Multiple sequence alignment - TraesCS2A01G145800

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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 TraesCS2A01G145800 chr2A 100.000 3841 0 0 1 3841 90598087 90594247 0.000000e+00 7094.0
1 TraesCS2A01G145800 chr2A 97.071 751 20 2 2936 3685 377027267 377026518 0.000000e+00 1264.0
2 TraesCS2A01G145800 chr2A 96.282 753 23 2 2939 3687 672973820 672973069 0.000000e+00 1230.0
3 TraesCS2A01G145800 chr2A 89.731 409 37 3 2936 3343 475141641 475141237 5.690000e-143 518.0
4 TraesCS2A01G145800 chr2A 91.020 245 16 2 3440 3683 475140994 475140755 3.700000e-85 326.0
5 TraesCS2A01G145800 chr2D 93.722 2230 105 19 682 2900 92921459 92919254 0.000000e+00 3310.0
6 TraesCS2A01G145800 chr2D 92.105 228 15 2 67 293 92921956 92921731 6.190000e-83 318.0
7 TraesCS2A01G145800 chr2D 95.625 160 5 2 3683 3841 92919252 92919094 4.920000e-64 255.0
8 TraesCS2A01G145800 chr2D 85.306 245 21 7 364 606 92921725 92921494 4.960000e-59 239.0
9 TraesCS2A01G145800 chr2B 91.524 2277 116 36 666 2910 144434327 144432096 0.000000e+00 3064.0
10 TraesCS2A01G145800 chr2B 91.034 145 5 3 3683 3827 144432101 144431965 5.070000e-44 189.0
11 TraesCS2A01G145800 chr3A 96.419 754 23 3 2934 3684 572149830 572150582 0.000000e+00 1240.0
12 TraesCS2A01G145800 chr4A 95.767 756 28 2 2931 3683 75223696 75222942 0.000000e+00 1216.0
13 TraesCS2A01G145800 chr4A 86.607 336 32 4 3020 3343 545610940 545611274 3.650000e-95 359.0
14 TraesCS2A01G145800 chr4A 87.687 268 22 6 3440 3701 545611511 545611773 6.240000e-78 302.0
15 TraesCS2A01G145800 chr7A 89.614 414 34 4 2935 3343 62730660 62730251 5.690000e-143 518.0
16 TraesCS2A01G145800 chr7A 88.642 405 40 5 2934 3335 316009527 316009126 4.460000e-134 488.0
17 TraesCS2A01G145800 chr7A 91.566 249 16 2 3440 3687 62730008 62729764 4.750000e-89 339.0
18 TraesCS2A01G145800 chr5D 82.409 523 66 15 2936 3445 292680101 292679592 2.120000e-117 433.0
19 TraesCS2A01G145800 chr5D 81.679 524 63 20 2933 3445 384630577 384631078 4.620000e-109 405.0
20 TraesCS2A01G145800 chr5D 92.095 253 18 2 3440 3690 292679250 292678998 4.720000e-94 355.0
21 TraesCS2A01G145800 chr5D 92.653 245 18 0 3440 3684 384631418 384631662 1.700000e-93 353.0
22 TraesCS2A01G145800 chr4D 85.893 319 40 5 2938 3253 391053791 391053475 6.150000e-88 335.0
23 TraesCS2A01G145800 chr1B 83.036 336 35 9 3127 3445 675262259 675262589 6.280000e-73 285.0
24 TraesCS2A01G145800 chr1B 91.163 215 8 3 3240 3445 100633293 100633081 8.120000e-72 281.0
25 TraesCS2A01G145800 chr6B 78.830 359 64 11 1643 1995 200009040 200008688 8.300000e-57 231.0
26 TraesCS2A01G145800 chr7D 73.228 635 117 37 1037 1637 593368960 593369575 8.480000e-42 182.0
27 TraesCS2A01G145800 chr6A 85.714 84 10 2 2437 2520 492283683 492283602 1.900000e-13 87.9


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 TraesCS2A01G145800 chr2A 90594247 90598087 3840 True 7094.0 7094 100.0000 1 3841 1 chr2A.!!$R1 3840
1 TraesCS2A01G145800 chr2A 377026518 377027267 749 True 1264.0 1264 97.0710 2936 3685 1 chr2A.!!$R2 749
2 TraesCS2A01G145800 chr2A 672973069 672973820 751 True 1230.0 1230 96.2820 2939 3687 1 chr2A.!!$R3 748
3 TraesCS2A01G145800 chr2A 475140755 475141641 886 True 422.0 518 90.3755 2936 3683 2 chr2A.!!$R4 747
4 TraesCS2A01G145800 chr2D 92919094 92921956 2862 True 1030.5 3310 91.6895 67 3841 4 chr2D.!!$R1 3774
5 TraesCS2A01G145800 chr2B 144431965 144434327 2362 True 1626.5 3064 91.2790 666 3827 2 chr2B.!!$R1 3161
6 TraesCS2A01G145800 chr3A 572149830 572150582 752 False 1240.0 1240 96.4190 2934 3684 1 chr3A.!!$F1 750
7 TraesCS2A01G145800 chr4A 75222942 75223696 754 True 1216.0 1216 95.7670 2931 3683 1 chr4A.!!$R1 752
8 TraesCS2A01G145800 chr4A 545610940 545611773 833 False 330.5 359 87.1470 3020 3701 2 chr4A.!!$F1 681
9 TraesCS2A01G145800 chr7A 62729764 62730660 896 True 428.5 518 90.5900 2935 3687 2 chr7A.!!$R2 752
10 TraesCS2A01G145800 chr5D 292678998 292680101 1103 True 394.0 433 87.2520 2936 3690 2 chr5D.!!$R1 754
11 TraesCS2A01G145800 chr5D 384630577 384631662 1085 False 379.0 405 87.1660 2933 3684 2 chr5D.!!$F1 751

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
939 970 0.035056 CCCCCACTGTTCCACTGATC 60.035 60.0 0.00 0.00 0.00 2.92 F
979 1010 0.108329 CCAGCCGTAAACGATCCAGT 60.108 55.0 3.65 0.00 43.02 4.00 F
1801 1832 0.647410 CGACACGGTCAAGATGATGC 59.353 55.0 5.15 0.00 32.09 3.91 F
2608 2650 0.390209 TCTTAACAACGGCCGGCTAC 60.390 55.0 31.76 9.89 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2074 0.108992 TAACTGGCATGGTCGTCGTC 60.109 55.000 0.00 0.0 0.00 4.20 R
2586 2619 0.386352 GCCGGCCGTTGTTAAGAAAC 60.386 55.000 26.12 0.0 36.07 2.78 R
2827 2869 0.598419 GCATCATCAGCACGATCCGA 60.598 55.000 0.00 0.0 29.21 4.55 R
3699 4204 3.616076 CGATCCTTGCTCACACTCTCTTT 60.616 47.826 0.00 0.0 0.00 2.52 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
19 20 4.547367 CCGATTCGCCCCCAGACC 62.547 72.222 0.00 0.00 0.00 3.85
20 21 4.891727 CGATTCGCCCCCAGACCG 62.892 72.222 0.00 0.00 0.00 4.79
26 27 4.035102 GCCCCCAGACCGCTCTTT 62.035 66.667 0.00 0.00 0.00 2.52
27 28 2.757077 CCCCCAGACCGCTCTTTT 59.243 61.111 0.00 0.00 0.00 2.27
28 29 1.074951 CCCCCAGACCGCTCTTTTT 59.925 57.895 0.00 0.00 0.00 1.94
51 52 4.637771 CCTTGGGAGGCTAAACGG 57.362 61.111 0.00 0.00 35.94 4.44
52 53 1.749258 CCTTGGGAGGCTAAACGGC 60.749 63.158 0.00 0.00 35.94 5.68
61 62 2.892784 GGCTAAACGGCTAGAGATGT 57.107 50.000 0.00 0.00 34.85 3.06
62 63 3.180891 GGCTAAACGGCTAGAGATGTT 57.819 47.619 0.00 0.00 34.85 2.71
63 64 3.124560 GGCTAAACGGCTAGAGATGTTC 58.875 50.000 0.00 0.00 34.85 3.18
64 65 3.181474 GGCTAAACGGCTAGAGATGTTCT 60.181 47.826 0.00 0.00 40.06 3.01
65 66 4.037684 GGCTAAACGGCTAGAGATGTTCTA 59.962 45.833 0.00 0.00 37.36 2.10
80 81 2.161808 TGTTCTAAGACTCGAAGCTCCG 59.838 50.000 0.00 0.00 0.00 4.63
81 82 1.380524 TCTAAGACTCGAAGCTCCGG 58.619 55.000 0.00 0.00 0.00 5.14
96 97 0.245539 TCCGGCCTTTAGTGAGTTCG 59.754 55.000 0.00 0.00 0.00 3.95
110 111 5.300752 AGTGAGTTCGTCTGATGATGTTTT 58.699 37.500 0.00 0.00 0.00 2.43
129 130 9.255304 GATGTTTTTGTAGCTGTAATTTTTCCA 57.745 29.630 0.00 0.00 0.00 3.53
144 145 7.835634 AATTTTTCCAAAGCAAAACGACTTA 57.164 28.000 0.00 0.00 0.00 2.24
145 146 7.835634 ATTTTTCCAAAGCAAAACGACTTAA 57.164 28.000 0.00 0.00 0.00 1.85
174 175 3.317149 ATGTATGGCACATGCATTGACTC 59.683 43.478 13.55 7.01 46.41 3.36
177 178 3.070476 TGGCACATGCATTGACTCTAA 57.930 42.857 13.55 0.00 44.36 2.10
203 204 9.630098 AATGTCGTCGTAGAATTTAAGAACTAA 57.370 29.630 0.00 0.00 39.69 2.24
204 205 9.798994 ATGTCGTCGTAGAATTTAAGAACTAAT 57.201 29.630 0.00 0.00 39.69 1.73
231 232 0.674581 TCTTTCTCTGCACATGCCCG 60.675 55.000 0.49 0.00 41.18 6.13
240 241 0.385390 GCACATGCCCGGAAAATAGG 59.615 55.000 0.73 0.00 34.31 2.57
259 261 4.965200 AGGGATAAAGCTAGATGGTGAC 57.035 45.455 0.00 0.00 0.00 3.67
351 353 8.804688 AATCATTACTAGTGATCTAAACGCTC 57.195 34.615 5.39 0.00 35.35 5.03
352 354 7.569639 TCATTACTAGTGATCTAAACGCTCT 57.430 36.000 5.39 0.00 0.00 4.09
353 355 7.997482 TCATTACTAGTGATCTAAACGCTCTT 58.003 34.615 5.39 0.00 0.00 2.85
354 356 9.117183 TCATTACTAGTGATCTAAACGCTCTTA 57.883 33.333 5.39 0.00 0.00 2.10
355 357 9.171701 CATTACTAGTGATCTAAACGCTCTTAC 57.828 37.037 5.39 0.00 0.00 2.34
356 358 6.754702 ACTAGTGATCTAAACGCTCTTACA 57.245 37.500 0.00 0.00 0.00 2.41
357 359 7.336161 ACTAGTGATCTAAACGCTCTTACAT 57.664 36.000 0.00 0.00 0.00 2.29
358 360 7.773149 ACTAGTGATCTAAACGCTCTTACATT 58.227 34.615 0.00 0.00 0.00 2.71
359 361 8.251721 ACTAGTGATCTAAACGCTCTTACATTT 58.748 33.333 0.00 0.00 0.00 2.32
360 362 7.907214 AGTGATCTAAACGCTCTTACATTTT 57.093 32.000 0.00 0.00 0.00 1.82
361 363 8.324163 AGTGATCTAAACGCTCTTACATTTTT 57.676 30.769 0.00 0.00 0.00 1.94
392 395 5.557891 GAGTAGTACTCACTCCGCTTTTA 57.442 43.478 22.85 0.00 44.45 1.52
397 400 8.189460 AGTAGTACTCACTCCGCTTTTATTTAG 58.811 37.037 0.00 0.00 36.14 1.85
400 403 4.863131 ACTCACTCCGCTTTTATTTAGTCG 59.137 41.667 0.00 0.00 0.00 4.18
401 404 5.063180 TCACTCCGCTTTTATTTAGTCGA 57.937 39.130 0.00 0.00 0.00 4.20
408 411 9.188588 CTCCGCTTTTATTTAGTCGACATATTA 57.811 33.333 19.50 0.00 0.00 0.98
523 526 8.491950 TGTTTTCTTCTACAAACTTTTTGTTGC 58.508 29.630 9.44 0.00 39.13 4.17
525 528 8.594881 TTTCTTCTACAAACTTTTTGTTGCAA 57.405 26.923 9.44 0.00 39.13 4.08
526 529 7.575332 TCTTCTACAAACTTTTTGTTGCAAC 57.425 32.000 22.83 22.83 39.13 4.17
585 588 5.646577 TTGACTCTAGACAAAGCTAGTCC 57.353 43.478 13.82 1.30 39.10 3.85
587 590 2.424246 ACTCTAGACAAAGCTAGTCCGC 59.576 50.000 13.82 0.00 39.10 5.54
597 600 1.679680 AGCTAGTCCGCGCAGTAAATA 59.320 47.619 8.75 0.00 34.40 1.40
606 609 5.227184 GTCCGCGCAGTAAATAAAAATGAAG 59.773 40.000 8.75 0.00 0.00 3.02
608 611 4.499040 CGCGCAGTAAATAAAAATGAAGGG 59.501 41.667 8.75 0.00 0.00 3.95
610 613 6.096695 GCGCAGTAAATAAAAATGAAGGGAA 58.903 36.000 0.30 0.00 0.00 3.97
611 614 6.756542 GCGCAGTAAATAAAAATGAAGGGAAT 59.243 34.615 0.30 0.00 0.00 3.01
613 616 9.233232 CGCAGTAAATAAAAATGAAGGGAATAC 57.767 33.333 0.00 0.00 0.00 1.89
614 617 9.529325 GCAGTAAATAAAAATGAAGGGAATACC 57.471 33.333 0.00 0.00 40.67 2.73
630 633 6.896883 GGGAATACCTTATATACATCCCACC 58.103 44.000 2.70 0.00 43.83 4.61
631 634 6.126565 GGGAATACCTTATATACATCCCACCC 60.127 46.154 2.70 0.00 43.83 4.61
632 635 6.445786 GGAATACCTTATATACATCCCACCCA 59.554 42.308 0.00 0.00 0.00 4.51
635 638 4.601857 ACCTTATATACATCCCACCCAAGG 59.398 45.833 0.00 0.00 36.83 3.61
636 639 4.849810 CCTTATATACATCCCACCCAAGGA 59.150 45.833 0.00 0.00 37.93 3.36
638 641 2.587060 ATACATCCCACCCAAGGAGA 57.413 50.000 0.00 0.00 36.67 3.71
639 642 2.352561 TACATCCCACCCAAGGAGAA 57.647 50.000 0.00 0.00 36.67 2.87
640 643 1.455822 ACATCCCACCCAAGGAGAAA 58.544 50.000 0.00 0.00 36.67 2.52
641 644 1.786441 ACATCCCACCCAAGGAGAAAA 59.214 47.619 0.00 0.00 36.67 2.29
642 645 2.178984 ACATCCCACCCAAGGAGAAAAA 59.821 45.455 0.00 0.00 36.67 1.94
643 646 2.375014 TCCCACCCAAGGAGAAAAAC 57.625 50.000 0.00 0.00 0.00 2.43
644 647 1.571457 TCCCACCCAAGGAGAAAAACA 59.429 47.619 0.00 0.00 0.00 2.83
645 648 2.178984 TCCCACCCAAGGAGAAAAACAT 59.821 45.455 0.00 0.00 0.00 2.71
646 649 2.972021 CCCACCCAAGGAGAAAAACATT 59.028 45.455 0.00 0.00 0.00 2.71
647 650 3.390967 CCCACCCAAGGAGAAAAACATTT 59.609 43.478 0.00 0.00 0.00 2.32
648 651 4.141505 CCCACCCAAGGAGAAAAACATTTT 60.142 41.667 0.00 0.00 0.00 1.82
649 652 5.071115 CCCACCCAAGGAGAAAAACATTTTA 59.929 40.000 0.00 0.00 0.00 1.52
650 653 6.239858 CCCACCCAAGGAGAAAAACATTTTAT 60.240 38.462 0.00 0.00 0.00 1.40
651 654 7.038658 CCCACCCAAGGAGAAAAACATTTTATA 60.039 37.037 0.00 0.00 0.00 0.98
652 655 8.539544 CCACCCAAGGAGAAAAACATTTTATAT 58.460 33.333 0.00 0.00 0.00 0.86
653 656 9.586435 CACCCAAGGAGAAAAACATTTTATATC 57.414 33.333 0.00 0.00 0.00 1.63
654 657 9.547279 ACCCAAGGAGAAAAACATTTTATATCT 57.453 29.630 0.00 0.00 0.00 1.98
680 683 2.671396 AGTTTATTCATGTGCCGACGTC 59.329 45.455 5.18 5.18 0.00 4.34
718 726 1.967762 CACGTGTGAAATGCATGTCC 58.032 50.000 14.44 6.43 34.23 4.02
770 792 1.071605 CCGAGCTTTCTTCCACGAAG 58.928 55.000 0.00 0.00 40.65 3.79
847 875 3.133365 AAACGCCACTGCCTCCCTT 62.133 57.895 0.00 0.00 0.00 3.95
867 895 5.105837 CCCTTCGCTATCTATAAGTACCACC 60.106 48.000 0.00 0.00 0.00 4.61
892 920 0.617249 AGCTCCTTCCACTCCTCAGG 60.617 60.000 0.00 0.00 0.00 3.86
894 922 1.190643 CTCCTTCCACTCCTCAGGAC 58.809 60.000 0.00 0.00 32.62 3.85
895 923 0.487325 TCCTTCCACTCCTCAGGACA 59.513 55.000 0.00 0.00 32.62 4.02
896 924 1.132849 TCCTTCCACTCCTCAGGACAA 60.133 52.381 0.00 0.00 32.62 3.18
897 925 1.002544 CCTTCCACTCCTCAGGACAAC 59.997 57.143 0.00 0.00 32.62 3.32
898 926 1.974236 CTTCCACTCCTCAGGACAACT 59.026 52.381 0.00 0.00 32.62 3.16
899 927 1.633774 TCCACTCCTCAGGACAACTC 58.366 55.000 0.00 0.00 0.00 3.01
900 928 0.244994 CCACTCCTCAGGACAACTCG 59.755 60.000 0.00 0.00 0.00 4.18
901 929 0.244994 CACTCCTCAGGACAACTCGG 59.755 60.000 0.00 0.00 0.00 4.63
909 940 1.096416 AGGACAACTCGGTCGATCTC 58.904 55.000 0.00 0.00 38.70 2.75
934 965 2.597510 GTGCCCCCACTGTTCCAC 60.598 66.667 0.00 0.00 38.93 4.02
935 966 2.776526 TGCCCCCACTGTTCCACT 60.777 61.111 0.00 0.00 0.00 4.00
936 967 2.282462 GCCCCCACTGTTCCACTG 60.282 66.667 0.00 0.00 0.00 3.66
937 968 2.829384 GCCCCCACTGTTCCACTGA 61.829 63.158 0.00 0.00 0.00 3.41
938 969 2.078452 CCCCCACTGTTCCACTGAT 58.922 57.895 0.00 0.00 0.00 2.90
939 970 0.035056 CCCCCACTGTTCCACTGATC 60.035 60.000 0.00 0.00 0.00 2.92
960 991 0.883833 CACAGCTCCACCAACCAATC 59.116 55.000 0.00 0.00 0.00 2.67
979 1010 0.108329 CCAGCCGTAAACGATCCAGT 60.108 55.000 3.65 0.00 43.02 4.00
1044 1075 2.125912 CAGCAGGTCGTCTTCCGG 60.126 66.667 0.00 0.00 37.11 5.14
1242 1273 3.058160 GTCCGCAATGGCAGCACT 61.058 61.111 0.00 0.00 41.24 4.40
1488 1519 3.417275 CTGCGCCTCGTTCTCCGAT 62.417 63.158 4.18 0.00 46.23 4.18
1517 1548 4.103103 CGACGACTCGGCTCTGCA 62.103 66.667 2.10 0.00 36.16 4.41
1801 1832 0.647410 CGACACGGTCAAGATGATGC 59.353 55.000 5.15 0.00 32.09 3.91
1923 1954 2.501128 CGCATGGTCATCTCCGGT 59.499 61.111 0.00 0.00 0.00 5.28
1998 2029 3.546407 CGTGCTCGGACAGGTATAC 57.454 57.895 0.00 0.00 0.00 1.47
2043 2074 5.105752 GTGCTTTGACCATGACTAGTCTAG 58.894 45.833 23.01 14.77 34.02 2.43
2108 2141 1.302033 GCAGGGCTATGGGATGACG 60.302 63.158 0.00 0.00 0.00 4.35
2339 2372 1.812686 CGGAGACCGTGGACAAGGAA 61.813 60.000 11.22 0.00 42.73 3.36
2586 2619 5.757320 CCTCATTGAGCTGTAAGAGTTATGG 59.243 44.000 8.23 0.00 34.07 2.74
2608 2650 0.390209 TCTTAACAACGGCCGGCTAC 60.390 55.000 31.76 9.89 0.00 3.58
2660 2702 3.041940 GTCCCTGTGGCGTTCGTG 61.042 66.667 0.00 0.00 0.00 4.35
2766 2808 2.440539 GAAGGTCTTCTTCGTGAGCA 57.559 50.000 3.65 0.00 41.95 4.26
2852 2894 3.457610 TCGTGCTGATGATGCTTGATA 57.542 42.857 0.00 0.00 0.00 2.15
2860 2902 8.724229 GTGCTGATGATGCTTGATATATTTGTA 58.276 33.333 0.00 0.00 0.00 2.41
2861 2903 8.724229 TGCTGATGATGCTTGATATATTTGTAC 58.276 33.333 0.00 0.00 0.00 2.90
2862 2904 8.724229 GCTGATGATGCTTGATATATTTGTACA 58.276 33.333 0.00 0.00 0.00 2.90
2883 2927 6.939551 ACACGAAATATATAATCGGTTCGG 57.060 37.500 19.22 11.15 41.49 4.30
2900 2945 4.209112 GTTCGGTTTTTGTTCTCGTCATC 58.791 43.478 0.00 0.00 0.00 2.92
2907 2952 6.403636 GGTTTTTGTTCTCGTCATCATGCTAT 60.404 38.462 0.00 0.00 0.00 2.97
2908 2953 6.741992 TTTTGTTCTCGTCATCATGCTATT 57.258 33.333 0.00 0.00 0.00 1.73
2909 2954 6.741992 TTTGTTCTCGTCATCATGCTATTT 57.258 33.333 0.00 0.00 0.00 1.40
2910 2955 6.741992 TTGTTCTCGTCATCATGCTATTTT 57.258 33.333 0.00 0.00 0.00 1.82
2911 2956 6.741992 TGTTCTCGTCATCATGCTATTTTT 57.258 33.333 0.00 0.00 0.00 1.94
3005 3051 3.655777 TGGTCCCTCAACTAGAAAACCAT 59.344 43.478 0.00 0.00 30.52 3.55
3018 3064 8.250143 ACTAGAAAACCATCAAAATTTGGTCT 57.750 30.769 5.83 0.00 45.44 3.85
3048 3094 9.511272 AACTATTCAAACCGGATAAGTTTAGTT 57.489 29.630 9.46 10.11 35.71 2.24
3229 3290 6.751514 TGCCACATGTTTCGAACTTAATAT 57.248 33.333 0.00 0.00 0.00 1.28
3236 3297 7.548075 ACATGTTTCGAACTTAATATCGGAAGT 59.452 33.333 0.00 1.37 37.23 3.01
3404 3538 4.019860 AGTTTCAGTCCTCTGCACATATGT 60.020 41.667 1.41 1.41 41.10 2.29
3652 4157 7.715249 TGAGGGACCATTTCTATATTTTCGAAG 59.285 37.037 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.547367 GGTCTGGGGGCGAATCGG 62.547 72.222 4.35 0.00 0.00 4.18
3 4 4.891727 CGGTCTGGGGGCGAATCG 62.892 72.222 0.00 0.00 0.00 3.34
9 10 3.569200 AAAAGAGCGGTCTGGGGGC 62.569 63.158 19.39 0.00 31.37 5.80
10 11 1.074951 AAAAAGAGCGGTCTGGGGG 59.925 57.895 19.39 0.00 31.37 5.40
11 12 4.821935 AAAAAGAGCGGTCTGGGG 57.178 55.556 19.39 0.00 31.37 4.96
25 26 1.406860 GCCTCCCAAGGTGCCAAAAA 61.407 55.000 0.00 0.00 45.34 1.94
26 27 1.836604 GCCTCCCAAGGTGCCAAAA 60.837 57.895 0.00 0.00 45.34 2.44
27 28 1.431195 TAGCCTCCCAAGGTGCCAAA 61.431 55.000 0.00 0.00 45.34 3.28
28 29 1.431195 TTAGCCTCCCAAGGTGCCAA 61.431 55.000 0.00 0.00 45.34 4.52
29 30 1.431195 TTTAGCCTCCCAAGGTGCCA 61.431 55.000 0.00 0.00 45.34 4.92
30 31 0.965866 GTTTAGCCTCCCAAGGTGCC 60.966 60.000 0.00 0.00 45.34 5.01
31 32 1.305930 CGTTTAGCCTCCCAAGGTGC 61.306 60.000 0.00 0.00 45.34 5.01
32 33 0.676782 CCGTTTAGCCTCCCAAGGTG 60.677 60.000 0.00 0.00 45.34 4.00
33 34 1.683441 CCGTTTAGCCTCCCAAGGT 59.317 57.895 0.00 0.00 45.34 3.50
34 35 1.749258 GCCGTTTAGCCTCCCAAGG 60.749 63.158 0.00 0.00 46.44 3.61
35 36 0.539986 TAGCCGTTTAGCCTCCCAAG 59.460 55.000 0.00 0.00 0.00 3.61
36 37 0.539986 CTAGCCGTTTAGCCTCCCAA 59.460 55.000 0.00 0.00 0.00 4.12
37 38 0.324923 TCTAGCCGTTTAGCCTCCCA 60.325 55.000 0.00 0.00 0.00 4.37
38 39 0.389757 CTCTAGCCGTTTAGCCTCCC 59.610 60.000 0.00 0.00 0.00 4.30
39 40 1.400737 TCTCTAGCCGTTTAGCCTCC 58.599 55.000 0.00 0.00 0.00 4.30
40 41 2.362717 ACATCTCTAGCCGTTTAGCCTC 59.637 50.000 0.00 0.00 0.00 4.70
41 42 2.389715 ACATCTCTAGCCGTTTAGCCT 58.610 47.619 0.00 0.00 0.00 4.58
42 43 2.892784 ACATCTCTAGCCGTTTAGCC 57.107 50.000 0.00 0.00 0.00 3.93
43 44 4.048241 AGAACATCTCTAGCCGTTTAGC 57.952 45.455 0.00 0.00 30.22 3.09
44 45 6.913673 GTCTTAGAACATCTCTAGCCGTTTAG 59.086 42.308 0.00 0.00 37.93 1.85
45 46 6.602406 AGTCTTAGAACATCTCTAGCCGTTTA 59.398 38.462 0.00 0.00 37.93 2.01
46 47 5.419471 AGTCTTAGAACATCTCTAGCCGTTT 59.581 40.000 0.00 0.00 37.93 3.60
47 48 4.951094 AGTCTTAGAACATCTCTAGCCGTT 59.049 41.667 0.00 0.00 37.93 4.44
48 49 4.528920 AGTCTTAGAACATCTCTAGCCGT 58.471 43.478 0.00 0.00 37.93 5.68
49 50 4.319190 CGAGTCTTAGAACATCTCTAGCCG 60.319 50.000 0.00 0.00 37.93 5.52
50 51 4.817464 TCGAGTCTTAGAACATCTCTAGCC 59.183 45.833 0.00 0.00 37.93 3.93
51 52 5.994887 TCGAGTCTTAGAACATCTCTAGC 57.005 43.478 0.00 0.00 37.93 3.42
52 53 6.260050 AGCTTCGAGTCTTAGAACATCTCTAG 59.740 42.308 0.00 0.00 37.93 2.43
53 54 6.116806 AGCTTCGAGTCTTAGAACATCTCTA 58.883 40.000 0.00 0.00 35.41 2.43
54 55 4.947388 AGCTTCGAGTCTTAGAACATCTCT 59.053 41.667 0.00 0.00 38.28 3.10
55 56 5.243426 AGCTTCGAGTCTTAGAACATCTC 57.757 43.478 0.00 0.00 0.00 2.75
56 57 4.097286 GGAGCTTCGAGTCTTAGAACATCT 59.903 45.833 0.00 0.00 0.00 2.90
57 58 4.356289 GGAGCTTCGAGTCTTAGAACATC 58.644 47.826 0.00 0.00 0.00 3.06
58 59 3.181495 CGGAGCTTCGAGTCTTAGAACAT 60.181 47.826 9.41 0.00 0.00 2.71
59 60 2.161808 CGGAGCTTCGAGTCTTAGAACA 59.838 50.000 9.41 0.00 0.00 3.18
60 61 2.478200 CCGGAGCTTCGAGTCTTAGAAC 60.478 54.545 18.24 0.00 0.00 3.01
61 62 1.743958 CCGGAGCTTCGAGTCTTAGAA 59.256 52.381 18.24 0.00 0.00 2.10
62 63 1.380524 CCGGAGCTTCGAGTCTTAGA 58.619 55.000 18.24 0.00 0.00 2.10
63 64 0.248702 GCCGGAGCTTCGAGTCTTAG 60.249 60.000 18.24 0.00 35.50 2.18
64 65 1.664321 GGCCGGAGCTTCGAGTCTTA 61.664 60.000 18.24 0.00 39.73 2.10
65 66 2.574399 GCCGGAGCTTCGAGTCTT 59.426 61.111 18.24 0.00 35.50 3.01
80 81 2.029290 TCAGACGAACTCACTAAAGGCC 60.029 50.000 0.00 0.00 0.00 5.19
81 82 3.299340 TCAGACGAACTCACTAAAGGC 57.701 47.619 0.00 0.00 0.00 4.35
96 97 6.246420 ACAGCTACAAAAACATCATCAGAC 57.754 37.500 0.00 0.00 0.00 3.51
110 111 6.810911 TGCTTTGGAAAAATTACAGCTACAA 58.189 32.000 0.00 0.00 0.00 2.41
129 130 6.431198 TTGTCTCTTAAGTCGTTTTGCTTT 57.569 33.333 1.63 0.00 0.00 3.51
174 175 9.882856 GTTCTTAAATTCTACGACGACATTTAG 57.117 33.333 0.00 0.00 0.00 1.85
177 178 9.630098 TTAGTTCTTAAATTCTACGACGACATT 57.370 29.630 0.00 0.00 0.00 2.71
203 204 6.344500 CATGTGCAGAGAAAGAGTAAGGTAT 58.656 40.000 0.00 0.00 0.00 2.73
204 205 5.724328 CATGTGCAGAGAAAGAGTAAGGTA 58.276 41.667 0.00 0.00 0.00 3.08
206 207 3.373439 GCATGTGCAGAGAAAGAGTAAGG 59.627 47.826 0.00 0.00 41.59 2.69
219 220 1.066002 CTATTTTCCGGGCATGTGCAG 59.934 52.381 0.00 0.31 44.36 4.41
231 232 7.391833 CACCATCTAGCTTTATCCCTATTTTCC 59.608 40.741 0.00 0.00 0.00 3.13
240 241 8.854614 ATTAATGTCACCATCTAGCTTTATCC 57.145 34.615 0.00 0.00 0.00 2.59
325 327 9.250624 GAGCGTTTAGATCACTAGTAATGATTT 57.749 33.333 0.00 0.00 36.92 2.17
326 328 8.634444 AGAGCGTTTAGATCACTAGTAATGATT 58.366 33.333 0.00 0.00 36.92 2.57
327 329 8.172352 AGAGCGTTTAGATCACTAGTAATGAT 57.828 34.615 0.00 0.00 39.54 2.45
328 330 7.569639 AGAGCGTTTAGATCACTAGTAATGA 57.430 36.000 0.00 0.00 37.82 2.57
329 331 9.171701 GTAAGAGCGTTTAGATCACTAGTAATG 57.828 37.037 0.00 0.00 37.82 1.90
330 332 8.900781 TGTAAGAGCGTTTAGATCACTAGTAAT 58.099 33.333 0.00 0.00 37.82 1.89
331 333 8.272545 TGTAAGAGCGTTTAGATCACTAGTAA 57.727 34.615 0.00 0.00 37.82 2.24
332 334 7.854557 TGTAAGAGCGTTTAGATCACTAGTA 57.145 36.000 0.00 0.00 37.82 1.82
333 335 6.754702 TGTAAGAGCGTTTAGATCACTAGT 57.245 37.500 0.00 0.00 37.82 2.57
334 336 8.635877 AAATGTAAGAGCGTTTAGATCACTAG 57.364 34.615 0.00 0.00 37.82 2.57
335 337 8.997621 AAAATGTAAGAGCGTTTAGATCACTA 57.002 30.769 0.00 0.00 37.82 2.74
336 338 7.907214 AAAATGTAAGAGCGTTTAGATCACT 57.093 32.000 0.00 0.00 37.82 3.41
359 361 6.006449 AGTGAGTACTACTCCTCCGTAAAAA 58.994 40.000 12.79 0.00 44.44 1.94
360 362 5.564550 AGTGAGTACTACTCCTCCGTAAAA 58.435 41.667 12.79 0.00 44.44 1.52
361 363 5.171339 AGTGAGTACTACTCCTCCGTAAA 57.829 43.478 12.79 0.00 44.44 2.01
362 364 4.764172 GAGTGAGTACTACTCCTCCGTAA 58.236 47.826 12.79 0.00 44.44 3.18
363 365 4.399004 GAGTGAGTACTACTCCTCCGTA 57.601 50.000 12.79 0.00 44.44 4.02
364 366 3.264998 GAGTGAGTACTACTCCTCCGT 57.735 52.381 12.79 0.00 44.44 4.69
371 373 6.527057 AATAAAAGCGGAGTGAGTACTACT 57.473 37.500 0.00 0.00 37.25 2.57
377 379 4.863131 CGACTAAATAAAAGCGGAGTGAGT 59.137 41.667 0.00 0.00 0.00 3.41
397 400 9.601971 GACTTCAGTAGAATCTAATATGTCGAC 57.398 37.037 9.11 9.11 32.31 4.20
519 522 9.900264 CAAGTTTGTAGAAAAATTAGTTGCAAC 57.100 29.630 22.17 22.17 0.00 4.17
557 560 6.610741 AGCTTTGTCTAGAGTCAAACTTTG 57.389 37.500 4.79 0.00 31.74 2.77
566 569 2.424246 GCGGACTAGCTTTGTCTAGAGT 59.576 50.000 15.85 0.91 38.61 3.24
570 573 0.179145 GCGCGGACTAGCTTTGTCTA 60.179 55.000 8.83 0.00 35.04 2.59
585 588 4.499040 CCCTTCATTTTTATTTACTGCGCG 59.501 41.667 0.00 0.00 0.00 6.86
587 590 9.233232 GTATTCCCTTCATTTTTATTTACTGCG 57.767 33.333 0.00 0.00 0.00 5.18
606 609 6.126565 GGGTGGGATGTATATAAGGTATTCCC 60.127 46.154 0.00 0.00 0.00 3.97
608 611 7.504926 TGGGTGGGATGTATATAAGGTATTC 57.495 40.000 0.00 0.00 0.00 1.75
610 613 6.447084 CCTTGGGTGGGATGTATATAAGGTAT 59.553 42.308 0.00 0.00 0.00 2.73
611 614 5.788533 CCTTGGGTGGGATGTATATAAGGTA 59.211 44.000 0.00 0.00 0.00 3.08
613 616 4.849810 TCCTTGGGTGGGATGTATATAAGG 59.150 45.833 0.00 0.00 34.84 2.69
614 617 5.785423 TCTCCTTGGGTGGGATGTATATAAG 59.215 44.000 0.00 0.00 31.89 1.73
615 618 5.733000 TCTCCTTGGGTGGGATGTATATAA 58.267 41.667 0.00 0.00 31.89 0.98
619 622 2.587060 TCTCCTTGGGTGGGATGTAT 57.413 50.000 0.00 0.00 31.89 2.29
621 624 1.455822 TTTCTCCTTGGGTGGGATGT 58.544 50.000 0.00 0.00 31.89 3.06
622 625 2.562738 GTTTTTCTCCTTGGGTGGGATG 59.437 50.000 0.00 0.00 31.89 3.51
623 626 2.178984 TGTTTTTCTCCTTGGGTGGGAT 59.821 45.455 0.00 0.00 31.89 3.85
624 627 1.571457 TGTTTTTCTCCTTGGGTGGGA 59.429 47.619 0.00 0.00 0.00 4.37
625 628 2.080654 TGTTTTTCTCCTTGGGTGGG 57.919 50.000 0.00 0.00 0.00 4.61
626 629 4.687901 AAATGTTTTTCTCCTTGGGTGG 57.312 40.909 0.00 0.00 0.00 4.61
627 630 9.586435 GATATAAAATGTTTTTCTCCTTGGGTG 57.414 33.333 0.00 0.00 0.00 4.61
628 631 9.547279 AGATATAAAATGTTTTTCTCCTTGGGT 57.453 29.630 0.00 0.00 0.00 4.51
649 652 8.939929 CGGCACATGAATAAACTTGATAGATAT 58.060 33.333 0.00 0.00 0.00 1.63
650 653 8.147704 TCGGCACATGAATAAACTTGATAGATA 58.852 33.333 0.00 0.00 0.00 1.98
651 654 6.992123 TCGGCACATGAATAAACTTGATAGAT 59.008 34.615 0.00 0.00 0.00 1.98
652 655 6.257849 GTCGGCACATGAATAAACTTGATAGA 59.742 38.462 0.00 0.00 0.00 1.98
653 656 6.422223 GTCGGCACATGAATAAACTTGATAG 58.578 40.000 0.00 0.00 0.00 2.08
654 657 5.006261 CGTCGGCACATGAATAAACTTGATA 59.994 40.000 0.00 0.00 0.00 2.15
655 658 4.201812 CGTCGGCACATGAATAAACTTGAT 60.202 41.667 0.00 0.00 0.00 2.57
656 659 3.124466 CGTCGGCACATGAATAAACTTGA 59.876 43.478 0.00 0.00 0.00 3.02
657 660 3.120338 ACGTCGGCACATGAATAAACTTG 60.120 43.478 0.00 0.00 0.00 3.16
658 661 3.071479 ACGTCGGCACATGAATAAACTT 58.929 40.909 0.00 0.00 0.00 2.66
659 662 2.671396 GACGTCGGCACATGAATAAACT 59.329 45.455 0.00 0.00 0.00 2.66
660 663 2.534150 CGACGTCGGCACATGAATAAAC 60.534 50.000 29.70 0.00 35.37 2.01
661 664 1.656594 CGACGTCGGCACATGAATAAA 59.343 47.619 29.70 0.00 35.37 1.40
662 665 1.273688 CGACGTCGGCACATGAATAA 58.726 50.000 29.70 0.00 35.37 1.40
663 666 2.952273 CGACGTCGGCACATGAATA 58.048 52.632 29.70 0.00 35.37 1.75
664 667 3.780693 CGACGTCGGCACATGAAT 58.219 55.556 29.70 0.00 35.37 2.57
680 683 1.374252 CGAAGGAACCACACCTCCG 60.374 63.158 0.00 0.00 36.67 4.63
718 726 0.958091 ACTCTAGCCGAGCAGCATAG 59.042 55.000 0.00 0.00 43.85 2.23
736 744 2.770532 GCTCGGTGCGAATTTCTAAAC 58.229 47.619 0.00 0.00 34.74 2.01
817 845 3.056328 GCGTTTGGTGGGGAGCTC 61.056 66.667 4.71 4.71 0.00 4.09
847 875 4.338879 GGGGTGGTACTTATAGATAGCGA 58.661 47.826 0.00 0.00 0.00 4.93
867 895 4.821589 GTGGAAGGAGCTCGCGGG 62.822 72.222 6.13 2.60 0.00 6.13
892 920 0.862283 GCGAGATCGACCGAGTTGTC 60.862 60.000 6.39 0.00 43.02 3.18
894 922 0.456142 TTGCGAGATCGACCGAGTTG 60.456 55.000 6.39 0.00 43.02 3.16
895 923 0.456312 GTTGCGAGATCGACCGAGTT 60.456 55.000 6.39 0.00 43.02 3.01
896 924 1.136984 GTTGCGAGATCGACCGAGT 59.863 57.895 6.39 0.00 43.02 4.18
897 925 1.586564 GGTTGCGAGATCGACCGAG 60.587 63.158 6.39 0.00 43.02 4.63
898 926 2.266376 CTGGTTGCGAGATCGACCGA 62.266 60.000 6.39 0.00 43.02 4.69
899 927 1.874019 CTGGTTGCGAGATCGACCG 60.874 63.158 6.39 0.00 43.02 4.79
900 928 1.078759 CACTGGTTGCGAGATCGACC 61.079 60.000 6.39 6.30 43.02 4.79
901 929 1.687494 GCACTGGTTGCGAGATCGAC 61.687 60.000 6.39 0.00 42.79 4.20
925 956 1.349026 CTGTGGGATCAGTGGAACAGT 59.651 52.381 0.00 0.00 46.79 3.55
926 957 1.947678 GCTGTGGGATCAGTGGAACAG 60.948 57.143 0.00 0.00 41.80 3.16
927 958 0.036732 GCTGTGGGATCAGTGGAACA 59.963 55.000 0.00 0.00 41.43 3.18
928 959 0.326264 AGCTGTGGGATCAGTGGAAC 59.674 55.000 0.00 0.00 37.70 3.62
929 960 0.615331 GAGCTGTGGGATCAGTGGAA 59.385 55.000 0.00 0.00 37.70 3.53
930 961 1.267574 GGAGCTGTGGGATCAGTGGA 61.268 60.000 0.00 0.00 37.70 4.02
931 962 1.222936 GGAGCTGTGGGATCAGTGG 59.777 63.158 0.00 0.00 37.70 4.00
932 963 0.392193 GTGGAGCTGTGGGATCAGTG 60.392 60.000 0.00 0.00 37.70 3.66
933 964 1.557269 GGTGGAGCTGTGGGATCAGT 61.557 60.000 0.00 0.00 37.70 3.41
934 965 1.222936 GGTGGAGCTGTGGGATCAG 59.777 63.158 0.00 0.00 38.35 2.90
935 966 1.133181 TTGGTGGAGCTGTGGGATCA 61.133 55.000 0.00 0.00 30.93 2.92
936 967 0.678048 GTTGGTGGAGCTGTGGGATC 60.678 60.000 0.00 0.00 0.00 3.36
937 968 1.380302 GTTGGTGGAGCTGTGGGAT 59.620 57.895 0.00 0.00 0.00 3.85
938 969 2.829384 GGTTGGTGGAGCTGTGGGA 61.829 63.158 0.00 0.00 0.00 4.37
939 970 2.282462 GGTTGGTGGAGCTGTGGG 60.282 66.667 0.00 0.00 0.00 4.61
960 991 0.108329 ACTGGATCGTTTACGGCTGG 60.108 55.000 0.00 0.00 40.29 4.85
979 1010 3.035576 CTCGCCGCGTCTGTCTGTA 62.036 63.158 13.39 0.00 0.00 2.74
1044 1075 4.796231 ATGTCCGGCAGCGTCGAC 62.796 66.667 5.18 5.18 29.41 4.20
1064 1095 2.365105 GGAGGTGGTCCGGGATGA 60.365 66.667 0.00 0.00 34.84 2.92
1231 1262 1.888018 GCATCACAGTGCTGCCATT 59.112 52.632 17.12 0.00 41.82 3.16
1242 1273 2.673200 GGGGAGGAGCAGCATCACA 61.673 63.158 0.00 0.00 30.71 3.58
1996 2027 5.361857 CGAGGAAGGAAAGGTTAGGTATGTA 59.638 44.000 0.00 0.00 0.00 2.29
1998 2029 4.161754 ACGAGGAAGGAAAGGTTAGGTATG 59.838 45.833 0.00 0.00 0.00 2.39
2043 2074 0.108992 TAACTGGCATGGTCGTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
2550 2583 3.824133 CTCAATGAGGACCCATGCATTA 58.176 45.455 1.53 0.00 30.45 1.90
2586 2619 0.386352 GCCGGCCGTTGTTAAGAAAC 60.386 55.000 26.12 0.00 36.07 2.78
2676 2718 4.498520 CTCGGTCATGTCGGCGCT 62.499 66.667 7.64 0.00 0.00 5.92
2816 2858 2.125106 GATCCGACGGCCAGCTTT 60.125 61.111 9.66 0.00 0.00 3.51
2827 2869 0.598419 GCATCATCAGCACGATCCGA 60.598 55.000 0.00 0.00 29.21 4.55
2860 2902 6.449698 ACCGAACCGATTATATATTTCGTGT 58.550 36.000 11.84 7.98 35.26 4.49
2861 2903 6.939551 ACCGAACCGATTATATATTTCGTG 57.060 37.500 11.84 7.54 35.26 4.35
2862 2904 7.951530 AAACCGAACCGATTATATATTTCGT 57.048 32.000 11.84 0.00 35.26 3.85
2874 2918 2.222445 CGAGAACAAAAACCGAACCGAT 59.778 45.455 0.00 0.00 0.00 4.18
2875 2919 1.593933 CGAGAACAAAAACCGAACCGA 59.406 47.619 0.00 0.00 0.00 4.69
2883 2927 4.787598 AGCATGATGACGAGAACAAAAAC 58.212 39.130 0.00 0.00 0.00 2.43
2915 2960 9.425248 TCTCCCTTTAAATTAGCATGATTTCAT 57.575 29.630 0.00 0.00 36.96 2.57
2916 2961 8.821686 TCTCCCTTTAAATTAGCATGATTTCA 57.178 30.769 0.00 0.00 0.00 2.69
2917 2962 9.741647 CTTCTCCCTTTAAATTAGCATGATTTC 57.258 33.333 0.00 0.00 0.00 2.17
2918 2963 9.259832 ACTTCTCCCTTTAAATTAGCATGATTT 57.740 29.630 0.00 0.00 0.00 2.17
2919 2964 8.829373 ACTTCTCCCTTTAAATTAGCATGATT 57.171 30.769 0.00 0.00 0.00 2.57
3018 3064 9.729281 AAACTTATCCGGTTTGAATAGTTAAGA 57.271 29.630 0.00 0.00 35.84 2.10
3048 3094 4.974645 AACAGTCAAAGTGGTATGAGGA 57.025 40.909 0.00 0.00 0.00 3.71
3128 3187 3.736213 CACATTTGTACACGCTGATGTC 58.264 45.455 0.00 0.00 33.85 3.06
3229 3290 1.342076 ACTGATCTGGCCTACTTCCGA 60.342 52.381 3.32 0.00 0.00 4.55
3236 3297 3.052414 TGGTTACCTACTGATCTGGCCTA 60.052 47.826 3.32 0.00 0.00 3.93
3699 4204 3.616076 CGATCCTTGCTCACACTCTCTTT 60.616 47.826 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.