Multiple sequence alignment - TraesCS3B01G214700

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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 TraesCS3B01G214700 chr3B 100.000 5960 0 0 1 5960 255035696 255041655 0.000000e+00 11007.0
1 TraesCS3B01G214700 chr3B 91.156 147 11 1 192 336 523945974 523946120 1.310000e-46 198.0
2 TraesCS3B01G214700 chr3D 92.374 2426 134 23 3217 5621 175660881 175663276 0.000000e+00 3408.0
3 TraesCS3B01G214700 chr3D 93.686 1362 43 7 883 2222 175658321 175659661 0.000000e+00 1999.0
4 TraesCS3B01G214700 chr3D 92.102 899 44 10 2342 3233 175659811 175660689 0.000000e+00 1242.0
5 TraesCS3B01G214700 chr3D 89.102 679 65 9 1 674 175657097 175657771 0.000000e+00 835.0
6 TraesCS3B01G214700 chr3D 87.678 211 16 6 683 893 175657972 175658172 2.780000e-58 237.0
7 TraesCS3B01G214700 chr3D 91.608 143 12 0 195 337 115208228 115208086 1.310000e-46 198.0
8 TraesCS3B01G214700 chr3A 95.679 1921 57 7 2970 4874 216136164 216138074 0.000000e+00 3064.0
9 TraesCS3B01G214700 chr3A 90.830 2301 126 35 683 2940 216133905 216136163 0.000000e+00 3001.0
10 TraesCS3B01G214700 chr3A 90.571 1103 89 9 4867 5960 216152038 216153134 0.000000e+00 1447.0
11 TraesCS3B01G214700 chr3A 90.491 631 53 6 44 671 216133075 216133701 0.000000e+00 826.0
12 TraesCS3B01G214700 chr1A 83.113 302 45 6 376 674 358768453 358768155 2.740000e-68 270.0
13 TraesCS3B01G214700 chr2D 90.625 192 14 4 1 191 152512962 152512774 9.920000e-63 252.0
14 TraesCS3B01G214700 chr1B 89.583 192 16 4 1 191 332264014 332264202 2.150000e-59 241.0
15 TraesCS3B01G214700 chr1B 80.488 205 33 6 5171 5372 457026627 457026827 3.720000e-32 150.0
16 TraesCS3B01G214700 chr1B 80.791 177 27 7 5225 5396 489807778 489807604 1.350000e-26 132.0
17 TraesCS3B01G214700 chr6B 83.858 254 33 6 92 340 139946062 139945812 9.990000e-58 235.0
18 TraesCS3B01G214700 chr1D 89.062 192 17 4 1 191 331503936 331504124 9.990000e-58 235.0
19 TraesCS3B01G214700 chr4D 89.062 192 14 5 1 191 456091405 456091220 1.290000e-56 231.0
20 TraesCS3B01G214700 chr4D 85.185 216 21 10 1 212 67297450 67297242 1.680000e-50 211.0
21 TraesCS3B01G214700 chr4D 81.538 195 31 3 348 540 489125405 489125596 8.000000e-34 156.0
22 TraesCS3B01G214700 chr5B 88.601 193 13 8 1 191 62912543 62912358 6.010000e-55 226.0
23 TraesCS3B01G214700 chr6A 93.007 143 8 1 195 335 188452890 188452748 2.180000e-49 207.0
24 TraesCS3B01G214700 chr6A 84.466 103 15 1 447 548 70975894 70975996 3.800000e-17 100.0
25 TraesCS3B01G214700 chr5D 92.308 143 11 0 195 337 116753206 116753064 2.820000e-48 204.0
26 TraesCS3B01G214700 chr5D 77.670 309 64 5 348 652 503500244 503500551 3.670000e-42 183.0
27 TraesCS3B01G214700 chr4B 91.837 147 11 1 192 338 510165746 510165891 2.820000e-48 204.0
28 TraesCS3B01G214700 chr4B 76.946 334 64 13 349 674 601096276 601095948 1.710000e-40 178.0
29 TraesCS3B01G214700 chr4B 81.000 200 36 2 350 547 626466006 626466205 2.220000e-34 158.0
30 TraesCS3B01G214700 chr4A 91.549 142 12 0 195 336 608239353 608239494 4.710000e-46 196.0
31 TraesCS3B01G214700 chr6D 75.758 330 59 11 348 674 97257684 97257995 4.810000e-31 147.0
32 TraesCS3B01G214700 chr2A 100.000 28 0 0 625 652 733895480 733895507 1.100000e-02 52.8


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 TraesCS3B01G214700 chr3B 255035696 255041655 5959 False 11007.0 11007 100.000000 1 5960 1 chr3B.!!$F1 5959
1 TraesCS3B01G214700 chr3D 175657097 175663276 6179 False 1544.2 3408 90.988400 1 5621 5 chr3D.!!$F1 5620
2 TraesCS3B01G214700 chr3A 216133075 216138074 4999 False 2297.0 3064 92.333333 44 4874 3 chr3A.!!$F2 4830
3 TraesCS3B01G214700 chr3A 216152038 216153134 1096 False 1447.0 1447 90.571000 4867 5960 1 chr3A.!!$F1 1093

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
458 461 0.176910 TTCCGCTGACGCCAATATGA 59.823 50.000 0.00 0.0 38.22 2.15 F
737 934 0.821517 TCGTGTGTTGTCCAGTCACT 59.178 50.000 0.00 0.0 33.82 3.41 F
1879 2259 0.759436 GCGGGGAGAGTCCATAGGAA 60.759 60.000 0.00 0.0 38.64 3.36 F
2511 2973 0.242286 ACAGCTAGCGACAGTGACAG 59.758 55.000 9.55 0.0 0.00 3.51 F
4172 4865 1.079819 CACGAGGTACCAGCACCAG 60.080 63.158 15.94 0.0 41.40 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 2062 0.041386 AGACCCAGTACCTCCCTGAC 59.959 60.0 0.00 0.0 31.38 3.51 R
2486 2941 0.522286 CTGTCGCTAGCTGTGAGTCG 60.522 60.0 13.93 0.0 35.65 4.18 R
3349 4025 0.326238 ATAAGGTCCTTCCAGCCGGA 60.326 55.0 7.61 0.0 40.60 5.14 R
4175 4868 0.167908 GTGTGTGTGTGTGTGTGGTG 59.832 55.0 0.00 0.0 0.00 4.17 R
5716 6431 0.109412 GTGCAACCTCATCAGCAAGC 60.109 55.0 0.00 0.0 38.91 4.01 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
82 83 7.036220 ACTTAGTCTTGATCAACCTTGTATCG 58.964 38.462 3.38 0.00 0.00 2.92
95 96 8.784994 TCAACCTTGTATCGTATATTCTCTCTC 58.215 37.037 0.00 0.00 0.00 3.20
96 97 8.788806 CAACCTTGTATCGTATATTCTCTCTCT 58.211 37.037 0.00 0.00 0.00 3.10
97 98 8.556213 ACCTTGTATCGTATATTCTCTCTCTC 57.444 38.462 0.00 0.00 0.00 3.20
136 137 6.489700 TCTTGAAGGTAAACATCAATGCTCAA 59.510 34.615 0.00 0.00 33.03 3.02
137 138 6.012658 TGAAGGTAAACATCAATGCTCAAC 57.987 37.500 0.00 0.00 0.00 3.18
138 139 4.685169 AGGTAAACATCAATGCTCAACG 57.315 40.909 0.00 0.00 0.00 4.10
148 149 3.935203 TCAATGCTCAACGAATCCTCTTC 59.065 43.478 0.00 0.00 0.00 2.87
158 159 5.215252 ACGAATCCTCTTCTTCAAGACAA 57.785 39.130 0.00 0.00 34.71 3.18
241 243 3.018856 TGGTCTTCAAGCAATGCCTATG 58.981 45.455 0.00 0.00 30.91 2.23
285 287 8.579850 AACTCAAAGCAATCATTAGTCCATAA 57.420 30.769 0.00 0.00 0.00 1.90
286 288 8.579850 ACTCAAAGCAATCATTAGTCCATAAA 57.420 30.769 0.00 0.00 0.00 1.40
319 321 0.471617 TGCCAAAACCAAACATGGGG 59.528 50.000 0.00 0.00 33.45 4.96
341 343 2.162408 GCACCATGTTCTTTCAGCTACC 59.838 50.000 0.00 0.00 0.00 3.18
346 348 1.145803 GTTCTTTCAGCTACCGCGTT 58.854 50.000 4.92 0.00 42.32 4.84
370 372 1.806461 GAGGCGATGCGGTCCATCTA 61.806 60.000 0.00 0.00 46.61 1.98
458 461 0.176910 TTCCGCTGACGCCAATATGA 59.823 50.000 0.00 0.00 38.22 2.15
527 531 1.291184 CCTCGCTGCGTGAATGTTGA 61.291 55.000 23.74 0.00 0.00 3.18
540 544 2.504244 GTTGACGAGGCGGAGTCG 60.504 66.667 0.00 0.00 43.25 4.18
658 663 3.414700 GTTCACCGGCAGCGTGAG 61.415 66.667 0.00 0.00 41.10 3.51
731 928 3.075148 TCAACTTTTCGTGTGTTGTCCA 58.925 40.909 0.00 0.00 41.05 4.02
732 929 3.126171 TCAACTTTTCGTGTGTTGTCCAG 59.874 43.478 0.00 0.00 41.05 3.86
733 930 2.706890 ACTTTTCGTGTGTTGTCCAGT 58.293 42.857 0.00 0.00 0.00 4.00
734 931 2.676342 ACTTTTCGTGTGTTGTCCAGTC 59.324 45.455 0.00 0.00 0.00 3.51
735 932 2.388310 TTTCGTGTGTTGTCCAGTCA 57.612 45.000 0.00 0.00 0.00 3.41
736 933 1.647346 TTCGTGTGTTGTCCAGTCAC 58.353 50.000 0.00 0.00 0.00 3.67
737 934 0.821517 TCGTGTGTTGTCCAGTCACT 59.178 50.000 0.00 0.00 33.82 3.41
738 935 0.930310 CGTGTGTTGTCCAGTCACTG 59.070 55.000 0.00 0.00 33.82 3.66
739 936 1.739035 CGTGTGTTGTCCAGTCACTGT 60.739 52.381 3.56 0.00 33.82 3.55
740 937 2.356135 GTGTGTTGTCCAGTCACTGTT 58.644 47.619 3.56 0.00 33.82 3.16
741 938 2.747446 GTGTGTTGTCCAGTCACTGTTT 59.253 45.455 3.56 0.00 33.82 2.83
809 1006 7.284489 GGATTTAGGCAATTGTGGTTGTAGATA 59.716 37.037 7.40 0.00 0.00 1.98
810 1007 8.766994 ATTTAGGCAATTGTGGTTGTAGATAT 57.233 30.769 7.40 0.00 0.00 1.63
895 1251 3.869065 TCAAACGTGTCCTGAGAACTTT 58.131 40.909 0.00 0.00 0.00 2.66
910 1266 6.395629 TGAGAACTTTAGATTTCCGTTCGAT 58.604 36.000 0.00 0.00 39.05 3.59
944 1300 4.500116 GGCGTGCTCTCCGTCTCC 62.500 72.222 0.00 0.00 0.00 3.71
1064 1420 1.355066 CGCGAGCTTCTTCCAGTTCC 61.355 60.000 0.00 0.00 0.00 3.62
1069 1425 1.299976 CTTCTTCCAGTTCCCCCGG 59.700 63.158 0.00 0.00 0.00 5.73
1247 1603 2.269883 GCCCACGATTACCCCGTT 59.730 61.111 0.00 0.00 38.29 4.44
1321 1683 4.405671 ACGCGTCTCCTCCTCCGA 62.406 66.667 5.58 0.00 0.00 4.55
1328 1690 4.501285 TCCTCCTCCGACGGCGAT 62.501 66.667 15.16 0.00 40.82 4.58
1682 2062 2.747855 GCTGGAAAGCCGGTCCTG 60.748 66.667 10.68 10.83 42.93 3.86
1687 2067 1.376037 GAAAGCCGGTCCTGTCAGG 60.376 63.158 13.21 13.21 36.46 3.86
1879 2259 0.759436 GCGGGGAGAGTCCATAGGAA 60.759 60.000 0.00 0.00 38.64 3.36
2096 2488 1.896660 GCCCGTTCTTGTGCAGGAA 60.897 57.895 0.00 0.00 0.00 3.36
2179 2575 8.977412 CAGGTAAATAATAGTTTCCCCATGTTT 58.023 33.333 0.00 0.00 0.00 2.83
2180 2576 9.197306 AGGTAAATAATAGTTTCCCCATGTTTC 57.803 33.333 0.00 0.00 0.00 2.78
2181 2577 8.132995 GGTAAATAATAGTTTCCCCATGTTTCG 58.867 37.037 0.00 0.00 0.00 3.46
2184 2580 7.712204 ATAATAGTTTCCCCATGTTTCGTTT 57.288 32.000 0.00 0.00 0.00 3.60
2215 2611 8.970859 AATATTTGTTGATTGTGGGTTTCAAA 57.029 26.923 0.00 0.00 31.66 2.69
2217 2613 5.413309 TTGTTGATTGTGGGTTTCAAACT 57.587 34.783 0.00 0.00 31.66 2.66
2222 2618 8.043710 TGTTGATTGTGGGTTTCAAACTAAATT 58.956 29.630 0.00 0.00 31.66 1.82
2225 2621 8.260818 TGATTGTGGGTTTCAAACTAAATTCAA 58.739 29.630 0.00 0.00 0.00 2.69
2226 2622 9.271828 GATTGTGGGTTTCAAACTAAATTCAAT 57.728 29.630 0.00 3.95 0.00 2.57
2229 2625 9.703892 TGTGGGTTTCAAACTAAATTCAATATG 57.296 29.630 0.00 0.00 0.00 1.78
2230 2626 8.655970 GTGGGTTTCAAACTAAATTCAATATGC 58.344 33.333 0.00 0.00 0.00 3.14
2231 2627 8.370940 TGGGTTTCAAACTAAATTCAATATGCA 58.629 29.630 0.00 0.00 0.00 3.96
2232 2628 8.872845 GGGTTTCAAACTAAATTCAATATGCAG 58.127 33.333 0.00 0.00 0.00 4.41
2233 2629 9.423061 GGTTTCAAACTAAATTCAATATGCAGT 57.577 29.630 0.00 0.00 0.00 4.40
2325 2780 8.414778 AGTATTTGTTTTGAACCGTCCAATTTA 58.585 29.630 0.00 0.00 0.00 1.40
2361 2816 6.496524 GTCAAAGATTCAAAAGTTTGACCG 57.503 37.500 13.39 0.00 46.89 4.79
2364 2819 6.750039 TCAAAGATTCAAAAGTTTGACCGTTC 59.250 34.615 5.98 2.61 45.99 3.95
2391 2846 2.029838 AGAGTTTGGGCATCATCGAC 57.970 50.000 0.00 0.00 0.00 4.20
2399 2854 1.143305 GGCATCATCGACGGATTGAG 58.857 55.000 0.00 0.00 0.00 3.02
2401 2856 2.611473 GGCATCATCGACGGATTGAGAT 60.611 50.000 0.00 0.00 0.00 2.75
2402 2857 3.062763 GCATCATCGACGGATTGAGATT 58.937 45.455 0.00 0.00 0.00 2.40
2404 2859 3.097877 TCATCGACGGATTGAGATTGG 57.902 47.619 0.00 0.00 0.00 3.16
2405 2860 2.693074 TCATCGACGGATTGAGATTGGA 59.307 45.455 0.00 0.00 0.00 3.53
2406 2861 3.132111 TCATCGACGGATTGAGATTGGAA 59.868 43.478 0.00 0.00 0.00 3.53
2432 2887 1.073025 TGGTCGCTTGTTGCATCCT 59.927 52.632 0.00 0.00 43.06 3.24
2471 2926 7.068692 ACGTACAAGTATTTAAGATGGCAAC 57.931 36.000 0.00 0.00 0.00 4.17
2477 2932 5.437060 AGTATTTAAGATGGCAACGATGGT 58.563 37.500 0.00 0.00 42.51 3.55
2486 2941 1.463444 GGCAACGATGGTGAGTGTAAC 59.537 52.381 0.00 0.00 0.00 2.50
2511 2973 0.242286 ACAGCTAGCGACAGTGACAG 59.758 55.000 9.55 0.00 0.00 3.51
2538 3004 1.813753 AGTTGTCTTGCGCGTGTGT 60.814 52.632 8.43 0.00 0.00 3.72
2556 3022 1.623811 TGTGCTTGGAACTCCTACTCC 59.376 52.381 0.00 0.00 36.82 3.85
2606 3072 4.218312 AGCCAGACAAGGAGATTTTGTTT 58.782 39.130 0.00 0.00 38.78 2.83
2607 3073 4.651045 AGCCAGACAAGGAGATTTTGTTTT 59.349 37.500 0.00 0.00 38.78 2.43
2622 3088 9.786105 AGATTTTGTTTTTGTTGCCATTTTAAG 57.214 25.926 0.00 0.00 0.00 1.85
2627 3093 6.150140 TGTTTTTGTTGCCATTTTAAGCAGTT 59.850 30.769 0.00 0.00 40.73 3.16
2632 3098 2.627221 TGCCATTTTAAGCAGTTCTGCA 59.373 40.909 23.69 5.99 37.25 4.41
2633 3099 3.248266 GCCATTTTAAGCAGTTCTGCAG 58.752 45.455 23.69 7.63 37.25 4.41
2635 3101 4.082787 GCCATTTTAAGCAGTTCTGCAGTA 60.083 41.667 23.69 13.75 37.25 2.74
2636 3102 5.393962 CCATTTTAAGCAGTTCTGCAGTAC 58.606 41.667 23.69 15.08 37.25 2.73
2639 3105 6.693315 TTTTAAGCAGTTCTGCAGTACTTT 57.307 33.333 21.95 16.92 37.25 2.66
2640 3106 6.693315 TTTAAGCAGTTCTGCAGTACTTTT 57.307 33.333 21.95 19.63 37.25 2.27
2641 3107 6.693315 TTAAGCAGTTCTGCAGTACTTTTT 57.307 33.333 21.95 19.34 37.25 1.94
2642 3108 4.820284 AGCAGTTCTGCAGTACTTTTTC 57.180 40.909 21.95 11.96 37.25 2.29
2643 3109 3.248602 AGCAGTTCTGCAGTACTTTTTCG 59.751 43.478 21.95 12.27 37.25 3.46
2644 3110 3.002348 GCAGTTCTGCAGTACTTTTTCGT 59.998 43.478 21.95 0.00 34.41 3.85
2645 3111 4.210537 GCAGTTCTGCAGTACTTTTTCGTA 59.789 41.667 21.95 0.00 34.41 3.43
2667 3133 7.041303 TCGTAGTATTTCGAGTATGAGATGCTT 60.041 37.037 0.00 0.00 30.21 3.91
2697 3164 4.279659 GTGTTCAACTCGTGGTGATTTTC 58.720 43.478 5.98 0.00 0.00 2.29
2700 3167 2.548057 TCAACTCGTGGTGATTTTCTGC 59.452 45.455 0.06 0.00 0.00 4.26
2845 3313 3.019564 GTGCAGATTCAGGTAGCCATTT 58.980 45.455 0.00 0.00 0.00 2.32
2850 3318 4.514441 CAGATTCAGGTAGCCATTTAGCAG 59.486 45.833 0.00 0.00 34.23 4.24
2941 3409 2.661537 TCAACTCCGCTGTGCACG 60.662 61.111 13.13 8.32 0.00 5.34
3028 3496 1.753463 GGGAGAGTCACCGACCGAT 60.753 63.158 0.09 0.00 32.18 4.18
3213 3681 2.497675 TCTCCGGTCTGAAGGAATCAAG 59.502 50.000 0.00 0.00 37.67 3.02
3250 3926 1.613925 CTCGACTCCCAACTCTGAACA 59.386 52.381 0.00 0.00 0.00 3.18
3467 4149 1.271934 CCGATCGATCAGAGCTCCAAT 59.728 52.381 24.40 3.87 32.02 3.16
3473 4155 3.127548 TCGATCAGAGCTCCAATTTTTGC 59.872 43.478 10.93 0.00 0.00 3.68
3499 4181 5.803020 AAATTCCTTGTGATCGAGCTTAC 57.197 39.130 0.90 0.00 0.00 2.34
3500 4182 3.953712 TTCCTTGTGATCGAGCTTACA 57.046 42.857 0.90 0.00 0.00 2.41
3501 4183 4.471904 TTCCTTGTGATCGAGCTTACAT 57.528 40.909 0.90 0.00 0.00 2.29
3997 4690 1.994467 CATCAAGAGCAGCGTCGTC 59.006 57.895 0.00 0.00 0.00 4.20
4170 4863 2.264794 CCACGAGGTACCAGCACC 59.735 66.667 15.94 0.00 39.02 5.01
4171 4864 2.579657 CCACGAGGTACCAGCACCA 61.580 63.158 15.94 0.00 41.40 4.17
4172 4865 1.079819 CACGAGGTACCAGCACCAG 60.080 63.158 15.94 0.00 41.40 4.00
4173 4866 1.533273 ACGAGGTACCAGCACCAGT 60.533 57.895 15.94 0.01 41.40 4.00
4174 4867 1.079819 CGAGGTACCAGCACCAGTG 60.080 63.158 15.94 0.00 41.40 3.66
4368 5063 2.901042 CCTGGGAGTTCTACCGCC 59.099 66.667 0.00 0.00 0.00 6.13
4388 5083 1.374758 CCAGCTCGTCAAGGTCCAC 60.375 63.158 0.00 0.00 31.91 4.02
4685 5381 1.301479 GTGGACCGGCGAAGAGTTT 60.301 57.895 9.30 0.00 0.00 2.66
4898 5594 6.575162 ACCAAACAGTTGATAATTGGACTC 57.425 37.500 9.63 0.00 42.46 3.36
4901 5597 6.370442 CCAAACAGTTGATAATTGGACTCGTA 59.630 38.462 0.00 0.00 42.46 3.43
4939 5636 0.957395 CATTGCAGCCGTCTTGGAGT 60.957 55.000 0.00 0.00 42.00 3.85
4956 5653 4.072131 TGGAGTAGTGGCAAGTTTCATTC 58.928 43.478 0.00 0.00 0.00 2.67
5061 5763 6.861144 ACTAATAGTCGACCTTTAGTTCCAC 58.139 40.000 24.37 0.00 32.43 4.02
5066 5768 1.659098 CGACCTTTAGTTCCACGCATC 59.341 52.381 0.00 0.00 0.00 3.91
5094 5796 4.384846 GCATACCTAACGACATATCCAACG 59.615 45.833 0.00 0.00 0.00 4.10
5107 5809 2.702592 TCCAACGCGGATCCTAAAAT 57.297 45.000 12.47 0.00 39.64 1.82
5129 5831 3.986006 ACGTGTCCGTCCGCACAT 61.986 61.111 0.00 0.00 46.28 3.21
5200 5911 4.881273 TCATACCGCATACATTTCAAAGCT 59.119 37.500 0.00 0.00 0.00 3.74
5203 5914 3.119849 ACCGCATACATTTCAAAGCTGAC 60.120 43.478 0.00 0.00 0.00 3.51
5216 5927 4.704540 TCAAAGCTGACTTGAACAAAAGGA 59.295 37.500 0.00 0.00 35.85 3.36
5333 6044 8.351461 ACGCTATTCTAACCTAGTCTAAATGAC 58.649 37.037 0.00 0.00 45.67 3.06
5357 6068 3.707458 TCGCGGTGGCACCCATTA 61.707 61.111 30.03 11.09 39.92 1.90
5450 6161 2.285743 GGGAGGGGGAAGAGTGCT 60.286 66.667 0.00 0.00 0.00 4.40
5520 6231 2.774799 GCGGTGGCATCCCATGTTC 61.775 63.158 0.00 0.00 44.51 3.18
5601 6315 1.940758 CGTGAACGACGTTGACGGT 60.941 57.895 34.72 6.07 45.98 4.83
5603 6317 0.866906 GTGAACGACGTTGACGGTGA 60.867 55.000 19.60 0.00 44.95 4.02
5631 6345 3.124686 GAGCTGCCGAGGTCCTAG 58.875 66.667 0.00 0.00 40.31 3.02
5652 6367 2.431057 GGTCTCGCCTCAAATTCCTCTA 59.569 50.000 0.00 0.00 0.00 2.43
5658 6373 2.939640 GCCTCAAATTCCTCTACGGCAA 60.940 50.000 0.00 0.00 36.37 4.52
5687 6402 7.921214 TCGATGTCCATAAATAGAGTGTCTTTC 59.079 37.037 0.00 0.00 0.00 2.62
5689 6404 9.255304 GATGTCCATAAATAGAGTGTCTTTCTC 57.745 37.037 0.00 0.00 0.00 2.87
5693 6408 4.810191 AAATAGAGTGTCTTTCTCCGCT 57.190 40.909 0.00 0.00 32.93 5.52
5716 6431 3.406361 GACGCATAGCCGCCATCG 61.406 66.667 0.00 0.00 0.00 3.84
5775 6490 8.610035 CATGAAGATCCAATACAATATGATCCG 58.390 37.037 0.00 0.00 33.86 4.18
5778 6493 6.409704 AGATCCAATACAATATGATCCGTGG 58.590 40.000 0.00 0.00 33.86 4.94
5802 6517 5.344396 GGTCTACAACTCAAGTTACGCTAAC 59.656 44.000 0.00 0.00 36.32 2.34
5856 6571 0.504384 CAACGCGCTCTATCATTCGG 59.496 55.000 5.73 0.00 0.00 4.30
5884 6599 5.660417 AGGAACTCTTAGATGCTCAGATGAA 59.340 40.000 0.00 0.00 0.00 2.57
5901 6616 5.406477 CAGATGAACAAATCACTCGAAGACA 59.594 40.000 0.00 0.00 41.93 3.41
5934 6649 2.002127 CACGAAGAGCATCCGAAGC 58.998 57.895 0.00 0.00 33.66 3.86
5943 6658 1.299850 CATCCGAAGCGTCGCCATA 60.300 57.895 16.96 2.02 46.28 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.436080 AGTTGATCAACACACAAAGCATAAAAG 59.564 33.333 33.92 0.00 43.47 2.27
17 18 6.389830 AGTTGATCAACACACAAAGCATAA 57.610 33.333 33.92 0.00 43.47 1.90
20 21 4.157472 TCAAGTTGATCAACACACAAAGCA 59.843 37.500 33.92 9.55 43.47 3.91
21 22 4.671377 TCAAGTTGATCAACACACAAAGC 58.329 39.130 33.92 9.67 43.47 3.51
108 109 7.989826 AGCATTGATGTTTACCTTCAAGATAC 58.010 34.615 0.00 0.00 39.67 2.24
110 111 6.660521 TGAGCATTGATGTTTACCTTCAAGAT 59.339 34.615 0.00 0.00 39.67 2.40
127 128 3.937706 AGAAGAGGATTCGTTGAGCATTG 59.062 43.478 0.00 0.00 0.00 2.82
136 137 4.873746 TGTCTTGAAGAAGAGGATTCGT 57.126 40.909 0.00 0.00 38.95 3.85
137 138 4.092675 GCTTGTCTTGAAGAAGAGGATTCG 59.907 45.833 0.00 0.00 38.95 3.34
138 139 5.244755 AGCTTGTCTTGAAGAAGAGGATTC 58.755 41.667 0.00 0.00 38.95 2.52
158 159 4.020751 TGAGAGTTGAGACTATTGCAAGCT 60.021 41.667 4.94 0.00 35.88 3.74
241 243 7.696992 TGAGTTATATTTGAAGGGTTTGTCC 57.303 36.000 0.00 0.00 0.00 4.02
285 287 5.179182 GGTTTTGGCAATCGATCACAATTTT 59.821 36.000 0.00 0.00 0.00 1.82
286 288 4.690280 GGTTTTGGCAATCGATCACAATTT 59.310 37.500 0.00 0.00 0.00 1.82
319 321 1.251251 AGCTGAAAGAACATGGTGCC 58.749 50.000 0.00 0.00 34.07 5.01
357 359 1.364171 GACGCTAGATGGACCGCAT 59.636 57.895 0.00 0.00 0.00 4.73
514 517 1.565156 GCCTCGTCAACATTCACGCA 61.565 55.000 0.00 0.00 35.93 5.24
586 591 2.089854 GTGATGTCCACCATGACGC 58.910 57.895 0.00 0.00 39.86 5.19
620 625 5.027293 ACGTGAGATCAATGATGGATTCA 57.973 39.130 0.00 0.00 39.12 2.57
674 679 9.097257 CATAAACACCATTTTCAAAGTTGAAGT 57.903 29.630 6.58 0.00 46.68 3.01
675 680 8.550376 CCATAAACACCATTTTCAAAGTTGAAG 58.450 33.333 6.58 0.00 46.68 3.02
676 681 8.043710 ACCATAAACACCATTTTCAAAGTTGAA 58.956 29.630 2.32 2.32 44.78 2.69
677 682 7.560368 ACCATAAACACCATTTTCAAAGTTGA 58.440 30.769 0.00 0.00 34.92 3.18
678 683 7.784633 ACCATAAACACCATTTTCAAAGTTG 57.215 32.000 0.00 0.00 0.00 3.16
681 686 7.493971 TCACAACCATAAACACCATTTTCAAAG 59.506 33.333 0.00 0.00 0.00 2.77
735 932 2.713154 GCCGCGTTCACAAACAGT 59.287 55.556 4.92 0.00 34.93 3.55
736 933 2.051345 GGCCGCGTTCACAAACAG 60.051 61.111 4.92 0.00 34.93 3.16
737 934 3.943034 CGGCCGCGTTCACAAACA 61.943 61.111 14.67 0.00 34.93 2.83
738 935 4.676586 CCGGCCGCGTTCACAAAC 62.677 66.667 22.85 0.00 0.00 2.93
798 995 8.933653 TGGATGATGTTAGAATATCTACAACCA 58.066 33.333 0.00 0.00 0.00 3.67
809 1006 3.711704 ACCGAGGTGGATGATGTTAGAAT 59.288 43.478 0.00 0.00 42.00 2.40
810 1007 3.104512 ACCGAGGTGGATGATGTTAGAA 58.895 45.455 0.00 0.00 42.00 2.10
884 1081 5.062308 CGAACGGAAATCTAAAGTTCTCAGG 59.938 44.000 5.33 0.00 39.05 3.86
910 1266 0.658897 GCCTTCGTTTTTGACCGACA 59.341 50.000 0.00 0.00 31.95 4.35
963 1319 1.010046 TCCTGGAATGAGGGAGGATGT 59.990 52.381 0.00 0.00 33.41 3.06
1129 1485 1.851267 GGGAAGGGGTTGTTGAGGT 59.149 57.895 0.00 0.00 0.00 3.85
1667 2047 2.111999 CTGACAGGACCGGCTTTCCA 62.112 60.000 11.86 0.00 35.33 3.53
1682 2062 0.041386 AGACCCAGTACCTCCCTGAC 59.959 60.000 0.00 0.00 31.38 3.51
1687 2067 1.196012 CAGGAAGACCCAGTACCTCC 58.804 60.000 0.00 0.00 37.41 4.30
1866 2246 3.378512 TGCTCATGTTCCTATGGACTCT 58.621 45.455 0.00 0.00 0.00 3.24
1879 2259 4.002316 GAGCTTCTTCTTCTTGCTCATGT 58.998 43.478 8.19 0.00 46.41 3.21
2096 2488 3.350163 CCCCTGCCAATCCCCTGT 61.350 66.667 0.00 0.00 0.00 4.00
2199 2595 7.786030 TGAATTTAGTTTGAAACCCACAATCA 58.214 30.769 4.14 0.82 0.00 2.57
2222 2618 9.899661 AGGTAAAAACATAGTACTGCATATTGA 57.100 29.630 5.39 0.00 0.00 2.57
2300 2754 7.471657 AAATTGGACGGTTCAAAACAAATAC 57.528 32.000 5.85 0.00 0.00 1.89
2302 2756 9.936759 ATATAAATTGGACGGTTCAAAACAAAT 57.063 25.926 5.85 0.00 0.00 2.32
2332 2787 9.447157 TCAAACTTTTGAATCTTTGACCAAAAT 57.553 25.926 1.81 0.00 43.62 1.82
2333 2788 8.839310 TCAAACTTTTGAATCTTTGACCAAAA 57.161 26.923 1.81 0.00 43.62 2.44
2361 2816 3.569701 TGCCCAAACTCTTGAATCTGAAC 59.430 43.478 0.00 0.00 34.14 3.18
2364 2819 3.760151 TGATGCCCAAACTCTTGAATCTG 59.240 43.478 0.00 0.00 34.14 2.90
2391 2846 5.063944 CACACTAAGTTCCAATCTCAATCCG 59.936 44.000 0.00 0.00 0.00 4.18
2399 2854 2.415512 GCGACCACACTAAGTTCCAATC 59.584 50.000 0.00 0.00 0.00 2.67
2401 2856 1.414919 AGCGACCACACTAAGTTCCAA 59.585 47.619 0.00 0.00 0.00 3.53
2402 2857 1.045407 AGCGACCACACTAAGTTCCA 58.955 50.000 0.00 0.00 0.00 3.53
2404 2859 2.480845 ACAAGCGACCACACTAAGTTC 58.519 47.619 0.00 0.00 0.00 3.01
2405 2860 2.612212 CAACAAGCGACCACACTAAGTT 59.388 45.455 0.00 0.00 0.00 2.66
2406 2861 2.210116 CAACAAGCGACCACACTAAGT 58.790 47.619 0.00 0.00 0.00 2.24
2432 2887 5.527511 TTGTACGTTTCAAGTTCGTTCAA 57.472 34.783 0.00 0.00 40.40 2.69
2471 2926 2.095415 TGAGTCGTTACACTCACCATCG 60.095 50.000 11.54 0.00 46.43 3.84
2486 2941 0.522286 CTGTCGCTAGCTGTGAGTCG 60.522 60.000 13.93 0.00 35.65 4.18
2511 2973 2.908634 CGCAAGACAACTGTGACAATC 58.091 47.619 0.00 0.00 43.02 2.67
2538 3004 2.024176 TGGAGTAGGAGTTCCAAGCA 57.976 50.000 0.28 0.00 40.41 3.91
2556 3022 3.674528 AGTGAGAGAACTGTGGACATG 57.325 47.619 0.00 0.00 0.00 3.21
2627 3093 7.061441 CGAAATACTACGAAAAAGTACTGCAGA 59.939 37.037 23.35 0.48 32.47 4.26
2635 3101 9.286946 CTCATACTCGAAATACTACGAAAAAGT 57.713 33.333 0.00 0.00 38.05 2.66
2636 3102 9.499585 TCTCATACTCGAAATACTACGAAAAAG 57.500 33.333 0.00 0.00 38.05 2.27
2639 3105 7.590322 GCATCTCATACTCGAAATACTACGAAA 59.410 37.037 0.00 0.00 38.05 3.46
2640 3106 7.041303 AGCATCTCATACTCGAAATACTACGAA 60.041 37.037 0.00 0.00 38.05 3.85
2641 3107 6.427242 AGCATCTCATACTCGAAATACTACGA 59.573 38.462 0.00 0.00 37.03 3.43
2642 3108 6.604012 AGCATCTCATACTCGAAATACTACG 58.396 40.000 0.00 0.00 0.00 3.51
2643 3109 8.695284 CAAAGCATCTCATACTCGAAATACTAC 58.305 37.037 0.00 0.00 0.00 2.73
2644 3110 8.414003 ACAAAGCATCTCATACTCGAAATACTA 58.586 33.333 0.00 0.00 0.00 1.82
2645 3111 7.268586 ACAAAGCATCTCATACTCGAAATACT 58.731 34.615 0.00 0.00 0.00 2.12
2667 3133 2.160615 CACGAGTTGAACACCACAACAA 59.839 45.455 12.15 0.00 46.58 2.83
2697 3164 1.376037 GTTTCCTCCCGACCTGCAG 60.376 63.158 6.78 6.78 0.00 4.41
2700 3167 1.192146 TCCAGTTTCCTCCCGACCTG 61.192 60.000 0.00 0.00 0.00 4.00
2845 3313 8.752005 AAAAGAAAATGCATATAGACCTGCTA 57.248 30.769 0.00 0.00 39.16 3.49
2941 3409 2.600792 GCATGGAATCGCTGAATCGTTC 60.601 50.000 0.00 0.00 0.00 3.95
3028 3496 0.733150 CCGTGTAGCTCGTGATCAGA 59.267 55.000 0.00 0.00 0.00 3.27
3213 3681 3.060205 GTCGAGTGTTTCTCAAGTGCTTC 60.060 47.826 0.00 0.00 42.88 3.86
3233 3701 3.134458 CACTTGTTCAGAGTTGGGAGTC 58.866 50.000 0.00 0.00 0.00 3.36
3238 3861 1.003545 CACGCACTTGTTCAGAGTTGG 60.004 52.381 0.00 0.00 0.00 3.77
3239 3862 1.665679 ACACGCACTTGTTCAGAGTTG 59.334 47.619 0.00 0.00 0.00 3.16
3349 4025 0.326238 ATAAGGTCCTTCCAGCCGGA 60.326 55.000 7.61 0.00 40.60 5.14
3467 4149 6.200665 CGATCACAAGGAATTTTGAGCAAAAA 59.799 34.615 11.86 0.47 42.71 1.94
3473 4155 4.394300 AGCTCGATCACAAGGAATTTTGAG 59.606 41.667 0.00 0.00 0.00 3.02
3475 4157 4.691860 AGCTCGATCACAAGGAATTTTG 57.308 40.909 0.00 0.00 0.00 2.44
3499 4181 6.476706 CACCCATCTGCACATATACGTATATG 59.523 42.308 36.95 36.95 46.85 1.78
3500 4182 6.379988 TCACCCATCTGCACATATACGTATAT 59.620 38.462 20.08 20.08 0.00 0.86
3501 4183 5.712917 TCACCCATCTGCACATATACGTATA 59.287 40.000 17.24 17.24 0.00 1.47
3604 4291 0.732571 CCGTGTTGGGCATCATGTAC 59.267 55.000 0.00 0.00 0.00 2.90
3862 4549 2.122167 CCCTTCCTCCTCGTCCTCG 61.122 68.421 0.00 0.00 38.55 4.63
3863 4550 2.428085 GCCCTTCCTCCTCGTCCTC 61.428 68.421 0.00 0.00 0.00 3.71
3864 4551 2.364448 GCCCTTCCTCCTCGTCCT 60.364 66.667 0.00 0.00 0.00 3.85
3865 4552 2.364448 AGCCCTTCCTCCTCGTCC 60.364 66.667 0.00 0.00 0.00 4.79
3866 4553 2.726351 CCAGCCCTTCCTCCTCGTC 61.726 68.421 0.00 0.00 0.00 4.20
3867 4554 2.685380 CCAGCCCTTCCTCCTCGT 60.685 66.667 0.00 0.00 0.00 4.18
4114 4807 1.745489 GGCGTTCACCTCCATCCAC 60.745 63.158 0.00 0.00 0.00 4.02
4173 4866 1.302832 TGTGTGTGTGTGTGGTGCA 60.303 52.632 0.00 0.00 0.00 4.57
4174 4867 1.136565 GTGTGTGTGTGTGTGGTGC 59.863 57.895 0.00 0.00 0.00 5.01
4175 4868 0.167908 GTGTGTGTGTGTGTGTGGTG 59.832 55.000 0.00 0.00 0.00 4.17
4176 4869 0.250510 TGTGTGTGTGTGTGTGTGGT 60.251 50.000 0.00 0.00 0.00 4.16
4177 4870 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
4178 4871 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
4179 4872 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4340 5035 3.844211 AGAACTCCCAGGCTTTGTACATA 59.156 43.478 0.00 0.00 0.00 2.29
4368 5063 1.216710 GGACCTTGACGAGCTGGAG 59.783 63.158 1.44 0.00 0.00 3.86
4548 5244 1.267121 AGGAACTGCTGGTACGTCAT 58.733 50.000 0.00 0.00 37.18 3.06
4571 5267 3.461773 ACCAGCATCTCCGTCCCG 61.462 66.667 0.00 0.00 0.00 5.14
4772 5468 2.280524 CTCACAAACACGGCCGGA 60.281 61.111 31.76 14.04 0.00 5.14
4898 5594 4.573201 TGACTTTTCCACTTTCCAGTTACG 59.427 41.667 0.00 0.00 0.00 3.18
4901 5597 5.682212 GCAATGACTTTTCCACTTTCCAGTT 60.682 40.000 0.00 0.00 0.00 3.16
4939 5636 2.742053 GCTCGAATGAAACTTGCCACTA 59.258 45.455 0.00 0.00 0.00 2.74
4956 5653 0.942962 GGGATTTGCTCTCATGCTCG 59.057 55.000 0.00 0.00 0.00 5.03
5066 5768 5.348724 GGATATGTCGTTAGGTATGCATGTG 59.651 44.000 10.16 0.00 0.00 3.21
5094 5796 1.597663 CGTGTCCATTTTAGGATCCGC 59.402 52.381 5.98 0.00 40.42 5.54
5129 5831 2.264480 CGGACCCATCTGTTCGCA 59.736 61.111 0.00 0.00 29.13 5.10
5156 5858 1.131638 TGGATGACCAGCTCCCATAC 58.868 55.000 0.00 0.00 41.77 2.39
5200 5911 4.436317 CGTTCGTTCCTTTTGTTCAAGTCA 60.436 41.667 0.00 0.00 0.00 3.41
5203 5914 4.011058 ACGTTCGTTCCTTTTGTTCAAG 57.989 40.909 0.00 0.00 0.00 3.02
5216 5927 1.070443 CGGTTTGCATGTACGTTCGTT 60.070 47.619 2.62 0.00 0.00 3.85
5308 6019 7.808856 GGTCATTTAGACTAGGTTAGAATAGCG 59.191 40.741 0.00 0.00 46.72 4.26
5350 6061 0.988832 ACATGTCGTGGGTAATGGGT 59.011 50.000 0.00 0.00 0.00 4.51
5354 6065 2.838202 AGGAAGACATGTCGTGGGTAAT 59.162 45.455 19.32 0.00 34.09 1.89
5357 6068 0.608640 GAGGAAGACATGTCGTGGGT 59.391 55.000 19.32 4.82 34.09 4.51
5450 6161 3.135994 GTTTGCCTGGAGTTTCGTAGAA 58.864 45.455 0.00 0.00 45.90 2.10
5454 6165 1.134220 TGAGTTTGCCTGGAGTTTCGT 60.134 47.619 0.00 0.00 0.00 3.85
5459 6170 1.071471 CGGTGAGTTTGCCTGGAGT 59.929 57.895 0.00 0.00 0.00 3.85
5585 6299 0.593008 CTCACCGTCAACGTCGTTCA 60.593 55.000 7.86 0.00 37.74 3.18
5587 6301 1.299620 CCTCACCGTCAACGTCGTT 60.300 57.895 4.40 4.40 37.74 3.85
5590 6304 1.728426 CGACCTCACCGTCAACGTC 60.728 63.158 1.48 0.00 37.74 4.34
5591 6305 2.188829 TCGACCTCACCGTCAACGT 61.189 57.895 1.48 0.00 37.74 3.99
5601 6315 4.361971 AGCTCCCCGTCGACCTCA 62.362 66.667 10.58 0.00 0.00 3.86
5631 6345 1.208293 AGAGGAATTTGAGGCGAGACC 59.792 52.381 0.00 0.00 39.61 3.85
5658 6373 5.067413 ACACTCTATTTATGGACATCGACGT 59.933 40.000 0.00 0.00 0.00 4.34
5716 6431 0.109412 GTGCAACCTCATCAGCAAGC 60.109 55.000 0.00 0.00 38.91 4.01
5751 6466 7.603784 CACGGATCATATTGTATTGGATCTTCA 59.396 37.037 0.00 0.00 35.76 3.02
5775 6490 3.985925 CGTAACTTGAGTTGTAGACCCAC 59.014 47.826 6.64 0.00 38.90 4.61
5778 6493 3.910648 AGCGTAACTTGAGTTGTAGACC 58.089 45.455 6.64 0.00 38.90 3.85
5805 6520 0.679505 TCCTTTCAGGGTCACGTCTG 59.320 55.000 0.00 0.00 35.59 3.51
5856 6571 3.378742 TGAGCATCTAAGAGTTCCTCGTC 59.621 47.826 0.00 0.00 33.42 4.20
5866 6581 7.279536 GTGATTTGTTCATCTGAGCATCTAAGA 59.720 37.037 0.00 0.00 36.54 2.10
5869 6584 6.647229 AGTGATTTGTTCATCTGAGCATCTA 58.353 36.000 0.00 0.00 36.54 1.98
5881 6596 5.356426 TCTTGTCTTCGAGTGATTTGTTCA 58.644 37.500 0.00 0.00 0.00 3.18
5884 6599 5.601662 TCTTCTTGTCTTCGAGTGATTTGT 58.398 37.500 0.00 0.00 0.00 2.83
5901 6616 0.959553 TCGTGCTCGTTCCTCTTCTT 59.040 50.000 8.17 0.00 38.33 2.52
5931 6646 2.361119 TCTATCAACTATGGCGACGCTT 59.639 45.455 20.77 10.30 0.00 4.68
5934 6649 2.287608 TGCTCTATCAACTATGGCGACG 60.288 50.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.