Multiple sequence alignment - TraesCS2B01G484700

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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 TraesCS2B01G484700 chr2B 100.000 4538 0 0 1 4538 682020164 682015627 0.000000e+00 8381
1 TraesCS2B01G484700 chr2D 94.289 3992 185 25 1 3965 569198806 569194831 0.000000e+00 6069
2 TraesCS2B01G484700 chr2D 87.072 526 51 9 3964 4485 569194794 569194282 3.040000e-161 579
3 TraesCS2B01G484700 chr2A 93.552 3908 201 19 80 3964 709031672 709027793 0.000000e+00 5773
4 TraesCS2B01G484700 chr2A 85.284 299 28 7 4186 4481 709027585 709027300 1.230000e-75 294


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 TraesCS2B01G484700 chr2B 682015627 682020164 4537 True 8381.0 8381 100.0000 1 4538 1 chr2B.!!$R1 4537
1 TraesCS2B01G484700 chr2D 569194282 569198806 4524 True 3324.0 6069 90.6805 1 4485 2 chr2D.!!$R1 4484
2 TraesCS2B01G484700 chr2A 709027300 709031672 4372 True 3033.5 5773 89.4180 80 4481 2 chr2A.!!$R1 4401

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
839 860 0.539986 GCCGTTCCCATTCTACCTCA 59.460 55.0 0.0 0.0 0.0 3.86 F
1912 1933 0.179192 CAATGTGACATGGCGGTTCG 60.179 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2112 0.320771 AGTCTACCTGTTGCGGCAAG 60.321 55.0 16.97 7.29 0.0 4.01 R
3581 3603 0.527817 CCAAGACCACGGCTACGATC 60.528 60.0 0.00 0.00 44.6 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
142 143 9.816787 TTAAAAAGTTACATTTCAGTCCCCTAT 57.183 29.630 0.00 0.00 0.00 2.57
143 144 8.721133 AAAAAGTTACATTTCAGTCCCCTATT 57.279 30.769 0.00 0.00 0.00 1.73
162 163 5.182570 CCTATTGTCGACCGTCAATATCCTA 59.817 44.000 14.12 3.39 36.27 2.94
164 165 3.281158 TGTCGACCGTCAATATCCTACA 58.719 45.455 14.12 0.00 0.00 2.74
174 175 4.341235 GTCAATATCCTACAAAAAGGGCCC 59.659 45.833 16.46 16.46 37.24 5.80
175 176 2.721425 TATCCTACAAAAAGGGCCCG 57.279 50.000 18.44 3.62 37.24 6.13
179 180 1.165270 CTACAAAAAGGGCCCGTGAG 58.835 55.000 18.44 9.47 0.00 3.51
236 240 5.625721 CGGTCTATCATTGTTGATCGTAGAC 59.374 44.000 8.08 8.08 42.51 2.59
256 260 2.293399 ACGAAAAGTCATCAAGGCAACC 59.707 45.455 0.00 0.00 37.17 3.77
262 277 2.147958 GTCATCAAGGCAACCGTAACA 58.852 47.619 0.00 0.00 37.17 2.41
267 282 4.274602 TCAAGGCAACCGTAACATCTTA 57.725 40.909 0.00 0.00 37.17 2.10
282 297 5.840940 ACATCTTAGAAAAGAAACCGTCG 57.159 39.130 0.00 0.00 44.75 5.12
297 312 1.301716 GTCGCCACTGAAAGAGCCA 60.302 57.895 0.00 0.00 37.43 4.75
303 318 2.159114 GCCACTGAAAGAGCCACAAAAA 60.159 45.455 0.00 0.00 37.43 1.94
309 324 6.638468 CACTGAAAGAGCCACAAAAATAAGAC 59.362 38.462 0.00 0.00 37.43 3.01
310 325 6.547510 ACTGAAAGAGCCACAAAAATAAGACT 59.452 34.615 0.00 0.00 37.43 3.24
332 348 9.620259 AGACTAAAATCTCCATTATTTCTCACC 57.380 33.333 0.00 0.00 0.00 4.02
335 351 9.401058 CTAAAATCTCCATTATTTCTCACCAGT 57.599 33.333 0.00 0.00 0.00 4.00
336 352 7.636150 AAATCTCCATTATTTCTCACCAGTG 57.364 36.000 0.00 0.00 0.00 3.66
340 356 6.065976 TCCATTATTTCTCACCAGTGTCAT 57.934 37.500 0.00 0.00 0.00 3.06
343 359 5.762179 TTATTTCTCACCAGTGTCATCCT 57.238 39.130 0.00 0.00 0.00 3.24
370 391 2.100879 GAGGGTGCACCGACTTGACT 62.101 60.000 29.08 18.28 46.96 3.41
375 396 0.969149 TGCACCGACTTGACTGAGAT 59.031 50.000 0.00 0.00 0.00 2.75
394 415 6.582636 TGAGATGCTGGAATAATACTTTCGT 58.417 36.000 0.00 0.00 0.00 3.85
440 461 4.181309 ACGGTGCAAGTTTCTTGAAAAA 57.819 36.364 12.77 0.00 0.00 1.94
463 484 9.651913 AAAAACAAATTTATACATGCCCTGTAG 57.348 29.630 0.00 0.00 43.44 2.74
632 653 4.179599 CTCCCTCCCTCCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
649 670 3.756783 CCCCTCCCTCTCCCGAGT 61.757 72.222 0.00 0.00 35.43 4.18
699 720 2.492773 CCCTCAATCCAATGCGGCC 61.493 63.158 0.00 0.00 33.14 6.13
839 860 0.539986 GCCGTTCCCATTCTACCTCA 59.460 55.000 0.00 0.00 0.00 3.86
847 868 1.065701 CCATTCTACCTCACTCGTCGG 59.934 57.143 0.00 0.00 0.00 4.79
903 924 1.376037 CTCCTTGCCTTCCGGTGAC 60.376 63.158 0.00 0.00 0.00 3.67
1074 1095 2.434428 CTGCAGTTCTTGAAGGCTCAT 58.566 47.619 5.25 0.00 0.00 2.90
1188 1209 3.801997 CTGAGCAGCCCGGGGATT 61.802 66.667 25.28 0.00 0.00 3.01
1197 1218 2.203126 CCGGGGATTGCTGCTCTC 60.203 66.667 0.00 0.00 0.00 3.20
1198 1219 2.739996 CCGGGGATTGCTGCTCTCT 61.740 63.158 0.00 0.00 0.00 3.10
1211 1232 3.672295 CTCTCTTGGCCGGGAGCAC 62.672 68.421 16.93 0.00 46.50 4.40
1233 1254 2.761767 CAATGGGAGTGAAATCATGGCA 59.238 45.455 0.00 0.00 0.00 4.92
1282 1303 2.565391 ACCACGACATCTTGGTATGACA 59.435 45.455 8.22 0.00 45.27 3.58
1288 1309 3.461061 ACATCTTGGTATGACATCAGCG 58.539 45.455 0.00 0.00 0.00 5.18
1308 1329 2.955881 GCTGCCGGGGAACTACTGT 61.956 63.158 2.18 0.00 0.00 3.55
1339 1360 1.017177 TTTCTTCCCGTCCGCATTCG 61.017 55.000 0.00 0.00 0.00 3.34
1356 1377 4.497300 CATTCGGGAATTTCAGTGCAAAT 58.503 39.130 0.00 0.00 0.00 2.32
1386 1407 1.358877 TTGATGTCGTCGCCAATGAG 58.641 50.000 0.00 0.00 0.00 2.90
1401 1422 1.800805 ATGAGTTCAAGCTGGTGTCG 58.199 50.000 0.00 0.00 0.00 4.35
1413 1434 2.286025 GCTGGTGTCGAAGTTTAACGTT 59.714 45.455 5.88 5.88 0.00 3.99
1437 1458 4.019321 TCGGAGGAGATTGTTTGGAGAAAT 60.019 41.667 0.00 0.00 0.00 2.17
1548 1569 2.765122 CCCGGTTCATTTGCATTTGTT 58.235 42.857 0.00 0.00 0.00 2.83
1591 1612 6.373005 TCACTCCAGATAATTCCTTCAACA 57.627 37.500 0.00 0.00 0.00 3.33
1596 1617 4.701651 CCAGATAATTCCTTCAACAGCACA 59.298 41.667 0.00 0.00 0.00 4.57
1669 1690 4.082190 GCCGAGCTATTGAGACCATGTATA 60.082 45.833 0.00 0.00 0.00 1.47
1674 1695 5.186797 AGCTATTGAGACCATGTATAGGCTC 59.813 44.000 0.00 0.00 33.06 4.70
1720 1741 7.052248 TGCATCTTCACATGATCAGTATCTTT 58.948 34.615 0.00 0.00 32.93 2.52
1761 1782 2.030893 TGAAGCCTTCATGTTTTCTGCG 60.031 45.455 2.24 0.00 34.08 5.18
1775 1796 0.518636 TCTGCGAATGCTGCTTTGAC 59.481 50.000 5.43 0.00 43.34 3.18
1776 1797 0.455633 CTGCGAATGCTGCTTTGACC 60.456 55.000 5.43 0.00 43.34 4.02
1788 1809 1.127951 GCTTTGACCGTGTCCAATACG 59.872 52.381 0.00 0.00 40.98 3.06
1813 1834 4.025396 CAGCCATAAAGTATGTCTCAAGCG 60.025 45.833 0.00 0.00 34.36 4.68
1814 1835 3.248602 GCCATAAAGTATGTCTCAAGCGG 59.751 47.826 0.00 0.00 34.36 5.52
1838 1859 0.181114 TCCTCAATTGCTCCCATCGG 59.819 55.000 0.00 0.00 0.00 4.18
1851 1872 2.091830 TCCCATCGGTGTCTATGAGACT 60.092 50.000 8.04 0.00 45.27 3.24
1887 1908 3.492309 GCAACAACATGGTCATGGACAAA 60.492 43.478 14.49 0.00 42.91 2.83
1912 1933 0.179192 CAATGTGACATGGCGGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
1920 1941 1.002624 ATGGCGGTTCGTTGTCCAT 60.003 52.632 0.00 0.00 33.04 3.41
1929 1950 3.366985 GGTTCGTTGTCCATCCCAATTTC 60.367 47.826 0.00 0.00 0.00 2.17
1936 1957 4.849518 TGTCCATCCCAATTTCGATTACA 58.150 39.130 0.00 0.00 0.00 2.41
1944 1965 3.625764 CCAATTTCGATTACATGGTCCGT 59.374 43.478 0.00 0.00 0.00 4.69
2040 2061 4.734989 GCTGCTGAGAACTACGATGTGTAT 60.735 45.833 0.00 0.00 31.20 2.29
2041 2062 4.672409 TGCTGAGAACTACGATGTGTATG 58.328 43.478 0.00 0.00 31.20 2.39
2049 2070 3.447586 ACTACGATGTGTATGACAAGGCT 59.552 43.478 0.00 0.00 38.36 4.58
2055 2076 1.555075 GTGTATGACAAGGCTGGAGGA 59.445 52.381 0.00 0.00 0.00 3.71
2088 2109 5.698545 GGCATATCATGAGGACTACTTTGAC 59.301 44.000 0.09 0.00 0.00 3.18
2091 2112 4.193826 TCATGAGGACTACTTTGACAGC 57.806 45.455 0.00 0.00 0.00 4.40
2100 2121 1.359833 CTTTGACAGCTTGCCGCAA 59.640 52.632 5.52 5.52 42.61 4.85
2157 2178 1.310933 CCATGACCAGTGCTTCAGGC 61.311 60.000 0.00 0.00 42.22 4.85
2194 2215 7.632861 TCTCAATGGTTTGGAGATATTCAAGA 58.367 34.615 0.00 0.00 33.44 3.02
2217 2238 1.518903 GCAGGAGTGGCAACCTTGAC 61.519 60.000 11.08 2.36 33.91 3.18
2256 2277 1.138859 GATATGGGCAACAAAAGGGGC 59.861 52.381 0.00 0.00 39.74 5.80
2278 2299 3.322466 CCAAGGGTCGGAGCAGGT 61.322 66.667 9.66 0.00 0.00 4.00
2310 2331 3.561313 GGGAAGAAGTTGGTATTGGCTCA 60.561 47.826 0.00 0.00 0.00 4.26
2373 2394 3.195661 GTGCTATGTAAGGAGGAAACGG 58.804 50.000 0.00 0.00 0.00 4.44
2382 2403 1.157585 GGAGGAAACGGAAAGCTGTC 58.842 55.000 0.00 0.00 31.81 3.51
2383 2404 0.790814 GAGGAAACGGAAAGCTGTCG 59.209 55.000 0.00 0.00 31.81 4.35
2421 2442 1.774217 TTGGCACCCTCTGGTCCTT 60.774 57.895 0.00 0.00 45.57 3.36
2528 2549 1.089920 GGCAGACGATTCAGCATTGT 58.910 50.000 0.00 0.00 35.98 2.71
2538 2559 8.031864 AGACGATTCAGCATTGTAGATATTAGG 58.968 37.037 0.00 0.00 28.30 2.69
2550 2571 3.825328 AGATATTAGGGCTGCCACAAAG 58.175 45.455 22.05 0.00 0.00 2.77
2631 2652 3.118261 AGGTCGATGATGGCATTACAGTT 60.118 43.478 0.00 0.00 34.11 3.16
2898 2919 0.685097 GCCTTCACTACCTCCACACA 59.315 55.000 0.00 0.00 0.00 3.72
2910 2931 2.574018 CCACACAGGAGCAGACCGA 61.574 63.158 0.00 0.00 41.22 4.69
3102 3123 3.187022 GGCAGCAATTGACACAAAAATCC 59.813 43.478 10.34 0.00 33.76 3.01
3105 3126 4.148696 CAGCAATTGACACAAAAATCCGAC 59.851 41.667 10.34 0.00 0.00 4.79
3208 3229 0.672342 CTTGGCAGAATGGGCTATGC 59.328 55.000 0.00 0.00 35.86 3.14
3303 3324 4.574892 TGAAGAAGTTTGGTGATATCGCA 58.425 39.130 17.68 1.89 0.00 5.10
3376 3397 0.324943 GTGGCACCTGGAGTATGTGT 59.675 55.000 6.29 0.00 32.62 3.72
3420 3441 1.416049 CAACGTGGATTGCGAGTCG 59.584 57.895 8.54 8.54 0.00 4.18
3480 3501 1.558294 AGCATGCCTCACATCAGAGAA 59.442 47.619 15.66 0.00 36.64 2.87
3510 3531 3.011032 AGGAGCATCACCCAAAGAAATCT 59.989 43.478 0.00 0.00 36.25 2.40
3581 3603 4.848357 ACCCACTGAACTATCTTGATTGG 58.152 43.478 0.00 0.00 0.00 3.16
3599 3621 0.527817 GGATCGTAGCCGTGGTCTTG 60.528 60.000 0.00 0.00 35.01 3.02
3799 3825 3.258372 TCATGTAGTTCTCCTGTGTGACC 59.742 47.826 0.00 0.00 0.00 4.02
3809 3835 6.222038 TCTCCTGTGTGACCTGTATAAATC 57.778 41.667 0.00 0.00 0.00 2.17
3811 3837 6.096987 TCTCCTGTGTGACCTGTATAAATCTC 59.903 42.308 0.00 0.00 0.00 2.75
3848 3874 4.016444 TCCATCCCTCAACTTATTTGTGC 58.984 43.478 0.00 0.00 36.49 4.57
3850 3876 3.410631 TCCCTCAACTTATTTGTGCGA 57.589 42.857 0.00 0.00 36.49 5.10
3855 3881 2.096466 TCAACTTATTTGTGCGAGTGCG 60.096 45.455 0.00 0.00 37.74 5.34
3872 3899 1.847890 GCGGCGCAACTGTTTCCTTA 61.848 55.000 29.21 0.00 0.00 2.69
3880 3907 5.739161 GCGCAACTGTTTCCTTATATTTCAG 59.261 40.000 0.30 0.00 0.00 3.02
3910 3937 5.160607 TGGTGTATTAAACTCCTGTCCAG 57.839 43.478 9.02 0.00 41.50 3.86
3920 3947 3.837355 ACTCCTGTCCAGCAATTCTTTT 58.163 40.909 0.00 0.00 0.00 2.27
3923 3950 2.611224 CCTGTCCAGCAATTCTTTTGCC 60.611 50.000 6.69 0.00 45.98 4.52
3924 3951 2.036217 CTGTCCAGCAATTCTTTTGCCA 59.964 45.455 6.69 0.00 45.98 4.92
3926 3953 2.997986 GTCCAGCAATTCTTTTGCCATG 59.002 45.455 6.69 0.53 45.98 3.66
3929 3956 3.055963 CCAGCAATTCTTTTGCCATGGTA 60.056 43.478 14.67 5.86 45.98 3.25
3934 3961 4.660789 ATTCTTTTGCCATGGTATCTGC 57.339 40.909 14.67 0.00 0.00 4.26
3942 3969 1.299541 CATGGTATCTGCGTTCCCAC 58.700 55.000 0.00 0.00 0.00 4.61
4034 4099 8.894592 ACTTTGATGTACCCAATCCTCATATAT 58.105 33.333 0.00 0.00 0.00 0.86
4040 4105 5.344743 ACCCAATCCTCATATATACTGCG 57.655 43.478 0.00 0.00 0.00 5.18
4047 4112 3.381590 CCTCATATATACTGCGGCAGCTA 59.618 47.826 28.80 20.18 45.42 3.32
4083 4148 1.526917 CCCTCCATGCAATCCGACC 60.527 63.158 0.00 0.00 0.00 4.79
4089 4154 0.374758 CATGCAATCCGACCGAACAG 59.625 55.000 0.00 0.00 0.00 3.16
4099 4164 2.353406 CCGACCGAACAGTTAGTGGATT 60.353 50.000 5.85 0.00 0.00 3.01
4104 4169 5.861727 ACCGAACAGTTAGTGGATTACTTT 58.138 37.500 5.85 0.00 40.89 2.66
4143 4208 4.080243 TGGACTTTCAGTTCTTGGTGGTAA 60.080 41.667 0.00 0.00 0.00 2.85
4158 4223 6.783708 TGGTGGTAATGTTTTTCAAGTTCT 57.216 33.333 0.00 0.00 0.00 3.01
4175 4240 1.361204 TCTGGGCTCTTGGTGATCAA 58.639 50.000 0.00 0.00 0.00 2.57
4176 4241 1.704628 TCTGGGCTCTTGGTGATCAAA 59.295 47.619 0.00 0.00 34.56 2.69
4182 4247 3.129988 GGCTCTTGGTGATCAAATTCAGG 59.870 47.826 0.00 0.00 34.56 3.86
4192 4340 4.943705 TGATCAAATTCAGGGCTAACAGTC 59.056 41.667 0.00 0.00 0.00 3.51
4202 4350 1.267121 GCTAACAGTCACTCCCCTGA 58.733 55.000 0.00 0.00 32.93 3.86
4210 4358 3.088789 GTCACTCCCCTGACTAGAAGA 57.911 52.381 0.00 0.00 38.05 2.87
4258 4406 3.629398 CAGGAAAGAAAGCAGTTGACACT 59.371 43.478 0.00 0.00 0.00 3.55
4266 4414 2.851195 AGCAGTTGACACTAAACCCAG 58.149 47.619 0.00 0.00 0.00 4.45
4280 4428 7.151976 CACTAAACCCAGAAACCTAAAATTGG 58.848 38.462 0.00 0.00 0.00 3.16
4328 4478 2.179517 GCTCACTCCCTCGACACG 59.820 66.667 0.00 0.00 0.00 4.49
4407 4557 5.897377 ATAAACACAAGAGCCAATACACC 57.103 39.130 0.00 0.00 0.00 4.16
4410 4560 2.224426 ACACAAGAGCCAATACACCGAA 60.224 45.455 0.00 0.00 0.00 4.30
4411 4561 3.009723 CACAAGAGCCAATACACCGAAT 58.990 45.455 0.00 0.00 0.00 3.34
4413 4563 4.271049 CACAAGAGCCAATACACCGAATAG 59.729 45.833 0.00 0.00 0.00 1.73
4418 4568 4.694339 AGCCAATACACCGAATAGAACTC 58.306 43.478 0.00 0.00 0.00 3.01
4423 4573 6.700520 CCAATACACCGAATAGAACTCCTAAC 59.299 42.308 0.00 0.00 0.00 2.34
4424 4574 4.367386 ACACCGAATAGAACTCCTAACG 57.633 45.455 0.00 0.00 33.95 3.18
4425 4575 3.114065 CACCGAATAGAACTCCTAACGC 58.886 50.000 0.00 0.00 33.34 4.84
4428 4578 3.550678 CCGAATAGAACTCCTAACGCAAC 59.449 47.826 0.00 0.00 33.34 4.17
4440 4590 6.025749 TCCTAACGCAACTATGATATCTGG 57.974 41.667 3.98 0.00 0.00 3.86
4476 4626 5.590259 TCCTCCCGATTTCATGAGAATTTTC 59.410 40.000 0.00 0.00 32.89 2.29
4477 4627 5.357878 CCTCCCGATTTCATGAGAATTTTCA 59.642 40.000 0.54 0.54 32.89 2.69
4478 4628 6.194796 TCCCGATTTCATGAGAATTTTCAC 57.805 37.500 0.00 0.00 32.89 3.18
4482 4632 5.664457 GATTTCATGAGAATTTTCACCCCC 58.336 41.667 0.00 0.00 32.89 5.40
4483 4633 2.722094 TCATGAGAATTTTCACCCCCG 58.278 47.619 0.00 0.00 0.00 5.73
4496 4646 3.420482 CCCCGGGGCTTTGGAGAT 61.420 66.667 31.01 0.00 0.00 2.75
4497 4647 2.683475 CCCGGGGCTTTGGAGATT 59.317 61.111 14.71 0.00 0.00 2.40
4498 4648 1.453928 CCCGGGGCTTTGGAGATTC 60.454 63.158 14.71 0.00 0.00 2.52
4499 4649 1.609783 CCGGGGCTTTGGAGATTCT 59.390 57.895 0.00 0.00 0.00 2.40
4500 4650 0.034089 CCGGGGCTTTGGAGATTCTT 60.034 55.000 0.00 0.00 0.00 2.52
4501 4651 1.616994 CCGGGGCTTTGGAGATTCTTT 60.617 52.381 0.00 0.00 0.00 2.52
4502 4652 1.745653 CGGGGCTTTGGAGATTCTTTC 59.254 52.381 0.00 0.00 0.00 2.62
4503 4653 2.619074 CGGGGCTTTGGAGATTCTTTCT 60.619 50.000 0.00 0.00 37.41 2.52
4526 4676 9.656040 TTCTCATTACAATGAAATTTCAATGGG 57.344 29.630 30.29 24.06 44.20 4.00
4527 4677 9.033711 TCTCATTACAATGAAATTTCAATGGGA 57.966 29.630 30.29 25.47 44.20 4.37
4528 4678 9.656040 CTCATTACAATGAAATTTCAATGGGAA 57.344 29.630 30.29 24.66 44.20 3.97
4529 4679 9.656040 TCATTACAATGAAATTTCAATGGGAAG 57.344 29.630 30.29 20.38 41.28 3.46
4530 4680 9.439500 CATTACAATGAAATTTCAATGGGAAGT 57.561 29.630 30.29 17.04 41.28 3.01
4534 4684 9.657419 ACAATGAAATTTCAATGGGAAGTAATC 57.343 29.630 30.29 0.00 41.28 1.75
4535 4685 9.101655 CAATGAAATTTCAATGGGAAGTAATCC 57.898 33.333 23.91 0.00 43.40 3.01
4536 4686 7.789202 TGAAATTTCAATGGGAAGTAATCCA 57.211 32.000 18.45 0.00 41.38 3.41
4537 4687 8.378115 TGAAATTTCAATGGGAAGTAATCCAT 57.622 30.769 18.45 0.00 44.90 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.481871 GGTCGACAATAGGGGACTGA 58.518 55.000 18.91 0.00 43.88 3.41
132 133 0.102481 CGGTCGACAATAGGGGACTG 59.898 60.000 18.91 0.00 43.88 3.51
142 143 3.695556 TGTAGGATATTGACGGTCGACAA 59.304 43.478 18.91 10.13 34.74 3.18
143 144 3.281158 TGTAGGATATTGACGGTCGACA 58.719 45.455 18.91 0.00 0.00 4.35
162 163 1.530655 CCTCACGGGCCCTTTTTGT 60.531 57.895 22.43 6.86 0.00 2.83
213 217 5.625721 CGTCTACGATCAACAATGATAGACC 59.374 44.000 11.65 0.73 46.30 3.85
236 240 2.665519 CGGTTGCCTTGATGACTTTTCG 60.666 50.000 0.00 0.00 0.00 3.46
256 260 7.113704 ACGGTTTCTTTTCTAAGATGTTACG 57.886 36.000 0.00 0.00 40.01 3.18
262 277 3.683340 GGCGACGGTTTCTTTTCTAAGAT 59.317 43.478 0.00 0.00 40.01 2.40
267 282 0.942252 GTGGCGACGGTTTCTTTTCT 59.058 50.000 0.00 0.00 0.00 2.52
282 297 1.032014 TTTGTGGCTCTTTCAGTGGC 58.968 50.000 0.00 0.00 35.22 5.01
309 324 9.401058 ACTGGTGAGAAATAATGGAGATTTTAG 57.599 33.333 0.00 0.00 0.00 1.85
310 325 9.177608 CACTGGTGAGAAATAATGGAGATTTTA 57.822 33.333 0.00 0.00 0.00 1.52
332 348 0.179100 CCGGTGCTAGGATGACACTG 60.179 60.000 0.00 0.00 39.81 3.66
335 351 1.043116 CCTCCGGTGCTAGGATGACA 61.043 60.000 0.00 0.00 37.13 3.58
336 352 1.742768 CCTCCGGTGCTAGGATGAC 59.257 63.158 0.00 0.00 37.13 3.06
360 376 1.638133 CAGCATCTCAGTCAAGTCGG 58.362 55.000 0.00 0.00 0.00 4.79
370 391 6.582636 ACGAAAGTATTATTCCAGCATCTCA 58.417 36.000 0.00 0.00 46.88 3.27
440 461 8.588290 TTCTACAGGGCATGTATAAATTTGTT 57.412 30.769 12.88 0.00 43.44 2.83
441 462 8.588290 TTTCTACAGGGCATGTATAAATTTGT 57.412 30.769 12.88 0.00 43.44 2.83
457 478 9.565213 CTTTTAGAGCAATCATTTTTCTACAGG 57.435 33.333 0.00 0.00 0.00 4.00
463 484 9.696917 TTTCTCCTTTTAGAGCAATCATTTTTC 57.303 29.630 0.00 0.00 33.66 2.29
510 531 7.254590 CCACACTGTAGACTGAGAAAAGAAAAG 60.255 40.741 0.00 0.00 0.00 2.27
640 661 3.013327 TCGGGAGGACTCGGGAGA 61.013 66.667 2.08 0.00 40.79 3.71
641 662 2.829458 GTCGGGAGGACTCGGGAG 60.829 72.222 0.00 0.00 42.62 4.30
649 670 2.361771 GTGGGTAGGTCGGGAGGA 59.638 66.667 0.00 0.00 0.00 3.71
699 720 1.839994 TGCTAGTGGAGGGATTTCAGG 59.160 52.381 0.00 0.00 0.00 3.86
903 924 0.326264 ACTCAGCTGGGCTTAACTGG 59.674 55.000 15.27 0.00 36.40 4.00
1030 1051 1.008875 GCGAACACGATGCTCACAGA 61.009 55.000 0.00 0.00 0.00 3.41
1074 1095 0.473694 TCAGAAACAGCTCCCTCCCA 60.474 55.000 0.00 0.00 0.00 4.37
1188 1209 4.399395 CCGGCCAAGAGAGCAGCA 62.399 66.667 2.24 0.00 0.00 4.41
1197 1218 3.944250 ATTGGTGCTCCCGGCCAAG 62.944 63.158 14.64 4.76 44.29 3.61
1198 1219 3.978193 ATTGGTGCTCCCGGCCAA 61.978 61.111 12.18 12.18 45.02 4.52
1211 1232 2.101917 GCCATGATTTCACTCCCATTGG 59.898 50.000 0.00 0.00 0.00 3.16
1218 1239 0.734889 CCGGTGCCATGATTTCACTC 59.265 55.000 0.00 0.00 0.00 3.51
1248 1269 2.479198 GTGGTAAAGAAGCGCGCC 59.521 61.111 30.33 14.19 0.00 6.53
1288 1309 2.436115 GTAGTTCCCCGGCAGCAC 60.436 66.667 0.00 0.00 0.00 4.40
1308 1329 1.538047 GGAAGAAATGCAGCCTGACA 58.462 50.000 0.00 0.00 0.00 3.58
1339 1360 3.683365 ACCATTTGCACTGAAATTCCC 57.317 42.857 0.00 0.00 0.00 3.97
1356 1377 2.869801 GACGACATCAAACACTGAACCA 59.130 45.455 0.00 0.00 37.67 3.67
1386 1407 1.583054 ACTTCGACACCAGCTTGAAC 58.417 50.000 0.00 0.00 0.00 3.18
1401 1422 4.301628 TCTCCTCCGAAACGTTAAACTTC 58.698 43.478 0.00 0.00 0.00 3.01
1413 1434 2.903784 TCTCCAAACAATCTCCTCCGAA 59.096 45.455 0.00 0.00 0.00 4.30
1437 1458 1.538512 GCAGCTGAATTGCTCACTGAA 59.461 47.619 20.43 0.00 41.98 3.02
1548 1569 1.341209 AGCATCACCTCGATCGCATTA 59.659 47.619 11.09 0.00 33.28 1.90
1591 1612 2.164219 CACCAACTTTGTTCACTGTGCT 59.836 45.455 2.12 0.00 0.00 4.40
1596 1617 2.491693 CACACCACCAACTTTGTTCACT 59.508 45.455 0.00 0.00 0.00 3.41
1654 1675 5.130975 TGTTGAGCCTATACATGGTCTCAAT 59.869 40.000 16.30 0.00 42.94 2.57
1669 1690 1.000396 GCCCTCCAATGTTGAGCCT 60.000 57.895 0.00 0.00 0.00 4.58
1674 1695 1.607178 TGCAGGCCCTCCAATGTTG 60.607 57.895 0.00 0.00 33.74 3.33
1720 1741 6.239317 GCTTCATCAGTGTACCATGGTCTATA 60.239 42.308 23.76 0.00 0.00 1.31
1746 1767 3.606777 CAGCATTCGCAGAAAACATGAAG 59.393 43.478 0.00 0.00 45.90 3.02
1761 1782 0.593128 ACACGGTCAAAGCAGCATTC 59.407 50.000 0.00 0.00 0.00 2.67
1775 1796 1.082117 GGCTGACGTATTGGACACGG 61.082 60.000 0.00 0.00 43.59 4.94
1776 1797 0.389296 TGGCTGACGTATTGGACACG 60.389 55.000 0.00 0.00 44.80 4.49
1813 1834 1.092345 GGAGCAATTGAGGAGTCGCC 61.092 60.000 10.34 0.00 0.00 5.54
1814 1835 1.092345 GGGAGCAATTGAGGAGTCGC 61.092 60.000 10.34 2.02 0.00 5.19
1851 1872 1.630223 TGTTGCCCATGATTCTTGCA 58.370 45.000 0.00 0.00 0.00 4.08
1887 1908 0.881118 GCCATGTCACATTGAACCGT 59.119 50.000 0.00 0.00 0.00 4.83
1912 1933 4.718940 AATCGAAATTGGGATGGACAAC 57.281 40.909 0.00 0.00 0.00 3.32
1920 1941 4.204012 GGACCATGTAATCGAAATTGGGA 58.796 43.478 0.00 0.00 0.00 4.37
1929 1950 3.159353 TGAAGACGGACCATGTAATCG 57.841 47.619 0.00 0.00 0.00 3.34
1936 1957 2.095263 CGCAAAAATGAAGACGGACCAT 60.095 45.455 0.00 0.00 0.00 3.55
1944 1965 3.565482 AGACAAGCTCGCAAAAATGAAGA 59.435 39.130 0.00 0.00 0.00 2.87
2040 2061 3.073798 TGTTAATTCCTCCAGCCTTGTCA 59.926 43.478 0.00 0.00 0.00 3.58
2041 2062 3.686016 TGTTAATTCCTCCAGCCTTGTC 58.314 45.455 0.00 0.00 0.00 3.18
2049 2070 6.012337 TGATATGCCTTGTTAATTCCTCCA 57.988 37.500 0.00 0.00 0.00 3.86
2055 2076 7.293073 AGTCCTCATGATATGCCTTGTTAATT 58.707 34.615 0.00 0.00 0.00 1.40
2091 2112 0.320771 AGTCTACCTGTTGCGGCAAG 60.321 55.000 16.97 7.29 0.00 4.01
2100 2121 1.076350 AGCCAGAGTGAGTCTACCTGT 59.924 52.381 0.00 0.00 32.51 4.00
2157 2178 1.399440 CCATTGAGAAGTGCATCCGTG 59.601 52.381 0.00 0.00 0.00 4.94
2194 2215 1.001641 GGTTGCCACTCCTGCTGAT 60.002 57.895 0.00 0.00 0.00 2.90
2217 2238 7.066645 CCCATATCAATATGACCAAGCACATAG 59.933 40.741 10.85 0.00 42.05 2.23
2256 2277 2.264794 CTCCGACCCTTGGAACGG 59.735 66.667 14.51 14.51 42.88 4.44
2278 2299 6.208840 ACCAACTTCTTCCCATAAACCTAA 57.791 37.500 0.00 0.00 0.00 2.69
2373 2394 0.456995 CCTCCTCGTCGACAGCTTTC 60.457 60.000 17.16 0.00 0.00 2.62
2382 2403 3.827898 GCAGGGACCTCCTCGTCG 61.828 72.222 0.00 0.00 46.12 5.12
2383 2404 2.363147 AGCAGGGACCTCCTCGTC 60.363 66.667 0.00 0.00 46.12 4.20
2421 2442 4.226427 AGTGCTTTTCATAGCCTCATGA 57.774 40.909 0.00 0.00 40.49 3.07
2472 2493 2.159198 GGAAGATGAATTGCGTGCCAAT 60.159 45.455 0.00 0.00 45.90 3.16
2528 2549 4.658435 TCTTTGTGGCAGCCCTAATATCTA 59.342 41.667 9.64 0.00 0.00 1.98
2538 2559 1.408702 TCAAAGTTCTTTGTGGCAGCC 59.591 47.619 20.05 3.66 33.82 4.85
2550 2571 3.807622 TGACCAATGACTCGTCAAAGTTC 59.192 43.478 3.60 0.00 43.58 3.01
2631 2652 1.669502 GGATTTGCACGCTTGATTGCA 60.670 47.619 0.00 0.00 46.93 4.08
2661 2682 2.528564 TCAAATTCTTTCAGGCCCTGG 58.471 47.619 11.68 0.00 31.51 4.45
2898 2919 2.750141 TTATACCTCGGTCTGCTCCT 57.250 50.000 0.00 0.00 0.00 3.69
2907 2928 6.546428 ACATCCCTATGAATTATACCTCGG 57.454 41.667 0.00 0.00 36.54 4.63
3102 3123 3.363575 CCACACCAAAAGAATACACGTCG 60.364 47.826 0.00 0.00 0.00 5.12
3105 3126 3.851838 GCACCACACCAAAAGAATACACG 60.852 47.826 0.00 0.00 0.00 4.49
3303 3324 4.505808 CATCATCAGCAAGACACTTCTCT 58.494 43.478 0.00 0.00 0.00 3.10
3354 3375 1.423541 ACATACTCCAGGTGCCACAAA 59.576 47.619 0.00 0.00 0.00 2.83
3420 3441 1.338020 CCCAGTTCACTGCTTCCAAAC 59.662 52.381 1.01 0.00 42.47 2.93
3480 3501 1.494960 GGTGATGCTCCTCTTCTCCT 58.505 55.000 0.00 0.00 32.71 3.69
3510 3531 3.389329 GGGCTGAATCTTCTCTGATACCA 59.611 47.826 0.00 0.00 0.00 3.25
3581 3603 0.527817 CCAAGACCACGGCTACGATC 60.528 60.000 0.00 0.00 44.60 3.69
3739 3764 6.347969 CGAACAAATCACATGATATAGCAGGG 60.348 42.308 7.62 0.00 33.73 4.45
3833 3859 3.482786 GCACTCGCACAAATAAGTTGAG 58.517 45.455 0.00 0.00 40.74 3.02
3850 3876 3.181169 GAAACAGTTGCGCCGCACT 62.181 57.895 13.21 10.01 38.71 4.40
3855 3881 4.632538 AATATAAGGAAACAGTTGCGCC 57.367 40.909 4.18 0.00 0.00 6.53
3858 3884 7.816640 TCACTGAAATATAAGGAAACAGTTGC 58.183 34.615 0.00 0.00 35.43 4.17
3859 3885 9.778993 CATCACTGAAATATAAGGAAACAGTTG 57.221 33.333 0.00 0.00 35.43 3.16
3880 3907 7.040686 ACAGGAGTTTAATACACCAAACATCAC 60.041 37.037 0.00 0.00 39.71 3.06
3910 3937 4.807304 CAGATACCATGGCAAAAGAATTGC 59.193 41.667 13.04 4.64 44.22 3.56
3920 3947 0.463654 GGAACGCAGATACCATGGCA 60.464 55.000 13.04 0.00 0.00 4.92
3923 3950 1.299541 GTGGGAACGCAGATACCATG 58.700 55.000 0.00 0.00 41.67 3.66
3924 3951 0.179084 CGTGGGAACGCAGATACCAT 60.179 55.000 0.00 0.00 42.37 3.55
3926 3953 4.104143 CGTGGGAACGCAGATACC 57.896 61.111 0.00 0.00 42.37 2.73
3934 3961 3.423154 GAGGCTTGCGTGGGAACG 61.423 66.667 0.00 0.00 0.00 3.95
3942 3969 2.956987 CAAAGGGTGAGGCTTGCG 59.043 61.111 0.00 0.00 0.00 4.85
3947 3974 1.269723 GTTTACAGCAAAGGGTGAGGC 59.730 52.381 0.42 0.00 45.29 4.70
3949 3976 2.814336 GAGGTTTACAGCAAAGGGTGAG 59.186 50.000 0.42 0.00 45.29 3.51
3979 4044 1.808945 AGCTAGTGCAACATCACAAGC 59.191 47.619 0.00 0.00 41.43 4.01
3985 4050 5.551760 ACAACATTAGCTAGTGCAACATC 57.448 39.130 15.57 0.00 41.43 3.06
4034 4099 0.108329 GAGGTTTAGCTGCCGCAGTA 60.108 55.000 21.29 9.87 39.10 2.74
4035 4100 1.376037 GAGGTTTAGCTGCCGCAGT 60.376 57.895 21.29 10.81 39.10 4.40
4040 4105 0.615850 ACTCCAGAGGTTTAGCTGCC 59.384 55.000 0.00 0.00 0.00 4.85
4047 4112 2.070639 GAGGCCACTCCAGAGGTTT 58.929 57.895 5.01 0.00 37.79 3.27
4083 4148 7.042321 TGTTGAAAGTAATCCACTAACTGTTCG 60.042 37.037 0.00 0.00 36.04 3.95
4089 4154 9.959749 TTCAATTGTTGAAAGTAATCCACTAAC 57.040 29.630 5.13 0.00 45.94 2.34
4104 4169 7.780064 TGAAAGTCCATTTCTTCAATTGTTGA 58.220 30.769 5.13 2.36 46.34 3.18
4136 4201 5.983118 CCAGAACTTGAAAAACATTACCACC 59.017 40.000 0.00 0.00 0.00 4.61
4143 4208 4.218312 AGAGCCCAGAACTTGAAAAACAT 58.782 39.130 0.00 0.00 0.00 2.71
4158 4223 2.905415 ATTTGATCACCAAGAGCCCA 57.095 45.000 0.00 0.00 35.94 5.36
4175 4240 3.307762 GGAGTGACTGTTAGCCCTGAATT 60.308 47.826 0.00 0.00 0.00 2.17
4176 4241 2.237392 GGAGTGACTGTTAGCCCTGAAT 59.763 50.000 0.00 0.00 0.00 2.57
4182 4247 0.250513 CAGGGGAGTGACTGTTAGCC 59.749 60.000 0.00 0.00 0.00 3.93
4192 4340 3.196685 CCTTTCTTCTAGTCAGGGGAGTG 59.803 52.174 0.00 0.00 0.00 3.51
4202 4350 2.303311 GGTGGTCTGCCTTTCTTCTAGT 59.697 50.000 0.00 0.00 35.27 2.57
4209 4357 3.075148 GTTTAGAGGTGGTCTGCCTTTC 58.925 50.000 0.00 0.00 36.64 2.62
4210 4358 2.441750 TGTTTAGAGGTGGTCTGCCTTT 59.558 45.455 0.00 0.00 36.64 3.11
4258 4406 5.602978 TGCCAATTTTAGGTTTCTGGGTTTA 59.397 36.000 0.00 0.00 0.00 2.01
4266 4414 4.257267 AGCTGTGCCAATTTTAGGTTTC 57.743 40.909 0.00 0.00 0.00 2.78
4328 4478 4.451096 TGACATTTAAACGAGAAGCTCCAC 59.549 41.667 0.00 0.00 0.00 4.02
4367 4517 8.540388 TGTGTTTATTTCTAGAGTGGATTAGCT 58.460 33.333 0.00 0.00 0.00 3.32
4407 4557 4.421948 AGTTGCGTTAGGAGTTCTATTCG 58.578 43.478 0.83 0.83 0.00 3.34
4410 4560 6.710597 TCATAGTTGCGTTAGGAGTTCTAT 57.289 37.500 0.00 0.00 0.00 1.98
4411 4561 6.710597 ATCATAGTTGCGTTAGGAGTTCTA 57.289 37.500 0.00 0.00 0.00 2.10
4413 4563 7.327275 CAGATATCATAGTTGCGTTAGGAGTTC 59.673 40.741 5.32 0.00 0.00 3.01
4418 4568 5.635280 CACCAGATATCATAGTTGCGTTAGG 59.365 44.000 5.32 0.00 0.00 2.69
4423 4573 5.755375 AGAAACACCAGATATCATAGTTGCG 59.245 40.000 5.32 0.00 0.00 4.85
4424 4574 6.989169 AGAGAAACACCAGATATCATAGTTGC 59.011 38.462 5.32 3.28 0.00 4.17
4425 4575 7.042187 GCAGAGAAACACCAGATATCATAGTTG 60.042 40.741 5.32 0.00 0.00 3.16
4428 4578 6.757237 AGCAGAGAAACACCAGATATCATAG 58.243 40.000 5.32 0.00 0.00 2.23
4440 4590 0.390472 CGGGAGGAGCAGAGAAACAC 60.390 60.000 0.00 0.00 0.00 3.32
4482 4632 1.745653 GAAAGAATCTCCAAAGCCCCG 59.254 52.381 0.00 0.00 0.00 5.73
4483 4633 3.093057 AGAAAGAATCTCCAAAGCCCC 57.907 47.619 0.00 0.00 30.46 5.80
4500 4650 9.656040 CCCATTGAAATTTCATTGTAATGAGAA 57.344 29.630 28.25 11.16 45.35 2.87
4501 4651 9.033711 TCCCATTGAAATTTCATTGTAATGAGA 57.966 29.630 28.25 19.29 45.35 3.27
4502 4652 9.656040 TTCCCATTGAAATTTCATTGTAATGAG 57.344 29.630 28.25 17.84 45.35 2.90
4503 4653 9.656040 CTTCCCATTGAAATTTCATTGTAATGA 57.344 29.630 28.25 20.03 36.74 2.57
4504 4654 9.439500 ACTTCCCATTGAAATTTCATTGTAATG 57.561 29.630 28.25 23.05 37.03 1.90
4508 4658 9.657419 GATTACTTCCCATTGAAATTTCATTGT 57.343 29.630 28.25 18.21 37.03 2.71
4509 4659 9.101655 GGATTACTTCCCATTGAAATTTCATTG 57.898 33.333 25.76 25.76 38.75 2.82
4510 4660 8.824783 TGGATTACTTCCCATTGAAATTTCATT 58.175 29.630 21.10 14.84 44.77 2.57
4511 4661 8.378115 TGGATTACTTCCCATTGAAATTTCAT 57.622 30.769 21.10 9.11 44.77 2.57
4512 4662 7.789202 TGGATTACTTCCCATTGAAATTTCA 57.211 32.000 16.91 16.91 44.77 2.69


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

AutoCloner maintained by Alex Coulton.