Multiple sequence alignment - TraesCS7A01G017300

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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 TraesCS7A01G017300 chr7A 100.000 4678 0 0 1 4678 7520990 7525667 0.000000e+00 8639
1 TraesCS7A01G017300 chr7A 99.610 513 0 1 882 1394 7510506 7511016 0.000000e+00 935
2 TraesCS7A01G017300 chr7A 96.923 325 10 0 3779 4103 7543254 7543578 3.180000e-151 545
3 TraesCS7A01G017300 chr7A 90.333 300 23 3 1625 1924 388776334 388776041 5.680000e-104 388
4 TraesCS7A01G017300 chr7A 92.488 213 14 2 2197 2408 388772012 388771801 2.120000e-78 303
5 TraesCS7A01G017300 chr7A 95.082 183 5 3 4103 4282 7543621 7543802 7.660000e-73 285
6 TraesCS7A01G017300 chr7A 93.985 133 8 0 2983 3115 388769699 388769567 7.940000e-48 202
7 TraesCS7A01G017300 chr7A 93.893 131 7 1 2499 2628 388771527 388771397 3.690000e-46 196
8 TraesCS7A01G017300 chr7A 92.969 128 7 1 2856 2981 388770549 388770422 7.990000e-43 185
9 TraesCS7A01G017300 chr7A 90.833 120 3 4 2743 2862 388771107 388770996 2.250000e-33 154
10 TraesCS7A01G017300 chr7A 93.407 91 6 0 2407 2497 388771714 388771624 8.160000e-28 135
11 TraesCS7A01G017300 chr4A 94.219 3944 124 44 753 4678 734053923 734050066 0.000000e+00 5925
12 TraesCS7A01G017300 chr7D 93.697 2364 67 42 773 3115 6131208 6133510 0.000000e+00 3465
13 TraesCS7A01G017300 chr7D 95.766 496 21 0 3232 3727 6133611 6134106 0.000000e+00 800
14 TraesCS7A01G017300 chr7D 93.040 546 21 6 1054 1591 559087589 559087053 0.000000e+00 782
15 TraesCS7A01G017300 chr7D 97.853 326 7 0 3779 4104 6134245 6134570 8.790000e-157 564
16 TraesCS7A01G017300 chr7D 92.857 364 12 5 1236 1591 123240435 123240078 2.500000e-142 516
17 TraesCS7A01G017300 chr7D 92.162 370 15 5 1230 1591 118612150 118612513 1.160000e-140 510
18 TraesCS7A01G017300 chr7D 92.254 284 16 3 1625 1908 332255936 332256213 9.430000e-107 398
19 TraesCS7A01G017300 chr7D 96.685 181 5 1 4103 4282 6134612 6134792 2.740000e-77 300
20 TraesCS7A01G017300 chr7D 92.019 213 15 2 2197 2408 332260275 332260486 9.840000e-77 298
21 TraesCS7A01G017300 chr7D 94.656 131 6 1 2499 2628 332260758 332260888 7.940000e-48 202
22 TraesCS7A01G017300 chr7D 93.985 133 8 0 2983 3115 332262624 332262756 7.940000e-48 202
23 TraesCS7A01G017300 chr7D 92.188 128 8 1 2856 2981 332261769 332261896 3.720000e-41 180
24 TraesCS7A01G017300 chr7D 94.340 106 6 0 2633 2738 332260987 332261092 3.750000e-36 163
25 TraesCS7A01G017300 chr7D 90.833 120 3 4 2743 2862 332261178 332261289 2.250000e-33 154
26 TraesCS7A01G017300 chrUn 95.918 1176 41 5 3121 4290 341303662 341304836 0.000000e+00 1899
27 TraesCS7A01G017300 chrUn 96.224 874 32 1 3121 3994 354467218 354468090 0.000000e+00 1430
28 TraesCS7A01G017300 chrUn 95.137 329 15 1 3779 4107 391284062 391283735 6.940000e-143 518
29 TraesCS7A01G017300 chrUn 95.399 326 14 1 3779 4104 460727099 460727423 6.940000e-143 518
30 TraesCS7A01G017300 chrUn 98.230 113 1 1 4103 4214 391283696 391283584 3.690000e-46 196
31 TraesCS7A01G017300 chrUn 98.230 113 1 1 4103 4214 460727465 460727577 3.690000e-46 196
32 TraesCS7A01G017300 chr7B 93.445 717 33 11 1 713 679384404 679383698 0.000000e+00 1051
33 TraesCS7A01G017300 chr7B 90.878 296 21 3 1625 1920 300089683 300089394 4.390000e-105 392
34 TraesCS7A01G017300 chr7B 92.958 213 13 2 2197 2408 300085633 300085422 4.550000e-80 309
35 TraesCS7A01G017300 chr7B 93.985 133 8 0 2983 3115 300083294 300083162 7.940000e-48 202
36 TraesCS7A01G017300 chr7B 93.893 131 7 1 2499 2628 300085150 300085020 3.690000e-46 196
37 TraesCS7A01G017300 chr7B 92.969 128 7 1 2856 2981 300084137 300084010 7.990000e-43 185
38 TraesCS7A01G017300 chr7B 95.283 106 5 0 2633 2738 300084920 300084815 8.050000e-38 169
39 TraesCS7A01G017300 chr7B 90.833 120 3 4 2743 2862 300084729 300084618 2.250000e-33 154
40 TraesCS7A01G017300 chr3B 92.673 737 42 9 1 732 22888079 22888808 0.000000e+00 1051
41 TraesCS7A01G017300 chr3B 91.734 738 46 13 4 733 806668366 806669096 0.000000e+00 1011
42 TraesCS7A01G017300 chr2B 90.786 738 58 8 1 732 525251115 525251848 0.000000e+00 977
43 TraesCS7A01G017300 chr1B 87.821 739 58 18 1 732 144875673 144874960 0.000000e+00 837
44 TraesCS7A01G017300 chr1B 93.870 261 16 0 3779 4039 252371251 252371511 1.220000e-105 394
45 TraesCS7A01G017300 chr1B 86.592 179 24 0 4497 4675 252326551 252326729 1.030000e-46 198
46 TraesCS7A01G017300 chr6B 87.169 756 62 17 1 732 513799488 513798744 0.000000e+00 826
47 TraesCS7A01G017300 chr6B 85.695 748 76 18 1 726 646940477 646941215 0.000000e+00 760
48 TraesCS7A01G017300 chr6B 94.091 220 11 1 1484 1703 243493221 243493004 2.700000e-87 333
49 TraesCS7A01G017300 chr4B 86.774 620 67 13 118 732 602335840 602335231 0.000000e+00 676
50 TraesCS7A01G017300 chr1D 86.780 590 67 9 143 727 16685042 16684459 0.000000e+00 647
51 TraesCS7A01G017300 chr1D 87.805 369 13 7 1230 1590 431532245 431532589 2.030000e-108 403
52 TraesCS7A01G017300 chr4D 92.703 370 13 5 1230 1591 407245023 407244660 5.360000e-144 521
53 TraesCS7A01G017300 chr4D 92.432 370 14 5 1230 1591 58372215 58372578 2.500000e-142 516
54 TraesCS7A01G017300 chr4D 92.432 370 14 5 1230 1591 286304715 286305078 2.500000e-142 516
55 TraesCS7A01G017300 chr2A 85.742 519 40 15 4180 4678 503442257 503441753 6.940000e-143 518
56 TraesCS7A01G017300 chr2A 91.892 370 19 4 1230 1591 145271337 145271703 1.500000e-139 507
57 TraesCS7A01G017300 chr6D 92.432 370 14 5 1230 1591 463099361 463099724 2.500000e-142 516
58 TraesCS7A01G017300 chr5D 92.857 364 12 5 1236 1591 401976302 401975945 2.500000e-142 516
59 TraesCS7A01G017300 chr2D 92.432 370 13 5 1230 1591 521627917 521628279 8.980000e-142 514
60 TraesCS7A01G017300 chr3A 92.694 219 12 3 3779 3996 715829398 715829613 3.510000e-81 313
61 TraesCS7A01G017300 chr3A 89.157 166 11 3 4103 4267 715879488 715879647 2.850000e-47 200


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 TraesCS7A01G017300 chr7A 7520990 7525667 4677 False 8639.000000 8639 100.000000 1 4678 1 chr7A.!!$F2 4677
1 TraesCS7A01G017300 chr7A 7510506 7511016 510 False 935.000000 935 99.610000 882 1394 1 chr7A.!!$F1 512
2 TraesCS7A01G017300 chr7A 7543254 7543802 548 False 415.000000 545 96.002500 3779 4282 2 chr7A.!!$F3 503
3 TraesCS7A01G017300 chr4A 734050066 734053923 3857 True 5925.000000 5925 94.219000 753 4678 1 chr4A.!!$R1 3925
4 TraesCS7A01G017300 chr7D 6131208 6134792 3584 False 1282.250000 3465 96.000250 773 4282 4 chr7D.!!$F3 3509
5 TraesCS7A01G017300 chr7D 559087053 559087589 536 True 782.000000 782 93.040000 1054 1591 1 chr7D.!!$R2 537
6 TraesCS7A01G017300 chrUn 341303662 341304836 1174 False 1899.000000 1899 95.918000 3121 4290 1 chrUn.!!$F1 1169
7 TraesCS7A01G017300 chrUn 354467218 354468090 872 False 1430.000000 1430 96.224000 3121 3994 1 chrUn.!!$F2 873
8 TraesCS7A01G017300 chr7B 679383698 679384404 706 True 1051.000000 1051 93.445000 1 713 1 chr7B.!!$R1 712
9 TraesCS7A01G017300 chr7B 300083162 300089683 6521 True 229.571429 392 92.971286 1625 3115 7 chr7B.!!$R2 1490
10 TraesCS7A01G017300 chr3B 22888079 22888808 729 False 1051.000000 1051 92.673000 1 732 1 chr3B.!!$F1 731
11 TraesCS7A01G017300 chr3B 806668366 806669096 730 False 1011.000000 1011 91.734000 4 733 1 chr3B.!!$F2 729
12 TraesCS7A01G017300 chr2B 525251115 525251848 733 False 977.000000 977 90.786000 1 732 1 chr2B.!!$F1 731
13 TraesCS7A01G017300 chr1B 144874960 144875673 713 True 837.000000 837 87.821000 1 732 1 chr1B.!!$R1 731
14 TraesCS7A01G017300 chr6B 513798744 513799488 744 True 826.000000 826 87.169000 1 732 1 chr6B.!!$R2 731
15 TraesCS7A01G017300 chr6B 646940477 646941215 738 False 760.000000 760 85.695000 1 726 1 chr6B.!!$F1 725
16 TraesCS7A01G017300 chr4B 602335231 602335840 609 True 676.000000 676 86.774000 118 732 1 chr4B.!!$R1 614
17 TraesCS7A01G017300 chr1D 16684459 16685042 583 True 647.000000 647 86.780000 143 727 1 chr1D.!!$R1 584
18 TraesCS7A01G017300 chr2A 503441753 503442257 504 True 518.000000 518 85.742000 4180 4678 1 chr2A.!!$R1 498

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
796 960 0.040351 TCATTTGGGGGCGGAAATGA 59.960 50.0 11.11 11.11 43.18 2.57 F
803 967 0.178990 GGGGCGGAAATGAGGCTTAT 60.179 55.0 0.00 0.00 0.00 1.73 F
864 1028 1.325476 ATTACCAGGGACGACGGGAC 61.325 60.0 0.00 0.00 0.00 4.46 F
3497 8741 1.444836 TTTCAACGCTTGGTATCGGG 58.555 50.0 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 6444 1.462627 TCCGAACTTGGTTCCCCCT 60.463 57.895 5.06 0.0 39.14 4.79 R
3141 8385 3.301835 GCGCACATGAACTAAGTATCACG 60.302 47.826 0.30 0.0 0.00 4.35 R
3633 8877 3.896888 TCAACTGGAGAAATGGCAAATGT 59.103 39.130 0.00 0.0 0.00 2.71 R
4571 9990 0.108138 GATCAAGGGTGACTGGGACG 60.108 60.000 0.00 0.0 36.31 4.79 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
41 42 8.927315 TTCGCGCAGTTAAACATTAATATATG 57.073 30.769 8.75 0.00 0.00 1.78
509 658 6.126623 GGAGAAAAGAGGGAAGGACATAGAAT 60.127 42.308 0.00 0.00 0.00 2.40
529 679 2.863401 AAAAACGTGAAGAAGGGCAC 57.137 45.000 0.00 0.00 0.00 5.01
571 721 4.831155 TGTAGTCTAGTGGTTAGTGCAGTT 59.169 41.667 0.00 0.00 0.00 3.16
733 897 2.094675 GCGCCAAATAGGATATGCCAT 58.905 47.619 0.00 0.00 41.22 4.40
734 898 2.098117 GCGCCAAATAGGATATGCCATC 59.902 50.000 0.00 0.00 41.22 3.51
735 899 2.684881 CGCCAAATAGGATATGCCATCC 59.315 50.000 6.36 6.36 41.22 3.51
736 900 3.700538 GCCAAATAGGATATGCCATCCA 58.299 45.455 14.93 3.96 41.22 3.41
737 901 4.284178 GCCAAATAGGATATGCCATCCAT 58.716 43.478 14.93 5.72 41.22 3.41
738 902 5.448654 GCCAAATAGGATATGCCATCCATA 58.551 41.667 14.93 6.63 41.22 2.74
739 903 5.893255 GCCAAATAGGATATGCCATCCATAA 59.107 40.000 14.93 2.99 41.22 1.90
740 904 6.552350 GCCAAATAGGATATGCCATCCATAAT 59.448 38.462 14.93 4.81 41.22 1.28
741 905 7.255730 GCCAAATAGGATATGCCATCCATAATC 60.256 40.741 14.93 0.00 41.22 1.75
742 906 7.040892 CCAAATAGGATATGCCATCCATAATCG 60.041 40.741 14.93 1.76 39.71 3.34
743 907 3.813443 AGGATATGCCATCCATAATCGC 58.187 45.455 14.93 0.00 39.71 4.58
744 908 2.545526 GGATATGCCATCCATAATCGCG 59.454 50.000 0.00 0.00 39.71 5.87
745 909 1.368641 TATGCCATCCATAATCGCGC 58.631 50.000 0.00 0.00 33.56 6.86
746 910 0.321919 ATGCCATCCATAATCGCGCT 60.322 50.000 5.56 0.00 30.69 5.92
747 911 0.320050 TGCCATCCATAATCGCGCTA 59.680 50.000 5.56 0.00 0.00 4.26
748 912 1.066215 TGCCATCCATAATCGCGCTAT 60.066 47.619 5.56 0.00 0.00 2.97
749 913 2.167487 TGCCATCCATAATCGCGCTATA 59.833 45.455 5.56 0.00 0.00 1.31
750 914 2.797156 GCCATCCATAATCGCGCTATAG 59.203 50.000 5.56 0.00 0.00 1.31
751 915 3.384668 CCATCCATAATCGCGCTATAGG 58.615 50.000 5.56 3.74 0.00 2.57
756 920 0.815734 TAATCGCGCTATAGGGGAGC 59.184 55.000 17.62 0.00 36.54 4.70
794 958 0.687427 CCTCATTTGGGGGCGGAAAT 60.687 55.000 0.00 0.00 0.00 2.17
795 959 0.461135 CTCATTTGGGGGCGGAAATG 59.539 55.000 0.00 0.00 39.79 2.32
796 960 0.040351 TCATTTGGGGGCGGAAATGA 59.960 50.000 11.11 11.11 43.18 2.57
797 961 0.461135 CATTTGGGGGCGGAAATGAG 59.539 55.000 8.13 0.00 40.53 2.90
799 963 3.955543 TTGGGGGCGGAAATGAGGC 62.956 63.158 0.00 0.00 0.00 4.70
800 964 4.129148 GGGGGCGGAAATGAGGCT 62.129 66.667 0.00 0.00 0.00 4.58
801 965 2.043953 GGGGCGGAAATGAGGCTT 60.044 61.111 0.00 0.00 0.00 4.35
802 966 1.226262 GGGGCGGAAATGAGGCTTA 59.774 57.895 0.00 0.00 0.00 3.09
803 967 0.178990 GGGGCGGAAATGAGGCTTAT 60.179 55.000 0.00 0.00 0.00 1.73
804 968 1.692411 GGGCGGAAATGAGGCTTATT 58.308 50.000 0.00 0.00 0.00 1.40
805 969 2.031870 GGGCGGAAATGAGGCTTATTT 58.968 47.619 16.16 16.16 0.00 1.40
806 970 2.034685 GGGCGGAAATGAGGCTTATTTC 59.965 50.000 27.52 27.52 41.53 2.17
811 975 4.105486 GGAAATGAGGCTTATTTCGTTGC 58.895 43.478 27.94 16.35 42.59 4.17
813 977 4.622701 AATGAGGCTTATTTCGTTGCTC 57.377 40.909 0.00 0.00 0.00 4.26
836 1000 3.011517 AGCCCACGAAGAGCCCAT 61.012 61.111 0.00 0.00 0.00 4.00
853 1017 3.873910 CCCATCGGCTAATATTACCAGG 58.126 50.000 11.97 10.12 0.00 4.45
854 1018 3.370527 CCCATCGGCTAATATTACCAGGG 60.371 52.174 14.57 14.57 0.00 4.45
855 1019 3.517901 CCATCGGCTAATATTACCAGGGA 59.482 47.826 11.97 0.00 0.00 4.20
856 1020 4.504858 CATCGGCTAATATTACCAGGGAC 58.495 47.826 11.97 0.00 0.00 4.46
857 1021 2.559668 TCGGCTAATATTACCAGGGACG 59.440 50.000 11.97 7.44 0.00 4.79
858 1022 2.559668 CGGCTAATATTACCAGGGACGA 59.440 50.000 1.68 0.00 0.00 4.20
859 1023 3.613432 CGGCTAATATTACCAGGGACGAC 60.613 52.174 1.68 0.00 0.00 4.34
864 1028 1.325476 ATTACCAGGGACGACGGGAC 61.325 60.000 0.00 0.00 0.00 4.46
1367 1545 5.604231 TGTCTCATATCCCTAAAGCACTGAT 59.396 40.000 0.00 0.00 0.00 2.90
1403 1591 3.197983 GGTGATATCCCTAGTATGTGGCC 59.802 52.174 0.00 0.00 0.00 5.36
1510 1707 6.145535 CCTTTTTGTTGACTGCTTGTAGATC 58.854 40.000 0.00 0.00 0.00 2.75
1527 1724 7.661536 TGTAGATCTTGTCTATGCCTTTAGT 57.338 36.000 0.00 0.00 41.33 2.24
1700 1897 2.505407 TCAGCCATGCATTAGTGTACCT 59.495 45.455 0.00 0.00 0.00 3.08
1701 1898 3.709141 TCAGCCATGCATTAGTGTACCTA 59.291 43.478 0.00 0.00 0.00 3.08
1813 2010 3.748568 GGTCAAGTTCTTGTGAGGATGAC 59.251 47.826 11.52 0.00 36.18 3.06
2229 5911 5.680229 CAGTTTCGATAATTGATTGCTCAGC 59.320 40.000 0.00 0.00 31.68 4.26
2578 6444 2.586425 CTCCTTTCTTTGCAACTCCCA 58.414 47.619 0.00 0.00 0.00 4.37
2826 6868 4.079787 ACAAGTGTATCCCCAACAGCATAT 60.080 41.667 0.00 0.00 0.00 1.78
2884 7412 3.442625 CACATCCAAGATCAACTGTGCAT 59.557 43.478 0.00 0.00 0.00 3.96
3141 8385 6.846350 GCATAGACATCATGCTTTTATACCC 58.154 40.000 0.18 0.00 44.35 3.69
3366 8610 8.552469 TCTTTATTTCTATTGTAGCGTACGAC 57.448 34.615 21.65 9.98 0.00 4.34
3497 8741 1.444836 TTTCAACGCTTGGTATCGGG 58.555 50.000 0.00 0.00 0.00 5.14
3632 8876 4.937620 TCAGCTATTGTGGTGAAAGTCATC 59.062 41.667 0.00 0.00 40.82 2.92
3633 8877 4.696877 CAGCTATTGTGGTGAAAGTCATCA 59.303 41.667 0.00 0.00 34.65 3.07
3671 8915 3.519510 CAGTTGAGGAACCCAAGGAGATA 59.480 47.826 0.00 0.00 31.81 1.98
3682 8926 4.353191 ACCCAAGGAGATAGCATGATCATT 59.647 41.667 5.16 0.00 0.00 2.57
3685 8929 5.585445 CCAAGGAGATAGCATGATCATTAGC 59.415 44.000 5.16 7.72 0.00 3.09
3720 8964 9.878599 AGTCATATGAACTTTTTGTTTAAGTCG 57.121 29.630 7.07 0.00 39.30 4.18
3721 8965 8.627428 GTCATATGAACTTTTTGTTTAAGTCGC 58.373 33.333 7.07 0.00 39.30 5.19
3747 8991 6.465781 CGTGTTATGTACTGCAATTTGTGATC 59.534 38.462 0.00 0.00 0.00 2.92
3838 9169 1.964223 GGAGCTCCATCGACCTATCAA 59.036 52.381 28.43 0.00 35.64 2.57
3847 9178 4.262207 CCATCGACCTATCAACACTGCTAT 60.262 45.833 0.00 0.00 0.00 2.97
3945 9276 6.395426 TTGAGCTTGACATTCATTTTGTCT 57.605 33.333 5.52 0.00 43.12 3.41
3978 9309 2.213499 CTCTTGGTGCTGTTCGAGTTT 58.787 47.619 0.00 0.00 0.00 2.66
3994 9325 4.338118 TCGAGTTTTGCATGTTCCTTCTTT 59.662 37.500 0.00 0.00 0.00 2.52
4067 9398 0.969894 AGTTCCGGTCCAGTCTTCAG 59.030 55.000 0.00 0.00 0.00 3.02
4290 9675 8.547481 TTCCTATCTGTCTTACATGGTATCAA 57.453 34.615 0.00 0.00 0.00 2.57
4291 9676 7.952671 TCCTATCTGTCTTACATGGTATCAAC 58.047 38.462 0.00 0.00 0.00 3.18
4292 9677 7.785028 TCCTATCTGTCTTACATGGTATCAACT 59.215 37.037 0.00 0.00 0.00 3.16
4293 9678 9.078990 CCTATCTGTCTTACATGGTATCAACTA 57.921 37.037 0.00 0.00 0.00 2.24
4354 9755 1.486211 TCGATCCTCCTCCTCAAACC 58.514 55.000 0.00 0.00 0.00 3.27
4355 9756 0.466124 CGATCCTCCTCCTCAAACCC 59.534 60.000 0.00 0.00 0.00 4.11
4356 9757 0.840617 GATCCTCCTCCTCAAACCCC 59.159 60.000 0.00 0.00 0.00 4.95
4357 9758 0.423544 ATCCTCCTCCTCAAACCCCT 59.576 55.000 0.00 0.00 0.00 4.79
4397 9798 0.172127 CTGAAGAGCTCGCAGCACTA 59.828 55.000 21.28 0.08 45.56 2.74
4417 9819 4.569180 ACCCAGCTGCAGCAACGT 62.569 61.111 38.24 26.39 45.16 3.99
4418 9820 4.034258 CCCAGCTGCAGCAACGTG 62.034 66.667 38.24 26.85 45.16 4.49
4419 9821 2.974148 CCAGCTGCAGCAACGTGA 60.974 61.111 38.24 0.00 45.16 4.35
4420 9822 2.554775 CAGCTGCAGCAACGTGAG 59.445 61.111 38.24 15.70 45.16 3.51
4421 9823 2.667536 AGCTGCAGCAACGTGAGG 60.668 61.111 38.24 0.00 45.16 3.86
4422 9824 4.395583 GCTGCAGCAACGTGAGGC 62.396 66.667 33.36 2.16 41.59 4.70
4423 9825 2.667536 CTGCAGCAACGTGAGGCT 60.668 61.111 0.00 4.01 42.06 4.58
4429 9831 3.414700 CAACGTGAGGCTGCCGTC 61.415 66.667 13.96 11.66 32.95 4.79
4450 9866 2.665603 GAACGGGAGGCTGAGCTT 59.334 61.111 3.72 0.00 0.00 3.74
4545 9964 1.130054 ATACCATCCCGCAGCATCCT 61.130 55.000 0.00 0.00 0.00 3.24
4571 9990 5.856126 TCGTCCACTCAATCAAAACATAC 57.144 39.130 0.00 0.00 0.00 2.39
4619 10038 1.134818 TCGAACTATGCTCAATGGCGT 60.135 47.619 0.00 0.00 35.47 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
414 560 5.404466 TCTTTTGGCCAAATCGAATGATT 57.596 34.783 30.78 0.00 46.75 2.57
415 561 5.404466 TTCTTTTGGCCAAATCGAATGAT 57.596 34.783 30.78 0.00 35.98 2.45
509 658 3.547746 AGTGCCCTTCTTCACGTTTTTA 58.452 40.909 0.00 0.00 38.19 1.52
546 696 3.762288 TGCACTAACCACTAGACTACAGG 59.238 47.826 0.00 0.00 0.00 4.00
571 721 2.279073 CCTCCTGCTCGAGGGGTA 59.721 66.667 15.58 0.00 41.60 3.69
733 897 1.754803 CCCCTATAGCGCGATTATGGA 59.245 52.381 12.10 0.00 0.00 3.41
734 898 1.754803 TCCCCTATAGCGCGATTATGG 59.245 52.381 12.10 8.85 0.00 2.74
735 899 2.799917 GCTCCCCTATAGCGCGATTATG 60.800 54.545 12.10 0.00 0.00 1.90
736 900 1.409427 GCTCCCCTATAGCGCGATTAT 59.591 52.381 12.10 9.65 0.00 1.28
737 901 0.815734 GCTCCCCTATAGCGCGATTA 59.184 55.000 12.10 0.74 0.00 1.75
738 902 0.900647 AGCTCCCCTATAGCGCGATT 60.901 55.000 12.10 0.00 44.87 3.34
739 903 1.304547 AGCTCCCCTATAGCGCGAT 60.305 57.895 12.10 5.99 44.87 4.58
740 904 1.972223 GAGCTCCCCTATAGCGCGA 60.972 63.158 12.10 0.00 44.87 5.87
741 905 2.569134 GAGCTCCCCTATAGCGCG 59.431 66.667 0.00 0.00 44.87 6.86
742 906 2.974717 GGAGCTCCCCTATAGCGC 59.025 66.667 23.19 0.00 44.87 5.92
756 920 2.703798 CCCGCACATTGCAAGGGAG 61.704 63.158 16.45 8.66 43.93 4.30
777 941 0.040351 TCATTTCCGCCCCCAAATGA 59.960 50.000 3.50 3.50 43.54 2.57
787 951 2.354821 ACGAAATAAGCCTCATTTCCGC 59.645 45.455 0.00 0.00 38.58 5.54
794 958 1.999735 CGAGCAACGAAATAAGCCTCA 59.000 47.619 0.00 0.00 45.77 3.86
795 959 1.327764 CCGAGCAACGAAATAAGCCTC 59.672 52.381 4.96 0.00 45.77 4.70
796 960 1.338769 ACCGAGCAACGAAATAAGCCT 60.339 47.619 4.96 0.00 45.77 4.58
797 961 1.084289 ACCGAGCAACGAAATAAGCC 58.916 50.000 4.96 0.00 45.77 4.35
799 963 3.725010 GCTGAACCGAGCAACGAAATAAG 60.725 47.826 4.96 0.00 45.77 1.73
800 964 2.158841 GCTGAACCGAGCAACGAAATAA 59.841 45.455 4.96 0.00 45.77 1.40
801 965 1.730064 GCTGAACCGAGCAACGAAATA 59.270 47.619 4.96 0.00 45.77 1.40
802 966 0.517316 GCTGAACCGAGCAACGAAAT 59.483 50.000 4.96 0.00 45.77 2.17
803 967 1.503818 GGCTGAACCGAGCAACGAAA 61.504 55.000 4.96 0.00 45.77 3.46
804 968 1.959226 GGCTGAACCGAGCAACGAA 60.959 57.895 4.96 0.00 45.77 3.85
805 969 2.357034 GGCTGAACCGAGCAACGA 60.357 61.111 4.96 0.00 45.77 3.85
806 970 3.423154 GGGCTGAACCGAGCAACG 61.423 66.667 0.00 0.00 41.08 4.10
811 975 1.738099 CTTCGTGGGCTGAACCGAG 60.738 63.158 0.00 0.00 40.62 4.63
813 977 1.738099 CTCTTCGTGGGCTGAACCG 60.738 63.158 0.00 0.00 40.62 4.44
836 1000 2.559668 CGTCCCTGGTAATATTAGCCGA 59.440 50.000 19.31 10.81 0.00 5.54
847 1011 2.361610 GTCCCGTCGTCCCTGGTA 60.362 66.667 0.00 0.00 0.00 3.25
879 1043 0.869454 CGCGATGTCTCTGGAAGCTC 60.869 60.000 0.00 0.00 0.00 4.09
880 1044 1.140589 CGCGATGTCTCTGGAAGCT 59.859 57.895 0.00 0.00 0.00 3.74
1403 1591 9.029243 CATTTCTACAATCAAGTACAGAGCTAG 57.971 37.037 0.00 0.00 0.00 3.42
1531 1728 6.131264 TGTTCATGGAAGCCTTTGATCATAT 58.869 36.000 0.00 0.00 0.00 1.78
1700 1897 7.882791 TGAGGCAGAGTTCAAACAGAAAATATA 59.117 33.333 0.00 0.00 38.13 0.86
1701 1898 6.716628 TGAGGCAGAGTTCAAACAGAAAATAT 59.283 34.615 0.00 0.00 38.13 1.28
1813 2010 2.742428 ATGATCCAATGGACACTGGG 57.258 50.000 3.09 0.00 32.98 4.45
2397 6081 3.056832 AGGAAAGGAGGAGTTGGAAAGT 58.943 45.455 0.00 0.00 0.00 2.66
2578 6444 1.462627 TCCGAACTTGGTTCCCCCT 60.463 57.895 5.06 0.00 39.14 4.79
3141 8385 3.301835 GCGCACATGAACTAAGTATCACG 60.302 47.826 0.30 0.00 0.00 4.35
3632 8876 3.947910 ACTGGAGAAATGGCAAATGTG 57.052 42.857 0.00 0.00 0.00 3.21
3633 8877 3.896888 TCAACTGGAGAAATGGCAAATGT 59.103 39.130 0.00 0.00 0.00 2.71
3671 8915 2.305343 GGAGGGAGCTAATGATCATGCT 59.695 50.000 17.83 17.83 38.59 3.79
3682 8926 2.450886 TCATATGACTGGGAGGGAGCTA 59.549 50.000 0.00 0.00 0.00 3.32
3685 8929 3.312890 AGTTCATATGACTGGGAGGGAG 58.687 50.000 4.48 0.00 0.00 4.30
3720 8964 3.757745 AATTGCAGTACATAACACGGC 57.242 42.857 0.00 0.00 37.57 5.68
3721 8965 4.851014 CACAAATTGCAGTACATAACACGG 59.149 41.667 0.00 0.00 0.00 4.94
3747 8991 4.801891 TCTTAAGTTATGCCGGTATAGCG 58.198 43.478 18.07 17.19 0.00 4.26
3945 9276 1.229428 CCAAGAGCAACTTTCTCGCA 58.771 50.000 0.00 0.00 36.61 5.10
3978 9309 3.698539 TGTGACAAAGAAGGAACATGCAA 59.301 39.130 0.00 0.00 0.00 4.08
3994 9325 4.276431 TGAATATATCCGCGTACTGTGACA 59.724 41.667 4.92 0.00 0.00 3.58
4026 9357 5.182001 ACTCATGAAACAATACAGCTGGAAC 59.818 40.000 19.93 0.00 0.00 3.62
4290 9675 3.259123 AGGAACGACCGGTGTTTAATAGT 59.741 43.478 14.63 0.00 44.74 2.12
4291 9676 3.853475 AGGAACGACCGGTGTTTAATAG 58.147 45.455 14.63 0.00 44.74 1.73
4292 9677 3.511146 AGAGGAACGACCGGTGTTTAATA 59.489 43.478 14.63 0.00 44.74 0.98
4293 9678 2.301009 AGAGGAACGACCGGTGTTTAAT 59.699 45.455 14.63 6.96 44.74 1.40
4294 9679 1.688197 AGAGGAACGACCGGTGTTTAA 59.312 47.619 14.63 0.00 44.74 1.52
4295 9680 1.331214 AGAGGAACGACCGGTGTTTA 58.669 50.000 14.63 0.00 44.74 2.01
4296 9681 0.466963 AAGAGGAACGACCGGTGTTT 59.533 50.000 14.63 3.86 44.74 2.83
4297 9682 0.033090 GAAGAGGAACGACCGGTGTT 59.967 55.000 14.63 17.15 44.74 3.32
4354 9755 3.728305 ATGGCAGAGGGAGGGAGGG 62.728 68.421 0.00 0.00 0.00 4.30
4355 9756 2.040043 ATGGCAGAGGGAGGGAGG 60.040 66.667 0.00 0.00 0.00 4.30
4356 9757 1.383664 TCATGGCAGAGGGAGGGAG 60.384 63.158 0.00 0.00 0.00 4.30
4357 9758 1.690633 GTCATGGCAGAGGGAGGGA 60.691 63.158 0.00 0.00 0.00 4.20
4397 9798 1.900498 GTTGCTGCAGCTGGGTCTT 60.900 57.895 36.61 0.00 42.66 3.01
4430 9832 4.821589 CTCAGCCTCCCGTTCGGC 62.822 72.222 5.66 0.00 46.65 5.54
4545 9964 3.762407 TTTGATTGAGTGGACGAAGGA 57.238 42.857 0.00 0.00 0.00 3.36
4571 9990 0.108138 GATCAAGGGTGACTGGGACG 60.108 60.000 0.00 0.00 36.31 4.79
4619 10038 2.701780 GGCGACGAGGAAGAGCTCA 61.702 63.158 17.77 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.