Multiple sequence alignment - TraesCS2B01G268200

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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 TraesCS2B01G268200 chr2B 100.000 6008 0 0 1 6008 362017342 362023349 0.000000e+00 11095.0
1 TraesCS2B01G268200 chr2B 97.436 39 0 1 2942 2979 362020174 362020212 1.400000e-06 65.8
2 TraesCS2B01G268200 chr2B 97.436 39 0 1 2833 2871 362020283 362020320 1.400000e-06 65.8
3 TraesCS2B01G268200 chr2D 97.032 2325 51 10 629 2947 310305481 310303169 0.000000e+00 3895.0
4 TraesCS2B01G268200 chr2D 95.587 1994 63 9 3843 5828 310302121 310300145 0.000000e+00 3171.0
5 TraesCS2B01G268200 chr2D 93.258 712 18 7 3127 3810 310302832 310302123 0.000000e+00 1022.0
6 TraesCS2B01G268200 chr2D 100.000 29 0 0 2996 3024 310302908 310302880 3.000000e-03 54.7
7 TraesCS2B01G268200 chr2A 94.567 1767 55 10 3033 4758 426378501 426376735 0.000000e+00 2693.0
8 TraesCS2B01G268200 chr2A 98.206 1226 18 3 632 1853 426381502 426380277 0.000000e+00 2139.0
9 TraesCS2B01G268200 chr2A 94.750 1219 55 8 4794 6008 426376733 426375520 0.000000e+00 1888.0
10 TraesCS2B01G268200 chr2A 96.407 1002 27 6 1949 2947 426380266 426379271 0.000000e+00 1642.0
11 TraesCS2B01G268200 chr2A 97.436 39 0 1 2942 2979 426379385 426379347 1.400000e-06 65.8
12 TraesCS2B01G268200 chr4A 92.371 603 38 8 3 597 648754183 648753581 0.000000e+00 852.0
13 TraesCS2B01G268200 chr4A 97.826 92 1 1 3796 3887 597739879 597739969 2.240000e-34 158.0
14 TraesCS2B01G268200 chr1B 92.230 592 40 6 3 588 268798326 268798917 0.000000e+00 833.0
15 TraesCS2B01G268200 chr1B 90.909 605 45 9 3 597 538199253 538198649 0.000000e+00 804.0
16 TraesCS2B01G268200 chr5D 91.556 604 41 9 3 597 205117564 205118166 0.000000e+00 824.0
17 TraesCS2B01G268200 chr5D 91.457 597 41 8 3 590 370623030 370623625 0.000000e+00 811.0
18 TraesCS2B01G268200 chr5D 91.045 603 42 11 5 597 241111016 241110416 0.000000e+00 804.0
19 TraesCS2B01G268200 chr5D 93.878 98 6 0 3787 3884 111788632 111788729 1.350000e-31 148.0
20 TraesCS2B01G268200 chr5D 89.474 114 8 4 3773 3886 216627746 216627855 2.260000e-29 141.0
21 TraesCS2B01G268200 chr5D 96.774 31 1 0 4857 4887 311903632 311903602 1.100000e-02 52.8
22 TraesCS2B01G268200 chr3D 91.556 604 41 9 3 597 571056186 571056788 0.000000e+00 824.0
23 TraesCS2B01G268200 chr4B 91.723 592 43 6 3 588 645056898 645057489 0.000000e+00 817.0
24 TraesCS2B01G268200 chr4B 81.250 240 41 4 5587 5824 311801845 311802082 2.210000e-44 191.0
25 TraesCS2B01G268200 chr5B 91.261 595 44 8 3 590 474580444 474579851 0.000000e+00 804.0
26 TraesCS2B01G268200 chr1A 84.454 238 37 0 5587 5824 539709478 539709241 1.010000e-57 235.0
27 TraesCS2B01G268200 chr1A 82.379 227 39 1 5588 5814 11790056 11790281 4.750000e-46 196.0
28 TraesCS2B01G268200 chr1A 81.092 238 43 2 5588 5824 58304049 58304285 7.950000e-44 189.0
29 TraesCS2B01G268200 chr5A 82.278 237 42 0 5588 5824 263654961 263655197 7.890000e-49 206.0
30 TraesCS2B01G268200 chr5A 81.013 237 45 0 5588 5824 18779938 18780174 7.950000e-44 189.0
31 TraesCS2B01G268200 chr7B 81.435 237 44 0 5588 5824 137560152 137560388 1.710000e-45 195.0
32 TraesCS2B01G268200 chr3B 95.050 101 3 2 3789 3888 723452849 723452948 2.240000e-34 158.0
33 TraesCS2B01G268200 chr6D 94.118 102 3 2 3785 3883 168293856 168293755 1.040000e-32 152.0
34 TraesCS2B01G268200 chr4D 95.699 93 4 0 3792 3884 398430809 398430901 3.750000e-32 150.0
35 TraesCS2B01G268200 chr7D 93.878 98 6 0 3787 3884 289566341 289566438 1.350000e-31 148.0
36 TraesCS2B01G268200 chr7D 91.429 105 9 0 3782 3886 5068187 5068083 1.750000e-30 145.0


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 TraesCS2B01G268200 chr2B 362017342 362023349 6007 False 3742.200 11095 98.290667 1 6008 3 chr2B.!!$F1 6007
1 TraesCS2B01G268200 chr2D 310300145 310305481 5336 True 2035.675 3895 96.469250 629 5828 4 chr2D.!!$R1 5199
2 TraesCS2B01G268200 chr2A 426375520 426381502 5982 True 1685.560 2693 96.273200 632 6008 5 chr2A.!!$R1 5376
3 TraesCS2B01G268200 chr4A 648753581 648754183 602 True 852.000 852 92.371000 3 597 1 chr4A.!!$R1 594
4 TraesCS2B01G268200 chr1B 268798326 268798917 591 False 833.000 833 92.230000 3 588 1 chr1B.!!$F1 585
5 TraesCS2B01G268200 chr1B 538198649 538199253 604 True 804.000 804 90.909000 3 597 1 chr1B.!!$R1 594
6 TraesCS2B01G268200 chr5D 205117564 205118166 602 False 824.000 824 91.556000 3 597 1 chr5D.!!$F2 594
7 TraesCS2B01G268200 chr5D 370623030 370623625 595 False 811.000 811 91.457000 3 590 1 chr5D.!!$F4 587
8 TraesCS2B01G268200 chr5D 241110416 241111016 600 True 804.000 804 91.045000 5 597 1 chr5D.!!$R1 592
9 TraesCS2B01G268200 chr3D 571056186 571056788 602 False 824.000 824 91.556000 3 597 1 chr3D.!!$F1 594
10 TraesCS2B01G268200 chr4B 645056898 645057489 591 False 817.000 817 91.723000 3 588 1 chr4B.!!$F2 585
11 TraesCS2B01G268200 chr5B 474579851 474580444 593 True 804.000 804 91.261000 3 590 1 chr5B.!!$R1 587

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
622 634 0.320073 CCCAGGACGCGTTACAGAAA 60.320 55.000 15.53 0.00 0.00 2.52 F
623 635 0.788391 CCAGGACGCGTTACAGAAAC 59.212 55.000 15.53 0.00 34.52 2.78 F
1965 1983 0.533755 CTCCGGATGATTGAGGTGGC 60.534 60.000 3.57 0.00 0.00 5.01 F
2813 2834 1.079336 GTTGCCAGGGGACGACTAC 60.079 63.158 0.00 0.00 0.00 2.73 F
4110 4918 0.039256 CAACTGACAAACCATGGCCG 60.039 55.000 13.04 2.47 35.52 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1583 0.673333 GGCATGGTGTGTGTGATCGA 60.673 55.0 0.00 0.0 0.00 3.59 R
2537 2558 2.325583 TTTGCGAGACTGGAACACTT 57.674 45.0 0.00 0.0 0.00 3.16 R
3087 3839 0.551131 AGAGGCCAGGGACAATCCTT 60.551 55.0 5.01 0.0 36.57 3.36 R
4772 5587 0.242555 CCACATTAACCAACCGGCAC 59.757 55.0 0.00 0.0 34.57 5.01 R
5901 6724 0.107848 ACTACGTACAGGGCCAATGC 60.108 55.0 6.18 0.0 0.00 3.56 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 4.611310 TCATCAAGGTAACGACGTAGAG 57.389 45.455 0.00 0.00 46.39 2.43
87 88 4.717629 CGCCTGTCGTCGGCTCAA 62.718 66.667 0.00 0.00 45.37 3.02
91 92 0.721718 CCTGTCGTCGGCTCAATTTC 59.278 55.000 0.00 0.00 0.00 2.17
116 117 1.586154 GCAACCATGTCTCCCCAACG 61.586 60.000 0.00 0.00 0.00 4.10
210 214 1.754745 CACCACCACTGGCTACACT 59.245 57.895 0.00 0.00 42.08 3.55
269 273 2.176055 CAGACCCTCGACGTCACG 59.824 66.667 17.16 2.92 32.41 4.35
293 297 4.202050 GCCGATCTAAAGCCAAATGACATT 60.202 41.667 0.00 0.00 0.00 2.71
330 334 4.451150 GCCACCGTCCGATGCAGA 62.451 66.667 0.00 0.00 0.00 4.26
476 484 3.626596 AGGGAGGAAGAGCCCCCA 61.627 66.667 0.00 0.00 45.89 4.96
606 618 4.323477 CGGAGCGGAAACACCCCA 62.323 66.667 0.00 0.00 34.64 4.96
607 619 2.359975 GGAGCGGAAACACCCCAG 60.360 66.667 0.00 0.00 34.64 4.45
608 620 2.359975 GAGCGGAAACACCCCAGG 60.360 66.667 0.00 0.00 34.64 4.45
609 621 2.852075 AGCGGAAACACCCCAGGA 60.852 61.111 0.00 0.00 34.64 3.86
610 622 2.671963 GCGGAAACACCCCAGGAC 60.672 66.667 0.00 0.00 34.64 3.85
611 623 2.358247 CGGAAACACCCCAGGACG 60.358 66.667 0.00 0.00 34.64 4.79
612 624 2.671963 GGAAACACCCCAGGACGC 60.672 66.667 0.00 0.00 0.00 5.19
613 625 3.047877 GAAACACCCCAGGACGCG 61.048 66.667 3.53 3.53 0.00 6.01
614 626 3.819877 GAAACACCCCAGGACGCGT 62.820 63.158 13.85 13.85 0.00 6.01
615 627 3.409605 AAACACCCCAGGACGCGTT 62.410 57.895 15.53 0.00 0.00 4.84
616 628 2.042404 AAACACCCCAGGACGCGTTA 62.042 55.000 15.53 0.00 0.00 3.18
617 629 2.433664 CACCCCAGGACGCGTTAC 60.434 66.667 15.53 10.33 0.00 2.50
618 630 2.918802 ACCCCAGGACGCGTTACA 60.919 61.111 15.53 0.00 0.00 2.41
619 631 2.125673 CCCCAGGACGCGTTACAG 60.126 66.667 15.53 6.76 0.00 2.74
620 632 2.642254 CCCCAGGACGCGTTACAGA 61.642 63.158 15.53 0.00 0.00 3.41
621 633 1.290955 CCCAGGACGCGTTACAGAA 59.709 57.895 15.53 0.00 0.00 3.02
622 634 0.320073 CCCAGGACGCGTTACAGAAA 60.320 55.000 15.53 0.00 0.00 2.52
623 635 0.788391 CCAGGACGCGTTACAGAAAC 59.212 55.000 15.53 0.00 34.52 2.78
624 636 1.493772 CAGGACGCGTTACAGAAACA 58.506 50.000 15.53 0.00 38.03 2.83
625 637 2.066262 CAGGACGCGTTACAGAAACAT 58.934 47.619 15.53 0.00 38.03 2.71
626 638 2.092211 CAGGACGCGTTACAGAAACATC 59.908 50.000 15.53 0.00 38.03 3.06
627 639 2.063266 GGACGCGTTACAGAAACATCA 58.937 47.619 15.53 0.00 38.03 3.07
704 716 2.064762 GCTGCTAGTATTCCATGCGAG 58.935 52.381 0.00 0.00 0.00 5.03
880 896 3.562176 GCCCATTAATATCCACCTCCCTG 60.562 52.174 0.00 0.00 0.00 4.45
976 992 9.030452 AGCTCTATTTTTCTCTCTCTTCTTACA 57.970 33.333 0.00 0.00 0.00 2.41
1221 1237 1.053835 TCCACCACCACAAGAGCAGA 61.054 55.000 0.00 0.00 0.00 4.26
1425 1441 3.301515 CGCGTTTTTCTTTTGCGTGATTT 60.302 39.130 0.00 0.00 43.50 2.17
1567 1583 2.302157 ACGTCTTCTTCTTCCCCGATTT 59.698 45.455 0.00 0.00 0.00 2.17
1608 1624 4.339247 CCATGGCCGTTTAATTCTTCATCT 59.661 41.667 0.00 0.00 0.00 2.90
1613 1629 3.242739 CCGTTTAATTCTTCATCTGCCGG 60.243 47.826 0.00 0.00 0.00 6.13
1745 1761 1.225704 GGAGGCCATGGAGTTCCTG 59.774 63.158 18.40 0.00 36.82 3.86
1836 1852 3.435026 CGGTAAACCATCCCTTCCATGAT 60.435 47.826 0.00 0.00 35.14 2.45
1853 1869 5.016675 TCCATGATCCATCCCATCTACTAGA 59.983 44.000 0.00 0.00 0.00 2.43
1965 1983 0.533755 CTCCGGATGATTGAGGTGGC 60.534 60.000 3.57 0.00 0.00 5.01
2011 2029 8.377034 TGTTAGCCTGTTCTTAATTAACCTGTA 58.623 33.333 0.00 0.00 0.00 2.74
2161 2182 1.928868 AGCTAGCTTTGGTTGGCATT 58.071 45.000 12.68 0.00 33.05 3.56
2262 2283 4.715896 CACACTACACATGCTAGCTTTTG 58.284 43.478 17.23 15.11 0.00 2.44
2272 2293 6.094603 CACATGCTAGCTTTTGAACTAATCCT 59.905 38.462 17.23 0.00 0.00 3.24
2274 2295 6.743575 TGCTAGCTTTTGAACTAATCCTTC 57.256 37.500 17.23 0.00 0.00 3.46
2388 2409 3.212685 GCTAGCTTGCAGGAGAATCATT 58.787 45.455 15.53 0.00 36.25 2.57
2446 2467 1.205655 TCTTGCACCAGCTACTAGCAG 59.794 52.381 10.73 2.17 45.56 4.24
2524 2545 3.498774 ACTCCATTATGGCTAGCAAGG 57.501 47.619 18.24 2.57 37.47 3.61
2631 2652 7.200434 TCTTTATTGTTCTTCCCAGCTCTAT 57.800 36.000 0.00 0.00 0.00 1.98
2812 2833 1.534476 TGTTGCCAGGGGACGACTA 60.534 57.895 0.00 0.00 0.00 2.59
2813 2834 1.079336 GTTGCCAGGGGACGACTAC 60.079 63.158 0.00 0.00 0.00 2.73
2935 2956 8.660373 CAGAGAATAATTCCTTGTGTACAGAAC 58.340 37.037 0.45 0.00 0.00 3.01
2937 2958 9.167311 GAGAATAATTCCTTGTGTACAGAACAT 57.833 33.333 0.45 0.00 41.10 2.71
2960 2981 2.212869 CCATGTTGTGGTATGCATGC 57.787 50.000 11.82 11.82 43.44 4.06
2962 2983 2.101750 CCATGTTGTGGTATGCATGCAT 59.898 45.455 33.92 33.92 43.44 3.96
2963 2984 3.431068 CCATGTTGTGGTATGCATGCATT 60.431 43.478 36.23 20.71 43.44 3.56
2964 2985 3.507103 TGTTGTGGTATGCATGCATTC 57.493 42.857 36.23 29.98 37.82 2.67
2965 2986 2.166050 TGTTGTGGTATGCATGCATTCC 59.834 45.455 36.44 36.44 42.08 3.01
2969 2990 2.033372 TGGTATGCATGCATTCCAAGG 58.967 47.619 40.68 0.00 46.15 3.61
2982 3527 5.357878 TGCATTCCAAGGAGATCAACATTAC 59.642 40.000 0.00 0.00 0.00 1.89
2984 3529 6.459298 GCATTCCAAGGAGATCAACATTACAG 60.459 42.308 0.00 0.00 0.00 2.74
2985 3530 6.373005 TTCCAAGGAGATCAACATTACAGA 57.627 37.500 0.00 0.00 0.00 3.41
2986 3531 6.373005 TCCAAGGAGATCAACATTACAGAA 57.627 37.500 0.00 0.00 0.00 3.02
2987 3532 6.962182 TCCAAGGAGATCAACATTACAGAAT 58.038 36.000 0.00 0.00 0.00 2.40
2989 3534 8.717717 TCCAAGGAGATCAACATTACAGAATAT 58.282 33.333 0.00 0.00 0.00 1.28
2990 3535 9.347240 CCAAGGAGATCAACATTACAGAATATT 57.653 33.333 0.00 0.00 0.00 1.28
2992 3537 8.915057 AGGAGATCAACATTACAGAATATTGG 57.085 34.615 0.00 0.00 31.52 3.16
2993 3538 7.446625 AGGAGATCAACATTACAGAATATTGGC 59.553 37.037 0.00 0.00 31.52 4.52
2994 3539 7.308830 GGAGATCAACATTACAGAATATTGGCC 60.309 40.741 0.00 0.00 31.52 5.36
3032 3784 9.866655 ATCTAGATCTTGTTTATTTATTGGCCA 57.133 29.630 0.00 0.00 0.00 5.36
3033 3785 9.866655 TCTAGATCTTGTTTATTTATTGGCCAT 57.133 29.630 6.09 0.00 0.00 4.40
3036 3788 9.603921 AGATCTTGTTTATTTATTGGCCATTTG 57.396 29.630 6.09 0.00 0.00 2.32
3037 3789 8.735692 ATCTTGTTTATTTATTGGCCATTTGG 57.264 30.769 6.09 0.00 38.53 3.28
3038 3790 7.684529 TCTTGTTTATTTATTGGCCATTTGGT 58.315 30.769 6.09 0.00 37.57 3.67
3039 3791 7.605691 TCTTGTTTATTTATTGGCCATTTGGTG 59.394 33.333 6.09 0.00 37.57 4.17
3040 3792 7.009179 TGTTTATTTATTGGCCATTTGGTGA 57.991 32.000 6.09 0.00 37.57 4.02
3041 3793 7.628234 TGTTTATTTATTGGCCATTTGGTGAT 58.372 30.769 6.09 0.00 37.57 3.06
3042 3794 8.762645 TGTTTATTTATTGGCCATTTGGTGATA 58.237 29.630 6.09 0.00 37.57 2.15
3048 3800 6.655078 ATTGGCCATTTGGTGATAATCTAC 57.345 37.500 6.09 0.00 37.57 2.59
3072 3824 5.856126 TCTTGTTTATTCAGCAACTACGG 57.144 39.130 0.00 0.00 0.00 4.02
3290 4067 7.094205 ACCATGTGTCAATTAAGAGATCAAACC 60.094 37.037 0.00 0.00 0.00 3.27
3485 4263 7.773489 TTGAGGAAATATTGTGGACATTTCA 57.227 32.000 8.14 0.00 39.40 2.69
3613 4396 7.064609 TGTTTATTCTTAAGGCGATCTTCACTG 59.935 37.037 1.85 0.00 36.93 3.66
3622 4405 4.813161 AGGCGATCTTCACTGTATTCAATG 59.187 41.667 0.00 0.00 0.00 2.82
3715 4498 7.012894 TCTCTTTCCTTTCGTTTGCTCATTTTA 59.987 33.333 0.00 0.00 0.00 1.52
3787 4595 7.836479 TTGTTCCAATATTCATCATGCCATA 57.164 32.000 0.00 0.00 0.00 2.74
3821 4629 9.629649 AATTACTCCCTCAGTCCCATAATATAA 57.370 33.333 0.00 0.00 36.43 0.98
3825 4633 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3894 4702 1.981495 GAGGGAGTATATTGCAGGGCT 59.019 52.381 0.00 0.00 0.00 5.19
4051 4859 7.169476 TGTGATACGTTCAAATAAACACTTCGA 59.831 33.333 0.00 0.00 35.70 3.71
4110 4918 0.039256 CAACTGACAAACCATGGCCG 60.039 55.000 13.04 2.47 35.52 6.13
4150 4958 5.798934 GTCTTATTCAGCTCATTGCAAAGTG 59.201 40.000 1.71 0.44 45.94 3.16
4380 5189 8.025243 ACAAAACACGTGTATCTTACCATTAG 57.975 34.615 23.69 4.99 0.00 1.73
4416 5225 0.527565 GATGGCAAATGTGAAGGCGT 59.472 50.000 0.00 0.00 0.00 5.68
4426 5235 1.302511 TGAAGGCGTTGGCTCTTCC 60.303 57.895 0.00 0.00 41.66 3.46
4534 5343 5.971763 CTTCTGAAGAAGTACAGTGGCTAT 58.028 41.667 12.01 0.00 44.80 2.97
4535 5344 6.360370 TTCTGAAGAAGTACAGTGGCTATT 57.640 37.500 0.00 0.00 35.84 1.73
4674 5483 4.263462 GGTATGATACATGCTTCCATCCCA 60.263 45.833 4.83 0.00 0.00 4.37
4687 5496 5.068591 GCTTCCATCCCATAAAATTTACGGT 59.931 40.000 0.00 0.00 0.00 4.83
4734 5549 2.362077 GGAGCCGCATGTAATTTCCATT 59.638 45.455 0.00 0.00 0.00 3.16
4772 5587 8.600625 TGCGTTATGTATTCTTACTAAAGCTTG 58.399 33.333 0.00 0.00 33.34 4.01
4788 5603 1.668628 GCTTGTGCCGGTTGGTTAATG 60.669 52.381 1.90 0.00 37.67 1.90
4815 5630 6.459923 GTGAGTGTAGGAGACAGAAAAGATT 58.540 40.000 0.00 0.00 39.29 2.40
4971 5786 1.191535 CCCTCTACATGGACGGTCAA 58.808 55.000 10.76 0.00 0.00 3.18
5115 5931 7.512992 TGGACATTGTTATTGAATTTTTGGGT 58.487 30.769 0.00 0.00 0.00 4.51
5117 5933 7.148656 GGACATTGTTATTGAATTTTTGGGTCG 60.149 37.037 0.00 0.00 0.00 4.79
5287 6103 6.149973 TGTTCAAAGTTGCCTATCTGAATCAG 59.850 38.462 3.38 3.38 0.00 2.90
5307 6123 9.906660 GAATCAGTTATGTACATTGGTTTTTCA 57.093 29.630 14.77 0.00 0.00 2.69
5330 6146 7.629157 TCATTTAACAGTTGAGGTGGATATGA 58.371 34.615 0.00 0.00 0.00 2.15
5472 6293 3.891366 CCCTGTGGAATTTCTGAAACACT 59.109 43.478 17.67 3.39 0.00 3.55
5612 6434 3.091545 TCATGTGGAATCTTTGAAGGGC 58.908 45.455 0.00 0.00 0.00 5.19
5684 6506 6.259167 AGCGACAAATGTAGTTTTTGTACTCA 59.741 34.615 2.10 0.00 44.90 3.41
5749 6571 5.380043 CATATTCTAGGTGGCCAGTCATTT 58.620 41.667 5.11 0.00 0.00 2.32
5780 6603 6.347725 GCGTCTAATTTGTATCTGCCCATAAG 60.348 42.308 0.00 0.00 0.00 1.73
5798 6621 9.184523 GCCCATAAGTGTTGCCAATATATATTA 57.815 33.333 7.65 0.00 0.00 0.98
5812 6635 9.561270 CCAATATATATTATCATAGGCTCGACG 57.439 37.037 7.65 0.00 0.00 5.12
5814 6637 9.516546 AATATATATTATCATAGGCTCGACGGA 57.483 33.333 6.16 0.00 0.00 4.69
5824 6647 1.865340 GGCTCGACGGAATACCAAATC 59.135 52.381 0.00 0.00 35.59 2.17
5843 6666 2.045340 GCCTTAGGCCGCTTTCCA 60.045 61.111 13.12 0.00 44.06 3.53
5851 6674 1.004277 AGGCCGCTTTCCAATGTAGAA 59.996 47.619 0.00 0.00 0.00 2.10
5915 6738 2.749839 TGCGCATTGGCCCTGTAC 60.750 61.111 5.66 0.00 36.38 2.90
5924 6747 2.742428 TGGCCCTGTACGTAGTCTAT 57.258 50.000 0.00 0.00 43.93 1.98
5925 6748 2.304092 TGGCCCTGTACGTAGTCTATG 58.696 52.381 0.00 0.00 43.93 2.23
5936 6759 7.466805 TGTACGTAGTCTATGTTACACATCAC 58.533 38.462 10.00 1.15 43.93 3.06
5943 6766 7.952671 AGTCTATGTTACACATCACGGAATAT 58.047 34.615 0.00 0.00 39.88 1.28
5944 6767 8.082852 AGTCTATGTTACACATCACGGAATATC 58.917 37.037 0.00 0.00 39.88 1.63
5955 6778 6.706270 ACATCACGGAATATCAACCACTATTC 59.294 38.462 0.00 0.00 34.85 1.75
5960 6783 6.055588 CGGAATATCAACCACTATTCAAGGT 58.944 40.000 0.00 0.00 36.50 3.50
5967 6790 3.939066 ACCACTATTCAAGGTAGTGTGC 58.061 45.455 11.12 0.00 44.72 4.57
5982 6805 4.539083 TGCGTGCGGTTGGAGTGT 62.539 61.111 0.00 0.00 0.00 3.55
5990 6813 0.250295 CGGTTGGAGTGTGTGGACAT 60.250 55.000 0.00 0.00 33.63 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 0.607620 CATGGTTGCCGGTGGAAATT 59.392 50.000 1.90 0.00 0.00 1.82
87 88 0.541764 ACATGGTTGCCGGTGGAAAT 60.542 50.000 1.90 0.00 0.00 2.17
91 92 2.034066 AGACATGGTTGCCGGTGG 59.966 61.111 1.90 0.00 0.00 4.61
116 117 3.917760 ATCTAGTCCCGGCTGCGC 61.918 66.667 0.00 0.00 0.00 6.09
186 187 1.152756 GCCAGTGGTGGTGGTCTTT 60.153 57.895 11.74 0.00 46.96 2.52
210 214 3.055963 CCATGGCAGATTTGTTTTGGCTA 60.056 43.478 0.00 0.00 38.14 3.93
269 273 2.033424 GTCATTTGGCTTTAGATCGGCC 59.967 50.000 12.71 12.71 45.45 6.13
285 289 1.369625 GTCTTCGGCGGAATGTCATT 58.630 50.000 7.21 0.00 0.00 2.57
293 297 4.508128 GATGCGGTCTTCGGCGGA 62.508 66.667 7.21 0.00 41.74 5.54
320 324 4.147449 CGGCTGGTCTGCATCGGA 62.147 66.667 0.00 0.00 34.04 4.55
451 458 3.391382 CTTCCTCCCTCCCGCGTT 61.391 66.667 4.92 0.00 0.00 4.84
562 571 3.480133 CTCCCCAACCCTAGCCGG 61.480 72.222 0.00 0.00 0.00 6.13
594 606 2.358247 CGTCCTGGGGTGTTTCCG 60.358 66.667 0.00 0.00 37.00 4.30
595 607 2.671963 GCGTCCTGGGGTGTTTCC 60.672 66.667 0.00 0.00 0.00 3.13
597 609 2.042404 TAACGCGTCCTGGGGTGTTT 62.042 55.000 14.44 0.00 37.90 2.83
598 610 2.509651 TAACGCGTCCTGGGGTGTT 61.510 57.895 14.44 17.33 39.85 3.32
599 611 2.918802 TAACGCGTCCTGGGGTGT 60.919 61.111 14.44 0.00 32.94 4.16
600 612 2.433664 GTAACGCGTCCTGGGGTG 60.434 66.667 14.44 0.00 32.94 4.61
601 613 2.918802 TGTAACGCGTCCTGGGGT 60.919 61.111 14.44 0.00 34.15 4.95
602 614 2.125673 CTGTAACGCGTCCTGGGG 60.126 66.667 14.44 0.00 34.15 4.96
603 615 0.320073 TTTCTGTAACGCGTCCTGGG 60.320 55.000 14.44 2.29 0.00 4.45
604 616 0.788391 GTTTCTGTAACGCGTCCTGG 59.212 55.000 14.44 3.89 0.00 4.45
605 617 1.493772 TGTTTCTGTAACGCGTCCTG 58.506 50.000 14.44 10.77 39.72 3.86
606 618 2.288579 TGATGTTTCTGTAACGCGTCCT 60.289 45.455 14.44 0.00 39.72 3.85
607 619 2.063266 TGATGTTTCTGTAACGCGTCC 58.937 47.619 14.44 7.13 39.72 4.79
608 620 2.472397 GCTGATGTTTCTGTAACGCGTC 60.472 50.000 14.44 0.25 39.72 5.19
609 621 1.459592 GCTGATGTTTCTGTAACGCGT 59.540 47.619 5.58 5.58 39.72 6.01
610 622 1.459209 TGCTGATGTTTCTGTAACGCG 59.541 47.619 3.53 3.53 39.72 6.01
611 623 3.747099 ATGCTGATGTTTCTGTAACGC 57.253 42.857 0.00 0.00 39.72 4.84
612 624 4.568359 AGCTATGCTGATGTTTCTGTAACG 59.432 41.667 0.00 0.00 37.21 3.18
976 992 5.538433 TGAGCAAATTAACAAACCCTAGCTT 59.462 36.000 0.00 0.00 0.00 3.74
1567 1583 0.673333 GGCATGGTGTGTGTGATCGA 60.673 55.000 0.00 0.00 0.00 3.59
1608 1624 4.473643 CTGGAACAAGAACCGGCA 57.526 55.556 0.00 0.00 38.70 5.69
1613 1629 6.921914 TCTTAGTACTAGCTGGAACAAGAAC 58.078 40.000 3.17 0.00 38.70 3.01
1836 1852 7.260387 CTAGTAGTCTAGTAGATGGGATGGA 57.740 44.000 14.41 0.00 38.91 3.41
1853 1869 5.640189 ACGAACAAGCATGTACTAGTAGT 57.360 39.130 8.14 8.14 39.40 2.73
2011 2029 6.977244 AGCCCTCCCATCATAAACTAATAT 57.023 37.500 0.00 0.00 0.00 1.28
2161 2182 2.587247 GCTCCTCACTGTGCCCTCA 61.587 63.158 2.12 0.00 0.00 3.86
2383 2404 4.218635 GCTTCATGCATGGAGATCAATGAT 59.781 41.667 34.79 0.00 42.31 2.45
2388 2409 3.211865 GAAGCTTCATGCATGGAGATCA 58.788 45.455 34.79 9.29 45.94 2.92
2524 2545 5.073311 TGGAACACTTGTGATCTAGCTAC 57.927 43.478 7.83 0.00 0.00 3.58
2537 2558 2.325583 TTTGCGAGACTGGAACACTT 57.674 45.000 0.00 0.00 0.00 3.16
2631 2652 1.302752 CTGCACTGCACCCAAGCTA 60.303 57.895 0.00 0.00 33.79 3.32
2691 2712 2.360165 GCAGAATAGTGCCCCTTGAATG 59.640 50.000 0.00 0.00 37.49 2.67
2812 2833 3.136443 TGGAGATTGGAAGAACACAGTGT 59.864 43.478 0.00 0.00 0.00 3.55
2813 2834 3.743521 TGGAGATTGGAAGAACACAGTG 58.256 45.455 0.00 0.00 0.00 3.66
2947 2968 2.140839 TGGAATGCATGCATACCACA 57.859 45.000 32.36 23.51 35.31 4.17
2948 2969 2.223876 CCTTGGAATGCATGCATACCAC 60.224 50.000 32.36 21.45 35.31 4.16
2950 2971 2.295349 CTCCTTGGAATGCATGCATACC 59.705 50.000 32.36 24.79 35.31 2.73
2951 2972 3.216800 TCTCCTTGGAATGCATGCATAC 58.783 45.455 32.36 26.34 35.31 2.39
2952 2973 3.581265 TCTCCTTGGAATGCATGCATA 57.419 42.857 32.36 15.49 35.31 3.14
2953 2974 2.447408 TCTCCTTGGAATGCATGCAT 57.553 45.000 27.46 27.46 38.46 3.96
2954 2975 2.304092 GATCTCCTTGGAATGCATGCA 58.696 47.619 25.04 25.04 0.00 3.96
2955 2976 2.304092 TGATCTCCTTGGAATGCATGC 58.696 47.619 11.82 11.82 0.00 4.06
2956 2977 3.697542 TGTTGATCTCCTTGGAATGCATG 59.302 43.478 0.00 0.00 0.00 4.06
2957 2978 3.972133 TGTTGATCTCCTTGGAATGCAT 58.028 40.909 0.00 0.00 0.00 3.96
2958 2979 3.438216 TGTTGATCTCCTTGGAATGCA 57.562 42.857 0.00 0.00 0.00 3.96
2959 2980 4.996788 AATGTTGATCTCCTTGGAATGC 57.003 40.909 0.00 0.00 0.00 3.56
2960 2981 6.825213 TCTGTAATGTTGATCTCCTTGGAATG 59.175 38.462 0.00 0.00 0.00 2.67
2962 2983 6.373005 TCTGTAATGTTGATCTCCTTGGAA 57.627 37.500 0.00 0.00 0.00 3.53
2963 2984 6.373005 TTCTGTAATGTTGATCTCCTTGGA 57.627 37.500 0.00 0.00 0.00 3.53
2964 2985 8.915057 ATATTCTGTAATGTTGATCTCCTTGG 57.085 34.615 0.00 0.00 0.00 3.61
2967 2988 7.446625 GCCAATATTCTGTAATGTTGATCTCCT 59.553 37.037 8.58 0.00 43.26 3.69
2969 2990 7.229306 TGGCCAATATTCTGTAATGTTGATCTC 59.771 37.037 0.61 0.00 43.26 2.75
2982 3527 5.341872 TTCACCAAATGGCCAATATTCTG 57.658 39.130 10.96 0.98 39.32 3.02
2984 3529 7.049754 AGATTTTCACCAAATGGCCAATATTC 58.950 34.615 10.96 0.00 35.02 1.75
2985 3530 6.961042 AGATTTTCACCAAATGGCCAATATT 58.039 32.000 10.96 2.11 35.02 1.28
2986 3531 6.564557 AGATTTTCACCAAATGGCCAATAT 57.435 33.333 10.96 0.00 35.02 1.28
2987 3532 6.894654 TCTAGATTTTCACCAAATGGCCAATA 59.105 34.615 10.96 0.00 35.02 1.90
2989 3534 5.083122 TCTAGATTTTCACCAAATGGCCAA 58.917 37.500 10.96 0.00 35.02 4.52
2990 3535 4.671831 TCTAGATTTTCACCAAATGGCCA 58.328 39.130 8.56 8.56 35.02 5.36
2992 3537 6.705863 AGATCTAGATTTTCACCAAATGGC 57.294 37.500 6.70 0.00 35.02 4.40
2993 3538 8.059798 ACAAGATCTAGATTTTCACCAAATGG 57.940 34.615 6.70 0.00 35.02 3.16
2994 3539 9.918630 AAACAAGATCTAGATTTTCACCAAATG 57.081 29.630 6.70 0.00 35.02 2.32
3024 3776 7.293828 TGTAGATTATCACCAAATGGCCAATA 58.706 34.615 10.96 0.00 39.32 1.90
3026 3778 5.514169 TGTAGATTATCACCAAATGGCCAA 58.486 37.500 10.96 0.00 39.32 4.52
3027 3779 5.122707 TGTAGATTATCACCAAATGGCCA 57.877 39.130 8.56 8.56 39.32 5.36
3028 3780 6.006449 AGATGTAGATTATCACCAAATGGCC 58.994 40.000 0.00 0.00 39.32 5.36
3029 3781 7.013655 ACAAGATGTAGATTATCACCAAATGGC 59.986 37.037 0.00 0.00 39.32 4.40
3030 3782 8.455903 ACAAGATGTAGATTATCACCAAATGG 57.544 34.615 0.00 0.00 42.17 3.16
3042 3794 9.236006 AGTTGCTGAATAAACAAGATGTAGATT 57.764 29.630 0.00 0.00 0.00 2.40
3048 3800 6.128282 ACCGTAGTTGCTGAATAAACAAGATG 60.128 38.462 0.00 0.00 0.00 2.90
3083 3835 1.272704 GGCCAGGGACAATCCTTCTTT 60.273 52.381 0.00 0.00 36.57 2.52
3087 3839 0.551131 AGAGGCCAGGGACAATCCTT 60.551 55.000 5.01 0.00 36.57 3.36
3094 3846 2.191641 GATGCAGAGGCCAGGGAC 59.808 66.667 5.01 0.00 40.13 4.46
3290 4067 3.262420 CGTCATCCCTTAAACCTCACTG 58.738 50.000 0.00 0.00 0.00 3.66
3765 4573 7.218228 TGTATGGCATGATGAATATTGGAAC 57.782 36.000 10.98 0.00 0.00 3.62
3787 4595 5.535030 GGACTGAGGGAGTAATTGTTTTTGT 59.465 40.000 0.00 0.00 33.83 2.83
3894 4702 3.007614 GGAGTCAGGGTAACAAAGCAGTA 59.992 47.826 0.00 0.00 39.74 2.74
4051 4859 5.487488 TGACCATTACCTGATAGACCAGTTT 59.513 40.000 0.00 0.00 32.43 2.66
4110 4918 2.365408 AGACCGAATCAGACCGAAAC 57.635 50.000 0.00 0.00 0.00 2.78
4119 4927 4.736126 TGAGCTGAATAAGACCGAATCA 57.264 40.909 0.00 0.00 0.00 2.57
4150 4958 1.943340 GCTACAGTCCCAATTAGCTGC 59.057 52.381 0.00 0.00 35.15 5.25
4426 5235 2.398498 CTAGCGTCCATTTCATCCTCG 58.602 52.381 0.00 0.00 0.00 4.63
4734 5549 4.735662 ACATAACGCAGCTTTCGTTTTA 57.264 36.364 23.18 11.00 46.47 1.52
4772 5587 0.242555 CCACATTAACCAACCGGCAC 59.757 55.000 0.00 0.00 34.57 5.01
4788 5603 2.515854 TCTGTCTCCTACACTCACCAC 58.484 52.381 0.00 0.00 33.45 4.16
4815 5630 3.487202 GTCGATTCCGCAAGCGCA 61.487 61.111 11.47 0.00 41.30 6.09
4971 5786 0.394762 ACATGCCGTCAGCCATGAAT 60.395 50.000 7.53 0.00 42.71 2.57
5006 5821 6.149474 CCAGATCGATTGTTCAAAGTAGGTTT 59.851 38.462 0.00 0.00 0.00 3.27
5014 5829 2.694213 TCGCCAGATCGATTGTTCAAA 58.306 42.857 0.00 0.00 33.02 2.69
5024 5839 1.328680 CAATCACCTTTCGCCAGATCG 59.671 52.381 0.00 0.00 0.00 3.69
5063 5878 9.575868 TGTATTTTTAACCAGTCCTGAATACAA 57.424 29.630 11.49 0.00 36.41 2.41
5073 5888 8.303876 ACAATGTCCATGTATTTTTAACCAGTC 58.696 33.333 0.00 0.00 0.00 3.51
5117 5933 0.744771 GAGCCTGTGAATCCGGGAAC 60.745 60.000 0.00 0.00 0.00 3.62
5307 6123 8.274322 TGATCATATCCACCTCAACTGTTAAAT 58.726 33.333 0.00 0.00 0.00 1.40
5384 6200 2.835764 TCAACTGGGTAACGCTAAGGAT 59.164 45.455 0.00 0.00 37.60 3.24
5530 6351 9.139174 GGTGTTTAAGAAATTCCATTACATGTG 57.861 33.333 9.11 0.00 0.00 3.21
5612 6434 6.970484 AGGTTGTCTTTAGTTAGCACAAATG 58.030 36.000 0.00 0.00 0.00 2.32
5684 6506 9.186837 AGAAAAGCTATTTGATTGTCTCATCAT 57.813 29.630 0.00 0.00 33.72 2.45
5727 6549 5.653255 AAATGACTGGCCACCTAGAATAT 57.347 39.130 0.00 0.00 0.00 1.28
5728 6550 6.569127 TTAAATGACTGGCCACCTAGAATA 57.431 37.500 0.00 0.00 0.00 1.75
5749 6571 7.386848 GGGCAGATACAAATTAGACGCTATTTA 59.613 37.037 0.00 0.00 0.00 1.40
5798 6621 2.492484 GGTATTCCGTCGAGCCTATGAT 59.508 50.000 0.00 0.00 0.00 2.45
5802 6625 1.766494 TTGGTATTCCGTCGAGCCTA 58.234 50.000 0.00 0.00 36.30 3.93
5812 6635 3.146847 CCTAAGGCCGATTTGGTATTCC 58.853 50.000 0.00 0.00 41.21 3.01
5814 6637 2.583143 GCCTAAGGCCGATTTGGTATT 58.417 47.619 0.00 0.00 44.06 1.89
5835 6658 9.013490 CAATTCTAATTTCTACATTGGAAAGCG 57.987 33.333 0.00 0.00 37.24 4.68
5878 6701 8.770438 TGCGCACAATGATATATAAACATAGA 57.230 30.769 5.66 0.00 0.00 1.98
5879 6702 9.992910 AATGCGCACAATGATATATAAACATAG 57.007 29.630 14.90 3.06 0.00 2.23
5880 6703 9.771915 CAATGCGCACAATGATATATAAACATA 57.228 29.630 14.90 0.00 0.00 2.29
5881 6704 7.756272 CCAATGCGCACAATGATATATAAACAT 59.244 33.333 14.90 0.00 0.00 2.71
5882 6705 7.083230 CCAATGCGCACAATGATATATAAACA 58.917 34.615 14.90 0.00 0.00 2.83
5883 6706 6.033831 GCCAATGCGCACAATGATATATAAAC 59.966 38.462 14.90 0.00 0.00 2.01
5884 6707 6.092092 GCCAATGCGCACAATGATATATAAA 58.908 36.000 14.90 0.00 0.00 1.40
5901 6724 0.107848 ACTACGTACAGGGCCAATGC 60.108 55.000 6.18 0.00 0.00 3.56
5925 6748 5.583061 TGGTTGATATTCCGTGATGTGTAAC 59.417 40.000 0.00 0.00 37.35 2.50
5936 6759 6.055588 ACCTTGAATAGTGGTTGATATTCCG 58.944 40.000 0.00 0.00 37.52 4.30
5955 6778 2.667318 CCGCACGCACACTACCTTG 61.667 63.158 0.00 0.00 0.00 3.61
5960 6783 2.663520 CCAACCGCACGCACACTA 60.664 61.111 0.00 0.00 0.00 2.74
5967 6790 2.587753 ACACACTCCAACCGCACG 60.588 61.111 0.00 0.00 0.00 5.34
5982 6805 3.117701 TCAGGAAAACCTCAATGTCCACA 60.118 43.478 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.