Multiple sequence alignment - TraesCS6D01G149200

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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 TraesCS6D01G149200 chr6D 100.000 3166 0 0 1 3166 122988649 122991814 0.000000e+00 5847.0
1 TraesCS6D01G149200 chr6D 95.175 974 37 5 877 1841 124609472 124608500 0.000000e+00 1530.0
2 TraesCS6D01G149200 chr6D 92.455 888 39 15 953 1821 122979578 122980456 0.000000e+00 1243.0
3 TraesCS6D01G149200 chr6D 85.436 872 96 12 1 847 124610411 124609546 0.000000e+00 878.0
4 TraesCS6D01G149200 chr6D 92.040 402 28 3 2721 3122 122982244 122982641 2.130000e-156 562.0
5 TraesCS6D01G149200 chr6D 82.344 657 52 33 1911 2539 122980462 122981082 2.180000e-141 512.0
6 TraesCS6D01G149200 chr6D 92.574 202 14 1 2535 2735 122982029 122982230 4.000000e-74 289.0
7 TraesCS6D01G149200 chr6D 96.552 58 2 0 871 928 122979521 122979578 2.600000e-16 97.1
8 TraesCS6D01G149200 chr6A 91.718 2270 124 28 865 3111 158245612 158243384 0.000000e+00 3092.0
9 TraesCS6D01G149200 chr6A 85.523 898 103 9 960 1840 107264414 107265301 0.000000e+00 913.0
10 TraesCS6D01G149200 chr6A 85.047 214 9 10 876 1089 158246112 158245922 2.490000e-46 196.0
11 TraesCS6D01G149200 chr6B 92.007 2152 128 24 871 3007 216631587 216633709 0.000000e+00 2981.0
12 TraesCS6D01G149200 chr7D 85.827 1397 99 51 1752 3122 518774637 518775960 0.000000e+00 1391.0
13 TraesCS6D01G149200 chr7D 87.213 1220 71 19 1911 3122 545652594 545653736 0.000000e+00 1310.0
14 TraesCS6D01G149200 chr7D 83.960 1197 121 38 962 2123 545647062 545648222 0.000000e+00 1081.0
15 TraesCS6D01G149200 chr7D 89.152 719 60 4 1046 1749 518768995 518769710 0.000000e+00 880.0
16 TraesCS6D01G149200 chr7D 79.887 1243 142 44 960 2135 518766195 518767396 0.000000e+00 811.0
17 TraesCS6D01G149200 chr7D 86.610 351 27 14 1796 2135 509597981 509597640 1.390000e-98 370.0
18 TraesCS6D01G149200 chr7D 86.645 307 41 0 2 308 385424595 385424901 1.090000e-89 340.0
19 TraesCS6D01G149200 chr7D 84.797 296 42 3 1 295 617657298 617657591 8.590000e-76 294.0
20 TraesCS6D01G149200 chr7D 83.673 294 48 0 3 296 532604097 532603804 8.650000e-71 278.0
21 TraesCS6D01G149200 chr7D 85.214 257 38 0 7 263 87503314 87503058 6.730000e-67 265.0
22 TraesCS6D01G149200 chr7D 87.970 133 13 3 2258 2389 546777955 546778085 1.520000e-33 154.0
23 TraesCS6D01G149200 chr7D 97.727 44 1 0 2433 2476 545651919 545651962 3.390000e-10 76.8
24 TraesCS6D01G149200 chr7A 84.846 1399 100 51 1746 3122 594449126 594450434 0.000000e+00 1306.0
25 TraesCS6D01G149200 chr7A 89.126 892 50 13 2172 3043 169955551 169954687 0.000000e+00 1066.0
26 TraesCS6D01G149200 chr7A 85.645 1024 94 31 1051 2058 626992528 626991542 0.000000e+00 1027.0
27 TraesCS6D01G149200 chr7A 83.029 1096 96 46 1053 2123 628492196 628491166 0.000000e+00 911.0
28 TraesCS6D01G149200 chr7A 92.383 407 21 3 2627 3031 628647683 628648081 3.540000e-159 571.0
29 TraesCS6D01G149200 chr7A 83.230 322 20 13 2123 2437 628647205 628647499 6.730000e-67 265.0
30 TraesCS6D01G149200 chr7A 77.344 512 58 39 1911 2392 629771927 629771444 1.890000e-62 250.0
31 TraesCS6D01G149200 chr7A 80.180 222 22 15 1995 2206 628485177 628484968 2.540000e-31 147.0
32 TraesCS6D01G149200 chr7A 88.710 62 7 0 874 935 628390066 628390005 3.390000e-10 76.8
33 TraesCS6D01G149200 chr7B 89.385 1008 45 20 1911 2904 589937084 589938043 0.000000e+00 1212.0
34 TraesCS6D01G149200 chr7B 85.740 1122 106 28 962 2058 589700700 589699608 0.000000e+00 1136.0
35 TraesCS6D01G149200 chr7B 86.937 222 15 4 2901 3122 589938112 589938319 1.470000e-58 237.0
36 TraesCS6D01G149200 chr7B 87.019 208 18 4 1851 2056 589737532 589737732 3.180000e-55 226.0
37 TraesCS6D01G149200 chr7B 78.333 180 25 12 2062 2231 589897845 589898020 1.550000e-18 104.0
38 TraesCS6D01G149200 chr7B 97.727 44 1 0 2433 2476 589936404 589936447 3.390000e-10 76.8
39 TraesCS6D01G149200 chr5D 87.253 910 72 15 962 1846 331837765 331838655 0.000000e+00 998.0
40 TraesCS6D01G149200 chr5D 81.887 530 64 19 2517 3039 331839058 331839562 4.880000e-113 418.0
41 TraesCS6D01G149200 chr5D 85.227 264 37 2 6 268 472461817 472461555 1.450000e-68 270.0
42 TraesCS6D01G149200 chr5D 92.982 57 4 0 874 930 331837712 331837768 2.020000e-12 84.2
43 TraesCS6D01G149200 chr5D 97.727 44 1 0 2433 2476 331839165 331839208 3.390000e-10 76.8
44 TraesCS6D01G149200 chr1B 85.192 1013 90 30 874 1846 398840513 398839521 0.000000e+00 985.0
45 TraesCS6D01G149200 chr1B 85.099 859 76 18 871 1705 398899469 398900299 0.000000e+00 830.0
46 TraesCS6D01G149200 chr1B 84.034 238 24 4 1877 2107 133109657 133109427 1.910000e-52 217.0
47 TraesCS6D01G149200 chr1B 83.193 238 26 4 1877 2107 426480248 426480018 4.140000e-49 206.0
48 TraesCS6D01G149200 chr1B 78.970 233 30 11 1994 2217 398838448 398838226 1.180000e-29 141.0
49 TraesCS6D01G149200 chr1B 95.918 49 1 1 3001 3049 398901997 398902044 9.420000e-11 78.7
50 TraesCS6D01G149200 chr2D 85.382 301 42 2 1 301 550629320 550629022 8.530000e-81 311.0
51 TraesCS6D01G149200 chr3B 83.284 335 43 8 3 325 7601667 7601334 2.390000e-76 296.0
52 TraesCS6D01G149200 chr2B 82.965 317 53 1 1 316 793409343 793409027 5.170000e-73 285.0
53 TraesCS6D01G149200 chr3D 83.333 156 16 3 874 1029 43727645 43727500 5.510000e-28 135.0
54 TraesCS6D01G149200 chr3A 83.333 150 13 7 880 1029 55501495 55501358 9.220000e-26 128.0


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 TraesCS6D01G149200 chr6D 122988649 122991814 3165 False 5847.00 5847 100.000000 1 3166 1 chr6D.!!$F1 3165
1 TraesCS6D01G149200 chr6D 124608500 124610411 1911 True 1204.00 1530 90.305500 1 1841 2 chr6D.!!$R1 1840
2 TraesCS6D01G149200 chr6D 122979521 122982641 3120 False 540.62 1243 91.193000 871 3122 5 chr6D.!!$F2 2251
3 TraesCS6D01G149200 chr6A 158243384 158246112 2728 True 1644.00 3092 88.382500 865 3111 2 chr6A.!!$R1 2246
4 TraesCS6D01G149200 chr6A 107264414 107265301 887 False 913.00 913 85.523000 960 1840 1 chr6A.!!$F1 880
5 TraesCS6D01G149200 chr6B 216631587 216633709 2122 False 2981.00 2981 92.007000 871 3007 1 chr6B.!!$F1 2136
6 TraesCS6D01G149200 chr7D 518774637 518775960 1323 False 1391.00 1391 85.827000 1752 3122 1 chr7D.!!$F2 1370
7 TraesCS6D01G149200 chr7D 518766195 518769710 3515 False 845.50 880 84.519500 960 2135 2 chr7D.!!$F5 1175
8 TraesCS6D01G149200 chr7D 545647062 545653736 6674 False 822.60 1310 89.633333 962 3122 3 chr7D.!!$F6 2160
9 TraesCS6D01G149200 chr7A 594449126 594450434 1308 False 1306.00 1306 84.846000 1746 3122 1 chr7A.!!$F1 1376
10 TraesCS6D01G149200 chr7A 169954687 169955551 864 True 1066.00 1066 89.126000 2172 3043 1 chr7A.!!$R1 871
11 TraesCS6D01G149200 chr7A 626991542 626992528 986 True 1027.00 1027 85.645000 1051 2058 1 chr7A.!!$R2 1007
12 TraesCS6D01G149200 chr7A 628491166 628492196 1030 True 911.00 911 83.029000 1053 2123 1 chr7A.!!$R5 1070
13 TraesCS6D01G149200 chr7A 628647205 628648081 876 False 418.00 571 87.806500 2123 3031 2 chr7A.!!$F2 908
14 TraesCS6D01G149200 chr7B 589699608 589700700 1092 True 1136.00 1136 85.740000 962 2058 1 chr7B.!!$R1 1096
15 TraesCS6D01G149200 chr7B 589936404 589938319 1915 False 508.60 1212 91.349667 1911 3122 3 chr7B.!!$F3 1211
16 TraesCS6D01G149200 chr5D 331837712 331839562 1850 False 394.25 998 89.962250 874 3039 4 chr5D.!!$F1 2165
17 TraesCS6D01G149200 chr1B 398838226 398840513 2287 True 563.00 985 82.081000 874 2217 2 chr1B.!!$R3 1343
18 TraesCS6D01G149200 chr1B 398899469 398902044 2575 False 454.35 830 90.508500 871 3049 2 chr1B.!!$F1 2178

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
564 565 0.036952 AGCAGCAGTAAGACACGCAT 60.037 50.000 0.0 0.0 31.69 4.73 F
699 725 1.003839 CCACAGCGACTTTGCCCTA 60.004 57.895 0.0 0.0 34.65 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1849 0.389025 TGAGTTGAGCTTGAGCACGA 59.611 50.000 5.7 0.0 45.16 4.35 R
2495 8496 1.419762 TGGCAGGTACACATGAGTTGT 59.580 47.619 0.0 0.0 39.91 3.32 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
60 61 1.299165 GATATGGACGCGCACGACT 60.299 57.895 5.73 0.00 43.93 4.18
76 77 3.908978 CACGACTGGATTCTATTCGATCG 59.091 47.826 14.97 9.36 33.87 3.69
81 82 6.036191 CGACTGGATTCTATTCGATCGAGATA 59.964 42.308 18.54 16.20 0.00 1.98
104 105 2.544685 CTTGGGCAAGATCTACGACAG 58.455 52.381 0.00 0.00 40.79 3.51
110 111 9.869779 CTTGGGCAAGATCTACGACAGTAGTTT 62.870 44.444 0.00 0.00 43.87 2.66
153 154 0.103937 GAGGAGGACCGATCAAGCAG 59.896 60.000 0.00 0.00 41.83 4.24
188 189 1.405526 GCGATAAGAGCACAAGGACCA 60.406 52.381 0.00 0.00 34.19 4.02
193 194 1.600916 GAGCACAAGGACCACCACC 60.601 63.158 0.00 0.00 38.94 4.61
217 218 1.966451 GTTGCCTCCACCAAGTCGG 60.966 63.158 0.00 0.00 42.50 4.79
247 248 4.308458 CACGGCGGAGGACACCAA 62.308 66.667 13.24 0.00 0.00 3.67
256 257 4.382320 GGACACCAACCCGCGCTA 62.382 66.667 5.56 0.00 0.00 4.26
263 264 3.943691 AACCCGCGCTACCCACAA 61.944 61.111 5.56 0.00 0.00 3.33
301 302 2.416566 CCAGATCTGACAGAACCGACAG 60.417 54.545 24.62 0.00 0.00 3.51
338 339 1.229076 GGTCCACCACACCACCTTT 59.771 57.895 0.00 0.00 33.63 3.11
343 344 1.756561 ACCACACCACCTTTGCCAC 60.757 57.895 0.00 0.00 0.00 5.01
372 373 2.300967 CCCCAACCTAGAGCAGCCA 61.301 63.158 0.00 0.00 0.00 4.75
453 454 3.005539 GAGGGAGACAGGCCAGCA 61.006 66.667 5.01 0.00 0.00 4.41
459 460 0.952984 GAGACAGGCCAGCACTTGAC 60.953 60.000 5.01 0.00 0.00 3.18
461 462 3.730761 CAGGCCAGCACTTGACGC 61.731 66.667 5.01 0.00 0.00 5.19
530 531 1.349542 ACCACCACCTAGCACACCAA 61.350 55.000 0.00 0.00 0.00 3.67
537 538 4.610714 TAGCACACCAACGCCGCA 62.611 61.111 0.00 0.00 0.00 5.69
540 541 3.582120 CACACCAACGCCGCACTT 61.582 61.111 0.00 0.00 0.00 3.16
556 557 1.463831 CACTTGAGCAGCAGCAGTAAG 59.536 52.381 3.17 7.11 45.49 2.34
564 565 0.036952 AGCAGCAGTAAGACACGCAT 60.037 50.000 0.00 0.00 31.69 4.73
578 579 2.280457 GCATACGAGGAGGCAGGC 60.280 66.667 0.00 0.00 0.00 4.85
609 611 4.717629 TGCCGAACCGAGCAGTCG 62.718 66.667 0.00 0.00 46.39 4.18
619 621 1.282875 GAGCAGTCGCCCAAAACAC 59.717 57.895 0.00 0.00 39.83 3.32
621 623 2.637025 CAGTCGCCCAAAACACCG 59.363 61.111 0.00 0.00 0.00 4.94
628 630 4.341502 CCAAAACACCGCCGCCTG 62.342 66.667 0.00 0.00 0.00 4.85
629 631 4.999939 CAAAACACCGCCGCCTGC 63.000 66.667 0.00 0.00 0.00 4.85
647 650 1.216710 CCGTTGCTGAGGGAGACTC 59.783 63.158 0.00 0.00 46.78 3.36
650 653 1.228894 TTGCTGAGGGAGACTCCGT 60.229 57.895 16.55 16.55 46.01 4.69
693 719 2.034879 CATCGGCCACAGCGACTTT 61.035 57.895 2.24 0.00 41.24 2.66
699 725 1.003839 CCACAGCGACTTTGCCCTA 60.004 57.895 0.00 0.00 34.65 3.53
711 737 2.512515 GCCCTACAGCTTGCTCCG 60.513 66.667 0.00 0.00 0.00 4.63
713 739 2.187946 CCTACAGCTTGCTCCGGG 59.812 66.667 0.00 0.00 0.00 5.73
764 790 1.376037 GCAGTGGCGCTAGGTTTCT 60.376 57.895 7.64 0.00 0.00 2.52
785 811 9.977762 GTTTCTTTCCGAATGTAATTATAACGT 57.022 29.630 9.72 0.00 36.07 3.99
803 829 3.921677 ACGTTGAGTAATGTGGGTACTG 58.078 45.455 0.00 0.00 34.81 2.74
805 831 4.174009 CGTTGAGTAATGTGGGTACTGAG 58.826 47.826 0.00 0.00 31.88 3.35
814 840 5.615925 ATGTGGGTACTGAGGTTATTCTC 57.384 43.478 0.00 0.00 0.00 2.87
845 871 7.851822 AAAAATATTTCAGCACGTACAAGTG 57.148 32.000 0.10 0.00 44.47 3.16
847 873 7.661127 AAATATTTCAGCACGTACAAGTGTA 57.339 32.000 0.00 0.00 43.61 2.90
848 874 7.661127 AATATTTCAGCACGTACAAGTGTAA 57.339 32.000 0.00 0.00 43.61 2.41
849 875 5.994887 ATTTCAGCACGTACAAGTGTAAA 57.005 34.783 0.00 3.14 43.61 2.01
852 878 3.799963 TCAGCACGTACAAGTGTAAAGTG 59.200 43.478 17.27 17.27 43.61 3.16
853 879 3.554324 CAGCACGTACAAGTGTAAAGTGT 59.446 43.478 20.17 10.78 43.61 3.55
855 881 4.033587 AGCACGTACAAGTGTAAAGTGTTG 59.966 41.667 20.17 5.64 43.61 3.33
856 882 4.201744 GCACGTACAAGTGTAAAGTGTTGT 60.202 41.667 20.17 0.00 43.61 3.32
859 885 7.623770 CACGTACAAGTGTAAAGTGTTGTTAT 58.376 34.615 14.98 0.00 37.01 1.89
860 886 7.790673 CACGTACAAGTGTAAAGTGTTGTTATC 59.209 37.037 14.98 0.00 37.01 1.75
861 887 6.999627 CGTACAAGTGTAAAGTGTTGTTATCG 59.000 38.462 0.00 0.00 34.92 2.92
862 888 6.295039 ACAAGTGTAAAGTGTTGTTATCGG 57.705 37.500 0.00 0.00 28.62 4.18
864 890 6.985645 ACAAGTGTAAAGTGTTGTTATCGGTA 59.014 34.615 0.00 0.00 28.62 4.02
865 891 7.495279 ACAAGTGTAAAGTGTTGTTATCGGTAA 59.505 33.333 0.00 0.00 28.62 2.85
866 892 8.336806 CAAGTGTAAAGTGTTGTTATCGGTAAA 58.663 33.333 0.00 0.00 0.00 2.01
868 894 8.500773 AGTGTAAAGTGTTGTTATCGGTAAATG 58.499 33.333 0.00 0.00 0.00 2.32
869 895 8.284693 GTGTAAAGTGTTGTTATCGGTAAATGT 58.715 33.333 0.00 0.00 0.00 2.71
872 949 5.801380 AGTGTTGTTATCGGTAAATGTCCT 58.199 37.500 0.00 0.00 0.00 3.85
936 1020 1.377725 CCTGATTGCCGCCAGTTCT 60.378 57.895 0.00 0.00 0.00 3.01
1018 1102 4.550076 ATTCCCGATCCATCTGAATCTC 57.450 45.455 0.00 0.00 0.00 2.75
1034 1136 4.104261 TGAATCTCATTGGCATCCTCATCT 59.896 41.667 0.00 0.00 0.00 2.90
1167 1301 3.368190 CTGCACTCCTGCTCCTCCG 62.368 68.421 0.00 0.00 44.57 4.63
1185 1319 2.125431 GCGTGCGCCTAAACCCTA 60.125 61.111 4.18 0.00 34.56 3.53
1408 1557 1.258445 AACCAGGTCGCCGAATCTCT 61.258 55.000 0.00 0.00 0.00 3.10
1611 1787 1.302511 CAGTTCAACGACCCCTGGG 60.303 63.158 5.50 5.50 42.03 4.45
1673 1849 2.295349 CCAAGCAAGACAAGAAGCATGT 59.705 45.455 0.00 0.00 0.00 3.21
1959 2541 2.493278 GCATGTTTTCCAGTAGTGCCAT 59.507 45.455 0.00 0.00 0.00 4.40
2008 2898 7.160547 TCAGTGTGCATTATGATCACAATTT 57.839 32.000 17.06 0.00 41.66 1.82
2049 7521 7.226523 AGGGTTTTGTTTCATGTAAAAGCATTC 59.773 33.333 19.80 10.50 41.18 2.67
2267 7830 7.649306 CCTTGAGAAAAATTTACACCTCAACAG 59.351 37.037 14.82 9.75 36.21 3.16
2389 8090 4.114794 GCTGTCTGAAATTTTGCAACTGT 58.885 39.130 0.00 0.00 0.00 3.55
2487 8488 9.817809 GATCCACTGAGTTAACATATTCAGTAA 57.182 33.333 21.24 15.26 46.14 2.24
2547 9500 3.810941 ACTGCTGCAAATTTTGTTCCATG 59.189 39.130 3.02 0.00 0.00 3.66
2557 9510 3.834489 TTTGTTCCATGCAAATGGTGT 57.166 38.095 6.24 0.00 42.28 4.16
2626 9583 5.355910 ACTTGACGACAATGGTGTTTACTTT 59.644 36.000 0.00 0.00 38.41 2.66
2700 9658 7.068226 ACAAGGGAATTACAATGCCTAATACAC 59.932 37.037 0.00 0.00 37.69 2.90
2716 9678 7.095439 GCCTAATACACAATCTGAACTCATAGC 60.095 40.741 0.00 0.00 0.00 2.97
2885 9933 3.689347 CTGGGAAATGACATGACCAAGA 58.311 45.455 0.00 0.00 0.00 3.02
2986 10848 6.433404 ATGGTTTTTATCCATTGCATTTTGCA 59.567 30.769 0.00 0.00 43.29 4.08
3039 11729 3.386768 TTCAGAATACTAGCCATCGCC 57.613 47.619 0.00 0.00 34.57 5.54
3041 11731 1.000163 CAGAATACTAGCCATCGCCGT 60.000 52.381 0.00 0.00 34.57 5.68
3042 11732 1.269998 AGAATACTAGCCATCGCCGTC 59.730 52.381 0.00 0.00 34.57 4.79
3043 11733 0.317479 AATACTAGCCATCGCCGTCC 59.683 55.000 0.00 0.00 34.57 4.79
3045 11735 4.647615 CTAGCCATCGCCGTCCGG 62.648 72.222 0.24 0.24 37.59 5.14
3122 11816 3.771577 AGTCAAACTGGGAGTACCTTG 57.228 47.619 0.00 0.00 41.11 3.61
3123 11817 3.314693 AGTCAAACTGGGAGTACCTTGA 58.685 45.455 0.00 0.00 41.11 3.02
3124 11818 3.714798 AGTCAAACTGGGAGTACCTTGAA 59.285 43.478 0.00 0.00 41.11 2.69
3125 11819 3.813724 GTCAAACTGGGAGTACCTTGAAC 59.186 47.826 0.00 0.00 41.11 3.18
3127 11821 4.080243 TCAAACTGGGAGTACCTTGAACAA 60.080 41.667 0.00 0.00 41.11 2.83
3128 11822 4.724279 AACTGGGAGTACCTTGAACAAT 57.276 40.909 0.00 0.00 41.11 2.71
3129 11823 4.287766 ACTGGGAGTACCTTGAACAATC 57.712 45.455 0.00 0.00 41.11 2.67
3130 11824 3.910627 ACTGGGAGTACCTTGAACAATCT 59.089 43.478 0.00 0.00 41.11 2.40
3131 11825 5.091552 ACTGGGAGTACCTTGAACAATCTA 58.908 41.667 0.00 0.00 41.11 1.98
3132 11826 5.187967 ACTGGGAGTACCTTGAACAATCTAG 59.812 44.000 0.00 0.00 41.11 2.43
3133 11827 4.081087 TGGGAGTACCTTGAACAATCTAGC 60.081 45.833 0.00 0.00 41.11 3.42
3134 11828 4.443621 GGAGTACCTTGAACAATCTAGCC 58.556 47.826 0.00 0.00 0.00 3.93
3136 11830 4.833390 AGTACCTTGAACAATCTAGCCAC 58.167 43.478 0.00 0.00 0.00 5.01
3137 11831 2.699954 ACCTTGAACAATCTAGCCACG 58.300 47.619 0.00 0.00 0.00 4.94
3138 11832 2.009774 CCTTGAACAATCTAGCCACGG 58.990 52.381 0.00 0.00 0.00 4.94
3139 11833 2.615493 CCTTGAACAATCTAGCCACGGT 60.615 50.000 0.00 0.00 0.00 4.83
3140 11834 2.380084 TGAACAATCTAGCCACGGTC 57.620 50.000 0.00 0.00 0.00 4.79
3141 11835 1.621317 TGAACAATCTAGCCACGGTCA 59.379 47.619 0.00 0.00 0.00 4.02
3143 11837 1.557099 ACAATCTAGCCACGGTCAGA 58.443 50.000 0.00 0.00 0.00 3.27
3144 11838 1.478510 ACAATCTAGCCACGGTCAGAG 59.521 52.381 0.00 0.00 0.00 3.35
3145 11839 0.461961 AATCTAGCCACGGTCAGAGC 59.538 55.000 0.00 0.00 0.00 4.09
3146 11840 1.395826 ATCTAGCCACGGTCAGAGCC 61.396 60.000 0.00 0.00 0.00 4.70
3148 11842 2.564553 CTAGCCACGGTCAGAGCCAC 62.565 65.000 0.00 0.00 0.00 5.01
3149 11843 4.314440 GCCACGGTCAGAGCCACA 62.314 66.667 0.00 0.00 0.00 4.17
3151 11845 2.740055 CACGGTCAGAGCCACAGC 60.740 66.667 0.00 0.00 40.32 4.40
3152 11846 3.233980 ACGGTCAGAGCCACAGCA 61.234 61.111 0.00 0.00 43.56 4.41
3153 11847 2.740055 CGGTCAGAGCCACAGCAC 60.740 66.667 0.00 0.00 43.56 4.40
3155 11849 1.670406 GGTCAGAGCCACAGCACAG 60.670 63.158 0.00 0.00 43.56 3.66
3156 11850 2.031616 TCAGAGCCACAGCACAGC 59.968 61.111 0.00 0.00 43.56 4.40
3157 11851 2.281276 CAGAGCCACAGCACAGCA 60.281 61.111 0.00 0.00 43.56 4.41
3158 11852 1.895231 CAGAGCCACAGCACAGCAA 60.895 57.895 0.00 0.00 43.56 3.91
3159 11853 1.895707 AGAGCCACAGCACAGCAAC 60.896 57.895 0.00 0.00 43.56 4.17
3160 11854 1.895707 GAGCCACAGCACAGCAACT 60.896 57.895 0.00 0.00 43.56 3.16
3164 11858 1.270550 GCCACAGCACAGCAACTTTAT 59.729 47.619 0.00 0.00 39.53 1.40
3165 11859 2.487762 GCCACAGCACAGCAACTTTATA 59.512 45.455 0.00 0.00 39.53 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.929806 TAGAATCCAGTCGTGCGCGT 61.930 55.000 20.50 0.00 39.49 6.01
60 61 7.057264 AGGATATCTCGATCGAATAGAATCCA 58.943 38.462 28.06 11.63 33.74 3.41
76 77 4.906747 AGATCTTGCCCAAGGATATCTC 57.093 45.455 8.06 0.00 38.88 2.75
81 82 2.103263 GTCGTAGATCTTGCCCAAGGAT 59.897 50.000 0.00 1.48 40.67 3.24
104 105 4.382160 GCTGTCTACGTGTTCTGAAACTAC 59.618 45.833 0.00 0.00 36.30 2.73
110 111 1.269723 CTGGCTGTCTACGTGTTCTGA 59.730 52.381 0.00 0.00 0.00 3.27
166 167 2.346803 GTCCTTGTGCTCTTATCGCAA 58.653 47.619 0.00 0.00 39.39 4.85
170 171 2.027192 TGGTGGTCCTTGTGCTCTTATC 60.027 50.000 0.00 0.00 34.23 1.75
188 189 3.767630 GAGGCAACGGTGTGGTGGT 62.768 63.158 0.66 0.00 46.39 4.16
193 194 2.978010 GGTGGAGGCAACGGTGTG 60.978 66.667 0.66 0.00 46.39 3.82
247 248 4.692475 GTTGTGGGTAGCGCGGGT 62.692 66.667 8.83 0.00 0.00 5.28
256 257 4.265056 GAGCCGTGGGTTGTGGGT 62.265 66.667 0.00 0.00 35.91 4.51
279 280 1.134965 GTCGGTTCTGTCAGATCTGGG 60.135 57.143 22.42 12.75 0.00 4.45
330 331 2.906897 CTGCGTGGCAAAGGTGGT 60.907 61.111 0.00 0.00 38.41 4.16
443 444 2.281070 CGTCAAGTGCTGGCCTGT 60.281 61.111 11.69 0.00 0.00 4.00
453 454 3.515316 CTCGGGTGTGGCGTCAAGT 62.515 63.158 0.00 0.00 0.00 3.16
537 538 1.345741 TCTTACTGCTGCTGCTCAAGT 59.654 47.619 17.00 13.64 40.48 3.16
540 541 0.681175 TGTCTTACTGCTGCTGCTCA 59.319 50.000 17.00 0.00 40.48 4.26
556 557 1.589196 GCCTCCTCGTATGCGTGTC 60.589 63.158 2.37 0.00 39.49 3.67
564 565 3.075005 GTGGCCTGCCTCCTCGTA 61.075 66.667 9.97 0.00 36.94 3.43
584 585 4.760047 CGGTTCGGCAGGTCAGGG 62.760 72.222 0.00 0.00 0.00 4.45
627 629 2.922503 TCTCCCTCAGCAACGGCA 60.923 61.111 0.00 0.00 44.61 5.69
628 630 2.435059 GTCTCCCTCAGCAACGGC 60.435 66.667 0.00 0.00 41.61 5.68
629 631 1.216710 GAGTCTCCCTCAGCAACGG 59.783 63.158 0.00 0.00 40.17 4.44
631 633 1.216710 CGGAGTCTCCCTCAGCAAC 59.783 63.158 13.54 0.00 42.40 4.17
632 634 1.228894 ACGGAGTCTCCCTCAGCAA 60.229 57.895 13.54 0.00 42.40 3.91
633 635 2.441051 ACGGAGTCTCCCTCAGCA 59.559 61.111 13.54 0.00 42.40 4.41
650 653 4.308458 CACGGACCTTGGGCACGA 62.308 66.667 9.68 0.00 0.00 4.35
676 702 2.034879 CAAAGTCGCTGTGGCCGAT 61.035 57.895 0.00 0.00 34.44 4.18
683 709 0.320771 CTGTAGGGCAAAGTCGCTGT 60.321 55.000 0.00 0.00 0.00 4.40
689 715 0.111253 AGCAAGCTGTAGGGCAAAGT 59.889 50.000 0.00 0.00 34.17 2.66
693 719 2.671070 GGAGCAAGCTGTAGGGCA 59.329 61.111 0.00 0.00 34.17 5.36
741 767 4.393155 CTAGCGCCACTGCCACCA 62.393 66.667 2.29 0.00 34.65 4.17
748 774 1.610886 GGAAAGAAACCTAGCGCCACT 60.611 52.381 2.29 0.00 0.00 4.00
750 776 0.672401 CGGAAAGAAACCTAGCGCCA 60.672 55.000 2.29 0.00 0.00 5.69
764 790 9.153721 ACTCAACGTTATAATTACATTCGGAAA 57.846 29.630 0.00 0.00 0.00 3.13
785 811 4.164981 ACCTCAGTACCCACATTACTCAA 58.835 43.478 0.00 0.00 0.00 3.02
827 853 5.526111 ACTTTACACTTGTACGTGCTGAAAT 59.474 36.000 4.97 0.00 38.45 2.17
830 856 3.799963 CACTTTACACTTGTACGTGCTGA 59.200 43.478 4.97 0.00 38.45 4.26
831 857 3.554324 ACACTTTACACTTGTACGTGCTG 59.446 43.478 4.97 0.00 38.45 4.41
832 858 3.788937 ACACTTTACACTTGTACGTGCT 58.211 40.909 4.97 0.00 38.45 4.40
833 859 4.201744 ACAACACTTTACACTTGTACGTGC 60.202 41.667 0.00 0.00 38.45 5.34
834 860 5.459110 ACAACACTTTACACTTGTACGTG 57.541 39.130 0.00 12.90 40.67 4.49
835 861 7.306167 CGATAACAACACTTTACACTTGTACGT 60.306 37.037 0.00 0.00 0.00 3.57
836 862 6.999627 CGATAACAACACTTTACACTTGTACG 59.000 38.462 0.00 0.00 0.00 3.67
837 863 7.042523 ACCGATAACAACACTTTACACTTGTAC 60.043 37.037 0.00 0.00 0.00 2.90
838 864 6.985645 ACCGATAACAACACTTTACACTTGTA 59.014 34.615 0.00 0.00 0.00 2.41
839 865 5.818857 ACCGATAACAACACTTTACACTTGT 59.181 36.000 0.00 0.00 0.00 3.16
840 866 6.295039 ACCGATAACAACACTTTACACTTG 57.705 37.500 0.00 0.00 0.00 3.16
842 868 8.500773 CATTTACCGATAACAACACTTTACACT 58.499 33.333 0.00 0.00 0.00 3.55
843 869 8.284693 ACATTTACCGATAACAACACTTTACAC 58.715 33.333 0.00 0.00 0.00 2.90
844 870 8.380743 ACATTTACCGATAACAACACTTTACA 57.619 30.769 0.00 0.00 0.00 2.41
845 871 7.959109 GGACATTTACCGATAACAACACTTTAC 59.041 37.037 0.00 0.00 0.00 2.01
847 873 6.713450 AGGACATTTACCGATAACAACACTTT 59.287 34.615 0.00 0.00 0.00 2.66
848 874 6.148811 CAGGACATTTACCGATAACAACACTT 59.851 38.462 0.00 0.00 0.00 3.16
849 875 5.642063 CAGGACATTTACCGATAACAACACT 59.358 40.000 0.00 0.00 0.00 3.55
852 878 4.493545 CGCAGGACATTTACCGATAACAAC 60.494 45.833 0.00 0.00 0.00 3.32
853 879 3.619483 CGCAGGACATTTACCGATAACAA 59.381 43.478 0.00 0.00 0.00 2.83
855 881 2.033151 GCGCAGGACATTTACCGATAAC 60.033 50.000 0.30 0.00 0.00 1.89
856 882 2.159014 AGCGCAGGACATTTACCGATAA 60.159 45.455 11.47 0.00 0.00 1.75
859 885 0.036765 AAGCGCAGGACATTTACCGA 60.037 50.000 11.47 0.00 0.00 4.69
860 886 0.802494 AAAGCGCAGGACATTTACCG 59.198 50.000 11.47 0.00 0.00 4.02
861 887 1.202031 CGAAAGCGCAGGACATTTACC 60.202 52.381 11.47 0.00 0.00 2.85
862 888 1.730064 TCGAAAGCGCAGGACATTTAC 59.270 47.619 11.47 0.00 37.46 2.01
864 890 0.798776 CTCGAAAGCGCAGGACATTT 59.201 50.000 11.47 0.00 37.46 2.32
865 891 1.639298 GCTCGAAAGCGCAGGACATT 61.639 55.000 11.47 0.00 42.44 2.71
866 892 2.103042 GCTCGAAAGCGCAGGACAT 61.103 57.895 11.47 0.00 42.44 3.06
1018 1102 3.563223 AGGAAAGATGAGGATGCCAATG 58.437 45.455 0.00 0.00 0.00 2.82
1185 1319 2.355115 GGGGTTCGCCATCAAGGT 59.645 61.111 0.99 0.00 40.61 3.50
1284 1421 3.474570 GACATGGAGCTCGGCCCT 61.475 66.667 7.83 0.00 0.00 5.19
1347 1496 1.012086 CACGTCGGACTCTTCGGATA 58.988 55.000 6.57 0.00 33.95 2.59
1673 1849 0.389025 TGAGTTGAGCTTGAGCACGA 59.611 50.000 5.70 0.00 45.16 4.35
1985 2578 9.177304 GATAAATTGTGATCATAATGCACACTG 57.823 33.333 17.26 0.00 41.72 3.66
2008 2898 9.566432 AAACAAAACCCTTTGCATTAATTGATA 57.434 25.926 0.00 0.00 44.96 2.15
2049 7521 4.858140 GCATACATCAGACTGATCAGATCG 59.142 45.833 29.27 15.31 34.28 3.69
2267 7830 5.094812 TGATGCGACAAATAAATTCTGCAC 58.905 37.500 0.00 0.00 33.47 4.57
2495 8496 1.419762 TGGCAGGTACACATGAGTTGT 59.580 47.619 0.00 0.00 39.91 3.32
2547 9500 5.953183 TGATTTGATACTGACACCATTTGC 58.047 37.500 0.00 0.00 0.00 3.68
2557 9510 6.714356 TGACATGTGGTTTGATTTGATACTGA 59.286 34.615 1.15 0.00 0.00 3.41
2700 9658 4.867047 AGTTGACGCTATGAGTTCAGATTG 59.133 41.667 0.00 0.00 0.00 2.67
2716 9678 6.527722 CCCATTGTAATTGATTGAAGTTGACG 59.472 38.462 0.00 0.00 0.00 4.35
2986 10848 7.309438 GCTGGAAGTTTTGAAGTATTGATCCTT 60.309 37.037 0.00 0.00 35.30 3.36
2988 10850 6.071952 TGCTGGAAGTTTTGAAGTATTGATCC 60.072 38.462 0.00 0.00 35.30 3.36
3102 11796 3.314693 TCAAGGTACTCCCAGTTTGACT 58.685 45.455 0.00 0.00 38.49 3.41
3122 11816 2.094182 TCTGACCGTGGCTAGATTGTTC 60.094 50.000 0.00 0.00 0.00 3.18
3123 11817 1.899814 TCTGACCGTGGCTAGATTGTT 59.100 47.619 0.00 0.00 0.00 2.83
3124 11818 1.478510 CTCTGACCGTGGCTAGATTGT 59.521 52.381 0.00 0.00 0.00 2.71
3125 11819 1.804372 GCTCTGACCGTGGCTAGATTG 60.804 57.143 0.00 0.00 0.00 2.67
3127 11821 1.395826 GGCTCTGACCGTGGCTAGAT 61.396 60.000 0.00 0.00 0.00 1.98
3128 11822 2.052690 GGCTCTGACCGTGGCTAGA 61.053 63.158 0.00 0.00 0.00 2.43
3129 11823 2.351244 TGGCTCTGACCGTGGCTAG 61.351 63.158 0.00 0.00 33.34 3.42
3130 11824 2.283604 TGGCTCTGACCGTGGCTA 60.284 61.111 0.00 0.00 33.34 3.93
3131 11825 4.008933 GTGGCTCTGACCGTGGCT 62.009 66.667 0.00 0.00 33.34 4.75
3132 11826 4.314440 TGTGGCTCTGACCGTGGC 62.314 66.667 0.00 0.00 0.00 5.01
3133 11827 2.047844 CTGTGGCTCTGACCGTGG 60.048 66.667 0.00 0.00 0.00 4.94
3134 11828 2.740055 GCTGTGGCTCTGACCGTG 60.740 66.667 0.00 0.00 35.22 4.94
3136 11830 2.740055 GTGCTGTGGCTCTGACCG 60.740 66.667 0.00 0.00 39.59 4.79
3137 11831 1.670406 CTGTGCTGTGGCTCTGACC 60.670 63.158 0.00 0.00 39.59 4.02
3138 11832 2.323580 GCTGTGCTGTGGCTCTGAC 61.324 63.158 0.00 0.00 39.59 3.51
3139 11833 2.031616 GCTGTGCTGTGGCTCTGA 59.968 61.111 0.00 0.00 39.59 3.27
3140 11834 1.895231 TTGCTGTGCTGTGGCTCTG 60.895 57.895 0.00 0.00 39.59 3.35
3141 11835 1.895707 GTTGCTGTGCTGTGGCTCT 60.896 57.895 0.00 0.00 39.59 4.09
3143 11837 1.039233 AAAGTTGCTGTGCTGTGGCT 61.039 50.000 0.00 0.00 39.59 4.75
3144 11838 0.667993 TAAAGTTGCTGTGCTGTGGC 59.332 50.000 0.00 0.00 39.26 5.01


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

AutoCloner maintained by Alex Coulton.