Multiple sequence alignment - TraesCS3D01G271200

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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 TraesCS3D01G271200 chr3D 100.000 5502 0 0 1 5502 376161379 376166880 0.000000e+00 10161.0
1 TraesCS3D01G271200 chr3D 95.035 705 33 2 4799 5502 300917965 300918668 0.000000e+00 1107.0
2 TraesCS3D01G271200 chr3A 93.075 2888 87 28 820 3657 500973939 500976763 0.000000e+00 4120.0
3 TraesCS3D01G271200 chr3A 91.734 871 44 13 3920 4778 500977070 500977924 0.000000e+00 1184.0
4 TraesCS3D01G271200 chr3A 90.196 816 43 22 1 793 500972961 500973762 0.000000e+00 1029.0
5 TraesCS3D01G271200 chr3A 95.567 203 9 0 3672 3874 500976870 500977072 5.320000e-85 326.0
6 TraesCS3D01G271200 chr3A 97.500 40 1 0 3638 3677 500976808 500976769 9.890000e-08 69.4
7 TraesCS3D01G271200 chr3B 92.700 2904 104 32 820 3677 490595220 490598061 0.000000e+00 4089.0
8 TraesCS3D01G271200 chr3B 93.025 1104 50 5 3671 4768 490598182 490599264 0.000000e+00 1587.0
9 TraesCS3D01G271200 chr3B 89.791 813 49 18 1 790 490594237 490595038 0.000000e+00 1011.0
10 TraesCS3D01G271200 chr3B 93.333 45 2 1 3638 3681 490598113 490598069 1.280000e-06 65.8
11 TraesCS3D01G271200 chr7D 95.851 723 30 0 4780 5502 484338446 484337724 0.000000e+00 1170.0
12 TraesCS3D01G271200 chr7D 95.436 723 32 1 4780 5502 574912527 574913248 0.000000e+00 1151.0
13 TraesCS3D01G271200 chr2D 95.304 724 28 2 4779 5502 398462271 398461554 0.000000e+00 1144.0
14 TraesCS3D01G271200 chr6D 94.437 719 40 0 4778 5496 396006488 396005770 0.000000e+00 1107.0
15 TraesCS3D01G271200 chr6D 94.207 725 32 7 4780 5502 346273018 346273734 0.000000e+00 1098.0
16 TraesCS3D01G271200 chr4B 94.452 721 36 3 4782 5502 52585752 52585036 0.000000e+00 1107.0
17 TraesCS3D01G271200 chr5D 94.329 723 36 1 4780 5502 331545597 331546314 0.000000e+00 1103.0
18 TraesCS3D01G271200 chr1D 94.183 722 34 4 4782 5502 494455795 494456509 0.000000e+00 1094.0


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 TraesCS3D01G271200 chr3D 376161379 376166880 5501 False 10161.00 10161 100.000000 1 5502 1 chr3D.!!$F2 5501
1 TraesCS3D01G271200 chr3D 300917965 300918668 703 False 1107.00 1107 95.035000 4799 5502 1 chr3D.!!$F1 703
2 TraesCS3D01G271200 chr3A 500972961 500977924 4963 False 1664.75 4120 92.643000 1 4778 4 chr3A.!!$F1 4777
3 TraesCS3D01G271200 chr3B 490594237 490599264 5027 False 2229.00 4089 91.838667 1 4768 3 chr3B.!!$F1 4767
4 TraesCS3D01G271200 chr7D 484337724 484338446 722 True 1170.00 1170 95.851000 4780 5502 1 chr7D.!!$R1 722
5 TraesCS3D01G271200 chr7D 574912527 574913248 721 False 1151.00 1151 95.436000 4780 5502 1 chr7D.!!$F1 722
6 TraesCS3D01G271200 chr2D 398461554 398462271 717 True 1144.00 1144 95.304000 4779 5502 1 chr2D.!!$R1 723
7 TraesCS3D01G271200 chr6D 396005770 396006488 718 True 1107.00 1107 94.437000 4778 5496 1 chr6D.!!$R1 718
8 TraesCS3D01G271200 chr6D 346273018 346273734 716 False 1098.00 1098 94.207000 4780 5502 1 chr6D.!!$F1 722
9 TraesCS3D01G271200 chr4B 52585036 52585752 716 True 1107.00 1107 94.452000 4782 5502 1 chr4B.!!$R1 720
10 TraesCS3D01G271200 chr5D 331545597 331546314 717 False 1103.00 1103 94.329000 4780 5502 1 chr5D.!!$F1 722
11 TraesCS3D01G271200 chr1D 494455795 494456509 714 False 1094.00 1094 94.183000 4782 5502 1 chr1D.!!$F1 720

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
815 845 0.323633 TCATGGTGGCAATGGAGGTG 60.324 55.000 0.0 0.0 0.00 4.00 F
1677 1879 1.136695 CTCTCACCTCACCTCATCTGC 59.863 57.143 0.0 0.0 0.00 4.26 F
3069 3296 1.739067 GCTTTCATAGCCCGTCTGTT 58.261 50.000 0.0 0.0 44.48 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 2956 1.912043 AGGCAGCACTTTGGAGATAGT 59.088 47.619 0.00 0.00 0.0 2.12 R
3177 3404 0.538057 TCTTGACAGGCCAGGCAAAG 60.538 55.000 18.17 11.67 0.0 2.77 R
4777 5156 0.107654 GCGATGGAGTTGGCCTAAGT 60.108 55.000 3.32 0.00 0.0 2.24 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
198 200 3.311486 AACATATTTTTGTGGGTGCGG 57.689 42.857 0.00 0.00 0.00 5.69
313 315 0.963962 CTGCAGCACCTGTTGGAATT 59.036 50.000 0.00 0.00 37.04 2.17
358 361 1.066430 GCCATTTCGACACTCCTGGTA 60.066 52.381 0.00 0.00 0.00 3.25
363 366 2.577593 GACACTCCTGGTACCGCC 59.422 66.667 7.57 0.00 37.90 6.13
408 413 0.958382 GTTACACAATGCTGGCCGGA 60.958 55.000 18.31 2.96 0.00 5.14
417 422 2.420890 CTGGCCGGATCTCTCTGC 59.579 66.667 5.28 0.00 0.00 4.26
418 423 3.496875 CTGGCCGGATCTCTCTGCG 62.497 68.421 5.28 0.00 0.00 5.18
419 424 4.959596 GGCCGGATCTCTCTGCGC 62.960 72.222 5.05 0.00 0.00 6.09
421 426 4.637489 CCGGATCTCTCTGCGCGG 62.637 72.222 10.86 10.86 0.00 6.46
422 427 3.893763 CGGATCTCTCTGCGCGGT 61.894 66.667 17.37 0.00 0.00 5.68
423 428 2.279120 GGATCTCTCTGCGCGGTG 60.279 66.667 17.37 14.57 0.00 4.94
447 452 3.461061 CAGTGAGCAGAGAGTGTTTGAA 58.539 45.455 0.00 0.00 0.00 2.69
500 511 3.257933 CTGCGAGAAACAGGGCAC 58.742 61.111 0.00 0.00 0.00 5.01
551 563 3.517296 TTTTTGTGCAGGGGAGATGTA 57.483 42.857 0.00 0.00 0.00 2.29
562 574 4.346418 CAGGGGAGATGTATGATATAGCCC 59.654 50.000 0.00 0.00 0.00 5.19
602 614 2.766828 GCCCTGTCCTGTAGTAGTGAAT 59.233 50.000 0.00 0.00 0.00 2.57
643 655 3.007290 TGCTGCAGACTTGTAGTTCATCT 59.993 43.478 20.43 0.00 39.03 2.90
645 657 4.564041 CTGCAGACTTGTAGTTCATCTGT 58.436 43.478 8.42 0.00 36.26 3.41
647 659 6.096673 TGCAGACTTGTAGTTCATCTGTTA 57.903 37.500 0.00 0.00 36.26 2.41
656 668 5.958380 TGTAGTTCATCTGTTACTGGGATCT 59.042 40.000 0.00 0.00 0.00 2.75
657 669 5.606348 AGTTCATCTGTTACTGGGATCTC 57.394 43.478 0.00 0.00 0.00 2.75
661 673 4.895889 TCATCTGTTACTGGGATCTCGAAT 59.104 41.667 0.00 0.00 0.00 3.34
664 676 6.978674 TCTGTTACTGGGATCTCGAATTAT 57.021 37.500 0.00 0.00 0.00 1.28
665 677 7.361457 TCTGTTACTGGGATCTCGAATTATT 57.639 36.000 0.00 0.00 0.00 1.40
668 680 8.473358 TGTTACTGGGATCTCGAATTATTAGA 57.527 34.615 0.00 0.00 0.00 2.10
670 682 9.930693 GTTACTGGGATCTCGAATTATTAGAAT 57.069 33.333 0.00 0.00 0.00 2.40
718 743 3.055094 TCCAGCCTGGTTCTTCAGTAATC 60.055 47.826 11.27 0.00 39.03 1.75
748 778 1.303888 CTGTCATGCCTGGCAACCT 60.304 57.895 27.24 6.43 43.62 3.50
749 779 0.896940 CTGTCATGCCTGGCAACCTT 60.897 55.000 27.24 5.99 43.62 3.50
754 784 1.895131 CATGCCTGGCAACCTTTAAGT 59.105 47.619 27.24 2.08 43.62 2.24
779 809 6.898041 TCGAACCAGTAAATTGTTCAGAATG 58.102 36.000 6.46 0.00 38.59 2.67
782 812 7.519809 CGAACCAGTAAATTGTTCAGAATGTCA 60.520 37.037 6.46 0.00 38.59 3.58
784 814 8.862325 ACCAGTAAATTGTTCAGAATGTCATA 57.138 30.769 0.00 0.00 37.40 2.15
795 825 9.500785 TGTTCAGAATGTCATATTACTTTGTGA 57.499 29.630 9.91 9.91 36.01 3.58
798 828 9.889128 TCAGAATGTCATATTACTTTGTGATCA 57.111 29.630 9.91 0.00 34.19 2.92
801 831 9.888878 GAATGTCATATTACTTTGTGATCATGG 57.111 33.333 0.00 0.00 0.00 3.66
802 832 8.985315 ATGTCATATTACTTTGTGATCATGGT 57.015 30.769 0.00 0.00 0.00 3.55
805 835 4.989279 ATTACTTTGTGATCATGGTGGC 57.011 40.909 0.00 0.00 0.00 5.01
806 836 2.291209 ACTTTGTGATCATGGTGGCA 57.709 45.000 0.00 0.00 0.00 4.92
808 838 3.167485 ACTTTGTGATCATGGTGGCAAT 58.833 40.909 0.00 0.00 0.00 3.56
809 839 3.056393 ACTTTGTGATCATGGTGGCAATG 60.056 43.478 0.00 2.55 0.00 2.82
810 840 1.476477 TGTGATCATGGTGGCAATGG 58.524 50.000 0.00 0.00 0.00 3.16
811 841 1.005687 TGTGATCATGGTGGCAATGGA 59.994 47.619 0.00 0.00 0.00 3.41
813 843 1.325355 GATCATGGTGGCAATGGAGG 58.675 55.000 0.00 0.00 0.00 4.30
814 844 0.632835 ATCATGGTGGCAATGGAGGT 59.367 50.000 0.00 0.00 0.00 3.85
815 845 0.323633 TCATGGTGGCAATGGAGGTG 60.324 55.000 0.00 0.00 0.00 4.00
841 1023 8.978874 AAAATCAGCTGTATGTAATCATGGTA 57.021 30.769 14.67 0.00 35.70 3.25
843 1025 5.853936 TCAGCTGTATGTAATCATGGTACC 58.146 41.667 14.67 4.43 35.70 3.34
847 1029 7.331934 CAGCTGTATGTAATCATGGTACCATAC 59.668 40.741 26.91 20.63 34.91 2.39
866 1048 1.818674 ACGGCAATGGAGGTGAAAATC 59.181 47.619 0.00 0.00 0.00 2.17
870 1052 3.259123 GGCAATGGAGGTGAAAATCACTT 59.741 43.478 10.06 2.69 46.19 3.16
974 1158 1.600485 TCGATACGCTGATAACTCGCA 59.400 47.619 0.00 0.00 0.00 5.10
976 1160 2.320367 GATACGCTGATAACTCGCAGG 58.680 52.381 0.00 0.00 32.83 4.85
1510 1707 4.838486 GCGTCTCAGTCCCGCTCG 62.838 72.222 0.00 0.00 43.81 5.03
1558 1755 1.187567 AAATGTTCTGCAGTGGGGGC 61.188 55.000 14.67 0.00 0.00 5.80
1560 1757 2.674380 GTTCTGCAGTGGGGGCTG 60.674 66.667 14.67 0.00 39.37 4.85
1568 1765 1.755179 CAGTGGGGGCTGTTATTCTG 58.245 55.000 0.00 0.00 0.00 3.02
1601 1798 1.896220 AGCAATTCGTTTGAGCAGGA 58.104 45.000 5.27 0.00 37.53 3.86
1676 1878 2.455557 ACTCTCACCTCACCTCATCTG 58.544 52.381 0.00 0.00 0.00 2.90
1677 1879 1.136695 CTCTCACCTCACCTCATCTGC 59.863 57.143 0.00 0.00 0.00 4.26
1936 2158 4.290093 TGTAGGCTGTCAATAGATCCACT 58.710 43.478 0.00 0.00 0.00 4.00
2028 2250 2.080693 CGGTGGCATTGTAAGCTGTTA 58.919 47.619 0.00 0.00 0.00 2.41
2396 2621 1.973812 GCCAAGTGCTCAAGGTCCC 60.974 63.158 0.00 0.00 36.87 4.46
2424 2649 7.007725 GTGTTCTTCAAGAATGAAATATGCACG 59.992 37.037 2.39 0.00 44.64 5.34
2439 2664 8.447787 AAATATGCACGAATTTGTGTTACTTC 57.552 30.769 23.70 9.21 41.94 3.01
2611 2836 7.077605 TGAATTCACTTTTGATTAGTGCTTCG 58.922 34.615 3.38 0.00 42.12 3.79
2622 2847 9.651913 TTTGATTAGTGCTTCGCATATATGATA 57.348 29.630 17.10 0.13 41.91 2.15
2731 2956 6.092122 CAGGATTAGTTTGCGTCTTGTTCATA 59.908 38.462 0.00 0.00 0.00 2.15
2885 3110 3.409026 AGCAGCTGCCAAGTATATACC 57.591 47.619 34.39 2.87 43.38 2.73
2914 3139 7.373493 AGCTGTTTCTCTTACAAATTGGATTG 58.627 34.615 0.00 0.00 36.37 2.67
2920 3145 7.645058 TCTCTTACAAATTGGATTGGGAATC 57.355 36.000 0.00 0.00 34.56 2.52
2938 3163 5.463724 GGGAATCACACTCGATAAGCTTTAG 59.536 44.000 3.20 0.08 0.00 1.85
3069 3296 1.739067 GCTTTCATAGCCCGTCTGTT 58.261 50.000 0.00 0.00 44.48 3.16
3070 3297 2.901249 GCTTTCATAGCCCGTCTGTTA 58.099 47.619 0.00 0.00 44.48 2.41
3071 3298 2.866762 GCTTTCATAGCCCGTCTGTTAG 59.133 50.000 0.00 0.00 44.48 2.34
3072 3299 3.430374 GCTTTCATAGCCCGTCTGTTAGA 60.430 47.826 0.00 0.00 44.48 2.10
3073 3300 4.740934 GCTTTCATAGCCCGTCTGTTAGAT 60.741 45.833 0.00 0.00 44.48 1.98
3074 3301 5.509163 GCTTTCATAGCCCGTCTGTTAGATA 60.509 44.000 0.00 0.00 44.48 1.98
3075 3302 5.707242 TTCATAGCCCGTCTGTTAGATAG 57.293 43.478 0.00 0.00 0.00 2.08
3076 3303 4.981812 TCATAGCCCGTCTGTTAGATAGA 58.018 43.478 0.00 0.00 0.00 1.98
3077 3304 5.571285 TCATAGCCCGTCTGTTAGATAGAT 58.429 41.667 0.00 0.00 0.00 1.98
3078 3305 6.718294 TCATAGCCCGTCTGTTAGATAGATA 58.282 40.000 0.00 0.00 0.00 1.98
3079 3306 6.824196 TCATAGCCCGTCTGTTAGATAGATAG 59.176 42.308 0.00 0.00 0.00 2.08
3080 3307 5.244189 AGCCCGTCTGTTAGATAGATAGA 57.756 43.478 0.00 0.00 0.00 1.98
3081 3308 5.005094 AGCCCGTCTGTTAGATAGATAGAC 58.995 45.833 0.00 0.00 35.58 2.59
3082 3309 4.760715 GCCCGTCTGTTAGATAGATAGACA 59.239 45.833 0.00 0.00 38.07 3.41
3083 3310 5.241064 GCCCGTCTGTTAGATAGATAGACAA 59.759 44.000 0.00 0.00 38.07 3.18
3084 3311 6.238953 GCCCGTCTGTTAGATAGATAGACAAA 60.239 42.308 0.00 0.00 38.07 2.83
3085 3312 7.140048 CCCGTCTGTTAGATAGATAGACAAAC 58.860 42.308 0.00 0.00 38.07 2.93
3086 3313 7.140048 CCGTCTGTTAGATAGATAGACAAACC 58.860 42.308 0.00 0.00 38.07 3.27
3087 3314 7.013464 CCGTCTGTTAGATAGATAGACAAACCT 59.987 40.741 0.00 0.00 38.07 3.50
3090 3317 8.904834 TCTGTTAGATAGATAGACAAACCTCAC 58.095 37.037 0.00 0.00 0.00 3.51
3111 3338 6.472016 TCACATAGATAGACAAACCTGCAAA 58.528 36.000 0.00 0.00 0.00 3.68
3163 3390 7.993183 TCTTTCAGACAAACCATTCTAGTCTTT 59.007 33.333 0.00 0.00 37.45 2.52
3177 3404 7.781548 TTCTAGTCTTTGACTTACACCAAAC 57.218 36.000 5.52 0.00 40.28 2.93
3193 3420 0.396974 AAACTTTGCCTGGCCTGTCA 60.397 50.000 17.53 0.00 0.00 3.58
3197 3424 0.538057 TTTGCCTGGCCTGTCAAGAG 60.538 55.000 17.53 0.00 0.00 2.85
3461 3698 8.792830 ACATACTTACAGCATATTTTGACTGT 57.207 30.769 0.00 0.00 41.96 3.55
3472 3709 9.683069 AGCATATTTTGACTGTGTTTAGAAAAG 57.317 29.630 0.00 0.00 0.00 2.27
3478 3715 6.169557 TGACTGTGTTTAGAAAAGGCTAGA 57.830 37.500 0.00 0.00 0.00 2.43
3551 3788 1.304713 CTGGAATGCTTGCAGGGGT 60.305 57.895 0.00 0.00 44.32 4.95
3667 3904 7.958088 ACTTCCTCTGCCTCTAAATATAAGAC 58.042 38.462 0.00 0.00 0.00 3.01
3677 3914 8.129211 GCCTCTAAATATAAGACGTTTTTGCAT 58.871 33.333 0.00 0.00 0.00 3.96
3815 4179 3.392947 TCAGTACCTGATGTTGGAAACCA 59.607 43.478 0.00 0.00 39.98 3.67
3840 4204 3.848726 AGTTTGAACACTGTTTTGGCTG 58.151 40.909 0.00 0.00 0.00 4.85
3841 4205 2.929398 GTTTGAACACTGTTTTGGCTGG 59.071 45.455 0.00 0.00 0.00 4.85
3874 4238 1.609072 GAGAAGGTTGTTGTTGCCCTC 59.391 52.381 0.00 0.00 0.00 4.30
3895 4259 1.221021 GGGGAGATTGGTCACCGTC 59.779 63.158 0.00 0.00 36.10 4.79
4078 4443 9.450807 CGTTTGAAATGAAGTAACTTGATTCTT 57.549 29.630 0.00 0.00 26.82 2.52
4108 4473 5.163561 TGCCGATCCCATTCTTGTTATTTTC 60.164 40.000 0.00 0.00 0.00 2.29
4290 4663 3.559655 GGCAAACACAAATTCAAGTTCCC 59.440 43.478 0.00 0.00 0.00 3.97
4321 4694 3.795877 CACCTTTGAACTTTTGGTGCAT 58.204 40.909 0.00 0.00 41.09 3.96
4328 4701 2.086610 ACTTTTGGTGCATTGACCCT 57.913 45.000 0.00 0.00 34.79 4.34
4434 4807 3.255888 CGGGCTGTCAATATACTAGCTCA 59.744 47.826 0.00 0.00 34.59 4.26
4435 4808 4.561105 GGGCTGTCAATATACTAGCTCAC 58.439 47.826 0.00 0.00 35.03 3.51
4522 4895 4.166011 GGAACGCGGTCTGCATGC 62.166 66.667 25.41 11.82 46.97 4.06
4541 4914 2.946329 TGCGTTGTGTGGTGAGTTTAAT 59.054 40.909 0.00 0.00 0.00 1.40
4542 4915 4.127907 TGCGTTGTGTGGTGAGTTTAATA 58.872 39.130 0.00 0.00 0.00 0.98
4543 4916 4.212425 TGCGTTGTGTGGTGAGTTTAATAG 59.788 41.667 0.00 0.00 0.00 1.73
4643 5016 5.463392 TCGTTGACAATGAGAAGAAGAACAG 59.537 40.000 5.98 0.00 0.00 3.16
4701 5074 4.365514 TGGCTAAAAGTGGAAGTGATGA 57.634 40.909 0.00 0.00 0.00 2.92
4729 5102 2.159254 CCTGTTTGTTGGGATAATGCGG 60.159 50.000 0.00 0.00 0.00 5.69
4736 5109 0.472471 TGGGATAATGCGGACCTTCC 59.528 55.000 0.00 0.00 0.00 3.46
4759 5138 3.454082 CAGGTAGATGCCTCCTTTCTTCT 59.546 47.826 0.00 0.00 36.58 2.85
4769 5148 4.323104 GCCTCCTTTCTTCTTCTTGCTAGA 60.323 45.833 0.00 0.00 0.00 2.43
4770 5149 5.175127 CCTCCTTTCTTCTTCTTGCTAGAC 58.825 45.833 0.00 0.00 0.00 2.59
4772 5151 3.929610 CCTTTCTTCTTCTTGCTAGACGG 59.070 47.826 0.00 0.00 0.00 4.79
4773 5152 4.561105 CTTTCTTCTTCTTGCTAGACGGT 58.439 43.478 0.00 0.00 0.00 4.83
4774 5153 5.336531 CCTTTCTTCTTCTTGCTAGACGGTA 60.337 44.000 0.00 0.00 0.00 4.02
4775 5154 4.966965 TCTTCTTCTTGCTAGACGGTAG 57.033 45.455 0.00 0.00 0.00 3.18
4776 5155 4.333690 TCTTCTTCTTGCTAGACGGTAGT 58.666 43.478 0.00 0.00 0.00 2.73
4777 5156 5.494724 TCTTCTTCTTGCTAGACGGTAGTA 58.505 41.667 0.00 0.00 0.00 1.82
4793 5172 3.710165 GGTAGTACTTAGGCCAACTCCAT 59.290 47.826 5.01 0.00 0.00 3.41
4831 5210 1.941975 ACGTTCGTTTTGTCCGGATTT 59.058 42.857 7.81 0.00 0.00 2.17
4860 5239 1.153025 GGTAGGGATTTGGGGTCGC 60.153 63.158 0.00 0.00 0.00 5.19
4938 5317 4.530857 CCCATCCTGTCCGCGTCC 62.531 72.222 4.92 0.00 0.00 4.79
4991 5372 2.592308 GCCCTAGTTCAGGCCAGG 59.408 66.667 5.01 0.46 43.98 4.45
5161 5543 3.191162 CCAGAATGAATGTTTTCTCGCCA 59.809 43.478 0.00 0.00 39.69 5.69
5374 5756 2.929903 GCTTTGGTGGCGGCATTGA 61.930 57.895 17.19 0.31 0.00 2.57
5477 5859 0.250234 ATGTCGAGCTGCCTTTGCTA 59.750 50.000 0.00 0.00 41.30 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.347490 GCGGCTTTCTCCCTGACA 59.653 61.111 0.00 0.00 0.00 3.58
37 38 1.134580 CATATAGGGCAGGGCTCATCG 60.135 57.143 0.00 0.00 0.00 3.84
40 41 1.492133 GGCATATAGGGCAGGGCTCA 61.492 60.000 6.02 0.00 0.00 4.26
217 219 1.191489 TCATCCGAAGCCACCTGTCA 61.191 55.000 0.00 0.00 0.00 3.58
363 366 3.427528 ACATTACAAGTTGTCTACGCACG 59.572 43.478 12.82 0.00 0.00 5.34
408 413 2.804167 CTCACCGCGCAGAGAGAT 59.196 61.111 17.79 0.00 33.74 2.75
418 423 3.117171 CTGCTCACTGCTCACCGC 61.117 66.667 0.00 0.00 43.37 5.68
419 424 1.445754 CTCTGCTCACTGCTCACCG 60.446 63.158 0.00 0.00 43.37 4.94
420 425 0.108709 CTCTCTGCTCACTGCTCACC 60.109 60.000 0.00 0.00 43.37 4.02
421 426 0.602562 ACTCTCTGCTCACTGCTCAC 59.397 55.000 0.00 0.00 43.37 3.51
422 427 0.602060 CACTCTCTGCTCACTGCTCA 59.398 55.000 0.00 0.00 43.37 4.26
423 428 0.602562 ACACTCTCTGCTCACTGCTC 59.397 55.000 0.00 0.00 43.37 4.26
438 443 1.470098 GCTCCGCATCATTCAAACACT 59.530 47.619 0.00 0.00 0.00 3.55
447 452 2.447379 AGAGGGGCTCCGCATCAT 60.447 61.111 9.79 0.00 38.33 2.45
458 463 3.440127 ACAGAAGAGAAAGAGAGAGGGG 58.560 50.000 0.00 0.00 0.00 4.79
459 464 4.819769 CAACAGAAGAGAAAGAGAGAGGG 58.180 47.826 0.00 0.00 0.00 4.30
465 476 2.483491 GCAGGCAACAGAAGAGAAAGAG 59.517 50.000 0.00 0.00 41.41 2.85
469 480 0.392706 TCGCAGGCAACAGAAGAGAA 59.607 50.000 0.00 0.00 41.41 2.87
502 513 6.018016 GCAGCAAAAAGGAACACAATATTTGT 60.018 34.615 0.00 0.00 46.75 2.83
535 547 1.878211 TCATACATCTCCCCTGCACA 58.122 50.000 0.00 0.00 0.00 4.57
551 563 5.045651 TGACATGGAAATCGGGCTATATCAT 60.046 40.000 0.00 0.00 0.00 2.45
562 574 1.066002 GCCCACATGACATGGAAATCG 59.934 52.381 19.39 2.33 39.87 3.34
602 614 4.706476 CAGCAGAATAAACCTTTCATCCCA 59.294 41.667 0.00 0.00 0.00 4.37
643 655 8.473358 TCTAATAATTCGAGATCCCAGTAACA 57.527 34.615 0.00 0.00 0.00 2.41
668 680 8.246871 GCTTTCAGCTAAAAAGACCAGATAATT 58.753 33.333 19.71 0.00 38.45 1.40
670 682 6.714810 TGCTTTCAGCTAAAAAGACCAGATAA 59.285 34.615 19.71 0.00 42.97 1.75
674 686 4.836125 TGCTTTCAGCTAAAAAGACCAG 57.164 40.909 19.71 0.18 42.97 4.00
675 687 4.218417 GGATGCTTTCAGCTAAAAAGACCA 59.782 41.667 19.71 11.81 42.97 4.02
676 688 4.218417 TGGATGCTTTCAGCTAAAAAGACC 59.782 41.667 19.71 17.63 42.97 3.85
677 689 5.376854 TGGATGCTTTCAGCTAAAAAGAC 57.623 39.130 19.71 13.08 42.97 3.01
700 725 3.944087 ACAGATTACTGAAGAACCAGGC 58.056 45.455 0.00 0.00 46.03 4.85
748 778 8.675504 TGAACAATTTACTGGTTCGAACTTAAA 58.324 29.630 26.32 23.38 42.86 1.52
749 779 8.211116 TGAACAATTTACTGGTTCGAACTTAA 57.789 30.769 26.32 17.61 42.86 1.85
754 784 6.928979 TTCTGAACAATTTACTGGTTCGAA 57.071 33.333 0.00 0.00 42.86 3.71
779 809 7.642669 CCACCATGATCACAAAGTAATATGAC 58.357 38.462 0.00 0.00 0.00 3.06
782 812 6.128486 TGCCACCATGATCACAAAGTAATAT 58.872 36.000 0.00 0.00 0.00 1.28
784 814 4.343231 TGCCACCATGATCACAAAGTAAT 58.657 39.130 0.00 0.00 0.00 1.89
793 823 1.410507 CCTCCATTGCCACCATGATCA 60.411 52.381 0.00 0.00 0.00 2.92
794 824 1.325355 CCTCCATTGCCACCATGATC 58.675 55.000 0.00 0.00 0.00 2.92
795 825 0.632835 ACCTCCATTGCCACCATGAT 59.367 50.000 0.00 0.00 0.00 2.45
796 826 0.323633 CACCTCCATTGCCACCATGA 60.324 55.000 0.00 0.00 0.00 3.07
797 827 0.323633 TCACCTCCATTGCCACCATG 60.324 55.000 0.00 0.00 0.00 3.66
798 828 0.409092 TTCACCTCCATTGCCACCAT 59.591 50.000 0.00 0.00 0.00 3.55
799 829 0.187117 TTTCACCTCCATTGCCACCA 59.813 50.000 0.00 0.00 0.00 4.17
800 830 1.337118 TTTTCACCTCCATTGCCACC 58.663 50.000 0.00 0.00 0.00 4.61
801 831 2.562298 TGATTTTCACCTCCATTGCCAC 59.438 45.455 0.00 0.00 0.00 5.01
802 832 2.827322 CTGATTTTCACCTCCATTGCCA 59.173 45.455 0.00 0.00 0.00 4.92
805 835 3.508793 ACAGCTGATTTTCACCTCCATTG 59.491 43.478 23.35 0.00 0.00 2.82
806 836 3.771216 ACAGCTGATTTTCACCTCCATT 58.229 40.909 23.35 0.00 0.00 3.16
808 838 2.957402 ACAGCTGATTTTCACCTCCA 57.043 45.000 23.35 0.00 0.00 3.86
809 839 4.265073 ACATACAGCTGATTTTCACCTCC 58.735 43.478 23.35 0.00 0.00 4.30
810 840 6.985188 TTACATACAGCTGATTTTCACCTC 57.015 37.500 23.35 0.00 0.00 3.85
811 841 7.112122 TGATTACATACAGCTGATTTTCACCT 58.888 34.615 23.35 0.00 0.00 4.00
813 843 7.859377 CCATGATTACATACAGCTGATTTTCAC 59.141 37.037 23.35 5.97 35.09 3.18
814 844 7.557358 ACCATGATTACATACAGCTGATTTTCA 59.443 33.333 23.35 13.24 35.09 2.69
815 845 7.934457 ACCATGATTACATACAGCTGATTTTC 58.066 34.615 23.35 8.08 35.09 2.29
830 1012 3.997762 TGCCGTATGGTACCATGATTAC 58.002 45.455 33.41 22.91 37.82 1.89
841 1023 0.107214 CACCTCCATTGCCGTATGGT 60.107 55.000 2.17 0.00 44.48 3.55
843 1025 2.036958 TTCACCTCCATTGCCGTATG 57.963 50.000 0.00 0.00 0.00 2.39
847 1029 1.818060 TGATTTTCACCTCCATTGCCG 59.182 47.619 0.00 0.00 0.00 5.69
866 1048 2.166459 TCCGAGTTGCATAGGAGAAGTG 59.834 50.000 0.00 0.00 0.00 3.16
870 1052 3.197766 ACATTTCCGAGTTGCATAGGAGA 59.802 43.478 0.00 0.00 33.89 3.71
921 1105 5.923204 ACTGCTGGAAAATATCTACTCCTG 58.077 41.667 0.00 0.00 0.00 3.86
923 1107 6.481644 CAGAACTGCTGGAAAATATCTACTCC 59.518 42.308 0.00 0.00 41.07 3.85
1442 1639 3.583086 GAATGGGCTTACCGGCGC 61.583 66.667 0.00 0.00 44.64 6.53
1499 1696 0.673644 AAATTCACCGAGCGGGACTG 60.674 55.000 14.07 2.83 39.97 3.51
1558 1755 5.734720 TGGTTAGGAGCTTCAGAATAACAG 58.265 41.667 0.00 0.00 0.00 3.16
1560 1757 5.065346 GCTTGGTTAGGAGCTTCAGAATAAC 59.935 44.000 0.00 0.00 36.01 1.89
1568 1765 3.181506 CGAATTGCTTGGTTAGGAGCTTC 60.182 47.826 0.00 0.00 39.60 3.86
1601 1798 0.178929 AAACCCTGAGTCCTCGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
1676 1878 4.626628 GCGAAACGATTGTCGAGC 57.373 55.556 6.34 2.89 43.74 5.03
1815 2037 2.167693 TGATCGAATAACCTCAACGCCT 59.832 45.455 0.00 0.00 0.00 5.52
1816 2038 2.546778 TGATCGAATAACCTCAACGCC 58.453 47.619 0.00 0.00 0.00 5.68
1936 2158 5.615289 GGAGCTAGCTTCCATCTAATGAAA 58.385 41.667 20.42 0.00 0.00 2.69
2079 2301 3.072330 TGTTAGAAGGGTCTCACATGCAA 59.928 43.478 0.00 0.00 33.89 4.08
2311 2536 3.065648 GGAGGAAACTAGCAGTACTCGAG 59.934 52.174 11.84 11.84 44.43 4.04
2396 2621 8.024865 TGCATATTTCATTCTTGAAGAACACTG 58.975 33.333 10.18 5.27 42.60 3.66
2439 2664 6.403636 GCAAAACACCCTCAGTATCAGTAATG 60.404 42.308 0.00 0.00 0.00 1.90
2731 2956 1.912043 AGGCAGCACTTTGGAGATAGT 59.088 47.619 0.00 0.00 0.00 2.12
2885 3110 7.604164 TCCAATTTGTAAGAGAAACAGCTAGAG 59.396 37.037 0.00 0.00 0.00 2.43
2914 3139 3.460857 AGCTTATCGAGTGTGATTCCC 57.539 47.619 0.00 0.00 0.00 3.97
2920 3145 9.517609 AAGTATTACTAAAGCTTATCGAGTGTG 57.482 33.333 0.00 0.00 0.00 3.82
2972 3197 5.491982 CAGTGTAGCTCTCCCAAACTAAAT 58.508 41.667 0.00 0.00 0.00 1.40
3013 3238 6.886459 ACCAGAGTGCAATGTTATAAATGAGT 59.114 34.615 0.00 0.00 0.00 3.41
3063 3290 8.904834 TGAGGTTTGTCTATCTATCTAACAGAC 58.095 37.037 0.00 0.00 36.89 3.51
3070 3297 9.821240 ATCTATGTGAGGTTTGTCTATCTATCT 57.179 33.333 0.00 0.00 0.00 1.98
3074 3301 9.073475 GTCTATCTATGTGAGGTTTGTCTATCT 57.927 37.037 0.00 0.00 0.00 1.98
3075 3302 8.851145 TGTCTATCTATGTGAGGTTTGTCTATC 58.149 37.037 0.00 0.00 0.00 2.08
3076 3303 8.768501 TGTCTATCTATGTGAGGTTTGTCTAT 57.231 34.615 0.00 0.00 0.00 1.98
3077 3304 8.589701 TTGTCTATCTATGTGAGGTTTGTCTA 57.410 34.615 0.00 0.00 0.00 2.59
3078 3305 7.482169 TTGTCTATCTATGTGAGGTTTGTCT 57.518 36.000 0.00 0.00 0.00 3.41
3079 3306 7.064728 GGTTTGTCTATCTATGTGAGGTTTGTC 59.935 40.741 0.00 0.00 0.00 3.18
3080 3307 6.879458 GGTTTGTCTATCTATGTGAGGTTTGT 59.121 38.462 0.00 0.00 0.00 2.83
3081 3308 7.065085 CAGGTTTGTCTATCTATGTGAGGTTTG 59.935 40.741 0.00 0.00 0.00 2.93
3082 3309 7.106239 CAGGTTTGTCTATCTATGTGAGGTTT 58.894 38.462 0.00 0.00 0.00 3.27
3083 3310 6.644347 CAGGTTTGTCTATCTATGTGAGGTT 58.356 40.000 0.00 0.00 0.00 3.50
3084 3311 5.395768 GCAGGTTTGTCTATCTATGTGAGGT 60.396 44.000 0.00 0.00 0.00 3.85
3085 3312 5.053145 GCAGGTTTGTCTATCTATGTGAGG 58.947 45.833 0.00 0.00 0.00 3.86
3086 3313 5.664457 TGCAGGTTTGTCTATCTATGTGAG 58.336 41.667 0.00 0.00 0.00 3.51
3087 3314 5.675684 TGCAGGTTTGTCTATCTATGTGA 57.324 39.130 0.00 0.00 0.00 3.58
3090 3317 6.741992 TGTTTGCAGGTTTGTCTATCTATG 57.258 37.500 0.00 0.00 0.00 2.23
3163 3390 3.380004 CAGGCAAAGTTTGGTGTAAGTCA 59.620 43.478 17.11 0.00 0.00 3.41
3177 3404 0.538057 TCTTGACAGGCCAGGCAAAG 60.538 55.000 18.17 11.67 0.00 2.77
3193 3420 2.952310 GGTGAAAACAGAACCAGCTCTT 59.048 45.455 0.00 0.00 33.94 2.85
3197 3424 3.821033 ACATAGGTGAAAACAGAACCAGC 59.179 43.478 0.00 0.00 36.37 4.85
3461 3698 7.334421 CAGCAGTTATCTAGCCTTTTCTAAACA 59.666 37.037 0.00 0.00 0.00 2.83
3472 3709 4.054671 CAAGTAGCAGCAGTTATCTAGCC 58.945 47.826 0.00 0.00 0.00 3.93
3478 3715 5.923733 AGTAGACAAGTAGCAGCAGTTAT 57.076 39.130 0.00 0.00 0.00 1.89
3677 3914 6.382859 TGGAACTAGTATCCTGCATCAGTTAA 59.617 38.462 18.78 0.00 37.85 2.01
3679 3916 4.716784 TGGAACTAGTATCCTGCATCAGTT 59.283 41.667 18.78 0.00 37.85 3.16
3680 3917 4.290093 TGGAACTAGTATCCTGCATCAGT 58.710 43.478 18.78 0.00 37.85 3.41
3815 4179 4.481463 CCAAAACAGTGTTCAAACTTCGT 58.519 39.130 9.40 0.00 0.00 3.85
3840 4204 7.096884 ACAACCTTCTCTTTGTTTTTCTACC 57.903 36.000 0.00 0.00 31.78 3.18
3841 4205 8.027189 ACAACAACCTTCTCTTTGTTTTTCTAC 58.973 33.333 0.00 0.00 42.04 2.59
3884 4248 3.924114 ATATTGATGGACGGTGACCAA 57.076 42.857 1.11 0.00 40.93 3.67
3895 4259 5.182001 GCTTGGCACCTTACTATATTGATGG 59.818 44.000 0.00 0.00 0.00 3.51
3996 4361 6.460261 GCTTAAAGGGAAGGATGAGCATAAAC 60.460 42.308 0.00 0.00 0.00 2.01
4078 4443 4.136796 CAAGAATGGGATCGGCATTAGAA 58.863 43.478 0.00 0.00 0.00 2.10
4080 4445 3.480470 ACAAGAATGGGATCGGCATTAG 58.520 45.455 0.00 0.00 0.00 1.73
4124 4489 6.576442 GCTCCAGATTAGACCCTTCTAAAACA 60.576 42.308 0.00 0.00 45.52 2.83
4135 4501 1.691434 CTCCAGGCTCCAGATTAGACC 59.309 57.143 0.00 0.00 0.00 3.85
4211 4581 1.667724 CGGAATGCTGTCAATCAGTCC 59.332 52.381 9.84 9.84 45.23 3.85
4290 4663 6.920569 AAAGTTCAAAGGTGTACACTACAG 57.079 37.500 24.55 13.01 39.77 2.74
4321 4694 2.571653 CAACCATAGGACTCAGGGTCAA 59.428 50.000 1.94 0.00 46.16 3.18
4328 4701 1.833630 CCAGCTCAACCATAGGACTCA 59.166 52.381 0.00 0.00 0.00 3.41
4434 4807 9.326413 AGCACTTTGTAAAATATATAGCTTCGT 57.674 29.630 0.00 0.00 0.00 3.85
4479 4852 3.509575 GTGGCATTTGAACAGGGTCAATA 59.490 43.478 0.00 0.00 37.36 1.90
4522 4895 5.917541 ACTATTAAACTCACCACACAACG 57.082 39.130 0.00 0.00 0.00 4.10
4541 4914 3.513515 TCATCACATGGTGCAGTGTACTA 59.486 43.478 11.32 5.52 37.07 1.82
4542 4915 2.302733 TCATCACATGGTGCAGTGTACT 59.697 45.455 11.32 0.00 37.07 2.73
4543 4916 2.698803 TCATCACATGGTGCAGTGTAC 58.301 47.619 2.25 2.25 37.07 2.90
4643 5016 6.509418 TGGCATAGTGTCAATTTCTTTACC 57.491 37.500 0.00 0.00 0.00 2.85
4701 5074 0.465287 CCCAACAAACAGGCAAGCTT 59.535 50.000 0.00 0.00 0.00 3.74
4729 5102 0.470341 GGCATCTACCTGGGAAGGTC 59.530 60.000 0.00 0.00 42.99 3.85
4736 5109 2.122768 AGAAAGGAGGCATCTACCTGG 58.877 52.381 0.00 0.00 41.32 4.45
4759 5138 5.587844 CCTAAGTACTACCGTCTAGCAAGAA 59.412 44.000 0.00 0.00 32.16 2.52
4769 5148 2.757314 GAGTTGGCCTAAGTACTACCGT 59.243 50.000 3.32 0.00 0.00 4.83
4770 5149 2.100418 GGAGTTGGCCTAAGTACTACCG 59.900 54.545 3.32 0.00 0.00 4.02
4772 5151 4.499357 CGATGGAGTTGGCCTAAGTACTAC 60.499 50.000 3.32 1.07 0.00 2.73
4773 5152 3.635373 CGATGGAGTTGGCCTAAGTACTA 59.365 47.826 3.32 0.00 0.00 1.82
4774 5153 2.431057 CGATGGAGTTGGCCTAAGTACT 59.569 50.000 3.32 0.00 0.00 2.73
4775 5154 2.822764 CGATGGAGTTGGCCTAAGTAC 58.177 52.381 3.32 0.93 0.00 2.73
4776 5155 1.138266 GCGATGGAGTTGGCCTAAGTA 59.862 52.381 3.32 0.00 0.00 2.24
4777 5156 0.107654 GCGATGGAGTTGGCCTAAGT 60.108 55.000 3.32 0.00 0.00 2.24
4831 5210 1.364269 ATCCCTACCCAAACGGACAA 58.636 50.000 0.00 0.00 34.64 3.18
4867 5246 4.838152 CCGCATCCCAGGACACGG 62.838 72.222 13.16 13.16 38.80 4.94
5035 5416 2.031616 CTGATGCCGGCGATGGAT 59.968 61.111 23.90 9.28 0.00 3.41
5076 5457 5.874810 CGAGGACAACTATTCATTTTGGAGA 59.125 40.000 0.00 0.00 0.00 3.71
5129 5510 3.261897 ACATTCATTCTGGAGACCGTCTT 59.738 43.478 1.71 0.00 0.00 3.01
5132 5513 3.703001 AACATTCATTCTGGAGACCGT 57.297 42.857 0.00 0.00 0.00 4.83
5477 5859 2.039624 ACATGGAGGAGACGGCCT 59.960 61.111 0.00 0.00 42.17 5.19


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

AutoCloner maintained by Alex Coulton.