Multiple sequence alignment - TraesCS3D01G439000

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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 TraesCS3D01G439000 chr3D 100.000 3368 0 0 1 3368 549517124 549513757 0.000000e+00 6220.0
1 TraesCS3D01G439000 chr3B 93.183 2934 139 19 87 3003 728921459 728918570 0.000000e+00 4253.0
2 TraesCS3D01G439000 chr3A 95.886 2528 89 6 87 2609 686786455 686783938 0.000000e+00 4078.0
3 TraesCS3D01G439000 chr3A 90.374 374 29 5 2634 3002 686783945 686783574 5.050000e-133 484.0
4 TraesCS3D01G439000 chr3A 91.892 185 11 2 3185 3368 686783244 686783063 4.310000e-64 255.0
5 TraesCS3D01G439000 chr7D 100.000 50 0 0 1 50 60693422 60693373 3.580000e-15 93.5
6 TraesCS3D01G439000 chr7B 100.000 50 0 0 1 50 218545907 218545858 3.580000e-15 93.5
7 TraesCS3D01G439000 chr6B 100.000 50 0 0 1 50 204159186 204159137 3.580000e-15 93.5
8 TraesCS3D01G439000 chr6B 98.113 53 1 0 1 53 506128032 506127980 3.580000e-15 93.5
9 TraesCS3D01G439000 chr5D 100.000 50 0 0 5 54 493900677 493900726 3.580000e-15 93.5
10 TraesCS3D01G439000 chr5D 100.000 49 0 0 4 52 477332438 477332390 1.290000e-14 91.6
11 TraesCS3D01G439000 chr5A 100.000 50 0 0 1 50 658993754 658993803 3.580000e-15 93.5
12 TraesCS3D01G439000 chr1A 100.000 50 0 0 1 50 498166930 498166881 3.580000e-15 93.5
13 TraesCS3D01G439000 chr2D 94.828 58 2 1 4 61 7649532 7649476 4.630000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G439000 chr3D 549513757 549517124 3367 True 6220.000000 6220 100.000000 1 3368 1 chr3D.!!$R1 3367
1 TraesCS3D01G439000 chr3B 728918570 728921459 2889 True 4253.000000 4253 93.183000 87 3003 1 chr3B.!!$R1 2916
2 TraesCS3D01G439000 chr3A 686783063 686786455 3392 True 1605.666667 4078 92.717333 87 3368 3 chr3A.!!$R1 3281

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
199 200 1.822990 CCATTTCACCTGCAGAGCATT 59.177 47.619 17.39 0.00 38.13 3.56 F
1087 1093 1.001641 CTCAAGTCCCCAAGGCCAG 60.002 63.158 5.01 0.00 0.00 4.85 F
1128 1134 1.019673 CACAAGGGGATTGCGATCAG 58.980 55.000 15.92 2.76 43.15 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2147 0.322816 TCCAGGAATTGTCTGCTGGC 60.323 55.0 6.29 0.0 34.70 4.85 R
2190 2198 0.731514 CGAGAGAAAACCGCGTGCTA 60.732 55.0 4.92 0.0 0.00 3.49 R
2983 3005 0.842635 GGATGCTCCAGGATTGAGGT 59.157 55.0 0.00 0.0 36.28 3.85 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
21 22 4.437682 ACCCTGTCTGAAATGTCTTCAA 57.562 40.909 0.00 0.00 0.00 2.69
22 23 4.392940 ACCCTGTCTGAAATGTCTTCAAG 58.607 43.478 0.00 0.00 0.00 3.02
23 24 3.755378 CCCTGTCTGAAATGTCTTCAAGG 59.245 47.826 0.00 0.00 0.00 3.61
24 25 3.190118 CCTGTCTGAAATGTCTTCAAGGC 59.810 47.826 0.00 0.00 0.00 4.35
25 26 3.149196 TGTCTGAAATGTCTTCAAGGCC 58.851 45.455 0.00 0.00 0.00 5.19
26 27 3.181440 TGTCTGAAATGTCTTCAAGGCCT 60.181 43.478 0.00 0.00 0.00 5.19
27 28 3.823304 GTCTGAAATGTCTTCAAGGCCTT 59.177 43.478 13.78 13.78 0.00 4.35
28 29 5.003804 GTCTGAAATGTCTTCAAGGCCTTA 58.996 41.667 20.00 2.00 0.00 2.69
29 30 5.649831 GTCTGAAATGTCTTCAAGGCCTTAT 59.350 40.000 20.00 3.68 0.00 1.73
30 31 6.823689 GTCTGAAATGTCTTCAAGGCCTTATA 59.176 38.462 20.00 6.65 0.00 0.98
31 32 7.336931 GTCTGAAATGTCTTCAAGGCCTTATAA 59.663 37.037 20.00 14.54 0.00 0.98
32 33 7.888021 TCTGAAATGTCTTCAAGGCCTTATAAA 59.112 33.333 20.00 11.96 0.00 1.40
33 34 8.415950 TGAAATGTCTTCAAGGCCTTATAAAA 57.584 30.769 20.00 9.43 0.00 1.52
34 35 8.522830 TGAAATGTCTTCAAGGCCTTATAAAAG 58.477 33.333 20.00 18.05 0.00 2.27
35 36 8.422577 AAATGTCTTCAAGGCCTTATAAAAGT 57.577 30.769 20.00 0.00 0.00 2.66
36 37 6.817765 TGTCTTCAAGGCCTTATAAAAGTG 57.182 37.500 20.00 3.72 0.00 3.16
37 38 6.539173 TGTCTTCAAGGCCTTATAAAAGTGA 58.461 36.000 20.00 6.54 0.00 3.41
38 39 7.001674 TGTCTTCAAGGCCTTATAAAAGTGAA 58.998 34.615 20.00 14.48 0.00 3.18
39 40 7.040686 TGTCTTCAAGGCCTTATAAAAGTGAAC 60.041 37.037 20.00 13.04 0.00 3.18
40 41 7.001674 TCTTCAAGGCCTTATAAAAGTGAACA 58.998 34.615 20.00 0.21 0.00 3.18
41 42 6.817765 TCAAGGCCTTATAAAAGTGAACAG 57.182 37.500 20.00 0.00 0.00 3.16
42 43 6.539173 TCAAGGCCTTATAAAAGTGAACAGA 58.461 36.000 20.00 2.74 0.00 3.41
43 44 6.655003 TCAAGGCCTTATAAAAGTGAACAGAG 59.345 38.462 20.00 0.00 0.00 3.35
44 45 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
45 46 4.640647 GGCCTTATAAAAGTGAACAGAGGG 59.359 45.833 0.00 0.00 0.00 4.30
46 47 5.497474 GCCTTATAAAAGTGAACAGAGGGA 58.503 41.667 0.00 0.00 0.00 4.20
47 48 5.586643 GCCTTATAAAAGTGAACAGAGGGAG 59.413 44.000 0.00 0.00 0.00 4.30
48 49 6.712276 CCTTATAAAAGTGAACAGAGGGAGT 58.288 40.000 0.00 0.00 0.00 3.85
49 50 7.580882 GCCTTATAAAAGTGAACAGAGGGAGTA 60.581 40.741 0.00 0.00 0.00 2.59
50 51 8.487028 CCTTATAAAAGTGAACAGAGGGAGTAT 58.513 37.037 0.00 0.00 0.00 2.12
51 52 9.892130 CTTATAAAAGTGAACAGAGGGAGTATT 57.108 33.333 0.00 0.00 0.00 1.89
53 54 6.884280 AAAAGTGAACAGAGGGAGTATTTG 57.116 37.500 0.00 0.00 0.00 2.32
54 55 5.568620 AAGTGAACAGAGGGAGTATTTGT 57.431 39.130 0.00 0.00 0.00 2.83
55 56 5.568620 AGTGAACAGAGGGAGTATTTGTT 57.431 39.130 0.00 0.00 34.91 2.83
56 57 5.941788 AGTGAACAGAGGGAGTATTTGTTT 58.058 37.500 0.00 0.00 32.58 2.83
57 58 5.765182 AGTGAACAGAGGGAGTATTTGTTTG 59.235 40.000 0.00 0.00 32.58 2.93
58 59 5.531287 GTGAACAGAGGGAGTATTTGTTTGT 59.469 40.000 0.00 0.00 32.58 2.83
59 60 5.530915 TGAACAGAGGGAGTATTTGTTTGTG 59.469 40.000 0.00 0.00 32.58 3.33
60 61 5.048846 ACAGAGGGAGTATTTGTTTGTGT 57.951 39.130 0.00 0.00 0.00 3.72
61 62 5.063880 ACAGAGGGAGTATTTGTTTGTGTC 58.936 41.667 0.00 0.00 0.00 3.67
62 63 5.063204 CAGAGGGAGTATTTGTTTGTGTCA 58.937 41.667 0.00 0.00 0.00 3.58
63 64 5.707298 CAGAGGGAGTATTTGTTTGTGTCAT 59.293 40.000 0.00 0.00 0.00 3.06
64 65 5.707298 AGAGGGAGTATTTGTTTGTGTCATG 59.293 40.000 0.00 0.00 0.00 3.07
65 66 4.766891 AGGGAGTATTTGTTTGTGTCATGG 59.233 41.667 0.00 0.00 0.00 3.66
66 67 4.485163 GGAGTATTTGTTTGTGTCATGGC 58.515 43.478 0.00 0.00 0.00 4.40
67 68 4.022416 GGAGTATTTGTTTGTGTCATGGCA 60.022 41.667 0.00 0.00 0.00 4.92
68 69 5.125100 AGTATTTGTTTGTGTCATGGCAG 57.875 39.130 0.00 0.00 0.00 4.85
69 70 4.826733 AGTATTTGTTTGTGTCATGGCAGA 59.173 37.500 0.00 0.00 0.00 4.26
70 71 3.713858 TTTGTTTGTGTCATGGCAGAG 57.286 42.857 0.00 0.00 0.00 3.35
71 72 2.636647 TGTTTGTGTCATGGCAGAGA 57.363 45.000 0.00 0.00 0.00 3.10
72 73 2.497138 TGTTTGTGTCATGGCAGAGAG 58.503 47.619 0.00 0.00 0.00 3.20
73 74 2.104622 TGTTTGTGTCATGGCAGAGAGA 59.895 45.455 0.00 0.00 0.00 3.10
74 75 3.244665 TGTTTGTGTCATGGCAGAGAGAT 60.245 43.478 0.00 0.00 0.00 2.75
75 76 3.708403 TTGTGTCATGGCAGAGAGATT 57.292 42.857 0.00 0.00 0.00 2.40
76 77 3.257469 TGTGTCATGGCAGAGAGATTC 57.743 47.619 0.00 0.00 0.00 2.52
77 78 2.568509 TGTGTCATGGCAGAGAGATTCA 59.431 45.455 0.00 0.00 0.00 2.57
78 79 3.199289 TGTGTCATGGCAGAGAGATTCAT 59.801 43.478 0.00 0.00 0.00 2.57
79 80 4.197750 GTGTCATGGCAGAGAGATTCATT 58.802 43.478 0.00 0.00 0.00 2.57
80 81 4.639310 GTGTCATGGCAGAGAGATTCATTT 59.361 41.667 0.00 0.00 0.00 2.32
81 82 5.125097 GTGTCATGGCAGAGAGATTCATTTT 59.875 40.000 0.00 0.00 0.00 1.82
82 83 5.713389 TGTCATGGCAGAGAGATTCATTTTT 59.287 36.000 0.00 0.00 0.00 1.94
124 125 7.883833 ACGATGGACTAGTCTATATTTGCTCTA 59.116 37.037 20.46 0.00 30.61 2.43
140 141 4.086457 TGCTCTATCTGTTGGTAGTGTCA 58.914 43.478 0.00 0.00 0.00 3.58
152 153 3.071023 TGGTAGTGTCAAACCTCAGGAAG 59.929 47.826 0.00 0.00 36.67 3.46
168 169 4.524714 TCAGGAAGTTCTTGTGTCTCCTAG 59.475 45.833 14.03 0.00 0.00 3.02
199 200 1.822990 CCATTTCACCTGCAGAGCATT 59.177 47.619 17.39 0.00 38.13 3.56
387 388 7.218963 GTGACTAATATTAAACAAAGCTGCTGC 59.781 37.037 1.35 7.62 40.05 5.25
462 463 5.911752 ACAGTATCACAGGATTGCTTCTAG 58.088 41.667 0.00 0.00 34.89 2.43
463 464 5.423610 ACAGTATCACAGGATTGCTTCTAGT 59.576 40.000 0.00 0.00 34.89 2.57
464 465 6.070538 ACAGTATCACAGGATTGCTTCTAGTT 60.071 38.462 0.00 0.00 34.89 2.24
465 466 6.478344 CAGTATCACAGGATTGCTTCTAGTTC 59.522 42.308 0.00 0.00 34.89 3.01
466 467 5.690464 ATCACAGGATTGCTTCTAGTTCT 57.310 39.130 0.00 0.00 0.00 3.01
467 468 6.798427 ATCACAGGATTGCTTCTAGTTCTA 57.202 37.500 0.00 0.00 0.00 2.10
637 640 9.709495 TTGACTGCAAATTTAGCTGATATTTTT 57.291 25.926 18.85 3.20 35.29 1.94
719 722 7.268586 TCTACTTCATCAATAAGGAGACAAGC 58.731 38.462 0.00 0.00 38.69 4.01
813 816 5.235186 ACAGAGACATCAAAGTTGAAGAACG 59.765 40.000 3.46 0.00 41.13 3.95
869 872 3.073062 CCATTCCCATAGGAGACGGATTT 59.927 47.826 0.00 0.00 45.19 2.17
1087 1093 1.001641 CTCAAGTCCCCAAGGCCAG 60.002 63.158 5.01 0.00 0.00 4.85
1128 1134 1.019673 CACAAGGGGATTGCGATCAG 58.980 55.000 15.92 2.76 43.15 2.90
1131 1137 2.439507 ACAAGGGGATTGCGATCAGTAT 59.560 45.455 15.92 0.00 43.15 2.12
1245 1251 3.276857 CAAGAGGTGGATGTCATTCCTG 58.723 50.000 9.03 0.00 36.68 3.86
1484 1490 1.188863 GCTGACCATGGCAAGGAATT 58.811 50.000 16.88 0.00 0.00 2.17
1524 1530 8.739972 GTTTACCAGTATGATTGTTTCCTCAAT 58.260 33.333 0.00 0.00 39.69 2.57
1550 1556 5.888161 GGTATGTTTCTTGTGGATCCTCATT 59.112 40.000 16.93 0.76 0.00 2.57
1563 1569 7.398047 TGTGGATCCTCATTCATCAGAAAAATT 59.602 33.333 14.23 0.00 37.29 1.82
1608 1616 7.175990 TGACAAACTTTAGAACTTCACCTTGTT 59.824 33.333 0.00 0.00 0.00 2.83
1896 1904 7.598493 CCAGAACAAAATAAATGGACGTTGATT 59.402 33.333 0.00 0.00 0.00 2.57
1898 1906 8.356657 AGAACAAAATAAATGGACGTTGATTGA 58.643 29.630 0.00 0.00 0.00 2.57
2026 2034 4.984205 TGACGTGTACGATACAAATAGCA 58.016 39.130 11.79 0.00 40.93 3.49
2139 2147 2.675348 GAGGTCTCTGGCGATTTTTGAG 59.325 50.000 0.00 0.00 0.00 3.02
2190 2198 1.067071 GTGCCGCTTACTGGTAGTTCT 60.067 52.381 0.00 0.00 0.00 3.01
2211 2219 1.663702 CACGCGGTTTTCTCTCGGT 60.664 57.895 12.47 0.00 0.00 4.69
2213 2221 0.529378 ACGCGGTTTTCTCTCGGTAT 59.471 50.000 12.47 0.00 0.00 2.73
2262 2270 0.906282 TGGAGGAAGAACCCGGGTAC 60.906 60.000 30.52 18.16 40.05 3.34
2319 2327 2.668457 CTCTGAATGGTGCACGTCTAAC 59.332 50.000 11.45 0.00 0.00 2.34
2402 2410 1.603172 GGTCGCTGAAGGATGATACCG 60.603 57.143 0.00 0.00 34.73 4.02
2440 2448 3.706698 TCATCTTCCGCAGTTAAGATCG 58.293 45.455 0.00 0.00 39.79 3.69
2506 2514 2.620112 CGCTTGTTGCTCCACCCAG 61.620 63.158 0.00 0.00 40.11 4.45
2552 2560 0.463654 TTCGGTTGCTTGCTGACAGT 60.464 50.000 3.99 0.00 0.00 3.55
2725 2737 4.280929 TGAGTGTGGGAATATGTATCCTCG 59.719 45.833 0.00 0.00 37.14 4.63
2858 2879 5.947228 TTGTTCTTTCTAACCATGCTCTG 57.053 39.130 0.00 0.00 0.00 3.35
2862 2883 1.742761 TTCTAACCATGCTCTGCTGC 58.257 50.000 0.00 0.00 0.00 5.25
2875 2896 3.129988 GCTCTGCTGCAAGGATTTATGTT 59.870 43.478 3.02 0.00 29.63 2.71
2919 2940 2.027192 TCCTCTCCTTCCAAATGTTCCG 60.027 50.000 0.00 0.00 0.00 4.30
2930 2951 5.492895 TCCAAATGTTCCGAGCAGTAATAA 58.507 37.500 0.00 0.00 0.00 1.40
2931 2952 5.941058 TCCAAATGTTCCGAGCAGTAATAAA 59.059 36.000 0.00 0.00 0.00 1.40
2937 2958 6.460781 TGTTCCGAGCAGTAATAAAGAAGAA 58.539 36.000 0.00 0.00 0.00 2.52
2940 2961 7.400599 TCCGAGCAGTAATAAAGAAGAACTA 57.599 36.000 0.00 0.00 0.00 2.24
2983 3005 5.202004 TGGTTTTGTTTAGCCCTTTGACTA 58.798 37.500 0.00 0.00 0.00 2.59
3023 3045 3.431922 CAATCACATTGGGCACATCTC 57.568 47.619 0.00 0.00 36.63 2.75
3024 3046 2.756207 CAATCACATTGGGCACATCTCA 59.244 45.455 0.00 0.00 36.63 3.27
3051 3173 6.182627 TCATTGCCAATCTGATAGTGTCTTT 58.817 36.000 0.00 0.00 0.00 2.52
3085 3207 2.906389 TCCTAGTGTTCAGCCTGTCAAT 59.094 45.455 0.00 0.00 0.00 2.57
3095 3217 6.538742 TGTTCAGCCTGTCAATAAGTAATAGC 59.461 38.462 0.00 0.00 0.00 2.97
3096 3218 5.611374 TCAGCCTGTCAATAAGTAATAGCC 58.389 41.667 0.00 0.00 0.00 3.93
3097 3219 5.130311 TCAGCCTGTCAATAAGTAATAGCCA 59.870 40.000 0.00 0.00 0.00 4.75
3098 3220 5.237344 CAGCCTGTCAATAAGTAATAGCCAC 59.763 44.000 0.00 0.00 0.00 5.01
3099 3221 5.104527 AGCCTGTCAATAAGTAATAGCCACA 60.105 40.000 0.00 0.00 0.00 4.17
3100 3222 5.765182 GCCTGTCAATAAGTAATAGCCACAT 59.235 40.000 0.00 0.00 0.00 3.21
3101 3223 6.263168 GCCTGTCAATAAGTAATAGCCACATT 59.737 38.462 0.00 0.00 0.00 2.71
3102 3224 7.444183 GCCTGTCAATAAGTAATAGCCACATTA 59.556 37.037 0.00 0.00 0.00 1.90
3103 3225 9.337396 CCTGTCAATAAGTAATAGCCACATTAA 57.663 33.333 0.00 0.00 0.00 1.40
3113 3235 5.700402 ATAGCCACATTAAGACCTTGAGT 57.300 39.130 0.00 0.00 0.00 3.41
3116 3238 5.140454 AGCCACATTAAGACCTTGAGTTTT 58.860 37.500 0.00 0.00 0.00 2.43
3122 3244 8.915654 CACATTAAGACCTTGAGTTTTATTTGC 58.084 33.333 0.00 0.00 0.00 3.68
3154 3364 1.746157 TCCCCATGGATATGACCAGG 58.254 55.000 15.22 1.97 43.49 4.45
3155 3365 1.060640 TCCCCATGGATATGACCAGGT 60.061 52.381 15.22 0.00 43.49 4.00
3156 3366 1.074405 CCCCATGGATATGACCAGGTG 59.926 57.143 15.22 0.00 43.49 4.00
3157 3367 1.776667 CCCATGGATATGACCAGGTGT 59.223 52.381 15.22 0.00 43.49 4.16
3158 3368 2.224621 CCCATGGATATGACCAGGTGTC 60.225 54.545 15.22 0.00 43.49 3.67
3159 3369 2.224621 CCATGGATATGACCAGGTGTCC 60.225 54.545 5.56 0.00 43.78 4.02
3160 3370 2.262266 TGGATATGACCAGGTGTCCA 57.738 50.000 0.00 2.47 43.78 4.02
3161 3371 2.556766 TGGATATGACCAGGTGTCCAA 58.443 47.619 0.00 0.00 43.78 3.53
3162 3372 2.916269 TGGATATGACCAGGTGTCCAAA 59.084 45.455 0.00 0.00 43.78 3.28
3163 3373 3.527253 TGGATATGACCAGGTGTCCAAAT 59.473 43.478 0.00 0.00 43.78 2.32
3164 3374 4.137543 GGATATGACCAGGTGTCCAAATC 58.862 47.826 0.00 0.00 43.78 2.17
3165 3375 4.385199 GGATATGACCAGGTGTCCAAATCA 60.385 45.833 0.00 0.00 43.78 2.57
3166 3376 2.270352 TGACCAGGTGTCCAAATCAC 57.730 50.000 0.00 0.00 43.78 3.06
3198 3408 2.283298 CGGATGAGGTGTCCAAATCAG 58.717 52.381 0.00 0.00 35.41 2.90
3207 3417 4.351111 AGGTGTCCAAATCAGTTAACTCCT 59.649 41.667 4.77 2.26 0.00 3.69
3208 3418 4.695928 GGTGTCCAAATCAGTTAACTCCTC 59.304 45.833 4.77 0.00 0.00 3.71
3209 3419 5.305585 GTGTCCAAATCAGTTAACTCCTCA 58.694 41.667 4.77 0.00 0.00 3.86
3230 3440 5.260424 TCAATGCTGGAAGGTTTGCTAATA 58.740 37.500 0.00 0.00 0.00 0.98
3239 3449 5.009110 GGAAGGTTTGCTAATAATGAGGCTC 59.991 44.000 7.79 7.79 0.00 4.70
3287 3497 3.930634 AGTGGCAAATTGAAGAGAAGC 57.069 42.857 0.00 0.00 0.00 3.86
3301 3511 3.663198 AGAGAAGCCTTGGGTCATCTAT 58.337 45.455 4.61 0.00 0.00 1.98
3310 3520 5.474876 GCCTTGGGTCATCTATGGAATAAAG 59.525 44.000 0.00 0.00 0.00 1.85
3312 3522 6.410853 CCTTGGGTCATCTATGGAATAAAGGT 60.411 42.308 0.00 0.00 0.00 3.50
3317 3527 7.420214 GGGTCATCTATGGAATAAAGGTTCTGA 60.420 40.741 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.392940 CTTGAAGACATTTCAGACAGGGT 58.607 43.478 0.00 0.00 0.00 4.34
1 2 3.755378 CCTTGAAGACATTTCAGACAGGG 59.245 47.826 0.00 0.00 0.00 4.45
2 3 3.190118 GCCTTGAAGACATTTCAGACAGG 59.810 47.826 0.00 3.03 30.77 4.00
3 4 3.190118 GGCCTTGAAGACATTTCAGACAG 59.810 47.826 0.00 0.00 0.00 3.51
4 5 3.149196 GGCCTTGAAGACATTTCAGACA 58.851 45.455 0.00 0.00 0.00 3.41
5 6 3.416156 AGGCCTTGAAGACATTTCAGAC 58.584 45.455 0.00 0.00 0.00 3.51
6 7 3.795688 AGGCCTTGAAGACATTTCAGA 57.204 42.857 0.00 0.00 0.00 3.27
7 8 7.630242 TTATAAGGCCTTGAAGACATTTCAG 57.370 36.000 28.77 0.00 0.00 3.02
8 9 8.415950 TTTTATAAGGCCTTGAAGACATTTCA 57.584 30.769 28.77 3.15 0.00 2.69
9 10 8.523658 ACTTTTATAAGGCCTTGAAGACATTTC 58.476 33.333 28.77 0.00 35.61 2.17
10 11 8.306761 CACTTTTATAAGGCCTTGAAGACATTT 58.693 33.333 28.77 0.00 35.61 2.32
11 12 7.669722 TCACTTTTATAAGGCCTTGAAGACATT 59.330 33.333 28.77 0.00 35.61 2.71
12 13 7.175104 TCACTTTTATAAGGCCTTGAAGACAT 58.825 34.615 28.77 14.50 35.61 3.06
13 14 6.539173 TCACTTTTATAAGGCCTTGAAGACA 58.461 36.000 28.77 7.10 35.61 3.41
14 15 7.040686 TGTTCACTTTTATAAGGCCTTGAAGAC 60.041 37.037 28.77 17.56 35.61 3.01
15 16 7.001674 TGTTCACTTTTATAAGGCCTTGAAGA 58.998 34.615 28.77 15.87 35.61 2.87
16 17 7.174946 TCTGTTCACTTTTATAAGGCCTTGAAG 59.825 37.037 28.77 24.09 35.61 3.02
17 18 7.001674 TCTGTTCACTTTTATAAGGCCTTGAA 58.998 34.615 28.77 17.44 35.61 2.69
18 19 6.539173 TCTGTTCACTTTTATAAGGCCTTGA 58.461 36.000 28.77 11.98 35.61 3.02
19 20 6.127897 CCTCTGTTCACTTTTATAAGGCCTTG 60.128 42.308 28.77 12.48 35.61 3.61
20 21 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
21 22 5.501156 CCTCTGTTCACTTTTATAAGGCCT 58.499 41.667 0.00 0.00 35.61 5.19
22 23 4.640647 CCCTCTGTTCACTTTTATAAGGCC 59.359 45.833 0.00 0.00 35.61 5.19
23 24 5.497474 TCCCTCTGTTCACTTTTATAAGGC 58.503 41.667 0.00 0.00 35.61 4.35
24 25 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
25 26 9.892130 AATACTCCCTCTGTTCACTTTTATAAG 57.108 33.333 0.00 0.00 37.40 1.73
27 28 9.667107 CAAATACTCCCTCTGTTCACTTTTATA 57.333 33.333 0.00 0.00 0.00 0.98
28 29 8.164070 ACAAATACTCCCTCTGTTCACTTTTAT 58.836 33.333 0.00 0.00 0.00 1.40
29 30 7.514721 ACAAATACTCCCTCTGTTCACTTTTA 58.485 34.615 0.00 0.00 0.00 1.52
30 31 6.365520 ACAAATACTCCCTCTGTTCACTTTT 58.634 36.000 0.00 0.00 0.00 2.27
31 32 5.941788 ACAAATACTCCCTCTGTTCACTTT 58.058 37.500 0.00 0.00 0.00 2.66
32 33 5.568620 ACAAATACTCCCTCTGTTCACTT 57.431 39.130 0.00 0.00 0.00 3.16
33 34 5.568620 AACAAATACTCCCTCTGTTCACT 57.431 39.130 0.00 0.00 0.00 3.41
34 35 5.531287 ACAAACAAATACTCCCTCTGTTCAC 59.469 40.000 0.00 0.00 30.16 3.18
35 36 5.530915 CACAAACAAATACTCCCTCTGTTCA 59.469 40.000 0.00 0.00 30.16 3.18
36 37 5.531287 ACACAAACAAATACTCCCTCTGTTC 59.469 40.000 0.00 0.00 30.16 3.18
37 38 5.445964 ACACAAACAAATACTCCCTCTGTT 58.554 37.500 0.00 0.00 0.00 3.16
38 39 5.048846 ACACAAACAAATACTCCCTCTGT 57.951 39.130 0.00 0.00 0.00 3.41
39 40 5.063204 TGACACAAACAAATACTCCCTCTG 58.937 41.667 0.00 0.00 0.00 3.35
40 41 5.304686 TGACACAAACAAATACTCCCTCT 57.695 39.130 0.00 0.00 0.00 3.69
41 42 5.106157 CCATGACACAAACAAATACTCCCTC 60.106 44.000 0.00 0.00 0.00 4.30
42 43 4.766891 CCATGACACAAACAAATACTCCCT 59.233 41.667 0.00 0.00 0.00 4.20
43 44 4.618227 GCCATGACACAAACAAATACTCCC 60.618 45.833 0.00 0.00 0.00 4.30
44 45 4.022416 TGCCATGACACAAACAAATACTCC 60.022 41.667 0.00 0.00 0.00 3.85
45 46 5.048782 TCTGCCATGACACAAACAAATACTC 60.049 40.000 0.00 0.00 0.00 2.59
46 47 4.826733 TCTGCCATGACACAAACAAATACT 59.173 37.500 0.00 0.00 0.00 2.12
47 48 5.048782 TCTCTGCCATGACACAAACAAATAC 60.049 40.000 0.00 0.00 0.00 1.89
48 49 5.069318 TCTCTGCCATGACACAAACAAATA 58.931 37.500 0.00 0.00 0.00 1.40
49 50 3.890756 TCTCTGCCATGACACAAACAAAT 59.109 39.130 0.00 0.00 0.00 2.32
50 51 3.286353 TCTCTGCCATGACACAAACAAA 58.714 40.909 0.00 0.00 0.00 2.83
51 52 2.880268 CTCTCTGCCATGACACAAACAA 59.120 45.455 0.00 0.00 0.00 2.83
52 53 2.104622 TCTCTCTGCCATGACACAAACA 59.895 45.455 0.00 0.00 0.00 2.83
53 54 2.771089 TCTCTCTGCCATGACACAAAC 58.229 47.619 0.00 0.00 0.00 2.93
54 55 3.708403 ATCTCTCTGCCATGACACAAA 57.292 42.857 0.00 0.00 0.00 2.83
55 56 3.008266 TGAATCTCTCTGCCATGACACAA 59.992 43.478 0.00 0.00 0.00 3.33
56 57 2.568509 TGAATCTCTCTGCCATGACACA 59.431 45.455 0.00 0.00 0.00 3.72
57 58 3.257469 TGAATCTCTCTGCCATGACAC 57.743 47.619 0.00 0.00 0.00 3.67
58 59 4.498894 AATGAATCTCTCTGCCATGACA 57.501 40.909 0.00 0.00 0.00 3.58
59 60 5.831702 AAAATGAATCTCTCTGCCATGAC 57.168 39.130 0.00 0.00 0.00 3.06
80 81 5.349270 CCATCGTCATGTACGGTAAGAAAAA 59.651 40.000 14.72 0.00 45.15 1.94
81 82 4.865925 CCATCGTCATGTACGGTAAGAAAA 59.134 41.667 14.72 0.00 45.15 2.29
82 83 4.158209 TCCATCGTCATGTACGGTAAGAAA 59.842 41.667 14.72 0.00 45.15 2.52
83 84 3.695556 TCCATCGTCATGTACGGTAAGAA 59.304 43.478 14.72 0.00 45.15 2.52
84 85 3.065786 GTCCATCGTCATGTACGGTAAGA 59.934 47.826 14.72 7.78 45.15 2.10
85 86 3.066342 AGTCCATCGTCATGTACGGTAAG 59.934 47.826 14.72 6.07 45.15 2.34
96 97 6.490381 AGCAAATATAGACTAGTCCATCGTCA 59.510 38.462 19.38 0.00 0.00 4.35
124 125 4.102524 TGAGGTTTGACACTACCAACAGAT 59.897 41.667 8.28 0.00 36.87 2.90
140 141 4.080299 AGACACAAGAACTTCCTGAGGTTT 60.080 41.667 0.00 0.00 30.37 3.27
152 153 8.254508 ACATCTAATTCTAGGAGACACAAGAAC 58.745 37.037 0.00 0.00 31.20 3.01
168 169 5.357878 TGCAGGTGAAATGGACATCTAATTC 59.642 40.000 0.00 0.00 0.00 2.17
274 275 0.758734 CACCCACAGTGTGAAGAGGA 59.241 55.000 24.99 0.00 41.93 3.71
462 463 3.995048 GCACCAAGTAGGAACTGTAGAAC 59.005 47.826 0.00 0.00 41.52 3.01
463 464 3.901844 AGCACCAAGTAGGAACTGTAGAA 59.098 43.478 0.00 0.00 41.52 2.10
464 465 3.507411 AGCACCAAGTAGGAACTGTAGA 58.493 45.455 0.00 0.00 41.52 2.59
465 466 3.963428 AGCACCAAGTAGGAACTGTAG 57.037 47.619 0.00 0.00 41.52 2.74
466 467 5.811796 TTTAGCACCAAGTAGGAACTGTA 57.188 39.130 0.00 0.00 41.52 2.74
467 468 4.699925 TTTAGCACCAAGTAGGAACTGT 57.300 40.909 0.00 0.00 41.52 3.55
588 591 4.010349 AGTTGCTAGGAACAAATAGGTGC 58.990 43.478 26.40 0.00 0.00 5.01
813 816 4.866486 GGGTTTGAATGATGCTGAAATGAC 59.134 41.667 0.00 0.00 0.00 3.06
1128 1134 3.954258 AGCCAGGGATTAAAGCACAATAC 59.046 43.478 0.00 0.00 0.00 1.89
1131 1137 2.562298 CAAGCCAGGGATTAAAGCACAA 59.438 45.455 0.00 0.00 0.00 3.33
1407 1413 1.760480 AACCACACCAAACCCAGCC 60.760 57.895 0.00 0.00 0.00 4.85
1484 1490 5.690865 ACTGGTAAACCTCATCAGAAACAA 58.309 37.500 0.02 0.00 36.82 2.83
1524 1530 3.517901 AGGATCCACAAGAAACATACCGA 59.482 43.478 15.82 0.00 0.00 4.69
1525 1531 3.871594 GAGGATCCACAAGAAACATACCG 59.128 47.826 15.82 0.00 0.00 4.02
1566 1572 8.798859 AAGTTTGTCAGACTAATAAGATGCAT 57.201 30.769 0.00 0.00 0.00 3.96
1701 1709 2.885135 ATGAGCTGGTCCAACATTCA 57.115 45.000 4.17 0.00 0.00 2.57
1715 1723 3.434984 GCGGAATCAGAGGATAAATGAGC 59.565 47.826 0.00 0.00 32.09 4.26
2026 2034 1.005924 CCTAAACTCACCCCAGGCATT 59.994 52.381 0.00 0.00 0.00 3.56
2136 2144 0.694771 AGGAATTGTCTGCTGGCTCA 59.305 50.000 0.00 0.00 0.00 4.26
2139 2147 0.322816 TCCAGGAATTGTCTGCTGGC 60.323 55.000 6.29 0.00 34.70 4.85
2190 2198 0.731514 CGAGAGAAAACCGCGTGCTA 60.732 55.000 4.92 0.00 0.00 3.49
2211 2219 3.808265 GCAGCAGCTTCCCATCATGTATA 60.808 47.826 0.00 0.00 37.91 1.47
2213 2221 1.748244 GCAGCAGCTTCCCATCATGTA 60.748 52.381 0.00 0.00 37.91 2.29
2262 2270 2.298446 AGGATCATACATCAGCGTCTGG 59.702 50.000 6.95 0.00 31.51 3.86
2346 2354 0.981183 AGGCTTTGATGGTCACGGTA 59.019 50.000 0.00 0.00 0.00 4.02
2402 2410 5.346181 AGATGAGGCAGGTAGTAAACTTC 57.654 43.478 0.00 0.00 0.00 3.01
2440 2448 3.653539 ACGATAAACCAAACAAAGCCC 57.346 42.857 0.00 0.00 0.00 5.19
2506 2514 8.668353 TGAACTGAAGCATGAACATTCTATTAC 58.332 33.333 0.00 0.00 0.00 1.89
2552 2560 3.780294 AGAGTACATTATGGCAAGGTCCA 59.220 43.478 0.00 0.00 40.97 4.02
2648 2656 7.336396 GGAGCCTTTCCTACTATTTCAAAGTA 58.664 38.462 0.00 0.00 43.16 2.24
2712 2724 5.620206 TGAACCAATGCGAGGATACATATT 58.380 37.500 0.00 0.00 41.41 1.28
2725 2737 6.446318 TGTTTACAAATCTCTGAACCAATGC 58.554 36.000 0.00 0.00 0.00 3.56
2858 2879 4.808558 TCAACAACATAAATCCTTGCAGC 58.191 39.130 0.00 0.00 0.00 5.25
2875 2896 9.883142 AGGAAGAAAACAATTACATTTTCAACA 57.117 25.926 17.38 0.00 43.99 3.33
2892 2913 5.705400 ACATTTGGAAGGAGAGGAAGAAAA 58.295 37.500 0.00 0.00 0.00 2.29
2896 2917 4.013050 GGAACATTTGGAAGGAGAGGAAG 58.987 47.826 0.00 0.00 0.00 3.46
2948 2969 6.037062 GCTAAACAAAACCATTCTGCAAAAGT 59.963 34.615 0.00 0.00 0.00 2.66
2949 2970 6.421405 GCTAAACAAAACCATTCTGCAAAAG 58.579 36.000 0.00 0.00 0.00 2.27
2954 2975 3.006859 AGGGCTAAACAAAACCATTCTGC 59.993 43.478 0.00 0.00 0.00 4.26
2983 3005 0.842635 GGATGCTCCAGGATTGAGGT 59.157 55.000 0.00 0.00 36.28 3.85
3003 3025 2.756207 TGAGATGTGCCCAATGTGATTG 59.244 45.455 0.00 0.00 39.94 2.67
3004 3026 3.090210 TGAGATGTGCCCAATGTGATT 57.910 42.857 0.00 0.00 0.00 2.57
3006 3028 2.161855 GTTGAGATGTGCCCAATGTGA 58.838 47.619 0.00 0.00 0.00 3.58
3007 3029 2.163010 GAGTTGAGATGTGCCCAATGTG 59.837 50.000 0.00 0.00 0.00 3.21
3008 3030 2.224843 TGAGTTGAGATGTGCCCAATGT 60.225 45.455 0.00 0.00 0.00 2.71
3009 3031 2.439409 TGAGTTGAGATGTGCCCAATG 58.561 47.619 0.00 0.00 0.00 2.82
3010 3032 2.885135 TGAGTTGAGATGTGCCCAAT 57.115 45.000 0.00 0.00 0.00 3.16
3011 3033 2.821378 CAATGAGTTGAGATGTGCCCAA 59.179 45.455 0.00 0.00 37.53 4.12
3012 3034 2.439409 CAATGAGTTGAGATGTGCCCA 58.561 47.619 0.00 0.00 37.53 5.36
3013 3035 1.133790 GCAATGAGTTGAGATGTGCCC 59.866 52.381 0.00 0.00 37.53 5.36
3014 3036 1.133790 GGCAATGAGTTGAGATGTGCC 59.866 52.381 0.00 0.00 42.88 5.01
3016 3038 4.398358 AGATTGGCAATGAGTTGAGATGTG 59.602 41.667 19.07 0.00 37.53 3.21
3018 3040 4.638865 TCAGATTGGCAATGAGTTGAGATG 59.361 41.667 19.07 2.68 37.53 2.90
3019 3041 4.851843 TCAGATTGGCAATGAGTTGAGAT 58.148 39.130 19.07 0.00 37.53 2.75
3020 3042 4.290711 TCAGATTGGCAATGAGTTGAGA 57.709 40.909 19.07 2.00 37.53 3.27
3022 3044 5.587443 CACTATCAGATTGGCAATGAGTTGA 59.413 40.000 19.07 14.99 37.53 3.18
3023 3045 5.356190 ACACTATCAGATTGGCAATGAGTTG 59.644 40.000 19.07 11.39 38.39 3.16
3024 3046 5.503927 ACACTATCAGATTGGCAATGAGTT 58.496 37.500 19.07 7.29 0.00 3.01
3051 3173 7.362056 GCTGAACACTAGGAATATGCTCAAAAA 60.362 37.037 0.00 0.00 0.00 1.94
3058 3180 3.812053 CAGGCTGAACACTAGGAATATGC 59.188 47.826 9.42 0.00 0.00 3.14
3067 3189 5.483685 ACTTATTGACAGGCTGAACACTA 57.516 39.130 23.66 15.12 0.00 2.74
3085 3207 8.764558 TCAAGGTCTTAATGTGGCTATTACTTA 58.235 33.333 0.00 0.00 0.00 2.24
3095 3217 9.410556 CAAATAAAACTCAAGGTCTTAATGTGG 57.589 33.333 0.00 0.00 0.00 4.17
3096 3218 8.915654 GCAAATAAAACTCAAGGTCTTAATGTG 58.084 33.333 0.00 0.00 0.00 3.21
3097 3219 8.637986 TGCAAATAAAACTCAAGGTCTTAATGT 58.362 29.630 0.00 0.00 0.00 2.71
3098 3220 9.474920 TTGCAAATAAAACTCAAGGTCTTAATG 57.525 29.630 0.00 0.00 0.00 1.90
3099 3221 9.476202 GTTGCAAATAAAACTCAAGGTCTTAAT 57.524 29.630 0.00 0.00 0.00 1.40
3100 3222 8.691797 AGTTGCAAATAAAACTCAAGGTCTTAA 58.308 29.630 0.00 0.00 30.87 1.85
3101 3223 8.232913 AGTTGCAAATAAAACTCAAGGTCTTA 57.767 30.769 0.00 0.00 30.87 2.10
3102 3224 7.112452 AGTTGCAAATAAAACTCAAGGTCTT 57.888 32.000 0.00 0.00 30.87 3.01
3103 3225 6.715347 AGTTGCAAATAAAACTCAAGGTCT 57.285 33.333 0.00 0.00 30.87 3.85
3104 3226 6.200854 CCAAGTTGCAAATAAAACTCAAGGTC 59.799 38.462 0.00 0.00 35.60 3.85
3113 3235 2.365617 TCGGGCCAAGTTGCAAATAAAA 59.634 40.909 4.39 0.00 0.00 1.52
3116 3238 1.748493 GATCGGGCCAAGTTGCAAATA 59.252 47.619 4.39 0.00 0.00 1.40
3122 3244 2.440247 GGGGATCGGGCCAAGTTG 60.440 66.667 4.39 0.00 0.00 3.16
3169 3379 2.882137 GACACCTCATCCGGAACAAAAA 59.118 45.455 9.01 0.00 0.00 1.94
3170 3380 2.500229 GACACCTCATCCGGAACAAAA 58.500 47.619 9.01 0.00 0.00 2.44
3171 3381 1.271163 GGACACCTCATCCGGAACAAA 60.271 52.381 9.01 0.00 0.00 2.83
3172 3382 0.323629 GGACACCTCATCCGGAACAA 59.676 55.000 9.01 0.00 0.00 2.83
3173 3383 0.834261 TGGACACCTCATCCGGAACA 60.834 55.000 9.01 0.00 39.30 3.18
3174 3384 0.323629 TTGGACACCTCATCCGGAAC 59.676 55.000 9.01 0.00 39.30 3.62
3175 3385 1.060729 TTTGGACACCTCATCCGGAA 58.939 50.000 9.01 0.00 39.30 4.30
3176 3386 1.209504 GATTTGGACACCTCATCCGGA 59.790 52.381 6.61 6.61 39.30 5.14
3177 3387 1.065491 TGATTTGGACACCTCATCCGG 60.065 52.381 0.00 0.00 39.30 5.14
3178 3388 2.283298 CTGATTTGGACACCTCATCCG 58.717 52.381 0.00 0.00 39.30 4.18
3179 3389 3.356529 ACTGATTTGGACACCTCATCC 57.643 47.619 0.00 0.00 36.70 3.51
3180 3390 5.940470 AGTTAACTGATTTGGACACCTCATC 59.060 40.000 7.48 0.00 0.00 2.92
3181 3391 5.880901 AGTTAACTGATTTGGACACCTCAT 58.119 37.500 7.48 0.00 0.00 2.90
3182 3392 5.304686 AGTTAACTGATTTGGACACCTCA 57.695 39.130 7.48 0.00 0.00 3.86
3183 3393 4.695928 GGAGTTAACTGATTTGGACACCTC 59.304 45.833 14.14 0.00 0.00 3.85
3198 3408 3.691609 CCTTCCAGCATTGAGGAGTTAAC 59.308 47.826 0.00 0.00 34.91 2.01
3207 3417 1.999648 AGCAAACCTTCCAGCATTGA 58.000 45.000 0.00 0.00 0.00 2.57
3208 3418 3.940209 TTAGCAAACCTTCCAGCATTG 57.060 42.857 0.00 0.00 0.00 2.82
3209 3419 6.380846 TCATTATTAGCAAACCTTCCAGCATT 59.619 34.615 0.00 0.00 0.00 3.56
3230 3440 3.136763 CGCTGAATATGTGAGCCTCATT 58.863 45.455 0.00 0.00 0.00 2.57
3259 3469 5.188434 TCTTCAATTTGCCACTATCTCCTG 58.812 41.667 0.00 0.00 0.00 3.86
3267 3477 2.560105 GGCTTCTCTTCAATTTGCCACT 59.440 45.455 0.00 0.00 38.79 4.00
3287 3497 6.006449 CCTTTATTCCATAGATGACCCAAGG 58.994 44.000 0.00 0.00 0.00 3.61
3310 3520 6.351327 CTGAAGATATTTCGGTTCAGAACC 57.649 41.667 21.18 21.18 45.87 3.62
3317 3527 6.659242 ACACCAAATCTGAAGATATTTCGGTT 59.341 34.615 0.00 0.00 33.73 4.44
3321 3531 8.964476 TCCTACACCAAATCTGAAGATATTTC 57.036 34.615 0.00 0.00 33.73 2.17


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

AutoCloner maintained by Alex Coulton.