Multiple sequence alignment - TraesCS6D01G327800

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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 TraesCS6D01G327800 chr6D 100.000 3348 0 0 1 3348 432894608 432897955 0.000000e+00 6183.0
1 TraesCS6D01G327800 chr6D 100.000 34 0 0 3575 3608 432898182 432898215 3.010000e-06 63.9
2 TraesCS6D01G327800 chr6A 90.854 2471 161 29 234 2681 579004486 579006914 0.000000e+00 3251.0
3 TraesCS6D01G327800 chr6A 92.870 575 37 2 2117 2691 579009146 579009716 0.000000e+00 832.0
4 TraesCS6D01G327800 chr6A 85.458 612 77 8 2741 3348 579007077 579007680 8.500000e-176 627.0
5 TraesCS6D01G327800 chr6A 85.517 435 52 7 2916 3348 579012816 579013241 9.190000e-121 444.0
6 TraesCS6D01G327800 chr6A 90.446 314 30 0 1816 2129 579008784 579009097 7.210000e-112 414.0
7 TraesCS6D01G327800 chr6A 95.745 188 4 1 29 216 579003151 579003334 2.110000e-77 300.0
8 TraesCS6D01G327800 chr6A 95.349 43 2 0 207 249 579004404 579004446 6.460000e-08 69.4
9 TraesCS6D01G327800 chr6B 90.585 1572 124 16 1134 2691 653072167 653073728 0.000000e+00 2061.0
10 TraesCS6D01G327800 chr6B 89.696 922 60 4 1 895 653057104 653058017 0.000000e+00 1144.0
11 TraesCS6D01G327800 chr6B 94.349 407 23 0 1225 1631 653070395 653070801 3.060000e-175 625.0
12 TraesCS6D01G327800 chr6B 85.835 473 52 9 2811 3281 653097251 653097710 4.190000e-134 488.0
13 TraesCS6D01G327800 chr6B 93.115 305 17 1 923 1227 653058017 653058317 9.190000e-121 444.0
14 TraesCS6D01G327800 chr6B 89.781 137 8 2 1001 1131 653071776 653071912 1.720000e-38 171.0
15 TraesCS6D01G327800 chr6B 78.970 233 44 5 236 464 228662575 228662806 1.730000e-33 154.0
16 TraesCS6D01G327800 chr6B 93.258 89 5 1 816 904 653071635 653071722 2.920000e-26 130.0
17 TraesCS6D01G327800 chr6B 90.323 93 5 2 706 798 653071420 653071508 6.330000e-23 119.0
18 TraesCS6D01G327800 chr4A 81.022 822 140 12 1705 2521 713729368 713730178 1.090000e-179 640.0
19 TraesCS6D01G327800 chr1A 81.346 327 44 12 236 547 554341778 554341454 2.150000e-62 250.0
20 TraesCS6D01G327800 chr5A 80.294 340 53 14 211 546 613566968 613566639 1.000000e-60 244.0
21 TraesCS6D01G327800 chr3D 86.301 219 28 2 248 464 304352914 304353132 1.670000e-58 237.0
22 TraesCS6D01G327800 chr3D 77.429 350 61 12 211 547 9757574 9757230 3.680000e-45 193.0
23 TraesCS6D01G327800 chr3D 81.301 246 38 8 231 470 58109859 58109616 3.680000e-45 193.0
24 TraesCS6D01G327800 chr1D 81.413 269 45 5 282 547 63427442 63427708 7.850000e-52 215.0


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 TraesCS6D01G327800 chr6D 432894608 432898215 3607 False 3123.45 6183 100.000000 1 3608 2 chr6D.!!$F1 3607
1 TraesCS6D01G327800 chr6A 579003151 579013241 10090 False 848.20 3251 90.891286 29 3348 7 chr6A.!!$F1 3319
2 TraesCS6D01G327800 chr6B 653057104 653058317 1213 False 794.00 1144 91.405500 1 1227 2 chr6B.!!$F3 1226
3 TraesCS6D01G327800 chr6B 653070395 653073728 3333 False 621.20 2061 91.659200 706 2691 5 chr6B.!!$F4 1985
4 TraesCS6D01G327800 chr4A 713729368 713730178 810 False 640.00 640 81.022000 1705 2521 1 chr4A.!!$F1 816

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
962 2251 0.26023 CCACTCCTGCTCCTCCTCTA 59.74 60.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 7168 0.671251 GGTGCTCGGACATCTAGGAG 59.329 60.0 0.0 0.0 0.0 3.69 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
56 57 7.355017 CACACCATGAAATCCTAAATGATACG 58.645 38.462 0.00 0.00 0.00 3.06
57 58 7.012327 CACACCATGAAATCCTAAATGATACGT 59.988 37.037 0.00 0.00 0.00 3.57
58 59 8.208224 ACACCATGAAATCCTAAATGATACGTA 58.792 33.333 0.00 0.00 0.00 3.57
190 218 3.937814 AGGACATGATGTTGCGTTCTAA 58.062 40.909 0.00 0.00 0.00 2.10
198 226 8.677300 ACATGATGTTGCGTTCTAATTAAAGAT 58.323 29.630 0.00 0.00 0.00 2.40
239 1346 5.357257 TCTATTGTCGGACTTAGCAAATCC 58.643 41.667 9.88 0.00 0.00 3.01
279 1441 2.867855 GCACCCAGTCAGTGACCGA 61.868 63.158 19.71 0.00 37.42 4.69
313 1475 3.250744 TGAGCCTCTATTTGTTCGTTCG 58.749 45.455 0.00 0.00 0.00 3.95
324 1486 3.306917 TGTTCGTTCGTACATCCACAT 57.693 42.857 0.96 0.00 0.00 3.21
327 1489 4.512198 TGTTCGTTCGTACATCCACATTTT 59.488 37.500 0.96 0.00 0.00 1.82
425 1591 3.296854 ACAAAGAGAAAAAGGTGGTCCC 58.703 45.455 0.00 0.00 0.00 4.46
522 1690 1.752683 ACTGAGAGTTCGCGGATAGT 58.247 50.000 6.13 0.00 0.00 2.12
569 1737 7.732222 AGAGTTCTGATTCCACTCTCTTATT 57.268 36.000 4.33 0.00 43.10 1.40
570 1738 8.830915 AGAGTTCTGATTCCACTCTCTTATTA 57.169 34.615 4.33 0.00 43.10 0.98
641 1809 3.759086 TCCGGATATAGATGCTCTCACAC 59.241 47.826 0.00 0.00 0.00 3.82
703 1871 1.889105 AACGCGGCCATCTAGCATG 60.889 57.895 12.47 0.00 0.00 4.06
763 1931 2.658285 GCTCAAGTTGCAATCACACAG 58.342 47.619 0.59 0.00 0.00 3.66
764 1932 2.291465 GCTCAAGTTGCAATCACACAGA 59.709 45.455 0.59 0.00 0.00 3.41
765 1933 3.851105 GCTCAAGTTGCAATCACACAGAC 60.851 47.826 0.59 0.00 0.00 3.51
766 1934 3.277715 TCAAGTTGCAATCACACAGACA 58.722 40.909 0.59 0.00 0.00 3.41
767 1935 3.313249 TCAAGTTGCAATCACACAGACAG 59.687 43.478 0.59 0.00 0.00 3.51
772 1940 2.613595 TGCAATCACACAGACAGAACAC 59.386 45.455 0.00 0.00 0.00 3.32
962 2251 0.260230 CCACTCCTGCTCCTCCTCTA 59.740 60.000 0.00 0.00 0.00 2.43
963 2252 1.133199 CCACTCCTGCTCCTCCTCTAT 60.133 57.143 0.00 0.00 0.00 1.98
964 2253 2.109128 CCACTCCTGCTCCTCCTCTATA 59.891 54.545 0.00 0.00 0.00 1.31
1034 2330 2.857186 TGCTTAGTGGCAGTCATGAA 57.143 45.000 0.00 0.00 37.29 2.57
1119 2417 4.586841 AGGCTTCAGGTCTCATACTGTATC 59.413 45.833 0.00 0.00 36.17 2.24
1135 2685 9.210329 CATACTGTATCTCTTCTCACGTACTAT 57.790 37.037 0.00 0.00 0.00 2.12
1146 2696 4.212847 TCTCACGTACTATTATCTGCCGTC 59.787 45.833 0.00 0.00 0.00 4.79
1186 2736 1.897133 TGGATTCAGCTGCAATTGCTT 59.103 42.857 29.37 13.50 42.66 3.91
1387 2940 3.259374 GGTCAGTCACCATCTTGAGAAGA 59.741 47.826 0.00 0.00 45.98 2.87
1397 2950 0.250234 CTTGAGAAGATCGGTGGCCA 59.750 55.000 0.00 0.00 0.00 5.36
1410 2963 4.496336 GGCCATCCCGCTGAGCTT 62.496 66.667 1.78 0.00 0.00 3.74
1435 2988 8.690203 TCAGTTCTTTCTCAATGATTTACCAA 57.310 30.769 0.00 0.00 0.00 3.67
1437 2990 7.540055 CAGTTCTTTCTCAATGATTTACCAAGC 59.460 37.037 0.00 0.00 0.00 4.01
1502 3058 1.407618 CTCGATTGGTATGGGTCGTCA 59.592 52.381 0.00 0.00 35.71 4.35
1534 3090 5.028549 GGAGATACCTGCTTTCTTCATCA 57.971 43.478 0.00 0.00 35.41 3.07
1540 3096 0.960364 TGCTTTCTTCATCACCGGGC 60.960 55.000 6.32 0.00 0.00 6.13
1666 3228 6.751514 ACACACGGCTTATTCATATTTTGA 57.248 33.333 0.00 0.00 0.00 2.69
1773 3339 1.055849 TGGAGCCAAGTTGACAGCTA 58.944 50.000 3.87 0.00 35.23 3.32
1785 3351 8.299570 CCAAGTTGACAGCTAAAAATAATGTCT 58.700 33.333 3.87 0.00 40.67 3.41
1848 3415 2.485479 GCAGCTTCCCGATGGATTAGAA 60.485 50.000 0.00 0.00 41.40 2.10
1860 3427 5.220931 CGATGGATTAGAAGGCAAGAAAAGG 60.221 44.000 0.00 0.00 0.00 3.11
1869 3436 1.401905 GGCAAGAAAAGGCCGTATCTG 59.598 52.381 7.81 0.00 40.93 2.90
1951 3518 2.157738 AGCAGTTTCAGAAGGACATGC 58.842 47.619 0.00 0.00 0.00 4.06
1972 3539 2.954684 TTGTTCCTCCGGCTGCGAT 61.955 57.895 0.00 0.00 0.00 4.58
1984 3551 3.579709 CGGCTGCGATATGAAGAACTAT 58.420 45.455 0.00 0.00 0.00 2.12
2034 3601 0.539986 TAGGGAGGAAACATGGCGAC 59.460 55.000 0.00 0.00 0.00 5.19
2082 3649 2.574399 GGTCTGCTCTCACGGTCC 59.426 66.667 0.00 0.00 0.00 4.46
2125 3692 6.150396 AGGTACGCAAGGATATAGCATATC 57.850 41.667 7.31 7.31 46.39 1.63
2145 3714 7.880195 GCATATCTGTGGTAATTAACTCAGGAT 59.120 37.037 24.96 19.61 33.83 3.24
2148 3717 6.338146 TCTGTGGTAATTAACTCAGGATTCG 58.662 40.000 24.96 6.78 33.83 3.34
2151 3720 7.335627 TGTGGTAATTAACTCAGGATTCGAAT 58.664 34.615 11.20 11.20 0.00 3.34
2267 3836 1.716581 GAAGTCAAAGCAGTCGTCGAG 59.283 52.381 0.00 0.00 0.00 4.04
2448 4017 2.488355 GCGAATCCGTCCTCGACA 59.512 61.111 1.94 0.00 37.23 4.35
2477 4046 7.199766 TCTTCAAGAAATTTGCATACAACGTT 58.800 30.769 0.00 0.00 34.87 3.99
2522 4091 4.084287 AGACCAAGTACTCCGTCATTACA 58.916 43.478 19.17 0.00 0.00 2.41
2556 6918 5.533903 ACAAGGATTTGAGGCATATGTGATC 59.466 40.000 4.29 1.18 37.73 2.92
2591 6953 9.494271 TTTGCTTGCAATTTATGTATTTACCAA 57.506 25.926 8.93 0.00 0.00 3.67
2601 6963 9.762381 ATTTATGTATTTACCAACTCCCTTGAA 57.238 29.630 0.00 0.00 30.42 2.69
2647 7009 1.518572 GCATCTACGTGGACACCCG 60.519 63.158 2.80 0.00 34.29 5.28
2671 7034 6.814644 CGGACATGTACTTCCACAACTAAATA 59.185 38.462 6.49 0.00 30.84 1.40
2709 7164 6.578163 TGGATCCGTTTAAAGGTTTAAAGG 57.422 37.500 7.39 15.79 41.66 3.11
2713 7168 7.596248 GGATCCGTTTAAAGGTTTAAAGGTTTC 59.404 37.037 18.97 15.61 42.44 2.78
2735 7190 2.076622 CTAGATGTCCGAGCACCCCG 62.077 65.000 0.00 0.00 0.00 5.73
2736 7191 2.849096 TAGATGTCCGAGCACCCCGT 62.849 60.000 0.00 0.00 0.00 5.28
2737 7192 3.310860 GATGTCCGAGCACCCCGTT 62.311 63.158 0.00 0.00 0.00 4.44
2738 7193 3.605749 ATGTCCGAGCACCCCGTTG 62.606 63.158 0.00 0.00 0.00 4.10
2740 7195 3.691342 TCCGAGCACCCCGTTGAG 61.691 66.667 0.00 0.00 0.00 3.02
2741 7196 3.691342 CCGAGCACCCCGTTGAGA 61.691 66.667 0.00 0.00 0.00 3.27
2742 7197 2.125912 CGAGCACCCCGTTGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
2744 7209 2.203788 AGCACCCCGTTGAGAGGA 60.204 61.111 0.00 0.00 0.00 3.71
2755 7220 1.045350 TTGAGAGGAGGAGGCGGATG 61.045 60.000 0.00 0.00 0.00 3.51
2768 7233 0.740149 GCGGATGCCACAAATGATGA 59.260 50.000 0.00 0.00 33.98 2.92
2771 7236 3.192001 GCGGATGCCACAAATGATGATAT 59.808 43.478 0.00 0.00 33.98 1.63
2784 7249 8.153550 ACAAATGATGATATACTTCTCTCCCAC 58.846 37.037 0.00 0.00 0.00 4.61
2810 7275 1.004918 GTGAGGTCACGGAGGTTGG 60.005 63.158 0.00 0.00 37.10 3.77
2811 7276 1.152419 TGAGGTCACGGAGGTTGGA 60.152 57.895 0.00 0.00 0.00 3.53
2813 7278 0.108138 GAGGTCACGGAGGTTGGATG 60.108 60.000 0.00 0.00 0.00 3.51
2815 7280 1.078426 GTCACGGAGGTTGGATGGG 60.078 63.158 0.00 0.00 0.00 4.00
2816 7281 2.272146 CACGGAGGTTGGATGGGG 59.728 66.667 0.00 0.00 0.00 4.96
2831 7296 0.478072 TGGGGTGAAGCAAGACATGT 59.522 50.000 0.00 0.00 0.00 3.21
2832 7297 0.883833 GGGGTGAAGCAAGACATGTG 59.116 55.000 1.15 0.00 0.00 3.21
2833 7298 1.609208 GGGTGAAGCAAGACATGTGT 58.391 50.000 1.15 0.00 0.00 3.72
2835 7300 1.537202 GGTGAAGCAAGACATGTGTCC 59.463 52.381 1.15 0.00 45.85 4.02
2836 7301 2.221169 GTGAAGCAAGACATGTGTCCA 58.779 47.619 1.15 0.00 45.85 4.02
2845 7310 5.692814 CAAGACATGTGTCCAGTATTTGTG 58.307 41.667 1.15 0.00 45.85 3.33
2849 7314 6.014584 AGACATGTGTCCAGTATTTGTGACTA 60.015 38.462 1.15 0.00 45.85 2.59
2926 10165 3.476552 CACAAGAAGGCTAAGGTCACAA 58.523 45.455 0.00 0.00 0.00 3.33
2948 10187 2.591311 CCACACGGGTTTCGACACG 61.591 63.158 0.00 0.00 42.43 4.49
2960 10199 2.442212 TCGACACGAAAGGCATGTTA 57.558 45.000 0.00 0.00 31.06 2.41
2961 10200 2.063266 TCGACACGAAAGGCATGTTAC 58.937 47.619 0.00 0.00 31.06 2.50
2964 10203 2.477375 GACACGAAAGGCATGTTACGAA 59.523 45.455 0.00 0.00 0.00 3.85
2968 10207 5.163893 ACACGAAAGGCATGTTACGAAATAG 60.164 40.000 0.00 0.00 0.00 1.73
2991 10231 7.366847 AGCATAGATCTTTTAGACTTGGCTA 57.633 36.000 0.00 0.00 0.00 3.93
2992 10232 7.796054 AGCATAGATCTTTTAGACTTGGCTAA 58.204 34.615 0.00 0.00 0.00 3.09
3006 10246 8.142994 AGACTTGGCTAAACATAAATATGTCG 57.857 34.615 6.53 1.16 45.55 4.35
3007 10247 7.985184 AGACTTGGCTAAACATAAATATGTCGA 59.015 33.333 6.53 0.00 45.55 4.20
3013 10253 9.760660 GGCTAAACATAAATATGTCGATGATTC 57.239 33.333 6.53 0.00 45.55 2.52
3018 10258 9.546428 AACATAAATATGTCGATGATTCTGTGA 57.454 29.630 6.53 0.00 45.55 3.58
3020 10260 8.654215 CATAAATATGTCGATGATTCTGTGAGG 58.346 37.037 0.00 0.00 0.00 3.86
3027 10267 3.620374 CGATGATTCTGTGAGGGAACTTG 59.380 47.826 0.00 0.00 44.43 3.16
3028 10268 4.583871 GATGATTCTGTGAGGGAACTTGT 58.416 43.478 0.00 0.00 44.43 3.16
3042 10282 5.245977 AGGGAACTTGTGTTGGATTTTATGG 59.754 40.000 0.00 0.00 37.44 2.74
3043 10283 4.929211 GGAACTTGTGTTGGATTTTATGGC 59.071 41.667 0.00 0.00 36.39 4.40
3045 10285 3.823873 ACTTGTGTTGGATTTTATGGCGA 59.176 39.130 0.00 0.00 0.00 5.54
3063 10303 2.165167 CGATTTCCATGGCTGGCATAT 58.835 47.619 16.84 6.64 42.80 1.78
3064 10304 3.346315 CGATTTCCATGGCTGGCATATA 58.654 45.455 16.84 5.03 42.80 0.86
3065 10305 3.949754 CGATTTCCATGGCTGGCATATAT 59.050 43.478 16.84 7.64 42.80 0.86
3071 10311 3.054582 CCATGGCTGGCATATATGAGACT 60.055 47.826 16.84 0.00 35.23 3.24
3077 10317 4.934602 GCTGGCATATATGAGACTTCCTTC 59.065 45.833 17.10 0.40 0.00 3.46
3095 10335 3.551863 CCTTCAGTATGTCCTCGAGCATC 60.552 52.174 6.99 0.00 37.40 3.91
3099 10339 0.952280 TATGTCCTCGAGCATCCGTC 59.048 55.000 6.99 0.00 0.00 4.79
3101 10341 2.124860 TCCTCGAGCATCCGTCGA 60.125 61.111 6.99 0.00 43.97 4.20
3110 10350 1.683790 GCATCCGTCGAGTGGTTTCG 61.684 60.000 0.00 0.00 41.79 3.46
3117 10357 2.693797 TCGAGTGGTTTCGACTACAC 57.306 50.000 4.81 4.81 44.00 2.90
3156 10396 0.035056 CGTGGAAGGGCTGGAAGAAT 60.035 55.000 0.00 0.00 34.07 2.40
3160 10400 2.291153 TGGAAGGGCTGGAAGAATCTTG 60.291 50.000 0.00 0.00 34.07 3.02
3174 10414 6.038050 GGAAGAATCTTGCTTGGAATACAGAG 59.962 42.308 7.27 0.00 0.00 3.35
3175 10415 5.435291 AGAATCTTGCTTGGAATACAGAGG 58.565 41.667 0.00 0.00 0.00 3.69
3177 10417 4.908601 TCTTGCTTGGAATACAGAGGAA 57.091 40.909 0.00 0.00 0.00 3.36
3185 10425 3.118261 TGGAATACAGAGGAAGACCATGC 60.118 47.826 0.00 0.00 38.94 4.06
3187 10427 4.445448 GGAATACAGAGGAAGACCATGCAT 60.445 45.833 0.00 0.00 38.94 3.96
3188 10428 2.414994 ACAGAGGAAGACCATGCATG 57.585 50.000 20.19 20.19 38.94 4.06
3205 10445 4.870363 TGCATGGACTTGTTAGCTTTTTC 58.130 39.130 0.00 0.00 0.00 2.29
3206 10446 3.914364 GCATGGACTTGTTAGCTTTTTCG 59.086 43.478 0.00 0.00 0.00 3.46
3211 10451 5.529430 TGGACTTGTTAGCTTTTTCGATTGA 59.471 36.000 0.00 0.00 0.00 2.57
3220 10460 9.128107 GTTAGCTTTTTCGATTGATGAATTTCA 57.872 29.630 0.75 0.75 0.00 2.69
3221 10461 9.859427 TTAGCTTTTTCGATTGATGAATTTCAT 57.141 25.926 11.64 11.64 40.34 2.57
3248 10488 7.556844 TCAAATCTAACCTTCGAAATAGAGCT 58.443 34.615 15.79 0.00 0.00 4.09
3254 10494 8.308931 TCTAACCTTCGAAATAGAGCTTACAAA 58.691 33.333 0.00 0.00 0.00 2.83
3284 10524 1.741770 CCTGTTGGCAGTCTACGGC 60.742 63.158 0.00 0.00 41.02 5.68
3310 10550 5.601662 TGCCTAGAACGAGAATAAATCTGG 58.398 41.667 0.00 0.00 38.96 3.86
3318 10558 7.492994 AGAACGAGAATAAATCTGGCTTTCTAC 59.507 37.037 0.00 0.00 38.96 2.59
3320 10560 5.977725 CGAGAATAAATCTGGCTTTCTACGA 59.022 40.000 0.00 0.00 38.96 3.43
3595 10835 4.061570 GTACCAACGAGAAAAATGACGG 57.938 45.455 0.00 0.00 0.00 4.79
3596 10836 1.265905 ACCAACGAGAAAAATGACGGC 59.734 47.619 0.00 0.00 0.00 5.68
3597 10837 1.401018 CCAACGAGAAAAATGACGGCC 60.401 52.381 0.00 0.00 0.00 6.13
3598 10838 0.515564 AACGAGAAAAATGACGGCCG 59.484 50.000 26.86 26.86 0.00 6.13
3599 10839 1.226018 CGAGAAAAATGACGGCCGC 60.226 57.895 28.58 19.01 0.00 6.53
3600 10840 1.635663 CGAGAAAAATGACGGCCGCT 61.636 55.000 28.58 13.18 0.00 5.52
3601 10841 0.521735 GAGAAAAATGACGGCCGCTT 59.478 50.000 28.58 14.08 0.00 4.68
3602 10842 0.958822 AGAAAAATGACGGCCGCTTT 59.041 45.000 28.58 19.47 0.00 3.51
3603 10843 1.059942 GAAAAATGACGGCCGCTTTG 58.940 50.000 28.58 0.00 0.00 2.77
3604 10844 0.671251 AAAAATGACGGCCGCTTTGA 59.329 45.000 28.58 0.00 0.00 2.69
3605 10845 0.039527 AAAATGACGGCCGCTTTGAC 60.040 50.000 28.58 10.44 0.00 3.18
3606 10846 1.169661 AAATGACGGCCGCTTTGACA 61.170 50.000 28.58 15.88 0.00 3.58
3607 10847 1.852067 AATGACGGCCGCTTTGACAC 61.852 55.000 28.58 7.12 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.526846 CCCTTCTCATTTCTCAGCTCAATAC 59.473 44.000 0.00 0.00 0.00 1.89
57 58 5.678583 CCCTTCTCATTTCTCAGCTCAATA 58.321 41.667 0.00 0.00 0.00 1.90
58 59 4.525024 CCCTTCTCATTTCTCAGCTCAAT 58.475 43.478 0.00 0.00 0.00 2.57
190 218 5.747248 GCTCTGACCAGGCCATATCTTTAAT 60.747 44.000 5.01 0.00 0.00 1.40
198 226 0.761187 GATGCTCTGACCAGGCCATA 59.239 55.000 5.01 0.00 0.00 2.74
239 1346 2.892334 CGCGGGCATTTATGGGTCG 61.892 63.158 0.00 0.00 0.00 4.79
279 1441 1.940613 GAGGCTCAAAACAGACACGTT 59.059 47.619 10.25 0.00 0.00 3.99
327 1489 9.706691 GACCGGACATATGAGATAGAAAATAAA 57.293 33.333 9.46 0.00 0.00 1.40
465 1631 1.005630 AGGATATGAAGGCTCGCGC 60.006 57.895 0.00 0.00 0.00 6.86
474 1640 9.093458 TGAGCATAAATGTAGAGAGGATATGAA 57.907 33.333 0.00 0.00 0.00 2.57
522 1690 7.888424 TCTCATATCATTTTTATACGTCCGGA 58.112 34.615 0.00 0.00 0.00 5.14
534 1702 9.118300 GTGGAATCAGAACTCTCATATCATTTT 57.882 33.333 0.00 0.00 0.00 1.82
569 1737 0.251922 AGTGCCCGGTTAGTGACCTA 60.252 55.000 0.00 0.00 46.92 3.08
570 1738 1.125711 AAGTGCCCGGTTAGTGACCT 61.126 55.000 0.00 0.00 46.92 3.85
586 1754 1.663702 CTCAAACGTCCGCGGAAGT 60.664 57.895 36.13 36.13 43.45 3.01
692 1860 2.818432 GGATGAAAGCCATGCTAGATGG 59.182 50.000 13.78 13.78 46.15 3.51
703 1871 1.087501 GGACAGAACGGATGAAAGCC 58.912 55.000 0.00 0.00 40.71 4.35
763 1931 2.143925 CCTTTTCCCTCGTGTTCTGTC 58.856 52.381 0.00 0.00 0.00 3.51
764 1932 1.202770 CCCTTTTCCCTCGTGTTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
765 1933 1.523758 CCCTTTTCCCTCGTGTTCTG 58.476 55.000 0.00 0.00 0.00 3.02
766 1934 0.400594 CCCCTTTTCCCTCGTGTTCT 59.599 55.000 0.00 0.00 0.00 3.01
767 1935 0.399075 TCCCCTTTTCCCTCGTGTTC 59.601 55.000 0.00 0.00 0.00 3.18
772 1940 1.908483 CCTCTCCCCTTTTCCCTCG 59.092 63.158 0.00 0.00 0.00 4.63
964 2253 8.690884 CCGATCAGAGGACAGTTGAATATATAT 58.309 37.037 0.00 0.00 0.00 0.86
1034 2330 4.263374 CCATATGGAAGTCATGCTCCATCT 60.263 45.833 17.49 12.48 41.56 2.90
1119 2417 6.375377 GGCAGATAATAGTACGTGAGAAGAG 58.625 44.000 0.00 0.00 0.00 2.85
1146 2696 3.488047 CCAGCAATCAAATTAGGACTGCG 60.488 47.826 7.53 4.19 33.61 5.18
1186 2736 8.720537 AGATAAACGGGAAGGGAAATCTTTATA 58.279 33.333 0.00 0.00 0.00 0.98
1250 2803 4.436998 CTCGTGTCACGGCCTCCC 62.437 72.222 24.33 0.00 42.81 4.30
1276 2829 2.507058 TCATTGTTGGATGGAGGAGAGG 59.493 50.000 0.00 0.00 0.00 3.69
1328 2881 0.733223 GACGAAGAGGAGCGTGTTCC 60.733 60.000 0.00 0.00 41.34 3.62
1410 2963 8.690203 TTGGTAAATCATTGAGAAAGAACTGA 57.310 30.769 0.00 0.00 0.00 3.41
1435 2988 0.884704 ACGCGGTTGAAGTCATTGCT 60.885 50.000 12.47 0.00 0.00 3.91
1437 2990 1.148310 AGACGCGGTTGAAGTCATTG 58.852 50.000 12.47 0.00 37.36 2.82
1502 3058 2.957312 GCAGGTATCTCCTCTCCCTTGT 60.957 54.545 0.00 0.00 46.24 3.16
1540 3096 0.382515 GTGTAGTAGGAGCTCGGCAG 59.617 60.000 7.83 0.00 0.00 4.85
1666 3228 3.192212 GCAAGCAGTCCTTTTTCTAGCAT 59.808 43.478 0.00 0.00 0.00 3.79
1751 3316 1.612726 GCTGTCAACTTGGCTCCATCT 60.613 52.381 0.00 0.00 0.00 2.90
1848 3415 1.282157 AGATACGGCCTTTTCTTGCCT 59.718 47.619 0.00 0.00 45.71 4.75
1860 3427 2.288961 TTCCTTCGTTCAGATACGGC 57.711 50.000 0.00 0.00 41.67 5.68
1863 3430 5.004535 GTCGATGTTTCCTTCGTTCAGATAC 59.995 44.000 0.00 0.00 38.83 2.24
1869 3436 4.394795 CAATGTCGATGTTTCCTTCGTTC 58.605 43.478 0.00 0.00 38.83 3.95
1972 3539 5.880332 GTCCACCTGCAAATAGTTCTTCATA 59.120 40.000 0.00 0.00 0.00 2.15
1984 3551 2.439409 CATCATCTGTCCACCTGCAAA 58.561 47.619 0.00 0.00 0.00 3.68
2034 3601 1.139095 GAGACCTCCGTTGTAGGCG 59.861 63.158 0.00 0.00 37.67 5.52
2067 3634 2.282251 ACGGACCGTGAGAGCAGA 60.282 61.111 21.02 0.00 39.18 4.26
2082 3649 1.792367 TCGTCAACAAGAGATTGCACG 59.208 47.619 0.00 0.00 34.65 5.34
2125 3692 6.338146 TCGAATCCTGAGTTAATTACCACAG 58.662 40.000 1.27 1.27 33.96 3.66
2137 3706 3.055530 AGCAACAGATTCGAATCCTGAGT 60.056 43.478 29.82 21.05 36.04 3.41
2138 3707 3.529533 AGCAACAGATTCGAATCCTGAG 58.470 45.455 29.82 22.53 36.04 3.35
2176 3745 2.187946 CCACGAGGCCCTGTCATC 59.812 66.667 0.00 0.00 0.00 2.92
2178 3747 2.997315 CTCCACGAGGCCCTGTCA 60.997 66.667 0.00 0.00 33.74 3.58
2267 3836 2.018324 GCGAAACTGCTGGCTTTGC 61.018 57.895 0.00 0.30 0.00 3.68
2448 4017 6.985117 TGTATGCAAATTTCTTGAAGAGCTT 58.015 32.000 0.00 2.14 0.00 3.74
2477 4046 1.556373 CCATCTCCAGGTGCACCTCA 61.556 60.000 35.79 23.04 46.65 3.86
2494 4063 2.168496 CGGAGTACTTGGTCTTCTCCA 58.832 52.381 0.00 0.00 43.17 3.86
2522 4091 4.755123 CCTCAAATCCTTGTTAACGACAGT 59.245 41.667 0.26 0.00 39.94 3.55
2556 6918 4.455917 AATTGCAAGCAAACATGAAACG 57.544 36.364 11.89 0.00 39.55 3.60
2647 7009 8.732746 ATATTTAGTTGTGGAAGTACATGTCC 57.267 34.615 0.00 0.00 0.00 4.02
2691 7054 6.919662 GGAGAAACCTTTAAACCTTTAAACGG 59.080 38.462 12.48 12.48 37.61 4.44
2709 7164 2.427453 TGCTCGGACATCTAGGAGAAAC 59.573 50.000 0.00 0.00 0.00 2.78
2713 7168 0.671251 GGTGCTCGGACATCTAGGAG 59.329 60.000 0.00 0.00 0.00 3.69
2719 7174 3.310860 AACGGGGTGCTCGGACATC 62.311 63.158 0.00 0.00 0.00 3.06
2725 7180 2.125912 CTCTCAACGGGGTGCTCG 60.126 66.667 0.00 0.00 0.00 5.03
2735 7190 1.045911 ATCCGCCTCCTCCTCTCAAC 61.046 60.000 0.00 0.00 0.00 3.18
2736 7191 1.045350 CATCCGCCTCCTCCTCTCAA 61.045 60.000 0.00 0.00 0.00 3.02
2737 7192 1.456518 CATCCGCCTCCTCCTCTCA 60.457 63.158 0.00 0.00 0.00 3.27
2738 7193 2.866726 GCATCCGCCTCCTCCTCTC 61.867 68.421 0.00 0.00 0.00 3.20
2755 7220 7.118971 GGAGAGAAGTATATCATCATTTGTGGC 59.881 40.741 0.00 0.00 0.00 5.01
2757 7222 8.152898 TGGGAGAGAAGTATATCATCATTTGTG 58.847 37.037 0.00 0.00 0.00 3.33
2758 7223 8.153550 GTGGGAGAGAAGTATATCATCATTTGT 58.846 37.037 0.00 0.00 0.00 2.83
2761 7226 8.503428 AAGTGGGAGAGAAGTATATCATCATT 57.497 34.615 0.00 0.00 0.00 2.57
2768 7233 7.070074 CACCAACTAAGTGGGAGAGAAGTATAT 59.930 40.741 1.14 0.00 43.56 0.86
2771 7236 4.527038 CACCAACTAAGTGGGAGAGAAGTA 59.473 45.833 1.14 0.00 43.56 2.24
2784 7249 1.616865 TCCGTGACCTCACCAACTAAG 59.383 52.381 0.00 0.00 43.66 2.18
2810 7275 1.747355 CATGTCTTGCTTCACCCCATC 59.253 52.381 0.00 0.00 0.00 3.51
2811 7276 1.076024 ACATGTCTTGCTTCACCCCAT 59.924 47.619 0.00 0.00 0.00 4.00
2813 7278 0.883833 CACATGTCTTGCTTCACCCC 59.116 55.000 0.00 0.00 0.00 4.95
2815 7280 1.537202 GGACACATGTCTTGCTTCACC 59.463 52.381 11.63 0.00 44.20 4.02
2816 7281 2.221169 TGGACACATGTCTTGCTTCAC 58.779 47.619 11.63 0.00 44.20 3.18
2855 7320 9.878599 AATGAAACTTAGATTTACACAAAGACG 57.121 29.630 0.00 0.00 0.00 4.18
2902 7368 2.040278 TGACCTTAGCCTTCTTGTGCAT 59.960 45.455 0.00 0.00 0.00 3.96
2904 7370 1.807142 GTGACCTTAGCCTTCTTGTGC 59.193 52.381 0.00 0.00 0.00 4.57
2948 10187 5.229921 TGCTATTTCGTAACATGCCTTTC 57.770 39.130 0.00 0.00 0.00 2.62
2964 10203 8.435982 AGCCAAGTCTAAAAGATCTATGCTATT 58.564 33.333 0.00 0.00 0.00 1.73
2968 10207 8.338986 GTTTAGCCAAGTCTAAAAGATCTATGC 58.661 37.037 0.00 0.00 39.43 3.14
2992 10232 9.546428 TCACAGAATCATCGACATATTTATGTT 57.454 29.630 4.79 0.00 46.20 2.71
3000 10240 4.215109 TCCCTCACAGAATCATCGACATA 58.785 43.478 0.00 0.00 0.00 2.29
3006 10246 4.394300 CACAAGTTCCCTCACAGAATCATC 59.606 45.833 0.00 0.00 0.00 2.92
3007 10247 4.202503 ACACAAGTTCCCTCACAGAATCAT 60.203 41.667 0.00 0.00 0.00 2.45
3013 10253 1.949525 CCAACACAAGTTCCCTCACAG 59.050 52.381 0.00 0.00 35.28 3.66
3018 10258 5.245977 CCATAAAATCCAACACAAGTTCCCT 59.754 40.000 0.00 0.00 35.28 4.20
3020 10260 4.929211 GCCATAAAATCCAACACAAGTTCC 59.071 41.667 0.00 0.00 35.28 3.62
3027 10267 4.803613 GGAAATCGCCATAAAATCCAACAC 59.196 41.667 0.00 0.00 0.00 3.32
3028 10268 4.464244 TGGAAATCGCCATAAAATCCAACA 59.536 37.500 0.00 0.00 32.84 3.33
3052 10292 3.008375 GGAAGTCTCATATATGCCAGCCA 59.992 47.826 7.92 0.00 0.00 4.75
3063 10303 6.436027 AGGACATACTGAAGGAAGTCTCATA 58.564 40.000 0.00 0.00 0.00 2.15
3064 10304 5.276440 AGGACATACTGAAGGAAGTCTCAT 58.724 41.667 0.00 0.00 0.00 2.90
3065 10305 4.678256 AGGACATACTGAAGGAAGTCTCA 58.322 43.478 0.00 0.00 0.00 3.27
3071 10311 2.427453 GCTCGAGGACATACTGAAGGAA 59.573 50.000 15.58 0.00 0.00 3.36
3077 10317 1.335415 CGGATGCTCGAGGACATACTG 60.335 57.143 15.58 5.72 0.00 2.74
3099 10339 2.410785 TGTGTAGTCGAAACCACTCG 57.589 50.000 9.96 0.00 40.25 4.18
3101 10341 2.870435 GCCATGTGTAGTCGAAACCACT 60.870 50.000 9.96 0.00 0.00 4.00
3110 10350 3.871594 GGTAGACAATGCCATGTGTAGTC 59.128 47.826 0.00 0.00 30.64 2.59
3117 10357 2.024918 GGCGGTAGACAATGCCATG 58.975 57.895 0.00 0.00 46.76 3.66
3146 10386 2.440409 TCCAAGCAAGATTCTTCCAGC 58.560 47.619 0.00 0.00 0.00 4.85
3147 10387 5.649395 TGTATTCCAAGCAAGATTCTTCCAG 59.351 40.000 0.00 0.00 0.00 3.86
3148 10388 5.569355 TGTATTCCAAGCAAGATTCTTCCA 58.431 37.500 0.00 0.00 0.00 3.53
3156 10396 4.532126 TCTTCCTCTGTATTCCAAGCAAGA 59.468 41.667 0.00 0.00 0.00 3.02
3160 10400 3.055094 TGGTCTTCCTCTGTATTCCAAGC 60.055 47.826 0.00 0.00 34.23 4.01
3185 10425 5.356882 TCGAAAAAGCTAACAAGTCCATG 57.643 39.130 0.00 0.00 0.00 3.66
3187 10427 5.529430 TCAATCGAAAAAGCTAACAAGTCCA 59.471 36.000 0.00 0.00 0.00 4.02
3188 10428 5.997385 TCAATCGAAAAAGCTAACAAGTCC 58.003 37.500 0.00 0.00 0.00 3.85
3189 10429 7.298122 TCATCAATCGAAAAAGCTAACAAGTC 58.702 34.615 0.00 0.00 0.00 3.01
3190 10430 7.202016 TCATCAATCGAAAAAGCTAACAAGT 57.798 32.000 0.00 0.00 0.00 3.16
3193 10433 9.128107 GAAATTCATCAATCGAAAAAGCTAACA 57.872 29.630 0.00 0.00 0.00 2.41
3195 10435 9.859427 ATGAAATTCATCAATCGAAAAAGCTAA 57.141 25.926 2.07 0.00 29.59 3.09
3221 10461 9.477484 GCTCTATTTCGAAGGTTAGATTTGATA 57.523 33.333 12.25 0.00 0.00 2.15
3231 10471 7.923414 ATTTGTAAGCTCTATTTCGAAGGTT 57.077 32.000 0.00 0.59 0.00 3.50
3236 10476 7.386573 TGTGTGAATTTGTAAGCTCTATTTCGA 59.613 33.333 0.00 0.00 0.00 3.71
3248 10488 5.590530 ACAGGCTTTGTGTGAATTTGTAA 57.409 34.783 0.00 0.00 38.99 2.41
3254 10494 1.069049 GCCAACAGGCTTTGTGTGAAT 59.931 47.619 0.00 0.00 45.21 2.57
3284 10524 4.402056 TTTATTCTCGTTCTAGGCAGGG 57.598 45.455 0.00 0.00 0.00 4.45
3288 10528 4.449405 GCCAGATTTATTCTCGTTCTAGGC 59.551 45.833 0.00 0.00 29.93 3.93
3291 10531 7.556844 AGAAAGCCAGATTTATTCTCGTTCTA 58.443 34.615 0.00 0.00 30.54 2.10
3293 10533 6.670077 AGAAAGCCAGATTTATTCTCGTTC 57.330 37.500 0.00 0.00 29.93 3.95
3294 10534 6.255887 CGTAGAAAGCCAGATTTATTCTCGTT 59.744 38.462 0.00 0.00 32.87 3.85
3310 10550 5.642491 AGGTTAACCAATTCTCGTAGAAAGC 59.358 40.000 26.26 0.00 36.73 3.51
3318 10558 5.163754 CCTTTGCTAGGTTAACCAATTCTCG 60.164 44.000 26.26 9.45 39.39 4.04
3320 10560 5.887754 TCCTTTGCTAGGTTAACCAATTCT 58.112 37.500 26.26 7.96 45.03 2.40
3574 10814 3.666111 GCCGTCATTTTTCTCGTTGGTAC 60.666 47.826 0.00 0.00 0.00 3.34
3575 10815 2.481185 GCCGTCATTTTTCTCGTTGGTA 59.519 45.455 0.00 0.00 0.00 3.25
3576 10816 1.265905 GCCGTCATTTTTCTCGTTGGT 59.734 47.619 0.00 0.00 0.00 3.67
3577 10817 1.401018 GGCCGTCATTTTTCTCGTTGG 60.401 52.381 0.00 0.00 0.00 3.77
3578 10818 1.724654 CGGCCGTCATTTTTCTCGTTG 60.725 52.381 19.50 0.00 0.00 4.10
3579 10819 0.515564 CGGCCGTCATTTTTCTCGTT 59.484 50.000 19.50 0.00 0.00 3.85
3580 10820 1.908066 GCGGCCGTCATTTTTCTCGT 61.908 55.000 28.70 0.00 0.00 4.18
3581 10821 1.226018 GCGGCCGTCATTTTTCTCG 60.226 57.895 28.70 0.00 0.00 4.04
3582 10822 0.521735 AAGCGGCCGTCATTTTTCTC 59.478 50.000 28.70 5.38 0.00 2.87
3583 10823 0.958822 AAAGCGGCCGTCATTTTTCT 59.041 45.000 28.70 9.64 0.00 2.52
3584 10824 1.059942 CAAAGCGGCCGTCATTTTTC 58.940 50.000 28.70 7.06 0.00 2.29
3585 10825 0.671251 TCAAAGCGGCCGTCATTTTT 59.329 45.000 28.70 15.98 0.00 1.94
3586 10826 0.039527 GTCAAAGCGGCCGTCATTTT 60.040 50.000 28.70 18.39 0.00 1.82
3587 10827 1.169661 TGTCAAAGCGGCCGTCATTT 61.170 50.000 28.70 21.30 0.00 2.32
3588 10828 1.599518 TGTCAAAGCGGCCGTCATT 60.600 52.632 28.70 16.49 0.00 2.57
3589 10829 2.031919 TGTCAAAGCGGCCGTCAT 59.968 55.556 28.70 10.69 0.00 3.06
3590 10830 2.970324 GTGTCAAAGCGGCCGTCA 60.970 61.111 28.70 13.28 0.00 4.35


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

AutoCloner maintained by Alex Coulton.