Multiple sequence alignment - TraesCS4B01G054000

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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 TraesCS4B01G054000 chr4B 100.000 3644 0 0 1 3644 42778095 42774452 0.000000e+00 6730.0
1 TraesCS4B01G054000 chr4B 78.431 153 30 3 1761 1911 30862303 30862454 3.000000e-16 97.1
2 TraesCS4B01G054000 chr4D 90.450 2691 139 53 966 3589 30004272 30006911 0.000000e+00 3437.0
3 TraesCS4B01G054000 chr4D 88.806 268 20 7 614 876 30003695 30003957 1.630000e-83 320.0
4 TraesCS4B01G054000 chr4D 78.571 154 30 3 1761 1912 18781986 18782138 8.330000e-17 99.0
5 TraesCS4B01G054000 chr4A 93.090 2026 91 15 659 2656 573174055 573172051 0.000000e+00 2920.0
6 TraesCS4B01G054000 chr4A 85.246 610 82 7 1 605 69996053 69995447 4.000000e-174 621.0
7 TraesCS4B01G054000 chr4A 85.880 517 26 22 2705 3200 573172050 573171560 1.170000e-139 507.0
8 TraesCS4B01G054000 chr4A 93.478 138 9 0 3205 3342 573171522 573171385 4.770000e-49 206.0
9 TraesCS4B01G054000 chr4A 94.845 97 5 0 3470 3566 573171387 573171291 6.300000e-33 152.0
10 TraesCS4B01G054000 chr4A 79.085 153 29 3 1761 1911 582478660 582478509 6.440000e-18 102.0
11 TraesCS4B01G054000 chr1D 89.439 606 55 7 1 600 353644687 353644085 0.000000e+00 756.0
12 TraesCS4B01G054000 chr1D 87.769 605 69 5 1 600 223469618 223470222 0.000000e+00 702.0
13 TraesCS4B01G054000 chr1D 86.393 610 75 5 2 603 448219944 448220553 0.000000e+00 660.0
14 TraesCS4B01G054000 chr5D 88.264 605 65 5 1 600 134914143 134913540 0.000000e+00 719.0
15 TraesCS4B01G054000 chr5D 85.738 610 79 8 1 604 192549784 192549177 3.970000e-179 638.0
16 TraesCS4B01G054000 chr3B 86.393 610 73 6 1 600 416802968 416803577 0.000000e+00 658.0
17 TraesCS4B01G054000 chr5B 86.757 589 72 5 15 599 639667606 639668192 0.000000e+00 651.0
18 TraesCS4B01G054000 chr2D 85.927 604 81 4 1 600 620213774 620214377 3.070000e-180 641.0
19 TraesCS4B01G054000 chr3D 95.833 168 7 0 1817 1984 581540462 581540629 4.640000e-69 272.0
20 TraesCS4B01G054000 chr3D 97.260 73 2 0 2338 2410 581541042 581541114 1.370000e-24 124.0


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 TraesCS4B01G054000 chr4B 42774452 42778095 3643 True 6730.00 6730 100.00000 1 3644 1 chr4B.!!$R1 3643
1 TraesCS4B01G054000 chr4D 30003695 30006911 3216 False 1878.50 3437 89.62800 614 3589 2 chr4D.!!$F2 2975
2 TraesCS4B01G054000 chr4A 573171291 573174055 2764 True 946.25 2920 91.82325 659 3566 4 chr4A.!!$R3 2907
3 TraesCS4B01G054000 chr4A 69995447 69996053 606 True 621.00 621 85.24600 1 605 1 chr4A.!!$R1 604
4 TraesCS4B01G054000 chr1D 353644085 353644687 602 True 756.00 756 89.43900 1 600 1 chr1D.!!$R1 599
5 TraesCS4B01G054000 chr1D 223469618 223470222 604 False 702.00 702 87.76900 1 600 1 chr1D.!!$F1 599
6 TraesCS4B01G054000 chr1D 448219944 448220553 609 False 660.00 660 86.39300 2 603 1 chr1D.!!$F2 601
7 TraesCS4B01G054000 chr5D 134913540 134914143 603 True 719.00 719 88.26400 1 600 1 chr5D.!!$R1 599
8 TraesCS4B01G054000 chr5D 192549177 192549784 607 True 638.00 638 85.73800 1 604 1 chr5D.!!$R2 603
9 TraesCS4B01G054000 chr3B 416802968 416803577 609 False 658.00 658 86.39300 1 600 1 chr3B.!!$F1 599
10 TraesCS4B01G054000 chr5B 639667606 639668192 586 False 651.00 651 86.75700 15 599 1 chr5B.!!$F1 584
11 TraesCS4B01G054000 chr2D 620213774 620214377 603 False 641.00 641 85.92700 1 600 1 chr2D.!!$F1 599

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
606 623 0.107703 CGCTGGAGTTGGCATAAGGA 60.108 55.0 0.0 0.0 0.0 3.36 F
1761 2026 0.958822 TCACGCTCTGCTACAAGACA 59.041 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2795 1.174783 GAGTCGTAGTCCCAGAGCAA 58.825 55.0 0.0 0.00 0.00 3.91 R
2685 2950 0.317938 CCTCCGTGGATCGATCGAAC 60.318 60.0 23.5 19.61 42.86 3.95 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
83 84 3.402681 CTCCGTGGGGGTGATGCT 61.403 66.667 0.00 0.00 37.00 3.79
175 177 1.598962 CAGTGCTCCACCACACCAG 60.599 63.158 0.00 0.00 38.18 4.00
207 209 2.470362 CGGCGAGCTCGAGTAAGGA 61.470 63.158 38.74 0.00 43.02 3.36
233 241 1.351350 GAGAGCTAGGGTTTGGGTGTT 59.649 52.381 0.00 0.00 0.00 3.32
320 329 1.669999 TAAGAAGGACGCCTACCGCC 61.670 60.000 0.00 0.00 41.76 6.13
340 351 2.942796 AAGCGCGGATGACAGGTGA 61.943 57.895 8.83 0.00 0.00 4.02
384 399 0.838987 GTTGGGTGGTGGGAGGTAGA 60.839 60.000 0.00 0.00 0.00 2.59
387 402 0.620700 GGGTGGTGGGAGGTAGATGT 60.621 60.000 0.00 0.00 0.00 3.06
392 407 2.125326 TGGGAGGTAGATGTCCGCG 61.125 63.158 0.00 0.00 33.13 6.46
439 454 1.207593 GCGCATTCGTTTGCTGTCT 59.792 52.632 0.30 0.00 40.54 3.41
499 515 0.889186 GTCGGGCCAGACACAAACAT 60.889 55.000 28.45 0.00 40.65 2.71
507 523 4.218417 GGCCAGACACAAACATACAAGATT 59.782 41.667 0.00 0.00 0.00 2.40
554 570 1.425066 TGAGGTCTGTCCATTTTGCCT 59.575 47.619 0.00 0.00 39.02 4.75
562 579 4.588106 TCTGTCCATTTTGCCTCAAATGAA 59.412 37.500 12.43 0.00 33.19 2.57
569 586 1.305213 GCCTCAAATGAAGGGGCCA 60.305 57.895 4.39 0.00 37.12 5.36
605 622 0.392998 ACGCTGGAGTTGGCATAAGG 60.393 55.000 0.00 0.00 0.00 2.69
606 623 0.107703 CGCTGGAGTTGGCATAAGGA 60.108 55.000 0.00 0.00 0.00 3.36
607 624 1.678728 CGCTGGAGTTGGCATAAGGAA 60.679 52.381 0.00 0.00 0.00 3.36
608 625 2.446435 GCTGGAGTTGGCATAAGGAAA 58.554 47.619 0.00 0.00 0.00 3.13
609 626 2.164422 GCTGGAGTTGGCATAAGGAAAC 59.836 50.000 0.00 0.00 0.00 2.78
610 627 2.755103 CTGGAGTTGGCATAAGGAAACC 59.245 50.000 0.00 0.00 0.00 3.27
611 628 1.743394 GGAGTTGGCATAAGGAAACCG 59.257 52.381 0.00 0.00 0.00 4.44
612 629 2.433436 GAGTTGGCATAAGGAAACCGT 58.567 47.619 0.00 0.00 0.00 4.83
642 659 1.092921 GTGACACCGGTTGCTCACAA 61.093 55.000 23.20 0.00 36.77 3.33
688 709 2.978010 CCCACCTGAACACCGCAC 60.978 66.667 0.00 0.00 0.00 5.34
777 808 3.422796 AGACCAGTACAGTCCAGTACAG 58.577 50.000 11.29 0.00 45.25 2.74
785 816 1.982938 GTCCAGTACAGCCCGAGGT 60.983 63.158 0.00 0.00 0.00 3.85
791 822 3.533079 TACAGCCCGAGGTCACCCA 62.533 63.158 0.00 0.00 0.00 4.51
802 833 1.959226 GTCACCCACGTCATTGCGT 60.959 57.895 0.00 1.20 46.88 5.24
806 837 3.124921 CCACGTCATTGCGTCCCC 61.125 66.667 3.67 0.00 43.83 4.81
876 907 3.542969 ACTGTTTTAAATCCCCCTGCT 57.457 42.857 0.00 0.00 0.00 4.24
881 912 0.998928 TTAAATCCCCCTGCTGCTCA 59.001 50.000 0.00 0.00 0.00 4.26
887 918 4.463879 CCCTGCTGCTCACCTCCG 62.464 72.222 0.00 0.00 0.00 4.63
913 949 2.543637 TTCCCTCCCCTCCCCTCT 60.544 66.667 0.00 0.00 0.00 3.69
916 962 3.039526 CCTCCCCTCCCCTCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
935 981 1.752694 CAAACCCGCCCCGATTCAT 60.753 57.895 0.00 0.00 0.00 2.57
1090 1346 1.895231 CACAACCAGCAGCAGCAGA 60.895 57.895 3.17 0.00 45.49 4.26
1117 1379 4.928140 ACCACCACCTCGTCCCGT 62.928 66.667 0.00 0.00 0.00 5.28
1377 1639 1.811266 CCGCCTCATCTTCACCACG 60.811 63.158 0.00 0.00 0.00 4.94
1383 1645 4.778143 ATCTTCACCACGCCGCCC 62.778 66.667 0.00 0.00 0.00 6.13
1419 1681 4.443266 GCTGAAGCCGAGGACGCT 62.443 66.667 0.00 0.00 38.29 5.07
1501 1766 2.046217 GTTCTTCCCCGGGCTCAC 60.046 66.667 17.73 2.55 0.00 3.51
1536 1801 2.367512 GCCCCCATCCTCCAGTCT 60.368 66.667 0.00 0.00 0.00 3.24
1605 1870 2.342648 GAACTCGCCAAGGTCCGT 59.657 61.111 0.00 0.00 35.49 4.69
1761 2026 0.958822 TCACGCTCTGCTACAAGACA 59.041 50.000 0.00 0.00 0.00 3.41
1788 2053 2.966732 CGCCTGCCCCTACTCCAAA 61.967 63.158 0.00 0.00 0.00 3.28
1980 2245 4.569180 CCATACCTGGGGCCGCAG 62.569 72.222 36.42 36.42 39.04 5.18
2090 2355 4.357947 GGTGCACGAGCTCGACCA 62.358 66.667 40.58 30.36 43.02 4.02
2382 2647 4.166011 GAGCGGTGCATGTTCGGC 62.166 66.667 0.00 11.52 0.00 5.54
2547 2812 1.133407 CTCTTGCTCTGGGACTACGAC 59.867 57.143 0.00 0.00 0.00 4.34
2548 2813 1.178276 CTTGCTCTGGGACTACGACT 58.822 55.000 0.00 0.00 0.00 4.18
2571 2836 3.303495 CCAAGTACAAGTATTCGCTCGTG 59.697 47.826 0.00 0.00 0.00 4.35
2572 2837 3.146618 AGTACAAGTATTCGCTCGTGG 57.853 47.619 0.00 0.00 0.00 4.94
2631 2896 2.347322 GCCTCTGCTCACCGTCTCT 61.347 63.158 0.00 0.00 33.53 3.10
2634 2899 1.594194 CTCTGCTCACCGTCTCTGCT 61.594 60.000 0.00 0.00 0.00 4.24
2685 2950 2.544685 CAGTATTTGCTCCTCCTCGTG 58.455 52.381 0.00 0.00 0.00 4.35
2695 2960 0.663688 CCTCCTCGTGTTCGATCGAT 59.336 55.000 20.18 0.00 45.21 3.59
2696 2961 1.334239 CCTCCTCGTGTTCGATCGATC 60.334 57.143 20.18 18.57 45.21 3.69
2697 2962 0.661552 TCCTCGTGTTCGATCGATCC 59.338 55.000 20.18 13.12 45.21 3.36
2699 2964 1.467875 CTCGTGTTCGATCGATCCAC 58.532 55.000 26.37 26.37 45.21 4.02
2701 2966 1.200474 CGTGTTCGATCGATCCACGG 61.200 60.000 37.27 27.11 41.65 4.94
2702 2967 0.099968 GTGTTCGATCGATCCACGGA 59.900 55.000 23.92 8.14 42.82 4.69
2703 2968 0.380733 TGTTCGATCGATCCACGGAG 59.619 55.000 20.18 4.69 42.82 4.63
2748 3013 3.616379 CAGATCGTTCTCCTTGAAGCTTC 59.384 47.826 19.89 19.89 35.01 3.86
2749 3014 2.457366 TCGTTCTCCTTGAAGCTTCC 57.543 50.000 23.42 6.48 35.01 3.46
2763 3028 8.306761 CCTTGAAGCTTCCTTTGTAATTTGTAT 58.693 33.333 23.42 0.00 0.00 2.29
2765 3030 9.474920 TTGAAGCTTCCTTTGTAATTTGTATTG 57.525 29.630 23.42 0.00 0.00 1.90
2814 3084 9.929180 AAAAAGCTCTGTTTATTTAGGATTTCC 57.071 29.630 0.00 0.00 0.00 3.13
2815 3085 6.927294 AGCTCTGTTTATTTAGGATTTCCG 57.073 37.500 0.00 0.00 42.08 4.30
2861 3144 5.069119 GGCTAGGATTGGGAAATTTAGTTGG 59.931 44.000 0.00 0.00 0.00 3.77
2863 3146 6.379988 GCTAGGATTGGGAAATTTAGTTGGAA 59.620 38.462 0.00 0.00 0.00 3.53
2864 3147 6.605471 AGGATTGGGAAATTTAGTTGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
2865 3148 5.483937 AGGATTGGGAAATTTAGTTGGAACC 59.516 40.000 0.00 0.00 0.00 3.62
2932 3217 6.760298 GGGTTAAGTAGTAGACCAAATGTAGC 59.240 42.308 5.04 0.00 33.81 3.58
2945 3230 7.385205 AGACCAAATGTAGCGCTAATTGTATAG 59.615 37.037 20.73 13.10 0.00 1.31
2946 3231 6.426937 ACCAAATGTAGCGCTAATTGTATAGG 59.573 38.462 20.73 15.23 0.00 2.57
2947 3232 6.649141 CCAAATGTAGCGCTAATTGTATAGGA 59.351 38.462 20.73 0.00 0.00 2.94
2964 3249 6.881065 TGTATAGGATGAATTTAGAGCATGCC 59.119 38.462 15.66 6.03 31.70 4.40
3056 3349 2.674954 TGCCGCACATGAAATTGAAAG 58.325 42.857 0.00 0.00 0.00 2.62
3057 3350 1.994779 GCCGCACATGAAATTGAAAGG 59.005 47.619 0.00 0.00 0.00 3.11
3061 3354 3.391965 GCACATGAAATTGAAAGGTGCA 58.608 40.909 15.83 0.00 46.75 4.57
3062 3355 3.998341 GCACATGAAATTGAAAGGTGCAT 59.002 39.130 15.83 0.00 46.75 3.96
3063 3356 4.453136 GCACATGAAATTGAAAGGTGCATT 59.547 37.500 15.83 0.00 46.75 3.56
3065 3358 6.183360 GCACATGAAATTGAAAGGTGCATTAG 60.183 38.462 15.83 0.00 46.75 1.73
3069 3362 6.158598 TGAAATTGAAAGGTGCATTAGCTTC 58.841 36.000 0.00 0.00 45.88 3.86
3070 3363 5.990120 AATTGAAAGGTGCATTAGCTTCT 57.010 34.783 0.00 0.00 45.88 2.85
3071 3364 5.573337 ATTGAAAGGTGCATTAGCTTCTC 57.427 39.130 0.00 0.00 45.88 2.87
3072 3365 4.292186 TGAAAGGTGCATTAGCTTCTCT 57.708 40.909 0.00 0.00 45.88 3.10
3073 3366 5.420725 TGAAAGGTGCATTAGCTTCTCTA 57.579 39.130 0.00 0.00 45.88 2.43
3074 3367 5.804639 TGAAAGGTGCATTAGCTTCTCTAA 58.195 37.500 0.00 0.00 45.88 2.10
3075 3368 5.643777 TGAAAGGTGCATTAGCTTCTCTAAC 59.356 40.000 0.00 0.00 45.88 2.34
3076 3369 4.826274 AGGTGCATTAGCTTCTCTAACA 57.174 40.909 0.00 0.00 39.86 2.41
3077 3370 5.365021 AGGTGCATTAGCTTCTCTAACAT 57.635 39.130 0.00 0.00 39.86 2.71
3078 3371 5.749462 AGGTGCATTAGCTTCTCTAACATT 58.251 37.500 0.00 0.00 39.86 2.71
3079 3372 6.889198 AGGTGCATTAGCTTCTCTAACATTA 58.111 36.000 0.00 0.00 39.86 1.90
3080 3373 7.338710 AGGTGCATTAGCTTCTCTAACATTAA 58.661 34.615 0.00 0.00 39.86 1.40
3081 3374 7.995488 AGGTGCATTAGCTTCTCTAACATTAAT 59.005 33.333 0.00 0.00 39.86 1.40
3085 3378 9.657121 GCATTAGCTTCTCTAACATTAATTGTC 57.343 33.333 0.00 0.00 39.86 3.18
3109 3402 4.269183 TGGTGGTAATATTGCTGTCAAGG 58.731 43.478 3.46 0.00 35.37 3.61
3121 3414 2.678190 GCTGTCAAGGTGTGGAGGATAC 60.678 54.545 0.00 0.00 0.00 2.24
3187 3483 3.913799 TGAACTCCCCTTTCCATGTTCTA 59.086 43.478 0.00 0.00 35.99 2.10
3195 3491 7.290061 TCCCCTTTCCATGTTCTATTATGAAG 58.710 38.462 0.00 0.00 0.00 3.02
3196 3492 6.015940 CCCCTTTCCATGTTCTATTATGAAGC 60.016 42.308 0.00 0.00 0.00 3.86
3197 3493 6.774656 CCCTTTCCATGTTCTATTATGAAGCT 59.225 38.462 0.00 0.00 0.00 3.74
3198 3494 7.040823 CCCTTTCCATGTTCTATTATGAAGCTC 60.041 40.741 0.00 0.00 0.00 4.09
3199 3495 7.718753 CCTTTCCATGTTCTATTATGAAGCTCT 59.281 37.037 0.00 0.00 0.00 4.09
3201 3497 9.466497 TTTCCATGTTCTATTATGAAGCTCTTT 57.534 29.630 0.00 0.00 0.00 2.52
3203 3499 9.547753 TCCATGTTCTATTATGAAGCTCTTTAC 57.452 33.333 0.00 0.00 0.00 2.01
3259 3589 0.397254 TCTGAGTAGGTAGCCAGGCC 60.397 60.000 8.22 0.00 0.00 5.19
3298 3628 4.580995 TGAGCTAATTTTGGGTTTTGTCGA 59.419 37.500 0.00 0.00 0.00 4.20
3347 3677 3.119673 CGTGCATTACCATTGTAGCCAAA 60.120 43.478 0.00 0.00 33.44 3.28
3348 3678 4.439974 CGTGCATTACCATTGTAGCCAAAT 60.440 41.667 0.00 0.00 33.44 2.32
3349 3679 5.043248 GTGCATTACCATTGTAGCCAAATC 58.957 41.667 0.00 0.00 33.44 2.17
3351 3681 5.186603 TGCATTACCATTGTAGCCAAATCAA 59.813 36.000 0.00 0.00 33.44 2.57
3352 3682 6.127111 TGCATTACCATTGTAGCCAAATCAAT 60.127 34.615 0.00 0.00 33.44 2.57
3353 3683 6.762661 GCATTACCATTGTAGCCAAATCAATT 59.237 34.615 0.00 0.00 33.44 2.32
3368 3698 7.870445 GCCAAATCAATTAGGTGAACTTTGTAA 59.130 33.333 0.00 0.00 30.58 2.41
3405 3745 8.083462 TGTTACAAAGTATTGACTTAGCTGTG 57.917 34.615 0.00 0.00 45.50 3.66
3438 3783 8.926710 CAAGCTGTATATACTGTATTTAGCACC 58.073 37.037 17.87 1.69 0.00 5.01
3459 3804 3.710437 GCAATTTGAGGTTTGCGAATG 57.290 42.857 0.00 0.00 38.88 2.67
3513 3858 6.128499 GCAGCAAATCAATCAAAGCAAATGTA 60.128 34.615 0.00 0.00 0.00 2.29
3548 3893 8.499162 AGTTATGTCTTGAAAATTGTTCTCTCG 58.501 33.333 0.00 0.00 0.00 4.04
3568 3913 9.958234 TCTCTCGTCGTATACTGTATATATACC 57.042 37.037 18.20 3.16 33.63 2.73
3569 3914 9.741647 CTCTCGTCGTATACTGTATATATACCA 57.258 37.037 18.20 6.04 33.63 3.25
3589 3934 4.580580 ACCAAGTTAAAGTCTCCTTTGCAG 59.419 41.667 0.00 0.00 41.03 4.41
3590 3935 4.540824 CAAGTTAAAGTCTCCTTTGCAGC 58.459 43.478 0.00 0.00 41.03 5.25
3591 3936 4.092116 AGTTAAAGTCTCCTTTGCAGCT 57.908 40.909 0.00 0.00 41.03 4.24
3592 3937 4.464947 AGTTAAAGTCTCCTTTGCAGCTT 58.535 39.130 0.00 0.00 41.03 3.74
3593 3938 4.517075 AGTTAAAGTCTCCTTTGCAGCTTC 59.483 41.667 0.00 0.00 41.03 3.86
3594 3939 2.947127 AAGTCTCCTTTGCAGCTTCT 57.053 45.000 0.00 0.00 0.00 2.85
3595 3940 2.181954 AGTCTCCTTTGCAGCTTCTG 57.818 50.000 0.00 0.00 34.12 3.02
3596 3941 1.696336 AGTCTCCTTTGCAGCTTCTGA 59.304 47.619 0.00 0.00 32.44 3.27
3597 3942 2.105477 AGTCTCCTTTGCAGCTTCTGAA 59.895 45.455 0.00 0.00 32.44 3.02
3598 3943 2.225255 GTCTCCTTTGCAGCTTCTGAAC 59.775 50.000 0.00 0.00 32.44 3.18
3599 3944 2.105477 TCTCCTTTGCAGCTTCTGAACT 59.895 45.455 0.00 0.00 32.44 3.01
3600 3945 2.483491 CTCCTTTGCAGCTTCTGAACTC 59.517 50.000 0.00 0.00 32.44 3.01
3601 3946 2.105477 TCCTTTGCAGCTTCTGAACTCT 59.895 45.455 0.00 0.00 32.44 3.24
3602 3947 2.883386 CCTTTGCAGCTTCTGAACTCTT 59.117 45.455 0.00 0.00 32.44 2.85
3603 3948 3.317430 CCTTTGCAGCTTCTGAACTCTTT 59.683 43.478 0.00 0.00 32.44 2.52
3604 3949 4.202090 CCTTTGCAGCTTCTGAACTCTTTT 60.202 41.667 0.00 0.00 32.44 2.27
3605 3950 4.989279 TTGCAGCTTCTGAACTCTTTTT 57.011 36.364 0.00 0.00 32.44 1.94
3625 3970 3.988379 TTCCATGTTCTGTTGTGAAGC 57.012 42.857 0.00 0.00 0.00 3.86
3626 3971 3.213206 TCCATGTTCTGTTGTGAAGCT 57.787 42.857 0.00 0.00 0.00 3.74
3627 3972 3.141398 TCCATGTTCTGTTGTGAAGCTC 58.859 45.455 0.00 0.00 0.00 4.09
3628 3973 3.144506 CCATGTTCTGTTGTGAAGCTCT 58.855 45.455 0.00 0.00 0.00 4.09
3629 3974 4.040339 TCCATGTTCTGTTGTGAAGCTCTA 59.960 41.667 0.00 0.00 0.00 2.43
3630 3975 4.940046 CCATGTTCTGTTGTGAAGCTCTAT 59.060 41.667 0.00 0.00 0.00 1.98
3631 3976 6.070824 TCCATGTTCTGTTGTGAAGCTCTATA 60.071 38.462 0.00 0.00 0.00 1.31
3632 3977 6.595326 CCATGTTCTGTTGTGAAGCTCTATAA 59.405 38.462 0.00 0.00 0.00 0.98
3633 3978 7.201591 CCATGTTCTGTTGTGAAGCTCTATAAG 60.202 40.741 0.00 0.00 0.00 1.73
3634 3979 6.759272 TGTTCTGTTGTGAAGCTCTATAAGT 58.241 36.000 0.00 0.00 0.00 2.24
3635 3980 7.892609 TGTTCTGTTGTGAAGCTCTATAAGTA 58.107 34.615 0.00 0.00 0.00 2.24
3636 3981 8.029522 TGTTCTGTTGTGAAGCTCTATAAGTAG 58.970 37.037 0.00 0.00 0.00 2.57
3637 3982 7.704578 TCTGTTGTGAAGCTCTATAAGTAGT 57.295 36.000 0.00 0.00 0.00 2.73
3638 3983 8.123639 TCTGTTGTGAAGCTCTATAAGTAGTT 57.876 34.615 0.00 0.00 0.00 2.24
3639 3984 8.244802 TCTGTTGTGAAGCTCTATAAGTAGTTC 58.755 37.037 0.00 0.00 0.00 3.01
3640 3985 8.123639 TGTTGTGAAGCTCTATAAGTAGTTCT 57.876 34.615 0.00 0.00 0.00 3.01
3641 3986 8.244802 TGTTGTGAAGCTCTATAAGTAGTTCTC 58.755 37.037 0.00 0.00 0.00 2.87
3642 3987 7.939784 TGTGAAGCTCTATAAGTAGTTCTCA 57.060 36.000 0.00 0.00 0.00 3.27
3643 3988 7.990917 TGTGAAGCTCTATAAGTAGTTCTCAG 58.009 38.462 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.519302 CCATTCACCATCGCCCCC 60.519 66.667 0.00 0.00 0.00 5.40
83 84 2.669569 GGCGTCAAAGCAGAGCCA 60.670 61.111 0.00 0.00 46.48 4.75
112 113 3.382832 CTGGTTCGTCCTCGGGCT 61.383 66.667 1.80 0.00 37.69 5.19
158 160 2.822637 CCTGGTGTGGTGGAGCACT 61.823 63.158 10.14 0.00 36.03 4.40
202 204 2.178106 CCCTAGCTCTCCCTTCTCCTTA 59.822 54.545 0.00 0.00 0.00 2.69
207 209 2.192263 CAAACCCTAGCTCTCCCTTCT 58.808 52.381 0.00 0.00 0.00 2.85
233 241 3.068881 CTGCCTCCTCGAAACCCA 58.931 61.111 0.00 0.00 0.00 4.51
320 329 3.197790 CCTGTCATCCGCGCTTGG 61.198 66.667 5.56 0.00 0.00 3.61
323 334 3.362399 CTCACCTGTCATCCGCGCT 62.362 63.158 5.56 0.00 0.00 5.92
325 336 2.202797 CCTCACCTGTCATCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
439 454 2.520458 CTGGTTTGGGTCCAGGCA 59.480 61.111 4.27 0.00 46.03 4.75
478 493 2.448582 TTTGTGTCTGGCCCGACCT 61.449 57.895 22.86 0.00 40.22 3.85
499 515 0.251916 CGGCCTGGACCAATCTTGTA 59.748 55.000 0.00 0.00 0.00 2.41
536 552 1.425066 TGAGGCAAAATGGACAGACCT 59.575 47.619 0.00 0.00 39.86 3.85
554 570 0.322456 CGTCTGGCCCCTTCATTTGA 60.322 55.000 0.00 0.00 0.00 2.69
605 622 0.739813 ACAGCATCGCCTACGGTTTC 60.740 55.000 0.00 0.00 40.63 2.78
606 623 1.019278 CACAGCATCGCCTACGGTTT 61.019 55.000 0.00 0.00 40.63 3.27
607 624 1.447838 CACAGCATCGCCTACGGTT 60.448 57.895 0.00 0.00 40.63 4.44
608 625 2.184322 CACAGCATCGCCTACGGT 59.816 61.111 0.00 0.00 40.63 4.83
609 626 1.878522 GTCACAGCATCGCCTACGG 60.879 63.158 0.00 0.00 40.63 4.02
610 627 1.153842 TGTCACAGCATCGCCTACG 60.154 57.895 0.00 0.00 42.01 3.51
611 628 1.084370 GGTGTCACAGCATCGCCTAC 61.084 60.000 0.95 0.00 0.00 3.18
612 629 1.218047 GGTGTCACAGCATCGCCTA 59.782 57.895 0.95 0.00 0.00 3.93
619 636 2.899838 GCAACCGGTGTCACAGCA 60.900 61.111 8.52 0.00 0.00 4.41
623 640 1.092921 TTGTGAGCAACCGGTGTCAC 61.093 55.000 26.81 26.81 38.09 3.67
625 642 1.647084 GTTGTGAGCAACCGGTGTC 59.353 57.895 8.52 6.37 46.81 3.67
642 659 2.842462 TGCACAGAGGGTCACCGT 60.842 61.111 0.00 0.00 43.47 4.83
655 672 0.615331 TGGGAGGATCTTCTGTGCAC 59.385 55.000 10.75 10.75 33.73 4.57
785 816 2.423874 ACGCAATGACGTGGGTGA 59.576 55.556 0.00 0.00 46.28 4.02
806 837 3.349006 GGCACGCTCACACTGTGG 61.349 66.667 13.09 1.42 33.87 4.17
916 962 2.045731 GAATCGGGGCGGGTTTGA 60.046 61.111 0.00 0.00 0.00 2.69
1090 1346 4.204028 GTGGTGGTGGTGGTGCCT 62.204 66.667 0.00 0.00 38.35 4.75
1427 1692 4.514577 CCGGCGCATTCTCGACCT 62.515 66.667 10.83 0.00 32.97 3.85
1590 1855 4.681978 GCACGGACCTTGGCGAGT 62.682 66.667 0.12 0.00 0.00 4.18
1761 2026 4.681978 GGGCAGGCGTCGTTGAGT 62.682 66.667 0.00 0.00 0.00 3.41
1917 2182 4.570874 GATGGCTTCCCCTCGGGC 62.571 72.222 0.00 0.00 43.94 6.13
1944 2209 2.203451 GAGGGGACGCCGGAGATA 60.203 66.667 13.83 0.00 0.00 1.98
2013 2278 3.666253 TGCGCGAAGTCACGGAGA 61.666 61.111 12.10 0.00 0.00 3.71
2019 2284 1.734477 GAGAAGCTGCGCGAAGTCA 60.734 57.895 17.19 0.00 0.00 3.41
2188 2453 3.682292 ATTTGGCGAGGCGGAGGAC 62.682 63.158 0.00 0.00 0.00 3.85
2226 2491 1.379576 CTCGTACTCCCCGAGGGTT 60.380 63.158 7.48 1.22 46.09 4.11
2530 2795 1.174783 GAGTCGTAGTCCCAGAGCAA 58.825 55.000 0.00 0.00 0.00 3.91
2547 2812 3.791887 CGAGCGAATACTTGTACTTGGAG 59.208 47.826 0.00 0.00 0.00 3.86
2548 2813 3.192001 ACGAGCGAATACTTGTACTTGGA 59.808 43.478 0.00 0.00 32.28 3.53
2634 2899 3.961414 GGAAGGGGTCACCGCCAA 61.961 66.667 7.41 0.00 45.93 4.52
2680 2945 1.467875 GTGGATCGATCGAACACGAG 58.532 55.000 28.54 0.00 41.63 4.18
2685 2950 0.317938 CCTCCGTGGATCGATCGAAC 60.318 60.000 23.50 19.61 42.86 3.95
2695 2960 6.428295 ACCATTAATTAATTTCCTCCGTGGA 58.572 36.000 8.01 0.00 44.51 4.02
2696 2961 6.709018 ACCATTAATTAATTTCCTCCGTGG 57.291 37.500 8.01 7.42 37.10 4.94
2697 2962 7.860872 GCTAACCATTAATTAATTTCCTCCGTG 59.139 37.037 8.01 0.00 0.00 4.94
2699 2964 7.936584 TGCTAACCATTAATTAATTTCCTCCG 58.063 34.615 8.01 0.00 0.00 4.63
2701 2966 8.413229 TGCTGCTAACCATTAATTAATTTCCTC 58.587 33.333 8.01 0.00 0.00 3.71
2702 2967 8.305046 TGCTGCTAACCATTAATTAATTTCCT 57.695 30.769 8.01 0.00 0.00 3.36
2703 2968 8.413229 TCTGCTGCTAACCATTAATTAATTTCC 58.587 33.333 8.01 0.00 0.00 3.13
2748 3013 9.906660 TGAAACTAGCAATACAAATTACAAAGG 57.093 29.630 0.00 0.00 0.00 3.11
2763 3028 2.562296 AGGGAGGGATGAAACTAGCAA 58.438 47.619 0.00 0.00 0.00 3.91
2765 3030 2.505819 TCAAGGGAGGGATGAAACTAGC 59.494 50.000 0.00 0.00 0.00 3.42
2821 3091 8.982723 CAATCCTAGCCATTACTACTACCATAT 58.017 37.037 0.00 0.00 0.00 1.78
2822 3092 7.399191 CCAATCCTAGCCATTACTACTACCATA 59.601 40.741 0.00 0.00 0.00 2.74
2823 3093 6.213600 CCAATCCTAGCCATTACTACTACCAT 59.786 42.308 0.00 0.00 0.00 3.55
2825 3095 5.046520 CCCAATCCTAGCCATTACTACTACC 60.047 48.000 0.00 0.00 0.00 3.18
2826 3096 5.778750 TCCCAATCCTAGCCATTACTACTAC 59.221 44.000 0.00 0.00 0.00 2.73
2827 3097 5.972698 TCCCAATCCTAGCCATTACTACTA 58.027 41.667 0.00 0.00 0.00 1.82
2828 3098 4.827789 TCCCAATCCTAGCCATTACTACT 58.172 43.478 0.00 0.00 0.00 2.57
2830 3100 6.780198 ATTTCCCAATCCTAGCCATTACTA 57.220 37.500 0.00 0.00 0.00 1.82
2831 3101 5.669798 ATTTCCCAATCCTAGCCATTACT 57.330 39.130 0.00 0.00 0.00 2.24
2846 3129 3.576550 GCTGGTTCCAACTAAATTTCCCA 59.423 43.478 0.00 0.00 0.00 4.37
2861 3144 0.807496 GGCATCTGACAAGCTGGTTC 59.193 55.000 0.00 0.00 0.00 3.62
2863 3146 0.322277 CAGGCATCTGACAAGCTGGT 60.322 55.000 0.00 0.00 43.49 4.00
2864 3147 0.322277 ACAGGCATCTGACAAGCTGG 60.322 55.000 0.00 0.00 43.49 4.85
2865 3148 1.531423 AACAGGCATCTGACAAGCTG 58.469 50.000 0.00 0.00 43.49 4.24
2945 3230 4.806330 CATGGCATGCTCTAAATTCATCC 58.194 43.478 18.92 0.00 0.00 3.51
2964 3249 3.319031 AAATCTCCCCCTAAAGGCATG 57.681 47.619 0.00 0.00 0.00 4.06
3028 3321 2.275134 TCATGTGCGGCATCCATAAT 57.725 45.000 5.72 0.00 35.19 1.28
3056 3349 7.553881 TTAATGTTAGAGAAGCTAATGCACC 57.446 36.000 0.00 0.00 40.94 5.01
3057 3350 9.443283 CAATTAATGTTAGAGAAGCTAATGCAC 57.557 33.333 0.00 0.00 40.94 4.57
3063 3356 9.383519 CCAAGACAATTAATGTTAGAGAAGCTA 57.616 33.333 0.00 0.00 44.12 3.32
3065 3358 7.965107 CACCAAGACAATTAATGTTAGAGAAGC 59.035 37.037 0.00 0.00 44.12 3.86
3068 3361 7.458397 ACCACCAAGACAATTAATGTTAGAGA 58.542 34.615 0.00 0.00 44.12 3.10
3069 3362 7.687941 ACCACCAAGACAATTAATGTTAGAG 57.312 36.000 0.00 0.00 44.12 2.43
3070 3363 9.747898 ATTACCACCAAGACAATTAATGTTAGA 57.252 29.630 0.00 0.00 44.12 2.10
3075 3368 9.248291 GCAATATTACCACCAAGACAATTAATG 57.752 33.333 0.00 0.00 0.00 1.90
3076 3369 9.200817 AGCAATATTACCACCAAGACAATTAAT 57.799 29.630 0.00 0.00 0.00 1.40
3077 3370 8.465999 CAGCAATATTACCACCAAGACAATTAA 58.534 33.333 0.00 0.00 0.00 1.40
3078 3371 7.613801 ACAGCAATATTACCACCAAGACAATTA 59.386 33.333 0.00 0.00 0.00 1.40
3079 3372 6.437162 ACAGCAATATTACCACCAAGACAATT 59.563 34.615 0.00 0.00 0.00 2.32
3080 3373 5.951747 ACAGCAATATTACCACCAAGACAAT 59.048 36.000 0.00 0.00 0.00 2.71
3081 3374 5.321102 ACAGCAATATTACCACCAAGACAA 58.679 37.500 0.00 0.00 0.00 3.18
3085 3378 5.163622 CCTTGACAGCAATATTACCACCAAG 60.164 44.000 0.00 0.00 32.68 3.61
3109 3402 4.649674 TGTAGATGGAAGTATCCTCCACAC 59.350 45.833 0.00 0.00 46.70 3.82
3187 3483 8.467598 TGAGAACTACGTAAAGAGCTTCATAAT 58.532 33.333 0.00 0.00 0.00 1.28
3195 3491 7.347508 TCAAATTGAGAACTACGTAAAGAGC 57.652 36.000 0.00 0.00 0.00 4.09
3196 3492 8.979574 ACTTCAAATTGAGAACTACGTAAAGAG 58.020 33.333 0.00 0.00 0.00 2.85
3197 3493 8.882415 ACTTCAAATTGAGAACTACGTAAAGA 57.118 30.769 0.00 0.00 0.00 2.52
3198 3494 9.370126 CAACTTCAAATTGAGAACTACGTAAAG 57.630 33.333 0.00 0.00 0.00 1.85
3199 3495 8.885722 ACAACTTCAAATTGAGAACTACGTAAA 58.114 29.630 0.00 0.00 0.00 2.01
3201 3497 7.096353 CGACAACTTCAAATTGAGAACTACGTA 60.096 37.037 0.00 0.00 0.00 3.57
3202 3498 6.292168 CGACAACTTCAAATTGAGAACTACGT 60.292 38.462 0.00 0.00 0.00 3.57
3203 3499 6.065153 CGACAACTTCAAATTGAGAACTACG 58.935 40.000 0.00 0.00 0.00 3.51
3259 3589 9.559958 AAATTAGCTCATGTAAGAACAAATTCG 57.440 29.630 0.00 0.00 39.58 3.34
3298 3628 1.131303 TGGAGATCACCGGGGTTTGT 61.131 55.000 2.12 0.00 0.00 2.83
3376 3706 9.991906 AGCTAAGTCAATACTTTGTAACAACTA 57.008 29.630 0.00 0.00 43.60 2.24
3377 3707 8.774586 CAGCTAAGTCAATACTTTGTAACAACT 58.225 33.333 0.00 0.00 43.60 3.16
3378 3708 8.557029 ACAGCTAAGTCAATACTTTGTAACAAC 58.443 33.333 0.00 0.00 43.60 3.32
3379 3709 8.556194 CACAGCTAAGTCAATACTTTGTAACAA 58.444 33.333 0.00 0.00 43.60 2.83
3380 3710 7.929245 TCACAGCTAAGTCAATACTTTGTAACA 59.071 33.333 0.00 0.00 43.60 2.41
3381 3711 8.221766 GTCACAGCTAAGTCAATACTTTGTAAC 58.778 37.037 0.00 0.00 43.60 2.50
3399 3739 1.134280 ACAGCTTGACAAGTCACAGCT 60.134 47.619 22.47 22.47 45.61 4.24
3400 3740 1.303309 ACAGCTTGACAAGTCACAGC 58.697 50.000 16.39 20.01 39.66 4.40
3405 3745 9.751542 AATACAGTATATACAGCTTGACAAGTC 57.248 33.333 16.39 8.92 0.00 3.01
3452 3797 1.129624 GTACCGAATTGCACATTCGCA 59.870 47.619 25.43 17.50 46.60 5.10
3453 3798 1.396996 AGTACCGAATTGCACATTCGC 59.603 47.619 25.43 17.40 46.60 4.70
3602 3947 5.105392 AGCTTCACAACAGAACATGGAAAAA 60.105 36.000 0.00 0.00 0.00 1.94
3603 3948 4.402155 AGCTTCACAACAGAACATGGAAAA 59.598 37.500 0.00 0.00 0.00 2.29
3604 3949 3.953612 AGCTTCACAACAGAACATGGAAA 59.046 39.130 0.00 0.00 0.00 3.13
3605 3950 3.554934 AGCTTCACAACAGAACATGGAA 58.445 40.909 0.00 0.00 0.00 3.53
3606 3951 3.141398 GAGCTTCACAACAGAACATGGA 58.859 45.455 0.00 0.00 0.00 3.41
3607 3952 3.144506 AGAGCTTCACAACAGAACATGG 58.855 45.455 0.00 0.00 0.00 3.66
3608 3953 7.332926 ACTTATAGAGCTTCACAACAGAACATG 59.667 37.037 0.00 0.00 0.00 3.21
3609 3954 7.390027 ACTTATAGAGCTTCACAACAGAACAT 58.610 34.615 0.00 0.00 0.00 2.71
3610 3955 6.759272 ACTTATAGAGCTTCACAACAGAACA 58.241 36.000 0.00 0.00 0.00 3.18
3611 3956 8.030106 ACTACTTATAGAGCTTCACAACAGAAC 58.970 37.037 0.00 0.00 32.23 3.01
3612 3957 8.123639 ACTACTTATAGAGCTTCACAACAGAA 57.876 34.615 0.00 0.00 32.23 3.02
3613 3958 7.704578 ACTACTTATAGAGCTTCACAACAGA 57.295 36.000 0.00 0.00 32.23 3.41
3614 3959 8.247562 AGAACTACTTATAGAGCTTCACAACAG 58.752 37.037 0.00 0.00 32.23 3.16
3615 3960 8.123639 AGAACTACTTATAGAGCTTCACAACA 57.876 34.615 0.00 0.00 32.23 3.33
3616 3961 8.244802 TGAGAACTACTTATAGAGCTTCACAAC 58.755 37.037 0.00 0.00 32.23 3.32
3617 3962 8.349568 TGAGAACTACTTATAGAGCTTCACAA 57.650 34.615 0.00 0.00 32.23 3.33
3618 3963 7.939784 TGAGAACTACTTATAGAGCTTCACA 57.060 36.000 0.00 0.00 32.23 3.58


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

AutoCloner maintained by Alex Coulton.