Multiple sequence alignment - TraesCS5D01G249900

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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 TraesCS5D01G249900 chr5D 100.000 2300 0 0 1 2300 356205693 356207992 0.000000e+00 4248
1 TraesCS5D01G249900 chr5B 89.740 1579 93 30 1 1541 421186668 421188215 0.000000e+00 1954
2 TraesCS5D01G249900 chr5B 87.169 756 71 10 1488 2218 421188260 421189014 0.000000e+00 835
3 TraesCS5D01G249900 chr5B 84.375 544 53 18 833 1368 421275447 421275966 2.640000e-139 505
4 TraesCS5D01G249900 chr5A 90.883 691 42 10 854 1528 457908239 457908924 0.000000e+00 907
5 TraesCS5D01G249900 chr5A 89.333 600 34 10 1 597 457904707 457905279 0.000000e+00 726
6 TraesCS5D01G249900 chr5A 88.774 579 47 6 1543 2116 457909260 457909825 0.000000e+00 693
7 TraesCS5D01G249900 chr5A 83.936 691 46 34 116 784 457907568 457908215 3.270000e-168 601
8 TraesCS5D01G249900 chr5A 80.560 679 68 35 850 1487 457915124 457915779 4.480000e-127 464
9 TraesCS5D01G249900 chr5A 81.416 226 18 10 600 819 457905474 457905681 1.830000e-36 163
10 TraesCS5D01G249900 chr5A 90.598 117 10 1 1 117 457906351 457906466 1.100000e-33 154


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 TraesCS5D01G249900 chr5D 356205693 356207992 2299 False 4248.000000 4248 100.0000 1 2300 1 chr5D.!!$F1 2299
1 TraesCS5D01G249900 chr5B 421186668 421189014 2346 False 1394.500000 1954 88.4545 1 2218 2 chr5B.!!$F2 2217
2 TraesCS5D01G249900 chr5B 421275447 421275966 519 False 505.000000 505 84.3750 833 1368 1 chr5B.!!$F1 535
3 TraesCS5D01G249900 chr5A 457904707 457909825 5118 False 540.666667 907 87.4900 1 2116 6 chr5A.!!$F2 2115
4 TraesCS5D01G249900 chr5A 457915124 457915779 655 False 464.000000 464 80.5600 850 1487 1 chr5A.!!$F1 637

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
224 227 0.541863 TGCCCTTTTCCGAGATCCTC 59.458 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 4888 0.621571 TCAAGCTCCCTACCAGCCAT 60.622 55.0 0.0 0.0 37.63 4.4 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
75 76 9.368416 TCTAGTCATAGGCTACATATGAAGTTT 57.632 33.333 10.38 0.00 40.40 2.66
100 103 1.144913 TCAAAAGGTGACCCCTCCTTG 59.855 52.381 0.00 0.00 45.47 3.61
101 104 1.133482 CAAAAGGTGACCCCTCCTTGT 60.133 52.381 0.00 0.00 45.47 3.16
104 107 1.134438 AGGTGACCCCTCCTTGTTCC 61.134 60.000 0.00 0.00 40.71 3.62
224 227 0.541863 TGCCCTTTTCCGAGATCCTC 59.458 55.000 0.00 0.00 0.00 3.71
282 287 8.697507 ACTTTTCCTTTCTGATGATGTTAGTT 57.302 30.769 0.00 0.00 0.00 2.24
283 288 9.793259 ACTTTTCCTTTCTGATGATGTTAGTTA 57.207 29.630 0.00 0.00 0.00 2.24
285 290 9.793259 TTTTCCTTTCTGATGATGTTAGTTACT 57.207 29.630 0.00 0.00 0.00 2.24
286 291 9.793259 TTTCCTTTCTGATGATGTTAGTTACTT 57.207 29.630 0.00 0.00 0.00 2.24
303 308 6.183347 AGTTACTTTTCCCTCCATGAGAATG 58.817 40.000 0.00 0.00 0.00 2.67
304 309 3.359950 ACTTTTCCCTCCATGAGAATGC 58.640 45.455 0.00 0.00 0.00 3.56
307 312 3.454719 TTCCCTCCATGAGAATGCAAA 57.545 42.857 0.00 0.00 0.00 3.68
313 318 5.299148 CCTCCATGAGAATGCAAAAACAAA 58.701 37.500 0.00 0.00 0.00 2.83
334 339 7.141363 ACAAATTGAGTTTAACAGACTGCATC 58.859 34.615 1.25 0.00 0.00 3.91
362 367 2.981898 TCTGTCCATGCATCAGTTCAG 58.018 47.619 12.22 11.69 0.00 3.02
440 448 8.682936 AGATGAACATTTAGTTTCTTGACTGT 57.317 30.769 0.00 0.00 41.51 3.55
459 470 1.340889 GTGGCAGAGGCATGTGAAAAA 59.659 47.619 0.00 0.00 43.71 1.94
548 559 2.611224 GCTTCTTCATGTGGCCTTTTGG 60.611 50.000 3.32 0.00 44.18 3.28
562 573 1.344438 CTTTTGGGTTTTGAGGAGCCC 59.656 52.381 0.00 0.00 41.42 5.19
598 804 1.139853 CTGGGCTGGCTACCTTTCTAG 59.860 57.143 0.00 0.00 0.00 2.43
599 805 1.205055 GGGCTGGCTACCTTTCTAGT 58.795 55.000 0.00 0.00 0.00 2.57
600 806 2.292653 TGGGCTGGCTACCTTTCTAGTA 60.293 50.000 0.00 0.00 0.00 1.82
601 807 2.365941 GGGCTGGCTACCTTTCTAGTAG 59.634 54.545 0.00 0.00 40.19 2.57
611 817 8.911965 GGCTACCTTTCTAGTAGTTTGTATACT 58.088 37.037 4.17 0.00 39.54 2.12
615 821 9.544579 ACCTTTCTAGTAGTTTGTATACTCCTT 57.455 33.333 4.17 0.00 35.20 3.36
623 829 9.047947 AGTAGTTTGTATACTCCTTGGATCTTT 57.952 33.333 4.17 0.00 0.00 2.52
626 832 9.892130 AGTTTGTATACTCCTTGGATCTTTAAG 57.108 33.333 4.17 0.00 0.00 1.85
633 839 7.368198 ACTCCTTGGATCTTTAAGATAGGTC 57.632 40.000 17.13 4.09 34.53 3.85
635 841 7.625682 ACTCCTTGGATCTTTAAGATAGGTCTT 59.374 37.037 17.13 5.32 46.22 3.01
636 842 7.796054 TCCTTGGATCTTTAAGATAGGTCTTG 58.204 38.462 17.13 2.65 44.27 3.02
637 843 6.484977 CCTTGGATCTTTAAGATAGGTCTTGC 59.515 42.308 7.52 0.00 44.27 4.01
638 844 5.930135 TGGATCTTTAAGATAGGTCTTGCC 58.070 41.667 7.52 3.14 44.27 4.52
696 903 1.362406 GCCGCTCTGTTGGTAAGCTC 61.362 60.000 0.00 0.00 33.83 4.09
730 943 4.048470 GCCCACCCAGGTTCCTCC 62.048 72.222 0.00 0.00 34.66 4.30
779 3546 5.526111 TCTTCTACTACAAAAATATGCCGCC 59.474 40.000 0.00 0.00 0.00 6.13
780 3547 4.771903 TCTACTACAAAAATATGCCGCCA 58.228 39.130 0.00 0.00 0.00 5.69
781 3548 5.373222 TCTACTACAAAAATATGCCGCCAT 58.627 37.500 0.00 0.00 35.44 4.40
782 3549 4.305989 ACTACAAAAATATGCCGCCATG 57.694 40.909 0.00 0.00 32.85 3.66
783 3550 2.600470 ACAAAAATATGCCGCCATGG 57.400 45.000 7.63 7.63 42.50 3.66
784 3551 1.138661 ACAAAAATATGCCGCCATGGG 59.861 47.619 15.13 3.37 38.63 4.00
785 3552 0.758123 AAAAATATGCCGCCATGGGG 59.242 50.000 21.60 21.60 38.63 4.96
809 3576 0.976073 GGCTAGTGTCCTGGCTGGTA 60.976 60.000 10.44 0.00 44.10 3.25
821 3588 3.127030 CCTGGCTGGTATCGTTCTTTTTC 59.873 47.826 1.62 0.00 0.00 2.29
827 3594 6.084277 GCTGGTATCGTTCTTTTTCGAAAAT 58.916 36.000 23.05 9.66 39.45 1.82
875 3643 4.310769 CTCTCCTATAAATTGACGCTGGG 58.689 47.826 0.00 0.00 0.00 4.45
936 3714 2.482142 GGAGTAGCAGCATACCAGTGTC 60.482 54.545 0.00 0.00 0.00 3.67
939 3717 3.634448 AGTAGCAGCATACCAGTGTCTAG 59.366 47.826 0.00 0.00 0.00 2.43
949 3727 1.225855 CAGTGTCTAGTGCCGCAAAA 58.774 50.000 0.00 0.00 0.00 2.44
952 3730 0.887387 TGTCTAGTGCCGCAAAACCC 60.887 55.000 0.00 0.00 0.00 4.11
962 3740 1.363807 GCAAAACCCTGTCTGTGCC 59.636 57.895 0.00 0.00 0.00 5.01
967 3745 1.352622 AACCCTGTCTGTGCCTCCAA 61.353 55.000 0.00 0.00 0.00 3.53
1047 3834 2.776312 GCACCTGCATTCTGATCATG 57.224 50.000 0.00 0.00 41.59 3.07
1155 3945 3.640407 ATGTCAGCTGGGTGCCGT 61.640 61.111 15.13 0.00 44.23 5.68
1182 3972 2.496470 GCAAGGTACTGCTAGTGGTACT 59.504 50.000 19.18 8.92 40.86 2.73
1187 3977 0.611062 ACTGCTAGTGGTACTGCGGA 60.611 55.000 0.00 0.00 34.75 5.54
1510 4335 5.336849 GGAGTGCTACTGTGTTATTGTCTCT 60.337 44.000 0.00 0.00 0.00 3.10
1528 4453 3.007940 TCTCTGACAACATAAGGGTGTGG 59.992 47.826 0.00 0.00 31.49 4.17
1533 4458 1.272212 CAACATAAGGGTGTGGTTGGC 59.728 52.381 0.00 0.00 36.19 4.52
1558 4717 5.174395 ACATTCTAAGACATGCTGAGTGTC 58.826 41.667 0.00 5.14 44.85 3.67
1564 4723 3.150848 GACATGCTGAGTGTCGACATA 57.849 47.619 23.12 10.49 36.92 2.29
1610 4770 3.541996 TGGTAGTGATGTATGTGCTGG 57.458 47.619 0.00 0.00 0.00 4.85
1659 4820 1.302993 GGAGCGGGTTAGTTGCCAA 60.303 57.895 0.00 0.00 0.00 4.52
1697 4865 0.909610 TTGCCATCGAGGAGAAGGGT 60.910 55.000 0.00 0.00 41.22 4.34
1700 4868 0.687757 CCATCGAGGAGAAGGGTGGA 60.688 60.000 0.00 0.00 41.22 4.02
1720 4888 3.695606 GCGGCTGGGTGTCTCTCA 61.696 66.667 0.00 0.00 0.00 3.27
1756 4924 3.446799 CTTGAGAGCGAGAGGAGAAATG 58.553 50.000 0.00 0.00 0.00 2.32
1758 4926 2.028130 GAGAGCGAGAGGAGAAATGGA 58.972 52.381 0.00 0.00 0.00 3.41
1764 4932 2.622942 CGAGAGGAGAAATGGAGAGGAG 59.377 54.545 0.00 0.00 0.00 3.69
1767 4935 2.965147 GAGGAGAAATGGAGAGGAGAGG 59.035 54.545 0.00 0.00 0.00 3.69
1785 4953 2.177451 GAGGTAACCCTAGTAGGCCTCT 59.823 54.545 23.57 9.43 42.86 3.69
1882 5051 2.194868 GAGGGGTATTTGGGCCGG 59.805 66.667 0.00 0.00 0.00 6.13
1931 5100 4.458989 TGCAGGCTAAAGAAACGAATGATT 59.541 37.500 0.00 0.00 0.00 2.57
1949 5122 5.255710 TGATTGATTTGTGGTCGTGTTTT 57.744 34.783 0.00 0.00 0.00 2.43
1984 5157 2.191400 CTCCATTCCTTCCTCTGGTGA 58.809 52.381 0.00 0.00 0.00 4.02
2001 5174 2.162408 GGTGATTTCTTCTTTGCCTCGG 59.838 50.000 0.00 0.00 0.00 4.63
2041 5215 3.855255 TCATGGTTGACTTCACCTTCA 57.145 42.857 0.00 0.00 0.00 3.02
2090 5264 3.885297 CTCTGATTTGTGTTGTCCACCTT 59.115 43.478 0.00 0.00 43.85 3.50
2147 5321 2.590575 CGGCGGTGTGGTCTTGTT 60.591 61.111 0.00 0.00 0.00 2.83
2153 5327 1.279840 GTGTGGTCTTGTTGCTCGC 59.720 57.895 0.00 0.00 0.00 5.03
2156 5330 1.597854 TGGTCTTGTTGCTCGCTGG 60.598 57.895 0.00 0.00 0.00 4.85
2159 5348 4.748679 CTTGTTGCTCGCTGGCGC 62.749 66.667 10.28 0.00 39.59 6.53
2178 5367 1.066257 GCAAGTGGTGTTGGCACTG 59.934 57.895 0.00 0.00 44.65 3.66
2179 5368 1.066257 CAAGTGGTGTTGGCACTGC 59.934 57.895 0.00 0.00 44.65 4.40
2202 5391 1.455959 TTGGTGGTTTTGTCCCGGG 60.456 57.895 16.85 16.85 0.00 5.73
2218 5407 1.304282 GGGGATGCTTGAGCTCCAA 59.696 57.895 12.15 4.89 42.66 3.53
2219 5408 0.106318 GGGGATGCTTGAGCTCCAAT 60.106 55.000 12.15 0.00 42.66 3.16
2220 5409 1.687368 GGGGATGCTTGAGCTCCAATT 60.687 52.381 12.15 0.00 42.66 2.32
2221 5410 2.423373 GGGGATGCTTGAGCTCCAATTA 60.423 50.000 12.15 0.00 42.66 1.40
2222 5411 2.620585 GGGATGCTTGAGCTCCAATTAC 59.379 50.000 12.15 0.00 42.66 1.89
2223 5412 2.620585 GGATGCTTGAGCTCCAATTACC 59.379 50.000 12.15 4.85 42.66 2.85
2224 5413 2.877097 TGCTTGAGCTCCAATTACCA 57.123 45.000 12.15 0.00 42.66 3.25
2225 5414 3.370840 TGCTTGAGCTCCAATTACCAT 57.629 42.857 12.15 0.00 42.66 3.55
2226 5415 3.700538 TGCTTGAGCTCCAATTACCATT 58.299 40.909 12.15 0.00 42.66 3.16
2227 5416 4.854173 TGCTTGAGCTCCAATTACCATTA 58.146 39.130 12.15 0.00 42.66 1.90
2228 5417 5.448654 TGCTTGAGCTCCAATTACCATTAT 58.551 37.500 12.15 0.00 42.66 1.28
2229 5418 5.300034 TGCTTGAGCTCCAATTACCATTATG 59.700 40.000 12.15 0.00 42.66 1.90
2230 5419 5.278660 GCTTGAGCTCCAATTACCATTATGG 60.279 44.000 12.15 10.08 39.97 2.74
2231 5420 5.829924 CTTGAGCTCCAATTACCATTATGGT 59.170 40.000 21.38 21.38 43.26 3.55
2232 5421 6.238842 CTTGAGCTCCAATTACCATTATGGTG 60.239 42.308 25.61 9.51 41.85 4.17
2233 5422 9.079367 CTTGAGCTCCAATTACCATTATGGTGG 62.079 44.444 25.61 17.88 41.85 4.61
2240 5429 3.873781 CCATTATGGTGGTGGTCGT 57.126 52.632 2.48 0.00 34.46 4.34
2241 5430 1.663695 CCATTATGGTGGTGGTCGTC 58.336 55.000 2.48 0.00 34.46 4.20
2242 5431 1.286501 CATTATGGTGGTGGTCGTCG 58.713 55.000 0.00 0.00 0.00 5.12
2243 5432 0.899720 ATTATGGTGGTGGTCGTCGT 59.100 50.000 0.00 0.00 0.00 4.34
2244 5433 1.543607 TTATGGTGGTGGTCGTCGTA 58.456 50.000 0.00 0.00 0.00 3.43
2245 5434 1.097232 TATGGTGGTGGTCGTCGTAG 58.903 55.000 0.00 0.00 0.00 3.51
2246 5435 0.896940 ATGGTGGTGGTCGTCGTAGT 60.897 55.000 0.00 0.00 0.00 2.73
2247 5436 0.250684 TGGTGGTGGTCGTCGTAGTA 60.251 55.000 0.00 0.00 0.00 1.82
2248 5437 0.449388 GGTGGTGGTCGTCGTAGTAG 59.551 60.000 0.00 0.00 0.00 2.57
2249 5438 1.160137 GTGGTGGTCGTCGTAGTAGT 58.840 55.000 0.00 0.00 0.00 2.73
2250 5439 1.129437 GTGGTGGTCGTCGTAGTAGTC 59.871 57.143 0.00 0.00 0.00 2.59
2251 5440 0.371645 GGTGGTCGTCGTAGTAGTCG 59.628 60.000 0.00 0.00 0.00 4.18
2252 5441 1.071605 GTGGTCGTCGTAGTAGTCGT 58.928 55.000 0.00 0.00 0.00 4.34
2253 5442 1.070821 TGGTCGTCGTAGTAGTCGTG 58.929 55.000 0.00 0.00 0.00 4.35
2254 5443 1.071605 GGTCGTCGTAGTAGTCGTGT 58.928 55.000 0.00 0.00 0.00 4.49
2255 5444 1.461127 GGTCGTCGTAGTAGTCGTGTT 59.539 52.381 0.00 0.00 0.00 3.32
2256 5445 2.096218 GGTCGTCGTAGTAGTCGTGTTT 60.096 50.000 0.00 0.00 0.00 2.83
2257 5446 2.898832 GTCGTCGTAGTAGTCGTGTTTG 59.101 50.000 0.00 0.00 0.00 2.93
2258 5447 2.096268 TCGTCGTAGTAGTCGTGTTTGG 60.096 50.000 0.00 0.00 0.00 3.28
2259 5448 2.589014 GTCGTAGTAGTCGTGTTTGGG 58.411 52.381 0.00 0.00 0.00 4.12
2260 5449 2.030805 GTCGTAGTAGTCGTGTTTGGGT 60.031 50.000 0.00 0.00 0.00 4.51
2261 5450 2.622942 TCGTAGTAGTCGTGTTTGGGTT 59.377 45.455 0.00 0.00 0.00 4.11
2262 5451 2.727798 CGTAGTAGTCGTGTTTGGGTTG 59.272 50.000 0.00 0.00 0.00 3.77
2263 5452 2.249844 AGTAGTCGTGTTTGGGTTGG 57.750 50.000 0.00 0.00 0.00 3.77
2264 5453 1.487558 AGTAGTCGTGTTTGGGTTGGT 59.512 47.619 0.00 0.00 0.00 3.67
2265 5454 1.600485 GTAGTCGTGTTTGGGTTGGTG 59.400 52.381 0.00 0.00 0.00 4.17
2266 5455 0.750182 AGTCGTGTTTGGGTTGGTGG 60.750 55.000 0.00 0.00 0.00 4.61
2267 5456 2.122167 TCGTGTTTGGGTTGGTGGC 61.122 57.895 0.00 0.00 0.00 5.01
2268 5457 2.124693 CGTGTTTGGGTTGGTGGCT 61.125 57.895 0.00 0.00 0.00 4.75
2269 5458 1.441311 GTGTTTGGGTTGGTGGCTG 59.559 57.895 0.00 0.00 0.00 4.85
2270 5459 1.760086 TGTTTGGGTTGGTGGCTGG 60.760 57.895 0.00 0.00 0.00 4.85
2271 5460 2.841988 TTTGGGTTGGTGGCTGGC 60.842 61.111 0.00 0.00 0.00 4.85
2272 5461 3.387609 TTTGGGTTGGTGGCTGGCT 62.388 57.895 2.00 0.00 0.00 4.75
2273 5462 4.601794 TGGGTTGGTGGCTGGCTG 62.602 66.667 2.00 0.00 0.00 4.85
2274 5463 4.603535 GGGTTGGTGGCTGGCTGT 62.604 66.667 2.00 0.00 0.00 4.40
2275 5464 2.521708 GGTTGGTGGCTGGCTGTT 60.522 61.111 2.00 0.00 0.00 3.16
2276 5465 2.564721 GGTTGGTGGCTGGCTGTTC 61.565 63.158 2.00 0.00 0.00 3.18
2277 5466 1.529244 GTTGGTGGCTGGCTGTTCT 60.529 57.895 2.00 0.00 0.00 3.01
2278 5467 1.109323 GTTGGTGGCTGGCTGTTCTT 61.109 55.000 2.00 0.00 0.00 2.52
2279 5468 1.108727 TTGGTGGCTGGCTGTTCTTG 61.109 55.000 2.00 0.00 0.00 3.02
2280 5469 1.228245 GGTGGCTGGCTGTTCTTGA 60.228 57.895 2.00 0.00 0.00 3.02
2281 5470 1.239968 GGTGGCTGGCTGTTCTTGAG 61.240 60.000 2.00 0.00 0.00 3.02
2282 5471 1.073722 TGGCTGGCTGTTCTTGAGG 59.926 57.895 2.00 0.00 0.00 3.86
2283 5472 1.073897 GGCTGGCTGTTCTTGAGGT 59.926 57.895 0.00 0.00 0.00 3.85
2284 5473 0.538287 GGCTGGCTGTTCTTGAGGTT 60.538 55.000 0.00 0.00 0.00 3.50
2285 5474 0.877743 GCTGGCTGTTCTTGAGGTTC 59.122 55.000 0.00 0.00 0.00 3.62
2286 5475 1.544314 GCTGGCTGTTCTTGAGGTTCT 60.544 52.381 0.00 0.00 0.00 3.01
2287 5476 2.421619 CTGGCTGTTCTTGAGGTTCTC 58.578 52.381 0.00 0.00 0.00 2.87
2288 5477 1.270305 TGGCTGTTCTTGAGGTTCTCG 60.270 52.381 0.00 0.00 32.35 4.04
2289 5478 0.793250 GCTGTTCTTGAGGTTCTCGC 59.207 55.000 0.00 0.00 32.35 5.03
2290 5479 1.873903 GCTGTTCTTGAGGTTCTCGCA 60.874 52.381 0.00 0.00 32.35 5.10
2291 5480 2.064762 CTGTTCTTGAGGTTCTCGCAG 58.935 52.381 0.00 0.00 32.35 5.18
2292 5481 1.412710 TGTTCTTGAGGTTCTCGCAGT 59.587 47.619 0.00 0.00 32.35 4.40
2293 5482 1.795286 GTTCTTGAGGTTCTCGCAGTG 59.205 52.381 0.00 0.00 32.35 3.66
2294 5483 0.318441 TCTTGAGGTTCTCGCAGTGG 59.682 55.000 0.00 0.00 32.35 4.00
2295 5484 0.318441 CTTGAGGTTCTCGCAGTGGA 59.682 55.000 0.00 0.00 32.35 4.02
2296 5485 0.976641 TTGAGGTTCTCGCAGTGGAT 59.023 50.000 0.00 0.00 32.35 3.41
2297 5486 0.247460 TGAGGTTCTCGCAGTGGATG 59.753 55.000 0.00 0.00 32.35 3.51
2298 5487 0.247736 GAGGTTCTCGCAGTGGATGT 59.752 55.000 0.00 0.00 0.00 3.06
2299 5488 0.687354 AGGTTCTCGCAGTGGATGTT 59.313 50.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 103 1.984288 ATTAGCTGGCTCCCCGGAAC 61.984 60.000 0.73 0.00 40.14 3.62
101 104 1.692749 ATTAGCTGGCTCCCCGGAA 60.693 57.895 0.73 0.00 40.14 4.30
104 107 1.524621 CACATTAGCTGGCTCCCCG 60.525 63.158 0.00 0.00 0.00 5.73
224 227 4.051922 AGAGTTGAGAAACACTTACTGCG 58.948 43.478 0.00 0.00 0.00 5.18
282 287 4.018506 TGCATTCTCATGGAGGGAAAAGTA 60.019 41.667 0.00 0.00 0.00 2.24
283 288 3.245371 TGCATTCTCATGGAGGGAAAAGT 60.245 43.478 0.00 0.00 0.00 2.66
284 289 3.359033 TGCATTCTCATGGAGGGAAAAG 58.641 45.455 0.00 0.00 0.00 2.27
285 290 3.454719 TGCATTCTCATGGAGGGAAAA 57.545 42.857 0.00 0.00 0.00 2.29
286 291 3.454719 TTGCATTCTCATGGAGGGAAA 57.545 42.857 0.00 0.00 31.42 3.13
290 295 4.524316 TGTTTTTGCATTCTCATGGAGG 57.476 40.909 0.00 0.00 31.42 4.30
303 308 8.655970 AGTCTGTTAAACTCAATTTGTTTTTGC 58.344 29.630 10.42 4.47 38.41 3.68
304 309 9.956797 CAGTCTGTTAAACTCAATTTGTTTTTG 57.043 29.630 10.42 0.00 38.41 2.44
307 312 7.319646 TGCAGTCTGTTAAACTCAATTTGTTT 58.680 30.769 0.93 10.13 40.27 2.83
313 318 5.564550 AGGATGCAGTCTGTTAAACTCAAT 58.435 37.500 0.93 0.00 0.00 2.57
334 339 2.704108 GCATGGACAGATGCAGAGG 58.296 57.895 0.00 0.00 46.77 3.69
355 360 6.293135 GCAGAAAAAGGAAGAGTACTGAACTG 60.293 42.308 0.00 0.00 39.07 3.16
358 363 5.527582 GTGCAGAAAAAGGAAGAGTACTGAA 59.472 40.000 0.00 0.00 0.00 3.02
362 367 7.604545 AGATTAGTGCAGAAAAAGGAAGAGTAC 59.395 37.037 0.00 0.00 0.00 2.73
440 448 1.702182 TTTTTCACATGCCTCTGCCA 58.298 45.000 0.00 0.00 36.33 4.92
459 470 5.139727 TGTCATTTTCACCAGAGTCCAATT 58.860 37.500 0.00 0.00 0.00 2.32
460 471 4.728772 TGTCATTTTCACCAGAGTCCAAT 58.271 39.130 0.00 0.00 0.00 3.16
471 482 3.916761 ACACCATGCATGTCATTTTCAC 58.083 40.909 24.58 0.00 31.79 3.18
472 483 4.603989 AACACCATGCATGTCATTTTCA 57.396 36.364 24.58 0.00 31.79 2.69
562 573 1.088340 CCAGCTCCGTGCAATCTGAG 61.088 60.000 0.00 0.00 45.94 3.35
600 806 9.892130 CTTAAAGATCCAAGGAGTATACAAACT 57.108 33.333 5.50 0.00 0.00 2.66
601 807 9.886132 TCTTAAAGATCCAAGGAGTATACAAAC 57.114 33.333 5.50 0.00 0.00 2.93
611 817 7.635971 GCAAGACCTATCTTAAAGATCCAAGGA 60.636 40.741 0.00 0.00 43.69 3.36
615 821 5.930135 GGCAAGACCTATCTTAAAGATCCA 58.070 41.667 0.00 0.00 43.69 3.41
630 836 9.678941 GCAATATTTTAAGTAATAGGCAAGACC 57.321 33.333 0.00 0.00 39.61 3.85
633 839 9.169468 CGTGCAATATTTTAAGTAATAGGCAAG 57.831 33.333 0.00 8.16 36.67 4.01
635 841 7.136119 GCGTGCAATATTTTAAGTAATAGGCA 58.864 34.615 0.00 0.00 34.55 4.75
636 842 6.581166 GGCGTGCAATATTTTAAGTAATAGGC 59.419 38.462 0.00 0.00 0.00 3.93
637 843 7.644490 TGGCGTGCAATATTTTAAGTAATAGG 58.356 34.615 0.00 0.00 0.00 2.57
640 846 9.624697 CATATGGCGTGCAATATTTTAAGTAAT 57.375 29.630 0.00 0.00 0.00 1.89
643 849 7.228507 TCTCATATGGCGTGCAATATTTTAAGT 59.771 33.333 2.13 0.00 0.00 2.24
644 850 7.584108 TCTCATATGGCGTGCAATATTTTAAG 58.416 34.615 2.13 0.00 0.00 1.85
779 3546 1.529948 CACTAGCCCATGCCCCATG 60.530 63.158 0.00 0.00 41.10 3.66
780 3547 1.999634 GACACTAGCCCATGCCCCAT 62.000 60.000 0.00 0.00 38.69 4.00
781 3548 2.613696 ACACTAGCCCATGCCCCA 60.614 61.111 0.00 0.00 38.69 4.96
782 3549 2.193248 GACACTAGCCCATGCCCC 59.807 66.667 0.00 0.00 38.69 5.80
783 3550 2.193248 GGACACTAGCCCATGCCC 59.807 66.667 0.00 0.00 38.69 5.36
784 3551 1.153086 CAGGACACTAGCCCATGCC 60.153 63.158 0.00 0.00 38.69 4.40
785 3552 1.153086 CCAGGACACTAGCCCATGC 60.153 63.158 0.00 0.00 37.95 4.06
791 3558 1.069358 GATACCAGCCAGGACACTAGC 59.931 57.143 0.00 0.00 41.22 3.42
821 3588 7.201376 GCTATGGCATTGCAATGTATATTTTCG 60.201 37.037 33.67 20.99 38.65 3.46
875 3643 0.443869 TTGATTTGAGAGCTTCGCGC 59.556 50.000 0.00 0.00 39.57 6.86
879 3647 7.131565 GCTTATTAGCTTGATTTGAGAGCTTC 58.868 38.462 2.16 0.00 43.84 3.86
882 3650 5.278218 GGGCTTATTAGCTTGATTTGAGAGC 60.278 44.000 3.39 0.00 46.90 4.09
936 3714 0.889186 ACAGGGTTTTGCGGCACTAG 60.889 55.000 0.05 0.00 0.00 2.57
939 3717 2.193536 AGACAGGGTTTTGCGGCAC 61.194 57.895 0.05 0.00 0.00 5.01
949 3727 1.352622 TTTGGAGGCACAGACAGGGT 61.353 55.000 0.00 0.00 0.00 4.34
952 3730 1.876156 GTCTTTTGGAGGCACAGACAG 59.124 52.381 0.00 0.00 35.04 3.51
962 3740 4.461198 ACAACTAAGGTGGTCTTTTGGAG 58.539 43.478 0.00 0.00 36.93 3.86
967 3745 4.245251 ACCAACAACTAAGGTGGTCTTT 57.755 40.909 0.00 0.00 36.93 2.52
1047 3834 2.028484 TGGCTCGACACGACCAAC 59.972 61.111 10.90 0.00 35.45 3.77
1155 3945 1.822114 TAGCAGTACCTTGCACGGCA 61.822 55.000 9.57 0.00 46.47 5.69
1187 3977 2.579201 CCATCTTCCACGTCGCCT 59.421 61.111 0.00 0.00 0.00 5.52
1279 4073 3.422732 GCTTAGTTTCGCTTAACGGTGAC 60.423 47.826 0.00 0.00 43.89 3.67
1282 4076 1.723003 CGCTTAGTTTCGCTTAACGGT 59.277 47.619 0.00 0.00 43.89 4.83
1510 4335 3.218453 CAACCACACCCTTATGTTGTCA 58.782 45.455 0.00 0.00 33.42 3.58
1528 4453 4.082571 AGCATGTCTTAGAATGTTGCCAAC 60.083 41.667 0.00 0.00 0.00 3.77
1533 4458 5.410746 ACACTCAGCATGTCTTAGAATGTTG 59.589 40.000 11.66 11.66 36.63 3.33
1540 4465 3.175152 GTCGACACTCAGCATGTCTTAG 58.825 50.000 11.55 0.00 43.60 2.18
1558 4717 5.693555 ACAGATGCATGTACTCAATATGTCG 59.306 40.000 2.46 0.00 0.00 4.35
1564 4723 5.474532 ACAACAACAGATGCATGTACTCAAT 59.525 36.000 2.46 0.00 32.41 2.57
1610 4770 4.453819 ACAAAGTCTTAGCTCAGCATGTTC 59.546 41.667 0.00 0.00 37.40 3.18
1659 4820 2.236395 CAACCTACTCCGGTGATTCCTT 59.764 50.000 11.17 0.00 37.36 3.36
1678 4839 0.909610 ACCCTTCTCCTCGATGGCAA 60.910 55.000 0.00 0.00 36.01 4.52
1700 4868 4.008933 GAGACACCCAGCCGCACT 62.009 66.667 0.00 0.00 0.00 4.40
1720 4888 0.621571 TCAAGCTCCCTACCAGCCAT 60.622 55.000 0.00 0.00 37.63 4.40
1756 4924 2.515005 ACTAGGGTTACCTCTCCTCTCC 59.485 54.545 0.00 0.00 46.95 3.71
1758 4926 3.723154 CCTACTAGGGTTACCTCTCCTCT 59.277 52.174 0.00 0.00 46.95 3.69
1764 4932 2.177451 AGAGGCCTACTAGGGTTACCTC 59.823 54.545 4.42 14.52 46.95 3.85
1767 4935 3.134262 CCAAAGAGGCCTACTAGGGTTAC 59.866 52.174 4.42 0.00 35.37 2.50
1785 4953 4.055227 GGATCCCCACGCCCCAAA 62.055 66.667 0.00 0.00 0.00 3.28
1931 5100 2.164422 TGCAAAACACGACCACAAATCA 59.836 40.909 0.00 0.00 0.00 2.57
1984 5157 0.804989 CGCCGAGGCAAAGAAGAAAT 59.195 50.000 15.03 0.00 42.06 2.17
2001 5174 3.468140 GACTACCAGGGGTCCCGC 61.468 72.222 0.48 0.00 41.95 6.13
2090 5264 2.717639 GCCATAGAAGGAAGGCAAGA 57.282 50.000 0.00 0.00 46.26 3.02
2141 5315 3.043713 CGCCAGCGAGCAACAAGA 61.044 61.111 6.06 0.00 42.83 3.02
2156 5330 4.980903 CCAACACCACTTGCGCGC 62.981 66.667 27.26 27.26 0.00 6.86
2159 5348 2.026014 GTGCCAACACCACTTGCG 59.974 61.111 0.00 0.00 41.21 4.85
2178 5367 2.656973 CAAAACCACCAACGGCGC 60.657 61.111 6.90 0.00 0.00 6.53
2179 5368 1.298788 GACAAAACCACCAACGGCG 60.299 57.895 4.80 4.80 0.00 6.46
2202 5391 2.620585 GGTAATTGGAGCTCAAGCATCC 59.379 50.000 17.19 7.20 45.16 3.51
2222 5411 1.663695 GACGACCACCACCATAATGG 58.336 55.000 0.00 0.00 46.10 3.16
2223 5412 1.286501 CGACGACCACCACCATAATG 58.713 55.000 0.00 0.00 0.00 1.90
2224 5413 0.899720 ACGACGACCACCACCATAAT 59.100 50.000 0.00 0.00 0.00 1.28
2225 5414 1.473677 CTACGACGACCACCACCATAA 59.526 52.381 0.00 0.00 0.00 1.90
2226 5415 1.097232 CTACGACGACCACCACCATA 58.903 55.000 0.00 0.00 0.00 2.74
2227 5416 0.896940 ACTACGACGACCACCACCAT 60.897 55.000 0.00 0.00 0.00 3.55
2228 5417 0.250684 TACTACGACGACCACCACCA 60.251 55.000 0.00 0.00 0.00 4.17
2229 5418 0.449388 CTACTACGACGACCACCACC 59.551 60.000 0.00 0.00 0.00 4.61
2230 5419 1.129437 GACTACTACGACGACCACCAC 59.871 57.143 0.00 0.00 0.00 4.16
2231 5420 1.442769 GACTACTACGACGACCACCA 58.557 55.000 0.00 0.00 0.00 4.17
2232 5421 0.371645 CGACTACTACGACGACCACC 59.628 60.000 0.00 0.00 0.00 4.61
2233 5422 1.071605 ACGACTACTACGACGACCAC 58.928 55.000 0.00 0.00 34.70 4.16
2234 5423 1.070821 CACGACTACTACGACGACCA 58.929 55.000 0.00 0.00 34.70 4.02
2235 5424 1.071605 ACACGACTACTACGACGACC 58.928 55.000 0.00 0.00 34.70 4.79
2236 5425 2.863658 AACACGACTACTACGACGAC 57.136 50.000 0.00 0.00 34.70 4.34
2237 5426 2.096268 CCAAACACGACTACTACGACGA 60.096 50.000 0.00 0.00 34.70 4.20
2238 5427 2.236690 CCAAACACGACTACTACGACG 58.763 52.381 0.00 0.00 34.70 5.12
2239 5428 2.030805 ACCCAAACACGACTACTACGAC 60.031 50.000 0.00 0.00 34.70 4.34
2240 5429 2.229792 ACCCAAACACGACTACTACGA 58.770 47.619 0.00 0.00 34.70 3.43
2241 5430 2.712057 ACCCAAACACGACTACTACG 57.288 50.000 0.00 0.00 0.00 3.51
2242 5431 3.062042 CCAACCCAAACACGACTACTAC 58.938 50.000 0.00 0.00 0.00 2.73
2243 5432 2.699846 ACCAACCCAAACACGACTACTA 59.300 45.455 0.00 0.00 0.00 1.82
2244 5433 1.487558 ACCAACCCAAACACGACTACT 59.512 47.619 0.00 0.00 0.00 2.57
2245 5434 1.600485 CACCAACCCAAACACGACTAC 59.400 52.381 0.00 0.00 0.00 2.73
2246 5435 1.475392 CCACCAACCCAAACACGACTA 60.475 52.381 0.00 0.00 0.00 2.59
2247 5436 0.750182 CCACCAACCCAAACACGACT 60.750 55.000 0.00 0.00 0.00 4.18
2248 5437 1.731093 CCACCAACCCAAACACGAC 59.269 57.895 0.00 0.00 0.00 4.34
2249 5438 2.122167 GCCACCAACCCAAACACGA 61.122 57.895 0.00 0.00 0.00 4.35
2250 5439 2.124693 AGCCACCAACCCAAACACG 61.125 57.895 0.00 0.00 0.00 4.49
2251 5440 1.441311 CAGCCACCAACCCAAACAC 59.559 57.895 0.00 0.00 0.00 3.32
2252 5441 1.760086 CCAGCCACCAACCCAAACA 60.760 57.895 0.00 0.00 0.00 2.83
2253 5442 3.137687 CCAGCCACCAACCCAAAC 58.862 61.111 0.00 0.00 0.00 2.93
2254 5443 2.841988 GCCAGCCACCAACCCAAA 60.842 61.111 0.00 0.00 0.00 3.28
2255 5444 3.831637 AGCCAGCCACCAACCCAA 61.832 61.111 0.00 0.00 0.00 4.12
2256 5445 4.601794 CAGCCAGCCACCAACCCA 62.602 66.667 0.00 0.00 0.00 4.51
2257 5446 4.603535 ACAGCCAGCCACCAACCC 62.604 66.667 0.00 0.00 0.00 4.11
2258 5447 2.521708 AACAGCCAGCCACCAACC 60.522 61.111 0.00 0.00 0.00 3.77
2259 5448 1.109323 AAGAACAGCCAGCCACCAAC 61.109 55.000 0.00 0.00 0.00 3.77
2260 5449 1.108727 CAAGAACAGCCAGCCACCAA 61.109 55.000 0.00 0.00 0.00 3.67
2261 5450 1.529010 CAAGAACAGCCAGCCACCA 60.529 57.895 0.00 0.00 0.00 4.17
2262 5451 1.228245 TCAAGAACAGCCAGCCACC 60.228 57.895 0.00 0.00 0.00 4.61
2263 5452 1.239968 CCTCAAGAACAGCCAGCCAC 61.240 60.000 0.00 0.00 0.00 5.01
2264 5453 1.073722 CCTCAAGAACAGCCAGCCA 59.926 57.895 0.00 0.00 0.00 4.75
2265 5454 0.538287 AACCTCAAGAACAGCCAGCC 60.538 55.000 0.00 0.00 0.00 4.85
2266 5455 0.877743 GAACCTCAAGAACAGCCAGC 59.122 55.000 0.00 0.00 0.00 4.85
2267 5456 2.421619 GAGAACCTCAAGAACAGCCAG 58.578 52.381 0.00 0.00 0.00 4.85
2268 5457 1.270305 CGAGAACCTCAAGAACAGCCA 60.270 52.381 0.00 0.00 0.00 4.75
2269 5458 1.433534 CGAGAACCTCAAGAACAGCC 58.566 55.000 0.00 0.00 0.00 4.85
2270 5459 0.793250 GCGAGAACCTCAAGAACAGC 59.207 55.000 0.00 0.00 0.00 4.40
2271 5460 2.064762 CTGCGAGAACCTCAAGAACAG 58.935 52.381 0.00 0.00 0.00 3.16
2272 5461 1.412710 ACTGCGAGAACCTCAAGAACA 59.587 47.619 0.00 0.00 0.00 3.18
2273 5462 1.795286 CACTGCGAGAACCTCAAGAAC 59.205 52.381 0.00 0.00 0.00 3.01
2274 5463 1.270305 CCACTGCGAGAACCTCAAGAA 60.270 52.381 0.00 0.00 0.00 2.52
2275 5464 0.318441 CCACTGCGAGAACCTCAAGA 59.682 55.000 0.00 0.00 0.00 3.02
2276 5465 0.318441 TCCACTGCGAGAACCTCAAG 59.682 55.000 0.00 0.00 0.00 3.02
2277 5466 0.976641 ATCCACTGCGAGAACCTCAA 59.023 50.000 0.00 0.00 0.00 3.02
2278 5467 0.247460 CATCCACTGCGAGAACCTCA 59.753 55.000 0.00 0.00 0.00 3.86
2279 5468 0.247736 ACATCCACTGCGAGAACCTC 59.752 55.000 0.00 0.00 0.00 3.85
2280 5469 0.687354 AACATCCACTGCGAGAACCT 59.313 50.000 0.00 0.00 0.00 3.50
2281 5470 3.233355 AACATCCACTGCGAGAACC 57.767 52.632 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.