Multiple sequence alignment - TraesCS5D01G473000

Loading Multiple Alignment...

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 TraesCS5D01G473000 chr5D 100.000 5097 0 0 1 5097 513472428 513467332 0.000000e+00 9413.0
1 TraesCS5D01G473000 chr5D 75.410 305 46 17 4077 4360 513026718 513026422 2.490000e-23 121.0
2 TraesCS5D01G473000 chr5D 88.298 94 11 0 3988 4081 513027072 513026979 4.170000e-21 113.0
3 TraesCS5D01G473000 chr5B 91.870 4551 218 55 24 4512 643982850 643978390 0.000000e+00 6215.0
4 TraesCS5D01G473000 chr5B 76.484 455 73 18 4664 5095 643978281 643977838 3.090000e-52 217.0
5 TraesCS5D01G473000 chr5B 89.610 77 8 0 3988 4064 643974082 643974006 1.170000e-16 99.0
6 TraesCS5D01G473000 chr5A 90.137 4512 204 86 677 5095 641122665 641118302 0.000000e+00 5644.0
7 TraesCS5D01G473000 chr5A 75.896 307 52 12 4020 4322 641114603 641114315 2.470000e-28 137.0
8 TraesCS5D01G473000 chr7D 92.576 1778 85 19 1316 3070 491344289 491342536 0.000000e+00 2508.0
9 TraesCS5D01G473000 chr7D 93.353 1023 49 7 3066 4074 491342415 491341398 0.000000e+00 1495.0
10 TraesCS5D01G473000 chr7D 76.456 412 74 15 4536 4925 495830694 495831104 8.650000e-48 202.0
11 TraesCS5D01G473000 chr3B 91.220 1640 93 21 1094 2721 782743551 782741951 0.000000e+00 2183.0
12 TraesCS5D01G473000 chr3B 95.491 377 16 1 3313 3689 782741765 782741390 7.300000e-168 601.0
13 TraesCS5D01G473000 chr3B 93.194 191 5 3 3067 3249 782741953 782741763 1.810000e-69 274.0
14 TraesCS5D01G473000 chr3B 76.695 236 35 16 4550 4771 808972136 808972365 4.170000e-21 113.0
15 TraesCS5D01G473000 chr6A 90.340 1646 105 22 1088 2721 428676148 428677751 0.000000e+00 2109.0
16 TraesCS5D01G473000 chr6A 93.939 759 34 7 3320 4071 428677942 428678695 0.000000e+00 1136.0
17 TraesCS5D01G473000 chr6A 92.553 188 6 1 3067 3246 428677749 428677936 3.910000e-66 263.0
18 TraesCS5D01G473000 chr6B 92.713 494 29 4 3587 4074 25590717 25590225 0.000000e+00 706.0
19 TraesCS5D01G473000 chr6B 84.848 231 28 2 1774 2004 637485961 637485738 5.130000e-55 226.0
20 TraesCS5D01G473000 chr6B 77.037 270 50 5 2277 2544 205437829 205437570 1.480000e-30 145.0
21 TraesCS5D01G473000 chr2A 76.942 412 70 15 4540 4928 83018617 83019026 1.440000e-50 211.0
22 TraesCS5D01G473000 chr7B 76.515 396 68 16 4536 4907 524057982 524058376 5.210000e-45 193.0
23 TraesCS5D01G473000 chr2D 76.486 387 59 21 4569 4926 82336972 82337355 1.130000e-41 182.0
24 TraesCS5D01G473000 chr2D 86.765 68 6 1 1385 1449 231603535 231603468 7.080000e-09 73.1
25 TraesCS5D01G473000 chr7A 76.420 352 60 17 4542 4874 237383624 237383277 8.780000e-38 169.0
26 TraesCS5D01G473000 chr7A 79.565 230 40 7 4536 4761 561598348 561598574 1.900000e-34 158.0
27 TraesCS5D01G473000 chr2B 86.765 68 6 1 1385 1449 366839893 366839826 7.080000e-09 73.1


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 TraesCS5D01G473000 chr5D 513467332 513472428 5096 True 9413.000000 9413 100.000000 1 5097 1 chr5D.!!$R1 5096
1 TraesCS5D01G473000 chr5B 643974006 643982850 8844 True 2177.000000 6215 85.988000 24 5095 3 chr5B.!!$R1 5071
2 TraesCS5D01G473000 chr5A 641114315 641122665 8350 True 2890.500000 5644 83.016500 677 5095 2 chr5A.!!$R1 4418
3 TraesCS5D01G473000 chr7D 491341398 491344289 2891 True 2001.500000 2508 92.964500 1316 4074 2 chr7D.!!$R1 2758
4 TraesCS5D01G473000 chr3B 782741390 782743551 2161 True 1019.333333 2183 93.301667 1094 3689 3 chr3B.!!$R1 2595
5 TraesCS5D01G473000 chr6A 428676148 428678695 2547 False 1169.333333 2109 92.277333 1088 4071 3 chr6A.!!$F1 2983

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
541 544 0.245539 CCGTTCGCTTTGAGAGGGTA 59.754 55.0 0.00 0.0 39.25 3.69 F
628 644 0.324943 TTAGAGGCTCTGGCGCTTTT 59.675 50.0 26.95 0.0 39.16 2.27 F
629 645 0.391661 TAGAGGCTCTGGCGCTTTTG 60.392 55.0 26.95 0.0 39.16 2.44 F
634 650 0.455126 GCTCTGGCGCTTTTGCTAAC 60.455 55.0 7.64 0.0 44.80 2.34 F
2141 2207 0.684535 TCAGGTTCGCATCCTTGTCA 59.315 50.0 0.00 0.0 32.37 3.58 F
3775 3998 0.908198 AAGAGCTAGCCCAGAAGGTG 59.092 55.0 12.13 0.0 38.26 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2183 0.036952 AGGATGCGAACCTGACACAG 60.037 55.000 0.00 0.00 36.30 3.66 R
2258 2337 1.243342 TTGTCTTCCAATGGCGGCTG 61.243 55.000 11.43 0.00 0.00 4.85 R
2330 2409 1.394266 AAGTTTGGTGCAGCACTGGG 61.394 55.000 24.75 0.00 34.40 4.45 R
2404 2483 2.996168 AAGAAGCTGCGGCGTTCACT 62.996 55.000 23.06 13.08 44.37 3.41 R
4039 4263 1.448540 CGCTTCGACCTGGATGCTT 60.449 57.895 0.00 0.00 35.57 3.91 R
4610 4853 3.868661 CCAATCCACATTCGTATTCGACA 59.131 43.478 0.00 0.00 46.03 4.35 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
118 120 9.692749 GTCTTTGATCCGAGACATATTATACAA 57.307 33.333 16.48 0.00 41.45 2.41
127 129 7.274468 CCGAGACATATTATACAAGTGAGATGC 59.726 40.741 0.00 0.00 0.00 3.91
128 130 7.274468 CGAGACATATTATACAAGTGAGATGCC 59.726 40.741 0.00 0.00 0.00 4.40
138 140 5.482908 ACAAGTGAGATGCCTGTTAACTAG 58.517 41.667 7.22 2.92 0.00 2.57
160 162 9.183368 ACTAGGATCAATGAGAAAATTTTCCTC 57.817 33.333 24.01 19.85 37.92 3.71
162 164 6.382282 AGGATCAATGAGAAAATTTTCCTCCC 59.618 38.462 24.01 15.41 37.92 4.30
164 166 5.321102 TCAATGAGAAAATTTTCCTCCCGA 58.679 37.500 24.01 14.26 37.92 5.14
173 175 5.835113 AATTTTCCTCCCGATTACATGTG 57.165 39.130 9.11 0.00 0.00 3.21
174 176 3.992943 TTTCCTCCCGATTACATGTGT 57.007 42.857 9.11 0.00 0.00 3.72
210 212 9.999883 CACGTTTATTAGTTCACTTAGTTGTAC 57.000 33.333 0.00 0.00 0.00 2.90
221 223 8.665685 GTTCACTTAGTTGTACAATCTTATGGG 58.334 37.037 12.26 8.56 0.00 4.00
224 226 7.280205 CACTTAGTTGTACAATCTTATGGGTCC 59.720 40.741 12.26 0.00 0.00 4.46
299 301 0.662619 ACACGATGCGCATATTTGGG 59.337 50.000 25.40 16.74 38.75 4.12
301 303 1.870402 CACGATGCGCATATTTGGGTA 59.130 47.619 25.40 0.00 38.05 3.69
303 305 2.289547 ACGATGCGCATATTTGGGTAAC 59.710 45.455 25.40 5.55 38.05 2.50
331 333 1.708341 ATTTGGCTTGCCAACACTCT 58.292 45.000 24.65 6.66 0.00 3.24
341 343 4.128925 TGCCAACACTCTAAGATAGCAG 57.871 45.455 0.00 0.00 0.00 4.24
348 350 6.307031 ACACTCTAAGATAGCAGTATCACG 57.693 41.667 0.00 0.00 38.04 4.35
351 353 5.475220 ACTCTAAGATAGCAGTATCACGCAT 59.525 40.000 0.00 0.00 38.04 4.73
357 359 5.802451 AGATAGCAGTATCACGCATAAATCG 59.198 40.000 0.00 0.00 38.04 3.34
362 364 7.088272 AGCAGTATCACGCATAAATCGTATAA 58.912 34.615 0.00 0.00 38.19 0.98
385 388 6.864560 AAAAAGTCTGACGTAAAGCAAAAC 57.135 33.333 1.52 0.00 0.00 2.43
405 408 9.146984 GCAAAACTATTAATTTTGGACCCTAAC 57.853 33.333 11.15 0.00 43.96 2.34
408 411 8.589701 AACTATTAATTTTGGACCCTAACAGG 57.410 34.615 0.00 0.00 34.30 4.00
409 412 7.935405 ACTATTAATTTTGGACCCTAACAGGA 58.065 34.615 0.00 0.00 37.67 3.86
436 439 3.617284 ACTTTCTCTCCGTGGTGTTTTT 58.383 40.909 0.00 0.00 0.00 1.94
444 447 1.336755 CCGTGGTGTTTTTGGAGGAAG 59.663 52.381 0.00 0.00 0.00 3.46
464 467 1.303309 CAATGCTTTAGGAGGCTCCG 58.697 55.000 27.11 14.40 42.75 4.63
477 480 2.864931 GCTCCGCGAGCGAAAGATG 61.865 63.158 19.72 0.80 45.85 2.90
483 486 1.528748 GCGAGCGAAAGATGCTTTTC 58.471 50.000 0.00 0.00 44.18 2.29
490 493 2.916111 GAAAGATGCTTTTCGCGTTGA 58.084 42.857 5.77 0.00 43.27 3.18
491 494 2.601481 AAGATGCTTTTCGCGTTGAG 57.399 45.000 5.77 3.40 43.27 3.02
494 497 0.517316 ATGCTTTTCGCGTTGAGGAC 59.483 50.000 5.77 0.00 43.27 3.85
503 506 2.660064 CGTTGAGGACCTCCCCCAG 61.660 68.421 19.11 2.44 36.42 4.45
515 518 1.697432 CTCCCCCAGGCGAATAATGTA 59.303 52.381 0.00 0.00 0.00 2.29
521 524 2.930040 CCAGGCGAATAATGTATAGCGG 59.070 50.000 0.00 0.00 0.00 5.52
523 526 1.664151 GGCGAATAATGTATAGCGGCC 59.336 52.381 0.00 0.00 36.42 6.13
536 539 2.736995 CGGCCGTTCGCTTTGAGA 60.737 61.111 19.50 0.00 37.74 3.27
537 540 2.730672 CGGCCGTTCGCTTTGAGAG 61.731 63.158 19.50 0.00 37.74 3.20
538 541 2.391389 GGCCGTTCGCTTTGAGAGG 61.391 63.158 0.00 0.00 37.74 3.69
539 542 2.391389 GCCGTTCGCTTTGAGAGGG 61.391 63.158 0.00 0.00 39.55 4.30
540 543 1.004918 CCGTTCGCTTTGAGAGGGT 60.005 57.895 0.00 0.00 39.25 4.34
541 544 0.245539 CCGTTCGCTTTGAGAGGGTA 59.754 55.000 0.00 0.00 39.25 3.69
542 545 1.134788 CCGTTCGCTTTGAGAGGGTAT 60.135 52.381 0.00 0.00 39.25 2.73
543 546 1.927174 CGTTCGCTTTGAGAGGGTATG 59.073 52.381 0.00 0.00 39.25 2.39
544 547 2.674177 CGTTCGCTTTGAGAGGGTATGT 60.674 50.000 0.00 0.00 39.25 2.29
545 548 2.672961 TCGCTTTGAGAGGGTATGTG 57.327 50.000 0.00 0.00 39.25 3.21
552 555 1.906574 TGAGAGGGTATGTGGTGAACC 59.093 52.381 0.00 0.00 0.00 3.62
561 564 4.395519 TGGTGAACCATTCCGCTG 57.604 55.556 0.00 0.00 42.01 5.18
568 571 2.003301 GAACCATTCCGCTGTTCTCTC 58.997 52.381 0.00 0.00 36.36 3.20
576 579 0.739112 CGCTGTTCTCTCAGAAGGGC 60.739 60.000 0.00 0.00 34.42 5.19
594 610 2.395690 GATGGAAGCGAACGCACG 59.604 61.111 20.66 0.00 44.88 5.34
606 622 1.463444 GAACGCACGCAAAATAGGACT 59.537 47.619 0.00 0.00 0.00 3.85
608 624 2.901249 ACGCACGCAAAATAGGACTAT 58.099 42.857 0.00 0.00 0.00 2.12
616 632 5.758784 ACGCAAAATAGGACTATTTAGAGGC 59.241 40.000 15.47 14.70 42.91 4.70
618 634 6.146347 CGCAAAATAGGACTATTTAGAGGCTC 59.854 42.308 15.47 6.34 42.91 4.70
624 640 1.069358 ACTATTTAGAGGCTCTGGCGC 59.931 52.381 26.95 0.00 39.81 6.53
628 644 0.324943 TTAGAGGCTCTGGCGCTTTT 59.675 50.000 26.95 0.00 39.16 2.27
629 645 0.391661 TAGAGGCTCTGGCGCTTTTG 60.392 55.000 26.95 0.00 39.16 2.44
630 646 3.333898 GAGGCTCTGGCGCTTTTGC 62.334 63.158 7.64 7.41 43.23 3.68
631 647 3.368571 GGCTCTGGCGCTTTTGCT 61.369 61.111 7.64 0.00 44.80 3.91
633 649 1.586154 GGCTCTGGCGCTTTTGCTAA 61.586 55.000 7.64 0.00 44.80 3.09
634 650 0.455126 GCTCTGGCGCTTTTGCTAAC 60.455 55.000 7.64 0.00 44.80 2.34
649 665 4.153958 TGCTAACAAAACGTTGCATAGG 57.846 40.909 0.00 0.00 38.63 2.57
650 666 2.914838 GCTAACAAAACGTTGCATAGGC 59.085 45.455 0.00 0.00 38.63 3.93
651 667 7.450225 TTGCTAACAAAACGTTGCATAGGCA 62.450 40.000 0.00 0.00 39.61 4.75
669 705 4.201679 CGTGGCGTCGGGATAGCA 62.202 66.667 0.00 0.00 0.00 3.49
694 730 6.761242 ACAAATTTTGGTAGCCAAGTTCTTTC 59.239 34.615 13.42 0.00 44.84 2.62
735 771 4.439776 CGAAAATTTGAACCGGACTTGAAC 59.560 41.667 9.46 0.00 0.00 3.18
744 780 1.303643 GGACTTGAACCTGGGCCAG 60.304 63.158 27.04 27.04 0.00 4.85
983 1022 4.271816 CCGCAGATCGACCCCTCG 62.272 72.222 0.00 0.00 41.67 4.63
1210 1249 2.519780 ACGCGATCCTCCTCTCCC 60.520 66.667 15.93 0.00 0.00 4.30
1211 1250 3.299190 CGCGATCCTCCTCTCCCC 61.299 72.222 0.00 0.00 0.00 4.81
1212 1251 2.920384 GCGATCCTCCTCTCCCCC 60.920 72.222 0.00 0.00 0.00 5.40
1213 1252 2.598985 CGATCCTCCTCTCCCCCG 60.599 72.222 0.00 0.00 0.00 5.73
1214 1253 2.936007 GATCCTCCTCTCCCCCGA 59.064 66.667 0.00 0.00 0.00 5.14
1215 1254 1.228737 GATCCTCCTCTCCCCCGAG 60.229 68.421 0.00 0.00 37.48 4.63
1216 1255 3.460478 ATCCTCCTCTCCCCCGAGC 62.460 68.421 0.00 0.00 35.94 5.03
1280 1330 2.581726 CTTGTTGGTGGGGTGGTGGT 62.582 60.000 0.00 0.00 0.00 4.16
1293 1343 1.326213 TGGTGGTGTTGCCTTGTTGG 61.326 55.000 0.00 0.00 38.35 3.77
1301 1351 4.645921 GCCTTGTTGGTGGCGTGC 62.646 66.667 0.00 0.00 39.71 5.34
1305 1355 2.406452 CTTGTTGGTGGCGTGCCTTC 62.406 60.000 12.84 5.36 36.94 3.46
1321 1371 3.244215 TGCCTTCGAGTTCTGATCAGTTT 60.244 43.478 21.92 9.08 0.00 2.66
1566 1619 2.020720 TGTTGTGAAATTGTCTGCCGT 58.979 42.857 0.00 0.00 0.00 5.68
1709 1770 1.891919 TGCGTGGTTTCTGTGCTCC 60.892 57.895 0.00 0.00 0.00 4.70
1824 1889 3.223435 GTCATCGGAGAAGGGAGATACA 58.777 50.000 0.00 0.00 43.58 2.29
1827 1892 1.569548 TCGGAGAAGGGAGATACAGGT 59.430 52.381 0.00 0.00 0.00 4.00
1866 1931 4.159377 TCGTTTGGCATTGTCTGAATTC 57.841 40.909 0.00 0.00 0.00 2.17
2075 2141 1.178276 AGACGATGACAGGACCAGTC 58.822 55.000 10.01 10.01 36.55 3.51
2086 2152 1.887198 AGGACCAGTCACACTTCGTAG 59.113 52.381 0.00 0.00 0.00 3.51
2092 2158 3.255149 CCAGTCACACTTCGTAGTAAGGT 59.745 47.826 0.00 0.00 31.96 3.50
2096 2162 6.093771 CAGTCACACTTCGTAGTAAGGTAGAT 59.906 42.308 0.00 0.00 31.96 1.98
2103 2169 2.035576 CGTAGTAAGGTAGATGTGGGCC 59.964 54.545 0.00 0.00 0.00 5.80
2106 2172 2.116238 GTAAGGTAGATGTGGGCCTGA 58.884 52.381 4.53 0.00 0.00 3.86
2117 2183 1.000274 GTGGGCCTGAATTTGTGTCAC 60.000 52.381 4.53 0.00 0.00 3.67
2124 2190 3.627123 CCTGAATTTGTGTCACTGTGTCA 59.373 43.478 7.79 5.61 0.00 3.58
2140 2206 1.079503 GTCAGGTTCGCATCCTTGTC 58.920 55.000 0.00 0.00 32.37 3.18
2141 2207 0.684535 TCAGGTTCGCATCCTTGTCA 59.315 50.000 0.00 0.00 32.37 3.58
2177 2256 6.625520 GCACCCTAAGAGAGTAGTTTGTCTAC 60.626 46.154 0.00 0.00 46.68 2.59
2632 2712 2.474032 GCATTTACTTGCGACTCGGTTC 60.474 50.000 0.00 0.00 32.06 3.62
2741 2821 3.573772 TTGAGGCCGTGACGAGCAG 62.574 63.158 6.54 0.00 0.00 4.24
2863 2943 1.524621 CTCATGACCACCCGGATGC 60.525 63.158 0.73 0.00 35.59 3.91
2865 2945 3.014538 ATGACCACCCGGATGCCA 61.015 61.111 0.73 0.00 35.59 4.92
3000 3080 5.057819 TCAAGATTACGCAAACAGGTACAA 58.942 37.500 0.00 0.00 0.00 2.41
3126 3344 6.478344 GTGGCACTAGAAGTAGAGAAATGATG 59.522 42.308 11.13 0.00 0.00 3.07
3492 3711 9.528018 TTGATTTGTTTTAACTGGACTTGATTC 57.472 29.630 0.00 0.00 0.00 2.52
3597 3816 3.827008 TTCTGAACTCAGCTGAACAGT 57.173 42.857 28.14 18.39 43.46 3.55
3637 3856 5.621193 AGGCAAGTAAGACAACACTGTATT 58.379 37.500 0.00 0.00 40.11 1.89
3724 3947 9.967451 TTGAAACAGTATTACTAATTGATCCCA 57.033 29.630 0.00 0.00 0.00 4.37
3742 3965 7.577303 TGATCCCAATTTCTTCTTATGCTACT 58.423 34.615 0.00 0.00 0.00 2.57
3775 3998 0.908198 AAGAGCTAGCCCAGAAGGTG 59.092 55.000 12.13 0.00 38.26 4.00
3901 4124 3.095163 CCCCTCTCTGGCCATGCT 61.095 66.667 5.51 0.00 0.00 3.79
3920 4143 6.018262 CCATGCTCTTGATGGCAAATTTATTG 60.018 38.462 0.00 0.00 41.90 1.90
4024 4248 1.687493 GCAGTCAGAGGGCCCTAGT 60.687 63.158 28.78 13.25 0.00 2.57
4039 4263 3.705051 CCCTAGTGTTGTGACTACCCTA 58.295 50.000 0.00 0.00 0.00 3.53
4147 4371 2.420129 GGATCGAGTGCCAACCAGTAAT 60.420 50.000 0.00 0.00 0.00 1.89
4443 4668 2.949644 AGCTTTGCTTCGTTAGTGGTTT 59.050 40.909 0.00 0.00 33.89 3.27
4444 4669 4.131596 AGCTTTGCTTCGTTAGTGGTTTA 58.868 39.130 0.00 0.00 33.89 2.01
4445 4670 4.213482 AGCTTTGCTTCGTTAGTGGTTTAG 59.787 41.667 0.00 0.00 33.89 1.85
4534 4777 1.692749 GGACATGGAGGTAGGGGCA 60.693 63.158 0.00 0.00 0.00 5.36
4547 4790 2.513897 GGGCAGAAACGGATCGGG 60.514 66.667 5.18 0.00 0.00 5.14
4554 4797 3.254024 AAACGGATCGGGCAGTGCT 62.254 57.895 16.11 0.00 0.00 4.40
4558 4801 1.823295 GGATCGGGCAGTGCTCTTA 59.177 57.895 14.31 0.78 0.00 2.10
4571 4814 5.446073 GCAGTGCTCTTACCGTTTCTATTTC 60.446 44.000 8.18 0.00 0.00 2.17
4620 4863 6.252655 TGCGAATATGGATATTGTCGAATACG 59.747 38.462 5.35 0.00 35.67 3.06
4640 4883 4.007659 ACGAATGTGGATTGGGTTTACTC 58.992 43.478 0.00 0.00 0.00 2.59
4873 5181 5.473162 TGTTCGATAATTGGCATATTGAGGG 59.527 40.000 0.00 0.00 0.00 4.30
4914 5222 6.438425 AGCTCATGGAATTTTATTTGGACACT 59.562 34.615 0.00 0.00 0.00 3.55
4945 5265 7.897575 TCCATATTTGTGTTTAAAATGCCAC 57.102 32.000 0.00 0.00 0.00 5.01
4946 5266 7.445121 TCCATATTTGTGTTTAAAATGCCACA 58.555 30.769 5.52 5.52 36.12 4.17
4947 5267 8.099537 TCCATATTTGTGTTTAAAATGCCACAT 58.900 29.630 9.41 0.93 37.63 3.21
4948 5268 8.728833 CCATATTTGTGTTTAAAATGCCACATT 58.271 29.630 9.41 4.82 37.63 2.71
4949 5269 9.544314 CATATTTGTGTTTAAAATGCCACATTG 57.456 29.630 9.41 3.96 37.63 2.82
4950 5270 6.992063 TTTGTGTTTAAAATGCCACATTGT 57.008 29.167 9.41 0.00 37.63 2.71
4951 5271 8.668510 ATTTGTGTTTAAAATGCCACATTGTA 57.331 26.923 9.41 0.00 37.63 2.41
4955 5275 7.172190 TGTGTTTAAAATGCCACATTGTATTGG 59.828 33.333 5.52 0.00 33.19 3.16
4956 5276 7.386299 GTGTTTAAAATGCCACATTGTATTGGA 59.614 33.333 0.00 0.00 34.46 3.53
4957 5277 8.099537 TGTTTAAAATGCCACATTGTATTGGAT 58.900 29.630 0.00 0.00 34.46 3.41
4958 5278 8.945057 GTTTAAAATGCCACATTGTATTGGATT 58.055 29.630 0.00 0.00 34.46 3.01
4959 5279 9.512588 TTTAAAATGCCACATTGTATTGGATTT 57.487 25.926 6.74 6.74 34.46 2.17
4960 5280 6.988622 AAATGCCACATTGTATTGGATTTG 57.011 33.333 9.98 0.00 34.46 2.32
4961 5281 5.680594 ATGCCACATTGTATTGGATTTGT 57.319 34.783 0.00 0.00 34.46 2.83
4962 5282 6.788598 ATGCCACATTGTATTGGATTTGTA 57.211 33.333 0.00 0.00 34.46 2.41
4963 5283 6.788598 TGCCACATTGTATTGGATTTGTAT 57.211 33.333 0.00 0.00 34.46 2.29
4964 5284 7.180322 TGCCACATTGTATTGGATTTGTATT 57.820 32.000 0.00 0.00 34.46 1.89
4965 5285 7.619050 TGCCACATTGTATTGGATTTGTATTT 58.381 30.769 0.00 0.00 34.46 1.40
4966 5286 8.753133 TGCCACATTGTATTGGATTTGTATTTA 58.247 29.630 0.00 0.00 34.46 1.40
5008 5328 3.401033 TTGTCTTGGTCATGTCGATGT 57.599 42.857 0.00 0.00 0.00 3.06
5030 5353 4.341235 GTGTGGCTACTCCTATACACATGA 59.659 45.833 0.00 0.00 40.42 3.07
5059 5382 8.515414 CCCAATATAATTACTTTGAGCTTAGCC 58.485 37.037 0.00 0.00 0.00 3.93
5075 5398 8.840321 TGAGCTTAGCCATATAAAGAAAATCAC 58.160 33.333 0.00 0.00 0.00 3.06
5077 5400 7.779798 AGCTTAGCCATATAAAGAAAATCACCA 59.220 33.333 0.00 0.00 0.00 4.17
5095 5418 6.585695 TCACCAGAACGAATCTAAACTACT 57.414 37.500 0.00 0.00 36.32 2.57
5096 5419 6.618811 TCACCAGAACGAATCTAAACTACTC 58.381 40.000 0.00 0.00 36.32 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.230309 TGAAAATAACACCAGATTCACACATGA 59.770 33.333 0.00 0.00 0.00 3.07
19 20 7.369607 TGAAAATAACACCAGATTCACACATG 58.630 34.615 0.00 0.00 0.00 3.21
20 21 7.523293 TGAAAATAACACCAGATTCACACAT 57.477 32.000 0.00 0.00 0.00 3.21
21 22 6.951062 TGAAAATAACACCAGATTCACACA 57.049 33.333 0.00 0.00 0.00 3.72
22 23 8.816640 AAATGAAAATAACACCAGATTCACAC 57.183 30.769 0.00 0.00 30.46 3.82
93 95 9.914131 CTTGTATAATATGTCTCGGATCAAAGA 57.086 33.333 0.00 0.00 0.00 2.52
118 120 4.353777 TCCTAGTTAACAGGCATCTCACT 58.646 43.478 8.61 0.00 32.82 3.41
127 129 8.792830 TTTTCTCATTGATCCTAGTTAACAGG 57.207 34.615 8.61 12.22 34.20 4.00
138 140 6.577103 GGGAGGAAAATTTTCTCATTGATCC 58.423 40.000 25.86 19.64 37.35 3.36
156 158 3.605634 CAAACACATGTAATCGGGAGGA 58.394 45.455 0.00 0.00 0.00 3.71
160 162 3.781079 ATGCAAACACATGTAATCGGG 57.219 42.857 0.00 0.00 0.00 5.14
162 164 5.794650 GCATATGCAAACACATGTAATCG 57.205 39.130 22.84 0.00 41.59 3.34
210 212 2.210116 CCGAACGGACCCATAAGATTG 58.790 52.381 7.53 0.00 37.50 2.67
221 223 1.161563 TGGCTCAAAACCGAACGGAC 61.162 55.000 20.14 0.62 38.96 4.79
224 226 2.196295 TTTTGGCTCAAAACCGAACG 57.804 45.000 8.46 0.00 38.24 3.95
274 276 2.272918 TATGCGCATCGTGTGGTCGA 62.273 55.000 29.11 1.32 43.86 4.20
279 281 1.597690 CCCAAATATGCGCATCGTGTG 60.598 52.381 29.11 20.73 0.00 3.82
289 291 5.897377 AGTTGTCTGTTACCCAAATATGC 57.103 39.130 0.00 0.00 0.00 3.14
299 301 5.154222 GCAAGCCAAATAGTTGTCTGTTAC 58.846 41.667 1.80 0.00 32.40 2.50
301 303 3.005791 GGCAAGCCAAATAGTTGTCTGTT 59.994 43.478 6.14 0.00 35.81 3.16
303 305 2.557924 TGGCAAGCCAAATAGTTGTCTG 59.442 45.455 12.11 0.00 44.12 3.51
331 333 7.484959 CGATTTATGCGTGATACTGCTATCTTA 59.515 37.037 0.00 0.00 31.36 2.10
362 364 6.617879 AGTTTTGCTTTACGTCAGACTTTTT 58.382 32.000 0.00 0.00 0.00 1.94
375 378 9.713713 GGGTCCAAAATTAATAGTTTTGCTTTA 57.286 29.630 13.38 0.00 42.38 1.85
379 382 9.146984 GTTAGGGTCCAAAATTAATAGTTTTGC 57.853 33.333 13.38 3.74 42.38 3.68
384 387 7.935405 TCCTGTTAGGGTCCAAAATTAATAGT 58.065 34.615 0.00 0.00 35.59 2.12
385 388 8.817092 TTCCTGTTAGGGTCCAAAATTAATAG 57.183 34.615 0.00 0.00 35.59 1.73
396 399 4.368565 AGTTCTTTTCCTGTTAGGGTCC 57.631 45.455 0.00 0.00 35.59 4.46
405 408 4.212214 CACGGAGAGAAAGTTCTTTTCCTG 59.788 45.833 16.88 13.91 45.15 3.86
408 411 4.024809 CACCACGGAGAGAAAGTTCTTTTC 60.025 45.833 0.00 0.00 44.52 2.29
409 412 3.877508 CACCACGGAGAGAAAGTTCTTTT 59.122 43.478 0.00 0.00 37.73 2.27
444 447 1.028130 GGAGCCTCCTAAAGCATTGC 58.972 55.000 2.64 0.00 32.53 3.56
464 467 1.528748 GAAAAGCATCTTTCGCTCGC 58.471 50.000 0.00 0.00 39.29 5.03
477 480 1.206831 GGTCCTCAACGCGAAAAGC 59.793 57.895 15.93 0.00 43.95 3.51
483 486 4.452733 GGGGAGGTCCTCAACGCG 62.453 72.222 20.72 3.53 36.20 6.01
484 487 4.097361 GGGGGAGGTCCTCAACGC 62.097 72.222 20.72 15.88 38.61 4.84
494 497 0.250901 CATTATTCGCCTGGGGGAGG 60.251 60.000 11.17 0.00 46.13 4.30
503 506 1.664151 GGCCGCTATACATTATTCGCC 59.336 52.381 0.00 0.00 0.00 5.54
521 524 2.391389 CCCTCTCAAAGCGAACGGC 61.391 63.158 0.00 0.00 44.05 5.68
523 526 1.927174 CATACCCTCTCAAAGCGAACG 59.073 52.381 0.00 0.00 0.00 3.95
545 548 0.521735 GAACAGCGGAATGGTTCACC 59.478 55.000 0.00 0.00 40.39 4.02
552 555 2.662006 TCTGAGAGAACAGCGGAATG 57.338 50.000 0.00 0.00 37.75 2.67
558 561 0.739112 CGCCCTTCTGAGAGAACAGC 60.739 60.000 0.00 0.00 37.75 4.40
559 562 0.891373 TCGCCCTTCTGAGAGAACAG 59.109 55.000 0.00 0.00 39.02 3.16
560 563 1.205655 CATCGCCCTTCTGAGAGAACA 59.794 52.381 0.00 0.00 29.89 3.18
561 564 1.472376 CCATCGCCCTTCTGAGAGAAC 60.472 57.143 0.00 0.00 29.89 3.01
568 571 2.176273 CGCTTCCATCGCCCTTCTG 61.176 63.158 0.00 0.00 0.00 3.02
576 579 2.395690 GTGCGTTCGCTTCCATCG 59.604 61.111 17.63 0.00 0.00 3.84
591 607 6.292919 GCCTCTAAATAGTCCTATTTTGCGTG 60.293 42.308 15.38 8.08 41.49 5.34
594 610 7.172361 CAGAGCCTCTAAATAGTCCTATTTTGC 59.828 40.741 15.38 12.99 41.49 3.68
596 612 7.690549 GCCAGAGCCTCTAAATAGTCCTATTTT 60.691 40.741 15.38 0.00 41.49 1.82
602 618 2.288518 CGCCAGAGCCTCTAAATAGTCC 60.289 54.545 0.00 0.00 34.57 3.85
606 622 1.414158 AGCGCCAGAGCCTCTAAATA 58.586 50.000 2.29 0.00 38.01 1.40
608 624 0.324943 AAAGCGCCAGAGCCTCTAAA 59.675 50.000 2.29 0.00 38.01 1.85
616 632 0.874390 TGTTAGCAAAAGCGCCAGAG 59.126 50.000 2.29 0.00 0.00 3.35
618 634 2.132740 TTTGTTAGCAAAAGCGCCAG 57.867 45.000 2.29 0.00 41.15 4.85
624 640 9.593442 GCCTATGCAACGTTTTGTTAGCAAAAG 62.593 40.741 16.61 12.98 44.37 2.27
628 644 3.610585 GCCTATGCAACGTTTTGTTAGCA 60.611 43.478 10.61 10.61 43.57 3.49
629 645 2.914838 GCCTATGCAACGTTTTGTTAGC 59.085 45.455 0.00 0.00 39.29 3.09
630 646 4.153958 TGCCTATGCAACGTTTTGTTAG 57.846 40.909 0.00 0.00 46.66 2.34
643 659 3.564027 GACGCCACGTGCCTATGC 61.564 66.667 10.91 6.86 41.37 3.14
645 661 4.508128 CCGACGCCACGTGCCTAT 62.508 66.667 10.91 0.00 41.37 2.57
649 665 4.501714 TATCCCGACGCCACGTGC 62.502 66.667 10.91 4.89 41.37 5.34
650 666 2.278596 CTATCCCGACGCCACGTG 60.279 66.667 9.08 9.08 41.37 4.49
651 667 4.203076 GCTATCCCGACGCCACGT 62.203 66.667 0.00 0.00 45.10 4.49
652 668 4.201679 TGCTATCCCGACGCCACG 62.202 66.667 0.00 0.00 0.00 4.94
653 669 2.585247 GTGCTATCCCGACGCCAC 60.585 66.667 0.00 0.00 0.00 5.01
655 671 0.814010 ATTTGTGCTATCCCGACGCC 60.814 55.000 0.00 0.00 0.00 5.68
669 705 5.869649 AGAACTTGGCTACCAAAATTTGT 57.130 34.783 4.92 0.00 43.44 2.83
1244 1294 4.531426 GGCAACACCACCACCCCA 62.531 66.667 0.00 0.00 38.86 4.96
1254 1304 1.441311 CCCACCAACAAGGCAACAC 59.559 57.895 0.00 0.00 43.14 3.32
1293 1343 2.665185 AACTCGAAGGCACGCCAC 60.665 61.111 11.35 3.09 38.92 5.01
1299 1349 1.895798 ACTGATCAGAACTCGAAGGCA 59.104 47.619 29.27 0.00 0.00 4.75
1301 1351 5.931441 AAAAACTGATCAGAACTCGAAGG 57.069 39.130 29.27 0.00 0.00 3.46
1709 1770 3.425713 AAGAGCACGCACGCATGG 61.426 61.111 0.00 0.00 0.00 3.66
1824 1889 0.610232 GCACCTTCTGATTGGCACCT 60.610 55.000 0.00 0.00 0.00 4.00
1827 1892 0.322816 GAGGCACCTTCTGATTGGCA 60.323 55.000 9.59 0.00 38.25 4.92
1884 1950 7.537596 TGGATCAACCAAAACTAACAATCAT 57.462 32.000 0.00 0.00 46.75 2.45
2075 2141 6.028368 CACATCTACCTTACTACGAAGTGTG 58.972 44.000 0.00 0.00 45.73 3.82
2086 2152 2.116238 TCAGGCCCACATCTACCTTAC 58.884 52.381 0.00 0.00 0.00 2.34
2092 2158 3.245229 ACACAAATTCAGGCCCACATCTA 60.245 43.478 0.00 0.00 0.00 1.98
2096 2162 1.327303 GACACAAATTCAGGCCCACA 58.673 50.000 0.00 0.00 0.00 4.17
2103 2169 4.260907 CCTGACACAGTGACACAAATTCAG 60.261 45.833 7.81 12.89 0.00 3.02
2106 2172 3.620488 ACCTGACACAGTGACACAAATT 58.380 40.909 7.81 0.00 0.00 1.82
2117 2183 0.036952 AGGATGCGAACCTGACACAG 60.037 55.000 0.00 0.00 36.30 3.66
2124 2190 3.540211 CTGACAAGGATGCGAACCT 57.460 52.632 0.00 0.00 39.69 3.50
2149 2215 4.538746 AACTACTCTCTTAGGGTGCAAC 57.461 45.455 0.00 0.00 0.00 4.17
2177 2256 9.254133 CTGTCATTCTCACATATACTACCAAAG 57.746 37.037 0.00 0.00 0.00 2.77
2178 2257 8.758829 ACTGTCATTCTCACATATACTACCAAA 58.241 33.333 0.00 0.00 0.00 3.28
2186 2265 5.988287 TGCCAACTGTCATTCTCACATATA 58.012 37.500 0.00 0.00 0.00 0.86
2187 2266 4.847198 TGCCAACTGTCATTCTCACATAT 58.153 39.130 0.00 0.00 0.00 1.78
2253 2332 3.762247 CCAATGGCGGCTGGGTTG 61.762 66.667 11.43 9.87 0.00 3.77
2258 2337 1.243342 TTGTCTTCCAATGGCGGCTG 61.243 55.000 11.43 0.00 0.00 4.85
2330 2409 1.394266 AAGTTTGGTGCAGCACTGGG 61.394 55.000 24.75 0.00 34.40 4.45
2404 2483 2.996168 AAGAAGCTGCGGCGTTCACT 62.996 55.000 23.06 13.08 44.37 3.41
2768 2848 3.492102 TTCTGACTTAGGTGCTGCTTT 57.508 42.857 0.00 0.00 0.00 3.51
2863 2943 2.053627 GCAAAAATTCACTCGCACTGG 58.946 47.619 0.00 0.00 0.00 4.00
2865 2945 3.435105 TTGCAAAAATTCACTCGCACT 57.565 38.095 0.00 0.00 0.00 4.40
2974 3054 3.370978 ACCTGTTTGCGTAATCTTGATCG 59.629 43.478 0.00 0.00 0.00 3.69
3000 3080 7.827701 TGAGATTGTTCGTCTTTAGTACTGAT 58.172 34.615 5.39 0.00 0.00 2.90
3346 3565 4.678509 TTGCATACTTTCCTACAAAGCG 57.321 40.909 0.00 0.00 0.00 4.68
3357 3576 9.260002 CCAAAACTTTTAGTGATTGCATACTTT 57.740 29.630 4.42 0.00 29.54 2.66
3492 3711 5.178797 CACTTGACTAAACATCCCTACTGG 58.821 45.833 0.00 0.00 0.00 4.00
3597 3816 6.245408 ACTTGCCTAAACTGGATATGTTTCA 58.755 36.000 0.00 0.00 38.41 2.69
3637 3856 4.343231 TCATTTGCTGGCCTAGAAAATCA 58.657 39.130 14.76 3.90 41.79 2.57
3807 4030 4.220821 TCTTAAGCTGGTCGAGTTCTGATT 59.779 41.667 0.00 0.00 0.00 2.57
3856 4079 5.039333 GCATTCACCATCAGCTGTTTATTC 58.961 41.667 14.67 0.00 0.00 1.75
3901 4124 9.585099 GTTATGACAATAAATTTGCCATCAAGA 57.415 29.630 0.00 0.00 30.19 3.02
3920 4143 7.009999 CAGTCAGCAGTAAGATTGAGTTATGAC 59.990 40.741 0.00 0.00 33.98 3.06
4024 4248 3.055385 GGATGCTTAGGGTAGTCACAACA 60.055 47.826 0.00 0.00 0.00 3.33
4039 4263 1.448540 CGCTTCGACCTGGATGCTT 60.449 57.895 0.00 0.00 35.57 3.91
4147 4371 6.043243 ACTCCACCAATCTTCTTGACTTCTAA 59.957 38.462 0.00 0.00 0.00 2.10
4443 4668 9.529325 CTATTGCACTTTTAGCATGTACTACTA 57.471 33.333 0.00 0.00 42.33 1.82
4444 4669 8.258007 TCTATTGCACTTTTAGCATGTACTACT 58.742 33.333 0.00 0.00 42.33 2.57
4445 4670 8.420374 TCTATTGCACTTTTAGCATGTACTAC 57.580 34.615 0.00 0.00 42.33 2.73
4534 4777 1.079127 CACTGCCCGATCCGTTTCT 60.079 57.895 0.00 0.00 0.00 2.52
4547 4790 1.797025 AGAAACGGTAAGAGCACTGC 58.203 50.000 0.00 0.00 0.00 4.40
4610 4853 3.868661 CCAATCCACATTCGTATTCGACA 59.131 43.478 0.00 0.00 46.03 4.35
4620 4863 4.258543 TCGAGTAAACCCAATCCACATTC 58.741 43.478 0.00 0.00 0.00 2.67
4640 4883 8.587111 CAAACATCTGATATGTATCCGTATTCG 58.413 37.037 0.00 0.00 31.71 3.34
4820 5128 7.651027 AGCCTAATGAGCTGTCAAATTAAAT 57.349 32.000 0.00 0.00 39.69 1.40
4823 5131 7.466746 AAAAGCCTAATGAGCTGTCAAATTA 57.533 32.000 0.00 0.00 40.49 1.40
4833 5141 5.734855 TCGAACATAAAAGCCTAATGAGC 57.265 39.130 0.00 0.00 0.00 4.26
4922 5230 7.664082 TGTGGCATTTTAAACACAAATATGG 57.336 32.000 6.84 0.00 40.50 2.74
4935 5255 8.099537 ACAAATCCAATACAATGTGGCATTTTA 58.900 29.630 0.00 0.00 34.68 1.52
4939 5259 5.680594 ACAAATCCAATACAATGTGGCAT 57.319 34.783 0.00 0.00 34.68 4.40
4940 5260 6.788598 ATACAAATCCAATACAATGTGGCA 57.211 33.333 0.00 0.00 34.68 4.92
4972 5292 8.934023 ACCAAGACAAAAGATATCCAAAACTA 57.066 30.769 0.00 0.00 0.00 2.24
4974 5294 7.657336 TGACCAAGACAAAAGATATCCAAAAC 58.343 34.615 0.00 0.00 0.00 2.43
4975 5295 7.831691 TGACCAAGACAAAAGATATCCAAAA 57.168 32.000 0.00 0.00 0.00 2.44
5008 5328 4.542697 TCATGTGTATAGGAGTAGCCACA 58.457 43.478 0.00 0.00 40.02 4.17
5064 5387 6.884280 AGATTCGTTCTGGTGATTTTCTTT 57.116 33.333 0.00 0.00 31.79 2.52


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

AutoCloner maintained by Alex Coulton.