Multiple sequence alignment - TraesCS3D01G380900

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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 TraesCS3D01G380900 chr3D 100.000 3035 0 0 1 3035 497016279 497013245 0.000000e+00 5605.0
1 TraesCS3D01G380900 chr3D 93.805 1146 56 6 909 2043 497231897 497230756 0.000000e+00 1709.0
2 TraesCS3D01G380900 chr3D 95.300 766 27 8 2277 3035 446066555 446067318 0.000000e+00 1206.0
3 TraesCS3D01G380900 chr3D 82.143 112 17 3 125 236 323724266 323724374 3.220000e-15 93.5
4 TraesCS3D01G380900 chr3D 91.111 45 3 1 2124 2168 497156511 497156468 3.270000e-05 60.2
5 TraesCS3D01G380900 chr3B 95.118 1823 89 0 265 2087 656741500 656739678 0.000000e+00 2874.0
6 TraesCS3D01G380900 chr3B 92.786 1206 74 5 927 2122 656917732 656916530 0.000000e+00 1733.0
7 TraesCS3D01G380900 chr3B 90.226 266 26 0 1 266 656741727 656741462 6.230000e-92 348.0
8 TraesCS3D01G380900 chr3B 84.615 117 12 4 2164 2274 656915154 656915038 8.890000e-21 111.0
9 TraesCS3D01G380900 chr3B 93.750 48 1 2 2124 2171 656738859 656738814 1.510000e-08 71.3
10 TraesCS3D01G380900 chr3B 100.000 33 0 0 2126 2158 656916475 656916443 9.090000e-06 62.1
11 TraesCS3D01G380900 chr3A 90.844 1398 95 17 745 2124 637470944 637472326 0.000000e+00 1842.0
12 TraesCS3D01G380900 chr3A 96.960 954 29 0 1094 2047 637603986 637604939 0.000000e+00 1602.0
13 TraesCS3D01G380900 chr3A 92.712 837 53 4 265 1101 637588348 637589176 0.000000e+00 1201.0
14 TraesCS3D01G380900 chr3A 93.971 763 35 7 2281 3035 298092612 298093371 0.000000e+00 1144.0
15 TraesCS3D01G380900 chr3A 91.339 254 22 0 1 254 637588121 637588374 6.230000e-92 348.0
16 TraesCS3D01G380900 chr3A 88.144 194 21 2 2274 2466 728045922 728045730 2.350000e-56 230.0
17 TraesCS3D01G380900 chr3A 100.000 33 0 0 2124 2156 637472733 637472765 9.090000e-06 62.1
18 TraesCS3D01G380900 chr1D 95.795 761 24 6 2281 3035 437009697 437008939 0.000000e+00 1221.0
19 TraesCS3D01G380900 chr1D 93.273 773 32 8 2282 3035 437004836 437004065 0.000000e+00 1122.0
20 TraesCS3D01G380900 chr1D 94.608 408 16 4 2282 2685 77797638 77797233 7.140000e-176 627.0
21 TraesCS3D01G380900 chr1D 97.087 309 8 1 2728 3035 77797228 77796920 1.250000e-143 520.0
22 TraesCS3D01G380900 chr7D 94.163 771 34 7 2272 3034 20622903 20622136 0.000000e+00 1164.0
23 TraesCS3D01G380900 chr7D 85.019 267 35 5 2263 2528 578066247 578066509 1.790000e-67 267.0
24 TraesCS3D01G380900 chr7D 80.189 106 20 1 67 171 429554000 429553895 9.020000e-11 78.7
25 TraesCS3D01G380900 chr6B 94.034 771 34 9 2274 3035 4663189 4663956 0.000000e+00 1158.0
26 TraesCS3D01G380900 chr5A 86.686 1044 127 6 994 2031 550656007 550654970 0.000000e+00 1147.0
27 TraesCS3D01G380900 chr5A 85.994 357 36 9 2273 2626 369853801 369853456 1.330000e-98 370.0
28 TraesCS3D01G380900 chr6A 90.789 760 46 10 2282 3035 614156399 614157140 0.000000e+00 994.0
29 TraesCS3D01G380900 chr5D 87.116 683 81 1 1352 2027 436207166 436206484 0.000000e+00 767.0
30 TraesCS3D01G380900 chr5D 86.992 369 35 6 994 1356 436212755 436212394 1.310000e-108 403.0
31 TraesCS3D01G380900 chr7B 83.696 644 80 19 2282 2907 2950839 2951475 4.360000e-163 584.0
32 TraesCS3D01G380900 chr7B 82.923 650 74 20 2277 2907 644553975 644553344 4.420000e-153 551.0
33 TraesCS3D01G380900 chr2B 82.043 607 81 15 2273 2868 512195500 512194911 2.720000e-135 492.0
34 TraesCS3D01G380900 chr2B 91.667 72 6 0 1226 1297 1749897 1749968 1.930000e-17 100.0
35 TraesCS3D01G380900 chr2B 91.549 71 6 0 1227 1297 1765061 1765131 6.920000e-17 99.0
36 TraesCS3D01G380900 chr7A 79.651 516 88 14 2277 2778 82213877 82214389 3.720000e-94 355.0
37 TraesCS3D01G380900 chr7A 92.486 173 10 2 2863 3035 736591377 736591208 8.410000e-61 244.0
38 TraesCS3D01G380900 chr6D 78.244 501 100 7 1487 1986 324571451 324571943 2.270000e-81 313.0
39 TraesCS3D01G380900 chr4D 91.908 173 11 3 2863 3035 402321516 402321347 3.910000e-59 239.0
40 TraesCS3D01G380900 chr5B 77.612 134 29 1 67 199 661251953 661252086 2.510000e-11 80.5
41 TraesCS3D01G380900 chr5B 77.444 133 29 1 40 171 661278335 661278467 9.020000e-11 78.7
42 TraesCS3D01G380900 chrUn 74.269 171 34 4 67 228 76224138 76223969 2.530000e-06 63.9
43 TraesCS3D01G380900 chrUn 74.269 171 34 4 67 228 446491034 446490865 2.530000e-06 63.9
44 TraesCS3D01G380900 chr2D 95.000 40 2 0 1483 1522 13856670 13856709 2.530000e-06 63.9


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 TraesCS3D01G380900 chr3D 497013245 497016279 3034 True 5605.000000 5605 100.000000 1 3035 1 chr3D.!!$R1 3034
1 TraesCS3D01G380900 chr3D 497230756 497231897 1141 True 1709.000000 1709 93.805000 909 2043 1 chr3D.!!$R3 1134
2 TraesCS3D01G380900 chr3D 446066555 446067318 763 False 1206.000000 1206 95.300000 2277 3035 1 chr3D.!!$F2 758
3 TraesCS3D01G380900 chr3B 656738814 656741727 2913 True 1097.766667 2874 93.031333 1 2171 3 chr3B.!!$R1 2170
4 TraesCS3D01G380900 chr3B 656915038 656917732 2694 True 635.366667 1733 92.467000 927 2274 3 chr3B.!!$R2 1347
5 TraesCS3D01G380900 chr3A 637603986 637604939 953 False 1602.000000 1602 96.960000 1094 2047 1 chr3A.!!$F2 953
6 TraesCS3D01G380900 chr3A 298092612 298093371 759 False 1144.000000 1144 93.971000 2281 3035 1 chr3A.!!$F1 754
7 TraesCS3D01G380900 chr3A 637470944 637472765 1821 False 952.050000 1842 95.422000 745 2156 2 chr3A.!!$F3 1411
8 TraesCS3D01G380900 chr3A 637588121 637589176 1055 False 774.500000 1201 92.025500 1 1101 2 chr3A.!!$F4 1100
9 TraesCS3D01G380900 chr1D 437008939 437009697 758 True 1221.000000 1221 95.795000 2281 3035 1 chr1D.!!$R2 754
10 TraesCS3D01G380900 chr1D 437004065 437004836 771 True 1122.000000 1122 93.273000 2282 3035 1 chr1D.!!$R1 753
11 TraesCS3D01G380900 chr1D 77796920 77797638 718 True 573.500000 627 95.847500 2282 3035 2 chr1D.!!$R3 753
12 TraesCS3D01G380900 chr7D 20622136 20622903 767 True 1164.000000 1164 94.163000 2272 3034 1 chr7D.!!$R1 762
13 TraesCS3D01G380900 chr6B 4663189 4663956 767 False 1158.000000 1158 94.034000 2274 3035 1 chr6B.!!$F1 761
14 TraesCS3D01G380900 chr5A 550654970 550656007 1037 True 1147.000000 1147 86.686000 994 2031 1 chr5A.!!$R2 1037
15 TraesCS3D01G380900 chr6A 614156399 614157140 741 False 994.000000 994 90.789000 2282 3035 1 chr6A.!!$F1 753
16 TraesCS3D01G380900 chr5D 436206484 436207166 682 True 767.000000 767 87.116000 1352 2027 1 chr5D.!!$R1 675
17 TraesCS3D01G380900 chr7B 2950839 2951475 636 False 584.000000 584 83.696000 2282 2907 1 chr7B.!!$F1 625
18 TraesCS3D01G380900 chr7B 644553344 644553975 631 True 551.000000 551 82.923000 2277 2907 1 chr7B.!!$R1 630
19 TraesCS3D01G380900 chr2B 512194911 512195500 589 True 492.000000 492 82.043000 2273 2868 1 chr2B.!!$R1 595
20 TraesCS3D01G380900 chr7A 82213877 82214389 512 False 355.000000 355 79.651000 2277 2778 1 chr7A.!!$F1 501

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
637 638 0.107214 GGGCCGAGATCCATTGTTCA 60.107 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 3420 0.036732 AAAGCAAGAGCATGGGACGA 59.963 50.0 0.0 0.0 45.49 4.2 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
21 22 1.064803 GTCGCAAACACCATTGTCACA 59.935 47.619 0.00 0.00 33.55 3.58
62 63 1.020437 TGCAGCAATTGACAACGACA 58.980 45.000 10.34 0.00 0.00 4.35
64 65 1.678360 CAGCAATTGACAACGACAGC 58.322 50.000 10.34 0.00 0.00 4.40
112 113 4.954118 TGGCCTCACCCTGGTCGT 62.954 66.667 3.32 0.00 37.83 4.34
114 115 4.436998 GCCTCACCCTGGTCGTCG 62.437 72.222 0.00 0.00 0.00 5.12
241 242 3.817148 CGTTGCCGGTTGTAGTATTTT 57.183 42.857 1.90 0.00 0.00 1.82
242 243 3.739494 CGTTGCCGGTTGTAGTATTTTC 58.261 45.455 1.90 0.00 0.00 2.29
243 244 3.425227 CGTTGCCGGTTGTAGTATTTTCC 60.425 47.826 1.90 0.00 0.00 3.13
244 245 3.420300 TGCCGGTTGTAGTATTTTCCA 57.580 42.857 1.90 0.00 0.00 3.53
245 246 3.752665 TGCCGGTTGTAGTATTTTCCAA 58.247 40.909 1.90 0.00 0.00 3.53
246 247 3.502979 TGCCGGTTGTAGTATTTTCCAAC 59.497 43.478 1.90 0.00 37.14 3.77
247 248 3.502979 GCCGGTTGTAGTATTTTCCAACA 59.497 43.478 1.90 0.00 39.08 3.33
248 249 4.023021 GCCGGTTGTAGTATTTTCCAACAA 60.023 41.667 1.90 0.00 39.08 2.83
249 250 5.454520 CCGGTTGTAGTATTTTCCAACAAC 58.545 41.667 7.86 7.86 45.72 3.32
250 251 5.141568 CGGTTGTAGTATTTTCCAACAACG 58.858 41.667 9.69 3.46 46.81 4.10
251 252 5.454520 GGTTGTAGTATTTTCCAACAACGG 58.545 41.667 9.69 0.00 46.81 4.44
252 253 5.008911 GGTTGTAGTATTTTCCAACAACGGT 59.991 40.000 9.69 0.00 46.81 4.83
253 254 6.459985 GGTTGTAGTATTTTCCAACAACGGTT 60.460 38.462 9.69 0.00 46.81 4.44
254 255 6.303021 TGTAGTATTTTCCAACAACGGTTC 57.697 37.500 0.00 0.00 34.21 3.62
255 256 4.841443 AGTATTTTCCAACAACGGTTCC 57.159 40.909 0.00 0.00 34.21 3.62
256 257 4.208746 AGTATTTTCCAACAACGGTTCCA 58.791 39.130 0.00 0.00 34.21 3.53
257 258 4.645588 AGTATTTTCCAACAACGGTTCCAA 59.354 37.500 0.00 0.00 34.21 3.53
258 259 2.943449 TTTCCAACAACGGTTCCAAC 57.057 45.000 0.00 0.00 34.21 3.77
259 260 2.131776 TTCCAACAACGGTTCCAACT 57.868 45.000 0.00 0.00 34.21 3.16
260 261 1.670791 TCCAACAACGGTTCCAACTC 58.329 50.000 0.00 0.00 34.21 3.01
261 262 0.306533 CCAACAACGGTTCCAACTCG 59.693 55.000 0.00 0.00 34.21 4.18
262 263 0.306533 CAACAACGGTTCCAACTCGG 59.693 55.000 0.00 0.00 34.21 4.63
263 264 1.441732 AACAACGGTTCCAACTCGGC 61.442 55.000 0.00 0.00 29.00 5.54
281 282 1.065272 GGCCGGTTGTAGTATTTCCCA 60.065 52.381 1.90 0.00 0.00 4.37
294 295 1.848652 TTTCCCAACAACGGTTCCAA 58.151 45.000 0.00 0.00 34.21 3.53
298 299 0.306533 CCAACAACGGTTCCAACTCG 59.693 55.000 0.00 0.00 34.21 4.18
332 333 0.447801 CCAGCAAATGTAGACACGGC 59.552 55.000 0.00 0.00 0.00 5.68
359 360 1.448497 GACGTCAGGGTGGTTCCAA 59.552 57.895 11.55 0.00 38.11 3.53
532 533 2.356793 CCGGAGATGATGGAGCGC 60.357 66.667 0.00 0.00 0.00 5.92
597 598 0.250295 TGTTGAGAGGGCGTTGAAGG 60.250 55.000 0.00 0.00 0.00 3.46
632 633 3.479203 TGCGGGCCGAGATCCATT 61.479 61.111 33.44 0.00 0.00 3.16
637 638 0.107214 GGGCCGAGATCCATTGTTCA 60.107 55.000 0.00 0.00 0.00 3.18
682 683 2.356553 CGACCGGCCGAAGTTTCA 60.357 61.111 30.73 0.00 0.00 2.69
691 692 0.955919 CCGAAGTTTCAGCCAGTCCC 60.956 60.000 0.00 0.00 0.00 4.46
708 709 3.527665 AGTCCCCTGGCTACAAACATTAT 59.472 43.478 0.00 0.00 0.00 1.28
710 711 3.117663 TCCCCTGGCTACAAACATTATCC 60.118 47.826 0.00 0.00 0.00 2.59
975 1011 1.068417 TGGAGCGCTGTACAAACGT 59.932 52.632 18.48 6.36 0.00 3.99
1031 1077 1.127343 CCACAATCCTCCTCCTCCTC 58.873 60.000 0.00 0.00 0.00 3.71
1094 1143 1.892474 CTATGACCAGCTCCTAGAGGC 59.108 57.143 0.00 0.00 34.44 4.70
1368 1423 1.005215 CACCAGCTCATCCCTTTCCTT 59.995 52.381 0.00 0.00 0.00 3.36
1552 1614 0.250467 GCTCTGGCACTTCTGGAACA 60.250 55.000 0.00 0.00 38.54 3.18
1626 1688 2.975799 GTTTCGCTGTTCGGGCCA 60.976 61.111 4.39 0.00 39.05 5.36
2007 2069 1.963464 GAGGATCGGGGTTGGCGTTA 61.963 60.000 0.00 0.00 0.00 3.18
2047 2109 4.476297 TCAGAACTAGTGGGTTCAGTACA 58.524 43.478 0.00 0.00 45.52 2.90
2158 3368 1.647213 CGTTATCACGTGGTGTCTTCG 59.353 52.381 17.00 7.07 41.84 3.79
2164 3374 1.536766 CACGTGGTGTCTTCGGTACTA 59.463 52.381 7.95 0.00 0.00 1.82
2165 3375 1.808945 ACGTGGTGTCTTCGGTACTAG 59.191 52.381 0.00 0.00 0.00 2.57
2166 3376 1.808945 CGTGGTGTCTTCGGTACTAGT 59.191 52.381 0.00 0.00 0.00 2.57
2167 3377 2.413765 CGTGGTGTCTTCGGTACTAGTG 60.414 54.545 5.39 0.00 0.00 2.74
2168 3378 2.816087 GTGGTGTCTTCGGTACTAGTGA 59.184 50.000 5.39 0.00 0.00 3.41
2169 3379 3.442977 GTGGTGTCTTCGGTACTAGTGAT 59.557 47.826 5.39 0.00 0.00 3.06
2170 3380 3.693085 TGGTGTCTTCGGTACTAGTGATC 59.307 47.826 5.39 0.00 0.00 2.92
2171 3381 3.242673 GGTGTCTTCGGTACTAGTGATCG 60.243 52.174 5.39 6.81 0.00 3.69
2172 3382 3.373439 GTGTCTTCGGTACTAGTGATCGT 59.627 47.826 5.39 0.00 0.00 3.73
2173 3383 3.620374 TGTCTTCGGTACTAGTGATCGTC 59.380 47.826 5.39 1.71 0.00 4.20
2174 3384 3.870419 GTCTTCGGTACTAGTGATCGTCT 59.130 47.826 5.39 0.00 0.00 4.18
2176 3386 4.331992 TCTTCGGTACTAGTGATCGTCTTG 59.668 45.833 5.39 0.00 0.00 3.02
2177 3387 3.603532 TCGGTACTAGTGATCGTCTTGT 58.396 45.455 5.39 8.97 0.00 3.16
2178 3388 4.005650 TCGGTACTAGTGATCGTCTTGTT 58.994 43.478 5.39 0.00 0.00 2.83
2179 3389 4.096311 CGGTACTAGTGATCGTCTTGTTG 58.904 47.826 5.39 0.40 0.00 3.33
2180 3390 3.858238 GGTACTAGTGATCGTCTTGTTGC 59.142 47.826 5.39 4.99 0.00 4.17
2183 3393 1.800805 AGTGATCGTCTTGTTGCCTG 58.199 50.000 0.00 0.00 0.00 4.85
2184 3394 0.166814 GTGATCGTCTTGTTGCCTGC 59.833 55.000 0.00 0.00 0.00 4.85
2187 3397 4.389576 CGTCTTGTTGCCTGCGCC 62.390 66.667 4.18 0.00 0.00 6.53
2202 3412 4.379143 GCCGCGTGGGTTTTCGTC 62.379 66.667 18.41 0.00 38.44 4.20
2204 3414 2.663852 CGCGTGGGTTTTCGTCCT 60.664 61.111 0.00 0.00 0.00 3.85
2207 3417 1.848932 GCGTGGGTTTTCGTCCTTCC 61.849 60.000 0.00 0.00 0.00 3.46
2210 3420 0.841289 TGGGTTTTCGTCCTTCCAGT 59.159 50.000 0.00 0.00 0.00 4.00
2212 3422 1.145803 GGTTTTCGTCCTTCCAGTCG 58.854 55.000 0.00 0.00 0.00 4.18
2213 3423 1.539712 GGTTTTCGTCCTTCCAGTCGT 60.540 52.381 0.00 0.00 0.00 4.34
2215 3425 0.316204 TTTCGTCCTTCCAGTCGTCC 59.684 55.000 0.00 0.00 0.00 4.79
2217 3427 2.273179 CGTCCTTCCAGTCGTCCCA 61.273 63.158 0.00 0.00 0.00 4.37
2218 3428 1.605058 CGTCCTTCCAGTCGTCCCAT 61.605 60.000 0.00 0.00 0.00 4.00
2219 3429 0.108138 GTCCTTCCAGTCGTCCCATG 60.108 60.000 0.00 0.00 0.00 3.66
2220 3430 1.450312 CCTTCCAGTCGTCCCATGC 60.450 63.158 0.00 0.00 0.00 4.06
2221 3431 1.599047 CTTCCAGTCGTCCCATGCT 59.401 57.895 0.00 0.00 0.00 3.79
2223 3433 0.904865 TTCCAGTCGTCCCATGCTCT 60.905 55.000 0.00 0.00 0.00 4.09
2224 3434 0.904865 TCCAGTCGTCCCATGCTCTT 60.905 55.000 0.00 0.00 0.00 2.85
2225 3435 0.742281 CCAGTCGTCCCATGCTCTTG 60.742 60.000 0.00 0.00 0.00 3.02
2227 3437 1.078848 GTCGTCCCATGCTCTTGCT 60.079 57.895 0.00 0.00 40.48 3.91
2228 3438 0.674895 GTCGTCCCATGCTCTTGCTT 60.675 55.000 0.00 0.00 40.48 3.91
2232 3442 2.289002 CGTCCCATGCTCTTGCTTTATC 59.711 50.000 0.00 0.00 40.48 1.75
2233 3443 2.620585 GTCCCATGCTCTTGCTTTATCC 59.379 50.000 0.00 0.00 40.48 2.59
2235 3445 2.883386 CCCATGCTCTTGCTTTATCCTC 59.117 50.000 0.00 0.00 40.48 3.71
2236 3446 3.434739 CCCATGCTCTTGCTTTATCCTCT 60.435 47.826 0.00 0.00 40.48 3.69
2237 3447 4.205587 CCATGCTCTTGCTTTATCCTCTT 58.794 43.478 0.00 0.00 40.48 2.85
2239 3449 3.525537 TGCTCTTGCTTTATCCTCTTCG 58.474 45.455 0.00 0.00 40.48 3.79
2240 3450 2.869192 GCTCTTGCTTTATCCTCTTCGG 59.131 50.000 0.00 0.00 36.03 4.30
2241 3451 2.869192 CTCTTGCTTTATCCTCTTCGGC 59.131 50.000 0.00 0.00 0.00 5.54
2242 3452 2.236146 TCTTGCTTTATCCTCTTCGGCA 59.764 45.455 0.00 0.00 0.00 5.69
2243 3453 2.779755 TGCTTTATCCTCTTCGGCAA 57.220 45.000 0.00 0.00 0.00 4.52
2244 3454 2.356135 TGCTTTATCCTCTTCGGCAAC 58.644 47.619 0.00 0.00 0.00 4.17
2246 3456 2.681097 GCTTTATCCTCTTCGGCAACCT 60.681 50.000 0.00 0.00 0.00 3.50
2247 3457 2.691409 TTATCCTCTTCGGCAACCTG 57.309 50.000 0.00 0.00 0.00 4.00
2248 3458 0.178068 TATCCTCTTCGGCAACCTGC 59.822 55.000 0.00 0.00 44.08 4.85
2261 3471 4.298744 GCAACCTGCCTCTTGAATAATC 57.701 45.455 0.00 0.00 37.42 1.75
2262 3472 3.950395 GCAACCTGCCTCTTGAATAATCT 59.050 43.478 0.00 0.00 37.42 2.40
2263 3473 4.400567 GCAACCTGCCTCTTGAATAATCTT 59.599 41.667 0.00 0.00 37.42 2.40
2264 3474 5.678107 GCAACCTGCCTCTTGAATAATCTTG 60.678 44.000 0.00 0.00 37.42 3.02
2265 3475 4.530875 ACCTGCCTCTTGAATAATCTTGG 58.469 43.478 0.00 0.00 0.00 3.61
2266 3476 3.317430 CCTGCCTCTTGAATAATCTTGGC 59.683 47.826 0.00 0.00 39.53 4.52
2267 3477 3.949754 CTGCCTCTTGAATAATCTTGGCA 59.050 43.478 0.00 0.00 45.51 4.92
2268 3478 3.949754 TGCCTCTTGAATAATCTTGGCAG 59.050 43.478 0.00 0.00 43.29 4.85
2269 3479 3.950395 GCCTCTTGAATAATCTTGGCAGT 59.050 43.478 0.00 0.00 38.99 4.40
2270 3480 4.400567 GCCTCTTGAATAATCTTGGCAGTT 59.599 41.667 0.00 0.00 38.99 3.16
2271 3481 5.449725 GCCTCTTGAATAATCTTGGCAGTTC 60.450 44.000 0.00 0.00 38.99 3.01
2339 3549 4.175787 ACGGTCACTTTAGTGCTAGAAG 57.824 45.455 5.00 0.00 45.25 2.85
2364 3574 4.036971 TGCGGTATACATTAAAATGGTGCC 59.963 41.667 5.01 7.31 40.70 5.01
2435 3645 0.744414 GGCAAAGCTGACGAGGCATA 60.744 55.000 0.00 0.00 0.00 3.14
2490 3703 3.364441 TGCAGATTGGGCGTGTGC 61.364 61.111 0.00 0.00 41.71 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.336451 GCAACCAATTTTTAAGATCCGAGGT 60.336 40.000 0.00 0.00 0.00 3.85
56 57 1.197721 GCATTTGCTACTGCTGTCGTT 59.802 47.619 0.00 0.00 40.48 3.85
62 63 1.134907 GCAATGGCATTTGCTACTGCT 60.135 47.619 13.90 0.00 46.66 4.24
112 113 0.179132 TATAAAAGCTGCGACGCCGA 60.179 50.000 18.69 0.00 38.22 5.54
114 115 1.567504 TCTATAAAAGCTGCGACGCC 58.432 50.000 18.69 2.18 0.00 5.68
226 227 5.454520 GTTGTTGGAAAATACTACAACCGG 58.545 41.667 0.00 0.00 41.49 5.28
227 228 5.141568 CGTTGTTGGAAAATACTACAACCG 58.858 41.667 12.30 6.17 43.32 4.44
228 229 5.008911 ACCGTTGTTGGAAAATACTACAACC 59.991 40.000 12.30 0.00 43.32 3.77
229 230 6.063640 ACCGTTGTTGGAAAATACTACAAC 57.936 37.500 9.16 9.16 43.00 3.32
230 231 6.238703 GGAACCGTTGTTGGAAAATACTACAA 60.239 38.462 0.00 0.00 33.97 2.41
231 232 5.239087 GGAACCGTTGTTGGAAAATACTACA 59.761 40.000 0.00 0.00 33.97 2.74
232 233 5.239087 TGGAACCGTTGTTGGAAAATACTAC 59.761 40.000 0.00 0.00 33.97 2.73
233 234 5.374921 TGGAACCGTTGTTGGAAAATACTA 58.625 37.500 0.00 0.00 33.97 1.82
234 235 4.208746 TGGAACCGTTGTTGGAAAATACT 58.791 39.130 0.00 0.00 33.97 2.12
235 236 4.571372 TGGAACCGTTGTTGGAAAATAC 57.429 40.909 0.00 0.00 33.97 1.89
236 237 4.645588 AGTTGGAACCGTTGTTGGAAAATA 59.354 37.500 0.00 0.00 33.97 1.40
237 238 3.449377 AGTTGGAACCGTTGTTGGAAAAT 59.551 39.130 0.00 0.00 33.97 1.82
238 239 2.826725 AGTTGGAACCGTTGTTGGAAAA 59.173 40.909 0.00 0.00 33.97 2.29
239 240 2.424246 GAGTTGGAACCGTTGTTGGAAA 59.576 45.455 0.00 0.00 33.97 3.13
240 241 2.018515 GAGTTGGAACCGTTGTTGGAA 58.981 47.619 0.00 0.00 33.97 3.53
241 242 1.670791 GAGTTGGAACCGTTGTTGGA 58.329 50.000 0.00 0.00 33.97 3.53
242 243 0.306533 CGAGTTGGAACCGTTGTTGG 59.693 55.000 0.00 0.00 33.97 3.77
243 244 0.306533 CCGAGTTGGAACCGTTGTTG 59.693 55.000 0.00 0.00 42.00 3.33
244 245 1.441732 GCCGAGTTGGAACCGTTGTT 61.442 55.000 0.00 0.00 42.00 2.83
245 246 1.890510 GCCGAGTTGGAACCGTTGT 60.891 57.895 0.00 0.00 42.00 3.32
246 247 2.613506 GGCCGAGTTGGAACCGTTG 61.614 63.158 0.00 0.00 42.00 4.10
247 248 2.281276 GGCCGAGTTGGAACCGTT 60.281 61.111 0.00 0.00 42.00 4.44
248 249 4.675029 CGGCCGAGTTGGAACCGT 62.675 66.667 24.07 0.00 42.00 4.83
250 251 3.837570 AACCGGCCGAGTTGGAACC 62.838 63.158 30.73 0.00 42.00 3.62
251 252 2.281276 AACCGGCCGAGTTGGAAC 60.281 61.111 30.73 0.00 42.00 3.62
252 253 2.281208 CAACCGGCCGAGTTGGAA 60.281 61.111 33.72 0.00 40.73 3.53
256 257 1.188863 ATACTACAACCGGCCGAGTT 58.811 50.000 30.73 25.14 0.00 3.01
257 258 1.188863 AATACTACAACCGGCCGAGT 58.811 50.000 30.73 23.72 0.00 4.18
258 259 2.199236 GAAATACTACAACCGGCCGAG 58.801 52.381 30.73 18.62 0.00 4.63
259 260 1.134729 GGAAATACTACAACCGGCCGA 60.135 52.381 30.73 4.63 0.00 5.54
260 261 1.292992 GGAAATACTACAACCGGCCG 58.707 55.000 21.04 21.04 0.00 6.13
261 262 1.065272 TGGGAAATACTACAACCGGCC 60.065 52.381 0.00 0.00 0.00 6.13
262 263 2.406596 TGGGAAATACTACAACCGGC 57.593 50.000 0.00 0.00 0.00 6.13
263 264 3.677190 TGTTGGGAAATACTACAACCGG 58.323 45.455 0.00 0.00 41.74 5.28
281 282 1.441732 GCCGAGTTGGAACCGTTGTT 61.442 55.000 0.00 0.00 42.00 2.83
332 333 2.126307 CCTGACGTCGTGCTGGAG 60.126 66.667 11.62 0.17 0.00 3.86
359 360 0.388649 GTGCTCCAACGACGAGATGT 60.389 55.000 0.00 0.00 0.00 3.06
490 491 0.538516 GAGCTCTCGCATCTCCCCTA 60.539 60.000 6.43 0.00 39.10 3.53
515 516 2.356793 GCGCTCCATCATCTCCGG 60.357 66.667 0.00 0.00 0.00 5.14
532 533 3.190849 CTCCCGCACAGTGCATCG 61.191 66.667 25.19 11.30 45.36 3.84
597 598 2.225727 CGCACTTTTCCCTTGTCCTTAC 59.774 50.000 0.00 0.00 0.00 2.34
632 633 5.309638 TGTCGATTTAAGTGGGATTGAACA 58.690 37.500 0.00 0.00 0.00 3.18
637 638 4.192317 GAGCTGTCGATTTAAGTGGGATT 58.808 43.478 0.00 0.00 0.00 3.01
686 687 1.372501 ATGTTTGTAGCCAGGGGACT 58.627 50.000 0.00 0.00 46.44 3.85
691 692 7.823745 ATAAAGGATAATGTTTGTAGCCAGG 57.176 36.000 0.00 0.00 28.96 4.45
975 1011 1.960417 TTGTGTGATTCGTGAAGGCA 58.040 45.000 0.00 0.00 0.00 4.75
1031 1077 3.726517 CGTCGGCTTTGGGTGCAG 61.727 66.667 0.00 0.00 0.00 4.41
1094 1143 2.677524 TCGGGTAGGTGGACACGG 60.678 66.667 0.00 0.00 46.38 4.94
1368 1423 1.118965 TGGCGAAGACCTGGAACTCA 61.119 55.000 0.00 0.00 25.51 3.41
1401 1456 2.039624 GGGAGGGAGCTCAGGTCA 59.960 66.667 17.19 0.00 0.00 4.02
1927 1989 2.738521 CGGCGTCAGGTGGTTCTG 60.739 66.667 0.00 0.00 36.17 3.02
2095 2858 7.320399 TCATGACTGACGTTCATAGTACAATT 58.680 34.615 1.04 0.00 0.00 2.32
2109 2872 6.672147 TCATGTATACTGATCATGACTGACG 58.328 40.000 0.00 0.00 41.59 4.35
2115 2878 7.661040 ACGATGTTCATGTATACTGATCATGA 58.339 34.615 21.10 12.90 43.71 3.07
2158 3368 3.858238 GCAACAAGACGATCACTAGTACC 59.142 47.826 0.00 0.00 0.00 3.34
2164 3374 1.800805 CAGGCAACAAGACGATCACT 58.199 50.000 0.00 0.00 41.41 3.41
2165 3375 0.166814 GCAGGCAACAAGACGATCAC 59.833 55.000 0.00 0.00 41.41 3.06
2166 3376 1.291184 CGCAGGCAACAAGACGATCA 61.291 55.000 0.00 0.00 41.41 2.92
2167 3377 1.421485 CGCAGGCAACAAGACGATC 59.579 57.895 0.00 0.00 41.41 3.69
2168 3378 2.680913 GCGCAGGCAACAAGACGAT 61.681 57.895 0.30 0.00 39.62 3.73
2169 3379 3.345808 GCGCAGGCAACAAGACGA 61.346 61.111 0.30 0.00 39.62 4.20
2187 3397 2.166584 GAAGGACGAAAACCCACGCG 62.167 60.000 3.53 3.53 0.00 6.01
2190 3400 1.235724 CTGGAAGGACGAAAACCCAC 58.764 55.000 0.00 0.00 0.00 4.61
2192 3402 1.520494 GACTGGAAGGACGAAAACCC 58.480 55.000 0.00 0.00 39.30 4.11
2193 3403 1.145803 CGACTGGAAGGACGAAAACC 58.854 55.000 0.00 0.00 39.43 3.27
2194 3404 1.791204 GACGACTGGAAGGACGAAAAC 59.209 52.381 0.00 0.00 39.43 2.43
2199 3409 1.605058 ATGGGACGACTGGAAGGACG 61.605 60.000 0.00 0.00 41.86 4.79
2201 3411 1.899437 GCATGGGACGACTGGAAGGA 61.899 60.000 0.00 0.00 39.30 3.36
2202 3412 1.450312 GCATGGGACGACTGGAAGG 60.450 63.158 0.00 0.00 39.30 3.46
2204 3414 0.904865 AGAGCATGGGACGACTGGAA 60.905 55.000 0.00 0.00 0.00 3.53
2207 3417 1.364626 GCAAGAGCATGGGACGACTG 61.365 60.000 0.00 0.00 41.58 3.51
2210 3420 0.036732 AAAGCAAGAGCATGGGACGA 59.963 50.000 0.00 0.00 45.49 4.20
2212 3422 2.620585 GGATAAAGCAAGAGCATGGGAC 59.379 50.000 0.00 0.00 45.49 4.46
2213 3423 2.511218 AGGATAAAGCAAGAGCATGGGA 59.489 45.455 0.00 0.00 45.49 4.37
2215 3425 3.818180 AGAGGATAAAGCAAGAGCATGG 58.182 45.455 0.00 0.00 45.49 3.66
2217 3427 4.125703 CGAAGAGGATAAAGCAAGAGCAT 58.874 43.478 0.00 0.00 45.49 3.79
2218 3428 3.525537 CGAAGAGGATAAAGCAAGAGCA 58.474 45.455 0.00 0.00 45.49 4.26
2219 3429 2.869192 CCGAAGAGGATAAAGCAAGAGC 59.131 50.000 0.00 0.00 45.00 4.09
2220 3430 2.869192 GCCGAAGAGGATAAAGCAAGAG 59.131 50.000 0.00 0.00 45.00 2.85
2221 3431 2.236146 TGCCGAAGAGGATAAAGCAAGA 59.764 45.455 0.00 0.00 45.00 3.02
2223 3433 2.747446 GTTGCCGAAGAGGATAAAGCAA 59.253 45.455 0.00 0.00 45.00 3.91
2224 3434 2.356135 GTTGCCGAAGAGGATAAAGCA 58.644 47.619 0.00 0.00 45.00 3.91
2225 3435 1.671328 GGTTGCCGAAGAGGATAAAGC 59.329 52.381 0.00 0.00 45.00 3.51
2227 3437 2.939640 GCAGGTTGCCGAAGAGGATAAA 60.940 50.000 0.00 0.00 45.00 1.40
2228 3438 1.406887 GCAGGTTGCCGAAGAGGATAA 60.407 52.381 0.00 0.00 45.00 1.75
2240 3450 3.950395 AGATTATTCAAGAGGCAGGTTGC 59.050 43.478 0.00 0.00 44.08 4.17
2241 3451 5.163581 CCAAGATTATTCAAGAGGCAGGTTG 60.164 44.000 0.00 0.00 0.00 3.77
2242 3452 4.952335 CCAAGATTATTCAAGAGGCAGGTT 59.048 41.667 0.00 0.00 0.00 3.50
2243 3453 4.530875 CCAAGATTATTCAAGAGGCAGGT 58.469 43.478 0.00 0.00 0.00 4.00
2244 3454 3.317430 GCCAAGATTATTCAAGAGGCAGG 59.683 47.826 0.00 0.00 40.50 4.85
2247 3457 3.950395 ACTGCCAAGATTATTCAAGAGGC 59.050 43.478 0.00 0.00 41.15 4.70
2248 3458 5.884792 AGAACTGCCAAGATTATTCAAGAGG 59.115 40.000 0.00 0.00 0.00 3.69
2249 3459 6.998968 AGAACTGCCAAGATTATTCAAGAG 57.001 37.500 0.00 0.00 0.00 2.85
2250 3460 7.765695 AAAGAACTGCCAAGATTATTCAAGA 57.234 32.000 0.00 0.00 0.00 3.02
2259 3469 9.771534 GACTCTATATAAAAGAACTGCCAAGAT 57.228 33.333 0.05 0.00 0.00 2.40
2260 3470 8.758829 TGACTCTATATAAAAGAACTGCCAAGA 58.241 33.333 0.05 0.00 0.00 3.02
2261 3471 8.948631 TGACTCTATATAAAAGAACTGCCAAG 57.051 34.615 0.05 0.00 0.00 3.61
2262 3472 9.905713 ATTGACTCTATATAAAAGAACTGCCAA 57.094 29.630 0.05 0.00 0.00 4.52
2263 3473 9.905713 AATTGACTCTATATAAAAGAACTGCCA 57.094 29.630 0.05 0.00 0.00 4.92
2339 3549 5.457473 GCACCATTTTAATGTATACCGCAAC 59.543 40.000 0.00 0.00 34.60 4.17
2364 3574 3.196463 TGCATGTTCAAGCCAAGTTTTG 58.804 40.909 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.