Multiple sequence alignment - TraesCS1D01G398600

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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 TraesCS1D01G398600 chr1D 100.000 4737 0 0 1 4737 465541145 465536409 0.000000e+00 8748.0
1 TraesCS1D01G398600 chr1D 84.848 66 10 0 279 344 180954811 180954746 3.060000e-07 67.6
2 TraesCS1D01G398600 chr1B 92.907 3468 180 41 806 4228 642479509 642476063 0.000000e+00 4981.0
3 TraesCS1D01G398600 chr1B 87.407 405 30 6 4333 4737 642476062 642475679 3.360000e-121 446.0
4 TraesCS1D01G398600 chr1B 80.300 533 77 16 1 508 642482328 642481799 1.240000e-100 377.0
5 TraesCS1D01G398600 chr1B 91.045 134 12 0 412 545 642481774 642481641 1.050000e-41 182.0
6 TraesCS1D01G398600 chr1B 81.140 228 22 11 568 778 642479735 642479512 3.790000e-36 163.0
7 TraesCS1D01G398600 chr1A 93.603 2126 88 24 2637 4735 557955022 557952918 0.000000e+00 3129.0
8 TraesCS1D01G398600 chr1A 85.672 1005 93 30 851 1843 557957142 557956177 0.000000e+00 1011.0
9 TraesCS1D01G398600 chr1A 93.916 526 22 3 1853 2371 557956124 557955602 0.000000e+00 785.0
10 TraesCS1D01G398600 chr1A 89.850 266 16 5 2368 2627 557955345 557955085 9.830000e-87 331.0
11 TraesCS1D01G398600 chr4D 88.235 85 7 3 566 649 82727579 82727661 1.080000e-16 99.0
12 TraesCS1D01G398600 chr4A 88.235 85 7 3 566 649 494006824 494006906 1.080000e-16 99.0
13 TraesCS1D01G398600 chr4A 92.500 40 3 0 17 56 596063260 596063299 1.840000e-04 58.4
14 TraesCS1D01G398600 chr2A 86.047 86 8 3 568 653 204198634 204198715 6.530000e-14 89.8
15 TraesCS1D01G398600 chr3B 85.714 84 11 1 566 649 447622293 447622211 2.350000e-13 87.9
16 TraesCS1D01G398600 chrUn 84.270 89 10 4 566 653 60954929 60954844 3.040000e-12 84.2
17 TraesCS1D01G398600 chr7A 84.091 88 12 2 566 653 579808425 579808510 3.040000e-12 84.2
18 TraesCS1D01G398600 chr5B 82.979 94 11 5 568 660 432254323 432254412 3.930000e-11 80.5
19 TraesCS1D01G398600 chr3A 81.188 101 15 4 562 661 80223502 80223405 1.410000e-10 78.7


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 TraesCS1D01G398600 chr1D 465536409 465541145 4736 True 8748.0 8748 100.00000 1 4737 1 chr1D.!!$R2 4736
1 TraesCS1D01G398600 chr1B 642475679 642482328 6649 True 1229.8 4981 86.55980 1 4737 5 chr1B.!!$R1 4736
2 TraesCS1D01G398600 chr1A 557952918 557957142 4224 True 1314.0 3129 90.76025 851 4735 4 chr1A.!!$R1 3884

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
549 697 0.177141 GTCATACGCCCCACTTGCTA 59.823 55.0 0.00 0.0 0.00 3.49 F
1276 3328 0.237235 TTCATGCGGCTGAAAACGTC 59.763 50.0 10.89 0.0 32.35 4.34 F
2258 4392 0.029834 CAGCAAAGCAACTTCAGCGT 59.970 50.0 0.00 0.0 37.01 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 3471 0.322456 TCTGAACCAATCGCCAAGGG 60.322 55.0 0.00 0.00 0.00 3.95 R
2507 4902 2.092753 CCAGGTGCTATGAGGTCATGTT 60.093 50.0 2.56 0.00 37.15 2.71 R
4242 6710 0.547471 TGGAGATGGCCTTCCTGTCA 60.547 55.0 14.77 5.99 0.00 3.58 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
60 61 3.964909 AGAGTTGACCAAACGCAAAATC 58.035 40.909 0.00 0.00 44.04 2.17
62 63 2.098443 AGTTGACCAAACGCAAAATCGT 59.902 40.909 0.00 0.00 44.04 3.73
67 68 3.254892 ACCAAACGCAAAATCGTGTTTT 58.745 36.364 0.15 0.00 44.90 2.43
70 71 4.434857 CCAAACGCAAAATCGTGTTTTTGT 60.435 37.500 14.29 8.85 44.90 2.83
76 77 6.746364 ACGCAAAATCGTGTTTTTGTAAAGTA 59.254 30.769 14.29 0.00 44.62 2.24
79 80 9.909043 GCAAAATCGTGTTTTTGTAAAGTATTT 57.091 25.926 14.29 0.00 44.62 1.40
206 212 8.600449 AAAATCTTTGTGTGTTTCAAACTTGA 57.400 26.923 1.10 0.00 34.92 3.02
207 213 8.776376 AAATCTTTGTGTGTTTCAAACTTGAT 57.224 26.923 1.10 0.00 37.00 2.57
208 214 8.776376 AATCTTTGTGTGTTTCAAACTTGATT 57.224 26.923 1.10 0.00 37.00 2.57
209 215 7.579589 TCTTTGTGTGTTTCAAACTTGATTG 57.420 32.000 1.10 0.00 37.00 2.67
214 239 8.818141 TGTGTGTTTCAAACTTGATTGTTTTA 57.182 26.923 1.10 0.00 37.98 1.52
267 292 8.801882 TCCTCAAATTCTAATAAATGTTCCGT 57.198 30.769 0.00 0.00 0.00 4.69
268 293 8.673711 TCCTCAAATTCTAATAAATGTTCCGTG 58.326 33.333 0.00 0.00 0.00 4.94
307 333 5.961421 TCGGGAATTAAAATGATTTTCCCCT 59.039 36.000 16.06 0.00 38.86 4.79
321 347 8.586879 TGATTTTCCCCTTTTTCAAAATTTGT 57.413 26.923 5.56 0.00 30.35 2.83
327 353 6.942576 TCCCCTTTTTCAAAATTTGTTCACAA 59.057 30.769 5.56 0.00 0.00 3.33
344 370 3.189080 TCACAAATGCAGAACATCTTCCG 59.811 43.478 0.00 0.00 38.34 4.30
417 565 8.034058 ACGTGTTTTTCAAATGATTTTTGGAA 57.966 26.923 0.00 0.00 0.00 3.53
484 632 8.202461 AGTCAAATAATATTCCGATCTACCCA 57.798 34.615 0.00 0.00 0.00 4.51
493 641 8.840200 ATATTCCGATCTACCCATGTAGTTAT 57.160 34.615 0.00 0.00 44.08 1.89
496 644 6.989659 TCCGATCTACCCATGTAGTTATTTC 58.010 40.000 0.00 0.00 44.08 2.17
526 674 1.522676 CACGCGGCATTATAGTCACAG 59.477 52.381 12.47 0.00 0.00 3.66
536 684 6.159988 GCATTATAGTCACAGAGGGTCATAC 58.840 44.000 0.00 0.00 0.00 2.39
539 687 0.179108 GTCACAGAGGGTCATACGCC 60.179 60.000 0.00 0.00 0.00 5.68
545 693 2.995547 GGGTCATACGCCCCACTT 59.004 61.111 0.00 0.00 40.88 3.16
546 694 1.451387 GGGTCATACGCCCCACTTG 60.451 63.158 0.00 0.00 40.88 3.16
547 695 2.112815 GGTCATACGCCCCACTTGC 61.113 63.158 0.00 0.00 0.00 4.01
548 696 1.078426 GTCATACGCCCCACTTGCT 60.078 57.895 0.00 0.00 0.00 3.91
549 697 0.177141 GTCATACGCCCCACTTGCTA 59.823 55.000 0.00 0.00 0.00 3.49
550 698 0.464036 TCATACGCCCCACTTGCTAG 59.536 55.000 0.00 0.00 0.00 3.42
684 2729 1.724623 TCAGATTTTTCGGCGAGTTCG 59.275 47.619 10.46 0.00 43.27 3.95
691 2736 0.249155 TTCGGCGAGTTCGTTCAGTT 60.249 50.000 10.46 0.00 42.22 3.16
693 2738 1.860078 GGCGAGTTCGTTCAGTTGG 59.140 57.895 3.27 0.00 42.22 3.77
695 2740 1.214367 GCGAGTTCGTTCAGTTGGAA 58.786 50.000 3.27 0.00 42.22 3.53
696 2741 1.595794 GCGAGTTCGTTCAGTTGGAAA 59.404 47.619 3.27 0.00 42.22 3.13
697 2742 2.223377 GCGAGTTCGTTCAGTTGGAAAT 59.777 45.455 3.27 0.00 42.22 2.17
698 2743 3.799035 CGAGTTCGTTCAGTTGGAAATG 58.201 45.455 0.00 0.00 37.23 2.32
699 2744 3.247648 CGAGTTCGTTCAGTTGGAAATGT 59.752 43.478 0.00 0.00 37.23 2.71
701 2746 5.169836 AGTTCGTTCAGTTGGAAATGTTC 57.830 39.130 0.00 0.00 37.23 3.18
703 2748 5.007724 AGTTCGTTCAGTTGGAAATGTTCTC 59.992 40.000 0.00 0.00 37.23 2.87
704 2749 3.493129 TCGTTCAGTTGGAAATGTTCTCG 59.507 43.478 0.00 0.00 37.23 4.04
705 2750 3.247648 CGTTCAGTTGGAAATGTTCTCGT 59.752 43.478 0.00 0.00 37.23 4.18
706 2751 4.608445 CGTTCAGTTGGAAATGTTCTCGTC 60.608 45.833 0.00 0.00 37.23 4.20
713 2760 3.177487 GGAAATGTTCTCGTCGGACTAC 58.823 50.000 6.57 0.35 0.00 2.73
730 2777 4.177026 GACTACAAGACGCTTGTGATGAT 58.823 43.478 25.49 12.32 34.11 2.45
733 2780 4.410492 ACAAGACGCTTGTGATGATTTC 57.590 40.909 19.72 0.00 0.00 2.17
734 2781 3.814842 ACAAGACGCTTGTGATGATTTCA 59.185 39.130 19.72 0.00 0.00 2.69
770 2817 8.475331 AATATTATACCGGCTCAGTATTTTCG 57.525 34.615 0.00 0.00 32.71 3.46
778 2825 3.003480 GCTCAGTATTTTCGAGGTGCTT 58.997 45.455 0.00 0.00 0.00 3.91
779 2826 3.181516 GCTCAGTATTTTCGAGGTGCTTG 60.182 47.826 0.00 0.00 0.00 4.01
780 2827 3.997021 CTCAGTATTTTCGAGGTGCTTGT 59.003 43.478 0.00 0.00 0.00 3.16
781 2828 5.142061 TCAGTATTTTCGAGGTGCTTGTA 57.858 39.130 0.00 0.00 0.00 2.41
782 2829 5.168569 TCAGTATTTTCGAGGTGCTTGTAG 58.831 41.667 0.00 0.00 0.00 2.74
783 2830 4.330074 CAGTATTTTCGAGGTGCTTGTAGG 59.670 45.833 0.00 0.00 0.00 3.18
784 2831 2.178912 TTTTCGAGGTGCTTGTAGGG 57.821 50.000 0.00 0.00 0.00 3.53
785 2832 1.344065 TTTCGAGGTGCTTGTAGGGA 58.656 50.000 0.00 0.00 0.00 4.20
786 2833 1.568504 TTCGAGGTGCTTGTAGGGAT 58.431 50.000 0.00 0.00 0.00 3.85
787 2834 2.447408 TCGAGGTGCTTGTAGGGATA 57.553 50.000 0.00 0.00 0.00 2.59
788 2835 2.958818 TCGAGGTGCTTGTAGGGATAT 58.041 47.619 0.00 0.00 0.00 1.63
789 2836 2.628178 TCGAGGTGCTTGTAGGGATATG 59.372 50.000 0.00 0.00 0.00 1.78
790 2837 2.628178 CGAGGTGCTTGTAGGGATATGA 59.372 50.000 0.00 0.00 0.00 2.15
791 2838 3.259374 CGAGGTGCTTGTAGGGATATGAT 59.741 47.826 0.00 0.00 0.00 2.45
792 2839 4.573900 GAGGTGCTTGTAGGGATATGATG 58.426 47.826 0.00 0.00 0.00 3.07
793 2840 4.234550 AGGTGCTTGTAGGGATATGATGA 58.765 43.478 0.00 0.00 0.00 2.92
794 2841 4.285517 AGGTGCTTGTAGGGATATGATGAG 59.714 45.833 0.00 0.00 0.00 2.90
795 2842 3.999663 GTGCTTGTAGGGATATGATGAGC 59.000 47.826 0.00 0.00 0.00 4.26
796 2843 3.647590 TGCTTGTAGGGATATGATGAGCA 59.352 43.478 0.00 0.00 35.49 4.26
797 2844 4.252073 GCTTGTAGGGATATGATGAGCAG 58.748 47.826 0.00 0.00 0.00 4.24
798 2845 4.020751 GCTTGTAGGGATATGATGAGCAGA 60.021 45.833 0.00 0.00 0.00 4.26
799 2846 5.722263 CTTGTAGGGATATGATGAGCAGAG 58.278 45.833 0.00 0.00 0.00 3.35
800 2847 4.092279 TGTAGGGATATGATGAGCAGAGG 58.908 47.826 0.00 0.00 0.00 3.69
801 2848 2.549082 AGGGATATGATGAGCAGAGGG 58.451 52.381 0.00 0.00 0.00 4.30
802 2849 2.113233 AGGGATATGATGAGCAGAGGGA 59.887 50.000 0.00 0.00 0.00 4.20
803 2850 2.500910 GGGATATGATGAGCAGAGGGAG 59.499 54.545 0.00 0.00 0.00 4.30
804 2851 3.172339 GGATATGATGAGCAGAGGGAGT 58.828 50.000 0.00 0.00 0.00 3.85
811 2858 4.343526 TGATGAGCAGAGGGAGTATTCTTC 59.656 45.833 0.00 0.00 0.00 2.87
816 2863 5.524535 AGCAGAGGGAGTATTCTTCTAACT 58.475 41.667 0.00 0.00 0.00 2.24
825 2872 7.829706 GGGAGTATTCTTCTAACTGTGGAATTT 59.170 37.037 0.00 0.00 0.00 1.82
826 2873 9.886132 GGAGTATTCTTCTAACTGTGGAATTTA 57.114 33.333 0.00 0.00 0.00 1.40
935 2985 0.609662 TGCGAGTGTACTTTACCCCC 59.390 55.000 0.00 0.00 0.00 5.40
940 2990 1.897802 AGTGTACTTTACCCCCAGACG 59.102 52.381 0.00 0.00 0.00 4.18
1145 3195 7.391554 TGTTCTTCAACCTCCTATTCATTTCTG 59.608 37.037 0.00 0.00 0.00 3.02
1151 3201 4.410555 ACCTCCTATTCATTTCTGTCCTCC 59.589 45.833 0.00 0.00 0.00 4.30
1161 3211 1.216710 CTGTCCTCCTGTTCTCGGC 59.783 63.158 0.00 0.00 0.00 5.54
1183 3233 3.936203 TTTCGGTGTGGCGAGCCT 61.936 61.111 15.75 0.00 36.94 4.58
1219 3269 3.760684 GGAAACTGATTGATTGGTGCTCT 59.239 43.478 0.00 0.00 0.00 4.09
1222 3272 4.778534 ACTGATTGATTGGTGCTCTTTG 57.221 40.909 0.00 0.00 0.00 2.77
1243 3295 8.653191 TCTTTGTGAGTTCTTAGTGGGTATTTA 58.347 33.333 0.00 0.00 0.00 1.40
1263 3315 1.212616 CTAGCGCTACTGGTTCATGC 58.787 55.000 14.45 0.00 0.00 4.06
1276 3328 0.237235 TTCATGCGGCTGAAAACGTC 59.763 50.000 10.89 0.00 32.35 4.34
1278 3330 1.599518 ATGCGGCTGAAAACGTCCA 60.600 52.632 0.00 0.00 0.00 4.02
1280 3332 0.320858 TGCGGCTGAAAACGTCCATA 60.321 50.000 0.00 0.00 0.00 2.74
1301 3353 8.700973 TCCATAGATTTTAATTTAACCTTGGGC 58.299 33.333 0.00 0.00 0.00 5.36
1358 3417 4.770010 CCAGCTTACAATTGTTTCCCCTTA 59.230 41.667 17.78 0.00 0.00 2.69
1392 3451 7.979537 AGGAGTTTGGTTCTTGAATTTTGTTAC 59.020 33.333 0.00 0.00 0.00 2.50
1393 3452 7.762159 GGAGTTTGGTTCTTGAATTTTGTTACA 59.238 33.333 0.00 0.00 0.00 2.41
1410 3469 1.967319 ACAAGTTGCCGATTCACTGT 58.033 45.000 1.81 0.00 0.00 3.55
1412 3471 0.593128 AAGTTGCCGATTCACTGTGC 59.407 50.000 2.12 0.00 0.00 4.57
1413 3472 1.210155 GTTGCCGATTCACTGTGCC 59.790 57.895 2.12 0.00 0.00 5.01
1440 3499 2.225019 CGATTGGTTCAGATATGCCAGC 59.775 50.000 0.00 0.00 32.09 4.85
1600 3665 6.472686 ACCTGACTATCTAATCCTGTGAAC 57.527 41.667 0.00 0.00 0.00 3.18
1601 3666 6.198639 ACCTGACTATCTAATCCTGTGAACT 58.801 40.000 0.00 0.00 0.00 3.01
1602 3667 6.097554 ACCTGACTATCTAATCCTGTGAACTG 59.902 42.308 0.00 0.00 0.00 3.16
1605 3674 7.548097 TGACTATCTAATCCTGTGAACTGTTC 58.452 38.462 13.49 13.49 0.00 3.18
1623 3692 6.357367 ACTGTTCCTCTGTAGTTTTTGTGAT 58.643 36.000 0.00 0.00 0.00 3.06
1630 3699 7.656137 TCCTCTGTAGTTTTTGTGATACAGTTC 59.344 37.037 10.13 0.00 43.53 3.01
1656 3725 4.093998 CACTGAAGCTGCGATTCTGTAAAT 59.906 41.667 14.65 0.00 36.91 1.40
1711 3789 6.021626 GCTTGTACTTGTACGAAATCTACTCG 60.022 42.308 6.46 0.00 42.06 4.18
1810 3893 1.816074 CCGGTAGCTGCCAAACTTTA 58.184 50.000 21.56 0.00 0.00 1.85
1845 3929 6.744993 GGTGATTTCGTTTGTTGCAAAATTTT 59.255 30.769 0.00 0.00 0.00 1.82
1923 4056 2.692709 TTGGCAAGAGAATTTGGGGA 57.307 45.000 0.00 0.00 0.00 4.81
2090 4224 0.894835 ACCGGAAATCCAAATGCACC 59.105 50.000 9.46 0.00 35.14 5.01
2258 4392 0.029834 CAGCAAAGCAACTTCAGCGT 59.970 50.000 0.00 0.00 37.01 5.07
2423 4817 5.876612 TGTTGCTGCTTTTGATTTGTTTT 57.123 30.435 0.00 0.00 0.00 2.43
2427 4822 6.680874 TGCTGCTTTTGATTTGTTTTCATT 57.319 29.167 0.00 0.00 0.00 2.57
2466 4861 5.514274 TCCAACATTTCTGAAAACAGACC 57.486 39.130 6.95 0.00 0.00 3.85
2473 4868 8.181904 ACATTTCTGAAAACAGACCATAATGT 57.818 30.769 15.80 15.80 35.66 2.71
2480 4875 5.886960 AAACAGACCATAATGTGCTCTTC 57.113 39.130 0.00 0.00 0.00 2.87
2538 4933 3.832490 TCATAGCACCTGGAGCGTAATAT 59.168 43.478 10.48 0.61 37.01 1.28
2660 5113 5.899547 AGTATCAGTGTGGACAAGATATGGA 59.100 40.000 6.51 0.00 31.94 3.41
2707 5160 8.202137 CGAAAGAATAAGGAAAGTATGGTCCTA 58.798 37.037 0.00 0.00 43.75 2.94
2760 5213 4.158209 TGCCATGTGTTTATTCATGACCTG 59.842 41.667 0.00 0.00 42.52 4.00
2861 5315 4.546570 TCCTGACATAGCAAATATCGTCG 58.453 43.478 0.00 0.00 30.65 5.12
2872 5326 5.006746 AGCAAATATCGTCGACCTGATTTTC 59.993 40.000 10.58 7.46 0.00 2.29
3322 5777 0.618458 TAAGGCATCGCTTGGACCTT 59.382 50.000 0.00 0.00 43.10 3.50
3345 5800 3.499918 ACTTTTGCTCGGTCAGAAGAATG 59.500 43.478 12.49 0.00 33.78 2.67
3417 5872 1.609208 GAACAGCAAGAGGCCTTTGA 58.391 50.000 23.58 0.00 46.50 2.69
3451 5906 2.033194 GGTGCCTTCCTCGAAACCG 61.033 63.158 0.00 0.00 0.00 4.44
3643 6098 0.758734 TACTTGATCCGGCATCCCTG 59.241 55.000 0.00 0.00 0.00 4.45
3685 6140 3.768757 CCATTGCATTTGGTTCCTTCCTA 59.231 43.478 7.82 0.00 0.00 2.94
3693 6148 5.646692 TTTGGTTCCTTCCTATGGGATAG 57.353 43.478 0.00 0.00 41.87 2.08
3764 6219 4.653341 GGATCTCCAGAAGATTCCTGAAGA 59.347 45.833 0.00 0.00 45.06 2.87
3815 6270 3.683802 AGTTTGCAGAAGATTCCTGAGG 58.316 45.455 0.00 0.00 33.65 3.86
3836 6291 9.965902 CTGAGGCCTTGTATATATTTTAGGAAT 57.034 33.333 6.77 0.18 0.00 3.01
3839 6294 9.025041 AGGCCTTGTATATATTTTAGGAATTGC 57.975 33.333 0.00 0.00 0.00 3.56
3873 6328 4.937620 TCTGTGCATGTAAATCTTGACCTC 59.062 41.667 0.00 0.00 0.00 3.85
4141 6605 2.190538 TGGATTGATCTCCAGACAGCA 58.809 47.619 0.00 0.00 40.43 4.41
4173 6637 0.253160 TAAGGGGAGGAGCCACACAT 60.253 55.000 0.00 0.00 45.20 3.21
4177 6641 0.678048 GGGAGGAGCCACACATCAAC 60.678 60.000 0.00 0.00 38.95 3.18
4179 6643 1.160137 GAGGAGCCACACATCAACAC 58.840 55.000 0.00 0.00 0.00 3.32
4180 6644 0.767375 AGGAGCCACACATCAACACT 59.233 50.000 0.00 0.00 0.00 3.55
4182 6646 0.792640 GAGCCACACATCAACACTCG 59.207 55.000 0.00 0.00 0.00 4.18
4183 6647 1.207593 GCCACACATCAACACTCGC 59.792 57.895 0.00 0.00 0.00 5.03
4235 6703 1.153429 GCACCCTAACCTACCTGCG 60.153 63.158 0.00 0.00 0.00 5.18
4242 6710 2.368875 CCTAACCTACCTGCGATTGGAT 59.631 50.000 0.00 0.00 0.00 3.41
4246 6714 1.138859 CCTACCTGCGATTGGATGACA 59.861 52.381 0.00 0.00 0.00 3.58
4263 6731 0.842635 ACAGGAAGGCCATCTCCATC 59.157 55.000 17.96 0.00 36.29 3.51
4272 6740 4.615815 ATCTCCATCGCCGCCAGC 62.616 66.667 0.00 0.00 38.52 4.85
4288 6756 2.357517 GCCACCTCACAGTGACGG 60.358 66.667 14.31 14.31 40.34 4.79
4300 6768 4.124351 TGACGGGGCGACGATGAC 62.124 66.667 0.00 0.00 37.61 3.06
4303 6771 2.658593 CGGGGCGACGATGACATC 60.659 66.667 5.28 5.28 35.47 3.06
4317 6785 3.221964 TGACATCGTCATCTGACAGTG 57.778 47.619 10.69 9.86 44.99 3.66
4318 6786 2.819608 TGACATCGTCATCTGACAGTGA 59.180 45.455 14.95 3.22 44.99 3.41
4319 6787 3.175152 GACATCGTCATCTGACAGTGAC 58.825 50.000 19.74 19.74 44.99 3.67
4327 6804 3.916392 CTGACAGTGACGGGGCGAC 62.916 68.421 0.00 0.00 0.00 5.19
4497 6974 6.521527 AGGTGCTCCAATTCTAGGATTATT 57.478 37.500 7.70 0.00 33.99 1.40
4528 7005 6.481643 TCAAGTTAAACCTAAGGATTCCCTG 58.518 40.000 0.00 0.00 43.48 4.45
4587 7069 4.396166 CCTGTGACCAAGCTTAAGTAATGG 59.604 45.833 16.79 16.79 37.19 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.698545 GCAGAGAGCGTCATATAGGATTTTT 59.301 40.000 0.00 0.00 0.00 1.94
39 40 3.548014 CGATTTTGCGTTTGGTCAACTCT 60.548 43.478 0.00 0.00 32.53 3.24
187 193 7.721286 AACAATCAAGTTTGAAACACACAAA 57.279 28.000 11.02 0.00 41.13 2.83
245 270 8.455682 GGACACGGAACATTTATTAGAATTTGA 58.544 33.333 0.00 0.00 0.00 2.69
246 271 8.240682 TGGACACGGAACATTTATTAGAATTTG 58.759 33.333 0.00 0.00 0.00 2.32
256 281 8.361139 ACAAATATTTTGGACACGGAACATTTA 58.639 29.630 0.00 0.00 0.00 1.40
266 291 5.379732 TCCCGAACAAATATTTTGGACAC 57.620 39.130 0.00 0.00 29.70 3.67
267 292 6.597832 ATTCCCGAACAAATATTTTGGACA 57.402 33.333 0.00 0.00 29.70 4.02
268 293 8.989653 TTAATTCCCGAACAAATATTTTGGAC 57.010 30.769 0.00 0.00 29.70 4.02
296 322 8.586879 ACAAATTTTGAAAAAGGGGAAAATCA 57.413 26.923 15.81 0.00 29.76 2.57
321 347 4.320421 CGGAAGATGTTCTGCATTTGTGAA 60.320 41.667 2.24 0.00 38.06 3.18
327 353 6.515272 AAAATACGGAAGATGTTCTGCATT 57.485 33.333 11.21 7.60 42.18 3.56
389 415 9.760660 CCAAAAATCATTTGAAAAACACGTTTA 57.239 25.926 2.64 0.00 31.63 2.01
392 418 7.602517 TCCAAAAATCATTTGAAAAACACGT 57.397 28.000 2.64 0.00 0.00 4.49
393 419 9.500864 AATTCCAAAAATCATTTGAAAAACACG 57.499 25.926 2.64 0.00 0.00 4.49
484 632 9.821662 GCGTGAAAGTTTAAGAAATAACTACAT 57.178 29.630 0.00 0.00 33.66 2.29
493 641 2.355132 TGCCGCGTGAAAGTTTAAGAAA 59.645 40.909 4.92 0.00 0.00 2.52
496 644 2.611974 ATGCCGCGTGAAAGTTTAAG 57.388 45.000 4.92 0.00 0.00 1.85
536 684 0.249398 AGTTACTAGCAAGTGGGGCG 59.751 55.000 0.00 0.00 36.36 6.13
656 2687 6.967199 ACTCGCCGAAAAATCTGAATAAATTC 59.033 34.615 0.00 0.00 37.31 2.17
657 2688 6.852664 ACTCGCCGAAAAATCTGAATAAATT 58.147 32.000 0.00 0.00 0.00 1.82
658 2689 6.436843 ACTCGCCGAAAAATCTGAATAAAT 57.563 33.333 0.00 0.00 0.00 1.40
659 2690 5.873179 ACTCGCCGAAAAATCTGAATAAA 57.127 34.783 0.00 0.00 0.00 1.40
661 2692 4.032445 CGAACTCGCCGAAAAATCTGAATA 59.968 41.667 0.00 0.00 0.00 1.75
662 2693 3.181520 CGAACTCGCCGAAAAATCTGAAT 60.182 43.478 0.00 0.00 0.00 2.57
667 2712 2.096614 TGAACGAACTCGCCGAAAAATC 60.097 45.455 0.00 0.00 44.43 2.17
684 2729 4.608445 CGACGAGAACATTTCCAACTGAAC 60.608 45.833 0.00 0.00 31.05 3.18
691 2736 1.616865 AGTCCGACGAGAACATTTCCA 59.383 47.619 0.00 0.00 0.00 3.53
693 2738 3.829948 TGTAGTCCGACGAGAACATTTC 58.170 45.455 0.00 0.00 0.00 2.17
695 2740 3.504906 TCTTGTAGTCCGACGAGAACATT 59.495 43.478 0.00 0.00 36.99 2.71
696 2741 3.079578 TCTTGTAGTCCGACGAGAACAT 58.920 45.455 0.00 0.00 36.99 2.71
697 2742 2.225019 GTCTTGTAGTCCGACGAGAACA 59.775 50.000 0.00 0.00 40.74 3.18
698 2743 2.849110 GTCTTGTAGTCCGACGAGAAC 58.151 52.381 0.00 0.00 40.74 3.01
704 2749 1.335689 ACAAGCGTCTTGTAGTCCGAC 60.336 52.381 19.21 0.00 0.00 4.79
705 2750 0.956633 ACAAGCGTCTTGTAGTCCGA 59.043 50.000 19.21 0.00 0.00 4.55
706 2751 1.060713 CACAAGCGTCTTGTAGTCCG 58.939 55.000 19.88 8.14 0.00 4.79
713 2760 4.408993 TGAAATCATCACAAGCGTCTTG 57.591 40.909 15.16 15.16 31.50 3.02
748 2795 6.092955 TCGAAAATACTGAGCCGGTATAAT 57.907 37.500 1.90 0.00 35.18 1.28
753 2800 1.134788 CCTCGAAAATACTGAGCCGGT 60.135 52.381 1.90 0.00 0.00 5.28
756 2803 1.666189 GCACCTCGAAAATACTGAGCC 59.334 52.381 0.00 0.00 0.00 4.70
760 2807 4.330074 CCTACAAGCACCTCGAAAATACTG 59.670 45.833 0.00 0.00 0.00 2.74
770 2817 4.284490 TCATCATATCCCTACAAGCACCTC 59.716 45.833 0.00 0.00 0.00 3.85
778 2825 4.092279 CCTCTGCTCATCATATCCCTACA 58.908 47.826 0.00 0.00 0.00 2.74
779 2826 3.450457 CCCTCTGCTCATCATATCCCTAC 59.550 52.174 0.00 0.00 0.00 3.18
780 2827 3.337909 TCCCTCTGCTCATCATATCCCTA 59.662 47.826 0.00 0.00 0.00 3.53
781 2828 2.113233 TCCCTCTGCTCATCATATCCCT 59.887 50.000 0.00 0.00 0.00 4.20
782 2829 2.500910 CTCCCTCTGCTCATCATATCCC 59.499 54.545 0.00 0.00 0.00 3.85
783 2830 3.172339 ACTCCCTCTGCTCATCATATCC 58.828 50.000 0.00 0.00 0.00 2.59
784 2831 6.380846 AGAATACTCCCTCTGCTCATCATATC 59.619 42.308 0.00 0.00 0.00 1.63
785 2832 6.262980 AGAATACTCCCTCTGCTCATCATAT 58.737 40.000 0.00 0.00 0.00 1.78
786 2833 5.649265 AGAATACTCCCTCTGCTCATCATA 58.351 41.667 0.00 0.00 0.00 2.15
787 2834 4.491675 AGAATACTCCCTCTGCTCATCAT 58.508 43.478 0.00 0.00 0.00 2.45
788 2835 3.921104 AGAATACTCCCTCTGCTCATCA 58.079 45.455 0.00 0.00 0.00 3.07
789 2836 4.588528 AGAAGAATACTCCCTCTGCTCATC 59.411 45.833 0.00 0.00 0.00 2.92
790 2837 4.555689 AGAAGAATACTCCCTCTGCTCAT 58.444 43.478 0.00 0.00 0.00 2.90
791 2838 3.987745 AGAAGAATACTCCCTCTGCTCA 58.012 45.455 0.00 0.00 0.00 4.26
792 2839 5.596772 AGTTAGAAGAATACTCCCTCTGCTC 59.403 44.000 0.00 0.00 29.84 4.26
793 2840 5.362430 CAGTTAGAAGAATACTCCCTCTGCT 59.638 44.000 0.00 0.00 32.06 4.24
794 2841 5.128008 ACAGTTAGAAGAATACTCCCTCTGC 59.872 44.000 0.00 0.00 0.00 4.26
795 2842 6.406400 CCACAGTTAGAAGAATACTCCCTCTG 60.406 46.154 0.00 0.00 0.00 3.35
796 2843 5.659079 CCACAGTTAGAAGAATACTCCCTCT 59.341 44.000 0.00 0.00 0.00 3.69
797 2844 5.657302 TCCACAGTTAGAAGAATACTCCCTC 59.343 44.000 0.00 0.00 0.00 4.30
798 2845 5.590818 TCCACAGTTAGAAGAATACTCCCT 58.409 41.667 0.00 0.00 0.00 4.20
799 2846 5.934402 TCCACAGTTAGAAGAATACTCCC 57.066 43.478 0.00 0.00 0.00 4.30
800 2847 8.794335 AAATTCCACAGTTAGAAGAATACTCC 57.206 34.615 0.00 0.00 0.00 3.85
845 2894 8.462016 CCCTCAGAAGATAATTTTCATCGTTTT 58.538 33.333 0.00 0.00 0.00 2.43
940 2990 2.125269 AGGATAACGCCGTGTGCC 60.125 61.111 0.00 0.00 36.24 5.01
1078 3128 1.224039 CGGAGGAGAGGTACGAGGT 59.776 63.158 0.00 0.00 0.00 3.85
1145 3195 2.182030 CGCCGAGAACAGGAGGAC 59.818 66.667 0.00 0.00 0.00 3.85
1151 3201 2.032071 AAACCCCGCCGAGAACAG 59.968 61.111 0.00 0.00 0.00 3.16
1174 3224 2.819984 GATTGAACCCAGGCTCGCCA 62.820 60.000 11.02 0.00 38.92 5.69
1177 3227 0.250234 TCTGATTGAACCCAGGCTCG 59.750 55.000 0.00 0.00 0.00 5.03
1183 3233 3.394274 TCAGTTTCCTCTGATTGAACCCA 59.606 43.478 0.00 0.00 39.20 4.51
1219 3269 8.434392 AGTAAATACCCACTAAGAACTCACAAA 58.566 33.333 0.00 0.00 0.00 2.83
1222 3272 7.705752 GCTAGTAAATACCCACTAAGAACTCAC 59.294 40.741 0.00 0.00 0.00 3.51
1243 3295 1.471676 GCATGAACCAGTAGCGCTAGT 60.472 52.381 19.48 19.29 0.00 2.57
1263 3315 2.004583 TCTATGGACGTTTTCAGCCG 57.995 50.000 0.00 0.00 0.00 5.52
1276 3328 8.482128 TGCCCAAGGTTAAATTAAAATCTATGG 58.518 33.333 0.00 0.00 0.00 2.74
1278 3330 9.487442 TCTGCCCAAGGTTAAATTAAAATCTAT 57.513 29.630 0.00 0.00 0.00 1.98
1280 3332 7.790782 TCTGCCCAAGGTTAAATTAAAATCT 57.209 32.000 0.00 0.00 0.00 2.40
1301 3353 4.912317 ATTCAGATCATCCCTCCATCTG 57.088 45.455 0.00 2.32 43.38 2.90
1358 3417 2.450886 AGAACCAAACTCCTCCCCAAAT 59.549 45.455 0.00 0.00 0.00 2.32
1392 3451 1.664016 GCACAGTGAATCGGCAACTTG 60.664 52.381 4.15 0.00 0.00 3.16
1393 3452 0.593128 GCACAGTGAATCGGCAACTT 59.407 50.000 4.15 0.00 0.00 2.66
1412 3471 0.322456 TCTGAACCAATCGCCAAGGG 60.322 55.000 0.00 0.00 0.00 3.95
1413 3472 1.755179 ATCTGAACCAATCGCCAAGG 58.245 50.000 0.00 0.00 0.00 3.61
1440 3499 0.327924 TGACTGGTGTATTGGGCCTG 59.672 55.000 4.53 0.00 0.00 4.85
1593 3658 4.592485 ACTACAGAGGAACAGTTCACAG 57.408 45.455 15.36 7.84 0.00 3.66
1600 3665 6.867662 ATCACAAAAACTACAGAGGAACAG 57.132 37.500 0.00 0.00 0.00 3.16
1601 3666 7.276658 TGTATCACAAAAACTACAGAGGAACA 58.723 34.615 0.00 0.00 0.00 3.18
1602 3667 7.441458 ACTGTATCACAAAAACTACAGAGGAAC 59.559 37.037 13.75 0.00 42.25 3.62
1605 3674 7.095187 GGAACTGTATCACAAAAACTACAGAGG 60.095 40.741 13.75 0.00 42.25 3.69
1630 3699 1.005340 GAATCGCAGCTTCAGTGAGG 58.995 55.000 0.00 0.00 0.00 3.86
1656 3725 8.157476 GGCCTCCAACTTAAGATAAGATCATTA 58.843 37.037 10.09 0.00 0.00 1.90
1711 3789 7.849804 TGGAGAGTGCAGAACTTAATAATTC 57.150 36.000 0.00 0.00 40.07 2.17
1806 3889 5.049405 ACGAAATCACCAGTCTTTGCTAAAG 60.049 40.000 0.00 0.00 39.88 1.85
1810 3893 2.851195 ACGAAATCACCAGTCTTTGCT 58.149 42.857 0.00 0.00 0.00 3.91
1845 3929 3.255921 TGCCCATAGGATAGTGGCA 57.744 52.632 0.00 0.00 45.43 4.92
1848 3932 4.356405 TGACAATGCCCATAGGATAGTG 57.644 45.455 0.00 0.00 33.47 2.74
1849 3933 5.515534 GGATTGACAATGCCCATAGGATAGT 60.516 44.000 5.14 0.00 33.47 2.12
2090 4224 4.021894 ACAGTAGTCAGTAGCTTTCTGGTG 60.022 45.833 15.34 9.63 34.15 4.17
2131 4265 6.594284 TGACGCTATCAAATTCAGATTCAG 57.406 37.500 0.00 0.00 33.02 3.02
2258 4392 5.926542 CGTGTCTTTCCTTTGAATAGACAGA 59.073 40.000 14.66 0.00 42.48 3.41
2473 4868 7.877612 TGTGTTTGTCATTCTTATAGAAGAGCA 59.122 33.333 0.00 0.00 42.66 4.26
2507 4902 2.092753 CCAGGTGCTATGAGGTCATGTT 60.093 50.000 2.56 0.00 37.15 2.71
2538 4933 6.053005 CCTCACTTACAAGGTAAAACACTCA 58.947 40.000 0.00 0.00 0.00 3.41
2681 5134 7.048512 AGGACCATACTTTCCTTATTCTTTCG 58.951 38.462 0.00 0.00 39.36 3.46
2695 5148 7.394816 CCGGATTGAATATTAGGACCATACTT 58.605 38.462 0.00 0.00 0.00 2.24
2700 5153 4.236195 TCCCGGATTGAATATTAGGACCA 58.764 43.478 0.73 0.00 0.00 4.02
2707 5160 6.183361 TGGAAGAGAATCCCGGATTGAATATT 60.183 38.462 17.76 6.76 38.82 1.28
2796 5249 9.905713 AGCTACTTAATGGATTCAGTTAAATCA 57.094 29.630 0.00 0.00 37.38 2.57
2861 5315 8.479313 AAAAGAACAAAACAGAAAATCAGGTC 57.521 30.769 0.00 0.00 0.00 3.85
2872 5326 9.791838 GTAACAAAAGTGAAAAGAACAAAACAG 57.208 29.630 0.00 0.00 0.00 3.16
3322 5777 4.330944 TTCTTCTGACCGAGCAAAAGTA 57.669 40.909 0.00 0.00 0.00 2.24
3345 5800 4.216257 TGAGAAGCTGAATTGGCTGTAAAC 59.784 41.667 3.66 0.00 40.19 2.01
3417 5872 0.812412 CACCGTTTCCACAGAACCGT 60.812 55.000 0.00 0.00 36.28 4.83
3451 5906 0.802607 GAGGATCAACGACAGACCGC 60.803 60.000 0.00 0.00 33.17 5.68
3643 6098 2.606551 GGCTTCAAGCAGCAGTCTTTTC 60.607 50.000 12.53 0.00 44.75 2.29
3685 6140 4.588951 TCAACATAGTCTTCGCTATCCCAT 59.411 41.667 0.00 0.00 29.89 4.00
3693 6148 8.023706 TGTATATCTCATCAACATAGTCTTCGC 58.976 37.037 0.00 0.00 0.00 4.70
3764 6219 1.334243 GCGAGCTCCGTATCTACAGTT 59.666 52.381 8.47 0.00 41.15 3.16
3815 6270 9.025041 AGGCAATTCCTAAAATATATACAAGGC 57.975 33.333 0.00 0.00 45.41 4.35
3848 6303 5.769662 AGGTCAAGATTTACATGCACAGAAA 59.230 36.000 0.00 0.00 0.00 2.52
4141 6605 2.434702 CTCCCCTTACGTTATTGCTCCT 59.565 50.000 0.00 0.00 0.00 3.69
4173 6637 4.373116 GAGGGGCGCGAGTGTTGA 62.373 66.667 12.10 0.00 0.00 3.18
4182 6646 2.552231 ATTAGTTGGGTGAGGGGCGC 62.552 60.000 0.00 0.00 0.00 6.53
4183 6647 0.748005 CATTAGTTGGGTGAGGGGCG 60.748 60.000 0.00 0.00 0.00 6.13
4232 6700 1.407299 CCTTCCTGTCATCCAATCGCA 60.407 52.381 0.00 0.00 0.00 5.10
4235 6703 1.064463 TGGCCTTCCTGTCATCCAATC 60.064 52.381 3.32 0.00 0.00 2.67
4242 6710 0.547471 TGGAGATGGCCTTCCTGTCA 60.547 55.000 14.77 5.99 0.00 3.58
4246 6714 2.049627 GCGATGGAGATGGCCTTCCT 62.050 60.000 14.77 3.43 0.00 3.36
4268 6736 1.302033 GTCACTGTGAGGTGGCTGG 60.302 63.158 11.41 0.00 38.61 4.85
4272 6740 2.343758 CCCGTCACTGTGAGGTGG 59.656 66.667 23.94 20.41 37.75 4.61
4304 6772 0.108615 CCCCGTCACTGTCAGATGAC 60.109 60.000 18.23 18.23 44.97 3.06
4305 6773 1.888436 GCCCCGTCACTGTCAGATGA 61.888 60.000 6.91 4.04 0.00 2.92
4308 6776 3.680786 CGCCCCGTCACTGTCAGA 61.681 66.667 6.91 0.00 0.00 3.27
4309 6777 3.680786 TCGCCCCGTCACTGTCAG 61.681 66.667 0.00 0.00 0.00 3.51
4311 6779 4.736896 GGTCGCCCCGTCACTGTC 62.737 72.222 0.00 0.00 0.00 3.51
4316 6784 3.691342 CTTCAGGTCGCCCCGTCA 61.691 66.667 0.00 0.00 38.74 4.35
4317 6785 4.452733 CCTTCAGGTCGCCCCGTC 62.453 72.222 0.00 0.00 38.74 4.79
4319 6787 3.470888 ATCCTTCAGGTCGCCCCG 61.471 66.667 0.00 0.00 38.74 5.73
4320 6788 2.190578 CATCCTTCAGGTCGCCCC 59.809 66.667 0.00 0.00 36.34 5.80
4327 6804 1.146263 GGTACCGGCATCCTTCAGG 59.854 63.158 0.00 0.00 0.00 3.86
4395 6872 1.995646 GAGTCGAAGCGAGGTCCCTC 61.996 65.000 3.09 3.09 36.23 4.30
4542 7019 8.287350 ACAGGTTTGATACTTACTATCCCTAGA 58.713 37.037 0.00 0.00 31.42 2.43
4546 7023 6.985059 GTCACAGGTTTGATACTTACTATCCC 59.015 42.308 0.00 0.00 31.42 3.85
4553 7030 5.001232 GCTTGGTCACAGGTTTGATACTTA 58.999 41.667 0.00 0.00 0.00 2.24
4587 7069 6.092807 GGAATACCTGAGACACAACTGAAATC 59.907 42.308 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.