Multiple sequence alignment - TraesCS1D01G199000

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 TraesCS1D01G199000 chr1D 100.000 6852 0 0 1 6852 281373999 281380850 0.000000e+00 12654.0
1 TraesCS1D01G199000 chr1D 100.000 50 0 0 5636 5685 281379592 281379641 7.320000e-15 93.5
2 TraesCS1D01G199000 chr1D 100.000 50 0 0 5594 5643 281379634 281379683 7.320000e-15 93.5
3 TraesCS1D01G199000 chr1A 93.533 5644 202 55 80 5643 353632035 353626475 0.000000e+00 8250.0
4 TraesCS1D01G199000 chr1A 90.248 1251 55 21 5636 6852 353626524 353625307 0.000000e+00 1572.0
5 TraesCS1D01G199000 chr1A 96.970 66 2 0 9 74 353632269 353632204 2.020000e-20 111.0
6 TraesCS1D01G199000 chr1B 93.245 5285 195 50 1 5230 382227448 382222271 0.000000e+00 7633.0
7 TraesCS1D01G199000 chr1B 93.571 700 23 5 5228 5905 382222246 382221547 0.000000e+00 1024.0
8 TraesCS1D01G199000 chr1B 95.848 289 9 1 5936 6224 382221550 382221265 1.350000e-126 464.0
9 TraesCS1D01G199000 chr1B 98.000 50 1 0 5636 5685 382221868 382221819 3.400000e-13 87.9
10 TraesCS1D01G199000 chr4D 81.272 283 38 10 6578 6846 356322344 356322063 1.500000e-51 215.0
11 TraesCS1D01G199000 chr5B 83.168 202 33 1 6567 6768 371269281 371269081 4.220000e-42 183.0
12 TraesCS1D01G199000 chrUn 75.850 294 50 12 6568 6843 34063652 34063942 5.580000e-26 130.0
13 TraesCS1D01G199000 chrUn 75.932 295 48 13 6568 6843 35845883 35846173 5.580000e-26 130.0
14 TraesCS1D01G199000 chr6B 100.000 29 0 0 789 817 711857470 711857442 3.000000e-03 54.7


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 TraesCS1D01G199000 chr1D 281373999 281380850 6851 False 4280.333333 12654 100.000000 1 6852 3 chr1D.!!$F1 6851
1 TraesCS1D01G199000 chr1A 353625307 353632269 6962 True 3311.000000 8250 93.583667 9 6852 3 chr1A.!!$R1 6843
2 TraesCS1D01G199000 chr1B 382221265 382227448 6183 True 2302.225000 7633 95.166000 1 6224 4 chr1B.!!$R1 6223

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
85 250 0.682852 TTGGTCTCCGGTTACACAGG 59.317 55.0 0.00 0.0 34.60 4.00 F
1085 1284 0.035915 GCGCCTTTTCTCCTTCTCCT 60.036 55.0 0.00 0.0 0.00 3.69 F
1242 1441 0.035915 TTCATGGATTCCGCCACGAA 60.036 50.0 0.00 0.0 41.56 3.85 F
2918 3150 0.319083 TTTATGAGTGGACGGTGCGT 59.681 50.0 0.00 0.0 45.10 5.24 F
4740 4995 1.360820 TGACGTCTTTTGCACAACGA 58.639 45.0 17.92 1.3 38.44 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1441 0.039618 ATTCTCCCAATTGGCGTGGT 59.960 50.000 19.75 1.58 34.01 4.16 R
2594 2825 0.394352 CGAATTCCTCCTTGGTGGGG 60.394 60.000 7.78 0.10 37.07 4.96 R
3177 3409 1.888512 TGCTTTTCCCAAGCTGATCAC 59.111 47.619 8.00 0.00 43.38 3.06 R
4753 5008 0.595095 CTGACCTTTGGTTCTGCAGC 59.405 55.000 9.47 0.00 35.25 5.25 R
6614 6947 0.179174 CGCCGGTTGTAATTTCAGCC 60.179 55.000 1.90 7.74 35.77 4.85 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
39 41 2.135933 GAGGCGAATATACCTGCACAC 58.864 52.381 0.00 0.00 36.05 3.82
78 80 3.339547 CCAACATTGGTCTCCGGTT 57.660 52.632 0.00 0.00 43.43 4.44
85 250 0.682852 TTGGTCTCCGGTTACACAGG 59.317 55.000 0.00 0.00 34.60 4.00
90 255 1.896122 CTCCGGTTACACAGGGGTCC 61.896 65.000 0.00 0.00 34.05 4.46
109 274 1.514553 CTCTCATCTCACGCAGGCA 59.485 57.895 0.00 0.00 0.00 4.75
139 304 1.267533 GCGAGCTAACCTAGGAGTAGC 59.732 57.143 27.86 27.86 0.00 3.58
321 486 2.421314 CCTCGTGTCACACAGGCA 59.579 61.111 9.06 0.00 34.28 4.75
333 498 2.757508 CAGGCAGGCGAGAGGAGA 60.758 66.667 0.00 0.00 0.00 3.71
334 499 2.441901 AGGCAGGCGAGAGGAGAG 60.442 66.667 0.00 0.00 0.00 3.20
361 526 4.092116 AGTCCCACCAGAAAGAAAGAAG 57.908 45.455 0.00 0.00 0.00 2.85
378 543 1.915078 AAGGACAATGGGCGAGGAGG 61.915 60.000 0.00 0.00 0.00 4.30
381 546 3.411517 CAATGGGCGAGGAGGGGT 61.412 66.667 0.00 0.00 0.00 4.95
382 547 3.411517 AATGGGCGAGGAGGGGTG 61.412 66.667 0.00 0.00 0.00 4.61
419 584 1.682684 GCAGGACGGGGAGAGAGAA 60.683 63.158 0.00 0.00 0.00 2.87
420 585 1.258445 GCAGGACGGGGAGAGAGAAA 61.258 60.000 0.00 0.00 0.00 2.52
421 586 0.820871 CAGGACGGGGAGAGAGAAAG 59.179 60.000 0.00 0.00 0.00 2.62
422 587 0.705253 AGGACGGGGAGAGAGAAAGA 59.295 55.000 0.00 0.00 0.00 2.52
423 588 1.107945 GGACGGGGAGAGAGAAAGAG 58.892 60.000 0.00 0.00 0.00 2.85
424 589 1.341187 GGACGGGGAGAGAGAAAGAGA 60.341 57.143 0.00 0.00 0.00 3.10
425 590 2.021457 GACGGGGAGAGAGAAAGAGAG 58.979 57.143 0.00 0.00 0.00 3.20
426 591 1.636519 ACGGGGAGAGAGAAAGAGAGA 59.363 52.381 0.00 0.00 0.00 3.10
514 697 4.507916 TCGCCTCCCTCTCCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
519 703 3.347590 TCCCTCTCCCTCGCCTCA 61.348 66.667 0.00 0.00 0.00 3.86
617 801 2.438614 TGGGGCTCTCTCGTCTCG 60.439 66.667 0.00 0.00 0.00 4.04
687 883 2.743718 CACAGCCAGAGACCCGTT 59.256 61.111 0.00 0.00 0.00 4.44
808 1004 2.122729 CCTCCACCTCCACCTCCA 59.877 66.667 0.00 0.00 0.00 3.86
809 1005 2.294078 CCTCCACCTCCACCTCCAC 61.294 68.421 0.00 0.00 0.00 4.02
846 1042 2.784547 GGGAAAATAACCGACGGGG 58.215 57.895 20.00 0.00 43.62 5.73
847 1043 1.378882 GGGAAAATAACCGACGGGGC 61.379 60.000 20.00 0.00 40.62 5.80
940 1139 3.090532 GAGGGGAATGCGGGACCT 61.091 66.667 0.00 0.00 0.00 3.85
1005 1204 3.151710 CCCGCCGGAGTCATGGTA 61.152 66.667 5.05 0.00 0.00 3.25
1023 1222 1.103803 TAAGTCGCGAGATCTGCCTT 58.896 50.000 10.24 10.23 45.19 4.35
1064 1263 2.811799 GCTCGCTCCCTCTTCCTC 59.188 66.667 0.00 0.00 0.00 3.71
1084 1283 1.362406 CGCGCCTTTTCTCCTTCTCC 61.362 60.000 0.00 0.00 0.00 3.71
1085 1284 0.035915 GCGCCTTTTCTCCTTCTCCT 60.036 55.000 0.00 0.00 0.00 3.69
1086 1285 2.009542 GCGCCTTTTCTCCTTCTCCTC 61.010 57.143 0.00 0.00 0.00 3.71
1130 1329 4.670735 GCCTTAATTAATGCGTGTTCGTGT 60.671 41.667 9.31 0.00 39.49 4.49
1178 1377 6.000219 TCGTAGGCCTAGTATTCGAATTACT 59.000 40.000 17.19 17.77 0.00 2.24
1179 1378 6.072838 TCGTAGGCCTAGTATTCGAATTACTG 60.073 42.308 17.19 11.19 0.00 2.74
1194 1393 2.696409 TACTGCGCGTCGTTTTCCCA 62.696 55.000 8.43 0.00 0.00 4.37
1204 1403 4.555116 GCGTCGTTTTCCCAGTAAATTTCA 60.555 41.667 0.00 0.00 0.00 2.69
1206 1405 6.146898 CGTCGTTTTCCCAGTAAATTTCATT 58.853 36.000 0.00 0.00 0.00 2.57
1242 1441 0.035915 TTCATGGATTCCGCCACGAA 60.036 50.000 0.00 0.00 41.56 3.85
1267 1466 3.315191 ACGCCAATTGGGAGAATTATTCG 59.685 43.478 25.73 17.38 39.08 3.34
1296 1495 2.651232 GAATCCGCGTCCGTCGAG 60.651 66.667 4.92 0.00 42.86 4.04
1478 1683 2.158623 TCGCCCCGTTAGGATTAGTAGA 60.159 50.000 0.00 0.00 41.02 2.59
1479 1684 2.824341 CGCCCCGTTAGGATTAGTAGAT 59.176 50.000 0.00 0.00 41.02 1.98
1480 1685 4.012374 CGCCCCGTTAGGATTAGTAGATA 58.988 47.826 0.00 0.00 41.02 1.98
1481 1686 4.096081 CGCCCCGTTAGGATTAGTAGATAG 59.904 50.000 0.00 0.00 41.02 2.08
1482 1687 5.259632 GCCCCGTTAGGATTAGTAGATAGA 58.740 45.833 0.00 0.00 41.02 1.98
1483 1688 5.892686 GCCCCGTTAGGATTAGTAGATAGAT 59.107 44.000 0.00 0.00 41.02 1.98
1484 1689 7.059156 GCCCCGTTAGGATTAGTAGATAGATA 58.941 42.308 0.00 0.00 41.02 1.98
1688 1900 1.600107 CCAAGCAGGCAATGGCATT 59.400 52.632 6.96 6.96 43.71 3.56
1704 1916 2.540383 GCATTTTCCTCCCCTTTTCCT 58.460 47.619 0.00 0.00 0.00 3.36
1835 2047 1.661341 ATGCAGAACCTCGCTCAATC 58.339 50.000 0.00 0.00 0.00 2.67
1836 2048 0.321346 TGCAGAACCTCGCTCAATCA 59.679 50.000 0.00 0.00 0.00 2.57
1837 2049 1.005340 GCAGAACCTCGCTCAATCAG 58.995 55.000 0.00 0.00 0.00 2.90
1838 2050 1.674221 GCAGAACCTCGCTCAATCAGT 60.674 52.381 0.00 0.00 0.00 3.41
1839 2051 2.266554 CAGAACCTCGCTCAATCAGTC 58.733 52.381 0.00 0.00 0.00 3.51
1840 2052 1.895798 AGAACCTCGCTCAATCAGTCA 59.104 47.619 0.00 0.00 0.00 3.41
1841 2053 2.300152 AGAACCTCGCTCAATCAGTCAA 59.700 45.455 0.00 0.00 0.00 3.18
1842 2054 3.055530 AGAACCTCGCTCAATCAGTCAAT 60.056 43.478 0.00 0.00 0.00 2.57
1843 2055 2.898705 ACCTCGCTCAATCAGTCAATC 58.101 47.619 0.00 0.00 0.00 2.67
1844 2056 2.234661 ACCTCGCTCAATCAGTCAATCA 59.765 45.455 0.00 0.00 0.00 2.57
1845 2057 3.264947 CCTCGCTCAATCAGTCAATCAA 58.735 45.455 0.00 0.00 0.00 2.57
1846 2058 3.063180 CCTCGCTCAATCAGTCAATCAAC 59.937 47.826 0.00 0.00 0.00 3.18
1969 2195 1.337387 GCCACGAGATACAGTAGGACC 59.663 57.143 0.00 0.00 0.00 4.46
2047 2276 1.002624 GATGGTCGTGGCAGGGAAA 60.003 57.895 7.42 0.00 0.00 3.13
2083 2312 2.360483 ACATCAATGTGCCGTGTTTGAA 59.640 40.909 0.00 0.00 40.03 2.69
2307 2538 0.969917 GAGCTGTCTCCCTGCAGAGA 60.970 60.000 17.39 6.50 40.62 3.10
2321 2552 1.133853 GCAGAGATCAGGAATGGGCTT 60.134 52.381 0.00 0.00 0.00 4.35
2376 2607 2.866156 CGTTTGAGTGCTCAGAAAGACA 59.134 45.455 1.98 0.00 41.13 3.41
2594 2825 1.089920 CAGAGTGCCCTGTGTATTGC 58.910 55.000 0.00 0.00 0.00 3.56
2698 2929 5.221362 CCGTTTACCTCAAACCCATTTTTCT 60.221 40.000 0.00 0.00 43.09 2.52
2856 3088 3.834813 AGTTCATGACTAGAGTTCAGCCA 59.165 43.478 0.00 0.00 36.65 4.75
2918 3150 0.319083 TTTATGAGTGGACGGTGCGT 59.681 50.000 0.00 0.00 45.10 5.24
2942 3174 7.066043 CGTTACTCTCTGTCTATTTCAGTACCT 59.934 40.741 0.00 0.00 34.86 3.08
2943 3175 9.393512 GTTACTCTCTGTCTATTTCAGTACCTA 57.606 37.037 0.00 0.00 34.86 3.08
3177 3409 1.821753 TGCCTTCTCTTCTTCTCCTCG 59.178 52.381 0.00 0.00 0.00 4.63
3178 3410 1.822371 GCCTTCTCTTCTTCTCCTCGT 59.178 52.381 0.00 0.00 0.00 4.18
3255 3505 2.493035 CTGTGTGTGATGTTGGCTACA 58.507 47.619 3.86 3.86 41.97 2.74
3263 3513 3.753272 GTGATGTTGGCTACATGACAGTT 59.247 43.478 21.92 0.00 46.67 3.16
3417 3670 7.780008 ATGGATTCGTCGTGATTGTAATTAA 57.220 32.000 0.00 0.00 0.00 1.40
3424 3677 8.642908 TCGTCGTGATTGTAATTAATCTGATT 57.357 30.769 8.14 8.14 37.81 2.57
3425 3678 8.539674 TCGTCGTGATTGTAATTAATCTGATTG 58.460 33.333 13.01 0.00 37.81 2.67
3531 3784 5.350504 ACAGGTACTCATCCTCATTCTTG 57.649 43.478 0.00 0.00 34.60 3.02
3920 4173 8.543774 TCTATCTTCTTCTGCTTGGTAATTTCT 58.456 33.333 0.00 0.00 0.00 2.52
4016 4269 1.379527 CTATTGGCGACTGGTTTCCC 58.620 55.000 0.00 0.00 0.00 3.97
4076 4329 2.624838 CAGAACACCCTTTCTTGCACAT 59.375 45.455 0.00 0.00 33.31 3.21
4100 4353 1.387084 GAGCTACTTTGTCGTTCTGCG 59.613 52.381 0.00 0.00 43.01 5.18
4190 4443 4.081142 TGTGTGAAGTCTTCCTTTGTGAGA 60.081 41.667 10.12 0.00 32.03 3.27
4257 4510 8.554490 AATGGGTTCTCAGATATACTACAAGT 57.446 34.615 0.00 0.00 0.00 3.16
4280 4533 8.786826 AGTCAAAAATGTATTCGAACCTATCA 57.213 30.769 0.00 0.00 0.00 2.15
4737 4992 1.732809 TCGTTGACGTCTTTTGCACAA 59.267 42.857 17.92 0.00 40.80 3.33
4740 4995 1.360820 TGACGTCTTTTGCACAACGA 58.639 45.000 17.92 1.30 38.44 3.85
4778 5033 3.883489 GCAGAACCAAAGGTCAGTTTACT 59.117 43.478 0.00 0.00 33.12 2.24
4785 5040 4.130118 CAAAGGTCAGTTTACTGCACTCT 58.870 43.478 5.00 2.82 43.46 3.24
4849 5104 6.307077 GGTAACGATATTGTTGTTTTTCAGGC 59.693 38.462 17.22 0.00 35.94 4.85
4911 5166 9.844790 CTAAGCAGTTCATAAAAACATCATCAA 57.155 29.630 0.00 0.00 0.00 2.57
4927 5182 5.197224 TCATCAATGGAAGGAAATGGTCT 57.803 39.130 0.00 0.00 0.00 3.85
4929 5184 3.091545 TCAATGGAAGGAAATGGTCTGC 58.908 45.455 0.00 0.00 0.00 4.26
4932 5187 1.272092 TGGAAGGAAATGGTCTGCTGG 60.272 52.381 0.00 0.00 0.00 4.85
5027 5282 4.643784 AGTGGCAATTCTGATTCTGATTCC 59.356 41.667 0.00 0.00 0.00 3.01
5032 5287 5.970023 GCAATTCTGATTCTGATTCCGAAAG 59.030 40.000 9.41 7.39 0.00 2.62
5039 5294 1.009829 CTGATTCCGAAAGCTTCCGG 58.990 55.000 19.34 19.34 46.57 5.14
5152 5408 6.263168 ACCTCGAAATTTGAGAACAGATTGTT 59.737 34.615 11.68 0.00 44.37 2.83
5153 5409 6.580041 CCTCGAAATTTGAGAACAGATTGTTG 59.420 38.462 11.68 0.00 41.28 3.33
5156 5412 8.352201 TCGAAATTTGAGAACAGATTGTTGAAT 58.648 29.630 0.00 0.00 41.28 2.57
5157 5413 8.422457 CGAAATTTGAGAACAGATTGTTGAATG 58.578 33.333 0.00 0.00 41.28 2.67
5158 5414 9.467258 GAAATTTGAGAACAGATTGTTGAATGA 57.533 29.630 0.00 0.00 41.28 2.57
5197 5457 2.238084 ACTCATCTGACCCTGTAGCA 57.762 50.000 0.00 0.00 0.00 3.49
5211 5471 6.687604 ACCCTGTAGCAACAATTTTGATTAC 58.312 36.000 0.00 6.56 34.49 1.89
5225 5512 5.843673 TTTGATTACTTTTGTCACTGCCA 57.156 34.783 0.00 0.00 0.00 4.92
5226 5513 6.403866 TTTGATTACTTTTGTCACTGCCAT 57.596 33.333 0.00 0.00 0.00 4.40
5233 5520 2.885135 TTGTCACTGCCATCCTCATT 57.115 45.000 0.00 0.00 0.00 2.57
5242 5529 3.483421 TGCCATCCTCATTTGCTGATAG 58.517 45.455 0.00 0.00 32.10 2.08
5250 5537 8.843262 CATCCTCATTTGCTGATAGATTGTTAA 58.157 33.333 0.00 0.00 32.10 2.01
5277 5564 7.648510 GCTTAGGCGTGTATCATATTATAGGTC 59.351 40.741 0.00 0.00 0.00 3.85
5305 5592 4.678509 TGCGTGATTGGTAATTGAGAAC 57.321 40.909 0.00 0.00 0.00 3.01
5592 5894 1.740296 GCGACACCAGTTATGCCGT 60.740 57.895 0.00 0.00 0.00 5.68
5660 5962 3.318275 GCAGTCGAAGGTGTATCCATCTA 59.682 47.826 0.00 0.00 39.02 1.98
5710 6012 2.244000 GGCAACTAAAGACGCAGCA 58.756 52.632 0.00 0.00 0.00 4.41
5759 6061 2.017559 GATCCGGTTGCCTCGTAGCT 62.018 60.000 0.00 0.00 0.00 3.32
5760 6062 0.754217 ATCCGGTTGCCTCGTAGCTA 60.754 55.000 0.00 0.00 0.00 3.32
5761 6063 0.754217 TCCGGTTGCCTCGTAGCTAT 60.754 55.000 0.00 0.00 0.00 2.97
5910 6221 8.887717 CAGATAGGACTCAATTCTTTGTTTAGG 58.112 37.037 0.00 0.00 34.32 2.69
6014 6329 2.760092 GGGCTGATTGCTTGGTTAATCA 59.240 45.455 0.00 0.00 40.06 2.57
6076 6392 3.770933 AGGTAGGCACACGGTTATTAGAA 59.229 43.478 0.00 0.00 0.00 2.10
6077 6393 4.117685 GGTAGGCACACGGTTATTAGAAG 58.882 47.826 0.00 0.00 0.00 2.85
6078 6394 3.261981 AGGCACACGGTTATTAGAAGG 57.738 47.619 0.00 0.00 0.00 3.46
6092 6408 8.411683 GGTTATTAGAAGGAGACAAGACGATTA 58.588 37.037 0.00 0.00 0.00 1.75
6309 6628 2.677902 CGCTTACCTGCTCCTGATGAAA 60.678 50.000 0.00 0.00 0.00 2.69
6313 6632 5.767168 GCTTACCTGCTCCTGATGAAATATT 59.233 40.000 0.00 0.00 0.00 1.28
6314 6633 6.072783 GCTTACCTGCTCCTGATGAAATATTC 60.073 42.308 0.00 0.00 0.00 1.75
6315 6634 5.378230 ACCTGCTCCTGATGAAATATTCA 57.622 39.130 0.00 0.00 45.01 2.57
6316 6635 5.759059 ACCTGCTCCTGATGAAATATTCAA 58.241 37.500 0.00 0.00 43.95 2.69
6317 6636 6.371278 ACCTGCTCCTGATGAAATATTCAAT 58.629 36.000 0.00 0.00 43.95 2.57
6318 6637 6.489361 ACCTGCTCCTGATGAAATATTCAATC 59.511 38.462 0.00 0.00 43.95 2.67
6319 6638 6.348295 CCTGCTCCTGATGAAATATTCAATCG 60.348 42.308 0.00 0.00 43.95 3.34
6320 6639 6.290605 TGCTCCTGATGAAATATTCAATCGA 58.709 36.000 0.00 0.00 43.95 3.59
6357 6676 0.690192 ATGTTGACGGGATGGTGTGA 59.310 50.000 0.00 0.00 0.00 3.58
6362 6682 1.628340 TGACGGGATGGTGTGAGAAAT 59.372 47.619 0.00 0.00 0.00 2.17
6414 6734 6.668541 ATTGAACTAATCAGTGTGGAATCG 57.331 37.500 0.00 0.00 39.77 3.34
6421 6742 4.753516 ATCAGTGTGGAATCGAACCATA 57.246 40.909 15.78 11.47 39.69 2.74
6437 6758 6.035217 CGAACCATATTCATGTGAAATGCAA 58.965 36.000 0.00 0.00 37.61 4.08
6443 6764 4.495911 TTCATGTGAAATGCAAGCGTTA 57.504 36.364 0.00 0.00 0.00 3.18
6475 6796 6.615726 AGGCCTATGGAGTATGAGACTTTTTA 59.384 38.462 1.29 0.00 39.06 1.52
6512 6833 2.632996 AGCACTGGAAAGTACTACAGCA 59.367 45.455 17.29 2.15 34.40 4.41
6550 6871 2.048603 GCATCTCCAACAGCCCCAC 61.049 63.158 0.00 0.00 0.00 4.61
6605 6938 3.103742 GCCCCCATATCCTTGTTTTTCA 58.896 45.455 0.00 0.00 0.00 2.69
6606 6939 3.711190 GCCCCCATATCCTTGTTTTTCAT 59.289 43.478 0.00 0.00 0.00 2.57
6609 6942 4.887071 CCCCATATCCTTGTTTTTCATCGA 59.113 41.667 0.00 0.00 0.00 3.59
6614 6947 7.436080 CCATATCCTTGTTTTTCATCGATTTGG 59.564 37.037 0.00 0.00 32.60 3.28
6647 6980 2.899044 CGGCGAACCCAAGCGAAAA 61.899 57.895 0.00 0.00 0.00 2.29
6663 6996 0.542702 AAAACCAGCACATCAGGGGG 60.543 55.000 0.00 0.00 0.00 5.40
6664 6997 3.590466 AACCAGCACATCAGGGGGC 62.590 63.158 0.00 0.00 0.00 5.80
6693 7026 1.070786 ACCGGCTGAAGCGAAAAGA 59.929 52.632 0.00 0.00 43.26 2.52
6695 7028 1.227999 CCGGCTGAAGCGAAAAGACA 61.228 55.000 0.00 0.00 43.26 3.41
6700 7033 0.934496 TGAAGCGAAAAGACACGTGG 59.066 50.000 21.57 0.44 0.00 4.94
6705 7038 2.593436 AAAAGACACGTGGGCCCG 60.593 61.111 21.57 8.84 0.00 6.13
6723 7056 2.048222 CACAGTCGGCGACACCAT 60.048 61.111 37.71 17.81 39.03 3.55
6724 7057 2.094659 CACAGTCGGCGACACCATC 61.095 63.158 37.71 13.69 39.03 3.51
6750 7094 2.919772 TCCCCTTTCCCTCCATTTTC 57.080 50.000 0.00 0.00 0.00 2.29
6781 7125 4.168291 CCTTCTCCCCCGCAGCTC 62.168 72.222 0.00 0.00 0.00 4.09
6793 7137 4.154347 CAGCTCCCGCCACTCTCC 62.154 72.222 0.00 0.00 36.60 3.71
6812 7156 2.842462 TAGATCCGCCCGCCATGT 60.842 61.111 0.00 0.00 0.00 3.21
6822 7166 3.554692 CGCCATGTCGCCGAAGAC 61.555 66.667 0.00 3.73 41.30 3.01
6827 7171 1.556564 CATGTCGCCGAAGACGTATT 58.443 50.000 0.00 0.00 43.70 1.89
6836 7180 1.202268 CGAAGACGTATTCGCTCCCTT 60.202 52.381 29.33 6.23 44.73 3.95
6846 7190 2.922234 GCTCCCTTGCCTAGCCAT 59.078 61.111 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 3.550678 GGCTTGACTCGGATTTAGTTACG 59.449 47.826 0.00 0.00 0.00 3.18
74 76 1.916777 AGGGACCCCTGTGTAACCG 60.917 63.158 7.00 0.00 46.22 4.44
85 250 2.022240 GCGTGAGATGAGAGGGACCC 62.022 65.000 0.59 0.59 0.00 4.46
90 255 1.227205 GCCTGCGTGAGATGAGAGG 60.227 63.158 0.00 0.00 0.00 3.69
109 274 2.911484 TTAGCTCGCCACGTGTCGT 61.911 57.895 19.21 2.10 42.36 4.34
139 304 7.362747 CCTCCTCCTTTTTCTTGATTGAATGAG 60.363 40.741 0.00 0.00 0.00 2.90
321 486 0.252284 TTTTCCCTCTCCTCTCGCCT 60.252 55.000 0.00 0.00 0.00 5.52
361 526 2.190578 CCTCCTCGCCCATTGTCC 59.809 66.667 0.00 0.00 0.00 4.02
378 543 4.048470 GGCTTCCCACCTCCACCC 62.048 72.222 0.00 0.00 0.00 4.61
419 584 4.761058 TCCCCCGCGCTCTCTCTT 62.761 66.667 5.56 0.00 0.00 2.85
473 656 4.776322 CATGGGAGCGGCGTTGGA 62.776 66.667 9.37 0.00 0.00 3.53
514 697 3.462678 GGTCGGAGGAGGTGAGGC 61.463 72.222 0.00 0.00 0.00 4.70
617 801 3.125573 GGGAAACCGCGGAGAAGC 61.126 66.667 35.90 15.50 43.64 3.86
658 842 4.741239 GCTGTGGGGGAGGGGAGA 62.741 72.222 0.00 0.00 0.00 3.71
803 999 3.528370 CTACGCGGGAGGTGGAGG 61.528 72.222 12.47 0.00 33.15 4.30
805 1001 4.753662 AGCTACGCGGGAGGTGGA 62.754 66.667 12.47 0.00 0.00 4.02
1005 1204 0.179124 GAAGGCAGATCTCGCGACTT 60.179 55.000 3.71 4.94 0.00 3.01
1023 1222 2.418197 CGGAAGCGGAAATTACAGAGGA 60.418 50.000 0.00 0.00 0.00 3.71
1064 1263 1.362406 GAGAAGGAGAAAAGGCGCGG 61.362 60.000 8.83 0.00 0.00 6.46
1084 1283 1.681486 GGCGGAAGAGGAAGAGGGAG 61.681 65.000 0.00 0.00 0.00 4.30
1085 1284 1.686110 GGCGGAAGAGGAAGAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
1086 1285 2.904131 GGCGGAAGAGGAAGAGGG 59.096 66.667 0.00 0.00 0.00 4.30
1130 1329 3.508793 AGAGGAATCGAACAGTAACCGAA 59.491 43.478 0.00 0.00 35.87 4.30
1178 1377 2.696409 TACTGGGAAAACGACGCGCA 62.696 55.000 5.73 0.00 0.00 6.09
1179 1378 1.559149 TTACTGGGAAAACGACGCGC 61.559 55.000 5.73 0.00 0.00 6.86
1194 1393 3.288092 GCGAGGGGGAATGAAATTTACT 58.712 45.455 0.00 0.00 36.07 2.24
1242 1441 0.039618 ATTCTCCCAATTGGCGTGGT 59.960 50.000 19.75 1.58 34.01 4.16
1267 1466 0.042448 GCGGATTCGTGCGTAATTCC 60.042 55.000 0.00 0.00 38.89 3.01
1296 1495 1.805945 CAGAGGGCGTACGAGCAAC 60.806 63.158 21.65 5.66 39.27 4.17
1378 1577 6.855763 ATCCAAAAACAAAGAGATGGCATA 57.144 33.333 0.00 0.00 0.00 3.14
1478 1683 2.619177 ACTTCTCACGCAGCGTATCTAT 59.381 45.455 22.49 1.76 38.32 1.98
1479 1684 2.014857 ACTTCTCACGCAGCGTATCTA 58.985 47.619 22.49 5.71 38.32 1.98
1480 1685 0.811915 ACTTCTCACGCAGCGTATCT 59.188 50.000 22.49 0.00 38.32 1.98
1481 1686 1.192793 GACTTCTCACGCAGCGTATC 58.807 55.000 22.49 7.83 38.32 2.24
1482 1687 0.526211 TGACTTCTCACGCAGCGTAT 59.474 50.000 22.49 1.72 38.32 3.06
1483 1688 0.312729 TTGACTTCTCACGCAGCGTA 59.687 50.000 22.49 1.50 38.32 4.42
1484 1689 0.529773 TTTGACTTCTCACGCAGCGT 60.530 50.000 16.61 16.61 42.36 5.07
1529 1737 9.871238 GAGGGGAAAAGGAAGAAAAATAAATAC 57.129 33.333 0.00 0.00 0.00 1.89
1530 1738 9.837681 AGAGGGGAAAAGGAAGAAAAATAAATA 57.162 29.630 0.00 0.00 0.00 1.40
1531 1739 8.742125 AGAGGGGAAAAGGAAGAAAAATAAAT 57.258 30.769 0.00 0.00 0.00 1.40
1688 1900 2.789399 ACTTGAGGAAAAGGGGAGGAAA 59.211 45.455 0.00 0.00 0.00 3.13
1704 1916 4.039973 ACGACCATTGGAGTAGAAACTTGA 59.960 41.667 10.37 0.00 35.56 3.02
1835 2047 1.603802 AGCACAACGGTTGATTGACTG 59.396 47.619 26.39 13.98 0.00 3.51
1836 2048 1.967319 AGCACAACGGTTGATTGACT 58.033 45.000 26.39 13.14 0.00 3.41
1837 2049 2.774439 AAGCACAACGGTTGATTGAC 57.226 45.000 26.39 11.39 32.95 3.18
1844 2056 0.383949 AAATCGCAAGCACAACGGTT 59.616 45.000 0.00 0.00 35.07 4.44
1845 2057 1.231221 TAAATCGCAAGCACAACGGT 58.769 45.000 0.00 0.00 37.18 4.83
1846 2058 2.323939 TTAAATCGCAAGCACAACGG 57.676 45.000 0.00 0.00 37.18 4.44
1969 2195 8.027771 AGCCGTTCTATATTCGAGGTATAAAAG 58.972 37.037 0.00 0.00 0.00 2.27
2083 2312 6.421485 AGTCAAGAAAGCAATAGTCATGGAT 58.579 36.000 0.00 0.00 0.00 3.41
2244 2475 6.633500 AGCTAGATACATCAGAGAGTGAAC 57.367 41.667 0.00 0.00 39.19 3.18
2307 2538 2.172293 GAGTCTCAAGCCCATTCCTGAT 59.828 50.000 0.00 0.00 0.00 2.90
2376 2607 1.852157 ATGGCAGGATTGTCACCGGT 61.852 55.000 0.00 0.00 42.67 5.28
2594 2825 0.394352 CGAATTCCTCCTTGGTGGGG 60.394 60.000 7.78 0.10 37.07 4.96
2698 2929 3.055021 TCCATTCGGTAATACACTGGCAA 60.055 43.478 0.00 0.00 33.95 4.52
2740 2972 4.267536 CAAATGCCTGGAGAGAAAGATGA 58.732 43.478 0.00 0.00 0.00 2.92
2956 3188 7.202526 GTGAAAAATGTGATGAGACTTGGAAA 58.797 34.615 0.00 0.00 0.00 3.13
3177 3409 1.888512 TGCTTTTCCCAAGCTGATCAC 59.111 47.619 8.00 0.00 43.38 3.06
3178 3410 2.291209 TGCTTTTCCCAAGCTGATCA 57.709 45.000 8.00 0.00 43.38 2.92
3255 3505 9.512588 AGAGAAGAACATCAATAAAACTGTCAT 57.487 29.630 0.00 0.00 0.00 3.06
3263 3513 7.229306 ACAAGCACAGAGAAGAACATCAATAAA 59.771 33.333 0.00 0.00 0.00 1.40
3417 3670 5.006386 GTCACTCCCTGTTTTCAATCAGAT 58.994 41.667 0.00 0.00 34.02 2.90
3424 3677 3.244561 GGATCTGTCACTCCCTGTTTTCA 60.245 47.826 0.00 0.00 0.00 2.69
3425 3678 3.244561 TGGATCTGTCACTCCCTGTTTTC 60.245 47.826 0.00 0.00 0.00 2.29
3492 3745 8.362464 AGTACCTGTACAAATAGTGATCTTCA 57.638 34.615 9.90 0.00 38.48 3.02
3531 3784 7.907214 ACGAGGAATAGCCATTATCAATAAC 57.093 36.000 0.00 0.00 40.02 1.89
3540 3793 3.933861 AAGGAACGAGGAATAGCCATT 57.066 42.857 0.00 0.00 40.02 3.16
3904 4157 8.102800 CATATATGCAGAAATTACCAAGCAGA 57.897 34.615 0.00 0.00 35.26 4.26
3942 4195 6.279513 TGGGTAATTCAAACATTGCTTAGG 57.720 37.500 0.00 0.00 0.00 2.69
4016 4269 2.806009 GCTAGCCAGAGAGCCCAGG 61.806 68.421 2.29 0.00 32.25 4.45
4076 4329 2.891580 AGAACGACAAAGTAGCTCCTCA 59.108 45.455 0.00 0.00 0.00 3.86
4100 4353 2.227388 CAGTTTGTGGGACAGAAGCATC 59.773 50.000 0.00 0.00 44.67 3.91
4257 4510 9.173021 ACATGATAGGTTCGAATACATTTTTGA 57.827 29.630 0.00 0.00 0.00 2.69
4280 4533 2.896854 CGCCGGCACATGCTACAT 60.897 61.111 28.98 0.00 41.70 2.29
4687 4942 2.047830 AGGAGAACTCTTTCCACCGTT 58.952 47.619 1.86 0.00 35.24 4.44
4740 4995 3.386237 GCAGCCAGAGACCCGTCT 61.386 66.667 0.00 0.00 43.78 4.18
4753 5008 0.595095 CTGACCTTTGGTTCTGCAGC 59.405 55.000 9.47 0.00 35.25 5.25
4778 5033 6.489700 TGGAAACAAGATTTGATAAGAGTGCA 59.510 34.615 0.00 0.00 37.44 4.57
4849 5104 3.197790 CGGTTCGAGCTGCATGGG 61.198 66.667 1.02 0.00 0.00 4.00
4911 5166 2.622452 CCAGCAGACCATTTCCTTCCAT 60.622 50.000 0.00 0.00 0.00 3.41
4932 5187 2.288825 CCATGCAGGATGAATTGCCATC 60.289 50.000 0.00 0.00 39.69 3.51
5027 5282 1.912371 GCTTGACCCGGAAGCTTTCG 61.912 60.000 20.64 20.64 42.21 3.46
5039 5294 2.467826 GCTGGATCTGCGCTTGACC 61.468 63.158 9.73 8.12 0.00 4.02
5152 5408 7.722949 AAAATAGATTGGCTTCCTTCATTCA 57.277 32.000 0.00 0.00 0.00 2.57
5153 5409 9.521503 GTAAAAATAGATTGGCTTCCTTCATTC 57.478 33.333 0.00 0.00 0.00 2.67
5156 5412 7.888021 TGAGTAAAAATAGATTGGCTTCCTTCA 59.112 33.333 0.00 0.00 0.00 3.02
5157 5413 8.281212 TGAGTAAAAATAGATTGGCTTCCTTC 57.719 34.615 0.00 0.00 0.00 3.46
5158 5414 8.829373 ATGAGTAAAAATAGATTGGCTTCCTT 57.171 30.769 0.00 0.00 0.00 3.36
5197 5457 8.603181 GCAGTGACAAAAGTAATCAAAATTGTT 58.397 29.630 0.00 0.00 31.68 2.83
5211 5471 2.507484 TGAGGATGGCAGTGACAAAAG 58.493 47.619 0.77 0.00 0.00 2.27
5225 5512 8.985315 TTAACAATCTATCAGCAAATGAGGAT 57.015 30.769 0.00 0.00 42.53 3.24
5226 5513 7.012704 GCTTAACAATCTATCAGCAAATGAGGA 59.987 37.037 0.00 0.00 42.53 3.71
5233 5520 6.260936 GCCTAAGCTTAACAATCTATCAGCAA 59.739 38.462 7.74 0.00 35.50 3.91
5242 5529 5.522460 TGATACACGCCTAAGCTTAACAATC 59.478 40.000 7.74 5.04 36.60 2.67
5250 5537 7.342284 ACCTATAATATGATACACGCCTAAGCT 59.658 37.037 0.00 0.00 36.60 3.74
5277 5564 4.621068 ATTACCAATCACGCATTCAGTG 57.379 40.909 0.00 0.00 40.71 3.66
5284 5571 3.438781 GGTTCTCAATTACCAATCACGCA 59.561 43.478 0.00 0.00 34.48 5.24
5312 5599 3.947834 CCTACACAAACTCCATGGATTCC 59.052 47.826 16.63 0.00 0.00 3.01
5592 5894 0.608130 ATACACCTTCGACTGCTGCA 59.392 50.000 0.88 0.88 0.00 4.41
5910 6221 3.124636 CCCTCGTGTAGTTAACAATGCAC 59.875 47.826 8.61 7.14 40.63 4.57
6014 6329 0.319405 GCCCTGCTGCACAAAGAATT 59.681 50.000 0.00 0.00 0.00 2.17
6076 6392 6.276847 GTGATGAATAATCGTCTTGTCTCCT 58.723 40.000 1.82 0.00 41.37 3.69
6077 6393 5.174035 CGTGATGAATAATCGTCTTGTCTCC 59.826 44.000 1.82 0.00 41.37 3.71
6078 6394 5.744345 ACGTGATGAATAATCGTCTTGTCTC 59.256 40.000 1.82 0.00 41.37 3.36
6092 6408 4.579869 AGCCTCTAAACAACGTGATGAAT 58.420 39.130 0.00 0.00 0.00 2.57
6242 6561 0.313672 TAGCGCTGCCCTTGTTTTTG 59.686 50.000 22.90 0.00 0.00 2.44
6243 6562 0.598065 CTAGCGCTGCCCTTGTTTTT 59.402 50.000 22.90 0.00 0.00 1.94
6266 6585 5.061311 GCGTACGAAAGAATACAGTTAGCAA 59.939 40.000 21.65 0.00 0.00 3.91
6313 6632 6.538381 TCCGAAAAGAATGATTGATCGATTGA 59.462 34.615 0.00 0.00 0.00 2.57
6314 6633 6.718388 TCCGAAAAGAATGATTGATCGATTG 58.282 36.000 0.00 0.00 0.00 2.67
6315 6634 6.925610 TCCGAAAAGAATGATTGATCGATT 57.074 33.333 0.00 0.00 0.00 3.34
6316 6635 6.484643 ACATCCGAAAAGAATGATTGATCGAT 59.515 34.615 0.00 0.00 0.00 3.59
6317 6636 5.817296 ACATCCGAAAAGAATGATTGATCGA 59.183 36.000 0.00 0.00 0.00 3.59
6318 6637 6.052840 ACATCCGAAAAGAATGATTGATCG 57.947 37.500 0.00 0.00 0.00 3.69
6319 6638 7.430502 GTCAACATCCGAAAAGAATGATTGATC 59.569 37.037 0.00 0.00 0.00 2.92
6320 6639 7.253422 GTCAACATCCGAAAAGAATGATTGAT 58.747 34.615 0.00 0.00 0.00 2.57
6414 6734 6.019318 GCTTGCATTTCACATGAATATGGTTC 60.019 38.462 0.00 0.00 38.66 3.62
6421 6742 3.581024 ACGCTTGCATTTCACATGAAT 57.419 38.095 0.00 0.00 33.54 2.57
6437 6758 3.206150 CATAGGCCTCAATTGTAACGCT 58.794 45.455 9.68 0.00 0.00 5.07
6443 6764 4.660303 TCATACTCCATAGGCCTCAATTGT 59.340 41.667 9.68 7.23 0.00 2.71
6475 6796 4.290155 CAGTGCTTCGCTGTGTAAATTTT 58.710 39.130 0.00 0.00 37.23 1.82
6497 6818 6.737254 TTTGCTTATGCTGTAGTACTTTCC 57.263 37.500 0.00 0.00 40.48 3.13
6530 6851 1.452833 GGGGCTGTTGGAGATGCTC 60.453 63.158 0.00 0.00 0.00 4.26
6532 6853 2.048603 GTGGGGCTGTTGGAGATGC 61.049 63.158 0.00 0.00 0.00 3.91
6587 6920 6.639632 ATCGATGAAAAACAAGGATATGGG 57.360 37.500 0.00 0.00 0.00 4.00
6588 6921 7.436080 CCAAATCGATGAAAAACAAGGATATGG 59.564 37.037 0.00 0.00 0.00 2.74
6591 6924 6.627065 GCCCAAATCGATGAAAAACAAGGATA 60.627 38.462 0.00 0.00 0.00 2.59
6605 6938 5.394115 GGTTGTAATTTCAGCCCAAATCGAT 60.394 40.000 6.68 0.00 33.56 3.59
6606 6939 4.082463 GGTTGTAATTTCAGCCCAAATCGA 60.082 41.667 6.68 0.00 33.56 3.59
6609 6942 3.056179 CCGGTTGTAATTTCAGCCCAAAT 60.056 43.478 11.46 0.00 35.72 2.32
6614 6947 0.179174 CGCCGGTTGTAATTTCAGCC 60.179 55.000 1.90 7.74 35.77 4.85
6644 6977 0.542702 CCCCCTGATGTGCTGGTTTT 60.543 55.000 0.00 0.00 34.00 2.43
6647 6980 4.052518 GCCCCCTGATGTGCTGGT 62.053 66.667 0.00 0.00 34.00 4.00
6673 7006 2.786564 CTTTTCGCTTCAGCCGGTGC 62.787 60.000 1.90 0.00 37.91 5.01
6674 7007 1.207593 CTTTTCGCTTCAGCCGGTG 59.792 57.895 1.90 0.00 37.91 4.94
6705 7038 4.961511 TGGTGTCGCCGACTGTGC 62.962 66.667 19.12 6.03 41.21 4.57
6723 7056 1.283905 GAGGGAAAGGGGAAAATCGGA 59.716 52.381 0.00 0.00 0.00 4.55
6724 7057 1.685180 GGAGGGAAAGGGGAAAATCGG 60.685 57.143 0.00 0.00 0.00 4.18
6750 7094 4.426528 AAGGGGGTCGGTAGGGGG 62.427 72.222 0.00 0.00 0.00 5.40
6781 7125 1.152440 ATCTAGGGAGAGTGGCGGG 60.152 63.158 0.00 0.00 34.35 6.13
6788 7132 1.974343 CGGGCGGATCTAGGGAGAG 60.974 68.421 0.00 0.00 34.35 3.20
6793 7137 3.314331 ATGGCGGGCGGATCTAGG 61.314 66.667 0.00 0.00 0.00 3.02
6795 7139 2.842462 ACATGGCGGGCGGATCTA 60.842 61.111 0.00 0.00 0.00 1.98
6812 7156 1.584483 GCGAATACGTCTTCGGCGA 60.584 57.895 29.50 4.99 46.18 5.54
6815 7159 0.594284 GGGAGCGAATACGTCTTCGG 60.594 60.000 29.50 16.03 46.18 4.30
6822 7166 0.387929 TAGGCAAGGGAGCGAATACG 59.612 55.000 0.00 0.00 42.93 3.06
6827 7171 3.470888 GGCTAGGCAAGGGAGCGA 61.471 66.667 12.16 0.00 37.07 4.93
6829 7173 1.228094 GATGGCTAGGCAAGGGAGC 60.228 63.158 24.12 0.00 35.39 4.70
6831 7175 0.764369 ATCGATGGCTAGGCAAGGGA 60.764 55.000 24.12 19.29 0.00 4.20


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

AutoCloner maintained by Alex Coulton.