Multiple sequence alignment - TraesCS5D01G301300

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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 TraesCS5D01G301300 chr5D 100.000 2660 0 0 1 2660 398304003 398306662 0.000000e+00 4913.0
1 TraesCS5D01G301300 chr5D 90.711 1701 108 20 145 1823 398199826 398201498 0.000000e+00 2220.0
2 TraesCS5D01G301300 chr5D 98.333 120 2 0 2541 2660 449350038 449349919 7.460000e-51 211.0
3 TraesCS5D01G301300 chr5D 87.500 160 11 4 1 160 398199663 398199813 2.720000e-40 176.0
4 TraesCS5D01G301300 chr5B 94.847 1863 73 5 1 1843 478328025 478329884 0.000000e+00 2887.0
5 TraesCS5D01G301300 chr5B 77.513 1134 174 41 219 1305 478373598 478374697 8.140000e-170 606.0
6 TraesCS5D01G301300 chr5B 80.294 477 60 22 1355 1817 478374707 478375163 1.970000e-86 329.0
7 TraesCS5D01G301300 chr5B 94.737 57 3 0 1843 1899 629771976 629771920 3.650000e-14 89.8
8 TraesCS5D01G301300 chr5A 90.677 1727 124 13 145 1843 503324948 503326665 0.000000e+00 2263.0
9 TraesCS5D01G301300 chr5A 91.908 1174 54 11 1 1144 503255423 503256585 0.000000e+00 1604.0
10 TraesCS5D01G301300 chr5A 96.464 707 23 2 1843 2548 542543252 542542547 0.000000e+00 1166.0
11 TraesCS5D01G301300 chr5A 89.698 728 48 7 1834 2548 469299230 469299943 0.000000e+00 904.0
12 TraesCS5D01G301300 chr5A 88.125 160 10 3 1 160 503324784 503324934 5.850000e-42 182.0
13 TraesCS5D01G301300 chr5A 92.857 112 8 0 2549 2660 576293272 576293161 2.120000e-36 163.0
14 TraesCS5D01G301300 chr5A 90.323 124 11 1 2537 2660 2357742 2357620 7.620000e-36 161.0
15 TraesCS5D01G301300 chr6A 96.192 709 19 6 1843 2548 12880672 12879969 0.000000e+00 1153.0
16 TraesCS5D01G301300 chr6A 89.592 490 35 6 2061 2548 606596455 606596930 2.260000e-170 608.0
17 TraesCS5D01G301300 chr6A 93.662 142 9 0 1834 1975 606595994 606596135 2.070000e-51 213.0
18 TraesCS5D01G301300 chr6A 91.525 118 10 0 2543 2660 3648223 3648340 2.120000e-36 163.0
19 TraesCS5D01G301300 chr2A 88.462 728 57 6 1834 2548 4670469 4671182 0.000000e+00 854.0
20 TraesCS5D01G301300 chr6D 97.664 428 8 2 1894 2320 463771102 463771528 0.000000e+00 734.0
21 TraesCS5D01G301300 chr6D 96.825 63 2 0 1834 1896 463771067 463771129 3.620000e-19 106.0
22 TraesCS5D01G301300 chr7B 88.831 573 39 9 1988 2548 204157801 204158360 0.000000e+00 680.0
23 TraesCS5D01G301300 chr1B 88.328 574 38 11 1988 2548 664597321 664597878 0.000000e+00 662.0
24 TraesCS5D01G301300 chr1B 88.764 534 33 10 1988 2507 646680100 646679580 1.740000e-176 628.0
25 TraesCS5D01G301300 chr1B 93.043 115 8 0 2546 2660 576887 576773 4.550000e-38 169.0
26 TraesCS5D01G301300 chr1B 92.857 112 8 0 2549 2660 231337307 231337196 2.120000e-36 163.0
27 TraesCS5D01G301300 chr1B 84.211 133 3 5 1843 1975 646680517 646680403 2.160000e-21 113.0
28 TraesCS5D01G301300 chr3B 88.577 534 34 13 1988 2507 554032551 554033071 8.090000e-175 623.0
29 TraesCS5D01G301300 chr2B 88.889 378 26 3 1988 2352 797244439 797244065 4.040000e-123 451.0
30 TraesCS5D01G301300 chr6B 91.270 252 16 5 2293 2541 13337584 13337832 3.280000e-89 339.0
31 TraesCS5D01G301300 chr6B 90.909 253 16 6 2293 2541 13225760 13226009 1.530000e-87 333.0
32 TraesCS5D01G301300 chr6B 90.909 253 16 6 2293 2541 13270380 13270629 1.530000e-87 333.0
33 TraesCS5D01G301300 chr6B 95.536 112 5 0 1865 1976 6502001 6501890 2.100000e-41 180.0
34 TraesCS5D01G301300 chrUn 90.909 253 16 6 2293 2541 445608969 445609218 1.530000e-87 333.0
35 TraesCS5D01G301300 chr7A 92.857 112 8 0 2549 2660 46179551 46179440 2.120000e-36 163.0
36 TraesCS5D01G301300 chr7A 90.323 124 11 1 2537 2660 116543228 116543106 7.620000e-36 161.0
37 TraesCS5D01G301300 chr4A 90.323 124 11 1 2537 2660 715964252 715964374 7.620000e-36 161.0
38 TraesCS5D01G301300 chr4A 84.507 142 4 5 1834 1975 702626957 702627080 1.000000e-24 124.0


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 TraesCS5D01G301300 chr5D 398304003 398306662 2659 False 4913.0 4913 100.0000 1 2660 1 chr5D.!!$F1 2659
1 TraesCS5D01G301300 chr5D 398199663 398201498 1835 False 1198.0 2220 89.1055 1 1823 2 chr5D.!!$F2 1822
2 TraesCS5D01G301300 chr5B 478328025 478329884 1859 False 2887.0 2887 94.8470 1 1843 1 chr5B.!!$F1 1842
3 TraesCS5D01G301300 chr5B 478373598 478375163 1565 False 467.5 606 78.9035 219 1817 2 chr5B.!!$F2 1598
4 TraesCS5D01G301300 chr5A 503255423 503256585 1162 False 1604.0 1604 91.9080 1 1144 1 chr5A.!!$F2 1143
5 TraesCS5D01G301300 chr5A 503324784 503326665 1881 False 1222.5 2263 89.4010 1 1843 2 chr5A.!!$F3 1842
6 TraesCS5D01G301300 chr5A 542542547 542543252 705 True 1166.0 1166 96.4640 1843 2548 1 chr5A.!!$R2 705
7 TraesCS5D01G301300 chr5A 469299230 469299943 713 False 904.0 904 89.6980 1834 2548 1 chr5A.!!$F1 714
8 TraesCS5D01G301300 chr6A 12879969 12880672 703 True 1153.0 1153 96.1920 1843 2548 1 chr6A.!!$R1 705
9 TraesCS5D01G301300 chr6A 606595994 606596930 936 False 410.5 608 91.6270 1834 2548 2 chr6A.!!$F2 714
10 TraesCS5D01G301300 chr2A 4670469 4671182 713 False 854.0 854 88.4620 1834 2548 1 chr2A.!!$F1 714
11 TraesCS5D01G301300 chr7B 204157801 204158360 559 False 680.0 680 88.8310 1988 2548 1 chr7B.!!$F1 560
12 TraesCS5D01G301300 chr1B 664597321 664597878 557 False 662.0 662 88.3280 1988 2548 1 chr1B.!!$F1 560
13 TraesCS5D01G301300 chr1B 646679580 646680517 937 True 370.5 628 86.4875 1843 2507 2 chr1B.!!$R3 664
14 TraesCS5D01G301300 chr3B 554032551 554033071 520 False 623.0 623 88.5770 1988 2507 1 chr3B.!!$F1 519

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
114 115 0.320374 AGAATCACGAAACCAGCCGA 59.680 50.0 0.0 0.0 0.00 5.54 F
1127 1254 0.322277 AAGGTGGCTGAGACATGCAG 60.322 55.0 0.0 0.0 36.47 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1577 0.249120 TCGTCCACCTCGCAATCATT 59.751 50.0 0.0 0.0 0.00 2.57 R
2565 3194 0.175073 CCCAGTCGGTGGTAACTAGC 59.825 60.0 4.3 0.0 46.37 3.42 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
114 115 0.320374 AGAATCACGAAACCAGCCGA 59.680 50.000 0.00 0.00 0.00 5.54
127 128 1.450848 AGCCGACACATCCATGCAG 60.451 57.895 0.00 0.00 0.00 4.41
170 226 5.601583 TGCCGATACTTTAACATGGACTA 57.398 39.130 0.00 0.00 0.00 2.59
336 404 2.672874 CGACGCCATGAGAAAAGATTGA 59.327 45.455 0.00 0.00 0.00 2.57
397 465 1.787847 CACGTTTGGATGGACGAGC 59.212 57.895 2.69 0.00 41.53 5.03
460 534 2.285660 GGCGTCTGCGATTTAACTAAGC 60.286 50.000 0.00 0.00 44.10 3.09
489 563 1.068417 CGGGAATTCGGTATCGGCA 59.932 57.895 0.00 0.00 36.95 5.69
665 763 5.377478 TGAGATCGTAGAGAGCCAATCTAA 58.623 41.667 0.00 0.00 43.63 2.10
689 787 2.380064 TGGGGCATGTGTCTTTTCTT 57.620 45.000 0.00 0.00 0.00 2.52
896 1014 3.009723 CGGGACATGAGCAAAGTTGTAT 58.990 45.455 0.00 0.00 0.00 2.29
962 1088 1.931007 GCCTCAGGAGAAGGCCCATT 61.931 60.000 0.00 0.00 42.52 3.16
1065 1192 2.328099 GCAGTTTGGCCACCTCTCG 61.328 63.158 3.88 1.05 0.00 4.04
1127 1254 0.322277 AAGGTGGCTGAGACATGCAG 60.322 55.000 0.00 0.00 36.47 4.41
1215 1342 4.021925 GGCGCCTTCTCCCACAGT 62.022 66.667 22.15 0.00 0.00 3.55
1431 1558 3.054434 ACCCCATCTTCAATGACGATGAA 60.054 43.478 25.27 2.96 39.61 2.57
1432 1559 3.313526 CCCCATCTTCAATGACGATGAAC 59.686 47.826 25.27 0.00 39.61 3.18
1450 1577 4.072839 TGAACACAACTGTTGTTACACCA 58.927 39.130 22.66 13.28 43.23 4.17
1452 1579 5.184096 TGAACACAACTGTTGTTACACCAAT 59.816 36.000 22.66 4.16 43.23 3.16
1599 1738 5.106712 GGAGTTCAGCATTGACAACGAAATA 60.107 40.000 0.00 0.00 31.71 1.40
1722 1861 1.003545 TGAAGCGTACGTATACCGAGC 60.004 52.381 17.90 0.00 40.70 5.03
1727 1866 2.413112 GCGTACGTATACCGAGCTATCA 59.587 50.000 17.90 0.00 40.70 2.15
1784 1924 7.076983 GTGAGCTAGACTTGTATACCGTATTC 58.923 42.308 0.00 0.00 0.00 1.75
2557 3186 8.980143 TCCTTACTCAACTTTTGAAAAACTTG 57.020 30.769 0.00 0.00 39.58 3.16
2558 3187 8.798402 TCCTTACTCAACTTTTGAAAAACTTGA 58.202 29.630 9.03 9.03 39.58 3.02
2559 3188 9.076596 CCTTACTCAACTTTTGAAAAACTTGAG 57.923 33.333 23.19 23.19 44.84 3.02
2562 3191 7.281991 CTCAACTTTTGAAAAACTTGAGTGG 57.718 36.000 19.73 2.76 40.28 4.00
2563 3192 6.162777 TCAACTTTTGAAAAACTTGAGTGGG 58.837 36.000 6.41 0.00 36.59 4.61
2564 3193 5.738619 ACTTTTGAAAAACTTGAGTGGGT 57.261 34.783 0.00 0.00 0.00 4.51
2565 3194 5.478407 ACTTTTGAAAAACTTGAGTGGGTG 58.522 37.500 0.00 0.00 0.00 4.61
2566 3195 3.518634 TTGAAAAACTTGAGTGGGTGC 57.481 42.857 0.00 0.00 0.00 5.01
2567 3196 2.733956 TGAAAAACTTGAGTGGGTGCT 58.266 42.857 0.00 0.00 0.00 4.40
2568 3197 3.892284 TGAAAAACTTGAGTGGGTGCTA 58.108 40.909 0.00 0.00 0.00 3.49
2569 3198 3.882888 TGAAAAACTTGAGTGGGTGCTAG 59.117 43.478 0.00 0.00 0.00 3.42
2570 3199 3.577805 AAAACTTGAGTGGGTGCTAGT 57.422 42.857 0.00 0.00 0.00 2.57
2571 3200 3.577805 AAACTTGAGTGGGTGCTAGTT 57.422 42.857 0.00 0.00 32.84 2.24
2572 3201 4.699925 AAACTTGAGTGGGTGCTAGTTA 57.300 40.909 0.00 0.00 31.61 2.24
2573 3202 3.679824 ACTTGAGTGGGTGCTAGTTAC 57.320 47.619 0.00 0.00 0.00 2.50
2574 3203 2.302157 ACTTGAGTGGGTGCTAGTTACC 59.698 50.000 9.15 9.15 37.48 2.85
2575 3204 2.018355 TGAGTGGGTGCTAGTTACCA 57.982 50.000 16.76 8.50 40.03 3.25
2580 3209 3.430779 GGTGCTAGTTACCACCGAC 57.569 57.895 11.90 0.00 41.75 4.79
2581 3210 0.893447 GGTGCTAGTTACCACCGACT 59.107 55.000 11.90 0.00 41.75 4.18
2582 3211 1.403780 GGTGCTAGTTACCACCGACTG 60.404 57.143 11.90 0.00 41.75 3.51
2584 3213 0.175073 GCTAGTTACCACCGACTGGG 59.825 60.000 4.34 0.00 45.78 4.45
2585 3214 1.843368 CTAGTTACCACCGACTGGGA 58.157 55.000 4.34 0.00 45.78 4.37
2586 3215 2.173519 CTAGTTACCACCGACTGGGAA 58.826 52.381 4.34 0.00 45.78 3.97
2587 3216 1.652947 AGTTACCACCGACTGGGAAT 58.347 50.000 0.50 0.00 45.49 3.01
2588 3217 1.982958 AGTTACCACCGACTGGGAATT 59.017 47.619 0.50 0.00 45.49 2.17
2589 3218 2.374170 AGTTACCACCGACTGGGAATTT 59.626 45.455 0.50 0.00 45.49 1.82
2590 3219 3.583966 AGTTACCACCGACTGGGAATTTA 59.416 43.478 0.50 0.00 45.49 1.40
2591 3220 4.041938 AGTTACCACCGACTGGGAATTTAA 59.958 41.667 0.50 0.00 45.49 1.52
2592 3221 3.512219 ACCACCGACTGGGAATTTAAA 57.488 42.857 4.34 0.00 45.78 1.52
2593 3222 4.042271 ACCACCGACTGGGAATTTAAAT 57.958 40.909 0.00 0.00 45.78 1.40
2594 3223 5.182169 ACCACCGACTGGGAATTTAAATA 57.818 39.130 0.01 0.00 45.78 1.40
2595 3224 4.945543 ACCACCGACTGGGAATTTAAATAC 59.054 41.667 0.01 0.00 45.78 1.89
2596 3225 4.337274 CCACCGACTGGGAATTTAAATACC 59.663 45.833 12.62 12.62 40.75 2.73
2597 3226 4.337274 CACCGACTGGGAATTTAAATACCC 59.663 45.833 15.47 12.70 40.75 3.69
2599 3228 4.337274 CCGACTGGGAATTTAAATACCCAC 59.663 45.833 16.69 6.29 46.04 4.61
2600 3229 5.190677 CGACTGGGAATTTAAATACCCACT 58.809 41.667 16.69 0.00 46.04 4.00
2601 3230 6.350906 CGACTGGGAATTTAAATACCCACTA 58.649 40.000 16.69 6.25 46.04 2.74
2602 3231 6.482308 CGACTGGGAATTTAAATACCCACTAG 59.518 42.308 16.69 13.87 46.04 2.57
2603 3232 6.127101 ACTGGGAATTTAAATACCCACTAGC 58.873 40.000 16.69 4.76 46.04 3.42
2604 3233 5.127491 TGGGAATTTAAATACCCACTAGCG 58.873 41.667 16.69 0.00 46.04 4.26
2605 3234 5.128205 GGGAATTTAAATACCCACTAGCGT 58.872 41.667 16.69 0.00 41.72 5.07
2606 3235 5.237996 GGGAATTTAAATACCCACTAGCGTC 59.762 44.000 16.69 2.15 41.72 5.19
2607 3236 5.818857 GGAATTTAAATACCCACTAGCGTCA 59.181 40.000 0.01 0.00 0.00 4.35
2608 3237 6.018180 GGAATTTAAATACCCACTAGCGTCAG 60.018 42.308 0.01 0.00 0.00 3.51
2609 3238 5.410355 TTTAAATACCCACTAGCGTCAGT 57.590 39.130 0.00 0.00 0.00 3.41
2610 3239 2.961526 AATACCCACTAGCGTCAGTG 57.038 50.000 10.51 10.51 44.60 3.66
2611 3240 0.460311 ATACCCACTAGCGTCAGTGC 59.540 55.000 11.66 0.00 43.82 4.40
2612 3241 1.929806 TACCCACTAGCGTCAGTGCG 61.930 60.000 11.66 7.18 43.82 5.34
2613 3242 2.507102 CCACTAGCGTCAGTGCGG 60.507 66.667 11.66 0.00 43.82 5.69
2614 3243 2.507102 CACTAGCGTCAGTGCGGG 60.507 66.667 5.75 0.00 39.54 6.13
2615 3244 4.436998 ACTAGCGTCAGTGCGGGC 62.437 66.667 8.63 1.25 40.67 6.13
2616 3245 4.135153 CTAGCGTCAGTGCGGGCT 62.135 66.667 8.63 8.00 40.67 5.19
2617 3246 4.129737 TAGCGTCAGTGCGGGCTC 62.130 66.667 5.80 0.00 40.67 4.70
2621 3250 3.695606 GTCAGTGCGGGCTCTGGA 61.696 66.667 19.12 6.78 37.91 3.86
2622 3251 3.385384 TCAGTGCGGGCTCTGGAG 61.385 66.667 19.12 0.00 37.91 3.86
2623 3252 3.385384 CAGTGCGGGCTCTGGAGA 61.385 66.667 13.41 0.00 34.88 3.71
2624 3253 3.073735 AGTGCGGGCTCTGGAGAG 61.074 66.667 1.35 0.00 44.75 3.20
2625 3254 3.071206 GTGCGGGCTCTGGAGAGA 61.071 66.667 7.89 0.00 44.74 3.10
2626 3255 2.283894 TGCGGGCTCTGGAGAGAA 60.284 61.111 7.89 0.00 44.74 2.87
2627 3256 1.687146 TGCGGGCTCTGGAGAGAAT 60.687 57.895 7.89 0.00 44.74 2.40
2628 3257 1.267574 TGCGGGCTCTGGAGAGAATT 61.268 55.000 7.89 0.00 44.74 2.17
2629 3258 0.813210 GCGGGCTCTGGAGAGAATTG 60.813 60.000 7.89 0.00 44.74 2.32
2630 3259 0.826715 CGGGCTCTGGAGAGAATTGA 59.173 55.000 7.89 0.00 44.74 2.57
2631 3260 1.202510 CGGGCTCTGGAGAGAATTGAG 60.203 57.143 7.89 0.00 44.74 3.02
2632 3261 1.140652 GGGCTCTGGAGAGAATTGAGG 59.859 57.143 7.89 0.00 44.74 3.86
2633 3262 1.474855 GGCTCTGGAGAGAATTGAGGC 60.475 57.143 7.89 0.00 44.74 4.70
2634 3263 1.474855 GCTCTGGAGAGAATTGAGGCC 60.475 57.143 7.89 0.00 44.74 5.19
2635 3264 2.117865 CTCTGGAGAGAATTGAGGCCT 58.882 52.381 3.86 3.86 44.74 5.19
2636 3265 2.504996 CTCTGGAGAGAATTGAGGCCTT 59.495 50.000 6.77 0.00 44.74 4.35
2637 3266 3.708631 CTCTGGAGAGAATTGAGGCCTTA 59.291 47.826 6.77 0.00 44.74 2.69
2638 3267 4.302067 TCTGGAGAGAATTGAGGCCTTAT 58.698 43.478 6.77 0.08 0.00 1.73
2639 3268 4.346418 TCTGGAGAGAATTGAGGCCTTATC 59.654 45.833 6.77 3.10 0.00 1.75
2640 3269 3.070159 TGGAGAGAATTGAGGCCTTATCG 59.930 47.826 6.77 0.00 0.00 2.92
2641 3270 3.556004 GGAGAGAATTGAGGCCTTATCGG 60.556 52.174 6.77 0.00 0.00 4.18
2642 3271 3.309296 AGAGAATTGAGGCCTTATCGGA 58.691 45.455 6.77 0.00 33.16 4.55
2643 3272 3.906846 AGAGAATTGAGGCCTTATCGGAT 59.093 43.478 6.77 0.00 33.16 4.18
2644 3273 4.020662 AGAGAATTGAGGCCTTATCGGATC 60.021 45.833 6.77 0.27 33.16 3.36
2645 3274 3.648067 AGAATTGAGGCCTTATCGGATCA 59.352 43.478 6.77 0.00 33.16 2.92
2646 3275 4.288105 AGAATTGAGGCCTTATCGGATCAT 59.712 41.667 6.77 0.00 32.22 2.45
2647 3276 3.407424 TTGAGGCCTTATCGGATCATG 57.593 47.619 6.77 0.00 32.22 3.07
2648 3277 1.002430 TGAGGCCTTATCGGATCATGC 59.998 52.381 6.77 0.00 33.16 4.06
2649 3278 1.277557 GAGGCCTTATCGGATCATGCT 59.722 52.381 6.77 0.00 33.16 3.79
2650 3279 1.277557 AGGCCTTATCGGATCATGCTC 59.722 52.381 0.00 0.00 33.16 4.26
2651 3280 1.677217 GGCCTTATCGGATCATGCTCC 60.677 57.143 5.46 5.46 33.16 4.70
2652 3281 1.002430 GCCTTATCGGATCATGCTCCA 59.998 52.381 15.63 3.65 34.78 3.86
2653 3282 2.355513 GCCTTATCGGATCATGCTCCAT 60.356 50.000 15.63 10.15 34.78 3.41
2654 3283 3.871463 GCCTTATCGGATCATGCTCCATT 60.871 47.826 15.63 4.69 34.78 3.16
2655 3284 3.688185 CCTTATCGGATCATGCTCCATTG 59.312 47.826 15.63 0.00 34.78 2.82
2656 3285 1.531423 ATCGGATCATGCTCCATTGC 58.469 50.000 15.63 0.00 34.78 3.56
2657 3286 0.471191 TCGGATCATGCTCCATTGCT 59.529 50.000 15.63 0.00 34.78 3.91
2658 3287 1.134007 TCGGATCATGCTCCATTGCTT 60.134 47.619 15.63 0.00 34.78 3.91
2659 3288 2.104622 TCGGATCATGCTCCATTGCTTA 59.895 45.455 15.63 0.00 34.78 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 5.332707 GCAAGATATTTTCCGTTGAAGTCC 58.667 41.667 0.00 0.00 0.00 3.85
133 134 4.552166 ATCGGCAAGATATTTTCCGTTG 57.448 40.909 9.50 0.00 40.81 4.10
170 226 2.325082 GGCGGATCGTGTTTGCAGT 61.325 57.895 0.00 0.00 0.00 4.40
336 404 1.076485 GCATGGGTGGGAGCTTCAT 60.076 57.895 0.00 0.00 0.00 2.57
389 457 0.318441 CTTCTGGTTCTGCTCGTCCA 59.682 55.000 0.00 0.00 0.00 4.02
397 465 0.795085 CGCAGCTTCTTCTGGTTCTG 59.205 55.000 0.00 0.00 34.74 3.02
460 534 1.683790 GAATTCCCGTGTGCGTCTCG 61.684 60.000 0.00 0.00 36.15 4.04
489 563 1.244019 GCACCCGGAGAATTTGCAGT 61.244 55.000 0.73 0.00 33.24 4.40
665 763 0.188342 AAGACACATGCCCCAAGGTT 59.812 50.000 0.00 0.00 34.57 3.50
840 958 3.969976 TCTAGCTCTCCCAAAGCATATGT 59.030 43.478 4.29 0.00 42.35 2.29
877 995 3.191162 TGCATACAACTTTGCTCATGTCC 59.809 43.478 0.00 0.00 39.60 4.02
914 1032 9.449719 CAAGGTTGTATTTATAGTGAGGAACTT 57.550 33.333 0.00 0.00 41.55 2.66
922 1040 6.357367 AGGCTCCAAGGTTGTATTTATAGTG 58.643 40.000 0.00 0.00 0.00 2.74
962 1088 6.656902 AGATGAGGCAAGATGTTTCAGATTA 58.343 36.000 0.00 0.00 0.00 1.75
1065 1192 2.031333 GCCAATCTTCATCTTCGATGCC 60.031 50.000 0.00 0.00 0.00 4.40
1118 1245 1.421268 TGGTCTTGTTCCTGCATGTCT 59.579 47.619 0.00 0.00 0.00 3.41
1127 1254 3.655481 CCACGCTGGTCTTGTTCC 58.345 61.111 0.00 0.00 31.35 3.62
1215 1342 3.826221 GCCACAAGCGCATGGATA 58.174 55.556 24.60 0.00 38.34 2.59
1292 1419 2.125912 CTGGCGTCTTCTGGACCG 60.126 66.667 0.00 0.00 41.64 4.79
1353 1480 1.522668 TCCCTTGATCAAACAGTGCG 58.477 50.000 9.88 0.00 0.00 5.34
1431 1558 4.702612 TCATTGGTGTAACAACAGTTGTGT 59.297 37.500 19.84 11.95 44.59 3.72
1432 1559 5.242069 TCATTGGTGTAACAACAGTTGTG 57.758 39.130 19.84 4.22 44.59 3.33
1450 1577 0.249120 TCGTCCACCTCGCAATCATT 59.751 50.000 0.00 0.00 0.00 2.57
1452 1579 1.080093 GTCGTCCACCTCGCAATCA 60.080 57.895 0.00 0.00 0.00 2.57
1554 1693 0.834687 AACCCTGTGCCTCTCGGTTA 60.835 55.000 0.00 0.00 35.07 2.85
1722 1861 6.207025 ACCGTACCTCTATTAGCAACTGATAG 59.793 42.308 1.10 1.10 33.23 2.08
1727 1866 5.688807 TCTACCGTACCTCTATTAGCAACT 58.311 41.667 0.00 0.00 0.00 3.16
1784 1924 3.135530 CCATCTCCTTTTCTCCCTACCTG 59.864 52.174 0.00 0.00 0.00 4.00
2128 2750 2.562738 GGGTTGACATTTTCCCTCCTTG 59.437 50.000 0.00 0.00 37.18 3.61
2543 3172 4.329801 GCACCCACTCAAGTTTTTCAAAAG 59.670 41.667 0.00 0.00 0.00 2.27
2548 3177 3.883489 ACTAGCACCCACTCAAGTTTTTC 59.117 43.478 0.00 0.00 0.00 2.29
2549 3178 3.898482 ACTAGCACCCACTCAAGTTTTT 58.102 40.909 0.00 0.00 0.00 1.94
2550 3179 3.577805 ACTAGCACCCACTCAAGTTTT 57.422 42.857 0.00 0.00 0.00 2.43
2551 3180 3.577805 AACTAGCACCCACTCAAGTTT 57.422 42.857 0.00 0.00 0.00 2.66
2552 3181 3.244457 GGTAACTAGCACCCACTCAAGTT 60.244 47.826 3.18 0.00 0.00 2.66
2553 3182 2.302157 GGTAACTAGCACCCACTCAAGT 59.698 50.000 3.18 0.00 0.00 3.16
2554 3183 2.301870 TGGTAACTAGCACCCACTCAAG 59.698 50.000 10.76 0.00 34.99 3.02
2555 3184 2.038033 GTGGTAACTAGCACCCACTCAA 59.962 50.000 14.77 0.00 46.01 3.02
2556 3185 1.621814 GTGGTAACTAGCACCCACTCA 59.378 52.381 14.77 0.00 46.01 3.41
2557 3186 2.381725 GTGGTAACTAGCACCCACTC 57.618 55.000 14.77 1.21 46.01 3.51
2564 3193 0.892755 CCAGTCGGTGGTAACTAGCA 59.107 55.000 0.00 0.00 42.17 3.49
2565 3194 0.175073 CCCAGTCGGTGGTAACTAGC 59.825 60.000 4.30 0.00 46.37 3.42
2566 3195 1.843368 TCCCAGTCGGTGGTAACTAG 58.157 55.000 4.30 0.00 46.37 2.57
2567 3196 2.307496 TTCCCAGTCGGTGGTAACTA 57.693 50.000 4.30 0.00 46.37 2.24
2568 3197 1.652947 ATTCCCAGTCGGTGGTAACT 58.347 50.000 4.30 0.00 46.37 2.24
2569 3198 2.484742 AATTCCCAGTCGGTGGTAAC 57.515 50.000 4.30 0.00 46.37 2.50
2570 3199 4.637387 TTAAATTCCCAGTCGGTGGTAA 57.363 40.909 4.30 0.00 46.37 2.85
2571 3200 4.637387 TTTAAATTCCCAGTCGGTGGTA 57.363 40.909 4.30 0.00 46.37 3.25
2572 3201 3.512219 TTTAAATTCCCAGTCGGTGGT 57.488 42.857 4.30 0.00 46.37 4.16
2573 3202 6.666227 GGGTATTTAAATTCCCAGTCGGTGG 61.666 48.000 28.81 0.00 43.40 4.61
2574 3203 4.337274 GGGTATTTAAATTCCCAGTCGGTG 59.663 45.833 28.81 0.00 43.40 4.94
2575 3204 4.529897 GGGTATTTAAATTCCCAGTCGGT 58.470 43.478 28.81 0.00 43.40 4.69
2582 3211 5.128205 ACGCTAGTGGGTATTTAAATTCCC 58.872 41.667 27.69 27.69 43.99 3.97
2583 3212 5.818857 TGACGCTAGTGGGTATTTAAATTCC 59.181 40.000 13.90 13.90 39.55 3.01
2584 3213 6.537660 ACTGACGCTAGTGGGTATTTAAATTC 59.462 38.462 5.91 0.78 39.55 2.17
2585 3214 6.315393 CACTGACGCTAGTGGGTATTTAAATT 59.685 38.462 5.91 0.00 43.35 1.82
2586 3215 5.815740 CACTGACGCTAGTGGGTATTTAAAT 59.184 40.000 8.42 5.89 43.35 1.40
2587 3216 5.172934 CACTGACGCTAGTGGGTATTTAAA 58.827 41.667 8.42 0.00 43.35 1.52
2588 3217 4.751060 CACTGACGCTAGTGGGTATTTAA 58.249 43.478 8.42 0.00 43.35 1.52
2589 3218 3.429822 GCACTGACGCTAGTGGGTATTTA 60.430 47.826 17.94 0.00 46.32 1.40
2590 3219 2.677037 GCACTGACGCTAGTGGGTATTT 60.677 50.000 17.94 0.00 46.32 1.40
2591 3220 1.134788 GCACTGACGCTAGTGGGTATT 60.135 52.381 17.94 0.00 46.32 1.89
2592 3221 0.460311 GCACTGACGCTAGTGGGTAT 59.540 55.000 17.94 0.00 46.32 2.73
2593 3222 1.888018 GCACTGACGCTAGTGGGTA 59.112 57.895 17.94 0.00 46.32 3.69
2594 3223 2.657237 GCACTGACGCTAGTGGGT 59.343 61.111 17.94 0.85 46.32 4.51
2596 3225 2.507102 CCGCACTGACGCTAGTGG 60.507 66.667 17.94 10.01 46.32 4.00
2598 3227 4.436998 GCCCGCACTGACGCTAGT 62.437 66.667 0.00 0.00 0.00 2.57
2599 3228 4.135153 AGCCCGCACTGACGCTAG 62.135 66.667 0.00 0.00 0.00 3.42
2600 3229 4.129737 GAGCCCGCACTGACGCTA 62.130 66.667 0.00 0.00 0.00 4.26
2604 3233 3.655810 CTCCAGAGCCCGCACTGAC 62.656 68.421 14.65 0.00 36.90 3.51
2605 3234 3.385384 CTCCAGAGCCCGCACTGA 61.385 66.667 14.65 2.00 36.90 3.41
2606 3235 3.368190 CTCTCCAGAGCCCGCACTG 62.368 68.421 7.10 7.10 35.13 3.66
2607 3236 3.073735 CTCTCCAGAGCCCGCACT 61.074 66.667 0.00 0.00 35.13 4.40
2608 3237 1.965754 ATTCTCTCCAGAGCCCGCAC 61.966 60.000 0.00 0.00 41.80 5.34
2609 3238 1.267574 AATTCTCTCCAGAGCCCGCA 61.268 55.000 0.00 0.00 41.80 5.69
2610 3239 0.813210 CAATTCTCTCCAGAGCCCGC 60.813 60.000 0.00 0.00 41.80 6.13
2611 3240 0.826715 TCAATTCTCTCCAGAGCCCG 59.173 55.000 0.00 0.00 41.80 6.13
2612 3241 1.140652 CCTCAATTCTCTCCAGAGCCC 59.859 57.143 0.00 0.00 41.80 5.19
2613 3242 1.474855 GCCTCAATTCTCTCCAGAGCC 60.475 57.143 0.00 0.00 41.80 4.70
2614 3243 1.474855 GGCCTCAATTCTCTCCAGAGC 60.475 57.143 0.00 0.00 41.80 4.09
2615 3244 2.117865 AGGCCTCAATTCTCTCCAGAG 58.882 52.381 0.00 0.00 43.36 3.35
2616 3245 2.260639 AGGCCTCAATTCTCTCCAGA 57.739 50.000 0.00 0.00 0.00 3.86
2617 3246 4.640364 GATAAGGCCTCAATTCTCTCCAG 58.360 47.826 5.23 0.00 0.00 3.86
2618 3247 3.070159 CGATAAGGCCTCAATTCTCTCCA 59.930 47.826 5.23 0.00 0.00 3.86
2619 3248 3.556004 CCGATAAGGCCTCAATTCTCTCC 60.556 52.174 5.23 0.00 0.00 3.71
2620 3249 3.322254 TCCGATAAGGCCTCAATTCTCTC 59.678 47.826 5.23 0.00 40.77 3.20
2621 3250 3.309296 TCCGATAAGGCCTCAATTCTCT 58.691 45.455 5.23 0.00 40.77 3.10
2622 3251 3.753294 TCCGATAAGGCCTCAATTCTC 57.247 47.619 5.23 0.00 40.77 2.87
2623 3252 3.648067 TGATCCGATAAGGCCTCAATTCT 59.352 43.478 5.23 0.00 40.77 2.40
2624 3253 4.008074 TGATCCGATAAGGCCTCAATTC 57.992 45.455 5.23 0.00 40.77 2.17
2625 3254 4.330250 CATGATCCGATAAGGCCTCAATT 58.670 43.478 5.23 0.00 40.77 2.32
2626 3255 3.871463 GCATGATCCGATAAGGCCTCAAT 60.871 47.826 5.23 2.18 40.77 2.57
2627 3256 2.550855 GCATGATCCGATAAGGCCTCAA 60.551 50.000 5.23 0.00 40.77 3.02
2628 3257 1.002430 GCATGATCCGATAAGGCCTCA 59.998 52.381 5.23 0.00 40.77 3.86
2629 3258 1.277557 AGCATGATCCGATAAGGCCTC 59.722 52.381 5.23 0.00 40.77 4.70
2630 3259 1.277557 GAGCATGATCCGATAAGGCCT 59.722 52.381 0.00 0.00 40.77 5.19
2631 3260 1.677217 GGAGCATGATCCGATAAGGCC 60.677 57.143 15.42 0.00 40.77 5.19
2632 3261 1.002430 TGGAGCATGATCCGATAAGGC 59.998 52.381 24.26 0.00 42.77 4.35
2633 3262 3.623906 ATGGAGCATGATCCGATAAGG 57.376 47.619 24.26 0.00 42.77 2.69
2634 3263 3.126514 GCAATGGAGCATGATCCGATAAG 59.873 47.826 24.26 13.20 42.77 1.73
2635 3264 3.076621 GCAATGGAGCATGATCCGATAA 58.923 45.455 24.26 7.88 42.77 1.75
2636 3265 2.303890 AGCAATGGAGCATGATCCGATA 59.696 45.455 24.26 8.26 42.77 2.92
2637 3266 1.073444 AGCAATGGAGCATGATCCGAT 59.927 47.619 24.26 15.66 42.77 4.18
2638 3267 0.471191 AGCAATGGAGCATGATCCGA 59.529 50.000 24.26 14.11 42.77 4.55
2639 3268 1.315690 AAGCAATGGAGCATGATCCG 58.684 50.000 24.26 11.88 42.77 4.18


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

AutoCloner maintained by Alex Coulton.