Multiple sequence alignment - TraesCS5A01G330900

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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 TraesCS5A01G330900 chr5A 100.000 6887 0 0 1 6887 540279820 540286706 0.000000e+00 12718.0
1 TraesCS5A01G330900 chr5D 95.753 5157 106 39 421 5531 425999527 426004616 0.000000e+00 8205.0
2 TraesCS5A01G330900 chr5D 95.652 1219 36 6 5685 6887 426004898 426006115 0.000000e+00 1941.0
3 TraesCS5A01G330900 chr5D 88.780 410 41 3 12 421 425998799 425999203 1.330000e-136 497.0
4 TraesCS5A01G330900 chr5B 95.516 3546 108 17 3367 6887 515576823 515580342 0.000000e+00 5620.0
5 TraesCS5A01G330900 chr5B 93.840 3182 92 33 210 3354 515573724 515576838 0.000000e+00 4695.0
6 TraesCS5A01G330900 chr5B 95.745 47 1 1 2683 2729 556781934 556781979 2.660000e-09 75.0
7 TraesCS5A01G330900 chr3D 95.652 46 1 1 2683 2728 590082907 590082863 9.580000e-09 73.1
8 TraesCS5A01G330900 chr3D 95.652 46 1 1 2683 2728 593338018 593337974 9.580000e-09 73.1
9 TraesCS5A01G330900 chr3B 95.556 45 2 0 2682 2726 52711094 52711138 9.580000e-09 73.1
10 TraesCS5A01G330900 chr3A 95.556 45 2 0 2683 2727 662401412 662401456 9.580000e-09 73.1
11 TraesCS5A01G330900 chr2D 95.652 46 1 1 2683 2728 37959469 37959513 9.580000e-09 73.1
12 TraesCS5A01G330900 chr6D 92.157 51 3 1 2683 2733 49270680 49270631 3.450000e-08 71.3


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 TraesCS5A01G330900 chr5A 540279820 540286706 6886 False 12718.000000 12718 100.000 1 6887 1 chr5A.!!$F1 6886
1 TraesCS5A01G330900 chr5D 425998799 426006115 7316 False 3547.666667 8205 93.395 12 6887 3 chr5D.!!$F1 6875
2 TraesCS5A01G330900 chr5B 515573724 515580342 6618 False 5157.500000 5620 94.678 210 6887 2 chr5B.!!$F2 6677

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
48 49 0.462789 GCCATGGGCTTTGAGATTGG 59.537 55.000 15.13 0.00 46.69 3.16 F
550 880 0.467844 TCAAAGCACCACACAGGCAT 60.468 50.000 0.00 0.00 43.14 4.40 F
764 1102 0.955919 CGGCAGGAGTGAGAAAACCC 60.956 60.000 0.00 0.00 0.00 4.11 F
1894 2267 0.250234 CGCATCTCAAGGAGGGAACA 59.750 55.000 0.00 0.00 0.00 3.18 F
2075 2448 1.474077 CAAGTACCTTGAATGGGCTGC 59.526 52.381 0.00 0.00 43.42 5.25 F
3806 4183 2.744202 CACAAAGAGAGTATGTGCACCC 59.256 50.000 15.69 1.97 38.14 4.61 F
4878 5274 0.251787 GCCAAATTGGAGGGTGAGGT 60.252 55.000 17.47 0.00 40.96 3.85 F
5593 6001 0.110056 GTCATGCGCCAACTTCACTG 60.110 55.000 4.18 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1732 1.059657 CGAAATTGAACTGCGGTGCG 61.060 55.000 0.00 0.00 0.00 5.34 R
1870 2243 1.339055 CCCTCCTTGAGATGCGAACAA 60.339 52.381 0.00 0.00 0.00 2.83 R
2075 2448 2.101783 TGGTGCTAATGGCCATTTCAG 58.898 47.619 34.85 26.60 40.92 3.02 R
3497 3874 1.296002 GTTCCCAACCTCATACCCCT 58.704 55.000 0.00 0.00 0.00 4.79 R
3938 4315 2.306847 ACATTGTTCTTGGTCGCCTTT 58.693 42.857 0.00 0.00 0.00 3.11 R
5170 5576 0.179018 AGCGACTTTGCCAGGAGTTT 60.179 50.000 0.00 0.00 34.65 2.66 R
5784 6320 1.312371 AAAACGTGTGCAGCACTGGT 61.312 50.000 25.83 19.41 45.57 4.00 R
6714 7267 2.805671 CACACTCATGGCGAAAACACTA 59.194 45.455 0.00 0.00 0.00 2.74 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
31 32 2.945668 AGAAAACATGCTTATCGAGGCC 59.054 45.455 0.00 0.00 0.00 5.19
33 34 2.645838 AACATGCTTATCGAGGCCAT 57.354 45.000 5.01 0.00 0.00 4.40
48 49 0.462789 GCCATGGGCTTTGAGATTGG 59.537 55.000 15.13 0.00 46.69 3.16
57 58 4.384208 GGGCTTTGAGATTGGTAGCTCTAA 60.384 45.833 0.00 0.00 37.68 2.10
62 63 5.344743 TGAGATTGGTAGCTCTAACCTTG 57.655 43.478 5.75 0.00 37.68 3.61
80 81 5.824904 CCTTGAAGATGAAGGTACAATGG 57.175 43.478 0.00 0.00 36.05 3.16
117 118 2.617308 GTCTCCGTTATCTCCATGACGA 59.383 50.000 4.13 0.00 43.05 4.20
122 123 2.983136 CGTTATCTCCATGACGATGCTC 59.017 50.000 0.00 0.00 43.05 4.26
135 136 1.586422 GATGCTCGCATACACACCAT 58.414 50.000 4.10 0.00 36.70 3.55
176 177 2.120312 TGGACCACACCTTGACAGTTA 58.880 47.619 0.00 0.00 0.00 2.24
194 195 5.942236 ACAGTTAGAAGCAATGATCACATGT 59.058 36.000 0.00 0.00 36.79 3.21
196 197 5.356190 AGTTAGAAGCAATGATCACATGTGG 59.644 40.000 25.16 9.41 36.79 4.17
269 270 2.871096 ATGTCGTGGGGTGTGTAATT 57.129 45.000 0.00 0.00 0.00 1.40
270 271 3.985019 ATGTCGTGGGGTGTGTAATTA 57.015 42.857 0.00 0.00 0.00 1.40
271 272 3.766068 TGTCGTGGGGTGTGTAATTAA 57.234 42.857 0.00 0.00 0.00 1.40
272 273 4.289238 TGTCGTGGGGTGTGTAATTAAT 57.711 40.909 0.00 0.00 0.00 1.40
273 274 5.417754 TGTCGTGGGGTGTGTAATTAATA 57.582 39.130 0.00 0.00 0.00 0.98
274 275 5.991861 TGTCGTGGGGTGTGTAATTAATAT 58.008 37.500 0.00 0.00 0.00 1.28
324 325 7.093289 CCCAAGAATAGACCTGAAAAGTCTCTA 60.093 40.741 0.00 0.00 43.48 2.43
327 328 8.602472 AGAATAGACCTGAAAAGTCTCTACAT 57.398 34.615 0.00 0.00 43.48 2.29
347 348 2.651382 ACCACGCTAAAGAAACCCTT 57.349 45.000 0.00 0.00 36.47 3.95
369 374 0.687920 TATGGTTCCTTGACACGGCA 59.312 50.000 0.00 0.00 0.00 5.69
377 382 1.575244 CTTGACACGGCATCATCGAT 58.425 50.000 0.00 0.00 0.00 3.59
430 760 2.365237 AAGACCTAGGGACCGGGC 60.365 66.667 14.81 0.21 0.00 6.13
431 761 3.248248 AAGACCTAGGGACCGGGCA 62.248 63.158 11.00 0.00 28.77 5.36
432 762 3.155167 GACCTAGGGACCGGGCAG 61.155 72.222 11.00 0.00 0.00 4.85
433 763 3.674050 GACCTAGGGACCGGGCAGA 62.674 68.421 11.00 0.00 0.00 4.26
442 772 1.616374 GGACCGGGCAGAAATGAAAAA 59.384 47.619 11.00 0.00 0.00 1.94
445 775 2.432510 ACCGGGCAGAAATGAAAAACAA 59.567 40.909 6.32 0.00 0.00 2.83
492 822 4.738998 CCAACCGGCAGGCATGGA 62.739 66.667 19.53 0.00 45.65 3.41
499 829 0.819582 CGGCAGGCATGGAAAATCTT 59.180 50.000 0.00 0.00 0.00 2.40
527 857 2.282674 ACCCTGTCGACGTGGCTA 60.283 61.111 19.76 0.00 0.00 3.93
529 859 2.181021 CCTGTCGACGTGGCTACC 59.819 66.667 11.62 0.00 0.00 3.18
543 873 0.882927 GCTACCGTCAAAGCACCACA 60.883 55.000 0.00 0.00 38.63 4.17
547 877 1.648720 CGTCAAAGCACCACACAGG 59.351 57.895 0.00 0.00 45.67 4.00
548 878 1.360192 GTCAAAGCACCACACAGGC 59.640 57.895 0.00 0.00 43.14 4.85
549 879 1.077140 TCAAAGCACCACACAGGCA 60.077 52.632 0.00 0.00 43.14 4.75
550 880 0.467844 TCAAAGCACCACACAGGCAT 60.468 50.000 0.00 0.00 43.14 4.40
573 903 1.906574 AGGCCAGTCGAATTTAGGACA 59.093 47.619 5.01 0.00 35.63 4.02
590 920 5.614324 AGGACATCGGATGAATCACTTAA 57.386 39.130 23.98 0.00 0.00 1.85
591 921 5.989477 AGGACATCGGATGAATCACTTAAA 58.011 37.500 23.98 0.00 0.00 1.52
593 923 6.540189 AGGACATCGGATGAATCACTTAAAAG 59.460 38.462 23.98 0.00 0.00 2.27
594 924 6.124088 ACATCGGATGAATCACTTAAAAGC 57.876 37.500 23.98 0.00 0.00 3.51
596 926 6.319658 ACATCGGATGAATCACTTAAAAGCAT 59.680 34.615 23.98 0.00 0.00 3.79
634 967 5.526846 GTGCATTTTGAAGAAACAATGGGAA 59.473 36.000 0.00 0.00 0.00 3.97
635 968 6.205270 GTGCATTTTGAAGAAACAATGGGAAT 59.795 34.615 0.00 0.00 0.00 3.01
636 969 7.387397 GTGCATTTTGAAGAAACAATGGGAATA 59.613 33.333 0.00 0.00 0.00 1.75
762 1100 1.149148 GACGGCAGGAGTGAGAAAAC 58.851 55.000 0.00 0.00 0.00 2.43
764 1102 0.955919 CGGCAGGAGTGAGAAAACCC 60.956 60.000 0.00 0.00 0.00 4.11
765 1103 0.955919 GGCAGGAGTGAGAAAACCCG 60.956 60.000 0.00 0.00 0.00 5.28
769 1107 3.211045 CAGGAGTGAGAAAACCCGAAAA 58.789 45.455 0.00 0.00 0.00 2.29
770 1108 3.821033 CAGGAGTGAGAAAACCCGAAAAT 59.179 43.478 0.00 0.00 0.00 1.82
771 1109 4.072839 AGGAGTGAGAAAACCCGAAAATC 58.927 43.478 0.00 0.00 0.00 2.17
772 1110 3.818773 GGAGTGAGAAAACCCGAAAATCA 59.181 43.478 0.00 0.00 0.00 2.57
773 1111 4.320275 GGAGTGAGAAAACCCGAAAATCAC 60.320 45.833 0.00 0.00 36.65 3.06
774 1112 3.568430 AGTGAGAAAACCCGAAAATCACC 59.432 43.478 0.00 0.00 36.99 4.02
775 1113 2.550606 TGAGAAAACCCGAAAATCACCG 59.449 45.455 0.00 0.00 0.00 4.94
776 1114 1.883926 AGAAAACCCGAAAATCACCGG 59.116 47.619 0.00 0.00 44.94 5.28
797 1135 4.319549 CGGAAAAAGACGAAAAGAGGAAGG 60.320 45.833 0.00 0.00 0.00 3.46
802 1140 6.769134 AAAGACGAAAAGAGGAAGGAAAAA 57.231 33.333 0.00 0.00 0.00 1.94
973 1317 1.882189 TACTCCCCGTCCCCACATCT 61.882 60.000 0.00 0.00 0.00 2.90
1211 1555 2.672651 CACGCAGATGTGGCCCAA 60.673 61.111 0.00 0.00 36.20 4.12
1302 1655 4.078516 GAGCCCGGCAAGGTACGT 62.079 66.667 13.15 0.00 38.74 3.57
1303 1656 2.681064 AGCCCGGCAAGGTACGTA 60.681 61.111 13.15 0.00 38.74 3.57
1304 1657 2.510012 GCCCGGCAAGGTACGTAC 60.510 66.667 17.56 17.56 38.74 3.67
1305 1658 3.010413 GCCCGGCAAGGTACGTACT 62.010 63.158 24.07 8.57 38.74 2.73
1306 1659 1.140375 CCCGGCAAGGTACGTACTC 59.860 63.158 24.07 14.56 38.74 2.59
1307 1660 1.318158 CCCGGCAAGGTACGTACTCT 61.318 60.000 24.07 16.45 38.74 3.24
1308 1661 1.382522 CCGGCAAGGTACGTACTCTA 58.617 55.000 24.07 0.00 34.51 2.43
1309 1662 1.064654 CCGGCAAGGTACGTACTCTAC 59.935 57.143 24.07 14.30 34.51 2.59
1310 1663 4.434899 CCGGCAAGGTACGTACTCTACG 62.435 59.091 24.07 19.84 45.82 3.51
1322 1675 4.367023 TCTACGCACGCACACCCC 62.367 66.667 0.00 0.00 0.00 4.95
1375 1728 3.058160 ATGCAGCTCACCCGTTGC 61.058 61.111 0.00 0.00 37.09 4.17
1376 1729 4.560743 TGCAGCTCACCCGTTGCA 62.561 61.111 0.00 0.00 43.62 4.08
1379 1732 2.591715 AGCTCACCCGTTGCACAC 60.592 61.111 0.00 0.00 0.00 3.82
1622 1995 1.338973 CATGTGGCTGCTTCTGTTTGT 59.661 47.619 0.00 0.00 0.00 2.83
1623 1996 1.473258 TGTGGCTGCTTCTGTTTGTT 58.527 45.000 0.00 0.00 0.00 2.83
1624 1997 1.824230 TGTGGCTGCTTCTGTTTGTTT 59.176 42.857 0.00 0.00 0.00 2.83
1625 1998 2.195922 GTGGCTGCTTCTGTTTGTTTG 58.804 47.619 0.00 0.00 0.00 2.93
1626 1999 1.824230 TGGCTGCTTCTGTTTGTTTGT 59.176 42.857 0.00 0.00 0.00 2.83
1627 2000 2.233431 TGGCTGCTTCTGTTTGTTTGTT 59.767 40.909 0.00 0.00 0.00 2.83
1628 2001 3.261580 GGCTGCTTCTGTTTGTTTGTTT 58.738 40.909 0.00 0.00 0.00 2.83
1629 2002 3.062504 GGCTGCTTCTGTTTGTTTGTTTG 59.937 43.478 0.00 0.00 0.00 2.93
1870 2243 6.014840 AGTGCAAATGTTGAAGGATGAGAATT 60.015 34.615 0.00 0.00 0.00 2.17
1891 2264 0.537188 GTTCGCATCTCAAGGAGGGA 59.463 55.000 0.00 0.00 0.00 4.20
1894 2267 0.250234 CGCATCTCAAGGAGGGAACA 59.750 55.000 0.00 0.00 0.00 3.18
2075 2448 1.474077 CAAGTACCTTGAATGGGCTGC 59.526 52.381 0.00 0.00 43.42 5.25
2364 2737 4.361783 TGATCCAGAGTGTATTCCCTTGA 58.638 43.478 0.00 0.00 0.00 3.02
2800 3175 8.887717 CAACTTTTCCTCTAAAGATGATACTGG 58.112 37.037 0.00 0.00 39.10 4.00
2981 3358 4.702131 GGAATACACAGGTTCAGAGCATTT 59.298 41.667 0.00 0.00 0.00 2.32
3162 3539 3.256631 ACTTTTCATGGAGTTGCATGGTC 59.743 43.478 12.72 0.00 0.00 4.02
3329 3706 3.734463 TGTTGCCTCGATTGTGTCTAAA 58.266 40.909 0.00 0.00 0.00 1.85
3456 3833 6.317140 ACAATGTAATCAAGTCATACAGCAGG 59.683 38.462 0.00 0.00 33.44 4.85
3497 3874 4.129380 CAATCATTCGAGCTATTGGGTCA 58.871 43.478 0.12 0.00 42.06 4.02
3806 4183 2.744202 CACAAAGAGAGTATGTGCACCC 59.256 50.000 15.69 1.97 38.14 4.61
3849 4226 3.788227 AAGGACATTGCTTCAGTGGTA 57.212 42.857 0.00 0.00 0.00 3.25
3938 4315 3.644966 AGGTCATTCCATAAAGCCGAA 57.355 42.857 0.00 0.00 39.02 4.30
3978 4355 3.648067 TGTTTGGGAGATGTTCTCAGAGT 59.352 43.478 6.83 0.00 45.12 3.24
4003 4380 8.385858 GTTGATTCCGAGGTATAAACAAACTAC 58.614 37.037 4.63 0.00 0.00 2.73
4206 4583 2.085320 TGTTTACAACAACCGTGCAGT 58.915 42.857 0.00 0.00 38.72 4.40
4258 4635 2.662596 GTGACATCCGGCCTGTGA 59.337 61.111 13.42 3.36 0.00 3.58
4263 4640 2.514592 ATCCGGCCTGTGATTGCG 60.515 61.111 0.00 0.00 0.00 4.85
4274 4651 1.268999 TGTGATTGCGGTCAAAAGCAC 60.269 47.619 0.00 0.00 43.69 4.40
4276 4653 1.001487 TGATTGCGGTCAAAAGCACTG 60.001 47.619 0.00 0.00 43.69 3.66
4437 4814 1.341285 TGCAGGGAATGGTCATGGAAG 60.341 52.381 0.00 0.00 0.00 3.46
4451 4828 4.759183 GTCATGGAAGCAAGAAAGAGAAGT 59.241 41.667 0.00 0.00 0.00 3.01
4452 4829 5.240403 GTCATGGAAGCAAGAAAGAGAAGTT 59.760 40.000 0.00 0.00 0.00 2.66
4465 4842 7.590279 AGAAAGAGAAGTTTTTCACGTTTGAA 58.410 30.769 0.00 0.00 40.14 2.69
4476 4853 4.822036 TCACGTTTGAAACACCCATTAG 57.178 40.909 8.93 0.00 0.00 1.73
4507 4884 1.737735 TGTCAACCATCTCGCGCTG 60.738 57.895 5.56 0.00 0.00 5.18
4539 4919 8.461685 TCATCCATGGGAATGAAGGTAATATA 57.538 34.615 13.02 0.00 34.34 0.86
4554 4934 9.780186 GAAGGTAATATATAAGTGTTTCAGGCT 57.220 33.333 0.00 0.00 0.00 4.58
4567 4947 0.260230 TCAGGCTCTAGCTGGCTAGT 59.740 55.000 23.49 6.99 44.59 2.57
4612 5000 3.041211 TGGAATCCTGACCAGTCATAGG 58.959 50.000 0.00 0.41 39.13 2.57
4848 5244 5.378230 AGAAATGATCACCTCCATGCTTA 57.622 39.130 0.00 0.00 0.00 3.09
4878 5274 0.251787 GCCAAATTGGAGGGTGAGGT 60.252 55.000 17.47 0.00 40.96 3.85
5017 5423 8.566260 CATTCAGTCTCTTCAATCTTTGTTTCT 58.434 33.333 0.00 0.00 0.00 2.52
5022 5428 9.050601 AGTCTCTTCAATCTTTGTTTCTAACTG 57.949 33.333 0.00 0.00 0.00 3.16
5026 5432 9.173021 TCTTCAATCTTTGTTTCTAACTGTCAA 57.827 29.630 0.00 0.00 0.00 3.18
5167 5573 1.019673 GGTCGCTACTGGACGTCATA 58.980 55.000 18.91 4.66 35.24 2.15
5170 5576 2.086094 TCGCTACTGGACGTCATACAA 58.914 47.619 18.91 0.00 0.00 2.41
5206 5612 0.749454 GCTTCCCAGGCAGTGTATGG 60.749 60.000 8.37 8.37 0.00 2.74
5222 5628 0.607489 ATGGAAGTTCTGCGCTGCTT 60.607 50.000 9.73 7.94 0.00 3.91
5232 5638 0.893270 TGCGCTGCTTAACAACCCAT 60.893 50.000 9.73 0.00 0.00 4.00
5233 5639 0.243636 GCGCTGCTTAACAACCCATT 59.756 50.000 0.00 0.00 0.00 3.16
5234 5640 1.732405 GCGCTGCTTAACAACCCATTC 60.732 52.381 0.00 0.00 0.00 2.67
5269 5677 6.150976 TGGCCTACAATGTATTTTCACTCTTG 59.849 38.462 3.32 0.00 0.00 3.02
5313 5721 4.062991 GGTACCATATTCCACGGACATTC 58.937 47.826 7.15 0.00 0.00 2.67
5559 5967 2.553247 GGAGGTAGTCTTTGCCAGCTTT 60.553 50.000 0.00 0.00 33.26 3.51
5593 6001 0.110056 GTCATGCGCCAACTTCACTG 60.110 55.000 4.18 0.00 0.00 3.66
5594 6002 0.534877 TCATGCGCCAACTTCACTGT 60.535 50.000 4.18 0.00 0.00 3.55
5625 6033 0.400213 ACACTCCCAATGCGAAGGAA 59.600 50.000 0.00 0.00 0.00 3.36
5643 6051 1.987770 GAAATCGTCGCGAAGGTACAA 59.012 47.619 21.64 2.38 39.99 2.41
5644 6052 2.068837 AATCGTCGCGAAGGTACAAA 57.931 45.000 21.64 1.60 39.99 2.83
5672 6080 2.287788 CCCCTTAACAATGCGCATCATC 60.288 50.000 25.53 0.00 33.40 2.92
5707 6243 4.340381 AGCTTATCCTGGATCACATTTTGC 59.660 41.667 13.54 7.14 0.00 3.68
5710 6246 4.730949 ATCCTGGATCACATTTTGCTTG 57.269 40.909 2.57 0.00 0.00 4.01
5784 6320 1.003839 CAAGAAGGGGTGCGTGCTA 60.004 57.895 0.00 0.00 0.00 3.49
6067 6603 1.589716 GAATGAAACTGCTGGGCGCT 61.590 55.000 7.64 0.00 40.11 5.92
6123 6660 6.308766 CACCTCTTTCTTCTTTTGTTGTGTTG 59.691 38.462 0.00 0.00 0.00 3.33
6210 6747 4.550577 CCAAATTTGGTGCAAAAGAACC 57.449 40.909 26.34 0.00 43.43 3.62
6247 6784 7.118390 CCGAGTGGATAGAATAATTCAATGACC 59.882 40.741 0.00 0.00 37.49 4.02
6313 6850 3.503363 CCTTCTGCTGCTTGATTTGTACA 59.497 43.478 0.00 0.00 0.00 2.90
6315 6852 4.952262 TCTGCTGCTTGATTTGTACATC 57.048 40.909 0.00 0.00 0.00 3.06
6316 6853 4.582869 TCTGCTGCTTGATTTGTACATCT 58.417 39.130 0.00 0.00 0.00 2.90
6317 6854 4.633126 TCTGCTGCTTGATTTGTACATCTC 59.367 41.667 0.00 0.00 0.00 2.75
6318 6855 4.325972 TGCTGCTTGATTTGTACATCTCA 58.674 39.130 0.00 0.00 0.00 3.27
6319 6856 4.945543 TGCTGCTTGATTTGTACATCTCAT 59.054 37.500 0.00 0.00 0.00 2.90
6320 6857 5.065602 TGCTGCTTGATTTGTACATCTCATC 59.934 40.000 0.00 0.00 0.00 2.92
6321 6858 5.296283 GCTGCTTGATTTGTACATCTCATCT 59.704 40.000 0.00 0.00 0.00 2.90
6493 7044 7.378728 TGCAAATTCGTCTACATTCTATACTCG 59.621 37.037 0.00 0.00 0.00 4.18
6498 7049 5.177142 TCGTCTACATTCTATACTCGAGTGC 59.823 44.000 28.12 3.09 0.00 4.40
6516 7067 5.014808 AGTGCAATTTCAAGCTCAAACTT 57.985 34.783 0.00 0.00 0.00 2.66
6565 7116 7.231317 ACAACAACAGATTCAAACATGGATAGT 59.769 33.333 0.00 0.00 0.00 2.12
6592 7144 9.687210 GGTTTTTCTGGTTCTATCGTTTATTTT 57.313 29.630 0.00 0.00 0.00 1.82
6599 7151 9.158233 CTGGTTCTATCGTTTATTTTCCTGTTA 57.842 33.333 0.00 0.00 0.00 2.41
6623 7175 7.144722 AGATTGTTTTTCATGCTCACGAATA 57.855 32.000 0.00 0.00 0.00 1.75
6660 7212 7.059945 GCATTTGTAGAAATCAACTTCTCAACG 59.940 37.037 0.00 0.00 36.95 4.10
6792 7345 4.510571 TCAAAATTCCCTACGAAGCCTAC 58.489 43.478 0.00 0.00 32.78 3.18
6806 7359 5.419471 ACGAAGCCTACAGATTCTAGAACTT 59.581 40.000 7.48 3.93 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.946085 TCGATAAGCATGTTTTCTGTCTTTATT 58.054 29.630 0.00 0.00 0.00 1.40
2 3 8.492673 TCGATAAGCATGTTTTCTGTCTTTAT 57.507 30.769 0.00 0.00 0.00 1.40
3 4 7.064609 CCTCGATAAGCATGTTTTCTGTCTTTA 59.935 37.037 0.00 0.00 0.00 1.85
4 5 6.128172 CCTCGATAAGCATGTTTTCTGTCTTT 60.128 38.462 0.00 0.00 0.00 2.52
5 6 5.352569 CCTCGATAAGCATGTTTTCTGTCTT 59.647 40.000 0.00 0.00 0.00 3.01
6 7 4.872691 CCTCGATAAGCATGTTTTCTGTCT 59.127 41.667 0.00 0.00 0.00 3.41
7 8 4.494855 GCCTCGATAAGCATGTTTTCTGTC 60.495 45.833 0.00 0.00 0.00 3.51
8 9 3.375299 GCCTCGATAAGCATGTTTTCTGT 59.625 43.478 0.00 0.00 0.00 3.41
9 10 3.242870 GGCCTCGATAAGCATGTTTTCTG 60.243 47.826 0.00 0.00 0.00 3.02
10 11 2.945668 GGCCTCGATAAGCATGTTTTCT 59.054 45.455 0.00 0.00 0.00 2.52
15 16 1.544093 CCATGGCCTCGATAAGCATGT 60.544 52.381 3.32 0.00 0.00 3.21
19 20 1.968540 GCCCATGGCCTCGATAAGC 60.969 63.158 6.09 0.00 44.06 3.09
20 21 4.386413 GCCCATGGCCTCGATAAG 57.614 61.111 6.09 0.00 44.06 1.73
31 32 2.360165 GCTACCAATCTCAAAGCCCATG 59.640 50.000 0.00 0.00 0.00 3.66
33 34 1.635487 AGCTACCAATCTCAAAGCCCA 59.365 47.619 0.00 0.00 33.63 5.36
38 39 6.013725 TCAAGGTTAGAGCTACCAATCTCAAA 60.014 38.462 6.91 0.00 38.16 2.69
48 49 6.045955 CCTTCATCTTCAAGGTTAGAGCTAC 58.954 44.000 0.00 0.00 36.40 3.58
62 63 9.010029 TCTTTTAACCATTGTACCTTCATCTTC 57.990 33.333 0.00 0.00 0.00 2.87
93 94 4.215613 CGTCATGGAGATAACGGAGACATA 59.784 45.833 0.00 0.00 0.00 2.29
99 100 2.288213 GCATCGTCATGGAGATAACGGA 60.288 50.000 2.98 0.00 35.89 4.69
100 101 2.061773 GCATCGTCATGGAGATAACGG 58.938 52.381 2.98 0.00 35.89 4.44
101 102 2.983136 GAGCATCGTCATGGAGATAACG 59.017 50.000 0.00 0.00 36.50 3.18
117 118 1.134431 TGATGGTGTGTATGCGAGCAT 60.134 47.619 15.28 15.28 40.19 3.79
122 123 4.597079 GGTAAATTGATGGTGTGTATGCG 58.403 43.478 0.00 0.00 0.00 4.73
135 136 7.390440 GGTCCATGATATCAATCGGTAAATTGA 59.610 37.037 9.99 2.13 46.60 2.57
153 154 1.072173 CTGTCAAGGTGTGGTCCATGA 59.928 52.381 0.00 0.00 33.63 3.07
176 177 3.693807 ACCACATGTGATCATTGCTTCT 58.306 40.909 27.46 0.00 31.15 2.85
194 195 6.150976 CACTTGCTTTGGACTTATCATTACCA 59.849 38.462 0.00 0.00 0.00 3.25
196 197 6.030228 GCACTTGCTTTGGACTTATCATTAC 58.970 40.000 0.00 0.00 38.21 1.89
269 270 9.029368 CCTCTGTCATCAAGATACCAGATATTA 57.971 37.037 9.78 0.00 31.00 0.98
270 271 7.732140 TCCTCTGTCATCAAGATACCAGATATT 59.268 37.037 9.78 0.00 31.00 1.28
271 272 7.244558 TCCTCTGTCATCAAGATACCAGATAT 58.755 38.462 9.78 0.00 31.00 1.63
272 273 6.614657 TCCTCTGTCATCAAGATACCAGATA 58.385 40.000 9.78 2.55 31.00 1.98
273 274 5.462240 TCCTCTGTCATCAAGATACCAGAT 58.538 41.667 9.78 0.00 31.00 2.90
274 275 4.871822 TCCTCTGTCATCAAGATACCAGA 58.128 43.478 9.25 9.25 0.00 3.86
324 325 3.008704 AGGGTTTCTTTAGCGTGGTATGT 59.991 43.478 0.00 0.00 0.00 2.29
327 328 3.775261 AAGGGTTTCTTTAGCGTGGTA 57.225 42.857 0.00 0.00 29.99 3.25
347 348 3.055021 TGCCGTGTCAAGGAACCATAATA 60.055 43.478 9.22 0.00 0.00 0.98
369 374 4.517952 AGCGAAGATCAGAATCGATGAT 57.482 40.909 0.00 0.00 40.08 2.45
377 382 3.089284 TCTGGTGTAGCGAAGATCAGAA 58.911 45.455 0.00 0.00 0.00 3.02
430 760 7.591057 TCGTAAGATGCTTGTTTTTCATTTCTG 59.409 33.333 0.00 0.00 45.01 3.02
431 761 7.648142 TCGTAAGATGCTTGTTTTTCATTTCT 58.352 30.769 0.00 0.00 45.01 2.52
432 762 7.851822 TCGTAAGATGCTTGTTTTTCATTTC 57.148 32.000 0.00 0.00 45.01 2.17
492 822 0.451783 GTCATGCGGCGGAAGATTTT 59.548 50.000 9.94 0.00 0.00 1.82
527 857 1.078072 TGTGTGGTGCTTTGACGGT 60.078 52.632 0.00 0.00 0.00 4.83
529 859 1.648720 CCTGTGTGGTGCTTTGACG 59.351 57.895 0.00 0.00 0.00 4.35
547 877 1.660560 AATTCGACTGGCCTGCATGC 61.661 55.000 11.82 11.82 0.00 4.06
548 878 0.813184 AAATTCGACTGGCCTGCATG 59.187 50.000 9.95 0.00 0.00 4.06
549 879 2.292267 CTAAATTCGACTGGCCTGCAT 58.708 47.619 9.95 0.00 0.00 3.96
550 880 1.678728 CCTAAATTCGACTGGCCTGCA 60.679 52.381 9.95 0.00 0.00 4.41
573 903 6.949352 ATGCTTTTAAGTGATTCATCCGAT 57.051 33.333 0.00 0.00 0.00 4.18
602 935 6.766944 TGTTTCTTCAAAATGCACATCCAAAT 59.233 30.769 0.00 0.00 0.00 2.32
635 968 9.158233 CCTTCTCCGTGTTGAAAATAACTTATA 57.842 33.333 0.00 0.00 0.00 0.98
636 969 7.120726 CCCTTCTCCGTGTTGAAAATAACTTAT 59.879 37.037 0.00 0.00 0.00 1.73
660 993 6.887002 ACTTTCTCAACCAAATATTCTCTCCC 59.113 38.462 0.00 0.00 0.00 4.30
737 1075 1.944024 CTCACTCCTGCCGTCTAGTAG 59.056 57.143 0.00 0.00 0.00 2.57
762 1100 2.554893 TCTTTTTCCGGTGATTTTCGGG 59.445 45.455 0.00 0.00 45.69 5.14
764 1102 3.059461 TCGTCTTTTTCCGGTGATTTTCG 60.059 43.478 0.00 1.09 0.00 3.46
765 1103 4.477302 TCGTCTTTTTCCGGTGATTTTC 57.523 40.909 0.00 0.00 0.00 2.29
769 1107 4.131596 TCTTTTCGTCTTTTTCCGGTGAT 58.868 39.130 0.00 0.00 0.00 3.06
770 1108 3.533547 TCTTTTCGTCTTTTTCCGGTGA 58.466 40.909 0.00 0.00 0.00 4.02
771 1109 3.303791 CCTCTTTTCGTCTTTTTCCGGTG 60.304 47.826 0.00 0.00 0.00 4.94
772 1110 2.876550 CCTCTTTTCGTCTTTTTCCGGT 59.123 45.455 0.00 0.00 0.00 5.28
773 1111 3.135994 TCCTCTTTTCGTCTTTTTCCGG 58.864 45.455 0.00 0.00 0.00 5.14
774 1112 4.319549 CCTTCCTCTTTTCGTCTTTTTCCG 60.320 45.833 0.00 0.00 0.00 4.30
775 1113 4.820173 TCCTTCCTCTTTTCGTCTTTTTCC 59.180 41.667 0.00 0.00 0.00 3.13
776 1114 6.373186 TTCCTTCCTCTTTTCGTCTTTTTC 57.627 37.500 0.00 0.00 0.00 2.29
777 1115 6.769134 TTTCCTTCCTCTTTTCGTCTTTTT 57.231 33.333 0.00 0.00 0.00 1.94
778 1116 6.769134 TTTTCCTTCCTCTTTTCGTCTTTT 57.231 33.333 0.00 0.00 0.00 2.27
779 1117 6.769134 TTTTTCCTTCCTCTTTTCGTCTTT 57.231 33.333 0.00 0.00 0.00 2.52
802 1140 4.832608 GGGATCGCGGCCGTTCTT 62.833 66.667 28.70 9.51 34.47 2.52
1195 1539 2.360350 CTTGGGCCACATCTGCGT 60.360 61.111 5.23 0.00 0.00 5.24
1211 1555 3.182590 TTGGCGGTCTTGAGCAGCT 62.183 57.895 0.00 0.00 34.54 4.24
1302 1655 1.210931 GGTGTGCGTGCGTAGAGTA 59.789 57.895 0.00 0.00 0.00 2.59
1303 1656 2.049433 GGTGTGCGTGCGTAGAGT 60.049 61.111 0.00 0.00 0.00 3.24
1304 1657 2.809601 GGGTGTGCGTGCGTAGAG 60.810 66.667 0.00 0.00 0.00 2.43
1305 1658 4.367023 GGGGTGTGCGTGCGTAGA 62.367 66.667 0.00 0.00 0.00 2.59
1375 1728 2.116736 ATTGAACTGCGGTGCGTGTG 62.117 55.000 0.00 0.00 0.00 3.82
1376 1729 1.444119 AATTGAACTGCGGTGCGTGT 61.444 50.000 0.00 0.00 0.00 4.49
1379 1732 1.059657 CGAAATTGAACTGCGGTGCG 61.060 55.000 0.00 0.00 0.00 5.34
1622 1995 6.203723 CACTGAAGGGAAAACAAACAAACAAA 59.796 34.615 0.00 0.00 0.00 2.83
1623 1996 5.698545 CACTGAAGGGAAAACAAACAAACAA 59.301 36.000 0.00 0.00 0.00 2.83
1624 1997 5.233988 CACTGAAGGGAAAACAAACAAACA 58.766 37.500 0.00 0.00 0.00 2.83
1625 1998 4.092821 GCACTGAAGGGAAAACAAACAAAC 59.907 41.667 0.00 0.00 0.00 2.93
1626 1999 4.249661 GCACTGAAGGGAAAACAAACAAA 58.750 39.130 0.00 0.00 0.00 2.83
1627 2000 3.259374 TGCACTGAAGGGAAAACAAACAA 59.741 39.130 0.00 0.00 0.00 2.83
1628 2001 2.828520 TGCACTGAAGGGAAAACAAACA 59.171 40.909 0.00 0.00 0.00 2.83
1629 2002 3.518634 TGCACTGAAGGGAAAACAAAC 57.481 42.857 0.00 0.00 0.00 2.93
1870 2243 1.339055 CCCTCCTTGAGATGCGAACAA 60.339 52.381 0.00 0.00 0.00 2.83
1891 2264 4.475016 ACTGACCTGGGCTAGAATAATGTT 59.525 41.667 0.00 0.00 0.00 2.71
1894 2267 6.824958 TTAACTGACCTGGGCTAGAATAAT 57.175 37.500 0.00 0.00 0.00 1.28
2075 2448 2.101783 TGGTGCTAATGGCCATTTCAG 58.898 47.619 34.85 26.60 40.92 3.02
2364 2737 5.279206 CGAGGCACATATTAAGAGATGGAGT 60.279 44.000 0.00 0.00 0.00 3.85
2750 3124 4.900635 AATATTTTGCGTGATCCACTCC 57.099 40.909 0.00 0.00 31.34 3.85
2981 3358 4.137116 ACGCTGAGCTAAATCATTACCA 57.863 40.909 1.78 0.00 0.00 3.25
3162 3539 7.594758 CCACCATAATACTGTTCAAAACAAGTG 59.405 37.037 0.00 0.00 41.61 3.16
3329 3706 7.606456 ACAGTACATTGACCGAATAACTGATTT 59.394 33.333 12.87 0.00 38.43 2.17
3497 3874 1.296002 GTTCCCAACCTCATACCCCT 58.704 55.000 0.00 0.00 0.00 4.79
3806 4183 8.223769 CCTTACTAATTAGACGCAAATGCATAG 58.776 37.037 19.38 0.00 42.21 2.23
3813 4190 7.413657 GCAATGTCCTTACTAATTAGACGCAAA 60.414 37.037 19.38 4.63 0.00 3.68
3849 4226 7.831193 ACAAGTCAGGAATGTATGCTCTTTATT 59.169 33.333 0.00 0.00 0.00 1.40
3938 4315 2.306847 ACATTGTTCTTGGTCGCCTTT 58.693 42.857 0.00 0.00 0.00 3.11
3978 4355 8.316214 AGTAGTTTGTTTATACCTCGGAATCAA 58.684 33.333 0.00 0.00 0.00 2.57
4003 4380 4.576330 AAGGGTTCCTTGTTCCTGATAG 57.424 45.455 0.00 0.00 42.96 2.08
4206 4583 1.167851 CATCTGCCTCCAAGCGAAAA 58.832 50.000 0.00 0.00 34.65 2.29
4258 4635 0.318955 GCAGTGCTTTTGACCGCAAT 60.319 50.000 8.18 0.00 37.97 3.56
4263 4640 1.774639 CATGTGCAGTGCTTTTGACC 58.225 50.000 17.60 0.00 0.00 4.02
4276 4653 3.119029 ACAAATCCTACCATTGCATGTGC 60.119 43.478 0.00 0.00 42.50 4.57
4285 4662 4.586001 GGCATCATTGACAAATCCTACCAT 59.414 41.667 0.00 0.00 0.00 3.55
4292 4669 4.852609 GCAAAGGCATCATTGACAAATC 57.147 40.909 0.00 0.00 40.72 2.17
4349 4726 3.831333 TGCAATTGGTATCTGCTTTTGGA 59.169 39.130 7.72 0.00 37.00 3.53
4437 4814 5.332707 ACGTGAAAAACTTCTCTTTCTTGC 58.667 37.500 0.00 0.00 33.55 4.01
4465 4842 7.565680 CACCTAATCTTAGACTAATGGGTGTT 58.434 38.462 16.23 2.47 36.66 3.32
4467 4844 7.125792 ACACCTAATCTTAGACTAATGGGTG 57.874 40.000 20.16 20.16 43.93 4.61
4476 4853 6.879400 AGATGGTTGACACCTAATCTTAGAC 58.121 40.000 0.00 0.00 44.61 2.59
4507 4884 2.353357 TTCCCATGGATGATGACAGC 57.647 50.000 15.22 0.00 33.31 4.40
4539 4919 4.383552 CCAGCTAGAGCCTGAAACACTTAT 60.384 45.833 0.00 0.00 43.38 1.73
4554 4934 1.195115 CCACCAACTAGCCAGCTAGA 58.805 55.000 28.73 0.00 46.56 2.43
4567 4947 4.100035 TCATAAATTGTGTGCAACCACCAA 59.900 37.500 5.11 1.21 41.35 3.67
4632 5020 1.102978 ACCACTGTCCTGCAAACAAC 58.897 50.000 3.45 0.00 0.00 3.32
4848 5244 4.019411 CCTCCAATTTGGCCTGGTTAAAAT 60.019 41.667 10.76 0.00 37.47 1.82
4878 5274 5.477607 TTTCTCCGTGTAAATCTCCTTCA 57.522 39.130 0.00 0.00 0.00 3.02
5017 5423 5.276461 ACAGACAGTGACATTGACAGTTA 57.724 39.130 4.78 0.00 0.00 2.24
5022 5428 5.008019 ACATGAAACAGACAGTGACATTGAC 59.992 40.000 4.78 0.00 0.00 3.18
5026 5432 4.707105 TGACATGAAACAGACAGTGACAT 58.293 39.130 0.00 0.00 0.00 3.06
5167 5573 1.676006 CGACTTTGCCAGGAGTTTTGT 59.324 47.619 0.00 0.00 0.00 2.83
5170 5576 0.179018 AGCGACTTTGCCAGGAGTTT 60.179 50.000 0.00 0.00 34.65 2.66
5206 5612 1.531149 TGTTAAGCAGCGCAGAACTTC 59.469 47.619 11.47 0.00 0.00 3.01
5222 5628 6.071051 GCCAATAAAGGAAGAATGGGTTGTTA 60.071 38.462 0.00 0.00 0.00 2.41
5232 5638 6.252995 ACATTGTAGGCCAATAAAGGAAGAA 58.747 36.000 5.01 0.00 41.93 2.52
5233 5639 5.826643 ACATTGTAGGCCAATAAAGGAAGA 58.173 37.500 5.01 0.00 41.93 2.87
5234 5640 7.823745 ATACATTGTAGGCCAATAAAGGAAG 57.176 36.000 5.01 0.00 41.93 3.46
5289 5697 2.432874 TGTCCGTGGAATATGGTACCTG 59.567 50.000 14.36 0.00 36.76 4.00
5313 5721 7.092716 CCAATAGGTTGTTCTTGGATTTCAAG 58.907 38.462 0.00 0.00 42.32 3.02
5531 5939 2.501723 GCAAAGACTACCTCCTGGATGA 59.498 50.000 5.95 0.00 37.04 2.92
5625 6033 1.723003 GTTTGTACCTTCGCGACGATT 59.277 47.619 14.93 3.09 35.23 3.34
5633 6041 2.089201 GGGGGAATGTTTGTACCTTCG 58.911 52.381 0.00 0.00 31.83 3.79
5672 6080 7.526142 TCCAGGATAAGCTACAGTATTACAG 57.474 40.000 0.00 0.00 0.00 2.74
5707 6243 1.474077 GCAACCATAGGCAGGAACAAG 59.526 52.381 0.00 0.00 0.00 3.16
5710 6246 1.376609 CGGCAACCATAGGCAGGAAC 61.377 60.000 0.00 0.00 0.00 3.62
5784 6320 1.312371 AAAACGTGTGCAGCACTGGT 61.312 50.000 25.83 19.41 45.57 4.00
6067 6603 4.322080 AAATACATCTTCGAGCCGATCA 57.678 40.909 0.00 0.00 35.23 2.92
6123 6660 4.300189 TGGTTAACATGAAACAGCACAC 57.700 40.909 8.10 0.00 0.00 3.82
6210 6747 2.310233 CCACTCGGTCAGCACAACG 61.310 63.158 0.00 0.00 0.00 4.10
6247 6784 9.859427 AACATGATAAAACATTTACAGGACATG 57.141 29.630 0.00 0.00 37.06 3.21
6313 6850 8.844244 GGCAATATAAACTTGTCAAGATGAGAT 58.156 33.333 19.53 0.49 0.00 2.75
6315 6852 7.988737 TGGCAATATAAACTTGTCAAGATGAG 58.011 34.615 19.53 0.00 35.43 2.90
6316 6853 7.936496 TGGCAATATAAACTTGTCAAGATGA 57.064 32.000 19.53 0.51 35.43 2.92
6317 6854 8.984891 TTTGGCAATATAAACTTGTCAAGATG 57.015 30.769 19.53 7.17 45.70 2.90
6319 6856 9.995003 AAATTTGGCAATATAAACTTGTCAAGA 57.005 25.926 19.53 0.00 45.70 3.02
6321 6858 9.995003 AGAAATTTGGCAATATAAACTTGTCAA 57.005 25.926 0.00 1.39 44.10 3.18
6351 6901 7.444183 ACAAATACAACACTTACATACAGCTGT 59.556 33.333 25.12 25.12 0.00 4.40
6493 7044 4.614946 AGTTTGAGCTTGAAATTGCACTC 58.385 39.130 0.00 0.00 0.00 3.51
6565 7116 7.989416 ATAAACGATAGAACCAGAAAAACCA 57.011 32.000 0.00 0.00 41.38 3.67
6592 7144 6.489700 TGAGCATGAAAAACAATCTAACAGGA 59.510 34.615 0.00 0.00 0.00 3.86
6593 7145 6.583806 GTGAGCATGAAAAACAATCTAACAGG 59.416 38.462 0.00 0.00 0.00 4.00
6599 7151 5.437289 TTCGTGAGCATGAAAAACAATCT 57.563 34.783 0.00 0.00 0.00 2.40
6675 7228 9.565213 CCAAATTCAGAAAGTTTCAGATGATAC 57.435 33.333 17.65 0.00 0.00 2.24
6714 7267 2.805671 CACACTCATGGCGAAAACACTA 59.194 45.455 0.00 0.00 0.00 2.74
6782 7335 4.951094 AGTTCTAGAATCTGTAGGCTTCGT 59.049 41.667 8.75 0.00 0.00 3.85
6792 7345 6.939132 ATGCAATGGAAGTTCTAGAATCTG 57.061 37.500 8.75 0.00 0.00 2.90
6806 7359 6.418057 AAACAGAAAGGTTTATGCAATGGA 57.582 33.333 0.00 0.00 39.10 3.41


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

AutoCloner maintained by Alex Coulton.