Multiple sequence alignment - TraesCS4D01G265700

Loading Multiple Alignment...

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 TraesCS4D01G265700 chr4D 100.000 3444 0 0 2145 5588 435654061 435650618 0.000000e+00 6360.0
1 TraesCS4D01G265700 chr4D 100.000 1934 0 0 1 1934 435656205 435654272 0.000000e+00 3572.0
2 TraesCS4D01G265700 chr4B 95.538 3474 101 27 2145 5588 536922430 536918981 0.000000e+00 5507.0
3 TraesCS4D01G265700 chr4B 94.077 2752 101 21 2331 5060 537156392 537153681 0.000000e+00 4122.0
4 TraesCS4D01G265700 chr4B 92.877 1053 45 11 886 1928 536923719 536922687 0.000000e+00 1502.0
5 TraesCS4D01G265700 chr4B 92.027 903 46 15 903 1789 537157785 537156893 0.000000e+00 1245.0
6 TraesCS4D01G265700 chr4B 86.036 666 79 8 1 659 536924529 536923871 0.000000e+00 702.0
7 TraesCS4D01G265700 chr4B 86.014 572 62 12 66 626 536926470 536925906 1.040000e-166 597.0
8 TraesCS4D01G265700 chr4B 84.044 633 83 10 49 673 537158891 537158269 1.340000e-165 593.0
9 TraesCS4D01G265700 chr4B 91.919 99 8 0 2334 2432 537156489 537156391 7.550000e-29 139.0
10 TraesCS4D01G265700 chr4B 91.919 99 6 1 2179 2275 537156605 537156507 2.720000e-28 137.0
11 TraesCS4D01G265700 chr4B 79.605 152 24 4 518 663 570117306 570117156 9.900000e-18 102.0
12 TraesCS4D01G265700 chr4B 100.000 47 0 0 790 836 537157840 537157794 2.770000e-13 87.9
13 TraesCS4D01G265700 chr4B 88.235 68 5 3 725 790 537157935 537157869 1.670000e-10 78.7
14 TraesCS4D01G265700 chr4A 94.821 3051 90 28 2145 5161 37035700 37032684 0.000000e+00 4697.0
15 TraesCS4D01G265700 chr4A 94.377 1067 34 15 886 1934 37036877 37035819 0.000000e+00 1615.0
16 TraesCS4D01G265700 chr4A 96.032 504 17 1 5085 5588 37032682 37032182 0.000000e+00 817.0
17 TraesCS4D01G265700 chr4A 87.519 673 66 7 1 662 37037768 37037103 0.000000e+00 761.0
18 TraesCS4D01G265700 chr4A 85.870 184 6 9 668 836 37037052 37036874 1.600000e-40 178.0
19 TraesCS4D01G265700 chr4A 76.882 186 29 12 487 662 619957676 619957495 5.960000e-15 93.5
20 TraesCS4D01G265700 chr5D 83.511 843 124 14 3753 4587 428675806 428674971 0.000000e+00 773.0
21 TraesCS4D01G265700 chr5A 83.254 842 126 14 3754 4587 544513019 544512185 0.000000e+00 760.0
22 TraesCS4D01G265700 chr5A 80.259 694 116 19 3826 4509 544459127 544458445 2.320000e-138 503.0
23 TraesCS4D01G265700 chr7A 77.626 219 38 6 446 657 654067290 654067504 7.600000e-24 122.0
24 TraesCS4D01G265700 chr7B 76.419 229 44 5 436 657 119258593 119258818 1.270000e-21 115.0
25 TraesCS4D01G265700 chr2A 75.877 228 45 7 446 666 516417400 516417176 2.130000e-19 108.0
26 TraesCS4D01G265700 chr2A 87.654 81 10 0 5382 5462 157547455 157547375 1.660000e-15 95.3
27 TraesCS4D01G265700 chr5B 75.566 221 43 10 446 657 18522307 18522089 1.280000e-16 99.0
28 TraesCS4D01G265700 chr5B 75.566 221 43 9 446 657 18528127 18528345 1.280000e-16 99.0
29 TraesCS4D01G265700 chr2D 87.654 81 10 0 5382 5462 143757806 143757886 1.660000e-15 95.3
30 TraesCS4D01G265700 chr2B 87.654 81 10 0 5382 5462 201769353 201769433 1.660000e-15 95.3
31 TraesCS4D01G265700 chr3B 75.397 126 30 1 436 560 123607436 123607561 6.050000e-05 60.2


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 TraesCS4D01G265700 chr4D 435650618 435656205 5587 True 4966.000000 6360 100.000000 1 5588 2 chr4D.!!$R1 5587
1 TraesCS4D01G265700 chr4B 536918981 536926470 7489 True 2077.000000 5507 90.116250 1 5588 4 chr4B.!!$R2 5587
2 TraesCS4D01G265700 chr4B 537153681 537158891 5210 True 914.657143 4122 91.745857 49 5060 7 chr4B.!!$R3 5011
3 TraesCS4D01G265700 chr4A 37032182 37037768 5586 True 1613.600000 4697 91.723800 1 5588 5 chr4A.!!$R2 5587
4 TraesCS4D01G265700 chr5D 428674971 428675806 835 True 773.000000 773 83.511000 3753 4587 1 chr5D.!!$R1 834
5 TraesCS4D01G265700 chr5A 544512185 544513019 834 True 760.000000 760 83.254000 3754 4587 1 chr5A.!!$R2 833
6 TraesCS4D01G265700 chr5A 544458445 544459127 682 True 503.000000 503 80.259000 3826 4509 1 chr5A.!!$R1 683

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
611 2574 0.106708 TCTTTGGCTCGCTTCAGTGT 59.893 50.0 0.00 0.0 0.0 3.55 F
632 2595 1.237533 TGTAGTCGTCGCTTGTGGTA 58.762 50.0 0.00 0.0 0.0 3.25 F
989 3309 1.627297 AATTCTCCGCACTCTCCCCC 61.627 60.0 0.00 0.0 0.0 5.40 F
1399 3734 1.877637 TTGTCATGACCCACGACTTG 58.122 50.0 22.85 0.0 0.0 3.16 F
3183 5691 2.030457 GCTGAAATTCGTGGGTATGTCG 59.970 50.0 0.00 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 4505 0.035458 CAACGGCTCTGGTTCTTCCT 59.965 55.000 0.00 0.00 37.07 3.36 R
2222 4634 1.479323 TCACGTATAAAAGGGAGCGCT 59.521 47.619 11.27 11.27 0.00 5.92 R
2649 5156 2.482142 GCTCCTGACATAGAAAGGTCGG 60.482 54.545 0.00 0.00 41.46 4.79 R
3312 5820 2.540383 ACTACCTGACCAAGCTCATCA 58.460 47.619 0.00 0.00 0.00 3.07 R
5028 7594 1.146982 TGCCTGGAGTTTTTAGGGCTT 59.853 47.619 0.00 0.00 40.15 4.35 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
43 1985 3.766051 GACTTGAGGATTGGCAGGATTTT 59.234 43.478 0.00 0.00 0.00 1.82
46 1988 1.678101 GAGGATTGGCAGGATTTTCGG 59.322 52.381 0.00 0.00 0.00 4.30
47 1989 1.284785 AGGATTGGCAGGATTTTCGGA 59.715 47.619 0.00 0.00 0.00 4.55
59 2001 1.131303 TTTTCGGAAGGGCTCAGGGA 61.131 55.000 0.00 0.00 0.00 4.20
115 2057 3.655481 GCAACTGCTTGCGGTAGT 58.345 55.556 7.56 0.00 43.42 2.73
127 2077 1.749638 CGGTAGTGAGAGAGCGGGT 60.750 63.158 0.00 0.00 33.10 5.28
193 2143 4.381505 GGATCATAGGAAGATTCGAGAGGC 60.382 50.000 0.00 0.00 0.00 4.70
215 2169 4.020128 GCTAAGGGTGAAAAGGAGAGAGAA 60.020 45.833 0.00 0.00 0.00 2.87
261 2216 2.588034 GTAGCGGTGCGGGGATTC 60.588 66.667 0.00 0.00 0.00 2.52
297 2253 0.388907 CAGGCAGCCGACAAAAATGG 60.389 55.000 5.55 0.00 0.00 3.16
298 2254 0.827507 AGGCAGCCGACAAAAATGGT 60.828 50.000 5.55 0.00 0.00 3.55
317 2273 0.680618 TGTATCAACCGGTTGGACGT 59.319 50.000 39.46 26.47 40.78 4.34
322 2278 3.096633 AACCGGTTGGACGTGAGCA 62.097 57.895 21.56 0.00 39.21 4.26
440 2396 7.554835 TGTACTTGATATGTATTTTGGGTGTCC 59.445 37.037 0.00 0.00 0.00 4.02
476 2432 7.938715 TCCTTCTAATCTACGGTTATCTTCAC 58.061 38.462 0.00 0.00 0.00 3.18
480 2436 5.934402 AATCTACGGTTATCTTCACCAGT 57.066 39.130 0.00 0.00 33.36 4.00
496 2452 2.092646 ACCAGTGGTGTTTGCTGTTCTA 60.093 45.455 15.86 0.00 32.98 2.10
516 2473 0.464452 GTGCGCTGGTCCTATAAGGT 59.536 55.000 9.73 0.00 36.53 3.50
522 2479 3.391049 GCTGGTCCTATAAGGTTTAGCG 58.609 50.000 0.00 0.00 36.53 4.26
525 2482 2.401351 GTCCTATAAGGTTTAGCGCGG 58.599 52.381 8.83 0.00 36.53 6.46
531 2488 3.849953 GGTTTAGCGCGGCGACTG 61.850 66.667 28.54 0.00 0.00 3.51
563 2520 5.130350 ACTACTACAACAAGGTTTGCATGT 58.870 37.500 0.00 6.23 37.63 3.21
566 2523 3.715628 ACAACAAGGTTTGCATGTCTC 57.284 42.857 0.00 0.00 30.95 3.36
582 2543 2.528127 TCCGGTGAGAAAGGGGCA 60.528 61.111 0.00 0.00 0.00 5.36
591 2554 2.309755 TGAGAAAGGGGCAATGATGACT 59.690 45.455 0.00 0.00 33.84 3.41
611 2574 0.106708 TCTTTGGCTCGCTTCAGTGT 59.893 50.000 0.00 0.00 0.00 3.55
632 2595 1.237533 TGTAGTCGTCGCTTGTGGTA 58.762 50.000 0.00 0.00 0.00 3.25
640 2603 2.223735 CGTCGCTTGTGGTATATGGACT 60.224 50.000 0.00 0.00 0.00 3.85
653 2616 8.567948 GTGGTATATGGACTTGGATGTAATTTG 58.432 37.037 0.00 0.00 0.00 2.32
655 2618 9.131791 GGTATATGGACTTGGATGTAATTTGTT 57.868 33.333 0.00 0.00 0.00 2.83
659 2622 8.650143 ATGGACTTGGATGTAATTTGTTACTT 57.350 30.769 0.73 0.00 0.00 2.24
661 2624 7.942341 TGGACTTGGATGTAATTTGTTACTTCT 59.058 33.333 11.50 0.00 34.15 2.85
662 2625 8.793592 GGACTTGGATGTAATTTGTTACTTCTT 58.206 33.333 11.50 0.00 34.15 2.52
663 2626 9.612620 GACTTGGATGTAATTTGTTACTTCTTG 57.387 33.333 11.50 6.91 34.15 3.02
664 2627 9.131791 ACTTGGATGTAATTTGTTACTTCTTGT 57.868 29.630 11.50 7.31 34.15 3.16
665 2628 9.398170 CTTGGATGTAATTTGTTACTTCTTGTG 57.602 33.333 11.50 0.00 34.15 3.33
666 2629 7.881142 TGGATGTAATTTGTTACTTCTTGTGG 58.119 34.615 11.50 0.00 34.15 4.17
667 2630 7.504238 TGGATGTAATTTGTTACTTCTTGTGGT 59.496 33.333 11.50 0.00 34.15 4.16
671 2634 9.930693 TGTAATTTGTTACTTCTTGTGGTTTTT 57.069 25.926 0.73 0.00 0.00 1.94
673 2636 6.713792 TTTGTTACTTCTTGTGGTTTTTGC 57.286 33.333 0.00 0.00 0.00 3.68
674 2637 5.392767 TGTTACTTCTTGTGGTTTTTGCA 57.607 34.783 0.00 0.00 0.00 4.08
675 2638 5.784177 TGTTACTTCTTGTGGTTTTTGCAA 58.216 33.333 0.00 0.00 0.00 4.08
677 2640 6.706270 TGTTACTTCTTGTGGTTTTTGCAAAA 59.294 30.769 20.46 20.46 0.00 2.44
678 2641 7.389053 TGTTACTTCTTGTGGTTTTTGCAAAAT 59.611 29.630 24.39 8.26 0.00 1.82
679 2642 8.874816 GTTACTTCTTGTGGTTTTTGCAAAATA 58.125 29.630 24.39 12.91 0.00 1.40
680 2643 7.913674 ACTTCTTGTGGTTTTTGCAAAATAA 57.086 28.000 24.39 8.79 0.00 1.40
681 2644 8.329203 ACTTCTTGTGGTTTTTGCAAAATAAA 57.671 26.923 24.39 8.04 0.00 1.40
683 2646 9.786105 CTTCTTGTGGTTTTTGCAAAATAAAAT 57.214 25.926 24.39 0.00 0.00 1.82
836 3152 7.865530 ATTTTCCAAAATACCCCTTTGTAGT 57.134 32.000 0.00 0.00 36.88 2.73
837 3153 7.678207 TTTTCCAAAATACCCCTTTGTAGTT 57.322 32.000 0.00 0.00 32.87 2.24
838 3154 6.904463 TTCCAAAATACCCCTTTGTAGTTC 57.096 37.500 0.00 0.00 32.87 3.01
839 3155 5.954757 TCCAAAATACCCCTTTGTAGTTCA 58.045 37.500 0.00 0.00 32.87 3.18
840 3156 6.007703 TCCAAAATACCCCTTTGTAGTTCAG 58.992 40.000 0.00 0.00 32.87 3.02
841 3157 5.773176 CCAAAATACCCCTTTGTAGTTCAGT 59.227 40.000 0.00 0.00 32.87 3.41
842 3158 6.266786 CCAAAATACCCCTTTGTAGTTCAGTT 59.733 38.462 0.00 0.00 32.87 3.16
843 3159 7.201965 CCAAAATACCCCTTTGTAGTTCAGTTT 60.202 37.037 0.00 0.00 32.87 2.66
844 3160 7.907841 AAATACCCCTTTGTAGTTCAGTTTT 57.092 32.000 0.00 0.00 0.00 2.43
845 3161 7.907841 AATACCCCTTTGTAGTTCAGTTTTT 57.092 32.000 0.00 0.00 0.00 1.94
869 3185 7.553881 TTTTTGAGAGACTTTGTAGTTCAGG 57.446 36.000 0.00 0.00 33.84 3.86
870 3186 5.871396 TTGAGAGACTTTGTAGTTCAGGT 57.129 39.130 0.00 0.00 33.84 4.00
871 3187 5.871396 TGAGAGACTTTGTAGTTCAGGTT 57.129 39.130 0.00 0.00 33.84 3.50
872 3188 5.601662 TGAGAGACTTTGTAGTTCAGGTTG 58.398 41.667 0.00 0.00 33.84 3.77
873 3189 5.128827 TGAGAGACTTTGTAGTTCAGGTTGT 59.871 40.000 0.00 0.00 33.84 3.32
874 3190 5.360591 AGAGACTTTGTAGTTCAGGTTGTG 58.639 41.667 0.00 0.00 33.84 3.33
875 3191 5.128827 AGAGACTTTGTAGTTCAGGTTGTGA 59.871 40.000 0.00 0.00 33.84 3.58
876 3192 5.741011 AGACTTTGTAGTTCAGGTTGTGAA 58.259 37.500 0.00 0.00 43.26 3.18
877 3193 6.357367 AGACTTTGTAGTTCAGGTTGTGAAT 58.643 36.000 0.00 0.00 46.99 2.57
878 3194 6.483640 AGACTTTGTAGTTCAGGTTGTGAATC 59.516 38.462 0.00 0.00 46.99 2.52
879 3195 5.531287 ACTTTGTAGTTCAGGTTGTGAATCC 59.469 40.000 0.00 0.00 46.99 3.01
880 3196 4.698201 TGTAGTTCAGGTTGTGAATCCA 57.302 40.909 0.00 0.00 46.99 3.41
881 3197 5.042463 TGTAGTTCAGGTTGTGAATCCAA 57.958 39.130 0.00 0.00 46.99 3.53
882 3198 5.063204 TGTAGTTCAGGTTGTGAATCCAAG 58.937 41.667 0.00 0.00 46.99 3.61
883 3199 4.437682 AGTTCAGGTTGTGAATCCAAGA 57.562 40.909 0.00 0.00 46.99 3.02
884 3200 4.392940 AGTTCAGGTTGTGAATCCAAGAG 58.607 43.478 0.00 0.00 46.99 2.85
885 3201 3.423539 TCAGGTTGTGAATCCAAGAGG 57.576 47.619 0.00 0.00 29.64 3.69
886 3202 2.711009 TCAGGTTGTGAATCCAAGAGGT 59.289 45.455 0.00 0.00 31.32 3.85
887 3203 3.907474 TCAGGTTGTGAATCCAAGAGGTA 59.093 43.478 0.00 0.00 31.32 3.08
888 3204 4.020218 TCAGGTTGTGAATCCAAGAGGTAG 60.020 45.833 0.00 0.00 31.32 3.18
889 3205 3.010420 GGTTGTGAATCCAAGAGGTAGC 58.990 50.000 0.00 0.00 35.89 3.58
913 3229 3.933861 AAGTGTGAGGTGACCTTCTTT 57.066 42.857 5.21 0.00 31.76 2.52
921 3241 2.152016 GGTGACCTTCTTTAGCCACAC 58.848 52.381 0.00 0.00 31.54 3.82
922 3242 2.486548 GGTGACCTTCTTTAGCCACACA 60.487 50.000 0.00 0.00 31.54 3.72
923 3243 3.211045 GTGACCTTCTTTAGCCACACAA 58.789 45.455 0.00 0.00 0.00 3.33
924 3244 3.251004 GTGACCTTCTTTAGCCACACAAG 59.749 47.826 0.00 0.00 0.00 3.16
925 3245 3.118038 TGACCTTCTTTAGCCACACAAGT 60.118 43.478 0.00 0.00 0.00 3.16
926 3246 4.101898 TGACCTTCTTTAGCCACACAAGTA 59.898 41.667 0.00 0.00 0.00 2.24
989 3309 1.627297 AATTCTCCGCACTCTCCCCC 61.627 60.000 0.00 0.00 0.00 5.40
1399 3734 1.877637 TTGTCATGACCCACGACTTG 58.122 50.000 22.85 0.00 0.00 3.16
1454 3789 3.070159 TCTCACTGCCTCCATATAGTTGC 59.930 47.826 0.00 0.00 0.00 4.17
1542 3880 9.630098 CAGTCTTAGTTTCATTTTTGCATATGT 57.370 29.630 4.29 0.00 0.00 2.29
2222 4634 4.098914 AGAAAAGGCACCTGACACATAA 57.901 40.909 0.00 0.00 0.00 1.90
2304 4716 3.711190 TCCTATGGCAAGTATCTTGCTGA 59.289 43.478 26.11 17.02 44.36 4.26
2373 4785 7.435068 TGCCTTCAGTTAGTAATTCTGTTTC 57.565 36.000 1.65 0.00 0.00 2.78
2641 5148 4.575885 TGTCAGGAAGCTTGTTACATACC 58.424 43.478 2.10 0.00 0.00 2.73
2649 5156 8.039538 AGGAAGCTTGTTACATACCTAGTTAAC 58.960 37.037 2.10 0.00 0.00 2.01
2664 5171 6.127507 ACCTAGTTAACCGACCTTTCTATGTC 60.128 42.308 0.88 0.00 0.00 3.06
3183 5691 2.030457 GCTGAAATTCGTGGGTATGTCG 59.970 50.000 0.00 0.00 0.00 4.35
3312 5820 7.886629 ACATAGAATGGCAACTTTACATCAT 57.113 32.000 0.00 0.00 33.47 2.45
3350 5858 4.755629 GGTAGTTCTGTTTTCCTGGTTCTC 59.244 45.833 0.00 0.00 0.00 2.87
3445 5953 1.004440 GCTCAACCTGCTTCTCCGT 60.004 57.895 0.00 0.00 0.00 4.69
3451 5959 5.353394 TCAACCTGCTTCTCCGTAATTAT 57.647 39.130 0.00 0.00 0.00 1.28
3658 6171 8.981659 AGCTATTCTTTTAAAATGCCTTATGGT 58.018 29.630 0.09 0.00 35.27 3.55
3659 6172 9.599866 GCTATTCTTTTAAAATGCCTTATGGTT 57.400 29.630 0.09 0.00 35.27 3.67
4257 6789 3.273434 TGCTGATATTGCGAAGAAGCTT 58.727 40.909 0.00 0.00 38.13 3.74
4633 7184 4.537688 TGAAATCACTGAATTCTCCCCTCT 59.462 41.667 7.05 0.00 0.00 3.69
4864 7418 2.452600 TTCCTGCCCTGTTTCTTTGT 57.547 45.000 0.00 0.00 0.00 2.83
4905 7459 7.563724 AGTTACCACCTTTCTCCTGTAATTA 57.436 36.000 0.00 0.00 0.00 1.40
4907 7461 4.844884 ACCACCTTTCTCCTGTAATTAGC 58.155 43.478 0.00 0.00 0.00 3.09
4908 7462 4.288626 ACCACCTTTCTCCTGTAATTAGCA 59.711 41.667 0.00 0.00 0.00 3.49
4938 7498 7.015226 TCTGTGGATCTTAATAATTTGTGCG 57.985 36.000 0.00 0.00 0.00 5.34
4949 7509 6.801539 AATAATTTGTGCGACTCAAGAGAA 57.198 33.333 3.73 0.00 0.00 2.87
4950 7510 6.992063 ATAATTTGTGCGACTCAAGAGAAT 57.008 33.333 3.73 0.00 0.00 2.40
4968 7528 9.447040 CAAGAGAATATATTGTGCAAATGACAG 57.553 33.333 1.78 0.00 0.00 3.51
4984 7546 4.422073 TGACAGAGTTTCCTGATGTGTT 57.578 40.909 0.00 0.00 37.59 3.32
5004 7566 7.168219 TGTGTTAGCTGATGTAAATCCTTCTT 58.832 34.615 0.00 0.00 0.00 2.52
5032 7598 5.457140 TGAACGAATTTCACACATTAAGCC 58.543 37.500 0.00 0.00 39.45 4.35
5072 7640 6.922247 ACTCAAATGTAGAAGCAGATCATG 57.078 37.500 0.00 0.00 0.00 3.07
5077 7645 8.260114 TCAAATGTAGAAGCAGATCATGAAGTA 58.740 33.333 0.00 0.00 0.00 2.24
5079 7647 9.624373 AAATGTAGAAGCAGATCATGAAGTAAT 57.376 29.630 0.00 0.00 0.00 1.89
5109 7733 6.617879 TGCAGTAGTACACTATGTTACACAG 58.382 40.000 2.52 0.00 34.98 3.66
5228 7853 3.070018 CCTTAGTGAGGCAAACAGAGTG 58.930 50.000 0.00 0.00 39.09 3.51
5256 7881 1.594836 CAGCCTAGCTAGCAGCAGC 60.595 63.158 18.83 15.25 45.56 5.25
5275 7903 1.470494 GCAGCAACTTAGAAGAAGGCC 59.530 52.381 0.00 0.00 0.00 5.19
5349 7977 2.735663 TCTCTGTTGTACTCGAGTCGAC 59.264 50.000 23.89 21.32 0.00 4.20
5370 7998 2.308690 GTTATCAGCCGAGGGACTACT 58.691 52.381 0.00 0.00 41.55 2.57
5546 8174 1.141881 GGCGCCTCAGAAGAATCGA 59.858 57.895 22.15 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 1985 2.364317 CTCCCTGAGCCCTTCCGA 60.364 66.667 0.00 0.00 0.00 4.55
59 2001 0.539438 TTGCAACTTCCCAATCCGCT 60.539 50.000 0.00 0.00 0.00 5.52
115 2057 0.393673 CTCTCTCACCCGCTCTCTCA 60.394 60.000 0.00 0.00 0.00 3.27
127 2077 1.836166 CATTTGCCCTCCTCTCTCTCA 59.164 52.381 0.00 0.00 0.00 3.27
193 2143 5.746990 TTCTCTCTCCTTTTCACCCTTAG 57.253 43.478 0.00 0.00 0.00 2.18
225 2180 3.868985 AACCACGAGCCCACGGTT 61.869 61.111 0.00 0.00 36.91 4.44
259 2214 2.583441 CCTCGGGTGACAGCCAGAA 61.583 63.158 22.92 7.28 34.89 3.02
261 2216 4.767255 GCCTCGGGTGACAGCCAG 62.767 72.222 22.92 17.37 34.89 4.85
292 2247 2.823154 CCAACCGGTTGATACACCATTT 59.177 45.455 41.95 4.64 42.93 2.32
297 2253 1.073177 CGTCCAACCGGTTGATACAC 58.927 55.000 41.95 29.43 42.93 2.90
298 2254 0.680618 ACGTCCAACCGGTTGATACA 59.319 50.000 41.95 22.78 42.93 2.29
317 2273 6.488006 GCTGATAGAAATAAGGGAAATGCTCA 59.512 38.462 0.00 0.00 0.00 4.26
322 2278 9.259832 ACTTTTGCTGATAGAAATAAGGGAAAT 57.740 29.630 0.00 0.00 0.00 2.17
411 2367 8.352201 CACCCAAAATACATATCAAGTACATGG 58.648 37.037 0.00 0.00 0.00 3.66
440 2396 5.365021 AGATTAGAAGGATCCAACTGGTG 57.635 43.478 15.82 0.00 36.34 4.17
444 2400 5.209659 ACCGTAGATTAGAAGGATCCAACT 58.790 41.667 15.82 14.54 0.00 3.16
458 2414 5.395324 CCACTGGTGAAGATAACCGTAGATT 60.395 44.000 1.93 0.00 40.86 2.40
476 2432 1.392589 AGAACAGCAAACACCACTGG 58.607 50.000 0.00 0.00 35.70 4.00
480 2436 1.946768 GCACTAGAACAGCAAACACCA 59.053 47.619 0.00 0.00 0.00 4.17
496 2452 0.753262 CCTTATAGGACCAGCGCACT 59.247 55.000 11.47 1.70 37.67 4.40
525 2482 0.456995 GTAGTCTGTCAGGCAGTCGC 60.457 60.000 7.30 0.00 45.23 5.19
531 2488 3.936372 TGTTGTAGTAGTCTGTCAGGC 57.064 47.619 0.00 0.00 0.00 4.85
566 2523 1.000896 ATTGCCCCTTTCTCACCGG 60.001 57.895 0.00 0.00 0.00 5.28
575 2532 3.463048 AAGAAGTCATCATTGCCCCTT 57.537 42.857 0.00 0.00 0.00 3.95
582 2543 2.421424 GCGAGCCAAAGAAGTCATCATT 59.579 45.455 0.00 0.00 0.00 2.57
591 2554 1.229428 CACTGAAGCGAGCCAAAGAA 58.771 50.000 0.00 0.00 0.00 2.52
611 2574 1.202440 ACCACAAGCGACGACTACAAA 60.202 47.619 0.00 0.00 0.00 2.83
632 2595 9.920946 AGTAACAAATTACATCCAAGTCCATAT 57.079 29.630 0.44 0.00 42.83 1.78
640 2603 8.356657 CCACAAGAAGTAACAAATTACATCCAA 58.643 33.333 0.44 0.00 42.83 3.53
653 2616 6.713792 TTTGCAAAAACCACAAGAAGTAAC 57.286 33.333 10.02 0.00 0.00 2.50
655 2618 9.436957 TTTATTTTGCAAAAACCACAAGAAGTA 57.563 25.926 27.10 8.73 0.00 2.24
656 2619 7.913674 TTATTTTGCAAAAACCACAAGAAGT 57.086 28.000 27.10 9.69 0.00 3.01
657 2620 9.786105 ATTTTATTTTGCAAAAACCACAAGAAG 57.214 25.926 27.10 0.00 0.00 2.85
742 2814 9.834628 CACCAAAATACTCGCTCTTTTTATAAA 57.165 29.630 0.00 0.00 0.00 1.40
845 3161 7.110155 ACCTGAACTACAAAGTCTCTCAAAAA 58.890 34.615 0.00 0.00 33.75 1.94
846 3162 6.650120 ACCTGAACTACAAAGTCTCTCAAAA 58.350 36.000 0.00 0.00 33.75 2.44
847 3163 6.235231 ACCTGAACTACAAAGTCTCTCAAA 57.765 37.500 0.00 0.00 33.75 2.69
848 3164 5.871396 ACCTGAACTACAAAGTCTCTCAA 57.129 39.130 0.00 0.00 33.75 3.02
849 3165 5.128827 ACAACCTGAACTACAAAGTCTCTCA 59.871 40.000 0.00 0.00 33.75 3.27
850 3166 5.463724 CACAACCTGAACTACAAAGTCTCTC 59.536 44.000 0.00 0.00 33.75 3.20
851 3167 5.128827 TCACAACCTGAACTACAAAGTCTCT 59.871 40.000 0.00 0.00 33.75 3.10
852 3168 5.357257 TCACAACCTGAACTACAAAGTCTC 58.643 41.667 0.00 0.00 33.75 3.36
853 3169 5.353394 TCACAACCTGAACTACAAAGTCT 57.647 39.130 0.00 0.00 33.75 3.24
854 3170 6.293462 GGATTCACAACCTGAACTACAAAGTC 60.293 42.308 0.00 0.00 41.87 3.01
855 3171 5.531287 GGATTCACAACCTGAACTACAAAGT 59.469 40.000 0.00 0.00 41.87 2.66
856 3172 5.530915 TGGATTCACAACCTGAACTACAAAG 59.469 40.000 0.00 0.00 41.87 2.77
857 3173 5.441500 TGGATTCACAACCTGAACTACAAA 58.558 37.500 0.00 0.00 41.87 2.83
858 3174 5.042463 TGGATTCACAACCTGAACTACAA 57.958 39.130 0.00 0.00 41.87 2.41
859 3175 4.698201 TGGATTCACAACCTGAACTACA 57.302 40.909 0.00 0.00 41.87 2.74
860 3176 5.305585 TCTTGGATTCACAACCTGAACTAC 58.694 41.667 0.00 0.00 41.87 2.73
861 3177 5.513094 CCTCTTGGATTCACAACCTGAACTA 60.513 44.000 0.00 0.00 41.87 2.24
862 3178 4.392940 CTCTTGGATTCACAACCTGAACT 58.607 43.478 0.00 0.00 41.87 3.01
863 3179 3.503748 CCTCTTGGATTCACAACCTGAAC 59.496 47.826 0.00 0.00 41.87 3.18
864 3180 3.138283 ACCTCTTGGATTCACAACCTGAA 59.862 43.478 0.00 0.00 38.88 3.02
865 3181 2.711009 ACCTCTTGGATTCACAACCTGA 59.289 45.455 0.00 0.00 37.04 3.86
866 3182 3.146104 ACCTCTTGGATTCACAACCTG 57.854 47.619 0.00 0.00 37.04 4.00
867 3183 3.307762 GCTACCTCTTGGATTCACAACCT 60.308 47.826 0.00 0.00 37.04 3.50
868 3184 3.010420 GCTACCTCTTGGATTCACAACC 58.990 50.000 0.00 0.00 37.04 3.77
869 3185 3.686726 CAGCTACCTCTTGGATTCACAAC 59.313 47.826 0.00 0.00 37.04 3.32
870 3186 3.582647 TCAGCTACCTCTTGGATTCACAA 59.417 43.478 0.00 0.00 37.04 3.33
871 3187 3.173151 TCAGCTACCTCTTGGATTCACA 58.827 45.455 0.00 0.00 37.04 3.58
872 3188 3.895232 TCAGCTACCTCTTGGATTCAC 57.105 47.619 0.00 0.00 37.04 3.18
873 3189 4.287067 ACTTTCAGCTACCTCTTGGATTCA 59.713 41.667 0.00 0.00 37.04 2.57
874 3190 4.633565 CACTTTCAGCTACCTCTTGGATTC 59.366 45.833 0.00 0.00 37.04 2.52
875 3191 4.042187 ACACTTTCAGCTACCTCTTGGATT 59.958 41.667 0.00 0.00 37.04 3.01
876 3192 3.584848 ACACTTTCAGCTACCTCTTGGAT 59.415 43.478 0.00 0.00 37.04 3.41
877 3193 2.972713 ACACTTTCAGCTACCTCTTGGA 59.027 45.455 0.00 0.00 37.04 3.53
878 3194 3.070018 CACACTTTCAGCTACCTCTTGG 58.930 50.000 0.00 0.00 39.83 3.61
879 3195 3.993081 CTCACACTTTCAGCTACCTCTTG 59.007 47.826 0.00 0.00 0.00 3.02
880 3196 3.007398 CCTCACACTTTCAGCTACCTCTT 59.993 47.826 0.00 0.00 0.00 2.85
881 3197 2.564947 CCTCACACTTTCAGCTACCTCT 59.435 50.000 0.00 0.00 0.00 3.69
882 3198 2.300437 ACCTCACACTTTCAGCTACCTC 59.700 50.000 0.00 0.00 0.00 3.85
883 3199 2.037772 CACCTCACACTTTCAGCTACCT 59.962 50.000 0.00 0.00 0.00 3.08
884 3200 2.037251 TCACCTCACACTTTCAGCTACC 59.963 50.000 0.00 0.00 0.00 3.18
885 3201 3.060602 GTCACCTCACACTTTCAGCTAC 58.939 50.000 0.00 0.00 0.00 3.58
886 3202 2.037251 GGTCACCTCACACTTTCAGCTA 59.963 50.000 0.00 0.00 0.00 3.32
887 3203 1.202698 GGTCACCTCACACTTTCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
888 3204 1.202698 AGGTCACCTCACACTTTCAGC 60.203 52.381 0.00 0.00 0.00 4.26
889 3205 2.918712 AGGTCACCTCACACTTTCAG 57.081 50.000 0.00 0.00 0.00 3.02
913 3229 4.425180 TTGTTCCTTACTTGTGTGGCTA 57.575 40.909 0.00 0.00 0.00 3.93
921 3241 4.507756 GCCTTTTGCTTTGTTCCTTACTTG 59.492 41.667 0.00 0.00 36.87 3.16
922 3242 4.693283 GCCTTTTGCTTTGTTCCTTACTT 58.307 39.130 0.00 0.00 36.87 2.24
923 3243 4.322080 GCCTTTTGCTTTGTTCCTTACT 57.678 40.909 0.00 0.00 36.87 2.24
1068 3394 1.559682 AGCTTACGTTGGATGGTGGAT 59.440 47.619 0.00 0.00 0.00 3.41
1325 3660 4.509737 GGAGTGAGGCGGGCGTAC 62.510 72.222 0.00 0.00 0.00 3.67
1399 3734 0.536006 AGCAACTGCAGTGGAAGACC 60.536 55.000 25.91 6.56 45.16 3.85
1454 3789 1.739466 ACTGTGAATTACGCATGGCAG 59.261 47.619 0.00 0.00 38.38 4.85
1542 3880 0.035534 ATGCAAGTATGTGCCCGTCA 60.036 50.000 0.00 0.00 44.26 4.35
1614 3952 3.815809 TCACCCAGTACAAAACAGGAAG 58.184 45.455 0.00 0.00 36.90 3.46
2144 4496 1.981495 CTGGTTCTTCCTTCCACCTCT 59.019 52.381 0.00 0.00 37.07 3.69
2145 4497 1.978580 TCTGGTTCTTCCTTCCACCTC 59.021 52.381 0.00 0.00 37.07 3.85
2146 4498 1.981495 CTCTGGTTCTTCCTTCCACCT 59.019 52.381 0.00 0.00 37.07 4.00
2147 4499 1.611936 GCTCTGGTTCTTCCTTCCACC 60.612 57.143 0.00 0.00 37.07 4.61
2150 4502 0.391793 CGGCTCTGGTTCTTCCTTCC 60.392 60.000 0.00 0.00 37.07 3.46
2153 4505 0.035458 CAACGGCTCTGGTTCTTCCT 59.965 55.000 0.00 0.00 37.07 3.36
2185 4594 2.910688 TTCTTTTGCTCTCAGTCCGT 57.089 45.000 0.00 0.00 0.00 4.69
2186 4595 3.058639 CCTTTTCTTTTGCTCTCAGTCCG 60.059 47.826 0.00 0.00 0.00 4.79
2198 4607 3.096092 TGTGTCAGGTGCCTTTTCTTTT 58.904 40.909 0.00 0.00 0.00 2.27
2222 4634 1.479323 TCACGTATAAAAGGGAGCGCT 59.521 47.619 11.27 11.27 0.00 5.92
2373 4785 6.562270 GCGACTAGAATTTAATCACACGATGG 60.562 42.308 0.00 0.00 30.13 3.51
2524 5030 7.160726 TCATCATAACAGACACACAGATTTGA 58.839 34.615 0.00 0.00 0.00 2.69
2641 5148 6.860080 TGACATAGAAAGGTCGGTTAACTAG 58.140 40.000 5.42 0.49 39.28 2.57
2649 5156 2.482142 GCTCCTGACATAGAAAGGTCGG 60.482 54.545 0.00 0.00 41.46 4.79
2690 5198 4.943705 GGTGGCAGAAGTCTAAATTGATCA 59.056 41.667 0.00 0.00 0.00 2.92
3183 5691 5.451354 AGAGTAGGGGAAGATGTAGAAGTC 58.549 45.833 0.00 0.00 0.00 3.01
3312 5820 2.540383 ACTACCTGACCAAGCTCATCA 58.460 47.619 0.00 0.00 0.00 3.07
3350 5858 4.329801 TGACAGCATAACACTTAATCAGCG 59.670 41.667 0.00 0.00 0.00 5.18
3451 5959 6.323996 CCTGGTCATACAAGTTATAGTGGAGA 59.676 42.308 0.00 0.00 0.00 3.71
3648 6161 5.736951 AAGCAACATTAAACCATAAGGCA 57.263 34.783 0.00 0.00 39.06 4.75
3649 6162 5.351189 CCAAAGCAACATTAAACCATAAGGC 59.649 40.000 0.00 0.00 39.06 4.35
3650 6163 5.874261 CCCAAAGCAACATTAAACCATAAGG 59.126 40.000 0.00 0.00 42.21 2.69
3651 6164 5.874261 CCCCAAAGCAACATTAAACCATAAG 59.126 40.000 0.00 0.00 0.00 1.73
3652 6165 5.308237 ACCCCAAAGCAACATTAAACCATAA 59.692 36.000 0.00 0.00 0.00 1.90
3653 6166 4.841246 ACCCCAAAGCAACATTAAACCATA 59.159 37.500 0.00 0.00 0.00 2.74
3654 6167 3.650461 ACCCCAAAGCAACATTAAACCAT 59.350 39.130 0.00 0.00 0.00 3.55
3655 6168 3.041946 ACCCCAAAGCAACATTAAACCA 58.958 40.909 0.00 0.00 0.00 3.67
3656 6169 3.070302 TCACCCCAAAGCAACATTAAACC 59.930 43.478 0.00 0.00 0.00 3.27
3657 6170 4.329462 TCACCCCAAAGCAACATTAAAC 57.671 40.909 0.00 0.00 0.00 2.01
3658 6171 5.070981 TCAATCACCCCAAAGCAACATTAAA 59.929 36.000 0.00 0.00 0.00 1.52
3659 6172 4.590647 TCAATCACCCCAAAGCAACATTAA 59.409 37.500 0.00 0.00 0.00 1.40
3660 6173 4.155709 TCAATCACCCCAAAGCAACATTA 58.844 39.130 0.00 0.00 0.00 1.90
3661 6174 2.971330 TCAATCACCCCAAAGCAACATT 59.029 40.909 0.00 0.00 0.00 2.71
3662 6175 2.607499 TCAATCACCCCAAAGCAACAT 58.393 42.857 0.00 0.00 0.00 2.71
3663 6176 2.079170 TCAATCACCCCAAAGCAACA 57.921 45.000 0.00 0.00 0.00 3.33
3664 6177 2.299867 ACATCAATCACCCCAAAGCAAC 59.700 45.455 0.00 0.00 0.00 4.17
3665 6178 2.299582 CACATCAATCACCCCAAAGCAA 59.700 45.455 0.00 0.00 0.00 3.91
3764 6295 6.273730 TGATTTTCCCCAAGTAGAAGAGGTAA 59.726 38.462 0.00 0.00 0.00 2.85
4257 6789 4.211125 CAGGATTCTCAGTGTCTAGCCTA 58.789 47.826 0.00 0.00 0.00 3.93
4633 7184 9.753674 AAAGTTTACATGATTCAAATCTCCCTA 57.246 29.630 0.00 0.00 36.39 3.53
4864 7418 3.610040 AACTCGACCACTGCATAATCA 57.390 42.857 0.00 0.00 0.00 2.57
4933 7493 6.476706 CACAATATATTCTCTTGAGTCGCACA 59.523 38.462 0.00 0.00 0.00 4.57
4938 7498 9.661187 CATTTGCACAATATATTCTCTTGAGTC 57.339 33.333 0.00 0.00 0.00 3.36
4949 7509 8.408601 GGAAACTCTGTCATTTGCACAATATAT 58.591 33.333 0.00 0.00 0.00 0.86
4950 7510 7.611467 AGGAAACTCTGTCATTTGCACAATATA 59.389 33.333 0.00 0.00 32.90 0.86
4968 7528 4.569943 TCAGCTAACACATCAGGAAACTC 58.430 43.478 0.00 0.00 40.21 3.01
5028 7594 1.146982 TGCCTGGAGTTTTTAGGGCTT 59.853 47.619 0.00 0.00 40.15 4.35
5032 7598 3.486383 TGAGTTGCCTGGAGTTTTTAGG 58.514 45.455 0.00 0.00 34.67 2.69
5083 7707 7.608153 TGTGTAACATAGTGTACTACTGCATT 58.392 34.615 7.85 0.00 45.67 3.56
5161 7786 8.154649 ACTTGTATTGCTAATAGTGTTATGCC 57.845 34.615 0.00 0.00 0.00 4.40
5228 7853 0.755686 AGCTAGGCTGGCTCATACAC 59.244 55.000 20.63 0.00 37.57 2.90
5256 7881 2.087646 GGGCCTTCTTCTAAGTTGCTG 58.912 52.381 0.84 0.00 0.00 4.41
5275 7903 2.122768 AGGGTCTTCTATGGAAGCAGG 58.877 52.381 13.67 0.00 46.12 4.85
5323 7951 2.229062 CTCGAGTACAACAGAGAAGCCA 59.771 50.000 3.62 0.00 32.84 4.75
5349 7977 1.001597 GTAGTCCCTCGGCTGATAACG 60.002 57.143 0.00 0.00 0.00 3.18
5370 7998 1.215382 CCGCTGGATGTCGAGAACA 59.785 57.895 0.00 0.00 43.51 3.18
5546 8174 0.743097 GTTACTACGGATGGCGAGGT 59.257 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.