Multiple sequence alignment - TraesCS3B01G303500

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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 TraesCS3B01G303500 chr3B 100.000 3904 0 0 1 3904 487766983 487770886 0.000000e+00 7210.0
1 TraesCS3B01G303500 chr3B 79.495 317 63 2 3582 3897 773491051 773491366 1.410000e-54 224.0
2 TraesCS3B01G303500 chr3B 90.196 51 4 1 2265 2314 487769205 487769255 9.050000e-07 65.8
3 TraesCS3B01G303500 chr3B 90.196 51 4 1 2223 2273 487769247 487769296 9.050000e-07 65.8
4 TraesCS3B01G303500 chr3D 95.227 3394 122 26 24 3396 374011199 374014573 0.000000e+00 5334.0
5 TraesCS3B01G303500 chr3D 79.379 354 62 7 3546 3889 603310968 603311320 5.040000e-59 239.0
6 TraesCS3B01G303500 chr3D 92.000 50 4 0 2265 2314 374013405 374013454 1.950000e-08 71.3
7 TraesCS3B01G303500 chr3D 90.196 51 4 1 2223 2273 374013446 374013495 9.050000e-07 65.8
8 TraesCS3B01G303500 chr3A 88.619 1854 110 51 20 1836 496035737 496037526 0.000000e+00 2161.0
9 TraesCS3B01G303500 chr3A 97.447 1136 23 3 2265 3396 496038007 496039140 0.000000e+00 1932.0
10 TraesCS3B01G303500 chr3A 88.839 448 31 8 1843 2273 496037611 496038056 2.070000e-147 532.0
11 TraesCS3B01G303500 chr3A 90.560 339 24 3 3401 3733 208638781 208639117 3.580000e-120 442.0
12 TraesCS3B01G303500 chr6A 100.000 336 0 0 3398 3733 184739875 184740210 4.280000e-174 621.0
13 TraesCS3B01G303500 chr6A 77.737 274 50 9 24 289 562138742 562139012 1.450000e-34 158.0
14 TraesCS3B01G303500 chr5B 100.000 334 0 0 3400 3733 531375182 531374849 5.540000e-173 617.0
15 TraesCS3B01G303500 chr5B 99.438 178 0 1 3728 3904 531370876 531370699 4.870000e-84 322.0
16 TraesCS3B01G303500 chr5B 80.831 313 60 0 3582 3894 678041787 678041475 3.010000e-61 246.0
17 TraesCS3B01G303500 chr5B 78.142 366 69 6 3535 3889 259542588 259542953 5.080000e-54 222.0
18 TraesCS3B01G303500 chr5B 74.046 262 55 11 23 281 455812649 455812900 1.150000e-15 95.3
19 TraesCS3B01G303500 chr5B 76.056 142 33 1 502 642 585736619 585736760 5.410000e-09 73.1
20 TraesCS3B01G303500 chr1A 99.701 335 1 0 3399 3733 1689341 1689675 7.170000e-172 614.0
21 TraesCS3B01G303500 chr1A 97.753 178 3 1 3728 3904 1693648 1693825 4.900000e-79 305.0
22 TraesCS3B01G303500 chr7B 92.216 334 25 1 3400 3733 720078387 720078719 4.570000e-129 472.0
23 TraesCS3B01G303500 chr7B 93.220 177 10 2 3728 3903 720082691 720082866 3.870000e-65 259.0
24 TraesCS3B01G303500 chr2B 90.671 343 22 5 3398 3733 577206374 577206035 7.690000e-122 448.0
25 TraesCS3B01G303500 chr4A 90.407 344 25 4 3396 3733 3997719 3998060 2.770000e-121 446.0
26 TraesCS3B01G303500 chr4A 79.612 309 61 2 3582 3889 626957334 626957641 1.830000e-53 220.0
27 TraesCS3B01G303500 chr6B 90.379 343 25 3 3397 3733 29927358 29927018 9.950000e-121 444.0
28 TraesCS3B01G303500 chr6B 82.680 306 53 0 3583 3888 114964780 114965085 4.970000e-69 272.0
29 TraesCS3B01G303500 chr4B 90.407 344 24 6 3397 3733 237909475 237909816 9.950000e-121 444.0
30 TraesCS3B01G303500 chr4B 74.689 241 45 13 47 283 52404040 52403812 4.150000e-15 93.5
31 TraesCS3B01G303500 chr1D 76.384 271 45 16 25 279 461003182 461003449 1.140000e-25 128.0
32 TraesCS3B01G303500 chr1D 89.091 55 4 2 61 113 115015393 115015339 2.520000e-07 67.6
33 TraesCS3B01G303500 chr6D 74.806 258 53 10 25 279 304117236 304117484 5.330000e-19 106.0
34 TraesCS3B01G303500 chr2D 74.621 264 51 11 23 279 481604361 481604107 6.900000e-18 102.0
35 TraesCS3B01G303500 chr2D 90.566 53 5 0 24 76 37219708 37219760 1.950000e-08 71.3
36 TraesCS3B01G303500 chr7D 85.393 89 12 1 22 109 138087470 138087382 1.490000e-14 91.6
37 TraesCS3B01G303500 chr7D 80.165 121 17 6 22 138 178831836 178831953 2.500000e-12 84.2
38 TraesCS3B01G303500 chr5D 93.182 44 3 0 557 600 478119747 478119790 9.050000e-07 65.8


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 TraesCS3B01G303500 chr3B 487766983 487770886 3903 False 2447.200000 7210 93.464000 1 3904 3 chr3B.!!$F2 3903
1 TraesCS3B01G303500 chr3D 374011199 374014573 3374 False 1823.700000 5334 92.474333 24 3396 3 chr3D.!!$F2 3372
2 TraesCS3B01G303500 chr3A 496035737 496039140 3403 False 1541.666667 2161 91.635000 20 3396 3 chr3A.!!$F2 3376
3 TraesCS3B01G303500 chr5B 531370699 531375182 4483 True 469.500000 617 99.719000 3400 3904 2 chr5B.!!$R2 504
4 TraesCS3B01G303500 chr1A 1689341 1693825 4484 False 459.500000 614 98.727000 3399 3904 2 chr1A.!!$F1 505
5 TraesCS3B01G303500 chr7B 720078387 720082866 4479 False 365.500000 472 92.718000 3400 3903 2 chr7B.!!$F1 503

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
173 177 0.108615 AAGACCGCTGACCGAATCTG 60.109 55.000 0.0 0.0 40.02 2.90 F
284 292 0.605589 TCTTCAGAGAGCCGTCGTCA 60.606 55.000 0.0 0.0 0.00 4.35 F
740 753 1.996898 CTACGTGCAAATTACTCGCCA 59.003 47.619 0.0 0.0 0.00 5.69 F
1904 2024 2.233922 CCGTTCTCTTGCTTCTTCCCTA 59.766 50.000 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1995 0.246635 GCAAGAGAACGGGTAGAGCA 59.753 55.000 0.00 0.0 0.00 4.26 R
2080 2216 5.163513 GTGCATATGGAAGAACAAACAAGG 58.836 41.667 4.56 0.0 0.00 3.61 R
2307 2485 2.618709 GTTGCAGTTGTTAGTTGGAGCT 59.381 45.455 0.00 0.0 0.00 4.09 R
3094 3275 4.166725 TCCATCTTGTGCCTCTGGATAAAT 59.833 41.667 0.00 0.0 31.19 1.40 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
74 77 1.678360 CGCAGCAGAACAACAATCAC 58.322 50.000 0.00 0.00 0.00 3.06
92 95 0.736325 ACCGCCGATGAAGAGAAACG 60.736 55.000 0.00 0.00 0.00 3.60
118 122 4.451629 TCGAAGGATCAAACTGGTAGTC 57.548 45.455 0.00 0.00 0.00 2.59
122 126 4.974645 AGGATCAAACTGGTAGTCACAA 57.025 40.909 0.00 0.00 0.00 3.33
132 136 4.202161 ACTGGTAGTCACAAGAACACAGAG 60.202 45.833 0.00 0.00 29.44 3.35
142 146 4.119862 CAAGAACACAGAGGAACGAAGAA 58.880 43.478 0.00 0.00 0.00 2.52
144 148 4.962155 AGAACACAGAGGAACGAAGAAAT 58.038 39.130 0.00 0.00 0.00 2.17
151 155 5.121811 CAGAGGAACGAAGAAATGATCCAT 58.878 41.667 0.00 0.00 0.00 3.41
159 163 4.210120 CGAAGAAATGATCCATCGAAGACC 59.790 45.833 0.00 0.00 42.51 3.85
160 164 3.722147 AGAAATGATCCATCGAAGACCG 58.278 45.455 0.00 0.00 42.51 4.79
161 165 1.871080 AATGATCCATCGAAGACCGC 58.129 50.000 0.00 0.00 42.51 5.68
162 166 1.043816 ATGATCCATCGAAGACCGCT 58.956 50.000 0.00 0.00 42.51 5.52
164 168 0.385751 GATCCATCGAAGACCGCTGA 59.614 55.000 0.00 0.00 42.51 4.26
166 170 1.519455 CCATCGAAGACCGCTGACC 60.519 63.158 0.00 0.00 42.51 4.02
167 171 1.874019 CATCGAAGACCGCTGACCG 60.874 63.158 0.00 0.00 42.51 4.79
168 172 2.044555 ATCGAAGACCGCTGACCGA 61.045 57.895 0.00 0.00 42.51 4.69
169 173 1.592400 ATCGAAGACCGCTGACCGAA 61.592 55.000 0.00 0.00 42.51 4.30
170 174 1.153823 CGAAGACCGCTGACCGAAT 60.154 57.895 0.00 0.00 40.02 3.34
171 175 1.140407 CGAAGACCGCTGACCGAATC 61.140 60.000 0.00 0.00 40.02 2.52
172 176 0.173708 GAAGACCGCTGACCGAATCT 59.826 55.000 0.00 0.00 40.02 2.40
173 177 0.108615 AAGACCGCTGACCGAATCTG 60.109 55.000 0.00 0.00 40.02 2.90
195 203 2.738846 CAAGATCCACCAGAGACAAACG 59.261 50.000 0.00 0.00 0.00 3.60
202 210 1.416401 ACCAGAGACAAACGTCCACAT 59.584 47.619 0.00 0.00 33.60 3.21
220 228 1.131638 ATGCCCTCCGAAGATGCTAA 58.868 50.000 0.00 0.00 0.00 3.09
226 234 4.392940 CCCTCCGAAGATGCTAAAATCAT 58.607 43.478 0.00 0.00 0.00 2.45
232 240 4.507756 CGAAGATGCTAAAATCATCACCGA 59.492 41.667 5.87 0.00 41.98 4.69
233 241 5.006649 CGAAGATGCTAAAATCATCACCGAA 59.993 40.000 5.87 0.00 41.98 4.30
262 270 6.659668 GGGACTAAGCAGGAAGAACTTTATTT 59.340 38.462 0.00 0.00 0.00 1.40
277 285 7.552330 AGAACTTTATTTCATCTTCAGAGAGCC 59.448 37.037 0.00 0.00 34.85 4.70
284 292 0.605589 TCTTCAGAGAGCCGTCGTCA 60.606 55.000 0.00 0.00 0.00 4.35
308 316 8.999431 TCACCTCTACTAATTTTGTTGTTGATC 58.001 33.333 0.00 0.00 0.00 2.92
325 334 4.607293 TGATCCCAAATGATACGAGAGG 57.393 45.455 0.00 0.00 0.00 3.69
342 351 4.481463 GAGAGGTCGAAGAGTCAAGAAAG 58.519 47.826 0.00 0.00 36.95 2.62
356 365 5.775701 AGTCAAGAAAGAACTGCCTCTACTA 59.224 40.000 0.00 0.00 0.00 1.82
362 371 6.720288 AGAAAGAACTGCCTCTACTAGTGTTA 59.280 38.462 5.39 0.00 0.00 2.41
364 373 7.483580 AAGAACTGCCTCTACTAGTGTTAAT 57.516 36.000 5.39 0.00 0.00 1.40
370 379 4.372656 CCTCTACTAGTGTTAATGCCAGC 58.627 47.826 5.39 0.00 0.00 4.85
374 383 3.955471 ACTAGTGTTAATGCCAGCACAT 58.045 40.909 0.00 0.00 32.58 3.21
376 385 2.794103 AGTGTTAATGCCAGCACATGA 58.206 42.857 0.00 0.00 32.58 3.07
390 399 5.389778 CAGCACATGAACGTAGCAAAATTA 58.610 37.500 0.00 0.00 0.00 1.40
393 402 6.747280 AGCACATGAACGTAGCAAAATTAATC 59.253 34.615 0.00 0.00 0.00 1.75
423 432 8.237811 ACCAATGCTTTATTTATCGGAAATCT 57.762 30.769 0.26 0.00 0.00 2.40
462 474 4.857037 GGATTTTTAAGCACGACAATGACC 59.143 41.667 0.00 0.00 0.00 4.02
485 498 7.734942 ACCTTTTGGATGACAATTATGTTGTT 58.265 30.769 0.64 0.00 44.07 2.83
514 527 5.622914 GCATAGCAATTTCCTTCAGCAAAGA 60.623 40.000 0.74 0.00 37.12 2.52
583 596 7.276218 TGCTTGCTAAATAAATTTGTCATGCTC 59.724 33.333 18.64 0.00 36.16 4.26
602 615 4.092237 TGCTCGTGACAACATAATTTACCG 59.908 41.667 0.00 0.00 0.00 4.02
609 622 6.579666 GTGACAACATAATTTACCGTCCAAAC 59.420 38.462 0.00 0.00 0.00 2.93
629 642 4.996788 ACCATCAGATTTTCCATGCTTC 57.003 40.909 0.00 0.00 0.00 3.86
638 651 6.657836 GATTTTCCATGCTTCAAAATCTGG 57.342 37.500 15.87 0.00 40.81 3.86
664 677 8.850452 GCATTTGTAGCGAATTATTTATTAGCC 58.150 33.333 0.00 0.00 43.46 3.93
685 698 6.296026 AGCCGATTTCCTGCTATATTTGTTA 58.704 36.000 0.00 0.00 32.56 2.41
687 700 7.448469 AGCCGATTTCCTGCTATATTTGTTATT 59.552 33.333 0.00 0.00 32.56 1.40
737 750 6.421821 GAGTATCTACGTGCAAATTACTCG 57.578 41.667 0.00 0.00 0.00 4.18
740 753 1.996898 CTACGTGCAAATTACTCGCCA 59.003 47.619 0.00 0.00 0.00 5.69
825 838 3.817647 TGCATTGCCCGCTTTTAAAATTT 59.182 34.783 6.12 0.00 0.00 1.82
828 841 5.350091 GCATTGCCCGCTTTTAAAATTTCTA 59.650 36.000 0.09 0.00 0.00 2.10
913 927 6.162079 CCATGCCACTAGAATACTAGATGTG 58.838 44.000 10.60 0.00 46.34 3.21
918 933 8.486210 TGCCACTAGAATACTAGATGTGATTTT 58.514 33.333 10.60 0.00 46.34 1.82
1370 1388 2.486982 CAGCCTCAATTTGGTGAGTGAG 59.513 50.000 0.00 0.00 43.02 3.51
1446 1464 3.657015 TGGATTTGCTTGCGATTTTCA 57.343 38.095 0.00 0.00 0.00 2.69
1556 1574 2.746375 CCCATCGTCCCCCTTCCAG 61.746 68.421 0.00 0.00 0.00 3.86
1629 1647 3.091545 TGTCATCTTTTCCCCTTCATGC 58.908 45.455 0.00 0.00 0.00 4.06
1692 1723 9.368416 GGATATAGGTATCTATATGTGGAAGCA 57.632 37.037 18.41 0.00 44.73 3.91
1706 1737 4.574828 TGTGGAAGCAAGTAGAAACAAGTC 59.425 41.667 0.00 0.00 0.00 3.01
1772 1814 6.319658 AGTGAGATTTTGAGCTTCTTTGTGAA 59.680 34.615 0.00 0.00 0.00 3.18
1773 1815 7.014038 AGTGAGATTTTGAGCTTCTTTGTGAAT 59.986 33.333 0.00 0.00 33.71 2.57
1774 1816 7.650903 GTGAGATTTTGAGCTTCTTTGTGAATT 59.349 33.333 0.00 0.00 33.71 2.17
1775 1817 7.650504 TGAGATTTTGAGCTTCTTTGTGAATTG 59.349 33.333 0.00 0.00 33.71 2.32
1776 1818 7.495055 AGATTTTGAGCTTCTTTGTGAATTGT 58.505 30.769 0.00 0.00 33.71 2.71
1777 1819 6.890663 TTTTGAGCTTCTTTGTGAATTGTG 57.109 33.333 0.00 0.00 33.71 3.33
1778 1820 5.833406 TTGAGCTTCTTTGTGAATTGTGA 57.167 34.783 0.00 0.00 33.71 3.58
1779 1821 6.395426 TTGAGCTTCTTTGTGAATTGTGAT 57.605 33.333 0.00 0.00 33.71 3.06
1780 1822 7.509141 TTGAGCTTCTTTGTGAATTGTGATA 57.491 32.000 0.00 0.00 33.71 2.15
1781 1823 7.137490 TGAGCTTCTTTGTGAATTGTGATAG 57.863 36.000 0.00 0.00 33.71 2.08
1796 1838 8.485976 AATTGTGATAGAGTGAAGAAACTAGC 57.514 34.615 0.00 0.00 0.00 3.42
1875 1995 3.290948 TGTTTCCAGTTAGGTGTGCTT 57.709 42.857 0.00 0.00 39.02 3.91
1904 2024 2.233922 CCGTTCTCTTGCTTCTTCCCTA 59.766 50.000 0.00 0.00 0.00 3.53
2113 2249 3.030668 TCCATATGCACGTGAGCTATG 57.969 47.619 22.23 19.56 34.99 2.23
2141 2277 5.168647 AGATCTCTTACGATATCTCCGGT 57.831 43.478 0.00 0.00 29.89 5.28
2235 2413 4.968259 AGGTACTGCACACACTTCATTAA 58.032 39.130 0.00 0.00 37.18 1.40
2267 2445 3.706600 ACCCGGAATAACAAGCTACAA 57.293 42.857 0.73 0.00 0.00 2.41
2268 2446 3.340928 ACCCGGAATAACAAGCTACAAC 58.659 45.455 0.73 0.00 0.00 3.32
2269 2447 3.008704 ACCCGGAATAACAAGCTACAACT 59.991 43.478 0.73 0.00 0.00 3.16
2270 2448 3.621715 CCCGGAATAACAAGCTACAACTC 59.378 47.826 0.73 0.00 0.00 3.01
2271 2449 3.621715 CCGGAATAACAAGCTACAACTCC 59.378 47.826 0.00 0.00 0.00 3.85
2272 2450 4.250464 CGGAATAACAAGCTACAACTCCA 58.750 43.478 0.00 0.00 0.00 3.86
2273 2451 4.876107 CGGAATAACAAGCTACAACTCCAT 59.124 41.667 0.00 0.00 0.00 3.41
2274 2452 5.354234 CGGAATAACAAGCTACAACTCCATT 59.646 40.000 0.00 0.00 0.00 3.16
2275 2453 6.537301 CGGAATAACAAGCTACAACTCCATTA 59.463 38.462 0.00 0.00 0.00 1.90
2276 2454 7.226720 CGGAATAACAAGCTACAACTCCATTAT 59.773 37.037 0.00 0.00 0.00 1.28
2277 2455 8.903820 GGAATAACAAGCTACAACTCCATTATT 58.096 33.333 0.00 0.00 0.00 1.40
2278 2456 9.937175 GAATAACAAGCTACAACTCCATTATTC 57.063 33.333 0.00 0.00 32.48 1.75
2279 2457 6.759497 AACAAGCTACAACTCCATTATTCC 57.241 37.500 0.00 0.00 0.00 3.01
2280 2458 6.067217 ACAAGCTACAACTCCATTATTCCT 57.933 37.500 0.00 0.00 0.00 3.36
2281 2459 6.485171 ACAAGCTACAACTCCATTATTCCTT 58.515 36.000 0.00 0.00 0.00 3.36
2282 2460 6.375455 ACAAGCTACAACTCCATTATTCCTTG 59.625 38.462 0.00 0.00 0.00 3.61
2283 2461 6.313519 AGCTACAACTCCATTATTCCTTGA 57.686 37.500 0.00 0.00 0.00 3.02
2284 2462 6.721318 AGCTACAACTCCATTATTCCTTGAA 58.279 36.000 0.00 0.00 0.00 2.69
2285 2463 7.349598 AGCTACAACTCCATTATTCCTTGAAT 58.650 34.615 0.00 0.00 36.20 2.57
2286 2464 7.836183 AGCTACAACTCCATTATTCCTTGAATT 59.164 33.333 0.00 0.00 33.95 2.17
2287 2465 8.470002 GCTACAACTCCATTATTCCTTGAATTT 58.530 33.333 0.00 0.00 33.95 1.82
2290 2468 8.749354 ACAACTCCATTATTCCTTGAATTTACC 58.251 33.333 0.00 0.00 33.95 2.85
2291 2469 7.898014 ACTCCATTATTCCTTGAATTTACCC 57.102 36.000 0.00 0.00 33.95 3.69
2292 2470 6.546034 ACTCCATTATTCCTTGAATTTACCCG 59.454 38.462 0.00 0.00 33.95 5.28
2293 2471 5.830991 TCCATTATTCCTTGAATTTACCCGG 59.169 40.000 0.00 0.00 33.95 5.73
2294 2472 5.830991 CCATTATTCCTTGAATTTACCCGGA 59.169 40.000 0.73 0.00 33.95 5.14
2295 2473 6.322712 CCATTATTCCTTGAATTTACCCGGAA 59.677 38.462 0.73 0.00 33.95 4.30
2296 2474 7.015195 CCATTATTCCTTGAATTTACCCGGAAT 59.985 37.037 0.73 0.00 42.22 3.01
2297 2475 9.073475 CATTATTCCTTGAATTTACCCGGAATA 57.927 33.333 0.73 0.00 40.57 1.75
2299 2477 6.762702 TTCCTTGAATTTACCCGGAATAAC 57.237 37.500 0.73 0.00 0.00 1.89
2300 2478 5.817784 TCCTTGAATTTACCCGGAATAACA 58.182 37.500 0.73 0.00 0.00 2.41
2301 2479 6.246919 TCCTTGAATTTACCCGGAATAACAA 58.753 36.000 0.73 5.08 0.00 2.83
2302 2480 6.376018 TCCTTGAATTTACCCGGAATAACAAG 59.624 38.462 0.73 13.40 34.55 3.16
2303 2481 5.570234 TGAATTTACCCGGAATAACAAGC 57.430 39.130 0.73 0.00 0.00 4.01
2304 2482 5.258051 TGAATTTACCCGGAATAACAAGCT 58.742 37.500 0.73 0.00 0.00 3.74
2305 2483 6.416415 TGAATTTACCCGGAATAACAAGCTA 58.584 36.000 0.73 0.00 0.00 3.32
2306 2484 7.057894 TGAATTTACCCGGAATAACAAGCTAT 58.942 34.615 0.73 0.00 0.00 2.97
2307 2485 8.212312 TGAATTTACCCGGAATAACAAGCTATA 58.788 33.333 0.73 0.00 0.00 1.31
2504 2684 6.914757 GGCTGATCAAAAAGCATTATACACTC 59.085 38.462 6.95 0.00 41.36 3.51
3000 3181 4.148871 CACTGACACAGTTTCGTACATGAG 59.851 45.833 0.00 0.00 42.59 2.90
3085 3266 0.392060 TGAGCACTTGCATCGCAGAT 60.392 50.000 3.62 0.00 45.16 2.90
3317 3498 0.752658 TGTGTCGATCTGGCTATGGG 59.247 55.000 0.00 0.00 0.00 4.00
3396 3581 7.871853 AGTATTTTGTCGTGCTTTCAGTTATT 58.128 30.769 0.00 0.00 0.00 1.40
3397 3582 8.349983 AGTATTTTGTCGTGCTTTCAGTTATTT 58.650 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.025145 CCTTAGCACGACGACTTTCTTTTT 60.025 41.667 0.00 0.00 0.00 1.94
18 19 3.493503 CCTTAGCACGACGACTTTCTTTT 59.506 43.478 0.00 0.00 0.00 2.27
19 20 3.057734 CCTTAGCACGACGACTTTCTTT 58.942 45.455 0.00 0.00 0.00 2.52
20 21 2.673833 CCTTAGCACGACGACTTTCTT 58.326 47.619 0.00 0.00 0.00 2.52
21 22 1.669211 GCCTTAGCACGACGACTTTCT 60.669 52.381 0.00 0.00 39.53 2.52
22 23 0.714439 GCCTTAGCACGACGACTTTC 59.286 55.000 0.00 0.00 39.53 2.62
67 70 0.249120 TCTTCATCGGCGGTGATTGT 59.751 50.000 25.04 0.00 0.00 2.71
74 77 0.736325 ACGTTTCTCTTCATCGGCGG 60.736 55.000 7.21 0.00 0.00 6.13
92 95 5.012328 ACCAGTTTGATCCTTCGATCTAC 57.988 43.478 2.11 1.24 44.61 2.59
112 116 3.321111 TCCTCTGTGTTCTTGTGACTACC 59.679 47.826 0.00 0.00 0.00 3.18
118 122 2.821546 TCGTTCCTCTGTGTTCTTGTG 58.178 47.619 0.00 0.00 0.00 3.33
122 126 4.402056 TTTCTTCGTTCCTCTGTGTTCT 57.598 40.909 0.00 0.00 0.00 3.01
132 136 4.119862 TCGATGGATCATTTCTTCGTTCC 58.880 43.478 0.00 0.00 34.07 3.62
142 146 1.414181 AGCGGTCTTCGATGGATCATT 59.586 47.619 0.00 0.00 42.43 2.57
144 148 2.504920 AGCGGTCTTCGATGGATCA 58.495 52.632 0.00 0.00 42.43 2.92
151 155 1.592400 ATTCGGTCAGCGGTCTTCGA 61.592 55.000 0.00 0.00 42.43 3.71
159 163 0.737367 TCTTGCAGATTCGGTCAGCG 60.737 55.000 0.00 0.00 41.83 5.18
160 164 1.596727 GATCTTGCAGATTCGGTCAGC 59.403 52.381 0.00 0.46 34.53 4.26
161 165 2.208431 GGATCTTGCAGATTCGGTCAG 58.792 52.381 0.00 0.00 34.53 3.51
162 166 1.554617 TGGATCTTGCAGATTCGGTCA 59.445 47.619 0.00 0.00 34.53 4.02
164 168 1.407437 GGTGGATCTTGCAGATTCGGT 60.407 52.381 0.00 0.00 34.53 4.69
166 170 1.938577 CTGGTGGATCTTGCAGATTCG 59.061 52.381 0.00 0.00 34.53 3.34
167 171 3.118482 TCTCTGGTGGATCTTGCAGATTC 60.118 47.826 0.00 0.00 34.53 2.52
168 172 2.842496 TCTCTGGTGGATCTTGCAGATT 59.158 45.455 0.00 0.00 34.53 2.40
169 173 2.170187 GTCTCTGGTGGATCTTGCAGAT 59.830 50.000 0.00 0.00 37.73 2.90
170 174 1.552337 GTCTCTGGTGGATCTTGCAGA 59.448 52.381 0.00 0.00 0.00 4.26
171 175 1.277273 TGTCTCTGGTGGATCTTGCAG 59.723 52.381 0.00 0.00 0.00 4.41
172 176 1.351076 TGTCTCTGGTGGATCTTGCA 58.649 50.000 0.00 0.00 0.00 4.08
173 177 2.479566 TTGTCTCTGGTGGATCTTGC 57.520 50.000 0.00 0.00 0.00 4.01
175 179 2.368875 ACGTTTGTCTCTGGTGGATCTT 59.631 45.455 0.00 0.00 0.00 2.40
185 193 1.512926 GCATGTGGACGTTTGTCTCT 58.487 50.000 0.00 0.00 44.83 3.10
195 203 1.450312 CTTCGGAGGGCATGTGGAC 60.450 63.158 0.00 0.00 0.00 4.02
202 210 0.908910 TTTAGCATCTTCGGAGGGCA 59.091 50.000 10.33 0.00 32.74 5.36
220 228 1.003812 TCCCCGTTTCGGTGATGATTT 59.996 47.619 7.40 0.00 46.80 2.17
226 234 0.604578 CTTAGTCCCCGTTTCGGTGA 59.395 55.000 7.40 0.00 46.80 4.02
232 240 1.003233 CTTCCTGCTTAGTCCCCGTTT 59.997 52.381 0.00 0.00 0.00 3.60
233 241 0.613777 CTTCCTGCTTAGTCCCCGTT 59.386 55.000 0.00 0.00 0.00 4.44
262 270 0.735471 CGACGGCTCTCTGAAGATGA 59.265 55.000 0.00 0.00 0.00 2.92
277 285 5.159209 ACAAAATTAGTAGAGGTGACGACG 58.841 41.667 0.00 0.00 0.00 5.12
284 292 7.393515 GGGATCAACAACAAAATTAGTAGAGGT 59.606 37.037 0.00 0.00 0.00 3.85
308 316 2.361119 TCGACCTCTCGTATCATTTGGG 59.639 50.000 0.00 0.00 41.02 4.12
325 334 4.084797 GCAGTTCTTTCTTGACTCTTCGAC 60.085 45.833 0.00 0.00 0.00 4.20
331 340 4.001618 AGAGGCAGTTCTTTCTTGACTC 57.998 45.455 0.00 0.00 0.00 3.36
338 347 5.394224 ACACTAGTAGAGGCAGTTCTTTC 57.606 43.478 3.59 0.00 0.00 2.62
342 351 5.520649 GCATTAACACTAGTAGAGGCAGTTC 59.479 44.000 3.59 0.00 0.00 3.01
356 365 2.794103 TCATGTGCTGGCATTAACACT 58.206 42.857 0.00 0.00 34.14 3.55
362 371 1.739466 CTACGTTCATGTGCTGGCATT 59.261 47.619 0.00 0.00 0.00 3.56
364 373 1.298157 GCTACGTTCATGTGCTGGCA 61.298 55.000 0.00 0.00 0.00 4.92
370 379 8.446489 TTGATTAATTTTGCTACGTTCATGTG 57.554 30.769 0.00 0.00 0.00 3.21
374 383 7.806014 GGTTCTTGATTAATTTTGCTACGTTCA 59.194 33.333 0.00 0.00 0.00 3.18
376 385 7.653647 TGGTTCTTGATTAATTTTGCTACGTT 58.346 30.769 0.00 0.00 0.00 3.99
390 399 9.520204 CGATAAATAAAGCATTGGTTCTTGATT 57.480 29.630 0.90 0.00 0.00 2.57
393 402 7.479980 TCCGATAAATAAAGCATTGGTTCTTG 58.520 34.615 0.90 0.00 0.00 3.02
429 438 7.915397 GTCGTGCTTAAAAATCCAACATATGAT 59.085 33.333 10.38 0.00 0.00 2.45
431 440 7.026562 TGTCGTGCTTAAAAATCCAACATATG 58.973 34.615 0.00 0.00 0.00 1.78
432 441 7.151999 TGTCGTGCTTAAAAATCCAACATAT 57.848 32.000 0.00 0.00 0.00 1.78
439 448 4.857037 GGTCATTGTCGTGCTTAAAAATCC 59.143 41.667 0.00 0.00 0.00 3.01
462 474 7.512297 GCAACAACATAATTGTCATCCAAAAG 58.488 34.615 0.00 0.00 36.44 2.27
485 498 1.462616 AGGAAATTGCTATGCACGCA 58.537 45.000 8.32 8.32 38.71 5.24
555 568 8.392612 GCATGACAAATTTATTTAGCAAGCATT 58.607 29.630 0.00 0.00 32.25 3.56
583 596 4.389382 TGGACGGTAAATTATGTTGTCACG 59.611 41.667 0.00 0.00 0.00 4.35
602 615 5.413499 CATGGAAAATCTGATGGTTTGGAC 58.587 41.667 0.00 0.00 0.00 4.02
609 622 4.994907 TGAAGCATGGAAAATCTGATGG 57.005 40.909 0.00 0.00 0.00 3.51
629 642 4.095410 TCGCTACAAATGCCAGATTTTG 57.905 40.909 0.00 0.00 38.49 2.44
638 651 8.850452 GGCTAATAAATAATTCGCTACAAATGC 58.150 33.333 0.00 0.00 36.69 3.56
687 700 9.719355 TTCTTTAAGTCACTATTCAATGCTACA 57.281 29.630 0.00 0.00 0.00 2.74
737 750 2.858745 TGTCTCCTTGGTTACTTTGGC 58.141 47.619 0.00 0.00 0.00 4.52
740 753 6.209391 CCATCAATTGTCTCCTTGGTTACTTT 59.791 38.462 5.13 0.00 0.00 2.66
825 838 9.273016 CCCTATCGCTTGAAATAAAAATCTAGA 57.727 33.333 0.00 0.00 0.00 2.43
828 841 7.881775 ACCCTATCGCTTGAAATAAAAATCT 57.118 32.000 0.00 0.00 0.00 2.40
913 927 8.777413 AGCTTTTCTTGCCTCAAATTTAAAATC 58.223 29.630 0.00 0.00 0.00 2.17
1328 1346 1.363744 CCGTTCTGTGGATCAAGCTC 58.636 55.000 0.00 0.00 0.00 4.09
1370 1388 1.881973 TCAGCTTTGCAAGATGTGTCC 59.118 47.619 0.00 0.00 44.86 4.02
1446 1464 4.580580 GGAATCAGAAACGCCCAATCTTAT 59.419 41.667 0.00 0.00 0.00 1.73
1678 1709 8.492673 TTGTTTCTACTTGCTTCCACATATAG 57.507 34.615 0.00 0.00 0.00 1.31
1692 1723 9.620259 AAAGAAGATCAAGACTTGTTTCTACTT 57.380 29.630 21.33 15.30 36.57 2.24
1772 1814 7.763528 CAGCTAGTTTCTTCACTCTATCACAAT 59.236 37.037 0.00 0.00 0.00 2.71
1773 1815 7.093354 CAGCTAGTTTCTTCACTCTATCACAA 58.907 38.462 0.00 0.00 0.00 3.33
1774 1816 6.209589 ACAGCTAGTTTCTTCACTCTATCACA 59.790 38.462 0.00 0.00 0.00 3.58
1775 1817 6.626302 ACAGCTAGTTTCTTCACTCTATCAC 58.374 40.000 0.00 0.00 0.00 3.06
1776 1818 6.661377 AGACAGCTAGTTTCTTCACTCTATCA 59.339 38.462 0.00 0.00 0.00 2.15
1777 1819 7.095695 AGACAGCTAGTTTCTTCACTCTATC 57.904 40.000 0.00 0.00 0.00 2.08
1778 1820 7.475137 AAGACAGCTAGTTTCTTCACTCTAT 57.525 36.000 0.00 0.00 0.00 1.98
1779 1821 6.902771 AAGACAGCTAGTTTCTTCACTCTA 57.097 37.500 0.00 0.00 0.00 2.43
1780 1822 5.799827 AAGACAGCTAGTTTCTTCACTCT 57.200 39.130 0.00 0.00 0.00 3.24
1781 1823 5.986135 TCAAAGACAGCTAGTTTCTTCACTC 59.014 40.000 0.00 0.00 0.00 3.51
1875 1995 0.246635 GCAAGAGAACGGGTAGAGCA 59.753 55.000 0.00 0.00 0.00 4.26
2080 2216 5.163513 GTGCATATGGAAGAACAAACAAGG 58.836 41.667 4.56 0.00 0.00 3.61
2141 2277 7.333323 CCATATGCCATCTGTACATGATAAGA 58.667 38.462 0.00 0.00 0.00 2.10
2235 2413 6.428295 TGTTATTCCGGGTAAATTCAAGGAT 58.572 36.000 0.00 0.00 0.00 3.24
2267 2445 6.546034 CGGGTAAATTCAAGGAATAATGGAGT 59.454 38.462 0.00 0.00 31.46 3.85
2268 2446 6.016276 CCGGGTAAATTCAAGGAATAATGGAG 60.016 42.308 0.00 0.00 31.46 3.86
2269 2447 5.830991 CCGGGTAAATTCAAGGAATAATGGA 59.169 40.000 0.00 0.00 31.46 3.41
2270 2448 5.830991 TCCGGGTAAATTCAAGGAATAATGG 59.169 40.000 0.00 0.00 31.46 3.16
2271 2449 6.952773 TCCGGGTAAATTCAAGGAATAATG 57.047 37.500 0.00 0.00 31.46 1.90
2272 2450 9.649316 TTATTCCGGGTAAATTCAAGGAATAAT 57.351 29.630 18.12 0.00 46.77 1.28
2274 2452 8.053963 TGTTATTCCGGGTAAATTCAAGGAATA 58.946 33.333 0.00 9.80 43.99 1.75
2275 2453 6.893005 TGTTATTCCGGGTAAATTCAAGGAAT 59.107 34.615 0.00 11.54 46.44 3.01
2276 2454 6.246919 TGTTATTCCGGGTAAATTCAAGGAA 58.753 36.000 0.00 0.00 41.29 3.36
2277 2455 5.817784 TGTTATTCCGGGTAAATTCAAGGA 58.182 37.500 0.00 0.00 0.00 3.36
2278 2456 6.518208 TTGTTATTCCGGGTAAATTCAAGG 57.482 37.500 0.00 0.00 0.00 3.61
2279 2457 6.033966 GCTTGTTATTCCGGGTAAATTCAAG 58.966 40.000 0.00 12.81 34.18 3.02
2280 2458 5.712917 AGCTTGTTATTCCGGGTAAATTCAA 59.287 36.000 0.00 3.56 0.00 2.69
2281 2459 5.258051 AGCTTGTTATTCCGGGTAAATTCA 58.742 37.500 0.00 0.00 0.00 2.57
2282 2460 5.830000 AGCTTGTTATTCCGGGTAAATTC 57.170 39.130 0.00 0.00 0.00 2.17
2283 2461 7.174426 GCTATAGCTTGTTATTCCGGGTAAATT 59.826 37.037 17.75 0.00 38.21 1.82
2284 2462 6.653740 GCTATAGCTTGTTATTCCGGGTAAAT 59.346 38.462 17.75 0.00 38.21 1.40
2285 2463 5.993441 GCTATAGCTTGTTATTCCGGGTAAA 59.007 40.000 17.75 0.00 38.21 2.01
2286 2464 5.544650 GCTATAGCTTGTTATTCCGGGTAA 58.455 41.667 17.75 0.00 38.21 2.85
2287 2465 5.143376 GCTATAGCTTGTTATTCCGGGTA 57.857 43.478 17.75 0.00 38.21 3.69
2288 2466 4.004196 GCTATAGCTTGTTATTCCGGGT 57.996 45.455 17.75 0.00 38.21 5.28
2302 2480 4.271291 GCAGTTGTTAGTTGGAGCTATAGC 59.729 45.833 17.33 17.33 42.49 2.97
2303 2481 5.419542 TGCAGTTGTTAGTTGGAGCTATAG 58.580 41.667 0.00 0.00 0.00 1.31
2304 2482 5.414789 TGCAGTTGTTAGTTGGAGCTATA 57.585 39.130 0.00 0.00 0.00 1.31
2305 2483 4.286297 TGCAGTTGTTAGTTGGAGCTAT 57.714 40.909 0.00 0.00 0.00 2.97
2306 2484 3.762407 TGCAGTTGTTAGTTGGAGCTA 57.238 42.857 0.00 0.00 0.00 3.32
2307 2485 2.618709 GTTGCAGTTGTTAGTTGGAGCT 59.381 45.455 0.00 0.00 0.00 4.09
2470 2648 4.992951 GCTTTTTGATCAGCCATTCAACTT 59.007 37.500 0.00 0.00 31.87 2.66
2504 2684 7.962918 CCACATGAGTTAAAAAGATAACTTCGG 59.037 37.037 0.00 0.00 44.14 4.30
3094 3275 4.166725 TCCATCTTGTGCCTCTGGATAAAT 59.833 41.667 0.00 0.00 31.19 1.40
3368 3549 5.989777 ACTGAAAGCACGACAAAATACTACT 59.010 36.000 0.00 0.00 37.60 2.57


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

AutoCloner maintained by Alex Coulton.