Multiple sequence alignment - TraesCS5B01G232200

Loading Multiple Alignment...

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 TraesCS5B01G232200 chr5B 100.000 4969 0 0 1 4969 409871927 409876895 0.000000e+00 9177
1 TraesCS5B01G232200 chr5B 90.878 296 19 2 2249 2536 323645923 323645628 1.680000e-104 390
2 TraesCS5B01G232200 chr5B 91.065 291 20 2 2251 2535 64420421 64420711 6.030000e-104 388
3 TraesCS5B01G232200 chr5A 93.798 2193 98 18 2797 4968 449256308 449258483 0.000000e+00 3262
4 TraesCS5B01G232200 chr5A 91.000 1500 64 35 757 2212 449254823 449256295 0.000000e+00 1956
5 TraesCS5B01G232200 chr5A 87.632 760 40 25 1 731 449253755 449254489 0.000000e+00 833
6 TraesCS5B01G232200 chr5D 93.718 1942 48 25 331 2228 349376329 349378240 0.000000e+00 2843
7 TraesCS5B01G232200 chr5D 95.138 1666 56 13 2782 4429 349378237 349379895 0.000000e+00 2604
8 TraesCS5B01G232200 chr5D 94.316 563 22 2 4415 4969 349379917 349380477 0.000000e+00 854
9 TraesCS5B01G232200 chr5D 89.617 549 37 7 2241 2780 301123872 301124409 0.000000e+00 680
10 TraesCS5B01G232200 chr5D 92.150 293 15 2 2250 2534 397006165 397005873 1.670000e-109 407
11 TraesCS5B01G232200 chr5D 87.634 186 8 8 1 181 349374818 349374993 8.430000e-48 202
12 TraesCS5B01G232200 chr3A 96.800 250 8 0 2531 2780 656134037 656134286 7.690000e-113 418
13 TraesCS5B01G232200 chr3A 96.000 250 10 0 2531 2780 742770522 742770273 1.670000e-109 407
14 TraesCS5B01G232200 chr3A 76.961 408 89 4 1239 1645 362202181 362201778 1.390000e-55 228
15 TraesCS5B01G232200 chr6A 96.400 250 9 0 2531 2780 371732418 371732667 3.580000e-111 412
16 TraesCS5B01G232200 chr7A 96.000 250 10 0 2531 2780 182858025 182858274 1.670000e-109 407
17 TraesCS5B01G232200 chr6B 96.000 250 10 0 2531 2780 143176359 143176110 1.670000e-109 407
18 TraesCS5B01G232200 chr4B 96.000 250 10 0 2531 2780 637577443 637577692 1.670000e-109 407
19 TraesCS5B01G232200 chr4B 90.157 254 23 2 1395 1646 482137849 482138102 3.710000e-86 329
20 TraesCS5B01G232200 chr2A 96.000 250 10 0 2531 2780 70704051 70704300 1.670000e-109 407
21 TraesCS5B01G232200 chr1B 96.000 250 10 0 2531 2780 167110277 167110526 1.670000e-109 407
22 TraesCS5B01G232200 chr1D 91.958 286 17 2 2253 2532 45867239 45866954 3.600000e-106 396
23 TraesCS5B01G232200 chr1D 91.409 291 18 1 2251 2534 318339889 318340179 4.660000e-105 392
24 TraesCS5B01G232200 chr1D 91.459 281 22 2 2253 2532 71013899 71013620 7.800000e-103 385
25 TraesCS5B01G232200 chr7B 91.468 293 16 3 2249 2532 200825539 200825247 1.300000e-105 394
26 TraesCS5B01G232200 chr2D 91.126 293 19 1 2251 2536 77445769 77445477 1.680000e-104 390
27 TraesCS5B01G232200 chr7D 91.549 284 20 1 2253 2532 48195482 48195199 6.030000e-104 388
28 TraesCS5B01G232200 chr6D 79.534 601 74 31 1042 1602 86013808 86014399 2.810000e-102 383
29 TraesCS5B01G232200 chr4A 90.551 254 22 2 1395 1646 74009958 74010211 7.970000e-88 335
30 TraesCS5B01G232200 chr4D 89.764 254 24 2 1395 1646 392537963 392538216 1.730000e-84 324
31 TraesCS5B01G232200 chr4D 90.968 155 14 0 1239 1393 392537755 392537909 5.040000e-50 209
32 TraesCS5B01G232200 chr3B 91.189 227 14 1 1236 1462 821233076 821232856 2.250000e-78 303
33 TraesCS5B01G232200 chr3B 80.049 406 73 6 1237 1641 222318457 222318855 1.350000e-75 294
34 TraesCS5B01G232200 chr3B 76.961 408 89 4 1239 1645 372896587 372896184 1.390000e-55 228
35 TraesCS5B01G232200 chr3D 77.206 408 88 4 1239 1645 277222115 277222518 2.990000e-57 233


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 TraesCS5B01G232200 chr5B 409871927 409876895 4968 False 9177.00 9177 100.0000 1 4969 1 chr5B.!!$F2 4968
1 TraesCS5B01G232200 chr5A 449253755 449258483 4728 False 2017.00 3262 90.8100 1 4968 3 chr5A.!!$F1 4967
2 TraesCS5B01G232200 chr5D 349374818 349380477 5659 False 1625.75 2843 92.7015 1 4969 4 chr5D.!!$F2 4968
3 TraesCS5B01G232200 chr5D 301123872 301124409 537 False 680.00 680 89.6170 2241 2780 1 chr5D.!!$F1 539
4 TraesCS5B01G232200 chr6D 86013808 86014399 591 False 383.00 383 79.5340 1042 1602 1 chr6D.!!$F1 560

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
904 2451 0.026285 CGCATTCCGTTTCCATCGTC 59.974 55.0 0.00 0.00 0.00 4.20 F
945 2492 0.387565 GCGAGCTAGAGAGGGAAAGG 59.612 60.0 0.00 0.00 0.00 3.11 F
2132 3841 0.459063 TCATACTCGCACTGCTGCTG 60.459 55.0 4.89 4.89 41.77 4.41 F
2941 4687 0.314302 GACCAGACGTGTAGCAGTGT 59.686 55.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 3950 0.035458 CCTCCCCATTATGACGAGCC 59.965 60.0 0.00 0.0 0.00 4.70 R
2431 4154 0.736053 AGAGAGAGAAGGTAAGCGCG 59.264 55.0 0.00 0.0 0.00 6.86 R
2963 4709 0.655733 GGCCACGAATAATCACACCG 59.344 55.0 0.00 0.0 0.00 4.94 R
4412 6162 0.450482 CGTGTCGACGTTTGCAATCC 60.450 55.0 11.62 0.0 40.91 3.01 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
57 58 2.619074 GGCAGCTTGATTACCAGTTCCT 60.619 50.000 0.00 0.00 0.00 3.36
60 61 4.616835 GCAGCTTGATTACCAGTTCCTTTG 60.617 45.833 0.00 0.00 0.00 2.77
61 62 3.507622 AGCTTGATTACCAGTTCCTTTGC 59.492 43.478 0.00 0.00 0.00 3.68
62 63 3.507622 GCTTGATTACCAGTTCCTTTGCT 59.492 43.478 0.00 0.00 0.00 3.91
63 64 4.700213 GCTTGATTACCAGTTCCTTTGCTA 59.300 41.667 0.00 0.00 0.00 3.49
64 65 5.358160 GCTTGATTACCAGTTCCTTTGCTAT 59.642 40.000 0.00 0.00 0.00 2.97
65 66 6.542370 GCTTGATTACCAGTTCCTTTGCTATA 59.458 38.462 0.00 0.00 0.00 1.31
66 67 7.067008 GCTTGATTACCAGTTCCTTTGCTATAA 59.933 37.037 0.00 0.00 0.00 0.98
139 140 1.042229 GCATGCAAGCATTCCCCATA 58.958 50.000 14.21 0.00 33.90 2.74
165 170 6.153851 TGACGGTTATGTTGGAGAAGATCTTA 59.846 38.462 8.25 0.00 0.00 2.10
168 173 7.495934 ACGGTTATGTTGGAGAAGATCTTATTG 59.504 37.037 8.25 0.00 0.00 1.90
199 204 4.790962 CCGCTGCATGCCCAGAGT 62.791 66.667 16.68 0.00 38.78 3.24
218 223 5.527582 CAGAGTATGGCAACCCAAATAGTAC 59.472 44.000 0.00 0.00 46.14 2.73
219 224 5.428783 AGAGTATGGCAACCCAAATAGTACT 59.571 40.000 0.00 0.00 46.14 2.73
220 225 6.614087 AGAGTATGGCAACCCAAATAGTACTA 59.386 38.462 4.77 4.77 46.14 1.82
233 238 8.798402 CCCAAATAGTACTATAGTGGAAGAGAG 58.202 40.741 30.18 17.41 34.90 3.20
247 252 7.911651 AGTGGAAGAGAGAGAAAATATGTTCA 58.088 34.615 8.36 0.00 0.00 3.18
301 311 9.944376 TTTAAAGCTCATTGTACAGTATTCTCT 57.056 29.630 0.00 0.00 0.00 3.10
304 314 7.416964 AGCTCATTGTACAGTATTCTCTTCT 57.583 36.000 0.00 0.00 0.00 2.85
306 316 7.341769 AGCTCATTGTACAGTATTCTCTTCTCT 59.658 37.037 0.00 0.00 0.00 3.10
308 318 8.815565 TCATTGTACAGTATTCTCTTCTCTCT 57.184 34.615 0.00 0.00 0.00 3.10
309 319 8.898761 TCATTGTACAGTATTCTCTTCTCTCTC 58.101 37.037 0.00 0.00 0.00 3.20
311 321 8.500753 TTGTACAGTATTCTCTTCTCTCTCTC 57.499 38.462 0.00 0.00 0.00 3.20
312 322 7.857456 TGTACAGTATTCTCTTCTCTCTCTCT 58.143 38.462 0.00 0.00 0.00 3.10
313 323 7.985184 TGTACAGTATTCTCTTCTCTCTCTCTC 59.015 40.741 0.00 0.00 0.00 3.20
314 324 7.200434 ACAGTATTCTCTTCTCTCTCTCTCT 57.800 40.000 0.00 0.00 0.00 3.10
323 333 5.362143 TCTTCTCTCTCTCTCTCTCTCTCTG 59.638 48.000 0.00 0.00 0.00 3.35
324 334 3.386078 TCTCTCTCTCTCTCTCTCTCTGC 59.614 52.174 0.00 0.00 0.00 4.26
472 1682 0.826715 TGCATCTTCCTTCTCCCTCG 59.173 55.000 0.00 0.00 0.00 4.63
487 1697 4.144727 TCGCTCCCCTCTCCTCCC 62.145 72.222 0.00 0.00 0.00 4.30
510 1723 2.429250 GTCTTCCTCCTGTCCTTAGCTC 59.571 54.545 0.00 0.00 0.00 4.09
512 1725 0.710588 TCCTCCTGTCCTTAGCTCCA 59.289 55.000 0.00 0.00 0.00 3.86
785 2327 5.083821 CCTTTCCACCTTTAATTCCTTCCA 58.916 41.667 0.00 0.00 0.00 3.53
838 2385 2.846827 CCCTTCCTCCAATTACCACTCT 59.153 50.000 0.00 0.00 0.00 3.24
850 2397 1.222936 CCACTCTCCCACATCTGGC 59.777 63.158 0.00 0.00 36.00 4.85
904 2451 0.026285 CGCATTCCGTTTCCATCGTC 59.974 55.000 0.00 0.00 0.00 4.20
945 2492 0.387565 GCGAGCTAGAGAGGGAAAGG 59.612 60.000 0.00 0.00 0.00 3.11
946 2493 2.024825 GCGAGCTAGAGAGGGAAAGGA 61.025 57.143 0.00 0.00 0.00 3.36
947 2494 2.379972 CGAGCTAGAGAGGGAAAGGAA 58.620 52.381 0.00 0.00 0.00 3.36
948 2495 2.761208 CGAGCTAGAGAGGGAAAGGAAA 59.239 50.000 0.00 0.00 0.00 3.13
949 2496 3.181480 CGAGCTAGAGAGGGAAAGGAAAG 60.181 52.174 0.00 0.00 0.00 2.62
955 2502 2.503765 GAGAGGGAAAGGAAAGGAGGAG 59.496 54.545 0.00 0.00 0.00 3.69
959 2508 2.645297 GGGAAAGGAAAGGAGGAGTCTT 59.355 50.000 0.00 0.00 0.00 3.01
974 2523 4.200092 GGAGTCTTTCTCTCTCTCCTCTC 58.800 52.174 0.00 0.00 42.40 3.20
976 2525 3.591527 AGTCTTTCTCTCTCTCCTCTCCA 59.408 47.826 0.00 0.00 0.00 3.86
997 2547 1.795170 GCGAGTTGCTGGCAAGGAAA 61.795 55.000 8.34 0.00 41.73 3.13
1008 2558 1.047801 GCAAGGAAACCATGTTGGGT 58.952 50.000 0.00 0.00 40.89 4.51
1016 2566 1.178534 ACCATGTTGGGTTCTTGCGG 61.179 55.000 0.00 0.00 43.37 5.69
1157 2707 2.321333 CGCACCGTACACCATTGCA 61.321 57.895 0.00 0.00 32.51 4.08
1158 2708 1.643868 CGCACCGTACACCATTGCAT 61.644 55.000 0.00 0.00 32.51 3.96
1159 2709 1.374560 GCACCGTACACCATTGCATA 58.625 50.000 0.00 0.00 33.24 3.14
1160 2710 1.946768 GCACCGTACACCATTGCATAT 59.053 47.619 0.00 0.00 33.24 1.78
1161 2711 2.286950 GCACCGTACACCATTGCATATG 60.287 50.000 0.00 0.00 33.24 1.78
1188 2757 6.934083 TCTAATTGCATGATAGTTCGGCAATA 59.066 34.615 10.15 0.00 46.25 1.90
1508 3190 2.358737 AAGAAGCACTTCCGCCGG 60.359 61.111 0.00 0.00 40.33 6.13
1662 3348 4.324267 CCGGTAAACAATCAACCTCTCTT 58.676 43.478 0.00 0.00 0.00 2.85
1663 3349 4.392138 CCGGTAAACAATCAACCTCTCTTC 59.608 45.833 0.00 0.00 0.00 2.87
1673 3359 2.909662 CAACCTCTCTTCCTTCTTCCCT 59.090 50.000 0.00 0.00 0.00 4.20
1691 3377 0.613777 CTACCACCCCTCCAACTCAC 59.386 60.000 0.00 0.00 0.00 3.51
1874 3573 2.759795 GGCTGGGGCTCACTTCTT 59.240 61.111 0.00 0.00 38.73 2.52
1995 3700 1.202405 CCGTTGGTTTCTTGCTTGCTT 60.202 47.619 0.00 0.00 0.00 3.91
2132 3841 0.459063 TCATACTCGCACTGCTGCTG 60.459 55.000 4.89 4.89 41.77 4.41
2133 3842 1.812922 ATACTCGCACTGCTGCTGC 60.813 57.895 8.89 8.89 41.77 5.25
2134 3843 2.236223 ATACTCGCACTGCTGCTGCT 62.236 55.000 17.00 0.00 41.77 4.24
2193 3916 6.650807 CGCCCTGGATCGCAATATAATAATAT 59.349 38.462 0.00 0.00 0.00 1.28
2216 3939 0.473755 TCACAAGTCATGGCACTGGT 59.526 50.000 0.00 0.00 29.76 4.00
2219 3942 1.075482 AAGTCATGGCACTGGTGGG 59.925 57.895 0.00 0.00 0.00 4.61
2224 3947 3.808218 ATGGCACTGGTGGGCGTTT 62.808 57.895 0.00 0.00 0.00 3.60
2225 3948 3.977244 GGCACTGGTGGGCGTTTG 61.977 66.667 2.84 0.00 0.00 2.93
2226 3949 4.645921 GCACTGGTGGGCGTTTGC 62.646 66.667 2.84 0.00 41.71 3.68
2227 3950 4.326766 CACTGGTGGGCGTTTGCG 62.327 66.667 0.00 0.00 44.10 4.85
2236 3959 3.788766 GCGTTTGCGGCTCGTCAT 61.789 61.111 0.00 0.00 38.78 3.06
2237 3960 2.449525 GCGTTTGCGGCTCGTCATA 61.450 57.895 0.00 0.00 38.78 2.15
2238 3961 1.962092 GCGTTTGCGGCTCGTCATAA 61.962 55.000 0.00 0.00 38.78 1.90
2239 3962 0.650512 CGTTTGCGGCTCGTCATAAT 59.349 50.000 0.00 0.00 0.00 1.28
2306 4029 4.380233 GCTATAAGCCAATGCCATGTCATC 60.380 45.833 0.00 0.00 38.69 2.92
2311 4034 2.689471 GCCAATGCCATGTCATCTACAA 59.311 45.455 0.00 0.00 42.70 2.41
2317 4040 2.880890 GCCATGTCATCTACAACCCATC 59.119 50.000 0.00 0.00 42.70 3.51
2323 4046 7.821359 CCATGTCATCTACAACCCATCTTATAG 59.179 40.741 0.00 0.00 42.70 1.31
2324 4047 6.759272 TGTCATCTACAACCCATCTTATAGC 58.241 40.000 0.00 0.00 34.29 2.97
2325 4048 6.554982 TGTCATCTACAACCCATCTTATAGCT 59.445 38.462 0.00 0.00 34.29 3.32
2334 4057 8.660435 ACAACCCATCTTATAGCTAACATGTAT 58.340 33.333 0.00 0.00 0.00 2.29
2385 4108 6.441088 TTTTTATTATGTGGCCCACCTTTT 57.559 33.333 12.25 0.00 36.63 2.27
2393 4116 3.245586 TGTGGCCCACCTTTTATTCTCAT 60.246 43.478 12.25 0.00 36.63 2.90
2401 4124 6.405842 CCCACCTTTTATTCTCATAAAGTGCC 60.406 42.308 0.00 0.00 36.43 5.01
2450 4180 0.736053 CGCGCTTACCTTCTCTCTCT 59.264 55.000 5.56 0.00 0.00 3.10
2462 4192 6.314917 ACCTTCTCTCTCTTCTTCTCTTTCT 58.685 40.000 0.00 0.00 0.00 2.52
2531 4261 6.378564 TGACTAAGCTCTATTGTACTTGCTCT 59.621 38.462 0.00 0.00 0.00 4.09
2532 4262 7.093727 TGACTAAGCTCTATTGTACTTGCTCTT 60.094 37.037 0.00 0.00 0.00 2.85
2533 4263 8.294954 ACTAAGCTCTATTGTACTTGCTCTTA 57.705 34.615 0.00 0.00 0.00 2.10
2534 4264 8.410141 ACTAAGCTCTATTGTACTTGCTCTTAG 58.590 37.037 0.00 0.00 36.81 2.18
2535 4265 6.155475 AGCTCTATTGTACTTGCTCTTAGG 57.845 41.667 0.00 0.00 0.00 2.69
2561 4291 7.168219 AGTAACATCACACACTCCAATACAAT 58.832 34.615 0.00 0.00 0.00 2.71
2566 4296 6.707440 TCACACACTCCAATACAATTTTGT 57.293 33.333 1.08 1.08 44.86 2.83
2574 4304 8.924691 CACTCCAATACAATTTTGTTTATGTGG 58.075 33.333 0.63 3.51 42.35 4.17
2590 4320 9.800433 TGTTTATGTGGCACATATTTAATGAAG 57.200 29.630 33.89 0.00 44.52 3.02
2635 4366 3.370061 GCTAAGTTACCGGAACATCACAC 59.630 47.826 9.46 0.00 40.86 3.82
2652 4383 4.522114 TCACACACTCCAAGAAACAATGA 58.478 39.130 0.00 0.00 0.00 2.57
2657 4388 4.818546 ACACTCCAAGAAACAATGAGTCTG 59.181 41.667 0.00 0.00 34.21 3.51
2694 4425 8.907222 ATACATCATTGCATGACACTACATAA 57.093 30.769 0.00 0.00 43.01 1.90
2700 4431 8.522003 TCATTGCATGACACTACATAAATGTTT 58.478 29.630 0.00 0.00 36.98 2.83
2705 4436 8.883731 GCATGACACTACATAAATGTTTCTACT 58.116 33.333 0.00 0.00 41.97 2.57
2780 4511 2.203972 CTTGCCCATTGTGACCAGCG 62.204 60.000 0.00 0.00 0.00 5.18
2927 4667 2.027377 AGTTCATGCTCCTCTTGACCAG 60.027 50.000 0.00 0.00 0.00 4.00
2931 4671 0.827925 TGCTCCTCTTGACCAGACGT 60.828 55.000 0.00 0.00 0.00 4.34
2935 4675 2.160205 TCCTCTTGACCAGACGTGTAG 58.840 52.381 0.00 0.00 0.00 2.74
2936 4676 1.402984 CCTCTTGACCAGACGTGTAGC 60.403 57.143 0.00 0.00 0.00 3.58
2941 4687 0.314302 GACCAGACGTGTAGCAGTGT 59.686 55.000 0.00 0.00 0.00 3.55
2951 4697 3.362986 CGTGTAGCAGTGTTGTTGTGATC 60.363 47.826 0.00 0.00 0.00 2.92
2955 4701 3.141398 AGCAGTGTTGTTGTGATCGATT 58.859 40.909 0.00 0.00 0.00 3.34
2956 4702 3.187227 AGCAGTGTTGTTGTGATCGATTC 59.813 43.478 0.00 0.00 0.00 2.52
2957 4703 3.725356 CAGTGTTGTTGTGATCGATTCG 58.275 45.455 0.00 0.00 0.00 3.34
2958 4704 3.428534 CAGTGTTGTTGTGATCGATTCGA 59.571 43.478 11.73 11.73 41.13 3.71
2976 4725 3.624900 TCGATCGTCGGTGTGATTATTC 58.375 45.455 15.94 0.00 40.88 1.75
2979 4728 2.521996 TCGTCGGTGTGATTATTCGTG 58.478 47.619 0.00 0.00 0.00 4.35
3297 5046 2.665185 ACCGGTTCGAACAGCAGC 60.665 61.111 28.24 10.65 0.00 5.25
3535 5284 2.315386 GCGACAACCGTGGAAGGAC 61.315 63.158 0.00 0.00 41.15 3.85
3544 5293 1.668151 GTGGAAGGACAGACGTGGC 60.668 63.158 0.00 0.00 0.00 5.01
3821 5570 4.697756 CGCCAGAAGTTCCGGGCA 62.698 66.667 26.73 0.00 46.75 5.36
4412 6162 6.563222 TTCTTTAACTTGGACCATTTACCG 57.437 37.500 0.00 0.00 0.00 4.02
4499 6286 3.182967 CAAGCCTACATCTGACGAAGAC 58.817 50.000 0.00 0.00 37.88 3.01
4522 6309 8.790718 AGACAAATCCATAAATATCATGACTGC 58.209 33.333 0.00 0.00 0.00 4.40
4564 6351 2.937519 TGTGGGTGTAAATGTGAGCAA 58.062 42.857 0.00 0.00 0.00 3.91
4571 6358 5.971202 GGGTGTAAATGTGAGCAATAAATCG 59.029 40.000 0.00 0.00 0.00 3.34
4651 6439 3.851105 GCTTGTTGCTCACAGTTGATGTC 60.851 47.826 0.00 0.00 38.31 3.06
4659 6447 4.260132 GCTCACAGTTGATGTCGATGAATC 60.260 45.833 0.00 0.00 41.41 2.52
4685 6473 9.557061 CCTTCAGATCAGATTTCATTCTATTCA 57.443 33.333 0.00 0.00 0.00 2.57
4707 6495 3.881220 TGCCCTAGTAACATAACAAGCC 58.119 45.455 0.00 0.00 0.00 4.35
4730 6518 5.048782 CCTTAAGCACAGCAAAGTTGTATCA 60.049 40.000 0.00 0.00 0.00 2.15
4876 6672 3.467803 AGTATGGCGATTGTAAAGGAGC 58.532 45.455 0.00 0.00 0.00 4.70
4891 6687 1.992557 AGGAGCAGGGTTTGGTAATGA 59.007 47.619 0.00 0.00 37.72 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 6.595682 AGTGATTCTATTCCACCAGGTAATG 58.404 40.000 0.00 0.00 35.89 1.90
139 140 4.819105 TCTTCTCCAACATAACCGTCAT 57.181 40.909 0.00 0.00 0.00 3.06
165 170 3.005367 CAGCGGGGTCTTGTTAAAACAAT 59.995 43.478 8.62 0.00 46.71 2.71
168 173 1.335597 GCAGCGGGGTCTTGTTAAAAC 60.336 52.381 0.00 0.00 0.00 2.43
199 204 8.372459 CACTATAGTACTATTTGGGTTGCCATA 58.628 37.037 20.21 0.00 0.00 2.74
205 210 8.849543 TCTTCCACTATAGTACTATTTGGGTT 57.150 34.615 27.45 8.58 32.51 4.11
300 310 5.599732 CAGAGAGAGAGAGAGAGAGAGAAG 58.400 50.000 0.00 0.00 0.00 2.85
301 311 4.141846 GCAGAGAGAGAGAGAGAGAGAGAA 60.142 50.000 0.00 0.00 0.00 2.87
304 314 2.435805 GGCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
306 316 2.481441 AGGCAGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
308 318 2.104792 GCTAGGCAGAGAGAGAGAGAGA 59.895 54.545 0.00 0.00 0.00 3.10
309 319 2.158769 TGCTAGGCAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 33.32 3.20
311 321 2.346766 TGCTAGGCAGAGAGAGAGAG 57.653 55.000 0.00 0.00 33.32 3.20
312 322 3.311167 AATGCTAGGCAGAGAGAGAGA 57.689 47.619 0.00 0.00 43.65 3.10
313 323 3.132646 ACAAATGCTAGGCAGAGAGAGAG 59.867 47.826 0.00 0.00 43.65 3.20
314 324 3.102972 ACAAATGCTAGGCAGAGAGAGA 58.897 45.455 0.00 0.00 43.65 3.10
323 333 3.429881 GCACAAAAGAACAAATGCTAGGC 59.570 43.478 0.00 0.00 0.00 3.93
324 334 3.670055 CGCACAAAAGAACAAATGCTAGG 59.330 43.478 0.00 0.00 0.00 3.02
487 1697 1.751924 CTAAGGACAGGAGGAAGACGG 59.248 57.143 0.00 0.00 0.00 4.79
489 1699 2.429250 GAGCTAAGGACAGGAGGAAGAC 59.571 54.545 0.00 0.00 0.00 3.01
510 1723 1.341080 AATTGTCCTTGCAGGGTTGG 58.659 50.000 15.41 0.25 35.59 3.77
512 1725 3.165071 CCTTAATTGTCCTTGCAGGGTT 58.835 45.455 15.41 4.20 35.59 4.11
785 2327 1.260561 CTACAACAACAGCGAGCGTTT 59.739 47.619 0.00 0.00 0.00 3.60
827 2374 3.200825 CCAGATGTGGGAGAGTGGTAATT 59.799 47.826 0.00 0.00 40.67 1.40
838 2385 1.126488 GAGATCAGCCAGATGTGGGA 58.874 55.000 11.47 0.31 45.17 4.37
850 2397 2.773525 AGGGAGGGAGAAGAGATCAG 57.226 55.000 0.00 0.00 0.00 2.90
904 2451 5.122239 CGCCTGATCAAGAGAGTCTATCTAG 59.878 48.000 0.00 0.00 38.84 2.43
945 2492 5.016831 AGAGAGAGAAAGACTCCTCCTTTC 58.983 45.833 0.00 0.00 45.96 2.62
946 2493 5.010708 AGAGAGAGAAAGACTCCTCCTTT 57.989 43.478 0.00 0.00 45.96 3.11
947 2494 4.569865 GGAGAGAGAGAAAGACTCCTCCTT 60.570 50.000 17.04 0.00 45.96 3.36
948 2495 3.053619 GGAGAGAGAGAAAGACTCCTCCT 60.054 52.174 17.04 4.57 45.96 3.69
949 2496 3.288092 GGAGAGAGAGAAAGACTCCTCC 58.712 54.545 0.00 0.00 45.96 4.30
955 2502 3.963129 TGGAGAGGAGAGAGAGAAAGAC 58.037 50.000 0.00 0.00 0.00 3.01
959 2508 2.733956 GCTTGGAGAGGAGAGAGAGAA 58.266 52.381 0.00 0.00 0.00 2.87
997 2547 1.178534 CCGCAAGAACCCAACATGGT 61.179 55.000 0.00 0.00 41.55 3.55
1038 2588 4.710167 TCCGCCGTCTCCTCGTCA 62.710 66.667 0.00 0.00 0.00 4.35
1149 2699 6.904463 TGCAATTAGATCATATGCAATGGT 57.096 33.333 11.48 0.00 43.39 3.55
1157 2707 9.322773 CCGAACTATCATGCAATTAGATCATAT 57.677 33.333 0.00 0.00 0.00 1.78
1158 2708 7.278646 GCCGAACTATCATGCAATTAGATCATA 59.721 37.037 0.00 0.00 0.00 2.15
1159 2709 6.093219 GCCGAACTATCATGCAATTAGATCAT 59.907 38.462 0.00 0.00 0.00 2.45
1160 2710 5.409520 GCCGAACTATCATGCAATTAGATCA 59.590 40.000 0.00 0.00 0.00 2.92
1161 2711 5.409520 TGCCGAACTATCATGCAATTAGATC 59.590 40.000 0.00 0.00 32.05 2.75
1188 2757 3.197983 GCCACTAGTATTTCCACTCCACT 59.802 47.826 0.00 0.00 0.00 4.00
1662 3348 0.253020 GGGGTGGTAGGGAAGAAGGA 60.253 60.000 0.00 0.00 0.00 3.36
1663 3349 0.253207 AGGGGTGGTAGGGAAGAAGG 60.253 60.000 0.00 0.00 0.00 3.46
1673 3359 0.838987 GGTGAGTTGGAGGGGTGGTA 60.839 60.000 0.00 0.00 0.00 3.25
1691 3377 2.989422 AGAAAGAAAATGGCGTTCGG 57.011 45.000 0.00 0.00 0.00 4.30
1874 3573 7.676947 TCCGATAAAGAAAGAGAAAAGGAAGA 58.323 34.615 0.00 0.00 0.00 2.87
2132 3841 0.453390 GGCAGCAATTGTCAGGTAGC 59.547 55.000 7.40 1.47 0.00 3.58
2133 3842 2.119801 AGGCAGCAATTGTCAGGTAG 57.880 50.000 7.40 0.00 32.36 3.18
2134 3843 2.676750 CGTAGGCAGCAATTGTCAGGTA 60.677 50.000 7.40 0.00 32.36 3.08
2193 3916 0.953727 GTGCCATGACTTGTGAGCAA 59.046 50.000 0.00 0.00 31.03 3.91
2195 3918 0.520404 CAGTGCCATGACTTGTGAGC 59.480 55.000 0.00 0.00 0.00 4.26
2219 3942 1.962092 TTATGACGAGCCGCAAACGC 61.962 55.000 0.00 0.00 38.22 4.84
2224 3947 1.227527 CCCATTATGACGAGCCGCA 60.228 57.895 0.00 0.00 0.00 5.69
2225 3948 1.961277 CCCCATTATGACGAGCCGC 60.961 63.158 0.00 0.00 0.00 6.53
2226 3949 0.319900 CTCCCCATTATGACGAGCCG 60.320 60.000 0.00 0.00 0.00 5.52
2227 3950 0.035458 CCTCCCCATTATGACGAGCC 59.965 60.000 0.00 0.00 0.00 4.70
2228 3951 1.048601 TCCTCCCCATTATGACGAGC 58.951 55.000 0.00 0.00 0.00 5.03
2229 3952 2.700897 AGTTCCTCCCCATTATGACGAG 59.299 50.000 0.00 0.00 0.00 4.18
2230 3953 2.759355 AGTTCCTCCCCATTATGACGA 58.241 47.619 0.00 0.00 0.00 4.20
2231 3954 3.560636 AAGTTCCTCCCCATTATGACG 57.439 47.619 0.00 0.00 0.00 4.35
2232 3955 5.743422 GCTCTAAGTTCCTCCCCATTATGAC 60.743 48.000 0.00 0.00 0.00 3.06
2233 3956 4.348168 GCTCTAAGTTCCTCCCCATTATGA 59.652 45.833 0.00 0.00 0.00 2.15
2234 3957 4.103153 TGCTCTAAGTTCCTCCCCATTATG 59.897 45.833 0.00 0.00 0.00 1.90
2235 3958 4.307259 TGCTCTAAGTTCCTCCCCATTAT 58.693 43.478 0.00 0.00 0.00 1.28
2236 3959 3.731431 TGCTCTAAGTTCCTCCCCATTA 58.269 45.455 0.00 0.00 0.00 1.90
2237 3960 2.562296 TGCTCTAAGTTCCTCCCCATT 58.438 47.619 0.00 0.00 0.00 3.16
2238 3961 2.270434 TGCTCTAAGTTCCTCCCCAT 57.730 50.000 0.00 0.00 0.00 4.00
2239 3962 1.839994 CATGCTCTAAGTTCCTCCCCA 59.160 52.381 0.00 0.00 0.00 4.96
2294 4017 2.241941 TGGGTTGTAGATGACATGGCAT 59.758 45.455 15.73 15.73 38.07 4.40
2295 4018 1.632920 TGGGTTGTAGATGACATGGCA 59.367 47.619 2.18 2.18 38.07 4.92
2296 4019 2.418368 TGGGTTGTAGATGACATGGC 57.582 50.000 0.00 0.00 38.07 4.40
2297 4020 4.428294 AGATGGGTTGTAGATGACATGG 57.572 45.455 0.00 0.00 38.07 3.66
2298 4021 7.332926 GCTATAAGATGGGTTGTAGATGACATG 59.667 40.741 0.00 0.00 38.07 3.21
2299 4022 7.236432 AGCTATAAGATGGGTTGTAGATGACAT 59.764 37.037 0.00 0.00 38.07 3.06
2306 4029 8.150945 ACATGTTAGCTATAAGATGGGTTGTAG 58.849 37.037 10.22 0.00 43.55 2.74
2371 4094 2.109128 TGAGAATAAAAGGTGGGCCACA 59.891 45.455 35.69 17.34 35.86 4.17
2380 4103 7.993183 TCCTAGGCACTTTATGAGAATAAAAGG 59.007 37.037 2.96 0.00 41.75 3.11
2385 4108 5.602561 TGCTCCTAGGCACTTTATGAGAATA 59.397 40.000 2.96 0.00 41.75 1.75
2431 4154 0.736053 AGAGAGAGAAGGTAAGCGCG 59.264 55.000 0.00 0.00 0.00 6.86
2450 4180 6.591935 TGCTTAGTTGGAAGAAAGAGAAGAA 58.408 36.000 0.00 0.00 0.00 2.52
2493 4223 3.463944 GCTTAGTCAGCGGGCTATAAAA 58.536 45.455 0.00 0.00 39.29 1.52
2494 4224 3.107642 GCTTAGTCAGCGGGCTATAAA 57.892 47.619 0.00 0.00 39.29 1.40
2506 4236 6.378564 AGAGCAAGTACAATAGAGCTTAGTCA 59.621 38.462 0.00 0.00 31.61 3.41
2507 4237 6.801575 AGAGCAAGTACAATAGAGCTTAGTC 58.198 40.000 0.00 0.00 31.61 2.59
2511 4241 6.381420 TCCTAAGAGCAAGTACAATAGAGCTT 59.619 38.462 0.00 0.00 31.61 3.74
2513 4243 6.150396 TCCTAAGAGCAAGTACAATAGAGC 57.850 41.667 0.00 0.00 0.00 4.09
2521 4251 6.752815 GTGATGTTACTCCTAAGAGCAAGTAC 59.247 42.308 0.00 0.00 44.65 2.73
2535 4265 6.163476 TGTATTGGAGTGTGTGATGTTACTC 58.837 40.000 0.00 0.00 38.98 2.59
2574 4304 7.519649 GCACCTCTCTCTTCATTAAATATGTGC 60.520 40.741 0.00 0.00 35.67 4.57
2587 4317 1.346068 ACCACAAGCACCTCTCTCTTC 59.654 52.381 0.00 0.00 0.00 2.87
2590 4320 2.300437 AGTTACCACAAGCACCTCTCTC 59.700 50.000 0.00 0.00 0.00 3.20
2635 4366 4.818546 ACAGACTCATTGTTTCTTGGAGTG 59.181 41.667 0.00 0.00 38.82 3.51
2676 4407 8.742777 AGAAACATTTATGTAGTGTCATGCAAT 58.257 29.630 0.00 0.00 40.80 3.56
2729 4460 8.186709 AGCTAGTAACTTACACACTTTCCTAA 57.813 34.615 1.79 0.00 0.00 2.69
2733 4464 9.420551 ACATAAGCTAGTAACTTACACACTTTC 57.579 33.333 1.79 0.00 32.67 2.62
2734 4465 9.774413 AACATAAGCTAGTAACTTACACACTTT 57.226 29.630 1.79 0.00 32.67 2.66
2780 4511 3.232213 TCTACATGGAAGAGAACGCAC 57.768 47.619 0.00 0.00 0.00 5.34
2927 4667 1.931172 ACAACAACACTGCTACACGTC 59.069 47.619 0.00 0.00 0.00 4.34
2931 4671 2.799978 CGATCACAACAACACTGCTACA 59.200 45.455 0.00 0.00 0.00 2.74
2935 4675 3.482786 GAATCGATCACAACAACACTGC 58.517 45.455 0.00 0.00 0.00 4.40
2936 4676 3.428534 TCGAATCGATCACAACAACACTG 59.571 43.478 0.00 0.00 0.00 3.66
2955 4701 3.624900 GAATAATCACACCGACGATCGA 58.375 45.455 24.34 0.00 43.74 3.59
2956 4702 2.400735 CGAATAATCACACCGACGATCG 59.599 50.000 14.88 14.88 40.07 3.69
2957 4703 3.179795 CACGAATAATCACACCGACGATC 59.820 47.826 0.00 0.00 0.00 3.69
2958 4704 3.113322 CACGAATAATCACACCGACGAT 58.887 45.455 0.00 0.00 0.00 3.73
2959 4705 2.521996 CACGAATAATCACACCGACGA 58.478 47.619 0.00 0.00 0.00 4.20
2960 4706 1.586578 CCACGAATAATCACACCGACG 59.413 52.381 0.00 0.00 0.00 5.12
2961 4707 1.326548 GCCACGAATAATCACACCGAC 59.673 52.381 0.00 0.00 0.00 4.79
2962 4708 1.647346 GCCACGAATAATCACACCGA 58.353 50.000 0.00 0.00 0.00 4.69
2963 4709 0.655733 GGCCACGAATAATCACACCG 59.344 55.000 0.00 0.00 0.00 4.94
2965 4711 0.655733 CCGGCCACGAATAATCACAC 59.344 55.000 2.24 0.00 44.60 3.82
2979 4728 2.444140 TTAGAGAGAGGGCCGGCC 60.444 66.667 38.57 38.57 0.00 6.13
3005 4754 2.452813 CCACATTTCGACGAGCCCG 61.453 63.158 0.00 0.00 42.50 6.13
3106 4855 4.248842 CCGCCACTCCACCACACA 62.249 66.667 0.00 0.00 0.00 3.72
3425 5174 4.386951 TGTGGCGCTGCGTACCAT 62.387 61.111 24.04 0.00 35.53 3.55
4150 5900 1.825090 AGCGAAAGATTCCATGCACA 58.175 45.000 0.00 0.00 0.00 4.57
4409 6159 1.301087 TCGACGTTTGCAATCCGGT 60.301 52.632 19.26 7.68 0.00 5.28
4410 6160 1.131826 GTCGACGTTTGCAATCCGG 59.868 57.895 19.26 0.00 0.00 5.14
4412 6162 0.450482 CGTGTCGACGTTTGCAATCC 60.450 55.000 11.62 0.00 40.91 3.01
4435 6222 2.677003 GGCGTGTGTTCGGATGTGG 61.677 63.158 0.00 0.00 0.00 4.17
4499 6286 8.789762 TGAGCAGTCATGATATTTATGGATTTG 58.210 33.333 0.00 0.00 0.00 2.32
4521 6308 8.266682 CACATGTACACGTTTAGTATAATGAGC 58.733 37.037 0.00 0.00 0.00 4.26
4522 6309 8.752254 CCACATGTACACGTTTAGTATAATGAG 58.248 37.037 0.00 7.94 0.00 2.90
4564 6351 5.067153 TGAATTGCGGTCCATTTCGATTTAT 59.933 36.000 0.00 0.00 36.88 1.40
4571 6358 1.818674 AGGTGAATTGCGGTCCATTTC 59.181 47.619 0.00 0.00 35.43 2.17
4659 6447 9.557061 TGAATAGAATGAAATCTGATCTGAAGG 57.443 33.333 6.37 0.00 0.00 3.46
4685 6473 4.166144 AGGCTTGTTATGTTACTAGGGCAT 59.834 41.667 0.00 0.00 0.00 4.40
4707 6495 6.000891 TGATACAACTTTGCTGTGCTTAAG 57.999 37.500 0.00 0.00 0.00 1.85
4854 6650 3.495001 GCTCCTTTACAATCGCCATACTC 59.505 47.826 0.00 0.00 0.00 2.59
4876 6672 5.009631 TGTCATCTTCATTACCAAACCCTG 58.990 41.667 0.00 0.00 0.00 4.45
4891 6687 2.746277 GGGCGCCGTTGTCATCTT 60.746 61.111 22.54 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.