Multiple sequence alignment - TraesCS5D01G357400

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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 TraesCS5D01G357400 chr5D 100.000 3083 0 0 1 3083 438156387 438153305 0.000000e+00 5694.0
1 TraesCS5D01G357400 chr5D 73.900 341 83 6 2657 2994 521086583 521086920 6.940000e-27 132.0
2 TraesCS5D01G357400 chr5D 76.991 226 46 6 2752 2973 411611062 411610839 1.160000e-24 124.0
3 TraesCS5D01G357400 chr5D 81.731 104 9 6 2135 2228 437993645 437993748 9.170000e-11 78.7
4 TraesCS5D01G357400 chr5B 91.205 1046 51 15 1314 2348 532730344 532729329 0.000000e+00 1384.0
5 TraesCS5D01G357400 chr5B 90.747 897 51 12 429 1319 532731485 532730615 0.000000e+00 1168.0
6 TraesCS5D01G357400 chr5B 87.126 668 67 12 2350 3014 532729291 532728640 0.000000e+00 739.0
7 TraesCS5D01G357400 chr5A 92.694 917 47 6 744 1656 553145664 553144764 0.000000e+00 1304.0
8 TraesCS5D01G357400 chr5A 92.453 424 31 1 2661 3083 553144077 553143654 3.400000e-169 604.0
9 TraesCS5D01G357400 chr5A 95.473 243 9 2 2108 2348 553144770 553144528 1.340000e-103 387.0
10 TraesCS5D01G357400 chr5A 92.647 136 9 1 2528 2663 553144505 553144371 8.720000e-46 195.0
11 TraesCS5D01G357400 chr5A 77.381 336 60 14 2663 2991 616917840 616917514 5.250000e-43 185.0
12 TraesCS5D01G357400 chrUn 90.372 457 13 5 1 428 12354353 12354807 3.450000e-159 571.0
13 TraesCS5D01G357400 chrUn 88.399 431 43 6 1 428 412640271 412639845 2.120000e-141 512.0
14 TraesCS5D01G357400 chr7B 89.120 432 41 5 1 429 712731039 712730611 1.630000e-147 532.0
15 TraesCS5D01G357400 chr7B 88.863 431 42 5 1 428 712732561 712732134 2.720000e-145 525.0
16 TraesCS5D01G357400 chr7B 88.863 431 41 6 1 428 31376343 31375917 9.800000e-145 523.0
17 TraesCS5D01G357400 chr7B 88.631 431 42 6 1 428 31374801 31374375 4.560000e-143 518.0
18 TraesCS5D01G357400 chr7B 87.248 149 15 2 2511 2658 619095400 619095545 1.900000e-37 167.0
19 TraesCS5D01G357400 chr7B 83.708 178 19 5 2483 2658 605978658 605978827 3.180000e-35 159.0
20 TraesCS5D01G357400 chr2B 88.710 434 41 7 1 431 759181418 759180990 9.800000e-145 523.0
21 TraesCS5D01G357400 chr2B 82.123 179 30 2 2676 2853 91592210 91592387 5.320000e-33 152.0
22 TraesCS5D01G357400 chr1D 88.785 428 45 3 1 428 135396401 135396825 3.520000e-144 521.0
23 TraesCS5D01G357400 chr4B 88.167 431 44 6 1 428 664086884 664087310 9.860000e-140 507.0
24 TraesCS5D01G357400 chr4B 78.448 232 49 1 2764 2994 98700568 98700337 1.920000e-32 150.0
25 TraesCS5D01G357400 chr3B 84.444 180 19 4 2479 2657 9646996 9646825 5.290000e-38 169.0
26 TraesCS5D01G357400 chr7D 84.091 176 20 4 2483 2657 632637841 632637673 2.460000e-36 163.0
27 TraesCS5D01G357400 chr7D 82.320 181 23 5 2479 2657 621743876 621744049 6.890000e-32 148.0
28 TraesCS5D01G357400 chr7D 83.051 118 18 2 2822 2938 23186288 23186404 4.200000e-19 106.0
29 TraesCS5D01G357400 chr2A 83.708 178 19 5 2480 2657 44797208 44797041 3.180000e-35 159.0
30 TraesCS5D01G357400 chr6A 82.123 179 26 4 2477 2655 55366339 55366511 6.890000e-32 148.0
31 TraesCS5D01G357400 chr3A 76.018 221 45 6 2782 2996 730912607 730912389 1.170000e-19 108.0
32 TraesCS5D01G357400 chr6B 74.272 206 41 7 429 631 718597686 718597882 3.300000e-10 76.8
33 TraesCS5D01G357400 chr6D 77.305 141 22 5 493 631 473115626 473115758 1.190000e-09 75.0


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 TraesCS5D01G357400 chr5D 438153305 438156387 3082 True 5694.0 5694 100.000000 1 3083 1 chr5D.!!$R2 3082
1 TraesCS5D01G357400 chr5B 532728640 532731485 2845 True 1097.0 1384 89.692667 429 3014 3 chr5B.!!$R1 2585
2 TraesCS5D01G357400 chr5A 553143654 553145664 2010 True 622.5 1304 93.316750 744 3083 4 chr5A.!!$R2 2339
3 TraesCS5D01G357400 chr7B 712730611 712732561 1950 True 528.5 532 88.991500 1 429 2 chr7B.!!$R2 428
4 TraesCS5D01G357400 chr7B 31374375 31376343 1968 True 520.5 523 88.747000 1 428 2 chr7B.!!$R1 427

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
80 1624 0.036306 CCTGGAGCCGGTTGTTAAGT 59.964 55.0 1.9 0.0 0.00 2.24 F
240 1784 0.036765 GTTGCCGAGTATGGTGTCCA 60.037 55.0 0.0 0.0 38.19 4.02 F
1631 3461 0.036671 GGGTCAGTTAAGGTCGTGGG 60.037 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 2690 0.036732 TTAGGCCGCATGGATCATCC 59.963 55.0 0.0 0.0 37.49 3.51 R
1744 3574 0.107456 CCTGGCATCGATGGTAGCTT 59.893 55.0 26.0 0.0 0.00 3.74 R
2940 5115 0.035820 GTGGATACCGGCCTTTGTCA 60.036 55.0 0.0 0.0 0.00 3.58 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
20 21 4.853507 CGTGAAGCCATGCAACAG 57.146 55.556 0.00 0.00 0.00 3.16
31 32 1.127397 CATGCAACAGCGACAGTACAG 59.873 52.381 0.00 0.00 0.00 2.74
43 1587 1.362932 ACAGTACAGGAGGTGGAGGAT 59.637 52.381 0.00 0.00 0.00 3.24
74 1618 2.046892 CAGTCCTGGAGCCGGTTG 60.047 66.667 1.90 0.00 0.00 3.77
79 1623 0.323629 TCCTGGAGCCGGTTGTTAAG 59.676 55.000 1.90 0.00 0.00 1.85
80 1624 0.036306 CCTGGAGCCGGTTGTTAAGT 59.964 55.000 1.90 0.00 0.00 2.24
103 1647 6.841755 AGTTAAGTAGCCAAGTAGATCAGGAT 59.158 38.462 0.00 0.00 0.00 3.24
113 1657 6.926272 CCAAGTAGATCAGGATTAGTAGTTGC 59.074 42.308 0.00 0.00 0.00 4.17
135 1679 1.827789 ATGCACGTTGTGTTGGCCT 60.828 52.632 3.32 0.00 35.75 5.19
139 1683 1.822186 ACGTTGTGTTGGCCTGGTC 60.822 57.895 3.32 0.00 0.00 4.02
152 1696 1.296392 CTGGTCATGAGGCCGTTGA 59.704 57.895 0.00 0.00 0.00 3.18
158 1702 0.179089 CATGAGGCCGTTGAGAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
176 1720 3.605664 GTTGCGCAAGGGCCAAGT 61.606 61.111 25.78 0.00 36.38 3.16
181 1725 1.595093 GCGCAAGGGCCAAGTATTGT 61.595 55.000 6.18 0.00 41.30 2.71
185 1729 2.937873 GCAAGGGCCAAGTATTGTCGTA 60.938 50.000 6.18 0.00 46.99 3.43
217 1761 2.052104 GGTGCATGGGTTAGTGGCC 61.052 63.158 0.00 0.00 0.00 5.36
237 1781 2.093658 CCTTAGTTGCCGAGTATGGTGT 60.094 50.000 0.00 0.00 0.00 4.16
239 1783 0.249398 AGTTGCCGAGTATGGTGTCC 59.751 55.000 0.00 0.00 0.00 4.02
240 1784 0.036765 GTTGCCGAGTATGGTGTCCA 60.037 55.000 0.00 0.00 38.19 4.02
255 1799 2.516695 CCAGGCTGTGTGTGTGCA 60.517 61.111 14.43 0.00 0.00 4.57
257 1801 1.284715 CAGGCTGTGTGTGTGCATG 59.715 57.895 6.28 0.00 32.42 4.06
289 1833 6.529463 AACTTGTAATCATGTTTGCTTTGC 57.471 33.333 6.23 0.00 38.28 3.68
290 1834 5.599732 ACTTGTAATCATGTTTGCTTTGCA 58.400 33.333 6.23 0.00 36.47 4.08
306 1850 6.175471 TGCTTTGCATCAAGAGAAATAGAGA 58.825 36.000 2.23 0.00 31.71 3.10
307 1851 6.315642 TGCTTTGCATCAAGAGAAATAGAGAG 59.684 38.462 2.23 0.00 31.71 3.20
328 1875 1.692411 AGAAAAGGTTGGGCTGTGAC 58.308 50.000 0.00 0.00 0.00 3.67
347 1894 1.153329 AGTCCGACGCCAAAACACA 60.153 52.632 0.00 0.00 0.00 3.72
359 1906 3.612479 GCCAAAACACATGTGTCTCCATC 60.612 47.826 30.64 14.86 44.13 3.51
360 1907 3.365264 CCAAAACACATGTGTCTCCATCG 60.365 47.826 30.64 14.72 44.13 3.84
366 1913 2.300152 ACATGTGTCTCCATCGTCTTGT 59.700 45.455 0.00 0.00 0.00 3.16
369 1916 2.061773 GTGTCTCCATCGTCTTGTGTG 58.938 52.381 0.00 0.00 0.00 3.82
370 1917 1.686587 TGTCTCCATCGTCTTGTGTGT 59.313 47.619 0.00 0.00 0.00 3.72
373 1920 1.794701 CTCCATCGTCTTGTGTGTGTG 59.205 52.381 0.00 0.00 0.00 3.82
374 1921 1.138069 TCCATCGTCTTGTGTGTGTGT 59.862 47.619 0.00 0.00 0.00 3.72
381 1928 3.000041 GTCTTGTGTGTGTGTTGTGAGA 59.000 45.455 0.00 0.00 0.00 3.27
382 1929 3.435327 GTCTTGTGTGTGTGTTGTGAGAA 59.565 43.478 0.00 0.00 0.00 2.87
383 1930 3.684305 TCTTGTGTGTGTGTTGTGAGAAG 59.316 43.478 0.00 0.00 0.00 2.85
384 1931 1.737236 TGTGTGTGTGTTGTGAGAAGC 59.263 47.619 0.00 0.00 0.00 3.86
385 1932 1.737236 GTGTGTGTGTTGTGAGAAGCA 59.263 47.619 0.00 0.00 0.00 3.91
386 1933 2.161410 GTGTGTGTGTTGTGAGAAGCAA 59.839 45.455 0.00 0.00 0.00 3.91
387 1934 2.161410 TGTGTGTGTTGTGAGAAGCAAC 59.839 45.455 0.00 0.00 44.50 4.17
388 1935 1.742831 TGTGTGTTGTGAGAAGCAACC 59.257 47.619 5.84 0.00 43.86 3.77
389 1936 1.742831 GTGTGTTGTGAGAAGCAACCA 59.257 47.619 5.84 1.82 43.86 3.67
391 1938 2.822561 TGTGTTGTGAGAAGCAACCAAA 59.177 40.909 5.84 0.00 43.86 3.28
392 1939 3.256879 TGTGTTGTGAGAAGCAACCAAAA 59.743 39.130 5.84 0.00 43.86 2.44
398 1945 4.336433 TGTGAGAAGCAACCAAAAGAGAAG 59.664 41.667 0.00 0.00 0.00 2.85
399 1946 3.885297 TGAGAAGCAACCAAAAGAGAAGG 59.115 43.478 0.00 0.00 0.00 3.46
400 1947 3.885901 GAGAAGCAACCAAAAGAGAAGGT 59.114 43.478 0.00 0.00 37.20 3.50
434 1981 2.763448 GAGTCAGCTCCAACACTCCTAT 59.237 50.000 0.00 0.00 35.76 2.57
442 1989 5.104193 AGCTCCAACACTCCTATGATGAAAT 60.104 40.000 0.00 0.00 0.00 2.17
505 2052 1.669440 GCGGTGTAGTCTTGGACCA 59.331 57.895 0.00 0.00 32.18 4.02
510 2057 0.601558 TGTAGTCTTGGACCACGAGC 59.398 55.000 0.00 0.00 32.18 5.03
525 2072 0.389391 CGAGCAGGTGGTACCCATAG 59.611 60.000 10.07 0.00 39.75 2.23
633 2180 1.372997 GGCGAGTCTGCGAGTTGAA 60.373 57.895 0.00 0.00 35.06 2.69
657 2204 3.017232 CGAGACGCACAAGTAGACC 57.983 57.895 0.00 0.00 0.00 3.85
664 2211 1.944024 CGCACAAGTAGACCCAACAAA 59.056 47.619 0.00 0.00 0.00 2.83
665 2212 2.032030 CGCACAAGTAGACCCAACAAAG 60.032 50.000 0.00 0.00 0.00 2.77
666 2213 2.287608 GCACAAGTAGACCCAACAAAGC 60.288 50.000 0.00 0.00 0.00 3.51
667 2214 2.032030 CACAAGTAGACCCAACAAAGCG 60.032 50.000 0.00 0.00 0.00 4.68
668 2215 2.158871 ACAAGTAGACCCAACAAAGCGA 60.159 45.455 0.00 0.00 0.00 4.93
669 2216 2.875933 CAAGTAGACCCAACAAAGCGAA 59.124 45.455 0.00 0.00 0.00 4.70
670 2217 3.202829 AGTAGACCCAACAAAGCGAAA 57.797 42.857 0.00 0.00 0.00 3.46
671 2218 2.876550 AGTAGACCCAACAAAGCGAAAC 59.123 45.455 0.00 0.00 0.00 2.78
684 2231 2.753966 CGAAACAGGCCGCTGGATG 61.754 63.158 0.00 0.00 0.00 3.51
720 2267 1.523758 AACTCACGTTCAATCTGGGC 58.476 50.000 0.00 0.00 0.00 5.36
722 2269 1.361668 CTCACGTTCAATCTGGGCGG 61.362 60.000 0.00 0.00 0.00 6.13
723 2270 2.046314 ACGTTCAATCTGGGCGGG 60.046 61.111 0.00 0.00 0.00 6.13
724 2271 2.824041 CGTTCAATCTGGGCGGGG 60.824 66.667 0.00 0.00 0.00 5.73
725 2272 3.140814 GTTCAATCTGGGCGGGGC 61.141 66.667 0.00 0.00 0.00 5.80
726 2273 3.338250 TTCAATCTGGGCGGGGCT 61.338 61.111 0.00 0.00 0.00 5.19
727 2274 1.998438 TTCAATCTGGGCGGGGCTA 60.998 57.895 0.00 0.00 0.00 3.93
728 2275 2.203209 CAATCTGGGCGGGGCTAC 60.203 66.667 0.00 0.00 0.00 3.58
729 2276 2.690881 AATCTGGGCGGGGCTACA 60.691 61.111 0.00 0.00 0.00 2.74
730 2277 2.078665 AATCTGGGCGGGGCTACAT 61.079 57.895 0.00 0.00 0.00 2.29
731 2278 2.343475 AATCTGGGCGGGGCTACATG 62.343 60.000 0.00 0.00 0.00 3.21
732 2279 3.797353 CTGGGCGGGGCTACATGT 61.797 66.667 2.69 2.69 0.00 3.21
733 2280 2.365768 TGGGCGGGGCTACATGTA 60.366 61.111 5.25 5.25 0.00 2.29
734 2281 1.768482 TGGGCGGGGCTACATGTAT 60.768 57.895 5.91 0.00 0.00 2.29
735 2282 0.472161 TGGGCGGGGCTACATGTATA 60.472 55.000 5.91 0.00 0.00 1.47
736 2283 0.909623 GGGCGGGGCTACATGTATAT 59.090 55.000 5.91 0.00 0.00 0.86
737 2284 1.280998 GGGCGGGGCTACATGTATATT 59.719 52.381 5.91 0.00 0.00 1.28
738 2285 2.290705 GGGCGGGGCTACATGTATATTT 60.291 50.000 5.91 0.00 0.00 1.40
739 2286 3.054948 GGGCGGGGCTACATGTATATTTA 60.055 47.826 5.91 0.00 0.00 1.40
745 2292 7.385205 GCGGGGCTACATGTATATTTATAGATG 59.615 40.741 5.91 11.27 42.42 2.90
845 2395 6.591448 GGCAGAACCAAATTCAAATAGAAAGG 59.409 38.462 0.00 0.00 40.09 3.11
947 2497 1.911357 TCAGCTGGAGATCAACCACAT 59.089 47.619 15.13 0.00 33.57 3.21
949 2499 3.713248 TCAGCTGGAGATCAACCACATAT 59.287 43.478 15.13 0.00 33.57 1.78
950 2500 4.901250 TCAGCTGGAGATCAACCACATATA 59.099 41.667 15.13 0.00 33.57 0.86
951 2501 5.366477 TCAGCTGGAGATCAACCACATATAA 59.634 40.000 15.13 0.00 33.57 0.98
958 2510 8.097038 TGGAGATCAACCACATATAAATAGAGC 58.903 37.037 7.43 0.00 32.03 4.09
1066 2619 1.678970 AGCTGCGTTGGGGAAATCC 60.679 57.895 0.00 0.00 0.00 3.01
1084 2637 1.979155 CTCCTCTCTGCCGGTGACA 60.979 63.158 1.90 0.00 0.00 3.58
1327 3156 1.676746 CGACGGTCTTATCCTCCTGA 58.323 55.000 6.57 0.00 0.00 3.86
1349 3178 0.392998 GTGGACACTGGGTATGGCTG 60.393 60.000 0.00 0.00 0.00 4.85
1356 3185 0.392706 CTGGGTATGGCTGCGACATA 59.607 55.000 0.71 0.71 31.56 2.29
1359 3188 0.798776 GGTATGGCTGCGACATATGC 59.201 55.000 1.58 0.00 35.84 3.14
1481 3310 4.621991 CCACTCGTCTTTCTCTTTCTTGA 58.378 43.478 0.00 0.00 0.00 3.02
1489 3318 7.435488 TCGTCTTTCTCTTTCTTGACTGTTTAG 59.565 37.037 0.00 0.00 0.00 1.85
1540 3369 2.744709 CCCGGTGGTTTAGTGCCG 60.745 66.667 0.00 0.00 43.40 5.69
1607 3437 1.273887 GCGCATATATCGCCGATGC 59.726 57.895 10.41 5.00 46.18 3.91
1631 3461 0.036671 GGGTCAGTTAAGGTCGTGGG 60.037 60.000 0.00 0.00 0.00 4.61
1658 3488 4.123545 GGGGCCGCATACCAACCT 62.124 66.667 16.21 0.00 0.00 3.50
1872 3702 3.463944 CGGAAACCGTGCTATATTCCTT 58.536 45.455 1.80 0.00 42.73 3.36
1877 3707 2.104281 ACCGTGCTATATTCCTTGGTCC 59.896 50.000 0.00 0.00 0.00 4.46
1881 3711 1.610886 GCTATATTCCTTGGTCCCGGC 60.611 57.143 0.00 0.00 0.00 6.13
1900 3730 1.177401 CCACTGTCTCTCCATCGACA 58.823 55.000 0.00 0.00 37.79 4.35
1947 3777 7.589958 AGCTAACTGCATCTACTACTACAAT 57.410 36.000 0.00 0.00 45.94 2.71
1962 3792 8.379457 ACTACTACAATGTCAAGGAAAAAGAC 57.621 34.615 0.00 0.00 0.00 3.01
2023 3853 0.107459 GTTGCTCACATCTCCCCCTC 60.107 60.000 0.00 0.00 0.00 4.30
2040 3870 0.392729 CTCTACACGGTCCCTCGAGT 60.393 60.000 12.31 0.00 37.65 4.18
2048 3878 2.989253 TCCCTCGAGTCTTGCGCA 60.989 61.111 5.66 5.66 0.00 6.09
2056 3886 1.789464 CGAGTCTTGCGCAGATTATCC 59.211 52.381 11.31 0.00 32.60 2.59
2058 3888 3.304726 CGAGTCTTGCGCAGATTATCCTA 60.305 47.826 11.31 0.00 32.60 2.94
2080 3910 2.429933 ATACTGCAGGGGGAGATCAT 57.570 50.000 19.93 0.00 36.18 2.45
2081 3911 3.567375 ATACTGCAGGGGGAGATCATA 57.433 47.619 19.93 0.00 36.18 2.15
2129 3959 4.821805 AGACACAAAATGGTGACTTAGGTG 59.178 41.667 0.00 0.00 40.04 4.00
2133 3963 5.995282 CACAAAATGGTGACTTAGGTGACTA 59.005 40.000 0.00 0.00 40.75 2.59
2340 4179 7.926018 ACTTTTTGTTGGCTTCAAACCTAATAG 59.074 33.333 7.04 0.00 35.05 1.73
2348 4187 3.560636 TCAAACCTAATAGGGCTGAGC 57.439 47.619 11.52 0.00 40.58 4.26
2391 4266 7.695480 AACTGCACCATGTACAATGTTATTA 57.305 32.000 0.00 0.00 0.00 0.98
2425 4300 7.596749 ACTATTGTTATCGGCTGTTATATGC 57.403 36.000 0.00 0.00 0.00 3.14
2426 4301 7.158697 ACTATTGTTATCGGCTGTTATATGCA 58.841 34.615 0.00 0.00 0.00 3.96
2427 4302 7.824289 ACTATTGTTATCGGCTGTTATATGCAT 59.176 33.333 3.79 3.79 0.00 3.96
2428 4303 5.861222 TGTTATCGGCTGTTATATGCATG 57.139 39.130 10.16 0.00 0.00 4.06
2472 4347 4.161333 GACAAAGATTTTGTCATGCCGAG 58.839 43.478 22.85 0.00 45.89 4.63
2482 4357 2.224281 TGTCATGCCGAGACTTGTTTCT 60.224 45.455 0.00 0.00 36.94 2.52
2515 4392 8.462016 CGGGAAACTTTTCATCTATTCATCTTT 58.538 33.333 4.18 0.00 38.92 2.52
2543 4420 6.818142 TCATGAATCATGACAGTACAACGAAT 59.182 34.615 20.85 0.00 44.60 3.34
2548 4425 5.785243 TCATGACAGTACAACGAATACCAA 58.215 37.500 0.00 0.00 0.00 3.67
2604 4481 3.195825 ACCTAGTGATGACTACAAGCACC 59.804 47.826 0.00 0.00 36.64 5.01
2732 4905 5.815233 ATACCACATTCGAGAAGATCCAT 57.185 39.130 0.00 0.00 0.00 3.41
2754 4927 2.131776 AAGACAACCACCAACCGAAA 57.868 45.000 0.00 0.00 0.00 3.46
2756 4929 1.064979 AGACAACCACCAACCGAAACT 60.065 47.619 0.00 0.00 0.00 2.66
2796 4969 2.203252 CATCCACATGCCCTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
2878 5053 3.644884 AACTGATGTCGTCTCGTCTTT 57.355 42.857 0.00 0.00 0.00 2.52
2900 5075 1.623811 TGAGCAGGACAGAAACCCTAC 59.376 52.381 0.00 0.00 0.00 3.18
2905 5080 3.146847 CAGGACAGAAACCCTACCAAAC 58.853 50.000 0.00 0.00 0.00 2.93
2940 5115 1.716028 AAAAACCGAGCCCTCCCACT 61.716 55.000 0.00 0.00 0.00 4.00
2947 5122 0.322008 GAGCCCTCCCACTGACAAAG 60.322 60.000 0.00 0.00 0.00 2.77
2948 5123 1.303643 GCCCTCCCACTGACAAAGG 60.304 63.158 0.00 0.00 0.00 3.11
2949 5124 1.303643 CCCTCCCACTGACAAAGGC 60.304 63.158 0.00 0.00 0.00 4.35
2950 5125 1.303643 CCTCCCACTGACAAAGGCC 60.304 63.158 0.00 0.00 0.00 5.19
2978 5157 3.100545 CATGCACCCATGGTCCTAC 57.899 57.895 11.73 0.00 44.07 3.18
2997 5176 0.242825 CGGCCACAGAAGAAGACGTA 59.757 55.000 2.24 0.00 0.00 3.57
3036 5215 1.035932 TCCCTAGCCGTCTTTCCTCG 61.036 60.000 0.00 0.00 0.00 4.63
3053 5232 0.408309 TCGGGAGGAGAGACAAAGGA 59.592 55.000 0.00 0.00 0.00 3.36
3070 5249 3.358076 GAAGGAGAGACGCACGGGG 62.358 68.421 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.215647 CCACCTCCTGTACTGTCGC 59.784 63.158 0.00 0.00 0.00 5.19
31 32 1.486726 CACAGGTTATCCTCCACCTCC 59.513 57.143 0.00 0.00 41.86 4.30
43 1587 2.104111 CAGGACTGGTTCACACAGGTTA 59.896 50.000 0.00 0.00 40.23 2.85
74 1618 9.303537 CTGATCTACTTGGCTACTTAACTTAAC 57.696 37.037 0.00 0.00 0.00 2.01
79 1623 6.466885 TCCTGATCTACTTGGCTACTTAAC 57.533 41.667 0.00 0.00 0.00 2.01
80 1624 7.676683 AATCCTGATCTACTTGGCTACTTAA 57.323 36.000 0.00 0.00 0.00 1.85
113 1657 0.935831 CCAACACAACGTGCATGCAG 60.936 55.000 23.41 17.33 36.98 4.41
126 1670 0.962356 CCTCATGACCAGGCCAACAC 60.962 60.000 5.01 0.00 0.00 3.32
135 1679 1.191489 TCTCAACGGCCTCATGACCA 61.191 55.000 0.00 0.00 0.00 4.02
139 1683 0.179089 CTCCTCTCAACGGCCTCATG 60.179 60.000 0.00 0.00 0.00 3.07
152 1696 2.348998 CCTTGCGCAACCTCCTCT 59.651 61.111 21.02 0.00 0.00 3.69
158 1702 4.362476 CTTGGCCCTTGCGCAACC 62.362 66.667 21.02 19.61 38.85 3.77
176 1720 5.106442 CCACTAACTGCATGTACGACAATA 58.894 41.667 0.00 0.00 0.00 1.90
181 1725 1.897133 ACCCACTAACTGCATGTACGA 59.103 47.619 0.00 0.00 0.00 3.43
185 1729 0.110295 TGCACCCACTAACTGCATGT 59.890 50.000 0.00 0.00 36.00 3.21
217 1761 3.187700 GACACCATACTCGGCAACTAAG 58.812 50.000 0.00 0.00 0.00 2.18
237 1781 2.203195 GCACACACACAGCCTGGA 60.203 61.111 0.00 0.00 0.00 3.86
239 1783 1.284715 CATGCACACACACAGCCTG 59.715 57.895 0.00 0.00 0.00 4.85
240 1784 1.152902 ACATGCACACACACAGCCT 60.153 52.632 0.00 0.00 0.00 4.58
288 1832 8.715191 TTTCTTCTCTCTATTTCTCTTGATGC 57.285 34.615 0.00 0.00 0.00 3.91
290 1834 9.889128 CCTTTTCTTCTCTCTATTTCTCTTGAT 57.111 33.333 0.00 0.00 0.00 2.57
306 1850 2.091885 TCACAGCCCAACCTTTTCTTCT 60.092 45.455 0.00 0.00 0.00 2.85
307 1851 2.034685 GTCACAGCCCAACCTTTTCTTC 59.965 50.000 0.00 0.00 0.00 2.87
328 1875 1.278637 GTGTTTTGGCGTCGGACTG 59.721 57.895 6.57 1.33 0.00 3.51
359 1906 1.729517 TCACAACACACACACAAGACG 59.270 47.619 0.00 0.00 0.00 4.18
360 1907 3.000041 TCTCACAACACACACACAAGAC 59.000 45.455 0.00 0.00 0.00 3.01
366 1913 2.106477 TGCTTCTCACAACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
373 1920 4.096382 TCTCTTTTGGTTGCTTCTCACAAC 59.904 41.667 0.00 0.00 45.30 3.32
374 1921 4.269183 TCTCTTTTGGTTGCTTCTCACAA 58.731 39.130 0.00 0.00 0.00 3.33
381 1928 3.631250 TCACCTTCTCTTTTGGTTGCTT 58.369 40.909 0.00 0.00 30.72 3.91
382 1929 3.217626 CTCACCTTCTCTTTTGGTTGCT 58.782 45.455 0.00 0.00 30.72 3.91
383 1930 2.294512 CCTCACCTTCTCTTTTGGTTGC 59.705 50.000 0.00 0.00 30.72 4.17
384 1931 2.887152 CCCTCACCTTCTCTTTTGGTTG 59.113 50.000 0.00 0.00 30.72 3.77
385 1932 2.158460 CCCCTCACCTTCTCTTTTGGTT 60.158 50.000 0.00 0.00 30.72 3.67
386 1933 1.425448 CCCCTCACCTTCTCTTTTGGT 59.575 52.381 0.00 0.00 33.87 3.67
387 1934 1.888391 GCCCCTCACCTTCTCTTTTGG 60.888 57.143 0.00 0.00 0.00 3.28
388 1935 1.074566 AGCCCCTCACCTTCTCTTTTG 59.925 52.381 0.00 0.00 0.00 2.44
389 1936 1.074566 CAGCCCCTCACCTTCTCTTTT 59.925 52.381 0.00 0.00 0.00 2.27
391 1938 0.178891 TCAGCCCCTCACCTTCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
392 1939 0.617249 CTCAGCCCCTCACCTTCTCT 60.617 60.000 0.00 0.00 0.00 3.10
398 1945 1.305718 ACTCTCTCAGCCCCTCACC 60.306 63.158 0.00 0.00 0.00 4.02
399 1946 0.613292 TGACTCTCTCAGCCCCTCAC 60.613 60.000 0.00 0.00 0.00 3.51
400 1947 0.324183 CTGACTCTCTCAGCCCCTCA 60.324 60.000 0.00 0.00 40.23 3.86
434 1981 2.682836 TCAACTCGCGTCATTTCATCA 58.317 42.857 5.77 0.00 0.00 3.07
442 1989 0.733909 CAGAGCATCAACTCGCGTCA 60.734 55.000 5.77 0.00 41.77 4.35
542 2089 2.252260 CTTGCGCCGAGTTGTTGG 59.748 61.111 4.18 0.00 0.00 3.77
591 2138 3.041940 GCGTCCTTCACCGGTGTG 61.042 66.667 32.74 24.75 44.18 3.82
622 2169 2.802667 CGCCGGATTCAACTCGCAG 61.803 63.158 5.05 0.00 0.00 5.18
652 2199 2.875933 CTGTTTCGCTTTGTTGGGTCTA 59.124 45.455 0.00 0.00 0.00 2.59
657 2204 0.597377 GGCCTGTTTCGCTTTGTTGG 60.597 55.000 0.00 0.00 0.00 3.77
666 2213 2.436646 ATCCAGCGGCCTGTTTCG 60.437 61.111 0.00 0.00 37.38 3.46
667 2214 2.409870 CCATCCAGCGGCCTGTTTC 61.410 63.158 0.00 0.00 37.38 2.78
668 2215 2.361610 CCATCCAGCGGCCTGTTT 60.362 61.111 0.00 0.00 37.38 2.83
720 2267 8.638873 TCATCTATAAATATACATGTAGCCCCG 58.361 37.037 11.91 0.00 0.00 5.73
776 2323 1.541670 GGTTCAAACAGTGTCCGGCTA 60.542 52.381 0.00 0.00 0.00 3.93
821 2371 6.591448 CCCTTTCTATTTGAATTTGGTTCTGC 59.409 38.462 0.00 0.00 37.72 4.26
845 2395 1.529865 CAGAAACGGTCGGTCTTTTCC 59.470 52.381 0.00 0.00 0.00 3.13
947 2497 9.481340 CTGACATTGCTACTTGCTCTATTTATA 57.519 33.333 0.00 0.00 43.37 0.98
949 2499 7.492669 GTCTGACATTGCTACTTGCTCTATTTA 59.507 37.037 2.24 0.00 43.37 1.40
950 2500 6.314896 GTCTGACATTGCTACTTGCTCTATTT 59.685 38.462 2.24 0.00 43.37 1.40
951 2501 5.814705 GTCTGACATTGCTACTTGCTCTATT 59.185 40.000 2.24 0.00 43.37 1.73
958 2510 2.417933 GCTGGTCTGACATTGCTACTTG 59.582 50.000 10.38 0.00 0.00 3.16
1066 2619 1.326213 ATGTCACCGGCAGAGAGGAG 61.326 60.000 0.00 0.00 0.00 3.69
1084 2637 2.959707 GGAAGGTCATGTAGGAGTCGAT 59.040 50.000 0.00 0.00 0.00 3.59
1137 2690 0.036732 TTAGGCCGCATGGATCATCC 59.963 55.000 0.00 0.00 37.49 3.51
1327 3156 1.271926 GCCATACCCAGTGTCCACTTT 60.272 52.381 0.00 0.00 40.20 2.66
1349 3178 1.532868 GGTTGAGGATGCATATGTCGC 59.467 52.381 0.00 0.00 0.00 5.19
1356 3185 1.002069 TGAAGGGGTTGAGGATGCAT 58.998 50.000 0.00 0.00 0.00 3.96
1359 3188 0.392998 CCGTGAAGGGGTTGAGGATG 60.393 60.000 0.00 0.00 35.97 3.51
1481 3310 0.602905 GCACACTCCGCCTAAACAGT 60.603 55.000 0.00 0.00 0.00 3.55
1489 3318 0.601311 GGATCATAGCACACTCCGCC 60.601 60.000 0.00 0.00 0.00 6.13
1540 3369 0.949105 ATGTTGACCGGACTGCGTTC 60.949 55.000 9.46 0.00 0.00 3.95
1607 3437 1.337823 CGACCTTAACTGACCCACCAG 60.338 57.143 0.00 0.00 39.93 4.00
1638 3468 2.119029 GTTGGTATGCGGCCCCTTC 61.119 63.158 0.00 0.00 0.00 3.46
1658 3488 6.595326 GTGTTTGATGATGGTAGTGATCTCAA 59.405 38.462 0.00 0.00 0.00 3.02
1739 3569 1.270305 GCATCGATGGTAGCTTGCCTA 60.270 52.381 26.00 0.00 0.00 3.93
1740 3570 0.533755 GCATCGATGGTAGCTTGCCT 60.534 55.000 26.00 0.00 0.00 4.75
1741 3571 1.510480 GGCATCGATGGTAGCTTGCC 61.510 60.000 26.00 16.37 42.40 4.52
1742 3572 0.815213 TGGCATCGATGGTAGCTTGC 60.815 55.000 26.00 11.03 0.00 4.01
1743 3573 1.224075 CTGGCATCGATGGTAGCTTG 58.776 55.000 26.00 0.41 0.00 4.01
1744 3574 0.107456 CCTGGCATCGATGGTAGCTT 59.893 55.000 26.00 0.00 0.00 3.74
1745 3575 1.750930 CCTGGCATCGATGGTAGCT 59.249 57.895 26.00 0.00 0.00 3.32
1746 3576 1.963338 GCCTGGCATCGATGGTAGC 60.963 63.158 26.00 11.99 0.00 3.58
1747 3577 1.302033 GGCCTGGCATCGATGGTAG 60.302 63.158 26.00 1.57 0.00 3.18
1872 3702 4.954118 AGACAGTGGCCGGGACCA 62.954 66.667 2.18 0.00 37.38 4.02
1877 3707 2.303549 GATGGAGAGACAGTGGCCGG 62.304 65.000 0.00 0.00 0.00 6.13
1881 3711 1.135257 GTGTCGATGGAGAGACAGTGG 60.135 57.143 0.00 0.00 46.49 4.00
1900 3730 2.158900 CGATGGCAGGAAGATGGTTAGT 60.159 50.000 0.00 0.00 0.00 2.24
1947 3777 6.547141 ACATCTGAATGTCTTTTTCCTTGACA 59.453 34.615 0.00 0.00 42.59 3.58
1962 3792 7.336679 TCAAGGTGGTACAAATACATCTGAATG 59.663 37.037 0.00 0.00 44.16 2.67
1965 3795 6.367374 TCAAGGTGGTACAAATACATCTGA 57.633 37.500 0.00 0.00 44.16 3.27
2019 3849 2.119655 CGAGGGACCGTGTAGAGGG 61.120 68.421 0.00 0.00 0.00 4.30
2023 3853 0.392729 AGACTCGAGGGACCGTGTAG 60.393 60.000 18.41 0.00 36.56 2.74
2040 3870 4.937201 TTCTAGGATAATCTGCGCAAGA 57.063 40.909 13.05 11.87 39.94 3.02
2048 3878 5.723887 CCCCTGCAGTATTCTAGGATAATCT 59.276 44.000 13.81 0.00 31.91 2.40
2056 3886 2.964209 TCTCCCCCTGCAGTATTCTAG 58.036 52.381 13.81 2.54 0.00 2.43
2058 3888 2.334023 GATCTCCCCCTGCAGTATTCT 58.666 52.381 13.81 0.00 0.00 2.40
2080 3910 8.871629 TTTAAGACAAGGCCACTCATAATTTA 57.128 30.769 5.01 0.00 0.00 1.40
2081 3911 7.775053 TTTAAGACAAGGCCACTCATAATTT 57.225 32.000 5.01 0.00 0.00 1.82
2151 3987 5.277779 GCACATGTCCGCTAGCAAAATATAA 60.278 40.000 16.45 0.00 0.00 0.98
2340 4179 1.755179 ACATTGTACATGCTCAGCCC 58.245 50.000 0.00 0.00 0.00 5.19
2366 4241 4.935352 AACATTGTACATGGTGCAGTTT 57.065 36.364 0.00 0.00 28.83 2.66
2425 4300 3.655276 AGCAAGAAAAAGAGCACCATG 57.345 42.857 0.00 0.00 0.00 3.66
2426 4301 4.401925 ACTAGCAAGAAAAAGAGCACCAT 58.598 39.130 0.00 0.00 0.00 3.55
2427 4302 3.820557 ACTAGCAAGAAAAAGAGCACCA 58.179 40.909 0.00 0.00 0.00 4.17
2428 4303 4.275936 TCAACTAGCAAGAAAAAGAGCACC 59.724 41.667 0.00 0.00 0.00 5.01
2488 4363 5.560966 TGAATAGATGAAAAGTTTCCCGC 57.439 39.130 1.46 0.00 36.36 6.13
2604 4481 4.196826 CGCTTTCGGCTCGCTTCG 62.197 66.667 0.00 0.00 39.13 3.79
2655 4532 7.013750 GGTTGGATCCTTTCAATCTAAGATTCC 59.986 40.741 14.23 0.00 0.00 3.01
2701 4874 6.288941 TCTCGAATGTGGTATTTGTTCCTA 57.711 37.500 0.00 0.00 0.00 2.94
2732 4905 1.065345 TCGGTTGGTGGTTGTCTTTGA 60.065 47.619 0.00 0.00 0.00 2.69
2770 4943 1.709147 GCATGTGGATGTGCGTCCTC 61.709 60.000 11.28 8.42 39.12 3.71
2775 4948 2.438975 AGGGCATGTGGATGTGCG 60.439 61.111 0.00 0.00 42.15 5.34
2801 4974 1.001764 TCCCGGTGAAGCGTCTAGA 60.002 57.895 0.00 0.00 0.00 2.43
2856 5031 3.644884 AGACGAGACGACATCAGTTTT 57.355 42.857 0.00 0.00 0.00 2.43
2863 5038 2.414824 GCTCAGAAAGACGAGACGACAT 60.415 50.000 0.00 0.00 0.00 3.06
2878 5053 0.687354 GGGTTTCTGTCCTGCTCAGA 59.313 55.000 0.00 0.00 39.71 3.27
2900 5075 0.875059 GGTGCTTCTTCGAGGTTTGG 59.125 55.000 0.00 0.00 0.00 3.28
2905 5080 3.188667 GGTTTTTAGGTGCTTCTTCGAGG 59.811 47.826 0.00 0.00 0.00 4.63
2940 5115 0.035820 GTGGATACCGGCCTTTGTCA 60.036 55.000 0.00 0.00 0.00 3.58
2978 5157 0.242825 TACGTCTTCTTCTGTGGCCG 59.757 55.000 0.00 0.00 0.00 6.13
2997 5176 0.036765 TTTTGCCGCCACGATCTACT 60.037 50.000 0.00 0.00 0.00 2.57
3036 5215 1.557371 CCTTCCTTTGTCTCTCCTCCC 59.443 57.143 0.00 0.00 0.00 4.30
3053 5232 3.382832 CCCCGTGCGTCTCTCCTT 61.383 66.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.