Multiple sequence alignment - TraesCS2A01G288900

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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 TraesCS2A01G288900 chr2A 100.000 2895 0 0 1 2895 497015664 497012770 0.000000e+00 5347.0
1 TraesCS2A01G288900 chr2D 88.326 1679 121 17 1063 2721 367224165 367222542 0.000000e+00 1945.0
2 TraesCS2A01G288900 chr2D 92.575 431 25 6 652 1081 367224601 367224177 1.910000e-171 612.0
3 TraesCS2A01G288900 chr2D 90.331 362 33 2 2536 2895 367222546 367222185 9.390000e-130 473.0
4 TraesCS2A01G288900 chr2D 74.438 489 118 7 2375 2858 431531185 431530699 1.360000e-48 204.0
5 TraesCS2A01G288900 chr2B 89.438 1316 63 16 998 2298 436016449 436015195 0.000000e+00 1591.0
6 TraesCS2A01G288900 chr2B 90.305 557 52 2 2341 2895 436007015 436006459 0.000000e+00 728.0
7 TraesCS2A01G288900 chr2B 88.723 603 54 6 1 602 436017413 436016824 0.000000e+00 725.0
8 TraesCS2A01G288900 chr2B 88.736 364 20 5 651 1008 436016814 436016466 2.670000e-115 425.0
9 TraesCS2A01G288900 chr2B 100.000 29 0 0 2610 2638 81396807 81396835 1.000000e-03 54.7
10 TraesCS2A01G288900 chr1A 74.887 665 145 18 2204 2858 558984322 558983670 1.700000e-72 283.0
11 TraesCS2A01G288900 chr1A 88.136 59 7 0 2589 2647 341012190 341012248 1.440000e-08 71.3
12 TraesCS2A01G288900 chr6A 74.551 668 151 16 2201 2858 559444243 559444901 1.020000e-69 274.0
13 TraesCS2A01G288900 chr6A 89.474 57 6 0 2589 2645 574288342 574288398 4.000000e-09 73.1
14 TraesCS2A01G288900 chr6B 75.387 581 123 16 2204 2774 687091927 687091357 2.210000e-66 263.0
15 TraesCS2A01G288900 chr1B 73.423 666 161 13 2204 2859 282046168 282045509 4.820000e-58 235.0
16 TraesCS2A01G288900 chr1B 75.066 377 80 11 2490 2858 172424600 172424230 2.310000e-36 163.0
17 TraesCS2A01G288900 chr6D 92.045 88 6 1 562 648 8545389 8545476 3.920000e-24 122.0
18 TraesCS2A01G288900 chr3A 91.071 56 5 0 2589 2644 560689884 560689829 3.090000e-10 76.8
19 TraesCS2A01G288900 chr1D 86.000 50 7 0 2589 2638 335357805 335357854 1.000000e-03 54.7


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 TraesCS2A01G288900 chr2A 497012770 497015664 2894 True 5347.000000 5347 100.000000 1 2895 1 chr2A.!!$R1 2894
1 TraesCS2A01G288900 chr2D 367222185 367224601 2416 True 1010.000000 1945 90.410667 652 2895 3 chr2D.!!$R2 2243
2 TraesCS2A01G288900 chr2B 436015195 436017413 2218 True 913.666667 1591 88.965667 1 2298 3 chr2B.!!$R2 2297
3 TraesCS2A01G288900 chr2B 436006459 436007015 556 True 728.000000 728 90.305000 2341 2895 1 chr2B.!!$R1 554
4 TraesCS2A01G288900 chr1A 558983670 558984322 652 True 283.000000 283 74.887000 2204 2858 1 chr1A.!!$R1 654
5 TraesCS2A01G288900 chr6A 559444243 559444901 658 False 274.000000 274 74.551000 2201 2858 1 chr6A.!!$F1 657
6 TraesCS2A01G288900 chr6B 687091357 687091927 570 True 263.000000 263 75.387000 2204 2774 1 chr6B.!!$R1 570
7 TraesCS2A01G288900 chr1B 282045509 282046168 659 True 235.000000 235 73.423000 2204 2859 1 chr1B.!!$R2 655

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
641 643 0.106967 GTTGCAGAGGGGAGGGATTC 60.107 60.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1988 0.107945 AGGCTTCGAAGAGATGGTGC 60.108 55.0 28.95 11.14 38.43 5.01 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 3.694043 TGTTCGAATTGTGGATCTCCA 57.306 42.857 0.00 0.00 45.30 3.86
69 70 1.666872 GCACGCCGTGGTACTTCTT 60.667 57.895 20.07 0.00 33.64 2.52
71 72 1.080974 ACGCCGTGGTACTTCTTCG 60.081 57.895 0.00 0.00 0.00 3.79
74 75 1.804326 CCGTGGTACTTCTTCGGCG 60.804 63.158 0.00 0.00 35.01 6.46
108 109 2.356793 CATGGATCTCGAGCGGGC 60.357 66.667 7.81 0.00 0.00 6.13
184 185 3.866582 GGGTGGCCCTCCTCATCG 61.867 72.222 12.79 0.00 41.34 3.84
203 204 0.741326 GACGAGCTCATGGTAGCAGA 59.259 55.000 15.40 0.00 45.30 4.26
204 205 1.339610 GACGAGCTCATGGTAGCAGAT 59.660 52.381 15.40 0.00 45.30 2.90
205 206 1.068281 ACGAGCTCATGGTAGCAGATG 59.932 52.381 15.40 0.00 45.30 2.90
208 209 1.140452 AGCTCATGGTAGCAGATGTGG 59.860 52.381 8.91 0.00 45.30 4.17
214 215 1.757118 TGGTAGCAGATGTGGCTAGAC 59.243 52.381 0.00 0.00 43.96 2.59
227 228 2.033424 TGGCTAGACTCATCGATTCACG 59.967 50.000 0.00 0.00 44.09 4.35
231 232 3.138205 AGACTCATCGATTCACGTGAC 57.862 47.619 19.90 6.95 43.13 3.67
235 236 1.198178 TCATCGATTCACGTGACGTCA 59.802 47.619 19.90 15.76 38.32 4.35
243 244 2.874780 CGTGACGTCAGTAGGCGC 60.875 66.667 20.73 0.00 0.00 6.53
252 253 0.613260 TCAGTAGGCGCTGGTCAATT 59.387 50.000 7.64 0.00 37.12 2.32
261 262 2.668279 GCGCTGGTCAATTAAAGTGTGG 60.668 50.000 0.00 0.00 0.00 4.17
262 263 2.668279 CGCTGGTCAATTAAAGTGTGGC 60.668 50.000 0.00 0.00 0.00 5.01
263 264 2.295909 GCTGGTCAATTAAAGTGTGGCA 59.704 45.455 0.00 0.00 0.00 4.92
264 265 3.857010 GCTGGTCAATTAAAGTGTGGCAC 60.857 47.826 11.55 11.55 34.10 5.01
316 317 0.538746 GGGAAAGGAAAGTGGCGGAA 60.539 55.000 0.00 0.00 0.00 4.30
377 378 2.434884 AGCGACATCCAAGCCACG 60.435 61.111 0.00 0.00 0.00 4.94
378 379 3.499737 GCGACATCCAAGCCACGG 61.500 66.667 0.00 0.00 0.00 4.94
382 383 1.899437 GACATCCAAGCCACGGAGGA 61.899 60.000 5.43 0.00 41.22 3.71
412 413 1.294780 CTGAGAAGTGGCTTCGGCT 59.705 57.895 3.60 0.00 44.34 5.52
439 440 7.936496 TCAAATTTGAGGCACAACTGATATA 57.064 32.000 16.91 0.00 38.29 0.86
444 445 1.484653 AGGCACAACTGATATACCGCA 59.515 47.619 0.00 0.00 0.00 5.69
451 452 6.677920 GCACAACTGATATACCGCATTCTTTT 60.678 38.462 0.00 0.00 0.00 2.27
452 453 7.250569 CACAACTGATATACCGCATTCTTTTT 58.749 34.615 0.00 0.00 0.00 1.94
486 487 4.851639 ACTGGATGAGAGTTTGGCTATT 57.148 40.909 0.00 0.00 0.00 1.73
524 525 5.163099 TGTCTATGCATGTTAGGCCCTATTT 60.163 40.000 10.16 0.00 0.00 1.40
526 527 2.665165 TGCATGTTAGGCCCTATTTGG 58.335 47.619 0.00 0.00 0.00 3.28
558 559 4.361971 TCCAGGACGGAGCGGAGT 62.362 66.667 0.00 0.00 39.64 3.85
559 560 4.135153 CCAGGACGGAGCGGAGTG 62.135 72.222 0.00 0.00 36.56 3.51
560 561 4.803426 CAGGACGGAGCGGAGTGC 62.803 72.222 0.00 0.00 46.98 4.40
595 597 5.828328 GGGTTAGCAGCTCCTAAATTACAAT 59.172 40.000 0.00 0.00 0.00 2.71
602 604 7.557719 AGCAGCTCCTAAATTACAATTACATGT 59.442 33.333 2.69 2.69 37.32 3.21
603 605 7.857885 GCAGCTCCTAAATTACAATTACATGTC 59.142 37.037 0.00 0.00 34.75 3.06
606 608 7.254795 GCTCCTAAATTACAATTACATGTCGCT 60.255 37.037 0.00 0.00 34.75 4.93
607 609 8.138365 TCCTAAATTACAATTACATGTCGCTC 57.862 34.615 0.00 0.00 34.75 5.03
608 610 7.225931 TCCTAAATTACAATTACATGTCGCTCC 59.774 37.037 0.00 0.00 34.75 4.70
609 611 5.403897 AATTACAATTACATGTCGCTCCG 57.596 39.130 0.00 0.00 34.75 4.63
610 612 1.006832 ACAATTACATGTCGCTCCGC 58.993 50.000 0.00 0.00 0.00 5.54
611 613 1.290203 CAATTACATGTCGCTCCGCT 58.710 50.000 0.00 0.00 0.00 5.52
612 614 1.258982 CAATTACATGTCGCTCCGCTC 59.741 52.381 0.00 0.00 0.00 5.03
613 615 0.249489 ATTACATGTCGCTCCGCTCC 60.249 55.000 0.00 0.00 0.00 4.70
614 616 1.600511 TTACATGTCGCTCCGCTCCA 61.601 55.000 0.00 0.00 0.00 3.86
615 617 2.004808 TACATGTCGCTCCGCTCCAG 62.005 60.000 0.00 0.00 0.00 3.86
616 618 2.755876 ATGTCGCTCCGCTCCAGA 60.756 61.111 0.00 0.00 0.00 3.86
617 619 2.780094 ATGTCGCTCCGCTCCAGAG 61.780 63.158 0.00 0.00 0.00 3.35
628 630 2.659016 TCCAGAGCGGAGTTGCAG 59.341 61.111 0.00 0.00 39.64 4.41
629 631 1.908299 TCCAGAGCGGAGTTGCAGA 60.908 57.895 0.00 0.00 39.64 4.26
630 632 1.447489 CCAGAGCGGAGTTGCAGAG 60.447 63.158 0.00 0.00 36.56 3.35
631 633 1.447489 CAGAGCGGAGTTGCAGAGG 60.447 63.158 0.00 0.00 37.31 3.69
632 634 2.125350 GAGCGGAGTTGCAGAGGG 60.125 66.667 0.00 0.00 37.31 4.30
633 635 3.672295 GAGCGGAGTTGCAGAGGGG 62.672 68.421 0.00 0.00 37.31 4.79
634 636 3.706373 GCGGAGTTGCAGAGGGGA 61.706 66.667 0.00 0.00 34.15 4.81
635 637 2.581354 CGGAGTTGCAGAGGGGAG 59.419 66.667 0.00 0.00 0.00 4.30
636 638 2.993853 GGAGTTGCAGAGGGGAGG 59.006 66.667 0.00 0.00 0.00 4.30
637 639 2.674220 GGAGTTGCAGAGGGGAGGG 61.674 68.421 0.00 0.00 0.00 4.30
638 640 1.613630 GAGTTGCAGAGGGGAGGGA 60.614 63.158 0.00 0.00 0.00 4.20
639 641 0.985490 GAGTTGCAGAGGGGAGGGAT 60.985 60.000 0.00 0.00 0.00 3.85
640 642 0.551131 AGTTGCAGAGGGGAGGGATT 60.551 55.000 0.00 0.00 0.00 3.01
641 643 0.106967 GTTGCAGAGGGGAGGGATTC 60.107 60.000 0.00 0.00 0.00 2.52
642 644 1.281925 TTGCAGAGGGGAGGGATTCC 61.282 60.000 0.00 0.00 46.00 3.01
654 656 3.369997 GGAGGGATTCCAAACAGACTCTC 60.370 52.174 4.80 0.00 46.01 3.20
684 686 5.931532 ACAAATTCGTCTGTGTCATCAATC 58.068 37.500 0.00 0.00 0.00 2.67
750 752 2.299013 AGACTTGCGATTCCAGTACACA 59.701 45.455 0.00 0.00 0.00 3.72
793 795 4.069304 CCATTTCGGTTAGGTTCTTGTGA 58.931 43.478 0.00 0.00 0.00 3.58
818 820 1.593196 GCATATAGGCCAGCGTTGAA 58.407 50.000 5.01 0.00 0.00 2.69
856 861 2.351418 CACAGTTGCTGTTTCTTCGTCA 59.649 45.455 0.00 0.00 42.59 4.35
922 927 6.363357 GGCGGCATTAAATATTCAACAGAATC 59.637 38.462 3.07 0.00 34.08 2.52
981 989 0.179086 TCGCTTGCCATCTATTCGCA 60.179 50.000 0.00 0.00 0.00 5.10
1058 1093 1.596727 CACCAAACCAAATGCAAACCG 59.403 47.619 0.00 0.00 0.00 4.44
1060 1095 2.284190 CCAAACCAAATGCAAACCGTT 58.716 42.857 0.00 0.00 0.00 4.44
1141 1206 3.637229 CCTCTCCGGCATCTACTTAAGAA 59.363 47.826 10.09 0.00 37.89 2.52
1144 1209 4.098044 TCTCCGGCATCTACTTAAGAACTG 59.902 45.833 10.09 2.46 37.89 3.16
1159 1224 7.759886 ACTTAAGAACTGCAAAGGTTTTTCTTC 59.240 33.333 10.09 0.00 35.48 2.87
1163 1228 3.181490 ACTGCAAAGGTTTTTCTTCCGAC 60.181 43.478 0.00 0.00 0.00 4.79
1166 1231 4.177783 GCAAAGGTTTTTCTTCCGACAAA 58.822 39.130 0.00 0.00 0.00 2.83
1170 1235 6.465439 AAGGTTTTTCTTCCGACAAAGAAT 57.535 33.333 7.96 0.00 43.02 2.40
1195 1260 4.517075 GCAAAGGTGAGCTTACTTCTTCTT 59.483 41.667 8.70 0.21 0.00 2.52
1223 1288 4.202315 TGCAAAGGTGAGCTTACTTCTGTA 60.202 41.667 8.70 0.00 0.00 2.74
1226 1291 2.498078 AGGTGAGCTTACTTCTGTAGCC 59.502 50.000 8.70 0.00 0.00 3.93
1230 1295 3.583086 TGAGCTTACTTCTGTAGCCCTTT 59.417 43.478 0.00 0.00 0.00 3.11
1231 1296 4.185394 GAGCTTACTTCTGTAGCCCTTTC 58.815 47.826 0.00 0.00 0.00 2.62
1238 1303 1.203440 TCTGTAGCCCTTTCCCCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
1245 1310 0.605083 CCTTTCCCCTTCTGCTTTGC 59.395 55.000 0.00 0.00 0.00 3.68
1260 1325 2.297033 GCTTTGCTGAATCCAGAACCAA 59.703 45.455 0.00 0.00 43.02 3.67
1265 1330 3.269178 GCTGAATCCAGAACCAAGAGAG 58.731 50.000 0.00 0.00 43.02 3.20
1280 1345 1.408340 AGAGAGACATGACGCTGGATG 59.592 52.381 6.13 0.00 0.00 3.51
1307 1372 3.760035 GCCGTTCCTGAGCCGAGA 61.760 66.667 0.00 0.00 0.00 4.04
1340 1405 2.827604 CAGAAGATGCCGACGTTGT 58.172 52.632 1.30 0.00 0.00 3.32
1606 1671 2.816672 CAAGCCCAAGAAGAAAGAGGAC 59.183 50.000 0.00 0.00 0.00 3.85
1616 1681 1.003233 AAAGAGGACAAGCCCGAGC 60.003 57.895 0.00 0.00 37.37 5.03
1657 1722 2.103538 CTGGTGCCGTACGCGTAT 59.896 61.111 23.56 0.00 42.08 3.06
1658 1723 1.942712 CTGGTGCCGTACGCGTATC 60.943 63.158 23.56 14.60 42.08 2.24
1659 1724 2.656328 GGTGCCGTACGCGTATCC 60.656 66.667 23.56 15.17 42.08 2.59
1660 1725 3.020665 GTGCCGTACGCGTATCCG 61.021 66.667 23.56 20.90 42.08 4.18
1716 1781 3.433453 TGGCTGCGCTACGTCGTA 61.433 61.111 9.73 4.78 0.00 3.43
1745 1810 1.298014 CACTCCAAGCCACCTCCTC 59.702 63.158 0.00 0.00 0.00 3.71
1746 1811 1.920835 ACTCCAAGCCACCTCCTCC 60.921 63.158 0.00 0.00 0.00 4.30
1747 1812 3.003173 TCCAAGCCACCTCCTCCG 61.003 66.667 0.00 0.00 0.00 4.63
1748 1813 4.101448 CCAAGCCACCTCCTCCGG 62.101 72.222 0.00 0.00 0.00 5.14
1749 1814 4.785453 CAAGCCACCTCCTCCGGC 62.785 72.222 0.00 0.00 46.62 6.13
1793 1858 4.778143 GCCCGGCGTGGTCATCTT 62.778 66.667 6.01 0.00 35.15 2.40
1794 1859 2.819595 CCCGGCGTGGTCATCTTG 60.820 66.667 6.01 0.00 35.15 3.02
1795 1860 3.499737 CCGGCGTGGTCATCTTGC 61.500 66.667 6.01 0.00 0.00 4.01
1796 1861 3.499737 CGGCGTGGTCATCTTGCC 61.500 66.667 0.00 0.00 42.29 4.52
1797 1862 2.359850 GGCGTGGTCATCTTGCCA 60.360 61.111 0.00 0.00 45.06 4.92
1801 1866 4.402851 TGGTCATCTTGCCACTGC 57.597 55.556 0.00 0.00 38.26 4.40
1802 1867 1.303561 TGGTCATCTTGCCACTGCC 60.304 57.895 0.00 0.00 36.33 4.85
1803 1868 1.303561 GGTCATCTTGCCACTGCCA 60.304 57.895 0.00 0.00 36.33 4.92
1804 1869 1.589716 GGTCATCTTGCCACTGCCAC 61.590 60.000 0.00 0.00 36.33 5.01
1805 1870 0.890542 GTCATCTTGCCACTGCCACA 60.891 55.000 0.00 0.00 36.33 4.17
1806 1871 0.890542 TCATCTTGCCACTGCCACAC 60.891 55.000 0.00 0.00 36.33 3.82
1900 1965 1.011968 GCACCGTCATGTAACTGCGA 61.012 55.000 0.00 0.00 0.00 5.10
1901 1966 0.713883 CACCGTCATGTAACTGCGAC 59.286 55.000 0.00 0.00 0.00 5.19
1909 1988 0.872451 TGTAACTGCGACACGGTGTG 60.872 55.000 20.06 11.88 38.15 3.82
1940 2019 2.329267 TCGAAGCCTCCATGTATCCAT 58.671 47.619 0.00 0.00 0.00 3.41
2003 2082 5.575606 CCTTAAACGTCTTCGAGCTTAATGA 59.424 40.000 0.00 0.00 40.62 2.57
2025 2104 2.561733 TCTGTCGAATAAGTGAGCGG 57.438 50.000 0.00 0.00 0.00 5.52
2093 2172 6.044682 AGAGCAATTTTCACCTTGTTCAAAG 58.955 36.000 0.00 0.00 35.72 2.77
2190 2269 6.377146 CACCACTTAAATTACAATGCCTACCT 59.623 38.462 0.00 0.00 0.00 3.08
2299 2379 0.890542 GGCGGCCATTGATGCTATGA 60.891 55.000 15.62 0.00 0.00 2.15
2305 2385 3.496692 GGCCATTGATGCTATGACAGGTA 60.497 47.826 0.00 0.00 0.00 3.08
2323 2403 2.474133 TAACAAGGCCCCGGGACCTA 62.474 60.000 30.86 10.89 34.31 3.08
2336 2416 1.291272 GACCTAACGGCTTCACGGT 59.709 57.895 0.00 0.00 38.39 4.83
2390 2472 3.063510 AGATGATGGCATGGGTTATCG 57.936 47.619 3.81 0.00 34.11 2.92
2413 2495 4.497291 ACAGTTCAGTAACCTCCAAACA 57.503 40.909 0.00 0.00 36.15 2.83
2416 2498 6.597562 ACAGTTCAGTAACCTCCAAACAATA 58.402 36.000 0.00 0.00 36.15 1.90
2436 2518 7.002276 ACAATAAACCTACACTGGCTTAACTT 58.998 34.615 0.00 0.00 0.00 2.66
2510 2592 2.972348 TCCGCCCCATTAGTCTTATCT 58.028 47.619 0.00 0.00 0.00 1.98
2520 2602 7.989741 CCCCATTAGTCTTATCTATGCTATTGG 59.010 40.741 0.00 0.00 35.04 3.16
2563 2829 1.453155 CAGTCCGTCTTTCCCCATTG 58.547 55.000 0.00 0.00 0.00 2.82
2638 2905 6.602179 CATTCACGACAACTTCATGTATGTT 58.398 36.000 0.00 0.00 32.57 2.71
2644 2911 8.443160 CACGACAACTTCATGTATGTTAGAAAT 58.557 33.333 0.00 0.00 32.57 2.17
2655 2922 3.454371 TGTTAGAAATCTAGCGAGGCC 57.546 47.619 0.00 0.00 33.12 5.19
2668 2937 2.732001 CGAGGCCGCTAAATAAACAC 57.268 50.000 4.53 0.00 0.00 3.32
2669 2938 1.329599 CGAGGCCGCTAAATAAACACC 59.670 52.381 4.53 0.00 0.00 4.16
2670 2939 2.640184 GAGGCCGCTAAATAAACACCT 58.360 47.619 0.00 0.00 0.00 4.00
2671 2940 3.014623 GAGGCCGCTAAATAAACACCTT 58.985 45.455 0.00 0.00 0.00 3.50
2727 2996 0.248661 CTTCGACTCGGTGCGATGAT 60.249 55.000 0.00 0.00 36.31 2.45
2728 2997 0.525455 TTCGACTCGGTGCGATGATG 60.525 55.000 0.00 0.00 36.31 3.07
2785 3054 4.785453 CCGCTTCCAGGAGTGGGC 62.785 72.222 9.56 3.98 45.11 5.36
2830 3099 4.552355 TCTTCGTGCGTTCTTCTTAATGA 58.448 39.130 0.00 0.00 0.00 2.57
2863 3132 1.152984 CCATCTACCATGGCCGCAA 60.153 57.895 13.04 0.00 31.75 4.85
2865 3134 0.179048 CATCTACCATGGCCGCAAGA 60.179 55.000 13.04 7.69 43.02 3.02
2871 3140 1.143684 ACCATGGCCGCAAGATTAGAT 59.856 47.619 13.04 0.00 43.02 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.941483 GGAGATCCACAATTCGAACATGT 59.059 43.478 11.53 11.53 35.64 3.21
54 55 1.804326 CCGAAGAAGTACCACGGCG 60.804 63.158 4.80 4.80 37.32 6.46
59 60 2.263540 GCCGCCGAAGAAGTACCA 59.736 61.111 0.00 0.00 0.00 3.25
60 61 1.810030 CTGCCGCCGAAGAAGTACC 60.810 63.158 0.00 0.00 0.00 3.34
71 72 4.819761 TCTGTCATCGCTGCCGCC 62.820 66.667 0.00 0.00 0.00 6.13
74 75 0.179089 ATGTCTCTGTCATCGCTGCC 60.179 55.000 0.00 0.00 0.00 4.85
86 87 0.950836 CGCTCGAGATCCATGTCTCT 59.049 55.000 18.75 3.38 41.95 3.10
144 145 1.738830 TCCGCATTTCGTCCGGAAC 60.739 57.895 5.23 0.00 46.95 3.62
184 185 0.741326 TCTGCTACCATGAGCTCGTC 59.259 55.000 5.16 0.00 43.27 4.20
203 204 3.638627 TGAATCGATGAGTCTAGCCACAT 59.361 43.478 0.00 0.00 0.00 3.21
204 205 3.023832 TGAATCGATGAGTCTAGCCACA 58.976 45.455 0.00 0.00 0.00 4.17
205 206 3.376540 GTGAATCGATGAGTCTAGCCAC 58.623 50.000 0.00 0.00 0.00 5.01
208 209 3.039405 CACGTGAATCGATGAGTCTAGC 58.961 50.000 10.90 0.00 42.86 3.42
214 215 1.840741 GACGTCACGTGAATCGATGAG 59.159 52.381 28.50 12.63 41.37 2.90
227 228 1.801913 CAGCGCCTACTGACGTCAC 60.802 63.158 15.76 3.34 40.25 3.67
231 232 2.202623 GACCAGCGCCTACTGACG 60.203 66.667 2.29 0.00 40.25 4.35
235 236 3.270877 CTTTAATTGACCAGCGCCTACT 58.729 45.455 2.29 0.00 0.00 2.57
243 244 3.609175 CGTGCCACACTTTAATTGACCAG 60.609 47.826 0.00 0.00 31.34 4.00
252 253 1.338674 CCATCCTCGTGCCACACTTTA 60.339 52.381 0.00 0.00 31.34 1.85
294 295 1.465172 GCCACTTTCCTTTCCCCCT 59.535 57.895 0.00 0.00 0.00 4.79
309 310 1.150536 AACCTTCTTGCTTCCGCCA 59.849 52.632 0.00 0.00 34.43 5.69
316 317 0.825010 CAGGCACCAACCTTCTTGCT 60.825 55.000 0.00 0.00 38.26 3.91
324 325 4.947147 TCCACGCAGGCACCAACC 62.947 66.667 0.00 0.00 37.29 3.77
353 354 0.179089 CTTGGATGTCGCTCTCCCTG 60.179 60.000 0.00 0.00 0.00 4.45
362 363 1.811266 CTCCGTGGCTTGGATGTCG 60.811 63.158 0.00 0.00 34.32 4.35
393 394 1.004440 GCCGAAGCCACTTCTCAGT 60.004 57.895 5.85 0.00 38.24 3.41
428 429 7.391148 AAAAAGAATGCGGTATATCAGTTGT 57.609 32.000 0.00 0.00 0.00 3.32
451 452 7.993183 ACTCTCATCCAGTTTAACTTCTCAAAA 59.007 33.333 0.00 0.00 0.00 2.44
452 453 7.509546 ACTCTCATCCAGTTTAACTTCTCAAA 58.490 34.615 0.00 0.00 0.00 2.69
468 469 4.439289 GCAACAATAGCCAAACTCTCATCC 60.439 45.833 0.00 0.00 0.00 3.51
486 487 3.129113 GCATAGACATGTTCATGGCAACA 59.871 43.478 18.99 2.76 42.62 3.33
524 525 0.467290 GGAGGAGTGGTGTTTTGCCA 60.467 55.000 0.00 0.00 0.00 4.92
526 527 0.954452 CTGGAGGAGTGGTGTTTTGC 59.046 55.000 0.00 0.00 0.00 3.68
530 531 1.472662 CGTCCTGGAGGAGTGGTGTT 61.473 60.000 10.85 0.00 46.49 3.32
533 534 2.283966 CCGTCCTGGAGGAGTGGT 60.284 66.667 17.56 0.00 46.49 4.16
573 574 8.889717 TGTAATTGTAATTTAGGAGCTGCTAAC 58.110 33.333 25.40 15.98 0.00 2.34
612 614 1.447489 CTCTGCAACTCCGCTCTGG 60.447 63.158 0.00 0.00 40.09 3.86
613 615 1.447489 CCTCTGCAACTCCGCTCTG 60.447 63.158 0.00 0.00 0.00 3.35
614 616 2.654079 CCCTCTGCAACTCCGCTCT 61.654 63.158 0.00 0.00 0.00 4.09
615 617 2.125350 CCCTCTGCAACTCCGCTC 60.125 66.667 0.00 0.00 0.00 5.03
616 618 3.710722 CCCCTCTGCAACTCCGCT 61.711 66.667 0.00 0.00 0.00 5.52
617 619 3.672295 CTCCCCTCTGCAACTCCGC 62.672 68.421 0.00 0.00 0.00 5.54
618 620 2.581354 CTCCCCTCTGCAACTCCG 59.419 66.667 0.00 0.00 0.00 4.63
619 621 2.674220 CCCTCCCCTCTGCAACTCC 61.674 68.421 0.00 0.00 0.00 3.85
620 622 0.985490 ATCCCTCCCCTCTGCAACTC 60.985 60.000 0.00 0.00 0.00 3.01
621 623 0.551131 AATCCCTCCCCTCTGCAACT 60.551 55.000 0.00 0.00 0.00 3.16
622 624 0.106967 GAATCCCTCCCCTCTGCAAC 60.107 60.000 0.00 0.00 0.00 4.17
623 625 1.281925 GGAATCCCTCCCCTCTGCAA 61.282 60.000 0.00 0.00 38.44 4.08
624 626 1.694169 GGAATCCCTCCCCTCTGCA 60.694 63.158 0.00 0.00 38.44 4.41
625 627 1.281925 TTGGAATCCCTCCCCTCTGC 61.282 60.000 0.00 0.00 44.69 4.26
626 628 1.064389 GTTTGGAATCCCTCCCCTCTG 60.064 57.143 0.00 0.00 44.69 3.35
627 629 1.299939 GTTTGGAATCCCTCCCCTCT 58.700 55.000 0.00 0.00 44.69 3.69
628 630 0.999712 TGTTTGGAATCCCTCCCCTC 59.000 55.000 0.00 0.00 44.69 4.30
629 631 1.002857 CTGTTTGGAATCCCTCCCCT 58.997 55.000 0.00 0.00 44.69 4.79
630 632 0.999712 TCTGTTTGGAATCCCTCCCC 59.000 55.000 0.00 0.00 44.69 4.81
631 633 1.636003 AGTCTGTTTGGAATCCCTCCC 59.364 52.381 0.00 0.00 44.69 4.30
632 634 2.573915 AGAGTCTGTTTGGAATCCCTCC 59.426 50.000 0.00 0.00 45.64 4.30
633 635 3.261897 TGAGAGTCTGTTTGGAATCCCTC 59.738 47.826 0.00 0.00 31.64 4.30
634 636 3.251484 TGAGAGTCTGTTTGGAATCCCT 58.749 45.455 0.00 0.00 31.64 4.20
635 637 3.008485 ACTGAGAGTCTGTTTGGAATCCC 59.992 47.826 0.00 0.00 31.64 3.85
636 638 4.249661 GACTGAGAGTCTGTTTGGAATCC 58.750 47.826 0.00 0.00 41.88 3.01
637 639 4.020662 AGGACTGAGAGTCTGTTTGGAATC 60.021 45.833 0.00 0.00 44.46 2.52
638 640 3.906846 AGGACTGAGAGTCTGTTTGGAAT 59.093 43.478 0.00 0.00 44.46 3.01
639 641 3.309296 AGGACTGAGAGTCTGTTTGGAA 58.691 45.455 0.00 0.00 44.46 3.53
640 642 2.964209 AGGACTGAGAGTCTGTTTGGA 58.036 47.619 0.00 0.00 44.46 3.53
641 643 3.574396 TGTAGGACTGAGAGTCTGTTTGG 59.426 47.826 0.00 0.00 44.46 3.28
642 644 4.855715 TGTAGGACTGAGAGTCTGTTTG 57.144 45.455 0.00 0.00 44.46 2.93
643 645 5.871396 TTTGTAGGACTGAGAGTCTGTTT 57.129 39.130 0.00 0.00 44.46 2.83
644 646 6.426646 AATTTGTAGGACTGAGAGTCTGTT 57.573 37.500 0.00 0.00 44.46 3.16
645 647 5.336055 CGAATTTGTAGGACTGAGAGTCTGT 60.336 44.000 0.00 0.00 44.46 3.41
646 648 5.098893 CGAATTTGTAGGACTGAGAGTCTG 58.901 45.833 0.00 0.00 44.46 3.51
649 651 4.767928 AGACGAATTTGTAGGACTGAGAGT 59.232 41.667 0.00 0.00 0.00 3.24
654 656 4.307432 ACACAGACGAATTTGTAGGACTG 58.693 43.478 9.61 9.61 0.00 3.51
684 686 2.032924 AGAAAAGGAAAAGCCAACGACG 59.967 45.455 0.00 0.00 40.02 5.12
724 726 3.589988 ACTGGAATCGCAAGTCTTACAG 58.410 45.455 0.00 0.00 43.17 2.74
750 752 2.755876 TCGCCTCTGCATCGACCT 60.756 61.111 0.00 0.00 37.32 3.85
827 829 6.699575 AGAAACAGCAACTGTGAACTAAAT 57.300 33.333 0.15 0.00 44.62 1.40
831 833 3.063997 CGAAGAAACAGCAACTGTGAACT 59.936 43.478 0.15 0.00 44.62 3.01
832 834 3.181510 ACGAAGAAACAGCAACTGTGAAC 60.182 43.478 0.15 0.00 44.62 3.18
835 840 2.351418 TGACGAAGAAACAGCAACTGTG 59.649 45.455 0.15 0.00 44.62 3.66
856 861 3.270877 GAGCGGTGACAATTAGTGGAAT 58.729 45.455 0.00 0.00 0.00 3.01
922 927 4.031765 CGATCACATCTCAACGGTTAACAG 59.968 45.833 8.10 6.02 0.00 3.16
967 975 1.887242 GCGGTGCGAATAGATGGCA 60.887 57.895 0.00 0.00 0.00 4.92
981 989 1.990160 TTCTGAAACCCTGGTGCGGT 61.990 55.000 0.00 0.00 34.07 5.68
1058 1093 5.912955 CGAAGGTGTTTATGTTTTCTCCAAC 59.087 40.000 0.00 0.00 0.00 3.77
1060 1095 5.127491 ACGAAGGTGTTTATGTTTTCTCCA 58.873 37.500 0.00 0.00 0.00 3.86
1141 1206 3.020984 TCGGAAGAAAAACCTTTGCAGT 58.979 40.909 0.00 0.00 37.03 4.40
1144 1209 3.430333 TGTCGGAAGAAAAACCTTTGC 57.570 42.857 0.00 0.00 45.01 3.68
1159 1224 3.052036 CACCTTTGCAATTCTTTGTCGG 58.948 45.455 0.00 0.00 35.17 4.79
1163 1228 3.986277 AGCTCACCTTTGCAATTCTTTG 58.014 40.909 0.00 0.00 35.85 2.77
1166 1231 4.401925 AGTAAGCTCACCTTTGCAATTCT 58.598 39.130 0.00 0.00 34.95 2.40
1170 1235 3.820557 AGAAGTAAGCTCACCTTTGCAA 58.179 40.909 0.00 0.00 34.95 4.08
1195 1260 2.645838 AAGCTCACCTTTGCAGAAGA 57.354 45.000 9.37 0.00 0.00 2.87
1223 1288 1.438686 AAGCAGAAGGGGAAAGGGCT 61.439 55.000 0.00 0.00 0.00 5.19
1226 1291 0.605083 GCAAAGCAGAAGGGGAAAGG 59.395 55.000 0.00 0.00 0.00 3.11
1230 1295 0.478072 TTCAGCAAAGCAGAAGGGGA 59.522 50.000 0.00 0.00 30.93 4.81
1231 1296 1.475682 GATTCAGCAAAGCAGAAGGGG 59.524 52.381 3.38 0.00 37.47 4.79
1238 1303 1.888512 GGTTCTGGATTCAGCAAAGCA 59.111 47.619 0.00 0.00 40.69 3.91
1245 1310 4.020751 TGTCTCTCTTGGTTCTGGATTCAG 60.021 45.833 0.00 0.00 42.21 3.02
1260 1325 1.408340 CATCCAGCGTCATGTCTCTCT 59.592 52.381 0.00 0.00 0.00 3.10
1265 1330 1.091771 CCACCATCCAGCGTCATGTC 61.092 60.000 0.00 0.00 0.00 3.06
1307 1372 6.862711 CATCTTCTGCACATCAAGATACAT 57.137 37.500 5.53 0.00 35.16 2.29
1340 1405 1.377072 CCATGTCCACCGTGATGCA 60.377 57.895 0.00 0.00 31.20 3.96
1716 1781 2.721971 CTTGGAGTGGCACTCGCAGT 62.722 60.000 34.23 8.06 45.96 4.40
1724 1789 3.177884 AGGTGGCTTGGAGTGGCA 61.178 61.111 0.00 0.00 37.66 4.92
1784 1849 1.303561 GGCAGTGGCAAGATGACCA 60.304 57.895 12.58 0.00 43.71 4.02
1785 1850 1.303561 TGGCAGTGGCAAGATGACC 60.304 57.895 18.31 0.00 43.71 4.02
1786 1851 0.890542 TGTGGCAGTGGCAAGATGAC 60.891 55.000 22.39 8.36 43.71 3.06
1787 1852 0.890542 GTGTGGCAGTGGCAAGATGA 60.891 55.000 22.39 0.23 43.71 2.92
1788 1853 1.582968 GTGTGGCAGTGGCAAGATG 59.417 57.895 22.39 0.00 43.71 2.90
1789 1854 1.604593 GGTGTGGCAGTGGCAAGAT 60.605 57.895 22.39 0.00 43.71 2.40
1790 1855 1.414866 TAGGTGTGGCAGTGGCAAGA 61.415 55.000 22.39 8.31 43.71 3.02
1791 1856 1.073025 TAGGTGTGGCAGTGGCAAG 59.927 57.895 22.39 0.00 43.71 4.01
1792 1857 1.228124 GTAGGTGTGGCAGTGGCAA 60.228 57.895 22.39 9.10 43.71 4.52
1793 1858 2.429930 GTAGGTGTGGCAGTGGCA 59.570 61.111 16.56 16.56 43.71 4.92
1794 1859 2.359975 GGTAGGTGTGGCAGTGGC 60.360 66.667 10.30 10.30 40.13 5.01
1795 1860 2.351276 GGGTAGGTGTGGCAGTGG 59.649 66.667 0.00 0.00 0.00 4.00
1796 1861 2.047274 CGGGTAGGTGTGGCAGTG 60.047 66.667 0.00 0.00 0.00 3.66
1797 1862 4.016706 GCGGGTAGGTGTGGCAGT 62.017 66.667 0.00 0.00 0.00 4.40
1798 1863 4.778143 GGCGGGTAGGTGTGGCAG 62.778 72.222 0.00 0.00 0.00 4.85
1801 1866 3.069946 TACGGCGGGTAGGTGTGG 61.070 66.667 13.24 0.00 0.00 4.17
1802 1867 2.182537 GTACGGCGGGTAGGTGTG 59.817 66.667 13.24 0.00 0.00 3.82
1803 1868 3.070576 GGTACGGCGGGTAGGTGT 61.071 66.667 13.24 0.00 0.00 4.16
1804 1869 3.069946 TGGTACGGCGGGTAGGTG 61.070 66.667 13.24 0.00 0.00 4.00
1805 1870 2.757099 CTGGTACGGCGGGTAGGT 60.757 66.667 13.24 0.00 0.00 3.08
1828 1893 4.501714 GTGCACGGCATGGGCATG 62.502 66.667 8.44 0.00 41.91 4.06
1883 1948 0.315886 TGTCGCAGTTACATGACGGT 59.684 50.000 0.00 0.00 34.11 4.83
1909 1988 0.107945 AGGCTTCGAAGAGATGGTGC 60.108 55.000 28.95 11.14 38.43 5.01
1915 1994 1.561643 ACATGGAGGCTTCGAAGAGA 58.438 50.000 28.95 6.89 38.43 3.10
1940 2019 8.859090 AGAATTACAAACAAATCACTCATGGAA 58.141 29.630 0.00 0.00 0.00 3.53
2003 2082 3.865745 CCGCTCACTTATTCGACAGAAAT 59.134 43.478 0.00 0.00 40.15 2.17
2144 2223 8.573035 GTGGTGAAAGAAATCCATTACACTTTA 58.427 33.333 0.00 0.00 32.45 1.85
2145 2224 7.287696 AGTGGTGAAAGAAATCCATTACACTTT 59.712 33.333 0.00 0.00 30.96 2.66
2190 2269 3.005472 CCGAATTTAGATCAGTCGGCCTA 59.995 47.826 7.37 0.00 44.13 3.93
2197 2276 3.964031 AGGCTCTCCGAATTTAGATCAGT 59.036 43.478 0.00 0.00 37.47 3.41
2299 2379 2.754375 CGGGGCCTTGTTACCTGT 59.246 61.111 0.84 0.00 0.00 4.00
2323 2403 1.314730 AAAATGACCGTGAAGCCGTT 58.685 45.000 0.00 0.00 0.00 4.44
2367 2447 5.003160 CGATAACCCATGCCATCATCTTTA 58.997 41.667 0.00 0.00 0.00 1.85
2378 2458 3.006940 TGAACTGTTCGATAACCCATGC 58.993 45.455 15.18 0.00 34.49 4.06
2390 2472 4.879545 TGTTTGGAGGTTACTGAACTGTTC 59.120 41.667 13.49 13.49 35.74 3.18
2413 2495 9.006839 GTTAAGTTAAGCCAGTGTAGGTTTATT 57.993 33.333 0.00 0.00 34.84 1.40
2416 2498 5.766670 GGTTAAGTTAAGCCAGTGTAGGTTT 59.233 40.000 12.83 0.00 36.07 3.27
2436 2518 3.829026 TGGCAATAGCACAATGTTGGTTA 59.171 39.130 0.00 0.00 44.61 2.85
2510 2592 7.494922 TGGCTATGATCTTACCAATAGCATA 57.505 36.000 17.44 7.34 38.84 3.14
2520 2602 3.812053 CAGCACCTTGGCTATGATCTTAC 59.188 47.826 0.00 0.00 43.68 2.34
2545 2627 1.358152 TCAATGGGGAAAGACGGACT 58.642 50.000 0.00 0.00 0.00 3.85
2563 2829 9.515020 TGTTTATTGAAGACAAAGTTGTTCATC 57.485 29.630 0.00 0.00 42.43 2.92
2586 2852 6.772716 TCTCCTCTTATTGAAAGCACTTTGTT 59.227 34.615 0.00 0.00 32.11 2.83
2655 2922 4.457949 ACAAGGGAAGGTGTTTATTTAGCG 59.542 41.667 0.00 0.00 0.00 4.26
2660 2927 3.826729 GCAGACAAGGGAAGGTGTTTATT 59.173 43.478 0.00 0.00 0.00 1.40
2668 2937 1.349026 TGAAGAGCAGACAAGGGAAGG 59.651 52.381 0.00 0.00 0.00 3.46
2669 2938 2.847327 TGAAGAGCAGACAAGGGAAG 57.153 50.000 0.00 0.00 0.00 3.46
2670 2939 3.131709 CTTGAAGAGCAGACAAGGGAA 57.868 47.619 0.00 0.00 37.80 3.97
2671 2940 2.847327 CTTGAAGAGCAGACAAGGGA 57.153 50.000 0.00 0.00 37.80 4.20
2693 2962 0.108138 CGAAGGCCTTCCGAATGTCT 60.108 55.000 34.54 2.52 36.27 3.41
2727 2996 1.656587 AGCAGGTCAAGGATGTACCA 58.343 50.000 0.00 0.00 42.04 3.25
2728 2997 2.481449 CGTAGCAGGTCAAGGATGTACC 60.481 54.545 0.00 0.00 39.35 3.34
2785 3054 2.434185 TGCAAAGTAGAGCCGCCG 60.434 61.111 0.00 0.00 0.00 6.46
2830 3099 3.210012 ATGGGAGGCACGGCAACTT 62.210 57.895 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.