Multiple sequence alignment - TraesCS3B01G509900

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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 TraesCS3B01G509900 chr3B 100.000 3158 0 0 1 3158 753915231 753918388 0.000000e+00 5832.0
1 TraesCS3B01G509900 chr3B 79.704 877 145 21 1579 2447 753951685 753952536 1.250000e-168 603.0
2 TraesCS3B01G509900 chr3B 78.208 982 183 23 1539 2508 753867873 753868835 1.620000e-167 599.0
3 TraesCS3B01G509900 chr3B 77.345 693 112 29 163 828 820089918 820090592 4.980000e-98 368.0
4 TraesCS3B01G509900 chr3B 76.675 403 70 18 1105 1483 753951223 753951625 5.340000e-48 202.0
5 TraesCS3B01G509900 chr3B 73.936 564 98 33 926 1462 752122984 752122443 6.960000e-42 182.0
6 TraesCS3B01G509900 chr3B 74.580 476 91 25 996 1459 753964638 753964181 6.960000e-42 182.0
7 TraesCS3B01G509900 chr3B 82.258 186 32 1 1017 1202 754879562 754879746 3.260000e-35 159.0
8 TraesCS3B01G509900 chr3B 78.995 219 40 5 978 1193 753560985 753561200 9.130000e-31 145.0
9 TraesCS3B01G509900 chr3B 75.573 262 59 4 1635 1895 754220463 754220720 1.190000e-24 124.0
10 TraesCS3B01G509900 chr3A 90.451 2283 158 24 908 3147 699982320 699984585 0.000000e+00 2953.0
11 TraesCS3B01G509900 chr3A 78.586 990 166 38 1539 2508 699976454 699977417 2.080000e-171 612.0
12 TraesCS3B01G509900 chr3A 79.904 209 42 0 996 1204 697585517 697585309 1.520000e-33 154.0
13 TraesCS3B01G509900 chr3A 86.301 146 14 4 988 1130 699462238 699462096 1.520000e-33 154.0
14 TraesCS3B01G509900 chr3A 100.000 35 0 0 1306 1340 702012774 702012740 7.310000e-07 65.8
15 TraesCS3B01G509900 chr5D 94.817 849 29 6 1 846 304349206 304350042 0.000000e+00 1310.0
16 TraesCS3B01G509900 chr5D 88.418 708 56 10 142 844 465898754 465898068 0.000000e+00 830.0
17 TraesCS3B01G509900 chr5D 90.248 605 43 9 239 840 439639738 439639147 0.000000e+00 776.0
18 TraesCS3B01G509900 chr7B 91.222 843 70 4 1 841 291939414 291938574 0.000000e+00 1144.0
19 TraesCS3B01G509900 chr7B 85.111 853 90 25 1 832 706852172 706853008 0.000000e+00 837.0
20 TraesCS3B01G509900 chr7B 81.560 846 107 22 1 832 207903960 207903150 0.000000e+00 652.0
21 TraesCS3B01G509900 chr7B 81.464 847 109 20 1 832 57266862 57266049 0.000000e+00 651.0
22 TraesCS3B01G509900 chr4D 85.431 858 94 16 1 840 88092235 88091391 0.000000e+00 863.0
23 TraesCS3B01G509900 chr3D 79.469 1281 214 28 937 2185 565675327 565676590 0.000000e+00 863.0
24 TraesCS3B01G509900 chr3D 88.304 684 55 12 1 668 325975368 325976042 0.000000e+00 797.0
25 TraesCS3B01G509900 chr3D 87.237 713 60 16 149 840 359455406 359454704 0.000000e+00 784.0
26 TraesCS3B01G509900 chr3D 77.273 1012 194 25 1537 2532 565642449 565643440 2.130000e-156 562.0
27 TraesCS3B01G509900 chr3D 77.337 984 187 22 1528 2493 565831266 565832231 1.660000e-152 549.0
28 TraesCS3B01G509900 chr3D 87.850 214 23 2 984 1197 564905438 564905228 6.760000e-62 248.0
29 TraesCS3B01G509900 chr6A 88.244 706 65 11 142 840 555929783 555929089 0.000000e+00 828.0
30 TraesCS3B01G509900 chr6B 84.571 862 95 24 1 841 261526651 261525807 0.000000e+00 821.0
31 TraesCS3B01G509900 chr5A 85.509 766 90 16 1 760 51906646 51905896 0.000000e+00 780.0
32 TraesCS3B01G509900 chr5A 81.551 851 103 27 1 832 389155412 389154597 0.000000e+00 652.0
33 TraesCS3B01G509900 chr2A 87.407 675 62 11 150 818 69306727 69306070 0.000000e+00 754.0
34 TraesCS3B01G509900 chr5B 85.835 713 71 15 1 696 429438258 429437559 0.000000e+00 730.0
35 TraesCS3B01G509900 chrUn 78.034 651 123 14 1610 2247 48323992 48323349 2.950000e-105 392.0
36 TraesCS3B01G509900 chrUn 83.827 371 51 6 2253 2616 48292870 48292502 8.390000e-91 344.0
37 TraesCS3B01G509900 chrUn 81.720 186 33 1 1017 1202 279459090 279458906 1.520000e-33 154.0
38 TraesCS3B01G509900 chr4A 78.219 629 119 12 1623 2239 611418056 611417434 1.370000e-103 387.0
39 TraesCS3B01G509900 chr4A 77.448 572 112 9 1685 2247 611378787 611378224 3.040000e-85 326.0
40 TraesCS3B01G509900 chr1B 77.914 163 30 5 1303 1462 41840921 41841080 2.590000e-16 97.1


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 TraesCS3B01G509900 chr3B 753915231 753918388 3157 False 5832.0 5832 100.0000 1 3158 1 chr3B.!!$F3 3157
1 TraesCS3B01G509900 chr3B 753867873 753868835 962 False 599.0 599 78.2080 1539 2508 1 chr3B.!!$F2 969
2 TraesCS3B01G509900 chr3B 753951223 753952536 1313 False 402.5 603 78.1895 1105 2447 2 chr3B.!!$F7 1342
3 TraesCS3B01G509900 chr3B 820089918 820090592 674 False 368.0 368 77.3450 163 828 1 chr3B.!!$F6 665
4 TraesCS3B01G509900 chr3A 699982320 699984585 2265 False 2953.0 2953 90.4510 908 3147 1 chr3A.!!$F2 2239
5 TraesCS3B01G509900 chr3A 699976454 699977417 963 False 612.0 612 78.5860 1539 2508 1 chr3A.!!$F1 969
6 TraesCS3B01G509900 chr5D 304349206 304350042 836 False 1310.0 1310 94.8170 1 846 1 chr5D.!!$F1 845
7 TraesCS3B01G509900 chr5D 465898068 465898754 686 True 830.0 830 88.4180 142 844 1 chr5D.!!$R2 702
8 TraesCS3B01G509900 chr5D 439639147 439639738 591 True 776.0 776 90.2480 239 840 1 chr5D.!!$R1 601
9 TraesCS3B01G509900 chr7B 291938574 291939414 840 True 1144.0 1144 91.2220 1 841 1 chr7B.!!$R3 840
10 TraesCS3B01G509900 chr7B 706852172 706853008 836 False 837.0 837 85.1110 1 832 1 chr7B.!!$F1 831
11 TraesCS3B01G509900 chr7B 207903150 207903960 810 True 652.0 652 81.5600 1 832 1 chr7B.!!$R2 831
12 TraesCS3B01G509900 chr7B 57266049 57266862 813 True 651.0 651 81.4640 1 832 1 chr7B.!!$R1 831
13 TraesCS3B01G509900 chr4D 88091391 88092235 844 True 863.0 863 85.4310 1 840 1 chr4D.!!$R1 839
14 TraesCS3B01G509900 chr3D 565675327 565676590 1263 False 863.0 863 79.4690 937 2185 1 chr3D.!!$F3 1248
15 TraesCS3B01G509900 chr3D 325975368 325976042 674 False 797.0 797 88.3040 1 668 1 chr3D.!!$F1 667
16 TraesCS3B01G509900 chr3D 359454704 359455406 702 True 784.0 784 87.2370 149 840 1 chr3D.!!$R1 691
17 TraesCS3B01G509900 chr3D 565642449 565643440 991 False 562.0 562 77.2730 1537 2532 1 chr3D.!!$F2 995
18 TraesCS3B01G509900 chr3D 565831266 565832231 965 False 549.0 549 77.3370 1528 2493 1 chr3D.!!$F4 965
19 TraesCS3B01G509900 chr6A 555929089 555929783 694 True 828.0 828 88.2440 142 840 1 chr6A.!!$R1 698
20 TraesCS3B01G509900 chr6B 261525807 261526651 844 True 821.0 821 84.5710 1 841 1 chr6B.!!$R1 840
21 TraesCS3B01G509900 chr5A 51905896 51906646 750 True 780.0 780 85.5090 1 760 1 chr5A.!!$R1 759
22 TraesCS3B01G509900 chr5A 389154597 389155412 815 True 652.0 652 81.5510 1 832 1 chr5A.!!$R2 831
23 TraesCS3B01G509900 chr2A 69306070 69306727 657 True 754.0 754 87.4070 150 818 1 chr2A.!!$R1 668
24 TraesCS3B01G509900 chr5B 429437559 429438258 699 True 730.0 730 85.8350 1 696 1 chr5B.!!$R1 695
25 TraesCS3B01G509900 chrUn 48323349 48323992 643 True 392.0 392 78.0340 1610 2247 1 chrUn.!!$R2 637
26 TraesCS3B01G509900 chr4A 611417434 611418056 622 True 387.0 387 78.2190 1623 2239 1 chr4A.!!$R2 616
27 TraesCS3B01G509900 chr4A 611378224 611378787 563 True 326.0 326 77.4480 1685 2247 1 chr4A.!!$R1 562

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
907 1007 0.039618 AGGCCCATTCCATTGACGTT 59.960 50.0 0.00 0.00 0.00 3.99 F
1098 1207 0.596577 TCCGCCTCGATCCTAAATCG 59.403 55.0 1.13 1.13 42.38 3.34 F
1402 1559 0.608640 GTATGCTCCCCTCCGTATGG 59.391 60.0 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2148 0.459489 TTTGACCAGCACAAGCAACC 59.541 50.000 0.0 0.0 45.49 3.77 R
2048 2223 0.674895 AGGACAGATGCCTTTGCGAC 60.675 55.000 0.0 0.0 41.78 5.19 R
2659 2871 1.871408 GCCACATCTCATCGCTAGGTG 60.871 57.143 0.0 0.0 0.00 4.00 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
137 140 4.142988 CGCAAAAAGCTTCAACCGTAGATA 60.143 41.667 0.00 0.00 42.61 1.98
174 177 1.904287 AGCCGATTTTTGCTACCACA 58.096 45.000 0.00 0.00 35.69 4.17
767 867 0.991146 TACCAGATCCAAAGGCTGCA 59.009 50.000 0.50 0.00 0.00 4.41
861 961 3.536075 AAAAACCCTAAGCTAAGCCCA 57.464 42.857 0.00 0.00 0.00 5.36
862 962 3.757947 AAAACCCTAAGCTAAGCCCAT 57.242 42.857 0.00 0.00 0.00 4.00
863 963 3.757947 AAACCCTAAGCTAAGCCCATT 57.242 42.857 0.00 0.00 0.00 3.16
864 964 4.873724 AAACCCTAAGCTAAGCCCATTA 57.126 40.909 0.00 0.00 0.00 1.90
865 965 4.873724 AACCCTAAGCTAAGCCCATTAA 57.126 40.909 0.00 0.00 0.00 1.40
866 966 5.403558 AACCCTAAGCTAAGCCCATTAAT 57.596 39.130 0.00 0.00 0.00 1.40
867 967 6.524545 AACCCTAAGCTAAGCCCATTAATA 57.475 37.500 0.00 0.00 0.00 0.98
868 968 6.720217 ACCCTAAGCTAAGCCCATTAATAT 57.280 37.500 0.00 0.00 0.00 1.28
869 969 7.103745 ACCCTAAGCTAAGCCCATTAATATT 57.896 36.000 0.00 0.00 0.00 1.28
870 970 7.535738 ACCCTAAGCTAAGCCCATTAATATTT 58.464 34.615 0.00 0.00 0.00 1.40
871 971 7.670140 ACCCTAAGCTAAGCCCATTAATATTTC 59.330 37.037 0.00 0.00 0.00 2.17
872 972 7.890655 CCCTAAGCTAAGCCCATTAATATTTCT 59.109 37.037 0.00 0.00 0.00 2.52
873 973 8.951243 CCTAAGCTAAGCCCATTAATATTTCTC 58.049 37.037 0.00 0.00 0.00 2.87
874 974 9.507329 CTAAGCTAAGCCCATTAATATTTCTCA 57.493 33.333 0.00 0.00 0.00 3.27
875 975 8.766994 AAGCTAAGCCCATTAATATTTCTCAA 57.233 30.769 0.00 0.00 0.00 3.02
876 976 8.766994 AGCTAAGCCCATTAATATTTCTCAAA 57.233 30.769 0.00 0.00 0.00 2.69
877 977 9.200817 AGCTAAGCCCATTAATATTTCTCAAAA 57.799 29.630 0.00 0.00 0.00 2.44
878 978 9.816354 GCTAAGCCCATTAATATTTCTCAAAAA 57.184 29.630 0.00 0.00 0.00 1.94
892 992 5.391312 TCTCAAAAAGAAAATGCTAGGCC 57.609 39.130 0.00 0.00 0.00 5.19
893 993 4.220602 TCTCAAAAAGAAAATGCTAGGCCC 59.779 41.667 0.00 0.00 0.00 5.80
894 994 3.900601 TCAAAAAGAAAATGCTAGGCCCA 59.099 39.130 0.00 0.00 0.00 5.36
895 995 4.531732 TCAAAAAGAAAATGCTAGGCCCAT 59.468 37.500 0.00 0.00 0.00 4.00
896 996 5.012975 TCAAAAAGAAAATGCTAGGCCCATT 59.987 36.000 0.00 0.00 34.56 3.16
897 997 4.743057 AAAGAAAATGCTAGGCCCATTC 57.257 40.909 0.00 0.00 32.07 2.67
898 998 2.670939 AGAAAATGCTAGGCCCATTCC 58.329 47.619 0.00 0.00 32.07 3.01
899 999 2.024080 AGAAAATGCTAGGCCCATTCCA 60.024 45.455 0.00 0.00 32.07 3.53
900 1000 2.781403 AAATGCTAGGCCCATTCCAT 57.219 45.000 0.00 0.00 32.07 3.41
901 1001 2.781403 AATGCTAGGCCCATTCCATT 57.219 45.000 0.00 0.00 0.00 3.16
902 1002 2.005370 ATGCTAGGCCCATTCCATTG 57.995 50.000 0.00 0.00 0.00 2.82
903 1003 0.925558 TGCTAGGCCCATTCCATTGA 59.074 50.000 0.00 0.00 0.00 2.57
904 1004 1.322442 GCTAGGCCCATTCCATTGAC 58.678 55.000 0.00 0.00 0.00 3.18
905 1005 1.597742 CTAGGCCCATTCCATTGACG 58.402 55.000 0.00 0.00 0.00 4.35
906 1006 0.916086 TAGGCCCATTCCATTGACGT 59.084 50.000 0.00 0.00 0.00 4.34
907 1007 0.039618 AGGCCCATTCCATTGACGTT 59.960 50.000 0.00 0.00 0.00 3.99
908 1008 0.894835 GGCCCATTCCATTGACGTTT 59.105 50.000 0.00 0.00 0.00 3.60
909 1009 1.135112 GGCCCATTCCATTGACGTTTC 60.135 52.381 0.00 0.00 0.00 2.78
910 1010 1.818674 GCCCATTCCATTGACGTTTCT 59.181 47.619 0.00 0.00 0.00 2.52
911 1011 2.415893 GCCCATTCCATTGACGTTTCTG 60.416 50.000 0.00 0.00 0.00 3.02
923 1023 2.009774 ACGTTTCTGCTGTATCCATGC 58.990 47.619 0.00 0.00 0.00 4.06
927 1027 1.228367 CTGCTGTATCCATGCCCCC 60.228 63.158 0.00 0.00 0.00 5.40
928 1028 1.697394 TGCTGTATCCATGCCCCCT 60.697 57.895 0.00 0.00 0.00 4.79
929 1029 1.073897 GCTGTATCCATGCCCCCTC 59.926 63.158 0.00 0.00 0.00 4.30
965 1065 3.168528 AACCGCACCTCCACCTGT 61.169 61.111 0.00 0.00 0.00 4.00
978 1079 4.007644 CCTGTGGACGGAGCAGCA 62.008 66.667 0.00 0.00 0.00 4.41
1041 1150 1.630126 AAGCCACGCCTCTCATCCAT 61.630 55.000 0.00 0.00 0.00 3.41
1053 1162 1.150081 CATCCATGGCCTCCCAGAC 59.850 63.158 6.96 0.00 46.24 3.51
1089 1198 2.203365 ATCCTCGTCCGCCTCGAT 60.203 61.111 0.00 0.00 36.73 3.59
1092 1201 2.902846 CTCGTCCGCCTCGATCCT 60.903 66.667 0.00 0.00 36.73 3.24
1098 1207 0.596577 TCCGCCTCGATCCTAAATCG 59.403 55.000 1.13 1.13 42.38 3.34
1402 1559 0.608640 GTATGCTCCCCTCCGTATGG 59.391 60.000 0.00 0.00 0.00 2.74
1484 1641 2.002586 CATGCACTCTTCGAAATCCGT 58.997 47.619 0.00 0.00 39.75 4.69
1505 1665 2.371841 TGAAGCAGGCCTCTGTTCTTTA 59.628 45.455 0.00 0.00 42.78 1.85
1577 1737 3.753434 ACTCGGCTCTGGTCAGCG 61.753 66.667 0.00 0.00 40.68 5.18
1749 1912 3.718480 GATGCGCGCTCCGGTTTTC 62.718 63.158 33.29 11.63 37.44 2.29
1761 1927 4.056125 GTTTTCCCTGGCGGCTGC 62.056 66.667 9.72 9.72 41.71 5.25
1845 2014 1.600511 TTCGTATCTGGGTGCTGCGA 61.601 55.000 0.00 0.00 0.00 5.10
1883 2052 4.393371 GGACTGGATCTTAAAGTGCAAGAC 59.607 45.833 0.00 0.00 34.96 3.01
1973 2148 4.802051 CGTGCCTGGGGATGGTGG 62.802 72.222 0.00 0.00 0.00 4.61
2003 2178 2.754552 TGCTGGTCAAATATGCCAAGTC 59.245 45.455 0.00 0.00 34.02 3.01
2004 2179 2.099756 GCTGGTCAAATATGCCAAGTCC 59.900 50.000 0.00 0.00 34.02 3.85
2012 2187 5.191722 TCAAATATGCCAAGTCCCTACTTCT 59.808 40.000 0.00 0.00 44.28 2.85
2027 2202 4.080919 CCTACTTCTGGTTGACATGGATGA 60.081 45.833 0.00 0.00 0.00 2.92
2037 2212 4.632327 TGACATGGATGACAAGTTGGTA 57.368 40.909 7.96 0.00 29.85 3.25
2048 2223 1.535462 CAAGTTGGTAGCCACTTTCCG 59.465 52.381 8.56 0.00 30.78 4.30
2062 2237 0.605319 TTTCCGTCGCAAAGGCATCT 60.605 50.000 0.00 0.00 41.24 2.90
2127 2302 3.432890 CCTTCTTTCCATCACTAGAGGGC 60.433 52.174 0.00 0.00 45.23 5.19
2142 2317 2.000447 GAGGGCTATGTTGTGAACGAC 59.000 52.381 0.00 0.00 0.00 4.34
2397 2600 5.376854 AATTACAAGTCATTCTGGTGTGC 57.623 39.130 0.00 0.00 31.88 4.57
2411 2614 4.390603 TCTGGTGTGCGTTTGTAATATGTC 59.609 41.667 0.00 0.00 0.00 3.06
2415 2618 6.036626 TGGTGTGCGTTTGTAATATGTCATAG 59.963 38.462 0.00 0.00 0.00 2.23
2537 2749 1.355720 CCTCCCTGGTGTCTCCATTTT 59.644 52.381 0.00 0.00 46.12 1.82
2604 2816 6.814954 TTAATTAGAGATTCTCTGGTGGCT 57.185 37.500 23.60 7.00 41.37 4.75
2620 2832 5.299148 TGGTGGCTTTCTTGAAAATCAATG 58.701 37.500 0.00 0.00 35.59 2.82
2627 2839 6.238429 GCTTTCTTGAAAATCAATGTTTGGCA 60.238 34.615 0.00 0.00 35.59 4.92
2630 2842 7.192148 TCTTGAAAATCAATGTTTGGCAATG 57.808 32.000 0.00 0.00 35.59 2.82
2642 2854 4.807834 TGTTTGGCAATGTACATGTGTTTG 59.192 37.500 9.63 10.30 0.00 2.93
2643 2855 4.662468 TTGGCAATGTACATGTGTTTGT 57.338 36.364 9.63 0.00 0.00 2.83
2645 2857 4.615949 TGGCAATGTACATGTGTTTGTTC 58.384 39.130 9.63 7.06 0.00 3.18
2687 2899 5.308014 AGCGATGAGATGTGGCAAATTATA 58.692 37.500 0.00 0.00 0.00 0.98
2731 2943 4.068599 GCACCTGAGTTTTAGAAGAGCTT 58.931 43.478 0.00 0.00 0.00 3.74
2735 2947 5.013599 ACCTGAGTTTTAGAAGAGCTTGGAT 59.986 40.000 0.00 0.00 0.00 3.41
2748 2960 1.141858 GCTTGGATCCCTACTCCTTGG 59.858 57.143 9.90 0.00 33.69 3.61
2771 2983 6.320164 TGGTTAAATGATTGCACCATAGGTAC 59.680 38.462 4.95 0.00 32.11 3.34
2808 3021 3.557898 CCACTGCATATGGTTAGCTAGGG 60.558 52.174 4.56 0.00 32.08 3.53
2821 3034 2.764269 AGCTAGGGGATTAAGCTCACA 58.236 47.619 0.00 0.00 42.89 3.58
2822 3035 2.703007 AGCTAGGGGATTAAGCTCACAG 59.297 50.000 0.00 0.00 42.89 3.66
2823 3036 2.808567 GCTAGGGGATTAAGCTCACAGC 60.809 54.545 0.60 0.60 42.84 4.40
2824 3037 0.548510 AGGGGATTAAGCTCACAGCC 59.451 55.000 0.00 0.00 43.77 4.85
2825 3038 0.548510 GGGGATTAAGCTCACAGCCT 59.451 55.000 0.00 0.00 43.77 4.58
2826 3039 1.475930 GGGGATTAAGCTCACAGCCTC 60.476 57.143 0.00 0.00 43.77 4.70
2827 3040 1.210478 GGGATTAAGCTCACAGCCTCA 59.790 52.381 0.00 0.00 43.77 3.86
2832 3045 1.342074 AAGCTCACAGCCTCACACTA 58.658 50.000 0.00 0.00 43.77 2.74
2844 3057 4.040461 AGCCTCACACTAAAGCAAGAGTTA 59.960 41.667 0.00 0.00 0.00 2.24
2847 3060 6.402658 GCCTCACACTAAAGCAAGAGTTAATC 60.403 42.308 0.00 0.00 0.00 1.75
2848 3061 6.650807 CCTCACACTAAAGCAAGAGTTAATCA 59.349 38.462 0.00 0.00 0.00 2.57
2850 3063 9.371136 CTCACACTAAAGCAAGAGTTAATCATA 57.629 33.333 0.00 0.00 0.00 2.15
2856 3069 6.917217 AAGCAAGAGTTAATCATAGCAGAC 57.083 37.500 0.00 0.00 0.00 3.51
2872 3085 2.554032 GCAGACATGGTTAAGCAGTTGT 59.446 45.455 13.51 12.93 0.00 3.32
2876 3089 4.644685 AGACATGGTTAAGCAGTTGTTGTT 59.355 37.500 13.51 1.92 0.00 2.83
2883 3096 7.152645 TGGTTAAGCAGTTGTTGTTGTTTTTA 58.847 30.769 2.54 0.00 0.00 1.52
2950 3164 6.842163 ACATTAGTTGATCCGTTGACAAATC 58.158 36.000 0.00 0.00 0.00 2.17
2951 3165 6.429692 ACATTAGTTGATCCGTTGACAAATCA 59.570 34.615 0.00 0.00 0.00 2.57
2970 3184 9.325198 ACAAATCAAACTGGAAGGTTAATTTTC 57.675 29.630 0.00 0.00 46.52 2.29
2973 3187 7.654022 TCAAACTGGAAGGTTAATTTTCTGT 57.346 32.000 0.00 0.00 46.52 3.41
2983 3197 7.595819 AGGTTAATTTTCTGTTTCCATGTCA 57.404 32.000 0.00 0.00 0.00 3.58
2998 3212 8.680903 GTTTCCATGTCATGTTCAGAATTATCT 58.319 33.333 11.84 0.00 35.88 1.98
3024 3238 6.996509 ACATCATTTCACTTTAGGTGCAAAT 58.003 32.000 0.00 0.00 44.98 2.32
3028 3242 7.669427 TCATTTCACTTTAGGTGCAAATCATT 58.331 30.769 0.00 0.00 44.98 2.57
3063 3277 5.178096 TCATGTAACTGGTTCATGGTCAT 57.822 39.130 11.64 0.00 39.25 3.06
3072 3286 0.918258 TTCATGGTCATAGCCAGGCA 59.082 50.000 15.80 0.00 42.47 4.75
3073 3287 1.142936 TCATGGTCATAGCCAGGCAT 58.857 50.000 15.80 2.05 42.47 4.40
3074 3288 2.337849 TCATGGTCATAGCCAGGCATA 58.662 47.619 15.80 3.51 42.47 3.14
3078 3292 3.247162 TGGTCATAGCCAGGCATATGTA 58.753 45.455 15.80 0.00 33.97 2.29
3081 3295 3.007940 GTCATAGCCAGGCATATGTACCA 59.992 47.826 15.80 0.82 32.37 3.25
3088 3302 4.582656 GCCAGGCATATGTACCACATTTTA 59.417 41.667 6.55 0.00 39.88 1.52
3096 3310 8.850156 GCATATGTACCACATTTTATTCCTCTT 58.150 33.333 4.29 0.00 39.88 2.85
3101 3315 9.444600 TGTACCACATTTTATTCCTCTTAAGAC 57.555 33.333 0.00 0.00 0.00 3.01
3102 3316 9.444600 GTACCACATTTTATTCCTCTTAAGACA 57.555 33.333 0.00 0.00 0.00 3.41
3103 3317 8.336801 ACCACATTTTATTCCTCTTAAGACAC 57.663 34.615 0.00 0.00 0.00 3.67
3104 3318 8.164070 ACCACATTTTATTCCTCTTAAGACACT 58.836 33.333 0.00 0.00 0.00 3.55
3122 3336 8.574251 AAGACACTGTAATTGCCATATTTGTA 57.426 30.769 0.00 0.00 0.00 2.41
3148 3362 9.369904 ACCATGTTTATTTTCATCTGTATTTGC 57.630 29.630 0.00 0.00 0.00 3.68
3149 3363 8.819974 CCATGTTTATTTTCATCTGTATTTGCC 58.180 33.333 0.00 0.00 0.00 4.52
3150 3364 9.368674 CATGTTTATTTTCATCTGTATTTGCCA 57.631 29.630 0.00 0.00 0.00 4.92
3151 3365 8.755696 TGTTTATTTTCATCTGTATTTGCCAC 57.244 30.769 0.00 0.00 0.00 5.01
3152 3366 8.584157 TGTTTATTTTCATCTGTATTTGCCACT 58.416 29.630 0.00 0.00 0.00 4.00
3155 3369 9.679661 TTATTTTCATCTGTATTTGCCACTAGA 57.320 29.630 0.00 0.00 0.00 2.43
3156 3370 6.985188 TTTCATCTGTATTTGCCACTAGAC 57.015 37.500 0.00 0.00 0.00 2.59
3157 3371 5.939764 TCATCTGTATTTGCCACTAGACT 57.060 39.130 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 140 5.180271 TCGGCTACGGTTGAATCTTTATTT 58.820 37.500 0.00 0.00 41.39 1.40
464 505 1.153628 GCGATGGTTGTAGCTCCGT 60.154 57.895 0.00 0.00 0.00 4.69
624 699 3.877450 TGGCCATCCTCATCGCCC 61.877 66.667 0.00 0.00 35.45 6.13
767 867 1.750399 GCCATTGGATGTGAGCCGT 60.750 57.895 6.95 0.00 0.00 5.68
844 944 4.873724 TTAATGGGCTTAGCTTAGGGTT 57.126 40.909 3.59 0.00 0.00 4.11
846 946 7.890655 AGAAATATTAATGGGCTTAGCTTAGGG 59.109 37.037 3.59 0.00 0.00 3.53
847 947 8.870075 AGAAATATTAATGGGCTTAGCTTAGG 57.130 34.615 3.59 0.00 0.00 2.69
848 948 9.507329 TGAGAAATATTAATGGGCTTAGCTTAG 57.493 33.333 3.59 0.00 0.00 2.18
849 949 9.860650 TTGAGAAATATTAATGGGCTTAGCTTA 57.139 29.630 3.59 0.00 0.00 3.09
850 950 8.766994 TTGAGAAATATTAATGGGCTTAGCTT 57.233 30.769 3.59 0.00 0.00 3.74
851 951 8.766994 TTTGAGAAATATTAATGGGCTTAGCT 57.233 30.769 3.59 0.00 0.00 3.32
852 952 9.816354 TTTTTGAGAAATATTAATGGGCTTAGC 57.184 29.630 0.00 0.00 0.00 3.09
869 969 5.279456 GGGCCTAGCATTTTCTTTTTGAGAA 60.279 40.000 0.84 0.00 42.56 2.87
870 970 4.220602 GGGCCTAGCATTTTCTTTTTGAGA 59.779 41.667 0.84 0.00 0.00 3.27
871 971 4.021192 TGGGCCTAGCATTTTCTTTTTGAG 60.021 41.667 4.53 0.00 0.00 3.02
872 972 3.900601 TGGGCCTAGCATTTTCTTTTTGA 59.099 39.130 4.53 0.00 0.00 2.69
873 973 4.270245 TGGGCCTAGCATTTTCTTTTTG 57.730 40.909 4.53 0.00 0.00 2.44
874 974 5.491070 GAATGGGCCTAGCATTTTCTTTTT 58.509 37.500 4.53 0.00 0.00 1.94
875 975 4.080919 GGAATGGGCCTAGCATTTTCTTTT 60.081 41.667 4.53 0.00 0.00 2.27
876 976 3.452264 GGAATGGGCCTAGCATTTTCTTT 59.548 43.478 4.53 0.00 0.00 2.52
877 977 3.033909 GGAATGGGCCTAGCATTTTCTT 58.966 45.455 4.53 0.00 0.00 2.52
878 978 2.024080 TGGAATGGGCCTAGCATTTTCT 60.024 45.455 4.53 0.00 0.00 2.52
879 979 2.387757 TGGAATGGGCCTAGCATTTTC 58.612 47.619 4.53 0.00 0.00 2.29
880 980 2.548464 TGGAATGGGCCTAGCATTTT 57.452 45.000 4.53 0.00 0.00 1.82
881 981 2.701951 CAATGGAATGGGCCTAGCATTT 59.298 45.455 4.53 0.00 0.00 2.32
882 982 2.091166 TCAATGGAATGGGCCTAGCATT 60.091 45.455 4.53 3.70 0.00 3.56
883 983 1.500303 TCAATGGAATGGGCCTAGCAT 59.500 47.619 4.53 0.00 0.00 3.79
884 984 0.925558 TCAATGGAATGGGCCTAGCA 59.074 50.000 4.53 0.00 0.00 3.49
885 985 1.322442 GTCAATGGAATGGGCCTAGC 58.678 55.000 4.53 0.00 0.00 3.42
886 986 1.134098 ACGTCAATGGAATGGGCCTAG 60.134 52.381 4.53 0.00 0.00 3.02
887 987 0.916086 ACGTCAATGGAATGGGCCTA 59.084 50.000 4.53 0.00 0.00 3.93
888 988 0.039618 AACGTCAATGGAATGGGCCT 59.960 50.000 4.53 0.00 0.00 5.19
889 989 0.894835 AAACGTCAATGGAATGGGCC 59.105 50.000 0.00 0.00 0.00 5.80
890 990 1.818674 AGAAACGTCAATGGAATGGGC 59.181 47.619 0.00 0.00 0.00 5.36
891 991 2.415893 GCAGAAACGTCAATGGAATGGG 60.416 50.000 0.00 0.00 0.00 4.00
892 992 2.489329 AGCAGAAACGTCAATGGAATGG 59.511 45.455 0.00 0.00 0.00 3.16
893 993 3.058016 ACAGCAGAAACGTCAATGGAATG 60.058 43.478 0.00 0.00 0.00 2.67
894 994 3.149196 ACAGCAGAAACGTCAATGGAAT 58.851 40.909 0.00 0.00 0.00 3.01
895 995 2.571212 ACAGCAGAAACGTCAATGGAA 58.429 42.857 0.00 0.00 0.00 3.53
896 996 2.254546 ACAGCAGAAACGTCAATGGA 57.745 45.000 0.00 0.00 0.00 3.41
897 997 3.063997 GGATACAGCAGAAACGTCAATGG 59.936 47.826 0.00 0.00 0.00 3.16
898 998 3.684305 TGGATACAGCAGAAACGTCAATG 59.316 43.478 0.00 0.00 46.17 2.82
899 999 3.937814 TGGATACAGCAGAAACGTCAAT 58.062 40.909 0.00 0.00 46.17 2.57
900 1000 3.394674 TGGATACAGCAGAAACGTCAA 57.605 42.857 0.00 0.00 46.17 3.18
1022 1131 1.630126 ATGGATGAGAGGCGTGGCTT 61.630 55.000 0.00 0.00 0.00 4.35
1053 1162 0.748367 TCTCCCAGATGACGACCTCG 60.748 60.000 0.00 0.00 46.33 4.63
1089 1198 0.755698 AGCGGAGGAGCGATTTAGGA 60.756 55.000 0.00 0.00 43.00 2.94
1092 1201 1.227263 GCAGCGGAGGAGCGATTTA 60.227 57.895 0.00 0.00 43.00 1.40
1156 1265 4.803426 GTGGTGCGCGAGGAGGAG 62.803 72.222 12.10 0.00 0.00 3.69
1293 1450 3.217743 GCCTCCGGACGGACTAGG 61.218 72.222 20.27 10.98 39.76 3.02
1332 1489 1.758514 GGTGCCGAGGATGGAGAGA 60.759 63.158 0.00 0.00 0.00 3.10
1402 1559 4.943705 TCCCAATATGCTGAACTCAGAAAC 59.056 41.667 10.95 0.00 46.59 2.78
1484 1641 0.767375 AAGAACAGAGGCCTGCTTCA 59.233 50.000 12.00 0.00 44.16 3.02
1505 1665 2.606587 GGTCTGGTGCAGGGACCAT 61.607 63.158 20.88 0.00 45.19 3.55
1577 1737 0.249398 ACACTCAATGTACCTCGGCC 59.751 55.000 0.00 0.00 40.88 6.13
1761 1927 3.251479 TCCATCTCAAACAGGTCATCG 57.749 47.619 0.00 0.00 0.00 3.84
1845 2014 2.428890 CCAGTCCTCGCTTTCATAGTCT 59.571 50.000 0.00 0.00 0.00 3.24
1883 2052 2.917933 TCTCCATAACCGGCAATTCAG 58.082 47.619 0.00 0.00 0.00 3.02
1926 2095 3.613910 CGTCCCAAAAATTGTCATGGTCC 60.614 47.826 0.00 0.00 0.00 4.46
1973 2148 0.459489 TTTGACCAGCACAAGCAACC 59.541 50.000 0.00 0.00 45.49 3.77
2003 2178 2.571653 TCCATGTCAACCAGAAGTAGGG 59.428 50.000 0.00 0.00 0.00 3.53
2004 2179 3.981071 TCCATGTCAACCAGAAGTAGG 57.019 47.619 0.00 0.00 0.00 3.18
2012 2187 3.507162 ACTTGTCATCCATGTCAACCA 57.493 42.857 0.00 0.00 33.52 3.67
2027 2202 2.583143 GGAAAGTGGCTACCAACTTGT 58.417 47.619 0.00 0.00 34.18 3.16
2048 2223 0.674895 AGGACAGATGCCTTTGCGAC 60.675 55.000 0.00 0.00 41.78 5.19
2062 2237 1.273606 GAGCTGCAACTGAGTAGGACA 59.726 52.381 1.02 0.00 0.00 4.02
2127 2302 1.732259 GGCCAGTCGTTCACAACATAG 59.268 52.381 0.00 0.00 0.00 2.23
2142 2317 1.101331 GCCTTCAGATGAAAGGCCAG 58.899 55.000 14.51 0.00 39.86 4.85
2185 2375 3.000727 GGATAGAAACACCAAGGACACG 58.999 50.000 0.00 0.00 0.00 4.49
2186 2376 4.254492 GAGGATAGAAACACCAAGGACAC 58.746 47.826 0.00 0.00 0.00 3.67
2411 2614 5.948162 AGATACATGGGGCAAATTAGCTATG 59.052 40.000 0.00 0.00 34.17 2.23
2415 2618 6.840780 AATAGATACATGGGGCAAATTAGC 57.159 37.500 0.00 0.00 0.00 3.09
2537 2749 5.453198 GGGAAAGGCATTTCTTGAGTTCAAA 60.453 40.000 21.84 0.00 43.67 2.69
2594 2806 4.279169 TGATTTTCAAGAAAGCCACCAGAG 59.721 41.667 0.00 0.00 0.00 3.35
2604 2816 7.621428 TTGCCAAACATTGATTTTCAAGAAA 57.379 28.000 0.00 0.00 40.05 2.52
2620 2832 4.808364 ACAAACACATGTACATTGCCAAAC 59.192 37.500 5.37 0.00 0.00 2.93
2659 2871 1.871408 GCCACATCTCATCGCTAGGTG 60.871 57.143 0.00 0.00 0.00 4.00
2662 2874 2.229675 TTGCCACATCTCATCGCTAG 57.770 50.000 0.00 0.00 0.00 3.42
2664 2876 2.048444 ATTTGCCACATCTCATCGCT 57.952 45.000 0.00 0.00 0.00 4.93
2667 2879 7.976135 AGAGTATAATTTGCCACATCTCATC 57.024 36.000 0.00 0.00 0.00 2.92
2687 2899 4.023707 GCAACTTGCAAGTCAACATAGAGT 60.024 41.667 31.20 9.82 44.26 3.24
2715 2927 4.878971 GGGATCCAAGCTCTTCTAAAACTC 59.121 45.833 15.23 0.00 0.00 3.01
2731 2943 2.661176 AACCAAGGAGTAGGGATCCA 57.339 50.000 15.23 0.00 39.47 3.41
2735 2947 6.423182 CAATCATTTAACCAAGGAGTAGGGA 58.577 40.000 0.00 0.00 0.00 4.20
2748 2960 7.568199 AGTACCTATGGTGCAATCATTTAAC 57.432 36.000 8.78 4.33 40.76 2.01
2771 2983 9.459640 CATATGCAGTGGATTCATAAAGAAAAG 57.540 33.333 1.20 0.00 40.22 2.27
2808 3021 2.284190 GTGAGGCTGTGAGCTTAATCC 58.716 52.381 0.00 0.00 41.99 3.01
2821 3034 2.370189 ACTCTTGCTTTAGTGTGAGGCT 59.630 45.455 0.00 0.00 0.00 4.58
2822 3035 2.772287 ACTCTTGCTTTAGTGTGAGGC 58.228 47.619 0.00 0.00 0.00 4.70
2823 3036 6.650807 TGATTAACTCTTGCTTTAGTGTGAGG 59.349 38.462 0.00 0.00 0.00 3.86
2824 3037 7.658179 TGATTAACTCTTGCTTTAGTGTGAG 57.342 36.000 0.00 0.00 0.00 3.51
2825 3038 9.371136 CTATGATTAACTCTTGCTTTAGTGTGA 57.629 33.333 0.00 0.00 0.00 3.58
2826 3039 8.119226 GCTATGATTAACTCTTGCTTTAGTGTG 58.881 37.037 0.00 0.00 0.00 3.82
2827 3040 7.824289 TGCTATGATTAACTCTTGCTTTAGTGT 59.176 33.333 0.00 0.00 0.00 3.55
2832 3045 6.881065 TGTCTGCTATGATTAACTCTTGCTTT 59.119 34.615 0.00 0.00 0.00 3.51
2844 3057 5.439721 TGCTTAACCATGTCTGCTATGATT 58.560 37.500 0.00 0.00 0.00 2.57
2847 3060 4.194640 ACTGCTTAACCATGTCTGCTATG 58.805 43.478 0.00 0.00 0.00 2.23
2848 3061 4.494091 ACTGCTTAACCATGTCTGCTAT 57.506 40.909 0.00 0.00 0.00 2.97
2850 3063 2.816087 CAACTGCTTAACCATGTCTGCT 59.184 45.455 0.00 0.00 0.00 4.24
2856 3069 4.681744 ACAACAACAACTGCTTAACCATG 58.318 39.130 0.00 0.00 0.00 3.66
2912 3126 5.347342 CAACTAATGTTGCAACAAGGACAA 58.653 37.500 34.06 11.15 45.57 3.18
2939 3153 4.202010 ACCTTCCAGTTTGATTTGTCAACG 60.202 41.667 0.00 0.00 0.00 4.10
2945 3159 9.546428 AGAAAATTAACCTTCCAGTTTGATTTG 57.454 29.630 0.00 0.00 30.89 2.32
2950 3164 8.716646 AAACAGAAAATTAACCTTCCAGTTTG 57.283 30.769 13.27 3.05 33.07 2.93
2951 3165 7.985184 GGAAACAGAAAATTAACCTTCCAGTTT 59.015 33.333 13.62 13.62 35.11 2.66
2973 3187 8.812513 AGATAATTCTGAACATGACATGGAAA 57.187 30.769 19.39 6.54 33.60 3.13
3024 3238 9.890629 AGTTACATGAAGCATTACTTAGAATGA 57.109 29.630 0.00 0.00 39.29 2.57
3028 3242 7.620880 ACCAGTTACATGAAGCATTACTTAGA 58.379 34.615 0.00 0.00 39.29 2.10
3049 3263 2.569059 CTGGCTATGACCATGAACCAG 58.431 52.381 0.00 10.98 39.54 4.00
3063 3277 2.403561 TGTGGTACATATGCCTGGCTA 58.596 47.619 21.03 10.05 44.52 3.93
3078 3292 8.164070 AGTGTCTTAAGAGGAATAAAATGTGGT 58.836 33.333 5.12 0.00 0.00 4.16
3088 3302 6.599638 GGCAATTACAGTGTCTTAAGAGGAAT 59.400 38.462 5.12 0.00 0.00 3.01
3096 3310 8.574251 ACAAATATGGCAATTACAGTGTCTTA 57.426 30.769 0.00 0.00 0.00 2.10
3097 3311 7.466746 ACAAATATGGCAATTACAGTGTCTT 57.533 32.000 0.00 0.00 0.00 3.01
3098 3312 7.067008 GGTACAAATATGGCAATTACAGTGTCT 59.933 37.037 0.00 0.00 0.00 3.41
3099 3313 7.148154 TGGTACAAATATGGCAATTACAGTGTC 60.148 37.037 0.00 0.00 31.92 3.67
3100 3314 6.661377 TGGTACAAATATGGCAATTACAGTGT 59.339 34.615 0.00 0.00 31.92 3.55
3101 3315 7.094508 TGGTACAAATATGGCAATTACAGTG 57.905 36.000 0.00 0.00 31.92 3.66
3122 3336 9.369904 GCAAATACAGATGAAAATAAACATGGT 57.630 29.630 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.