Multiple sequence alignment - TraesCS5B01G113800

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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 TraesCS5B01G113800 chr5B 100.000 4361 0 0 1 4361 182988747 182993107 0.000000e+00 8054
1 TraesCS5B01G113800 chr5B 91.099 382 31 3 240 619 276897803 276897423 8.360000e-142 514
2 TraesCS5B01G113800 chr5B 89.406 387 38 3 240 623 445179238 445179624 6.560000e-133 484
3 TraesCS5B01G113800 chr5A 94.664 3373 99 29 617 3964 198653243 198649927 0.000000e+00 5156
4 TraesCS5B01G113800 chr5A 94.030 335 15 5 3955 4286 198648994 198648662 1.810000e-138 503
5 TraesCS5B01G113800 chr5A 90.099 202 19 1 39 240 198653454 198653254 1.200000e-65 261
6 TraesCS5B01G113800 chr5D 94.099 2559 116 14 40 2585 174801166 174798630 0.000000e+00 3856
7 TraesCS5B01G113800 chr5D 94.240 1059 47 7 3231 4286 174796461 174795414 0.000000e+00 1605
8 TraesCS5B01G113800 chr5D 97.838 370 8 0 2815 3184 174796930 174796561 1.320000e-179 640
9 TraesCS5B01G113800 chr5D 95.565 248 7 3 2584 2830 174798580 174798336 1.140000e-105 394
10 TraesCS5B01G113800 chr6B 90.263 380 35 2 240 617 260600930 260601309 3.030000e-136 496
11 TraesCS5B01G113800 chr3B 90.263 380 33 3 240 617 758628483 758628860 1.090000e-135 494
12 TraesCS5B01G113800 chr2D 90.263 380 33 4 240 617 364977683 364978060 1.090000e-135 494
13 TraesCS5B01G113800 chr2D 89.791 382 36 3 240 619 405280877 405281257 1.820000e-133 486
14 TraesCS5B01G113800 chr1B 89.844 384 36 3 240 621 330838182 330837800 1.410000e-134 490
15 TraesCS5B01G113800 chr1B 89.610 385 37 3 240 622 655851285 655850902 1.820000e-133 486


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 TraesCS5B01G113800 chr5B 182988747 182993107 4360 False 8054.000000 8054 100.0000 1 4361 1 chr5B.!!$F1 4360
1 TraesCS5B01G113800 chr5A 198648662 198653454 4792 True 1973.333333 5156 92.9310 39 4286 3 chr5A.!!$R1 4247
2 TraesCS5B01G113800 chr5D 174795414 174801166 5752 True 1623.750000 3856 95.4355 40 4286 4 chr5D.!!$R1 4246

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
373 374 0.317160 TCTTCATCTGCGACGGTTGT 59.683 50.000 0.00 0.0 0.00 3.32 F
512 515 0.949397 TCAGTGCTTGTAGTCGTCGT 59.051 50.000 0.00 0.0 0.00 4.34 F
1176 1184 1.296722 CGAGGACGACGACGATGAC 60.297 63.158 15.32 1.0 42.66 3.06 F
1178 1186 1.690283 GAGGACGACGACGATGACGA 61.690 60.000 15.32 0.0 42.66 4.20 F
3133 4652 0.792640 ACGCAGCACTTCAGAATTCG 59.207 50.000 0.00 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2031 0.033920 AGCACTTCTGCACGACATGA 59.966 50.000 0.00 0.0 46.97 3.07 R
2430 2476 1.669115 CTCCTTGTGCTCACCCGTG 60.669 63.158 0.00 0.0 0.00 4.94 R
3035 4554 1.211457 GAGCTCCAGGATGATGTTGGT 59.789 52.381 0.87 0.0 39.69 3.67 R
3157 4676 2.160205 CGGTCTCTGGTTGACTCTGTA 58.840 52.381 0.00 0.0 35.04 2.74 R
4287 6808 0.242017 GCCTGATGCAAAGCGTTTCT 59.758 50.000 0.00 0.0 40.77 2.52 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
39 40 8.424274 AAAGTTTTGCAGTTCATAAAAGAAGG 57.576 30.769 0.00 0.00 0.00 3.46
40 41 7.112452 AGTTTTGCAGTTCATAAAAGAAGGT 57.888 32.000 0.00 0.00 0.00 3.50
41 42 7.555965 AGTTTTGCAGTTCATAAAAGAAGGTT 58.444 30.769 0.00 0.00 0.00 3.50
42 43 7.492344 AGTTTTGCAGTTCATAAAAGAAGGTTG 59.508 33.333 0.00 0.00 0.00 3.77
48 49 2.739913 TCATAAAAGAAGGTTGACGCCG 59.260 45.455 0.00 0.00 0.00 6.46
101 102 4.017808 ACTAGACACGTTTAGCATCCTCT 58.982 43.478 0.00 0.00 0.00 3.69
244 245 1.931172 CTACCGTCACTATTTTGGGCG 59.069 52.381 0.00 0.00 0.00 6.13
254 255 1.178534 ATTTTGGGCGTGTGGAGGTG 61.179 55.000 0.00 0.00 0.00 4.00
258 259 2.665185 GGCGTGTGGAGGTGTGTC 60.665 66.667 0.00 0.00 0.00 3.67
261 262 0.814010 GCGTGTGGAGGTGTGTCTTT 60.814 55.000 0.00 0.00 0.00 2.52
262 263 0.937304 CGTGTGGAGGTGTGTCTTTG 59.063 55.000 0.00 0.00 0.00 2.77
266 267 2.617274 GGAGGTGTGTCTTTGGCGC 61.617 63.158 0.00 0.00 0.00 6.53
273 274 2.009051 TGTGTCTTTGGCGCATCTATG 58.991 47.619 10.83 0.00 0.00 2.23
280 281 1.093972 TGGCGCATCTATGTTTGGTG 58.906 50.000 10.83 0.00 0.00 4.17
282 283 1.378531 GCGCATCTATGTTTGGTGGA 58.621 50.000 0.30 0.00 0.00 4.02
294 295 3.013921 GTTTGGTGGATTTGCTCGGATA 58.986 45.455 0.00 0.00 0.00 2.59
295 296 3.358111 TTGGTGGATTTGCTCGGATAA 57.642 42.857 0.00 0.00 0.00 1.75
299 300 2.676342 GTGGATTTGCTCGGATAACGTT 59.324 45.455 5.88 5.88 44.69 3.99
302 303 3.126343 GGATTTGCTCGGATAACGTTGTT 59.874 43.478 11.99 0.00 44.69 2.83
313 314 4.681025 GGATAACGTTGTTGTTCGTCTACA 59.319 41.667 11.99 0.00 39.39 2.74
316 317 4.703899 ACGTTGTTGTTCGTCTACATTC 57.296 40.909 0.00 0.00 35.30 2.67
331 332 2.662700 ACATTCGTGTGTCTTCGAGTC 58.337 47.619 0.00 0.00 37.38 3.36
345 346 3.487120 TCGAGTCGGATCCTTCTGATA 57.513 47.619 13.54 0.00 39.43 2.15
349 350 4.201734 CGAGTCGGATCCTTCTGATATACG 60.202 50.000 10.75 3.24 39.43 3.06
355 356 7.697291 GTCGGATCCTTCTGATATACGTTATTC 59.303 40.741 10.75 0.00 39.43 1.75
365 366 7.750903 TCTGATATACGTTATTCTTCATCTGCG 59.249 37.037 0.00 0.00 0.00 5.18
366 367 7.590279 TGATATACGTTATTCTTCATCTGCGA 58.410 34.615 0.00 0.00 0.00 5.10
373 374 0.317160 TCTTCATCTGCGACGGTTGT 59.683 50.000 0.00 0.00 0.00 3.32
379 380 1.083657 CTGCGACGGTTGTTGTTCG 60.084 57.895 0.00 0.00 0.00 3.95
382 383 1.214373 GCGACGGTTGTTGTTCGGTA 61.214 55.000 0.00 0.00 0.00 4.02
415 418 1.077089 GGCCTTAGCACGACGACTTC 61.077 60.000 0.00 0.00 42.56 3.01
416 419 1.077089 GCCTTAGCACGACGACTTCC 61.077 60.000 0.00 0.00 39.53 3.46
423 426 1.598962 ACGACGACTTCCCGACTGA 60.599 57.895 0.00 0.00 0.00 3.41
436 439 3.504906 TCCCGACTGACTACTACAACAAG 59.495 47.826 0.00 0.00 0.00 3.16
450 453 1.261619 CAACAAGTTGTGCTCGACTCC 59.738 52.381 9.79 0.00 37.32 3.85
512 515 0.949397 TCAGTGCTTGTAGTCGTCGT 59.051 50.000 0.00 0.00 0.00 4.34
516 519 2.810274 AGTGCTTGTAGTCGTCGTTAGA 59.190 45.455 0.00 0.00 0.00 2.10
519 522 3.106672 GCTTGTAGTCGTCGTTAGATGG 58.893 50.000 0.00 0.00 34.23 3.51
521 524 4.730657 CTTGTAGTCGTCGTTAGATGGTT 58.269 43.478 0.00 0.00 34.23 3.67
531 534 4.738740 GTCGTTAGATGGTTTACGGATCTG 59.261 45.833 0.00 0.00 34.93 2.90
580 583 4.068599 TCGTTGTACTGCCATGATTGAAA 58.931 39.130 0.00 0.00 0.00 2.69
591 594 8.701895 ACTGCCATGATTGAAAATGAATAGATT 58.298 29.630 0.00 0.00 0.00 2.40
592 595 8.880878 TGCCATGATTGAAAATGAATAGATTG 57.119 30.769 0.00 0.00 0.00 2.67
593 596 8.697292 TGCCATGATTGAAAATGAATAGATTGA 58.303 29.630 0.00 0.00 0.00 2.57
606 609 7.953305 TGAATAGATTGAAAATTTTCTCGCG 57.047 32.000 26.73 0.00 38.02 5.87
607 610 6.966632 TGAATAGATTGAAAATTTTCTCGCGG 59.033 34.615 26.73 0.00 38.02 6.46
636 639 5.992217 AGAAACTAAGTGGTACAGAGCTTTG 59.008 40.000 2.03 2.03 41.80 2.77
648 651 1.926511 GAGCTTTGTGGCATGGTCGG 61.927 60.000 0.00 0.00 34.17 4.79
696 699 6.814506 AAATGAAGACCTCTGATGTCAAAG 57.185 37.500 14.20 0.00 35.15 2.77
845 853 2.025699 TGTATAAAACCACCCCCTCTGC 60.026 50.000 0.00 0.00 0.00 4.26
846 854 1.382914 ATAAAACCACCCCCTCTGCT 58.617 50.000 0.00 0.00 0.00 4.24
1131 1139 3.128938 CCGTCGACTTCTCTTACCTCATT 59.871 47.826 14.70 0.00 0.00 2.57
1174 1182 3.087176 TCGAGGACGACGACGATG 58.913 61.111 15.32 0.00 43.81 3.84
1175 1183 1.446618 TCGAGGACGACGACGATGA 60.447 57.895 15.32 1.32 43.81 2.92
1176 1184 1.296722 CGAGGACGACGACGATGAC 60.297 63.158 15.32 1.00 42.66 3.06
1177 1185 1.296722 GAGGACGACGACGATGACG 60.297 63.158 15.32 4.49 42.66 4.35
1178 1186 1.690283 GAGGACGACGACGATGACGA 61.690 60.000 15.32 0.00 42.66 4.20
1672 1698 1.905215 ACTACCTCATGCAGAAGCTGT 59.095 47.619 0.00 0.00 42.74 4.40
1985 2031 8.224620 AGCTCATAAAGGATCCTAATGGTAAT 57.775 34.615 25.83 13.69 34.23 1.89
2021 2067 2.033448 TTGCAATCGTTCGGGGCT 59.967 55.556 0.00 0.00 0.00 5.19
2052 2098 6.104146 ACAAGGTATACATGTGTGTGTGTA 57.896 37.500 9.11 0.00 39.39 2.90
2231 2277 5.356882 TGCAGCTTGTACTGTTAATTGTC 57.643 39.130 0.00 0.00 39.96 3.18
2259 2305 4.392921 TGACCTGAATTTTCGGCAAAAA 57.607 36.364 0.00 0.00 40.98 1.94
2430 2476 2.398036 CGGTGTATTGCGCGTTCC 59.602 61.111 8.43 0.00 0.00 3.62
2643 2741 2.821969 AGCATGCCTTTGTAAAGTGGAG 59.178 45.455 15.66 0.00 34.20 3.86
2791 2889 7.713764 AAGAATGCATTCAACAAGTTTTACC 57.286 32.000 34.59 9.18 39.23 2.85
2905 4424 9.809096 AACTATGTTGTTCAGTATGTGATAGAG 57.191 33.333 0.00 0.00 37.40 2.43
2986 4505 2.027377 CCTCTCCATGCAGAAGTTCAGT 60.027 50.000 5.50 0.00 0.00 3.41
3035 4554 3.445805 AGTTTTCAAGGAAGCCGACAAAA 59.554 39.130 0.00 0.00 0.00 2.44
3067 4586 2.046892 GAGCTCCTTTCTGCGCCA 60.047 61.111 4.18 0.00 0.00 5.69
3133 4652 0.792640 ACGCAGCACTTCAGAATTCG 59.207 50.000 0.00 0.00 0.00 3.34
3157 4676 7.827236 TCGAAGGTAAATAACATCTCAACCAAT 59.173 33.333 0.00 0.00 0.00 3.16
3372 4944 3.009363 TGAAGAAGTGATGGCCTGATGAA 59.991 43.478 3.32 0.00 0.00 2.57
3450 5024 8.884124 ATTCAAAAGGGATAAAAGTGATCTCA 57.116 30.769 0.00 0.00 0.00 3.27
3525 5099 3.181434 ACCTTTATTGGGTGCACTCTTCA 60.181 43.478 19.48 8.32 35.51 3.02
3560 5135 2.629051 CTGGAATGGTAAGTTCCGGTC 58.371 52.381 0.00 0.00 46.49 4.79
3631 5206 8.845227 TGATGCTTCTTGTAACTTAATGTTTGA 58.155 29.630 0.88 0.00 39.89 2.69
3646 5221 6.875948 AATGTTTGAATTTTTACTTGCCCC 57.124 33.333 0.00 0.00 0.00 5.80
3647 5222 5.622346 TGTTTGAATTTTTACTTGCCCCT 57.378 34.783 0.00 0.00 0.00 4.79
3815 5390 0.586319 AACACAACATGAACGGAGCG 59.414 50.000 0.00 0.00 0.00 5.03
3828 5403 1.597663 ACGGAGCGTGAACTTTCAAAG 59.402 47.619 0.00 0.00 39.18 2.77
3831 5406 1.604278 GAGCGTGAACTTTCAAAGGCT 59.396 47.619 1.31 11.21 40.70 4.58
3896 5474 0.692476 AGCTATGAGCCACCACAACA 59.308 50.000 0.00 0.00 43.77 3.33
3910 5488 6.204495 GCCACCACAACAATTCAATATGTTTT 59.796 34.615 0.00 0.00 37.66 2.43
3911 5489 7.574496 CCACCACAACAATTCAATATGTTTTG 58.426 34.615 0.00 0.00 37.66 2.44
3966 6486 0.240945 CAATTGTCCCACAAGCGTCC 59.759 55.000 0.00 0.00 41.94 4.79
3984 6504 3.368739 CGTCCCTACGTTATTTTCACCCT 60.369 47.826 0.00 0.00 44.21 4.34
3990 6510 3.731089 ACGTTATTTTCACCCTTCACGA 58.269 40.909 0.00 0.00 0.00 4.35
4076 6596 6.491403 GCCCAATTTGTATCTTACATCATCCT 59.509 38.462 0.00 0.00 38.68 3.24
4110 6630 1.308746 TTCCCCCTTCCATCCCCTC 60.309 63.158 0.00 0.00 0.00 4.30
4147 6668 4.344978 TCCCTTCCATGTCTCGATATAGG 58.655 47.826 0.00 0.00 0.00 2.57
4156 6677 3.659195 TGTCTCGATATAGGGACCCCTTA 59.341 47.826 13.61 6.24 45.70 2.69
4210 6731 2.771943 GTCATCCTCATTCACCCTGGTA 59.228 50.000 0.00 0.00 0.00 3.25
4218 6739 1.956297 TTCACCCTGGTACGTGTTTG 58.044 50.000 0.00 0.00 0.00 2.93
4257 6778 0.823356 TGGAACAGTCTGCCCTTTGC 60.823 55.000 11.74 0.69 41.77 3.68
4299 6820 6.934561 ATTTAAGATTGAGAAACGCTTTGC 57.065 33.333 0.00 0.00 0.00 3.68
4300 6821 3.988379 AAGATTGAGAAACGCTTTGCA 57.012 38.095 0.00 0.00 0.00 4.08
4301 6822 4.510038 AAGATTGAGAAACGCTTTGCAT 57.490 36.364 0.00 0.00 0.00 3.96
4302 6823 4.088823 AGATTGAGAAACGCTTTGCATC 57.911 40.909 0.00 0.00 0.00 3.91
4303 6824 3.503363 AGATTGAGAAACGCTTTGCATCA 59.497 39.130 0.00 0.00 0.00 3.07
4304 6825 2.975410 TGAGAAACGCTTTGCATCAG 57.025 45.000 0.00 0.00 0.00 2.90
4305 6826 1.536766 TGAGAAACGCTTTGCATCAGG 59.463 47.619 0.00 0.00 0.00 3.86
4306 6827 0.242017 AGAAACGCTTTGCATCAGGC 59.758 50.000 0.00 0.00 45.13 4.85
4315 6836 2.663188 GCATCAGGCGTCCGATCC 60.663 66.667 0.00 0.00 0.00 3.36
4316 6837 2.029666 CATCAGGCGTCCGATCCC 59.970 66.667 0.00 0.00 0.00 3.85
4317 6838 2.443952 ATCAGGCGTCCGATCCCA 60.444 61.111 0.00 0.00 0.00 4.37
4318 6839 2.797278 ATCAGGCGTCCGATCCCAC 61.797 63.158 0.00 0.00 0.00 4.61
4319 6840 4.873129 CAGGCGTCCGATCCCACG 62.873 72.222 6.71 6.71 39.09 4.94
4321 6842 4.446413 GGCGTCCGATCCCACGTT 62.446 66.667 11.57 0.00 38.32 3.99
4322 6843 2.884207 GCGTCCGATCCCACGTTC 60.884 66.667 11.57 0.00 38.32 3.95
4323 6844 2.578713 CGTCCGATCCCACGTTCG 60.579 66.667 0.41 0.41 35.19 3.95
4324 6845 2.570181 GTCCGATCCCACGTTCGT 59.430 61.111 6.62 0.00 33.60 3.85
4325 6846 1.804326 GTCCGATCCCACGTTCGTG 60.804 63.158 16.87 16.87 33.60 4.35
4326 6847 2.260434 CCGATCCCACGTTCGTGT 59.740 61.111 20.93 5.74 34.59 4.49
4327 6848 1.804326 CCGATCCCACGTTCGTGTC 60.804 63.158 20.93 12.62 34.59 3.67
4328 6849 1.081041 CGATCCCACGTTCGTGTCA 60.081 57.895 20.93 9.55 34.59 3.58
4329 6850 1.071019 CGATCCCACGTTCGTGTCAG 61.071 60.000 20.93 11.30 34.59 3.51
4330 6851 0.242825 GATCCCACGTTCGTGTCAGA 59.757 55.000 20.93 15.32 34.59 3.27
4331 6852 0.038526 ATCCCACGTTCGTGTCAGAC 60.039 55.000 20.93 0.00 34.59 3.51
4332 6853 1.663702 CCCACGTTCGTGTCAGACC 60.664 63.158 20.93 0.00 34.59 3.85
4333 6854 1.066752 CCACGTTCGTGTCAGACCA 59.933 57.895 20.93 0.00 34.59 4.02
4334 6855 1.213094 CCACGTTCGTGTCAGACCAC 61.213 60.000 20.93 0.00 34.59 4.16
4335 6856 0.526739 CACGTTCGTGTCAGACCACA 60.527 55.000 15.81 0.00 34.98 4.17
4336 6857 0.387929 ACGTTCGTGTCAGACCACAT 59.612 50.000 0.00 0.00 34.98 3.21
4337 6858 1.060713 CGTTCGTGTCAGACCACATC 58.939 55.000 0.00 0.00 34.98 3.06
4338 6859 1.429463 GTTCGTGTCAGACCACATCC 58.571 55.000 0.00 0.00 34.98 3.51
4339 6860 0.320374 TTCGTGTCAGACCACATCCC 59.680 55.000 0.00 0.00 34.98 3.85
4340 6861 0.541998 TCGTGTCAGACCACATCCCT 60.542 55.000 0.00 0.00 34.98 4.20
4341 6862 0.321671 CGTGTCAGACCACATCCCTT 59.678 55.000 0.00 0.00 34.98 3.95
4342 6863 1.673033 CGTGTCAGACCACATCCCTTC 60.673 57.143 0.00 0.00 34.98 3.46
4343 6864 0.984230 TGTCAGACCACATCCCTTCC 59.016 55.000 0.00 0.00 0.00 3.46
4344 6865 0.984230 GTCAGACCACATCCCTTCCA 59.016 55.000 0.00 0.00 0.00 3.53
4345 6866 1.561542 GTCAGACCACATCCCTTCCAT 59.438 52.381 0.00 0.00 0.00 3.41
4346 6867 2.025887 GTCAGACCACATCCCTTCCATT 60.026 50.000 0.00 0.00 0.00 3.16
4347 6868 2.025981 TCAGACCACATCCCTTCCATTG 60.026 50.000 0.00 0.00 0.00 2.82
4348 6869 1.285962 AGACCACATCCCTTCCATTGG 59.714 52.381 0.00 0.00 0.00 3.16
4349 6870 1.284785 GACCACATCCCTTCCATTGGA 59.715 52.381 0.00 0.00 34.54 3.53
4350 6871 1.932338 ACCACATCCCTTCCATTGGAT 59.068 47.619 6.15 0.00 42.12 3.41
4351 6872 2.315763 ACCACATCCCTTCCATTGGATT 59.684 45.455 6.15 0.00 39.36 3.01
4352 6873 3.246094 ACCACATCCCTTCCATTGGATTT 60.246 43.478 6.15 0.00 39.36 2.17
4353 6874 3.776417 CCACATCCCTTCCATTGGATTTT 59.224 43.478 6.15 0.00 39.36 1.82
4354 6875 4.383335 CCACATCCCTTCCATTGGATTTTG 60.383 45.833 6.15 3.58 39.36 2.44
4355 6876 4.223477 CACATCCCTTCCATTGGATTTTGT 59.777 41.667 6.15 4.17 39.36 2.83
4356 6877 4.223477 ACATCCCTTCCATTGGATTTTGTG 59.777 41.667 6.15 6.33 39.36 3.33
4357 6878 4.125124 TCCCTTCCATTGGATTTTGTGA 57.875 40.909 6.15 0.00 0.00 3.58
4358 6879 4.487804 TCCCTTCCATTGGATTTTGTGAA 58.512 39.130 6.15 0.00 0.00 3.18
4359 6880 4.904251 TCCCTTCCATTGGATTTTGTGAAA 59.096 37.500 6.15 0.00 0.00 2.69
4360 6881 4.996758 CCCTTCCATTGGATTTTGTGAAAC 59.003 41.667 6.15 0.00 37.35 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.528018 CCTTCTTTTATGAACTGCAAAACTTTA 57.472 29.630 0.00 0.00 0.00 1.85
14 15 8.040727 ACCTTCTTTTATGAACTGCAAAACTTT 58.959 29.630 0.00 0.00 0.00 2.66
15 16 7.555965 ACCTTCTTTTATGAACTGCAAAACTT 58.444 30.769 0.00 0.00 0.00 2.66
16 17 7.112452 ACCTTCTTTTATGAACTGCAAAACT 57.888 32.000 0.00 0.00 0.00 2.66
17 18 7.491048 TCAACCTTCTTTTATGAACTGCAAAAC 59.509 33.333 0.00 0.00 0.00 2.43
18 19 7.491048 GTCAACCTTCTTTTATGAACTGCAAAA 59.509 33.333 0.00 0.00 0.00 2.44
19 20 6.978080 GTCAACCTTCTTTTATGAACTGCAAA 59.022 34.615 0.00 0.00 0.00 3.68
20 21 6.503524 GTCAACCTTCTTTTATGAACTGCAA 58.496 36.000 0.00 0.00 0.00 4.08
21 22 5.277779 CGTCAACCTTCTTTTATGAACTGCA 60.278 40.000 0.00 0.00 0.00 4.41
22 23 5.147162 CGTCAACCTTCTTTTATGAACTGC 58.853 41.667 0.00 0.00 0.00 4.40
23 24 5.147162 GCGTCAACCTTCTTTTATGAACTG 58.853 41.667 0.00 0.00 0.00 3.16
24 25 4.215613 GGCGTCAACCTTCTTTTATGAACT 59.784 41.667 0.00 0.00 0.00 3.01
25 26 4.473199 GGCGTCAACCTTCTTTTATGAAC 58.527 43.478 0.00 0.00 0.00 3.18
26 27 3.187637 CGGCGTCAACCTTCTTTTATGAA 59.812 43.478 0.00 0.00 0.00 2.57
27 28 2.739913 CGGCGTCAACCTTCTTTTATGA 59.260 45.455 0.00 0.00 0.00 2.15
28 29 2.727916 GCGGCGTCAACCTTCTTTTATG 60.728 50.000 9.37 0.00 0.00 1.90
29 30 1.467342 GCGGCGTCAACCTTCTTTTAT 59.533 47.619 9.37 0.00 0.00 1.40
30 31 0.869730 GCGGCGTCAACCTTCTTTTA 59.130 50.000 9.37 0.00 0.00 1.52
31 32 0.818040 AGCGGCGTCAACCTTCTTTT 60.818 50.000 9.37 0.00 0.00 2.27
32 33 1.227853 AGCGGCGTCAACCTTCTTT 60.228 52.632 9.37 0.00 0.00 2.52
33 34 1.668151 GAGCGGCGTCAACCTTCTT 60.668 57.895 9.37 0.00 0.00 2.52
34 35 1.248785 TAGAGCGGCGTCAACCTTCT 61.249 55.000 9.37 2.39 0.00 2.85
35 36 0.802607 CTAGAGCGGCGTCAACCTTC 60.803 60.000 9.37 0.00 0.00 3.46
36 37 1.215647 CTAGAGCGGCGTCAACCTT 59.784 57.895 9.37 0.00 0.00 3.50
37 38 1.977544 ACTAGAGCGGCGTCAACCT 60.978 57.895 9.37 0.00 0.00 3.50
38 39 1.805945 CACTAGAGCGGCGTCAACC 60.806 63.158 9.37 0.00 0.00 3.77
39 40 0.666577 AACACTAGAGCGGCGTCAAC 60.667 55.000 9.37 0.00 0.00 3.18
40 41 0.032952 AAACACTAGAGCGGCGTCAA 59.967 50.000 9.37 0.00 0.00 3.18
41 42 0.883153 TAAACACTAGAGCGGCGTCA 59.117 50.000 9.37 0.00 0.00 4.35
42 43 1.546834 CTAAACACTAGAGCGGCGTC 58.453 55.000 9.37 5.00 0.00 5.19
228 229 1.136085 CACACGCCCAAAATAGTGACG 60.136 52.381 1.24 0.00 37.95 4.35
235 236 1.152830 ACCTCCACACGCCCAAAAT 59.847 52.632 0.00 0.00 0.00 1.82
244 245 1.308998 CCAAAGACACACCTCCACAC 58.691 55.000 0.00 0.00 0.00 3.82
254 255 2.009774 ACATAGATGCGCCAAAGACAC 58.990 47.619 4.18 0.00 0.00 3.67
258 259 2.164219 ACCAAACATAGATGCGCCAAAG 59.836 45.455 4.18 0.00 0.00 2.77
261 262 1.093972 CACCAAACATAGATGCGCCA 58.906 50.000 4.18 0.00 0.00 5.69
262 263 0.381801 CCACCAAACATAGATGCGCC 59.618 55.000 4.18 0.00 0.00 6.53
266 267 5.585390 GAGCAAATCCACCAAACATAGATG 58.415 41.667 0.00 0.00 0.00 2.90
273 274 1.243902 TCCGAGCAAATCCACCAAAC 58.756 50.000 0.00 0.00 0.00 2.93
280 281 2.676342 ACAACGTTATCCGAGCAAATCC 59.324 45.455 0.00 0.00 40.70 3.01
282 283 3.500680 ACAACAACGTTATCCGAGCAAAT 59.499 39.130 0.00 0.00 40.70 2.32
294 295 4.317558 CGAATGTAGACGAACAACAACGTT 60.318 41.667 0.00 0.00 42.74 3.99
295 296 3.180980 CGAATGTAGACGAACAACAACGT 59.819 43.478 0.00 0.00 45.32 3.99
299 300 3.487942 CACACGAATGTAGACGAACAACA 59.512 43.478 0.00 0.00 36.72 3.33
302 303 3.004002 AGACACACGAATGTAGACGAACA 59.996 43.478 0.00 0.00 36.72 3.18
313 314 1.401148 CCGACTCGAAGACACACGAAT 60.401 52.381 0.00 0.00 38.05 3.34
316 317 0.168348 ATCCGACTCGAAGACACACG 59.832 55.000 0.00 0.00 0.00 4.49
331 332 7.763356 AGAATAACGTATATCAGAAGGATCCG 58.237 38.462 5.98 0.00 37.44 4.18
365 366 0.503961 CGTACCGAACAACAACCGTC 59.496 55.000 0.00 0.00 0.00 4.79
366 367 1.489881 GCGTACCGAACAACAACCGT 61.490 55.000 0.00 0.00 0.00 4.83
373 374 1.005867 GGACCAGCGTACCGAACAA 60.006 57.895 0.00 0.00 0.00 2.83
379 380 1.814527 CCTGTAGGACCAGCGTACC 59.185 63.158 0.00 0.00 37.11 3.34
382 383 3.391382 GGCCTGTAGGACCAGCGT 61.391 66.667 1.17 0.00 37.19 5.07
395 397 1.533469 AAGTCGTCGTGCTAAGGCCT 61.533 55.000 0.00 0.00 37.74 5.19
415 418 3.255149 ACTTGTTGTAGTAGTCAGTCGGG 59.745 47.826 0.00 0.00 0.00 5.14
416 419 4.500603 ACTTGTTGTAGTAGTCAGTCGG 57.499 45.455 0.00 0.00 0.00 4.79
423 426 4.049186 CGAGCACAACTTGTTGTAGTAGT 58.951 43.478 17.26 2.85 33.17 2.73
436 439 3.112709 GCCGGAGTCGAGCACAAC 61.113 66.667 5.05 0.00 39.00 3.32
443 446 3.209812 CTCCATCGCCGGAGTCGA 61.210 66.667 5.05 5.08 46.40 4.20
485 488 0.397941 TACAAGCACTGAAGCAGGCT 59.602 50.000 0.00 0.00 38.78 4.58
488 491 1.723542 CGACTACAAGCACTGAAGCAG 59.276 52.381 0.00 0.00 37.52 4.24
489 492 1.068588 ACGACTACAAGCACTGAAGCA 59.931 47.619 0.00 0.00 36.85 3.91
512 515 5.365605 ACATCCAGATCCGTAAACCATCTAA 59.634 40.000 0.00 0.00 0.00 2.10
516 519 5.623956 TTACATCCAGATCCGTAAACCAT 57.376 39.130 0.00 0.00 0.00 3.55
551 554 2.967362 TGGCAGTACAACGAATACCAG 58.033 47.619 0.00 0.00 0.00 4.00
553 556 3.527533 TCATGGCAGTACAACGAATACC 58.472 45.455 0.00 0.00 0.00 2.73
554 557 5.293324 TCAATCATGGCAGTACAACGAATAC 59.707 40.000 0.00 0.00 0.00 1.89
580 583 9.013490 CGCGAGAAAATTTTCAATCTATTCATT 57.987 29.630 28.00 7.07 39.61 2.57
604 607 4.563337 ACCACTTAGTTTCTTTTTCCGC 57.437 40.909 0.00 0.00 0.00 5.54
605 608 6.480981 TCTGTACCACTTAGTTTCTTTTTCCG 59.519 38.462 0.00 0.00 0.00 4.30
606 609 7.520131 GCTCTGTACCACTTAGTTTCTTTTTCC 60.520 40.741 0.00 0.00 0.00 3.13
607 610 7.226918 AGCTCTGTACCACTTAGTTTCTTTTTC 59.773 37.037 0.00 0.00 0.00 2.29
613 616 5.758784 ACAAAGCTCTGTACCACTTAGTTTC 59.241 40.000 0.00 0.00 0.00 2.78
615 618 5.057149 CACAAAGCTCTGTACCACTTAGTT 58.943 41.667 0.00 0.00 0.00 2.24
636 639 0.887933 ATGTTTTCCGACCATGCCAC 59.112 50.000 0.00 0.00 0.00 5.01
680 683 7.201478 CGATTTTCTACTTTGACATCAGAGGTC 60.201 40.741 8.34 8.34 32.89 3.85
682 685 6.036517 CCGATTTTCTACTTTGACATCAGAGG 59.963 42.308 4.61 0.00 32.89 3.69
692 695 6.002062 AGCACTTTCCGATTTTCTACTTTG 57.998 37.500 0.00 0.00 0.00 2.77
696 699 5.163784 GGGTAAGCACTTTCCGATTTTCTAC 60.164 44.000 0.63 0.00 31.66 2.59
845 853 0.926293 AGTGGGAGGAGGAGAGAGAG 59.074 60.000 0.00 0.00 0.00 3.20
846 854 0.923358 GAGTGGGAGGAGGAGAGAGA 59.077 60.000 0.00 0.00 0.00 3.10
1131 1139 0.173481 CCATCTCGCCGAGTTCTTGA 59.827 55.000 14.64 0.00 0.00 3.02
1167 1175 1.708375 CGTTGTCGTCGTCATCGTCG 61.708 60.000 12.67 1.62 46.06 5.12
1168 1176 1.393597 CCGTTGTCGTCGTCATCGTC 61.394 60.000 17.32 0.60 38.33 4.20
1169 1177 1.441515 CCGTTGTCGTCGTCATCGT 60.442 57.895 17.32 0.00 38.33 3.73
1170 1178 1.000233 AACCGTTGTCGTCGTCATCG 61.000 55.000 13.57 13.57 38.55 3.84
1171 1179 1.123756 GAAACCGTTGTCGTCGTCATC 59.876 52.381 0.00 0.00 35.01 2.92
1172 1180 1.134226 GAAACCGTTGTCGTCGTCAT 58.866 50.000 0.00 0.00 35.01 3.06
1173 1181 0.871163 GGAAACCGTTGTCGTCGTCA 60.871 55.000 0.00 0.00 35.01 4.35
1174 1182 0.595825 AGGAAACCGTTGTCGTCGTC 60.596 55.000 0.00 0.00 35.01 4.20
1175 1183 0.179103 AAGGAAACCGTTGTCGTCGT 60.179 50.000 0.00 0.00 35.01 4.34
1176 1184 0.505655 GAAGGAAACCGTTGTCGTCG 59.494 55.000 0.00 0.00 35.01 5.12
1177 1185 1.259770 GTGAAGGAAACCGTTGTCGTC 59.740 52.381 0.00 0.00 35.01 4.20
1178 1186 1.292992 GTGAAGGAAACCGTTGTCGT 58.707 50.000 0.00 0.00 35.01 4.34
1352 1372 2.675772 GGAGGTCCCAGTCGTCGT 60.676 66.667 0.00 0.00 34.14 4.34
1644 1670 1.066430 TGCATGAGGTAGTTCCCGAAC 60.066 52.381 0.00 0.00 41.45 3.95
1672 1698 2.181777 CTCGCTGCAGACGGCTAA 59.818 61.111 20.43 3.87 46.69 3.09
1985 2031 0.033920 AGCACTTCTGCACGACATGA 59.966 50.000 0.00 0.00 46.97 3.07
2021 2067 8.264347 ACACACATGTATACCTTGTTATCATCA 58.736 33.333 0.00 0.00 37.26 3.07
2052 2098 6.882610 TTCAGAACTTGTTAAGATGCATGT 57.117 33.333 2.46 0.00 0.00 3.21
2231 2277 6.098679 TGCCGAAAATTCAGGTCAATAATTG 58.901 36.000 0.00 0.00 0.00 2.32
2287 2333 6.212589 TGTCTGACCAGGAACATATCAGTTTA 59.787 38.462 5.17 0.00 38.35 2.01
2430 2476 1.669115 CTCCTTGTGCTCACCCGTG 60.669 63.158 0.00 0.00 0.00 4.94
2643 2741 5.105146 ACAGAGGTCTCTACAATCAATGGTC 60.105 44.000 0.00 0.00 37.98 4.02
2905 4424 1.722011 TTGCAGTAGCGACCTTTAGC 58.278 50.000 0.00 0.00 46.23 3.09
2986 4505 2.156891 GCATTTCTCGACAACGTTGCTA 59.843 45.455 27.61 12.35 40.69 3.49
3035 4554 1.211457 GAGCTCCAGGATGATGTTGGT 59.789 52.381 0.87 0.00 39.69 3.67
3157 4676 2.160205 CGGTCTCTGGTTGACTCTGTA 58.840 52.381 0.00 0.00 35.04 2.74
3372 4944 7.888021 TCTTTATTGTTACATGGTGAGATGGTT 59.112 33.333 0.00 0.00 0.00 3.67
3423 4997 9.183368 GAGATCACTTTTATCCCTTTTGAATCT 57.817 33.333 0.00 0.00 0.00 2.40
3525 5099 4.831155 CCATTCCAGATGGATTATGCAACT 59.169 41.667 1.61 0.00 44.98 3.16
3631 5206 5.003160 GCAATTGAGGGGCAAGTAAAAATT 58.997 37.500 10.34 0.00 40.42 1.82
3646 5221 2.523015 GCATTCGGTTGAGCAATTGAG 58.477 47.619 10.34 0.00 0.00 3.02
3647 5222 1.202114 GGCATTCGGTTGAGCAATTGA 59.798 47.619 10.34 0.00 0.00 2.57
3749 5324 8.160765 TGTGATTTCCTTTGTCCAGATACTTAA 58.839 33.333 0.00 0.00 0.00 1.85
3764 5339 8.866970 AATGGCATTTTAATTGTGATTTCCTT 57.133 26.923 6.96 0.00 0.00 3.36
3885 5463 4.819769 ACATATTGAATTGTTGTGGTGGC 58.180 39.130 0.00 0.00 0.00 5.01
3896 5474 4.156922 TCGGACGGCAAAACATATTGAATT 59.843 37.500 0.00 0.00 31.84 2.17
3910 5488 2.209273 CAATTATGTGATCGGACGGCA 58.791 47.619 0.00 0.00 0.00 5.69
3911 5489 1.531149 CCAATTATGTGATCGGACGGC 59.469 52.381 0.00 0.00 0.00 5.68
3966 6486 4.092383 CGTGAAGGGTGAAAATAACGTAGG 59.908 45.833 0.00 0.00 0.00 3.18
3973 6493 3.438781 GCATGTCGTGAAGGGTGAAAATA 59.561 43.478 0.00 0.00 0.00 1.40
3984 6504 0.950836 CAAGTTGGGCATGTCGTGAA 59.049 50.000 0.00 0.00 0.00 3.18
3990 6510 1.341080 CCCTTTCAAGTTGGGCATGT 58.659 50.000 2.34 0.00 33.88 3.21
4095 6615 0.709992 TTTTGAGGGGATGGAAGGGG 59.290 55.000 0.00 0.00 0.00 4.79
4218 6739 0.593128 CCTTATATTGCTGCCGTGGC 59.407 55.000 3.30 3.30 42.35 5.01
4226 6747 5.431765 CAGACTGTTCCACCTTATATTGCT 58.568 41.667 0.00 0.00 0.00 3.91
4257 6778 7.931948 TCTTAAATTAAGATAGAAGCGGAAGGG 59.068 37.037 11.10 0.00 39.73 3.95
4286 6807 1.730446 GCCTGATGCAAAGCGTTTCTC 60.730 52.381 0.00 0.00 40.77 2.87
4287 6808 0.242017 GCCTGATGCAAAGCGTTTCT 59.758 50.000 0.00 0.00 40.77 2.52
4288 6809 1.067199 CGCCTGATGCAAAGCGTTTC 61.067 55.000 12.95 0.00 43.45 2.78
4289 6810 1.081242 CGCCTGATGCAAAGCGTTT 60.081 52.632 12.95 0.00 43.45 3.60
4290 6811 2.562912 CGCCTGATGCAAAGCGTT 59.437 55.556 12.95 0.00 43.45 4.84
4293 6814 2.486966 GGACGCCTGATGCAAAGC 59.513 61.111 0.00 0.00 41.33 3.51
4294 6815 1.091771 ATCGGACGCCTGATGCAAAG 61.092 55.000 0.00 0.00 41.33 2.77
4295 6816 1.078497 ATCGGACGCCTGATGCAAA 60.078 52.632 0.00 0.00 41.33 3.68
4296 6817 1.521457 GATCGGACGCCTGATGCAA 60.521 57.895 0.00 0.00 38.47 4.08
4297 6818 2.106938 GATCGGACGCCTGATGCA 59.893 61.111 0.00 0.00 38.47 3.96
4298 6819 2.663188 GGATCGGACGCCTGATGC 60.663 66.667 0.00 0.00 38.47 3.91
4299 6820 2.029666 GGGATCGGACGCCTGATG 59.970 66.667 0.00 0.00 38.47 3.07
4300 6821 2.443952 TGGGATCGGACGCCTGAT 60.444 61.111 0.00 0.00 40.96 2.90
4301 6822 3.458163 GTGGGATCGGACGCCTGA 61.458 66.667 0.00 0.00 0.00 3.86
4302 6823 4.873129 CGTGGGATCGGACGCCTG 62.873 72.222 2.60 0.00 0.00 4.85
4304 6825 4.446413 AACGTGGGATCGGACGCC 62.446 66.667 13.39 0.00 39.22 5.68
4305 6826 2.884207 GAACGTGGGATCGGACGC 60.884 66.667 13.39 0.55 39.22 5.19
4306 6827 2.578713 CGAACGTGGGATCGGACG 60.579 66.667 12.22 12.22 41.41 4.79
4307 6828 1.804326 CACGAACGTGGGATCGGAC 60.804 63.158 17.83 0.00 42.09 4.79
4308 6829 2.569657 CACGAACGTGGGATCGGA 59.430 61.111 17.83 0.00 42.09 4.55
4317 6838 0.387929 ATGTGGTCTGACACGAACGT 59.612 50.000 10.38 0.00 44.21 3.99
4318 6839 1.060713 GATGTGGTCTGACACGAACG 58.939 55.000 10.38 0.00 44.21 3.95
4319 6840 1.429463 GGATGTGGTCTGACACGAAC 58.571 55.000 10.38 3.07 44.21 3.95
4320 6841 0.320374 GGGATGTGGTCTGACACGAA 59.680 55.000 10.38 0.00 44.21 3.85
4321 6842 0.541998 AGGGATGTGGTCTGACACGA 60.542 55.000 10.38 0.00 44.21 4.35
4322 6843 0.321671 AAGGGATGTGGTCTGACACG 59.678 55.000 10.38 0.00 44.21 4.49
4323 6844 1.339151 GGAAGGGATGTGGTCTGACAC 60.339 57.143 10.38 6.76 41.68 3.67
4324 6845 0.984230 GGAAGGGATGTGGTCTGACA 59.016 55.000 10.38 0.00 0.00 3.58
4325 6846 0.984230 TGGAAGGGATGTGGTCTGAC 59.016 55.000 0.00 0.00 0.00 3.51
4326 6847 1.971149 ATGGAAGGGATGTGGTCTGA 58.029 50.000 0.00 0.00 0.00 3.27
4327 6848 2.372264 CAATGGAAGGGATGTGGTCTG 58.628 52.381 0.00 0.00 0.00 3.51
4328 6849 1.285962 CCAATGGAAGGGATGTGGTCT 59.714 52.381 0.00 0.00 0.00 3.85
4329 6850 1.284785 TCCAATGGAAGGGATGTGGTC 59.715 52.381 0.00 0.00 0.00 4.02
4330 6851 1.381867 TCCAATGGAAGGGATGTGGT 58.618 50.000 0.00 0.00 0.00 4.16
4331 6852 2.761786 ATCCAATGGAAGGGATGTGG 57.238 50.000 5.89 0.00 42.24 4.17
4332 6853 4.223477 ACAAAATCCAATGGAAGGGATGTG 59.777 41.667 5.89 0.78 43.01 3.21
4333 6854 4.223477 CACAAAATCCAATGGAAGGGATGT 59.777 41.667 5.89 4.98 43.01 3.06
4334 6855 4.467082 TCACAAAATCCAATGGAAGGGATG 59.533 41.667 5.89 2.98 43.01 3.51
4335 6856 4.686891 TCACAAAATCCAATGGAAGGGAT 58.313 39.130 5.89 0.00 45.71 3.85
4336 6857 4.125124 TCACAAAATCCAATGGAAGGGA 57.875 40.909 5.89 0.37 34.34 4.20
4337 6858 4.888326 TTCACAAAATCCAATGGAAGGG 57.112 40.909 5.89 0.00 34.34 3.95


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

AutoCloner maintained by Alex Coulton.