Multiple sequence alignment - TraesCS7A01G391000

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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 TraesCS7A01G391000 chr7A 100.000 8838 0 0 1 8838 567001156 567009993 0.000000e+00 16321
1 TraesCS7A01G391000 chr7A 90.428 2173 152 27 5700 7845 567379121 567381264 0.000000e+00 2809
2 TraesCS7A01G391000 chr7A 86.135 916 72 24 2258 3166 567375498 567376365 0.000000e+00 937
3 TraesCS7A01G391000 chr7A 88.415 751 56 10 3791 4510 567377032 567377782 0.000000e+00 876
4 TraesCS7A01G391000 chr7A 84.435 938 91 32 4569 5469 567377817 567378736 0.000000e+00 872
5 TraesCS7A01G391000 chr7A 93.450 458 29 1 3258 3715 567376374 567376830 0.000000e+00 678
6 TraesCS7A01G391000 chr7A 85.106 470 50 16 1631 2095 567375044 567375498 6.250000e-126 462
7 TraesCS7A01G391000 chr7A 89.730 185 11 2 5449 5631 567378789 567378967 6.900000e-56 230
8 TraesCS7A01G391000 chr7D 94.355 8681 303 81 1 8537 500818209 500826846 0.000000e+00 13143
9 TraesCS7A01G391000 chr7D 89.739 2183 164 27 5699 7845 500892533 500894691 0.000000e+00 2736
10 TraesCS7A01G391000 chr7D 88.131 1466 104 37 2283 3715 500888780 500890208 0.000000e+00 1679
11 TraesCS7A01G391000 chr7D 85.625 1433 130 39 4089 5469 500890744 500892152 0.000000e+00 1435
12 TraesCS7A01G391000 chr7D 92.282 298 23 0 3791 4088 500890395 500890692 2.950000e-114 424
13 TraesCS7A01G391000 chr7D 83.403 476 54 20 1638 2103 500888209 500888669 1.370000e-112 418
14 TraesCS7A01G391000 chr7D 82.402 483 47 24 962 1432 500887740 500888196 3.870000e-103 387
15 TraesCS7A01G391000 chr7D 83.562 146 14 3 304 440 500815565 500815709 2.590000e-25 128
16 TraesCS7A01G391000 chrUn 95.062 5873 138 40 2315 8106 86622414 86628215 0.000000e+00 9099
17 TraesCS7A01G391000 chrUn 91.093 1437 76 26 173 1559 86620323 86621757 0.000000e+00 1897
18 TraesCS7A01G391000 chrUn 92.286 700 20 7 8140 8834 86628211 86628881 0.000000e+00 963
19 TraesCS7A01G391000 chrUn 90.909 539 33 6 1561 2095 86621863 86622389 0.000000e+00 710
20 TraesCS7A01G391000 chr7B 89.437 2168 177 23 5696 7845 529673632 529675765 0.000000e+00 2687
21 TraesCS7A01G391000 chr7B 86.189 1745 151 45 3791 5469 529671534 529673254 0.000000e+00 1805
22 TraesCS7A01G391000 chr7B 86.328 1024 74 38 2166 3166 529669808 529670788 0.000000e+00 1055
23 TraesCS7A01G391000 chr7B 93.450 458 29 1 3258 3715 529670797 529671253 0.000000e+00 678
24 TraesCS7A01G391000 chr7B 83.682 478 56 17 1631 2103 529669330 529669790 1.760000e-116 431
25 TraesCS7A01G391000 chr7B 84.273 337 37 10 1102 1433 529668992 529669317 1.850000e-81 315
26 TraesCS7A01G391000 chr7B 90.270 185 10 4 5449 5631 529673302 529673480 1.480000e-57 235


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 TraesCS7A01G391000 chr7A 567001156 567009993 8837 False 16321.000000 16321 100.000000 1 8838 1 chr7A.!!$F1 8837
1 TraesCS7A01G391000 chr7A 567375044 567381264 6220 False 980.571429 2809 88.242714 1631 7845 7 chr7A.!!$F2 6214
2 TraesCS7A01G391000 chr7D 500815565 500826846 11281 False 6635.500000 13143 88.958500 1 8537 2 chr7D.!!$F1 8536
3 TraesCS7A01G391000 chr7D 500887740 500894691 6951 False 1179.833333 2736 86.930333 962 7845 6 chr7D.!!$F2 6883
4 TraesCS7A01G391000 chrUn 86620323 86628881 8558 False 3167.250000 9099 92.337500 173 8834 4 chrUn.!!$F1 8661
5 TraesCS7A01G391000 chr7B 529668992 529675765 6773 False 1029.428571 2687 87.661286 1102 7845 7 chr7B.!!$F1 6743

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
165 2813 0.755698 TACCTCCTCCATCTCCACGC 60.756 60.000 0.00 0.00 0.00 5.34 F
1377 4108 0.704664 TAGACAGGTGGCTCCTCTCA 59.295 55.000 12.45 0.00 46.24 3.27 F
1753 4597 0.969149 AGGACGTCAACAGCAGATGA 59.031 50.000 18.91 0.00 0.00 2.92 F
3157 6059 2.289547 GCAAACGTGTCACAACTGGTAT 59.710 45.455 3.42 0.00 0.00 2.73 F
3756 6691 2.119801 AGCCTCATGATGTTGGTCAC 57.880 50.000 0.00 0.00 0.00 3.67 F
4108 7315 2.517959 CTCCCATTTCAGTTCAGGCAA 58.482 47.619 0.00 0.00 0.00 4.52 F
5635 8996 0.175531 GCCTGCGGTAATGCCAAAAT 59.824 50.000 0.00 0.00 36.97 1.82 F
6257 9742 0.452184 GGAAGAGACTGACGATCGCA 59.548 55.000 16.60 13.18 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 4118 0.386985 GCAAAGCAGAGCAGAGCAAC 60.387 55.000 0.00 0.00 0.00 4.17 R
3071 5973 1.264020 GTGTCAGCGCAAATGTCAAGA 59.736 47.619 11.47 0.00 0.00 3.02 R
3236 6164 4.834496 TCCAGAAAAACTCTTGGCAATGAT 59.166 37.500 0.00 0.00 29.07 2.45 R
5093 8379 0.325933 CCCTGGACTTGAGCACATCA 59.674 55.000 0.00 0.00 35.62 3.07 R
5213 8499 6.360329 AGAAGCTTTGAATTACGTACGTTTG 58.640 36.000 27.92 4.98 0.00 2.93 R
6020 9499 2.295070 TCTTGTTTCCGACTCGACATCA 59.705 45.455 0.00 0.00 0.00 3.07 R
7027 10558 1.039856 GGTGTTGTTTCCACAGGCAT 58.960 50.000 0.00 0.00 33.22 4.40 R
8121 11662 0.755686 GCAGTCCTCTCCCATACCTG 59.244 60.000 0.00 0.00 0.00 4.00 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
17 2662 2.820479 CGACCTCGAGCTCCGACT 60.820 66.667 6.99 0.00 43.23 4.18
21 2666 2.766400 CCTCGAGCTCCGACTGGAC 61.766 68.421 6.99 0.00 43.23 4.02
37 2682 1.439644 GACTGACTCGAGGATGGCC 59.560 63.158 18.41 0.00 0.00 5.36
48 2693 3.885521 GATGGCCTGCTGCTTCGC 61.886 66.667 3.32 0.00 40.92 4.70
54 2699 3.184683 CTGCTGCTTCGCCGAGTC 61.185 66.667 0.00 0.00 0.00 3.36
64 2709 4.373116 GCCGAGTCCACCGCTTGA 62.373 66.667 0.00 0.00 0.00 3.02
81 2726 2.672307 AGCGACCTCGAACTCCGT 60.672 61.111 0.00 0.00 43.02 4.69
83 2728 2.097918 CGACCTCGAACTCCGTCG 59.902 66.667 0.00 0.00 43.02 5.12
86 2731 3.441290 CCTCGAACTCCGTCGGCT 61.441 66.667 6.34 0.00 41.43 5.52
87 2732 2.567049 CTCGAACTCCGTCGGCTT 59.433 61.111 6.34 0.00 41.43 4.35
89 2734 3.479269 CGAACTCCGTCGGCTTGC 61.479 66.667 6.34 0.00 37.37 4.01
140 2788 1.424635 CTCGTCCTCTTCGTCCGAC 59.575 63.158 0.00 0.00 0.00 4.79
143 2791 3.437795 TCCTCTTCGTCCGACGGC 61.438 66.667 20.35 3.45 42.81 5.68
146 2794 2.359602 TCTTCGTCCGACGGCTCT 60.360 61.111 20.35 0.00 42.81 4.09
165 2813 0.755698 TACCTCCTCCATCTCCACGC 60.756 60.000 0.00 0.00 0.00 5.34
170 2818 3.746949 CTCCATCTCCACGCCCAGC 62.747 68.421 0.00 0.00 0.00 4.85
207 2855 4.501571 GCGCACATCTCCTAATAGGAAGAA 60.502 45.833 10.62 0.00 45.28 2.52
212 2860 6.928492 CACATCTCCTAATAGGAAGAAAGAGC 59.072 42.308 10.62 0.00 45.28 4.09
313 2961 2.183478 TGCACATGGTCTTCACGAAT 57.817 45.000 0.00 0.00 0.00 3.34
315 2963 2.226200 TGCACATGGTCTTCACGAATTG 59.774 45.455 0.00 0.00 0.00 2.32
318 2966 4.083537 GCACATGGTCTTCACGAATTGTTA 60.084 41.667 0.00 0.00 0.00 2.41
354 3002 2.506472 GGGGTCAAGCCGGATCTC 59.494 66.667 5.05 0.00 38.44 2.75
370 3025 5.507985 CCGGATCTCTTTTTGCCCATTATTC 60.508 44.000 0.00 0.00 0.00 1.75
372 3027 4.370364 TCTCTTTTTGCCCATTATTCGC 57.630 40.909 0.00 0.00 0.00 4.70
399 3054 4.326766 CTTGGCGCGGTTGGTGTG 62.327 66.667 8.83 0.00 0.00 3.82
453 3136 2.817423 GCGATTGCTTGGCGAGAGG 61.817 63.158 5.76 0.00 38.39 3.69
538 3227 1.463674 CCTCCTATGCCACCACAAAC 58.536 55.000 0.00 0.00 0.00 2.93
622 3311 2.939022 GTGTTCCACACTGCGCTC 59.061 61.111 9.73 0.00 45.27 5.03
623 3312 1.595382 GTGTTCCACACTGCGCTCT 60.595 57.895 9.73 0.00 45.27 4.09
759 3461 3.465403 CCACCTGCTCCCTCCTCG 61.465 72.222 0.00 0.00 0.00 4.63
846 3561 2.589014 CCAGTAACGACCAACGAGTAC 58.411 52.381 0.00 0.00 45.77 2.73
1086 3807 4.100084 TCCTCGTACCGGGAGCGA 62.100 66.667 6.32 11.71 0.00 4.93
1105 3829 3.379445 GGGCCGACGTCTTCTCCA 61.379 66.667 14.70 0.00 0.00 3.86
1336 4066 1.079750 GAGGACCACGAGCACTTCC 60.080 63.158 0.00 0.00 0.00 3.46
1377 4108 0.704664 TAGACAGGTGGCTCCTCTCA 59.295 55.000 12.45 0.00 46.24 3.27
1387 4118 1.294659 GCTCCTCTCACCTGTTTGCG 61.295 60.000 0.00 0.00 0.00 4.85
1450 4188 4.518211 CACCTATTTGCCATCAATCTCTCC 59.482 45.833 0.00 0.00 31.33 3.71
1493 4231 7.730364 TGAAGTTCTTCATTTGTCCTAACTC 57.270 36.000 10.67 0.00 0.00 3.01
1502 4240 6.361433 TCATTTGTCCTAACTCAAACTTCCA 58.639 36.000 0.00 0.00 36.58 3.53
1630 4474 9.573166 CCTAATGATGAATAGGTGAAAATGGTA 57.427 33.333 0.00 0.00 35.06 3.25
1677 4521 9.859427 TTTGAACATTTTCACCATTCATAGATC 57.141 29.630 0.00 0.00 41.64 2.75
1685 4529 6.416631 TCACCATTCATAGATCTCCTCTTG 57.583 41.667 0.00 0.00 35.28 3.02
1686 4530 5.901853 TCACCATTCATAGATCTCCTCTTGT 59.098 40.000 0.00 0.00 35.28 3.16
1687 4531 6.385176 TCACCATTCATAGATCTCCTCTTGTT 59.615 38.462 0.00 0.00 35.28 2.83
1696 4540 3.319137 TCTCCTCTTGTTGTCAATCCG 57.681 47.619 0.00 0.00 32.82 4.18
1704 4548 1.376683 TTGTCAATCCGAAGCCCCG 60.377 57.895 0.00 0.00 0.00 5.73
1715 4559 3.894547 AAGCCCCGATCACGCGTTT 62.895 57.895 10.22 0.00 38.29 3.60
1724 4568 3.143279 CGATCACGCGTTTGTTAGAAAC 58.857 45.455 10.22 0.97 0.00 2.78
1738 4582 7.435068 TTGTTAGAAACTAAGCATGAAGGAC 57.565 36.000 0.00 0.00 0.00 3.85
1753 4597 0.969149 AGGACGTCAACAGCAGATGA 59.031 50.000 18.91 0.00 0.00 2.92
1764 4608 6.527023 GTCAACAGCAGATGATGAATTTCTTG 59.473 38.462 4.89 0.00 41.78 3.02
1792 4636 4.230455 TCATTTGTTTCAGGGTTGGGATT 58.770 39.130 0.00 0.00 0.00 3.01
1926 4774 3.435186 GCCAGGAGCGTTGAAGCC 61.435 66.667 0.00 0.00 38.01 4.35
1997 4848 2.943036 TTTTTGTACCCGCCTTCTCT 57.057 45.000 0.00 0.00 0.00 3.10
2053 4904 5.044179 TCCCAACAAGAAGATACCCATCAAT 60.044 40.000 0.00 0.00 33.21 2.57
2168 5019 2.955660 GGGTGATCAGAGTAGTCTCCAG 59.044 54.545 0.00 0.00 41.26 3.86
2213 5064 6.441093 TCTGGAATCATGATAGCACAAAAC 57.559 37.500 9.04 0.00 0.00 2.43
2214 5065 5.945191 TCTGGAATCATGATAGCACAAAACA 59.055 36.000 9.04 0.00 0.00 2.83
2818 5715 8.928448 TCCTCTCTATAATTGTGTGCTAATTCT 58.072 33.333 0.00 0.00 0.00 2.40
3071 5973 3.690460 CTGAACCCTGCAGATTTTAGGT 58.310 45.455 17.39 9.97 35.39 3.08
3157 6059 2.289547 GCAAACGTGTCACAACTGGTAT 59.710 45.455 3.42 0.00 0.00 2.73
3183 6102 5.479724 TCTGGTATTGCAAAATTGTCATGGA 59.520 36.000 1.71 0.00 0.00 3.41
3236 6164 9.118300 ACAAAAATGCCAAATTTCTTGAACATA 57.882 25.926 0.00 0.00 0.00 2.29
3249 6182 6.688637 TCTTGAACATATCATTGCCAAGAG 57.311 37.500 0.00 0.00 38.03 2.85
3255 6188 7.814107 TGAACATATCATTGCCAAGAGTTTTTC 59.186 33.333 0.00 0.00 31.50 2.29
3282 6217 6.238484 GGAACCACAACATATACTTCTCATGC 60.238 42.308 0.00 0.00 0.00 4.06
3344 6279 8.567285 TCTCATCTCGTTATCATAGCAGAATA 57.433 34.615 0.00 0.00 0.00 1.75
3451 6386 2.439507 GGATGAAATCTCCACTGGCCTA 59.560 50.000 3.32 0.00 44.71 3.93
3756 6691 2.119801 AGCCTCATGATGTTGGTCAC 57.880 50.000 0.00 0.00 0.00 3.67
4108 7315 2.517959 CTCCCATTTCAGTTCAGGCAA 58.482 47.619 0.00 0.00 0.00 4.52
4460 7692 5.124936 GGGTTACTATGTCATTGGGTTTGAC 59.875 44.000 0.00 0.00 43.04 3.18
4491 7723 2.798847 GGAAGGTACGCGTCAAATATCC 59.201 50.000 18.63 13.79 0.00 2.59
4991 8264 2.676342 GGGTATGTAGCTGTTGTTTCCG 59.324 50.000 0.00 0.00 0.00 4.30
5093 8379 6.071320 GGGCTCCAACAATATCTTAGGAATT 58.929 40.000 0.00 0.00 0.00 2.17
5213 8499 2.025898 ACCTTCGCTCTAAGCTACCTC 58.974 52.381 0.00 0.00 39.60 3.85
5314 8601 2.014128 GTATAACATGCAGCGTTGGGT 58.986 47.619 13.16 3.90 0.00 4.51
5635 8996 0.175531 GCCTGCGGTAATGCCAAAAT 59.824 50.000 0.00 0.00 36.97 1.82
5636 8997 1.405391 GCCTGCGGTAATGCCAAAATT 60.405 47.619 0.00 0.00 36.97 1.82
5644 9112 4.499040 CGGTAATGCCAAAATTAGCTTTCG 59.501 41.667 0.00 0.00 38.03 3.46
5649 9117 4.698575 TGCCAAAATTAGCTTTCGGTTTT 58.301 34.783 0.00 0.00 0.00 2.43
5678 9146 9.950496 AAGAATAAGAACATCATGTGAAGTACT 57.050 29.630 0.00 0.00 0.00 2.73
6245 9730 2.029828 GTCGACAGAGCAAAGGAAGAGA 60.030 50.000 11.55 0.00 0.00 3.10
6257 9742 0.452184 GGAAGAGACTGACGATCGCA 59.548 55.000 16.60 13.18 0.00 5.10
6377 9862 2.920645 CGTCGACACAGGCAGGACT 61.921 63.158 17.16 0.00 0.00 3.85
6505 9992 3.426695 CGTGATCCTGACATTCTTTTGGC 60.427 47.826 0.00 0.00 0.00 4.52
6515 10002 1.993956 TTCTTTTGGCCTTGCAGCTA 58.006 45.000 3.32 0.00 0.00 3.32
6862 10370 9.762933 AAGTAGTCATTAATTTTGCATGTTTGT 57.237 25.926 0.00 0.00 0.00 2.83
6934 10465 3.297134 TTTTGCAGGAGAAACCAGAGT 57.703 42.857 0.00 0.00 42.04 3.24
7009 10540 0.734253 CGCAGTACTCGCAAAGCTCT 60.734 55.000 14.77 0.00 0.00 4.09
7027 10558 2.983030 GTCACCCAATGCACGGCA 60.983 61.111 0.00 1.01 44.86 5.69
7108 10639 2.525629 TTCTCCCTCGTGGTGGCA 60.526 61.111 2.33 0.00 34.77 4.92
7303 10834 0.176680 CTGGGATGTACTCAGCGCTT 59.823 55.000 7.50 0.00 40.42 4.68
7366 10897 2.509336 GTGCAGTCGCTGGCGTAT 60.509 61.111 14.55 2.20 40.74 3.06
7406 10937 1.899437 GATCGGCTTCCAGTGGGACA 61.899 60.000 9.92 0.00 44.89 4.02
7603 11134 1.550130 CGGTGTGGTGGAGGTGGTAT 61.550 60.000 0.00 0.00 0.00 2.73
7723 11254 5.024785 ACGTCTTCCTCAAGAACTTCTTT 57.975 39.130 0.92 0.00 40.49 2.52
7830 11361 2.172505 TCAAGGTGCTCAACTTCCAGAA 59.827 45.455 0.00 0.00 35.91 3.02
7860 11391 2.614734 CCATCACAGAGTGCACAGATGT 60.615 50.000 21.04 16.80 32.98 3.06
7902 11433 9.435688 TGATCTGCACATGTATACATATAAACC 57.564 33.333 17.86 4.98 34.26 3.27
8055 11596 0.178861 TTTTCTCTCCAGCCCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
8138 11679 0.639392 AGCAGGTATGGGAGAGGACT 59.361 55.000 0.00 0.00 0.00 3.85
8141 11682 0.757188 AGGTATGGGAGAGGACTGCG 60.757 60.000 0.00 0.00 35.29 5.18
8315 11857 1.495069 GAGACTGCAAAGCTGACGC 59.505 57.895 2.86 0.00 0.00 5.19
8408 11976 9.802039 TTATTCTATTGTAAACAAGGTCCAAGT 57.198 29.630 1.62 0.00 39.47 3.16
8410 11978 9.975218 ATTCTATTGTAAACAAGGTCCAAGTAT 57.025 29.630 1.62 0.00 39.47 2.12
8411 11979 9.444600 TTCTATTGTAAACAAGGTCCAAGTATC 57.555 33.333 1.62 0.00 39.47 2.24
8412 11980 8.598916 TCTATTGTAAACAAGGTCCAAGTATCA 58.401 33.333 1.62 0.00 39.47 2.15
8413 11981 6.870971 TTGTAAACAAGGTCCAAGTATCAC 57.129 37.500 0.00 0.00 0.00 3.06
8414 11982 5.931294 TGTAAACAAGGTCCAAGTATCACA 58.069 37.500 0.00 0.00 0.00 3.58
8415 11983 6.358178 TGTAAACAAGGTCCAAGTATCACAA 58.642 36.000 0.00 0.00 0.00 3.33
8416 11984 6.485313 TGTAAACAAGGTCCAAGTATCACAAG 59.515 38.462 0.00 0.00 0.00 3.16
8417 11985 4.021102 ACAAGGTCCAAGTATCACAAGG 57.979 45.455 0.00 0.00 0.00 3.61
8418 11986 3.394606 ACAAGGTCCAAGTATCACAAGGT 59.605 43.478 0.00 0.00 0.00 3.50
8419 11987 4.141251 ACAAGGTCCAAGTATCACAAGGTT 60.141 41.667 0.00 0.00 0.00 3.50
8420 11988 4.287766 AGGTCCAAGTATCACAAGGTTC 57.712 45.455 0.00 0.00 0.00 3.62
8421 11989 3.650942 AGGTCCAAGTATCACAAGGTTCA 59.349 43.478 0.00 0.00 0.00 3.18
8422 11990 4.104102 AGGTCCAAGTATCACAAGGTTCAA 59.896 41.667 0.00 0.00 0.00 2.69
8509 12078 3.090210 ACCTTCATGCATCACCAATCA 57.910 42.857 0.00 0.00 0.00 2.57
8521 12090 6.176183 GCATCACCAATCATACTAATAGGCT 58.824 40.000 0.00 0.00 0.00 4.58
8552 12121 6.034898 CCAAATCGGTTGAATAAATCACAAGC 59.965 38.462 0.00 0.00 39.87 4.01
8583 12153 2.355756 CCATTAGTTGCATCCAAGACCG 59.644 50.000 0.00 0.00 0.00 4.79
8698 12271 5.857268 AGAGCTTGTTTATTTGCCATGTTT 58.143 33.333 0.00 0.00 0.00 2.83
8744 12317 2.204244 GGGAAGGTGGAGGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
8745 12318 2.309504 GGGAAGGTGGAGGGGGAAG 61.310 68.421 0.00 0.00 0.00 3.46
8746 12319 2.309504 GGAAGGTGGAGGGGGAAGG 61.310 68.421 0.00 0.00 0.00 3.46
8747 12320 1.541620 GAAGGTGGAGGGGGAAGGT 60.542 63.158 0.00 0.00 0.00 3.50
8748 12321 1.852626 AAGGTGGAGGGGGAAGGTG 60.853 63.158 0.00 0.00 0.00 4.00
8749 12322 3.339093 GGTGGAGGGGGAAGGTGG 61.339 72.222 0.00 0.00 0.00 4.61
8750 12323 2.204090 GTGGAGGGGGAAGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
8751 12324 2.124996 TGGAGGGGGAAGGTGGAG 59.875 66.667 0.00 0.00 0.00 3.86
8752 12325 2.692741 GGAGGGGGAAGGTGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
8753 12326 2.692741 GAGGGGGAAGGTGGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
8754 12327 4.371231 AGGGGGAAGGTGGAGGGG 62.371 72.222 0.00 0.00 0.00 4.79
8766 12339 1.327690 TGGAGGGGGAAGATCGAACG 61.328 60.000 0.00 0.00 0.00 3.95
8824 12397 3.705638 CTCAGTGGCGTGTGTGCG 61.706 66.667 0.00 0.00 35.06 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.041115 CAGTCCAGTCGGAGCTCGA 61.041 63.158 7.83 5.90 43.99 4.04
13 2658 0.673956 TCCTCGAGTCAGTCCAGTCG 60.674 60.000 12.31 0.00 40.07 4.18
17 2662 1.323271 GCCATCCTCGAGTCAGTCCA 61.323 60.000 12.31 0.00 0.00 4.02
21 2666 1.440893 CAGGCCATCCTCGAGTCAG 59.559 63.158 12.31 0.00 41.93 3.51
48 2693 2.125912 CTCAAGCGGTGGACTCGG 60.126 66.667 0.00 0.00 0.00 4.63
64 2709 2.672307 ACGGAGTTCGAGGTCGCT 60.672 61.111 0.00 0.00 37.78 4.93
125 2770 2.484203 CCGTCGGACGAAGAGGAC 59.516 66.667 30.33 0.00 46.05 3.85
140 2788 0.178975 AGATGGAGGAGGTAGAGCCG 60.179 60.000 0.00 0.00 43.70 5.52
143 2791 2.593026 GTGGAGATGGAGGAGGTAGAG 58.407 57.143 0.00 0.00 0.00 2.43
146 2794 0.755698 GCGTGGAGATGGAGGAGGTA 60.756 60.000 0.00 0.00 0.00 3.08
185 2833 4.855715 TCTTCCTATTAGGAGATGTGCG 57.144 45.455 12.16 0.00 46.73 5.34
252 2900 0.319297 GTATGTACCCGGCGTGATCC 60.319 60.000 6.01 0.00 0.00 3.36
313 2961 1.614413 GCACCACCCGGAAAATAACAA 59.386 47.619 0.73 0.00 35.59 2.83
315 2963 0.169451 CGCACCACCCGGAAAATAAC 59.831 55.000 0.73 0.00 35.59 1.89
318 2966 1.969589 GTCGCACCACCCGGAAAAT 60.970 57.895 0.73 0.00 35.59 1.82
354 3002 2.929398 GTGGCGAATAATGGGCAAAAAG 59.071 45.455 0.00 0.00 41.36 2.27
453 3136 1.411493 GGCGACCGAATCACGAGTTC 61.411 60.000 0.00 0.00 45.77 3.01
622 3311 4.201208 AGCGCAATTGAATATGAACGAG 57.799 40.909 11.47 0.00 0.00 4.18
623 3312 3.302415 CGAGCGCAATTGAATATGAACGA 60.302 43.478 11.47 0.00 0.00 3.85
721 3423 2.270297 CTGGCGAGGAAAAATGGCGG 62.270 60.000 0.00 0.00 0.00 6.13
772 3474 3.428282 GGTTTGAACGGCGGCGAT 61.428 61.111 38.93 28.08 0.00 4.58
794 3496 2.360475 GTTGGTGGAGGGAGCAGC 60.360 66.667 0.00 0.00 0.00 5.25
846 3561 1.814527 GGCGCGTAGATATAGGGGG 59.185 63.158 8.43 0.00 0.00 5.40
1086 3807 3.069318 GAGAAGACGTCGGCCCCT 61.069 66.667 10.46 4.03 0.00 4.79
1336 4066 3.800863 CTGCTTGAGCCTGCGCAG 61.801 66.667 30.52 30.52 43.10 5.18
1373 4103 0.463654 AGCAACGCAAACAGGTGAGA 60.464 50.000 0.00 0.00 0.00 3.27
1377 4108 2.024918 CAGAGCAACGCAAACAGGT 58.975 52.632 0.00 0.00 0.00 4.00
1387 4118 0.386985 GCAAAGCAGAGCAGAGCAAC 60.387 55.000 0.00 0.00 0.00 4.17
1677 4521 3.319137 TCGGATTGACAACAAGAGGAG 57.681 47.619 0.00 0.00 39.46 3.69
1685 4529 1.644786 CGGGGCTTCGGATTGACAAC 61.645 60.000 0.00 0.00 0.00 3.32
1686 4530 1.376683 CGGGGCTTCGGATTGACAA 60.377 57.895 0.00 0.00 0.00 3.18
1687 4531 1.622607 ATCGGGGCTTCGGATTGACA 61.623 55.000 1.61 0.00 32.40 3.58
1704 4548 4.385244 AGTTTCTAACAAACGCGTGATC 57.615 40.909 14.98 1.27 35.42 2.92
1715 4559 5.637810 CGTCCTTCATGCTTAGTTTCTAACA 59.362 40.000 0.00 0.00 0.00 2.41
1724 4568 3.325870 TGTTGACGTCCTTCATGCTTAG 58.674 45.455 14.12 0.00 0.00 2.18
1738 4582 4.611310 AATTCATCATCTGCTGTTGACG 57.389 40.909 6.51 0.00 34.15 4.35
1753 4597 5.175859 CAAATGAGCAGGCAAGAAATTCAT 58.824 37.500 0.00 0.00 0.00 2.57
1764 4608 1.067354 CCCTGAAACAAATGAGCAGGC 60.067 52.381 0.00 0.00 43.65 4.85
1792 4636 0.530744 CCTGGATCGTCGGAAAGTCA 59.469 55.000 0.00 0.00 0.00 3.41
1919 4763 9.797642 ATTCATGATAACATATAGTGGCTTCAA 57.202 29.630 0.00 0.00 35.09 2.69
1979 4830 2.943036 AAGAGAAGGCGGGTACAAAA 57.057 45.000 0.00 0.00 0.00 2.44
1985 4836 2.759985 TCTGAAAGAGAAGGCGGGT 58.240 52.632 0.00 0.00 38.67 5.28
1997 4848 6.942005 TGAAGAAGATTGGCTAATGTCTGAAA 59.058 34.615 0.00 0.00 0.00 2.69
2053 4904 2.485302 CCCGTTGACATCATGCAGGATA 60.485 50.000 14.40 0.00 0.00 2.59
2151 5002 6.116806 TGAAGTACTGGAGACTACTCTGATC 58.883 44.000 0.00 0.00 42.28 2.92
2158 5009 7.868906 ATCTAACTGAAGTACTGGAGACTAC 57.131 40.000 0.00 0.00 0.00 2.73
2225 5077 7.871973 TCATTTGACATACAATTTTTCACCTGG 59.128 33.333 0.00 0.00 38.36 4.45
2245 5100 7.147312 ACAACATAAACAGTGGTGATCATTTG 58.853 34.615 0.00 0.00 36.38 2.32
2818 5715 4.641396 CATGTCTAGGACAAGTTCACCAA 58.359 43.478 4.46 0.00 45.96 3.67
3071 5973 1.264020 GTGTCAGCGCAAATGTCAAGA 59.736 47.619 11.47 0.00 0.00 3.02
3157 6059 5.781210 TGACAATTTTGCAATACCAGACA 57.219 34.783 0.00 0.00 0.00 3.41
3201 6120 9.949174 GAAATTTGGCATTTTTGTTCTACAATT 57.051 25.926 0.00 0.00 38.00 2.32
3218 6137 7.404203 GCAATGATATGTTCAAGAAATTTGGC 58.596 34.615 0.00 0.00 38.03 4.52
3236 6164 4.834496 TCCAGAAAAACTCTTGGCAATGAT 59.166 37.500 0.00 0.00 29.07 2.45
3249 6182 7.882179 AGTATATGTTGTGGTTCCAGAAAAAC 58.118 34.615 3.03 2.40 0.00 2.43
3255 6188 6.406370 TGAGAAGTATATGTTGTGGTTCCAG 58.594 40.000 0.00 0.00 0.00 3.86
3451 6386 5.326283 TCTGGTATGTGGTAGAGCTATCT 57.674 43.478 0.00 0.00 39.75 1.98
3756 6691 5.977129 GGTGTCAGTAACCAAAATTGTGAAG 59.023 40.000 0.00 0.00 37.65 3.02
3933 7075 1.140312 ACTGGCTCCTGTCAAAAGGA 58.860 50.000 0.00 0.00 44.35 3.36
4409 7641 1.177401 CTGTGATGGAGACCTCGACA 58.823 55.000 0.00 0.00 0.00 4.35
4460 7692 2.012051 GCGTACCTTCCAACATCTGGG 61.012 57.143 0.00 0.00 46.44 4.45
4491 7723 4.489810 CTGTTAGTCTGCCACAGTAAGAG 58.510 47.826 0.00 0.00 34.39 2.85
4597 7852 2.099592 TGAACAGCCTGCAAGAAAACAG 59.900 45.455 0.00 0.00 34.07 3.16
4991 8264 1.463444 GACCAATACTGTTGTCACGGC 59.537 52.381 0.00 0.00 31.56 5.68
5093 8379 0.325933 CCCTGGACTTGAGCACATCA 59.674 55.000 0.00 0.00 35.62 3.07
5213 8499 6.360329 AGAAGCTTTGAATTACGTACGTTTG 58.640 36.000 27.92 4.98 0.00 2.93
5314 8601 6.652481 CCTCTGAAAGAATTTGCTGAGACTTA 59.348 38.462 0.00 0.00 46.34 2.24
5635 8996 8.842280 TCTTATTCTTTGAAAACCGAAAGCTAA 58.158 29.630 0.00 0.00 0.00 3.09
5636 8997 8.385898 TCTTATTCTTTGAAAACCGAAAGCTA 57.614 30.769 0.00 0.00 0.00 3.32
5644 9112 9.696917 ACATGATGTTCTTATTCTTTGAAAACC 57.303 29.630 0.00 0.00 0.00 3.27
5649 9117 9.288576 ACTTCACATGATGTTCTTATTCTTTGA 57.711 29.630 0.00 0.00 0.00 2.69
6020 9499 2.295070 TCTTGTTTCCGACTCGACATCA 59.705 45.455 0.00 0.00 0.00 3.07
6245 9730 1.425825 CTCGACTGCGATCGTCAGT 59.574 57.895 31.31 31.31 46.80 3.41
6505 9992 3.204306 TCATCAGGAATAGCTGCAAGG 57.796 47.619 1.02 0.00 0.00 3.61
6515 10002 3.316501 CCCTCCTCTCTTCATCAGGAAT 58.683 50.000 0.00 0.00 35.84 3.01
6771 10279 6.607600 TGACACCTAGTATATCTTCTTGTGCT 59.392 38.462 0.00 0.00 0.00 4.40
6934 10465 1.208776 CTGCTGATGTCCCTGATCACA 59.791 52.381 0.00 0.00 0.00 3.58
7009 10540 2.983030 GCCGTGCATTGGGTGACA 60.983 61.111 9.69 0.00 0.00 3.58
7027 10558 1.039856 GGTGTTGTTTCCACAGGCAT 58.960 50.000 0.00 0.00 33.22 4.40
7075 10606 1.273886 GAGAAGAAGAAGCGGACCACT 59.726 52.381 0.00 0.00 0.00 4.00
7108 10639 3.118261 AGAATATGGTGCCGAACATGAGT 60.118 43.478 0.00 0.00 0.00 3.41
7366 10897 2.420568 GGCGTAGACGATCACCCCA 61.421 63.158 6.19 0.00 43.02 4.96
7406 10937 2.224548 GGTACCAGCAGAACTTCTTGGT 60.225 50.000 16.21 16.21 39.96 3.67
7723 11254 1.079405 GAAGTCGTGGCGGAATCCA 60.079 57.895 0.00 0.00 0.00 3.41
7830 11361 4.197750 GCACTCTGTGATGGATCATCTTT 58.802 43.478 9.00 0.00 41.06 2.52
8003 11542 2.423898 AAGAGCCGCTAGCCGCTTA 61.424 57.895 27.53 0.00 45.47 3.09
8055 11596 5.006649 CGAGTCATCACAAACAACTCTCAAA 59.993 40.000 0.00 0.00 35.35 2.69
8115 11656 1.047002 CTCTCCCATACCTGCTCTGG 58.953 60.000 0.00 0.00 0.00 3.86
8121 11662 0.755686 GCAGTCCTCTCCCATACCTG 59.244 60.000 0.00 0.00 0.00 4.00
8125 11666 1.457643 CCCGCAGTCCTCTCCCATA 60.458 63.158 0.00 0.00 0.00 2.74
8138 11679 1.909459 ATGCACAGGACATACCCGCA 61.909 55.000 0.00 0.00 41.03 5.69
8141 11682 3.134804 AGACTTATGCACAGGACATACCC 59.865 47.826 0.00 0.00 40.05 3.69
8315 11857 3.999663 GCCTTCGATCTTATTCATGGAGG 59.000 47.826 0.00 0.00 0.00 4.30
8360 11905 6.824958 AATTAGTAATAGGTTGGCTGAGGA 57.175 37.500 0.00 0.00 0.00 3.71
8403 11971 4.062293 TCGTTGAACCTTGTGATACTTGG 58.938 43.478 0.00 0.00 0.00 3.61
8407 11975 6.774354 TTACTTCGTTGAACCTTGTGATAC 57.226 37.500 0.00 0.00 0.00 2.24
8408 11976 7.972832 ATTTACTTCGTTGAACCTTGTGATA 57.027 32.000 0.00 0.00 0.00 2.15
8409 11977 6.877611 ATTTACTTCGTTGAACCTTGTGAT 57.122 33.333 0.00 0.00 0.00 3.06
8410 11978 7.789273 TTATTTACTTCGTTGAACCTTGTGA 57.211 32.000 0.00 0.00 0.00 3.58
8411 11979 8.844441 TTTTATTTACTTCGTTGAACCTTGTG 57.156 30.769 0.00 0.00 0.00 3.33
8412 11980 7.646526 GCTTTTATTTACTTCGTTGAACCTTGT 59.353 33.333 0.00 0.00 0.00 3.16
8413 11981 7.114388 GGCTTTTATTTACTTCGTTGAACCTTG 59.886 37.037 0.00 0.00 0.00 3.61
8414 11982 7.143340 GGCTTTTATTTACTTCGTTGAACCTT 58.857 34.615 0.00 0.00 0.00 3.50
8415 11983 6.263617 TGGCTTTTATTTACTTCGTTGAACCT 59.736 34.615 0.00 0.00 0.00 3.50
8416 11984 6.361481 GTGGCTTTTATTTACTTCGTTGAACC 59.639 38.462 0.00 0.00 0.00 3.62
8417 11985 6.913673 TGTGGCTTTTATTTACTTCGTTGAAC 59.086 34.615 0.00 0.00 0.00 3.18
8418 11986 7.028926 TGTGGCTTTTATTTACTTCGTTGAA 57.971 32.000 0.00 0.00 0.00 2.69
8419 11987 6.621316 TGTGGCTTTTATTTACTTCGTTGA 57.379 33.333 0.00 0.00 0.00 3.18
8489 12058 3.090210 TGATTGGTGATGCATGAAGGT 57.910 42.857 2.46 0.00 0.00 3.50
8509 12078 6.874134 CGATTTGGTTAGCAGCCTATTAGTAT 59.126 38.462 0.00 0.00 0.00 2.12
8552 12121 1.670811 GCAACTAATGGGTGATGGTCG 59.329 52.381 0.00 0.00 33.74 4.79
8609 12179 0.391263 GACGTGGTCCTTAGCCCTTG 60.391 60.000 0.00 0.00 0.00 3.61
8698 12271 2.540383 ACCATGGTGACTAAGAGAGCA 58.460 47.619 18.99 0.00 0.00 4.26
8744 12317 1.383248 CGATCTTCCCCCTCCACCT 60.383 63.158 0.00 0.00 0.00 4.00
8745 12318 0.981277 TTCGATCTTCCCCCTCCACC 60.981 60.000 0.00 0.00 0.00 4.61
8746 12319 0.178301 GTTCGATCTTCCCCCTCCAC 59.822 60.000 0.00 0.00 0.00 4.02
8747 12320 1.327690 CGTTCGATCTTCCCCCTCCA 61.328 60.000 0.00 0.00 0.00 3.86
8748 12321 1.328430 ACGTTCGATCTTCCCCCTCC 61.328 60.000 0.00 0.00 0.00 4.30
8749 12322 0.102663 GACGTTCGATCTTCCCCCTC 59.897 60.000 0.00 0.00 0.00 4.30
8750 12323 1.328430 GGACGTTCGATCTTCCCCCT 61.328 60.000 7.61 0.00 0.00 4.79
8751 12324 1.143401 GGACGTTCGATCTTCCCCC 59.857 63.158 7.61 0.00 0.00 5.40
8752 12325 1.226888 CGGACGTTCGATCTTCCCC 60.227 63.158 11.86 0.00 0.00 4.81
8753 12326 0.525029 GTCGGACGTTCGATCTTCCC 60.525 60.000 23.87 4.17 41.40 3.97
8754 12327 0.169672 TGTCGGACGTTCGATCTTCC 59.830 55.000 23.87 9.62 41.40 3.46
8755 12328 1.536149 CTGTCGGACGTTCGATCTTC 58.464 55.000 23.87 10.03 41.40 2.87
8766 12339 0.591659 GGCTTCAAAACCTGTCGGAC 59.408 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.