Multiple sequence alignment - TraesCS5B01G174700

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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 TraesCS5B01G174700 chr5B 100.000 5622 0 0 1 5622 321124776 321130397 0.000000e+00 10382
1 TraesCS5B01G174700 chr5B 92.067 416 29 2 1 413 634675789 634675375 2.920000e-162 582
2 TraesCS5B01G174700 chr5D 96.733 4469 129 14 795 5254 282845115 282849575 0.000000e+00 7428
3 TraesCS5B01G174700 chr5D 94.040 302 15 3 5254 5554 282850280 282850579 6.640000e-124 455
4 TraesCS5B01G174700 chr5D 86.423 383 44 4 419 794 534877550 534877169 4.050000e-111 412
5 TraesCS5B01G174700 chr5D 98.485 66 1 0 5555 5620 526139176 526139241 3.560000e-22 117
6 TraesCS5B01G174700 chr5A 96.691 4472 124 16 796 5254 375247931 375252391 0.000000e+00 7417
7 TraesCS5B01G174700 chr5A 92.208 308 18 6 5254 5559 375252975 375253278 1.120000e-116 431
8 TraesCS5B01G174700 chr5A 86.494 385 46 6 414 794 651807957 651808339 8.710000e-113 418
9 TraesCS5B01G174700 chr7B 92.326 417 27 3 1 413 628777971 628777556 6.270000e-164 588
10 TraesCS5B01G174700 chr7B 90.028 361 33 2 419 778 628777293 628776935 1.100000e-126 464
11 TraesCS5B01G174700 chr7B 98.462 65 1 0 5556 5620 508189385 508189449 1.280000e-21 115
12 TraesCS5B01G174700 chr7D 92.271 414 28 2 1 413 166264565 166264155 8.120000e-163 584
13 TraesCS5B01G174700 chr7D 88.620 413 40 4 1 413 53187830 53188235 3.910000e-136 496
14 TraesCS5B01G174700 chr7D 98.462 65 1 0 5555 5619 58788035 58787971 1.280000e-21 115
15 TraesCS5B01G174700 chr1B 92.647 408 27 2 6 413 27994601 27995005 8.120000e-163 584
16 TraesCS5B01G174700 chr1B 88.251 383 37 4 419 794 27995272 27995653 8.590000e-123 451
17 TraesCS5B01G174700 chr1D 89.855 414 38 2 1 413 375180578 375180988 3.860000e-146 529
18 TraesCS5B01G174700 chr1D 88.268 358 35 6 414 769 466134945 466134593 6.730000e-114 422
19 TraesCS5B01G174700 chr3D 89.831 413 38 1 1 413 167509772 167510180 1.390000e-145 527
20 TraesCS5B01G174700 chr3D 97.015 67 2 0 5553 5619 348973371 348973305 4.600000e-21 113
21 TraesCS5B01G174700 chr3D 94.521 73 4 0 5548 5620 582933392 582933464 4.600000e-21 113
22 TraesCS5B01G174700 chr2A 89.681 407 37 3 1 407 492922991 492923392 1.080000e-141 514
23 TraesCS5B01G174700 chr1A 89.435 407 38 2 1 406 455052382 455051980 5.030000e-140 508
24 TraesCS5B01G174700 chr2B 87.240 384 39 7 414 794 700203935 700204311 4.020000e-116 429
25 TraesCS5B01G174700 chr6D 86.856 388 40 7 414 794 411399160 411399543 1.870000e-114 424
26 TraesCS5B01G174700 chr2D 86.945 383 39 6 419 794 41779503 41779881 2.420000e-113 420
27 TraesCS5B01G174700 chr2D 86.340 388 41 8 414 794 491336881 491337263 4.050000e-111 412
28 TraesCS5B01G174700 chr2D 95.890 73 3 0 5548 5620 52051372 52051444 9.890000e-23 119
29 TraesCS5B01G174700 chr3A 98.507 67 1 0 5553 5619 467651386 467651320 9.890000e-23 119
30 TraesCS5B01G174700 chrUn 95.714 70 3 0 5549 5618 71312850 71312919 4.600000e-21 113
31 TraesCS5B01G174700 chr3B 96.970 66 2 0 5555 5620 119469107 119469042 1.660000e-20 111


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 TraesCS5B01G174700 chr5B 321124776 321130397 5621 False 10382.0 10382 100.0000 1 5622 1 chr5B.!!$F1 5621
1 TraesCS5B01G174700 chr5D 282845115 282850579 5464 False 3941.5 7428 95.3865 795 5554 2 chr5D.!!$F2 4759
2 TraesCS5B01G174700 chr5A 375247931 375253278 5347 False 3924.0 7417 94.4495 796 5559 2 chr5A.!!$F2 4763
3 TraesCS5B01G174700 chr7B 628776935 628777971 1036 True 526.0 588 91.1770 1 778 2 chr7B.!!$R1 777
4 TraesCS5B01G174700 chr1B 27994601 27995653 1052 False 517.5 584 90.4490 6 794 2 chr1B.!!$F1 788

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
928 1200 0.032815 TCGCTCCATTCGTGTTCACA 59.967 50.0 3.87 0.0 0.00 3.58 F
2037 2309 0.035056 ATGGGTAAGTGTCTGCCTGC 60.035 55.0 0.00 0.0 0.00 4.85 F
3136 3411 2.740981 GAGCATCAACCTCAGTCTGTTG 59.259 50.0 0.00 0.0 42.46 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 2818 1.515952 TGCACGCAGTTTGCACAAC 60.516 52.632 1.69 0.0 45.06 3.32 R
3138 3413 1.086696 GTATGAACGCATGGCAGTGT 58.913 50.000 0.00 0.0 35.94 3.55 R
5015 5299 2.775384 AGGAACACAAACTACAGGGACA 59.225 45.455 0.00 0.0 0.00 4.02 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
64 65 3.432186 GCCTTTTGCACGACCTGT 58.568 55.556 0.00 0.00 40.77 4.00
112 113 2.126071 CATGACGTTCCCTCGCGT 60.126 61.111 5.77 0.00 44.50 6.01
131 132 2.733593 GGAGGCGTCGTGTCACAC 60.734 66.667 0.00 0.00 0.00 3.82
148 149 2.202440 CGACGATGGAGAACGCGT 60.202 61.111 5.58 5.58 39.99 6.01
258 263 1.801913 CGAGCAAGACGTTCCCTCG 60.802 63.158 12.16 12.16 39.28 4.63
404 557 2.182030 GAGCAGGACGTTCCCTCG 59.818 66.667 0.00 0.00 37.19 4.63
417 570 4.554363 CCTCGCGCCGGAGTACAG 62.554 72.222 5.05 0.00 31.98 2.74
457 722 9.717892 GTTTCTTCCTTACTTAAAAGTTCACAG 57.282 33.333 0.00 0.00 40.37 3.66
465 730 9.813080 CTTACTTAAAAGTTCACAGTTGATAGC 57.187 33.333 0.00 0.00 40.37 2.97
476 741 3.510360 ACAGTTGATAGCGTTGGTAGTCT 59.490 43.478 0.00 0.00 0.00 3.24
500 765 4.385532 CCACCCGTAACTACCCCATAAATT 60.386 45.833 0.00 0.00 0.00 1.82
605 870 2.768698 TGTTTAATCGCACGGAAAGGA 58.231 42.857 0.00 0.00 0.00 3.36
667 932 0.179161 CGCACGAAACCACAAACCAA 60.179 50.000 0.00 0.00 0.00 3.67
680 945 4.762251 CCACAAACCAAAAAGGAAAAACCA 59.238 37.500 0.00 0.00 41.22 3.67
681 946 5.241728 CCACAAACCAAAAAGGAAAAACCAA 59.758 36.000 0.00 0.00 41.22 3.67
708 973 2.908073 CGCGCCAGCTGTTTTTCCT 61.908 57.895 13.81 0.00 42.32 3.36
713 978 1.490621 CCAGCTGTTTTTCCTTTGCG 58.509 50.000 13.81 0.00 0.00 4.85
746 1012 3.391631 CGACACTTTCACGCGCGA 61.392 61.111 39.36 13.15 0.00 5.87
779 1045 3.642901 GATCGTTAGGAGCGCTCAA 57.357 52.632 36.27 21.68 0.00 3.02
813 1085 2.846193 GCCTATTGCGGTCCTATTTCA 58.154 47.619 0.00 0.00 0.00 2.69
902 1174 0.385751 TTCGCGATCCCATCTGACTC 59.614 55.000 10.88 0.00 0.00 3.36
928 1200 0.032815 TCGCTCCATTCGTGTTCACA 59.967 50.000 3.87 0.00 0.00 3.58
1539 1811 2.035626 CCCACCTTCCGCATTGGT 59.964 61.111 0.00 0.00 39.52 3.67
2037 2309 0.035056 ATGGGTAAGTGTCTGCCTGC 60.035 55.000 0.00 0.00 0.00 4.85
2090 2362 7.613585 TGAATGTTGCATTACTTGGAATGAAT 58.386 30.769 9.55 0.00 38.01 2.57
2129 2401 2.975410 TGAATGCTCAAAGACTTGCG 57.025 45.000 0.00 0.00 32.14 4.85
2210 2482 6.065374 TGTTGGTTTGTTGTACTATCCACAT 58.935 36.000 0.00 0.00 0.00 3.21
2392 2665 7.094118 TGCTTAGTTTACTTTTGGACAGTTGTT 60.094 33.333 0.00 0.00 0.00 2.83
2407 2681 6.020971 ACAGTTGTTCTTTTTCCTCGTTTT 57.979 33.333 0.00 0.00 0.00 2.43
2544 2818 6.194796 TGCTAATTCCATTTCTTTTCTCCG 57.805 37.500 0.00 0.00 0.00 4.63
2695 2969 4.404715 TGACCCAGAGTAAGTAGCATTACC 59.595 45.833 3.66 0.00 36.49 2.85
2759 3033 6.542735 GGAAGTGTTTGAAGTCTTTAGTCCTT 59.457 38.462 0.00 0.00 0.00 3.36
2837 3112 5.366477 TCAGACATGGGCAATCTCTAACATA 59.634 40.000 0.00 0.00 0.00 2.29
3136 3411 2.740981 GAGCATCAACCTCAGTCTGTTG 59.259 50.000 0.00 0.00 42.46 3.33
3138 3413 2.550855 GCATCAACCTCAGTCTGTTGGA 60.551 50.000 17.28 4.10 41.64 3.53
3381 3656 6.145534 TGCTCTTTTATCGAAAGTGTGTACTG 59.854 38.462 0.00 0.00 44.17 2.74
3391 3666 6.203915 TCGAAAGTGTGTACTGTTGCATTAAT 59.796 34.615 0.00 0.00 37.19 1.40
3569 3844 4.823989 CCAGAGAACAGATTGTCTTTTGGT 59.176 41.667 0.00 0.00 36.33 3.67
3647 3925 7.172019 GCAAAGATTCAACTGATGGATTTTGTT 59.828 33.333 11.54 0.00 32.89 2.83
3846 4125 9.859427 CTCATTTTACATCATGTATTTTGTGGT 57.141 29.630 0.00 0.00 32.20 4.16
3852 4131 8.642432 TTACATCATGTATTTTGTGGTTTTCCA 58.358 29.630 0.00 0.00 39.07 3.53
3958 4237 3.117888 AGTCGCCATGATGGAGGTATTTT 60.118 43.478 17.22 0.00 40.96 1.82
4027 4306 3.829601 ACATTTTTAGGTTTGGCCATCGA 59.170 39.130 6.09 0.00 40.61 3.59
4178 4457 5.391312 AAGCCATGTCAATGTCTAAAACC 57.609 39.130 0.00 0.00 31.27 3.27
4217 4496 3.047857 TGATGGAGTATTGGCCTGATGA 58.952 45.455 3.32 0.00 0.00 2.92
4339 4618 1.275010 TGCTAGATGGTGCGTTCTTGA 59.725 47.619 0.00 0.00 0.00 3.02
4503 4784 4.336889 TCGACACTTGATGAAGGAAGTT 57.663 40.909 0.00 0.00 32.95 2.66
4582 4863 5.091552 ACTTGAAGTGGGGATCTTACACTA 58.908 41.667 14.63 2.24 44.08 2.74
4583 4864 5.546499 ACTTGAAGTGGGGATCTTACACTAA 59.454 40.000 14.63 8.16 44.08 2.24
4787 5070 5.416271 ACCAGTTAGTAACCCAGTATGTG 57.584 43.478 9.46 0.00 0.00 3.21
5070 5354 3.051081 TGTTTGGCCATAATGTTTGCC 57.949 42.857 6.09 0.00 44.27 4.52
5193 5477 6.721208 TGCCCTTTTCTTCATCTTCAATAAGT 59.279 34.615 0.00 0.00 34.13 2.24
5200 5484 9.650539 TTTCTTCATCTTCAATAAGTCTCTCTG 57.349 33.333 0.00 0.00 34.13 3.35
5218 5505 0.700564 TGATTCCTTGCCCTTGAGCT 59.299 50.000 0.00 0.00 0.00 4.09
5239 5526 0.032813 CCCATCATGGCCTCACCTTT 60.033 55.000 3.32 0.00 40.22 3.11
5243 5530 0.250234 TCATGGCCTCACCTTTCTCG 59.750 55.000 3.32 0.00 40.22 4.04
5259 6252 6.149807 ACCTTTCTCGTTTTTGTGTTGTAAGA 59.850 34.615 0.00 0.00 0.00 2.10
5273 6267 5.571357 GTGTTGTAAGAATAATTTGTGCCGG 59.429 40.000 0.00 0.00 0.00 6.13
5278 6272 8.057536 TGTAAGAATAATTTGTGCCGGTTTAT 57.942 30.769 1.90 0.00 0.00 1.40
5309 6303 1.996191 CTGTTCGCTTTCTACTCAGCC 59.004 52.381 0.00 0.00 31.82 4.85
5312 6306 0.532573 TCGCTTTCTACTCAGCCTGG 59.467 55.000 0.00 0.00 31.82 4.45
5366 6360 2.413601 TGGATGGGGATCCAACGATAA 58.586 47.619 15.23 0.00 46.90 1.75
5372 6366 3.257375 TGGGGATCCAACGATAATAGACG 59.743 47.826 15.23 0.00 40.73 4.18
5452 6446 8.422577 AGTTAGGAATGCCTATTTTGTTTCTT 57.577 30.769 0.00 0.00 45.96 2.52
5453 6447 8.523658 AGTTAGGAATGCCTATTTTGTTTCTTC 58.476 33.333 0.00 0.00 45.96 2.87
5508 6503 7.041721 TCAGCTCATCAACGAGTATTAACATT 58.958 34.615 0.00 0.00 35.33 2.71
5511 6506 6.292919 GCTCATCAACGAGTATTAACATTCCC 60.293 42.308 0.00 0.00 35.33 3.97
5512 6507 6.645306 TCATCAACGAGTATTAACATTCCCA 58.355 36.000 0.00 0.00 0.00 4.37
5513 6508 6.537301 TCATCAACGAGTATTAACATTCCCAC 59.463 38.462 0.00 0.00 0.00 4.61
5514 6509 6.045072 TCAACGAGTATTAACATTCCCACT 57.955 37.500 0.00 0.00 0.00 4.00
5515 6510 7.172868 TCAACGAGTATTAACATTCCCACTA 57.827 36.000 0.00 0.00 0.00 2.74
5516 6511 7.262772 TCAACGAGTATTAACATTCCCACTAG 58.737 38.462 0.00 0.00 0.00 2.57
5517 6512 6.786967 ACGAGTATTAACATTCCCACTAGT 57.213 37.500 0.00 0.00 0.00 2.57
5518 6513 6.570692 ACGAGTATTAACATTCCCACTAGTG 58.429 40.000 16.34 16.34 0.00 2.74
5519 6514 6.154021 ACGAGTATTAACATTCCCACTAGTGT 59.846 38.462 21.18 3.73 0.00 3.55
5559 6554 3.243301 CCTCATTTGCATGCCACATACTC 60.243 47.826 16.68 0.00 0.00 2.59
5560 6555 2.689471 TCATTTGCATGCCACATACTCC 59.311 45.455 16.68 0.00 0.00 3.85
5561 6556 1.473258 TTTGCATGCCACATACTCCC 58.527 50.000 16.68 0.00 0.00 4.30
5562 6557 0.625316 TTGCATGCCACATACTCCCT 59.375 50.000 16.68 0.00 0.00 4.20
5563 6558 0.181114 TGCATGCCACATACTCCCTC 59.819 55.000 16.68 0.00 0.00 4.30
5564 6559 0.536006 GCATGCCACATACTCCCTCC 60.536 60.000 6.36 0.00 0.00 4.30
5565 6560 0.250038 CATGCCACATACTCCCTCCG 60.250 60.000 0.00 0.00 0.00 4.63
5566 6561 0.691078 ATGCCACATACTCCCTCCGT 60.691 55.000 0.00 0.00 0.00 4.69
5567 6562 1.327690 TGCCACATACTCCCTCCGTC 61.328 60.000 0.00 0.00 0.00 4.79
5568 6563 1.043673 GCCACATACTCCCTCCGTCT 61.044 60.000 0.00 0.00 0.00 4.18
5569 6564 1.033574 CCACATACTCCCTCCGTCTC 58.966 60.000 0.00 0.00 0.00 3.36
5570 6565 1.685180 CCACATACTCCCTCCGTCTCA 60.685 57.143 0.00 0.00 0.00 3.27
5571 6566 1.678627 CACATACTCCCTCCGTCTCAG 59.321 57.143 0.00 0.00 0.00 3.35
5572 6567 1.564818 ACATACTCCCTCCGTCTCAGA 59.435 52.381 0.00 0.00 0.00 3.27
5573 6568 2.025226 ACATACTCCCTCCGTCTCAGAA 60.025 50.000 0.00 0.00 0.00 3.02
5574 6569 3.226777 CATACTCCCTCCGTCTCAGAAT 58.773 50.000 0.00 0.00 0.00 2.40
5575 6570 4.141228 ACATACTCCCTCCGTCTCAGAATA 60.141 45.833 0.00 0.00 0.00 1.75
5576 6571 3.383698 ACTCCCTCCGTCTCAGAATAA 57.616 47.619 0.00 0.00 0.00 1.40
5577 6572 3.292460 ACTCCCTCCGTCTCAGAATAAG 58.708 50.000 0.00 0.00 0.00 1.73
5578 6573 3.292460 CTCCCTCCGTCTCAGAATAAGT 58.708 50.000 0.00 0.00 0.00 2.24
5579 6574 3.024547 TCCCTCCGTCTCAGAATAAGTG 58.975 50.000 0.00 0.00 0.00 3.16
5580 6575 2.761208 CCCTCCGTCTCAGAATAAGTGT 59.239 50.000 0.00 0.00 0.00 3.55
5581 6576 3.181485 CCCTCCGTCTCAGAATAAGTGTC 60.181 52.174 0.00 0.00 0.00 3.67
5582 6577 3.697045 CCTCCGTCTCAGAATAAGTGTCT 59.303 47.826 0.00 0.00 0.00 3.41
5583 6578 4.201970 CCTCCGTCTCAGAATAAGTGTCTC 60.202 50.000 0.00 0.00 0.00 3.36
5584 6579 4.332828 TCCGTCTCAGAATAAGTGTCTCA 58.667 43.478 0.00 0.00 0.00 3.27
5585 6580 4.765339 TCCGTCTCAGAATAAGTGTCTCAA 59.235 41.667 0.00 0.00 0.00 3.02
5586 6581 4.859798 CCGTCTCAGAATAAGTGTCTCAAC 59.140 45.833 0.00 0.00 0.00 3.18
5587 6582 5.336055 CCGTCTCAGAATAAGTGTCTCAACT 60.336 44.000 0.00 0.00 0.00 3.16
5588 6583 6.153067 CGTCTCAGAATAAGTGTCTCAACTT 58.847 40.000 0.00 0.00 42.89 2.66
5589 6584 6.642950 CGTCTCAGAATAAGTGTCTCAACTTT 59.357 38.462 0.00 0.00 40.77 2.66
5590 6585 7.358765 CGTCTCAGAATAAGTGTCTCAACTTTG 60.359 40.741 0.00 0.00 40.77 2.77
5591 6586 7.439655 GTCTCAGAATAAGTGTCTCAACTTTGT 59.560 37.037 0.00 0.00 40.77 2.83
5592 6587 8.638873 TCTCAGAATAAGTGTCTCAACTTTGTA 58.361 33.333 0.00 0.00 40.77 2.41
5593 6588 8.589335 TCAGAATAAGTGTCTCAACTTTGTAC 57.411 34.615 0.00 0.00 40.77 2.90
5594 6589 8.421784 TCAGAATAAGTGTCTCAACTTTGTACT 58.578 33.333 0.00 0.00 40.77 2.73
5595 6590 9.692749 CAGAATAAGTGTCTCAACTTTGTACTA 57.307 33.333 0.00 0.00 40.77 1.82
5600 6595 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
5601 6596 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
5602 6597 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
5603 6598 9.310716 GTGTCTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 7.964011 CCTTCGGCTCGTTTAATTTTTATACAA 59.036 33.333 0.00 0.00 0.00 2.41
97 98 2.355363 CAACGCGAGGGAACGTCA 60.355 61.111 15.93 0.00 44.35 4.35
112 113 2.028484 GTGACACGACGCCTCCAA 59.972 61.111 0.00 0.00 0.00 3.53
131 132 2.202440 ACGCGTTCTCCATCGTCG 60.202 61.111 5.58 0.00 34.74 5.12
213 218 9.573133 CCTTCAGCTCGTTTAATTTTCATAAAT 57.427 29.630 0.00 0.00 35.49 1.40
234 239 0.944311 GAACGTCTTGCTCGCCTTCA 60.944 55.000 0.00 0.00 0.00 3.02
313 463 1.078778 TGTGTGTTGGTCGTGCAGT 60.079 52.632 0.00 0.00 0.00 4.40
365 518 3.571571 GCCTTCGGCTCGTTTAATTTTT 58.428 40.909 0.00 0.00 46.69 1.94
404 557 1.648504 ATTTAACTGTACTCCGGCGC 58.351 50.000 0.00 0.00 0.00 6.53
414 567 9.185680 AGGAAGAAACAACAACTATTTAACTGT 57.814 29.630 0.00 0.00 0.00 3.55
457 722 3.119245 TGGAGACTACCAACGCTATCAAC 60.119 47.826 0.00 0.00 36.96 3.18
476 741 0.043032 ATGGGGTAGTTACGGGTGGA 59.957 55.000 0.00 0.00 0.00 4.02
500 765 9.815306 TTCCCATTATATTTCCGGATAATGAAA 57.185 29.630 26.46 19.50 43.90 2.69
613 878 7.989416 TGACCCTCGAACTAACATAATTTTT 57.011 32.000 0.00 0.00 0.00 1.94
620 885 4.315803 CAGTTTGACCCTCGAACTAACAT 58.684 43.478 4.83 0.00 46.47 2.71
623 888 2.103432 TGCAGTTTGACCCTCGAACTAA 59.897 45.455 4.83 0.00 46.47 2.24
667 932 5.250200 GGTTGGTTCTTGGTTTTTCCTTTT 58.750 37.500 0.00 0.00 37.07 2.27
680 945 2.978010 CTGGCGCGGTTGGTTCTT 60.978 61.111 8.83 0.00 0.00 2.52
730 995 1.154836 CTTCGCGCGTGAAAGTGTC 60.155 57.895 32.05 0.26 0.00 3.67
778 1044 4.110482 CAATAGGCTAGTTAACGAGCGTT 58.890 43.478 31.24 23.48 44.07 4.84
779 1045 3.703420 CAATAGGCTAGTTAACGAGCGT 58.297 45.455 29.73 29.73 44.07 5.07
812 1084 3.636929 TTGTGTGGGGCGCCCTATG 62.637 63.158 42.70 0.00 45.70 2.23
813 1085 3.334891 TTGTGTGGGGCGCCCTAT 61.335 61.111 42.70 0.00 45.70 2.57
821 1093 3.258123 CCTGGTTATTTTCTTGTGTGGGG 59.742 47.826 0.00 0.00 0.00 4.96
850 1122 1.823899 CAGGCCGGGCAGGAATAAC 60.824 63.158 31.59 0.00 45.00 1.89
902 1174 1.391485 CACGAATGGAGCGACAAAGAG 59.609 52.381 0.00 0.00 0.00 2.85
928 1200 3.409605 GACGGGTGTGGTGGTGGTT 62.410 63.158 0.00 0.00 0.00 3.67
1200 1472 1.585006 GAGGAAGTCGACGAAGGCA 59.415 57.895 10.46 0.00 0.00 4.75
1539 1811 2.528127 TTCGTTGCCTCCCCCTCA 60.528 61.111 0.00 0.00 0.00 3.86
2037 2309 5.647589 ACATAGCATGCAGAAAGAAACATG 58.352 37.500 21.98 8.87 42.20 3.21
2090 2362 9.212641 GCATTCATTTAGTCTCTATGCATTCTA 57.787 33.333 3.54 0.00 37.45 2.10
2129 2401 7.223387 ACAAATTTCTCAATCTTGTTGCAACTC 59.777 33.333 28.61 5.59 0.00 3.01
2173 2445 4.638865 ACAAACCAACAAAGTAGGTCAGAC 59.361 41.667 0.00 0.00 33.74 3.51
2210 2482 7.811653 TCAACAGATAAATTGTGCATTCGTAA 58.188 30.769 0.00 0.00 0.00 3.18
2392 2665 6.824704 TGACTTTAGGAAAACGAGGAAAAAGA 59.175 34.615 0.00 0.00 0.00 2.52
2531 2805 4.647424 TTGCACAACGGAGAAAAGAAAT 57.353 36.364 0.00 0.00 0.00 2.17
2544 2818 1.515952 TGCACGCAGTTTGCACAAC 60.516 52.632 1.69 0.00 45.06 3.32
2674 2948 3.383825 CGGTAATGCTACTTACTCTGGGT 59.616 47.826 0.00 0.00 33.13 4.51
2837 3112 6.483640 GGATGAGAAGTAACAGTCAAAGTTGT 59.516 38.462 0.00 0.00 0.00 3.32
2984 3259 4.634883 AGATGATGTCTGCAATCACACTTC 59.365 41.667 1.70 0.00 35.31 3.01
3136 3411 1.308069 ATGAACGCATGGCAGTGTCC 61.308 55.000 0.00 0.00 32.31 4.02
3138 3413 1.086696 GTATGAACGCATGGCAGTGT 58.913 50.000 0.00 0.00 35.94 3.55
3351 3626 6.312426 CACACTTTCGATAAAAGAGCAGATCT 59.688 38.462 2.42 0.00 46.18 2.75
3381 3656 9.042008 TCTCCTAGTTTCGATAATTAATGCAAC 57.958 33.333 0.00 0.00 0.00 4.17
3391 3666 5.109903 GCTGCTTTCTCCTAGTTTCGATAA 58.890 41.667 0.00 0.00 0.00 1.75
3569 3844 2.268920 GGATGTCTCCAAGGCGCA 59.731 61.111 10.83 0.00 41.64 6.09
3647 3925 8.783093 CCAAATTCTGTGTTTACATAAGACTGA 58.217 33.333 0.00 0.00 35.97 3.41
3852 4131 9.614792 ACACACAAATAAGAACTCTAAAACTCT 57.385 29.630 0.00 0.00 0.00 3.24
4027 4306 9.013229 TGTAGATGTTGCTGATGTTTTCTATTT 57.987 29.630 0.00 0.00 0.00 1.40
4178 4457 4.142534 CCATCAGAGTTTGCAATGTAGGTG 60.143 45.833 0.00 0.00 0.00 4.00
4503 4784 9.204337 TCTTATATACCTTGTTACTTGTAGCCA 57.796 33.333 0.00 0.00 0.00 4.75
4544 4825 9.492973 CCCACTTCAAGTTCAAATGAATTAATT 57.507 29.630 0.00 0.00 35.20 1.40
5015 5299 2.775384 AGGAACACAAACTACAGGGACA 59.225 45.455 0.00 0.00 0.00 4.02
5070 5354 3.753272 CACAAGGTAGGACACATTTGGAG 59.247 47.826 0.00 0.00 31.21 3.86
5162 5446 4.681484 AGATGAAGAAAAGGGCAAGGAAT 58.319 39.130 0.00 0.00 0.00 3.01
5193 5477 2.238144 CAAGGGCAAGGAATCAGAGAGA 59.762 50.000 0.00 0.00 0.00 3.10
5200 5484 1.747924 GAAGCTCAAGGGCAAGGAATC 59.252 52.381 0.00 0.00 34.17 2.52
5218 5505 0.920763 AGGTGAGGCCATGATGGGAA 60.921 55.000 14.26 0.00 38.19 3.97
5259 6252 7.781056 AGAATGATAAACCGGCACAAATTATT 58.219 30.769 0.00 0.00 0.00 1.40
5264 6257 4.075682 TGAGAATGATAAACCGGCACAAA 58.924 39.130 0.00 0.00 0.00 2.83
5273 6267 4.569029 CGAACAGCGTGAGAATGATAAAC 58.431 43.478 0.00 0.00 34.64 2.01
5278 6272 2.445274 GCGAACAGCGTGAGAATGA 58.555 52.632 0.00 0.00 43.41 2.57
5309 6303 2.293677 CCGTACTGTATCTGCCTACCAG 59.706 54.545 0.00 0.00 43.17 4.00
5312 6306 3.379372 TGTTCCGTACTGTATCTGCCTAC 59.621 47.826 0.00 0.00 0.00 3.18
5328 6322 5.449041 CCATCCAGTGTATTCAAATGTTCCG 60.449 44.000 0.00 0.00 0.00 4.30
5366 6360 7.361799 GCCCAATTTTCTACTTGAAACGTCTAT 60.362 37.037 0.00 0.00 43.55 1.98
5372 6366 6.983890 TCAAAGCCCAATTTTCTACTTGAAAC 59.016 34.615 0.00 0.00 43.55 2.78
5383 6377 5.549742 TGAAGACATCAAAGCCCAATTTT 57.450 34.783 0.00 0.00 34.30 1.82
5452 6446 7.223584 TGTCTTCTTCCAAGTATTCACATTGA 58.776 34.615 0.00 0.00 0.00 2.57
5453 6447 7.173907 ACTGTCTTCTTCCAAGTATTCACATTG 59.826 37.037 0.00 0.00 0.00 2.82
5559 6554 2.761208 ACACTTATTCTGAGACGGAGGG 59.239 50.000 0.00 0.00 0.00 4.30
5560 6555 3.697045 AGACACTTATTCTGAGACGGAGG 59.303 47.826 0.00 0.00 0.00 4.30
5561 6556 4.396478 TGAGACACTTATTCTGAGACGGAG 59.604 45.833 0.00 0.00 0.00 4.63
5562 6557 4.332828 TGAGACACTTATTCTGAGACGGA 58.667 43.478 0.00 0.00 0.00 4.69
5563 6558 4.703645 TGAGACACTTATTCTGAGACGG 57.296 45.455 0.00 0.00 0.00 4.79
5564 6559 5.704888 AGTTGAGACACTTATTCTGAGACG 58.295 41.667 0.00 0.00 0.00 4.18
5565 6560 7.439655 ACAAAGTTGAGACACTTATTCTGAGAC 59.560 37.037 0.00 0.00 35.87 3.36
5566 6561 7.500992 ACAAAGTTGAGACACTTATTCTGAGA 58.499 34.615 0.00 0.00 35.87 3.27
5567 6562 7.721286 ACAAAGTTGAGACACTTATTCTGAG 57.279 36.000 0.00 0.00 35.87 3.35
5568 6563 8.421784 AGTACAAAGTTGAGACACTTATTCTGA 58.578 33.333 0.00 0.00 35.87 3.27
5569 6564 8.594881 AGTACAAAGTTGAGACACTTATTCTG 57.405 34.615 0.00 0.00 35.87 3.02
5574 6569 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
5575 6570 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
5576 6571 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
5577 6572 9.310716 ACTAAAGTTAGTACAAAGTTGAGACAC 57.689 33.333 1.81 0.00 41.92 3.67


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

AutoCloner maintained by Alex Coulton.