Multiple sequence alignment - TraesCS6D01G223600

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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 TraesCS6D01G223600 chr6D 100.000 4865 0 0 1 4865 315651337 315646473 0.000000e+00 8985.0
1 TraesCS6D01G223600 chr6D 85.955 356 29 14 121 467 176820500 176820843 1.290000e-95 361.0
2 TraesCS6D01G223600 chr6D 87.500 192 15 6 479 665 36127793 36127606 3.810000e-51 213.0
3 TraesCS6D01G223600 chr6A 96.122 3533 92 16 658 4164 452957916 452954403 0.000000e+00 5723.0
4 TraesCS6D01G223600 chr6A 87.269 487 53 6 4387 4865 452782510 452782025 9.210000e-152 547.0
5 TraesCS6D01G223600 chr6A 87.288 354 30 10 121 468 229993808 229993464 1.640000e-104 390.0
6 TraesCS6D01G223600 chr6A 86.486 333 31 10 4 330 452958912 452958588 2.150000e-93 353.0
7 TraesCS6D01G223600 chr6B 95.581 3553 107 17 717 4243 511422390 511425918 0.000000e+00 5646.0
8 TraesCS6D01G223600 chr6B 87.654 567 44 10 4314 4864 511427026 511427582 1.910000e-178 636.0
9 TraesCS6D01G223600 chr6B 86.133 375 34 13 104 467 511421857 511422224 5.900000e-104 388.0
10 TraesCS6D01G223600 chr6B 89.503 181 19 0 479 659 511422209 511422389 3.790000e-56 230.0
11 TraesCS6D01G223600 chr3A 86.383 470 49 11 4 467 595464748 595464288 2.610000e-137 499.0
12 TraesCS6D01G223600 chr5B 85.650 446 49 11 31 468 469983834 469983396 5.740000e-124 455.0
13 TraesCS6D01G223600 chr5B 84.136 353 41 11 121 467 493727679 493727336 1.310000e-85 327.0
14 TraesCS6D01G223600 chr7D 88.788 330 21 10 9 326 638418936 638419261 1.640000e-104 390.0
15 TraesCS6D01G223600 chr7D 92.000 100 4 4 496 594 638419382 638419478 2.360000e-28 137.0
16 TraesCS6D01G223600 chr7D 94.444 36 1 1 4124 4159 440053238 440053272 2.000000e-03 54.7
17 TraesCS6D01G223600 chr1D 83.262 466 36 22 9 459 382224692 382224254 1.640000e-104 390.0
18 TraesCS6D01G223600 chr1D 83.298 467 34 24 9 459 401146022 401146460 1.640000e-104 390.0
19 TraesCS6D01G223600 chr1D 86.979 192 18 5 479 665 382224262 382224073 4.930000e-50 209.0
20 TraesCS6D01G223600 chr1D 88.571 175 13 5 496 665 401146468 401146640 6.380000e-49 206.0
21 TraesCS6D01G223600 chr2D 83.226 465 36 24 9 459 429104044 429104480 5.900000e-104 388.0
22 TraesCS6D01G223600 chr2D 88.571 175 13 5 496 665 484559120 484558948 6.380000e-49 206.0
23 TraesCS6D01G223600 chr2B 83.668 349 26 13 4 324 787280307 787280652 2.850000e-77 300.0
24 TraesCS6D01G223600 chr2B 83.668 349 26 13 4 324 787297384 787297729 2.850000e-77 300.0
25 TraesCS6D01G223600 chr7B 91.729 133 9 2 479 610 681525394 681525525 2.990000e-42 183.0
26 TraesCS6D01G223600 chr4B 76.786 336 60 14 4537 4865 167337484 167337808 6.470000e-39 172.0
27 TraesCS6D01G223600 chr4B 96.875 32 1 0 4188 4219 14016248 14016279 2.000000e-03 54.7


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 TraesCS6D01G223600 chr6D 315646473 315651337 4864 True 8985.0 8985 100.00000 1 4865 1 chr6D.!!$R2 4864
1 TraesCS6D01G223600 chr6A 452954403 452958912 4509 True 3038.0 5723 91.30400 4 4164 2 chr6A.!!$R3 4160
2 TraesCS6D01G223600 chr6B 511421857 511427582 5725 False 1725.0 5646 89.71775 104 4864 4 chr6B.!!$F1 4760
3 TraesCS6D01G223600 chr7D 638418936 638419478 542 False 263.5 390 90.39400 9 594 2 chr7D.!!$F2 585
4 TraesCS6D01G223600 chr1D 382224073 382224692 619 True 299.5 390 85.12050 9 665 2 chr1D.!!$R1 656
5 TraesCS6D01G223600 chr1D 401146022 401146640 618 False 298.0 390 85.93450 9 665 2 chr1D.!!$F1 656

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
353 376 0.038021 TGGCAATGTGGAGCAAGCTA 59.962 50.000 0.00 0.0 34.14 3.32 F
699 1146 0.236711 ACCACTCGTAGTTCGTGACG 59.763 55.000 0.00 0.0 40.80 4.35 F
1389 1843 0.533085 TTGTGCCCGTGAATCGTGAA 60.533 50.000 0.00 0.0 37.94 3.18 F
2296 2752 1.054978 CCCCTGGTTAGTAGGCCCTC 61.055 65.000 0.00 0.0 33.86 4.30 F
3398 3871 1.136141 GCATGCTGAACTGAACACTCG 60.136 52.381 11.37 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2720 2.117423 AGGGGAGGCAAAAACGGG 59.883 61.111 0.00 0.0 0.00 5.28 R
2590 3046 2.282674 CCAGCTGCAGGGAAGCAA 60.283 61.111 17.12 0.0 45.13 3.91 R
3156 3629 5.048846 ACCAAATAGCCACCCAAGTATAG 57.951 43.478 0.00 0.0 0.00 1.31 R
3808 4289 1.854743 CATACACTCCTGCATCGTTCG 59.145 52.381 0.00 0.0 0.00 3.95 R
4527 6082 0.107459 GGAGTTGTCCTGAGATGGCC 60.107 60.000 0.00 0.0 40.17 5.36 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
68 69 7.282332 AGAGTTTTCCTCCAGAATTTCTTTG 57.718 36.000 0.00 0.00 41.47 2.77
72 73 6.639632 TTTCCTCCAGAATTTCTTTGTCAG 57.360 37.500 0.00 0.00 33.44 3.51
85 86 9.855021 AATTTCTTTGTCAGATATTAAAACCGG 57.145 29.630 0.00 0.00 32.91 5.28
112 114 3.665409 CACTTAACAATGCAAGTGCTTCG 59.335 43.478 13.13 0.00 43.57 3.79
117 119 2.187599 AATGCAAGTGCTTCGCGGAC 62.188 55.000 6.13 0.00 42.66 4.79
143 149 8.385111 CAGATGAATTGCAAAAATATGAACACC 58.615 33.333 1.71 0.00 0.00 4.16
150 156 4.979197 GCAAAAATATGAACACCGTTGACA 59.021 37.500 0.00 0.00 0.00 3.58
208 214 3.008923 TCACCATCACATGCAGTTCCTAA 59.991 43.478 0.00 0.00 0.00 2.69
210 216 3.949754 ACCATCACATGCAGTTCCTAATG 59.050 43.478 0.00 0.00 0.00 1.90
234 247 1.825090 TTGCGATGCCATCACTTCTT 58.175 45.000 5.40 0.00 0.00 2.52
238 251 2.223203 GCGATGCCATCACTTCTTTCTG 60.223 50.000 5.40 0.00 0.00 3.02
275 288 4.142752 GCACTAATCCTCCCGTTTACAAAC 60.143 45.833 0.00 0.00 35.59 2.93
276 289 5.243207 CACTAATCCTCCCGTTTACAAACT 58.757 41.667 3.55 0.00 36.77 2.66
277 290 6.400568 CACTAATCCTCCCGTTTACAAACTA 58.599 40.000 3.55 0.00 36.77 2.24
304 318 8.519799 AGAGTAAAATTTTCACAGAACTTGGA 57.480 30.769 6.72 0.00 0.00 3.53
325 340 5.040635 GGACGATTGTTTCTTGCAGAAAAA 58.959 37.500 11.33 5.49 44.84 1.94
348 371 1.412079 AAGTTTGGCAATGTGGAGCA 58.588 45.000 0.00 0.00 0.00 4.26
353 376 0.038021 TGGCAATGTGGAGCAAGCTA 59.962 50.000 0.00 0.00 34.14 3.32
365 388 3.556004 GGAGCAAGCTATGTACCATCCTC 60.556 52.174 0.00 0.00 0.00 3.71
377 400 5.630121 TGTACCATCCTCACTCAATTGTTT 58.370 37.500 5.13 0.00 0.00 2.83
378 401 5.705441 TGTACCATCCTCACTCAATTGTTTC 59.295 40.000 5.13 0.00 0.00 2.78
381 404 2.778299 TCCTCACTCAATTGTTTCCGG 58.222 47.619 5.13 0.00 0.00 5.14
383 406 1.200020 CTCACTCAATTGTTTCCGGGC 59.800 52.381 0.00 0.00 0.00 6.13
385 408 1.613437 CACTCAATTGTTTCCGGGCTT 59.387 47.619 0.00 0.00 0.00 4.35
386 409 1.886542 ACTCAATTGTTTCCGGGCTTC 59.113 47.619 0.00 0.00 0.00 3.86
387 410 2.162681 CTCAATTGTTTCCGGGCTTCT 58.837 47.619 0.00 0.00 0.00 2.85
389 412 1.067635 CAATTGTTTCCGGGCTTCTGG 60.068 52.381 0.00 0.00 38.29 3.86
618 733 5.428496 AGCATCGGATGTGAATTATGTTG 57.572 39.130 18.54 0.00 0.00 3.33
623 738 4.097714 CGGATGTGAATTATGTTGCACAC 58.902 43.478 0.00 0.00 43.17 3.82
642 757 4.742167 CACACAATTGATGTTTTGCCGTTA 59.258 37.500 13.59 0.00 41.46 3.18
645 760 4.742659 ACAATTGATGTTTTGCCGTTACAC 59.257 37.500 13.59 0.00 40.06 2.90
672 787 1.287425 GCATTTAGCTAGCCGAACGT 58.713 50.000 12.13 0.00 41.15 3.99
673 788 2.466846 GCATTTAGCTAGCCGAACGTA 58.533 47.619 12.13 0.00 41.15 3.57
699 1146 0.236711 ACCACTCGTAGTTCGTGACG 59.763 55.000 0.00 0.00 40.80 4.35
764 1211 8.873830 CATCATAAATCCACTAATCACGGATAC 58.126 37.037 0.00 0.00 38.62 2.24
782 1229 2.930826 ACTTGTGGATCACCTTCGTT 57.069 45.000 0.00 0.00 37.04 3.85
783 1230 3.208747 ACTTGTGGATCACCTTCGTTT 57.791 42.857 0.00 0.00 37.04 3.60
784 1231 3.139077 ACTTGTGGATCACCTTCGTTTC 58.861 45.455 0.00 0.00 37.04 2.78
785 1232 2.178912 TGTGGATCACCTTCGTTTCC 57.821 50.000 0.00 0.00 37.04 3.13
786 1233 1.418264 TGTGGATCACCTTCGTTTCCA 59.582 47.619 0.00 0.00 37.04 3.53
787 1234 2.158740 TGTGGATCACCTTCGTTTCCAA 60.159 45.455 0.00 0.00 34.83 3.53
788 1235 2.882137 GTGGATCACCTTCGTTTCCAAA 59.118 45.455 0.00 0.00 34.83 3.28
803 1250 5.878116 CGTTTCCAAATTCCATCTACCACTA 59.122 40.000 0.00 0.00 0.00 2.74
937 1387 1.341209 CCACCACTTGCTTTTCTTCCC 59.659 52.381 0.00 0.00 0.00 3.97
968 1418 8.637986 CCAAATCCCCAATTTTCTTCGATATAA 58.362 33.333 0.00 0.00 35.32 0.98
1389 1843 0.533085 TTGTGCCCGTGAATCGTGAA 60.533 50.000 0.00 0.00 37.94 3.18
1430 1885 6.071952 TGCCAATCAGATTCAGGAGTAAAAAC 60.072 38.462 4.04 0.00 0.00 2.43
1433 1888 8.526147 CCAATCAGATTCAGGAGTAAAAACATT 58.474 33.333 0.00 0.00 0.00 2.71
1436 1891 9.965902 ATCAGATTCAGGAGTAAAAACATTACT 57.034 29.630 0.73 0.73 37.89 2.24
1437 1892 9.219603 TCAGATTCAGGAGTAAAAACATTACTG 57.780 33.333 5.65 0.00 35.54 2.74
1541 1996 2.044793 TGAACTTCTGGGGACTGGAT 57.955 50.000 0.00 0.00 0.00 3.41
1551 2006 3.053077 TGGGGACTGGATATTTAGGTGG 58.947 50.000 0.00 0.00 0.00 4.61
1552 2007 3.053826 GGGGACTGGATATTTAGGTGGT 58.946 50.000 0.00 0.00 0.00 4.16
1553 2008 4.237018 GGGGACTGGATATTTAGGTGGTA 58.763 47.826 0.00 0.00 0.00 3.25
1779 2234 1.268625 CTGCTTGATTGTGAGCTTGCA 59.731 47.619 0.00 0.00 39.60 4.08
1986 2442 4.820173 AGGTACAACAAACTTGGAACTAGC 59.180 41.667 0.00 0.00 26.04 3.42
2065 2521 4.334552 TCTGTTTATGATTCAGCTTGGCA 58.665 39.130 0.00 0.00 0.00 4.92
2098 2554 1.707632 CCTTCGAGTGAGTTCTGCTG 58.292 55.000 0.00 0.00 0.00 4.41
2114 2570 5.450592 TCTGCTGTGCAATAATGTCAAAA 57.549 34.783 0.00 0.00 38.41 2.44
2264 2720 5.832060 ACTCCCAGATTTTCCATCATTCATC 59.168 40.000 0.00 0.00 0.00 2.92
2296 2752 1.054978 CCCCTGGTTAGTAGGCCCTC 61.055 65.000 0.00 0.00 33.86 4.30
2513 2969 7.283625 TGCACCAATTGTAAGTTACATTCTT 57.716 32.000 16.26 8.06 38.68 2.52
2921 3394 1.632269 TACCCCCTCCCCCTCTCAT 60.632 63.158 0.00 0.00 0.00 2.90
3032 3505 3.628942 ACCGTCTAAACCCAGTTTCAAAC 59.371 43.478 0.00 0.00 37.01 2.93
3059 3532 5.243207 AGACGGGTAAACTTACTTCATTGG 58.757 41.667 0.00 0.00 34.16 3.16
3083 3556 5.220567 GCTGCTTAGTCTAAGATCAAACAGC 60.221 44.000 21.56 21.55 37.30 4.40
3156 3629 3.754965 TGATAGCTTATTGTGCATCCCC 58.245 45.455 0.00 0.00 0.00 4.81
3177 3650 4.398319 CCTATACTTGGGTGGCTATTTGG 58.602 47.826 0.00 0.00 0.00 3.28
3396 3869 1.971481 TGCATGCTGAACTGAACACT 58.029 45.000 20.33 0.00 0.00 3.55
3398 3871 1.136141 GCATGCTGAACTGAACACTCG 60.136 52.381 11.37 0.00 0.00 4.18
3424 3897 4.336433 CCTGTTTCTGAATCAACACACACT 59.664 41.667 3.07 0.00 0.00 3.55
3425 3898 5.484173 TGTTTCTGAATCAACACACACTC 57.516 39.130 0.00 0.00 0.00 3.51
3429 3902 5.929697 TCTGAATCAACACACACTCAATC 57.070 39.130 0.00 0.00 0.00 2.67
3435 3908 6.992063 ATCAACACACACTCAATCCTAATC 57.008 37.500 0.00 0.00 0.00 1.75
3447 3920 7.664731 CACTCAATCCTAATCAATATTGGCTCT 59.335 37.037 15.36 0.99 31.66 4.09
3485 3958 1.973515 CTACCCTGCATGCTATCTGGA 59.026 52.381 20.33 0.00 0.00 3.86
3486 3959 1.216064 ACCCTGCATGCTATCTGGAA 58.784 50.000 20.33 0.00 0.00 3.53
3499 3972 6.656902 TGCTATCTGGAATTGAGACTCAAAT 58.343 36.000 21.29 13.69 40.12 2.32
3514 3987 6.675026 AGACTCAAATGAAACATGACATGTG 58.325 36.000 21.49 7.62 44.07 3.21
3517 3990 6.039605 ACTCAAATGAAACATGACATGTGACA 59.960 34.615 21.49 21.59 44.07 3.58
3523 3996 6.324042 TGAAACATGACATGTGACAATATGC 58.676 36.000 21.49 3.69 44.07 3.14
3747 4220 8.905660 TGTATACTAGTGAATCTGAGTAGACC 57.094 38.462 5.39 0.00 36.32 3.85
3808 4289 2.086054 ACTGATCAGTCGCTTGAACC 57.914 50.000 22.89 0.00 36.92 3.62
3856 4337 5.460646 CCAAAGCAAATAAATCGTGTCACT 58.539 37.500 0.65 0.00 0.00 3.41
3943 4424 5.837437 TGTAAACGAAATTTCAATGGCACT 58.163 33.333 17.99 0.00 0.00 4.40
4172 4654 4.909284 AGTTACTATTCCCTCCTTCCCAT 58.091 43.478 0.00 0.00 0.00 4.00
4183 4665 6.639938 TCCCTCCTTCCCATAATATAAGACA 58.360 40.000 0.00 0.00 0.00 3.41
4273 5823 5.517054 GCAAACACGGAAGTAAAATGTTTGA 59.483 36.000 24.65 0.00 46.85 2.69
4279 5829 5.401079 ACGGAAGTAAAATGTTTGATTTGCG 59.599 36.000 9.38 9.38 46.88 4.85
4284 5834 9.123709 GAAGTAAAATGTTTGATTTGCGACATA 57.876 29.630 0.00 0.00 32.77 2.29
4366 5916 6.332735 AGTTTTGAACTTTCTTATCCCAGC 57.667 37.500 0.00 0.00 39.04 4.85
4367 5917 5.833131 AGTTTTGAACTTTCTTATCCCAGCA 59.167 36.000 0.00 0.00 39.04 4.41
4368 5918 5.964958 TTTGAACTTTCTTATCCCAGCAG 57.035 39.130 0.00 0.00 0.00 4.24
4369 5919 4.640771 TGAACTTTCTTATCCCAGCAGT 57.359 40.909 0.00 0.00 0.00 4.40
4370 5920 4.985538 TGAACTTTCTTATCCCAGCAGTT 58.014 39.130 0.00 0.00 0.00 3.16
4387 5937 3.181486 GCAGTTTAAAGGAATAGCTGGGC 60.181 47.826 0.00 0.00 0.00 5.36
4442 5992 4.080186 GGAAAAAGTACTAGCCCATGGGTA 60.080 45.833 31.58 20.09 37.65 3.69
4457 6007 0.472471 GGGTATGAGATTTGGCCCGA 59.528 55.000 0.00 0.00 0.00 5.14
4490 6040 0.752054 CAGCCAGCCCAAGAACAAAA 59.248 50.000 0.00 0.00 0.00 2.44
4495 6045 2.223805 CCAGCCCAAGAACAAAACTGAC 60.224 50.000 0.00 0.00 0.00 3.51
4497 6047 3.131046 CAGCCCAAGAACAAAACTGACTT 59.869 43.478 0.00 0.00 0.00 3.01
4526 6081 3.097614 GCTTGAACTAGGGGACTGACTA 58.902 50.000 0.00 0.00 43.88 2.59
4527 6082 3.131400 GCTTGAACTAGGGGACTGACTAG 59.869 52.174 0.00 0.00 43.88 2.57
4528 6083 3.383698 TGAACTAGGGGACTGACTAGG 57.616 52.381 0.00 0.00 43.88 3.02
4529 6084 2.033372 GAACTAGGGGACTGACTAGGC 58.967 57.143 0.00 0.00 43.88 3.93
4538 6093 1.686052 GACTGACTAGGCCATCTCAGG 59.314 57.143 21.28 8.87 0.00 3.86
4539 6094 1.289231 ACTGACTAGGCCATCTCAGGA 59.711 52.381 21.28 0.00 0.00 3.86
4540 6095 1.686052 CTGACTAGGCCATCTCAGGAC 59.314 57.143 5.01 0.00 36.73 3.85
4541 6096 1.007118 TGACTAGGCCATCTCAGGACA 59.993 52.381 5.01 0.00 40.05 4.02
4542 6097 2.111384 GACTAGGCCATCTCAGGACAA 58.889 52.381 5.01 0.00 40.05 3.18
4543 6098 1.834263 ACTAGGCCATCTCAGGACAAC 59.166 52.381 5.01 0.00 40.05 3.32
4550 6105 2.304180 CCATCTCAGGACAACTCCAACT 59.696 50.000 0.00 0.00 39.39 3.16
4553 6108 0.108585 TCAGGACAACTCCAACTGGC 59.891 55.000 0.00 0.00 39.39 4.85
4555 6110 1.150536 GGACAACTCCAACTGGCCA 59.849 57.895 4.71 4.71 40.83 5.36
4564 6119 1.067250 CAACTGGCCAACCCAAACG 59.933 57.895 7.01 0.00 44.81 3.60
4567 6122 2.519780 TGGCCAACCCAAACGGAC 60.520 61.111 0.61 0.00 41.82 4.79
4572 6127 1.032657 CCAACCCAAACGGACACACA 61.033 55.000 0.00 0.00 34.64 3.72
4589 6144 5.508124 CACACAATGTGTTCGTTTTTGTT 57.492 34.783 17.31 0.00 45.08 2.83
4591 6146 5.782684 CACACAATGTGTTCGTTTTTGTTTG 59.217 36.000 17.31 0.00 45.08 2.93
4594 6149 6.299499 CACAATGTGTTCGTTTTTGTTTGTTG 59.701 34.615 5.00 0.00 0.00 3.33
4595 6150 4.974103 TGTGTTCGTTTTTGTTTGTTGG 57.026 36.364 0.00 0.00 0.00 3.77
4596 6151 4.617959 TGTGTTCGTTTTTGTTTGTTGGA 58.382 34.783 0.00 0.00 0.00 3.53
4597 6152 5.047847 TGTGTTCGTTTTTGTTTGTTGGAA 58.952 33.333 0.00 0.00 0.00 3.53
4628 6183 2.113139 CACCAGGGCCGTCTTGTT 59.887 61.111 0.00 0.00 0.00 2.83
4724 6279 3.536956 TCACTTCGTCACCAAAAGTCT 57.463 42.857 0.00 0.00 31.04 3.24
4781 6336 8.699283 ATAAAATCTTACGTCTAGTTGTGGTC 57.301 34.615 0.00 0.00 0.00 4.02
4784 6339 3.187227 TCTTACGTCTAGTTGTGGTCGTC 59.813 47.826 0.00 0.00 33.70 4.20
4787 6342 1.682982 GTCTAGTTGTGGTCGTCGTG 58.317 55.000 0.00 0.00 0.00 4.35
4790 6345 0.746063 TAGTTGTGGTCGTCGTGGTT 59.254 50.000 0.00 0.00 0.00 3.67
4794 6353 2.026445 TGGTCGTCGTGGTTGTCG 59.974 61.111 0.00 0.00 0.00 4.35
4821 6380 3.351450 TCACTGGTGAGGTCGACG 58.649 61.111 9.92 0.00 34.14 5.12
4864 6423 1.078708 AACCATGGAACTACCGCCG 60.079 57.895 21.47 0.00 42.61 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.592105 TTGGCATATTAGCAATTAATCAAAGC 57.408 30.769 0.00 0.00 33.96 3.51
2 3 9.970395 TCTTGGCATATTAGCAATTAATCAAAG 57.030 29.630 0.00 0.00 33.96 2.77
3 4 9.748708 GTCTTGGCATATTAGCAATTAATCAAA 57.251 29.630 0.00 0.00 33.96 2.69
4 5 9.135189 AGTCTTGGCATATTAGCAATTAATCAA 57.865 29.630 0.00 0.00 33.96 2.57
68 69 8.209917 AGTGATTTCCGGTTTTAATATCTGAC 57.790 34.615 0.00 0.00 0.00 3.51
112 114 2.634982 TTTGCAATTCATCTGTCCGC 57.365 45.000 0.00 0.00 0.00 5.54
117 119 8.385111 GGTGTTCATATTTTTGCAATTCATCTG 58.615 33.333 0.00 0.00 0.00 2.90
143 149 3.052036 CCCTGCATTCTTTTTGTCAACG 58.948 45.455 0.00 0.00 0.00 4.10
208 214 2.030540 GTGATGGCATCGCAATTAGCAT 60.031 45.455 30.57 0.00 46.13 3.79
210 216 1.605710 AGTGATGGCATCGCAATTAGC 59.394 47.619 34.84 13.14 42.11 3.09
238 251 9.425577 GGAGGATTAGTGCAATAGTCTAATTAC 57.574 37.037 15.01 8.37 35.42 1.89
277 290 8.624776 CCAAGTTCTGTGAAAATTTTACTCTCT 58.375 33.333 2.75 0.00 0.00 3.10
365 388 1.247567 AGCCCGGAAACAATTGAGTG 58.752 50.000 13.59 0.00 0.00 3.51
377 400 1.602237 CTAAAGCCAGAAGCCCGGA 59.398 57.895 0.73 0.00 45.47 5.14
378 401 2.115291 GCTAAAGCCAGAAGCCCGG 61.115 63.158 0.00 0.00 45.47 5.73
389 412 0.812412 TATTGGCGGTCGGCTAAAGC 60.812 55.000 17.23 0.00 45.74 3.51
580 691 6.331845 TCCGATGCTAGTATTTTAAACGACA 58.668 36.000 0.00 0.00 0.00 4.35
618 733 2.096811 CGGCAAAACATCAATTGTGTGC 60.097 45.455 5.13 2.90 44.07 4.57
623 738 4.149747 GGTGTAACGGCAAAACATCAATTG 59.850 41.667 0.00 0.00 38.12 2.32
642 757 2.032834 TAAATGCCCGTGCGGTGT 59.967 55.556 9.90 0.00 41.78 4.16
645 760 1.498865 CTAGCTAAATGCCCGTGCGG 61.499 60.000 3.25 3.25 44.23 5.69
682 1129 0.453950 CCCGTCACGAACTACGAGTG 60.454 60.000 0.00 0.00 45.77 3.51
683 1130 0.886490 ACCCGTCACGAACTACGAGT 60.886 55.000 0.00 0.00 45.77 4.18
684 1131 0.453950 CACCCGTCACGAACTACGAG 60.454 60.000 0.00 0.00 45.77 4.18
685 1132 1.165907 ACACCCGTCACGAACTACGA 61.166 55.000 0.00 0.00 45.77 3.43
687 1134 1.788886 GAAACACCCGTCACGAACTAC 59.211 52.381 0.00 0.00 0.00 2.73
699 1146 2.098831 GCGACGCCTAGAAACACCC 61.099 63.158 9.14 0.00 0.00 4.61
764 1211 2.484264 GGAAACGAAGGTGATCCACAAG 59.516 50.000 0.00 0.00 35.86 3.16
782 1229 7.206789 TGATAGTGGTAGATGGAATTTGGAA 57.793 36.000 0.00 0.00 0.00 3.53
783 1230 6.823286 TGATAGTGGTAGATGGAATTTGGA 57.177 37.500 0.00 0.00 0.00 3.53
784 1231 7.941238 AGAATGATAGTGGTAGATGGAATTTGG 59.059 37.037 0.00 0.00 0.00 3.28
785 1232 8.915057 AGAATGATAGTGGTAGATGGAATTTG 57.085 34.615 0.00 0.00 0.00 2.32
786 1233 8.943085 AGAGAATGATAGTGGTAGATGGAATTT 58.057 33.333 0.00 0.00 0.00 1.82
787 1234 8.503428 AGAGAATGATAGTGGTAGATGGAATT 57.497 34.615 0.00 0.00 0.00 2.17
788 1235 8.503428 AAGAGAATGATAGTGGTAGATGGAAT 57.497 34.615 0.00 0.00 0.00 3.01
833 1280 8.641541 TGGAGCTCAAATTTTCTACTCAATTTT 58.358 29.630 17.19 0.00 31.54 1.82
937 1387 1.194218 AAATTGGGGATTTGGAGCGG 58.806 50.000 0.00 0.00 36.61 5.52
1329 1782 6.435277 ACCAACTGCTCACAAAATAGATCAAT 59.565 34.615 0.00 0.00 0.00 2.57
1436 1891 9.922477 AGCATGTTCCTATATATAGCTACTACA 57.078 33.333 13.49 11.60 0.00 2.74
1541 1996 8.145767 CCGAATCATTACTGTACCACCTAAATA 58.854 37.037 0.00 0.00 0.00 1.40
1551 2006 4.189231 AGTTGCCCGAATCATTACTGTAC 58.811 43.478 0.00 0.00 0.00 2.90
1552 2007 4.081365 TGAGTTGCCCGAATCATTACTGTA 60.081 41.667 0.00 0.00 0.00 2.74
1553 2008 3.270877 GAGTTGCCCGAATCATTACTGT 58.729 45.455 0.00 0.00 0.00 3.55
1766 2221 6.477688 GCAAATTGTATATGCAAGCTCACAAT 59.522 34.615 11.95 0.00 39.81 2.71
1986 2442 7.417513 CCTAAAGGATCCATGGATGTTCCAAG 61.418 46.154 32.05 21.90 43.89 3.61
2021 2477 5.129650 AGAAAGAAGATACACTAGAAGGGCC 59.870 44.000 0.00 0.00 0.00 5.80
2065 2521 7.770897 ACTCACTCGAAGGCATAATTAAAAGAT 59.229 33.333 0.00 0.00 0.00 2.40
2098 2554 7.312154 TGATAGTGGTTTTGACATTATTGCAC 58.688 34.615 0.00 0.00 0.00 4.57
2114 2570 6.686484 TGCCAGAATGTATATGATAGTGGT 57.314 37.500 0.00 0.00 0.00 4.16
2264 2720 2.117423 AGGGGAGGCAAAAACGGG 59.883 61.111 0.00 0.00 0.00 5.28
2296 2752 3.316308 GCATAATAGCTTTGGGTCTGGTG 59.684 47.826 0.00 0.00 0.00 4.17
2513 2969 5.943706 CAACAATTGCCAATCCAAAATCA 57.056 34.783 5.05 0.00 0.00 2.57
2550 3006 3.004210 CCACCACGTTGTTTCATGATGAA 59.996 43.478 3.29 3.29 34.03 2.57
2590 3046 2.282674 CCAGCTGCAGGGAAGCAA 60.283 61.111 17.12 0.00 45.13 3.91
3059 3532 5.220567 GCTGTTTGATCTTAGACTAAGCAGC 60.221 44.000 22.97 22.97 37.80 5.25
3083 3556 6.615264 ATCAATCCATCTGAGATTTGTTCG 57.385 37.500 0.00 0.00 31.56 3.95
3125 3598 7.825761 TGCACAATAAGCTATCATGTATATGCT 59.174 33.333 0.00 0.00 34.21 3.79
3156 3629 5.048846 ACCAAATAGCCACCCAAGTATAG 57.951 43.478 0.00 0.00 0.00 1.31
3177 3650 7.116519 CCTCAGTGAGTTTAAACTTACAGCTAC 59.883 40.741 32.52 15.87 45.03 3.58
3183 3656 8.834749 AATCTCCTCAGTGAGTTTAAACTTAC 57.165 34.615 27.26 27.26 43.52 2.34
3396 3869 3.181459 TGTTGATTCAGAAACAGGGTCGA 60.181 43.478 0.00 0.00 32.66 4.20
3398 3871 3.882888 TGTGTTGATTCAGAAACAGGGTC 59.117 43.478 0.00 0.00 36.98 4.46
3447 3920 7.441836 CAGGGTAGCATGTAACATACTGATAA 58.558 38.462 0.00 0.00 0.00 1.75
3451 3924 3.809832 GCAGGGTAGCATGTAACATACTG 59.190 47.826 8.51 4.63 0.00 2.74
3485 3958 7.944061 TGTCATGTTTCATTTGAGTCTCAATT 58.056 30.769 15.95 9.86 36.11 2.32
3486 3959 7.514784 TGTCATGTTTCATTTGAGTCTCAAT 57.485 32.000 15.95 4.22 36.11 2.57
3499 3972 6.151480 AGCATATTGTCACATGTCATGTTTCA 59.849 34.615 15.98 14.13 42.70 2.69
3514 3987 3.379372 ACATCACCTGCAAGCATATTGTC 59.621 43.478 0.00 0.00 0.00 3.18
3517 3990 2.100252 GCACATCACCTGCAAGCATATT 59.900 45.455 0.00 0.00 34.56 1.28
3523 3996 2.345760 GGGGCACATCACCTGCAAG 61.346 63.158 0.00 0.00 36.27 4.01
3808 4289 1.854743 CATACACTCCTGCATCGTTCG 59.145 52.381 0.00 0.00 0.00 3.95
4000 4481 7.019774 ACACATCACACAAATAGTCATATGC 57.980 36.000 0.00 0.00 0.00 3.14
4147 4629 6.273889 TGGGAAGGAGGGAATAGTAACTTTA 58.726 40.000 0.00 0.00 0.00 1.85
4166 4648 8.380099 AGGCGTAAATGTCTTATATTATGGGAA 58.620 33.333 0.00 0.00 0.00 3.97
4183 4665 7.913789 TCTGTCCCATAATATAAGGCGTAAAT 58.086 34.615 0.00 0.00 0.00 1.40
4211 4693 3.642848 ACTTCCGTCCCAAAGTTGTACTA 59.357 43.478 0.00 0.00 31.81 1.82
4243 4725 4.451629 TTACTTCCGTGTTTGCCAAAAA 57.548 36.364 0.00 0.00 0.00 1.94
4244 4726 4.451629 TTTACTTCCGTGTTTGCCAAAA 57.548 36.364 0.00 0.00 0.00 2.44
4248 4730 3.972403 ACATTTTACTTCCGTGTTTGCC 58.028 40.909 0.00 0.00 0.00 4.52
4249 4731 5.723237 CAAACATTTTACTTCCGTGTTTGC 58.277 37.500 13.97 0.00 46.84 3.68
4251 4733 8.599774 CAAATCAAACATTTTACTTCCGTGTTT 58.400 29.630 0.00 0.00 41.98 2.83
4254 4736 6.580476 GCAAATCAAACATTTTACTTCCGTG 58.420 36.000 0.00 0.00 0.00 4.94
4255 4737 5.401079 CGCAAATCAAACATTTTACTTCCGT 59.599 36.000 0.00 0.00 0.00 4.69
4256 4738 5.627367 TCGCAAATCAAACATTTTACTTCCG 59.373 36.000 0.00 0.00 0.00 4.30
4257 4739 6.419413 TGTCGCAAATCAAACATTTTACTTCC 59.581 34.615 0.00 0.00 0.00 3.46
4258 4740 7.388290 TGTCGCAAATCAAACATTTTACTTC 57.612 32.000 0.00 0.00 0.00 3.01
4260 4742 8.296713 AGTATGTCGCAAATCAAACATTTTACT 58.703 29.630 0.00 0.00 34.39 2.24
4261 4743 8.447787 AGTATGTCGCAAATCAAACATTTTAC 57.552 30.769 0.00 0.00 34.39 2.01
4265 5815 7.750458 CAGTTAGTATGTCGCAAATCAAACATT 59.250 33.333 0.00 0.00 34.39 2.71
4273 5823 5.818136 AATGCAGTTAGTATGTCGCAAAT 57.182 34.783 0.00 0.00 32.38 2.32
4318 5868 9.539825 CTTCATATTACTCTGACTAATGCAGTT 57.460 33.333 0.00 0.00 37.72 3.16
4319 5869 8.700051 ACTTCATATTACTCTGACTAATGCAGT 58.300 33.333 0.00 0.00 41.47 4.40
4320 5870 9.539825 AACTTCATATTACTCTGACTAATGCAG 57.460 33.333 0.00 0.00 34.71 4.41
4321 5871 9.890629 AAACTTCATATTACTCTGACTAATGCA 57.109 29.630 0.00 0.00 0.00 3.96
4363 5913 4.096984 CCCAGCTATTCCTTTAAACTGCTG 59.903 45.833 0.00 0.00 44.09 4.41
4364 5914 4.273318 CCCAGCTATTCCTTTAAACTGCT 58.727 43.478 0.00 0.00 0.00 4.24
4365 5915 3.181486 GCCCAGCTATTCCTTTAAACTGC 60.181 47.826 0.00 0.00 0.00 4.40
4366 5916 3.381590 GGCCCAGCTATTCCTTTAAACTG 59.618 47.826 0.00 0.00 0.00 3.16
4367 5917 3.627492 GGGCCCAGCTATTCCTTTAAACT 60.627 47.826 19.95 0.00 0.00 2.66
4368 5918 2.693591 GGGCCCAGCTATTCCTTTAAAC 59.306 50.000 19.95 0.00 0.00 2.01
4369 5919 2.585432 AGGGCCCAGCTATTCCTTTAAA 59.415 45.455 27.56 0.00 0.00 1.52
4370 5920 2.214201 AGGGCCCAGCTATTCCTTTAA 58.786 47.619 27.56 0.00 0.00 1.52
4387 5937 3.483869 GGTCTGGGCTGCCTAGGG 61.484 72.222 28.69 8.52 32.70 3.53
4412 5962 3.607741 GCTAGTACTTTTTCCACTCCCC 58.392 50.000 0.00 0.00 0.00 4.81
4416 5966 4.567747 CCATGGGCTAGTACTTTTTCCACT 60.568 45.833 2.85 0.00 0.00 4.00
4442 5992 1.152881 GCCTCGGGCCAAATCTCAT 60.153 57.895 4.39 0.00 44.06 2.90
4467 6017 1.073722 TTCTTGGGCTGGCTGTCTG 59.926 57.895 0.00 0.00 0.00 3.51
4490 6040 2.603021 TCAAGCTCCTCTCAAGTCAGT 58.397 47.619 0.00 0.00 0.00 3.41
4495 6045 3.118811 CCCTAGTTCAAGCTCCTCTCAAG 60.119 52.174 0.00 0.00 0.00 3.02
4497 6047 2.461695 CCCTAGTTCAAGCTCCTCTCA 58.538 52.381 0.00 0.00 0.00 3.27
4526 6081 0.908198 GAGTTGTCCTGAGATGGCCT 59.092 55.000 3.32 0.00 0.00 5.19
4527 6082 0.107459 GGAGTTGTCCTGAGATGGCC 60.107 60.000 0.00 0.00 40.17 5.36
4528 6083 0.615331 TGGAGTTGTCCTGAGATGGC 59.385 55.000 0.00 0.00 44.30 4.40
4529 6084 2.304180 AGTTGGAGTTGTCCTGAGATGG 59.696 50.000 0.00 0.00 44.30 3.51
4530 6085 3.332919 CAGTTGGAGTTGTCCTGAGATG 58.667 50.000 0.00 0.00 44.30 2.90
4531 6086 2.304180 CCAGTTGGAGTTGTCCTGAGAT 59.696 50.000 0.00 0.00 44.30 2.75
4532 6087 1.694150 CCAGTTGGAGTTGTCCTGAGA 59.306 52.381 0.00 0.00 44.30 3.27
4534 6089 0.108585 GCCAGTTGGAGTTGTCCTGA 59.891 55.000 1.45 0.00 44.30 3.86
4535 6090 0.890996 GGCCAGTTGGAGTTGTCCTG 60.891 60.000 0.00 0.00 44.30 3.86
4536 6091 1.352622 TGGCCAGTTGGAGTTGTCCT 61.353 55.000 0.00 0.00 44.30 3.85
4537 6092 0.467290 TTGGCCAGTTGGAGTTGTCC 60.467 55.000 5.11 0.00 44.24 4.02
4538 6093 0.668535 GTTGGCCAGTTGGAGTTGTC 59.331 55.000 5.11 0.00 37.39 3.18
4539 6094 0.755327 GGTTGGCCAGTTGGAGTTGT 60.755 55.000 5.11 0.00 37.39 3.32
4540 6095 1.463553 GGGTTGGCCAGTTGGAGTTG 61.464 60.000 5.11 0.00 37.39 3.16
4541 6096 1.152546 GGGTTGGCCAGTTGGAGTT 60.153 57.895 5.11 0.00 37.39 3.01
4542 6097 1.943730 TTGGGTTGGCCAGTTGGAGT 61.944 55.000 5.11 0.00 37.39 3.85
4543 6098 0.758685 TTTGGGTTGGCCAGTTGGAG 60.759 55.000 5.11 0.00 37.39 3.86
4550 6105 2.519780 GTCCGTTTGGGTTGGCCA 60.520 61.111 0.00 0.00 37.00 5.36
4553 6108 1.032657 TGTGTGTCCGTTTGGGTTGG 61.033 55.000 0.00 0.00 37.00 3.77
4555 6110 1.407258 CATTGTGTGTCCGTTTGGGTT 59.593 47.619 0.00 0.00 37.00 4.11
4572 6127 5.696724 TCCAACAAACAAAAACGAACACATT 59.303 32.000 0.00 0.00 0.00 2.71
4587 6142 1.934849 GCTTGGCCGATTCCAACAAAC 60.935 52.381 0.00 0.00 40.92 2.93
4589 6144 1.861542 CGCTTGGCCGATTCCAACAA 61.862 55.000 0.00 0.00 40.92 2.83
4591 6146 2.485122 CGCTTGGCCGATTCCAAC 59.515 61.111 0.00 0.00 40.92 3.77
4594 6149 3.202706 GTCCGCTTGGCCGATTCC 61.203 66.667 0.00 0.00 0.00 3.01
4595 6150 2.435938 TGTCCGCTTGGCCGATTC 60.436 61.111 0.00 0.00 0.00 2.52
4596 6151 2.746277 GTGTCCGCTTGGCCGATT 60.746 61.111 0.00 0.00 0.00 3.34
4597 6152 4.778143 GGTGTCCGCTTGGCCGAT 62.778 66.667 0.00 0.00 0.00 4.18
4619 6174 1.883021 GGGCCATCAAACAAGACGG 59.117 57.895 4.39 0.00 0.00 4.79
4621 6176 1.737793 CTACGGGCCATCAAACAAGAC 59.262 52.381 4.39 0.00 0.00 3.01
4628 6183 2.270850 GCACCTACGGGCCATCAA 59.729 61.111 4.39 0.00 35.63 2.57
4656 6211 0.447801 AATCTGAAATGCACGTCCGC 59.552 50.000 0.00 0.00 0.00 5.54
4657 6212 2.900122 AAATCTGAAATGCACGTCCG 57.100 45.000 0.00 0.00 0.00 4.79
4661 6216 8.619146 AATATTGTGTAAATCTGAAATGCACG 57.381 30.769 0.00 0.00 0.00 5.34
4710 6265 0.600255 AGCCGAGACTTTTGGTGACG 60.600 55.000 0.00 0.00 32.26 4.35
4762 6317 3.141398 ACGACCACAACTAGACGTAAGA 58.859 45.455 0.00 0.00 43.62 2.10
4768 6323 1.665161 CCACGACGACCACAACTAGAC 60.665 57.143 0.00 0.00 0.00 2.59
4781 6336 2.645510 GACAGCGACAACCACGACG 61.646 63.158 0.00 0.00 0.00 5.12
4784 6339 2.645510 GACGACAGCGACAACCACG 61.646 63.158 0.00 0.00 41.64 4.94
4787 6342 1.733399 GAGGACGACAGCGACAACC 60.733 63.158 0.00 0.00 41.64 3.77
4790 6345 1.897137 AGTGAGGACGACAGCGACA 60.897 57.895 0.00 0.00 41.64 4.35
4794 6353 1.373497 CACCAGTGAGGACGACAGC 60.373 63.158 0.00 0.00 41.22 4.40
4818 6377 1.410517 TGAGATCATCTGGCCTTCGTC 59.589 52.381 3.32 0.00 0.00 4.20
4821 6380 2.371179 TCCATGAGATCATCTGGCCTTC 59.629 50.000 3.32 0.00 33.61 3.46


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

AutoCloner maintained by Alex Coulton.