Multiple sequence alignment - TraesCS5D01G564100

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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 TraesCS5D01G564100 chr5D 100.000 5050 0 0 1 5050 562830922 562835971 0.000000e+00 9326.0
1 TraesCS5D01G564100 chr5D 94.710 586 25 3 4458 5039 563001556 563000973 0.000000e+00 905.0
2 TraesCS5D01G564100 chr5D 94.539 586 26 3 4458 5039 562946956 562947539 0.000000e+00 900.0
3 TraesCS5D01G564100 chr5D 97.095 482 13 1 1 482 562821755 562822235 0.000000e+00 811.0
4 TraesCS5D01G564100 chr5D 88.048 502 31 16 1 482 18176797 18177289 7.340000e-158 568.0
5 TraesCS5D01G564100 chr5D 83.044 519 42 17 1 486 500441182 500440677 3.610000e-116 429.0
6 TraesCS5D01G564100 chr5D 93.916 263 9 3 4204 4459 562946653 562946915 1.700000e-104 390.0
7 TraesCS5D01G564100 chr5D 93.916 263 9 3 4204 4459 563001859 563001597 1.700000e-104 390.0
8 TraesCS5D01G564100 chr5D 82.707 399 29 17 3150 3519 450205868 450205481 8.160000e-83 318.0
9 TraesCS5D01G564100 chr5D 94.737 114 5 1 3557 3669 561820396 561820283 5.200000e-40 176.0
10 TraesCS5D01G564100 chr5D 92.958 71 5 0 3861 3931 561820174 561820104 2.490000e-18 104.0
11 TraesCS5D01G564100 chr7B 94.578 3873 73 41 657 4459 36826 33021 0.000000e+00 5862.0
12 TraesCS5D01G564100 chr7B 93.266 594 19 3 4458 5048 32979 32404 0.000000e+00 856.0
13 TraesCS5D01G564100 chr7B 85.876 177 13 6 2862 3029 1045616 1045789 1.440000e-40 178.0
14 TraesCS5D01G564100 chr7B 92.308 117 8 1 3554 3669 965031 965147 1.120000e-36 165.0
15 TraesCS5D01G564100 chr7B 92.982 57 4 0 3554 3610 1145009 1145065 3.240000e-12 84.2
16 TraesCS5D01G564100 chr7B 100.000 44 0 0 595 638 36916 36873 1.170000e-11 82.4
17 TraesCS5D01G564100 chr5B 87.713 1408 93 38 1673 3016 713015033 713016424 0.000000e+00 1568.0
18 TraesCS5D01G564100 chr5B 94.184 705 23 5 3077 3766 713016558 713017259 0.000000e+00 1059.0
19 TraesCS5D01G564100 chr5B 86.342 637 35 13 3857 4459 713017368 713017986 0.000000e+00 647.0
20 TraesCS5D01G564100 chr5B 88.832 394 30 9 1199 1586 713014534 713014919 5.920000e-129 472.0
21 TraesCS5D01G564100 chr5B 84.498 458 28 16 4524 4958 713018135 713018572 3.640000e-111 412.0
22 TraesCS5D01G564100 chr5B 81.766 521 47 18 1 486 621841752 621841245 4.740000e-105 392.0
23 TraesCS5D01G564100 chr5B 83.450 429 28 17 3147 3546 550223907 550223493 4.810000e-95 359.0
24 TraesCS5D01G564100 chr5B 81.308 321 32 16 880 1192 713014167 713014467 8.450000e-58 235.0
25 TraesCS5D01G564100 chr5B 76.298 443 43 25 2942 3349 550225765 550225350 4.020000e-41 180.0
26 TraesCS5D01G564100 chr5B 97.297 74 2 0 3794 3867 713017259 713017332 5.310000e-25 126.0
27 TraesCS5D01G564100 chr5B 97.674 43 0 1 3031 3072 713016494 713016536 7.010000e-09 73.1
28 TraesCS5D01G564100 chr5B 100.000 31 0 0 4754 4784 641098301 641098331 1.960000e-04 58.4
29 TraesCS5D01G564100 chr4A 89.879 494 32 10 1 482 615694584 615694097 2.000000e-173 619.0
30 TraesCS5D01G564100 chr4A 85.017 574 54 23 1701 2250 615561707 615561142 5.710000e-154 555.0
31 TraesCS5D01G564100 chr4A 86.364 308 9 10 878 1183 615567827 615567551 6.350000e-79 305.0
32 TraesCS5D01G564100 chr4A 93.805 113 5 2 1461 1573 615567449 615567339 8.700000e-38 169.0
33 TraesCS5D01G564100 chr5A 88.048 502 31 9 1 482 11942419 11942911 7.340000e-158 568.0
34 TraesCS5D01G564100 chr5A 83.622 519 42 9 1 486 626966695 626966187 9.970000e-122 448.0
35 TraesCS5D01G564100 chr5A 80.680 647 53 27 2926 3519 569546015 569545388 2.160000e-118 436.0
36 TraesCS5D01G564100 chr5A 87.313 134 10 3 4801 4933 569545379 569545252 4.070000e-31 147.0
37 TraesCS5D01G564100 chr5A 90.476 84 4 4 479 562 11943132 11943211 1.920000e-19 108.0
38 TraesCS5D01G564100 chr5A 100.000 29 0 0 4750 4778 396105003 396105031 3.000000e-03 54.7
39 TraesCS5D01G564100 chr3A 86.441 118 9 4 2925 3035 30182270 30182387 6.870000e-24 122.0
40 TraesCS5D01G564100 chr3A 85.714 112 12 2 3141 3250 30182554 30182663 1.150000e-21 115.0
41 TraesCS5D01G564100 chr3D 94.444 72 4 0 4979 5050 301344330 301344401 1.490000e-20 111.0
42 TraesCS5D01G564100 chr7D 93.056 72 5 0 4979 5050 509067763 509067692 6.910000e-19 106.0
43 TraesCS5D01G564100 chr7D 100.000 29 0 0 4748 4776 157131905 157131877 3.000000e-03 54.7
44 TraesCS5D01G564100 chr2D 92.857 70 3 2 4978 5046 20845033 20845101 3.220000e-17 100.0
45 TraesCS5D01G564100 chr2D 89.231 65 7 0 4983 5047 357129930 357129994 1.170000e-11 82.4
46 TraesCS5D01G564100 chr6D 89.231 65 7 0 4983 5047 287635240 287635304 1.170000e-11 82.4
47 TraesCS5D01G564100 chr6D 85.915 71 8 2 4979 5048 338995038 338995107 1.950000e-09 75.0
48 TraesCS5D01G564100 chr1B 100.000 31 0 0 4748 4778 330486064 330486034 1.960000e-04 58.4
49 TraesCS5D01G564100 chr3B 100.000 28 0 0 4748 4775 152580330 152580357 9.000000e-03 52.8
50 TraesCS5D01G564100 chr1A 100.000 28 0 0 918 945 581440152 581440179 9.000000e-03 52.8


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 TraesCS5D01G564100 chr5D 562830922 562835971 5049 False 9326.0000 9326 100.0000 1 5050 1 chr5D.!!$F3 5049
1 TraesCS5D01G564100 chr5D 563000973 563001859 886 True 647.5000 905 94.3130 4204 5039 2 chr5D.!!$R4 835
2 TraesCS5D01G564100 chr5D 562946653 562947539 886 False 645.0000 900 94.2275 4204 5039 2 chr5D.!!$F4 835
3 TraesCS5D01G564100 chr5D 500440677 500441182 505 True 429.0000 429 83.0440 1 486 1 chr5D.!!$R2 485
4 TraesCS5D01G564100 chr7B 32404 36916 4512 True 2266.8000 5862 95.9480 595 5048 3 chr7B.!!$R1 4453
5 TraesCS5D01G564100 chr5B 713014167 713018572 4405 False 574.0125 1568 89.7310 880 4958 8 chr5B.!!$F2 4078
6 TraesCS5D01G564100 chr5B 621841245 621841752 507 True 392.0000 392 81.7660 1 486 1 chr5B.!!$R1 485
7 TraesCS5D01G564100 chr5B 550223493 550225765 2272 True 269.5000 359 79.8740 2942 3546 2 chr5B.!!$R2 604
8 TraesCS5D01G564100 chr4A 615561142 615561707 565 True 555.0000 555 85.0170 1701 2250 1 chr4A.!!$R1 549
9 TraesCS5D01G564100 chr5A 626966187 626966695 508 True 448.0000 448 83.6220 1 486 1 chr5A.!!$R1 485
10 TraesCS5D01G564100 chr5A 11942419 11943211 792 False 338.0000 568 89.2620 1 562 2 chr5A.!!$F2 561
11 TraesCS5D01G564100 chr5A 569545252 569546015 763 True 291.5000 436 83.9965 2926 4933 2 chr5A.!!$R2 2007

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
855 1145 0.178767 CAGGCGGACAGATCCATTCA 59.821 55.0 0.00 0.00 46.67 2.57 F
2392 2872 0.034756 TCGGTACACACTGCATGCTT 59.965 50.0 20.33 2.49 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2952 2.165030 CTGTGTGCATCTGAAATTCCCC 59.835 50.0 0.0 0.0 0.0 4.81 R
4191 6567 0.905357 TTGGTTGGTTGGTTGGTTGG 59.095 50.0 0.0 0.0 0.0 3.77 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
25 26 4.019858 TCAACCACTTCACATTGTTTGGA 58.980 39.130 9.43 0.00 0.00 3.53
34 35 6.209192 ACTTCACATTGTTTGGAATGATGCTA 59.791 34.615 0.00 0.00 36.89 3.49
61 62 0.255033 TGAGCTCATCTGCCATGCTT 59.745 50.000 13.74 0.00 33.83 3.91
77 78 5.754406 GCCATGCTTGCAAACATAATCATAA 59.246 36.000 14.67 0.00 0.00 1.90
125 126 1.719529 TTCCTGGGTTCCTCGTTACA 58.280 50.000 0.00 0.00 0.00 2.41
144 145 2.289257 ACAAGACCGGTAAGTAAGCCAC 60.289 50.000 7.34 0.00 0.00 5.01
145 146 1.636148 AGACCGGTAAGTAAGCCACA 58.364 50.000 7.34 0.00 0.00 4.17
209 233 3.320541 TGATGATGGTTGGTTGGTTGTTC 59.679 43.478 0.00 0.00 0.00 3.18
314 338 2.953020 GCAATTTGGCGATAACACCAA 58.047 42.857 0.00 0.00 44.11 3.67
349 387 0.673437 CGGTGGTGGTGAAGCAATTT 59.327 50.000 0.00 0.00 38.21 1.82
371 409 2.948115 TGGAGGACAATATGGGCATTG 58.052 47.619 0.00 0.00 40.93 2.82
455 493 2.162408 GTGTTTGCCTACTCCATCAAGC 59.838 50.000 0.00 0.00 0.00 4.01
466 504 3.567164 ACTCCATCAAGCTGTTGAACTTG 59.433 43.478 0.00 0.00 45.88 3.16
498 760 2.887152 AGGAAGCGGATTTATCATTGGC 59.113 45.455 0.00 0.00 0.00 4.52
512 774 4.314522 TCATTGGCCTCTGTTAATTCCA 57.685 40.909 3.32 0.00 0.00 3.53
513 775 4.671831 TCATTGGCCTCTGTTAATTCCAA 58.328 39.130 3.32 0.00 37.89 3.53
562 824 7.006865 TCATGTGGGTCAATTCAATTCAATT 57.993 32.000 0.00 0.00 0.00 2.32
563 825 7.451732 TCATGTGGGTCAATTCAATTCAATTT 58.548 30.769 0.00 0.00 0.00 1.82
564 826 8.591940 TCATGTGGGTCAATTCAATTCAATTTA 58.408 29.630 0.00 0.00 0.00 1.40
565 827 9.217278 CATGTGGGTCAATTCAATTCAATTTAA 57.783 29.630 0.00 0.00 0.00 1.52
566 828 9.962809 ATGTGGGTCAATTCAATTCAATTTAAT 57.037 25.926 0.00 0.00 0.00 1.40
567 829 9.434420 TGTGGGTCAATTCAATTCAATTTAATC 57.566 29.630 0.00 0.00 0.00 1.75
568 830 9.434420 GTGGGTCAATTCAATTCAATTTAATCA 57.566 29.630 0.00 0.00 0.00 2.57
569 831 9.434420 TGGGTCAATTCAATTCAATTTAATCAC 57.566 29.630 0.00 0.00 0.00 3.06
570 832 8.594687 GGGTCAATTCAATTCAATTTAATCACG 58.405 33.333 0.00 0.00 0.00 4.35
571 833 9.139174 GGTCAATTCAATTCAATTTAATCACGT 57.861 29.630 0.00 0.00 0.00 4.49
572 834 9.941991 GTCAATTCAATTCAATTTAATCACGTG 57.058 29.630 9.94 9.94 0.00 4.49
573 835 9.905171 TCAATTCAATTCAATTTAATCACGTGA 57.095 25.926 22.48 22.48 0.00 4.35
577 839 9.773328 TTCAATTCAATTTAATCACGTGATCTC 57.227 29.630 30.06 0.00 32.75 2.75
578 840 8.945057 TCAATTCAATTTAATCACGTGATCTCA 58.055 29.630 30.06 17.04 32.75 3.27
579 841 9.726232 CAATTCAATTTAATCACGTGATCTCAT 57.274 29.630 30.06 17.46 32.75 2.90
582 844 9.558648 TTCAATTTAATCACGTGATCTCATTTG 57.441 29.630 30.06 25.13 32.75 2.32
583 845 8.945057 TCAATTTAATCACGTGATCTCATTTGA 58.055 29.630 30.06 26.55 32.75 2.69
584 846 9.726232 CAATTTAATCACGTGATCTCATTTGAT 57.274 29.630 30.06 14.27 33.97 2.57
587 849 9.558648 TTTAATCACGTGATCTCATTTGATTTG 57.441 29.630 30.06 0.00 39.18 2.32
588 850 6.990341 ATCACGTGATCTCATTTGATTTGA 57.010 33.333 25.18 0.00 30.62 2.69
589 851 6.990341 TCACGTGATCTCATTTGATTTGAT 57.010 33.333 15.76 0.00 0.00 2.57
590 852 7.381766 TCACGTGATCTCATTTGATTTGATT 57.618 32.000 15.76 0.00 0.00 2.57
591 853 7.819644 TCACGTGATCTCATTTGATTTGATTT 58.180 30.769 15.76 0.00 0.00 2.17
592 854 8.298854 TCACGTGATCTCATTTGATTTGATTTT 58.701 29.630 15.76 0.00 0.00 1.82
593 855 8.918658 CACGTGATCTCATTTGATTTGATTTTT 58.081 29.630 10.90 0.00 0.00 1.94
638 900 0.615331 TTTGAGAGGCAGGCAGGTAG 59.385 55.000 0.00 0.00 0.00 3.18
639 901 0.545309 TTGAGAGGCAGGCAGGTAGT 60.545 55.000 0.00 0.00 0.00 2.73
640 902 0.335019 TGAGAGGCAGGCAGGTAGTA 59.665 55.000 0.00 0.00 0.00 1.82
651 936 3.052033 AGGCAGGTAGTACATCTTAGGGT 60.052 47.826 2.06 0.00 0.00 4.34
652 937 4.169461 AGGCAGGTAGTACATCTTAGGGTA 59.831 45.833 2.06 0.00 0.00 3.69
653 938 4.523558 GGCAGGTAGTACATCTTAGGGTAG 59.476 50.000 2.06 0.00 0.00 3.18
654 939 5.139001 GCAGGTAGTACATCTTAGGGTAGT 58.861 45.833 2.06 0.00 0.00 2.73
655 940 6.302269 GCAGGTAGTACATCTTAGGGTAGTA 58.698 44.000 2.06 0.00 0.00 1.82
679 969 2.671070 GCTTTACCGCCAACAAGGAATG 60.671 50.000 0.00 0.00 41.22 2.67
681 971 3.420300 TTACCGCCAACAAGGAATGTA 57.580 42.857 0.00 0.00 42.99 2.29
682 972 1.821216 ACCGCCAACAAGGAATGTAG 58.179 50.000 0.00 0.00 42.99 2.74
684 974 2.159382 CCGCCAACAAGGAATGTAGTT 58.841 47.619 0.00 0.00 42.99 2.24
685 975 2.095263 CCGCCAACAAGGAATGTAGTTG 60.095 50.000 0.00 0.00 42.99 3.16
686 976 2.552315 CGCCAACAAGGAATGTAGTTGT 59.448 45.455 0.00 0.00 42.99 3.32
687 977 3.749088 CGCCAACAAGGAATGTAGTTGTA 59.251 43.478 0.00 0.00 42.99 2.41
688 978 4.394920 CGCCAACAAGGAATGTAGTTGTAT 59.605 41.667 0.00 0.00 42.99 2.29
692 982 9.116067 GCCAACAAGGAATGTAGTTGTATTATA 57.884 33.333 0.00 0.00 42.99 0.98
760 1050 0.829182 AGTCAAAGGCAAGGCAAGGG 60.829 55.000 0.00 0.00 0.00 3.95
772 1062 1.774300 GCAAGGGAAGGGAAGGGAA 59.226 57.895 0.00 0.00 0.00 3.97
773 1063 0.323816 GCAAGGGAAGGGAAGGGAAG 60.324 60.000 0.00 0.00 0.00 3.46
774 1064 0.332972 CAAGGGAAGGGAAGGGAAGG 59.667 60.000 0.00 0.00 0.00 3.46
775 1065 0.851332 AAGGGAAGGGAAGGGAAGGG 60.851 60.000 0.00 0.00 0.00 3.95
776 1066 1.230182 GGGAAGGGAAGGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
851 1141 3.785859 GGCAGGCGGACAGATCCA 61.786 66.667 0.00 0.00 46.67 3.41
852 1142 2.507944 GCAGGCGGACAGATCCAT 59.492 61.111 0.00 0.00 46.67 3.41
853 1143 1.153086 GCAGGCGGACAGATCCATT 60.153 57.895 0.00 0.00 46.67 3.16
854 1144 1.162800 GCAGGCGGACAGATCCATTC 61.163 60.000 0.00 0.00 46.67 2.67
855 1145 0.178767 CAGGCGGACAGATCCATTCA 59.821 55.000 0.00 0.00 46.67 2.57
856 1146 1.135094 AGGCGGACAGATCCATTCAT 58.865 50.000 0.00 0.00 46.67 2.57
857 1147 1.492176 AGGCGGACAGATCCATTCATT 59.508 47.619 0.00 0.00 46.67 2.57
858 1148 1.876156 GGCGGACAGATCCATTCATTC 59.124 52.381 0.00 0.00 46.67 2.67
859 1149 2.564771 GCGGACAGATCCATTCATTCA 58.435 47.619 0.00 0.00 46.67 2.57
860 1150 3.144506 GCGGACAGATCCATTCATTCAT 58.855 45.455 0.00 0.00 46.67 2.57
861 1151 3.567164 GCGGACAGATCCATTCATTCATT 59.433 43.478 0.00 0.00 46.67 2.57
865 1155 4.477249 ACAGATCCATTCATTCATTCCCC 58.523 43.478 0.00 0.00 0.00 4.81
968 1265 3.347216 CAAGATCCAACCTTGTACCAGG 58.653 50.000 11.42 11.42 40.23 4.45
969 1266 2.915869 AGATCCAACCTTGTACCAGGA 58.084 47.619 19.49 4.02 37.39 3.86
970 1267 2.840651 AGATCCAACCTTGTACCAGGAG 59.159 50.000 19.49 10.80 37.39 3.69
981 1287 4.180946 CCAGGAGAGCGTCGTCGG 62.181 72.222 3.90 0.00 37.56 4.79
982 1288 3.125573 CAGGAGAGCGTCGTCGGA 61.126 66.667 3.90 0.00 37.56 4.55
983 1289 2.359602 AGGAGAGCGTCGTCGGAA 60.360 61.111 3.90 0.00 37.56 4.30
1127 1433 6.472016 AGATCAAGGTCTCTTCTTTCCTTTC 58.528 40.000 0.00 0.00 38.09 2.62
1129 1435 4.660771 TCAAGGTCTCTTCTTTCCTTTCCT 59.339 41.667 0.00 0.00 38.09 3.36
1130 1436 4.901197 AGGTCTCTTCTTTCCTTTCCTC 57.099 45.455 0.00 0.00 0.00 3.71
1131 1437 4.498493 AGGTCTCTTCTTTCCTTTCCTCT 58.502 43.478 0.00 0.00 0.00 3.69
1132 1438 4.910913 AGGTCTCTTCTTTCCTTTCCTCTT 59.089 41.667 0.00 0.00 0.00 2.85
1336 1701 1.968493 GGATTCAGAGCGGGGTATGTA 59.032 52.381 0.00 0.00 0.00 2.29
1353 1722 5.358442 GGTATGTATGTCTGTCTGTCTGTCT 59.642 44.000 0.00 0.00 0.00 3.41
1355 1724 4.145052 TGTATGTCTGTCTGTCTGTCTGT 58.855 43.478 0.00 0.00 0.00 3.41
1363 1732 2.030363 GTCTGTCTGTCTGTCTGTCAGG 60.030 54.545 0.00 0.00 43.76 3.86
1421 1796 1.058404 GTCGTCGTCTAACACAAGCC 58.942 55.000 0.00 0.00 0.00 4.35
1426 1801 1.202592 TCGTCTAACACAAGCCAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
1682 2096 2.038295 TGACCACCGATATATGCATGCA 59.962 45.455 25.04 25.04 0.00 3.96
1683 2097 3.273434 GACCACCGATATATGCATGCAT 58.727 45.455 33.92 33.92 40.19 3.96
1684 2098 3.011818 ACCACCGATATATGCATGCATG 58.988 45.455 37.43 23.89 37.82 4.06
2022 2491 5.560722 ATGTCATGTCGTGGGGATAATAA 57.439 39.130 0.00 0.00 0.00 1.40
2025 2494 7.252612 TGTCATGTCGTGGGGATAATAATAT 57.747 36.000 0.00 0.00 0.00 1.28
2391 2871 0.670546 GTCGGTACACACTGCATGCT 60.671 55.000 20.33 0.00 0.00 3.79
2392 2872 0.034756 TCGGTACACACTGCATGCTT 59.965 50.000 20.33 2.49 0.00 3.91
2393 2873 0.443869 CGGTACACACTGCATGCTTC 59.556 55.000 20.33 0.00 0.00 3.86
2394 2874 1.813513 GGTACACACTGCATGCTTCT 58.186 50.000 20.33 0.00 0.00 2.85
2395 2875 1.734465 GGTACACACTGCATGCTTCTC 59.266 52.381 20.33 1.49 0.00 2.87
2396 2876 1.734465 GTACACACTGCATGCTTCTCC 59.266 52.381 20.33 0.00 0.00 3.71
2397 2877 0.109153 ACACACTGCATGCTTCTCCA 59.891 50.000 20.33 0.00 0.00 3.86
2399 2879 1.400846 CACACTGCATGCTTCTCCATC 59.599 52.381 20.33 0.00 0.00 3.51
2400 2880 1.003928 ACACTGCATGCTTCTCCATCA 59.996 47.619 20.33 0.00 0.00 3.07
2403 2883 1.941294 CTGCATGCTTCTCCATCAGTC 59.059 52.381 20.33 0.00 0.00 3.51
2461 2952 9.651718 GTTATCTATCTGTGATTTTTAAAGCGG 57.348 33.333 0.00 0.00 0.00 5.52
2599 3098 3.425162 AATCAACACTCAAGGAGGGAC 57.575 47.619 1.91 0.00 34.53 4.46
2698 3197 1.482278 GAGGCGACTATCTCTTTGCG 58.518 55.000 0.00 0.00 44.43 4.85
2836 3335 2.286365 TTTCATCCGGGTGAGCTTTT 57.714 45.000 18.64 0.00 0.00 2.27
2923 3426 0.875059 CCTGGGCTGAACGTCTTTTC 59.125 55.000 0.00 0.00 0.00 2.29
2936 3439 3.875134 ACGTCTTTTCGTTCAAATGGACT 59.125 39.130 0.00 0.00 41.37 3.85
2937 3440 4.334481 ACGTCTTTTCGTTCAAATGGACTT 59.666 37.500 0.00 0.00 41.37 3.01
2938 3441 4.904154 CGTCTTTTCGTTCAAATGGACTTC 59.096 41.667 0.00 0.00 30.79 3.01
2939 3442 5.503357 CGTCTTTTCGTTCAAATGGACTTCA 60.503 40.000 0.00 0.00 30.79 3.02
2940 3443 5.681543 GTCTTTTCGTTCAAATGGACTTCAC 59.318 40.000 0.00 0.00 30.55 3.18
3001 5096 8.908786 TCATTCTCTTTAATGATACCATGACC 57.091 34.615 0.00 0.00 40.17 4.02
3239 5496 0.821517 ACTGTTGTGTGTCCACGAGA 59.178 50.000 0.00 0.00 44.92 4.04
3281 5538 3.272574 ACTATGAGCCTGGTTGTCATG 57.727 47.619 14.74 9.40 33.05 3.07
3718 6006 5.741388 AATATGAGCGAAAACAGGCTAAG 57.259 39.130 0.00 0.00 40.16 2.18
3733 6021 5.534654 ACAGGCTAAGCTTCACATAACAAAA 59.465 36.000 0.00 0.00 0.00 2.44
3925 6259 2.453773 CTTGCGCTGGTGCACTGAAG 62.454 60.000 17.98 12.94 46.25 3.02
4191 6567 1.303309 AGTTTCAGATATGCGCCAGC 58.697 50.000 4.18 0.00 45.41 4.85
4192 6568 0.308993 GTTTCAGATATGCGCCAGCC 59.691 55.000 4.18 0.00 44.33 4.85
4193 6569 0.107263 TTTCAGATATGCGCCAGCCA 60.107 50.000 4.18 0.00 44.33 4.75
4194 6570 0.107263 TTCAGATATGCGCCAGCCAA 60.107 50.000 4.18 0.00 44.33 4.52
4503 6954 3.990318 AAGCACCTGTGTTTTTAGCTC 57.010 42.857 0.00 0.00 29.58 4.09
4511 6962 5.239525 ACCTGTGTTTTTAGCTCTGTTGATC 59.760 40.000 0.00 0.00 0.00 2.92
4589 7096 9.144298 CTTGTATGATAGTAGAAAAGGGTAGGA 57.856 37.037 0.00 0.00 0.00 2.94
5002 7529 8.904099 ATACTCCCTCCATTTTTATTTACTCG 57.096 34.615 0.00 0.00 0.00 4.18
5019 7546 7.908827 TTTACTCGGCATATTAAGTTTGACA 57.091 32.000 0.00 0.00 0.00 3.58
5020 7547 7.908827 TTACTCGGCATATTAAGTTTGACAA 57.091 32.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.119588 GCATCATTCCAAACAATGTGAAGTG 59.880 40.000 0.00 0.00 35.56 3.16
25 26 2.283298 CTCAACGCCACTAGCATCATT 58.717 47.619 0.00 0.00 44.04 2.57
34 35 0.390866 CAGATGAGCTCAACGCCACT 60.391 55.000 22.50 10.27 40.39 4.00
61 62 9.019656 AGTACAAAGGTTATGATTATGTTTGCA 57.980 29.630 0.00 0.00 0.00 4.08
77 78 3.323775 TCCAAAGAGGGAGTACAAAGGT 58.676 45.455 0.00 0.00 38.24 3.50
108 109 1.621814 TCTTGTAACGAGGAACCCAGG 59.378 52.381 0.00 0.00 0.00 4.45
125 126 1.972795 TGTGGCTTACTTACCGGTCTT 59.027 47.619 12.40 0.00 0.00 3.01
173 194 1.852633 TCATCATGACCTCACCTCGT 58.147 50.000 0.00 0.00 0.00 4.18
209 233 6.036300 CCAAATTGGTATTAACTGCATGCAAG 59.964 38.462 22.88 17.38 31.35 4.01
349 387 3.686227 ATGCCCATATTGTCCTCCAAA 57.314 42.857 0.00 0.00 36.44 3.28
371 409 4.210331 ACATACCCAAGGAAATCATGCTC 58.790 43.478 0.00 0.00 0.00 4.26
376 414 3.605634 CACGACATACCCAAGGAAATCA 58.394 45.455 0.00 0.00 0.00 2.57
411 449 1.816835 AGAAGAAGCCGATGACGTACA 59.183 47.619 0.00 0.00 37.88 2.90
455 493 3.405170 ACGTTTCTGCAAGTTCAACAG 57.595 42.857 0.00 0.00 33.76 3.16
466 504 0.442699 CCGCTTCCTAACGTTTCTGC 59.557 55.000 5.91 3.85 0.00 4.26
498 760 2.747446 CCCGTGTTGGAATTAACAGAGG 59.253 50.000 7.87 7.87 40.89 3.69
513 775 9.798994 GAATAAATCTCGTATATATTCCCGTGT 57.201 33.333 0.00 0.00 30.41 4.49
523 785 8.593679 TGACCCACATGAATAAATCTCGTATAT 58.406 33.333 0.00 0.00 0.00 0.86
524 786 7.958088 TGACCCACATGAATAAATCTCGTATA 58.042 34.615 0.00 0.00 0.00 1.47
525 787 6.826668 TGACCCACATGAATAAATCTCGTAT 58.173 36.000 0.00 0.00 0.00 3.06
526 788 6.228616 TGACCCACATGAATAAATCTCGTA 57.771 37.500 0.00 0.00 0.00 3.43
527 789 5.097742 TGACCCACATGAATAAATCTCGT 57.902 39.130 0.00 0.00 0.00 4.18
528 790 6.624352 ATTGACCCACATGAATAAATCTCG 57.376 37.500 0.00 0.00 0.00 4.04
562 824 8.945057 TCAAATCAAATGAGATCACGTGATTAA 58.055 29.630 30.46 19.27 39.65 1.40
563 825 8.491331 TCAAATCAAATGAGATCACGTGATTA 57.509 30.769 30.46 20.04 39.65 1.75
564 826 7.381766 TCAAATCAAATGAGATCACGTGATT 57.618 32.000 30.46 20.01 41.02 2.57
565 827 6.990341 TCAAATCAAATGAGATCACGTGAT 57.010 33.333 30.37 30.37 35.46 3.06
566 828 6.990341 ATCAAATCAAATGAGATCACGTGA 57.010 33.333 22.48 22.48 0.00 4.35
567 829 8.456904 AAAATCAAATCAAATGAGATCACGTG 57.543 30.769 9.94 9.94 0.00 4.49
638 900 6.712179 AAGCACTACTACCCTAAGATGTAC 57.288 41.667 0.00 0.00 0.00 2.90
639 901 7.286316 GGTAAAGCACTACTACCCTAAGATGTA 59.714 40.741 0.00 0.00 30.69 2.29
640 902 6.097981 GGTAAAGCACTACTACCCTAAGATGT 59.902 42.308 0.00 0.00 30.69 3.06
651 936 2.299582 TGTTGGCGGTAAAGCACTACTA 59.700 45.455 0.00 0.00 39.27 1.82
652 937 1.071071 TGTTGGCGGTAAAGCACTACT 59.929 47.619 0.00 0.00 39.27 2.57
653 938 1.515081 TGTTGGCGGTAAAGCACTAC 58.485 50.000 0.00 0.00 39.27 2.73
654 939 2.147958 CTTGTTGGCGGTAAAGCACTA 58.852 47.619 0.00 0.00 39.27 2.74
655 940 0.951558 CTTGTTGGCGGTAAAGCACT 59.048 50.000 0.00 0.00 39.27 4.40
760 1050 0.033991 GCTTCCCTTCCCTTCCCTTC 60.034 60.000 0.00 0.00 0.00 3.46
772 1062 3.397613 GAGATGCGCTGGCTTCCCT 62.398 63.158 9.73 0.00 42.61 4.20
773 1063 2.899339 GAGATGCGCTGGCTTCCC 60.899 66.667 9.73 0.00 42.61 3.97
774 1064 2.899339 GGAGATGCGCTGGCTTCC 60.899 66.667 9.73 5.10 42.61 3.46
775 1065 2.899339 GGGAGATGCGCTGGCTTC 60.899 66.667 9.73 1.34 42.11 3.86
776 1066 3.397613 GAGGGAGATGCGCTGGCTT 62.398 63.158 9.73 0.00 40.28 4.35
851 1141 2.867746 AGGGGAAGGGGAATGAATGAAT 59.132 45.455 0.00 0.00 0.00 2.57
852 1142 2.244769 GAGGGGAAGGGGAATGAATGAA 59.755 50.000 0.00 0.00 0.00 2.57
853 1143 1.852965 GAGGGGAAGGGGAATGAATGA 59.147 52.381 0.00 0.00 0.00 2.57
854 1144 1.477558 CGAGGGGAAGGGGAATGAATG 60.478 57.143 0.00 0.00 0.00 2.67
855 1145 0.846693 CGAGGGGAAGGGGAATGAAT 59.153 55.000 0.00 0.00 0.00 2.57
856 1146 0.252974 TCGAGGGGAAGGGGAATGAA 60.253 55.000 0.00 0.00 0.00 2.57
857 1147 0.981277 GTCGAGGGGAAGGGGAATGA 60.981 60.000 0.00 0.00 0.00 2.57
858 1148 1.527370 GTCGAGGGGAAGGGGAATG 59.473 63.158 0.00 0.00 0.00 2.67
859 1149 1.693103 GGTCGAGGGGAAGGGGAAT 60.693 63.158 0.00 0.00 0.00 3.01
860 1150 2.285144 GGTCGAGGGGAAGGGGAA 60.285 66.667 0.00 0.00 0.00 3.97
861 1151 4.772231 CGGTCGAGGGGAAGGGGA 62.772 72.222 0.00 0.00 0.00 4.81
865 1155 1.442148 GATTCCGGTCGAGGGGAAG 59.558 63.158 18.76 0.00 44.93 3.46
954 1251 1.673033 CGCTCTCCTGGTACAAGGTTG 60.673 57.143 16.29 10.40 38.70 3.77
968 1265 2.100603 CCTTCCGACGACGCTCTC 59.899 66.667 0.64 0.00 38.29 3.20
969 1266 3.441290 CCCTTCCGACGACGCTCT 61.441 66.667 0.64 0.00 38.29 4.09
970 1267 2.868999 CTTCCCTTCCGACGACGCTC 62.869 65.000 0.64 0.00 38.29 5.03
981 1287 0.253207 TCCTCCCTTCCCTTCCCTTC 60.253 60.000 0.00 0.00 0.00 3.46
982 1288 0.427685 ATCCTCCCTTCCCTTCCCTT 59.572 55.000 0.00 0.00 0.00 3.95
983 1289 0.327964 CATCCTCCCTTCCCTTCCCT 60.328 60.000 0.00 0.00 0.00 4.20
1127 1433 6.699204 GGAAAGAAAGCAAAGAAAGAAAGAGG 59.301 38.462 0.00 0.00 0.00 3.69
1129 1435 7.410120 AGGAAAGAAAGCAAAGAAAGAAAGA 57.590 32.000 0.00 0.00 0.00 2.52
1130 1436 7.465111 GCAAGGAAAGAAAGCAAAGAAAGAAAG 60.465 37.037 0.00 0.00 0.00 2.62
1131 1437 6.313658 GCAAGGAAAGAAAGCAAAGAAAGAAA 59.686 34.615 0.00 0.00 0.00 2.52
1132 1438 5.812127 GCAAGGAAAGAAAGCAAAGAAAGAA 59.188 36.000 0.00 0.00 0.00 2.52
1336 1701 3.255395 CAGACAGACAGACAGACAGACAT 59.745 47.826 0.00 0.00 0.00 3.06
1353 1722 0.836606 TGGTTTGAGCCTGACAGACA 59.163 50.000 3.32 0.00 0.00 3.41
1355 1724 2.957402 ATTGGTTTGAGCCTGACAGA 57.043 45.000 3.32 0.00 0.00 3.41
1363 1732 5.200368 TGAGGAAGAAAATTGGTTTGAGC 57.800 39.130 0.00 0.00 0.00 4.26
1421 1796 5.240713 ACAAACAAGAGAGAGTTTTGCTG 57.759 39.130 0.00 0.00 35.90 4.41
1426 1801 9.178758 ACATAGAAAACAAACAAGAGAGAGTTT 57.821 29.630 0.00 0.00 38.40 2.66
1450 1825 8.529424 GGTGCACACCCTAGTATATATATACA 57.471 38.462 27.07 15.79 45.68 2.29
1597 2003 6.950842 TCTTATTGAAGCATTGAGGAGAAGA 58.049 36.000 0.00 0.00 32.21 2.87
1601 2007 5.678583 TCCTCTTATTGAAGCATTGAGGAG 58.321 41.667 0.00 0.00 42.24 3.69
1682 2096 5.105023 CCATCTAGCATACTGTATCCTGCAT 60.105 44.000 12.78 0.00 37.09 3.96
1683 2097 4.221482 CCATCTAGCATACTGTATCCTGCA 59.779 45.833 12.78 0.00 37.09 4.41
1684 2098 4.464244 TCCATCTAGCATACTGTATCCTGC 59.536 45.833 1.46 2.93 34.85 4.85
1685 2099 6.350864 CCTTCCATCTAGCATACTGTATCCTG 60.351 46.154 1.46 0.00 0.00 3.86
1886 2329 5.629849 CCATTCGATAGTCTGTTTATCCGTC 59.370 44.000 0.00 0.00 37.40 4.79
2025 2494 7.145985 GCGAAGAACATCAAGACCTGTATATA 58.854 38.462 0.00 0.00 0.00 0.86
2391 2871 5.013495 AGAGACCAAAATGACTGATGGAGAA 59.987 40.000 0.00 0.00 36.75 2.87
2392 2872 4.533707 AGAGACCAAAATGACTGATGGAGA 59.466 41.667 0.00 0.00 36.75 3.71
2393 2873 4.841422 AGAGACCAAAATGACTGATGGAG 58.159 43.478 0.00 0.00 36.75 3.86
2394 2874 4.916041 AGAGACCAAAATGACTGATGGA 57.084 40.909 0.00 0.00 36.75 3.41
2395 2875 5.251764 AGAAGAGACCAAAATGACTGATGG 58.748 41.667 0.00 0.00 38.91 3.51
2396 2876 7.102346 ACTAGAAGAGACCAAAATGACTGATG 58.898 38.462 0.00 0.00 0.00 3.07
2397 2877 7.251321 ACTAGAAGAGACCAAAATGACTGAT 57.749 36.000 0.00 0.00 0.00 2.90
2399 2879 7.442364 TGAAACTAGAAGAGACCAAAATGACTG 59.558 37.037 0.00 0.00 0.00 3.51
2400 2880 7.442666 GTGAAACTAGAAGAGACCAAAATGACT 59.557 37.037 0.00 0.00 0.00 3.41
2461 2952 2.165030 CTGTGTGCATCTGAAATTCCCC 59.835 50.000 0.00 0.00 0.00 4.81
2698 3197 3.128589 ACAATACCATGAACATGCGGAAC 59.871 43.478 9.03 0.00 37.49 3.62
2923 3426 5.862924 ACATAGTGAAGTCCATTTGAACG 57.137 39.130 0.00 0.00 0.00 3.95
3001 5096 5.174395 TGGTTTTCAACACCTTTGAACATG 58.826 37.500 0.00 0.00 38.05 3.21
3239 5496 1.285078 GGGTGGCCTTTTACTGGAGAT 59.715 52.381 3.32 0.00 0.00 2.75
3322 5579 8.023128 GTCAATCTTTATTTGCAAAGCAGAGTA 58.977 33.333 18.19 0.83 40.61 2.59
3718 6006 4.317769 GCCAAACGTTTTGTTATGTGAAGC 60.318 41.667 11.66 0.00 40.84 3.86
3733 6021 2.446435 AGCCATAATTGAGCCAAACGT 58.554 42.857 0.00 0.00 0.00 3.99
3774 6062 4.439837 GCTACGTACGGAAAATCCTCTCTT 60.440 45.833 21.06 0.00 33.30 2.85
3775 6063 3.066481 GCTACGTACGGAAAATCCTCTCT 59.934 47.826 21.06 0.00 33.30 3.10
3776 6064 3.181493 TGCTACGTACGGAAAATCCTCTC 60.181 47.826 21.06 0.00 33.30 3.20
3925 6259 4.695560 AGGTACTTGGCGTGAAGC 57.304 55.556 0.00 0.00 40.67 3.86
4191 6567 0.905357 TTGGTTGGTTGGTTGGTTGG 59.095 50.000 0.00 0.00 0.00 3.77
4192 6568 1.406205 GGTTGGTTGGTTGGTTGGTTG 60.406 52.381 0.00 0.00 0.00 3.77
4193 6569 0.906066 GGTTGGTTGGTTGGTTGGTT 59.094 50.000 0.00 0.00 0.00 3.67
4194 6570 1.324005 CGGTTGGTTGGTTGGTTGGT 61.324 55.000 0.00 0.00 0.00 3.67
4391 6791 4.097892 TCTTTTCTTCTCTTTTGGCACACC 59.902 41.667 0.00 0.00 39.29 4.16
4455 6860 3.106242 TGCATCCGACCATACATACAC 57.894 47.619 0.00 0.00 0.00 2.90
4589 7096 9.781425 ATCTCTTGATAGATAGTGGTATGGAAT 57.219 33.333 0.00 0.00 34.40 3.01
4735 7247 5.360714 GGCAATGGAGGAAGATTCAACATTA 59.639 40.000 7.71 0.00 30.60 1.90
4869 7396 4.679662 CTTGTTGAATGGATGCAATCTCC 58.320 43.478 3.80 0.00 44.71 3.71
4960 7487 2.301870 AGTATTCTTGTCCAAGCGTCCA 59.698 45.455 2.09 0.00 38.28 4.02


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

AutoCloner maintained by Alex Coulton.