Multiple sequence alignment - TraesCS7B01G208200

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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 TraesCS7B01G208200 chr7B 100.000 2522 0 0 1 2522 380864885 380862364 0.000000e+00 4658.0
1 TraesCS7B01G208200 chr7B 94.030 871 40 3 654 1516 380856642 380855776 0.000000e+00 1310.0
2 TraesCS7B01G208200 chr7B 84.211 266 29 3 112 377 380837007 380836755 1.940000e-61 246.0
3 TraesCS7B01G208200 chr7B 81.413 269 42 7 375 639 682235398 682235662 1.970000e-51 213.0
4 TraesCS7B01G208200 chr7A 90.083 1684 102 32 562 2214 435865659 435864010 0.000000e+00 2124.0
5 TraesCS7B01G208200 chr7A 92.940 864 43 4 659 1517 435827737 435826887 0.000000e+00 1242.0
6 TraesCS7B01G208200 chr7A 84.848 594 47 13 1 575 435866245 435865676 2.190000e-155 558.0
7 TraesCS7B01G208200 chr7A 76.496 685 112 23 1789 2452 435821964 435821308 6.730000e-86 327.0
8 TraesCS7B01G208200 chr7A 87.310 197 24 1 435 631 543069343 543069538 9.080000e-55 224.0
9 TraesCS7B01G208200 chr7D 90.458 1551 93 17 1 1530 386564326 386562810 0.000000e+00 1993.0
10 TraesCS7B01G208200 chr7D 79.558 362 53 12 2094 2452 386560455 386560112 3.240000e-59 239.0
11 TraesCS7B01G208200 chr7D 92.754 69 5 0 2454 2522 578161977 578161909 1.600000e-17 100.0
12 TraesCS7B01G208200 chr7D 95.000 40 1 1 1682 1721 386562658 386562620 7.530000e-06 62.1
13 TraesCS7B01G208200 chr3A 82.154 325 47 9 326 645 393917848 393917530 4.140000e-68 268.0
14 TraesCS7B01G208200 chr5D 81.538 325 52 7 326 646 128663372 128663692 6.920000e-66 261.0
15 TraesCS7B01G208200 chr6A 81.366 322 52 6 326 645 60161536 60161851 3.220000e-64 255.0
16 TraesCS7B01G208200 chr6A 92.754 69 5 0 2454 2522 464506809 464506741 1.600000e-17 100.0
17 TraesCS7B01G208200 chr3D 80.062 321 61 3 326 645 463114151 463113833 4.190000e-58 235.0
18 TraesCS7B01G208200 chr2A 80.062 321 58 4 326 643 81166010 81165693 1.510000e-57 233.0
19 TraesCS7B01G208200 chr2A 92.754 69 4 1 2454 2521 288959150 288959218 5.740000e-17 99.0
20 TraesCS7B01G208200 chr1D 80.124 322 57 5 326 645 466941039 466940723 1.510000e-57 233.0
21 TraesCS7B01G208200 chr1D 87.952 83 7 3 2442 2522 431627485 431627404 7.430000e-16 95.3
22 TraesCS7B01G208200 chr6B 94.203 69 4 0 2454 2522 91130310 91130242 3.430000e-19 106.0
23 TraesCS7B01G208200 chr6B 92.754 69 5 0 2454 2522 631847740 631847672 1.600000e-17 100.0
24 TraesCS7B01G208200 chr2B 92.754 69 5 0 2454 2522 556849502 556849434 1.600000e-17 100.0
25 TraesCS7B01G208200 chr2B 86.747 83 9 2 2441 2522 109923505 109923586 9.610000e-15 91.6
26 TraesCS7B01G208200 chr1B 92.857 70 4 1 2454 2522 30008198 30008267 1.600000e-17 100.0


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 TraesCS7B01G208200 chr7B 380862364 380864885 2521 True 4658.0 4658 100.000000 1 2522 1 chr7B.!!$R3 2521
1 TraesCS7B01G208200 chr7B 380855776 380856642 866 True 1310.0 1310 94.030000 654 1516 1 chr7B.!!$R2 862
2 TraesCS7B01G208200 chr7A 435864010 435866245 2235 True 1341.0 2124 87.465500 1 2214 2 chr7A.!!$R3 2213
3 TraesCS7B01G208200 chr7A 435826887 435827737 850 True 1242.0 1242 92.940000 659 1517 1 chr7A.!!$R2 858
4 TraesCS7B01G208200 chr7A 435821308 435821964 656 True 327.0 327 76.496000 1789 2452 1 chr7A.!!$R1 663
5 TraesCS7B01G208200 chr7D 386560112 386564326 4214 True 764.7 1993 88.338667 1 2452 3 chr7D.!!$R2 2451

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
897 959 0.179018 AACACAACCAGTCCAGAGCC 60.179 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 4115 0.034896 TCTTGAAGCGGAACAGTCCC 59.965 55.0 0.0 0.0 41.44 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
30 31 2.599875 TCTGGCGCCCAATGCAAA 60.600 55.556 26.77 0.19 41.33 3.68
87 88 2.362397 GGATCTCATCAACGTCCAGCTA 59.638 50.000 0.00 0.00 0.00 3.32
108 109 5.507985 GCTACAAGAAATGTTGGTGAAGCTT 60.508 40.000 0.00 0.00 43.63 3.74
109 110 4.936891 ACAAGAAATGTTGGTGAAGCTTC 58.063 39.130 19.89 19.89 40.06 3.86
122 140 3.552294 GTGAAGCTTCATCGGTTAGTAGC 59.448 47.826 30.65 10.59 39.73 3.58
142 160 0.686441 TCAGCTACCCGGCAGTATGT 60.686 55.000 0.00 0.00 39.31 2.29
148 166 3.508793 GCTACCCGGCAGTATGTATAGAA 59.491 47.826 0.00 0.00 39.31 2.10
149 167 4.021719 GCTACCCGGCAGTATGTATAGAAA 60.022 45.833 0.00 0.00 39.31 2.52
150 168 5.510179 GCTACCCGGCAGTATGTATAGAAAA 60.510 44.000 0.00 0.00 39.31 2.29
194 212 4.826274 TGTCTAAACCTTCTCCCATGAG 57.174 45.455 0.00 0.00 40.17 2.90
219 237 9.545105 AGTAATGAAAATGACAAATCTTTTGCA 57.455 25.926 0.06 0.00 40.20 4.08
230 248 8.816144 TGACAAATCTTTTGCATTGTTTAGAAC 58.184 29.630 2.85 0.00 36.22 3.01
271 290 1.808343 GCAACCGTTGGTAAACCTAGG 59.192 52.381 7.41 7.41 33.12 3.02
273 292 2.809696 CAACCGTTGGTAAACCTAGGTG 59.190 50.000 17.14 1.46 37.62 4.00
274 293 2.328319 ACCGTTGGTAAACCTAGGTGA 58.672 47.619 17.14 3.58 36.76 4.02
275 294 2.908351 ACCGTTGGTAAACCTAGGTGAT 59.092 45.455 17.14 10.51 36.76 3.06
276 295 3.055602 ACCGTTGGTAAACCTAGGTGATC 60.056 47.826 17.14 7.83 36.76 2.92
277 296 3.528532 CGTTGGTAAACCTAGGTGATCC 58.471 50.000 17.14 17.35 36.82 3.36
278 297 3.197116 CGTTGGTAAACCTAGGTGATCCT 59.803 47.826 17.14 0.00 39.18 3.24
279 298 4.403432 CGTTGGTAAACCTAGGTGATCCTA 59.597 45.833 17.14 11.71 43.17 2.94
280 299 5.105228 CGTTGGTAAACCTAGGTGATCCTAA 60.105 44.000 17.14 11.31 44.63 2.69
338 357 4.363991 AGGATCTTGCTTCACTGACTTT 57.636 40.909 0.00 0.00 0.00 2.66
404 424 8.374743 TCATCCATTAAAGATCCGACATATCAA 58.625 33.333 0.00 0.00 0.00 2.57
506 526 8.973835 TTCGTTTTGTATTCTGTGAAAGTTTT 57.026 26.923 0.00 0.00 0.00 2.43
535 555 1.136891 TGGATGTATCGCCTGTGAGTG 59.863 52.381 0.00 0.00 0.00 3.51
572 622 2.479566 TGAGCTCCAAAGGCTAGTTG 57.520 50.000 12.15 0.00 40.40 3.16
690 740 5.862323 GCAGTACGTATGTATGGAATCGATT 59.138 40.000 11.20 11.20 32.11 3.34
754 807 5.629020 CGCCACATTTTAATTATGCGCTATT 59.371 36.000 9.73 8.51 34.06 1.73
767 820 3.325870 TGCGCTATTATTTCCAGATCGG 58.674 45.455 9.73 0.00 0.00 4.18
860 920 6.198687 GTCTCATCTGTATATATCGCAGAGC 58.801 44.000 18.66 8.23 43.63 4.09
861 921 5.882557 TCTCATCTGTATATATCGCAGAGCA 59.117 40.000 18.66 10.68 43.63 4.26
862 922 6.375455 TCTCATCTGTATATATCGCAGAGCAA 59.625 38.462 18.66 10.04 43.63 3.91
863 923 6.924111 TCATCTGTATATATCGCAGAGCAAA 58.076 36.000 18.66 7.33 43.63 3.68
864 924 7.378181 TCATCTGTATATATCGCAGAGCAAAA 58.622 34.615 18.66 6.17 43.63 2.44
897 959 0.179018 AACACAACCAGTCCAGAGCC 60.179 55.000 0.00 0.00 0.00 4.70
914 976 1.440518 CCGCGACCTCGATCATACG 60.441 63.158 8.23 0.00 43.02 3.06
970 1032 3.194062 GGTCATCTTCTCAAGTGCTAGC 58.806 50.000 8.10 8.10 0.00 3.42
971 1033 3.118811 GGTCATCTTCTCAAGTGCTAGCT 60.119 47.826 17.23 0.00 0.00 3.32
1006 1068 3.846180 GGCATTCATCCATGGCGT 58.154 55.556 6.96 0.00 39.67 5.68
1215 1277 1.145156 CAACGTGGTGGAGGTGACA 59.855 57.895 0.00 0.00 0.00 3.58
1217 1279 0.179056 AACGTGGTGGAGGTGACAAG 60.179 55.000 0.00 0.00 0.00 3.16
1228 1290 1.542187 GGTGACAAGGACGGCCTACT 61.542 60.000 12.33 0.00 46.28 2.57
1324 1386 2.230940 CGGTACTTCATCTGCGGCG 61.231 63.158 0.51 0.51 0.00 6.46
1530 1592 6.378280 TGATGCTTCTCTACTAGTCATCAACA 59.622 38.462 15.14 2.77 36.07 3.33
1543 1605 5.003804 AGTCATCAACAACAACCTCCATAC 58.996 41.667 0.00 0.00 0.00 2.39
1545 1607 2.773487 TCAACAACAACCTCCATACGG 58.227 47.619 0.00 0.00 0.00 4.02
1607 1674 5.047377 GTGATGACTTTCTCCTCTCTCAAGT 60.047 44.000 0.00 0.00 0.00 3.16
1628 1697 2.674357 TGTGATTGATCGTGCACATGAG 59.326 45.455 18.64 0.00 36.44 2.90
1629 1698 2.931969 GTGATTGATCGTGCACATGAGA 59.068 45.455 18.64 6.11 0.00 3.27
1630 1699 3.558829 GTGATTGATCGTGCACATGAGAT 59.441 43.478 18.64 11.13 0.00 2.75
1632 1701 4.271776 TGATTGATCGTGCACATGAGATTC 59.728 41.667 18.64 6.66 0.00 2.52
1634 1703 3.865446 TGATCGTGCACATGAGATTCTT 58.135 40.909 18.64 0.00 0.00 2.52
1636 1705 4.093850 TGATCGTGCACATGAGATTCTTTG 59.906 41.667 18.64 0.00 0.00 2.77
1648 1717 9.725019 ACATGAGATTCTTTGTAGTCAAATGTA 57.275 29.630 0.00 0.00 41.77 2.29
1743 1837 4.098960 ACAGTGGATCAATTTCATGGCATC 59.901 41.667 0.00 0.00 0.00 3.91
1787 2118 6.554334 TTTAGAACATAGACACAAGTTGGC 57.446 37.500 7.96 0.00 0.00 4.52
1812 2143 5.887598 CCCATGAGATACAACCAAGATCAAA 59.112 40.000 0.00 0.00 0.00 2.69
1816 2147 8.733458 CATGAGATACAACCAAGATCAAAGAAA 58.267 33.333 0.00 0.00 0.00 2.52
1879 2212 3.006940 GTGAAATCACCAATGGCGACTA 58.993 45.455 0.00 0.00 40.85 2.59
1880 2213 3.627577 GTGAAATCACCAATGGCGACTAT 59.372 43.478 0.00 0.00 40.85 2.12
1881 2214 4.814234 GTGAAATCACCAATGGCGACTATA 59.186 41.667 0.00 0.00 40.85 1.31
1882 2215 5.470098 GTGAAATCACCAATGGCGACTATAT 59.530 40.000 0.00 0.00 40.85 0.86
1883 2216 5.469760 TGAAATCACCAATGGCGACTATATG 59.530 40.000 0.00 0.00 0.00 1.78
1884 2217 4.623932 ATCACCAATGGCGACTATATGT 57.376 40.909 0.00 0.00 0.00 2.29
1885 2218 3.990092 TCACCAATGGCGACTATATGTC 58.010 45.455 0.00 0.00 42.06 3.06
1886 2219 3.641436 TCACCAATGGCGACTATATGTCT 59.359 43.478 0.00 0.00 43.25 3.41
1887 2220 4.830600 TCACCAATGGCGACTATATGTCTA 59.169 41.667 0.00 0.00 43.25 2.59
1909 3111 0.250467 TCCAGCTGCTTGTTGAGGAC 60.250 55.000 8.66 0.00 0.00 3.85
1911 3113 1.073897 AGCTGCTTGTTGAGGACCC 59.926 57.895 0.00 0.00 0.00 4.46
1921 3123 0.035820 TTGAGGACCCGCCATACAAC 60.036 55.000 0.00 0.00 40.02 3.32
1928 3131 2.752903 GACCCGCCATACAACAAGAAAT 59.247 45.455 0.00 0.00 0.00 2.17
1956 3161 8.811994 ACAAAGTTTATAAATGGCACCAATAGT 58.188 29.630 0.31 0.00 0.00 2.12
1960 3165 9.030452 AGTTTATAAATGGCACCAATAGTTTCA 57.970 29.630 0.31 0.00 0.00 2.69
2069 3281 3.802948 CGTGAGCTAGTCCTATTGGTT 57.197 47.619 0.00 0.00 34.23 3.67
2072 3284 4.567159 CGTGAGCTAGTCCTATTGGTTTTC 59.433 45.833 0.00 0.00 34.23 2.29
2073 3285 5.624738 CGTGAGCTAGTCCTATTGGTTTTCT 60.625 44.000 0.00 0.00 34.23 2.52
2074 3286 6.405508 CGTGAGCTAGTCCTATTGGTTTTCTA 60.406 42.308 0.00 0.00 34.23 2.10
2075 3287 7.328737 GTGAGCTAGTCCTATTGGTTTTCTAA 58.671 38.462 0.00 0.00 34.23 2.10
2076 3288 7.492994 GTGAGCTAGTCCTATTGGTTTTCTAAG 59.507 40.741 0.00 0.00 34.23 2.18
2077 3289 7.399191 TGAGCTAGTCCTATTGGTTTTCTAAGA 59.601 37.037 0.00 0.00 34.23 2.10
2078 3290 7.787028 AGCTAGTCCTATTGGTTTTCTAAGAG 58.213 38.462 0.00 0.00 34.23 2.85
2080 3292 8.041919 GCTAGTCCTATTGGTTTTCTAAGAGTT 58.958 37.037 0.00 0.00 29.59 3.01
2081 3293 9.945904 CTAGTCCTATTGGTTTTCTAAGAGTTT 57.054 33.333 0.00 0.00 29.59 2.66
2091 3997 9.720769 TGGTTTTCTAAGAGTTTTAGTAGGATG 57.279 33.333 0.74 0.00 0.00 3.51
2136 4042 4.260170 TGAAAGCAGCACCACAAAAATTT 58.740 34.783 0.00 0.00 0.00 1.82
2209 4115 1.715585 GCGGACAACGGTCATCATG 59.284 57.895 0.00 0.00 46.17 3.07
2212 4118 0.251916 GGACAACGGTCATCATGGGA 59.748 55.000 0.00 0.00 46.17 4.37
2214 4120 0.984230 ACAACGGTCATCATGGGACT 59.016 50.000 15.08 0.00 35.61 3.85
2218 4124 1.656652 CGGTCATCATGGGACTGTTC 58.343 55.000 15.19 2.43 36.98 3.18
2219 4125 1.743772 CGGTCATCATGGGACTGTTCC 60.744 57.143 15.19 0.00 41.95 3.62
2221 4127 0.107703 TCATCATGGGACTGTTCCGC 60.108 55.000 0.00 0.00 43.94 5.54
2252 4158 3.829601 CTCTTGACCAGAGTAAGACCACT 59.170 47.826 0.00 0.00 43.96 4.00
2254 4160 5.580998 TCTTGACCAGAGTAAGACCACTAT 58.419 41.667 0.00 0.00 0.00 2.12
2255 4161 5.419155 TCTTGACCAGAGTAAGACCACTATG 59.581 44.000 0.00 0.00 37.47 2.23
2256 4162 4.930696 TGACCAGAGTAAGACCACTATGA 58.069 43.478 0.00 0.00 39.58 2.15
2267 4173 8.321353 AGTAAGACCACTATGAATCAATTGTCA 58.679 33.333 5.13 3.18 0.00 3.58
2268 4174 6.992063 AGACCACTATGAATCAATTGTCAC 57.008 37.500 5.13 0.00 0.00 3.67
2269 4175 6.715280 AGACCACTATGAATCAATTGTCACT 58.285 36.000 5.13 0.00 0.00 3.41
2270 4176 6.596888 AGACCACTATGAATCAATTGTCACTG 59.403 38.462 5.13 2.67 0.00 3.66
2271 4177 6.475504 ACCACTATGAATCAATTGTCACTGA 58.524 36.000 5.13 0.00 0.00 3.41
2272 4178 6.942005 ACCACTATGAATCAATTGTCACTGAA 59.058 34.615 5.13 0.00 0.00 3.02
2273 4179 7.448161 ACCACTATGAATCAATTGTCACTGAAA 59.552 33.333 5.13 0.00 0.00 2.69
2274 4180 7.966753 CCACTATGAATCAATTGTCACTGAAAG 59.033 37.037 5.13 0.54 42.29 2.62
2275 4181 8.724229 CACTATGAATCAATTGTCACTGAAAGA 58.276 33.333 5.13 0.00 37.43 2.52
2276 4182 9.458727 ACTATGAATCAATTGTCACTGAAAGAT 57.541 29.630 5.13 0.00 37.43 2.40
2277 4183 9.932699 CTATGAATCAATTGTCACTGAAAGATC 57.067 33.333 5.13 0.00 37.43 2.75
2278 4184 7.149569 TGAATCAATTGTCACTGAAAGATCC 57.850 36.000 5.13 0.00 37.43 3.36
2279 4185 6.716173 TGAATCAATTGTCACTGAAAGATCCA 59.284 34.615 5.13 0.00 37.43 3.41
2294 4200 4.796038 AGATCCAAATTTTGAGTGGCAG 57.204 40.909 10.72 0.00 32.10 4.85
2309 4215 0.745845 GGCAGCTTGATCGACCACAT 60.746 55.000 0.00 0.00 0.00 3.21
2310 4216 1.089920 GCAGCTTGATCGACCACATT 58.910 50.000 0.00 0.00 0.00 2.71
2311 4217 1.470098 GCAGCTTGATCGACCACATTT 59.530 47.619 0.00 0.00 0.00 2.32
2316 4222 4.037923 AGCTTGATCGACCACATTTTTGTT 59.962 37.500 0.00 0.00 0.00 2.83
2321 4227 6.434596 TGATCGACCACATTTTTGTTAGTTG 58.565 36.000 0.00 0.00 0.00 3.16
2327 4233 3.420576 CACATTTTTGTTAGTTGCGTCGG 59.579 43.478 0.00 0.00 0.00 4.79
2332 4238 2.047655 TTAGTTGCGTCGGGCCAG 60.048 61.111 4.39 0.00 42.61 4.85
2336 4242 2.517402 TTGCGTCGGGCCAGTTTT 60.517 55.556 4.39 0.00 42.61 2.43
2347 4253 0.388520 GCCAGTTTTAGCCAAAGCGG 60.389 55.000 0.00 0.23 46.67 5.52
2349 4255 1.068541 CCAGTTTTAGCCAAAGCGGTC 60.069 52.381 0.00 0.00 46.67 4.79
2378 4284 2.879026 GAGACCTTGTGGAGAAACAACC 59.121 50.000 0.00 0.00 35.16 3.77
2379 4285 2.241176 AGACCTTGTGGAGAAACAACCA 59.759 45.455 0.00 0.00 35.16 3.67
2387 4293 1.611936 GGAGAAACAACCAGAGGGCTC 60.612 57.143 0.00 0.00 37.90 4.70
2390 4296 2.108952 AGAAACAACCAGAGGGCTCAAT 59.891 45.455 0.00 0.00 37.90 2.57
2395 4301 1.516110 ACCAGAGGGCTCAATATGCT 58.484 50.000 0.00 0.00 37.90 3.79
2407 4313 7.946776 AGGGCTCAATATGCTAGTAATCAAATT 59.053 33.333 0.00 0.00 0.00 1.82
2408 4314 9.231297 GGGCTCAATATGCTAGTAATCAAATTA 57.769 33.333 0.00 0.00 0.00 1.40
2418 4324 9.905713 TGCTAGTAATCAAATTAGGTTTCATCT 57.094 29.630 0.00 0.00 0.00 2.90
2434 4340 5.337956 TTCATCTATGGCATAACCCCATT 57.662 39.130 8.79 0.00 42.78 3.16
2442 4348 2.622977 GGCATAACCCCATTCAGGTCAA 60.623 50.000 0.00 0.00 36.27 3.18
2444 4350 3.131046 GCATAACCCCATTCAGGTCAAAG 59.869 47.826 0.00 0.00 36.27 2.77
2452 4358 3.760151 CCATTCAGGTCAAAGATCAAGCA 59.240 43.478 0.00 0.00 0.00 3.91
2453 4359 4.401519 CCATTCAGGTCAAAGATCAAGCAT 59.598 41.667 0.00 0.00 0.00 3.79
2454 4360 5.591472 CCATTCAGGTCAAAGATCAAGCATA 59.409 40.000 0.00 0.00 0.00 3.14
2455 4361 6.459298 CCATTCAGGTCAAAGATCAAGCATAC 60.459 42.308 0.00 0.00 0.00 2.39
2456 4362 4.517285 TCAGGTCAAAGATCAAGCATACC 58.483 43.478 0.00 0.00 0.00 2.73
2457 4363 4.019411 TCAGGTCAAAGATCAAGCATACCA 60.019 41.667 0.00 0.00 0.00 3.25
2458 4364 4.701651 CAGGTCAAAGATCAAGCATACCAA 59.298 41.667 0.00 0.00 0.00 3.67
2459 4365 5.183713 CAGGTCAAAGATCAAGCATACCAAA 59.816 40.000 0.00 0.00 0.00 3.28
2460 4366 5.774690 AGGTCAAAGATCAAGCATACCAAAA 59.225 36.000 0.00 0.00 0.00 2.44
2461 4367 6.267471 AGGTCAAAGATCAAGCATACCAAAAA 59.733 34.615 0.00 0.00 0.00 1.94
2476 4382 1.745890 AAAAAGGCTTTCACCCCGC 59.254 52.632 13.76 0.00 0.00 6.13
2477 4383 0.759060 AAAAAGGCTTTCACCCCGCT 60.759 50.000 13.76 0.00 0.00 5.52
2478 4384 0.759060 AAAAGGCTTTCACCCCGCTT 60.759 50.000 13.76 0.00 0.00 4.68
2479 4385 0.759060 AAAGGCTTTCACCCCGCTTT 60.759 50.000 6.68 0.00 0.00 3.51
2480 4386 0.111639 AAGGCTTTCACCCCGCTTTA 59.888 50.000 0.00 0.00 0.00 1.85
2481 4387 0.331616 AGGCTTTCACCCCGCTTTAT 59.668 50.000 0.00 0.00 0.00 1.40
2482 4388 1.562475 AGGCTTTCACCCCGCTTTATA 59.438 47.619 0.00 0.00 0.00 0.98
2483 4389 2.174854 AGGCTTTCACCCCGCTTTATAT 59.825 45.455 0.00 0.00 0.00 0.86
2484 4390 3.393278 AGGCTTTCACCCCGCTTTATATA 59.607 43.478 0.00 0.00 0.00 0.86
2485 4391 4.042934 AGGCTTTCACCCCGCTTTATATAT 59.957 41.667 0.00 0.00 0.00 0.86
2486 4392 5.249852 AGGCTTTCACCCCGCTTTATATATA 59.750 40.000 0.00 0.00 0.00 0.86
2487 4393 5.941647 GGCTTTCACCCCGCTTTATATATAA 59.058 40.000 0.81 0.81 0.00 0.98
2488 4394 6.431852 GGCTTTCACCCCGCTTTATATATAAA 59.568 38.462 15.47 15.47 0.00 1.40
2507 4413 4.996788 AAAGCAAAGATCATCATCACCC 57.003 40.909 0.00 0.00 0.00 4.61
2508 4414 2.569059 AGCAAAGATCATCATCACCCG 58.431 47.619 0.00 0.00 0.00 5.28
2509 4415 2.171237 AGCAAAGATCATCATCACCCGA 59.829 45.455 0.00 0.00 0.00 5.14
2510 4416 3.144506 GCAAAGATCATCATCACCCGAT 58.855 45.455 0.00 0.00 0.00 4.18
2511 4417 4.040829 AGCAAAGATCATCATCACCCGATA 59.959 41.667 0.00 0.00 0.00 2.92
2512 4418 4.153117 GCAAAGATCATCATCACCCGATAC 59.847 45.833 0.00 0.00 0.00 2.24
2513 4419 5.299949 CAAAGATCATCATCACCCGATACA 58.700 41.667 0.00 0.00 0.00 2.29
2514 4420 5.551305 AAGATCATCATCACCCGATACAA 57.449 39.130 0.00 0.00 0.00 2.41
2515 4421 5.551305 AGATCATCATCACCCGATACAAA 57.449 39.130 0.00 0.00 0.00 2.83
2516 4422 5.300752 AGATCATCATCACCCGATACAAAC 58.699 41.667 0.00 0.00 0.00 2.93
2517 4423 4.479786 TCATCATCACCCGATACAAACA 57.520 40.909 0.00 0.00 0.00 2.83
2518 4424 4.188462 TCATCATCACCCGATACAAACAC 58.812 43.478 0.00 0.00 0.00 3.32
2519 4425 3.686916 TCATCACCCGATACAAACACA 57.313 42.857 0.00 0.00 0.00 3.72
2520 4426 3.331150 TCATCACCCGATACAAACACAC 58.669 45.455 0.00 0.00 0.00 3.82
2521 4427 1.785768 TCACCCGATACAAACACACG 58.214 50.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.949525 GGCTGGATGACGTATTTGCAT 59.050 47.619 0.00 0.00 0.00 3.96
87 88 4.402155 TGAAGCTTCACCAACATTTCTTGT 59.598 37.500 25.16 0.00 34.07 3.16
108 109 2.656002 AGCTGAGCTACTAACCGATGA 58.344 47.619 4.49 0.00 36.99 2.92
122 140 0.032678 CATACTGCCGGGTAGCTGAG 59.967 60.000 12.41 0.00 35.80 3.35
142 160 7.280356 GGTCCCTACTGCTTGATTTTTCTATA 58.720 38.462 0.00 0.00 0.00 1.31
148 166 2.378547 TGGGTCCCTACTGCTTGATTTT 59.621 45.455 10.00 0.00 0.00 1.82
149 167 1.992557 TGGGTCCCTACTGCTTGATTT 59.007 47.619 10.00 0.00 0.00 2.17
150 168 1.668826 TGGGTCCCTACTGCTTGATT 58.331 50.000 10.00 0.00 0.00 2.57
271 290 5.510520 GGTCATCTGGATCACTTAGGATCAC 60.511 48.000 11.02 4.03 44.38 3.06
273 292 4.837860 AGGTCATCTGGATCACTTAGGATC 59.162 45.833 0.00 0.00 42.36 3.36
274 293 4.825445 AGGTCATCTGGATCACTTAGGAT 58.175 43.478 0.00 0.00 0.00 3.24
275 294 4.271807 AGGTCATCTGGATCACTTAGGA 57.728 45.455 0.00 0.00 0.00 2.94
276 295 5.104776 TGAAAGGTCATCTGGATCACTTAGG 60.105 44.000 0.00 0.00 0.00 2.69
277 296 5.982356 TGAAAGGTCATCTGGATCACTTAG 58.018 41.667 0.00 0.00 0.00 2.18
278 297 6.566079 ATGAAAGGTCATCTGGATCACTTA 57.434 37.500 0.00 0.00 40.69 2.24
279 298 4.916041 TGAAAGGTCATCTGGATCACTT 57.084 40.909 0.00 0.00 0.00 3.16
280 299 5.901853 TCTATGAAAGGTCATCTGGATCACT 59.098 40.000 0.00 0.00 43.69 3.41
315 334 5.690464 AAGTCAGTGAAGCAAGATCCTAT 57.310 39.130 0.00 0.00 0.00 2.57
338 357 6.455647 AGTCACGTTGAGATTTGACTTCATA 58.544 36.000 0.00 0.00 45.06 2.15
345 364 4.753107 GGGTTAAGTCACGTTGAGATTTGA 59.247 41.667 0.00 0.00 0.00 2.69
349 368 4.618920 AAGGGTTAAGTCACGTTGAGAT 57.381 40.909 0.00 0.00 0.00 2.75
378 398 7.906327 TGATATGTCGGATCTTTAATGGATGA 58.094 34.615 0.00 0.00 0.00 2.92
404 424 4.905456 TCCAGTTCGGAATATGGGTCTATT 59.095 41.667 19.04 0.00 42.52 1.73
407 427 2.759355 TCCAGTTCGGAATATGGGTCT 58.241 47.619 19.04 0.00 42.52 3.85
546 566 6.900194 ACTAGCCTTTGGAGCTCAAATAATA 58.100 36.000 17.19 1.25 43.57 0.98
547 567 5.760131 ACTAGCCTTTGGAGCTCAAATAAT 58.240 37.500 17.19 0.04 43.57 1.28
560 580 4.321230 GGGTTTGTGATCAACTAGCCTTTG 60.321 45.833 0.00 0.00 35.67 2.77
572 622 3.573967 AGTTGGATGTTGGGTTTGTGATC 59.426 43.478 0.00 0.00 0.00 2.92
650 700 7.377766 ACGTACTGCACAATAATCAGATTTT 57.622 32.000 0.00 0.00 0.00 1.82
651 701 6.985188 ACGTACTGCACAATAATCAGATTT 57.015 33.333 0.00 0.00 0.00 2.17
652 702 7.710907 ACATACGTACTGCACAATAATCAGATT 59.289 33.333 0.00 0.20 0.00 2.40
664 714 4.381863 CGATTCCATACATACGTACTGCAC 59.618 45.833 0.00 0.00 0.00 4.57
690 740 0.105964 AGCTGCTAGCCTACTGCCTA 60.106 55.000 13.29 0.00 43.77 3.93
754 807 1.342174 GTACGGGCCGATCTGGAAATA 59.658 52.381 35.78 8.12 42.00 1.40
860 920 7.359431 GGTTGTGTTGTAGCATGATGATTTTTG 60.359 37.037 0.00 0.00 0.00 2.44
861 921 6.646240 GGTTGTGTTGTAGCATGATGATTTTT 59.354 34.615 0.00 0.00 0.00 1.94
862 922 6.158598 GGTTGTGTTGTAGCATGATGATTTT 58.841 36.000 0.00 0.00 0.00 1.82
863 923 5.243507 TGGTTGTGTTGTAGCATGATGATTT 59.756 36.000 0.00 0.00 0.00 2.17
864 924 4.766373 TGGTTGTGTTGTAGCATGATGATT 59.234 37.500 0.00 0.00 0.00 2.57
897 959 0.721811 GACGTATGATCGAGGTCGCG 60.722 60.000 0.00 0.00 39.60 5.87
914 976 3.742433 ATGTTGAGATGATCGAGGGAC 57.258 47.619 0.00 0.00 0.00 4.46
970 1032 2.350007 GCCAATCGAGCGACTAGTAGAG 60.350 54.545 7.23 0.00 0.00 2.43
971 1033 1.602851 GCCAATCGAGCGACTAGTAGA 59.397 52.381 7.23 0.00 0.00 2.59
1071 1133 3.056458 CCGACTGTGTAGGTGGCA 58.944 61.111 0.00 0.00 0.00 4.92
1215 1277 1.549170 CAGTTGTAGTAGGCCGTCCTT 59.451 52.381 0.00 0.00 40.66 3.36
1217 1279 0.459759 GCAGTTGTAGTAGGCCGTCC 60.460 60.000 0.00 0.00 0.00 4.79
1228 1290 1.895798 ACTAGAGCTGCTGCAGTTGTA 59.104 47.619 28.50 23.60 42.74 2.41
1499 1561 5.725362 ACTAGTAGAGAAGCATCAAACCAC 58.275 41.667 3.59 0.00 0.00 4.16
1567 1632 6.234177 AGTCATCACGGAAAGAAAGAGAAAT 58.766 36.000 0.00 0.00 0.00 2.17
1607 1674 2.674357 CTCATGTGCACGATCAATCACA 59.326 45.455 13.13 11.63 42.66 3.58
1785 2116 0.550914 TGGTTGTATCTCATGGGGCC 59.449 55.000 0.00 0.00 0.00 5.80
1787 2118 3.931907 TCTTGGTTGTATCTCATGGGG 57.068 47.619 0.00 0.00 0.00 4.96
1812 2143 0.600255 CTCACTCGGCCGTTGTTTCT 60.600 55.000 27.15 0.46 0.00 2.52
1816 2147 4.681978 GCCTCACTCGGCCGTTGT 62.682 66.667 27.15 21.73 44.41 3.32
1879 2212 6.617782 ACAAGCAGCTGGATATAGACATAT 57.382 37.500 17.12 0.00 0.00 1.78
1880 2213 6.041979 TCAACAAGCAGCTGGATATAGACATA 59.958 38.462 17.12 0.00 0.00 2.29
1881 2214 4.970860 ACAAGCAGCTGGATATAGACAT 57.029 40.909 17.12 0.00 0.00 3.06
1882 2215 4.162131 TCAACAAGCAGCTGGATATAGACA 59.838 41.667 17.12 0.00 0.00 3.41
1883 2216 4.697514 TCAACAAGCAGCTGGATATAGAC 58.302 43.478 17.12 0.00 0.00 2.59
1884 2217 4.202295 CCTCAACAAGCAGCTGGATATAGA 60.202 45.833 17.12 0.00 0.00 1.98
1885 2218 4.063689 CCTCAACAAGCAGCTGGATATAG 58.936 47.826 17.12 0.00 0.00 1.31
1886 2219 3.711190 TCCTCAACAAGCAGCTGGATATA 59.289 43.478 17.12 0.00 0.00 0.86
1887 2220 2.507058 TCCTCAACAAGCAGCTGGATAT 59.493 45.455 17.12 0.00 0.00 1.63
1909 3111 2.752354 TGATTTCTTGTTGTATGGCGGG 59.248 45.455 0.00 0.00 0.00 6.13
1911 3113 4.418013 TGTGATTTCTTGTTGTATGGCG 57.582 40.909 0.00 0.00 0.00 5.69
1928 3131 6.656632 TGGTGCCATTTATAAACTTTGTGA 57.343 33.333 0.00 0.00 0.00 3.58
1956 3161 3.333029 TGAGAATGCTCATCGGTGAAA 57.667 42.857 0.00 0.00 45.88 2.69
1989 3198 5.992217 GTCCTTGACTAGACACTGACAATTT 59.008 40.000 14.28 0.00 33.08 1.82
2067 3279 8.666573 GGCATCCTACTAAAACTCTTAGAAAAC 58.333 37.037 0.00 0.00 0.00 2.43
2069 3281 7.336396 GGGCATCCTACTAAAACTCTTAGAAA 58.664 38.462 0.00 0.00 0.00 2.52
2072 3284 5.367060 AGGGGCATCCTACTAAAACTCTTAG 59.633 44.000 0.00 0.00 45.98 2.18
2073 3285 5.286221 AGGGGCATCCTACTAAAACTCTTA 58.714 41.667 0.00 0.00 45.98 2.10
2074 3286 4.112331 AGGGGCATCCTACTAAAACTCTT 58.888 43.478 0.00 0.00 45.98 2.85
2075 3287 3.737263 AGGGGCATCCTACTAAAACTCT 58.263 45.455 0.00 0.00 45.98 3.24
2091 3997 3.181458 TGAAATCGTAGGATACAAGGGGC 60.181 47.826 0.00 0.00 43.24 5.80
2136 4042 3.688694 ATTCACTTGCGTTACCACCTA 57.311 42.857 0.00 0.00 0.00 3.08
2156 4062 7.870954 GTCATCGAGGACAATAACCACATATTA 59.129 37.037 24.24 0.00 37.73 0.98
2209 4115 0.034896 TCTTGAAGCGGAACAGTCCC 59.965 55.000 0.00 0.00 41.44 4.46
2212 4118 0.759346 AGGTCTTGAAGCGGAACAGT 59.241 50.000 0.00 0.00 0.00 3.55
2214 4120 1.048601 AGAGGTCTTGAAGCGGAACA 58.951 50.000 0.00 0.00 0.00 3.18
2239 4145 8.543774 ACAATTGATTCATAGTGGTCTTACTCT 58.456 33.333 13.59 0.00 32.19 3.24
2241 4147 8.321353 TGACAATTGATTCATAGTGGTCTTACT 58.679 33.333 13.59 0.00 34.71 2.24
2243 4149 8.321353 AGTGACAATTGATTCATAGTGGTCTTA 58.679 33.333 13.59 0.00 0.00 2.10
2249 4155 8.724229 TCTTTCAGTGACAATTGATTCATAGTG 58.276 33.333 13.59 6.16 0.00 2.74
2252 4158 8.896744 GGATCTTTCAGTGACAATTGATTCATA 58.103 33.333 13.59 0.00 0.00 2.15
2254 4160 6.716173 TGGATCTTTCAGTGACAATTGATTCA 59.284 34.615 13.59 3.31 0.00 2.57
2255 4161 7.149569 TGGATCTTTCAGTGACAATTGATTC 57.850 36.000 13.59 0.24 0.00 2.52
2256 4162 7.528996 TTGGATCTTTCAGTGACAATTGATT 57.471 32.000 13.59 0.00 0.00 2.57
2267 4173 6.739565 GCCACTCAAAATTTGGATCTTTCAGT 60.740 38.462 5.83 0.00 31.39 3.41
2268 4174 5.636543 GCCACTCAAAATTTGGATCTTTCAG 59.363 40.000 5.83 0.00 31.39 3.02
2269 4175 5.070180 TGCCACTCAAAATTTGGATCTTTCA 59.930 36.000 5.83 0.00 31.39 2.69
2270 4176 5.540911 TGCCACTCAAAATTTGGATCTTTC 58.459 37.500 5.83 0.00 31.39 2.62
2271 4177 5.544650 CTGCCACTCAAAATTTGGATCTTT 58.455 37.500 5.83 0.00 31.39 2.52
2272 4178 4.562143 GCTGCCACTCAAAATTTGGATCTT 60.562 41.667 5.83 0.00 31.39 2.40
2273 4179 3.056322 GCTGCCACTCAAAATTTGGATCT 60.056 43.478 5.83 0.00 31.39 2.75
2274 4180 3.056322 AGCTGCCACTCAAAATTTGGATC 60.056 43.478 5.83 0.00 31.39 3.36
2275 4181 2.901839 AGCTGCCACTCAAAATTTGGAT 59.098 40.909 5.83 0.00 31.39 3.41
2276 4182 2.318908 AGCTGCCACTCAAAATTTGGA 58.681 42.857 5.83 0.00 31.39 3.53
2277 4183 2.803956 CAAGCTGCCACTCAAAATTTGG 59.196 45.455 5.83 0.00 0.00 3.28
2278 4184 3.719924 TCAAGCTGCCACTCAAAATTTG 58.280 40.909 0.00 0.00 0.00 2.32
2279 4185 4.563061 GATCAAGCTGCCACTCAAAATTT 58.437 39.130 0.00 0.00 0.00 1.82
2294 4200 3.900941 ACAAAAATGTGGTCGATCAAGC 58.099 40.909 0.00 0.00 0.00 4.01
2309 4215 1.268640 GCCCGACGCAACTAACAAAAA 60.269 47.619 0.00 0.00 37.47 1.94
2310 4216 0.308376 GCCCGACGCAACTAACAAAA 59.692 50.000 0.00 0.00 37.47 2.44
2311 4217 1.508808 GGCCCGACGCAACTAACAAA 61.509 55.000 0.00 0.00 40.31 2.83
2316 4222 2.386064 AAACTGGCCCGACGCAACTA 62.386 55.000 0.00 0.00 40.31 2.24
2321 4227 3.035576 GCTAAAACTGGCCCGACGC 62.036 63.158 0.00 0.00 0.00 5.19
2332 4238 1.877443 TCAGACCGCTTTGGCTAAAAC 59.123 47.619 0.00 0.00 43.94 2.43
2336 4242 2.362397 CTCTATCAGACCGCTTTGGCTA 59.638 50.000 0.00 0.00 43.94 3.93
2347 4253 4.274147 TCCACAAGGTCTCTCTATCAGAC 58.726 47.826 0.00 0.00 39.78 3.51
2349 4255 4.531854 TCTCCACAAGGTCTCTCTATCAG 58.468 47.826 0.00 0.00 35.89 2.90
2378 4284 5.474578 TTACTAGCATATTGAGCCCTCTG 57.525 43.478 0.00 0.00 0.00 3.35
2379 4285 5.782331 TGATTACTAGCATATTGAGCCCTCT 59.218 40.000 0.00 0.00 0.00 3.69
2407 4313 5.222048 GGGGTTATGCCATAGATGAAACCTA 60.222 44.000 5.12 0.00 39.65 3.08
2408 4314 4.447762 GGGGTTATGCCATAGATGAAACCT 60.448 45.833 5.12 0.00 39.65 3.50
2413 4319 4.353489 TGAATGGGGTTATGCCATAGATGA 59.647 41.667 0.00 0.00 39.65 2.92
2415 4321 4.264083 CCTGAATGGGGTTATGCCATAGAT 60.264 45.833 0.00 0.00 39.65 1.98
2418 4324 2.788807 ACCTGAATGGGGTTATGCCATA 59.211 45.455 0.00 0.00 41.11 2.74
2422 4328 2.435372 TGACCTGAATGGGGTTATGC 57.565 50.000 0.00 0.00 41.11 3.14
2434 4340 4.019411 TGGTATGCTTGATCTTTGACCTGA 60.019 41.667 0.00 0.00 0.00 3.86
2463 4369 7.361799 CTTTATATATAAAGCGGGGTGAAAGCC 60.362 40.741 25.10 0.00 46.46 4.35
2464 4370 7.443259 TTTATATATAAAGCGGGGTGAAAGC 57.557 36.000 12.90 0.00 0.00 3.51
2481 4387 9.453572 GGGTGATGATGATCTTTGCTTTATATA 57.546 33.333 0.00 0.00 0.00 0.86
2482 4388 7.120285 CGGGTGATGATGATCTTTGCTTTATAT 59.880 37.037 0.00 0.00 0.00 0.86
2483 4389 6.427853 CGGGTGATGATGATCTTTGCTTTATA 59.572 38.462 0.00 0.00 0.00 0.98
2484 4390 5.240183 CGGGTGATGATGATCTTTGCTTTAT 59.760 40.000 0.00 0.00 0.00 1.40
2485 4391 4.576053 CGGGTGATGATGATCTTTGCTTTA 59.424 41.667 0.00 0.00 0.00 1.85
2486 4392 3.379372 CGGGTGATGATGATCTTTGCTTT 59.621 43.478 0.00 0.00 0.00 3.51
2487 4393 2.947652 CGGGTGATGATGATCTTTGCTT 59.052 45.455 0.00 0.00 0.00 3.91
2488 4394 2.171237 TCGGGTGATGATGATCTTTGCT 59.829 45.455 0.00 0.00 0.00 3.91
2489 4395 2.564771 TCGGGTGATGATGATCTTTGC 58.435 47.619 0.00 0.00 0.00 3.68
2490 4396 5.299949 TGTATCGGGTGATGATGATCTTTG 58.700 41.667 0.00 0.00 35.99 2.77
2491 4397 5.551305 TGTATCGGGTGATGATGATCTTT 57.449 39.130 0.00 0.00 35.99 2.52
2492 4398 5.551305 TTGTATCGGGTGATGATGATCTT 57.449 39.130 0.00 0.00 35.99 2.40
2493 4399 5.163311 TGTTTGTATCGGGTGATGATGATCT 60.163 40.000 0.00 0.00 35.99 2.75
2494 4400 5.050091 GTGTTTGTATCGGGTGATGATGATC 60.050 44.000 0.00 0.00 35.99 2.92
2495 4401 4.816385 GTGTTTGTATCGGGTGATGATGAT 59.184 41.667 0.00 0.00 35.99 2.45
2496 4402 4.188462 GTGTTTGTATCGGGTGATGATGA 58.812 43.478 0.00 0.00 35.99 2.92
2497 4403 3.938334 TGTGTTTGTATCGGGTGATGATG 59.062 43.478 0.00 0.00 35.99 3.07
2498 4404 3.938963 GTGTGTTTGTATCGGGTGATGAT 59.061 43.478 0.00 0.00 35.99 2.45
2499 4405 3.331150 GTGTGTTTGTATCGGGTGATGA 58.669 45.455 0.00 0.00 35.99 2.92
2500 4406 2.093625 CGTGTGTTTGTATCGGGTGATG 59.906 50.000 0.00 0.00 35.99 3.07
2501 4407 2.343101 CGTGTGTTTGTATCGGGTGAT 58.657 47.619 0.00 0.00 38.67 3.06
2502 4408 1.785768 CGTGTGTTTGTATCGGGTGA 58.214 50.000 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.