Multiple sequence alignment - TraesCS1B01G419100

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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 TraesCS1B01G419100 chr1B 100.000 4875 0 0 1 4875 642674782 642679656 0.000000e+00 9003.0
1 TraesCS1B01G419100 chr1B 100.000 85 0 0 4781 4865 642734858 642734942 1.820000e-34 158.0
2 TraesCS1B01G419100 chr1D 94.518 2426 84 15 2075 4471 465887260 465889665 0.000000e+00 3698.0
3 TraesCS1B01G419100 chr1D 93.487 2088 87 35 1 2073 465885094 465887147 0.000000e+00 3057.0
4 TraesCS1B01G419100 chr1D 90.187 214 18 3 4665 4875 465889852 465890065 4.810000e-70 276.0
5 TraesCS1B01G419100 chr1D 96.875 96 2 1 4780 4875 362603831 362603737 5.050000e-35 159.0
6 TraesCS1B01G419100 chr1D 100.000 84 0 0 4781 4864 465942180 465942263 6.530000e-34 156.0
7 TraesCS1B01G419100 chr1A 91.083 2456 152 29 43 2473 558184385 558186798 0.000000e+00 3260.0
8 TraesCS1B01G419100 chr1A 87.955 1071 72 36 3517 4580 558188349 558189369 0.000000e+00 1210.0
9 TraesCS1B01G419100 chr1A 88.413 1027 59 20 2515 3500 558187225 558188232 0.000000e+00 1182.0
10 TraesCS1B01G419100 chr1A 87.143 210 25 2 4658 4865 558189500 558189709 2.270000e-58 237.0
11 TraesCS1B01G419100 chr1A 96.875 96 3 0 4780 4875 462120054 462119959 1.400000e-35 161.0
12 TraesCS1B01G419100 chr1A 97.917 48 0 1 11 57 558184321 558184368 1.120000e-11 82.4
13 TraesCS1B01G419100 chr5B 95.918 98 2 2 4780 4875 685441436 685441339 1.820000e-34 158.0
14 TraesCS1B01G419100 chr5D 96.774 93 3 0 4782 4874 543608516 543608424 6.530000e-34 156.0
15 TraesCS1B01G419100 chr4A 95.833 96 3 1 4769 4863 625489813 625489908 2.350000e-33 154.0


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 TraesCS1B01G419100 chr1B 642674782 642679656 4874 False 9003.000000 9003 100.000000 1 4875 1 chr1B.!!$F1 4874
1 TraesCS1B01G419100 chr1D 465885094 465890065 4971 False 2343.666667 3698 92.730667 1 4875 3 chr1D.!!$F2 4874
2 TraesCS1B01G419100 chr1A 558184321 558189709 5388 False 1194.280000 3260 90.502200 11 4865 5 chr1A.!!$F1 4854

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
86 120 0.521735 GATGGAAAGAACACCGTGGC 59.478 55.000 3.03 0.0 0.00 5.01 F
607 668 0.681243 GGGGTTCCAGTTCATGCTCC 60.681 60.000 0.00 0.0 0.00 4.70 F
610 671 1.003580 GGTTCCAGTTCATGCTCCTGA 59.996 52.381 7.43 0.0 0.00 3.86 F
950 1022 1.008329 GCATGAGCAGAAGAGACAGC 58.992 55.000 0.00 0.0 41.58 4.40 F
1119 1191 1.078759 CGCCGTCTCCTAAACTGCTG 61.079 60.000 0.00 0.0 0.00 4.41 F
1179 1251 1.088340 CGCTGGCATCTCTGGACTTG 61.088 60.000 0.00 0.0 0.00 3.16 F
3321 3905 2.413837 CAGGTGAGTTTGTCCCTAACG 58.586 52.381 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1827 0.723981 GACAGACAGCAATCTTCCGC 59.276 55.000 0.00 0.0 0.00 5.54 R
2167 2353 1.342074 AGGTGCTGTCTCTGCTTACA 58.658 50.000 0.00 0.0 0.00 2.41 R
2268 2454 2.731572 ACTTGCTTCATTGGCTGCTAT 58.268 42.857 0.00 0.0 0.00 2.97 R
2922 3506 6.457159 TCACCTCCTAAACCAAATTCCTAA 57.543 37.500 0.00 0.0 0.00 2.69 R
3321 3905 7.148755 CCATTAAAACATAGTGCTGAAGTTTGC 60.149 37.037 0.00 0.0 33.19 3.68 R
3367 3965 4.826274 AATTCAACTAGCCTGCAGTAGA 57.174 40.909 13.81 0.0 0.00 2.59 R
4206 4923 0.032952 GAAAAAGGCCGTGGGGAAAC 59.967 55.000 0.00 0.0 34.06 2.78 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
47 81 2.571212 TGGTACACACAAAGCAAGAGG 58.429 47.619 0.00 0.00 0.00 3.69
48 82 1.880027 GGTACACACAAAGCAAGAGGG 59.120 52.381 0.00 0.00 0.00 4.30
52 86 1.228675 CACAAAGCAAGAGGGGGCT 60.229 57.895 0.00 0.00 43.46 5.19
54 88 1.381851 CAAAGCAAGAGGGGGCTCT 59.618 57.895 0.00 0.00 40.01 4.09
57 91 1.372501 AAGCAAGAGGGGGCTCTTTA 58.627 50.000 0.00 0.00 41.28 1.85
70 104 4.158579 GGGGCTCTTTAAAAGAACTGGATG 59.841 45.833 0.00 0.00 37.02 3.51
86 120 0.521735 GATGGAAAGAACACCGTGGC 59.478 55.000 3.03 0.00 0.00 5.01
161 195 2.603173 CGAGAAAAAGGTCACAGCTTGC 60.603 50.000 0.00 0.00 35.89 4.01
293 341 3.054361 ACCAACTCCTCTCTCTCTCTCTC 60.054 52.174 0.00 0.00 0.00 3.20
294 342 3.200825 CCAACTCCTCTCTCTCTCTCTCT 59.799 52.174 0.00 0.00 0.00 3.10
327 375 3.532155 TGGTTGCGCCACCAAACC 61.532 61.111 29.42 22.90 44.30 3.27
475 530 3.931375 TACCCCCACCCGTCCAGT 61.931 66.667 0.00 0.00 0.00 4.00
476 531 3.910784 TACCCCCACCCGTCCAGTC 62.911 68.421 0.00 0.00 0.00 3.51
482 537 3.602030 ACCCGTCCAGTCCTCCCT 61.602 66.667 0.00 0.00 0.00 4.20
486 541 2.365768 GTCCAGTCCTCCCTCCCC 60.366 72.222 0.00 0.00 0.00 4.81
509 568 1.338020 CCCTGTTCTGTTCTGGTTTGC 59.662 52.381 0.00 0.00 0.00 3.68
510 569 2.301346 CCTGTTCTGTTCTGGTTTGCT 58.699 47.619 0.00 0.00 0.00 3.91
511 570 2.689983 CCTGTTCTGTTCTGGTTTGCTT 59.310 45.455 0.00 0.00 0.00 3.91
512 571 3.489738 CCTGTTCTGTTCTGGTTTGCTTG 60.490 47.826 0.00 0.00 0.00 4.01
513 572 2.159254 TGTTCTGTTCTGGTTTGCTTGC 60.159 45.455 0.00 0.00 0.00 4.01
607 668 0.681243 GGGGTTCCAGTTCATGCTCC 60.681 60.000 0.00 0.00 0.00 4.70
609 670 1.457346 GGTTCCAGTTCATGCTCCTG 58.543 55.000 0.00 0.00 0.00 3.86
610 671 1.003580 GGTTCCAGTTCATGCTCCTGA 59.996 52.381 7.43 0.00 0.00 3.86
615 676 3.265221 TCCAGTTCATGCTCCTGATTCTT 59.735 43.478 7.43 0.00 0.00 2.52
627 688 5.486526 CTCCTGATTCTTTACTTCTGCTGT 58.513 41.667 0.00 0.00 0.00 4.40
631 692 5.482908 TGATTCTTTACTTCTGCTGTCCTC 58.517 41.667 0.00 0.00 0.00 3.71
644 705 2.293399 GCTGTCCTCGATTTTTGTTGGT 59.707 45.455 0.00 0.00 0.00 3.67
655 716 1.180907 TTTGTTGGTGCTGTTGCTGA 58.819 45.000 0.00 0.00 40.48 4.26
664 725 2.031012 TGTTGCTGAGCGGTGGAG 59.969 61.111 0.00 0.00 0.00 3.86
700 762 1.209504 TGGATCGGAAATCGGCTCTTT 59.790 47.619 0.00 0.00 39.77 2.52
736 799 4.351874 TTCTTGAAGTCTGGGGTTAGTG 57.648 45.455 0.00 0.00 0.00 2.74
744 807 1.854280 TCTGGGGTTAGTGGTTGGTTT 59.146 47.619 0.00 0.00 0.00 3.27
754 817 2.812011 AGTGGTTGGTTTAGTCGATTGC 59.188 45.455 0.00 0.00 0.00 3.56
764 832 2.361104 TCGATTGCTGTTGGGGGC 60.361 61.111 0.00 0.00 0.00 5.80
774 842 1.450312 GTTGGGGGCAGATGTCTCG 60.450 63.158 0.00 0.00 0.00 4.04
785 853 2.872858 CAGATGTCTCGTCTCCGTGATA 59.127 50.000 0.00 0.00 38.65 2.15
788 856 2.277969 TGTCTCGTCTCCGTGATACTC 58.722 52.381 0.00 0.00 38.65 2.59
795 863 3.376234 CGTCTCCGTGATACTCTTTGGTA 59.624 47.826 0.00 0.00 0.00 3.25
857 925 7.334421 ACAAGTGGTTATAATTGCTGTACTGAG 59.666 37.037 3.61 0.00 0.00 3.35
880 952 4.681744 CTCTACTTTCAGCTGAGCTAAGG 58.318 47.826 23.84 11.45 36.40 2.69
885 957 2.322355 TCAGCTGAGCTAAGGCAATC 57.678 50.000 13.74 0.00 36.40 2.67
950 1022 1.008329 GCATGAGCAGAAGAGACAGC 58.992 55.000 0.00 0.00 41.58 4.40
963 1035 3.172339 AGAGACAGCAGGAGAAGTGATT 58.828 45.455 0.00 0.00 0.00 2.57
971 1043 3.190118 GCAGGAGAAGTGATTTTGGACTG 59.810 47.826 0.00 0.00 0.00 3.51
991 1063 7.162082 GGACTGAACTTCTGAGAAATTTAGGA 58.838 38.462 11.84 0.00 0.00 2.94
1119 1191 1.078759 CGCCGTCTCCTAAACTGCTG 61.079 60.000 0.00 0.00 0.00 4.41
1179 1251 1.088340 CGCTGGCATCTCTGGACTTG 61.088 60.000 0.00 0.00 0.00 3.16
1344 1416 3.303725 CGGTCGATGTCTCTCAGAAGATC 60.304 52.174 0.00 0.00 0.00 2.75
1740 1812 2.617308 CAGGCATATTGTCTGCAGGAAG 59.383 50.000 15.13 0.00 43.65 3.46
1749 1821 5.489792 TTGTCTGCAGGAAGAATCTTACT 57.510 39.130 15.13 0.98 0.00 2.24
1755 1827 5.724328 TGCAGGAAGAATCTTACTAGTGTG 58.276 41.667 7.52 0.00 0.00 3.82
1782 1854 4.660168 AGATTGCTGTCTGTCAAAGGAAT 58.340 39.130 0.00 0.00 35.05 3.01
2050 2125 5.470098 TGTAGATTCTGGTTTCTTTGCTCAC 59.530 40.000 0.00 0.00 0.00 3.51
2119 2305 6.472016 TGTTACATCTTCCTTGCTTATGACA 58.528 36.000 0.00 0.00 0.00 3.58
2167 2353 3.872511 TGATCCTTGCGCATGAAATTT 57.127 38.095 23.56 3.15 0.00 1.82
2195 2381 4.621747 GCAGAGACAGCACCTAGTAAATGT 60.622 45.833 0.00 0.00 0.00 2.71
2223 2409 7.704472 GTCTTCTCAAGGAATATATGGCTATCG 59.296 40.741 0.00 0.00 33.01 2.92
2268 2454 2.886913 TGGATGCCACTTGGATTTTGA 58.113 42.857 0.00 0.00 37.39 2.69
2309 2498 6.932356 AGTTTAATCTCATACACATGGCTG 57.068 37.500 0.00 0.00 32.61 4.85
2442 2631 5.112686 CCTTCTCTCCACTAGAAAAATCCG 58.887 45.833 0.00 0.00 32.77 4.18
2478 2667 6.315891 TCCCTTTTCTTTTTGCAACAAATCAG 59.684 34.615 0.00 0.00 0.00 2.90
2891 3475 9.672086 CTTTTTATTAAGAAAACGGACATGTCA 57.328 29.630 26.47 2.93 0.00 3.58
2895 3479 6.869315 TTAAGAAAACGGACATGTCATGAA 57.131 33.333 26.47 5.03 0.00 2.57
3321 3905 2.413837 CAGGTGAGTTTGTCCCTAACG 58.586 52.381 0.00 0.00 0.00 3.18
3331 3915 2.489971 TGTCCCTAACGCAAACTTCAG 58.510 47.619 0.00 0.00 0.00 3.02
3367 3965 5.612725 TGGAACTTCCTTTCTGCAAAATT 57.387 34.783 9.31 0.00 37.46 1.82
3394 3992 6.889198 ACTGCAGGCTAGTTGAATTTCTATA 58.111 36.000 19.93 0.00 0.00 1.31
3439 4039 7.145932 ACTGCACAGTACCTATCAATTTTTC 57.854 36.000 0.35 0.00 40.43 2.29
3525 4222 1.880027 GATCAAGACAAAACCAGCCGT 59.120 47.619 0.00 0.00 0.00 5.68
3548 4261 7.660208 CCGTGGGATATTTTAAGCAACTATAGT 59.340 37.037 0.00 0.00 0.00 2.12
3587 4300 5.857471 AGAAAATGCTGCATTATGGCTAA 57.143 34.783 26.48 0.00 32.43 3.09
3615 4328 4.993584 GTGACCTGATATGAAGCCATACAG 59.006 45.833 0.00 0.00 38.02 2.74
3664 4377 8.837788 TGGATAACAGAATTCATGTAGCATAG 57.162 34.615 8.44 0.00 0.00 2.23
3670 4383 6.204301 ACAGAATTCATGTAGCATAGCATCAC 59.796 38.462 8.44 0.00 0.00 3.06
3678 4391 8.724229 TCATGTAGCATAGCATCACATTATTTC 58.276 33.333 0.00 0.00 29.80 2.17
3679 4392 7.439157 TGTAGCATAGCATCACATTATTTCC 57.561 36.000 0.00 0.00 0.00 3.13
3680 4393 7.226441 TGTAGCATAGCATCACATTATTTCCT 58.774 34.615 0.00 0.00 0.00 3.36
3681 4394 6.570672 AGCATAGCATCACATTATTTCCTG 57.429 37.500 0.00 0.00 0.00 3.86
3682 4395 6.301486 AGCATAGCATCACATTATTTCCTGA 58.699 36.000 0.00 0.00 0.00 3.86
3683 4396 6.206243 AGCATAGCATCACATTATTTCCTGAC 59.794 38.462 0.00 0.00 0.00 3.51
3685 4398 5.121380 AGCATCACATTATTTCCTGACCT 57.879 39.130 0.00 0.00 0.00 3.85
3686 4399 4.885907 AGCATCACATTATTTCCTGACCTG 59.114 41.667 0.00 0.00 0.00 4.00
3687 4400 4.883585 GCATCACATTATTTCCTGACCTGA 59.116 41.667 0.00 0.00 0.00 3.86
3688 4401 5.220931 GCATCACATTATTTCCTGACCTGAC 60.221 44.000 0.00 0.00 0.00 3.51
3689 4402 5.497464 TCACATTATTTCCTGACCTGACA 57.503 39.130 0.00 0.00 0.00 3.58
3694 4407 6.879458 ACATTATTTCCTGACCTGACAACTAC 59.121 38.462 0.00 0.00 0.00 2.73
3909 4622 2.726351 CCGGAAGTCCTCTGCTCCC 61.726 68.421 0.00 0.00 0.00 4.30
3910 4623 1.684049 CGGAAGTCCTCTGCTCCCT 60.684 63.158 0.00 0.00 0.00 4.20
3911 4624 1.904032 GGAAGTCCTCTGCTCCCTG 59.096 63.158 0.00 0.00 0.00 4.45
3927 4643 1.004560 CTGCAGGCCGTTTCTCTCA 60.005 57.895 5.57 0.00 0.00 3.27
3931 4647 0.603707 CAGGCCGTTTCTCTCAGCAA 60.604 55.000 0.00 0.00 0.00 3.91
3932 4648 0.321122 AGGCCGTTTCTCTCAGCAAG 60.321 55.000 0.00 0.00 0.00 4.01
3933 4649 1.499502 GCCGTTTCTCTCAGCAAGC 59.500 57.895 0.00 0.00 0.00 4.01
3934 4650 1.916697 GCCGTTTCTCTCAGCAAGCC 61.917 60.000 0.00 0.00 0.00 4.35
3964 4680 1.724582 ATGATAAACCTTGCGGCGGC 61.725 55.000 9.78 9.68 40.52 6.53
4032 4748 1.915078 AACCGATTGCCCTCCTCCTG 61.915 60.000 0.00 0.00 0.00 3.86
4039 4755 2.993853 CCCTCCTCCTGAACAGCC 59.006 66.667 0.00 0.00 0.00 4.85
4040 4756 2.674220 CCCTCCTCCTGAACAGCCC 61.674 68.421 0.00 0.00 0.00 5.19
4041 4757 2.581354 CTCCTCCTGAACAGCCCG 59.419 66.667 0.00 0.00 0.00 6.13
4042 4758 3.672295 CTCCTCCTGAACAGCCCGC 62.672 68.421 0.00 0.00 0.00 6.13
4073 4789 1.623973 GACCCGCAAAGTCGTAGTGC 61.624 60.000 0.00 0.00 34.87 4.40
4089 4805 4.213694 CGTAGTGCCAGTCATACTAGTAGG 59.786 50.000 8.27 8.27 0.00 3.18
4123 4839 1.133668 ACTGCCTGACCAGCTTTTTCT 60.134 47.619 0.00 0.00 36.29 2.52
4165 4882 3.643159 ATTCTTTTTGTGCCCTTCGTC 57.357 42.857 0.00 0.00 0.00 4.20
4166 4883 1.314730 TCTTTTTGTGCCCTTCGTCC 58.685 50.000 0.00 0.00 0.00 4.79
4206 4923 3.081061 TGCATACTGCCCTGTAGTTTTG 58.919 45.455 0.00 0.00 44.23 2.44
4325 5042 5.699097 TTGTAACTGTTAACCCAGCAATC 57.301 39.130 2.48 0.00 35.83 2.67
4326 5043 4.980573 TGTAACTGTTAACCCAGCAATCT 58.019 39.130 2.48 0.00 35.83 2.40
4331 5048 4.192317 CTGTTAACCCAGCAATCTAGTCC 58.808 47.826 2.48 0.00 0.00 3.85
4332 5049 3.195661 GTTAACCCAGCAATCTAGTCCG 58.804 50.000 0.00 0.00 0.00 4.79
4335 5052 0.179000 CCCAGCAATCTAGTCCGCTT 59.821 55.000 0.73 0.00 30.72 4.68
4336 5053 1.412710 CCCAGCAATCTAGTCCGCTTA 59.587 52.381 0.73 0.00 30.72 3.09
4338 5055 2.546795 CCAGCAATCTAGTCCGCTTAGG 60.547 54.545 0.73 0.00 42.97 2.69
4339 5056 1.069358 AGCAATCTAGTCCGCTTAGGC 59.931 52.381 0.00 0.00 40.77 3.93
4340 5057 1.069358 GCAATCTAGTCCGCTTAGGCT 59.931 52.381 0.00 0.00 40.77 4.58
4341 5058 2.748605 CAATCTAGTCCGCTTAGGCTG 58.251 52.381 0.00 0.00 40.77 4.85
4342 5059 2.074729 ATCTAGTCCGCTTAGGCTGT 57.925 50.000 0.00 0.00 40.77 4.40
4343 5060 2.723322 TCTAGTCCGCTTAGGCTGTA 57.277 50.000 0.00 0.00 40.77 2.74
4370 5087 2.552315 GCTGTGTCAAATTCCTTTCGGA 59.448 45.455 0.00 0.00 37.60 4.55
4386 5103 5.811100 CCTTTCGGAGTCTTAACTGTAATCC 59.189 44.000 0.00 0.00 35.28 3.01
4403 5120 2.654749 TCCTACATGACGCTGTGAAG 57.345 50.000 0.00 0.00 0.00 3.02
4426 5143 7.730364 AGTTGTACATGAAACCTGTAAAGAG 57.270 36.000 0.00 0.00 31.27 2.85
4475 5192 1.676006 GCCGTCCCAACCTTTATCATG 59.324 52.381 0.00 0.00 0.00 3.07
4478 5195 3.761752 CCGTCCCAACCTTTATCATGTTT 59.238 43.478 0.00 0.00 0.00 2.83
4485 5202 6.014669 CCCAACCTTTATCATGTTTTCTCCAA 60.015 38.462 0.00 0.00 0.00 3.53
4516 5233 6.974795 ACCTTTATCATAAGAAGAAGCCCTT 58.025 36.000 0.00 0.00 37.93 3.95
4517 5234 8.102484 ACCTTTATCATAAGAAGAAGCCCTTA 57.898 34.615 0.00 0.00 34.68 2.69
4526 5243 4.542697 AGAAGAAGCCCTTAACCAAACAA 58.457 39.130 0.00 0.00 34.68 2.83
4528 5245 2.628178 AGAAGCCCTTAACCAAACAAGC 59.372 45.455 0.00 0.00 0.00 4.01
4529 5246 1.338107 AGCCCTTAACCAAACAAGCC 58.662 50.000 0.00 0.00 0.00 4.35
4622 5358 4.081198 TCAACCAGTTTGATGCAAAAGGTT 60.081 37.500 17.85 17.85 42.10 3.50
4630 5366 2.253603 GATGCAAAAGGTTCATGCGAC 58.746 47.619 0.00 0.00 42.91 5.19
4631 5367 0.040514 TGCAAAAGGTTCATGCGACG 60.041 50.000 0.00 0.00 42.91 5.12
4632 5368 0.040425 GCAAAAGGTTCATGCGACGT 60.040 50.000 0.00 0.00 0.00 4.34
4634 5370 2.726633 CAAAAGGTTCATGCGACGTTT 58.273 42.857 11.46 11.46 36.86 3.60
4636 5372 3.430333 AAAGGTTCATGCGACGTTTTT 57.570 38.095 11.46 3.24 32.92 1.94
4637 5373 2.681152 AGGTTCATGCGACGTTTTTC 57.319 45.000 0.00 0.00 0.00 2.29
4640 5376 2.286772 GGTTCATGCGACGTTTTTCACT 60.287 45.455 0.00 0.00 0.00 3.41
4642 5378 3.247563 TCATGCGACGTTTTTCACTTC 57.752 42.857 0.00 0.00 0.00 3.01
4643 5379 2.869801 TCATGCGACGTTTTTCACTTCT 59.130 40.909 0.00 0.00 0.00 2.85
4645 5381 3.750639 TGCGACGTTTTTCACTTCTTT 57.249 38.095 0.00 0.00 0.00 2.52
4646 5382 4.086199 TGCGACGTTTTTCACTTCTTTT 57.914 36.364 0.00 0.00 0.00 2.27
4694 5472 2.352715 GCACTAGTTTGGAAATGGTGGC 60.353 50.000 0.00 0.00 0.00 5.01
4705 5483 2.905415 AATGGTGGCAGAAATCCAGA 57.095 45.000 0.17 0.00 33.63 3.86
4708 5486 2.449464 TGGTGGCAGAAATCCAGAATG 58.551 47.619 0.00 0.00 33.63 2.67
4710 5488 1.820519 GTGGCAGAAATCCAGAATGCA 59.179 47.619 0.00 0.00 38.63 3.96
4733 5511 1.762708 ATACATTTGGACCTTGGCCG 58.237 50.000 0.00 0.00 29.56 6.13
4739 5517 0.893270 TTGGACCTTGGCCGTCAATG 60.893 55.000 10.87 0.00 34.45 2.82
4744 5522 1.366111 CCTTGGCCGTCAATGGTACG 61.366 60.000 0.00 0.00 40.01 3.67
4778 5557 3.637998 TCTAAGTGAGTGTTGACGTCC 57.362 47.619 14.12 0.00 0.00 4.79
4865 5644 1.482278 GAATCCTGCTGTCGACGATC 58.518 55.000 11.62 2.83 0.00 3.69
4867 5646 0.753479 ATCCTGCTGTCGACGATCCT 60.753 55.000 11.62 0.00 0.00 3.24
4868 5647 0.965866 TCCTGCTGTCGACGATCCTT 60.966 55.000 11.62 0.00 0.00 3.36
4869 5648 0.526524 CCTGCTGTCGACGATCCTTC 60.527 60.000 11.62 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.931661 AAGGATGCAATTATTCAGCTGG 57.068 40.909 15.13 0.00 0.00 4.85
6 7 5.047847 CCAAAGGATGCAATTATTCAGCTG 58.952 41.667 7.63 7.63 0.00 4.24
47 81 3.763057 TCCAGTTCTTTTAAAGAGCCCC 58.237 45.455 15.99 3.59 39.29 5.80
48 82 4.158579 CCATCCAGTTCTTTTAAAGAGCCC 59.841 45.833 15.99 5.70 39.29 5.19
52 86 8.630037 GTTCTTTCCATCCAGTTCTTTTAAAGA 58.370 33.333 2.94 2.94 35.26 2.52
54 88 8.194769 GTGTTCTTTCCATCCAGTTCTTTTAAA 58.805 33.333 0.00 0.00 0.00 1.52
57 91 5.069119 GGTGTTCTTTCCATCCAGTTCTTTT 59.931 40.000 0.00 0.00 0.00 2.27
70 104 2.613506 CCGCCACGGTGTTCTTTCC 61.614 63.158 7.45 0.00 42.73 3.13
86 120 1.028905 TGGTTGTTTTGCTCCTTCCG 58.971 50.000 0.00 0.00 0.00 4.30
89 123 1.000274 GCGATGGTTGTTTTGCTCCTT 60.000 47.619 0.00 0.00 0.00 3.36
144 178 1.388547 TCGCAAGCTGTGACCTTTTT 58.611 45.000 0.00 0.00 31.05 1.94
223 263 2.058705 GATAGGGAGGGAAGGGGAAAG 58.941 57.143 0.00 0.00 0.00 2.62
226 266 0.939443 TGGATAGGGAGGGAAGGGGA 60.939 60.000 0.00 0.00 0.00 4.81
230 270 1.132500 GTGGTGGATAGGGAGGGAAG 58.868 60.000 0.00 0.00 0.00 3.46
232 272 1.316969 GGTGGTGGATAGGGAGGGA 59.683 63.158 0.00 0.00 0.00 4.20
293 341 1.690219 CCAATCGAGGGGGACAGGAG 61.690 65.000 0.00 0.00 0.00 3.69
294 342 1.689233 CCAATCGAGGGGGACAGGA 60.689 63.158 0.00 0.00 0.00 3.86
475 530 4.761304 AGGGGAGGGGAGGGAGGA 62.761 72.222 0.00 0.00 0.00 3.71
476 531 4.505970 CAGGGGAGGGGAGGGAGG 62.506 77.778 0.00 0.00 0.00 4.30
477 532 3.274550 AACAGGGGAGGGGAGGGAG 62.275 68.421 0.00 0.00 0.00 4.30
478 533 3.216371 AACAGGGGAGGGGAGGGA 61.216 66.667 0.00 0.00 0.00 4.20
482 537 0.840722 GAACAGAACAGGGGAGGGGA 60.841 60.000 0.00 0.00 0.00 4.81
486 541 1.059913 ACCAGAACAGAACAGGGGAG 58.940 55.000 0.00 0.00 0.00 4.30
513 572 4.114997 ATTTCCGCCGCAAAGCCG 62.115 61.111 0.00 0.00 0.00 5.52
556 617 1.787012 GGCAGCACAATTTCACCAAG 58.213 50.000 0.00 0.00 0.00 3.61
589 650 0.329596 AGGAGCATGAACTGGAACCC 59.670 55.000 0.00 0.00 0.00 4.11
607 668 5.486526 AGGACAGCAGAAGTAAAGAATCAG 58.513 41.667 0.00 0.00 0.00 2.90
609 670 4.564769 CGAGGACAGCAGAAGTAAAGAATC 59.435 45.833 0.00 0.00 0.00 2.52
610 671 4.220821 TCGAGGACAGCAGAAGTAAAGAAT 59.779 41.667 0.00 0.00 0.00 2.40
615 676 4.537135 AAATCGAGGACAGCAGAAGTAA 57.463 40.909 0.00 0.00 0.00 2.24
627 688 2.293122 CAGCACCAACAAAAATCGAGGA 59.707 45.455 0.00 0.00 0.00 3.71
631 692 2.033832 GCAACAGCACCAACAAAAATCG 60.034 45.455 0.00 0.00 0.00 3.34
644 705 2.974148 CACCGCTCAGCAACAGCA 60.974 61.111 0.00 0.00 36.61 4.41
700 762 0.400213 AAGAAACAGGATCGGCACCA 59.600 50.000 0.00 0.00 0.00 4.17
736 799 2.812011 ACAGCAATCGACTAAACCAACC 59.188 45.455 0.00 0.00 0.00 3.77
744 807 0.251916 CCCCCAACAGCAATCGACTA 59.748 55.000 0.00 0.00 0.00 2.59
754 817 0.393537 GAGACATCTGCCCCCAACAG 60.394 60.000 0.00 0.00 36.44 3.16
774 842 3.870633 ACCAAAGAGTATCACGGAGAC 57.129 47.619 0.00 0.00 37.82 3.36
832 900 7.609760 TCAGTACAGCAATTATAACCACTTG 57.390 36.000 0.00 0.00 0.00 3.16
880 952 4.946784 ATACAACGAGTTGAAGGATTGC 57.053 40.909 21.14 0.00 42.93 3.56
885 957 4.466828 CTGCAAATACAACGAGTTGAAGG 58.533 43.478 21.14 7.85 42.93 3.46
950 1022 4.645535 TCAGTCCAAAATCACTTCTCCTG 58.354 43.478 0.00 0.00 0.00 3.86
963 1035 7.645058 AAATTTCTCAGAAGTTCAGTCCAAA 57.355 32.000 5.50 0.00 0.00 3.28
971 1043 6.431234 TGCCTTCCTAAATTTCTCAGAAGTTC 59.569 38.462 0.00 0.00 31.01 3.01
1029 1101 1.957113 GCCCCTGTGGAATTCCTTCTG 60.957 57.143 24.73 18.80 35.39 3.02
1104 1176 3.760537 CGAGTACAGCAGTTTAGGAGAC 58.239 50.000 0.00 0.00 0.00 3.36
1119 1191 1.669779 ACGACATAGGACTGCGAGTAC 59.330 52.381 0.00 0.00 0.00 2.73
1179 1251 2.985847 GTGCTTGACCACAGGGCC 60.986 66.667 0.00 0.00 37.90 5.80
1344 1416 3.398353 GAACGGGAGCCTCGAGACG 62.398 68.421 15.71 12.27 0.00 4.18
1713 1785 3.878699 TGCAGACAATATGCCTGTACATG 59.121 43.478 0.00 0.00 43.18 3.21
1740 1812 4.995124 TCTTCCGCACACTAGTAAGATTC 58.005 43.478 0.00 0.00 0.00 2.52
1749 1821 1.001974 ACAGCAATCTTCCGCACACTA 59.998 47.619 0.00 0.00 0.00 2.74
1755 1827 0.723981 GACAGACAGCAATCTTCCGC 59.276 55.000 0.00 0.00 0.00 5.54
2119 2305 2.700897 ACTCAACCTAGTGCTGACTTGT 59.299 45.455 0.00 0.00 33.21 3.16
2167 2353 1.342074 AGGTGCTGTCTCTGCTTACA 58.658 50.000 0.00 0.00 0.00 2.41
2195 2381 7.141758 AGCCATATATTCCTTGAGAAGACAA 57.858 36.000 0.00 0.00 38.07 3.18
2231 2417 5.392380 GGCATCCAACTGAAGAAACTACATG 60.392 44.000 0.00 0.00 0.00 3.21
2268 2454 2.731572 ACTTGCTTCATTGGCTGCTAT 58.268 42.857 0.00 0.00 0.00 2.97
2442 2631 7.643764 GCAAAAAGAAAAGGGAAATTTACAAGC 59.356 33.333 2.10 0.00 0.00 4.01
2919 3503 7.953493 TCACCTCCTAAACCAAATTCCTAATTT 59.047 33.333 0.00 0.00 41.57 1.82
2922 3506 6.457159 TCACCTCCTAAACCAAATTCCTAA 57.543 37.500 0.00 0.00 0.00 2.69
3321 3905 7.148755 CCATTAAAACATAGTGCTGAAGTTTGC 60.149 37.037 0.00 0.00 33.19 3.68
3331 3915 7.158099 AGGAAGTTCCATTAAAACATAGTGC 57.842 36.000 23.87 0.00 39.61 4.40
3367 3965 4.826274 AATTCAACTAGCCTGCAGTAGA 57.174 40.909 13.81 0.00 0.00 2.59
3394 3992 4.411540 AGTTTGCTCCATGGAGATCTACAT 59.588 41.667 40.29 15.18 44.53 2.29
3439 4039 7.972832 TTACTTCATTACAGTGTTACCCAAG 57.027 36.000 0.00 0.86 0.00 3.61
3525 4222 9.555727 GTGACTATAGTTGCTTAAAATATCCCA 57.444 33.333 6.88 0.00 31.71 4.37
3533 4246 8.258007 ACATGCTAGTGACTATAGTTGCTTAAA 58.742 33.333 6.88 0.00 0.00 1.52
3548 4261 4.783764 TTTCTTCGAGACATGCTAGTGA 57.216 40.909 0.00 0.00 0.00 3.41
3555 4268 3.120095 TGCAGCATTTTCTTCGAGACATG 60.120 43.478 0.00 0.00 0.00 3.21
3587 4300 5.263599 TGGCTTCATATCAGGTCACAAAAT 58.736 37.500 0.00 0.00 0.00 1.82
3659 4372 6.376978 GTCAGGAAATAATGTGATGCTATGC 58.623 40.000 0.00 0.00 0.00 3.14
3664 4377 4.883585 TCAGGTCAGGAAATAATGTGATGC 59.116 41.667 0.00 0.00 0.00 3.91
3670 4383 6.036083 CGTAGTTGTCAGGTCAGGAAATAATG 59.964 42.308 0.00 0.00 0.00 1.90
3678 4391 1.340248 ACACGTAGTTGTCAGGTCAGG 59.660 52.381 0.00 0.00 41.61 3.86
3679 4392 2.034179 TGACACGTAGTTGTCAGGTCAG 59.966 50.000 2.71 0.00 41.61 3.51
3680 4393 2.025898 TGACACGTAGTTGTCAGGTCA 58.974 47.619 2.71 0.00 41.61 4.02
3681 4394 2.787601 TGACACGTAGTTGTCAGGTC 57.212 50.000 2.71 0.00 41.61 3.85
3682 4395 3.390135 CAATGACACGTAGTTGTCAGGT 58.610 45.455 11.58 1.18 45.79 4.00
3683 4396 2.157668 GCAATGACACGTAGTTGTCAGG 59.842 50.000 11.58 7.90 45.79 3.86
3685 4398 2.799978 CTGCAATGACACGTAGTTGTCA 59.200 45.455 8.78 8.78 46.29 3.58
3686 4399 2.157668 CCTGCAATGACACGTAGTTGTC 59.842 50.000 0.00 0.00 41.61 3.18
3687 4400 2.143122 CCTGCAATGACACGTAGTTGT 58.857 47.619 0.00 0.00 41.61 3.32
3688 4401 2.412870 TCCTGCAATGACACGTAGTTG 58.587 47.619 0.00 0.00 41.61 3.16
3689 4402 2.037251 ACTCCTGCAATGACACGTAGTT 59.963 45.455 0.00 0.00 41.61 2.24
3694 4407 0.792640 GTGACTCCTGCAATGACACG 59.207 55.000 0.00 0.00 0.00 4.49
3909 4622 1.004560 TGAGAGAAACGGCCTGCAG 60.005 57.895 6.78 6.78 0.00 4.41
3910 4623 1.004560 CTGAGAGAAACGGCCTGCA 60.005 57.895 0.00 0.00 0.00 4.41
3911 4624 2.394563 GCTGAGAGAAACGGCCTGC 61.395 63.158 0.00 0.00 34.04 4.85
3927 4643 4.729918 CCTTCCGGCTGGCTTGCT 62.730 66.667 6.73 0.00 34.14 3.91
3931 4647 0.764369 TATCATCCTTCCGGCTGGCT 60.764 55.000 6.73 0.00 34.14 4.75
3932 4648 0.108585 TTATCATCCTTCCGGCTGGC 59.891 55.000 6.73 0.00 34.14 4.85
3933 4649 2.222027 GTTTATCATCCTTCCGGCTGG 58.778 52.381 4.71 4.71 0.00 4.85
3934 4650 2.158755 AGGTTTATCATCCTTCCGGCTG 60.159 50.000 0.00 0.00 0.00 4.85
3964 4680 0.248825 CGAGATCCAGAACCTCTGCG 60.249 60.000 0.00 0.00 42.98 5.18
3977 4693 2.220761 GCATCGCCAAGTCGAGATC 58.779 57.895 0.00 0.00 42.14 2.75
4073 4789 3.570550 GGCACTCCTACTAGTATGACTGG 59.429 52.174 2.33 0.84 32.47 4.00
4089 4805 0.807496 GGCAGTTCTGATTGGCACTC 59.193 55.000 3.84 0.00 37.88 3.51
4123 4839 3.138304 ACAGCGAGCACACAAAAATAGA 58.862 40.909 0.00 0.00 0.00 1.98
4166 4883 3.626924 CGGCGAATAGGGAGGGGG 61.627 72.222 0.00 0.00 0.00 5.40
4174 4891 1.139989 CAGTATGCACCGGCGAATAG 58.860 55.000 9.30 0.00 45.35 1.73
4206 4923 0.032952 GAAAAAGGCCGTGGGGAAAC 59.967 55.000 0.00 0.00 34.06 2.78
4325 5042 2.623889 ACATACAGCCTAAGCGGACTAG 59.376 50.000 0.00 0.00 46.67 2.57
4326 5043 2.662866 ACATACAGCCTAAGCGGACTA 58.337 47.619 0.00 0.00 46.67 2.59
4331 5048 2.797156 CAGCTTACATACAGCCTAAGCG 59.203 50.000 0.00 0.00 44.72 4.68
4332 5049 3.557595 CACAGCTTACATACAGCCTAAGC 59.442 47.826 0.00 0.00 41.78 3.09
4335 5052 3.767131 TGACACAGCTTACATACAGCCTA 59.233 43.478 0.00 0.00 38.09 3.93
4336 5053 2.567169 TGACACAGCTTACATACAGCCT 59.433 45.455 0.00 0.00 38.09 4.58
4338 5055 5.551760 ATTTGACACAGCTTACATACAGC 57.448 39.130 0.00 0.00 37.56 4.40
4339 5056 6.372659 AGGAATTTGACACAGCTTACATACAG 59.627 38.462 0.00 0.00 0.00 2.74
4340 5057 6.237901 AGGAATTTGACACAGCTTACATACA 58.762 36.000 0.00 0.00 0.00 2.29
4341 5058 6.743575 AGGAATTTGACACAGCTTACATAC 57.256 37.500 0.00 0.00 0.00 2.39
4342 5059 7.360861 CGAAAGGAATTTGACACAGCTTACATA 60.361 37.037 0.00 0.00 0.00 2.29
4343 5060 6.568462 CGAAAGGAATTTGACACAGCTTACAT 60.568 38.462 0.00 0.00 0.00 2.29
4370 5087 7.481642 CGTCATGTAGGATTACAGTTAAGACT 58.518 38.462 0.00 0.00 42.72 3.24
4386 5103 3.059884 ACAACTTCACAGCGTCATGTAG 58.940 45.455 0.00 0.00 0.00 2.74
4403 5120 7.492352 ACTCTTTACAGGTTTCATGTACAAC 57.508 36.000 0.00 0.00 33.01 3.32
4491 5208 6.596621 AGGGCTTCTTCTTATGATAAAGGTC 58.403 40.000 0.00 0.00 0.00 3.85
4498 5215 6.327386 TGGTTAAGGGCTTCTTCTTATGAT 57.673 37.500 0.00 0.00 36.93 2.45
4499 5216 5.772393 TGGTTAAGGGCTTCTTCTTATGA 57.228 39.130 0.00 0.00 36.93 2.15
4500 5217 6.208599 TGTTTGGTTAAGGGCTTCTTCTTATG 59.791 38.462 0.00 0.00 36.93 1.90
4501 5218 6.311735 TGTTTGGTTAAGGGCTTCTTCTTAT 58.688 36.000 0.00 0.00 36.93 1.73
4502 5219 5.697067 TGTTTGGTTAAGGGCTTCTTCTTA 58.303 37.500 0.00 0.00 36.93 2.10
4503 5220 4.542697 TGTTTGGTTAAGGGCTTCTTCTT 58.457 39.130 0.00 0.00 36.93 2.52
4505 5222 4.796290 GCTTGTTTGGTTAAGGGCTTCTTC 60.796 45.833 0.00 0.00 36.93 2.87
4516 5233 0.752009 TGCACCGGCTTGTTTGGTTA 60.752 50.000 0.00 0.00 41.91 2.85
4517 5234 1.608717 TTGCACCGGCTTGTTTGGTT 61.609 50.000 0.00 0.00 41.91 3.67
4547 5266 7.384932 CCAGTAATGTTCGAATCACATGCTATA 59.615 37.037 0.00 0.00 34.97 1.31
4611 5347 1.401409 CGTCGCATGAACCTTTTGCAT 60.401 47.619 0.00 0.00 36.15 3.96
4622 5358 2.869801 AGAAGTGAAAAACGTCGCATGA 59.130 40.909 0.00 0.00 41.62 3.07
4646 5382 9.320406 CGCAAAATTGTACTACGATTAAGAAAA 57.680 29.630 2.57 0.00 31.20 2.29
4649 5385 6.455913 GCCGCAAAATTGTACTACGATTAAGA 60.456 38.462 2.57 0.00 31.20 2.10
4650 5386 5.675444 GCCGCAAAATTGTACTACGATTAAG 59.325 40.000 2.57 0.96 31.20 1.85
4651 5387 5.121925 TGCCGCAAAATTGTACTACGATTAA 59.878 36.000 2.57 0.00 31.20 1.40
4653 5389 3.437395 TGCCGCAAAATTGTACTACGATT 59.563 39.130 0.00 0.00 33.76 3.34
4655 5391 2.158058 GTGCCGCAAAATTGTACTACGA 59.842 45.455 0.00 0.00 0.00 3.43
4656 5392 2.158841 AGTGCCGCAAAATTGTACTACG 59.841 45.455 0.00 0.00 0.00 3.51
4659 5395 3.408634 ACTAGTGCCGCAAAATTGTACT 58.591 40.909 0.00 0.00 0.00 2.73
4694 5472 7.500720 TGTATACATGCATTCTGGATTTCTG 57.499 36.000 0.08 0.00 0.00 3.02
4705 5483 6.183360 CCAAGGTCCAAATGTATACATGCATT 60.183 38.462 18.94 7.24 43.42 3.56
4708 5486 4.499696 GCCAAGGTCCAAATGTATACATGC 60.500 45.833 18.94 9.91 36.56 4.06
4710 5488 4.215109 GGCCAAGGTCCAAATGTATACAT 58.785 43.478 12.75 12.75 38.41 2.29
4775 5554 2.358267 ACTCGGACATATCGACTTGGAC 59.642 50.000 0.00 0.00 32.86 4.02
4778 5557 2.099263 ACCACTCGGACATATCGACTTG 59.901 50.000 0.00 0.00 35.59 3.16


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

AutoCloner maintained by Alex Coulton.