Multiple sequence alignment - TraesCS4B01G091500

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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 TraesCS4B01G091500 chr4B 100.000 4984 0 0 1 4984 94763059 94768042 0.000000e+00 9204.0
1 TraesCS4B01G091500 chr4B 97.397 730 14 3 4260 4984 28682346 28681617 0.000000e+00 1238.0
2 TraesCS4B01G091500 chr4B 97.131 732 15 3 4258 4984 665293821 665293091 0.000000e+00 1230.0
3 TraesCS4B01G091500 chr4B 87.500 56 5 2 760 813 94763782 94763837 4.170000e-06 63.9
4 TraesCS4B01G091500 chr4B 87.500 56 5 2 724 779 94763818 94763871 4.170000e-06 63.9
5 TraesCS4B01G091500 chr4D 94.658 3426 122 22 881 4260 64187672 64191082 0.000000e+00 5256.0
6 TraesCS4B01G091500 chr4D 95.111 675 20 4 1 675 64186813 64187474 0.000000e+00 1051.0
7 TraesCS4B01G091500 chr4A 96.324 3183 108 6 881 4061 532353481 532350306 0.000000e+00 5221.0
8 TraesCS4B01G091500 chr4A 88.497 539 35 11 247 779 532354173 532353656 1.180000e-175 627.0
9 TraesCS4B01G091500 chr4A 94.677 263 14 0 1 263 532354450 532354188 4.640000e-110 409.0
10 TraesCS4B01G091500 chr3B 97.684 734 10 2 4258 4984 171120076 171120809 0.000000e+00 1254.0
11 TraesCS4B01G091500 chr3B 97.390 728 15 2 4261 4984 247808974 247809701 0.000000e+00 1236.0
12 TraesCS4B01G091500 chr5A 97.531 729 16 2 4258 4984 482426301 482427029 0.000000e+00 1245.0
13 TraesCS4B01G091500 chr3A 97.524 727 16 2 4260 4984 522043381 522044107 0.000000e+00 1242.0
14 TraesCS4B01G091500 chr2B 97.527 728 14 3 4260 4984 683096048 683096774 0.000000e+00 1242.0
15 TraesCS4B01G091500 chr2B 97.260 730 17 2 4258 4984 699182429 699181700 0.000000e+00 1234.0
16 TraesCS4B01G091500 chr2B 97.007 735 14 5 4256 4984 123108463 123109195 0.000000e+00 1229.0
17 TraesCS4B01G091500 chr1A 79.747 158 23 9 3315 3467 497504848 497504695 6.820000e-19 106.0
18 TraesCS4B01G091500 chr6B 91.026 78 4 3 4165 4240 279908110 279908186 8.830000e-18 102.0
19 TraesCS4B01G091500 chr6B 81.000 100 15 4 3320 3417 24916704 24916607 5.350000e-10 76.8
20 TraesCS4B01G091500 chr1B 79.114 158 24 9 3315 3467 539547863 539547710 3.170000e-17 100.0
21 TraesCS4B01G091500 chr6D 85.149 101 9 5 4165 4261 157156603 157156701 1.140000e-16 99.0
22 TraesCS4B01G091500 chrUn 80.682 88 11 5 3378 3463 372039634 372039551 4.170000e-06 63.9
23 TraesCS4B01G091500 chrUn 93.023 43 3 0 3375 3417 372064324 372064366 4.170000e-06 63.9
24 TraesCS4B01G091500 chr7D 88.000 50 6 0 3642 3691 509699889 509699938 5.390000e-05 60.2
25 TraesCS4B01G091500 chr6A 75.524 143 24 11 3327 3463 14411604 14411467 5.390000e-05 60.2
26 TraesCS4B01G091500 chr7A 100.000 31 0 0 4211 4241 511538129 511538099 1.940000e-04 58.4
27 TraesCS4B01G091500 chr7A 91.892 37 3 0 3642 3678 580655210 580655174 9.000000e-03 52.8


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 TraesCS4B01G091500 chr4B 94763059 94768042 4983 False 9204.000000 9204 100.0000 1 4984 1 chr4B.!!$F1 4983
1 TraesCS4B01G091500 chr4B 28681617 28682346 729 True 1238.000000 1238 97.3970 4260 4984 1 chr4B.!!$R1 724
2 TraesCS4B01G091500 chr4B 665293091 665293821 730 True 1230.000000 1230 97.1310 4258 4984 1 chr4B.!!$R2 726
3 TraesCS4B01G091500 chr4D 64186813 64191082 4269 False 3153.500000 5256 94.8845 1 4260 2 chr4D.!!$F1 4259
4 TraesCS4B01G091500 chr4A 532350306 532354450 4144 True 2085.666667 5221 93.1660 1 4061 3 chr4A.!!$R1 4060
5 TraesCS4B01G091500 chr3B 171120076 171120809 733 False 1254.000000 1254 97.6840 4258 4984 1 chr3B.!!$F1 726
6 TraesCS4B01G091500 chr3B 247808974 247809701 727 False 1236.000000 1236 97.3900 4261 4984 1 chr3B.!!$F2 723
7 TraesCS4B01G091500 chr5A 482426301 482427029 728 False 1245.000000 1245 97.5310 4258 4984 1 chr5A.!!$F1 726
8 TraesCS4B01G091500 chr3A 522043381 522044107 726 False 1242.000000 1242 97.5240 4260 4984 1 chr3A.!!$F1 724
9 TraesCS4B01G091500 chr2B 683096048 683096774 726 False 1242.000000 1242 97.5270 4260 4984 1 chr2B.!!$F2 724
10 TraesCS4B01G091500 chr2B 699181700 699182429 729 True 1234.000000 1234 97.2600 4258 4984 1 chr2B.!!$R1 726
11 TraesCS4B01G091500 chr2B 123108463 123109195 732 False 1229.000000 1229 97.0070 4256 4984 1 chr2B.!!$F1 728

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
543 575 0.392327 GTCTCTTGAGGCCTTGGAGC 60.392 60.0 6.77 7.76 0.00 4.70 F
1101 1268 0.035458 AAACCGAGGCACTTCTCCAG 59.965 55.0 0.00 0.00 41.55 3.86 F
1600 1767 0.322975 GAACTGCAGCTTGAGAGGGA 59.677 55.0 15.27 0.00 0.00 4.20 F
3216 3383 0.368227 GCGAGCTCAACTTCATCGTG 59.632 55.0 15.40 0.00 35.87 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1569 0.394488 CTCTCTAGCACCGTCAGGGA 60.394 60.0 0.00 0.0 43.47 4.20 R
2136 2303 0.690192 TGATCCGGAACCTTTGCAGA 59.310 50.0 9.01 0.0 0.00 4.26 R
3599 3777 0.033991 AGTAGGCGAGCTCTGAGGAA 60.034 55.0 12.85 0.0 0.00 3.36 R
4242 4454 0.744771 CCTTTACTCGGGCAGCTTCC 60.745 60.0 0.00 0.0 0.00 3.46 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
36 37 6.864685 GGTCGGTCATATCGTGTCATTTATAA 59.135 38.462 0.00 0.00 0.00 0.98
57 58 1.829222 GTTCCACTGGTTATCCCTCGA 59.171 52.381 0.00 0.00 0.00 4.04
66 67 1.066430 GTTATCCCTCGAAGCACCACA 60.066 52.381 0.00 0.00 0.00 4.17
275 307 6.094603 GGAGAAAATAGTTGATGTGTCATGCT 59.905 38.462 0.00 0.00 33.56 3.79
280 312 0.522626 TTGATGTGTCATGCTTGGCG 59.477 50.000 0.00 0.00 33.56 5.69
305 337 1.382420 TGCAGTTTTGGCCCTGGTT 60.382 52.632 0.00 0.00 0.00 3.67
375 407 5.105146 AGGTCATCTTCTCTGGAACATGTAC 60.105 44.000 0.00 0.00 38.20 2.90
376 408 4.800993 GTCATCTTCTCTGGAACATGTACG 59.199 45.833 0.00 0.00 38.20 3.67
377 409 4.462834 TCATCTTCTCTGGAACATGTACGT 59.537 41.667 0.00 0.00 38.20 3.57
378 410 5.650703 TCATCTTCTCTGGAACATGTACGTA 59.349 40.000 0.00 0.00 38.20 3.57
443 475 8.074370 CAGATGCCAATTATACAATGTTCTGAG 58.926 37.037 0.00 0.00 0.00 3.35
543 575 0.392327 GTCTCTTGAGGCCTTGGAGC 60.392 60.000 6.77 7.76 0.00 4.70
584 616 7.873719 TTTGTTGGTTTTATCTGAAGAGACA 57.126 32.000 0.00 0.00 0.00 3.41
585 617 7.873719 TTGTTGGTTTTATCTGAAGAGACAA 57.126 32.000 0.00 0.00 0.00 3.18
586 618 7.496529 TGTTGGTTTTATCTGAAGAGACAAG 57.503 36.000 0.00 0.00 0.00 3.16
587 619 7.279615 TGTTGGTTTTATCTGAAGAGACAAGA 58.720 34.615 0.00 0.00 0.00 3.02
588 620 7.442364 TGTTGGTTTTATCTGAAGAGACAAGAG 59.558 37.037 0.00 0.00 0.00 2.85
589 621 7.303182 TGGTTTTATCTGAAGAGACAAGAGA 57.697 36.000 0.00 0.00 0.00 3.10
611 643 6.821388 AGAGGTATGATTAGCAAACAGTAGG 58.179 40.000 0.00 0.00 0.00 3.18
664 696 8.274322 TCCATTAATGTACAGTGAGGAATGAAT 58.726 33.333 14.85 0.00 0.00 2.57
675 730 7.066284 ACAGTGAGGAATGAATATACAAAGCAC 59.934 37.037 0.00 0.00 0.00 4.40
676 731 7.281774 CAGTGAGGAATGAATATACAAAGCACT 59.718 37.037 0.00 0.00 0.00 4.40
677 732 7.497249 AGTGAGGAATGAATATACAAAGCACTC 59.503 37.037 0.00 0.00 0.00 3.51
678 733 6.767902 TGAGGAATGAATATACAAAGCACTCC 59.232 38.462 0.00 0.00 0.00 3.85
679 734 6.904626 AGGAATGAATATACAAAGCACTCCT 58.095 36.000 0.00 0.00 0.00 3.69
680 735 8.034313 AGGAATGAATATACAAAGCACTCCTA 57.966 34.615 0.00 0.00 0.00 2.94
686 741 8.755028 TGAATATACAAAGCACTCCTAAGTACA 58.245 33.333 0.00 0.00 33.25 2.90
695 750 3.935203 CACTCCTAAGTACAAGTGCCATG 59.065 47.826 0.00 0.00 33.42 3.66
697 752 4.184629 CTCCTAAGTACAAGTGCCATGAC 58.815 47.826 0.00 0.00 0.00 3.06
698 753 3.580895 TCCTAAGTACAAGTGCCATGACA 59.419 43.478 0.00 0.00 0.00 3.58
703 758 4.655963 AGTACAAGTGCCATGACAAGAAT 58.344 39.130 0.00 0.00 0.00 2.40
705 760 2.029649 ACAAGTGCCATGACAAGAATGC 60.030 45.455 0.00 0.00 0.00 3.56
706 761 2.211250 AGTGCCATGACAAGAATGCT 57.789 45.000 0.00 0.00 0.00 3.79
707 762 1.816835 AGTGCCATGACAAGAATGCTG 59.183 47.619 0.00 0.00 0.00 4.41
708 763 1.814394 GTGCCATGACAAGAATGCTGA 59.186 47.619 0.00 0.00 0.00 4.26
709 764 2.426024 GTGCCATGACAAGAATGCTGAT 59.574 45.455 0.00 0.00 0.00 2.90
710 765 2.425668 TGCCATGACAAGAATGCTGATG 59.574 45.455 0.00 0.00 0.00 3.07
711 766 2.223735 GCCATGACAAGAATGCTGATGG 60.224 50.000 0.00 0.00 34.91 3.51
713 768 3.446161 CCATGACAAGAATGCTGATGGTT 59.554 43.478 0.00 0.00 30.58 3.67
714 769 4.641541 CCATGACAAGAATGCTGATGGTTA 59.358 41.667 0.00 0.00 30.58 2.85
715 770 5.125900 CCATGACAAGAATGCTGATGGTTAA 59.874 40.000 0.00 0.00 30.58 2.01
716 771 5.885230 TGACAAGAATGCTGATGGTTAAG 57.115 39.130 0.00 0.00 0.00 1.85
717 772 4.701651 TGACAAGAATGCTGATGGTTAAGG 59.298 41.667 0.00 0.00 0.00 2.69
719 774 4.460382 ACAAGAATGCTGATGGTTAAGGTG 59.540 41.667 0.00 0.00 0.00 4.00
720 775 4.307032 AGAATGCTGATGGTTAAGGTGT 57.693 40.909 0.00 0.00 0.00 4.16
721 776 4.012374 AGAATGCTGATGGTTAAGGTGTG 58.988 43.478 0.00 0.00 0.00 3.82
722 777 3.719268 ATGCTGATGGTTAAGGTGTGA 57.281 42.857 0.00 0.00 0.00 3.58
724 779 2.371841 TGCTGATGGTTAAGGTGTGAGT 59.628 45.455 0.00 0.00 0.00 3.41
727 782 5.001232 GCTGATGGTTAAGGTGTGAGTTTA 58.999 41.667 0.00 0.00 0.00 2.01
728 783 5.648092 GCTGATGGTTAAGGTGTGAGTTTAT 59.352 40.000 0.00 0.00 0.00 1.40
729 784 6.151144 GCTGATGGTTAAGGTGTGAGTTTATT 59.849 38.462 0.00 0.00 0.00 1.40
754 812 6.522625 TTTTCCGATTAATGCCATTTCAGA 57.477 33.333 0.00 0.00 0.00 3.27
755 813 5.756195 TTCCGATTAATGCCATTTCAGAG 57.244 39.130 0.00 0.00 0.00 3.35
756 814 5.034852 TCCGATTAATGCCATTTCAGAGA 57.965 39.130 0.00 0.00 0.00 3.10
757 815 5.059161 TCCGATTAATGCCATTTCAGAGAG 58.941 41.667 0.00 0.00 0.00 3.20
758 816 4.818546 CCGATTAATGCCATTTCAGAGAGT 59.181 41.667 0.00 0.00 0.00 3.24
759 817 5.277683 CCGATTAATGCCATTTCAGAGAGTG 60.278 44.000 0.00 0.00 0.00 3.51
760 818 5.295292 CGATTAATGCCATTTCAGAGAGTGT 59.705 40.000 0.00 0.00 0.00 3.55
761 819 6.183360 CGATTAATGCCATTTCAGAGAGTGTT 60.183 38.462 0.00 0.00 0.00 3.32
762 820 6.899393 TTAATGCCATTTCAGAGAGTGTTT 57.101 33.333 0.00 0.00 0.00 2.83
763 821 4.778534 ATGCCATTTCAGAGAGTGTTTG 57.221 40.909 0.00 0.00 0.00 2.93
764 822 3.554934 TGCCATTTCAGAGAGTGTTTGT 58.445 40.909 0.00 0.00 0.00 2.83
765 823 4.713553 TGCCATTTCAGAGAGTGTTTGTA 58.286 39.130 0.00 0.00 0.00 2.41
766 824 5.316167 TGCCATTTCAGAGAGTGTTTGTAT 58.684 37.500 0.00 0.00 0.00 2.29
767 825 5.769662 TGCCATTTCAGAGAGTGTTTGTATT 59.230 36.000 0.00 0.00 0.00 1.89
768 826 6.265196 TGCCATTTCAGAGAGTGTTTGTATTT 59.735 34.615 0.00 0.00 0.00 1.40
769 827 7.147976 GCCATTTCAGAGAGTGTTTGTATTTT 58.852 34.615 0.00 0.00 0.00 1.82
770 828 7.653311 GCCATTTCAGAGAGTGTTTGTATTTTT 59.347 33.333 0.00 0.00 0.00 1.94
771 829 9.185192 CCATTTCAGAGAGTGTTTGTATTTTTC 57.815 33.333 0.00 0.00 0.00 2.29
772 830 9.734620 CATTTCAGAGAGTGTTTGTATTTTTCA 57.265 29.630 0.00 0.00 0.00 2.69
773 831 9.956720 ATTTCAGAGAGTGTTTGTATTTTTCAG 57.043 29.630 0.00 0.00 0.00 3.02
774 832 8.731275 TTCAGAGAGTGTTTGTATTTTTCAGA 57.269 30.769 0.00 0.00 0.00 3.27
775 833 8.142994 TCAGAGAGTGTTTGTATTTTTCAGAC 57.857 34.615 0.00 0.00 0.00 3.51
776 834 7.768582 TCAGAGAGTGTTTGTATTTTTCAGACA 59.231 33.333 0.00 0.00 0.00 3.41
777 835 8.397906 CAGAGAGTGTTTGTATTTTTCAGACAA 58.602 33.333 0.00 0.00 33.10 3.18
800 858 7.285401 ACAAACCATTTCAGAGAGTGTTTGTAT 59.715 33.333 16.21 1.37 39.63 2.29
804 862 8.695456 ACCATTTCAGAGAGTGTTTGTATTTTT 58.305 29.630 0.00 0.00 0.00 1.94
805 863 9.185192 CCATTTCAGAGAGTGTTTGTATTTTTC 57.815 33.333 0.00 0.00 0.00 2.29
843 901 8.213518 TCCATTTCAGAGAATATACAAAGCAC 57.786 34.615 0.00 0.00 0.00 4.40
845 903 8.341173 CCATTTCAGAGAATATACAAAGCACTC 58.659 37.037 0.00 0.00 0.00 3.51
847 905 6.798427 TCAGAGAATATACAAAGCACTCCT 57.202 37.500 0.00 0.00 0.00 3.69
848 906 7.898014 TCAGAGAATATACAAAGCACTCCTA 57.102 36.000 0.00 0.00 0.00 2.94
850 908 8.417106 TCAGAGAATATACAAAGCACTCCTAAG 58.583 37.037 0.00 0.00 0.00 2.18
854 912 9.203163 AGAATATACAAAGCACTCCTAAGTAGT 57.797 33.333 0.00 0.00 33.25 2.73
857 915 7.713734 ATACAAAGCACTCCTAAGTAGTACA 57.286 36.000 2.52 0.00 33.25 2.90
859 917 6.456501 ACAAAGCACTCCTAAGTAGTACAAG 58.543 40.000 2.52 0.00 33.25 3.16
861 919 5.646577 AGCACTCCTAAGTAGTACAAGTG 57.353 43.478 2.52 8.71 36.58 3.16
862 920 5.078256 AGCACTCCTAAGTAGTACAAGTGT 58.922 41.667 2.52 0.00 36.05 3.55
865 923 6.350277 GCACTCCTAAGTAGTACAAGTGTCAT 60.350 42.308 2.52 0.00 36.05 3.06
866 924 7.030165 CACTCCTAAGTAGTACAAGTGTCATG 58.970 42.308 2.52 0.00 33.25 3.07
867 925 6.946583 ACTCCTAAGTAGTACAAGTGTCATGA 59.053 38.462 2.52 0.00 32.59 3.07
868 926 7.094291 ACTCCTAAGTAGTACAAGTGTCATGAC 60.094 40.741 19.27 19.27 32.59 3.06
869 927 6.717997 TCCTAAGTAGTACAAGTGTCATGACA 59.282 38.462 24.56 24.56 39.32 3.58
870 928 7.231925 TCCTAAGTAGTACAAGTGTCATGACAA 59.768 37.037 29.42 11.59 43.77 3.18
871 929 7.870954 CCTAAGTAGTACAAGTGTCATGACAAA 59.129 37.037 29.42 5.89 43.77 2.83
872 930 9.256477 CTAAGTAGTACAAGTGTCATGACAAAA 57.744 33.333 29.42 10.86 43.77 2.44
873 931 8.500753 AAGTAGTACAAGTGTCATGACAAAAA 57.499 30.769 29.42 11.20 43.77 1.94
875 933 8.559536 AGTAGTACAAGTGTCATGACAAAAATG 58.440 33.333 29.42 24.12 43.77 2.32
877 935 5.266733 ACAAGTGTCATGACAAAAATGCT 57.733 34.783 29.42 17.93 43.77 3.79
878 936 5.045215 ACAAGTGTCATGACAAAAATGCTG 58.955 37.500 29.42 18.70 43.77 4.41
879 937 5.163530 ACAAGTGTCATGACAAAAATGCTGA 60.164 36.000 29.42 0.25 43.77 4.26
894 1060 9.462174 CAAAAATGCTGATCTGTTAACTAACAA 57.538 29.630 7.22 0.00 44.67 2.83
932 1099 4.654091 TTTTTCAGGTCTTCCAAAGCAG 57.346 40.909 0.00 0.00 35.89 4.24
938 1105 2.646798 AGGTCTTCCAAAGCAGAATCCT 59.353 45.455 0.00 0.00 35.89 3.24
986 1153 4.834496 TCAGTTCTTTCCAGATTTGCCAAT 59.166 37.500 0.00 0.00 0.00 3.16
993 1160 5.596836 TTCCAGATTTGCCAATACCAATC 57.403 39.130 0.00 0.00 0.00 2.67
994 1161 4.870636 TCCAGATTTGCCAATACCAATCT 58.129 39.130 0.00 0.00 0.00 2.40
1066 1233 0.972134 CCTCTCTGTGAGCTCAACCA 59.028 55.000 20.19 12.50 41.35 3.67
1086 1253 0.608130 GCCAAACTGATCCCCAAACC 59.392 55.000 0.00 0.00 0.00 3.27
1101 1268 0.035458 AAACCGAGGCACTTCTCCAG 59.965 55.000 0.00 0.00 41.55 3.86
1108 1275 2.037772 GAGGCACTTCTCCAGTTCAAGA 59.962 50.000 0.00 0.00 41.55 3.02
1159 1326 2.126888 CATGGACAAACGCCACGC 60.127 61.111 0.00 0.00 38.44 5.34
1197 1364 1.968017 CATCCAGTGCAACGCAGGT 60.968 57.895 0.00 0.00 45.86 4.00
1213 1380 2.341257 CAGGTTTGGTGACTGAGATCG 58.659 52.381 0.00 0.00 34.21 3.69
1398 1565 1.884926 CGGAGAGCTGCCGGATTTC 60.885 63.158 5.05 0.00 44.87 2.17
1402 1569 1.153549 GAGCTGCCGGATTTCTCGT 60.154 57.895 5.05 0.00 0.00 4.18
1404 1571 2.174319 GCTGCCGGATTTCTCGTCC 61.174 63.158 5.05 0.00 0.00 4.79
1450 1617 1.226128 GCGAACAATGGCTTCTCGC 60.226 57.895 0.00 0.00 46.69 5.03
1600 1767 0.322975 GAACTGCAGCTTGAGAGGGA 59.677 55.000 15.27 0.00 0.00 4.20
1638 1805 2.947532 CGAGCTGACCCTGCTGGAA 61.948 63.158 11.88 0.00 38.70 3.53
1654 1821 1.202879 TGGAAACGCTGGATTTGTCCT 60.203 47.619 0.00 0.00 0.00 3.85
1818 1985 3.733344 TAACCAGATCAGCGGCGGC 62.733 63.158 9.78 8.43 40.37 6.53
1930 2097 1.984570 CTCCGGTCCCTGAAGAGCA 60.985 63.158 0.00 0.00 33.83 4.26
1986 2153 3.351416 GCGAACTTCGGCCGGTTT 61.351 61.111 27.83 15.92 40.84 3.27
2136 2303 1.666872 GTACTCGGCGTGCCAAACT 60.667 57.895 12.06 0.00 35.37 2.66
2184 2351 4.864334 CTCACCGGCAGCATCCCC 62.864 72.222 0.00 0.00 0.00 4.81
2451 2618 0.957395 CGCTGCACCTGGAAGACAAT 60.957 55.000 0.00 0.00 34.07 2.71
2518 2685 3.702253 TCGAGATCGACGTCTCCG 58.298 61.111 14.70 10.78 44.22 4.63
2563 2730 3.485431 CTTCGCTGTCGCTGCTGG 61.485 66.667 0.00 0.00 35.26 4.85
2751 2918 2.982130 GGTCTCTGCGTCCATGGT 59.018 61.111 12.58 0.00 0.00 3.55
3216 3383 0.368227 GCGAGCTCAACTTCATCGTG 59.632 55.000 15.40 0.00 35.87 4.35
3414 3581 3.056749 AGTCCACCAACATACTTCTCGAC 60.057 47.826 0.00 0.00 0.00 4.20
3553 3729 8.926710 CCGACATTTATATTGTCTATCCAGTTC 58.073 37.037 12.12 0.00 41.05 3.01
3565 3741 7.402054 TGTCTATCCAGTTCATTAACCATGTT 58.598 34.615 0.00 0.00 36.15 2.71
3574 3750 6.942576 AGTTCATTAACCATGTTAGTGAGCTT 59.057 34.615 17.07 7.32 31.69 3.74
3595 3771 2.742053 TCAGCTTACAAATTCTCCGTGC 59.258 45.455 0.00 0.00 0.00 5.34
3599 3777 3.119495 GCTTACAAATTCTCCGTGCCATT 60.119 43.478 0.00 0.00 0.00 3.16
3626 3804 1.746220 GAGCTCGCCTACTCTCTCAAA 59.254 52.381 0.00 0.00 0.00 2.69
3857 4035 1.523258 GATCGCCATGCTCTGCACT 60.523 57.895 0.00 0.00 43.04 4.40
3917 4095 3.071459 GAACATGCTCACGGACGCG 62.071 63.158 3.53 3.53 0.00 6.01
3990 4168 4.285291 GCGCGCGCTGAATTTTAT 57.715 50.000 44.38 0.00 38.26 1.40
3991 4169 2.565868 GCGCGCGCTGAATTTTATT 58.434 47.368 44.38 0.00 38.26 1.40
3992 4170 1.737249 GCGCGCGCTGAATTTTATTA 58.263 45.000 44.38 0.00 38.26 0.98
4000 4178 6.128795 GCGCGCTGAATTTTATTAGAGTAGAT 60.129 38.462 26.67 0.00 0.00 1.98
4015 4193 1.409427 GTAGATTCTGACTCCGGGGTG 59.591 57.143 14.62 0.00 0.00 4.61
4033 4211 0.175760 TGCCACCGTCTTATCTCTGC 59.824 55.000 0.00 0.00 0.00 4.26
4073 4281 6.942005 TCTGATGTGATCTTTGTGGTGTATTT 59.058 34.615 0.00 0.00 0.00 1.40
4104 4312 9.326413 GGGTCATATGTTTGCAGGTATATATAC 57.674 37.037 13.60 13.60 0.00 1.47
4131 4343 6.472163 GTCAAGTATTTGCGACCATATTTTGG 59.528 38.462 0.00 0.00 41.64 3.28
4152 4364 7.461182 TTGGGTGGATAATGAAGTGTTTTAG 57.539 36.000 0.00 0.00 0.00 1.85
4165 4377 8.853077 TGAAGTGTTTTAGACTTGATGATGAT 57.147 30.769 0.00 0.00 33.71 2.45
4244 4456 4.967036 TGATGCAAATATACATCACCGGA 58.033 39.130 9.46 0.00 45.79 5.14
4247 4459 3.563808 TGCAAATATACATCACCGGAAGC 59.436 43.478 9.46 0.00 0.00 3.86
4251 4463 0.179045 ATACATCACCGGAAGCTGCC 60.179 55.000 9.46 0.00 0.00 4.85
4906 5127 5.122512 AGTTTTGAAGATCTCGTCGAGAA 57.877 39.130 27.50 9.19 42.27 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.177836 GGCAAAAACCTGTGGTGCTT 59.822 50.000 0.00 0.00 35.34 3.91
66 67 0.681564 TGACACGTGGGCAAAAACCT 60.682 50.000 21.57 0.00 0.00 3.50
275 307 0.537143 AAACTGCACTGGATCGCCAA 60.537 50.000 0.00 0.00 45.41 4.52
280 312 0.244721 GGCCAAAACTGCACTGGATC 59.755 55.000 0.00 0.00 31.38 3.36
305 337 3.920197 TCCCCTGTTTCCCTCTCATTTTA 59.080 43.478 0.00 0.00 0.00 1.52
375 407 6.715344 TGCTTTGGTCTGTTAATTACTACG 57.285 37.500 0.00 0.00 0.00 3.51
376 408 8.095937 AGTTGCTTTGGTCTGTTAATTACTAC 57.904 34.615 0.00 0.00 0.00 2.73
377 409 8.685838 AAGTTGCTTTGGTCTGTTAATTACTA 57.314 30.769 0.00 0.00 0.00 1.82
378 410 7.582667 AAGTTGCTTTGGTCTGTTAATTACT 57.417 32.000 0.00 0.00 0.00 2.24
583 615 6.820656 ACTGTTTGCTAATCATACCTCTCTTG 59.179 38.462 0.00 0.00 0.00 3.02
584 616 6.951971 ACTGTTTGCTAATCATACCTCTCTT 58.048 36.000 0.00 0.00 0.00 2.85
585 617 6.552445 ACTGTTTGCTAATCATACCTCTCT 57.448 37.500 0.00 0.00 0.00 3.10
586 618 6.926272 CCTACTGTTTGCTAATCATACCTCTC 59.074 42.308 0.00 0.00 0.00 3.20
587 619 6.183361 CCCTACTGTTTGCTAATCATACCTCT 60.183 42.308 0.00 0.00 0.00 3.69
588 620 5.992217 CCCTACTGTTTGCTAATCATACCTC 59.008 44.000 0.00 0.00 0.00 3.85
589 621 5.687706 GCCCTACTGTTTGCTAATCATACCT 60.688 44.000 0.00 0.00 0.00 3.08
611 643 4.449068 GTGTGTGCACTATATATGTCTGCC 59.551 45.833 19.41 0.00 42.13 4.85
636 668 8.933653 TCATTCCTCACTGTACATTAATGGATA 58.066 33.333 19.37 8.64 0.00 2.59
638 670 7.194112 TCATTCCTCACTGTACATTAATGGA 57.806 36.000 19.37 8.49 0.00 3.41
664 696 8.033038 CACTTGTACTTAGGAGTGCTTTGTATA 58.967 37.037 0.00 0.00 39.04 1.47
667 699 5.057149 CACTTGTACTTAGGAGTGCTTTGT 58.943 41.667 0.00 0.00 39.04 2.83
675 730 4.184629 GTCATGGCACTTGTACTTAGGAG 58.815 47.826 0.00 0.00 0.00 3.69
676 731 3.580895 TGTCATGGCACTTGTACTTAGGA 59.419 43.478 0.00 0.00 0.00 2.94
677 732 3.937814 TGTCATGGCACTTGTACTTAGG 58.062 45.455 0.00 0.00 0.00 2.69
678 733 5.237815 TCTTGTCATGGCACTTGTACTTAG 58.762 41.667 0.00 0.00 0.00 2.18
679 734 5.222079 TCTTGTCATGGCACTTGTACTTA 57.778 39.130 0.00 0.00 0.00 2.24
680 735 4.085357 TCTTGTCATGGCACTTGTACTT 57.915 40.909 0.00 0.00 0.00 2.24
686 741 2.230508 CAGCATTCTTGTCATGGCACTT 59.769 45.455 0.00 0.00 0.00 3.16
691 746 3.021695 ACCATCAGCATTCTTGTCATGG 58.978 45.455 0.00 0.00 36.23 3.66
695 750 4.702131 ACCTTAACCATCAGCATTCTTGTC 59.298 41.667 0.00 0.00 0.00 3.18
697 752 4.460382 ACACCTTAACCATCAGCATTCTTG 59.540 41.667 0.00 0.00 0.00 3.02
698 753 4.460382 CACACCTTAACCATCAGCATTCTT 59.540 41.667 0.00 0.00 0.00 2.52
703 758 2.371841 ACTCACACCTTAACCATCAGCA 59.628 45.455 0.00 0.00 0.00 4.41
705 760 7.687941 AATAAACTCACACCTTAACCATCAG 57.312 36.000 0.00 0.00 0.00 2.90
706 761 8.472007 AAAATAAACTCACACCTTAACCATCA 57.528 30.769 0.00 0.00 0.00 3.07
736 794 5.295292 ACACTCTCTGAAATGGCATTAATCG 59.705 40.000 14.05 5.49 0.00 3.34
744 802 5.886960 ATACAAACACTCTCTGAAATGGC 57.113 39.130 0.00 0.00 0.00 4.40
745 803 9.185192 GAAAAATACAAACACTCTCTGAAATGG 57.815 33.333 0.00 0.00 0.00 3.16
746 804 9.734620 TGAAAAATACAAACACTCTCTGAAATG 57.265 29.630 0.00 0.00 0.00 2.32
747 805 9.956720 CTGAAAAATACAAACACTCTCTGAAAT 57.043 29.630 0.00 0.00 0.00 2.17
748 806 9.173021 TCTGAAAAATACAAACACTCTCTGAAA 57.827 29.630 0.00 0.00 0.00 2.69
749 807 8.612619 GTCTGAAAAATACAAACACTCTCTGAA 58.387 33.333 0.00 0.00 0.00 3.02
750 808 7.768582 TGTCTGAAAAATACAAACACTCTCTGA 59.231 33.333 0.00 0.00 0.00 3.27
751 809 7.919690 TGTCTGAAAAATACAAACACTCTCTG 58.080 34.615 0.00 0.00 0.00 3.35
752 810 8.506168 TTGTCTGAAAAATACAAACACTCTCT 57.494 30.769 0.00 0.00 30.54 3.10
760 818 9.658799 TGAAATGGTTTGTCTGAAAAATACAAA 57.341 25.926 0.00 0.00 39.95 2.83
761 819 9.311916 CTGAAATGGTTTGTCTGAAAAATACAA 57.688 29.630 0.00 0.00 0.00 2.41
762 820 8.690884 TCTGAAATGGTTTGTCTGAAAAATACA 58.309 29.630 0.00 0.38 0.00 2.29
763 821 9.185192 CTCTGAAATGGTTTGTCTGAAAAATAC 57.815 33.333 0.00 0.00 0.00 1.89
764 822 9.130661 TCTCTGAAATGGTTTGTCTGAAAAATA 57.869 29.630 0.00 0.00 0.00 1.40
765 823 8.010733 TCTCTGAAATGGTTTGTCTGAAAAAT 57.989 30.769 0.00 0.00 0.00 1.82
766 824 7.122650 ACTCTCTGAAATGGTTTGTCTGAAAAA 59.877 33.333 0.00 0.00 0.00 1.94
767 825 6.603201 ACTCTCTGAAATGGTTTGTCTGAAAA 59.397 34.615 0.00 0.00 0.00 2.29
768 826 6.038603 CACTCTCTGAAATGGTTTGTCTGAAA 59.961 38.462 0.00 0.00 0.00 2.69
769 827 5.528690 CACTCTCTGAAATGGTTTGTCTGAA 59.471 40.000 0.00 0.00 0.00 3.02
770 828 5.059161 CACTCTCTGAAATGGTTTGTCTGA 58.941 41.667 0.00 0.00 0.00 3.27
771 829 4.818546 ACACTCTCTGAAATGGTTTGTCTG 59.181 41.667 0.00 0.00 0.00 3.51
772 830 5.041191 ACACTCTCTGAAATGGTTTGTCT 57.959 39.130 0.00 0.00 0.00 3.41
773 831 5.757850 AACACTCTCTGAAATGGTTTGTC 57.242 39.130 0.00 0.00 0.00 3.18
774 832 5.418840 ACAAACACTCTCTGAAATGGTTTGT 59.581 36.000 17.26 17.26 46.82 2.83
775 833 5.894807 ACAAACACTCTCTGAAATGGTTTG 58.105 37.500 16.40 16.40 45.34 2.93
776 834 7.823745 ATACAAACACTCTCTGAAATGGTTT 57.176 32.000 0.00 0.00 0.00 3.27
777 835 7.823745 AATACAAACACTCTCTGAAATGGTT 57.176 32.000 0.00 0.00 0.00 3.67
820 878 8.341173 GGAGTGCTTTGTATATTCTCTGAAATG 58.659 37.037 0.00 0.00 0.00 2.32
821 879 8.270744 AGGAGTGCTTTGTATATTCTCTGAAAT 58.729 33.333 0.00 0.00 0.00 2.17
827 885 9.685828 CTACTTAGGAGTGCTTTGTATATTCTC 57.314 37.037 0.00 0.00 36.60 2.87
831 889 9.417561 TGTACTACTTAGGAGTGCTTTGTATAT 57.582 33.333 13.58 0.00 36.60 0.86
833 891 7.713734 TGTACTACTTAGGAGTGCTTTGTAT 57.286 36.000 13.58 0.00 36.60 2.29
834 892 7.232127 ACTTGTACTACTTAGGAGTGCTTTGTA 59.768 37.037 13.58 0.00 36.60 2.41
835 893 6.041751 ACTTGTACTACTTAGGAGTGCTTTGT 59.958 38.462 13.58 7.01 36.60 2.83
839 897 5.078256 ACACTTGTACTACTTAGGAGTGCT 58.922 41.667 13.58 0.00 36.60 4.40
840 898 5.048224 TGACACTTGTACTACTTAGGAGTGC 60.048 44.000 7.48 6.55 36.60 4.40
841 899 6.570672 TGACACTTGTACTACTTAGGAGTG 57.429 41.667 7.48 2.93 36.60 3.51
843 901 7.094334 TGTCATGACACTTGTACTACTTAGGAG 60.094 40.741 24.56 0.00 36.21 3.69
845 903 6.920817 TGTCATGACACTTGTACTACTTAGG 58.079 40.000 24.56 0.00 36.21 2.69
847 905 9.602568 TTTTTGTCATGACACTTGTACTACTTA 57.397 29.630 27.88 5.99 41.67 2.24
848 906 8.500753 TTTTTGTCATGACACTTGTACTACTT 57.499 30.769 27.88 0.00 41.67 2.24
850 908 7.323656 GCATTTTTGTCATGACACTTGTACTAC 59.676 37.037 27.88 8.74 41.67 2.73
854 912 6.039159 TCAGCATTTTTGTCATGACACTTGTA 59.961 34.615 27.88 10.60 41.67 2.41
856 914 5.283294 TCAGCATTTTTGTCATGACACTTG 58.717 37.500 27.88 20.89 41.67 3.16
857 915 5.518848 TCAGCATTTTTGTCATGACACTT 57.481 34.783 27.88 10.23 41.67 3.16
859 917 5.571741 CAGATCAGCATTTTTGTCATGACAC 59.428 40.000 27.88 15.11 41.67 3.67
861 919 5.706916 ACAGATCAGCATTTTTGTCATGAC 58.293 37.500 19.27 19.27 0.00 3.06
862 920 5.970317 ACAGATCAGCATTTTTGTCATGA 57.030 34.783 0.00 0.00 0.00 3.07
865 923 7.275888 AGTTAACAGATCAGCATTTTTGTCA 57.724 32.000 8.61 0.00 0.00 3.58
866 924 9.118236 GTTAGTTAACAGATCAGCATTTTTGTC 57.882 33.333 8.61 0.00 36.25 3.18
867 925 8.629158 TGTTAGTTAACAGATCAGCATTTTTGT 58.371 29.630 8.61 0.00 40.93 2.83
868 926 9.462174 TTGTTAGTTAACAGATCAGCATTTTTG 57.538 29.630 8.61 0.00 45.77 2.44
869 927 9.683069 CTTGTTAGTTAACAGATCAGCATTTTT 57.317 29.630 8.61 0.00 45.77 1.94
870 928 8.850156 ACTTGTTAGTTAACAGATCAGCATTTT 58.150 29.630 8.61 0.00 45.77 1.82
871 929 8.396272 ACTTGTTAGTTAACAGATCAGCATTT 57.604 30.769 8.61 0.00 45.77 2.32
872 930 7.986085 ACTTGTTAGTTAACAGATCAGCATT 57.014 32.000 8.61 0.00 45.77 3.56
873 931 7.986085 AACTTGTTAGTTAACAGATCAGCAT 57.014 32.000 8.61 0.00 45.77 3.79
875 933 7.861630 TGAAACTTGTTAGTTAACAGATCAGC 58.138 34.615 8.61 0.00 45.77 4.26
877 935 9.778741 AGATGAAACTTGTTAGTTAACAGATCA 57.221 29.630 8.61 6.91 45.77 2.92
894 1060 6.927381 CCTGAAAAATTGCAAGAGATGAAACT 59.073 34.615 4.94 0.00 25.93 2.66
932 1099 5.710567 GGGTATTTAGTATTGCCCAGGATTC 59.289 44.000 0.00 0.00 36.25 2.52
986 1153 7.392953 TGTGTATTCTCATTGCAAAGATTGGTA 59.607 33.333 1.71 0.00 0.00 3.25
993 1160 6.446781 AGGATGTGTATTCTCATTGCAAAG 57.553 37.500 1.71 0.00 0.00 2.77
994 1161 8.523915 AATAGGATGTGTATTCTCATTGCAAA 57.476 30.769 1.71 0.00 0.00 3.68
1066 1233 1.632589 GTTTGGGGATCAGTTTGGCT 58.367 50.000 0.00 0.00 0.00 4.75
1086 1253 0.318441 TGAACTGGAGAAGTGCCTCG 59.682 55.000 0.00 0.00 39.81 4.63
1159 1326 4.047125 ATGGAACTGGCACGGGGG 62.047 66.667 0.00 0.00 40.47 5.40
1197 1364 1.014044 GCGCGATCTCAGTCACCAAA 61.014 55.000 12.10 0.00 0.00 3.28
1402 1569 0.394488 CTCTCTAGCACCGTCAGGGA 60.394 60.000 0.00 0.00 43.47 4.20
1539 1706 2.205022 TCTTGAGGTTCCCAATGCTG 57.795 50.000 0.00 0.00 0.00 4.41
1654 1821 2.387445 CGCCGGCGAGATTGTTCAA 61.387 57.895 44.86 0.00 42.83 2.69
1818 1985 3.957535 GCGAATGCTGCCGGGATG 61.958 66.667 2.18 0.00 38.39 3.51
1930 2097 1.297664 CGGTTCTCGTAGACGGAGAT 58.702 55.000 1.67 0.00 40.29 2.75
2136 2303 0.690192 TGATCCGGAACCTTTGCAGA 59.310 50.000 9.01 0.00 0.00 4.26
2184 2351 3.316573 GAGCCCCCACAACCTCTCG 62.317 68.421 0.00 0.00 0.00 4.04
2298 2465 1.233019 CACTGAGCCTGTTGTTCTGG 58.767 55.000 0.00 0.00 38.06 3.86
2402 2569 0.899717 TGCCAAGTTCCCAATCTGCC 60.900 55.000 0.00 0.00 0.00 4.85
2451 2618 2.996153 AATGCGCCACCCAATGCA 60.996 55.556 4.18 0.00 42.22 3.96
2518 2685 4.452733 CCCCGTGAGCTCGTTCCC 62.453 72.222 9.64 0.00 0.00 3.97
2563 2730 2.055100 GTTGAGTGAGTTCAGAGACGC 58.945 52.381 0.00 0.00 0.00 5.19
2751 2918 4.742201 GCGCCGAGCTCAGACCAA 62.742 66.667 15.40 0.00 44.04 3.67
2988 3155 2.645567 CCGACGCCGCATATCTCT 59.354 61.111 0.00 0.00 0.00 3.10
3216 3383 0.040958 CCCGCGGTATGTACTCGTAC 60.041 60.000 26.12 0.35 35.86 3.67
3414 3581 1.030488 TCTTGGCCTCGTAGTCCTCG 61.030 60.000 3.32 0.00 0.00 4.63
3553 3729 6.676456 GCTGAAGCTCACTAACATGGTTAATG 60.676 42.308 0.00 0.00 39.06 1.90
3574 3750 2.742053 GCACGGAGAATTTGTAAGCTGA 59.258 45.455 0.00 0.00 0.00 4.26
3595 3771 0.813210 GGCGAGCTCTGAGGAAATGG 60.813 60.000 12.85 0.00 0.00 3.16
3599 3777 0.033991 AGTAGGCGAGCTCTGAGGAA 60.034 55.000 12.85 0.00 0.00 3.36
3626 3804 1.575576 CGTCCGTCTTCTCCGTCACT 61.576 60.000 0.00 0.00 0.00 3.41
3917 4095 4.814294 CTACAGGACCCCGCGCAC 62.814 72.222 8.75 0.00 0.00 5.34
3990 4168 4.462133 CCCGGAGTCAGAATCTACTCTAA 58.538 47.826 0.73 0.00 41.53 2.10
3991 4169 3.181442 CCCCGGAGTCAGAATCTACTCTA 60.181 52.174 0.73 0.00 41.53 2.43
3992 4170 2.423660 CCCCGGAGTCAGAATCTACTCT 60.424 54.545 0.73 1.86 41.53 3.24
4000 4178 3.319198 GGCACCCCGGAGTCAGAA 61.319 66.667 0.73 0.00 0.00 3.02
4010 4188 1.153229 GATAAGACGGTGGCACCCC 60.153 63.158 30.03 21.34 33.75 4.95
4015 4193 0.461961 AGCAGAGATAAGACGGTGGC 59.538 55.000 0.00 0.00 0.00 5.01
4073 4281 4.719773 ACCTGCAAACATATGACCCTACTA 59.280 41.667 10.38 0.00 0.00 1.82
4104 4312 5.991328 ATATGGTCGCAAATACTTGACAG 57.009 39.130 0.00 0.00 34.14 3.51
4105 4313 6.751514 AAATATGGTCGCAAATACTTGACA 57.248 33.333 0.00 0.00 34.14 3.58
4106 4314 6.472163 CCAAAATATGGTCGCAAATACTTGAC 59.528 38.462 0.00 0.00 44.85 3.18
4107 4315 6.559810 CCAAAATATGGTCGCAAATACTTGA 58.440 36.000 0.00 0.00 44.85 3.02
4108 4316 6.810888 CCAAAATATGGTCGCAAATACTTG 57.189 37.500 0.00 0.00 44.85 3.16
4131 4343 7.923414 AGTCTAAAACACTTCATTATCCACC 57.077 36.000 0.00 0.00 0.00 4.61
4242 4454 0.744771 CCTTTACTCGGGCAGCTTCC 60.745 60.000 0.00 0.00 0.00 3.46
4244 4456 1.299976 CCCTTTACTCGGGCAGCTT 59.700 57.895 0.00 0.00 34.32 3.74
4247 4459 1.153628 CGACCCTTTACTCGGGCAG 60.154 63.158 0.00 0.00 46.04 4.85
4251 4463 1.996786 TAGCGCGACCCTTTACTCGG 61.997 60.000 12.10 0.00 0.00 4.63
4402 4614 7.722795 AAAACGGATTTTCAATCGGATTTTT 57.277 28.000 0.00 5.70 32.29 1.94
4433 4646 2.029470 AGATCTCATCGCGAGGGATTTC 60.029 50.000 21.76 15.34 42.55 2.17
4862 5083 6.731467 ACTAGACCCCATGTTGATATGTTTT 58.269 36.000 0.00 0.00 0.00 2.43
4906 5127 6.850752 AATCCGTTTTCACCATTAAATCCT 57.149 33.333 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.