Multiple sequence alignment - TraesCS3A01G356800

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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 TraesCS3A01G356800 chr3A 100.000 4129 0 0 1 4129 604567273 604571401 0.000000e+00 7625
1 TraesCS3A01G356800 chr3A 89.234 1737 113 29 1 1722 605051149 605049472 0.000000e+00 2104
2 TraesCS3A01G356800 chr3A 92.378 1207 61 15 1804 2988 605049354 605048157 0.000000e+00 1690
3 TraesCS3A01G356800 chr3A 82.604 983 132 30 291 1257 605051927 605050968 0.000000e+00 832
4 TraesCS3A01G356800 chr3A 84.950 804 98 20 291 1087 605122972 605122185 0.000000e+00 793
5 TraesCS3A01G356800 chr3A 86.688 631 66 8 1304 1934 554943598 554944210 0.000000e+00 684
6 TraesCS3A01G356800 chr3A 81.664 649 94 18 615 1257 605052834 605052205 2.200000e-142 516
7 TraesCS3A01G356800 chr3A 94.898 98 2 3 3424 3520 604691522 604691617 2.570000e-32 150
8 TraesCS3A01G356800 chr3D 90.854 3149 199 33 1 3125 462071127 462074210 0.000000e+00 4137
9 TraesCS3A01G356800 chr3D 90.284 3067 208 33 1 3031 462205945 462202933 0.000000e+00 3930
10 TraesCS3A01G356800 chr3D 91.608 858 48 10 3142 3997 462074193 462075028 0.000000e+00 1164
11 TraesCS3A01G356800 chr3D 85.641 975 119 14 290 1257 462206724 462205764 0.000000e+00 1005
12 TraesCS3A01G356800 chr3D 84.693 993 124 21 272 1257 462070337 462071308 0.000000e+00 966
13 TraesCS3A01G356800 chr3D 90.726 248 22 1 1 247 462206973 462206726 3.080000e-86 329
14 TraesCS3A01G356800 chr3D 92.105 228 18 0 1 228 462069762 462069989 5.150000e-84 322
15 TraesCS3A01G356800 chr3D 82.143 392 38 8 55 445 462051863 462052223 1.440000e-79 307
16 TraesCS3A01G356800 chr3D 80.135 443 60 15 2937 3378 462200657 462201072 5.190000e-79 305
17 TraesCS3A01G356800 chr3D 95.238 84 4 0 4046 4129 462075013 462075096 2.590000e-27 134
18 TraesCS3A01G356800 chr3D 93.333 90 5 1 3424 3513 462201135 462201223 9.310000e-27 132
19 TraesCS3A01G356800 chr3B 91.802 2220 124 22 779 2956 613638057 613640260 0.000000e+00 3038
20 TraesCS3A01G356800 chr3B 87.349 332 39 3 1 330 613637718 613638048 1.080000e-100 377
21 TraesCS3A01G356800 chr3B 88.699 292 28 3 3146 3437 613742313 613742599 6.570000e-93 351
22 TraesCS3A01G356800 chr3B 90.055 181 17 1 3817 3997 613640150 613640329 2.480000e-57 233
23 TraesCS3A01G356800 chr3B 90.265 113 10 1 3424 3536 613742621 613742732 3.330000e-31 147
24 TraesCS3A01G356800 chr4A 85.261 631 69 13 1304 1934 142122244 142122850 2.710000e-176 628
25 TraesCS3A01G356800 chr6A 85.032 628 69 14 1305 1932 409818351 409817749 2.110000e-172 616
26 TraesCS3A01G356800 chr2B 81.193 771 115 24 1913 2683 784848925 784848185 9.880000e-166 593
27 TraesCS3A01G356800 chr2A 84.152 631 63 14 1304 1934 379364824 379365417 9.950000e-161 577
28 TraesCS3A01G356800 chr5A 79.972 704 130 11 1952 2650 631504497 631505194 3.680000e-140 508
29 TraesCS3A01G356800 chr5D 78.884 753 142 16 1943 2688 503049189 503049931 1.030000e-135 494
30 TraesCS3A01G356800 chr5D 89.459 351 35 2 1923 2272 449115024 449115373 3.790000e-120 442
31 TraesCS3A01G356800 chr7D 87.855 387 45 2 1889 2274 401548370 401547985 1.750000e-123 453
32 TraesCS3A01G356800 chr7D 78.947 494 83 13 1189 1672 401548947 401548465 2.400000e-82 316
33 TraesCS3A01G356800 chr7B 87.404 389 47 2 1887 2274 411057615 411057228 2.930000e-121 446
34 TraesCS3A01G356800 chr7B 79.614 363 60 13 2365 2718 411057200 411056843 8.860000e-62 248
35 TraesCS3A01G356800 chr5B 89.174 351 36 2 1923 2272 548817850 548817501 1.760000e-118 436
36 TraesCS3A01G356800 chr5B 89.174 351 36 2 1923 2272 548826276 548825927 1.760000e-118 436
37 TraesCS3A01G356800 chr5B 80.690 290 48 8 2365 2650 98845228 98844943 6.950000e-53 219


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 TraesCS3A01G356800 chr3A 604567273 604571401 4128 False 7625.000000 7625 100.000000 1 4129 1 chr3A.!!$F2 4128
1 TraesCS3A01G356800 chr3A 605048157 605052834 4677 True 1285.500000 2104 86.470000 1 2988 4 chr3A.!!$R2 2987
2 TraesCS3A01G356800 chr3A 605122185 605122972 787 True 793.000000 793 84.950000 291 1087 1 chr3A.!!$R1 796
3 TraesCS3A01G356800 chr3A 554943598 554944210 612 False 684.000000 684 86.688000 1304 1934 1 chr3A.!!$F1 630
4 TraesCS3A01G356800 chr3D 462202933 462206973 4040 True 1754.666667 3930 88.883667 1 3031 3 chr3D.!!$R1 3030
5 TraesCS3A01G356800 chr3D 462069762 462075096 5334 False 1344.600000 4137 90.899600 1 4129 5 chr3D.!!$F2 4128
6 TraesCS3A01G356800 chr3D 462200657 462201223 566 False 218.500000 305 86.734000 2937 3513 2 chr3D.!!$F3 576
7 TraesCS3A01G356800 chr3B 613637718 613640329 2611 False 1216.000000 3038 89.735333 1 3997 3 chr3B.!!$F1 3996
8 TraesCS3A01G356800 chr4A 142122244 142122850 606 False 628.000000 628 85.261000 1304 1934 1 chr4A.!!$F1 630
9 TraesCS3A01G356800 chr6A 409817749 409818351 602 True 616.000000 616 85.032000 1305 1932 1 chr6A.!!$R1 627
10 TraesCS3A01G356800 chr2B 784848185 784848925 740 True 593.000000 593 81.193000 1913 2683 1 chr2B.!!$R1 770
11 TraesCS3A01G356800 chr2A 379364824 379365417 593 False 577.000000 577 84.152000 1304 1934 1 chr2A.!!$F1 630
12 TraesCS3A01G356800 chr5A 631504497 631505194 697 False 508.000000 508 79.972000 1952 2650 1 chr5A.!!$F1 698
13 TraesCS3A01G356800 chr5D 503049189 503049931 742 False 494.000000 494 78.884000 1943 2688 1 chr5D.!!$F2 745
14 TraesCS3A01G356800 chr7D 401547985 401548947 962 True 384.500000 453 83.401000 1189 2274 2 chr7D.!!$R1 1085
15 TraesCS3A01G356800 chr7B 411056843 411057615 772 True 347.000000 446 83.509000 1887 2718 2 chr7B.!!$R1 831

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
487 1257 0.317160 GAGACACGACACACCCATCA 59.683 55.0 0.00 0.0 0.00 3.07 F
2025 3998 0.452452 GACGACCTCGACGACTTCAC 60.452 60.0 0.78 0.0 43.02 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 4419 0.396417 CCAGGTGGTTGGTGGTGAAA 60.396 55.0 0.0 0.0 33.38 2.69 R
3151 5202 0.188834 GCTAGCTAGGGGAGGAAGGA 59.811 60.0 22.1 0.0 0.00 3.36 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
41 491 4.292178 GATGGGGAGAGCGCTCGG 62.292 72.222 30.39 0.00 42.25 4.63
63 513 0.610232 ACTTCCACTCCTTGGCATGC 60.610 55.000 9.90 9.90 46.47 4.06
193 644 2.729360 CGTTCGACATGTACAAAGAGCA 59.271 45.455 0.00 0.00 0.00 4.26
396 1160 8.183536 TCAAATGCATAACACATTCTACATGTC 58.816 33.333 0.00 0.00 36.74 3.06
400 1164 7.880105 TGCATAACACATTCTACATGTCAAAA 58.120 30.769 0.00 0.00 0.00 2.44
403 1167 8.800972 CATAACACATTCTACATGTCAAAATGC 58.199 33.333 19.68 0.00 31.96 3.56
405 1169 5.243507 ACACATTCTACATGTCAAAATGCCA 59.756 36.000 19.68 0.00 31.96 4.92
418 1182 4.070716 CAAAATGCCAGCCCAAAAATGTA 58.929 39.130 0.00 0.00 0.00 2.29
456 1220 1.221840 GTGATGTGCCTCACCGGAT 59.778 57.895 9.46 0.00 39.72 4.18
465 1229 1.654954 CCTCACCGGATCGTCGAAGT 61.655 60.000 9.46 0.00 33.16 3.01
483 1253 0.386478 GTACGAGACACGACACACCC 60.386 60.000 0.00 0.00 45.77 4.61
484 1254 0.818852 TACGAGACACGACACACCCA 60.819 55.000 0.00 0.00 45.77 4.51
485 1255 1.289066 CGAGACACGACACACCCAT 59.711 57.895 0.00 0.00 45.77 4.00
487 1257 0.317160 GAGACACGACACACCCATCA 59.683 55.000 0.00 0.00 0.00 3.07
492 1262 1.118965 ACGACACACCCATCAGTCCA 61.119 55.000 0.00 0.00 0.00 4.02
523 1293 0.991920 GTTGTTGGATGGAGGAGGGA 59.008 55.000 0.00 0.00 0.00 4.20
532 1302 0.487325 TGGAGGAGGGAACAGAGACA 59.513 55.000 0.00 0.00 0.00 3.41
534 1304 1.551329 GGAGGAGGGAACAGAGACAGT 60.551 57.143 0.00 0.00 0.00 3.55
536 1306 1.148027 AGGAGGGAACAGAGACAGTGA 59.852 52.381 0.00 0.00 0.00 3.41
541 1311 2.028930 GGGAACAGAGACAGTGACGATT 60.029 50.000 0.00 0.00 0.00 3.34
548 1318 5.706369 ACAGAGACAGTGACGATTACTTAGT 59.294 40.000 0.00 0.00 0.00 2.24
553 1323 6.883217 AGACAGTGACGATTACTTAGTCCTAA 59.117 38.462 0.00 0.00 34.24 2.69
578 1348 1.671054 GGTGTGGTGGTGTCCATCG 60.671 63.158 0.00 0.00 37.47 3.84
585 1355 2.813908 GGTGTCCATCGTGACGGC 60.814 66.667 4.70 0.00 38.11 5.68
621 1391 1.673033 GCCTAGAGAAGCTTGCGACAA 60.673 52.381 2.10 0.00 0.00 3.18
624 1394 2.533266 AGAGAAGCTTGCGACAAAGA 57.467 45.000 2.10 0.00 0.00 2.52
696 2529 2.024941 ACATTGGGTTCTGGGAGGAATC 60.025 50.000 0.00 0.00 0.00 2.52
708 2541 5.541868 TCTGGGAGGAATCATTCTGAGATAC 59.458 44.000 0.00 0.00 0.00 2.24
719 2552 6.663734 TCATTCTGAGATACACAGTAGAGGA 58.336 40.000 0.00 0.00 36.81 3.71
781 2614 1.659794 GTGCACGGTTTGGATGCTT 59.340 52.632 0.00 0.00 40.13 3.91
839 2672 2.802792 CGAGCGGGATACACGGAA 59.197 61.111 0.00 0.00 39.74 4.30
885 2718 4.764050 TGGTAAAAGTGGAAGTGACAGA 57.236 40.909 0.00 0.00 0.00 3.41
903 2736 8.348507 AGTGACAGATTGAAATTCTCTTTGAAC 58.651 33.333 0.00 0.00 37.52 3.18
1035 2891 1.123928 ATAGCCAAAGACGGGGAGAG 58.876 55.000 0.00 0.00 0.00 3.20
1276 3162 2.125310 ATCGACATCGCGGCCAAA 60.125 55.556 6.13 0.00 39.60 3.28
1467 3362 3.119096 GGACGACTTCAAGGGCGC 61.119 66.667 0.00 0.00 0.00 6.53
1711 3621 6.874288 ATCAATTACCTCTGCAATTAGCTC 57.126 37.500 0.00 0.00 45.94 4.09
1722 3632 6.775088 TCTGCAATTAGCTCGTTCTTAATTG 58.225 36.000 10.25 10.25 45.94 2.32
1731 3641 9.659830 TTAGCTCGTTCTTAATTGTTTTTCTTC 57.340 29.630 0.00 0.00 0.00 2.87
1732 3642 7.931275 AGCTCGTTCTTAATTGTTTTTCTTCT 58.069 30.769 0.00 0.00 0.00 2.85
1733 3643 8.070769 AGCTCGTTCTTAATTGTTTTTCTTCTC 58.929 33.333 0.00 0.00 0.00 2.87
1734 3644 7.855904 GCTCGTTCTTAATTGTTTTTCTTCTCA 59.144 33.333 0.00 0.00 0.00 3.27
1735 3645 9.884465 CTCGTTCTTAATTGTTTTTCTTCTCAT 57.116 29.630 0.00 0.00 0.00 2.90
1763 3673 3.728076 TCCGATAATCCGAAGTTCTGG 57.272 47.619 0.56 4.50 0.00 3.86
1795 3713 1.938577 CCTGAGTGAGCAATGGATTCG 59.061 52.381 0.00 0.00 0.00 3.34
1822 3785 6.764560 AGCAATGTGAAGCATTTTCTCTTTTT 59.235 30.769 0.00 0.00 44.82 1.94
1960 3933 1.342672 ACTTCGACCACCCAACCACT 61.343 55.000 0.00 0.00 0.00 4.00
2025 3998 0.452452 GACGACCTCGACGACTTCAC 60.452 60.000 0.78 0.00 43.02 3.18
2027 4000 1.575576 CGACCTCGACGACTTCACCT 61.576 60.000 0.00 0.00 43.02 4.00
2122 4095 2.009108 CAAGTCCACCATGATCGCG 58.991 57.895 0.00 0.00 0.00 5.87
2434 4419 3.264897 GGCGAGCGCATCATCGTT 61.265 61.111 17.16 0.00 44.11 3.85
2603 4588 4.463879 CCGTGGAGGAGCTGCTGG 62.464 72.222 14.48 3.22 45.00 4.85
2931 4952 6.832384 ACTTCTACCGACCATTATCTGTCTTA 59.168 38.462 0.00 0.00 0.00 2.10
2932 4953 6.879276 TCTACCGACCATTATCTGTCTTAG 57.121 41.667 0.00 0.00 0.00 2.18
2933 4954 6.598503 TCTACCGACCATTATCTGTCTTAGA 58.401 40.000 0.00 0.00 40.37 2.10
2934 4955 5.776173 ACCGACCATTATCTGTCTTAGAG 57.224 43.478 0.00 0.00 39.20 2.43
3037 5073 1.036707 TTTTTCAGGTTTCTGCCGGG 58.963 50.000 2.18 0.00 40.69 5.73
3072 5108 5.983720 TCTCGAATAGATTTCAACCGATTCC 59.016 40.000 0.00 0.00 0.00 3.01
3125 5176 3.359950 GCCAATGTTCATCTCCTTCCTT 58.640 45.455 0.00 0.00 0.00 3.36
3126 5177 3.766051 GCCAATGTTCATCTCCTTCCTTT 59.234 43.478 0.00 0.00 0.00 3.11
3128 5179 4.400567 CCAATGTTCATCTCCTTCCTTTCC 59.599 45.833 0.00 0.00 0.00 3.13
3129 5180 3.334583 TGTTCATCTCCTTCCTTTCCG 57.665 47.619 0.00 0.00 0.00 4.30
3130 5181 2.010497 GTTCATCTCCTTCCTTTCCGC 58.990 52.381 0.00 0.00 0.00 5.54
3131 5182 1.275666 TCATCTCCTTCCTTTCCGCA 58.724 50.000 0.00 0.00 0.00 5.69
3132 5183 1.628340 TCATCTCCTTCCTTTCCGCAA 59.372 47.619 0.00 0.00 0.00 4.85
3133 5184 2.039746 TCATCTCCTTCCTTTCCGCAAA 59.960 45.455 0.00 0.00 0.00 3.68
3134 5185 2.649531 TCTCCTTCCTTTCCGCAAAA 57.350 45.000 0.00 0.00 0.00 2.44
3135 5186 2.938838 TCTCCTTCCTTTCCGCAAAAA 58.061 42.857 0.00 0.00 0.00 1.94
3161 5212 4.308526 AAAAGTTCATCTCCTTCCTCCC 57.691 45.455 0.00 0.00 0.00 4.30
3162 5213 1.886422 AGTTCATCTCCTTCCTCCCC 58.114 55.000 0.00 0.00 0.00 4.81
3163 5214 1.367848 AGTTCATCTCCTTCCTCCCCT 59.632 52.381 0.00 0.00 0.00 4.79
3164 5215 2.592512 AGTTCATCTCCTTCCTCCCCTA 59.407 50.000 0.00 0.00 0.00 3.53
3165 5216 2.969262 GTTCATCTCCTTCCTCCCCTAG 59.031 54.545 0.00 0.00 0.00 3.02
3242 5293 1.296056 GCCGCTACGAAAAGGCTTCA 61.296 55.000 0.00 0.00 45.67 3.02
3264 5315 6.342111 TCACACCCAAATTTGTTAAACCTTC 58.658 36.000 16.73 0.00 0.00 3.46
3326 5388 1.004440 GTCTCGCCTTGGCTTCACT 60.004 57.895 10.12 0.00 0.00 3.41
3331 5393 0.392193 CGCCTTGGCTTCACTCATCT 60.392 55.000 10.12 0.00 0.00 2.90
3332 5394 1.831580 GCCTTGGCTTCACTCATCTT 58.168 50.000 4.11 0.00 0.00 2.40
3333 5395 2.165998 GCCTTGGCTTCACTCATCTTT 58.834 47.619 4.11 0.00 0.00 2.52
3334 5396 2.163211 GCCTTGGCTTCACTCATCTTTC 59.837 50.000 4.11 0.00 0.00 2.62
3335 5397 2.417933 CCTTGGCTTCACTCATCTTTCG 59.582 50.000 0.00 0.00 0.00 3.46
3336 5398 1.442769 TGGCTTCACTCATCTTTCGC 58.557 50.000 0.00 0.00 0.00 4.70
3337 5399 0.729690 GGCTTCACTCATCTTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54
3338 5400 0.729690 GCTTCACTCATCTTTCGCCC 59.270 55.000 0.00 0.00 0.00 6.13
3339 5401 1.945819 GCTTCACTCATCTTTCGCCCA 60.946 52.381 0.00 0.00 0.00 5.36
3340 5402 2.636830 CTTCACTCATCTTTCGCCCAT 58.363 47.619 0.00 0.00 0.00 4.00
3341 5403 2.315925 TCACTCATCTTTCGCCCATC 57.684 50.000 0.00 0.00 0.00 3.51
3369 5431 2.567615 GGGTTGTCTCCTTTCTCTAGCA 59.432 50.000 0.00 0.00 0.00 3.49
3385 5447 0.108615 AGCAGAAATCGACTGACCGG 60.109 55.000 0.00 0.00 37.54 5.28
3426 5489 1.999735 CGAGGATTTGCAAAGCTCGTA 59.000 47.619 26.49 4.57 0.00 3.43
3448 5538 4.551702 AAATAATGTTGGGACTTTGGGC 57.448 40.909 0.00 0.00 0.00 5.36
3492 5582 3.244596 GCTACTTGAGGGTTGAAAGAGGT 60.245 47.826 0.00 0.00 0.00 3.85
3531 5621 3.067106 CGGCAAGCCACCAACTATATAG 58.933 50.000 12.19 8.27 35.37 1.31
3607 5697 3.000041 TCGCCATCTTTGATGTGTGTAC 59.000 45.455 6.78 0.00 0.00 2.90
3622 5712 5.254901 TGTGTGTACGGGGCTATTTAATTT 58.745 37.500 0.00 0.00 0.00 1.82
3632 5722 6.406370 GGGGCTATTTAATTTGCTCAAACTT 58.594 36.000 6.11 0.00 32.51 2.66
3654 5744 8.409358 ACTTTTAAGTGCATGATTACCTTTCT 57.591 30.769 0.00 0.00 37.98 2.52
3685 5775 4.866486 AGTTACAAATTAGTAGAACGCCGG 59.134 41.667 0.00 0.00 0.00 6.13
3686 5776 3.323751 ACAAATTAGTAGAACGCCGGT 57.676 42.857 1.90 0.00 0.00 5.28
3687 5777 4.454728 ACAAATTAGTAGAACGCCGGTA 57.545 40.909 1.90 0.00 0.00 4.02
3688 5778 5.014808 ACAAATTAGTAGAACGCCGGTAT 57.985 39.130 1.90 0.00 0.00 2.73
3696 5786 1.066430 AGAACGCCGGTATGTTGTCAT 60.066 47.619 12.54 0.00 38.00 3.06
3711 5801 9.301153 GTATGTTGTCATGGGCTTTTATTAAAG 57.699 33.333 0.00 0.00 38.46 1.85
3755 5845 6.176183 AGAGCTAACATAACAAGAGCAATGT 58.824 36.000 0.00 0.00 35.55 2.71
3809 5900 6.388259 AAAACAACACATGTCTGTTTTTCG 57.612 33.333 27.44 10.63 42.99 3.46
3848 5939 0.615331 AGTCATGACCAACGGAGCAT 59.385 50.000 22.21 0.00 0.00 3.79
3876 5967 0.664767 GCGAGTGGTGTGAGTGTCTC 60.665 60.000 0.00 0.00 0.00 3.36
3877 5968 0.955178 CGAGTGGTGTGAGTGTCTCT 59.045 55.000 0.00 0.00 0.00 3.10
3878 5969 1.335415 CGAGTGGTGTGAGTGTCTCTG 60.335 57.143 0.00 0.00 0.00 3.35
3999 6090 5.703876 CAGTTAACTGATTCTCCTTTTGGC 58.296 41.667 28.17 0.00 46.59 4.52
4000 6091 5.474876 CAGTTAACTGATTCTCCTTTTGGCT 59.525 40.000 28.17 0.00 46.59 4.75
4001 6092 5.474876 AGTTAACTGATTCTCCTTTTGGCTG 59.525 40.000 7.48 0.00 40.12 4.85
4002 6093 3.515602 ACTGATTCTCCTTTTGGCTGT 57.484 42.857 0.00 0.00 40.12 4.40
4003 6094 4.640771 ACTGATTCTCCTTTTGGCTGTA 57.359 40.909 0.00 0.00 40.12 2.74
4004 6095 5.184892 ACTGATTCTCCTTTTGGCTGTAT 57.815 39.130 0.00 0.00 40.12 2.29
4005 6096 4.946157 ACTGATTCTCCTTTTGGCTGTATG 59.054 41.667 0.00 0.00 40.12 2.39
4006 6097 3.696051 TGATTCTCCTTTTGGCTGTATGC 59.304 43.478 0.00 0.00 40.12 3.14
4007 6098 2.877097 TCTCCTTTTGGCTGTATGCA 57.123 45.000 0.00 0.00 45.15 3.96
4008 6099 2.436417 TCTCCTTTTGGCTGTATGCAC 58.564 47.619 0.00 0.00 45.15 4.57
4009 6100 1.474077 CTCCTTTTGGCTGTATGCACC 59.526 52.381 0.00 0.00 45.15 5.01
4010 6101 0.171007 CCTTTTGGCTGTATGCACCG 59.829 55.000 0.00 0.00 45.15 4.94
4011 6102 0.881118 CTTTTGGCTGTATGCACCGT 59.119 50.000 0.00 0.00 45.15 4.83
4012 6103 1.269448 CTTTTGGCTGTATGCACCGTT 59.731 47.619 0.00 0.00 45.15 4.44
4013 6104 0.878416 TTTGGCTGTATGCACCGTTC 59.122 50.000 0.00 0.00 45.15 3.95
4014 6105 0.250510 TTGGCTGTATGCACCGTTCA 60.251 50.000 0.00 0.00 45.15 3.18
4015 6106 0.673333 TGGCTGTATGCACCGTTCAG 60.673 55.000 0.00 0.00 45.15 3.02
4016 6107 0.391130 GGCTGTATGCACCGTTCAGA 60.391 55.000 0.00 0.00 45.15 3.27
4017 6108 1.656652 GCTGTATGCACCGTTCAGAT 58.343 50.000 0.00 0.00 42.31 2.90
4018 6109 2.483013 GGCTGTATGCACCGTTCAGATA 60.483 50.000 0.00 0.00 45.15 1.98
4019 6110 2.797156 GCTGTATGCACCGTTCAGATAG 59.203 50.000 0.00 0.00 42.31 2.08
4020 6111 3.384668 CTGTATGCACCGTTCAGATAGG 58.615 50.000 0.00 0.00 0.00 2.57
4021 6112 2.102420 TGTATGCACCGTTCAGATAGGG 59.898 50.000 0.00 0.00 0.00 3.53
4022 6113 1.496060 ATGCACCGTTCAGATAGGGA 58.504 50.000 0.00 0.00 0.00 4.20
4023 6114 0.824109 TGCACCGTTCAGATAGGGAG 59.176 55.000 0.00 0.00 0.00 4.30
4024 6115 0.824759 GCACCGTTCAGATAGGGAGT 59.175 55.000 0.00 0.00 0.00 3.85
4025 6116 1.471676 GCACCGTTCAGATAGGGAGTG 60.472 57.143 0.00 0.00 0.00 3.51
4026 6117 0.824759 ACCGTTCAGATAGGGAGTGC 59.175 55.000 0.00 0.00 0.00 4.40
4027 6118 0.824109 CCGTTCAGATAGGGAGTGCA 59.176 55.000 0.00 0.00 0.00 4.57
4028 6119 1.414181 CCGTTCAGATAGGGAGTGCAT 59.586 52.381 0.00 0.00 0.00 3.96
4029 6120 2.546795 CCGTTCAGATAGGGAGTGCATC 60.547 54.545 0.00 0.00 0.00 3.91
4039 6130 2.797177 GGAGTGCATCCTCCTTTTCT 57.203 50.000 14.62 0.00 46.34 2.52
4040 6131 3.914426 GGAGTGCATCCTCCTTTTCTA 57.086 47.619 14.62 0.00 46.34 2.10
4041 6132 4.222124 GGAGTGCATCCTCCTTTTCTAA 57.778 45.455 14.62 0.00 46.34 2.10
4042 6133 4.589908 GGAGTGCATCCTCCTTTTCTAAA 58.410 43.478 14.62 0.00 46.34 1.85
4043 6134 5.010282 GGAGTGCATCCTCCTTTTCTAAAA 58.990 41.667 14.62 0.00 46.34 1.52
4044 6135 5.476945 GGAGTGCATCCTCCTTTTCTAAAAA 59.523 40.000 14.62 0.00 46.34 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 471 4.959596 GAGCGCTCTCCCCATCGC 62.960 72.222 29.88 0.00 46.95 4.58
37 487 1.831652 AAGGAGTGGAAGTGGCCGAG 61.832 60.000 0.00 0.00 0.00 4.63
50 500 1.065126 GGTAGAAGCATGCCAAGGAGT 60.065 52.381 15.66 0.00 0.00 3.85
63 513 3.114065 GACAATCGGCGTTAGGTAGAAG 58.886 50.000 6.85 0.00 0.00 2.85
103 553 2.294074 GAGATACGTCCAGAGCACTCT 58.706 52.381 0.00 0.00 41.37 3.24
105 555 2.130272 TGAGATACGTCCAGAGCACT 57.870 50.000 0.00 0.00 0.00 4.40
193 644 3.511146 ACATGGCAATCGACCTTTTCAAT 59.489 39.130 0.00 0.00 0.00 2.57
366 1130 8.355913 TGTAGAATGTGTTATGCATTTGACAAA 58.644 29.630 3.54 2.48 36.77 2.83
396 1160 2.885894 ACATTTTTGGGCTGGCATTTTG 59.114 40.909 2.88 0.00 0.00 2.44
400 1164 2.171027 CCATACATTTTTGGGCTGGCAT 59.829 45.455 2.88 0.00 0.00 4.40
403 1167 3.099141 AGTCCATACATTTTTGGGCTGG 58.901 45.455 0.00 0.00 46.01 4.85
418 1182 3.760151 CACATCCATGTTGACAAGTCCAT 59.240 43.478 0.00 0.00 39.39 3.41
465 1229 0.818852 TGGGTGTGTCGTGTCTCGTA 60.819 55.000 0.00 0.00 40.80 3.43
483 1253 2.897436 ACATGACGTGATGGACTGATG 58.103 47.619 19.29 0.00 0.00 3.07
523 1293 5.455056 AAGTAATCGTCACTGTCTCTGTT 57.545 39.130 0.00 0.00 0.00 3.16
548 1318 1.628340 CACCACACCCATGACTTAGGA 59.372 52.381 0.00 0.00 0.00 2.94
553 1323 1.352622 ACACCACCACACCCATGACT 61.353 55.000 0.00 0.00 0.00 3.41
555 1325 1.454104 GACACCACCACACCCATGA 59.546 57.895 0.00 0.00 0.00 3.07
562 1332 1.070615 CACGATGGACACCACCACA 59.929 57.895 0.00 0.00 43.03 4.17
564 1334 1.369692 GTCACGATGGACACCACCA 59.630 57.895 0.00 0.00 44.41 4.17
578 1348 2.262915 CCTCACCTCTGCCGTCAC 59.737 66.667 0.00 0.00 0.00 3.67
585 1355 4.767255 GCCGTGCCCTCACCTCTG 62.767 72.222 0.00 0.00 40.04 3.35
696 2529 6.770303 TCTCCTCTACTGTGTATCTCAGAATG 59.230 42.308 5.95 0.00 36.81 2.67
708 2541 6.279513 ACATCTTTTCTCTCCTCTACTGTG 57.720 41.667 0.00 0.00 0.00 3.66
719 2552 5.396213 GGAGGCATGACTACATCTTTTCTCT 60.396 44.000 5.68 0.00 34.15 3.10
781 2614 2.093500 AGTCGCCATGTGCTAATCTCAA 60.093 45.455 4.92 0.00 38.05 3.02
857 2690 8.750298 TGTCACTTCCACTTTTACCAAAAATTA 58.250 29.630 0.00 0.00 34.18 1.40
885 2718 8.137437 ACACAATCGTTCAAAGAGAATTTCAAT 58.863 29.630 0.00 0.00 38.76 2.57
903 2736 3.066380 TCACATTCCAGTGACACAATCG 58.934 45.455 8.59 0.00 43.18 3.34
1035 2891 3.430862 TTCATGCCGCGCTTGGTC 61.431 61.111 5.56 0.00 34.99 4.02
1448 3343 2.342648 GCCCTTGAAGTCGTCCGT 59.657 61.111 0.00 0.00 0.00 4.69
1773 3691 2.414994 ATCCATTGCTCACTCAGGTG 57.585 50.000 0.00 0.00 44.23 4.00
1774 3692 2.679059 CGAATCCATTGCTCACTCAGGT 60.679 50.000 0.00 0.00 0.00 4.00
1775 3693 1.938577 CGAATCCATTGCTCACTCAGG 59.061 52.381 0.00 0.00 0.00 3.86
1780 3698 0.659957 GCTCCGAATCCATTGCTCAC 59.340 55.000 0.00 0.00 0.00 3.51
1793 3711 3.556817 ATGCTTCACATTGCTCCGA 57.443 47.368 0.00 0.00 34.40 4.55
1960 3933 1.303236 CATGGCCAGGGTGTCGAAA 60.303 57.895 13.05 0.00 0.00 3.46
2025 3998 2.308690 GGTAGTAGTCCCTGCTGTAGG 58.691 57.143 4.63 4.63 46.88 3.18
2027 4000 2.020694 GCGGTAGTAGTCCCTGCTGTA 61.021 57.143 0.00 0.00 0.00 2.74
2434 4419 0.396417 CCAGGTGGTTGGTGGTGAAA 60.396 55.000 0.00 0.00 33.38 2.69
2603 4588 2.789203 GCGTCATCTTCACGTCGCC 61.789 63.158 2.94 0.00 39.54 5.54
2612 4597 4.814294 GTCCGCCGGCGTCATCTT 62.814 66.667 43.12 0.00 37.81 2.40
2887 4908 0.881796 TAGAGACGCTCACACCACTG 59.118 55.000 9.09 0.00 32.06 3.66
2931 4952 1.821088 AACAACCTCCCTCAACCTCT 58.179 50.000 0.00 0.00 0.00 3.69
2932 4953 2.638363 ACTAACAACCTCCCTCAACCTC 59.362 50.000 0.00 0.00 0.00 3.85
2933 4954 2.702748 ACTAACAACCTCCCTCAACCT 58.297 47.619 0.00 0.00 0.00 3.50
2934 4955 3.503800 AACTAACAACCTCCCTCAACC 57.496 47.619 0.00 0.00 0.00 3.77
3044 5080 9.542462 AATCGGTTGAAATCTATTCGAGATAAA 57.458 29.630 0.00 0.00 44.68 1.40
3046 5082 7.813148 GGAATCGGTTGAAATCTATTCGAGATA 59.187 37.037 0.00 0.00 44.68 1.98
3049 5085 5.107837 CGGAATCGGTTGAAATCTATTCGAG 60.108 44.000 0.00 0.00 0.00 4.04
3051 5087 4.506654 ACGGAATCGGTTGAAATCTATTCG 59.493 41.667 0.00 0.00 41.39 3.34
3139 5190 4.509302 GGGGAGGAAGGAGATGAACTTTTT 60.509 45.833 0.00 0.00 0.00 1.94
3140 5191 3.010696 GGGGAGGAAGGAGATGAACTTTT 59.989 47.826 0.00 0.00 0.00 2.27
3141 5192 2.578480 GGGGAGGAAGGAGATGAACTTT 59.422 50.000 0.00 0.00 0.00 2.66
3142 5193 2.200955 GGGGAGGAAGGAGATGAACTT 58.799 52.381 0.00 0.00 0.00 2.66
3143 5194 1.367848 AGGGGAGGAAGGAGATGAACT 59.632 52.381 0.00 0.00 0.00 3.01
3144 5195 1.886422 AGGGGAGGAAGGAGATGAAC 58.114 55.000 0.00 0.00 0.00 3.18
3145 5196 2.694303 GCTAGGGGAGGAAGGAGATGAA 60.694 54.545 0.00 0.00 0.00 2.57
3146 5197 1.133009 GCTAGGGGAGGAAGGAGATGA 60.133 57.143 0.00 0.00 0.00 2.92
3147 5198 1.132881 AGCTAGGGGAGGAAGGAGATG 60.133 57.143 0.00 0.00 0.00 2.90
3148 5199 1.250165 AGCTAGGGGAGGAAGGAGAT 58.750 55.000 0.00 0.00 0.00 2.75
3149 5200 1.783979 CTAGCTAGGGGAGGAAGGAGA 59.216 57.143 13.32 0.00 0.00 3.71
3150 5201 1.825641 GCTAGCTAGGGGAGGAAGGAG 60.826 61.905 22.10 0.00 0.00 3.69
3151 5202 0.188834 GCTAGCTAGGGGAGGAAGGA 59.811 60.000 22.10 0.00 0.00 3.36
3152 5203 0.834261 GGCTAGCTAGGGGAGGAAGG 60.834 65.000 22.10 0.00 0.00 3.46
3153 5204 1.182385 CGGCTAGCTAGGGGAGGAAG 61.182 65.000 22.10 0.00 0.00 3.46
3154 5205 1.152525 CGGCTAGCTAGGGGAGGAA 60.153 63.158 22.10 0.00 0.00 3.36
3155 5206 2.521479 CGGCTAGCTAGGGGAGGA 59.479 66.667 22.10 0.00 0.00 3.71
3156 5207 3.307108 GCGGCTAGCTAGGGGAGG 61.307 72.222 22.10 0.00 44.04 4.30
3239 5290 6.301169 AGGTTTAACAAATTTGGGTGTGAA 57.699 33.333 21.74 0.00 0.00 3.18
3242 5293 5.127356 TCGAAGGTTTAACAAATTTGGGTGT 59.873 36.000 21.74 7.07 0.00 4.16
3290 5341 2.446848 CGGGGATGATGTGGCTCCT 61.447 63.158 0.00 0.00 0.00 3.69
3326 5388 2.363680 GAGAGAGATGGGCGAAAGATGA 59.636 50.000 0.00 0.00 0.00 2.92
3331 5393 1.676678 CCCGAGAGAGATGGGCGAAA 61.677 60.000 0.00 0.00 35.82 3.46
3332 5394 2.127869 CCCGAGAGAGATGGGCGAA 61.128 63.158 0.00 0.00 35.82 4.70
3333 5395 2.519541 CCCGAGAGAGATGGGCGA 60.520 66.667 0.00 0.00 35.82 5.54
3337 5399 1.407258 GAGACAACCCGAGAGAGATGG 59.593 57.143 0.00 0.00 0.00 3.51
3338 5400 1.407258 GGAGACAACCCGAGAGAGATG 59.593 57.143 0.00 0.00 0.00 2.90
3339 5401 1.286553 AGGAGACAACCCGAGAGAGAT 59.713 52.381 0.00 0.00 0.00 2.75
3340 5402 0.699399 AGGAGACAACCCGAGAGAGA 59.301 55.000 0.00 0.00 0.00 3.10
3341 5403 1.551452 AAGGAGACAACCCGAGAGAG 58.449 55.000 0.00 0.00 0.00 3.20
3369 5431 3.396260 TTTTCCGGTCAGTCGATTTCT 57.604 42.857 0.00 0.00 0.00 2.52
3426 5489 4.562552 CGCCCAAAGTCCCAACATTATTTT 60.563 41.667 0.00 0.00 0.00 1.82
3448 5538 4.161333 CAAGATGCAAGCCTTAAAAGTCG 58.839 43.478 0.00 0.00 0.00 4.18
3492 5582 2.863137 GCCGCAGTTTGAAATTTCAACA 59.137 40.909 28.78 18.40 45.99 3.33
3531 5621 6.943718 ACCTACTCTACTCCTGAAGCATATAC 59.056 42.308 0.00 0.00 0.00 1.47
3551 5641 3.802685 GGCACAGTCGATAATTCACCTAC 59.197 47.826 0.00 0.00 0.00 3.18
3607 5697 4.647424 TTGAGCAAATTAAATAGCCCCG 57.353 40.909 0.00 0.00 0.00 5.73
3622 5712 5.512753 TCATGCACTTAAAAGTTTGAGCA 57.487 34.783 7.71 7.71 38.19 4.26
3658 5748 8.598075 CGGCGTTCTACTAATTTGTAACTAAAT 58.402 33.333 0.00 0.00 31.87 1.40
3659 5749 7.063308 CCGGCGTTCTACTAATTTGTAACTAAA 59.937 37.037 6.01 0.00 0.00 1.85
3671 5761 3.193267 ACAACATACCGGCGTTCTACTAA 59.807 43.478 6.01 0.00 0.00 2.24
3680 5770 1.436195 CCCATGACAACATACCGGCG 61.436 60.000 0.00 0.00 35.09 6.46
3685 5775 9.301153 CTTTAATAAAAGCCCATGACAACATAC 57.699 33.333 0.00 0.00 35.98 2.39
3749 5839 2.284190 GGGTTAGCTGAGAGACATTGC 58.716 52.381 0.00 0.00 0.00 3.56
3755 5845 0.461548 CATGCGGGTTAGCTGAGAGA 59.538 55.000 0.00 0.00 38.13 3.10
3788 5879 5.092781 GTCGAAAAACAGACATGTGTTGTT 58.907 37.500 15.91 15.91 40.02 2.83
3789 5880 4.155099 TGTCGAAAAACAGACATGTGTTGT 59.845 37.500 1.15 4.78 41.81 3.32
3797 5888 4.196193 AGGTGATTGTCGAAAAACAGACA 58.804 39.130 0.00 0.00 44.57 3.41
3798 5889 4.813296 AGGTGATTGTCGAAAAACAGAC 57.187 40.909 0.00 0.00 37.85 3.51
3809 5900 2.668457 CTCTGCGTGTTAGGTGATTGTC 59.332 50.000 0.00 0.00 0.00 3.18
3876 5967 5.911752 ACAGATAATGGTCAGTAGAAGCAG 58.088 41.667 0.00 0.00 0.00 4.24
3877 5968 5.658634 AGACAGATAATGGTCAGTAGAAGCA 59.341 40.000 0.00 0.00 36.50 3.91
3878 5969 6.155475 AGACAGATAATGGTCAGTAGAAGC 57.845 41.667 0.00 0.00 36.50 3.86
3993 6084 1.268352 GAACGGTGCATACAGCCAAAA 59.732 47.619 0.00 0.00 44.83 2.44
3994 6085 0.878416 GAACGGTGCATACAGCCAAA 59.122 50.000 0.00 0.00 44.83 3.28
3995 6086 0.250510 TGAACGGTGCATACAGCCAA 60.251 50.000 0.00 0.00 44.83 4.52
3996 6087 0.673333 CTGAACGGTGCATACAGCCA 60.673 55.000 0.00 0.00 44.83 4.75
3997 6088 0.391130 TCTGAACGGTGCATACAGCC 60.391 55.000 0.00 0.00 44.83 4.85
3998 6089 1.656652 ATCTGAACGGTGCATACAGC 58.343 50.000 0.00 0.00 45.96 4.40
3999 6090 3.384668 CCTATCTGAACGGTGCATACAG 58.615 50.000 0.00 0.00 0.00 2.74
4000 6091 2.102420 CCCTATCTGAACGGTGCATACA 59.898 50.000 0.00 0.00 0.00 2.29
4001 6092 2.364324 TCCCTATCTGAACGGTGCATAC 59.636 50.000 0.00 0.00 0.00 2.39
4002 6093 2.628178 CTCCCTATCTGAACGGTGCATA 59.372 50.000 0.00 0.00 0.00 3.14
4003 6094 1.414181 CTCCCTATCTGAACGGTGCAT 59.586 52.381 0.00 0.00 0.00 3.96
4004 6095 0.824109 CTCCCTATCTGAACGGTGCA 59.176 55.000 0.00 0.00 0.00 4.57
4005 6096 0.824759 ACTCCCTATCTGAACGGTGC 59.175 55.000 0.00 0.00 0.00 5.01
4006 6097 1.471676 GCACTCCCTATCTGAACGGTG 60.472 57.143 0.00 0.00 0.00 4.94
4007 6098 0.824759 GCACTCCCTATCTGAACGGT 59.175 55.000 0.00 0.00 0.00 4.83
4008 6099 0.824109 TGCACTCCCTATCTGAACGG 59.176 55.000 0.00 0.00 0.00 4.44
4009 6100 2.546795 GGATGCACTCCCTATCTGAACG 60.547 54.545 0.00 0.00 38.19 3.95
4010 6101 2.703007 AGGATGCACTCCCTATCTGAAC 59.297 50.000 10.46 0.00 46.27 3.18
4011 6102 2.968574 GAGGATGCACTCCCTATCTGAA 59.031 50.000 10.46 0.00 46.27 3.02
4012 6103 2.603021 GAGGATGCACTCCCTATCTGA 58.397 52.381 10.46 0.00 46.27 3.27
4021 6112 6.575162 TTTTTAGAAAAGGAGGATGCACTC 57.425 37.500 0.00 0.00 36.76 3.51
4056 6147 7.665145 GGGGAGAAATTGATTGATTTGGAAAAA 59.335 33.333 0.00 0.00 29.75 1.94
4088 6179 2.698803 TGAACACTAGCATGCATCGTT 58.301 42.857 21.98 16.48 0.00 3.85


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

AutoCloner maintained by Alex Coulton.