Multiple sequence alignment - TraesCS3A01G102400

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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 TraesCS3A01G102400 chr3A 100.000 3008 0 0 1 3008 66248816 66251823 0.000000e+00 5555.0
1 TraesCS3A01G102400 chr3A 85.849 106 15 0 128 233 658884822 658884927 2.450000e-21 113.0
2 TraesCS3A01G102400 chr6D 88.167 2138 163 36 908 3008 16510486 16512570 0.000000e+00 2464.0
3 TraesCS3A01G102400 chr6D 89.057 795 75 9 1097 1884 16390170 16389381 0.000000e+00 976.0
4 TraesCS3A01G102400 chr6D 82.604 1006 116 39 915 1884 16502638 16503620 0.000000e+00 833.0
5 TraesCS3A01G102400 chr6D 90.385 104 10 0 2544 2647 16388568 16388465 1.450000e-28 137.0
6 TraesCS3A01G102400 chr6D 83.846 130 20 1 2 131 460096924 460096796 4.070000e-24 122.0
7 TraesCS3A01G102400 chr6A 91.746 1054 77 7 908 1955 16700708 16701757 0.000000e+00 1456.0
8 TraesCS3A01G102400 chr6A 87.972 848 84 12 1053 1884 16658816 16657971 0.000000e+00 985.0
9 TraesCS3A01G102400 chr6A 90.138 507 44 4 2400 2900 16702599 16703105 0.000000e+00 654.0
10 TraesCS3A01G102400 chr6A 84.884 172 26 0 2010 2181 16662564 16662393 1.110000e-39 174.0
11 TraesCS3A01G102400 chr6A 92.222 90 0 2 2400 2486 16702172 16702257 1.460000e-23 121.0
12 TraesCS3A01G102400 chr6B 85.522 1409 120 39 1001 2378 28713882 28715237 0.000000e+00 1395.0
13 TraesCS3A01G102400 chr6B 86.633 980 89 23 933 1884 28925785 28926750 0.000000e+00 1046.0
14 TraesCS3A01G102400 chr6B 88.058 896 76 18 1006 1888 59294774 59295651 0.000000e+00 1033.0
15 TraesCS3A01G102400 chr6B 85.507 966 114 19 931 1884 28517568 28516617 0.000000e+00 985.0
16 TraesCS3A01G102400 chr6B 87.531 818 68 19 933 1732 28256874 28256073 0.000000e+00 915.0
17 TraesCS3A01G102400 chr6B 85.040 869 73 40 931 1772 59232561 59233399 0.000000e+00 832.0
18 TraesCS3A01G102400 chr6B 90.212 613 46 6 2400 3008 28715293 28715895 0.000000e+00 787.0
19 TraesCS3A01G102400 chr6B 92.879 323 23 0 2686 3008 28720008 28720330 1.260000e-128 470.0
20 TraesCS3A01G102400 chr6B 79.138 441 52 24 2202 2622 28516376 28515956 4.940000e-68 268.0
21 TraesCS3A01G102400 chr6B 93.056 72 4 1 908 979 59294706 59294776 1.480000e-18 104.0
22 TraesCS3A01G102400 chr6B 90.625 64 6 0 2202 2265 28926882 28926945 5.340000e-13 86.1
23 TraesCS3A01G102400 chr4D 92.105 342 25 2 128 469 40121205 40120866 5.830000e-132 481.0
24 TraesCS3A01G102400 chr4D 90.625 352 32 1 559 910 40120863 40120513 1.630000e-127 466.0
25 TraesCS3A01G102400 chr4D 79.851 268 47 6 128 393 40119161 40119423 3.960000e-44 189.0
26 TraesCS3A01G102400 chr4D 85.714 56 6 2 649 703 40120072 40120018 1.160000e-04 58.4
27 TraesCS3A01G102400 chr2A 77.320 291 52 11 629 910 543766858 543767143 3.100000e-35 159.0
28 TraesCS3A01G102400 chr3B 91.964 112 9 0 128 239 787612294 787612183 1.120000e-34 158.0
29 TraesCS3A01G102400 chr3B 91.964 112 9 0 128 239 787651526 787651415 1.120000e-34 158.0
30 TraesCS3A01G102400 chr3B 81.944 144 24 2 5 147 174904343 174904201 1.460000e-23 121.0
31 TraesCS3A01G102400 chr5A 86.508 126 15 2 765 889 94303918 94304042 1.450000e-28 137.0
32 TraesCS3A01G102400 chr5A 86.400 125 15 2 128 251 30005133 30005010 5.230000e-28 135.0
33 TraesCS3A01G102400 chr5A 86.792 106 14 0 128 233 377139406 377139301 5.270000e-23 119.0
34 TraesCS3A01G102400 chr5A 84.810 79 10 2 777 854 709174612 709174535 8.940000e-11 78.7
35 TraesCS3A01G102400 chr5A 84.615 78 10 2 778 854 659372150 659372226 3.220000e-10 76.8
36 TraesCS3A01G102400 chrUn 85.271 129 18 1 3 131 34137272 34137399 6.770000e-27 132.0
37 TraesCS3A01G102400 chr2D 79.293 198 31 8 671 861 42897677 42897483 2.430000e-26 130.0
38 TraesCS3A01G102400 chr2D 77.844 167 25 10 669 828 585435386 585435547 3.190000e-15 93.5
39 TraesCS3A01G102400 chr2D 92.453 53 2 1 775 827 595530357 595530307 1.160000e-09 75.0
40 TraesCS3A01G102400 chr2B 84.615 130 20 0 5 134 572570255 572570126 2.430000e-26 130.0
41 TraesCS3A01G102400 chr7D 85.039 127 18 1 5 131 498501943 498501818 8.750000e-26 128.0
42 TraesCS3A01G102400 chr7D 100.000 29 0 0 801 829 499789349 499789377 2.000000e-03 54.7
43 TraesCS3A01G102400 chr5B 84.091 132 21 0 3 134 704110904 704110773 8.750000e-26 128.0
44 TraesCS3A01G102400 chr4B 86.842 114 15 0 128 241 624156279 624156392 8.750000e-26 128.0
45 TraesCS3A01G102400 chr4B 82.836 134 23 0 2 135 307461987 307462120 1.460000e-23 121.0
46 TraesCS3A01G102400 chr7A 83.969 131 21 0 1 131 214644180 214644310 3.150000e-25 126.0
47 TraesCS3A01G102400 chr1A 87.736 106 13 0 128 233 64854813 64854708 1.130000e-24 124.0
48 TraesCS3A01G102400 chr1A 84.375 128 18 2 5 131 144783028 144782902 1.130000e-24 124.0
49 TraesCS3A01G102400 chr5D 81.982 111 14 5 764 872 551420997 551421103 4.130000e-14 89.8


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 TraesCS3A01G102400 chr3A 66248816 66251823 3007 False 5555.000000 5555 100.000000 1 3008 1 chr3A.!!$F1 3007
1 TraesCS3A01G102400 chr6D 16510486 16512570 2084 False 2464.000000 2464 88.167000 908 3008 1 chr6D.!!$F2 2100
2 TraesCS3A01G102400 chr6D 16502638 16503620 982 False 833.000000 833 82.604000 915 1884 1 chr6D.!!$F1 969
3 TraesCS3A01G102400 chr6D 16388465 16390170 1705 True 556.500000 976 89.721000 1097 2647 2 chr6D.!!$R2 1550
4 TraesCS3A01G102400 chr6A 16700708 16703105 2397 False 743.666667 1456 91.368667 908 2900 3 chr6A.!!$F1 1992
5 TraesCS3A01G102400 chr6A 16657971 16662564 4593 True 579.500000 985 86.428000 1053 2181 2 chr6A.!!$R1 1128
6 TraesCS3A01G102400 chr6B 28713882 28715895 2013 False 1091.000000 1395 87.867000 1001 3008 2 chr6B.!!$F3 2007
7 TraesCS3A01G102400 chr6B 28256073 28256874 801 True 915.000000 915 87.531000 933 1732 1 chr6B.!!$R1 799
8 TraesCS3A01G102400 chr6B 59232561 59233399 838 False 832.000000 832 85.040000 931 1772 1 chr6B.!!$F2 841
9 TraesCS3A01G102400 chr6B 28515956 28517568 1612 True 626.500000 985 82.322500 931 2622 2 chr6B.!!$R2 1691
10 TraesCS3A01G102400 chr6B 59294706 59295651 945 False 568.500000 1033 90.557000 908 1888 2 chr6B.!!$F5 980
11 TraesCS3A01G102400 chr6B 28925785 28926945 1160 False 566.050000 1046 88.629000 933 2265 2 chr6B.!!$F4 1332
12 TraesCS3A01G102400 chr4D 40120018 40121205 1187 True 335.133333 481 89.481333 128 910 3 chr4D.!!$R1 782

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
485 486 0.320683 TCTGCCATGGACACACGAAG 60.321 55.0 18.4 0.47 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 4949 0.037882 TGCAGGACTTCTGAAGCTCG 60.038 55.0 17.0 5.06 46.18 5.03 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
24 25 7.844493 AATAAGGGCATGTACAATGATTGAT 57.156 32.000 12.80 0.00 0.00 2.57
26 27 8.938801 ATAAGGGCATGTACAATGATTGATAA 57.061 30.769 12.80 0.00 0.00 1.75
27 28 6.889301 AGGGCATGTACAATGATTGATAAG 57.111 37.500 12.80 0.00 0.00 1.73
28 29 6.604171 AGGGCATGTACAATGATTGATAAGA 58.396 36.000 12.80 0.00 0.00 2.10
29 30 7.236529 AGGGCATGTACAATGATTGATAAGAT 58.763 34.615 12.80 0.00 0.00 2.40
30 31 8.385491 AGGGCATGTACAATGATTGATAAGATA 58.615 33.333 12.80 0.00 0.00 1.98
68 69 8.969260 ATCTTGCATGTAATTTAGAGATGACA 57.031 30.769 0.00 0.00 0.00 3.58
69 70 8.791327 TCTTGCATGTAATTTAGAGATGACAA 57.209 30.769 0.00 0.00 0.00 3.18
70 71 9.399797 TCTTGCATGTAATTTAGAGATGACAAT 57.600 29.630 0.00 0.00 0.00 2.71
98 99 7.581213 TTTTGTCTACAATGAACCATCACTT 57.419 32.000 0.00 0.00 38.69 3.16
101 102 7.667043 TGTCTACAATGAACCATCACTTAAC 57.333 36.000 0.00 0.00 38.69 2.01
104 105 7.390718 GTCTACAATGAACCATCACTTAACCTT 59.609 37.037 0.00 0.00 38.69 3.50
105 106 8.598916 TCTACAATGAACCATCACTTAACCTTA 58.401 33.333 0.00 0.00 38.69 2.69
107 108 8.650143 ACAATGAACCATCACTTAACCTTATT 57.350 30.769 0.00 0.00 38.69 1.40
108 109 9.088987 ACAATGAACCATCACTTAACCTTATTT 57.911 29.630 0.00 0.00 38.69 1.40
109 110 9.927668 CAATGAACCATCACTTAACCTTATTTT 57.072 29.630 0.00 0.00 38.69 1.82
112 113 9.137459 TGAACCATCACTTAACCTTATTTTCAA 57.863 29.630 0.00 0.00 0.00 2.69
233 234 2.934887 TGTCCTCCCGTTCATATACGA 58.065 47.619 0.00 0.00 43.99 3.43
293 294 3.827634 GCGGAGGCCCATTGTTAG 58.172 61.111 0.00 0.00 0.00 2.34
315 316 1.227380 CTATCAGTGGCGGAGGTGC 60.227 63.158 0.00 0.00 0.00 5.01
328 329 0.391793 GAGGTGCTTGGTCTAGTGCC 60.392 60.000 0.00 0.00 0.00 5.01
393 394 6.623353 CGTAATTATGTCTGTGTAAACGCATG 59.377 38.462 0.00 0.00 35.63 4.06
401 402 4.454161 TCTGTGTAAACGCATGTAGCAATT 59.546 37.500 0.00 0.00 46.13 2.32
406 407 6.464834 GTGTAAACGCATGTAGCAATTACTTC 59.535 38.462 0.00 0.00 46.13 3.01
414 415 8.547894 CGCATGTAGCAATTACTTCTATTTACA 58.452 33.333 0.00 0.00 46.13 2.41
421 422 8.616076 AGCAATTACTTCTATTTACATCTGTGC 58.384 33.333 0.00 0.00 0.00 4.57
476 477 1.427809 CAGGACCTATCTGCCATGGA 58.572 55.000 18.40 0.00 0.00 3.41
477 478 1.071385 CAGGACCTATCTGCCATGGAC 59.929 57.143 18.40 7.64 0.00 4.02
479 480 1.202698 GGACCTATCTGCCATGGACAC 60.203 57.143 18.40 0.00 0.00 3.67
480 481 1.486310 GACCTATCTGCCATGGACACA 59.514 52.381 18.40 2.70 0.00 3.72
482 483 1.575244 CTATCTGCCATGGACACACG 58.425 55.000 18.40 1.92 0.00 4.49
483 484 1.136891 CTATCTGCCATGGACACACGA 59.863 52.381 18.40 7.42 0.00 4.35
484 485 0.324614 ATCTGCCATGGACACACGAA 59.675 50.000 18.40 0.00 0.00 3.85
485 486 0.320683 TCTGCCATGGACACACGAAG 60.321 55.000 18.40 0.47 0.00 3.79
486 487 1.300971 CTGCCATGGACACACGAAGG 61.301 60.000 18.40 0.00 0.00 3.46
487 488 1.003839 GCCATGGACACACGAAGGA 60.004 57.895 18.40 0.00 0.00 3.36
488 489 0.605319 GCCATGGACACACGAAGGAA 60.605 55.000 18.40 0.00 0.00 3.36
490 491 2.436417 CCATGGACACACGAAGGAATT 58.564 47.619 5.56 0.00 0.00 2.17
491 492 2.819608 CCATGGACACACGAAGGAATTT 59.180 45.455 5.56 0.00 0.00 1.82
492 493 4.006989 CCATGGACACACGAAGGAATTTA 58.993 43.478 5.56 0.00 0.00 1.40
497 498 6.001460 TGGACACACGAAGGAATTTAAGATT 58.999 36.000 0.00 0.00 0.00 2.40
498 499 6.488683 TGGACACACGAAGGAATTTAAGATTT 59.511 34.615 0.00 0.00 0.00 2.17
499 500 7.662258 TGGACACACGAAGGAATTTAAGATTTA 59.338 33.333 0.00 0.00 0.00 1.40
500 501 8.508875 GGACACACGAAGGAATTTAAGATTTAA 58.491 33.333 0.00 0.00 0.00 1.52
501 502 9.887406 GACACACGAAGGAATTTAAGATTTAAA 57.113 29.630 0.00 0.00 0.00 1.52
525 526 8.463930 AAAAATATTGCCTATGAGGATTCGAA 57.536 30.769 0.00 0.00 37.67 3.71
529 530 3.572642 TGCCTATGAGGATTCGAACCTA 58.427 45.455 16.15 8.11 37.67 3.08
530 531 4.160329 TGCCTATGAGGATTCGAACCTAT 58.840 43.478 16.15 12.76 37.67 2.57
532 533 5.419155 TGCCTATGAGGATTCGAACCTATAG 59.581 44.000 16.15 18.30 37.67 1.31
533 534 5.163499 GCCTATGAGGATTCGAACCTATAGG 60.163 48.000 27.29 27.29 37.67 2.57
536 537 7.614583 CCTATGAGGATTCGAACCTATAGGTAA 59.385 40.741 24.84 15.65 42.81 2.85
546 547 2.977914 CCTATAGGTAATGCATGCGCT 58.022 47.619 14.09 4.78 39.64 5.92
547 548 4.123497 CCTATAGGTAATGCATGCGCTA 57.877 45.455 14.09 3.68 39.64 4.26
548 549 4.503910 CCTATAGGTAATGCATGCGCTAA 58.496 43.478 14.09 0.00 39.64 3.09
549 550 4.330074 CCTATAGGTAATGCATGCGCTAAC 59.670 45.833 14.09 9.44 39.64 2.34
550 551 1.308998 AGGTAATGCATGCGCTAACC 58.691 50.000 14.09 16.77 39.64 2.85
552 553 1.268539 GGTAATGCATGCGCTAACCAC 60.269 52.381 20.23 9.20 39.64 4.16
553 554 0.655208 TAATGCATGCGCTAACCACG 59.345 50.000 14.09 0.00 39.64 4.94
555 556 1.431488 ATGCATGCGCTAACCACGAG 61.431 55.000 14.09 0.00 39.64 4.18
556 557 1.809619 GCATGCGCTAACCACGAGA 60.810 57.895 9.73 0.00 34.30 4.04
557 558 1.756375 GCATGCGCTAACCACGAGAG 61.756 60.000 9.73 0.00 34.30 3.20
593 594 2.914941 TGCCCCATACAGAGATGCATAT 59.085 45.455 0.00 0.00 0.00 1.78
610 611 5.687780 TGCATATCATATTCTATGGGCCAG 58.312 41.667 13.78 0.00 0.00 4.85
611 612 4.518211 GCATATCATATTCTATGGGCCAGC 59.482 45.833 13.78 0.00 0.00 4.85
627 628 2.165437 GCCAGCCCGACAAATAAATTCA 59.835 45.455 0.00 0.00 0.00 2.57
874 875 9.722056 GTCCAACAGAATTTACATACATTCATC 57.278 33.333 1.71 0.00 32.61 2.92
892 1194 9.851686 ACATTCATCCTGAACTATATTTTAGCA 57.148 29.630 0.00 0.00 39.45 3.49
955 1257 3.567797 GCGCTCTGATTGGTCGGC 61.568 66.667 0.00 0.00 0.00 5.54
1100 3799 3.496131 CCGCCGTCCAATTCCACG 61.496 66.667 0.00 0.00 35.72 4.94
1103 3802 1.366111 CGCCGTCCAATTCCACGAAT 61.366 55.000 7.18 0.00 38.32 3.34
1111 3810 2.223112 CCAATTCCACGAATTCAGAGCG 60.223 50.000 6.22 0.00 39.82 5.03
1257 3965 2.686106 GGGCTCCAGTTCCCCGTA 60.686 66.667 0.00 0.00 36.50 4.02
1350 4058 2.799371 GCCGTCCTCGAGTACCTG 59.201 66.667 12.31 0.00 39.71 4.00
1441 4169 4.359706 ACTGATTTCGTTGGCTTTTGAAC 58.640 39.130 0.00 0.00 0.00 3.18
1603 4332 2.355108 CGTCATCCCCAACATCAACTCT 60.355 50.000 0.00 0.00 0.00 3.24
1699 4428 1.679898 CCCCAAGAAGAAGGTCGCT 59.320 57.895 0.00 0.00 0.00 4.93
1711 4440 2.281484 GTCGCTGCCACCAAGGAA 60.281 61.111 0.00 0.00 41.22 3.36
1726 4463 0.770557 AGGAATAGCCGCCCCCATAA 60.771 55.000 0.00 0.00 43.43 1.90
1732 4469 2.449450 GCCGCCCCCATAACCTAGT 61.449 63.158 0.00 0.00 0.00 2.57
1733 4470 1.991339 GCCGCCCCCATAACCTAGTT 61.991 60.000 0.00 0.00 0.00 2.24
1734 4471 0.179029 CCGCCCCCATAACCTAGTTG 60.179 60.000 0.00 0.00 0.00 3.16
1778 4515 4.282957 TCATGGACTAAGATGAGATCCTGC 59.717 45.833 0.00 0.00 0.00 4.85
1855 4594 4.271696 TGTACCTGTGATTTCTGTGAGG 57.728 45.455 0.00 0.00 0.00 3.86
1892 4631 5.391449 CAATCATTTCAGTCTGCTGTTCTG 58.609 41.667 0.00 10.37 43.05 3.02
1909 4648 2.910199 TCTGTCTATGGCTGCAATCAC 58.090 47.619 0.50 0.00 0.00 3.06
1923 4662 5.366829 TGCAATCACTTCAATCTCTTGTG 57.633 39.130 0.00 0.00 33.87 3.33
1924 4663 4.823442 TGCAATCACTTCAATCTCTTGTGT 59.177 37.500 0.00 0.00 33.87 3.72
1934 4673 8.254508 ACTTCAATCTCTTGTGTTCTACCTATC 58.745 37.037 0.00 0.00 33.87 2.08
1940 4679 1.136305 TGTGTTCTACCTATCGCTGCC 59.864 52.381 0.00 0.00 0.00 4.85
1955 4694 1.135315 GCTGCCATTGATCTTGCGAAA 60.135 47.619 0.00 0.00 0.00 3.46
1956 4695 2.480759 GCTGCCATTGATCTTGCGAAAT 60.481 45.455 0.00 0.00 0.00 2.17
1957 4696 3.777478 CTGCCATTGATCTTGCGAAATT 58.223 40.909 0.00 0.00 0.00 1.82
1960 4699 4.626604 TGCCATTGATCTTGCGAAATTTTC 59.373 37.500 0.00 0.00 0.00 2.29
1962 4701 4.266029 CCATTGATCTTGCGAAATTTTCCG 59.734 41.667 3.61 0.00 0.00 4.30
1992 4736 4.563184 CGTCTCAAGGTCACTGCTAAATAC 59.437 45.833 0.00 0.00 0.00 1.89
1993 4737 5.479306 GTCTCAAGGTCACTGCTAAATACA 58.521 41.667 0.00 0.00 0.00 2.29
1994 4738 5.578727 GTCTCAAGGTCACTGCTAAATACAG 59.421 44.000 0.00 0.00 41.08 2.74
2044 4788 4.917415 GTGTCATCTGAAATTTTCCGTTGG 59.083 41.667 6.68 0.00 0.00 3.77
2055 4799 7.650104 TGAAATTTTCCGTTGGTCTGTAATTTC 59.350 33.333 6.68 0.00 39.43 2.17
2114 4858 4.649674 TCGGTCTTATTCCTATCAAGCTGT 59.350 41.667 0.00 0.00 0.00 4.40
2118 4869 4.721776 TCTTATTCCTATCAAGCTGTGGGT 59.278 41.667 0.00 0.00 0.00 4.51
2130 4881 4.473477 AGCTGTGGGTAACTGAATCTAC 57.527 45.455 0.00 0.00 0.00 2.59
2139 4890 5.805994 GGGTAACTGAATCTACGAAGAACTG 59.194 44.000 0.00 0.00 34.73 3.16
2146 4897 1.968493 TCTACGAAGAACTGGCACCTT 59.032 47.619 0.00 0.00 0.00 3.50
2171 4922 0.107456 CCCAATCATCCTCCACCTCG 59.893 60.000 0.00 0.00 0.00 4.63
2176 4927 2.765807 ATCCTCCACCTCGCCCTG 60.766 66.667 0.00 0.00 0.00 4.45
2198 4949 0.521291 TGCGTGGCAGCTTACAAATC 59.479 50.000 9.68 0.00 38.13 2.17
2232 5019 4.586001 AGTCCTGCAGTCAAACATTTCAAT 59.414 37.500 13.81 0.00 0.00 2.57
2247 5035 6.681777 ACATTTCAATTTAGAGCTTGACCAC 58.318 36.000 0.00 0.00 31.41 4.16
2271 5060 5.437263 GCTGAAACATTTTGCAGAAATGTG 58.563 37.500 26.29 19.20 46.62 3.21
2281 5070 3.753815 TGCAGAAATGTGACCTTGATCA 58.246 40.909 0.00 0.00 0.00 2.92
2283 5072 4.397103 TGCAGAAATGTGACCTTGATCATC 59.603 41.667 0.00 0.00 0.00 2.92
2317 5125 4.393834 TGAGCTGGTTACATGTTGCTTTA 58.606 39.130 2.30 0.00 0.00 1.85
2343 5158 8.816640 TTCATGAGCCAAAAGAATTCTTAAAC 57.183 30.769 20.76 10.88 34.61 2.01
2367 5182 1.210155 GTTGAGCCGACAACATGCC 59.790 57.895 12.10 0.00 46.19 4.40
2504 5805 5.770162 CCCTTGAAAGACTCCAGTACAAAAT 59.230 40.000 0.00 0.00 0.00 1.82
2526 5827 0.249868 TTCTTCACCGGAGTGCACAG 60.250 55.000 21.04 9.77 44.16 3.66
2530 5831 1.742880 CACCGGAGTGCACAGGATG 60.743 63.158 25.87 17.70 38.84 3.51
2658 6277 9.042450 TGGGTATTCCGTATATTCATCAGTTAT 57.958 33.333 0.00 0.00 38.76 1.89
2768 6389 5.163513 CAGGCATGTGGTATTTTTGAAGTC 58.836 41.667 0.00 0.00 0.00 3.01
2795 6416 7.307989 CGGCGGATGATTGTTTAGATATTTTCT 60.308 37.037 0.00 0.00 38.57 2.52
2796 6417 8.999431 GGCGGATGATTGTTTAGATATTTTCTA 58.001 33.333 0.00 0.00 35.79 2.10
2817 6438 8.691661 TTCTACTTTAGAAAAACAAGCCAGAT 57.308 30.769 0.00 0.00 41.53 2.90
2866 6487 9.654663 CTAGCTAAAAGTTTTCTAAAGGAGCTA 57.345 33.333 18.72 18.72 37.66 3.32
2904 6525 4.783764 TCCGCATATACTGACAGGTATG 57.216 45.455 18.55 18.55 34.65 2.39
2920 6541 5.163591 ACAGGTATGTTTGATGCATGATGTG 60.164 40.000 2.46 0.00 35.63 3.21
2976 6597 1.996191 GAGCTGTGATTCTGGTTCGAC 59.004 52.381 0.00 0.00 0.00 4.20
2988 6609 2.993899 CTGGTTCGACTTGTGGTATGAC 59.006 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.217111 TCTTATCAATCATTGTACATGCCCTTA 58.783 33.333 0.00 0.00 0.00 2.69
3 4 7.062322 TCTTATCAATCATTGTACATGCCCTT 58.938 34.615 0.00 0.00 0.00 3.95
4 5 6.604171 TCTTATCAATCATTGTACATGCCCT 58.396 36.000 0.00 0.00 0.00 5.19
5 6 6.882610 TCTTATCAATCATTGTACATGCCC 57.117 37.500 0.00 0.00 0.00 5.36
43 44 8.969260 TGTCATCTCTAAATTACATGCAAGAT 57.031 30.769 0.00 0.00 0.00 2.40
73 74 7.581213 AGTGATGGTTCATTGTAGACAAAAA 57.419 32.000 0.00 0.00 39.55 1.94
74 75 7.581213 AAGTGATGGTTCATTGTAGACAAAA 57.419 32.000 0.00 0.00 39.55 2.44
75 76 8.564574 GTTAAGTGATGGTTCATTGTAGACAAA 58.435 33.333 0.00 0.00 39.55 2.83
78 79 6.879458 AGGTTAAGTGATGGTTCATTGTAGAC 59.121 38.462 0.00 0.00 33.56 2.59
79 80 7.016153 AGGTTAAGTGATGGTTCATTGTAGA 57.984 36.000 0.00 0.00 33.56 2.59
82 83 8.650143 AATAAGGTTAAGTGATGGTTCATTGT 57.350 30.769 0.00 0.00 33.56 2.71
86 87 8.698973 TGAAAATAAGGTTAAGTGATGGTTCA 57.301 30.769 0.00 0.00 0.00 3.18
118 119 9.256228 TGACTCCTAGTGTATTTAAGAATGTCT 57.744 33.333 0.00 0.00 0.00 3.41
145 146 1.593933 GACCGTCACGTGCAAGTTTTA 59.406 47.619 11.67 0.00 0.00 1.52
193 194 4.655963 ACAAGTTAGCTGACCACAATCAT 58.344 39.130 4.79 0.00 0.00 2.45
233 234 3.390135 CACGGAATACATACGGAAGCAT 58.610 45.455 0.00 0.00 0.00 3.79
293 294 0.103208 CCTCCGCCACTGATAGTCAC 59.897 60.000 0.00 0.00 0.00 3.67
315 316 3.540211 CCACAGGCACTAGACCAAG 57.460 57.895 0.00 0.00 36.02 3.61
368 369 6.085121 TGCGTTTACACAGACATAATTACG 57.915 37.500 0.00 0.00 0.00 3.18
401 402 7.145985 GGATCGCACAGATGTAAATAGAAGTA 58.854 38.462 0.00 0.00 40.26 2.24
406 407 5.292765 AGTGGATCGCACAGATGTAAATAG 58.707 41.667 14.31 0.00 40.26 1.73
414 415 1.737029 CGACAAGTGGATCGCACAGAT 60.737 52.381 14.31 2.10 43.51 2.90
421 422 0.797249 GTCGACCGACAAGTGGATCG 60.797 60.000 16.57 0.00 44.02 3.69
471 472 5.411361 TCTTAAATTCCTTCGTGTGTCCATG 59.589 40.000 0.00 0.00 0.00 3.66
474 475 6.496338 AATCTTAAATTCCTTCGTGTGTCC 57.504 37.500 0.00 0.00 0.00 4.02
475 476 9.887406 TTTAAATCTTAAATTCCTTCGTGTGTC 57.113 29.630 0.00 0.00 0.00 3.67
500 501 8.352942 GTTCGAATCCTCATAGGCAATATTTTT 58.647 33.333 0.00 0.00 34.61 1.94
501 502 7.040409 GGTTCGAATCCTCATAGGCAATATTTT 60.040 37.037 0.00 0.00 34.61 1.82
502 503 6.431234 GGTTCGAATCCTCATAGGCAATATTT 59.569 38.462 0.00 0.00 34.61 1.40
505 506 4.593206 AGGTTCGAATCCTCATAGGCAATA 59.407 41.667 4.40 0.00 34.61 1.90
507 508 2.771943 AGGTTCGAATCCTCATAGGCAA 59.228 45.455 4.40 0.00 34.61 4.52
508 509 2.398588 AGGTTCGAATCCTCATAGGCA 58.601 47.619 4.40 0.00 34.61 4.75
522 523 6.186224 GCGCATGCATTACCTATAGGTTCG 62.186 50.000 29.09 17.88 43.48 3.95
523 524 3.125316 GCGCATGCATTACCTATAGGTTC 59.875 47.826 29.09 15.77 43.48 3.62
524 525 3.074412 GCGCATGCATTACCTATAGGTT 58.926 45.455 29.09 10.11 43.48 3.50
525 526 2.699954 GCGCATGCATTACCTATAGGT 58.300 47.619 27.24 27.24 46.12 3.08
529 530 3.074412 GGTTAGCGCATGCATTACCTAT 58.926 45.455 19.57 0.00 46.23 2.57
530 531 2.158885 TGGTTAGCGCATGCATTACCTA 60.159 45.455 19.57 6.70 46.23 3.08
532 533 1.021202 TGGTTAGCGCATGCATTACC 58.979 50.000 19.57 18.03 46.23 2.85
533 534 1.594518 CGTGGTTAGCGCATGCATTAC 60.595 52.381 19.57 9.34 46.23 1.89
536 537 1.431488 CTCGTGGTTAGCGCATGCAT 61.431 55.000 19.57 8.14 46.23 3.96
537 538 2.047750 TCGTGGTTAGCGCATGCA 60.048 55.556 19.57 0.00 46.23 3.96
538 539 1.756375 CTCTCGTGGTTAGCGCATGC 61.756 60.000 11.47 7.91 43.24 4.06
539 540 0.458543 ACTCTCGTGGTTAGCGCATG 60.459 55.000 11.47 0.00 0.00 4.06
540 541 0.179134 GACTCTCGTGGTTAGCGCAT 60.179 55.000 11.47 0.00 0.00 4.73
541 542 1.211969 GACTCTCGTGGTTAGCGCA 59.788 57.895 11.47 0.00 0.00 6.09
542 543 1.868251 CGACTCTCGTGGTTAGCGC 60.868 63.158 0.00 0.00 34.72 5.92
544 545 0.520827 CGTCGACTCTCGTGGTTAGC 60.521 60.000 14.70 0.00 41.35 3.09
546 547 0.952497 AGCGTCGACTCTCGTGGTTA 60.952 55.000 14.70 0.00 41.35 2.85
547 548 0.952497 TAGCGTCGACTCTCGTGGTT 60.952 55.000 12.07 0.00 41.35 3.67
548 549 0.952497 TTAGCGTCGACTCTCGTGGT 60.952 55.000 12.07 3.54 41.35 4.16
549 550 0.377554 ATTAGCGTCGACTCTCGTGG 59.622 55.000 12.07 0.00 41.35 4.94
550 551 1.840741 CAATTAGCGTCGACTCTCGTG 59.159 52.381 12.07 5.11 41.35 4.35
552 553 0.840729 GCAATTAGCGTCGACTCTCG 59.159 55.000 12.07 0.00 42.10 4.04
610 611 3.194755 ACCCTTGAATTTATTTGTCGGGC 59.805 43.478 0.00 0.00 32.40 6.13
611 612 5.067283 CCTACCCTTGAATTTATTTGTCGGG 59.933 44.000 0.00 0.00 35.32 5.14
852 853 9.685276 TCAGGATGAATGTATGTAAATTCTGTT 57.315 29.630 4.94 0.00 45.97 3.16
906 1208 9.862371 TTTTGTTTTAGCACTTGATTCACTTTA 57.138 25.926 0.00 0.00 0.00 1.85
962 1264 3.861797 GGGCGTGATCCGTGGGAT 61.862 66.667 0.00 0.00 46.28 3.85
1094 3793 0.037326 AGCGCTCTGAATTCGTGGAA 60.037 50.000 2.64 0.00 0.00 3.53
1095 3794 0.458543 GAGCGCTCTGAATTCGTGGA 60.459 55.000 29.88 0.00 0.00 4.02
1100 3799 1.135867 GATCGGAGCGCTCTGAATTC 58.864 55.000 43.25 34.19 46.84 2.17
1103 3802 2.052104 TGGATCGGAGCGCTCTGAA 61.052 57.895 43.25 29.14 46.84 3.02
1135 3834 1.199558 GACTCTCGAGGTGTGGTGTAC 59.800 57.143 13.56 0.00 0.00 2.90
1136 3835 1.531423 GACTCTCGAGGTGTGGTGTA 58.469 55.000 13.56 0.00 0.00 2.90
1203 3911 1.118965 TCACCGCCTTCTTCCTGTCA 61.119 55.000 0.00 0.00 0.00 3.58
1603 4332 1.073722 CTTCTTGGGGAGCAGCACA 59.926 57.895 0.00 0.00 0.00 4.57
1699 4428 1.077787 CGGCTATTCCTTGGTGGCA 60.078 57.895 0.00 0.00 35.26 4.92
1711 4440 0.178885 TAGGTTATGGGGGCGGCTAT 60.179 55.000 9.56 4.06 0.00 2.97
1732 4469 5.324409 AGAAATGGATCTAAGCAACACCAA 58.676 37.500 0.00 0.00 0.00 3.67
1733 4470 4.922206 AGAAATGGATCTAAGCAACACCA 58.078 39.130 0.00 0.00 0.00 4.17
1734 4471 4.943705 TGAGAAATGGATCTAAGCAACACC 59.056 41.667 0.00 0.00 0.00 4.16
1778 4515 6.018425 CACTAAAGACTAGCAGGCATTACATG 60.018 42.308 0.00 0.00 0.00 3.21
1855 4594 6.509656 TGAAATGATTGCATCTTTAGCCATC 58.490 36.000 0.00 0.00 35.41 3.51
1885 4624 2.391616 TGCAGCCATAGACAGAACAG 57.608 50.000 0.00 0.00 0.00 3.16
1892 4631 3.273434 TGAAGTGATTGCAGCCATAGAC 58.727 45.455 0.00 0.00 0.00 2.59
1909 4648 7.433719 CGATAGGTAGAACACAAGAGATTGAAG 59.566 40.741 0.00 0.00 0.00 3.02
1934 4673 1.298116 CGCAAGATCAATGGCAGCG 60.298 57.895 0.00 0.00 43.02 5.18
1962 4701 4.731193 GCAGTGACCTTGAGACGTATAGAC 60.731 50.000 0.00 0.00 0.00 2.59
1974 4718 5.288712 CGTACTGTATTTAGCAGTGACCTTG 59.711 44.000 8.05 0.00 45.59 3.61
1992 4736 8.240883 AGAGAATTTACAAGTAAAGCGTACTG 57.759 34.615 10.70 2.57 38.30 2.74
1993 4737 8.305317 AGAGAGAATTTACAAGTAAAGCGTACT 58.695 33.333 10.70 6.69 38.30 2.73
1994 4738 8.463456 AGAGAGAATTTACAAGTAAAGCGTAC 57.537 34.615 10.70 2.96 38.30 3.67
1995 4739 8.922676 CAAGAGAGAATTTACAAGTAAAGCGTA 58.077 33.333 10.70 0.00 38.30 4.42
2044 4788 7.484035 AGATAAATCGCTGGAAATTACAGAC 57.516 36.000 9.83 0.00 38.20 3.51
2055 4799 4.962155 AGGAGGTAAAGATAAATCGCTGG 58.038 43.478 0.00 0.00 0.00 4.85
2093 4837 5.059833 CCACAGCTTGATAGGAATAAGACC 58.940 45.833 0.00 0.00 0.00 3.85
2094 4838 5.059833 CCCACAGCTTGATAGGAATAAGAC 58.940 45.833 0.00 0.00 0.00 3.01
2095 4839 4.721776 ACCCACAGCTTGATAGGAATAAGA 59.278 41.667 0.00 0.00 0.00 2.10
2114 4858 5.479375 AGTTCTTCGTAGATTCAGTTACCCA 59.521 40.000 0.00 0.00 35.04 4.51
2118 4869 5.047590 TGCCAGTTCTTCGTAGATTCAGTTA 60.048 40.000 0.00 0.00 35.04 2.24
2130 4881 0.250295 TCCAAGGTGCCAGTTCTTCG 60.250 55.000 0.00 0.00 0.00 3.79
2146 4897 2.175499 GTGGAGGATGATTGGGAATCCA 59.825 50.000 0.09 0.00 44.17 3.41
2176 4927 4.445545 GTAAGCTGCCACGCACGC 62.446 66.667 0.00 0.00 33.79 5.34
2177 4928 2.111932 TTTGTAAGCTGCCACGCACG 62.112 55.000 0.00 0.00 33.79 5.34
2178 4929 0.240945 ATTTGTAAGCTGCCACGCAC 59.759 50.000 0.00 0.00 33.79 5.34
2179 4930 0.521291 GATTTGTAAGCTGCCACGCA 59.479 50.000 0.00 0.00 36.92 5.24
2198 4949 0.037882 TGCAGGACTTCTGAAGCTCG 60.038 55.000 17.00 5.06 46.18 5.03
2232 5019 1.343142 TCAGCGTGGTCAAGCTCTAAA 59.657 47.619 8.34 0.00 44.04 1.85
2247 5035 4.209703 ACATTTCTGCAAAATGTTTCAGCG 59.790 37.500 22.96 7.68 45.52 5.18
2271 5060 4.892934 ACTACAGAGAGGATGATCAAGGTC 59.107 45.833 0.00 0.00 0.00 3.85
2281 5070 3.030291 CCAGCTCAACTACAGAGAGGAT 58.970 50.000 0.00 0.00 35.09 3.24
2283 5072 2.175202 ACCAGCTCAACTACAGAGAGG 58.825 52.381 0.00 0.00 36.50 3.69
2317 5125 9.428097 GTTTAAGAATTCTTTTGGCTCATGAAT 57.572 29.630 25.02 0.00 37.40 2.57
2343 5158 0.868406 GTTGTCGGCTCAACTCCAAG 59.132 55.000 12.73 0.00 42.76 3.61
2378 5193 3.356290 ACCTGCATCAAACAACTATCCC 58.644 45.455 0.00 0.00 0.00 3.85
2504 5805 0.179234 TGCACTCCGGTGAAGAACAA 59.821 50.000 11.17 0.00 45.61 2.83
2526 5827 4.164843 TGCTTATTTACCCAGGACATCC 57.835 45.455 0.00 0.00 0.00 3.51
2530 5831 7.122204 ACATTAACTTGCTTATTTACCCAGGAC 59.878 37.037 0.00 0.00 0.00 3.85
2614 6233 3.780294 ACCCACTCTGCATTCAACCTATA 59.220 43.478 0.00 0.00 0.00 1.31
2622 6241 2.213499 CGGAATACCCACTCTGCATTC 58.787 52.381 0.00 0.00 34.14 2.67
2768 6389 1.948104 TCTAAACAATCATCCGCCGG 58.052 50.000 0.00 0.00 0.00 6.13
2796 6417 9.529325 GTTTTATCTGGCTTGTTTTTCTAAAGT 57.471 29.630 0.00 0.00 0.00 2.66
2904 6525 3.853831 TGTCCACATCATGCATCAAAC 57.146 42.857 0.00 0.00 0.00 2.93
2920 6541 6.534793 ACAAAGTGTTTCATTTGAACATGTCC 59.465 34.615 0.00 0.00 38.42 4.02
2976 6597 0.719465 GCGTTCGGTCATACCACAAG 59.281 55.000 0.00 0.00 38.47 3.16
2988 6609 2.202690 TGGTATGAGCGCGTTCGG 60.203 61.111 18.23 0.00 35.95 4.30


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

AutoCloner maintained by Alex Coulton.