Multiple sequence alignment - TraesCS6D01G246800

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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 TraesCS6D01G246800 chr6D 100.000 8001 0 0 1 8001 349930993 349922993 0.000000e+00 14776.0
1 TraesCS6D01G246800 chr6D 90.099 606 44 5 2 594 68725681 68725079 0.000000e+00 773.0
2 TraesCS6D01G246800 chr6D 88.961 616 46 9 2 600 78765708 78765098 0.000000e+00 741.0
3 TraesCS6D01G246800 chr6D 88.216 611 57 13 1 599 192100792 192100185 0.000000e+00 715.0
4 TraesCS6D01G246800 chr6D 100.000 141 0 0 8454 8594 349922540 349922400 2.380000e-65 261.0
5 TraesCS6D01G246800 chr6D 100.000 31 0 0 3255 3285 10171020 10171050 3.350000e-04 58.4
6 TraesCS6D01G246800 chr6D 100.000 30 0 0 3267 3296 366679095 366679124 1.000000e-03 56.5
7 TraesCS6D01G246800 chr6D 81.538 65 10 2 3257 3320 101241954 101241891 1.600000e-02 52.8
8 TraesCS6D01G246800 chr6B 96.143 4615 119 21 786 5365 530557938 530562528 0.000000e+00 7481.0
9 TraesCS6D01G246800 chr6B 97.031 1044 26 4 5895 6936 530563054 530564094 0.000000e+00 1751.0
10 TraesCS6D01G246800 chr6B 95.480 885 15 5 6960 7826 530564432 530565309 0.000000e+00 1389.0
11 TraesCS6D01G246800 chr6B 97.211 502 12 1 5394 5895 530562523 530563022 0.000000e+00 848.0
12 TraesCS6D01G246800 chr6B 89.482 618 45 6 1 599 640694409 640695025 0.000000e+00 763.0
13 TraesCS6D01G246800 chr6B 100.000 66 0 0 8515 8580 530565599 530565664 1.170000e-23 122.0
14 TraesCS6D01G246800 chr6B 90.698 86 8 0 7915 8000 68903743 68903658 1.960000e-21 115.0
15 TraesCS6D01G246800 chr6A 97.996 3642 46 9 1508 5133 494463281 494466911 0.000000e+00 6296.0
16 TraesCS6D01G246800 chr6A 97.587 1948 24 7 5895 7826 494467888 494469828 0.000000e+00 3315.0
17 TraesCS6D01G246800 chr6A 91.667 936 38 19 601 1521 494462194 494463104 0.000000e+00 1260.0
18 TraesCS6D01G246800 chr6A 98.974 585 6 0 5311 5895 494467272 494467856 0.000000e+00 1048.0
19 TraesCS6D01G246800 chr6A 95.885 243 7 2 5073 5315 494466912 494467151 2.910000e-104 390.0
20 TraesCS6D01G246800 chr6A 92.208 154 12 0 7827 7980 494469891 494470044 1.450000e-52 219.0
21 TraesCS6D01G246800 chr6A 89.262 149 8 2 8454 8594 494470322 494470470 6.850000e-41 180.0
22 TraesCS6D01G246800 chr6A 86.517 89 12 0 7912 8000 96144820 96144908 1.970000e-16 99.0
23 TraesCS6D01G246800 chr6A 83.333 96 16 0 7905 8000 519213086 519213181 1.190000e-13 89.8
24 TraesCS6D01G246800 chr7B 89.984 619 42 5 1 600 710727561 710728178 0.000000e+00 782.0
25 TraesCS6D01G246800 chr7B 89.268 615 48 5 2 601 228361 228972 0.000000e+00 754.0
26 TraesCS6D01G246800 chr7B 88.293 615 47 10 1 594 121112529 121111919 0.000000e+00 713.0
27 TraesCS6D01G246800 chr7B 87.061 626 46 15 1 594 121163885 121163263 0.000000e+00 675.0
28 TraesCS6D01G246800 chr7B 92.784 97 7 0 3224 3320 33076094 33075998 3.230000e-29 141.0
29 TraesCS6D01G246800 chr7B 88.785 107 11 1 3215 3320 156958903 156958797 7.000000e-26 130.0
30 TraesCS6D01G246800 chr1D 90.049 613 48 4 1 600 379151384 379151996 0.000000e+00 782.0
31 TraesCS6D01G246800 chr1D 89.216 102 9 2 3221 3320 373419715 373419614 9.060000e-25 126.0
32 TraesCS6D01G246800 chr1D 89.583 96 10 0 7905 8000 307210215 307210120 1.170000e-23 122.0
33 TraesCS6D01G246800 chr1D 85.714 105 15 0 3224 3328 154021317 154021213 2.540000e-20 111.0
34 TraesCS6D01G246800 chr1D 84.848 99 11 3 3224 3320 31154765 31154861 7.100000e-16 97.1
35 TraesCS6D01G246800 chr1D 83.000 100 17 0 3223 3322 447920727 447920826 3.300000e-14 91.6
36 TraesCS6D01G246800 chr1D 84.536 97 7 1 3224 3320 444347475 444347387 1.190000e-13 89.8
37 TraesCS6D01G246800 chr5D 89.286 616 50 5 2 604 238781139 238780527 0.000000e+00 758.0
38 TraesCS6D01G246800 chr5D 89.216 102 11 0 7899 8000 377177227 377177328 2.520000e-25 128.0
39 TraesCS6D01G246800 chr5A 88.925 614 50 13 2 601 75341674 75341065 0.000000e+00 741.0
40 TraesCS6D01G246800 chr5A 86.458 96 13 0 7905 8000 431896723 431896628 1.180000e-18 106.0
41 TraesCS6D01G246800 chr4D 88.655 617 51 7 2 603 509444220 509443608 0.000000e+00 734.0
42 TraesCS6D01G246800 chr4D 88.119 101 11 1 3221 3320 503868681 503868581 1.520000e-22 119.0
43 TraesCS6D01G246800 chr4D 88.660 97 9 2 7905 8000 111131775 111131680 5.450000e-22 117.0
44 TraesCS6D01G246800 chr4D 85.321 109 15 1 3224 3332 484680064 484680171 2.540000e-20 111.0
45 TraesCS6D01G246800 chr2D 87.774 638 54 11 2 621 73828115 73827484 0.000000e+00 725.0
46 TraesCS6D01G246800 chr3D 88.293 615 54 6 2 601 461601364 461601975 0.000000e+00 721.0
47 TraesCS6D01G246800 chr3D 93.814 97 6 0 3224 3320 352795403 352795499 6.950000e-31 147.0
48 TraesCS6D01G246800 chr2A 88.293 615 54 8 1 600 498083925 498084536 0.000000e+00 721.0
49 TraesCS6D01G246800 chr2A 94.118 51 3 0 2868 2918 205194331 205194281 2.570000e-10 78.7
50 TraesCS6D01G246800 chr3B 88.084 621 52 9 1 599 331623885 331624505 0.000000e+00 717.0
51 TraesCS6D01G246800 chr3A 87.188 601 62 11 7 600 596296022 596295430 0.000000e+00 669.0
52 TraesCS6D01G246800 chr1B 79.675 615 95 13 4902 5505 427070703 427070108 4.800000e-112 416.0
53 TraesCS6D01G246800 chr1B 89.720 107 10 1 3225 3330 67444644 67444538 1.500000e-27 135.0
54 TraesCS6D01G246800 chr1B 87.255 102 13 0 7899 8000 90310186 90310287 5.450000e-22 117.0
55 TraesCS6D01G246800 chr7D 95.876 97 4 0 3224 3320 83625759 83625663 3.210000e-34 158.0
56 TraesCS6D01G246800 chr7D 89.720 107 10 1 3215 3320 193409951 193409845 1.500000e-27 135.0
57 TraesCS6D01G246800 chr7D 85.294 102 15 0 7899 8000 376356196 376356095 1.180000e-18 106.0
58 TraesCS6D01G246800 chr7A 95.876 97 4 0 3224 3320 85209398 85209302 3.210000e-34 158.0
59 TraesCS6D01G246800 chr4B 93.814 97 6 0 3224 3320 609499535 609499439 6.950000e-31 147.0
60 TraesCS6D01G246800 chr4B 90.816 98 9 0 3224 3321 472388264 472388167 1.950000e-26 132.0
61 TraesCS6D01G246800 chr4B 89.583 96 10 0 7905 8000 500109058 500109153 1.170000e-23 122.0
62 TraesCS6D01G246800 chr4B 90.385 52 5 0 7949 8000 584051366 584051417 1.550000e-07 69.4
63 TraesCS6D01G246800 chr2B 92.000 100 8 0 3221 3320 679898248 679898347 3.230000e-29 141.0
64 TraesCS6D01G246800 chr2B 87.288 118 13 1 3216 3333 97569967 97569852 5.410000e-27 134.0
65 TraesCS6D01G246800 chr5B 88.119 101 12 0 3221 3321 595228558 595228458 4.210000e-23 121.0
66 TraesCS6D01G246800 chr5B 85.526 76 11 0 7915 7990 672809330 672809405 7.150000e-11 80.5
67 TraesCS6D01G246800 chrUn 86.047 86 12 0 7915 8000 23375141 23375056 9.190000e-15 93.5
68 TraesCS6D01G246800 chrUn 92.857 42 3 0 3247 3288 371796272 371796313 2.590000e-05 62.1


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 TraesCS6D01G246800 chr6D 349922400 349930993 8593 True 7518.500000 14776 100.000 1 8594 2 chr6D.!!$R5 8593
1 TraesCS6D01G246800 chr6D 68725079 68725681 602 True 773.000000 773 90.099 2 594 1 chr6D.!!$R1 592
2 TraesCS6D01G246800 chr6D 78765098 78765708 610 True 741.000000 741 88.961 2 600 1 chr6D.!!$R2 598
3 TraesCS6D01G246800 chr6D 192100185 192100792 607 True 715.000000 715 88.216 1 599 1 chr6D.!!$R4 598
4 TraesCS6D01G246800 chr6B 530557938 530565664 7726 False 2318.200000 7481 97.173 786 8580 5 chr6B.!!$F2 7794
5 TraesCS6D01G246800 chr6B 640694409 640695025 616 False 763.000000 763 89.482 1 599 1 chr6B.!!$F1 598
6 TraesCS6D01G246800 chr6A 494462194 494470470 8276 False 1815.428571 6296 94.797 601 8594 7 chr6A.!!$F3 7993
7 TraesCS6D01G246800 chr7B 710727561 710728178 617 False 782.000000 782 89.984 1 600 1 chr7B.!!$F2 599
8 TraesCS6D01G246800 chr7B 228361 228972 611 False 754.000000 754 89.268 2 601 1 chr7B.!!$F1 599
9 TraesCS6D01G246800 chr7B 121111919 121112529 610 True 713.000000 713 88.293 1 594 1 chr7B.!!$R2 593
10 TraesCS6D01G246800 chr7B 121163263 121163885 622 True 675.000000 675 87.061 1 594 1 chr7B.!!$R3 593
11 TraesCS6D01G246800 chr1D 379151384 379151996 612 False 782.000000 782 90.049 1 600 1 chr1D.!!$F2 599
12 TraesCS6D01G246800 chr5D 238780527 238781139 612 True 758.000000 758 89.286 2 604 1 chr5D.!!$R1 602
13 TraesCS6D01G246800 chr5A 75341065 75341674 609 True 741.000000 741 88.925 2 601 1 chr5A.!!$R1 599
14 TraesCS6D01G246800 chr4D 509443608 509444220 612 True 734.000000 734 88.655 2 603 1 chr4D.!!$R3 601
15 TraesCS6D01G246800 chr2D 73827484 73828115 631 True 725.000000 725 87.774 2 621 1 chr2D.!!$R1 619
16 TraesCS6D01G246800 chr3D 461601364 461601975 611 False 721.000000 721 88.293 2 601 1 chr3D.!!$F2 599
17 TraesCS6D01G246800 chr2A 498083925 498084536 611 False 721.000000 721 88.293 1 600 1 chr2A.!!$F1 599
18 TraesCS6D01G246800 chr3B 331623885 331624505 620 False 717.000000 717 88.084 1 599 1 chr3B.!!$F1 598
19 TraesCS6D01G246800 chr3A 596295430 596296022 592 True 669.000000 669 87.188 7 600 1 chr3A.!!$R1 593
20 TraesCS6D01G246800 chr1B 427070108 427070703 595 True 416.000000 416 79.675 4902 5505 1 chr1B.!!$R2 603

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
770 833 0.103282 TCCCCCTCAACCCCCTTTAA 60.103 55.000 0.00 0.00 0.00 1.52 F
1730 1998 1.000233 CAGGCCCTGCACCCATTTA 60.000 57.895 0.00 0.00 0.00 1.40 F
2048 2317 1.828595 ACACACTGCATACATACGGGA 59.171 47.619 0.00 0.00 0.00 5.14 F
3610 3906 0.623194 TGCCTTATTGCCAGCACCTA 59.377 50.000 0.00 0.00 0.00 3.08 F
4179 4475 8.427276 TGCATGATTGTGATAAACTAGATCTCT 58.573 33.333 0.00 0.00 0.00 3.10 F
4885 5189 3.488047 CCTTCACTGCAGGATTTATTGCG 60.488 47.826 19.93 0.25 43.13 4.85 F
5152 5513 1.017387 GTGCCCACTAGTAGCATTGC 58.983 55.000 19.41 0.00 39.04 3.56 F
6783 7345 1.016130 ATTCTGCGTGTGAGAAGGCG 61.016 55.000 0.00 0.00 33.01 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2365 0.036388 TAGAAACAGAAGGGCAGCGG 60.036 55.000 0.0 0.0 0.00 5.52 R
3551 3827 4.512944 ACGATGCTGATGGACATAAATGAC 59.487 41.667 0.0 0.0 0.00 3.06 R
4055 4351 5.826601 TGCATCAAACACTCAAAGTTACA 57.173 34.783 0.0 0.0 0.00 2.41 R
4885 5189 3.019564 AGGTCAAATGGCAATACAGCTC 58.980 45.455 0.0 0.0 34.17 4.09 R
5152 5513 4.330074 AGCGTAATTCAAGAATGAGAACCG 59.670 41.667 0.0 0.0 36.78 4.44 R
6607 7169 4.283467 ACAAGCAATTCTTTACCCCCTTTC 59.717 41.667 0.0 0.0 31.27 2.62 R
6814 7376 4.595781 ACACCACCATTTCTCAGTTACCTA 59.404 41.667 0.0 0.0 0.00 3.08 R
7866 8841 1.063469 AGTTTGGCAGTTTCGTGTTCG 59.937 47.619 0.0 0.0 38.55 3.95 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
43 44 0.392193 CCACATCTTCTTCGCCTGCT 60.392 55.000 0.00 0.00 0.00 4.24
390 407 2.123683 CGCCTCCTCCAGAGCCTA 60.124 66.667 0.00 0.00 41.74 3.93
507 557 3.477210 ACTTCTGGACCTCTTGTTGTC 57.523 47.619 0.00 0.00 0.00 3.18
543 597 7.231925 TGTGTGTTCTGAACTAGTCCTTGTATA 59.768 37.037 20.18 0.00 0.00 1.47
550 604 7.124298 TCTGAACTAGTCCTTGTATATGTGCTT 59.876 37.037 0.00 0.00 0.00 3.91
609 663 6.506147 AGCCTTTTTCGGTAATAACGTTTTT 58.494 32.000 5.91 7.78 0.00 1.94
642 696 1.401931 CCGAGGCAAGCAAAACTCATG 60.402 52.381 0.00 0.00 0.00 3.07
650 704 4.585364 CAAGCAAAACTCATGATCTAGCG 58.415 43.478 0.00 0.00 0.00 4.26
664 718 8.775527 TCATGATCTAGCGAGTAGTAGTAAAAG 58.224 37.037 0.00 0.00 0.00 2.27
665 719 8.775527 CATGATCTAGCGAGTAGTAGTAAAAGA 58.224 37.037 0.00 0.00 0.00 2.52
666 720 8.728337 TGATCTAGCGAGTAGTAGTAAAAGAA 57.272 34.615 0.00 0.00 0.00 2.52
667 721 8.828644 TGATCTAGCGAGTAGTAGTAAAAGAAG 58.171 37.037 0.00 0.00 0.00 2.85
672 726 8.745464 AGCGAGTAGTAGTAAAAGAAGAAAAG 57.255 34.615 0.00 0.00 0.00 2.27
674 728 8.852380 GCGAGTAGTAGTAAAAGAAGAAAAGAG 58.148 37.037 0.00 0.00 0.00 2.85
700 754 3.063045 CGTAAGGCCTTGTTCGGTTAATC 59.937 47.826 28.77 3.10 0.00 1.75
706 765 3.369576 GCCTTGTTCGGTTAATCTCCTCT 60.370 47.826 0.00 0.00 0.00 3.69
711 770 4.770531 TGTTCGGTTAATCTCCTCTCAAGA 59.229 41.667 0.00 0.00 0.00 3.02
763 826 2.958818 GGATTTAATCCCCCTCAACCC 58.041 52.381 12.74 0.00 43.88 4.11
764 827 2.425829 GGATTTAATCCCCCTCAACCCC 60.426 54.545 12.74 0.00 43.88 4.95
765 828 1.012395 TTTAATCCCCCTCAACCCCC 58.988 55.000 0.00 0.00 0.00 5.40
766 829 0.124522 TTAATCCCCCTCAACCCCCT 59.875 55.000 0.00 0.00 0.00 4.79
767 830 0.124522 TAATCCCCCTCAACCCCCTT 59.875 55.000 0.00 0.00 0.00 3.95
768 831 0.784154 AATCCCCCTCAACCCCCTTT 60.784 55.000 0.00 0.00 0.00 3.11
769 832 0.124522 ATCCCCCTCAACCCCCTTTA 59.875 55.000 0.00 0.00 0.00 1.85
770 833 0.103282 TCCCCCTCAACCCCCTTTAA 60.103 55.000 0.00 0.00 0.00 1.52
782 845 2.094752 CCCCCTTTAAATCAGCACAACG 60.095 50.000 0.00 0.00 0.00 4.10
909 972 3.681835 ACCACTCGTCGCCACTCC 61.682 66.667 0.00 0.00 0.00 3.85
1555 1819 2.414138 GCATGCTTGAATTGTTGGAAGC 59.586 45.455 11.37 0.00 41.03 3.86
1577 1841 3.626217 CAGCAGTTGAGTGATGTATGCAT 59.374 43.478 3.79 3.79 38.18 3.96
1667 1935 9.524106 GGTTTGTTTTTACTGCTTAGTTAACAT 57.476 29.630 8.61 0.00 0.00 2.71
1675 1943 6.969828 ACTGCTTAGTTAACATTGTAGCTC 57.030 37.500 8.61 0.00 0.00 4.09
1691 1959 2.906354 AGCTCCAATAAGCCAGTAACG 58.094 47.619 0.00 0.00 43.56 3.18
1692 1960 1.330829 GCTCCAATAAGCCAGTAACGC 59.669 52.381 0.00 0.00 36.22 4.84
1693 1961 2.906354 CTCCAATAAGCCAGTAACGCT 58.094 47.619 0.00 0.00 38.53 5.07
1694 1962 2.866762 CTCCAATAAGCCAGTAACGCTC 59.133 50.000 0.00 0.00 34.84 5.03
1695 1963 1.940613 CCAATAAGCCAGTAACGCTCC 59.059 52.381 0.00 0.00 34.84 4.70
1696 1964 2.420129 CCAATAAGCCAGTAACGCTCCT 60.420 50.000 0.00 0.00 34.84 3.69
1697 1965 3.181469 CCAATAAGCCAGTAACGCTCCTA 60.181 47.826 0.00 0.00 34.84 2.94
1698 1966 4.439057 CAATAAGCCAGTAACGCTCCTAA 58.561 43.478 0.00 0.00 34.84 2.69
1699 1967 4.957684 ATAAGCCAGTAACGCTCCTAAT 57.042 40.909 0.00 0.00 34.84 1.73
1730 1998 1.000233 CAGGCCCTGCACCCATTTA 60.000 57.895 0.00 0.00 0.00 1.40
1750 2018 8.017373 CCATTTAAGTAAGATATGCATCCGTTG 58.983 37.037 0.19 0.00 0.00 4.10
2015 2284 2.378547 TGGGCAATTTAGGAGAACAGGT 59.621 45.455 0.00 0.00 0.00 4.00
2048 2317 1.828595 ACACACTGCATACATACGGGA 59.171 47.619 0.00 0.00 0.00 5.14
2096 2365 3.431486 CCACTGGAGAAAGAGTATGGCTC 60.431 52.174 0.00 0.00 44.45 4.70
2521 2790 7.929941 TGTTGTTAATGAATGCAGTATACCA 57.070 32.000 0.00 0.00 0.00 3.25
2557 2826 6.183361 ACCAGTTTTAAGTTCCATCTCAGTCT 60.183 38.462 0.00 0.00 0.00 3.24
2711 2980 9.617523 TCTTGAAAGATCATAATCACTGCATTA 57.382 29.630 0.00 0.00 34.96 1.90
3370 3646 3.931907 TCCTTGACAATACCTCCATGG 57.068 47.619 4.97 4.97 42.93 3.66
3459 3735 3.197333 ACTGCTAGAGTCAGTGATGCAAT 59.803 43.478 0.00 0.00 42.63 3.56
3551 3827 1.873591 AGCAGCGGTACTTGTTTTGAG 59.126 47.619 0.00 0.00 0.00 3.02
3610 3906 0.623194 TGCCTTATTGCCAGCACCTA 59.377 50.000 0.00 0.00 0.00 3.08
3919 4215 9.185680 ACTTTTGTTCATCTGTAATATTACCCC 57.814 33.333 20.35 0.00 32.72 4.95
4179 4475 8.427276 TGCATGATTGTGATAAACTAGATCTCT 58.573 33.333 0.00 0.00 0.00 3.10
4885 5189 3.488047 CCTTCACTGCAGGATTTATTGCG 60.488 47.826 19.93 0.25 43.13 4.85
5152 5513 1.017387 GTGCCCACTAGTAGCATTGC 58.983 55.000 19.41 0.00 39.04 3.56
6607 7169 6.128200 TGTGTAAGTCAAATTGCAGCATAGAG 60.128 38.462 0.00 0.00 0.00 2.43
6783 7345 1.016130 ATTCTGCGTGTGAGAAGGCG 61.016 55.000 0.00 0.00 33.01 5.52
6987 7863 9.631257 TGTTGTTCATATGGTTGATTGATATCT 57.369 29.630 2.13 0.00 0.00 1.98
6997 7873 5.921408 GGTTGATTGATATCTCGTACACCTC 59.079 44.000 3.98 0.00 0.00 3.85
7256 8132 8.417106 TGCCATTTCTGACATTTACTTTGTTTA 58.583 29.630 0.00 0.00 0.00 2.01
7257 8133 9.255304 GCCATTTCTGACATTTACTTTGTTTAA 57.745 29.630 0.00 0.00 0.00 1.52
7527 8403 0.613012 ATGGGAAGCTGCTTTGGGTC 60.613 55.000 17.10 2.86 0.00 4.46
7866 8841 4.585955 TCACTTGTACTTCTCTGGTGTC 57.414 45.455 0.00 0.00 0.00 3.67
7902 8877 0.256752 AACTGGCTATGGCATGCTCA 59.743 50.000 18.92 14.25 40.87 4.26
7907 8882 1.958579 GGCTATGGCATGCTCATTTCA 59.041 47.619 21.59 10.15 40.87 2.69
7909 8884 2.621998 GCTATGGCATGCTCATTTCAGT 59.378 45.455 21.59 5.34 38.54 3.41
7941 8916 5.636965 GTCGTCGCTAGGTAGTCTATGAATA 59.363 44.000 0.00 0.00 0.00 1.75
7944 8919 6.313164 CGTCGCTAGGTAGTCTATGAATATGA 59.687 42.308 0.00 0.00 0.00 2.15
7982 8957 6.843069 ATTTTTGATGTTTGTTGTACTGCC 57.157 33.333 0.00 0.00 0.00 4.85
7983 8958 4.991153 TTTGATGTTTGTTGTACTGCCA 57.009 36.364 0.00 0.00 0.00 4.92
7984 8959 5.528043 TTTGATGTTTGTTGTACTGCCAT 57.472 34.783 0.00 0.00 0.00 4.40
7985 8960 4.502171 TGATGTTTGTTGTACTGCCATG 57.498 40.909 0.00 0.00 0.00 3.66
7986 8961 4.140536 TGATGTTTGTTGTACTGCCATGA 58.859 39.130 0.00 0.00 0.00 3.07
7987 8962 4.766373 TGATGTTTGTTGTACTGCCATGAT 59.234 37.500 0.00 0.00 0.00 2.45
7988 8963 5.243507 TGATGTTTGTTGTACTGCCATGATT 59.756 36.000 0.00 0.00 0.00 2.57
7989 8964 4.869215 TGTTTGTTGTACTGCCATGATTG 58.131 39.130 0.00 0.00 0.00 2.67
7990 8965 4.236935 GTTTGTTGTACTGCCATGATTGG 58.763 43.478 0.00 0.00 46.66 3.16
7991 8966 3.431673 TGTTGTACTGCCATGATTGGA 57.568 42.857 0.00 0.00 46.92 3.53
7992 8967 3.346315 TGTTGTACTGCCATGATTGGAG 58.654 45.455 0.00 0.00 46.92 3.86
7993 8968 3.008923 TGTTGTACTGCCATGATTGGAGA 59.991 43.478 0.00 0.00 46.92 3.71
7994 8969 4.202441 GTTGTACTGCCATGATTGGAGAT 58.798 43.478 0.00 0.00 46.92 2.75
7995 8970 5.104569 TGTTGTACTGCCATGATTGGAGATA 60.105 40.000 0.00 0.00 46.92 1.98
7996 8971 5.628797 TGTACTGCCATGATTGGAGATAA 57.371 39.130 0.00 0.00 46.92 1.75
7997 8972 6.000246 TGTACTGCCATGATTGGAGATAAA 58.000 37.500 0.00 0.00 46.92 1.40
7998 8973 6.604171 TGTACTGCCATGATTGGAGATAAAT 58.396 36.000 0.00 0.00 46.92 1.40
7999 8974 7.744733 TGTACTGCCATGATTGGAGATAAATA 58.255 34.615 0.00 0.00 46.92 1.40
8000 8975 8.385491 TGTACTGCCATGATTGGAGATAAATAT 58.615 33.333 0.00 0.00 46.92 1.28
8492 9469 1.152777 CACACCCCAGCAACAAGGA 60.153 57.895 0.00 0.00 0.00 3.36
8580 9563 6.977502 CGGCAATAATGTGATAACCAATGAAA 59.022 34.615 0.00 0.00 0.00 2.69
8581 9564 7.490725 CGGCAATAATGTGATAACCAATGAAAA 59.509 33.333 0.00 0.00 0.00 2.29
8583 9566 9.971744 GCAATAATGTGATAACCAATGAAAAAC 57.028 29.630 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.210227 TCCAAACGAATTGAGCAGACAA 58.790 40.909 7.17 0.00 41.85 3.18
390 407 3.335579 GGGAGCAAACAGACGTCTAATT 58.664 45.455 19.57 12.94 0.00 1.40
439 469 4.269844 GCCCAACACACACACAAAATAAAG 59.730 41.667 0.00 0.00 0.00 1.85
489 538 3.038280 TCAGACAACAAGAGGTCCAGAA 58.962 45.455 0.00 0.00 34.58 3.02
507 557 1.942657 CAGAACACACACCCAAGTCAG 59.057 52.381 0.00 0.00 0.00 3.51
543 597 0.879839 GCAAACCGCCAAAAGCACAT 60.880 50.000 0.00 0.00 44.04 3.21
550 604 8.245701 CTTTATAAATAAAGCAAACCGCCAAA 57.754 30.769 9.01 0.00 41.69 3.28
609 663 6.058833 TGCTTGCCTCGGTATTTATTTATCA 58.941 36.000 0.00 0.00 0.00 2.15
624 678 3.442977 AGATCATGAGTTTTGCTTGCCTC 59.557 43.478 0.09 0.00 0.00 4.70
642 696 9.044150 TCTTCTTTTACTACTACTCGCTAGATC 57.956 37.037 0.00 0.00 0.00 2.75
664 718 3.436015 GGCCTTACGGTTCTCTTTTCTTC 59.564 47.826 0.00 0.00 0.00 2.87
665 719 3.072622 AGGCCTTACGGTTCTCTTTTCTT 59.927 43.478 0.00 0.00 0.00 2.52
666 720 2.638363 AGGCCTTACGGTTCTCTTTTCT 59.362 45.455 0.00 0.00 0.00 2.52
667 721 3.055209 AGGCCTTACGGTTCTCTTTTC 57.945 47.619 0.00 0.00 0.00 2.29
672 726 2.074576 GAACAAGGCCTTACGGTTCTC 58.925 52.381 27.74 12.71 35.99 2.87
674 728 0.794473 CGAACAAGGCCTTACGGTTC 59.206 55.000 26.28 26.28 35.65 3.62
678 732 2.083167 TAACCGAACAAGGCCTTACG 57.917 50.000 20.00 21.99 33.69 3.18
706 765 5.048083 CGTCCAAATTTCCTCCAATTCTTGA 60.048 40.000 0.00 0.00 0.00 3.02
711 770 6.358974 AATTCGTCCAAATTTCCTCCAATT 57.641 33.333 0.00 0.00 0.00 2.32
721 780 3.125658 CCGTACCGAAATTCGTCCAAATT 59.874 43.478 14.58 0.00 38.40 1.82
729 788 5.333568 GGATTAAATCCCGTACCGAAATTCG 60.334 44.000 8.62 8.62 43.88 3.34
751 814 0.103282 TTAAAGGGGGTTGAGGGGGA 60.103 55.000 0.00 0.00 0.00 4.81
756 819 3.193479 GTGCTGATTTAAAGGGGGTTGAG 59.807 47.826 0.00 0.00 0.00 3.02
761 824 2.094752 CGTTGTGCTGATTTAAAGGGGG 60.095 50.000 0.00 0.00 0.00 5.40
762 825 2.094752 CCGTTGTGCTGATTTAAAGGGG 60.095 50.000 0.00 0.00 0.00 4.79
763 826 2.094752 CCCGTTGTGCTGATTTAAAGGG 60.095 50.000 0.00 0.00 35.93 3.95
764 827 2.817258 TCCCGTTGTGCTGATTTAAAGG 59.183 45.455 0.00 0.00 0.00 3.11
765 828 3.119849 CCTCCCGTTGTGCTGATTTAAAG 60.120 47.826 0.00 0.00 0.00 1.85
766 829 2.817258 CCTCCCGTTGTGCTGATTTAAA 59.183 45.455 0.00 0.00 0.00 1.52
767 830 2.039216 TCCTCCCGTTGTGCTGATTTAA 59.961 45.455 0.00 0.00 0.00 1.52
768 831 1.626321 TCCTCCCGTTGTGCTGATTTA 59.374 47.619 0.00 0.00 0.00 1.40
769 832 0.400213 TCCTCCCGTTGTGCTGATTT 59.600 50.000 0.00 0.00 0.00 2.17
770 833 0.036010 CTCCTCCCGTTGTGCTGATT 60.036 55.000 0.00 0.00 0.00 2.57
782 845 1.152419 GTCCCCTCTAGCTCCTCCC 60.152 68.421 0.00 0.00 0.00 4.30
1464 1538 4.226113 AGATGGTCTAGAACGCGATTAC 57.774 45.455 15.93 1.45 0.00 1.89
1555 1819 3.004862 TGCATACATCACTCAACTGCTG 58.995 45.455 0.00 0.00 0.00 4.41
1577 1841 2.472695 AGGTGTAAAATGCTCTGCGA 57.527 45.000 0.00 0.00 0.00 5.10
1640 1907 8.521176 TGTTAACTAAGCAGTAAAAACAAACCA 58.479 29.630 7.22 0.00 33.01 3.67
1667 1935 5.183228 GTTACTGGCTTATTGGAGCTACAA 58.817 41.667 15.23 15.23 42.32 2.41
1671 1939 2.906354 CGTTACTGGCTTATTGGAGCT 58.094 47.619 0.00 0.00 42.32 4.09
1675 1943 1.940613 GGAGCGTTACTGGCTTATTGG 59.059 52.381 0.00 0.00 41.72 3.16
1691 1959 2.094442 GCGGTCATAGGAGATTAGGAGC 60.094 54.545 0.00 0.00 0.00 4.70
1692 1960 3.157881 TGCGGTCATAGGAGATTAGGAG 58.842 50.000 0.00 0.00 0.00 3.69
1693 1961 3.157881 CTGCGGTCATAGGAGATTAGGA 58.842 50.000 0.00 0.00 0.00 2.94
1694 1962 2.232452 CCTGCGGTCATAGGAGATTAGG 59.768 54.545 0.00 0.00 36.11 2.69
1695 1963 2.353208 GCCTGCGGTCATAGGAGATTAG 60.353 54.545 0.00 0.00 36.11 1.73
1696 1964 1.618837 GCCTGCGGTCATAGGAGATTA 59.381 52.381 0.00 0.00 36.11 1.75
1697 1965 0.394565 GCCTGCGGTCATAGGAGATT 59.605 55.000 0.00 0.00 36.11 2.40
1698 1966 1.476007 GGCCTGCGGTCATAGGAGAT 61.476 60.000 0.00 0.00 36.11 2.75
1699 1967 2.134287 GGCCTGCGGTCATAGGAGA 61.134 63.158 0.00 0.00 36.11 3.71
1730 1998 7.250569 CAAAACAACGGATGCATATCTTACTT 58.749 34.615 0.00 0.00 33.68 2.24
1750 2018 8.573885 AGAATAAAAGTGTAAGGTAGGCAAAAC 58.426 33.333 0.00 0.00 0.00 2.43
1972 2241 3.902261 TGTGAGCTGTACTTGCAAATG 57.098 42.857 0.00 0.00 0.00 2.32
2048 2317 3.511540 GGACCAAGGCAGCTAAGATTTTT 59.488 43.478 0.00 0.00 0.00 1.94
2096 2365 0.036388 TAGAAACAGAAGGGCAGCGG 60.036 55.000 0.00 0.00 0.00 5.52
2521 2790 7.393515 GGAACTTAAAACTGGTAGGAATGTCAT 59.606 37.037 0.00 0.00 0.00 3.06
2711 2980 4.945246 ACAGACGACAGAAAGTGTTACAT 58.055 39.130 0.00 0.00 40.56 2.29
2924 3200 7.481798 GCACTGTTCGGAACTAATTTTCATTAG 59.518 37.037 20.53 8.30 45.37 1.73
2942 3218 9.801873 AATTACAAATATACCAATGCACTGTTC 57.198 29.630 0.00 0.00 0.00 3.18
3459 3735 7.195374 ACAAGATAGTTAAGGCTGGTTCATA 57.805 36.000 0.00 0.00 0.00 2.15
3551 3827 4.512944 ACGATGCTGATGGACATAAATGAC 59.487 41.667 0.00 0.00 0.00 3.06
4055 4351 5.826601 TGCATCAAACACTCAAAGTTACA 57.173 34.783 0.00 0.00 0.00 2.41
4179 4475 4.081198 AGCATTTTGGTCCAACAGTGAAAA 60.081 37.500 2.98 0.00 0.00 2.29
4885 5189 3.019564 AGGTCAAATGGCAATACAGCTC 58.980 45.455 0.00 0.00 34.17 4.09
5152 5513 4.330074 AGCGTAATTCAAGAATGAGAACCG 59.670 41.667 0.00 0.00 36.78 4.44
5308 5678 7.695480 AATGCATTGGTTACACATGTACTTA 57.305 32.000 12.09 0.00 0.00 2.24
5824 6352 8.198109 CCCTTAGGGTTGATAATATAGTCATCG 58.802 40.741 9.64 0.00 38.25 3.84
6607 7169 4.283467 ACAAGCAATTCTTTACCCCCTTTC 59.717 41.667 0.00 0.00 31.27 2.62
6771 7333 6.535508 AGATAGAAATAAACGCCTTCTCACAC 59.464 38.462 0.00 0.00 31.91 3.82
6814 7376 4.595781 ACACCACCATTTCTCAGTTACCTA 59.404 41.667 0.00 0.00 0.00 3.08
6950 7662 8.948631 ACCATATGAACAACAATGTAGTAGAG 57.051 34.615 3.65 0.00 39.40 2.43
6987 7863 8.133627 GCTACAAAAGATATTAGAGGTGTACGA 58.866 37.037 0.00 0.00 0.00 3.43
7229 8105 6.449698 ACAAAGTAAATGTCAGAAATGGCAG 58.550 36.000 0.00 0.00 0.00 4.85
7256 8132 6.059484 TCGAGGTTTCCTTTCACTAAACATT 58.941 36.000 0.00 0.00 35.33 2.71
7257 8133 5.617252 TCGAGGTTTCCTTTCACTAAACAT 58.383 37.500 0.00 0.00 35.33 2.71
7258 8134 5.026038 TCGAGGTTTCCTTTCACTAAACA 57.974 39.130 0.00 0.00 35.33 2.83
7259 8135 5.996669 TTCGAGGTTTCCTTTCACTAAAC 57.003 39.130 0.00 0.00 31.76 2.01
7260 8136 6.531021 AGATTCGAGGTTTCCTTTCACTAAA 58.469 36.000 0.00 0.00 31.76 1.85
7261 8137 6.110411 AGATTCGAGGTTTCCTTTCACTAA 57.890 37.500 0.00 0.00 31.76 2.24
7262 8138 5.245301 TGAGATTCGAGGTTTCCTTTCACTA 59.755 40.000 0.00 0.00 31.76 2.74
7527 8403 0.947180 GCAGCACAAGTTGGCCATTG 60.947 55.000 16.02 16.02 0.00 2.82
7662 8541 2.527100 CGAGGTTTTGGCTACGTCTAG 58.473 52.381 0.00 0.00 0.00 2.43
7709 8594 4.786609 GCCTGCTTCCTTCGATTATTTTCG 60.787 45.833 0.00 0.00 40.46 3.46
7792 8677 5.484715 TGCTGAAATTAGTACACCACTACC 58.515 41.667 0.00 0.00 39.52 3.18
7866 8841 1.063469 AGTTTGGCAGTTTCGTGTTCG 59.937 47.619 0.00 0.00 38.55 3.95
7889 8864 4.579340 AGAACTGAAATGAGCATGCCATAG 59.421 41.667 15.66 13.40 0.00 2.23
7894 8869 2.417933 ACGAGAACTGAAATGAGCATGC 59.582 45.455 10.51 10.51 0.00 4.06
7902 8877 3.744987 CGACGACTACGAGAACTGAAAT 58.255 45.455 0.00 0.00 42.66 2.17
7907 8882 1.925847 CTAGCGACGACTACGAGAACT 59.074 52.381 0.00 0.00 42.66 3.01
7909 8884 1.284657 CCTAGCGACGACTACGAGAA 58.715 55.000 0.00 0.00 42.66 2.87
7963 8938 4.582240 TCATGGCAGTACAACAAACATCAA 59.418 37.500 0.00 0.00 0.00 2.57
7965 8940 4.764679 TCATGGCAGTACAACAAACATC 57.235 40.909 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.