Multiple sequence alignment - TraesCS1D01G407600

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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 TraesCS1D01G407600 chr1D 100.000 3014 0 0 1 3014 470521250 470524263 0.000000e+00 5566.0
1 TraesCS1D01G407600 chr1D 87.500 272 27 3 994 1261 470530191 470530459 1.050000e-79 307.0
2 TraesCS1D01G407600 chr1D 89.427 227 18 2 2788 3014 470199719 470199499 6.360000e-72 281.0
3 TraesCS1D01G407600 chr1D 88.942 208 17 4 2044 2251 470535853 470536054 4.990000e-63 252.0
4 TraesCS1D01G407600 chr1D 87.500 224 17 6 43 265 460596032 460596245 6.450000e-62 248.0
5 TraesCS1D01G407600 chr1D 92.157 153 12 0 1295 1447 470539981 470540133 1.820000e-52 217.0
6 TraesCS1D01G407600 chr1D 91.339 127 11 0 1489 1615 470530623 470530749 1.110000e-39 174.0
7 TraesCS1D01G407600 chr1D 83.246 191 21 5 1406 1596 460596690 460596869 6.680000e-37 165.0
8 TraesCS1D01G407600 chr1D 95.789 95 4 0 2920 3014 470191282 470191188 1.450000e-33 154.0
9 TraesCS1D01G407600 chr1D 78.641 206 26 11 2265 2455 470536366 470536568 1.470000e-23 121.0
10 TraesCS1D01G407600 chr1D 75.714 210 30 7 2265 2456 470544507 470544713 5.350000e-13 86.1
11 TraesCS1D01G407600 chr1A 88.813 2199 110 42 1 2170 564116029 564118120 0.000000e+00 2573.0
12 TraesCS1D01G407600 chr1A 82.039 206 18 12 2265 2456 564130659 564130859 1.120000e-34 158.0
13 TraesCS1D01G407600 chr1A 87.255 102 13 0 1776 1877 564142793 564142894 1.900000e-22 117.0
14 TraesCS1D01G407600 chr1A 77.251 211 25 10 2265 2456 564140008 564140214 5.320000e-18 102.0
15 TraesCS1D01G407600 chr1B 89.736 1588 75 43 1269 2789 653235641 653237207 0.000000e+00 1949.0
16 TraesCS1D01G407600 chr1B 86.917 879 39 30 3 845 653234388 653235226 0.000000e+00 917.0
17 TraesCS1D01G407600 chr1B 81.552 786 82 34 994 1755 653263930 653264676 9.310000e-165 590.0
18 TraesCS1D01G407600 chr1B 83.821 513 58 13 1047 1551 653321493 653321988 5.890000e-127 464.0
19 TraesCS1D01G407600 chr1B 95.781 237 8 2 2780 3014 653237231 653237467 6.100000e-102 381.0
20 TraesCS1D01G407600 chr1B 84.450 373 26 15 2660 3014 652576208 652575850 3.720000e-89 339.0
21 TraesCS1D01G407600 chr1B 89.764 254 15 5 2761 3014 652634463 652634221 6.270000e-82 315.0
22 TraesCS1D01G407600 chr1B 90.222 225 16 2 2790 3014 652640159 652639941 3.800000e-74 289.0
23 TraesCS1D01G407600 chr1B 82.534 292 47 2 995 1286 469173594 469173881 1.390000e-63 254.0
24 TraesCS1D01G407600 chr1B 87.302 189 24 0 2265 2453 683109278 683109466 1.820000e-52 217.0
25 TraesCS1D01G407600 chr1B 84.103 195 28 2 2265 2456 653683369 653683563 5.130000e-43 185.0
26 TraesCS1D01G407600 chr1B 80.952 252 27 13 1004 1236 653312277 653312526 2.390000e-41 180.0
27 TraesCS1D01G407600 chr1B 84.375 192 20 7 2265 2456 653526607 653526788 2.390000e-41 180.0
28 TraesCS1D01G407600 chr1B 80.786 229 21 15 2568 2789 652577477 652577265 1.120000e-34 158.0
29 TraesCS1D01G407600 chr1B 86.713 143 13 3 2786 2927 652577234 652577097 1.450000e-33 154.0
30 TraesCS1D01G407600 chr1B 77.143 210 27 10 2265 2456 653836226 653836020 5.320000e-18 102.0
31 TraesCS1D01G407600 chr1B 88.710 62 2 2 1692 1752 653322155 653322212 1.500000e-08 71.3
32 TraesCS1D01G407600 chr1B 91.489 47 4 0 2476 2522 652577538 652577492 6.970000e-07 65.8
33 TraesCS1D01G407600 chr7D 83.480 454 53 7 995 1430 561004496 561004945 1.300000e-108 403.0
34 TraesCS1D01G407600 chr7B 83.493 418 50 6 1028 1430 608904510 608904923 3.670000e-99 372.0
35 TraesCS1D01G407600 chr3B 81.153 451 63 13 995 1430 672672156 672672599 2.880000e-90 342.0
36 TraesCS1D01G407600 chr2B 79.393 461 65 18 995 1433 234826806 234826354 6.320000e-77 298.0
37 TraesCS1D01G407600 chr2A 79.457 258 34 6 1157 1396 138143257 138143513 6.680000e-37 165.0
38 TraesCS1D01G407600 chr3A 79.231 260 35 4 1157 1397 80495170 80495429 2.400000e-36 163.0
39 TraesCS1D01G407600 chr7A 87.302 63 7 1 1106 1168 645092354 645092415 1.500000e-08 71.3


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 TraesCS1D01G407600 chr1D 470521250 470524263 3013 False 5566.000000 5566 100.000000 1 3014 1 chr1D.!!$F1 3013
1 TraesCS1D01G407600 chr1D 470530191 470530749 558 False 240.500000 307 89.419500 994 1615 2 chr1D.!!$F4 621
2 TraesCS1D01G407600 chr1D 460596032 460596869 837 False 206.500000 248 85.373000 43 1596 2 chr1D.!!$F3 1553
3 TraesCS1D01G407600 chr1A 564116029 564118120 2091 False 2573.000000 2573 88.813000 1 2170 1 chr1A.!!$F1 2169
4 TraesCS1D01G407600 chr1B 653234388 653237467 3079 False 1082.333333 1949 90.811333 3 3014 3 chr1B.!!$F7 3011
5 TraesCS1D01G407600 chr1B 653263930 653264676 746 False 590.000000 590 81.552000 994 1755 1 chr1B.!!$F2 761
6 TraesCS1D01G407600 chr1B 653321493 653322212 719 False 267.650000 464 86.265500 1047 1752 2 chr1B.!!$F8 705

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
485 513 0.181350 ATCCGGCTTGCTAAAGGAGG 59.819 55.0 0.0 0.0 34.14 4.30 F
1526 1654 0.534203 TCACCAACTTCCAGAACGCC 60.534 55.0 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1744 0.179094 GTTCGTCCATGTATCCGCCA 60.179 55.0 0.0 0.0 0.00 5.69 R
2818 3103 0.107312 CTATGCAAGCTGCTCCCTGT 60.107 55.0 1.0 0.0 45.31 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
38 39 9.604626 CAAAATGAACACAAAACTAAAGCAAAA 57.395 25.926 0.00 0.00 0.00 2.44
39 40 9.824534 AAAATGAACACAAAACTAAAGCAAAAG 57.175 25.926 0.00 0.00 0.00 2.27
40 41 8.770438 AATGAACACAAAACTAAAGCAAAAGA 57.230 26.923 0.00 0.00 0.00 2.52
48 49 8.510505 ACAAAACTAAAGCAAAAGAAAAATGCA 58.489 25.926 0.00 0.00 42.45 3.96
132 133 3.242712 CACGATCAACTTTGCCAAACAAC 59.757 43.478 0.00 0.00 38.23 3.32
155 156 0.317770 AATGGCGCAGTTGAACAACG 60.318 50.000 10.83 1.65 45.50 4.10
171 172 2.510238 CGCCCAGCTTTCTCCGAG 60.510 66.667 0.00 0.00 0.00 4.63
176 177 1.807573 CAGCTTTCTCCGAGACCGC 60.808 63.158 0.00 3.91 0.00 5.68
177 178 1.979693 AGCTTTCTCCGAGACCGCT 60.980 57.895 12.64 12.64 0.00 5.52
178 179 1.079750 GCTTTCTCCGAGACCGCTT 60.080 57.895 0.00 0.00 0.00 4.68
179 180 0.670854 GCTTTCTCCGAGACCGCTTT 60.671 55.000 0.00 0.00 0.00 3.51
189 190 2.157863 CGAGACCGCTTTCTTTCTTTCC 59.842 50.000 0.00 0.00 0.00 3.13
255 257 2.350197 GCATCCAACAATATCTCGCTGC 60.350 50.000 0.00 0.00 0.00 5.25
325 335 0.753262 CCTTCCACTCCATACCCTCG 59.247 60.000 0.00 0.00 0.00 4.63
385 395 4.643387 ACGCCCAACCCTGCTCAC 62.643 66.667 0.00 0.00 0.00 3.51
485 513 0.181350 ATCCGGCTTGCTAAAGGAGG 59.819 55.000 0.00 0.00 34.14 4.30
486 514 1.452108 CCGGCTTGCTAAAGGAGGG 60.452 63.158 0.00 0.00 33.68 4.30
487 515 1.452108 CGGCTTGCTAAAGGAGGGG 60.452 63.158 0.00 0.00 33.68 4.79
568 596 1.098869 TGCGTTCCTGAACTTGCAAA 58.901 45.000 0.00 0.00 39.08 3.68
658 690 0.955428 GGCGTTGATTGGTCTCTGCA 60.955 55.000 0.00 0.00 0.00 4.41
793 847 1.826054 TAGCGGGAGAGAGCAGAGC 60.826 63.158 0.00 0.00 35.48 4.09
795 849 3.535962 CGGGAGAGAGCAGAGCCC 61.536 72.222 0.00 0.00 35.40 5.19
820 877 1.820519 GCTTGCCCTGTTCATTCATCA 59.179 47.619 0.00 0.00 0.00 3.07
822 879 1.838112 TGCCCTGTTCATTCATCACC 58.162 50.000 0.00 0.00 0.00 4.02
832 889 5.221904 TGTTCATTCATCACCTTCTCCTTCA 60.222 40.000 0.00 0.00 0.00 3.02
864 981 2.654404 GTGTAGGCGCGTCGATCC 60.654 66.667 5.57 0.00 0.00 3.36
874 991 1.009829 GCGTCGATCCATCTTGCTTT 58.990 50.000 0.00 0.00 0.00 3.51
899 1016 5.284079 GTTTGATCTTTTGCTGCTCAAGAA 58.716 37.500 15.05 1.54 35.84 2.52
905 1027 1.597742 TTGCTGCTCAAGAAGTCCAC 58.402 50.000 0.00 0.00 0.00 4.02
906 1028 0.761187 TGCTGCTCAAGAAGTCCACT 59.239 50.000 0.00 0.00 0.00 4.00
907 1029 1.141657 TGCTGCTCAAGAAGTCCACTT 59.858 47.619 0.00 0.00 39.23 3.16
908 1030 2.225467 GCTGCTCAAGAAGTCCACTTT 58.775 47.619 0.00 0.00 36.11 2.66
909 1031 2.031333 GCTGCTCAAGAAGTCCACTTTG 60.031 50.000 0.00 0.00 36.11 2.77
910 1032 2.551459 CTGCTCAAGAAGTCCACTTTGG 59.449 50.000 0.00 0.00 39.43 3.28
911 1033 2.092429 TGCTCAAGAAGTCCACTTTGGT 60.092 45.455 0.00 0.00 39.03 3.67
912 1034 2.952310 GCTCAAGAAGTCCACTTTGGTT 59.048 45.455 0.00 0.00 39.03 3.67
913 1035 3.003793 GCTCAAGAAGTCCACTTTGGTTC 59.996 47.826 0.00 0.00 39.03 3.62
914 1036 4.199310 CTCAAGAAGTCCACTTTGGTTCA 58.801 43.478 0.00 0.00 39.03 3.18
915 1037 4.199310 TCAAGAAGTCCACTTTGGTTCAG 58.801 43.478 0.00 0.00 39.03 3.02
916 1038 3.933861 AGAAGTCCACTTTGGTTCAGT 57.066 42.857 0.00 0.00 39.03 3.41
917 1039 4.236527 AGAAGTCCACTTTGGTTCAGTT 57.763 40.909 0.00 0.00 39.03 3.16
918 1040 4.200092 AGAAGTCCACTTTGGTTCAGTTC 58.800 43.478 0.00 0.00 39.03 3.01
919 1041 3.644966 AGTCCACTTTGGTTCAGTTCA 57.355 42.857 0.00 0.00 39.03 3.18
929 1051 1.269257 GGTTCAGTTCAGTTGCTTGCC 60.269 52.381 0.00 0.00 0.00 4.52
930 1052 1.405105 GTTCAGTTCAGTTGCTTGCCA 59.595 47.619 0.00 0.00 0.00 4.92
949 1071 3.691609 GCCATTTTCGATCTTCTTGGAGT 59.308 43.478 0.00 0.00 0.00 3.85
969 1091 0.686789 TGCTTGCTCTGTTCCTGCTA 59.313 50.000 0.00 0.00 0.00 3.49
1143 1265 2.161609 CGTTCAGCCATTGGAGGTAAAC 59.838 50.000 6.95 2.34 0.00 2.01
1150 1272 3.745975 GCCATTGGAGGTAAACAAAAAGC 59.254 43.478 6.95 0.00 0.00 3.51
1266 1392 5.871524 CACAACTGCTATCACTGACTAACAT 59.128 40.000 0.00 0.00 0.00 2.71
1355 1483 2.726351 CGCCTTCCTCCTCTGGTCC 61.726 68.421 0.00 0.00 0.00 4.46
1370 1498 2.754658 TCCTCCGTCGGCTTCCTC 60.755 66.667 6.34 0.00 0.00 3.71
1518 1646 1.079503 GCTGTCGATCACCAACTTCC 58.920 55.000 0.00 0.00 0.00 3.46
1526 1654 0.534203 TCACCAACTTCCAGAACGCC 60.534 55.000 0.00 0.00 0.00 5.68
1629 1761 2.099141 CAGGTATGGCGGATACATGG 57.901 55.000 9.97 0.00 42.94 3.66
1632 1764 1.671850 GGTATGGCGGATACATGGACG 60.672 57.143 0.00 0.00 39.08 4.79
1638 1770 1.567504 CGGATACATGGACGAACACC 58.432 55.000 0.00 0.00 0.00 4.16
1643 1775 2.631160 ACATGGACGAACACCTTGAA 57.369 45.000 0.00 0.00 36.71 2.69
1646 1778 3.888930 ACATGGACGAACACCTTGAATTT 59.111 39.130 0.00 0.00 36.71 1.82
1649 1781 3.146847 GGACGAACACCTTGAATTTCCT 58.853 45.455 0.00 0.00 0.00 3.36
1653 1785 4.216257 ACGAACACCTTGAATTTCCTCATG 59.784 41.667 0.00 0.00 0.00 3.07
1654 1786 4.455533 CGAACACCTTGAATTTCCTCATGA 59.544 41.667 0.00 0.00 0.00 3.07
1659 1851 6.032094 CACCTTGAATTTCCTCATGAATTCG 58.968 40.000 11.41 3.03 31.67 3.34
1669 1861 4.100529 CCTCATGAATTCGTGATGTTTGC 58.899 43.478 26.52 0.00 40.69 3.68
1672 1864 4.455190 TCATGAATTCGTGATGTTTGCTGA 59.545 37.500 23.51 0.83 37.00 4.26
1673 1865 4.145876 TGAATTCGTGATGTTTGCTGAC 57.854 40.909 0.04 0.00 0.00 3.51
1688 1889 4.871933 TGCTGACTGATCTCTTGTTGTA 57.128 40.909 0.00 0.00 0.00 2.41
2023 2240 4.538233 TGCCGTAGCATGACCATG 57.462 55.556 0.00 5.67 46.52 3.66
2024 2241 1.153188 TGCCGTAGCATGACCATGG 60.153 57.895 11.19 11.19 46.52 3.66
2025 2242 1.893808 GCCGTAGCATGACCATGGG 60.894 63.158 18.09 0.00 39.16 4.00
2026 2243 1.829456 CCGTAGCATGACCATGGGA 59.171 57.895 18.09 1.83 39.16 4.37
2028 2245 0.882042 CGTAGCATGACCATGGGAGC 60.882 60.000 18.09 13.77 39.16 4.70
2029 2246 0.471617 GTAGCATGACCATGGGAGCT 59.528 55.000 18.09 19.86 39.16 4.09
2030 2247 0.761187 TAGCATGACCATGGGAGCTC 59.239 55.000 20.81 4.71 39.16 4.09
2084 2303 2.165167 CAGTTCATGTGTGCTTGGGAT 58.835 47.619 0.00 0.00 0.00 3.85
2087 2306 0.889994 TCATGTGTGCTTGGGATTGC 59.110 50.000 0.00 0.00 0.00 3.56
2147 2372 6.626302 ACAGCTTTTCAGTGAGAGTAGATAC 58.374 40.000 0.00 0.00 0.00 2.24
2150 2375 7.763528 CAGCTTTTCAGTGAGAGTAGATACAAT 59.236 37.037 0.00 0.00 0.00 2.71
2164 2389 5.916661 AGATACAATACAACTCTCGGTGT 57.083 39.130 0.00 0.00 0.00 4.16
2199 2424 1.965643 CCGGGGATTGCATGATCAATT 59.034 47.619 0.00 0.00 36.85 2.32
2213 2438 9.955208 TGCATGATCAATTAACATGAGATTTAC 57.045 29.630 17.09 4.37 42.41 2.01
2214 2439 9.110617 GCATGATCAATTAACATGAGATTTACG 57.889 33.333 17.09 0.00 42.41 3.18
2222 2447 8.766000 ATTAACATGAGATTTACGTACACACA 57.234 30.769 0.00 0.00 0.00 3.72
2254 2479 3.499918 CAGTGAGACATTCCAGGAACAAC 59.500 47.826 3.18 0.00 0.00 3.32
2269 2494 5.527214 CAGGAACAACAGTCACAGTATCAAA 59.473 40.000 0.00 0.00 0.00 2.69
2334 2559 3.322466 CGACTTCCCCTGCCACCT 61.322 66.667 0.00 0.00 0.00 4.00
2368 2603 2.094894 TCGAGTCGGTGTAGACGAAATC 59.905 50.000 13.54 0.00 45.26 2.17
2369 2604 2.438583 GAGTCGGTGTAGACGAAATCG 58.561 52.381 0.48 0.48 45.26 3.34
2378 2613 1.078759 AGACGAAATCGAGCAAGGCG 61.079 55.000 10.16 0.00 43.02 5.52
2394 2629 1.574428 GCGTTGAACACATTCGGCT 59.426 52.632 0.00 0.00 37.69 5.52
2493 2729 2.030371 TGGCAACTTGAGCATGAAACA 58.970 42.857 0.00 0.00 37.61 2.83
2504 2740 2.290641 AGCATGAAACAACCTGACGTTC 59.709 45.455 0.00 0.00 29.93 3.95
2508 2744 2.680841 TGAAACAACCTGACGTTCAAGG 59.319 45.455 10.41 10.41 29.93 3.61
2511 2757 0.535102 CAACCTGACGTTCAAGGGCT 60.535 55.000 14.98 2.23 29.93 5.19
2515 2761 1.002087 CCTGACGTTCAAGGGCTACTT 59.998 52.381 5.26 0.00 41.00 2.24
2517 2763 3.118738 CCTGACGTTCAAGGGCTACTTAT 60.119 47.826 5.26 0.00 37.29 1.73
2532 2778 5.221461 GGCTACTTATTTGCTAGCTACAGGA 60.221 44.000 17.23 0.37 34.48 3.86
2540 2786 4.063998 TGCTAGCTACAGGATGACAATG 57.936 45.455 17.23 0.00 39.69 2.82
2541 2787 2.805099 GCTAGCTACAGGATGACAATGC 59.195 50.000 7.70 0.00 39.69 3.56
2560 2806 2.172505 TGCAGACCAAGAAAGAGACCAA 59.827 45.455 0.00 0.00 0.00 3.67
2568 2814 3.228188 AGAAAGAGACCAACATGCCAA 57.772 42.857 0.00 0.00 0.00 4.52
2569 2815 3.565307 AGAAAGAGACCAACATGCCAAA 58.435 40.909 0.00 0.00 0.00 3.28
2570 2816 3.571401 AGAAAGAGACCAACATGCCAAAG 59.429 43.478 0.00 0.00 0.00 2.77
2571 2817 2.957402 AGAGACCAACATGCCAAAGA 57.043 45.000 0.00 0.00 0.00 2.52
2572 2818 3.446442 AGAGACCAACATGCCAAAGAT 57.554 42.857 0.00 0.00 0.00 2.40
2573 2819 4.574674 AGAGACCAACATGCCAAAGATA 57.425 40.909 0.00 0.00 0.00 1.98
2574 2820 4.521146 AGAGACCAACATGCCAAAGATAG 58.479 43.478 0.00 0.00 0.00 2.08
2575 2821 4.018960 AGAGACCAACATGCCAAAGATAGT 60.019 41.667 0.00 0.00 0.00 2.12
2576 2822 5.189736 AGAGACCAACATGCCAAAGATAGTA 59.810 40.000 0.00 0.00 0.00 1.82
2577 2823 5.431765 AGACCAACATGCCAAAGATAGTAG 58.568 41.667 0.00 0.00 0.00 2.57
2578 2824 4.526970 ACCAACATGCCAAAGATAGTAGG 58.473 43.478 0.00 0.00 0.00 3.18
2595 2841 2.431954 AGGCAGATAAGCAGCAACAT 57.568 45.000 0.00 0.00 35.83 2.71
2597 2843 1.066605 GGCAGATAAGCAGCAACATGG 59.933 52.381 0.00 0.00 35.83 3.66
2602 2848 4.624024 CAGATAAGCAGCAACATGGTTTTG 59.376 41.667 0.00 0.00 41.01 2.44
2629 2879 3.354948 TTCATCCACAGTAGCAGCAAT 57.645 42.857 0.00 0.00 0.00 3.56
2735 2986 6.201044 CACTTACACAGAGTAACCAAGTTCAG 59.799 42.308 0.00 0.00 37.77 3.02
2768 3019 2.751436 GCATTCCCGGCTTGCAGA 60.751 61.111 14.38 0.00 36.40 4.26
2782 3033 3.503748 GCTTGCAGAATAACCACAGAACT 59.496 43.478 0.00 0.00 0.00 3.01
2795 3080 4.762765 ACCACAGAACTACAACAACAACAA 59.237 37.500 0.00 0.00 0.00 2.83
2817 3102 4.630644 CCATAGCATGGTCAGATAACCT 57.369 45.455 0.00 0.00 45.54 3.50
2818 3103 5.745312 CCATAGCATGGTCAGATAACCTA 57.255 43.478 0.00 0.00 45.54 3.08
2933 3219 0.742990 CGCACCGCTTCCAGGAAATA 60.743 55.000 2.72 0.00 0.00 1.40
2989 3275 2.232941 TGGAATAGACGCCGAAAGAAGT 59.767 45.455 0.00 0.00 0.00 3.01
2990 3276 2.858941 GGAATAGACGCCGAAAGAAGTC 59.141 50.000 0.00 0.00 37.50 3.01
2991 3277 3.429135 GGAATAGACGCCGAAAGAAGTCT 60.429 47.826 0.00 2.50 44.96 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.604626 TTTTGCTTTAGTTTTGTGTTCATTTTG 57.395 25.926 0.00 0.00 0.00 2.44
48 49 1.941975 GCTGCTTTTGTTTGTGCCATT 59.058 42.857 0.00 0.00 0.00 3.16
132 133 0.109597 GTTCAACTGCGCCATTGAGG 60.110 55.000 19.10 0.00 36.26 3.86
155 156 1.448717 GTCTCGGAGAAAGCTGGGC 60.449 63.158 9.72 0.00 34.09 5.36
171 172 1.399855 GCGGAAAGAAAGAAAGCGGTC 60.400 52.381 0.00 0.00 0.00 4.79
202 203 8.703522 GGCATCTAGCGAGGGATTTTATCCTT 62.704 46.154 5.74 0.00 46.56 3.36
203 204 7.318278 GGCATCTAGCGAGGGATTTTATCCT 62.318 48.000 5.74 0.00 46.56 3.24
204 205 5.158618 GGCATCTAGCGAGGGATTTTATCC 61.159 50.000 0.00 0.00 46.61 2.59
276 278 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
277 279 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
278 280 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
342 352 0.598065 GAGCACATTTTTGGCTCGGT 59.402 50.000 0.00 0.00 43.83 4.69
375 385 0.622738 AGATGGGATGTGAGCAGGGT 60.623 55.000 0.00 0.00 0.00 4.34
385 395 4.662966 TGGGATGGAATAAGATGGGATG 57.337 45.455 0.00 0.00 0.00 3.51
485 513 1.268066 GCTAGCTACCACCTATCCCC 58.732 60.000 7.70 0.00 0.00 4.81
486 514 2.011122 TGCTAGCTACCACCTATCCC 57.989 55.000 17.23 0.00 0.00 3.85
487 515 3.702045 CCTATGCTAGCTACCACCTATCC 59.298 52.174 17.23 0.00 0.00 2.59
568 596 1.687368 GGGGAATGCAAGAATCTGGCT 60.687 52.381 11.36 0.00 30.50 4.75
658 690 2.821969 CCTGGCTGAGCTTAAACAATGT 59.178 45.455 3.72 0.00 0.00 2.71
793 847 1.228675 AACAGGGCAAGCTTCTGGG 60.229 57.895 15.73 0.00 33.19 4.45
795 849 1.542492 ATGAACAGGGCAAGCTTCTG 58.458 50.000 11.11 11.11 34.91 3.02
820 877 1.615384 GCAATGGCTGAAGGAGAAGGT 60.615 52.381 0.00 0.00 36.96 3.50
845 902 3.405592 GATCGACGCGCCTACACCA 62.406 63.158 5.73 0.00 0.00 4.17
846 903 2.654404 GATCGACGCGCCTACACC 60.654 66.667 5.73 0.00 0.00 4.16
847 904 2.654404 GGATCGACGCGCCTACAC 60.654 66.667 5.73 0.00 0.00 2.90
848 905 2.402282 GATGGATCGACGCGCCTACA 62.402 60.000 5.73 0.00 0.00 2.74
864 981 6.565247 GCAAAAGATCAAACCAAAGCAAGATG 60.565 38.462 0.00 0.00 0.00 2.90
874 991 2.957680 TGAGCAGCAAAAGATCAAACCA 59.042 40.909 0.00 0.00 0.00 3.67
899 1016 3.054361 ACTGAACTGAACCAAAGTGGACT 60.054 43.478 0.18 0.00 40.96 3.85
905 1027 4.107622 CAAGCAACTGAACTGAACCAAAG 58.892 43.478 0.00 0.00 0.00 2.77
906 1028 3.675775 GCAAGCAACTGAACTGAACCAAA 60.676 43.478 0.00 0.00 0.00 3.28
907 1029 2.159254 GCAAGCAACTGAACTGAACCAA 60.159 45.455 0.00 0.00 0.00 3.67
908 1030 1.405105 GCAAGCAACTGAACTGAACCA 59.595 47.619 0.00 0.00 0.00 3.67
909 1031 1.269257 GGCAAGCAACTGAACTGAACC 60.269 52.381 0.00 0.00 0.00 3.62
910 1032 1.405105 TGGCAAGCAACTGAACTGAAC 59.595 47.619 0.00 0.00 0.00 3.18
911 1033 1.761449 TGGCAAGCAACTGAACTGAA 58.239 45.000 0.00 0.00 0.00 3.02
912 1034 1.985473 ATGGCAAGCAACTGAACTGA 58.015 45.000 0.00 0.00 0.00 3.41
913 1035 2.806608 AATGGCAAGCAACTGAACTG 57.193 45.000 0.00 0.00 0.00 3.16
914 1036 3.721035 GAAAATGGCAAGCAACTGAACT 58.279 40.909 0.00 0.00 0.00 3.01
915 1037 2.472488 CGAAAATGGCAAGCAACTGAAC 59.528 45.455 0.00 0.00 0.00 3.18
916 1038 2.360483 TCGAAAATGGCAAGCAACTGAA 59.640 40.909 0.00 0.00 0.00 3.02
917 1039 1.952990 TCGAAAATGGCAAGCAACTGA 59.047 42.857 0.00 0.00 0.00 3.41
918 1040 2.420628 TCGAAAATGGCAAGCAACTG 57.579 45.000 0.00 0.00 0.00 3.16
919 1041 2.821969 AGATCGAAAATGGCAAGCAACT 59.178 40.909 0.00 0.00 0.00 3.16
929 1051 5.091431 GCAACTCCAAGAAGATCGAAAATG 58.909 41.667 0.00 0.00 0.00 2.32
930 1052 5.006386 AGCAACTCCAAGAAGATCGAAAAT 58.994 37.500 0.00 0.00 0.00 1.82
949 1071 0.179009 AGCAGGAACAGAGCAAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
1143 1265 5.745769 GGAGAGAAAACTTGACAGCTTTTTG 59.254 40.000 0.00 0.00 0.00 2.44
1150 1272 3.181450 ACAGGGGAGAGAAAACTTGACAG 60.181 47.826 0.00 0.00 0.00 3.51
1266 1392 8.402472 CAACAGTTCATCCAAGTGTAAGTTTTA 58.598 33.333 0.00 0.00 46.36 1.52
1355 1483 1.227089 CATGAGGAAGCCGACGGAG 60.227 63.158 20.50 0.00 0.00 4.63
1518 1646 1.268539 GGTGTTGTTGAAGGCGTTCTG 60.269 52.381 19.07 0.00 33.38 3.02
1526 1654 0.385390 GCTGGTGGGTGTTGTTGAAG 59.615 55.000 0.00 0.00 0.00 3.02
1616 1744 0.179094 GTTCGTCCATGTATCCGCCA 60.179 55.000 0.00 0.00 0.00 5.69
1618 1746 0.928229 GTGTTCGTCCATGTATCCGC 59.072 55.000 0.00 0.00 0.00 5.54
1619 1747 1.136305 AGGTGTTCGTCCATGTATCCG 59.864 52.381 0.00 0.00 0.00 4.18
1629 1761 3.813166 TGAGGAAATTCAAGGTGTTCGTC 59.187 43.478 0.00 0.00 36.12 4.20
1632 1764 5.964958 TCATGAGGAAATTCAAGGTGTTC 57.035 39.130 0.00 0.00 0.00 3.18
1638 1770 6.845302 TCACGAATTCATGAGGAAATTCAAG 58.155 36.000 14.97 8.50 39.39 3.02
1643 1775 6.764308 AACATCACGAATTCATGAGGAAAT 57.236 33.333 21.42 5.78 39.39 2.17
1646 1778 4.142622 GCAAACATCACGAATTCATGAGGA 60.143 41.667 21.42 3.92 31.25 3.71
1649 1781 4.455190 TCAGCAAACATCACGAATTCATGA 59.545 37.500 6.68 6.68 0.00 3.07
1653 1785 4.083855 TCAGTCAGCAAACATCACGAATTC 60.084 41.667 0.00 0.00 0.00 2.17
1654 1786 3.814842 TCAGTCAGCAAACATCACGAATT 59.185 39.130 0.00 0.00 0.00 2.17
1659 1851 4.252073 AGAGATCAGTCAGCAAACATCAC 58.748 43.478 0.00 0.00 0.00 3.06
1669 1861 6.450545 TGAAGTACAACAAGAGATCAGTCAG 58.549 40.000 0.00 0.00 0.00 3.51
1672 1864 5.279708 CCCTGAAGTACAACAAGAGATCAGT 60.280 44.000 0.00 0.00 33.04 3.41
1673 1865 5.174395 CCCTGAAGTACAACAAGAGATCAG 58.826 45.833 0.00 0.00 34.33 2.90
1688 1889 2.750350 CCTTCACGCCCCTGAAGT 59.250 61.111 11.27 0.00 43.95 3.01
1903 2117 2.187946 CGCCTCTTCTTGCCGGAT 59.812 61.111 5.05 0.00 0.00 4.18
1959 2173 3.525545 GGGTACGACGGCTCCTCC 61.526 72.222 0.00 0.00 0.00 4.30
2020 2237 4.218578 AGCGAGCGAGCTCCCATG 62.219 66.667 18.19 6.45 45.67 3.66
2028 2245 3.049674 TTTGCCCAAGCGAGCGAG 61.050 61.111 0.00 0.00 44.31 5.03
2029 2246 3.353836 GTTTGCCCAAGCGAGCGA 61.354 61.111 0.00 0.00 44.31 4.93
2084 2303 3.249080 GCTAACAAGTTACCAAGACGCAA 59.751 43.478 0.00 0.00 0.00 4.85
2087 2306 4.304110 TCAGCTAACAAGTTACCAAGACG 58.696 43.478 0.00 0.00 0.00 4.18
2147 2372 2.805671 TGCAACACCGAGAGTTGTATTG 59.194 45.455 13.43 0.00 46.09 1.90
2150 2375 2.831685 ATGCAACACCGAGAGTTGTA 57.168 45.000 13.43 10.58 46.09 2.41
2164 2389 2.282039 CCGGCCAGGGAAAATGCAA 61.282 57.895 2.24 0.00 35.97 4.08
2199 2424 7.372714 ACTGTGTGTACGTAAATCTCATGTTA 58.627 34.615 0.00 0.00 0.00 2.41
2222 2447 5.483937 TGGAATGTCTCACTGTATTGGTACT 59.516 40.000 0.00 0.00 0.00 2.73
2232 2457 3.407424 TGTTCCTGGAATGTCTCACTG 57.593 47.619 13.07 0.00 0.00 3.66
2254 2479 5.043903 CGGATAGGTTTGATACTGTGACTG 58.956 45.833 0.00 0.00 0.00 3.51
2330 2555 0.816825 CGATGCCCAAGATGGAGGTG 60.817 60.000 0.00 0.00 40.96 4.00
2331 2556 0.982852 TCGATGCCCAAGATGGAGGT 60.983 55.000 0.00 0.00 40.96 3.85
2334 2559 0.465705 GACTCGATGCCCAAGATGGA 59.534 55.000 0.00 0.00 40.96 3.41
2368 2603 1.082756 GTGTTCAACGCCTTGCTCG 60.083 57.895 0.00 0.00 0.00 5.03
2369 2604 0.593128 ATGTGTTCAACGCCTTGCTC 59.407 50.000 0.00 0.00 0.00 4.26
2378 2613 1.234821 TGGAGCCGAATGTGTTCAAC 58.765 50.000 0.00 0.00 33.86 3.18
2394 2629 4.408596 TGCCATACAGATACAAGACATGGA 59.591 41.667 0.00 0.00 34.64 3.41
2493 2729 1.053424 TAGCCCTTGAACGTCAGGTT 58.947 50.000 7.44 0.00 42.96 3.50
2504 2740 4.455606 AGCTAGCAAATAAGTAGCCCTTG 58.544 43.478 18.83 0.00 40.11 3.61
2508 2744 4.991687 CCTGTAGCTAGCAAATAAGTAGCC 59.008 45.833 18.83 0.00 40.11 3.93
2511 2757 7.069455 TGTCATCCTGTAGCTAGCAAATAAGTA 59.931 37.037 18.83 0.00 0.00 2.24
2515 2761 5.869649 TGTCATCCTGTAGCTAGCAAATA 57.130 39.130 18.83 1.80 0.00 1.40
2517 2763 4.551702 TTGTCATCCTGTAGCTAGCAAA 57.448 40.909 18.83 0.86 0.00 3.68
2532 2778 4.401022 TCTTTCTTGGTCTGCATTGTCAT 58.599 39.130 0.00 0.00 0.00 3.06
2540 2786 2.550180 GTTGGTCTCTTTCTTGGTCTGC 59.450 50.000 0.00 0.00 0.00 4.26
2541 2787 3.808728 TGTTGGTCTCTTTCTTGGTCTG 58.191 45.455 0.00 0.00 0.00 3.51
2568 2814 4.590647 TGCTGCTTATCTGCCTACTATCTT 59.409 41.667 0.00 0.00 38.68 2.40
2569 2815 4.155709 TGCTGCTTATCTGCCTACTATCT 58.844 43.478 0.00 0.00 38.68 1.98
2570 2816 4.527509 TGCTGCTTATCTGCCTACTATC 57.472 45.455 0.00 0.00 38.68 2.08
2571 2817 4.101585 TGTTGCTGCTTATCTGCCTACTAT 59.898 41.667 0.00 0.00 38.68 2.12
2572 2818 3.450817 TGTTGCTGCTTATCTGCCTACTA 59.549 43.478 0.00 0.00 38.68 1.82
2573 2819 2.237143 TGTTGCTGCTTATCTGCCTACT 59.763 45.455 0.00 0.00 38.68 2.57
2574 2820 2.632377 TGTTGCTGCTTATCTGCCTAC 58.368 47.619 0.00 0.00 38.68 3.18
2575 2821 3.208594 CATGTTGCTGCTTATCTGCCTA 58.791 45.455 0.00 0.00 38.68 3.93
2576 2822 2.022195 CATGTTGCTGCTTATCTGCCT 58.978 47.619 0.00 0.00 38.68 4.75
2577 2823 1.066605 CCATGTTGCTGCTTATCTGCC 59.933 52.381 0.00 0.00 38.68 4.85
2578 2824 1.747355 ACCATGTTGCTGCTTATCTGC 59.253 47.619 0.00 0.00 39.73 4.26
2579 2825 4.445452 AAACCATGTTGCTGCTTATCTG 57.555 40.909 0.00 0.00 0.00 2.90
2595 2841 5.323581 TGTGGATGAATGATCTCAAAACCA 58.676 37.500 0.00 0.39 0.00 3.67
2597 2843 6.506500 ACTGTGGATGAATGATCTCAAAAC 57.493 37.500 0.00 0.00 0.00 2.43
2602 2848 4.953667 TGCTACTGTGGATGAATGATCTC 58.046 43.478 0.00 0.00 0.00 2.75
2629 2879 2.568956 AGCTGTTATCTGCACAAGAGGA 59.431 45.455 5.59 0.00 38.67 3.71
2735 2986 7.675637 GCCGGGAATGCGTTAGTATAAATTATC 60.676 40.741 2.18 0.00 0.00 1.75
2747 2998 2.403378 GCAAGCCGGGAATGCGTTA 61.403 57.895 2.18 0.00 0.00 3.18
2750 3001 4.183686 CTGCAAGCCGGGAATGCG 62.184 66.667 16.42 9.64 42.91 4.73
2768 3019 7.121463 TGTTGTTGTTGTAGTTCTGTGGTTATT 59.879 33.333 0.00 0.00 0.00 1.40
2782 3033 5.278709 CCATGCTATGGTTGTTGTTGTTGTA 60.279 40.000 6.93 0.00 45.54 2.41
2817 3102 1.139654 CTATGCAAGCTGCTCCCTGTA 59.860 52.381 1.00 0.00 45.31 2.74
2818 3103 0.107312 CTATGCAAGCTGCTCCCTGT 60.107 55.000 1.00 0.00 45.31 4.00
2933 3219 0.616371 TCGGTTCCGGTGATCCAAAT 59.384 50.000 11.37 0.00 31.66 2.32
2989 3275 5.649265 ACTATGCCTATGATGAGGAGAAGA 58.351 41.667 0.00 0.00 39.15 2.87
2990 3276 5.964758 GACTATGCCTATGATGAGGAGAAG 58.035 45.833 0.00 0.00 39.15 2.85
2991 3277 5.991933 GACTATGCCTATGATGAGGAGAA 57.008 43.478 0.00 0.00 39.15 2.87


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

AutoCloner maintained by Alex Coulton.