Multiple sequence alignment - TraesCS5B01G010600

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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 TraesCS5B01G010600 chr5B 100.000 3763 0 0 1 3763 10429305 10433067 0.000000e+00 6950.0
1 TraesCS5B01G010600 chr5B 91.691 2082 109 27 1736 3763 10525793 10523722 0.000000e+00 2828.0
2 TraesCS5B01G010600 chr5B 91.985 1073 39 6 712 1737 10526900 10525828 0.000000e+00 1461.0
3 TraesCS5B01G010600 chr5B 91.096 146 9 4 1 143 10527549 10527405 1.070000e-45 195.0
4 TraesCS5B01G010600 chr5B 79.375 320 28 16 223 534 10527375 10527086 1.380000e-44 191.0
5 TraesCS5B01G010600 chr5A 82.252 1803 226 46 1737 3501 8186949 8188695 0.000000e+00 1471.0
6 TraesCS5B01G010600 chr5A 86.614 635 60 15 977 1588 8186098 8186730 0.000000e+00 678.0
7 TraesCS5B01G010600 chr5A 87.654 243 30 0 715 957 8180380 8180622 2.210000e-72 283.0
8 TraesCS5B01G010600 chr5A 82.759 116 13 5 361 472 8180044 8180156 3.090000e-16 97.1
9 TraesCS5B01G010600 chr5D 80.692 1445 198 47 2090 3500 10471481 10472878 0.000000e+00 1048.0
10 TraesCS5B01G010600 chr5D 87.209 602 55 16 711 1305 10468642 10469228 0.000000e+00 665.0
11 TraesCS5B01G010600 chr5D 96.029 277 11 0 1312 1588 10469265 10469541 5.730000e-123 451.0
12 TraesCS5B01G010600 chr5D 81.675 573 62 26 1574 2111 10469558 10470122 1.600000e-118 436.0
13 TraesCS5B01G010600 chr5D 83.483 333 24 13 223 531 10468005 10468330 7.960000e-72 281.0
14 TraesCS5B01G010600 chr5D 88.112 143 14 1 1 143 10467836 10467975 2.320000e-37 167.0
15 TraesCS5B01G010600 chr5D 98.413 63 1 0 146 208 560508994 560509056 1.100000e-20 111.0
16 TraesCS5B01G010600 chr2B 90.099 101 7 3 615 714 192907625 192907723 1.100000e-25 128.0
17 TraesCS5B01G010600 chr2A 90.099 101 7 3 614 713 25042513 25042415 1.100000e-25 128.0
18 TraesCS5B01G010600 chr2A 86.538 104 9 4 614 715 611763460 611763560 3.970000e-20 110.0
19 TraesCS5B01G010600 chr2A 88.889 63 7 0 3096 3158 608779192 608779130 1.120000e-10 78.7
20 TraesCS5B01G010600 chr1D 92.308 91 5 1 615 705 3952558 3952646 1.100000e-25 128.0
21 TraesCS5B01G010600 chr1D 86.408 103 11 2 613 714 483018358 483018258 3.970000e-20 110.0
22 TraesCS5B01G010600 chr3A 88.000 100 9 2 615 713 699542068 699541971 8.540000e-22 115.0
23 TraesCS5B01G010600 chr3A 98.413 63 1 0 146 208 737369173 737369235 1.100000e-20 111.0
24 TraesCS5B01G010600 chr1B 98.462 65 1 0 147 211 684089123 684089059 8.540000e-22 115.0
25 TraesCS5B01G010600 chr1B 98.413 63 1 0 146 208 17540241 17540303 1.100000e-20 111.0
26 TraesCS5B01G010600 chr7D 87.255 102 10 3 613 713 401097374 401097275 3.070000e-21 113.0
27 TraesCS5B01G010600 chr7D 87.000 100 10 2 615 713 140326027 140326124 3.970000e-20 110.0
28 TraesCS5B01G010600 chr7D 87.000 100 10 2 615 713 474338818 474338721 3.970000e-20 110.0
29 TraesCS5B01G010600 chr7D 84.524 84 11 2 3101 3184 547491327 547491246 8.660000e-12 82.4
30 TraesCS5B01G010600 chr7D 100.000 29 0 0 2976 3004 528886312 528886284 2.000000e-03 54.7
31 TraesCS5B01G010600 chr4A 97.015 67 2 0 145 211 603447675 603447609 3.070000e-21 113.0
32 TraesCS5B01G010600 chr2D 98.438 64 1 0 148 211 32020805 32020742 3.070000e-21 113.0
33 TraesCS5B01G010600 chr2D 89.024 82 5 4 3101 3180 207902958 207903037 8.600000e-17 99.0
34 TraesCS5B01G010600 chr6D 98.413 63 1 0 146 208 304097607 304097669 1.100000e-20 111.0
35 TraesCS5B01G010600 chr6D 96.875 64 1 1 142 205 199210322 199210384 5.140000e-19 106.0
36 TraesCS5B01G010600 chr3B 96.970 66 2 0 146 211 753744246 753744181 1.100000e-20 111.0
37 TraesCS5B01G010600 chr3D 89.474 57 5 1 3094 3150 488391739 488391794 1.880000e-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 TraesCS5B01G010600 chr5B 10429305 10433067 3762 False 6950.00 6950 100.00000 1 3763 1 chr5B.!!$F1 3762
1 TraesCS5B01G010600 chr5B 10523722 10527549 3827 True 1168.75 2828 88.53675 1 3763 4 chr5B.!!$R1 3762
2 TraesCS5B01G010600 chr5A 8186098 8188695 2597 False 1074.50 1471 84.43300 977 3501 2 chr5A.!!$F2 2524
3 TraesCS5B01G010600 chr5D 10467836 10472878 5042 False 508.00 1048 86.20000 1 3500 6 chr5D.!!$F2 3499

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
411 460 0.038599 TCGTGGTGTAGGGCTCTGTA 59.961 55.000 0.00 0.0 0.00 2.74 F
490 552 0.325203 GCTCCTCCTTCTGTCCTCCT 60.325 60.000 0.00 0.0 0.00 3.69 F
845 1050 0.693049 AGGCGGGAATTCTTGACACT 59.307 50.000 5.23 0.0 0.00 3.55 F
2118 3854 1.228552 GCTGGAAGGCAACAGGGAA 60.229 57.895 5.48 0.0 41.41 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 4020 0.179076 CACCAGCACCGCTATGATCA 60.179 55.000 0.00 0.00 36.4 2.92 R
2377 4114 0.319900 CTCCGACACCTCCAACACAG 60.320 60.000 0.00 0.00 0.0 3.66 R
2383 4120 1.152419 TTCACCTCCGACACCTCCA 60.152 57.895 0.00 0.00 0.0 3.86 R
3360 5136 0.038159 AGGCGCGCATCTATAACTCC 60.038 55.000 34.42 10.63 0.0 3.85 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
66 67 3.194062 CGCTCCTTCTCATCCTTTCTTC 58.806 50.000 0.00 0.00 0.00 2.87
67 68 3.540617 GCTCCTTCTCATCCTTTCTTCC 58.459 50.000 0.00 0.00 0.00 3.46
68 69 3.791245 CTCCTTCTCATCCTTTCTTCCG 58.209 50.000 0.00 0.00 0.00 4.30
69 70 2.501723 TCCTTCTCATCCTTTCTTCCGG 59.498 50.000 0.00 0.00 0.00 5.14
72 73 0.543749 CTCATCCTTTCTTCCGGCCT 59.456 55.000 0.00 0.00 0.00 5.19
97 104 3.085533 ACGTACTTGAGTCATGAGCTCT 58.914 45.455 16.19 5.64 34.30 4.09
100 107 4.260990 CGTACTTGAGTCATGAGCTCTAGG 60.261 50.000 24.93 16.98 39.14 3.02
107 114 5.717178 TGAGTCATGAGCTCTAGGTAAGTTT 59.283 40.000 16.19 0.00 34.30 2.66
152 159 4.149910 GAAGCTATCCACGCTAGTACTC 57.850 50.000 0.00 0.00 36.56 2.59
153 160 2.506444 AGCTATCCACGCTAGTACTCC 58.494 52.381 0.00 0.00 35.63 3.85
154 161 1.540707 GCTATCCACGCTAGTACTCCC 59.459 57.143 0.00 0.00 0.00 4.30
155 162 2.814842 GCTATCCACGCTAGTACTCCCT 60.815 54.545 0.00 0.00 0.00 4.20
158 165 1.025812 CCACGCTAGTACTCCCTCTG 58.974 60.000 0.00 0.00 0.00 3.35
161 168 3.276857 CACGCTAGTACTCCCTCTGTAA 58.723 50.000 0.00 0.00 0.00 2.41
162 169 3.693085 CACGCTAGTACTCCCTCTGTAAA 59.307 47.826 0.00 0.00 0.00 2.01
163 170 3.693578 ACGCTAGTACTCCCTCTGTAAAC 59.306 47.826 0.00 0.00 0.00 2.01
164 171 3.693085 CGCTAGTACTCCCTCTGTAAACA 59.307 47.826 0.00 0.00 0.00 2.83
165 172 4.157289 CGCTAGTACTCCCTCTGTAAACAA 59.843 45.833 0.00 0.00 0.00 2.83
166 173 5.336213 CGCTAGTACTCCCTCTGTAAACAAA 60.336 44.000 0.00 0.00 0.00 2.83
167 174 6.627508 CGCTAGTACTCCCTCTGTAAACAAAT 60.628 42.308 0.00 0.00 0.00 2.32
169 176 8.422566 GCTAGTACTCCCTCTGTAAACAAATAT 58.577 37.037 0.00 0.00 0.00 1.28
175 182 9.047947 ACTCCCTCTGTAAACAAATATAAGAGT 57.952 33.333 0.00 0.00 0.00 3.24
176 183 9.319143 CTCCCTCTGTAAACAAATATAAGAGTG 57.681 37.037 0.00 0.00 0.00 3.51
177 184 8.822805 TCCCTCTGTAAACAAATATAAGAGTGT 58.177 33.333 0.00 0.00 0.00 3.55
178 185 9.449719 CCCTCTGTAAACAAATATAAGAGTGTT 57.550 33.333 0.00 0.00 35.77 3.32
216 223 9.545105 TTTAGTGATCTAAACACTTTTTACGGA 57.455 29.630 0.00 0.00 44.69 4.69
217 224 7.653767 AGTGATCTAAACACTTTTTACGGAG 57.346 36.000 0.00 0.00 44.69 4.63
218 225 6.649557 AGTGATCTAAACACTTTTTACGGAGG 59.350 38.462 0.00 0.00 44.69 4.30
219 226 5.935789 TGATCTAAACACTTTTTACGGAGGG 59.064 40.000 0.00 0.00 0.00 4.30
220 227 5.549742 TCTAAACACTTTTTACGGAGGGA 57.450 39.130 0.00 0.00 0.00 4.20
221 228 5.544650 TCTAAACACTTTTTACGGAGGGAG 58.455 41.667 0.00 0.00 0.00 4.30
264 271 3.506067 GGTTGGATTTTTGTGTCGAGGAT 59.494 43.478 0.00 0.00 0.00 3.24
265 272 4.379499 GGTTGGATTTTTGTGTCGAGGATC 60.379 45.833 0.00 0.00 0.00 3.36
266 273 3.343617 TGGATTTTTGTGTCGAGGATCC 58.656 45.455 2.48 2.48 33.78 3.36
267 274 3.244735 TGGATTTTTGTGTCGAGGATCCA 60.245 43.478 15.82 0.00 39.24 3.41
268 275 3.947834 GGATTTTTGTGTCGAGGATCCAT 59.052 43.478 15.82 0.00 33.48 3.41
285 292 2.093500 TCCATTCCATTCACACCTCTCG 60.093 50.000 0.00 0.00 0.00 4.04
305 351 2.396157 CCAAAAGCGTACTCCGGCC 61.396 63.158 0.00 0.00 36.94 6.13
306 352 2.433664 AAAAGCGTACTCCGGCCG 60.434 61.111 21.04 21.04 36.94 6.13
307 353 3.945304 AAAAGCGTACTCCGGCCGG 62.945 63.158 39.13 39.13 36.94 6.13
323 369 4.011517 GGCGAGGTTCCCGTTCCA 62.012 66.667 0.00 0.00 0.00 3.53
324 370 2.434359 GCGAGGTTCCCGTTCCAG 60.434 66.667 0.00 0.00 0.00 3.86
325 371 3.057337 CGAGGTTCCCGTTCCAGT 58.943 61.111 0.00 0.00 0.00 4.00
326 372 1.080025 CGAGGTTCCCGTTCCAGTC 60.080 63.158 0.00 0.00 0.00 3.51
327 373 1.533469 CGAGGTTCCCGTTCCAGTCT 61.533 60.000 0.00 0.00 0.00 3.24
328 374 0.246910 GAGGTTCCCGTTCCAGTCTC 59.753 60.000 0.00 0.00 0.00 3.36
329 375 1.192803 AGGTTCCCGTTCCAGTCTCC 61.193 60.000 0.00 0.00 0.00 3.71
330 376 1.080025 GTTCCCGTTCCAGTCTCCG 60.080 63.158 0.00 0.00 0.00 4.63
331 377 2.280552 TTCCCGTTCCAGTCTCCGG 61.281 63.158 0.00 0.00 40.12 5.14
332 378 4.452733 CCCGTTCCAGTCTCCGGC 62.453 72.222 0.00 0.00 39.12 6.13
333 379 4.796231 CCGTTCCAGTCTCCGGCG 62.796 72.222 0.00 0.00 33.20 6.46
334 380 3.744719 CGTTCCAGTCTCCGGCGA 61.745 66.667 9.30 0.00 0.00 5.54
335 381 2.182030 GTTCCAGTCTCCGGCGAG 59.818 66.667 9.30 4.01 37.48 5.03
336 382 3.068691 TTCCAGTCTCCGGCGAGG 61.069 66.667 9.30 0.00 42.97 4.63
339 385 3.068691 CAGTCTCCGGCGAGGGAA 61.069 66.667 9.30 0.00 41.52 3.97
340 386 2.756283 AGTCTCCGGCGAGGGAAG 60.756 66.667 9.30 0.00 41.52 3.46
341 387 4.516195 GTCTCCGGCGAGGGAAGC 62.516 72.222 9.30 0.00 41.52 3.86
385 434 2.027192 TCCTCTTATTTTGCTGGTCGCT 60.027 45.455 0.00 0.00 40.11 4.93
411 460 0.038599 TCGTGGTGTAGGGCTCTGTA 59.961 55.000 0.00 0.00 0.00 2.74
486 548 0.823460 CTCTGCTCCTCCTTCTGTCC 59.177 60.000 0.00 0.00 0.00 4.02
489 551 0.616111 TGCTCCTCCTTCTGTCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
490 552 0.325203 GCTCCTCCTTCTGTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
491 553 1.899438 GCTCCTCCTTCTGTCCTCCTT 60.899 57.143 0.00 0.00 0.00 3.36
519 583 1.583054 CTATAGTTTGGTGCTCCGGC 58.417 55.000 0.00 0.00 36.30 6.13
544 633 1.477553 TGCTTTCAGGGCATGATTCC 58.522 50.000 1.35 0.00 37.89 3.01
564 653 4.543689 TCCCACTCTCTATTTATCCACGT 58.456 43.478 0.00 0.00 0.00 4.49
568 657 7.946219 TCCCACTCTCTATTTATCCACGTATTA 59.054 37.037 0.00 0.00 0.00 0.98
582 671 6.107343 TCCACGTATTATTTTCATCCGTTCA 58.893 36.000 0.00 0.00 0.00 3.18
584 673 6.189567 CACGTATTATTTTCATCCGTTCACC 58.810 40.000 0.00 0.00 0.00 4.02
585 674 5.005971 ACGTATTATTTTCATCCGTTCACCG 59.994 40.000 0.00 0.00 0.00 4.94
595 685 2.027625 CGTTCACCGGCTTGGAGTC 61.028 63.158 0.00 0.00 42.00 3.36
612 702 1.139058 AGTCTTCTTTGCTCACGGTGT 59.861 47.619 8.17 0.00 0.00 4.16
613 703 2.364324 AGTCTTCTTTGCTCACGGTGTA 59.636 45.455 8.17 0.00 0.00 2.90
618 744 4.530710 TCTTTGCTCACGGTGTATACTT 57.469 40.909 8.17 0.00 0.00 2.24
690 884 9.821662 AATAAAATTAGTACAAAGTTGAGACGC 57.178 29.630 0.00 0.00 0.00 5.19
692 886 7.492352 AAATTAGTACAAAGTTGAGACGCTT 57.508 32.000 0.00 0.00 0.00 4.68
693 887 8.597662 AAATTAGTACAAAGTTGAGACGCTTA 57.402 30.769 0.00 0.00 0.00 3.09
694 888 8.773404 AATTAGTACAAAGTTGAGACGCTTAT 57.227 30.769 0.00 0.00 0.00 1.73
695 889 8.773404 ATTAGTACAAAGTTGAGACGCTTATT 57.227 30.769 0.00 0.00 0.00 1.40
696 890 8.597662 TTAGTACAAAGTTGAGACGCTTATTT 57.402 30.769 0.00 0.00 0.00 1.40
697 891 7.492352 AGTACAAAGTTGAGACGCTTATTTT 57.508 32.000 0.00 0.00 0.00 1.82
700 894 6.430451 ACAAAGTTGAGACGCTTATTTTGAG 58.570 36.000 0.00 0.00 0.00 3.02
701 895 6.260050 ACAAAGTTGAGACGCTTATTTTGAGA 59.740 34.615 0.00 0.00 0.00 3.27
702 896 5.847670 AGTTGAGACGCTTATTTTGAGAC 57.152 39.130 0.00 0.00 0.00 3.36
704 898 3.250744 TGAGACGCTTATTTTGAGACGG 58.749 45.455 0.00 0.00 0.00 4.79
705 899 2.603560 GAGACGCTTATTTTGAGACGGG 59.396 50.000 0.00 0.00 0.00 5.28
706 900 1.664151 GACGCTTATTTTGAGACGGGG 59.336 52.381 0.00 0.00 0.00 5.73
723 928 2.525368 GGGGGAGTATGTGCTTTTGTT 58.475 47.619 0.00 0.00 0.00 2.83
735 940 6.019779 TGTGCTTTTGTTGAGTTAGTTTGT 57.980 33.333 0.00 0.00 0.00 2.83
845 1050 0.693049 AGGCGGGAATTCTTGACACT 59.307 50.000 5.23 0.00 0.00 3.55
859 1064 2.803956 TGACACTACTCCACTCGGATT 58.196 47.619 0.00 0.00 41.79 3.01
892 1097 2.677902 CGACAAATCTCTTGGCTAGGCA 60.678 50.000 16.16 16.16 0.00 4.75
904 1109 2.235155 TGGCTAGGCACGACTTAATCAA 59.765 45.455 16.16 0.00 0.00 2.57
914 1119 8.827677 AGGCACGACTTAATCAAATATACTTTC 58.172 33.333 0.00 0.00 0.00 2.62
965 1170 7.938140 TTAATTTGAATGGAAGGGAGTAGTG 57.062 36.000 0.00 0.00 0.00 2.74
969 1174 7.743116 TTTGAATGGAAGGGAGTAGTGTATA 57.257 36.000 0.00 0.00 0.00 1.47
1058 1284 3.912563 CCCGTCGTCGAGTAATCATATTG 59.087 47.826 2.98 0.00 39.71 1.90
1268 1502 3.314553 ACTGGTATGCACGCGATATTAC 58.685 45.455 15.93 9.21 0.00 1.89
1308 1542 3.875134 CCTCCGGTCAACCAATAATGTAC 59.125 47.826 0.00 0.00 35.14 2.90
1601 1906 5.602628 ACTTTCTGTCAGTAGTCAAGGAAC 58.397 41.667 0.00 0.00 0.00 3.62
1709 2018 5.333875 CGCTAAACTTGAAACCTAGGAACAC 60.334 44.000 17.98 4.50 0.00 3.32
1723 2032 3.305720 AGGAACACAACAGTCCAGTAGA 58.694 45.455 0.00 0.00 0.00 2.59
1757 2103 6.697455 CACGCTATGTTAGAAGTGTCACATAT 59.303 38.462 5.62 0.00 34.32 1.78
1802 2148 3.391626 AGAGAAACGGGAGAAAAGGTCTT 59.608 43.478 0.00 0.00 36.41 3.01
1817 2163 9.727859 AGAAAAGGTCTTCTTTCTCCTAATTAC 57.272 33.333 0.00 0.00 44.30 1.89
1954 2304 2.119495 ACCACTCTACATGCCCTTAGG 58.881 52.381 0.00 0.00 0.00 2.69
2059 2411 2.099263 GCATCATGATCATATGGCTGCC 59.901 50.000 12.87 12.87 34.21 4.85
2118 3854 1.228552 GCTGGAAGGCAACAGGGAA 60.229 57.895 5.48 0.00 41.41 3.97
2137 3873 2.150397 ACCAGGAGAAAGTTCGTTCG 57.850 50.000 0.00 0.00 32.50 3.95
2183 3920 7.648142 CACCTCTGTTTAAAATTTGCAGACTA 58.352 34.615 9.49 0.00 33.34 2.59
2195 3932 7.992180 AATTTGCAGACTAAAGTTCAACAAG 57.008 32.000 0.00 0.00 0.00 3.16
2202 3939 9.334693 GCAGACTAAAGTTCAACAAGATTTATG 57.665 33.333 0.00 0.00 0.00 1.90
2283 4020 6.077993 TCATGTATACTTGCAGGATCCTAGT 58.922 40.000 15.67 16.95 0.00 2.57
2348 4085 7.972301 AGGGATTGAAGGATATACAGAGAAAG 58.028 38.462 0.00 0.00 0.00 2.62
2349 4086 7.570607 AGGGATTGAAGGATATACAGAGAAAGT 59.429 37.037 0.00 0.00 0.00 2.66
2377 4114 4.331992 GGGAAAACTATTGAGAACGGTAGC 59.668 45.833 0.00 0.00 0.00 3.58
2383 4120 2.902705 TTGAGAACGGTAGCTGTGTT 57.097 45.000 0.00 0.00 0.00 3.32
2485 4222 9.958234 TCGTATCTTCTTATTCAGAAAGATGAG 57.042 33.333 6.69 2.03 41.25 2.90
2576 4313 4.275443 CAGCTTCTTCTAAAGATGATGCCC 59.725 45.833 20.64 5.09 43.62 5.36
2622 4359 0.985549 CAAGTCTGACGTTAGCTCGC 59.014 55.000 1.76 0.00 0.00 5.03
2710 4448 1.487231 CACTCGTTGCGGTCTTTCG 59.513 57.895 0.00 0.00 0.00 3.46
2711 4449 0.937699 CACTCGTTGCGGTCTTTCGA 60.938 55.000 0.00 0.00 0.00 3.71
2795 4534 7.931015 AAGGAGGGAGTACATGTTTATCATA 57.069 36.000 2.30 0.00 34.67 2.15
2864 4604 8.246180 GGGCTATTTTATGTCATATGGATTGTG 58.754 37.037 2.13 0.00 0.00 3.33
2963 4706 7.147976 AGCTTATGTTTGATGTGTCCTTTTTC 58.852 34.615 0.00 0.00 0.00 2.29
3312 5088 2.619177 CAATTGTGTTGTTGGGACGGTA 59.381 45.455 0.00 0.00 0.00 4.02
3360 5136 5.447954 CGCGATGGTCTATCTCACTATAAGG 60.448 48.000 0.00 0.00 33.44 2.69
3477 5253 2.543777 AGTGCATGTCGTTAACTGGT 57.456 45.000 3.71 0.00 0.00 4.00
3480 5256 0.871722 GCATGTCGTTAACTGGTGCA 59.128 50.000 3.71 0.00 34.10 4.57
3507 5292 1.065126 GCTCTTACCTGGCCAGTTGAT 60.065 52.381 30.63 15.55 0.00 2.57
3511 5296 4.298626 TCTTACCTGGCCAGTTGATCTAT 58.701 43.478 30.63 8.36 0.00 1.98
3520 5305 3.873952 GCCAGTTGATCTATGTCTGGAAC 59.126 47.826 13.91 0.00 45.76 3.62
3637 5455 9.738832 TTCCTTTTTATTTGGTTCTACTTTTCG 57.261 29.630 0.00 0.00 0.00 3.46
3638 5456 8.905850 TCCTTTTTATTTGGTTCTACTTTTCGT 58.094 29.630 0.00 0.00 0.00 3.85
3639 5457 9.524106 CCTTTTTATTTGGTTCTACTTTTCGTT 57.476 29.630 0.00 0.00 0.00 3.85
3649 5467 9.558648 TGGTTCTACTTTTCGTTTTACTTTTTC 57.441 29.630 0.00 0.00 0.00 2.29
3650 5468 9.013490 GGTTCTACTTTTCGTTTTACTTTTTCC 57.987 33.333 0.00 0.00 0.00 3.13
3675 5493 6.752335 TTTTTCTTGAGAAATGCACGAATG 57.248 33.333 6.98 0.00 42.83 2.67
3694 5516 9.605955 CACGAATGTTAAATGTGATGAACTTTA 57.394 29.630 0.00 0.00 32.39 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.941333 CGACCGATGCATGATGCC 59.059 61.111 15.70 0.00 44.23 4.40
66 67 0.320073 TCAAGTACGTTTCAGGCCGG 60.320 55.000 0.00 0.00 0.00 6.13
67 68 1.068474 CTCAAGTACGTTTCAGGCCG 58.932 55.000 0.00 0.00 0.00 6.13
68 69 2.067013 GACTCAAGTACGTTTCAGGCC 58.933 52.381 0.00 0.00 0.00 5.19
69 70 2.750948 TGACTCAAGTACGTTTCAGGC 58.249 47.619 0.00 0.00 0.00 4.85
72 73 3.987868 GCTCATGACTCAAGTACGTTTCA 59.012 43.478 0.00 0.00 0.00 2.69
97 104 6.449956 AGTGGATAGGATGGAAACTTACCTA 58.550 40.000 0.00 0.00 37.57 3.08
100 107 7.939784 AAAAGTGGATAGGATGGAAACTTAC 57.060 36.000 0.00 0.00 0.00 2.34
143 150 5.656213 TTGTTTACAGAGGGAGTACTAGC 57.344 43.478 0.00 0.00 0.00 3.42
150 157 9.319143 CACTCTTATATTTGTTTACAGAGGGAG 57.681 37.037 0.00 0.00 0.00 4.30
152 159 9.449719 AACACTCTTATATTTGTTTACAGAGGG 57.550 33.333 0.00 0.00 0.00 4.30
190 197 9.545105 TCCGTAAAAAGTGTTTAGATCACTAAA 57.455 29.630 0.00 0.00 44.03 1.85
191 198 9.199982 CTCCGTAAAAAGTGTTTAGATCACTAA 57.800 33.333 0.00 0.00 44.03 2.24
192 199 7.816031 CCTCCGTAAAAAGTGTTTAGATCACTA 59.184 37.037 0.00 0.00 44.03 2.74
193 200 6.649557 CCTCCGTAAAAAGTGTTTAGATCACT 59.350 38.462 0.00 0.00 46.30 3.41
194 201 6.128363 CCCTCCGTAAAAAGTGTTTAGATCAC 60.128 42.308 0.00 0.00 36.22 3.06
195 202 5.935789 CCCTCCGTAAAAAGTGTTTAGATCA 59.064 40.000 0.00 0.00 0.00 2.92
196 203 6.168389 TCCCTCCGTAAAAAGTGTTTAGATC 58.832 40.000 0.00 0.00 0.00 2.75
197 204 6.117975 TCCCTCCGTAAAAAGTGTTTAGAT 57.882 37.500 0.00 0.00 0.00 1.98
198 205 5.070847 ACTCCCTCCGTAAAAAGTGTTTAGA 59.929 40.000 0.00 0.00 0.00 2.10
199 206 5.303165 ACTCCCTCCGTAAAAAGTGTTTAG 58.697 41.667 0.00 0.00 0.00 1.85
200 207 5.294734 ACTCCCTCCGTAAAAAGTGTTTA 57.705 39.130 0.00 0.00 0.00 2.01
201 208 4.160642 ACTCCCTCCGTAAAAAGTGTTT 57.839 40.909 0.00 0.00 0.00 2.83
202 209 3.851458 ACTCCCTCCGTAAAAAGTGTT 57.149 42.857 0.00 0.00 0.00 3.32
203 210 5.494390 AATACTCCCTCCGTAAAAAGTGT 57.506 39.130 0.00 0.00 0.00 3.55
204 211 8.502105 AATAAATACTCCCTCCGTAAAAAGTG 57.498 34.615 0.00 0.00 0.00 3.16
205 212 9.828039 CTAATAAATACTCCCTCCGTAAAAAGT 57.172 33.333 0.00 0.00 0.00 2.66
206 213 9.828039 ACTAATAAATACTCCCTCCGTAAAAAG 57.172 33.333 0.00 0.00 0.00 2.27
207 214 9.603921 CACTAATAAATACTCCCTCCGTAAAAA 57.396 33.333 0.00 0.00 0.00 1.94
208 215 8.980596 TCACTAATAAATACTCCCTCCGTAAAA 58.019 33.333 0.00 0.00 0.00 1.52
209 216 8.537728 TCACTAATAAATACTCCCTCCGTAAA 57.462 34.615 0.00 0.00 0.00 2.01
210 217 8.716674 ATCACTAATAAATACTCCCTCCGTAA 57.283 34.615 0.00 0.00 0.00 3.18
211 218 9.458727 CTATCACTAATAAATACTCCCTCCGTA 57.541 37.037 0.00 0.00 0.00 4.02
212 219 7.949006 ACTATCACTAATAAATACTCCCTCCGT 59.051 37.037 0.00 0.00 0.00 4.69
213 220 8.350852 ACTATCACTAATAAATACTCCCTCCG 57.649 38.462 0.00 0.00 0.00 4.63
264 271 2.093500 CGAGAGGTGTGAATGGAATGGA 60.093 50.000 0.00 0.00 0.00 3.41
265 272 2.093500 TCGAGAGGTGTGAATGGAATGG 60.093 50.000 0.00 0.00 0.00 3.16
266 273 2.932614 GTCGAGAGGTGTGAATGGAATG 59.067 50.000 0.00 0.00 0.00 2.67
267 274 2.093447 GGTCGAGAGGTGTGAATGGAAT 60.093 50.000 0.00 0.00 0.00 3.01
268 275 1.275291 GGTCGAGAGGTGTGAATGGAA 59.725 52.381 0.00 0.00 0.00 3.53
285 292 1.632948 GCCGGAGTACGCTTTTGGTC 61.633 60.000 5.05 0.00 42.52 4.02
314 360 2.678934 CCGGAGACTGGAACGGGA 60.679 66.667 0.00 0.00 42.48 5.14
315 361 4.452733 GCCGGAGACTGGAACGGG 62.453 72.222 5.05 0.00 46.04 5.28
317 363 3.685214 CTCGCCGGAGACTGGAACG 62.685 68.421 5.05 0.00 43.27 3.95
318 364 2.182030 CTCGCCGGAGACTGGAAC 59.818 66.667 5.05 0.00 43.27 3.62
319 365 3.068691 CCTCGCCGGAGACTGGAA 61.069 66.667 5.05 0.00 43.27 3.53
322 368 3.068691 TTCCCTCGCCGGAGACTG 61.069 66.667 5.05 0.00 43.27 3.51
323 369 2.756283 CTTCCCTCGCCGGAGACT 60.756 66.667 5.05 0.00 43.27 3.24
324 370 4.516195 GCTTCCCTCGCCGGAGAC 62.516 72.222 5.05 0.00 43.27 3.36
348 394 4.767255 GACGGCCACCAGGAGCAG 62.767 72.222 2.24 6.68 36.89 4.24
385 434 0.032403 CCCTACACCACGAACACGAA 59.968 55.000 0.00 0.00 0.00 3.85
519 583 2.494471 TCATGCCCTGAAAGCAAATCTG 59.506 45.455 0.00 0.00 44.83 2.90
577 666 2.027625 GACTCCAAGCCGGTGAACG 61.028 63.158 1.90 0.00 43.80 3.95
582 671 0.765510 AAAGAAGACTCCAAGCCGGT 59.234 50.000 1.90 0.00 35.57 5.28
584 673 0.519077 GCAAAGAAGACTCCAAGCCG 59.481 55.000 0.00 0.00 0.00 5.52
585 674 1.809547 GAGCAAAGAAGACTCCAAGCC 59.190 52.381 0.00 0.00 0.00 4.35
589 678 1.270305 CCGTGAGCAAAGAAGACTCCA 60.270 52.381 0.00 0.00 0.00 3.86
595 685 4.495422 AGTATACACCGTGAGCAAAGAAG 58.505 43.478 5.28 0.00 0.00 2.85
612 702 8.195436 CACTTATTTTGAGACGGAGGAAGTATA 58.805 37.037 0.00 0.00 0.00 1.47
613 703 7.042335 CACTTATTTTGAGACGGAGGAAGTAT 58.958 38.462 0.00 0.00 0.00 2.12
618 744 4.527038 AGACACTTATTTTGAGACGGAGGA 59.473 41.667 0.00 0.00 0.00 3.71
665 859 9.216117 AGCGTCTCAACTTTGTACTAATTTTAT 57.784 29.630 0.00 0.00 0.00 1.40
667 861 7.492352 AGCGTCTCAACTTTGTACTAATTTT 57.508 32.000 0.00 0.00 0.00 1.82
672 866 8.492748 CAAAATAAGCGTCTCAACTTTGTACTA 58.507 33.333 0.00 0.00 0.00 1.82
674 868 7.349711 TCAAAATAAGCGTCTCAACTTTGTAC 58.650 34.615 0.00 0.00 0.00 2.90
677 871 6.575201 GTCTCAAAATAAGCGTCTCAACTTTG 59.425 38.462 0.00 0.00 0.00 2.77
683 877 3.250744 CCGTCTCAAAATAAGCGTCTCA 58.749 45.455 0.00 0.00 0.00 3.27
684 878 2.603560 CCCGTCTCAAAATAAGCGTCTC 59.396 50.000 0.00 0.00 0.00 3.36
685 879 2.618053 CCCGTCTCAAAATAAGCGTCT 58.382 47.619 0.00 0.00 0.00 4.18
686 880 1.664151 CCCCGTCTCAAAATAAGCGTC 59.336 52.381 0.00 0.00 0.00 5.19
687 881 1.677820 CCCCCGTCTCAAAATAAGCGT 60.678 52.381 0.00 0.00 0.00 5.07
688 882 1.014352 CCCCCGTCTCAAAATAAGCG 58.986 55.000 0.00 0.00 0.00 4.68
689 883 2.289565 CTCCCCCGTCTCAAAATAAGC 58.710 52.381 0.00 0.00 0.00 3.09
690 884 3.629142 ACTCCCCCGTCTCAAAATAAG 57.371 47.619 0.00 0.00 0.00 1.73
692 886 4.035112 ACATACTCCCCCGTCTCAAAATA 58.965 43.478 0.00 0.00 0.00 1.40
693 887 2.844348 ACATACTCCCCCGTCTCAAAAT 59.156 45.455 0.00 0.00 0.00 1.82
694 888 2.027561 CACATACTCCCCCGTCTCAAAA 60.028 50.000 0.00 0.00 0.00 2.44
695 889 1.553248 CACATACTCCCCCGTCTCAAA 59.447 52.381 0.00 0.00 0.00 2.69
696 890 1.191535 CACATACTCCCCCGTCTCAA 58.808 55.000 0.00 0.00 0.00 3.02
697 891 1.327690 GCACATACTCCCCCGTCTCA 61.328 60.000 0.00 0.00 0.00 3.27
700 894 0.252197 AAAGCACATACTCCCCCGTC 59.748 55.000 0.00 0.00 0.00 4.79
701 895 0.696501 AAAAGCACATACTCCCCCGT 59.303 50.000 0.00 0.00 0.00 5.28
702 896 1.094785 CAAAAGCACATACTCCCCCG 58.905 55.000 0.00 0.00 0.00 5.73
704 898 3.153919 TCAACAAAAGCACATACTCCCC 58.846 45.455 0.00 0.00 0.00 4.81
705 899 3.821033 ACTCAACAAAAGCACATACTCCC 59.179 43.478 0.00 0.00 0.00 4.30
706 900 5.438761 AACTCAACAAAAGCACATACTCC 57.561 39.130 0.00 0.00 0.00 3.85
723 928 1.073284 GAGGCCCCACAAACTAACTCA 59.927 52.381 0.00 0.00 0.00 3.41
735 940 0.560688 AAACCTCAAAAGAGGCCCCA 59.439 50.000 11.29 0.00 46.05 4.96
859 1064 1.999735 GATTTGTCGAGGATTCACGCA 59.000 47.619 0.00 0.00 0.00 5.24
892 1097 8.199449 TCCCGAAAGTATATTTGATTAAGTCGT 58.801 33.333 0.00 0.00 0.00 4.34
914 1119 3.306166 CGCAACTCTAATACAACTTCCCG 59.694 47.826 0.00 0.00 0.00 5.14
1058 1284 3.142174 GCAGGAATACAATGGTAGCTCC 58.858 50.000 0.00 3.77 36.41 4.70
1268 1502 0.955919 GGTTGCAACCGAGGAAGAGG 60.956 60.000 31.73 0.00 39.66 3.69
1308 1542 7.969508 TGCATGAATAATTGTACACAGTGATTG 59.030 33.333 7.81 0.00 0.00 2.67
1325 1594 4.321527 CCTCATAGCGTCTCTGCATGAATA 60.322 45.833 0.00 0.00 34.42 1.75
1555 1829 4.775236 AGTTGAGATATGGAGGTTTCAGC 58.225 43.478 0.00 0.00 0.00 4.26
1709 2018 7.009631 CGTGATTTTCTATCTACTGGACTGTTG 59.990 40.741 0.00 0.00 0.00 3.33
1723 2032 9.035607 CACTTCTAACATAGCGTGATTTTCTAT 57.964 33.333 0.00 0.00 32.39 1.98
1757 2103 8.044574 TCTCCCATTCACCTCAATATTTATCA 57.955 34.615 0.00 0.00 0.00 2.15
1802 2148 9.751542 GAAATCATCTCGTAATTAGGAGAAAGA 57.248 33.333 31.02 29.04 46.37 2.52
1817 2163 8.986847 AGATATTGTTGCTAAGAAATCATCTCG 58.013 33.333 0.00 0.00 37.42 4.04
1859 2205 3.493767 TGGTGTACAACAGGTTATGCA 57.506 42.857 10.22 0.00 0.00 3.96
1861 2207 9.352784 CAATAAAATGGTGTACAACAGGTTATG 57.647 33.333 22.87 16.22 0.00 1.90
1954 2304 4.201551 CGATTTGAATTGTGAGTTGCATGC 60.202 41.667 11.82 11.82 0.00 4.06
1955 2305 4.201551 GCGATTTGAATTGTGAGTTGCATG 60.202 41.667 0.00 0.00 0.00 4.06
1956 2306 3.922240 GCGATTTGAATTGTGAGTTGCAT 59.078 39.130 0.00 0.00 0.00 3.96
1957 2307 3.004629 AGCGATTTGAATTGTGAGTTGCA 59.995 39.130 0.00 0.00 0.00 4.08
2059 2411 0.591170 AATTTTGACTCACGGCCGTG 59.409 50.000 45.04 45.04 46.64 4.94
2118 3854 1.872653 GCGAACGAACTTTCTCCTGGT 60.873 52.381 0.00 0.00 0.00 4.00
2195 3932 7.391148 ACAATCCACCAAGTGTACATAAATC 57.609 36.000 0.00 0.00 0.00 2.17
2202 3939 4.911514 ACAAACAATCCACCAAGTGTAC 57.088 40.909 0.00 0.00 0.00 2.90
2205 3942 6.337356 ACTTAAACAAACAATCCACCAAGTG 58.663 36.000 0.00 0.00 0.00 3.16
2283 4020 0.179076 CACCAGCACCGCTATGATCA 60.179 55.000 0.00 0.00 36.40 2.92
2340 4077 9.846248 CAATAGTTTTCCCAATAACTTTCTCTG 57.154 33.333 0.00 0.00 36.16 3.35
2341 4078 9.807921 TCAATAGTTTTCCCAATAACTTTCTCT 57.192 29.630 0.00 0.00 36.16 3.10
2348 4085 7.094506 ACCGTTCTCAATAGTTTTCCCAATAAC 60.095 37.037 0.00 0.00 0.00 1.89
2349 4086 6.943718 ACCGTTCTCAATAGTTTTCCCAATAA 59.056 34.615 0.00 0.00 0.00 1.40
2377 4114 0.319900 CTCCGACACCTCCAACACAG 60.320 60.000 0.00 0.00 0.00 3.66
2383 4120 1.152419 TTCACCTCCGACACCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
2558 4295 3.797039 CGTGGGCATCATCTTTAGAAGA 58.203 45.455 0.00 0.00 42.69 2.87
2560 4297 2.288666 GCGTGGGCATCATCTTTAGAA 58.711 47.619 0.00 0.00 39.62 2.10
2704 4442 6.488683 ACCACAAAGTATTTTGGATCGAAAGA 59.511 34.615 14.38 0.00 46.33 2.52
2710 4448 9.406828 GACTAAAACCACAAAGTATTTTGGATC 57.593 33.333 14.38 0.00 46.33 3.36
2711 4449 8.364894 GGACTAAAACCACAAAGTATTTTGGAT 58.635 33.333 14.38 0.00 46.33 3.41
2848 4588 7.114866 TGAAATTGCACAATCCATATGACAT 57.885 32.000 3.65 0.00 0.00 3.06
3014 4760 9.020731 ACGAAGGGACTATTTGAAAAATGTTAT 57.979 29.630 0.00 0.00 38.49 1.89
3256 5030 7.623268 TTTTCCGTTCGTTAACTTAGTCTAC 57.377 36.000 3.71 0.00 33.15 2.59
3312 5088 0.603707 CTGAAGTGGCGTGGTCATGT 60.604 55.000 0.00 0.00 0.00 3.21
3336 5112 5.447954 CCTTATAGTGAGATAGACCATCGCG 60.448 48.000 0.00 0.00 38.81 5.87
3360 5136 0.038159 AGGCGCGCATCTATAACTCC 60.038 55.000 34.42 10.63 0.00 3.85
3477 5253 2.143122 CAGGTAAGAGCGTCTTTTGCA 58.857 47.619 5.74 0.00 37.89 4.08
3480 5256 1.610886 GGCCAGGTAAGAGCGTCTTTT 60.611 52.381 0.00 0.00 37.89 2.27
3507 5292 4.489306 TCTCTCTCGTTCCAGACATAGA 57.511 45.455 0.00 0.00 0.00 1.98
3511 5296 2.814919 GAGTTCTCTCTCGTTCCAGACA 59.185 50.000 0.00 0.00 37.68 3.41
3535 5320 6.828502 AATTGAAGAAAGAAAAACGAAGGC 57.171 33.333 0.00 0.00 0.00 4.35
3589 5407 8.678199 AGGAAAAGAGTACAGAACAAAGAAAAG 58.322 33.333 0.00 0.00 0.00 2.27
3624 5442 9.013490 GGAAAAAGTAAAACGAAAAGTAGAACC 57.987 33.333 0.00 0.00 0.00 3.62
3656 5474 6.552859 TTAACATTCGTGCATTTCTCAAGA 57.447 33.333 0.00 0.00 0.00 3.02
3657 5475 7.326789 ACATTTAACATTCGTGCATTTCTCAAG 59.673 33.333 0.00 0.00 0.00 3.02
3659 5477 6.581919 CACATTTAACATTCGTGCATTTCTCA 59.418 34.615 0.00 0.00 0.00 3.27
3660 5478 6.801377 TCACATTTAACATTCGTGCATTTCTC 59.199 34.615 0.00 0.00 0.00 2.87
3661 5479 6.676950 TCACATTTAACATTCGTGCATTTCT 58.323 32.000 0.00 0.00 0.00 2.52
3662 5480 6.926280 TCACATTTAACATTCGTGCATTTC 57.074 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.