Multiple sequence alignment - TraesCS3D01G170100

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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 TraesCS3D01G170100 chr3D 100.000 3134 0 0 1 3134 148253629 148250496 0.000000e+00 5788.0
1 TraesCS3D01G170100 chr3D 86.948 521 57 11 14 526 551002142 551001625 2.710000e-160 575.0
2 TraesCS3D01G170100 chr3D 90.511 274 24 2 2375 2648 4579079 4579350 8.260000e-96 361.0
3 TraesCS3D01G170100 chr3B 93.137 1763 66 18 649 2389 213723102 213724831 0.000000e+00 2534.0
4 TraesCS3D01G170100 chr3B 90.438 502 29 6 2645 3134 213724828 213725322 0.000000e+00 643.0
5 TraesCS3D01G170100 chr3B 94.000 50 2 1 513 561 213713803 213713852 1.210000e-09 75.0
6 TraesCS3D01G170100 chr3A 92.865 1724 66 15 521 2228 164928456 164930138 0.000000e+00 2449.0
7 TraesCS3D01G170100 chr3A 85.669 949 64 36 2219 3134 164931623 164932532 0.000000e+00 933.0
8 TraesCS3D01G170100 chr6D 87.549 514 58 6 14 523 146943248 146943759 9.680000e-165 590.0
9 TraesCS3D01G170100 chr6D 93.233 266 15 3 2387 2651 472139316 472139053 3.790000e-104 388.0
10 TraesCS3D01G170100 chr2D 87.160 514 59 5 14 523 642304039 642304549 7.540000e-161 577.0
11 TraesCS3D01G170100 chr6B 86.847 517 59 7 14 526 565219055 565218544 1.260000e-158 569.0
12 TraesCS3D01G170100 chr2B 86.381 514 61 7 14 523 61598689 61599197 1.270000e-153 553.0
13 TraesCS3D01G170100 chr7B 86.019 515 66 6 14 523 400643570 400644083 5.910000e-152 547.0
14 TraesCS3D01G170100 chr4D 86.047 516 64 8 14 525 51959655 51960166 5.910000e-152 547.0
15 TraesCS3D01G170100 chr2A 86.042 523 58 12 15 531 471222504 471221991 5.910000e-152 547.0
16 TraesCS3D01G170100 chr2A 92.720 261 19 0 2388 2648 487746144 487745884 8.200000e-101 377.0
17 TraesCS3D01G170100 chr2A 90.335 269 26 0 2388 2656 625011940 625011672 1.380000e-93 353.0
18 TraesCS3D01G170100 chr2A 84.211 76 10 2 3026 3099 194125740 194125665 4.340000e-09 73.1
19 TraesCS3D01G170100 chr6A 85.714 518 71 3 14 528 125881218 125881735 7.640000e-151 544.0
20 TraesCS3D01G170100 chr7A 93.487 261 17 0 2388 2648 218936186 218936446 3.790000e-104 388.0
21 TraesCS3D01G170100 chr5D 93.487 261 17 0 2388 2648 546697975 546697715 3.790000e-104 388.0
22 TraesCS3D01G170100 chr4B 92.424 264 20 0 2385 2648 121191551 121191814 8.200000e-101 377.0
23 TraesCS3D01G170100 chr7D 92.424 264 19 1 2385 2648 393625086 393624824 2.950000e-100 375.0
24 TraesCS3D01G170100 chr1A 92.337 261 20 0 2388 2648 592535638 592535898 3.820000e-99 372.0


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 TraesCS3D01G170100 chr3D 148250496 148253629 3133 True 5788.0 5788 100.0000 1 3134 1 chr3D.!!$R1 3133
1 TraesCS3D01G170100 chr3D 551001625 551002142 517 True 575.0 575 86.9480 14 526 1 chr3D.!!$R2 512
2 TraesCS3D01G170100 chr3B 213723102 213725322 2220 False 1588.5 2534 91.7875 649 3134 2 chr3B.!!$F2 2485
3 TraesCS3D01G170100 chr3A 164928456 164932532 4076 False 1691.0 2449 89.2670 521 3134 2 chr3A.!!$F1 2613
4 TraesCS3D01G170100 chr6D 146943248 146943759 511 False 590.0 590 87.5490 14 523 1 chr6D.!!$F1 509
5 TraesCS3D01G170100 chr2D 642304039 642304549 510 False 577.0 577 87.1600 14 523 1 chr2D.!!$F1 509
6 TraesCS3D01G170100 chr6B 565218544 565219055 511 True 569.0 569 86.8470 14 526 1 chr6B.!!$R1 512
7 TraesCS3D01G170100 chr2B 61598689 61599197 508 False 553.0 553 86.3810 14 523 1 chr2B.!!$F1 509
8 TraesCS3D01G170100 chr7B 400643570 400644083 513 False 547.0 547 86.0190 14 523 1 chr7B.!!$F1 509
9 TraesCS3D01G170100 chr4D 51959655 51960166 511 False 547.0 547 86.0470 14 525 1 chr4D.!!$F1 511
10 TraesCS3D01G170100 chr2A 471221991 471222504 513 True 547.0 547 86.0420 15 531 1 chr2A.!!$R2 516
11 TraesCS3D01G170100 chr6A 125881218 125881735 517 False 544.0 544 85.7140 14 528 1 chr6A.!!$F1 514

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
495 513 0.109919 GCGGACAAAAACATCGTCCC 60.110 55.0 0.00 0.0 45.34 4.46 F
642 661 0.248661 CGATCGATCTCCGTGCTGTT 60.249 55.0 22.43 0.0 39.75 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2172 0.320508 GAAAACGAGCCCGGAAGAGT 60.321 55.0 0.73 0.0 40.78 3.24 R
2515 4108 0.800631 TCGTTAGATGCGTCGTGACT 59.199 50.0 0.00 0.0 0.00 3.41 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
211 219 0.321830 CGAACTCCCGCCCCTTTTTA 60.322 55.000 0.00 0.00 0.00 1.52
299 310 2.676744 CATTGTATGCCGACGCTGA 58.323 52.632 0.00 0.00 35.36 4.26
361 374 2.283476 GCATAATCTATGGCCGCAGGG 61.283 57.143 0.00 0.00 41.99 4.45
380 394 3.318557 AGGGGTTTTTCGAAATTTGCGTA 59.681 39.130 12.12 0.00 0.00 4.42
381 395 3.671459 GGGGTTTTTCGAAATTTGCGTAG 59.329 43.478 12.12 0.00 0.00 3.51
448 465 1.259609 TTAAAGAGGAGGACGCCGAA 58.740 50.000 0.00 0.00 0.00 4.30
486 504 6.237861 CCAAACGAATAAAAAGCGGACAAAAA 60.238 34.615 0.00 0.00 0.00 1.94
495 513 0.109919 GCGGACAAAAACATCGTCCC 60.110 55.000 0.00 0.00 45.34 4.46
499 517 2.882137 GGACAAAAACATCGTCCCTTCA 59.118 45.455 0.00 0.00 42.87 3.02
507 525 1.541310 ATCGTCCCTTCAAGTCGGCA 61.541 55.000 0.00 0.00 0.00 5.69
563 581 0.374758 AGCGCACAATGTTGCTATCG 59.625 50.000 11.47 0.00 40.62 2.92
580 598 2.084610 TCGAGAAATGACCAGCACAG 57.915 50.000 0.00 0.00 0.00 3.66
583 601 3.195610 TCGAGAAATGACCAGCACAGTAT 59.804 43.478 0.00 0.00 0.00 2.12
585 603 5.069119 TCGAGAAATGACCAGCACAGTATAT 59.931 40.000 0.00 0.00 0.00 0.86
586 604 6.264518 TCGAGAAATGACCAGCACAGTATATA 59.735 38.462 0.00 0.00 0.00 0.86
587 605 6.584184 CGAGAAATGACCAGCACAGTATATAG 59.416 42.308 0.00 0.00 0.00 1.31
642 661 0.248661 CGATCGATCTCCGTGCTGTT 60.249 55.000 22.43 0.00 39.75 3.16
646 665 1.421485 GATCTCCGTGCTGTTTGCG 59.579 57.895 0.00 0.00 46.63 4.85
734 768 3.241530 TGCACCTCCGCAGTTCCT 61.242 61.111 0.00 0.00 36.86 3.36
735 769 2.435059 GCACCTCCGCAGTTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
736 770 2.266055 CACCTCCGCAGTTCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
737 771 3.382832 ACCTCCGCAGTTCCTCCG 61.383 66.667 0.00 0.00 0.00 4.63
738 772 4.821589 CCTCCGCAGTTCCTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
797 831 3.113322 CGCAAAAGATAGCTAGCGTACA 58.887 45.455 9.55 0.00 40.25 2.90
798 832 3.061139 CGCAAAAGATAGCTAGCGTACAC 60.061 47.826 9.55 0.89 40.25 2.90
832 891 1.190643 CTTCGCTCTCTTCCTCCCTT 58.809 55.000 0.00 0.00 0.00 3.95
834 893 0.684805 TCGCTCTCTTCCTCCCTTCC 60.685 60.000 0.00 0.00 0.00 3.46
835 894 1.681486 CGCTCTCTTCCTCCCTTCCC 61.681 65.000 0.00 0.00 0.00 3.97
836 895 1.341913 GCTCTCTTCCTCCCTTCCCC 61.342 65.000 0.00 0.00 0.00 4.81
837 896 0.692756 CTCTCTTCCTCCCTTCCCCC 60.693 65.000 0.00 0.00 0.00 5.40
938 998 3.159472 CAACCAAACCCCTAAACCCTAC 58.841 50.000 0.00 0.00 0.00 3.18
967 1027 0.472734 CCCATTCCCACCCAACCAAA 60.473 55.000 0.00 0.00 0.00 3.28
968 1028 0.975887 CCATTCCCACCCAACCAAAG 59.024 55.000 0.00 0.00 0.00 2.77
969 1029 0.321346 CATTCCCACCCAACCAAAGC 59.679 55.000 0.00 0.00 0.00 3.51
970 1030 1.184970 ATTCCCACCCAACCAAAGCG 61.185 55.000 0.00 0.00 0.00 4.68
971 1031 3.989787 CCCACCCAACCAAAGCGC 61.990 66.667 0.00 0.00 0.00 5.92
972 1032 3.989787 CCACCCAACCAAAGCGCC 61.990 66.667 2.29 0.00 0.00 6.53
973 1033 3.989787 CACCCAACCAAAGCGCCC 61.990 66.667 2.29 0.00 0.00 6.13
974 1034 4.531426 ACCCAACCAAAGCGCCCA 62.531 61.111 2.29 0.00 0.00 5.36
975 1035 3.683937 CCCAACCAAAGCGCCCAG 61.684 66.667 2.29 0.00 0.00 4.45
1512 1578 1.515020 CACCCTCCTCTGCTTCTCG 59.485 63.158 0.00 0.00 0.00 4.04
1863 1929 4.373116 GACCCGAGCACCGCAGAA 62.373 66.667 0.00 0.00 36.84 3.02
1999 2065 3.130693 AGACGTGGTATACTTCTTCCTGC 59.869 47.826 0.00 0.00 34.53 4.85
2103 2169 1.142748 CAGCTACTCTTCCGGGCTG 59.857 63.158 11.40 11.40 43.03 4.85
2104 2170 2.202946 GCTACTCTTCCGGGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
2105 2171 2.726351 GCTACTCTTCCGGGCTGCT 61.726 63.158 0.00 0.00 0.00 4.24
2106 2172 1.392710 GCTACTCTTCCGGGCTGCTA 61.393 60.000 0.00 0.00 0.00 3.49
2107 2173 0.386113 CTACTCTTCCGGGCTGCTAC 59.614 60.000 0.00 0.00 0.00 3.58
2108 2174 0.033405 TACTCTTCCGGGCTGCTACT 60.033 55.000 0.00 0.00 0.00 2.57
2109 2175 1.324005 ACTCTTCCGGGCTGCTACTC 61.324 60.000 0.00 0.00 0.00 2.59
2110 2176 1.000486 TCTTCCGGGCTGCTACTCT 60.000 57.895 0.00 0.00 0.00 3.24
2111 2177 0.614979 TCTTCCGGGCTGCTACTCTT 60.615 55.000 0.00 0.00 0.00 2.85
2112 2178 0.179097 CTTCCGGGCTGCTACTCTTC 60.179 60.000 0.00 0.00 0.00 2.87
2113 2179 1.614241 TTCCGGGCTGCTACTCTTCC 61.614 60.000 0.00 0.00 0.00 3.46
2114 2180 2.105128 CGGGCTGCTACTCTTCCG 59.895 66.667 0.00 0.00 0.00 4.30
2115 2181 2.501610 GGGCTGCTACTCTTCCGG 59.498 66.667 0.00 0.00 0.00 5.14
2116 2182 2.501610 GGCTGCTACTCTTCCGGG 59.498 66.667 0.00 0.00 0.00 5.73
2117 2183 2.202946 GCTGCTACTCTTCCGGGC 60.203 66.667 0.00 0.00 0.00 6.13
2118 2184 2.726351 GCTGCTACTCTTCCGGGCT 61.726 63.158 0.00 0.00 0.00 5.19
2288 3851 1.375396 ATGTGGCGTGTGCGTATGT 60.375 52.632 0.00 0.00 44.10 2.29
2355 3918 2.234908 AGTGTGGATTGGTCTACTGCTC 59.765 50.000 0.00 0.00 36.83 4.26
2364 3927 3.431415 TGGTCTACTGCTCAGAGCTTAA 58.569 45.455 23.15 7.39 42.97 1.85
2365 3928 4.026744 TGGTCTACTGCTCAGAGCTTAAT 58.973 43.478 23.15 8.48 42.97 1.40
2366 3929 4.467795 TGGTCTACTGCTCAGAGCTTAATT 59.532 41.667 23.15 5.64 42.97 1.40
2367 3930 5.656859 TGGTCTACTGCTCAGAGCTTAATTA 59.343 40.000 23.15 0.68 42.97 1.40
2368 3931 5.980715 GGTCTACTGCTCAGAGCTTAATTAC 59.019 44.000 23.15 13.26 42.97 1.89
2370 3933 4.826274 ACTGCTCAGAGCTTAATTACCA 57.174 40.909 23.15 0.00 42.97 3.25
2371 3934 5.365021 ACTGCTCAGAGCTTAATTACCAT 57.635 39.130 23.15 0.00 42.97 3.55
2372 3935 6.485830 ACTGCTCAGAGCTTAATTACCATA 57.514 37.500 23.15 0.00 42.97 2.74
2373 3936 7.072263 ACTGCTCAGAGCTTAATTACCATAT 57.928 36.000 23.15 0.00 42.97 1.78
2374 3937 8.195165 ACTGCTCAGAGCTTAATTACCATATA 57.805 34.615 23.15 0.00 42.97 0.86
2375 3938 8.091449 ACTGCTCAGAGCTTAATTACCATATAC 58.909 37.037 23.15 0.00 42.97 1.47
2376 3939 7.386851 TGCTCAGAGCTTAATTACCATATACC 58.613 38.462 23.15 0.00 42.97 2.73
2377 3940 6.531948 GCTCAGAGCTTAATTACCATATACCG 59.468 42.308 15.78 0.00 38.45 4.02
2378 3941 7.534723 TCAGAGCTTAATTACCATATACCGT 57.465 36.000 0.00 0.00 0.00 4.83
2379 3942 7.959175 TCAGAGCTTAATTACCATATACCGTT 58.041 34.615 0.00 0.00 0.00 4.44
2380 3943 7.870954 TCAGAGCTTAATTACCATATACCGTTG 59.129 37.037 0.00 0.00 0.00 4.10
2381 3944 7.870954 CAGAGCTTAATTACCATATACCGTTGA 59.129 37.037 0.00 0.00 0.00 3.18
2382 3945 8.088981 AGAGCTTAATTACCATATACCGTTGAG 58.911 37.037 0.00 0.00 0.00 3.02
2383 3946 6.649557 AGCTTAATTACCATATACCGTTGAGC 59.350 38.462 0.00 0.00 0.00 4.26
2384 3947 6.649557 GCTTAATTACCATATACCGTTGAGCT 59.350 38.462 0.00 0.00 0.00 4.09
2385 3948 7.816031 GCTTAATTACCATATACCGTTGAGCTA 59.184 37.037 0.00 0.00 0.00 3.32
2386 3949 9.355215 CTTAATTACCATATACCGTTGAGCTAG 57.645 37.037 0.00 0.00 0.00 3.42
2396 3959 2.366533 CGTTGAGCTAGTACTCCCTCA 58.633 52.381 17.00 17.00 35.72 3.86
2408 3971 4.531339 AGTACTCCCTCAGGTCCTTTTTAC 59.469 45.833 0.00 0.00 0.00 2.01
2410 3973 3.583526 ACTCCCTCAGGTCCTTTTTACTC 59.416 47.826 0.00 0.00 0.00 2.59
2411 3974 3.841255 CTCCCTCAGGTCCTTTTTACTCT 59.159 47.826 0.00 0.00 0.00 3.24
2421 3984 7.987458 CAGGTCCTTTTTACTCTGCATATAAGA 59.013 37.037 0.00 0.00 0.00 2.10
2422 3985 8.548877 AGGTCCTTTTTACTCTGCATATAAGAA 58.451 33.333 0.00 0.00 0.00 2.52
2432 3995 8.659925 ACTCTGCATATAAGAATTGTCTGAAG 57.340 34.615 0.00 0.00 33.05 3.02
2437 4000 9.230122 TGCATATAAGAATTGTCTGAAGTCAAA 57.770 29.630 0.00 0.00 33.05 2.69
2497 4090 9.811995 ATATCAACATCTACAACGCTAAAGTTA 57.188 29.630 0.00 0.00 32.35 2.24
2498 4091 8.718102 ATCAACATCTACAACGCTAAAGTTAT 57.282 30.769 0.00 0.00 32.35 1.89
2500 4093 9.079833 TCAACATCTACAACGCTAAAGTTATAC 57.920 33.333 0.00 0.00 32.35 1.47
2502 4095 8.991243 ACATCTACAACGCTAAAGTTATACAA 57.009 30.769 0.00 0.00 32.35 2.41
2524 4117 8.874745 ACAATATGAAAATTTAAGTCACGACG 57.125 30.769 0.00 0.00 36.20 5.12
2525 4118 7.480542 ACAATATGAAAATTTAAGTCACGACGC 59.519 33.333 0.00 0.00 36.20 5.19
2526 4119 4.797693 TGAAAATTTAAGTCACGACGCA 57.202 36.364 0.00 0.00 36.20 5.24
2527 4120 5.351233 TGAAAATTTAAGTCACGACGCAT 57.649 34.783 0.00 0.00 36.20 4.73
2528 4121 5.379003 TGAAAATTTAAGTCACGACGCATC 58.621 37.500 0.00 0.00 36.20 3.91
2529 4122 5.178623 TGAAAATTTAAGTCACGACGCATCT 59.821 36.000 0.00 0.00 36.20 2.90
2530 4123 6.366604 TGAAAATTTAAGTCACGACGCATCTA 59.633 34.615 0.00 0.00 36.20 1.98
2531 4124 6.715344 AAATTTAAGTCACGACGCATCTAA 57.285 33.333 0.00 0.00 36.20 2.10
2532 4125 5.697848 ATTTAAGTCACGACGCATCTAAC 57.302 39.130 0.00 0.00 36.20 2.34
2533 4126 1.614385 AAGTCACGACGCATCTAACG 58.386 50.000 0.00 0.00 36.20 3.18
2534 4127 0.800631 AGTCACGACGCATCTAACGA 59.199 50.000 0.00 0.00 36.20 3.85
2535 4128 1.400846 AGTCACGACGCATCTAACGAT 59.599 47.619 0.00 0.00 36.20 3.73
2536 4129 2.610833 AGTCACGACGCATCTAACGATA 59.389 45.455 0.00 0.00 36.20 2.92
2537 4130 3.064408 AGTCACGACGCATCTAACGATAA 59.936 43.478 0.00 0.00 36.20 1.75
2538 4131 3.973135 GTCACGACGCATCTAACGATAAT 59.027 43.478 0.00 0.00 0.00 1.28
2539 4132 3.972502 TCACGACGCATCTAACGATAATG 59.027 43.478 0.00 0.00 0.00 1.90
2540 4133 3.972502 CACGACGCATCTAACGATAATGA 59.027 43.478 0.00 0.00 0.00 2.57
2541 4134 4.617223 CACGACGCATCTAACGATAATGAT 59.383 41.667 0.00 0.00 0.00 2.45
2542 4135 5.117135 CACGACGCATCTAACGATAATGATT 59.883 40.000 0.00 0.00 0.00 2.57
2543 4136 5.690409 ACGACGCATCTAACGATAATGATTT 59.310 36.000 0.00 0.00 0.00 2.17
2544 4137 6.129168 ACGACGCATCTAACGATAATGATTTC 60.129 38.462 0.00 0.00 0.00 2.17
2545 4138 6.129194 CGACGCATCTAACGATAATGATTTCA 60.129 38.462 0.00 0.00 0.00 2.69
2546 4139 6.877855 ACGCATCTAACGATAATGATTTCAC 58.122 36.000 0.00 0.00 0.00 3.18
2547 4140 6.478673 ACGCATCTAACGATAATGATTTCACA 59.521 34.615 0.00 0.00 0.00 3.58
2548 4141 7.171508 ACGCATCTAACGATAATGATTTCACAT 59.828 33.333 0.00 0.00 0.00 3.21
2549 4142 8.011673 CGCATCTAACGATAATGATTTCACATT 58.988 33.333 0.00 0.00 42.17 2.71
2550 4143 9.110617 GCATCTAACGATAATGATTTCACATTG 57.889 33.333 0.00 0.00 40.15 2.82
2553 4146 9.377312 TCTAACGATAATGATTTCACATTGTGA 57.623 29.630 15.41 15.41 41.09 3.58
2595 4188 9.769093 CCTATAAAATTGGTCAAACTTTACGAG 57.231 33.333 0.00 5.38 0.00 4.18
2609 4202 6.541111 ACTTTACGAGGTTTGATTTCAGAC 57.459 37.500 0.00 0.00 0.00 3.51
2612 4205 6.928979 TTACGAGGTTTGATTTCAGACAAA 57.071 33.333 3.96 0.00 33.14 2.83
2616 4209 6.263168 ACGAGGTTTGATTTCAGACAAATCTT 59.737 34.615 0.00 0.00 44.16 2.40
2623 4216 9.720667 TTTGATTTCAGACAAATCTTATATGCG 57.279 29.630 8.21 0.00 37.50 4.73
2624 4217 8.661352 TGATTTCAGACAAATCTTATATGCGA 57.339 30.769 8.21 0.00 37.50 5.10
2626 4219 9.591404 GATTTCAGACAAATCTTATATGCGAAG 57.409 33.333 0.00 0.00 34.65 3.79
2758 4367 4.096382 AGGCTTAATTGACGTATTTGCTGG 59.904 41.667 0.00 0.00 0.00 4.85
2768 4377 3.435671 ACGTATTTGCTGGCACTTTAGTC 59.564 43.478 0.00 0.00 0.00 2.59
2773 4382 1.082690 GCTGGCACTTTAGTCTGAGC 58.917 55.000 0.00 0.00 0.00 4.26
2869 4478 5.362556 ACTTGTTCTAATGTGTGATGTGC 57.637 39.130 0.00 0.00 0.00 4.57
2870 4479 4.216257 ACTTGTTCTAATGTGTGATGTGCC 59.784 41.667 0.00 0.00 0.00 5.01
3048 4660 5.401531 TTTAAATAGGGCGCTATCTCGAT 57.598 39.130 22.17 5.03 0.00 3.59
3088 4710 2.415893 GCATCATGCTAAGCCGTTTTGT 60.416 45.455 1.02 0.00 40.96 2.83
3119 4741 5.251764 AGCATGCTATAGCTCCAATTTAGG 58.748 41.667 21.21 5.58 42.66 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.972660 GATCTCCACCCCCGTTGAGG 61.973 65.000 0.00 0.00 33.53 3.86
9 10 1.264749 TGATCTCCACCCCCGTTGAG 61.265 60.000 0.00 0.00 33.91 3.02
10 11 0.620410 ATGATCTCCACCCCCGTTGA 60.620 55.000 0.00 0.00 0.00 3.18
11 12 0.464373 CATGATCTCCACCCCCGTTG 60.464 60.000 0.00 0.00 0.00 4.10
12 13 0.620410 TCATGATCTCCACCCCCGTT 60.620 55.000 0.00 0.00 0.00 4.44
147 149 2.332514 CAACACACTTGCCAGCGG 59.667 61.111 0.00 0.00 0.00 5.52
148 150 2.332514 CCAACACACTTGCCAGCG 59.667 61.111 0.00 0.00 0.00 5.18
211 219 2.967397 GCACACATGCCAGCACAT 59.033 55.556 0.00 0.00 46.97 3.21
293 304 2.359107 CCAGCACCATGTCAGCGT 60.359 61.111 0.00 0.00 0.00 5.07
299 310 0.251474 AGTTCATGCCAGCACCATGT 60.251 50.000 0.00 0.00 40.63 3.21
345 357 1.645402 AACCCCTGCGGCCATAGATT 61.645 55.000 2.24 0.00 33.26 2.40
358 371 2.101750 ACGCAAATTTCGAAAAACCCCT 59.898 40.909 15.66 0.00 0.00 4.79
361 374 4.538917 TCCTACGCAAATTTCGAAAAACC 58.461 39.130 15.66 3.19 0.00 3.27
362 375 5.456173 TGTTCCTACGCAAATTTCGAAAAAC 59.544 36.000 15.66 10.68 0.00 2.43
380 394 4.708177 CTCGATACCCATTTCATGTTCCT 58.292 43.478 0.00 0.00 0.00 3.36
381 395 3.251004 GCTCGATACCCATTTCATGTTCC 59.749 47.826 0.00 0.00 0.00 3.62
453 470 2.835580 TTATTCGTTTGGGTCGGTCA 57.164 45.000 0.00 0.00 0.00 4.02
486 504 0.246635 CCGACTTGAAGGGACGATGT 59.753 55.000 9.40 0.00 0.00 3.06
495 513 2.317609 CCCACGTGCCGACTTGAAG 61.318 63.158 10.91 0.00 0.00 3.02
499 517 2.803817 AACTCCCACGTGCCGACTT 61.804 57.895 10.91 0.38 0.00 3.01
507 525 0.608640 CCTAAGAGCAACTCCCACGT 59.391 55.000 0.00 0.00 0.00 4.49
511 529 2.489722 CAAAAGCCTAAGAGCAACTCCC 59.510 50.000 0.00 0.00 34.23 4.30
563 581 6.870965 CCTATATACTGTGCTGGTCATTTCTC 59.129 42.308 0.00 0.00 0.00 2.87
580 598 4.043750 TGCGCACGTTTGTACCTATATAC 58.956 43.478 5.66 0.00 0.00 1.47
583 601 2.261345 GTGCGCACGTTTGTACCTATA 58.739 47.619 26.77 0.00 0.00 1.31
585 603 2.519826 GTGCGCACGTTTGTACCTA 58.480 52.632 26.77 0.00 0.00 3.08
586 604 3.326109 GTGCGCACGTTTGTACCT 58.674 55.556 26.77 0.00 0.00 3.08
728 762 2.362632 AGCTACGGCGGAGGAACT 60.363 61.111 22.54 6.59 43.58 3.01
729 763 2.104530 GAGCTACGGCGGAGGAAC 59.895 66.667 22.54 3.93 44.37 3.62
730 764 2.044252 AGAGCTACGGCGGAGGAA 60.044 61.111 22.54 0.00 44.37 3.36
731 765 2.829003 CAGAGCTACGGCGGAGGA 60.829 66.667 22.54 0.00 44.37 3.71
732 766 4.577246 GCAGAGCTACGGCGGAGG 62.577 72.222 22.54 4.86 44.37 4.30
733 767 3.356639 TTGCAGAGCTACGGCGGAG 62.357 63.158 16.49 16.49 42.31 4.63
734 768 3.378602 TTGCAGAGCTACGGCGGA 61.379 61.111 13.24 0.00 42.31 5.54
735 769 3.188786 GTTGCAGAGCTACGGCGG 61.189 66.667 13.24 0.00 42.31 6.13
736 770 3.188786 GGTTGCAGAGCTACGGCG 61.189 66.667 4.80 4.80 42.31 6.46
737 771 2.820037 GGGTTGCAGAGCTACGGC 60.820 66.667 0.00 0.00 35.33 5.68
738 772 2.125106 GGGGTTGCAGAGCTACGG 60.125 66.667 0.00 0.00 35.33 4.02
794 828 1.379977 CAGGCGAGGAGGAGGTGTA 60.380 63.158 0.00 0.00 0.00 2.90
795 829 2.681778 CAGGCGAGGAGGAGGTGT 60.682 66.667 0.00 0.00 0.00 4.16
797 831 3.914551 AAGCAGGCGAGGAGGAGGT 62.915 63.158 0.00 0.00 0.00 3.85
798 832 3.080121 AAGCAGGCGAGGAGGAGG 61.080 66.667 0.00 0.00 0.00 4.30
834 893 1.001248 TTGAGACGGTAGGAGGGGG 59.999 63.158 0.00 0.00 0.00 5.40
835 894 0.324460 AGTTGAGACGGTAGGAGGGG 60.324 60.000 0.00 0.00 0.00 4.79
836 895 1.104630 GAGTTGAGACGGTAGGAGGG 58.895 60.000 0.00 0.00 0.00 4.30
837 896 0.733729 CGAGTTGAGACGGTAGGAGG 59.266 60.000 0.00 0.00 0.00 4.30
838 897 0.099082 GCGAGTTGAGACGGTAGGAG 59.901 60.000 0.00 0.00 0.00 3.69
839 898 1.310933 GGCGAGTTGAGACGGTAGGA 61.311 60.000 0.00 0.00 0.00 2.94
840 899 1.139095 GGCGAGTTGAGACGGTAGG 59.861 63.158 0.00 0.00 0.00 3.18
841 900 0.456312 GTGGCGAGTTGAGACGGTAG 60.456 60.000 0.00 0.00 0.00 3.18
842 901 1.582968 GTGGCGAGTTGAGACGGTA 59.417 57.895 0.00 0.00 0.00 4.02
843 902 2.338984 GTGGCGAGTTGAGACGGT 59.661 61.111 0.00 0.00 0.00 4.83
844 903 2.432628 GGTGGCGAGTTGAGACGG 60.433 66.667 0.00 0.00 0.00 4.79
847 906 3.691342 CGGGGTGGCGAGTTGAGA 61.691 66.667 0.00 0.00 0.00 3.27
899 958 9.533253 GTTTGGTTGTTGAAGTACTAGTAGTAA 57.467 33.333 11.64 0.09 31.62 2.24
900 959 8.143835 GGTTTGGTTGTTGAAGTACTAGTAGTA 58.856 37.037 10.68 5.90 0.00 1.82
901 960 6.988580 GGTTTGGTTGTTGAAGTACTAGTAGT 59.011 38.462 8.14 8.14 0.00 2.73
975 1035 3.223589 GAGGGAGAGCGGAGGAGC 61.224 72.222 0.00 0.00 37.41 4.70
976 1036 2.520741 GGAGGGAGAGCGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1448 1514 2.039746 TGGAACTCGACCACCATGAATT 59.960 45.455 0.00 0.00 32.03 2.17
1848 1914 3.197790 CATTCTGCGGTGCTCGGG 61.198 66.667 0.00 0.00 39.69 5.14
1863 1929 1.403780 GCCTCGTACTCAAACGTCCAT 60.404 52.381 0.00 0.00 43.31 3.41
2020 2086 2.202932 CTCCCTAGCGCGCATGTT 60.203 61.111 35.10 15.58 0.00 2.71
2031 2097 1.681327 GCACTCCACGACCTCCCTA 60.681 63.158 0.00 0.00 0.00 3.53
2103 2169 1.946475 AACGAGCCCGGAAGAGTAGC 61.946 60.000 0.73 0.00 40.78 3.58
2104 2170 0.531200 AAACGAGCCCGGAAGAGTAG 59.469 55.000 0.73 0.00 40.78 2.57
2105 2171 0.971386 AAAACGAGCCCGGAAGAGTA 59.029 50.000 0.73 0.00 40.78 2.59
2106 2172 0.320508 GAAAACGAGCCCGGAAGAGT 60.321 55.000 0.73 0.00 40.78 3.24
2107 2173 1.019805 GGAAAACGAGCCCGGAAGAG 61.020 60.000 0.73 0.00 40.78 2.85
2108 2174 1.004200 GGAAAACGAGCCCGGAAGA 60.004 57.895 0.73 0.00 40.78 2.87
2109 2175 2.038837 GGGAAAACGAGCCCGGAAG 61.039 63.158 0.73 0.00 40.78 3.46
2110 2176 2.032987 GGGAAAACGAGCCCGGAA 59.967 61.111 0.73 0.00 40.78 4.30
2114 2180 1.202348 CTCAAATGGGAAAACGAGCCC 59.798 52.381 0.00 0.00 44.93 5.19
2115 2181 1.402852 GCTCAAATGGGAAAACGAGCC 60.403 52.381 0.00 0.00 39.93 4.70
2116 2182 1.541588 AGCTCAAATGGGAAAACGAGC 59.458 47.619 0.00 0.00 44.83 5.03
2117 2183 3.366374 GGAAGCTCAAATGGGAAAACGAG 60.366 47.826 0.00 0.00 0.00 4.18
2118 2184 2.556622 GGAAGCTCAAATGGGAAAACGA 59.443 45.455 0.00 0.00 0.00 3.85
2355 3918 7.870954 TCAACGGTATATGGTAATTAAGCTCTG 59.129 37.037 0.00 0.00 0.00 3.35
2364 3927 6.912951 ACTAGCTCAACGGTATATGGTAAT 57.087 37.500 0.00 0.00 0.00 1.89
2365 3928 7.000472 AGTACTAGCTCAACGGTATATGGTAA 59.000 38.462 0.00 0.00 0.00 2.85
2366 3929 6.537355 AGTACTAGCTCAACGGTATATGGTA 58.463 40.000 0.00 0.00 0.00 3.25
2367 3930 5.383476 AGTACTAGCTCAACGGTATATGGT 58.617 41.667 0.00 0.00 0.00 3.55
2368 3931 5.106237 GGAGTACTAGCTCAACGGTATATGG 60.106 48.000 0.00 0.00 37.24 2.74
2370 3933 5.008980 GGGAGTACTAGCTCAACGGTATAT 58.991 45.833 0.00 0.00 37.24 0.86
2371 3934 4.103785 AGGGAGTACTAGCTCAACGGTATA 59.896 45.833 0.00 0.00 37.24 1.47
2372 3935 3.117587 AGGGAGTACTAGCTCAACGGTAT 60.118 47.826 0.00 0.00 37.24 2.73
2373 3936 2.240667 AGGGAGTACTAGCTCAACGGTA 59.759 50.000 0.00 0.00 37.24 4.02
2374 3937 1.005687 AGGGAGTACTAGCTCAACGGT 59.994 52.381 0.00 0.00 37.24 4.83
2375 3938 1.677052 GAGGGAGTACTAGCTCAACGG 59.323 57.143 0.00 0.00 37.24 4.44
2376 3939 2.356382 CTGAGGGAGTACTAGCTCAACG 59.644 54.545 0.00 0.00 37.24 4.10
2377 3940 2.691011 CCTGAGGGAGTACTAGCTCAAC 59.309 54.545 0.00 0.00 37.24 3.18
2378 3941 2.312140 ACCTGAGGGAGTACTAGCTCAA 59.688 50.000 2.38 0.00 37.24 3.02
2379 3942 1.923850 ACCTGAGGGAGTACTAGCTCA 59.076 52.381 2.38 0.00 37.24 4.26
2380 3943 2.578786 GACCTGAGGGAGTACTAGCTC 58.421 57.143 2.38 0.00 36.25 4.09
2381 3944 1.215924 GGACCTGAGGGAGTACTAGCT 59.784 57.143 2.38 0.00 36.25 3.32
2382 3945 1.215924 AGGACCTGAGGGAGTACTAGC 59.784 57.143 2.38 0.00 36.25 3.42
2383 3946 3.673543 AAGGACCTGAGGGAGTACTAG 57.326 52.381 2.38 0.00 36.25 2.57
2384 3947 4.415224 AAAAGGACCTGAGGGAGTACTA 57.585 45.455 2.38 0.00 36.25 1.82
2385 3948 3.277416 AAAAGGACCTGAGGGAGTACT 57.723 47.619 2.38 0.00 36.25 2.73
2386 3949 4.531339 AGTAAAAAGGACCTGAGGGAGTAC 59.469 45.833 2.38 0.00 36.25 2.73
2396 3959 8.090788 TCTTATATGCAGAGTAAAAAGGACCT 57.909 34.615 0.00 0.00 0.00 3.85
2408 3971 8.659925 ACTTCAGACAATTCTTATATGCAGAG 57.340 34.615 0.00 0.00 0.00 3.35
2410 3973 8.429493 TGACTTCAGACAATTCTTATATGCAG 57.571 34.615 0.00 0.00 0.00 4.41
2411 3974 8.791327 TTGACTTCAGACAATTCTTATATGCA 57.209 30.769 0.00 0.00 0.00 3.96
2471 4034 8.718102 AACTTTAGCGTTGTAGATGTTGATAT 57.282 30.769 0.00 0.00 0.00 1.63
2473 4036 8.718102 ATAACTTTAGCGTTGTAGATGTTGAT 57.282 30.769 0.00 0.00 0.00 2.57
2498 4091 9.961266 CGTCGTGACTTAAATTTTCATATTGTA 57.039 29.630 0.00 0.00 0.00 2.41
2500 4093 7.480229 TGCGTCGTGACTTAAATTTTCATATTG 59.520 33.333 0.00 0.00 0.00 1.90
2502 4095 7.067532 TGCGTCGTGACTTAAATTTTCATAT 57.932 32.000 0.00 0.00 0.00 1.78
2506 4099 5.618561 AGATGCGTCGTGACTTAAATTTTC 58.381 37.500 0.00 0.00 0.00 2.29
2507 4100 5.607119 AGATGCGTCGTGACTTAAATTTT 57.393 34.783 0.00 0.00 0.00 1.82
2510 4103 4.264614 CGTTAGATGCGTCGTGACTTAAAT 59.735 41.667 0.00 0.00 0.00 1.40
2515 4108 0.800631 TCGTTAGATGCGTCGTGACT 59.199 50.000 0.00 0.00 0.00 3.41
2516 4109 1.823828 ATCGTTAGATGCGTCGTGAC 58.176 50.000 0.00 0.15 35.40 3.67
2517 4110 3.678915 TTATCGTTAGATGCGTCGTGA 57.321 42.857 0.00 0.00 37.70 4.35
2518 4111 3.972502 TCATTATCGTTAGATGCGTCGTG 59.027 43.478 0.00 0.00 37.70 4.35
2519 4112 4.219143 TCATTATCGTTAGATGCGTCGT 57.781 40.909 0.00 0.00 37.70 4.34
2520 4113 5.747262 AATCATTATCGTTAGATGCGTCG 57.253 39.130 0.00 0.00 37.70 5.12
2521 4114 7.004225 GTGAAATCATTATCGTTAGATGCGTC 58.996 38.462 0.00 0.00 37.70 5.19
2523 4116 6.876804 TGTGAAATCATTATCGTTAGATGCG 58.123 36.000 0.00 0.00 37.70 4.73
2524 4117 9.110617 CAATGTGAAATCATTATCGTTAGATGC 57.889 33.333 0.00 0.00 37.70 3.91
2527 4120 9.377312 TCACAATGTGAAATCATTATCGTTAGA 57.623 29.630 14.37 0.00 39.78 2.10
2570 4163 9.769093 CCTCGTAAAGTTTGACCAATTTTATAG 57.231 33.333 0.00 0.00 0.00 1.31
2591 4184 5.765182 AGATTTGTCTGAAATCAAACCTCGT 59.235 36.000 9.24 0.00 38.70 4.18
2592 4185 6.246420 AGATTTGTCTGAAATCAAACCTCG 57.754 37.500 9.24 0.00 38.70 4.63
2602 4195 8.492673 ACTTCGCATATAAGATTTGTCTGAAA 57.507 30.769 0.00 0.00 0.00 2.69
2612 4205 7.170998 CGGTCCTTTTTACTTCGCATATAAGAT 59.829 37.037 0.00 0.00 0.00 2.40
2616 4209 5.051816 CCGGTCCTTTTTACTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
2623 4216 2.303890 TCCCTCCGGTCCTTTTTACTTC 59.696 50.000 0.00 0.00 0.00 3.01
2624 4217 2.305052 CTCCCTCCGGTCCTTTTTACTT 59.695 50.000 0.00 0.00 0.00 2.24
2626 4219 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
2698 4305 8.801715 TCAGCAAAATAAATGAAGTTTCTCAC 57.198 30.769 0.00 0.00 0.00 3.51
2758 4367 4.457834 TTCCTAGCTCAGACTAAAGTGC 57.542 45.455 0.00 0.00 0.00 4.40
2768 4377 5.843673 TCACACTTCTATTCCTAGCTCAG 57.156 43.478 0.00 0.00 0.00 3.35
2869 4478 0.756294 TGGTACCACACAGTCACAGG 59.244 55.000 11.60 0.00 0.00 4.00
2870 4479 2.839486 ATGGTACCACACAGTCACAG 57.161 50.000 19.09 0.00 0.00 3.66
2948 4560 2.536803 CGGCAAATGAATTATGCAGCAC 59.463 45.455 0.00 0.00 41.80 4.40
3018 4630 9.181061 AGATAGCGCCCTATTTAAAAGTTAAAA 57.819 29.630 2.29 0.00 34.44 1.52
3019 4631 8.741603 AGATAGCGCCCTATTTAAAAGTTAAA 57.258 30.769 2.29 0.00 34.44 1.52
3020 4632 7.170320 CGAGATAGCGCCCTATTTAAAAGTTAA 59.830 37.037 2.29 0.00 34.44 2.01
3021 4633 6.643770 CGAGATAGCGCCCTATTTAAAAGTTA 59.356 38.462 2.29 0.00 34.44 2.24
3022 4634 5.465724 CGAGATAGCGCCCTATTTAAAAGTT 59.534 40.000 2.29 0.00 34.44 2.66
3023 4635 4.989168 CGAGATAGCGCCCTATTTAAAAGT 59.011 41.667 2.29 0.00 34.44 2.66
3024 4636 5.227908 TCGAGATAGCGCCCTATTTAAAAG 58.772 41.667 2.29 0.00 34.44 2.27
3088 4710 4.005650 GAGCTATAGCATGCTAAATGGCA 58.994 43.478 29.44 12.85 45.16 4.92


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

AutoCloner maintained by Alex Coulton.