Multiple sequence alignment - TraesCS6A01G222100

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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 TraesCS6A01G222100 chr6A 100.000 4807 0 0 1 4807 414879302 414874496 0.000000e+00 8877.0
1 TraesCS6A01G222100 chr6A 85.000 140 21 0 2782 2921 456750647 456750508 5.010000e-30 143.0
2 TraesCS6A01G222100 chr6B 93.138 1982 63 24 574 2521 467447530 467449472 0.000000e+00 2839.0
3 TraesCS6A01G222100 chr6B 91.193 1760 109 23 3075 4804 467449979 467451722 0.000000e+00 2350.0
4 TraesCS6A01G222100 chr6B 90.769 585 33 12 1 575 467446907 467447480 0.000000e+00 761.0
5 TraesCS6A01G222100 chr6B 95.914 465 12 2 2507 2971 467449493 467449950 0.000000e+00 747.0
6 TraesCS6A01G222100 chr6B 86.014 143 20 0 2776 2918 504586218 504586360 2.320000e-33 154.0
7 TraesCS6A01G222100 chr6D 93.095 1231 54 12 1755 2966 302038275 302039493 0.000000e+00 1773.0
8 TraesCS6A01G222100 chr6D 93.448 1160 34 22 574 1733 302036713 302037830 0.000000e+00 1683.0
9 TraesCS6A01G222100 chr6D 94.040 1057 36 13 3075 4113 302039522 302040569 0.000000e+00 1578.0
10 TraesCS6A01G222100 chr6D 95.652 276 6 2 85 360 302035426 302035695 5.710000e-119 438.0
11 TraesCS6A01G222100 chr6D 97.087 103 3 0 1 103 302033917 302034019 1.780000e-39 174.0
12 TraesCS6A01G222100 chr6D 85.816 141 18 2 2782 2921 318953105 318952966 1.080000e-31 148.0
13 TraesCS6A01G222100 chr2D 93.069 303 21 0 1428 1730 480325215 480324913 1.230000e-120 444.0
14 TraesCS6A01G222100 chr2D 91.582 297 25 0 1434 1730 480181347 480181051 1.250000e-110 411.0
15 TraesCS6A01G222100 chr2D 88.438 320 34 1 1001 1317 480181671 480181352 2.710000e-102 383.0
16 TraesCS6A01G222100 chr2D 86.293 321 41 1 1001 1318 480325533 480325213 3.560000e-91 346.0
17 TraesCS6A01G222100 chr2D 87.542 297 36 1 1431 1726 159574134 159574430 4.610000e-90 342.0
18 TraesCS6A01G222100 chr2D 85.714 287 38 1 1031 1314 159573844 159574130 2.810000e-77 300.0
19 TraesCS6A01G222100 chr2D 92.568 148 11 0 2775 2922 480180551 480180404 3.770000e-51 213.0
20 TraesCS6A01G222100 chr2D 89.241 158 14 3 2776 2931 159575980 159576136 1.370000e-45 195.0
21 TraesCS6A01G222100 chr2D 92.079 101 7 1 3692 3791 480323768 480323668 1.800000e-29 141.0
22 TraesCS6A01G222100 chr2D 90.722 97 9 0 3695 3791 480179671 480179575 3.900000e-26 130.0
23 TraesCS6A01G222100 chr2B 92.079 303 24 0 1428 1730 563184639 563184337 1.240000e-115 427.0
24 TraesCS6A01G222100 chr2B 90.365 301 28 1 1431 1730 563046121 563045821 1.250000e-105 394.0
25 TraesCS6A01G222100 chr2B 87.500 320 37 1 1001 1317 563046441 563046122 2.730000e-97 366.0
26 TraesCS6A01G222100 chr2B 91.216 148 13 0 2776 2923 216710516 216710663 8.160000e-48 202.0
27 TraesCS6A01G222100 chr2B 92.079 101 7 1 3692 3791 563182882 563182782 1.800000e-29 141.0
28 TraesCS6A01G222100 chr2B 90.722 97 9 0 3695 3791 563043975 563043879 3.900000e-26 130.0
29 TraesCS6A01G222100 chr2A 91.749 303 25 0 1428 1730 622853424 622853122 5.750000e-114 422.0
30 TraesCS6A01G222100 chr2A 90.759 303 28 0 1428 1730 622747736 622747434 5.790000e-109 405.0
31 TraesCS6A01G222100 chr2A 88.162 321 35 1 1001 1318 622748054 622747734 3.510000e-101 379.0
32 TraesCS6A01G222100 chr2A 88.162 321 35 2 1001 1318 622853742 622853422 3.510000e-101 379.0
33 TraesCS6A01G222100 chr2A 86.760 287 35 1 1031 1314 170602949 170603235 2.790000e-82 316.0
34 TraesCS6A01G222100 chr2A 89.189 148 16 0 2776 2923 170604806 170604953 8.220000e-43 185.0
35 TraesCS6A01G222100 chr2A 90.722 97 9 0 3695 3791 622746081 622745985 3.900000e-26 130.0
36 TraesCS6A01G222100 chr2A 90.426 94 7 1 2982 3075 385298772 385298863 6.530000e-24 122.0
37 TraesCS6A01G222100 chr2A 91.111 90 8 0 2986 3075 752101551 752101640 6.530000e-24 122.0
38 TraesCS6A01G222100 chr5D 90.816 98 9 0 2988 3085 505817122 505817025 1.090000e-26 132.0
39 TraesCS6A01G222100 chr5D 78.495 93 15 4 4514 4601 118581720 118581628 6.720000e-04 56.5
40 TraesCS6A01G222100 chr3A 92.941 85 6 0 2991 3075 489193085 489193169 1.820000e-24 124.0
41 TraesCS6A01G222100 chr4A 90.323 93 9 0 2983 3075 659629620 659629712 6.530000e-24 122.0
42 TraesCS6A01G222100 chr1D 91.111 90 8 0 2989 3078 307830189 307830100 6.530000e-24 122.0
43 TraesCS6A01G222100 chr1D 90.323 93 7 1 2990 3082 183020037 183020127 2.350000e-23 121.0
44 TraesCS6A01G222100 chr1A 91.011 89 8 0 2990 3078 405482978 405482890 2.350000e-23 121.0
45 TraesCS6A01G222100 chr1B 88.235 102 9 3 2976 3075 684089021 684089121 8.450000e-23 119.0


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 TraesCS6A01G222100 chr6A 414874496 414879302 4806 True 8877.000000 8877 100.000000 1 4807 1 chr6A.!!$R1 4806
1 TraesCS6A01G222100 chr6B 467446907 467451722 4815 False 1674.250000 2839 92.753500 1 4804 4 chr6B.!!$F2 4803
2 TraesCS6A01G222100 chr6D 302033917 302040569 6652 False 1129.200000 1773 94.664400 1 4113 5 chr6D.!!$F1 4112
3 TraesCS6A01G222100 chr2D 480323668 480325533 1865 True 310.333333 444 90.480333 1001 3791 3 chr2D.!!$R2 2790
4 TraesCS6A01G222100 chr2D 480179575 480181671 2096 True 284.250000 411 90.827500 1001 3791 4 chr2D.!!$R1 2790
5 TraesCS6A01G222100 chr2D 159573844 159576136 2292 False 279.000000 342 87.499000 1031 2931 3 chr2D.!!$F1 1900
6 TraesCS6A01G222100 chr2B 563043879 563046441 2562 True 296.666667 394 89.529000 1001 3791 3 chr2B.!!$R1 2790
7 TraesCS6A01G222100 chr2B 563182782 563184639 1857 True 284.000000 427 92.079000 1428 3791 2 chr2B.!!$R2 2363
8 TraesCS6A01G222100 chr2A 622853122 622853742 620 True 400.500000 422 89.955500 1001 1730 2 chr2A.!!$R2 729
9 TraesCS6A01G222100 chr2A 622745985 622748054 2069 True 304.666667 405 89.881000 1001 3791 3 chr2A.!!$R1 2790
10 TraesCS6A01G222100 chr2A 170602949 170604953 2004 False 250.500000 316 87.974500 1031 2923 2 chr2A.!!$F3 1892

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
432 2591 0.110486 ACTGCCAAATTGTCCCGAGT 59.890 50.0 0.00 0.0 0.00 4.18 F
1338 3582 0.942252 CGTCCATCGATCGACCACTA 59.058 55.0 22.06 1.5 42.86 2.74 F
2146 4897 0.764890 AGTAGGGCAAGCAAGTCACA 59.235 50.0 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 3634 0.244994 AGTCAGTCTCACGCATGACC 59.755 55.0 0.00 0.0 42.39 4.02 R
3288 7977 0.756442 TGGCAAGCATTATCCTGCCC 60.756 55.0 9.32 0.0 43.33 5.36 R
3916 8665 2.355132 CTGATGATGCAAAGACTGGAGC 59.645 50.0 0.00 0.0 31.39 4.70 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
46 47 8.492748 TGTTTCGTTGTTATACTTGTCTTGATC 58.507 33.333 0.00 0.00 0.00 2.92
147 1573 3.416490 CACGTTTTGTGCGAGGGT 58.584 55.556 0.00 0.00 42.70 4.34
151 1577 0.878523 CGTTTTGTGCGAGGGTGAGA 60.879 55.000 0.00 0.00 0.00 3.27
152 1578 1.305201 GTTTTGTGCGAGGGTGAGAA 58.695 50.000 0.00 0.00 0.00 2.87
153 1579 1.264288 GTTTTGTGCGAGGGTGAGAAG 59.736 52.381 0.00 0.00 0.00 2.85
154 1580 0.756294 TTTGTGCGAGGGTGAGAAGA 59.244 50.000 0.00 0.00 0.00 2.87
155 1581 0.318441 TTGTGCGAGGGTGAGAAGAG 59.682 55.000 0.00 0.00 0.00 2.85
156 1582 0.539669 TGTGCGAGGGTGAGAAGAGA 60.540 55.000 0.00 0.00 0.00 3.10
169 1595 0.325203 GAAGAGAGAGGGGGACAGCT 60.325 60.000 0.00 0.00 0.00 4.24
185 1611 2.283298 CAGCTTATGCCTTCACGTCAT 58.717 47.619 0.00 0.00 40.80 3.06
360 1786 7.710907 TGAGCATGTATATACTGAACCTGTTTC 59.289 37.037 13.89 5.66 34.41 2.78
361 1787 7.796054 AGCATGTATATACTGAACCTGTTTCT 58.204 34.615 13.89 0.00 34.97 2.52
362 1788 7.712639 AGCATGTATATACTGAACCTGTTTCTG 59.287 37.037 13.89 0.00 38.73 3.02
365 1791 9.959721 ATGTATATACTGAACCTGTTTCTGTTT 57.040 29.630 13.89 0.00 42.14 2.83
373 2531 7.342026 ACTGAACCTGTTTCTGTTTAAATTCCT 59.658 33.333 0.00 0.00 42.14 3.36
376 2534 7.418337 ACCTGTTTCTGTTTAAATTCCTGTT 57.582 32.000 0.00 0.00 0.00 3.16
377 2535 7.847096 ACCTGTTTCTGTTTAAATTCCTGTTT 58.153 30.769 0.00 0.00 0.00 2.83
381 2539 9.712305 TGTTTCTGTTTAAATTCCTGTTTTTGA 57.288 25.926 0.00 0.00 0.00 2.69
432 2591 0.110486 ACTGCCAAATTGTCCCGAGT 59.890 50.000 0.00 0.00 0.00 4.18
460 2619 5.001232 GGCACCACAGTAAAAGTTATCTGA 58.999 41.667 8.26 0.00 0.00 3.27
469 2632 6.965500 CAGTAAAAGTTATCTGAAGCTGCATG 59.035 38.462 0.00 0.00 0.00 4.06
522 2685 2.573009 TGATCCTTCCAAGACATCTGCA 59.427 45.455 0.00 0.00 0.00 4.41
547 2715 1.134818 CCATGCTAACTCTACACGCCA 60.135 52.381 0.00 0.00 0.00 5.69
562 2730 2.098607 CACGCCACTAGATAAAGGTCGA 59.901 50.000 0.00 0.00 0.00 4.20
568 2736 7.133513 CGCCACTAGATAAAGGTCGATATATC 58.866 42.308 2.34 2.34 0.00 1.63
570 2738 8.688151 GCCACTAGATAAAGGTCGATATATCTT 58.312 37.037 10.93 0.90 36.68 2.40
578 2815 7.484035 AAAGGTCGATATATCTTTTCTGTGC 57.516 36.000 10.93 0.00 0.00 4.57
603 2840 3.063180 CGCTTTCTGACCTTTCTGCATAG 59.937 47.826 0.00 0.00 0.00 2.23
605 2842 5.178797 GCTTTCTGACCTTTCTGCATAGTA 58.821 41.667 0.00 0.00 0.00 1.82
631 2868 4.697756 GGCGGCACAGGCACAGTA 62.698 66.667 3.07 0.00 43.71 2.74
632 2869 3.121030 GCGGCACAGGCACAGTAG 61.121 66.667 0.00 0.00 43.71 2.57
633 2870 2.343758 CGGCACAGGCACAGTAGT 59.656 61.111 0.00 0.00 43.71 2.73
851 3088 2.076863 CTTAACAGGCCAAACTCGAGG 58.923 52.381 18.41 0.00 0.00 4.63
852 3089 1.053424 TAACAGGCCAAACTCGAGGT 58.947 50.000 18.41 7.47 0.00 3.85
856 3093 1.207089 CAGGCCAAACTCGAGGTGATA 59.793 52.381 18.41 0.00 0.00 2.15
968 3209 2.030007 GCAGCAAACACCATTCAAGCTA 60.030 45.455 0.00 0.00 0.00 3.32
969 3210 3.829948 CAGCAAACACCATTCAAGCTAG 58.170 45.455 0.00 0.00 0.00 3.42
970 3211 2.229784 AGCAAACACCATTCAAGCTAGC 59.770 45.455 6.62 6.62 0.00 3.42
971 3212 2.229784 GCAAACACCATTCAAGCTAGCT 59.770 45.455 12.68 12.68 0.00 3.32
1324 3568 3.371063 GCGTCTCAGGTCCGTCCA 61.371 66.667 0.00 0.00 39.02 4.02
1325 3569 2.711922 GCGTCTCAGGTCCGTCCAT 61.712 63.158 0.00 0.00 39.02 3.41
1326 3570 1.433879 CGTCTCAGGTCCGTCCATC 59.566 63.158 0.00 0.00 39.02 3.51
1327 3571 1.433879 GTCTCAGGTCCGTCCATCG 59.566 63.158 0.00 0.00 39.02 3.84
1328 3572 1.030488 GTCTCAGGTCCGTCCATCGA 61.030 60.000 0.00 0.00 42.86 3.59
1338 3582 0.942252 CGTCCATCGATCGACCACTA 59.058 55.000 22.06 1.50 42.86 2.74
1364 3612 1.682867 TTCTCGCGCGTGCATAACTG 61.683 55.000 30.98 3.12 42.97 3.16
1733 3985 1.687054 CCCACATCCCGGTGAGTACTA 60.687 57.143 0.00 0.00 41.32 1.82
1734 3986 2.317040 CCACATCCCGGTGAGTACTAT 58.683 52.381 0.00 0.00 41.32 2.12
1736 3988 3.492656 CCACATCCCGGTGAGTACTATTG 60.493 52.174 0.00 0.00 41.32 1.90
1785 4464 7.133513 CCATAGAGTACACTTTACGATGTCTC 58.866 42.308 0.00 0.00 0.00 3.36
1900 4589 3.244112 CGTTGACCTTGTCCTTAACTCCT 60.244 47.826 0.00 0.00 0.00 3.69
1911 4600 6.173339 TGTCCTTAACTCCTTATTCTGCTTG 58.827 40.000 0.00 0.00 0.00 4.01
1921 4610 5.046304 TCCTTATTCTGCTTGTGACTTAGCT 60.046 40.000 10.61 0.00 38.22 3.32
2146 4897 0.764890 AGTAGGGCAAGCAAGTCACA 59.235 50.000 0.00 0.00 0.00 3.58
2183 5026 9.696917 AAATGAAGCATTTTAGTGAACCTAAAG 57.303 29.630 0.00 0.00 44.36 1.85
2184 5027 7.214467 TGAAGCATTTTAGTGAACCTAAAGG 57.786 36.000 0.00 0.00 44.36 3.11
2185 5028 5.644977 AGCATTTTAGTGAACCTAAAGGC 57.355 39.130 0.00 0.00 44.36 4.35
2186 5029 5.325239 AGCATTTTAGTGAACCTAAAGGCT 58.675 37.500 13.01 13.01 44.36 4.58
2187 5030 6.481643 AGCATTTTAGTGAACCTAAAGGCTA 58.518 36.000 15.40 0.00 45.86 3.93
2188 5031 6.946009 AGCATTTTAGTGAACCTAAAGGCTAA 59.054 34.615 15.40 0.00 45.86 3.09
2189 5032 7.450323 AGCATTTTAGTGAACCTAAAGGCTAAA 59.550 33.333 15.40 0.00 45.86 1.85
2288 5131 3.515104 TGTATCTGCTTGTCTGATCCACA 59.485 43.478 0.00 0.00 35.39 4.17
2289 5132 2.756840 TCTGCTTGTCTGATCCACAG 57.243 50.000 0.00 0.00 46.97 3.66
2317 5160 6.371595 CCAATAGGCAGATAGGAAGATTCT 57.628 41.667 0.00 0.00 0.00 2.40
2320 5163 7.256619 CCAATAGGCAGATAGGAAGATTCTCTT 60.257 40.741 0.00 0.00 39.87 2.85
2390 5244 2.230992 TGAGGTGGCAAATCGAAAATGG 59.769 45.455 0.00 0.00 0.00 3.16
2432 5348 6.266103 AGGAAATATGTTGCATGGGTATGAAG 59.734 38.462 0.00 0.00 36.36 3.02
2464 5380 2.779430 AGTCCAGGGATAATGTCATGCA 59.221 45.455 0.00 0.00 0.00 3.96
2545 5873 7.213216 TCAAACAAGTATGCTCTTATTTGCA 57.787 32.000 12.25 0.00 39.88 4.08
2749 6226 6.653526 TGATGTGTTTCATGGTTTGATCTT 57.346 33.333 0.00 0.00 36.83 2.40
2937 7155 3.918591 CCAAGTACGACACATCAGTACAC 59.081 47.826 7.57 0.00 42.12 2.90
2967 7185 9.565090 CATGGCCAATACAGTTATATGCTATAT 57.435 33.333 10.96 0.00 0.00 0.86
2997 7215 7.149202 TGGCATAAAATATTGAGTACTCCCT 57.851 36.000 20.11 9.66 0.00 4.20
2998 7216 7.224297 TGGCATAAAATATTGAGTACTCCCTC 58.776 38.462 20.11 0.00 0.00 4.30
2999 7217 6.655425 GGCATAAAATATTGAGTACTCCCTCC 59.345 42.308 20.11 0.00 0.00 4.30
3000 7218 6.369065 GCATAAAATATTGAGTACTCCCTCCG 59.631 42.308 20.11 0.28 0.00 4.63
3001 7219 5.952347 AAAATATTGAGTACTCCCTCCGT 57.048 39.130 20.11 0.00 0.00 4.69
3002 7220 8.582437 CATAAAATATTGAGTACTCCCTCCGTA 58.418 37.037 20.11 5.25 0.00 4.02
3003 7221 7.427989 AAAATATTGAGTACTCCCTCCGTAA 57.572 36.000 20.11 6.24 0.00 3.18
3005 7223 6.651975 ATATTGAGTACTCCCTCCGTAAAG 57.348 41.667 20.11 0.00 0.00 1.85
3009 7227 5.021458 TGAGTACTCCCTCCGTAAAGAAAT 58.979 41.667 20.11 0.00 0.00 2.17
3011 7229 6.837568 TGAGTACTCCCTCCGTAAAGAAATAT 59.162 38.462 20.11 0.00 0.00 1.28
3012 7230 8.000709 TGAGTACTCCCTCCGTAAAGAAATATA 58.999 37.037 20.11 0.00 0.00 0.86
3014 7232 9.205513 AGTACTCCCTCCGTAAAGAAATATAAA 57.794 33.333 0.00 0.00 0.00 1.40
3016 7234 8.959705 ACTCCCTCCGTAAAGAAATATAAAAG 57.040 34.615 0.00 0.00 0.00 2.27
3017 7235 8.546322 ACTCCCTCCGTAAAGAAATATAAAAGT 58.454 33.333 0.00 0.00 0.00 2.66
3018 7236 8.726870 TCCCTCCGTAAAGAAATATAAAAGTG 57.273 34.615 0.00 0.00 0.00 3.16
3019 7237 8.323567 TCCCTCCGTAAAGAAATATAAAAGTGT 58.676 33.333 0.00 0.00 0.00 3.55
3020 7238 8.953313 CCCTCCGTAAAGAAATATAAAAGTGTT 58.047 33.333 0.00 0.00 0.00 3.32
3049 7644 5.148651 ACTACTTTAGTGATCCAAACGCT 57.851 39.130 0.00 0.00 37.69 5.07
3050 7645 5.548406 ACTACTTTAGTGATCCAAACGCTT 58.452 37.500 0.00 0.00 37.69 4.68
3051 7646 5.995897 ACTACTTTAGTGATCCAAACGCTTT 59.004 36.000 0.00 0.00 37.69 3.51
3053 7648 6.870971 ACTTTAGTGATCCAAACGCTTTTA 57.129 33.333 0.00 0.00 0.00 1.52
3054 7649 7.448748 ACTTTAGTGATCCAAACGCTTTTAT 57.551 32.000 0.00 0.00 0.00 1.40
3055 7650 8.556213 ACTTTAGTGATCCAAACGCTTTTATA 57.444 30.769 0.00 0.00 0.00 0.98
3056 7651 9.174166 ACTTTAGTGATCCAAACGCTTTTATAT 57.826 29.630 0.00 0.00 0.00 0.86
3061 7656 9.174166 AGTGATCCAAACGCTTTTATATTAGTT 57.826 29.630 0.00 0.00 0.00 2.24
3134 7785 5.819379 TCACGGTCGACTAGTACTTGATAAT 59.181 40.000 16.46 0.00 0.00 1.28
3270 7959 2.181426 CAAACGAACGGTTGCTTTCA 57.819 45.000 11.81 0.00 39.30 2.69
3288 7977 8.246908 TGCTTTCAAAGATATTGCAAATGAAG 57.753 30.769 1.71 0.00 0.00 3.02
3447 8156 8.736097 ATATAACCTAATCCATACCTCACACA 57.264 34.615 0.00 0.00 0.00 3.72
3468 8177 2.009774 CACCTAAAAGATGCTCCGTGG 58.990 52.381 0.00 0.00 0.00 4.94
3481 8190 2.159627 GCTCCGTGGAACATAACAACAG 59.840 50.000 0.00 0.00 44.52 3.16
3612 8361 1.620819 AGATTGCTTCGTCTGTCCTGT 59.379 47.619 0.00 0.00 0.00 4.00
3613 8362 2.826128 AGATTGCTTCGTCTGTCCTGTA 59.174 45.455 0.00 0.00 0.00 2.74
3614 8363 2.433868 TTGCTTCGTCTGTCCTGTAC 57.566 50.000 0.00 0.00 0.00 2.90
3719 8468 3.406595 GATCTTCTGGGTGGGGCCG 62.407 68.421 0.00 0.00 38.44 6.13
3808 8557 2.894902 GTCCTACAGGAGCAACTAAGC 58.105 52.381 0.00 0.00 46.49 3.09
3810 8559 1.471676 CCTACAGGAGCAACTAAGCCG 60.472 57.143 0.00 0.00 37.39 5.52
3811 8560 0.535335 TACAGGAGCAACTAAGCCGG 59.465 55.000 0.00 0.00 34.23 6.13
3916 8665 1.949525 CACCTTTGTCCTGTTCAGTGG 59.050 52.381 0.00 0.00 0.00 4.00
4051 8800 4.072131 GTTTCTTCCAAGTGTGCTATCCA 58.928 43.478 0.00 0.00 0.00 3.41
4118 8875 7.807433 TGTGAATCAAAGAATTGGTATCGTTTG 59.193 33.333 0.00 0.00 37.15 2.93
4122 8879 7.265647 TCAAAGAATTGGTATCGTTTGTGAA 57.734 32.000 0.00 0.00 37.15 3.18
4171 8928 2.436417 TCCACAGCTTCCATTAACTGC 58.564 47.619 0.00 0.00 33.35 4.40
4187 8944 4.813296 AACTGCTTTTAGAACCAAGACG 57.187 40.909 0.00 0.00 0.00 4.18
4200 8957 6.159988 AGAACCAAGACGAAATAAGAGTCTG 58.840 40.000 0.00 0.00 43.60 3.51
4201 8958 4.246458 ACCAAGACGAAATAAGAGTCTGC 58.754 43.478 0.00 0.00 43.60 4.26
4242 8999 4.940654 CCAACATAATTTCCCCGCAAAAAT 59.059 37.500 0.00 0.00 0.00 1.82
4243 9000 5.163774 CCAACATAATTTCCCCGCAAAAATG 60.164 40.000 0.00 0.00 0.00 2.32
4256 9015 5.757320 CCCGCAAAAATGCCAATATAATTGA 59.243 36.000 1.23 0.00 0.00 2.57
4265 9024 8.801715 AATGCCAATATAATTGACGAATGTTC 57.198 30.769 1.23 0.00 0.00 3.18
4277 9036 6.662414 TGACGAATGTTCTGTATTTCATCC 57.338 37.500 0.00 0.00 0.00 3.51
4282 9041 6.479990 CGAATGTTCTGTATTTCATCCTAGCA 59.520 38.462 0.00 0.00 0.00 3.49
4295 9054 3.637821 TCCTAGCACCTAATGGATCCT 57.362 47.619 14.23 0.00 37.04 3.24
4300 9059 0.179048 CACCTAATGGATCCTGCGCA 60.179 55.000 10.98 10.98 37.04 6.09
4301 9060 0.767375 ACCTAATGGATCCTGCGCAT 59.233 50.000 12.24 0.00 37.04 4.73
4309 9069 1.590932 GATCCTGCGCATCTGATTGT 58.409 50.000 12.24 0.00 0.00 2.71
4334 9094 3.118992 TCGCATTGCTGTGATCTAAGAGT 60.119 43.478 7.12 0.00 36.99 3.24
4335 9095 3.001026 CGCATTGCTGTGATCTAAGAGTG 59.999 47.826 7.12 0.00 34.71 3.51
4340 9100 4.082125 TGCTGTGATCTAAGAGTGAGTCA 58.918 43.478 0.00 0.00 0.00 3.41
4344 9104 4.142071 TGTGATCTAAGAGTGAGTCATGGC 60.142 45.833 0.00 0.00 0.00 4.40
4353 9113 0.478072 TGAGTCATGGCCTGTGGTTT 59.522 50.000 3.32 0.00 0.00 3.27
4398 9158 9.824534 AATGTTCACAAACTTGAAATGTTTTTC 57.175 25.926 0.00 0.00 40.77 2.29
4399 9159 8.370493 TGTTCACAAACTTGAAATGTTTTTCA 57.630 26.923 0.00 0.00 40.77 2.69
4433 9193 8.637281 AATCTTCACGAAATTAAAAACCGTTT 57.363 26.923 0.00 0.00 0.00 3.60
4468 9228 9.084164 CAAAAATTGTTCATGAATTGCCAAAAA 57.916 25.926 12.12 0.00 0.00 1.94
4534 9294 9.927668 ATAAAAATGTCCACGATTTCAAAAGAT 57.072 25.926 0.00 0.00 0.00 2.40
4635 9397 8.503458 TGTTCATGATTCCAATTTTTGTTTGT 57.497 26.923 0.00 0.00 0.00 2.83
4636 9398 8.954350 TGTTCATGATTCCAATTTTTGTTTGTT 58.046 25.926 0.00 0.00 0.00 2.83
4678 9453 8.364129 TGTCCAAAAATCTAAGAAATGTTTGC 57.636 30.769 0.00 0.00 0.00 3.68
4685 9460 9.474920 AAAATCTAAGAAATGTTTGCGAATTCA 57.525 25.926 6.22 0.00 0.00 2.57
4686 9461 9.474920 AAATCTAAGAAATGTTTGCGAATTCAA 57.525 25.926 6.22 0.00 0.00 2.69
4689 9464 9.307121 TCTAAGAAATGTTTGCGAATTCAAAAA 57.693 25.926 6.22 2.52 37.65 1.94
4692 9467 8.770850 AGAAATGTTTGCGAATTCAAAAATTG 57.229 26.923 6.22 0.00 40.88 2.32
4697 9472 6.958193 TGTTTGCGAATTCAAAAATTGTTCAC 59.042 30.769 6.22 0.00 37.65 3.18
4700 9475 7.065216 TGCGAATTCAAAAATTGTTCACAAA 57.935 28.000 6.22 0.00 39.55 2.83
4727 9502 6.900568 AAAACATCAGCGTGAATTTGAAAA 57.099 29.167 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.108615 ATCGGTGGTCGCTTTCTCTG 60.109 55.000 0.00 0.00 39.05 3.35
147 1573 1.006519 CTGTCCCCCTCTCTCTTCTCA 59.993 57.143 0.00 0.00 0.00 3.27
151 1577 0.118144 AAGCTGTCCCCCTCTCTCTT 59.882 55.000 0.00 0.00 0.00 2.85
152 1578 1.011595 TAAGCTGTCCCCCTCTCTCT 58.988 55.000 0.00 0.00 0.00 3.10
153 1579 1.691434 CATAAGCTGTCCCCCTCTCTC 59.309 57.143 0.00 0.00 0.00 3.20
154 1580 1.799933 CATAAGCTGTCCCCCTCTCT 58.200 55.000 0.00 0.00 0.00 3.10
155 1581 0.107643 GCATAAGCTGTCCCCCTCTC 59.892 60.000 0.00 0.00 37.91 3.20
156 1582 1.348775 GGCATAAGCTGTCCCCCTCT 61.349 60.000 0.00 0.00 41.70 3.69
185 1611 0.883153 CAACCTGCATGCAAGCTGTA 59.117 50.000 22.88 0.00 34.99 2.74
335 1761 7.928706 AGAAACAGGTTCAGTATATACATGCTC 59.071 37.037 15.18 2.27 38.86 4.26
394 2552 5.123027 GGCAGTCCTATCTTTCAGAAAACAG 59.877 44.000 0.00 0.00 0.00 3.16
428 2587 1.154016 CTGTGGTGCCGACTACTCG 60.154 63.158 0.00 0.00 39.83 4.18
432 2591 2.366266 ACTTTTACTGTGGTGCCGACTA 59.634 45.455 0.00 0.00 0.00 2.59
478 2641 0.521291 ATGTGTCCGTTCCAAATGCG 59.479 50.000 0.00 0.00 0.00 4.73
522 2685 4.000988 CGTGTAGAGTTAGCATGGGTTTT 58.999 43.478 0.00 0.00 0.00 2.43
578 2815 1.196354 CAGAAAGGTCAGAAAGCGCAG 59.804 52.381 11.47 0.00 0.00 5.18
851 3088 3.305064 GGAGAGGACGAGCTCATTATCAC 60.305 52.174 15.40 4.89 32.83 3.06
852 3089 2.887783 GGAGAGGACGAGCTCATTATCA 59.112 50.000 15.40 0.00 32.83 2.15
856 3093 1.045911 GGGGAGAGGACGAGCTCATT 61.046 60.000 15.40 0.00 32.83 2.57
968 3209 4.796408 AGCTAGTGCCCTGTAGCT 57.204 55.556 0.00 0.00 45.81 3.32
969 3210 1.338655 GTCTAGCTAGTGCCCTGTAGC 59.661 57.143 20.10 0.00 41.77 3.58
970 3211 2.621055 CTGTCTAGCTAGTGCCCTGTAG 59.379 54.545 20.10 4.78 40.80 2.74
971 3212 2.241430 TCTGTCTAGCTAGTGCCCTGTA 59.759 50.000 20.10 0.00 40.80 2.74
1324 3568 3.811083 AGAGAACTAGTGGTCGATCGAT 58.189 45.455 22.50 7.70 0.00 3.59
1325 3569 3.263489 AGAGAACTAGTGGTCGATCGA 57.737 47.619 15.15 15.15 0.00 3.59
1326 3570 3.623960 AGAAGAGAACTAGTGGTCGATCG 59.376 47.826 9.36 9.36 0.00 3.69
1327 3571 4.260456 CGAGAAGAGAACTAGTGGTCGATC 60.260 50.000 0.00 0.00 0.00 3.69
1328 3572 3.623960 CGAGAAGAGAACTAGTGGTCGAT 59.376 47.826 0.00 0.00 0.00 3.59
1338 3582 1.442857 CACGCGCGAGAAGAGAACT 60.443 57.895 39.36 6.60 0.00 3.01
1385 3633 0.737715 GTCAGTCTCACGCATGACCC 60.738 60.000 0.00 0.00 36.83 4.46
1386 3634 0.244994 AGTCAGTCTCACGCATGACC 59.755 55.000 0.00 0.00 42.39 4.02
1389 3637 1.723542 GAACAGTCAGTCTCACGCATG 59.276 52.381 0.00 0.00 0.00 4.06
1390 3638 1.615883 AGAACAGTCAGTCTCACGCAT 59.384 47.619 0.00 0.00 0.00 4.73
1778 4457 7.442666 AGTGTACTTTTCCTTTTGAGAGACATC 59.557 37.037 0.00 0.00 0.00 3.06
1785 4464 9.110502 ACTCTAAAGTGTACTTTTCCTTTTGAG 57.889 33.333 14.47 15.69 43.07 3.02
1900 4589 6.072508 CCAAAGCTAAGTCACAAGCAGAATAA 60.073 38.462 5.09 0.00 41.32 1.40
1911 4600 5.500645 AAGTTGTTCCAAAGCTAAGTCAC 57.499 39.130 0.00 0.00 0.00 3.67
1921 4610 7.413219 CGTTGTCAAGTAGTAAGTTGTTCCAAA 60.413 37.037 0.00 0.00 37.33 3.28
2010 4701 5.897377 ATCGCTTTTTACCAGCAATTAGT 57.103 34.783 0.00 0.00 37.07 2.24
2011 4702 8.128582 TGATAATCGCTTTTTACCAGCAATTAG 58.871 33.333 0.00 0.00 31.31 1.73
2184 5027 2.900716 TTTTTGGGTGGCACTTTAGC 57.099 45.000 18.45 0.00 0.00 3.09
2210 5053 7.664082 TTCGTACAATTTTGGACCGTAAATA 57.336 32.000 0.13 0.00 38.85 1.40
2216 5059 4.153475 AGTGATTCGTACAATTTTGGACCG 59.847 41.667 0.13 0.00 38.85 4.79
2317 5160 3.024547 ACTAGTGCCTAATCGAGCAAGA 58.975 45.455 0.00 0.00 41.48 3.02
2320 5163 1.333931 CGACTAGTGCCTAATCGAGCA 59.666 52.381 0.00 0.00 37.81 4.26
2390 5244 2.639065 TCCTCATTAATTGGTGGCGAC 58.361 47.619 0.00 0.00 0.00 5.19
2432 5348 2.795329 TCCCTGGACTTCTGCAATTTC 58.205 47.619 0.00 0.00 0.00 2.17
2464 5380 7.630242 AATCTGAATGACAAAATACGTCCAT 57.370 32.000 0.00 0.00 32.15 3.41
2545 5873 9.725019 TGAGTATACATCTCAACACAAAAGAAT 57.275 29.630 5.50 0.00 38.71 2.40
2749 6226 9.362539 GAGTAGATCGGTAAGTTCAAAACATTA 57.637 33.333 0.00 0.00 0.00 1.90
2937 7155 7.772292 AGCATATAACTGTATTGGCCATGATAG 59.228 37.037 6.09 7.99 0.00 2.08
2971 7189 8.890472 AGGGAGTACTCAATATTTTATGCCATA 58.110 33.333 23.91 0.00 0.00 2.74
2974 7192 6.655425 GGAGGGAGTACTCAATATTTTATGCC 59.345 42.308 23.91 11.07 39.27 4.40
2975 7193 6.369065 CGGAGGGAGTACTCAATATTTTATGC 59.631 42.308 23.91 2.31 39.27 3.14
2976 7194 7.442656 ACGGAGGGAGTACTCAATATTTTATG 58.557 38.462 23.91 5.79 39.27 1.90
2978 7196 8.537728 TTACGGAGGGAGTACTCAATATTTTA 57.462 34.615 23.91 4.49 39.27 1.52
2980 7198 7.343833 TCTTTACGGAGGGAGTACTCAATATTT 59.656 37.037 23.91 6.82 39.27 1.40
2981 7199 6.837568 TCTTTACGGAGGGAGTACTCAATATT 59.162 38.462 23.91 6.33 39.27 1.28
2982 7200 6.371278 TCTTTACGGAGGGAGTACTCAATAT 58.629 40.000 23.91 6.64 39.27 1.28
2984 7202 4.607239 TCTTTACGGAGGGAGTACTCAAT 58.393 43.478 23.91 11.72 39.27 2.57
2985 7203 4.038271 TCTTTACGGAGGGAGTACTCAA 57.962 45.455 23.91 5.40 39.27 3.02
2986 7204 3.726557 TCTTTACGGAGGGAGTACTCA 57.273 47.619 23.91 0.00 39.27 3.41
2987 7205 5.595257 ATTTCTTTACGGAGGGAGTACTC 57.405 43.478 14.87 14.87 36.76 2.59
2989 7207 9.822185 TTTTATATTTCTTTACGGAGGGAGTAC 57.178 33.333 0.00 0.00 0.00 2.73
2991 7209 8.546322 ACTTTTATATTTCTTTACGGAGGGAGT 58.454 33.333 0.00 0.00 0.00 3.85
2992 7210 8.827677 CACTTTTATATTTCTTTACGGAGGGAG 58.172 37.037 0.00 0.00 0.00 4.30
2993 7211 8.323567 ACACTTTTATATTTCTTTACGGAGGGA 58.676 33.333 0.00 0.00 0.00 4.20
3027 7245 5.148651 AGCGTTTGGATCACTAAAGTAGT 57.851 39.130 0.00 0.00 40.28 2.73
3028 7246 6.481954 AAAGCGTTTGGATCACTAAAGTAG 57.518 37.500 0.00 0.00 0.00 2.57
3029 7247 6.870971 AAAAGCGTTTGGATCACTAAAGTA 57.129 33.333 0.00 0.00 0.00 2.24
3071 7666 9.930693 GCCAAGTAGTAGCTGATAAATATTACT 57.069 33.333 0.00 0.00 0.00 2.24
3072 7667 9.930693 AGCCAAGTAGTAGCTGATAAATATTAC 57.069 33.333 0.00 0.00 34.99 1.89
3134 7785 6.366061 CGTGTGATTGTCAATTCAGTCTAGAA 59.634 38.462 0.00 0.00 0.00 2.10
3270 7959 5.395990 CCTGCCCTTCATTTGCAATATCTTT 60.396 40.000 0.00 0.00 34.06 2.52
3288 7977 0.756442 TGGCAAGCATTATCCTGCCC 60.756 55.000 9.32 0.00 43.33 5.36
3436 8145 5.818678 TCTTTTAGGTGTGTGTGAGGTAT 57.181 39.130 0.00 0.00 0.00 2.73
3447 8156 2.615493 CCACGGAGCATCTTTTAGGTGT 60.615 50.000 0.00 0.00 33.73 4.16
3481 8190 4.588805 GCATGCAGCAGATTTTAAAACC 57.411 40.909 14.21 0.00 44.79 3.27
3612 8361 8.035984 TCATTGGAAGTTTATGTGATGTACGTA 58.964 33.333 0.00 0.00 0.00 3.57
3613 8362 6.876789 TCATTGGAAGTTTATGTGATGTACGT 59.123 34.615 0.00 0.00 0.00 3.57
3614 8363 7.302350 TCATTGGAAGTTTATGTGATGTACG 57.698 36.000 0.00 0.00 0.00 3.67
3916 8665 2.355132 CTGATGATGCAAAGACTGGAGC 59.645 50.000 0.00 0.00 31.39 4.70
4149 8906 3.119708 GCAGTTAATGGAAGCTGTGGAAG 60.120 47.826 0.00 0.00 0.00 3.46
4171 8928 8.989980 ACTCTTATTTCGTCTTGGTTCTAAAAG 58.010 33.333 0.00 0.00 0.00 2.27
4200 8957 7.583860 TGTTGGCGTTTATTAATTTAAAGGC 57.416 32.000 15.32 15.32 45.41 4.35
4229 8986 0.689623 ATTGGCATTTTTGCGGGGAA 59.310 45.000 0.00 0.00 35.24 3.97
4231 8988 2.618442 ATATTGGCATTTTTGCGGGG 57.382 45.000 0.00 0.00 35.24 5.73
4242 8999 7.066887 ACAGAACATTCGTCAATTATATTGGCA 59.933 33.333 5.04 0.00 0.00 4.92
4243 9000 7.417612 ACAGAACATTCGTCAATTATATTGGC 58.582 34.615 0.00 0.00 0.00 4.52
4256 9015 6.480320 GCTAGGATGAAATACAGAACATTCGT 59.520 38.462 0.00 0.00 0.00 3.85
4265 9024 6.652481 CCATTAGGTGCTAGGATGAAATACAG 59.348 42.308 0.00 0.00 0.00 2.74
4277 9036 2.611473 CGCAGGATCCATTAGGTGCTAG 60.611 54.545 15.82 0.00 32.57 3.42
4282 9041 0.767375 ATGCGCAGGATCCATTAGGT 59.233 50.000 18.32 0.00 25.85 3.08
4295 9054 0.932399 CGATCACAATCAGATGCGCA 59.068 50.000 14.96 14.96 31.76 6.09
4300 9059 3.003378 CAGCAATGCGATCACAATCAGAT 59.997 43.478 0.00 0.00 31.76 2.90
4301 9060 2.353579 CAGCAATGCGATCACAATCAGA 59.646 45.455 0.00 0.00 31.76 3.27
4309 9069 2.320745 AGATCACAGCAATGCGATCA 57.679 45.000 18.80 0.00 37.36 2.92
4334 9094 0.478072 AAACCACAGGCCATGACTCA 59.522 50.000 5.01 0.00 0.00 3.41
4335 9095 1.168714 GAAACCACAGGCCATGACTC 58.831 55.000 5.01 0.00 0.00 3.36
4340 9100 2.299867 GTGAAATGAAACCACAGGCCAT 59.700 45.455 5.01 0.00 0.00 4.40
4344 9104 6.538021 TCAAAATTGTGAAATGAAACCACAGG 59.462 34.615 0.00 0.00 41.17 4.00
4409 9169 8.132995 AGAAACGGTTTTTAATTTCGTGAAGAT 58.867 29.630 7.65 0.00 36.41 2.40
4411 9171 7.673810 AGAAACGGTTTTTAATTTCGTGAAG 57.326 32.000 7.65 0.00 36.41 3.02
4468 9228 9.442047 TTTCAAATACACTTGAATTTGTGGTTT 57.558 25.926 7.44 8.43 43.12 3.27
4471 9231 8.417780 TGTTTCAAATACACTTGAATTTGTGG 57.582 30.769 7.44 0.00 43.12 4.17
4508 9268 9.927668 ATCTTTTGAAATCGTGGACATTTTTAT 57.072 25.926 0.00 0.00 0.00 1.40
4516 9276 5.757886 TGAACATCTTTTGAAATCGTGGAC 58.242 37.500 0.00 0.00 0.00 4.02
4521 9281 9.131416 TGAAATCATGAACATCTTTTGAAATCG 57.869 29.630 0.00 0.00 0.00 3.34
4652 9414 8.992073 GCAAACATTTCTTAGATTTTTGGACAT 58.008 29.630 0.00 0.00 29.36 3.06
4653 9415 7.168972 CGCAAACATTTCTTAGATTTTTGGACA 59.831 33.333 0.00 0.00 29.36 4.02
4654 9416 7.381139 TCGCAAACATTTCTTAGATTTTTGGAC 59.619 33.333 0.00 0.00 29.36 4.02
4655 9417 7.429633 TCGCAAACATTTCTTAGATTTTTGGA 58.570 30.769 0.00 0.00 29.36 3.53
4656 9418 7.636259 TCGCAAACATTTCTTAGATTTTTGG 57.364 32.000 0.00 0.00 29.36 3.28
4659 9421 9.474920 TGAATTCGCAAACATTTCTTAGATTTT 57.525 25.926 0.04 0.00 0.00 1.82
4677 9452 9.643652 TTATTTGTGAACAATTTTTGAATTCGC 57.356 25.926 0.04 0.00 35.55 4.70
4712 9487 6.272698 GTGAACATTTTTCAAATTCACGCT 57.727 33.333 0.00 0.00 39.65 5.07


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

AutoCloner maintained by Alex Coulton.