Multiple sequence alignment - TraesCS1A01G221000

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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 TraesCS1A01G221000 chr1A 100.000 7705 0 0 1 7705 389868228 389875932 0.000000e+00 14229.0
1 TraesCS1A01G221000 chr1A 99.785 932 2 0 4623 5554 149512080 149511149 0.000000e+00 1711.0
2 TraesCS1A01G221000 chr1A 99.457 921 5 0 4623 5543 520766862 520765942 0.000000e+00 1674.0
3 TraesCS1A01G221000 chr1A 82.189 1005 85 38 4622 5554 575690979 575691961 0.000000e+00 778.0
4 TraesCS1A01G221000 chr1A 74.618 327 62 8 7167 7478 555174234 555174554 2.920000e-24 124.0
5 TraesCS1A01G221000 chr1A 92.857 84 6 0 3705 3788 572331619 572331702 1.050000e-23 122.0
6 TraesCS1A01G221000 chr3A 97.765 3937 79 8 692 4623 128528106 128524174 0.000000e+00 6774.0
7 TraesCS1A01G221000 chr3A 93.811 2165 107 17 5550 7705 128524186 128522040 0.000000e+00 3230.0
8 TraesCS1A01G221000 chr3A 88.953 688 63 7 1 687 128528981 128528306 0.000000e+00 837.0
9 TraesCS1A01G221000 chr3A 84.576 590 51 24 4993 5554 46568345 46568922 4.060000e-152 549.0
10 TraesCS1A01G221000 chr3A 84.576 590 51 24 4993 5554 163805021 163805598 4.060000e-152 549.0
11 TraesCS1A01G221000 chr3A 93.976 83 5 0 3705 3787 696209565 696209647 8.120000e-25 126.0
12 TraesCS1A01G221000 chr3A 85.714 77 9 2 3884 3958 35669039 35668963 6.410000e-11 80.5
13 TraesCS1A01G221000 chr1D 91.994 2111 113 15 3 2100 310139495 310141562 0.000000e+00 2911.0
14 TraesCS1A01G221000 chr1D 94.280 1591 49 20 5550 7121 310143761 310145328 0.000000e+00 2396.0
15 TraesCS1A01G221000 chr1D 95.396 695 32 0 3929 4623 310143079 310143773 0.000000e+00 1107.0
16 TraesCS1A01G221000 chr1D 91.486 599 27 13 3111 3704 310142294 310142873 0.000000e+00 802.0
17 TraesCS1A01G221000 chr1D 83.995 756 69 29 4829 5555 354768450 354769182 0.000000e+00 678.0
18 TraesCS1A01G221000 chr1D 84.783 598 72 15 7110 7705 310146838 310147418 4.010000e-162 582.0
19 TraesCS1A01G221000 chr1D 86.965 491 28 14 2114 2572 310141605 310142091 3.190000e-143 520.0
20 TraesCS1A01G221000 chr1D 80.505 277 32 10 4623 4881 398943482 398943754 7.890000e-45 193.0
21 TraesCS1A01G221000 chr1D 79.853 273 47 8 7223 7491 462749591 462749323 7.890000e-45 193.0
22 TraesCS1A01G221000 chr1D 93.023 86 6 0 2633 2718 310142088 310142173 8.120000e-25 126.0
23 TraesCS1A01G221000 chr1B 89.282 1866 94 37 789 2572 420231539 420233380 0.000000e+00 2241.0
24 TraesCS1A01G221000 chr1B 94.569 1381 51 7 5550 6920 420235330 420236696 0.000000e+00 2113.0
25 TraesCS1A01G221000 chr1B 92.123 914 56 10 2800 3704 420233575 420234481 0.000000e+00 1275.0
26 TraesCS1A01G221000 chr1B 92.883 843 51 5 3783 4623 420234507 420235342 0.000000e+00 1216.0
27 TraesCS1A01G221000 chr1B 83.166 998 83 33 4623 5554 657187193 657186215 0.000000e+00 833.0
28 TraesCS1A01G221000 chr1B 89.205 176 16 3 2641 2814 420233386 420233560 4.680000e-52 217.0
29 TraesCS1A01G221000 chr1B 75.897 390 80 7 7116 7492 499660028 499660416 3.670000e-43 187.0
30 TraesCS1A01G221000 chr1B 89.831 59 3 2 2577 2632 300749859 300749801 1.070000e-08 73.1
31 TraesCS1A01G221000 chr1B 100.000 32 0 0 6912 6943 420249953 420249984 8.350000e-05 60.2
32 TraesCS1A01G221000 chr4B 99.893 935 1 0 4623 5557 500254338 500253404 0.000000e+00 1722.0
33 TraesCS1A01G221000 chr4B 83.811 593 54 25 4993 5555 124595960 124596540 6.850000e-145 525.0
34 TraesCS1A01G221000 chr4B 79.899 199 34 6 7116 7311 633749634 633749439 2.900000e-29 141.0
35 TraesCS1A01G221000 chr2D 99.893 932 1 0 4623 5554 542779062 542779993 0.000000e+00 1716.0
36 TraesCS1A01G221000 chr2D 90.187 214 21 0 7492 7705 481060890 481060677 5.890000e-71 279.0
37 TraesCS1A01G221000 chr2D 89.720 214 22 0 7492 7705 619421501 619421714 2.740000e-69 274.0
38 TraesCS1A01G221000 chr2D 78.049 369 71 8 7113 7477 103463430 103463792 2.800000e-54 224.0
39 TraesCS1A01G221000 chr2D 93.902 82 5 0 3701 3782 487495832 487495913 2.920000e-24 124.0
40 TraesCS1A01G221000 chr2D 83.516 91 14 1 3881 3970 380407767 380407677 4.950000e-12 84.2
41 TraesCS1A01G221000 chrUn 97.863 936 16 3 4623 5554 307772982 307772047 0.000000e+00 1615.0
42 TraesCS1A01G221000 chrUn 100.000 393 0 0 2798 3190 479646003 479646395 0.000000e+00 726.0
43 TraesCS1A01G221000 chrUn 94.937 79 4 0 3705 3783 378382014 378382092 2.920000e-24 124.0
44 TraesCS1A01G221000 chrUn 85.714 91 10 3 3884 3972 19227907 19227818 8.230000e-15 93.5
45 TraesCS1A01G221000 chr6B 92.696 753 38 12 4623 5373 4550984 4551721 0.000000e+00 1070.0
46 TraesCS1A01G221000 chr6B 78.559 555 58 34 5003 5545 4817430 4816925 7.510000e-80 309.0
47 TraesCS1A01G221000 chr6B 75.322 543 124 8 201 737 448340419 448340957 1.280000e-62 252.0
48 TraesCS1A01G221000 chr6B 95.122 41 0 2 2581 2619 667782419 667782379 6.450000e-06 63.9
49 TraesCS1A01G221000 chr4D 80.362 387 62 12 7113 7491 385488871 385489251 1.640000e-71 281.0
50 TraesCS1A01G221000 chr4D 80.052 381 60 7 7116 7492 39296676 39296308 1.270000e-67 268.0
51 TraesCS1A01G221000 chr4D 80.198 202 37 3 7116 7316 28845962 28846161 1.730000e-31 148.0
52 TraesCS1A01G221000 chr5A 89.815 216 21 1 7491 7705 543569919 543570134 7.620000e-70 276.0
53 TraesCS1A01G221000 chr3D 89.767 215 22 0 7491 7705 6522412 6522198 7.620000e-70 276.0
54 TraesCS1A01G221000 chr3D 77.212 373 76 9 7111 7478 464321006 464321374 7.830000e-50 209.0
55 TraesCS1A01G221000 chr3D 80.505 277 32 10 4623 4881 19290067 19289795 7.890000e-45 193.0
56 TraesCS1A01G221000 chr3D 78.829 222 45 2 7115 7335 400324415 400324635 1.730000e-31 148.0
57 TraesCS1A01G221000 chr3D 79.798 198 36 4 7116 7311 517395814 517396009 2.900000e-29 141.0
58 TraesCS1A01G221000 chr3D 93.902 82 5 0 3705 3786 110497006 110496925 2.920000e-24 124.0
59 TraesCS1A01G221000 chr5D 89.498 219 20 3 7489 7705 486993025 486992808 2.740000e-69 274.0
60 TraesCS1A01G221000 chr5D 83.838 99 11 5 3881 3976 520287108 520287012 1.060000e-13 89.8
61 TraesCS1A01G221000 chr4A 89.401 217 23 0 7489 7705 520823951 520824167 2.740000e-69 274.0
62 TraesCS1A01G221000 chr4A 90.000 210 21 0 7496 7705 705615347 705615138 9.850000e-69 272.0
63 TraesCS1A01G221000 chr4A 95.181 83 4 0 3705 3787 439012997 439012915 1.740000e-26 132.0
64 TraesCS1A01G221000 chr5B 90.000 210 21 0 7496 7705 103489920 103489711 9.850000e-69 272.0
65 TraesCS1A01G221000 chr5B 81.522 92 17 0 459 550 360808858 360808949 8.290000e-10 76.8
66 TraesCS1A01G221000 chr5B 91.071 56 2 3 2581 2633 234194911 234194856 1.070000e-08 73.1
67 TraesCS1A01G221000 chr2A 80.930 215 32 8 7103 7311 19611963 19612174 2.230000e-35 161.0
68 TraesCS1A01G221000 chr2A 89.831 59 3 2 2578 2633 673059745 673059803 1.070000e-08 73.1
69 TraesCS1A01G221000 chr6D 77.061 279 55 7 7220 7491 49775662 49775386 1.340000e-32 152.0
70 TraesCS1A01G221000 chr6D 97.297 37 0 1 2584 2619 441784379 441784343 2.320000e-05 62.1
71 TraesCS1A01G221000 chr2B 79.500 200 38 2 7116 7314 793501738 793501935 1.040000e-28 139.0
72 TraesCS1A01G221000 chr2B 84.314 102 11 5 3881 3978 169856245 169856145 2.290000e-15 95.3
73 TraesCS1A01G221000 chr2B 83.696 92 12 3 3881 3970 451818373 451818283 4.950000e-12 84.2
74 TraesCS1A01G221000 chr7A 95.062 81 4 0 3705 3785 452751218 452751138 2.260000e-25 128.0
75 TraesCS1A01G221000 chr3B 93.902 82 5 0 3705 3786 161691457 161691376 2.920000e-24 124.0
76 TraesCS1A01G221000 chr3B 89.831 59 3 3 2581 2636 546836626 546836684 1.070000e-08 73.1
77 TraesCS1A01G221000 chr7D 83.516 91 14 1 3884 3973 20285658 20285568 4.950000e-12 84.2
78 TraesCS1A01G221000 chr7B 89.474 57 6 0 2575 2631 86882247 86882303 1.070000e-08 73.1
79 TraesCS1A01G221000 chr6A 91.837 49 3 1 2584 2632 384043914 384043961 4.990000e-07 67.6


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 TraesCS1A01G221000 chr1A 389868228 389875932 7704 False 14229.000000 14229 100.000000 1 7705 1 chr1A.!!$F1 7704
1 TraesCS1A01G221000 chr1A 149511149 149512080 931 True 1711.000000 1711 99.785000 4623 5554 1 chr1A.!!$R1 931
2 TraesCS1A01G221000 chr1A 520765942 520766862 920 True 1674.000000 1674 99.457000 4623 5543 1 chr1A.!!$R2 920
3 TraesCS1A01G221000 chr1A 575690979 575691961 982 False 778.000000 778 82.189000 4622 5554 1 chr1A.!!$F4 932
4 TraesCS1A01G221000 chr3A 128522040 128528981 6941 True 3613.666667 6774 93.509667 1 7705 3 chr3A.!!$R2 7704
5 TraesCS1A01G221000 chr3A 46568345 46568922 577 False 549.000000 549 84.576000 4993 5554 1 chr3A.!!$F1 561
6 TraesCS1A01G221000 chr3A 163805021 163805598 577 False 549.000000 549 84.576000 4993 5554 1 chr3A.!!$F2 561
7 TraesCS1A01G221000 chr1D 310139495 310147418 7923 False 1206.285714 2911 91.132429 3 7705 7 chr1D.!!$F3 7702
8 TraesCS1A01G221000 chr1D 354768450 354769182 732 False 678.000000 678 83.995000 4829 5555 1 chr1D.!!$F1 726
9 TraesCS1A01G221000 chr1B 420231539 420236696 5157 False 1412.400000 2241 91.612400 789 6920 5 chr1B.!!$F3 6131
10 TraesCS1A01G221000 chr1B 657186215 657187193 978 True 833.000000 833 83.166000 4623 5554 1 chr1B.!!$R2 931
11 TraesCS1A01G221000 chr4B 500253404 500254338 934 True 1722.000000 1722 99.893000 4623 5557 1 chr4B.!!$R1 934
12 TraesCS1A01G221000 chr4B 124595960 124596540 580 False 525.000000 525 83.811000 4993 5555 1 chr4B.!!$F1 562
13 TraesCS1A01G221000 chr2D 542779062 542779993 931 False 1716.000000 1716 99.893000 4623 5554 1 chr2D.!!$F3 931
14 TraesCS1A01G221000 chrUn 307772047 307772982 935 True 1615.000000 1615 97.863000 4623 5554 1 chrUn.!!$R2 931
15 TraesCS1A01G221000 chr6B 4550984 4551721 737 False 1070.000000 1070 92.696000 4623 5373 1 chr6B.!!$F1 750
16 TraesCS1A01G221000 chr6B 4816925 4817430 505 True 309.000000 309 78.559000 5003 5545 1 chr6B.!!$R1 542
17 TraesCS1A01G221000 chr6B 448340419 448340957 538 False 252.000000 252 75.322000 201 737 1 chr6B.!!$F2 536

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
539 544 0.323633 CATCCCCACCAAGCACATGA 60.324 55.000 0.00 0.00 0.00 3.07 F
1009 1216 0.096976 CTCGCGTTAACCAGCCAATG 59.903 55.000 5.77 0.00 0.00 2.82 F
2205 2484 0.248907 CGTCCTATGAACGTCGCCAT 60.249 55.000 0.00 6.09 35.47 4.40 F
2255 2547 0.817634 CACCACCAAAGAAGCCGTCA 60.818 55.000 0.00 0.00 0.00 4.35 F
3547 3904 1.098050 GGATGTAGGCTGCCTTTGTG 58.902 55.000 28.55 0.00 34.61 3.33 F
3658 4019 1.542547 CGCCACTTAACAACTGGGTCT 60.543 52.381 0.00 0.00 0.00 3.85 F
4620 5015 1.783284 TGAGAATGTCACTGTCACGC 58.217 50.000 0.00 0.00 0.00 5.34 F
6607 7154 0.041839 GAATAAGTGGCATCGCAGCG 60.042 55.000 9.06 9.06 34.64 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2547 0.673644 GTACGCAAGCCTGTGGTCAT 60.674 55.000 0.19 0.00 45.62 3.06 R
2606 2922 3.462483 TGAGCTGAAACCGTAGAACAA 57.538 42.857 0.00 0.00 0.00 2.83 R
3941 4304 0.813184 TCCCGAATTACTCGTCGCTT 59.187 50.000 0.00 0.00 46.65 4.68 R
4620 5015 1.115930 ATCCTAGCTACGCCACTGGG 61.116 60.000 0.00 0.00 35.95 4.45 R
5199 5673 3.605664 GGCGGCAAACAGGCTGTT 61.606 61.111 26.54 26.54 43.41 3.16 R
6040 6583 1.077501 CCACGATGCCCTTGGTGAT 60.078 57.895 0.00 0.00 32.23 3.06 R
6644 7191 0.673644 CGCCGTGGAAGGATCACTTT 60.674 55.000 0.00 0.00 40.21 2.66 R
7523 9616 0.597568 CCTGCGCATTTTGTTCTCCA 59.402 50.000 12.24 0.00 0.00 3.86 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
50 51 2.787249 CTTGCATCTCGTTGGCCG 59.213 61.111 0.00 0.00 38.13 6.13
63 64 4.065281 GGCCGTGCAGTCTACCGT 62.065 66.667 0.00 0.00 0.00 4.83
65 66 2.959372 CCGTGCAGTCTACCGTGA 59.041 61.111 0.00 0.00 0.00 4.35
69 70 0.388649 GTGCAGTCTACCGTGACCTG 60.389 60.000 0.00 0.00 37.66 4.00
113 114 2.342279 CGAAGAACGCCTCCACCA 59.658 61.111 0.00 0.00 34.51 4.17
146 147 1.068741 GGTCGGAGTTGTCTTCTGTGT 59.931 52.381 0.00 0.00 0.00 3.72
197 198 2.617274 GCGGTGGAGTTTGCTGACC 61.617 63.158 0.00 0.00 0.00 4.02
253 254 3.319198 AACCAGTCGGCGGACCAT 61.319 61.111 19.68 4.04 44.54 3.55
260 261 2.358125 CGGCGGACCATGTCAACA 60.358 61.111 0.00 0.00 33.68 3.33
294 296 4.221422 CATCCGGGTCGATGGCGT 62.221 66.667 0.00 0.00 36.74 5.68
359 361 0.817634 CGGCAACTTCAACCTCCACA 60.818 55.000 0.00 0.00 0.00 4.17
424 426 2.295070 GGAAGGCGTAGAAGAGATCCTC 59.705 54.545 0.00 0.00 0.00 3.71
426 428 1.215673 AGGCGTAGAAGAGATCCTCCA 59.784 52.381 0.00 0.00 0.00 3.86
492 497 4.585879 GGCCACACCAAGACTTTTATCTA 58.414 43.478 0.00 0.00 38.86 1.98
501 506 6.045955 CCAAGACTTTTATCTACTGGCTCTC 58.954 44.000 0.00 0.00 0.00 3.20
539 544 0.323633 CATCCCCACCAAGCACATGA 60.324 55.000 0.00 0.00 0.00 3.07
554 559 3.272364 ATGATGTGGGTGCTGCCGT 62.272 57.895 0.00 0.00 38.44 5.68
592 597 1.765314 GAGGAGATGCAGGGCTTCTTA 59.235 52.381 7.86 0.00 41.89 2.10
711 911 3.157252 ATCGCACTCGGGGCAGAT 61.157 61.111 0.00 0.00 36.13 2.90
729 929 2.859273 ATCGGCTTGCCGTCTTCCAG 62.859 60.000 29.41 3.50 34.52 3.86
769 970 1.324740 CGTTCCCCACGTGATCCCTA 61.325 60.000 19.30 0.00 44.49 3.53
856 1063 4.020485 GGGTACTTCTCCACTTTTGAGCTA 60.020 45.833 0.00 0.00 0.00 3.32
904 1111 8.199449 CAGGTCTTAATCCATGTATTGCATTTT 58.801 33.333 0.00 0.00 35.19 1.82
952 1159 1.204467 CCCATCCACCCGTCAAAATTG 59.796 52.381 0.00 0.00 0.00 2.32
1009 1216 0.096976 CTCGCGTTAACCAGCCAATG 59.903 55.000 5.77 0.00 0.00 2.82
1022 1229 0.613012 GCCAATGGTTGCTCCTCCTT 60.613 55.000 0.00 0.00 37.07 3.36
1125 1340 2.679059 CGAGCCTGATTGAACATGTCCT 60.679 50.000 0.00 0.00 0.00 3.85
1135 1350 1.816863 AACATGTCCTCCTCACGCGT 61.817 55.000 5.58 5.58 0.00 6.01
1293 1508 1.228769 ACTGTGCCGGTGACCTCTA 60.229 57.895 1.90 0.00 0.00 2.43
1964 2212 7.331193 TGCGAGAGAAAGGTAAATTTAGACTTC 59.669 37.037 12.84 9.11 0.00 3.01
1970 2218 8.515414 AGAAAGGTAAATTTAGACTTCACATGC 58.485 33.333 12.84 0.00 0.00 4.06
2198 2477 6.071463 GCTAAATTATTGCGTCCTATGAACG 58.929 40.000 0.00 0.00 42.87 3.95
2199 2478 6.292703 GCTAAATTATTGCGTCCTATGAACGT 60.293 38.462 0.00 0.00 42.02 3.99
2205 2484 0.248907 CGTCCTATGAACGTCGCCAT 60.249 55.000 0.00 6.09 35.47 4.40
2255 2547 0.817634 CACCACCAAAGAAGCCGTCA 60.818 55.000 0.00 0.00 0.00 4.35
2338 2630 5.012046 TCTCCTTTTCTGTCAGCTCATACAA 59.988 40.000 0.00 0.00 0.00 2.41
2524 2839 7.145932 ACGATTTTCAGGATAGGTTTTCTTG 57.854 36.000 0.00 0.00 0.00 3.02
2541 2856 2.228822 TCTTGGAAAAATCAGCCTTCGC 59.771 45.455 0.00 0.00 0.00 4.70
2754 3072 7.939784 ATAAACAAATGTACCTCCCTCTTTC 57.060 36.000 0.00 0.00 0.00 2.62
3221 3570 2.814280 TTCTCTGGTCCACTTTCGTC 57.186 50.000 0.00 0.00 0.00 4.20
3237 3586 1.345415 TCGTCGGGCTTTACCTTTCTT 59.655 47.619 0.00 0.00 39.10 2.52
3282 3632 3.065371 CAGGATGATGCCTTTTTCGTACC 59.935 47.826 0.00 0.00 39.69 3.34
3439 3796 4.402056 TTTAGTGCTACATGTAGAGGCC 57.598 45.455 32.39 16.99 35.21 5.19
3449 3806 1.271856 TGTAGAGGCCAAATCGGTCA 58.728 50.000 5.01 0.00 44.49 4.02
3524 3881 2.955660 TGCGTTGTCAAGGAGGAAATTT 59.044 40.909 9.42 0.00 0.00 1.82
3547 3904 1.098050 GGATGTAGGCTGCCTTTGTG 58.902 55.000 28.55 0.00 34.61 3.33
3658 4019 1.542547 CGCCACTTAACAACTGGGTCT 60.543 52.381 0.00 0.00 0.00 3.85
3740 4101 7.755373 GCATGAAACTTCAACCCTATACTTTTC 59.245 37.037 0.00 0.00 41.13 2.29
3807 4168 5.749462 AGCAGTGTTTCCAATCTAGCTATT 58.251 37.500 0.00 0.00 0.00 1.73
3941 4304 9.967346 GTATTGTAGTGCTAGATCATCTGTTTA 57.033 33.333 0.00 0.00 0.00 2.01
4559 4954 2.833943 TCAGGCAGCTCTTGATGTCTTA 59.166 45.455 0.00 0.00 42.34 2.10
4614 5009 4.999311 TGGTTCTTCATGAGAATGTCACTG 59.001 41.667 9.75 0.00 45.66 3.66
4615 5010 4.999950 GGTTCTTCATGAGAATGTCACTGT 59.000 41.667 9.75 0.00 45.66 3.55
4616 5011 5.121454 GGTTCTTCATGAGAATGTCACTGTC 59.879 44.000 9.75 0.00 45.66 3.51
4617 5012 5.473066 TCTTCATGAGAATGTCACTGTCA 57.527 39.130 0.00 0.00 38.28 3.58
4618 5013 5.233225 TCTTCATGAGAATGTCACTGTCAC 58.767 41.667 0.00 0.00 38.28 3.67
4619 5014 3.578688 TCATGAGAATGTCACTGTCACG 58.421 45.455 0.00 0.00 38.28 4.35
4620 5015 1.783284 TGAGAATGTCACTGTCACGC 58.217 50.000 0.00 0.00 0.00 5.34
5199 5673 2.224744 TGCTCAACCTAATGCTTCACCA 60.225 45.455 0.00 0.00 0.00 4.17
6401 6944 0.981277 GGGAACATCCTCGGGGAGAA 60.981 60.000 11.27 0.00 45.86 2.87
6607 7154 0.041839 GAATAAGTGGCATCGCAGCG 60.042 55.000 9.06 9.06 34.64 5.18
6608 7155 0.461870 AATAAGTGGCATCGCAGCGA 60.462 50.000 22.06 22.06 41.13 4.93
6680 7227 2.118294 GCCTTGGTTTGGCCTCCT 59.882 61.111 3.32 0.00 44.32 3.69
6753 7309 3.533913 GCCTAGCGCTTGTTTATGC 57.466 52.632 18.68 8.38 0.00 3.14
6860 7422 9.283768 TGTATGTAATGGTGATGATGATTTACC 57.716 33.333 0.00 0.00 0.00 2.85
6861 7423 9.507329 GTATGTAATGGTGATGATGATTTACCT 57.493 33.333 0.00 0.00 32.68 3.08
6862 7424 7.806409 TGTAATGGTGATGATGATTTACCTG 57.194 36.000 0.00 0.00 32.68 4.00
6863 7425 6.772233 TGTAATGGTGATGATGATTTACCTGG 59.228 38.462 0.00 0.00 32.68 4.45
6864 7426 3.554934 TGGTGATGATGATTTACCTGGC 58.445 45.455 0.00 0.00 32.68 4.85
6865 7427 3.053768 TGGTGATGATGATTTACCTGGCA 60.054 43.478 0.00 0.00 32.68 4.92
6866 7428 4.147321 GGTGATGATGATTTACCTGGCAT 58.853 43.478 0.00 0.00 0.00 4.40
7048 7613 1.271762 GGTGGGAAACTCCAGGGTAAC 60.272 57.143 0.00 0.00 38.64 2.50
7080 7645 1.661463 ACATCAGCTGGGAGAAGGAA 58.339 50.000 15.13 0.00 0.00 3.36
7081 7646 2.203584 ACATCAGCTGGGAGAAGGAAT 58.796 47.619 15.13 0.00 0.00 3.01
7156 9243 3.190535 GCACAAACCCATCTCATACGTTT 59.809 43.478 0.00 0.00 0.00 3.60
7160 9247 2.710096 CCCATCTCATACGTTTGGGT 57.290 50.000 5.76 0.00 41.78 4.51
7162 9249 2.093181 CCCATCTCATACGTTTGGGTGA 60.093 50.000 5.76 3.37 41.78 4.02
7163 9250 3.605634 CCATCTCATACGTTTGGGTGAA 58.394 45.455 5.76 0.00 0.00 3.18
7177 9264 0.535335 GGTGAACTGCCCGATCACTA 59.465 55.000 11.43 0.00 42.94 2.74
7195 9282 4.862574 TCACTATCTGGTCACGATTTTTCG 59.137 41.667 0.00 0.00 39.31 3.46
7198 9285 3.380479 TCTGGTCACGATTTTTCGACT 57.620 42.857 1.96 0.00 36.85 4.18
7203 9290 3.121445 GGTCACGATTTTTCGACTCAGAC 59.879 47.826 1.96 0.00 36.85 3.51
7228 9315 1.691196 CCTCAAACAGGCCTCAAACA 58.309 50.000 0.00 0.00 34.56 2.83
7232 9319 1.962807 CAAACAGGCCTCAAACATCCA 59.037 47.619 0.00 0.00 0.00 3.41
7235 9322 0.038744 CAGGCCTCAAACATCCAGGT 59.961 55.000 0.00 0.00 0.00 4.00
7248 9337 2.282462 CAGGTTGACTGGCACCCC 60.282 66.667 0.00 0.00 43.70 4.95
7269 9358 5.222316 CCCCTCATATCCAACCCAAATATGA 60.222 44.000 0.00 0.00 39.09 2.15
7273 9362 7.147958 TCATATCCAACCCAAATATGAGACA 57.852 36.000 0.00 0.00 37.43 3.41
7286 9375 1.004440 GAGACAGATATGGGGGCGC 60.004 63.158 0.00 0.00 0.00 6.53
7287 9376 1.460305 AGACAGATATGGGGGCGCT 60.460 57.895 7.64 0.00 0.00 5.92
7325 9414 3.308705 GACCCGACAACCCGACCT 61.309 66.667 0.00 0.00 0.00 3.85
7368 9458 1.562672 CCCCCAAGACCTGTCGGATT 61.563 60.000 0.00 0.00 34.09 3.01
7385 9475 3.999663 CGGATTCATTTGCTATCTCCTCC 59.000 47.826 0.00 0.00 0.00 4.30
7402 9495 0.178944 TCCCTTCTTCCTCCACGTCA 60.179 55.000 0.00 0.00 0.00 4.35
7403 9496 0.905357 CCCTTCTTCCTCCACGTCAT 59.095 55.000 0.00 0.00 0.00 3.06
7417 9510 1.153745 GTCATCCGTCTCGCAGCTT 60.154 57.895 0.00 0.00 0.00 3.74
7418 9511 0.737715 GTCATCCGTCTCGCAGCTTT 60.738 55.000 0.00 0.00 0.00 3.51
7465 9558 3.356639 CTAGCCTCTGCGTCGCCAA 62.357 63.158 15.88 1.25 44.33 4.52
7470 9563 1.506718 CTCTGCGTCGCCAACTCTA 59.493 57.895 15.88 0.00 0.00 2.43
7523 9616 3.910627 AGGTGTTTGGACCTGAGTATCTT 59.089 43.478 0.00 0.00 45.20 2.40
7531 9624 3.769844 GGACCTGAGTATCTTGGAGAACA 59.230 47.826 0.00 0.00 34.46 3.18
7553 9646 2.357034 GCGCAGGACACGGAGAAA 60.357 61.111 0.30 0.00 0.00 2.52
7556 9649 2.004583 CGCAGGACACGGAGAAATTA 57.995 50.000 0.00 0.00 0.00 1.40
7571 9664 6.073003 CGGAGAAATTATTGGCTATTGGAGAC 60.073 42.308 0.00 0.00 0.00 3.36
7588 9681 0.611714 GACGCAAGGGGGTTTCTAGA 59.388 55.000 0.00 0.00 40.72 2.43
7646 9739 4.398319 GGAAGAACTGTCCCAAAGATTCA 58.602 43.478 0.00 0.00 0.00 2.57
7670 9763 5.130477 ACGGGGAATGTATCAAGATAACACT 59.870 40.000 0.00 0.00 0.00 3.55
7689 9782 3.837146 CACTAGAGAGGCCACCATCATAT 59.163 47.826 5.01 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.388649 CAGGTCACGGTAGACTGCAC 60.389 60.000 9.47 0.00 38.57 4.57
113 114 2.656069 CCGACCCCCACAACGATCT 61.656 63.158 0.00 0.00 0.00 2.75
173 174 3.647771 AAACTCCACCGCCCCCTC 61.648 66.667 0.00 0.00 0.00 4.30
253 254 0.817229 TGCGCCTGACAATGTTGACA 60.817 50.000 4.18 0.00 0.00 3.58
260 261 0.322816 ATGGAGTTGCGCCTGACAAT 60.323 50.000 4.18 0.00 0.00 2.71
294 296 3.179048 CATGACGCAATGTAGAAGACGA 58.821 45.455 0.00 0.00 0.00 4.20
302 304 1.941975 CTCATGCCATGACGCAATGTA 59.058 47.619 2.53 0.00 43.24 2.29
359 361 1.276421 CTTCTCAATGACGACCCTGGT 59.724 52.381 0.00 0.00 0.00 4.00
397 399 1.123928 CTTCTACGCCTTCCAGGGAT 58.876 55.000 0.00 0.00 35.37 3.85
492 497 3.790437 CCCATGCCGAGAGCCAGT 61.790 66.667 0.00 0.00 42.71 4.00
729 929 4.933064 CATCGCCCTCGTCGGAGC 62.933 72.222 0.00 0.00 39.06 4.70
769 970 2.573869 CTCCATCGTCCACGTGCT 59.426 61.111 10.91 0.00 40.80 4.40
856 1063 2.443255 AGAGGAACACACCAGGAAACAT 59.557 45.455 0.00 0.00 0.00 2.71
904 1111 1.513975 TTATTGCTTGGGGGCCCTGA 61.514 55.000 24.38 10.50 36.94 3.86
952 1159 4.161565 GGTGGAGGTTATTTTGGGGAAATC 59.838 45.833 0.00 0.00 38.80 2.17
1009 1216 0.884514 GCAAAGAAGGAGGAGCAACC 59.115 55.000 0.00 0.00 39.35 3.77
1022 1229 4.576463 GTCTTTTCTCTGTTGAGGCAAAGA 59.424 41.667 12.80 12.80 41.84 2.52
1125 1340 2.750637 GAGGAGGACGCGTGAGGA 60.751 66.667 20.70 0.00 0.00 3.71
1478 1693 4.193334 CCGCTCCGCACGATGAGA 62.193 66.667 0.00 0.00 0.00 3.27
2049 2297 0.756903 TTCGCTGGCTAATACCCTCC 59.243 55.000 0.00 0.00 0.00 4.30
2110 2360 9.308318 GAATTTACTTTTGAGCTTTTGTGGTTA 57.692 29.630 0.00 0.00 0.00 2.85
2111 2361 8.040727 AGAATTTACTTTTGAGCTTTTGTGGTT 58.959 29.630 0.00 0.00 0.00 3.67
2112 2362 7.492344 CAGAATTTACTTTTGAGCTTTTGTGGT 59.508 33.333 0.00 0.00 0.00 4.16
2198 2477 2.279517 CCCTAGCGACATGGCGAC 60.280 66.667 28.68 16.54 38.18 5.19
2199 2478 4.221422 GCCCTAGCGACATGGCGA 62.221 66.667 28.68 2.93 38.18 5.54
2255 2547 0.673644 GTACGCAAGCCTGTGGTCAT 60.674 55.000 0.19 0.00 45.62 3.06
2338 2630 8.587608 TCAGAAAACAGCAAATCTAATTTCCAT 58.412 29.630 0.00 0.00 32.93 3.41
2606 2922 3.462483 TGAGCTGAAACCGTAGAACAA 57.538 42.857 0.00 0.00 0.00 2.83
2754 3072 4.632538 ACTTTTCCTCCGTTTTCAACAG 57.367 40.909 0.00 0.00 0.00 3.16
3221 3570 2.500229 TCACAAGAAAGGTAAAGCCCG 58.500 47.619 0.00 0.00 38.26 6.13
3237 3586 2.816672 TGATTTGCAACCGCTTATCACA 59.183 40.909 0.00 0.00 39.64 3.58
3282 3632 5.551760 AATAGTTTTGCACAGATTCCTCG 57.448 39.130 0.00 0.00 0.00 4.63
3417 3774 4.408921 TGGCCTCTACATGTAGCACTAAAT 59.591 41.667 25.31 0.00 33.32 1.40
3439 3796 6.435430 TCCAAAATATCAGTGACCGATTTG 57.565 37.500 0.00 5.38 0.00 2.32
3449 3806 6.655078 AGCAACAAGTTCCAAAATATCAGT 57.345 33.333 0.00 0.00 0.00 3.41
3524 3881 1.216064 AAGGCAGCCTACATCCATCA 58.784 50.000 16.56 0.00 31.13 3.07
3761 4122 1.485066 GGGCCTCTTTGATTCGTAGGA 59.515 52.381 0.84 0.00 0.00 2.94
3815 4176 9.219603 GTAAACATGCAAGATAGGAGCATAATA 57.780 33.333 0.00 0.00 46.39 0.98
3941 4304 0.813184 TCCCGAATTACTCGTCGCTT 59.187 50.000 0.00 0.00 46.65 4.68
4620 5015 1.115930 ATCCTAGCTACGCCACTGGG 61.116 60.000 0.00 0.00 35.95 4.45
5199 5673 3.605664 GGCGGCAAACAGGCTGTT 61.606 61.111 26.54 26.54 43.41 3.16
6040 6583 1.077501 CCACGATGCCCTTGGTGAT 60.078 57.895 0.00 0.00 32.23 3.06
6301 6844 2.307137 CTGACGTCGACCTCGTAGGC 62.307 65.000 10.58 0.00 39.63 3.93
6644 7191 0.673644 CGCCGTGGAAGGATCACTTT 60.674 55.000 0.00 0.00 40.21 2.66
6680 7227 7.022055 ACACACACATCGTTCTTATTCAAAA 57.978 32.000 0.00 0.00 0.00 2.44
7048 7613 1.593006 GCTGATGTTCACCGGTTATCG 59.407 52.381 2.97 0.00 38.88 2.92
7112 7679 1.620819 CCCGGCTGTAGATGCTCTTAT 59.379 52.381 0.00 0.00 0.00 1.73
7144 9231 4.253685 CAGTTCACCCAAACGTATGAGAT 58.746 43.478 0.00 0.00 34.27 2.75
7145 9232 3.659786 CAGTTCACCCAAACGTATGAGA 58.340 45.455 0.00 0.00 34.27 3.27
7160 9247 2.101415 CAGATAGTGATCGGGCAGTTCA 59.899 50.000 0.00 0.00 37.15 3.18
7162 9249 1.414181 CCAGATAGTGATCGGGCAGTT 59.586 52.381 0.00 0.00 40.05 3.16
7163 9250 1.043816 CCAGATAGTGATCGGGCAGT 58.956 55.000 0.00 0.00 40.05 4.40
7177 9264 3.926616 AGTCGAAAAATCGTGACCAGAT 58.073 40.909 0.00 0.00 31.75 2.90
7195 9282 3.462678 GAGGGGGCCGTCTGAGTC 61.463 72.222 0.00 0.00 0.00 3.36
7198 9285 2.528127 TTTGAGGGGGCCGTCTGA 60.528 61.111 0.00 0.00 0.00 3.27
7235 9322 1.490490 GATATGAGGGGTGCCAGTCAA 59.510 52.381 0.00 0.00 0.00 3.18
7242 9331 0.178990 GGGTTGGATATGAGGGGTGC 60.179 60.000 0.00 0.00 0.00 5.01
7269 9358 1.056700 AAGCGCCCCCATATCTGTCT 61.057 55.000 2.29 0.00 0.00 3.41
7273 9362 0.179018 GTTCAAGCGCCCCCATATCT 60.179 55.000 2.29 0.00 0.00 1.98
7286 9375 2.568090 GTGGCGGGCATGTTCAAG 59.432 61.111 7.75 0.00 0.00 3.02
7287 9376 3.361158 CGTGGCGGGCATGTTCAA 61.361 61.111 15.03 0.00 0.00 2.69
7325 9414 7.012894 GGGTGGAATTGATGTAATTTACGATGA 59.987 37.037 2.30 0.00 39.06 2.92
7340 9429 0.407918 GGTCTTGGGGGTGGAATTGA 59.592 55.000 0.00 0.00 0.00 2.57
7368 9458 4.302067 AGAAGGGAGGAGATAGCAAATGA 58.698 43.478 0.00 0.00 0.00 2.57
7385 9475 1.134670 GGATGACGTGGAGGAAGAAGG 60.135 57.143 0.00 0.00 0.00 3.46
7402 9495 2.103042 GCAAAGCTGCGAGACGGAT 61.103 57.895 0.00 0.00 39.20 4.18
7403 9496 2.738521 GCAAAGCTGCGAGACGGA 60.739 61.111 0.00 0.00 39.20 4.69
7441 9534 1.654954 GACGCAGAGGCTAGGAACGA 61.655 60.000 0.00 0.00 38.10 3.85
7465 9558 5.124036 AGAGTGGATTGCTCTACTAGAGT 57.876 43.478 13.60 0.00 42.67 3.24
7470 9563 2.393646 GGGAGAGTGGATTGCTCTACT 58.606 52.381 4.77 0.00 45.01 2.57
7523 9616 0.597568 CCTGCGCATTTTGTTCTCCA 59.402 50.000 12.24 0.00 0.00 3.86
7531 9624 1.577328 CTCCGTGTCCTGCGCATTTT 61.577 55.000 12.24 0.00 0.00 1.82
7553 9646 4.085357 TGCGTCTCCAATAGCCAATAAT 57.915 40.909 0.00 0.00 0.00 1.28
7556 9649 2.292267 CTTGCGTCTCCAATAGCCAAT 58.708 47.619 0.00 0.00 0.00 3.16
7571 9664 2.194201 TTTCTAGAAACCCCCTTGCG 57.806 50.000 13.99 0.00 0.00 4.85
7588 9681 5.722263 TGCAATCAATTGATCCGAACATTT 58.278 33.333 20.95 0.42 40.14 2.32
7628 9721 2.484264 CCGTGAATCTTTGGGACAGTTC 59.516 50.000 0.00 0.00 42.39 3.01
7642 9735 4.771114 TCTTGATACATTCCCCGTGAAT 57.229 40.909 0.00 0.00 44.67 2.57
7645 9738 5.236478 GTGTTATCTTGATACATTCCCCGTG 59.764 44.000 0.00 0.00 0.00 4.94
7646 9739 5.130477 AGTGTTATCTTGATACATTCCCCGT 59.870 40.000 0.00 0.00 0.00 5.28
7670 9763 5.903923 TCTAATATGATGGTGGCCTCTCTA 58.096 41.667 3.32 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.