Multiple sequence alignment - TraesCS6D01G066000

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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 TraesCS6D01G066000 chr6D 100.000 3140 0 0 1 3140 32321001 32317862 0.000000e+00 5799.0
1 TraesCS6D01G066000 chr6A 89.428 1731 109 40 925 2626 36704204 36702519 0.000000e+00 2115.0
2 TraesCS6D01G066000 chr6B 91.842 1520 83 22 843 2325 68111788 68110273 0.000000e+00 2082.0
3 TraesCS6D01G066000 chr6B 87.095 1759 110 27 928 2626 68006152 68004451 0.000000e+00 1882.0
4 TraesCS6D01G066000 chr6B 84.335 549 52 18 2623 3140 68004413 68003868 1.000000e-139 507.0
5 TraesCS6D01G066000 chr6B 85.084 476 48 10 2623 3077 68108393 68107920 6.130000e-127 464.0
6 TraesCS6D01G066000 chr6B 92.400 250 18 1 469 717 68115357 68115108 3.850000e-94 355.0
7 TraesCS6D01G066000 chr6B 84.887 311 24 7 2321 2608 68108775 68108465 3.060000e-75 292.0
8 TraesCS6D01G066000 chr6B 96.774 31 1 0 786 816 68112139 68112109 6.000000e-03 52.8
9 TraesCS6D01G066000 chr1D 94.589 462 19 4 3 464 468018817 468019272 0.000000e+00 710.0
10 TraesCS6D01G066000 chr2D 93.347 481 13 4 3 464 13243743 13243263 0.000000e+00 693.0
11 TraesCS6D01G066000 chr2A 91.974 461 29 6 6 463 460340095 460339640 9.500000e-180 640.0
12 TraesCS6D01G066000 chr2A 92.199 282 19 1 182 463 81477565 81477287 2.270000e-106 396.0
13 TraesCS6D01G066000 chr4B 91.489 470 31 5 3 463 667640780 667641249 3.420000e-179 638.0
14 TraesCS6D01G066000 chr3B 89.316 468 43 5 4 469 13610854 13610392 5.840000e-162 580.0
15 TraesCS6D01G066000 chr3B 89.062 64 5 1 477 538 573303210 573303147 9.340000e-11 78.7
16 TraesCS6D01G066000 chrUn 89.671 426 31 10 3 422 43777373 43776955 5.960000e-147 531.0
17 TraesCS6D01G066000 chr5D 97.761 268 6 0 3 270 556427384 556427117 2.210000e-126 462.0
18 TraesCS6D01G066000 chr5D 90.545 275 10 5 202 463 556427138 556426867 1.790000e-92 350.0
19 TraesCS6D01G066000 chr7D 96.654 269 7 1 3 271 628617644 628617910 2.220000e-121 446.0
20 TraesCS6D01G066000 chr7D 89.734 263 19 5 202 463 574229316 574229061 2.330000e-86 329.0
21 TraesCS6D01G066000 chr4D 96.642 268 8 1 3 270 378424519 378424785 7.990000e-121 444.0
22 TraesCS6D01G066000 chr3D 90.909 275 9 5 202 463 588120995 588121266 3.850000e-94 355.0
23 TraesCS6D01G066000 chr5A 87.594 266 24 4 203 468 473007718 473007974 1.830000e-77 300.0
24 TraesCS6D01G066000 chr3A 92.208 77 5 1 838 914 518538226 518538301 1.190000e-19 108.0
25 TraesCS6D01G066000 chr2B 81.395 86 12 3 470 553 793520099 793520182 2.020000e-07 67.6


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 TraesCS6D01G066000 chr6D 32317862 32321001 3139 True 5799.00 5799 100.0000 1 3140 1 chr6D.!!$R1 3139
1 TraesCS6D01G066000 chr6A 36702519 36704204 1685 True 2115.00 2115 89.4280 925 2626 1 chr6A.!!$R1 1701
2 TraesCS6D01G066000 chr6B 68003868 68006152 2284 True 1194.50 1882 85.7150 928 3140 2 chr6B.!!$R1 2212
3 TraesCS6D01G066000 chr6B 68107920 68115357 7437 True 649.16 2082 90.1974 469 3077 5 chr6B.!!$R2 2608
4 TraesCS6D01G066000 chr5D 556426867 556427384 517 True 406.00 462 94.1530 3 463 2 chr5D.!!$R1 460

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
729 788 0.037975 GGTACTCGGCGAACAGGAAA 60.038 55.0 12.13 0.0 0.0 3.13 F
732 791 0.391597 ACTCGGCGAACAGGAAAGAA 59.608 50.0 12.13 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 5262 0.608856 GCCACCATCATGTGTGACCA 60.609 55.0 12.28 0.0 37.14 4.02 R
2719 7653 1.318576 AACTTGCTCTTTCGGTTGGG 58.681 50.0 0.00 0.0 0.00 4.12 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
174 175 3.806316 AAACTGAAAAGGCGATACACG 57.194 42.857 0.00 0.00 45.66 4.49
177 178 0.609151 TGAAAAGGCGATACACGGGA 59.391 50.000 0.00 0.00 42.83 5.14
182 183 3.925090 GCGATACACGGGAGGGGG 61.925 72.222 0.00 0.00 42.83 5.40
184 185 2.792947 CGATACACGGGAGGGGGTG 61.793 68.421 0.00 0.00 37.82 4.61
199 200 2.642311 GGGGGTGGGATTTGAAAATTGT 59.358 45.455 0.00 0.00 0.00 2.71
320 378 0.323087 GGCACCAACCGGGACTAAAT 60.323 55.000 6.32 0.00 41.15 1.40
353 411 0.742505 CGGGAGTAATGCCTGTACGA 59.257 55.000 0.00 0.00 0.00 3.43
425 483 5.504994 CGTAATGCAACCGGTATTAATGCTT 60.505 40.000 24.44 17.42 36.10 3.91
463 521 5.476945 CCAAAGCCCATTTTTCTACTAGTGT 59.523 40.000 5.39 0.00 0.00 3.55
464 522 6.657541 CCAAAGCCCATTTTTCTACTAGTGTA 59.342 38.462 5.39 0.00 0.00 2.90
465 523 7.175990 CCAAAGCCCATTTTTCTACTAGTGTAA 59.824 37.037 5.39 0.00 0.00 2.41
466 524 7.923414 AAGCCCATTTTTCTACTAGTGTAAG 57.077 36.000 5.39 0.00 0.00 2.34
467 525 7.017319 AGCCCATTTTTCTACTAGTGTAAGT 57.983 36.000 5.39 0.00 0.00 2.24
508 566 8.627208 AGATTGACAAAATCATTACAGACACT 57.373 30.769 0.00 0.00 37.11 3.55
520 578 2.216046 ACAGACACTTCGTAGTCGACA 58.784 47.619 19.50 0.48 46.03 4.35
524 582 3.501062 AGACACTTCGTAGTCGACATGAA 59.499 43.478 19.50 17.58 46.03 2.57
528 586 5.106436 ACACTTCGTAGTCGACATGAACATA 60.106 40.000 19.50 0.00 46.03 2.29
529 587 5.971792 CACTTCGTAGTCGACATGAACATAT 59.028 40.000 19.50 0.00 46.03 1.78
543 601 4.998788 TGAACATATCCTCTCACTGAACG 58.001 43.478 0.00 0.00 0.00 3.95
545 603 2.760650 ACATATCCTCTCACTGAACGCA 59.239 45.455 0.00 0.00 0.00 5.24
567 625 3.008049 ACATCGCCTTTGACTAGGTTCTT 59.992 43.478 0.00 0.00 37.63 2.52
577 636 7.225538 CCTTTGACTAGGTTCTTGCATACTATG 59.774 40.741 0.00 0.00 0.00 2.23
599 658 4.666237 GCATAAGCAAGTTCCTTCATGTC 58.334 43.478 0.00 0.00 41.58 3.06
600 659 4.439289 GCATAAGCAAGTTCCTTCATGTCC 60.439 45.833 0.00 0.00 41.58 4.02
602 661 0.804989 GCAAGTTCCTTCATGTCCGG 59.195 55.000 0.00 0.00 0.00 5.14
614 673 0.248907 ATGTCCGGCGAGTATGTTCG 60.249 55.000 9.30 0.00 43.23 3.95
645 704 4.372656 CTCGATAGTGTCTCCCATTTTCC 58.627 47.826 0.00 0.00 37.40 3.13
717 776 5.824429 TGTAATCCTATGTTTCGGTACTCG 58.176 41.667 0.00 0.00 40.90 4.18
718 777 4.317671 AATCCTATGTTTCGGTACTCGG 57.682 45.455 0.00 0.00 39.77 4.63
719 778 1.406539 TCCTATGTTTCGGTACTCGGC 59.593 52.381 0.00 0.00 39.77 5.54
720 779 1.474017 CTATGTTTCGGTACTCGGCG 58.526 55.000 0.00 0.00 39.77 6.46
721 780 1.064505 CTATGTTTCGGTACTCGGCGA 59.935 52.381 10.14 10.14 39.77 5.54
722 781 0.244450 ATGTTTCGGTACTCGGCGAA 59.756 50.000 12.13 0.00 39.77 4.70
723 782 0.664166 TGTTTCGGTACTCGGCGAAC 60.664 55.000 12.13 7.17 39.77 3.95
724 783 0.664166 GTTTCGGTACTCGGCGAACA 60.664 55.000 12.13 0.00 39.77 3.18
725 784 0.387622 TTTCGGTACTCGGCGAACAG 60.388 55.000 12.13 8.34 39.77 3.16
727 786 2.693762 CGGTACTCGGCGAACAGGA 61.694 63.158 12.13 0.00 34.75 3.86
729 788 0.037975 GGTACTCGGCGAACAGGAAA 60.038 55.000 12.13 0.00 0.00 3.13
730 789 1.347320 GTACTCGGCGAACAGGAAAG 58.653 55.000 12.13 0.00 0.00 2.62
732 791 0.391597 ACTCGGCGAACAGGAAAGAA 59.608 50.000 12.13 0.00 0.00 2.52
733 792 0.790814 CTCGGCGAACAGGAAAGAAC 59.209 55.000 12.13 0.00 0.00 3.01
734 793 0.391597 TCGGCGAACAGGAAAGAACT 59.608 50.000 7.35 0.00 0.00 3.01
735 794 0.790814 CGGCGAACAGGAAAGAACTC 59.209 55.000 0.00 0.00 0.00 3.01
736 795 0.790814 GGCGAACAGGAAAGAACTCG 59.209 55.000 0.00 0.00 0.00 4.18
738 797 1.872653 GCGAACAGGAAAGAACTCGGT 60.873 52.381 0.00 0.00 0.00 4.69
739 798 2.608752 GCGAACAGGAAAGAACTCGGTA 60.609 50.000 0.00 0.00 0.00 4.02
744 803 4.124970 ACAGGAAAGAACTCGGTAACAAC 58.875 43.478 0.00 0.00 0.00 3.32
746 805 3.135167 AGGAAAGAACTCGGTAACAACCA 59.865 43.478 0.00 0.00 0.00 3.67
747 806 4.070009 GGAAAGAACTCGGTAACAACCAT 58.930 43.478 0.00 0.00 0.00 3.55
748 807 4.517832 GGAAAGAACTCGGTAACAACCATT 59.482 41.667 0.00 0.00 0.00 3.16
749 808 5.009310 GGAAAGAACTCGGTAACAACCATTT 59.991 40.000 0.00 0.00 0.00 2.32
750 809 6.459670 AAAGAACTCGGTAACAACCATTTT 57.540 33.333 0.00 0.00 0.00 1.82
751 810 6.459670 AAGAACTCGGTAACAACCATTTTT 57.540 33.333 0.00 0.00 0.00 1.94
752 811 6.068473 AGAACTCGGTAACAACCATTTTTC 57.932 37.500 0.00 0.00 0.00 2.29
753 812 4.841443 ACTCGGTAACAACCATTTTTCC 57.159 40.909 0.00 0.00 0.00 3.13
754 813 4.208746 ACTCGGTAACAACCATTTTTCCA 58.791 39.130 0.00 0.00 0.00 3.53
755 814 4.277423 ACTCGGTAACAACCATTTTTCCAG 59.723 41.667 0.00 0.00 0.00 3.86
757 816 5.374921 TCGGTAACAACCATTTTTCCAGTA 58.625 37.500 0.00 0.00 0.00 2.74
758 817 5.470777 TCGGTAACAACCATTTTTCCAGTAG 59.529 40.000 0.00 0.00 0.00 2.57
759 818 5.239963 CGGTAACAACCATTTTTCCAGTAGT 59.760 40.000 0.00 0.00 0.00 2.73
761 820 6.263617 GGTAACAACCATTTTTCCAGTAGTGA 59.736 38.462 0.00 0.00 0.00 3.41
777 3744 0.464452 GTGAGGCTGGGCGTACTTAT 59.536 55.000 0.00 0.00 0.00 1.73
778 3745 1.684983 GTGAGGCTGGGCGTACTTATA 59.315 52.381 0.00 0.00 0.00 0.98
779 3746 2.299297 GTGAGGCTGGGCGTACTTATAT 59.701 50.000 0.00 0.00 0.00 0.86
780 3747 3.508793 GTGAGGCTGGGCGTACTTATATA 59.491 47.826 0.00 0.00 0.00 0.86
781 3748 3.508793 TGAGGCTGGGCGTACTTATATAC 59.491 47.826 0.00 0.00 0.00 1.47
782 3749 3.503365 AGGCTGGGCGTACTTATATACA 58.497 45.455 0.00 0.00 0.00 2.29
783 3750 3.510360 AGGCTGGGCGTACTTATATACAG 59.490 47.826 0.00 0.00 0.00 2.74
784 3751 3.257624 GGCTGGGCGTACTTATATACAGT 59.742 47.826 0.00 3.95 0.00 3.55
813 3780 3.680937 CGCGTACAAACCCAAGAGATAAA 59.319 43.478 0.00 0.00 0.00 1.40
816 3783 6.255950 GCGTACAAACCCAAGAGATAAATTC 58.744 40.000 0.00 0.00 0.00 2.17
818 3785 7.279313 GCGTACAAACCCAAGAGATAAATTCTA 59.721 37.037 0.00 0.00 33.74 2.10
819 3786 8.601476 CGTACAAACCCAAGAGATAAATTCTAC 58.399 37.037 0.00 0.00 33.74 2.59
823 3790 8.462016 CAAACCCAAGAGATAAATTCTACTTGG 58.538 37.037 14.36 14.36 46.33 3.61
824 3791 7.272144 ACCCAAGAGATAAATTCTACTTGGT 57.728 36.000 18.14 7.59 45.92 3.67
825 3792 7.699878 ACCCAAGAGATAAATTCTACTTGGTT 58.300 34.615 18.14 5.70 45.92 3.67
826 3793 7.829706 ACCCAAGAGATAAATTCTACTTGGTTC 59.170 37.037 18.14 0.00 45.92 3.62
828 3795 9.454859 CCAAGAGATAAATTCTACTTGGTTCTT 57.545 33.333 0.00 0.00 44.45 2.52
831 3798 8.951243 AGAGATAAATTCTACTTGGTTCTTTGC 58.049 33.333 0.00 0.00 33.74 3.68
833 3800 9.247861 AGATAAATTCTACTTGGTTCTTTGCAT 57.752 29.630 0.00 0.00 30.96 3.96
834 3801 9.294030 GATAAATTCTACTTGGTTCTTTGCATG 57.706 33.333 0.00 0.00 0.00 4.06
835 3802 6.899393 AATTCTACTTGGTTCTTTGCATGA 57.101 33.333 0.00 0.00 0.00 3.07
837 3804 6.707440 TTCTACTTGGTTCTTTGCATGAAA 57.293 33.333 0.00 0.00 0.00 2.69
838 3805 6.707440 TCTACTTGGTTCTTTGCATGAAAA 57.293 33.333 0.00 0.00 0.00 2.29
839 3806 7.288810 TCTACTTGGTTCTTTGCATGAAAAT 57.711 32.000 0.00 0.00 0.00 1.82
840 3807 7.725251 TCTACTTGGTTCTTTGCATGAAAATT 58.275 30.769 0.00 0.00 0.00 1.82
841 3808 6.849588 ACTTGGTTCTTTGCATGAAAATTC 57.150 33.333 0.00 0.00 0.00 2.17
871 4134 6.875195 CGGTTTACAACTCCTAATCCTACAAA 59.125 38.462 0.00 0.00 0.00 2.83
882 4145 5.579511 CCTAATCCTACAAAACCACGTACAG 59.420 44.000 0.00 0.00 0.00 2.74
892 4155 1.286570 CACGTACAGGTGCCGTGTA 59.713 57.895 14.39 3.19 45.00 2.90
899 4162 1.067142 ACAGGTGCCGTGTACATACTG 60.067 52.381 0.00 4.58 33.62 2.74
905 4168 1.997606 GCCGTGTACATACTGGTGTTC 59.002 52.381 0.00 0.00 33.62 3.18
911 4174 5.539048 GTGTACATACTGGTGTTCAAGTCT 58.461 41.667 0.00 0.00 32.38 3.24
915 4178 6.169557 ACATACTGGTGTTCAAGTCTAACA 57.830 37.500 0.00 0.00 34.56 2.41
916 4179 6.769512 ACATACTGGTGTTCAAGTCTAACAT 58.230 36.000 0.00 0.00 38.95 2.71
917 4180 7.903145 ACATACTGGTGTTCAAGTCTAACATA 58.097 34.615 0.00 0.00 38.95 2.29
921 4184 8.773404 ACTGGTGTTCAAGTCTAACATATAAC 57.227 34.615 0.00 0.00 38.95 1.89
922 4185 7.822822 ACTGGTGTTCAAGTCTAACATATAACC 59.177 37.037 0.00 0.00 38.95 2.85
923 4186 7.107542 TGGTGTTCAAGTCTAACATATAACCC 58.892 38.462 0.00 0.00 38.95 4.11
924 4187 7.107542 GGTGTTCAAGTCTAACATATAACCCA 58.892 38.462 0.00 0.00 38.95 4.51
925 4188 7.065443 GGTGTTCAAGTCTAACATATAACCCAC 59.935 40.741 0.00 0.00 38.95 4.61
944 4224 2.223377 CACCTAACAAACTTCTCGGTGC 59.777 50.000 0.00 0.00 34.72 5.01
951 4231 3.380004 ACAAACTTCTCGGTGCATCAAAA 59.620 39.130 0.00 0.00 0.00 2.44
957 4237 0.953471 TCGGTGCATCAAAACCCTCG 60.953 55.000 0.00 0.00 32.44 4.63
972 4252 1.587054 CTCGTCCCCCATCGATAGC 59.413 63.158 0.00 0.00 35.57 2.97
1028 4323 2.355837 GCACTCGCCTGAACGTCA 60.356 61.111 0.00 0.00 0.00 4.35
1132 4430 1.135257 AGCTCATCTTCGACGTCCTTG 60.135 52.381 10.58 0.00 0.00 3.61
1372 4670 2.297129 GGCCTCAGGTTGCTCTCCT 61.297 63.158 0.00 0.00 35.45 3.69
1505 4803 3.218453 ACATCATGTTTGGTTTCGGTCA 58.782 40.909 0.00 0.00 0.00 4.02
1628 4932 2.030401 CCCCAATTCGCGTCAACGA 61.030 57.895 5.77 0.00 43.02 3.85
1635 4939 2.019951 TCGCGTCAACGAAAGCTCC 61.020 57.895 5.77 0.00 43.02 4.70
1730 5034 3.176728 TCGAGAGCGAAGAGTGGAT 57.823 52.632 0.00 0.00 44.78 3.41
1737 5041 2.268920 GAAGAGTGGATGCCGGCA 59.731 61.111 34.80 34.80 0.00 5.69
1888 5192 4.506005 CCAACGTATGGCTGCGTA 57.494 55.556 0.00 0.00 43.16 4.42
1947 5251 4.323562 GCAGCCCCTTCGTCCTATTATTAT 60.324 45.833 0.00 0.00 0.00 1.28
1949 5253 6.338937 CAGCCCCTTCGTCCTATTATTATAC 58.661 44.000 0.00 0.00 0.00 1.47
1953 5257 5.032863 CCTTCGTCCTATTATTATACGCCG 58.967 45.833 0.00 0.00 33.75 6.46
1958 5262 6.032094 CGTCCTATTATTATACGCCGTTGAT 58.968 40.000 0.00 0.00 0.00 2.57
1980 5284 1.068333 GTCACACATGATGGTGGCAAC 60.068 52.381 11.86 0.00 43.08 4.17
1995 5299 4.035675 GGTGGCAACTTGATATTCTACTGC 59.964 45.833 0.00 0.00 37.61 4.40
2016 5320 3.259123 GCTTTTTCCATGGACAAGGACAT 59.741 43.478 22.98 0.00 32.62 3.06
2019 5323 6.518200 GCTTTTTCCATGGACAAGGACATTTA 60.518 38.462 22.98 2.69 32.62 1.40
2026 5330 5.160607 TGGACAAGGACATTTACTTCGAT 57.839 39.130 0.00 0.00 0.00 3.59
2038 5342 6.040616 ACATTTACTTCGATCCTACGATCCTT 59.959 38.462 0.00 0.00 41.77 3.36
2039 5343 7.230108 ACATTTACTTCGATCCTACGATCCTTA 59.770 37.037 0.00 0.00 41.77 2.69
2100 5404 4.709886 AGTACTGAAAAAGTTGGCCTTTGT 59.290 37.500 3.32 0.00 42.62 2.83
2256 5562 0.879765 AAGACATCGTCCGACTCGTT 59.120 50.000 0.00 0.00 32.18 3.85
2411 7251 6.990341 AATTGGCTAATGCATTTTCTTTCC 57.010 33.333 18.75 10.13 41.91 3.13
2448 7288 7.042797 AGGTTTTACATGCATATCATTGTCC 57.957 36.000 0.00 0.00 31.79 4.02
2470 7312 7.935210 TGTCCTTTTCCGAAGTAGAAATAAACT 59.065 33.333 0.00 0.00 0.00 2.66
2474 7316 8.680039 TTTTCCGAAGTAGAAATAAACTTGGA 57.320 30.769 0.00 0.00 0.00 3.53
2477 7319 8.857694 TCCGAAGTAGAAATAAACTTGGAAAT 57.142 30.769 0.00 0.00 0.00 2.17
2478 7320 9.947433 TCCGAAGTAGAAATAAACTTGGAAATA 57.053 29.630 0.00 0.00 0.00 1.40
2479 7321 9.983804 CCGAAGTAGAAATAAACTTGGAAATAC 57.016 33.333 0.00 0.00 0.00 1.89
2513 7355 6.755542 AATCCAAACTAAACCCAATCCAAA 57.244 33.333 0.00 0.00 0.00 3.28
2515 7357 5.212745 TCCAAACTAAACCCAATCCAAACT 58.787 37.500 0.00 0.00 0.00 2.66
2516 7358 5.663556 TCCAAACTAAACCCAATCCAAACTT 59.336 36.000 0.00 0.00 0.00 2.66
2517 7359 5.757808 CCAAACTAAACCCAATCCAAACTTG 59.242 40.000 0.00 0.00 0.00 3.16
2518 7360 6.407525 CCAAACTAAACCCAATCCAAACTTGA 60.408 38.462 0.00 0.00 0.00 3.02
2533 7397 3.113260 ACTTGAAGTGCTACAGTCCAC 57.887 47.619 0.00 0.00 0.00 4.02
2612 7487 1.064003 AGGTCAGGGTTACATGTGCA 58.936 50.000 9.11 0.00 0.00 4.57
2666 7591 5.401531 ACATCGTCTAGGAAGCAAAGTAA 57.598 39.130 0.00 0.00 0.00 2.24
2667 7592 5.169295 ACATCGTCTAGGAAGCAAAGTAAC 58.831 41.667 0.00 0.00 0.00 2.50
2672 7606 4.152580 GTCTAGGAAGCAAAGTAACTGCAC 59.847 45.833 0.00 0.00 42.48 4.57
2719 7653 4.883585 TGCTACAAAATCATCATCCTCACC 59.116 41.667 0.00 0.00 0.00 4.02
2723 7657 4.025360 CAAAATCATCATCCTCACCCCAA 58.975 43.478 0.00 0.00 0.00 4.12
2749 7684 6.237595 CCGAAAGAGCAAGTTAATAAGAGACG 60.238 42.308 0.00 0.00 0.00 4.18
2767 7702 3.308866 AGACGGTGTTTTCAAAAGAGACG 59.691 43.478 3.38 3.38 0.00 4.18
2783 7718 0.320771 GACGGTGCTCAACATCCAGT 60.321 55.000 0.00 0.00 0.00 4.00
2784 7719 0.603707 ACGGTGCTCAACATCCAGTG 60.604 55.000 0.00 0.00 0.00 3.66
2798 7733 3.140325 TCCAGTGGGAACATTCAACTC 57.860 47.619 9.92 0.00 46.14 3.01
2842 7777 9.638239 GTTTTAAAATATGCTTGAGATCAACCA 57.362 29.630 3.52 0.00 0.00 3.67
2848 7783 5.627182 ATGCTTGAGATCAACCAGTAGAT 57.373 39.130 0.00 0.00 0.00 1.98
2981 7922 1.890041 CAAACCAGGCGACAACCGA 60.890 57.895 0.00 0.00 41.76 4.69
3017 7963 4.934075 ACACTGAATGAACATGATCACG 57.066 40.909 7.94 0.00 30.82 4.35
3021 7968 3.598299 TGAATGAACATGATCACGCTGA 58.402 40.909 7.94 0.00 30.82 4.26
3030 7977 1.878734 TGATCACGCTGATTGCACAAA 59.121 42.857 0.00 0.00 37.20 2.83
3073 8020 0.755686 TGGTTGGACCCAAAACATGC 59.244 50.000 2.62 0.00 37.50 4.06
3078 8025 2.323599 TGGACCCAAAACATGCATTGA 58.676 42.857 11.52 0.00 0.00 2.57
3080 8027 3.327172 TGGACCCAAAACATGCATTGAAT 59.673 39.130 11.52 1.12 0.00 2.57
3081 8028 4.202440 TGGACCCAAAACATGCATTGAATT 60.202 37.500 11.52 0.00 0.00 2.17
3082 8029 4.154556 GGACCCAAAACATGCATTGAATTG 59.845 41.667 11.52 0.33 0.00 2.32
3088 8045 7.094720 CCCAAAACATGCATTGAATTGTACATT 60.095 33.333 11.52 0.00 0.00 2.71
3108 8065 7.749539 ACATTGTACTTTCTTTTGTTTTCGG 57.250 32.000 0.00 0.00 0.00 4.30
3109 8066 7.317390 ACATTGTACTTTCTTTTGTTTTCGGT 58.683 30.769 0.00 0.00 0.00 4.69
3112 8069 6.324042 TGTACTTTCTTTTGTTTTCGGTTCC 58.676 36.000 0.00 0.00 0.00 3.62
3113 8070 4.417506 ACTTTCTTTTGTTTTCGGTTCCG 58.582 39.130 4.74 4.74 0.00 4.30
3130 8087 1.346395 TCCGCCTCTGCTTGAACTTTA 59.654 47.619 0.00 0.00 34.43 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.457436 AGGGAAAATGTAAAACGACTATAACAT 57.543 29.630 0.00 0.00 0.00 2.71
1 2 8.851541 AGGGAAAATGTAAAACGACTATAACA 57.148 30.769 0.00 0.00 0.00 2.41
9 10 7.571080 AAAGTGTAGGGAAAATGTAAAACGA 57.429 32.000 0.00 0.00 0.00 3.85
174 175 1.514864 TTCAAATCCCACCCCCTCCC 61.515 60.000 0.00 0.00 0.00 4.30
177 178 2.912295 CAATTTTCAAATCCCACCCCCT 59.088 45.455 0.00 0.00 0.00 4.79
199 200 2.426738 CCACGAACCGGTACTAATGGTA 59.573 50.000 8.00 0.00 34.11 3.25
320 378 0.037590 CTCCCGGTTCAAATGGGACA 59.962 55.000 0.00 0.00 46.96 4.02
377 435 3.199071 ACCGGGACTAATGTGAGCATTAA 59.801 43.478 6.32 0.00 44.23 1.40
463 521 9.093458 TCAATCTCAAGATGATATGCCTACTTA 57.907 33.333 0.00 0.00 34.49 2.24
464 522 7.877097 GTCAATCTCAAGATGATATGCCTACTT 59.123 37.037 0.00 0.00 34.49 2.24
465 523 7.015974 TGTCAATCTCAAGATGATATGCCTACT 59.984 37.037 0.00 0.00 34.49 2.57
466 524 7.157347 TGTCAATCTCAAGATGATATGCCTAC 58.843 38.462 0.00 0.00 34.49 3.18
467 525 7.307131 TGTCAATCTCAAGATGATATGCCTA 57.693 36.000 0.00 0.00 34.49 3.93
520 578 5.595885 CGTTCAGTGAGAGGATATGTTCAT 58.404 41.667 0.00 0.00 0.00 2.57
524 582 2.760650 TGCGTTCAGTGAGAGGATATGT 59.239 45.455 0.00 0.00 0.00 2.29
528 586 0.969149 TGTGCGTTCAGTGAGAGGAT 59.031 50.000 0.00 0.00 0.00 3.24
529 587 0.969149 ATGTGCGTTCAGTGAGAGGA 59.031 50.000 0.00 0.00 0.00 3.71
543 601 1.009829 CCTAGTCAAAGGCGATGTGC 58.990 55.000 0.00 0.00 45.38 4.57
545 603 2.567615 AGAACCTAGTCAAAGGCGATGT 59.432 45.455 0.00 0.00 40.62 3.06
599 658 2.960129 GCCGAACATACTCGCCGG 60.960 66.667 0.00 0.00 42.74 6.13
600 659 3.320078 CGCCGAACATACTCGCCG 61.320 66.667 0.00 0.00 37.51 6.46
602 661 3.972803 CGCGCCGAACATACTCGC 61.973 66.667 0.00 0.00 42.05 5.03
685 744 7.280205 CCGAAACATAGGATTACAGTAAAAGCT 59.720 37.037 0.00 0.00 0.00 3.74
702 761 1.093972 TCGCCGAGTACCGAAACATA 58.906 50.000 5.46 0.00 41.76 2.29
717 776 0.790814 CGAGTTCTTTCCTGTTCGCC 59.209 55.000 0.00 0.00 0.00 5.54
718 777 0.790814 CCGAGTTCTTTCCTGTTCGC 59.209 55.000 0.00 0.00 0.00 4.70
719 778 2.150397 ACCGAGTTCTTTCCTGTTCG 57.850 50.000 0.00 0.00 0.00 3.95
720 779 4.374399 TGTTACCGAGTTCTTTCCTGTTC 58.626 43.478 0.00 0.00 0.00 3.18
721 780 4.411256 TGTTACCGAGTTCTTTCCTGTT 57.589 40.909 0.00 0.00 0.00 3.16
722 781 4.124970 GTTGTTACCGAGTTCTTTCCTGT 58.875 43.478 0.00 0.00 0.00 4.00
723 782 3.497262 GGTTGTTACCGAGTTCTTTCCTG 59.503 47.826 0.00 0.00 34.01 3.86
724 783 3.736720 GGTTGTTACCGAGTTCTTTCCT 58.263 45.455 0.00 0.00 34.01 3.36
736 795 6.263617 TCACTACTGGAAAAATGGTTGTTACC 59.736 38.462 0.00 0.00 45.26 2.85
738 797 6.488683 CCTCACTACTGGAAAAATGGTTGTTA 59.511 38.462 0.00 0.00 0.00 2.41
739 798 5.301805 CCTCACTACTGGAAAAATGGTTGTT 59.698 40.000 0.00 0.00 0.00 2.83
744 803 3.441572 CAGCCTCACTACTGGAAAAATGG 59.558 47.826 0.00 0.00 0.00 3.16
753 812 1.320344 TACGCCCAGCCTCACTACTG 61.320 60.000 0.00 0.00 0.00 2.74
754 813 1.000019 TACGCCCAGCCTCACTACT 60.000 57.895 0.00 0.00 0.00 2.57
755 814 1.141234 GTACGCCCAGCCTCACTAC 59.859 63.158 0.00 0.00 0.00 2.73
757 816 0.613853 TAAGTACGCCCAGCCTCACT 60.614 55.000 0.00 0.00 0.00 3.41
758 817 0.464452 ATAAGTACGCCCAGCCTCAC 59.536 55.000 0.00 0.00 0.00 3.51
759 818 2.076207 TATAAGTACGCCCAGCCTCA 57.924 50.000 0.00 0.00 0.00 3.86
761 820 3.503365 TGTATATAAGTACGCCCAGCCT 58.497 45.455 0.00 0.00 0.00 4.58
777 3744 6.690957 GGTTTGTACGCGTGTATAACTGTATA 59.309 38.462 24.59 8.42 32.27 1.47
778 3745 5.516339 GGTTTGTACGCGTGTATAACTGTAT 59.484 40.000 24.59 0.00 32.27 2.29
779 3746 4.856487 GGTTTGTACGCGTGTATAACTGTA 59.144 41.667 24.59 9.24 32.27 2.74
780 3747 3.674753 GGTTTGTACGCGTGTATAACTGT 59.325 43.478 24.59 0.00 32.27 3.55
781 3748 3.061161 GGGTTTGTACGCGTGTATAACTG 59.939 47.826 24.59 0.00 32.27 3.16
782 3749 3.253230 GGGTTTGTACGCGTGTATAACT 58.747 45.455 24.59 0.00 32.27 2.24
783 3750 2.992543 TGGGTTTGTACGCGTGTATAAC 59.007 45.455 24.59 18.74 39.90 1.89
784 3751 3.309961 TGGGTTTGTACGCGTGTATAA 57.690 42.857 24.59 13.10 39.90 0.98
813 3780 6.899393 TTCATGCAAAGAACCAAGTAGAAT 57.101 33.333 0.00 0.00 0.00 2.40
816 3783 7.869429 AGAATTTTCATGCAAAGAACCAAGTAG 59.131 33.333 4.62 0.00 0.00 2.57
818 3785 6.585416 AGAATTTTCATGCAAAGAACCAAGT 58.415 32.000 4.62 0.00 0.00 3.16
819 3786 7.869429 AGTAGAATTTTCATGCAAAGAACCAAG 59.131 33.333 4.62 0.00 0.00 3.61
823 3790 6.524586 CCGAGTAGAATTTTCATGCAAAGAAC 59.475 38.462 4.62 0.00 0.00 3.01
824 3791 6.206634 ACCGAGTAGAATTTTCATGCAAAGAA 59.793 34.615 0.00 0.00 0.00 2.52
825 3792 5.705441 ACCGAGTAGAATTTTCATGCAAAGA 59.295 36.000 0.00 0.00 0.00 2.52
826 3793 5.942872 ACCGAGTAGAATTTTCATGCAAAG 58.057 37.500 0.00 0.00 0.00 2.77
828 3795 5.957842 AACCGAGTAGAATTTTCATGCAA 57.042 34.783 0.00 0.00 0.00 4.08
829 3796 5.957842 AAACCGAGTAGAATTTTCATGCA 57.042 34.783 0.00 0.00 0.00 3.96
831 3798 8.655378 GTTGTAAACCGAGTAGAATTTTCATG 57.345 34.615 0.00 0.00 42.21 3.07
871 4134 2.029964 CGGCACCTGTACGTGGTT 59.970 61.111 7.53 0.00 35.28 3.67
882 4145 0.248289 ACCAGTATGTACACGGCACC 59.752 55.000 0.00 0.00 0.00 5.01
892 4155 6.169557 TGTTAGACTTGAACACCAGTATGT 57.830 37.500 0.00 0.00 31.92 2.29
899 4162 7.065443 GTGGGTTATATGTTAGACTTGAACACC 59.935 40.741 0.00 0.00 39.51 4.16
905 4168 8.262227 TGTTAGGTGGGTTATATGTTAGACTTG 58.738 37.037 0.00 0.00 0.00 3.16
911 4174 9.452287 GAAGTTTGTTAGGTGGGTTATATGTTA 57.548 33.333 0.00 0.00 0.00 2.41
915 4178 7.046033 CGAGAAGTTTGTTAGGTGGGTTATAT 58.954 38.462 0.00 0.00 0.00 0.86
916 4179 6.400568 CGAGAAGTTTGTTAGGTGGGTTATA 58.599 40.000 0.00 0.00 0.00 0.98
917 4180 5.243207 CGAGAAGTTTGTTAGGTGGGTTAT 58.757 41.667 0.00 0.00 0.00 1.89
919 4182 3.473625 CGAGAAGTTTGTTAGGTGGGTT 58.526 45.455 0.00 0.00 0.00 4.11
920 4183 2.224450 CCGAGAAGTTTGTTAGGTGGGT 60.224 50.000 0.00 0.00 0.00 4.51
921 4184 2.224450 ACCGAGAAGTTTGTTAGGTGGG 60.224 50.000 0.00 0.00 0.00 4.61
922 4185 2.806244 CACCGAGAAGTTTGTTAGGTGG 59.194 50.000 3.98 0.00 42.65 4.61
924 4187 2.158871 TGCACCGAGAAGTTTGTTAGGT 60.159 45.455 0.00 0.00 0.00 3.08
925 4188 2.489971 TGCACCGAGAAGTTTGTTAGG 58.510 47.619 0.00 0.00 0.00 2.69
944 4224 0.679960 GGGGGACGAGGGTTTTGATG 60.680 60.000 0.00 0.00 0.00 3.07
951 4231 2.015243 TATCGATGGGGGACGAGGGT 62.015 60.000 8.54 0.00 41.63 4.34
957 4237 1.128188 AAGGGCTATCGATGGGGGAC 61.128 60.000 8.54 0.00 0.00 4.46
972 4252 3.846430 GGCGGTAGACGGGAAGGG 61.846 72.222 0.00 0.00 44.51 3.95
1197 4495 4.480480 AGGAAGGCCTGATCGGAA 57.520 55.556 5.69 0.00 44.90 4.30
1255 4553 3.866582 CGGGGAGGAGGTGATGGC 61.867 72.222 0.00 0.00 0.00 4.40
1349 4647 2.674380 GCAACCTGAGGCCACCAG 60.674 66.667 15.84 15.84 0.00 4.00
1350 4648 3.177884 AGCAACCTGAGGCCACCA 61.178 61.111 5.01 0.71 0.00 4.17
1351 4649 2.360475 GAGCAACCTGAGGCCACC 60.360 66.667 5.01 0.00 0.00 4.61
1372 4670 2.801421 GAGCTCATCCGTGCTCGA 59.199 61.111 9.40 0.00 45.72 4.04
1407 4705 0.316607 CGATCACGCGAGAGGAAGAG 60.317 60.000 15.93 0.00 0.00 2.85
1628 4932 1.600916 GCGGTGACTTGGGAGCTTT 60.601 57.895 0.00 0.00 0.00 3.51
1635 4939 2.993471 GCCATTGGCGGTGACTTGG 61.993 63.158 12.82 0.00 39.62 3.61
1730 5034 3.293702 GGCCTTTTATTGCCGGCA 58.706 55.556 29.03 29.03 44.23 5.69
1737 5041 1.951602 GTTATCGGCGGGCCTTTTATT 59.048 47.619 7.21 0.00 0.00 1.40
1819 5123 4.578871 TCCGATTGAATCACACACAAGAT 58.421 39.130 5.95 0.00 0.00 2.40
1884 5188 2.941453 TCCAAGAGTCATCAGTACGC 57.059 50.000 0.00 0.00 0.00 4.42
1888 5192 4.260170 GCTTTGATCCAAGAGTCATCAGT 58.740 43.478 10.62 0.00 0.00 3.41
1947 5251 0.668096 GTGTGACCATCAACGGCGTA 60.668 55.000 15.20 0.00 0.00 4.42
1949 5253 1.298157 ATGTGTGACCATCAACGGCG 61.298 55.000 4.80 4.80 0.00 6.46
1953 5257 3.084039 ACCATCATGTGTGACCATCAAC 58.916 45.455 0.00 0.00 37.14 3.18
1958 5262 0.608856 GCCACCATCATGTGTGACCA 60.609 55.000 12.28 0.00 37.14 4.02
1980 5284 8.133627 CCATGGAAAAAGCAGTAGAATATCAAG 58.866 37.037 5.56 0.00 0.00 3.02
1995 5299 5.473066 AATGTCCTTGTCCATGGAAAAAG 57.527 39.130 18.20 21.40 36.55 2.27
2026 5330 3.194116 GTGTTGGTGTAAGGATCGTAGGA 59.806 47.826 0.00 0.00 0.00 2.94
2038 5342 2.544686 GCGTTGTACATGTGTTGGTGTA 59.455 45.455 9.11 0.00 0.00 2.90
2039 5343 1.332375 GCGTTGTACATGTGTTGGTGT 59.668 47.619 9.11 0.00 0.00 4.16
2100 5404 2.335316 AACGGTCCAAGTGCAAACTA 57.665 45.000 0.00 0.00 0.00 2.24
2256 5562 9.587772 TCGAAACATTCCATAAAACTTTCAAAA 57.412 25.926 0.00 0.00 0.00 2.44
2342 7180 2.965831 TCAGTCAAGTAGTCAAGTGCCT 59.034 45.455 0.00 0.00 0.00 4.75
2411 7251 6.311200 GCATGTAAAACCTAATGCTTTCCAAG 59.689 38.462 0.00 0.00 41.71 3.61
2448 7288 8.780249 TCCAAGTTTATTTCTACTTCGGAAAAG 58.220 33.333 0.00 0.00 36.47 2.27
2470 7312 9.575868 TTGGATTACAAACTACAGTATTTCCAA 57.424 29.630 0.00 0.00 38.80 3.53
2513 7355 2.434336 TGTGGACTGTAGCACTTCAAGT 59.566 45.455 0.00 0.00 0.00 3.16
2515 7357 2.434336 AGTGTGGACTGTAGCACTTCAA 59.566 45.455 5.82 0.00 38.86 2.69
2516 7358 2.039418 AGTGTGGACTGTAGCACTTCA 58.961 47.619 5.82 0.00 38.86 3.02
2517 7359 2.408050 CAGTGTGGACTGTAGCACTTC 58.592 52.381 8.13 0.00 44.15 3.01
2518 7360 2.533266 CAGTGTGGACTGTAGCACTT 57.467 50.000 8.13 0.00 44.15 3.16
2533 7397 2.929398 GGTTTGGCTTGAAAACACAGTG 59.071 45.455 0.00 0.00 38.91 3.66
2651 7576 4.065088 TGTGCAGTTACTTTGCTTCCTAG 58.935 43.478 0.00 0.00 42.02 3.02
2652 7577 3.813166 GTGTGCAGTTACTTTGCTTCCTA 59.187 43.478 0.00 0.00 42.02 2.94
2666 7591 3.569277 TGCATCTTGTAATTGTGTGCAGT 59.431 39.130 0.00 0.00 36.33 4.40
2667 7592 4.163458 TGCATCTTGTAATTGTGTGCAG 57.837 40.909 0.00 0.00 36.33 4.41
2672 7606 6.910972 CAGCTTAGATGCATCTTGTAATTGTG 59.089 38.462 32.94 15.76 38.32 3.33
2719 7653 1.318576 AACTTGCTCTTTCGGTTGGG 58.681 50.000 0.00 0.00 0.00 4.12
2723 7657 6.590677 GTCTCTTATTAACTTGCTCTTTCGGT 59.409 38.462 0.00 0.00 0.00 4.69
2749 7684 3.691498 CACCGTCTCTTTTGAAAACACC 58.309 45.455 0.00 0.00 0.00 4.16
2767 7702 0.962356 CCCACTGGATGTTGAGCACC 60.962 60.000 0.00 0.00 0.00 5.01
2783 7718 8.642935 TGTAATAATTGAGTTGAATGTTCCCA 57.357 30.769 0.00 0.00 0.00 4.37
2830 7765 5.485353 ACCTCAATCTACTGGTTGATCTCAA 59.515 40.000 0.00 0.00 34.18 3.02
2842 7777 3.697045 CGGAGTCTCAACCTCAATCTACT 59.303 47.826 1.47 0.00 0.00 2.57
2848 7783 1.671742 GCCGGAGTCTCAACCTCAA 59.328 57.895 5.05 0.00 0.00 3.02
2880 7815 4.508461 TCGGATTCAAGTCGTCTTTGTA 57.492 40.909 0.00 0.00 0.00 2.41
2881 7816 3.380479 TCGGATTCAAGTCGTCTTTGT 57.620 42.857 0.00 0.00 0.00 2.83
2884 7819 2.233922 ACCATCGGATTCAAGTCGTCTT 59.766 45.455 0.00 0.00 0.00 3.01
2919 7860 6.129874 ACACTATACTAGTCATTGAGGCTGA 58.870 40.000 0.00 0.00 36.76 4.26
2929 7870 6.884836 TCTGCTTCTCAACACTATACTAGTCA 59.115 38.462 0.00 0.00 36.76 3.41
2947 7888 5.693555 CCTGGTTTGATTTCTTTTCTGCTTC 59.306 40.000 0.00 0.00 0.00 3.86
2953 7894 3.981416 GTCGCCTGGTTTGATTTCTTTTC 59.019 43.478 0.00 0.00 0.00 2.29
2981 7922 7.431249 TCATTCAGTGTTAGAACTAGTCGTTT 58.569 34.615 0.00 0.00 35.56 3.60
3017 7963 5.910637 TGATTTCTTTTTGTGCAATCAGC 57.089 34.783 0.00 0.00 45.96 4.26
3021 7968 6.063404 ACCCATTGATTTCTTTTTGTGCAAT 58.937 32.000 0.00 0.00 0.00 3.56
3062 8009 5.699915 TGTACAATTCAATGCATGTTTTGGG 59.300 36.000 0.00 0.00 0.00 4.12
3070 8017 9.357652 GAAAGTACAATGTACAATTCAATGCAT 57.642 29.630 23.52 0.00 0.00 3.96
3081 8028 9.279904 CGAAAACAAAAGAAAGTACAATGTACA 57.720 29.630 23.52 0.00 0.00 2.90
3082 8029 8.739461 CCGAAAACAAAAGAAAGTACAATGTAC 58.261 33.333 15.22 15.22 0.00 2.90
3088 8045 6.324042 GGAACCGAAAACAAAAGAAAGTACA 58.676 36.000 0.00 0.00 0.00 2.90
3113 8070 6.149474 TGACTAAATAAAGTTCAAGCAGAGGC 59.851 38.462 0.00 0.00 41.61 4.70


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

AutoCloner maintained by Alex Coulton.