Multiple sequence alignment - TraesCS5D01G436400

Loading Multiple Alignment...

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 TraesCS5D01G436400 chr5D 100.000 2537 0 0 1 2537 490967597 490970133 0.000000e+00 4686.0
1 TraesCS5D01G436400 chr5D 91.971 411 29 3 1211 1620 491846737 491846330 7.870000e-160 573.0
2 TraesCS5D01G436400 chr5D 90.777 412 32 5 1211 1620 491796835 491796428 1.720000e-151 545.0
3 TraesCS5D01G436400 chr5D 90.260 154 15 0 1026 1179 492222502 492222349 4.280000e-48 202.0
4 TraesCS5D01G436400 chr5D 88.816 152 14 3 1026 1177 491796987 491796839 1.550000e-42 183.0
5 TraesCS5D01G436400 chr5D 88.235 153 16 2 1026 1177 491846892 491846741 5.580000e-42 182.0
6 TraesCS5D01G436400 chr5D 87.662 154 19 0 1026 1179 492068052 492067899 2.010000e-41 180.0
7 TraesCS5D01G436400 chr5D 78.151 119 20 5 701 818 492222853 492222740 1.260000e-08 71.3
8 TraesCS5D01G436400 chr5D 91.489 47 2 2 880 925 492068234 492068189 2.110000e-06 63.9
9 TraesCS5D01G436400 chr5A 88.723 2013 136 50 575 2537 613456825 613458796 0.000000e+00 2375.0
10 TraesCS5D01G436400 chr5A 89.451 455 38 5 1222 1674 614367120 614366674 1.320000e-157 566.0
11 TraesCS5D01G436400 chr5A 88.564 376 40 2 1211 1586 614408870 614408498 1.070000e-123 453.0
12 TraesCS5D01G436400 chr5A 91.532 248 21 0 1301 1548 613374355 613374602 2.420000e-90 342.0
13 TraesCS5D01G436400 chr5A 88.014 292 31 3 1 291 613456304 613456592 2.420000e-90 342.0
14 TraesCS5D01G436400 chr5A 83.333 306 38 8 34 338 2387925 2387632 1.160000e-68 270.0
15 TraesCS5D01G436400 chr5A 90.845 142 9 3 284 422 613456616 613456756 1.200000e-43 187.0
16 TraesCS5D01G436400 chr5A 88.312 154 18 0 1026 1179 614367283 614367130 4.310000e-43 185.0
17 TraesCS5D01G436400 chr5A 87.662 154 19 0 1026 1179 614409025 614408872 2.010000e-41 180.0
18 TraesCS5D01G436400 chr5A 92.982 57 3 1 464 520 613456775 613456830 5.820000e-12 82.4
19 TraesCS5D01G436400 chr5A 92.593 54 1 3 873 925 614409212 614409161 9.730000e-10 75.0
20 TraesCS5D01G436400 chr5B 90.287 1637 94 33 447 2042 605517823 605519435 0.000000e+00 2082.0
21 TraesCS5D01G436400 chr5B 90.826 436 34 4 1222 1653 606853511 606853078 1.690000e-161 579.0
22 TraesCS5D01G436400 chr5B 87.302 504 37 16 2042 2537 605519465 605519949 3.690000e-153 551.0
23 TraesCS5D01G436400 chr5B 90.426 376 33 2 1211 1586 606871000 606870628 2.270000e-135 492.0
24 TraesCS5D01G436400 chr5B 88.535 157 18 0 1023 1179 606871158 606871002 9.260000e-45 191.0
25 TraesCS5D01G436400 chr5B 85.542 83 9 3 2046 2127 68813636 68813716 1.620000e-12 84.2
26 TraesCS5D01G436400 chr5B 83.333 84 11 3 2045 2127 611700951 611700870 9.730000e-10 75.0
27 TraesCS5D01G436400 chr5B 90.741 54 0 3 874 923 606871342 606871290 1.630000e-07 67.6
28 TraesCS5D01G436400 chr2D 90.236 297 26 3 44 338 112888188 112887893 3.960000e-103 385.0
29 TraesCS5D01G436400 chr2D 75.691 181 35 7 159 337 102538924 102538751 5.820000e-12 82.4
30 TraesCS5D01G436400 chr2B 90.580 138 11 2 184 320 163368668 163368804 5.580000e-42 182.0
31 TraesCS5D01G436400 chr2B 86.452 155 21 0 34 188 163334579 163334733 1.210000e-38 171.0
32 TraesCS5D01G436400 chr7A 80.000 200 35 4 126 324 46638457 46638262 2.630000e-30 143.0
33 TraesCS5D01G436400 chr7A 86.667 75 7 3 2045 2118 457571240 457571312 2.090000e-11 80.5
34 TraesCS5D01G436400 chr7A 83.333 84 11 3 2045 2127 67666654 67666573 9.730000e-10 75.0
35 TraesCS5D01G436400 chr7A 89.286 56 5 1 284 338 708606439 708606494 4.530000e-08 69.4
36 TraesCS5D01G436400 chr4A 77.232 224 45 6 117 337 678136170 678136390 2.650000e-25 126.0
37 TraesCS5D01G436400 chr6B 84.524 84 10 3 2045 2127 698066634 698066715 2.090000e-11 80.5
38 TraesCS5D01G436400 chr3A 86.667 75 7 3 2045 2118 485901852 485901780 2.090000e-11 80.5
39 TraesCS5D01G436400 chr1A 84.524 84 10 3 2045 2127 301554415 301554334 2.090000e-11 80.5
40 TraesCS5D01G436400 chr7B 84.810 79 9 3 2041 2118 39915774 39915850 2.710000e-10 76.8


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 TraesCS5D01G436400 chr5D 490967597 490970133 2536 False 4686.0 4686 100.000000 1 2537 1 chr5D.!!$F1 2536
1 TraesCS5D01G436400 chr5D 491846330 491846892 562 True 377.5 573 90.103000 1026 1620 2 chr5D.!!$R2 594
2 TraesCS5D01G436400 chr5D 491796428 491796987 559 True 364.0 545 89.796500 1026 1620 2 chr5D.!!$R1 594
3 TraesCS5D01G436400 chr5A 613456304 613458796 2492 False 746.6 2375 90.141000 1 2537 4 chr5A.!!$F2 2536
4 TraesCS5D01G436400 chr5A 614366674 614367283 609 True 375.5 566 88.881500 1026 1674 2 chr5A.!!$R2 648
5 TraesCS5D01G436400 chr5A 614408498 614409212 714 True 236.0 453 89.606333 873 1586 3 chr5A.!!$R3 713
6 TraesCS5D01G436400 chr5B 605517823 605519949 2126 False 1316.5 2082 88.794500 447 2537 2 chr5B.!!$F2 2090
7 TraesCS5D01G436400 chr5B 606870628 606871342 714 True 250.2 492 89.900667 874 1586 3 chr5B.!!$R3 712

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
262 263 0.03213 GACAGTCACGTCTGGCTTGA 59.968 55.0 8.89 0.0 40.07 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2359 0.248289 GGCACCCGCTTACTAGACAA 59.752 55.0 0.0 0.0 38.6 3.18 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
40 41 5.288952 GTCGCACTAGGTAAAACAAGATCTC 59.711 44.000 0.00 0.00 0.00 2.75
42 43 4.567159 GCACTAGGTAAAACAAGATCTCCG 59.433 45.833 0.00 0.00 0.00 4.63
45 46 2.572104 AGGTAAAACAAGATCTCCGCCT 59.428 45.455 0.00 0.00 0.00 5.52
53 54 0.757188 AGATCTCCGCCTCCATCGTT 60.757 55.000 0.00 0.00 0.00 3.85
54 55 0.105039 GATCTCCGCCTCCATCGTTT 59.895 55.000 0.00 0.00 0.00 3.60
67 68 2.415893 CCATCGTTTGGTCATTGCTTCC 60.416 50.000 0.00 0.00 40.99 3.46
75 76 0.924090 GTCATTGCTTCCGACGCTAG 59.076 55.000 0.00 0.00 0.00 3.42
79 80 0.388134 TTGCTTCCGACGCTAGACAC 60.388 55.000 0.00 0.00 0.00 3.67
84 85 1.511464 CCGACGCTAGACACGTGAC 60.511 63.158 25.01 17.23 45.24 3.67
87 88 0.454620 GACGCTAGACACGTGACTGG 60.455 60.000 27.01 24.92 45.24 4.00
94 95 0.389948 GACACGTGACTGGGGACATC 60.390 60.000 25.01 0.58 41.51 3.06
107 108 0.698818 GGACATCCAGAAAGGTGGGT 59.301 55.000 0.00 0.00 38.26 4.51
117 118 2.243736 AGAAAGGTGGGTGAGGAAACAA 59.756 45.455 0.00 0.00 0.00 2.83
122 123 2.593026 GTGGGTGAGGAAACAATGGAA 58.407 47.619 0.00 0.00 0.00 3.53
148 149 7.169982 ACAATTATTAGCGAGATCAAGCTACAC 59.830 37.037 17.97 0.00 44.54 2.90
150 151 0.526524 AGCGAGATCAAGCTACACGC 60.527 55.000 12.40 13.39 42.60 5.34
163 164 2.096417 GCTACACGCGTTGTCTTTTGAT 60.096 45.455 10.22 0.00 39.91 2.57
189 190 6.797995 TGTATTTTTAATTTCGAAGGTCGTGC 59.202 34.615 0.00 0.00 41.35 5.34
210 211 4.277921 TGCTGTCAATGTTGAAGCACATAA 59.722 37.500 19.25 6.03 41.62 1.90
217 218 7.756722 GTCAATGTTGAAGCACATAATTTAGCT 59.243 33.333 0.00 0.00 39.21 3.32
240 241 4.830826 AGTTTTCATTTTCGTCAGGTCC 57.169 40.909 0.00 0.00 0.00 4.46
242 243 2.536761 TTCATTTTCGTCAGGTCCGT 57.463 45.000 0.00 0.00 0.00 4.69
246 247 0.460722 TTTTCGTCAGGTCCGTGACA 59.539 50.000 17.31 5.08 46.19 3.58
251 252 0.318784 GTCAGGTCCGTGACAGTCAC 60.319 60.000 22.09 22.09 45.34 3.67
262 263 0.032130 GACAGTCACGTCTGGCTTGA 59.968 55.000 8.89 0.00 40.07 3.02
282 284 3.573538 TGACCAATCCATGACCAAAACTG 59.426 43.478 0.00 0.00 0.00 3.16
291 322 4.526262 CCATGACCAAAACTGTATCCCAAA 59.474 41.667 0.00 0.00 0.00 3.28
296 327 6.015519 TGACCAAAACTGTATCCCAAATTCTG 60.016 38.462 0.00 0.00 0.00 3.02
321 352 5.988561 TGGTGTTTGATGAATAAAACTTGGC 59.011 36.000 5.14 0.00 37.22 4.52
326 357 8.637986 TGTTTGATGAATAAAACTTGGCTTACT 58.362 29.630 5.14 0.00 37.22 2.24
329 360 6.377146 TGATGAATAAAACTTGGCTTACTCCC 59.623 38.462 0.00 0.00 0.00 4.30
330 361 5.014202 TGAATAAAACTTGGCTTACTCCCC 58.986 41.667 0.00 0.00 0.00 4.81
369 400 3.284323 TCGTCTTTCTTCTTCCACGAG 57.716 47.619 0.00 0.00 32.75 4.18
371 402 3.317149 TCGTCTTTCTTCTTCCACGAGAA 59.683 43.478 0.00 0.00 32.75 2.87
398 429 2.614829 AACGATAGCCCTAATTGCGT 57.385 45.000 0.00 0.00 42.67 5.24
399 430 2.614829 ACGATAGCCCTAATTGCGTT 57.385 45.000 0.00 0.00 42.67 4.84
400 431 2.210116 ACGATAGCCCTAATTGCGTTG 58.790 47.619 0.00 0.00 42.67 4.10
418 451 4.735132 GCGCACGTGTCTGCCCTA 62.735 66.667 18.38 0.00 33.18 3.53
420 453 1.447838 CGCACGTGTCTGCCCTAAT 60.448 57.895 18.38 0.00 33.18 1.73
423 456 2.352388 GCACGTGTCTGCCCTAATTTA 58.648 47.619 18.38 0.00 0.00 1.40
425 458 3.377172 GCACGTGTCTGCCCTAATTTAAT 59.623 43.478 18.38 0.00 0.00 1.40
426 459 4.142469 GCACGTGTCTGCCCTAATTTAATT 60.142 41.667 18.38 0.00 0.00 1.40
427 460 5.621329 GCACGTGTCTGCCCTAATTTAATTT 60.621 40.000 18.38 0.00 0.00 1.82
428 461 6.403855 GCACGTGTCTGCCCTAATTTAATTTA 60.404 38.462 18.38 0.00 0.00 1.40
429 462 7.531716 CACGTGTCTGCCCTAATTTAATTTAA 58.468 34.615 7.58 0.00 0.00 1.52
430 463 7.696453 CACGTGTCTGCCCTAATTTAATTTAAG 59.304 37.037 7.58 0.00 0.00 1.85
431 464 7.608761 ACGTGTCTGCCCTAATTTAATTTAAGA 59.391 33.333 0.00 0.00 0.00 2.10
432 465 8.455682 CGTGTCTGCCCTAATTTAATTTAAGAA 58.544 33.333 0.00 0.00 0.00 2.52
433 466 9.788960 GTGTCTGCCCTAATTTAATTTAAGAAG 57.211 33.333 0.00 0.00 0.00 2.85
434 467 8.966868 TGTCTGCCCTAATTTAATTTAAGAAGG 58.033 33.333 0.00 0.00 0.00 3.46
435 468 9.185680 GTCTGCCCTAATTTAATTTAAGAAGGA 57.814 33.333 5.32 0.00 0.00 3.36
436 469 9.762381 TCTGCCCTAATTTAATTTAAGAAGGAA 57.238 29.630 5.32 0.00 0.00 3.36
438 471 9.762381 TGCCCTAATTTAATTTAAGAAGGAAGA 57.238 29.630 5.32 0.00 0.00 2.87
452 485 2.556766 AGGAAGAAGGAAGGAGGAAGG 58.443 52.381 0.00 0.00 0.00 3.46
459 492 2.556766 AGGAAGGAGGAAGGAAGGAAG 58.443 52.381 0.00 0.00 0.00 3.46
460 493 1.562008 GGAAGGAGGAAGGAAGGAAGG 59.438 57.143 0.00 0.00 0.00 3.46
461 494 2.552367 GAAGGAGGAAGGAAGGAAGGA 58.448 52.381 0.00 0.00 0.00 3.36
462 495 1.959710 AGGAGGAAGGAAGGAAGGAC 58.040 55.000 0.00 0.00 0.00 3.85
469 502 0.719623 AGGAAGGAAGGACTAGCCCT 59.280 55.000 0.00 0.00 38.42 5.19
471 504 2.090999 AGGAAGGAAGGACTAGCCCTAG 60.091 54.545 0.00 0.88 34.95 3.02
501 534 2.441750 TGTGTCTGCCCTAGTTTCCTTT 59.558 45.455 0.00 0.00 0.00 3.11
503 536 3.502595 GTGTCTGCCCTAGTTTCCTTTTC 59.497 47.826 0.00 0.00 0.00 2.29
521 554 3.885724 TTCATAGGCGACAACTGATCA 57.114 42.857 0.00 0.00 0.00 2.92
522 555 3.165058 TCATAGGCGACAACTGATCAC 57.835 47.619 0.00 0.00 0.00 3.06
523 556 1.854743 CATAGGCGACAACTGATCACG 59.145 52.381 0.00 0.00 0.00 4.35
524 557 0.885879 TAGGCGACAACTGATCACGT 59.114 50.000 0.00 0.00 0.00 4.49
525 558 0.885879 AGGCGACAACTGATCACGTA 59.114 50.000 0.00 0.00 0.00 3.57
526 559 1.135373 AGGCGACAACTGATCACGTAG 60.135 52.381 0.00 0.00 0.00 3.51
528 561 2.159476 GGCGACAACTGATCACGTAGTA 60.159 50.000 0.00 0.00 41.61 1.82
541 574 7.019418 TGATCACGTAGTATATCATGTAACGC 58.981 38.462 0.00 0.00 41.61 4.84
557 590 2.981400 ACGCAAATTTACGGGTTGAG 57.019 45.000 14.93 0.00 0.00 3.02
558 591 1.068816 ACGCAAATTTACGGGTTGAGC 60.069 47.619 14.93 0.00 0.00 4.26
594 628 6.157211 ACGTACTCATGAAACTTCCTTGTAG 58.843 40.000 0.00 0.00 0.00 2.74
595 629 6.157211 CGTACTCATGAAACTTCCTTGTAGT 58.843 40.000 0.00 0.00 0.00 2.73
596 630 7.040201 ACGTACTCATGAAACTTCCTTGTAGTA 60.040 37.037 0.00 0.00 0.00 1.82
598 632 9.088512 GTACTCATGAAACTTCCTTGTAGTATG 57.911 37.037 0.00 0.00 0.00 2.39
599 633 7.680730 ACTCATGAAACTTCCTTGTAGTATGT 58.319 34.615 0.00 0.00 0.00 2.29
601 635 8.918202 TCATGAAACTTCCTTGTAGTATGTTT 57.082 30.769 0.00 0.00 0.00 2.83
602 636 8.783093 TCATGAAACTTCCTTGTAGTATGTTTG 58.217 33.333 0.00 0.00 0.00 2.93
603 637 8.567948 CATGAAACTTCCTTGTAGTATGTTTGT 58.432 33.333 0.00 0.00 0.00 2.83
604 638 9.787435 ATGAAACTTCCTTGTAGTATGTTTGTA 57.213 29.630 0.00 0.00 0.00 2.41
752 801 0.935196 GTTGAACTGACGCTCGGTTT 59.065 50.000 11.72 0.11 45.29 3.27
761 810 3.504863 TGACGCTCGGTTTAGTGTTATC 58.495 45.455 0.00 0.00 40.22 1.75
825 874 1.812922 GCACAGATGCGAGTCCTGG 60.813 63.158 0.00 0.00 43.33 4.45
839 888 1.043116 TCCTGGCAGGACTATGACGG 61.043 60.000 32.01 3.73 40.06 4.79
842 891 2.279517 GCAGGACTATGACGGGCG 60.280 66.667 0.00 0.00 0.00 6.13
1251 1355 1.201429 AGAAGGCCAGGATGACCGTT 61.201 55.000 5.01 0.00 39.69 4.44
1265 1369 3.751246 CGTTGCCGTCCCGTCCTA 61.751 66.667 0.00 0.00 0.00 2.94
1269 1373 1.952102 TTGCCGTCCCGTCCTATGAC 61.952 60.000 0.00 0.00 38.18 3.06
1447 1551 0.099082 CTACTCGGAGAAGCACGACC 59.901 60.000 12.86 0.00 34.09 4.79
1640 1751 7.907214 TCTTCTTTGTATTTGCTAGGTCTTC 57.093 36.000 0.00 0.00 0.00 2.87
1739 1851 7.834881 TCAGAGATATAGGAATTTGTACCGT 57.165 36.000 0.00 0.00 0.00 4.83
1747 1859 5.733620 AGGAATTTGTACCGTGAGTCTTA 57.266 39.130 0.00 0.00 0.00 2.10
1755 1867 8.659925 TTTGTACCGTGAGTCTTAAAACATTA 57.340 30.769 0.00 0.00 0.00 1.90
1761 1873 7.660208 ACCGTGAGTCTTAAAACATTAGTTCAT 59.340 33.333 0.00 0.00 36.84 2.57
1763 1875 8.708742 CGTGAGTCTTAAAACATTAGTTCATCA 58.291 33.333 0.00 0.00 36.84 3.07
1787 1901 8.898761 TCACGATTTATACATAAAGCAAACCAT 58.101 29.630 9.80 0.00 38.24 3.55
1797 1911 4.685169 AAAGCAAACCATCACGTCTATG 57.315 40.909 0.00 0.00 0.00 2.23
1821 1935 7.192913 TGCAACAAGTTTCAGTGTAACATAAG 58.807 34.615 14.18 4.38 41.43 1.73
1824 1938 9.438291 CAACAAGTTTCAGTGTAACATAAGAAG 57.562 33.333 14.18 0.31 41.43 2.85
1895 2009 9.321562 GGTAATACATTTATTTTCAGACGGAGA 57.678 33.333 0.00 0.00 0.00 3.71
1919 2033 9.382275 AGAAAATATCACAAATATGCCCAAAAC 57.618 29.630 0.00 0.00 0.00 2.43
2078 2225 4.901197 TGTCCTCTACAAATAAGCACCA 57.099 40.909 0.00 0.00 34.29 4.17
2189 2359 1.336887 CCAAGTCACTCGATGTTCCGT 60.337 52.381 0.00 0.00 0.00 4.69
2232 2403 2.332654 ACATCGCAAAAGACCCGCC 61.333 57.895 0.00 0.00 0.00 6.13
2261 2433 3.978217 CCATTTGTTACGCGTTGTTCATT 59.022 39.130 20.78 0.00 0.00 2.57
2290 2462 1.291184 CCATCGCTGCGAACACTCAA 61.291 55.000 29.48 3.20 39.99 3.02
2348 2520 3.101437 TGGGCTTATACGAACTCTCCAA 58.899 45.455 0.00 0.00 0.00 3.53
2428 2600 0.318762 AGCGGACCTGAGAAGACAAC 59.681 55.000 0.00 0.00 0.00 3.32
2429 2601 0.033504 GCGGACCTGAGAAGACAACA 59.966 55.000 0.00 0.00 0.00 3.33
2472 2644 2.289819 ACACACGGGAAAATACCATCGT 60.290 45.455 0.00 0.00 0.00 3.73
2521 2693 2.525629 TGAGGGGAAGTGACCGCA 60.526 61.111 0.00 0.00 43.85 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.064296 CTAGTGCGACCTACAGCCG 59.936 63.158 0.00 0.00 0.00 5.52
53 54 1.573829 GCGTCGGAAGCAATGACCAA 61.574 55.000 11.07 0.00 34.19 3.67
54 55 2.032634 GCGTCGGAAGCAATGACCA 61.033 57.895 11.07 0.00 34.19 4.02
67 68 0.789753 CAGTCACGTGTCTAGCGTCG 60.790 60.000 16.51 0.00 40.90 5.12
75 76 0.389948 GATGTCCCCAGTCACGTGTC 60.390 60.000 16.51 10.42 0.00 3.67
79 80 1.219124 CTGGATGTCCCCAGTCACG 59.781 63.158 0.00 0.00 46.62 4.35
87 88 0.034089 CCCACCTTTCTGGATGTCCC 60.034 60.000 0.00 0.00 39.71 4.46
94 95 0.771127 TTCCTCACCCACCTTTCTGG 59.229 55.000 0.00 0.00 42.93 3.86
107 108 8.250332 GCTAATAATTGTTCCATTGTTTCCTCA 58.750 33.333 0.00 0.00 0.00 3.86
117 118 7.308229 GCTTGATCTCGCTAATAATTGTTCCAT 60.308 37.037 0.00 0.00 0.00 3.41
122 123 7.169982 GTGTAGCTTGATCTCGCTAATAATTGT 59.830 37.037 15.07 0.00 40.12 2.71
138 139 0.031585 AGACAACGCGTGTAGCTTGA 59.968 50.000 14.98 0.00 41.96 3.02
148 149 6.432802 AAAATACAATCAAAAGACAACGCG 57.567 33.333 3.53 3.53 0.00 6.01
163 164 7.324135 GCACGACCTTCGAAATTAAAAATACAA 59.676 33.333 0.00 0.00 43.74 2.41
178 179 0.439985 CATTGACAGCACGACCTTCG 59.560 55.000 0.00 0.00 46.93 3.79
185 186 1.002576 TGCTTCAACATTGACAGCACG 60.003 47.619 18.94 0.00 41.62 5.34
189 190 7.878477 AAATTATGTGCTTCAACATTGACAG 57.122 32.000 0.00 0.00 41.09 3.51
210 211 9.612620 CTGACGAAAATGAAAACTTAGCTAAAT 57.387 29.630 7.74 0.00 0.00 1.40
217 218 5.049954 CGGACCTGACGAAAATGAAAACTTA 60.050 40.000 0.00 0.00 0.00 2.24
224 225 1.341852 TCACGGACCTGACGAAAATGA 59.658 47.619 0.00 0.00 34.93 2.57
227 228 0.460722 TGTCACGGACCTGACGAAAA 59.539 50.000 15.14 0.97 43.14 2.29
234 235 4.655527 GTGACTGTCACGGACCTG 57.344 61.111 23.54 0.00 37.67 4.00
242 243 0.249447 CAAGCCAGACGTGACTGTCA 60.249 55.000 6.36 6.36 41.41 3.58
262 263 3.575805 ACAGTTTTGGTCATGGATTGGT 58.424 40.909 0.00 0.00 0.00 3.67
282 284 5.242838 TCAAACACCACAGAATTTGGGATAC 59.757 40.000 0.00 0.00 38.59 2.24
291 322 8.641541 AGTTTTATTCATCAAACACCACAGAAT 58.358 29.630 0.00 0.00 35.66 2.40
296 327 6.073819 GCCAAGTTTTATTCATCAAACACCAC 60.074 38.462 0.00 0.00 35.66 4.16
369 400 6.980051 TTAGGGCTATCGTTTTCTTTCTTC 57.020 37.500 0.00 0.00 0.00 2.87
371 402 6.183360 GCAATTAGGGCTATCGTTTTCTTTCT 60.183 38.462 0.00 0.00 0.00 2.52
404 437 5.560966 AATTAAATTAGGGCAGACACGTG 57.439 39.130 15.48 15.48 0.00 4.49
423 456 7.018650 TCCTCCTTCCTTCTTCCTTCTTAAATT 59.981 37.037 0.00 0.00 0.00 1.82
425 458 5.850028 TCCTCCTTCCTTCTTCCTTCTTAAA 59.150 40.000 0.00 0.00 0.00 1.52
426 459 5.412384 TCCTCCTTCCTTCTTCCTTCTTAA 58.588 41.667 0.00 0.00 0.00 1.85
427 460 5.024803 TCCTCCTTCCTTCTTCCTTCTTA 57.975 43.478 0.00 0.00 0.00 2.10
428 461 3.875571 TCCTCCTTCCTTCTTCCTTCTT 58.124 45.455 0.00 0.00 0.00 2.52
429 462 3.569135 TCCTCCTTCCTTCTTCCTTCT 57.431 47.619 0.00 0.00 0.00 2.85
430 463 3.054728 CCTTCCTCCTTCCTTCTTCCTTC 60.055 52.174 0.00 0.00 0.00 3.46
431 464 2.916269 CCTTCCTCCTTCCTTCTTCCTT 59.084 50.000 0.00 0.00 0.00 3.36
432 465 2.114506 TCCTTCCTCCTTCCTTCTTCCT 59.885 50.000 0.00 0.00 0.00 3.36
433 466 2.552367 TCCTTCCTCCTTCCTTCTTCC 58.448 52.381 0.00 0.00 0.00 3.46
434 467 3.054728 CCTTCCTTCCTCCTTCCTTCTTC 60.055 52.174 0.00 0.00 0.00 2.87
435 468 2.916269 CCTTCCTTCCTCCTTCCTTCTT 59.084 50.000 0.00 0.00 0.00 2.52
436 469 2.114506 TCCTTCCTTCCTCCTTCCTTCT 59.885 50.000 0.00 0.00 0.00 2.85
437 470 2.552367 TCCTTCCTTCCTCCTTCCTTC 58.448 52.381 0.00 0.00 0.00 3.46
438 471 2.743131 TCCTTCCTTCCTCCTTCCTT 57.257 50.000 0.00 0.00 0.00 3.36
439 472 2.556766 CTTCCTTCCTTCCTCCTTCCT 58.443 52.381 0.00 0.00 0.00 3.36
440 473 1.562008 CCTTCCTTCCTTCCTCCTTCC 59.438 57.143 0.00 0.00 0.00 3.46
441 474 2.237643 GTCCTTCCTTCCTTCCTCCTTC 59.762 54.545 0.00 0.00 0.00 3.46
442 475 2.157926 AGTCCTTCCTTCCTTCCTCCTT 60.158 50.000 0.00 0.00 0.00 3.36
443 476 1.439143 AGTCCTTCCTTCCTTCCTCCT 59.561 52.381 0.00 0.00 0.00 3.69
444 477 1.959710 AGTCCTTCCTTCCTTCCTCC 58.040 55.000 0.00 0.00 0.00 4.30
445 478 2.432874 GCTAGTCCTTCCTTCCTTCCTC 59.567 54.545 0.00 0.00 0.00 3.71
452 485 1.689813 GCTAGGGCTAGTCCTTCCTTC 59.310 57.143 23.65 2.81 38.30 3.46
469 502 0.167470 GCAGACACACGTACGAGCTA 59.833 55.000 24.41 0.00 0.00 3.32
471 504 2.087009 GGCAGACACACGTACGAGC 61.087 63.158 24.41 12.67 0.00 5.03
501 534 3.521560 GTGATCAGTTGTCGCCTATGAA 58.478 45.455 0.00 0.00 0.00 2.57
503 536 1.854743 CGTGATCAGTTGTCGCCTATG 59.145 52.381 0.00 0.00 0.00 2.23
521 554 8.583810 AATTTGCGTTACATGATATACTACGT 57.416 30.769 0.00 0.00 0.00 3.57
525 558 8.492748 CCGTAAATTTGCGTTACATGATATACT 58.507 33.333 23.91 0.00 34.39 2.12
526 559 7.742963 CCCGTAAATTTGCGTTACATGATATAC 59.257 37.037 23.91 0.00 34.39 1.47
527 560 7.441760 ACCCGTAAATTTGCGTTACATGATATA 59.558 33.333 23.91 0.00 34.39 0.86
528 561 6.261381 ACCCGTAAATTTGCGTTACATGATAT 59.739 34.615 23.91 0.00 34.39 1.63
541 574 5.949735 ACAATAGCTCAACCCGTAAATTTG 58.050 37.500 0.00 0.00 0.00 2.32
550 583 4.110482 CGTACTGTACAATAGCTCAACCC 58.890 47.826 17.35 0.00 0.00 4.11
594 628 7.226128 GTGCCCTAAGGATTACTACAAACATAC 59.774 40.741 0.00 0.00 33.47 2.39
595 629 7.277396 GTGCCCTAAGGATTACTACAAACATA 58.723 38.462 0.00 0.00 33.47 2.29
596 630 6.120220 GTGCCCTAAGGATTACTACAAACAT 58.880 40.000 0.00 0.00 33.47 2.71
598 632 4.880120 GGTGCCCTAAGGATTACTACAAAC 59.120 45.833 0.00 0.00 33.47 2.93
599 633 4.786454 AGGTGCCCTAAGGATTACTACAAA 59.214 41.667 0.00 0.00 33.47 2.83
601 635 3.965347 GAGGTGCCCTAAGGATTACTACA 59.035 47.826 0.00 0.00 31.76 2.74
602 636 3.005578 CGAGGTGCCCTAAGGATTACTAC 59.994 52.174 0.00 0.00 31.76 2.73
603 637 3.117398 TCGAGGTGCCCTAAGGATTACTA 60.117 47.826 0.00 0.00 31.76 1.82
604 638 2.040178 CGAGGTGCCCTAAGGATTACT 58.960 52.381 0.00 0.00 31.76 2.24
627 663 0.247695 GCGCTCTTATGCCGTTTGAC 60.248 55.000 0.00 0.00 0.00 3.18
674 719 6.093404 CGTTCTACGTCGGGATAGTAGTATA 58.907 44.000 0.00 0.00 38.99 1.47
676 721 4.299155 CGTTCTACGTCGGGATAGTAGTA 58.701 47.826 0.00 3.43 38.99 1.82
677 722 3.126831 CGTTCTACGTCGGGATAGTAGT 58.873 50.000 0.00 0.00 38.99 2.73
678 723 3.784883 CGTTCTACGTCGGGATAGTAG 57.215 52.381 0.00 7.52 39.20 2.57
718 767 1.950630 CAACGCAACAAGGCAAGGC 60.951 57.895 0.00 0.00 0.00 4.35
719 768 0.102120 TTCAACGCAACAAGGCAAGG 59.898 50.000 0.00 0.00 0.00 3.61
811 860 2.729479 CCTGCCAGGACTCGCATCT 61.729 63.158 4.15 0.00 37.67 2.90
825 874 2.279517 CGCCCGTCATAGTCCTGC 60.280 66.667 0.00 0.00 0.00 4.85
1190 1294 3.207669 CAGCAGGGCCGATGAAGC 61.208 66.667 10.61 1.52 0.00 3.86
1447 1551 1.278238 GCCTTGTAGTCGAATCCACG 58.722 55.000 0.00 0.00 0.00 4.94
1640 1751 8.123445 AGCCTAAACTAATATTTACACGTTCG 57.877 34.615 0.00 0.00 0.00 3.95
1715 1827 7.504574 TCACGGTACAAATTCCTATATCTCTGA 59.495 37.037 0.00 0.00 0.00 3.27
1716 1828 7.658261 TCACGGTACAAATTCCTATATCTCTG 58.342 38.462 0.00 0.00 0.00 3.35
1717 1829 7.506261 ACTCACGGTACAAATTCCTATATCTCT 59.494 37.037 0.00 0.00 0.00 3.10
1739 1851 8.708742 CGTGATGAACTAATGTTTTAAGACTCA 58.291 33.333 0.00 0.00 36.39 3.41
1755 1867 9.325198 TGCTTTATGTATAAATCGTGATGAACT 57.675 29.630 0.00 0.00 32.36 3.01
1761 1873 8.270080 TGGTTTGCTTTATGTATAAATCGTGA 57.730 30.769 0.00 0.00 32.36 4.35
1763 1875 8.898761 TGATGGTTTGCTTTATGTATAAATCGT 58.101 29.630 0.00 0.00 32.36 3.73
1771 1885 5.242434 AGACGTGATGGTTTGCTTTATGTA 58.758 37.500 0.00 0.00 0.00 2.29
1773 1887 4.685169 AGACGTGATGGTTTGCTTTATG 57.315 40.909 0.00 0.00 0.00 1.90
1787 1901 4.123506 TGAAACTTGTTGCATAGACGTGA 58.876 39.130 0.00 0.00 0.00 4.35
1797 1911 7.414436 TCTTATGTTACACTGAAACTTGTTGC 58.586 34.615 0.00 0.00 0.00 4.17
1886 2000 7.800380 GCATATTTGTGATATTTTCTCCGTCTG 59.200 37.037 0.00 0.00 0.00 3.51
1895 2009 8.037758 TCGTTTTGGGCATATTTGTGATATTTT 58.962 29.630 0.00 0.00 0.00 1.82
2036 2151 7.593644 AGGACAAACGCTTAATTAAACATGTTC 59.406 33.333 12.39 0.00 0.00 3.18
2037 2152 7.430441 AGGACAAACGCTTAATTAAACATGTT 58.570 30.769 4.92 4.92 0.00 2.71
2039 2154 7.305474 AGAGGACAAACGCTTAATTAAACATG 58.695 34.615 0.00 0.00 0.00 3.21
2043 2190 7.966246 TGTAGAGGACAAACGCTTAATTAAA 57.034 32.000 0.00 0.00 34.15 1.52
2129 2276 8.836413 GCGCATATCCTTTTAGGCATTATATTA 58.164 33.333 0.30 0.00 34.61 0.98
2130 2277 7.339212 TGCGCATATCCTTTTAGGCATTATATT 59.661 33.333 5.66 0.00 34.61 1.28
2131 2278 6.828273 TGCGCATATCCTTTTAGGCATTATAT 59.172 34.615 5.66 0.00 34.61 0.86
2189 2359 0.248289 GGCACCCGCTTACTAGACAA 59.752 55.000 0.00 0.00 38.60 3.18
2228 2399 0.607620 AACAAATGGTGATTGGGCGG 59.392 50.000 0.00 0.00 32.02 6.13
2232 2403 2.095466 ACGCGTAACAAATGGTGATTGG 60.095 45.455 11.67 0.00 32.02 3.16
2261 2433 1.897423 CAGCGATGGTCTACACCCA 59.103 57.895 0.00 0.00 42.99 4.51
2348 2520 1.006281 TGAATGGCAGGCCTCAAATCT 59.994 47.619 0.00 0.00 36.94 2.40
2376 2548 1.340991 TGGAGCTTTGTCCATAAGGCC 60.341 52.381 0.00 0.00 41.99 5.19
2428 2600 0.539051 GTCTGAGTCCTGGACCCATG 59.461 60.000 22.81 11.43 32.18 3.66
2429 2601 0.117140 TGTCTGAGTCCTGGACCCAT 59.883 55.000 22.81 4.91 32.18 4.00
2491 2663 4.816109 CCTCAGGGATGGAGGTCA 57.184 61.111 0.00 0.00 45.59 4.02


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

AutoCloner maintained by Alex Coulton.