Multiple sequence alignment - TraesCS2B01G164800

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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 TraesCS2B01G164800 chr2B 100.000 3474 0 0 1 3474 136816023 136812550 0.000000e+00 6416
1 TraesCS2B01G164800 chr2B 95.940 2931 79 18 394 3316 137622977 137620079 0.000000e+00 4717
2 TraesCS2B01G164800 chr2B 95.078 2580 92 14 731 3301 136639125 136636572 0.000000e+00 4028
3 TraesCS2B01G164800 chr2B 97.825 1747 33 4 394 2139 137015284 137013542 0.000000e+00 3011
4 TraesCS2B01G164800 chr2B 97.217 1150 22 5 2167 3316 137013547 137012408 0.000000e+00 1938
5 TraesCS2B01G164800 chr2B 92.276 971 53 11 2161 3118 135464706 135465667 0.000000e+00 1358
6 TraesCS2B01G164800 chr2B 91.796 963 68 9 2161 3118 182132935 182131979 0.000000e+00 1330
7 TraesCS2B01G164800 chr2B 88.254 630 41 13 1 617 137131867 137131258 0.000000e+00 723
8 TraesCS2B01G164800 chr2B 87.917 629 42 11 1 617 137703155 137702549 0.000000e+00 710
9 TraesCS2B01G164800 chr2B 86.777 605 48 21 1 585 137463472 137462880 0.000000e+00 645
10 TraesCS2B01G164800 chr2B 86.712 444 53 4 613 1055 137130903 137130465 4.030000e-134 488
11 TraesCS2B01G164800 chr2B 86.207 406 46 9 1 400 137015781 137015380 6.890000e-117 431
12 TraesCS2B01G164800 chr2B 86.207 406 46 9 1 400 137623472 137623071 6.890000e-117 431
13 TraesCS2B01G164800 chr2B 94.737 76 4 0 3126 3201 182131588 182131513 6.090000e-23 119
14 TraesCS2B01G164800 chr2B 91.139 79 7 0 3123 3201 135515463 135515541 1.320000e-19 108
15 TraesCS2B01G164800 chr2B 97.674 43 1 0 3253 3295 136634674 136634632 1.340000e-09 75
16 TraesCS2B01G164800 chr2D 94.860 1790 72 5 394 2166 85409287 85407501 0.000000e+00 2778
17 TraesCS2B01G164800 chr2D 94.850 1437 58 4 731 2166 84780549 84779128 0.000000e+00 2230
18 TraesCS2B01G164800 chr2D 95.994 1373 48 4 800 2166 84938075 84936704 0.000000e+00 2224
19 TraesCS2B01G164800 chr2D 92.247 1019 56 3 739 1752 85252000 85251000 0.000000e+00 1423
20 TraesCS2B01G164800 chr2D 92.111 900 52 5 853 1752 85703786 85702906 0.000000e+00 1251
21 TraesCS2B01G164800 chr2D 86.881 1151 82 23 2161 3301 85250909 85249818 0.000000e+00 1225
22 TraesCS2B01G164800 chr2D 86.667 720 66 20 1 713 85252851 85252155 0.000000e+00 771
23 TraesCS2B01G164800 chr2D 91.520 342 20 7 394 733 84938436 84938102 2.440000e-126 462
24 TraesCS2B01G164800 chr2D 87.293 362 37 8 1 355 84939011 84938652 4.180000e-109 405
25 TraesCS2B01G164800 chr2D 81.250 464 69 13 3 454 332513507 332513964 3.300000e-95 359
26 TraesCS2B01G164800 chr2D 97.516 161 3 1 3315 3474 102542473 102542633 1.230000e-69 274
27 TraesCS2B01G164800 chr2D 94.375 160 8 1 3135 3294 84935457 84935299 9.630000e-61 244
28 TraesCS2B01G164800 chr2D 93.750 160 9 1 3135 3294 85406253 85406095 4.480000e-59 239
29 TraesCS2B01G164800 chr2A 96.570 1137 21 9 2167 3301 85612506 85611386 0.000000e+00 1868
30 TraesCS2B01G164800 chr2A 93.306 1240 52 3 838 2070 85613727 85612512 0.000000e+00 1801
31 TraesCS2B01G164800 chr2A 93.306 1240 52 3 838 2070 85927152 85925937 0.000000e+00 1801
32 TraesCS2B01G164800 chr2A 92.984 1240 56 3 838 2070 85811245 85810030 0.000000e+00 1779
33 TraesCS2B01G164800 chr2A 91.615 966 65 12 2161 3118 84144623 84145580 0.000000e+00 1321
34 TraesCS2B01G164800 chr2A 91.131 981 70 12 2161 3132 83991119 83992091 0.000000e+00 1314
35 TraesCS2B01G164800 chr2A 87.882 1081 101 11 2161 3237 134866475 134865421 0.000000e+00 1243
36 TraesCS2B01G164800 chr2A 97.516 161 3 1 3315 3474 86445806 86445646 1.230000e-69 274
37 TraesCS2B01G164800 chr2A 93.578 109 7 0 3123 3231 84146006 84146114 2.770000e-36 163
38 TraesCS2B01G164800 chr7A 93.659 1230 60 8 533 1752 618195694 618194473 0.000000e+00 1823
39 TraesCS2B01G164800 chr7A 91.325 415 30 5 59 471 618196529 618196119 2.340000e-156 562
40 TraesCS2B01G164800 chr7A 95.000 80 3 1 2060 2139 627006928 627006850 1.310000e-24 124
41 TraesCS2B01G164800 chr4A 93.145 1240 54 3 838 2070 349806780 349805565 0.000000e+00 1790
42 TraesCS2B01G164800 chr7D 86.297 343 33 6 1824 2153 518766779 518767120 9.170000e-96 361
43 TraesCS2B01G164800 chr7D 97.516 161 3 1 3315 3474 614432499 614432339 1.230000e-69 274
44 TraesCS2B01G164800 chrUn 96.951 164 4 1 3310 3472 341557028 341557191 1.230000e-69 274
45 TraesCS2B01G164800 chrUn 96.951 164 4 1 3310 3472 341575571 341575408 1.230000e-69 274
46 TraesCS2B01G164800 chr6A 97.516 161 3 1 3315 3474 579515348 579515188 1.230000e-69 274
47 TraesCS2B01G164800 chr5B 97.516 161 3 1 3315 3474 681629771 681629611 1.230000e-69 274
48 TraesCS2B01G164800 chr5D 96.914 162 4 1 3314 3474 505210339 505210178 1.590000e-68 270
49 TraesCS2B01G164800 chr4B 96.894 161 4 1 3315 3474 107681081 107680921 5.720000e-68 268
50 TraesCS2B01G164800 chr7B 92.233 103 2 1 2070 2166 588876413 588876311 1.300000e-29 141


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 TraesCS2B01G164800 chr2B 136812550 136816023 3473 True 6416.000000 6416 100.000000 1 3474 1 chr2B.!!$R1 3473
1 TraesCS2B01G164800 chr2B 137620079 137623472 3393 True 2574.000000 4717 91.073500 1 3316 2 chr2B.!!$R7 3315
2 TraesCS2B01G164800 chr2B 136634632 136639125 4493 True 2051.500000 4028 96.376000 731 3301 2 chr2B.!!$R4 2570
3 TraesCS2B01G164800 chr2B 137012408 137015781 3373 True 1793.333333 3011 93.749667 1 3316 3 chr2B.!!$R5 3315
4 TraesCS2B01G164800 chr2B 135464706 135465667 961 False 1358.000000 1358 92.276000 2161 3118 1 chr2B.!!$F1 957
5 TraesCS2B01G164800 chr2B 182131513 182132935 1422 True 724.500000 1330 93.266500 2161 3201 2 chr2B.!!$R8 1040
6 TraesCS2B01G164800 chr2B 137702549 137703155 606 True 710.000000 710 87.917000 1 617 1 chr2B.!!$R3 616
7 TraesCS2B01G164800 chr2B 137462880 137463472 592 True 645.000000 645 86.777000 1 585 1 chr2B.!!$R2 584
8 TraesCS2B01G164800 chr2B 137130465 137131867 1402 True 605.500000 723 87.483000 1 1055 2 chr2B.!!$R6 1054
9 TraesCS2B01G164800 chr2D 84779128 84780549 1421 True 2230.000000 2230 94.850000 731 2166 1 chr2D.!!$R1 1435
10 TraesCS2B01G164800 chr2D 85406095 85409287 3192 True 1508.500000 2778 94.305000 394 3294 2 chr2D.!!$R5 2900
11 TraesCS2B01G164800 chr2D 85702906 85703786 880 True 1251.000000 1251 92.111000 853 1752 1 chr2D.!!$R2 899
12 TraesCS2B01G164800 chr2D 85249818 85252851 3033 True 1139.666667 1423 88.598333 1 3301 3 chr2D.!!$R4 3300
13 TraesCS2B01G164800 chr2D 84935299 84939011 3712 True 833.750000 2224 92.295500 1 3294 4 chr2D.!!$R3 3293
14 TraesCS2B01G164800 chr2A 85611386 85613727 2341 True 1834.500000 1868 94.938000 838 3301 2 chr2A.!!$R5 2463
15 TraesCS2B01G164800 chr2A 85925937 85927152 1215 True 1801.000000 1801 93.306000 838 2070 1 chr2A.!!$R2 1232
16 TraesCS2B01G164800 chr2A 85810030 85811245 1215 True 1779.000000 1779 92.984000 838 2070 1 chr2A.!!$R1 1232
17 TraesCS2B01G164800 chr2A 83991119 83992091 972 False 1314.000000 1314 91.131000 2161 3132 1 chr2A.!!$F1 971
18 TraesCS2B01G164800 chr2A 134865421 134866475 1054 True 1243.000000 1243 87.882000 2161 3237 1 chr2A.!!$R4 1076
19 TraesCS2B01G164800 chr2A 84144623 84146114 1491 False 742.000000 1321 92.596500 2161 3231 2 chr2A.!!$F2 1070
20 TraesCS2B01G164800 chr7A 618194473 618196529 2056 True 1192.500000 1823 92.492000 59 1752 2 chr7A.!!$R2 1693
21 TraesCS2B01G164800 chr4A 349805565 349806780 1215 True 1790.000000 1790 93.145000 838 2070 1 chr4A.!!$R1 1232

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
187 194 3.626670 GTCAGCAAAATCAGGATCAGAGG 59.373 47.826 0.0 0.0 0.00 3.69 F
1240 2364 4.373116 GGACGCCGACTTCCAGCA 62.373 66.667 0.0 0.0 34.35 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 2807 1.001641 AGCAAGCCTTGGAAGCGAT 60.002 52.632 6.57 0.00 34.64 4.58 R
2582 4354 1.327690 CCTGCTACAAGCCGGGTAGA 61.328 60.000 17.53 1.78 41.27 2.59 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
122 127 5.181811 CCTTAATCAATAGCGCATGATCCAA 59.818 40.000 19.30 15.54 35.29 3.53
187 194 3.626670 GTCAGCAAAATCAGGATCAGAGG 59.373 47.826 0.00 0.00 0.00 3.69
210 217 4.505039 GCGAAAGGGACCATCTATAACCAT 60.505 45.833 0.00 0.00 0.00 3.55
307 315 7.729116 AGGATTGACAAGATTCAAACACATTT 58.271 30.769 0.00 0.00 38.95 2.32
438 626 9.656323 AGATACTCATGGTTATTAGGTTAGTGA 57.344 33.333 0.00 0.00 0.00 3.41
443 631 6.821665 TCATGGTTATTAGGTTAGTGAAGTGC 59.178 38.462 0.00 0.00 0.00 4.40
496 704 6.310149 AGACCTTCTGAAAGTTGGAATGATT 58.690 36.000 0.92 0.00 33.19 2.57
497 705 7.461749 AGACCTTCTGAAAGTTGGAATGATTA 58.538 34.615 0.92 0.00 33.19 1.75
1240 2364 4.373116 GGACGCCGACTTCCAGCA 62.373 66.667 0.00 0.00 34.35 4.41
1683 2807 2.814919 GTGAAGAAGGTCTCTCGTCAGA 59.185 50.000 0.00 0.00 31.02 3.27
2668 4442 2.811101 CTGCCTAGCGTCTGGAGG 59.189 66.667 0.00 0.00 0.00 4.30
2710 4484 5.520376 AAATTAATCTTGGCTGAATCGGG 57.480 39.130 0.00 0.00 0.00 5.14
3239 5594 1.602311 CAGTCTTGCATATCCAGGCC 58.398 55.000 0.00 0.00 0.00 5.19
3264 7563 6.183360 CCCCCTAAGAAATTTTCATGTCCATC 60.183 42.308 11.53 0.00 0.00 3.51
3316 7615 3.197983 AGTTACCTGGAGTGGAATGCTAC 59.802 47.826 0.00 0.00 0.00 3.58
3317 7616 1.958288 ACCTGGAGTGGAATGCTACT 58.042 50.000 0.00 0.00 38.69 2.57
3322 7621 2.900716 GAGTGGAATGCTACTCCCTC 57.099 55.000 5.90 0.00 44.27 4.30
3323 7622 1.414550 GAGTGGAATGCTACTCCCTCC 59.585 57.143 5.90 0.00 44.27 4.30
3324 7623 1.204146 GTGGAATGCTACTCCCTCCA 58.796 55.000 0.00 0.00 33.77 3.86
3325 7624 1.771255 GTGGAATGCTACTCCCTCCAT 59.229 52.381 0.00 0.00 38.41 3.41
3326 7625 2.173569 GTGGAATGCTACTCCCTCCATT 59.826 50.000 0.00 0.00 38.41 3.16
3327 7626 2.439507 TGGAATGCTACTCCCTCCATTC 59.560 50.000 0.00 0.00 41.57 2.67
3328 7627 3.133141 GAATGCTACTCCCTCCATTCC 57.867 52.381 0.00 0.00 38.25 3.01
3329 7628 1.439543 ATGCTACTCCCTCCATTCCC 58.560 55.000 0.00 0.00 0.00 3.97
3330 7629 0.343372 TGCTACTCCCTCCATTCCCT 59.657 55.000 0.00 0.00 0.00 4.20
3331 7630 1.274416 TGCTACTCCCTCCATTCCCTT 60.274 52.381 0.00 0.00 0.00 3.95
3332 7631 2.022428 TGCTACTCCCTCCATTCCCTTA 60.022 50.000 0.00 0.00 0.00 2.69
3333 7632 3.252351 GCTACTCCCTCCATTCCCTTAT 58.748 50.000 0.00 0.00 0.00 1.73
3334 7633 4.140543 TGCTACTCCCTCCATTCCCTTATA 60.141 45.833 0.00 0.00 0.00 0.98
3335 7634 4.223255 GCTACTCCCTCCATTCCCTTATAC 59.777 50.000 0.00 0.00 0.00 1.47
3336 7635 4.295905 ACTCCCTCCATTCCCTTATACA 57.704 45.455 0.00 0.00 0.00 2.29
3337 7636 4.641868 ACTCCCTCCATTCCCTTATACAA 58.358 43.478 0.00 0.00 0.00 2.41
3338 7637 4.660771 ACTCCCTCCATTCCCTTATACAAG 59.339 45.833 0.00 0.00 0.00 3.16
3352 7651 7.639113 CCTTATACAAGGCCACTATCAAAAA 57.361 36.000 5.01 0.00 44.90 1.94
3353 7652 8.237811 CCTTATACAAGGCCACTATCAAAAAT 57.762 34.615 5.01 0.00 44.90 1.82
3354 7653 9.349713 CCTTATACAAGGCCACTATCAAAAATA 57.650 33.333 5.01 0.00 44.90 1.40
3356 7655 9.688091 TTATACAAGGCCACTATCAAAAATACA 57.312 29.630 5.01 0.00 0.00 2.29
3357 7656 8.766994 ATACAAGGCCACTATCAAAAATACAT 57.233 30.769 5.01 0.00 0.00 2.29
3358 7657 7.480760 ACAAGGCCACTATCAAAAATACATT 57.519 32.000 5.01 0.00 0.00 2.71
3359 7658 7.906327 ACAAGGCCACTATCAAAAATACATTT 58.094 30.769 5.01 0.00 0.00 2.32
3360 7659 8.374743 ACAAGGCCACTATCAAAAATACATTTT 58.625 29.630 5.01 0.00 41.93 1.82
3375 7674 7.775397 AATACATTTTGCATCAATACAAGGC 57.225 32.000 0.00 0.00 0.00 4.35
3376 7675 4.506758 ACATTTTGCATCAATACAAGGCC 58.493 39.130 0.00 0.00 0.00 5.19
3377 7676 4.020396 ACATTTTGCATCAATACAAGGCCA 60.020 37.500 5.01 0.00 0.00 5.36
3378 7677 3.591196 TTTGCATCAATACAAGGCCAC 57.409 42.857 5.01 0.00 0.00 5.01
3379 7678 1.473258 TGCATCAATACAAGGCCACC 58.527 50.000 5.01 0.00 0.00 4.61
3380 7679 1.272369 TGCATCAATACAAGGCCACCA 60.272 47.619 5.01 0.00 0.00 4.17
3381 7680 1.824230 GCATCAATACAAGGCCACCAA 59.176 47.619 5.01 0.00 0.00 3.67
3382 7681 2.417243 GCATCAATACAAGGCCACCAAC 60.417 50.000 5.01 0.00 0.00 3.77
3383 7682 2.666272 TCAATACAAGGCCACCAACA 57.334 45.000 5.01 0.00 0.00 3.33
3384 7683 2.513753 TCAATACAAGGCCACCAACAG 58.486 47.619 5.01 0.00 0.00 3.16
3385 7684 2.158534 TCAATACAAGGCCACCAACAGT 60.159 45.455 5.01 0.00 0.00 3.55
3386 7685 3.073209 TCAATACAAGGCCACCAACAGTA 59.927 43.478 5.01 0.00 0.00 2.74
3387 7686 3.799432 ATACAAGGCCACCAACAGTAA 57.201 42.857 5.01 0.00 0.00 2.24
3388 7687 2.675658 ACAAGGCCACCAACAGTAAT 57.324 45.000 5.01 0.00 0.00 1.89
3389 7688 2.514803 ACAAGGCCACCAACAGTAATC 58.485 47.619 5.01 0.00 0.00 1.75
3390 7689 1.468520 CAAGGCCACCAACAGTAATCG 59.531 52.381 5.01 0.00 0.00 3.34
3391 7690 0.981183 AGGCCACCAACAGTAATCGA 59.019 50.000 5.01 0.00 0.00 3.59
3392 7691 1.066143 AGGCCACCAACAGTAATCGAG 60.066 52.381 5.01 0.00 0.00 4.04
3393 7692 1.369625 GCCACCAACAGTAATCGAGG 58.630 55.000 0.00 0.00 0.00 4.63
3394 7693 1.369625 CCACCAACAGTAATCGAGGC 58.630 55.000 0.00 0.00 0.00 4.70
3395 7694 1.338674 CCACCAACAGTAATCGAGGCA 60.339 52.381 0.00 0.00 0.00 4.75
3396 7695 2.422597 CACCAACAGTAATCGAGGCAA 58.577 47.619 0.00 0.00 0.00 4.52
3397 7696 2.811431 CACCAACAGTAATCGAGGCAAA 59.189 45.455 0.00 0.00 0.00 3.68
3398 7697 3.252215 CACCAACAGTAATCGAGGCAAAA 59.748 43.478 0.00 0.00 0.00 2.44
3399 7698 3.886505 ACCAACAGTAATCGAGGCAAAAA 59.113 39.130 0.00 0.00 0.00 1.94
3400 7699 4.522789 ACCAACAGTAATCGAGGCAAAAAT 59.477 37.500 0.00 0.00 0.00 1.82
3401 7700 5.010617 ACCAACAGTAATCGAGGCAAAAATT 59.989 36.000 0.00 0.00 0.00 1.82
3402 7701 6.207810 ACCAACAGTAATCGAGGCAAAAATTA 59.792 34.615 0.00 0.00 0.00 1.40
3403 7702 7.087639 CCAACAGTAATCGAGGCAAAAATTAA 58.912 34.615 0.00 0.00 0.00 1.40
3404 7703 7.759433 CCAACAGTAATCGAGGCAAAAATTAAT 59.241 33.333 0.00 0.00 0.00 1.40
3405 7704 8.586273 CAACAGTAATCGAGGCAAAAATTAATG 58.414 33.333 0.00 0.00 36.36 1.90
3406 7705 8.050778 ACAGTAATCGAGGCAAAAATTAATGA 57.949 30.769 12.44 0.00 34.81 2.57
3407 7706 8.686334 ACAGTAATCGAGGCAAAAATTAATGAT 58.314 29.630 12.44 0.00 34.81 2.45
3408 7707 8.961092 CAGTAATCGAGGCAAAAATTAATGATG 58.039 33.333 0.00 0.00 33.69 3.07
3409 7708 8.686334 AGTAATCGAGGCAAAAATTAATGATGT 58.314 29.630 0.00 0.00 0.00 3.06
3410 7709 9.301153 GTAATCGAGGCAAAAATTAATGATGTT 57.699 29.630 0.00 0.00 0.00 2.71
3411 7710 8.776376 AATCGAGGCAAAAATTAATGATGTTT 57.224 26.923 0.00 0.00 0.00 2.83
3412 7711 7.810766 TCGAGGCAAAAATTAATGATGTTTC 57.189 32.000 0.00 0.00 0.00 2.78
3413 7712 6.811170 TCGAGGCAAAAATTAATGATGTTTCC 59.189 34.615 0.00 0.00 0.00 3.13
3414 7713 6.813152 CGAGGCAAAAATTAATGATGTTTCCT 59.187 34.615 0.00 0.00 31.07 3.36
3415 7714 7.331687 CGAGGCAAAAATTAATGATGTTTCCTT 59.668 33.333 0.00 0.00 29.76 3.36
3416 7715 8.326680 AGGCAAAAATTAATGATGTTTCCTTG 57.673 30.769 0.00 0.00 27.22 3.61
3417 7716 7.938490 AGGCAAAAATTAATGATGTTTCCTTGT 59.062 29.630 0.00 0.00 27.22 3.16
3418 7717 9.213799 GGCAAAAATTAATGATGTTTCCTTGTA 57.786 29.630 0.00 0.00 0.00 2.41
3424 7723 9.461312 AATTAATGATGTTTCCTTGTACTAGCA 57.539 29.630 0.00 0.00 0.00 3.49
3425 7724 8.856153 TTAATGATGTTTCCTTGTACTAGCAA 57.144 30.769 0.00 0.00 0.00 3.91
3426 7725 6.743575 ATGATGTTTCCTTGTACTAGCAAC 57.256 37.500 0.00 5.06 0.00 4.17
3427 7726 5.865085 TGATGTTTCCTTGTACTAGCAACT 58.135 37.500 14.29 5.16 0.00 3.16
3428 7727 6.296026 TGATGTTTCCTTGTACTAGCAACTT 58.704 36.000 14.29 10.24 0.00 2.66
3429 7728 6.770785 TGATGTTTCCTTGTACTAGCAACTTT 59.229 34.615 14.29 6.40 0.00 2.66
3430 7729 7.284489 TGATGTTTCCTTGTACTAGCAACTTTT 59.716 33.333 14.29 4.78 0.00 2.27
3431 7730 8.685838 ATGTTTCCTTGTACTAGCAACTTTTA 57.314 30.769 14.29 1.33 0.00 1.52
3432 7731 8.508883 TGTTTCCTTGTACTAGCAACTTTTAA 57.491 30.769 14.29 0.00 0.00 1.52
3433 7732 9.127277 TGTTTCCTTGTACTAGCAACTTTTAAT 57.873 29.630 14.29 0.00 0.00 1.40
3444 7743 9.226606 ACTAGCAACTTTTAATACTTACATGCA 57.773 29.630 0.00 0.00 32.76 3.96
3446 7745 8.915871 AGCAACTTTTAATACTTACATGCATG 57.084 30.769 25.09 25.09 32.76 4.06
3447 7746 8.522830 AGCAACTTTTAATACTTACATGCATGT 58.477 29.630 33.20 33.20 44.48 3.21
3448 7747 9.781834 GCAACTTTTAATACTTACATGCATGTA 57.218 29.630 31.03 31.03 41.97 2.29
3459 7758 8.370493 ACTTACATGCATGTAGTCATAATGAC 57.630 34.615 32.09 0.00 43.44 3.06
3460 7759 7.986889 ACTTACATGCATGTAGTCATAATGACA 59.013 33.333 32.09 16.51 44.34 3.58
3461 7760 6.609237 ACATGCATGTAGTCATAATGACAC 57.391 37.500 30.50 0.00 42.13 3.67
3462 7761 6.351711 ACATGCATGTAGTCATAATGACACT 58.648 36.000 30.50 0.00 42.13 3.55
3463 7762 6.825213 ACATGCATGTAGTCATAATGACACTT 59.175 34.615 30.50 0.00 42.13 3.16
3464 7763 7.986889 ACATGCATGTAGTCATAATGACACTTA 59.013 33.333 30.50 0.00 42.13 2.24
3472 7771 6.351327 GTCATAATGACACTTAGCCACTTC 57.649 41.667 0.00 0.00 46.22 3.01
3473 7772 5.294552 GTCATAATGACACTTAGCCACTTCC 59.705 44.000 0.00 0.00 46.22 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 194 3.181458 TGGTTATAGATGGTCCCTTTCGC 60.181 47.826 0.00 0.00 0.00 4.70
307 315 3.865446 CCTCTGTGCTCACATAATCACA 58.135 45.455 2.90 0.00 41.01 3.58
335 343 1.658686 CTCCTTCTCACCCTCGTCGG 61.659 65.000 0.00 0.00 0.00 4.79
497 705 7.890655 GCTTGGGAAATAAAGACTGGGATATAT 59.109 37.037 0.00 0.00 0.00 0.86
506 1077 4.021981 GCAAGTGCTTGGGAAATAAAGACT 60.022 41.667 13.07 0.00 40.74 3.24
956 2061 1.710013 GAACGAATCGAGTTGGAGCA 58.290 50.000 10.55 0.00 31.14 4.26
1354 2478 1.676635 GCAGGAGCAGCCACATCAA 60.677 57.895 0.00 0.00 41.58 2.57
1683 2807 1.001641 AGCAAGCCTTGGAAGCGAT 60.002 52.632 6.57 0.00 34.64 4.58
2582 4354 1.327690 CCTGCTACAAGCCGGGTAGA 61.328 60.000 17.53 1.78 41.27 2.59
2668 4442 4.392921 TTTACAGGAGAGTCAGCATAGC 57.607 45.455 0.00 0.00 0.00 2.97
2710 4484 4.884164 ACTAAGATGCCAATGCCTAAGAAC 59.116 41.667 0.00 0.00 36.33 3.01
3239 5594 5.022787 TGGACATGAAAATTTCTTAGGGGG 58.977 41.667 7.29 0.00 0.00 5.40
3264 7563 8.469200 ACATGGTGGAATTTGTAACATATTCAG 58.531 33.333 10.38 0.00 34.89 3.02
3316 7615 5.234466 CTTGTATAAGGGAATGGAGGGAG 57.766 47.826 0.00 0.00 0.00 4.30
3330 7629 9.688091 TGTATTTTTGATAGTGGCCTTGTATAA 57.312 29.630 3.32 0.00 0.00 0.98
3331 7630 9.860650 ATGTATTTTTGATAGTGGCCTTGTATA 57.139 29.630 3.32 0.00 0.00 1.47
3332 7631 8.766994 ATGTATTTTTGATAGTGGCCTTGTAT 57.233 30.769 3.32 0.00 0.00 2.29
3333 7632 8.588290 AATGTATTTTTGATAGTGGCCTTGTA 57.412 30.769 3.32 0.00 0.00 2.41
3334 7633 7.480760 AATGTATTTTTGATAGTGGCCTTGT 57.519 32.000 3.32 0.00 0.00 3.16
3335 7634 8.776376 AAAATGTATTTTTGATAGTGGCCTTG 57.224 30.769 3.32 0.00 36.65 3.61
3349 7648 8.667463 GCCTTGTATTGATGCAAAATGTATTTT 58.333 29.630 7.96 0.00 40.37 1.82
3350 7649 7.280652 GGCCTTGTATTGATGCAAAATGTATTT 59.719 33.333 0.00 0.00 32.12 1.40
3351 7650 6.762661 GGCCTTGTATTGATGCAAAATGTATT 59.237 34.615 0.00 0.00 32.12 1.89
3352 7651 6.127111 TGGCCTTGTATTGATGCAAAATGTAT 60.127 34.615 3.32 0.00 32.12 2.29
3353 7652 5.186603 TGGCCTTGTATTGATGCAAAATGTA 59.813 36.000 3.32 0.00 32.12 2.29
3354 7653 4.020396 TGGCCTTGTATTGATGCAAAATGT 60.020 37.500 3.32 0.00 32.12 2.71
3355 7654 4.330620 GTGGCCTTGTATTGATGCAAAATG 59.669 41.667 3.32 0.00 32.12 2.32
3356 7655 4.506758 GTGGCCTTGTATTGATGCAAAAT 58.493 39.130 3.32 0.00 32.12 1.82
3357 7656 3.306641 GGTGGCCTTGTATTGATGCAAAA 60.307 43.478 3.32 0.00 32.12 2.44
3358 7657 2.233431 GGTGGCCTTGTATTGATGCAAA 59.767 45.455 3.32 0.00 32.12 3.68
3359 7658 1.824230 GGTGGCCTTGTATTGATGCAA 59.176 47.619 3.32 0.00 0.00 4.08
3360 7659 1.272369 TGGTGGCCTTGTATTGATGCA 60.272 47.619 3.32 0.00 0.00 3.96
3361 7660 1.473258 TGGTGGCCTTGTATTGATGC 58.527 50.000 3.32 0.00 0.00 3.91
3362 7661 2.824936 TGTTGGTGGCCTTGTATTGATG 59.175 45.455 3.32 0.00 0.00 3.07
3363 7662 3.091545 CTGTTGGTGGCCTTGTATTGAT 58.908 45.455 3.32 0.00 0.00 2.57
3364 7663 2.158534 ACTGTTGGTGGCCTTGTATTGA 60.159 45.455 3.32 0.00 0.00 2.57
3365 7664 2.238521 ACTGTTGGTGGCCTTGTATTG 58.761 47.619 3.32 0.00 0.00 1.90
3366 7665 2.675658 ACTGTTGGTGGCCTTGTATT 57.324 45.000 3.32 0.00 0.00 1.89
3367 7666 3.799432 TTACTGTTGGTGGCCTTGTAT 57.201 42.857 3.32 0.00 0.00 2.29
3368 7667 3.681593 GATTACTGTTGGTGGCCTTGTA 58.318 45.455 3.32 0.00 0.00 2.41
3369 7668 2.514803 GATTACTGTTGGTGGCCTTGT 58.485 47.619 3.32 0.00 0.00 3.16
3370 7669 1.468520 CGATTACTGTTGGTGGCCTTG 59.531 52.381 3.32 0.00 0.00 3.61
3371 7670 1.349688 TCGATTACTGTTGGTGGCCTT 59.650 47.619 3.32 0.00 0.00 4.35
3372 7671 0.981183 TCGATTACTGTTGGTGGCCT 59.019 50.000 3.32 0.00 0.00 5.19
3373 7672 1.369625 CTCGATTACTGTTGGTGGCC 58.630 55.000 0.00 0.00 0.00 5.36
3374 7673 1.369625 CCTCGATTACTGTTGGTGGC 58.630 55.000 0.00 0.00 0.00 5.01
3375 7674 1.338674 TGCCTCGATTACTGTTGGTGG 60.339 52.381 0.00 0.00 0.00 4.61
3376 7675 2.093306 TGCCTCGATTACTGTTGGTG 57.907 50.000 0.00 0.00 0.00 4.17
3377 7676 2.851263 TTGCCTCGATTACTGTTGGT 57.149 45.000 0.00 0.00 0.00 3.67
3378 7677 4.497473 TTTTTGCCTCGATTACTGTTGG 57.503 40.909 0.00 0.00 0.00 3.77
3379 7678 8.586273 CATTAATTTTTGCCTCGATTACTGTTG 58.414 33.333 0.00 0.00 0.00 3.33
3380 7679 8.519526 TCATTAATTTTTGCCTCGATTACTGTT 58.480 29.630 0.00 0.00 0.00 3.16
3381 7680 8.050778 TCATTAATTTTTGCCTCGATTACTGT 57.949 30.769 0.00 0.00 0.00 3.55
3382 7681 8.961092 CATCATTAATTTTTGCCTCGATTACTG 58.039 33.333 0.00 0.00 0.00 2.74
3383 7682 8.686334 ACATCATTAATTTTTGCCTCGATTACT 58.314 29.630 0.00 0.00 0.00 2.24
3384 7683 8.856490 ACATCATTAATTTTTGCCTCGATTAC 57.144 30.769 0.00 0.00 0.00 1.89
3385 7684 9.868277 AAACATCATTAATTTTTGCCTCGATTA 57.132 25.926 0.00 0.00 0.00 1.75
3386 7685 8.776376 AAACATCATTAATTTTTGCCTCGATT 57.224 26.923 0.00 0.00 0.00 3.34
3387 7686 7.492344 GGAAACATCATTAATTTTTGCCTCGAT 59.508 33.333 0.00 0.00 0.00 3.59
3388 7687 6.811170 GGAAACATCATTAATTTTTGCCTCGA 59.189 34.615 0.00 0.00 0.00 4.04
3389 7688 6.813152 AGGAAACATCATTAATTTTTGCCTCG 59.187 34.615 0.00 0.00 28.59 4.63
3390 7689 8.445493 CAAGGAAACATCATTAATTTTTGCCTC 58.555 33.333 0.00 0.00 28.59 4.70
3391 7690 7.938490 ACAAGGAAACATCATTAATTTTTGCCT 59.062 29.630 0.00 0.00 28.59 4.75
3392 7691 8.098220 ACAAGGAAACATCATTAATTTTTGCC 57.902 30.769 0.00 0.00 28.59 4.52
3398 7697 9.461312 TGCTAGTACAAGGAAACATCATTAATT 57.539 29.630 0.00 0.00 0.00 1.40
3399 7698 9.461312 TTGCTAGTACAAGGAAACATCATTAAT 57.539 29.630 0.00 0.00 0.00 1.40
3400 7699 8.726988 GTTGCTAGTACAAGGAAACATCATTAA 58.273 33.333 0.00 0.00 0.00 1.40
3401 7700 8.100791 AGTTGCTAGTACAAGGAAACATCATTA 58.899 33.333 0.00 0.00 0.00 1.90
3402 7701 6.942576 AGTTGCTAGTACAAGGAAACATCATT 59.057 34.615 0.00 0.00 0.00 2.57
3403 7702 6.476378 AGTTGCTAGTACAAGGAAACATCAT 58.524 36.000 0.00 0.00 0.00 2.45
3404 7703 5.865085 AGTTGCTAGTACAAGGAAACATCA 58.135 37.500 0.00 0.00 0.00 3.07
3405 7704 6.803154 AAGTTGCTAGTACAAGGAAACATC 57.197 37.500 0.00 0.00 0.00 3.06
3406 7705 7.582667 AAAAGTTGCTAGTACAAGGAAACAT 57.417 32.000 0.00 0.00 0.00 2.71
3407 7706 8.508883 TTAAAAGTTGCTAGTACAAGGAAACA 57.491 30.769 0.00 0.00 0.00 2.83
3418 7717 9.226606 TGCATGTAAGTATTAAAAGTTGCTAGT 57.773 29.630 0.00 0.00 28.70 2.57
3421 7720 8.522830 ACATGCATGTAAGTATTAAAAGTTGCT 58.477 29.630 30.50 0.00 39.68 3.91
3422 7721 8.687824 ACATGCATGTAAGTATTAAAAGTTGC 57.312 30.769 30.50 0.00 39.68 4.17
3433 7732 9.476202 GTCATTATGACTACATGCATGTAAGTA 57.524 33.333 33.05 23.37 43.73 2.24
3434 7733 8.370493 GTCATTATGACTACATGCATGTAAGT 57.630 34.615 33.05 29.88 43.73 2.24
3450 7749 5.428253 GGAAGTGGCTAAGTGTCATTATGA 58.572 41.667 0.00 0.00 30.58 2.15
3451 7750 5.741388 GGAAGTGGCTAAGTGTCATTATG 57.259 43.478 0.00 0.00 30.58 1.90


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

AutoCloner maintained by Alex Coulton.