Multiple sequence alignment - TraesCS2D01G301300

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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 TraesCS2D01G301300 chr2D 100.000 4165 0 0 1 4165 384244645 384248809 0.000000e+00 7692.0
1 TraesCS2D01G301300 chr2D 94.058 589 32 3 185 772 118538254 118538840 0.000000e+00 891.0
2 TraesCS2D01G301300 chr2D 94.316 563 31 1 210 772 647842934 647842373 0.000000e+00 861.0
3 TraesCS2D01G301300 chr2D 97.041 169 5 0 1 169 372502953 372502785 6.820000e-73 285.0
4 TraesCS2D01G301300 chr2D 96.450 169 6 0 1 169 638356652 638356820 3.170000e-71 279.0
5 TraesCS2D01G301300 chr2D 96.450 169 6 0 1 169 647843297 647843129 3.170000e-71 279.0
6 TraesCS2D01G301300 chr2D 100.000 30 0 0 159 188 15827209 15827238 5.820000e-04 56.5
7 TraesCS2D01G301300 chr2D 100.000 29 0 0 3714 3742 439391576 439391548 2.000000e-03 54.7
8 TraesCS2D01G301300 chr2A 93.450 2000 90 19 1452 3438 519404001 519405972 0.000000e+00 2929.0
9 TraesCS2D01G301300 chr2A 95.178 477 16 3 769 1239 519403063 519403538 0.000000e+00 747.0
10 TraesCS2D01G301300 chr2A 97.333 225 5 1 1238 1461 519403566 519403790 8.450000e-102 381.0
11 TraesCS2D01G301300 chr2A 84.585 253 30 5 1665 1911 687814142 687813893 4.160000e-60 243.0
12 TraesCS2D01G301300 chr2A 89.529 191 11 5 3443 3629 519406184 519406369 2.500000e-57 233.0
13 TraesCS2D01G301300 chr2A 78.571 294 30 14 3787 4057 519407478 519407761 3.330000e-36 163.0
14 TraesCS2D01G301300 chr2A 91.860 86 7 0 3615 3700 519407360 519407445 2.030000e-23 121.0
15 TraesCS2D01G301300 chr2A 84.848 99 14 1 3707 3804 667229713 667229615 9.530000e-17 99.0
16 TraesCS2D01G301300 chr2A 100.000 32 0 0 3646 3677 519406279 519406310 4.500000e-05 60.2
17 TraesCS2D01G301300 chr2B 90.919 1806 77 33 1682 3438 454338331 454340098 0.000000e+00 2346.0
18 TraesCS2D01G301300 chr2B 84.812 744 54 19 3443 4159 454340220 454340931 0.000000e+00 693.0
19 TraesCS2D01G301300 chr2B 90.580 414 26 2 769 1182 454337394 454337794 1.700000e-148 536.0
20 TraesCS2D01G301300 chr2B 90.659 364 26 6 1240 1601 454337971 454338328 1.050000e-130 477.0
21 TraesCS2D01G301300 chr2B 86.239 109 11 4 3696 3804 615331711 615331607 9.460000e-22 115.0
22 TraesCS2D01G301300 chr2B 96.875 32 1 0 3646 3677 454340316 454340347 2.000000e-03 54.7
23 TraesCS2D01G301300 chr3D 93.356 587 34 4 185 770 363853248 363853830 0.000000e+00 863.0
24 TraesCS2D01G301300 chr3D 92.869 589 41 1 185 773 300539759 300539172 0.000000e+00 854.0
25 TraesCS2D01G301300 chr3D 85.616 292 38 3 1696 1985 598941570 598941281 1.880000e-78 303.0
26 TraesCS2D01G301300 chr3D 96.450 169 6 0 1 169 13252382 13252214 3.170000e-71 279.0
27 TraesCS2D01G301300 chr3D 80.328 183 27 8 3694 3874 410375538 410375713 3.380000e-26 130.0
28 TraesCS2D01G301300 chr6D 93.174 586 38 2 187 772 383215167 383214584 0.000000e+00 859.0
29 TraesCS2D01G301300 chr1D 92.542 590 42 2 185 773 249021543 249020955 0.000000e+00 845.0
30 TraesCS2D01G301300 chr7D 92.437 595 33 7 185 776 505150089 505150674 0.000000e+00 839.0
31 TraesCS2D01G301300 chr7D 96.450 169 6 0 1 169 136988780 136988948 3.170000e-71 279.0
32 TraesCS2D01G301300 chr3A 92.203 590 43 3 185 773 176138616 176139203 0.000000e+00 832.0
33 TraesCS2D01G301300 chr3A 92.334 587 42 3 185 770 715533929 715534513 0.000000e+00 832.0
34 TraesCS2D01G301300 chr3A 86.301 292 36 3 1696 1985 728998407 728998118 8.690000e-82 315.0
35 TraesCS2D01G301300 chr3A 100.000 29 0 0 160 188 60078603 60078575 2.000000e-03 54.7
36 TraesCS2D01G301300 chr3A 100.000 29 0 0 160 188 681454056 681454028 2.000000e-03 54.7
37 TraesCS2D01G301300 chr1A 84.404 327 41 7 1665 1985 517121326 517121648 3.130000e-81 313.0
38 TraesCS2D01G301300 chr1A 100.000 29 0 0 160 188 381288081 381288109 2.000000e-03 54.7
39 TraesCS2D01G301300 chr5B 85.959 292 37 2 1696 1985 103635129 103635418 4.040000e-80 309.0
40 TraesCS2D01G301300 chr7A 83.486 327 45 6 1665 1985 21011246 21010923 3.150000e-76 296.0
41 TraesCS2D01G301300 chr5D 97.633 169 4 0 1 169 44170707 44170875 1.460000e-74 291.0
42 TraesCS2D01G301300 chr5D 97.041 169 5 0 1 169 426793221 426793389 6.820000e-73 285.0
43 TraesCS2D01G301300 chr5D 97.041 169 5 0 1 169 525173990 525173822 6.820000e-73 285.0
44 TraesCS2D01G301300 chr5D 86.538 104 11 3 3703 3804 426039362 426039464 1.220000e-20 111.0
45 TraesCS2D01G301300 chr5D 100.000 29 0 0 160 188 4239499 4239471 2.000000e-03 54.7
46 TraesCS2D01G301300 chr5D 100.000 29 0 0 160 188 44170954 44170982 2.000000e-03 54.7
47 TraesCS2D01G301300 chr1B 84.247 292 42 2 1696 1985 79197501 79197790 8.820000e-72 281.0
48 TraesCS2D01G301300 chrUn 96.450 169 6 0 1 169 220600899 220601067 3.170000e-71 279.0
49 TraesCS2D01G301300 chrUn 100.000 29 0 0 160 188 220601145 220601173 2.000000e-03 54.7
50 TraesCS2D01G301300 chr4A 86.905 84 9 2 3704 3786 618186238 618186320 4.430000e-15 93.5
51 TraesCS2D01G301300 chr6A 100.000 29 0 0 160 188 579991293 579991321 2.000000e-03 54.7
52 TraesCS2D01G301300 chr5A 100.000 29 0 0 160 188 599464343 599464315 2.000000e-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 TraesCS2D01G301300 chr2D 384244645 384248809 4164 False 7692.000000 7692 100.000000 1 4165 1 chr2D.!!$F3 4164
1 TraesCS2D01G301300 chr2D 118538254 118538840 586 False 891.000000 891 94.058000 185 772 1 chr2D.!!$F2 587
2 TraesCS2D01G301300 chr2D 647842373 647843297 924 True 570.000000 861 95.383000 1 772 2 chr2D.!!$R3 771
3 TraesCS2D01G301300 chr2A 519403063 519407761 4698 False 662.028571 2929 92.274429 769 4057 7 chr2A.!!$F1 3288
4 TraesCS2D01G301300 chr2B 454337394 454340931 3537 False 821.340000 2346 90.769000 769 4159 5 chr2B.!!$F1 3390
5 TraesCS2D01G301300 chr3D 363853248 363853830 582 False 863.000000 863 93.356000 185 770 1 chr3D.!!$F1 585
6 TraesCS2D01G301300 chr3D 300539172 300539759 587 True 854.000000 854 92.869000 185 773 1 chr3D.!!$R2 588
7 TraesCS2D01G301300 chr6D 383214584 383215167 583 True 859.000000 859 93.174000 187 772 1 chr6D.!!$R1 585
8 TraesCS2D01G301300 chr1D 249020955 249021543 588 True 845.000000 845 92.542000 185 773 1 chr1D.!!$R1 588
9 TraesCS2D01G301300 chr7D 505150089 505150674 585 False 839.000000 839 92.437000 185 776 1 chr7D.!!$F2 591
10 TraesCS2D01G301300 chr3A 176138616 176139203 587 False 832.000000 832 92.203000 185 773 1 chr3A.!!$F1 588
11 TraesCS2D01G301300 chr3A 715533929 715534513 584 False 832.000000 832 92.334000 185 770 1 chr3A.!!$F2 585

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
526 690 0.178932 GGGAAGTGGGGGAAAAAGCT 60.179 55.000 0.00 0.0 0.00 3.74 F
826 998 0.252881 TTCCATGCAGTCCTCTCCCT 60.253 55.000 0.00 0.0 0.00 4.20 F
1012 1190 0.599558 GCCCACTATGGTACGCGATA 59.400 55.000 15.93 0.0 35.17 2.92 F
1209 1478 1.203758 TGTGGCGTAGTTGATCGTGAT 59.796 47.619 0.00 0.0 0.00 3.06 F
2736 3280 2.997980 TGTGCTCCTGTCTTGTTTTGA 58.002 42.857 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2824 2.504367 CAAGGAGTACACAACCCCTTG 58.496 52.381 4.35 4.35 45.11 3.61 R
2580 3124 0.389391 CACCATACCTAGGCCTGTCG 59.611 60.000 17.99 4.58 0.00 4.35 R
2712 3256 2.469274 ACAAGACAGGAGCACATCAG 57.531 50.000 0.00 0.00 0.00 2.90 R
3147 3702 0.251341 GTTCACTCCATTGGGCCAGT 60.251 55.000 6.23 0.00 0.00 4.00 R
3616 5410 0.038166 TGAGGTCCATTTGGTGAGGC 59.962 55.000 0.00 0.00 36.34 4.70 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
67 68 4.821589 GCCGAGGTGCGAGAAGGG 62.822 72.222 0.00 0.00 44.57 3.95
71 72 2.925170 AGGTGCGAGAAGGGCAGT 60.925 61.111 0.00 0.00 41.83 4.40
142 143 5.371526 CGAGTAGTTGTATGGAGGGTACTA 58.628 45.833 0.00 0.00 0.00 1.82
264 428 1.990160 TTGTCACGGGCCTTCTTGGT 61.990 55.000 0.84 0.00 38.35 3.67
266 430 3.365265 CACGGGCCTTCTTGGTGC 61.365 66.667 0.84 0.00 38.35 5.01
489 653 2.506472 GAGGGAGATTGGCGGGAC 59.494 66.667 0.00 0.00 0.00 4.46
523 687 0.485543 GGAGGGAAGTGGGGGAAAAA 59.514 55.000 0.00 0.00 0.00 1.94
526 690 0.178932 GGGAAGTGGGGGAAAAAGCT 60.179 55.000 0.00 0.00 0.00 3.74
535 699 2.906389 GGGGGAAAAAGCTGGAAGAAAT 59.094 45.455 0.00 0.00 34.07 2.17
598 763 2.026522 CCCTTTTCGTTTGTGCCGA 58.973 52.632 0.00 0.00 0.00 5.54
685 855 1.512156 GGCGAAAAACGGGCTTCTGA 61.512 55.000 0.00 0.00 42.83 3.27
690 862 2.426305 AAAACGGGCTTCTGAGGGGG 62.426 60.000 0.00 0.00 0.00 5.40
817 989 1.003580 CGGGCCTATATTCCATGCAGT 59.996 52.381 0.84 0.00 0.00 4.40
820 992 2.307098 GGCCTATATTCCATGCAGTCCT 59.693 50.000 0.00 0.00 0.00 3.85
826 998 0.252881 TTCCATGCAGTCCTCTCCCT 60.253 55.000 0.00 0.00 0.00 4.20
1012 1190 0.599558 GCCCACTATGGTACGCGATA 59.400 55.000 15.93 0.00 35.17 2.92
1025 1203 1.968493 ACGCGATAACCACTGGGATAT 59.032 47.619 15.93 0.00 35.06 1.63
1161 1339 5.250543 TCCAAGGTCAGTAATTCTCAATCCA 59.749 40.000 0.00 0.00 0.00 3.41
1209 1478 1.203758 TGTGGCGTAGTTGATCGTGAT 59.796 47.619 0.00 0.00 0.00 3.06
1241 1510 3.143515 TGCGCCCACAGCAACAAA 61.144 55.556 4.18 0.00 44.04 2.83
1252 1551 6.648725 GCCCACAGCAACAAAGAAAATAAATA 59.351 34.615 0.00 0.00 42.97 1.40
1278 1577 8.575649 TTTTAAGGGAAGAGGTGAATTGTATC 57.424 34.615 0.00 0.00 0.00 2.24
1316 1615 5.470437 TGATTCGTTGGTACAGTTTTGCATA 59.530 36.000 0.00 0.00 42.39 3.14
1468 1988 3.379372 CCATGGCTTGTTATGACTTCCTG 59.621 47.826 0.00 0.00 0.00 3.86
1510 2030 7.719483 ACTGAATTCACCTAATGCCATATTTG 58.281 34.615 3.38 0.00 0.00 2.32
1603 2123 7.016153 TCCATACTCTGGTTTGTCATAACTT 57.984 36.000 0.00 0.00 46.08 2.66
2045 2587 6.855836 TCATCTCTTTTGTTACAATGCCATC 58.144 36.000 0.00 0.00 0.00 3.51
2068 2610 5.597182 TCGTCCTTGCTATACCTTTCAGTAT 59.403 40.000 0.00 0.00 36.84 2.12
2069 2611 6.097839 TCGTCCTTGCTATACCTTTCAGTATT 59.902 38.462 0.00 0.00 34.74 1.89
2072 2614 7.769044 GTCCTTGCTATACCTTTCAGTATTTCA 59.231 37.037 0.00 0.00 34.74 2.69
2073 2615 7.987458 TCCTTGCTATACCTTTCAGTATTTCAG 59.013 37.037 0.00 0.00 34.74 3.02
2074 2616 7.770897 CCTTGCTATACCTTTCAGTATTTCAGT 59.229 37.037 0.00 0.00 34.74 3.41
2075 2617 9.817809 CTTGCTATACCTTTCAGTATTTCAGTA 57.182 33.333 0.00 0.00 34.74 2.74
2076 2618 9.595823 TTGCTATACCTTTCAGTATTTCAGTAC 57.404 33.333 0.00 0.00 34.74 2.73
2077 2619 8.202137 TGCTATACCTTTCAGTATTTCAGTACC 58.798 37.037 0.00 0.00 34.74 3.34
2078 2620 8.422566 GCTATACCTTTCAGTATTTCAGTACCT 58.577 37.037 0.00 0.00 34.74 3.08
2079 2621 9.968870 CTATACCTTTCAGTATTTCAGTACCTC 57.031 37.037 0.00 0.00 34.74 3.85
2080 2622 6.936968 ACCTTTCAGTATTTCAGTACCTCT 57.063 37.500 0.00 0.00 0.00 3.69
2116 2658 7.042051 TCAGTTGCACTTACTTGACTAATGAAC 60.042 37.037 0.00 0.00 0.00 3.18
2208 2750 9.371136 TCTGACTGTATGTGATTTGACTTAATC 57.629 33.333 0.00 0.00 35.54 1.75
2238 2780 4.496673 GGTGCAGACTCTAATCTGTAGACG 60.497 50.000 4.80 0.00 46.65 4.18
2247 2789 8.680039 ACTCTAATCTGTAGACGTAGCTTTAT 57.320 34.615 0.00 0.00 0.00 1.40
2282 2824 9.468532 AGTATGAACTTGAAAATTCTCTTTTGC 57.531 29.630 0.00 0.00 29.00 3.68
2425 2969 9.403583 TGGTCCTTTGATTTTATTATGTAGACC 57.596 33.333 0.00 0.00 38.38 3.85
2426 2970 9.403583 GGTCCTTTGATTTTATTATGTAGACCA 57.596 33.333 0.00 0.00 37.92 4.02
2428 2972 9.967451 TCCTTTGATTTTATTATGTAGACCACA 57.033 29.630 0.00 0.00 42.69 4.17
2533 3077 4.676546 GCCAAGGCAATCTCTTAATGTTC 58.323 43.478 6.14 0.00 41.49 3.18
2712 3256 8.429641 TCATTCAGGGTAATCAACTTATCTACC 58.570 37.037 0.00 0.00 32.78 3.18
2736 3280 2.997980 TGTGCTCCTGTCTTGTTTTGA 58.002 42.857 0.00 0.00 0.00 2.69
2739 3283 4.402155 TGTGCTCCTGTCTTGTTTTGATTT 59.598 37.500 0.00 0.00 0.00 2.17
2815 3359 6.808008 TCTGTTTGAATCCTCATCTGTTTC 57.192 37.500 0.00 0.00 0.00 2.78
2817 3361 7.679783 TCTGTTTGAATCCTCATCTGTTTCTA 58.320 34.615 0.00 0.00 0.00 2.10
2877 3421 9.743057 TTTGTATTCACCTGTATTTTGTTTCAG 57.257 29.630 0.00 0.00 0.00 3.02
2878 3422 8.684386 TGTATTCACCTGTATTTTGTTTCAGA 57.316 30.769 0.00 0.00 0.00 3.27
2879 3423 8.783093 TGTATTCACCTGTATTTTGTTTCAGAG 58.217 33.333 0.00 0.00 0.00 3.35
2881 3425 7.639113 TTCACCTGTATTTTGTTTCAGAGTT 57.361 32.000 0.00 0.00 0.00 3.01
2882 3426 7.639113 TCACCTGTATTTTGTTTCAGAGTTT 57.361 32.000 0.00 0.00 0.00 2.66
2883 3427 7.479980 TCACCTGTATTTTGTTTCAGAGTTTG 58.520 34.615 0.00 0.00 0.00 2.93
2932 3483 8.134895 CACTTTTCTTTGCAAAAGGTCTATACA 58.865 33.333 13.84 0.00 44.49 2.29
3016 3567 5.931441 AGAAAACTAAGTGACTGCATGTC 57.069 39.130 8.75 8.75 45.54 3.06
3169 3724 1.133199 TGGCCCAATGGAGTGAACTTT 60.133 47.619 0.00 0.00 0.00 2.66
3245 3800 2.263077 AGTGATGTTTGCGAGATCGAC 58.737 47.619 6.39 0.00 43.02 4.20
3300 3855 8.972127 TGATTCACTCTAGTAAAATAGCTCTGT 58.028 33.333 0.00 0.00 0.00 3.41
3321 3876 6.318648 TCTGTGAAATACTTCTGTTGCTGTTT 59.681 34.615 0.00 0.00 32.33 2.83
3322 3877 6.264832 TGTGAAATACTTCTGTTGCTGTTTG 58.735 36.000 0.00 0.00 32.33 2.93
3332 3887 2.233431 TGTTGCTGTTTGGTTTCTGCTT 59.767 40.909 0.00 0.00 0.00 3.91
3373 3944 2.633967 TGGTAGACGTTTGTATGGTGGT 59.366 45.455 0.00 0.00 0.00 4.16
3400 3978 0.608130 GGTTTTTGCCCCATGGACTC 59.392 55.000 15.22 1.84 0.00 3.36
3417 3995 0.674581 CTCCGTCTTGATTGCAGGCA 60.675 55.000 0.00 0.00 0.00 4.75
3429 4007 2.646175 GCAGGCAGTAGGTGGTCGA 61.646 63.158 0.00 0.00 0.00 4.20
3438 4016 1.553704 GTAGGTGGTCGATTTCCTGGT 59.446 52.381 13.08 0.00 0.00 4.00
3439 4017 1.064825 AGGTGGTCGATTTCCTGGTT 58.935 50.000 4.81 0.00 0.00 3.67
3440 4018 1.423921 AGGTGGTCGATTTCCTGGTTT 59.576 47.619 4.81 0.00 0.00 3.27
3441 4019 2.158519 AGGTGGTCGATTTCCTGGTTTT 60.159 45.455 4.81 0.00 0.00 2.43
3482 4271 3.262405 AGGTGGTTGAATTTACGAGCCTA 59.738 43.478 0.00 0.00 0.00 3.93
3487 4276 5.708230 TGGTTGAATTTACGAGCCTAATTGT 59.292 36.000 0.00 0.00 0.00 2.71
3530 4320 8.347035 GCCAAAACTAGAACTTGTAAACATGTA 58.653 33.333 0.00 0.00 34.38 2.29
3560 4350 4.298103 TGCCAACCAATTTTTATGCCAT 57.702 36.364 0.00 0.00 0.00 4.40
3568 4358 7.878547 ACCAATTTTTATGCCATTATTTGGG 57.121 32.000 0.00 0.00 46.55 4.12
3580 4370 5.408299 GCCATTATTTGGGAAAACAACAGTC 59.592 40.000 0.00 0.00 46.55 3.51
3581 4371 5.633182 CCATTATTTGGGAAAACAACAGTCG 59.367 40.000 0.00 0.00 42.33 4.18
3582 4372 2.570442 TTTGGGAAAACAACAGTCGC 57.430 45.000 0.00 0.00 0.00 5.19
3583 4373 1.757682 TTGGGAAAACAACAGTCGCT 58.242 45.000 0.00 0.00 0.00 4.93
3584 4374 2.623878 TGGGAAAACAACAGTCGCTA 57.376 45.000 0.00 0.00 0.00 4.26
3585 4375 3.134574 TGGGAAAACAACAGTCGCTAT 57.865 42.857 0.00 0.00 0.00 2.97
3612 4402 3.161866 GGTTAGGGCAACTCCATCAAAA 58.838 45.455 0.00 0.00 37.30 2.44
3613 4403 3.769300 GGTTAGGGCAACTCCATCAAAAT 59.231 43.478 0.00 0.00 37.30 1.82
3639 5433 1.002134 ACCAAATGGACCTCAGCCG 60.002 57.895 6.42 0.00 38.94 5.52
3810 5628 8.349983 TCAAGTTTGAATTCAACTTAGTTAGGC 58.650 33.333 20.35 2.03 35.28 3.93
3811 5629 7.817418 AGTTTGAATTCAACTTAGTTAGGCA 57.183 32.000 20.35 0.00 35.28 4.75
3812 5630 8.232913 AGTTTGAATTCAACTTAGTTAGGCAA 57.767 30.769 20.35 0.00 35.28 4.52
3813 5631 8.860088 AGTTTGAATTCAACTTAGTTAGGCAAT 58.140 29.630 20.35 0.00 35.28 3.56
3814 5632 8.915654 GTTTGAATTCAACTTAGTTAGGCAATG 58.084 33.333 20.35 0.00 35.28 2.82
3816 5634 6.208402 TGAATTCAACTTAGTTAGGCAATGCA 59.792 34.615 5.45 0.00 0.00 3.96
3817 5635 5.371115 TTCAACTTAGTTAGGCAATGCAC 57.629 39.130 7.79 0.00 0.00 4.57
3818 5636 4.651778 TCAACTTAGTTAGGCAATGCACT 58.348 39.130 7.79 4.66 0.00 4.40
3819 5637 5.800296 TCAACTTAGTTAGGCAATGCACTA 58.200 37.500 7.79 3.57 0.00 2.74
3826 5644 5.605534 AGTTAGGCAATGCACTATAGTCTG 58.394 41.667 7.79 0.00 0.00 3.51
3829 5647 3.070734 AGGCAATGCACTATAGTCTGGAG 59.929 47.826 7.79 0.00 0.00 3.86
3833 5651 5.295950 CAATGCACTATAGTCTGGAGGAAG 58.704 45.833 1.26 0.00 0.00 3.46
3838 5656 2.445682 ATAGTCTGGAGGAAGCGTCT 57.554 50.000 0.00 0.00 0.00 4.18
3874 5692 2.168936 AGATCTTTCTGGAGCTGCTCAG 59.831 50.000 28.95 22.45 30.29 3.35
3896 5714 2.420129 GCATTCATCTACTGGACGGGTT 60.420 50.000 0.00 0.00 0.00 4.11
3900 5718 0.824759 ATCTACTGGACGGGTTCTGC 59.175 55.000 0.00 0.00 0.00 4.26
3944 5762 3.834231 CCCATGTTTGAAAATCCAGACCT 59.166 43.478 0.00 0.00 0.00 3.85
3961 5779 1.078918 CTTGGCGAGCTCCATCACA 60.079 57.895 8.47 0.00 35.77 3.58
3967 5785 1.741732 GCGAGCTCCATCACACTCATT 60.742 52.381 8.47 0.00 0.00 2.57
3983 5821 5.121298 ACACTCATTCTCGACAATCATGTTG 59.879 40.000 0.00 0.00 40.74 3.33
4040 5878 3.369681 CCCACCCCATCATCACAATTTTG 60.370 47.826 0.00 0.00 0.00 2.44
4071 5909 7.967771 TTATGCATATGAACAATGACGTTTG 57.032 32.000 7.36 0.00 0.00 2.93
4077 5916 8.523464 GCATATGAACAATGACGTTTGTAAATC 58.477 33.333 6.97 2.04 38.85 2.17
4085 5924 6.991485 ATGACGTTTGTAAATCTTGCTTTG 57.009 33.333 0.00 0.00 0.00 2.77
4086 5925 6.125327 TGACGTTTGTAAATCTTGCTTTGA 57.875 33.333 0.00 0.00 0.00 2.69
4096 5935 4.722700 TGCTTTGAGCCGGCCCTC 62.723 66.667 26.15 16.53 41.51 4.30
4109 5948 0.466372 GGCCCTCCCTAGCATCAAAC 60.466 60.000 0.00 0.00 0.00 2.93
4133 5972 1.748879 GCAATCCTGCCTACGCCAA 60.749 57.895 0.00 0.00 43.26 4.52
4138 5977 2.764314 CCTGCCTACGCCAATGCAC 61.764 63.158 0.00 0.00 37.32 4.57
4142 5981 0.878523 GCCTACGCCAATGCACGATA 60.879 55.000 1.06 0.00 37.32 2.92
4143 5982 1.795768 CCTACGCCAATGCACGATAT 58.204 50.000 1.06 0.00 37.32 1.63
4150 5989 2.355756 GCCAATGCACGATATCACAAGT 59.644 45.455 3.12 0.00 37.47 3.16
4155 5994 3.658709 TGCACGATATCACAAGTTGTCA 58.341 40.909 5.27 0.00 0.00 3.58
4159 5998 5.007039 GCACGATATCACAAGTTGTCATCAT 59.993 40.000 5.27 0.00 0.00 2.45
4160 5999 6.457392 GCACGATATCACAAGTTGTCATCATT 60.457 38.462 5.27 0.00 0.00 2.57
4161 6000 7.121911 CACGATATCACAAGTTGTCATCATTC 58.878 38.462 5.27 0.00 0.00 2.67
4162 6001 6.258727 ACGATATCACAAGTTGTCATCATTCC 59.741 38.462 5.27 0.00 0.00 3.01
4163 6002 6.293081 CGATATCACAAGTTGTCATCATTCCC 60.293 42.308 5.27 0.00 0.00 3.97
4164 6003 3.420893 TCACAAGTTGTCATCATTCCCC 58.579 45.455 5.27 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.222847 CCCGCCTACGCTTCCTCC 62.223 72.222 0.00 0.00 38.22 4.30
99 100 4.893601 GCCCGCCTACGCTTCCTC 62.894 72.222 0.00 0.00 38.22 3.71
264 428 4.329545 GACGGAACAGGGCCAGCA 62.330 66.667 6.18 0.00 0.00 4.41
266 430 4.760047 CCGACGGAACAGGGCCAG 62.760 72.222 8.64 0.00 0.00 4.85
489 653 2.026262 TCCCTCCCATTTTCTCCTTTCG 60.026 50.000 0.00 0.00 0.00 3.46
523 687 1.379044 CCCGCCATTTCTTCCAGCT 60.379 57.895 0.00 0.00 0.00 4.24
526 690 2.422803 CCTATTCCCGCCATTTCTTCCA 60.423 50.000 0.00 0.00 0.00 3.53
589 754 2.664851 CTGGAGCGTCGGCACAAA 60.665 61.111 0.00 0.00 43.41 2.83
733 905 2.286121 CCCCAACAGGCCCTCCTA 60.286 66.667 0.00 0.00 41.93 2.94
817 989 4.567747 GGCAGAAATGTAAAAGGGAGAGGA 60.568 45.833 0.00 0.00 0.00 3.71
820 992 3.563479 GGGGCAGAAATGTAAAAGGGAGA 60.563 47.826 0.00 0.00 0.00 3.71
826 998 1.816224 GCGAGGGGCAGAAATGTAAAA 59.184 47.619 0.00 0.00 42.87 1.52
999 1177 2.034939 CCAGTGGTTATCGCGTACCATA 59.965 50.000 24.92 7.34 45.53 2.74
1012 1190 4.464008 CAGCATGTTATATCCCAGTGGTT 58.536 43.478 8.74 0.00 0.00 3.67
1161 1339 1.267261 CTACTAGCCTACAAGCGCGAT 59.733 52.381 12.10 0.00 38.01 4.58
1191 1460 2.665649 AATCACGATCAACTACGCCA 57.334 45.000 0.00 0.00 0.00 5.69
1209 1478 2.550855 GGGCGCATCAGATCAATCCTAA 60.551 50.000 10.83 0.00 0.00 2.69
1252 1551 9.190317 GATACAATTCACCTCTTCCCTTAAAAT 57.810 33.333 0.00 0.00 0.00 1.82
1278 1577 7.930217 ACCAACGAATCAAATCCTATACATTG 58.070 34.615 0.00 0.00 0.00 2.82
1316 1615 2.044630 AGAGCCTACTAGGTTTCCTGGT 59.955 50.000 9.53 9.53 46.84 4.00
1468 1988 3.071479 TCAGTTTCGTATTTCCTGGTGC 58.929 45.455 0.00 0.00 0.00 5.01
1541 2061 7.920160 TTTCTGATGTACTACATGATTTGCA 57.080 32.000 6.41 0.00 39.27 4.08
1542 2062 8.615211 TGATTTCTGATGTACTACATGATTTGC 58.385 33.333 6.41 0.00 39.27 3.68
1584 2104 8.747538 AGTTAAAAGTTATGACAAACCAGAGT 57.252 30.769 0.00 0.00 0.00 3.24
1603 2123 8.470805 TCAAAATTTCTGGTGTAGCAAGTTAAA 58.529 29.630 0.00 0.00 0.00 1.52
1659 2179 7.646526 ACATGCATCAGATAAAATGATTTCACG 59.353 33.333 0.00 0.00 35.20 4.35
1666 2186 7.364970 GCACATACATGCATCAGATAAAATGA 58.635 34.615 0.00 0.00 45.39 2.57
1950 2470 3.637273 GGTGGGCCAGAACCGAGT 61.637 66.667 6.40 0.00 34.09 4.18
2045 2587 4.124851 ACTGAAAGGTATAGCAAGGACG 57.875 45.455 4.48 0.00 39.30 4.79
2073 2615 4.762289 ACTGAAATCATCCCAGAGGTAC 57.238 45.455 0.00 0.00 0.00 3.34
2074 2616 4.626287 GCAACTGAAATCATCCCAGAGGTA 60.626 45.833 0.00 0.00 0.00 3.08
2075 2617 3.875369 GCAACTGAAATCATCCCAGAGGT 60.875 47.826 0.00 0.00 0.00 3.85
2076 2618 2.686915 GCAACTGAAATCATCCCAGAGG 59.313 50.000 0.00 0.00 0.00 3.69
2077 2619 3.128242 GTGCAACTGAAATCATCCCAGAG 59.872 47.826 0.00 0.00 0.00 3.35
2078 2620 3.084039 GTGCAACTGAAATCATCCCAGA 58.916 45.455 0.00 0.00 0.00 3.86
2079 2621 3.498927 GTGCAACTGAAATCATCCCAG 57.501 47.619 0.00 0.00 0.00 4.45
2208 2750 5.289675 CAGATTAGAGTCTGCACCTTAAACG 59.710 44.000 1.86 0.00 39.19 3.60
2282 2824 2.504367 CAAGGAGTACACAACCCCTTG 58.496 52.381 4.35 4.35 45.11 3.61
2425 2969 7.381766 TCCTGAATACAAACATCTTGATGTG 57.618 36.000 15.83 8.03 34.56 3.21
2426 2970 8.585471 AATCCTGAATACAAACATCTTGATGT 57.415 30.769 10.15 10.15 36.10 3.06
2427 2971 9.297586 CAAATCCTGAATACAAACATCTTGATG 57.702 33.333 8.87 8.87 0.00 3.07
2428 2972 7.977853 GCAAATCCTGAATACAAACATCTTGAT 59.022 33.333 0.00 0.00 0.00 2.57
2433 2977 7.887996 TTTGCAAATCCTGAATACAAACATC 57.112 32.000 8.05 0.00 0.00 3.06
2524 3068 9.586435 GGTCCAATCAAAATAAGGAACATTAAG 57.414 33.333 0.00 0.00 36.12 1.85
2533 3077 8.034804 CCTACAAAAGGTCCAATCAAAATAAGG 58.965 37.037 0.00 0.00 40.94 2.69
2580 3124 0.389391 CACCATACCTAGGCCTGTCG 59.611 60.000 17.99 4.58 0.00 4.35
2712 3256 2.469274 ACAAGACAGGAGCACATCAG 57.531 50.000 0.00 0.00 0.00 2.90
2739 3283 7.225145 GCTGGAAATTGCAATGCTAAATCATAA 59.775 33.333 13.82 0.00 0.00 1.90
2753 3297 5.680594 ATTTATCTTGGCTGGAAATTGCA 57.319 34.783 0.00 0.00 0.00 4.08
2761 3305 6.107901 AGCTAGAGTATTTATCTTGGCTGG 57.892 41.667 0.00 0.00 35.13 4.85
2826 3370 4.580167 AGCTGCTGAAATGTACAGAACAAA 59.420 37.500 0.00 0.00 42.70 2.83
2836 3380 6.421801 GTGAATACAAAAAGCTGCTGAAATGT 59.578 34.615 1.35 9.18 0.00 2.71
2839 3383 5.068987 AGGTGAATACAAAAAGCTGCTGAAA 59.931 36.000 1.35 0.00 0.00 2.69
2842 3386 4.232221 CAGGTGAATACAAAAAGCTGCTG 58.768 43.478 1.35 0.00 32.10 4.41
2878 3422 9.899226 GCAAACTATGAAACTAAGAATCAAACT 57.101 29.630 0.00 0.00 0.00 2.66
2879 3423 9.677567 TGCAAACTATGAAACTAAGAATCAAAC 57.322 29.630 0.00 0.00 0.00 2.93
2881 3425 8.845227 TGTGCAAACTATGAAACTAAGAATCAA 58.155 29.630 0.00 0.00 0.00 2.57
2882 3426 8.289618 GTGTGCAAACTATGAAACTAAGAATCA 58.710 33.333 0.00 0.00 0.00 2.57
2883 3427 8.507249 AGTGTGCAAACTATGAAACTAAGAATC 58.493 33.333 8.09 0.00 0.00 2.52
2989 3540 6.545504 TGCAGTCACTTAGTTTTCTTCATC 57.454 37.500 0.00 0.00 0.00 2.92
3016 3567 9.674068 ATCAGAGAAATCATCCATATCAATGAG 57.326 33.333 0.00 0.00 35.49 2.90
3147 3702 0.251341 GTTCACTCCATTGGGCCAGT 60.251 55.000 6.23 0.00 0.00 4.00
3150 3705 1.546029 GAAAGTTCACTCCATTGGGCC 59.454 52.381 2.09 0.00 0.00 5.80
3169 3724 3.189606 ACATCACATCCAAACTAGGGGA 58.810 45.455 0.00 0.00 37.64 4.81
3300 3855 5.359576 ACCAAACAGCAACAGAAGTATTTCA 59.640 36.000 0.44 0.00 35.70 2.69
3321 3876 4.021544 AGTTCAAAACACAAGCAGAAACCA 60.022 37.500 0.00 0.00 0.00 3.67
3322 3877 4.327087 CAGTTCAAAACACAAGCAGAAACC 59.673 41.667 0.00 0.00 0.00 3.27
3332 3887 4.196193 CCACCTAGACAGTTCAAAACACA 58.804 43.478 0.00 0.00 0.00 3.72
3373 3944 3.922640 GGCAAAAACCTGGCGCCA 61.923 61.111 30.59 30.59 42.50 5.69
3400 3978 0.957395 ACTGCCTGCAATCAAGACGG 60.957 55.000 0.00 0.00 0.00 4.79
3417 3995 1.831736 CCAGGAAATCGACCACCTACT 59.168 52.381 5.92 0.00 0.00 2.57
3429 4007 5.338300 GGCATCATACCAAAAACCAGGAAAT 60.338 40.000 0.00 0.00 0.00 2.17
3475 4264 2.031682 GGCTGCATAACAATTAGGCTCG 60.032 50.000 0.50 0.36 42.91 5.03
3482 4271 5.883503 CCAAAATTGGCTGCATAACAATT 57.116 34.783 14.11 14.11 44.18 2.32
3530 4320 6.772360 AAAAATTGGTTGGCAAAAGTTGAT 57.228 29.167 0.00 0.00 0.00 2.57
3531 4321 7.680588 GCATAAAAATTGGTTGGCAAAAGTTGA 60.681 33.333 0.00 0.00 0.00 3.18
3560 4350 4.339814 AGCGACTGTTGTTTTCCCAAATAA 59.660 37.500 0.00 0.00 0.00 1.40
3568 4358 5.569059 CCAATTGATAGCGACTGTTGTTTTC 59.431 40.000 7.12 0.00 0.00 2.29
3580 4370 2.571212 TGCCCTAACCAATTGATAGCG 58.429 47.619 7.12 3.15 0.00 4.26
3581 4371 3.954258 AGTTGCCCTAACCAATTGATAGC 59.046 43.478 7.12 1.75 40.24 2.97
3582 4372 4.580580 GGAGTTGCCCTAACCAATTGATAG 59.419 45.833 7.12 8.89 40.24 2.08
3583 4373 4.017958 TGGAGTTGCCCTAACCAATTGATA 60.018 41.667 7.12 0.00 40.24 2.15
3584 4374 3.245586 TGGAGTTGCCCTAACCAATTGAT 60.246 43.478 7.12 0.00 40.24 2.57
3585 4375 2.109128 TGGAGTTGCCCTAACCAATTGA 59.891 45.455 7.12 0.00 40.24 2.57
3612 4402 0.324645 GTCCATTTGGTGAGGCCCAT 60.325 55.000 0.00 0.00 33.60 4.00
3613 4403 1.076549 GTCCATTTGGTGAGGCCCA 59.923 57.895 0.00 0.00 36.04 5.36
3616 5410 0.038166 TGAGGTCCATTTGGTGAGGC 59.962 55.000 0.00 0.00 36.34 4.70
3639 5433 6.859420 AATTGGTTGGCAAAAGTTTATGAC 57.141 33.333 0.00 0.00 0.00 3.06
3791 5607 6.208402 TGCATTGCCTAACTAAGTTGAATTCA 59.792 34.615 3.38 3.38 0.00 2.57
3808 5626 3.397482 CTCCAGACTATAGTGCATTGCC 58.603 50.000 10.90 0.00 0.00 4.52
3809 5627 3.070159 TCCTCCAGACTATAGTGCATTGC 59.930 47.826 10.90 0.46 0.00 3.56
3810 5628 4.944619 TCCTCCAGACTATAGTGCATTG 57.055 45.455 10.90 3.50 0.00 2.82
3811 5629 4.202305 GCTTCCTCCAGACTATAGTGCATT 60.202 45.833 10.90 0.00 0.00 3.56
3812 5630 3.323403 GCTTCCTCCAGACTATAGTGCAT 59.677 47.826 10.90 0.00 0.00 3.96
3813 5631 2.695666 GCTTCCTCCAGACTATAGTGCA 59.304 50.000 10.90 0.00 0.00 4.57
3814 5632 2.287909 CGCTTCCTCCAGACTATAGTGC 60.288 54.545 10.90 3.09 0.00 4.40
3816 5634 3.117813 AGACGCTTCCTCCAGACTATAGT 60.118 47.826 4.68 4.68 0.00 2.12
3817 5635 3.482436 AGACGCTTCCTCCAGACTATAG 58.518 50.000 0.00 0.00 0.00 1.31
3818 5636 3.579534 AGACGCTTCCTCCAGACTATA 57.420 47.619 0.00 0.00 0.00 1.31
3819 5637 2.445682 AGACGCTTCCTCCAGACTAT 57.554 50.000 0.00 0.00 0.00 2.12
3826 5644 2.159028 AGCATCTTTAGACGCTTCCTCC 60.159 50.000 0.00 0.00 41.15 4.30
3829 5647 2.893637 TGAGCATCTTTAGACGCTTCC 58.106 47.619 1.54 0.00 44.23 3.46
3833 5651 2.346803 TGGTTGAGCATCTTTAGACGC 58.653 47.619 0.00 0.00 34.92 5.19
3838 5656 6.715280 AGAAAGATCTGGTTGAGCATCTTTA 58.285 36.000 0.00 0.00 42.83 1.85
3874 5692 1.541233 CCCGTCCAGTAGATGAATGCC 60.541 57.143 0.00 0.00 32.76 4.40
3896 5714 6.918572 TGATCCTATCAAGCTTCTAGAGCAGA 60.919 42.308 12.26 11.77 43.51 4.26
3900 5718 5.047377 GGGTGATCCTATCAAGCTTCTAGAG 60.047 48.000 12.26 4.15 41.69 2.43
3944 5762 1.375908 GTGTGATGGAGCTCGCCAA 60.376 57.895 7.83 0.00 42.16 4.52
3947 5765 0.179089 ATGAGTGTGATGGAGCTCGC 60.179 55.000 7.83 1.18 0.00 5.03
3951 5769 2.159184 TCGAGAATGAGTGTGATGGAGC 60.159 50.000 0.00 0.00 0.00 4.70
3961 5779 5.121298 CACAACATGATTGTCGAGAATGAGT 59.879 40.000 13.16 5.40 34.06 3.41
3967 5785 3.401033 ACCACAACATGATTGTCGAGA 57.599 42.857 0.00 0.00 34.06 4.04
3983 5821 1.335882 GCCACCCCTACCTCTACCAC 61.336 65.000 0.00 0.00 0.00 4.16
4059 5897 6.072112 AGCAAGATTTACAAACGTCATTGT 57.928 33.333 10.28 10.28 45.14 2.71
4065 5903 4.976116 GCTCAAAGCAAGATTTACAAACGT 59.024 37.500 0.00 0.00 41.89 3.99
4066 5904 4.382754 GGCTCAAAGCAAGATTTACAAACG 59.617 41.667 0.86 0.00 44.75 3.60
4071 5909 2.732282 GCCGGCTCAAAGCAAGATTTAC 60.732 50.000 22.15 0.00 44.75 2.01
4077 5916 3.752339 GGGCCGGCTCAAAGCAAG 61.752 66.667 28.56 0.00 44.75 4.01
4096 5935 3.620488 TGCCTAAAGTTTGATGCTAGGG 58.380 45.455 0.00 0.00 31.51 3.53
4127 5966 0.937304 GTGATATCGTGCATTGGCGT 59.063 50.000 0.00 0.00 45.35 5.68
4133 5972 4.252878 TGACAACTTGTGATATCGTGCAT 58.747 39.130 0.00 0.00 0.00 3.96
4138 5977 6.293081 GGGAATGATGACAACTTGTGATATCG 60.293 42.308 0.00 0.00 0.00 2.92
4142 5981 4.019174 GGGGAATGATGACAACTTGTGAT 58.981 43.478 0.00 0.00 0.00 3.06
4143 5982 3.420893 GGGGAATGATGACAACTTGTGA 58.579 45.455 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.