Multiple sequence alignment - TraesCS4A01G175900

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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 TraesCS4A01G175900 chr4A 100.000 5224 0 0 1 5224 446952708 446947485 0.000000e+00 9648.0
1 TraesCS4A01G175900 chr4B 90.566 2862 106 50 389 3209 187431884 187434622 0.000000e+00 3639.0
2 TraesCS4A01G175900 chr4B 94.784 786 32 6 3719 4500 187435262 187436042 0.000000e+00 1216.0
3 TraesCS4A01G175900 chr4B 89.474 741 71 4 4491 5224 187436293 187437033 0.000000e+00 929.0
4 TraesCS4A01G175900 chr4B 88.312 539 40 9 3191 3712 187434638 187435170 4.440000e-175 625.0
5 TraesCS4A01G175900 chr4B 89.526 401 18 10 1 391 187431085 187431471 2.190000e-133 486.0
6 TraesCS4A01G175900 chr4B 90.741 54 3 1 3670 3723 187435186 187435237 2.610000e-08 71.3
7 TraesCS4A01G175900 chr4D 93.427 2495 92 30 1235 3701 122758065 122760515 0.000000e+00 3633.0
8 TraesCS4A01G175900 chr4D 93.110 1611 49 23 1 1583 122756134 122757710 0.000000e+00 2303.0
9 TraesCS4A01G175900 chr4D 94.764 783 35 3 3719 4500 122760592 122761369 0.000000e+00 1214.0
10 TraesCS4A01G175900 chr4D 77.211 294 58 7 4937 5224 49307258 49306968 4.190000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G175900 chr4A 446947485 446952708 5223 True 9648.000000 9648 100.000000 1 5224 1 chr4A.!!$R1 5223
1 TraesCS4A01G175900 chr4B 187431085 187437033 5948 False 1161.050000 3639 90.567167 1 5224 6 chr4B.!!$F1 5223
2 TraesCS4A01G175900 chr4D 122756134 122761369 5235 False 2383.333333 3633 93.767000 1 4500 3 chr4D.!!$F1 4499


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
238 249 0.107897 CCATCCACCGTCCAAATCGA 60.108 55.000 0.00 0.0 0.00 3.59 F
420 846 0.528466 CATCGATACGCACACCAGCT 60.528 55.000 0.00 0.0 0.00 4.24 F
1743 2907 1.271054 GCCCAGATGGACGCAATCTAT 60.271 52.381 0.00 0.0 37.39 1.98 F
2596 3768 0.179018 AACGGCTGCCTTTCTTGACT 60.179 50.000 17.92 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 2907 0.179111 CGAGCTTCTTCATGGCGGTA 60.179 55.000 0.00 0.00 0.00 4.02 R
2007 3171 1.881602 GTAGACGGGCGTGAAGTCT 59.118 57.895 2.85 2.85 45.85 3.24 R
3570 4819 0.316204 CAAAGCAGGGCAAGTCCAAG 59.684 55.000 0.00 0.00 36.21 3.61 R
4318 5657 0.249238 CGGCAGTATGAGCAGTCCTC 60.249 60.000 0.00 0.00 39.69 3.71 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
71 72 2.815211 CCTGCCGACCACACGATG 60.815 66.667 0.00 0.00 35.09 3.84
156 163 0.165944 GAAGCGTCACAATCCAACCG 59.834 55.000 0.00 0.00 0.00 4.44
166 173 0.183971 AATCCAACCGGGTCAACACA 59.816 50.000 6.32 0.00 38.11 3.72
169 176 1.720694 CCAACCGGGTCAACACACAC 61.721 60.000 6.32 0.00 0.00 3.82
170 177 1.816259 AACCGGGTCAACACACACG 60.816 57.895 6.32 0.00 43.17 4.49
238 249 0.107897 CCATCCACCGTCCAAATCGA 60.108 55.000 0.00 0.00 0.00 3.59
262 273 7.952101 CGATGATTATCCAAGCAATACTTTACG 59.048 37.037 0.00 0.00 36.04 3.18
263 274 8.902540 ATGATTATCCAAGCAATACTTTACGA 57.097 30.769 0.00 0.00 36.04 3.43
264 275 8.365399 TGATTATCCAAGCAATACTTTACGAG 57.635 34.615 0.00 0.00 36.04 4.18
271 282 6.292168 CCAAGCAATACTTTACGAGTAATCGG 60.292 42.308 17.70 1.19 43.76 4.18
279 290 9.813446 ATACTTTACGAGTAATCGGAATTTTCT 57.187 29.630 17.70 0.00 43.76 2.52
285 296 6.183360 ACGAGTAATCGGAATTTTCTAGTCGA 60.183 38.462 17.70 6.67 33.95 4.20
294 305 2.807631 TTTCTAGTCGACGCGTGCCC 62.808 60.000 20.70 0.00 0.00 5.36
299 310 2.589442 TCGACGCGTGCCCTTTTT 60.589 55.556 20.70 0.00 0.00 1.94
302 313 3.263503 GACGCGTGCCCTTTTTCCC 62.264 63.158 20.70 0.00 0.00 3.97
303 314 3.291383 CGCGTGCCCTTTTTCCCA 61.291 61.111 0.00 0.00 0.00 4.37
304 315 2.338620 GCGTGCCCTTTTTCCCAC 59.661 61.111 0.00 0.00 0.00 4.61
305 316 2.642700 CGTGCCCTTTTTCCCACG 59.357 61.111 0.00 0.00 43.83 4.94
306 317 2.338620 GTGCCCTTTTTCCCACGC 59.661 61.111 0.00 0.00 0.00 5.34
386 397 3.558418 CCGTCGTTTCCTTTTTCTCTTCA 59.442 43.478 0.00 0.00 0.00 3.02
412 838 2.279186 CCGGCACATCGATACGCA 60.279 61.111 17.21 0.00 0.00 5.24
420 846 0.528466 CATCGATACGCACACCAGCT 60.528 55.000 0.00 0.00 0.00 4.24
431 857 5.364778 ACGCACACCAGCTGAATAATATTA 58.635 37.500 17.39 0.00 0.00 0.98
432 858 5.997746 ACGCACACCAGCTGAATAATATTAT 59.002 36.000 17.39 1.91 0.00 1.28
433 859 6.486657 ACGCACACCAGCTGAATAATATTATT 59.513 34.615 17.39 18.55 36.14 1.40
551 978 9.762381 TTCTTTAGAAAAGGCTTGGGATTATTA 57.238 29.630 0.00 0.00 0.00 0.98
556 983 8.608185 AGAAAAGGCTTGGGATTATTAATTCA 57.392 30.769 0.00 0.00 0.00 2.57
582 1013 1.737793 ACGCATGCTTTGGTTACTAGC 59.262 47.619 17.13 0.00 35.50 3.42
686 1121 4.976864 AGTAGTGTACCAACCCGAAAAAT 58.023 39.130 0.00 0.00 0.00 1.82
693 1131 9.856162 AGTGTACCAACCCGAAAAATATATTAT 57.144 29.630 0.00 0.00 0.00 1.28
826 1268 7.545265 AGCAAAGCGAGAAATAAAAATGCATTA 59.455 29.630 13.39 0.00 32.76 1.90
953 1411 1.836604 GGAAGCCCCAGTTGCCAAA 60.837 57.895 0.00 0.00 34.14 3.28
968 1426 3.237746 TGCCAAATCAGATTCAAACCCA 58.762 40.909 0.00 0.00 0.00 4.51
992 1450 2.923035 ACTCCACACTCCACCCCG 60.923 66.667 0.00 0.00 0.00 5.73
993 1451 3.706373 CTCCACACTCCACCCCGG 61.706 72.222 0.00 0.00 0.00 5.73
994 1452 4.242586 TCCACACTCCACCCCGGA 62.243 66.667 0.73 0.00 43.61 5.14
1188 1649 2.434359 CTCTTCGACGCCAACCCC 60.434 66.667 0.00 0.00 0.00 4.95
1557 2721 1.577328 CGGGCTACAACACCAAGCTG 61.577 60.000 0.00 0.00 36.48 4.24
1560 2724 1.681264 GGCTACAACACCAAGCTGTTT 59.319 47.619 0.00 0.00 36.48 2.83
1692 2856 4.603946 GGCATCTACGACCCGGCC 62.604 72.222 0.00 0.00 0.00 6.13
1695 2859 3.152400 ATCTACGACCCGGCCACC 61.152 66.667 2.24 0.00 0.00 4.61
1743 2907 1.271054 GCCCAGATGGACGCAATCTAT 60.271 52.381 0.00 0.00 37.39 1.98
2007 3171 0.555769 ACTTTGGCCTCTTCAACCCA 59.444 50.000 3.32 0.00 0.00 4.51
2173 3341 4.382040 GCTGGGGCCTAAAATCTTTTCTTC 60.382 45.833 0.84 0.00 0.00 2.87
2174 3342 5.010708 TGGGGCCTAAAATCTTTTCTTCT 57.989 39.130 0.84 0.00 0.00 2.85
2175 3343 5.402630 TGGGGCCTAAAATCTTTTCTTCTT 58.597 37.500 0.84 0.00 0.00 2.52
2178 3346 7.039293 TGGGGCCTAAAATCTTTTCTTCTTTAC 60.039 37.037 0.84 0.00 0.00 2.01
2252 3420 8.609176 GCCTGTCTTTACAATCGTGATTTTATA 58.391 33.333 0.00 0.00 34.49 0.98
2288 3456 5.600696 GGAGAATGTGGTTTCAATTGTGTT 58.399 37.500 5.13 0.00 0.00 3.32
2299 3467 9.743057 TGGTTTCAATTGTGTTAAATTCAGTAG 57.257 29.630 5.13 0.00 0.00 2.57
2356 3526 8.702819 GGATGAACCCAGTAAAAGTAGTATAGT 58.297 37.037 0.00 0.00 0.00 2.12
2407 3577 1.238439 GGCTGCAGCAACTCTGTTTA 58.762 50.000 37.63 0.00 44.66 2.01
2411 3581 1.603802 TGCAGCAACTCTGTTTACAGC 59.396 47.619 5.00 0.00 44.66 4.40
2564 3736 1.377994 GCTCCTATCCCCTGCATGG 59.622 63.158 0.13 0.13 0.00 3.66
2596 3768 0.179018 AACGGCTGCCTTTCTTGACT 60.179 50.000 17.92 0.00 0.00 3.41
2618 3790 2.176273 CCAGTATGACAGCAGGCGC 61.176 63.158 0.00 0.00 39.69 6.53
2648 3820 2.358737 GCCTTGGACACGTCTGGG 60.359 66.667 0.00 0.00 0.00 4.45
2825 4017 7.490000 ACGTAGTACTCCCTATCAAAATCTTG 58.510 38.462 0.00 0.00 41.94 3.02
2826 4018 7.123847 ACGTAGTACTCCCTATCAAAATCTTGT 59.876 37.037 0.00 0.00 41.94 3.16
2827 4019 8.627403 CGTAGTACTCCCTATCAAAATCTTGTA 58.373 37.037 0.00 0.00 33.94 2.41
2828 4020 9.968870 GTAGTACTCCCTATCAAAATCTTGTAG 57.031 37.037 0.00 0.00 33.94 2.74
2891 4086 9.566432 ACTAGGATCTGATATTTGAATTGGAAC 57.434 33.333 0.00 0.00 0.00 3.62
2894 4089 6.486657 GGATCTGATATTTGAATTGGAACGGA 59.513 38.462 0.00 0.00 0.00 4.69
2895 4090 7.175641 GGATCTGATATTTGAATTGGAACGGAT 59.824 37.037 0.00 0.00 0.00 4.18
2957 4152 7.306866 CGGTACTGTTTTGAGAAGAAGAAGAAG 60.307 40.741 0.00 0.00 0.00 2.85
2968 4163 9.177608 TGAGAAGAAGAAGAAGAAAAATCAACA 57.822 29.630 0.00 0.00 0.00 3.33
2982 4177 4.637483 AATCAACAGGTTGTCAACACTG 57.363 40.909 22.41 22.41 41.16 3.66
3209 4441 5.437289 TTGGACTTGCTATCTGTTGTTTG 57.563 39.130 0.00 0.00 0.00 2.93
3218 4450 4.201891 GCTATCTGTTGTTTGCTGAGATGG 60.202 45.833 0.00 0.00 0.00 3.51
3219 4451 3.213206 TCTGTTGTTTGCTGAGATGGT 57.787 42.857 0.00 0.00 0.00 3.55
3230 4462 2.357009 GCTGAGATGGTTGCCTATTGTG 59.643 50.000 0.00 0.00 0.00 3.33
3342 4580 2.364632 CTTTCCGTGGCATCCAATACA 58.635 47.619 0.00 0.00 34.18 2.29
3343 4581 2.036958 TTCCGTGGCATCCAATACAG 57.963 50.000 0.00 0.00 34.18 2.74
3344 4582 0.180171 TCCGTGGCATCCAATACAGG 59.820 55.000 0.00 0.00 34.18 4.00
3345 4583 0.180171 CCGTGGCATCCAATACAGGA 59.820 55.000 0.00 0.00 43.01 3.86
3347 4585 1.942657 CGTGGCATCCAATACAGGAAG 59.057 52.381 0.00 0.00 41.92 3.46
3409 4647 0.475906 GCATGTGGATTAGGCCCTCT 59.524 55.000 0.00 0.00 0.00 3.69
3467 4712 1.640428 TCGGATGCTTAGCGAAAGTG 58.360 50.000 0.00 0.00 37.53 3.16
3468 4713 1.203758 TCGGATGCTTAGCGAAAGTGA 59.796 47.619 0.00 0.00 37.53 3.41
3487 4732 1.566298 AACCATGTGGAGGAGAGGGC 61.566 60.000 5.96 0.00 38.94 5.19
3488 4733 2.750657 CCATGTGGAGGAGAGGGCC 61.751 68.421 0.00 0.00 37.39 5.80
3489 4734 1.692042 CATGTGGAGGAGAGGGCCT 60.692 63.158 5.25 5.25 42.17 5.19
3490 4735 1.692042 ATGTGGAGGAGAGGGCCTG 60.692 63.158 12.95 0.00 38.73 4.85
3492 4737 2.039624 TGGAGGAGAGGGCCTGAC 59.960 66.667 12.95 4.06 38.73 3.51
3494 4739 2.063378 GGAGGAGAGGGCCTGACTG 61.063 68.421 12.95 0.00 38.73 3.51
3495 4740 2.686835 AGGAGAGGGCCTGACTGC 60.687 66.667 12.95 8.46 36.76 4.40
3496 4741 3.005539 GGAGAGGGCCTGACTGCA 61.006 66.667 12.95 0.00 0.00 4.41
3497 4742 2.373707 GGAGAGGGCCTGACTGCAT 61.374 63.158 12.95 0.00 0.00 3.96
3500 4749 0.543749 AGAGGGCCTGACTGCATTAC 59.456 55.000 12.95 0.00 0.00 1.89
3503 4752 2.170607 GAGGGCCTGACTGCATTACTAA 59.829 50.000 12.95 0.00 0.00 2.24
3508 4757 5.450550 GGGCCTGACTGCATTACTAATTTTC 60.451 44.000 0.84 0.00 0.00 2.29
3515 4764 7.094248 TGACTGCATTACTAATTTTCAGCATGT 60.094 33.333 0.00 0.00 37.40 3.21
3527 4776 0.813184 CAGCATGTTGATTCGGCCTT 59.187 50.000 2.97 0.00 0.00 4.35
3529 4778 0.248215 GCATGTTGATTCGGCCTTCG 60.248 55.000 0.00 0.00 40.90 3.79
3530 4779 0.378257 CATGTTGATTCGGCCTTCGG 59.622 55.000 0.00 0.00 39.77 4.30
3531 4780 0.748005 ATGTTGATTCGGCCTTCGGG 60.748 55.000 0.00 0.00 39.77 5.14
3557 4806 5.468746 GGCTAGTGTGTGTCAACAATCTTAA 59.531 40.000 0.00 0.00 38.27 1.85
3559 4808 6.423905 GCTAGTGTGTGTCAACAATCTTAAGA 59.576 38.462 7.82 7.82 38.27 2.10
3570 4819 9.020813 GTCAACAATCTTAAGAAGAAAACCAAC 57.979 33.333 9.71 0.00 41.63 3.77
3574 4823 8.197439 ACAATCTTAAGAAGAAAACCAACTTGG 58.803 33.333 9.71 6.24 41.71 3.61
3578 4827 7.614192 TCTTAAGAAGAAAACCAACTTGGACTT 59.386 33.333 15.14 12.62 36.28 3.01
3644 4893 5.590530 TTTGTTGTCAAAGCACCACTAAT 57.409 34.783 0.00 0.00 38.44 1.73
3717 5022 5.128827 AGTTGAGAATCTAAAGTATGGCCGA 59.871 40.000 0.00 0.00 34.92 5.54
3765 5099 3.258372 TCCTGTGCTGTTACCTGACTTAG 59.742 47.826 0.00 0.00 0.00 2.18
3798 5133 2.548875 TGTTGTTTTGCATTGCAGTCC 58.451 42.857 11.76 4.23 40.61 3.85
3850 5185 2.808206 AATCCGAGCCCTAAGCCCG 61.808 63.158 0.00 0.00 45.47 6.13
4110 5445 0.462047 GCGACCCCAGTAAGTCCATG 60.462 60.000 0.00 0.00 0.00 3.66
4146 5481 0.538287 AGTTTCTGAACCTGGCTGCC 60.538 55.000 12.87 12.87 36.39 4.85
4167 5506 2.107953 GGCATCGGAGGAGCTGAC 59.892 66.667 0.00 0.00 33.94 3.51
4172 5511 1.459455 ATCGGAGGAGCTGACGATGG 61.459 60.000 9.69 0.00 43.55 3.51
4184 5523 0.889186 GACGATGGCACCCTTGTTGT 60.889 55.000 0.00 0.00 0.00 3.32
4185 5524 1.172180 ACGATGGCACCCTTGTTGTG 61.172 55.000 0.00 0.00 36.79 3.33
4186 5525 1.172180 CGATGGCACCCTTGTTGTGT 61.172 55.000 0.00 0.00 36.11 3.72
4436 5775 1.483424 CGCCTCTTAGCTTAGCGCAC 61.483 60.000 11.47 0.00 42.61 5.34
4467 5806 2.845752 TAGCGTGATGTTGGGCCGTC 62.846 60.000 0.00 0.00 0.00 4.79
4500 5839 8.317460 TGCATCGCATTAATTTATTTTTCGTTC 58.683 29.630 0.00 0.00 31.71 3.95
4501 5840 8.531530 GCATCGCATTAATTTATTTTTCGTTCT 58.468 29.630 0.00 0.00 0.00 3.01
4515 6114 6.598753 TTTTCGTTCTCTTCGACTCATTTT 57.401 33.333 0.00 0.00 37.05 1.82
4530 6129 5.559770 ACTCATTTTTGGCCCAAATTTAGG 58.440 37.500 10.24 0.00 33.19 2.69
4546 6145 1.895020 TAGGCCGAGTTTGCATCCGT 61.895 55.000 0.00 0.00 0.00 4.69
4580 6179 2.360980 CCCTCTCCCTGTCCTCGT 59.639 66.667 0.00 0.00 0.00 4.18
4582 6181 1.304952 CCTCTCCCTGTCCTCGTCT 59.695 63.158 0.00 0.00 0.00 4.18
4621 6220 2.031768 GCCATCGCCATCTCTCCC 59.968 66.667 0.00 0.00 0.00 4.30
4630 6229 1.590932 CCATCTCTCCCAATTCGCTG 58.409 55.000 0.00 0.00 0.00 5.18
4636 6235 3.012518 CTCTCCCAATTCGCTGTCAAAT 58.987 45.455 0.00 0.00 0.00 2.32
4638 6237 2.091541 TCCCAATTCGCTGTCAAATCC 58.908 47.619 0.00 0.00 0.00 3.01
4650 6249 2.124695 AAATCCTTCCGCGCTCCC 60.125 61.111 5.56 0.00 0.00 4.30
4724 6324 2.266055 GCCGTGGTCCTGAGGAAG 59.734 66.667 0.96 0.00 31.38 3.46
4725 6325 2.584391 GCCGTGGTCCTGAGGAAGT 61.584 63.158 0.96 0.00 31.38 3.01
4727 6327 1.185618 CCGTGGTCCTGAGGAAGTCA 61.186 60.000 0.96 0.00 31.38 3.41
4795 6398 1.299850 AAAAAGAAGCCGCCGTTGC 60.300 52.632 0.00 0.00 0.00 4.17
4865 6468 2.594592 GCCACGCAACAGGTCCTT 60.595 61.111 0.00 0.00 0.00 3.36
4907 6510 2.432628 CTTCTCGTCACCACCGCC 60.433 66.667 0.00 0.00 0.00 6.13
4908 6511 3.220999 CTTCTCGTCACCACCGCCA 62.221 63.158 0.00 0.00 0.00 5.69
4931 6534 1.378882 CCAACATGGGCTCATCGGTG 61.379 60.000 0.00 1.19 32.67 4.94
4950 6553 3.830192 CAAGCCCGCCCATGCTTC 61.830 66.667 0.00 0.00 45.59 3.86
4972 6575 1.421410 GAATCGTCGCGCCTGTCAAT 61.421 55.000 0.00 0.00 0.00 2.57
5003 6606 0.393077 CATACGGGTGCCTTCCTAGG 59.607 60.000 0.82 0.82 45.02 3.02
5012 6615 1.987855 CCTTCCTAGGCACGACCCA 60.988 63.158 2.96 0.00 40.58 4.51
5015 6618 0.970937 TTCCTAGGCACGACCCAGAG 60.971 60.000 2.96 0.00 40.58 3.35
5036 6639 2.159226 GGTGTCCTACTTCTCCATGTCG 60.159 54.545 0.00 0.00 0.00 4.35
5051 6654 4.043100 TCGCCTCGGGACCTCTCA 62.043 66.667 0.00 0.00 0.00 3.27
5052 6655 3.827898 CGCCTCGGGACCTCTCAC 61.828 72.222 0.00 0.00 0.00 3.51
5054 6657 2.037367 CCTCGGGACCTCTCACCA 59.963 66.667 0.00 0.00 0.00 4.17
5070 6673 2.043411 CACCAAAAATGCACGACTTCG 58.957 47.619 0.00 0.00 46.33 3.79
5120 6723 0.740868 ATCTCAACGCCACACCGATG 60.741 55.000 0.00 0.00 33.08 3.84
5136 6739 3.588511 TGGCCAGCCAATCCACCA 61.589 61.111 9.42 0.00 44.12 4.17
5142 6746 3.499737 GCCAATCCACCAGACGCG 61.500 66.667 3.53 3.53 0.00 6.01
5148 6752 3.691342 CCACCAGACGCGAAGGGA 61.691 66.667 15.93 0.00 46.37 4.20
5207 6811 2.548920 GCCTCCTTCCTATTCGATGGTG 60.549 54.545 0.00 0.00 0.00 4.17
5208 6812 2.548920 CCTCCTTCCTATTCGATGGTGC 60.549 54.545 0.00 0.00 0.00 5.01
5209 6813 1.416401 TCCTTCCTATTCGATGGTGCC 59.584 52.381 0.00 0.00 0.00 5.01
5210 6814 1.502231 CTTCCTATTCGATGGTGCCG 58.498 55.000 0.00 0.00 0.00 5.69
5211 6815 1.068588 CTTCCTATTCGATGGTGCCGA 59.931 52.381 0.00 0.00 0.00 5.54
5212 6816 0.387929 TCCTATTCGATGGTGCCGAC 59.612 55.000 0.00 0.00 35.61 4.79
5215 6819 0.821517 TATTCGATGGTGCCGACACT 59.178 50.000 0.81 0.00 46.57 3.55
5216 6820 0.740868 ATTCGATGGTGCCGACACTG 60.741 55.000 0.81 0.00 46.57 3.66
5217 6821 2.779951 TTCGATGGTGCCGACACTGG 62.780 60.000 0.81 0.00 46.57 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.328099 GCAGGGAGAAACGCACAGG 61.328 63.158 0.00 0.00 0.00 4.00
41 42 2.328099 GGCAGGGAGAAACGCACAG 61.328 63.158 0.00 0.00 0.00 3.66
42 43 2.281484 GGCAGGGAGAAACGCACA 60.281 61.111 0.00 0.00 0.00 4.57
43 44 3.423154 CGGCAGGGAGAAACGCAC 61.423 66.667 0.00 0.00 0.00 5.34
44 45 3.621805 TCGGCAGGGAGAAACGCA 61.622 61.111 0.00 0.00 0.00 5.24
45 46 3.119096 GTCGGCAGGGAGAAACGC 61.119 66.667 0.00 0.00 0.00 4.84
49 50 2.525629 TGTGGTCGGCAGGGAGAA 60.526 61.111 0.00 0.00 0.00 2.87
71 72 0.801067 GCACGTACACGGAGATGGAC 60.801 60.000 6.72 0.00 44.95 4.02
119 126 0.969149 TCTCAATCTCACCAGCGTGT 59.031 50.000 0.00 0.00 41.09 4.49
156 163 1.494824 GAGTACGTGTGTGTTGACCC 58.505 55.000 0.00 0.00 0.00 4.46
169 176 2.413142 GGTGGGGAGGACGAGTACG 61.413 68.421 0.00 0.00 45.75 3.67
170 177 2.413142 CGGTGGGGAGGACGAGTAC 61.413 68.421 0.00 0.00 0.00 2.73
238 249 8.902540 TCGTAAAGTATTGCTTGGATAATCAT 57.097 30.769 0.00 0.00 37.52 2.45
262 273 6.140422 CGTCGACTAGAAAATTCCGATTACTC 59.860 42.308 14.70 0.00 0.00 2.59
263 274 5.970023 CGTCGACTAGAAAATTCCGATTACT 59.030 40.000 14.70 0.00 0.00 2.24
264 275 5.331383 GCGTCGACTAGAAAATTCCGATTAC 60.331 44.000 14.70 0.00 0.00 1.89
271 282 2.532388 GCACGCGTCGACTAGAAAATTC 60.532 50.000 9.86 0.00 0.00 2.17
279 290 2.424705 AAAAGGGCACGCGTCGACTA 62.425 55.000 9.86 0.00 0.00 2.59
285 296 3.292159 GGGAAAAAGGGCACGCGT 61.292 61.111 5.58 5.58 0.00 6.01
294 305 1.524008 GAGGTGGGCGTGGGAAAAAG 61.524 60.000 0.00 0.00 0.00 2.27
302 313 3.423154 GAAAGCGAGGTGGGCGTG 61.423 66.667 0.00 0.00 35.00 5.34
303 314 3.178540 AAGAAAGCGAGGTGGGCGT 62.179 57.895 0.00 0.00 35.00 5.68
304 315 2.358737 AAGAAAGCGAGGTGGGCG 60.359 61.111 0.00 0.00 35.00 6.13
305 316 2.391389 CGAAGAAAGCGAGGTGGGC 61.391 63.158 0.00 0.00 0.00 5.36
306 317 1.292223 TCGAAGAAAGCGAGGTGGG 59.708 57.895 0.00 0.00 33.33 4.61
386 397 1.138859 TCGATGTGCCGGAGAATGAAT 59.861 47.619 5.05 0.00 0.00 2.57
431 857 3.149196 TGCTCGAAGCTTTCCTTTGAAT 58.851 40.909 0.00 0.00 42.12 2.57
432 858 2.549754 CTGCTCGAAGCTTTCCTTTGAA 59.450 45.455 0.00 0.00 42.12 2.69
433 859 2.146342 CTGCTCGAAGCTTTCCTTTGA 58.854 47.619 0.00 0.00 42.97 2.69
439 865 0.671781 TGCCTCTGCTCGAAGCTTTC 60.672 55.000 0.00 0.00 42.97 2.62
551 978 4.152759 CCAAAGCATGCGTTTGAATGAATT 59.847 37.500 28.78 8.76 37.10 2.17
555 982 2.406130 ACCAAAGCATGCGTTTGAATG 58.594 42.857 28.78 20.03 37.10 2.67
556 983 2.818130 ACCAAAGCATGCGTTTGAAT 57.182 40.000 28.78 19.54 37.10 2.57
582 1013 6.043411 GCAAGAAAGAGGGTATACTGTACTG 58.957 44.000 2.25 0.00 0.00 2.74
664 1099 4.420522 TTTTTCGGGTTGGTACACTACT 57.579 40.909 0.00 0.00 39.29 2.57
779 1221 2.564975 GCTGCCATGTGTCACTGC 59.435 61.111 4.27 5.28 0.00 4.40
826 1268 9.816787 TTACAGTATTCTTATTCCCTTGGTTTT 57.183 29.630 0.00 0.00 0.00 2.43
830 1272 7.040409 GCCATTACAGTATTCTTATTCCCTTGG 60.040 40.741 0.00 0.00 0.00 3.61
953 1411 4.396166 GTCGATTGTGGGTTTGAATCTGAT 59.604 41.667 0.00 0.00 0.00 2.90
968 1426 1.000955 GTGGAGTGTGGAGTCGATTGT 59.999 52.381 0.00 0.00 0.00 2.71
1012 1470 1.747145 CGAGCAGCATGAGGAGGAT 59.253 57.895 0.00 0.00 39.69 3.24
1188 1649 0.807667 CGAAGGCGGAGATGAAGGTG 60.808 60.000 0.00 0.00 0.00 4.00
1296 2460 4.161295 TTGGCGCGGATCCAGGAG 62.161 66.667 13.41 0.00 34.66 3.69
1557 2721 3.346631 CTGCAGCATGGCCGGAAAC 62.347 63.158 5.05 0.00 35.86 2.78
1560 2724 4.349503 AACTGCAGCATGGCCGGA 62.350 61.111 15.27 0.00 35.86 5.14
1692 2856 2.146342 CTGGTGTAGTTGAGCTTGGTG 58.854 52.381 0.00 0.00 0.00 4.17
1695 2859 1.882912 TGCTGGTGTAGTTGAGCTTG 58.117 50.000 0.00 0.00 32.41 4.01
1743 2907 0.179111 CGAGCTTCTTCATGGCGGTA 60.179 55.000 0.00 0.00 0.00 4.02
2007 3171 1.881602 GTAGACGGGCGTGAAGTCT 59.118 57.895 2.85 2.85 45.85 3.24
2181 3349 8.507249 GCAATCAACCAATCATTATACTCCTAC 58.493 37.037 0.00 0.00 0.00 3.18
2182 3350 8.217111 TGCAATCAACCAATCATTATACTCCTA 58.783 33.333 0.00 0.00 0.00 2.94
2184 3352 7.275888 TGCAATCAACCAATCATTATACTCC 57.724 36.000 0.00 0.00 0.00 3.85
2252 3420 4.142315 CCACATTCTCCGCAGAAATGAAAT 60.142 41.667 5.50 0.00 42.14 2.17
2256 3424 2.086869 ACCACATTCTCCGCAGAAATG 58.913 47.619 0.00 0.00 42.14 2.32
2350 3520 9.282247 CGGAATGTCCATTATTACGTACTATAC 57.718 37.037 0.00 0.00 37.15 1.47
2407 3577 2.101582 GTCGGATCATCTGTAAGGCTGT 59.898 50.000 0.00 0.00 0.00 4.40
2411 3581 4.655762 TCAAGTCGGATCATCTGTAAGG 57.344 45.455 0.00 0.00 0.00 2.69
2564 3736 2.644992 CCGTTTGGGCAAGCAGAC 59.355 61.111 0.00 0.00 0.00 3.51
2596 3768 1.139654 GCCTGCTGTCATACTGGATCA 59.860 52.381 0.00 0.00 0.00 2.92
2618 3790 0.729116 CCAAGGCTGCTATCAACACG 59.271 55.000 0.00 0.00 0.00 4.49
2648 3820 1.931705 TCCCACCCCACCCATAACC 60.932 63.158 0.00 0.00 0.00 2.85
2733 3925 2.083774 GGTACATTTACAGCAGCAGCA 58.916 47.619 3.17 0.00 45.49 4.41
2734 3926 2.083774 TGGTACATTTACAGCAGCAGC 58.916 47.619 0.00 0.00 42.56 5.25
2735 3927 3.338249 ACTGGTACATTTACAGCAGCAG 58.662 45.455 0.00 0.00 42.62 4.24
2736 3928 3.417069 ACTGGTACATTTACAGCAGCA 57.583 42.857 0.00 0.00 42.62 4.41
2737 3929 4.201822 GCTTACTGGTACATTTACAGCAGC 60.202 45.833 0.00 0.76 42.62 5.25
2738 3930 5.178797 AGCTTACTGGTACATTTACAGCAG 58.821 41.667 0.00 0.00 44.04 4.24
2739 3931 5.160607 AGCTTACTGGTACATTTACAGCA 57.839 39.130 0.00 0.00 38.20 4.41
2740 3932 5.673818 GCAAGCTTACTGGTACATTTACAGC 60.674 44.000 0.00 0.00 38.20 4.40
2741 3933 5.411361 TGCAAGCTTACTGGTACATTTACAG 59.589 40.000 0.00 0.00 38.20 2.74
2742 3934 5.180492 GTGCAAGCTTACTGGTACATTTACA 59.820 40.000 0.00 0.00 38.20 2.41
2743 3935 5.391629 GGTGCAAGCTTACTGGTACATTTAC 60.392 44.000 0.00 0.00 34.29 2.01
2744 3936 4.698304 GGTGCAAGCTTACTGGTACATTTA 59.302 41.667 0.00 0.00 34.29 1.40
2828 4020 9.021863 GCATGTACTCACTCTGTAAACTAATAC 57.978 37.037 0.00 0.00 0.00 1.89
2931 4126 5.983720 TCTTCTTCTTCTCAAAACAGTACCG 59.016 40.000 0.00 0.00 0.00 4.02
2957 4152 6.034898 CAGTGTTGACAACCTGTTGATTTTTC 59.965 38.462 16.41 4.18 42.93 2.29
2968 4163 1.210478 ACTCAGCAGTGTTGACAACCT 59.790 47.619 15.59 9.29 0.00 3.50
3026 4224 1.365699 CCCTTAACGTGTTGATCCGG 58.634 55.000 0.00 0.00 0.00 5.14
3029 4227 3.335579 AGAAGCCCTTAACGTGTTGATC 58.664 45.455 0.00 0.00 0.00 2.92
3132 4330 3.916989 AGACCACCAGAATCTTAAACCCT 59.083 43.478 0.00 0.00 0.00 4.34
3209 4441 2.357009 CACAATAGGCAACCATCTCAGC 59.643 50.000 0.00 0.00 37.17 4.26
3218 4450 8.601476 GTCATTTACTAGTACACAATAGGCAAC 58.399 37.037 0.91 0.00 0.00 4.17
3219 4451 8.315482 TGTCATTTACTAGTACACAATAGGCAA 58.685 33.333 0.91 0.00 0.00 4.52
3230 4462 5.857517 GCGCTATCCTGTCATTTACTAGTAC 59.142 44.000 0.91 0.00 0.00 2.73
3342 4580 1.284198 AGAACAGATGCATGCCTTCCT 59.716 47.619 16.68 3.80 0.00 3.36
3343 4581 1.404391 CAGAACAGATGCATGCCTTCC 59.596 52.381 16.68 1.28 0.00 3.46
3344 4582 1.202268 GCAGAACAGATGCATGCCTTC 60.202 52.381 16.68 12.33 43.31 3.46
3345 4583 0.815734 GCAGAACAGATGCATGCCTT 59.184 50.000 16.68 1.92 43.31 4.35
3347 4585 0.815734 AAGCAGAACAGATGCATGCC 59.184 50.000 16.68 0.00 46.31 4.40
3409 4647 2.440409 GCTGCTTCCTTCCTTTGATGA 58.560 47.619 0.00 0.00 0.00 2.92
3444 4688 3.125316 ACTTTCGCTAAGCATCCGAAAAG 59.875 43.478 12.74 6.44 46.24 2.27
3467 4712 0.543749 CCCTCTCCTCCACATGGTTC 59.456 60.000 0.00 0.00 36.34 3.62
3468 4713 1.566298 GCCCTCTCCTCCACATGGTT 61.566 60.000 0.00 0.00 36.34 3.67
3487 4732 6.127925 TGCTGAAAATTAGTAATGCAGTCAGG 60.128 38.462 17.98 7.89 32.48 3.86
3488 4733 6.845302 TGCTGAAAATTAGTAATGCAGTCAG 58.155 36.000 16.01 15.43 34.46 3.51
3489 4734 6.816134 TGCTGAAAATTAGTAATGCAGTCA 57.184 33.333 16.01 12.96 0.00 3.41
3490 4735 7.253422 ACATGCTGAAAATTAGTAATGCAGTC 58.747 34.615 16.01 11.46 32.65 3.51
3492 4737 7.756272 TCAACATGCTGAAAATTAGTAATGCAG 59.244 33.333 9.77 11.35 32.65 4.41
3494 4739 8.638685 ATCAACATGCTGAAAATTAGTAATGC 57.361 30.769 2.34 0.00 0.00 3.56
3496 4741 9.507280 CGAATCAACATGCTGAAAATTAGTAAT 57.493 29.630 2.34 0.00 0.00 1.89
3497 4742 7.967854 CCGAATCAACATGCTGAAAATTAGTAA 59.032 33.333 2.34 0.00 0.00 2.24
3500 4749 5.230726 GCCGAATCAACATGCTGAAAATTAG 59.769 40.000 2.34 0.00 0.00 1.73
3503 4752 3.514645 GCCGAATCAACATGCTGAAAAT 58.485 40.909 2.34 0.00 0.00 1.82
3508 4757 0.813184 AAGGCCGAATCAACATGCTG 59.187 50.000 0.00 0.00 0.00 4.41
3527 4776 4.063967 CACACACTAGCCGCCCGA 62.064 66.667 0.00 0.00 0.00 5.14
3529 4778 2.434359 GACACACACTAGCCGCCC 60.434 66.667 0.00 0.00 0.00 6.13
3530 4779 1.301401 TTGACACACACTAGCCGCC 60.301 57.895 0.00 0.00 0.00 6.13
3531 4780 0.878523 TGTTGACACACACTAGCCGC 60.879 55.000 0.00 0.00 0.00 6.53
3557 4806 4.142160 GCAAGTCCAAGTTGGTTTTCTTCT 60.142 41.667 21.35 7.17 39.03 2.85
3559 4808 3.118775 GGCAAGTCCAAGTTGGTTTTCTT 60.119 43.478 21.35 16.76 39.03 2.52
3570 4819 0.316204 CAAAGCAGGGCAAGTCCAAG 59.684 55.000 0.00 0.00 36.21 3.61
3574 4823 1.856265 CGTCCAAAGCAGGGCAAGTC 61.856 60.000 0.00 0.00 30.91 3.01
3578 4827 3.884774 ACCGTCCAAAGCAGGGCA 61.885 61.111 0.00 0.00 30.91 5.36
3644 4893 1.065926 CATACTGGAAGGCTGTGCAGA 60.066 52.381 19.27 0.00 39.16 4.26
3717 5022 5.078411 ACGAATCTAAGCATCAGAACTGT 57.922 39.130 0.00 0.00 0.00 3.55
3765 5099 0.596082 AACAACATAACGGCACCTGC 59.404 50.000 0.00 0.00 41.14 4.85
3798 5133 2.359975 GAAGGGGTTGGAGCCACG 60.360 66.667 0.00 0.00 37.54 4.94
3819 5154 2.186826 CGGATTGGGCGATGGGTTC 61.187 63.158 0.00 0.00 0.00 3.62
4053 5388 2.357517 CCCTTGAAGTCGCACGCT 60.358 61.111 0.00 0.00 0.00 5.07
4078 5413 2.885861 GTCGCTGGAGGTGACGAT 59.114 61.111 0.00 0.00 44.05 3.73
4110 5445 8.193250 TCAGAAACTTCACAAACTGTTAGTAC 57.807 34.615 0.00 0.00 0.00 2.73
4146 5481 2.202987 GCTCCTCCGATGCCACAG 60.203 66.667 0.00 0.00 0.00 3.66
4167 5506 1.172180 ACACAACAAGGGTGCCATCG 61.172 55.000 0.00 0.00 39.87 3.84
4172 5511 1.639280 CAACAACACAACAAGGGTGC 58.361 50.000 0.00 0.00 39.87 5.01
4184 5523 0.820074 CCCCGTAACCTGCAACAACA 60.820 55.000 0.00 0.00 0.00 3.33
4185 5524 1.520600 CCCCCGTAACCTGCAACAAC 61.521 60.000 0.00 0.00 0.00 3.32
4186 5525 1.228306 CCCCCGTAACCTGCAACAA 60.228 57.895 0.00 0.00 0.00 2.83
4318 5657 0.249238 CGGCAGTATGAGCAGTCCTC 60.249 60.000 0.00 0.00 39.69 3.71
4467 5806 5.398176 AAATTAATGCGATGCAATGCAAG 57.602 34.783 13.45 10.90 45.45 4.01
4500 5839 2.162408 GGGCCAAAAATGAGTCGAAGAG 59.838 50.000 4.39 0.00 36.95 2.85
4501 5840 2.159382 GGGCCAAAAATGAGTCGAAGA 58.841 47.619 4.39 0.00 0.00 2.87
4530 6129 2.480555 CACGGATGCAAACTCGGC 59.519 61.111 0.00 0.00 0.00 5.54
4571 6170 1.384989 ATACGGGCAGACGAGGACAG 61.385 60.000 0.00 0.00 37.61 3.51
4600 6199 2.969238 GAGATGGCGATGGCGTGG 60.969 66.667 0.00 0.00 41.24 4.94
4603 6202 2.356793 GGAGAGATGGCGATGGCG 60.357 66.667 0.00 0.00 41.24 5.69
4610 6209 0.179034 AGCGAATTGGGAGAGATGGC 60.179 55.000 0.00 0.00 0.00 4.40
4621 6220 3.728864 CGGAAGGATTTGACAGCGAATTG 60.729 47.826 0.00 0.00 0.00 2.32
4630 6229 1.706287 GGAGCGCGGAAGGATTTGAC 61.706 60.000 8.83 0.00 0.00 3.18
4650 6249 4.899239 GGGCATGTCGAGAGGGCG 62.899 72.222 14.36 0.00 0.00 6.13
4654 6253 2.105128 GGTCGGGCATGTCGAGAG 59.895 66.667 12.26 0.00 37.31 3.20
4656 6255 4.530857 GGGGTCGGGCATGTCGAG 62.531 72.222 12.26 0.00 37.31 4.04
4678 6278 3.943137 ATGACTGGGAAGGGGGCGA 62.943 63.158 0.00 0.00 0.00 5.54
4710 6310 2.368875 TCTTTGACTTCCTCAGGACCAC 59.631 50.000 0.00 0.00 0.00 4.16
4717 6317 2.172505 TGCACCTTCTTTGACTTCCTCA 59.827 45.455 0.00 0.00 0.00 3.86
4744 6344 3.838565 CTCTAGGCATCCCTCTACTTCA 58.161 50.000 0.00 0.00 41.75 3.02
4865 6468 1.267121 GCTCTTGGTACCCTGACAGA 58.733 55.000 10.07 2.33 0.00 3.41
4889 6492 3.112709 GCGGTGGTGACGAGAAGC 61.113 66.667 0.00 0.00 0.00 3.86
4918 6521 3.626996 CTTGCCACCGATGAGCCCA 62.627 63.158 0.00 0.00 0.00 5.36
4945 6548 2.508439 GCGACGATTCCGGAAGCA 60.508 61.111 30.16 4.82 40.78 3.91
4994 6597 1.961180 CTGGGTCGTGCCTAGGAAGG 61.961 65.000 14.75 8.32 46.76 3.46
5003 6606 2.048127 GACACCTCTGGGTCGTGC 60.048 66.667 0.00 0.00 45.41 5.34
5006 6609 0.323542 AGTAGGACACCTCTGGGTCG 60.324 60.000 0.00 0.00 45.41 4.79
5012 6615 3.245803 ACATGGAGAAGTAGGACACCTCT 60.246 47.826 0.00 0.00 34.61 3.69
5015 6618 2.159226 CGACATGGAGAAGTAGGACACC 60.159 54.545 0.00 0.00 0.00 4.16
5023 6626 1.513158 CGAGGCGACATGGAGAAGT 59.487 57.895 0.00 0.00 0.00 3.01
5027 6630 3.147595 TCCCGAGGCGACATGGAG 61.148 66.667 0.00 0.00 0.00 3.86
5036 6639 3.462678 GGTGAGAGGTCCCGAGGC 61.463 72.222 0.00 0.00 0.00 4.70
5051 6654 2.399396 CGAAGTCGTGCATTTTTGGT 57.601 45.000 0.00 0.00 34.11 3.67
5078 6681 4.269523 GCAGGCACCACTGGGACA 62.270 66.667 0.00 0.00 38.90 4.02
5084 6687 2.490270 GATCAAGGGCAGGCACCACT 62.490 60.000 0.00 0.00 0.00 4.00
5120 6723 2.757099 CTGGTGGATTGGCTGGCC 60.757 66.667 4.43 4.43 0.00 5.36



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

AutoCloner maintained by Alex Coulton.