Multiple sequence alignment - TraesCS3A01G380000

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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 TraesCS3A01G380000 chr3A 100.000 5987 0 0 1 5987 630047405 630041419 0.000000e+00 11057.0
1 TraesCS3A01G380000 chr3A 86.180 2576 203 66 3314 5850 630207655 630205194 0.000000e+00 2643.0
2 TraesCS3A01G380000 chr3A 89.765 1192 82 21 2082 3255 630209106 630207937 0.000000e+00 1489.0
3 TraesCS3A01G380000 chr3A 93.253 830 42 6 4 821 630211786 630210959 0.000000e+00 1210.0
4 TraesCS3A01G380000 chr3A 87.450 502 43 8 856 1353 630210966 630210481 1.460000e-155 560.0
5 TraesCS3A01G380000 chr3A 93.089 246 16 1 1526 1771 630209787 630209543 5.710000e-95 359.0
6 TraesCS3A01G380000 chr3A 87.781 311 17 13 1786 2083 630209439 630209137 1.600000e-90 344.0
7 TraesCS3A01G380000 chr3A 89.474 95 7 2 1440 1531 630210019 630209925 3.790000e-22 117.0
8 TraesCS3A01G380000 chr3D 97.004 4272 89 17 1566 5831 486739690 486735452 0.000000e+00 7143.0
9 TraesCS3A01G380000 chr3D 88.349 3416 247 76 2082 5424 486780598 486777261 0.000000e+00 3964.0
10 TraesCS3A01G380000 chr3D 97.691 823 17 2 1 823 486741364 486740544 0.000000e+00 1413.0
11 TraesCS3A01G380000 chr3D 92.892 830 45 6 4 821 486782956 486782129 0.000000e+00 1194.0
12 TraesCS3A01G380000 chr3D 93.122 727 15 13 854 1567 486740553 486739849 0.000000e+00 1033.0
13 TraesCS3A01G380000 chr3D 87.824 501 39 8 856 1352 486782136 486781654 8.710000e-158 568.0
14 TraesCS3A01G380000 chr3D 88.710 310 21 9 1786 2083 486780932 486780625 3.410000e-97 366.0
15 TraesCS3A01G380000 chr3D 92.308 247 17 2 1526 1771 486781281 486781036 3.430000e-92 350.0
16 TraesCS3A01G380000 chr3B 94.684 2295 89 13 2082 4352 649523892 649521607 0.000000e+00 3531.0
17 TraesCS3A01G380000 chr3B 87.398 2460 192 52 3314 5722 649645640 649643248 0.000000e+00 2717.0
18 TraesCS3A01G380000 chr3B 92.000 1500 71 16 4423 5918 649521606 649520152 0.000000e+00 2060.0
19 TraesCS3A01G380000 chr3B 90.201 1194 84 18 2082 3255 649647011 649645831 0.000000e+00 1526.0
20 TraesCS3A01G380000 chr3B 95.000 780 32 5 42 821 649526321 649525549 0.000000e+00 1218.0
21 TraesCS3A01G380000 chr3B 93.494 830 36 9 4 821 649649324 649648501 0.000000e+00 1218.0
22 TraesCS3A01G380000 chr3B 93.494 830 36 9 4 821 649681210 649680387 0.000000e+00 1218.0
23 TraesCS3A01G380000 chr3B 93.322 614 32 4 1471 2083 649524528 649523923 0.000000e+00 898.0
24 TraesCS3A01G380000 chr3B 88.029 543 26 11 856 1396 649525556 649525051 1.850000e-169 606.0
25 TraesCS3A01G380000 chr3B 88.247 502 40 6 856 1353 649648508 649648022 3.110000e-162 582.0
26 TraesCS3A01G380000 chr3B 88.247 502 40 6 856 1353 649680394 649679908 3.110000e-162 582.0
27 TraesCS3A01G380000 chr3B 87.097 310 25 9 1786 2083 649647348 649647042 2.670000e-88 337.0
28 TraesCS3A01G380000 chr3B 91.949 236 17 2 1536 1770 649647687 649647453 4.470000e-86 329.0
29 TraesCS3A01G380000 chr3B 87.662 154 18 1 1536 1688 649679573 649679420 1.710000e-40 178.0
30 TraesCS3A01G380000 chr1D 93.478 46 2 1 5942 5987 104461442 104461398 3.870000e-07 67.6


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 TraesCS3A01G380000 chr3A 630041419 630047405 5986 True 11057.000000 11057 100.000000 1 5987 1 chr3A.!!$R1 5986
1 TraesCS3A01G380000 chr3A 630205194 630211786 6592 True 960.285714 2643 89.570286 4 5850 7 chr3A.!!$R2 5846
2 TraesCS3A01G380000 chr3D 486735452 486741364 5912 True 3196.333333 7143 95.939000 1 5831 3 chr3D.!!$R1 5830
3 TraesCS3A01G380000 chr3D 486777261 486782956 5695 True 1288.400000 3964 90.016600 4 5424 5 chr3D.!!$R2 5420
4 TraesCS3A01G380000 chr3B 649520152 649526321 6169 True 1662.600000 3531 92.607000 42 5918 5 chr3B.!!$R1 5876
5 TraesCS3A01G380000 chr3B 649643248 649649324 6076 True 1118.166667 2717 89.731000 4 5722 6 chr3B.!!$R2 5718
6 TraesCS3A01G380000 chr3B 649679420 649681210 1790 True 659.333333 1218 89.801000 4 1688 3 chr3B.!!$R3 1684

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
264 265 1.272490 TGAGTGTTCTCCGGCTTACAG 59.728 52.381 0.00 0.0 39.75 2.74 F
787 800 1.555075 AGTTCTGGCTTATTCTCCGCA 59.445 47.619 0.00 0.0 0.00 5.69 F
1279 1296 0.554792 ATGCTATTCCTGCTTGGCCT 59.445 50.000 3.32 0.0 35.26 5.19 F
2790 3796 0.328592 TCTCGTCCAGGTGAGTAGCT 59.671 55.000 10.19 0.0 33.88 3.32 F
3297 4575 1.821216 ACTATTTGGTGCTGGGTTCG 58.179 50.000 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1296 2.361757 CAAAAGCATGAACAGGTGTGGA 59.638 45.455 0.00 0.00 0.00 4.02 R
2565 3571 0.392193 ATCAAGTCCCTTGCGCTCAG 60.392 55.000 9.73 4.36 40.84 3.35 R
3195 4218 0.180642 CACCTGCAGAGCATCCAGAT 59.819 55.000 17.39 0.00 38.13 2.90 R
4701 6006 5.301835 ACAATTGCCTGTATAGATCTGCT 57.698 39.130 5.18 0.00 0.00 4.24 R
5230 6546 0.038166 GATGGCACCAAGGACAAGGA 59.962 55.000 0.00 0.00 0.00 3.36 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
256 257 2.135933 GTTCCACTTGAGTGTTCTCCG 58.864 52.381 10.03 0.00 44.21 4.63
264 265 1.272490 TGAGTGTTCTCCGGCTTACAG 59.728 52.381 0.00 0.00 39.75 2.74
355 356 6.324561 TGCAAAGTATACATCTGCAACAAA 57.675 33.333 18.61 2.08 39.91 2.83
413 414 5.589855 TGTTGTGTTGACATGATTTCTCACT 59.410 36.000 0.00 0.00 33.22 3.41
454 455 4.457949 GCTAGAGCTCAGAGGGTAGAATAC 59.542 50.000 17.77 0.00 38.38 1.89
478 479 5.125900 CCTACTGTTGCATTCATTCCATTCA 59.874 40.000 0.00 0.00 0.00 2.57
561 562 6.811253 AACGAAAACTTAATGCTGATACCA 57.189 33.333 0.00 0.00 0.00 3.25
613 626 2.934887 TGATGAGGTGCATAATGGTGG 58.065 47.619 0.00 0.00 37.34 4.61
785 798 4.120589 GGTAAGTTCTGGCTTATTCTCCG 58.879 47.826 0.00 0.00 34.03 4.63
786 799 2.317530 AGTTCTGGCTTATTCTCCGC 57.682 50.000 0.00 0.00 0.00 5.54
787 800 1.555075 AGTTCTGGCTTATTCTCCGCA 59.445 47.619 0.00 0.00 0.00 5.69
1017 1032 6.545504 ACATACATGTGCTTTATTCGGATC 57.454 37.500 9.11 0.00 40.03 3.36
1030 1045 6.985188 TTATTCGGATCTGGAGTTTTTCTG 57.015 37.500 0.62 0.00 0.00 3.02
1279 1296 0.554792 ATGCTATTCCTGCTTGGCCT 59.445 50.000 3.32 0.00 35.26 5.19
1353 1376 4.258702 ACTGTGATTCGAGCTTACAAGT 57.741 40.909 0.00 0.00 0.00 3.16
1354 1382 3.990469 ACTGTGATTCGAGCTTACAAGTG 59.010 43.478 0.00 0.00 0.00 3.16
1626 2487 6.572167 TCTAACATGTGTTTGCAATCATCA 57.428 33.333 13.07 12.54 39.31 3.07
1838 2798 6.708054 CGATGGGCTCTAACTTATCTTTCATT 59.292 38.462 0.00 0.00 0.00 2.57
2269 3265 1.337167 GGCAATTGCTGGAAAGGTCAC 60.337 52.381 28.42 4.84 41.70 3.67
2286 3282 2.756207 GTCACTCAGGAGGTAGGACTTC 59.244 54.545 0.83 0.00 0.00 3.01
2339 3335 8.565896 AAACTATGATCTATGAGCAACACAAA 57.434 30.769 0.00 0.00 29.85 2.83
2340 3336 8.565896 AACTATGATCTATGAGCAACACAAAA 57.434 30.769 0.00 0.00 29.85 2.44
2457 3455 7.458409 TCTCAAAAAGAAGAAATATGCTGCT 57.542 32.000 0.00 0.00 0.00 4.24
2501 3507 5.390991 GCAGTTTATTAGAGGTGTGTGCTTC 60.391 44.000 0.00 0.00 0.00 3.86
2502 3508 5.934625 CAGTTTATTAGAGGTGTGTGCTTCT 59.065 40.000 0.00 0.00 0.00 2.85
2565 3571 6.968131 TCTAACATGCTTGATACAGAACAC 57.032 37.500 6.60 0.00 0.00 3.32
2625 3631 5.277011 GGAGTTTGCTGTCAAAAGAAATTGC 60.277 40.000 0.00 0.00 43.12 3.56
2790 3796 0.328592 TCTCGTCCAGGTGAGTAGCT 59.671 55.000 10.19 0.00 33.88 3.32
2948 3970 6.413892 TGAATATGAGTATTGTTGCAGGTCA 58.586 36.000 0.00 0.00 30.75 4.02
3195 4218 7.651704 GCTTTAAGACTGAAGCAAAATGGTTTA 59.348 33.333 15.36 0.00 45.74 2.01
3297 4575 1.821216 ACTATTTGGTGCTGGGTTCG 58.179 50.000 0.00 0.00 0.00 3.95
4414 5712 7.262772 TGATGGTAAGTATAGTTTCCACTTCG 58.737 38.462 17.98 0.00 34.48 3.79
4701 6006 3.535280 TTGCACTGACAGTACACAGAA 57.465 42.857 8.02 0.00 37.54 3.02
4754 6059 3.278574 GCTATGTACTTGATGCAACCCA 58.721 45.455 0.00 0.00 0.00 4.51
5181 6497 1.895131 GGAGTTGCCCACATCATGTTT 59.105 47.619 0.00 0.00 0.00 2.83
5183 6499 2.557924 GAGTTGCCCACATCATGTTTCA 59.442 45.455 0.00 0.00 0.00 2.69
5184 6500 3.167485 AGTTGCCCACATCATGTTTCAT 58.833 40.909 0.00 0.00 0.00 2.57
5185 6501 3.056393 AGTTGCCCACATCATGTTTCATG 60.056 43.478 0.00 3.65 0.00 3.07
5186 6502 2.527497 TGCCCACATCATGTTTCATGT 58.473 42.857 9.13 0.00 33.29 3.21
5187 6503 2.898612 TGCCCACATCATGTTTCATGTT 59.101 40.909 9.13 0.00 30.48 2.71
5230 6546 2.127708 ACCAGTTGTTTCAGAGACCCT 58.872 47.619 0.00 0.00 0.00 4.34
5231 6547 2.104963 ACCAGTTGTTTCAGAGACCCTC 59.895 50.000 0.00 0.00 0.00 4.30
5232 6548 2.551071 CCAGTTGTTTCAGAGACCCTCC 60.551 54.545 0.00 0.00 0.00 4.30
5233 6549 2.370189 CAGTTGTTTCAGAGACCCTCCT 59.630 50.000 0.00 0.00 0.00 3.69
5234 6550 3.049344 AGTTGTTTCAGAGACCCTCCTT 58.951 45.455 0.00 0.00 0.00 3.36
5235 6551 3.142174 GTTGTTTCAGAGACCCTCCTTG 58.858 50.000 0.00 0.00 0.00 3.61
5255 6577 0.988145 TCCTTGGTGCCATCCCTAGG 60.988 60.000 0.06 0.06 43.75 3.02
5261 6583 1.379527 GTGCCATCCCTAGGTTTTCG 58.620 55.000 8.29 0.00 0.00 3.46
5271 6593 7.172703 CCATCCCTAGGTTTTCGAAATGTATAC 59.827 40.741 12.12 6.27 0.00 1.47
5425 6751 7.862873 CGCTTACTGATTCTCATATCTGTAACA 59.137 37.037 10.23 0.00 40.72 2.41
5624 6987 6.017192 TCTTCCAGATACCTCACTTGTAGTT 58.983 40.000 0.00 0.00 0.00 2.24
5705 7068 5.755849 CCATACATTAGGGTTCTTGTCCTT 58.244 41.667 0.00 0.00 34.75 3.36
5715 7078 3.315470 GGTTCTTGTCCTTTGAACTCCAC 59.685 47.826 0.00 0.00 39.73 4.02
5770 7133 3.930336 GCATATGCCAGATGCTAGTACA 58.070 45.455 16.66 0.00 45.14 2.90
5779 7142 5.927115 GCCAGATGCTAGTACATACTAAACC 59.073 44.000 0.00 0.00 38.24 3.27
5786 7149 9.872684 ATGCTAGTACATACTAAACCCTAACTA 57.127 33.333 0.00 0.00 38.24 2.24
5818 7186 6.015940 AGTGCTGAAATCTTTCTAAACCAAGG 60.016 38.462 4.46 0.00 38.02 3.61
5845 7213 2.363683 AGCAGCAAGAGTTTAGCATCC 58.636 47.619 0.00 0.00 0.00 3.51
5856 7224 9.696917 CAAGAGTTTAGCATCCAAAACTTAAAT 57.303 29.630 2.34 0.00 43.97 1.40
5884 7252 8.072480 AGATCCTACATAGTAAACCTTAACCCT 58.928 37.037 0.00 0.00 0.00 4.34
5885 7253 9.372189 GATCCTACATAGTAAACCTTAACCCTA 57.628 37.037 0.00 0.00 0.00 3.53
5886 7254 9.733907 ATCCTACATAGTAAACCTTAACCCTAA 57.266 33.333 0.00 0.00 0.00 2.69
5923 7291 1.421480 AGGGGATTAACCTAGGACGC 58.579 55.000 17.98 9.07 36.32 5.19
5924 7292 1.062352 AGGGGATTAACCTAGGACGCT 60.062 52.381 17.98 8.65 36.32 5.07
5925 7293 1.070289 GGGGATTAACCTAGGACGCTG 59.930 57.143 17.98 0.00 38.98 5.18
5926 7294 2.037144 GGGATTAACCTAGGACGCTGA 58.963 52.381 17.98 0.00 38.98 4.26
5927 7295 2.633481 GGGATTAACCTAGGACGCTGAT 59.367 50.000 17.98 0.18 38.98 2.90
5928 7296 3.830755 GGGATTAACCTAGGACGCTGATA 59.169 47.826 17.98 0.00 38.98 2.15
5929 7297 4.282703 GGGATTAACCTAGGACGCTGATAA 59.717 45.833 17.98 3.57 38.98 1.75
5930 7298 5.046520 GGGATTAACCTAGGACGCTGATAAT 60.047 44.000 17.98 7.93 38.98 1.28
5931 7299 6.465084 GGATTAACCTAGGACGCTGATAATT 58.535 40.000 17.98 0.00 35.41 1.40
5932 7300 6.369065 GGATTAACCTAGGACGCTGATAATTG 59.631 42.308 17.98 0.00 35.41 2.32
5933 7301 3.113260 ACCTAGGACGCTGATAATTGC 57.887 47.619 17.98 0.00 0.00 3.56
5934 7302 2.224305 ACCTAGGACGCTGATAATTGCC 60.224 50.000 17.98 0.00 0.00 4.52
5935 7303 2.224281 CCTAGGACGCTGATAATTGCCA 60.224 50.000 1.05 0.00 0.00 4.92
5936 7304 2.645838 AGGACGCTGATAATTGCCAT 57.354 45.000 0.00 0.00 0.00 4.40
5937 7305 2.224606 AGGACGCTGATAATTGCCATG 58.775 47.619 0.00 0.00 0.00 3.66
5938 7306 1.949525 GGACGCTGATAATTGCCATGT 59.050 47.619 0.00 0.00 0.00 3.21
5939 7307 2.287188 GGACGCTGATAATTGCCATGTG 60.287 50.000 0.00 0.00 0.00 3.21
5940 7308 2.355756 GACGCTGATAATTGCCATGTGT 59.644 45.455 0.00 0.00 0.00 3.72
5941 7309 2.097954 ACGCTGATAATTGCCATGTGTG 59.902 45.455 0.00 0.00 0.00 3.82
5943 7311 2.223876 GCTGATAATTGCCATGTGTGGG 60.224 50.000 0.00 0.00 46.14 4.61
5951 7319 3.344703 CCATGTGTGGGCTGAAAGA 57.655 52.632 0.00 0.00 42.11 2.52
5952 7320 1.171308 CCATGTGTGGGCTGAAAGAG 58.829 55.000 0.00 0.00 42.11 2.85
5953 7321 1.171308 CATGTGTGGGCTGAAAGAGG 58.829 55.000 0.00 0.00 34.07 3.69
5954 7322 0.773644 ATGTGTGGGCTGAAAGAGGT 59.226 50.000 0.00 0.00 34.07 3.85
5955 7323 0.108585 TGTGTGGGCTGAAAGAGGTC 59.891 55.000 0.00 0.00 34.07 3.85
5956 7324 0.951040 GTGTGGGCTGAAAGAGGTCG 60.951 60.000 0.00 0.00 34.07 4.79
5957 7325 1.376037 GTGGGCTGAAAGAGGTCGG 60.376 63.158 0.00 0.00 34.07 4.79
5958 7326 2.269241 GGGCTGAAAGAGGTCGGG 59.731 66.667 0.00 0.00 34.07 5.14
5959 7327 2.269241 GGCTGAAAGAGGTCGGGG 59.731 66.667 0.00 0.00 34.07 5.73
5960 7328 2.436824 GCTGAAAGAGGTCGGGGC 60.437 66.667 0.00 0.00 34.07 5.80
5961 7329 2.269241 CTGAAAGAGGTCGGGGCC 59.731 66.667 0.00 0.00 34.07 5.80
5962 7330 3.665675 CTGAAAGAGGTCGGGGCCG 62.666 68.421 0.00 0.00 37.05 6.13
5963 7331 3.387947 GAAAGAGGTCGGGGCCGA 61.388 66.667 0.00 0.00 46.87 5.54
5976 7344 2.890961 GCCGAACGCCCTTCTAGC 60.891 66.667 0.00 0.00 0.00 3.42
5977 7345 2.202892 CCGAACGCCCTTCTAGCC 60.203 66.667 0.00 0.00 0.00 3.93
5978 7346 2.577059 CGAACGCCCTTCTAGCCA 59.423 61.111 0.00 0.00 0.00 4.75
5979 7347 1.810030 CGAACGCCCTTCTAGCCAC 60.810 63.158 0.00 0.00 0.00 5.01
5980 7348 1.449778 GAACGCCCTTCTAGCCACC 60.450 63.158 0.00 0.00 0.00 4.61
5981 7349 2.871216 GAACGCCCTTCTAGCCACCC 62.871 65.000 0.00 0.00 0.00 4.61
5982 7350 3.399181 CGCCCTTCTAGCCACCCA 61.399 66.667 0.00 0.00 0.00 4.51
5983 7351 2.746375 CGCCCTTCTAGCCACCCAT 61.746 63.158 0.00 0.00 0.00 4.00
5984 7352 1.615262 GCCCTTCTAGCCACCCATT 59.385 57.895 0.00 0.00 0.00 3.16
5985 7353 0.753111 GCCCTTCTAGCCACCCATTG 60.753 60.000 0.00 0.00 0.00 2.82
5986 7354 0.625849 CCCTTCTAGCCACCCATTGT 59.374 55.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 265 3.243068 CCGCTAATATTTGTCAGTTGGCC 60.243 47.826 0.00 0.00 0.00 5.36
284 285 3.418047 AGTTTTTCCCCACAGATTACCG 58.582 45.455 0.00 0.00 0.00 4.02
413 414 1.523154 GCACCCTGCGTCCATTTCAA 61.523 55.000 0.00 0.00 31.71 2.69
454 455 5.125900 TGAATGGAATGAATGCAACAGTAGG 59.874 40.000 0.00 0.00 30.96 3.18
561 562 0.465460 TCAGCAGCGTTTCCACCTTT 60.465 50.000 0.00 0.00 0.00 3.11
613 626 3.126073 CCTTTTCTTGCTTTGCCTTGAC 58.874 45.455 0.00 0.00 0.00 3.18
785 798 3.482786 CATCGCTTAACAGTTGACTTGC 58.517 45.455 0.00 0.00 0.00 4.01
786 799 3.482786 GCATCGCTTAACAGTTGACTTG 58.517 45.455 0.00 0.00 0.00 3.16
787 800 2.484264 GGCATCGCTTAACAGTTGACTT 59.516 45.455 0.00 0.00 0.00 3.01
860 873 9.436957 AGAAGAGAATAAAAGAAACAGCGAATA 57.563 29.630 0.00 0.00 0.00 1.75
861 874 8.329203 AGAAGAGAATAAAAGAAACAGCGAAT 57.671 30.769 0.00 0.00 0.00 3.34
862 875 7.095187 GGAGAAGAGAATAAAAGAAACAGCGAA 60.095 37.037 0.00 0.00 0.00 4.70
865 878 7.174080 AGTGGAGAAGAGAATAAAAGAAACAGC 59.826 37.037 0.00 0.00 0.00 4.40
1017 1032 3.821033 CCCCAAGTACAGAAAAACTCCAG 59.179 47.826 0.00 0.00 0.00 3.86
1030 1045 0.996583 TGTCCCATTCCCCCAAGTAC 59.003 55.000 0.00 0.00 0.00 2.73
1279 1296 2.361757 CAAAAGCATGAACAGGTGTGGA 59.638 45.455 0.00 0.00 0.00 4.02
1626 2487 6.058183 ACTCTTCAACAGCTGTTTCATTAGT 58.942 36.000 29.23 22.69 35.83 2.24
1838 2798 2.453521 AGCAACCGTACATACTGGAGA 58.546 47.619 0.00 0.00 0.00 3.71
1977 2938 6.815641 GGTCATCATGATGTATATCAGTCACC 59.184 42.308 30.01 22.30 45.89 4.02
2154 3150 9.912634 TCCAGTGAAATGAAAAGAAATATCAAC 57.087 29.630 0.00 0.00 0.00 3.18
2269 3265 2.421751 TCGAAGTCCTACCTCCTGAG 57.578 55.000 0.00 0.00 0.00 3.35
2339 3335 3.553508 GCAGTTGTGGCAAGATGATGTTT 60.554 43.478 0.00 0.00 0.00 2.83
2340 3336 2.029649 GCAGTTGTGGCAAGATGATGTT 60.030 45.455 0.00 0.00 0.00 2.71
2457 3455 5.104527 ACTGCCATCTAGTGCCACTTTAATA 60.105 40.000 1.02 0.00 0.00 0.98
2478 3476 5.934625 AGAAGCACACACCTCTAATAAACTG 59.065 40.000 0.00 0.00 0.00 3.16
2565 3571 0.392193 ATCAAGTCCCTTGCGCTCAG 60.392 55.000 9.73 4.36 40.84 3.35
2625 3631 8.347035 ACAAAATTTGATTCAGGCAAAAATCAG 58.653 29.630 13.19 1.76 41.50 2.90
2948 3970 3.953612 TCACCACTTTTCATCTGTGCTTT 59.046 39.130 0.00 0.00 0.00 3.51
3195 4218 0.180642 CACCTGCAGAGCATCCAGAT 59.819 55.000 17.39 0.00 38.13 2.90
3297 4575 6.072673 AGGTTAACAATAACAGCACAGTAAGC 60.073 38.462 8.10 0.00 42.66 3.09
3472 4766 8.540388 AGTTAGAATTGCCTCTTAATAGTCACA 58.460 33.333 0.00 0.00 0.00 3.58
4701 6006 5.301835 ACAATTGCCTGTATAGATCTGCT 57.698 39.130 5.18 0.00 0.00 4.24
5230 6546 0.038166 GATGGCACCAAGGACAAGGA 59.962 55.000 0.00 0.00 0.00 3.36
5231 6547 0.967380 GGATGGCACCAAGGACAAGG 60.967 60.000 0.00 0.00 0.00 3.61
5232 6548 0.967380 GGGATGGCACCAAGGACAAG 60.967 60.000 8.11 0.00 0.00 3.16
5233 6549 1.076549 GGGATGGCACCAAGGACAA 59.923 57.895 8.11 0.00 0.00 3.18
5234 6550 0.548926 TAGGGATGGCACCAAGGACA 60.549 55.000 8.11 0.00 0.00 4.02
5235 6551 0.181350 CTAGGGATGGCACCAAGGAC 59.819 60.000 8.11 0.00 0.00 3.85
5271 6593 7.069569 GCAACACATTTACAACAGTAGTACAG 58.930 38.462 2.52 0.00 0.00 2.74
5290 6615 5.068198 ACCATGAGATTTATGGATGCAACAC 59.932 40.000 10.72 0.00 46.42 3.32
5495 6827 7.892771 TCAGAGCACCAGTAATCTATCTGATAT 59.107 37.037 0.00 0.00 37.58 1.63
5512 6844 3.582208 AGGATTCCATCTATCAGAGCACC 59.418 47.826 5.29 0.00 0.00 5.01
5574 6937 7.972832 ATATAAAAGAACAAGACGAACACCA 57.027 32.000 0.00 0.00 0.00 4.17
5603 6966 5.580998 AGAACTACAAGTGAGGTATCTGGA 58.419 41.667 0.00 0.00 0.00 3.86
5611 6974 8.777865 TCATTTGATAAGAACTACAAGTGAGG 57.222 34.615 0.00 0.00 35.35 3.86
5624 6987 9.730705 ATTCAGTCAGTCTTTCATTTGATAAGA 57.269 29.630 0.00 0.00 0.00 2.10
5715 7078 2.320587 GGTTCGCACTGCCACAGAG 61.321 63.158 0.78 0.00 35.18 3.35
5856 7224 8.921205 GGTTAAGGTTTACTATGTAGGATCTGA 58.079 37.037 0.00 0.00 0.00 3.27
5862 7230 8.985922 AGTTAGGGTTAAGGTTTACTATGTAGG 58.014 37.037 0.00 0.00 0.00 3.18
5877 7245 9.871175 AGAACTTCCAAAATTAGTTAGGGTTAA 57.129 29.630 0.00 0.00 32.58 2.01
5884 7252 8.222138 TCCCCTAGAACTTCCAAAATTAGTTA 57.778 34.615 0.00 0.00 32.58 2.24
5885 7253 7.098845 TCCCCTAGAACTTCCAAAATTAGTT 57.901 36.000 0.00 0.00 34.97 2.24
5886 7254 6.713731 TCCCCTAGAACTTCCAAAATTAGT 57.286 37.500 0.00 0.00 0.00 2.24
5890 7258 6.895756 GGTTAATCCCCTAGAACTTCCAAAAT 59.104 38.462 0.00 0.00 0.00 1.82
5918 7286 1.949525 ACATGGCAATTATCAGCGTCC 59.050 47.619 0.00 0.00 0.00 4.79
5919 7287 2.355756 ACACATGGCAATTATCAGCGTC 59.644 45.455 0.00 0.00 0.00 5.19
5920 7288 2.097954 CACACATGGCAATTATCAGCGT 59.902 45.455 0.00 0.00 0.00 5.07
5921 7289 2.542205 CCACACATGGCAATTATCAGCG 60.542 50.000 0.00 0.00 39.82 5.18
5922 7290 2.223876 CCCACACATGGCAATTATCAGC 60.224 50.000 0.00 0.00 45.76 4.26
5923 7291 3.720949 CCCACACATGGCAATTATCAG 57.279 47.619 0.00 0.00 45.76 2.90
5933 7301 1.171308 CTCTTTCAGCCCACACATGG 58.829 55.000 0.00 0.00 46.81 3.66
5934 7302 1.171308 CCTCTTTCAGCCCACACATG 58.829 55.000 0.00 0.00 0.00 3.21
5935 7303 0.773644 ACCTCTTTCAGCCCACACAT 59.226 50.000 0.00 0.00 0.00 3.21
5936 7304 0.108585 GACCTCTTTCAGCCCACACA 59.891 55.000 0.00 0.00 0.00 3.72
5937 7305 0.951040 CGACCTCTTTCAGCCCACAC 60.951 60.000 0.00 0.00 0.00 3.82
5938 7306 1.371183 CGACCTCTTTCAGCCCACA 59.629 57.895 0.00 0.00 0.00 4.17
5939 7307 1.376037 CCGACCTCTTTCAGCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
5940 7308 2.592993 CCCGACCTCTTTCAGCCCA 61.593 63.158 0.00 0.00 0.00 5.36
5941 7309 2.269241 CCCGACCTCTTTCAGCCC 59.731 66.667 0.00 0.00 0.00 5.19
5942 7310 2.269241 CCCCGACCTCTTTCAGCC 59.731 66.667 0.00 0.00 0.00 4.85
5943 7311 2.436824 GCCCCGACCTCTTTCAGC 60.437 66.667 0.00 0.00 0.00 4.26
5944 7312 2.269241 GGCCCCGACCTCTTTCAG 59.731 66.667 0.00 0.00 0.00 3.02
5945 7313 3.702048 CGGCCCCGACCTCTTTCA 61.702 66.667 0.00 0.00 42.83 2.69
5946 7314 3.387947 TCGGCCCCGACCTCTTTC 61.388 66.667 5.12 0.00 44.01 2.62
5959 7327 2.890961 GCTAGAAGGGCGTTCGGC 60.891 66.667 18.82 18.82 40.49 5.54
5960 7328 2.202892 GGCTAGAAGGGCGTTCGG 60.203 66.667 13.65 11.64 40.49 4.30
5961 7329 1.810030 GTGGCTAGAAGGGCGTTCG 60.810 63.158 13.65 2.78 40.49 3.95
5962 7330 1.449778 GGTGGCTAGAAGGGCGTTC 60.450 63.158 11.81 11.81 35.08 3.95
5963 7331 2.669240 GGTGGCTAGAAGGGCGTT 59.331 61.111 0.00 0.00 34.31 4.84
5964 7332 3.400054 GGGTGGCTAGAAGGGCGT 61.400 66.667 0.00 0.00 34.31 5.68
5965 7333 2.270874 AATGGGTGGCTAGAAGGGCG 62.271 60.000 0.00 0.00 34.31 6.13
5966 7334 0.753111 CAATGGGTGGCTAGAAGGGC 60.753 60.000 0.00 0.00 0.00 5.19
5967 7335 0.625849 ACAATGGGTGGCTAGAAGGG 59.374 55.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.