Multiple sequence alignment - TraesCS7D01G341100

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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 TraesCS7D01G341100 chr7D 100.000 4969 0 0 900 5868 436951196 436956164 0.000000e+00 9177.0
1 TraesCS7D01G341100 chr7D 100.000 533 0 0 1 533 436950297 436950829 0.000000e+00 985.0
2 TraesCS7D01G341100 chr7B 97.268 3331 89 1 941 4269 453446620 453449950 0.000000e+00 5646.0
3 TraesCS7D01G341100 chr7B 94.254 1514 43 11 4393 5868 453449949 453451456 0.000000e+00 2274.0
4 TraesCS7D01G341100 chr7B 96.145 415 15 1 1 415 453444551 453444964 0.000000e+00 676.0
5 TraesCS7D01G341100 chr7B 89.744 156 12 4 4263 4416 126549094 126549247 4.640000e-46 196.0
6 TraesCS7D01G341100 chr7A 96.836 3192 91 6 1077 4267 485608319 485605137 0.000000e+00 5326.0
7 TraesCS7D01G341100 chr7A 92.449 1311 70 7 4393 5689 485605138 485603843 0.000000e+00 1845.0
8 TraesCS7D01G341100 chr7A 97.674 215 4 1 1 214 485610227 485610013 9.290000e-98 368.0
9 TraesCS7D01G341100 chr7A 97.861 187 4 0 293 479 485609997 485609811 2.040000e-84 324.0
10 TraesCS7D01G341100 chr7A 96.471 170 6 0 915 1084 485609440 485609271 1.250000e-71 281.0
11 TraesCS7D01G341100 chr5D 94.928 138 6 1 4266 4403 368983477 368983613 1.280000e-51 215.0
12 TraesCS7D01G341100 chr5D 72.236 407 90 13 3571 3973 553064129 553064516 2.890000e-18 104.0
13 TraesCS7D01G341100 chr5D 71.960 403 90 14 3571 3969 553472162 553472545 4.840000e-16 97.1
14 TraesCS7D01G341100 chr5D 71.253 407 94 15 3571 3973 553458936 553458549 1.360000e-11 82.4
15 TraesCS7D01G341100 chr5B 94.697 132 7 0 4263 4394 96879074 96878943 7.710000e-49 206.0
16 TraesCS7D01G341100 chr5B 89.032 155 15 2 4266 4419 109317135 109316982 2.160000e-44 191.0
17 TraesCS7D01G341100 chr5B 71.782 404 89 13 3571 3969 697344816 697344433 2.250000e-14 91.6
18 TraesCS7D01G341100 chr4A 94.697 132 7 0 4267 4398 27685673 27685542 7.710000e-49 206.0
19 TraesCS7D01G341100 chr3B 91.781 146 9 3 4263 4406 760588979 760589123 3.590000e-47 200.0
20 TraesCS7D01G341100 chr2A 92.254 142 10 1 4268 4409 321155659 321155519 3.590000e-47 200.0
21 TraesCS7D01G341100 chr1B 91.608 143 10 2 4252 4394 623950944 623951084 4.640000e-46 196.0
22 TraesCS7D01G341100 chr1D 87.952 166 16 4 4233 4394 368493646 368493811 6.000000e-45 193.0


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 TraesCS7D01G341100 chr7D 436950297 436956164 5867 False 5081.000000 9177 100.0000 1 5868 2 chr7D.!!$F1 5867
1 TraesCS7D01G341100 chr7B 453444551 453451456 6905 False 2865.333333 5646 95.8890 1 5868 3 chr7B.!!$F2 5867
2 TraesCS7D01G341100 chr7A 485603843 485610227 6384 True 1628.800000 5326 96.2582 1 5689 5 chr7A.!!$R1 5688

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
529 531 0.901124 AACTTGCCAACTTGTTGCCA 59.099 45.000 7.89 0.58 0.00 4.92 F
530 532 1.122227 ACTTGCCAACTTGTTGCCAT 58.878 45.000 7.89 0.00 0.00 4.40 F
2106 4197 0.890996 CAGGCACAGTTCCTCCAACC 60.891 60.000 0.00 0.00 35.28 3.77 F
2196 4287 1.638070 TCCATTGGCCATACACTTCCA 59.362 47.619 6.09 0.00 0.00 3.53 F
3409 5500 1.873698 TGTACACAGAAAGCGGGAAC 58.126 50.000 0.00 0.00 0.00 3.62 F
4594 6687 1.337118 TTGTGGAACTGGCATTTCCC 58.663 50.000 27.64 20.37 41.80 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 3734 0.313987 GGGGCCTGAAAGTTTGTTCG 59.686 55.000 0.84 0.0 0.0 3.95 R
2176 4267 1.638070 TGGAAGTGTATGGCCAATGGA 59.362 47.619 10.96 0.0 0.0 3.41 R
3831 5922 0.617413 AGGCAGCAGCTATGTCTGTT 59.383 50.000 4.52 0.0 41.7 3.16 R
3961 6052 7.122650 GGATGGATGGTCATAAAGAAACTTTGA 59.877 37.037 6.95 0.0 0.0 2.69 R
4627 6720 1.024271 CGCCCTGGTATTGTGGAATG 58.976 55.000 0.00 0.0 0.0 2.67 R
5810 7942 0.747852 TGCTTCGTGTCACAGGTGTA 59.252 50.000 3.42 0.0 0.0 2.90 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
111 113 8.726988 GCCATTTTGTCTGTTATTCTGTTACTA 58.273 33.333 0.00 0.00 0.00 1.82
259 261 3.731652 TTCCCGTTCGAGTTTGACTTA 57.268 42.857 0.00 0.00 0.00 2.24
479 481 0.943673 CACACGCATGTCTCAACCAA 59.056 50.000 0.00 0.00 36.72 3.67
480 482 0.944386 ACACGCATGTCTCAACCAAC 59.056 50.000 0.00 0.00 31.55 3.77
481 483 1.229428 CACGCATGTCTCAACCAACT 58.771 50.000 0.00 0.00 0.00 3.16
482 484 1.603802 CACGCATGTCTCAACCAACTT 59.396 47.619 0.00 0.00 0.00 2.66
484 486 1.664016 CGCATGTCTCAACCAACTTGC 60.664 52.381 0.00 0.00 40.93 4.01
486 488 1.955778 CATGTCTCAACCAACTTGCCA 59.044 47.619 0.00 0.00 0.00 4.92
487 489 2.136298 TGTCTCAACCAACTTGCCAA 57.864 45.000 0.00 0.00 0.00 4.52
488 490 1.748493 TGTCTCAACCAACTTGCCAAC 59.252 47.619 0.00 0.00 0.00 3.77
489 491 2.024414 GTCTCAACCAACTTGCCAACT 58.976 47.619 0.00 0.00 0.00 3.16
490 492 2.427095 GTCTCAACCAACTTGCCAACTT 59.573 45.455 0.00 0.00 0.00 2.66
491 493 2.426738 TCTCAACCAACTTGCCAACTTG 59.573 45.455 0.00 0.00 0.00 3.16
492 494 2.166254 CTCAACCAACTTGCCAACTTGT 59.834 45.455 0.00 0.00 0.00 3.16
493 495 2.564947 TCAACCAACTTGCCAACTTGTT 59.435 40.909 0.00 0.00 0.00 2.83
495 497 2.456577 ACCAACTTGCCAACTTGTTCT 58.543 42.857 0.00 0.00 0.00 3.01
496 498 2.831526 ACCAACTTGCCAACTTGTTCTT 59.168 40.909 0.00 0.00 0.00 2.52
497 499 3.260632 ACCAACTTGCCAACTTGTTCTTT 59.739 39.130 0.00 0.00 0.00 2.52
498 500 4.252878 CCAACTTGCCAACTTGTTCTTTT 58.747 39.130 0.00 0.00 0.00 2.27
527 529 1.136891 AGGAACTTGCCAACTTGTTGC 59.863 47.619 7.89 4.88 27.25 4.17
528 530 1.570813 GAACTTGCCAACTTGTTGCC 58.429 50.000 7.89 0.00 0.00 4.52
529 531 0.901124 AACTTGCCAACTTGTTGCCA 59.099 45.000 7.89 0.58 0.00 4.92
530 532 1.122227 ACTTGCCAACTTGTTGCCAT 58.878 45.000 7.89 0.00 0.00 4.40
531 533 1.485895 ACTTGCCAACTTGTTGCCATT 59.514 42.857 7.89 0.00 0.00 3.16
532 534 2.093021 ACTTGCCAACTTGTTGCCATTT 60.093 40.909 7.89 0.00 0.00 2.32
1042 2174 4.020543 ACTGCTTCTTTCTCTATCGACCT 58.979 43.478 0.00 0.00 0.00 3.85
1121 3212 1.745320 AACAACTCTGACGCCGACCT 61.745 55.000 0.00 0.00 0.00 3.85
1212 3303 1.153667 CGACTCCCAGAGCTTCTGC 60.154 63.158 7.44 0.00 42.98 4.26
1320 3411 2.577563 TCAGATTCCTCCTTGCATTGGA 59.422 45.455 8.42 8.42 0.00 3.53
1353 3444 3.010027 TCTTGACCAGGATAAACATGCCA 59.990 43.478 0.00 0.00 0.00 4.92
1543 3634 3.688673 CCCTTCAGATCTTGCTCAAAGTC 59.311 47.826 0.00 0.00 37.18 3.01
1660 3751 2.350484 GCTACGAACAAACTTTCAGGCC 60.350 50.000 0.00 0.00 0.00 5.19
1711 3802 2.610479 CGTCTTACCAAGCTTGCTCTCA 60.610 50.000 21.43 1.25 0.00 3.27
1799 3890 1.614903 CCTTGCATCAAACAAGCTCCA 59.385 47.619 0.00 0.00 42.57 3.86
2106 4197 0.890996 CAGGCACAGTTCCTCCAACC 60.891 60.000 0.00 0.00 35.28 3.77
2175 4266 4.101585 CAGCTATCTGGGAGAATACCAACA 59.898 45.833 0.00 0.00 37.59 3.33
2176 4267 4.910304 AGCTATCTGGGAGAATACCAACAT 59.090 41.667 0.00 0.00 37.59 2.71
2177 4268 5.012561 AGCTATCTGGGAGAATACCAACATC 59.987 44.000 0.00 0.00 37.59 3.06
2196 4287 1.638070 TCCATTGGCCATACACTTCCA 59.362 47.619 6.09 0.00 0.00 3.53
2669 4760 6.899393 TGTCCTGAATTTAGCAGAAAACAT 57.101 33.333 0.00 0.00 35.39 2.71
2877 4968 6.295349 CCTCACTTTCTGAAGGCTTAGACTTA 60.295 42.308 0.00 0.00 37.19 2.24
2941 5032 5.530543 AGCAGCTTAAATAATCTTGAGCTCC 59.469 40.000 12.15 0.00 44.03 4.70
3025 5116 3.254470 TGGAATCGCTTCGTTTGGATA 57.746 42.857 0.00 0.00 31.75 2.59
3409 5500 1.873698 TGTACACAGAAAGCGGGAAC 58.126 50.000 0.00 0.00 0.00 3.62
3539 5630 3.574826 GGAGGGTGTGGATCTGTCTATAC 59.425 52.174 0.00 0.00 0.00 1.47
3669 5760 2.098607 ACGCCATCGAAATCTCGTAAGA 59.901 45.455 0.00 0.00 45.62 2.10
3732 5823 6.582636 TGAGTTCAAAGCTCTAGTTCTTGAA 58.417 36.000 3.87 3.87 34.30 2.69
3775 5866 4.327680 AGAAAGTTGGCTTCATCCAGTAC 58.672 43.478 0.00 0.00 37.44 2.73
3831 5922 6.489603 TCTTGGGTTAAGGATAAGAATTGCA 58.510 36.000 0.00 0.00 37.01 4.08
3961 6052 4.647611 TCGTGTTGGTGACTTTGGATTAT 58.352 39.130 0.00 0.00 0.00 1.28
4152 6243 8.485578 AAAGGAAATCATGTTTACCTTTACCA 57.514 30.769 19.43 0.00 43.08 3.25
4154 6245 8.122472 AGGAAATCATGTTTACCTTTACCAAG 57.878 34.615 0.00 0.00 0.00 3.61
4198 6289 7.048512 AGCACCAGAATTATGTAGACCTAAAC 58.951 38.462 0.00 0.00 0.00 2.01
4230 6321 7.988737 TCCACTATAATGTGCTTTCAATGAAG 58.011 34.615 0.00 0.00 36.68 3.02
4278 6371 9.765295 AACTAATATTACATATACTCCCTCCGT 57.235 33.333 0.00 0.00 0.00 4.69
4279 6372 9.406113 ACTAATATTACATATACTCCCTCCGTC 57.594 37.037 0.00 0.00 0.00 4.79
4280 6373 9.629878 CTAATATTACATATACTCCCTCCGTCT 57.370 37.037 0.00 0.00 0.00 4.18
4281 6374 7.883391 ATATTACATATACTCCCTCCGTCTG 57.117 40.000 0.00 0.00 0.00 3.51
4282 6375 2.877866 ACATATACTCCCTCCGTCTGG 58.122 52.381 0.00 0.00 0.00 3.86
4283 6376 2.445905 ACATATACTCCCTCCGTCTGGA 59.554 50.000 0.00 0.00 43.88 3.86
4284 6377 3.117246 ACATATACTCCCTCCGTCTGGAA 60.117 47.826 0.00 0.00 45.87 3.53
4285 6378 2.544844 ATACTCCCTCCGTCTGGAAA 57.455 50.000 0.00 0.00 45.87 3.13
4286 6379 2.544844 TACTCCCTCCGTCTGGAAAT 57.455 50.000 0.00 0.00 45.87 2.17
4287 6380 2.544844 ACTCCCTCCGTCTGGAAATA 57.455 50.000 0.00 0.00 45.87 1.40
4288 6381 2.108970 ACTCCCTCCGTCTGGAAATAC 58.891 52.381 0.00 0.00 45.87 1.89
4289 6382 2.292323 ACTCCCTCCGTCTGGAAATACT 60.292 50.000 0.00 0.00 45.87 2.12
4290 6383 2.766828 CTCCCTCCGTCTGGAAATACTT 59.233 50.000 0.00 0.00 45.87 2.24
4291 6384 2.500098 TCCCTCCGTCTGGAAATACTTG 59.500 50.000 0.00 0.00 45.87 3.16
4292 6385 2.236395 CCCTCCGTCTGGAAATACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
4293 6386 3.522553 CCTCCGTCTGGAAATACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
4294 6387 3.056107 CCTCCGTCTGGAAATACTTGTCA 60.056 47.826 0.00 0.00 45.87 3.58
4295 6388 4.383118 CCTCCGTCTGGAAATACTTGTCAT 60.383 45.833 0.00 0.00 45.87 3.06
4296 6389 4.755411 TCCGTCTGGAAATACTTGTCATC 58.245 43.478 0.00 0.00 42.85 2.92
4297 6390 4.221924 TCCGTCTGGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 42.85 3.07
4298 6391 4.935205 CCGTCTGGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 37.49 2.57
4299 6392 5.411361 CCGTCTGGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 37.49 2.69
4300 6393 6.072728 CCGTCTGGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 37.49 2.44
4301 6394 7.362056 CCGTCTGGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 37.49 1.82
4302 6395 7.482743 CGTCTGGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
4303 6396 8.514594 GTCTGGAAATACTTGTCATCAAAATGA 58.485 33.333 0.00 0.00 39.63 2.57
4304 6397 9.076781 TCTGGAAATACTTGTCATCAAAATGAA 57.923 29.630 0.00 0.00 43.42 2.57
4305 6398 9.865321 CTGGAAATACTTGTCATCAAAATGAAT 57.135 29.630 0.00 0.00 43.42 2.57
4369 6462 9.643693 ACATCACCTTTTATTCATTTTGATGAC 57.356 29.630 13.63 0.00 40.95 3.06
4370 6463 9.642327 CATCACCTTTTATTCATTTTGATGACA 57.358 29.630 0.00 0.00 40.95 3.58
4372 6465 9.695526 TCACCTTTTATTCATTTTGATGACAAG 57.304 29.630 0.00 0.00 37.32 3.16
4373 6466 9.480053 CACCTTTTATTCATTTTGATGACAAGT 57.520 29.630 0.00 0.00 37.32 3.16
4381 6474 9.865321 ATTCATTTTGATGACAAGTATTTCCTG 57.135 29.630 0.00 0.00 37.32 3.86
4382 6475 8.634335 TCATTTTGATGACAAGTATTTCCTGA 57.366 30.769 0.00 0.00 37.32 3.86
4383 6476 8.514594 TCATTTTGATGACAAGTATTTCCTGAC 58.485 33.333 0.00 0.00 37.32 3.51
4384 6477 6.480524 TTTGATGACAAGTATTTCCTGACG 57.519 37.500 0.00 0.00 37.32 4.35
4385 6478 4.503910 TGATGACAAGTATTTCCTGACGG 58.496 43.478 0.00 0.00 0.00 4.79
4386 6479 4.221924 TGATGACAAGTATTTCCTGACGGA 59.778 41.667 0.00 0.00 37.60 4.69
4387 6480 4.188247 TGACAAGTATTTCCTGACGGAG 57.812 45.455 0.00 0.00 41.25 4.63
4388 6481 3.056107 TGACAAGTATTTCCTGACGGAGG 60.056 47.826 0.00 0.00 44.45 4.30
4389 6482 2.236395 ACAAGTATTTCCTGACGGAGGG 59.764 50.000 3.12 0.00 43.06 4.30
4390 6483 2.500098 CAAGTATTTCCTGACGGAGGGA 59.500 50.000 3.12 0.00 43.06 4.20
4391 6484 2.389715 AGTATTTCCTGACGGAGGGAG 58.610 52.381 3.12 0.00 43.06 4.30
4419 6512 6.594788 TGATTAAGCAGCTGAAAGGATTTT 57.405 33.333 20.43 0.60 39.27 1.82
4422 6515 7.394359 TGATTAAGCAGCTGAAAGGATTTTACT 59.606 33.333 20.43 0.00 39.27 2.24
4508 6601 8.250143 TGTCTACAGCTATGGAATTATTCTGA 57.750 34.615 4.87 0.00 0.00 3.27
4562 6655 8.152898 CAGATGAGATGTTTAAGGATGGACATA 58.847 37.037 0.00 0.00 33.21 2.29
4594 6687 1.337118 TTGTGGAACTGGCATTTCCC 58.663 50.000 27.64 20.37 41.80 3.97
4623 6716 4.963318 TTGGTGATATTCTAGAGCCCAG 57.037 45.455 0.00 0.00 0.00 4.45
4627 6720 4.219725 GGTGATATTCTAGAGCCCAGTCTC 59.780 50.000 0.00 0.00 0.00 3.36
4661 6754 2.552315 CAGGGCGAACACACAAGTAAAT 59.448 45.455 0.00 0.00 0.00 1.40
5096 7196 7.611855 ACACTTGCCTAAAAAGCACTATATTCT 59.388 33.333 0.00 0.00 40.69 2.40
5137 7237 0.508641 CTTCGCTGTTGACCTTCACG 59.491 55.000 0.00 0.00 0.00 4.35
5147 7247 5.547465 TGTTGACCTTCACGATATTTGAGT 58.453 37.500 0.00 0.00 0.00 3.41
5160 7260 8.708742 CACGATATTTGAGTGAAGAACTTTACA 58.291 33.333 11.00 0.00 40.07 2.41
5173 7273 8.139989 TGAAGAACTTTACACAGTAACCTCTAC 58.860 37.037 0.00 0.00 0.00 2.59
5217 7317 7.812690 AGCATGAAGATATGTTTTGATAGCA 57.187 32.000 0.00 0.00 0.00 3.49
5220 7320 8.294577 GCATGAAGATATGTTTTGATAGCATGA 58.705 33.333 0.00 0.00 32.31 3.07
5226 7330 9.000486 AGATATGTTTTGATAGCATGACTGATG 58.000 33.333 0.00 0.00 34.84 3.07
5228 7332 7.634671 ATGTTTTGATAGCATGACTGATGAA 57.365 32.000 0.00 0.00 33.31 2.57
5234 7338 9.563748 TTTGATAGCATGACTGATGAATATCAA 57.436 29.630 0.00 13.36 42.84 2.57
5247 7351 8.492673 TGATGAATATCAAGTTTACCTGACAC 57.507 34.615 0.00 0.00 40.26 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.403276 GTGCTACTCACAGACGGTC 57.597 57.895 0.00 0.00 44.98 4.79
111 113 3.637769 TCTTTTTGCCTGGGTGTTTACT 58.362 40.909 0.00 0.00 0.00 2.24
232 234 1.856629 ACTCGAACGGGAAAGGGATA 58.143 50.000 0.00 0.00 0.00 2.59
411 413 5.947228 TCTCTACCAAGTGCTTTTGAATG 57.053 39.130 2.84 0.00 0.00 2.67
449 451 4.696078 GCGTGTGCATTGCCATAG 57.304 55.556 6.12 4.23 42.15 2.23
497 499 4.559862 TGGCAAGTTCCTTTTCCAAAAA 57.440 36.364 0.00 0.00 0.00 1.94
498 500 4.019771 AGTTGGCAAGTTCCTTTTCCAAAA 60.020 37.500 0.00 0.00 36.22 2.44
500 502 3.103742 AGTTGGCAAGTTCCTTTTCCAA 58.896 40.909 0.00 0.00 33.87 3.53
501 503 2.745968 AGTTGGCAAGTTCCTTTTCCA 58.254 42.857 0.00 0.00 0.00 3.53
502 504 3.118775 ACAAGTTGGCAAGTTCCTTTTCC 60.119 43.478 17.14 0.00 0.00 3.13
504 506 4.252878 CAACAAGTTGGCAAGTTCCTTTT 58.747 39.130 17.14 6.09 36.95 2.27
505 507 3.860641 CAACAAGTTGGCAAGTTCCTTT 58.139 40.909 17.14 8.35 36.95 3.11
506 508 2.418609 GCAACAAGTTGGCAAGTTCCTT 60.419 45.455 17.14 8.98 40.74 3.36
508 510 1.570813 GCAACAAGTTGGCAAGTTCC 58.429 50.000 17.14 0.00 40.74 3.62
904 1324 0.548926 TTCTGTATGTGGCTGGGGGA 60.549 55.000 0.00 0.00 0.00 4.81
907 1327 1.098050 GCTTTCTGTATGTGGCTGGG 58.902 55.000 0.00 0.00 0.00 4.45
1042 2174 2.698274 GGAAGAAGAAGGCCACCAAAAA 59.302 45.455 5.01 0.00 0.00 1.94
1121 3212 1.000771 AGGCAGAGGAGCGTCTGTA 60.001 57.895 18.10 0.00 45.07 2.74
1212 3303 1.243342 ATGTCACACCACGCCATTGG 61.243 55.000 0.00 0.00 43.04 3.16
1320 3411 3.202151 TCCTGGTCAAGAAACTGAGGTTT 59.798 43.478 0.00 0.00 46.85 3.27
1353 3444 3.054875 TGCTGCCACTGATCTTATTGTCT 60.055 43.478 0.00 0.00 0.00 3.41
1452 3543 3.568538 GGAACACATTGACAGTGCATTC 58.431 45.455 0.00 2.60 40.59 2.67
1453 3544 2.297033 GGGAACACATTGACAGTGCATT 59.703 45.455 0.00 0.00 40.59 3.56
1529 3620 2.579860 AGGGATGGACTTTGAGCAAGAT 59.420 45.455 0.00 0.00 36.21 2.40
1543 3634 1.453379 CAAGCTGCTCCAGGGATGG 60.453 63.158 1.00 0.00 31.21 3.51
1643 3734 0.313987 GGGGCCTGAAAGTTTGTTCG 59.686 55.000 0.84 0.00 0.00 3.95
1660 3751 2.703007 CTCCTAGGAACTGAGGAATGGG 59.297 54.545 13.77 0.00 41.52 4.00
1711 3802 2.020720 TCCTGTGAACGCATTGTTGTT 58.979 42.857 0.00 0.00 42.09 2.83
2175 4266 2.244510 TGGAAGTGTATGGCCAATGGAT 59.755 45.455 10.96 0.00 0.00 3.41
2176 4267 1.638070 TGGAAGTGTATGGCCAATGGA 59.362 47.619 10.96 0.00 0.00 3.41
2177 4268 2.142356 TGGAAGTGTATGGCCAATGG 57.858 50.000 10.96 0.00 0.00 3.16
2185 4276 7.621428 ACATCTGAATTCTTGGAAGTGTATG 57.379 36.000 7.05 0.00 0.00 2.39
2196 4287 6.839124 TGCATTACCAACATCTGAATTCTT 57.161 33.333 7.05 0.00 0.00 2.52
2877 4968 6.325545 TCAGTCCGGTTAGTTGGTTATATGAT 59.674 38.462 0.00 0.00 0.00 2.45
2941 5032 4.583871 AGCTGGTTGTTGGAGAGATTAAG 58.416 43.478 0.00 0.00 0.00 1.85
3009 5100 5.560966 AATTTGTATCCAAACGAAGCGAT 57.439 34.783 0.00 0.00 43.03 4.58
3025 5116 6.351286 GGAATGCCACCTTGAAGATAATTTGT 60.351 38.462 0.00 0.00 0.00 2.83
3037 5128 1.064166 AGATCCAGGAATGCCACCTTG 60.064 52.381 0.00 0.00 35.35 3.61
3409 5500 5.269505 TGGTTGATTGGTTGTTTAGTTGG 57.730 39.130 0.00 0.00 0.00 3.77
3539 5630 3.320541 TGGTTCAGCCAAAAATGTACCTG 59.679 43.478 3.24 0.00 45.94 4.00
3732 5823 3.439857 AGGCTACCATTTGACATGTGT 57.560 42.857 1.15 0.00 0.00 3.72
3775 5866 4.933400 CCTTTTTGAGCCATGATTTTCTGG 59.067 41.667 0.00 0.00 35.53 3.86
3831 5922 0.617413 AGGCAGCAGCTATGTCTGTT 59.383 50.000 4.52 0.00 41.70 3.16
3961 6052 7.122650 GGATGGATGGTCATAAAGAAACTTTGA 59.877 37.037 6.95 0.00 0.00 2.69
4198 6289 9.764363 TGAAAGCACATTATAGTGGATACTTAG 57.236 33.333 0.00 0.00 39.87 2.18
4209 6300 9.844790 TGTTTCTTCATTGAAAGCACATTATAG 57.155 29.630 0.01 0.00 36.72 1.31
4211 6302 9.545105 TTTGTTTCTTCATTGAAAGCACATTAT 57.455 25.926 0.01 0.00 36.72 1.28
4216 6307 8.351495 TGTATTTGTTTCTTCATTGAAAGCAC 57.649 30.769 0.01 0.00 36.72 4.40
4254 6347 9.629878 AGACGGAGGGAGTATATGTAATATTAG 57.370 37.037 0.00 0.00 40.66 1.73
4263 6356 3.156288 TCCAGACGGAGGGAGTATATG 57.844 52.381 0.00 0.00 35.91 1.78
4267 6360 2.544844 ATTTCCAGACGGAGGGAGTA 57.455 50.000 0.00 0.00 44.10 2.59
4269 6362 2.389715 AGTATTTCCAGACGGAGGGAG 58.610 52.381 0.00 0.00 44.10 4.30
4270 6363 2.500098 CAAGTATTTCCAGACGGAGGGA 59.500 50.000 0.00 0.00 44.10 4.20
4271 6364 2.236395 ACAAGTATTTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
4272 6365 3.056107 TGACAAGTATTTCCAGACGGAGG 60.056 47.826 0.00 0.00 44.10 4.30
4273 6366 4.188247 TGACAAGTATTTCCAGACGGAG 57.812 45.455 0.00 0.00 44.10 4.63
4274 6367 4.221924 TGATGACAAGTATTTCCAGACGGA 59.778 41.667 0.00 0.00 40.60 4.69
4275 6368 4.503910 TGATGACAAGTATTTCCAGACGG 58.496 43.478 0.00 0.00 0.00 4.79
4276 6369 6.480524 TTTGATGACAAGTATTTCCAGACG 57.519 37.500 0.00 0.00 37.32 4.18
4277 6370 8.514594 TCATTTTGATGACAAGTATTTCCAGAC 58.485 33.333 0.00 0.00 37.32 3.51
4278 6371 8.634335 TCATTTTGATGACAAGTATTTCCAGA 57.366 30.769 0.00 0.00 37.32 3.86
4279 6372 9.865321 ATTCATTTTGATGACAAGTATTTCCAG 57.135 29.630 0.00 0.00 37.32 3.86
4343 6436 9.643693 GTCATCAAAATGAATAAAAGGTGATGT 57.356 29.630 9.42 0.00 43.42 3.06
4344 6437 9.642327 TGTCATCAAAATGAATAAAAGGTGATG 57.358 29.630 0.00 0.00 43.42 3.07
4346 6439 9.695526 CTTGTCATCAAAATGAATAAAAGGTGA 57.304 29.630 0.00 0.00 43.42 4.02
4347 6440 9.480053 ACTTGTCATCAAAATGAATAAAAGGTG 57.520 29.630 0.00 0.00 43.42 4.00
4355 6448 9.865321 CAGGAAATACTTGTCATCAAAATGAAT 57.135 29.630 0.00 0.00 43.42 2.57
4356 6449 9.076781 TCAGGAAATACTTGTCATCAAAATGAA 57.923 29.630 0.00 0.00 43.42 2.57
4357 6450 8.514594 GTCAGGAAATACTTGTCATCAAAATGA 58.485 33.333 0.00 0.00 39.63 2.57
4358 6451 7.482743 CGTCAGGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
4359 6452 7.362056 CCGTCAGGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 41.02 1.82
4360 6453 6.072728 CCGTCAGGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 41.02 2.44
4361 6454 5.411361 CCGTCAGGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 41.02 2.69
4362 6455 4.935205 CCGTCAGGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 41.02 2.57
4363 6456 4.221924 TCCGTCAGGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 45.12 3.07
4364 6457 4.755411 TCCGTCAGGAAATACTTGTCATC 58.245 43.478 0.00 0.00 45.12 2.92
4365 6458 4.819105 TCCGTCAGGAAATACTTGTCAT 57.181 40.909 0.00 0.00 45.12 3.06
4378 6471 2.108168 TCAATTACTCCCTCCGTCAGG 58.892 52.381 0.00 0.00 43.01 3.86
4379 6472 4.408182 AATCAATTACTCCCTCCGTCAG 57.592 45.455 0.00 0.00 0.00 3.51
4380 6473 5.684030 GCTTAATCAATTACTCCCTCCGTCA 60.684 44.000 0.00 0.00 0.00 4.35
4381 6474 4.750598 GCTTAATCAATTACTCCCTCCGTC 59.249 45.833 0.00 0.00 0.00 4.79
4382 6475 4.163458 TGCTTAATCAATTACTCCCTCCGT 59.837 41.667 0.00 0.00 0.00 4.69
4383 6476 4.703897 TGCTTAATCAATTACTCCCTCCG 58.296 43.478 0.00 0.00 0.00 4.63
4384 6477 4.517075 GCTGCTTAATCAATTACTCCCTCC 59.483 45.833 0.00 0.00 0.00 4.30
4385 6478 5.238214 CAGCTGCTTAATCAATTACTCCCTC 59.762 44.000 0.00 0.00 0.00 4.30
4386 6479 5.104360 TCAGCTGCTTAATCAATTACTCCCT 60.104 40.000 9.47 0.00 0.00 4.20
4387 6480 5.126067 TCAGCTGCTTAATCAATTACTCCC 58.874 41.667 9.47 0.00 0.00 4.30
4388 6481 6.683974 TTCAGCTGCTTAATCAATTACTCC 57.316 37.500 9.47 0.00 0.00 3.85
4389 6482 7.066284 TCCTTTCAGCTGCTTAATCAATTACTC 59.934 37.037 9.47 0.00 0.00 2.59
4390 6483 6.886459 TCCTTTCAGCTGCTTAATCAATTACT 59.114 34.615 9.47 0.00 0.00 2.24
4391 6484 7.088589 TCCTTTCAGCTGCTTAATCAATTAC 57.911 36.000 9.47 0.00 0.00 1.89
4508 6601 5.893824 GGTTCTTTCCCATCACCATTTCTAT 59.106 40.000 0.00 0.00 0.00 1.98
4594 6687 6.426328 GCTCTAGAATATCACCAATCTTGTGG 59.574 42.308 0.00 0.00 44.92 4.17
4623 6716 3.545703 CCCTGGTATTGTGGAATGAGAC 58.454 50.000 0.00 0.00 0.00 3.36
4627 6720 1.024271 CGCCCTGGTATTGTGGAATG 58.976 55.000 0.00 0.00 0.00 2.67
4661 6754 1.133181 TGTGTCCCATGGCCTGAAGA 61.133 55.000 6.09 0.00 0.00 2.87
4690 6783 3.676598 GCATTGTACATTCTTGCATGCCA 60.677 43.478 16.68 2.49 33.58 4.92
5096 7196 8.914654 CGAAGAAAGCAAATGAATAAACATCAA 58.085 29.630 0.00 0.00 0.00 2.57
5147 7247 7.120923 AGAGGTTACTGTGTAAAGTTCTTCA 57.879 36.000 0.00 0.00 0.00 3.02
5160 7260 9.531158 AGTTTCACTAATAGTAGAGGTTACTGT 57.469 33.333 3.83 0.00 0.00 3.55
5173 7273 9.803315 TCATGCTAGTTACAGTTTCACTAATAG 57.197 33.333 0.00 0.00 0.00 1.73
5181 7281 9.319143 ACATATCTTCATGCTAGTTACAGTTTC 57.681 33.333 0.00 0.00 0.00 2.78
5201 7301 8.996271 TCATCAGTCATGCTATCAAAACATATC 58.004 33.333 0.00 0.00 31.70 1.63
5217 7317 9.334947 CAGGTAAACTTGATATTCATCAGTCAT 57.665 33.333 0.00 0.00 42.11 3.06
5220 7320 8.321353 TGTCAGGTAAACTTGATATTCATCAGT 58.679 33.333 0.00 0.00 42.11 3.41
5226 7330 7.602644 TCAGTGTGTCAGGTAAACTTGATATTC 59.397 37.037 0.00 0.00 34.44 1.75
5228 7332 6.874134 GTCAGTGTGTCAGGTAAACTTGATAT 59.126 38.462 0.00 0.00 34.44 1.63
5234 7338 2.223971 CCGTCAGTGTGTCAGGTAAACT 60.224 50.000 0.00 0.00 0.00 2.66
5247 7351 4.001652 TCTACTCTGTTAGACCGTCAGTG 58.998 47.826 0.40 0.00 0.00 3.66
5495 7603 1.741706 ACGATCTTCTTCGCTTCCGTA 59.258 47.619 0.00 0.00 42.82 4.02
5798 7930 5.469760 TGTCACAGGTGTAACATCATTTGAG 59.530 40.000 0.00 0.00 39.98 3.02
5799 7931 5.238432 GTGTCACAGGTGTAACATCATTTGA 59.762 40.000 0.00 0.00 39.98 2.69
5800 7932 5.451908 GTGTCACAGGTGTAACATCATTTG 58.548 41.667 0.00 0.00 39.98 2.32
5801 7933 4.213270 CGTGTCACAGGTGTAACATCATTT 59.787 41.667 3.42 0.00 39.98 2.32
5804 7936 2.362717 TCGTGTCACAGGTGTAACATCA 59.637 45.455 3.42 0.00 39.98 3.07
5805 7937 3.021269 TCGTGTCACAGGTGTAACATC 57.979 47.619 3.42 0.00 39.98 3.06
5806 7938 3.390135 CTTCGTGTCACAGGTGTAACAT 58.610 45.455 3.42 0.00 39.98 2.71
5807 7939 2.816689 CTTCGTGTCACAGGTGTAACA 58.183 47.619 3.42 0.00 39.98 2.41
5808 7940 1.525619 GCTTCGTGTCACAGGTGTAAC 59.474 52.381 3.42 0.00 0.00 2.50
5809 7941 1.137282 TGCTTCGTGTCACAGGTGTAA 59.863 47.619 3.42 0.00 0.00 2.41
5810 7942 0.747852 TGCTTCGTGTCACAGGTGTA 59.252 50.000 3.42 0.00 0.00 2.90
5811 7943 0.810031 GTGCTTCGTGTCACAGGTGT 60.810 55.000 3.42 0.00 33.63 4.16


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

AutoCloner maintained by Alex Coulton.