Multiple sequence alignment - TraesCS6A01G262900

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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 TraesCS6A01G262900 chr6A 100.000 4256 0 0 1 4256 486004182 486008437 0.000000e+00 7860.0
1 TraesCS6A01G262900 chr6A 82.186 247 23 6 10 244 394638254 394638491 4.340000e-45 193.0
2 TraesCS6A01G262900 chr6D 97.546 2323 51 3 1865 4182 345389896 345392217 0.000000e+00 3969.0
3 TraesCS6A01G262900 chr6D 86.864 1081 85 33 460 1535 345388862 345389890 0.000000e+00 1157.0
4 TraesCS6A01G262900 chr6D 89.744 468 32 10 1 459 345388374 345388834 6.130000e-163 584.0
5 TraesCS6A01G262900 chr6D 98.611 72 1 0 4185 4256 345392247 345392318 1.240000e-25 128.0
6 TraesCS6A01G262900 chr6B 96.513 1950 49 7 1560 3501 521514307 521516245 0.000000e+00 3206.0
7 TraesCS6A01G262900 chr6B 88.548 1109 70 18 460 1564 521513222 521514277 0.000000e+00 1291.0
8 TraesCS6A01G262900 chr6B 95.199 729 29 3 3531 4253 521516246 521516974 0.000000e+00 1147.0
9 TraesCS6A01G262900 chr3D 90.278 216 15 1 2163 2378 32190911 32190702 1.170000e-70 278.0
10 TraesCS6A01G262900 chr7D 86.822 258 20 4 1 244 98997897 98997640 4.190000e-70 276.0
11 TraesCS6A01G262900 chr7D 83.984 256 25 8 1 244 91690003 91689752 9.200000e-57 231.0
12 TraesCS6A01G262900 chr7D 93.333 45 2 1 2 45 222146914 222146870 9.880000e-07 65.8
13 TraesCS6A01G262900 chr4A 86.047 258 22 4 1 244 620474639 620474896 9.070000e-67 265.0
14 TraesCS6A01G262900 chr4A 84.646 254 25 6 2 244 733630332 733630582 1.530000e-59 241.0
15 TraesCS6A01G262900 chr4A 83.984 256 19 9 1 244 574771660 574771415 4.280000e-55 226.0
16 TraesCS6A01G262900 chr4A 78.598 271 31 8 1 244 175849899 175850169 2.050000e-33 154.0
17 TraesCS6A01G262900 chr7A 85.214 257 24 4 1 244 93256718 93256463 7.060000e-63 252.0
18 TraesCS6A01G262900 chr3A 83.594 256 20 9 1 244 224963145 224963390 1.990000e-53 220.0
19 TraesCS6A01G262900 chr2D 82.331 266 23 8 1 244 119841069 119841332 4.310000e-50 209.0
20 TraesCS6A01G262900 chr1A 84.804 204 18 5 1 191 572678125 572678328 4.340000e-45 193.0
21 TraesCS6A01G262900 chr7B 80.408 245 38 9 3 244 43245323 43245560 1.220000e-40 178.0
22 TraesCS6A01G262900 chr4B 77.491 271 31 11 3 244 377950975 377950706 7.420000e-28 135.0


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 TraesCS6A01G262900 chr6A 486004182 486008437 4255 False 7860.000000 7860 100.00000 1 4256 1 chr6A.!!$F2 4255
1 TraesCS6A01G262900 chr6D 345388374 345392318 3944 False 1459.500000 3969 93.19125 1 4256 4 chr6D.!!$F1 4255
2 TraesCS6A01G262900 chr6B 521513222 521516974 3752 False 1881.333333 3206 93.42000 460 4253 3 chr6B.!!$F1 3793

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
308 316 0.253044 ATTGGCTTCAAGCTCCGCTA 59.747 50.0 9.83 0.00 41.99 4.26 F
905 941 0.317186 GCTAGCGGCTAGTCTTCGTC 60.317 60.0 31.34 14.04 36.53 4.20 F
1564 1642 0.099436 GCATGGCGAACTAGGCTTTG 59.901 55.0 0.00 0.00 37.59 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1254 0.105453 TATCTGGACCTCCTCCTGGC 60.105 60.000 0.0 0.0 40.26 4.85 R
1866 1982 1.602377 GGACGAACTCCAACAAACAGG 59.398 52.381 0.0 0.0 39.21 4.00 R
3348 3468 2.159028 CCAAACCGAACCAAACCAACAT 60.159 45.455 0.0 0.0 0.00 2.71 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
71 73 7.281100 GGGAGAATAGAGTTTGAAATACACCTG 59.719 40.741 0.00 0.00 0.00 4.00
72 74 7.281100 GGAGAATAGAGTTTGAAATACACCTGG 59.719 40.741 0.00 0.00 0.00 4.45
76 78 8.788325 ATAGAGTTTGAAATACACCTGGTAAC 57.212 34.615 0.00 0.00 35.14 2.50
79 81 6.597562 AGTTTGAAATACACCTGGTAACTGA 58.402 36.000 0.00 0.00 35.14 3.41
88 90 6.538945 ACACCTGGTAACTGAAAAACAAAT 57.461 33.333 0.00 0.00 37.83 2.32
103 105 6.635030 AAAACAAATGAGTGTTACTCTCCC 57.365 37.500 11.25 0.00 45.27 4.30
110 112 3.285484 GAGTGTTACTCTCCCGGTATGA 58.715 50.000 0.00 0.00 41.88 2.15
119 121 1.225983 CCCGGTATGATGTTGCCCA 59.774 57.895 0.00 0.00 0.00 5.36
135 137 1.560505 CCCAATTTCTTCACCCCCAG 58.439 55.000 0.00 0.00 0.00 4.45
139 141 2.041620 CAATTTCTTCACCCCCAGAGGA 59.958 50.000 0.00 0.00 38.24 3.71
162 164 5.083533 TGGCTTCACTTTTGATGTTGTTT 57.916 34.783 0.00 0.00 31.01 2.83
198 200 4.093556 GGAGGCATACTCTTTTGTCGAAAG 59.906 45.833 6.25 6.25 45.83 2.62
219 222 1.202722 ACCCAGACGTTCCGTTCATTT 60.203 47.619 0.00 0.00 41.37 2.32
226 229 4.513692 AGACGTTCCGTTCATTTCAAATGA 59.486 37.500 8.85 8.85 41.37 2.57
227 230 4.533222 ACGTTCCGTTCATTTCAAATGAC 58.467 39.130 12.58 7.34 36.35 3.06
279 287 7.119553 CCACATGCTATTTTATTTGTTTTGGCT 59.880 33.333 0.00 0.00 0.00 4.75
307 315 1.001641 ATTGGCTTCAAGCTCCGCT 60.002 52.632 9.83 0.00 41.99 5.52
308 316 0.253044 ATTGGCTTCAAGCTCCGCTA 59.747 50.000 9.83 0.00 41.99 4.26
309 317 0.391661 TTGGCTTCAAGCTCCGCTAG 60.392 55.000 9.83 0.00 41.99 3.42
329 337 0.384309 CAGTAGCGCGTCCCTTATGA 59.616 55.000 8.43 0.00 0.00 2.15
351 359 7.015226 TGACGCAACAATTAATGAGATTAGG 57.985 36.000 0.00 0.00 0.00 2.69
414 422 7.323049 TGAGTTTCGAACCTTAAATGTTGAA 57.677 32.000 0.00 0.00 0.00 2.69
423 431 7.165812 CGAACCTTAAATGTTGAAACTCACAAG 59.834 37.037 0.00 0.00 0.00 3.16
427 435 7.857885 CCTTAAATGTTGAAACTCACAAGTCTC 59.142 37.037 0.00 0.00 33.48 3.36
433 441 3.063452 TGAAACTCACAAGTCTCGCAAAC 59.937 43.478 0.00 0.00 33.48 2.93
450 458 3.433615 GCAAACACATGGTCTGACTCTAC 59.566 47.826 7.85 0.00 0.00 2.59
453 461 0.818296 ACATGGTCTGACTCTACGGC 59.182 55.000 7.85 0.00 0.00 5.68
454 462 1.107114 CATGGTCTGACTCTACGGCT 58.893 55.000 7.85 0.00 0.00 5.52
455 463 1.107114 ATGGTCTGACTCTACGGCTG 58.893 55.000 7.85 0.00 0.00 4.85
457 465 1.139947 GTCTGACTCTACGGCTGGC 59.860 63.158 0.00 0.00 0.00 4.85
534 570 2.229784 GCAGCAGGCAAAGTCAAAGTAT 59.770 45.455 0.00 0.00 43.97 2.12
697 733 2.695666 TCGGGTTCTCAGAATCTCATCC 59.304 50.000 0.00 0.00 0.00 3.51
699 735 3.739519 CGGGTTCTCAGAATCTCATCCAC 60.740 52.174 0.00 0.00 0.00 4.02
700 736 3.432890 GGGTTCTCAGAATCTCATCCACC 60.433 52.174 0.00 0.00 0.00 4.61
701 737 3.432890 GGTTCTCAGAATCTCATCCACCC 60.433 52.174 0.00 0.00 0.00 4.61
702 738 3.411454 TCTCAGAATCTCATCCACCCT 57.589 47.619 0.00 0.00 0.00 4.34
703 739 3.036819 TCTCAGAATCTCATCCACCCTG 58.963 50.000 0.00 0.00 0.00 4.45
727 763 2.065993 ATCATCGGGAGAATTACGCG 57.934 50.000 3.53 3.53 45.37 6.01
742 778 0.734253 ACGCGACTGCTCACTCATTC 60.734 55.000 15.93 0.00 39.65 2.67
747 783 3.178267 CGACTGCTCACTCATTCTCTTC 58.822 50.000 0.00 0.00 0.00 2.87
757 793 3.118592 ACTCATTCTCTTCGGTCAATCCC 60.119 47.826 0.00 0.00 0.00 3.85
762 798 1.898154 CTTCGGTCAATCCCGGAGT 59.102 57.895 0.73 0.00 46.60 3.85
763 799 1.108776 CTTCGGTCAATCCCGGAGTA 58.891 55.000 0.73 0.00 46.60 2.59
764 800 1.202382 CTTCGGTCAATCCCGGAGTAC 60.202 57.143 0.73 0.00 46.60 2.73
765 801 2.501492 CGGTCAATCCCGGAGTACT 58.499 57.895 0.73 0.00 44.32 2.73
766 802 0.384669 CGGTCAATCCCGGAGTACTC 59.615 60.000 14.87 14.87 44.32 2.59
767 803 1.777941 GGTCAATCCCGGAGTACTCT 58.222 55.000 21.88 0.00 0.00 3.24
768 804 1.409427 GGTCAATCCCGGAGTACTCTG 59.591 57.143 22.75 22.75 35.77 3.35
769 805 1.112113 TCAATCCCGGAGTACTCTGC 58.888 55.000 24.04 7.56 34.69 4.26
818 854 2.504681 GGGCACTGCAAATTCGCG 60.505 61.111 0.00 0.00 33.35 5.87
855 891 1.520787 GGACGAACCCGATGCGATT 60.521 57.895 0.00 0.00 39.50 3.34
863 899 2.016165 CCGATGCGATTCGATGCGA 61.016 57.895 10.88 0.00 41.62 5.10
864 900 1.347097 CCGATGCGATTCGATGCGAT 61.347 55.000 10.88 2.87 41.62 4.58
867 903 1.904852 ATGCGATTCGATGCGATGCC 61.905 55.000 10.88 0.00 35.23 4.40
869 905 1.490258 CGATTCGATGCGATGCCAG 59.510 57.895 0.00 0.00 35.23 4.85
870 906 1.206072 GATTCGATGCGATGCCAGC 59.794 57.895 0.00 0.00 35.23 4.85
872 908 4.512961 TCGATGCGATGCCAGCGT 62.513 61.111 3.63 0.00 44.21 5.07
873 909 3.993234 CGATGCGATGCCAGCGTC 61.993 66.667 3.63 1.59 44.66 5.19
874 910 2.891936 GATGCGATGCCAGCGTCA 60.892 61.111 3.63 2.89 46.64 4.35
875 911 2.879070 GATGCGATGCCAGCGTCAG 61.879 63.158 3.63 6.10 46.64 3.51
877 913 3.260483 GCGATGCCAGCGTCAGAG 61.260 66.667 3.63 0.00 32.55 3.35
879 915 1.588403 CGATGCCAGCGTCAGAGAG 60.588 63.158 12.10 0.00 32.55 3.20
884 920 2.487428 CAGCGTCAGAGAGGTCCG 59.513 66.667 0.00 0.00 0.00 4.79
903 939 1.369448 CGCTAGCGGCTAGTCTTCG 60.369 63.158 31.34 23.60 36.53 3.79
904 940 1.728672 GCTAGCGGCTAGTCTTCGT 59.271 57.895 31.34 0.00 36.53 3.85
905 941 0.317186 GCTAGCGGCTAGTCTTCGTC 60.317 60.000 31.34 14.04 36.53 4.20
906 942 1.015109 CTAGCGGCTAGTCTTCGTCA 58.985 55.000 25.36 0.00 30.16 4.35
907 943 0.731417 TAGCGGCTAGTCTTCGTCAC 59.269 55.000 5.42 0.00 0.00 3.67
908 944 1.211969 GCGGCTAGTCTTCGTCACA 59.788 57.895 0.00 0.00 0.00 3.58
910 946 0.793478 CGGCTAGTCTTCGTCACACG 60.793 60.000 0.00 0.00 44.19 4.49
982 1019 4.936411 GGAACAAAAAGGACTAGTAGGAGC 59.064 45.833 0.00 0.00 0.00 4.70
990 1027 2.650322 GACTAGTAGGAGCAGCTCTGT 58.350 52.381 21.99 12.11 0.00 3.41
991 1028 3.020984 GACTAGTAGGAGCAGCTCTGTT 58.979 50.000 21.99 10.54 0.00 3.16
992 1029 3.020984 ACTAGTAGGAGCAGCTCTGTTC 58.979 50.000 21.99 5.33 39.64 3.18
1025 1062 2.430921 CGAGACGACACAGTGCCC 60.431 66.667 0.00 0.00 0.00 5.36
1269 1306 0.667792 AGTTCGCTTCTGGTTCGAGC 60.668 55.000 0.00 0.00 33.56 5.03
1291 1328 2.861286 CGTGATGAGATATCTCGCTGG 58.139 52.381 24.27 11.02 45.72 4.85
1302 1339 0.250295 TCTCGCTGGTTCCTTGGTTG 60.250 55.000 0.00 0.00 0.00 3.77
1307 1344 2.351738 CGCTGGTTCCTTGGTTGAATTC 60.352 50.000 0.00 0.00 0.00 2.17
1338 1412 2.764572 ACGTGGAAACCCTGATAGTAGG 59.235 50.000 0.00 0.00 37.59 3.18
1349 1423 3.572255 CCTGATAGTAGGAGCTCACCTTC 59.428 52.174 17.19 2.86 40.42 3.46
1350 1424 4.211125 CTGATAGTAGGAGCTCACCTTCA 58.789 47.826 17.19 10.45 41.00 3.02
1364 1438 1.349627 CTTCATGATGTGGTCGCGC 59.650 57.895 0.00 0.00 0.00 6.86
1365 1439 2.352109 CTTCATGATGTGGTCGCGCG 62.352 60.000 26.76 26.76 0.00 6.86
1366 1440 3.928769 CATGATGTGGTCGCGCGG 61.929 66.667 31.69 11.75 0.00 6.46
1423 1501 7.547227 AGACAAACAAAACTGCTGTTTATCTT 58.453 30.769 20.29 11.44 44.24 2.40
1424 1502 7.489113 AGACAAACAAAACTGCTGTTTATCTTG 59.511 33.333 20.29 21.31 44.24 3.02
1525 1603 1.823470 GGCATCTTGGCCGTATGCA 60.823 57.895 27.82 0.00 46.18 3.96
1540 1618 5.074430 CGTATGCAGTAACGGGTTTATTC 57.926 43.478 10.28 0.00 35.51 1.75
1550 1628 1.330521 CGGGTTTATTCACGAGCATGG 59.669 52.381 0.00 0.00 36.20 3.66
1552 1630 1.268032 GGTTTATTCACGAGCATGGCG 60.268 52.381 0.00 0.00 0.00 5.69
1564 1642 0.099436 GCATGGCGAACTAGGCTTTG 59.901 55.000 0.00 0.00 37.59 2.77
1565 1643 0.734889 CATGGCGAACTAGGCTTTGG 59.265 55.000 0.00 0.00 37.59 3.28
1566 1644 0.618458 ATGGCGAACTAGGCTTTGGA 59.382 50.000 0.00 0.00 37.59 3.53
1567 1645 0.618458 TGGCGAACTAGGCTTTGGAT 59.382 50.000 0.00 0.00 37.59 3.41
1568 1646 1.004277 TGGCGAACTAGGCTTTGGATT 59.996 47.619 0.00 0.00 37.59 3.01
1569 1647 2.237643 TGGCGAACTAGGCTTTGGATTA 59.762 45.455 0.00 0.00 37.59 1.75
1570 1648 2.872858 GGCGAACTAGGCTTTGGATTAG 59.127 50.000 0.00 0.00 0.00 1.73
1571 1649 3.532542 GCGAACTAGGCTTTGGATTAGT 58.467 45.455 0.00 0.00 0.00 2.24
1572 1650 3.309954 GCGAACTAGGCTTTGGATTAGTG 59.690 47.826 0.00 0.00 0.00 2.74
1573 1651 4.504858 CGAACTAGGCTTTGGATTAGTGT 58.495 43.478 0.00 0.00 0.00 3.55
1574 1652 4.935808 CGAACTAGGCTTTGGATTAGTGTT 59.064 41.667 0.00 0.00 0.00 3.32
1575 1653 5.411669 CGAACTAGGCTTTGGATTAGTGTTT 59.588 40.000 0.00 0.00 0.00 2.83
1576 1654 6.402226 CGAACTAGGCTTTGGATTAGTGTTTC 60.402 42.308 0.00 0.00 0.00 2.78
1577 1655 5.254115 ACTAGGCTTTGGATTAGTGTTTCC 58.746 41.667 0.00 0.00 0.00 3.13
1578 1656 3.431415 AGGCTTTGGATTAGTGTTTCCC 58.569 45.455 0.00 0.00 0.00 3.97
1579 1657 3.076032 AGGCTTTGGATTAGTGTTTCCCT 59.924 43.478 0.00 0.00 0.00 4.20
1581 1659 4.321974 GGCTTTGGATTAGTGTTTCCCTTG 60.322 45.833 0.00 0.00 0.00 3.61
1594 1709 2.804986 TCCCTTGTAATCTGCATGCA 57.195 45.000 21.29 21.29 0.00 3.96
1615 1730 1.811965 CGAATGTGAGTGCCAAATCCA 59.188 47.619 0.00 0.00 0.00 3.41
1622 1737 2.228582 TGAGTGCCAAATCCATGTTTCG 59.771 45.455 0.00 0.00 0.00 3.46
1624 1739 2.030007 AGTGCCAAATCCATGTTTCGTG 60.030 45.455 0.00 0.00 0.00 4.35
1652 1768 1.002087 CTCTCCGGTGGTTAGCACTTT 59.998 52.381 14.31 0.00 0.00 2.66
1679 1795 2.858476 TGGTCATGCCACCCACCT 60.858 61.111 4.93 0.00 43.61 4.00
1680 1796 2.044946 GGTCATGCCACCCACCTC 60.045 66.667 1.78 0.00 37.17 3.85
1681 1797 2.606587 GGTCATGCCACCCACCTCT 61.607 63.158 1.78 0.00 37.17 3.69
1682 1798 1.271840 GGTCATGCCACCCACCTCTA 61.272 60.000 1.78 0.00 37.17 2.43
1683 1799 0.107654 GTCATGCCACCCACCTCTAC 60.108 60.000 0.00 0.00 0.00 2.59
1684 1800 1.224592 CATGCCACCCACCTCTACC 59.775 63.158 0.00 0.00 0.00 3.18
1685 1801 1.082954 ATGCCACCCACCTCTACCT 59.917 57.895 0.00 0.00 0.00 3.08
1722 1838 4.009675 GGAGTTCCATGTGCATTCAAGTA 58.990 43.478 0.00 0.00 35.64 2.24
1731 1847 6.309494 CCATGTGCATTCAAGTATTTTGTCAG 59.691 38.462 0.00 0.00 0.00 3.51
1774 1890 1.750193 CATCCACGTATTTGGCCAGT 58.250 50.000 5.11 1.00 36.48 4.00
1779 1895 0.398696 ACGTATTTGGCCAGTGGTGA 59.601 50.000 11.74 0.00 0.00 4.02
1784 1900 1.909700 TTTGGCCAGTGGTGAGAATC 58.090 50.000 11.74 0.00 0.00 2.52
1794 1910 3.117131 AGTGGTGAGAATCCCCTGTTTTT 60.117 43.478 0.00 0.00 0.00 1.94
1819 1935 4.301072 TCATCTGACAGGGTTTTAAGGG 57.699 45.455 1.81 0.00 0.00 3.95
1832 1948 3.719268 TTTAAGGGCTGATGAGAGCAA 57.281 42.857 0.00 0.00 41.08 3.91
1843 1959 3.130164 TGATGAGAGCAACAGCTAGACTC 59.870 47.826 0.00 0.00 39.10 3.36
1907 2023 6.359617 CGTCCAAACATTTTGTCATGTCTTAC 59.640 38.462 0.00 0.00 36.30 2.34
1941 2057 7.922505 TGTTCGGAATTTACAGTTTGATTTG 57.077 32.000 0.00 0.00 0.00 2.32
1953 2069 4.695455 CAGTTTGATTTGACCTGTCGGTAT 59.305 41.667 0.00 0.00 45.73 2.73
2195 2311 2.535331 CTGGTTTTCCGGTGTTGTTTG 58.465 47.619 0.00 0.00 44.36 2.93
2372 2488 2.164624 CCTGTCTCAACTTACTCCCTCG 59.835 54.545 0.00 0.00 0.00 4.63
3205 3325 6.659668 AGTTTCTTCCCTTTTCCTATGTAAGC 59.340 38.462 0.00 0.00 0.00 3.09
3267 3387 1.497991 TTTCTGAGACGTGCTTTCCG 58.502 50.000 0.00 0.00 0.00 4.30
3348 3468 6.125719 TGAACACTGCATAATGGGCTATTAA 58.874 36.000 7.41 0.00 35.03 1.40
3581 3701 6.582677 TCTTGTTCTTCCTTTTGTGTTCAA 57.417 33.333 0.00 0.00 0.00 2.69
3648 3769 7.274250 GCAAGAACACATGGAATAAATGTCTTC 59.726 37.037 0.00 0.00 36.10 2.87
3656 3777 9.525826 ACATGGAATAAATGTCTTCTCTCTTTT 57.474 29.630 0.00 0.00 32.83 2.27
3666 3787 6.129179 TGTCTTCTCTCTTTTTGTTTCCCAT 58.871 36.000 0.00 0.00 0.00 4.00
3690 3811 2.441750 ACCATAACATTGGCTACCCGAT 59.558 45.455 0.00 0.00 40.68 4.18
3830 3955 3.440872 TGTACAAAACCGCATTACATCCC 59.559 43.478 0.00 0.00 0.00 3.85
4001 4126 4.370917 CCAAAGAGGTCAACCATTGTTTG 58.629 43.478 1.33 3.50 38.89 2.93
4027 4152 0.538977 AAGAGGTCAACCGTCGAGGA 60.539 55.000 6.70 0.00 45.00 3.71
4031 4156 1.372623 GTCAACCGTCGAGGACCAC 60.373 63.158 6.70 0.00 45.00 4.16
4175 4300 6.265196 ACATAACCATTCTGTTTGCAAGAAGA 59.735 34.615 8.61 8.61 0.00 2.87
4182 4307 1.603802 TGTTTGCAAGAAGAGCTTCGG 59.396 47.619 0.00 3.25 43.97 4.30
4183 4308 0.593128 TTTGCAAGAAGAGCTTCGGC 59.407 50.000 17.26 17.26 43.97 5.54
4220 4372 4.044336 TGCAAGTTGAAGTTGACATTGG 57.956 40.909 16.41 0.00 30.18 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 9.016623 GTAACACTCATTTGTTTTTCAGTTACC 57.983 33.333 0.00 0.00 40.29 2.85
72 74 9.783256 AGTAACACTCATTTGTTTTTCAGTTAC 57.217 29.630 0.00 0.00 40.29 2.50
103 105 3.381272 AGAAATTGGGCAACATCATACCG 59.619 43.478 0.00 0.00 39.74 4.02
110 112 2.302733 GGGTGAAGAAATTGGGCAACAT 59.697 45.455 0.00 0.00 39.74 2.71
119 121 2.358258 TCCTCTGGGGGTGAAGAAATT 58.642 47.619 0.00 0.00 35.33 1.82
135 137 3.760684 ACATCAAAAGTGAAGCCATCCTC 59.239 43.478 0.00 0.00 37.30 3.71
139 141 4.942761 ACAACATCAAAAGTGAAGCCAT 57.057 36.364 0.00 0.00 37.30 4.40
150 152 5.982516 AGCGATTTTGCTAAACAACATCAAA 59.017 32.000 0.00 0.00 42.96 2.69
162 164 0.035534 TGCCTCCAGCGATTTTGCTA 60.036 50.000 0.00 0.00 45.23 3.49
219 222 5.645056 TGCTATTAGGATGGGTCATTTGA 57.355 39.130 0.00 0.00 0.00 2.69
226 229 4.446311 GGTGTTCATGCTATTAGGATGGGT 60.446 45.833 20.87 0.00 43.25 4.51
227 230 4.074970 GGTGTTCATGCTATTAGGATGGG 58.925 47.826 20.87 1.66 43.25 4.00
307 315 0.749091 TAAGGGACGCGCTACTGCTA 60.749 55.000 5.73 0.00 36.97 3.49
308 316 1.392710 ATAAGGGACGCGCTACTGCT 61.393 55.000 5.73 0.00 36.97 4.24
309 317 1.067582 ATAAGGGACGCGCTACTGC 59.932 57.895 5.73 0.00 0.00 4.40
310 318 0.384309 TCATAAGGGACGCGCTACTG 59.616 55.000 5.73 0.00 0.00 2.74
311 319 0.384669 GTCATAAGGGACGCGCTACT 59.615 55.000 5.73 0.00 0.00 2.57
329 337 6.119536 TCCCTAATCTCATTAATTGTTGCGT 58.880 36.000 0.00 0.00 0.00 5.24
388 396 8.610248 TCAACATTTAAGGTTCGAAACTCATA 57.390 30.769 17.67 3.04 0.00 2.15
397 405 6.491394 TGTGAGTTTCAACATTTAAGGTTCG 58.509 36.000 0.00 0.00 0.00 3.95
414 422 2.351726 GTGTTTGCGAGACTTGTGAGTT 59.648 45.455 0.00 0.00 35.88 3.01
423 431 1.195448 CAGACCATGTGTTTGCGAGAC 59.805 52.381 0.00 0.00 0.00 3.36
427 435 1.195448 GAGTCAGACCATGTGTTTGCG 59.805 52.381 0.00 0.00 0.00 4.85
433 441 1.469940 GCCGTAGAGTCAGACCATGTG 60.470 57.143 0.00 0.00 0.00 3.21
463 499 4.659874 GCGGTCACCACGTTTGCG 62.660 66.667 0.00 0.00 44.93 4.85
465 501 1.983196 TTGTGCGGTCACCACGTTTG 61.983 55.000 0.00 0.00 42.46 2.93
566 602 0.389757 GTAGATTCTCTGCGGTCCCC 59.610 60.000 0.00 0.00 0.00 4.81
697 733 0.681733 CCCGATGATAGGACAGGGTG 59.318 60.000 0.00 0.00 34.36 4.61
699 735 1.203063 TCTCCCGATGATAGGACAGGG 60.203 57.143 0.00 0.00 40.16 4.45
700 736 2.294449 TCTCCCGATGATAGGACAGG 57.706 55.000 0.00 0.00 0.00 4.00
701 737 4.881019 AATTCTCCCGATGATAGGACAG 57.119 45.455 0.00 0.00 0.00 3.51
702 738 4.217767 CGTAATTCTCCCGATGATAGGACA 59.782 45.833 0.00 0.00 0.00 4.02
703 739 4.734917 CGTAATTCTCCCGATGATAGGAC 58.265 47.826 0.00 0.00 0.00 3.85
727 763 3.178267 CGAAGAGAATGAGTGAGCAGTC 58.822 50.000 0.00 0.00 33.38 3.51
757 793 2.743195 GCAGTTGCAGAGTACTCCG 58.257 57.895 19.38 10.64 41.59 4.63
768 804 0.249031 GGACTTGTGGTTGCAGTTGC 60.249 55.000 0.00 0.00 42.50 4.17
769 805 1.102154 TGGACTTGTGGTTGCAGTTG 58.898 50.000 0.00 0.00 0.00 3.16
806 842 0.923403 TCGAGATCGCGAATTTGCAG 59.077 50.000 19.51 10.24 37.35 4.41
855 891 4.512961 ACGCTGGCATCGCATCGA 62.513 61.111 11.07 0.00 41.13 3.59
863 899 1.954362 GACCTCTCTGACGCTGGCAT 61.954 60.000 0.00 0.00 0.00 4.40
864 900 2.601666 ACCTCTCTGACGCTGGCA 60.602 61.111 0.00 0.00 0.00 4.92
867 903 2.487428 CGGACCTCTCTGACGCTG 59.513 66.667 0.00 0.00 0.00 5.18
869 905 4.838486 CGCGGACCTCTCTGACGC 62.838 72.222 0.00 0.00 46.04 5.19
870 906 4.838486 GCGCGGACCTCTCTGACG 62.838 72.222 8.83 0.00 0.00 4.35
872 908 1.820056 CTAGCGCGGACCTCTCTGA 60.820 63.158 8.83 0.00 0.00 3.27
873 909 2.718731 CTAGCGCGGACCTCTCTG 59.281 66.667 8.83 0.00 0.00 3.35
874 910 3.213402 GCTAGCGCGGACCTCTCT 61.213 66.667 8.83 0.00 0.00 3.10
903 939 0.374758 TCGCTATCGTACCGTGTGAC 59.625 55.000 0.00 0.00 36.96 3.67
904 940 0.374758 GTCGCTATCGTACCGTGTGA 59.625 55.000 0.00 0.00 36.96 3.58
905 941 0.922560 CGTCGCTATCGTACCGTGTG 60.923 60.000 0.00 0.00 36.96 3.82
906 942 1.349627 CGTCGCTATCGTACCGTGT 59.650 57.895 0.00 0.00 36.96 4.49
907 943 1.368493 CCGTCGCTATCGTACCGTG 60.368 63.158 0.00 0.00 36.96 4.94
908 944 3.017323 CCGTCGCTATCGTACCGT 58.983 61.111 0.00 0.00 36.96 4.83
910 946 2.378945 TTCGCCGTCGCTATCGTACC 62.379 60.000 0.00 0.00 36.96 3.34
971 1008 2.818751 ACAGAGCTGCTCCTACTAGT 57.181 50.000 25.09 11.79 0.00 2.57
982 1019 1.153939 CGGAGTCGGAACAGAGCTG 60.154 63.158 0.00 0.00 0.00 4.24
990 1027 3.796443 CGTCGCTCGGAGTCGGAA 61.796 66.667 17.35 2.04 36.95 4.30
994 1031 4.872485 CTCGCGTCGCTCGGAGTC 62.872 72.222 16.36 0.00 40.26 3.36
1025 1062 1.600636 TGTGGAAAAGAGGCCGCAG 60.601 57.895 9.88 0.00 39.58 5.18
1216 1253 2.905676 ATCTGGACCTCCTCCTGGCC 62.906 65.000 0.00 0.00 40.26 5.36
1217 1254 0.105453 TATCTGGACCTCCTCCTGGC 60.105 60.000 0.00 0.00 40.26 4.85
1269 1306 1.254882 GCGAGATATCTCATCACGCG 58.745 55.000 27.97 16.12 44.87 6.01
1291 1328 1.886542 AGGCGAATTCAACCAAGGAAC 59.113 47.619 15.05 0.00 0.00 3.62
1302 1339 1.129326 CACGTATCCGAGGCGAATTC 58.871 55.000 0.00 0.00 37.88 2.17
1307 1344 1.140161 TTTCCACGTATCCGAGGCG 59.860 57.895 0.00 0.00 43.54 5.52
1338 1412 2.286872 CCACATCATGAAGGTGAGCTC 58.713 52.381 24.55 6.82 34.52 4.09
1349 1423 3.928769 CCGCGCGACCACATCATG 61.929 66.667 34.63 6.11 0.00 3.07
1368 1442 4.659172 TGCCCCAGCCAAAGACGG 62.659 66.667 0.00 0.00 38.69 4.79
1396 1470 8.270026 GATAAACAGCAGTTTTGTTTGTCTAC 57.730 34.615 12.75 0.00 45.32 2.59
1405 1479 5.399301 CGAACCAAGATAAACAGCAGTTTTG 59.601 40.000 12.75 5.00 45.32 2.44
1406 1480 5.067283 ACGAACCAAGATAAACAGCAGTTTT 59.933 36.000 12.75 1.27 45.32 2.43
1408 1482 4.134563 ACGAACCAAGATAAACAGCAGTT 58.865 39.130 0.00 0.00 40.40 3.16
1423 1501 3.146066 CAAATTCCTTGGAGACGAACCA 58.854 45.455 0.00 0.00 35.47 3.67
1424 1502 3.831715 CAAATTCCTTGGAGACGAACC 57.168 47.619 0.00 0.00 0.00 3.62
1448 1526 4.692475 CCCCACCAACGGACGGAC 62.692 72.222 0.00 0.00 0.00 4.79
1451 1529 4.388499 CTCCCCCACCAACGGACG 62.388 72.222 0.00 0.00 0.00 4.79
1518 1596 4.567558 TGAATAAACCCGTTACTGCATACG 59.432 41.667 8.63 8.63 37.50 3.06
1525 1603 3.256558 GCTCGTGAATAAACCCGTTACT 58.743 45.455 0.00 0.00 0.00 2.24
1540 1618 1.148157 CCTAGTTCGCCATGCTCGTG 61.148 60.000 5.68 0.00 0.00 4.35
1550 1628 3.309954 CACTAATCCAAAGCCTAGTTCGC 59.690 47.826 0.00 0.00 0.00 4.70
1552 1630 6.127980 GGAAACACTAATCCAAAGCCTAGTTC 60.128 42.308 0.00 0.00 35.71 3.01
1564 1642 6.183360 GCAGATTACAAGGGAAACACTAATCC 60.183 42.308 0.00 0.00 34.85 3.01
1565 1643 6.374333 TGCAGATTACAAGGGAAACACTAATC 59.626 38.462 0.00 0.00 0.00 1.75
1566 1644 6.245408 TGCAGATTACAAGGGAAACACTAAT 58.755 36.000 0.00 0.00 0.00 1.73
1567 1645 5.626142 TGCAGATTACAAGGGAAACACTAA 58.374 37.500 0.00 0.00 0.00 2.24
1568 1646 5.235850 TGCAGATTACAAGGGAAACACTA 57.764 39.130 0.00 0.00 0.00 2.74
1569 1647 4.098914 TGCAGATTACAAGGGAAACACT 57.901 40.909 0.00 0.00 0.00 3.55
1570 1648 4.737054 CATGCAGATTACAAGGGAAACAC 58.263 43.478 0.00 0.00 0.00 3.32
1571 1649 3.193267 GCATGCAGATTACAAGGGAAACA 59.807 43.478 14.21 0.00 0.00 2.83
1572 1650 3.193267 TGCATGCAGATTACAAGGGAAAC 59.807 43.478 18.46 0.00 0.00 2.78
1573 1651 3.193267 GTGCATGCAGATTACAAGGGAAA 59.807 43.478 23.41 0.00 0.00 3.13
1574 1652 2.754552 GTGCATGCAGATTACAAGGGAA 59.245 45.455 23.41 0.00 0.00 3.97
1575 1653 2.368439 GTGCATGCAGATTACAAGGGA 58.632 47.619 23.41 0.00 0.00 4.20
1576 1654 1.064505 CGTGCATGCAGATTACAAGGG 59.935 52.381 23.41 0.00 0.00 3.95
1577 1655 2.009051 TCGTGCATGCAGATTACAAGG 58.991 47.619 23.41 1.89 0.00 3.61
1578 1656 3.745332 TTCGTGCATGCAGATTACAAG 57.255 42.857 23.41 5.41 0.00 3.16
1579 1657 3.439825 ACATTCGTGCATGCAGATTACAA 59.560 39.130 23.41 7.92 0.00 2.41
1581 1659 3.063861 TCACATTCGTGCATGCAGATTAC 59.936 43.478 23.41 8.01 43.28 1.89
1594 1709 1.812571 GGATTTGGCACTCACATTCGT 59.187 47.619 0.00 0.00 0.00 3.85
1624 1739 2.740055 CACCGGAGAGCACACAGC 60.740 66.667 9.46 0.00 46.19 4.40
1652 1768 2.542013 GCATGACCACACACGTGCA 61.542 57.895 17.22 4.42 44.99 4.57
1684 1800 1.064017 ACTCCTACTCCCTCAGCAGAG 60.064 57.143 0.00 0.00 41.72 3.35
1685 1801 1.003646 ACTCCTACTCCCTCAGCAGA 58.996 55.000 0.00 0.00 0.00 4.26
1694 1810 1.555075 TGCACATGGAACTCCTACTCC 59.445 52.381 0.00 0.00 36.82 3.85
1722 1838 4.491676 GCATCTTGCATGACTGACAAAAT 58.508 39.130 4.14 0.00 44.26 1.82
1758 1874 2.179764 CCACTGGCCAAATACGTGG 58.820 57.895 22.55 22.55 42.05 4.94
1774 1890 3.496331 GAAAAACAGGGGATTCTCACCA 58.504 45.455 0.00 0.00 44.30 4.17
1779 1895 3.827722 TGAACGAAAAACAGGGGATTCT 58.172 40.909 0.00 0.00 0.00 2.40
1784 1900 3.058224 GTCAGATGAACGAAAAACAGGGG 60.058 47.826 0.00 0.00 0.00 4.79
1794 1910 3.485463 AAAACCCTGTCAGATGAACGA 57.515 42.857 0.00 0.00 0.00 3.85
1832 1948 2.502947 TGGATGCATTGAGTCTAGCTGT 59.497 45.455 0.00 0.00 0.00 4.40
1866 1982 1.602377 GGACGAACTCCAACAAACAGG 59.398 52.381 0.00 0.00 39.21 4.00
1907 2023 7.442364 ACTGTAAATTCCGAACATGGATGATAG 59.558 37.037 0.00 0.00 38.00 2.08
1953 2069 4.876125 TGCAATTTACAATTGGAAAGCGA 58.124 34.783 20.15 8.19 0.00 4.93
2195 2311 3.057019 GACGGAAAAGAAATTGGGCAAC 58.943 45.455 0.00 0.00 0.00 4.17
3205 3325 4.397103 CCCAATTCCCATGATGATACATCG 59.603 45.833 0.00 0.00 0.00 3.84
3348 3468 2.159028 CCAAACCGAACCAAACCAACAT 60.159 45.455 0.00 0.00 0.00 2.71
3581 3701 7.547370 GCACTCTACAAGATGACAACTAGAAAT 59.453 37.037 0.00 0.00 0.00 2.17
3648 3769 6.003950 TGGTCTATGGGAAACAAAAAGAGAG 58.996 40.000 0.00 0.00 0.00 3.20
3656 3777 6.379703 CCAATGTTATGGTCTATGGGAAACAA 59.620 38.462 0.00 0.00 35.65 2.83
3666 3787 3.070446 CGGGTAGCCAATGTTATGGTCTA 59.930 47.826 12.31 0.00 42.75 2.59
3690 3811 6.239176 CCTTTTAACCAAGTATGTGCTTCCAA 60.239 38.462 0.00 0.00 0.00 3.53
4001 4126 3.059800 CGACGGTTGACCTCTTTTCTTTC 60.060 47.826 0.00 0.00 0.00 2.62
4027 4152 5.692115 TCCTTACATCATACACATGTGGT 57.308 39.130 28.64 17.60 35.95 4.16
4031 4156 9.716531 ATGTAGATTCCTTACATCATACACATG 57.283 33.333 0.00 0.00 29.28 3.21
4175 4300 2.936202 ACCATCAAATATGCCGAAGCT 58.064 42.857 0.00 0.00 40.80 3.74
4182 4307 5.353938 ACTTGCATGAACCATCAAATATGC 58.646 37.500 6.60 0.00 39.49 3.14
4183 4308 7.036829 TCAACTTGCATGAACCATCAAATATG 58.963 34.615 6.60 0.00 39.49 1.78
4220 4372 4.935885 ACACGATGAAGATTCTTTCAGC 57.064 40.909 0.00 2.85 40.16 4.26


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

AutoCloner maintained by Alex Coulton.