Multiple sequence alignment - TraesCS5D01G396600

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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 TraesCS5D01G396600 chr5D 100.000 6697 0 0 1 6697 464065716 464072412 0.000000e+00 12368.0
1 TraesCS5D01G396600 chr5D 89.024 164 16 2 166 327 150835731 150835568 1.140000e-47 202.0
2 TraesCS5D01G396600 chr5D 83.234 167 20 3 4670 4836 294634322 294634480 5.410000e-31 147.0
3 TraesCS5D01G396600 chr5D 80.105 191 25 6 635 813 218944661 218944850 5.450000e-26 130.0
4 TraesCS5D01G396600 chr5D 85.455 110 7 4 4728 4836 241947497 241947598 9.190000e-19 106.0
5 TraesCS5D01G396600 chr5D 93.750 64 4 0 612 675 5605888 5605825 5.530000e-16 97.1
6 TraesCS5D01G396600 chr5D 94.231 52 3 0 5259 5310 433387148 433387199 5.570000e-11 80.5
7 TraesCS5D01G396600 chr5D 91.379 58 4 1 4792 4849 207781527 207781583 2.000000e-10 78.7
8 TraesCS5D01G396600 chr5A 93.195 4879 213 60 1889 6697 584450608 584455437 0.000000e+00 7060.0
9 TraesCS5D01G396600 chr5A 90.016 1933 124 34 1 1895 584448652 584450553 0.000000e+00 2436.0
10 TraesCS5D01G396600 chr5A 88.820 161 16 2 170 328 320214403 320214243 5.300000e-46 196.0
11 TraesCS5D01G396600 chr5A 87.952 166 18 2 167 330 558675496 558675661 1.910000e-45 195.0
12 TraesCS5D01G396600 chr5A 80.909 220 29 4 614 820 538101260 538101479 1.930000e-35 161.0
13 TraesCS5D01G396600 chr5A 80.952 168 17 4 4670 4837 622051062 622051214 1.180000e-22 119.0
14 TraesCS5D01G396600 chr5B 93.294 2729 118 27 1889 4584 570925042 570927738 0.000000e+00 3965.0
15 TraesCS5D01G396600 chr5B 93.552 1985 74 23 4737 6697 570928124 570930078 0.000000e+00 2907.0
16 TraesCS5D01G396600 chr5B 90.627 1355 92 18 571 1894 570923629 570924979 0.000000e+00 1766.0
17 TraesCS5D01G396600 chr5B 91.537 579 39 6 1 574 570905567 570906140 0.000000e+00 789.0
18 TraesCS5D01G396600 chr5B 82.530 166 21 3 4671 4836 336241174 336241331 9.060000e-29 139.0
19 TraesCS5D01G396600 chr3D 89.937 159 14 2 171 327 549066794 549066952 3.170000e-48 204.0
20 TraesCS5D01G396600 chr3D 85.119 168 17 3 4669 4836 71517845 71517686 1.490000e-36 165.0
21 TraesCS5D01G396600 chr3D 84.431 167 18 3 4670 4836 426452025 426451867 2.500000e-34 158.0
22 TraesCS5D01G396600 chr3D 91.860 86 7 0 5149 5234 370115798 370115713 3.280000e-23 121.0
23 TraesCS5D01G396600 chr3D 89.655 87 9 0 5148 5234 45931418 45931332 1.970000e-20 111.0
24 TraesCS5D01G396600 chr3D 89.655 87 5 3 5147 5233 250931575 250931493 2.550000e-19 108.0
25 TraesCS5D01G396600 chr6D 87.719 171 19 2 159 327 90112229 90112399 1.470000e-46 198.0
26 TraesCS5D01G396600 chr6D 81.707 164 21 4 4673 4836 306053316 306053162 1.960000e-25 128.0
27 TraesCS5D01G396600 chr6D 88.372 86 8 2 5147 5231 13290764 13290848 1.190000e-17 102.0
28 TraesCS5D01G396600 chr6D 86.207 87 10 2 5148 5234 401309394 401309310 7.150000e-15 93.5
29 TraesCS5D01G396600 chr6D 85.882 85 4 1 5149 5233 211443945 211444021 4.300000e-12 84.2
30 TraesCS5D01G396600 chr6D 83.721 86 9 3 5149 5233 335373916 335373835 7.200000e-10 76.8
31 TraesCS5D01G396600 chr6D 95.349 43 2 0 5192 5234 35635065 35635023 1.210000e-07 69.4
32 TraesCS5D01G396600 chr6A 86.705 173 21 2 157 327 108947875 108947703 2.470000e-44 191.0
33 TraesCS5D01G396600 chr6A 79.907 214 31 7 614 815 490260315 490260102 5.410000e-31 147.0
34 TraesCS5D01G396600 chr6A 90.805 87 6 1 5148 5234 127186115 127186199 1.530000e-21 115.0
35 TraesCS5D01G396600 chr4D 85.955 178 22 3 153 328 508222931 508222755 3.190000e-43 187.0
36 TraesCS5D01G396600 chr4D 93.878 49 2 1 4788 4836 54811503 54811550 9.320000e-09 73.1
37 TraesCS5D01G396600 chr4D 97.500 40 1 0 5194 5233 394190395 394190356 1.210000e-07 69.4
38 TraesCS5D01G396600 chr4D 97.368 38 1 0 5196 5233 44749393 44749356 1.560000e-06 65.8
39 TraesCS5D01G396600 chr4B 81.818 220 26 6 612 817 237025809 237025590 8.930000e-39 172.0
40 TraesCS5D01G396600 chr4B 90.000 90 8 1 5148 5236 486282368 486282279 1.530000e-21 115.0
41 TraesCS5D01G396600 chr4B 85.870 92 9 4 5143 5233 450478052 450478140 1.990000e-15 95.3
42 TraesCS5D01G396600 chr4B 87.209 86 7 4 5149 5233 450478140 450478058 1.990000e-15 95.3
43 TraesCS5D01G396600 chr2D 85.629 167 19 1 4670 4836 12567241 12567080 3.210000e-38 171.0
44 TraesCS5D01G396600 chr2D 94.231 52 3 0 5259 5310 643859159 643859108 5.570000e-11 80.5
45 TraesCS5D01G396600 chr2A 85.629 167 19 1 4670 4836 13022783 13022622 3.210000e-38 171.0
46 TraesCS5D01G396600 chr7A 80.676 207 36 3 613 815 76831896 76832102 2.500000e-34 158.0
47 TraesCS5D01G396600 chr1D 84.524 168 17 4 4670 4836 190781410 190781251 2.500000e-34 158.0
48 TraesCS5D01G396600 chr1D 83.832 167 18 5 4670 4836 48391298 48391455 4.180000e-32 150.0
49 TraesCS5D01G396600 chr1D 90.588 85 8 0 5149 5233 279101376 279101460 5.490000e-21 113.0
50 TraesCS5D01G396600 chr1D 89.655 87 8 1 5148 5234 468830133 468830218 7.100000e-20 110.0
51 TraesCS5D01G396600 chr1D 87.640 89 7 2 5149 5234 493932304 493932391 4.270000e-17 100.0
52 TraesCS5D01G396600 chr1D 92.424 66 5 0 5169 5234 22976553 22976618 1.990000e-15 95.3
53 TraesCS5D01G396600 chr1D 82.558 86 14 1 5149 5234 302696422 302696506 2.590000e-09 75.0
54 TraesCS5D01G396600 chr1B 84.431 167 18 3 4670 4836 252288647 252288805 2.500000e-34 158.0
55 TraesCS5D01G396600 chr1B 84.431 167 17 5 4670 4836 68073312 68073469 8.990000e-34 156.0
56 TraesCS5D01G396600 chr1B 82.143 168 19 6 4670 4837 264360161 264360005 4.210000e-27 134.0
57 TraesCS5D01G396600 chr1B 90.805 87 4 2 5149 5235 539869528 539869610 5.490000e-21 113.0
58 TraesCS5D01G396600 chr1B 88.636 88 9 1 5147 5234 593924290 593924376 9.190000e-19 106.0
59 TraesCS5D01G396600 chr1B 88.372 86 10 0 5149 5234 658497429 658497514 3.300000e-18 104.0
60 TraesCS5D01G396600 chr7B 80.383 209 37 4 612 816 703714507 703714299 8.990000e-34 156.0
61 TraesCS5D01G396600 chr7B 94.118 85 5 0 5149 5233 490685182 490685098 5.450000e-26 130.0
62 TraesCS5D01G396600 chr3B 84.615 156 16 2 4681 4836 556089601 556089748 1.500000e-31 148.0
63 TraesCS5D01G396600 chr3B 79.630 216 31 5 612 815 593937701 593937487 7.000000e-30 143.0
64 TraesCS5D01G396600 chr1A 83.234 167 20 3 4670 4836 168583035 168582877 5.410000e-31 147.0
65 TraesCS5D01G396600 chr1A 87.500 96 7 2 5147 5242 501030275 501030185 9.190000e-19 106.0
66 TraesCS5D01G396600 chr1A 79.221 154 22 5 4684 4836 510394006 510393862 1.540000e-16 99.0
67 TraesCS5D01G396600 chr1A 86.111 72 8 2 4789 4859 47586234 47586304 7.200000e-10 76.8
68 TraesCS5D01G396600 chr3A 85.135 148 12 5 4689 4836 562286831 562286694 7.000000e-30 143.0
69 TraesCS5D01G396600 chr3A 90.698 86 8 0 5149 5234 491189426 491189511 1.530000e-21 115.0
70 TraesCS5D01G396600 chr3A 76.733 202 39 7 614 813 495020064 495019869 9.190000e-19 106.0
71 TraesCS5D01G396600 chr7D 83.230 161 14 7 4681 4836 83637793 83637641 1.170000e-27 135.0
72 TraesCS5D01G396600 chr7D 79.070 215 31 9 615 816 116789581 116789368 1.170000e-27 135.0
73 TraesCS5D01G396600 chr7D 81.366 161 15 9 4681 4834 79958151 79958303 4.240000e-22 117.0
74 TraesCS5D01G396600 chr2B 78.218 202 37 6 614 813 452778075 452778271 9.120000e-24 122.0
75 TraesCS5D01G396600 chr6B 91.954 87 5 1 5148 5234 191534633 191534717 3.280000e-23 121.0
76 TraesCS5D01G396600 chr6B 91.667 60 3 2 4777 4835 713699579 713699637 1.550000e-11 82.4
77 TraesCS5D01G396600 chr4A 90.805 87 8 0 5142 5228 695135011 695134925 4.240000e-22 117.0
78 TraesCS5D01G396600 chrUn 100.000 45 0 0 5190 5234 313622386 313622430 4.300000e-12 84.2
79 TraesCS5D01G396600 chrUn 83.908 87 12 2 5148 5234 10131510 10131426 1.550000e-11 82.4
80 TraesCS5D01G396600 chrUn 93.878 49 3 0 4788 4836 19230149 19230197 2.590000e-09 75.0
81 TraesCS5D01G396600 chrUn 100.000 33 0 0 5201 5233 32098221 32098253 2.020000e-05 62.1
82 TraesCS5D01G396600 chrUn 97.059 34 1 0 5200 5233 295853755 295853722 2.610000e-04 58.4


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 TraesCS5D01G396600 chr5D 464065716 464072412 6696 False 12368.000000 12368 100.0000 1 6697 1 chr5D.!!$F6 6696
1 TraesCS5D01G396600 chr5A 584448652 584455437 6785 False 4748.000000 7060 91.6055 1 6697 2 chr5A.!!$F4 6696
2 TraesCS5D01G396600 chr5B 570923629 570930078 6449 False 2879.333333 3965 92.4910 571 6697 3 chr5B.!!$F3 6126
3 TraesCS5D01G396600 chr5B 570905567 570906140 573 False 789.000000 789 91.5370 1 574 1 chr5B.!!$F2 573

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
725 743 0.752054 CTCAGTCCCTCAGAGATGCC 59.248 60.000 0.00 0.00 32.43 4.40 F
1520 1567 0.036732 TGGATGGCGTTTCTCAAGCT 59.963 50.000 0.00 0.00 0.00 3.74 F
1734 1782 1.493311 GGAGAAAGTGTTGCTCGCG 59.507 57.895 0.00 0.00 0.00 5.87 F
2249 2366 1.593196 TTTGGAAAGAGCACCGAGTG 58.407 50.000 0.25 0.25 36.51 3.51 F
3657 3807 2.171448 AGCCTTCAAGCCTAGTGGTATG 59.829 50.000 0.00 0.00 35.27 2.39 F
4040 4204 2.621526 TCCTCATGATCATGTGCAATGC 59.378 45.455 30.01 0.00 39.72 3.56 F
4836 5266 0.176910 GAGCTTCTAGCACTGGGTCC 59.823 60.000 1.09 0.00 45.56 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2039 1.134946 GGTCCATTATGTTGCAGGTGC 59.865 52.381 0.0 0.0 42.5 5.01 R
2708 2833 3.830744 TGAGGAAAAACTGAAGACGGA 57.169 42.857 0.0 0.0 0.0 4.69 R
3228 3355 3.883489 AGACAAGCTAAACTCCCACAAAC 59.117 43.478 0.0 0.0 0.0 2.93 R
4236 4431 1.334160 TTCGCCTCCTTCACACTGTA 58.666 50.000 0.0 0.0 0.0 2.74 R
4603 4802 0.535102 GTGAGTGTGTGTTGGGGAGG 60.535 60.000 0.0 0.0 0.0 4.30 R
4890 5327 0.965439 TGCCTTTGCTTATTTGGCGT 59.035 45.000 0.0 0.0 45.9 5.68 R
6223 6678 0.502275 CGTGACAAATGCAAAACCGC 59.498 50.000 0.0 0.0 0.0 5.68 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
175 180 6.584185 ATTAACGTTATTTTGTGCTCCCTT 57.416 33.333 9.18 0.00 0.00 3.95
176 181 7.690952 ATTAACGTTATTTTGTGCTCCCTTA 57.309 32.000 9.18 0.00 0.00 2.69
237 243 8.877779 ACGGACTACATACGAATGTATATAGAC 58.122 37.037 7.52 2.40 45.33 2.59
445 451 3.945285 AGGAAAACAGACGTGTTGAATGT 59.055 39.130 0.00 0.00 46.68 2.71
497 503 5.667644 GCATTACGCCAAATGTTGCTTTTAC 60.668 40.000 7.33 0.00 38.78 2.01
508 514 5.752892 TGTTGCTTTTACACATCGGTTTA 57.247 34.783 0.00 0.00 0.00 2.01
585 592 7.282585 CCTCAACAAGTAATATGGATTGGAGA 58.717 38.462 0.00 0.00 0.00 3.71
619 626 7.992180 AATCGCAACAAAATCAGGATTTATC 57.008 32.000 7.62 0.00 39.88 1.75
633 640 3.826729 GGATTTATCCCAGGATTTTCGGG 59.173 47.826 4.13 0.00 41.20 5.14
653 660 3.958147 ATGCGCGTTCAGTGGGAGG 62.958 63.158 8.43 0.00 0.00 4.30
661 668 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
725 743 0.752054 CTCAGTCCCTCAGAGATGCC 59.248 60.000 0.00 0.00 32.43 4.40
732 750 3.117888 GTCCCTCAGAGATGCCCATAAAA 60.118 47.826 0.00 0.00 0.00 1.52
736 754 6.070656 CCCTCAGAGATGCCCATAAAATTAA 58.929 40.000 0.00 0.00 0.00 1.40
737 755 6.550854 CCCTCAGAGATGCCCATAAAATTAAA 59.449 38.462 0.00 0.00 0.00 1.52
744 762 9.709495 GAGATGCCCATAAAATTAAAATATGCA 57.291 29.630 0.00 0.00 0.00 3.96
772 791 3.430374 GCGTTCATAGGGTGAGTGTATGT 60.430 47.826 0.00 0.00 38.29 2.29
774 793 3.819564 TCATAGGGTGAGTGTATGTGC 57.180 47.619 0.00 0.00 31.80 4.57
795 814 3.420162 GCGTTTATATGAGCGCTTACGTC 60.420 47.826 19.08 0.00 45.48 4.34
845 867 3.040099 CAGCGAAAACACCCGTTAAAAG 58.960 45.455 0.00 0.00 33.99 2.27
900 928 2.278245 TGGATGGGGATTAGGGCATAG 58.722 52.381 0.00 0.00 0.00 2.23
967 995 5.531122 TCGTCTCCTAACCAGATTAATGG 57.469 43.478 0.00 0.00 46.47 3.16
986 1016 3.738982 TGGCGTAATAATCATCACAGGG 58.261 45.455 0.00 0.00 0.00 4.45
998 1028 4.065088 TCATCACAGGGAAAAACTCTTCG 58.935 43.478 0.00 0.00 0.00 3.79
1142 1172 0.179215 CGTGTACGTGGACGACTACC 60.179 60.000 14.06 0.00 43.02 3.18
1168 1198 2.586357 GAGATTGCCGGCTCCGAC 60.586 66.667 29.70 14.11 42.83 4.79
1192 1222 5.289083 TGTTTCCCTTTTCCTTTCCATTG 57.711 39.130 0.00 0.00 0.00 2.82
1194 1224 3.913370 TCCCTTTTCCTTTCCATTGGA 57.087 42.857 0.00 0.00 0.00 3.53
1329 1363 2.236644 CCCATGGTGATGATTTTGCCAA 59.763 45.455 11.73 0.00 32.54 4.52
1422 1469 2.103263 GCTTTCCATCCTGACTCCGTAT 59.897 50.000 0.00 0.00 0.00 3.06
1452 1499 3.016736 CCATGCTTTAATTGTCGACCCT 58.983 45.455 14.12 0.00 0.00 4.34
1474 1521 4.017126 TGAGATATAATCCCGCGAGTGAT 58.983 43.478 8.23 3.49 0.00 3.06
1508 1555 4.397420 TGTTGTATATGATGGTGGATGGC 58.603 43.478 0.00 0.00 0.00 4.40
1510 1557 2.637382 TGTATATGATGGTGGATGGCGT 59.363 45.455 0.00 0.00 0.00 5.68
1520 1567 0.036732 TGGATGGCGTTTCTCAAGCT 59.963 50.000 0.00 0.00 0.00 3.74
1536 1584 5.637387 TCTCAAGCTTTGTTTTGTGGTTTTC 59.363 36.000 0.00 0.00 0.00 2.29
1590 1638 3.039011 GGGTCAGACTAAAGGGCAGATA 58.961 50.000 0.00 0.00 0.00 1.98
1734 1782 1.493311 GGAGAAAGTGTTGCTCGCG 59.507 57.895 0.00 0.00 0.00 5.87
1805 1853 8.549338 AGTTGTCCTGTAGCTTAAAGAATTAC 57.451 34.615 0.00 0.00 0.00 1.89
1836 1884 7.268447 GCAAAACTTTTAACTAGTGCATCTACG 59.732 37.037 0.00 0.00 0.00 3.51
1920 2036 4.452795 GCTTCCTTCCTTCAACTTGTAGTC 59.547 45.833 0.00 0.00 0.00 2.59
1921 2037 4.618920 TCCTTCCTTCAACTTGTAGTCC 57.381 45.455 0.00 0.00 0.00 3.85
1922 2038 4.232091 TCCTTCCTTCAACTTGTAGTCCT 58.768 43.478 0.00 0.00 0.00 3.85
1923 2039 4.040461 TCCTTCCTTCAACTTGTAGTCCTG 59.960 45.833 0.00 0.00 0.00 3.86
1924 2040 3.402628 TCCTTCAACTTGTAGTCCTGC 57.597 47.619 0.00 0.00 0.00 4.85
1925 2041 2.703536 TCCTTCAACTTGTAGTCCTGCA 59.296 45.455 0.00 0.00 0.00 4.41
1969 2085 4.827835 TGGATATCAGTTAGTTCTCCTCCG 59.172 45.833 4.83 0.00 0.00 4.63
2249 2366 1.593196 TTTGGAAAGAGCACCGAGTG 58.407 50.000 0.25 0.25 36.51 3.51
2361 2478 3.304829 ACCACCCAGCTGTTAAATTGTT 58.695 40.909 13.81 0.00 0.00 2.83
2369 2486 8.686334 ACCCAGCTGTTAAATTGTTATATTGAG 58.314 33.333 13.81 0.00 0.00 3.02
2401 2519 5.957842 CTAACACAGGATGCAAACCTAAA 57.042 39.130 14.08 0.80 36.74 1.85
2407 2525 5.047802 CACAGGATGCAAACCTAAATCTGTT 60.048 40.000 14.08 0.00 36.74 3.16
2408 2526 5.183904 ACAGGATGCAAACCTAAATCTGTTC 59.816 40.000 14.08 0.00 36.74 3.18
2420 2538 7.593825 ACCTAAATCTGTTCTTAACAATGCAC 58.406 34.615 0.00 0.00 41.61 4.57
2429 2547 8.800370 TGTTCTTAACAATGCACCTCATTATA 57.200 30.769 0.00 0.00 43.21 0.98
2480 2598 5.590259 CGAGGATCCAAACCAATCTACAAAT 59.410 40.000 15.82 0.00 0.00 2.32
2520 2643 6.426937 TGGCAGTTATCTCTTCAGTGTTAAAC 59.573 38.462 0.00 0.00 0.00 2.01
2708 2833 9.471702 AATCTTCACCAAACAGAATATCAGATT 57.528 29.630 0.00 0.00 0.00 2.40
2711 2836 5.817296 TCACCAAACAGAATATCAGATTCCG 59.183 40.000 0.00 0.00 0.00 4.30
2718 2843 6.511416 ACAGAATATCAGATTCCGTCTTCAG 58.489 40.000 0.00 0.00 34.00 3.02
3228 3355 5.426504 AGTGATGCCTTATCTTCTGAGTTG 58.573 41.667 0.00 0.00 36.71 3.16
3236 3363 5.182001 CCTTATCTTCTGAGTTGTTTGTGGG 59.818 44.000 0.00 0.00 0.00 4.61
3249 3376 3.630312 TGTTTGTGGGAGTTTAGCTTGTC 59.370 43.478 0.00 0.00 0.00 3.18
3291 3418 6.742559 TTTACCCTTATCAGGCCTAAGTAG 57.257 41.667 3.98 2.19 39.20 2.57
3317 3444 7.803079 GCTTTAGAGCTTTCCAAACTTATTG 57.197 36.000 0.00 0.00 45.65 1.90
3537 3687 8.856103 AGTTGGTACTTGCATTTTACAAACTAT 58.144 29.630 15.87 1.02 37.94 2.12
3538 3688 9.471084 GTTGGTACTTGCATTTTACAAACTATT 57.529 29.630 10.70 0.00 30.09 1.73
3656 3806 2.482494 AGCCTTCAAGCCTAGTGGTAT 58.518 47.619 0.00 0.00 35.27 2.73
3657 3807 2.171448 AGCCTTCAAGCCTAGTGGTATG 59.829 50.000 0.00 0.00 35.27 2.39
3667 3817 4.910304 AGCCTAGTGGTATGATTTCCAGAT 59.090 41.667 0.00 0.00 34.16 2.90
3810 3974 8.571336 CAAATATCTCCCCTAGCAACAAAATAG 58.429 37.037 0.00 0.00 0.00 1.73
4035 4199 4.616143 GCATCAATCCTCATGATCATGTGC 60.616 45.833 30.01 24.97 39.72 4.57
4036 4200 4.159244 TCAATCCTCATGATCATGTGCA 57.841 40.909 30.01 18.10 39.72 4.57
4037 4201 4.528920 TCAATCCTCATGATCATGTGCAA 58.471 39.130 30.01 19.71 39.72 4.08
4038 4202 5.137551 TCAATCCTCATGATCATGTGCAAT 58.862 37.500 30.01 20.77 39.72 3.56
4039 4203 5.009610 TCAATCCTCATGATCATGTGCAATG 59.990 40.000 30.01 23.42 39.72 2.82
4040 4204 2.621526 TCCTCATGATCATGTGCAATGC 59.378 45.455 30.01 0.00 39.72 3.56
4041 4205 2.623416 CCTCATGATCATGTGCAATGCT 59.377 45.455 30.01 0.00 39.72 3.79
4042 4206 3.304726 CCTCATGATCATGTGCAATGCTC 60.305 47.826 30.01 3.08 39.72 4.26
4043 4207 3.551846 TCATGATCATGTGCAATGCTCT 58.448 40.909 30.01 0.00 39.72 4.09
4044 4208 4.710324 TCATGATCATGTGCAATGCTCTA 58.290 39.130 30.01 8.18 39.72 2.43
4045 4209 5.313712 TCATGATCATGTGCAATGCTCTAT 58.686 37.500 30.01 0.00 39.72 1.98
4046 4210 5.181245 TCATGATCATGTGCAATGCTCTATG 59.819 40.000 30.01 8.48 39.72 2.23
4047 4211 3.818773 TGATCATGTGCAATGCTCTATGG 59.181 43.478 6.82 0.00 0.00 2.74
4048 4212 3.286329 TCATGTGCAATGCTCTATGGT 57.714 42.857 6.82 0.00 0.00 3.55
4099 4294 7.312899 AGGAAAAACATTAGATAAAAGGCACG 58.687 34.615 0.00 0.00 0.00 5.34
4140 4335 3.741344 GTGTCTTGCACTATCACTTTCGT 59.259 43.478 0.00 0.00 44.41 3.85
4236 4431 6.773976 TGCTAACTTTTTATATGCTTGCCT 57.226 33.333 0.00 0.00 0.00 4.75
4373 4568 8.045720 TCTCCTAAATTGGTAAGAGGCAATAT 57.954 34.615 0.00 0.00 0.00 1.28
4426 4621 8.689061 TCTTAGCTTACCTTATCACGTAAATCA 58.311 33.333 0.00 0.00 0.00 2.57
4438 4633 5.945155 TCACGTAAATCACCAAATAAAGCC 58.055 37.500 0.00 0.00 0.00 4.35
4557 4753 7.745620 TCCTTTTCAGAAAACCATCTAACTC 57.254 36.000 4.06 0.00 0.00 3.01
4588 4784 6.297582 TCAAAACCTCGAAATAACCCTACAA 58.702 36.000 0.00 0.00 0.00 2.41
4589 4785 6.771749 TCAAAACCTCGAAATAACCCTACAAA 59.228 34.615 0.00 0.00 0.00 2.83
4590 4786 7.449086 TCAAAACCTCGAAATAACCCTACAAAT 59.551 33.333 0.00 0.00 0.00 2.32
4591 4787 8.732531 CAAAACCTCGAAATAACCCTACAAATA 58.267 33.333 0.00 0.00 0.00 1.40
4592 4788 9.470399 AAAACCTCGAAATAACCCTACAAATAT 57.530 29.630 0.00 0.00 0.00 1.28
4593 4789 8.446599 AACCTCGAAATAACCCTACAAATATG 57.553 34.615 0.00 0.00 0.00 1.78
4594 4790 6.485648 ACCTCGAAATAACCCTACAAATATGC 59.514 38.462 0.00 0.00 0.00 3.14
4595 4791 6.072673 CCTCGAAATAACCCTACAAATATGCC 60.073 42.308 0.00 0.00 0.00 4.40
4618 4817 2.115266 CCCCTCCCCAACACACAC 59.885 66.667 0.00 0.00 0.00 3.82
4619 4818 2.460853 CCCCTCCCCAACACACACT 61.461 63.158 0.00 0.00 0.00 3.55
4678 4877 1.460689 AACGTGGGGGAAGGACAGA 60.461 57.895 0.00 0.00 0.00 3.41
4704 4903 2.444421 CGTAGTGGTGAAGTACTCCCT 58.556 52.381 0.00 0.00 33.16 4.20
4709 4908 4.490706 AGTGGTGAAGTACTCCCTACTTT 58.509 43.478 0.00 0.00 44.45 2.66
4720 4919 1.354368 TCCCTACTTTTGCCAAGAGGG 59.646 52.381 16.41 16.41 44.37 4.30
4729 4928 2.854076 CCAAGAGGGCCTGGGTTT 59.146 61.111 12.95 0.00 30.82 3.27
4732 4931 0.895559 CAAGAGGGCCTGGGTTTGAC 60.896 60.000 12.95 0.00 0.00 3.18
4766 5195 2.671619 GCACTGCGCAGGGGTAAA 60.672 61.111 38.56 0.00 41.79 2.01
4786 5215 3.550437 AGCACTAAGATTCGCCTCATT 57.450 42.857 0.00 0.00 0.00 2.57
4830 5260 0.610687 GTGTGGGAGCTTCTAGCACT 59.389 55.000 1.09 0.00 45.56 4.40
4836 5266 0.176910 GAGCTTCTAGCACTGGGTCC 59.823 60.000 1.09 0.00 45.56 4.46
4955 5392 4.475763 CACCGATAGTGTACAGCTAGAG 57.524 50.000 0.00 0.48 41.93 2.43
4981 5418 9.717942 GTTAAGCTTATCCAGAGACATATCAAT 57.282 33.333 7.08 0.00 0.00 2.57
5063 5501 8.899771 CATAAAGGCCCTATAATTAATTACCGG 58.100 37.037 10.07 12.34 0.00 5.28
5345 5783 3.714280 TCATCGGGATAATTCTTGGGTCA 59.286 43.478 0.00 0.00 0.00 4.02
5409 5847 1.947678 GCTCACCAGTGTTGATGAGGG 60.948 57.143 1.39 0.00 39.20 4.30
5461 5899 3.430042 ACATGCAGGACTCTTCAACAT 57.570 42.857 4.84 0.00 0.00 2.71
5531 5969 4.138290 TGTTTCAATTTGTAAGGAGGCGA 58.862 39.130 0.00 0.00 0.00 5.54
5542 5980 2.892784 AGGAGGCGATTACTTACAGC 57.107 50.000 0.00 0.00 0.00 4.40
5546 5984 0.300789 GGCGATTACTTACAGCGTGC 59.699 55.000 0.00 0.00 0.00 5.34
5776 6214 1.022735 CCATTGTCTGCTGCATCTCC 58.977 55.000 1.31 0.00 0.00 3.71
5777 6215 1.408405 CCATTGTCTGCTGCATCTCCT 60.408 52.381 1.31 0.00 0.00 3.69
5778 6216 1.941294 CATTGTCTGCTGCATCTCCTC 59.059 52.381 1.31 0.00 0.00 3.71
5779 6217 1.273759 TTGTCTGCTGCATCTCCTCT 58.726 50.000 1.31 0.00 0.00 3.69
5780 6218 0.535797 TGTCTGCTGCATCTCCTCTG 59.464 55.000 1.31 0.00 0.00 3.35
5781 6219 0.810823 GTCTGCTGCATCTCCTCTGC 60.811 60.000 1.31 0.00 40.10 4.26
5796 6234 2.357881 TGCTGAGCTGAAGGTGCG 60.358 61.111 5.83 0.00 35.28 5.34
5862 6300 5.756347 TGTGTAACTACAACTACAAAGCCTG 59.244 40.000 0.00 0.00 38.04 4.85
5885 6324 1.474077 GATCCCCTGTTTCACATGTGC 59.526 52.381 21.38 7.96 0.00 4.57
6094 6537 1.135575 CCGTACCACTCGTACTTGGAC 60.136 57.143 10.98 5.35 44.52 4.02
6223 6678 7.221452 CAGTTTTTCAGTTTTGTGATCCTTCTG 59.779 37.037 0.00 0.00 0.00 3.02
6225 6680 2.807967 TCAGTTTTGTGATCCTTCTGCG 59.192 45.455 0.00 0.00 0.00 5.18
6402 6857 1.739049 GGAGAGGAGCATGTCGAGG 59.261 63.158 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.016276 TGTCTTAGGAAAATTTCAAGCCTCAC 60.016 38.462 8.09 0.00 0.00 3.51
47 48 6.664515 TGGATGCTTAGTTTCAAAGTAAACG 58.335 36.000 0.00 0.00 42.83 3.60
155 160 5.067954 ACTAAGGGAGCACAAAATAACGTT 58.932 37.500 5.88 5.88 0.00 3.99
257 263 9.625747 TGGACTACATATGAAGCAAAATGAATA 57.374 29.630 10.38 0.00 0.00 1.75
324 330 6.795098 TCATCAACACACCACAACTAATAC 57.205 37.500 0.00 0.00 0.00 1.89
430 436 2.799978 TGTGCTACATTCAACACGTCTG 59.200 45.455 0.00 0.00 35.79 3.51
431 437 3.106242 TGTGCTACATTCAACACGTCT 57.894 42.857 0.00 0.00 35.79 4.18
434 440 4.975502 ACAAATTGTGCTACATTCAACACG 59.024 37.500 0.00 0.00 35.79 4.49
445 451 4.081365 TCCCGACTATGACAAATTGTGCTA 60.081 41.667 2.20 0.00 0.00 3.49
558 565 6.159575 TCCAATCCATATTACTTGTTGAGGGA 59.840 38.462 0.00 0.00 0.00 4.20
564 571 8.095452 AGTCTCTCCAATCCATATTACTTGTT 57.905 34.615 0.00 0.00 0.00 2.83
585 592 7.199766 TGATTTTGTTGCGATTTTTGTAGTCT 58.800 30.769 0.00 0.00 0.00 3.24
619 626 1.109323 GCATCCCCGAAAATCCTGGG 61.109 60.000 0.00 0.00 42.92 4.45
620 627 1.447317 CGCATCCCCGAAAATCCTGG 61.447 60.000 0.00 0.00 0.00 4.45
629 636 4.812476 CTGAACGCGCATCCCCGA 62.812 66.667 5.73 0.00 0.00 5.14
633 640 3.499737 CCCACTGAACGCGCATCC 61.500 66.667 5.73 0.00 0.00 3.51
693 711 5.132648 TGAGGGACTGAGCCAACATATTATT 59.867 40.000 0.00 0.00 41.55 1.40
696 714 2.846206 TGAGGGACTGAGCCAACATATT 59.154 45.455 0.00 0.00 41.55 1.28
703 721 0.337773 ATCTCTGAGGGACTGAGCCA 59.662 55.000 4.59 0.00 40.28 4.75
744 762 3.388024 ACTCACCCTATGAACGCATACAT 59.612 43.478 0.00 0.00 36.69 2.29
748 766 1.555075 ACACTCACCCTATGAACGCAT 59.445 47.619 0.00 0.00 36.69 4.73
755 773 2.159099 ACGCACATACACTCACCCTATG 60.159 50.000 0.00 0.00 0.00 2.23
774 793 3.973135 AGACGTAAGCGCTCATATAAACG 59.027 43.478 12.06 14.21 42.83 3.60
845 867 1.844544 TAAACTTGGGGCCTCCGGAC 61.845 60.000 0.00 0.00 38.76 4.79
859 882 5.191722 TCCATGGGCTCACTCTATTTAAACT 59.808 40.000 13.02 0.00 0.00 2.66
860 883 5.437060 TCCATGGGCTCACTCTATTTAAAC 58.563 41.667 13.02 0.00 0.00 2.01
863 886 4.042062 CCATCCATGGGCTCACTCTATTTA 59.958 45.833 13.02 0.00 44.31 1.40
900 928 1.067582 CCGTACGATGGAAGCCCTC 59.932 63.158 18.76 0.00 0.00 4.30
937 965 0.651031 GTTAGGAGACGATTTGCGCC 59.349 55.000 4.18 0.00 46.04 6.53
967 995 6.371809 TTTTCCCTGTGATGATTATTACGC 57.628 37.500 0.00 0.00 0.00 4.42
986 1016 5.765072 AATCTCGCTACGAAGAGTTTTTC 57.235 39.130 0.00 0.00 34.74 2.29
998 1028 0.179054 GGGTGGGGAAATCTCGCTAC 60.179 60.000 0.00 0.00 42.94 3.58
1142 1172 0.742281 CCGGCAATCTCACACTCCAG 60.742 60.000 0.00 0.00 0.00 3.86
1168 1198 5.551305 ATGGAAAGGAAAAGGGAAACAAG 57.449 39.130 0.00 0.00 0.00 3.16
1192 1222 1.704641 AAAGGTCCAAAAGCACCTCC 58.295 50.000 0.00 0.00 42.61 4.30
1194 1224 1.138859 GCAAAAGGTCCAAAAGCACCT 59.861 47.619 0.00 0.00 45.59 4.00
1383 1430 2.893424 AGCAAAATTCACTCCCCACAT 58.107 42.857 0.00 0.00 0.00 3.21
1389 1436 4.221482 AGGATGGAAAGCAAAATTCACTCC 59.779 41.667 0.00 0.00 32.93 3.85
1422 1469 6.543430 ACAATTAAAGCATGGCCAGATTAA 57.457 33.333 13.05 13.61 0.00 1.40
1452 1499 3.418047 TCACTCGCGGGATTATATCTCA 58.582 45.455 15.95 0.00 0.00 3.27
1474 1521 5.454966 TCATATACAACAGCCAGTCCTCTA 58.545 41.667 0.00 0.00 0.00 2.43
1508 1555 4.031652 CCACAAAACAAAGCTTGAGAAACG 59.968 41.667 0.00 0.00 0.00 3.60
1510 1557 5.146010 ACCACAAAACAAAGCTTGAGAAA 57.854 34.783 0.00 0.00 0.00 2.52
1536 1584 7.172190 CCTGCACCACAAAGATATATAAGACAG 59.828 40.741 0.00 0.00 0.00 3.51
1549 1597 1.868498 CAAAATGCCTGCACCACAAAG 59.132 47.619 0.00 0.00 0.00 2.77
1590 1638 1.644509 GCACCCCCAGGAGAAATTTT 58.355 50.000 0.00 0.00 36.73 1.82
1734 1782 1.718757 CCAGGTCATAAGCTTGGCGC 61.719 60.000 9.86 0.00 39.57 6.53
1805 1853 5.342259 GCACTAGTTAAAAGTTTTGCATCCG 59.658 40.000 11.18 0.00 0.00 4.18
1923 2039 1.134946 GGTCCATTATGTTGCAGGTGC 59.865 52.381 0.00 0.00 42.50 5.01
1924 2040 2.726821 AGGTCCATTATGTTGCAGGTG 58.273 47.619 0.00 0.00 0.00 4.00
1925 2041 4.464008 CATAGGTCCATTATGTTGCAGGT 58.536 43.478 0.00 0.00 0.00 4.00
1969 2085 2.030946 GCACTAGCGACATTTCCATCAC 59.969 50.000 0.00 0.00 0.00 3.06
2387 2504 5.904362 AGAACAGATTTAGGTTTGCATCC 57.096 39.130 0.00 0.00 0.00 3.51
2401 2519 5.316167 TGAGGTGCATTGTTAAGAACAGAT 58.684 37.500 0.00 0.00 43.27 2.90
2407 2525 7.342581 TGGTATAATGAGGTGCATTGTTAAGA 58.657 34.615 0.00 0.00 46.38 2.10
2408 2526 7.566760 TGGTATAATGAGGTGCATTGTTAAG 57.433 36.000 0.00 0.00 46.38 1.85
2429 2547 6.388619 ACCCTTCTGTATTTCTATGTTGGT 57.611 37.500 0.00 0.00 0.00 3.67
2680 2805 8.102676 TCTGATATTCTGTTTGGTGAAGATTCA 58.897 33.333 0.00 0.00 34.20 2.57
2690 2815 6.051717 AGACGGAATCTGATATTCTGTTTGG 58.948 40.000 12.20 0.00 44.86 3.28
2708 2833 3.830744 TGAGGAAAAACTGAAGACGGA 57.169 42.857 0.00 0.00 0.00 4.69
2711 2836 7.812669 TGTTCTTTTTGAGGAAAAACTGAAGAC 59.187 33.333 0.00 0.00 37.48 3.01
2718 2843 9.706846 CAATCAATGTTCTTTTTGAGGAAAAAC 57.293 29.630 0.00 0.00 37.48 2.43
3196 3322 6.678568 AGATAAGGCATCACTACTTAGCAT 57.321 37.500 0.00 0.00 36.01 3.79
3228 3355 3.883489 AGACAAGCTAAACTCCCACAAAC 59.117 43.478 0.00 0.00 0.00 2.93
3236 3363 9.595357 GTAATTTACAACAGACAAGCTAAACTC 57.405 33.333 1.62 0.00 0.00 3.01
3317 3444 8.550376 ACAACATCATTGTTCAAAAAGCAATAC 58.450 29.630 0.00 0.00 44.24 1.89
3392 3520 4.775236 AGCACATAATCCTCTTTCTGGAC 58.225 43.478 0.00 0.00 36.30 4.02
3400 3528 4.833478 AACAGTGAGCACATAATCCTCT 57.167 40.909 0.00 0.00 0.00 3.69
3537 3687 9.613428 CATTGACCACTAATTCTATTCCACTAA 57.387 33.333 0.00 0.00 0.00 2.24
3538 3688 7.715249 GCATTGACCACTAATTCTATTCCACTA 59.285 37.037 0.00 0.00 0.00 2.74
3656 3806 7.010160 AGAACAGGGTAAAAATCTGGAAATCA 58.990 34.615 0.00 0.00 33.19 2.57
3657 3807 7.468141 AGAACAGGGTAAAAATCTGGAAATC 57.532 36.000 0.00 0.00 33.19 2.17
4035 4199 6.278172 TCTAGCATAGACCATAGAGCATTG 57.722 41.667 0.00 0.00 44.15 2.82
4099 4294 3.197983 ACACTACTTTGTAGGGCTCCATC 59.802 47.826 6.88 0.00 0.00 3.51
4140 4335 2.469826 CGATAACAAGCATCGGCACTA 58.530 47.619 0.00 0.00 44.61 2.74
4181 4376 7.726216 AGAGATGGATGACGTTCATATAACAA 58.274 34.615 0.00 0.00 37.20 2.83
4236 4431 1.334160 TTCGCCTCCTTCACACTGTA 58.666 50.000 0.00 0.00 0.00 2.74
4373 4568 8.911918 TTCTACAGATTTAAAGCAGTTGGTAA 57.088 30.769 6.82 0.00 0.00 2.85
4381 4576 9.672673 AGCTAAGATTTCTACAGATTTAAAGCA 57.327 29.630 6.19 0.00 0.00 3.91
4426 4621 4.026052 CAGGAAGATGGGCTTTATTTGGT 58.974 43.478 0.00 0.00 36.83 3.67
4516 4711 9.528018 CTGAAAAGGAAAAGTTTGCACTAATAA 57.472 29.630 0.00 0.00 30.68 1.40
4532 4727 7.777910 TGAGTTAGATGGTTTTCTGAAAAGGAA 59.222 33.333 15.39 5.38 0.00 3.36
4557 4753 6.371389 GTTATTTCGAGGTTTTGAAGGACTG 58.629 40.000 0.00 0.00 0.00 3.51
4603 4802 0.535102 GTGAGTGTGTGTTGGGGAGG 60.535 60.000 0.00 0.00 0.00 4.30
4612 4811 4.863689 TGCAAAATTTGAAGTGAGTGTGTG 59.136 37.500 10.26 0.00 0.00 3.82
4646 4845 3.448301 CCCCACGTTCTACATGTAAGGTA 59.552 47.826 7.06 0.00 28.09 3.08
4647 4846 2.235402 CCCCACGTTCTACATGTAAGGT 59.765 50.000 7.06 4.05 32.53 3.50
4663 4862 1.920835 AGCTCTGTCCTTCCCCCAC 60.921 63.158 0.00 0.00 0.00 4.61
4678 4877 1.293498 CTTCACCACTACGCCAGCT 59.707 57.895 0.00 0.00 0.00 4.24
4720 4919 4.043200 GCTGCGTCAAACCCAGGC 62.043 66.667 0.00 0.00 0.00 4.85
4766 5195 3.550437 AATGAGGCGAATCTTAGTGCT 57.450 42.857 0.00 0.00 0.00 4.40
4786 5215 3.784202 GGTGGGTTCTAGGGAAGGATTAA 59.216 47.826 0.00 0.00 31.46 1.40
4856 5292 3.941188 CACCTGCACTCCCCACGT 61.941 66.667 0.00 0.00 0.00 4.49
4890 5327 0.965439 TGCCTTTGCTTATTTGGCGT 59.035 45.000 0.00 0.00 45.90 5.68
4955 5392 9.717942 ATTGATATGTCTCTGGATAAGCTTAAC 57.282 33.333 10.85 7.81 0.00 2.01
5017 5454 2.100584 TGTGAAATTGCAGTGGGTGTTC 59.899 45.455 0.00 0.00 0.00 3.18
5063 5501 7.094377 TGGGTGTTTTTCTCAATAGCTTATGTC 60.094 37.037 0.00 0.00 0.00 3.06
5383 5821 1.013596 CAACACTGGTGAGCAAACGA 58.986 50.000 7.78 0.00 0.00 3.85
5393 5831 0.987294 CTCCCCTCATCAACACTGGT 59.013 55.000 0.00 0.00 0.00 4.00
5461 5899 2.636893 AGAAAAGCTTCTGAGAGCCTCA 59.363 45.455 0.00 5.03 43.74 3.86
5531 5969 7.414098 CCAAAATAAGAGCACGCTGTAAGTAAT 60.414 37.037 0.00 0.00 35.30 1.89
5776 6214 1.020333 GCACCTTCAGCTCAGCAGAG 61.020 60.000 0.00 0.94 44.96 3.35
5777 6215 1.004080 GCACCTTCAGCTCAGCAGA 60.004 57.895 0.00 0.00 0.00 4.26
5778 6216 2.389020 CGCACCTTCAGCTCAGCAG 61.389 63.158 0.00 0.00 0.00 4.24
5779 6217 2.357881 CGCACCTTCAGCTCAGCA 60.358 61.111 0.00 0.00 0.00 4.41
5780 6218 3.123620 CCGCACCTTCAGCTCAGC 61.124 66.667 0.00 0.00 0.00 4.26
5781 6219 3.123620 GCCGCACCTTCAGCTCAG 61.124 66.667 0.00 0.00 0.00 3.35
5816 6254 9.364989 ACACAATAATTTAATACAATGTGTGCC 57.635 29.630 13.76 0.00 45.82 5.01
5853 6291 1.000396 GGGGATCAGCAGGCTTTGT 60.000 57.895 0.00 0.00 0.00 2.83
5862 6300 3.650647 TGTGAAACAGGGGATCAGC 57.349 52.632 0.00 0.00 45.67 4.26
5913 6352 5.584649 TGTAGATATACTGCAGCAACAAACC 59.415 40.000 15.27 0.00 36.38 3.27
5914 6353 6.662414 TGTAGATATACTGCAGCAACAAAC 57.338 37.500 15.27 5.18 36.38 2.93
5915 6354 7.680442 TTTGTAGATATACTGCAGCAACAAA 57.320 32.000 15.27 11.35 41.74 2.83
6094 6537 3.072468 TACGTCTTCAGCCCGGGG 61.072 66.667 25.28 9.31 0.00 5.73
6223 6678 0.502275 CGTGACAAATGCAAAACCGC 59.498 50.000 0.00 0.00 0.00 5.68
6225 6680 3.047093 GGTACGTGACAAATGCAAAACC 58.953 45.455 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.