Multiple sequence alignment - TraesCS5B01G265100

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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 TraesCS5B01G265100 chr5B 100.000 5854 0 0 1 5854 449127690 449133543 0.000000e+00 10811
1 TraesCS5B01G265100 chr5B 75.738 2304 510 34 2261 4544 316152143 316154417 0.000000e+00 1112
2 TraesCS5B01G265100 chr5B 90.090 111 11 0 2768 2878 37449588 37449478 1.700000e-30 145
3 TraesCS5B01G265100 chr5B 88.696 115 13 0 2946 3060 37449478 37449364 2.200000e-29 141
4 TraesCS5B01G265100 chr5D 96.637 3747 93 13 1157 4887 376177357 376181086 0.000000e+00 6191
5 TraesCS5B01G265100 chr5D 91.827 1199 51 15 1 1159 376175846 376177037 0.000000e+00 1628
6 TraesCS5B01G265100 chr5D 75.183 2325 528 36 2261 4565 278137562 278139857 0.000000e+00 1051
7 TraesCS5B01G265100 chr5D 88.136 472 44 9 5104 5572 376181085 376181547 8.570000e-153 551
8 TraesCS5B01G265100 chr5D 94.937 316 9 4 1 314 376174894 376175204 6.820000e-134 488
9 TraesCS5B01G265100 chr5D 84.354 294 28 9 5567 5854 376184127 376184408 7.480000e-69 272
10 TraesCS5B01G265100 chr5A 94.561 3971 150 38 1903 5854 477221791 477225714 0.000000e+00 6076
11 TraesCS5B01G265100 chr5A 91.191 806 39 13 625 1408 477220483 477221278 0.000000e+00 1066
12 TraesCS5B01G265100 chr5A 75.183 2325 528 35 2261 4565 367269835 367272130 0.000000e+00 1051
13 TraesCS5B01G265100 chr5A 86.614 635 67 12 4 626 477212469 477213097 0.000000e+00 686
14 TraesCS5B01G265100 chr5A 88.032 493 35 5 623 1098 477213129 477213614 3.960000e-156 562
15 TraesCS5B01G265100 chr5A 87.965 457 42 8 1449 1903 477221401 477221846 1.440000e-145 527
16 TraesCS5B01G265100 chr5A 88.759 427 39 6 103 524 477219942 477220364 1.120000e-141 514
17 TraesCS5B01G265100 chr1B 90.826 109 10 0 2946 3054 633293451 633293559 4.730000e-31 147
18 TraesCS5B01G265100 chr1B 93.151 73 5 0 2765 2837 633291771 633291843 2.230000e-19 108


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 TraesCS5B01G265100 chr5B 449127690 449133543 5853 False 10811.00 10811 100.0000 1 5854 1 chr5B.!!$F2 5853
1 TraesCS5B01G265100 chr5B 316152143 316154417 2274 False 1112.00 1112 75.7380 2261 4544 1 chr5B.!!$F1 2283
2 TraesCS5B01G265100 chr5D 376174894 376184408 9514 False 1826.00 6191 91.1782 1 5854 5 chr5D.!!$F2 5853
3 TraesCS5B01G265100 chr5D 278137562 278139857 2295 False 1051.00 1051 75.1830 2261 4565 1 chr5D.!!$F1 2304
4 TraesCS5B01G265100 chr5A 477219942 477225714 5772 False 2045.75 6076 90.6190 103 5854 4 chr5A.!!$F3 5751
5 TraesCS5B01G265100 chr5A 367269835 367272130 2295 False 1051.00 1051 75.1830 2261 4565 1 chr5A.!!$F1 2304
6 TraesCS5B01G265100 chr5A 477212469 477213614 1145 False 624.00 686 87.3230 4 1098 2 chr5A.!!$F2 1094

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
44 45 0.323629 TCAAATCTCCACACCGACCC 59.676 55.000 0.0 0.0 0.00 4.46 F
1091 2131 0.391793 GGGTTCTTGCCGAGGAGAAG 60.392 60.000 0.0 0.0 32.91 2.85 F
1360 2722 0.598065 CCCTGTCGCTTTTCCCTTTG 59.402 55.000 0.0 0.0 0.00 2.77 F
2134 3588 1.000394 GCAACCATTTAAAGGCCGTGT 60.000 47.619 0.0 0.0 0.00 4.49 F
3357 4827 1.208052 GAGCTGGGTATCTTGACTGCA 59.792 52.381 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 3118 0.184211 ACCCACGGCTTTAACTTGGT 59.816 50.000 0.00 0.00 0.0 3.67 R
2114 3568 1.000394 ACACGGCCTTTAAATGGTTGC 60.000 47.619 0.00 0.00 0.0 4.17 R
3048 4515 1.407989 CCTGGAGCAATCCTGTCTTCC 60.408 57.143 0.00 0.00 0.0 3.46 R
4002 5472 3.119316 AGTGACAGATCTGATCGAACCAC 60.119 47.826 29.27 19.92 0.0 4.16 R
5070 6552 0.096976 CATGAAGCGGCGTACAAAGG 59.903 55.000 9.37 0.00 0.0 3.11 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
44 45 0.323629 TCAAATCTCCACACCGACCC 59.676 55.000 0.00 0.00 0.00 4.46
56 58 4.039357 CGACCCGCGTCACTGTCT 62.039 66.667 4.92 0.00 39.11 3.41
163 1118 3.563390 GCACTTCTATTCCAGCTGGATTC 59.437 47.826 35.42 14.24 44.98 2.52
180 1135 3.879295 GGATTCGAGGAAATGATCAGCAA 59.121 43.478 0.09 0.00 0.00 3.91
338 1293 4.207891 TGATCCAAGCCTCTAACTTCAC 57.792 45.455 0.00 0.00 0.00 3.18
385 1345 1.063166 GTACCGACCATCGACGACC 59.937 63.158 0.00 0.00 43.74 4.79
389 1349 2.494918 GACCATCGACGACCTGGG 59.505 66.667 19.04 12.27 34.21 4.45
483 1445 4.378874 GGTCGAGCAAAAGAAAAGAGATGG 60.379 45.833 10.30 0.00 0.00 3.51
578 1550 4.562143 GCAGGATGGGGCAAATTATTCATC 60.562 45.833 0.00 0.00 35.86 2.92
590 1562 8.323140 GGCAAATTATTCATCAAGAATCAAACG 58.677 33.333 0.00 0.00 43.42 3.60
659 1667 2.543031 CCTGAATCGAGCGAACGGAATA 60.543 50.000 0.00 0.00 0.00 1.75
754 1765 7.362660 GGAAACAACTAAACAACTCACTTCCTT 60.363 37.037 0.00 0.00 0.00 3.36
846 1872 2.108976 ACACACGCACACCTCCTG 59.891 61.111 0.00 0.00 0.00 3.86
847 1873 3.349006 CACACGCACACCTCCTGC 61.349 66.667 0.00 0.00 0.00 4.85
1034 2060 1.248486 TCCACACTCTTCCTCAGTCG 58.752 55.000 0.00 0.00 0.00 4.18
1091 2131 0.391793 GGGTTCTTGCCGAGGAGAAG 60.392 60.000 0.00 0.00 32.91 2.85
1112 2152 1.071385 ACCCAAGAGATCGATCCATGC 59.929 52.381 21.66 9.13 0.00 4.06
1216 2578 1.377856 GCTCCCTTGCTCCTGTTCC 60.378 63.158 0.00 0.00 0.00 3.62
1243 2605 0.609957 TGGCCAACCTCTGCTGATTG 60.610 55.000 0.61 0.00 36.63 2.67
1360 2722 0.598065 CCCTGTCGCTTTTCCCTTTG 59.402 55.000 0.00 0.00 0.00 2.77
1411 2786 5.824904 TCTGTAGGAGTAAACGATGGTAC 57.175 43.478 0.00 0.00 0.00 3.34
1442 2817 3.727391 TGTAGTGGATGGAGGATCTAGGA 59.273 47.826 0.00 0.00 33.73 2.94
1467 2842 1.817357 GCCGCTAGGGTTTTACAAGT 58.183 50.000 6.02 0.00 38.44 3.16
1621 3066 1.442526 GGCGCACCATCCAGATCTTG 61.443 60.000 10.83 0.00 35.26 3.02
1623 3068 1.473257 GCGCACCATCCAGATCTTGTA 60.473 52.381 0.30 0.00 0.00 2.41
1625 3070 2.159043 CGCACCATCCAGATCTTGTACT 60.159 50.000 0.00 0.00 0.00 2.73
1626 3071 3.068165 CGCACCATCCAGATCTTGTACTA 59.932 47.826 0.00 0.00 0.00 1.82
1627 3072 4.626042 GCACCATCCAGATCTTGTACTAG 58.374 47.826 0.00 0.00 0.00 2.57
1628 3073 4.342378 GCACCATCCAGATCTTGTACTAGA 59.658 45.833 9.48 9.48 0.00 2.43
1629 3074 5.163405 GCACCATCCAGATCTTGTACTAGAA 60.163 44.000 11.06 0.00 0.00 2.10
1630 3075 6.511416 CACCATCCAGATCTTGTACTAGAAG 58.489 44.000 11.06 4.81 0.00 2.85
1660 3105 6.583912 TCTAGTTCATATGCGCTGTTTTAC 57.416 37.500 9.73 0.24 0.00 2.01
1673 3118 4.134563 GCTGTTTTACTTCTTCCTGGACA 58.865 43.478 0.00 0.00 0.00 4.02
1674 3119 4.023963 GCTGTTTTACTTCTTCCTGGACAC 60.024 45.833 0.00 0.00 0.00 3.67
1675 3120 4.457466 TGTTTTACTTCTTCCTGGACACC 58.543 43.478 0.00 0.00 0.00 4.16
1676 3121 4.080243 TGTTTTACTTCTTCCTGGACACCA 60.080 41.667 0.00 0.00 0.00 4.17
1718 3163 6.998074 TCTCTTCATGTTCCAACATTAACACT 59.002 34.615 2.01 0.00 46.95 3.55
1818 3265 6.661805 AGAATAGGGCTAGCATAACTCTACTC 59.338 42.308 18.24 7.28 0.00 2.59
1870 3320 8.375506 TGGATTTATGTTCTAGTGTTCTCAGTT 58.624 33.333 0.00 0.00 0.00 3.16
1941 3391 3.770666 TCAGTTCAGTCGCTATACTTGC 58.229 45.455 0.00 0.00 0.00 4.01
1953 3403 1.459450 ATACTTGCCGCGGATGTTTT 58.541 45.000 33.48 9.62 0.00 2.43
1954 3404 1.240256 TACTTGCCGCGGATGTTTTT 58.760 45.000 33.48 7.83 0.00 1.94
2009 3463 3.067742 CCACATGGCAGATGGAGAATTTC 59.932 47.826 13.27 0.00 35.33 2.17
2114 3568 5.138125 ACCATTCATTTTGTTGCCTACAG 57.862 39.130 0.00 0.00 38.19 2.74
2134 3588 1.000394 GCAACCATTTAAAGGCCGTGT 60.000 47.619 0.00 0.00 0.00 4.49
2213 3669 3.090037 TCCTTTTCCGACCTGAGTAGAG 58.910 50.000 0.00 0.00 0.00 2.43
3048 4515 2.227388 GGAGCACCTGATTTTGAGTGTG 59.773 50.000 0.00 0.00 32.75 3.82
3357 4827 1.208052 GAGCTGGGTATCTTGACTGCA 59.792 52.381 0.00 0.00 0.00 4.41
3528 4998 1.945394 GATCCATGCACTGTGATCACC 59.055 52.381 22.85 8.07 34.38 4.02
4002 5472 2.286872 CCTCTGATTGCAGTTGCTAGG 58.713 52.381 5.62 0.04 42.84 3.02
4041 5511 0.399949 ACTGGAGGAACCCACTGACA 60.400 55.000 0.00 0.00 38.00 3.58
4101 5571 1.055040 ATCCTGAGCTGATACTGCCC 58.945 55.000 0.00 0.00 0.00 5.36
4248 5718 3.650942 AGTTTGACACCTTCCCTACATCA 59.349 43.478 0.00 0.00 0.00 3.07
4266 5736 1.980232 ACGCCCACCTGACATCGTA 60.980 57.895 0.00 0.00 0.00 3.43
4350 5820 1.276421 GCAACACAAGGAGAGAGGCTA 59.724 52.381 0.00 0.00 0.00 3.93
4377 5847 3.074999 GCTGAGCTGGAGAGACCCG 62.075 68.421 0.00 0.00 38.00 5.28
4416 5886 0.737367 TGACCTTCTGCTTCATCGCG 60.737 55.000 0.00 0.00 0.00 5.87
4419 5889 2.047370 TTCTGCTTCATCGCGGCA 60.047 55.556 6.13 6.53 36.24 5.69
4589 6065 4.117661 AACCGTCTCTCGCTCCGC 62.118 66.667 0.00 0.00 38.35 5.54
4656 6132 5.859205 TCTATAGCTGCAACTGAGATGAA 57.141 39.130 1.02 0.00 0.00 2.57
4725 6201 7.331440 TGTCGTTGTTTGTAGTCTTTTCAGTTA 59.669 33.333 0.00 0.00 0.00 2.24
4776 6254 6.937436 ACCTTTCTTGTTAACGACTGAAAT 57.063 33.333 9.52 0.00 34.01 2.17
4779 6257 6.371809 TTTCTTGTTAACGACTGAAATGCT 57.628 33.333 0.26 0.00 31.60 3.79
4829 6307 0.109132 CCGCCTGAAGAAATTGTGCC 60.109 55.000 0.00 0.00 0.00 5.01
4867 6345 2.360165 CTGTGCCCTATCATCTTTTGCC 59.640 50.000 0.00 0.00 0.00 4.52
4892 6374 7.645340 CCTTTGCATGTAGTAATAGTTTGCATC 59.355 37.037 0.00 0.00 38.30 3.91
4903 6385 9.624373 AGTAATAGTTTGCATCAGAAGATTCAT 57.376 29.630 0.00 0.00 30.20 2.57
4908 6390 5.970317 TTGCATCAGAAGATTCATTGTGT 57.030 34.783 0.00 0.00 30.20 3.72
4930 6412 3.245229 TGCCTGGGACACTGTTAATGATT 60.245 43.478 0.00 0.00 0.00 2.57
4931 6413 3.763897 GCCTGGGACACTGTTAATGATTT 59.236 43.478 0.00 0.00 0.00 2.17
4932 6414 4.220602 GCCTGGGACACTGTTAATGATTTT 59.779 41.667 0.00 0.00 0.00 1.82
4933 6415 5.279456 GCCTGGGACACTGTTAATGATTTTT 60.279 40.000 0.00 0.00 0.00 1.94
4982 6464 2.166050 TGAATCCATGACGGCATTTTGG 59.834 45.455 0.00 0.62 30.68 3.28
5015 6497 2.682856 CTGGGTTGGTATATGTGTGCAC 59.317 50.000 10.75 10.75 0.00 4.57
5038 6520 7.033791 CACGTAGTTTCAGGTCAAGTATGTAT 58.966 38.462 0.00 0.00 41.61 2.29
5039 6521 7.009265 CACGTAGTTTCAGGTCAAGTATGTATG 59.991 40.741 0.00 0.00 41.61 2.39
5040 6522 7.033791 CGTAGTTTCAGGTCAAGTATGTATGT 58.966 38.462 0.00 0.00 0.00 2.29
5041 6523 8.186163 CGTAGTTTCAGGTCAAGTATGTATGTA 58.814 37.037 0.00 0.00 0.00 2.29
5042 6524 9.298774 GTAGTTTCAGGTCAAGTATGTATGTAC 57.701 37.037 0.00 0.00 0.00 2.90
5044 6526 8.372459 AGTTTCAGGTCAAGTATGTATGTACAA 58.628 33.333 0.00 0.00 39.99 2.41
5045 6527 8.656849 GTTTCAGGTCAAGTATGTATGTACAAG 58.343 37.037 0.00 0.00 39.99 3.16
5047 6529 8.584063 TCAGGTCAAGTATGTATGTACAAGTA 57.416 34.615 0.00 0.00 39.99 2.24
5048 6530 8.683615 TCAGGTCAAGTATGTATGTACAAGTAG 58.316 37.037 0.00 0.00 39.99 2.57
5049 6531 8.467598 CAGGTCAAGTATGTATGTACAAGTAGT 58.532 37.037 0.00 0.00 39.99 2.73
5052 6534 9.084164 GTCAAGTATGTATGTACAAGTAGTTGG 57.916 37.037 14.69 0.00 39.99 3.77
5053 6535 7.762615 TCAAGTATGTATGTACAAGTAGTTGGC 59.237 37.037 14.69 7.55 39.99 4.52
5055 6537 4.524316 TGTATGTACAAGTAGTTGGCGT 57.476 40.909 14.69 10.23 38.07 5.68
5057 6539 2.894763 TGTACAAGTAGTTGGCGTGT 57.105 45.000 14.69 0.00 38.07 4.49
5058 6540 3.182341 TGTACAAGTAGTTGGCGTGTT 57.818 42.857 14.69 0.00 38.07 3.32
5059 6541 2.867368 TGTACAAGTAGTTGGCGTGTTG 59.133 45.455 14.69 0.00 38.07 3.33
5060 6542 0.661020 ACAAGTAGTTGGCGTGTTGC 59.339 50.000 14.69 0.00 45.38 4.17
5078 6560 4.533566 GCACTTGCGCCTTTGTAC 57.466 55.556 4.18 0.00 0.00 2.90
5079 6561 1.440353 GCACTTGCGCCTTTGTACG 60.440 57.895 4.18 0.00 0.00 3.67
5085 6567 3.419759 CGCCTTTGTACGCCGCTT 61.420 61.111 0.00 0.00 0.00 4.68
5086 6568 2.479198 GCCTTTGTACGCCGCTTC 59.521 61.111 0.00 0.00 0.00 3.86
5087 6569 2.322081 GCCTTTGTACGCCGCTTCA 61.322 57.895 0.00 0.00 0.00 3.02
5088 6570 1.644786 GCCTTTGTACGCCGCTTCAT 61.645 55.000 0.00 0.00 0.00 2.57
5089 6571 0.096976 CCTTTGTACGCCGCTTCATG 59.903 55.000 0.00 0.00 0.00 3.07
5090 6572 0.796312 CTTTGTACGCCGCTTCATGT 59.204 50.000 0.00 0.00 0.00 3.21
5091 6573 1.996898 CTTTGTACGCCGCTTCATGTA 59.003 47.619 0.00 0.00 0.00 2.29
5092 6574 2.303163 TTGTACGCCGCTTCATGTAT 57.697 45.000 0.00 0.00 0.00 2.29
5093 6575 1.847818 TGTACGCCGCTTCATGTATC 58.152 50.000 0.00 0.00 0.00 2.24
5094 6576 1.407618 TGTACGCCGCTTCATGTATCT 59.592 47.619 0.00 0.00 0.00 1.98
5112 6594 7.316393 TGTATCTTCTTCTCTTTCTTCCCAA 57.684 36.000 0.00 0.00 0.00 4.12
5166 6648 0.887836 CTTCAGTTGGAGCTGCTGCA 60.888 55.000 20.33 20.33 42.74 4.41
5205 6689 3.383761 GTTTTTGCACTTCACAGATGGG 58.616 45.455 0.00 0.00 0.00 4.00
5215 6699 1.902508 TCACAGATGGGAGTGTTCCTC 59.097 52.381 0.00 0.00 43.49 3.71
5224 6708 1.534235 AGTGTTCCTCCACTCGCCT 60.534 57.895 0.00 0.00 41.84 5.52
5240 6724 1.789464 CGCCTGAATATGACGAAGAGC 59.211 52.381 0.00 0.00 0.00 4.09
5253 6738 3.873952 GACGAAGAGCTGGCATTTATCTT 59.126 43.478 0.00 0.00 33.07 2.40
5293 6778 3.849911 TCCTCGAATGCCAATCGATATC 58.150 45.455 5.17 0.00 46.98 1.63
5316 6801 0.598065 AGGAAATTGCGCTTGTCCAC 59.402 50.000 18.57 1.53 0.00 4.02
5318 6803 0.040425 GAAATTGCGCTTGTCCACGT 60.040 50.000 9.73 0.00 0.00 4.49
5320 6805 1.448985 AATTGCGCTTGTCCACGTAT 58.551 45.000 9.73 0.00 0.00 3.06
5325 6810 1.195900 GCGCTTGTCCACGTATTTTCA 59.804 47.619 0.00 0.00 0.00 2.69
5326 6811 2.159572 GCGCTTGTCCACGTATTTTCAT 60.160 45.455 0.00 0.00 0.00 2.57
5383 6869 8.492673 TCAACTTCTTAGGCTGTAATACATTG 57.507 34.615 0.00 0.00 0.00 2.82
5412 6898 3.947910 ATTGGTTCCTGTCTTTGCATG 57.052 42.857 0.00 0.00 0.00 4.06
5413 6899 0.961019 TGGTTCCTGTCTTTGCATGC 59.039 50.000 11.82 11.82 0.00 4.06
5419 6905 0.731514 CTGTCTTTGCATGCCAAGCG 60.732 55.000 23.21 12.07 34.34 4.68
5471 6957 9.981114 ACACATTTTATAAATATTTAGGCAGGC 57.019 29.630 13.15 0.00 0.00 4.85
5495 6981 1.335810 TCGGAAATATCGAGGTCCACG 59.664 52.381 1.78 1.78 32.51 4.94
5496 6982 1.066605 CGGAAATATCGAGGTCCACGT 59.933 52.381 8.62 0.00 0.00 4.49
5497 6983 2.291465 CGGAAATATCGAGGTCCACGTA 59.709 50.000 8.62 1.70 0.00 3.57
5522 7008 4.058817 ACTTGCTTACAGTTTTCCTCTCG 58.941 43.478 0.00 0.00 0.00 4.04
5540 7031 5.241728 CCTCTCGAAAAGAAATTTGTCCCTT 59.758 40.000 0.00 0.00 32.23 3.95
5578 9654 9.469097 AGTATATTCATGCTAGTTAGGTAGAGG 57.531 37.037 0.00 0.00 0.00 3.69
5588 9664 4.551671 AGTTAGGTAGAGGCATGTGAGAT 58.448 43.478 0.00 0.00 0.00 2.75
5589 9665 5.706447 AGTTAGGTAGAGGCATGTGAGATA 58.294 41.667 0.00 0.00 0.00 1.98
5590 9666 5.536916 AGTTAGGTAGAGGCATGTGAGATAC 59.463 44.000 0.00 0.00 0.00 2.24
5600 9676 9.499479 AGAGGCATGTGAGATACTATAAAAATG 57.501 33.333 0.00 0.00 0.00 2.32
5621 9703 0.890683 GCTGGCTGCCAACACTAAAT 59.109 50.000 23.51 0.00 30.80 1.40
5624 9706 3.056891 GCTGGCTGCCAACACTAAATTTA 60.057 43.478 23.51 0.00 30.80 1.40
5628 9710 6.529220 TGGCTGCCAACACTAAATTTAAATT 58.471 32.000 21.08 7.64 0.00 1.82
5631 9714 7.172361 GGCTGCCAACACTAAATTTAAATTGAA 59.828 33.333 15.17 5.33 0.00 2.69
5632 9715 8.720562 GCTGCCAACACTAAATTTAAATTGAAT 58.279 29.630 14.04 1.84 0.00 2.57
5634 9717 8.997323 TGCCAACACTAAATTTAAATTGAATGG 58.003 29.630 14.04 15.49 0.00 3.16
5635 9718 8.998377 GCCAACACTAAATTTAAATTGAATGGT 58.002 29.630 14.04 2.77 0.00 3.55
5689 9776 1.702886 ATCACGCTTCTTCAGACGTG 58.297 50.000 11.75 11.75 46.10 4.49
5734 9821 5.172205 AGTTCCAATCGAGCTTCTTAAGAC 58.828 41.667 4.18 0.00 0.00 3.01
5737 9824 4.929808 TCCAATCGAGCTTCTTAAGACAAC 59.070 41.667 4.18 0.00 0.00 3.32
5740 9827 1.390463 CGAGCTTCTTAAGACAACCGC 59.610 52.381 4.18 3.53 0.00 5.68
5838 9926 2.959071 GGCGAGATGAGACTGCGC 60.959 66.667 0.00 0.00 46.20 6.09
5840 9928 2.101185 CGAGATGAGACTGCGCGT 59.899 61.111 8.43 3.28 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.673341 AGTGGAGCGCGAGAGTCA 60.673 61.111 12.10 0.00 0.00 3.41
44 45 1.734477 CTTCCCAGACAGTGACGCG 60.734 63.158 3.53 3.53 0.00 6.01
56 58 1.978580 GACAGTTCCCTCTTCTTCCCA 59.021 52.381 0.00 0.00 0.00 4.37
163 1118 4.348656 CATGTTTGCTGATCATTTCCTCG 58.651 43.478 0.00 0.00 0.00 4.63
255 1210 3.508012 TGGATTGGTGGTTTGTAATTCGG 59.492 43.478 0.00 0.00 0.00 4.30
338 1293 1.134189 TGAGAAGCATGCCATGAGGAG 60.134 52.381 15.66 0.00 36.89 3.69
394 1354 1.207329 CCCTAGTTTTCTAGCCGCTGT 59.793 52.381 2.16 0.00 46.11 4.40
395 1355 1.207329 ACCCTAGTTTTCTAGCCGCTG 59.793 52.381 2.16 0.00 46.11 5.18
397 1357 2.277969 GAACCCTAGTTTTCTAGCCGC 58.722 52.381 0.00 0.00 46.11 6.53
398 1358 3.604875 TGAACCCTAGTTTTCTAGCCG 57.395 47.619 3.08 0.00 46.11 5.52
400 1360 7.336931 TCAAATGATGAACCCTAGTTTTCTAGC 59.663 37.037 3.08 0.00 40.70 3.42
401 1361 8.792830 TCAAATGATGAACCCTAGTTTTCTAG 57.207 34.615 3.08 0.00 41.18 2.43
498 1460 9.683870 ATTGCTATGAAATTCTTCTCTTTCTCT 57.316 29.630 0.00 0.00 33.50 3.10
754 1765 4.966787 GTTGGTGGGAAGCCGCCA 62.967 66.667 0.00 0.00 46.95 5.69
849 1875 3.876198 CACCGGCATTGCGTAGGC 61.876 66.667 0.00 0.00 40.52 3.93
850 1876 3.876198 GCACCGGCATTGCGTAGG 61.876 66.667 0.00 12.82 40.72 3.18
955 1981 1.019278 GCTTTTCTCATCGGCGTGGA 61.019 55.000 6.85 4.86 0.00 4.02
991 2017 3.894547 GAGGGAAAGCGGCGGACAA 62.895 63.158 9.78 0.00 0.00 3.18
1034 2060 1.338655 GGATAAGCGAGAGAGTGGGAC 59.661 57.143 0.00 0.00 0.00 4.46
1091 2131 2.869636 GCATGGATCGATCTCTTGGGTC 60.870 54.545 23.96 6.26 0.00 4.46
1200 2562 2.592993 CGGGAACAGGAGCAAGGGA 61.593 63.158 0.00 0.00 0.00 4.20
1216 2578 3.316573 GAGGTTGGCCAGGAGTCGG 62.317 68.421 5.11 0.00 37.19 4.79
1243 2605 1.535833 TCGGAGGAGGAGATATTCGC 58.464 55.000 0.00 0.00 0.00 4.70
1411 2786 5.887598 TCCTCCATCCACTACAAATTCATTG 59.112 40.000 0.00 0.00 44.95 2.82
1414 2789 5.429762 AGATCCTCCATCCACTACAAATTCA 59.570 40.000 0.00 0.00 30.71 2.57
1424 2799 1.899142 GCTCCTAGATCCTCCATCCAC 59.101 57.143 0.00 0.00 30.71 4.02
1626 3071 8.552034 GCGCATATGAACTAGAAAAATACTTCT 58.448 33.333 6.97 0.00 39.09 2.85
1627 3072 8.552034 AGCGCATATGAACTAGAAAAATACTTC 58.448 33.333 11.47 0.00 0.00 3.01
1628 3073 8.338259 CAGCGCATATGAACTAGAAAAATACTT 58.662 33.333 11.47 0.00 0.00 2.24
1629 3074 7.495934 ACAGCGCATATGAACTAGAAAAATACT 59.504 33.333 11.47 0.00 0.00 2.12
1630 3075 7.630924 ACAGCGCATATGAACTAGAAAAATAC 58.369 34.615 11.47 0.00 0.00 1.89
1660 3105 2.938956 ACTTGGTGTCCAGGAAGAAG 57.061 50.000 4.97 0.00 34.05 2.85
1673 3118 0.184211 ACCCACGGCTTTAACTTGGT 59.816 50.000 0.00 0.00 0.00 3.67
1674 3119 1.268625 GAACCCACGGCTTTAACTTGG 59.731 52.381 0.00 0.00 0.00 3.61
1675 3120 2.225727 GAGAACCCACGGCTTTAACTTG 59.774 50.000 0.00 0.00 0.00 3.16
1676 3121 2.105993 AGAGAACCCACGGCTTTAACTT 59.894 45.455 0.00 0.00 0.00 2.66
1718 3163 3.432749 GGATCATGAAGAACAGCTAGCCA 60.433 47.826 12.13 0.00 0.00 4.75
1856 3306 9.991388 GTATAACTACTGAACTGAGAACACTAG 57.009 37.037 0.00 0.00 0.00 2.57
1863 3313 8.675504 GCTACAAGTATAACTACTGAACTGAGA 58.324 37.037 0.00 0.00 38.23 3.27
1870 3320 6.544931 ACATCCGCTACAAGTATAACTACTGA 59.455 38.462 0.00 0.00 38.23 3.41
1960 3410 8.306761 GGAAAAACATCTACATCACCAATCTTT 58.693 33.333 0.00 0.00 0.00 2.52
2114 3568 1.000394 ACACGGCCTTTAAATGGTTGC 60.000 47.619 0.00 0.00 0.00 4.17
2213 3669 5.499139 TGACAGTCTTCAACCAAACAATC 57.501 39.130 1.31 0.00 0.00 2.67
3048 4515 1.407989 CCTGGAGCAATCCTGTCTTCC 60.408 57.143 0.00 0.00 0.00 3.46
3528 4998 4.236935 GGCAGTTGTCAAATACACCAATG 58.763 43.478 0.00 0.00 38.00 2.82
4002 5472 3.119316 AGTGACAGATCTGATCGAACCAC 60.119 47.826 29.27 19.92 0.00 4.16
4041 5511 6.814954 AACAGGACATGGATCAGTATAGTT 57.185 37.500 0.00 0.00 0.00 2.24
4101 5571 7.786030 TCAGGAATAGGTAGAGAAAGATTGTG 58.214 38.462 0.00 0.00 0.00 3.33
4248 5718 1.537814 TTACGATGTCAGGTGGGCGT 61.538 55.000 0.00 0.00 35.95 5.68
4350 5820 0.541530 TCCAGCTCAGCAGAGACTGT 60.542 55.000 20.60 0.00 44.98 3.55
4591 6067 4.699522 ACAAGGAAGGCGCCGGAC 62.700 66.667 23.20 15.09 0.00 4.79
4725 6201 1.745827 CGTCCCAAAACAGACACAGGT 60.746 52.381 0.00 0.00 33.08 4.00
4760 6238 5.743026 TCAAGCATTTCAGTCGTTAACAA 57.257 34.783 6.39 0.00 0.00 2.83
4765 6243 3.565482 ACACATCAAGCATTTCAGTCGTT 59.435 39.130 0.00 0.00 0.00 3.85
4776 6254 7.011389 GCATAATAACTAGTCACACATCAAGCA 59.989 37.037 0.00 0.00 0.00 3.91
4779 6257 8.829612 CATGCATAATAACTAGTCACACATCAA 58.170 33.333 0.00 0.00 0.00 2.57
4867 6345 8.183536 TGATGCAAACTATTACTACATGCAAAG 58.816 33.333 1.40 0.00 44.39 2.77
4883 6361 6.015688 ACACAATGAATCTTCTGATGCAAACT 60.016 34.615 0.00 0.00 41.27 2.66
4886 6364 5.705902 CACACAATGAATCTTCTGATGCAA 58.294 37.500 0.00 0.00 41.27 4.08
4892 6374 3.119602 CCAGGCACACAATGAATCTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
4903 6385 1.152984 CAGTGTCCCAGGCACACAA 60.153 57.895 16.48 0.00 45.67 3.33
4908 6390 1.702401 TCATTAACAGTGTCCCAGGCA 59.298 47.619 0.00 0.00 0.00 4.75
4947 6429 0.723981 GATTCAGTTCACGCTCCAGC 59.276 55.000 0.00 0.00 37.78 4.85
4951 6433 2.349886 GTCATGGATTCAGTTCACGCTC 59.650 50.000 0.00 0.00 0.00 5.03
4982 6464 1.308998 CAACCCAGGTTCAGTGACAC 58.691 55.000 0.00 0.00 36.00 3.67
5015 6497 7.033791 ACATACATACTTGACCTGAAACTACG 58.966 38.462 0.00 0.00 0.00 3.51
5038 6520 2.867368 CAACACGCCAACTACTTGTACA 59.133 45.455 0.00 0.00 0.00 2.90
5039 6521 2.349155 GCAACACGCCAACTACTTGTAC 60.349 50.000 0.00 0.00 32.94 2.90
5040 6522 1.868498 GCAACACGCCAACTACTTGTA 59.132 47.619 0.00 0.00 32.94 2.41
5041 6523 0.661020 GCAACACGCCAACTACTTGT 59.339 50.000 0.00 0.00 32.94 3.16
5042 6524 0.384230 CGCAACACGCCAACTACTTG 60.384 55.000 0.00 0.00 37.30 3.16
5044 6526 3.637714 CGCAACACGCCAACTACT 58.362 55.556 0.00 0.00 37.30 2.57
5061 6543 1.440353 CGTACAAAGGCGCAAGTGC 60.440 57.895 10.83 4.24 41.68 4.40
5062 6544 4.818417 CGTACAAAGGCGCAAGTG 57.182 55.556 10.83 5.74 41.68 3.16
5070 6552 0.096976 CATGAAGCGGCGTACAAAGG 59.903 55.000 9.37 0.00 0.00 3.11
5071 6553 0.796312 ACATGAAGCGGCGTACAAAG 59.204 50.000 9.37 6.57 0.00 2.77
5073 6555 2.159156 AGATACATGAAGCGGCGTACAA 60.159 45.455 9.37 0.00 0.00 2.41
5076 6558 2.361119 AGAAGATACATGAAGCGGCGTA 59.639 45.455 9.37 0.00 0.00 4.42
5078 6560 1.858091 AGAAGATACATGAAGCGGCG 58.142 50.000 0.51 0.51 0.00 6.46
5079 6561 3.462021 AGAAGAAGATACATGAAGCGGC 58.538 45.455 0.00 0.00 0.00 6.53
5080 6562 4.942852 AGAGAAGAAGATACATGAAGCGG 58.057 43.478 0.00 0.00 0.00 5.52
5081 6563 6.756074 AGAAAGAGAAGAAGATACATGAAGCG 59.244 38.462 0.00 0.00 0.00 4.68
5082 6564 8.491331 AAGAAAGAGAAGAAGATACATGAAGC 57.509 34.615 0.00 0.00 0.00 3.86
5083 6565 9.097257 GGAAGAAAGAGAAGAAGATACATGAAG 57.903 37.037 0.00 0.00 0.00 3.02
5084 6566 8.043710 GGGAAGAAAGAGAAGAAGATACATGAA 58.956 37.037 0.00 0.00 0.00 2.57
5085 6567 7.180946 TGGGAAGAAAGAGAAGAAGATACATGA 59.819 37.037 0.00 0.00 0.00 3.07
5086 6568 7.334090 TGGGAAGAAAGAGAAGAAGATACATG 58.666 38.462 0.00 0.00 0.00 3.21
5087 6569 7.502060 TGGGAAGAAAGAGAAGAAGATACAT 57.498 36.000 0.00 0.00 0.00 2.29
5088 6570 6.935240 TGGGAAGAAAGAGAAGAAGATACA 57.065 37.500 0.00 0.00 0.00 2.29
5089 6571 8.800370 AATTGGGAAGAAAGAGAAGAAGATAC 57.200 34.615 0.00 0.00 0.00 2.24
5090 6572 9.813826 AAAATTGGGAAGAAAGAGAAGAAGATA 57.186 29.630 0.00 0.00 0.00 1.98
5091 6573 8.718158 AAAATTGGGAAGAAAGAGAAGAAGAT 57.282 30.769 0.00 0.00 0.00 2.40
5092 6574 8.539117 AAAAATTGGGAAGAAAGAGAAGAAGA 57.461 30.769 0.00 0.00 0.00 2.87
5119 6601 6.212388 ACTGAAGATAGATCGGCATTCCTATT 59.788 38.462 0.00 0.00 0.00 1.73
5130 6612 5.347342 ACTGAAGCAACTGAAGATAGATCG 58.653 41.667 0.00 0.00 0.00 3.69
5139 6621 1.949525 GCTCCAACTGAAGCAACTGAA 59.050 47.619 0.00 0.00 0.00 3.02
5166 6648 6.677913 CAAAAACGAGTTGGATCCAATACTT 58.322 36.000 29.37 16.54 38.28 2.24
5175 6657 3.380004 TGAAGTGCAAAAACGAGTTGGAT 59.620 39.130 0.00 0.00 0.00 3.41
5176 6658 2.750166 TGAAGTGCAAAAACGAGTTGGA 59.250 40.909 0.00 0.00 0.00 3.53
5177 6659 2.851824 GTGAAGTGCAAAAACGAGTTGG 59.148 45.455 0.00 0.00 0.00 3.77
5179 6661 3.438781 TCTGTGAAGTGCAAAAACGAGTT 59.561 39.130 0.00 0.00 0.00 3.01
5180 6662 3.006940 TCTGTGAAGTGCAAAAACGAGT 58.993 40.909 0.00 0.00 0.00 4.18
5181 6663 3.673746 TCTGTGAAGTGCAAAAACGAG 57.326 42.857 0.00 0.00 0.00 4.18
5182 6664 3.243035 CCATCTGTGAAGTGCAAAAACGA 60.243 43.478 0.00 0.00 0.00 3.85
5183 6665 3.044986 CCATCTGTGAAGTGCAAAAACG 58.955 45.455 0.00 0.00 0.00 3.60
5184 6666 3.068024 TCCCATCTGTGAAGTGCAAAAAC 59.932 43.478 0.00 0.00 0.00 2.43
5215 6699 1.067060 TCGTCATATTCAGGCGAGTGG 59.933 52.381 0.00 0.00 0.00 4.00
5224 6708 2.168313 TGCCAGCTCTTCGTCATATTCA 59.832 45.455 0.00 0.00 0.00 2.57
5240 6724 8.609176 CATTCAAATTTGGAAGATAAATGCCAG 58.391 33.333 17.90 0.00 0.00 4.85
5253 6738 5.048782 CGAGGAGTTGACATTCAAATTTGGA 60.049 40.000 17.90 10.24 38.22 3.53
5293 6778 2.589014 GACAAGCGCAATTTCCTCAAG 58.411 47.619 11.47 0.00 0.00 3.02
5348 6834 5.536161 AGCCTAAGAAGTTGATTTTTGAGCA 59.464 36.000 0.00 0.00 0.00 4.26
5350 6836 6.974965 ACAGCCTAAGAAGTTGATTTTTGAG 58.025 36.000 0.00 0.00 0.00 3.02
5383 6869 7.518848 GCAAAGACAGGAACCAATTGATTTTTC 60.519 37.037 7.12 4.03 0.00 2.29
5389 6875 3.295093 TGCAAAGACAGGAACCAATTGA 58.705 40.909 7.12 0.00 0.00 2.57
5390 6876 3.731652 TGCAAAGACAGGAACCAATTG 57.268 42.857 0.00 0.00 0.00 2.32
5397 6883 1.614903 CTTGGCATGCAAAGACAGGAA 59.385 47.619 27.92 0.00 0.00 3.36
5412 6898 1.595093 AATTGGTGTAGGCGCTTGGC 61.595 55.000 7.64 0.00 42.51 4.52
5413 6899 0.887933 AAATTGGTGTAGGCGCTTGG 59.112 50.000 7.64 0.00 0.00 3.61
5458 6944 2.438021 TCCGACAAGCCTGCCTAAATAT 59.562 45.455 0.00 0.00 0.00 1.28
5459 6945 1.834896 TCCGACAAGCCTGCCTAAATA 59.165 47.619 0.00 0.00 0.00 1.40
5467 6953 2.797156 CTCGATATTTCCGACAAGCCTG 59.203 50.000 0.00 0.00 32.18 4.85
5469 6955 2.135933 CCTCGATATTTCCGACAAGCC 58.864 52.381 0.00 0.00 32.18 4.35
5471 6957 3.181479 TGGACCTCGATATTTCCGACAAG 60.181 47.826 0.00 0.00 32.18 3.16
5472 6958 2.761767 TGGACCTCGATATTTCCGACAA 59.238 45.455 0.00 0.00 32.18 3.18
5495 6981 7.153315 AGAGGAAAACTGTAAGCAAGTACTAC 58.847 38.462 0.00 0.00 37.60 2.73
5496 6982 7.299246 AGAGGAAAACTGTAAGCAAGTACTA 57.701 36.000 0.00 0.00 37.60 1.82
5497 6983 6.176014 AGAGGAAAACTGTAAGCAAGTACT 57.824 37.500 0.00 0.00 37.60 2.73
5522 7008 8.607441 AAAGCATAAGGGACAAATTTCTTTTC 57.393 30.769 0.00 0.00 0.00 2.29
5533 7024 9.474313 AATATACTTTGAAAAGCATAAGGGACA 57.526 29.630 2.69 0.00 39.63 4.02
5534 7025 9.952188 GAATATACTTTGAAAAGCATAAGGGAC 57.048 33.333 2.69 0.00 39.63 4.46
5535 7026 9.693739 TGAATATACTTTGAAAAGCATAAGGGA 57.306 29.630 2.69 0.00 39.63 4.20
5577 9653 7.805071 GCACATTTTTATAGTATCTCACATGCC 59.195 37.037 0.00 0.00 0.00 4.40
5578 9654 8.562892 AGCACATTTTTATAGTATCTCACATGC 58.437 33.333 0.00 0.00 0.00 4.06
5588 9664 5.499139 GCAGCCAGCACATTTTTATAGTA 57.501 39.130 0.00 0.00 44.79 1.82
5589 9665 4.376340 GCAGCCAGCACATTTTTATAGT 57.624 40.909 0.00 0.00 44.79 2.12
5668 9751 2.864968 ACGTCTGAAGAAGCGTGATAC 58.135 47.619 0.00 0.00 37.30 2.24
5683 9766 2.983930 GCCTCGCTGTCTCACGTCT 61.984 63.158 0.00 0.00 0.00 4.18
5689 9776 2.034685 TGTATGTATGCCTCGCTGTCTC 59.965 50.000 0.00 0.00 0.00 3.36
5734 9821 1.447317 GCAGTATGGATGGGCGGTTG 61.447 60.000 0.00 0.00 35.86 3.77
5737 9824 2.281761 GGCAGTATGGATGGGCGG 60.282 66.667 0.00 0.00 35.86 6.13
5740 9827 0.106569 TTGCTGGCAGTATGGATGGG 60.107 55.000 17.16 0.00 35.86 4.00


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

AutoCloner maintained by Alex Coulton.