Multiple sequence alignment - TraesCS2A01G549000

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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 TraesCS2A01G549000 chr2A 100.000 4384 0 0 1 4384 756484064 756488447 0.000000e+00 8096.0
1 TraesCS2A01G549000 chr2A 78.383 1212 200 35 948 2130 755740925 755742103 0.000000e+00 730.0
2 TraesCS2A01G549000 chr2A 81.317 562 78 17 2283 2832 755742457 755743003 8.710000e-117 431.0
3 TraesCS2A01G549000 chr2A 96.203 79 3 0 769 847 607518798 607518876 3.560000e-26 130.0
4 TraesCS2A01G549000 chr2A 96.104 77 3 0 771 847 715299526 715299602 4.600000e-25 126.0
5 TraesCS2A01G549000 chr2A 85.507 69 9 1 23 90 755740363 755740431 2.190000e-08 71.3
6 TraesCS2A01G549000 chr2D 92.524 2100 86 28 845 2924 626114806 626112758 0.000000e+00 2942.0
7 TraesCS2A01G549000 chr2D 93.928 774 43 3 3614 4384 626112122 626111350 0.000000e+00 1166.0
8 TraesCS2A01G549000 chr2D 91.149 644 37 8 131 774 626115425 626114802 0.000000e+00 856.0
9 TraesCS2A01G549000 chr2D 87.963 648 37 18 2850 3464 626112758 626112119 0.000000e+00 726.0
10 TraesCS2A01G549000 chr2D 77.778 1188 171 52 878 2023 624348857 624349993 0.000000e+00 645.0
11 TraesCS2A01G549000 chr2D 83.397 524 83 2 3794 4317 626108488 626107969 2.370000e-132 483.0
12 TraesCS2A01G549000 chr2D 79.900 602 89 22 2243 2832 624350282 624350863 3.160000e-111 412.0
13 TraesCS2A01G549000 chr2D 84.615 377 46 8 2443 2813 625565621 625565251 8.960000e-97 364.0
14 TraesCS2A01G549000 chr2D 79.433 282 42 11 3145 3421 625541281 625541011 7.490000e-43 185.0
15 TraesCS2A01G549000 chr2D 86.667 165 18 3 3241 3402 624351341 624351504 3.480000e-41 180.0
16 TraesCS2A01G549000 chr2D 76.955 243 42 7 877 1108 625565862 625565623 4.600000e-25 126.0
17 TraesCS2A01G549000 chr2D 88.235 85 6 3 22 106 626115504 626115424 1.000000e-16 99.0
18 TraesCS2A01G549000 chr2D 91.667 48 3 1 25 71 624348348 624348395 1.020000e-06 65.8
19 TraesCS2A01G549000 chr2B 93.564 1274 64 9 854 2119 767696001 767694738 0.000000e+00 1882.0
20 TraesCS2A01G549000 chr2B 95.355 818 25 8 2116 2924 767694422 767693609 0.000000e+00 1288.0
21 TraesCS2A01G549000 chr2B 88.699 761 43 23 2850 3577 767693609 767692859 0.000000e+00 889.0
22 TraesCS2A01G549000 chr2B 94.504 564 31 0 3821 4384 767692529 767691966 0.000000e+00 870.0
23 TraesCS2A01G549000 chr2B 78.552 1105 176 32 948 2023 766527586 766528658 0.000000e+00 671.0
24 TraesCS2A01G549000 chr2B 92.151 344 24 1 422 765 767696340 767696000 2.370000e-132 483.0
25 TraesCS2A01G549000 chr2B 82.290 559 96 3 3759 4317 767688582 767688027 8.530000e-132 481.0
26 TraesCS2A01G549000 chr2B 80.198 606 85 23 2243 2832 766528947 766529533 5.240000e-114 422.0
27 TraesCS2A01G549000 chr2B 87.467 375 23 9 22 388 767696693 767696335 1.130000e-110 411.0
28 TraesCS2A01G549000 chr2B 92.344 209 12 2 3576 3783 767692737 767692532 1.190000e-75 294.0
29 TraesCS2A01G549000 chr2B 97.333 75 2 0 773 847 794534955 794534881 1.280000e-25 128.0
30 TraesCS2A01G549000 chr2B 85.507 69 9 1 23 90 766526993 766527061 2.190000e-08 71.3
31 TraesCS2A01G549000 chr1A 97.368 76 2 0 772 847 459516906 459516831 3.560000e-26 130.0
32 TraesCS2A01G549000 chr7B 96.154 78 3 0 770 847 656482258 656482335 1.280000e-25 128.0
33 TraesCS2A01G549000 chr5B 97.333 75 2 0 773 847 268959427 268959501 1.280000e-25 128.0
34 TraesCS2A01G549000 chr4B 96.154 78 3 0 770 847 183611087 183611164 1.280000e-25 128.0
35 TraesCS2A01G549000 chr5D 91.860 86 5 2 763 847 461071770 461071686 7.700000e-23 119.0
36 TraesCS2A01G549000 chr4A 86.239 109 10 5 740 847 677435883 677435987 3.580000e-21 113.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G549000 chr2A 756484064 756488447 4383 False 8096.000000 8096 100.000000 1 4384 1 chr2A.!!$F3 4383
1 TraesCS2A01G549000 chr2A 755740363 755743003 2640 False 410.766667 730 81.735667 23 2832 3 chr2A.!!$F4 2809
2 TraesCS2A01G549000 chr2D 626107969 626115504 7535 True 1045.333333 2942 89.532667 22 4384 6 chr2D.!!$R3 4362
3 TraesCS2A01G549000 chr2D 624348348 624351504 3156 False 325.700000 645 84.003000 25 3402 4 chr2D.!!$F1 3377
4 TraesCS2A01G549000 chr2D 625565251 625565862 611 True 245.000000 364 80.785000 877 2813 2 chr2D.!!$R2 1936
5 TraesCS2A01G549000 chr2B 767688027 767696693 8666 True 824.750000 1882 90.796750 22 4384 8 chr2B.!!$R2 4362
6 TraesCS2A01G549000 chr2B 766526993 766529533 2540 False 388.100000 671 81.419000 23 2832 3 chr2B.!!$F1 2809

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
789 814 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.00 0.0 0.00 3.46 F
1727 1807 0.109597 CCACCGTGTCGTAGTGGTAC 60.110 60.0 0.18 0.0 44.95 3.34 F
3211 4050 1.153353 CGACAACCGGCACTTATGTT 58.847 50.0 0.00 0.0 33.91 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2132 0.462759 GCACACAGGCAGGATAGGTC 60.463 60.0 0.0 0.0 0.00 3.85 R
3288 4127 0.032615 AAACCCTTGCTGACCACCAA 60.033 50.0 0.0 0.0 0.00 3.67 R
4043 5014 0.533491 CCGGGATGGTAACTTCGACA 59.467 55.0 0.0 0.0 41.51 4.35 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
19 20 1.272807 TTACTCTCAAACCCTCCCGG 58.727 55.000 0.00 0.00 37.81 5.73
20 21 0.410663 TACTCTCAAACCCTCCCGGA 59.589 55.000 0.73 0.00 34.64 5.14
92 101 4.753662 AGCGTGCCGAGGGGACTA 62.754 66.667 4.79 0.00 41.99 2.59
102 111 0.755686 GAGGGGACTAGGTGCATCAG 59.244 60.000 0.00 0.00 44.43 2.90
103 112 0.043334 AGGGGACTAGGTGCATCAGT 59.957 55.000 0.00 0.12 40.61 3.41
256 269 1.339151 GGGGAGAAGTTCGCTGATTGT 60.339 52.381 6.57 0.00 38.70 2.71
394 411 4.099881 TGCATTTGGGAGATTAGCATTTCC 59.900 41.667 0.00 0.00 33.54 3.13
463 487 1.463056 TCAGGATAGTTTTGCAACGCG 59.537 47.619 3.53 3.53 38.03 6.01
480 504 1.757306 CGGGCATTAGGATGAGGCT 59.243 57.895 0.00 0.00 35.16 4.58
541 565 7.391554 TCTGTTTGATGAAATGCTTAAGCTAGT 59.608 33.333 26.90 12.38 42.66 2.57
542 566 8.560355 TGTTTGATGAAATGCTTAAGCTAGTA 57.440 30.769 26.90 8.34 42.66 1.82
543 567 8.668353 TGTTTGATGAAATGCTTAAGCTAGTAG 58.332 33.333 26.90 0.00 42.66 2.57
567 591 3.720818 CGCGATGATTACAAATGTGCTTC 59.279 43.478 0.00 0.00 0.00 3.86
627 651 5.120830 ACTTGCATTTACTCGCTTAGTGAAG 59.879 40.000 0.00 0.00 37.15 3.02
735 759 7.440856 TGCTTATTTCGATATGCTGTTACATCA 59.559 33.333 0.00 0.00 0.00 3.07
744 769 7.062722 CGATATGCTGTTACATCAATAGTGGAG 59.937 40.741 0.00 0.00 0.00 3.86
782 807 9.629878 ATGTATAATAAGATAGTACTCCCTCCG 57.370 37.037 0.00 0.00 0.00 4.63
783 808 8.609483 TGTATAATAAGATAGTACTCCCTCCGT 58.391 37.037 0.00 0.00 0.00 4.69
784 809 9.108284 GTATAATAAGATAGTACTCCCTCCGTC 57.892 40.741 0.00 0.00 0.00 4.79
785 810 2.955342 AGATAGTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
786 811 1.072015 AGATAGTACTCCCTCCGTCCG 59.928 57.143 0.00 0.00 0.00 4.79
787 812 1.071385 GATAGTACTCCCTCCGTCCGA 59.929 57.143 0.00 0.00 0.00 4.55
788 813 0.911769 TAGTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
789 814 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
790 815 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
791 816 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
792 817 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
793 818 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
794 819 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
795 820 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
796 821 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
797 822 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
798 823 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
799 824 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
800 825 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
801 826 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
802 827 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
803 828 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
804 829 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
810 835 3.027419 GCTTGTCCCAAGCTTGTCT 57.973 52.632 24.35 0.00 40.01 3.41
811 836 0.877743 GCTTGTCCCAAGCTTGTCTC 59.122 55.000 24.35 13.85 40.01 3.36
812 837 1.544314 GCTTGTCCCAAGCTTGTCTCT 60.544 52.381 24.35 0.00 40.01 3.10
813 838 2.421619 CTTGTCCCAAGCTTGTCTCTC 58.578 52.381 24.35 10.65 0.00 3.20
814 839 1.423584 TGTCCCAAGCTTGTCTCTCA 58.576 50.000 24.35 12.85 0.00 3.27
815 840 1.768275 TGTCCCAAGCTTGTCTCTCAA 59.232 47.619 24.35 1.41 34.61 3.02
816 841 2.172505 TGTCCCAAGCTTGTCTCTCAAA 59.827 45.455 24.35 0.00 35.48 2.69
817 842 3.181440 TGTCCCAAGCTTGTCTCTCAAAT 60.181 43.478 24.35 0.00 35.48 2.32
818 843 3.190118 GTCCCAAGCTTGTCTCTCAAATG 59.810 47.826 24.35 5.47 35.48 2.32
819 844 2.490903 CCCAAGCTTGTCTCTCAAATGG 59.509 50.000 24.35 10.71 35.48 3.16
820 845 3.415212 CCAAGCTTGTCTCTCAAATGGA 58.585 45.455 24.35 0.00 36.92 3.41
821 846 4.015084 CCAAGCTTGTCTCTCAAATGGAT 58.985 43.478 24.35 0.00 36.92 3.41
822 847 4.142447 CCAAGCTTGTCTCTCAAATGGATG 60.142 45.833 24.35 0.00 36.92 3.51
823 848 4.298103 AGCTTGTCTCTCAAATGGATGT 57.702 40.909 0.00 0.00 35.48 3.06
824 849 5.426689 AGCTTGTCTCTCAAATGGATGTA 57.573 39.130 0.00 0.00 35.48 2.29
825 850 5.181748 AGCTTGTCTCTCAAATGGATGTAC 58.818 41.667 0.00 0.00 35.48 2.90
826 851 4.333926 GCTTGTCTCTCAAATGGATGTACC 59.666 45.833 0.00 0.00 35.48 3.34
827 852 5.738909 CTTGTCTCTCAAATGGATGTACCT 58.261 41.667 0.00 0.00 36.19 3.08
828 853 6.630413 GCTTGTCTCTCAAATGGATGTACCTA 60.630 42.308 0.00 0.00 36.19 3.08
829 854 6.471233 TGTCTCTCAAATGGATGTACCTAG 57.529 41.667 0.00 0.00 39.86 3.02
830 855 5.163405 TGTCTCTCAAATGGATGTACCTAGC 60.163 44.000 0.00 0.00 39.86 3.42
831 856 4.962362 TCTCTCAAATGGATGTACCTAGCA 59.038 41.667 0.00 0.00 39.86 3.49
832 857 5.604231 TCTCTCAAATGGATGTACCTAGCAT 59.396 40.000 0.00 0.00 39.86 3.79
833 858 6.100279 TCTCTCAAATGGATGTACCTAGCATT 59.900 38.462 0.00 0.00 39.86 3.56
834 859 7.290014 TCTCTCAAATGGATGTACCTAGCATTA 59.710 37.037 0.00 0.00 39.86 1.90
835 860 7.801104 TCTCAAATGGATGTACCTAGCATTAA 58.199 34.615 0.00 0.00 39.86 1.40
836 861 7.715249 TCTCAAATGGATGTACCTAGCATTAAC 59.285 37.037 0.00 0.00 39.86 2.01
837 862 7.573710 TCAAATGGATGTACCTAGCATTAACT 58.426 34.615 0.00 0.00 39.86 2.24
838 863 8.052748 TCAAATGGATGTACCTAGCATTAACTT 58.947 33.333 0.00 0.00 39.86 2.66
839 864 7.807977 AATGGATGTACCTAGCATTAACTTG 57.192 36.000 0.00 0.00 39.86 3.16
840 865 6.553953 TGGATGTACCTAGCATTAACTTGA 57.446 37.500 0.00 0.00 39.86 3.02
841 866 7.136822 TGGATGTACCTAGCATTAACTTGAT 57.863 36.000 0.00 0.00 39.86 2.57
842 867 6.992123 TGGATGTACCTAGCATTAACTTGATG 59.008 38.462 0.00 0.00 39.86 3.07
843 868 6.073003 GGATGTACCTAGCATTAACTTGATGC 60.073 42.308 9.92 9.92 41.64 3.91
872 897 3.357079 GTGCAGGGCTTGTGTCGG 61.357 66.667 0.00 0.00 0.00 4.79
873 898 4.641645 TGCAGGGCTTGTGTCGGG 62.642 66.667 0.00 0.00 0.00 5.14
908 946 2.689471 TCTTGTTTGTTGCAGCATGTCT 59.311 40.909 3.36 0.00 39.31 3.41
938 976 5.276348 GCACTCAAAGAACAAATTGGTTTCG 60.276 40.000 0.00 0.00 0.00 3.46
980 1019 2.620242 CTTTGCACTTGTGGCTGTTTT 58.380 42.857 2.81 0.00 0.00 2.43
1050 1090 2.010497 GCTCCCTTTCTTTCTAAGCGG 58.990 52.381 0.00 0.00 0.00 5.52
1088 1146 1.026182 TCACCATCATGCTCGGCAAC 61.026 55.000 2.68 0.00 43.62 4.17
1197 1255 3.703556 TGTTTGAAATTCAGGTGGCTCAA 59.296 39.130 0.00 0.00 0.00 3.02
1214 1273 8.682710 GGTGGCTCAACTTTATTGTCATAATTA 58.317 33.333 0.00 0.00 0.00 1.40
1379 1438 6.931281 ACGTTCCTCTTTACTTTTAGGGTAAC 59.069 38.462 0.00 0.00 0.00 2.50
1389 1448 6.869206 ACTTTTAGGGTAACTGATGCTCTA 57.131 37.500 0.00 0.00 0.00 2.43
1405 1467 8.621532 TGATGCTCTATTTTCAAGTACAAAGT 57.378 30.769 0.00 0.00 0.00 2.66
1461 1523 1.380246 GCAGGGATGGTTGATGGCA 60.380 57.895 0.00 0.00 0.00 4.92
1727 1807 0.109597 CCACCGTGTCGTAGTGGTAC 60.110 60.000 0.18 0.00 44.95 3.34
1776 1856 4.192317 GACACCTTAGATTGGCTAACTGG 58.808 47.826 0.00 0.00 35.32 4.00
1780 1860 4.786454 ACCTTAGATTGGCTAACTGGGTTA 59.214 41.667 0.00 0.00 33.63 2.85
1853 1933 5.237996 AGTTCTTCGTTTACAACCTAAAGGC 59.762 40.000 0.00 0.00 39.32 4.35
1894 1974 7.933215 ATGGGTCAGTAAACCTTACATTTAC 57.067 36.000 0.00 0.00 41.06 2.01
1913 1993 3.675467 ACGTGCTTTGTGAAAGAGTTC 57.325 42.857 0.16 0.00 41.02 3.01
1914 1994 3.270877 ACGTGCTTTGTGAAAGAGTTCT 58.729 40.909 0.16 0.00 41.02 3.01
1915 1995 4.439057 ACGTGCTTTGTGAAAGAGTTCTA 58.561 39.130 0.16 0.00 41.02 2.10
1916 1996 5.057149 ACGTGCTTTGTGAAAGAGTTCTAT 58.943 37.500 0.16 0.00 41.02 1.98
1917 1997 5.527582 ACGTGCTTTGTGAAAGAGTTCTATT 59.472 36.000 0.16 0.00 41.02 1.73
1918 1998 6.038271 ACGTGCTTTGTGAAAGAGTTCTATTT 59.962 34.615 0.16 0.00 41.02 1.40
1919 1999 6.575201 CGTGCTTTGTGAAAGAGTTCTATTTC 59.425 38.462 11.47 11.47 41.02 2.17
1920 2000 7.417612 GTGCTTTGTGAAAGAGTTCTATTTCA 58.582 34.615 15.55 15.55 41.76 2.69
2026 2107 6.823689 GCTCTGGAATTCATCAGGTTAAGTTA 59.176 38.462 7.93 0.00 0.00 2.24
2051 2132 7.770801 TCAAGATTGTGATATTCGTACTTGG 57.229 36.000 0.00 0.00 34.81 3.61
2201 2653 9.730420 ACTACATTTCTTGTTTGTTGTTGTATC 57.270 29.630 0.00 0.00 39.87 2.24
2528 3147 2.290641 CGAGAATTTGGCCGATTAAGGG 59.709 50.000 0.00 0.00 0.00 3.95
2704 3329 7.913789 ACGGGTATAAAATCTCCATTGCTATA 58.086 34.615 0.00 0.00 0.00 1.31
2712 3338 8.773033 AAAATCTCCATTGCTATAATCCTTGT 57.227 30.769 0.00 0.00 0.00 3.16
2733 3359 8.730680 CCTTGTGTTCTAGTTTAATGTTATGCT 58.269 33.333 0.00 0.00 0.00 3.79
2838 3469 8.274322 TGGATGATTGTGTTCATTAACTAGGAT 58.726 33.333 0.00 0.00 36.48 3.24
2845 3476 9.787435 TTGTGTTCATTAACTAGGATAAGTGTT 57.213 29.630 0.00 0.00 36.51 3.32
2852 3483 9.326413 CATTAACTAGGATAAGTGTTACCAAGG 57.674 37.037 0.00 0.00 0.00 3.61
2856 3487 5.678955 AGGATAAGTGTTACCAAGGAGTC 57.321 43.478 0.00 0.00 0.00 3.36
2905 3611 8.485976 AGCTCTGTGTTCTATTGACTTTAATC 57.514 34.615 0.00 0.00 0.00 1.75
2950 3664 4.615170 TGCATGGTCCCTGCAAAA 57.385 50.000 18.40 0.00 46.06 2.44
3088 3918 7.753132 GTGTGTCAAACTGAAAACAATCTTACA 59.247 33.333 0.00 0.00 30.23 2.41
3158 3997 6.681729 AGTGTTCCTTCCACATAGTAGAAA 57.318 37.500 0.00 0.00 35.24 2.52
3161 4000 7.181125 AGTGTTCCTTCCACATAGTAGAAAGAT 59.819 37.037 0.00 0.00 35.24 2.40
3209 4048 2.835605 ACGACAACCGGCACTTATG 58.164 52.632 0.00 0.00 43.93 1.90
3211 4050 1.153353 CGACAACCGGCACTTATGTT 58.847 50.000 0.00 0.00 33.91 2.71
3212 4051 1.533731 CGACAACCGGCACTTATGTTT 59.466 47.619 0.00 0.00 33.91 2.83
3213 4052 2.737783 CGACAACCGGCACTTATGTTTA 59.262 45.455 0.00 0.00 33.91 2.01
3219 4058 6.422400 ACAACCGGCACTTATGTTTATTTTTG 59.578 34.615 0.00 0.00 0.00 2.44
3288 4127 0.326264 GGGTGCTGACATCCTGAAGT 59.674 55.000 0.00 0.00 44.47 3.01
3410 4251 2.158784 ACTACGAACCGCTCCTCTAGAT 60.159 50.000 0.00 0.00 0.00 1.98
3454 4295 5.620429 GCTCTTCCAGTATTATCTAGACGGC 60.620 48.000 0.00 0.00 0.00 5.68
3455 4296 4.454847 TCTTCCAGTATTATCTAGACGGCG 59.545 45.833 4.80 4.80 0.00 6.46
3465 4310 1.404391 TCTAGACGGCGGAATTGACTC 59.596 52.381 13.24 0.00 0.00 3.36
3501 4346 6.475402 CGAGGTGGCACCAATTTATTTATTTC 59.525 38.462 36.28 19.30 41.95 2.17
3570 4415 9.730705 ATGTTGAGCAATATAGCTAACATGTAT 57.269 29.630 0.00 0.00 46.75 2.29
3607 4575 3.508402 TGGTACACGCTTGACTATTCAGA 59.492 43.478 0.00 0.00 31.71 3.27
3632 4600 2.239402 TGTGACCTGATGTGTATGGCAT 59.761 45.455 4.88 4.88 0.00 4.40
3654 4622 0.237761 CTGTGAACAGCAGCTTCAGC 59.762 55.000 0.00 0.00 37.15 4.26
3690 4658 6.493166 TCCACATCAGTATCTTCCCAAAAAT 58.507 36.000 0.00 0.00 0.00 1.82
3743 4711 2.793288 TCAATTGATGCAGAGGCTGA 57.207 45.000 3.38 0.00 41.91 4.26
3830 4801 9.906660 GAAGGAAAACACACAATAACATATGAA 57.093 29.630 10.38 0.00 0.00 2.57
3904 4875 4.200838 TGCTCCTGAACAACAATATCGA 57.799 40.909 0.00 0.00 0.00 3.59
3953 4924 5.063564 CGAACTTGAAGGGTATGTTAGCTTC 59.936 44.000 0.00 0.00 0.00 3.86
3981 4952 3.620966 GCCTACTCAGCTCCTTCACAAAT 60.621 47.826 0.00 0.00 0.00 2.32
4043 5014 2.249139 GTATACCTTCTCGGGAGCCAT 58.751 52.381 0.00 0.00 36.97 4.40
4077 5048 2.283529 CCGGTACACCACCTGCTCT 61.284 63.158 0.00 0.00 46.19 4.09
4126 5097 1.217244 GTAGTCGGCACCATCGGTT 59.783 57.895 0.00 0.00 31.02 4.44
4146 5117 4.016444 GTTGGTCAATTCCCAGCTTCATA 58.984 43.478 0.00 0.00 32.49 2.15
4190 5161 1.153329 TGTTCAAACCGAGTGCCGT 60.153 52.632 0.00 0.00 36.31 5.68
4215 5186 4.965532 AGGAAGTCCTTGTAGTCATATGCT 59.034 41.667 0.00 1.43 46.09 3.79
4296 5267 0.107165 GGGATAAAAGGGTGCTCGCT 60.107 55.000 0.00 0.00 38.50 4.93
4317 5288 0.110486 AGGTTCTCCACATTTGCCGT 59.890 50.000 0.00 0.00 35.89 5.68
4344 5315 4.090588 GGCGGAACCGATGGGACA 62.091 66.667 17.63 0.00 42.83 4.02
4372 5343 2.680352 GTCCCGAGGTGAGGCTCA 60.680 66.667 14.43 14.43 0.00 4.26
4373 5344 2.680352 TCCCGAGGTGAGGCTCAC 60.680 66.667 34.21 34.21 46.23 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.255667 CCTTTCTTCTCCGTCCGGGA 61.256 60.000 0.00 0.00 44.68 5.14
15 16 1.218316 CCTTTCTTCTCCGTCCGGG 59.782 63.158 0.00 0.00 35.59 5.73
16 17 1.448013 GCCTTTCTTCTCCGTCCGG 60.448 63.158 0.00 0.00 0.00 5.14
17 18 1.805945 CGCCTTTCTTCTCCGTCCG 60.806 63.158 0.00 0.00 0.00 4.79
18 19 0.736672 GTCGCCTTTCTTCTCCGTCC 60.737 60.000 0.00 0.00 0.00 4.79
19 20 1.071567 CGTCGCCTTTCTTCTCCGTC 61.072 60.000 0.00 0.00 0.00 4.79
20 21 1.080705 CGTCGCCTTTCTTCTCCGT 60.081 57.895 0.00 0.00 0.00 4.69
92 101 2.267006 CGCTCCACTGATGCACCT 59.733 61.111 0.00 0.00 0.00 4.00
142 151 1.011131 GGCGCCGAAAATAAGCTCG 60.011 57.895 12.58 0.00 34.83 5.03
177 186 3.311110 TTCGGAACCGGAGCTGCT 61.311 61.111 9.46 0.00 40.25 4.24
415 439 4.013267 GATCATGGATTTGATCGGACCT 57.987 45.455 0.00 0.00 41.77 3.85
438 462 4.378459 CGTTGCAAAACTATCCTGAACTCC 60.378 45.833 0.00 0.00 0.00 3.85
463 487 0.251077 CCAGCCTCATCCTAATGCCC 60.251 60.000 0.00 0.00 32.58 5.36
480 504 0.744771 TGCAACACTAACACGCACCA 60.745 50.000 0.00 0.00 0.00 4.17
511 535 9.043444 GCTTAAGCATTTCATCAAACAGATGCC 62.043 40.741 22.59 0.00 45.92 4.40
515 539 6.579666 AGCTTAAGCATTTCATCAAACAGA 57.420 33.333 28.39 0.00 45.16 3.41
541 565 4.026062 GCACATTTGTAATCATCGCGTCTA 60.026 41.667 5.77 0.00 0.00 2.59
542 566 3.242413 GCACATTTGTAATCATCGCGTCT 60.242 43.478 5.77 0.00 0.00 4.18
543 567 3.029074 GCACATTTGTAATCATCGCGTC 58.971 45.455 5.77 0.00 0.00 5.19
567 591 1.066573 AGCTCGAACAGTCATGGAAGG 60.067 52.381 0.00 0.00 0.00 3.46
636 660 1.352156 GCCACAGTAGAACCGAAGCG 61.352 60.000 0.00 0.00 0.00 4.68
639 663 0.320374 CTGGCCACAGTAGAACCGAA 59.680 55.000 0.00 0.00 39.92 4.30
735 759 7.200434 ACATCACTAAATGACCTCCACTATT 57.800 36.000 0.00 0.00 41.24 1.73
769 794 0.911769 TTCGGACGGAGGGAGTACTA 59.088 55.000 0.00 0.00 0.00 1.82
770 795 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
771 796 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
772 797 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
773 798 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
774 799 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
775 800 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
776 801 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
777 802 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
778 803 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
779 804 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
780 805 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
781 806 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
782 807 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
783 808 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
793 818 3.745480 TTGAGAGACAAGCTTGGGACAAG 60.745 47.826 29.18 3.71 37.48 3.16
794 819 2.172505 TTGAGAGACAAGCTTGGGACAA 59.827 45.455 29.18 21.59 37.48 3.18
795 820 1.423584 TGAGAGACAAGCTTGGGACA 58.576 50.000 29.18 17.71 0.00 4.02
796 821 2.550830 TTGAGAGACAAGCTTGGGAC 57.449 50.000 29.18 19.11 34.20 4.46
797 822 3.415212 CATTTGAGAGACAAGCTTGGGA 58.585 45.455 29.18 7.03 39.77 4.37
798 823 2.490903 CCATTTGAGAGACAAGCTTGGG 59.509 50.000 29.18 13.19 39.77 4.12
799 824 3.415212 TCCATTTGAGAGACAAGCTTGG 58.585 45.455 29.18 12.28 39.77 3.61
800 825 4.458295 ACATCCATTTGAGAGACAAGCTTG 59.542 41.667 24.84 24.84 39.77 4.01
801 826 4.660168 ACATCCATTTGAGAGACAAGCTT 58.340 39.130 0.00 0.00 39.77 3.74
802 827 4.298103 ACATCCATTTGAGAGACAAGCT 57.702 40.909 0.00 0.00 39.77 3.74
803 828 4.333926 GGTACATCCATTTGAGAGACAAGC 59.666 45.833 0.00 0.00 36.65 4.01
804 829 5.738909 AGGTACATCCATTTGAGAGACAAG 58.261 41.667 0.00 0.00 38.01 3.16
805 830 5.762179 AGGTACATCCATTTGAGAGACAA 57.238 39.130 0.00 0.00 39.02 3.18
806 831 5.163405 GCTAGGTACATCCATTTGAGAGACA 60.163 44.000 0.00 0.00 39.02 3.41
807 832 5.163405 TGCTAGGTACATCCATTTGAGAGAC 60.163 44.000 0.00 0.00 39.02 3.36
808 833 4.962362 TGCTAGGTACATCCATTTGAGAGA 59.038 41.667 0.00 0.00 39.02 3.10
809 834 5.282055 TGCTAGGTACATCCATTTGAGAG 57.718 43.478 0.00 0.00 39.02 3.20
810 835 5.894298 ATGCTAGGTACATCCATTTGAGA 57.106 39.130 0.00 0.00 39.02 3.27
811 836 7.716998 AGTTAATGCTAGGTACATCCATTTGAG 59.283 37.037 10.35 0.00 39.02 3.02
812 837 7.573710 AGTTAATGCTAGGTACATCCATTTGA 58.426 34.615 10.35 1.01 39.02 2.69
813 838 7.807977 AGTTAATGCTAGGTACATCCATTTG 57.192 36.000 10.35 0.00 39.02 2.32
814 839 8.052748 TCAAGTTAATGCTAGGTACATCCATTT 58.947 33.333 10.35 0.00 39.02 2.32
815 840 7.573710 TCAAGTTAATGCTAGGTACATCCATT 58.426 34.615 10.06 10.06 39.02 3.16
816 841 7.136822 TCAAGTTAATGCTAGGTACATCCAT 57.863 36.000 0.00 0.00 39.02 3.41
817 842 6.553953 TCAAGTTAATGCTAGGTACATCCA 57.446 37.500 0.00 0.00 39.02 3.41
818 843 6.073003 GCATCAAGTTAATGCTAGGTACATCC 60.073 42.308 3.54 0.00 44.83 3.51
819 844 6.892691 GCATCAAGTTAATGCTAGGTACATC 58.107 40.000 3.54 0.00 44.83 3.06
820 845 6.867662 GCATCAAGTTAATGCTAGGTACAT 57.132 37.500 3.54 0.00 44.83 2.29
830 855 9.049523 ACATCACATACTAGCATCAAGTTAATG 57.950 33.333 0.00 0.00 0.00 1.90
831 856 9.049523 CACATCACATACTAGCATCAAGTTAAT 57.950 33.333 0.00 0.00 0.00 1.40
832 857 7.011389 GCACATCACATACTAGCATCAAGTTAA 59.989 37.037 0.00 0.00 0.00 2.01
833 858 6.479990 GCACATCACATACTAGCATCAAGTTA 59.520 38.462 0.00 0.00 0.00 2.24
834 859 5.295292 GCACATCACATACTAGCATCAAGTT 59.705 40.000 0.00 0.00 0.00 2.66
835 860 4.813161 GCACATCACATACTAGCATCAAGT 59.187 41.667 0.00 0.00 0.00 3.16
836 861 4.812626 TGCACATCACATACTAGCATCAAG 59.187 41.667 0.00 0.00 0.00 3.02
837 862 4.768583 TGCACATCACATACTAGCATCAA 58.231 39.130 0.00 0.00 0.00 2.57
838 863 4.374399 CTGCACATCACATACTAGCATCA 58.626 43.478 0.00 0.00 0.00 3.07
839 864 3.744942 CCTGCACATCACATACTAGCATC 59.255 47.826 0.00 0.00 0.00 3.91
840 865 3.495629 CCCTGCACATCACATACTAGCAT 60.496 47.826 0.00 0.00 0.00 3.79
841 866 2.158914 CCCTGCACATCACATACTAGCA 60.159 50.000 0.00 0.00 0.00 3.49
842 867 2.487934 CCCTGCACATCACATACTAGC 58.512 52.381 0.00 0.00 0.00 3.42
843 868 2.103771 AGCCCTGCACATCACATACTAG 59.896 50.000 0.00 0.00 0.00 2.57
872 897 2.433436 ACAAGAGGCCGAAACATAACC 58.567 47.619 0.00 0.00 0.00 2.85
873 898 4.226761 CAAACAAGAGGCCGAAACATAAC 58.773 43.478 0.00 0.00 0.00 1.89
908 946 6.238731 CCAATTTGTTCTTTGAGTGCTCACTA 60.239 38.462 2.07 0.00 42.66 2.74
980 1019 7.609146 GCATCATTTACAGGATCATAGGAATGA 59.391 37.037 11.37 11.37 46.01 2.57
1050 1090 5.069648 TGGTGATGATGAGGAAGAGACATAC 59.930 44.000 0.00 0.00 0.00 2.39
1088 1146 2.431782 CCAATAAAGAGCCATGGTTGGG 59.568 50.000 14.67 0.24 43.84 4.12
1372 1431 6.313519 TGAAAATAGAGCATCAGTTACCCT 57.686 37.500 0.00 0.00 37.82 4.34
1379 1438 8.725148 ACTTTGTACTTGAAAATAGAGCATCAG 58.275 33.333 0.00 0.00 37.82 2.90
1389 1448 9.868277 TCAATTCAACACTTTGTACTTGAAAAT 57.132 25.926 9.06 1.34 31.11 1.82
1405 1467 3.953612 AGCACCTTCAGTTCAATTCAACA 59.046 39.130 0.00 0.00 0.00 3.33
1461 1523 1.345415 CTTGGCAAGCAAAACAGGGAT 59.655 47.619 15.25 0.00 0.00 3.85
1727 1807 6.489675 CAAGGAAGATTGGATCATAAACACG 58.510 40.000 0.00 0.00 0.00 4.49
1776 1856 6.555315 CCTGAAACTCATACAGCAAATAACC 58.445 40.000 0.00 0.00 0.00 2.85
1780 1860 4.081406 TGCCTGAAACTCATACAGCAAAT 58.919 39.130 0.00 0.00 0.00 2.32
1853 1933 2.135139 CCATTGTGACGTCCATATCCG 58.865 52.381 14.12 0.00 0.00 4.18
1894 1974 3.951979 AGAACTCTTTCACAAAGCACG 57.048 42.857 0.00 0.00 38.39 5.34
1920 2000 7.164230 TGGAAACTTTTGACACACAAATAGT 57.836 32.000 0.00 0.00 45.99 2.12
2012 2093 9.166173 TCACAATCTTGATAACTTAACCTGATG 57.834 33.333 0.00 0.00 0.00 3.07
2026 2107 8.204160 TCCAAGTACGAATATCACAATCTTGAT 58.796 33.333 0.00 0.00 39.61 2.57
2051 2132 0.462759 GCACACAGGCAGGATAGGTC 60.463 60.000 0.00 0.00 0.00 3.85
2220 2684 8.824781 CAAGTAAGGATCATGTTGAGATGTAAG 58.175 37.037 0.00 0.00 0.00 2.34
2528 3147 2.685897 TGCAGTTGTCAAACCTACCAAC 59.314 45.455 0.00 0.00 36.94 3.77
2591 3216 6.055588 CGTCCAATCCCTACATAAGACAAAT 58.944 40.000 0.00 0.00 0.00 2.32
2845 3476 1.061546 GGGTGTTGGACTCCTTGGTA 58.938 55.000 0.00 0.00 32.60 3.25
2851 3482 1.603739 GCCAAGGGTGTTGGACTCC 60.604 63.158 7.99 0.00 42.06 3.85
2852 3483 0.690762 TAGCCAAGGGTGTTGGACTC 59.309 55.000 7.99 0.00 42.06 3.36
2856 3487 3.821033 GCTTATATAGCCAAGGGTGTTGG 59.179 47.826 0.13 0.00 44.48 3.77
3061 3891 5.650543 AGATTGTTTTCAGTTTGACACACC 58.349 37.500 0.00 0.00 0.00 4.16
3132 3963 3.412386 ACTATGTGGAAGGAACACTTGC 58.588 45.455 0.00 0.00 46.60 4.01
3133 3964 6.037786 TCTACTATGTGGAAGGAACACTTG 57.962 41.667 0.00 0.00 40.21 3.16
3174 4013 3.312973 TGTCGTCCGCAATTTAAAACAGT 59.687 39.130 0.00 0.00 0.00 3.55
3184 4023 2.740826 CCGGTTGTCGTCCGCAAT 60.741 61.111 0.00 0.00 45.71 3.56
3202 4041 8.055402 GCACACACACAAAAATAAACATAAGTG 58.945 33.333 0.00 0.00 0.00 3.16
3203 4042 7.761704 TGCACACACACAAAAATAAACATAAGT 59.238 29.630 0.00 0.00 0.00 2.24
3204 4043 8.124586 TGCACACACACAAAAATAAACATAAG 57.875 30.769 0.00 0.00 0.00 1.73
3205 4044 8.654230 ATGCACACACACAAAAATAAACATAA 57.346 26.923 0.00 0.00 0.00 1.90
3207 4046 6.985645 AGATGCACACACACAAAAATAAACAT 59.014 30.769 0.00 0.00 0.00 2.71
3208 4047 6.336566 AGATGCACACACACAAAAATAAACA 58.663 32.000 0.00 0.00 0.00 2.83
3209 4048 6.826893 AGATGCACACACACAAAAATAAAC 57.173 33.333 0.00 0.00 0.00 2.01
3211 4050 7.682824 CAAAAGATGCACACACACAAAAATAA 58.317 30.769 0.00 0.00 0.00 1.40
3212 4051 7.231705 CAAAAGATGCACACACACAAAAATA 57.768 32.000 0.00 0.00 0.00 1.40
3213 4052 6.109320 CAAAAGATGCACACACACAAAAAT 57.891 33.333 0.00 0.00 0.00 1.82
3288 4127 0.032615 AAACCCTTGCTGACCACCAA 60.033 50.000 0.00 0.00 0.00 3.67
3410 4251 3.786516 CACAGCATGCATGACCATTTA 57.213 42.857 30.64 0.00 42.53 1.40
3465 4310 1.816835 TGCCACCTCGTACTCAAGTAG 59.183 52.381 0.00 0.00 0.00 2.57
3530 4375 6.358118 TGCTCAACATAACCGATGAAATAC 57.642 37.500 0.00 0.00 39.06 1.89
3532 4377 5.895636 TTGCTCAACATAACCGATGAAAT 57.104 34.783 0.00 0.00 39.06 2.17
3547 4392 7.661027 TGCATACATGTTAGCTATATTGCTCAA 59.339 33.333 15.09 6.06 42.97 3.02
3548 4393 7.160726 TGCATACATGTTAGCTATATTGCTCA 58.839 34.615 15.09 8.75 42.97 4.26
3570 4415 3.944650 GTGTACCATTGGACATACATGCA 59.055 43.478 10.37 0.00 30.67 3.96
3586 4554 4.106029 TCTGAATAGTCAAGCGTGTACC 57.894 45.455 0.00 0.00 31.88 3.34
3607 4575 4.264253 CCATACACATCAGGTCACAACAT 58.736 43.478 0.00 0.00 0.00 2.71
3690 4658 8.034215 GGACATTGTTGTGGAATATGATTTTCA 58.966 33.333 0.00 0.00 35.79 2.69
3754 4723 6.857777 TGTAATTGGGCATTGTTTTTGAAG 57.142 33.333 0.00 0.00 0.00 3.02
3757 4726 6.798315 TCATGTAATTGGGCATTGTTTTTG 57.202 33.333 0.00 0.00 0.00 2.44
3904 4875 4.878397 GGAGATTGCTAATGCTACACACTT 59.122 41.667 0.00 0.00 40.48 3.16
3953 4924 1.277557 AGGAGCTGAGTAGGCAACAAG 59.722 52.381 0.00 0.00 41.41 3.16
3981 4952 2.791383 ATTTGTTTAGCGTGCTTGCA 57.209 40.000 0.00 0.00 37.31 4.08
4043 5014 0.533491 CCGGGATGGTAACTTCGACA 59.467 55.000 0.00 0.00 41.51 4.35
4094 5065 2.102420 CCGACTACATACCTCAATGGCA 59.898 50.000 0.00 0.00 40.22 4.92
4126 5097 2.905415 ATGAAGCTGGGAATTGACCA 57.095 45.000 0.00 0.00 36.38 4.02
4196 5167 4.959210 ACTCAGCATATGACTACAAGGACT 59.041 41.667 6.97 0.00 33.22 3.85
4215 5186 3.452990 TCACCAACCACAAGAACTACTCA 59.547 43.478 0.00 0.00 0.00 3.41
4296 5267 2.224670 ACGGCAAATGTGGAGAACCTTA 60.225 45.455 0.00 0.00 37.04 2.69
4317 5288 2.125673 GTTCCGCCGCTGCTTCTA 60.126 61.111 0.00 0.00 34.43 2.10
4344 5315 1.542187 CCTCGGGACCGTCTTTCCTT 61.542 60.000 10.90 0.00 40.74 3.36
4350 5321 2.361357 CTCACCTCGGGACCGTCT 60.361 66.667 10.90 0.00 40.74 4.18


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

AutoCloner maintained by Alex Coulton.