54.545 16.47 0.00 45.05 4.02
2122 2202 3.484407 GAGTATACTGCTCCCTCCGTAA 58.516 50.000 10.90 0.00 0.00 3.18
2123 2203 3.887716 GAGTATACTGCTCCCTCCGTAAA 59.112 47.826 10.90 0.00 0.00 2.01
2124 2204 3.890147 AGTATACTGCTCCCTCCGTAAAG 59.110 47.826 4.10 0.00 0.00 1.85
2125 2205 2.519771 TACTGCTCCCTCCGTAAAGA 57.480 50.000 0.00 0.00 0.00 2.52
2126 2206 1.640917 ACTGCTCCCTCCGTAAAGAA 58.359 50.000 0.00 0.00 0.00 2.52
2127 2207 1.975680 ACTGCTCCCTCCGTAAAGAAA 59.024 47.619 0.00 0.00 0.00 2.52
2128 2208 2.572104 ACTGCTCCCTCCGTAAAGAAAT 59.428 45.455 0.00 0.00 0.00 2.17
2129 2209 3.773119 ACTGCTCCCTCCGTAAAGAAATA 59.227 43.478 0.00 0.00 0.00 1.40
2130 2210 4.409247 ACTGCTCCCTCCGTAAAGAAATAT 59.591 41.667 0.00 0.00 0.00 1.28
2131 2211 5.601313 ACTGCTCCCTCCGTAAAGAAATATA 59.399 40.000 0.00 0.00 0.00 0.86
2132 2212 6.099269 ACTGCTCCCTCCGTAAAGAAATATAA 59.901 38.462 0.00 0.00 0.00 0.98
2133 2213 6.285990 TGCTCCCTCCGTAAAGAAATATAAC 58.714 40.000 0.00 0.00 0.00 1.89
2134 2214 6.126997 TGCTCCCTCCGTAAAGAAATATAACA 60.127 38.462 0.00 0.00 0.00 2.41
2135 2215 6.424207 GCTCCCTCCGTAAAGAAATATAACAG 59.576 42.308 0.00 0.00 0.00 3.16
2136 2216 6.285990 TCCCTCCGTAAAGAAATATAACAGC 58.714 40.000 0.00 0.00 0.00 4.40
2137 2217 5.176958 CCCTCCGTAAAGAAATATAACAGCG 59.823 44.000 0.00 0.00 0.00 5.18
2138 2218 5.751990 CCTCCGTAAAGAAATATAACAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
2139 2219 6.257193 CCTCCGTAAAGAAATATAACAGCGTT 59.743 38.462 0.02 0.02 0.00 4.84
2140 2220 7.201582 CCTCCGTAAAGAAATATAACAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
2141 2221 8.700722 TCCGTAAAGAAATATAACAGCGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
2142 2222 8.810427 TCCGTAAAGAAATATAACAGCGTTTAG 58.190 33.333 0.00 0.00 0.00 1.85
2143 2223 8.810427 CCGTAAAGAAATATAACAGCGTTTAGA 58.190 33.333 0.00 0.00 0.00 2.10
2148 2228 9.614792 AAGAAATATAACAGCGTTTAGATTCCT 57.385 29.630 0.00 0.00 0.00 3.36
2149 2229 9.614792 AGAAATATAACAGCGTTTAGATTCCTT 57.385 29.630 0.00 0.00 0.00 3.36
2153 2233 9.826574 ATATAACAGCGTTTAGATTCCTTTACA 57.173 29.630 0.00 0.00 0.00 2.41
2154 2234 6.481954 AACAGCGTTTAGATTCCTTTACAG 57.518 37.500 0.00 0.00 0.00 2.74
2155 2235 5.790593 ACAGCGTTTAGATTCCTTTACAGA 58.209 37.500 0.00 0.00 0.00 3.41
2156 2236 5.869888 ACAGCGTTTAGATTCCTTTACAGAG 59.130 40.000 0.00 0.00 0.00 3.35
2157 2237 5.292101 CAGCGTTTAGATTCCTTTACAGAGG 59.708 44.000 0.00 0.00 38.20 3.69
2158 2238 5.187186 AGCGTTTAGATTCCTTTACAGAGGA 59.813 40.000 0.00 0.00 43.99 3.71
2169 2249 7.171630 TCCTTTACAGAGGAAGTACTGATTC 57.828 40.000 0.00 0.00 42.75 2.52
2170 2250 6.154706 TCCTTTACAGAGGAAGTACTGATTCC 59.845 42.308 0.00 0.00 42.75 3.01
2180 2260 6.342111 GGAAGTACTGATTCCTTTACAGAGG 58.658 44.000 0.00 0.00 42.52 3.69
2181 2261 6.154706 GGAAGTACTGATTCCTTTACAGAGGA 59.845 42.308 0.00 0.00 43.99 3.71
2194 2274 9.517868 TCCTTTACAGAGGAAGTACTATATAGC 57.482 37.037 9.78 0.00 42.75 2.97
2195 2275 9.523168 CCTTTACAGAGGAAGTACTATATAGCT 57.477 37.037 9.78 0.00 39.25 3.32
2241 2321 9.928236 TTTTGCAACATAAAAGAGTTTTATTGC 57.072 25.926 16.48 16.48 43.98 3.56
2242 2322 8.885494 TTGCAACATAAAAGAGTTTTATTGCT 57.115 26.923 20.41 3.56 44.01 3.91
2243 2323 8.885494 TGCAACATAAAAGAGTTTTATTGCTT 57.115 26.923 20.41 6.45 44.01 3.91
2244 2324 9.973450 TGCAACATAAAAGAGTTTTATTGCTTA 57.027 25.926 20.41 8.14 44.01 3.09
2263 2343 5.975410 CTTACTTAAGCAGGCATACAGTC 57.025 43.478 1.29 0.00 0.00 3.51
2264 2344 3.981071 ACTTAAGCAGGCATACAGTCA 57.019 42.857 1.29 0.00 0.00 3.41
2265 2345 3.600388 ACTTAAGCAGGCATACAGTCAC 58.400 45.455 1.29 0.00 0.00 3.67
2266 2346 2.293677 TAAGCAGGCATACAGTCACG 57.706 50.000 0.00 0.00 0.00 4.35
2267 2347 0.608130 AAGCAGGCATACAGTCACGA 59.392 50.000 0.00 0.00 0.00 4.35
2268 2348 0.826715 AGCAGGCATACAGTCACGAT 59.173 50.000 0.00 0.00 0.00 3.73
2269 2349 2.031870 AGCAGGCATACAGTCACGATA 58.968 47.619 0.00 0.00 0.00 2.92
2270 2350 2.128035 GCAGGCATACAGTCACGATAC 58.872 52.381 0.00 0.00 0.00 2.24
2271 2351 2.481276 GCAGGCATACAGTCACGATACA 60.481 50.000 0.00 0.00 0.00 2.29
2272 2352 3.780902 CAGGCATACAGTCACGATACAA 58.219 45.455 0.00 0.00 0.00 2.41
2273 2353 3.551890 CAGGCATACAGTCACGATACAAC 59.448 47.826 0.00 0.00 0.00 3.32
2274 2354 2.534349 GGCATACAGTCACGATACAACG 59.466 50.000 0.00 0.00 39.31 4.10
2286 2366 5.063180 ACGATACAACGTGTTCATTAGGA 57.937 39.130 0.00 0.00 44.84 2.94
2287 2367 5.472148 ACGATACAACGTGTTCATTAGGAA 58.528 37.500 0.00 0.00 44.84 3.36
2288 2368 5.927689 ACGATACAACGTGTTCATTAGGAAA 59.072 36.000 0.00 0.00 44.84 3.13
2289 2369 6.424509 ACGATACAACGTGTTCATTAGGAAAA 59.575 34.615 0.00 0.00 44.84 2.29
2290 2370 6.735063 CGATACAACGTGTTCATTAGGAAAAC 59.265 38.462 0.00 0.00 39.88 2.43
2291 2371 5.821516 ACAACGTGTTCATTAGGAAAACA 57.178 34.783 0.87 0.00 42.86 2.83
2292 2372 6.385649 ACAACGTGTTCATTAGGAAAACAT 57.614 33.333 0.87 0.00 42.86 2.71
2293 2373 6.205784 ACAACGTGTTCATTAGGAAAACATG 58.794 36.000 0.87 1.83 42.86 3.21
2294 2374 6.038825 ACAACGTGTTCATTAGGAAAACATGA 59.961 34.615 12.22 0.00 42.86 3.07
2295 2375 6.241207 ACGTGTTCATTAGGAAAACATGAG 57.759 37.500 12.22 1.48 42.86 2.90
2296 2376 5.763204 ACGTGTTCATTAGGAAAACATGAGT 59.237 36.000 12.22 1.99 42.86 3.41
2297 2377 6.079763 CGTGTTCATTAGGAAAACATGAGTG 58.920 40.000 0.00 0.00 42.86 3.51
2298 2378 6.293407 CGTGTTCATTAGGAAAACATGAGTGT 60.293 38.462 0.00 0.00 42.86 3.55
2299 2379 7.095397 CGTGTTCATTAGGAAAACATGAGTGTA 60.095 37.037 0.00 0.00 42.86 2.90
2300 2380 8.564574 GTGTTCATTAGGAAAACATGAGTGTAA 58.435 33.333 0.00 0.00 42.37 2.41
2301 2381 9.295825 TGTTCATTAGGAAAACATGAGTGTAAT 57.704 29.630 0.00 0.00 37.67 1.89
2307 2387 7.158099 AGGAAAACATGAGTGTAATTAAGCC 57.842 36.000 0.00 0.00 37.67 4.35
2308 2388 6.719370 AGGAAAACATGAGTGTAATTAAGCCA 59.281 34.615 0.00 0.00 37.67 4.75
2309 2389 7.397192 AGGAAAACATGAGTGTAATTAAGCCAT 59.603 33.333 0.00 0.00 37.67 4.40
2310 2390 8.682710 GGAAAACATGAGTGTAATTAAGCCATA 58.317 33.333 0.00 0.00 37.67 2.74
2313 2393 9.855021 AAACATGAGTGTAATTAAGCCATAAAC 57.145 29.630 0.00 0.00 37.67 2.01
2314 2394 8.574251 ACATGAGTGTAATTAAGCCATAAACA 57.426 30.769 0.00 0.00 36.63 2.83
2315 2395 9.189156 ACATGAGTGTAATTAAGCCATAAACAT 57.811 29.630 0.00 0.00 36.63 2.71
2316 2396 9.669353 CATGAGTGTAATTAAGCCATAAACATC 57.331 33.333 0.00 0.00 0.00 3.06
2317 2397 9.632638 ATGAGTGTAATTAAGCCATAAACATCT 57.367 29.630 0.00 0.00 0.00 2.90
2318 2398 9.461312 TGAGTGTAATTAAGCCATAAACATCTT 57.539 29.630 0.00 0.00 0.00 2.40
2319 2399 9.937175 GAGTGTAATTAAGCCATAAACATCTTC 57.063 33.333 0.00 0.00 0.00 2.87
2320 2400 9.686683 AGTGTAATTAAGCCATAAACATCTTCT 57.313 29.630 0.00 0.00 0.00 2.85
2327 2407 9.733556 TTAAGCCATAAACATCTTCTTCTAACA 57.266 29.630 0.00 0.00 0.00 2.41
2328 2408 7.617041 AGCCATAAACATCTTCTTCTAACAC 57.383 36.000 0.00 0.00 0.00 3.32
2329 2409 7.398024 AGCCATAAACATCTTCTTCTAACACT 58.602 34.615 0.00 0.00 0.00 3.55
2330 2410 7.885399 AGCCATAAACATCTTCTTCTAACACTT 59.115 33.333 0.00 0.00 0.00 3.16
2331 2411 7.965107 GCCATAAACATCTTCTTCTAACACTTG 59.035 37.037 0.00 0.00 0.00 3.16
2332 2412 9.003658 CCATAAACATCTTCTTCTAACACTTGT 57.996 33.333 0.00 0.00 0.00 3.16
2334 2414 6.771188 AACATCTTCTTCTAACACTTGTCG 57.229 37.500 0.00 0.00 0.00 4.35
2335 2415 4.686554 ACATCTTCTTCTAACACTTGTCGC 59.313 41.667 0.00 0.00 0.00 5.19
2336 2416 3.650139 TCTTCTTCTAACACTTGTCGCC 58.350 45.455 0.00 0.00 0.00 5.54
2337 2417 3.321111 TCTTCTTCTAACACTTGTCGCCT 59.679 43.478 0.00 0.00 0.00 5.52
2338 2418 3.026630 TCTTCTAACACTTGTCGCCTG 57.973 47.619 0.00 0.00 0.00 4.85
2339 2419 1.461127 CTTCTAACACTTGTCGCCTGC 59.539 52.381 0.00 0.00 0.00 4.85
2340 2420 0.666274 TCTAACACTTGTCGCCTGCG 60.666 55.000 4.92 4.92 41.35 5.18
2341 2421 0.944311 CTAACACTTGTCGCCTGCGT 60.944 55.000 11.68 0.00 40.74 5.24
2342 2422 0.942410 TAACACTTGTCGCCTGCGTC 60.942 55.000 11.68 6.63 40.74 5.19
2343 2423 3.767230 CACTTGTCGCCTGCGTCG 61.767 66.667 11.68 0.00 40.74 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.253422 CAAGAGATACAAAAATGTTGGCTAGG 58.747 38.462 0.00 0.00 0.00 3.02
20 21 5.185828 GGTCCAAGCCAAGAGATACAAAAAT 59.814 40.000 0.00 0.00 0.00 1.82
25 26 2.265367 TGGTCCAAGCCAAGAGATACA 58.735 47.619 0.00 0.00 35.25 2.29
117 118 8.632906 TGGGTTACCGATAAATTCAGTAAAAA 57.367 30.769 0.00 0.00 40.75 1.94
140 141 6.127140 CCCTAGTTATACCTCCCGATAAATGG 60.127 46.154 0.00 0.00 0.00 3.16
195 196 2.404215 ACACTCAGTACATTGCACGTC 58.596 47.619 0.00 0.00 0.00 4.34
198 199 6.727824 ATTTAGACACTCAGTACATTGCAC 57.272 37.500 0.00 0.00 0.00 4.57
259 260 5.393352 GCAACATCATTAGAACATCAAGGCA 60.393 40.000 0.00 0.00 0.00 4.75
280 281 2.574006 AACTTCCAGATCAGCTGCAA 57.426 45.000 9.47 0.00 43.50 4.08
314 315 4.086457 GCCATTCCCTTCCTACTTTTCAA 58.914 43.478 0.00 0.00 0.00 2.69
355 356 5.542779 CTGGGCTAATTAACTACTAGGCAG 58.457 45.833 0.00 0.00 39.36 4.85
372 373 3.116091 CCGAATTATTGGCTGGGCT 57.884 52.632 0.00 0.00 0.00 5.19
471 472 1.946984 ACTGTTATTCGGACCCCTCA 58.053 50.000 0.00 0.00 0.00 3.86
500 507 5.245751 TCCAAATACCGGTCAGTTAACTGTA 59.754 40.000 29.83 17.59 44.12 2.74
525 538 0.312102 GTTTGAGTCCAAGCCACTGC 59.688 55.000 0.00 0.00 33.23 4.40
618 631 2.159085 AGCTATACCAGGAAACTCGCAC 60.159 50.000 0.00 0.00 40.21 5.34
783 796 1.949847 CTGGTGTAGACAGGGAGCGG 61.950 65.000 0.00 0.00 32.38 5.52
797 810 3.457610 AACAAATTCTTGCCACTGGTG 57.542 42.857 0.00 0.00 35.84 4.17
803 816 8.674263 ACAATTCATAAAACAAATTCTTGCCA 57.326 26.923 0.00 0.00 35.84 4.92
869 882 6.073222 GCGGTCGATGTTAAAAATCAGGATAT 60.073 38.462 0.00 0.00 0.00 1.63
1092 1107 1.352622 GGGTATGGATGACCTGGGCA 61.353 60.000 3.79 3.79 37.13 5.36
1392 1407 6.647481 TGCAATCAGTCCAAAAATCAGAAATG 59.353 34.615 0.00 0.00 0.00 2.32
1402 1417 5.350914 CACAAAAGTTGCAATCAGTCCAAAA 59.649 36.000 0.59 0.00 0.00 2.44
1442 1461 0.863144 CCGGACAAACGTTCGTTCAT 59.137 50.000 10.90 2.82 33.24 2.57
1444 1463 0.875474 TCCCGGACAAACGTTCGTTC 60.875 55.000 0.73 0.00 33.24 3.95
1545 1569 3.578282 TCCTCAAGTCATCAAGTGCTACA 59.422 43.478 0.00 0.00 0.00 2.74
1562 1586 3.264193 ACATAACAGGCTGTTGATCCTCA 59.736 43.478 36.40 19.24 41.30 3.86
1569 1593 4.074970 AGGAGAAACATAACAGGCTGTTG 58.925 43.478 36.40 26.25 41.30 3.33
1602 1626 1.949525 CCAGCCCAATAATCTCCGTTG 59.050 52.381 0.00 0.00 0.00 4.10
1631 1655 0.111061 ATCACAGGCAAGCAAGTCCA 59.889 50.000 0.00 0.00 0.00 4.02
1639 1663 3.615496 GCAAATTTAGCATCACAGGCAAG 59.385 43.478 7.47 0.00 0.00 4.01
1661 1685 5.645067 TGCTCCATCAAACAGTCTTGAATAG 59.355 40.000 3.30 3.37 38.75 1.73
1677 1701 2.012673 GAAGTCACACCATGCTCCATC 58.987 52.381 0.00 0.00 0.00 3.51
1861 1934 4.755411 TGAGGTTTAGCATGTACTACTGC 58.245 43.478 7.33 7.33 38.69 4.40
1862 1935 6.631016 TCTTGAGGTTTAGCATGTACTACTG 58.369 40.000 0.00 0.00 0.00 2.74
1863 1936 6.852420 TCTTGAGGTTTAGCATGTACTACT 57.148 37.500 0.00 0.00 0.00 2.57
1864 1937 6.418226 CGATCTTGAGGTTTAGCATGTACTAC 59.582 42.308 0.00 0.00 0.00 2.73
1958 2031 7.069986 ACTACCTTCAAGATTAGCATCTCCTA 58.930 38.462 0.00 0.00 39.00 2.94
1975 2048 6.142817 CCGCAAATGCAATTATACTACCTTC 58.857 40.000 6.18 0.00 42.21 3.46
1983 2056 5.316327 TGAACACCGCAAATGCAATTATA 57.684 34.783 6.18 0.00 42.21 0.98
1984 2057 4.185467 TGAACACCGCAAATGCAATTAT 57.815 36.364 6.18 0.00 42.21 1.28
2042 2122 3.625313 CACACAAAGTCACACACCATGTA 59.375 43.478 0.00 0.00 40.64 2.29
2046 2126 0.808125 GCACACAAAGTCACACACCA 59.192 50.000 0.00 0.00 0.00 4.17
2101 2181 1.984066 ACGGAGGGAGCAGTATACTC 58.016 55.000 1.26 0.00 0.00 2.59
2110 2190 6.285990 TGTTATATTTCTTTACGGAGGGAGC 58.714 40.000 0.00 0.00 0.00 4.70
2122 2202 9.614792 AGGAATCTAAACGCTGTTATATTTCTT 57.385 29.630 0.00 0.00 0.00 2.52
2123 2203 9.614792 AAGGAATCTAAACGCTGTTATATTTCT 57.385 29.630 0.00 0.00 0.00 2.52
2127 2207 9.826574 TGTAAAGGAATCTAAACGCTGTTATAT 57.173 29.630 0.00 0.00 0.00 0.86
2128 2208 9.309516 CTGTAAAGGAATCTAAACGCTGTTATA 57.690 33.333 0.00 0.00 0.00 0.98
2129 2209 8.038944 TCTGTAAAGGAATCTAAACGCTGTTAT 58.961 33.333 0.00 0.00 0.00 1.89
2130 2210 7.380536 TCTGTAAAGGAATCTAAACGCTGTTA 58.619 34.615 0.00 0.00 0.00 2.41
2131 2211 6.228258 TCTGTAAAGGAATCTAAACGCTGTT 58.772 36.000 0.00 0.00 0.00 3.16
2132 2212 5.790593 TCTGTAAAGGAATCTAAACGCTGT 58.209 37.500 0.00 0.00 0.00 4.40
2133 2213 5.292101 CCTCTGTAAAGGAATCTAAACGCTG 59.708 44.000 0.00 0.00 38.87 5.18
2134 2214 5.187186 TCCTCTGTAAAGGAATCTAAACGCT 59.813 40.000 0.00 0.00 42.56 5.07
2135 2215 5.416947 TCCTCTGTAAAGGAATCTAAACGC 58.583 41.667 0.00 0.00 42.56 4.84
2145 2225 6.154706 GGAATCAGTACTTCCTCTGTAAAGGA 59.845 42.308 5.02 0.00 43.84 3.36
2146 2226 6.342111 GGAATCAGTACTTCCTCTGTAAAGG 58.658 44.000 5.02 0.00 39.30 3.11
2156 2236 6.154706 TCCTCTGTAAAGGAATCAGTACTTCC 59.845 42.308 4.16 4.16 42.56 3.46
2157 2237 7.171630 TCCTCTGTAAAGGAATCAGTACTTC 57.828 40.000 0.00 0.00 42.56 3.01
2168 2248 9.517868 GCTATATAGTACTTCCTCTGTAAAGGA 57.482 37.037 11.38 0.00 43.84 3.36
2169 2249 9.523168 AGCTATATAGTACTTCCTCTGTAAAGG 57.477 37.037 11.38 0.00 37.81 3.11
2215 2295 9.928236 GCAATAAAACTCTTTTATGTTGCAAAA 57.072 25.926 0.00 0.00 43.60 2.44
2216 2296 9.323985 AGCAATAAAACTCTTTTATGTTGCAAA 57.676 25.926 18.75 0.00 44.99 3.68
2217 2297 8.885494 AGCAATAAAACTCTTTTATGTTGCAA 57.115 26.923 18.75 0.00 44.99 4.08
2218 2298 8.885494 AAGCAATAAAACTCTTTTATGTTGCA 57.115 26.923 18.75 0.00 44.99 4.08
2241 2321 5.292101 GTGACTGTATGCCTGCTTAAGTAAG 59.708 44.000 4.02 2.55 36.40 2.34
2242 2322 5.175859 GTGACTGTATGCCTGCTTAAGTAA 58.824 41.667 4.02 0.00 0.00 2.24
2243 2323 4.676986 CGTGACTGTATGCCTGCTTAAGTA 60.677 45.833 4.02 0.00 0.00 2.24
2244 2324 3.600388 GTGACTGTATGCCTGCTTAAGT 58.400 45.455 4.02 0.00 0.00 2.24
2245 2325 2.604914 CGTGACTGTATGCCTGCTTAAG 59.395 50.000 0.00 0.00 0.00 1.85
2246 2326 2.232696 TCGTGACTGTATGCCTGCTTAA 59.767 45.455 0.00 0.00 0.00 1.85
2247 2327 1.822371 TCGTGACTGTATGCCTGCTTA 59.178 47.619 0.00 0.00 0.00 3.09
2248 2328 0.608130 TCGTGACTGTATGCCTGCTT 59.392 50.000 0.00 0.00 0.00 3.91
2249 2329 0.826715 ATCGTGACTGTATGCCTGCT 59.173 50.000 0.00 0.00 0.00 4.24
2250 2330 2.128035 GTATCGTGACTGTATGCCTGC 58.872 52.381 0.00 0.00 0.00 4.85
2251 2331 3.436700 TGTATCGTGACTGTATGCCTG 57.563 47.619 0.00 0.00 0.00 4.85
2252 2332 3.733988 CGTTGTATCGTGACTGTATGCCT 60.734 47.826 0.00 0.00 0.00 4.75
2253 2333 2.534349 CGTTGTATCGTGACTGTATGCC 59.466 50.000 0.00 0.00 0.00 4.40
2254 2334 3.176708 ACGTTGTATCGTGACTGTATGC 58.823 45.455 0.00 0.00 42.56 3.14
2264 2344 5.063180 TCCTAATGAACACGTTGTATCGT 57.937 39.130 0.00 0.00 45.10 3.73
2265 2345 6.397831 TTTCCTAATGAACACGTTGTATCG 57.602 37.500 0.00 0.00 31.05 2.92
2266 2346 7.577979 TGTTTTCCTAATGAACACGTTGTATC 58.422 34.615 0.00 0.00 36.61 2.24
2267 2347 7.499321 TGTTTTCCTAATGAACACGTTGTAT 57.501 32.000 0.00 0.00 36.61 2.29
2268 2348 6.922247 TGTTTTCCTAATGAACACGTTGTA 57.078 33.333 0.00 0.00 36.61 2.41
2269 2349 5.821516 TGTTTTCCTAATGAACACGTTGT 57.178 34.783 0.00 0.00 36.61 3.32
2270 2350 6.434596 TCATGTTTTCCTAATGAACACGTTG 58.565 36.000 0.00 0.00 36.61 4.10
2271 2351 6.262273 ACTCATGTTTTCCTAATGAACACGTT 59.738 34.615 0.00 0.00 36.61 3.99
2272 2352 5.763204 ACTCATGTTTTCCTAATGAACACGT 59.237 36.000 0.00 0.00 36.61 4.49
2273 2353 6.079763 CACTCATGTTTTCCTAATGAACACG 58.920 40.000 0.00 0.00 36.61 4.49
2274 2354 6.970484 ACACTCATGTTTTCCTAATGAACAC 58.030 36.000 0.00 0.00 34.46 3.32
2275 2355 8.684386 TTACACTCATGTTTTCCTAATGAACA 57.316 30.769 0.00 0.00 40.48 3.18
2281 2361 8.736244 GGCTTAATTACACTCATGTTTTCCTAA 58.264 33.333 0.00 0.00 40.48 2.69
2282 2362 7.885922 TGGCTTAATTACACTCATGTTTTCCTA 59.114 33.333 0.00 0.00 40.48 2.94
2283 2363 6.719370 TGGCTTAATTACACTCATGTTTTCCT 59.281 34.615 0.00 0.00 40.48 3.36
2284 2364 6.919721 TGGCTTAATTACACTCATGTTTTCC 58.080 36.000 0.00 0.00 40.48 3.13
2287 2367 9.855021 GTTTATGGCTTAATTACACTCATGTTT 57.145 29.630 0.00 0.00 40.48 2.83
2288 2368 9.019656 TGTTTATGGCTTAATTACACTCATGTT 57.980 29.630 0.00 0.00 40.48 2.71
2289 2369 8.574251 TGTTTATGGCTTAATTACACTCATGT 57.426 30.769 0.00 0.00 43.30 3.21
2290 2370 9.669353 GATGTTTATGGCTTAATTACACTCATG 57.331 33.333 1.21 0.00 0.00 3.07
2291 2371 9.632638 AGATGTTTATGGCTTAATTACACTCAT 57.367 29.630 1.21 0.00 0.00 2.90
2292 2372 9.461312 AAGATGTTTATGGCTTAATTACACTCA 57.539 29.630 1.21 0.00 0.00 3.41
2293 2373 9.937175 GAAGATGTTTATGGCTTAATTACACTC 57.063 33.333 1.21 2.07 0.00 3.51
2294 2374 9.686683 AGAAGATGTTTATGGCTTAATTACACT 57.313 29.630 1.21 0.17 0.00 3.55
2301 2381 9.733556 TGTTAGAAGAAGATGTTTATGGCTTAA 57.266 29.630 0.00 0.00 0.00 1.85
2302 2382 9.162764 GTGTTAGAAGAAGATGTTTATGGCTTA 57.837 33.333 0.00 0.00 0.00 3.09
2303 2383 7.885399 AGTGTTAGAAGAAGATGTTTATGGCTT 59.115 33.333 0.00 0.00 0.00 4.35
2304 2384 7.398024 AGTGTTAGAAGAAGATGTTTATGGCT 58.602 34.615 0.00 0.00 0.00 4.75
2305 2385 7.617041 AGTGTTAGAAGAAGATGTTTATGGC 57.383 36.000 0.00 0.00 0.00 4.40
2306 2386 9.003658 ACAAGTGTTAGAAGAAGATGTTTATGG 57.996 33.333 0.00 0.00 0.00 2.74
2308 2388 8.926710 CGACAAGTGTTAGAAGAAGATGTTTAT 58.073 33.333 0.00 0.00 0.00 1.40
2309 2389 7.095774 GCGACAAGTGTTAGAAGAAGATGTTTA 60.096 37.037 0.00 0.00 0.00 2.01
2310 2390 6.292919 GCGACAAGTGTTAGAAGAAGATGTTT 60.293 38.462 0.00 0.00 0.00 2.83
2311 2391 5.177696 GCGACAAGTGTTAGAAGAAGATGTT 59.822 40.000 0.00 0.00 0.00 2.71
2312 2392 4.686554 GCGACAAGTGTTAGAAGAAGATGT 59.313 41.667 0.00 0.00 0.00 3.06
2313 2393 4.092091 GGCGACAAGTGTTAGAAGAAGATG 59.908 45.833 0.00 0.00 0.00 2.90
2314 2394 4.021016 AGGCGACAAGTGTTAGAAGAAGAT 60.021 41.667 0.00 0.00 0.00 2.40
2315 2395 3.321111 AGGCGACAAGTGTTAGAAGAAGA 59.679 43.478 0.00 0.00 0.00 2.87
2316 2396 3.430218 CAGGCGACAAGTGTTAGAAGAAG 59.570 47.826 0.00 0.00 0.00 2.85
2317 2397 3.390135 CAGGCGACAAGTGTTAGAAGAA 58.610 45.455 0.00 0.00 0.00 2.52
2318 2398 2.866460 GCAGGCGACAAGTGTTAGAAGA 60.866 50.000 0.00 0.00 0.00 2.87
2319 2399 1.461127 GCAGGCGACAAGTGTTAGAAG 59.539 52.381 0.00 0.00 0.00 2.85
2320 2400 1.508632 GCAGGCGACAAGTGTTAGAA 58.491 50.000 0.00 0.00 0.00 2.10
2321 2401 0.666274 CGCAGGCGACAAGTGTTAGA 60.666 55.000 8.15 0.00 42.83 2.10
2322 2402 0.944311 ACGCAGGCGACAAGTGTTAG 60.944 55.000 21.62 0.00 42.83 2.34
2323 2403 0.942410 GACGCAGGCGACAAGTGTTA 60.942 55.000 21.62 0.00 42.83 2.41
2324 2404 2.203015 ACGCAGGCGACAAGTGTT 60.203 55.556 21.62 0.00 42.83 3.32
2325 2405 2.661866 GACGCAGGCGACAAGTGT 60.662 61.111 21.62 0.00 42.83 3.55
2326 2406 3.767230 CGACGCAGGCGACAAGTG 61.767 66.667 21.62 0.00 42.83 3.16


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

AutoCloner maintained by Alex Coulton.