Multiple sequence alignment - TraesCS4A01G260800

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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 TraesCS4A01G260800 chr4A 100.000 6341 0 0 1 6341 573320338 573326678 0.000000e+00 11710.0
1 TraesCS4A01G260800 chr4D 96.688 3140 76 10 2345 5465 29832945 29829815 0.000000e+00 5197.0
2 TraesCS4A01G260800 chr4D 91.496 2387 139 31 3 2347 29835609 29833245 0.000000e+00 3225.0
3 TraesCS4A01G260800 chr4D 92.707 617 37 4 5732 6340 29829458 29828842 0.000000e+00 883.0
4 TraesCS4A01G260800 chr4B 94.389 2709 85 20 2995 5666 42399080 42396402 0.000000e+00 4098.0
5 TraesCS4A01G260800 chr4B 92.155 2562 149 27 429 2966 42401611 42399078 0.000000e+00 3570.0
6 TraesCS4A01G260800 chr4B 93.269 624 33 2 5727 6341 42396398 42395775 0.000000e+00 911.0
7 TraesCS4A01G260800 chr3D 94.479 163 7 2 1947 2108 71517840 71517679 3.800000e-62 250.0
8 TraesCS4A01G260800 chr3D 93.168 161 9 2 1949 2108 426452019 426451860 1.060000e-57 235.0
9 TraesCS4A01G260800 chr3D 97.872 47 0 1 4427 4472 320835081 320835035 5.270000e-11 80.5
10 TraesCS4A01G260800 chr3A 93.865 163 8 2 1947 2108 34532611 34532450 1.770000e-60 244.0
11 TraesCS4A01G260800 chr3A 92.683 164 10 2 1947 2109 83748183 83748021 1.060000e-57 235.0
12 TraesCS4A01G260800 chr3B 93.252 163 9 2 1947 2108 42630980 42630819 8.220000e-59 239.0
13 TraesCS4A01G260800 chr3B 97.872 47 0 1 4427 4472 398840442 398840396 5.270000e-11 80.5
14 TraesCS4A01G260800 chr1D 92.638 163 10 2 1947 2108 175819998 175819837 3.820000e-57 233.0
15 TraesCS4A01G260800 chr1D 90.789 76 7 0 4481 4556 41508167 41508092 1.120000e-17 102.0
16 TraesCS4A01G260800 chr1D 88.750 80 8 1 4478 4556 260568859 260568938 5.230000e-16 97.1
17 TraesCS4A01G260800 chr1A 92.638 163 10 2 1947 2108 218527003 218526842 3.820000e-57 233.0
18 TraesCS4A01G260800 chr1B 93.056 72 5 0 4485 4556 92616643 92616714 8.690000e-19 106.0
19 TraesCS4A01G260800 chr7A 90.000 80 6 1 4478 4557 660539963 660540040 1.120000e-17 102.0
20 TraesCS4A01G260800 chr7A 94.000 50 2 1 4429 4477 16024979 16024930 2.450000e-09 75.0
21 TraesCS4A01G260800 chr2A 90.789 76 7 0 4482 4557 771545104 771545179 1.120000e-17 102.0
22 TraesCS4A01G260800 chr2A 86.885 61 7 1 4419 4478 176564411 176564471 4.100000e-07 67.6
23 TraesCS4A01G260800 chr6D 90.667 75 7 0 4482 4556 3025215 3025289 4.050000e-17 100.0
24 TraesCS4A01G260800 chr5D 89.610 77 8 0 4481 4557 118571888 118571964 1.450000e-16 99.0
25 TraesCS4A01G260800 chr5D 94.000 50 0 2 4419 4467 3238100 3238053 8.820000e-09 73.1
26 TraesCS4A01G260800 chr5B 92.308 52 3 1 4428 4478 582158137 582158188 8.820000e-09 73.1
27 TraesCS4A01G260800 chr2D 90.385 52 4 1 4428 4478 97219731 97219680 4.100000e-07 67.6


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 TraesCS4A01G260800 chr4A 573320338 573326678 6340 False 11710.000000 11710 100.000000 1 6341 1 chr4A.!!$F1 6340
1 TraesCS4A01G260800 chr4D 29828842 29835609 6767 True 3101.666667 5197 93.630333 3 6340 3 chr4D.!!$R1 6337
2 TraesCS4A01G260800 chr4B 42395775 42401611 5836 True 2859.666667 4098 93.271000 429 6341 3 chr4B.!!$R1 5912

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
96 97 0.259938 GGATCAGACCCAATGGCCTT 59.740 55.000 3.32 0.0 33.59 4.35 F
247 263 0.575390 CGTGTCGACGTTTCTTGCTT 59.425 50.000 11.62 0.0 40.91 3.91 F
1539 1577 0.745845 ACCGTGCTTGATGGATCTGC 60.746 55.000 0.00 0.0 34.36 4.26 F
2064 2107 1.067071 GCCTCGTATAATCCTTCCCCG 60.067 57.143 0.00 0.0 0.00 5.73 F
3603 3978 0.250295 TCTCGTGCAGGAACCTTTGG 60.250 55.000 10.76 0.0 0.00 3.28 F
3866 4241 0.179124 GCGTAGTTGAGAGGGAGCTG 60.179 60.000 0.00 0.0 0.00 4.24 F
4479 4855 2.619177 TGCAAGCTAAAACGGTTTGCTA 59.381 40.909 18.71 5.6 46.09 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2007 0.389948 GCACACTGGGGAGTACTTCG 60.390 60.000 0.0 0.0 0.00 3.79 R
2076 2119 1.153549 GTGCTAGAAGCTCCCACGG 60.154 63.158 0.0 0.0 42.97 4.94 R
2487 2840 2.619931 TCACTCTTTCTCATCCACCCA 58.380 47.619 0.0 0.0 0.00 4.51 R
3696 4071 4.280174 AGTGACAACCTGTAATGACGTACT 59.720 41.667 0.0 0.0 0.00 2.73 R
4786 5163 0.321346 ACGACATCCTGCATGACACA 59.679 50.000 0.0 0.0 36.21 3.72 R
5058 5438 0.462047 AGCCGAAGTAATGGAAGCGG 60.462 55.000 0.0 0.0 41.51 5.52 R
6053 6608 0.471780 TCACTCTGTCTGCCCTTGGA 60.472 55.000 0.0 0.0 0.00 3.53 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
23 24 0.613853 TTCCTGGATCCCGACGAGTT 60.614 55.000 9.90 0.00 0.00 3.01
32 33 1.733041 CCGACGAGTTGATGCGTGT 60.733 57.895 0.00 0.00 41.34 4.49
49 50 2.284798 CGTGTGTTATGGCGATGTAACG 60.285 50.000 0.00 0.00 34.37 3.18
79 80 1.753073 GCTACTACTTAGGCGGTTGGA 59.247 52.381 0.00 0.00 0.00 3.53
80 81 2.364647 GCTACTACTTAGGCGGTTGGAT 59.635 50.000 0.00 0.00 0.00 3.41
83 84 2.431057 ACTACTTAGGCGGTTGGATCAG 59.569 50.000 0.00 0.00 0.00 2.90
96 97 0.259938 GGATCAGACCCAATGGCCTT 59.740 55.000 3.32 0.00 33.59 4.35
110 111 5.233225 CAATGGCCTTTCTTCCTTTCTTTC 58.767 41.667 3.32 0.00 0.00 2.62
115 116 3.574396 CCTTTCTTCCTTTCTTTCCCCAC 59.426 47.826 0.00 0.00 0.00 4.61
116 117 3.963476 TTCTTCCTTTCTTTCCCCACA 57.037 42.857 0.00 0.00 0.00 4.17
123 124 2.561478 TTCTTTCCCCACAGCTACAC 57.439 50.000 0.00 0.00 0.00 2.90
124 125 1.429930 TCTTTCCCCACAGCTACACA 58.570 50.000 0.00 0.00 0.00 3.72
125 126 1.071699 TCTTTCCCCACAGCTACACAC 59.928 52.381 0.00 0.00 0.00 3.82
130 131 2.742372 CACAGCTACACACGGCCC 60.742 66.667 0.00 0.00 0.00 5.80
131 132 4.016706 ACAGCTACACACGGCCCC 62.017 66.667 0.00 0.00 0.00 5.80
136 137 3.324108 TACACACGGCCCCCTTCC 61.324 66.667 0.00 0.00 0.00 3.46
140 141 4.410400 CACGGCCCCCTTCCAGAC 62.410 72.222 0.00 0.00 0.00 3.51
153 154 4.164221 CCCTTCCAGACACCTAATGTACAT 59.836 45.833 1.41 1.41 43.56 2.29
191 192 3.268032 CTTCCACCTTGGGGGCCT 61.268 66.667 0.84 0.00 38.32 5.19
222 229 2.685380 CCTCTCAGGGCCGGTCTT 60.685 66.667 5.77 0.00 0.00 3.01
224 231 1.984570 CTCTCAGGGCCGGTCTTGA 60.985 63.158 20.69 20.69 0.00 3.02
233 249 2.100631 CCGGTCTTGATGCCGTGTC 61.101 63.158 0.00 0.00 45.91 3.67
239 255 1.282248 CTTGATGCCGTGTCGACGTT 61.282 55.000 11.62 0.00 44.54 3.99
246 262 1.213094 CCGTGTCGACGTTTCTTGCT 61.213 55.000 11.62 0.00 44.54 3.91
247 263 0.575390 CGTGTCGACGTTTCTTGCTT 59.425 50.000 11.62 0.00 40.91 3.91
255 271 3.618698 GACGTTTCTTGCTTTCTTGTCC 58.381 45.455 0.00 0.00 0.00 4.02
265 281 3.758973 TTCTTGTCCGTTGGCGCCA 62.759 57.895 29.03 29.03 36.67 5.69
303 319 5.577860 GCTGGTAGCGTAGAAATATGTTC 57.422 43.478 0.00 0.00 0.00 3.18
315 331 9.144085 CGTAGAAATATGTTCGCTAATTTTCAC 57.856 33.333 0.00 0.00 0.00 3.18
332 348 2.894902 TCACGCCGTTGCTAATGAATA 58.105 42.857 0.00 0.00 34.43 1.75
334 350 3.247411 TCACGCCGTTGCTAATGAATATG 59.753 43.478 0.00 0.00 34.43 1.78
339 355 4.083110 GCCGTTGCTAATGAATATGCTGAT 60.083 41.667 0.00 0.00 33.53 2.90
341 357 5.854866 CCGTTGCTAATGAATATGCTGATTG 59.145 40.000 0.00 0.00 0.00 2.67
344 362 7.531871 CGTTGCTAATGAATATGCTGATTGTAC 59.468 37.037 0.00 0.00 0.00 2.90
350 368 5.670485 TGAATATGCTGATTGTACCGTTCT 58.330 37.500 0.00 0.00 0.00 3.01
358 376 6.092122 TGCTGATTGTACCGTTCTATGAAAAG 59.908 38.462 0.00 0.00 0.00 2.27
406 424 8.192774 CCAACATGCATAACTAGATTGACAATT 58.807 33.333 0.00 0.00 0.00 2.32
524 546 0.955905 GTGGCCTTTAACTTTCGGCA 59.044 50.000 3.32 0.00 44.23 5.69
543 565 3.364964 GGCAACAACTCACCGACTTAATG 60.365 47.826 0.00 0.00 0.00 1.90
545 567 4.154195 GCAACAACTCACCGACTTAATGAT 59.846 41.667 0.00 0.00 0.00 2.45
552 574 5.092554 TCACCGACTTAATGATAAAGGCA 57.907 39.130 0.00 0.00 30.91 4.75
564 586 9.995003 TTAATGATAAAGGCAACAAAAGTTCAT 57.005 25.926 0.00 0.00 41.41 2.57
597 619 2.450609 ACGCAACAACGACTCCTTAT 57.549 45.000 0.00 0.00 36.70 1.73
598 620 2.334838 ACGCAACAACGACTCCTTATC 58.665 47.619 0.00 0.00 36.70 1.75
606 628 1.363080 GACTCCTTATCGCCGACCC 59.637 63.158 0.00 0.00 0.00 4.46
615 637 0.974010 ATCGCCGACCCTTTACCAGA 60.974 55.000 0.00 0.00 0.00 3.86
622 644 3.627577 CCGACCCTTTACCAGATTGATTG 59.372 47.826 0.00 0.00 0.00 2.67
665 687 6.545298 GGTCATGCTAATCTTCCTTTCAAGAT 59.455 38.462 0.00 0.00 43.70 2.40
666 688 7.416022 GTCATGCTAATCTTCCTTTCAAGATG 58.584 38.462 0.00 0.00 41.45 2.90
671 693 6.765512 GCTAATCTTCCTTTCAAGATGCTACT 59.234 38.462 0.00 0.00 41.45 2.57
672 694 6.998968 AATCTTCCTTTCAAGATGCTACTG 57.001 37.500 0.00 0.00 41.45 2.74
684 706 5.939764 AGATGCTACTGGTAGATCACAAA 57.060 39.130 11.44 0.00 35.21 2.83
685 707 6.491714 AGATGCTACTGGTAGATCACAAAT 57.508 37.500 11.44 0.00 35.21 2.32
692 719 8.148351 GCTACTGGTAGATCACAAATTACCATA 58.852 37.037 11.44 4.99 43.22 2.74
891 923 1.067821 GTCCATCAAAACCGCAACCAA 59.932 47.619 0.00 0.00 0.00 3.67
892 924 1.967066 TCCATCAAAACCGCAACCAAT 59.033 42.857 0.00 0.00 0.00 3.16
1215 1251 2.738521 CTCGAGGCCACCAACGTG 60.739 66.667 5.01 0.00 39.91 4.49
1266 1302 1.000521 CCTCATCCTGGCCAAGCAA 60.001 57.895 7.01 0.00 0.00 3.91
1311 1347 1.153208 CCTGCCCTGATCTGCTGTC 60.153 63.158 0.00 0.00 0.00 3.51
1346 1383 2.427245 CCTCAGATCTCCGGGCGTT 61.427 63.158 0.00 0.00 0.00 4.84
1394 1431 2.749839 TTCGGCGGAAATGGCTGG 60.750 61.111 7.21 0.00 37.38 4.85
1425 1463 6.217294 CGAGATTTTGATCCTAGGTTAGGTC 58.783 44.000 9.08 1.76 46.32 3.85
1469 1507 2.512515 GACGTCTGGGGCTGATGC 60.513 66.667 8.70 0.00 38.76 3.91
1539 1577 0.745845 ACCGTGCTTGATGGATCTGC 60.746 55.000 0.00 0.00 34.36 4.26
1573 1611 5.182001 ACTGCAATTCTTACATCACTGAACC 59.818 40.000 0.00 0.00 0.00 3.62
1578 1616 7.653311 GCAATTCTTACATCACTGAACCTTTTT 59.347 33.333 0.00 0.00 0.00 1.94
1579 1617 9.185192 CAATTCTTACATCACTGAACCTTTTTC 57.815 33.333 0.00 0.00 0.00 2.29
1615 1653 4.082081 CAGAAACCTGCATCAATGGCTAAA 60.082 41.667 0.00 0.00 0.00 1.85
1702 1740 2.872858 GAGGCCCGACTATTTCAATCAC 59.127 50.000 0.00 0.00 0.00 3.06
1791 1829 2.030805 AGTGAAATTGCTTCGTTGGCTC 60.031 45.455 0.00 0.00 36.78 4.70
1807 1845 1.377463 CTCTGAGTCCGGTCGAGGT 60.377 63.158 0.00 0.00 0.00 3.85
1911 1949 2.979130 GCAGATGGCCGAGTTCTAC 58.021 57.895 0.00 0.00 36.11 2.59
1927 1965 7.222224 CCGAGTTCTACAATAACAAGGTATGTC 59.778 40.741 0.00 0.00 42.99 3.06
1929 1967 9.654663 GAGTTCTACAATAACAAGGTATGTCTT 57.345 33.333 0.00 0.00 42.99 3.01
2041 2084 1.847968 ACTGTGCAGGGGTAAGGCT 60.848 57.895 4.11 0.00 0.00 4.58
2064 2107 1.067071 GCCTCGTATAATCCTTCCCCG 60.067 57.143 0.00 0.00 0.00 5.73
2213 2258 4.466015 TGCTGTTTCTTTTTGGAAAGGTCT 59.534 37.500 0.00 0.00 42.05 3.85
2214 2259 4.805719 GCTGTTTCTTTTTGGAAAGGTCTG 59.194 41.667 0.00 0.00 42.05 3.51
2250 2295 6.018425 GTGAGATGCATCTGTAACACTTATGG 60.018 42.308 33.33 0.00 37.25 2.74
2262 2307 7.217200 TGTAACACTTATGGCTATCATCCTTC 58.783 38.462 0.00 0.00 37.30 3.46
2291 2336 6.166984 TCAAGCAAAACAACCCATTTATCA 57.833 33.333 0.00 0.00 0.00 2.15
2453 2806 6.644347 AGCATCTAAAACAGTACATGCTACT 58.356 36.000 10.36 0.00 39.39 2.57
2487 2840 4.306600 GTCGCCAAATCAGGATTTTGTTT 58.693 39.130 4.57 0.00 38.84 2.83
2533 2886 9.512588 AAATGAGAGAATGAACTTGTATCTTGT 57.487 29.630 0.00 0.00 0.00 3.16
2713 3072 3.560636 ACATAATTCTGGAAGGGGACG 57.439 47.619 0.00 0.00 0.00 4.79
2733 3092 4.329392 ACGGTCGGGATTATGAAGTTTTT 58.671 39.130 0.00 0.00 0.00 1.94
2743 3102 9.406828 GGGATTATGAAGTTTTTGACAACTTAC 57.593 33.333 0.00 0.00 45.23 2.34
2807 3166 8.035448 AGGCCTAGAGTAGCATAAAGTTAATT 57.965 34.615 1.29 0.00 0.00 1.40
3085 3444 5.221541 TGGTTCATGATGCATATACACCGTA 60.222 40.000 0.00 0.00 0.00 4.02
3493 3868 5.508200 TTATTATTTTTACAGGGCTGCGG 57.492 39.130 0.00 0.00 0.00 5.69
3603 3978 0.250295 TCTCGTGCAGGAACCTTTGG 60.250 55.000 10.76 0.00 0.00 3.28
3664 4039 2.939756 TCGCAAGTGAGTGCTAAAAACA 59.060 40.909 0.00 0.00 42.62 2.83
3695 4070 9.947433 ACTGTTATCTAGCGTCTATTATCTACT 57.053 33.333 0.00 0.00 0.00 2.57
3866 4241 0.179124 GCGTAGTTGAGAGGGAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
4304 4680 9.965902 ACACTGATCTATTTTACATTTCCTCTT 57.034 29.630 0.00 0.00 0.00 2.85
4437 4813 4.431378 TCAAGTAAATGGTACTCCCTCCA 58.569 43.478 0.00 0.00 38.14 3.86
4471 4847 5.888412 AGATGTTTTTGCAAGCTAAAACG 57.112 34.783 26.86 0.00 46.54 3.60
4479 4855 2.619177 TGCAAGCTAAAACGGTTTGCTA 59.381 40.909 18.71 5.60 46.09 3.49
4772 5149 6.883756 TGGAATTAATATTGCATATGCCGAGA 59.116 34.615 24.54 11.20 37.20 4.04
4786 5163 8.936864 GCATATGCCGAGAGTAATTTAGTTAAT 58.063 33.333 17.26 0.00 34.31 1.40
4877 5254 5.869888 AGGTACTCGATTGTTCTGTGAATTC 59.130 40.000 0.00 0.00 0.00 2.17
5050 5430 7.227910 GGGTGTCAGTTATACTTGAACAAAGAA 59.772 37.037 0.00 0.00 39.38 2.52
5058 5438 4.574599 ACTTGAACAAAGAATCACTGGC 57.425 40.909 0.00 0.00 39.38 4.85
5222 5602 2.990066 ACACATAAGCTACAGGCCTC 57.010 50.000 0.00 0.00 43.05 4.70
5239 5619 1.880027 CCTCAACCTAACCTTGTGTGC 59.120 52.381 0.00 0.00 0.00 4.57
5383 5771 1.454201 TTTTGTGTGTGGCTGTTCGA 58.546 45.000 0.00 0.00 0.00 3.71
5525 5916 5.787953 TGTTTCTCTTGCCATTCATTTGA 57.212 34.783 0.00 0.00 0.00 2.69
5536 5927 4.379813 GCCATTCATTTGACCAGTGTGTAG 60.380 45.833 0.00 0.00 0.00 2.74
5575 5966 2.875296 TCCTTGCACTTGCTTGGTATT 58.125 42.857 2.33 0.00 42.66 1.89
5576 5967 3.230134 TCCTTGCACTTGCTTGGTATTT 58.770 40.909 2.33 0.00 42.66 1.40
5607 5998 5.752892 TTGTACGCCAACAAAATACTTCA 57.247 34.783 0.00 0.00 36.45 3.02
5619 6010 6.170506 ACAAAATACTTCAGTATGCTTCGGA 58.829 36.000 0.07 0.00 40.78 4.55
5642 6041 9.499585 CGGATGATGATTCTTTTTATGATATGC 57.500 33.333 0.00 0.00 0.00 3.14
5655 6054 3.303881 TGATATGCTATGACTGTCGGC 57.696 47.619 2.98 8.08 0.00 5.54
5666 6065 3.352338 CTGTCGGCGTGTCCCTACC 62.352 68.421 6.85 0.00 0.00 3.18
5672 6071 1.669440 GCGTGTCCCTACCTTGTCA 59.331 57.895 0.00 0.00 0.00 3.58
5683 6082 4.335416 CCTACCTTGTCATTGATGTTGGT 58.665 43.478 0.00 0.00 0.00 3.67
5684 6083 5.496556 CCTACCTTGTCATTGATGTTGGTA 58.503 41.667 0.00 1.02 0.00 3.25
5685 6084 5.354234 CCTACCTTGTCATTGATGTTGGTAC 59.646 44.000 0.00 0.00 0.00 3.34
5686 6085 4.724399 ACCTTGTCATTGATGTTGGTACA 58.276 39.130 0.00 0.00 38.95 2.90
5705 6109 7.264221 TGGTACACTGTTTCTTTAACGAACTA 58.736 34.615 0.00 0.00 39.72 2.24
5706 6110 7.436080 TGGTACACTGTTTCTTTAACGAACTAG 59.564 37.037 0.00 0.00 39.72 2.57
5708 6112 5.756833 ACACTGTTTCTTTAACGAACTAGGG 59.243 40.000 0.00 0.43 39.72 3.53
5709 6113 5.756833 CACTGTTTCTTTAACGAACTAGGGT 59.243 40.000 0.00 0.00 39.72 4.34
5711 6115 6.481313 ACTGTTTCTTTAACGAACTAGGGTTC 59.519 38.462 0.00 0.00 45.91 3.62
5713 6117 4.541973 TCTTTAACGAACTAGGGTTCCC 57.458 45.455 0.00 0.00 46.46 3.97
5715 6119 4.347583 TCTTTAACGAACTAGGGTTCCCAA 59.652 41.667 10.73 0.00 46.46 4.12
5722 6126 4.081309 CGAACTAGGGTTCCCAACTGATTA 60.081 45.833 10.73 0.00 46.46 1.75
5760 6305 4.494484 TGTTCACATCGTATCAGAGTTGG 58.506 43.478 0.00 0.00 0.00 3.77
5763 6308 3.761752 TCACATCGTATCAGAGTTGGACA 59.238 43.478 0.00 0.00 0.00 4.02
5764 6309 4.108336 CACATCGTATCAGAGTTGGACAG 58.892 47.826 0.00 0.00 0.00 3.51
5835 6388 6.712095 ACATTACAGAGATTGCAGACAGAAAA 59.288 34.615 0.00 0.00 0.00 2.29
5846 6399 3.406764 CAGACAGAAAAGGAAGGTCAGG 58.593 50.000 0.00 0.00 0.00 3.86
5887 6440 3.068590 AGAAACAAGCAAACACATGGAGG 59.931 43.478 0.00 0.00 0.00 4.30
5890 6443 0.469705 AAGCAAACACATGGAGGGCA 60.470 50.000 0.00 0.00 0.00 5.36
5929 6482 1.812922 AGCAGCACTACGAGCATGC 60.813 57.895 10.51 10.51 39.74 4.06
6053 6608 6.136541 AGAAACTTCGAAAGCAAACAAGAT 57.863 33.333 0.00 0.00 0.00 2.40
6065 6620 2.206576 AACAAGATCCAAGGGCAGAC 57.793 50.000 0.00 0.00 0.00 3.51
6066 6621 1.067295 ACAAGATCCAAGGGCAGACA 58.933 50.000 0.00 0.00 0.00 3.41
6069 6624 1.202330 AGATCCAAGGGCAGACAGAG 58.798 55.000 0.00 0.00 0.00 3.35
6070 6625 0.908198 GATCCAAGGGCAGACAGAGT 59.092 55.000 0.00 0.00 0.00 3.24
6202 6757 2.596338 TCGGTGAGCGTGGTCTGA 60.596 61.111 3.30 0.00 0.00 3.27
6205 6760 1.284982 CGGTGAGCGTGGTCTGAAAG 61.285 60.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.056223 GTCGGGATCCAGGAACGGA 61.056 63.158 15.23 6.29 40.07 4.69
1 2 2.499685 GTCGGGATCCAGGAACGG 59.500 66.667 15.23 4.30 0.00 4.44
9 10 0.876342 GCATCAACTCGTCGGGATCC 60.876 60.000 1.92 1.92 0.00 3.36
23 24 0.390472 TCGCCATAACACACGCATCA 60.390 50.000 0.00 0.00 0.00 3.07
55 56 2.454538 ACCGCCTAAGTAGTAGCAACT 58.545 47.619 0.00 0.00 39.91 3.16
57 58 2.093869 CCAACCGCCTAAGTAGTAGCAA 60.094 50.000 0.00 0.00 0.00 3.91
62 63 2.431057 CTGATCCAACCGCCTAAGTAGT 59.569 50.000 0.00 0.00 0.00 2.73
83 84 1.186200 GGAAGAAAGGCCATTGGGTC 58.814 55.000 5.01 0.00 39.90 4.46
96 97 3.832527 CTGTGGGGAAAGAAAGGAAGAA 58.167 45.455 0.00 0.00 0.00 2.52
110 111 2.047274 CCGTGTGTAGCTGTGGGG 60.047 66.667 0.00 0.00 0.00 4.96
115 116 4.778143 GGGGGCCGTGTGTAGCTG 62.778 72.222 0.00 0.00 0.00 4.24
123 124 4.410400 GTCTGGAAGGGGGCCGTG 62.410 72.222 0.00 0.00 0.00 4.94
124 125 4.974438 TGTCTGGAAGGGGGCCGT 62.974 66.667 0.00 0.00 0.00 5.68
125 126 4.410400 GTGTCTGGAAGGGGGCCG 62.410 72.222 0.00 0.00 0.00 6.13
130 131 3.517901 TGTACATTAGGTGTCTGGAAGGG 59.482 47.826 0.00 0.00 42.29 3.95
131 132 4.819105 TGTACATTAGGTGTCTGGAAGG 57.181 45.455 0.00 0.00 42.29 3.46
136 137 7.552458 TGCAATTATGTACATTAGGTGTCTG 57.448 36.000 14.77 2.49 42.29 3.51
140 141 8.009409 CACGTATGCAATTATGTACATTAGGTG 58.991 37.037 14.77 14.78 0.00 4.00
153 154 0.548989 AGCCCCCACGTATGCAATTA 59.451 50.000 0.00 0.00 0.00 1.40
207 214 1.306141 ATCAAGACCGGCCCTGAGA 60.306 57.895 0.00 1.81 0.00 3.27
218 225 1.674611 CGTCGACACGGCATCAAGAC 61.675 60.000 17.16 0.00 42.73 3.01
219 226 1.443702 CGTCGACACGGCATCAAGA 60.444 57.895 17.16 0.00 42.73 3.02
233 249 3.280775 GACAAGAAAGCAAGAAACGTCG 58.719 45.455 0.00 0.00 0.00 5.12
239 255 2.357637 CCAACGGACAAGAAAGCAAGAA 59.642 45.455 0.00 0.00 0.00 2.52
246 262 2.548295 GGCGCCAACGGACAAGAAA 61.548 57.895 24.80 0.00 40.57 2.52
247 263 2.975799 GGCGCCAACGGACAAGAA 60.976 61.111 24.80 0.00 40.57 2.52
303 319 1.246970 CAACGGCGTGAAAATTAGCG 58.753 50.000 15.70 0.00 0.00 4.26
332 348 5.276461 TCATAGAACGGTACAATCAGCAT 57.724 39.130 0.00 0.00 0.00 3.79
334 350 6.092259 ACTTTTCATAGAACGGTACAATCAGC 59.908 38.462 0.00 0.00 0.00 4.26
358 376 6.320944 TGGTTCCCGCGTAAATTTTTATAAC 58.679 36.000 4.92 0.00 0.00 1.89
366 384 1.606903 TGTTGGTTCCCGCGTAAATT 58.393 45.000 4.92 0.00 0.00 1.82
367 385 1.470890 CATGTTGGTTCCCGCGTAAAT 59.529 47.619 4.92 0.00 0.00 1.40
368 386 0.875728 CATGTTGGTTCCCGCGTAAA 59.124 50.000 4.92 0.00 0.00 2.01
369 387 1.579084 GCATGTTGGTTCCCGCGTAA 61.579 55.000 4.92 0.00 0.00 3.18
406 424 8.962884 TGTATTCGGTGTGTATAGTTAGAGTA 57.037 34.615 0.00 0.00 0.00 2.59
524 546 7.119262 CCTTTATCATTAAGTCGGTGAGTTGTT 59.881 37.037 0.00 0.00 0.00 2.83
543 565 7.713764 AACATGAACTTTTGTTGCCTTTATC 57.286 32.000 0.00 0.00 43.66 1.75
545 567 6.183360 GCAAACATGAACTTTTGTTGCCTTTA 60.183 34.615 0.00 0.00 43.66 1.85
552 574 4.201705 CGCTTGCAAACATGAACTTTTGTT 60.202 37.500 0.00 0.00 46.75 2.83
597 619 0.974010 ATCTGGTAAAGGGTCGGCGA 60.974 55.000 4.99 4.99 0.00 5.54
598 620 0.107848 AATCTGGTAAAGGGTCGGCG 60.108 55.000 0.00 0.00 0.00 6.46
606 628 9.177608 TCAGGAAATACAATCAATCTGGTAAAG 57.822 33.333 0.00 0.00 0.00 1.85
622 644 7.446625 AGCATGACCTAATCAATCAGGAAATAC 59.553 37.037 0.00 0.00 41.93 1.89
665 687 6.070481 TGGTAATTTGTGATCTACCAGTAGCA 60.070 38.462 5.42 3.81 39.06 3.49
666 688 6.346096 TGGTAATTTGTGATCTACCAGTAGC 58.654 40.000 5.42 1.89 39.06 3.58
759 787 9.952030 CCCCAAAATTAAAGTACCACATATTTT 57.048 29.630 0.00 0.00 0.00 1.82
760 788 9.327731 TCCCCAAAATTAAAGTACCACATATTT 57.672 29.630 0.00 0.00 0.00 1.40
761 789 8.903059 TCCCCAAAATTAAAGTACCACATATT 57.097 30.769 0.00 0.00 0.00 1.28
762 790 8.903059 TTCCCCAAAATTAAAGTACCACATAT 57.097 30.769 0.00 0.00 0.00 1.78
774 802 6.126911 GGCACTGGATAATTCCCCAAAATTAA 60.127 38.462 1.11 0.00 41.83 1.40
800 828 3.542648 ACATGAGATTGTGAGATGCTGG 58.457 45.455 0.00 0.00 0.00 4.85
891 923 4.408821 TGGCGCCGCTTCTCCAAT 62.409 61.111 23.90 0.00 0.00 3.16
1289 1325 3.117452 GCAGATCAGGGCAGGGAGG 62.117 68.421 0.00 0.00 0.00 4.30
1300 1336 1.133216 GCAGACGTAGACAGCAGATCA 59.867 52.381 0.00 0.00 34.72 2.92
1379 1416 3.508840 GACCAGCCATTTCCGCCG 61.509 66.667 0.00 0.00 0.00 6.46
1380 1417 3.508840 CGACCAGCCATTTCCGCC 61.509 66.667 0.00 0.00 0.00 6.13
1394 1431 2.159085 AGGATCAAAATCTCGGGTCGAC 60.159 50.000 7.13 7.13 32.12 4.20
1425 1463 5.531122 TCAACGAAACCCTATATCTCCTG 57.469 43.478 0.00 0.00 0.00 3.86
1469 1507 0.802494 GGACGCCATTACAACAGTGG 59.198 55.000 0.00 0.00 36.09 4.00
1504 1542 3.302221 GCACGGTAACATTGTACTATGCG 60.302 47.826 15.90 13.31 30.59 4.73
1702 1740 3.136763 ACTGTCAGCAACACTCTTCATG 58.863 45.455 0.00 0.00 33.24 3.07
1747 1785 1.087501 CGCAGCCTTTCCCTAAGAAC 58.912 55.000 0.00 0.00 35.80 3.01
1791 1829 1.171308 TAAACCTCGACCGGACTCAG 58.829 55.000 9.46 0.00 0.00 3.35
1807 1845 3.263261 TCAGGCGCGAAACATGTATAAA 58.737 40.909 12.10 0.00 0.00 1.40
1927 1965 6.967199 GCCTGTCGAAAATGGAATACTAAAAG 59.033 38.462 0.00 0.00 0.00 2.27
1929 1967 5.355910 GGCCTGTCGAAAATGGAATACTAAA 59.644 40.000 0.00 0.00 0.00 1.85
1932 1970 3.054361 AGGCCTGTCGAAAATGGAATACT 60.054 43.478 3.11 0.00 0.00 2.12
1933 1971 3.065371 CAGGCCTGTCGAAAATGGAATAC 59.935 47.826 25.53 0.00 0.00 1.89
1965 2007 0.389948 GCACACTGGGGAGTACTTCG 60.390 60.000 0.00 0.00 0.00 3.79
2041 2084 3.181448 GGGGAAGGATTATACGAGGCAAA 60.181 47.826 0.00 0.00 0.00 3.68
2076 2119 1.153549 GTGCTAGAAGCTCCCACGG 60.154 63.158 0.00 0.00 42.97 4.94
2213 2258 7.178097 ACAGATGCATCTCACTAATCTATAGCA 59.822 37.037 26.44 0.00 34.22 3.49
2214 2259 7.546358 ACAGATGCATCTCACTAATCTATAGC 58.454 38.462 26.44 0.00 34.22 2.97
2250 2295 7.502120 TGCTTGAATAAAGAAGGATGATAGC 57.498 36.000 0.00 0.00 38.24 2.97
2262 2307 7.495135 AATGGGTTGTTTTGCTTGAATAAAG 57.505 32.000 0.00 0.00 39.07 1.85
2360 2707 8.642908 AGGTTGTTCTAATGCTTTTGTTTTAC 57.357 30.769 0.00 0.00 0.00 2.01
2487 2840 2.619931 TCACTCTTTCTCATCCACCCA 58.380 47.619 0.00 0.00 0.00 4.51
2533 2886 7.389607 GGTGTGTCCTTTAGCTTTTATCTTGTA 59.610 37.037 0.00 0.00 0.00 2.41
2713 3072 5.182380 TGTCAAAAACTTCATAATCCCGACC 59.818 40.000 0.00 0.00 0.00 4.79
2733 3092 9.214957 CATGTGAACCTAATAAGTAAGTTGTCA 57.785 33.333 0.00 0.00 0.00 3.58
2807 3166 8.251721 TCAAAGGTTTCGGAAAAAGACATAAAA 58.748 29.630 4.46 0.00 0.00 1.52
2852 3211 5.951747 ACTATGAATTAGCATGTGTGGGTTT 59.048 36.000 0.00 0.00 0.00 3.27
2883 3242 9.487790 CATAAGTAAATGTTTCACCCAAAATGT 57.512 29.630 0.00 0.00 0.00 2.71
3085 3444 8.429641 TGTACTCAACAAGAACCTAAGAGAAAT 58.570 33.333 0.00 0.00 34.29 2.17
3122 3481 4.436515 CACTCAACGTGGTCAGCA 57.563 55.556 0.00 0.00 40.02 4.41
3493 3868 4.333926 GCCTTCATGTCATCAGTAACCTTC 59.666 45.833 0.00 0.00 0.00 3.46
3694 4069 5.798934 GTGACAACCTGTAATGACGTACTAG 59.201 44.000 0.00 0.00 0.00 2.57
3695 4070 5.474532 AGTGACAACCTGTAATGACGTACTA 59.525 40.000 0.00 0.00 0.00 1.82
3696 4071 4.280174 AGTGACAACCTGTAATGACGTACT 59.720 41.667 0.00 0.00 0.00 2.73
3866 4241 9.136323 AGGATTACAAATCCATATCCTGTTTTC 57.864 33.333 18.40 0.00 42.58 2.29
4187 4563 6.798476 CACCAAGCAGCATATGTAAATTATCG 59.202 38.462 4.29 0.00 0.00 2.92
4304 4680 3.096092 GACCACCCATCTGCCATTTTAA 58.904 45.455 0.00 0.00 0.00 1.52
4305 4681 2.733956 GACCACCCATCTGCCATTTTA 58.266 47.619 0.00 0.00 0.00 1.52
4437 4813 9.590451 CTTGCAAAAACATCTTATATTGTGGAT 57.410 29.630 0.00 0.00 0.00 3.41
4471 4847 1.530323 ATTGTGGGACGTAGCAAACC 58.470 50.000 0.00 0.00 0.00 3.27
4479 4855 8.349983 GCAAAAATATCTTATATTGTGGGACGT 58.650 33.333 0.00 0.00 0.00 4.34
4542 4918 2.725221 ATACGTTACTCCCTCCGTCT 57.275 50.000 0.00 0.00 34.95 4.18
4747 5124 6.883756 TCTCGGCATATGCAATATTAATTCCA 59.116 34.615 28.07 0.00 37.44 3.53
4772 5149 8.677300 CCTGCATGACACATTAACTAAATTACT 58.323 33.333 0.00 0.00 0.00 2.24
4786 5163 0.321346 ACGACATCCTGCATGACACA 59.679 50.000 0.00 0.00 36.21 3.72
4877 5254 3.314553 ACACTTTTAGACCGATGACACG 58.685 45.455 0.00 0.00 0.00 4.49
5050 5430 0.546122 TAATGGAAGCGGCCAGTGAT 59.454 50.000 2.24 0.00 42.15 3.06
5058 5438 0.462047 AGCCGAAGTAATGGAAGCGG 60.462 55.000 0.00 0.00 41.51 5.52
5222 5602 3.214328 AGAAGCACACAAGGTTAGGTTG 58.786 45.455 0.00 0.00 0.00 3.77
5239 5619 2.286872 CTCCACCTGCAGCATAAGAAG 58.713 52.381 8.66 0.00 0.00 2.85
5383 5771 1.403249 GCAAAGGCAGCATCGAACAAT 60.403 47.619 0.00 0.00 40.72 2.71
5414 5805 5.425217 TCTCAGCATACCACCATCTTAGAAA 59.575 40.000 0.00 0.00 0.00 2.52
5488 5879 2.295349 AGAAACAACAATCTGCAGGCAG 59.705 45.455 15.13 14.97 44.86 4.85
5525 5916 2.224159 CCAGGCCCTACACACTGGT 61.224 63.158 0.00 0.00 44.21 4.00
5575 5966 7.591006 TTTGTTGGCGTACAAATAACAAAAA 57.409 28.000 17.61 3.70 43.84 1.94
5607 5998 5.480642 AGAATCATCATCCGAAGCATACT 57.519 39.130 0.00 0.00 0.00 2.12
5642 6041 0.525668 GGACACGCCGACAGTCATAG 60.526 60.000 0.41 0.00 34.04 2.23
5643 6042 1.509463 GGACACGCCGACAGTCATA 59.491 57.895 0.41 0.00 34.04 2.15
5655 6054 2.028476 TCAATGACAAGGTAGGGACACG 60.028 50.000 0.00 0.00 0.00 4.49
5666 6065 5.239306 ACAGTGTACCAACATCAATGACAAG 59.761 40.000 0.00 0.00 38.08 3.16
5672 6071 6.959639 AAGAAACAGTGTACCAACATCAAT 57.040 33.333 0.00 0.00 38.08 2.57
5683 6082 6.925165 CCCTAGTTCGTTAAAGAAACAGTGTA 59.075 38.462 5.37 0.00 38.03 2.90
5684 6083 5.756833 CCCTAGTTCGTTAAAGAAACAGTGT 59.243 40.000 5.37 0.00 38.03 3.55
5685 6084 5.756833 ACCCTAGTTCGTTAAAGAAACAGTG 59.243 40.000 5.37 0.94 38.03 3.66
5686 6085 5.922053 ACCCTAGTTCGTTAAAGAAACAGT 58.078 37.500 5.37 0.00 38.03 3.55
5753 6298 2.024414 GGTTTTGCACTGTCCAACTCT 58.976 47.619 0.00 0.00 0.00 3.24
5760 6305 4.726416 CTCATATGTGGTTTTGCACTGTC 58.274 43.478 1.90 0.00 0.00 3.51
5763 6308 3.156293 TGCTCATATGTGGTTTTGCACT 58.844 40.909 1.90 0.00 0.00 4.40
5764 6309 3.191162 TCTGCTCATATGTGGTTTTGCAC 59.809 43.478 1.90 0.00 0.00 4.57
5835 6388 2.530151 TGCTGGCCTGACCTTCCT 60.530 61.111 14.77 0.00 40.22 3.36
5846 6399 1.467734 CTTGTTCATGTCTCTGCTGGC 59.532 52.381 0.00 0.00 0.00 4.85
6053 6608 0.471780 TCACTCTGTCTGCCCTTGGA 60.472 55.000 0.00 0.00 0.00 3.53
6202 6757 1.276705 GAGAAGTCCTTCGGCCTCTTT 59.723 52.381 0.00 0.00 43.97 2.52
6205 6760 1.518302 GGAGAAGTCCTTCGGCCTC 59.482 63.158 0.00 0.00 43.97 4.70
6208 6763 1.153804 GTCGGAGAAGTCCTTCGGC 60.154 63.158 1.59 0.00 44.04 5.54


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

AutoCloner maintained by Alex Coulton.