Multiple sequence alignment - TraesCS7A01G327400

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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 TraesCS7A01G327400 chr7A 100.000 2633 0 0 1 2633 475803358 475805990 0.000000e+00 4863
1 TraesCS7A01G327400 chr7A 84.956 113 15 2 2013 2125 638507716 638507826 2.140000e-21 113
2 TraesCS7A01G327400 chr7A 86.538 104 8 4 2365 2462 671955099 671954996 2.770000e-20 110
3 TraesCS7A01G327400 chr7D 92.052 1686 99 15 281 1949 413727971 413729638 0.000000e+00 2338
4 TraesCS7A01G327400 chr7D 89.655 493 42 4 2041 2529 413730006 413730493 1.040000e-173 619
5 TraesCS7A01G327400 chr7D 91.986 287 23 0 1 287 413725769 413726055 1.130000e-108 403
6 TraesCS7A01G327400 chr7D 84.483 116 16 2 2013 2128 382089747 382089634 2.140000e-21 113
7 TraesCS7A01G327400 chr7B 93.027 1133 46 18 635 1749 428162899 428164016 0.000000e+00 1624
8 TraesCS7A01G327400 chr7B 85.008 627 53 9 1741 2356 428165309 428165905 1.350000e-167 599
9 TraesCS7A01G327400 chr7B 81.909 503 68 9 132 614 428160758 428161257 1.130000e-108 403
10 TraesCS7A01G327400 chr6D 79.894 567 93 7 85 631 71997386 71997951 1.900000e-106 396
11 TraesCS7A01G327400 chr6D 81.899 337 59 2 165 499 145005615 145005279 1.540000e-72 283
12 TraesCS7A01G327400 chr6D 75.000 392 80 12 86 466 430866661 430866277 5.830000e-37 165
13 TraesCS7A01G327400 chr2D 82.254 417 71 3 85 499 293781418 293781833 8.960000e-95 357
14 TraesCS7A01G327400 chr2D 82.007 289 50 2 164 451 461559382 461559669 7.280000e-61 244
15 TraesCS7A01G327400 chr1A 80.815 417 77 2 85 499 332385469 332385054 9.090000e-85 324
16 TraesCS7A01G327400 chr1A 78.019 414 82 6 90 497 577884447 577884037 4.350000e-63 252
17 TraesCS7A01G327400 chr1A 99.091 110 1 0 2524 2633 111805947 111806056 5.750000e-47 198
18 TraesCS7A01G327400 chr1A 84.956 113 15 2 2013 2125 94663993 94664103 2.140000e-21 113
19 TraesCS7A01G327400 chr5B 98.214 112 2 0 2522 2633 283270497 283270386 2.070000e-46 196
20 TraesCS7A01G327400 chr6B 96.581 117 4 0 2517 2633 270808404 270808288 7.440000e-46 195
21 TraesCS7A01G327400 chr6B 95.041 121 5 1 2513 2633 244876332 244876451 3.460000e-44 189
22 TraesCS7A01G327400 chr3A 97.391 115 2 1 2520 2633 245563799 245563913 7.440000e-46 195
23 TraesCS7A01G327400 chr2A 95.122 123 5 1 2512 2633 776059380 776059502 2.670000e-45 193
24 TraesCS7A01G327400 chr2A 85.345 116 15 2 2013 2128 755482159 755482046 4.600000e-23 119
25 TraesCS7A01G327400 chrUn 91.971 137 7 4 2501 2633 47211682 47211818 3.460000e-44 189
26 TraesCS7A01G327400 chrUn 84.483 116 16 2 2013 2128 171008234 171008121 2.140000e-21 113
27 TraesCS7A01G327400 chrUn 84.483 116 16 2 2013 2128 432742302 432742189 2.140000e-21 113
28 TraesCS7A01G327400 chr5A 90.845 142 5 7 2496 2633 164680034 164679897 1.610000e-42 183
29 TraesCS7A01G327400 chr5A 90.845 142 5 7 2496 2633 164733711 164733574 1.610000e-42 183
30 TraesCS7A01G327400 chr3B 85.345 116 15 2 2013 2128 39877024 39876911 4.600000e-23 119


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 TraesCS7A01G327400 chr7A 475803358 475805990 2632 False 4863.000000 4863 100.000 1 2633 1 chr7A.!!$F1 2632
1 TraesCS7A01G327400 chr7D 413725769 413730493 4724 False 1120.000000 2338 91.231 1 2529 3 chr7D.!!$F1 2528
2 TraesCS7A01G327400 chr7B 428160758 428165905 5147 False 875.333333 1624 86.648 132 2356 3 chr7B.!!$F1 2224
3 TraesCS7A01G327400 chr6D 71997386 71997951 565 False 396.000000 396 79.894 85 631 1 chr6D.!!$F1 546

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
888 4464 0.10212 CCTGTCTGTCTCGATCTGCC 59.898 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 7793 0.250467 ACCTCACTTGCGACATTGCT 60.25 50.0 0.0 0.0 35.36 3.91 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
20 21 1.360931 CTCATCACGCATTGTCGGCA 61.361 55.000 0.00 0.00 0.00 5.69
21 22 0.744057 TCATCACGCATTGTCGGCAT 60.744 50.000 0.00 0.00 0.00 4.40
23 24 1.070376 CATCACGCATTGTCGGCATAG 60.070 52.381 0.00 0.00 0.00 2.23
60 61 6.618287 CCTCGCAAAGGTTCATTCATATTA 57.382 37.500 0.00 0.00 40.67 0.98
63 64 6.437928 TCGCAAAGGTTCATTCATATTATGC 58.562 36.000 0.00 0.00 0.00 3.14
108 109 2.203182 TGGGTGTCGTTCCCCTCT 59.797 61.111 9.10 0.00 44.00 3.69
111 112 0.978907 GGGTGTCGTTCCCCTCTTTA 59.021 55.000 0.00 0.00 39.08 1.85
196 197 2.642254 CCTACGTCTTGGACCGGCA 61.642 63.158 0.00 0.00 0.00 5.69
287 288 2.466140 GCGGTTGTTCGGTGTGTGT 61.466 57.895 0.00 0.00 0.00 3.72
311 2234 1.901591 TGTCCGAGTAGAGGTTCGTT 58.098 50.000 0.00 0.00 35.14 3.85
323 2246 0.450184 GGTTCGTTGGCGCAATGTAT 59.550 50.000 10.83 0.00 38.14 2.29
355 2280 2.094182 GTGACTCCAAGACGATGGCTTA 60.094 50.000 0.00 0.00 40.46 3.09
360 2285 3.628008 TCCAAGACGATGGCTTACTCTA 58.372 45.455 0.00 0.00 40.46 2.43
422 2347 1.894466 CATTCAAGGGTGGTTGATGCA 59.106 47.619 0.00 0.00 36.34 3.96
424 2349 2.307496 TCAAGGGTGGTTGATGCATT 57.693 45.000 0.00 0.00 31.31 3.56
455 2380 3.482436 AGTCCGGTTGAAATTGTTGCTA 58.518 40.909 0.00 0.00 0.00 3.49
495 2420 0.530744 TAGAGACGCGGCTTTGATGT 59.469 50.000 19.64 0.00 0.00 3.06
524 2469 2.032302 GTGTTTGTAATGTGTGCGGTGA 59.968 45.455 0.00 0.00 0.00 4.02
568 2514 2.166050 TGTGATGTTTGCACTGCACTTT 59.834 40.909 2.26 0.00 38.71 2.66
583 2529 0.944386 ACTTTGTTGTTCGCAGCGAT 59.056 45.000 20.32 0.00 35.23 4.58
647 4221 1.068333 GTACTCCGTACGTCTTTGGCA 60.068 52.381 15.21 0.00 29.20 4.92
657 4231 2.159366 ACGTCTTTGGCATACTCTCTCG 60.159 50.000 0.00 0.00 0.00 4.04
658 4232 2.796383 CGTCTTTGGCATACTCTCTCGG 60.796 54.545 0.00 0.00 0.00 4.63
695 4269 3.414700 GCACGCGTCCACTCAAGG 61.415 66.667 9.86 0.00 0.00 3.61
804 4380 1.081094 TCTTGCATGCACGATCACAG 58.919 50.000 22.58 13.52 0.00 3.66
835 4411 2.832129 TCTCCTACAAAAGTGGCGATCT 59.168 45.455 0.00 0.00 0.00 2.75
863 4439 1.736365 GCCTCCGACCACTAGCTACC 61.736 65.000 0.00 0.00 0.00 3.18
870 4446 1.265454 ACCACTAGCTACCACCTGCC 61.265 60.000 0.00 0.00 0.00 4.85
888 4464 0.102120 CCTGTCTGTCTCGATCTGCC 59.898 60.000 0.00 0.00 0.00 4.85
963 4539 2.853731 ATCACAAGACCTCGATCGAC 57.146 50.000 15.15 4.76 0.00 4.20
1110 4686 1.439228 CACCATCCTCGTCATCGCT 59.561 57.895 0.00 0.00 36.96 4.93
1164 4740 2.270205 CCGCACCTCATCCAAGCT 59.730 61.111 0.00 0.00 0.00 3.74
1203 4779 0.031585 TCAACGACTTCACCCTCACG 59.968 55.000 0.00 0.00 0.00 4.35
1550 5135 1.761174 GGGTTGACTGCCCTCTCAA 59.239 57.895 0.00 0.00 42.81 3.02
1552 5137 0.108585 GGTTGACTGCCCTCTCAACA 59.891 55.000 11.52 0.00 45.48 3.33
1609 5200 4.760047 CGCAGGAGTTCCACCCCG 62.760 72.222 0.28 0.00 38.89 5.73
1653 5244 5.128205 TGATTGATTCAGGCGATTCAGATT 58.872 37.500 0.00 0.00 34.07 2.40
1666 5257 5.505286 CGATTCAGATTGCCAGTTGATTAC 58.495 41.667 0.00 0.00 0.00 1.89
1674 5265 5.528043 TTGCCAGTTGATTACATGTTGTT 57.472 34.783 2.30 0.00 0.00 2.83
1675 5266 6.641169 TTGCCAGTTGATTACATGTTGTTA 57.359 33.333 2.30 0.00 0.00 2.41
1676 5267 6.252967 TGCCAGTTGATTACATGTTGTTAG 57.747 37.500 2.30 0.00 0.00 2.34
1739 5332 1.961394 CCATTCTCCCATGCATCTTGG 59.039 52.381 0.00 0.00 0.00 3.61
1816 6710 9.472361 TCTGTAGTAAGTATAAATTTGGATCGC 57.528 33.333 0.00 0.00 0.00 4.58
1856 6750 1.775385 TCACCATGTCCTCGCTCATA 58.225 50.000 0.00 0.00 0.00 2.15
1857 6751 2.107366 TCACCATGTCCTCGCTCATAA 58.893 47.619 0.00 0.00 0.00 1.90
1858 6752 2.700371 TCACCATGTCCTCGCTCATAAT 59.300 45.455 0.00 0.00 0.00 1.28
1859 6753 3.895041 TCACCATGTCCTCGCTCATAATA 59.105 43.478 0.00 0.00 0.00 0.98
1860 6754 3.990469 CACCATGTCCTCGCTCATAATAC 59.010 47.826 0.00 0.00 0.00 1.89
1919 6813 3.874383 TTGTTTGATCTGTTCCCTCCA 57.126 42.857 0.00 0.00 0.00 3.86
1924 6818 3.370840 TGATCTGTTCCCTCCAAATGG 57.629 47.619 0.00 0.00 0.00 3.16
1929 6823 3.019564 CTGTTCCCTCCAAATGGACATC 58.980 50.000 0.00 0.00 39.78 3.06
1949 6843 9.174166 GGACATCCATTTGTAGTTGTATAAGTT 57.826 33.333 0.00 0.00 35.64 2.66
1950 6844 9.988350 GACATCCATTTGTAGTTGTATAAGTTG 57.012 33.333 0.00 0.00 0.00 3.16
1951 6845 9.515226 ACATCCATTTGTAGTTGTATAAGTTGT 57.485 29.630 0.00 0.00 0.00 3.32
2029 7220 7.750903 GTGTATACACATTTTCTTCTTCCAAGC 59.249 37.037 27.37 0.00 45.75 4.01
2030 7221 4.590850 ACACATTTTCTTCTTCCAAGCC 57.409 40.909 0.00 0.00 0.00 4.35
2031 7222 3.004734 ACACATTTTCTTCTTCCAAGCCG 59.995 43.478 0.00 0.00 0.00 5.52
2032 7223 3.253188 CACATTTTCTTCTTCCAAGCCGA 59.747 43.478 0.00 0.00 0.00 5.54
2033 7224 3.253432 ACATTTTCTTCTTCCAAGCCGAC 59.747 43.478 0.00 0.00 0.00 4.79
2034 7225 1.508632 TTTCTTCTTCCAAGCCGACG 58.491 50.000 0.00 0.00 0.00 5.12
2035 7226 0.949105 TTCTTCTTCCAAGCCGACGC 60.949 55.000 0.00 0.00 0.00 5.19
2063 7254 5.734855 TTATACAAGAGAAAGCATTCGCC 57.265 39.130 1.66 0.00 40.63 5.54
2157 7348 4.589216 TGAAAACAGGAAGAAGGCATTG 57.411 40.909 0.00 0.00 0.00 2.82
2181 7372 5.512942 TGGAAGACAAACAATCCCTCATA 57.487 39.130 0.00 0.00 0.00 2.15
2197 7388 1.626321 TCATAGTGCAAACTTCGGGGA 59.374 47.619 0.00 0.00 0.00 4.81
2199 7390 3.452990 TCATAGTGCAAACTTCGGGGATA 59.547 43.478 0.00 0.00 0.00 2.59
2200 7391 2.109425 AGTGCAAACTTCGGGGATAC 57.891 50.000 0.00 0.00 0.00 2.24
2201 7392 1.628846 AGTGCAAACTTCGGGGATACT 59.371 47.619 0.00 0.00 0.00 2.12
2202 7393 2.835764 AGTGCAAACTTCGGGGATACTA 59.164 45.455 0.00 0.00 0.00 1.82
2210 7401 3.206185 ACTTCGGGGATACTAACTAGGGT 59.794 47.826 0.00 0.00 0.00 4.34
2217 7408 6.321321 GGGGATACTAACTAGGGTCTACATT 58.679 44.000 0.00 0.00 0.00 2.71
2220 7411 7.674772 GGGATACTAACTAGGGTCTACATTCAT 59.325 40.741 0.00 0.00 0.00 2.57
2249 7440 4.753107 ACATTTCTTCTGCAATGCAAAAGG 59.247 37.500 19.70 15.33 37.24 3.11
2259 7450 6.148150 TCTGCAATGCAAAAGGAAAATGATTC 59.852 34.615 9.92 0.00 38.41 2.52
2268 7459 8.850452 GCAAAAGGAAAATGATTCTAGTTAACG 58.150 33.333 0.00 0.00 0.00 3.18
2269 7460 8.850452 CAAAAGGAAAATGATTCTAGTTAACGC 58.150 33.333 0.00 0.00 0.00 4.84
2272 7463 8.336801 AGGAAAATGATTCTAGTTAACGCTTT 57.663 30.769 0.00 0.00 0.00 3.51
2292 7483 7.599998 ACGCTTTCAATTTGCTCTGAATTTAAT 59.400 29.630 0.00 0.00 31.85 1.40
2293 7484 7.896274 CGCTTTCAATTTGCTCTGAATTTAATG 59.104 33.333 0.00 0.00 31.85 1.90
2322 7513 8.540507 AATCAGACACCATATAACTCAGTAGT 57.459 34.615 0.00 0.00 37.65 2.73
2335 7526 3.244249 ACTCAGTAGTGTTTTGGAGCTCC 60.244 47.826 26.78 26.78 33.57 4.70
2372 7563 9.327628 GGACCAGTTCTCCTATTTAGAAAATAC 57.672 37.037 0.00 0.00 34.86 1.89
2414 7609 1.406903 GCCCATTCTCCAAATCAGGG 58.593 55.000 0.00 0.00 37.87 4.45
2479 7674 1.141019 TGTGCGCGAAGATACCTCC 59.859 57.895 12.10 0.00 0.00 4.30
2487 7682 2.872858 GCGAAGATACCTCCCAATTCAC 59.127 50.000 0.00 0.00 0.00 3.18
2509 7704 7.821652 TCACAACACATACAAGAAGAAAACAA 58.178 30.769 0.00 0.00 0.00 2.83
2536 7731 6.665465 ACTCCAAACTAGAAAATTGTAACGC 58.335 36.000 0.00 0.00 0.00 4.84
2537 7732 6.004408 TCCAAACTAGAAAATTGTAACGCC 57.996 37.500 0.00 0.00 0.00 5.68
2538 7733 5.048573 TCCAAACTAGAAAATTGTAACGCCC 60.049 40.000 0.00 0.00 0.00 6.13
2539 7734 5.048294 CCAAACTAGAAAATTGTAACGCCCT 60.048 40.000 0.00 0.00 0.00 5.19
2540 7735 5.874895 AACTAGAAAATTGTAACGCCCTC 57.125 39.130 0.00 0.00 0.00 4.30
2541 7736 3.930848 ACTAGAAAATTGTAACGCCCTCG 59.069 43.478 0.00 0.00 42.43 4.63
2542 7737 3.048337 AGAAAATTGTAACGCCCTCGA 57.952 42.857 0.00 0.00 39.41 4.04
2543 7738 3.606687 AGAAAATTGTAACGCCCTCGAT 58.393 40.909 0.00 0.00 39.41 3.59
2544 7739 3.374058 AGAAAATTGTAACGCCCTCGATG 59.626 43.478 0.00 0.00 39.41 3.84
2545 7740 1.014352 AATTGTAACGCCCTCGATGC 58.986 50.000 0.00 0.00 39.41 3.91
2552 7747 2.970639 GCCCTCGATGCGGCTATA 59.029 61.111 10.26 0.00 42.21 1.31
2553 7748 1.517832 GCCCTCGATGCGGCTATAT 59.482 57.895 10.26 0.00 42.21 0.86
2554 7749 0.528684 GCCCTCGATGCGGCTATATC 60.529 60.000 10.26 0.00 42.21 1.63
2555 7750 1.107114 CCCTCGATGCGGCTATATCT 58.893 55.000 0.00 0.00 0.00 1.98
2556 7751 1.066303 CCCTCGATGCGGCTATATCTC 59.934 57.143 0.00 0.00 0.00 2.75
2557 7752 1.066303 CCTCGATGCGGCTATATCTCC 59.934 57.143 0.00 0.00 0.00 3.71
2558 7753 1.066303 CTCGATGCGGCTATATCTCCC 59.934 57.143 0.00 0.00 0.00 4.30
2559 7754 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
2560 7755 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
2561 7756 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
2562 7757 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
2563 7758 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
2564 7759 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
2565 7760 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
2566 7761 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
2567 7762 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
2568 7763 2.292569 GCTATATCTCCCACGTGTCGAA 59.707 50.000 15.65 0.00 0.00 3.71
2569 7764 3.609644 GCTATATCTCCCACGTGTCGAAG 60.610 52.174 15.65 6.13 0.00 3.79
2570 7765 0.454600 TATCTCCCACGTGTCGAAGC 59.545 55.000 15.65 0.00 0.00 3.86
2571 7766 1.532604 ATCTCCCACGTGTCGAAGCA 61.533 55.000 15.65 0.00 0.00 3.91
2572 7767 2.022129 CTCCCACGTGTCGAAGCAC 61.022 63.158 15.65 0.00 36.12 4.40
2573 7768 2.279851 CCCACGTGTCGAAGCACA 60.280 61.111 15.65 0.00 39.19 4.57
2574 7769 1.885388 CCCACGTGTCGAAGCACAA 60.885 57.895 15.65 0.00 39.19 3.33
2575 7770 1.275657 CCACGTGTCGAAGCACAAC 59.724 57.895 15.65 0.00 39.19 3.32
2576 7771 1.151777 CCACGTGTCGAAGCACAACT 61.152 55.000 15.65 0.00 39.19 3.16
2577 7772 0.650512 CACGTGTCGAAGCACAACTT 59.349 50.000 7.58 0.00 42.98 2.66
2578 7773 1.855978 CACGTGTCGAAGCACAACTTA 59.144 47.619 7.58 0.00 39.29 2.24
2579 7774 2.097396 CACGTGTCGAAGCACAACTTAG 60.097 50.000 7.58 0.00 39.29 2.18
2580 7775 2.223641 ACGTGTCGAAGCACAACTTAGA 60.224 45.455 6.93 0.00 39.29 2.10
2581 7776 2.405357 CGTGTCGAAGCACAACTTAGAG 59.595 50.000 6.93 0.00 40.21 2.43
2582 7777 2.731976 GTGTCGAAGCACAACTTAGAGG 59.268 50.000 1.54 0.00 40.21 3.69
2583 7778 1.727335 GTCGAAGCACAACTTAGAGGC 59.273 52.381 0.00 0.00 40.21 4.70
2584 7779 1.343142 TCGAAGCACAACTTAGAGGCA 59.657 47.619 0.00 0.00 39.29 4.75
2585 7780 2.028112 TCGAAGCACAACTTAGAGGCAT 60.028 45.455 0.00 0.00 39.29 4.40
2586 7781 3.194755 TCGAAGCACAACTTAGAGGCATA 59.805 43.478 0.00 0.00 39.29 3.14
2587 7782 3.932710 CGAAGCACAACTTAGAGGCATAA 59.067 43.478 0.00 0.00 39.29 1.90
2588 7783 4.201724 CGAAGCACAACTTAGAGGCATAAC 60.202 45.833 0.00 0.00 39.29 1.89
2589 7784 3.610911 AGCACAACTTAGAGGCATAACC 58.389 45.455 0.00 0.00 39.61 2.85
2590 7785 2.351726 GCACAACTTAGAGGCATAACCG 59.648 50.000 0.00 0.00 46.52 4.44
2591 7786 2.351726 CACAACTTAGAGGCATAACCGC 59.648 50.000 0.00 0.00 46.52 5.68
2592 7787 2.027561 ACAACTTAGAGGCATAACCGCA 60.028 45.455 0.00 0.00 46.52 5.69
2593 7788 3.206150 CAACTTAGAGGCATAACCGCAT 58.794 45.455 0.00 0.00 46.52 4.73
2594 7789 3.560636 ACTTAGAGGCATAACCGCATT 57.439 42.857 0.00 0.00 46.52 3.56
2595 7790 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
2596 7791 3.118408 ACTTAGAGGCATAACCGCATTGA 60.118 43.478 0.00 0.00 46.52 2.57
2597 7792 2.418368 AGAGGCATAACCGCATTGAA 57.582 45.000 0.00 0.00 46.52 2.69
2598 7793 2.722094 AGAGGCATAACCGCATTGAAA 58.278 42.857 0.00 0.00 46.52 2.69
2599 7794 2.684881 AGAGGCATAACCGCATTGAAAG 59.315 45.455 0.00 0.00 46.52 2.62
2600 7795 1.134946 AGGCATAACCGCATTGAAAGC 59.865 47.619 0.00 0.00 46.52 3.51
2601 7796 1.135141 GGCATAACCGCATTGAAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
2602 7797 2.605030 GCATAACCGCATTGAAAGCAA 58.395 42.857 0.00 0.00 38.60 3.91
2603 7798 3.189285 GCATAACCGCATTGAAAGCAAT 58.811 40.909 0.00 0.00 45.33 3.56
2612 7807 3.648339 ATTGAAAGCAATGTCGCAAGT 57.352 38.095 0.00 0.00 42.91 3.16
2613 7808 2.404265 TGAAAGCAATGTCGCAAGTG 57.596 45.000 0.00 0.00 39.48 3.16
2614 7809 1.946081 TGAAAGCAATGTCGCAAGTGA 59.054 42.857 0.00 0.00 39.48 3.41
2615 7810 2.031769 TGAAAGCAATGTCGCAAGTGAG 60.032 45.455 0.00 0.00 39.48 3.51
2616 7811 0.877071 AAGCAATGTCGCAAGTGAGG 59.123 50.000 0.00 0.00 39.48 3.86
2617 7812 0.250467 AGCAATGTCGCAAGTGAGGT 60.250 50.000 0.00 0.00 39.48 3.85
2618 7813 1.001974 AGCAATGTCGCAAGTGAGGTA 59.998 47.619 0.00 0.00 39.48 3.08
2619 7814 1.804151 GCAATGTCGCAAGTGAGGTAA 59.196 47.619 0.00 0.00 39.48 2.85
2620 7815 2.420022 GCAATGTCGCAAGTGAGGTAAT 59.580 45.455 0.00 0.00 39.48 1.89
2621 7816 3.485877 GCAATGTCGCAAGTGAGGTAATC 60.486 47.826 0.00 0.00 39.48 1.75
2622 7817 3.895232 ATGTCGCAAGTGAGGTAATCT 57.105 42.857 0.00 0.00 39.48 2.40
2623 7818 3.678056 TGTCGCAAGTGAGGTAATCTT 57.322 42.857 0.00 0.00 39.48 2.40
2624 7819 3.585862 TGTCGCAAGTGAGGTAATCTTC 58.414 45.455 0.00 0.00 39.48 2.87
2625 7820 3.006430 TGTCGCAAGTGAGGTAATCTTCA 59.994 43.478 0.00 0.00 39.48 3.02
2626 7821 3.368236 GTCGCAAGTGAGGTAATCTTCAC 59.632 47.826 2.97 2.97 46.51 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.202521 TCTATGCCGACAATGCGTGAT 60.203 47.619 0.00 0.00 0.00 3.06
8 9 1.934463 GGTCTATGCCGACAATGCG 59.066 57.895 0.00 0.00 35.63 4.73
28 29 2.480224 CCTTTGCGAGGCATGTATTG 57.520 50.000 0.00 0.00 38.76 1.90
133 134 4.540715 CAATAAAGAAGGGGGAAGATGCT 58.459 43.478 0.00 0.00 0.00 3.79
202 203 3.554692 GAACGATGCCCAGACGCG 61.555 66.667 3.53 3.53 0.00 6.01
209 210 0.243636 CCAACAAAGGAACGATGCCC 59.756 55.000 0.00 0.00 0.00 5.36
287 288 1.629043 ACCTCTACTCGGACAAGCAA 58.371 50.000 0.00 0.00 0.00 3.91
311 2234 0.936600 CATCGACATACATTGCGCCA 59.063 50.000 4.18 0.00 0.00 5.69
323 2246 2.571757 GAGTCACCGGCATCGACA 59.428 61.111 0.00 0.00 39.00 4.35
355 2280 1.616456 GGGACTCGGTTGGTCTAGAGT 60.616 57.143 0.00 0.00 45.46 3.24
360 2285 3.692406 GCGGGACTCGGTTGGTCT 61.692 66.667 0.00 0.00 39.69 3.85
422 2347 1.000896 CCGGACTTCCCTTGCCAAT 60.001 57.895 0.00 0.00 0.00 3.16
424 2349 2.457323 AACCGGACTTCCCTTGCCA 61.457 57.895 9.46 0.00 0.00 4.92
455 2380 1.620524 CCAAGGCCAATCACCCTGAAT 60.621 52.381 5.01 0.00 0.00 2.57
495 2420 5.564768 CACACATTACAAACACAACGAGAA 58.435 37.500 0.00 0.00 0.00 2.87
535 2481 4.262420 GCAAACATCACACCCAACCTAATT 60.262 41.667 0.00 0.00 0.00 1.40
541 2487 1.408702 AGTGCAAACATCACACCCAAC 59.591 47.619 0.00 0.00 36.93 3.77
568 2514 0.037697 ACCTATCGCTGCGAACAACA 60.038 50.000 29.48 4.89 39.99 3.33
602 2548 9.868277 ACTATATTTTGACAGAAGACAGAGAAG 57.132 33.333 0.00 0.00 0.00 2.85
669 4243 2.563942 GACGCGTGCTCTCTGTCT 59.436 61.111 20.70 0.00 0.00 3.41
670 4244 2.505118 GGACGCGTGCTCTCTGTC 60.505 66.667 24.37 1.40 0.00 3.51
671 4245 3.295273 TGGACGCGTGCTCTCTGT 61.295 61.111 30.67 0.00 0.00 3.41
672 4246 2.807045 GTGGACGCGTGCTCTCTG 60.807 66.667 30.67 0.00 0.00 3.35
674 4248 2.505118 GAGTGGACGCGTGCTCTC 60.505 66.667 35.27 35.27 35.17 3.20
804 4380 4.527427 ACTTTTGTAGGAGAGGAGTGTACC 59.473 45.833 0.00 0.00 0.00 3.34
863 4439 1.080230 CGAGACAGACAGGCAGGTG 60.080 63.158 0.00 0.00 0.00 4.00
870 4446 0.102120 GGGCAGATCGAGACAGACAG 59.898 60.000 0.00 0.00 0.00 3.51
888 4464 2.036958 TTCATGGCGATTGGTGTAGG 57.963 50.000 0.00 0.00 0.00 3.18
981 4557 0.970640 TCGATCGGTTGGTTCCTTCA 59.029 50.000 16.41 0.00 0.00 3.02
1128 4704 2.510613 GGTCGGAAGAGGAGATAGAGG 58.489 57.143 0.00 0.00 43.49 3.69
1186 4762 1.300697 GCGTGAGGGTGAAGTCGTT 60.301 57.895 0.00 0.00 0.00 3.85
1203 4779 3.453070 GAGGATCCAGGTGCTCGGC 62.453 68.421 15.82 0.00 0.00 5.54
1532 5117 0.606673 GTTGAGAGGGCAGTCAACCC 60.607 60.000 12.39 0.00 44.54 4.11
1550 5135 2.260434 CGTTCCGTCGGTGGATGT 59.740 61.111 11.88 0.00 38.00 3.06
1552 5137 4.446413 GGCGTTCCGTCGGTGGAT 62.446 66.667 11.88 0.00 38.00 3.41
1609 5200 3.554692 CCAGACGCGGCATTCGAC 61.555 66.667 17.71 0.00 42.43 4.20
1653 5244 5.767665 ACTAACAACATGTAATCAACTGGCA 59.232 36.000 0.00 0.00 0.00 4.92
1708 5301 6.501805 TGCATGGGAGAATGGTAGACTATATT 59.498 38.462 0.00 0.00 0.00 1.28
1709 5302 6.025539 TGCATGGGAGAATGGTAGACTATAT 58.974 40.000 0.00 0.00 0.00 0.86
1710 5303 5.402630 TGCATGGGAGAATGGTAGACTATA 58.597 41.667 0.00 0.00 0.00 1.31
1722 5315 2.905415 AACCAAGATGCATGGGAGAA 57.095 45.000 2.46 0.00 42.48 2.87
1766 6660 0.659957 GCGATCAGGGAAACATGCTC 59.340 55.000 0.00 0.00 43.15 4.26
1828 6722 3.069300 CGAGGACATGGTGAAGAGATCAT 59.931 47.826 0.00 0.00 40.97 2.45
1839 6733 3.305403 CGTATTATGAGCGAGGACATGGT 60.305 47.826 0.00 0.00 0.00 3.55
1900 6794 3.874383 TTGGAGGGAACAGATCAAACA 57.126 42.857 0.00 0.00 0.00 2.83
1901 6795 4.082026 CCATTTGGAGGGAACAGATCAAAC 60.082 45.833 0.00 0.00 37.39 2.93
1924 6818 9.988350 CAACTTATACAACTACAAATGGATGTC 57.012 33.333 0.00 0.00 34.75 3.06
2000 7191 8.999431 TGGAAGAAGAAAATGTGTATACACTTC 58.001 33.333 30.69 25.23 46.55 3.01
2028 7219 3.615496 TCTTGTATAAAAAGAGCGTCGGC 59.385 43.478 0.00 0.00 40.37 5.54
2029 7220 5.100259 TCTCTTGTATAAAAAGAGCGTCGG 58.900 41.667 16.52 0.70 46.78 4.79
2030 7221 6.627690 TTCTCTTGTATAAAAAGAGCGTCG 57.372 37.500 16.52 0.00 46.78 5.12
2031 7222 6.956520 GCTTTCTCTTGTATAAAAAGAGCGTC 59.043 38.462 16.52 6.73 46.78 5.19
2032 7223 6.426937 TGCTTTCTCTTGTATAAAAAGAGCGT 59.573 34.615 16.52 0.00 46.78 5.07
2033 7224 6.831769 TGCTTTCTCTTGTATAAAAAGAGCG 58.168 36.000 16.52 10.85 46.78 5.03
2034 7225 9.283420 GAATGCTTTCTCTTGTATAAAAAGAGC 57.717 33.333 16.52 9.78 46.78 4.09
2036 7227 7.962918 GCGAATGCTTTCTCTTGTATAAAAAGA 59.037 33.333 10.29 0.55 38.39 2.52
2037 7228 7.218963 GGCGAATGCTTTCTCTTGTATAAAAAG 59.781 37.037 10.29 0.00 42.25 2.27
2038 7229 7.027161 GGCGAATGCTTTCTCTTGTATAAAAA 58.973 34.615 10.29 0.00 42.25 1.94
2039 7230 6.551736 GGCGAATGCTTTCTCTTGTATAAAA 58.448 36.000 10.29 0.00 42.25 1.52
2116 7307 4.278310 TCAAGAATACAGACCGATCCAGA 58.722 43.478 0.00 0.00 0.00 3.86
2124 7315 6.710744 TCTTCCTGTTTTCAAGAATACAGACC 59.289 38.462 25.10 0.00 46.36 3.85
2157 7348 3.888930 TGAGGGATTGTTTGTCTTCCAAC 59.111 43.478 0.00 0.00 31.20 3.77
2181 7372 1.628846 AGTATCCCCGAAGTTTGCACT 59.371 47.619 0.00 0.00 33.11 4.40
2197 7388 9.830186 ATGATGAATGTAGACCCTAGTTAGTAT 57.170 33.333 0.00 0.00 0.00 2.12
2199 7390 7.785028 TCATGATGAATGTAGACCCTAGTTAGT 59.215 37.037 0.00 0.00 37.56 2.24
2200 7391 8.183104 TCATGATGAATGTAGACCCTAGTTAG 57.817 38.462 0.00 0.00 37.56 2.34
2201 7392 8.421784 GTTCATGATGAATGTAGACCCTAGTTA 58.578 37.037 11.46 0.00 38.79 2.24
2202 7393 7.092891 TGTTCATGATGAATGTAGACCCTAGTT 60.093 37.037 11.46 0.00 38.79 2.24
2210 7401 9.676861 AGAAGAAATGTTCATGATGAATGTAGA 57.323 29.630 11.46 0.00 38.79 2.59
2217 7408 6.578163 TTGCAGAAGAAATGTTCATGATGA 57.422 33.333 0.00 0.00 0.00 2.92
2220 7411 5.165676 GCATTGCAGAAGAAATGTTCATGA 58.834 37.500 3.15 0.00 41.98 3.07
2249 7440 9.607285 TTGAAAGCGTTAACTAGAATCATTTTC 57.393 29.630 3.71 0.00 0.00 2.29
2259 7450 6.521133 CAGAGCAAATTGAAAGCGTTAACTAG 59.479 38.462 3.71 0.00 0.00 2.57
2268 7459 8.928733 TCATTAAATTCAGAGCAAATTGAAAGC 58.071 29.630 0.00 0.00 36.93 3.51
2292 7483 8.533569 TGAGTTATATGGTGTCTGATTACTCA 57.466 34.615 0.00 0.00 36.79 3.41
2293 7484 8.634444 ACTGAGTTATATGGTGTCTGATTACTC 58.366 37.037 0.00 0.00 0.00 2.59
2306 7497 7.011482 GCTCCAAAACACTACTGAGTTATATGG 59.989 40.741 0.00 0.00 31.73 2.74
2335 7526 2.375509 AGAACTGGTCCCCCTAAACAAG 59.624 50.000 0.00 0.00 0.00 3.16
2392 7583 0.395586 TGATTTGGAGAATGGGCCCG 60.396 55.000 19.37 0.00 0.00 6.13
2398 7589 5.244626 ACTTTTGACCCTGATTTGGAGAATG 59.755 40.000 0.00 0.00 0.00 2.67
2414 7609 2.289547 TGCTTAGCGTTCCACTTTTGAC 59.710 45.455 0.00 0.00 0.00 3.18
2479 7674 6.969366 TCTTCTTGTATGTGTTGTGAATTGG 58.031 36.000 0.00 0.00 0.00 3.16
2515 7710 5.048294 AGGGCGTTACAATTTTCTAGTTTGG 60.048 40.000 0.00 0.00 0.00 3.28
2536 7731 1.066303 GAGATATAGCCGCATCGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
2537 7732 1.066303 GGAGATATAGCCGCATCGAGG 59.934 57.143 0.00 0.00 0.00 4.63
2538 7733 1.066303 GGGAGATATAGCCGCATCGAG 59.934 57.143 0.00 0.00 0.00 4.04
2539 7734 1.103803 GGGAGATATAGCCGCATCGA 58.896 55.000 0.00 0.00 0.00 3.59
2540 7735 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
2541 7736 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
2542 7737 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
2543 7738 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
2544 7739 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
2545 7740 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
2546 7741 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
2547 7742 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
2548 7743 3.609644 GCTTCGACACGTGGGAGATATAG 60.610 52.174 21.57 11.01 0.00 1.31
2549 7744 2.292569 GCTTCGACACGTGGGAGATATA 59.707 50.000 21.57 0.63 0.00 0.86
2550 7745 1.067212 GCTTCGACACGTGGGAGATAT 59.933 52.381 21.57 0.00 0.00 1.63
2551 7746 0.454600 GCTTCGACACGTGGGAGATA 59.545 55.000 21.57 1.34 0.00 1.98
2552 7747 1.215647 GCTTCGACACGTGGGAGAT 59.784 57.895 21.57 0.00 0.00 2.75
2553 7748 2.197605 TGCTTCGACACGTGGGAGA 61.198 57.895 21.57 12.82 0.00 3.71
2554 7749 2.022129 GTGCTTCGACACGTGGGAG 61.022 63.158 21.57 8.15 0.00 4.30
2555 7750 2.028484 GTGCTTCGACACGTGGGA 59.972 61.111 21.57 13.88 0.00 4.37
2556 7751 1.885388 TTGTGCTTCGACACGTGGG 60.885 57.895 21.57 11.55 43.74 4.61
2557 7752 1.151777 AGTTGTGCTTCGACACGTGG 61.152 55.000 21.57 2.57 43.74 4.94
2558 7753 0.650512 AAGTTGTGCTTCGACACGTG 59.349 50.000 15.48 15.48 43.74 4.49
2559 7754 2.124903 CTAAGTTGTGCTTCGACACGT 58.875 47.619 2.18 0.00 43.74 4.49
2560 7755 2.390938 TCTAAGTTGTGCTTCGACACG 58.609 47.619 2.18 0.00 43.74 4.49
2561 7756 2.731976 CCTCTAAGTTGTGCTTCGACAC 59.268 50.000 0.00 0.00 41.10 3.67
2562 7757 2.866460 GCCTCTAAGTTGTGCTTCGACA 60.866 50.000 0.00 0.00 38.57 4.35
2563 7758 1.727335 GCCTCTAAGTTGTGCTTCGAC 59.273 52.381 0.00 0.00 38.57 4.20
2564 7759 1.343142 TGCCTCTAAGTTGTGCTTCGA 59.657 47.619 0.00 0.00 38.57 3.71
2565 7760 1.795768 TGCCTCTAAGTTGTGCTTCG 58.204 50.000 0.00 0.00 38.57 3.79
2566 7761 4.095036 GGTTATGCCTCTAAGTTGTGCTTC 59.905 45.833 0.00 0.00 38.57 3.86
2567 7762 4.010349 GGTTATGCCTCTAAGTTGTGCTT 58.990 43.478 0.00 0.00 41.05 3.91
2568 7763 3.610911 GGTTATGCCTCTAAGTTGTGCT 58.389 45.455 0.00 0.00 0.00 4.40
2569 7764 2.351726 CGGTTATGCCTCTAAGTTGTGC 59.648 50.000 0.00 0.00 34.25 4.57
2570 7765 2.351726 GCGGTTATGCCTCTAAGTTGTG 59.648 50.000 0.00 0.00 34.25 3.33
2571 7766 2.027561 TGCGGTTATGCCTCTAAGTTGT 60.028 45.455 0.00 0.00 34.25 3.32
2572 7767 2.627945 TGCGGTTATGCCTCTAAGTTG 58.372 47.619 0.00 0.00 34.25 3.16
2573 7768 3.560636 ATGCGGTTATGCCTCTAAGTT 57.439 42.857 0.00 0.00 34.25 2.66
2574 7769 3.118408 TCAATGCGGTTATGCCTCTAAGT 60.118 43.478 0.00 0.00 34.25 2.24
2575 7770 3.466836 TCAATGCGGTTATGCCTCTAAG 58.533 45.455 0.00 0.00 34.25 2.18
2576 7771 3.552132 TCAATGCGGTTATGCCTCTAA 57.448 42.857 0.00 0.00 34.25 2.10
2577 7772 3.552132 TTCAATGCGGTTATGCCTCTA 57.448 42.857 0.00 0.00 34.25 2.43
2578 7773 2.418368 TTCAATGCGGTTATGCCTCT 57.582 45.000 0.00 0.00 34.25 3.69
2579 7774 2.796032 GCTTTCAATGCGGTTATGCCTC 60.796 50.000 0.00 0.00 34.25 4.70
2580 7775 1.134946 GCTTTCAATGCGGTTATGCCT 59.865 47.619 0.00 0.00 34.25 4.75
2581 7776 1.135141 TGCTTTCAATGCGGTTATGCC 60.135 47.619 0.00 0.00 0.00 4.40
2582 7777 2.276472 TGCTTTCAATGCGGTTATGC 57.724 45.000 0.00 0.00 0.00 3.14
2592 7787 3.004629 TCACTTGCGACATTGCTTTCAAT 59.995 39.130 0.00 0.00 43.31 2.57
2593 7788 2.357323 TCACTTGCGACATTGCTTTCAA 59.643 40.909 0.00 0.00 36.51 2.69
2594 7789 1.946081 TCACTTGCGACATTGCTTTCA 59.054 42.857 0.00 0.00 35.36 2.69
2595 7790 2.578495 CTCACTTGCGACATTGCTTTC 58.422 47.619 0.00 0.00 35.36 2.62
2596 7791 1.267806 CCTCACTTGCGACATTGCTTT 59.732 47.619 0.00 0.00 35.36 3.51
2597 7792 0.877071 CCTCACTTGCGACATTGCTT 59.123 50.000 0.00 0.00 35.36 3.91
2598 7793 0.250467 ACCTCACTTGCGACATTGCT 60.250 50.000 0.00 0.00 35.36 3.91
2599 7794 1.438651 TACCTCACTTGCGACATTGC 58.561 50.000 0.00 0.00 0.00 3.56
2600 7795 3.935203 AGATTACCTCACTTGCGACATTG 59.065 43.478 0.00 0.00 0.00 2.82
2601 7796 4.207891 AGATTACCTCACTTGCGACATT 57.792 40.909 0.00 0.00 0.00 2.71
2602 7797 3.895232 AGATTACCTCACTTGCGACAT 57.105 42.857 0.00 0.00 0.00 3.06
2603 7798 3.006430 TGAAGATTACCTCACTTGCGACA 59.994 43.478 0.00 0.00 0.00 4.35
2604 7799 3.368236 GTGAAGATTACCTCACTTGCGAC 59.632 47.826 0.00 0.00 0.00 5.19
2605 7800 3.006430 TGTGAAGATTACCTCACTTGCGA 59.994 43.478 4.07 0.00 34.51 5.10
2606 7801 3.123621 GTGTGAAGATTACCTCACTTGCG 59.876 47.826 4.07 0.00 34.51 4.85
2607 7802 4.065088 TGTGTGAAGATTACCTCACTTGC 58.935 43.478 4.07 0.00 34.51 4.01
2608 7803 5.049405 GGTTGTGTGAAGATTACCTCACTTG 60.049 44.000 4.07 0.00 34.51 3.16
2609 7804 5.063880 GGTTGTGTGAAGATTACCTCACTT 58.936 41.667 4.07 0.00 34.51 3.16
2610 7805 4.642429 GGTTGTGTGAAGATTACCTCACT 58.358 43.478 4.07 0.00 34.51 3.41


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

AutoCloner maintained by Alex Coulton.