Multiple sequence alignment - TraesCS6D01G214800

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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 TraesCS6D01G214800 chr6D 100.000 4778 0 0 1 4778 305183014 305178237 0.000000e+00 8824.0
1 TraesCS6D01G214800 chr6D 78.100 758 127 20 4016 4753 194208181 194208919 1.220000e-120 444.0
2 TraesCS6D01G214800 chr6A 89.477 4875 288 91 1 4762 409410593 409415355 0.000000e+00 5952.0
3 TraesCS6D01G214800 chr6B 94.089 3079 131 26 736 3797 471628038 471631082 0.000000e+00 4630.0
4 TraesCS6D01G214800 chr6B 90.107 657 53 11 4015 4663 471638071 471638723 0.000000e+00 843.0
5 TraesCS6D01G214800 chr6B 88.961 308 24 7 6 310 471552722 471553022 5.840000e-99 372.0
6 TraesCS6D01G214800 chr6B 85.207 338 37 6 301 637 471553290 471553615 7.660000e-88 335.0
7 TraesCS6D01G214800 chr5B 79.468 677 116 17 4092 4751 160129053 160129723 4.360000e-125 459.0
8 TraesCS6D01G214800 chr2D 78.496 758 108 33 4016 4753 169968418 169969140 3.390000e-121 446.0
9 TraesCS6D01G214800 chr7A 78.146 755 122 29 4025 4753 26387053 26386316 1.580000e-119 440.0
10 TraesCS6D01G214800 chr7A 80.380 158 29 2 3259 3415 256213519 256213363 8.400000e-23 119.0
11 TraesCS6D01G214800 chr2A 78.278 755 109 35 4016 4753 180348865 180348149 7.340000e-118 435.0
12 TraesCS6D01G214800 chr2B 77.910 756 110 36 4016 4753 227845617 227844901 7.400000e-113 418.0
13 TraesCS6D01G214800 chr7D 81.879 149 25 2 3259 3406 241883129 241883276 1.810000e-24 124.0
14 TraesCS6D01G214800 chr7B 81.879 149 25 2 3259 3406 217625990 217626137 1.810000e-24 124.0
15 TraesCS6D01G214800 chr4A 72.857 210 48 9 294 500 519675142 519675345 3.990000e-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 TraesCS6D01G214800 chr6D 305178237 305183014 4777 True 8824.0 8824 100.000 1 4778 1 chr6D.!!$R1 4777
1 TraesCS6D01G214800 chr6D 194208181 194208919 738 False 444.0 444 78.100 4016 4753 1 chr6D.!!$F1 737
2 TraesCS6D01G214800 chr6A 409410593 409415355 4762 False 5952.0 5952 89.477 1 4762 1 chr6A.!!$F1 4761
3 TraesCS6D01G214800 chr6B 471628038 471631082 3044 False 4630.0 4630 94.089 736 3797 1 chr6B.!!$F1 3061
4 TraesCS6D01G214800 chr6B 471638071 471638723 652 False 843.0 843 90.107 4015 4663 1 chr6B.!!$F2 648
5 TraesCS6D01G214800 chr6B 471552722 471553615 893 False 353.5 372 87.084 6 637 2 chr6B.!!$F3 631
6 TraesCS6D01G214800 chr5B 160129053 160129723 670 False 459.0 459 79.468 4092 4751 1 chr5B.!!$F1 659
7 TraesCS6D01G214800 chr2D 169968418 169969140 722 False 446.0 446 78.496 4016 4753 1 chr2D.!!$F1 737
8 TraesCS6D01G214800 chr7A 26386316 26387053 737 True 440.0 440 78.146 4025 4753 1 chr7A.!!$R1 728
9 TraesCS6D01G214800 chr2A 180348149 180348865 716 True 435.0 435 78.278 4016 4753 1 chr2A.!!$R1 737
10 TraesCS6D01G214800 chr2B 227844901 227845617 716 True 418.0 418 77.910 4016 4753 1 chr2B.!!$R1 737

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
628 907 0.106719 ACCCTAACATTGCCATCCCG 60.107 55.0 0.0 0.0 0.0 5.14 F
1673 1990 0.107312 CCTCCTCGGTCGGTCTCTAA 60.107 60.0 0.0 0.0 0.0 2.10 F
3233 3592 0.390340 GCTTCTGACTGACATCGGCA 60.390 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2399 0.104120 CGCCATCCGAGGTGATGTAA 59.896 55.0 0.0 0.0 41.75 2.41 R
3244 3603 0.035152 TCAAGCGTGAATCCCTGCAT 60.035 50.0 0.0 0.0 0.00 3.96 R
4238 4657 0.888736 TGACATTTGGGTGTGCTCCG 60.889 55.0 0.0 0.0 31.16 4.63 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
22 23 5.310720 CTAGGGTTGTGCTAAAATTGGAC 57.689 43.478 0.00 0.00 0.00 4.02
55 56 6.660521 TGGATAGCTCTCAAATGTCACAAAAT 59.339 34.615 1.14 0.00 0.00 1.82
56 57 7.828717 TGGATAGCTCTCAAATGTCACAAAATA 59.171 33.333 1.14 0.00 0.00 1.40
57 58 8.341173 GGATAGCTCTCAAATGTCACAAAATAG 58.659 37.037 1.14 0.00 0.00 1.73
124 126 9.696917 GAAAGAAGTTATTCACCATTTGACAAT 57.303 29.630 0.00 0.00 37.94 2.71
242 246 4.020128 GCTAGGGTATTATTCCTGAGGTGG 60.020 50.000 0.00 0.00 34.75 4.61
308 313 9.807921 TTCTATTGAGTCAACCCTTCTTTTTAT 57.192 29.630 7.96 0.00 0.00 1.40
363 641 1.263217 AGTACAAAGCGCCTCAAAACG 59.737 47.619 2.29 0.00 0.00 3.60
373 651 5.705902 AGCGCCTCAAAACGTAATAAAAAT 58.294 33.333 2.29 0.00 0.00 1.82
404 683 0.971386 TCCCTAGACCACGGAACAAC 59.029 55.000 0.00 0.00 0.00 3.32
459 738 2.101415 CTCTGTCGTTGCTCCCATATGA 59.899 50.000 3.65 0.00 0.00 2.15
468 747 2.177594 CTCCCATATGAGAGCCGCCC 62.178 65.000 3.65 0.00 34.11 6.13
505 784 1.606668 GTCGGGAAGTTTTCATGCACA 59.393 47.619 0.00 0.00 0.00 4.57
518 797 1.546923 CATGCACATGCCCTTGAGAAA 59.453 47.619 0.49 0.00 41.18 2.52
536 815 3.969250 ATAACACCCCGCAGCCACG 62.969 63.158 0.00 0.00 0.00 4.94
587 866 7.254050 CGATCTCAAGAATCTCACATCAAAGTC 60.254 40.741 0.00 0.00 0.00 3.01
588 867 6.169094 TCTCAAGAATCTCACATCAAAGTCC 58.831 40.000 0.00 0.00 0.00 3.85
603 882 2.342910 AGTCCGTCATTGTGTACGAC 57.657 50.000 0.00 0.00 41.55 4.34
624 903 3.016736 CGAGAAACCCTAACATTGCCAT 58.983 45.455 0.00 0.00 0.00 4.40
628 907 0.106719 ACCCTAACATTGCCATCCCG 60.107 55.000 0.00 0.00 0.00 5.14
638 917 2.998097 CCATCCCGAGGAAGGCAA 59.002 61.111 1.96 0.00 33.69 4.52
639 918 1.302949 CCATCCCGAGGAAGGCAAA 59.697 57.895 1.96 0.00 33.69 3.68
642 921 1.202348 CATCCCGAGGAAGGCAAAAAC 59.798 52.381 0.00 0.00 34.34 2.43
672 951 0.316689 GCGCATTTTAATCCGTCCCG 60.317 55.000 0.30 0.00 0.00 5.14
674 953 1.666700 CGCATTTTAATCCGTCCCGAA 59.333 47.619 0.00 0.00 0.00 4.30
675 954 2.286184 CGCATTTTAATCCGTCCCGAAG 60.286 50.000 0.00 0.00 0.00 3.79
688 972 3.259064 GTCCCGAAGAACAAATGATCGA 58.741 45.455 0.00 0.00 35.65 3.59
692 976 3.485877 CCGAAGAACAAATGATCGAAGCC 60.486 47.826 0.00 0.00 35.65 4.35
701 985 1.821216 TGATCGAAGCCCAAAAGACC 58.179 50.000 0.00 0.00 0.00 3.85
732 1016 1.455383 AAAAAGCAGAGCACCACCCG 61.455 55.000 0.00 0.00 0.00 5.28
754 1038 3.524541 CGGGCTAAAACCGTAACATAGT 58.475 45.455 0.00 0.00 46.03 2.12
755 1039 4.681744 CGGGCTAAAACCGTAACATAGTA 58.318 43.478 0.00 0.00 46.03 1.82
760 1044 8.309656 GGGCTAAAACCGTAACATAGTATCTAT 58.690 37.037 0.00 0.00 0.00 1.98
766 1050 9.909644 AAACCGTAACATAGTATCTATTAGCTG 57.090 33.333 0.00 0.00 0.00 4.24
767 1051 8.859236 ACCGTAACATAGTATCTATTAGCTGA 57.141 34.615 0.00 0.00 0.00 4.26
823 1107 1.004799 ACAGCAGCAGCAGACAGAG 60.005 57.895 3.17 0.00 45.49 3.35
879 1163 1.632965 AAAGGCGTGGTCCCTATCCC 61.633 60.000 0.00 0.00 30.93 3.85
940 1224 2.125912 CGAGCAGCGGTGTAGCTT 60.126 61.111 17.07 0.00 46.80 3.74
979 1263 4.280174 CAGCAATAATTTGGCTATGGCTCT 59.720 41.667 0.00 0.00 34.40 4.09
1001 1285 0.953727 TGTGGTTGCTGATTCTGCAC 59.046 50.000 16.67 11.92 37.99 4.57
1007 1291 0.251033 TGCTGATTCTGCACCAAGCT 60.251 50.000 13.50 0.00 45.94 3.74
1183 1467 5.652014 TGATTTCATACACCATTGTTCCCTC 59.348 40.000 0.00 0.00 37.15 4.30
1205 1489 3.763057 GAAAAGGAAAGAACCAGCCCTA 58.237 45.455 0.00 0.00 0.00 3.53
1207 1491 0.613777 AGGAAAGAACCAGCCCTACG 59.386 55.000 0.00 0.00 0.00 3.51
1208 1492 0.611714 GGAAAGAACCAGCCCTACGA 59.388 55.000 0.00 0.00 0.00 3.43
1209 1493 1.405661 GGAAAGAACCAGCCCTACGAG 60.406 57.143 0.00 0.00 0.00 4.18
1233 1521 7.521669 AGGATTCCAGGTATTTCTTTATCCTG 58.478 38.462 5.29 0.00 43.46 3.86
1285 1596 7.099764 TCTAAGCAAGTATCCTTGTTTCTGAG 58.900 38.462 3.42 0.00 45.50 3.35
1305 1616 4.566759 TGAGATTGATTCGAAATGTCCGAC 59.433 41.667 0.00 0.00 35.61 4.79
1338 1649 3.760035 CGCAGGTACCAGCTCCGT 61.760 66.667 24.85 0.00 0.00 4.69
1341 1652 1.019805 GCAGGTACCAGCTCCGTTTC 61.020 60.000 21.21 0.00 0.00 2.78
1671 1988 2.272797 CCTCCTCGGTCGGTCTCT 59.727 66.667 0.00 0.00 0.00 3.10
1672 1989 1.525923 CCTCCTCGGTCGGTCTCTA 59.474 63.158 0.00 0.00 0.00 2.43
1673 1990 0.107312 CCTCCTCGGTCGGTCTCTAA 60.107 60.000 0.00 0.00 0.00 2.10
1674 1991 1.477195 CCTCCTCGGTCGGTCTCTAAT 60.477 57.143 0.00 0.00 0.00 1.73
1675 1992 1.604755 CTCCTCGGTCGGTCTCTAATG 59.395 57.143 0.00 0.00 0.00 1.90
1676 1993 1.064906 TCCTCGGTCGGTCTCTAATGT 60.065 52.381 0.00 0.00 0.00 2.71
1677 1994 2.171237 TCCTCGGTCGGTCTCTAATGTA 59.829 50.000 0.00 0.00 0.00 2.29
1678 1995 3.147629 CCTCGGTCGGTCTCTAATGTAT 58.852 50.000 0.00 0.00 0.00 2.29
1679 1996 3.568853 CCTCGGTCGGTCTCTAATGTATT 59.431 47.826 0.00 0.00 0.00 1.89
1680 1997 4.320348 CCTCGGTCGGTCTCTAATGTATTC 60.320 50.000 0.00 0.00 0.00 1.75
1681 1998 4.458397 TCGGTCGGTCTCTAATGTATTCT 58.542 43.478 0.00 0.00 0.00 2.40
1682 1999 4.514441 TCGGTCGGTCTCTAATGTATTCTC 59.486 45.833 0.00 0.00 0.00 2.87
1699 2016 8.425577 TGTATTCTCTAATTAAGCTGCAGAAC 57.574 34.615 20.43 0.00 0.00 3.01
1703 2020 5.877012 TCTCTAATTAAGCTGCAGAACTTGG 59.123 40.000 20.43 4.75 0.00 3.61
1711 2028 2.030805 GCTGCAGAACTTGGTCGATTTT 60.031 45.455 20.43 0.00 0.00 1.82
1713 2030 2.287547 TGCAGAACTTGGTCGATTTTGC 60.288 45.455 4.71 4.71 0.00 3.68
1730 2047 4.898829 TTTGCTCATCATCCGGTTTATG 57.101 40.909 0.00 0.11 0.00 1.90
1741 2058 3.857052 TCCGGTTTATGTGTCATCACTC 58.143 45.455 0.00 0.00 44.14 3.51
1754 2071 3.031013 TCATCACTCGCTGGAAATCCTA 58.969 45.455 0.44 0.00 36.82 2.94
1781 2098 0.861837 CTGCTCTTGACACGGTGAAC 59.138 55.000 16.29 8.92 0.00 3.18
1863 2180 7.384524 AAGGATCATCTGAATTCATCCTGTA 57.615 36.000 22.41 3.76 37.17 2.74
1869 2186 6.608808 TCATCTGAATTCATCCTGTACAGAGA 59.391 38.462 24.68 18.58 36.59 3.10
1880 2197 3.192422 CCTGTACAGAGACAAGAGACAGG 59.808 52.174 24.68 0.28 44.62 4.00
1881 2198 3.157881 TGTACAGAGACAAGAGACAGGG 58.842 50.000 0.00 0.00 0.00 4.45
1885 2202 2.754552 CAGAGACAAGAGACAGGGAGAG 59.245 54.545 0.00 0.00 0.00 3.20
1888 2205 3.161866 AGACAAGAGACAGGGAGAGAAC 58.838 50.000 0.00 0.00 0.00 3.01
1898 2215 3.257393 CAGGGAGAGAACATTTCACTCG 58.743 50.000 7.11 0.00 44.91 4.18
1899 2216 2.003301 GGGAGAGAACATTTCACTCGC 58.997 52.381 12.31 12.31 46.58 5.03
1900 2217 2.966050 GGAGAGAACATTTCACTCGCT 58.034 47.619 7.11 0.00 44.91 4.93
2033 2391 1.137872 GCGATCTTGACCTCACCATCT 59.862 52.381 0.00 0.00 0.00 2.90
2041 2399 2.373169 TGACCTCACCATCTTGAAAGCT 59.627 45.455 0.00 0.00 0.00 3.74
2142 2500 7.617041 AGAGCATCATTACTCCAACTTAAAC 57.383 36.000 0.00 0.00 37.82 2.01
2159 2518 1.170290 AACTGTTACACGGCCTTGCC 61.170 55.000 9.57 0.00 46.75 4.52
2275 2634 3.253188 TCGAGAAGGTTTGCAAATTCCAG 59.747 43.478 16.21 12.00 0.00 3.86
2327 2686 5.439721 TGAGACATTCGATTGATTTGGGAT 58.560 37.500 13.92 0.00 0.00 3.85
2328 2687 5.528690 TGAGACATTCGATTGATTTGGGATC 59.471 40.000 13.92 0.00 0.00 3.36
2414 2773 9.409312 TGAATAGCTGAATTATTGTTGTTTGTG 57.591 29.630 0.00 0.00 0.00 3.33
2593 2952 2.029844 GGAGCTCCAGTGCAACGTC 61.030 63.158 28.43 0.00 45.86 4.34
2954 3313 2.110213 TGGTGAACGTGAGGTGCC 59.890 61.111 0.00 0.00 0.00 5.01
3053 3412 2.499205 CCGAAGGCATCTACGGCA 59.501 61.111 0.00 0.00 46.14 5.69
3172 3531 1.909781 GTCCGAGGTGGGTGGTACA 60.910 63.158 0.00 0.00 38.76 2.90
3208 3567 0.536687 TCAGTTCTCTGGTCGACGGT 60.537 55.000 9.92 0.00 41.59 4.83
3210 3569 1.733399 GTTCTCTGGTCGACGGTGC 60.733 63.158 9.92 0.00 0.00 5.01
3227 3586 1.665916 GCGCTGCTTCTGACTGACA 60.666 57.895 0.00 0.00 0.00 3.58
3228 3587 1.018226 GCGCTGCTTCTGACTGACAT 61.018 55.000 0.00 0.00 0.00 3.06
3233 3592 0.390340 GCTTCTGACTGACATCGGCA 60.390 55.000 0.00 0.00 0.00 5.69
3641 4016 1.065926 TCAGTATGGCAGCTCTTGGTG 60.066 52.381 0.00 0.00 38.78 4.17
3642 4017 0.254178 AGTATGGCAGCTCTTGGTGG 59.746 55.000 0.00 0.00 41.57 4.61
3643 4018 0.253044 GTATGGCAGCTCTTGGTGGA 59.747 55.000 0.00 0.00 41.57 4.02
3797 4172 4.084223 TCTCAACCTCGCGTATTTTTGTTC 60.084 41.667 5.77 0.00 0.00 3.18
3798 4173 3.810941 TCAACCTCGCGTATTTTTGTTCT 59.189 39.130 5.77 0.00 0.00 3.01
3799 4174 4.989797 TCAACCTCGCGTATTTTTGTTCTA 59.010 37.500 5.77 0.00 0.00 2.10
3800 4175 5.466058 TCAACCTCGCGTATTTTTGTTCTAA 59.534 36.000 5.77 0.00 0.00 2.10
3801 4176 5.927954 ACCTCGCGTATTTTTGTTCTAAA 57.072 34.783 5.77 0.00 0.00 1.85
3802 4177 6.490566 ACCTCGCGTATTTTTGTTCTAAAT 57.509 33.333 5.77 0.00 0.00 1.40
3803 4178 6.905578 ACCTCGCGTATTTTTGTTCTAAATT 58.094 32.000 5.77 0.00 0.00 1.82
3804 4179 7.364970 ACCTCGCGTATTTTTGTTCTAAATTT 58.635 30.769 5.77 0.00 0.00 1.82
3805 4180 7.863877 ACCTCGCGTATTTTTGTTCTAAATTTT 59.136 29.630 5.77 0.00 0.00 1.82
3806 4181 8.696175 CCTCGCGTATTTTTGTTCTAAATTTTT 58.304 29.630 5.77 0.00 0.00 1.94
3867 4243 9.678941 ACTTTTTCTTTATTTCCTCGTCATTTC 57.321 29.630 0.00 0.00 0.00 2.17
3868 4244 9.899226 CTTTTTCTTTATTTCCTCGTCATTTCT 57.101 29.630 0.00 0.00 0.00 2.52
3870 4246 9.677567 TTTTCTTTATTTCCTCGTCATTTCTTG 57.322 29.630 0.00 0.00 0.00 3.02
3876 4252 3.399330 TCCTCGTCATTTCTTGTGGAAC 58.601 45.455 0.00 0.00 33.13 3.62
3894 4270 3.282021 GAACATAAGGGCATCTGAGCAA 58.718 45.455 0.00 0.00 35.83 3.91
3899 4275 5.893255 ACATAAGGGCATCTGAGCAATTTTA 59.107 36.000 0.00 0.00 35.83 1.52
3900 4276 6.380846 ACATAAGGGCATCTGAGCAATTTTAA 59.619 34.615 0.00 0.00 35.83 1.52
3901 4277 4.725790 AGGGCATCTGAGCAATTTTAAC 57.274 40.909 0.00 0.00 35.83 2.01
3911 4289 6.723977 TCTGAGCAATTTTAACATTTAGGGGT 59.276 34.615 0.00 0.00 0.00 4.95
3917 4295 8.450180 GCAATTTTAACATTTAGGGGTCATTTG 58.550 33.333 0.00 0.00 0.00 2.32
3929 4307 5.402630 AGGGGTCATTTGGTAAGTTTTCAT 58.597 37.500 0.00 0.00 0.00 2.57
3930 4308 6.557568 AGGGGTCATTTGGTAAGTTTTCATA 58.442 36.000 0.00 0.00 0.00 2.15
3934 4312 7.393515 GGGTCATTTGGTAAGTTTTCATAGTCT 59.606 37.037 0.00 0.00 0.00 3.24
3936 4314 9.220767 GTCATTTGGTAAGTTTTCATAGTCTCT 57.779 33.333 0.00 0.00 0.00 3.10
3945 4323 5.046950 AGTTTTCATAGTCTCTGTGGACCTC 60.047 44.000 0.00 0.00 36.95 3.85
3950 4328 1.360852 AGTCTCTGTGGACCTCCTCAT 59.639 52.381 0.00 0.00 38.64 2.90
3953 4331 1.222936 CTGTGGACCTCCTCATGGC 59.777 63.158 0.00 0.00 38.64 4.40
3954 4332 2.262774 CTGTGGACCTCCTCATGGCC 62.263 65.000 0.00 0.00 38.64 5.36
3955 4333 1.997874 GTGGACCTCCTCATGGCCT 60.998 63.158 3.32 0.00 36.82 5.19
3956 4334 1.997311 TGGACCTCCTCATGGCCTG 60.997 63.158 3.32 0.00 36.82 4.85
3957 4335 2.191641 GACCTCCTCATGGCCTGC 59.808 66.667 3.32 0.00 0.00 4.85
3958 4336 3.412624 GACCTCCTCATGGCCTGCC 62.413 68.421 3.32 0.00 0.00 4.85
3967 4359 3.442441 TGGCCTGCCACTTTTTCG 58.558 55.556 6.80 0.00 41.89 3.46
3997 4389 9.189156 AGTATTATGGCTCAAATGTATTGTGTT 57.811 29.630 0.00 0.00 0.00 3.32
4002 4394 6.851609 TGGCTCAAATGTATTGTGTTATGTC 58.148 36.000 0.00 0.00 0.00 3.06
4003 4395 6.432472 TGGCTCAAATGTATTGTGTTATGTCA 59.568 34.615 0.00 0.00 0.00 3.58
4004 4396 6.968904 GGCTCAAATGTATTGTGTTATGTCAG 59.031 38.462 0.00 0.00 0.00 3.51
4005 4397 6.470235 GCTCAAATGTATTGTGTTATGTCAGC 59.530 38.462 0.00 0.00 0.00 4.26
4006 4398 6.851609 TCAAATGTATTGTGTTATGTCAGCC 58.148 36.000 0.00 0.00 0.00 4.85
4008 4400 7.122501 TCAAATGTATTGTGTTATGTCAGCCAT 59.877 33.333 0.00 0.00 37.58 4.40
4012 4425 9.791801 ATGTATTGTGTTATGTCAGCCATATTA 57.208 29.630 0.00 0.00 35.96 0.98
4022 4435 7.618019 ATGTCAGCCATATTAGAAGACCTTA 57.382 36.000 0.00 0.00 29.82 2.69
4098 4513 5.140747 TGGAAGAAGAGAAGTACAAGAGC 57.859 43.478 0.00 0.00 0.00 4.09
4159 4577 1.847088 AGGAGGAAGGGGAAAGTATGC 59.153 52.381 0.00 0.00 0.00 3.14
4182 4600 5.988561 GCTAACTATCTCCCACATCTCTTTG 59.011 44.000 0.00 0.00 0.00 2.77
4222 4641 7.942341 ACTTGAGGAGGTAAATTTGTGTATTGA 59.058 33.333 0.00 0.00 0.00 2.57
4238 4657 7.535139 TGTGTATTGAGCTTATTGTAAAAGGC 58.465 34.615 0.00 0.00 0.00 4.35
4240 4659 4.695217 TTGAGCTTATTGTAAAAGGCGG 57.305 40.909 0.00 0.00 0.00 6.13
4288 4707 6.764308 AGCAAATGCATGTGTCTTATTAGT 57.236 33.333 18.15 0.00 45.16 2.24
4377 4797 5.929697 TGACTTAACTTCATGAGCAAGTG 57.070 39.130 14.32 1.04 35.33 3.16
4416 4836 6.931838 TCACTACCGAATGAGTACAAAAGAT 58.068 36.000 0.00 0.00 0.00 2.40
4420 4850 8.041323 ACTACCGAATGAGTACAAAAGATCATT 58.959 33.333 5.69 5.69 43.26 2.57
4421 4851 7.687941 ACCGAATGAGTACAAAAGATCATTT 57.312 32.000 7.08 0.00 41.27 2.32
4492 4933 7.996098 AATATTAGCCCATATGTTGTACCAC 57.004 36.000 1.24 0.00 0.00 4.16
4524 4965 4.039124 ACGCCAAAGAAAGATGGATTTTGT 59.961 37.500 0.00 0.00 39.12 2.83
4530 4971 7.656948 CCAAAGAAAGATGGATTTTGTTGCTTA 59.343 33.333 0.00 0.00 39.12 3.09
4701 5146 2.095919 GGAGATGAACGAAAAACCACCG 60.096 50.000 0.00 0.00 0.00 4.94
4753 5198 4.038271 TGATCAAGCCATTTGGACTCTT 57.962 40.909 0.00 0.00 37.39 2.85
4758 5203 3.228188 AGCCATTTGGACTCTTGAACA 57.772 42.857 0.00 0.00 37.39 3.18
4762 5207 4.262164 GCCATTTGGACTCTTGAACACATT 60.262 41.667 0.00 0.00 37.39 2.71
4763 5208 5.739935 GCCATTTGGACTCTTGAACACATTT 60.740 40.000 0.00 0.00 37.39 2.32
4764 5209 6.516527 GCCATTTGGACTCTTGAACACATTTA 60.517 38.462 0.00 0.00 37.39 1.40
4765 5210 7.605449 CCATTTGGACTCTTGAACACATTTAT 58.395 34.615 0.00 0.00 37.39 1.40
4766 5211 7.543172 CCATTTGGACTCTTGAACACATTTATG 59.457 37.037 0.00 0.00 37.39 1.90
4767 5212 5.627499 TGGACTCTTGAACACATTTATGC 57.373 39.130 0.00 0.00 0.00 3.14
4768 5213 5.069318 TGGACTCTTGAACACATTTATGCA 58.931 37.500 0.00 0.00 0.00 3.96
4769 5214 5.048782 TGGACTCTTGAACACATTTATGCAC 60.049 40.000 0.00 0.00 0.00 4.57
4770 5215 5.182001 GGACTCTTGAACACATTTATGCACT 59.818 40.000 0.00 0.00 0.00 4.40
4771 5216 6.294176 GGACTCTTGAACACATTTATGCACTT 60.294 38.462 0.00 0.00 0.00 3.16
4772 5217 6.441274 ACTCTTGAACACATTTATGCACTTG 58.559 36.000 0.00 0.00 0.00 3.16
4773 5218 6.262944 ACTCTTGAACACATTTATGCACTTGA 59.737 34.615 0.00 0.00 0.00 3.02
4774 5219 7.040201 ACTCTTGAACACATTTATGCACTTGAT 60.040 33.333 0.00 0.00 0.00 2.57
4775 5220 7.085746 TCTTGAACACATTTATGCACTTGATG 58.914 34.615 0.00 0.00 0.00 3.07
4776 5221 6.572167 TGAACACATTTATGCACTTGATGA 57.428 33.333 0.00 0.00 0.00 2.92
4777 5222 6.979465 TGAACACATTTATGCACTTGATGAA 58.021 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.318141 ACATTTGAGAGCTATCCAAATTGTTG 58.682 34.615 5.78 5.57 35.72 3.33
119 121 8.948853 TGAAAGTTTCATTTCGTCATATTGTC 57.051 30.769 14.35 0.00 41.21 3.18
170 173 4.201881 TGACCGTGTGTATCTCATAAGTCG 60.202 45.833 0.00 0.00 30.74 4.18
237 241 2.972713 AGAGAATGTGTGTGTACCACCT 59.027 45.455 10.70 2.43 43.85 4.00
242 246 3.963428 AGGGAGAGAATGTGTGTGTAC 57.037 47.619 0.00 0.00 0.00 2.90
459 738 3.553095 GACAAGGTTGGGCGGCTCT 62.553 63.158 9.56 0.00 0.00 4.09
466 745 1.270839 ACTGTCATCGACAAGGTTGGG 60.271 52.381 0.00 0.00 42.26 4.12
468 747 1.721389 CGACTGTCATCGACAAGGTTG 59.279 52.381 8.73 0.00 45.13 3.77
505 784 3.365472 GGGTGTTATTTCTCAAGGGCAT 58.635 45.455 0.00 0.00 0.00 4.40
518 797 2.045340 GTGGCTGCGGGGTGTTAT 60.045 61.111 0.00 0.00 0.00 1.89
536 815 2.100605 AGGATTCAGCAACGAAGACC 57.899 50.000 0.00 0.00 0.00 3.85
547 826 8.654230 TTCTTGAGATCGATTTAAGGATTCAG 57.346 34.615 0.00 0.00 0.00 3.02
603 882 2.432444 TGGCAATGTTAGGGTTTCTCG 58.568 47.619 0.00 0.00 0.00 4.04
624 903 0.476771 AGTTTTTGCCTTCCTCGGGA 59.523 50.000 0.00 0.00 0.00 5.14
672 951 3.440173 TGGGCTTCGATCATTTGTTCTTC 59.560 43.478 0.00 0.00 0.00 2.87
674 953 3.071874 TGGGCTTCGATCATTTGTTCT 57.928 42.857 0.00 0.00 0.00 3.01
675 954 3.848272 TTGGGCTTCGATCATTTGTTC 57.152 42.857 0.00 0.00 0.00 3.18
688 972 1.133915 TCGAGTTGGTCTTTTGGGCTT 60.134 47.619 0.00 0.00 0.00 4.35
713 997 1.455383 CGGGTGGTGCTCTGCTTTTT 61.455 55.000 0.00 0.00 0.00 1.94
714 998 1.898574 CGGGTGGTGCTCTGCTTTT 60.899 57.895 0.00 0.00 0.00 2.27
715 999 2.281761 CGGGTGGTGCTCTGCTTT 60.282 61.111 0.00 0.00 0.00 3.51
734 1018 6.519382 AGATACTATGTTACGGTTTTAGCCC 58.481 40.000 0.00 0.00 0.00 5.19
753 1037 5.011125 TGCCTCCACTTCAGCTAATAGATAC 59.989 44.000 0.00 0.00 0.00 2.24
754 1038 5.011125 GTGCCTCCACTTCAGCTAATAGATA 59.989 44.000 0.00 0.00 38.93 1.98
755 1039 3.969976 TGCCTCCACTTCAGCTAATAGAT 59.030 43.478 0.00 0.00 0.00 1.98
760 1044 0.324943 GGTGCCTCCACTTCAGCTAA 59.675 55.000 0.00 0.00 41.75 3.09
762 1046 2.149383 TGGTGCCTCCACTTCAGCT 61.149 57.895 0.00 0.00 41.93 4.24
810 1094 1.981636 CCTTCCTCTGTCTGCTGCT 59.018 57.895 0.00 0.00 0.00 4.24
823 1107 1.338105 GGCAATTGGACAAAGCCTTCC 60.338 52.381 18.71 0.00 40.32 3.46
940 1224 5.620738 ATTGCTGGAATCTGACTAGCTAA 57.379 39.130 0.00 0.00 41.29 3.09
979 1263 1.881973 GCAGAATCAGCAACCACAAGA 59.118 47.619 0.00 0.00 0.00 3.02
1001 1285 2.634815 ATGTGCTCCTGATAGCTTGG 57.365 50.000 0.00 0.00 43.19 3.61
1007 1291 6.994421 TGGATACTTTATGTGCTCCTGATA 57.006 37.500 0.00 0.00 34.70 2.15
1183 1467 1.269723 GGGCTGGTTCTTTCCTTTTCG 59.730 52.381 0.00 0.00 0.00 3.46
1205 1489 5.437191 AAAGAAATACCTGGAATCCTCGT 57.563 39.130 0.00 0.00 0.00 4.18
1207 1491 7.663493 CAGGATAAAGAAATACCTGGAATCCTC 59.337 40.741 0.00 0.00 42.77 3.71
1208 1492 7.521669 CAGGATAAAGAAATACCTGGAATCCT 58.478 38.462 0.00 0.00 42.77 3.24
1209 1493 7.751768 CAGGATAAAGAAATACCTGGAATCC 57.248 40.000 0.00 0.00 42.77 3.01
1233 1521 0.537188 TGAATTCAGAGACCGAGGCC 59.463 55.000 3.38 0.00 0.00 5.19
1285 1596 3.550275 TCGTCGGACATTTCGAATCAATC 59.450 43.478 9.10 0.00 38.42 2.67
1305 1616 1.927174 CTGCGGTATCCTGAAAAGTCG 59.073 52.381 0.00 0.00 0.00 4.18
1672 1989 9.618890 TTCTGCAGCTTAATTAGAGAATACATT 57.381 29.630 9.47 0.00 0.00 2.71
1673 1990 9.050601 GTTCTGCAGCTTAATTAGAGAATACAT 57.949 33.333 9.47 0.00 0.00 2.29
1674 1991 8.260818 AGTTCTGCAGCTTAATTAGAGAATACA 58.739 33.333 9.47 0.00 0.00 2.29
1675 1992 8.655651 AGTTCTGCAGCTTAATTAGAGAATAC 57.344 34.615 9.47 0.00 0.00 1.89
1676 1993 9.102757 CAAGTTCTGCAGCTTAATTAGAGAATA 57.897 33.333 9.47 0.00 0.00 1.75
1677 1994 7.066766 CCAAGTTCTGCAGCTTAATTAGAGAAT 59.933 37.037 9.47 0.00 0.00 2.40
1678 1995 6.372659 CCAAGTTCTGCAGCTTAATTAGAGAA 59.627 38.462 9.47 0.00 0.00 2.87
1679 1996 5.877012 CCAAGTTCTGCAGCTTAATTAGAGA 59.123 40.000 9.47 0.00 0.00 3.10
1680 1997 5.645497 ACCAAGTTCTGCAGCTTAATTAGAG 59.355 40.000 9.47 0.00 0.00 2.43
1681 1998 5.560724 ACCAAGTTCTGCAGCTTAATTAGA 58.439 37.500 9.47 0.00 0.00 2.10
1682 1999 5.446473 CGACCAAGTTCTGCAGCTTAATTAG 60.446 44.000 9.47 0.00 0.00 1.73
1693 2010 2.030805 AGCAAAATCGACCAAGTTCTGC 60.031 45.455 0.00 0.00 0.00 4.26
1699 2016 4.497006 GGATGATGAGCAAAATCGACCAAG 60.497 45.833 0.00 0.00 0.00 3.61
1703 2020 2.032549 CCGGATGATGAGCAAAATCGAC 60.033 50.000 0.00 0.00 0.00 4.20
1711 2028 3.205338 CACATAAACCGGATGATGAGCA 58.795 45.455 15.74 0.00 0.00 4.26
1713 2030 4.441792 TGACACATAAACCGGATGATGAG 58.558 43.478 15.74 10.21 0.00 2.90
1730 2047 1.795768 TTTCCAGCGAGTGATGACAC 58.204 50.000 0.00 0.00 46.24 3.67
1741 2058 5.277538 GCAGAAATTAGTAGGATTTCCAGCG 60.278 44.000 0.00 0.00 41.97 5.18
1754 2071 3.997021 CCGTGTCAAGAGCAGAAATTAGT 59.003 43.478 0.00 0.00 0.00 2.24
1863 2180 2.109128 TCTCCCTGTCTCTTGTCTCTGT 59.891 50.000 0.00 0.00 0.00 3.41
1869 2186 2.964209 TGTTCTCTCCCTGTCTCTTGT 58.036 47.619 0.00 0.00 0.00 3.16
1880 2197 2.670414 CAGCGAGTGAAATGTTCTCTCC 59.330 50.000 12.17 7.17 43.72 3.71
1881 2198 2.670414 CCAGCGAGTGAAATGTTCTCTC 59.330 50.000 9.11 9.11 43.37 3.20
1885 2202 1.808411 TCCCAGCGAGTGAAATGTTC 58.192 50.000 0.00 0.00 0.00 3.18
1888 2205 2.028420 TGATCCCAGCGAGTGAAATG 57.972 50.000 0.00 0.00 0.00 2.32
1898 2215 4.741321 TGGATTTTGAAATGATCCCAGC 57.259 40.909 6.26 0.00 38.84 4.85
1899 2216 8.455682 CAAATTTGGATTTTGAAATGATCCCAG 58.544 33.333 10.49 0.00 38.84 4.45
1900 2217 7.943447 ACAAATTTGGATTTTGAAATGATCCCA 59.057 29.630 21.74 0.00 38.84 4.37
2033 2391 3.007506 TCCGAGGTGATGTAAGCTTTCAA 59.992 43.478 9.99 0.00 0.00 2.69
2041 2399 0.104120 CGCCATCCGAGGTGATGTAA 59.896 55.000 0.00 0.00 41.75 2.41
2142 2500 3.263941 GGCAAGGCCGTGTAACAG 58.736 61.111 20.23 0.00 39.62 3.16
2159 2518 5.663795 AGTCGCAATATACAGCTCAAATG 57.336 39.130 0.00 0.00 0.00 2.32
2275 2634 6.790285 TTAAGAGTTAAAACGGATGGTGAC 57.210 37.500 0.00 0.00 0.00 3.67
2323 2682 8.624776 CATGGAAAACTAATTAACAGAGATCCC 58.375 37.037 0.00 0.00 0.00 3.85
2414 2773 2.732619 CCGGACCTAAGGCCTGTCC 61.733 68.421 24.61 24.61 44.12 4.02
3053 3412 2.101582 GACGAATGTACAGCTCCTGGAT 59.898 50.000 0.33 0.00 35.51 3.41
3172 3531 2.213499 CTGAACCGAGTTCTGTTGCTT 58.787 47.619 14.95 0.00 42.39 3.91
3208 3567 1.665916 GTCAGTCAGAAGCAGCGCA 60.666 57.895 11.47 0.00 0.00 6.09
3210 3569 0.997932 GATGTCAGTCAGAAGCAGCG 59.002 55.000 0.00 0.00 0.00 5.18
3215 3574 1.354040 GTGCCGATGTCAGTCAGAAG 58.646 55.000 0.00 0.00 0.00 2.85
3227 3586 1.091537 CATTGTAAACCCGTGCCGAT 58.908 50.000 0.00 0.00 0.00 4.18
3228 3587 1.579084 GCATTGTAAACCCGTGCCGA 61.579 55.000 0.00 0.00 0.00 5.54
3233 3592 0.402504 TCCCTGCATTGTAAACCCGT 59.597 50.000 0.00 0.00 0.00 5.28
3238 3597 2.163412 GCGTGAATCCCTGCATTGTAAA 59.837 45.455 0.00 0.00 0.00 2.01
3244 3603 0.035152 TCAAGCGTGAATCCCTGCAT 60.035 50.000 0.00 0.00 0.00 3.96
3584 3943 4.274459 GGCCATTTTACAACAATTTGCACA 59.726 37.500 0.00 0.00 36.00 4.57
3641 4016 5.847111 AACTTGTTGGAAAAAGGTACTCC 57.153 39.130 0.00 0.00 38.49 3.85
3642 4017 6.270815 GGAAACTTGTTGGAAAAAGGTACTC 58.729 40.000 0.00 0.00 38.49 2.59
3851 4227 5.800296 TCCACAAGAAATGACGAGGAAATA 58.200 37.500 0.00 0.00 0.00 1.40
3860 4236 5.622233 GCCCTTATGTTCCACAAGAAATGAC 60.622 44.000 0.00 0.00 35.85 3.06
3862 4238 4.220382 TGCCCTTATGTTCCACAAGAAATG 59.780 41.667 0.00 0.00 35.85 2.32
3867 4243 3.379372 CAGATGCCCTTATGTTCCACAAG 59.621 47.826 0.00 0.00 0.00 3.16
3868 4244 3.010027 TCAGATGCCCTTATGTTCCACAA 59.990 43.478 0.00 0.00 0.00 3.33
3870 4246 3.209410 CTCAGATGCCCTTATGTTCCAC 58.791 50.000 0.00 0.00 0.00 4.02
3876 4252 4.931661 AAATTGCTCAGATGCCCTTATG 57.068 40.909 0.00 0.00 0.00 1.90
3894 4270 8.213489 ACCAAATGACCCCTAAATGTTAAAAT 57.787 30.769 0.00 0.00 0.00 1.82
3899 4275 6.319715 ACTTACCAAATGACCCCTAAATGTT 58.680 36.000 0.00 0.00 0.00 2.71
3900 4276 5.899278 ACTTACCAAATGACCCCTAAATGT 58.101 37.500 0.00 0.00 0.00 2.71
3901 4277 6.850752 AACTTACCAAATGACCCCTAAATG 57.149 37.500 0.00 0.00 0.00 2.32
3911 4289 9.219603 CAGAGACTATGAAAACTTACCAAATGA 57.780 33.333 0.00 0.00 0.00 2.57
3917 4295 6.590677 GTCCACAGAGACTATGAAAACTTACC 59.409 42.308 3.62 0.00 33.79 2.85
3929 4307 1.993301 TGAGGAGGTCCACAGAGACTA 59.007 52.381 0.00 0.00 38.89 2.59
3930 4308 0.780637 TGAGGAGGTCCACAGAGACT 59.219 55.000 0.00 0.00 38.89 3.24
3934 4312 1.267574 GCCATGAGGAGGTCCACAGA 61.268 60.000 0.00 0.00 39.88 3.41
3936 4314 2.300967 GGCCATGAGGAGGTCCACA 61.301 63.158 0.00 0.00 40.76 4.17
3950 4328 2.199652 CCGAAAAAGTGGCAGGCCA 61.200 57.895 9.35 9.35 45.02 5.36
3957 4335 5.339990 CCATAATACTTGCCGAAAAAGTGG 58.660 41.667 7.38 0.00 38.32 4.00
3958 4336 4.798387 GCCATAATACTTGCCGAAAAAGTG 59.202 41.667 7.38 0.00 38.32 3.16
3959 4337 4.705023 AGCCATAATACTTGCCGAAAAAGT 59.295 37.500 3.43 3.43 40.82 2.66
3960 4338 5.163663 TGAGCCATAATACTTGCCGAAAAAG 60.164 40.000 0.00 0.00 0.00 2.27
3966 4358 4.036734 ACATTTGAGCCATAATACTTGCCG 59.963 41.667 0.00 0.00 0.00 5.69
3967 4359 5.520376 ACATTTGAGCCATAATACTTGCC 57.480 39.130 0.00 0.00 0.00 4.52
3969 4361 9.454585 CACAATACATTTGAGCCATAATACTTG 57.545 33.333 0.00 0.00 0.00 3.16
3979 4371 6.851609 TGACATAACACAATACATTTGAGCC 58.148 36.000 0.00 0.00 0.00 4.70
3997 4389 7.618019 AAGGTCTTCTAATATGGCTGACATA 57.382 36.000 5.53 5.53 45.60 2.29
4002 4394 8.682936 ATTGTTAAGGTCTTCTAATATGGCTG 57.317 34.615 0.00 0.00 0.00 4.85
4003 4395 9.700831 AAATTGTTAAGGTCTTCTAATATGGCT 57.299 29.630 0.00 0.00 0.00 4.75
4004 4396 9.736023 CAAATTGTTAAGGTCTTCTAATATGGC 57.264 33.333 0.00 0.00 0.00 4.40
4012 4425 5.716703 CCCCATCAAATTGTTAAGGTCTTCT 59.283 40.000 0.00 0.00 0.00 2.85
4081 4496 7.426929 TGATTTTGCTCTTGTACTTCTCTTC 57.573 36.000 0.00 0.00 0.00 2.87
4150 4568 6.817184 TGTGGGAGATAGTTAGCATACTTTC 58.183 40.000 0.00 0.00 0.00 2.62
4159 4577 6.325028 TCCAAAGAGATGTGGGAGATAGTTAG 59.675 42.308 0.00 0.00 35.46 2.34
4182 4600 5.422214 TCCTCAAGTCTTCCATAAACTCC 57.578 43.478 0.00 0.00 0.00 3.85
4222 4641 2.683362 GCTCCGCCTTTTACAATAAGCT 59.317 45.455 0.00 0.00 0.00 3.74
4238 4657 0.888736 TGACATTTGGGTGTGCTCCG 60.889 55.000 0.00 0.00 31.16 4.63
4240 4659 3.451141 TTTTGACATTTGGGTGTGCTC 57.549 42.857 0.00 0.00 31.16 4.26
4288 4707 8.656849 GCTTTCGAAGTATGTTCTGAAATTCTA 58.343 33.333 0.00 0.00 0.00 2.10
4351 4770 7.864379 CACTTGCTCATGAAGTTAAGTCAATTT 59.136 33.333 0.00 0.00 34.44 1.82
4377 4797 6.628185 TCGGTAGTGAGGAAGATTAGAAAAC 58.372 40.000 0.00 0.00 0.00 2.43
4439 4879 8.099364 TCAAATGTGCCTTTTTACAACAAAAA 57.901 26.923 0.00 0.00 0.00 1.94
4524 4965 4.811024 GCTCTACTATGCACACATAAGCAA 59.189 41.667 0.00 0.00 44.88 3.91
4530 4971 3.389002 TGATGGCTCTACTATGCACACAT 59.611 43.478 0.00 0.00 40.49 3.21
4701 5146 3.288092 ACAACCCTTCCTTTGTCTTGAC 58.712 45.455 0.00 0.00 29.75 3.18
4753 5198 6.572167 TCATCAAGTGCATAAATGTGTTCA 57.428 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.