Multiple sequence alignment - TraesCS3D01G399900

Loading Multiple Alignment...

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 TraesCS3D01G399900 chr3D 100.000 4706 0 0 1 4706 514918949 514923654 0.000000e+00 8691.0
1 TraesCS3D01G399900 chr3D 86.207 58 8 0 3996 4053 590764958 590765015 3.930000e-06 63.9
2 TraesCS3D01G399900 chr3D 87.755 49 6 0 4005 4053 363248079 363248127 1.830000e-04 58.4
3 TraesCS3D01G399900 chr3B 95.381 3659 123 18 347 3992 677312858 677316483 0.000000e+00 5779.0
4 TraesCS3D01G399900 chr3B 91.197 284 12 7 4423 4706 677316710 677316980 1.600000e-99 374.0
5 TraesCS3D01G399900 chr3B 84.132 334 30 12 16 328 677312018 677312349 7.650000e-78 302.0
6 TraesCS3D01G399900 chr3B 84.127 63 7 2 3987 4049 819562086 819562145 1.830000e-04 58.4
7 TraesCS3D01G399900 chr3A 94.730 3207 145 10 690 3882 649605484 649608680 0.000000e+00 4964.0
8 TraesCS3D01G399900 chr3A 94.234 555 28 4 3880 4433 649612431 649612982 0.000000e+00 845.0
9 TraesCS3D01G399900 chr3A 94.505 182 10 0 1 182 649605303 649605484 9.970000e-72 281.0
10 TraesCS3D01G399900 chr3A 96.667 90 2 1 4525 4614 649613172 649613260 1.060000e-31 148.0
11 TraesCS3D01G399900 chr3A 100.000 38 0 0 4421 4458 649613025 649613062 2.350000e-08 71.3
12 TraesCS3D01G399900 chr3A 95.455 44 2 0 4498 4541 649613067 649613110 2.350000e-08 71.3
13 TraesCS3D01G399900 chr4A 87.500 80 9 1 204 283 733427492 733427570 1.800000e-14 91.6
14 TraesCS3D01G399900 chr4A 91.667 48 2 2 4005 4051 742428789 742428743 1.090000e-06 65.8
15 TraesCS3D01G399900 chr6A 87.143 70 5 3 212 278 383479455 383479387 5.050000e-10 76.8
16 TraesCS3D01G399900 chr7D 87.879 66 4 3 207 269 71314541 71314477 1.820000e-09 75.0
17 TraesCS3D01G399900 chr2D 97.619 42 1 0 238 279 348190593 348190634 6.530000e-09 73.1
18 TraesCS3D01G399900 chr7B 88.679 53 3 3 4000 4051 585577105 585577155 1.410000e-05 62.1
19 TraesCS3D01G399900 chr7B 85.455 55 7 1 3995 4049 451093741 451093688 6.580000e-04 56.5
20 TraesCS3D01G399900 chr2A 84.127 63 8 2 3991 4053 763278448 763278388 5.090000e-05 60.2
21 TraesCS3D01G399900 chr5B 84.127 63 7 2 3992 4053 283018432 283018372 1.830000e-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 TraesCS3D01G399900 chr3D 514918949 514923654 4705 False 8691.000000 8691 100.000000 1 4706 1 chr3D.!!$F2 4705
1 TraesCS3D01G399900 chr3B 677312018 677316980 4962 False 2151.666667 5779 90.236667 16 4706 3 chr3B.!!$F2 4690
2 TraesCS3D01G399900 chr3A 649605303 649613260 7957 False 1063.433333 4964 95.931833 1 4614 6 chr3A.!!$F1 4613

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
240 241 1.668751 TGTGAGACGTTTTGGCAGTTC 59.331 47.619 0.0 0.0 0.00 3.01 F
2008 2531 1.000955 GGTGTCTGCGGGTCCATATAG 59.999 57.143 0.0 0.0 0.00 1.31 F
2412 2935 0.453793 CTACCTGCCTCGACAGTGAG 59.546 60.000 0.0 0.0 35.83 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2603 0.029700 TTCGTCGTCTTTCGCTGACA 59.970 50.0 0.00 0.00 39.67 3.58 R
3064 3587 0.169672 CTTTTCCGCATGCTCCACAG 59.830 55.0 17.13 2.41 0.00 3.66 R
3841 4367 0.179094 AACCGAGTCTTGCAACACGA 60.179 50.0 9.52 0.00 35.62 4.35 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
97 98 1.882623 CAGGTGCTTCAGTTTTCCTCC 59.117 52.381 0.00 0.00 0.00 4.30
102 103 1.946283 GCTTCAGTTTTCCTCCCCGAG 60.946 57.143 0.00 0.00 0.00 4.63
120 121 2.360801 CGAGATCCTTTCCCTGAGACTC 59.639 54.545 0.00 0.00 0.00 3.36
160 161 2.514803 ACGCAGGCCCATATATTTTCC 58.485 47.619 0.00 0.00 0.00 3.13
203 204 4.995124 AGAGTGCTGAAATTTGCATCATC 58.005 39.130 6.49 6.05 41.45 2.92
206 207 3.615496 GTGCTGAAATTTGCATCATCCAC 59.385 43.478 6.49 0.00 41.45 4.02
207 208 3.192466 GCTGAAATTTGCATCATCCACC 58.808 45.455 0.00 0.00 0.00 4.61
208 209 3.118884 GCTGAAATTTGCATCATCCACCT 60.119 43.478 0.00 0.00 0.00 4.00
209 210 4.679662 CTGAAATTTGCATCATCCACCTC 58.320 43.478 0.00 0.00 0.00 3.85
210 211 4.346730 TGAAATTTGCATCATCCACCTCT 58.653 39.130 0.00 0.00 0.00 3.69
211 212 4.158949 TGAAATTTGCATCATCCACCTCTG 59.841 41.667 0.00 0.00 0.00 3.35
213 214 2.885135 TTGCATCATCCACCTCTGTT 57.115 45.000 0.00 0.00 0.00 3.16
216 217 2.012673 GCATCATCCACCTCTGTTCAC 58.987 52.381 0.00 0.00 0.00 3.18
218 219 3.118629 GCATCATCCACCTCTGTTCACTA 60.119 47.826 0.00 0.00 0.00 2.74
219 220 4.623886 GCATCATCCACCTCTGTTCACTAA 60.624 45.833 0.00 0.00 0.00 2.24
220 221 5.678583 CATCATCCACCTCTGTTCACTAAT 58.321 41.667 0.00 0.00 0.00 1.73
222 223 4.532126 TCATCCACCTCTGTTCACTAATGT 59.468 41.667 0.00 0.00 0.00 2.71
223 224 4.271696 TCCACCTCTGTTCACTAATGTG 57.728 45.455 0.00 0.00 45.07 3.21
235 236 3.810373 CACTAATGTGAGACGTTTTGGC 58.190 45.455 0.00 0.00 46.55 4.52
236 237 3.249799 CACTAATGTGAGACGTTTTGGCA 59.750 43.478 0.00 0.00 46.55 4.92
237 238 3.498397 ACTAATGTGAGACGTTTTGGCAG 59.502 43.478 0.00 0.00 0.00 4.85
238 239 1.967319 ATGTGAGACGTTTTGGCAGT 58.033 45.000 0.00 0.00 0.00 4.40
239 240 1.745232 TGTGAGACGTTTTGGCAGTT 58.255 45.000 0.00 0.00 0.00 3.16
240 241 1.668751 TGTGAGACGTTTTGGCAGTTC 59.331 47.619 0.00 0.00 0.00 3.01
242 243 2.290641 GTGAGACGTTTTGGCAGTTCAT 59.709 45.455 0.00 0.00 0.00 2.57
259 279 3.347958 TCATTGAACTGCCAAAACGTC 57.652 42.857 0.00 0.00 0.00 4.34
266 286 7.908827 TTGAACTGCCAAAACGTCTTATATA 57.091 32.000 0.00 0.00 0.00 0.86
275 295 8.709646 GCCAAAACGTCTTATATATAGGAACAG 58.290 37.037 6.16 4.51 0.00 3.16
280 300 7.468496 ACGTCTTATATATAGGAACAGAGGGT 58.532 38.462 6.16 0.00 0.00 4.34
282 302 7.393796 CGTCTTATATATAGGAACAGAGGGTGT 59.606 40.741 6.16 0.00 43.24 4.16
290 310 2.417719 GAACAGAGGGTGTACTTGCAG 58.582 52.381 0.00 0.00 39.03 4.41
316 336 4.580167 GGCAGCATATGTGAAACTATGGAA 59.420 41.667 4.29 0.00 38.04 3.53
328 348 7.450014 TGTGAAACTATGGAATTAGGCTTGAAA 59.550 33.333 0.00 0.00 38.04 2.69
331 351 9.875691 GAAACTATGGAATTAGGCTTGAAAAAT 57.124 29.630 0.00 0.00 0.00 1.82
333 353 8.593945 ACTATGGAATTAGGCTTGAAAAATGA 57.406 30.769 0.00 0.00 0.00 2.57
338 358 9.874205 TGGAATTAGGCTTGAAAAATGAATTAG 57.126 29.630 0.00 0.00 0.00 1.73
341 361 5.743636 AGGCTTGAAAAATGAATTAGGCA 57.256 34.783 0.00 0.00 0.00 4.75
342 362 5.727434 AGGCTTGAAAAATGAATTAGGCAG 58.273 37.500 0.00 0.00 0.00 4.85
343 363 4.330894 GGCTTGAAAAATGAATTAGGCAGC 59.669 41.667 0.00 0.00 0.00 5.25
344 364 4.931002 GCTTGAAAAATGAATTAGGCAGCA 59.069 37.500 0.00 0.00 0.00 4.41
346 366 6.757947 GCTTGAAAAATGAATTAGGCAGCATA 59.242 34.615 0.00 0.00 0.00 3.14
347 367 7.440255 GCTTGAAAAATGAATTAGGCAGCATAT 59.560 33.333 0.00 0.00 0.00 1.78
348 368 8.651391 TTGAAAAATGAATTAGGCAGCATATG 57.349 30.769 0.00 0.00 0.00 1.78
382 893 7.611855 CAGATTAAAGGGGTGAAGTAATCAACT 59.388 37.037 0.00 0.00 45.60 3.16
436 947 9.492973 CTTTTGGGTTCTGTATTCAAAATTGAT 57.507 29.630 0.00 0.00 36.92 2.57
465 977 9.787435 TTCAACTTACTGTAATAAAGTGATGGT 57.213 29.630 0.00 0.00 33.85 3.55
544 1056 9.974980 TTTAAAGAGGCAAACCATTTACTTAAG 57.025 29.630 0.00 0.00 39.06 1.85
566 1078 7.809880 AAGGTTTAAGAGTAACTGGTCCTAT 57.190 36.000 0.00 0.00 0.00 2.57
644 1156 3.752747 CAGGGTGCATTGAAATTTTTCCC 59.247 43.478 0.00 0.00 36.36 3.97
667 1179 8.228206 TCCCAAGTATGAATACTCTGATCTAGT 58.772 37.037 3.51 6.54 42.47 2.57
770 1284 9.988815 ATCCAGATATACATTGTGAGAACTTAC 57.011 33.333 0.00 0.00 0.00 2.34
904 1421 5.596836 TTGCTGTGTCTTTTTGAAGGATT 57.403 34.783 0.00 0.00 0.00 3.01
906 1423 5.591099 TGCTGTGTCTTTTTGAAGGATTTC 58.409 37.500 0.00 0.00 0.00 2.17
1043 1566 1.810151 GGAAGTTGTAAGCGCCAATGA 59.190 47.619 2.29 0.00 0.00 2.57
1113 1636 3.879998 TGCTGACCAAAGTTTCACTACA 58.120 40.909 0.00 0.00 0.00 2.74
1114 1637 4.460263 TGCTGACCAAAGTTTCACTACAT 58.540 39.130 0.00 0.00 0.00 2.29
1148 1671 2.838202 AGGTTCGATGTCCTGTATGGTT 59.162 45.455 3.98 0.00 37.07 3.67
1159 1682 2.159085 CCTGTATGGTTCGAGAAGACCC 60.159 54.545 1.62 0.00 31.14 4.46
1171 1694 3.744660 GAGAAGACCCTGTTTGATGTGT 58.255 45.455 0.00 0.00 0.00 3.72
1255 1778 3.888930 CTGCCAGTTTTTCCTTGGTAAGA 59.111 43.478 0.00 0.00 34.43 2.10
1459 1982 2.451132 CGGATGCTGTAGTCAAGTACG 58.549 52.381 0.00 0.00 0.00 3.67
1938 2461 2.361992 TGGTTAGAGGCGAGCGGA 60.362 61.111 0.00 0.00 0.00 5.54
2008 2531 1.000955 GGTGTCTGCGGGTCCATATAG 59.999 57.143 0.00 0.00 0.00 1.31
2056 2579 5.565439 GCATGTGGAAGCAAAATTGTAGAGT 60.565 40.000 0.00 0.00 0.00 3.24
2080 2603 1.502690 TGTCACAGTGGTGGTAGGTT 58.497 50.000 0.00 0.00 45.32 3.50
2227 2750 0.957888 GCCTGGCAGAGACAAGGTTC 60.958 60.000 17.94 0.00 0.00 3.62
2383 2906 3.842126 CTGTGTCATCGTGCCGCG 61.842 66.667 0.00 0.00 43.01 6.46
2412 2935 0.453793 CTACCTGCCTCGACAGTGAG 59.546 60.000 0.00 0.00 35.83 3.51
2455 2978 1.927174 GAGACCACACGGATGAAATCG 59.073 52.381 0.00 0.00 46.86 3.34
2565 3088 1.023502 CGCATCCATATTGTGTGGCA 58.976 50.000 0.00 0.00 36.66 4.92
2609 3132 3.547868 CGAACTCGTACCATCATCAACAG 59.452 47.826 0.00 0.00 34.11 3.16
2721 3244 2.614229 GGAAGAGTCAAGTTCAGGAGGC 60.614 54.545 0.00 0.00 0.00 4.70
2808 3331 3.827008 TGTCATGCATACCCTCTTCTC 57.173 47.619 0.00 0.00 0.00 2.87
2856 3379 1.344953 TGGGTGAACTGTGCCTGTCT 61.345 55.000 0.00 0.00 0.00 3.41
2874 3397 6.402983 GCCTGTCTGTGAGATTTACATCAAAG 60.403 42.308 0.00 0.00 32.87 2.77
2960 3483 4.378774 CCACTGCAGATTCTGATAGAAGG 58.621 47.826 23.35 15.27 37.69 3.46
3064 3587 0.318955 GTGTGATGTGCAAAGCCACC 60.319 55.000 9.04 0.00 34.85 4.61
3124 3647 0.877649 CATGTCCGCCCTCTCAATCG 60.878 60.000 0.00 0.00 0.00 3.34
3210 3733 2.229784 GGTCCATGCTGTTTTCCTCTTG 59.770 50.000 0.00 0.00 0.00 3.02
3227 3750 3.797039 TCTTGGCTCTTATGTTCCATCG 58.203 45.455 0.00 0.00 0.00 3.84
3246 3769 2.117137 CGATTCATACTCCCGTCAACG 58.883 52.381 0.00 0.00 39.44 4.10
3330 3853 5.051441 CCACGTCGACATCAAGATATCTTTG 60.051 44.000 15.49 14.26 33.11 2.77
3390 3913 4.246712 TGATACCTTCCCTACTTCTCGT 57.753 45.455 0.00 0.00 0.00 4.18
3397 3920 2.920524 TCCCTACTTCTCGTAGCTCTG 58.079 52.381 0.00 0.00 43.48 3.35
3465 3988 1.471119 TACAGACGGTCATGGGAGAC 58.529 55.000 11.27 0.00 37.80 3.36
3474 3997 1.683917 GTCATGGGAGACGTAGCATCT 59.316 52.381 0.00 0.00 0.00 2.90
3564 4087 2.280628 ACTTTAGCAGCAGCCGTTATC 58.719 47.619 0.00 0.00 43.56 1.75
3635 4158 2.436109 GAGGCACCCCAAGCTTCA 59.564 61.111 0.00 0.00 37.93 3.02
3656 4179 1.086696 CGGAAGATGCCGTCATTTGT 58.913 50.000 0.00 0.00 46.07 2.83
3679 4202 5.353394 TTGGAACTTCTATAGGCGATTGT 57.647 39.130 0.00 0.00 0.00 2.71
3681 4204 3.982058 GGAACTTCTATAGGCGATTGTCG 59.018 47.826 0.00 0.00 43.89 4.35
3722 4245 8.918116 TGTGCTCTGAATATCTTCTGTACTATT 58.082 33.333 0.00 0.00 33.42 1.73
3768 4294 4.890088 TGCTCTCGTTTGTGGTAACTATT 58.110 39.130 0.00 0.00 37.61 1.73
3769 4295 5.302360 TGCTCTCGTTTGTGGTAACTATTT 58.698 37.500 0.00 0.00 37.61 1.40
3821 4347 2.325484 TGGTTGCAACTCTCTCCTGTA 58.675 47.619 27.64 0.00 0.00 2.74
3824 4350 3.935828 GGTTGCAACTCTCTCCTGTAATC 59.064 47.826 27.64 3.39 0.00 1.75
3827 4353 3.449018 TGCAACTCTCTCCTGTAATCTCC 59.551 47.826 0.00 0.00 0.00 3.71
3829 4355 4.441356 GCAACTCTCTCCTGTAATCTCCTG 60.441 50.000 0.00 0.00 0.00 3.86
3830 4356 4.601406 ACTCTCTCCTGTAATCTCCTGT 57.399 45.455 0.00 0.00 0.00 4.00
3832 4358 4.709397 ACTCTCTCCTGTAATCTCCTGTTG 59.291 45.833 0.00 0.00 0.00 3.33
3833 4359 4.678256 TCTCTCCTGTAATCTCCTGTTGT 58.322 43.478 0.00 0.00 0.00 3.32
3834 4360 4.464244 TCTCTCCTGTAATCTCCTGTTGTG 59.536 45.833 0.00 0.00 0.00 3.33
3835 4361 4.160329 TCTCCTGTAATCTCCTGTTGTGT 58.840 43.478 0.00 0.00 0.00 3.72
3836 4362 4.220821 TCTCCTGTAATCTCCTGTTGTGTC 59.779 45.833 0.00 0.00 0.00 3.67
3837 4363 3.901222 TCCTGTAATCTCCTGTTGTGTCA 59.099 43.478 0.00 0.00 0.00 3.58
3838 4364 4.532126 TCCTGTAATCTCCTGTTGTGTCAT 59.468 41.667 0.00 0.00 0.00 3.06
3839 4365 4.872691 CCTGTAATCTCCTGTTGTGTCATC 59.127 45.833 0.00 0.00 0.00 2.92
3840 4366 4.494484 TGTAATCTCCTGTTGTGTCATCG 58.506 43.478 0.00 0.00 0.00 3.84
3841 4367 3.685139 AATCTCCTGTTGTGTCATCGT 57.315 42.857 0.00 0.00 0.00 3.73
3842 4368 2.724977 TCTCCTGTTGTGTCATCGTC 57.275 50.000 0.00 0.00 0.00 4.20
3843 4369 1.068541 TCTCCTGTTGTGTCATCGTCG 60.069 52.381 0.00 0.00 0.00 5.12
3844 4370 0.671796 TCCTGTTGTGTCATCGTCGT 59.328 50.000 0.00 0.00 0.00 4.34
3856 4382 1.125021 CATCGTCGTGTTGCAAGACTC 59.875 52.381 22.68 14.70 39.87 3.36
3874 4400 2.053627 CTCGGTTTTCATGCAAAGCAC 58.946 47.619 17.84 0.00 43.04 4.40
3906 8185 4.578928 TGTTGTAAGCCTTTTTCTCTCCAC 59.421 41.667 0.00 0.00 0.00 4.02
3914 8193 3.558505 CTTTTTCTCTCCACGCATGTTG 58.441 45.455 0.00 0.00 0.00 3.33
3918 8197 1.069978 TCTCTCCACGCATGTTGAACA 59.930 47.619 0.00 0.00 0.00 3.18
3933 8212 6.214191 TGTTGAACAATACACACCAATTGT 57.786 33.333 4.43 0.00 45.75 2.71
3988 8267 5.694910 TGAGAATTTTGTTCGTGTACTCCTC 59.305 40.000 0.00 0.00 0.00 3.71
4003 8282 8.106348 CGTGTACTCCTCGATTTGTTTATTTAC 58.894 37.037 0.00 0.00 0.00 2.01
4062 8341 5.126067 CGGAAATACATCCAAATCCAGAGT 58.874 41.667 0.00 0.00 39.61 3.24
4066 8345 6.575244 AATACATCCAAATCCAGAGTACCA 57.425 37.500 0.00 0.00 0.00 3.25
4067 8346 6.770286 ATACATCCAAATCCAGAGTACCAT 57.230 37.500 0.00 0.00 0.00 3.55
4068 8347 5.041191 ACATCCAAATCCAGAGTACCATC 57.959 43.478 0.00 0.00 0.00 3.51
4121 8401 4.992688 TGCGGCAGTCCTTTAAATTAATG 58.007 39.130 0.00 0.00 0.00 1.90
4128 8408 6.905609 GCAGTCCTTTAAATTAATGCGACTAC 59.094 38.462 15.32 10.47 30.24 2.73
4142 8422 7.566858 AATGCGACTACATGTTTCAAATTTC 57.433 32.000 2.30 0.00 0.00 2.17
4154 8434 5.984926 TGTTTCAAATTTCAGTGGCATCTTC 59.015 36.000 0.00 0.00 0.00 2.87
4157 8437 5.072055 TCAAATTTCAGTGGCATCTTCAGA 58.928 37.500 0.00 0.00 0.00 3.27
4164 8444 3.063180 CAGTGGCATCTTCAGAATCGAAC 59.937 47.826 0.00 0.00 0.00 3.95
4169 8449 4.393062 GGCATCTTCAGAATCGAACTTCAA 59.607 41.667 1.86 0.00 0.00 2.69
4171 8451 6.404074 GGCATCTTCAGAATCGAACTTCAAAT 60.404 38.462 1.86 0.00 0.00 2.32
4203 8483 5.983540 ACTAAAGCTCAAAGTAGGATCAGG 58.016 41.667 0.00 0.00 0.00 3.86
4243 8523 2.148768 TCAGCAGCAAGACAATGACTG 58.851 47.619 0.00 0.00 0.00 3.51
4292 8572 0.733909 GCCAAAAGCGCAATCTGGAC 60.734 55.000 11.47 3.63 0.00 4.02
4301 8581 1.933181 CGCAATCTGGACGCAAGATTA 59.067 47.619 8.53 0.00 41.39 1.75
4302 8582 2.033407 CGCAATCTGGACGCAAGATTAG 60.033 50.000 8.53 5.95 41.39 1.73
4303 8583 3.198068 GCAATCTGGACGCAAGATTAGA 58.802 45.455 8.53 0.00 41.39 2.10
4368 8648 0.747644 CAACACCCACAGCACTGTCA 60.748 55.000 0.00 0.00 42.83 3.58
4465 8801 2.750637 TCTCACCGGCTCGTCTCC 60.751 66.667 0.00 0.00 0.00 3.71
4466 8802 3.062466 CTCACCGGCTCGTCTCCA 61.062 66.667 0.00 0.00 0.00 3.86
4467 8803 3.057547 CTCACCGGCTCGTCTCCAG 62.058 68.421 0.00 0.00 0.00 3.86
4468 8804 4.135153 CACCGGCTCGTCTCCAGG 62.135 72.222 0.00 0.00 0.00 4.45
4471 8807 3.382832 CGGCTCGTCTCCAGGGTT 61.383 66.667 0.00 0.00 0.00 4.11
4472 8808 2.943978 CGGCTCGTCTCCAGGGTTT 61.944 63.158 0.00 0.00 0.00 3.27
4473 8809 1.601419 CGGCTCGTCTCCAGGGTTTA 61.601 60.000 0.00 0.00 0.00 2.01
4474 8810 0.611714 GGCTCGTCTCCAGGGTTTAA 59.388 55.000 0.00 0.00 0.00 1.52
4475 8811 1.675116 GGCTCGTCTCCAGGGTTTAAC 60.675 57.143 0.00 0.00 0.00 2.01
4478 8814 3.675502 GCTCGTCTCCAGGGTTTAACTAC 60.676 52.174 0.00 0.00 0.00 2.73
4491 8827 2.852714 TAACTACTCATTCCCCGGGA 57.147 50.000 26.32 1.94 0.00 5.14
4492 8828 1.961133 AACTACTCATTCCCCGGGAA 58.039 50.000 26.32 21.61 46.39 3.97
4555 8969 7.854557 TCAGAATCCTCTTGTAATGATTGTG 57.145 36.000 0.00 0.00 38.89 3.33
4573 8987 5.628797 TTGTGGCTACATAATCAGATGGA 57.371 39.130 2.83 0.00 36.53 3.41
4619 9034 9.372369 GGCTGTGTGATAGGACTAATAATTATC 57.628 37.037 0.00 0.00 0.00 1.75
4675 9090 1.026182 TGAATGCTGATTTCGCGGCT 61.026 50.000 6.13 0.00 40.79 5.52
4695 9110 1.616865 TCGGTGTTCCTGGTCTACTTG 59.383 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 0.755686 CTCAGGGAAAGGATCTCGGG 59.244 60.000 0.00 0.00 31.91 5.14
102 103 4.959839 AGTAAGAGTCTCAGGGAAAGGATC 59.040 45.833 1.94 0.00 0.00 3.36
120 121 5.106712 TGCGTTTTGGATTGAAGCTAGTAAG 60.107 40.000 0.00 0.00 0.00 2.34
160 161 7.383572 CACTCTCTAATTGATTCCACGGATAAG 59.616 40.741 0.00 0.00 0.00 1.73
216 217 3.498397 ACTGCCAAAACGTCTCACATTAG 59.502 43.478 0.00 0.00 0.00 1.73
218 219 2.297701 ACTGCCAAAACGTCTCACATT 58.702 42.857 0.00 0.00 0.00 2.71
219 220 1.967319 ACTGCCAAAACGTCTCACAT 58.033 45.000 0.00 0.00 0.00 3.21
220 221 1.668751 GAACTGCCAAAACGTCTCACA 59.331 47.619 0.00 0.00 0.00 3.58
222 223 2.031258 TGAACTGCCAAAACGTCTCA 57.969 45.000 0.00 0.00 0.00 3.27
223 224 3.003275 TCAATGAACTGCCAAAACGTCTC 59.997 43.478 0.00 0.00 0.00 3.36
224 225 2.948979 TCAATGAACTGCCAAAACGTCT 59.051 40.909 0.00 0.00 0.00 4.18
225 226 3.347958 TCAATGAACTGCCAAAACGTC 57.652 42.857 0.00 0.00 0.00 4.34
226 227 3.443976 GTTCAATGAACTGCCAAAACGT 58.556 40.909 18.03 0.00 39.23 3.99
237 238 3.443976 ACGTTTTGGCAGTTCAATGAAC 58.556 40.909 17.67 17.67 42.25 3.18
238 239 3.380004 AGACGTTTTGGCAGTTCAATGAA 59.620 39.130 0.00 0.00 0.00 2.57
239 240 2.948979 AGACGTTTTGGCAGTTCAATGA 59.051 40.909 0.00 0.00 0.00 2.57
240 241 3.354089 AGACGTTTTGGCAGTTCAATG 57.646 42.857 0.00 0.00 0.00 2.82
242 243 6.811253 ATATAAGACGTTTTGGCAGTTCAA 57.189 33.333 0.83 0.00 0.00 2.69
259 279 9.756571 AGTACACCCTCTGTTCCTATATATAAG 57.243 37.037 0.00 0.00 33.91 1.73
266 286 3.197983 GCAAGTACACCCTCTGTTCCTAT 59.802 47.826 0.00 0.00 33.91 2.57
275 295 0.321653 CCACCTGCAAGTACACCCTC 60.322 60.000 0.00 0.00 0.00 4.30
290 310 2.094675 AGTTTCACATATGCTGCCACC 58.905 47.619 1.58 0.00 0.00 4.61
316 336 7.850193 TGCCTAATTCATTTTTCAAGCCTAAT 58.150 30.769 0.00 0.00 0.00 1.73
328 348 6.964807 TCACATATGCTGCCTAATTCATTT 57.035 33.333 1.58 0.00 0.00 2.32
331 351 5.683681 TCTTCACATATGCTGCCTAATTCA 58.316 37.500 1.58 0.00 0.00 2.57
333 353 6.301486 TGATCTTCACATATGCTGCCTAATT 58.699 36.000 1.58 0.00 0.00 1.40
336 356 4.590222 TCTGATCTTCACATATGCTGCCTA 59.410 41.667 1.58 0.00 0.00 3.93
337 357 3.390311 TCTGATCTTCACATATGCTGCCT 59.610 43.478 1.58 0.00 0.00 4.75
338 358 3.736720 TCTGATCTTCACATATGCTGCC 58.263 45.455 1.58 0.00 0.00 4.85
341 361 7.664731 CCCTTTAATCTGATCTTCACATATGCT 59.335 37.037 1.58 0.00 0.00 3.79
342 362 7.094463 CCCCTTTAATCTGATCTTCACATATGC 60.094 40.741 1.58 0.00 0.00 3.14
343 363 7.941238 ACCCCTTTAATCTGATCTTCACATATG 59.059 37.037 0.00 0.00 0.00 1.78
344 364 7.941238 CACCCCTTTAATCTGATCTTCACATAT 59.059 37.037 0.00 0.00 0.00 1.78
346 366 6.069440 TCACCCCTTTAATCTGATCTTCACAT 60.069 38.462 0.00 0.00 0.00 3.21
347 367 5.250543 TCACCCCTTTAATCTGATCTTCACA 59.749 40.000 0.00 0.00 0.00 3.58
348 368 5.745227 TCACCCCTTTAATCTGATCTTCAC 58.255 41.667 0.00 0.00 0.00 3.18
457 969 9.060347 CAAATATTGCTGATTACTACCATCACT 57.940 33.333 0.00 0.00 0.00 3.41
494 1006 5.597182 ACCTGACTTTGAACTGTAGTACTCA 59.403 40.000 0.00 0.00 0.00 3.41
495 1007 6.086785 ACCTGACTTTGAACTGTAGTACTC 57.913 41.667 0.00 0.00 0.00 2.59
496 1008 6.481434 AACCTGACTTTGAACTGTAGTACT 57.519 37.500 0.00 0.00 0.00 2.73
544 1056 7.046652 GGAATAGGACCAGTTACTCTTAAACC 58.953 42.308 0.00 0.00 0.00 3.27
566 1078 6.775629 AGCACCAGTTACTTCTTTTTATGGAA 59.224 34.615 0.00 0.00 0.00 3.53
589 1101 8.989980 GTTAGGTTGATATTCCAGTTACATAGC 58.010 37.037 0.00 0.00 0.00 2.97
635 1147 9.753674 TCAGAGTATTCATACTTGGGAAAAATT 57.246 29.630 0.97 0.00 43.27 1.82
636 1148 9.927081 ATCAGAGTATTCATACTTGGGAAAAAT 57.073 29.630 0.97 0.00 43.27 1.82
641 1153 8.228206 ACTAGATCAGAGTATTCATACTTGGGA 58.772 37.037 0.00 1.09 43.27 4.37
683 1195 5.362717 ACCAATCCTCTGATCGTGTATGTAA 59.637 40.000 0.00 0.00 0.00 2.41
761 1275 6.425114 TCTGAAGCATGTTTGAGTAAGTTCTC 59.575 38.462 8.48 0.00 35.28 2.87
770 1284 6.766944 AGGATATCTTCTGAAGCATGTTTGAG 59.233 38.462 12.54 0.09 0.00 3.02
904 1421 6.353323 TGATGGCCTACGAGAATAAATTGAA 58.647 36.000 3.32 0.00 0.00 2.69
906 1423 6.128172 GGATGATGGCCTACGAGAATAAATTG 60.128 42.308 3.32 0.00 0.00 2.32
1113 1636 1.204941 CGAACCTTCCTCTTGACCGAT 59.795 52.381 0.00 0.00 0.00 4.18
1114 1637 0.601558 CGAACCTTCCTCTTGACCGA 59.398 55.000 0.00 0.00 0.00 4.69
1148 1671 2.632996 ACATCAAACAGGGTCTTCTCGA 59.367 45.455 0.00 0.00 0.00 4.04
1159 1682 3.631686 TCCTTGTCCAACACATCAAACAG 59.368 43.478 0.00 0.00 33.90 3.16
1255 1778 1.059913 CTAGCCCCAGAAATCCGGAT 58.940 55.000 12.38 12.38 0.00 4.18
1459 1982 5.901552 TCCATCTTCAAAGTTTGGTTGAAC 58.098 37.500 15.47 0.00 39.46 3.18
2008 2531 6.524586 GCTAGTGCAATACATTTGAACTCAAC 59.475 38.462 2.28 0.00 39.04 3.18
2056 2579 3.450817 CCTACCACCACTGTGACATATGA 59.549 47.826 10.38 0.00 45.76 2.15
2080 2603 0.029700 TTCGTCGTCTTTCGCTGACA 59.970 50.000 0.00 0.00 39.67 3.58
2121 2644 6.070021 TCAGTTCTTCATCCCAGACATAATGT 60.070 38.462 0.00 0.00 0.00 2.71
2227 2750 1.673033 GGGTATGATGATTCGGCCGAG 60.673 57.143 29.20 0.00 0.00 4.63
2383 2906 2.480416 CGAGGCAGGTAGTGAGATGAAC 60.480 54.545 0.00 0.00 0.00 3.18
2565 3088 0.474184 CCCACTTCCGGCCATATCTT 59.526 55.000 2.24 0.00 0.00 2.40
2609 3132 1.264288 CTTGGAATAAAGGATCGCGGC 59.736 52.381 6.13 0.00 0.00 6.53
2721 3244 3.517901 TCCCTATGTTGACACCCTTGTAG 59.482 47.826 0.00 0.00 35.47 2.74
2808 3331 1.000955 ACACCTGAAGGCTGTAGAACG 59.999 52.381 0.00 0.00 39.32 3.95
2874 3397 3.896122 ACGCACCATGTTTGTTAATGAC 58.104 40.909 0.00 0.00 0.00 3.06
2960 3483 1.198637 GGACAGCATGAAACTGCAGAC 59.801 52.381 23.35 11.72 44.77 3.51
3064 3587 0.169672 CTTTTCCGCATGCTCCACAG 59.830 55.000 17.13 2.41 0.00 3.66
3124 3647 1.621107 CGCTGCCAAAATGTGATGAC 58.379 50.000 0.00 0.00 0.00 3.06
3246 3769 8.862085 ACTATACTGAAGAAGGTAAATAGGAGC 58.138 37.037 0.00 0.00 0.00 4.70
3330 3853 1.961394 TCTGGGTGTACAGTGTCTGTC 59.039 52.381 0.00 0.29 41.21 3.51
3390 3913 6.115446 CCTCATCATTGTTAAACCAGAGCTA 58.885 40.000 0.00 0.00 0.00 3.32
3397 3920 9.003658 CCTATCATACCTCATCATTGTTAAACC 57.996 37.037 0.00 0.00 0.00 3.27
3465 3988 0.179137 TCTCGCCACAAGATGCTACG 60.179 55.000 0.00 0.00 0.00 3.51
3474 3997 0.247460 CAGTGATCCTCTCGCCACAA 59.753 55.000 0.00 0.00 34.78 3.33
3579 4102 2.004583 TCGCGACGAGAATTTTCCAT 57.995 45.000 3.71 0.00 0.00 3.41
3644 4167 2.028130 AGTTCCAAACAAATGACGGCA 58.972 42.857 0.00 0.00 0.00 5.69
3654 4177 4.811969 TCGCCTATAGAAGTTCCAAACA 57.188 40.909 0.00 0.00 0.00 2.83
3656 4179 5.741011 ACAATCGCCTATAGAAGTTCCAAA 58.259 37.500 0.00 0.00 0.00 3.28
3679 4202 3.923864 ACTGTCGGCCTTGTGCGA 61.924 61.111 0.00 0.00 42.61 5.10
3681 4204 2.591715 ACACTGTCGGCCTTGTGC 60.592 61.111 0.00 0.00 40.16 4.57
3689 4212 2.654749 TATTCAGAGCACACTGTCGG 57.345 50.000 0.00 0.00 38.79 4.79
3722 4245 1.005097 AGCAGACTCAATGGGCATCAA 59.995 47.619 0.00 0.00 0.00 2.57
3768 4294 8.516234 TCAAGAAACTGTACAAAGTAGCAAAAA 58.484 29.630 0.00 0.00 0.00 1.94
3769 4295 8.046294 TCAAGAAACTGTACAAAGTAGCAAAA 57.954 30.769 0.00 0.00 0.00 2.44
3785 4311 4.402155 TGCAACCAACAGATTCAAGAAACT 59.598 37.500 0.00 0.00 0.00 2.66
3821 4347 3.589988 GACGATGACACAACAGGAGATT 58.410 45.455 0.00 0.00 0.00 2.40
3824 4350 1.335964 ACGACGATGACACAACAGGAG 60.336 52.381 0.00 0.00 0.00 3.69
3827 4353 1.487482 ACACGACGATGACACAACAG 58.513 50.000 0.00 0.00 0.00 3.16
3829 4355 1.656429 GCAACACGACGATGACACAAC 60.656 52.381 0.00 0.00 0.00 3.32
3830 4356 0.579630 GCAACACGACGATGACACAA 59.420 50.000 0.00 0.00 0.00 3.33
3832 4358 0.579630 TTGCAACACGACGATGACAC 59.420 50.000 0.00 0.00 0.00 3.67
3833 4359 0.858583 CTTGCAACACGACGATGACA 59.141 50.000 0.00 0.00 0.00 3.58
3834 4360 1.136611 GTCTTGCAACACGACGATGAC 60.137 52.381 0.00 0.00 0.00 3.06
3835 4361 1.136690 GTCTTGCAACACGACGATGA 58.863 50.000 0.00 0.00 0.00 2.92
3836 4362 1.125021 GAGTCTTGCAACACGACGATG 59.875 52.381 0.00 0.00 37.64 3.84
3837 4363 1.419374 GAGTCTTGCAACACGACGAT 58.581 50.000 0.00 0.00 37.64 3.73
3838 4364 0.933047 CGAGTCTTGCAACACGACGA 60.933 55.000 16.85 1.50 37.64 4.20
3839 4365 1.482955 CGAGTCTTGCAACACGACG 59.517 57.895 10.60 10.88 37.64 5.12
3840 4366 0.874607 ACCGAGTCTTGCAACACGAC 60.875 55.000 9.52 9.16 35.62 4.34
3841 4367 0.179094 AACCGAGTCTTGCAACACGA 60.179 50.000 9.52 0.00 35.62 4.35
3842 4368 0.655733 AAACCGAGTCTTGCAACACG 59.344 50.000 0.00 0.00 33.76 4.49
3843 4369 2.096819 TGAAAACCGAGTCTTGCAACAC 59.903 45.455 0.00 0.00 0.00 3.32
3844 4370 2.360844 TGAAAACCGAGTCTTGCAACA 58.639 42.857 0.00 0.00 0.00 3.33
3856 4382 1.850377 TGTGCTTTGCATGAAAACCG 58.150 45.000 0.00 0.00 41.91 4.44
3874 4400 7.439056 AGAAAAAGGCTTACAACAACATGATTG 59.561 33.333 0.00 3.00 0.00 2.67
3906 8185 3.233578 GGTGTGTATTGTTCAACATGCG 58.766 45.455 0.00 0.00 0.00 4.73
3933 8212 2.107378 TCAGGTACTTCCAAATGGTGCA 59.893 45.455 0.00 0.00 34.60 4.57
3988 8267 6.525280 CCCGGTTCAAGTAAATAAACAAATCG 59.475 38.462 0.00 0.00 0.00 3.34
4003 8282 4.313819 GGGTTAGCCCGGTTCAAG 57.686 61.111 0.00 0.00 46.51 3.02
4062 8341 3.448277 AGGGGGTTAATGGAGATGGTA 57.552 47.619 0.00 0.00 0.00 3.25
4066 8345 4.232820 ACATGAAAGGGGGTTAATGGAGAT 59.767 41.667 0.00 0.00 0.00 2.75
4067 8346 3.596046 ACATGAAAGGGGGTTAATGGAGA 59.404 43.478 0.00 0.00 0.00 3.71
4068 8347 3.981212 ACATGAAAGGGGGTTAATGGAG 58.019 45.455 0.00 0.00 0.00 3.86
4121 8401 6.086765 CACTGAAATTTGAAACATGTAGTCGC 59.913 38.462 0.00 0.00 0.00 5.19
4128 8408 5.929992 AGATGCCACTGAAATTTGAAACATG 59.070 36.000 0.00 0.00 0.00 3.21
4142 8422 2.897436 TCGATTCTGAAGATGCCACTG 58.103 47.619 0.00 0.00 0.00 3.66
4203 8483 4.065088 TGAACAGACACAGTGCCTATTTC 58.935 43.478 0.00 2.25 0.00 2.17
4243 8523 2.288948 TGGCTCCATGTTCAAAATGTGC 60.289 45.455 0.00 0.00 0.00 4.57
4269 8549 1.135199 CAGATTGCGCTTTTGGCATCT 60.135 47.619 9.73 1.31 40.62 2.90
4292 8572 5.342806 TGTTGTTCAGTTCTAATCTTGCG 57.657 39.130 0.00 0.00 0.00 4.85
4301 8581 4.764823 TCTGGTTTGTTGTTGTTCAGTTCT 59.235 37.500 0.00 0.00 0.00 3.01
4302 8582 5.054390 TCTGGTTTGTTGTTGTTCAGTTC 57.946 39.130 0.00 0.00 0.00 3.01
4303 8583 5.461032 TTCTGGTTTGTTGTTGTTCAGTT 57.539 34.783 0.00 0.00 0.00 3.16
4368 8648 5.138125 ACTGAAAATGCATGATTCGGTTT 57.862 34.783 24.10 10.85 39.08 3.27
4403 8683 2.110213 TTCTTCCAGTGCCGCGTT 59.890 55.556 4.92 0.00 0.00 4.84
4465 8801 4.524053 GGGGAATGAGTAGTTAAACCCTG 58.476 47.826 0.00 0.00 36.66 4.45
4466 8802 3.199289 CGGGGAATGAGTAGTTAAACCCT 59.801 47.826 0.00 0.00 36.66 4.34
4467 8803 3.538591 CGGGGAATGAGTAGTTAAACCC 58.461 50.000 0.00 0.00 35.80 4.11
4468 8804 3.538591 CCGGGGAATGAGTAGTTAAACC 58.461 50.000 0.00 0.00 0.00 3.27
4469 8805 3.198417 TCCCGGGGAATGAGTAGTTAAAC 59.802 47.826 23.50 0.00 0.00 2.01
4470 8806 3.452878 TCCCGGGGAATGAGTAGTTAAA 58.547 45.455 23.50 0.00 0.00 1.52
4471 8807 3.119009 TCCCGGGGAATGAGTAGTTAA 57.881 47.619 23.50 0.00 0.00 2.01
4472 8808 2.852714 TCCCGGGGAATGAGTAGTTA 57.147 50.000 23.50 0.00 0.00 2.24
4473 8809 1.961133 TTCCCGGGGAATGAGTAGTT 58.039 50.000 24.64 0.00 36.71 2.24
4474 8810 1.961133 TTTCCCGGGGAATGAGTAGT 58.039 50.000 28.41 0.00 41.71 2.73
4475 8811 3.359695 TTTTTCCCGGGGAATGAGTAG 57.640 47.619 28.41 0.00 41.71 2.57
4496 8832 7.444487 GGTTCAGTACTTCATTAACTCACCTTT 59.556 37.037 0.00 0.00 0.00 3.11
4555 8969 6.291377 TGAAGTTCCATCTGATTATGTAGCC 58.709 40.000 0.00 0.00 0.00 3.93
4573 8987 6.888632 ACAGCCATGATATTTCTTCTGAAGTT 59.111 34.615 16.43 6.44 33.28 2.66
4675 9090 1.616865 CAAGTAGACCAGGAACACCGA 59.383 52.381 0.00 0.00 0.00 4.69
4684 9099 2.941064 TCGATCGTACCAAGTAGACCAG 59.059 50.000 15.94 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.