Multiple sequence alignment - TraesCS6D01G269400

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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 TraesCS6D01G269400 chr6D 100.000 5250 0 0 1 5250 379562641 379567890 0.000000e+00 9696.0
1 TraesCS6D01G269400 chr6B 93.611 5290 211 54 2 5211 567412320 567407078 0.000000e+00 7779.0
2 TraesCS6D01G269400 chr6A 95.034 3484 97 25 1222 4651 521461897 521458436 0.000000e+00 5406.0
3 TraesCS6D01G269400 chr6A 90.571 1050 37 21 94 1117 521463154 521462141 0.000000e+00 1334.0
4 TraesCS6D01G269400 chr6A 94.024 502 26 1 4649 5146 521458321 521457820 0.000000e+00 758.0
5 TraesCS6D01G269400 chr6A 97.059 34 1 0 5172 5205 521457819 521457786 2.040000e-04 58.4
6 TraesCS6D01G269400 chr7A 90.476 84 8 0 2038 2121 174196412 174196495 1.550000e-20 111.0
7 TraesCS6D01G269400 chr7B 94.118 68 2 2 4273 4339 537019939 537019873 9.300000e-18 102.0
8 TraesCS6D01G269400 chr1B 100.000 31 0 0 4370 4400 30227765 30227795 2.040000e-04 58.4


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 TraesCS6D01G269400 chr6D 379562641 379567890 5249 False 9696.0 9696 100.000 1 5250 1 chr6D.!!$F1 5249
1 TraesCS6D01G269400 chr6B 567407078 567412320 5242 True 7779.0 7779 93.611 2 5211 1 chr6B.!!$R1 5209
2 TraesCS6D01G269400 chr6A 521457786 521463154 5368 True 1889.1 5406 94.172 94 5205 4 chr6A.!!$R1 5111

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
147 149 0.039618 TCCCTTGTCCATTTGCCTCC 59.960 55.000 0.00 0.00 0.00 4.30 F
481 505 0.460284 AGGCCACTCGATTAACAGCG 60.460 55.000 5.01 0.00 0.00 5.18 F
1554 1774 0.108424 CTCCAAGCCAGAACCTCTCG 60.108 60.000 0.00 0.00 0.00 4.04 F
1927 2153 0.831711 TCTACTGTGCCACTGCCAGA 60.832 55.000 0.00 2.53 38.43 3.86 F
2274 2520 1.203052 GTAAGGCCGCAGTACTGTGTA 59.797 52.381 29.42 15.77 39.31 2.90 F
3795 4049 1.002033 CAGACTGCACTTGAGTTTGGC 60.002 52.381 0.00 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 1082 0.478507 GAGGAGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69 R
1823 2049 0.689623 AGAAGTGGTTGCTGGAGAGG 59.310 55.000 0.00 0.00 0.00 3.69 R
3525 3779 1.351076 TCTTGGGATCACACTGCTCA 58.649 50.000 0.00 0.00 0.00 4.26 R
3774 4028 2.292267 CCAAACTCAAGTGCAGTCTGT 58.708 47.619 0.93 0.00 0.00 3.41 R
4030 4288 0.036010 GATACTGGGTGCACAGCAGT 60.036 55.000 20.43 10.41 40.08 4.40 R
4869 5246 0.250901 ACAGGGCAACATCACTGACC 60.251 55.000 0.00 0.00 43.00 4.02 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
38 39 2.267642 GCCACTGGATGCGGTGTA 59.732 61.111 22.85 0.00 0.00 2.90
57 58 7.262772 CGGTGTATTTATCTTCCTTGTCACTA 58.737 38.462 0.00 0.00 0.00 2.74
89 90 9.442047 CTAGGGTTTATCTGCTATTTAATCTGG 57.558 37.037 0.00 0.00 0.00 3.86
90 91 7.816411 AGGGTTTATCTGCTATTTAATCTGGT 58.184 34.615 0.00 0.00 0.00 4.00
92 93 7.363431 GGTTTATCTGCTATTTAATCTGGTGC 58.637 38.462 0.00 0.00 0.00 5.01
101 102 7.340232 TGCTATTTAATCTGGTGCTTGATTCTT 59.660 33.333 0.00 0.00 35.01 2.52
145 147 1.632589 GTTCCCTTGTCCATTTGCCT 58.367 50.000 0.00 0.00 0.00 4.75
147 149 0.039618 TCCCTTGTCCATTTGCCTCC 59.960 55.000 0.00 0.00 0.00 4.30
148 150 1.315257 CCCTTGTCCATTTGCCTCCG 61.315 60.000 0.00 0.00 0.00 4.63
155 162 0.962356 CCATTTGCCTCCGCTTCAGT 60.962 55.000 0.00 0.00 35.36 3.41
437 460 6.726299 TCTCGGATGGGATCAATACTAATCTT 59.274 38.462 0.00 0.00 0.00 2.40
481 505 0.460284 AGGCCACTCGATTAACAGCG 60.460 55.000 5.01 0.00 0.00 5.18
503 527 4.098416 GCACTCTCACTGTTTTTCACAAC 58.902 43.478 0.00 0.00 33.87 3.32
506 530 6.238484 GCACTCTCACTGTTTTTCACAACTAT 60.238 38.462 0.00 0.00 33.87 2.12
507 531 7.042051 GCACTCTCACTGTTTTTCACAACTATA 60.042 37.037 0.00 0.00 33.87 1.31
508 532 8.491152 CACTCTCACTGTTTTTCACAACTATAG 58.509 37.037 0.00 0.00 33.87 1.31
509 533 8.204836 ACTCTCACTGTTTTTCACAACTATAGT 58.795 33.333 0.00 0.00 33.87 2.12
522 547 9.676861 TTCACAACTATAGTAGTACTAGCTTGA 57.323 33.333 20.71 12.89 38.26 3.02
590 615 8.506168 AAAAGGGTGGAAAAGAAGAATTTTTC 57.494 30.769 0.46 0.46 41.53 2.29
591 616 7.437713 AAGGGTGGAAAAGAAGAATTTTTCT 57.562 32.000 5.43 5.43 41.80 2.52
595 620 6.223852 GTGGAAAAGAAGAATTTTTCTCCCC 58.776 40.000 11.34 12.28 41.80 4.81
596 621 6.042093 GTGGAAAAGAAGAATTTTTCTCCCCT 59.958 38.462 11.34 0.00 41.80 4.79
612 641 1.075482 CCTCCTTTGCCTTGCTCCA 59.925 57.895 0.00 0.00 0.00 3.86
616 645 2.424956 CTCCTTTGCCTTGCTCCAATAC 59.575 50.000 0.00 0.00 0.00 1.89
726 763 2.796593 CTGCTTTTGTACCTTTGCTTGC 59.203 45.455 0.00 0.00 0.00 4.01
800 842 1.214062 GTGAGTGAGGTGAGAGGCG 59.786 63.158 0.00 0.00 0.00 5.52
801 843 1.979155 TGAGTGAGGTGAGAGGCGG 60.979 63.158 0.00 0.00 0.00 6.13
803 845 3.695606 GTGAGGTGAGAGGCGGCA 61.696 66.667 13.08 0.00 0.00 5.69
804 846 2.685017 TGAGGTGAGAGGCGGCAT 60.685 61.111 13.08 0.00 0.00 4.40
805 847 2.107953 GAGGTGAGAGGCGGCATC 59.892 66.667 13.08 6.52 0.00 3.91
808 850 3.474570 GTGAGAGGCGGCATCCCT 61.475 66.667 13.08 1.98 34.77 4.20
812 854 2.524394 GAGGCGGCATCCCTCCTA 60.524 66.667 13.08 0.00 46.38 2.94
1029 1081 4.486503 CCCCTGCTGCTGCTCCTC 62.487 72.222 17.00 0.00 40.48 3.71
1030 1082 4.486503 CCCTGCTGCTGCTCCTCC 62.487 72.222 17.00 0.00 40.48 4.30
1031 1083 3.400928 CCTGCTGCTGCTCCTCCT 61.401 66.667 17.00 0.00 40.48 3.69
1032 1084 2.187424 CTGCTGCTGCTCCTCCTC 59.813 66.667 17.00 0.00 40.48 3.71
1033 1085 3.388703 CTGCTGCTGCTCCTCCTCC 62.389 68.421 17.00 0.00 40.48 4.30
1034 1086 3.082701 GCTGCTGCTCCTCCTCCT 61.083 66.667 8.53 0.00 36.03 3.69
1035 1087 3.092780 GCTGCTGCTCCTCCTCCTC 62.093 68.421 8.53 0.00 36.03 3.71
1156 1211 5.104259 AGAGCCCTACTGGTTATTCTTTG 57.896 43.478 0.00 0.00 36.04 2.77
1158 1213 2.688446 GCCCTACTGGTTATTCTTTGGC 59.312 50.000 0.00 0.00 36.04 4.52
1172 1229 1.132262 CTTTGGCGTCTGTGTGTGTTT 59.868 47.619 0.00 0.00 0.00 2.83
1201 1365 3.267860 CTTGCATCGGAGCTCGCC 61.268 66.667 7.83 0.00 39.05 5.54
1202 1366 4.081185 TTGCATCGGAGCTCGCCA 62.081 61.111 7.83 0.00 39.05 5.69
1230 1426 6.687105 CCTTGTTTTGTTTGTACTCTTCTTCG 59.313 38.462 0.00 0.00 0.00 3.79
1254 1457 1.795170 TTTGTTCCTCTTGCGCTGGC 61.795 55.000 9.73 0.00 40.52 4.85
1404 1607 1.679311 GACCATGGTCACCTGCTCA 59.321 57.895 35.21 0.00 44.02 4.26
1450 1653 0.601558 AGTTTTCTGTCGCGGCTAGA 59.398 50.000 13.81 10.61 0.00 2.43
1457 1660 1.371881 GTCGCGGCTAGACTATGGC 60.372 63.158 1.90 0.00 35.84 4.40
1489 1706 6.268387 ACACACCAATCATTTCCTTTTGATCT 59.732 34.615 0.00 0.00 31.48 2.75
1506 1723 7.452880 TTTGATCTTAACCCTTTGTCATCTG 57.547 36.000 0.00 0.00 0.00 2.90
1507 1724 5.500234 TGATCTTAACCCTTTGTCATCTGG 58.500 41.667 0.00 0.00 0.00 3.86
1513 1733 1.815003 CCCTTTGTCATCTGGCTGTTC 59.185 52.381 0.00 0.00 0.00 3.18
1536 1756 4.077822 CAATTTGTTCTCTCAGGGAAGCT 58.922 43.478 0.00 0.00 0.00 3.74
1554 1774 0.108424 CTCCAAGCCAGAACCTCTCG 60.108 60.000 0.00 0.00 0.00 4.04
1613 1833 5.492895 TCTCGAGATAGTGTGAGTTTCTCT 58.507 41.667 12.08 0.00 32.50 3.10
1682 1906 5.514274 TTTCTTTTGAGAACACATGGGAC 57.486 39.130 0.00 0.00 0.00 4.46
1823 2049 0.992802 CGAAGCTTAGGACGCTTGAC 59.007 55.000 0.00 0.00 46.85 3.18
1927 2153 0.831711 TCTACTGTGCCACTGCCAGA 60.832 55.000 0.00 2.53 38.43 3.86
2159 2392 3.142951 TGTTATGTGGTTGTGTACTGCC 58.857 45.455 0.00 0.00 0.00 4.85
2274 2520 1.203052 GTAAGGCCGCAGTACTGTGTA 59.797 52.381 29.42 15.77 39.31 2.90
2278 2524 1.396996 GGCCGCAGTACTGTGTAATTG 59.603 52.381 29.42 17.50 39.31 2.32
2331 2577 7.500227 CAGTGGAGACATGTTCACCATAAATAT 59.500 37.037 17.82 1.63 45.64 1.28
2525 2772 9.289782 GATTAATTTCTACCCTGCACTGATATT 57.710 33.333 0.00 0.00 0.00 1.28
2656 2905 3.978718 GCATCAGCATCCTTTTCCTAC 57.021 47.619 0.00 0.00 41.58 3.18
2688 2937 1.833630 CTGTTCTGGTGGAGGCATAGA 59.166 52.381 0.00 0.00 0.00 1.98
2735 2984 7.462856 CGATGTCGATGGTAAGTAAAAAGTCTG 60.463 40.741 0.00 0.00 43.02 3.51
2990 3240 2.233431 AGTAGCAGTCAAGAGGCTGAAG 59.767 50.000 0.62 0.00 38.55 3.02
3367 3620 7.412853 AGATTTGCATTCGATTCTCACATTAC 58.587 34.615 0.00 0.00 0.00 1.89
3525 3779 3.551635 AGAGGCCTACTATACCTGCAT 57.448 47.619 4.42 0.00 32.67 3.96
3774 4028 1.751351 CTGCTAGAACTGATCACCGGA 59.249 52.381 9.46 0.00 0.00 5.14
3795 4049 1.002033 CAGACTGCACTTGAGTTTGGC 60.002 52.381 0.00 0.00 0.00 4.52
3836 4090 1.075374 AGCCATGCTTGACTGGGTAAA 59.925 47.619 0.22 0.00 41.30 2.01
3837 4091 2.102578 GCCATGCTTGACTGGGTAAAT 58.897 47.619 0.22 0.00 32.90 1.40
3905 4163 8.791675 TGATCTCATCATACATGAGTCTTACTC 58.208 37.037 0.00 0.01 44.30 2.59
3921 4179 2.814805 ACTCATATGGCACTGGCTTT 57.185 45.000 2.13 0.00 40.87 3.51
3931 4189 2.164422 GGCACTGGCTTTTATTCAGGTC 59.836 50.000 0.00 0.00 40.87 3.85
4054 4312 0.252696 TGTGCACCCAGTATCTCCCT 60.253 55.000 15.69 0.00 0.00 4.20
4525 4785 6.633500 TTTGAGATGTAAGTTTTGGTCCTG 57.367 37.500 0.00 0.00 0.00 3.86
4540 4800 1.961394 GTCCTGTTTCCCCCTTTTGTC 59.039 52.381 0.00 0.00 0.00 3.18
4541 4801 1.856920 TCCTGTTTCCCCCTTTTGTCT 59.143 47.619 0.00 0.00 0.00 3.41
4542 4802 2.246327 TCCTGTTTCCCCCTTTTGTCTT 59.754 45.455 0.00 0.00 0.00 3.01
4543 4803 2.628178 CCTGTTTCCCCCTTTTGTCTTC 59.372 50.000 0.00 0.00 0.00 2.87
4545 4805 3.562182 TGTTTCCCCCTTTTGTCTTCTC 58.438 45.455 0.00 0.00 0.00 2.87
4546 4806 3.204382 TGTTTCCCCCTTTTGTCTTCTCT 59.796 43.478 0.00 0.00 0.00 3.10
4547 4807 3.508845 TTCCCCCTTTTGTCTTCTCTG 57.491 47.619 0.00 0.00 0.00 3.35
4548 4808 1.073923 TCCCCCTTTTGTCTTCTCTGC 59.926 52.381 0.00 0.00 0.00 4.26
4549 4809 1.539157 CCCCTTTTGTCTTCTCTGCC 58.461 55.000 0.00 0.00 0.00 4.85
4550 4810 1.074566 CCCCTTTTGTCTTCTCTGCCT 59.925 52.381 0.00 0.00 0.00 4.75
4551 4811 2.489802 CCCCTTTTGTCTTCTCTGCCTT 60.490 50.000 0.00 0.00 0.00 4.35
4552 4812 2.816672 CCCTTTTGTCTTCTCTGCCTTC 59.183 50.000 0.00 0.00 0.00 3.46
4553 4813 3.480470 CCTTTTGTCTTCTCTGCCTTCA 58.520 45.455 0.00 0.00 0.00 3.02
4554 4814 3.251972 CCTTTTGTCTTCTCTGCCTTCAC 59.748 47.826 0.00 0.00 0.00 3.18
4555 4815 3.845781 TTTGTCTTCTCTGCCTTCACT 57.154 42.857 0.00 0.00 0.00 3.41
4556 4816 4.955811 TTTGTCTTCTCTGCCTTCACTA 57.044 40.909 0.00 0.00 0.00 2.74
4557 4817 5.489792 TTTGTCTTCTCTGCCTTCACTAT 57.510 39.130 0.00 0.00 0.00 2.12
4558 4818 5.489792 TTGTCTTCTCTGCCTTCACTATT 57.510 39.130 0.00 0.00 0.00 1.73
4559 4819 5.489792 TGTCTTCTCTGCCTTCACTATTT 57.510 39.130 0.00 0.00 0.00 1.40
4560 4820 5.869579 TGTCTTCTCTGCCTTCACTATTTT 58.130 37.500 0.00 0.00 0.00 1.82
4561 4821 6.299141 TGTCTTCTCTGCCTTCACTATTTTT 58.701 36.000 0.00 0.00 0.00 1.94
4562 4822 7.450074 TGTCTTCTCTGCCTTCACTATTTTTA 58.550 34.615 0.00 0.00 0.00 1.52
4563 4823 7.604164 TGTCTTCTCTGCCTTCACTATTTTTAG 59.396 37.037 0.00 0.00 0.00 1.85
4564 4824 7.604545 GTCTTCTCTGCCTTCACTATTTTTAGT 59.395 37.037 0.00 0.00 0.00 2.24
4565 4825 8.157476 TCTTCTCTGCCTTCACTATTTTTAGTT 58.843 33.333 0.00 0.00 0.00 2.24
4566 4826 8.691661 TTCTCTGCCTTCACTATTTTTAGTTT 57.308 30.769 0.00 0.00 0.00 2.66
4567 4827 8.099364 TCTCTGCCTTCACTATTTTTAGTTTG 57.901 34.615 0.00 0.00 0.00 2.93
4568 4828 7.719633 TCTCTGCCTTCACTATTTTTAGTTTGT 59.280 33.333 0.00 0.00 0.00 2.83
4593 4853 0.823356 ATTGCAACGACCTGGCAGTT 60.823 50.000 14.43 0.00 38.97 3.16
4609 4869 4.159321 TGGCAGTTTCATGTTGTCTTCAAA 59.841 37.500 0.00 0.00 35.20 2.69
4624 4884 5.108517 GTCTTCAAACTGATAGAGCTCCAG 58.891 45.833 10.93 13.23 0.00 3.86
4694 5071 7.552687 TCTTTGTCAAGAAAGTAGTGAACATGT 59.447 33.333 0.00 0.00 35.99 3.21
4712 5089 6.832520 ACATGTTATGTGCATTTCCAACTA 57.167 33.333 0.00 0.00 43.01 2.24
4759 5136 6.759356 TGATGGCAAAGATCTGCATTAATTTG 59.241 34.615 8.97 9.15 44.52 2.32
4811 5188 3.124976 GCAGCAAACAAAAGAACAAGCAA 59.875 39.130 0.00 0.00 0.00 3.91
4827 5204 1.406539 AGCAAGAAACAACCACAGCAG 59.593 47.619 0.00 0.00 0.00 4.24
4835 5212 2.880443 ACAACCACAGCAGATGGAATT 58.120 42.857 7.81 0.00 39.87 2.17
4845 5222 2.292845 GCAGATGGAATTAGGCTCTTGC 59.707 50.000 0.00 0.00 38.76 4.01
4847 5224 1.265365 GATGGAATTAGGCTCTTGCGC 59.735 52.381 0.00 0.00 40.82 6.09
4849 5226 1.010685 GAATTAGGCTCTTGCGCGC 60.011 57.895 27.26 27.26 40.82 6.86
4868 5245 2.414559 CGCTTTTATGTTCCACCAGCAG 60.415 50.000 0.00 0.00 0.00 4.24
4869 5246 2.094545 GCTTTTATGTTCCACCAGCAGG 60.095 50.000 0.00 0.00 42.21 4.85
4890 5267 1.537202 GTCAGTGATGTTGCCCTGTTC 59.463 52.381 0.00 0.00 0.00 3.18
4926 5303 1.446907 CACAGAGTCAACCCAGCATC 58.553 55.000 0.00 0.00 0.00 3.91
4959 5336 0.173481 TCGCTCAGCCACTGTATGAC 59.827 55.000 0.00 0.00 32.61 3.06
4976 5353 1.589716 GACAGTGCAGGAATGTGGCC 61.590 60.000 0.00 0.00 0.00 5.36
5157 5538 1.517242 GGTCACTTTCAGACAGGCAG 58.483 55.000 0.00 0.00 37.74 4.85
5166 5547 0.319728 CAGACAGGCAGTGTAGTGCT 59.680 55.000 11.13 0.00 43.45 4.40
5170 5551 0.033920 CAGGCAGTGTAGTGCTGTCA 59.966 55.000 11.13 0.00 43.45 3.58
5208 5589 3.998672 GACACGCTCCACCCGGAA 61.999 66.667 0.73 0.00 42.21 4.30
5209 5590 4.309950 ACACGCTCCACCCGGAAC 62.310 66.667 0.73 0.00 42.21 3.62
5210 5591 4.003788 CACGCTCCACCCGGAACT 62.004 66.667 0.73 0.00 42.21 3.01
5211 5592 4.003788 ACGCTCCACCCGGAACTG 62.004 66.667 0.73 0.00 42.21 3.16
5212 5593 4.760047 CGCTCCACCCGGAACTGG 62.760 72.222 0.73 4.51 42.21 4.00
5213 5594 3.319198 GCTCCACCCGGAACTGGA 61.319 66.667 0.73 9.25 42.21 3.86
5214 5595 2.670148 GCTCCACCCGGAACTGGAT 61.670 63.158 0.73 0.00 42.21 3.41
5215 5596 1.522569 CTCCACCCGGAACTGGATC 59.477 63.158 0.73 0.00 42.21 3.36
5216 5597 1.972660 CTCCACCCGGAACTGGATCC 61.973 65.000 0.73 4.20 42.21 3.36
5217 5598 1.995626 CCACCCGGAACTGGATCCT 60.996 63.158 14.23 0.00 37.34 3.24
5218 5599 1.522569 CACCCGGAACTGGATCCTC 59.477 63.158 14.23 1.71 37.34 3.71
5219 5600 1.080354 ACCCGGAACTGGATCCTCA 59.920 57.895 14.23 0.00 37.34 3.86
5220 5601 0.546747 ACCCGGAACTGGATCCTCAA 60.547 55.000 14.23 0.00 37.34 3.02
5221 5602 0.618458 CCCGGAACTGGATCCTCAAA 59.382 55.000 14.23 0.00 37.34 2.69
5222 5603 1.679032 CCCGGAACTGGATCCTCAAAC 60.679 57.143 14.23 0.00 37.34 2.93
5223 5604 1.003118 CCGGAACTGGATCCTCAAACA 59.997 52.381 14.23 0.00 37.34 2.83
5224 5605 2.356125 CCGGAACTGGATCCTCAAACAT 60.356 50.000 14.23 0.00 37.34 2.71
5225 5606 3.118408 CCGGAACTGGATCCTCAAACATA 60.118 47.826 14.23 0.00 37.34 2.29
5226 5607 4.122776 CGGAACTGGATCCTCAAACATAG 58.877 47.826 14.23 1.33 37.34 2.23
5227 5608 4.141937 CGGAACTGGATCCTCAAACATAGA 60.142 45.833 14.23 0.00 37.34 1.98
5228 5609 5.363939 GGAACTGGATCCTCAAACATAGAG 58.636 45.833 14.23 0.00 36.50 2.43
5229 5610 5.129485 GGAACTGGATCCTCAAACATAGAGA 59.871 44.000 14.23 0.00 36.50 3.10
5230 5611 6.352222 GGAACTGGATCCTCAAACATAGAGAA 60.352 42.308 14.23 0.00 36.50 2.87
5231 5612 6.232581 ACTGGATCCTCAAACATAGAGAAG 57.767 41.667 14.23 0.00 35.09 2.85
5232 5613 5.028549 TGGATCCTCAAACATAGAGAAGC 57.971 43.478 14.23 0.00 35.09 3.86
5233 5614 4.718774 TGGATCCTCAAACATAGAGAAGCT 59.281 41.667 14.23 0.00 35.09 3.74
5234 5615 5.899547 TGGATCCTCAAACATAGAGAAGCTA 59.100 40.000 14.23 0.00 35.09 3.32
5235 5616 6.183360 TGGATCCTCAAACATAGAGAAGCTAC 60.183 42.308 14.23 0.00 35.09 3.58
5236 5617 6.183360 GGATCCTCAAACATAGAGAAGCTACA 60.183 42.308 3.84 0.00 35.09 2.74
5237 5618 6.214191 TCCTCAAACATAGAGAAGCTACAG 57.786 41.667 0.00 0.00 35.09 2.74
5238 5619 5.717178 TCCTCAAACATAGAGAAGCTACAGT 59.283 40.000 0.00 0.00 35.09 3.55
5239 5620 6.890268 TCCTCAAACATAGAGAAGCTACAGTA 59.110 38.462 0.00 0.00 35.09 2.74
5240 5621 6.975772 CCTCAAACATAGAGAAGCTACAGTAC 59.024 42.308 0.00 0.00 35.09 2.73
5241 5622 6.864342 TCAAACATAGAGAAGCTACAGTACC 58.136 40.000 0.00 0.00 0.00 3.34
5242 5623 5.855740 AACATAGAGAAGCTACAGTACCC 57.144 43.478 0.00 0.00 0.00 3.69
5243 5624 5.132043 ACATAGAGAAGCTACAGTACCCT 57.868 43.478 0.00 0.00 0.00 4.34
5244 5625 6.263412 ACATAGAGAAGCTACAGTACCCTA 57.737 41.667 0.00 0.00 0.00 3.53
5245 5626 6.670617 ACATAGAGAAGCTACAGTACCCTAA 58.329 40.000 0.00 0.00 0.00 2.69
5246 5627 6.546772 ACATAGAGAAGCTACAGTACCCTAAC 59.453 42.308 0.00 0.00 0.00 2.34
5247 5628 5.195848 AGAGAAGCTACAGTACCCTAACT 57.804 43.478 0.00 0.00 0.00 2.24
5248 5629 5.581975 AGAGAAGCTACAGTACCCTAACTT 58.418 41.667 0.00 0.00 0.00 2.66
5249 5630 6.017830 AGAGAAGCTACAGTACCCTAACTTT 58.982 40.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.795889 GCTGTCGTCTACTGTAGCAGC 60.796 57.143 21.17 21.17 40.48 5.25
5 6 0.956902 TGGCGCTGTCGTCTACTGTA 60.957 55.000 7.64 0.00 41.64 2.74
12 13 3.649277 ATCCAGTGGCGCTGTCGTC 62.649 63.158 25.05 0.00 43.55 4.20
30 31 4.839121 ACAAGGAAGATAAATACACCGCA 58.161 39.130 0.00 0.00 0.00 5.69
33 34 7.711339 CCTAGTGACAAGGAAGATAAATACACC 59.289 40.741 0.00 0.00 36.08 4.16
34 35 8.475639 TCCTAGTGACAAGGAAGATAAATACAC 58.524 37.037 0.00 0.00 40.23 2.90
38 39 9.440761 AGTATCCTAGTGACAAGGAAGATAAAT 57.559 33.333 0.00 0.00 46.06 1.40
57 58 8.743636 AAATAGCAGATAAACCCTAGTATCCT 57.256 34.615 0.00 0.00 0.00 3.24
63 64 9.442047 CCAGATTAAATAGCAGATAAACCCTAG 57.558 37.037 0.00 0.00 0.00 3.02
64 65 8.945193 ACCAGATTAAATAGCAGATAAACCCTA 58.055 33.333 0.00 0.00 0.00 3.53
66 67 7.522236 GCACCAGATTAAATAGCAGATAAACCC 60.522 40.741 0.00 0.00 0.00 4.11
67 68 7.229506 AGCACCAGATTAAATAGCAGATAAACC 59.770 37.037 0.00 0.00 0.00 3.27
68 69 8.159344 AGCACCAGATTAAATAGCAGATAAAC 57.841 34.615 0.00 0.00 0.00 2.01
69 70 8.623903 CAAGCACCAGATTAAATAGCAGATAAA 58.376 33.333 0.00 0.00 0.00 1.40
70 71 7.992608 TCAAGCACCAGATTAAATAGCAGATAA 59.007 33.333 0.00 0.00 0.00 1.75
72 73 6.359804 TCAAGCACCAGATTAAATAGCAGAT 58.640 36.000 0.00 0.00 0.00 2.90
74 75 6.630444 ATCAAGCACCAGATTAAATAGCAG 57.370 37.500 0.00 0.00 0.00 4.24
75 76 6.830324 AGAATCAAGCACCAGATTAAATAGCA 59.170 34.615 0.00 0.00 34.79 3.49
76 77 7.269477 AGAATCAAGCACCAGATTAAATAGC 57.731 36.000 0.00 0.00 34.79 2.97
80 81 7.148018 GGATGAAGAATCAAGCACCAGATTAAA 60.148 37.037 0.00 0.00 39.49 1.52
82 83 5.824624 GGATGAAGAATCAAGCACCAGATTA 59.175 40.000 0.00 0.00 39.49 1.75
83 84 4.643784 GGATGAAGAATCAAGCACCAGATT 59.356 41.667 0.00 0.00 39.49 2.40
84 85 4.205587 GGATGAAGAATCAAGCACCAGAT 58.794 43.478 0.00 0.00 39.49 2.90
85 86 3.614092 GGATGAAGAATCAAGCACCAGA 58.386 45.455 0.00 0.00 39.49 3.86
86 87 2.353889 CGGATGAAGAATCAAGCACCAG 59.646 50.000 0.00 0.00 39.49 4.00
87 88 2.290260 ACGGATGAAGAATCAAGCACCA 60.290 45.455 0.00 0.00 39.49 4.17
88 89 2.359900 ACGGATGAAGAATCAAGCACC 58.640 47.619 0.00 0.00 39.49 5.01
89 90 5.505286 CATTACGGATGAAGAATCAAGCAC 58.495 41.667 0.00 0.00 39.49 4.40
90 91 4.035558 GCATTACGGATGAAGAATCAAGCA 59.964 41.667 5.36 0.00 39.49 3.91
92 93 5.739752 TGCATTACGGATGAAGAATCAAG 57.260 39.130 5.36 0.00 39.49 3.02
101 102 2.560504 GTCACCATGCATTACGGATGA 58.439 47.619 8.47 5.85 45.87 2.92
145 147 4.069232 CGGCCTGACTGAAGCGGA 62.069 66.667 0.00 0.00 0.00 5.54
437 460 4.906060 GGCTAATCCTACCCTAAAAGGAGA 59.094 45.833 0.00 0.00 44.92 3.71
481 505 4.098416 GTTGTGAAAAACAGTGAGAGTGC 58.902 43.478 0.00 0.00 40.74 4.40
506 530 8.295288 GTGTGAAAACTCAAGCTAGTACTACTA 58.705 37.037 0.00 0.00 0.00 1.82
507 531 7.146648 GTGTGAAAACTCAAGCTAGTACTACT 58.853 38.462 0.00 0.00 0.00 2.57
508 532 6.921857 TGTGTGAAAACTCAAGCTAGTACTAC 59.078 38.462 0.00 0.00 0.00 2.73
509 533 7.046292 TGTGTGAAAACTCAAGCTAGTACTA 57.954 36.000 1.89 1.89 0.00 1.82
522 547 0.032615 TTGGGGCCTGTGTGAAAACT 60.033 50.000 0.84 0.00 0.00 2.66
589 614 2.078452 CAAGGCAAAGGAGGGGAGA 58.922 57.895 0.00 0.00 0.00 3.71
590 615 1.680314 GCAAGGCAAAGGAGGGGAG 60.680 63.158 0.00 0.00 0.00 4.30
591 616 2.142292 GAGCAAGGCAAAGGAGGGGA 62.142 60.000 0.00 0.00 0.00 4.81
595 620 1.553706 ATTGGAGCAAGGCAAAGGAG 58.446 50.000 0.00 0.00 0.00 3.69
596 621 2.041620 AGTATTGGAGCAAGGCAAAGGA 59.958 45.455 0.00 0.00 0.00 3.36
612 641 6.153924 AGAATATTGGAGGGACCTCAGTATT 58.846 40.000 19.30 17.14 44.40 1.89
616 645 5.151454 AGTAGAATATTGGAGGGACCTCAG 58.849 45.833 19.30 0.00 44.40 3.35
672 705 4.704833 GACTTGCCTGCCGCCTGA 62.705 66.667 0.00 0.00 36.24 3.86
686 719 4.423209 GGAGGGAGGGGGCAGACT 62.423 72.222 0.00 0.00 0.00 3.24
800 842 2.823758 GCAGGGTAGGAGGGATGCC 61.824 68.421 0.00 0.00 0.00 4.40
801 843 2.823758 GGCAGGGTAGGAGGGATGC 61.824 68.421 0.00 0.00 0.00 3.91
803 845 2.290745 GGGCAGGGTAGGAGGGAT 59.709 66.667 0.00 0.00 0.00 3.85
804 846 3.289211 TGGGCAGGGTAGGAGGGA 61.289 66.667 0.00 0.00 0.00 4.20
805 847 3.090532 GTGGGCAGGGTAGGAGGG 61.091 72.222 0.00 0.00 0.00 4.30
808 850 3.009115 GCAGTGGGCAGGGTAGGA 61.009 66.667 0.00 0.00 43.97 2.94
918 970 2.362077 GTGTTCAAACATGGAAGCAGGT 59.638 45.455 0.00 0.00 41.59 4.00
1029 1081 0.998945 AGGAGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
1030 1082 0.478507 GAGGAGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
1031 1083 0.996762 GGAGGAGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1032 1084 1.541672 GGAGGAGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1033 1085 1.541672 GGGAGGAGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1034 1086 2.015726 GGGGAGGAGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1035 1087 2.018086 AGGGGAGGAGAGGAGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
1156 1211 1.014352 AGAAAACACACACAGACGCC 58.986 50.000 0.00 0.00 0.00 5.68
1158 1213 3.119990 ACCAAAGAAAACACACACAGACG 60.120 43.478 0.00 0.00 0.00 4.18
1172 1229 3.634448 TCCGATGCAAGAAAACCAAAGAA 59.366 39.130 0.00 0.00 0.00 2.52
1201 1365 5.949735 AGAGTACAAACAAAACAAGGTGTG 58.050 37.500 0.00 0.00 0.00 3.82
1202 1366 6.433093 AGAAGAGTACAAACAAAACAAGGTGT 59.567 34.615 0.00 0.00 0.00 4.16
1230 1426 1.852280 GCGCAAGAGGAACAAACAAAC 59.148 47.619 0.30 0.00 43.02 2.93
1450 1653 1.210478 GGTGTGTGATGGAGCCATAGT 59.790 52.381 1.21 0.00 36.70 2.12
1457 1660 4.142315 GGAAATGATTGGTGTGTGATGGAG 60.142 45.833 0.00 0.00 0.00 3.86
1489 1706 3.181434 ACAGCCAGATGACAAAGGGTTAA 60.181 43.478 0.00 0.00 0.00 2.01
1506 1723 3.569701 TGAGAGAACAAATTGGAACAGCC 59.430 43.478 0.00 0.00 42.39 4.85
1507 1724 4.320788 CCTGAGAGAACAAATTGGAACAGC 60.321 45.833 0.00 0.00 42.39 4.40
1513 1733 3.192212 GCTTCCCTGAGAGAACAAATTGG 59.808 47.826 0.00 0.00 0.00 3.16
1536 1756 1.975327 CGAGAGGTTCTGGCTTGGA 59.025 57.895 0.00 0.00 0.00 3.53
1613 1833 1.849977 TGCAAGGCTAATGATGGCAA 58.150 45.000 0.00 0.00 34.13 4.52
1682 1906 4.766891 TCTTCCAGCCCAAAAGAAACATAG 59.233 41.667 0.00 0.00 0.00 2.23
1823 2049 0.689623 AGAAGTGGTTGCTGGAGAGG 59.310 55.000 0.00 0.00 0.00 3.69
2159 2392 0.900421 TCCATCTGACAGTGAGCAGG 59.100 55.000 14.61 4.03 33.05 4.85
2331 2577 7.398618 TCAATTAATTTCCCATAAGCTCAACCA 59.601 33.333 0.00 0.00 0.00 3.67
2333 2579 9.822185 AATCAATTAATTTCCCATAAGCTCAAC 57.178 29.630 0.00 0.00 0.00 3.18
2656 2905 2.009774 CCAGAACAGCAATCCCGTAAG 58.990 52.381 0.00 0.00 0.00 2.34
2735 2984 6.073548 CCATTATGAGCTCGGTGAGTAATTTC 60.074 42.308 9.64 0.00 31.39 2.17
2990 3240 3.122850 CCTGCGGCATTTCCATCC 58.877 61.111 1.75 0.00 34.01 3.51
3367 3620 3.317430 GCTATGCCCAAAGGAGAAGAATG 59.683 47.826 0.00 0.00 33.47 2.67
3525 3779 1.351076 TCTTGGGATCACACTGCTCA 58.649 50.000 0.00 0.00 0.00 4.26
3774 4028 2.292267 CCAAACTCAAGTGCAGTCTGT 58.708 47.619 0.93 0.00 0.00 3.41
3795 4049 4.096081 GCTCCCTTCTGATTTGATGACTTG 59.904 45.833 0.00 0.00 0.00 3.16
3836 4090 6.148315 CGTGCCATATGAGTATGACAATGAAT 59.852 38.462 3.65 0.00 40.12 2.57
3837 4091 5.466393 CGTGCCATATGAGTATGACAATGAA 59.534 40.000 3.65 0.00 40.12 2.57
3861 4118 2.722094 TCATATGCCTGAAACCACACC 58.278 47.619 0.00 0.00 0.00 4.16
3905 4163 5.508489 CCTGAATAAAAGCCAGTGCCATATG 60.508 44.000 0.00 0.00 38.69 1.78
3914 4172 5.707298 TCTTCTTGACCTGAATAAAAGCCAG 59.293 40.000 0.00 0.00 0.00 4.85
3921 4179 4.943705 GGTGCATCTTCTTGACCTGAATAA 59.056 41.667 0.00 0.00 0.00 1.40
3931 4189 2.775911 TCTCCTGGTGCATCTTCTTG 57.224 50.000 0.00 0.00 0.00 3.02
4030 4288 0.036010 GATACTGGGTGCACAGCAGT 60.036 55.000 20.43 10.41 40.08 4.40
4054 4312 1.555075 GACATCTTAGGCCTGTGACCA 59.445 52.381 17.99 0.00 0.00 4.02
4467 4727 6.371548 TCTGTCATCTTTATTGTACCAACAGC 59.628 38.462 0.00 0.00 36.83 4.40
4511 4771 3.568443 GGGGAAACAGGACCAAAACTTA 58.432 45.455 0.00 0.00 0.00 2.24
4525 4785 3.570125 CAGAGAAGACAAAAGGGGGAAAC 59.430 47.826 0.00 0.00 0.00 2.78
4540 4800 7.913674 ACTAAAAATAGTGAAGGCAGAGAAG 57.086 36.000 0.00 0.00 0.00 2.85
4541 4801 8.567948 CAAACTAAAAATAGTGAAGGCAGAGAA 58.432 33.333 0.00 0.00 0.00 2.87
4542 4802 7.719633 ACAAACTAAAAATAGTGAAGGCAGAGA 59.280 33.333 0.00 0.00 0.00 3.10
4543 4803 7.875971 ACAAACTAAAAATAGTGAAGGCAGAG 58.124 34.615 0.00 0.00 0.00 3.35
4546 4806 9.906660 CAATACAAACTAAAAATAGTGAAGGCA 57.093 29.630 0.00 0.00 0.00 4.75
4547 4807 9.353999 CCAATACAAACTAAAAATAGTGAAGGC 57.646 33.333 0.00 0.00 0.00 4.35
4556 4816 8.707839 CGTTGCAATCCAATACAAACTAAAAAT 58.292 29.630 0.59 0.00 35.55 1.82
4557 4817 7.921214 TCGTTGCAATCCAATACAAACTAAAAA 59.079 29.630 0.59 0.00 35.55 1.94
4558 4818 7.380065 GTCGTTGCAATCCAATACAAACTAAAA 59.620 33.333 0.59 0.00 35.55 1.52
4559 4819 6.858993 GTCGTTGCAATCCAATACAAACTAAA 59.141 34.615 0.59 0.00 35.55 1.85
4560 4820 6.375377 GTCGTTGCAATCCAATACAAACTAA 58.625 36.000 0.59 0.00 35.55 2.24
4561 4821 5.106475 GGTCGTTGCAATCCAATACAAACTA 60.106 40.000 0.59 0.00 35.55 2.24
4562 4822 4.320935 GGTCGTTGCAATCCAATACAAACT 60.321 41.667 0.59 0.00 35.55 2.66
4563 4823 3.917985 GGTCGTTGCAATCCAATACAAAC 59.082 43.478 0.59 0.00 35.55 2.93
4564 4824 3.823873 AGGTCGTTGCAATCCAATACAAA 59.176 39.130 0.59 0.00 35.55 2.83
4565 4825 3.190327 CAGGTCGTTGCAATCCAATACAA 59.810 43.478 0.59 0.00 35.55 2.41
4566 4826 2.746904 CAGGTCGTTGCAATCCAATACA 59.253 45.455 0.59 0.00 35.55 2.29
4567 4827 2.097466 CCAGGTCGTTGCAATCCAATAC 59.903 50.000 0.59 0.00 35.55 1.89
4568 4828 2.364632 CCAGGTCGTTGCAATCCAATA 58.635 47.619 0.59 0.00 35.55 1.90
4593 4853 7.095060 GCTCTATCAGTTTGAAGACAACATGAA 60.095 37.037 0.00 0.00 35.68 2.57
4609 4869 3.951563 AGAGTCTGGAGCTCTATCAGT 57.048 47.619 14.64 0.00 41.10 3.41
4712 5089 7.218228 TCAAGTTATGATGTCAGTTGCATTT 57.782 32.000 0.00 0.00 31.50 2.32
4759 5136 7.840342 TTGATGCAGATCTTCTTTTCTAGAC 57.160 36.000 0.00 0.00 30.90 2.59
4811 5188 2.158623 TCCATCTGCTGTGGTTGTTTCT 60.159 45.455 10.43 0.00 37.96 2.52
4827 5204 1.265365 GCGCAAGAGCCTAATTCCATC 59.735 52.381 0.30 0.00 43.02 3.51
4845 5222 0.519519 TGGTGGAACATAAAAGCGCG 59.480 50.000 0.00 0.00 44.52 6.86
4847 5224 1.539388 TGCTGGTGGAACATAAAAGCG 59.461 47.619 0.00 0.00 44.52 4.68
4849 5226 2.493278 CCCTGCTGGTGGAACATAAAAG 59.507 50.000 9.00 0.00 44.52 2.27
4868 5245 0.962356 CAGGGCAACATCACTGACCC 60.962 60.000 0.00 0.00 43.82 4.46
4869 5246 0.250901 ACAGGGCAACATCACTGACC 60.251 55.000 0.00 0.00 43.00 4.02
4890 5267 4.191544 TCTGTGGAGTTTGTCAAGAAGTG 58.808 43.478 0.00 0.00 0.00 3.16
4926 5303 1.068588 TGAGCGAGGAAATATGGTCCG 59.931 52.381 0.00 0.00 40.36 4.79
4959 5336 2.345760 GGGCCACATTCCTGCACTG 61.346 63.158 4.39 0.00 0.00 3.66
4976 5353 2.365582 ACTAAAATAGCTTGCACCCGG 58.634 47.619 0.00 0.00 0.00 5.73
5093 5470 2.251642 GCTATTTAGCCGTGCCCCG 61.252 63.158 0.00 0.00 43.39 5.73
5157 5538 2.678324 GTCCTTCTGACAGCACTACAC 58.322 52.381 0.00 0.00 43.85 2.90
5170 5551 0.605589 CCTGCTCGTTCTGTCCTTCT 59.394 55.000 0.00 0.00 0.00 2.85
5205 5586 5.129485 TCTCTATGTTTGAGGATCCAGTTCC 59.871 44.000 15.82 0.00 35.90 3.62
5207 5588 6.627087 TTCTCTATGTTTGAGGATCCAGTT 57.373 37.500 15.82 0.00 32.78 3.16
5208 5589 5.396213 GCTTCTCTATGTTTGAGGATCCAGT 60.396 44.000 15.82 0.00 32.78 4.00
5209 5590 5.055812 GCTTCTCTATGTTTGAGGATCCAG 58.944 45.833 15.82 0.00 32.78 3.86
5210 5591 4.718774 AGCTTCTCTATGTTTGAGGATCCA 59.281 41.667 15.82 0.00 32.78 3.41
5211 5592 5.289083 AGCTTCTCTATGTTTGAGGATCC 57.711 43.478 2.48 2.48 32.78 3.36
5212 5593 6.810911 TGTAGCTTCTCTATGTTTGAGGATC 58.189 40.000 0.00 0.00 32.78 3.36
5213 5594 6.382570 ACTGTAGCTTCTCTATGTTTGAGGAT 59.617 38.462 0.00 0.00 32.78 3.24
5214 5595 5.717178 ACTGTAGCTTCTCTATGTTTGAGGA 59.283 40.000 0.00 0.00 32.78 3.71
5215 5596 5.971763 ACTGTAGCTTCTCTATGTTTGAGG 58.028 41.667 0.00 0.00 32.78 3.86
5216 5597 6.975772 GGTACTGTAGCTTCTCTATGTTTGAG 59.024 42.308 9.64 0.00 0.00 3.02
5217 5598 6.127423 GGGTACTGTAGCTTCTCTATGTTTGA 60.127 42.308 15.74 0.00 0.00 2.69
5218 5599 6.043411 GGGTACTGTAGCTTCTCTATGTTTG 58.957 44.000 15.74 0.00 0.00 2.93
5219 5600 5.958987 AGGGTACTGTAGCTTCTCTATGTTT 59.041 40.000 15.74 0.00 0.00 2.83
5220 5601 5.520751 AGGGTACTGTAGCTTCTCTATGTT 58.479 41.667 15.74 0.00 0.00 2.71
5221 5602 5.132043 AGGGTACTGTAGCTTCTCTATGT 57.868 43.478 15.74 0.00 0.00 2.29
5222 5603 6.773685 AGTTAGGGTACTGTAGCTTCTCTATG 59.226 42.308 15.74 0.00 0.00 2.23
5223 5604 6.913545 AGTTAGGGTACTGTAGCTTCTCTAT 58.086 40.000 15.74 0.00 0.00 1.98
5224 5605 6.324601 AGTTAGGGTACTGTAGCTTCTCTA 57.675 41.667 15.74 6.77 0.00 2.43
5225 5606 5.195848 AGTTAGGGTACTGTAGCTTCTCT 57.804 43.478 15.74 7.64 0.00 3.10
5226 5607 5.918426 AAGTTAGGGTACTGTAGCTTCTC 57.082 43.478 15.74 6.27 0.00 2.87


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

AutoCloner maintained by Alex Coulton.