Multiple sequence alignment - TraesCS3B01G278100

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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 TraesCS3B01G278100 chr3B 100.000 3320 0 0 1 3320 448315709 448312390 0.000000e+00 6131.0
1 TraesCS3B01G278100 chr3A 93.253 1749 78 18 684 2404 467404451 467402715 0.000000e+00 2540.0
2 TraesCS3B01G278100 chr3A 92.336 274 13 5 1 266 467405132 467404859 1.870000e-102 383.0
3 TraesCS3B01G278100 chr3A 93.976 166 8 1 2601 2764 467402720 467402555 1.980000e-62 250.0
4 TraesCS3B01G278100 chr3A 82.609 207 36 0 2398 2604 728367660 728367454 2.030000e-42 183.0
5 TraesCS3B01G278100 chr3D 93.891 1555 75 15 858 2404 348913258 348911716 0.000000e+00 2327.0
6 TraesCS3B01G278100 chr3D 91.713 893 55 9 1 882 348915811 348914927 0.000000e+00 1221.0
7 TraesCS3B01G278100 chr3D 85.740 561 66 10 2764 3317 90351059 90351612 6.170000e-162 580.0
8 TraesCS3B01G278100 chr3D 84.602 565 68 17 2766 3317 8688572 8688014 8.100000e-151 544.0
9 TraesCS3B01G278100 chr3D 93.069 101 5 1 2601 2699 348911721 348911621 2.670000e-31 147.0
10 TraesCS3B01G278100 chr6D 85.689 566 67 11 2764 3317 405819404 405819967 4.770000e-163 584.0
11 TraesCS3B01G278100 chr6D 84.480 567 72 13 2764 3317 359522073 359522636 2.250000e-151 545.0
12 TraesCS3B01G278100 chr2D 84.574 564 72 13 2765 3317 456961729 456961170 2.250000e-151 545.0
13 TraesCS3B01G278100 chr2D 84.468 573 65 17 2764 3317 103169389 103169956 8.100000e-151 544.0
14 TraesCS3B01G278100 chr2D 94.286 35 1 1 1464 1498 643878760 643878793 6.000000e-03 52.8
15 TraesCS3B01G278100 chr7A 84.698 562 67 14 2764 3317 9200021 9199471 8.100000e-151 544.0
16 TraesCS3B01G278100 chr7A 84.058 207 32 1 2398 2604 614080968 614081173 7.260000e-47 198.0
17 TraesCS3B01G278100 chr1A 84.683 568 62 21 2764 3317 583608388 583607832 8.100000e-151 544.0
18 TraesCS3B01G278100 chr6A 84.369 563 71 12 2764 3317 71530044 71530598 1.360000e-148 536.0
19 TraesCS3B01G278100 chr6A 91.787 207 16 1 2398 2603 196951372 196951578 1.510000e-73 287.0
20 TraesCS3B01G278100 chr6A 89.604 202 20 1 2403 2604 521465293 521465093 4.250000e-64 255.0
21 TraesCS3B01G278100 chr6A 85.047 214 29 3 2398 2611 117126339 117126549 7.210000e-52 215.0
22 TraesCS3B01G278100 chr4A 91.176 204 17 1 2401 2604 96449861 96449659 3.260000e-70 276.0
23 TraesCS3B01G278100 chr4A 100.000 30 0 0 1595 1624 164687991 164687962 4.630000e-04 56.5
24 TraesCS3B01G278100 chr5A 88.350 206 22 2 2399 2603 397753517 397753313 2.560000e-61 246.0
25 TraesCS3B01G278100 chr5A 85.572 201 28 1 2401 2601 592604799 592604600 3.360000e-50 209.0
26 TraesCS3B01G278100 chr2A 85.784 204 27 2 2401 2604 502954824 502954623 7.210000e-52 215.0
27 TraesCS3B01G278100 chr4D 100.000 30 0 0 1595 1624 309943995 309944024 4.630000e-04 56.5
28 TraesCS3B01G278100 chr2B 94.286 35 1 1 1464 1498 793169492 793169459 6.000000e-03 52.8


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 TraesCS3B01G278100 chr3B 448312390 448315709 3319 True 6131.000000 6131 100.000000 1 3320 1 chr3B.!!$R1 3319
1 TraesCS3B01G278100 chr3A 467402555 467405132 2577 True 1057.666667 2540 93.188333 1 2764 3 chr3A.!!$R2 2763
2 TraesCS3B01G278100 chr3D 348911621 348915811 4190 True 1231.666667 2327 92.891000 1 2699 3 chr3D.!!$R2 2698
3 TraesCS3B01G278100 chr3D 90351059 90351612 553 False 580.000000 580 85.740000 2764 3317 1 chr3D.!!$F1 553
4 TraesCS3B01G278100 chr3D 8688014 8688572 558 True 544.000000 544 84.602000 2766 3317 1 chr3D.!!$R1 551
5 TraesCS3B01G278100 chr6D 405819404 405819967 563 False 584.000000 584 85.689000 2764 3317 1 chr6D.!!$F2 553
6 TraesCS3B01G278100 chr6D 359522073 359522636 563 False 545.000000 545 84.480000 2764 3317 1 chr6D.!!$F1 553
7 TraesCS3B01G278100 chr2D 456961170 456961729 559 True 545.000000 545 84.574000 2765 3317 1 chr2D.!!$R1 552
8 TraesCS3B01G278100 chr2D 103169389 103169956 567 False 544.000000 544 84.468000 2764 3317 1 chr2D.!!$F1 553
9 TraesCS3B01G278100 chr7A 9199471 9200021 550 True 544.000000 544 84.698000 2764 3317 1 chr7A.!!$R1 553
10 TraesCS3B01G278100 chr1A 583607832 583608388 556 True 544.000000 544 84.683000 2764 3317 1 chr1A.!!$R1 553
11 TraesCS3B01G278100 chr6A 71530044 71530598 554 False 536.000000 536 84.369000 2764 3317 1 chr6A.!!$F1 553

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
928 2698 0.597072 TATTTTCCCGCGCCGTTTTT 59.403 45.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 4194 0.603065 AATCGCCCAAAAGAACTGGC 59.397 50.0 0.0 0.0 40.54 4.85 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
42 43 1.263217 ACACGCATTTGTTCCGACTTC 59.737 47.619 0.00 0.00 0.00 3.01
56 57 1.336517 CGACTTCGGTACCTCTGCAAA 60.337 52.381 10.90 0.00 35.37 3.68
61 62 0.748005 CGGTACCTCTGCAAATGGGG 60.748 60.000 10.90 0.00 0.00 4.96
286 297 1.067776 ACCGATCCTTCACACGAGAAC 60.068 52.381 0.00 0.00 0.00 3.01
303 314 2.124736 CCGGTGGCCGTCATTGAT 60.125 61.111 0.00 0.00 46.80 2.57
336 347 4.494855 GCTGCGGAGTCACTGATTTATTTC 60.495 45.833 5.62 0.00 0.00 2.17
359 370 1.669115 CCTTGCCACTGTCCAGTCG 60.669 63.158 0.00 0.00 40.20 4.18
360 371 1.669115 CTTGCCACTGTCCAGTCGG 60.669 63.158 0.00 4.56 40.20 4.79
361 372 3.825160 TTGCCACTGTCCAGTCGGC 62.825 63.158 22.85 22.85 46.36 5.54
362 373 4.314440 GCCACTGTCCAGTCGGCA 62.314 66.667 23.85 0.00 45.91 5.69
435 447 6.383415 TGCCAAACGGTGAAATATTCTTTAC 58.617 36.000 0.00 0.00 0.00 2.01
446 458 6.371548 TGAAATATTCTTTACGCACTTGAGCT 59.628 34.615 0.00 0.00 0.00 4.09
509 525 1.876156 GCGGACATGAATTCAGGATCC 59.124 52.381 25.68 23.20 0.00 3.36
516 532 4.353191 ACATGAATTCAGGATCCTATGGCT 59.647 41.667 25.68 0.00 0.00 4.75
530 546 4.102996 TCCTATGGCTGCACAAATATCTGA 59.897 41.667 0.50 0.00 0.00 3.27
531 547 5.008331 CCTATGGCTGCACAAATATCTGAT 58.992 41.667 0.50 0.00 0.00 2.90
533 549 6.656270 CCTATGGCTGCACAAATATCTGATTA 59.344 38.462 0.50 0.00 0.00 1.75
580 596 9.965824 GAAGATCTGGTTGAATTTCAAGTAAAA 57.034 29.630 12.02 0.00 37.00 1.52
581 597 9.750125 AAGATCTGGTTGAATTTCAAGTAAAAC 57.250 29.630 12.02 0.51 37.00 2.43
598 614 2.131776 AACTTTTGGTCCGTTCACCA 57.868 45.000 0.00 0.00 45.25 4.17
604 620 2.060050 TGGTCCGTTCACCAAAATGT 57.940 45.000 0.00 0.00 43.88 2.71
610 637 6.088173 GGTCCGTTCACCAAAATGTAAATAC 58.912 40.000 0.00 0.00 36.32 1.89
616 643 7.322699 CGTTCACCAAAATGTAAATACTGTCAC 59.677 37.037 0.00 0.00 0.00 3.67
645 672 5.743636 ATTTGATTACAGTTGTGGCCAAT 57.256 34.783 7.24 0.00 32.11 3.16
725 797 0.599204 TTCTGACGAAACCTCACCGC 60.599 55.000 0.00 0.00 0.00 5.68
748 820 6.562640 CGCAAGTGAAAAACCATGATTCTTTG 60.563 38.462 0.00 4.70 0.00 2.77
768 840 3.831715 GGTGCTACCAAGAATCAACAC 57.168 47.619 1.01 0.00 38.42 3.32
780 852 6.128336 CCAAGAATCAACACTCTGAATCAGAC 60.128 42.308 9.18 0.00 35.39 3.51
811 884 1.529244 AACAGGACAAGCCACAGCC 60.529 57.895 0.00 0.00 41.25 4.85
905 2675 1.694133 CCCAAGGCCCACAAAGCAAA 61.694 55.000 0.00 0.00 0.00 3.68
928 2698 0.597072 TATTTTCCCGCGCCGTTTTT 59.403 45.000 0.00 0.00 0.00 1.94
958 2728 1.076332 CCTTGACGCCTTAACTTCCG 58.924 55.000 0.00 0.00 0.00 4.30
1072 2845 1.233285 CCTGTGCACAGACAAGCTCC 61.233 60.000 41.50 1.67 46.59 4.70
1077 2850 1.595109 CACAGACAAGCTCCGCACA 60.595 57.895 0.00 0.00 0.00 4.57
1116 2889 2.876645 GCGCTTCTGGTCGACGAG 60.877 66.667 20.34 20.34 0.00 4.18
1117 2890 2.202492 CGCTTCTGGTCGACGAGG 60.202 66.667 24.82 12.60 0.00 4.63
1118 2891 2.687805 CGCTTCTGGTCGACGAGGA 61.688 63.158 24.82 17.28 0.00 3.71
1119 2892 1.137825 GCTTCTGGTCGACGAGGAG 59.862 63.158 26.73 26.73 31.27 3.69
1120 2893 1.803943 CTTCTGGTCGACGAGGAGG 59.196 63.158 24.22 11.98 0.00 4.30
1121 2894 0.677098 CTTCTGGTCGACGAGGAGGA 60.677 60.000 24.22 5.65 0.00 3.71
1122 2895 0.677098 TTCTGGTCGACGAGGAGGAG 60.677 60.000 24.82 2.02 0.00 3.69
1125 2898 1.820481 GGTCGACGAGGAGGAGGAG 60.820 68.421 9.92 0.00 0.00 3.69
1133 2906 2.829458 GGAGGAGGAGGACGACGG 60.829 72.222 0.00 0.00 0.00 4.79
1134 2907 2.045143 GAGGAGGAGGACGACGGT 60.045 66.667 0.00 0.00 0.00 4.83
1136 2909 3.450115 GGAGGAGGACGACGGTGG 61.450 72.222 0.00 0.00 0.00 4.61
1445 3218 3.119495 ACGCTGTGCTCTGTTTTCTTTTT 60.119 39.130 0.00 0.00 0.00 1.94
1521 3297 3.760035 GGCGGCAAGTCGGAGAGA 61.760 66.667 3.07 0.00 36.95 3.10
1582 3358 2.740447 GTCGACAAAATTAAGGCGAGGT 59.260 45.455 11.55 0.00 0.00 3.85
1734 3510 1.081041 CGACGACGTGAACATCCCA 60.081 57.895 4.58 0.00 34.56 4.37
1827 3603 1.888736 GCTCTTAGGTCCGTCCGTT 59.111 57.895 0.00 0.00 41.99 4.44
1832 3608 1.271656 CTTAGGTCCGTCCGTTTGTCT 59.728 52.381 0.00 0.00 41.99 3.41
1839 3615 1.508632 CGTCCGTTTGTCTGTCCATT 58.491 50.000 0.00 0.00 0.00 3.16
1884 3675 7.751732 TGTGTTAATTGATTGATTCTTCTCGG 58.248 34.615 0.00 0.00 0.00 4.63
2345 4136 0.179032 TGAGGGCTTTTTGTCAGCGA 60.179 50.000 0.00 0.00 38.24 4.93
2401 4192 7.064134 TCACATACGAATTGTAGCAAGGTTTAG 59.936 37.037 0.00 0.00 36.25 1.85
2402 4193 6.315393 ACATACGAATTGTAGCAAGGTTTAGG 59.685 38.462 0.00 0.00 36.25 2.69
2403 4194 4.007659 ACGAATTGTAGCAAGGTTTAGGG 58.992 43.478 0.00 0.00 0.00 3.53
2404 4195 3.181500 CGAATTGTAGCAAGGTTTAGGGC 60.181 47.826 0.00 0.00 0.00 5.19
2405 4196 2.209690 TTGTAGCAAGGTTTAGGGCC 57.790 50.000 0.00 0.00 0.00 5.80
2406 4197 1.068948 TGTAGCAAGGTTTAGGGCCA 58.931 50.000 6.18 0.00 0.00 5.36
2407 4198 1.004277 TGTAGCAAGGTTTAGGGCCAG 59.996 52.381 6.18 0.00 0.00 4.85
2408 4199 1.004394 GTAGCAAGGTTTAGGGCCAGT 59.996 52.381 6.18 0.00 0.00 4.00
2409 4200 0.482887 AGCAAGGTTTAGGGCCAGTT 59.517 50.000 6.18 0.00 0.00 3.16
2410 4201 0.888619 GCAAGGTTTAGGGCCAGTTC 59.111 55.000 6.18 0.00 0.00 3.01
2411 4202 1.547901 GCAAGGTTTAGGGCCAGTTCT 60.548 52.381 6.18 0.00 0.00 3.01
2412 4203 2.876581 CAAGGTTTAGGGCCAGTTCTT 58.123 47.619 6.18 0.00 0.00 2.52
2413 4204 3.230976 CAAGGTTTAGGGCCAGTTCTTT 58.769 45.455 6.18 0.00 0.00 2.52
2414 4205 3.612795 AGGTTTAGGGCCAGTTCTTTT 57.387 42.857 6.18 0.00 0.00 2.27
2415 4206 3.230976 AGGTTTAGGGCCAGTTCTTTTG 58.769 45.455 6.18 0.00 0.00 2.44
2416 4207 2.299013 GGTTTAGGGCCAGTTCTTTTGG 59.701 50.000 6.18 0.00 38.78 3.28
2417 4208 2.299013 GTTTAGGGCCAGTTCTTTTGGG 59.701 50.000 6.18 0.00 36.19 4.12
2420 4211 3.758172 GCCAGTTCTTTTGGGCGA 58.242 55.556 0.00 0.00 36.58 5.54
2421 4212 2.267045 GCCAGTTCTTTTGGGCGAT 58.733 52.632 0.00 0.00 36.58 4.58
2422 4213 0.603065 GCCAGTTCTTTTGGGCGATT 59.397 50.000 0.00 0.00 36.58 3.34
2423 4214 1.402852 GCCAGTTCTTTTGGGCGATTC 60.403 52.381 0.00 0.00 36.58 2.52
2424 4215 2.162681 CCAGTTCTTTTGGGCGATTCT 58.837 47.619 0.00 0.00 31.87 2.40
2425 4216 2.558359 CCAGTTCTTTTGGGCGATTCTT 59.442 45.455 0.00 0.00 31.87 2.52
2426 4217 3.005791 CCAGTTCTTTTGGGCGATTCTTT 59.994 43.478 0.00 0.00 31.87 2.52
2427 4218 4.501400 CCAGTTCTTTTGGGCGATTCTTTT 60.501 41.667 0.00 0.00 31.87 2.27
2428 4219 5.278758 CCAGTTCTTTTGGGCGATTCTTTTA 60.279 40.000 0.00 0.00 31.87 1.52
2429 4220 5.858581 CAGTTCTTTTGGGCGATTCTTTTAG 59.141 40.000 0.00 0.00 0.00 1.85
2430 4221 5.768164 AGTTCTTTTGGGCGATTCTTTTAGA 59.232 36.000 0.00 0.00 0.00 2.10
2431 4222 6.264518 AGTTCTTTTGGGCGATTCTTTTAGAA 59.735 34.615 0.00 0.00 38.78 2.10
2432 4223 6.834168 TCTTTTGGGCGATTCTTTTAGAAT 57.166 33.333 1.73 1.73 46.84 2.40
2433 4224 7.227049 TCTTTTGGGCGATTCTTTTAGAATT 57.773 32.000 3.64 0.00 44.41 2.17
2434 4225 7.090173 TCTTTTGGGCGATTCTTTTAGAATTG 58.910 34.615 10.87 10.87 44.41 2.32
2439 4230 4.307443 CGATTCTTTTAGAATTGCCCCC 57.693 45.455 3.64 0.00 44.41 5.40
2547 4338 9.442047 GAAAATATATAGAGTGGTGATTCTGGG 57.558 37.037 0.00 0.00 0.00 4.45
2548 4339 8.742125 AAATATATAGAGTGGTGATTCTGGGA 57.258 34.615 0.00 0.00 0.00 4.37
2549 4340 7.969690 ATATATAGAGTGGTGATTCTGGGAG 57.030 40.000 0.00 0.00 0.00 4.30
2550 4341 2.630889 AGAGTGGTGATTCTGGGAGA 57.369 50.000 0.00 0.00 0.00 3.71
2551 4342 2.907892 AGAGTGGTGATTCTGGGAGAA 58.092 47.619 0.00 0.00 38.78 2.87
2552 4343 2.836981 AGAGTGGTGATTCTGGGAGAAG 59.163 50.000 0.00 0.00 37.69 2.85
2553 4344 1.280421 AGTGGTGATTCTGGGAGAAGC 59.720 52.381 0.00 0.00 40.77 3.86
2554 4345 1.280421 GTGGTGATTCTGGGAGAAGCT 59.720 52.381 3.49 0.00 40.96 3.74
2555 4346 1.280133 TGGTGATTCTGGGAGAAGCTG 59.720 52.381 3.49 0.00 40.96 4.24
2556 4347 1.407989 GGTGATTCTGGGAGAAGCTGG 60.408 57.143 3.49 0.00 40.96 4.85
2557 4348 1.556911 GTGATTCTGGGAGAAGCTGGA 59.443 52.381 3.49 0.00 40.96 3.86
2558 4349 1.836166 TGATTCTGGGAGAAGCTGGAG 59.164 52.381 3.49 0.00 40.96 3.86
2559 4350 2.114616 GATTCTGGGAGAAGCTGGAGA 58.885 52.381 0.00 0.00 37.62 3.71
2560 4351 2.030027 TTCTGGGAGAAGCTGGAGAA 57.970 50.000 0.00 0.00 29.50 2.87
2561 4352 1.566211 TCTGGGAGAAGCTGGAGAAG 58.434 55.000 0.00 0.00 0.00 2.85
2562 4353 1.077828 TCTGGGAGAAGCTGGAGAAGA 59.922 52.381 0.00 0.00 0.00 2.87
2563 4354 1.481772 CTGGGAGAAGCTGGAGAAGAG 59.518 57.143 0.00 0.00 0.00 2.85
2564 4355 0.829990 GGGAGAAGCTGGAGAAGAGG 59.170 60.000 0.00 0.00 0.00 3.69
2565 4356 1.621072 GGGAGAAGCTGGAGAAGAGGA 60.621 57.143 0.00 0.00 0.00 3.71
2566 4357 1.480545 GGAGAAGCTGGAGAAGAGGAC 59.519 57.143 0.00 0.00 0.00 3.85
2567 4358 1.134175 GAGAAGCTGGAGAAGAGGACG 59.866 57.143 0.00 0.00 0.00 4.79
2568 4359 1.178276 GAAGCTGGAGAAGAGGACGA 58.822 55.000 0.00 0.00 0.00 4.20
2569 4360 1.754226 GAAGCTGGAGAAGAGGACGAT 59.246 52.381 0.00 0.00 0.00 3.73
2570 4361 1.859302 AGCTGGAGAAGAGGACGATT 58.141 50.000 0.00 0.00 0.00 3.34
2571 4362 1.754226 AGCTGGAGAAGAGGACGATTC 59.246 52.381 0.00 0.00 0.00 2.52
2572 4363 1.754226 GCTGGAGAAGAGGACGATTCT 59.246 52.381 0.00 0.00 38.46 2.40
2573 4364 2.481104 GCTGGAGAAGAGGACGATTCTG 60.481 54.545 0.00 0.00 35.93 3.02
2574 4365 2.100584 CTGGAGAAGAGGACGATTCTGG 59.899 54.545 0.00 0.00 35.93 3.86
2575 4366 1.410882 GGAGAAGAGGACGATTCTGGG 59.589 57.143 0.00 0.00 35.93 4.45
2576 4367 2.379972 GAGAAGAGGACGATTCTGGGA 58.620 52.381 0.00 0.00 35.93 4.37
2577 4368 2.360801 GAGAAGAGGACGATTCTGGGAG 59.639 54.545 0.00 0.00 35.93 4.30
2578 4369 2.024846 AGAAGAGGACGATTCTGGGAGA 60.025 50.000 0.00 0.00 34.52 3.71
2579 4370 2.534042 AGAGGACGATTCTGGGAGAA 57.466 50.000 0.00 0.00 38.78 2.87
2580 4371 3.039252 AGAGGACGATTCTGGGAGAAT 57.961 47.619 0.00 0.00 46.84 2.40
2593 4384 3.748868 GGGAGAATCGCTGAAAAGAAC 57.251 47.619 0.00 0.00 45.72 3.01
2594 4385 3.339141 GGGAGAATCGCTGAAAAGAACT 58.661 45.455 0.00 0.00 45.72 3.01
2595 4386 3.126000 GGGAGAATCGCTGAAAAGAACTG 59.874 47.826 0.00 0.00 45.72 3.16
2596 4387 3.126000 GGAGAATCGCTGAAAAGAACTGG 59.874 47.826 0.00 0.00 34.37 4.00
2597 4388 2.485814 AGAATCGCTGAAAAGAACTGGC 59.514 45.455 0.00 0.00 0.00 4.85
2598 4389 1.168714 ATCGCTGAAAAGAACTGGCC 58.831 50.000 0.00 0.00 0.00 5.36
2599 4390 0.889186 TCGCTGAAAAGAACTGGCCC 60.889 55.000 0.00 0.00 0.00 5.80
2600 4391 0.890996 CGCTGAAAAGAACTGGCCCT 60.891 55.000 0.00 0.00 0.00 5.19
2601 4392 1.332195 GCTGAAAAGAACTGGCCCTT 58.668 50.000 0.00 0.00 0.00 3.95
2602 4393 2.514803 GCTGAAAAGAACTGGCCCTTA 58.485 47.619 0.00 0.00 0.00 2.69
2603 4394 2.489722 GCTGAAAAGAACTGGCCCTTAG 59.510 50.000 0.00 0.00 0.00 2.18
2628 4419 1.068741 GTTCATAGGATTCTCGCCGGT 59.931 52.381 1.90 0.00 0.00 5.28
2678 4471 3.692593 GTCTCACTCTCACCTACTCCTTC 59.307 52.174 0.00 0.00 0.00 3.46
2694 4487 1.299541 CTTCGCCACACACTTCTGTT 58.700 50.000 0.00 0.00 0.00 3.16
2705 4498 2.092646 ACACTTCTGTTAGGGCAACACA 60.093 45.455 0.00 0.00 42.29 3.72
2742 4535 8.948631 TTTAAAGATAGCTCAAGTATGACCTG 57.051 34.615 0.00 0.00 0.00 4.00
2750 4543 2.823747 TCAAGTATGACCTGCTACACGT 59.176 45.455 0.00 0.00 0.00 4.49
2753 4546 0.736636 TATGACCTGCTACACGTCGG 59.263 55.000 0.00 0.00 0.00 4.79
2779 4572 2.669434 TGCGTCAACTAATTAACGAGCC 59.331 45.455 10.75 0.00 37.31 4.70
2780 4573 2.928116 GCGTCAACTAATTAACGAGCCT 59.072 45.455 10.75 0.00 37.31 4.58
2796 4589 1.990060 CCTTCCTTCGGGAGCCTCA 60.990 63.158 0.00 0.00 45.95 3.86
2804 4599 0.690192 TCGGGAGCCTCACAAATCAA 59.310 50.000 0.00 0.00 0.00 2.57
2849 4644 1.161843 TCGTCATGTGTCGTGCTCTA 58.838 50.000 0.00 0.00 0.00 2.43
2938 4742 0.595567 GGGGTTTTCGACGTTTTGGC 60.596 55.000 0.00 0.00 0.00 4.52
2955 4759 1.674651 GCTTTCCACCGGTCTTCCC 60.675 63.158 2.59 0.00 0.00 3.97
2958 4762 1.626825 CTTTCCACCGGTCTTCCCTAA 59.373 52.381 2.59 0.00 0.00 2.69
2964 4768 3.483421 CACCGGTCTTCCCTAACTTTTT 58.517 45.455 2.59 0.00 0.00 1.94
3053 4869 2.634777 CGGTTTTGCTTCCGCGAA 59.365 55.556 8.23 0.00 40.28 4.70
3070 4886 1.451651 CGAAATGCACGGTTTTGCTTC 59.548 47.619 0.00 0.00 43.41 3.86
3083 4900 2.148916 TTGCTTCACGAGAATCACGT 57.851 45.000 0.00 0.00 44.83 4.49
3179 4999 3.460103 GAGAGGTACGGTTGTGTTTTCA 58.540 45.455 0.00 0.00 0.00 2.69
3319 5147 4.323477 CGTGCCTCCCGGAAACCA 62.323 66.667 0.73 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.748005 CCCCATTTGCAGAGGTACCG 60.748 60.000 6.18 0.00 0.00 4.02
45 46 1.077787 CGCCCCATTTGCAGAGGTA 60.078 57.895 0.00 0.00 0.00 3.08
48 49 2.420568 ATGCGCCCCATTTGCAGAG 61.421 57.895 4.18 0.00 42.65 3.35
61 62 2.050533 TGGTTTCGTTGCATGCGC 60.051 55.556 14.09 0.00 39.24 6.09
313 324 2.010145 TAAATCAGTGACTCCGCAGC 57.990 50.000 0.00 0.00 0.00 5.25
314 325 4.631377 TGAAATAAATCAGTGACTCCGCAG 59.369 41.667 0.00 0.00 0.00 5.18
336 347 0.250858 TGGACAGTGGCAAGGTGATG 60.251 55.000 0.00 0.00 0.00 3.07
359 370 1.961793 TTTACGGTCATATGCCTGCC 58.038 50.000 12.45 5.40 0.00 4.85
360 371 3.304659 CCATTTTACGGTCATATGCCTGC 60.305 47.826 12.45 0.00 0.00 4.85
361 372 3.882888 ACCATTTTACGGTCATATGCCTG 59.117 43.478 12.45 3.13 27.30 4.85
362 373 3.882888 CACCATTTTACGGTCATATGCCT 59.117 43.478 12.45 4.81 33.25 4.75
435 447 1.326852 CTGATGCTTAGCTCAAGTGCG 59.673 52.381 5.60 0.00 36.55 5.34
446 458 2.872245 GTCCGCTATTTGCTGATGCTTA 59.128 45.455 0.00 0.00 37.26 3.09
473 485 6.759356 TCATGTCCGCTATTATTCGAAGAAAA 59.241 34.615 9.57 1.12 45.90 2.29
475 487 5.838529 TCATGTCCGCTATTATTCGAAGAA 58.161 37.500 7.79 7.79 45.90 2.52
509 525 6.570672 AATCAGATATTTGTGCAGCCATAG 57.429 37.500 0.00 0.00 0.00 2.23
554 570 9.965824 TTTTACTTGAAATTCAACCAGATCTTC 57.034 29.630 4.03 0.00 32.21 2.87
560 576 9.971744 CAAAAGTTTTACTTGAAATTCAACCAG 57.028 29.630 4.03 0.00 38.66 4.00
580 596 3.886324 TGGTGAACGGACCAAAAGT 57.114 47.368 1.05 0.00 43.31 2.66
616 643 9.301153 GGCCACAACTGTAATCAAATAAATTAG 57.699 33.333 0.00 0.00 0.00 1.73
725 797 7.181143 CCAAAGAATCATGGTTTTTCACTTG 57.819 36.000 0.00 0.00 31.84 3.16
748 820 3.412386 AGTGTTGATTCTTGGTAGCACC 58.588 45.455 0.00 0.00 39.22 5.01
768 840 6.483307 TGTTTGTACCAAAGTCTGATTCAGAG 59.517 38.462 16.62 7.38 41.46 3.35
780 852 4.974368 TGTCCTGTTGTTTGTACCAAAG 57.026 40.909 0.00 0.00 0.00 2.77
811 884 4.811555 TTGACTGTGTTGAATTTCCGAG 57.188 40.909 0.00 0.00 0.00 4.63
905 2675 0.812549 ACGGCGCGGGAAAATATTTT 59.187 45.000 19.75 13.24 0.00 1.82
928 2698 1.365699 GCGTCAAGGCGAGGAATTTA 58.634 50.000 0.00 0.00 0.00 1.40
958 2728 3.813166 TCGATTTTTGAGTTGGAGGTGTC 59.187 43.478 0.00 0.00 0.00 3.67
1104 2877 1.078356 CTCCTCCTCGTCGACCAGA 60.078 63.158 12.11 2.26 0.00 3.86
1116 2889 2.829458 CCGTCGTCCTCCTCCTCC 60.829 72.222 0.00 0.00 0.00 4.30
1117 2890 2.045143 ACCGTCGTCCTCCTCCTC 60.045 66.667 0.00 0.00 0.00 3.71
1118 2891 2.361357 CACCGTCGTCCTCCTCCT 60.361 66.667 0.00 0.00 0.00 3.69
1119 2892 3.450115 CCACCGTCGTCCTCCTCC 61.450 72.222 0.00 0.00 0.00 4.30
1120 2893 4.131088 GCCACCGTCGTCCTCCTC 62.131 72.222 0.00 0.00 0.00 3.71
1151 2924 2.672307 AGAAGGACGACGAGCCGT 60.672 61.111 0.00 0.21 46.43 5.68
1314 3087 2.561976 CGAAGCAGTCGTGAAAGAAC 57.438 50.000 1.91 0.00 45.09 3.01
1582 3358 2.032528 CGGGCACTGCTTCTCCAA 59.967 61.111 0.00 0.00 0.00 3.53
1749 3525 2.517450 GCTGAGCGTCATGGCGTAC 61.517 63.158 22.33 15.46 38.18 3.67
1827 3603 1.003580 GGAGCTCCAATGGACAGACAA 59.996 52.381 28.43 0.00 35.64 3.18
1832 3608 1.993653 CAGGGAGCTCCAATGGACA 59.006 57.895 33.29 0.00 38.24 4.02
1839 3615 2.897271 TAAATTTGCAGGGAGCTCCA 57.103 45.000 33.29 13.04 45.94 3.86
1882 3673 4.124351 TACAAGCGGGTCGAGCCG 62.124 66.667 43.01 43.01 38.44 5.52
1884 3675 2.202756 CCTACAAGCGGGTCGAGC 60.203 66.667 5.93 5.93 0.00 5.03
2280 4071 3.866582 CTGATCCGGACCTGCCCC 61.867 72.222 6.12 0.00 0.00 5.80
2345 4136 4.135306 TGAGACCGAGTTAGAATCGCTAT 58.865 43.478 0.00 0.00 38.84 2.97
2349 4140 4.822036 ATCTGAGACCGAGTTAGAATCG 57.178 45.455 0.00 0.00 39.86 3.34
2401 4192 2.931068 CGCCCAAAAGAACTGGCCC 61.931 63.158 0.00 0.00 40.87 5.80
2402 4193 1.250840 ATCGCCCAAAAGAACTGGCC 61.251 55.000 0.00 0.00 40.87 5.36
2403 4194 0.603065 AATCGCCCAAAAGAACTGGC 59.397 50.000 0.00 0.00 40.54 4.85
2404 4195 2.162681 AGAATCGCCCAAAAGAACTGG 58.837 47.619 0.00 0.00 0.00 4.00
2405 4196 3.923017 AAGAATCGCCCAAAAGAACTG 57.077 42.857 0.00 0.00 0.00 3.16
2406 4197 4.937201 AAAAGAATCGCCCAAAAGAACT 57.063 36.364 0.00 0.00 0.00 3.01
2407 4198 6.009115 TCTAAAAGAATCGCCCAAAAGAAC 57.991 37.500 0.00 0.00 0.00 3.01
2408 4199 6.642707 TTCTAAAAGAATCGCCCAAAAGAA 57.357 33.333 0.00 0.00 0.00 2.52
2409 4200 6.834168 ATTCTAAAAGAATCGCCCAAAAGA 57.166 33.333 0.00 0.00 40.75 2.52
2410 4201 6.183360 GCAATTCTAAAAGAATCGCCCAAAAG 60.183 38.462 2.79 0.00 43.67 2.27
2411 4202 5.637387 GCAATTCTAAAAGAATCGCCCAAAA 59.363 36.000 2.79 0.00 43.67 2.44
2412 4203 5.167845 GCAATTCTAAAAGAATCGCCCAAA 58.832 37.500 2.79 0.00 43.67 3.28
2413 4204 4.743493 GCAATTCTAAAAGAATCGCCCAA 58.257 39.130 2.79 0.00 43.67 4.12
2414 4205 4.370364 GCAATTCTAAAAGAATCGCCCA 57.630 40.909 2.79 0.00 43.67 5.36
2417 4208 3.490933 GGGGGCAATTCTAAAAGAATCGC 60.491 47.826 4.37 4.37 43.67 4.58
2418 4209 4.307443 GGGGGCAATTCTAAAAGAATCG 57.693 45.455 2.79 0.00 43.67 3.34
2521 4312 9.442047 CCCAGAATCACCACTCTATATATTTTC 57.558 37.037 0.00 0.00 0.00 2.29
2522 4313 9.170890 TCCCAGAATCACCACTCTATATATTTT 57.829 33.333 0.00 0.00 0.00 1.82
2523 4314 8.742125 TCCCAGAATCACCACTCTATATATTT 57.258 34.615 0.00 0.00 0.00 1.40
2524 4315 8.180165 TCTCCCAGAATCACCACTCTATATATT 58.820 37.037 0.00 0.00 0.00 1.28
2525 4316 7.713518 TCTCCCAGAATCACCACTCTATATAT 58.286 38.462 0.00 0.00 0.00 0.86
2526 4317 7.103745 TCTCCCAGAATCACCACTCTATATA 57.896 40.000 0.00 0.00 0.00 0.86
2527 4318 5.970289 TCTCCCAGAATCACCACTCTATAT 58.030 41.667 0.00 0.00 0.00 0.86
2528 4319 5.403558 TCTCCCAGAATCACCACTCTATA 57.596 43.478 0.00 0.00 0.00 1.31
2529 4320 4.271807 TCTCCCAGAATCACCACTCTAT 57.728 45.455 0.00 0.00 0.00 1.98
2530 4321 3.757947 TCTCCCAGAATCACCACTCTA 57.242 47.619 0.00 0.00 0.00 2.43
2531 4322 2.630889 TCTCCCAGAATCACCACTCT 57.369 50.000 0.00 0.00 0.00 3.24
2532 4323 2.679349 GCTTCTCCCAGAATCACCACTC 60.679 54.545 0.00 0.00 33.13 3.51
2533 4324 1.280421 GCTTCTCCCAGAATCACCACT 59.720 52.381 0.00 0.00 33.13 4.00
2534 4325 1.280421 AGCTTCTCCCAGAATCACCAC 59.720 52.381 0.00 0.00 33.13 4.16
2535 4326 1.280133 CAGCTTCTCCCAGAATCACCA 59.720 52.381 0.00 0.00 33.13 4.17
2536 4327 1.407989 CCAGCTTCTCCCAGAATCACC 60.408 57.143 0.00 0.00 33.13 4.02
2537 4328 1.556911 TCCAGCTTCTCCCAGAATCAC 59.443 52.381 0.00 0.00 33.13 3.06
2538 4329 1.836166 CTCCAGCTTCTCCCAGAATCA 59.164 52.381 0.00 0.00 33.13 2.57
2539 4330 2.114616 TCTCCAGCTTCTCCCAGAATC 58.885 52.381 0.00 0.00 33.13 2.52
2540 4331 2.260639 TCTCCAGCTTCTCCCAGAAT 57.739 50.000 0.00 0.00 33.13 2.40
2541 4332 1.905215 CTTCTCCAGCTTCTCCCAGAA 59.095 52.381 0.00 0.00 32.50 3.02
2542 4333 1.077828 TCTTCTCCAGCTTCTCCCAGA 59.922 52.381 0.00 0.00 0.00 3.86
2543 4334 1.481772 CTCTTCTCCAGCTTCTCCCAG 59.518 57.143 0.00 0.00 0.00 4.45
2544 4335 1.566211 CTCTTCTCCAGCTTCTCCCA 58.434 55.000 0.00 0.00 0.00 4.37
2545 4336 0.829990 CCTCTTCTCCAGCTTCTCCC 59.170 60.000 0.00 0.00 0.00 4.30
2546 4337 1.480545 GTCCTCTTCTCCAGCTTCTCC 59.519 57.143 0.00 0.00 0.00 3.71
2547 4338 1.134175 CGTCCTCTTCTCCAGCTTCTC 59.866 57.143 0.00 0.00 0.00 2.87
2548 4339 1.181786 CGTCCTCTTCTCCAGCTTCT 58.818 55.000 0.00 0.00 0.00 2.85
2549 4340 1.178276 TCGTCCTCTTCTCCAGCTTC 58.822 55.000 0.00 0.00 0.00 3.86
2550 4341 1.859302 ATCGTCCTCTTCTCCAGCTT 58.141 50.000 0.00 0.00 0.00 3.74
2551 4342 1.754226 GAATCGTCCTCTTCTCCAGCT 59.246 52.381 0.00 0.00 0.00 4.24
2552 4343 1.754226 AGAATCGTCCTCTTCTCCAGC 59.246 52.381 0.00 0.00 0.00 4.85
2553 4344 2.100584 CCAGAATCGTCCTCTTCTCCAG 59.899 54.545 0.00 0.00 29.34 3.86
2554 4345 2.103373 CCAGAATCGTCCTCTTCTCCA 58.897 52.381 0.00 0.00 29.34 3.86
2555 4346 1.410882 CCCAGAATCGTCCTCTTCTCC 59.589 57.143 0.00 0.00 29.34 3.71
2556 4347 2.360801 CTCCCAGAATCGTCCTCTTCTC 59.639 54.545 0.00 0.00 29.34 2.87
2557 4348 2.024846 TCTCCCAGAATCGTCCTCTTCT 60.025 50.000 0.00 0.00 31.97 2.85
2558 4349 2.379972 TCTCCCAGAATCGTCCTCTTC 58.620 52.381 0.00 0.00 0.00 2.87
2559 4350 2.534042 TCTCCCAGAATCGTCCTCTT 57.466 50.000 0.00 0.00 0.00 2.85
2560 4351 2.534042 TTCTCCCAGAATCGTCCTCT 57.466 50.000 0.00 0.00 0.00 3.69
2568 4359 3.634397 TTTCAGCGATTCTCCCAGAAT 57.366 42.857 0.00 0.00 46.84 2.40
2569 4360 3.007940 TCTTTTCAGCGATTCTCCCAGAA 59.992 43.478 0.00 0.00 38.78 3.02
2570 4361 2.567169 TCTTTTCAGCGATTCTCCCAGA 59.433 45.455 0.00 0.00 0.00 3.86
2571 4362 2.977914 TCTTTTCAGCGATTCTCCCAG 58.022 47.619 0.00 0.00 0.00 4.45
2572 4363 3.074412 GTTCTTTTCAGCGATTCTCCCA 58.926 45.455 0.00 0.00 0.00 4.37
2573 4364 3.126000 CAGTTCTTTTCAGCGATTCTCCC 59.874 47.826 0.00 0.00 0.00 4.30
2574 4365 3.126000 CCAGTTCTTTTCAGCGATTCTCC 59.874 47.826 0.00 0.00 0.00 3.71
2575 4366 3.425492 GCCAGTTCTTTTCAGCGATTCTC 60.425 47.826 0.00 0.00 0.00 2.87
2576 4367 2.485814 GCCAGTTCTTTTCAGCGATTCT 59.514 45.455 0.00 0.00 0.00 2.40
2577 4368 2.414691 GGCCAGTTCTTTTCAGCGATTC 60.415 50.000 0.00 0.00 0.00 2.52
2578 4369 1.541588 GGCCAGTTCTTTTCAGCGATT 59.458 47.619 0.00 0.00 0.00 3.34
2579 4370 1.168714 GGCCAGTTCTTTTCAGCGAT 58.831 50.000 0.00 0.00 0.00 4.58
2580 4371 0.889186 GGGCCAGTTCTTTTCAGCGA 60.889 55.000 4.39 0.00 0.00 4.93
2581 4372 0.890996 AGGGCCAGTTCTTTTCAGCG 60.891 55.000 6.18 0.00 0.00 5.18
2582 4373 1.332195 AAGGGCCAGTTCTTTTCAGC 58.668 50.000 6.18 0.00 0.00 4.26
2583 4374 3.084786 CCTAAGGGCCAGTTCTTTTCAG 58.915 50.000 6.18 0.00 0.00 3.02
2584 4375 2.225017 CCCTAAGGGCCAGTTCTTTTCA 60.225 50.000 6.18 0.00 35.35 2.69
2585 4376 2.447443 CCCTAAGGGCCAGTTCTTTTC 58.553 52.381 6.18 0.00 35.35 2.29
2586 4377 2.604912 CCCTAAGGGCCAGTTCTTTT 57.395 50.000 6.18 0.00 35.35 2.27
2598 4389 4.660771 AGAATCCTATGAACCACCCTAAGG 59.339 45.833 0.00 0.00 40.04 2.69
2599 4390 5.509840 CGAGAATCCTATGAACCACCCTAAG 60.510 48.000 0.00 0.00 0.00 2.18
2600 4391 4.344102 CGAGAATCCTATGAACCACCCTAA 59.656 45.833 0.00 0.00 0.00 2.69
2601 4392 3.895656 CGAGAATCCTATGAACCACCCTA 59.104 47.826 0.00 0.00 0.00 3.53
2602 4393 2.700897 CGAGAATCCTATGAACCACCCT 59.299 50.000 0.00 0.00 0.00 4.34
2603 4394 2.807108 GCGAGAATCCTATGAACCACCC 60.807 54.545 0.00 0.00 0.00 4.61
2678 4471 1.148310 CCTAACAGAAGTGTGTGGCG 58.852 55.000 0.00 0.00 36.84 5.69
2816 4611 0.673333 TGACGAATGATTGGCAGCGT 60.673 50.000 0.00 0.00 41.94 5.07
2821 4616 2.537529 CGACACATGACGAATGATTGGC 60.538 50.000 0.00 0.99 38.72 4.52
2822 4617 2.672874 ACGACACATGACGAATGATTGG 59.327 45.455 10.57 0.00 38.72 3.16
2849 4644 2.474410 AAAATTCGAAGGGAGCGTCT 57.526 45.000 3.35 0.00 0.00 4.18
2922 4726 2.532723 GGAAAGCCAAAACGTCGAAAAC 59.467 45.455 0.00 0.00 0.00 2.43
2938 4742 1.272807 TAGGGAAGACCGGTGGAAAG 58.727 55.000 14.63 0.00 46.96 2.62
3070 4886 0.710567 GCACAGACGTGATTCTCGTG 59.289 55.000 17.49 7.65 46.80 4.35
3238 5066 1.494824 AAACCGTGACTCTTGCGTAC 58.505 50.000 0.00 0.00 0.00 3.67
3240 5068 0.655733 CAAAACCGTGACTCTTGCGT 59.344 50.000 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.