Multiple sequence alignment - TraesCS3B01G322000

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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 TraesCS3B01G322000 chr3B 100.000 2828 0 0 1 2828 521475243 521478070 0.000000e+00 5223.0
1 TraesCS3B01G322000 chr3B 95.983 1394 37 7 525 1915 521609207 521610584 0.000000e+00 2246.0
2 TraesCS3B01G322000 chr3B 95.445 1361 42 4 711 2058 521687801 521689154 0.000000e+00 2152.0
3 TraesCS3B01G322000 chr3B 94.466 1283 55 13 605 1877 521216745 521218021 0.000000e+00 1962.0
4 TraesCS3B01G322000 chr3B 94.987 1157 43 10 1678 2828 521413619 521414766 0.000000e+00 1801.0
5 TraesCS3B01G322000 chr3B 95.660 1083 37 6 612 1688 521404928 521406006 0.000000e+00 1731.0
6 TraesCS3B01G322000 chr3B 95.604 182 7 1 1 182 521608480 521608660 9.910000e-75 291.0
7 TraesCS3B01G322000 chr3B 92.347 196 15 0 525 720 521684897 521685092 2.150000e-71 279.0
8 TraesCS3B01G322000 chr3B 95.652 138 3 1 2041 2178 521610758 521610892 4.740000e-53 219.0
9 TraesCS3B01G322000 chr3B 96.970 99 1 2 171 269 521608696 521608792 6.270000e-37 165.0
10 TraesCS3B01G322000 chr3B 97.297 74 2 0 1928 2001 521610681 521610754 2.960000e-25 126.0
11 TraesCS3B01G322000 chr3B 97.297 74 2 0 1 74 814892293 814892366 2.960000e-25 126.0
12 TraesCS3B01G322000 chr3B 97.101 69 2 0 248 316 521684839 521684907 1.780000e-22 117.0
13 TraesCS3B01G322000 chr3B 90.476 84 6 1 525 606 521216385 521216468 2.980000e-20 110.0
14 TraesCS3B01G322000 chr3B 100.000 57 0 0 260 316 521609161 521609217 3.850000e-19 106.0
15 TraesCS3B01G322000 chr3B 79.762 168 13 4 1968 2122 521218025 521218184 4.980000e-18 102.0
16 TraesCS3B01G322000 chr3B 92.593 54 2 2 171 224 528520682 528520733 3.020000e-10 76.8
17 TraesCS3B01G322000 chr3D 93.148 1620 81 15 574 2174 396204740 396206348 0.000000e+00 2350.0
18 TraesCS3B01G322000 chr3D 92.018 1591 74 11 609 2178 395836975 395838533 0.000000e+00 2185.0
19 TraesCS3B01G322000 chr3D 91.981 1509 62 20 526 2018 395832518 395833983 0.000000e+00 2061.0
20 TraesCS3B01G322000 chr3D 87.313 134 8 5 2046 2178 395834698 395834823 8.170000e-31 145.0
21 TraesCS3B01G322000 chr3A 89.859 1637 94 42 525 2129 515860744 515862340 0.000000e+00 2037.0
22 TraesCS3B01G322000 chr3A 88.085 235 22 6 309 540 522180524 522180755 9.980000e-70 274.0
23 TraesCS3B01G322000 chr2D 90.635 598 52 4 2231 2826 462258946 462258351 0.000000e+00 791.0
24 TraesCS3B01G322000 chr2D 97.561 41 1 0 181 221 26539018 26539058 1.410000e-08 71.3
25 TraesCS3B01G322000 chr7D 89.782 597 54 6 2233 2826 624916422 624917014 0.000000e+00 758.0
26 TraesCS3B01G322000 chr7D 88.226 603 63 6 2231 2826 127678428 127677827 0.000000e+00 713.0
27 TraesCS3B01G322000 chr7D 96.203 79 2 1 1 79 614172389 614172312 8.220000e-26 128.0
28 TraesCS3B01G322000 chr7D 96.053 76 3 0 1 76 83378388 83378313 1.060000e-24 124.0
29 TraesCS3B01G322000 chr2B 88.796 598 59 7 2231 2826 2969562 2968971 0.000000e+00 726.0
30 TraesCS3B01G322000 chr2B 87.940 597 66 6 2231 2824 743203997 743204590 0.000000e+00 699.0
31 TraesCS3B01G322000 chr2B 88.496 226 20 6 303 525 27548150 27547928 4.640000e-68 268.0
32 TraesCS3B01G322000 chr2B 97.260 73 2 0 1 73 82717093 82717165 1.060000e-24 124.0
33 TraesCS3B01G322000 chr2B 86.916 107 14 0 74 180 3413765 3413871 1.380000e-23 121.0
34 TraesCS3B01G322000 chr2B 84.112 107 17 0 74 180 3480360 3480254 1.390000e-18 104.0
35 TraesCS3B01G322000 chr2B 97.674 43 1 0 181 223 140537400 140537358 1.090000e-09 75.0
36 TraesCS3B01G322000 chr2B 100.000 37 0 0 190 226 1752048 1752084 5.060000e-08 69.4
37 TraesCS3B01G322000 chr2B 100.000 37 0 0 190 226 1767212 1767248 5.060000e-08 69.4
38 TraesCS3B01G322000 chr6D 88.538 602 63 4 2231 2826 438696578 438695977 0.000000e+00 725.0
39 TraesCS3B01G322000 chr5D 88.519 601 60 7 2231 2826 247755474 247754878 0.000000e+00 719.0
40 TraesCS3B01G322000 chr7A 88.067 595 65 4 2237 2826 299305004 299305597 0.000000e+00 701.0
41 TraesCS3B01G322000 chr7A 97.333 75 2 0 1 75 225637725 225637799 8.220000e-26 128.0
42 TraesCS3B01G322000 chr7A 85.981 107 4 4 74 180 558105513 558105608 1.390000e-18 104.0
43 TraesCS3B01G322000 chr7A 94.340 53 1 2 171 223 558105646 558105696 2.340000e-11 80.5
44 TraesCS3B01G322000 chr4B 91.038 212 17 2 315 525 328323926 328323716 4.610000e-73 285.0
45 TraesCS3B01G322000 chr4B 91.080 213 15 3 316 527 462779382 462779173 4.610000e-73 285.0
46 TraesCS3B01G322000 chr6B 90.566 212 18 2 316 526 636742732 636742942 2.150000e-71 279.0
47 TraesCS3B01G322000 chr6B 89.815 216 19 3 316 530 720142062 720142275 9.980000e-70 274.0
48 TraesCS3B01G322000 chrUn 90.141 213 20 1 315 526 171112602 171112390 2.780000e-70 276.0
49 TraesCS3B01G322000 chr5B 90.476 210 18 2 313 520 686047993 686048202 2.780000e-70 276.0
50 TraesCS3B01G322000 chr1B 90.233 215 13 5 313 525 646178069 646177861 9.980000e-70 274.0
51 TraesCS3B01G322000 chr2A 97.297 74 2 0 1 74 61475895 61475968 2.960000e-25 126.0
52 TraesCS3B01G322000 chr1D 93.750 80 4 1 1 79 445221299 445221378 4.950000e-23 119.0
53 TraesCS3B01G322000 chr5A 89.130 92 8 2 1 90 552058444 552058353 2.300000e-21 113.0
54 TraesCS3B01G322000 chr5A 94.118 51 1 2 171 221 87883661 87883709 3.020000e-10 76.8
55 TraesCS3B01G322000 chr7B 85.047 107 5 5 74 180 734907140 734907045 6.450000e-17 99.0
56 TraesCS3B01G322000 chr7B 100.000 43 0 0 181 223 734906999 734906957 2.340000e-11 80.5


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 TraesCS3B01G322000 chr3B 521475243 521478070 2827 False 5223.000000 5223 100.000000 1 2828 1 chr3B.!!$F3 2827
1 TraesCS3B01G322000 chr3B 521413619 521414766 1147 False 1801.000000 1801 94.987000 1678 2828 1 chr3B.!!$F2 1150
2 TraesCS3B01G322000 chr3B 521404928 521406006 1078 False 1731.000000 1731 95.660000 612 1688 1 chr3B.!!$F1 1076
3 TraesCS3B01G322000 chr3B 521684839 521689154 4315 False 849.333333 2152 94.964333 248 2058 3 chr3B.!!$F8 1810
4 TraesCS3B01G322000 chr3B 521216385 521218184 1799 False 724.666667 1962 88.234667 525 2122 3 chr3B.!!$F6 1597
5 TraesCS3B01G322000 chr3B 521608480 521610892 2412 False 525.500000 2246 96.917667 1 2178 6 chr3B.!!$F7 2177
6 TraesCS3B01G322000 chr3D 396204740 396206348 1608 False 2350.000000 2350 93.148000 574 2174 1 chr3D.!!$F1 1600
7 TraesCS3B01G322000 chr3D 395832518 395838533 6015 False 1463.666667 2185 90.437333 526 2178 3 chr3D.!!$F2 1652
8 TraesCS3B01G322000 chr3A 515860744 515862340 1596 False 2037.000000 2037 89.859000 525 2129 1 chr3A.!!$F1 1604
9 TraesCS3B01G322000 chr2D 462258351 462258946 595 True 791.000000 791 90.635000 2231 2826 1 chr2D.!!$R1 595
10 TraesCS3B01G322000 chr7D 624916422 624917014 592 False 758.000000 758 89.782000 2233 2826 1 chr7D.!!$F1 593
11 TraesCS3B01G322000 chr7D 127677827 127678428 601 True 713.000000 713 88.226000 2231 2826 1 chr7D.!!$R2 595
12 TraesCS3B01G322000 chr2B 2968971 2969562 591 True 726.000000 726 88.796000 2231 2826 1 chr2B.!!$R1 595
13 TraesCS3B01G322000 chr2B 743203997 743204590 593 False 699.000000 699 87.940000 2231 2824 1 chr2B.!!$F5 593
14 TraesCS3B01G322000 chr6D 438695977 438696578 601 True 725.000000 725 88.538000 2231 2826 1 chr6D.!!$R1 595
15 TraesCS3B01G322000 chr5D 247754878 247755474 596 True 719.000000 719 88.519000 2231 2826 1 chr5D.!!$R1 595
16 TraesCS3B01G322000 chr7A 299305004 299305597 593 False 701.000000 701 88.067000 2237 2826 1 chr7A.!!$F2 589

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
438 862 0.041982 TGATTTTAAGGGGGTGGGGC 59.958 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 5382 1.611592 GGACGCCAAACTCGTACGTG 61.612 60.0 16.05 15.64 40.59 4.49 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
54 55 7.394016 TCATATAAGGTGCATATACAACCAGG 58.606 38.462 0.00 0.00 0.00 4.45
62 63 4.704540 TGCATATACAACCAGGAACCAAAG 59.295 41.667 0.00 0.00 0.00 2.77
107 108 3.502211 AGGAAAAACCGAACTACATGCAG 59.498 43.478 0.00 0.00 44.74 4.41
108 109 3.365969 GGAAAAACCGAACTACATGCAGG 60.366 47.826 0.00 0.00 0.00 4.85
126 127 4.079253 GCAGGTAAAGTTGATGGAGGAAA 58.921 43.478 0.00 0.00 0.00 3.13
170 171 0.532862 GTATGAGACCACCCCATGCG 60.533 60.000 0.00 0.00 0.00 4.73
332 756 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
333 757 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
334 758 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
337 761 4.729918 CGGCTTGCCTGCTCCCTT 62.730 66.667 10.12 0.00 0.00 3.95
338 762 2.753446 GGCTTGCCTGCTCCCTTC 60.753 66.667 4.11 0.00 0.00 3.46
339 763 2.753446 GCTTGCCTGCTCCCTTCC 60.753 66.667 0.00 0.00 0.00 3.46
340 764 2.044551 CTTGCCTGCTCCCTTCCC 60.045 66.667 0.00 0.00 0.00 3.97
341 765 2.858476 TTGCCTGCTCCCTTCCCA 60.858 61.111 0.00 0.00 0.00 4.37
342 766 2.220786 CTTGCCTGCTCCCTTCCCAT 62.221 60.000 0.00 0.00 0.00 4.00
343 767 2.123982 GCCTGCTCCCTTCCCATG 60.124 66.667 0.00 0.00 0.00 3.66
344 768 2.123982 CCTGCTCCCTTCCCATGC 60.124 66.667 0.00 0.00 0.00 4.06
345 769 2.687610 CCTGCTCCCTTCCCATGCT 61.688 63.158 0.00 0.00 0.00 3.79
346 770 1.305623 CTGCTCCCTTCCCATGCTT 59.694 57.895 0.00 0.00 0.00 3.91
347 771 0.750911 CTGCTCCCTTCCCATGCTTC 60.751 60.000 0.00 0.00 0.00 3.86
348 772 1.454663 GCTCCCTTCCCATGCTTCC 60.455 63.158 0.00 0.00 0.00 3.46
349 773 2.001803 CTCCCTTCCCATGCTTCCA 58.998 57.895 0.00 0.00 0.00 3.53
350 774 0.554792 CTCCCTTCCCATGCTTCCAT 59.445 55.000 0.00 0.00 0.00 3.41
351 775 0.552848 TCCCTTCCCATGCTTCCATC 59.447 55.000 0.00 0.00 0.00 3.51
352 776 0.468771 CCCTTCCCATGCTTCCATCC 60.469 60.000 0.00 0.00 0.00 3.51
353 777 0.820891 CCTTCCCATGCTTCCATCCG 60.821 60.000 0.00 0.00 0.00 4.18
354 778 0.107017 CTTCCCATGCTTCCATCCGT 60.107 55.000 0.00 0.00 0.00 4.69
355 779 0.394216 TTCCCATGCTTCCATCCGTG 60.394 55.000 0.00 0.00 0.00 4.94
356 780 2.484062 CCCATGCTTCCATCCGTGC 61.484 63.158 0.00 0.00 0.00 5.34
357 781 1.452651 CCATGCTTCCATCCGTGCT 60.453 57.895 0.00 0.00 0.00 4.40
358 782 1.442526 CCATGCTTCCATCCGTGCTC 61.443 60.000 0.00 0.00 0.00 4.26
359 783 1.153086 ATGCTTCCATCCGTGCTCC 60.153 57.895 0.00 0.00 0.00 4.70
360 784 2.514824 GCTTCCATCCGTGCTCCC 60.515 66.667 0.00 0.00 0.00 4.30
361 785 2.989639 CTTCCATCCGTGCTCCCA 59.010 61.111 0.00 0.00 0.00 4.37
362 786 1.450312 CTTCCATCCGTGCTCCCAC 60.450 63.158 0.00 0.00 38.62 4.61
363 787 1.903877 CTTCCATCCGTGCTCCCACT 61.904 60.000 0.00 0.00 39.86 4.00
364 788 1.488705 TTCCATCCGTGCTCCCACTT 61.489 55.000 0.00 0.00 39.86 3.16
365 789 1.450312 CCATCCGTGCTCCCACTTC 60.450 63.158 0.00 0.00 39.86 3.01
366 790 1.296392 CATCCGTGCTCCCACTTCA 59.704 57.895 0.00 0.00 39.86 3.02
367 791 0.107508 CATCCGTGCTCCCACTTCAT 60.108 55.000 0.00 0.00 39.86 2.57
368 792 0.179000 ATCCGTGCTCCCACTTCATC 59.821 55.000 0.00 0.00 39.86 2.92
369 793 1.450312 CCGTGCTCCCACTTCATCC 60.450 63.158 0.00 0.00 39.86 3.51
370 794 1.599047 CGTGCTCCCACTTCATCCT 59.401 57.895 0.00 0.00 39.86 3.24
371 795 0.824109 CGTGCTCCCACTTCATCCTA 59.176 55.000 0.00 0.00 39.86 2.94
372 796 1.471676 CGTGCTCCCACTTCATCCTAC 60.472 57.143 0.00 0.00 39.86 3.18
373 797 0.824109 TGCTCCCACTTCATCCTACG 59.176 55.000 0.00 0.00 0.00 3.51
374 798 0.105039 GCTCCCACTTCATCCTACGG 59.895 60.000 0.00 0.00 0.00 4.02
375 799 0.105039 CTCCCACTTCATCCTACGGC 59.895 60.000 0.00 0.00 0.00 5.68
376 800 0.325296 TCCCACTTCATCCTACGGCT 60.325 55.000 0.00 0.00 0.00 5.52
377 801 0.179073 CCCACTTCATCCTACGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
378 802 0.537188 CCACTTCATCCTACGGCTGT 59.463 55.000 2.42 2.42 0.00 4.40
379 803 1.066143 CCACTTCATCCTACGGCTGTT 60.066 52.381 1.99 0.00 0.00 3.16
380 804 2.615493 CCACTTCATCCTACGGCTGTTT 60.615 50.000 1.99 0.00 0.00 2.83
381 805 3.074412 CACTTCATCCTACGGCTGTTTT 58.926 45.455 1.99 0.00 0.00 2.43
382 806 3.502211 CACTTCATCCTACGGCTGTTTTT 59.498 43.478 1.99 0.00 0.00 1.94
421 845 9.439461 TTTCTAATCTAATCATCTTCTCCCTGA 57.561 33.333 0.00 0.00 0.00 3.86
422 846 9.612879 TTCTAATCTAATCATCTTCTCCCTGAT 57.387 33.333 0.00 0.00 0.00 2.90
423 847 9.612879 TCTAATCTAATCATCTTCTCCCTGATT 57.387 33.333 0.00 0.00 41.28 2.57
429 853 9.282569 CTAATCATCTTCTCCCTGATTTTAAGG 57.717 37.037 2.71 0.00 39.60 2.69
436 860 2.159179 CCTGATTTTAAGGGGGTGGG 57.841 55.000 0.00 0.00 0.00 4.61
437 861 1.342975 CCTGATTTTAAGGGGGTGGGG 60.343 57.143 0.00 0.00 0.00 4.96
438 862 0.041982 TGATTTTAAGGGGGTGGGGC 59.958 55.000 0.00 0.00 0.00 5.80
439 863 0.689745 GATTTTAAGGGGGTGGGGCC 60.690 60.000 0.00 0.00 0.00 5.80
440 864 1.456518 ATTTTAAGGGGGTGGGGCCA 61.457 55.000 4.39 0.00 39.65 5.36
441 865 2.100525 TTTTAAGGGGGTGGGGCCAG 62.101 60.000 4.39 0.00 39.65 4.85
456 880 2.972625 GGCCAGGCCTTATTTTGTTTC 58.027 47.619 24.99 0.00 46.69 2.78
457 881 2.301583 GGCCAGGCCTTATTTTGTTTCA 59.698 45.455 24.99 0.00 46.69 2.69
458 882 3.244387 GGCCAGGCCTTATTTTGTTTCAA 60.244 43.478 24.99 0.00 46.69 2.69
459 883 4.565444 GGCCAGGCCTTATTTTGTTTCAAT 60.565 41.667 24.99 0.00 46.69 2.57
460 884 4.631377 GCCAGGCCTTATTTTGTTTCAATC 59.369 41.667 0.00 0.00 0.00 2.67
461 885 5.792741 CCAGGCCTTATTTTGTTTCAATCA 58.207 37.500 0.00 0.00 0.00 2.57
462 886 6.229733 CCAGGCCTTATTTTGTTTCAATCAA 58.770 36.000 0.00 0.00 0.00 2.57
463 887 6.709846 CCAGGCCTTATTTTGTTTCAATCAAA 59.290 34.615 0.00 0.00 33.76 2.69
464 888 7.228308 CCAGGCCTTATTTTGTTTCAATCAAAA 59.772 33.333 0.00 8.47 44.83 2.44
473 897 7.489574 TTTGTTTCAATCAAAATAAGCCACC 57.510 32.000 0.00 0.00 32.86 4.61
474 898 6.418057 TGTTTCAATCAAAATAAGCCACCT 57.582 33.333 0.00 0.00 0.00 4.00
475 899 7.531857 TGTTTCAATCAAAATAAGCCACCTA 57.468 32.000 0.00 0.00 0.00 3.08
476 900 8.133024 TGTTTCAATCAAAATAAGCCACCTAT 57.867 30.769 0.00 0.00 0.00 2.57
477 901 8.034215 TGTTTCAATCAAAATAAGCCACCTATG 58.966 33.333 0.00 0.00 0.00 2.23
478 902 6.147864 TCAATCAAAATAAGCCACCTATGC 57.852 37.500 0.00 0.00 0.00 3.14
479 903 4.836125 ATCAAAATAAGCCACCTATGCG 57.164 40.909 0.00 0.00 0.00 4.73
480 904 2.948979 TCAAAATAAGCCACCTATGCGG 59.051 45.455 0.00 0.00 39.35 5.69
481 905 2.948979 CAAAATAAGCCACCTATGCGGA 59.051 45.455 0.00 0.00 36.31 5.54
482 906 3.290948 AAATAAGCCACCTATGCGGAA 57.709 42.857 0.00 0.00 36.31 4.30
483 907 2.550830 ATAAGCCACCTATGCGGAAG 57.449 50.000 0.00 0.00 36.31 3.46
495 919 2.745884 CGGAAGCACGAATGGGCA 60.746 61.111 0.00 0.00 35.47 5.36
496 920 2.877691 GGAAGCACGAATGGGCAC 59.122 61.111 0.00 0.00 0.00 5.01
497 921 1.971167 GGAAGCACGAATGGGCACA 60.971 57.895 0.00 0.00 0.00 4.57
498 922 1.210155 GAAGCACGAATGGGCACAC 59.790 57.895 0.00 0.00 0.00 3.82
499 923 2.513065 GAAGCACGAATGGGCACACG 62.513 60.000 0.00 0.00 0.00 4.49
500 924 4.759096 GCACGAATGGGCACACGC 62.759 66.667 0.00 0.00 37.44 5.34
511 935 3.114616 CACACGCCGGAAGAGCAG 61.115 66.667 5.05 0.00 0.00 4.24
512 936 4.379243 ACACGCCGGAAGAGCAGG 62.379 66.667 5.05 0.00 34.63 4.85
517 941 2.348998 CCGGAAGAGCAGGCAAGT 59.651 61.111 0.00 0.00 0.00 3.16
518 942 1.743252 CCGGAAGAGCAGGCAAGTC 60.743 63.158 0.00 0.00 0.00 3.01
519 943 1.294780 CGGAAGAGCAGGCAAGTCT 59.705 57.895 0.00 0.00 0.00 3.24
520 944 0.532573 CGGAAGAGCAGGCAAGTCTA 59.467 55.000 0.00 0.00 0.00 2.59
521 945 1.470632 CGGAAGAGCAGGCAAGTCTAG 60.471 57.143 0.00 0.00 0.00 2.43
522 946 1.552792 GGAAGAGCAGGCAAGTCTAGT 59.447 52.381 0.00 0.00 0.00 2.57
523 947 2.418060 GGAAGAGCAGGCAAGTCTAGTC 60.418 54.545 0.00 0.00 0.00 2.59
696 1400 4.082463 CCACGGCATAAACTACAACCAAAT 60.082 41.667 0.00 0.00 0.00 2.32
1914 5382 4.621991 CCTGATATGCTGGTGTGTAGTAC 58.378 47.826 0.00 0.00 0.00 2.73
2168 10135 6.346096 AGCTGCCACTACTTCGAATATTTTA 58.654 36.000 0.00 0.00 0.00 1.52
2379 10353 9.774742 GTTCAACATTTCACAGGTATTCTATTC 57.225 33.333 0.00 0.00 0.00 1.75
2428 10403 3.737266 CCGTACAAAGAAACGAGCAAGTA 59.263 43.478 0.00 0.00 41.55 2.24
2483 10459 4.943093 GGGTATTGTTAAGAGCCGGTAAAA 59.057 41.667 1.90 0.00 29.85 1.52
2500 10476 6.089150 CCGGTAAAAGAAAACGACAAAAACAA 59.911 34.615 0.00 0.00 0.00 2.83
2519 10495 3.188460 ACAAACGATGACACATTAGCACC 59.812 43.478 0.00 0.00 0.00 5.01
2543 10521 0.977627 AGAGACCCGTGCATCATGGA 60.978 55.000 6.64 0.00 42.73 3.41
2552 10530 2.414559 CGTGCATCATGGACAGTTTTCC 60.415 50.000 10.23 0.00 38.73 3.13
2557 10535 4.475944 CATCATGGACAGTTTTCCGTTTC 58.524 43.478 0.00 0.00 38.69 2.78
2760 10745 9.322773 CATCACTATTTCTTGTCATACATGTCT 57.677 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.267894 GGTTGTATATGCACCTTATATGAGGAT 58.732 37.037 19.88 6.06 39.25 3.24
29 30 7.236640 TCCTGGTTGTATATGCACCTTATATGA 59.763 37.037 11.54 0.00 0.00 2.15
54 55 4.070009 ACTCGGGAAATACACTTTGGTTC 58.930 43.478 0.00 0.00 0.00 3.62
62 63 1.732259 CAGCACACTCGGGAAATACAC 59.268 52.381 0.00 0.00 0.00 2.90
107 108 5.768164 TGACTTTTCCTCCATCAACTTTACC 59.232 40.000 0.00 0.00 0.00 2.85
108 109 6.294010 GGTGACTTTTCCTCCATCAACTTTAC 60.294 42.308 0.00 0.00 0.00 2.01
126 127 0.178941 ACTAGGTCCCACGGTGACTT 60.179 55.000 10.28 0.00 33.22 3.01
170 171 2.748209 ACTGCCCCATATTACCCAAC 57.252 50.000 0.00 0.00 0.00 3.77
307 731 4.530857 AGCCGGATCCCGCTTTCG 62.531 66.667 20.40 0.07 46.86 3.46
308 732 2.124695 AAGCCGGATCCCGCTTTC 60.125 61.111 28.18 1.51 46.86 2.62
309 733 2.438434 CAAGCCGGATCCCGCTTT 60.438 61.111 30.38 17.08 46.86 3.51
315 739 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
316 740 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
317 741 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
320 744 4.729918 AAGGGAGCAGGCAAGCCG 62.730 66.667 5.28 2.12 41.95 5.52
321 745 2.753446 GAAGGGAGCAGGCAAGCC 60.753 66.667 2.02 2.02 34.23 4.35
322 746 2.753446 GGAAGGGAGCAGGCAAGC 60.753 66.667 0.00 0.00 0.00 4.01
323 747 2.044551 GGGAAGGGAGCAGGCAAG 60.045 66.667 0.00 0.00 0.00 4.01
324 748 2.240918 ATGGGAAGGGAGCAGGCAA 61.241 57.895 0.00 0.00 0.00 4.52
325 749 2.614969 ATGGGAAGGGAGCAGGCA 60.615 61.111 0.00 0.00 0.00 4.75
326 750 2.123982 CATGGGAAGGGAGCAGGC 60.124 66.667 0.00 0.00 0.00 4.85
327 751 2.123982 GCATGGGAAGGGAGCAGG 60.124 66.667 0.00 0.00 0.00 4.85
328 752 0.750911 GAAGCATGGGAAGGGAGCAG 60.751 60.000 0.00 0.00 0.00 4.24
329 753 1.304282 GAAGCATGGGAAGGGAGCA 59.696 57.895 0.00 0.00 0.00 4.26
330 754 1.454663 GGAAGCATGGGAAGGGAGC 60.455 63.158 0.00 0.00 0.00 4.70
331 755 0.554792 ATGGAAGCATGGGAAGGGAG 59.445 55.000 0.00 0.00 0.00 4.30
332 756 0.552848 GATGGAAGCATGGGAAGGGA 59.447 55.000 0.00 0.00 0.00 4.20
333 757 0.468771 GGATGGAAGCATGGGAAGGG 60.469 60.000 0.00 0.00 0.00 3.95
334 758 0.820891 CGGATGGAAGCATGGGAAGG 60.821 60.000 0.00 0.00 0.00 3.46
335 759 0.107017 ACGGATGGAAGCATGGGAAG 60.107 55.000 0.00 0.00 0.00 3.46
336 760 0.394216 CACGGATGGAAGCATGGGAA 60.394 55.000 0.00 0.00 0.00 3.97
337 761 1.224315 CACGGATGGAAGCATGGGA 59.776 57.895 0.00 0.00 0.00 4.37
338 762 2.484062 GCACGGATGGAAGCATGGG 61.484 63.158 0.00 0.00 0.00 4.00
339 763 1.442526 GAGCACGGATGGAAGCATGG 61.443 60.000 0.00 0.00 0.00 3.66
340 764 1.442526 GGAGCACGGATGGAAGCATG 61.443 60.000 0.00 0.00 0.00 4.06
341 765 1.153086 GGAGCACGGATGGAAGCAT 60.153 57.895 0.00 0.00 0.00 3.79
342 766 2.268920 GGAGCACGGATGGAAGCA 59.731 61.111 0.00 0.00 0.00 3.91
343 767 2.514824 GGGAGCACGGATGGAAGC 60.515 66.667 0.00 0.00 0.00 3.86
344 768 1.450312 GTGGGAGCACGGATGGAAG 60.450 63.158 0.00 0.00 0.00 3.46
345 769 1.488705 AAGTGGGAGCACGGATGGAA 61.489 55.000 0.00 0.00 0.00 3.53
346 770 1.899437 GAAGTGGGAGCACGGATGGA 61.899 60.000 0.00 0.00 0.00 3.41
347 771 1.450312 GAAGTGGGAGCACGGATGG 60.450 63.158 0.00 0.00 0.00 3.51
348 772 0.107508 ATGAAGTGGGAGCACGGATG 60.108 55.000 0.00 0.00 0.00 3.51
349 773 0.179000 GATGAAGTGGGAGCACGGAT 59.821 55.000 0.00 0.00 0.00 4.18
350 774 1.596934 GATGAAGTGGGAGCACGGA 59.403 57.895 0.00 0.00 0.00 4.69
351 775 1.450312 GGATGAAGTGGGAGCACGG 60.450 63.158 0.00 0.00 0.00 4.94
352 776 0.824109 TAGGATGAAGTGGGAGCACG 59.176 55.000 0.00 0.00 0.00 5.34
353 777 1.471676 CGTAGGATGAAGTGGGAGCAC 60.472 57.143 0.00 0.00 0.00 4.40
354 778 0.824109 CGTAGGATGAAGTGGGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
355 779 3.669354 CGTAGGATGAAGTGGGAGC 57.331 57.895 0.00 0.00 0.00 4.70
395 819 9.439461 TCAGGGAGAAGATGATTAGATTAGAAA 57.561 33.333 0.00 0.00 0.00 2.52
396 820 9.612879 ATCAGGGAGAAGATGATTAGATTAGAA 57.387 33.333 0.00 0.00 29.42 2.10
397 821 9.612879 AATCAGGGAGAAGATGATTAGATTAGA 57.387 33.333 0.00 0.00 40.84 2.10
403 827 9.282569 CCTTAAAATCAGGGAGAAGATGATTAG 57.717 37.037 0.49 0.00 41.56 1.73
417 841 1.342975 CCCCACCCCCTTAAAATCAGG 60.343 57.143 0.00 0.00 0.00 3.86
418 842 1.964830 GCCCCACCCCCTTAAAATCAG 60.965 57.143 0.00 0.00 0.00 2.90
419 843 0.041982 GCCCCACCCCCTTAAAATCA 59.958 55.000 0.00 0.00 0.00 2.57
420 844 0.689745 GGCCCCACCCCCTTAAAATC 60.690 60.000 0.00 0.00 0.00 2.17
421 845 1.394557 GGCCCCACCCCCTTAAAAT 59.605 57.895 0.00 0.00 0.00 1.82
422 846 2.098376 TGGCCCCACCCCCTTAAAA 61.098 57.895 0.00 0.00 37.83 1.52
423 847 2.454714 TGGCCCCACCCCCTTAAA 60.455 61.111 0.00 0.00 37.83 1.52
424 848 2.944390 CTGGCCCCACCCCCTTAA 60.944 66.667 0.00 0.00 37.83 1.85
437 861 3.676291 TGAAACAAAATAAGGCCTGGC 57.324 42.857 5.69 11.05 0.00 4.85
438 862 5.792741 TGATTGAAACAAAATAAGGCCTGG 58.207 37.500 5.69 0.00 0.00 4.45
439 863 7.727331 TTTGATTGAAACAAAATAAGGCCTG 57.273 32.000 5.69 0.00 34.89 4.85
448 872 7.772757 AGGTGGCTTATTTTGATTGAAACAAAA 59.227 29.630 14.26 14.26 46.29 2.44
449 873 7.278875 AGGTGGCTTATTTTGATTGAAACAAA 58.721 30.769 0.00 0.00 35.81 2.83
450 874 6.825610 AGGTGGCTTATTTTGATTGAAACAA 58.174 32.000 0.00 0.00 0.00 2.83
451 875 6.418057 AGGTGGCTTATTTTGATTGAAACA 57.582 33.333 0.00 0.00 0.00 2.83
452 876 7.010460 GCATAGGTGGCTTATTTTGATTGAAAC 59.990 37.037 0.00 0.00 0.00 2.78
453 877 7.041107 GCATAGGTGGCTTATTTTGATTGAAA 58.959 34.615 0.00 0.00 0.00 2.69
454 878 6.572519 GCATAGGTGGCTTATTTTGATTGAA 58.427 36.000 0.00 0.00 0.00 2.69
455 879 5.221028 CGCATAGGTGGCTTATTTTGATTGA 60.221 40.000 0.00 0.00 0.00 2.57
456 880 4.977963 CGCATAGGTGGCTTATTTTGATTG 59.022 41.667 0.00 0.00 0.00 2.67
457 881 4.037923 CCGCATAGGTGGCTTATTTTGATT 59.962 41.667 0.00 0.00 37.98 2.57
458 882 3.569701 CCGCATAGGTGGCTTATTTTGAT 59.430 43.478 0.00 0.00 37.98 2.57
459 883 2.948979 CCGCATAGGTGGCTTATTTTGA 59.051 45.455 0.00 0.00 37.98 2.69
460 884 2.948979 TCCGCATAGGTGGCTTATTTTG 59.051 45.455 1.06 0.00 44.64 2.44
461 885 3.290948 TCCGCATAGGTGGCTTATTTT 57.709 42.857 1.06 0.00 44.64 1.82
462 886 3.214328 CTTCCGCATAGGTGGCTTATTT 58.786 45.455 1.06 0.00 44.64 1.40
463 887 2.851195 CTTCCGCATAGGTGGCTTATT 58.149 47.619 1.06 0.00 44.64 1.40
464 888 1.543429 GCTTCCGCATAGGTGGCTTAT 60.543 52.381 1.06 0.00 44.64 1.73
465 889 0.179056 GCTTCCGCATAGGTGGCTTA 60.179 55.000 1.06 0.00 44.64 3.09
466 890 1.452108 GCTTCCGCATAGGTGGCTT 60.452 57.895 1.06 0.00 44.64 4.35
467 891 2.190578 GCTTCCGCATAGGTGGCT 59.809 61.111 1.06 0.00 44.64 4.75
468 892 2.124736 TGCTTCCGCATAGGTGGC 60.125 61.111 1.06 0.00 44.64 5.01
476 900 2.745884 CCCATTCGTGCTTCCGCA 60.746 61.111 0.00 0.00 45.60 5.69
477 901 4.179579 GCCCATTCGTGCTTCCGC 62.180 66.667 0.00 0.00 0.00 5.54
478 902 2.745884 TGCCCATTCGTGCTTCCG 60.746 61.111 0.00 0.00 0.00 4.30
479 903 1.971167 TGTGCCCATTCGTGCTTCC 60.971 57.895 0.00 0.00 0.00 3.46
480 904 1.210155 GTGTGCCCATTCGTGCTTC 59.790 57.895 0.00 0.00 0.00 3.86
481 905 2.616330 CGTGTGCCCATTCGTGCTT 61.616 57.895 0.00 0.00 0.00 3.91
482 906 3.049674 CGTGTGCCCATTCGTGCT 61.050 61.111 0.00 0.00 0.00 4.40
483 907 4.759096 GCGTGTGCCCATTCGTGC 62.759 66.667 0.00 0.00 33.98 5.34
494 918 3.114616 CTGCTCTTCCGGCGTGTG 61.115 66.667 6.01 0.00 0.00 3.82
495 919 4.379243 CCTGCTCTTCCGGCGTGT 62.379 66.667 6.01 0.00 0.00 4.49
499 923 3.130160 CTTGCCTGCTCTTCCGGC 61.130 66.667 0.00 0.00 44.02 6.13
500 924 1.743252 GACTTGCCTGCTCTTCCGG 60.743 63.158 0.00 0.00 0.00 5.14
501 925 0.532573 TAGACTTGCCTGCTCTTCCG 59.467 55.000 0.00 0.00 0.00 4.30
502 926 1.552792 ACTAGACTTGCCTGCTCTTCC 59.447 52.381 0.00 0.00 0.00 3.46
503 927 2.418060 GGACTAGACTTGCCTGCTCTTC 60.418 54.545 0.00 0.00 0.00 2.87
504 928 1.552792 GGACTAGACTTGCCTGCTCTT 59.447 52.381 0.00 0.00 0.00 2.85
505 929 1.190643 GGACTAGACTTGCCTGCTCT 58.809 55.000 0.00 0.00 0.00 4.09
506 930 0.179124 CGGACTAGACTTGCCTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
507 931 1.893786 CGGACTAGACTTGCCTGCT 59.106 57.895 0.00 0.00 0.00 4.24
508 932 1.811679 GCGGACTAGACTTGCCTGC 60.812 63.158 0.00 0.00 0.00 4.85
509 933 1.517257 CGCGGACTAGACTTGCCTG 60.517 63.158 0.00 0.00 0.00 4.85
510 934 1.248785 TTCGCGGACTAGACTTGCCT 61.249 55.000 6.13 0.00 0.00 4.75
511 935 0.389426 TTTCGCGGACTAGACTTGCC 60.389 55.000 6.13 0.00 0.00 4.52
512 936 0.992802 CTTTCGCGGACTAGACTTGC 59.007 55.000 6.13 0.00 0.00 4.01
513 937 0.992802 GCTTTCGCGGACTAGACTTG 59.007 55.000 6.13 0.00 0.00 3.16
514 938 3.420397 GCTTTCGCGGACTAGACTT 57.580 52.632 6.13 0.00 0.00 3.01
593 1019 1.593209 GTGGCCGTGAACGTGAAGA 60.593 57.895 0.00 0.00 37.74 2.87
660 1364 2.241190 CCGTGGCATATGCGCGTTA 61.241 57.895 28.64 0.00 43.26 3.18
696 1400 0.400975 TTTTGGTTCCGGGGATTCGA 59.599 50.000 0.00 0.00 0.00 3.71
1273 4732 2.125512 GTTGGCGTCGCTGAGGAT 60.126 61.111 18.11 0.00 0.00 3.24
1670 5132 4.680237 CCTTGCCGTCGCTCCACA 62.680 66.667 0.00 0.00 35.36 4.17
1914 5382 1.611592 GGACGCCAAACTCGTACGTG 61.612 60.000 16.05 15.64 40.59 4.49
2001 9946 2.244382 CGGACGACACGCACAAAC 59.756 61.111 0.00 0.00 0.00 2.93
2076 10041 4.649088 TTCGTCGGATCAACTCATGTAT 57.351 40.909 0.00 0.00 0.00 2.29
2077 10042 4.142249 ACATTCGTCGGATCAACTCATGTA 60.142 41.667 0.00 0.00 0.00 2.29
2078 10043 3.190079 CATTCGTCGGATCAACTCATGT 58.810 45.455 0.00 0.00 0.00 3.21
2217 10184 2.102588 CACGGGCCTGCTATTTAGTACT 59.897 50.000 12.89 0.00 0.00 2.73
2225 10192 1.825191 CAATGCACGGGCCTGCTAT 60.825 57.895 22.57 14.27 40.13 2.97
2262 10234 7.485418 TTTTCTGTAAATTAAGAGCGTGTGA 57.515 32.000 0.00 0.00 0.00 3.58
2294 10268 8.983724 GGTCAGTAGCTACAAATTATGAGATTC 58.016 37.037 25.28 7.32 0.00 2.52
2359 10333 8.184192 GTGTTGGAATAGAATACCTGTGAAATG 58.816 37.037 0.00 0.00 0.00 2.32
2379 10353 2.287915 GTCTATATGCAAGCCGTGTTGG 59.712 50.000 0.00 0.00 42.50 3.77
2418 10393 4.970662 AAATGCATGATTACTTGCTCGT 57.029 36.364 0.00 0.00 44.15 4.18
2428 10403 7.820386 ACACACAACATGAATAAATGCATGATT 59.180 29.630 16.32 3.08 43.43 2.57
2483 10459 6.033091 GTCATCGTTTGTTTTTGTCGTTTTCT 59.967 34.615 0.00 0.00 0.00 2.52
2500 10476 2.027192 AGGGTGCTAATGTGTCATCGTT 60.027 45.455 0.00 0.00 0.00 3.85
2519 10495 0.103208 GATGCACGGGTCTCTGTAGG 59.897 60.000 0.00 0.00 0.00 3.18
2543 10521 2.948979 TGATGCTGAAACGGAAAACTGT 59.051 40.909 0.00 0.00 0.00 3.55
2552 10530 4.466828 CTTAAGTTGGTGATGCTGAAACG 58.533 43.478 0.00 0.00 0.00 3.60
2557 10535 5.003804 AGTTACCTTAAGTTGGTGATGCTG 58.996 41.667 0.97 0.00 38.42 4.41
2760 10745 7.252612 TGATGAAACAGAGACCAATACCTAA 57.747 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.