Multiple sequence alignment - TraesCS7D01G290800

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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 TraesCS7D01G290800 chr7D 100.000 4998 0 0 1 4998 345582000 345577003 0.000000e+00 9230.0
1 TraesCS7D01G290800 chr7B 97.483 1510 30 6 2816 4319 277651869 277653376 0.000000e+00 2571.0
2 TraesCS7D01G290800 chr7B 97.286 1400 25 7 1326 2722 277650481 277651870 0.000000e+00 2362.0
3 TraesCS7D01G290800 chr7B 91.489 1363 63 20 1 1338 277649130 277650464 0.000000e+00 1825.0
4 TraesCS7D01G290800 chr7B 97.115 104 3 0 2714 2817 159510595 159510698 5.140000e-40 176.0
5 TraesCS7D01G290800 chr7B 96.154 104 4 0 2721 2824 706811142 706811039 2.390000e-38 171.0
6 TraesCS7D01G290800 chr7A 98.385 1424 16 4 2816 4236 354431214 354429795 0.000000e+00 2495.0
7 TraesCS7D01G290800 chr7A 96.731 1407 28 8 1321 2722 354432606 354431213 0.000000e+00 2327.0
8 TraesCS7D01G290800 chr7A 97.484 636 10 5 699 1330 354433260 354432627 0.000000e+00 1081.0
9 TraesCS7D01G290800 chr7A 90.264 719 41 9 1 699 354434951 354434242 0.000000e+00 913.0
10 TraesCS7D01G290800 chr7A 90.996 522 37 5 4317 4830 580659091 580659610 0.000000e+00 695.0
11 TraesCS7D01G290800 chr7A 91.860 86 5 1 4239 4322 354429507 354429422 8.790000e-23 119.0
12 TraesCS7D01G290800 chr3D 88.547 716 39 9 4324 4998 499599031 499598318 0.000000e+00 828.0
13 TraesCS7D01G290800 chr3D 88.272 486 24 5 4543 4996 225358729 225358245 7.310000e-153 551.0
14 TraesCS7D01G290800 chr3B 87.849 716 42 16 4322 4998 660333556 660332847 0.000000e+00 798.0
15 TraesCS7D01G290800 chr3B 96.262 107 3 1 2716 2821 806367809 806367703 1.850000e-39 174.0
16 TraesCS7D01G290800 chr3B 95.283 106 5 0 2715 2820 561029416 561029521 8.600000e-38 169.0
17 TraesCS7D01G290800 chr5D 87.101 721 48 11 4319 4998 117352497 117351781 0.000000e+00 774.0
18 TraesCS7D01G290800 chr4D 87.101 721 46 14 4319 4998 25180654 25179940 0.000000e+00 773.0
19 TraesCS7D01G290800 chr4D 78.599 1042 223 0 2940 3981 478765 479806 0.000000e+00 689.0
20 TraesCS7D01G290800 chr4D 89.529 191 16 3 2490 2677 362791984 362792173 6.470000e-59 239.0
21 TraesCS7D01G290800 chr4D 94.231 104 6 0 2721 2824 109074971 109074868 5.180000e-35 159.0
22 TraesCS7D01G290800 chr6D 86.676 713 52 10 4319 4991 158871096 158871805 0.000000e+00 750.0
23 TraesCS7D01G290800 chr5A 88.604 623 47 8 4320 4920 262230977 262231597 0.000000e+00 736.0
24 TraesCS7D01G290800 chr5A 88.442 199 17 6 2489 2683 291594550 291594746 8.360000e-58 235.0
25 TraesCS7D01G290800 chr4B 88.387 620 49 8 4322 4920 660587122 660587739 0.000000e+00 725.0
26 TraesCS7D01G290800 chr4B 78.332 1043 224 2 2940 3981 1322625 1321584 0.000000e+00 673.0
27 TraesCS7D01G290800 chr2B 85.814 719 61 9 4320 4998 361568781 361568064 0.000000e+00 725.0
28 TraesCS7D01G290800 chr4A 78.599 1042 223 0 2940 3981 210782 211823 0.000000e+00 689.0
29 TraesCS7D01G290800 chr4A 89.894 188 15 4 2493 2677 457823951 457823765 6.470000e-59 239.0
30 TraesCS7D01G290800 chr1D 88.548 489 40 6 4446 4920 390426145 390426631 3.350000e-161 579.0
31 TraesCS7D01G290800 chr1B 81.970 660 85 7 4371 4998 262535114 262535771 3.430000e-146 529.0
32 TraesCS7D01G290800 chr1A 84.118 340 21 7 4691 4998 253288225 253288563 1.050000e-76 298.0
33 TraesCS7D01G290800 chr1A 90.761 184 14 3 2499 2679 7949504 7949687 5.000000e-60 243.0
34 TraesCS7D01G290800 chr1A 88.945 199 13 8 2490 2684 581544080 581543887 2.330000e-58 237.0
35 TraesCS7D01G290800 chr1A 98.000 100 2 0 2721 2820 435510126 435510027 1.850000e-39 174.0
36 TraesCS7D01G290800 chrUn 91.160 181 14 1 2499 2677 30689240 30689420 1.390000e-60 244.0
37 TraesCS7D01G290800 chr6A 87.793 213 17 9 2484 2688 4043500 4043711 1.800000e-59 241.0
38 TraesCS7D01G290800 chr6A 97.468 79 2 0 4918 4996 20546695 20546617 8.730000e-28 135.0
39 TraesCS7D01G290800 chr2A 97.115 104 3 0 2721 2824 13287305 13287408 5.140000e-40 176.0
40 TraesCS7D01G290800 chr2A 98.000 100 2 0 2721 2820 704122592 704122493 1.850000e-39 174.0
41 TraesCS7D01G290800 chr2D 95.413 109 4 1 2721 2828 107204080 107204188 6.650000e-39 172.0
42 TraesCS7D01G290800 chr2D 88.312 77 9 0 4922 4998 352188975 352188899 5.330000e-15 93.5


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 TraesCS7D01G290800 chr7D 345577003 345582000 4997 True 9230.000000 9230 100.000000 1 4998 1 chr7D.!!$R1 4997
1 TraesCS7D01G290800 chr7B 277649130 277653376 4246 False 2252.666667 2571 95.419333 1 4319 3 chr7B.!!$F2 4318
2 TraesCS7D01G290800 chr7A 354429422 354434951 5529 True 1387.000000 2495 94.944800 1 4322 5 chr7A.!!$R1 4321
3 TraesCS7D01G290800 chr7A 580659091 580659610 519 False 695.000000 695 90.996000 4317 4830 1 chr7A.!!$F1 513
4 TraesCS7D01G290800 chr3D 499598318 499599031 713 True 828.000000 828 88.547000 4324 4998 1 chr3D.!!$R2 674
5 TraesCS7D01G290800 chr3B 660332847 660333556 709 True 798.000000 798 87.849000 4322 4998 1 chr3B.!!$R1 676
6 TraesCS7D01G290800 chr5D 117351781 117352497 716 True 774.000000 774 87.101000 4319 4998 1 chr5D.!!$R1 679
7 TraesCS7D01G290800 chr4D 25179940 25180654 714 True 773.000000 773 87.101000 4319 4998 1 chr4D.!!$R1 679
8 TraesCS7D01G290800 chr4D 478765 479806 1041 False 689.000000 689 78.599000 2940 3981 1 chr4D.!!$F1 1041
9 TraesCS7D01G290800 chr6D 158871096 158871805 709 False 750.000000 750 86.676000 4319 4991 1 chr6D.!!$F1 672
10 TraesCS7D01G290800 chr5A 262230977 262231597 620 False 736.000000 736 88.604000 4320 4920 1 chr5A.!!$F1 600
11 TraesCS7D01G290800 chr4B 660587122 660587739 617 False 725.000000 725 88.387000 4322 4920 1 chr4B.!!$F1 598
12 TraesCS7D01G290800 chr4B 1321584 1322625 1041 True 673.000000 673 78.332000 2940 3981 1 chr4B.!!$R1 1041
13 TraesCS7D01G290800 chr2B 361568064 361568781 717 True 725.000000 725 85.814000 4320 4998 1 chr2B.!!$R1 678
14 TraesCS7D01G290800 chr4A 210782 211823 1041 False 689.000000 689 78.599000 2940 3981 1 chr4A.!!$F1 1041
15 TraesCS7D01G290800 chr1B 262535114 262535771 657 False 529.000000 529 81.970000 4371 4998 1 chr1B.!!$F1 627


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
133 134 0.179200 GCCTTGTAACATTGTCGCGG 60.179 55.000 6.13 0.0 0.0 6.46 F
334 335 0.179234 TGACCTTTGGAGCACGACAA 59.821 50.000 0.00 0.0 0.0 3.18 F
390 400 0.904649 TGCTGCATGCCACTACTAGT 59.095 50.000 16.68 0.0 42.0 2.57 F
1494 2546 2.361438 CCTGGAACCTATCTCGTACCAC 59.639 54.545 0.00 0.0 0.0 4.16 F
2735 3792 2.019807 AAGTTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 3093 0.250234 TAGCTAACCTGTGCAGCCAG 59.750 55.000 0.00 0.00 35.88 4.85 R
2088 3141 0.744414 ACCCGGATGAAATGCAGACG 60.744 55.000 0.73 0.00 32.20 4.18 R
2134 3187 3.748048 CGCCACCATCATCCTAAATAGTG 59.252 47.826 0.00 0.00 0.00 2.74 R
3196 4254 1.605710 GCAGATCCATGACCAAATCGG 59.394 52.381 0.00 0.00 42.50 4.18 R
4626 5984 1.539388 CTAACATTGGCGCAAAGGACA 59.461 47.619 17.41 1.72 0.00 4.02 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
107 108 2.910360 CCATCTCCGTGGCCATCA 59.090 61.111 9.72 0.00 31.43 3.07
122 123 2.355197 CCATCACATCACGCCTTGTAA 58.645 47.619 0.00 0.00 0.00 2.41
133 134 0.179200 GCCTTGTAACATTGTCGCGG 60.179 55.000 6.13 0.00 0.00 6.46
136 137 1.902716 TTGTAACATTGTCGCGGCCG 61.903 55.000 24.05 24.05 0.00 6.13
188 189 0.738389 CGTTGAAGCAGTTGGGTGTT 59.262 50.000 0.00 0.00 0.00 3.32
288 289 3.831112 CATCGTATGAGATGCGTCAGAT 58.169 45.455 8.99 1.90 41.09 2.90
329 330 0.674895 ATCGCTGACCTTTGGAGCAC 60.675 55.000 0.00 0.00 32.70 4.40
330 331 2.671177 CGCTGACCTTTGGAGCACG 61.671 63.158 0.00 0.00 32.70 5.34
331 332 1.301716 GCTGACCTTTGGAGCACGA 60.302 57.895 0.00 0.00 32.70 4.35
333 334 0.249868 CTGACCTTTGGAGCACGACA 60.250 55.000 0.00 0.00 0.00 4.35
334 335 0.179234 TGACCTTTGGAGCACGACAA 59.821 50.000 0.00 0.00 0.00 3.18
354 364 5.460646 ACAATGACGGCTGTTAATTTTGAG 58.539 37.500 0.00 0.00 0.00 3.02
390 400 0.904649 TGCTGCATGCCACTACTAGT 59.095 50.000 16.68 0.00 42.00 2.57
404 414 2.656560 ACTAGTTGAGGACGCATGTC 57.343 50.000 0.00 0.00 44.72 3.06
480 495 3.556775 TGAAAAAGGACGAGTTGTAACGG 59.443 43.478 0.00 0.00 0.00 4.44
666 697 9.910267 TTTTGAGGGGTAGGTATTTTAGATTAC 57.090 33.333 0.00 0.00 0.00 1.89
667 698 8.865244 TTGAGGGGTAGGTATTTTAGATTACT 57.135 34.615 0.00 0.00 0.00 2.24
813 1826 4.845811 ACCAGTAGTGAGCGGAGT 57.154 55.556 0.00 0.00 0.00 3.85
1232 2254 3.621558 GTTGAGATCCGATCCCCTTTTT 58.378 45.455 4.67 0.00 0.00 1.94
1377 2429 8.757982 ACAGATTGCTAGATCCATGTTAAATT 57.242 30.769 0.00 0.00 0.00 1.82
1494 2546 2.361438 CCTGGAACCTATCTCGTACCAC 59.639 54.545 0.00 0.00 0.00 4.16
1638 2690 7.112779 CCTCCTTCATACCAGTTGATTACTTT 58.887 38.462 0.00 0.00 33.85 2.66
1949 3002 5.985530 ACACATGGACATACATCATCTTACG 59.014 40.000 0.00 0.00 0.00 3.18
2040 3093 5.847304 AGTTGGAAAAGGAAGCTGAAATTC 58.153 37.500 0.00 0.00 0.00 2.17
2088 3141 9.521503 GAACTTCTATCTTTTTATTTGCCCATC 57.478 33.333 0.00 0.00 0.00 3.51
2134 3187 3.565905 AATTGCTTACACTTGCTGCTC 57.434 42.857 0.00 0.00 0.00 4.26
2720 3777 5.163195 ACACATCCTTCTACCTCACAAAGTT 60.163 40.000 0.00 0.00 0.00 2.66
2721 3778 6.042781 ACACATCCTTCTACCTCACAAAGTTA 59.957 38.462 0.00 0.00 0.00 2.24
2722 3779 6.369065 CACATCCTTCTACCTCACAAAGTTAC 59.631 42.308 0.00 0.00 0.00 2.50
2723 3780 6.270231 ACATCCTTCTACCTCACAAAGTTACT 59.730 38.462 0.00 0.00 0.00 2.24
2724 3781 6.342338 TCCTTCTACCTCACAAAGTTACTC 57.658 41.667 0.00 0.00 0.00 2.59
2725 3782 5.245526 TCCTTCTACCTCACAAAGTTACTCC 59.754 44.000 0.00 0.00 0.00 3.85
2726 3783 5.479124 TTCTACCTCACAAAGTTACTCCC 57.521 43.478 0.00 0.00 0.00 4.30
2727 3784 4.748701 TCTACCTCACAAAGTTACTCCCT 58.251 43.478 0.00 0.00 0.00 4.20
2728 3785 4.771054 TCTACCTCACAAAGTTACTCCCTC 59.229 45.833 0.00 0.00 0.00 4.30
2729 3786 2.638363 ACCTCACAAAGTTACTCCCTCC 59.362 50.000 0.00 0.00 0.00 4.30
2730 3787 2.353803 CCTCACAAAGTTACTCCCTCCG 60.354 54.545 0.00 0.00 0.00 4.63
2731 3788 2.299297 CTCACAAAGTTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
2732 3789 2.701951 TCACAAAGTTACTCCCTCCGTT 59.298 45.455 0.00 0.00 0.00 4.44
2733 3790 3.064931 CACAAAGTTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
2734 3791 2.038164 ACAAAGTTACTCCCTCCGTTCC 59.962 50.000 0.00 0.00 0.00 3.62
2735 3792 2.019807 AAGTTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2736 3793 2.019807 AGTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2737 3794 2.332117 AGTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
2738 3795 2.707257 AGTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
2739 3796 3.329814 AGTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
2740 3797 4.533311 AGTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
2741 3798 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2742 3799 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2743 3800 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2744 3801 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2745 3802 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2746 3803 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2747 3804 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2748 3805 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2749 3806 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2750 3807 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2751 3808 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2752 3809 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2753 3810 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2754 3811 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2755 3812 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2756 3813 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2757 3814 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2758 3815 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2759 3816 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2786 3843 8.502105 ACTTTAGTACAAAGTTAGTGCAAAGT 57.498 30.769 14.04 0.00 37.18 2.66
2787 3844 8.953313 ACTTTAGTACAAAGTTAGTGCAAAGTT 58.047 29.630 14.04 0.00 37.18 2.66
2788 3845 9.221775 CTTTAGTACAAAGTTAGTGCAAAGTTG 57.778 33.333 0.00 0.00 0.00 3.16
2789 3846 6.131544 AGTACAAAGTTAGTGCAAAGTTGG 57.868 37.500 0.00 0.00 0.00 3.77
2790 3847 4.385358 ACAAAGTTAGTGCAAAGTTGGG 57.615 40.909 0.00 0.00 0.00 4.12
2791 3848 3.767131 ACAAAGTTAGTGCAAAGTTGGGT 59.233 39.130 0.00 0.00 0.00 4.51
2792 3849 4.142249 ACAAAGTTAGTGCAAAGTTGGGTC 60.142 41.667 0.00 0.00 0.00 4.46
2793 3850 3.290948 AGTTAGTGCAAAGTTGGGTCA 57.709 42.857 0.00 0.00 0.00 4.02
2794 3851 3.832527 AGTTAGTGCAAAGTTGGGTCAT 58.167 40.909 0.00 0.00 0.00 3.06
2795 3852 3.821033 AGTTAGTGCAAAGTTGGGTCATC 59.179 43.478 0.00 0.00 0.00 2.92
2796 3853 2.664402 AGTGCAAAGTTGGGTCATCT 57.336 45.000 0.00 0.00 0.00 2.90
2797 3854 3.788227 AGTGCAAAGTTGGGTCATCTA 57.212 42.857 0.00 0.00 0.00 1.98
2798 3855 4.307032 AGTGCAAAGTTGGGTCATCTAT 57.693 40.909 0.00 0.00 0.00 1.98
2799 3856 4.666512 AGTGCAAAGTTGGGTCATCTATT 58.333 39.130 0.00 0.00 0.00 1.73
2800 3857 5.079643 AGTGCAAAGTTGGGTCATCTATTT 58.920 37.500 0.00 0.00 0.00 1.40
2801 3858 5.539955 AGTGCAAAGTTGGGTCATCTATTTT 59.460 36.000 0.00 0.00 0.00 1.82
2802 3859 5.634859 GTGCAAAGTTGGGTCATCTATTTTG 59.365 40.000 0.00 0.00 0.00 2.44
2803 3860 5.170748 GCAAAGTTGGGTCATCTATTTTGG 58.829 41.667 0.00 0.00 0.00 3.28
2804 3861 5.047377 GCAAAGTTGGGTCATCTATTTTGGA 60.047 40.000 0.00 0.00 0.00 3.53
2805 3862 6.518200 GCAAAGTTGGGTCATCTATTTTGGAA 60.518 38.462 0.00 0.00 0.00 3.53
2806 3863 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2807 3864 5.640147 AGTTGGGTCATCTATTTTGGAACA 58.360 37.500 0.00 0.00 0.00 3.18
2808 3865 5.711976 AGTTGGGTCATCTATTTTGGAACAG 59.288 40.000 0.00 0.00 42.39 3.16
2809 3866 5.512942 TGGGTCATCTATTTTGGAACAGA 57.487 39.130 0.00 0.00 42.39 3.41
2810 3867 5.500234 TGGGTCATCTATTTTGGAACAGAG 58.500 41.667 0.00 0.00 42.39 3.35
2811 3868 4.884164 GGGTCATCTATTTTGGAACAGAGG 59.116 45.833 0.00 0.00 42.39 3.69
2812 3869 4.884164 GGTCATCTATTTTGGAACAGAGGG 59.116 45.833 0.00 0.00 42.39 4.30
2813 3870 5.339200 GGTCATCTATTTTGGAACAGAGGGA 60.339 44.000 0.00 0.00 42.39 4.20
2814 3871 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
3196 4254 6.234177 AGCTAATATGAAGGAGTACATTGCC 58.766 40.000 0.00 0.00 0.00 4.52
4100 5161 7.489160 TCATTTAGCGTGACAAGTATGAGTAT 58.511 34.615 0.00 0.00 0.00 2.12
4173 5235 8.433421 ACGATCCGTGTTTAATTTCATATCTT 57.567 30.769 0.00 0.00 39.18 2.40
4201 5263 4.804868 TTGTTGATCCATGATGGTTTGG 57.195 40.909 11.87 0.00 39.03 3.28
4406 5763 7.381323 ACAATTTCATTTAAAGGCTCCTCAAG 58.619 34.615 0.00 0.00 0.00 3.02
4407 5764 7.015584 ACAATTTCATTTAAAGGCTCCTCAAGT 59.984 33.333 0.00 0.00 0.00 3.16
4529 5886 8.334263 TCACATGCATAATGAAAACAGTCTTA 57.666 30.769 9.77 0.00 38.72 2.10
4584 5941 6.540995 CCCTCCATCATTCATAGAGTCAATT 58.459 40.000 0.00 0.00 0.00 2.32
4648 6006 2.423538 GTCCTTTGCGCCAATGTTAGAT 59.576 45.455 4.18 0.00 0.00 1.98
4691 6049 2.179547 CCATTAGCACATCCGCGCA 61.180 57.895 8.75 0.00 36.85 6.09
4696 6054 0.167908 TAGCACATCCGCGCAAAAAG 59.832 50.000 8.75 0.00 36.85 2.27
4765 6124 1.621814 AGCATTGCTTTCATTGTGCCT 59.378 42.857 5.03 0.00 33.89 4.75
4806 6165 6.489700 TCAAAGGAAGCATCAACATTGAGTTA 59.510 34.615 0.23 0.00 41.08 2.24
4817 6176 9.097257 CATCAACATTGAGTTAAACAAAACCTT 57.903 29.630 0.23 0.00 41.08 3.50
4854 6217 3.014304 ACTCTCCTTCACATACGCCTA 57.986 47.619 0.00 0.00 0.00 3.93
4901 6277 4.161001 GCAAGGATTCCCATTGAAATCTGT 59.839 41.667 8.48 0.02 36.33 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.353103 CCCGCTGTTTCGATGATGC 59.647 57.895 0.00 0.00 0.00 3.91
107 108 3.146066 ACAATGTTACAAGGCGTGATGT 58.854 40.909 7.60 0.42 0.00 3.06
122 123 3.722295 CAACGGCCGCGACAATGT 61.722 61.111 28.58 0.00 0.00 2.71
133 134 4.090057 GGCGACTGCTTCAACGGC 62.090 66.667 0.00 0.00 42.25 5.68
136 137 1.461127 CTACAAGGCGACTGCTTCAAC 59.539 52.381 0.00 0.00 42.68 3.18
188 189 1.675310 CTGGATGGCGGTCTTTGCA 60.675 57.895 0.00 0.00 0.00 4.08
288 289 5.001237 TCGAGTGTTTGTTGTCTACAAGA 57.999 39.130 0.00 0.00 46.81 3.02
303 304 0.603569 AAAGGTCAGCGATCGAGTGT 59.396 50.000 21.57 0.00 0.00 3.55
329 330 3.740044 AATTAACAGCCGTCATTGTCG 57.260 42.857 0.00 0.00 0.00 4.35
330 331 5.457140 TCAAAATTAACAGCCGTCATTGTC 58.543 37.500 0.00 0.00 0.00 3.18
331 332 5.009610 ACTCAAAATTAACAGCCGTCATTGT 59.990 36.000 0.00 0.00 0.00 2.71
333 334 5.705609 ACTCAAAATTAACAGCCGTCATT 57.294 34.783 0.00 0.00 0.00 2.57
334 335 5.460646 CAACTCAAAATTAACAGCCGTCAT 58.539 37.500 0.00 0.00 0.00 3.06
404 414 0.863538 CTCATCGACGACTTCCAGCG 60.864 60.000 0.00 0.00 0.00 5.18
463 474 0.320160 GGCCGTTACAACTCGTCCTT 60.320 55.000 0.00 0.00 0.00 3.36
503 519 3.665675 GATCAGCCGCCTCGTTGGT 62.666 63.158 0.00 0.00 38.35 3.67
813 1826 4.030913 AGTGCTACTTGTATTGCCTCCTA 58.969 43.478 0.00 0.00 0.00 2.94
888 1902 0.031515 TTCTATTCCCCTCCCAGCGA 60.032 55.000 0.00 0.00 0.00 4.93
1232 2254 5.525012 CGATGGATGAATAGCAACAAGAAGA 59.475 40.000 0.00 0.00 0.00 2.87
1377 2429 9.905713 ATATAAAGAGCCAAGAAATCACAAGTA 57.094 29.630 0.00 0.00 0.00 2.24
1571 2623 7.714377 AGATCAGATATTCGCATTGAAGAACTT 59.286 33.333 0.00 0.00 40.65 2.66
1949 3002 1.005340 CAGAAGCCTCAATCTCACGC 58.995 55.000 0.00 0.00 0.00 5.34
2040 3093 0.250234 TAGCTAACCTGTGCAGCCAG 59.750 55.000 0.00 0.00 35.88 4.85
2088 3141 0.744414 ACCCGGATGAAATGCAGACG 60.744 55.000 0.73 0.00 32.20 4.18
2134 3187 3.748048 CGCCACCATCATCCTAAATAGTG 59.252 47.826 0.00 0.00 0.00 2.74
2446 3499 5.636121 TGTTAACGGTAGTCAAGCAATACAG 59.364 40.000 0.26 0.00 0.00 2.74
2532 3589 6.314896 GCTTGATTTAGTCACTTAGATGTGCT 59.685 38.462 0.00 0.00 36.32 4.40
2573 3630 9.945904 TTTGTGTGGGTATTTTCTTTTTACTTT 57.054 25.926 0.00 0.00 0.00 2.66
2662 3719 5.985530 GCCAAAGATTCAGTTTTGCTAAAGT 59.014 36.000 0.00 0.00 33.92 2.66
2720 3777 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2721 3778 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2722 3779 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2723 3780 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2724 3781 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2725 3782 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2726 3783 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2727 3784 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2728 3785 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2729 3786 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2730 3787 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2731 3788 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2732 3789 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2733 3790 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2761 3818 8.502105 ACTTTGCACTAACTTTGTACTAAAGT 57.498 30.769 14.04 14.04 41.82 2.66
2762 3819 9.221775 CAACTTTGCACTAACTTTGTACTAAAG 57.778 33.333 13.08 13.08 0.00 1.85
2763 3820 8.185505 CCAACTTTGCACTAACTTTGTACTAAA 58.814 33.333 0.00 0.00 0.00 1.85
2764 3821 7.201750 CCCAACTTTGCACTAACTTTGTACTAA 60.202 37.037 0.00 0.00 0.00 2.24
2765 3822 6.261381 CCCAACTTTGCACTAACTTTGTACTA 59.739 38.462 0.00 0.00 0.00 1.82
2766 3823 5.067283 CCCAACTTTGCACTAACTTTGTACT 59.933 40.000 0.00 0.00 0.00 2.73
2767 3824 5.163591 ACCCAACTTTGCACTAACTTTGTAC 60.164 40.000 0.00 0.00 0.00 2.90
2768 3825 4.951094 ACCCAACTTTGCACTAACTTTGTA 59.049 37.500 0.00 0.00 0.00 2.41
2769 3826 3.767131 ACCCAACTTTGCACTAACTTTGT 59.233 39.130 0.00 0.00 0.00 2.83
2770 3827 4.142271 TGACCCAACTTTGCACTAACTTTG 60.142 41.667 0.00 0.00 0.00 2.77
2771 3828 4.020543 TGACCCAACTTTGCACTAACTTT 58.979 39.130 0.00 0.00 0.00 2.66
2772 3829 3.626930 TGACCCAACTTTGCACTAACTT 58.373 40.909 0.00 0.00 0.00 2.66
2773 3830 3.290948 TGACCCAACTTTGCACTAACT 57.709 42.857 0.00 0.00 0.00 2.24
2774 3831 3.821033 AGATGACCCAACTTTGCACTAAC 59.179 43.478 0.00 0.00 0.00 2.34
2775 3832 4.098914 AGATGACCCAACTTTGCACTAA 57.901 40.909 0.00 0.00 0.00 2.24
2776 3833 3.788227 AGATGACCCAACTTTGCACTA 57.212 42.857 0.00 0.00 0.00 2.74
2777 3834 2.664402 AGATGACCCAACTTTGCACT 57.336 45.000 0.00 0.00 0.00 4.40
2778 3835 5.391312 AAATAGATGACCCAACTTTGCAC 57.609 39.130 0.00 0.00 0.00 4.57
2779 3836 5.279406 CCAAAATAGATGACCCAACTTTGCA 60.279 40.000 0.00 0.00 0.00 4.08
2780 3837 5.047377 TCCAAAATAGATGACCCAACTTTGC 60.047 40.000 0.00 0.00 0.00 3.68
2781 3838 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2782 3839 6.553100 TGTTCCAAAATAGATGACCCAACTTT 59.447 34.615 0.00 0.00 0.00 2.66
2783 3840 6.074648 TGTTCCAAAATAGATGACCCAACTT 58.925 36.000 0.00 0.00 0.00 2.66
2784 3841 5.640147 TGTTCCAAAATAGATGACCCAACT 58.360 37.500 0.00 0.00 0.00 3.16
2785 3842 5.710099 TCTGTTCCAAAATAGATGACCCAAC 59.290 40.000 0.00 0.00 28.72 3.77
2786 3843 5.886609 TCTGTTCCAAAATAGATGACCCAA 58.113 37.500 0.00 0.00 28.72 4.12
2787 3844 5.500234 CTCTGTTCCAAAATAGATGACCCA 58.500 41.667 0.00 0.00 32.88 4.51
2788 3845 4.884164 CCTCTGTTCCAAAATAGATGACCC 59.116 45.833 0.00 0.00 32.88 4.46
2789 3846 4.884164 CCCTCTGTTCCAAAATAGATGACC 59.116 45.833 0.00 0.00 32.88 4.02
2790 3847 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
2791 3848 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
2792 3849 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
2793 3850 7.698163 ATACTCCCTCTGTTCCAAAATAGAT 57.302 36.000 0.00 0.00 32.88 1.98
2794 3851 8.651389 CATATACTCCCTCTGTTCCAAAATAGA 58.349 37.037 0.00 0.00 32.42 1.98
2795 3852 7.880195 CCATATACTCCCTCTGTTCCAAAATAG 59.120 40.741 0.00 0.00 0.00 1.73
2796 3853 7.349859 ACCATATACTCCCTCTGTTCCAAAATA 59.650 37.037 0.00 0.00 0.00 1.40
2797 3854 6.160459 ACCATATACTCCCTCTGTTCCAAAAT 59.840 38.462 0.00 0.00 0.00 1.82
2798 3855 5.491078 ACCATATACTCCCTCTGTTCCAAAA 59.509 40.000 0.00 0.00 0.00 2.44
2799 3856 5.036916 ACCATATACTCCCTCTGTTCCAAA 58.963 41.667 0.00 0.00 0.00 3.28
2800 3857 4.631234 ACCATATACTCCCTCTGTTCCAA 58.369 43.478 0.00 0.00 0.00 3.53
2801 3858 4.280789 ACCATATACTCCCTCTGTTCCA 57.719 45.455 0.00 0.00 0.00 3.53
2802 3859 5.395611 AGTACCATATACTCCCTCTGTTCC 58.604 45.833 0.00 0.00 0.00 3.62
2803 3860 7.232910 AGTAGTACCATATACTCCCTCTGTTC 58.767 42.308 0.00 0.00 0.00 3.18
2804 3861 7.164233 AGTAGTACCATATACTCCCTCTGTT 57.836 40.000 0.00 0.00 0.00 3.16
2805 3862 6.783517 AGTAGTACCATATACTCCCTCTGT 57.216 41.667 0.00 0.00 0.00 3.41
2806 3863 9.835389 GTATAGTAGTACCATATACTCCCTCTG 57.165 40.741 10.41 0.00 34.21 3.35
2807 3864 9.571823 TGTATAGTAGTACCATATACTCCCTCT 57.428 37.037 15.45 0.00 34.76 3.69
3196 4254 1.605710 GCAGATCCATGACCAAATCGG 59.394 52.381 0.00 0.00 42.50 4.18
4129 5190 7.096189 CGGATCGTCTGGTTATAAAATAGTGTG 60.096 40.741 0.00 0.00 0.00 3.82
4173 5235 7.479352 ACCATCATGGATCAACAATGTTAAA 57.521 32.000 11.90 0.00 40.96 1.52
4201 5263 2.080286 TCTAGAACCGCAGAGCAAAC 57.920 50.000 0.00 0.00 0.00 2.93
4406 5763 6.903419 AGATTTTCTTTGACTTCGGATTGAC 58.097 36.000 0.00 0.00 0.00 3.18
4407 5764 7.148407 GCTAGATTTTCTTTGACTTCGGATTGA 60.148 37.037 0.00 0.00 0.00 2.57
4529 5886 2.690778 GCGGCGGCAACAATCTTCT 61.691 57.895 9.78 0.00 39.62 2.85
4554 5911 1.588239 TGAATGATGGAGGGCAGTCT 58.412 50.000 0.00 0.00 31.06 3.24
4626 5984 1.539388 CTAACATTGGCGCAAAGGACA 59.461 47.619 17.41 1.72 0.00 4.02
4648 6006 4.383552 GGAGGCTAGAGCTCTCAAATTTGA 60.384 45.833 22.17 19.45 38.92 2.69
4691 6049 7.037297 TGGAGGGAATGAGAGAATAGACTTTTT 60.037 37.037 0.00 0.00 0.00 1.94
4696 6054 4.262420 GCTGGAGGGAATGAGAGAATAGAC 60.262 50.000 0.00 0.00 0.00 2.59
4754 6112 4.579869 GACCTTCTTAGAGGCACAATGAA 58.420 43.478 0.00 0.00 40.65 2.57
4762 6120 2.427453 TGATCACGACCTTCTTAGAGGC 59.573 50.000 0.00 0.00 40.65 4.70
4765 6124 4.770531 TCCTTTGATCACGACCTTCTTAGA 59.229 41.667 0.00 0.00 0.00 2.10
4806 6165 2.573915 TGCCCTCCAAAAGGTTTTGTTT 59.426 40.909 12.90 0.00 44.56 2.83
4817 6176 0.555769 AGTTGGTCTTGCCCTCCAAA 59.444 50.000 0.00 0.00 41.86 3.28
4854 6217 8.598041 TGCCCTTACCATAAATTTTGTTAATGT 58.402 29.630 0.00 0.00 0.00 2.71
4901 6277 9.453325 GAAAGACGGAAAATACAAAATGTAACA 57.547 29.630 0.00 0.00 36.31 2.41
4967 6361 3.957497 GGATATTGGGTTGCCACAATGTA 59.043 43.478 1.13 0.00 37.80 2.29



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

AutoCloner maintained by Alex Coulton.