Multiple sequence alignment - TraesCS5D01G307800

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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 TraesCS5D01G307800 chr5D 100.000 5808 0 0 1 5808 404503632 404497825 0.000000e+00 10726.0
1 TraesCS5D01G307800 chr5D 82.028 434 45 19 392 816 554517370 554516961 7.210000e-89 339.0
2 TraesCS5D01G307800 chr5D 81.336 434 51 11 390 816 324595267 324595677 5.610000e-85 326.0
3 TraesCS5D01G307800 chr5D 81.050 438 51 15 389 817 434423570 434423984 2.610000e-83 320.0
4 TraesCS5D01G307800 chr5D 85.185 324 34 12 389 701 551073025 551073345 2.610000e-83 320.0
5 TraesCS5D01G307800 chr5D 88.593 263 19 9 1467 1718 480700043 480700305 5.650000e-80 309.0
6 TraesCS5D01G307800 chr5D 87.452 263 22 9 1467 1718 511472559 511472821 5.690000e-75 292.0
7 TraesCS5D01G307800 chr5D 87.500 64 6 2 74 136 8338361 8338423 8.070000e-09 73.1
8 TraesCS5D01G307800 chr5D 87.500 64 6 2 74 136 15236363 15236425 8.070000e-09 73.1
9 TraesCS5D01G307800 chr5D 87.500 64 6 2 74 136 408763769 408763831 8.070000e-09 73.1
10 TraesCS5D01G307800 chr5B 91.351 1688 83 32 315 1974 485913986 485912334 0.000000e+00 2250.0
11 TraesCS5D01G307800 chr5B 92.243 1070 63 12 4491 5541 485909319 485908251 0.000000e+00 1498.0
12 TraesCS5D01G307800 chr5B 90.835 611 53 3 1971 2579 485912070 485911461 0.000000e+00 815.0
13 TraesCS5D01G307800 chr5B 91.443 409 31 3 4086 4490 485909757 485909349 5.080000e-155 558.0
14 TraesCS5D01G307800 chr5B 93.421 228 14 1 1 227 485914214 485913987 2.590000e-88 337.0
15 TraesCS5D01G307800 chr5B 92.670 191 13 1 2578 2768 485909941 485909752 2.060000e-69 274.0
16 TraesCS5D01G307800 chr5B 90.741 54 5 0 83 136 643417330 643417277 8.070000e-09 73.1
17 TraesCS5D01G307800 chr2D 97.683 1295 28 1 2763 4057 136426810 136425518 0.000000e+00 2224.0
18 TraesCS5D01G307800 chr2D 87.293 362 38 7 5181 5538 12575771 12576128 1.950000e-109 407.0
19 TraesCS5D01G307800 chr2D 90.517 232 15 5 1467 1691 42209766 42209535 3.400000e-77 300.0
20 TraesCS5D01G307800 chr2D 82.573 241 23 9 4659 4886 683751 683985 1.650000e-45 195.0
21 TraesCS5D01G307800 chr2D 81.193 218 29 5 2360 2577 8479540 8479335 1.290000e-36 165.0
22 TraesCS5D01G307800 chr2D 78.030 264 51 6 5537 5797 12576428 12576687 6.020000e-35 159.0
23 TraesCS5D01G307800 chr2D 85.000 100 14 1 2065 2164 9791694 9791596 3.700000e-17 100.0
24 TraesCS5D01G307800 chr2D 88.406 69 6 2 4493 4559 683684 683752 1.340000e-11 82.4
25 TraesCS5D01G307800 chr2D 82.558 86 13 2 2062 2147 9753631 9753548 2.240000e-09 75.0
26 TraesCS5D01G307800 chr2D 93.182 44 3 0 2119 2162 9792367 9792324 1.350000e-06 65.8
27 TraesCS5D01G307800 chr1D 97.683 1295 28 1 2763 4057 223524576 223523284 0.000000e+00 2224.0
28 TraesCS5D01G307800 chr1D 90.265 226 16 4 1472 1691 31007859 31007634 2.050000e-74 291.0
29 TraesCS5D01G307800 chr1D 97.436 39 1 0 5545 5583 493030152 493030114 3.760000e-07 67.6
30 TraesCS5D01G307800 chr5A 97.676 1291 28 1 2767 4057 602839194 602837906 0.000000e+00 2217.0
31 TraesCS5D01G307800 chr5A 92.033 1318 67 13 1485 2768 509650207 509651520 0.000000e+00 1818.0
32 TraesCS5D01G307800 chr5A 88.583 1270 74 27 4103 5324 509651540 509652786 0.000000e+00 1476.0
33 TraesCS5D01G307800 chr5A 94.799 596 21 2 840 1434 509649613 509650199 0.000000e+00 920.0
34 TraesCS5D01G307800 chr5A 87.193 570 50 19 131 694 509648966 509649518 1.370000e-175 627.0
35 TraesCS5D01G307800 chr5A 95.575 113 5 0 12 124 509637434 509637546 1.290000e-41 182.0
36 TraesCS5D01G307800 chr5A 79.779 272 19 18 4637 4891 599798624 599798876 1.290000e-36 165.0
37 TraesCS5D01G307800 chr5A 91.150 113 8 2 5697 5808 509652784 509652895 1.010000e-32 152.0
38 TraesCS5D01G307800 chr5A 91.071 56 2 3 73 127 663189080 663189027 8.070000e-09 73.1
39 TraesCS5D01G307800 chr4D 97.676 1291 27 2 2768 4057 242938963 242937675 0.000000e+00 2215.0
40 TraesCS5D01G307800 chr4D 85.127 316 42 5 391 701 15347805 15347490 9.390000e-83 318.0
41 TraesCS5D01G307800 chr2A 97.606 1295 26 2 2763 4057 578390480 578391769 0.000000e+00 2215.0
42 TraesCS5D01G307800 chr2A 97.676 1291 25 2 2767 4057 101854859 101856144 0.000000e+00 2213.0
43 TraesCS5D01G307800 chr2A 85.399 363 43 7 5181 5538 13031463 13031820 9.190000e-98 368.0
44 TraesCS5D01G307800 chr2A 85.153 229 25 5 4637 4857 535757 535984 5.860000e-55 226.0
45 TraesCS5D01G307800 chr2A 77.736 265 50 7 5537 5797 13032372 13032631 2.800000e-33 154.0
46 TraesCS5D01G307800 chr7D 97.529 1295 29 2 2763 4057 511568924 511570215 0.000000e+00 2211.0
47 TraesCS5D01G307800 chr7D 97.383 1299 30 3 2760 4057 551828030 551826735 0.000000e+00 2207.0
48 TraesCS5D01G307800 chr7D 85.623 313 40 5 391 699 607213976 607214287 2.020000e-84 324.0
49 TraesCS5D01G307800 chr7D 87.833 263 21 9 1467 1718 620849511 620849773 1.220000e-76 298.0
50 TraesCS5D01G307800 chr3D 97.312 1302 32 2 2756 4057 357155621 357156919 0.000000e+00 2207.0
51 TraesCS5D01G307800 chr3D 90.517 232 15 5 1467 1691 26968007 26967776 3.400000e-77 300.0
52 TraesCS5D01G307800 chr2B 86.501 363 40 8 5181 5538 19067721 19068079 1.960000e-104 390.0
53 TraesCS5D01G307800 chr2B 81.173 324 41 16 4648 4959 10775086 10774771 5.810000e-60 243.0
54 TraesCS5D01G307800 chr2B 84.211 228 27 7 5541 5764 18931405 18931183 4.560000e-51 213.0
55 TraesCS5D01G307800 chr2B 83.333 228 31 5 5541 5765 19068367 19068590 2.740000e-48 204.0
56 TraesCS5D01G307800 chr2B 92.929 99 6 1 4515 4612 10775552 10775454 6.070000e-30 143.0
57 TraesCS5D01G307800 chr2B 85.827 127 17 1 2449 2575 11173140 11173015 3.650000e-27 134.0
58 TraesCS5D01G307800 chr2B 85.714 112 12 3 2581 2689 212577146 212577256 1.320000e-21 115.0
59 TraesCS5D01G307800 chr2B 94.231 52 3 0 1920 1971 13315258 13315207 4.820000e-11 80.5
60 TraesCS5D01G307800 chr2B 82.558 86 13 2 2062 2147 13059206 13059123 2.240000e-09 75.0
61 TraesCS5D01G307800 chr6B 85.635 362 43 8 5181 5537 49615581 49615224 7.110000e-99 372.0
62 TraesCS5D01G307800 chr3B 84.810 316 37 7 392 698 43042695 43043008 2.030000e-79 307.0
63 TraesCS5D01G307800 chr6D 90.222 225 16 4 1467 1686 22486317 22486540 7.360000e-74 289.0
64 TraesCS5D01G307800 chr6A 94.118 51 3 0 84 134 587553115 587553165 1.740000e-10 78.7
65 TraesCS5D01G307800 chr7B 87.500 64 6 2 74 136 707519440 707519378 8.070000e-09 73.1
66 TraesCS5D01G307800 chr7A 100.000 31 0 0 2017 2047 680681572 680681542 2.260000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G307800 chr5D 404497825 404503632 5807 True 10726.000000 10726 100.000000 1 5808 1 chr5D.!!$R1 5807
1 TraesCS5D01G307800 chr5B 485908251 485914214 5963 True 955.333333 2250 91.993833 1 5541 6 chr5B.!!$R2 5540
2 TraesCS5D01G307800 chr2D 136425518 136426810 1292 True 2224.000000 2224 97.683000 2763 4057 1 chr2D.!!$R4 1294
3 TraesCS5D01G307800 chr2D 12575771 12576687 916 False 283.000000 407 82.661500 5181 5797 2 chr2D.!!$F2 616
4 TraesCS5D01G307800 chr1D 223523284 223524576 1292 True 2224.000000 2224 97.683000 2763 4057 1 chr1D.!!$R2 1294
5 TraesCS5D01G307800 chr5A 602837906 602839194 1288 True 2217.000000 2217 97.676000 2767 4057 1 chr5A.!!$R1 1290
6 TraesCS5D01G307800 chr5A 509648966 509652895 3929 False 998.600000 1818 90.751600 131 5808 5 chr5A.!!$F3 5677
7 TraesCS5D01G307800 chr4D 242937675 242938963 1288 True 2215.000000 2215 97.676000 2768 4057 1 chr4D.!!$R2 1289
8 TraesCS5D01G307800 chr2A 578390480 578391769 1289 False 2215.000000 2215 97.606000 2763 4057 1 chr2A.!!$F3 1294
9 TraesCS5D01G307800 chr2A 101854859 101856144 1285 False 2213.000000 2213 97.676000 2767 4057 1 chr2A.!!$F2 1290
10 TraesCS5D01G307800 chr2A 13031463 13032631 1168 False 261.000000 368 81.567500 5181 5797 2 chr2A.!!$F4 616
11 TraesCS5D01G307800 chr7D 511568924 511570215 1291 False 2211.000000 2211 97.529000 2763 4057 1 chr7D.!!$F1 1294
12 TraesCS5D01G307800 chr7D 551826735 551828030 1295 True 2207.000000 2207 97.383000 2760 4057 1 chr7D.!!$R1 1297
13 TraesCS5D01G307800 chr3D 357155621 357156919 1298 False 2207.000000 2207 97.312000 2756 4057 1 chr3D.!!$F1 1301
14 TraesCS5D01G307800 chr2B 19067721 19068590 869 False 297.000000 390 84.917000 5181 5765 2 chr2B.!!$F2 584

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
617 624 0.172578 CGCACTGTTCTGACCCGATA 59.827 55.000 0.00 0.00 0.00 2.92 F
1838 1891 1.200948 GCAGAGGCCACTGAATTTGTC 59.799 52.381 31.50 9.86 39.94 3.18 F
3035 4879 1.229464 ACTGGAGCTTCTGGAGGCT 60.229 57.895 6.92 6.92 46.96 4.58 F
3843 5688 0.251787 GTTTCTCCAAGGCCCACCAT 60.252 55.000 0.00 0.00 39.06 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 2863 0.107508 TGATGAGGTAAGCTGCTGGC 60.108 55.0 1.35 0.00 42.19 4.85 R
3415 5259 0.104882 TGGTACCCCAGAAGGACACA 60.105 55.0 10.07 0.00 38.24 3.72 R
4756 6643 0.033781 CCGGTACCCTTTTGTCGACA 59.966 55.0 15.76 15.76 0.00 4.35 R
5698 8202 0.394899 GGTCTTCATTGGGGGAGCAG 60.395 60.0 0.00 0.00 0.00 4.24 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
49 50 6.150396 ACTCCTATAATCTCTTGTGTTCGG 57.850 41.667 0.00 0.00 0.00 4.30
64 65 5.074115 TGTGTTCGGGATTGTAAAAGGAAT 58.926 37.500 0.00 0.00 0.00 3.01
65 66 5.048364 TGTGTTCGGGATTGTAAAAGGAATG 60.048 40.000 0.00 0.00 0.00 2.67
186 188 7.037438 TCCTTCATTGCAAAGCTATTCATTTC 58.963 34.615 1.71 0.00 0.00 2.17
188 190 8.192774 CCTTCATTGCAAAGCTATTCATTTCTA 58.807 33.333 1.71 0.00 0.00 2.10
228 230 8.788325 ACCATTCACATTAGTTAACTCCTAAC 57.212 34.615 12.39 0.00 40.33 2.34
366 368 6.646653 GCGGGAATGAAAAAGAGAAAGAAAAT 59.353 34.615 0.00 0.00 0.00 1.82
429 431 1.067084 CGAGCTCATCTGCATCCGT 59.933 57.895 15.40 0.00 34.99 4.69
535 541 7.330700 GGTCCGCTTCAAATTTCAATTCATTTA 59.669 33.333 0.00 0.00 0.00 1.40
551 557 7.870509 ATTCATTTAAACATCTGAGCAGCTA 57.129 32.000 0.00 0.00 0.00 3.32
617 624 0.172578 CGCACTGTTCTGACCCGATA 59.827 55.000 0.00 0.00 0.00 2.92
620 627 2.826428 CACTGTTCTGACCCGATATGG 58.174 52.381 0.00 0.00 37.55 2.74
694 702 4.189231 ACCTCACGCATCAAATTACCTAC 58.811 43.478 0.00 0.00 0.00 3.18
705 713 7.679638 GCATCAAATTACCTACCACACATTCTC 60.680 40.741 0.00 0.00 0.00 2.87
710 719 8.472007 AATTACCTACCACACATTCTCAAAAA 57.528 30.769 0.00 0.00 0.00 1.94
735 744 9.940166 AAAATTACCTACGACACAAAAAGTTAG 57.060 29.630 0.00 0.00 0.00 2.34
736 745 8.891671 AATTACCTACGACACAAAAAGTTAGA 57.108 30.769 0.00 0.00 0.00 2.10
797 810 2.203181 GGAGCAGATGAGCCTGGC 60.203 66.667 11.65 11.65 34.82 4.85
818 831 1.451387 CCGAGTTGGATTTCCGGGG 60.451 63.158 0.00 0.00 42.00 5.73
897 910 4.849329 GCTACGACCCTGACCGCG 62.849 72.222 0.00 0.00 0.00 6.46
898 911 4.849329 CTACGACCCTGACCGCGC 62.849 72.222 0.00 0.00 0.00 6.86
1065 1078 2.203640 ATCGCCGCCTCCCTCATA 60.204 61.111 0.00 0.00 0.00 2.15
1207 1220 1.674322 ACAACCCGCCGGATTCTTG 60.674 57.895 5.05 2.98 0.00 3.02
1253 1266 3.925238 CGCCAGGTGAATACGCGC 61.925 66.667 5.73 0.00 36.02 6.86
1259 1272 1.740296 GGTGAATACGCGCTGGTGT 60.740 57.895 5.73 0.00 40.64 4.16
1444 1461 9.547753 CCGGATCTTGATTCTTTTTATCTTCTA 57.452 33.333 0.00 0.00 0.00 2.10
1474 1491 2.098770 GGATCTTGATTCTTGGTGCTGC 59.901 50.000 0.00 0.00 0.00 5.25
1480 1497 4.486125 TGATTCTTGGTGCTGCTGTATA 57.514 40.909 0.00 0.00 0.00 1.47
1815 1868 3.729966 GGAGTCTCTCCGAAACTTTGTT 58.270 45.455 0.00 0.00 41.08 2.83
1821 1874 2.357637 TCTCCGAAACTTTGTTTGGCAG 59.642 45.455 0.10 0.00 32.66 4.85
1838 1891 1.200948 GCAGAGGCCACTGAATTTGTC 59.799 52.381 31.50 9.86 39.94 3.18
1847 1900 4.841422 CCACTGAATTTGTCCTGAGAGAT 58.159 43.478 0.00 0.00 0.00 2.75
1855 1908 5.673337 TTTGTCCTGAGAGATTTGTTTCG 57.327 39.130 0.00 0.00 0.00 3.46
2096 2416 2.538141 CCCCCTGCTTTCTCCACCA 61.538 63.158 0.00 0.00 0.00 4.17
2117 2437 2.200373 AGTTCATCTGGAAAACCCCG 57.800 50.000 0.00 0.00 37.23 5.73
2176 2496 6.313905 AGTGCACATATGTAAAGTGTAGAAGC 59.686 38.462 21.04 3.84 35.75 3.86
2178 2498 6.652900 TGCACATATGTAAAGTGTAGAAGCAA 59.347 34.615 8.32 0.00 35.75 3.91
2184 2504 7.944729 ATGTAAAGTGTAGAAGCAATCCAAT 57.055 32.000 0.00 0.00 0.00 3.16
2219 2539 7.269084 CGTGCAAAGATAATTGACAACAGTTAG 59.731 37.037 0.00 0.00 33.15 2.34
2399 2720 4.022416 GGCTTGTCCATGTCACATGTTTTA 60.022 41.667 16.74 0.00 34.01 1.52
2436 2757 3.241530 TGAGTCTGCCGCCCACTT 61.242 61.111 0.00 0.00 0.00 3.16
2541 2863 2.122783 TAAATTTGTCCAGAGGCCGG 57.877 50.000 0.00 0.00 0.00 6.13
2673 4516 6.366061 GGAGTGCCAATCTAATTTTGTTTGAC 59.634 38.462 0.00 0.00 0.00 3.18
2902 4746 1.794714 CACCCCTGTCCATAGCTAGT 58.205 55.000 0.00 0.00 0.00 2.57
2972 4816 3.370527 CCATGTCAAATTCGGTCTACCCT 60.371 47.826 0.00 0.00 0.00 4.34
3035 4879 1.229464 ACTGGAGCTTCTGGAGGCT 60.229 57.895 6.92 6.92 46.96 4.58
3134 4978 5.710567 TCTCGTATATCATCATTCCGGACTT 59.289 40.000 1.83 0.00 0.00 3.01
3172 5016 2.098607 GCCACACATCCATCTCAACATG 59.901 50.000 0.00 0.00 0.00 3.21
3207 5051 4.574421 CACACCTAACTGTTGAACATGTCA 59.426 41.667 0.00 0.00 0.00 3.58
3223 5067 1.270625 TGTCACCTTTTAGTCGGCCAG 60.271 52.381 2.24 0.00 0.00 4.85
3225 5069 1.375523 ACCTTTTAGTCGGCCAGCG 60.376 57.895 2.24 0.00 0.00 5.18
3348 5192 1.303309 CACTTCATCCATCCGGCTTC 58.697 55.000 0.00 0.00 0.00 3.86
3415 5259 3.132111 GCATTGACCCCAAATACCGAAAT 59.868 43.478 0.00 0.00 35.67 2.17
3647 5491 6.968248 ACACCATGGGATATCTCCTTGTATAT 59.032 38.462 18.09 0.00 41.74 0.86
3648 5492 8.129001 ACACCATGGGATATCTCCTTGTATATA 58.871 37.037 18.09 0.00 41.74 0.86
3729 5573 4.832823 TGATGCAGTCCTATCTTAATCGGA 59.167 41.667 0.00 0.00 0.00 4.55
3843 5688 0.251787 GTTTCTCCAAGGCCCACCAT 60.252 55.000 0.00 0.00 39.06 3.55
4057 5902 3.938334 GACTCTCTCCCAAAGCTTCATTC 59.062 47.826 0.00 0.00 0.00 2.67
4058 5903 3.328931 ACTCTCTCCCAAAGCTTCATTCA 59.671 43.478 0.00 0.00 0.00 2.57
4059 5904 3.940221 CTCTCTCCCAAAGCTTCATTCAG 59.060 47.826 0.00 0.00 0.00 3.02
4060 5905 2.422832 CTCTCCCAAAGCTTCATTCAGC 59.577 50.000 0.00 0.00 40.44 4.26
4075 5920 9.928236 GCTTCATTCAGCTAAAAGTATTAAGAG 57.072 33.333 0.00 0.00 36.79 2.85
4080 5925 9.785982 ATTCAGCTAAAAGTATTAAGAGATCCC 57.214 33.333 0.00 0.00 0.00 3.85
4081 5926 8.319057 TCAGCTAAAAGTATTAAGAGATCCCA 57.681 34.615 0.00 0.00 0.00 4.37
4082 5927 8.768397 TCAGCTAAAAGTATTAAGAGATCCCAA 58.232 33.333 0.00 0.00 0.00 4.12
4083 5928 9.566432 CAGCTAAAAGTATTAAGAGATCCCAAT 57.434 33.333 0.00 0.00 0.00 3.16
4101 5946 6.013379 TCCCAATTACACCATTCAGCTAAAA 58.987 36.000 0.00 0.00 0.00 1.52
4169 6023 1.809567 GCAACCCCCTGCACTTCTTG 61.810 60.000 0.00 0.00 42.17 3.02
4219 6073 1.384222 GGTTCGGGCTTAAGCATGGG 61.384 60.000 27.83 13.64 44.36 4.00
4227 6081 1.542108 GCTTAAGCATGGGATCGAGCT 60.542 52.381 22.59 0.00 41.59 4.09
4256 6110 1.291588 CGCTCCTGTGCTCTGAGTT 59.708 57.895 6.53 0.00 0.00 3.01
4426 6283 6.016777 GCTATTTTTGATACTGCTATGGTGCT 60.017 38.462 0.00 0.00 0.00 4.40
4463 6320 7.147828 TGGTTACTGTCACCATTGAAATTGAAA 60.148 33.333 9.71 0.00 39.53 2.69
4464 6321 7.872483 GGTTACTGTCACCATTGAAATTGAAAT 59.128 33.333 6.29 0.00 34.04 2.17
4494 6380 7.912250 GTCCATCTGCAGTTTGAAATTATAGTG 59.088 37.037 14.67 0.00 0.00 2.74
4501 6387 8.547069 TGCAGTTTGAAATTATAGTGTTTTTGC 58.453 29.630 0.00 0.00 0.00 3.68
4726 6613 3.402681 CAGGGGAGGGTGACGCAT 61.403 66.667 1.61 0.00 0.00 4.73
4756 6643 2.505167 GCCCCGTAAGATAGGCCGT 61.505 63.158 0.00 0.00 40.53 5.68
4842 6729 2.203422 CCCGGTTGCTTTGTCCCA 60.203 61.111 0.00 0.00 0.00 4.37
4992 6881 0.824759 ACCGGCTGTAGGAACTCATC 59.175 55.000 0.00 0.00 41.75 2.92
5052 6942 0.742635 GCTAGGAGCTGTTGCCACTC 60.743 60.000 0.00 0.00 38.45 3.51
5057 6947 1.615392 GGAGCTGTTGCCACTCAATTT 59.385 47.619 0.00 0.00 40.80 1.82
5090 6981 5.856156 TCTATGTGTTTTCGGTGGTTAAGA 58.144 37.500 0.00 0.00 0.00 2.10
5110 7001 3.387374 AGATCCGCTTCTGATGAATCACT 59.613 43.478 0.00 0.00 32.50 3.41
5128 7020 3.996363 TCACTGTTGCTGTGATGATGTAC 59.004 43.478 5.03 0.00 37.40 2.90
5129 7021 2.995939 ACTGTTGCTGTGATGATGTACG 59.004 45.455 0.00 0.00 0.00 3.67
5131 7023 3.658709 TGTTGCTGTGATGATGTACGAA 58.341 40.909 0.00 0.00 0.00 3.85
5132 7024 3.431912 TGTTGCTGTGATGATGTACGAAC 59.568 43.478 0.00 0.00 0.00 3.95
5133 7025 2.258755 TGCTGTGATGATGTACGAACG 58.741 47.619 0.00 0.00 0.00 3.95
5296 7203 3.004315 GCACGAAAAGAAACCCTGATCAA 59.996 43.478 0.00 0.00 0.00 2.57
5299 7206 4.887655 ACGAAAAGAAACCCTGATCAACTT 59.112 37.500 0.00 0.00 0.00 2.66
5361 7268 1.434555 TTGGTCGTTTCAGTATGCCG 58.565 50.000 0.00 0.00 34.76 5.69
5418 7325 3.368948 GGTGACATCTTCAGGGTTCTCTC 60.369 52.174 0.00 0.00 33.71 3.20
5421 7328 2.232452 ACATCTTCAGGGTTCTCTCACG 59.768 50.000 0.00 0.00 0.00 4.35
5460 7367 5.598005 ACTTCTTCTGCTGCTATGATCTACT 59.402 40.000 0.00 0.00 0.00 2.57
5588 8054 4.415846 TCAGGTCTCTGAATACTAGGCCTA 59.584 45.833 13.09 13.09 43.48 3.93
5589 8055 5.103643 TCAGGTCTCTGAATACTAGGCCTAA 60.104 44.000 14.85 0.00 43.48 2.69
5596 8064 5.130311 TCTGAATACTAGGCCTAACAATGCA 59.870 40.000 14.85 10.89 0.00 3.96
5601 8069 3.701040 ACTAGGCCTAACAATGCAAATGG 59.299 43.478 14.85 0.00 0.00 3.16
5621 8089 6.683974 ATGGTGCAAGTATGTTTACTCATC 57.316 37.500 0.00 0.00 37.70 2.92
5631 8099 8.277490 AGTATGTTTACTCATCACTCGACTAA 57.723 34.615 0.00 0.00 33.18 2.24
5640 8108 3.759527 TCACTCGACTAACTGAATCCG 57.240 47.619 0.00 0.00 0.00 4.18
5649 8117 5.738225 CGACTAACTGAATCCGTAAGTCTTC 59.262 44.000 0.00 0.00 31.81 2.87
5650 8118 5.963594 ACTAACTGAATCCGTAAGTCTTCC 58.036 41.667 0.00 0.00 0.00 3.46
5651 8119 5.715753 ACTAACTGAATCCGTAAGTCTTCCT 59.284 40.000 0.00 0.00 0.00 3.36
5656 8124 7.621796 ACTGAATCCGTAAGTCTTCCTTTATT 58.378 34.615 0.00 0.00 34.46 1.40
5660 8128 9.163899 GAATCCGTAAGTCTTCCTTTATTCTTT 57.836 33.333 0.00 0.00 34.46 2.52
5695 8199 0.979665 TCTCTTGGCTGAAGGACCAG 59.020 55.000 0.00 0.00 37.24 4.00
5696 8200 0.979665 CTCTTGGCTGAAGGACCAGA 59.020 55.000 0.00 0.00 37.24 3.86
5697 8201 0.979665 TCTTGGCTGAAGGACCAGAG 59.020 55.000 0.00 0.00 37.24 3.35
5698 8202 0.676151 CTTGGCTGAAGGACCAGAGC 60.676 60.000 0.00 0.00 37.24 4.09
5703 8207 0.108233 CTGAAGGACCAGAGCTGCTC 60.108 60.000 21.72 21.72 36.29 4.26
5749 8254 5.513233 ACCAAGATGTAGAAGCAAATGGAT 58.487 37.500 0.00 0.00 0.00 3.41
5771 8311 1.896755 GCCCCCTGATGAACCAAACAT 60.897 52.381 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 188 7.496920 TGTGAATGGTCATCTCAGCTAATTTAG 59.503 37.037 0.00 0.00 35.80 1.85
188 190 6.182627 TGTGAATGGTCATCTCAGCTAATTT 58.817 36.000 0.00 0.00 35.80 1.82
366 368 6.800072 AAAACCCCTCATTTGTTTCTTGTA 57.200 33.333 0.00 0.00 31.37 2.41
375 377 3.337358 GCATCCAAAAACCCCTCATTTG 58.663 45.455 0.00 0.00 34.60 2.32
376 378 2.028203 CGCATCCAAAAACCCCTCATTT 60.028 45.455 0.00 0.00 0.00 2.32
379 381 0.897863 CCGCATCCAAAAACCCCTCA 60.898 55.000 0.00 0.00 0.00 3.86
489 495 5.934625 GGACCTCACGCATCAAATTATCTAT 59.065 40.000 0.00 0.00 0.00 1.98
535 541 2.831333 CCGATAGCTGCTCAGATGTTT 58.169 47.619 4.91 0.00 0.00 2.83
628 635 1.066286 GGACATCTGAGCAGCTCTTGT 60.066 52.381 23.15 21.15 0.00 3.16
630 637 1.273759 TGGACATCTGAGCAGCTCTT 58.726 50.000 23.15 5.67 0.00 2.85
710 719 9.328845 TCTAACTTTTTGTGTCGTAGGTAATTT 57.671 29.630 0.00 0.00 0.00 1.82
774 785 2.415010 CTCATCTGCTCCGGTCCG 59.585 66.667 3.60 3.60 0.00 4.79
775 786 2.107953 GCTCATCTGCTCCGGTCC 59.892 66.667 0.00 0.00 0.00 4.46
777 788 2.364842 AGGCTCATCTGCTCCGGT 60.365 61.111 0.00 0.00 0.00 5.28
778 789 2.108566 CAGGCTCATCTGCTCCGG 59.891 66.667 0.00 0.00 0.00 5.14
779 790 2.108566 CCAGGCTCATCTGCTCCG 59.891 66.667 0.00 0.00 33.64 4.63
780 791 2.203181 GCCAGGCTCATCTGCTCC 60.203 66.667 3.29 0.00 33.64 4.70
781 792 2.203181 GGCCAGGCTCATCTGCTC 60.203 66.667 12.43 0.00 33.64 4.26
797 810 1.024579 CCGGAAATCCAACTCGGTGG 61.025 60.000 0.00 0.00 40.33 4.61
924 937 1.901650 CTCGCCGTCAAAGTTGAGGC 61.902 60.000 17.54 17.54 42.67 4.70
925 938 1.901650 GCTCGCCGTCAAAGTTGAGG 61.902 60.000 6.74 6.74 41.39 3.86
1055 1068 1.124477 GGTGAGGCCTATGAGGGAGG 61.124 65.000 4.42 0.00 35.37 4.30
1207 1220 2.027688 CAGCGACGGTAAGAAATCGAAC 59.972 50.000 0.00 0.00 36.70 3.95
1253 1266 1.595382 GGCATAGCCGCTACACCAG 60.595 63.158 13.40 0.24 39.62 4.00
1267 1280 1.006805 GTCATAGCGCTCGAGGCAT 60.007 57.895 16.34 0.00 41.91 4.40
1367 1384 0.745845 CTGGAAGCATCAGGGAACGG 60.746 60.000 0.00 0.00 0.00 4.44
1437 1454 5.070981 TCAAGATCCGCCATTTCTAGAAGAT 59.929 40.000 5.12 3.96 0.00 2.40
1439 1456 4.697514 TCAAGATCCGCCATTTCTAGAAG 58.302 43.478 5.12 0.00 0.00 2.85
1444 1461 4.162040 AGAATCAAGATCCGCCATTTCT 57.838 40.909 0.00 0.00 0.00 2.52
1474 1491 6.528072 CGTCCTGCATACACACATATATACAG 59.472 42.308 0.00 0.00 0.00 2.74
1480 1497 2.483876 GCGTCCTGCATACACACATAT 58.516 47.619 0.00 0.00 45.45 1.78
1611 1628 1.002624 TGCCATTGTCCCCTTCGAC 60.003 57.895 0.00 0.00 0.00 4.20
1731 1752 9.403583 GGTGACATTCCAGGACTAAAATATTTA 57.596 33.333 0.01 0.00 0.00 1.40
1735 1756 5.251932 TGGGTGACATTCCAGGACTAAAATA 59.748 40.000 0.00 0.00 0.00 1.40
1772 1804 2.635915 AGGGGTGACTAAATCGTTGACA 59.364 45.455 0.00 0.00 0.00 3.58
1804 1857 2.731217 CCTCTGCCAAACAAAGTTTCG 58.269 47.619 0.00 0.00 0.00 3.46
1838 1891 6.341316 TCCTATTCGAAACAAATCTCTCAGG 58.659 40.000 0.00 0.00 0.00 3.86
1847 1900 7.282224 CCTGATGGTAATCCTATTCGAAACAAA 59.718 37.037 0.00 0.00 34.23 2.83
1855 1908 4.640771 TGGCCTGATGGTAATCCTATTC 57.359 45.455 3.32 0.00 35.27 1.75
2096 2416 2.890945 CGGGGTTTTCCAGATGAACTTT 59.109 45.455 0.00 0.00 42.91 2.66
2117 2437 4.301637 AGTTTGACCGTGGAAATTGTTC 57.698 40.909 0.00 0.00 0.00 3.18
2176 2496 3.236816 GCACGTGTCTTTCATTGGATTG 58.763 45.455 18.38 0.00 0.00 2.67
2178 2498 2.503331 TGCACGTGTCTTTCATTGGAT 58.497 42.857 18.38 0.00 0.00 3.41
2184 2504 5.940192 ATTATCTTTGCACGTGTCTTTCA 57.060 34.783 18.38 2.76 0.00 2.69
2256 2576 7.824289 TCTTTTCTCACTTTACATATGACTGGG 59.176 37.037 10.38 0.00 0.00 4.45
2399 2720 2.861935 CACGGACACTTGTCTAAACGTT 59.138 45.455 9.20 0.00 44.20 3.99
2436 2757 1.409064 ACTTTGACTCTGCGACTGACA 59.591 47.619 0.00 0.00 0.00 3.58
2482 2804 1.971695 TCTCGCGCAGACTCTTGGA 60.972 57.895 8.75 0.00 0.00 3.53
2541 2863 0.107508 TGATGAGGTAAGCTGCTGGC 60.108 55.000 1.35 0.00 42.19 4.85
2576 2898 6.636850 GCACGACTTGTAACAAAATGAGAAAT 59.363 34.615 0.00 0.00 0.00 2.17
2673 4516 6.711579 ACAACAAGTTACATTACACGAGTTG 58.288 36.000 0.00 0.00 37.96 3.16
2720 4563 5.184671 TGCTTTATGTCCATGCAAACACATA 59.815 36.000 9.70 9.70 31.83 2.29
2761 4604 4.848562 TGTTGTTGTTGTTGTTGGTGTA 57.151 36.364 0.00 0.00 0.00 2.90
2765 4608 3.120373 GGCTTTGTTGTTGTTGTTGTTGG 60.120 43.478 0.00 0.00 0.00 3.77
2972 4816 1.556911 GGAGAATGTCAAGAGAGGGCA 59.443 52.381 0.00 0.00 0.00 5.36
3134 4978 1.596934 GCCACACGAGGAAGGATCA 59.403 57.895 0.00 0.00 0.00 2.92
3207 5051 1.375523 CGCTGGCCGACTAAAAGGT 60.376 57.895 0.00 0.00 40.02 3.50
3348 5192 2.010145 AGATGTGAACCACCGAATCG 57.990 50.000 0.00 0.00 32.73 3.34
3415 5259 0.104882 TGGTACCCCAGAAGGACACA 60.105 55.000 10.07 0.00 38.24 3.72
3647 5491 3.129262 TGGATGAGGTCACAAGGGATA 57.871 47.619 0.00 0.00 0.00 2.59
3648 5492 1.971149 TGGATGAGGTCACAAGGGAT 58.029 50.000 0.00 0.00 0.00 3.85
3729 5573 2.289631 TGATGCCGACACTGATGACTTT 60.290 45.455 0.00 0.00 0.00 2.66
3843 5688 7.533289 TGATAAGATACCACGGAATGTCATA 57.467 36.000 0.00 0.00 0.00 2.15
4006 5851 4.142600 GCACCGCTTAAGAAGAATGACAAT 60.143 41.667 6.67 0.00 0.00 2.71
4057 5902 8.964476 TTGGGATCTCTTAATACTTTTAGCTG 57.036 34.615 0.00 0.00 0.00 4.24
4063 5908 9.628500 GGTGTAATTGGGATCTCTTAATACTTT 57.372 33.333 0.00 0.00 0.00 2.66
4064 5909 8.778059 TGGTGTAATTGGGATCTCTTAATACTT 58.222 33.333 0.00 0.00 0.00 2.24
4065 5910 8.331931 TGGTGTAATTGGGATCTCTTAATACT 57.668 34.615 0.00 0.00 0.00 2.12
4066 5911 9.574516 AATGGTGTAATTGGGATCTCTTAATAC 57.425 33.333 0.00 0.00 0.00 1.89
4067 5912 9.793259 GAATGGTGTAATTGGGATCTCTTAATA 57.207 33.333 0.00 0.00 0.00 0.98
4068 5913 8.281531 TGAATGGTGTAATTGGGATCTCTTAAT 58.718 33.333 0.00 0.00 0.00 1.40
4069 5914 7.638444 TGAATGGTGTAATTGGGATCTCTTAA 58.362 34.615 0.00 0.00 0.00 1.85
4070 5915 7.206789 TGAATGGTGTAATTGGGATCTCTTA 57.793 36.000 0.00 0.00 0.00 2.10
4071 5916 6.078456 TGAATGGTGTAATTGGGATCTCTT 57.922 37.500 0.00 0.00 0.00 2.85
4072 5917 5.688807 CTGAATGGTGTAATTGGGATCTCT 58.311 41.667 0.00 0.00 0.00 3.10
4073 5918 4.276926 GCTGAATGGTGTAATTGGGATCTC 59.723 45.833 0.00 0.00 0.00 2.75
4074 5919 4.079558 AGCTGAATGGTGTAATTGGGATCT 60.080 41.667 0.00 0.00 0.00 2.75
4075 5920 4.210331 AGCTGAATGGTGTAATTGGGATC 58.790 43.478 0.00 0.00 0.00 3.36
4076 5921 4.255510 AGCTGAATGGTGTAATTGGGAT 57.744 40.909 0.00 0.00 0.00 3.85
4077 5922 3.737559 AGCTGAATGGTGTAATTGGGA 57.262 42.857 0.00 0.00 0.00 4.37
4078 5923 5.913137 TTTAGCTGAATGGTGTAATTGGG 57.087 39.130 0.00 0.00 0.00 4.12
4079 5924 6.924111 ACTTTTAGCTGAATGGTGTAATTGG 58.076 36.000 0.00 0.00 0.00 3.16
4148 6001 1.973812 GAAGTGCAGGGGGTTGCTC 60.974 63.158 0.00 0.00 44.38 4.26
4169 6023 6.106003 GGTGATATTTGGGTTTCATTGGAAC 58.894 40.000 0.00 0.00 31.35 3.62
4219 6073 1.789464 CGGCTTCATGTTAGCTCGATC 59.211 52.381 17.70 4.86 38.67 3.69
4227 6081 0.613260 ACAGGAGCGGCTTCATGTTA 59.387 50.000 11.59 0.00 38.82 2.41
4256 6110 9.905713 ATAAACAGAGGAATACAAGATAGCAAA 57.094 29.630 0.00 0.00 0.00 3.68
4390 6247 4.742438 TCAAAAATAGCACCGAGACAAC 57.258 40.909 0.00 0.00 0.00 3.32
4426 6283 4.336993 GTGACAGTAACCAAATTGGACACA 59.663 41.667 20.25 6.66 40.96 3.72
4494 6380 5.063312 TGCTGCTACTTTTCAAAGCAAAAAC 59.937 36.000 0.00 0.00 45.04 2.43
4501 6387 4.291540 TGTGTGCTGCTACTTTTCAAAG 57.708 40.909 0.00 0.00 41.73 2.77
4575 6461 3.054802 ACCAAAATTGTGCAACCCAAGAA 60.055 39.130 0.00 0.00 34.36 2.52
4744 6631 1.753930 TGTCGACACGGCCTATCTTA 58.246 50.000 15.76 0.00 0.00 2.10
4756 6643 0.033781 CCGGTACCCTTTTGTCGACA 59.966 55.000 15.76 15.76 0.00 4.35
4842 6729 4.764823 TCCTGTGAGAACAAACAAAACTGT 59.235 37.500 0.00 0.00 0.00 3.55
4947 6834 8.596271 AAAGCTTACAGAAGAAGAAACTCTAC 57.404 34.615 0.00 0.00 34.25 2.59
4968 6857 1.066358 AGTTCCTACAGCCGGTAAAGC 60.066 52.381 1.90 0.00 0.00 3.51
4992 6881 2.019984 GCTCTGCTTCCCCTTACAATG 58.980 52.381 0.00 0.00 0.00 2.82
5052 6942 6.748333 ACACATAGATCCACAGACAAATTG 57.252 37.500 0.00 0.00 0.00 2.32
5057 6947 4.929211 CGAAAACACATAGATCCACAGACA 59.071 41.667 0.00 0.00 0.00 3.41
5069 6959 5.644636 GGATCTTAACCACCGAAAACACATA 59.355 40.000 0.00 0.00 0.00 2.29
5070 6960 4.457949 GGATCTTAACCACCGAAAACACAT 59.542 41.667 0.00 0.00 0.00 3.21
5090 6981 3.118482 ACAGTGATTCATCAGAAGCGGAT 60.118 43.478 0.00 0.00 42.93 4.18
5110 7001 3.311486 TCGTACATCATCACAGCAACA 57.689 42.857 0.00 0.00 0.00 3.33
5128 7020 2.719046 GCTTGTGGATTCAAAACGTTCG 59.281 45.455 0.00 0.00 0.00 3.95
5129 7021 3.049912 GGCTTGTGGATTCAAAACGTTC 58.950 45.455 0.00 0.00 0.00 3.95
5131 7023 1.001815 CGGCTTGTGGATTCAAAACGT 60.002 47.619 0.00 0.00 0.00 3.99
5132 7024 1.265635 TCGGCTTGTGGATTCAAAACG 59.734 47.619 0.00 0.00 0.00 3.60
5133 7025 3.575965 ATCGGCTTGTGGATTCAAAAC 57.424 42.857 0.00 0.00 0.00 2.43
5296 7203 7.168219 TGGTGCAAGAGTTCATAAGATTAAGT 58.832 34.615 0.00 0.00 0.00 2.24
5299 7206 5.586243 GCTGGTGCAAGAGTTCATAAGATTA 59.414 40.000 0.00 0.00 39.41 1.75
5361 7268 3.911661 AATCTGCTTGCACTTGTTCTC 57.088 42.857 0.00 0.00 0.00 2.87
5418 7325 4.585162 AGAAGTACCTCCATATCCTTCGTG 59.415 45.833 0.00 0.00 34.85 4.35
5421 7328 6.740122 GCAGAAGAAGTACCTCCATATCCTTC 60.740 46.154 0.00 0.00 0.00 3.46
5478 7385 3.243267 CCGGAAGACAAACGAACCAAAAT 60.243 43.478 0.00 0.00 0.00 1.82
5596 8064 6.892658 TGAGTAAACATACTTGCACCATTT 57.107 33.333 0.00 0.00 0.00 2.32
5601 8069 6.454318 CGAGTGATGAGTAAACATACTTGCAC 60.454 42.308 0.00 0.00 0.00 4.57
5605 8073 7.159322 AGTCGAGTGATGAGTAAACATACTT 57.841 36.000 0.00 0.00 0.00 2.24
5621 8089 3.489180 ACGGATTCAGTTAGTCGAGTG 57.511 47.619 2.10 0.00 0.00 3.51
5631 8099 5.485209 AAAGGAAGACTTACGGATTCAGT 57.515 39.130 0.00 0.00 38.85 3.41
5670 8138 4.137543 GTCCTTCAGCCAAGAGAGAAAAA 58.862 43.478 0.00 0.00 33.29 1.94
5677 8145 0.979665 TCTGGTCCTTCAGCCAAGAG 59.020 55.000 0.00 0.00 33.29 2.85
5695 8199 0.750911 CTTCATTGGGGGAGCAGCTC 60.751 60.000 14.69 14.69 0.00 4.09
5696 8200 1.210204 TCTTCATTGGGGGAGCAGCT 61.210 55.000 0.00 0.00 0.00 4.24
5697 8201 1.034292 GTCTTCATTGGGGGAGCAGC 61.034 60.000 0.00 0.00 0.00 5.25
5698 8202 0.394899 GGTCTTCATTGGGGGAGCAG 60.395 60.000 0.00 0.00 0.00 4.24
5703 8207 0.698238 TCTGTGGTCTTCATTGGGGG 59.302 55.000 0.00 0.00 0.00 5.40
5749 8254 1.005450 GTTTGGTTCATCAGGGGGCTA 59.995 52.381 0.00 0.00 0.00 3.93
5771 8311 1.252904 GGGCTTCCATTTGCTGCTGA 61.253 55.000 0.00 0.00 0.00 4.26
5775 8315 4.116926 TGGGGCTTCCATTTGCTG 57.883 55.556 0.00 0.00 41.46 4.41


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

AutoCloner maintained by Alex Coulton.