Multiple sequence alignment - TraesCS7B01G132100

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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 TraesCS7B01G132100 chr7B 100.000 4064 0 0 1 4064 159528168 159524105 0.000000e+00 7505.0
1 TraesCS7B01G132100 chr7B 95.238 63 3 0 364 426 159527746 159527684 2.580000e-17 100.0
2 TraesCS7B01G132100 chr7B 95.238 63 3 0 423 485 159527805 159527743 2.580000e-17 100.0
3 TraesCS7B01G132100 chr7D 93.836 3861 163 35 232 4051 195650403 195646577 0.000000e+00 5742.0
4 TraesCS7B01G132100 chr7D 93.514 185 7 2 1 181 195650596 195650413 1.860000e-68 270.0
5 TraesCS7B01G132100 chr7D 93.651 63 4 0 364 426 195650211 195650149 1.200000e-15 95.3
6 TraesCS7B01G132100 chr7A 95.005 3063 86 23 232 3279 205487814 205484804 0.000000e+00 4747.0
7 TraesCS7B01G132100 chr7A 94.054 185 7 1 1 181 205488008 205487824 1.110000e-70 278.0
8 TraesCS7B01G132100 chr7A 95.312 64 3 0 423 486 205487686 205487623 7.190000e-18 102.0
9 TraesCS7B01G132100 chr7A 93.750 64 3 1 364 426 205487627 205487564 1.200000e-15 95.3
10 TraesCS7B01G132100 chr7A 82.716 81 8 3 776 850 247256983 247257063 2.620000e-07 67.6
11 TraesCS7B01G132100 chr4A 79.310 435 74 11 2229 2649 396759852 396759420 1.430000e-74 291.0
12 TraesCS7B01G132100 chr4A 88.333 60 7 0 794 853 626981551 626981492 5.630000e-09 73.1
13 TraesCS7B01G132100 chr4B 77.573 379 76 8 2229 2602 193996249 193995875 1.900000e-53 220.0
14 TraesCS7B01G132100 chr3A 97.778 45 1 0 794 838 353182776 353182820 1.210000e-10 78.7
15 TraesCS7B01G132100 chr5D 94.000 50 2 1 776 825 501773163 501773211 1.570000e-09 75.0
16 TraesCS7B01G132100 chr5B 94.000 50 1 2 776 825 625522832 625522879 1.570000e-09 75.0
17 TraesCS7B01G132100 chr5A 87.879 66 5 3 776 839 629712510 629712446 1.570000e-09 75.0
18 TraesCS7B01G132100 chr5A 95.455 44 2 0 794 837 364712692 364712649 2.030000e-08 71.3
19 TraesCS7B01G132100 chr6A 90.741 54 5 0 797 850 420829872 420829925 5.630000e-09 73.1


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 TraesCS7B01G132100 chr7B 159524105 159528168 4063 True 2568.333333 7505 96.825333 1 4064 3 chr7B.!!$R1 4063
1 TraesCS7B01G132100 chr7D 195646577 195650596 4019 True 2035.766667 5742 93.667000 1 4051 3 chr7D.!!$R1 4050
2 TraesCS7B01G132100 chr7A 205484804 205488008 3204 True 1305.575000 4747 94.530250 1 3279 4 chr7A.!!$R1 3278

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
556 565 0.462759 CTTCCTCTCGGCACCATTCC 60.463 60.000 0.00 0.0 0.00 3.01 F
1433 1444 2.428171 TGCTGAGAAGCAAAGCAGTTTT 59.572 40.909 0.00 0.0 41.83 2.43 F
2005 2026 1.680338 ACTTGTTGAAGGCCAGACAC 58.320 50.000 5.01 0.0 32.95 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2008 0.954452 GGTGTCTGGCCTTCAACAAG 59.046 55.0 3.32 0.0 0.00 3.16 R
2835 2856 0.107848 GTACAGCGGGCATGGTAACT 60.108 55.0 0.00 0.0 37.61 2.24 R
3992 4041 0.321564 CTCGGTCCCATTGCACTCAA 60.322 55.0 0.00 0.0 36.51 3.02 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
37 38 6.531021 TCTTTTGTCCTTTTAGACGAGGATT 58.469 36.000 0.00 0.00 43.54 3.01
39 40 8.152246 TCTTTTGTCCTTTTAGACGAGGATTTA 58.848 33.333 0.00 0.00 43.54 1.40
52 53 4.841813 ACGAGGATTTATTTTTGGGGGTTT 59.158 37.500 0.00 0.00 0.00 3.27
80 81 2.084610 TGATGTACAGTGCTGTCTGC 57.915 50.000 8.23 2.00 43.74 4.26
181 186 4.612264 AGAAGGGCGTACTTTCTTTGTA 57.388 40.909 1.80 0.00 0.00 2.41
182 187 4.964593 AGAAGGGCGTACTTTCTTTGTAA 58.035 39.130 1.80 0.00 0.00 2.41
183 188 5.370679 AGAAGGGCGTACTTTCTTTGTAAA 58.629 37.500 1.80 0.00 0.00 2.01
185 190 6.489022 AGAAGGGCGTACTTTCTTTGTAAATT 59.511 34.615 1.80 0.00 0.00 1.82
187 192 5.533528 AGGGCGTACTTTCTTTGTAAATTGT 59.466 36.000 0.00 0.00 0.00 2.71
188 193 6.040054 AGGGCGTACTTTCTTTGTAAATTGTT 59.960 34.615 0.00 0.00 0.00 2.83
190 195 7.136772 GGCGTACTTTCTTTGTAAATTGTTCT 58.863 34.615 0.00 0.00 0.00 3.01
191 196 7.646526 GGCGTACTTTCTTTGTAAATTGTTCTT 59.353 33.333 0.00 0.00 0.00 2.52
192 197 8.469125 GCGTACTTTCTTTGTAAATTGTTCTTG 58.531 33.333 0.00 0.00 0.00 3.02
193 198 9.498307 CGTACTTTCTTTGTAAATTGTTCTTGT 57.502 29.630 0.00 0.00 0.00 3.16
200 205 9.809096 TCTTTGTAAATTGTTCTTGTTAATGCA 57.191 25.926 0.00 0.00 0.00 3.96
201 206 9.848172 CTTTGTAAATTGTTCTTGTTAATGCAC 57.152 29.630 0.00 0.00 0.00 4.57
202 207 8.932945 TTGTAAATTGTTCTTGTTAATGCACA 57.067 26.923 0.00 0.00 0.00 4.57
203 208 8.572828 TGTAAATTGTTCTTGTTAATGCACAG 57.427 30.769 0.00 0.00 0.00 3.66
204 209 8.409371 TGTAAATTGTTCTTGTTAATGCACAGA 58.591 29.630 0.00 0.00 0.00 3.41
205 210 7.935338 AAATTGTTCTTGTTAATGCACAGAG 57.065 32.000 0.00 0.00 0.00 3.35
206 211 6.882610 ATTGTTCTTGTTAATGCACAGAGA 57.117 33.333 0.00 0.00 0.00 3.10
207 212 6.691754 TTGTTCTTGTTAATGCACAGAGAA 57.308 33.333 0.00 0.00 0.00 2.87
208 213 6.691754 TGTTCTTGTTAATGCACAGAGAAA 57.308 33.333 0.00 0.00 31.49 2.52
209 214 6.728200 TGTTCTTGTTAATGCACAGAGAAAG 58.272 36.000 0.00 0.00 31.49 2.62
210 215 6.318648 TGTTCTTGTTAATGCACAGAGAAAGT 59.681 34.615 0.00 0.00 31.49 2.66
211 216 7.497579 TGTTCTTGTTAATGCACAGAGAAAGTA 59.502 33.333 0.00 0.00 31.49 2.24
212 217 7.421530 TCTTGTTAATGCACAGAGAAAGTAC 57.578 36.000 0.00 0.00 0.00 2.73
213 218 5.839262 TGTTAATGCACAGAGAAAGTACG 57.161 39.130 0.00 0.00 0.00 3.67
214 219 4.151689 TGTTAATGCACAGAGAAAGTACGC 59.848 41.667 0.00 0.00 0.00 4.42
215 220 1.726853 ATGCACAGAGAAAGTACGCC 58.273 50.000 0.00 0.00 0.00 5.68
216 221 0.679505 TGCACAGAGAAAGTACGCCT 59.320 50.000 0.00 0.00 0.00 5.52
217 222 1.071605 GCACAGAGAAAGTACGCCTG 58.928 55.000 0.00 0.00 0.00 4.85
218 223 1.336887 GCACAGAGAAAGTACGCCTGA 60.337 52.381 0.00 0.00 0.00 3.86
219 224 2.675317 GCACAGAGAAAGTACGCCTGAT 60.675 50.000 0.00 0.00 0.00 2.90
220 225 3.589988 CACAGAGAAAGTACGCCTGATT 58.410 45.455 0.00 0.00 0.00 2.57
221 226 4.744570 CACAGAGAAAGTACGCCTGATTA 58.255 43.478 0.00 0.00 0.00 1.75
222 227 4.563184 CACAGAGAAAGTACGCCTGATTAC 59.437 45.833 0.00 0.00 0.00 1.89
223 228 4.463186 ACAGAGAAAGTACGCCTGATTACT 59.537 41.667 0.00 0.00 0.00 2.24
224 229 5.047235 ACAGAGAAAGTACGCCTGATTACTT 60.047 40.000 0.00 0.00 39.69 2.24
225 230 5.869888 CAGAGAAAGTACGCCTGATTACTTT 59.130 40.000 6.47 6.47 46.46 2.66
226 231 5.869888 AGAGAAAGTACGCCTGATTACTTTG 59.130 40.000 10.63 0.00 44.73 2.77
227 232 5.548406 AGAAAGTACGCCTGATTACTTTGT 58.452 37.500 10.63 5.09 44.73 2.83
228 233 5.408604 AGAAAGTACGCCTGATTACTTTGTG 59.591 40.000 10.63 0.00 44.73 3.33
229 234 4.267349 AGTACGCCTGATTACTTTGTGT 57.733 40.909 0.00 0.00 0.00 3.72
230 235 5.395682 AGTACGCCTGATTACTTTGTGTA 57.604 39.130 0.00 0.00 0.00 2.90
244 249 3.806949 TTGTGTAAAGGAAGGCCATCT 57.193 42.857 5.01 0.00 36.29 2.90
282 287 5.717178 TCCAATTCTATCCCTAATCTCGAGG 59.283 44.000 13.56 0.00 0.00 4.63
295 300 2.048222 CGAGGTCACCATGCACGT 60.048 61.111 0.00 0.00 0.00 4.49
333 338 1.053264 AGCGCTTCATCTCCCTCCAT 61.053 55.000 2.64 0.00 0.00 3.41
336 341 1.347050 CGCTTCATCTCCCTCCATCAT 59.653 52.381 0.00 0.00 0.00 2.45
428 434 6.636454 TGGAGGAAGGAATTAACTACATGT 57.364 37.500 2.69 2.69 0.00 3.21
544 553 2.157989 ACTCCACCCCTAAACTTCCTCT 60.158 50.000 0.00 0.00 0.00 3.69
549 558 0.902531 CCCTAAACTTCCTCTCGGCA 59.097 55.000 0.00 0.00 0.00 5.69
556 565 0.462759 CTTCCTCTCGGCACCATTCC 60.463 60.000 0.00 0.00 0.00 3.01
629 638 6.668283 AGGGAGTAATGTGTACTGTCTATGTT 59.332 38.462 0.00 0.00 0.00 2.71
734 743 6.041979 ACTTGTTCCTGCCAGAAATGTTAAAT 59.958 34.615 0.00 0.00 0.00 1.40
774 783 7.861630 TGCTAACTTGTAGATTCAAACTTGAC 58.138 34.615 0.00 0.00 36.83 3.18
778 787 8.958119 AACTTGTAGATTCAAACTTGACACTA 57.042 30.769 0.00 0.00 36.83 2.74
850 859 5.717119 TCCTATAAAAGTGAACAGACGGAC 58.283 41.667 0.00 0.00 0.00 4.79
864 873 6.579666 ACAGACGGACTAGTTTGTAATGTA 57.420 37.500 0.00 0.00 37.63 2.29
1008 1017 3.639094 GGAGTGTATAGCTGATGTCTGGT 59.361 47.826 0.00 0.00 0.00 4.00
1091 1100 9.317936 GCTAAATGCTATTTATCAAGCCTTTTT 57.682 29.630 3.55 0.00 37.60 1.94
1336 1347 2.729028 AACCAAGGTACTGCACAACT 57.271 45.000 0.00 0.00 40.86 3.16
1433 1444 2.428171 TGCTGAGAAGCAAAGCAGTTTT 59.572 40.909 0.00 0.00 41.83 2.43
1495 1506 5.471456 GCCCTGTCTCCTCAATAATGTTATG 59.529 44.000 0.00 0.00 0.00 1.90
1496 1507 6.688922 GCCCTGTCTCCTCAATAATGTTATGA 60.689 42.308 0.00 0.00 0.00 2.15
1497 1508 7.456725 CCCTGTCTCCTCAATAATGTTATGAT 58.543 38.462 0.00 0.00 0.00 2.45
1498 1509 7.605691 CCCTGTCTCCTCAATAATGTTATGATC 59.394 40.741 0.00 0.00 0.00 2.92
1499 1510 7.330454 CCTGTCTCCTCAATAATGTTATGATCG 59.670 40.741 0.00 0.00 0.00 3.69
1500 1511 7.726216 TGTCTCCTCAATAATGTTATGATCGT 58.274 34.615 0.00 0.00 0.00 3.73
1501 1512 8.204160 TGTCTCCTCAATAATGTTATGATCGTT 58.796 33.333 0.00 0.00 0.00 3.85
1502 1513 9.692749 GTCTCCTCAATAATGTTATGATCGTTA 57.307 33.333 0.00 0.00 0.00 3.18
1519 1530 8.922058 TGATCGTTATCCAGTCTAAAAAGTAC 57.078 34.615 0.00 0.00 0.00 2.73
1601 1618 8.550376 GGTACGTTTTCTTCTAAACACATTGTA 58.450 33.333 0.00 0.00 37.77 2.41
1903 1920 9.258629 TCATTCTGGGATGAAAATCTATGTTTT 57.741 29.630 0.00 0.00 33.31 2.43
1987 2008 4.003648 CCAGAGACTTGGGTGTAATGAAC 58.996 47.826 0.00 0.00 34.46 3.18
2005 2026 1.680338 ACTTGTTGAAGGCCAGACAC 58.320 50.000 5.01 0.00 32.95 3.67
2094 2115 3.568181 CGTAGCTTTGTGCATGTCG 57.432 52.632 0.00 0.00 45.94 4.35
2160 2181 8.105829 ACTGAATCTGAAGGTTCAATGAAGTAT 58.894 33.333 7.39 0.00 36.64 2.12
2172 2193 6.566079 TCAATGAAGTATGAAGGAGATGGT 57.434 37.500 0.00 0.00 0.00 3.55
2199 2220 9.674824 CAATTTAGAGTGATGGAAAATGCTATC 57.325 33.333 0.00 0.00 0.00 2.08
2221 2242 4.647853 TCGGTAGCACAGTCATACCTAATT 59.352 41.667 8.48 0.00 37.42 1.40
2229 2250 6.586344 CACAGTCATACCTAATTCTGATGGT 58.414 40.000 0.00 0.00 36.66 3.55
2538 2559 3.747529 GGAACACAGATTTTTGCATTGGG 59.252 43.478 0.00 0.00 0.00 4.12
3008 3029 1.528824 CGGCTCCATCTGGATTGGT 59.471 57.895 0.00 0.00 44.46 3.67
3110 3132 3.003480 GGTTGTCTGCATAGAGTTGTCC 58.997 50.000 0.00 0.00 32.48 4.02
3208 3230 4.835615 ACTTGAGTCCTGTGAGTTGACTAT 59.164 41.667 0.00 0.00 39.36 2.12
3210 3232 6.493802 ACTTGAGTCCTGTGAGTTGACTATAA 59.506 38.462 0.00 0.00 39.36 0.98
3211 3233 6.911250 TGAGTCCTGTGAGTTGACTATAAA 57.089 37.500 0.00 0.00 39.36 1.40
3212 3234 6.688578 TGAGTCCTGTGAGTTGACTATAAAC 58.311 40.000 0.00 0.00 39.36 2.01
3279 3301 5.108027 GCACATTGTGGTTTACATTTCGTTC 60.108 40.000 18.05 0.00 39.48 3.95
3286 3308 4.209703 TGGTTTACATTTCGTTCGTCTGTC 59.790 41.667 0.00 0.00 0.00 3.51
3298 3320 0.660595 CGTCTGTCGTCTGCTCGTTT 60.661 55.000 0.00 0.00 34.52 3.60
3301 3323 1.337071 TCTGTCGTCTGCTCGTTTTCT 59.663 47.619 0.00 0.00 0.00 2.52
3353 3375 1.509703 GGCTCCCGATAATCCGAAAC 58.490 55.000 0.00 0.00 0.00 2.78
3358 3380 3.724374 TCCCGATAATCCGAAACATGTC 58.276 45.455 0.00 0.00 0.00 3.06
3370 3392 0.740868 AACATGTCCTCGGATGTGCG 60.741 55.000 0.00 0.00 33.03 5.34
3391 3414 4.993550 CGGATTTTCTCGCTTTGTTTTTG 58.006 39.130 0.00 0.00 0.00 2.44
3394 3417 6.184706 GGATTTTCTCGCTTTGTTTTTGTTG 58.815 36.000 0.00 0.00 0.00 3.33
3441 3464 2.953020 GCTCCAGGTAGCAGATTATCG 58.047 52.381 6.13 0.00 42.30 2.92
3455 3478 7.445121 AGCAGATTATCGTATTTCTCCATGAA 58.555 34.615 0.00 0.00 0.00 2.57
3537 3563 7.888250 ATCATCTCATTAAAAAGAAGGGTCC 57.112 36.000 0.00 0.00 0.00 4.46
3538 3564 5.880332 TCATCTCATTAAAAAGAAGGGTCCG 59.120 40.000 0.00 0.00 0.00 4.79
3539 3565 5.237236 TCTCATTAAAAAGAAGGGTCCGT 57.763 39.130 0.00 0.00 0.00 4.69
3540 3566 6.363167 TCTCATTAAAAAGAAGGGTCCGTA 57.637 37.500 0.00 0.00 0.00 4.02
3541 3567 6.403878 TCTCATTAAAAAGAAGGGTCCGTAG 58.596 40.000 0.00 0.00 0.00 3.51
3542 3568 6.013984 TCTCATTAAAAAGAAGGGTCCGTAGT 60.014 38.462 0.00 0.00 0.00 2.73
3555 3582 3.250521 GGTCCGTAGTATACTGTGCTCTC 59.749 52.174 15.90 0.69 40.12 3.20
3579 3606 4.838486 CGTCTCACCGAGCGAGCC 62.838 72.222 0.00 0.00 33.54 4.70
3612 3639 4.771590 CATCTTGTGCTGGTTATTGTGT 57.228 40.909 0.00 0.00 0.00 3.72
3626 3653 6.096987 TGGTTATTGTGTTTGTAAAGAAGGCA 59.903 34.615 0.00 0.00 0.00 4.75
3635 3662 2.832129 TGTAAAGAAGGCACGGAGAGAT 59.168 45.455 0.00 0.00 0.00 2.75
3639 3666 0.103937 GAAGGCACGGAGAGATCAGG 59.896 60.000 0.00 0.00 0.00 3.86
3642 3669 0.103937 GGCACGGAGAGATCAGGAAG 59.896 60.000 0.00 0.00 0.00 3.46
3656 3683 1.078848 GGAAGATGCTCAGCGGTGT 60.079 57.895 15.22 0.00 0.00 4.16
3666 3693 0.684535 TCAGCGGTGTGGATCTTTGA 59.315 50.000 15.22 0.00 0.00 2.69
3678 3707 5.538053 TGTGGATCTTTGAAACATAGCCAAA 59.462 36.000 0.00 0.00 0.00 3.28
3682 3711 5.726980 TCTTTGAAACATAGCCAAAGCAT 57.273 34.783 0.00 0.00 43.68 3.79
3694 3723 3.579586 AGCCAAAGCATCTGAATTGGAAA 59.420 39.130 14.81 0.00 44.01 3.13
3696 3725 4.390909 GCCAAAGCATCTGAATTGGAAAAG 59.609 41.667 14.81 0.00 44.01 2.27
3697 3726 4.390909 CCAAAGCATCTGAATTGGAAAAGC 59.609 41.667 8.07 0.00 44.01 3.51
3698 3727 4.877378 AAGCATCTGAATTGGAAAAGCA 57.123 36.364 0.00 0.00 0.00 3.91
3708 3741 7.986320 TCTGAATTGGAAAAGCATTCAAAAAGA 59.014 29.630 4.87 3.07 36.67 2.52
3711 3744 7.719778 ATTGGAAAAGCATTCAAAAAGAGTC 57.280 32.000 4.87 0.00 0.00 3.36
3712 3745 6.219417 TGGAAAAGCATTCAAAAAGAGTCA 57.781 33.333 4.87 0.00 0.00 3.41
3720 3753 7.967178 AGCATTCAAAAAGAGTCAAAACTTTG 58.033 30.769 0.00 0.00 36.62 2.77
3752 3789 2.889170 TTACCAAACATGGCCTAGCA 57.111 45.000 3.32 0.00 0.00 3.49
3760 3797 5.182001 CCAAACATGGCCTAGCATATTACTC 59.818 44.000 3.32 0.00 0.00 2.59
3763 3800 4.770531 ACATGGCCTAGCATATTACTCGTA 59.229 41.667 3.32 0.00 0.00 3.43
3764 3801 5.245301 ACATGGCCTAGCATATTACTCGTAA 59.755 40.000 3.32 0.00 0.00 3.18
3775 3814 8.166706 AGCATATTACTCGTAAAAAGTTTCACG 58.833 33.333 13.67 13.67 35.78 4.35
3796 3835 3.187700 GGATGAATGACTGTCGTGGTAC 58.812 50.000 2.78 0.00 0.00 3.34
3834 3879 6.160576 AGAAGCTAAATTGCAAGTCCAAAA 57.839 33.333 4.94 0.00 34.99 2.44
3886 3935 7.758528 GTCTACAATACAACGGTAGTCATTCTT 59.241 37.037 0.00 0.00 36.68 2.52
3887 3936 6.963049 ACAATACAACGGTAGTCATTCTTC 57.037 37.500 0.00 0.00 31.88 2.87
3888 3937 6.698380 ACAATACAACGGTAGTCATTCTTCT 58.302 36.000 0.00 0.00 31.88 2.85
3890 3939 3.326747 ACAACGGTAGTCATTCTTCTGC 58.673 45.455 0.00 0.00 0.00 4.26
3903 3952 3.585748 TCTTCTGCGAAACTTTTCACG 57.414 42.857 2.77 0.00 37.01 4.35
3904 3953 2.933906 TCTTCTGCGAAACTTTTCACGT 59.066 40.909 2.77 0.00 37.01 4.49
3905 3954 2.730183 TCTGCGAAACTTTTCACGTG 57.270 45.000 9.94 9.94 37.01 4.49
3912 3961 4.768145 CGAAACTTTTCACGTGAGCATTA 58.232 39.130 19.11 0.00 37.01 1.90
3927 3976 7.435488 ACGTGAGCATTACACTAAGTCATATTC 59.565 37.037 0.00 0.00 36.29 1.75
3943 3992 9.769093 AAGTCATATTCGTAACAAAATGTTAGC 57.231 29.630 3.32 0.00 42.78 3.09
3979 4028 8.292448 TGACTCTTTTTGATATTGCAAGTTCTC 58.708 33.333 4.94 0.00 0.00 2.87
3980 4029 8.401490 ACTCTTTTTGATATTGCAAGTTCTCT 57.599 30.769 4.94 0.00 0.00 3.10
3981 4030 8.854117 ACTCTTTTTGATATTGCAAGTTCTCTT 58.146 29.630 4.94 0.00 0.00 2.85
4024 4073 0.960286 GACCGAGACCCATAGGCTAC 59.040 60.000 0.00 0.00 36.11 3.58
4039 4088 1.269517 GGCTACTTCCGAGATGCTCAG 60.270 57.143 0.00 0.00 0.00 3.35
4051 4100 6.320418 TCCGAGATGCTCAGTGTATTTACTAA 59.680 38.462 0.00 0.00 0.00 2.24
4052 4101 6.418226 CCGAGATGCTCAGTGTATTTACTAAC 59.582 42.308 0.00 0.00 0.00 2.34
4053 4102 7.197017 CGAGATGCTCAGTGTATTTACTAACT 58.803 38.462 0.00 0.00 0.00 2.24
4054 4103 8.343366 CGAGATGCTCAGTGTATTTACTAACTA 58.657 37.037 0.00 0.00 0.00 2.24
4055 4104 9.672086 GAGATGCTCAGTGTATTTACTAACTAG 57.328 37.037 0.00 0.00 0.00 2.57
4056 4105 9.409918 AGATGCTCAGTGTATTTACTAACTAGA 57.590 33.333 0.00 0.00 0.00 2.43
4059 4108 8.343366 TGCTCAGTGTATTTACTAACTAGATCG 58.657 37.037 0.00 0.00 0.00 3.69
4060 4109 7.804129 GCTCAGTGTATTTACTAACTAGATCGG 59.196 40.741 0.00 0.00 0.00 4.18
4061 4110 7.646314 TCAGTGTATTTACTAACTAGATCGGC 58.354 38.462 0.00 0.00 0.00 5.54
4062 4111 7.283807 TCAGTGTATTTACTAACTAGATCGGCA 59.716 37.037 0.00 0.00 0.00 5.69
4063 4112 7.919091 CAGTGTATTTACTAACTAGATCGGCAA 59.081 37.037 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 9.301897 AGACAGCACTGTACATCATAGATTATA 57.698 33.333 2.68 0.00 45.05 0.98
80 81 1.065199 TCAAGGCTAAGCATGGACAGG 60.065 52.381 0.00 0.00 0.00 4.00
181 186 7.715657 TCTCTGTGCATTAACAAGAACAATTT 58.284 30.769 0.00 0.00 0.00 1.82
182 187 7.275888 TCTCTGTGCATTAACAAGAACAATT 57.724 32.000 0.00 0.00 0.00 2.32
183 188 6.882610 TCTCTGTGCATTAACAAGAACAAT 57.117 33.333 0.00 0.00 0.00 2.71
185 190 6.318648 ACTTTCTCTGTGCATTAACAAGAACA 59.681 34.615 0.00 0.00 32.23 3.18
187 192 6.942532 ACTTTCTCTGTGCATTAACAAGAA 57.057 33.333 0.00 0.00 31.42 2.52
188 193 6.145534 CGTACTTTCTCTGTGCATTAACAAGA 59.854 38.462 0.00 0.00 0.00 3.02
190 195 5.333798 GCGTACTTTCTCTGTGCATTAACAA 60.334 40.000 0.00 0.00 0.00 2.83
191 196 4.151689 GCGTACTTTCTCTGTGCATTAACA 59.848 41.667 0.00 0.00 0.00 2.41
192 197 4.435651 GGCGTACTTTCTCTGTGCATTAAC 60.436 45.833 0.00 0.00 0.00 2.01
193 198 3.682858 GGCGTACTTTCTCTGTGCATTAA 59.317 43.478 0.00 0.00 0.00 1.40
194 199 3.056107 AGGCGTACTTTCTCTGTGCATTA 60.056 43.478 0.00 0.00 0.00 1.90
195 200 2.076863 GGCGTACTTTCTCTGTGCATT 58.923 47.619 0.00 0.00 0.00 3.56
196 201 1.276421 AGGCGTACTTTCTCTGTGCAT 59.724 47.619 0.00 0.00 0.00 3.96
197 202 0.679505 AGGCGTACTTTCTCTGTGCA 59.320 50.000 0.00 0.00 0.00 4.57
198 203 1.071605 CAGGCGTACTTTCTCTGTGC 58.928 55.000 0.00 0.00 0.00 4.57
199 204 2.724977 TCAGGCGTACTTTCTCTGTG 57.275 50.000 0.00 0.00 0.00 3.66
200 205 3.963428 AATCAGGCGTACTTTCTCTGT 57.037 42.857 0.00 0.00 0.00 3.41
201 206 5.000012 AGTAATCAGGCGTACTTTCTCTG 58.000 43.478 0.00 0.00 0.00 3.35
202 207 5.662674 AAGTAATCAGGCGTACTTTCTCT 57.337 39.130 0.00 0.00 37.27 3.10
203 208 5.638234 ACAAAGTAATCAGGCGTACTTTCTC 59.362 40.000 12.56 0.00 44.72 2.87
204 209 5.408604 CACAAAGTAATCAGGCGTACTTTCT 59.591 40.000 12.56 3.42 44.72 2.52
205 210 5.178809 ACACAAAGTAATCAGGCGTACTTTC 59.821 40.000 12.56 0.00 44.72 2.62
206 211 5.061179 ACACAAAGTAATCAGGCGTACTTT 58.939 37.500 10.73 10.73 46.49 2.66
207 212 4.638304 ACACAAAGTAATCAGGCGTACTT 58.362 39.130 0.00 0.00 41.27 2.24
208 213 4.267349 ACACAAAGTAATCAGGCGTACT 57.733 40.909 0.00 0.00 31.81 2.73
209 214 6.401796 CCTTTACACAAAGTAATCAGGCGTAC 60.402 42.308 0.00 0.00 42.03 3.67
210 215 5.640357 CCTTTACACAAAGTAATCAGGCGTA 59.360 40.000 0.00 0.00 42.03 4.42
211 216 4.454504 CCTTTACACAAAGTAATCAGGCGT 59.545 41.667 0.00 0.00 42.03 5.68
212 217 4.693566 TCCTTTACACAAAGTAATCAGGCG 59.306 41.667 0.00 0.00 42.03 5.52
213 218 6.349363 CCTTCCTTTACACAAAGTAATCAGGC 60.349 42.308 0.00 0.00 42.03 4.85
214 219 6.349363 GCCTTCCTTTACACAAAGTAATCAGG 60.349 42.308 0.00 0.00 42.03 3.86
215 220 6.349363 GGCCTTCCTTTACACAAAGTAATCAG 60.349 42.308 0.00 0.00 42.03 2.90
216 221 5.475564 GGCCTTCCTTTACACAAAGTAATCA 59.524 40.000 0.00 0.00 42.03 2.57
217 222 5.475564 TGGCCTTCCTTTACACAAAGTAATC 59.524 40.000 3.32 0.00 42.03 1.75
218 223 5.390387 TGGCCTTCCTTTACACAAAGTAAT 58.610 37.500 3.32 0.00 42.03 1.89
219 224 4.794334 TGGCCTTCCTTTACACAAAGTAA 58.206 39.130 3.32 0.00 39.70 2.24
220 225 4.440826 TGGCCTTCCTTTACACAAAGTA 57.559 40.909 3.32 0.00 39.70 2.24
221 226 3.306472 TGGCCTTCCTTTACACAAAGT 57.694 42.857 3.32 0.00 39.70 2.66
222 227 4.082125 AGATGGCCTTCCTTTACACAAAG 58.918 43.478 14.77 0.00 40.80 2.77
223 228 3.826157 CAGATGGCCTTCCTTTACACAAA 59.174 43.478 14.77 0.00 0.00 2.83
224 229 3.420893 CAGATGGCCTTCCTTTACACAA 58.579 45.455 14.77 0.00 0.00 3.33
225 230 2.290896 CCAGATGGCCTTCCTTTACACA 60.291 50.000 14.77 0.00 0.00 3.72
226 231 2.026262 TCCAGATGGCCTTCCTTTACAC 60.026 50.000 14.77 0.00 34.44 2.90
227 232 2.239654 CTCCAGATGGCCTTCCTTTACA 59.760 50.000 14.77 0.00 34.44 2.41
228 233 2.505819 TCTCCAGATGGCCTTCCTTTAC 59.494 50.000 14.77 0.00 34.44 2.01
229 234 2.774234 CTCTCCAGATGGCCTTCCTTTA 59.226 50.000 14.77 0.00 34.44 1.85
230 235 1.563410 CTCTCCAGATGGCCTTCCTTT 59.437 52.381 14.77 0.00 34.44 3.11
244 249 7.995488 GGATAGAATTGGAAAGAAATCTCTCCA 59.005 37.037 1.26 1.26 0.00 3.86
428 434 0.896226 TTGCTATTGGCTGCATGCAA 59.104 45.000 22.88 7.10 45.15 4.08
503 510 2.412089 GTGACGAAAATGCTTAGCGAGT 59.588 45.455 0.00 0.00 0.00 4.18
504 511 2.668457 AGTGACGAAAATGCTTAGCGAG 59.332 45.455 0.00 0.00 0.00 5.03
505 512 2.666508 GAGTGACGAAAATGCTTAGCGA 59.333 45.455 0.00 0.00 0.00 4.93
544 553 1.304052 CCCAAAGGAATGGTGCCGA 60.304 57.895 0.00 0.00 38.91 5.54
549 558 2.104622 CTGTTTTGCCCAAAGGAATGGT 59.895 45.455 0.00 0.00 38.91 3.55
556 565 7.064966 GGATAAAATCATCTGTTTTGCCCAAAG 59.935 37.037 0.00 0.00 31.71 2.77
629 638 9.791820 GTACTACAAAAAGTGAAAGCCTTAAAA 57.208 29.630 0.00 0.00 0.00 1.52
689 698 2.482336 GTGGTATGCGAATGTTGACACA 59.518 45.455 0.00 0.00 37.31 3.72
829 838 7.536855 ACTAGTCCGTCTGTTCACTTTTATAG 58.463 38.462 0.00 0.00 0.00 1.31
839 848 5.924825 ACATTACAAACTAGTCCGTCTGTTC 59.075 40.000 0.00 0.00 0.00 3.18
840 849 5.850614 ACATTACAAACTAGTCCGTCTGTT 58.149 37.500 0.00 0.00 0.00 3.16
846 855 6.656314 TGCATTACATTACAAACTAGTCCG 57.344 37.500 0.00 0.00 0.00 4.79
864 873 8.668353 CCATTAGTTAGCGATACATATTGCATT 58.332 33.333 12.61 0.00 43.92 3.56
1495 1506 9.583765 AAGTACTTTTTAGACTGGATAACGATC 57.416 33.333 1.12 0.00 0.00 3.69
1496 1507 9.939802 AAAGTACTTTTTAGACTGGATAACGAT 57.060 29.630 15.22 0.00 0.00 3.73
1497 1508 9.415544 GAAAGTACTTTTTAGACTGGATAACGA 57.584 33.333 21.40 0.00 32.11 3.85
1498 1509 9.420551 AGAAAGTACTTTTTAGACTGGATAACG 57.579 33.333 21.40 0.00 32.11 3.18
1502 1513 8.871125 TCTCAGAAAGTACTTTTTAGACTGGAT 58.129 33.333 21.40 0.00 32.11 3.41
1503 1514 8.246430 TCTCAGAAAGTACTTTTTAGACTGGA 57.754 34.615 21.40 16.88 32.11 3.86
1601 1618 9.705290 GTTTGGACAAGTGTATAAAATTTGGAT 57.295 29.630 0.00 0.00 0.00 3.41
1674 1691 6.899393 ATTGCAGAAAAGGACAACTCATAA 57.101 33.333 0.00 0.00 0.00 1.90
1682 1699 5.538053 TCCAACATAATTGCAGAAAAGGACA 59.462 36.000 0.00 0.00 0.00 4.02
1811 1828 6.757897 TCTTATCCAAACTGCCAAACTATG 57.242 37.500 0.00 0.00 0.00 2.23
1815 1832 5.415701 TCTGATCTTATCCAAACTGCCAAAC 59.584 40.000 0.00 0.00 0.00 2.93
1899 1916 7.130269 AGAAAGATTACACACGCTACAAAAAC 58.870 34.615 0.00 0.00 0.00 2.43
1903 1920 5.534407 TGAGAAAGATTACACACGCTACAA 58.466 37.500 0.00 0.00 0.00 2.41
1987 2008 0.954452 GGTGTCTGGCCTTCAACAAG 59.046 55.000 3.32 0.00 0.00 3.16
2160 2181 6.213397 TCACTCTAAATTGACCATCTCCTTCA 59.787 38.462 0.00 0.00 0.00 3.02
2172 2193 7.707624 AGCATTTTCCATCACTCTAAATTGA 57.292 32.000 0.00 0.00 0.00 2.57
2199 2220 4.585955 ATTAGGTATGACTGTGCTACCG 57.414 45.455 8.82 0.00 39.91 4.02
2221 2242 4.067192 CACATCACAACTTCACCATCAGA 58.933 43.478 0.00 0.00 0.00 3.27
2229 2250 3.247411 CGTACTTGCACATCACAACTTCA 59.753 43.478 0.00 0.00 0.00 3.02
2424 2445 1.230324 GACCTTGACTGCTTCCACAC 58.770 55.000 0.00 0.00 0.00 3.82
2835 2856 0.107848 GTACAGCGGGCATGGTAACT 60.108 55.000 0.00 0.00 37.61 2.24
3068 3089 7.092891 ACAACCTTCATCTTCATGGACAGTATA 60.093 37.037 0.00 0.00 0.00 1.47
3110 3132 5.521010 TGTAACAGACTCAACCGTTTAGTTG 59.479 40.000 0.00 0.00 46.90 3.16
3208 3230 4.116961 CAGAACTCACAGTCAACCGTTTA 58.883 43.478 0.00 0.00 0.00 2.01
3210 3232 2.093658 ACAGAACTCACAGTCAACCGTT 60.094 45.455 0.00 0.00 0.00 4.44
3211 3233 1.480954 ACAGAACTCACAGTCAACCGT 59.519 47.619 0.00 0.00 0.00 4.83
3212 3234 1.860950 CACAGAACTCACAGTCAACCG 59.139 52.381 0.00 0.00 0.00 4.44
3353 3375 1.884464 CCGCACATCCGAGGACATG 60.884 63.158 0.00 0.00 0.00 3.21
3358 3380 0.657840 GAAAATCCGCACATCCGAGG 59.342 55.000 0.00 0.00 0.00 4.63
3370 3392 5.966636 ACAAAAACAAAGCGAGAAAATCC 57.033 34.783 0.00 0.00 0.00 3.01
3390 3413 1.160946 ACATACGTGCGGCAACAACA 61.161 50.000 3.23 0.00 0.00 3.33
3391 3414 0.791422 TACATACGTGCGGCAACAAC 59.209 50.000 3.23 0.00 0.00 3.32
3394 3417 2.724690 CTCTATACATACGTGCGGCAAC 59.275 50.000 3.23 0.00 0.00 4.17
3430 3453 6.997655 TCATGGAGAAATACGATAATCTGCT 58.002 36.000 0.00 0.00 32.23 4.24
3437 3460 7.465379 CGCAAGTTTTCATGGAGAAATACGATA 60.465 37.037 0.00 0.00 45.15 2.92
3441 3464 5.938322 TCGCAAGTTTTCATGGAGAAATAC 58.062 37.500 0.00 0.00 45.15 1.89
3513 3539 6.543831 CGGACCCTTCTTTTTAATGAGATGAT 59.456 38.462 0.00 0.00 0.00 2.45
3523 3549 7.397192 ACAGTATACTACGGACCCTTCTTTTTA 59.603 37.037 4.74 0.00 0.00 1.52
3529 3555 3.243334 GCACAGTATACTACGGACCCTTC 60.243 52.174 4.74 0.00 0.00 3.46
3530 3556 2.692041 GCACAGTATACTACGGACCCTT 59.308 50.000 4.74 0.00 0.00 3.95
3531 3557 2.091994 AGCACAGTATACTACGGACCCT 60.092 50.000 4.74 0.00 0.00 4.34
3533 3559 3.212685 AGAGCACAGTATACTACGGACC 58.787 50.000 4.74 0.00 0.00 4.46
3534 3560 3.875727 TGAGAGCACAGTATACTACGGAC 59.124 47.826 4.74 0.00 0.00 4.79
3537 3563 5.736486 TTCTGAGAGCACAGTATACTACG 57.264 43.478 4.74 0.64 38.79 3.51
3538 3564 6.853872 CGAATTCTGAGAGCACAGTATACTAC 59.146 42.308 4.74 0.00 38.79 2.73
3539 3565 6.542735 ACGAATTCTGAGAGCACAGTATACTA 59.457 38.462 4.74 0.00 38.79 1.82
3540 3566 5.358442 ACGAATTCTGAGAGCACAGTATACT 59.642 40.000 0.00 0.00 38.79 2.12
3541 3567 5.583495 ACGAATTCTGAGAGCACAGTATAC 58.417 41.667 3.52 0.00 38.79 1.47
3542 3568 5.590663 AGACGAATTCTGAGAGCACAGTATA 59.409 40.000 3.52 0.00 38.79 1.47
3555 3582 1.272781 GCTCGGTGAGACGAATTCTG 58.727 55.000 3.52 0.00 42.98 3.02
3579 3606 0.603707 ACAAGATGCGTGTGGAGGTG 60.604 55.000 0.00 0.00 0.00 4.00
3602 3629 6.419710 GTGCCTTCTTTACAAACACAATAACC 59.580 38.462 0.00 0.00 0.00 2.85
3603 3630 6.141685 CGTGCCTTCTTTACAAACACAATAAC 59.858 38.462 0.00 0.00 0.00 1.89
3607 3634 3.181495 CCGTGCCTTCTTTACAAACACAA 60.181 43.478 0.00 0.00 0.00 3.33
3608 3635 2.356382 CCGTGCCTTCTTTACAAACACA 59.644 45.455 0.00 0.00 0.00 3.72
3609 3636 2.614983 TCCGTGCCTTCTTTACAAACAC 59.385 45.455 0.00 0.00 0.00 3.32
3610 3637 2.875933 CTCCGTGCCTTCTTTACAAACA 59.124 45.455 0.00 0.00 0.00 2.83
3611 3638 3.135994 TCTCCGTGCCTTCTTTACAAAC 58.864 45.455 0.00 0.00 0.00 2.93
3612 3639 3.070446 TCTCTCCGTGCCTTCTTTACAAA 59.930 43.478 0.00 0.00 0.00 2.83
3626 3653 1.686052 GCATCTTCCTGATCTCTCCGT 59.314 52.381 0.00 0.00 32.05 4.69
3635 3662 1.260538 ACCGCTGAGCATCTTCCTGA 61.261 55.000 4.88 0.00 34.92 3.86
3639 3666 1.364626 CCACACCGCTGAGCATCTTC 61.365 60.000 4.88 0.00 34.92 2.87
3642 3669 1.153289 ATCCACACCGCTGAGCATC 60.153 57.895 4.88 0.00 0.00 3.91
3656 3683 5.336690 GCTTTGGCTATGTTTCAAAGATCCA 60.337 40.000 16.20 0.00 45.89 3.41
3666 3693 5.927281 ATTCAGATGCTTTGGCTATGTTT 57.073 34.783 0.00 0.00 39.59 2.83
3678 3707 5.046878 TGAATGCTTTTCCAATTCAGATGCT 60.047 36.000 0.00 0.00 0.00 3.79
3682 3711 7.986320 TCTTTTTGAATGCTTTTCCAATTCAGA 59.014 29.630 0.00 0.00 33.50 3.27
3694 3723 8.445493 CAAAGTTTTGACTCTTTTTGAATGCTT 58.555 29.630 0.00 0.00 40.55 3.91
3696 3725 7.689400 CACAAAGTTTTGACTCTTTTTGAATGC 59.311 33.333 11.29 0.00 40.55 3.56
3697 3726 8.924691 TCACAAAGTTTTGACTCTTTTTGAATG 58.075 29.630 11.29 0.00 37.39 2.67
3698 3727 9.487790 TTCACAAAGTTTTGACTCTTTTTGAAT 57.512 25.926 11.29 0.00 41.29 2.57
3741 3778 4.193826 ACGAGTAATATGCTAGGCCATG 57.806 45.455 5.01 0.00 0.00 3.66
3760 3797 6.302313 GTCATTCATCCGTGAAACTTTTTACG 59.698 38.462 11.01 11.01 46.67 3.18
3763 3800 6.183360 ACAGTCATTCATCCGTGAAACTTTTT 60.183 34.615 0.00 0.00 46.67 1.94
3764 3801 5.299279 ACAGTCATTCATCCGTGAAACTTTT 59.701 36.000 0.00 0.00 46.67 2.27
3775 3814 2.386661 ACCACGACAGTCATTCATCC 57.613 50.000 0.41 0.00 0.00 3.51
3863 3912 7.758076 CAGAAGAATGACTACCGTTGTATTGTA 59.242 37.037 0.00 0.00 0.00 2.41
3865 3914 6.455646 GCAGAAGAATGACTACCGTTGTATTG 60.456 42.308 0.00 0.00 0.00 1.90
3870 3919 2.345641 CGCAGAAGAATGACTACCGTTG 59.654 50.000 0.00 0.00 0.00 4.10
3871 3920 2.230508 TCGCAGAAGAATGACTACCGTT 59.769 45.455 0.00 0.00 0.00 4.44
3872 3921 1.816835 TCGCAGAAGAATGACTACCGT 59.183 47.619 0.00 0.00 0.00 4.83
3873 3922 2.561733 TCGCAGAAGAATGACTACCG 57.438 50.000 0.00 0.00 0.00 4.02
3878 3927 5.396654 GTGAAAAGTTTCGCAGAAGAATGAC 59.603 40.000 11.50 0.00 45.90 3.06
3886 3935 2.272678 TCACGTGAAAAGTTTCGCAGA 58.727 42.857 17.62 10.38 45.42 4.26
3887 3936 2.629022 CTCACGTGAAAAGTTTCGCAG 58.371 47.619 20.49 11.02 45.42 5.18
3888 3937 1.267832 GCTCACGTGAAAAGTTTCGCA 60.268 47.619 20.49 0.00 45.42 5.10
3890 3939 2.730183 TGCTCACGTGAAAAGTTTCG 57.270 45.000 20.49 6.26 40.01 3.46
3903 3952 7.435488 ACGAATATGACTTAGTGTAATGCTCAC 59.565 37.037 0.00 0.00 36.22 3.51
3904 3953 7.489160 ACGAATATGACTTAGTGTAATGCTCA 58.511 34.615 0.00 0.00 0.00 4.26
3905 3954 7.932120 ACGAATATGACTTAGTGTAATGCTC 57.068 36.000 0.00 0.00 0.00 4.26
3981 4030 4.820716 CCATTGCACTCAAATTGGGAAAAA 59.179 37.500 0.00 0.00 35.56 1.94
3992 4041 0.321564 CTCGGTCCCATTGCACTCAA 60.322 55.000 0.00 0.00 36.51 3.02
3993 4042 1.191489 TCTCGGTCCCATTGCACTCA 61.191 55.000 0.00 0.00 0.00 3.41
4006 4055 0.556747 AGTAGCCTATGGGTCTCGGT 59.443 55.000 0.00 0.00 34.28 4.69
4024 4073 3.724508 ATACACTGAGCATCTCGGAAG 57.275 47.619 9.43 4.53 39.05 3.46


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

AutoCloner maintained by Alex Coulton.