Multiple sequence alignment - TraesCS7B01G036100

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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 TraesCS7B01G036100 chr7B 100.000 5995 0 0 1 5995 35080606 35086600 0.000000e+00 11071.0
1 TraesCS7B01G036100 chr7B 91.848 184 13 2 2098 2280 644462169 644461987 7.710000e-64 255.0
2 TraesCS7B01G036100 chr7B 95.050 101 4 1 1 101 603668928 603669027 2.240000e-34 158.0
3 TraesCS7B01G036100 chr7D 96.389 4486 120 21 1344 5810 85909433 85913895 0.000000e+00 7348.0
4 TraesCS7B01G036100 chr7D 95.776 876 28 5 466 1337 85908470 85909340 0.000000e+00 1404.0
5 TraesCS7B01G036100 chr7D 91.892 370 12 2 100 466 85908036 85908390 8.970000e-138 501.0
6 TraesCS7B01G036100 chr7D 93.671 237 15 0 5759 5995 85913891 85914127 7.390000e-94 355.0
7 TraesCS7B01G036100 chr7D 91.848 184 13 2 2098 2280 382063404 382063222 7.710000e-64 255.0
8 TraesCS7B01G036100 chr7A 96.047 4452 136 24 1344 5771 87305675 87310110 0.000000e+00 7210.0
9 TraesCS7B01G036100 chr7A 95.317 662 20 6 679 1337 87304929 87305582 0.000000e+00 1040.0
10 TraesCS7B01G036100 chr7A 90.796 565 24 15 100 657 87304398 87304941 0.000000e+00 730.0
11 TraesCS7B01G036100 chr7A 94.348 230 13 0 5766 5995 87324430 87324659 2.660000e-93 353.0
12 TraesCS7B01G036100 chr3D 92.432 185 12 2 2098 2281 193390462 193390279 4.610000e-66 263.0
13 TraesCS7B01G036100 chrUn 91.848 184 13 2 2098 2280 189405809 189405627 7.710000e-64 255.0
14 TraesCS7B01G036100 chrUn 91.848 184 13 2 2098 2280 405354558 405354376 7.710000e-64 255.0
15 TraesCS7B01G036100 chrUn 94.175 103 6 0 1 103 79755264 79755162 2.240000e-34 158.0
16 TraesCS7B01G036100 chr6D 91.848 184 13 2 2098 2280 124530848 124530666 7.710000e-64 255.0
17 TraesCS7B01G036100 chr6D 91.848 184 13 2 2098 2280 458911504 458911322 7.710000e-64 255.0
18 TraesCS7B01G036100 chr3B 94.286 105 6 0 1 105 764239198 764239302 1.730000e-35 161.0
19 TraesCS7B01G036100 chr6B 94.231 104 4 2 1 102 383568594 383568491 2.240000e-34 158.0
20 TraesCS7B01G036100 chr6B 94.175 103 4 2 2 104 620468484 620468584 8.040000e-34 156.0
21 TraesCS7B01G036100 chr6A 95.000 100 5 0 1 100 102700 102799 2.240000e-34 158.0
22 TraesCS7B01G036100 chr6A 95.918 98 3 1 1 98 466703098 466703002 2.240000e-34 158.0
23 TraesCS7B01G036100 chr2A 95.918 98 3 1 1 98 422920598 422920694 2.240000e-34 158.0
24 TraesCS7B01G036100 chr2B 95.000 100 4 1 1 100 607064549 607064647 8.040000e-34 156.0
25 TraesCS7B01G036100 chr1D 94.231 52 3 0 5334 5385 244199692 244199743 4.980000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G036100 chr7B 35080606 35086600 5994 False 11071.000000 11071 100.000000 1 5995 1 chr7B.!!$F1 5994
1 TraesCS7B01G036100 chr7D 85908036 85914127 6091 False 2402.000000 7348 94.432000 100 5995 4 chr7D.!!$F1 5895
2 TraesCS7B01G036100 chr7A 87304398 87310110 5712 False 2993.333333 7210 94.053333 100 5771 3 chr7A.!!$F2 5671

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
64 65 0.473326 ATCTTCCAGATGCAGAGGCC 59.527 55.000 0.0 0.00 40.13 5.19 F
332 333 1.408822 GCTGAAGTGGGTAATCCTGGG 60.409 57.143 0.0 0.00 36.20 4.45 F
1938 2120 1.087202 TTGTGTCCACGTGACTGTGC 61.087 55.000 19.3 2.58 44.75 4.57 F
1939 2121 2.108157 TGTCCACGTGACTGTGCC 59.892 61.111 19.3 0.00 44.75 5.01 F
3118 3306 2.158623 TGGATCAAGCAACTCCACTGTT 60.159 45.455 0.0 0.00 34.17 3.16 F
3649 3837 0.172578 TAGGATTCTGCACGACACCG 59.827 55.000 0.0 0.00 42.50 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1134 1225 1.346395 TGACATTGCCTTACCGAGTGT 59.654 47.619 0.0 0.0 0.00 3.55 R
2189 2377 2.487762 TGGAAATGAGCACGAAATGTCC 59.512 45.455 0.0 0.0 0.00 4.02 R
3547 3735 0.611714 TTTCGCCTTCAGGACTACCC 59.388 55.000 0.0 0.0 37.39 3.69 R
3556 3744 0.887933 GGAAAGCCATTTCGCCTTCA 59.112 50.000 0.0 0.0 44.87 3.02 R
4850 5048 0.687757 CCTCCCACTGATCTTCCGGA 60.688 60.000 0.0 0.0 0.00 5.14 R
5493 5695 0.887933 GCCATCGTTGGTTGGTTGAT 59.112 50.000 13.9 0.0 45.57 2.57 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 6.540438 ACTTTGTATGGTCCTCGAGAATAA 57.460 37.500 15.71 0.00 0.00 1.40
25 26 7.125792 ACTTTGTATGGTCCTCGAGAATAAT 57.874 36.000 15.71 5.00 0.00 1.28
26 27 7.210873 ACTTTGTATGGTCCTCGAGAATAATC 58.789 38.462 15.71 0.00 0.00 1.75
27 28 6.724893 TTGTATGGTCCTCGAGAATAATCA 57.275 37.500 15.71 3.23 0.00 2.57
28 29 6.724893 TGTATGGTCCTCGAGAATAATCAA 57.275 37.500 15.71 0.00 0.00 2.57
29 30 7.303182 TGTATGGTCCTCGAGAATAATCAAT 57.697 36.000 15.71 0.00 0.00 2.57
30 31 8.417273 TGTATGGTCCTCGAGAATAATCAATA 57.583 34.615 15.71 0.00 0.00 1.90
31 32 8.866093 TGTATGGTCCTCGAGAATAATCAATAA 58.134 33.333 15.71 0.00 0.00 1.40
32 33 9.706691 GTATGGTCCTCGAGAATAATCAATAAA 57.293 33.333 15.71 0.00 0.00 1.40
33 34 8.839310 ATGGTCCTCGAGAATAATCAATAAAG 57.161 34.615 15.71 0.00 0.00 1.85
34 35 7.792032 TGGTCCTCGAGAATAATCAATAAAGT 58.208 34.615 15.71 0.00 0.00 2.66
35 36 7.710907 TGGTCCTCGAGAATAATCAATAAAGTG 59.289 37.037 15.71 0.00 0.00 3.16
36 37 7.926555 GGTCCTCGAGAATAATCAATAAAGTGA 59.073 37.037 15.71 0.00 0.00 3.41
37 38 8.756864 GTCCTCGAGAATAATCAATAAAGTGAC 58.243 37.037 15.71 2.41 0.00 3.67
38 39 7.926555 TCCTCGAGAATAATCAATAAAGTGACC 59.073 37.037 15.71 0.00 0.00 4.02
39 40 7.096023 CCTCGAGAATAATCAATAAAGTGACCG 60.096 40.741 15.71 0.00 0.00 4.79
40 41 7.262772 TCGAGAATAATCAATAAAGTGACCGT 58.737 34.615 0.00 0.00 0.00 4.83
41 42 8.407832 TCGAGAATAATCAATAAAGTGACCGTA 58.592 33.333 0.00 0.00 0.00 4.02
42 43 9.193133 CGAGAATAATCAATAAAGTGACCGTAT 57.807 33.333 0.00 0.00 0.00 3.06
48 49 8.964476 AATCAATAAAGTGACCGTATTCATCT 57.036 30.769 0.00 0.00 0.00 2.90
49 50 8.964476 ATCAATAAAGTGACCGTATTCATCTT 57.036 30.769 0.00 0.00 0.00 2.40
50 51 8.420374 TCAATAAAGTGACCGTATTCATCTTC 57.580 34.615 0.00 0.00 0.00 2.87
51 52 7.494625 TCAATAAAGTGACCGTATTCATCTTCC 59.505 37.037 0.00 0.00 0.00 3.46
52 53 4.819105 AAGTGACCGTATTCATCTTCCA 57.181 40.909 0.00 0.00 0.00 3.53
53 54 4.392921 AGTGACCGTATTCATCTTCCAG 57.607 45.455 0.00 0.00 0.00 3.86
54 55 4.023980 AGTGACCGTATTCATCTTCCAGA 58.976 43.478 0.00 0.00 0.00 3.86
55 56 4.651503 AGTGACCGTATTCATCTTCCAGAT 59.348 41.667 0.00 0.00 34.74 2.90
63 64 1.595466 CATCTTCCAGATGCAGAGGC 58.405 55.000 0.84 0.00 44.69 4.70
64 65 0.473326 ATCTTCCAGATGCAGAGGCC 59.527 55.000 0.00 0.00 40.13 5.19
65 66 1.523258 CTTCCAGATGCAGAGGCCG 60.523 63.158 0.00 0.00 40.13 6.13
66 67 2.937379 CTTCCAGATGCAGAGGCCGG 62.937 65.000 0.00 0.00 40.13 6.13
67 68 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
68 69 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
74 75 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
87 88 4.586306 GGGGTCATCCTCCTTTTCTTAA 57.414 45.455 0.00 0.00 35.33 1.85
88 89 4.930696 GGGGTCATCCTCCTTTTCTTAAA 58.069 43.478 0.00 0.00 35.33 1.52
89 90 5.330233 GGGGTCATCCTCCTTTTCTTAAAA 58.670 41.667 0.00 0.00 35.33 1.52
90 91 5.778241 GGGGTCATCCTCCTTTTCTTAAAAA 59.222 40.000 0.00 0.00 35.33 1.94
159 160 2.282040 GGTGCTGAGGTGCTGCTT 60.282 61.111 0.00 0.00 41.53 3.91
194 195 1.948145 GCTGATTCTGCTGATTGGAGG 59.052 52.381 8.16 0.00 34.66 4.30
237 238 1.529244 GCTGGTTGGAGTTGGTGCT 60.529 57.895 0.00 0.00 0.00 4.40
238 239 1.518903 GCTGGTTGGAGTTGGTGCTC 61.519 60.000 0.00 0.00 34.89 4.26
244 245 2.352805 GAGTTGGTGCTCCTGGGG 59.647 66.667 6.34 0.00 34.23 4.96
245 246 3.927481 GAGTTGGTGCTCCTGGGGC 62.927 68.421 12.83 12.83 34.23 5.80
246 247 4.284550 GTTGGTGCTCCTGGGGCA 62.285 66.667 19.38 19.38 37.36 5.36
247 248 3.970410 TTGGTGCTCCTGGGGCAG 61.970 66.667 24.26 0.00 40.54 4.85
249 250 4.729918 GGTGCTCCTGGGGCAGTG 62.730 72.222 24.26 0.00 40.54 3.66
250 251 4.729918 GTGCTCCTGGGGCAGTGG 62.730 72.222 24.26 0.00 40.54 4.00
321 322 3.929610 GCTAAACTGAGTAGCTGAAGTGG 59.070 47.826 0.00 0.00 40.71 4.00
324 325 3.170991 ACTGAGTAGCTGAAGTGGGTA 57.829 47.619 0.00 0.00 0.00 3.69
332 333 1.408822 GCTGAAGTGGGTAATCCTGGG 60.409 57.143 0.00 0.00 36.20 4.45
449 456 9.926158 ATATCAGTCATGAATCTTGATACTGAC 57.074 33.333 17.01 11.14 39.39 3.51
629 717 6.183360 TGTCTGAGATTCCGGCATTTAGAATA 60.183 38.462 0.00 0.00 30.52 1.75
695 783 4.046286 TGATAGGTTGCAATTGAACCCT 57.954 40.909 24.29 18.24 43.52 4.34
770 858 7.633193 TTTTCAGCTGTAGGTTCTGTAAAAA 57.367 32.000 14.67 5.59 28.81 1.94
826 914 7.355017 TGTGATTTTTCATTCTTCTCAGTTCG 58.645 34.615 0.00 0.00 0.00 3.95
945 1033 7.763985 TCGAGCAAACAGATACAGATTAAATCA 59.236 33.333 0.00 0.00 0.00 2.57
1085 1173 6.499436 ACAACCAAGGTAAAGCCCTTATATT 58.501 36.000 0.00 0.00 43.04 1.28
1088 1176 7.418337 ACCAAGGTAAAGCCCTTATATTTTG 57.582 36.000 0.00 0.00 43.04 2.44
1089 1177 7.186268 ACCAAGGTAAAGCCCTTATATTTTGA 58.814 34.615 0.00 0.00 43.04 2.69
1090 1178 7.123697 ACCAAGGTAAAGCCCTTATATTTTGAC 59.876 37.037 0.00 0.00 43.04 3.18
1134 1225 4.473196 TCAGGCATTATTCTACAAGGTCCA 59.527 41.667 0.00 0.00 0.00 4.02
1225 1316 4.705110 TCAGTTGGAGATTTGTCTTCCA 57.295 40.909 0.00 0.00 0.00 3.53
1317 1408 5.071788 TGGTGTTGTAATTGGGGCATAAAAA 59.928 36.000 0.00 0.00 0.00 1.94
1406 1583 1.338107 GGCCTACCTTTGGTTTGCTT 58.662 50.000 0.00 0.00 37.09 3.91
1433 1610 5.357742 TCAGTTAAGCTATCCAGATTGCA 57.642 39.130 14.85 0.00 41.01 4.08
1438 1615 3.920231 AGCTATCCAGATTGCAAGTGA 57.080 42.857 14.85 0.00 41.01 3.41
1511 1688 5.647589 TGCATTTAGTGTCTACCTCGTAAG 58.352 41.667 0.00 0.00 0.00 2.34
1529 1706 4.675114 CGTAAGACTGCAAACAAAATGACC 59.325 41.667 0.00 0.00 43.02 4.02
1590 1768 3.244281 ATGCTCACTGACAGCCGCA 62.244 57.895 13.93 13.93 35.89 5.69
1693 1871 9.490663 CGTTATTGGAATGTAAGTGAAAGAATC 57.509 33.333 0.00 0.00 0.00 2.52
1732 1910 7.352079 ACTTCAAGAAAATTCACATTCTGGT 57.648 32.000 0.00 0.00 36.09 4.00
1856 2036 6.697019 CAGAACAATGGTTTTACTTCAACAGG 59.303 38.462 0.00 0.00 37.36 4.00
1935 2117 2.502213 TACTTGTGTCCACGTGACTG 57.498 50.000 19.30 0.00 44.75 3.51
1938 2120 1.087202 TTGTGTCCACGTGACTGTGC 61.087 55.000 19.30 2.58 44.75 4.57
1939 2121 2.108157 TGTCCACGTGACTGTGCC 59.892 61.111 19.30 0.00 44.75 5.01
1940 2122 2.421739 GTCCACGTGACTGTGCCT 59.578 61.111 19.30 0.00 41.03 4.75
2136 2323 5.061920 TGGTGGTTGTTTCTTGTTGTAAC 57.938 39.130 0.00 0.00 0.00 2.50
2164 2351 9.455847 GAATTCAATGAAAAGATCCGGAAATAG 57.544 33.333 9.01 0.00 0.00 1.73
2204 2392 6.345298 TCATTTATAGGACATTTCGTGCTCA 58.655 36.000 0.00 0.00 44.03 4.26
2215 2403 6.686630 ACATTTCGTGCTCATTTCCAAATTA 58.313 32.000 0.00 0.00 0.00 1.40
2224 2412 5.745769 GCTCATTTCCAAATTACTGCTTAGC 59.254 40.000 0.00 0.00 0.00 3.09
2289 2477 9.449719 TCCTTTTAGTCAAAGATAAATCTCACC 57.550 33.333 0.00 0.00 44.40 4.02
2290 2478 8.391106 CCTTTTAGTCAAAGATAAATCTCACCG 58.609 37.037 0.00 0.00 44.40 4.94
2439 2627 4.406943 GAAGAAACAGCTTAAATGGCTCG 58.593 43.478 0.00 0.00 38.03 5.03
2457 2645 4.192317 GCTCGATACCTGAATCTTTTGGT 58.808 43.478 0.00 0.00 36.66 3.67
2458 2646 4.636206 GCTCGATACCTGAATCTTTTGGTT 59.364 41.667 0.00 0.00 34.33 3.67
2535 2723 5.885912 ACTGAACCACAACTCTAACAATGTT 59.114 36.000 3.43 3.43 0.00 2.71
2576 2764 3.221964 AGCGAAAATCTGTTGATTGGC 57.778 42.857 0.00 0.00 41.62 4.52
2609 2797 7.922278 CCAAACTCTTTGTCAAATCTTTCATCA 59.078 33.333 0.00 0.00 38.98 3.07
2642 2830 9.461312 AATATGTAAGTTGACCTTTTCATGCTA 57.539 29.630 0.00 0.00 32.84 3.49
2658 2846 9.995003 TTTTCATGCTAACAAATCCATAAAACT 57.005 25.926 0.00 0.00 0.00 2.66
2660 2848 9.995003 TTCATGCTAACAAATCCATAAAACTTT 57.005 25.926 0.00 0.00 0.00 2.66
2661 2849 9.995003 TCATGCTAACAAATCCATAAAACTTTT 57.005 25.926 0.00 0.00 0.00 2.27
2773 2961 7.042797 ACTCATTGTGTTTTGCAGTAATCTT 57.957 32.000 0.00 0.00 0.00 2.40
3118 3306 2.158623 TGGATCAAGCAACTCCACTGTT 60.159 45.455 0.00 0.00 34.17 3.16
3230 3418 7.819415 ACCGTCCTGATATATACATTGATGTTG 59.181 37.037 1.46 0.00 41.97 3.33
3255 3443 4.081420 AGGTTCGTTCAGCAAGATCACTAT 60.081 41.667 0.00 0.00 0.00 2.12
3336 3524 6.564328 ACTCTGAACATTTTTCAACCAAGAC 58.436 36.000 0.00 0.00 0.00 3.01
3406 3594 3.057526 AGTTTGGGCAGATAAAGCGTTTC 60.058 43.478 0.00 0.00 0.00 2.78
3413 3601 3.623060 GCAGATAAAGCGTTTCTCATGGA 59.377 43.478 0.00 0.00 0.00 3.41
3457 3645 7.933033 ACCAATAATTTCAGTGAGCAAAATGTT 59.067 29.630 0.00 0.00 0.00 2.71
3550 3738 2.556622 CAAACGGCTATTTGAAGTGGGT 59.443 45.455 7.25 0.00 41.28 4.51
3556 3744 3.200165 GGCTATTTGAAGTGGGTAGTCCT 59.800 47.826 0.00 0.00 36.20 3.85
3649 3837 0.172578 TAGGATTCTGCACGACACCG 59.827 55.000 0.00 0.00 42.50 4.94
3703 3891 1.949847 ATCTGAGTGTCGCTTCCCGG 61.950 60.000 0.00 0.00 37.59 5.73
3813 4004 4.735985 TGAGTTGATGCATGCAATTGTAC 58.264 39.130 26.68 17.26 0.00 2.90
3839 4030 3.821033 AGTGTATTGCCAGAAACTTGGAC 59.179 43.478 0.00 0.00 40.87 4.02
3990 4183 2.252976 TGTGCAACATACTGCTGACA 57.747 45.000 0.00 0.00 45.67 3.58
3996 4189 4.097741 TGCAACATACTGCTGACAAAACTT 59.902 37.500 0.00 0.00 43.07 2.66
4015 4209 9.864034 CAAAACTTAACAATACGCAGATATAGG 57.136 33.333 0.00 0.00 0.00 2.57
4054 4248 9.784531 AATATTAGATTGGACGACAAGAATGAT 57.215 29.630 0.00 0.00 43.48 2.45
4166 4360 3.447586 TCCTACTCGATGGGAACTTTGAG 59.552 47.826 0.00 0.00 46.50 3.02
4301 4495 0.179000 GGCCATCAGTGAAGACGGAT 59.821 55.000 0.00 0.00 37.48 4.18
4413 4607 6.641169 TGCTCATCGATCAAGTAAGATAGT 57.359 37.500 0.00 0.00 0.00 2.12
4985 5183 1.137086 GAAGCCGTTGAGCTATCTGGA 59.863 52.381 0.00 0.00 44.11 3.86
5079 5277 8.635765 AAGGAAATATAGAACTCAAAAGTGCA 57.364 30.769 0.00 0.00 35.36 4.57
5130 5332 5.054390 TCAAAACAAAGTTTTGCGAGACT 57.946 34.783 23.42 0.00 41.79 3.24
5136 5338 6.707599 ACAAAGTTTTGCGAGACTCTATAC 57.292 37.500 0.00 0.00 41.79 1.47
5184 5386 6.251471 AGTAACTGTACCTAGTATGTGGTGT 58.749 40.000 0.00 0.00 37.74 4.16
5562 5764 2.560542 CCCCACAAACATCCGAAATTGA 59.439 45.455 0.00 0.00 0.00 2.57
5749 5951 5.009310 GCAATGATCATATGGAGCTCAACAA 59.991 40.000 17.19 0.00 31.67 2.83
5806 6055 6.857777 AGACTGAGAAAGACATTTTCACTG 57.142 37.500 2.88 3.34 0.00 3.66
5835 6084 2.637521 CTGTGGTGCAGCTGACATT 58.362 52.632 20.43 0.00 38.52 2.71
5836 6085 1.812235 CTGTGGTGCAGCTGACATTA 58.188 50.000 20.43 5.65 38.52 1.90
5837 6086 2.362736 CTGTGGTGCAGCTGACATTAT 58.637 47.619 20.43 0.00 38.52 1.28
5846 6095 7.936301 TGGTGCAGCTGACATTATATAATAACA 59.064 33.333 20.43 9.69 0.00 2.41
5887 6136 4.340617 CAGTCCCCTTAAATACCAGCAAA 58.659 43.478 0.00 0.00 0.00 3.68
5888 6137 4.399303 CAGTCCCCTTAAATACCAGCAAAG 59.601 45.833 0.00 0.00 0.00 2.77
5909 6158 6.998968 AAGATCAAGATTTTGCTGACTAGG 57.001 37.500 0.00 0.00 34.21 3.02
5921 6170 2.620585 GCTGACTAGGCATGAATTTCCC 59.379 50.000 0.00 0.00 0.00 3.97
5932 6181 2.650322 TGAATTTCCCGAGTTATGGGC 58.350 47.619 0.00 0.00 46.92 5.36
5938 6187 2.404559 TCCCGAGTTATGGGCATACTT 58.595 47.619 0.00 0.00 46.92 2.24
5939 6188 2.104111 TCCCGAGTTATGGGCATACTTG 59.896 50.000 0.00 0.00 46.92 3.16
5960 6209 5.309323 TGTCTGTTTTGGTCAGTTTTCAG 57.691 39.130 0.00 0.00 34.86 3.02
5962 6211 4.157840 GTCTGTTTTGGTCAGTTTTCAGGT 59.842 41.667 0.00 0.00 34.86 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.649533 TTATTCTCGAGGACCATACAAAGTA 57.350 36.000 13.56 0.00 0.00 2.24
1 2 6.540438 TTATTCTCGAGGACCATACAAAGT 57.460 37.500 13.56 0.00 0.00 2.66
2 3 7.210174 TGATTATTCTCGAGGACCATACAAAG 58.790 38.462 13.56 0.00 0.00 2.77
3 4 7.119709 TGATTATTCTCGAGGACCATACAAA 57.880 36.000 13.56 0.00 0.00 2.83
4 5 6.724893 TGATTATTCTCGAGGACCATACAA 57.275 37.500 13.56 0.00 0.00 2.41
5 6 6.724893 TTGATTATTCTCGAGGACCATACA 57.275 37.500 13.56 3.04 0.00 2.29
6 7 9.706691 TTTATTGATTATTCTCGAGGACCATAC 57.293 33.333 13.56 0.40 0.00 2.39
7 8 9.929180 CTTTATTGATTATTCTCGAGGACCATA 57.071 33.333 13.56 1.81 0.00 2.74
8 9 8.432805 ACTTTATTGATTATTCTCGAGGACCAT 58.567 33.333 13.56 0.00 0.00 3.55
9 10 7.710907 CACTTTATTGATTATTCTCGAGGACCA 59.289 37.037 13.56 0.00 0.00 4.02
10 11 7.926555 TCACTTTATTGATTATTCTCGAGGACC 59.073 37.037 13.56 0.00 0.00 4.46
11 12 8.756864 GTCACTTTATTGATTATTCTCGAGGAC 58.243 37.037 13.56 1.82 0.00 3.85
12 13 7.926555 GGTCACTTTATTGATTATTCTCGAGGA 59.073 37.037 13.56 3.44 0.00 3.71
13 14 7.096023 CGGTCACTTTATTGATTATTCTCGAGG 60.096 40.741 13.56 0.00 0.00 4.63
14 15 7.435488 ACGGTCACTTTATTGATTATTCTCGAG 59.565 37.037 5.93 5.93 0.00 4.04
15 16 7.262772 ACGGTCACTTTATTGATTATTCTCGA 58.737 34.615 0.00 0.00 0.00 4.04
16 17 7.464830 ACGGTCACTTTATTGATTATTCTCG 57.535 36.000 0.00 0.00 0.00 4.04
23 24 8.964476 AGATGAATACGGTCACTTTATTGATT 57.036 30.769 0.00 0.00 0.00 2.57
24 25 8.964476 AAGATGAATACGGTCACTTTATTGAT 57.036 30.769 0.00 0.00 0.00 2.57
25 26 7.494625 GGAAGATGAATACGGTCACTTTATTGA 59.505 37.037 0.00 0.00 0.00 2.57
26 27 7.279981 TGGAAGATGAATACGGTCACTTTATTG 59.720 37.037 0.00 0.00 0.00 1.90
27 28 7.335627 TGGAAGATGAATACGGTCACTTTATT 58.664 34.615 0.00 0.00 0.00 1.40
28 29 6.884832 TGGAAGATGAATACGGTCACTTTAT 58.115 36.000 0.00 0.00 0.00 1.40
29 30 6.153851 TCTGGAAGATGAATACGGTCACTTTA 59.846 38.462 0.00 0.00 38.67 1.85
30 31 5.046591 TCTGGAAGATGAATACGGTCACTTT 60.047 40.000 0.00 0.00 38.67 2.66
31 32 4.466370 TCTGGAAGATGAATACGGTCACTT 59.534 41.667 0.00 0.00 38.67 3.16
32 33 4.023980 TCTGGAAGATGAATACGGTCACT 58.976 43.478 0.00 0.00 38.67 3.41
33 34 4.386867 TCTGGAAGATGAATACGGTCAC 57.613 45.455 0.00 0.00 38.67 3.67
47 48 1.523258 CGGCCTCTGCATCTGGAAG 60.523 63.158 0.00 0.00 40.13 3.46
48 49 2.586245 CGGCCTCTGCATCTGGAA 59.414 61.111 0.00 0.00 40.13 3.53
49 50 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
50 51 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
51 52 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
57 58 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
63 64 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
64 65 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
65 66 1.299939 AGAAAAGGAGGATGACCCCC 58.700 55.000 0.00 0.00 36.73 5.40
66 67 4.586306 TTAAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
67 68 6.911250 TTTTTAAGAAAAGGAGGATGACCC 57.089 37.500 0.00 0.00 32.16 4.46
95 96 2.102420 GCCCACTAAACCACAGCTTTTT 59.898 45.455 0.00 0.00 0.00 1.94
96 97 1.686587 GCCCACTAAACCACAGCTTTT 59.313 47.619 0.00 0.00 0.00 2.27
97 98 1.328279 GCCCACTAAACCACAGCTTT 58.672 50.000 0.00 0.00 0.00 3.51
98 99 0.889186 CGCCCACTAAACCACAGCTT 60.889 55.000 0.00 0.00 0.00 3.74
159 160 3.630013 AGCGGCAACTCCAGCTCA 61.630 61.111 1.45 0.00 39.37 4.26
194 195 0.947244 CAGCACAACACCTCCACTTC 59.053 55.000 0.00 0.00 0.00 3.01
237 238 3.009115 GTAGCCACTGCCCCAGGA 61.009 66.667 0.00 0.00 38.69 3.86
238 239 3.011517 AGTAGCCACTGCCCCAGG 61.012 66.667 0.00 0.00 38.69 4.45
239 240 2.270205 CAGTAGCCACTGCCCCAG 59.730 66.667 0.00 0.00 45.44 4.45
246 247 0.615850 GAAGCTTCCCAGTAGCCACT 59.384 55.000 15.97 0.00 39.47 4.00
247 248 0.741221 CGAAGCTTCCCAGTAGCCAC 60.741 60.000 20.62 0.00 39.47 5.01
248 249 1.192146 ACGAAGCTTCCCAGTAGCCA 61.192 55.000 20.62 0.00 39.47 4.75
249 250 0.741221 CACGAAGCTTCCCAGTAGCC 60.741 60.000 20.62 0.00 39.47 3.93
250 251 0.246635 TCACGAAGCTTCCCAGTAGC 59.753 55.000 20.62 0.00 38.93 3.58
251 252 2.969628 ATCACGAAGCTTCCCAGTAG 57.030 50.000 20.62 7.97 0.00 2.57
321 322 1.212250 ACACCACCCCCAGGATTACC 61.212 60.000 0.00 0.00 36.73 2.85
324 325 2.547595 CCACACCACCCCCAGGATT 61.548 63.158 0.00 0.00 36.73 3.01
332 333 3.574074 ATCAGCAGCCACACCACCC 62.574 63.158 0.00 0.00 0.00 4.61
466 473 5.205056 TCCCCAAATTCACAACTTGTTAGT 58.795 37.500 0.00 0.00 35.68 2.24
468 475 4.586841 CCTCCCCAAATTCACAACTTGTTA 59.413 41.667 0.00 0.00 0.00 2.41
629 717 4.756084 GCAAACTGCAGTGAGATAACTT 57.244 40.909 22.49 5.11 44.26 2.66
695 783 5.092554 TCCTACCTGCAACGATGAAAATA 57.907 39.130 0.00 0.00 0.00 1.40
770 858 7.114754 TCAAGCCATCAATTTACAGAGAGAAT 58.885 34.615 0.00 0.00 0.00 2.40
826 914 1.654317 CATGAGAAGACCAGCAGAGC 58.346 55.000 0.00 0.00 0.00 4.09
945 1033 6.478512 TTTTTGGGAATAGAAACACTGCTT 57.521 33.333 0.00 0.00 0.00 3.91
1106 1197 5.824624 CCTTGTAGAATAATGCCTGATGTGT 59.175 40.000 0.00 0.00 0.00 3.72
1115 1206 5.186198 AGTGTGGACCTTGTAGAATAATGC 58.814 41.667 0.00 0.00 0.00 3.56
1134 1225 1.346395 TGACATTGCCTTACCGAGTGT 59.654 47.619 0.00 0.00 0.00 3.55
1250 1341 7.667043 ATGGCAACTATATTGTTGTATACGG 57.333 36.000 24.44 4.90 46.33 4.02
1340 1431 9.546428 TCAATATTCGATGAGAAATTGCTTAGA 57.454 29.630 0.00 0.00 42.91 2.10
1406 1583 5.357742 TCTGGATAGCTTAACTGATGCAA 57.642 39.130 0.00 0.00 0.00 4.08
1511 1688 6.421377 AAAAAGGTCATTTTGTTTGCAGTC 57.579 33.333 0.00 0.00 40.27 3.51
1693 1871 4.631377 TCTTGAAGTACGCATTTGAGATGG 59.369 41.667 0.00 0.00 0.00 3.51
1856 2036 7.039784 AGGAGATAGTAGAGCATGAAGAATGTC 60.040 40.741 0.00 0.00 38.65 3.06
1935 2117 6.036408 GCATATTTGGAAATGAGAAAAGGCAC 59.964 38.462 0.00 0.00 0.00 5.01
1938 2120 7.549839 TCTGCATATTTGGAAATGAGAAAAGG 58.450 34.615 0.00 0.00 0.00 3.11
1939 2121 8.866956 GTTCTGCATATTTGGAAATGAGAAAAG 58.133 33.333 0.00 0.00 0.00 2.27
1940 2122 8.587608 AGTTCTGCATATTTGGAAATGAGAAAA 58.412 29.630 0.00 0.00 0.00 2.29
2112 2299 3.161866 ACAACAAGAAACAACCACCAGT 58.838 40.909 0.00 0.00 0.00 4.00
2136 2323 6.441093 TCCGGATCTTTTCATTGAATTCAG 57.559 37.500 8.41 0.00 0.00 3.02
2189 2377 2.487762 TGGAAATGAGCACGAAATGTCC 59.512 45.455 0.00 0.00 0.00 4.02
2197 2385 3.853671 GCAGTAATTTGGAAATGAGCACG 59.146 43.478 0.00 0.00 0.00 5.34
2200 2388 5.745769 GCTAAGCAGTAATTTGGAAATGAGC 59.254 40.000 0.00 0.00 0.00 4.26
2204 2392 8.633561 GGAATAGCTAAGCAGTAATTTGGAAAT 58.366 33.333 0.00 0.00 0.00 2.17
2215 2403 4.596643 AGATGATGGGAATAGCTAAGCAGT 59.403 41.667 0.00 0.00 0.00 4.40
2323 2511 6.777091 CCATCCAATAACCTGAAACCATATCA 59.223 38.462 0.00 0.00 0.00 2.15
2324 2512 6.777580 ACCATCCAATAACCTGAAACCATATC 59.222 38.462 0.00 0.00 0.00 1.63
2424 2612 3.496130 CAGGTATCGAGCCATTTAAGCTG 59.504 47.826 10.84 0.00 41.75 4.24
2457 2645 8.924511 ACAGATTTTGGAGTTCTGATAGAAAA 57.075 30.769 6.19 0.00 39.36 2.29
2535 2723 5.010719 CGCTTAGATCCCTGTCCAAGTTATA 59.989 44.000 0.00 0.00 0.00 0.98
2576 2764 7.707893 AGATTTGACAAAGAGTTTGGAATGTTG 59.292 33.333 6.77 0.00 44.81 3.33
2615 2803 9.461312 AGCATGAAAAGGTCAACTTACATATTA 57.539 29.630 0.00 0.00 40.50 0.98
2740 2928 9.577110 CTGCAAAACACAATGAGTTATGATATT 57.423 29.630 0.00 0.00 0.00 1.28
2773 2961 6.538945 TCACCACTAAGACTGTTATATGCA 57.461 37.500 0.00 0.00 0.00 3.96
2919 3107 5.677319 TGCCTGTATAGCTGTAAAGACTT 57.323 39.130 9.17 0.00 0.00 3.01
3118 3306 4.706476 CCAATGCTTCCAAGAATCACCTTA 59.294 41.667 0.00 0.00 0.00 2.69
3178 3366 3.316308 GCATTCTTTGCCACCATAGTAGG 59.684 47.826 0.00 0.00 46.15 3.18
3230 3418 1.129437 GATCTTGCTGAACGAACCTGC 59.871 52.381 0.00 0.00 0.00 4.85
3413 3601 1.001517 TCGCAGTCTGGAGCTCTCT 60.002 57.895 14.64 4.70 0.00 3.10
3457 3645 3.894547 GAAACCGCCCTTGCCGAGA 62.895 63.158 0.00 0.00 0.00 4.04
3547 3735 0.611714 TTTCGCCTTCAGGACTACCC 59.388 55.000 0.00 0.00 37.39 3.69
3550 3738 1.406887 GCCATTTCGCCTTCAGGACTA 60.407 52.381 0.00 0.00 37.39 2.59
3556 3744 0.887933 GGAAAGCCATTTCGCCTTCA 59.112 50.000 0.00 0.00 44.87 3.02
3649 3837 2.810439 ATATCAAGAGCCGCTCTGTC 57.190 50.000 23.58 0.00 40.28 3.51
3703 3891 6.210287 TCTTAGCTTAGCAGACCTCTTAAC 57.790 41.667 7.07 0.00 0.00 2.01
3813 4004 5.106555 CCAAGTTTCTGGCAATACACTACAG 60.107 44.000 0.00 0.00 0.00 2.74
3839 4030 7.977904 TCTCTTATTCAACACATAACATGCAG 58.022 34.615 0.00 0.00 0.00 4.41
3989 4182 9.864034 CCTATATCTGCGTATTGTTAAGTTTTG 57.136 33.333 0.00 0.00 0.00 2.44
3990 4183 9.826574 TCCTATATCTGCGTATTGTTAAGTTTT 57.173 29.630 0.00 0.00 0.00 2.43
4054 4248 1.742880 GCAGCTCCAAGTGCGATCA 60.743 57.895 0.00 0.00 35.28 2.92
4166 4360 2.420687 CCCAAAGTCTCCTATGACTGCC 60.421 54.545 0.00 0.00 45.49 4.85
4424 4618 6.382919 TTTGGGGTACTTATAAGCAGTTCT 57.617 37.500 12.54 0.00 0.00 3.01
4548 4743 6.904626 ACATCTTCCATTCTAAGCACCTAAT 58.095 36.000 0.00 0.00 0.00 1.73
4763 4961 1.273606 GTGCAGAGGAGTGCTACTTGA 59.726 52.381 0.00 0.00 44.32 3.02
4850 5048 0.687757 CCTCCCACTGATCTTCCGGA 60.688 60.000 0.00 0.00 0.00 5.14
5098 5296 8.655970 GCAAAACTTTGTTTTGATTCTGTACTT 58.344 29.630 28.79 0.00 40.73 2.24
5184 5386 8.664211 TGTATAAGTACAACATTGTGTCACAA 57.336 30.769 20.28 20.28 42.31 3.33
5214 5416 8.138074 GCATACAGATGTTAGTAATGTCTGAGA 58.862 37.037 23.44 15.42 38.81 3.27
5493 5695 0.887933 GCCATCGTTGGTTGGTTGAT 59.112 50.000 13.90 0.00 45.57 2.57
5495 5697 1.178534 AGGCCATCGTTGGTTGGTTG 61.179 55.000 13.90 0.00 45.57 3.77
5562 5764 3.695830 TCATTGCTCGAGTTACCCTTT 57.304 42.857 15.13 0.00 0.00 3.11
5776 6025 4.592485 TGTCTTTCTCAGTCTTGACCTC 57.408 45.455 0.00 0.00 0.00 3.85
5806 6055 1.066257 CACCACAGTTGTTGGCTGC 59.934 57.895 0.00 0.00 37.47 5.25
5835 6084 7.701924 GCGCCTACACGGTTATGTTATTATATA 59.298 37.037 0.00 0.00 33.85 0.86
5836 6085 6.532657 GCGCCTACACGGTTATGTTATTATAT 59.467 38.462 0.00 0.00 33.85 0.86
5837 6086 5.863397 GCGCCTACACGGTTATGTTATTATA 59.137 40.000 0.00 0.00 33.85 0.98
5846 6095 1.153509 GTGGCGCCTACACGGTTAT 60.154 57.895 29.70 0.00 34.25 1.89
5887 6136 4.880696 GCCTAGTCAGCAAAATCTTGATCT 59.119 41.667 0.00 0.00 34.14 2.75
5888 6137 4.637534 TGCCTAGTCAGCAAAATCTTGATC 59.362 41.667 0.00 0.00 37.28 2.92
5909 6158 4.228912 CCATAACTCGGGAAATTCATGC 57.771 45.455 0.00 0.00 0.00 4.06
5921 6170 3.804325 CAGACAAGTATGCCCATAACTCG 59.196 47.826 0.00 0.00 0.00 4.18
5932 6181 6.377327 AACTGACCAAAACAGACAAGTATG 57.623 37.500 0.00 0.00 38.55 2.39
5938 6187 4.157656 CCTGAAAACTGACCAAAACAGACA 59.842 41.667 0.00 0.00 38.55 3.41
5939 6188 4.157840 ACCTGAAAACTGACCAAAACAGAC 59.842 41.667 0.00 0.00 38.55 3.51


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

AutoCloner maintained by Alex Coulton.