Multiple sequence alignment - TraesCS5A01G184400

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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 TraesCS5A01G184400 chr5A 100.000 3635 0 0 1 3635 384185850 384189484 0.000000e+00 6713.0
1 TraesCS5A01G184400 chr5A 100.000 1206 0 0 3900 5105 384189749 384190954 0.000000e+00 2228.0
2 TraesCS5A01G184400 chr5A 77.698 139 28 3 622 760 482360784 482360919 1.180000e-11 82.4
3 TraesCS5A01G184400 chr5D 97.798 1953 29 6 1639 3591 291876091 291878029 0.000000e+00 3356.0
4 TraesCS5A01G184400 chr5D 96.281 1210 36 6 3900 5105 291878210 291879414 0.000000e+00 1977.0
5 TraesCS5A01G184400 chr5D 87.055 1460 117 39 1 1395 291874641 291876093 0.000000e+00 1583.0
6 TraesCS5A01G184400 chr5D 100.000 36 0 0 3600 3635 291878062 291878097 3.300000e-07 67.6
7 TraesCS5A01G184400 chr5B 93.696 1396 59 12 1671 3039 332427413 332428806 0.000000e+00 2063.0
8 TraesCS5A01G184400 chr5B 87.990 1224 78 32 3900 5105 332429317 332430489 0.000000e+00 1382.0
9 TraesCS5A01G184400 chr5B 89.327 787 50 12 885 1663 332426611 332427371 0.000000e+00 957.0
10 TraesCS5A01G184400 chr5B 81.870 524 41 18 3067 3565 332428800 332429294 4.790000e-105 392.0
11 TraesCS5A01G184400 chr5B 93.750 48 3 0 19 66 602240806 602240759 7.090000e-09 73.1
12 TraesCS5A01G184400 chr3B 86.826 167 20 2 2443 2609 57283624 57283460 8.730000e-43 185.0
13 TraesCS5A01G184400 chr3B 88.742 151 17 0 2459 2609 57350123 57349973 8.730000e-43 185.0
14 TraesCS5A01G184400 chr3B 81.507 146 21 3 369 509 780854119 780853975 1.160000e-21 115.0
15 TraesCS5A01G184400 chr3B 97.297 37 1 0 570 606 651378346 651378382 4.270000e-06 63.9
16 TraesCS5A01G184400 chr6A 84.795 171 24 2 2443 2613 259899681 259899513 2.440000e-38 171.0
17 TraesCS5A01G184400 chr6A 83.626 171 26 2 2443 2613 261284600 261284432 5.290000e-35 159.0
18 TraesCS5A01G184400 chr7A 82.584 178 21 6 2443 2613 577672081 577671907 1.150000e-31 148.0
19 TraesCS5A01G184400 chr7A 82.022 178 23 5 2443 2613 577496232 577496407 5.330000e-30 143.0
20 TraesCS5A01G184400 chr7A 77.778 162 31 2 370 530 643403972 643404129 1.510000e-15 95.3
21 TraesCS5A01G184400 chr7A 84.000 100 14 2 622 721 674313022 674313119 1.510000e-15 95.3
22 TraesCS5A01G184400 chr7A 85.106 94 11 2 418 509 60734033 60734125 5.440000e-15 93.5
23 TraesCS5A01G184400 chr4A 75.066 381 54 31 389 738 556232367 556232737 6.890000e-29 139.0
24 TraesCS5A01G184400 chr2A 79.429 175 27 6 369 535 438298110 438297937 1.160000e-21 115.0
25 TraesCS5A01G184400 chr2D 83.065 124 14 6 702 818 422094828 422094951 6.990000e-19 106.0
26 TraesCS5A01G184400 chr2D 78.235 170 26 10 445 605 634294625 634294792 1.170000e-16 99.0
27 TraesCS5A01G184400 chr4D 81.818 121 18 2 389 509 78935908 78935792 1.170000e-16 99.0
28 TraesCS5A01G184400 chr6D 76.804 194 32 10 621 806 381971636 381971824 4.210000e-16 97.1
29 TraesCS5A01G184400 chr6D 88.136 59 7 0 691 749 25854347 25854289 2.550000e-08 71.3
30 TraesCS5A01G184400 chr3D 79.054 148 26 4 389 531 142859351 142859204 4.210000e-16 97.1
31 TraesCS5A01G184400 chr3D 79.070 129 20 6 10 131 456542454 456542326 1.180000e-11 82.4
32 TraesCS5A01G184400 chr3D 81.818 88 15 1 687 774 422726525 422726611 7.090000e-09 73.1
33 TraesCS5A01G184400 chr3D 97.619 42 1 0 7 48 433828394 433828435 7.090000e-09 73.1
34 TraesCS5A01G184400 chr3A 88.608 79 7 2 456 533 735718438 735718361 1.510000e-15 95.3
35 TraesCS5A01G184400 chr1D 89.831 59 6 0 691 749 262035401 262035343 5.480000e-10 76.8
36 TraesCS5A01G184400 chr2B 76.582 158 18 15 467 606 20312362 20312206 9.170000e-08 69.4
37 TraesCS5A01G184400 chr1A 80.220 91 16 2 686 776 580965088 580965000 3.300000e-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 TraesCS5A01G184400 chr5A 384185850 384190954 5104 False 4470.5 6713 100.00000 1 5105 2 chr5A.!!$F2 5104
1 TraesCS5A01G184400 chr5D 291874641 291879414 4773 False 1745.9 3356 95.28350 1 5105 4 chr5D.!!$F1 5104
2 TraesCS5A01G184400 chr5B 332426611 332430489 3878 False 1198.5 2063 88.22075 885 5105 4 chr5B.!!$F1 4220

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
22 23 0.037232 GGACTAAGAGCACGCCAAGT 60.037 55.0 0.0 0.0 0.0 3.16 F
1417 1499 0.106708 TGAGTCCGCTTGCTTTCAGT 59.893 50.0 0.0 0.0 0.0 3.41 F
1420 1502 0.040067 GTCCGCTTGCTTTCAGTTGG 60.040 55.0 0.0 0.0 0.0 3.77 F
1422 1504 0.318107 CCGCTTGCTTTCAGTTGGTG 60.318 55.0 0.0 0.0 0.0 4.17 F
1425 1507 0.662619 CTTGCTTTCAGTTGGTGCGA 59.337 50.0 0.0 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1501 0.521735 GGGTTCTGAACAATCGCACC 59.478 55.000 21.01 8.19 0.0 5.01 R
3377 3525 3.572632 AGTAGGCGGTCATCAGTAGTA 57.427 47.619 0.00 0.00 0.0 1.82 R
3464 3630 4.510167 AATCTACAATGTGGAAGAGGGG 57.490 45.455 3.02 0.00 0.0 4.79 R
3963 4155 2.171003 TCTTCGAAGCAGACATCTCCA 58.829 47.619 20.56 0.00 0.0 3.86 R
4493 4686 3.754850 TGATGATTTCTGTGAGTTGGCTG 59.245 43.478 0.00 0.00 0.0 4.85 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
22 23 0.037232 GGACTAAGAGCACGCCAAGT 60.037 55.000 0.00 0.00 0.00 3.16
64 65 1.140804 GTTGCGTGTTGGGTGCTTT 59.859 52.632 0.00 0.00 0.00 3.51
70 71 1.608590 CGTGTTGGGTGCTTTCTCAAT 59.391 47.619 0.00 0.00 0.00 2.57
99 104 7.571080 TTTTAGGTGTTTTCGGTTTAGATGT 57.429 32.000 0.00 0.00 0.00 3.06
103 108 6.500910 AGGTGTTTTCGGTTTAGATGTTTTC 58.499 36.000 0.00 0.00 0.00 2.29
104 109 6.320418 AGGTGTTTTCGGTTTAGATGTTTTCT 59.680 34.615 0.00 0.00 38.57 2.52
105 110 6.976349 GGTGTTTTCGGTTTAGATGTTTTCTT 59.024 34.615 0.00 0.00 35.79 2.52
106 111 8.130469 GGTGTTTTCGGTTTAGATGTTTTCTTA 58.870 33.333 0.00 0.00 35.79 2.10
107 112 8.950961 GTGTTTTCGGTTTAGATGTTTTCTTAC 58.049 33.333 0.00 0.00 35.79 2.34
108 113 8.895737 TGTTTTCGGTTTAGATGTTTTCTTACT 58.104 29.630 0.00 0.00 35.79 2.24
115 120 9.940166 GGTTTAGATGTTTTCTTACTTTTTCGA 57.060 29.630 0.00 0.00 35.79 3.71
123 128 9.849166 TGTTTTCTTACTTTTTCGATTTTCACT 57.151 25.926 0.00 0.00 0.00 3.41
212 223 2.353269 AGAAGCACGACTATGACTCTCG 59.647 50.000 0.00 0.00 0.00 4.04
213 224 2.025589 AGCACGACTATGACTCTCGA 57.974 50.000 0.00 0.00 0.00 4.04
218 229 4.672024 GCACGACTATGACTCTCGAAAAGA 60.672 45.833 0.00 0.00 0.00 2.52
227 254 6.042638 TGACTCTCGAAAAGATTCTTCCAT 57.957 37.500 0.00 0.00 35.31 3.41
237 264 5.901413 AAGATTCTTCCATGAGAGGCATA 57.099 39.130 0.00 0.00 34.82 3.14
250 277 4.903649 TGAGAGGCATAGATTTGATCCTCA 59.096 41.667 8.56 0.00 41.79 3.86
272 299 4.572985 TGGAGACACAAATTTGCTTCAG 57.427 40.909 18.12 5.96 33.40 3.02
273 300 3.243501 TGGAGACACAAATTTGCTTCAGC 60.244 43.478 18.12 10.01 37.12 4.26
294 321 2.351455 GAGAAGCAAAGTAGTGCCTCC 58.649 52.381 0.00 0.00 46.14 4.30
297 324 1.745489 GCAAAGTAGTGCCTCCCGG 60.745 63.158 0.00 0.00 38.66 5.73
326 355 3.733443 AATGTGTCTTTTGGCTTCCAC 57.267 42.857 0.00 0.00 30.78 4.02
327 356 1.021202 TGTGTCTTTTGGCTTCCACG 58.979 50.000 0.00 0.00 30.78 4.94
339 368 2.565841 GCTTCCACGAGAGGCAAATAT 58.434 47.619 8.88 0.00 46.54 1.28
346 375 6.177610 TCCACGAGAGGCAAATATTTACTTT 58.822 36.000 0.00 0.00 0.00 2.66
353 382 6.879458 AGAGGCAAATATTTACTTTCACGAGT 59.121 34.615 0.00 0.00 0.00 4.18
354 383 7.064728 AGAGGCAAATATTTACTTTCACGAGTC 59.935 37.037 0.00 0.00 0.00 3.36
357 424 7.415206 GGCAAATATTTACTTTCACGAGTCCAT 60.415 37.037 0.00 0.00 0.00 3.41
370 437 2.616376 CGAGTCCATGAGAGAGACGAAT 59.384 50.000 0.00 0.00 35.65 3.34
371 438 3.066064 CGAGTCCATGAGAGAGACGAATT 59.934 47.826 0.00 0.00 35.65 2.17
372 439 4.439426 CGAGTCCATGAGAGAGACGAATTT 60.439 45.833 0.00 0.00 35.65 1.82
373 440 5.413309 AGTCCATGAGAGAGACGAATTTT 57.587 39.130 0.00 0.00 35.65 1.82
374 441 5.415221 AGTCCATGAGAGAGACGAATTTTC 58.585 41.667 0.00 0.00 35.65 2.29
375 442 5.186797 AGTCCATGAGAGAGACGAATTTTCT 59.813 40.000 0.00 0.00 35.65 2.52
376 443 5.872070 GTCCATGAGAGAGACGAATTTTCTT 59.128 40.000 0.00 0.00 0.00 2.52
377 444 6.035542 GTCCATGAGAGAGACGAATTTTCTTC 59.964 42.308 0.00 0.00 0.00 2.87
378 445 6.071108 TCCATGAGAGAGACGAATTTTCTTCT 60.071 38.462 0.00 0.00 38.35 2.85
379 446 6.255453 CCATGAGAGAGACGAATTTTCTTCTC 59.745 42.308 15.35 15.35 46.84 2.87
384 451 5.824243 GAGACGAATTTTCTTCTCGTGAA 57.176 39.130 10.03 0.00 45.25 3.18
385 452 5.830900 AGACGAATTTTCTTCTCGTGAAG 57.169 39.130 18.82 18.82 45.25 3.02
416 483 0.931005 CTTCCGCGAGAAGCATAACC 59.069 55.000 19.55 0.00 45.38 2.85
476 544 6.073548 CCACGAGAGGCACATATTTATTTCTC 60.074 42.308 0.00 0.00 0.00 2.87
488 556 3.627395 TTATTTCTCGTGGAGGCACAT 57.373 42.857 0.00 0.00 0.00 3.21
493 561 3.627395 TCTCGTGGAGGCACATATTTT 57.373 42.857 0.00 0.00 0.00 1.82
499 567 3.065371 GTGGAGGCACATATTTTCTTCCG 59.935 47.826 0.00 0.00 0.00 4.30
511 579 3.303605 CTTCCGCGAGAAGCATCG 58.696 61.111 19.55 2.05 45.38 3.84
528 596 3.558505 CATCGTTGTGCCTCTCAAAAAG 58.441 45.455 0.00 0.00 0.00 2.27
529 597 1.946768 TCGTTGTGCCTCTCAAAAAGG 59.053 47.619 0.00 0.00 36.95 3.11
530 598 1.946768 CGTTGTGCCTCTCAAAAAGGA 59.053 47.619 0.00 0.00 35.83 3.36
568 637 5.947503 TTCTTTCACGAAAAGCATTGTTG 57.052 34.783 9.29 0.00 43.48 3.33
579 648 1.503542 CATTGTTGCTCGTGGAGGC 59.496 57.895 0.00 0.00 0.00 4.70
581 650 1.237285 ATTGTTGCTCGTGGAGGCAC 61.237 55.000 0.00 0.00 38.23 5.01
594 663 2.818130 GAGGCACAAATTTGCTTCCA 57.182 45.000 18.12 0.00 41.54 3.53
610 679 4.159120 GCTTCCACGAAAAGCATAAGTTC 58.841 43.478 13.54 0.00 46.63 3.01
612 681 5.121768 GCTTCCACGAAAAGCATAAGTTCTA 59.878 40.000 13.54 0.00 46.63 2.10
618 687 7.148239 CCACGAAAAGCATAAGTTCTAGGAAAT 60.148 37.037 0.00 0.00 0.00 2.17
619 688 8.237267 CACGAAAAGCATAAGTTCTAGGAAATT 58.763 33.333 0.00 0.00 0.00 1.82
651 720 1.197949 GCTTCTGGCTCCGACTTTTTC 59.802 52.381 0.00 0.00 38.06 2.29
690 760 7.562454 TGAAAAAGAAGTTCATCGTAACCTT 57.438 32.000 5.50 0.00 30.08 3.50
757 827 2.969262 ACGGTGAAAATGGTTTGGGATT 59.031 40.909 0.00 0.00 0.00 3.01
762 832 5.825151 GGTGAAAATGGTTTGGGATTTGAAA 59.175 36.000 0.00 0.00 0.00 2.69
851 926 1.971357 AGAAGGTGGAGTGATCGTTGT 59.029 47.619 0.00 0.00 0.00 3.32
892 967 1.925847 CAAAGATGCGCTCAGAGAGAC 59.074 52.381 9.73 0.00 0.00 3.36
992 1071 1.154338 CTTCTCGGCAAAGCGCTTG 60.154 57.895 25.80 18.24 41.91 4.01
1134 1216 2.182030 GAGGACAAGGCGAGGACG 59.818 66.667 0.00 0.00 42.93 4.79
1337 1419 5.997746 GGATCAGTGATTTCGGGATTTCATA 59.002 40.000 7.16 0.00 0.00 2.15
1415 1497 1.230635 GCTGAGTCCGCTTGCTTTCA 61.231 55.000 0.00 0.00 0.00 2.69
1417 1499 0.106708 TGAGTCCGCTTGCTTTCAGT 59.893 50.000 0.00 0.00 0.00 3.41
1418 1500 1.230324 GAGTCCGCTTGCTTTCAGTT 58.770 50.000 0.00 0.00 0.00 3.16
1419 1501 0.947244 AGTCCGCTTGCTTTCAGTTG 59.053 50.000 0.00 0.00 0.00 3.16
1420 1502 0.040067 GTCCGCTTGCTTTCAGTTGG 60.040 55.000 0.00 0.00 0.00 3.77
1421 1503 0.465460 TCCGCTTGCTTTCAGTTGGT 60.465 50.000 0.00 0.00 0.00 3.67
1422 1504 0.318107 CCGCTTGCTTTCAGTTGGTG 60.318 55.000 0.00 0.00 0.00 4.17
1423 1505 0.936297 CGCTTGCTTTCAGTTGGTGC 60.936 55.000 0.00 0.00 0.00 5.01
1424 1506 0.936297 GCTTGCTTTCAGTTGGTGCG 60.936 55.000 0.00 0.00 0.00 5.34
1425 1507 0.662619 CTTGCTTTCAGTTGGTGCGA 59.337 50.000 0.00 0.00 0.00 5.10
1443 1525 1.133025 CGATTGTTCAGAACCCATGGC 59.867 52.381 6.09 0.00 0.00 4.40
1451 1533 2.863484 AACCCATGGCCACCCTGA 60.863 61.111 8.16 0.00 0.00 3.86
1454 1536 2.765969 CCATGGCCACCCTGAAGT 59.234 61.111 8.16 0.00 0.00 3.01
1459 1541 1.377333 GGCCACCCTGAAGTAGTGC 60.377 63.158 0.00 0.00 0.00 4.40
1526 1608 2.170397 TCTGAAAGTGGAAGCACTGTCA 59.830 45.455 0.00 0.00 44.58 3.58
1539 1621 4.863491 AGCACTGTCACATCAAAATGTTC 58.137 39.130 0.00 0.00 43.74 3.18
1552 1634 7.647715 ACATCAAAATGTTCGTTTAAACAGAGG 59.352 33.333 18.07 2.18 43.74 3.69
1553 1635 6.500041 TCAAAATGTTCGTTTAAACAGAGGG 58.500 36.000 18.07 1.82 42.09 4.30
1603 1690 9.632807 CTTCTTATACTGTCTAGTATTGATGCC 57.367 37.037 5.39 0.00 45.57 4.40
1618 1705 1.401905 GATGCCTCGATTTGGTTGGTC 59.598 52.381 0.00 0.00 0.00 4.02
1626 1713 3.074412 CGATTTGGTTGGTCTAGCTTGT 58.926 45.455 0.00 0.00 0.00 3.16
1901 2030 9.574516 ACTTTTCTTGGTCTTGTAGTTGATTAT 57.425 29.630 0.00 0.00 0.00 1.28
1959 2088 3.197766 TGCAGAGGACATAAGGTTACAGG 59.802 47.826 0.00 0.00 0.00 4.00
2273 2402 7.595819 AAAGGATGATGTTTGGTTTAGTTCA 57.404 32.000 0.00 0.00 0.00 3.18
2457 2598 5.072741 AGCTCTGTTCATCAAGCCTTTTAA 58.927 37.500 0.00 0.00 33.76 1.52
2461 2602 7.386025 GCTCTGTTCATCAAGCCTTTTAATTTT 59.614 33.333 0.00 0.00 0.00 1.82
2462 2603 9.912634 CTCTGTTCATCAAGCCTTTTAATTTTA 57.087 29.630 0.00 0.00 0.00 1.52
2853 3001 4.607293 CTGTAAGTGCTATCCATGCCTA 57.393 45.455 0.00 0.00 0.00 3.93
3065 3213 6.037500 TGCAGTATCACTTCTATTGCATGTTC 59.962 38.462 0.00 0.00 37.04 3.18
3066 3214 6.037500 GCAGTATCACTTCTATTGCATGTTCA 59.962 38.462 0.00 0.00 33.46 3.18
3278 3426 8.832521 CAATTTGTACTATTAAATCGCCACCTA 58.167 33.333 0.00 0.00 0.00 3.08
3411 3559 4.080526 ACCGCCTACTTTAATTCAGATGGT 60.081 41.667 0.00 0.00 0.00 3.55
3544 3710 1.200948 GGCTAGGCTTCTTTTGCAGTG 59.799 52.381 9.46 0.00 0.00 3.66
3598 3790 3.276857 TCTCAGCTTTCTTGATCCATGC 58.723 45.455 0.00 0.00 0.00 4.06
3963 4155 6.260936 CCAGTGATTTTGGCTATCGATTAACT 59.739 38.462 1.71 0.00 0.00 2.24
4111 4303 0.320771 CTTGAGTGACTGAACCCCCG 60.321 60.000 0.00 0.00 0.00 5.73
4126 4318 1.278537 CCCCGGAACTAAGGGTGTTA 58.721 55.000 0.73 0.00 46.17 2.41
4427 4620 6.597672 TGTATGCTTGATAATGTCCGAACTTT 59.402 34.615 0.00 0.00 0.00 2.66
4493 4686 4.811557 CCCAGTTTCTAGCATACTAGCAAC 59.188 45.833 7.25 7.25 46.68 4.17
4708 4916 7.103641 ACCAATATACGGATATTCGAATTGCT 58.896 34.615 17.19 1.49 36.31 3.91
4721 4931 2.618709 CGAATTGCTTCTGGGGGAATAC 59.381 50.000 0.00 0.00 33.01 1.89
4722 4932 3.631250 GAATTGCTTCTGGGGGAATACA 58.369 45.455 0.00 0.00 33.01 2.29
4786 4996 3.265791 CACCTATTCCTTCTGACTGCAC 58.734 50.000 0.00 0.00 0.00 4.57
4819 5029 8.301002 GTTTTTATGCCAGGTAGTTAATTGACA 58.699 33.333 2.93 0.00 0.00 3.58
4934 5145 2.784347 GCCCTTGCTTGTTTCTCTACT 58.216 47.619 0.00 0.00 33.53 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.278182 AAGCACCCAACACGCAACAC 62.278 55.000 0.00 0.00 0.00 3.32
50 51 1.021202 TTGAGAAAGCACCCAACACG 58.979 50.000 0.00 0.00 0.00 4.49
97 102 9.849166 AGTGAAAATCGAAAAAGTAAGAAAACA 57.151 25.926 0.00 0.00 0.00 2.83
119 124 9.231297 CTCCAATACCTAAGAAAAATCAAGTGA 57.769 33.333 0.00 0.00 0.00 3.41
121 126 9.807921 TTCTCCAATACCTAAGAAAAATCAAGT 57.192 29.630 0.00 0.00 0.00 3.16
206 217 6.042638 TCATGGAAGAATCTTTTCGAGAGT 57.957 37.500 0.00 0.00 37.93 3.24
212 223 4.946157 TGCCTCTCATGGAAGAATCTTTTC 59.054 41.667 0.00 0.00 0.00 2.29
213 224 4.927049 TGCCTCTCATGGAAGAATCTTTT 58.073 39.130 0.00 0.00 0.00 2.27
218 229 6.451292 AATCTATGCCTCTCATGGAAGAAT 57.549 37.500 0.00 0.00 44.27 2.40
227 254 4.903649 TGAGGATCAAATCTATGCCTCTCA 59.096 41.667 0.00 0.00 45.97 3.27
250 277 4.560108 GCTGAAGCAAATTTGTGTCTCCAT 60.560 41.667 19.03 0.00 41.59 3.41
270 297 1.127582 GCACTACTTTGCTTCTCGCTG 59.872 52.381 0.00 0.00 39.59 5.18
271 298 1.433534 GCACTACTTTGCTTCTCGCT 58.566 50.000 0.00 0.00 39.59 4.93
272 299 0.444260 GGCACTACTTTGCTTCTCGC 59.556 55.000 0.00 0.00 42.56 5.03
273 300 1.996191 GAGGCACTACTTTGCTTCTCG 59.004 52.381 0.36 0.00 43.46 4.04
313 342 1.160137 CCTCTCGTGGAAGCCAAAAG 58.840 55.000 0.00 0.00 34.18 2.27
326 355 6.035650 TCGTGAAAGTAAATATTTGCCTCTCG 59.964 38.462 21.24 21.24 0.00 4.04
327 356 7.064728 ACTCGTGAAAGTAAATATTTGCCTCTC 59.935 37.037 11.05 8.78 0.00 3.20
335 364 8.258007 TCTCATGGACTCGTGAAAGTAAATATT 58.742 33.333 0.00 0.00 38.33 1.28
339 368 5.243060 TCTCTCATGGACTCGTGAAAGTAAA 59.757 40.000 0.00 0.00 38.33 2.01
346 375 2.360844 GTCTCTCTCATGGACTCGTGA 58.639 52.381 0.00 0.00 37.37 4.35
353 382 5.667539 AGAAAATTCGTCTCTCTCATGGA 57.332 39.130 0.00 0.00 0.00 3.41
354 383 6.105333 AGAAGAAAATTCGTCTCTCTCATGG 58.895 40.000 5.88 0.00 41.15 3.66
375 442 4.819630 AGCAAATTTGTACCTTCACGAGAA 59.180 37.500 19.03 0.00 0.00 2.87
376 443 4.385825 AGCAAATTTGTACCTTCACGAGA 58.614 39.130 19.03 0.00 0.00 4.04
377 444 4.749245 AGCAAATTTGTACCTTCACGAG 57.251 40.909 19.03 0.00 0.00 4.18
378 445 4.023536 GGAAGCAAATTTGTACCTTCACGA 60.024 41.667 25.37 0.00 34.96 4.35
379 446 4.226761 GGAAGCAAATTTGTACCTTCACG 58.773 43.478 25.37 1.43 34.96 4.35
380 447 4.226761 CGGAAGCAAATTTGTACCTTCAC 58.773 43.478 25.37 18.02 34.96 3.18
381 448 4.497473 CGGAAGCAAATTTGTACCTTCA 57.503 40.909 25.37 0.00 34.96 3.02
439 507 2.069273 CTCTCGTGGAAAAAGACGCAT 58.931 47.619 0.00 0.00 35.53 4.73
440 508 1.497991 CTCTCGTGGAAAAAGACGCA 58.502 50.000 0.00 0.00 35.53 5.24
441 509 0.790814 CCTCTCGTGGAAAAAGACGC 59.209 55.000 0.00 0.00 35.53 5.19
442 510 0.790814 GCCTCTCGTGGAAAAAGACG 59.209 55.000 0.00 0.00 36.91 4.18
443 511 1.531578 GTGCCTCTCGTGGAAAAAGAC 59.468 52.381 0.00 0.00 0.00 3.01
444 512 1.140052 TGTGCCTCTCGTGGAAAAAGA 59.860 47.619 0.00 0.00 0.00 2.52
445 513 1.593196 TGTGCCTCTCGTGGAAAAAG 58.407 50.000 0.00 0.00 0.00 2.27
476 544 3.065371 GGAAGAAAATATGTGCCTCCACG 59.935 47.826 0.00 0.00 45.04 4.94
499 567 1.225854 GCACAACGATGCTTCTCGC 60.226 57.895 0.00 0.00 42.62 5.03
507 575 3.558505 CTTTTTGAGAGGCACAACGATG 58.441 45.455 0.00 0.00 0.00 3.84
510 578 1.946768 TCCTTTTTGAGAGGCACAACG 59.053 47.619 0.00 0.00 34.17 4.10
511 579 4.385358 TTTCCTTTTTGAGAGGCACAAC 57.615 40.909 0.00 0.00 34.17 3.32
537 606 8.641499 TGCTTTTCGTGAAAGAAAAATATGTT 57.359 26.923 15.01 0.00 46.24 2.71
538 607 8.816640 ATGCTTTTCGTGAAAGAAAAATATGT 57.183 26.923 15.01 0.00 46.24 2.29
539 608 9.519905 CAATGCTTTTCGTGAAAGAAAAATATG 57.480 29.630 15.01 1.12 46.24 1.78
540 609 9.260002 ACAATGCTTTTCGTGAAAGAAAAATAT 57.740 25.926 15.01 1.83 46.24 1.28
542 611 7.538303 ACAATGCTTTTCGTGAAAGAAAAAT 57.462 28.000 15.01 0.00 46.24 1.82
568 637 0.598065 AAATTTGTGCCTCCACGAGC 59.402 50.000 0.00 0.00 45.04 5.03
571 640 0.314935 AGCAAATTTGTGCCTCCACG 59.685 50.000 19.03 0.00 46.14 4.94
572 641 2.407090 GAAGCAAATTTGTGCCTCCAC 58.593 47.619 19.03 0.45 46.14 4.02
579 648 4.550639 GCTTTTCGTGGAAGCAAATTTGTG 60.551 41.667 19.03 0.00 46.67 3.33
581 650 4.119334 GCTTTTCGTGGAAGCAAATTTG 57.881 40.909 14.03 14.03 46.67 2.32
594 663 7.923414 ATTTCCTAGAACTTATGCTTTTCGT 57.077 32.000 0.00 0.00 0.00 3.85
636 705 1.876416 CGGAAGAAAAAGTCGGAGCCA 60.876 52.381 0.00 0.00 0.00 4.75
722 792 1.529438 TCACCGTTTGATTTCTCGTGC 59.471 47.619 0.00 0.00 0.00 5.34
734 804 2.766828 TCCCAAACCATTTTCACCGTTT 59.233 40.909 0.00 0.00 0.00 3.60
738 808 4.967036 TCAAATCCCAAACCATTTTCACC 58.033 39.130 0.00 0.00 0.00 4.02
1381 1463 4.691216 GGACTCAGCGTTCTTAAACTTCAT 59.309 41.667 0.00 0.00 32.95 2.57
1390 1472 0.946221 CAAGCGGACTCAGCGTTCTT 60.946 55.000 0.00 0.00 40.04 2.52
1395 1477 2.233007 GAAAGCAAGCGGACTCAGCG 62.233 60.000 0.00 0.00 40.04 5.18
1415 1497 2.254546 TCTGAACAATCGCACCAACT 57.745 45.000 0.00 0.00 0.00 3.16
1417 1499 1.606668 GGTTCTGAACAATCGCACCAA 59.393 47.619 21.01 0.00 0.00 3.67
1418 1500 1.234821 GGTTCTGAACAATCGCACCA 58.765 50.000 21.01 0.00 0.00 4.17
1419 1501 0.521735 GGGTTCTGAACAATCGCACC 59.478 55.000 21.01 8.19 0.00 5.01
1420 1502 1.234821 TGGGTTCTGAACAATCGCAC 58.765 50.000 21.01 2.93 0.00 5.34
1421 1503 1.811965 CATGGGTTCTGAACAATCGCA 59.188 47.619 21.01 9.86 0.00 5.10
1422 1504 1.133025 CCATGGGTTCTGAACAATCGC 59.867 52.381 21.01 4.28 0.00 4.58
1423 1505 1.133025 GCCATGGGTTCTGAACAATCG 59.867 52.381 21.01 8.77 0.00 3.34
1424 1506 1.478105 GGCCATGGGTTCTGAACAATC 59.522 52.381 21.01 10.83 0.00 2.67
1425 1507 1.203162 TGGCCATGGGTTCTGAACAAT 60.203 47.619 21.01 11.57 0.00 2.71
1443 1525 0.674895 GCAGCACTACTTCAGGGTGG 60.675 60.000 0.00 0.00 0.00 4.61
1451 1533 6.989169 CCTCTAAATCATTAGCAGCACTACTT 59.011 38.462 0.00 0.00 38.73 2.24
1454 1536 6.239430 CCTCCTCTAAATCATTAGCAGCACTA 60.239 42.308 0.00 0.00 38.73 2.74
1459 1541 7.872113 AAAACCTCCTCTAAATCATTAGCAG 57.128 36.000 0.00 0.00 38.73 4.24
1494 1576 6.266558 GCTTCCACTTTCAGAGGATAGAGATA 59.733 42.308 0.00 0.00 34.94 1.98
1495 1577 5.070313 GCTTCCACTTTCAGAGGATAGAGAT 59.930 44.000 0.00 0.00 34.94 2.75
1496 1578 4.404073 GCTTCCACTTTCAGAGGATAGAGA 59.596 45.833 0.00 0.00 34.94 3.10
1497 1579 4.161189 TGCTTCCACTTTCAGAGGATAGAG 59.839 45.833 0.00 0.00 34.94 2.43
1498 1580 4.081420 GTGCTTCCACTTTCAGAGGATAGA 60.081 45.833 0.00 0.00 34.94 1.98
1499 1581 4.187694 GTGCTTCCACTTTCAGAGGATAG 58.812 47.826 0.00 0.00 34.94 2.08
1500 1582 4.207891 GTGCTTCCACTTTCAGAGGATA 57.792 45.455 0.00 0.00 34.94 2.59
1501 1583 3.064900 GTGCTTCCACTTTCAGAGGAT 57.935 47.619 0.00 0.00 34.94 3.24
1502 1584 2.550830 GTGCTTCCACTTTCAGAGGA 57.449 50.000 0.00 0.00 38.93 3.71
1521 1603 7.906611 TTAAACGAACATTTTGATGTGACAG 57.093 32.000 0.00 0.00 34.56 3.51
1526 1608 7.647715 CCTCTGTTTAAACGAACATTTTGATGT 59.352 33.333 13.45 0.00 38.71 3.06
1539 1621 2.031157 CCACTTGCCCTCTGTTTAAACG 60.031 50.000 13.45 8.52 0.00 3.60
1552 1634 4.379918 GCTTCTAAACAATCTCCACTTGCC 60.380 45.833 0.00 0.00 0.00 4.52
1553 1635 4.457257 AGCTTCTAAACAATCTCCACTTGC 59.543 41.667 0.00 0.00 0.00 4.01
1596 1678 1.818060 CCAACCAAATCGAGGCATCAA 59.182 47.619 0.00 0.00 0.00 2.57
1597 1679 1.271871 ACCAACCAAATCGAGGCATCA 60.272 47.619 0.00 0.00 0.00 3.07
1603 1690 3.252974 AGCTAGACCAACCAAATCGAG 57.747 47.619 0.00 0.00 0.00 4.04
1618 1705 4.445452 TCGGGTACTTACAACAAGCTAG 57.555 45.455 0.00 0.00 0.00 3.42
1626 1713 7.999450 AAAACCATTATTCGGGTACTTACAA 57.001 32.000 0.00 0.00 36.05 2.41
1703 1824 2.305928 CACCATTTCACCAACCAGACA 58.694 47.619 0.00 0.00 0.00 3.41
1812 1937 4.940046 ACAATGAGATAAGGTGAAGCACAG 59.060 41.667 0.00 0.00 35.86 3.66
1901 2030 0.687920 TAATGGTTGCCGTGGACTCA 59.312 50.000 0.00 0.00 0.00 3.41
1959 2088 2.550830 TGAAGAACCTCCTCAGCAAC 57.449 50.000 0.00 0.00 0.00 4.17
2273 2402 8.773033 AAAAGGCTTTCATGGTATCAATCTAT 57.227 30.769 13.76 0.00 0.00 1.98
2462 2603 9.661563 ATGCTGATTTACACAAAATGATCAAAT 57.338 25.926 0.00 0.00 37.93 2.32
2841 2989 5.471456 GGATTTTCTGTGTAGGCATGGATAG 59.529 44.000 0.00 0.00 0.00 2.08
2853 3001 5.511386 AATCTCCTCTGGATTTTCTGTGT 57.489 39.130 0.00 0.00 30.26 3.72
3377 3525 3.572632 AGTAGGCGGTCATCAGTAGTA 57.427 47.619 0.00 0.00 0.00 1.82
3464 3630 4.510167 AATCTACAATGTGGAAGAGGGG 57.490 45.455 3.02 0.00 0.00 4.79
3963 4155 2.171003 TCTTCGAAGCAGACATCTCCA 58.829 47.619 20.56 0.00 0.00 3.86
4493 4686 3.754850 TGATGATTTCTGTGAGTTGGCTG 59.245 43.478 0.00 0.00 0.00 4.85
4681 4889 7.064134 GCAATTCGAATATCCGTATATTGGTCA 59.936 37.037 11.83 0.00 38.21 4.02
4708 4916 2.171870 GGTCGATTGTATTCCCCCAGAA 59.828 50.000 0.00 0.00 39.32 3.02
4786 4996 1.396996 CCTGGCATAAAAACGAGTCCG 59.603 52.381 0.00 0.00 42.50 4.79
4922 5133 8.395633 GTTGCTCTTTTTACAGTAGAGAAACAA 58.604 33.333 13.92 8.34 46.75 2.83
4934 5145 9.278978 TCTGTATGTATTGTTGCTCTTTTTACA 57.721 29.630 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.