Multiple sequence alignment - TraesCS6B01G294000

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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 TraesCS6B01G294000 chr6B 100.000 4351 0 0 1 4351 528280976 528285326 0.000000e+00 8035.0
1 TraesCS6B01G294000 chr6A 88.921 2067 135 42 5 2035 492279075 492281083 0.000000e+00 2462.0
2 TraesCS6B01G294000 chr6A 93.131 990 32 9 2610 3566 492281852 492282838 0.000000e+00 1419.0
3 TraesCS6B01G294000 chr6A 93.638 503 14 11 2075 2576 492281092 492281577 0.000000e+00 736.0
4 TraesCS6B01G294000 chr6A 95.251 379 15 1 3976 4351 492283129 492283507 8.050000e-167 597.0
5 TraesCS6B01G294000 chr6A 97.436 39 0 1 2579 2617 492281744 492281781 1.010000e-06 65.8
6 TraesCS6B01G294000 chr6D 91.569 1791 77 23 2610 4351 351139766 351138001 0.000000e+00 2403.0
7 TraesCS6B01G294000 chr6D 92.223 1543 62 23 389 1927 351142404 351140916 0.000000e+00 2132.0
8 TraesCS6B01G294000 chr6D 95.599 659 25 4 1923 2580 351140757 351140102 0.000000e+00 1053.0
9 TraesCS6B01G294000 chr6D 87.252 353 39 4 5 356 351143848 351143501 8.770000e-107 398.0
10 TraesCS6B01G294000 chr6D 100.000 35 0 0 2579 2613 351139913 351139879 1.010000e-06 65.8
11 TraesCS6B01G294000 chr6D 93.023 43 2 1 1666 1707 17109133 17109091 1.310000e-05 62.1
12 TraesCS6B01G294000 chr2D 85.932 526 74 0 997 1522 5684591 5684066 2.940000e-156 562.0
13 TraesCS6B01G294000 chr2D 82.495 457 58 13 1988 2441 5682678 5682241 8.830000e-102 381.0
14 TraesCS6B01G294000 chr2D 85.145 276 37 4 2168 2441 5709686 5709413 3.310000e-71 279.0
15 TraesCS6B01G294000 chr2D 91.837 49 4 0 1659 1707 643674134 643674086 7.810000e-08 69.4
16 TraesCS6B01G294000 chr2A 86.193 507 70 0 1016 1522 4171724 4171218 2.290000e-152 549.0
17 TraesCS6B01G294000 chr2A 82.456 456 52 15 1988 2441 4169699 4169270 1.480000e-99 374.0
18 TraesCS6B01G294000 chr2A 90.226 266 26 0 2132 2397 4204446 4204181 8.960000e-92 348.0
19 TraesCS6B01G294000 chr2B 85.380 513 75 0 1010 1522 5678125 5678637 2.300000e-147 532.0
20 TraesCS6B01G294000 chr2B 88.182 330 38 1 2113 2441 5680243 5680572 4.080000e-105 392.0
21 TraesCS6B01G294000 chr4D 87.500 112 10 3 3597 3706 335044863 335044972 4.570000e-25 126.0
22 TraesCS6B01G294000 chr7A 88.119 101 10 1 3599 3697 205167761 205167861 7.640000e-23 119.0
23 TraesCS6B01G294000 chr7B 87.129 101 11 1 3599 3697 707997406 707997506 3.560000e-21 113.0
24 TraesCS6B01G294000 chr3B 82.857 105 15 2 3602 3704 556986140 556986243 1.670000e-14 91.6
25 TraesCS6B01G294000 chr3B 85.507 69 9 1 18 85 778769370 778769302 2.170000e-08 71.3
26 TraesCS6B01G294000 chr7D 82.353 102 15 3 3602 3700 189320961 189320860 7.750000e-13 86.1
27 TraesCS6B01G294000 chr7D 82.105 95 13 4 3614 3706 213482481 213482573 1.300000e-10 78.7
28 TraesCS6B01G294000 chr4B 81.579 114 10 7 3597 3706 204718942 204718836 2.790000e-12 84.2
29 TraesCS6B01G294000 chr3A 83.000 100 10 7 3601 3697 467347299 467347394 2.790000e-12 84.2
30 TraesCS6B01G294000 chr4A 97.561 41 0 1 1668 1708 168924555 168924594 7.810000e-08 69.4
31 TraesCS6B01G294000 chr4A 93.023 43 2 1 1669 1711 618057931 618057972 1.310000e-05 62.1
32 TraesCS6B01G294000 chr3D 97.561 41 0 1 1668 1708 187853077 187853116 7.810000e-08 69.4
33 TraesCS6B01G294000 chr3D 97.500 40 0 1 1668 1707 528192470 528192508 2.810000e-07 67.6
34 TraesCS6B01G294000 chr1A 95.349 43 1 1 1665 1707 344132340 344132381 2.810000e-07 67.6


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 TraesCS6B01G294000 chr6B 528280976 528285326 4350 False 8035.00 8035 100.0000 1 4351 1 chr6B.!!$F1 4350
1 TraesCS6B01G294000 chr6A 492279075 492283507 4432 False 1055.96 2462 93.6754 5 4351 5 chr6A.!!$F1 4346
2 TraesCS6B01G294000 chr6D 351138001 351143848 5847 True 1210.36 2403 93.3286 5 4351 5 chr6D.!!$R2 4346
3 TraesCS6B01G294000 chr2D 5682241 5684591 2350 True 471.50 562 84.2135 997 2441 2 chr2D.!!$R3 1444
4 TraesCS6B01G294000 chr2A 4169270 4171724 2454 True 461.50 549 84.3245 1016 2441 2 chr2A.!!$R2 1425
5 TraesCS6B01G294000 chr2B 5678125 5680572 2447 False 462.00 532 86.7810 1010 2441 2 chr2B.!!$F1 1431

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
826 1914 0.038159 CGCCCTCTCTTTCTGTTCGT 60.038 55.000 0.00 0.0 0.00 3.85 F
961 2053 0.391130 TAATCTGACAGTGCCGTGGC 60.391 55.000 3.30 3.3 42.35 5.01 F
1293 2385 0.473326 GGATCATGCTCAAGGAGGCT 59.527 55.000 0.00 0.0 0.00 4.58 F
2098 4520 1.001269 GGTTAGGGCCTTGGTGGTC 60.001 63.158 13.45 0.0 40.45 4.02 F
2528 4952 2.274920 GCCTCAAGCAGCTTTTCATC 57.725 50.000 4.38 0.0 42.97 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 2819 1.510492 TGGGGCAGCAGAGATTATCA 58.490 50.000 0.00 0.0 0.00 2.15 R
2509 4933 1.817447 AGATGAAAAGCTGCTTGAGGC 59.183 47.619 16.73 6.4 42.22 4.70 R
3116 5879 0.033504 CCACTGGCTGTTCTGTACGT 59.966 55.000 0.00 0.0 0.00 3.57 R
3287 6050 0.966920 ACACGTCCTGGGAACTACTG 59.033 55.000 0.00 0.0 0.00 2.74 R
3673 6437 2.023695 ACTCCCTCCGTCCCAATAAGTA 60.024 50.000 0.00 0.0 0.00 2.24 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
88 89 0.040958 GGCAAGCCGCTTCAATATCG 60.041 55.000 1.56 0.00 41.91 2.92
119 121 1.129917 AGATCACATCTGCTCTGGGG 58.870 55.000 0.00 0.00 38.44 4.96
122 124 2.685017 ACATCTGCTCTGGGGCGA 60.685 61.111 0.00 0.00 34.52 5.54
191 193 1.377366 TTCAGGTGAAAAACGGCGCA 61.377 50.000 10.83 0.00 0.00 6.09
224 226 2.273557 GGTTTTGCATGTGCCATGATC 58.726 47.619 16.46 3.57 41.18 2.92
229 231 1.936658 CATGTGCCATGATCGTCGG 59.063 57.895 8.92 0.00 0.00 4.79
231 233 0.394192 ATGTGCCATGATCGTCGGAT 59.606 50.000 0.00 0.00 34.96 4.18
232 234 0.530431 TGTGCCATGATCGTCGGATG 60.530 55.000 0.00 0.00 31.51 3.51
233 235 1.595109 TGCCATGATCGTCGGATGC 60.595 57.895 0.00 0.00 31.51 3.91
251 254 2.358615 GTGCGTGGCATCAGTCCA 60.359 61.111 0.00 0.00 41.91 4.02
269 272 0.111704 CAGACACGAGCAAAACGTCG 60.112 55.000 0.00 0.00 42.07 5.12
270 273 1.200839 GACACGAGCAAAACGTCGG 59.799 57.895 0.00 0.00 42.07 4.79
271 274 1.210545 GACACGAGCAAAACGTCGGA 61.211 55.000 0.00 0.00 42.07 4.55
274 277 2.851104 GAGCAAAACGTCGGACCG 59.149 61.111 7.84 7.84 0.00 4.79
275 278 2.663852 AGCAAAACGTCGGACCGG 60.664 61.111 15.25 0.00 0.00 5.28
277 280 3.719144 CAAAACGTCGGACCGGCC 61.719 66.667 13.94 2.44 0.00 6.13
278 281 4.238654 AAAACGTCGGACCGGCCA 62.239 61.111 13.94 0.00 35.94 5.36
279 282 3.540367 AAAACGTCGGACCGGCCAT 62.540 57.895 13.94 0.00 35.94 4.40
280 283 3.945304 AAACGTCGGACCGGCCATC 62.945 63.158 13.94 0.00 35.94 3.51
287 290 1.303317 GGACCGGCCATCAGTTTGT 60.303 57.895 0.00 0.00 36.34 2.83
369 388 4.881850 GGGTTACCATACAAATCCACTGAG 59.118 45.833 2.98 0.00 36.50 3.35
411 1478 3.260884 AGAAGACATACGGGTCAATGTGT 59.739 43.478 6.86 0.00 40.29 3.72
441 1509 1.867166 GTCTGCCTAATCTAACCGGC 58.133 55.000 0.00 0.00 42.78 6.13
469 1538 3.391799 AGTGGCCCGGGTTATTTATTT 57.608 42.857 24.63 0.00 0.00 1.40
665 1753 1.369625 GGTCAAATCTACGCCACCAG 58.630 55.000 0.00 0.00 0.00 4.00
751 1839 1.721664 CGGAAGGTATCGTCTCGGCA 61.722 60.000 0.00 0.00 0.00 5.69
820 1908 1.003233 GGTTGCGCCCTCTCTTTCT 60.003 57.895 4.18 0.00 0.00 2.52
824 1912 0.320771 TGCGCCCTCTCTTTCTGTTC 60.321 55.000 4.18 0.00 0.00 3.18
825 1913 1.355066 GCGCCCTCTCTTTCTGTTCG 61.355 60.000 0.00 0.00 0.00 3.95
826 1914 0.038159 CGCCCTCTCTTTCTGTTCGT 60.038 55.000 0.00 0.00 0.00 3.85
827 1915 1.605712 CGCCCTCTCTTTCTGTTCGTT 60.606 52.381 0.00 0.00 0.00 3.85
828 1916 2.352421 CGCCCTCTCTTTCTGTTCGTTA 60.352 50.000 0.00 0.00 0.00 3.18
829 1917 3.676324 CGCCCTCTCTTTCTGTTCGTTAT 60.676 47.826 0.00 0.00 0.00 1.89
830 1918 3.866327 GCCCTCTCTTTCTGTTCGTTATC 59.134 47.826 0.00 0.00 0.00 1.75
831 1919 4.620803 GCCCTCTCTTTCTGTTCGTTATCA 60.621 45.833 0.00 0.00 0.00 2.15
832 1920 5.479306 CCCTCTCTTTCTGTTCGTTATCAA 58.521 41.667 0.00 0.00 0.00 2.57
833 1921 5.932303 CCCTCTCTTTCTGTTCGTTATCAAA 59.068 40.000 0.00 0.00 0.00 2.69
834 1922 6.595716 CCCTCTCTTTCTGTTCGTTATCAAAT 59.404 38.462 0.00 0.00 0.00 2.32
835 1923 7.201565 CCCTCTCTTTCTGTTCGTTATCAAATC 60.202 40.741 0.00 0.00 0.00 2.17
836 1924 7.547370 CCTCTCTTTCTGTTCGTTATCAAATCT 59.453 37.037 0.00 0.00 0.00 2.40
837 1925 8.467402 TCTCTTTCTGTTCGTTATCAAATCTC 57.533 34.615 0.00 0.00 0.00 2.75
838 1926 8.307483 TCTCTTTCTGTTCGTTATCAAATCTCT 58.693 33.333 0.00 0.00 0.00 3.10
839 1927 8.467402 TCTTTCTGTTCGTTATCAAATCTCTC 57.533 34.615 0.00 0.00 0.00 3.20
840 1928 7.545965 TCTTTCTGTTCGTTATCAAATCTCTCC 59.454 37.037 0.00 0.00 0.00 3.71
841 1929 5.340803 TCTGTTCGTTATCAAATCTCTCCG 58.659 41.667 0.00 0.00 0.00 4.63
842 1930 5.068234 TGTTCGTTATCAAATCTCTCCGT 57.932 39.130 0.00 0.00 0.00 4.69
843 1931 5.100259 TGTTCGTTATCAAATCTCTCCGTC 58.900 41.667 0.00 0.00 0.00 4.79
844 1932 4.303086 TCGTTATCAAATCTCTCCGTCC 57.697 45.455 0.00 0.00 0.00 4.79
845 1933 3.952323 TCGTTATCAAATCTCTCCGTCCT 59.048 43.478 0.00 0.00 0.00 3.85
846 1934 4.045104 CGTTATCAAATCTCTCCGTCCTG 58.955 47.826 0.00 0.00 0.00 3.86
847 1935 4.440250 CGTTATCAAATCTCTCCGTCCTGT 60.440 45.833 0.00 0.00 0.00 4.00
848 1936 5.220989 CGTTATCAAATCTCTCCGTCCTGTA 60.221 44.000 0.00 0.00 0.00 2.74
849 1937 4.657436 ATCAAATCTCTCCGTCCTGTAC 57.343 45.455 0.00 0.00 0.00 2.90
850 1938 3.427573 TCAAATCTCTCCGTCCTGTACA 58.572 45.455 0.00 0.00 0.00 2.90
851 1939 3.830178 TCAAATCTCTCCGTCCTGTACAA 59.170 43.478 0.00 0.00 0.00 2.41
852 1940 3.870633 AATCTCTCCGTCCTGTACAAC 57.129 47.619 0.00 0.00 0.00 3.32
853 1941 2.281539 TCTCTCCGTCCTGTACAACA 57.718 50.000 0.00 0.00 0.00 3.33
880 1968 7.760340 CCTCTGGTCTACTAACAATTCAACTAC 59.240 40.741 0.00 0.00 0.00 2.73
881 1969 8.418597 TCTGGTCTACTAACAATTCAACTACT 57.581 34.615 0.00 0.00 0.00 2.57
882 1970 8.521176 TCTGGTCTACTAACAATTCAACTACTC 58.479 37.037 0.00 0.00 0.00 2.59
918 2006 4.545823 AAGAAATTGCTTGTTCGTTCGA 57.454 36.364 0.00 0.00 0.00 3.71
923 2015 3.684103 TTGCTTGTTCGTTCGAATTGT 57.316 38.095 10.70 0.00 0.00 2.71
926 2018 3.059461 TGCTTGTTCGTTCGAATTGTACC 60.059 43.478 10.70 0.00 0.00 3.34
927 2019 3.666111 GCTTGTTCGTTCGAATTGTACCC 60.666 47.826 10.70 0.00 0.00 3.69
951 2043 1.074319 GCCGACGCGTTAATCTGACA 61.074 55.000 15.53 0.00 0.00 3.58
959 2051 1.390123 CGTTAATCTGACAGTGCCGTG 59.610 52.381 1.59 0.00 0.00 4.94
960 2052 1.732259 GTTAATCTGACAGTGCCGTGG 59.268 52.381 1.59 0.00 0.00 4.94
961 2053 0.391130 TAATCTGACAGTGCCGTGGC 60.391 55.000 3.30 3.30 42.35 5.01
962 2054 3.612247 ATCTGACAGTGCCGTGGCC 62.612 63.158 8.69 0.00 41.09 5.36
983 2075 1.467543 GCCTCCCGCGATTTTTCTTTC 60.468 52.381 8.23 0.00 0.00 2.62
984 2076 2.084546 CCTCCCGCGATTTTTCTTTCT 58.915 47.619 8.23 0.00 0.00 2.52
1014 2106 2.349886 AGCGAAAATGAGCGACAATCTC 59.650 45.455 0.00 0.00 38.61 2.75
1020 2112 3.548745 ATGAGCGACAATCTCATGGAA 57.451 42.857 4.86 0.00 46.27 3.53
1032 2124 3.476552 TCTCATGGAAAAAGTGAACGCT 58.523 40.909 0.00 0.00 0.00 5.07
1293 2385 0.473326 GGATCATGCTCAAGGAGGCT 59.527 55.000 0.00 0.00 0.00 4.58
1535 2627 7.703058 CCTACAAGGTAAAATCAATGTTCCT 57.297 36.000 0.00 0.00 0.00 3.36
1537 2629 8.244113 CCTACAAGGTAAAATCAATGTTCCTTC 58.756 37.037 0.00 0.00 32.48 3.46
1540 2632 8.793592 ACAAGGTAAAATCAATGTTCCTTCTAC 58.206 33.333 0.00 0.00 32.48 2.59
1551 2643 4.150359 TGTTCCTTCTACTTCGTTCCTCT 58.850 43.478 0.00 0.00 0.00 3.69
1552 2644 4.022242 TGTTCCTTCTACTTCGTTCCTCTG 60.022 45.833 0.00 0.00 0.00 3.35
1554 2646 4.150359 TCCTTCTACTTCGTTCCTCTGTT 58.850 43.478 0.00 0.00 0.00 3.16
1638 2730 4.837860 TGGCAGTGAGGTTAATTTTCCAAT 59.162 37.500 0.00 0.00 0.00 3.16
1748 2858 3.891366 CCCATTATGTAAGCAAGGAAGGG 59.109 47.826 0.00 0.00 0.00 3.95
1881 4139 6.071165 GGTTAGAAGCTGGTGGTTAGTACTTA 60.071 42.308 0.00 0.00 33.64 2.24
1882 4140 5.662674 AGAAGCTGGTGGTTAGTACTTAG 57.337 43.478 0.00 0.00 33.64 2.18
1883 4141 5.085219 AGAAGCTGGTGGTTAGTACTTAGT 58.915 41.667 0.00 0.00 33.64 2.24
1884 4142 6.251471 AGAAGCTGGTGGTTAGTACTTAGTA 58.749 40.000 0.00 0.00 33.64 1.82
1885 4143 5.911378 AGCTGGTGGTTAGTACTTAGTAC 57.089 43.478 14.13 14.13 39.10 2.73
1912 4170 4.201940 CGGTCATTGCTTTATTCATCAGCA 60.202 41.667 0.00 0.00 41.85 4.41
1966 4387 2.227149 TGCTGCTTATTCAGTTGTGCTG 59.773 45.455 0.00 0.00 46.34 4.41
2044 4465 9.605951 AATAAACCCATATGATTTATCCTTGCT 57.394 29.630 17.99 6.11 30.13 3.91
2098 4520 1.001269 GGTTAGGGCCTTGGTGGTC 60.001 63.158 13.45 0.00 40.45 4.02
2110 4532 3.331150 CTTGGTGGTCGCAAGTACATTA 58.669 45.455 0.00 0.00 39.48 1.90
2509 4933 4.929211 TGTTTCTATGTGTGAGATCGGTTG 59.071 41.667 0.00 0.00 0.00 3.77
2528 4952 2.274920 GCCTCAAGCAGCTTTTCATC 57.725 50.000 4.38 0.00 42.97 2.92
2541 4965 7.040201 AGCAGCTTTTCATCTGAACAATTTCTA 60.040 33.333 0.00 0.00 33.13 2.10
2635 5365 8.879427 ACTACCTAAACTGGATTGCTTATTTT 57.121 30.769 0.00 0.00 0.00 1.82
2696 5426 6.486248 GCTTTATTGAGCACGAATGATGTTA 58.514 36.000 0.00 0.00 42.25 2.41
2987 5750 5.156355 CAACAATGCTACCAATCTCAACAC 58.844 41.667 0.00 0.00 0.00 3.32
3104 5867 5.606348 AATACGAAGAGATGAAGAAGCCT 57.394 39.130 0.00 0.00 0.00 4.58
3260 6023 6.861144 TGATGATATCCTCGATGATCTTGAC 58.139 40.000 6.46 0.00 0.00 3.18
3284 6047 4.477249 AGATGATATTTGGCAAGAAGGGG 58.523 43.478 0.00 0.00 0.00 4.79
3502 6265 4.400884 TGGGTCGCTTGTTTATTTGCATAT 59.599 37.500 0.00 0.00 0.00 1.78
3503 6266 5.590663 TGGGTCGCTTGTTTATTTGCATATA 59.409 36.000 0.00 0.00 0.00 0.86
3555 6318 5.244755 TCAGTTGATAAGTTGCTGCATACA 58.755 37.500 1.84 0.00 0.00 2.29
3584 6347 6.538742 CGTCTTCTGGTTTCATGGTTATATGT 59.461 38.462 0.00 0.00 0.00 2.29
3616 6379 3.118038 TGAATTTTACTCCCTCCATCCCG 60.118 47.826 0.00 0.00 0.00 5.14
3619 6382 2.489528 TTACTCCCTCCATCCCGAAT 57.510 50.000 0.00 0.00 0.00 3.34
3650 6413 7.990886 TGTCTCAACTTTAGGACAACTTTGTAT 59.009 33.333 0.00 0.00 42.43 2.29
3652 6415 9.403583 TCTCAACTTTAGGACAACTTTGTATTT 57.596 29.630 0.00 0.00 42.43 1.40
3706 6470 6.212993 GGGACGGAGGGAGTATTATTTCTTAT 59.787 42.308 0.00 0.00 0.00 1.73
3707 6471 7.097834 GGACGGAGGGAGTATTATTTCTTATG 58.902 42.308 0.00 0.00 0.00 1.90
3753 6517 3.184541 ACGTAGTTATTCGCCACATGTC 58.815 45.455 0.00 0.00 37.78 3.06
3767 6561 3.304592 CCACATGTCGAATGCAAACAAGA 60.305 43.478 0.00 0.00 0.00 3.02
3774 6568 7.784633 TGTCGAATGCAAACAAGATGATATA 57.215 32.000 0.00 0.00 0.00 0.86
3804 6598 7.999679 TGAACCAATCCTGATTTAACATCATC 58.000 34.615 0.00 0.00 0.00 2.92
3814 6608 7.147863 CCTGATTTAACATCATCATGAACCCAA 60.148 37.037 0.00 0.00 33.72 4.12
3870 6678 1.530323 AAACATGGTACGGGCAGAAC 58.470 50.000 0.00 0.00 0.00 3.01
3871 6679 0.690762 AACATGGTACGGGCAGAACT 59.309 50.000 0.00 0.00 0.00 3.01
3872 6680 0.690762 ACATGGTACGGGCAGAACTT 59.309 50.000 0.00 0.00 0.00 2.66
3873 6681 1.073284 ACATGGTACGGGCAGAACTTT 59.927 47.619 0.00 0.00 0.00 2.66
3875 6683 0.759959 TGGTACGGGCAGAACTTTCA 59.240 50.000 0.00 0.00 0.00 2.69
3877 6685 2.007608 GGTACGGGCAGAACTTTCATC 58.992 52.381 0.00 0.00 0.00 2.92
3878 6686 2.354805 GGTACGGGCAGAACTTTCATCT 60.355 50.000 0.00 0.00 0.00 2.90
3879 6687 1.813513 ACGGGCAGAACTTTCATCTG 58.186 50.000 0.00 0.00 45.65 2.90
3889 6740 7.187244 CAGAACTTTCATCTGCATGGTATAG 57.813 40.000 0.00 0.00 38.03 1.31
3909 6760 4.590850 AGTCTTTCAAATGACAAAGGCC 57.409 40.909 0.00 0.00 35.23 5.19
3910 6761 3.960102 AGTCTTTCAAATGACAAAGGCCA 59.040 39.130 5.01 0.00 35.23 5.36
3911 6762 4.038402 AGTCTTTCAAATGACAAAGGCCAG 59.962 41.667 5.01 0.00 35.23 4.85
3942 6796 4.156477 TCCCTCCGTTCCAAAATTGAATT 58.844 39.130 0.00 0.00 0.00 2.17
3956 6810 3.372660 TTGAATTAAAACCACGGCACC 57.627 42.857 0.00 0.00 0.00 5.01
3959 6813 4.337145 TGAATTAAAACCACGGCACCTAT 58.663 39.130 0.00 0.00 0.00 2.57
4066 6928 0.108567 GGGAGACGAGTTTGGCTCTC 60.109 60.000 2.34 0.00 41.98 3.20
4200 7062 1.898472 AGAGATGGCCGATCGATTCAT 59.102 47.619 18.66 15.98 36.04 2.57
4233 7095 0.734253 GTAGCTGCTCTCGTGTGTGG 60.734 60.000 4.91 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.602257 TGTCGGAGATGCATTACAGG 57.398 50.000 0.00 0.00 40.67 4.00
1 2 4.122046 TCAATGTCGGAGATGCATTACAG 58.878 43.478 0.00 0.00 40.67 2.74
2 3 4.135747 TCAATGTCGGAGATGCATTACA 57.864 40.909 0.00 1.54 40.67 2.41
3 4 4.332543 TGTTCAATGTCGGAGATGCATTAC 59.667 41.667 0.00 0.00 40.67 1.89
7 8 2.470983 TGTTCAATGTCGGAGATGCA 57.529 45.000 0.00 0.00 40.67 3.96
17 18 1.266718 GTGTCCGCACATGTTCAATGT 59.733 47.619 0.00 0.00 44.64 2.71
86 87 3.608796 TGTGATCTTTCATTCATGCCGA 58.391 40.909 0.00 0.00 33.56 5.54
88 89 5.520632 CAGATGTGATCTTTCATTCATGCC 58.479 41.667 0.00 0.00 37.58 4.40
119 121 0.512952 AAACTCTGCATTGACGTCGC 59.487 50.000 11.62 9.03 0.00 5.19
122 124 1.148310 CGGAAACTCTGCATTGACGT 58.852 50.000 0.00 0.00 0.00 4.34
158 160 1.732917 CTGAAACAGTTGCCCGCAA 59.267 52.632 0.00 0.00 0.00 4.85
171 173 0.248702 GCGCCGTTTTTCACCTGAAA 60.249 50.000 0.00 0.00 41.77 2.69
176 178 0.506506 CATTTGCGCCGTTTTTCACC 59.493 50.000 4.18 0.00 0.00 4.02
185 187 1.709147 CCTCTTCCTCATTTGCGCCG 61.709 60.000 4.18 0.00 0.00 6.46
191 193 3.575805 TGCAAAACCCTCTTCCTCATTT 58.424 40.909 0.00 0.00 0.00 2.32
231 233 4.986645 ACTGATGCCACGCACGCA 62.987 61.111 0.00 0.00 43.04 5.24
232 234 4.152625 GACTGATGCCACGCACGC 62.153 66.667 0.00 0.00 43.04 5.34
233 235 3.490759 GGACTGATGCCACGCACG 61.491 66.667 0.00 0.00 43.04 5.34
246 249 1.583054 GTTTTGCTCGTGTCTGGACT 58.417 50.000 2.38 0.00 0.00 3.85
251 254 1.213094 CCGACGTTTTGCTCGTGTCT 61.213 55.000 0.00 0.00 41.64 3.41
269 272 1.303317 ACAAACTGATGGCCGGTCC 60.303 57.895 2.12 5.67 31.94 4.46
270 273 1.586154 CCACAAACTGATGGCCGGTC 61.586 60.000 0.00 0.00 31.94 4.79
271 274 1.603455 CCACAAACTGATGGCCGGT 60.603 57.895 1.90 0.00 35.44 5.28
274 277 1.337118 TTTCCCACAAACTGATGGCC 58.663 50.000 0.00 0.00 34.37 5.36
275 278 3.467374 TTTTTCCCACAAACTGATGGC 57.533 42.857 0.00 0.00 34.37 4.40
317 320 0.828022 TAATTCGCCCACATCCGTCT 59.172 50.000 0.00 0.00 0.00 4.18
369 388 8.171840 GTCTTCTGCTGATAAAGTGTTATGAAC 58.828 37.037 0.00 0.00 29.69 3.18
469 1538 4.758688 TCGCAGCATATTCTTCTCAGAAA 58.241 39.130 0.00 0.00 42.53 2.52
604 1684 4.697756 TGGAGTTCTTGCGCCCGG 62.698 66.667 4.18 0.00 0.00 5.73
606 1686 2.954611 GTTGGAGTTCTTGCGCCC 59.045 61.111 4.18 0.00 0.00 6.13
607 1687 1.503818 TTCGTTGGAGTTCTTGCGCC 61.504 55.000 4.18 0.00 0.00 6.53
608 1688 0.384353 GTTCGTTGGAGTTCTTGCGC 60.384 55.000 0.00 0.00 0.00 6.09
609 1689 0.934496 TGTTCGTTGGAGTTCTTGCG 59.066 50.000 0.00 0.00 0.00 4.85
610 1690 3.105937 GTTTGTTCGTTGGAGTTCTTGC 58.894 45.455 0.00 0.00 0.00 4.01
611 1691 3.127895 TGGTTTGTTCGTTGGAGTTCTTG 59.872 43.478 0.00 0.00 0.00 3.02
612 1692 3.128068 GTGGTTTGTTCGTTGGAGTTCTT 59.872 43.478 0.00 0.00 0.00 2.52
613 1693 2.681344 GTGGTTTGTTCGTTGGAGTTCT 59.319 45.455 0.00 0.00 0.00 3.01
709 1797 1.828660 GAGAATCGAGGGAGGCGGA 60.829 63.158 0.00 0.00 0.00 5.54
751 1839 0.464452 GGATCGATCGAGGGTTTGGT 59.536 55.000 23.84 3.38 0.00 3.67
814 1902 7.545965 GGAGAGATTTGATAACGAACAGAAAGA 59.454 37.037 0.00 0.00 0.00 2.52
820 1908 5.068234 ACGGAGAGATTTGATAACGAACA 57.932 39.130 0.00 0.00 0.00 3.18
824 1912 4.045104 CAGGACGGAGAGATTTGATAACG 58.955 47.826 0.00 0.00 0.00 3.18
825 1913 5.012328 ACAGGACGGAGAGATTTGATAAC 57.988 43.478 0.00 0.00 0.00 1.89
826 1914 5.655090 TGTACAGGACGGAGAGATTTGATAA 59.345 40.000 0.00 0.00 0.00 1.75
827 1915 5.198207 TGTACAGGACGGAGAGATTTGATA 58.802 41.667 0.00 0.00 0.00 2.15
828 1916 4.023980 TGTACAGGACGGAGAGATTTGAT 58.976 43.478 0.00 0.00 0.00 2.57
829 1917 3.427573 TGTACAGGACGGAGAGATTTGA 58.572 45.455 0.00 0.00 0.00 2.69
830 1918 3.868757 TGTACAGGACGGAGAGATTTG 57.131 47.619 0.00 0.00 0.00 2.32
831 1919 3.576982 TGTTGTACAGGACGGAGAGATTT 59.423 43.478 0.00 0.00 0.00 2.17
832 1920 3.056749 GTGTTGTACAGGACGGAGAGATT 60.057 47.826 0.00 0.00 0.00 2.40
833 1921 2.492484 GTGTTGTACAGGACGGAGAGAT 59.508 50.000 0.00 0.00 0.00 2.75
834 1922 1.884579 GTGTTGTACAGGACGGAGAGA 59.115 52.381 0.00 0.00 0.00 3.10
835 1923 1.067776 GGTGTTGTACAGGACGGAGAG 60.068 57.143 0.00 0.00 0.00 3.20
836 1924 0.963962 GGTGTTGTACAGGACGGAGA 59.036 55.000 0.00 0.00 0.00 3.71
837 1925 0.966920 AGGTGTTGTACAGGACGGAG 59.033 55.000 0.00 0.00 0.00 4.63
838 1926 0.963962 GAGGTGTTGTACAGGACGGA 59.036 55.000 0.00 0.00 0.00 4.69
839 1927 0.966920 AGAGGTGTTGTACAGGACGG 59.033 55.000 0.00 0.00 0.00 4.79
840 1928 1.336887 CCAGAGGTGTTGTACAGGACG 60.337 57.143 0.00 0.00 0.00 4.79
841 1929 1.692519 ACCAGAGGTGTTGTACAGGAC 59.307 52.381 0.00 0.00 32.98 3.85
842 1930 1.968493 GACCAGAGGTGTTGTACAGGA 59.032 52.381 0.00 0.00 35.25 3.86
843 1931 1.971357 AGACCAGAGGTGTTGTACAGG 59.029 52.381 0.00 0.00 35.25 4.00
844 1932 3.827302 AGTAGACCAGAGGTGTTGTACAG 59.173 47.826 0.00 0.00 35.25 2.74
845 1933 3.840991 AGTAGACCAGAGGTGTTGTACA 58.159 45.455 0.00 0.00 35.25 2.90
846 1934 5.242393 TGTTAGTAGACCAGAGGTGTTGTAC 59.758 44.000 0.00 0.00 35.25 2.90
847 1935 5.387788 TGTTAGTAGACCAGAGGTGTTGTA 58.612 41.667 0.00 0.00 35.25 2.41
848 1936 4.220724 TGTTAGTAGACCAGAGGTGTTGT 58.779 43.478 0.00 0.00 35.25 3.32
849 1937 4.866508 TGTTAGTAGACCAGAGGTGTTG 57.133 45.455 0.00 0.00 35.25 3.33
850 1938 6.042781 TGAATTGTTAGTAGACCAGAGGTGTT 59.957 38.462 0.00 0.00 35.25 3.32
851 1939 5.542635 TGAATTGTTAGTAGACCAGAGGTGT 59.457 40.000 0.00 0.00 35.25 4.16
852 1940 6.037786 TGAATTGTTAGTAGACCAGAGGTG 57.962 41.667 0.00 0.00 35.25 4.00
853 1941 6.270231 AGTTGAATTGTTAGTAGACCAGAGGT 59.730 38.462 0.00 0.00 39.44 3.85
908 1996 2.415776 GGGGTACAATTCGAACGAACA 58.584 47.619 11.71 0.00 36.91 3.18
963 2055 0.526211 AAAGAAAAATCGCGGGAGGC 59.474 50.000 6.13 0.00 38.69 4.70
964 2056 2.084546 AGAAAGAAAAATCGCGGGAGG 58.915 47.619 6.13 0.00 0.00 4.30
965 2057 2.484264 ACAGAAAGAAAAATCGCGGGAG 59.516 45.455 6.13 0.00 0.00 4.30
966 2058 2.500229 ACAGAAAGAAAAATCGCGGGA 58.500 42.857 6.13 4.03 0.00 5.14
967 2059 2.989422 ACAGAAAGAAAAATCGCGGG 57.011 45.000 6.13 0.00 0.00 6.13
968 2060 4.085107 CCAAAACAGAAAGAAAAATCGCGG 60.085 41.667 6.13 0.00 0.00 6.46
969 2061 4.502645 ACCAAAACAGAAAGAAAAATCGCG 59.497 37.500 0.00 0.00 0.00 5.87
983 2075 3.914364 GCTCATTTTCGCTACCAAAACAG 59.086 43.478 0.00 0.00 0.00 3.16
984 2076 3.608241 CGCTCATTTTCGCTACCAAAACA 60.608 43.478 0.00 0.00 0.00 2.83
1014 2106 3.665323 CGAGAGCGTTCACTTTTTCCATG 60.665 47.826 1.01 0.00 0.00 3.66
1020 2112 2.235546 GCCGAGAGCGTTCACTTTT 58.764 52.632 1.01 0.00 35.23 2.27
1069 2161 2.754658 GGCCTGCATCTGCTTGCT 60.755 61.111 13.44 0.00 43.18 3.91
1293 2385 1.262640 GGGCGAGGAACTGAACCCTA 61.263 60.000 0.00 0.00 41.55 3.53
1383 2475 2.171568 TCAGCCTGACCATCTCATCT 57.828 50.000 0.00 0.00 0.00 2.90
1461 2553 2.060980 ATCGCCAGACTCTCCCCAC 61.061 63.158 0.00 0.00 0.00 4.61
1526 2618 5.238583 AGGAACGAAGTAGAAGGAACATTG 58.761 41.667 0.00 0.00 45.00 2.82
1532 2624 3.764218 ACAGAGGAACGAAGTAGAAGGA 58.236 45.455 0.00 0.00 45.00 3.36
1535 2627 7.164122 TCTAGTAACAGAGGAACGAAGTAGAA 58.836 38.462 0.00 0.00 45.00 2.10
1537 2629 6.817641 TCTCTAGTAACAGAGGAACGAAGTAG 59.182 42.308 0.00 0.00 40.98 2.57
1540 2632 6.497785 TTCTCTAGTAACAGAGGAACGAAG 57.502 41.667 0.00 0.00 42.05 3.79
1551 2643 7.462571 TGTACTGCTGATTTCTCTAGTAACA 57.537 36.000 0.00 0.00 0.00 2.41
1552 2644 8.758633 TTTGTACTGCTGATTTCTCTAGTAAC 57.241 34.615 0.00 0.00 0.00 2.50
1554 2646 9.371136 CAATTTGTACTGCTGATTTCTCTAGTA 57.629 33.333 0.00 0.00 0.00 1.82
1638 2730 6.433716 TCATGGCTGATTTGTTTATGAACAGA 59.566 34.615 3.07 0.00 45.80 3.41
1650 2742 5.121925 CGAGGAGATTATCATGGCTGATTTG 59.878 44.000 5.07 0.00 42.23 2.32
1707 2816 2.224719 GGGGCAGCAGAGATTATCATGT 60.225 50.000 0.00 0.00 0.00 3.21
1710 2819 1.510492 TGGGGCAGCAGAGATTATCA 58.490 50.000 0.00 0.00 0.00 2.15
1748 2858 4.142160 GCAGGTTGGTCCTAAATTGGATTC 60.142 45.833 0.00 0.00 46.24 2.52
1798 3412 2.602257 TCCATGAAGCGATGTACCAG 57.398 50.000 0.00 0.00 0.00 4.00
1854 4111 3.587506 ACTAACCACCAGCTTCTAACCAT 59.412 43.478 0.00 0.00 0.00 3.55
1881 4139 3.611766 AAAGCAATGACCGCTAGTACT 57.388 42.857 0.00 0.00 39.29 2.73
1882 4140 5.522460 TGAATAAAGCAATGACCGCTAGTAC 59.478 40.000 0.00 0.00 39.29 2.73
1883 4141 5.666462 TGAATAAAGCAATGACCGCTAGTA 58.334 37.500 0.00 0.00 39.29 1.82
1884 4142 4.513442 TGAATAAAGCAATGACCGCTAGT 58.487 39.130 0.00 0.00 39.29 2.57
1885 4143 5.237127 TGATGAATAAAGCAATGACCGCTAG 59.763 40.000 0.00 0.00 39.29 3.42
1886 4144 5.122519 TGATGAATAAAGCAATGACCGCTA 58.877 37.500 0.00 0.00 39.29 4.26
2044 4465 5.911752 ACCAAAGCATGACAAATTTGTACA 58.088 33.333 23.33 20.74 42.43 2.90
2444 4868 5.185828 AAGCAGACAGACTGATATGTGTGTA 59.814 40.000 10.08 0.00 44.93 2.90
2450 4874 9.138062 GTCATAATAAGCAGACAGACTGATATG 57.862 37.037 10.08 5.77 44.93 1.78
2456 4880 8.470657 TCTATGTCATAATAAGCAGACAGACT 57.529 34.615 0.00 0.00 43.39 3.24
2509 4933 1.817447 AGATGAAAAGCTGCTTGAGGC 59.183 47.619 16.73 6.40 42.22 4.70
2526 4950 9.950496 ACAAGTACAGATAGAAATTGTTCAGAT 57.050 29.630 0.00 0.00 36.09 2.90
2527 4951 9.778741 AACAAGTACAGATAGAAATTGTTCAGA 57.221 29.630 0.00 0.00 35.16 3.27
2528 4952 9.817365 CAACAAGTACAGATAGAAATTGTTCAG 57.183 33.333 0.00 0.00 37.31 3.02
2541 4965 5.581605 CACAAAACAGCAACAAGTACAGAT 58.418 37.500 0.00 0.00 0.00 2.90
2696 5426 6.051717 GCTGTTAATGTCATCAGTATCAGGT 58.948 40.000 12.35 0.00 39.86 4.00
2814 5550 6.411203 GCTTCTCGTCAGTTTAAAGTTTGAAC 59.589 38.462 13.80 13.80 0.00 3.18
2987 5750 5.616645 CGTCTCGATGAATCTCTGGATAGTG 60.617 48.000 0.00 0.00 0.00 2.74
3116 5879 0.033504 CCACTGGCTGTTCTGTACGT 59.966 55.000 0.00 0.00 0.00 3.57
3260 6023 4.214971 CCCTTCTTGCCAAATATCATCTCG 59.785 45.833 0.00 0.00 0.00 4.04
3284 6047 1.602771 GTCCTGGGAACTACTGCCC 59.397 63.158 0.00 0.00 44.93 5.36
3287 6050 0.966920 ACACGTCCTGGGAACTACTG 59.033 55.000 0.00 0.00 0.00 2.74
3290 6053 2.662309 GGACACGTCCTGGGAACTA 58.338 57.895 9.04 0.00 46.16 2.24
3406 6169 6.649141 ACAGACATCGTTCAGCAGTATAAAAA 59.351 34.615 0.00 0.00 0.00 1.94
3502 6265 3.889538 CTGGAGGACAAGGTATCATCGTA 59.110 47.826 0.00 0.00 0.00 3.43
3503 6266 2.695666 CTGGAGGACAAGGTATCATCGT 59.304 50.000 0.00 0.00 0.00 3.73
3555 6318 3.261897 ACCATGAAACCAGAAGACGAGAT 59.738 43.478 0.00 0.00 0.00 2.75
3584 6347 4.943705 GGGAGTAAAATTCAGCATCTGACA 59.056 41.667 0.00 0.00 40.46 3.58
3616 6379 8.603242 TGTCCTAAAGTTGAGACACTTAATTC 57.397 34.615 0.00 0.00 35.87 2.17
3619 6382 7.562135 AGTTGTCCTAAAGTTGAGACACTTAA 58.438 34.615 3.14 0.00 38.88 1.85
3673 6437 2.023695 ACTCCCTCCGTCCCAATAAGTA 60.024 50.000 0.00 0.00 0.00 2.24
3706 6470 7.327975 ACGACAACAGAATATGAAGTATTCCA 58.672 34.615 0.00 0.00 46.93 3.53
3707 6471 7.772332 ACGACAACAGAATATGAAGTATTCC 57.228 36.000 0.00 0.00 46.93 3.01
3712 6476 5.706916 ACGTACGACAACAGAATATGAAGT 58.293 37.500 24.41 0.00 0.00 3.01
3726 6490 2.418280 TGGCGAATAACTACGTACGACA 59.582 45.455 24.41 5.55 36.44 4.35
3727 6491 2.778386 GTGGCGAATAACTACGTACGAC 59.222 50.000 24.41 0.22 0.00 4.34
3804 6598 7.040892 CCATTGAGTAGATGTATTGGGTTCATG 60.041 40.741 0.00 0.00 0.00 3.07
3843 6651 3.191791 GCCCGTACCATGTTTTTGTATGT 59.808 43.478 0.00 0.00 0.00 2.29
3870 6678 7.496920 TGAAAGACTATACCATGCAGATGAAAG 59.503 37.037 0.00 0.00 0.00 2.62
3871 6679 7.337938 TGAAAGACTATACCATGCAGATGAAA 58.662 34.615 0.00 0.00 0.00 2.69
3872 6680 6.888105 TGAAAGACTATACCATGCAGATGAA 58.112 36.000 0.00 0.00 0.00 2.57
3873 6681 6.484364 TGAAAGACTATACCATGCAGATGA 57.516 37.500 0.00 0.00 0.00 2.92
3875 6683 7.994911 TCATTTGAAAGACTATACCATGCAGAT 59.005 33.333 0.00 0.00 0.00 2.90
3877 6685 7.066163 TGTCATTTGAAAGACTATACCATGCAG 59.934 37.037 0.00 0.00 35.81 4.41
3878 6686 6.883756 TGTCATTTGAAAGACTATACCATGCA 59.116 34.615 0.00 0.00 35.81 3.96
3879 6687 7.320443 TGTCATTTGAAAGACTATACCATGC 57.680 36.000 8.29 0.00 35.81 4.06
3880 6688 9.778993 CTTTGTCATTTGAAAGACTATACCATG 57.221 33.333 8.29 0.00 35.81 3.66
3881 6689 8.960591 CCTTTGTCATTTGAAAGACTATACCAT 58.039 33.333 0.00 0.00 35.81 3.55
3882 6690 7.094377 GCCTTTGTCATTTGAAAGACTATACCA 60.094 37.037 0.00 0.00 35.81 3.25
3883 6691 7.251281 GCCTTTGTCATTTGAAAGACTATACC 58.749 38.462 0.00 0.00 35.81 2.73
3884 6692 7.094377 TGGCCTTTGTCATTTGAAAGACTATAC 60.094 37.037 3.32 0.00 35.81 1.47
3887 6738 5.136828 TGGCCTTTGTCATTTGAAAGACTA 58.863 37.500 3.32 0.63 35.81 2.59
3889 6740 4.037923 TCTGGCCTTTGTCATTTGAAAGAC 59.962 41.667 3.32 0.00 31.89 3.01
3909 6760 3.256136 GGAACGGAGGGAGTATATGTCTG 59.744 52.174 0.00 0.00 0.00 3.51
3910 6761 3.117246 TGGAACGGAGGGAGTATATGTCT 60.117 47.826 0.00 0.00 0.00 3.41
3911 6762 3.228453 TGGAACGGAGGGAGTATATGTC 58.772 50.000 0.00 0.00 0.00 3.06
3942 6796 3.256136 CCAAAATAGGTGCCGTGGTTTTA 59.744 43.478 0.00 0.00 0.00 1.52
3956 6810 8.368668 AGATATACTCCCTTCGTTCCAAAATAG 58.631 37.037 0.00 0.00 0.00 1.73
3959 6813 6.555463 AGATATACTCCCTTCGTTCCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
4066 6928 4.442753 GGGAAGATACTGAGGAAAGAGCTG 60.443 50.000 0.00 0.00 0.00 4.24
4200 7062 2.810400 GCAGCTACAGAACCTTGGTTGA 60.810 50.000 10.04 0.00 0.00 3.18
4233 7095 2.159085 AGTTCGTATCCAAGCAGGTAGC 60.159 50.000 0.00 0.00 46.19 3.58
4295 7157 3.186047 CCGGTCGCATTCGTGGTC 61.186 66.667 0.00 0.00 36.96 4.02


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

AutoCloner maintained by Alex Coulton.