Multiple sequence alignment - TraesCS1B01G311800

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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 TraesCS1B01G311800 chr1B 100.000 4676 0 0 1 4676 535387888 535383213 0.000000e+00 8636.0
1 TraesCS1B01G311800 chr1B 90.620 1759 128 15 1935 3676 535145000 535143262 0.000000e+00 2300.0
2 TraesCS1B01G311800 chr1B 87.207 852 90 5 876 1727 535146016 535145184 0.000000e+00 952.0
3 TraesCS1B01G311800 chr1B 87.912 182 20 2 1511 1692 534736232 534736053 3.670000e-51 213.0
4 TraesCS1B01G311800 chr1A 94.391 3976 160 19 1 3943 496047318 496043373 0.000000e+00 6048.0
5 TraesCS1B01G311800 chr1A 86.207 812 97 10 917 1727 495743873 495743076 0.000000e+00 865.0
6 TraesCS1B01G311800 chr1A 94.428 341 14 4 4185 4523 496042970 496042633 1.930000e-143 520.0
7 TraesCS1B01G311800 chr1A 88.321 411 41 3 1925 2331 495741536 495741129 1.960000e-133 486.0
8 TraesCS1B01G311800 chr1A 88.078 411 42 3 1925 2331 495742905 495742498 9.100000e-132 481.0
9 TraesCS1B01G311800 chr1A 87.835 411 43 2 1925 2331 495740141 495739734 4.230000e-130 475.0
10 TraesCS1B01G311800 chr1A 87.500 336 38 4 1400 1734 495740639 495740307 7.340000e-103 385.0
11 TraesCS1B01G311800 chr1A 82.090 335 40 5 1400 1734 495742014 495741700 7.710000e-68 268.0
12 TraesCS1B01G311800 chr1A 89.286 168 18 0 1229 1396 495742019 495742186 1.320000e-50 211.0
13 TraesCS1B01G311800 chr1A 88.800 125 14 0 4070 4194 496043123 496042999 2.250000e-33 154.0
14 TraesCS1B01G311800 chr1D 97.308 2637 65 5 3 2636 399192000 399189367 0.000000e+00 4471.0
15 TraesCS1B01G311800 chr1D 95.578 995 41 2 2783 3776 399189161 399188169 0.000000e+00 1591.0
16 TraesCS1B01G311800 chr1D 89.781 411 34 4 1925 2331 399063674 399063268 1.930000e-143 520.0
17 TraesCS1B01G311800 chr1D 93.143 350 12 7 4185 4527 399187706 399187362 1.940000e-138 503.0
18 TraesCS1B01G311800 chr1D 94.152 171 3 1 3773 3943 399188009 399187846 2.160000e-63 254.0
19 TraesCS1B01G311800 chr1D 88.690 168 19 0 1229 1396 399064239 399064406 6.130000e-49 206.0
20 TraesCS1B01G311800 chr1D 92.000 125 10 0 4552 4676 73760869 73760745 4.810000e-40 176.0
21 TraesCS1B01G311800 chr1D 94.340 106 6 0 4089 4194 399187840 399187735 3.740000e-36 163.0
22 TraesCS1B01G311800 chr3A 83.538 571 88 6 3039 3606 589395006 589395573 3.200000e-146 529.0
23 TraesCS1B01G311800 chr3A 93.443 122 8 0 4555 4676 449516417 449516296 1.030000e-41 182.0
24 TraesCS1B01G311800 chr3D 82.867 572 90 7 3039 3606 447991603 447992170 1.500000e-139 507.0
25 TraesCS1B01G311800 chr3D 92.857 126 8 1 4552 4676 418774556 418774431 1.030000e-41 182.0
26 TraesCS1B01G311800 chr3B 81.895 591 99 7 3039 3625 587567787 587568373 4.200000e-135 492.0
27 TraesCS1B01G311800 chr3B 94.215 121 7 0 4556 4676 548054189 548054069 7.990000e-43 185.0
28 TraesCS1B01G311800 chr4A 94.262 122 7 0 4555 4676 668116304 668116183 2.220000e-43 187.0
29 TraesCS1B01G311800 chr4A 76.577 222 45 6 3309 3528 60926386 60926170 1.060000e-21 115.0
30 TraesCS1B01G311800 chr7D 92.800 125 9 0 4552 4676 47906036 47906160 1.030000e-41 182.0
31 TraesCS1B01G311800 chr5B 92.800 125 9 0 4552 4676 265436318 265436194 1.030000e-41 182.0
32 TraesCS1B01G311800 chr5B 92.800 125 9 0 4552 4676 338933716 338933840 1.030000e-41 182.0
33 TraesCS1B01G311800 chr5B 88.889 72 8 0 3302 3373 369262336 369262265 6.440000e-14 89.8
34 TraesCS1B01G311800 chr6D 92.000 125 10 0 4552 4676 380589042 380589166 4.810000e-40 176.0
35 TraesCS1B01G311800 chr5D 83.962 106 15 2 3269 3373 319145960 319145856 2.980000e-17 100.0
36 TraesCS1B01G311800 chr5A 82.075 106 17 2 3269 3373 415322180 415322284 6.440000e-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 TraesCS1B01G311800 chr1B 535383213 535387888 4675 True 8636.000000 8636 100.000000 1 4676 1 chr1B.!!$R2 4675
1 TraesCS1B01G311800 chr1B 535143262 535146016 2754 True 1626.000000 2300 88.913500 876 3676 2 chr1B.!!$R3 2800
2 TraesCS1B01G311800 chr1A 496042633 496047318 4685 True 2240.666667 6048 92.539667 1 4523 3 chr1A.!!$R2 4522
3 TraesCS1B01G311800 chr1A 495739734 495743873 4139 True 493.333333 865 86.671833 917 2331 6 chr1A.!!$R1 1414
4 TraesCS1B01G311800 chr1D 399187362 399192000 4638 True 1396.400000 4471 94.904200 3 4527 5 chr1D.!!$R3 4524
5 TraesCS1B01G311800 chr3A 589395006 589395573 567 False 529.000000 529 83.538000 3039 3606 1 chr3A.!!$F1 567
6 TraesCS1B01G311800 chr3D 447991603 447992170 567 False 507.000000 507 82.867000 3039 3606 1 chr3D.!!$F1 567
7 TraesCS1B01G311800 chr3B 587567787 587568373 586 False 492.000000 492 81.895000 3039 3625 1 chr3B.!!$F1 586

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
203 208 0.875908 CATGTCGATGGGTGGTAGCG 60.876 60.0 0.0 0.0 0.0 4.26 F
1398 1427 0.387239 GCAACAACTTGTCGGGCATC 60.387 55.0 0.0 0.0 0.0 3.91 F
2849 4332 1.093159 CATTCTGAGGGAGTTGCTGC 58.907 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1655 1.251251 CCAAGAAAGAACTGGCTGGG 58.749 55.000 0.00 0.0 0.0 4.45 R
3348 4835 1.227089 CTTCCCCGTCAGCATCTCG 60.227 63.158 0.00 0.0 0.0 4.04 R
4001 6564 0.174389 TTTGCACAAGAAAAGCGGCA 59.826 45.000 1.45 0.0 0.0 5.69 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
26 27 1.701292 CATGATCAGACCTGCCCCATA 59.299 52.381 0.09 0.00 0.00 2.74
62 67 1.275010 TCAGAGCTGCACCGATTAACA 59.725 47.619 1.02 0.00 0.00 2.41
79 84 3.840132 AACGGGGGTGGGGCTTTT 61.840 61.111 0.00 0.00 0.00 2.27
80 85 2.471563 AACGGGGGTGGGGCTTTTA 61.472 57.895 0.00 0.00 0.00 1.52
203 208 0.875908 CATGTCGATGGGTGGTAGCG 60.876 60.000 0.00 0.00 0.00 4.26
321 326 1.134848 TGGAAAGCTGTTGGTGTTTGC 60.135 47.619 0.00 0.00 0.00 3.68
461 466 2.092968 TGATTGATAGCCTGACACACCC 60.093 50.000 0.00 0.00 0.00 4.61
510 515 4.550076 AGACTCCTTTCTGGTCATCAAG 57.450 45.455 0.00 0.00 37.07 3.02
528 533 5.125100 TCAAGTTTGCTATTCTTTGGCAG 57.875 39.130 0.00 0.00 37.28 4.85
686 692 9.467258 CTACATTATTGGTCCTTTATTGCAATG 57.533 33.333 22.27 5.15 0.00 2.82
787 793 7.735917 TCATGAAGTAACTATCTACATTGGGG 58.264 38.462 0.00 0.00 0.00 4.96
954 982 2.306805 AGGAGTGAAGCATTGATGACCA 59.693 45.455 0.00 0.00 0.00 4.02
1332 1361 2.679837 TCGTCTTACTGTTAGCCTACCG 59.320 50.000 0.00 0.00 0.00 4.02
1398 1427 0.387239 GCAACAACTTGTCGGGCATC 60.387 55.000 0.00 0.00 0.00 3.91
1494 1523 7.762615 CCATTGAAAGTGCAAAATATGACTGAT 59.237 33.333 0.00 0.00 0.00 2.90
1536 1565 2.821991 ACAACTCTCTTTCTGGACCG 57.178 50.000 0.00 0.00 0.00 4.79
1863 1895 1.337260 TGCAAGAGAAAGAGAGACGGC 60.337 52.381 0.00 0.00 0.00 5.68
2276 3695 1.125711 ACACCGGGTAGCCTTTCAGT 61.126 55.000 6.32 0.00 0.00 3.41
2381 3804 6.877611 TTTGAAACTTATTCTGACCTGGTC 57.122 37.500 19.96 19.96 0.00 4.02
2519 3942 4.215399 TGCAATCTAAGTAAGTGTGCCAAC 59.785 41.667 0.00 0.00 36.10 3.77
2705 4131 3.382832 CTGCCTTCGACCCTCGGT 61.383 66.667 0.00 0.00 40.88 4.69
2713 4139 3.281240 GACCCTCGGTCGTAAGCA 58.719 61.111 0.00 0.00 43.14 3.91
2721 4147 1.134818 TCGGTCGTAAGCATGCTGAAT 60.135 47.619 23.48 8.48 37.18 2.57
2726 4152 5.504010 CGGTCGTAAGCATGCTGAATAAAAT 60.504 40.000 23.48 5.10 37.18 1.82
2727 4153 5.682862 GGTCGTAAGCATGCTGAATAAAATG 59.317 40.000 23.48 6.72 37.18 2.32
2748 4175 4.693283 TGAAAGATAGATTACGGCAGTGG 58.307 43.478 0.00 0.00 0.00 4.00
2750 4177 5.070446 TGAAAGATAGATTACGGCAGTGGAT 59.930 40.000 0.00 0.00 0.00 3.41
2776 4203 2.833794 TGTCAACAAGTTCCTTCCTCG 58.166 47.619 0.00 0.00 0.00 4.63
2849 4332 1.093159 CATTCTGAGGGAGTTGCTGC 58.907 55.000 0.00 0.00 0.00 5.25
2869 4352 6.535150 TGCTGCTGTAGTTTTGTAGCTATAAG 59.465 38.462 3.00 0.00 39.53 1.73
2936 4419 4.251268 GTGTAGAAAAGAATAGGTGCCGT 58.749 43.478 0.00 0.00 0.00 5.68
2957 4440 6.620089 GCCGTTTTTCTTCACCTGTATAGTTC 60.620 42.308 0.00 0.00 0.00 3.01
3025 4508 8.928448 AGTTACATGATCACATACTTACCATCT 58.072 33.333 0.00 0.00 35.09 2.90
3048 4535 2.364632 TGTGAACACACAGGGAACAAG 58.635 47.619 3.39 0.00 39.23 3.16
3061 4548 2.147150 GGAACAAGTCTGCTGGAAGAC 58.853 52.381 0.60 0.60 45.82 3.01
3302 4789 3.732849 GGTCCTGGGGGCCAAGAG 61.733 72.222 4.39 0.00 30.80 2.85
3348 4835 4.742201 TTCGGCGTGCTGCTCCTC 62.742 66.667 6.85 0.00 45.43 3.71
3360 4847 1.299014 GCTCCTCGAGATGCTGACG 60.299 63.158 15.71 0.00 0.00 4.35
3588 5639 0.259065 AGCAGGTCGTCAGGAGGATA 59.741 55.000 0.00 0.00 0.00 2.59
3840 6207 1.880675 CTGCTGATCGTATCGTAGGGT 59.119 52.381 0.00 0.00 0.00 4.34
3841 6208 1.607148 TGCTGATCGTATCGTAGGGTG 59.393 52.381 0.00 0.00 0.00 4.61
3842 6209 1.607628 GCTGATCGTATCGTAGGGTGT 59.392 52.381 0.00 0.00 0.00 4.16
3843 6210 2.034305 GCTGATCGTATCGTAGGGTGTT 59.966 50.000 0.00 0.00 0.00 3.32
3844 6211 3.629058 CTGATCGTATCGTAGGGTGTTG 58.371 50.000 0.00 0.00 0.00 3.33
3845 6212 3.018856 TGATCGTATCGTAGGGTGTTGT 58.981 45.455 0.00 0.00 0.00 3.32
3846 6213 3.065786 TGATCGTATCGTAGGGTGTTGTC 59.934 47.826 0.00 0.00 0.00 3.18
3914 6281 6.352516 AGAGAGTGGTTGATATTGATTCACC 58.647 40.000 0.00 0.00 0.00 4.02
3943 6310 1.059098 ATCTGGTCTGTCACTTGCCA 58.941 50.000 0.00 0.00 0.00 4.92
3944 6311 0.836606 TCTGGTCTGTCACTTGCCAA 59.163 50.000 0.00 0.00 0.00 4.52
3945 6312 1.202687 TCTGGTCTGTCACTTGCCAAG 60.203 52.381 2.11 2.11 0.00 3.61
3946 6313 0.179020 TGGTCTGTCACTTGCCAAGG 60.179 55.000 9.64 0.00 0.00 3.61
3947 6314 0.179018 GGTCTGTCACTTGCCAAGGT 60.179 55.000 9.64 0.00 0.00 3.50
3948 6315 1.680338 GTCTGTCACTTGCCAAGGTT 58.320 50.000 9.64 0.00 0.00 3.50
3949 6316 1.334869 GTCTGTCACTTGCCAAGGTTG 59.665 52.381 9.64 0.00 0.00 3.77
3951 6318 2.158623 TCTGTCACTTGCCAAGGTTGAT 60.159 45.455 9.64 0.00 0.00 2.57
3952 6319 3.072330 TCTGTCACTTGCCAAGGTTGATA 59.928 43.478 9.64 2.21 0.00 2.15
3954 6321 4.211125 TGTCACTTGCCAAGGTTGATAAA 58.789 39.130 9.64 0.00 0.00 1.40
3955 6322 4.037446 TGTCACTTGCCAAGGTTGATAAAC 59.963 41.667 9.64 0.00 0.00 2.01
3956 6323 4.037446 GTCACTTGCCAAGGTTGATAAACA 59.963 41.667 9.64 0.00 0.00 2.83
3957 6324 4.646945 TCACTTGCCAAGGTTGATAAACAA 59.353 37.500 9.64 0.00 36.02 2.83
3967 6334 1.240256 TGATAAACAACGTGGCCACC 58.760 50.000 29.95 12.86 0.00 4.61
3968 6335 0.524414 GATAAACAACGTGGCCACCC 59.476 55.000 29.95 6.81 0.00 4.61
3969 6336 0.111639 ATAAACAACGTGGCCACCCT 59.888 50.000 29.95 14.47 0.00 4.34
3970 6337 0.820074 TAAACAACGTGGCCACCCTG 60.820 55.000 29.95 26.44 0.00 4.45
3971 6338 2.559922 AAACAACGTGGCCACCCTGA 62.560 55.000 29.51 0.00 0.00 3.86
3973 6340 1.826054 CAACGTGGCCACCCTGAAA 60.826 57.895 29.95 0.00 0.00 2.69
3974 6341 1.076632 AACGTGGCCACCCTGAAAA 60.077 52.632 29.95 0.00 0.00 2.29
3975 6342 0.684805 AACGTGGCCACCCTGAAAAA 60.685 50.000 29.95 0.00 0.00 1.94
4012 6575 8.848474 AATACTATATAATGTGCCGCTTTTCT 57.152 30.769 0.00 0.00 0.00 2.52
4014 6577 6.959361 ACTATATAATGTGCCGCTTTTCTTG 58.041 36.000 0.00 0.00 0.00 3.02
4017 6580 0.318955 ATGTGCCGCTTTTCTTGTGC 60.319 50.000 0.00 0.00 0.00 4.57
4018 6581 1.065600 GTGCCGCTTTTCTTGTGCA 59.934 52.632 0.00 0.00 0.00 4.57
4020 6583 0.174389 TGCCGCTTTTCTTGTGCAAA 59.826 45.000 0.00 0.00 0.00 3.68
4021 6584 1.285578 GCCGCTTTTCTTGTGCAAAA 58.714 45.000 0.00 0.00 0.00 2.44
4022 6585 1.866601 GCCGCTTTTCTTGTGCAAAAT 59.133 42.857 0.00 0.00 0.00 1.82
4023 6586 3.056304 GCCGCTTTTCTTGTGCAAAATA 58.944 40.909 0.00 0.00 0.00 1.40
4025 6588 4.152223 GCCGCTTTTCTTGTGCAAAATAAT 59.848 37.500 0.00 0.00 0.00 1.28
4026 6589 5.334028 GCCGCTTTTCTTGTGCAAAATAATT 60.334 36.000 0.00 0.00 0.00 1.40
4027 6590 6.298853 CCGCTTTTCTTGTGCAAAATAATTC 58.701 36.000 0.00 0.00 0.00 2.17
4028 6591 6.002911 CGCTTTTCTTGTGCAAAATAATTCG 58.997 36.000 0.00 0.00 0.00 3.34
4029 6592 6.129221 CGCTTTTCTTGTGCAAAATAATTCGA 60.129 34.615 0.00 0.00 0.00 3.71
4030 6593 7.003648 GCTTTTCTTGTGCAAAATAATTCGAC 58.996 34.615 0.00 0.00 0.00 4.20
4031 6594 7.096065 GCTTTTCTTGTGCAAAATAATTCGACT 60.096 33.333 0.00 0.00 0.00 4.18
4032 6595 7.851822 TTTCTTGTGCAAAATAATTCGACTC 57.148 32.000 0.00 0.00 0.00 3.36
4034 6597 7.899178 TCTTGTGCAAAATAATTCGACTCTA 57.101 32.000 0.00 0.00 0.00 2.43
4035 6598 8.492673 TCTTGTGCAAAATAATTCGACTCTAT 57.507 30.769 0.00 0.00 0.00 1.98
4036 6599 8.390354 TCTTGTGCAAAATAATTCGACTCTATG 58.610 33.333 0.00 0.00 0.00 2.23
4037 6600 7.841915 TGTGCAAAATAATTCGACTCTATGA 57.158 32.000 0.00 0.00 0.00 2.15
4038 6601 8.437360 TGTGCAAAATAATTCGACTCTATGAT 57.563 30.769 0.00 0.00 0.00 2.45
4043 6606 9.591404 CAAAATAATTCGACTCTATGATTGCTC 57.409 33.333 0.00 0.00 0.00 4.26
4044 6607 7.573916 AATAATTCGACTCTATGATTGCTCG 57.426 36.000 0.00 0.00 0.00 5.03
4045 6608 4.576216 ATTCGACTCTATGATTGCTCGT 57.424 40.909 0.00 0.00 0.00 4.18
4046 6609 5.690997 ATTCGACTCTATGATTGCTCGTA 57.309 39.130 0.00 0.00 0.00 3.43
4049 6612 6.796705 TCGACTCTATGATTGCTCGTAATA 57.203 37.500 0.00 0.00 0.00 0.98
4050 6613 7.379098 TCGACTCTATGATTGCTCGTAATAT 57.621 36.000 0.00 0.00 0.00 1.28
4051 6614 8.488651 TCGACTCTATGATTGCTCGTAATATA 57.511 34.615 0.00 0.00 0.00 0.86
4053 6616 9.556030 CGACTCTATGATTGCTCGTAATATAAA 57.444 33.333 0.00 0.00 0.00 1.40
4084 6647 9.198837 GTTAATAGTTATCCAAAGAGAGCTAGC 57.801 37.037 6.62 6.62 31.66 3.42
4168 6731 7.962964 TTAGGCGATGGTTAAGATGAATAAG 57.037 36.000 0.00 0.00 0.00 1.73
4241 6842 7.526142 AAGAACTAAAATCTTCCCCTCAAAC 57.474 36.000 0.00 0.00 31.61 2.93
4245 6846 7.290110 ACTAAAATCTTCCCCTCAAACAAAG 57.710 36.000 0.00 0.00 0.00 2.77
4364 6972 5.659525 TGCTACTACTAACCCTGCTATTTCA 59.340 40.000 0.00 0.00 0.00 2.69
4402 7010 0.538746 TGACGGGTGCAGTCTGTAGA 60.539 55.000 0.93 0.00 39.24 2.59
4403 7011 0.171455 GACGGGTGCAGTCTGTAGAG 59.829 60.000 0.93 0.00 35.84 2.43
4413 7022 2.492484 CAGTCTGTAGAGGTTAAGCCGT 59.508 50.000 0.00 0.00 43.70 5.68
4458 7067 5.674525 TCAATCAAAATCGCTATCAGGAGT 58.325 37.500 0.00 0.00 0.00 3.85
4534 7143 8.581253 AGGGAATTTGTTTAATCACTAGAAGG 57.419 34.615 0.00 0.00 0.00 3.46
4535 7144 7.615757 AGGGAATTTGTTTAATCACTAGAAGGG 59.384 37.037 0.00 0.00 0.00 3.95
4536 7145 7.396339 GGGAATTTGTTTAATCACTAGAAGGGT 59.604 37.037 0.00 0.00 0.00 4.34
4537 7146 8.803235 GGAATTTGTTTAATCACTAGAAGGGTT 58.197 33.333 0.00 0.00 0.00 4.11
4540 7149 8.857694 TTTGTTTAATCACTAGAAGGGTTAGG 57.142 34.615 0.00 0.00 0.00 2.69
4541 7150 7.563724 TGTTTAATCACTAGAAGGGTTAGGT 57.436 36.000 0.00 0.00 0.00 3.08
4542 7151 7.391620 TGTTTAATCACTAGAAGGGTTAGGTG 58.608 38.462 0.00 0.00 0.00 4.00
4543 7152 4.489306 AATCACTAGAAGGGTTAGGTGC 57.511 45.455 0.00 0.00 0.00 5.01
4544 7153 1.822990 TCACTAGAAGGGTTAGGTGCG 59.177 52.381 0.00 0.00 0.00 5.34
4545 7154 0.535797 ACTAGAAGGGTTAGGTGCGC 59.464 55.000 0.00 0.00 0.00 6.09
4546 7155 0.824759 CTAGAAGGGTTAGGTGCGCT 59.175 55.000 9.73 0.00 0.00 5.92
4547 7156 1.207329 CTAGAAGGGTTAGGTGCGCTT 59.793 52.381 9.73 0.00 40.94 4.68
4548 7157 0.400594 AGAAGGGTTAGGTGCGCTTT 59.599 50.000 9.73 0.00 38.86 3.51
4549 7158 1.202891 AGAAGGGTTAGGTGCGCTTTT 60.203 47.619 9.73 0.00 38.86 2.27
4550 7159 1.199327 GAAGGGTTAGGTGCGCTTTTC 59.801 52.381 9.73 0.00 38.86 2.29
4551 7160 0.400594 AGGGTTAGGTGCGCTTTTCT 59.599 50.000 9.73 3.24 0.00 2.52
4552 7161 1.626825 AGGGTTAGGTGCGCTTTTCTA 59.373 47.619 9.73 2.20 0.00 2.10
4553 7162 2.238898 AGGGTTAGGTGCGCTTTTCTAT 59.761 45.455 9.73 0.00 0.00 1.98
4554 7163 3.453353 AGGGTTAGGTGCGCTTTTCTATA 59.547 43.478 9.73 0.00 0.00 1.31
4555 7164 4.080751 AGGGTTAGGTGCGCTTTTCTATAA 60.081 41.667 9.73 0.00 0.00 0.98
4556 7165 4.637091 GGGTTAGGTGCGCTTTTCTATAAA 59.363 41.667 9.73 0.00 0.00 1.40
4557 7166 5.220796 GGGTTAGGTGCGCTTTTCTATAAAG 60.221 44.000 9.73 0.00 0.00 1.85
4558 7167 5.583457 GGTTAGGTGCGCTTTTCTATAAAGA 59.417 40.000 9.73 0.00 0.00 2.52
4559 7168 6.093082 GGTTAGGTGCGCTTTTCTATAAAGAA 59.907 38.462 9.73 0.00 40.03 2.52
4651 7260 8.526667 TTTTGATTTAATATTGGGGATGTCGA 57.473 30.769 0.00 0.00 0.00 4.20
4652 7261 8.704849 TTTGATTTAATATTGGGGATGTCGAT 57.295 30.769 0.00 0.00 0.00 3.59
4653 7262 9.800572 TTTGATTTAATATTGGGGATGTCGATA 57.199 29.630 0.00 0.00 0.00 2.92
4654 7263 9.973661 TTGATTTAATATTGGGGATGTCGATAT 57.026 29.630 0.00 0.00 0.00 1.63
4655 7264 9.973661 TGATTTAATATTGGGGATGTCGATATT 57.026 29.630 0.00 0.00 36.06 1.28
4660 7269 5.789643 ATTGGGGATGTCGATATTTTTGG 57.210 39.130 0.00 0.00 0.00 3.28
4661 7270 2.955660 TGGGGATGTCGATATTTTTGGC 59.044 45.455 0.00 0.00 0.00 4.52
4662 7271 3.222603 GGGGATGTCGATATTTTTGGCT 58.777 45.455 0.00 0.00 0.00 4.75
4663 7272 3.636764 GGGGATGTCGATATTTTTGGCTT 59.363 43.478 0.00 0.00 0.00 4.35
4664 7273 4.099419 GGGGATGTCGATATTTTTGGCTTT 59.901 41.667 0.00 0.00 0.00 3.51
4665 7274 5.300792 GGGGATGTCGATATTTTTGGCTTTA 59.699 40.000 0.00 0.00 0.00 1.85
4666 7275 6.183360 GGGGATGTCGATATTTTTGGCTTTAA 60.183 38.462 0.00 0.00 0.00 1.52
4667 7276 7.262048 GGGATGTCGATATTTTTGGCTTTAAA 58.738 34.615 0.00 0.00 0.00 1.52
4668 7277 7.222031 GGGATGTCGATATTTTTGGCTTTAAAC 59.778 37.037 0.00 0.00 0.00 2.01
4669 7278 7.973944 GGATGTCGATATTTTTGGCTTTAAACT 59.026 33.333 0.00 0.00 0.00 2.66
4670 7279 9.353999 GATGTCGATATTTTTGGCTTTAAACTT 57.646 29.630 0.00 0.00 0.00 2.66
4671 7280 8.514136 TGTCGATATTTTTGGCTTTAAACTTG 57.486 30.769 0.00 0.00 0.00 3.16
4672 7281 7.596995 TGTCGATATTTTTGGCTTTAAACTTGG 59.403 33.333 0.00 0.00 0.00 3.61
4673 7282 7.597369 GTCGATATTTTTGGCTTTAAACTTGGT 59.403 33.333 0.00 0.00 0.00 3.67
4674 7283 7.810759 TCGATATTTTTGGCTTTAAACTTGGTC 59.189 33.333 0.00 0.00 0.00 4.02
4675 7284 7.596995 CGATATTTTTGGCTTTAAACTTGGTCA 59.403 33.333 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.027792 CCACCCCCGTTGTTAATCGG 61.028 60.000 8.90 8.90 45.42 4.18
54 55 1.027792 CCCACCCCCGTTGTTAATCG 61.028 60.000 0.00 0.00 0.00 3.34
62 67 2.021318 TTAAAAGCCCCACCCCCGTT 62.021 55.000 0.00 0.00 0.00 4.44
80 85 8.990163 TTGTCTTTCCTTTAGACTAACCAATT 57.010 30.769 0.00 0.00 41.99 2.32
203 208 6.259829 ACAAACCCATAACAAAATGACAAAGC 59.740 34.615 0.00 0.00 0.00 3.51
277 282 4.925068 GCTTTGCGTCATAATTGATCCTT 58.075 39.130 0.00 0.00 33.56 3.36
321 326 5.008619 AGATACAGCATCTCTCAGTGTTG 57.991 43.478 0.00 0.00 40.09 3.33
335 340 4.591072 AGATCCAAGGAACCTAGATACAGC 59.409 45.833 0.00 0.00 0.00 4.40
461 466 8.722480 TGTGAGATTAATAGGATTTGACACAG 57.278 34.615 0.00 0.00 0.00 3.66
510 515 3.367395 GGTCCTGCCAAAGAATAGCAAAC 60.367 47.826 0.00 0.00 35.79 2.93
528 533 8.697507 AAAATGTAATATCAGATTCCTGGTCC 57.302 34.615 0.00 0.00 40.76 4.46
560 565 1.144708 TGTTTGCAATCCTGGGTCTGA 59.855 47.619 0.00 0.00 0.00 3.27
954 982 9.277783 CAAGGAGAACAAGAATTATAATCCGAT 57.722 33.333 0.00 0.00 0.00 4.18
1332 1361 2.157738 GGAATGGATGCTACATCAGGC 58.842 52.381 9.60 0.00 0.00 4.85
1398 1427 5.598416 TTGAGGACAGTGATGTAGGTATG 57.402 43.478 0.00 0.00 0.00 2.39
1494 1523 3.165875 CTGGAGAGACAACCCAGTAAGA 58.834 50.000 0.00 0.00 41.81 2.10
1536 1565 1.696884 GGGAGGTGAAGATCAGGGATC 59.303 57.143 0.00 0.00 39.17 3.36
1626 1655 1.251251 CCAAGAAAGAACTGGCTGGG 58.749 55.000 0.00 0.00 0.00 4.45
2368 3791 4.288105 AGTGATGAAAGACCAGGTCAGAAT 59.712 41.667 22.31 9.31 34.60 2.40
2371 3794 3.692257 AGTGATGAAAGACCAGGTCAG 57.308 47.619 22.31 0.00 34.60 3.51
2381 3804 9.429359 ACTTGTCATCTAAGTAAGTGATGAAAG 57.571 33.333 6.48 12.61 45.17 2.62
2409 3832 6.865205 GGCAATTTCTACCATAGAATTGCATC 59.135 38.462 25.86 16.49 46.52 3.91
2484 3907 9.683069 CTTACTTAGATTGCATTGAACAAACTT 57.317 29.630 0.00 0.00 33.00 2.66
2538 3961 2.743636 TAAAGGCGACCTCAGTTCTG 57.256 50.000 0.00 0.00 30.89 3.02
2705 4131 6.676237 TCATTTTATTCAGCATGCTTACGA 57.324 33.333 19.98 10.07 34.76 3.43
2711 4137 9.909644 ATCTATCTTTCATTTTATTCAGCATGC 57.090 29.630 10.51 10.51 34.76 4.06
2721 4147 8.826710 CACTGCCGTAATCTATCTTTCATTTTA 58.173 33.333 0.00 0.00 0.00 1.52
2726 4152 4.404394 TCCACTGCCGTAATCTATCTTTCA 59.596 41.667 0.00 0.00 0.00 2.69
2727 4153 4.945246 TCCACTGCCGTAATCTATCTTTC 58.055 43.478 0.00 0.00 0.00 2.62
2748 4175 3.755378 AGGAACTTGTTGACATCAGCATC 59.245 43.478 0.00 0.00 36.96 3.91
2750 4177 3.213206 AGGAACTTGTTGACATCAGCA 57.787 42.857 0.00 0.00 27.25 4.41
2809 4292 9.075678 AGAATGTTCATCAGAAGTTCAGAAAAT 57.924 29.630 5.50 2.13 34.47 1.82
2819 4302 5.095145 TCCCTCAGAATGTTCATCAGAAG 57.905 43.478 0.00 0.00 37.40 2.85
2936 4419 8.836413 CAAGTGAACTATACAGGTGAAGAAAAA 58.164 33.333 0.00 0.00 0.00 1.94
2957 4440 4.754618 TGTGGTAGTACAAAGATGCAAGTG 59.245 41.667 2.06 0.00 0.00 3.16
2991 4474 4.163552 TGTGATCATGTAACTTCGTCGTC 58.836 43.478 0.00 0.00 0.00 4.20
3061 4548 1.536418 TCTCCCAGTCCAGTGGTGG 60.536 63.158 9.54 10.50 46.63 4.61
3348 4835 1.227089 CTTCCCCGTCAGCATCTCG 60.227 63.158 0.00 0.00 0.00 4.04
3588 5639 1.152830 GGAGCTCCGGATCTCCTCT 59.847 63.158 36.50 14.65 44.19 3.69
3840 6207 2.080693 GTCACACCACAACAGACAACA 58.919 47.619 0.00 0.00 0.00 3.33
3841 6208 2.351726 GAGTCACACCACAACAGACAAC 59.648 50.000 0.00 0.00 0.00 3.32
3842 6209 2.236146 AGAGTCACACCACAACAGACAA 59.764 45.455 0.00 0.00 0.00 3.18
3843 6210 1.831106 AGAGTCACACCACAACAGACA 59.169 47.619 0.00 0.00 0.00 3.41
3844 6211 2.604046 AGAGTCACACCACAACAGAC 57.396 50.000 0.00 0.00 0.00 3.51
3845 6212 3.627395 AAAGAGTCACACCACAACAGA 57.373 42.857 0.00 0.00 0.00 3.41
3846 6213 4.693283 TCTAAAGAGTCACACCACAACAG 58.307 43.478 0.00 0.00 0.00 3.16
3895 6262 5.811399 TTCGGTGAATCAATATCAACCAC 57.189 39.130 0.00 0.00 30.56 4.16
3914 6281 2.606725 GACAGACCAGATTGCTCATTCG 59.393 50.000 0.00 0.00 0.00 3.34
3947 6314 1.609555 GGTGGCCACGTTGTTTATCAA 59.390 47.619 29.08 0.00 0.00 2.57
3948 6315 1.240256 GGTGGCCACGTTGTTTATCA 58.760 50.000 29.08 0.00 0.00 2.15
3949 6316 0.524414 GGGTGGCCACGTTGTTTATC 59.476 55.000 29.08 11.87 0.00 1.75
3951 6318 0.820074 CAGGGTGGCCACGTTGTTTA 60.820 55.000 29.08 0.00 0.00 2.01
3952 6319 2.124693 CAGGGTGGCCACGTTGTTT 61.125 57.895 29.08 8.08 0.00 2.83
3954 6321 2.559922 TTTCAGGGTGGCCACGTTGT 62.560 55.000 29.08 10.80 0.00 3.32
3955 6322 1.388065 TTTTCAGGGTGGCCACGTTG 61.388 55.000 29.08 26.55 0.00 4.10
3956 6323 0.684805 TTTTTCAGGGTGGCCACGTT 60.685 50.000 29.08 16.94 0.00 3.99
3957 6324 1.076632 TTTTTCAGGGTGGCCACGT 60.077 52.632 29.08 16.55 0.00 4.49
3994 6557 4.674101 GCACAAGAAAAGCGGCACATTATA 60.674 41.667 1.45 0.00 0.00 0.98
3996 6559 2.606795 GCACAAGAAAAGCGGCACATTA 60.607 45.455 1.45 0.00 0.00 1.90
3997 6560 1.869342 GCACAAGAAAAGCGGCACATT 60.869 47.619 1.45 0.00 0.00 2.71
3998 6561 0.318955 GCACAAGAAAAGCGGCACAT 60.319 50.000 1.45 0.00 0.00 3.21
4000 6563 0.527385 TTGCACAAGAAAAGCGGCAC 60.527 50.000 1.45 0.00 0.00 5.01
4001 6564 0.174389 TTTGCACAAGAAAAGCGGCA 59.826 45.000 1.45 0.00 0.00 5.69
4002 6565 1.285578 TTTTGCACAAGAAAAGCGGC 58.714 45.000 0.00 0.00 0.00 6.53
4003 6566 5.844301 ATTATTTTGCACAAGAAAAGCGG 57.156 34.783 0.00 0.00 0.00 5.52
4004 6567 6.002911 CGAATTATTTTGCACAAGAAAAGCG 58.997 36.000 0.00 0.00 0.00 4.68
4005 6568 7.003648 GTCGAATTATTTTGCACAAGAAAAGC 58.996 34.615 0.00 0.00 0.00 3.51
4006 6569 8.285776 AGTCGAATTATTTTGCACAAGAAAAG 57.714 30.769 0.00 0.00 0.00 2.27
4008 6571 7.648142 AGAGTCGAATTATTTTGCACAAGAAA 58.352 30.769 0.00 0.00 0.00 2.52
4010 6573 6.801539 AGAGTCGAATTATTTTGCACAAGA 57.198 33.333 0.00 0.00 0.00 3.02
4011 6574 8.390354 TCATAGAGTCGAATTATTTTGCACAAG 58.610 33.333 0.00 0.00 0.00 3.16
4012 6575 8.262715 TCATAGAGTCGAATTATTTTGCACAA 57.737 30.769 0.00 0.00 0.00 3.33
4014 6577 9.162793 CAATCATAGAGTCGAATTATTTTGCAC 57.837 33.333 0.00 0.00 0.00 4.57
4017 6580 9.591404 GAGCAATCATAGAGTCGAATTATTTTG 57.409 33.333 0.00 0.00 0.00 2.44
4018 6581 8.491152 CGAGCAATCATAGAGTCGAATTATTTT 58.509 33.333 0.00 0.00 0.00 1.82
4020 6583 7.148641 ACGAGCAATCATAGAGTCGAATTATT 58.851 34.615 0.00 0.00 0.00 1.40
4021 6584 6.682746 ACGAGCAATCATAGAGTCGAATTAT 58.317 36.000 0.00 0.00 0.00 1.28
4022 6585 6.073327 ACGAGCAATCATAGAGTCGAATTA 57.927 37.500 0.00 0.00 0.00 1.40
4023 6586 4.938080 ACGAGCAATCATAGAGTCGAATT 58.062 39.130 0.00 0.00 0.00 2.17
4025 6588 5.494632 TTACGAGCAATCATAGAGTCGAA 57.505 39.130 0.00 0.00 0.00 3.71
4026 6589 5.690997 ATTACGAGCAATCATAGAGTCGA 57.309 39.130 0.00 0.00 0.00 4.20
4027 6590 9.556030 TTTATATTACGAGCAATCATAGAGTCG 57.444 33.333 0.00 0.00 0.00 4.18
4059 6622 8.368668 GGCTAGCTCTCTTTGGATAACTATTAA 58.631 37.037 15.72 0.00 0.00 1.40
4060 6623 7.509318 TGGCTAGCTCTCTTTGGATAACTATTA 59.491 37.037 15.72 0.00 0.00 0.98
4061 6624 6.327626 TGGCTAGCTCTCTTTGGATAACTATT 59.672 38.462 15.72 0.00 0.00 1.73
4062 6625 5.841237 TGGCTAGCTCTCTTTGGATAACTAT 59.159 40.000 15.72 0.00 0.00 2.12
4063 6626 5.208890 TGGCTAGCTCTCTTTGGATAACTA 58.791 41.667 15.72 0.00 0.00 2.24
4064 6627 4.033709 TGGCTAGCTCTCTTTGGATAACT 58.966 43.478 15.72 0.00 0.00 2.24
4065 6628 4.376146 CTGGCTAGCTCTCTTTGGATAAC 58.624 47.826 15.72 0.00 0.00 1.89
4066 6629 3.181461 GCTGGCTAGCTCTCTTTGGATAA 60.181 47.826 15.78 0.00 46.57 1.75
4067 6630 2.366916 GCTGGCTAGCTCTCTTTGGATA 59.633 50.000 15.78 0.00 46.57 2.59
4068 6631 1.140652 GCTGGCTAGCTCTCTTTGGAT 59.859 52.381 15.78 0.00 46.57 3.41
4079 6642 5.474876 ATTGAACCAATATTAGCTGGCTAGC 59.525 40.000 15.23 15.23 40.12 3.42
4083 6646 5.284079 CACATTGAACCAATATTAGCTGGC 58.716 41.667 0.00 0.00 36.03 4.85
4084 6647 5.593909 TCCACATTGAACCAATATTAGCTGG 59.406 40.000 0.00 0.00 38.77 4.85
4090 6653 9.199645 TGTGATAATCCACATTGAACCAATATT 57.800 29.630 0.00 0.00 41.63 1.28
4168 6731 9.262472 CAATCGCTAAACAAACACTATAAAGAC 57.738 33.333 0.00 0.00 0.00 3.01
4364 6972 6.349611 CCCGTCAATTCTTCAATCAGAACAAT 60.350 38.462 0.00 0.00 35.57 2.71
4402 7010 3.116531 GCGCGAACGGCTTAACCT 61.117 61.111 12.10 0.00 40.44 3.50
4527 7136 0.824759 AGCGCACCTAACCCTTCTAG 59.175 55.000 11.47 0.00 0.00 2.43
4528 7137 1.272807 AAGCGCACCTAACCCTTCTA 58.727 50.000 11.47 0.00 0.00 2.10
4529 7138 0.400594 AAAGCGCACCTAACCCTTCT 59.599 50.000 11.47 0.00 0.00 2.85
4530 7139 1.199327 GAAAAGCGCACCTAACCCTTC 59.801 52.381 11.47 0.00 0.00 3.46
4531 7140 1.202891 AGAAAAGCGCACCTAACCCTT 60.203 47.619 11.47 0.00 0.00 3.95
4532 7141 0.400594 AGAAAAGCGCACCTAACCCT 59.599 50.000 11.47 0.00 0.00 4.34
4533 7142 2.103537 TAGAAAAGCGCACCTAACCC 57.896 50.000 11.47 0.00 0.00 4.11
4534 7143 5.583457 TCTTTATAGAAAAGCGCACCTAACC 59.417 40.000 11.47 0.00 0.00 2.85
4535 7144 6.657836 TCTTTATAGAAAAGCGCACCTAAC 57.342 37.500 11.47 0.00 0.00 2.34
4536 7145 7.675962 TTTCTTTATAGAAAAGCGCACCTAA 57.324 32.000 11.47 0.00 45.08 2.69
4625 7234 8.972127 TCGACATCCCCAATATTAAATCAAAAA 58.028 29.630 0.00 0.00 0.00 1.94
4626 7235 8.526667 TCGACATCCCCAATATTAAATCAAAA 57.473 30.769 0.00 0.00 0.00 2.44
4627 7236 8.704849 ATCGACATCCCCAATATTAAATCAAA 57.295 30.769 0.00 0.00 0.00 2.69
4628 7237 9.973661 ATATCGACATCCCCAATATTAAATCAA 57.026 29.630 0.00 0.00 0.00 2.57
4629 7238 9.973661 AATATCGACATCCCCAATATTAAATCA 57.026 29.630 0.00 0.00 0.00 2.57
4634 7243 9.019656 CCAAAAATATCGACATCCCCAATATTA 57.980 33.333 0.00 0.00 0.00 0.98
4635 7244 7.525360 GCCAAAAATATCGACATCCCCAATATT 60.525 37.037 0.00 0.00 0.00 1.28
4636 7245 6.071391 GCCAAAAATATCGACATCCCCAATAT 60.071 38.462 0.00 0.00 0.00 1.28
4637 7246 5.242838 GCCAAAAATATCGACATCCCCAATA 59.757 40.000 0.00 0.00 0.00 1.90
4638 7247 4.039124 GCCAAAAATATCGACATCCCCAAT 59.961 41.667 0.00 0.00 0.00 3.16
4639 7248 3.383185 GCCAAAAATATCGACATCCCCAA 59.617 43.478 0.00 0.00 0.00 4.12
4640 7249 2.955660 GCCAAAAATATCGACATCCCCA 59.044 45.455 0.00 0.00 0.00 4.96
4641 7250 3.222603 AGCCAAAAATATCGACATCCCC 58.777 45.455 0.00 0.00 0.00 4.81
4642 7251 4.918810 AAGCCAAAAATATCGACATCCC 57.081 40.909 0.00 0.00 0.00 3.85
4643 7252 7.973944 AGTTTAAAGCCAAAAATATCGACATCC 59.026 33.333 0.00 0.00 0.00 3.51
4644 7253 8.911247 AGTTTAAAGCCAAAAATATCGACATC 57.089 30.769 0.00 0.00 0.00 3.06
4645 7254 9.139174 CAAGTTTAAAGCCAAAAATATCGACAT 57.861 29.630 0.00 0.00 0.00 3.06
4646 7255 7.596995 CCAAGTTTAAAGCCAAAAATATCGACA 59.403 33.333 0.00 0.00 0.00 4.35
4647 7256 7.597369 ACCAAGTTTAAAGCCAAAAATATCGAC 59.403 33.333 0.00 0.00 0.00 4.20
4648 7257 7.662897 ACCAAGTTTAAAGCCAAAAATATCGA 58.337 30.769 0.00 0.00 0.00 3.59
4649 7258 7.596995 TGACCAAGTTTAAAGCCAAAAATATCG 59.403 33.333 0.00 0.00 0.00 2.92
4650 7259 8.825667 TGACCAAGTTTAAAGCCAAAAATATC 57.174 30.769 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.