Multiple sequence alignment - TraesCS7B01G109800

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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 TraesCS7B01G109800 chr7B 100.000 4521 0 0 1 4521 125505775 125510295 0.000000e+00 8349.0
1 TraesCS7B01G109800 chr7B 92.048 1748 91 29 1496 3222 133647902 133646182 0.000000e+00 2414.0
2 TraesCS7B01G109800 chr7B 87.607 1759 150 40 1496 3222 243793695 243791973 0.000000e+00 1978.0
3 TraesCS7B01G109800 chr7B 86.011 1780 155 61 1491 3222 171932577 171930844 0.000000e+00 1821.0
4 TraesCS7B01G109800 chr5B 97.920 1731 25 5 1500 3222 665593343 665591616 0.000000e+00 2987.0
5 TraesCS7B01G109800 chr5B 87.585 1756 166 33 1496 3222 708079687 708081419 0.000000e+00 1988.0
6 TraesCS7B01G109800 chr5B 85.931 1777 168 45 1495 3222 195161327 195163070 0.000000e+00 1821.0
7 TraesCS7B01G109800 chr3B 97.458 1731 33 5 1500 3222 62181730 62183457 0.000000e+00 2942.0
8 TraesCS7B01G109800 chr4B 97.405 1734 29 7 1497 3222 18120631 18122356 0.000000e+00 2939.0
9 TraesCS7B01G109800 chr4B 97.235 1736 31 7 1497 3222 18127663 18129391 0.000000e+00 2924.0
10 TraesCS7B01G109800 chr4B 85.642 1783 174 47 1496 3227 49805509 49807260 0.000000e+00 1799.0
11 TraesCS7B01G109800 chr4B 93.242 947 39 11 1496 2425 567945452 567946390 0.000000e+00 1371.0
12 TraesCS7B01G109800 chr2B 97.347 1734 30 9 1499 3222 731237977 731236250 0.000000e+00 2933.0
13 TraesCS7B01G109800 chr2B 97.116 1734 38 6 1500 3222 43323540 43321808 0.000000e+00 2915.0
14 TraesCS7B01G109800 chr2B 84.965 572 51 18 1491 2044 446030671 446031225 8.550000e-152 547.0
15 TraesCS7B01G109800 chr1B 97.715 1707 33 5 1518 3222 673560860 673559158 0.000000e+00 2931.0
16 TraesCS7B01G109800 chr1B 97.229 1732 36 4 1500 3222 641113392 641115120 0.000000e+00 2922.0
17 TraesCS7B01G109800 chr4A 97.286 1732 29 8 1500 3222 648862793 648861071 0.000000e+00 2922.0
18 TraesCS7B01G109800 chr4A 82.195 410 55 9 1495 1890 638455566 638455161 2.010000e-88 337.0
19 TraesCS7B01G109800 chr5D 97.468 1264 25 7 3223 4484 6201518 6200260 0.000000e+00 2150.0
20 TraesCS7B01G109800 chr5D 96.901 1065 30 3 3420 4484 329162138 329163199 0.000000e+00 1781.0
21 TraesCS7B01G109800 chr5D 97.959 490 10 0 1010 1499 240136982 240137471 0.000000e+00 850.0
22 TraesCS7B01G109800 chr5D 97.551 490 12 0 1010 1499 6202003 6201514 0.000000e+00 839.0
23 TraesCS7B01G109800 chr5D 100.000 37 0 0 4485 4521 6237197 6237161 8.120000e-08 69.4
24 TraesCS7B01G109800 chr5D 100.000 37 0 0 4485 4521 357559646 357559682 8.120000e-08 69.4
25 TraesCS7B01G109800 chr5D 100.000 37 0 0 4485 4521 503329613 503329649 8.120000e-08 69.4
26 TraesCS7B01G109800 chr3D 97.159 1267 28 5 3223 4484 21904386 21905649 0.000000e+00 2134.0
27 TraesCS7B01G109800 chr3D 97.347 490 12 1 1010 1499 21903902 21904390 0.000000e+00 832.0
28 TraesCS7B01G109800 chr1D 97.075 1265 32 4 3223 4484 254497758 254499020 0.000000e+00 2126.0
29 TraesCS7B01G109800 chr1D 94.778 1264 58 8 3223 4484 244484284 244483027 0.000000e+00 1962.0
30 TraesCS7B01G109800 chr1D 97.959 490 10 0 1010 1499 254497273 254497762 0.000000e+00 850.0
31 TraesCS7B01G109800 chr1D 97.755 490 10 1 1010 1499 19957310 19957798 0.000000e+00 843.0
32 TraesCS7B01G109800 chr1D 97.551 490 10 1 1010 1499 206072561 206072074 0.000000e+00 837.0
33 TraesCS7B01G109800 chr1D 100.000 37 0 0 4485 4521 100232304 100232268 8.120000e-08 69.4
34 TraesCS7B01G109800 chr1D 100.000 37 0 0 4485 4521 254475700 254475736 8.120000e-08 69.4
35 TraesCS7B01G109800 chr1D 100.000 37 0 0 4485 4521 290505870 290505906 8.120000e-08 69.4
36 TraesCS7B01G109800 chr6B 96.838 1265 34 5 3223 4484 22425705 22426966 0.000000e+00 2109.0
37 TraesCS7B01G109800 chr6B 85.971 1782 164 56 1496 3222 679316108 679314358 0.000000e+00 1827.0
38 TraesCS7B01G109800 chr6B 96.939 490 15 0 1010 1499 22425220 22425709 0.000000e+00 822.0
39 TraesCS7B01G109800 chr6B 81.701 623 101 9 1 620 576362660 576362048 1.450000e-139 507.0
40 TraesCS7B01G109800 chr4D 95.886 1264 44 8 3223 4484 19916258 19917515 0.000000e+00 2039.0
41 TraesCS7B01G109800 chr4D 100.000 37 0 0 4485 4521 39605487 39605523 8.120000e-08 69.4
42 TraesCS7B01G109800 chr1A 95.501 1267 46 6 3223 4484 168450806 168449546 0.000000e+00 2013.0
43 TraesCS7B01G109800 chr1A 97.031 640 16 2 3223 3860 112776273 112775635 0.000000e+00 1074.0
44 TraesCS7B01G109800 chr1A 97.143 490 13 1 1010 1499 112776757 112776269 0.000000e+00 826.0
45 TraesCS7B01G109800 chr7A 93.661 1262 75 5 3223 4483 352194261 352193004 0.000000e+00 1882.0
46 TraesCS7B01G109800 chr7A 96.032 882 30 2 1 878 164401581 164402461 0.000000e+00 1430.0
47 TraesCS7B01G109800 chr3A 85.971 1782 162 57 1498 3222 652101641 652099891 0.000000e+00 1825.0
48 TraesCS7B01G109800 chr7D 97.303 890 24 0 1 890 163258037 163258926 0.000000e+00 1511.0
49 TraesCS7B01G109800 chr7D 97.959 490 10 0 1010 1499 336507805 336507316 0.000000e+00 850.0
50 TraesCS7B01G109800 chr6D 82.075 636 90 16 1 627 385956461 385955841 5.180000e-144 521.0
51 TraesCS7B01G109800 chr6D 100.000 37 0 0 4485 4521 112849164 112849128 8.120000e-08 69.4
52 TraesCS7B01G109800 chr6A 81.300 631 104 12 1 627 530279831 530279211 2.430000e-137 499.0
53 TraesCS7B01G109800 chr2D 100.000 37 0 0 4485 4521 33931005 33930969 8.120000e-08 69.4


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 TraesCS7B01G109800 chr7B 125505775 125510295 4520 False 8349.0 8349 100.0000 1 4521 1 chr7B.!!$F1 4520
1 TraesCS7B01G109800 chr7B 133646182 133647902 1720 True 2414.0 2414 92.0480 1496 3222 1 chr7B.!!$R1 1726
2 TraesCS7B01G109800 chr7B 243791973 243793695 1722 True 1978.0 1978 87.6070 1496 3222 1 chr7B.!!$R3 1726
3 TraesCS7B01G109800 chr7B 171930844 171932577 1733 True 1821.0 1821 86.0110 1491 3222 1 chr7B.!!$R2 1731
4 TraesCS7B01G109800 chr5B 665591616 665593343 1727 True 2987.0 2987 97.9200 1500 3222 1 chr5B.!!$R1 1722
5 TraesCS7B01G109800 chr5B 708079687 708081419 1732 False 1988.0 1988 87.5850 1496 3222 1 chr5B.!!$F2 1726
6 TraesCS7B01G109800 chr5B 195161327 195163070 1743 False 1821.0 1821 85.9310 1495 3222 1 chr5B.!!$F1 1727
7 TraesCS7B01G109800 chr3B 62181730 62183457 1727 False 2942.0 2942 97.4580 1500 3222 1 chr3B.!!$F1 1722
8 TraesCS7B01G109800 chr4B 18120631 18122356 1725 False 2939.0 2939 97.4050 1497 3222 1 chr4B.!!$F1 1725
9 TraesCS7B01G109800 chr4B 18127663 18129391 1728 False 2924.0 2924 97.2350 1497 3222 1 chr4B.!!$F2 1725
10 TraesCS7B01G109800 chr4B 49805509 49807260 1751 False 1799.0 1799 85.6420 1496 3227 1 chr4B.!!$F3 1731
11 TraesCS7B01G109800 chr4B 567945452 567946390 938 False 1371.0 1371 93.2420 1496 2425 1 chr4B.!!$F4 929
12 TraesCS7B01G109800 chr2B 731236250 731237977 1727 True 2933.0 2933 97.3470 1499 3222 1 chr2B.!!$R2 1723
13 TraesCS7B01G109800 chr2B 43321808 43323540 1732 True 2915.0 2915 97.1160 1500 3222 1 chr2B.!!$R1 1722
14 TraesCS7B01G109800 chr2B 446030671 446031225 554 False 547.0 547 84.9650 1491 2044 1 chr2B.!!$F1 553
15 TraesCS7B01G109800 chr1B 673559158 673560860 1702 True 2931.0 2931 97.7150 1518 3222 1 chr1B.!!$R1 1704
16 TraesCS7B01G109800 chr1B 641113392 641115120 1728 False 2922.0 2922 97.2290 1500 3222 1 chr1B.!!$F1 1722
17 TraesCS7B01G109800 chr4A 648861071 648862793 1722 True 2922.0 2922 97.2860 1500 3222 1 chr4A.!!$R2 1722
18 TraesCS7B01G109800 chr5D 329162138 329163199 1061 False 1781.0 1781 96.9010 3420 4484 1 chr5D.!!$F2 1064
19 TraesCS7B01G109800 chr5D 6200260 6202003 1743 True 1494.5 2150 97.5095 1010 4484 2 chr5D.!!$R2 3474
20 TraesCS7B01G109800 chr3D 21903902 21905649 1747 False 1483.0 2134 97.2530 1010 4484 2 chr3D.!!$F1 3474
21 TraesCS7B01G109800 chr1D 244483027 244484284 1257 True 1962.0 1962 94.7780 3223 4484 1 chr1D.!!$R3 1261
22 TraesCS7B01G109800 chr1D 254497273 254499020 1747 False 1488.0 2126 97.5170 1010 4484 2 chr1D.!!$F4 3474
23 TraesCS7B01G109800 chr6B 679314358 679316108 1750 True 1827.0 1827 85.9710 1496 3222 1 chr6B.!!$R2 1726
24 TraesCS7B01G109800 chr6B 22425220 22426966 1746 False 1465.5 2109 96.8885 1010 4484 2 chr6B.!!$F1 3474
25 TraesCS7B01G109800 chr6B 576362048 576362660 612 True 507.0 507 81.7010 1 620 1 chr6B.!!$R1 619
26 TraesCS7B01G109800 chr4D 19916258 19917515 1257 False 2039.0 2039 95.8860 3223 4484 1 chr4D.!!$F1 1261
27 TraesCS7B01G109800 chr1A 168449546 168450806 1260 True 2013.0 2013 95.5010 3223 4484 1 chr1A.!!$R1 1261
28 TraesCS7B01G109800 chr1A 112775635 112776757 1122 True 950.0 1074 97.0870 1010 3860 2 chr1A.!!$R2 2850
29 TraesCS7B01G109800 chr7A 352193004 352194261 1257 True 1882.0 1882 93.6610 3223 4483 1 chr7A.!!$R1 1260
30 TraesCS7B01G109800 chr7A 164401581 164402461 880 False 1430.0 1430 96.0320 1 878 1 chr7A.!!$F1 877
31 TraesCS7B01G109800 chr3A 652099891 652101641 1750 True 1825.0 1825 85.9710 1498 3222 1 chr3A.!!$R1 1724
32 TraesCS7B01G109800 chr7D 163258037 163258926 889 False 1511.0 1511 97.3030 1 890 1 chr7D.!!$F1 889
33 TraesCS7B01G109800 chr6D 385955841 385956461 620 True 521.0 521 82.0750 1 627 1 chr6D.!!$R2 626
34 TraesCS7B01G109800 chr6A 530279211 530279831 620 True 499.0 499 81.3000 1 627 1 chr6A.!!$R1 626

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
955 960 0.318445 ACTACTGGTGACGTCGCAAC 60.318 55.000 28.67 13.27 0.0 4.17 F
1269 1274 0.102844 GCTTGTGTTTCTTGGCAGCA 59.897 50.000 0.00 0.00 0.0 4.41 F
2445 2546 0.250945 TCGGGCAATAACCAACAGCA 60.251 50.000 0.00 0.00 0.0 4.41 F
2816 2920 3.055385 TGCACCTTTATAGTCACCCAGTC 60.055 47.826 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2207 2.610859 GGGCTGAAGTGGGAGGGA 60.611 66.667 0.00 0.00 0.0 4.20 R
3186 3304 5.613358 CCCTAGAGGCAATAATAAAAGCG 57.387 43.478 0.00 0.00 0.0 4.68 R
3309 3432 0.454600 GCGGACGGACACTAAGATGA 59.545 55.000 0.00 0.00 0.0 2.92 R
3928 4059 2.018542 TTCCCCTAATTGAGAACGCG 57.981 50.000 3.53 3.53 0.0 6.01 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
455 456 2.352032 GCACTGGTAGAGGCCGACT 61.352 63.158 10.12 10.12 0.00 4.18
621 622 2.498761 GAACGCCGTGTAGTCGTCGA 62.499 60.000 0.00 0.00 35.80 4.20
722 723 3.188786 CGGCTTGGACGTGCTAGC 61.189 66.667 29.46 29.46 0.00 3.42
734 735 1.658596 CGTGCTAGCGTTTGATGCTTA 59.341 47.619 10.77 0.00 41.42 3.09
783 784 2.586245 CGGAGCAGAATGGCAGGA 59.414 61.111 0.00 0.00 35.86 3.86
809 810 2.965831 AGCTAGTGTTCTGAGTGTGGAA 59.034 45.455 0.00 0.00 0.00 3.53
811 812 4.772624 AGCTAGTGTTCTGAGTGTGGAATA 59.227 41.667 0.00 0.00 0.00 1.75
890 895 5.420739 TCACTGTCACCAGCATAGTATTGTA 59.579 40.000 0.00 0.00 42.81 2.41
891 896 5.520288 CACTGTCACCAGCATAGTATTGTAC 59.480 44.000 0.00 0.00 42.81 2.90
892 897 4.678622 TGTCACCAGCATAGTATTGTACG 58.321 43.478 0.00 0.00 0.00 3.67
893 898 4.158949 TGTCACCAGCATAGTATTGTACGT 59.841 41.667 0.00 0.00 0.00 3.57
894 899 5.357596 TGTCACCAGCATAGTATTGTACGTA 59.642 40.000 0.00 0.00 0.00 3.57
895 900 5.684626 GTCACCAGCATAGTATTGTACGTAC 59.315 44.000 18.90 18.90 0.00 3.67
896 901 4.980434 CACCAGCATAGTATTGTACGTACC 59.020 45.833 22.43 7.38 0.00 3.34
897 902 4.891756 ACCAGCATAGTATTGTACGTACCT 59.108 41.667 22.43 14.17 0.00 3.08
898 903 5.220381 CCAGCATAGTATTGTACGTACCTG 58.780 45.833 22.43 16.84 0.00 4.00
899 904 5.221185 CCAGCATAGTATTGTACGTACCTGT 60.221 44.000 22.43 10.89 0.00 4.00
900 905 5.685954 CAGCATAGTATTGTACGTACCTGTG 59.314 44.000 22.43 18.93 0.00 3.66
901 906 5.591472 AGCATAGTATTGTACGTACCTGTGA 59.409 40.000 22.43 0.64 0.00 3.58
902 907 6.095860 AGCATAGTATTGTACGTACCTGTGAA 59.904 38.462 22.43 10.28 0.00 3.18
903 908 6.921857 GCATAGTATTGTACGTACCTGTGAAT 59.078 38.462 22.43 16.22 0.00 2.57
904 909 7.096189 GCATAGTATTGTACGTACCTGTGAATG 60.096 40.741 22.43 18.08 0.00 2.67
905 910 6.276832 AGTATTGTACGTACCTGTGAATGT 57.723 37.500 22.43 5.25 0.00 2.71
906 911 6.694447 AGTATTGTACGTACCTGTGAATGTT 58.306 36.000 22.43 5.83 0.00 2.71
907 912 7.156673 AGTATTGTACGTACCTGTGAATGTTT 58.843 34.615 22.43 3.74 0.00 2.83
908 913 6.870971 ATTGTACGTACCTGTGAATGTTTT 57.129 33.333 22.43 0.00 0.00 2.43
909 914 6.680874 TTGTACGTACCTGTGAATGTTTTT 57.319 33.333 22.43 0.00 0.00 1.94
910 915 6.050454 TGTACGTACCTGTGAATGTTTTTG 57.950 37.500 22.43 0.00 0.00 2.44
911 916 3.959943 ACGTACCTGTGAATGTTTTTGC 58.040 40.909 0.00 0.00 0.00 3.68
912 917 3.243267 ACGTACCTGTGAATGTTTTTGCC 60.243 43.478 0.00 0.00 0.00 4.52
913 918 3.004315 CGTACCTGTGAATGTTTTTGCCT 59.996 43.478 0.00 0.00 0.00 4.75
914 919 3.733443 ACCTGTGAATGTTTTTGCCTC 57.267 42.857 0.00 0.00 0.00 4.70
915 920 2.365293 ACCTGTGAATGTTTTTGCCTCC 59.635 45.455 0.00 0.00 0.00 4.30
916 921 2.629617 CCTGTGAATGTTTTTGCCTCCT 59.370 45.455 0.00 0.00 0.00 3.69
917 922 3.305608 CCTGTGAATGTTTTTGCCTCCTC 60.306 47.826 0.00 0.00 0.00 3.71
918 923 2.627699 TGTGAATGTTTTTGCCTCCTCC 59.372 45.455 0.00 0.00 0.00 4.30
919 924 2.627699 GTGAATGTTTTTGCCTCCTCCA 59.372 45.455 0.00 0.00 0.00 3.86
920 925 2.627699 TGAATGTTTTTGCCTCCTCCAC 59.372 45.455 0.00 0.00 0.00 4.02
921 926 2.683211 ATGTTTTTGCCTCCTCCACT 57.317 45.000 0.00 0.00 0.00 4.00
922 927 3.806949 ATGTTTTTGCCTCCTCCACTA 57.193 42.857 0.00 0.00 0.00 2.74
923 928 3.586470 TGTTTTTGCCTCCTCCACTAA 57.414 42.857 0.00 0.00 0.00 2.24
924 929 3.904717 TGTTTTTGCCTCCTCCACTAAA 58.095 40.909 0.00 0.00 0.00 1.85
925 930 4.282496 TGTTTTTGCCTCCTCCACTAAAA 58.718 39.130 0.00 0.00 0.00 1.52
926 931 4.898861 TGTTTTTGCCTCCTCCACTAAAAT 59.101 37.500 0.00 0.00 0.00 1.82
927 932 6.071984 TGTTTTTGCCTCCTCCACTAAAATA 58.928 36.000 0.00 0.00 0.00 1.40
928 933 6.551601 TGTTTTTGCCTCCTCCACTAAAATAA 59.448 34.615 0.00 0.00 0.00 1.40
929 934 7.234577 TGTTTTTGCCTCCTCCACTAAAATAAT 59.765 33.333 0.00 0.00 0.00 1.28
930 935 8.745590 GTTTTTGCCTCCTCCACTAAAATAATA 58.254 33.333 0.00 0.00 0.00 0.98
931 936 7.875327 TTTGCCTCCTCCACTAAAATAATAC 57.125 36.000 0.00 0.00 0.00 1.89
932 937 6.824958 TGCCTCCTCCACTAAAATAATACT 57.175 37.500 0.00 0.00 0.00 2.12
933 938 7.924358 TGCCTCCTCCACTAAAATAATACTA 57.076 36.000 0.00 0.00 0.00 1.82
934 939 7.732996 TGCCTCCTCCACTAAAATAATACTAC 58.267 38.462 0.00 0.00 0.00 2.73
935 940 7.567622 TGCCTCCTCCACTAAAATAATACTACT 59.432 37.037 0.00 0.00 0.00 2.57
936 941 9.086758 GCCTCCTCCACTAAAATAATACTACTA 57.913 37.037 0.00 0.00 0.00 1.82
949 954 8.970859 AATAATACTACTACTACTGGTGACGT 57.029 34.615 0.00 0.00 0.00 4.34
950 955 6.917217 AATACTACTACTACTGGTGACGTC 57.083 41.667 9.11 9.11 0.00 4.34
951 956 3.257393 ACTACTACTACTGGTGACGTCG 58.743 50.000 11.62 0.00 0.00 5.12
952 957 0.801251 ACTACTACTGGTGACGTCGC 59.199 55.000 20.76 20.76 0.00 5.19
953 958 0.800631 CTACTACTGGTGACGTCGCA 59.199 55.000 28.67 14.72 0.00 5.10
954 959 1.198408 CTACTACTGGTGACGTCGCAA 59.802 52.381 28.67 18.53 0.00 4.85
955 960 0.318445 ACTACTGGTGACGTCGCAAC 60.318 55.000 28.67 13.27 0.00 4.17
964 969 4.925786 CGTCGCAACGCATCTTAC 57.074 55.556 0.00 0.00 42.82 2.34
965 970 2.359792 CGTCGCAACGCATCTTACT 58.640 52.632 0.00 0.00 42.82 2.24
966 971 0.713883 CGTCGCAACGCATCTTACTT 59.286 50.000 0.00 0.00 42.82 2.24
967 972 1.126113 CGTCGCAACGCATCTTACTTT 59.874 47.619 0.00 0.00 42.82 2.66
968 973 2.411031 CGTCGCAACGCATCTTACTTTT 60.411 45.455 0.00 0.00 42.82 2.27
969 974 3.153735 GTCGCAACGCATCTTACTTTTC 58.846 45.455 0.00 0.00 0.00 2.29
970 975 2.803386 TCGCAACGCATCTTACTTTTCA 59.197 40.909 0.00 0.00 0.00 2.69
971 976 3.248841 TCGCAACGCATCTTACTTTTCAA 59.751 39.130 0.00 0.00 0.00 2.69
972 977 3.599514 CGCAACGCATCTTACTTTTCAAG 59.400 43.478 0.00 0.00 0.00 3.02
973 978 4.537015 GCAACGCATCTTACTTTTCAAGT 58.463 39.130 0.00 0.00 45.40 3.16
974 979 4.976116 GCAACGCATCTTACTTTTCAAGTT 59.024 37.500 0.00 0.00 42.81 2.66
975 980 6.140110 GCAACGCATCTTACTTTTCAAGTTA 58.860 36.000 0.00 0.00 42.81 2.24
976 981 6.801862 GCAACGCATCTTACTTTTCAAGTTAT 59.198 34.615 0.00 0.00 42.81 1.89
977 982 7.007456 GCAACGCATCTTACTTTTCAAGTTATC 59.993 37.037 0.00 0.00 42.81 1.75
978 983 7.667043 ACGCATCTTACTTTTCAAGTTATCA 57.333 32.000 0.00 0.00 42.81 2.15
979 984 8.268850 ACGCATCTTACTTTTCAAGTTATCAT 57.731 30.769 0.00 0.00 42.81 2.45
980 985 8.391106 ACGCATCTTACTTTTCAAGTTATCATC 58.609 33.333 0.00 0.00 42.81 2.92
981 986 7.852945 CGCATCTTACTTTTCAAGTTATCATCC 59.147 37.037 0.00 0.00 42.81 3.51
982 987 8.897752 GCATCTTACTTTTCAAGTTATCATCCT 58.102 33.333 0.00 0.00 42.81 3.24
988 993 8.425577 ACTTTTCAAGTTATCATCCTATCACG 57.574 34.615 0.00 0.00 39.04 4.35
989 994 8.041323 ACTTTTCAAGTTATCATCCTATCACGT 58.959 33.333 0.00 0.00 39.04 4.49
990 995 9.529325 CTTTTCAAGTTATCATCCTATCACGTA 57.471 33.333 0.00 0.00 0.00 3.57
991 996 9.878667 TTTTCAAGTTATCATCCTATCACGTAA 57.121 29.630 0.00 0.00 0.00 3.18
993 998 7.658261 TCAAGTTATCATCCTATCACGTAAGG 58.342 38.462 4.75 4.75 46.39 2.69
994 999 7.287005 TCAAGTTATCATCCTATCACGTAAGGT 59.713 37.037 9.79 0.00 46.39 3.50
995 1000 8.573885 CAAGTTATCATCCTATCACGTAAGGTA 58.426 37.037 9.79 0.15 46.39 3.08
996 1001 8.701908 AGTTATCATCCTATCACGTAAGGTAA 57.298 34.615 9.79 1.03 46.39 2.85
997 1002 8.574737 AGTTATCATCCTATCACGTAAGGTAAC 58.425 37.037 9.79 10.34 46.39 2.50
998 1003 6.971726 ATCATCCTATCACGTAAGGTAACA 57.028 37.500 9.79 0.00 46.39 2.41
999 1004 6.778834 TCATCCTATCACGTAAGGTAACAA 57.221 37.500 9.79 0.00 46.39 2.83
1000 1005 7.172868 TCATCCTATCACGTAAGGTAACAAA 57.827 36.000 9.79 0.00 46.39 2.83
1001 1006 7.788026 TCATCCTATCACGTAAGGTAACAAAT 58.212 34.615 9.79 0.00 46.39 2.32
1002 1007 7.709182 TCATCCTATCACGTAAGGTAACAAATG 59.291 37.037 9.79 6.26 46.39 2.32
1003 1008 7.172868 TCCTATCACGTAAGGTAACAAATGA 57.827 36.000 9.79 0.00 46.39 2.57
1004 1009 7.788026 TCCTATCACGTAAGGTAACAAATGAT 58.212 34.615 9.79 0.00 46.39 2.45
1005 1010 7.709182 TCCTATCACGTAAGGTAACAAATGATG 59.291 37.037 9.79 0.00 46.39 3.07
1006 1011 7.494625 CCTATCACGTAAGGTAACAAATGATGT 59.505 37.037 0.00 0.00 44.37 3.06
1008 1013 7.124347 TCACGTAAGGTAACAAATGATGTTC 57.876 36.000 0.00 0.00 46.56 3.18
1028 1033 3.743521 TCATGCACACAGCTCTAGTTTT 58.256 40.909 0.00 0.00 45.94 2.43
1128 1133 5.801380 ACACAAGGTATGTTCGTAATTCCT 58.199 37.500 0.00 0.00 41.46 3.36
1224 1229 6.630863 CGGGTATTTGGAGTTATGAAGGTGTA 60.631 42.308 0.00 0.00 0.00 2.90
1269 1274 0.102844 GCTTGTGTTTCTTGGCAGCA 59.897 50.000 0.00 0.00 0.00 4.41
1355 1360 3.777087 TGGATTTGCCCAAGATCTTTGA 58.223 40.909 4.86 0.00 34.97 2.69
1531 1544 4.273969 ACGTTGCAGAAAATTTTCCTACGA 59.726 37.500 30.21 18.66 37.92 3.43
2026 2097 2.362889 CCCCCAAGGCATGTGGTC 60.363 66.667 0.00 0.00 34.01 4.02
2371 2471 1.153823 CCTAGCGTCACCGAACCTG 60.154 63.158 0.00 0.00 35.63 4.00
2445 2546 0.250945 TCGGGCAATAACCAACAGCA 60.251 50.000 0.00 0.00 0.00 4.41
2756 2860 3.099905 TGACAAATCCCAGTCTCGATCT 58.900 45.455 0.00 0.00 35.81 2.75
2816 2920 3.055385 TGCACCTTTATAGTCACCCAGTC 60.055 47.826 0.00 0.00 0.00 3.51
3309 3432 5.508280 TGGGTATATTAGCGGGCTTATTT 57.492 39.130 0.00 0.00 0.00 1.40
3359 3482 9.453572 ACGTCTATATAAAGGATTACGTATGGA 57.546 33.333 0.00 0.00 40.19 3.41
3477 3606 4.764050 TCGAATTATTTGGGCCTACTCA 57.236 40.909 4.53 0.00 0.00 3.41
3493 3622 5.221722 GCCTACTCATTATCAGTGGGATCAA 60.222 44.000 2.36 0.00 43.58 2.57
3693 3822 4.289672 AGTTGTTGGATGGTTAGGACATCT 59.710 41.667 5.52 0.00 43.25 2.90
3813 3943 4.056050 TGTTAGAGCAGACGTTCCTTTTC 58.944 43.478 0.00 0.00 0.00 2.29
3949 4080 2.943033 CGCGTTCTCAATTAGGGGAAAT 59.057 45.455 0.00 0.00 0.00 2.17
4316 4447 6.736110 ATCCCAAATGACAAATGAATAGGG 57.264 37.500 0.00 0.00 0.00 3.53
4328 4459 6.433093 ACAAATGAATAGGGTGTGGAAGTTAC 59.567 38.462 0.00 0.00 0.00 2.50
4353 4484 8.798402 ACAATTGTAAATAAACCAGGATCGAAA 58.202 29.630 9.97 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
734 735 1.130054 TCAGCTTCCCAAGTCTGCCT 61.130 55.000 0.00 0.00 34.67 4.75
783 784 4.022762 CACACTCAGAACACTAGCTACTGT 60.023 45.833 7.85 4.56 0.00 3.55
809 810 5.780958 AAACCCTTTCAAGCCTACTCTAT 57.219 39.130 0.00 0.00 0.00 1.98
811 812 5.780958 ATAAACCCTTTCAAGCCTACTCT 57.219 39.130 0.00 0.00 0.00 3.24
890 895 3.243267 GGCAAAAACATTCACAGGTACGT 60.243 43.478 0.00 0.00 0.00 3.57
891 896 3.004315 AGGCAAAAACATTCACAGGTACG 59.996 43.478 0.00 0.00 0.00 3.67
892 897 4.546570 GAGGCAAAAACATTCACAGGTAC 58.453 43.478 0.00 0.00 0.00 3.34
893 898 3.572255 GGAGGCAAAAACATTCACAGGTA 59.428 43.478 0.00 0.00 0.00 3.08
894 899 2.365293 GGAGGCAAAAACATTCACAGGT 59.635 45.455 0.00 0.00 0.00 4.00
895 900 2.629617 AGGAGGCAAAAACATTCACAGG 59.370 45.455 0.00 0.00 0.00 4.00
896 901 3.305608 GGAGGAGGCAAAAACATTCACAG 60.306 47.826 0.00 0.00 0.00 3.66
897 902 2.627699 GGAGGAGGCAAAAACATTCACA 59.372 45.455 0.00 0.00 0.00 3.58
898 903 2.627699 TGGAGGAGGCAAAAACATTCAC 59.372 45.455 0.00 0.00 0.00 3.18
899 904 2.627699 GTGGAGGAGGCAAAAACATTCA 59.372 45.455 0.00 0.00 0.00 2.57
900 905 2.893489 AGTGGAGGAGGCAAAAACATTC 59.107 45.455 0.00 0.00 0.00 2.67
901 906 2.962859 AGTGGAGGAGGCAAAAACATT 58.037 42.857 0.00 0.00 0.00 2.71
902 907 2.683211 AGTGGAGGAGGCAAAAACAT 57.317 45.000 0.00 0.00 0.00 2.71
903 908 3.586470 TTAGTGGAGGAGGCAAAAACA 57.414 42.857 0.00 0.00 0.00 2.83
904 909 4.929819 TTTTAGTGGAGGAGGCAAAAAC 57.070 40.909 0.00 0.00 0.00 2.43
905 910 7.790782 ATTATTTTAGTGGAGGAGGCAAAAA 57.209 32.000 0.00 0.00 0.00 1.94
906 911 8.113462 AGTATTATTTTAGTGGAGGAGGCAAAA 58.887 33.333 0.00 0.00 0.00 2.44
907 912 7.639378 AGTATTATTTTAGTGGAGGAGGCAAA 58.361 34.615 0.00 0.00 0.00 3.68
908 913 7.208064 AGTATTATTTTAGTGGAGGAGGCAA 57.792 36.000 0.00 0.00 0.00 4.52
909 914 6.824958 AGTATTATTTTAGTGGAGGAGGCA 57.175 37.500 0.00 0.00 0.00 4.75
910 915 7.964624 AGTAGTATTATTTTAGTGGAGGAGGC 58.035 38.462 0.00 0.00 0.00 4.70
923 928 9.401058 ACGTCACCAGTAGTAGTAGTATTATTT 57.599 33.333 0.00 0.00 0.00 1.40
924 929 8.970859 ACGTCACCAGTAGTAGTAGTATTATT 57.029 34.615 0.00 0.00 0.00 1.40
925 930 7.383572 CGACGTCACCAGTAGTAGTAGTATTAT 59.616 40.741 17.16 0.00 0.00 1.28
926 931 6.697455 CGACGTCACCAGTAGTAGTAGTATTA 59.303 42.308 17.16 0.00 0.00 0.98
927 932 5.521735 CGACGTCACCAGTAGTAGTAGTATT 59.478 44.000 17.16 0.00 0.00 1.89
928 933 5.046529 CGACGTCACCAGTAGTAGTAGTAT 58.953 45.833 17.16 0.00 0.00 2.12
929 934 4.424626 CGACGTCACCAGTAGTAGTAGTA 58.575 47.826 17.16 0.00 0.00 1.82
930 935 3.257393 CGACGTCACCAGTAGTAGTAGT 58.743 50.000 17.16 0.00 0.00 2.73
931 936 2.030213 GCGACGTCACCAGTAGTAGTAG 59.970 54.545 17.16 0.00 0.00 2.57
932 937 2.002586 GCGACGTCACCAGTAGTAGTA 58.997 52.381 17.16 0.00 0.00 1.82
933 938 0.801251 GCGACGTCACCAGTAGTAGT 59.199 55.000 17.16 0.00 0.00 2.73
934 939 0.800631 TGCGACGTCACCAGTAGTAG 59.199 55.000 17.16 0.00 0.00 2.57
935 940 1.069022 GTTGCGACGTCACCAGTAGTA 60.069 52.381 17.16 0.00 0.00 1.82
936 941 0.318445 GTTGCGACGTCACCAGTAGT 60.318 55.000 17.16 0.00 0.00 2.73
937 942 1.334992 CGTTGCGACGTCACCAGTAG 61.335 60.000 18.62 0.00 44.08 2.57
938 943 1.370778 CGTTGCGACGTCACCAGTA 60.371 57.895 18.62 0.00 44.08 2.74
939 944 2.657296 CGTTGCGACGTCACCAGT 60.657 61.111 18.62 0.00 44.08 4.00
948 953 2.875080 AAAGTAAGATGCGTTGCGAC 57.125 45.000 0.00 0.00 0.00 5.19
949 954 2.803386 TGAAAAGTAAGATGCGTTGCGA 59.197 40.909 0.00 0.00 0.00 5.10
950 955 3.181826 TGAAAAGTAAGATGCGTTGCG 57.818 42.857 0.00 0.00 0.00 4.85
965 970 9.878667 TTACGTGATAGGATGATAACTTGAAAA 57.121 29.630 0.00 0.00 0.00 2.29
966 971 9.529325 CTTACGTGATAGGATGATAACTTGAAA 57.471 33.333 0.00 0.00 0.00 2.69
967 972 8.141909 CCTTACGTGATAGGATGATAACTTGAA 58.858 37.037 0.00 0.00 33.13 2.69
968 973 7.287005 ACCTTACGTGATAGGATGATAACTTGA 59.713 37.037 16.97 0.00 35.45 3.02
969 974 7.434492 ACCTTACGTGATAGGATGATAACTTG 58.566 38.462 16.97 0.00 35.45 3.16
970 975 7.598759 ACCTTACGTGATAGGATGATAACTT 57.401 36.000 16.97 0.00 35.45 2.66
971 976 8.574737 GTTACCTTACGTGATAGGATGATAACT 58.425 37.037 16.97 0.00 35.45 2.24
972 977 8.355169 TGTTACCTTACGTGATAGGATGATAAC 58.645 37.037 16.97 14.32 35.45 1.89
973 978 8.467963 TGTTACCTTACGTGATAGGATGATAA 57.532 34.615 16.97 5.49 35.45 1.75
974 979 8.467963 TTGTTACCTTACGTGATAGGATGATA 57.532 34.615 16.97 0.53 35.45 2.15
975 980 6.971726 TGTTACCTTACGTGATAGGATGAT 57.028 37.500 16.97 1.30 35.45 2.45
976 981 6.778834 TTGTTACCTTACGTGATAGGATGA 57.221 37.500 16.97 2.99 35.45 2.92
977 982 7.709182 TCATTTGTTACCTTACGTGATAGGATG 59.291 37.037 16.97 10.31 35.45 3.51
978 983 7.788026 TCATTTGTTACCTTACGTGATAGGAT 58.212 34.615 16.97 6.79 35.45 3.24
979 984 7.172868 TCATTTGTTACCTTACGTGATAGGA 57.827 36.000 16.97 2.23 35.45 2.94
980 985 7.494625 ACATCATTTGTTACCTTACGTGATAGG 59.505 37.037 0.00 4.91 33.74 2.57
981 986 8.420374 ACATCATTTGTTACCTTACGTGATAG 57.580 34.615 0.00 0.00 33.74 2.08
982 987 8.780846 AACATCATTTGTTACCTTACGTGATA 57.219 30.769 0.00 0.00 46.75 2.15
983 988 7.681939 AACATCATTTGTTACCTTACGTGAT 57.318 32.000 0.00 0.00 46.75 3.06
993 998 9.186152 GCTGTGTGCATGAACATCATTTGTTAC 62.186 40.741 10.45 0.00 44.26 2.50
994 999 7.279491 GCTGTGTGCATGAACATCATTTGTTA 61.279 38.462 10.45 0.00 44.26 2.41
995 1000 6.528476 GCTGTGTGCATGAACATCATTTGTT 61.528 40.000 10.45 0.00 45.67 2.83
996 1001 4.552355 CTGTGTGCATGAACATCATTTGT 58.448 39.130 10.45 0.00 41.53 2.83
997 1002 3.366724 GCTGTGTGCATGAACATCATTTG 59.633 43.478 10.45 0.66 42.31 2.32
998 1003 3.257375 AGCTGTGTGCATGAACATCATTT 59.743 39.130 10.45 0.00 45.94 2.32
999 1004 2.823747 AGCTGTGTGCATGAACATCATT 59.176 40.909 10.45 0.00 45.94 2.57
1000 1005 2.422479 GAGCTGTGTGCATGAACATCAT 59.578 45.455 10.45 0.00 45.94 2.45
1001 1006 1.808343 GAGCTGTGTGCATGAACATCA 59.192 47.619 10.45 9.12 45.94 3.07
1002 1007 2.082231 AGAGCTGTGTGCATGAACATC 58.918 47.619 10.45 3.24 45.94 3.06
1003 1008 2.195741 AGAGCTGTGTGCATGAACAT 57.804 45.000 10.45 0.00 45.94 2.71
1004 1009 2.037641 ACTAGAGCTGTGTGCATGAACA 59.962 45.455 1.03 1.03 45.94 3.18
1005 1010 2.693069 ACTAGAGCTGTGTGCATGAAC 58.307 47.619 0.00 0.00 45.94 3.18
1006 1011 3.407424 AACTAGAGCTGTGTGCATGAA 57.593 42.857 0.00 0.00 45.94 2.57
1007 1012 3.407424 AAACTAGAGCTGTGTGCATGA 57.593 42.857 0.00 0.00 45.94 3.07
1008 1013 4.224433 CAAAAACTAGAGCTGTGTGCATG 58.776 43.478 0.00 0.00 45.94 4.06
1028 1033 1.155859 ATTGAGCCAGCCCAACCAA 59.844 52.632 0.00 0.00 0.00 3.67
1106 1111 6.737254 AAGGAATTACGAACATACCTTGTG 57.263 37.500 0.00 0.00 38.99 3.33
1224 1229 2.691409 ACACAATATGCGTACCTGCT 57.309 45.000 0.00 0.00 35.36 4.24
1269 1274 4.107798 TCCCAATATACCCAATGCCAGATT 59.892 41.667 0.00 0.00 0.00 2.40
1307 1312 0.035598 TTTTCCCGTCCGCTCATCAA 59.964 50.000 0.00 0.00 0.00 2.57
1355 1360 6.880529 CACCCCTGCAAGAAATAAATGAATTT 59.119 34.615 0.00 0.00 34.07 1.82
1531 1544 7.146715 ACTCATAGATGGATCTTGGTGAAAT 57.853 36.000 0.00 0.00 38.32 2.17
2110 2207 2.610859 GGGCTGAAGTGGGAGGGA 60.611 66.667 0.00 0.00 0.00 4.20
3186 3304 5.613358 CCCTAGAGGCAATAATAAAAGCG 57.387 43.478 0.00 0.00 0.00 4.68
3309 3432 0.454600 GCGGACGGACACTAAGATGA 59.545 55.000 0.00 0.00 0.00 2.92
3477 3606 7.639062 AAGTATCCTTGATCCCACTGATAAT 57.361 36.000 0.00 0.00 32.41 1.28
3620 3749 4.017591 TGCTCTGAATAATCCCCCTTTTGA 60.018 41.667 0.00 0.00 0.00 2.69
3752 3882 4.184629 CCAAAACAACCGGAAATGTTTCA 58.815 39.130 26.03 0.00 46.09 2.69
3813 3943 6.703607 ACACTATATTTGGATTCTGCTCTTCG 59.296 38.462 0.00 0.00 0.00 3.79
3928 4059 2.018542 TTCCCCTAATTGAGAACGCG 57.981 50.000 3.53 3.53 0.00 6.01
4328 4459 9.072294 GTTTCGATCCTGGTTTATTTACAATTG 57.928 33.333 3.24 3.24 0.00 2.32
4353 4484 6.354130 ACGTATAAACCAATGCTTCCATAGT 58.646 36.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.