Multiple sequence alignment - TraesCS2A01G177900

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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 TraesCS2A01G177900 chr2A 100.000 2375 0 0 1 2375 137130120 137132494 0.000000e+00 4386
1 TraesCS2A01G177900 chr2D 86.888 1533 153 34 583 2091 131075051 131076559 0.000000e+00 1674
2 TraesCS2A01G177900 chr2D 91.220 877 70 4 599 1469 130991691 130992566 0.000000e+00 1186
3 TraesCS2A01G177900 chr2D 83.892 776 95 19 785 1556 131120168 131120917 0.000000e+00 713
4 TraesCS2A01G177900 chr2D 84.848 726 54 14 250 936 131047450 131048158 0.000000e+00 680
5 TraesCS2A01G177900 chr2D 86.972 545 58 6 910 1443 131129071 131129613 3.380000e-168 601
6 TraesCS2A01G177900 chr2D 86.813 546 57 9 910 1443 131136258 131136800 1.570000e-166 595
7 TraesCS2A01G177900 chr2D 88.308 402 40 5 1636 2036 131050080 131050475 2.140000e-130 475
8 TraesCS2A01G177900 chr2D 87.255 306 25 3 2082 2375 131087841 131088144 1.050000e-88 337
9 TraesCS2A01G177900 chr2D 88.068 176 13 3 387 556 130991520 130991693 4.000000e-48 202
10 TraesCS2A01G177900 chr2B 84.846 1135 107 22 1001 2113 184496620 184497711 0.000000e+00 1083
11 TraesCS2A01G177900 chr2B 86.908 802 82 10 771 1556 184577324 184578118 0.000000e+00 878
12 TraesCS2A01G177900 chr2B 84.409 558 70 10 901 1443 184595913 184596468 1.250000e-147 532
13 TraesCS2A01G177900 chr2B 86.826 334 20 7 2 335 184496099 184496408 3.760000e-93 351
14 TraesCS2A01G177900 chr2B 86.017 236 21 6 2152 2375 184497705 184497940 2.360000e-60 243
15 TraesCS2A01G177900 chr2B 84.932 219 28 4 1899 2113 215498250 215498033 1.430000e-52 217
16 TraesCS2A01G177900 chr2B 85.106 188 16 1 2200 2375 215488009 215487822 5.210000e-42 182
17 TraesCS2A01G177900 chrUn 84.375 768 98 9 791 1553 326757707 326756957 0.000000e+00 734


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 TraesCS2A01G177900 chr2A 137130120 137132494 2374 False 4386.0 4386 100.000000 1 2375 1 chr2A.!!$F1 2374
1 TraesCS2A01G177900 chr2D 131075051 131076559 1508 False 1674.0 1674 86.888000 583 2091 1 chr2D.!!$F1 1508
2 TraesCS2A01G177900 chr2D 131120168 131120917 749 False 713.0 713 83.892000 785 1556 1 chr2D.!!$F3 771
3 TraesCS2A01G177900 chr2D 130991520 130992566 1046 False 694.0 1186 89.644000 387 1469 2 chr2D.!!$F6 1082
4 TraesCS2A01G177900 chr2D 131129071 131129613 542 False 601.0 601 86.972000 910 1443 1 chr2D.!!$F4 533
5 TraesCS2A01G177900 chr2D 131136258 131136800 542 False 595.0 595 86.813000 910 1443 1 chr2D.!!$F5 533
6 TraesCS2A01G177900 chr2D 131047450 131050475 3025 False 577.5 680 86.578000 250 2036 2 chr2D.!!$F7 1786
7 TraesCS2A01G177900 chr2B 184577324 184578118 794 False 878.0 878 86.908000 771 1556 1 chr2B.!!$F1 785
8 TraesCS2A01G177900 chr2B 184496099 184497940 1841 False 559.0 1083 85.896333 2 2375 3 chr2B.!!$F3 2373
9 TraesCS2A01G177900 chr2B 184595913 184596468 555 False 532.0 532 84.409000 901 1443 1 chr2B.!!$F2 542
10 TraesCS2A01G177900 chrUn 326756957 326757707 750 True 734.0 734 84.375000 791 1553 1 chrUn.!!$R1 762

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
202 203 0.036448 TGTTCCATTCGGCGGGTAAA 59.964 50.0 7.21 0.0 0.00 2.01 F
211 212 0.107081 CGGCGGGTAAATATGTCCCA 59.893 55.0 0.00 0.0 41.12 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1732 0.033601 GAGCTGTCTCCTCCTCCAGA 60.034 60.0 0.0 0.0 33.19 3.86 R
1957 3456 0.911769 TTGCTACCACCCATCTCCTG 59.088 55.0 0.0 0.0 0.00 3.86 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
32 33 6.239317 GCCTGGTCTCTCCTTTTGTAATTTTT 60.239 38.462 0.00 0.00 37.07 1.94
71 72 8.762426 GTCCTTATTTTAACTCCATGTCGTATC 58.238 37.037 0.00 0.00 0.00 2.24
120 121 2.437651 TGATCTGGGTGTCAAGTGTCAA 59.562 45.455 0.00 0.00 0.00 3.18
121 122 2.325583 TCTGGGTGTCAAGTGTCAAC 57.674 50.000 0.00 0.00 0.00 3.18
157 158 0.846693 AGGAGTGCAGGACCACTTTT 59.153 50.000 0.00 0.00 45.55 2.27
186 187 5.454966 ACCTTACTCCAGATTTTTGGTGTT 58.545 37.500 5.24 0.00 40.93 3.32
187 188 5.535030 ACCTTACTCCAGATTTTTGGTGTTC 59.465 40.000 5.24 0.00 40.93 3.18
188 189 5.048013 CCTTACTCCAGATTTTTGGTGTTCC 60.048 44.000 5.24 0.00 40.93 3.62
189 190 3.909732 ACTCCAGATTTTTGGTGTTCCA 58.090 40.909 0.00 0.00 40.93 3.53
190 191 4.482990 ACTCCAGATTTTTGGTGTTCCAT 58.517 39.130 0.00 0.00 40.93 3.41
191 192 4.901250 ACTCCAGATTTTTGGTGTTCCATT 59.099 37.500 0.00 0.00 40.93 3.16
192 193 5.011023 ACTCCAGATTTTTGGTGTTCCATTC 59.989 40.000 0.00 0.00 40.93 2.67
193 194 4.022416 TCCAGATTTTTGGTGTTCCATTCG 60.022 41.667 0.00 0.00 43.91 3.34
194 195 4.236935 CAGATTTTTGGTGTTCCATTCGG 58.763 43.478 0.00 0.00 43.91 4.30
195 196 2.517650 TTTTTGGTGTTCCATTCGGC 57.482 45.000 0.00 0.00 43.91 5.54
196 197 0.312416 TTTTGGTGTTCCATTCGGCG 59.688 50.000 0.00 0.00 43.91 6.46
197 198 1.519751 TTTGGTGTTCCATTCGGCGG 61.520 55.000 7.21 0.00 43.91 6.13
198 199 3.131478 GGTGTTCCATTCGGCGGG 61.131 66.667 7.21 0.00 0.00 6.13
199 200 2.359478 GTGTTCCATTCGGCGGGT 60.359 61.111 7.21 0.00 0.00 5.28
200 201 1.078988 GTGTTCCATTCGGCGGGTA 60.079 57.895 7.21 0.00 0.00 3.69
201 202 0.674269 GTGTTCCATTCGGCGGGTAA 60.674 55.000 7.21 0.00 0.00 2.85
202 203 0.036448 TGTTCCATTCGGCGGGTAAA 59.964 50.000 7.21 0.00 0.00 2.01
203 204 1.340211 TGTTCCATTCGGCGGGTAAAT 60.340 47.619 7.21 0.00 0.00 1.40
204 205 2.093075 TGTTCCATTCGGCGGGTAAATA 60.093 45.455 7.21 0.00 0.00 1.40
205 206 3.143728 GTTCCATTCGGCGGGTAAATAT 58.856 45.455 7.21 0.00 0.00 1.28
206 207 2.773487 TCCATTCGGCGGGTAAATATG 58.227 47.619 7.21 0.19 0.00 1.78
207 208 2.105134 TCCATTCGGCGGGTAAATATGT 59.895 45.455 7.21 0.00 0.00 2.29
211 212 0.107081 CGGCGGGTAAATATGTCCCA 59.893 55.000 0.00 0.00 41.12 4.37
214 215 2.817844 GGCGGGTAAATATGTCCCAATC 59.182 50.000 9.72 0.84 41.12 2.67
237 238 7.009179 TCTGTTCTTGTGTAGGATGAAATCT 57.991 36.000 0.00 0.00 44.71 2.40
238 239 8.134202 TCTGTTCTTGTGTAGGATGAAATCTA 57.866 34.615 0.00 0.00 44.71 1.98
267 268 3.624326 GGCCAAATTCAAAAGCCAAAC 57.376 42.857 0.00 0.00 43.32 2.93
296 297 3.923461 ACAACAACAATCAAACCAACGTG 59.077 39.130 0.00 0.00 0.00 4.49
311 312 1.299850 CGTGACCGAGTGCTCAACA 60.300 57.895 0.00 0.00 35.63 3.33
335 364 2.920384 TACCACACCGGCAGAGCA 60.920 61.111 0.00 0.00 39.03 4.26
357 386 4.687901 AGCAAATTAAGCAGGGTTTGTT 57.312 36.364 5.70 0.00 34.82 2.83
359 388 3.498018 GCAAATTAAGCAGGGTTTGTTGG 59.502 43.478 0.00 0.00 34.82 3.77
457 508 4.584874 TGAACCAGACACTGAACTCAAAA 58.415 39.130 0.00 0.00 32.44 2.44
464 515 8.352942 ACCAGACACTGAACTCAAAATTTTATC 58.647 33.333 2.44 1.34 32.44 1.75
552 609 7.113124 CGTGTTATTCTTATAGCGTAACCTCTG 59.887 40.741 0.00 0.00 0.00 3.35
576 633 2.407428 CCGCCAGTCGTCTAGCTCA 61.407 63.158 0.00 0.00 36.19 4.26
581 638 1.268999 CCAGTCGTCTAGCTCAGATGC 60.269 57.143 0.00 0.00 39.75 3.91
587 644 2.744352 TCTAGCTCAGATGCTGGAGA 57.256 50.000 0.00 0.00 43.81 3.71
588 645 3.023939 TCTAGCTCAGATGCTGGAGAA 57.976 47.619 0.00 0.00 43.81 2.87
597 654 4.042062 TCAGATGCTGGAGAAGGAAGAAAA 59.958 41.667 0.00 0.00 31.51 2.29
668 725 1.678101 ACTTGCTTGTGTTCTTCTGCC 59.322 47.619 0.00 0.00 0.00 4.85
673 730 2.810400 GCTTGTGTTCTTCTGCCACCTA 60.810 50.000 0.00 0.00 0.00 3.08
687 747 1.522900 CACCTAATGGTCCCCTGGAT 58.477 55.000 0.00 0.00 46.60 3.41
728 788 0.878416 TGGCCTAACAATTGCGTGTC 59.122 50.000 3.32 0.00 0.00 3.67
851 934 0.475044 TAAAACCGGGAACTGCAGGT 59.525 50.000 19.93 12.79 38.88 4.00
866 949 1.618837 GCAGGTGAGTAGGTGAACAGA 59.381 52.381 0.00 0.00 0.00 3.41
921 1009 9.907576 CTCAAGCGTTTCTTAACTCTATAAATG 57.092 33.333 0.00 0.00 29.53 2.32
950 1441 1.833630 CACCTGCTATCTCTCCCACAA 59.166 52.381 0.00 0.00 0.00 3.33
966 1457 2.093764 CCACAACAAAACCACACCACAT 60.094 45.455 0.00 0.00 0.00 3.21
968 1459 4.358851 CACAACAAAACCACACCACATAG 58.641 43.478 0.00 0.00 0.00 2.23
969 1460 3.181480 ACAACAAAACCACACCACATAGC 60.181 43.478 0.00 0.00 0.00 2.97
970 1461 2.944129 ACAAAACCACACCACATAGCT 58.056 42.857 0.00 0.00 0.00 3.32
1022 1635 0.110464 GCTTCGAGAAACACTGCTGC 60.110 55.000 0.00 0.00 0.00 5.25
1029 1642 2.555757 GAGAAACACTGCTGCATTCCTT 59.444 45.455 1.31 0.00 0.00 3.36
1077 1732 3.044059 GAGCAGCGCGGCAAGAATT 62.044 57.895 33.13 12.54 35.83 2.17
1080 1735 1.226211 CAGCGCGGCAAGAATTCTG 60.226 57.895 9.17 4.72 0.00 3.02
1081 1736 2.100991 GCGCGGCAAGAATTCTGG 59.899 61.111 9.17 7.18 0.00 3.86
1082 1737 2.398554 GCGCGGCAAGAATTCTGGA 61.399 57.895 14.40 0.00 0.00 3.86
1110 1771 2.358247 GCTCCGTCCAAAGGCGAA 60.358 61.111 0.00 0.00 0.00 4.70
1137 1798 1.452108 GCCGGAGCTACCAATGCTT 60.452 57.895 5.05 0.00 41.30 3.91
1182 2336 1.144057 GGAGGTACATCTGCCACCG 59.856 63.158 7.56 0.00 37.42 4.94
1462 2745 6.016276 GTCTTTCATGGGATTGTTTAGTGTGT 60.016 38.462 0.00 0.00 0.00 3.72
1493 2777 6.128309 CCGTGAGTCATTTGTGTGATATCAAA 60.128 38.462 7.07 0.00 37.82 2.69
1518 2806 5.661458 GCTTATCTATGGCGCCTATTTAGA 58.339 41.667 29.70 24.99 0.00 2.10
1519 2807 6.284459 GCTTATCTATGGCGCCTATTTAGAT 58.716 40.000 29.70 28.69 34.76 1.98
1520 2808 6.201806 GCTTATCTATGGCGCCTATTTAGATG 59.798 42.308 30.48 22.64 33.09 2.90
1521 2809 4.471904 TCTATGGCGCCTATTTAGATGG 57.528 45.455 29.70 12.80 0.00 3.51
1522 2810 4.093743 TCTATGGCGCCTATTTAGATGGA 58.906 43.478 29.70 15.07 0.00 3.41
1523 2811 3.788227 ATGGCGCCTATTTAGATGGAA 57.212 42.857 29.70 1.56 0.00 3.53
1524 2812 3.788227 TGGCGCCTATTTAGATGGAAT 57.212 42.857 29.70 0.00 0.00 3.01
1525 2813 3.411446 TGGCGCCTATTTAGATGGAATG 58.589 45.455 29.70 0.00 0.00 2.67
1526 2814 3.181445 TGGCGCCTATTTAGATGGAATGT 60.181 43.478 29.70 0.00 0.00 2.71
1527 2815 4.041075 TGGCGCCTATTTAGATGGAATGTA 59.959 41.667 29.70 0.00 0.00 2.29
1528 2816 4.392138 GGCGCCTATTTAGATGGAATGTAC 59.608 45.833 22.15 0.00 0.00 2.90
1532 2820 6.873605 CGCCTATTTAGATGGAATGTACATGA 59.126 38.462 9.63 0.00 0.00 3.07
1774 3271 4.501743 GGAACTTTTTGCCCGATAAACCAA 60.502 41.667 0.00 0.00 0.00 3.67
1838 3335 2.664916 CATTGTCCTTTGAGTTTGGCG 58.335 47.619 0.00 0.00 0.00 5.69
1886 3383 6.619329 ATTAAGTAGGGTTTGGTTACCGTA 57.381 37.500 0.00 0.00 39.18 4.02
1888 3385 2.606108 GTAGGGTTTGGTTACCGTACG 58.394 52.381 8.69 8.69 44.69 3.67
1894 3391 3.125146 GGTTTGGTTACCGTACGGAAATC 59.875 47.826 39.52 24.11 38.96 2.17
1896 3393 1.898472 TGGTTACCGTACGGAAATCCA 59.102 47.619 39.52 31.34 38.96 3.41
1897 3394 2.500910 TGGTTACCGTACGGAAATCCAT 59.499 45.455 39.52 18.41 38.96 3.41
1903 3400 1.745232 GTACGGAAATCCATGCACCA 58.255 50.000 0.00 0.00 35.14 4.17
1957 3456 0.250901 ATGGGCATGAAGGTATCGGC 60.251 55.000 0.00 0.00 0.00 5.54
1958 3457 1.148273 GGGCATGAAGGTATCGGCA 59.852 57.895 0.00 0.00 33.85 5.69
1994 3495 3.579586 AGCAAATTCTTGAAATCCTGCCA 59.420 39.130 0.00 0.00 34.14 4.92
1998 3499 6.690530 CAAATTCTTGAAATCCTGCCAGTTA 58.309 36.000 0.00 0.00 34.14 2.24
2011 3512 1.859302 CCAGTTAGAGGGCTCAGACT 58.141 55.000 0.00 0.00 0.00 3.24
2109 3611 2.496070 CGTCTCCACCTAGGTTTGATCA 59.504 50.000 13.15 0.00 39.02 2.92
2113 3615 6.463049 CGTCTCCACCTAGGTTTGATCAATAT 60.463 42.308 13.15 1.00 39.02 1.28
2114 3616 6.708054 GTCTCCACCTAGGTTTGATCAATATG 59.292 42.308 13.15 0.00 39.02 1.78
2116 3618 7.567250 TCTCCACCTAGGTTTGATCAATATGTA 59.433 37.037 13.15 0.00 39.02 2.29
2117 3619 7.735917 TCCACCTAGGTTTGATCAATATGTAG 58.264 38.462 13.15 8.04 39.02 2.74
2118 3620 7.567250 TCCACCTAGGTTTGATCAATATGTAGA 59.433 37.037 13.15 0.00 39.02 2.59
2119 3621 7.875041 CCACCTAGGTTTGATCAATATGTAGAG 59.125 40.741 13.15 1.27 0.00 2.43
2120 3622 7.386299 CACCTAGGTTTGATCAATATGTAGAGC 59.614 40.741 13.15 2.04 0.00 4.09
2121 3623 7.071196 ACCTAGGTTTGATCAATATGTAGAGCA 59.929 37.037 9.21 0.00 0.00 4.26
2122 3624 7.601886 CCTAGGTTTGATCAATATGTAGAGCAG 59.398 40.741 9.40 3.21 31.20 4.24
2123 3625 7.129457 AGGTTTGATCAATATGTAGAGCAGA 57.871 36.000 9.40 0.00 31.20 4.26
2124 3626 7.743749 AGGTTTGATCAATATGTAGAGCAGAT 58.256 34.615 9.40 0.00 31.20 2.90
2125 3627 7.877097 AGGTTTGATCAATATGTAGAGCAGATC 59.123 37.037 9.40 0.00 31.20 2.75
2126 3628 7.658982 GGTTTGATCAATATGTAGAGCAGATCA 59.341 37.037 9.40 0.00 38.74 2.92
2127 3629 8.494347 GTTTGATCAATATGTAGAGCAGATCAC 58.506 37.037 9.40 0.00 39.79 3.06
2128 3630 7.294017 TGATCAATATGTAGAGCAGATCACA 57.706 36.000 0.00 0.00 36.46 3.58
2129 3631 7.904205 TGATCAATATGTAGAGCAGATCACAT 58.096 34.615 0.00 8.26 36.46 3.21
2130 3632 9.028284 TGATCAATATGTAGAGCAGATCACATA 57.972 33.333 11.10 11.10 36.46 2.29
2131 3633 9.299963 GATCAATATGTAGAGCAGATCACATAC 57.700 37.037 10.99 0.00 36.06 2.39
2132 3634 7.606349 TCAATATGTAGAGCAGATCACATACC 58.394 38.462 10.99 0.00 36.06 2.73
2133 3635 7.233348 TCAATATGTAGAGCAGATCACATACCA 59.767 37.037 10.99 0.00 36.06 3.25
2134 3636 7.730672 ATATGTAGAGCAGATCACATACCAT 57.269 36.000 10.99 0.00 36.06 3.55
2135 3637 5.876651 TGTAGAGCAGATCACATACCATT 57.123 39.130 0.00 0.00 0.00 3.16
2136 3638 5.604565 TGTAGAGCAGATCACATACCATTG 58.395 41.667 0.00 0.00 0.00 2.82
2137 3639 4.082665 AGAGCAGATCACATACCATTGG 57.917 45.455 0.00 0.00 0.00 3.16
2138 3640 3.457380 AGAGCAGATCACATACCATTGGT 59.543 43.478 13.94 13.94 40.16 3.67
2139 3641 3.548770 AGCAGATCACATACCATTGGTG 58.451 45.455 18.83 5.17 36.19 4.17
2140 3642 3.054139 AGCAGATCACATACCATTGGTGT 60.054 43.478 18.83 9.12 36.19 4.16
2141 3643 4.164030 AGCAGATCACATACCATTGGTGTA 59.836 41.667 18.83 0.00 36.19 2.90
2142 3644 5.065914 GCAGATCACATACCATTGGTGTAT 58.934 41.667 18.83 1.71 36.19 2.29
2143 3645 5.532406 GCAGATCACATACCATTGGTGTATT 59.468 40.000 18.83 0.00 36.19 1.89
2144 3646 6.039717 GCAGATCACATACCATTGGTGTATTT 59.960 38.462 18.83 0.00 36.19 1.40
2145 3647 7.416664 GCAGATCACATACCATTGGTGTATTTT 60.417 37.037 18.83 0.00 36.19 1.82
2146 3648 7.916977 CAGATCACATACCATTGGTGTATTTTG 59.083 37.037 18.83 7.32 36.19 2.44
2147 3649 5.960113 TCACATACCATTGGTGTATTTTGC 58.040 37.500 18.83 0.00 36.19 3.68
2148 3650 4.797868 CACATACCATTGGTGTATTTTGCG 59.202 41.667 18.83 0.74 36.19 4.85
2149 3651 4.461081 ACATACCATTGGTGTATTTTGCGT 59.539 37.500 18.83 1.37 36.19 5.24
2150 3652 5.648526 ACATACCATTGGTGTATTTTGCGTA 59.351 36.000 18.83 0.00 36.19 4.42
2151 3653 6.151312 ACATACCATTGGTGTATTTTGCGTAA 59.849 34.615 18.83 0.00 36.19 3.18
2152 3654 5.652994 ACCATTGGTGTATTTTGCGTAAT 57.347 34.783 7.76 0.00 32.98 1.89
2153 3655 5.646606 ACCATTGGTGTATTTTGCGTAATC 58.353 37.500 7.76 0.00 32.98 1.75
2154 3656 5.184096 ACCATTGGTGTATTTTGCGTAATCA 59.816 36.000 7.76 0.00 32.98 2.57
2155 3657 6.096036 CCATTGGTGTATTTTGCGTAATCAA 58.904 36.000 0.00 0.00 0.00 2.57
2156 3658 6.756074 CCATTGGTGTATTTTGCGTAATCAAT 59.244 34.615 0.00 0.00 0.00 2.57
2157 3659 7.918033 CCATTGGTGTATTTTGCGTAATCAATA 59.082 33.333 0.00 0.00 0.00 1.90
2158 3660 9.295214 CATTGGTGTATTTTGCGTAATCAATAA 57.705 29.630 0.00 0.00 0.00 1.40
2159 3661 9.862371 ATTGGTGTATTTTGCGTAATCAATAAA 57.138 25.926 0.00 0.00 0.00 1.40
2160 3662 8.676454 TGGTGTATTTTGCGTAATCAATAAAC 57.324 30.769 3.61 3.61 0.00 2.01
2161 3663 7.755822 TGGTGTATTTTGCGTAATCAATAAACC 59.244 33.333 16.98 16.98 38.94 3.27
2162 3664 7.221259 GGTGTATTTTGCGTAATCAATAAACCC 59.779 37.037 14.53 3.78 34.96 4.11
2163 3665 7.755822 GTGTATTTTGCGTAATCAATAAACCCA 59.244 33.333 1.55 0.00 0.00 4.51
2210 3712 9.726438 ATAATAGCTCAATGGTGTTAATACTCC 57.274 33.333 2.17 0.00 38.21 3.85
2211 3713 4.781934 AGCTCAATGGTGTTAATACTCCC 58.218 43.478 2.17 0.00 37.16 4.30
2214 3716 3.520317 TCAATGGTGTTAATACTCCCGGT 59.480 43.478 0.00 0.00 37.16 5.28
2224 3726 8.680001 GTGTTAATACTCCCGGTCATAATTTTT 58.320 33.333 0.00 0.00 0.00 1.94
2229 3731 6.693315 ACTCCCGGTCATAATTTTTATGTG 57.307 37.500 0.00 0.82 0.00 3.21
2299 3801 2.050077 GCGGTGGAGTTTGCTTGC 60.050 61.111 0.00 0.00 0.00 4.01
2301 3803 1.234615 GCGGTGGAGTTTGCTTGCTA 61.235 55.000 0.00 0.00 0.00 3.49
2311 3825 0.804364 TTGCTTGCTATTGGTGAGCG 59.196 50.000 0.00 0.00 43.19 5.03
2313 3827 1.372087 GCTTGCTATTGGTGAGCGCT 61.372 55.000 11.27 11.27 43.19 5.92
2345 3859 0.995024 ATGGGTGCTTCTGCTAGGTT 59.005 50.000 0.00 0.00 40.48 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.041922 AGAGACCAGGCGGCCATA 60.042 61.111 23.09 0.00 34.57 2.74
6 7 0.035458 ACAAAAGGAGAGACCAGGCG 59.965 55.000 0.00 0.00 42.04 5.52
32 33 9.070179 GTTAAAATAAGGACCAGGTCAAGTAAA 57.930 33.333 21.75 2.33 33.68 2.01
35 36 6.849151 AGTTAAAATAAGGACCAGGTCAAGT 58.151 36.000 21.75 7.94 33.68 3.16
36 37 6.374613 GGAGTTAAAATAAGGACCAGGTCAAG 59.625 42.308 21.75 0.00 33.68 3.02
48 49 8.888579 AGGATACGACATGGAGTTAAAATAAG 57.111 34.615 0.00 0.00 46.39 1.73
51 52 6.929606 GCTAGGATACGACATGGAGTTAAAAT 59.070 38.462 0.00 0.00 46.39 1.82
71 72 0.315251 TCCATTCGCTCGATGCTAGG 59.685 55.000 5.53 0.00 40.11 3.02
84 85 1.211457 AGATCACTGCCACCTCCATTC 59.789 52.381 0.00 0.00 0.00 2.67
120 121 0.806868 CTCATCAGCGGCATTTGTGT 59.193 50.000 1.45 0.00 0.00 3.72
121 122 0.099968 CCTCATCAGCGGCATTTGTG 59.900 55.000 1.45 0.00 0.00 3.33
127 128 2.580815 CACTCCTCATCAGCGGCA 59.419 61.111 1.45 0.00 0.00 5.69
157 158 7.562088 ACCAAAAATCTGGAGTAAGGTAACAAA 59.438 33.333 0.00 0.00 38.96 2.83
186 187 2.105134 ACATATTTACCCGCCGAATGGA 59.895 45.455 0.00 0.00 37.49 3.41
187 188 2.482721 GACATATTTACCCGCCGAATGG 59.517 50.000 0.00 0.00 38.77 3.16
188 189 2.482721 GGACATATTTACCCGCCGAATG 59.517 50.000 0.00 0.00 0.00 2.67
189 190 2.551504 GGGACATATTTACCCGCCGAAT 60.552 50.000 0.00 0.00 34.03 3.34
190 191 1.202675 GGGACATATTTACCCGCCGAA 60.203 52.381 0.00 0.00 34.03 4.30
191 192 0.393820 GGGACATATTTACCCGCCGA 59.606 55.000 0.00 0.00 34.03 5.54
192 193 0.107081 TGGGACATATTTACCCGCCG 59.893 55.000 0.00 0.00 45.91 6.46
193 194 2.351706 TTGGGACATATTTACCCGCC 57.648 50.000 0.00 0.00 45.91 6.13
194 195 3.502211 CAGATTGGGACATATTTACCCGC 59.498 47.826 0.00 0.00 45.91 6.13
195 196 4.714632 ACAGATTGGGACATATTTACCCG 58.285 43.478 0.00 0.00 45.91 5.28
196 197 6.365520 AGAACAGATTGGGACATATTTACCC 58.634 40.000 0.00 0.00 43.51 3.69
197 198 7.339466 ACAAGAACAGATTGGGACATATTTACC 59.661 37.037 0.00 0.00 39.30 2.85
198 199 8.184192 CACAAGAACAGATTGGGACATATTTAC 58.816 37.037 0.00 0.00 39.30 2.01
199 200 7.888021 ACACAAGAACAGATTGGGACATATTTA 59.112 33.333 0.00 0.00 39.30 1.40
200 201 6.721208 ACACAAGAACAGATTGGGACATATTT 59.279 34.615 0.00 0.00 39.30 1.40
201 202 6.248433 ACACAAGAACAGATTGGGACATATT 58.752 36.000 0.00 0.00 39.30 1.28
202 203 5.819991 ACACAAGAACAGATTGGGACATAT 58.180 37.500 0.00 0.00 39.30 1.78
203 204 5.241403 ACACAAGAACAGATTGGGACATA 57.759 39.130 0.00 0.00 39.30 2.29
204 205 4.104383 ACACAAGAACAGATTGGGACAT 57.896 40.909 0.00 0.00 39.30 3.06
205 206 3.576078 ACACAAGAACAGATTGGGACA 57.424 42.857 0.00 0.00 34.59 4.02
206 207 4.003648 CCTACACAAGAACAGATTGGGAC 58.996 47.826 0.00 0.00 34.59 4.46
207 208 3.907474 TCCTACACAAGAACAGATTGGGA 59.093 43.478 0.00 0.00 34.59 4.37
211 212 8.105829 AGATTTCATCCTACACAAGAACAGATT 58.894 33.333 0.00 0.00 0.00 2.40
214 215 8.954950 ATAGATTTCATCCTACACAAGAACAG 57.045 34.615 0.00 0.00 0.00 3.16
237 238 7.418483 GGCTTTTGAATTTGGCCAACCTATATA 60.418 37.037 20.35 0.97 42.08 0.86
238 239 6.348498 GCTTTTGAATTTGGCCAACCTATAT 58.652 36.000 20.35 5.60 36.63 0.86
267 268 8.327429 GTTGGTTTGATTGTTGTTGTCTTATTG 58.673 33.333 0.00 0.00 0.00 1.90
311 312 1.001633 CTGCCGGTGTGGTACTTAAGT 59.998 52.381 13.68 13.68 41.21 2.24
319 320 3.832237 CTTGCTCTGCCGGTGTGGT 62.832 63.158 1.90 0.00 41.21 4.16
335 364 4.687901 ACAAACCCTGCTTAATTTGCTT 57.312 36.364 5.05 0.00 35.83 3.91
384 413 0.550914 TTGCCAAGGTCCTGAAGTGT 59.449 50.000 0.00 0.00 0.00 3.55
385 414 1.242076 CTTGCCAAGGTCCTGAAGTG 58.758 55.000 0.00 0.00 0.00 3.16
433 484 4.422073 TGAGTTCAGTGTCTGGTTCAAT 57.578 40.909 0.00 0.00 31.51 2.57
570 627 2.037901 CCTTCTCCAGCATCTGAGCTA 58.962 52.381 0.00 0.00 44.54 3.32
576 633 4.567327 CCTTTTCTTCCTTCTCCAGCATCT 60.567 45.833 0.00 0.00 0.00 2.90
581 638 3.308046 CCTCCCTTTTCTTCCTTCTCCAG 60.308 52.174 0.00 0.00 0.00 3.86
587 644 3.603697 AGACTCCTCCCTTTTCTTCCTT 58.396 45.455 0.00 0.00 0.00 3.36
588 645 3.283712 AGACTCCTCCCTTTTCTTCCT 57.716 47.619 0.00 0.00 0.00 3.36
597 654 0.684805 CGCCAACTAGACTCCTCCCT 60.685 60.000 0.00 0.00 0.00 4.20
682 742 4.745620 GCTAAGACTAAACGCCTTATCCAG 59.254 45.833 0.00 0.00 0.00 3.86
687 747 3.194968 AGCTGCTAAGACTAAACGCCTTA 59.805 43.478 0.00 0.00 0.00 2.69
728 788 1.202568 TGCGGCTGATGTTGAGGATAG 60.203 52.381 0.00 0.00 0.00 2.08
851 934 2.860009 ACGAGTCTGTTCACCTACTCA 58.140 47.619 0.00 0.00 38.60 3.41
866 949 1.001378 GTCCAATGCTTTGCAACGAGT 60.001 47.619 7.19 0.00 43.62 4.18
950 1441 2.944129 AGCTATGTGGTGTGGTTTTGT 58.056 42.857 0.00 0.00 0.00 2.83
966 1457 5.699915 CGACTATGGTTGTACTAGCTAGCTA 59.300 44.000 22.85 22.85 0.00 3.32
968 1459 4.275443 ACGACTATGGTTGTACTAGCTAGC 59.725 45.833 20.91 6.62 38.22 3.42
969 1460 5.049543 GGACGACTATGGTTGTACTAGCTAG 60.050 48.000 19.44 19.44 39.93 3.42
970 1461 4.818546 GGACGACTATGGTTGTACTAGCTA 59.181 45.833 4.55 0.00 39.93 3.32
1022 1635 1.372087 GAGCAGCCCGACAAGGAATG 61.372 60.000 0.00 0.00 45.00 2.67
1029 1642 3.071206 GAGAGGAGCAGCCCGACA 61.071 66.667 0.00 0.00 37.37 4.35
1077 1732 0.033601 GAGCTGTCTCCTCCTCCAGA 60.034 60.000 0.00 0.00 33.19 3.86
1128 1789 1.133199 TCAACCTTGGGAAGCATTGGT 60.133 47.619 0.00 0.00 0.00 3.67
1137 1798 2.436109 GGCAGCTCAACCTTGGGA 59.564 61.111 0.00 0.00 0.00 4.37
1170 2324 2.045926 GGCTTCGGTGGCAGATGT 60.046 61.111 0.00 0.00 0.00 3.06
1462 2745 5.760743 TCACACAAATGACTCACGGAAAATA 59.239 36.000 0.00 0.00 0.00 1.40
1518 2806 8.843262 CATCTGTATTGTTCATGTACATTCCAT 58.157 33.333 5.37 0.00 0.00 3.41
1519 2807 7.282901 CCATCTGTATTGTTCATGTACATTCCA 59.717 37.037 5.37 0.11 0.00 3.53
1520 2808 7.498900 TCCATCTGTATTGTTCATGTACATTCC 59.501 37.037 5.37 0.00 0.00 3.01
1521 2809 8.437360 TCCATCTGTATTGTTCATGTACATTC 57.563 34.615 5.37 0.75 0.00 2.67
1522 2810 8.843262 CATCCATCTGTATTGTTCATGTACATT 58.157 33.333 5.37 5.64 0.00 2.71
1523 2811 7.994911 ACATCCATCTGTATTGTTCATGTACAT 59.005 33.333 5.96 1.41 0.00 2.29
1524 2812 7.337938 ACATCCATCTGTATTGTTCATGTACA 58.662 34.615 0.00 0.00 0.00 2.90
1525 2813 7.792374 ACATCCATCTGTATTGTTCATGTAC 57.208 36.000 0.00 0.00 0.00 2.90
1526 2814 8.806429 AAACATCCATCTGTATTGTTCATGTA 57.194 30.769 0.00 0.00 30.62 2.29
1527 2815 7.707624 AAACATCCATCTGTATTGTTCATGT 57.292 32.000 0.00 0.00 30.62 3.21
1528 2816 8.676401 TGTAAACATCCATCTGTATTGTTCATG 58.324 33.333 0.00 0.00 30.62 3.07
1669 3159 5.977129 AGTTAAAAGGAAAAGTGTGCAATCG 59.023 36.000 0.00 0.00 0.00 3.34
1750 3247 3.239254 GTTTATCGGGCAAAAAGTTCCG 58.761 45.455 0.00 0.00 43.42 4.30
1755 3252 2.983803 CGTTGGTTTATCGGGCAAAAAG 59.016 45.455 0.00 0.00 0.00 2.27
1774 3271 1.135083 CAGAGTTAGGATTCCGTGCGT 60.135 52.381 0.00 0.00 0.00 5.24
1838 3335 4.127907 GCAAGGTATCTAGGCCTAACAAC 58.872 47.826 14.85 11.22 34.15 3.32
1851 3348 5.608449 ACCCTACTTAATTCGCAAGGTATC 58.392 41.667 0.00 0.00 38.47 2.24
1886 3383 1.750778 GAATGGTGCATGGATTTCCGT 59.249 47.619 0.00 0.00 39.43 4.69
1888 3385 3.025978 TCAGAATGGTGCATGGATTTCC 58.974 45.455 0.00 0.00 36.16 3.13
1894 3391 3.449737 AGGAATTTCAGAATGGTGCATGG 59.550 43.478 0.00 0.00 36.16 3.66
1896 3393 4.891756 CCTAGGAATTTCAGAATGGTGCAT 59.108 41.667 1.05 0.00 36.16 3.96
1897 3394 4.018506 TCCTAGGAATTTCAGAATGGTGCA 60.019 41.667 9.71 0.00 36.16 4.57
1903 3400 9.163894 TCATATCACTCCTAGGAATTTCAGAAT 57.836 33.333 13.77 2.86 0.00 2.40
1957 3456 0.911769 TTGCTACCACCCATCTCCTG 59.088 55.000 0.00 0.00 0.00 3.86
1958 3457 1.668826 TTTGCTACCACCCATCTCCT 58.331 50.000 0.00 0.00 0.00 3.69
1994 3495 3.243724 ACAAAGTCTGAGCCCTCTAACT 58.756 45.455 0.00 0.00 0.00 2.24
1998 3499 2.050144 TGAACAAAGTCTGAGCCCTCT 58.950 47.619 0.00 0.00 0.00 3.69
2011 3512 8.737168 AGGAGAATTCATCGAATATGAACAAA 57.263 30.769 8.44 0.00 40.37 2.83
2059 3561 1.948104 TTCCACAAGGTTGTCTCACG 58.052 50.000 0.00 0.00 39.91 4.35
2061 3563 2.622942 GCAATTCCACAAGGTTGTCTCA 59.377 45.455 0.00 0.00 39.91 3.27
2109 3611 7.544804 TGGTATGTGATCTGCTCTACATATT 57.455 36.000 5.04 0.00 38.04 1.28
2113 3615 5.453762 CCAATGGTATGTGATCTGCTCTACA 60.454 44.000 0.00 0.00 0.00 2.74
2114 3616 4.993584 CCAATGGTATGTGATCTGCTCTAC 59.006 45.833 0.00 0.00 0.00 2.59
2116 3618 3.457380 ACCAATGGTATGTGATCTGCTCT 59.543 43.478 1.52 0.00 32.11 4.09
2117 3619 3.562973 CACCAATGGTATGTGATCTGCTC 59.437 47.826 3.85 0.00 32.11 4.26
2118 3620 3.054139 ACACCAATGGTATGTGATCTGCT 60.054 43.478 3.85 0.00 32.11 4.24
2119 3621 3.282021 ACACCAATGGTATGTGATCTGC 58.718 45.455 3.85 0.00 32.11 4.26
2120 3622 7.572523 AAATACACCAATGGTATGTGATCTG 57.427 36.000 3.85 0.00 32.11 2.90
2121 3623 7.416664 GCAAAATACACCAATGGTATGTGATCT 60.417 37.037 3.85 0.00 32.11 2.75
2122 3624 6.697019 GCAAAATACACCAATGGTATGTGATC 59.303 38.462 3.85 0.00 32.11 2.92
2123 3625 6.572519 GCAAAATACACCAATGGTATGTGAT 58.427 36.000 3.85 0.00 32.11 3.06
2124 3626 5.392487 CGCAAAATACACCAATGGTATGTGA 60.392 40.000 3.85 0.00 32.11 3.58
2125 3627 4.797868 CGCAAAATACACCAATGGTATGTG 59.202 41.667 3.85 0.00 32.11 3.21
2126 3628 4.461081 ACGCAAAATACACCAATGGTATGT 59.539 37.500 3.85 2.24 32.11 2.29
2127 3629 4.992688 ACGCAAAATACACCAATGGTATG 58.007 39.130 3.85 0.00 32.11 2.39
2128 3630 6.761099 TTACGCAAAATACACCAATGGTAT 57.239 33.333 3.85 0.00 32.11 2.73
2129 3631 6.374613 TGATTACGCAAAATACACCAATGGTA 59.625 34.615 3.85 0.00 32.11 3.25
2130 3632 5.184096 TGATTACGCAAAATACACCAATGGT 59.816 36.000 0.00 0.00 35.62 3.55
2131 3633 5.645624 TGATTACGCAAAATACACCAATGG 58.354 37.500 0.00 0.00 0.00 3.16
2132 3634 7.754069 ATTGATTACGCAAAATACACCAATG 57.246 32.000 0.00 0.00 0.00 2.82
2133 3635 9.862371 TTTATTGATTACGCAAAATACACCAAT 57.138 25.926 0.00 0.00 0.00 3.16
2134 3636 9.130312 GTTTATTGATTACGCAAAATACACCAA 57.870 29.630 0.00 0.00 0.00 3.67
2135 3637 7.755822 GGTTTATTGATTACGCAAAATACACCA 59.244 33.333 0.00 0.00 36.23 4.17
2136 3638 7.221259 GGGTTTATTGATTACGCAAAATACACC 59.779 37.037 0.00 0.00 35.79 4.16
2137 3639 7.755822 TGGGTTTATTGATTACGCAAAATACAC 59.244 33.333 0.00 0.00 32.71 2.90
2138 3640 7.827701 TGGGTTTATTGATTACGCAAAATACA 58.172 30.769 0.00 0.00 32.71 2.29
2139 3641 8.690680 TTGGGTTTATTGATTACGCAAAATAC 57.309 30.769 0.00 0.00 40.34 1.89
2144 3646 8.908903 AGATATTTGGGTTTATTGATTACGCAA 58.091 29.630 0.00 0.00 41.17 4.85
2145 3647 8.458573 AGATATTTGGGTTTATTGATTACGCA 57.541 30.769 0.00 0.00 33.63 5.24
2146 3648 9.180678 CAAGATATTTGGGTTTATTGATTACGC 57.819 33.333 0.00 0.00 0.00 4.42
2196 3698 2.538222 TGACCGGGAGTATTAACACCA 58.462 47.619 6.32 0.00 38.04 4.17
2260 3762 4.504858 CCAAACTCGATTAGTAGTTGCCT 58.495 43.478 0.00 0.00 37.50 4.75
2262 3764 3.241995 CGCCAAACTCGATTAGTAGTTGC 60.242 47.826 0.00 0.00 37.50 4.17
2271 3773 0.673644 CTCCACCGCCAAACTCGATT 60.674 55.000 0.00 0.00 0.00 3.34
2299 3801 0.585357 GCATCAGCGCTCACCAATAG 59.415 55.000 7.13 0.00 0.00 1.73
2301 3803 2.117156 GGCATCAGCGCTCACCAAT 61.117 57.895 7.13 0.00 43.41 3.16
2329 3843 0.606401 TGCAACCTAGCAGAAGCACC 60.606 55.000 0.00 0.00 45.49 5.01
2330 3844 2.932663 TGCAACCTAGCAGAAGCAC 58.067 52.632 0.00 0.00 45.49 4.40
2341 3855 4.624125 GCAACTAGACCTAAGATGCAACCT 60.624 45.833 0.00 0.00 32.80 3.50
2345 3859 4.956700 AGTAGCAACTAGACCTAAGATGCA 59.043 41.667 0.00 0.00 32.84 3.96


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

AutoCloner maintained by Alex Coulton.