Multiple sequence alignment - TraesCS7D01G408500

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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 TraesCS7D01G408500 chr7D 100.000 4397 0 0 1 4397 526244845 526240449 0.000000e+00 8120.0
1 TraesCS7D01G408500 chr7B 90.370 3915 185 74 552 4397 562748264 562744473 0.000000e+00 4964.0
2 TraesCS7D01G408500 chr7B 84.522 575 30 20 1 555 562749057 562748522 8.430000e-142 514.0
3 TraesCS7D01G408500 chr7A 90.351 1710 94 25 2168 3829 606563206 606561520 0.000000e+00 2178.0
4 TraesCS7D01G408500 chr7A 93.658 1293 54 15 860 2138 606564612 606563334 0.000000e+00 1908.0
5 TraesCS7D01G408500 chr7A 91.756 279 11 7 80 346 606565271 606564993 1.150000e-100 377.0
6 TraesCS7D01G408500 chr7A 85.440 364 9 17 483 829 606564946 606564610 5.450000e-89 339.0
7 TraesCS7D01G408500 chr7A 92.754 138 9 1 3884 4020 606560779 606560642 9.650000e-47 198.0
8 TraesCS7D01G408500 chr5D 87.463 1021 65 26 3085 4064 388344353 388345351 0.000000e+00 1118.0
9 TraesCS7D01G408500 chr5D 83.417 199 25 4 2836 3034 388343871 388344061 1.260000e-40 178.0
10 TraesCS7D01G408500 chr5D 86.538 52 7 0 3042 3093 388344090 388344141 1.710000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G408500 chr7D 526240449 526244845 4396 True 8120.000000 8120 100.0000 1 4397 1 chr7D.!!$R1 4396
1 TraesCS7D01G408500 chr7B 562744473 562749057 4584 True 2739.000000 4964 87.4460 1 4397 2 chr7B.!!$R1 4396
2 TraesCS7D01G408500 chr7A 606560642 606565271 4629 True 1000.000000 2178 90.7918 80 4020 5 chr7A.!!$R1 3940
3 TraesCS7D01G408500 chr5D 388343871 388345351 1480 False 451.466667 1118 85.8060 2836 4064 3 chr5D.!!$F1 1228

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
981 1314 0.034896 GGCCAAGAAGAACGGAGTCA 59.965 55.0 0.00 0.0 45.0 3.41 F
2341 2813 0.038310 AGCTGGCAGAAGTAAACCCC 59.962 55.0 20.86 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 3076 1.139989 AACATCAGTCAACGAGCACG 58.860 50.0 0.76 0.76 45.75 5.34 R
4183 5666 0.179009 ACAGAAGGCAGAGCAAGCAA 60.179 50.0 0.00 0.00 0.00 3.91 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
28 29 7.616313 TCCTTTGTCCTTTTACATTTTGTTGT 58.384 30.769 0.00 0.00 0.00 3.32
29 30 7.547370 TCCTTTGTCCTTTTACATTTTGTTGTG 59.453 33.333 0.00 0.00 0.00 3.33
30 31 7.333174 CCTTTGTCCTTTTACATTTTGTTGTGT 59.667 33.333 0.00 0.00 0.00 3.72
31 32 8.608844 TTTGTCCTTTTACATTTTGTTGTGTT 57.391 26.923 0.00 0.00 0.00 3.32
34 35 6.036626 GTCCTTTTACATTTTGTTGTGTTGGG 59.963 38.462 0.00 0.00 0.00 4.12
35 36 5.220758 CCTTTTACATTTTGTTGTGTTGGGC 60.221 40.000 0.00 0.00 0.00 5.36
38 39 2.126467 CATTTTGTTGTGTTGGGCGAG 58.874 47.619 0.00 0.00 0.00 5.03
39 40 0.457851 TTTTGTTGTGTTGGGCGAGG 59.542 50.000 0.00 0.00 0.00 4.63
76 77 4.441356 CAAGTTTTTGAACTGCTAGGGCAA 60.441 41.667 0.00 0.00 41.30 4.52
77 78 5.910582 CAAGTTTTTGAACTGCTAGGGCAAA 60.911 40.000 0.00 0.00 41.30 3.68
78 79 7.877071 CAAGTTTTTGAACTGCTAGGGCAAAC 61.877 42.308 0.00 0.00 41.30 2.93
89 90 3.181450 GCTAGGGCAAACTATGTGGATCT 60.181 47.826 0.00 0.00 38.54 2.75
154 165 2.663188 GTCTCCGCATCGCATCCC 60.663 66.667 0.00 0.00 0.00 3.85
276 298 4.533222 CGTAAAAGAACAAAAGCGTGGAT 58.467 39.130 0.00 0.00 0.00 3.41
362 384 1.546923 CAGCATGCCTCCAATTGAACA 59.453 47.619 15.66 0.00 0.00 3.18
363 385 2.028839 CAGCATGCCTCCAATTGAACAA 60.029 45.455 15.66 0.00 0.00 2.83
365 387 2.932187 GCATGCCTCCAATTGAACAACC 60.932 50.000 6.36 0.00 0.00 3.77
366 388 1.337118 TGCCTCCAATTGAACAACCC 58.663 50.000 7.12 0.00 0.00 4.11
367 389 0.608130 GCCTCCAATTGAACAACCCC 59.392 55.000 7.12 0.00 0.00 4.95
368 390 2.008242 CCTCCAATTGAACAACCCCA 57.992 50.000 7.12 0.00 0.00 4.96
369 391 1.895131 CCTCCAATTGAACAACCCCAG 59.105 52.381 7.12 0.00 0.00 4.45
370 392 2.597455 CTCCAATTGAACAACCCCAGT 58.403 47.619 7.12 0.00 0.00 4.00
386 408 1.520494 CAGTAGTATCCTCGCGCCTA 58.480 55.000 0.00 0.00 0.00 3.93
390 412 0.108963 AGTATCCTCGCGCCTAGACT 59.891 55.000 0.00 0.00 0.00 3.24
391 413 0.238817 GTATCCTCGCGCCTAGACTG 59.761 60.000 0.00 0.00 0.00 3.51
392 414 0.889638 TATCCTCGCGCCTAGACTGG 60.890 60.000 0.00 0.00 0.00 4.00
399 421 4.375406 GCCTAGACTGGCCTGGTA 57.625 61.111 14.82 4.37 46.82 3.25
400 422 2.128729 GCCTAGACTGGCCTGGTAG 58.871 63.158 14.82 13.16 46.82 3.18
401 423 0.688087 GCCTAGACTGGCCTGGTAGT 60.688 60.000 14.82 3.56 46.82 2.73
402 424 1.411216 GCCTAGACTGGCCTGGTAGTA 60.411 57.143 14.82 3.38 46.82 1.82
403 425 2.308690 CCTAGACTGGCCTGGTAGTAC 58.691 57.143 14.82 0.00 0.00 2.73
404 426 2.308690 CTAGACTGGCCTGGTAGTACC 58.691 57.143 12.80 12.80 39.22 3.34
416 438 4.826274 TGGTAGTACCAGTAGACGTAGT 57.174 45.455 18.45 0.00 44.79 2.73
417 439 5.932619 TGGTAGTACCAGTAGACGTAGTA 57.067 43.478 18.45 0.00 44.79 1.82
418 440 5.907207 TGGTAGTACCAGTAGACGTAGTAG 58.093 45.833 18.45 0.00 44.79 2.57
419 441 5.422331 TGGTAGTACCAGTAGACGTAGTAGT 59.578 44.000 18.45 0.00 44.79 2.73
420 442 6.605995 TGGTAGTACCAGTAGACGTAGTAGTA 59.394 42.308 18.45 0.00 44.79 1.82
421 443 7.142680 GGTAGTACCAGTAGACGTAGTAGTAG 58.857 46.154 14.82 0.00 38.88 2.57
422 444 7.201839 GGTAGTACCAGTAGACGTAGTAGTAGT 60.202 44.444 14.82 0.00 38.88 2.73
536 559 2.688666 CACCCCTGCTAGCTCCCA 60.689 66.667 17.23 0.00 0.00 4.37
747 1032 2.309528 TTGAAGTGTGCACGTCTCTT 57.690 45.000 13.13 13.27 39.89 2.85
829 1155 4.236416 CGCCCCAGCAAATACGCG 62.236 66.667 3.53 3.53 39.83 6.01
830 1156 3.887868 GCCCCAGCAAATACGCGG 61.888 66.667 12.47 0.00 39.53 6.46
831 1157 2.124901 CCCCAGCAAATACGCGGA 60.125 61.111 12.47 0.00 36.85 5.54
835 1161 1.743623 CAGCAAATACGCGGACCCA 60.744 57.895 12.47 0.00 36.85 4.51
836 1162 1.003112 AGCAAATACGCGGACCCAA 60.003 52.632 12.47 0.00 36.85 4.12
837 1163 0.606944 AGCAAATACGCGGACCCAAA 60.607 50.000 12.47 0.00 36.85 3.28
838 1164 0.179174 GCAAATACGCGGACCCAAAG 60.179 55.000 12.47 0.00 0.00 2.77
839 1165 1.444836 CAAATACGCGGACCCAAAGA 58.555 50.000 12.47 0.00 0.00 2.52
840 1166 1.807742 CAAATACGCGGACCCAAAGAA 59.192 47.619 12.47 0.00 0.00 2.52
841 1167 1.445871 AATACGCGGACCCAAAGAAC 58.554 50.000 12.47 0.00 0.00 3.01
842 1168 0.392060 ATACGCGGACCCAAAGAACC 60.392 55.000 12.47 0.00 0.00 3.62
843 1169 1.756408 TACGCGGACCCAAAGAACCA 61.756 55.000 12.47 0.00 0.00 3.67
844 1170 1.894756 CGCGGACCCAAAGAACCAA 60.895 57.895 0.00 0.00 0.00 3.67
845 1171 1.658114 GCGGACCCAAAGAACCAAC 59.342 57.895 0.00 0.00 0.00 3.77
846 1172 1.802337 GCGGACCCAAAGAACCAACC 61.802 60.000 0.00 0.00 0.00 3.77
847 1173 0.466555 CGGACCCAAAGAACCAACCA 60.467 55.000 0.00 0.00 0.00 3.67
848 1174 1.783071 GGACCCAAAGAACCAACCAA 58.217 50.000 0.00 0.00 0.00 3.67
849 1175 1.411246 GGACCCAAAGAACCAACCAAC 59.589 52.381 0.00 0.00 0.00 3.77
850 1176 2.104170 GACCCAAAGAACCAACCAACA 58.896 47.619 0.00 0.00 0.00 3.33
851 1177 1.828595 ACCCAAAGAACCAACCAACAC 59.171 47.619 0.00 0.00 0.00 3.32
852 1178 1.827969 CCCAAAGAACCAACCAACACA 59.172 47.619 0.00 0.00 0.00 3.72
853 1179 2.234908 CCCAAAGAACCAACCAACACAA 59.765 45.455 0.00 0.00 0.00 3.33
854 1180 3.307059 CCCAAAGAACCAACCAACACAAA 60.307 43.478 0.00 0.00 0.00 2.83
855 1181 3.682377 CCAAAGAACCAACCAACACAAAC 59.318 43.478 0.00 0.00 0.00 2.93
856 1182 2.931512 AGAACCAACCAACACAAACG 57.068 45.000 0.00 0.00 0.00 3.60
857 1183 1.135228 AGAACCAACCAACACAAACGC 60.135 47.619 0.00 0.00 0.00 4.84
858 1184 0.108567 AACCAACCAACACAAACGCC 60.109 50.000 0.00 0.00 0.00 5.68
859 1185 1.227118 CCAACCAACACAAACGCCC 60.227 57.895 0.00 0.00 0.00 6.13
860 1186 1.587613 CAACCAACACAAACGCCCG 60.588 57.895 0.00 0.00 0.00 6.13
861 1187 3.418744 AACCAACACAAACGCCCGC 62.419 57.895 0.00 0.00 0.00 6.13
862 1188 4.639171 CCAACACAAACGCCCGCC 62.639 66.667 0.00 0.00 0.00 6.13
863 1189 4.639171 CAACACAAACGCCCGCCC 62.639 66.667 0.00 0.00 0.00 6.13
906 1232 3.065371 GCTTCAGTTCATCCCCATTAACG 59.935 47.826 0.00 0.00 0.00 3.18
911 1237 3.009695 AGTTCATCCCCATTAACGACCAA 59.990 43.478 0.00 0.00 0.00 3.67
971 1304 1.373570 GATCGTCCTTGGCCAAGAAG 58.626 55.000 41.10 29.95 40.79 2.85
981 1314 0.034896 GGCCAAGAAGAACGGAGTCA 59.965 55.000 0.00 0.00 45.00 3.41
1206 1539 4.496927 CCGCCGCCCATTTTCTGC 62.497 66.667 0.00 0.00 0.00 4.26
1528 1867 0.389391 ACATTCTCCGCCTCCGTATG 59.611 55.000 0.00 0.00 0.00 2.39
1571 1910 2.126189 GTACCAGGACACGGCGAC 60.126 66.667 16.62 4.28 0.00 5.19
1585 1924 3.041940 CGACCGACACCAGCAACC 61.042 66.667 0.00 0.00 0.00 3.77
1589 1928 2.669569 CGACACCAGCAACCCCAG 60.670 66.667 0.00 0.00 0.00 4.45
1638 1989 2.320587 GCACAGGCAGTTCTCCGTG 61.321 63.158 0.00 0.00 40.72 4.94
1998 2349 2.060980 GGTCTCCTGGATGTCCGCT 61.061 63.158 0.00 0.00 39.43 5.52
2079 2434 6.767902 TCAACCAATCCTTGCTATATTCAGAC 59.232 38.462 0.00 0.00 0.00 3.51
2085 2440 6.902771 TCCTTGCTATATTCAGACTCTACC 57.097 41.667 0.00 0.00 0.00 3.18
2086 2441 6.615617 TCCTTGCTATATTCAGACTCTACCT 58.384 40.000 0.00 0.00 0.00 3.08
2138 2495 4.336993 TGTACCAAACAAGACAACATCACC 59.663 41.667 0.00 0.00 34.29 4.02
2139 2496 3.360867 ACCAAACAAGACAACATCACCA 58.639 40.909 0.00 0.00 0.00 4.17
2140 2497 3.766591 ACCAAACAAGACAACATCACCAA 59.233 39.130 0.00 0.00 0.00 3.67
2141 2498 4.221703 ACCAAACAAGACAACATCACCAAA 59.778 37.500 0.00 0.00 0.00 3.28
2142 2499 5.174395 CCAAACAAGACAACATCACCAAAA 58.826 37.500 0.00 0.00 0.00 2.44
2143 2500 5.816777 CCAAACAAGACAACATCACCAAAAT 59.183 36.000 0.00 0.00 0.00 1.82
2144 2501 6.983307 CCAAACAAGACAACATCACCAAAATA 59.017 34.615 0.00 0.00 0.00 1.40
2145 2502 7.169645 CCAAACAAGACAACATCACCAAAATAG 59.830 37.037 0.00 0.00 0.00 1.73
2146 2503 6.959639 ACAAGACAACATCACCAAAATAGT 57.040 33.333 0.00 0.00 0.00 2.12
2147 2504 7.346751 ACAAGACAACATCACCAAAATAGTT 57.653 32.000 0.00 0.00 0.00 2.24
2148 2505 8.458573 ACAAGACAACATCACCAAAATAGTTA 57.541 30.769 0.00 0.00 0.00 2.24
2149 2506 8.567948 ACAAGACAACATCACCAAAATAGTTAG 58.432 33.333 0.00 0.00 0.00 2.34
2150 2507 8.783093 CAAGACAACATCACCAAAATAGTTAGA 58.217 33.333 0.00 0.00 0.00 2.10
2151 2508 9.520515 AAGACAACATCACCAAAATAGTTAGAT 57.479 29.630 0.00 0.00 0.00 1.98
2152 2509 8.950210 AGACAACATCACCAAAATAGTTAGATG 58.050 33.333 0.00 0.00 37.85 2.90
2153 2510 8.055279 ACAACATCACCAAAATAGTTAGATGG 57.945 34.615 0.00 2.72 36.59 3.51
2154 2511 7.888021 ACAACATCACCAAAATAGTTAGATGGA 59.112 33.333 0.00 0.00 36.59 3.41
2155 2512 8.906867 CAACATCACCAAAATAGTTAGATGGAT 58.093 33.333 0.00 0.00 36.59 3.41
2188 2545 9.747898 TCTAGCCCAAGAAATTACAATTTTAGA 57.252 29.630 1.69 1.53 38.64 2.10
2228 2700 6.777580 ACCATAAAACATGGACAGAGTTCTTT 59.222 34.615 10.19 0.00 41.64 2.52
2258 2730 7.649533 TCATGATGCTTTGGACTTGATTTAT 57.350 32.000 0.00 0.00 0.00 1.40
2298 2770 9.319143 GTAGTCAGTACTGATGAATGCTTATTT 57.681 33.333 27.54 1.59 42.18 1.40
2300 2772 9.539825 AGTCAGTACTGATGAATGCTTATTTAG 57.460 33.333 27.54 0.00 42.18 1.85
2301 2773 9.534565 GTCAGTACTGATGAATGCTTATTTAGA 57.465 33.333 27.54 0.00 42.18 2.10
2341 2813 0.038310 AGCTGGCAGAAGTAAACCCC 59.962 55.000 20.86 0.00 0.00 4.95
2384 2856 4.675146 CGAGATTGGCGTTTTGGATCAATT 60.675 41.667 0.00 0.00 0.00 2.32
2392 2864 5.637387 GGCGTTTTGGATCAATTTGTACAAT 59.363 36.000 9.56 0.00 0.00 2.71
2614 3086 2.949714 AACTTGATTCGTGCTCGTTG 57.050 45.000 8.17 0.00 38.33 4.10
2621 3093 1.418373 TTCGTGCTCGTTGACTGATG 58.582 50.000 8.17 0.00 38.33 3.07
2624 3096 1.526887 CGTGCTCGTTGACTGATGTTT 59.473 47.619 0.00 0.00 0.00 2.83
2625 3097 2.729360 CGTGCTCGTTGACTGATGTTTA 59.271 45.455 0.00 0.00 0.00 2.01
2627 3099 4.561213 CGTGCTCGTTGACTGATGTTTATA 59.439 41.667 0.00 0.00 0.00 0.98
2643 3143 9.013229 TGATGTTTATACTTTTGTGATGCTTCT 57.987 29.630 0.88 0.00 0.00 2.85
2644 3144 9.282247 GATGTTTATACTTTTGTGATGCTTCTG 57.718 33.333 0.88 0.00 0.00 3.02
2664 3164 6.403866 TCTGGTCTAACATTGTTGCAATTT 57.596 33.333 12.30 0.00 0.00 1.82
2826 3329 5.731599 TTGTTTGTTCATGAATGCAAACC 57.268 34.783 31.40 21.68 45.71 3.27
3040 3564 1.059942 GCACTACCATTTTGCAACGC 58.940 50.000 0.00 0.00 36.22 4.84
3048 3572 4.184629 ACCATTTTGCAACGCTTTTGTAA 58.815 34.783 0.00 0.00 0.00 2.41
3056 3580 4.979197 TGCAACGCTTTTGTAATTAACTGG 59.021 37.500 0.00 0.00 0.00 4.00
3357 4101 1.154073 CCCGTTCGACTCTCGGTTC 60.154 63.158 13.62 0.00 42.30 3.62
3424 4168 7.502895 TGGTAAGCTAAAATAGTGTCCAACAAA 59.497 33.333 0.00 0.00 0.00 2.83
3452 4197 6.506500 AATTTGCATTCTGAGTACTTCTGG 57.493 37.500 0.00 0.00 0.00 3.86
3520 4273 2.690497 GTCGAATCATCAGGTCAGAGGA 59.310 50.000 0.00 0.00 32.39 3.71
3563 4316 1.599542 GCTGTCGAACTGAGCTGTTTT 59.400 47.619 0.00 0.00 0.00 2.43
3600 4363 1.406069 GGTCTCGGATCACAAGTGCAT 60.406 52.381 0.00 0.00 0.00 3.96
3696 4486 3.270027 CACGTCAGCTGGATTAATTGGA 58.730 45.455 15.13 0.00 0.00 3.53
3753 4544 7.798516 CGCAAAATGTTGTATATGATAGTGGTC 59.201 37.037 0.00 0.00 37.06 4.02
3835 4630 5.483685 ACTGACAACATGTACTATGTGGT 57.516 39.130 14.53 14.53 38.78 4.16
3881 4730 5.126396 TCTGATCTGCGGTACTTATCATG 57.874 43.478 0.00 0.00 0.00 3.07
3882 4731 4.584743 TCTGATCTGCGGTACTTATCATGT 59.415 41.667 0.00 0.00 0.00 3.21
3933 5412 5.308825 AGGAAACCTAGATTGTTGACAGTG 58.691 41.667 0.00 0.00 28.47 3.66
4009 5489 4.021544 AGTTCAGCAGGTTTGTTTCAACAA 60.022 37.500 0.79 0.79 46.35 2.83
4022 5502 3.921119 TTCAACAATGGATCAGTGTGC 57.079 42.857 1.77 0.00 41.85 4.57
4026 5506 1.536766 ACAATGGATCAGTGTGCAACG 59.463 47.619 0.09 0.00 41.15 4.10
4066 5546 3.194542 CAGGAATCCTCAACTTCTCGTCT 59.805 47.826 0.00 0.00 0.00 4.18
4067 5547 4.399618 CAGGAATCCTCAACTTCTCGTCTA 59.600 45.833 0.00 0.00 0.00 2.59
4068 5548 5.017490 AGGAATCCTCAACTTCTCGTCTAA 58.983 41.667 0.00 0.00 0.00 2.10
4088 5568 6.474751 GTCTAAAATCCATTGAAAGATGCTGC 59.525 38.462 0.00 0.00 0.00 5.25
4091 5571 6.474140 AAATCCATTGAAAGATGCTGCATA 57.526 33.333 16.23 0.00 0.00 3.14
4138 5618 5.319140 TCAGTTGAAGGCATTCATTCATG 57.681 39.130 15.42 11.03 44.75 3.07
4139 5619 4.768448 TCAGTTGAAGGCATTCATTCATGT 59.232 37.500 15.42 0.00 44.75 3.21
4140 5620 4.862574 CAGTTGAAGGCATTCATTCATGTG 59.137 41.667 15.42 3.02 44.75 3.21
4142 5622 5.011329 AGTTGAAGGCATTCATTCATGTGTT 59.989 36.000 15.42 0.00 44.75 3.32
4163 5646 2.306341 ATCTCTGTTGCTCATGGTCG 57.694 50.000 0.00 0.00 0.00 4.79
4183 5666 3.687212 TCGTGACGATGCCAAAAATGTAT 59.313 39.130 2.39 0.00 0.00 2.29
4184 5667 4.155099 TCGTGACGATGCCAAAAATGTATT 59.845 37.500 2.39 0.00 0.00 1.89
4185 5668 4.262743 CGTGACGATGCCAAAAATGTATTG 59.737 41.667 0.00 0.00 0.00 1.90
4186 5669 4.031652 GTGACGATGCCAAAAATGTATTGC 59.968 41.667 0.00 0.00 0.00 3.56
4196 5679 3.515330 AAATGTATTGCTTGCTCTGCC 57.485 42.857 0.00 0.00 0.00 4.85
4198 5681 2.205022 TGTATTGCTTGCTCTGCCTT 57.795 45.000 0.00 0.00 0.00 4.35
4255 5738 7.607991 AGAAAGTACAGAAATTCCATGACGATT 59.392 33.333 0.00 0.00 0.00 3.34
4295 5778 2.697229 TGATCTCTTCACCGCATGATCT 59.303 45.455 0.00 0.00 37.11 2.75
4328 5811 0.027063 CGGAATTTACGCCGCGATTT 59.973 50.000 21.79 6.86 41.17 2.17
4329 5812 1.738432 GGAATTTACGCCGCGATTTC 58.262 50.000 21.79 14.76 0.00 2.17
4330 5813 1.372656 GAATTTACGCCGCGATTTCG 58.627 50.000 21.79 8.14 43.27 3.46
4362 5845 2.637382 TGTGAGAAATGCAGTCCCAGTA 59.363 45.455 0.00 0.00 0.00 2.74
4363 5846 3.072330 TGTGAGAAATGCAGTCCCAGTAA 59.928 43.478 0.00 0.00 0.00 2.24
4368 5851 1.926426 ATGCAGTCCCAGTAAGGCCC 61.926 60.000 0.00 0.00 35.39 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.130516 TCGCCCAACACAACAAAATGTAA 59.869 39.130 0.00 0.00 30.84 2.41
16 17 2.688446 TCGCCCAACACAACAAAATGTA 59.312 40.909 0.00 0.00 30.84 2.29
17 18 1.478510 TCGCCCAACACAACAAAATGT 59.521 42.857 0.00 0.00 0.00 2.71
18 19 2.126467 CTCGCCCAACACAACAAAATG 58.874 47.619 0.00 0.00 0.00 2.32
19 20 1.068434 CCTCGCCCAACACAACAAAAT 59.932 47.619 0.00 0.00 0.00 1.82
22 23 1.826054 CCCTCGCCCAACACAACAA 60.826 57.895 0.00 0.00 0.00 2.83
24 25 3.670377 GCCCTCGCCCAACACAAC 61.670 66.667 0.00 0.00 0.00 3.32
28 29 4.659172 CCTTGCCCTCGCCCAACA 62.659 66.667 0.00 0.00 0.00 3.33
29 30 3.860930 TTCCTTGCCCTCGCCCAAC 62.861 63.158 0.00 0.00 0.00 3.77
30 31 3.567579 CTTCCTTGCCCTCGCCCAA 62.568 63.158 0.00 0.00 0.00 4.12
31 32 4.033776 CTTCCTTGCCCTCGCCCA 62.034 66.667 0.00 0.00 0.00 5.36
34 35 3.569200 AACCCTTCCTTGCCCTCGC 62.569 63.158 0.00 0.00 0.00 5.03
35 36 1.377333 GAACCCTTCCTTGCCCTCG 60.377 63.158 0.00 0.00 0.00 4.63
38 39 0.178961 ACTTGAACCCTTCCTTGCCC 60.179 55.000 0.00 0.00 0.00 5.36
39 40 1.704641 AACTTGAACCCTTCCTTGCC 58.295 50.000 0.00 0.00 0.00 4.52
76 77 3.308402 CCCCAACACAGATCCACATAGTT 60.308 47.826 0.00 0.00 0.00 2.24
77 78 2.239654 CCCCAACACAGATCCACATAGT 59.760 50.000 0.00 0.00 0.00 2.12
78 79 2.239654 ACCCCAACACAGATCCACATAG 59.760 50.000 0.00 0.00 0.00 2.23
89 90 1.225983 CTGTCACCACCCCAACACA 59.774 57.895 0.00 0.00 0.00 3.72
122 129 0.169230 GAGACCGATGATCCCGATCG 59.831 60.000 8.51 8.51 41.94 3.69
184 200 2.357517 CCCAGCTTTCGTGTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
276 298 2.909965 GCGGTTGTTCCCTTGCCA 60.910 61.111 0.00 0.00 0.00 4.92
343 365 1.927487 TGTTCAATTGGAGGCATGCT 58.073 45.000 18.92 3.20 0.00 3.79
356 378 4.563140 GGATACTACTGGGGTTGTTCAA 57.437 45.455 0.00 0.00 33.82 2.69
386 408 0.412244 TGGTACTACCAGGCCAGTCT 59.588 55.000 5.01 0.00 44.79 3.24
398 420 7.339721 ACACTACTACTACGTCTACTGGTACTA 59.660 40.741 0.00 0.00 0.00 1.82
399 421 6.153680 ACACTACTACTACGTCTACTGGTACT 59.846 42.308 0.00 0.00 0.00 2.73
400 422 6.334202 ACACTACTACTACGTCTACTGGTAC 58.666 44.000 0.00 0.00 0.00 3.34
401 423 6.531503 ACACTACTACTACGTCTACTGGTA 57.468 41.667 0.00 0.00 0.00 3.25
402 424 5.413309 ACACTACTACTACGTCTACTGGT 57.587 43.478 0.00 0.00 0.00 4.00
403 425 5.461737 GCTACACTACTACTACGTCTACTGG 59.538 48.000 0.00 0.00 0.00 4.00
404 426 5.461737 GGCTACACTACTACTACGTCTACTG 59.538 48.000 0.00 0.00 0.00 2.74
405 427 5.362430 AGGCTACACTACTACTACGTCTACT 59.638 44.000 0.00 0.00 0.00 2.57
406 428 5.596845 AGGCTACACTACTACTACGTCTAC 58.403 45.833 0.00 0.00 0.00 2.59
407 429 5.506483 CGAGGCTACACTACTACTACGTCTA 60.506 48.000 0.00 0.00 0.00 2.59
408 430 4.692228 GAGGCTACACTACTACTACGTCT 58.308 47.826 0.00 0.00 0.00 4.18
409 431 3.489047 CGAGGCTACACTACTACTACGTC 59.511 52.174 0.00 0.00 0.00 4.34
410 432 3.452474 CGAGGCTACACTACTACTACGT 58.548 50.000 0.00 0.00 0.00 3.57
411 433 2.799412 CCGAGGCTACACTACTACTACG 59.201 54.545 0.00 0.00 0.00 3.51
412 434 2.547634 GCCGAGGCTACACTACTACTAC 59.452 54.545 6.90 0.00 38.26 2.73
413 435 2.843701 GCCGAGGCTACACTACTACTA 58.156 52.381 6.90 0.00 38.26 1.82
414 436 1.677942 GCCGAGGCTACACTACTACT 58.322 55.000 6.90 0.00 38.26 2.57
536 559 0.697854 ACCAAACCTCACCTGGGAGT 60.698 55.000 0.00 0.00 34.31 3.85
610 895 2.811317 GAGGCGCGACAACAGGAG 60.811 66.667 17.71 0.00 0.00 3.69
747 1032 3.884091 GCGAGTATTAACTGAGGAGGAGA 59.116 47.826 0.00 0.00 35.56 3.71
829 1155 1.411246 GTTGGTTGGTTCTTTGGGTCC 59.589 52.381 0.00 0.00 0.00 4.46
830 1156 2.104170 TGTTGGTTGGTTCTTTGGGTC 58.896 47.619 0.00 0.00 0.00 4.46
831 1157 1.828595 GTGTTGGTTGGTTCTTTGGGT 59.171 47.619 0.00 0.00 0.00 4.51
835 1161 3.580731 CGTTTGTGTTGGTTGGTTCTTT 58.419 40.909 0.00 0.00 0.00 2.52
836 1162 2.672760 GCGTTTGTGTTGGTTGGTTCTT 60.673 45.455 0.00 0.00 0.00 2.52
837 1163 1.135228 GCGTTTGTGTTGGTTGGTTCT 60.135 47.619 0.00 0.00 0.00 3.01
838 1164 1.273688 GCGTTTGTGTTGGTTGGTTC 58.726 50.000 0.00 0.00 0.00 3.62
839 1165 0.108567 GGCGTTTGTGTTGGTTGGTT 60.109 50.000 0.00 0.00 0.00 3.67
840 1166 1.513622 GGCGTTTGTGTTGGTTGGT 59.486 52.632 0.00 0.00 0.00 3.67
841 1167 1.227118 GGGCGTTTGTGTTGGTTGG 60.227 57.895 0.00 0.00 0.00 3.77
842 1168 1.587613 CGGGCGTTTGTGTTGGTTG 60.588 57.895 0.00 0.00 0.00 3.77
843 1169 2.802106 CGGGCGTTTGTGTTGGTT 59.198 55.556 0.00 0.00 0.00 3.67
844 1170 3.894947 GCGGGCGTTTGTGTTGGT 61.895 61.111 0.00 0.00 0.00 3.67
845 1171 4.639171 GGCGGGCGTTTGTGTTGG 62.639 66.667 0.00 0.00 0.00 3.77
846 1172 4.639171 GGGCGGGCGTTTGTGTTG 62.639 66.667 0.00 0.00 0.00 3.33
922 1255 0.963856 ACGTACCGCTGATGACTCCA 60.964 55.000 0.00 0.00 0.00 3.86
1194 1527 1.619807 ATGGCAGGCAGAAAATGGGC 61.620 55.000 1.89 0.00 0.00 5.36
1195 1528 0.462789 GATGGCAGGCAGAAAATGGG 59.537 55.000 1.89 0.00 0.00 4.00
1196 1529 0.462789 GGATGGCAGGCAGAAAATGG 59.537 55.000 1.89 0.00 0.00 3.16
1197 1530 1.481871 AGGATGGCAGGCAGAAAATG 58.518 50.000 1.89 0.00 0.00 2.32
1201 1534 1.000521 CCAAGGATGGCAGGCAGAA 60.001 57.895 1.89 0.00 40.58 3.02
1413 1746 4.421554 TGGGAGCAGAGGGGGAGG 62.422 72.222 0.00 0.00 0.00 4.30
1452 1785 2.025156 CGTACGTCGGATTCGGGG 59.975 66.667 7.22 0.00 36.95 5.73
1506 1843 2.514824 GGAGGCGGAGAATGTGGC 60.515 66.667 0.00 0.00 0.00 5.01
1571 1910 4.263572 TGGGGTTGCTGGTGTCGG 62.264 66.667 0.00 0.00 0.00 4.79
1585 1924 2.186384 CTTCTCCGCTCTGCTGGG 59.814 66.667 0.00 0.00 0.00 4.45
1977 2328 1.729470 CGGACATCCAGGAGACCTCG 61.729 65.000 0.00 0.00 35.14 4.63
1986 2337 1.153289 CTTCCCAGCGGACATCCAG 60.153 63.158 0.00 0.00 38.14 3.86
1998 2349 1.188219 ACTCGAGCTGCTTCTTCCCA 61.188 55.000 13.61 0.00 0.00 4.37
2102 2459 5.919755 TGTTTGGTACACTGTCACTGATTA 58.080 37.500 0.00 0.00 39.29 1.75
2103 2460 4.776349 TGTTTGGTACACTGTCACTGATT 58.224 39.130 0.00 0.00 39.29 2.57
2106 2463 4.034048 GTCTTGTTTGGTACACTGTCACTG 59.966 45.833 0.00 0.00 39.29 3.66
2107 2464 4.189231 GTCTTGTTTGGTACACTGTCACT 58.811 43.478 0.00 0.00 39.29 3.41
2108 2465 3.936453 TGTCTTGTTTGGTACACTGTCAC 59.064 43.478 0.00 0.00 39.29 3.67
2109 2466 4.209307 TGTCTTGTTTGGTACACTGTCA 57.791 40.909 0.00 0.00 39.29 3.58
2143 2500 9.869667 GGGCTAGAATCTATATCCATCTAACTA 57.130 37.037 0.00 0.00 0.00 2.24
2144 2501 8.347591 TGGGCTAGAATCTATATCCATCTAACT 58.652 37.037 0.00 0.00 0.00 2.24
2145 2502 8.540507 TGGGCTAGAATCTATATCCATCTAAC 57.459 38.462 0.00 0.00 0.00 2.34
2146 2503 9.206690 CTTGGGCTAGAATCTATATCCATCTAA 57.793 37.037 0.00 0.00 0.00 2.10
2147 2504 8.569596 TCTTGGGCTAGAATCTATATCCATCTA 58.430 37.037 0.00 0.00 0.00 1.98
2148 2505 7.425834 TCTTGGGCTAGAATCTATATCCATCT 58.574 38.462 0.00 0.00 0.00 2.90
2149 2506 7.667575 TCTTGGGCTAGAATCTATATCCATC 57.332 40.000 0.00 0.00 0.00 3.51
2150 2507 8.454859 TTTCTTGGGCTAGAATCTATATCCAT 57.545 34.615 0.00 0.00 34.33 3.41
2151 2508 7.872061 TTTCTTGGGCTAGAATCTATATCCA 57.128 36.000 0.00 0.00 34.33 3.41
2157 2514 9.920946 AATTGTAATTTCTTGGGCTAGAATCTA 57.079 29.630 0.00 0.00 34.33 1.98
2158 2515 8.829373 AATTGTAATTTCTTGGGCTAGAATCT 57.171 30.769 0.00 0.00 34.33 2.40
2159 2516 9.875691 AAAATTGTAATTTCTTGGGCTAGAATC 57.124 29.630 0.00 0.00 37.62 2.52
2188 2545 8.415950 TGTTTTATGGTATTCACACTTTGGAT 57.584 30.769 0.00 0.00 0.00 3.41
2197 2554 7.336931 ACTCTGTCCATGTTTTATGGTATTCAC 59.663 37.037 5.89 0.00 40.06 3.18
2271 2743 6.537453 AAGCATTCATCAGTACTGACTACT 57.463 37.500 27.41 15.37 43.11 2.57
2272 2744 8.879342 AATAAGCATTCATCAGTACTGACTAC 57.121 34.615 27.41 13.51 43.11 2.73
2274 2746 9.539825 CTAAATAAGCATTCATCAGTACTGACT 57.460 33.333 27.41 15.65 43.11 3.41
2275 2747 9.534565 TCTAAATAAGCATTCATCAGTACTGAC 57.465 33.333 27.41 13.62 43.11 3.51
2288 2760 6.044682 GCAACCTGCATTCTAAATAAGCATT 58.955 36.000 0.00 0.00 44.26 3.56
2341 2813 1.456678 CGTCGTCGCTGAGATGAACG 61.457 60.000 4.85 7.75 45.61 3.95
2392 2864 1.468127 CGTACATGCATCAACAAGGCA 59.532 47.619 0.00 0.00 42.43 4.75
2604 3076 1.139989 AACATCAGTCAACGAGCACG 58.860 50.000 0.76 0.76 45.75 5.34
2614 3086 8.454106 AGCATCACAAAAGTATAAACATCAGTC 58.546 33.333 0.00 0.00 0.00 3.51
2621 3093 7.593825 ACCAGAAGCATCACAAAAGTATAAAC 58.406 34.615 0.00 0.00 0.00 2.01
2624 3096 6.711277 AGACCAGAAGCATCACAAAAGTATA 58.289 36.000 0.00 0.00 0.00 1.47
2625 3097 5.564550 AGACCAGAAGCATCACAAAAGTAT 58.435 37.500 0.00 0.00 0.00 2.12
2627 3099 3.825328 AGACCAGAAGCATCACAAAAGT 58.175 40.909 0.00 0.00 0.00 2.66
2679 3182 6.152661 TGAATGAATTCCCTCCAATTGTGTAC 59.847 38.462 4.43 0.00 35.97 2.90
2826 3329 6.405216 CAAAACAAAGAAAAAGCTGTCATCG 58.595 36.000 0.00 0.00 0.00 3.84
3040 3564 7.867445 AACAATCGCCAGTTAATTACAAAAG 57.133 32.000 0.00 0.00 0.00 2.27
3048 3572 6.677920 GCAGTGATAAACAATCGCCAGTTAAT 60.678 38.462 0.00 0.00 44.75 1.40
3056 3580 2.420022 ACCTGCAGTGATAAACAATCGC 59.580 45.455 13.81 0.00 44.12 4.58
3168 3912 3.055602 GCATTTTGGGGATCAGAAGCTTT 60.056 43.478 0.00 0.00 0.00 3.51
3357 4101 1.209504 TCAGGCAGGAAAAGGTATCGG 59.790 52.381 0.00 0.00 0.00 4.18
3452 4197 5.314923 ACATGGAAATACACATGCTGTTC 57.685 39.130 0.00 0.00 46.35 3.18
3476 4229 7.063426 CGACTGTTACAACACACAGATATTCAT 59.937 37.037 6.32 0.00 42.74 2.57
3520 4273 3.495100 CGACAATATAGGGCTTCCTTGCT 60.495 47.826 0.00 0.00 41.96 3.91
3563 4316 2.031012 CTGGTCGAGCACTTGCCA 59.969 61.111 14.39 0.25 43.38 4.92
3600 4363 0.603065 CCGCGGATGATCACTGGATA 59.397 55.000 24.07 0.00 32.67 2.59
3659 4449 4.183865 TGACGTGCTCAAGATTTATCTGG 58.816 43.478 0.00 0.00 37.19 3.86
3696 4486 2.567615 ACAAGAGGTCGAGGCAAACTAT 59.432 45.455 0.00 0.00 0.00 2.12
3753 4544 8.575565 TTTATTTGCTAGCTAGTTAGACATCG 57.424 34.615 21.62 0.00 0.00 3.84
3835 4630 4.617995 GCTGCAGGCACACAATACATTTTA 60.618 41.667 17.12 0.00 41.35 1.52
3899 5378 7.175119 ACAATCTAGGTTTCCTTTCTTGCTTAC 59.825 37.037 0.00 0.00 34.61 2.34
3933 5412 1.742761 TGCTGAAGCTGCTATGTTCC 58.257 50.000 0.90 0.00 42.66 3.62
4009 5489 1.308069 GCCGTTGCACACTGATCCAT 61.308 55.000 0.00 0.00 37.47 3.41
4022 5502 1.197721 CTGTTTCTAGCCAAGCCGTTG 59.802 52.381 0.00 0.00 0.00 4.10
4026 5506 2.079925 CTGTCTGTTTCTAGCCAAGCC 58.920 52.381 0.00 0.00 0.00 4.35
4066 5546 6.283544 TGCAGCATCTTTCAATGGATTTTA 57.716 33.333 0.00 0.00 0.00 1.52
4067 5547 5.155278 TGCAGCATCTTTCAATGGATTTT 57.845 34.783 0.00 0.00 0.00 1.82
4068 5548 4.811969 TGCAGCATCTTTCAATGGATTT 57.188 36.364 0.00 0.00 0.00 2.17
4111 5591 6.660521 TGAATGAATGCCTTCAACTGATAACT 59.339 34.615 8.55 0.00 44.29 2.24
4138 5618 4.697352 ACCATGAGCAACAGAGATAAACAC 59.303 41.667 0.00 0.00 0.00 3.32
4139 5619 4.910195 ACCATGAGCAACAGAGATAAACA 58.090 39.130 0.00 0.00 0.00 2.83
4140 5620 4.033358 CGACCATGAGCAACAGAGATAAAC 59.967 45.833 0.00 0.00 0.00 2.01
4142 5622 3.195610 ACGACCATGAGCAACAGAGATAA 59.804 43.478 0.00 0.00 0.00 1.75
4163 5646 4.031652 GCAATACATTTTTGGCATCGTCAC 59.968 41.667 0.00 0.00 0.00 3.67
4183 5666 0.179009 ACAGAAGGCAGAGCAAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
4184 5667 0.887836 CACAGAAGGCAGAGCAAGCA 60.888 55.000 0.00 0.00 0.00 3.91
4185 5668 0.888285 ACACAGAAGGCAGAGCAAGC 60.888 55.000 0.00 0.00 0.00 4.01
4186 5669 1.155042 GACACAGAAGGCAGAGCAAG 58.845 55.000 0.00 0.00 0.00 4.01
4196 5679 6.199908 GCTTATAGCTGTACATGACACAGAAG 59.800 42.308 26.02 21.17 45.10 2.85
4198 5681 5.127031 TGCTTATAGCTGTACATGACACAGA 59.873 40.000 26.02 13.13 45.10 3.41
4255 5738 2.074579 CATAGTAGGGAGGGAGGGAGA 58.925 57.143 0.00 0.00 0.00 3.71
4328 5811 1.300620 CTCACAAGGAACCGCACGA 60.301 57.895 0.00 0.00 0.00 4.35
4329 5812 0.878523 TTCTCACAAGGAACCGCACG 60.879 55.000 0.00 0.00 0.00 5.34
4330 5813 1.305201 TTTCTCACAAGGAACCGCAC 58.695 50.000 0.00 0.00 0.00 5.34
4332 5815 1.401539 GCATTTCTCACAAGGAACCGC 60.402 52.381 0.00 0.00 0.00 5.68
4333 5816 1.879380 TGCATTTCTCACAAGGAACCG 59.121 47.619 0.00 0.00 0.00 4.44
4334 5817 2.887152 ACTGCATTTCTCACAAGGAACC 59.113 45.455 0.00 0.00 0.00 3.62
4335 5818 3.057946 GGACTGCATTTCTCACAAGGAAC 60.058 47.826 0.00 0.00 0.00 3.62
4336 5819 3.149196 GGACTGCATTTCTCACAAGGAA 58.851 45.455 0.00 0.00 0.00 3.36
4337 5820 2.553028 GGGACTGCATTTCTCACAAGGA 60.553 50.000 0.00 0.00 0.00 3.36
4338 5821 1.815003 GGGACTGCATTTCTCACAAGG 59.185 52.381 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.