Multiple sequence alignment - TraesCS5D01G213600

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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 TraesCS5D01G213600 chr5D 100.000 8399 0 0 1 8399 322954222 322962620 0.000000e+00 15511.0
1 TraesCS5D01G213600 chr5D 82.703 185 30 2 5719 5901 315936149 315935965 6.750000e-36 163.0
2 TraesCS5D01G213600 chr5D 92.661 109 6 2 4355 4462 565043082 565043189 1.130000e-33 156.0
3 TraesCS5D01G213600 chr5D 83.439 157 26 0 5741 5897 395733709 395733865 6.790000e-31 147.0
4 TraesCS5D01G213600 chr5D 84.375 64 8 2 5656 5718 508618998 508618936 2.530000e-05 62.1
5 TraesCS5D01G213600 chr5A 96.346 4707 95 15 360 5034 419681274 419685935 0.000000e+00 7668.0
6 TraesCS5D01G213600 chr5A 98.204 2839 32 9 5031 7862 419686192 419689018 0.000000e+00 4942.0
7 TraesCS5D01G213600 chr5A 89.216 306 20 1 8107 8399 419689314 419689619 3.700000e-98 370.0
8 TraesCS5D01G213600 chr5A 96.316 190 7 0 7862 8051 419689124 419689313 6.330000e-81 313.0
9 TraesCS5D01G213600 chr5A 78.889 180 28 6 4511 4689 682415132 682414962 6.890000e-21 113.0
10 TraesCS5D01G213600 chr5B 93.800 2000 67 16 336 2324 375167831 375169784 0.000000e+00 2953.0
11 TraesCS5D01G213600 chr5B 96.399 1333 41 4 6443 7773 375174239 375175566 0.000000e+00 2189.0
12 TraesCS5D01G213600 chr5B 91.518 1462 64 17 2949 4366 375170813 375172258 0.000000e+00 1958.0
13 TraesCS5D01G213600 chr5B 89.274 1212 69 27 5123 6308 375172892 375174068 0.000000e+00 1461.0
14 TraesCS5D01G213600 chr5B 89.026 647 47 4 7774 8397 375175609 375176254 0.000000e+00 780.0
15 TraesCS5D01G213600 chr5B 88.969 553 31 11 4511 5062 375172367 375172890 0.000000e+00 656.0
16 TraesCS5D01G213600 chr5B 92.953 298 19 2 2329 2626 375169927 375170222 4.660000e-117 433.0
17 TraesCS5D01G213600 chr5B 84.259 324 40 6 1 317 375167415 375167734 1.060000e-78 305.0
18 TraesCS5D01G213600 chr5B 94.030 134 6 1 2819 2952 375170483 375170614 1.430000e-47 202.0
19 TraesCS5D01G213600 chr5B 94.118 102 4 2 4365 4465 428958998 428958898 4.060000e-33 154.0
20 TraesCS5D01G213600 chr5B 92.857 70 5 0 4460 4529 375172257 375172326 1.490000e-17 102.0
21 TraesCS5D01G213600 chr5B 91.667 72 6 0 6309 6380 375174162 375174233 5.360000e-17 100.0
22 TraesCS5D01G213600 chr3A 80.632 253 37 9 5656 5897 186047772 186047521 1.440000e-42 185.0
23 TraesCS5D01G213600 chr3A 92.661 109 8 0 4353 4461 595454143 595454251 3.140000e-34 158.0
24 TraesCS5D01G213600 chr3A 91.453 117 7 3 4356 4472 614663642 614663529 3.140000e-34 158.0
25 TraesCS5D01G213600 chr3B 95.192 104 4 1 4359 4462 479298374 479298476 6.750000e-36 163.0
26 TraesCS5D01G213600 chr7A 92.174 115 8 1 4353 4467 164447452 164447339 2.430000e-35 161.0
27 TraesCS5D01G213600 chr6D 93.519 108 7 0 4362 4469 467773475 467773582 2.430000e-35 161.0
28 TraesCS5D01G213600 chr4B 85.350 157 20 3 5727 5881 317763379 317763534 8.730000e-35 159.0
29 TraesCS5D01G213600 chr4A 83.721 172 25 3 5727 5896 312683337 312683167 8.730000e-35 159.0
30 TraesCS5D01G213600 chr3D 84.906 159 22 2 5739 5897 159794657 159794501 8.730000e-35 159.0
31 TraesCS5D01G213600 chr3D 90.678 118 6 4 4345 4461 79532666 79532553 1.460000e-32 152.0
32 TraesCS5D01G213600 chr4D 86.325 117 14 2 5769 5884 212159257 212159142 8.850000e-25 126.0


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 TraesCS5D01G213600 chr5D 322954222 322962620 8398 False 15511.000000 15511 100.000000 1 8399 1 chr5D.!!$F1 8398
1 TraesCS5D01G213600 chr5A 419681274 419689619 8345 False 3323.250000 7668 95.020500 360 8399 4 chr5A.!!$F1 8039
2 TraesCS5D01G213600 chr5B 375167415 375176254 8839 False 1012.636364 2953 91.341091 1 8397 11 chr5B.!!$F1 8396

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
495 589 0.034896 AGATCACGTTTTGGCGAGGT 59.965 50.000 0.00 0.00 35.59 3.85 F
510 604 1.066143 CGAGGTTCTGCTATGGTTGGT 60.066 52.381 0.00 0.00 0.00 3.67 F
1112 1223 1.074566 CAAGGACAAGGGGAAGAAGCT 59.925 52.381 0.00 0.00 0.00 3.74 F
2445 2699 1.138859 TGATCCCTGAACAGCATACCG 59.861 52.381 0.00 0.00 0.00 4.02 F
3947 4545 2.034939 TGAAGCCAAAGATGTTGCTGTG 59.965 45.455 0.00 0.00 33.59 3.66 F
4317 4933 0.035439 ATGTGGCCGGAAGTACTTGG 60.035 55.000 14.14 10.25 0.00 3.61 F
5148 6092 2.090437 TGGGTGGTATAGTATCCTGCCA 60.090 50.000 0.00 0.00 0.00 4.92 F
6100 7068 1.531149 ACCTCGTTCATTGTTTCAGCG 59.469 47.619 0.00 0.00 0.00 5.18 F
6850 7916 2.388121 GCGATCATGCATACAAAAGCC 58.612 47.619 0.00 0.00 34.15 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1831 1.068055 GCGTTAGAGAACACGAGGGAA 60.068 52.381 0.00 0.0 38.76 3.97 R
1809 1923 2.579860 AGCCTGACCCAGATTTCAGAAT 59.420 45.455 0.08 0.0 41.65 2.40 R
2708 2979 1.009997 TCCCAAGGGAATGCAGGAAT 58.990 50.000 5.09 0.0 42.05 3.01 R
4081 4686 0.036388 CAGTATCCTGTGGGCAACGT 60.036 55.000 0.00 0.0 33.80 3.99 R
4782 5458 4.964593 AGTACGGTTGTAAAGAACATGGT 58.035 39.130 0.00 0.0 38.10 3.55 R
5624 6569 5.557866 ACAATACCACAGACCTAGGAAAAC 58.442 41.667 17.98 3.9 0.00 2.43 R
6389 7453 9.525409 ACTACACGTTCCAACTAAATATATCAC 57.475 33.333 0.00 0.0 0.00 3.06 R
7230 8296 1.059584 TCTGTGTGCCCCTTCCTTCA 61.060 55.000 0.00 0.0 0.00 3.02 R
8148 9372 0.546122 TGTCACTTGGTTGCCTCAGT 59.454 50.000 0.00 0.0 0.00 3.41 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
24 25 3.692593 ACCATTCTATTTACCGCCAACAC 59.307 43.478 0.00 0.00 0.00 3.32
25 26 3.692101 CCATTCTATTTACCGCCAACACA 59.308 43.478 0.00 0.00 0.00 3.72
33 34 1.672356 CCGCCAACACAGAGAAGGG 60.672 63.158 0.00 0.00 0.00 3.95
34 35 2.328099 CGCCAACACAGAGAAGGGC 61.328 63.158 0.00 0.00 38.04 5.19
35 36 1.228245 GCCAACACAGAGAAGGGCA 60.228 57.895 0.00 0.00 41.02 5.36
37 38 0.954452 CCAACACAGAGAAGGGCAAC 59.046 55.000 0.00 0.00 0.00 4.17
77 78 5.184864 AGGACGATCTTGCTAGGATCATTAG 59.815 44.000 7.85 0.00 39.42 1.73
105 106 3.756082 AGGTGCATGGGATTTTAAGGA 57.244 42.857 0.00 0.00 0.00 3.36
108 109 3.013921 GTGCATGGGATTTTAAGGACGA 58.986 45.455 0.00 0.00 0.00 4.20
136 137 9.899226 AGAAATATTTACAAGAAGAACACAAGC 57.101 29.630 0.00 0.00 0.00 4.01
137 138 9.129209 GAAATATTTACAAGAAGAACACAAGCC 57.871 33.333 0.00 0.00 0.00 4.35
138 139 7.759489 ATATTTACAAGAAGAACACAAGCCA 57.241 32.000 0.00 0.00 0.00 4.75
180 181 6.422223 CCAATTGATAACGTGCTAGCTTTAG 58.578 40.000 17.23 6.99 0.00 1.85
190 191 7.486802 ACGTGCTAGCTTTAGAAAAACTTAA 57.513 32.000 17.23 0.00 0.00 1.85
216 217 7.817418 TGTAACATCTCCAGTAAAAGCTTTT 57.183 32.000 26.50 26.50 0.00 2.27
218 219 7.719633 TGTAACATCTCCAGTAAAAGCTTTTCT 59.280 33.333 27.03 19.58 0.00 2.52
224 225 5.772521 TCCAGTAAAAGCTTTTCTTCATGC 58.227 37.500 27.03 6.98 32.88 4.06
225 226 5.536161 TCCAGTAAAAGCTTTTCTTCATGCT 59.464 36.000 27.03 9.24 37.37 3.79
226 227 5.632347 CCAGTAAAAGCTTTTCTTCATGCTG 59.368 40.000 27.03 19.45 35.75 4.41
227 228 6.211515 CAGTAAAAGCTTTTCTTCATGCTGT 58.788 36.000 27.03 2.29 35.79 4.40
228 229 6.361748 CAGTAAAAGCTTTTCTTCATGCTGTC 59.638 38.462 27.03 5.66 35.79 3.51
229 230 3.930634 AAGCTTTTCTTCATGCTGTCC 57.069 42.857 0.00 0.00 35.79 4.02
230 231 2.867624 AGCTTTTCTTCATGCTGTCCA 58.132 42.857 0.00 0.00 34.19 4.02
231 232 2.818432 AGCTTTTCTTCATGCTGTCCAG 59.182 45.455 0.00 0.00 34.19 3.86
232 233 2.816087 GCTTTTCTTCATGCTGTCCAGA 59.184 45.455 0.00 0.00 0.00 3.86
233 234 3.442977 GCTTTTCTTCATGCTGTCCAGAT 59.557 43.478 0.00 0.00 0.00 2.90
234 235 4.674623 GCTTTTCTTCATGCTGTCCAGATG 60.675 45.833 0.00 0.31 0.00 2.90
247 255 1.513158 CAGATGTCCCTCGCGTCTT 59.487 57.895 5.77 0.00 30.50 3.01
257 265 1.144969 CTCGCGTCTTGTTAAAGCCA 58.855 50.000 5.77 0.00 33.06 4.75
273 281 1.272769 AGCCACCGTTCTAGACAAGAC 59.727 52.381 0.00 0.00 32.51 3.01
274 282 1.978542 CCACCGTTCTAGACAAGACG 58.021 55.000 7.56 7.56 32.51 4.18
275 283 1.538512 CCACCGTTCTAGACAAGACGA 59.461 52.381 14.69 0.00 32.51 4.20
276 284 2.414293 CCACCGTTCTAGACAAGACGAG 60.414 54.545 14.69 8.35 32.51 4.18
277 285 1.811359 ACCGTTCTAGACAAGACGAGG 59.189 52.381 14.69 3.56 32.51 4.63
278 286 1.467713 CCGTTCTAGACAAGACGAGGC 60.468 57.143 14.69 0.00 32.51 4.70
279 287 1.467713 CGTTCTAGACAAGACGAGGCC 60.468 57.143 8.67 0.00 32.51 5.19
411 497 3.138884 TGCTCTGCACCTTGAATGTAA 57.861 42.857 0.00 0.00 31.71 2.41
412 498 3.485394 TGCTCTGCACCTTGAATGTAAA 58.515 40.909 0.00 0.00 31.71 2.01
413 499 3.253188 TGCTCTGCACCTTGAATGTAAAC 59.747 43.478 0.00 0.00 31.71 2.01
446 540 0.536460 ACCGTGCCAACCGAAAGATT 60.536 50.000 0.00 0.00 0.00 2.40
456 550 5.334337 GCCAACCGAAAGATTACGTTTTACT 60.334 40.000 0.00 0.00 0.00 2.24
495 589 0.034896 AGATCACGTTTTGGCGAGGT 59.965 50.000 0.00 0.00 35.59 3.85
502 596 1.519408 GTTTTGGCGAGGTTCTGCTA 58.481 50.000 0.00 0.00 0.00 3.49
510 604 1.066143 CGAGGTTCTGCTATGGTTGGT 60.066 52.381 0.00 0.00 0.00 3.67
532 626 4.446994 TCGCCATTATCATTTGTGCAAA 57.553 36.364 0.00 0.00 34.46 3.68
540 634 1.879380 TCATTTGTGCAAAGCTACGCT 59.121 42.857 8.58 0.00 42.56 5.07
570 664 4.078516 CCGTCCCCGTCCTTGACC 62.079 72.222 0.00 0.00 0.00 4.02
632 726 4.717313 GAACTCCGCCCCCACCAC 62.717 72.222 0.00 0.00 0.00 4.16
897 1007 3.615509 CTTAGGGTTTCGCGGGCCA 62.616 63.158 6.13 0.00 0.00 5.36
898 1008 3.615509 TTAGGGTTTCGCGGGCCAG 62.616 63.158 6.13 0.00 0.00 4.85
1112 1223 1.074566 CAAGGACAAGGGGAAGAAGCT 59.925 52.381 0.00 0.00 0.00 3.74
1560 1672 6.698766 GTCCGTTAAGTCTCTACTTTGTTTGA 59.301 38.462 0.00 0.00 43.60 2.69
1611 1723 6.748198 CGACGCTAGGATCCTTTAATAGAATC 59.252 42.308 22.03 10.32 0.00 2.52
1719 1831 3.972638 AGTCTGATTCCATAGGCTGTCAT 59.027 43.478 0.00 0.00 0.00 3.06
1755 1867 3.615224 AACGCCCTTTCCGTAGATTTA 57.385 42.857 0.00 0.00 38.06 1.40
1802 1916 2.355444 GCTGTAGGACTAGAGGTTCGTC 59.645 54.545 0.00 0.00 0.00 4.20
1809 1923 3.434739 GGACTAGAGGTTCGTCCCAGATA 60.435 52.174 0.00 0.00 41.00 1.98
1831 1945 1.556911 TCTGAAATCTGGGTCAGGCTC 59.443 52.381 1.14 0.00 41.38 4.70
1950 2066 2.563471 TGGTTGTTTTGTTACGGTGC 57.437 45.000 0.00 0.00 0.00 5.01
1960 2076 1.903860 TGTTACGGTGCAGGGATTAGT 59.096 47.619 0.00 0.00 0.00 2.24
2033 2149 8.741603 ACTGTTTAATTGTGTAAGTACTTGGT 57.258 30.769 18.56 0.00 0.00 3.67
2270 2386 4.974645 ATGTGTGTTCAGGTCCTTTAGA 57.025 40.909 0.00 0.00 0.00 2.10
2415 2669 2.438021 TGTTGCCTACTTTCTGGTGAGT 59.562 45.455 0.00 0.00 0.00 3.41
2445 2699 1.138859 TGATCCCTGAACAGCATACCG 59.861 52.381 0.00 0.00 0.00 4.02
2708 2979 5.392480 TTCGTTTCTTCGTTCAATTTCGA 57.608 34.783 0.00 0.00 0.00 3.71
2799 3070 4.756084 AAAGTTCAGCACTGTAGCAATC 57.244 40.909 0.00 0.00 35.12 2.67
3284 3845 4.884458 GCTAGAGCATTCTTTTGGGTAC 57.116 45.455 0.00 0.00 41.59 3.34
3322 3889 3.057736 TGCTTCTGCTTGCAATCTCTTTC 60.058 43.478 0.00 0.00 40.48 2.62
3334 3902 6.005823 TGCAATCTCTTTCATCCTCTTGAAA 58.994 36.000 0.00 0.31 41.92 2.69
3947 4545 2.034939 TGAAGCCAAAGATGTTGCTGTG 59.965 45.455 0.00 0.00 33.59 3.66
4081 4686 5.353956 ACGCACATTCTGAATTATGCTTGTA 59.646 36.000 23.58 0.00 0.00 2.41
4082 4687 5.678483 CGCACATTCTGAATTATGCTTGTAC 59.322 40.000 23.58 6.54 0.00 2.90
4115 4722 2.536761 TACTGTGCGTGCTTTAACCT 57.463 45.000 0.00 0.00 0.00 3.50
4317 4933 0.035439 ATGTGGCCGGAAGTACTTGG 60.035 55.000 14.14 10.25 0.00 3.61
4480 5096 3.543680 ATCTGATAACAGTGGTTCCCG 57.456 47.619 0.00 0.00 43.81 5.14
4635 5310 5.833406 TGATTGCACCCATGTTATAGTTG 57.167 39.130 0.00 0.00 0.00 3.16
4782 5458 7.531857 TGGTTTTGTATTTGCAGAATCCTTA 57.468 32.000 0.00 0.00 0.00 2.69
4801 5477 4.758165 CCTTACCATGTTCTTTACAACCGT 59.242 41.667 0.00 0.00 40.89 4.83
4824 5500 8.416329 CCGTACTAATACCAAAGTATAGGTTGT 58.584 37.037 0.00 0.00 38.27 3.32
4834 5510 9.969001 ACCAAAGTATAGGTTGTATTATGTTGT 57.031 29.630 0.00 0.00 33.39 3.32
4953 5636 6.434028 ACAACACTATCATGCATAAGGTGTTT 59.566 34.615 24.00 17.12 42.11 2.83
5148 6092 2.090437 TGGGTGGTATAGTATCCTGCCA 60.090 50.000 0.00 0.00 0.00 4.92
5624 6569 5.509716 ACCATCATACATGCAAATCACTG 57.490 39.130 0.00 0.00 0.00 3.66
5732 6696 9.985318 CTTTTCTAAGTTATCTGCAAAGATCTG 57.015 33.333 0.00 0.00 0.00 2.90
5873 6840 8.834749 AACTTAGGACAATTCTAAGACTTCAC 57.165 34.615 15.64 0.00 43.72 3.18
6100 7068 1.531149 ACCTCGTTCATTGTTTCAGCG 59.469 47.619 0.00 0.00 0.00 5.18
6305 7369 8.924303 TGTGATATATTTACCTGTCTTGCTAGT 58.076 33.333 0.00 0.00 0.00 2.57
6750 7814 5.201243 AGACAAAGTAAGAACCTTTTGCCT 58.799 37.500 0.00 0.00 34.69 4.75
6850 7916 2.388121 GCGATCATGCATACAAAAGCC 58.612 47.619 0.00 0.00 34.15 4.35
7101 8167 4.394920 GGTGTTTACATGTCGAATGGTGAT 59.605 41.667 0.00 0.00 0.00 3.06
7205 8271 6.598457 AGCAAGACTTACGTGAGAGAGTATAA 59.402 38.462 15.04 0.00 31.97 0.98
7230 8296 1.007238 TCTCCACCCTCGAATCTCCTT 59.993 52.381 0.00 0.00 0.00 3.36
7236 8302 2.111384 CCCTCGAATCTCCTTGAAGGA 58.889 52.381 14.16 14.16 43.43 3.36
7953 9167 7.123247 AGTTCAATTCCACCATAAGGAGAAATG 59.877 37.037 0.00 0.00 36.33 2.32
8065 9289 0.107654 GCCTCCCGGTATATGCATCC 60.108 60.000 0.19 0.00 0.00 3.51
8075 9299 7.292356 TCCCGGTATATGCATCCTGATAAATAT 59.708 37.037 0.19 0.00 0.00 1.28
8076 9300 7.388776 CCCGGTATATGCATCCTGATAAATATG 59.611 40.741 0.19 0.00 0.00 1.78
8077 9301 7.388776 CCGGTATATGCATCCTGATAAATATGG 59.611 40.741 0.19 0.00 0.00 2.74
8078 9302 7.095060 CGGTATATGCATCCTGATAAATATGGC 60.095 40.741 0.19 0.00 0.00 4.40
8148 9372 8.415950 TGGCATACAGAAAGGAAAGAAAATAA 57.584 30.769 0.00 0.00 0.00 1.40
8163 9387 5.140454 AGAAAATAACTGAGGCAACCAAGT 58.860 37.500 0.00 0.00 37.17 3.16
8179 9403 3.135712 ACCAAGTGACATGTGACCTAACA 59.864 43.478 12.11 0.00 0.00 2.41
8215 9439 2.958355 ACAACAACACCTTCAAGATGGG 59.042 45.455 6.90 0.00 0.00 4.00
8354 9591 5.717119 ACCTAGCCAGAAGGTTAAATCAT 57.283 39.130 0.00 0.00 45.26 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.857052 TCTCTGTGTTGGCGGTAAATAG 58.143 45.455 0.00 0.00 0.00 1.73
9 10 3.965379 TCTCTGTGTTGGCGGTAAATA 57.035 42.857 0.00 0.00 0.00 1.40
11 12 2.489971 CTTCTCTGTGTTGGCGGTAAA 58.510 47.619 0.00 0.00 0.00 2.01
15 16 1.672356 CCCTTCTCTGTGTTGGCGG 60.672 63.158 0.00 0.00 0.00 6.13
24 25 2.022195 CATGATGGTTGCCCTTCTCTG 58.978 52.381 0.00 0.00 36.20 3.35
25 26 1.064166 CCATGATGGTTGCCCTTCTCT 60.064 52.381 2.54 0.00 36.20 3.10
33 34 1.466856 TCTTCTGCCATGATGGTTGC 58.533 50.000 13.84 0.00 40.46 4.17
34 35 2.426024 CCTTCTTCTGCCATGATGGTTG 59.574 50.000 13.84 6.43 40.46 3.77
35 36 2.309755 TCCTTCTTCTGCCATGATGGTT 59.690 45.455 13.84 0.00 40.46 3.67
37 38 2.295885 GTCCTTCTTCTGCCATGATGG 58.704 52.381 7.21 7.21 41.55 3.51
44 45 2.275318 CAAGATCGTCCTTCTTCTGCC 58.725 52.381 0.00 0.00 31.11 4.85
45 46 1.663135 GCAAGATCGTCCTTCTTCTGC 59.337 52.381 0.00 0.00 31.11 4.26
77 78 1.375013 CCCATGCACCTTGCTTTGC 60.375 57.895 0.00 0.00 45.31 3.68
84 85 3.769300 GTCCTTAAAATCCCATGCACCTT 59.231 43.478 0.00 0.00 0.00 3.50
127 128 1.896220 TCATCCACTGGCTTGTGTTC 58.104 50.000 9.54 0.00 36.30 3.18
129 130 2.165167 CAATCATCCACTGGCTTGTGT 58.835 47.619 9.54 0.00 36.30 3.72
130 131 1.475280 CCAATCATCCACTGGCTTGTG 59.525 52.381 4.63 4.63 37.66 3.33
132 133 1.747355 GTCCAATCATCCACTGGCTTG 59.253 52.381 0.00 0.00 0.00 4.01
133 134 1.355381 TGTCCAATCATCCACTGGCTT 59.645 47.619 0.00 0.00 0.00 4.35
134 135 0.994247 TGTCCAATCATCCACTGGCT 59.006 50.000 0.00 0.00 0.00 4.75
136 137 1.679680 GCATGTCCAATCATCCACTGG 59.320 52.381 0.00 0.00 0.00 4.00
137 138 1.679680 GGCATGTCCAATCATCCACTG 59.320 52.381 0.00 0.00 34.01 3.66
138 139 1.285667 TGGCATGTCCAATCATCCACT 59.714 47.619 6.42 0.00 43.21 4.00
168 169 9.678941 ACATTTAAGTTTTTCTAAAGCTAGCAC 57.321 29.630 18.83 2.50 0.00 4.40
190 191 8.409358 AAAGCTTTTACTGGAGATGTTACATT 57.591 30.769 5.69 0.00 0.00 2.71
195 196 7.285401 TGAAGAAAAGCTTTTACTGGAGATGTT 59.715 33.333 23.90 4.23 36.83 2.71
196 197 6.772716 TGAAGAAAAGCTTTTACTGGAGATGT 59.227 34.615 23.90 6.77 36.83 3.06
200 201 5.860716 GCATGAAGAAAAGCTTTTACTGGAG 59.139 40.000 23.90 13.76 36.83 3.86
202 203 5.632347 CAGCATGAAGAAAAGCTTTTACTGG 59.368 40.000 23.90 12.52 39.69 4.00
203 204 6.211515 ACAGCATGAAGAAAAGCTTTTACTG 58.788 36.000 23.90 20.59 39.69 2.74
216 217 2.093288 GGACATCTGGACAGCATGAAGA 60.093 50.000 14.37 0.00 39.69 2.87
218 219 1.065199 GGGACATCTGGACAGCATGAA 60.065 52.381 14.37 0.00 39.69 2.57
224 225 1.142748 GCGAGGGACATCTGGACAG 59.857 63.158 0.00 0.00 0.00 3.51
225 226 2.710902 CGCGAGGGACATCTGGACA 61.711 63.158 0.00 0.00 0.00 4.02
226 227 2.105128 CGCGAGGGACATCTGGAC 59.895 66.667 0.00 0.00 0.00 4.02
227 228 2.362503 ACGCGAGGGACATCTGGA 60.363 61.111 15.93 0.00 0.00 3.86
228 229 1.949847 AAGACGCGAGGGACATCTGG 61.950 60.000 15.93 0.00 0.00 3.86
229 230 0.803768 CAAGACGCGAGGGACATCTG 60.804 60.000 15.93 0.00 0.00 2.90
230 231 1.251527 ACAAGACGCGAGGGACATCT 61.252 55.000 15.93 0.00 0.00 2.90
231 232 0.389948 AACAAGACGCGAGGGACATC 60.390 55.000 15.93 0.00 0.00 3.06
232 233 0.892755 TAACAAGACGCGAGGGACAT 59.107 50.000 15.93 0.00 0.00 3.06
233 234 0.675083 TTAACAAGACGCGAGGGACA 59.325 50.000 15.93 0.00 0.00 4.02
234 235 1.725164 CTTTAACAAGACGCGAGGGAC 59.275 52.381 15.93 0.00 30.57 4.46
247 255 3.069872 TGTCTAGAACGGTGGCTTTAACA 59.930 43.478 0.00 0.00 0.00 2.41
257 265 1.811359 CCTCGTCTTGTCTAGAACGGT 59.189 52.381 13.24 0.00 33.81 4.83
276 284 4.578516 AGTTGCAAATTTTAAGGTTTGGCC 59.421 37.500 0.00 0.00 36.19 5.36
277 285 5.749596 AGTTGCAAATTTTAAGGTTTGGC 57.250 34.783 0.00 8.35 36.19 4.52
278 286 9.535878 TTACTAGTTGCAAATTTTAAGGTTTGG 57.464 29.630 4.05 2.81 36.19 3.28
342 428 9.317936 GGGCTTGAAATAATTTAAATTCCTCTG 57.682 33.333 16.56 9.83 0.00 3.35
344 430 9.836864 ATGGGCTTGAAATAATTTAAATTCCTC 57.163 29.630 16.56 11.82 0.00 3.71
362 448 6.491062 TCCATTCTCATGTAATAATGGGCTTG 59.509 38.462 20.53 5.71 0.00 4.01
366 452 6.881065 ACGATCCATTCTCATGTAATAATGGG 59.119 38.462 20.53 12.83 0.00 4.00
468 562 2.228822 CCAAAACGTGATCTTTCTGGGG 59.771 50.000 0.00 0.00 0.00 4.96
495 589 1.448985 GCGAACCAACCATAGCAGAA 58.551 50.000 0.00 0.00 0.00 3.02
510 604 4.446994 TTGCACAAATGATAATGGCGAA 57.553 36.364 0.00 0.00 0.00 4.70
540 634 3.948719 GACGGTGAAGTGGGGCCA 61.949 66.667 4.39 0.00 0.00 5.36
587 681 4.498682 GCCTCTATTGATTGGAACATGTGC 60.499 45.833 0.00 0.00 39.30 4.57
630 724 3.625897 TGCGGGTGAGGTGAGGTG 61.626 66.667 0.00 0.00 0.00 4.00
631 725 3.626924 GTGCGGGTGAGGTGAGGT 61.627 66.667 0.00 0.00 0.00 3.85
632 726 4.394712 GGTGCGGGTGAGGTGAGG 62.395 72.222 0.00 0.00 0.00 3.86
633 727 4.742201 CGGTGCGGGTGAGGTGAG 62.742 72.222 0.00 0.00 0.00 3.51
970 1081 4.235762 CGGGCGAATGGGATCGGT 62.236 66.667 0.00 0.00 42.93 4.69
1560 1672 5.291905 ACTAAAGCAGCCCTAATAACGAT 57.708 39.130 0.00 0.00 0.00 3.73
1611 1723 5.047092 AGCCAAAAAGAATAACATGGGACTG 60.047 40.000 0.00 0.00 0.00 3.51
1719 1831 1.068055 GCGTTAGAGAACACGAGGGAA 60.068 52.381 0.00 0.00 38.76 3.97
1772 1886 4.633175 TCTAGTCCTACAGCTCAGATACG 58.367 47.826 0.00 0.00 0.00 3.06
1809 1923 2.579860 AGCCTGACCCAGATTTCAGAAT 59.420 45.455 0.08 0.00 41.65 2.40
1831 1945 2.969990 CTCGGCATTGAGGGATCATAG 58.030 52.381 0.00 0.00 32.18 2.23
1950 2066 9.627123 TCAAATTACCAAGAATACTAATCCCTG 57.373 33.333 0.00 0.00 0.00 4.45
2293 2409 6.480763 TCCCATGACTACATCAAAAGCTTTA 58.519 36.000 13.10 0.00 41.93 1.85
2361 2615 9.691362 TTTCCAGAAAAGCAGTATTTGAATAAC 57.309 29.630 0.00 0.00 0.00 1.89
2415 2669 5.408880 TGTTCAGGGATCACGTTATTACA 57.591 39.130 0.00 0.00 0.00 2.41
2708 2979 1.009997 TCCCAAGGGAATGCAGGAAT 58.990 50.000 5.09 0.00 42.05 3.01
2799 3070 4.832248 TGTAACAGCTAATCCCACAAGAG 58.168 43.478 0.00 0.00 0.00 2.85
3334 3902 4.322953 CCAGCATAAAGGCCTGAAAAATGT 60.323 41.667 5.69 0.00 0.00 2.71
4081 4686 0.036388 CAGTATCCTGTGGGCAACGT 60.036 55.000 0.00 0.00 33.80 3.99
4082 4687 2.767536 CAGTATCCTGTGGGCAACG 58.232 57.895 0.00 0.00 33.80 4.10
4115 4722 2.371841 ACTTGATGTCCTTGCCACTACA 59.628 45.455 0.00 0.00 0.00 2.74
4317 4933 7.916552 TGCAACTTCAAACTTCTAAACTAGAC 58.083 34.615 0.00 0.00 33.84 2.59
4425 5041 5.183713 TCCCAAAATAAGTGACTCAGCATTG 59.816 40.000 0.00 0.00 0.00 2.82
4635 5310 5.409826 ACACAGAATTGCTTAGACTGCTTAC 59.590 40.000 0.00 0.00 32.67 2.34
4690 5366 6.685527 TGTGCCGCATGATTACTTTAATTA 57.314 33.333 0.00 0.00 0.00 1.40
4782 5458 4.964593 AGTACGGTTGTAAAGAACATGGT 58.035 39.130 0.00 0.00 38.10 3.55
4838 5514 9.119329 GCGTAACAATGAACAACATAATAACAA 57.881 29.630 0.00 0.00 38.38 2.83
4839 5515 7.751348 GGCGTAACAATGAACAACATAATAACA 59.249 33.333 0.00 0.00 38.38 2.41
4840 5516 7.751348 TGGCGTAACAATGAACAACATAATAAC 59.249 33.333 0.00 0.00 38.38 1.89
4841 5517 7.817641 TGGCGTAACAATGAACAACATAATAA 58.182 30.769 0.00 0.00 38.38 1.40
5091 6034 7.504924 TTATGTTTCAAGTGAACCAGTAAGG 57.495 36.000 0.00 0.00 45.67 2.69
5092 6035 9.965824 AATTTATGTTTCAAGTGAACCAGTAAG 57.034 29.630 0.00 0.00 30.09 2.34
5624 6569 5.557866 ACAATACCACAGACCTAGGAAAAC 58.442 41.667 17.98 3.90 0.00 2.43
5848 6815 8.652290 AGTGAAGTCTTAGAATTGTCCTAAGTT 58.348 33.333 0.00 2.08 42.13 2.66
5873 6840 8.507249 CAAGTACTCCCTCAGTTCAAAAATAAG 58.493 37.037 0.00 0.00 36.43 1.73
6388 7452 9.745880 CTACACGTTCCAACTAAATATATCACT 57.254 33.333 0.00 0.00 0.00 3.41
6389 7453 9.525409 ACTACACGTTCCAACTAAATATATCAC 57.475 33.333 0.00 0.00 0.00 3.06
7205 8271 3.312890 AGATTCGAGGGTGGAGAATGAT 58.687 45.455 0.00 0.00 35.06 2.45
7230 8296 1.059584 TCTGTGTGCCCCTTCCTTCA 61.060 55.000 0.00 0.00 0.00 3.02
7236 8302 2.078665 ACCACTCTGTGTGCCCCTT 61.079 57.895 4.40 0.00 44.92 3.95
7684 8750 7.372714 TGTTATAGTCGACAAACATGTACAGT 58.627 34.615 19.50 0.00 0.00 3.55
7685 8751 7.806149 TGTTATAGTCGACAAACATGTACAG 57.194 36.000 19.50 0.00 0.00 2.74
7686 8752 7.490079 GGATGTTATAGTCGACAAACATGTACA 59.510 37.037 31.35 19.15 41.37 2.90
7687 8753 7.490079 TGGATGTTATAGTCGACAAACATGTAC 59.510 37.037 31.35 24.08 41.37 2.90
7953 9167 9.934190 AATGAAAATAGAAACAAATTGCACAAC 57.066 25.926 0.00 0.00 0.00 3.32
8148 9372 0.546122 TGTCACTTGGTTGCCTCAGT 59.454 50.000 0.00 0.00 0.00 3.41
8163 9387 4.698201 TCCTTTGTTAGGTCACATGTCA 57.302 40.909 0.00 0.00 45.03 3.58
8196 9420 3.593442 TCCCATCTTGAAGGTGTTGTT 57.407 42.857 4.56 0.00 0.00 2.83
8215 9439 3.744942 ACATTAGCATGTGAGCGATGATC 59.255 43.478 10.64 0.00 42.46 2.92


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

AutoCloner maintained by Alex Coulton.