Multiple sequence alignment - TraesCS1B01G256800

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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 TraesCS1B01G256800 chr1B 100.000 3951 0 0 1 3951 452492772 452496722 0.000000e+00 7297
1 TraesCS1B01G256800 chr1B 83.134 836 109 21 1048 1869 477410595 477409778 0.000000e+00 734
2 TraesCS1B01G256800 chr1B 83.745 769 97 15 1120 1865 477492866 477492103 0.000000e+00 702
3 TraesCS1B01G256800 chr1B 75.842 861 147 31 1945 2753 477409531 477408680 8.010000e-102 381
4 TraesCS1B01G256800 chr1A 92.762 2929 167 19 1037 3948 435083554 435086454 0.000000e+00 4193
5 TraesCS1B01G256800 chr1A 83.047 814 116 15 1058 1865 455042367 455041570 0.000000e+00 719
6 TraesCS1B01G256800 chr1A 76.754 727 126 19 2092 2779 455041343 455040621 2.240000e-97 366
7 TraesCS1B01G256800 chr1A 85.496 131 7 5 898 1023 435083385 435083508 4.140000e-25 126
8 TraesCS1B01G256800 chr7B 93.218 870 51 8 1 865 176221324 176220458 0.000000e+00 1273
9 TraesCS1B01G256800 chr6B 92.832 865 55 7 3 862 37769138 37770000 0.000000e+00 1247
10 TraesCS1B01G256800 chr6B 92.211 873 57 10 1 864 514830568 514831438 0.000000e+00 1225
11 TraesCS1B01G256800 chr6B 75.785 1784 297 74 1107 2796 80841121 80839379 0.000000e+00 776
12 TraesCS1B01G256800 chr6B 80.840 762 126 13 1107 1858 80781216 80780465 7.360000e-162 580
13 TraesCS1B01G256800 chr6B 80.309 777 134 14 1107 1869 80235954 80235183 1.590000e-158 569
14 TraesCS1B01G256800 chr6B 78.819 779 134 19 1107 1865 80822984 80822217 2.740000e-136 496
15 TraesCS1B01G256800 chr2B 92.652 871 54 8 1 863 761705135 761706003 0.000000e+00 1245
16 TraesCS1B01G256800 chr2B 91.230 878 61 16 1 868 195535367 195534496 0.000000e+00 1181
17 TraesCS1B01G256800 chr3B 92.635 869 54 10 1 863 813590491 813589627 0.000000e+00 1242
18 TraesCS1B01G256800 chr5B 92.529 870 56 8 1 863 673037640 673036773 0.000000e+00 1238
19 TraesCS1B01G256800 chr5B 92.211 873 60 8 1 868 692448328 692449197 0.000000e+00 1229
20 TraesCS1B01G256800 chr5B 92.173 856 58 9 1 850 563585566 563586418 0.000000e+00 1201
21 TraesCS1B01G256800 chr1D 78.128 1806 284 51 1056 2779 355185598 355183822 0.000000e+00 1044
22 TraesCS1B01G256800 chrUn 75.729 1784 301 63 1107 2796 27017436 27015691 0.000000e+00 774
23 TraesCS1B01G256800 chrUn 78.265 1118 178 43 1107 2176 27273315 27274415 0.000000e+00 658
24 TraesCS1B01G256800 chrUn 73.604 1307 228 60 1575 2796 27158895 27160169 1.030000e-105 394
25 TraesCS1B01G256800 chrUn 80.236 339 56 3 2021 2349 62700126 62700463 1.100000e-60 244
26 TraesCS1B01G256800 chr6A 79.437 817 151 11 1056 1865 5129766 5128960 2.670000e-156 562
27 TraesCS1B01G256800 chr6A 77.531 810 127 33 1107 1869 46784174 46783373 1.690000e-118 436
28 TraesCS1B01G256800 chr6A 79.646 339 58 3 2021 2349 4579472 4579809 2.370000e-57 233


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 TraesCS1B01G256800 chr1B 452492772 452496722 3950 False 7297.0 7297 100.0000 1 3951 1 chr1B.!!$F1 3950
1 TraesCS1B01G256800 chr1B 477492103 477492866 763 True 702.0 702 83.7450 1120 1865 1 chr1B.!!$R1 745
2 TraesCS1B01G256800 chr1B 477408680 477410595 1915 True 557.5 734 79.4880 1048 2753 2 chr1B.!!$R2 1705
3 TraesCS1B01G256800 chr1A 435083385 435086454 3069 False 2159.5 4193 89.1290 898 3948 2 chr1A.!!$F1 3050
4 TraesCS1B01G256800 chr1A 455040621 455042367 1746 True 542.5 719 79.9005 1058 2779 2 chr1A.!!$R1 1721
5 TraesCS1B01G256800 chr7B 176220458 176221324 866 True 1273.0 1273 93.2180 1 865 1 chr7B.!!$R1 864
6 TraesCS1B01G256800 chr6B 37769138 37770000 862 False 1247.0 1247 92.8320 3 862 1 chr6B.!!$F1 859
7 TraesCS1B01G256800 chr6B 514830568 514831438 870 False 1225.0 1225 92.2110 1 864 1 chr6B.!!$F2 863
8 TraesCS1B01G256800 chr6B 80839379 80841121 1742 True 776.0 776 75.7850 1107 2796 1 chr6B.!!$R4 1689
9 TraesCS1B01G256800 chr6B 80780465 80781216 751 True 580.0 580 80.8400 1107 1858 1 chr6B.!!$R2 751
10 TraesCS1B01G256800 chr6B 80235183 80235954 771 True 569.0 569 80.3090 1107 1869 1 chr6B.!!$R1 762
11 TraesCS1B01G256800 chr6B 80822217 80822984 767 True 496.0 496 78.8190 1107 1865 1 chr6B.!!$R3 758
12 TraesCS1B01G256800 chr2B 761705135 761706003 868 False 1245.0 1245 92.6520 1 863 1 chr2B.!!$F1 862
13 TraesCS1B01G256800 chr2B 195534496 195535367 871 True 1181.0 1181 91.2300 1 868 1 chr2B.!!$R1 867
14 TraesCS1B01G256800 chr3B 813589627 813590491 864 True 1242.0 1242 92.6350 1 863 1 chr3B.!!$R1 862
15 TraesCS1B01G256800 chr5B 673036773 673037640 867 True 1238.0 1238 92.5290 1 863 1 chr5B.!!$R1 862
16 TraesCS1B01G256800 chr5B 692448328 692449197 869 False 1229.0 1229 92.2110 1 868 1 chr5B.!!$F2 867
17 TraesCS1B01G256800 chr5B 563585566 563586418 852 False 1201.0 1201 92.1730 1 850 1 chr5B.!!$F1 849
18 TraesCS1B01G256800 chr1D 355183822 355185598 1776 True 1044.0 1044 78.1280 1056 2779 1 chr1D.!!$R1 1723
19 TraesCS1B01G256800 chrUn 27015691 27017436 1745 True 774.0 774 75.7290 1107 2796 1 chrUn.!!$R1 1689
20 TraesCS1B01G256800 chrUn 27273315 27274415 1100 False 658.0 658 78.2650 1107 2176 1 chrUn.!!$F2 1069
21 TraesCS1B01G256800 chrUn 27158895 27160169 1274 False 394.0 394 73.6040 1575 2796 1 chrUn.!!$F1 1221
22 TraesCS1B01G256800 chr6A 5128960 5129766 806 True 562.0 562 79.4370 1056 1865 1 chr6A.!!$R1 809
23 TraesCS1B01G256800 chr6A 46783373 46784174 801 True 436.0 436 77.5310 1107 1869 1 chr6A.!!$R2 762

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
912 934 0.096976 CAATTGCGCCGTTGTCCTAG 59.903 55.0 4.18 0.0 0.0 3.02 F
916 938 0.249953 TGCGCCGTTGTCCTAGAAAA 60.250 50.0 4.18 0.0 0.0 2.29 F
2128 2526 0.447801 AACGAATCATGCAGCCGAAC 59.552 50.0 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2521 0.320374 TTAGCACCCACTCTGTTCGG 59.68 55.0 0.00 0.0 0.00 4.30 R
2419 2848 0.480252 ATAGGCCATTCCCCTTGCTC 59.52 55.0 5.01 0.0 33.88 4.26 R
3917 4379 0.620410 CCCCTCTACCATGACACCCA 60.62 60.0 0.00 0.0 0.00 4.51 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
49 50 5.812127 GGCATGTAAGCATCGATCATACATA 59.188 40.000 19.18 2.46 35.91 2.29
58 60 8.081208 AGCATCGATCATACATAACTGAAAAG 57.919 34.615 0.00 0.00 0.00 2.27
166 169 1.006102 CTTCACCCAAGCTCGACGT 60.006 57.895 0.00 0.00 0.00 4.34
198 201 1.550524 TGATCAGCAGCTTTACGGACT 59.449 47.619 0.00 0.00 0.00 3.85
200 203 2.543777 TCAGCAGCTTTACGGACTTT 57.456 45.000 0.00 0.00 0.00 2.66
248 251 6.371278 ACCATAGCCATTGAAAGAATCAGAT 58.629 36.000 0.00 0.00 39.77 2.90
264 268 1.224592 GATCGGGGCAACATGTCCT 59.775 57.895 0.00 0.00 43.05 3.85
285 291 1.144969 GGACACGCATCGAACTTCAA 58.855 50.000 0.00 0.00 0.00 2.69
346 352 0.603707 CAGAACTGCCAGCCTTCGAA 60.604 55.000 0.00 0.00 0.00 3.71
361 367 2.310233 CGAACACAGACCCAGCACG 61.310 63.158 0.00 0.00 0.00 5.34
381 387 3.325135 ACGAAGAAACTCCATCTTCCAGT 59.675 43.478 9.89 2.10 46.47 4.00
454 463 2.184322 CTCCACCATGACGTCGGG 59.816 66.667 20.80 20.80 0.00 5.14
474 483 0.741574 AGACAACGCCACAACAACGA 60.742 50.000 0.00 0.00 0.00 3.85
475 484 0.306533 GACAACGCCACAACAACGAT 59.693 50.000 0.00 0.00 0.00 3.73
479 488 1.206578 CGCCACAACAACGATGACC 59.793 57.895 0.00 0.00 0.00 4.02
542 554 0.392863 TCGCCAACACCATCCATGAG 60.393 55.000 0.00 0.00 0.00 2.90
568 580 0.596083 CGCTGTCGATCTGTGGGATC 60.596 60.000 0.00 0.00 45.37 3.36
582 594 1.226717 GGATCGGCAGAGACACGAC 60.227 63.158 0.00 0.00 39.64 4.34
595 608 1.374125 CACGACGCCATCAACTCCA 60.374 57.895 0.00 0.00 0.00 3.86
708 721 5.768317 CACCACGACCTACAAATTCAAAAT 58.232 37.500 0.00 0.00 0.00 1.82
713 726 8.458843 CCACGACCTACAAATTCAAAATCTAAT 58.541 33.333 0.00 0.00 0.00 1.73
740 754 2.691252 GAGGAACGGGGTCCCCAT 60.691 66.667 27.45 15.01 45.83 4.00
754 769 4.113815 CCATTCCTCCTGCCGCCA 62.114 66.667 0.00 0.00 0.00 5.69
823 839 2.158234 AGGAAAGAGATCGCCTCCCTAT 60.158 50.000 10.46 0.00 42.97 2.57
865 887 4.182339 GCTAGGGTAGGAAAAAGTCTTCG 58.818 47.826 0.00 0.00 0.00 3.79
866 888 3.055209 AGGGTAGGAAAAAGTCTTCGC 57.945 47.619 0.00 0.00 0.00 4.70
867 889 2.638363 AGGGTAGGAAAAAGTCTTCGCT 59.362 45.455 0.00 0.00 0.00 4.93
868 890 3.836562 AGGGTAGGAAAAAGTCTTCGCTA 59.163 43.478 0.00 0.00 0.00 4.26
869 891 4.470304 AGGGTAGGAAAAAGTCTTCGCTAT 59.530 41.667 0.00 0.00 0.00 2.97
870 892 4.809958 GGGTAGGAAAAAGTCTTCGCTATC 59.190 45.833 0.00 0.00 0.00 2.08
871 893 5.416947 GGTAGGAAAAAGTCTTCGCTATCA 58.583 41.667 0.00 0.00 0.00 2.15
872 894 5.291371 GGTAGGAAAAAGTCTTCGCTATCAC 59.709 44.000 0.00 0.00 0.00 3.06
873 895 4.894784 AGGAAAAAGTCTTCGCTATCACA 58.105 39.130 0.00 0.00 0.00 3.58
874 896 5.305585 AGGAAAAAGTCTTCGCTATCACAA 58.694 37.500 0.00 0.00 0.00 3.33
875 897 5.409826 AGGAAAAAGTCTTCGCTATCACAAG 59.590 40.000 0.00 0.00 0.00 3.16
876 898 4.670227 AAAAGTCTTCGCTATCACAAGC 57.330 40.909 0.00 0.00 39.21 4.01
884 906 2.301577 GCTATCACAAGCGTCCTCTT 57.698 50.000 0.00 0.00 31.76 2.85
885 907 3.438297 GCTATCACAAGCGTCCTCTTA 57.562 47.619 0.00 0.00 31.76 2.10
886 908 3.376540 GCTATCACAAGCGTCCTCTTAG 58.623 50.000 0.00 0.00 31.76 2.18
887 909 2.301577 ATCACAAGCGTCCTCTTAGC 57.698 50.000 0.00 0.00 0.00 3.09
888 910 1.257743 TCACAAGCGTCCTCTTAGCT 58.742 50.000 0.00 0.00 43.90 3.32
893 915 2.371910 AGCGTCCTCTTAGCTTTGTC 57.628 50.000 0.00 0.00 38.13 3.18
894 916 1.618837 AGCGTCCTCTTAGCTTTGTCA 59.381 47.619 0.00 0.00 38.13 3.58
895 917 2.037251 AGCGTCCTCTTAGCTTTGTCAA 59.963 45.455 0.00 0.00 38.13 3.18
896 918 3.003480 GCGTCCTCTTAGCTTTGTCAAT 58.997 45.455 0.00 0.00 0.00 2.57
912 934 0.096976 CAATTGCGCCGTTGTCCTAG 59.903 55.000 4.18 0.00 0.00 3.02
916 938 0.249953 TGCGCCGTTGTCCTAGAAAA 60.250 50.000 4.18 0.00 0.00 2.29
921 943 3.242804 CGCCGTTGTCCTAGAAAACAAAA 60.243 43.478 6.81 0.00 37.15 2.44
939 961 1.649390 AACAGTTGCGCCGTTTGACA 61.649 50.000 4.18 0.00 0.00 3.58
944 966 2.740826 GCGCCGTTTGACAGCCTA 60.741 61.111 0.00 0.00 0.00 3.93
953 975 3.060363 CGTTTGACAGCCTACAATACGTC 59.940 47.826 0.00 0.00 32.26 4.34
954 976 2.953466 TGACAGCCTACAATACGTCC 57.047 50.000 0.00 0.00 0.00 4.79
955 977 1.133598 TGACAGCCTACAATACGTCCG 59.866 52.381 0.00 0.00 0.00 4.79
956 978 1.133790 GACAGCCTACAATACGTCCGT 59.866 52.381 0.00 0.00 0.00 4.69
957 979 2.355756 GACAGCCTACAATACGTCCGTA 59.644 50.000 1.60 1.60 34.87 4.02
958 980 2.098117 ACAGCCTACAATACGTCCGTAC 59.902 50.000 1.07 0.00 33.01 3.67
970 992 0.455005 GTCCGTACACTACTCCTGGC 59.545 60.000 0.00 0.00 0.00 4.85
984 1006 1.944676 CTGGCCGAATACGTCTCGC 60.945 63.158 13.05 9.19 37.88 5.03
1028 1060 1.410153 ACCACGTTCCAAGTAGTTCGT 59.590 47.619 0.00 0.00 0.00 3.85
1034 1066 5.176223 CACGTTCCAAGTAGTTCGTTAACAT 59.824 40.000 6.39 0.00 38.12 2.71
1042 1100 2.076863 AGTTCGTTAACATCTGCAGCC 58.923 47.619 9.47 0.00 38.12 4.85
1043 1101 2.076863 GTTCGTTAACATCTGCAGCCT 58.923 47.619 9.47 0.00 35.56 4.58
1086 1145 1.610038 TCGCAGACGACTGGAAACTAA 59.390 47.619 16.41 0.00 45.12 2.24
1089 1148 3.120991 CGCAGACGACTGGAAACTAAAAG 60.121 47.826 16.41 0.00 43.62 2.27
1091 1150 4.628074 CAGACGACTGGAAACTAAAAGGA 58.372 43.478 7.02 0.00 40.14 3.36
1092 1151 4.686554 CAGACGACTGGAAACTAAAAGGAG 59.313 45.833 7.02 0.00 40.14 3.69
1134 1205 4.100084 CCATGGCACCGGAGCTCA 62.100 66.667 23.40 18.73 34.17 4.26
1274 1345 3.877357 CTGCTCTCGCGCTCCGTA 61.877 66.667 5.56 0.00 39.65 4.02
1437 1565 4.212913 TCTGCCGCGATCAGAGCC 62.213 66.667 21.46 0.00 35.81 4.70
1553 1687 3.141488 CAGACCGCCTACCTCGCT 61.141 66.667 0.00 0.00 0.00 4.93
1637 1801 0.725686 AATCAGACGACGACGACGAT 59.274 50.000 25.15 10.95 42.66 3.73
1658 1822 1.300620 CAACCCGTTGCTCGAGTCA 60.301 57.895 15.13 9.82 42.86 3.41
1700 1864 2.474526 CGTGATGCATGTTTTCTCGTCC 60.475 50.000 2.46 0.00 0.00 4.79
1870 2052 7.603651 CATGGCTATCTTACGAGGTAAGTAAT 58.396 38.462 13.48 5.55 43.95 1.89
1909 2261 7.458397 TGGTCACCATTCTACTCTAACAAATT 58.542 34.615 0.00 0.00 0.00 1.82
1939 2303 6.258068 ACTCGGTTAGATTGCTTGCTATTAAC 59.742 38.462 0.00 4.59 0.00 2.01
2009 2392 5.228635 CACGTACAGTGTAATTAAGCTACCG 59.771 44.000 4.11 3.00 45.51 4.02
2010 2393 5.123820 ACGTACAGTGTAATTAAGCTACCGA 59.876 40.000 4.11 0.00 0.00 4.69
2029 2427 0.607620 AATGCCAAACATCCCAACCG 59.392 50.000 0.00 0.00 38.34 4.44
2046 2444 2.281345 GCCATCTGGGGCGATCAG 60.281 66.667 0.00 0.00 45.40 2.90
2123 2521 3.059325 GGTATCTCAACGAATCATGCAGC 60.059 47.826 0.00 0.00 0.00 5.25
2128 2526 0.447801 AACGAATCATGCAGCCGAAC 59.552 50.000 0.00 0.00 0.00 3.95
2155 2553 3.626930 GGGTGCTAAAACATGATACCCA 58.373 45.455 0.00 0.00 44.41 4.51
2160 2561 6.238759 GGTGCTAAAACATGATACCCATCTTC 60.239 42.308 0.00 0.00 31.94 2.87
2399 2827 9.479549 TTTCATCCTTATAAAGAGATTGCCTTT 57.520 29.630 0.00 0.00 37.57 3.11
2419 2848 5.126707 CCTTTTTGATTTCATCAGGGAGAGG 59.873 44.000 0.00 0.00 40.94 3.69
2466 2895 6.811954 TGGAACAACTTAAAATTTCAGGACC 58.188 36.000 0.00 0.00 31.92 4.46
2558 2990 1.820581 GTACACGCCCTGCTGGATA 59.179 57.895 11.88 0.00 35.39 2.59
2604 3036 4.942852 AGAATCGCTACTTGAAGATGAGG 58.057 43.478 0.00 0.00 0.00 3.86
2629 3061 7.554476 GGAGCTATCTATGAAAAAGTTGGAACT 59.446 37.037 0.00 0.00 42.04 3.01
2732 3176 1.361668 CCGCCAAGATTCGTCACAGG 61.362 60.000 0.00 0.00 0.00 4.00
2812 3258 0.179086 CACAAAGGCGGCCAAGTTTT 60.179 50.000 23.09 10.00 0.00 2.43
2813 3259 1.067821 CACAAAGGCGGCCAAGTTTTA 59.932 47.619 23.09 0.00 0.00 1.52
2814 3260 1.339929 ACAAAGGCGGCCAAGTTTTAG 59.660 47.619 23.09 9.79 0.00 1.85
2836 3282 1.207089 GTTTAGGGCCAAGGCAATTCC 59.793 52.381 13.87 4.71 44.11 3.01
2855 3301 1.693606 CCCATTGCCAAGTTTGACCTT 59.306 47.619 0.00 0.00 0.00 3.50
2872 3318 2.224867 ACCTTTGGCAAGCTACTGATGT 60.225 45.455 0.00 0.00 0.00 3.06
2876 3322 0.449388 GGCAAGCTACTGATGTGCAC 59.551 55.000 10.75 10.75 36.93 4.57
2920 3366 3.676873 GCCCTTGCATTGTAACTTGATGG 60.677 47.826 0.00 0.00 37.47 3.51
2976 3422 2.551912 CGCCAACCTTGTCCACCAC 61.552 63.158 0.00 0.00 0.00 4.16
2998 3444 6.718454 CCACTAATTCTGAAGGGCATATTCAT 59.282 38.462 0.00 0.00 36.16 2.57
3077 3523 6.325919 TCTTGAATTGGCAAAACGTCTTAT 57.674 33.333 3.01 0.00 0.00 1.73
3095 3541 8.141268 ACGTCTTATACAGAGGTAGTAGTACTC 58.859 40.741 5.96 0.00 46.68 2.59
3135 3581 2.480416 GCCGCATCCGATCCTCTATAAG 60.480 54.545 0.00 0.00 36.29 1.73
3307 3753 1.880027 GAAAATGTTCAGTGCCTCGGT 59.120 47.619 0.00 0.00 33.61 4.69
3336 3782 2.762745 TGAACTGGTTAGAGAAACGGC 58.237 47.619 0.00 0.00 39.13 5.68
3338 3784 0.963962 ACTGGTTAGAGAAACGGCGA 59.036 50.000 16.62 0.00 39.13 5.54
3353 3799 1.082104 GCGAAAGGAAGTGCCGTTG 60.082 57.895 0.00 0.00 43.43 4.10
3379 3825 3.222173 AGCTGAATACAACACCCAACA 57.778 42.857 0.00 0.00 0.00 3.33
3394 3840 4.991687 CACCCAACAGAGAGAAAGTAACTC 59.008 45.833 0.00 0.00 34.95 3.01
3401 3847 7.164230 ACAGAGAGAAAGTAACTCCACATAG 57.836 40.000 0.00 0.00 35.27 2.23
3404 3850 8.307483 CAGAGAGAAAGTAACTCCACATAGAAA 58.693 37.037 0.00 0.00 35.27 2.52
3441 3887 3.092301 GGGAAGCTTGAATTAACTGGCT 58.908 45.455 2.10 0.00 0.00 4.75
3538 3985 7.492614 CAAAGTTGTTTGTTTGTGTCTCTAC 57.507 36.000 0.00 0.00 38.64 2.59
3554 4001 8.773645 TGTGTCTCTACATTAGAAACAATTGTG 58.226 33.333 12.82 0.00 37.50 3.33
3555 4002 8.774586 GTGTCTCTACATTAGAAACAATTGTGT 58.225 33.333 12.82 6.37 37.50 3.72
3628 4075 5.677319 ATATTCAGACCCGAGACAGAAAA 57.323 39.130 0.00 0.00 0.00 2.29
3639 4086 3.546815 CGAGACAGAAAAGCAAAGTGTGG 60.547 47.826 0.00 0.00 0.00 4.17
3644 4091 3.865164 CAGAAAAGCAAAGTGTGGGAAAC 59.135 43.478 0.00 0.00 0.00 2.78
3666 4113 2.692741 CACCCCCTTCTCTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
3718 4165 3.496675 GGAACCCTAGTTGCCATCC 57.503 57.895 0.00 0.00 38.31 3.51
3748 4200 2.041405 CCCCTCCACCTCTCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
3753 4205 2.041405 CCACCTCTCCCTCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
3755 4207 1.075600 CACCTCTCCCTCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
3757 4209 2.695970 CCTCTCCCTCCTCCCTCGT 61.696 68.421 0.00 0.00 0.00 4.18
3758 4210 1.308326 CTCTCCCTCCTCCCTCGTT 59.692 63.158 0.00 0.00 0.00 3.85
3763 4215 2.125350 CTCCTCCCTCGTTGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
3789 4241 4.814294 GCGAACGGGCGATGTCCT 62.814 66.667 3.29 0.00 0.00 3.85
3792 4244 1.810030 GAACGGGCGATGTCCTGTC 60.810 63.158 0.00 0.00 44.63 3.51
3853 4305 1.540267 CGGCTGGTTGGGATTGTAAA 58.460 50.000 0.00 0.00 0.00 2.01
3854 4306 1.472480 CGGCTGGTTGGGATTGTAAAG 59.528 52.381 0.00 0.00 0.00 1.85
3863 4315 0.733150 GGATTGTAAAGCTGGGCGAC 59.267 55.000 0.00 0.00 29.39 5.19
3864 4316 1.448985 GATTGTAAAGCTGGGCGACA 58.551 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.418524 TGCTTACATGCCTTGTAACATGATT 59.581 36.000 9.77 0.00 44.08 2.57
29 30 7.657336 TCAGTTATGTATGATCGATGCTTACA 58.343 34.615 0.54 12.95 32.66 2.41
37 38 9.914131 CCTATCTTTTCAGTTATGTATGATCGA 57.086 33.333 0.00 0.00 0.00 3.59
128 131 6.147985 GTGAAGAGGTGATCTGTCTTTTTACC 59.852 42.308 0.00 0.00 38.67 2.85
166 169 1.444672 CTGATCAGCGATGGAGCCA 59.555 57.895 10.38 0.00 38.01 4.75
198 201 4.932146 GCTTCTGGCAAACTACTTTGAAA 58.068 39.130 0.00 0.00 39.43 2.69
248 251 2.668632 GAGGACATGTTGCCCCGA 59.331 61.111 0.00 0.00 0.00 5.14
264 268 0.731514 GAAGTTCGATGCGTGTCCGA 60.732 55.000 0.00 0.00 35.63 4.55
285 291 1.603455 CATGCGGGGGTGTCAGTTT 60.603 57.895 0.00 0.00 0.00 2.66
346 352 1.069765 CTTCGTGCTGGGTCTGTGT 59.930 57.895 0.00 0.00 0.00 3.72
361 367 5.066593 ACAACTGGAAGATGGAGTTTCTTC 58.933 41.667 5.13 5.13 41.61 2.87
381 387 1.742831 GGTTGTCTGTGCAAGTGACAA 59.257 47.619 19.69 19.69 44.96 3.18
418 424 1.029681 GCAGGGAGGTTTTGTCGTTT 58.970 50.000 0.00 0.00 0.00 3.60
454 463 0.315869 CGTTGTTGTGGCGTTGTCTC 60.316 55.000 0.00 0.00 0.00 3.36
474 483 1.110442 CTCTCCTTCTGCTCGGTCAT 58.890 55.000 0.00 0.00 0.00 3.06
475 484 0.038310 TCTCTCCTTCTGCTCGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
479 488 0.884514 TGTGTCTCTCCTTCTGCTCG 59.115 55.000 0.00 0.00 0.00 5.03
542 554 0.872021 CAGATCGACAGCGTTAGGGC 60.872 60.000 0.00 0.00 38.98 5.19
582 594 1.970917 GCGTCTTGGAGTTGATGGCG 61.971 60.000 0.00 0.00 0.00 5.69
595 608 2.436646 CCTTCATGGCGGCGTCTT 60.437 61.111 14.51 2.70 0.00 3.01
621 634 1.051812 CTCAACTCCACTCCCACACT 58.948 55.000 0.00 0.00 0.00 3.55
702 715 6.049149 CCTCCGCTCTGTAATTAGATTTTGA 58.951 40.000 0.00 0.00 0.00 2.69
708 721 3.066342 CGTTCCTCCGCTCTGTAATTAGA 59.934 47.826 0.00 0.00 0.00 2.10
713 726 1.601419 CCCGTTCCTCCGCTCTGTAA 61.601 60.000 0.00 0.00 0.00 2.41
739 753 2.273449 CTTGGCGGCAGGAGGAAT 59.727 61.111 16.59 0.00 0.00 3.01
740 754 4.722700 GCTTGGCGGCAGGAGGAA 62.723 66.667 25.57 1.39 0.00 3.36
754 769 2.664081 CCTCTCCCTTCGGCTGCTT 61.664 63.158 0.00 0.00 0.00 3.91
787 803 0.613853 TTCCTCCGATCTTCACCGGT 60.614 55.000 0.00 0.00 45.48 5.28
842 864 3.889520 AGACTTTTTCCTACCCTAGCG 57.110 47.619 0.00 0.00 0.00 4.26
865 887 2.301577 AAGAGGACGCTTGTGATAGC 57.698 50.000 0.00 0.00 37.80 2.97
866 888 3.067461 AGCTAAGAGGACGCTTGTGATAG 59.933 47.826 0.00 0.00 0.00 2.08
867 889 3.024547 AGCTAAGAGGACGCTTGTGATA 58.975 45.455 0.00 0.00 0.00 2.15
868 890 1.827969 AGCTAAGAGGACGCTTGTGAT 59.172 47.619 0.00 0.00 0.00 3.06
869 891 1.257743 AGCTAAGAGGACGCTTGTGA 58.742 50.000 0.00 0.00 0.00 3.58
870 892 2.086054 AAGCTAAGAGGACGCTTGTG 57.914 50.000 0.00 0.00 41.96 3.33
871 893 2.224305 ACAAAGCTAAGAGGACGCTTGT 60.224 45.455 0.00 0.00 42.65 3.16
872 894 2.413453 GACAAAGCTAAGAGGACGCTTG 59.587 50.000 0.00 0.00 42.65 4.01
873 895 2.037251 TGACAAAGCTAAGAGGACGCTT 59.963 45.455 0.00 0.00 45.13 4.68
874 896 1.618837 TGACAAAGCTAAGAGGACGCT 59.381 47.619 0.00 0.00 35.09 5.07
875 897 2.080286 TGACAAAGCTAAGAGGACGC 57.920 50.000 0.00 0.00 0.00 5.19
876 898 4.670221 GCAATTGACAAAGCTAAGAGGACG 60.670 45.833 10.34 0.00 0.00 4.79
877 899 4.670221 CGCAATTGACAAAGCTAAGAGGAC 60.670 45.833 10.34 0.00 0.00 3.85
878 900 3.436704 CGCAATTGACAAAGCTAAGAGGA 59.563 43.478 10.34 0.00 0.00 3.71
879 901 3.751621 CGCAATTGACAAAGCTAAGAGG 58.248 45.455 10.34 0.00 0.00 3.69
880 902 3.166657 GCGCAATTGACAAAGCTAAGAG 58.833 45.455 10.34 0.91 0.00 2.85
881 903 2.095263 GGCGCAATTGACAAAGCTAAGA 60.095 45.455 10.83 0.00 0.00 2.10
882 904 2.253603 GGCGCAATTGACAAAGCTAAG 58.746 47.619 10.83 0.00 0.00 2.18
883 905 1.400888 CGGCGCAATTGACAAAGCTAA 60.401 47.619 10.83 0.00 0.00 3.09
884 906 0.167908 CGGCGCAATTGACAAAGCTA 59.832 50.000 10.83 0.00 0.00 3.32
885 907 1.081242 CGGCGCAATTGACAAAGCT 60.081 52.632 10.83 0.00 0.00 3.74
886 908 0.939106 AACGGCGCAATTGACAAAGC 60.939 50.000 10.83 5.75 0.00 3.51
887 909 0.777631 CAACGGCGCAATTGACAAAG 59.222 50.000 15.67 0.00 0.00 2.77
888 910 0.101399 ACAACGGCGCAATTGACAAA 59.899 45.000 24.57 0.00 0.00 2.83
889 911 0.317436 GACAACGGCGCAATTGACAA 60.317 50.000 24.57 0.00 0.00 3.18
890 912 1.281353 GACAACGGCGCAATTGACA 59.719 52.632 24.57 0.00 0.00 3.58
891 913 1.442017 GGACAACGGCGCAATTGAC 60.442 57.895 24.57 19.11 0.00 3.18
892 914 0.320858 TAGGACAACGGCGCAATTGA 60.321 50.000 24.57 4.32 0.00 2.57
893 915 0.096976 CTAGGACAACGGCGCAATTG 59.903 55.000 18.27 18.27 0.00 2.32
894 916 0.036765 TCTAGGACAACGGCGCAATT 60.037 50.000 10.83 0.00 0.00 2.32
895 917 0.036765 TTCTAGGACAACGGCGCAAT 60.037 50.000 10.83 0.00 0.00 3.56
896 918 0.249953 TTTCTAGGACAACGGCGCAA 60.250 50.000 10.83 0.00 0.00 4.85
912 934 1.006494 CGGCGCAACTGTTTTGTTTTC 60.006 47.619 10.83 0.00 0.00 2.29
916 938 1.509004 AACGGCGCAACTGTTTTGT 59.491 47.368 10.83 0.00 46.01 2.83
921 943 2.047151 CTGTCAAACGGCGCAACTGT 62.047 55.000 10.83 0.00 40.66 3.55
939 961 2.098117 GTGTACGGACGTATTGTAGGCT 59.902 50.000 7.89 0.00 32.82 4.58
944 966 3.375299 GGAGTAGTGTACGGACGTATTGT 59.625 47.826 7.89 0.00 32.82 2.71
953 975 1.814527 GGCCAGGAGTAGTGTACGG 59.185 63.158 0.00 0.00 0.00 4.02
954 976 1.028330 TCGGCCAGGAGTAGTGTACG 61.028 60.000 2.24 0.00 0.00 3.67
955 977 1.180029 TTCGGCCAGGAGTAGTGTAC 58.820 55.000 2.24 0.00 0.00 2.90
956 978 2.154567 ATTCGGCCAGGAGTAGTGTA 57.845 50.000 2.24 0.00 0.00 2.90
957 979 1.755380 GTATTCGGCCAGGAGTAGTGT 59.245 52.381 2.24 0.00 0.00 3.55
958 980 1.269102 CGTATTCGGCCAGGAGTAGTG 60.269 57.143 2.24 0.00 0.00 2.74
984 1006 5.178623 TGCAATCTTGGACTTGTAACTAACG 59.821 40.000 0.00 0.00 0.00 3.18
985 1007 6.371389 GTGCAATCTTGGACTTGTAACTAAC 58.629 40.000 7.25 0.00 44.78 2.34
987 1009 5.001232 GGTGCAATCTTGGACTTGTAACTA 58.999 41.667 13.22 0.00 46.96 2.24
988 1010 3.821033 GGTGCAATCTTGGACTTGTAACT 59.179 43.478 13.22 0.00 46.96 2.24
989 1011 3.568007 TGGTGCAATCTTGGACTTGTAAC 59.432 43.478 13.22 0.00 46.96 2.50
990 1012 3.568007 GTGGTGCAATCTTGGACTTGTAA 59.432 43.478 13.22 0.00 46.96 2.41
992 1014 1.956477 GTGGTGCAATCTTGGACTTGT 59.044 47.619 13.22 0.00 46.96 3.16
993 1015 1.069022 CGTGGTGCAATCTTGGACTTG 60.069 52.381 13.22 1.94 46.96 3.16
994 1016 1.238439 CGTGGTGCAATCTTGGACTT 58.762 50.000 13.22 0.00 46.96 3.01
1028 1060 1.026182 CCGCAGGCTGCAGATGTTAA 61.026 55.000 35.94 0.00 46.14 2.01
1070 1128 4.262506 CCTCCTTTTAGTTTCCAGTCGTCT 60.263 45.833 0.00 0.00 0.00 4.18
1086 1145 3.775654 CTCGCCGCTCCCTCCTTT 61.776 66.667 0.00 0.00 0.00 3.11
1089 1148 3.724914 CTTTCTCGCCGCTCCCTCC 62.725 68.421 0.00 0.00 0.00 4.30
1091 1150 2.022240 GATCTTTCTCGCCGCTCCCT 62.022 60.000 0.00 0.00 0.00 4.20
1092 1151 1.592939 GATCTTTCTCGCCGCTCCC 60.593 63.158 0.00 0.00 0.00 4.30
1134 1205 4.157120 GTCGCCGGGTAGCATGGT 62.157 66.667 2.18 1.62 0.00 3.55
1274 1345 0.391661 AGTTGATGAAGATGCCGCGT 60.392 50.000 4.92 0.00 0.00 6.01
1615 1758 0.179230 GTCGTCGTCGTCTGATTCGT 60.179 55.000 1.33 0.00 38.33 3.85
1637 1801 1.300620 CTCGAGCAACGGGTTGTCA 60.301 57.895 12.65 1.85 42.31 3.58
1658 1822 3.474570 GATGCGGGAGGCCACTCT 61.475 66.667 5.01 0.00 43.46 3.24
1909 2261 6.346096 AGCAAGCAATCTAACCGAGTTATAA 58.654 36.000 0.00 0.00 0.00 0.98
1939 2303 2.159043 AGAGTAACCAGTCGGATGCATG 60.159 50.000 2.46 0.00 35.59 4.06
2009 2392 1.404047 CGGTTGGGATGTTTGGCATTC 60.404 52.381 0.00 0.00 38.06 2.67
2010 2393 0.607620 CGGTTGGGATGTTTGGCATT 59.392 50.000 0.00 0.00 38.06 3.56
2040 2438 1.763968 TACACCCCTCTCACTGATCG 58.236 55.000 0.00 0.00 0.00 3.69
2046 2444 1.066430 TGCGAAATACACCCCTCTCAC 60.066 52.381 0.00 0.00 0.00 3.51
2123 2521 0.320374 TTAGCACCCACTCTGTTCGG 59.680 55.000 0.00 0.00 0.00 4.30
2128 2526 3.411446 TCATGTTTTAGCACCCACTCTG 58.589 45.455 0.00 0.00 0.00 3.35
2155 2553 7.718753 GGTCCTCATGTTCAAATATCTGAAGAT 59.281 37.037 0.00 0.00 39.25 2.40
2160 2561 6.600822 AGTTGGTCCTCATGTTCAAATATCTG 59.399 38.462 0.00 0.00 0.00 2.90
2165 2566 3.828451 CCAGTTGGTCCTCATGTTCAAAT 59.172 43.478 0.00 0.00 0.00 2.32
2256 2666 1.300233 CCGGCGCTCTGTAATCTCC 60.300 63.158 7.64 0.00 0.00 3.71
2338 2760 3.426615 AGACCATCGTGATATCCCTCTC 58.573 50.000 0.00 0.00 0.00 3.20
2419 2848 0.480252 ATAGGCCATTCCCCTTGCTC 59.520 55.000 5.01 0.00 33.88 4.26
2452 2881 3.534357 TGCCCAGGTCCTGAAATTTTA 57.466 42.857 21.23 0.00 32.44 1.52
2466 2895 1.870055 GCTGGACACACATTGCCCAG 61.870 60.000 2.46 2.46 45.31 4.45
2514 2943 3.669036 CTGTGTCCGTCTCTCCGCG 62.669 68.421 0.00 0.00 0.00 6.46
2558 2990 0.602905 CGTTTCCAGGAAACTCGCCT 60.603 55.000 33.06 0.00 46.55 5.52
2604 3036 8.499403 AGTTCCAACTTTTTCATAGATAGCTC 57.501 34.615 0.00 0.00 35.21 4.09
2629 3061 6.500751 ACAGGTAAAGTTGGATTCCTCTTCTA 59.499 38.462 3.95 3.00 0.00 2.10
2812 3258 0.847314 TGCCTTGGCCCTAAACCCTA 60.847 55.000 9.35 0.00 0.00 3.53
2813 3259 1.735455 TTGCCTTGGCCCTAAACCCT 61.735 55.000 9.35 0.00 0.00 4.34
2814 3260 0.617535 ATTGCCTTGGCCCTAAACCC 60.618 55.000 9.35 0.00 0.00 4.11
2836 3282 3.132925 CAAAGGTCAAACTTGGCAATGG 58.867 45.455 0.00 0.00 33.59 3.16
2855 3301 1.167851 GCACATCAGTAGCTTGCCAA 58.832 50.000 0.00 0.00 0.00 4.52
2872 3318 2.491693 TGACATGAGTCTGATACGTGCA 59.508 45.455 0.00 0.00 45.20 4.57
2920 3366 3.942539 AAACTTTGTTTTCCATTGCGC 57.057 38.095 0.00 0.00 0.00 6.09
3077 3523 9.890629 TTTTATTCGAGTACTACTACCTCTGTA 57.109 33.333 0.00 0.00 0.00 2.74
3086 3532 5.261661 CGCGTCTTTTATTCGAGTACTACT 58.738 41.667 0.00 0.00 0.00 2.57
3095 3541 1.508725 GCAATGCGCGTCTTTTATTCG 59.491 47.619 8.43 0.00 0.00 3.34
3203 3649 5.103728 TGCCCCATAGGATTAGAAATGACAA 60.104 40.000 0.00 0.00 38.24 3.18
3204 3650 4.415179 TGCCCCATAGGATTAGAAATGACA 59.585 41.667 0.00 0.00 38.24 3.58
3221 3667 2.359850 GACGTGCTTCATGCCCCA 60.360 61.111 0.00 0.00 42.00 4.96
3287 3733 1.880027 ACCGAGGCACTGAACATTTTC 59.120 47.619 0.00 0.00 41.55 2.29
3296 3742 1.448540 GTGGATGACCGAGGCACTG 60.449 63.158 0.00 0.00 41.55 3.66
3307 3753 4.777366 TCTCTAACCAGTTCATGTGGATGA 59.223 41.667 7.78 2.65 38.57 2.92
3336 3782 1.459592 CTACAACGGCACTTCCTTTCG 59.540 52.381 0.00 0.00 0.00 3.46
3338 3784 1.235724 GCTACAACGGCACTTCCTTT 58.764 50.000 0.00 0.00 0.00 3.11
3353 3799 3.127030 GGGTGTTGTATTCAGCTTGCTAC 59.873 47.826 0.00 0.00 34.33 3.58
3379 3825 8.423906 TTTCTATGTGGAGTTACTTTCTCTCT 57.576 34.615 0.00 0.00 33.06 3.10
3394 3840 8.400947 CAAGGTTATCATGTTCTTTCTATGTGG 58.599 37.037 0.00 0.00 0.00 4.17
3401 3847 6.625960 GCTTCCCAAGGTTATCATGTTCTTTC 60.626 42.308 0.00 0.00 0.00 2.62
3404 3850 4.018050 AGCTTCCCAAGGTTATCATGTTCT 60.018 41.667 0.00 0.00 35.27 3.01
3453 3899 5.671493 ACCCGAGGTTAACATTCTCATTAG 58.329 41.667 8.10 0.00 27.29 1.73
3590 4037 6.659242 GTCTGAATATTTGGGTCCTTTCTTCA 59.341 38.462 0.00 0.00 0.00 3.02
3591 4038 6.095580 GGTCTGAATATTTGGGTCCTTTCTTC 59.904 42.308 0.00 0.00 0.00 2.87
3592 4039 5.952347 GGTCTGAATATTTGGGTCCTTTCTT 59.048 40.000 0.00 0.00 0.00 2.52
3593 4040 5.510430 GGTCTGAATATTTGGGTCCTTTCT 58.490 41.667 0.00 0.00 0.00 2.52
3594 4041 4.645136 GGGTCTGAATATTTGGGTCCTTTC 59.355 45.833 0.00 0.00 0.00 2.62
3595 4042 4.610333 GGGTCTGAATATTTGGGTCCTTT 58.390 43.478 0.00 0.00 0.00 3.11
3628 4075 1.106944 CCGGTTTCCCACACTTTGCT 61.107 55.000 0.00 0.00 0.00 3.91
3639 4086 2.759641 GAAGGGGGTGTCCGGTTTCC 62.760 65.000 0.00 1.93 36.01 3.13
3644 4091 2.284699 AGAGAAGGGGGTGTCCGG 60.285 66.667 0.00 0.00 36.01 5.14
3647 4094 1.996187 GGGGAGAGAAGGGGGTGTC 60.996 68.421 0.00 0.00 0.00 3.67
3748 4200 1.899437 TTAGGCTGCAACGAGGGAGG 61.899 60.000 0.50 0.00 0.00 4.30
3753 4205 4.208632 CCCTTAGGCTGCAACGAG 57.791 61.111 0.50 0.00 0.00 4.18
3774 4226 1.810030 GACAGGACATCGCCCGTTC 60.810 63.158 0.00 0.00 0.00 3.95
3775 4227 2.264794 GACAGGACATCGCCCGTT 59.735 61.111 0.00 0.00 0.00 4.44
3776 4228 4.129737 CGACAGGACATCGCCCGT 62.130 66.667 0.00 0.00 31.96 5.28
3781 4233 2.509336 GGTGGCGACAGGACATCG 60.509 66.667 0.00 0.00 44.46 3.84
3784 4236 3.936203 GGTGGTGGCGACAGGACA 61.936 66.667 0.00 0.00 44.46 4.02
3841 4293 1.555967 GCCCAGCTTTACAATCCCAA 58.444 50.000 0.00 0.00 0.00 4.12
3917 4379 0.620410 CCCCTCTACCATGACACCCA 60.620 60.000 0.00 0.00 0.00 4.51
3930 4392 2.833913 CCACCACTTGTGCCCCTCT 61.834 63.158 0.00 0.00 44.01 3.69


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

AutoCloner maintained by Alex Coulton.