Multiple sequence alignment - TraesCS1A01G210500

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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 TraesCS1A01G210500 chr1A 100.000 3359 0 0 1 3359 372908577 372911935 0.000000e+00 6204.0
1 TraesCS1A01G210500 chr1A 86.667 195 20 5 717 908 561115309 561115118 9.440000e-51 211.0
2 TraesCS1A01G210500 chr1A 87.013 77 10 0 553 629 310970615 310970691 1.660000e-13 87.9
3 TraesCS1A01G210500 chr1B 93.324 2037 78 25 732 2731 402797997 402800012 0.000000e+00 2955.0
4 TraesCS1A01G210500 chr1B 83.377 379 45 14 1 371 402795317 402795685 5.370000e-88 335.0
5 TraesCS1A01G210500 chr1D 96.650 1642 43 6 905 2543 298939548 298941180 0.000000e+00 2717.0
6 TraesCS1A01G210500 chr1D 90.050 794 50 8 2593 3359 298941195 298941986 0.000000e+00 1002.0
7 TraesCS1A01G210500 chr1D 93.103 58 4 0 572 629 226730020 226730077 5.970000e-13 86.1
8 TraesCS1A01G210500 chr4B 80.172 1281 230 22 1073 2344 9691123 9692388 0.000000e+00 937.0
9 TraesCS1A01G210500 chr4B 88.750 80 8 1 553 632 342858791 342858713 2.760000e-16 97.1
10 TraesCS1A01G210500 chr4D 80.156 1285 225 25 1073 2345 5566963 5568229 0.000000e+00 933.0
11 TraesCS1A01G210500 chr4D 85.246 61 7 2 2925 2984 9223092 9223033 1.010000e-05 62.1
12 TraesCS1A01G210500 chr4A 81.175 749 134 7 1601 2344 598045845 598045099 2.230000e-166 595.0
13 TraesCS1A01G210500 chr2D 81.421 366 59 5 558 915 114141414 114141778 1.180000e-74 291.0
14 TraesCS1A01G210500 chr2D 89.024 82 9 0 553 634 100753503 100753584 5.930000e-18 102.0
15 TraesCS1A01G210500 chr7D 81.185 287 42 9 627 908 2786288 2786567 1.570000e-53 220.0
16 TraesCS1A01G210500 chr7D 93.548 62 4 0 573 634 621211615 621211676 3.570000e-15 93.5
17 TraesCS1A01G210500 chr3A 85.202 223 21 7 717 930 744393014 744392795 5.640000e-53 219.0
18 TraesCS1A01G210500 chr3A 84.615 65 9 1 1 65 738947312 738947249 2.800000e-06 63.9
19 TraesCS1A01G210500 chr3B 87.179 195 19 5 717 908 248247909 248248100 2.030000e-52 217.0
20 TraesCS1A01G210500 chr3B 86.598 194 21 5 717 908 549666194 549666004 3.400000e-50 209.0
21 TraesCS1A01G210500 chr7A 86.667 195 20 5 717 908 399518442 399518633 9.440000e-51 211.0
22 TraesCS1A01G210500 chr7A 86.224 196 21 5 715 907 108947020 108946828 1.220000e-49 207.0
23 TraesCS1A01G210500 chr2B 86.667 195 20 5 717 908 614113754 614113945 9.440000e-51 211.0
24 TraesCS1A01G210500 chr6A 88.506 87 10 0 553 639 14658062 14658148 4.580000e-19 106.0
25 TraesCS1A01G210500 chr5A 86.207 87 12 0 553 639 18693647 18693733 9.920000e-16 95.3
26 TraesCS1A01G210500 chrUn 84.615 65 9 1 1 65 42510348 42510411 2.800000e-06 63.9


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 TraesCS1A01G210500 chr1A 372908577 372911935 3358 False 6204.0 6204 100.0000 1 3359 1 chr1A.!!$F2 3358
1 TraesCS1A01G210500 chr1B 402795317 402800012 4695 False 1645.0 2955 88.3505 1 2731 2 chr1B.!!$F1 2730
2 TraesCS1A01G210500 chr1D 298939548 298941986 2438 False 1859.5 2717 93.3500 905 3359 2 chr1D.!!$F2 2454
3 TraesCS1A01G210500 chr4B 9691123 9692388 1265 False 937.0 937 80.1720 1073 2344 1 chr4B.!!$F1 1271
4 TraesCS1A01G210500 chr4D 5566963 5568229 1266 False 933.0 933 80.1560 1073 2345 1 chr4D.!!$F1 1272
5 TraesCS1A01G210500 chr4A 598045099 598045845 746 True 595.0 595 81.1750 1601 2344 1 chr4A.!!$R1 743

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
259 264 0.461961 AAGCGAGTGATAGAGGCACC 59.538 55.000 0.00 0.00 36.95 5.01 F
274 279 0.463833 GCACCCGGGAAATCACCTAG 60.464 60.000 32.02 4.29 0.00 3.02 F
421 429 0.610785 TGCCCCCGTCCTGAAATTTC 60.611 55.000 11.41 11.41 0.00 2.17 F
629 2148 1.005394 CGACACAGGCTAAACGGGT 60.005 57.895 0.00 0.00 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1089 3112 0.561184 AGTCCCGGATGTGGATCCTA 59.439 55.000 14.23 2.2 45.68 2.94 R
1401 3424 2.119611 TTGAGGAGCGAGGGGTCA 59.880 61.111 0.00 0.0 42.46 4.02 R
2046 4069 2.674380 AACTCGTCGTACCGCCCT 60.674 61.111 0.00 0.0 0.00 5.19 R
2621 4649 1.806542 GTGATCACGACCAGTTTGCAT 59.193 47.619 10.69 0.0 0.00 3.96 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
201 206 2.873525 GCCTAGGTCGGCCCATCTC 61.874 68.421 11.31 0.00 44.41 2.75
202 207 2.565645 CCTAGGTCGGCCCATCTCG 61.566 68.421 0.08 0.00 34.66 4.04
214 219 0.811219 CCATCTCGCGCATCCTTCAA 60.811 55.000 8.75 0.00 0.00 2.69
243 248 2.783135 TCCCTTTGTCTCATGTGAAGC 58.217 47.619 0.00 0.00 0.00 3.86
246 251 2.414481 CCTTTGTCTCATGTGAAGCGAG 59.586 50.000 0.00 0.00 0.00 5.03
248 253 2.070262 TGTCTCATGTGAAGCGAGTG 57.930 50.000 0.00 0.00 0.00 3.51
257 262 1.135139 GTGAAGCGAGTGATAGAGGCA 59.865 52.381 0.00 0.00 0.00 4.75
259 264 0.461961 AAGCGAGTGATAGAGGCACC 59.538 55.000 0.00 0.00 36.95 5.01
260 265 1.068250 GCGAGTGATAGAGGCACCC 59.932 63.158 0.00 0.00 36.95 4.61
274 279 0.463833 GCACCCGGGAAATCACCTAG 60.464 60.000 32.02 4.29 0.00 3.02
277 282 2.502538 CACCCGGGAAATCACCTAGTAA 59.497 50.000 32.02 0.00 0.00 2.24
283 288 4.686122 CGGGAAATCACCTAGTAATGCCTT 60.686 45.833 0.00 0.00 0.00 4.35
284 289 5.454187 CGGGAAATCACCTAGTAATGCCTTA 60.454 44.000 0.00 0.00 0.00 2.69
285 290 5.763698 GGGAAATCACCTAGTAATGCCTTAC 59.236 44.000 3.89 3.89 37.99 2.34
332 340 1.005097 AGGAGCAATGCTGGATCAACA 59.995 47.619 14.48 0.00 39.88 3.33
333 341 1.404391 GGAGCAATGCTGGATCAACAG 59.596 52.381 14.48 0.00 39.88 3.16
337 345 2.159421 GCAATGCTGGATCAACAGACTG 60.159 50.000 0.00 0.00 40.97 3.51
338 346 1.747709 ATGCTGGATCAACAGACTGC 58.252 50.000 1.25 0.00 40.97 4.40
348 356 3.926616 TCAACAGACTGCTTACTAAGGC 58.073 45.455 1.25 0.00 0.00 4.35
375 383 3.554934 GGATCAATCCAACATGGTGCTA 58.445 45.455 4.81 0.00 46.38 3.49
378 386 4.508551 TCAATCCAACATGGTGCTATCT 57.491 40.909 4.81 0.00 39.03 1.98
383 391 4.201657 TCCAACATGGTGCTATCTGATTG 58.798 43.478 4.81 0.00 39.03 2.67
384 392 3.317149 CCAACATGGTGCTATCTGATTGG 59.683 47.826 4.81 0.00 31.35 3.16
385 393 4.201657 CAACATGGTGCTATCTGATTGGA 58.798 43.478 0.00 0.00 0.00 3.53
386 394 3.813443 ACATGGTGCTATCTGATTGGAC 58.187 45.455 13.56 13.56 0.00 4.02
387 395 2.602257 TGGTGCTATCTGATTGGACG 57.398 50.000 14.96 0.00 0.00 4.79
388 396 1.831106 TGGTGCTATCTGATTGGACGT 59.169 47.619 14.96 0.00 0.00 4.34
389 397 2.236146 TGGTGCTATCTGATTGGACGTT 59.764 45.455 14.96 0.00 0.00 3.99
390 398 2.609459 GGTGCTATCTGATTGGACGTTG 59.391 50.000 14.96 0.00 0.00 4.10
391 399 3.262420 GTGCTATCTGATTGGACGTTGT 58.738 45.455 7.82 0.00 0.00 3.32
392 400 3.684788 GTGCTATCTGATTGGACGTTGTT 59.315 43.478 7.82 0.00 0.00 2.83
393 401 4.154195 GTGCTATCTGATTGGACGTTGTTT 59.846 41.667 7.82 0.00 0.00 2.83
394 402 4.154015 TGCTATCTGATTGGACGTTGTTTG 59.846 41.667 0.00 0.00 0.00 2.93
395 403 4.437390 GCTATCTGATTGGACGTTGTTTGG 60.437 45.833 0.00 0.00 0.00 3.28
396 404 2.226330 TCTGATTGGACGTTGTTTGGG 58.774 47.619 0.00 0.00 0.00 4.12
397 405 1.269448 CTGATTGGACGTTGTTTGGGG 59.731 52.381 0.00 0.00 0.00 4.96
398 406 1.324383 GATTGGACGTTGTTTGGGGT 58.676 50.000 0.00 0.00 0.00 4.95
399 407 2.158652 TGATTGGACGTTGTTTGGGGTA 60.159 45.455 0.00 0.00 0.00 3.69
400 408 1.677942 TTGGACGTTGTTTGGGGTAC 58.322 50.000 0.00 0.00 0.00 3.34
414 422 3.782443 GTACCTGCCCCCGTCCTG 61.782 72.222 0.00 0.00 0.00 3.86
415 423 4.000620 TACCTGCCCCCGTCCTGA 62.001 66.667 0.00 0.00 0.00 3.86
416 424 3.549433 TACCTGCCCCCGTCCTGAA 62.549 63.158 0.00 0.00 0.00 3.02
417 425 3.646715 CCTGCCCCCGTCCTGAAA 61.647 66.667 0.00 0.00 0.00 2.69
418 426 2.677228 CTGCCCCCGTCCTGAAAT 59.323 61.111 0.00 0.00 0.00 2.17
419 427 1.000896 CTGCCCCCGTCCTGAAATT 60.001 57.895 0.00 0.00 0.00 1.82
420 428 0.611896 CTGCCCCCGTCCTGAAATTT 60.612 55.000 0.00 0.00 0.00 1.82
421 429 0.610785 TGCCCCCGTCCTGAAATTTC 60.611 55.000 11.41 11.41 0.00 2.17
422 430 0.610785 GCCCCCGTCCTGAAATTTCA 60.611 55.000 19.45 19.45 35.57 2.69
455 1974 3.340928 GGGGTTAGTTTGCACTCGTATT 58.659 45.455 0.00 0.00 34.06 1.89
456 1975 4.506758 GGGGTTAGTTTGCACTCGTATTA 58.493 43.478 0.00 0.00 34.06 0.98
457 1976 4.569564 GGGGTTAGTTTGCACTCGTATTAG 59.430 45.833 0.00 0.00 34.06 1.73
458 1977 4.033702 GGGTTAGTTTGCACTCGTATTAGC 59.966 45.833 0.00 0.00 34.06 3.09
459 1978 4.628333 GGTTAGTTTGCACTCGTATTAGCA 59.372 41.667 0.00 0.00 34.06 3.49
460 1979 5.445540 GGTTAGTTTGCACTCGTATTAGCAC 60.446 44.000 0.00 0.00 36.62 4.40
461 1980 3.000727 AGTTTGCACTCGTATTAGCACC 58.999 45.455 0.00 0.00 36.62 5.01
462 1981 2.739913 GTTTGCACTCGTATTAGCACCA 59.260 45.455 0.00 0.00 36.62 4.17
463 1982 2.979814 TGCACTCGTATTAGCACCAT 57.020 45.000 0.00 0.00 31.05 3.55
464 1983 4.394439 TTGCACTCGTATTAGCACCATA 57.606 40.909 0.00 0.00 36.62 2.74
465 1984 4.394439 TGCACTCGTATTAGCACCATAA 57.606 40.909 0.00 0.00 31.05 1.90
466 1985 4.956085 TGCACTCGTATTAGCACCATAAT 58.044 39.130 0.00 0.00 31.05 1.28
467 1986 4.749598 TGCACTCGTATTAGCACCATAATG 59.250 41.667 0.00 0.00 31.05 1.90
468 1987 4.152402 GCACTCGTATTAGCACCATAATGG 59.848 45.833 0.00 0.00 45.02 3.16
483 2002 6.060028 CCATAATGGTCCGTTGTTCTATTG 57.940 41.667 6.59 0.00 31.35 1.90
490 2009 4.979815 GGTCCGTTGTTCTATTGTTTTTGG 59.020 41.667 0.00 0.00 0.00 3.28
500 2019 3.843893 ATTGTTTTTGGGCTTTGAGCT 57.156 38.095 0.00 0.00 41.99 4.09
506 2025 5.220381 GTTTTTGGGCTTTGAGCTAGTTAC 58.780 41.667 0.00 0.00 41.99 2.50
517 2036 6.770746 TTGAGCTAGTTACGACCTTTCTAT 57.229 37.500 0.00 0.00 0.00 1.98
527 2046 7.544566 AGTTACGACCTTTCTATGTGTGTAATG 59.455 37.037 0.00 0.00 0.00 1.90
528 2047 6.032956 ACGACCTTTCTATGTGTGTAATGA 57.967 37.500 0.00 0.00 0.00 2.57
549 2068 6.037786 TGAAACAACCTCCTGACAGTATAG 57.962 41.667 0.93 0.00 0.00 1.31
577 2096 2.358125 CAATCACGCCGACCCACA 60.358 61.111 0.00 0.00 0.00 4.17
629 2148 1.005394 CGACACAGGCTAAACGGGT 60.005 57.895 0.00 0.00 0.00 5.28
631 2150 1.005394 ACACAGGCTAAACGGGTCG 60.005 57.895 0.00 0.00 0.00 4.79
634 2153 1.005394 CAGGCTAAACGGGTCGTGT 60.005 57.895 0.00 0.00 39.99 4.49
679 2199 2.048222 CAGCACGACACGACCCAT 60.048 61.111 0.00 0.00 0.00 4.00
683 2203 1.066430 AGCACGACACGACCCATTTAT 60.066 47.619 0.00 0.00 0.00 1.40
686 2206 3.371591 GCACGACACGACCCATTTATTAA 59.628 43.478 0.00 0.00 0.00 1.40
691 2211 7.539366 CACGACACGACCCATTTATTAATTTTT 59.461 33.333 0.00 0.00 0.00 1.94
711 2231 9.612066 AATTTTTATTTTTCCTGATGTGTGTGT 57.388 25.926 0.00 0.00 0.00 3.72
712 2232 8.417780 TTTTTATTTTTCCTGATGTGTGTGTG 57.582 30.769 0.00 0.00 0.00 3.82
713 2233 6.707440 TTATTTTTCCTGATGTGTGTGTGT 57.293 33.333 0.00 0.00 0.00 3.72
714 2234 4.368874 TTTTTCCTGATGTGTGTGTGTG 57.631 40.909 0.00 0.00 0.00 3.82
715 2235 2.998316 TTCCTGATGTGTGTGTGTGA 57.002 45.000 0.00 0.00 0.00 3.58
716 2236 2.238942 TCCTGATGTGTGTGTGTGAC 57.761 50.000 0.00 0.00 0.00 3.67
717 2237 1.202639 TCCTGATGTGTGTGTGTGACC 60.203 52.381 0.00 0.00 0.00 4.02
720 2240 3.494223 CCTGATGTGTGTGTGTGACCTAA 60.494 47.826 0.00 0.00 0.00 2.69
727 2247 5.525745 TGTGTGTGTGTGACCTAAATTACAG 59.474 40.000 0.00 0.00 0.00 2.74
751 2271 3.181397 CAATAGGCTGAAAAACATGCGG 58.819 45.455 0.00 0.00 0.00 5.69
757 2277 4.371590 AAAAACATGCGGCCCGGC 62.372 61.111 4.77 0.00 0.00 6.13
798 2318 1.404035 CGGCCTGTTTAATAACCAGGC 59.596 52.381 27.00 27.00 46.48 4.85
799 2319 2.735151 GGCCTGTTTAATAACCAGGCT 58.265 47.619 31.16 0.00 46.44 4.58
805 2325 4.377098 TGTTTAATAACCAGGCTGTGCCC 61.377 47.826 14.43 0.00 40.60 5.36
855 2376 3.717842 GGCATGGCCCGTCTATTAA 57.282 52.632 8.35 0.00 44.06 1.40
856 2377 1.975660 GGCATGGCCCGTCTATTAAA 58.024 50.000 8.35 0.00 44.06 1.52
857 2378 1.607148 GGCATGGCCCGTCTATTAAAC 59.393 52.381 8.35 0.00 44.06 2.01
858 2379 1.263217 GCATGGCCCGTCTATTAAACG 59.737 52.381 0.00 0.00 39.78 3.60
859 2380 2.557317 CATGGCCCGTCTATTAAACGT 58.443 47.619 0.00 0.00 38.44 3.99
1191 3214 1.674980 GTCCTCGTCGGTCACCTCT 60.675 63.158 0.00 0.00 0.00 3.69
1401 3424 2.308690 GACTCTATCCCCTACGTGCTT 58.691 52.381 0.00 0.00 0.00 3.91
1629 3652 2.664851 TTCACGTTCCTGGCGCTG 60.665 61.111 7.64 0.00 0.00 5.18
1692 3715 4.324991 ACGTCTTTCCACCCGGCC 62.325 66.667 0.00 0.00 0.00 6.13
2114 4137 4.891727 CGGGGGCGTGAAGATCGG 62.892 72.222 0.00 0.00 0.00 4.18
2238 4264 3.801997 CTGAGGGAGGCGGGCAAT 61.802 66.667 3.78 0.00 0.00 3.56
2253 4279 1.138036 CAATGACGCGGTCGACCTA 59.862 57.895 30.92 13.00 39.41 3.08
2365 4391 1.349973 GTCGACGCGTAGGACTACC 59.650 63.158 26.61 7.77 32.61 3.18
2421 4449 0.459899 GGTCCGGATTTGGGCATTTC 59.540 55.000 7.81 0.00 34.42 2.17
2433 4461 3.138304 TGGGCATTTCTATATCGTGCAC 58.862 45.455 6.82 6.82 39.56 4.57
2487 4515 7.278646 TGAAGAGTGTACATTTGCTATGTCATC 59.721 37.037 0.00 4.22 33.76 2.92
2488 4516 6.051717 AGAGTGTACATTTGCTATGTCATCC 58.948 40.000 0.00 4.60 33.76 3.51
2489 4517 5.744171 AGTGTACATTTGCTATGTCATCCA 58.256 37.500 0.00 1.16 33.76 3.41
2490 4518 5.586243 AGTGTACATTTGCTATGTCATCCAC 59.414 40.000 0.00 10.36 33.76 4.02
2491 4519 4.570369 TGTACATTTGCTATGTCATCCACG 59.430 41.667 8.07 0.00 33.76 4.94
2492 4520 3.872696 ACATTTGCTATGTCATCCACGA 58.127 40.909 0.00 0.00 0.00 4.35
2503 4531 2.098607 GTCATCCACGACCACGAGATTA 59.901 50.000 0.00 0.00 42.66 1.75
2549 4577 6.200665 GTCATTTGCATTTTCAAGTGTTGCTA 59.799 34.615 0.00 0.00 35.83 3.49
2570 4598 7.270779 TGCTATAGAACTAGACTACTGAACGA 58.729 38.462 3.21 0.00 0.00 3.85
2582 4610 3.305398 ACTGAACGAAGTGGCTAGAAG 57.695 47.619 0.00 0.00 45.00 2.85
2612 4640 9.533831 AATAGGATGGTTGAAGTCTGTATTTTT 57.466 29.630 0.00 0.00 0.00 1.94
2644 4672 3.000041 GCAAACTGGTCGTGATCACATA 59.000 45.455 24.93 10.06 0.00 2.29
2645 4673 3.435327 GCAAACTGGTCGTGATCACATAA 59.565 43.478 24.93 7.51 0.00 1.90
2646 4674 4.094887 GCAAACTGGTCGTGATCACATAAT 59.905 41.667 24.93 2.82 0.00 1.28
2647 4675 5.293324 GCAAACTGGTCGTGATCACATAATA 59.707 40.000 24.93 6.64 0.00 0.98
2650 4678 8.397906 CAAACTGGTCGTGATCACATAATAATT 58.602 33.333 24.93 9.57 0.00 1.40
2653 4681 7.987458 ACTGGTCGTGATCACATAATAATTCTT 59.013 33.333 24.93 0.00 0.00 2.52
2654 4682 8.731275 TGGTCGTGATCACATAATAATTCTTT 57.269 30.769 24.93 0.00 0.00 2.52
2744 4797 2.952978 CACGGTGCTACCTCTAGATCTT 59.047 50.000 0.00 0.00 35.66 2.40
2763 4816 4.101114 TCTTCCTGCTATTGGACCTTACA 58.899 43.478 0.00 0.00 32.65 2.41
2783 4836 7.336931 CCTTACAAGGTAGCAATTGACATAAGT 59.663 37.037 10.34 2.93 41.41 2.24
2787 4840 8.893727 ACAAGGTAGCAATTGACATAAGTATTC 58.106 33.333 10.34 0.00 0.00 1.75
2896 4950 5.376625 TGAGAAGTATTTTCCACTGCAACT 58.623 37.500 0.00 0.00 0.00 3.16
2905 4959 6.707440 TTTTCCACTGCAACTGAATAAGAA 57.293 33.333 0.00 0.00 0.00 2.52
2906 4960 5.689383 TTCCACTGCAACTGAATAAGAAC 57.311 39.130 0.00 0.00 0.00 3.01
2922 4976 7.172875 TGAATAAGAACATGCCATTGGTTTTTG 59.827 33.333 4.26 0.28 0.00 2.44
2951 5005 4.700365 GGGCAACTTCAACGCGCC 62.700 66.667 5.73 0.00 42.21 6.53
2954 5008 2.860293 CAACTTCAACGCGCCGAT 59.140 55.556 5.73 0.00 0.00 4.18
2994 5048 0.530211 TCCGCTTTTCGTCCGTTTGA 60.530 50.000 0.00 0.00 36.19 2.69
3003 5057 1.011968 CGTCCGTTTGAATCGGCTGA 61.012 55.000 9.70 0.00 46.49 4.26
3011 5065 0.955428 TGAATCGGCTGAAGGTGTGC 60.955 55.000 0.00 0.00 0.00 4.57
3019 5073 0.532862 CTGAAGGTGTGCTGTTCGGT 60.533 55.000 0.00 0.00 0.00 4.69
3037 5091 1.135199 GGTCGTGTCCGCTCAAATCTA 60.135 52.381 0.00 0.00 0.00 1.98
3040 5094 1.653151 GTGTCCGCTCAAATCTACCC 58.347 55.000 0.00 0.00 0.00 3.69
3073 5127 1.595929 GCCGACACCTTTTCGTCCA 60.596 57.895 0.00 0.00 34.56 4.02
3109 5163 9.317936 AGCAAATTTAATCTAAAATAAGCCAGC 57.682 29.630 0.00 0.00 33.03 4.85
3132 5186 2.742204 CGACCACTAGGATGTCTCTCGA 60.742 54.545 0.00 0.00 38.69 4.04
3159 5213 3.203086 TTTGCGCCCAGGTGGATGA 62.203 57.895 4.18 0.00 37.39 2.92
3191 5245 3.041940 GTGTGGCGTTGAGGTCGG 61.042 66.667 0.00 0.00 0.00 4.79
3198 5252 2.351276 GTTGAGGTCGGTGGCCAT 59.649 61.111 9.72 0.00 0.00 4.40
3237 5291 3.030209 CGATCACGCTTCCTTTCGA 57.970 52.632 0.00 0.00 0.00 3.71
3246 5300 1.195674 GCTTCCTTTCGACAAGCAGTC 59.804 52.381 11.02 0.00 41.87 3.51
3272 5326 4.974438 AGGTGGGGAAGCGGGACA 62.974 66.667 0.00 0.00 0.00 4.02
3337 5391 4.560856 GATGAGCGCGGCGACTCT 62.561 66.667 31.16 19.95 33.64 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 206 4.228097 CCGCTTGAAGGATGCGCG 62.228 66.667 0.00 0.00 44.70 6.86
202 207 3.880846 CCCGCTTGAAGGATGCGC 61.881 66.667 0.00 0.00 44.70 6.09
218 223 1.272147 ACATGAGACAAAGGGAAGCCC 60.272 52.381 0.00 0.00 45.90 5.19
235 240 2.223923 GCCTCTATCACTCGCTTCACAT 60.224 50.000 0.00 0.00 0.00 3.21
246 251 1.335132 TTCCCGGGTGCCTCTATCAC 61.335 60.000 22.86 0.00 0.00 3.06
248 253 0.765510 ATTTCCCGGGTGCCTCTATC 59.234 55.000 22.86 0.00 0.00 2.08
257 262 2.555732 TACTAGGTGATTTCCCGGGT 57.444 50.000 22.86 0.00 0.00 5.28
259 264 3.139077 GCATTACTAGGTGATTTCCCGG 58.861 50.000 0.00 0.00 0.00 5.73
260 265 3.139077 GGCATTACTAGGTGATTTCCCG 58.861 50.000 0.00 0.00 0.00 5.14
283 288 3.343617 CGAATCCTTTCAAAGCCAGGTA 58.656 45.455 0.00 0.00 0.00 3.08
284 289 2.162681 CGAATCCTTTCAAAGCCAGGT 58.837 47.619 0.00 0.00 0.00 4.00
285 290 1.474077 CCGAATCCTTTCAAAGCCAGG 59.526 52.381 0.00 0.00 0.00 4.45
332 340 4.381718 CCGTAAAGCCTTAGTAAGCAGTCT 60.382 45.833 4.22 0.00 0.00 3.24
333 341 3.864003 CCGTAAAGCCTTAGTAAGCAGTC 59.136 47.826 4.22 0.00 0.00 3.51
337 345 4.690122 TGATCCGTAAAGCCTTAGTAAGC 58.310 43.478 4.22 0.78 0.00 3.09
338 346 6.424207 GGATTGATCCGTAAAGCCTTAGTAAG 59.576 42.308 2.65 2.65 37.19 2.34
371 379 3.610040 ACAACGTCCAATCAGATAGCA 57.390 42.857 0.00 0.00 0.00 3.49
372 380 4.437390 CCAAACAACGTCCAATCAGATAGC 60.437 45.833 0.00 0.00 0.00 2.97
375 383 2.819608 CCCAAACAACGTCCAATCAGAT 59.180 45.455 0.00 0.00 0.00 2.90
378 386 1.323412 CCCCAAACAACGTCCAATCA 58.677 50.000 0.00 0.00 0.00 2.57
383 391 0.109153 AGGTACCCCAAACAACGTCC 59.891 55.000 8.74 0.00 0.00 4.79
384 392 1.232119 CAGGTACCCCAAACAACGTC 58.768 55.000 8.74 0.00 0.00 4.34
385 393 0.820482 GCAGGTACCCCAAACAACGT 60.820 55.000 8.74 0.00 0.00 3.99
386 394 1.520600 GGCAGGTACCCCAAACAACG 61.521 60.000 8.74 0.00 0.00 4.10
387 395 1.183030 GGGCAGGTACCCCAAACAAC 61.183 60.000 8.74 0.00 45.00 3.32
388 396 1.154221 GGGCAGGTACCCCAAACAA 59.846 57.895 8.74 0.00 45.00 2.83
389 397 2.848032 GGGCAGGTACCCCAAACA 59.152 61.111 8.74 0.00 45.00 2.83
397 405 3.782443 CAGGACGGGGGCAGGTAC 61.782 72.222 0.00 0.00 0.00 3.34
398 406 3.549433 TTCAGGACGGGGGCAGGTA 62.549 63.158 0.00 0.00 0.00 3.08
399 407 4.974438 TTCAGGACGGGGGCAGGT 62.974 66.667 0.00 0.00 0.00 4.00
400 408 2.499303 AATTTCAGGACGGGGGCAGG 62.499 60.000 0.00 0.00 0.00 4.85
401 409 0.611896 AAATTTCAGGACGGGGGCAG 60.612 55.000 0.00 0.00 0.00 4.85
402 410 0.610785 GAAATTTCAGGACGGGGGCA 60.611 55.000 13.40 0.00 0.00 5.36
403 411 0.610785 TGAAATTTCAGGACGGGGGC 60.611 55.000 16.91 0.00 32.50 5.80
404 412 3.662290 TGAAATTTCAGGACGGGGG 57.338 52.632 16.91 0.00 32.50 5.40
433 441 0.250597 ACGAGTGCAAACTAACCCCC 60.251 55.000 0.00 0.00 0.00 5.40
434 442 2.460757 TACGAGTGCAAACTAACCCC 57.539 50.000 0.00 0.00 0.00 4.95
435 443 4.033702 GCTAATACGAGTGCAAACTAACCC 59.966 45.833 0.00 0.00 0.00 4.11
460 1979 5.588648 ACAATAGAACAACGGACCATTATGG 59.411 40.000 10.08 10.08 45.02 2.74
461 1980 6.677781 ACAATAGAACAACGGACCATTATG 57.322 37.500 0.00 0.00 0.00 1.90
462 1981 7.696992 AAACAATAGAACAACGGACCATTAT 57.303 32.000 0.00 0.00 0.00 1.28
463 1982 7.513371 AAAACAATAGAACAACGGACCATTA 57.487 32.000 0.00 0.00 0.00 1.90
464 1983 6.399639 AAAACAATAGAACAACGGACCATT 57.600 33.333 0.00 0.00 0.00 3.16
465 1984 6.212955 CAAAAACAATAGAACAACGGACCAT 58.787 36.000 0.00 0.00 0.00 3.55
466 1985 5.450688 CCAAAAACAATAGAACAACGGACCA 60.451 40.000 0.00 0.00 0.00 4.02
467 1986 4.979815 CCAAAAACAATAGAACAACGGACC 59.020 41.667 0.00 0.00 0.00 4.46
468 1987 4.979815 CCCAAAAACAATAGAACAACGGAC 59.020 41.667 0.00 0.00 0.00 4.79
469 1988 4.500035 GCCCAAAAACAATAGAACAACGGA 60.500 41.667 0.00 0.00 0.00 4.69
470 1989 3.738791 GCCCAAAAACAATAGAACAACGG 59.261 43.478 0.00 0.00 0.00 4.44
483 2002 4.322080 AACTAGCTCAAAGCCCAAAAAC 57.678 40.909 0.00 0.00 43.77 2.43
490 2009 2.094130 AGGTCGTAACTAGCTCAAAGCC 60.094 50.000 0.00 0.00 43.77 4.35
500 2019 6.579666 ACACACATAGAAAGGTCGTAACTA 57.420 37.500 0.00 0.00 0.00 2.24
506 2025 6.961359 TTCATTACACACATAGAAAGGTCG 57.039 37.500 0.00 0.00 0.00 4.79
517 2036 4.578516 CAGGAGGTTGTTTCATTACACACA 59.421 41.667 0.00 0.00 0.00 3.72
527 2046 4.870991 GCTATACTGTCAGGAGGTTGTTTC 59.129 45.833 4.53 0.00 0.00 2.78
528 2047 4.532521 AGCTATACTGTCAGGAGGTTGTTT 59.467 41.667 4.53 0.00 0.00 2.83
604 2123 3.589654 TAGCCTGTGTCGTGCCTGC 62.590 63.158 0.00 0.00 0.00 4.85
629 2148 3.062466 CTCGAGGCCCAGACACGA 61.062 66.667 3.91 0.73 0.00 4.35
661 2180 3.589654 ATGGGTCGTGTCGTGCTGG 62.590 63.158 0.00 0.00 0.00 4.85
662 2181 1.227999 AAATGGGTCGTGTCGTGCTG 61.228 55.000 0.00 0.00 0.00 4.41
663 2182 0.319083 TAAATGGGTCGTGTCGTGCT 59.681 50.000 0.00 0.00 0.00 4.40
686 2206 9.044150 CACACACACATCAGGAAAAATAAAAAT 57.956 29.630 0.00 0.00 0.00 1.82
691 2211 5.825151 TCACACACACACATCAGGAAAAATA 59.175 36.000 0.00 0.00 0.00 1.40
700 2220 3.828875 TTAGGTCACACACACACATCA 57.171 42.857 0.00 0.00 0.00 3.07
703 2223 5.429130 TGTAATTTAGGTCACACACACACA 58.571 37.500 0.00 0.00 0.00 3.72
704 2224 5.560183 GCTGTAATTTAGGTCACACACACAC 60.560 44.000 0.00 0.00 0.00 3.82
705 2225 4.513692 GCTGTAATTTAGGTCACACACACA 59.486 41.667 0.00 0.00 0.00 3.72
706 2226 4.083484 GGCTGTAATTTAGGTCACACACAC 60.083 45.833 0.00 0.00 0.00 3.82
707 2227 4.069304 GGCTGTAATTTAGGTCACACACA 58.931 43.478 0.00 0.00 0.00 3.72
708 2228 3.439129 GGGCTGTAATTTAGGTCACACAC 59.561 47.826 0.00 0.00 0.00 3.82
709 2229 3.073209 TGGGCTGTAATTTAGGTCACACA 59.927 43.478 0.00 0.00 0.00 3.72
710 2230 3.681593 TGGGCTGTAATTTAGGTCACAC 58.318 45.455 0.00 0.00 0.00 3.82
711 2231 4.374689 TTGGGCTGTAATTTAGGTCACA 57.625 40.909 0.00 0.00 0.00 3.58
712 2232 5.531287 CCTATTGGGCTGTAATTTAGGTCAC 59.469 44.000 0.00 0.00 0.00 3.67
713 2233 5.690865 CCTATTGGGCTGTAATTTAGGTCA 58.309 41.667 0.00 0.00 0.00 4.02
738 2258 2.647875 CGGGCCGCATGTTTTTCA 59.352 55.556 15.42 0.00 0.00 2.69
773 2293 0.748729 TTATTAAACAGGCCGGCCCG 60.749 55.000 41.72 34.72 39.21 6.13
784 2304 3.503827 GGCACAGCCTGGTTATTAAAC 57.496 47.619 0.00 0.00 46.69 2.01
810 2331 2.801162 CACGTGTGTCGCTCCTCG 60.801 66.667 7.58 0.00 44.19 4.63
841 2362 2.012937 CACGTTTAATAGACGGGCCA 57.987 50.000 4.39 0.00 44.34 5.36
845 2366 1.322338 CGTGGCACGTTTAATAGACGG 59.678 52.381 30.56 0.00 44.34 4.79
846 2367 1.322338 CCGTGGCACGTTTAATAGACG 59.678 52.381 34.74 14.36 45.46 4.18
847 2368 1.061566 GCCGTGGCACGTTTAATAGAC 59.938 52.381 34.74 12.50 40.58 2.59
848 2369 1.361793 GCCGTGGCACGTTTAATAGA 58.638 50.000 34.74 0.00 40.58 1.98
849 2370 0.025770 CGCCGTGGCACGTTTAATAG 59.974 55.000 34.74 20.30 40.58 1.73
850 2371 1.360194 CCGCCGTGGCACGTTTAATA 61.360 55.000 34.74 0.00 40.58 0.98
851 2372 2.682876 CCGCCGTGGCACGTTTAAT 61.683 57.895 34.74 0.00 40.58 1.40
852 2373 3.347405 CCGCCGTGGCACGTTTAA 61.347 61.111 34.74 0.00 40.58 1.52
927 2458 3.366781 GGGGTTCTCGTGTACTAACTGTC 60.367 52.174 0.00 0.00 0.00 3.51
929 2460 2.559668 TGGGGTTCTCGTGTACTAACTG 59.440 50.000 0.00 0.00 0.00 3.16
932 2463 2.821969 GAGTGGGGTTCTCGTGTACTAA 59.178 50.000 0.00 0.00 0.00 2.24
934 2465 1.203025 AGAGTGGGGTTCTCGTGTACT 60.203 52.381 0.00 0.00 37.07 2.73
1089 3112 0.561184 AGTCCCGGATGTGGATCCTA 59.439 55.000 14.23 2.20 45.68 2.94
1284 3307 2.269241 CGGTGGAAGAAGGGCTCC 59.731 66.667 0.00 0.00 0.00 4.70
1401 3424 2.119611 TTGAGGAGCGAGGGGTCA 59.880 61.111 0.00 0.00 42.46 4.02
1473 3496 4.193334 CGACGCGCCAGGATCTGA 62.193 66.667 5.73 0.00 32.44 3.27
2046 4069 2.674380 AACTCGTCGTACCGCCCT 60.674 61.111 0.00 0.00 0.00 5.19
2238 4264 3.807538 GCTAGGTCGACCGCGTCA 61.808 66.667 28.26 11.62 42.08 4.35
2365 4391 7.646446 TCAAGAGCATTTCATTTGACATTTG 57.354 32.000 0.00 0.00 0.00 2.32
2487 4515 2.163815 AGAACTAATCTCGTGGTCGTGG 59.836 50.000 0.00 0.00 38.33 4.94
2488 4516 3.489180 AGAACTAATCTCGTGGTCGTG 57.511 47.619 0.00 0.00 38.33 4.35
2489 4517 3.255149 ACAAGAACTAATCTCGTGGTCGT 59.745 43.478 0.00 0.00 37.42 4.34
2490 4518 3.834610 ACAAGAACTAATCTCGTGGTCG 58.165 45.455 0.00 0.00 37.42 4.79
2491 4519 7.331193 ACATTTACAAGAACTAATCTCGTGGTC 59.669 37.037 0.00 0.00 37.42 4.02
2492 4520 7.117812 CACATTTACAAGAACTAATCTCGTGGT 59.882 37.037 0.00 0.00 37.42 4.16
2503 4531 4.215109 ACTTGCCCACATTTACAAGAACT 58.785 39.130 8.46 0.00 41.59 3.01
2549 4577 7.066043 CCACTTCGTTCAGTAGTCTAGTTCTAT 59.934 40.741 0.00 0.00 0.00 1.98
2570 4598 4.884961 TCCTATTCTCCTTCTAGCCACTT 58.115 43.478 0.00 0.00 0.00 3.16
2582 4610 5.104735 ACAGACTTCAACCATCCTATTCTCC 60.105 44.000 0.00 0.00 0.00 3.71
2621 4649 1.806542 GTGATCACGACCAGTTTGCAT 59.193 47.619 10.69 0.00 0.00 3.96
2744 4797 3.199946 CCTTGTAAGGTCCAATAGCAGGA 59.800 47.826 2.42 0.00 41.41 3.86
2763 4816 9.632638 ATGAATACTTATGTCAATTGCTACCTT 57.367 29.630 0.00 0.00 0.00 3.50
2810 4864 7.149307 TGTTATGTGAATCACGTAGAAAGACA 58.851 34.615 14.13 12.45 37.20 3.41
2811 4865 7.576750 TGTTATGTGAATCACGTAGAAAGAC 57.423 36.000 14.13 10.35 37.20 3.01
2812 4866 7.870954 ACTTGTTATGTGAATCACGTAGAAAGA 59.129 33.333 27.58 11.79 37.20 2.52
2896 4950 5.999205 AACCAATGGCATGTTCTTATTCA 57.001 34.783 0.00 0.00 0.00 2.57
2905 4959 1.773653 ACCCAAAAACCAATGGCATGT 59.226 42.857 0.00 0.00 35.28 3.21
2906 4960 2.565046 ACCCAAAAACCAATGGCATG 57.435 45.000 0.00 0.00 35.28 4.06
2942 4996 3.349808 TTTGCATCGGCGCGTTGA 61.350 55.556 8.43 6.41 45.35 3.18
2951 5005 0.041663 AAACACGTCCGTTTGCATCG 60.042 50.000 3.44 5.08 37.69 3.84
2994 5048 0.957395 CAGCACACCTTCAGCCGATT 60.957 55.000 0.00 0.00 0.00 3.34
3003 5057 1.594293 CGACCGAACAGCACACCTT 60.594 57.895 0.00 0.00 0.00 3.50
3019 5073 1.135199 GGTAGATTTGAGCGGACACGA 60.135 52.381 0.00 0.00 44.60 4.35
3102 5156 1.608717 CCTAGTGGTCGAGCTGGCTT 61.609 60.000 16.64 0.00 0.00 4.35
3103 5157 2.055042 CCTAGTGGTCGAGCTGGCT 61.055 63.158 16.64 13.02 0.00 4.75
3109 5163 2.875933 GAGAGACATCCTAGTGGTCGAG 59.124 54.545 0.00 0.00 36.68 4.04
3219 5273 0.640768 GTCGAAAGGAAGCGTGATCG 59.359 55.000 0.00 0.00 40.37 3.69
3225 5279 0.164647 CTGCTTGTCGAAAGGAAGCG 59.835 55.000 12.43 0.00 44.68 4.68
3229 5283 0.034896 GGGACTGCTTGTCGAAAGGA 59.965 55.000 8.68 5.74 46.24 3.36
3234 5288 3.691342 CCGGGGACTGCTTGTCGA 61.691 66.667 0.00 0.00 46.24 4.20


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

AutoCloner maintained by Alex Coulton.