Multiple sequence alignment - TraesCS5B01G320100

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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 TraesCS5B01G320100 chr5B 100.000 5513 0 0 1 5513 505486520 505481008 0.000000e+00 10181.0
1 TraesCS5B01G320100 chr5B 87.131 474 47 11 930 1401 324259799 324260260 4.890000e-145 525.0
2 TraesCS5B01G320100 chr5B 80.874 183 23 11 4979 5160 504810519 504810348 3.460000e-27 134.0
3 TraesCS5B01G320100 chr5A 95.729 4355 145 16 530 4872 533024781 533020456 0.000000e+00 6974.0
4 TraesCS5B01G320100 chr5A 89.313 524 50 5 6 528 533025473 533024955 0.000000e+00 652.0
5 TraesCS5B01G320100 chr5A 90.404 396 25 5 4908 5294 533020460 533020069 4.930000e-140 508.0
6 TraesCS5B01G320100 chr5A 94.545 220 9 2 5294 5510 533020114 533019895 2.460000e-88 337.0
7 TraesCS5B01G320100 chr5A 100.000 54 0 0 5460 5513 533013646 533013593 3.510000e-17 100.0
8 TraesCS5B01G320100 chr5A 84.615 65 6 1 705 769 533024664 533024604 1.660000e-05 62.1
9 TraesCS5B01G320100 chr5D 97.436 3471 72 7 1828 5294 418073715 418070258 0.000000e+00 5901.0
10 TraesCS5B01G320100 chr5D 93.297 1283 62 13 552 1832 418075048 418073788 0.000000e+00 1871.0
11 TraesCS5B01G320100 chr5D 92.176 524 37 4 6 528 418075665 418075145 0.000000e+00 737.0
12 TraesCS5B01G320100 chr5D 91.071 224 13 4 5294 5511 418070303 418070081 4.180000e-76 296.0
13 TraesCS5B01G320100 chr5D 72.727 473 111 18 62 525 509959288 509958825 5.760000e-30 143.0
14 TraesCS5B01G320100 chr5D 88.372 86 8 2 5102 5186 417620433 417620349 9.770000e-18 102.0
15 TraesCS5B01G320100 chr6B 86.842 342 36 6 1004 1344 14588790 14588457 1.880000e-99 374.0
16 TraesCS5B01G320100 chr3B 74.722 360 80 10 66 420 20479513 20479866 3.440000e-32 150.0
17 TraesCS5B01G320100 chr4A 72.907 454 104 19 81 525 675140122 675139679 7.450000e-29 139.0
18 TraesCS5B01G320100 chr4A 72.907 454 104 19 81 525 675162102 675161659 7.450000e-29 139.0
19 TraesCS5B01G320100 chr1A 71.730 474 112 22 62 525 339494207 339494668 4.510000e-21 113.0


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 TraesCS5B01G320100 chr5B 505481008 505486520 5512 True 10181.00 10181 100.0000 1 5513 1 chr5B.!!$R2 5512
1 TraesCS5B01G320100 chr5A 533019895 533025473 5578 True 1706.62 6974 90.9212 6 5510 5 chr5A.!!$R2 5504
2 TraesCS5B01G320100 chr5D 418070081 418075665 5584 True 2201.25 5901 93.4950 6 5511 4 chr5D.!!$R3 5505

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
318 319 0.250727 CCAAGACTTCTTTCCCCGCA 60.251 55.000 0.00 0.00 33.11 5.69 F
1200 1446 0.752658 ACTTTCCAGGCCACTTTTGC 59.247 50.000 5.01 0.00 0.00 3.68 F
1611 1860 1.239968 GCTCTCTTGGTGCCAGGTTG 61.240 60.000 0.28 0.00 0.00 3.77 F
1619 1868 1.354031 TGGTGCCAGGTTGTATGTCAT 59.646 47.619 0.00 0.00 0.00 3.06 F
3059 3388 0.161024 GTGTGCTGCGTCGAAAGTAC 59.839 55.000 0.00 3.02 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 1453 0.109342 CCATGGCATAGGGAGTGGTC 59.891 60.000 0.00 0.00 29.57 4.02 R
2460 2786 0.698238 CCTGAACCATCCTTGGGTGA 59.302 55.000 0.74 0.00 45.49 4.02 R
3001 3330 1.285078 TCTGCAGTAGCCTCTCCTACA 59.715 52.381 14.67 0.00 40.07 2.74 R
3109 3438 4.330074 CAGGTGCACTGTAAAGTAGCATAC 59.670 45.833 17.98 8.99 42.42 2.39 R
4949 5321 0.179111 TCGAATACTCCCAAGCAGCG 60.179 55.000 0.00 0.00 0.00 5.18 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
36 37 1.536766 CTTTCAAGAATGCGAGCACCA 59.463 47.619 0.00 0.00 0.00 4.17
126 127 4.614967 ATCCTTGAATCCCAAACCATCT 57.385 40.909 0.00 0.00 33.76 2.90
127 128 3.700538 TCCTTGAATCCCAAACCATCTG 58.299 45.455 0.00 0.00 33.76 2.90
130 131 3.805066 TGAATCCCAAACCATCTGTCA 57.195 42.857 0.00 0.00 0.00 3.58
152 153 4.396166 CACTTTGGGTTGTGTCATATCCTC 59.604 45.833 0.00 0.00 0.00 3.71
200 201 2.504175 GGCCATCTTTACAGTCCTACCA 59.496 50.000 0.00 0.00 0.00 3.25
259 260 1.556911 CCCTAGGAAGCTTGAAGCAGA 59.443 52.381 20.45 0.00 45.56 4.26
292 293 3.106552 GCACCACTTGCGACACAA 58.893 55.556 0.00 0.00 42.79 3.33
295 296 1.757574 CACCACTTGCGACACAAATG 58.242 50.000 0.00 0.00 37.96 2.32
301 302 2.946329 ACTTGCGACACAAATGTAACCA 59.054 40.909 0.00 0.00 39.95 3.67
308 309 5.440685 CGACACAAATGTAACCAAGACTTC 58.559 41.667 0.00 0.00 39.95 3.01
315 316 4.094830 TGTAACCAAGACTTCTTTCCCC 57.905 45.455 0.00 0.00 33.11 4.81
316 317 2.271944 AACCAAGACTTCTTTCCCCG 57.728 50.000 0.00 0.00 33.11 5.73
317 318 0.250770 ACCAAGACTTCTTTCCCCGC 60.251 55.000 0.00 0.00 33.11 6.13
318 319 0.250727 CCAAGACTTCTTTCCCCGCA 60.251 55.000 0.00 0.00 33.11 5.69
319 320 1.160137 CAAGACTTCTTTCCCCGCAG 58.840 55.000 0.00 0.00 33.11 5.18
320 321 0.765510 AAGACTTCTTTCCCCGCAGT 59.234 50.000 0.00 0.00 30.82 4.40
322 323 0.955919 GACTTCTTTCCCCGCAGTGG 60.956 60.000 0.00 0.00 37.55 4.00
369 371 5.499139 TGAATTTGCTCCATAAACGATCC 57.501 39.130 0.00 0.00 0.00 3.36
372 374 6.152661 TGAATTTGCTCCATAAACGATCCTTT 59.847 34.615 0.00 0.00 0.00 3.11
374 376 7.823745 ATTTGCTCCATAAACGATCCTTTAT 57.176 32.000 4.44 4.44 0.00 1.40
422 424 2.118679 TCCCACATCCGATGTCATTCT 58.881 47.619 11.24 0.00 42.70 2.40
446 448 8.236586 TCTCAAATATTTCTCATTCGGTGTTTG 58.763 33.333 0.00 0.00 0.00 2.93
462 464 2.510382 TGTTTGGTTGGGTACTTGGAGA 59.490 45.455 0.00 0.00 0.00 3.71
463 465 2.882761 GTTTGGTTGGGTACTTGGAGAC 59.117 50.000 0.00 0.00 0.00 3.36
515 517 2.278332 ACCCCTTTGCTGAAGAAGAC 57.722 50.000 2.50 0.00 37.57 3.01
528 693 2.115343 AGAAGACGGAAGATTTGCCC 57.885 50.000 0.00 0.00 0.00 5.36
558 732 5.204833 CCCGTTGCTTGACAATAAATATCG 58.795 41.667 0.00 0.00 41.27 2.92
559 797 5.204833 CCGTTGCTTGACAATAAATATCGG 58.795 41.667 0.00 0.00 41.27 4.18
592 831 1.321474 CTCATTTGCACCCACACTGT 58.679 50.000 0.00 0.00 0.00 3.55
668 907 2.455557 CCATCAATAAGGCACCAACCA 58.544 47.619 0.00 0.00 0.00 3.67
702 941 1.713830 GTGGGCTTCGATTGCGTAC 59.286 57.895 5.11 3.61 38.98 3.67
782 1021 1.400530 GGCCCAGATACCGCAGTACT 61.401 60.000 0.00 0.00 0.00 2.73
783 1022 1.325355 GCCCAGATACCGCAGTACTA 58.675 55.000 0.00 0.00 0.00 1.82
786 1025 1.612463 CCAGATACCGCAGTACTACCC 59.388 57.143 0.00 0.00 0.00 3.69
822 1061 2.395654 GATACGCGATCCTTCCTGAAC 58.604 52.381 15.93 0.00 0.00 3.18
829 1068 2.472029 GATCCTTCCTGAACTCCTCCA 58.528 52.381 0.00 0.00 0.00 3.86
861 1100 4.642488 TACCCCACGCCACTCCCA 62.642 66.667 0.00 0.00 0.00 4.37
1200 1446 0.752658 ACTTTCCAGGCCACTTTTGC 59.247 50.000 5.01 0.00 0.00 3.68
1207 1453 2.354259 CAGGCCACTTTTGCTAGAGAG 58.646 52.381 5.01 0.00 0.00 3.20
1214 1462 4.241681 CACTTTTGCTAGAGAGACCACTC 58.758 47.826 0.00 0.00 42.90 3.51
1278 1526 2.345760 GGGTCCCGTTGCGTCTAGA 61.346 63.158 0.00 0.00 0.00 2.43
1321 1569 3.423154 CTGGGCCGCGAGTTTGAC 61.423 66.667 8.23 0.00 0.00 3.18
1387 1636 3.340034 TCCGCCGTGTAGATTTGATTTT 58.660 40.909 0.00 0.00 0.00 1.82
1412 1661 4.702131 GTGGTTCAGGATTGTTATTCAGCT 59.298 41.667 0.00 0.00 0.00 4.24
1415 1664 6.767902 TGGTTCAGGATTGTTATTCAGCTATC 59.232 38.462 0.00 0.00 0.00 2.08
1577 1826 6.862608 CGTTCTGATTCAAGAGATCTGGATAG 59.137 42.308 0.00 0.00 0.00 2.08
1578 1827 7.469870 CGTTCTGATTCAAGAGATCTGGATAGT 60.470 40.741 0.00 0.00 0.00 2.12
1579 1828 7.287512 TCTGATTCAAGAGATCTGGATAGTG 57.712 40.000 0.00 0.00 0.00 2.74
1582 1831 8.539117 TGATTCAAGAGATCTGGATAGTGTTA 57.461 34.615 0.00 0.00 0.00 2.41
1611 1860 1.239968 GCTCTCTTGGTGCCAGGTTG 61.240 60.000 0.28 0.00 0.00 3.77
1619 1868 1.354031 TGGTGCCAGGTTGTATGTCAT 59.646 47.619 0.00 0.00 0.00 3.06
1697 1946 7.865889 TGGCATAGTAGTAGTGATAACAAATCG 59.134 37.037 0.00 0.00 0.00 3.34
1764 2013 7.814264 AAGGATAAGATTGTCTTAAGCATGG 57.186 36.000 0.00 0.00 41.72 3.66
1797 2046 7.702348 GTCTTTTGCTTTATCATCGGCTAAAAT 59.298 33.333 0.00 0.00 31.73 1.82
2117 2443 6.390721 GTCAGAACATCTTGCAGTTAGTAGA 58.609 40.000 0.00 0.00 0.00 2.59
2127 2453 4.023980 TGCAGTTAGTAGAGTACATGCCT 58.976 43.478 0.00 0.00 0.00 4.75
2289 2615 6.884836 TCTTCAGGTAATCGATGCTATAGCTA 59.115 38.462 24.61 12.11 42.66 3.32
2359 2685 4.353788 TCATCCCTCTCCTTCTTGGAAAAA 59.646 41.667 0.00 0.00 45.63 1.94
2626 2952 9.240734 CTCGAAGGGTAAGTAACTGGTATATAT 57.759 37.037 0.00 0.00 0.00 0.86
2627 2953 9.017509 TCGAAGGGTAAGTAACTGGTATATATG 57.982 37.037 0.00 0.00 0.00 1.78
2628 2954 8.800332 CGAAGGGTAAGTAACTGGTATATATGT 58.200 37.037 0.00 0.00 0.00 2.29
3059 3388 0.161024 GTGTGCTGCGTCGAAAGTAC 59.839 55.000 0.00 3.02 0.00 2.73
3073 3402 7.254017 GCGTCGAAAGTACTATTGCTTATTTCT 60.254 37.037 0.00 0.00 0.00 2.52
3074 3403 8.592998 CGTCGAAAGTACTATTGCTTATTTCTT 58.407 33.333 0.00 0.00 0.00 2.52
3109 3438 4.884164 ACCTTGTTCCTCTCTTTTCACAAG 59.116 41.667 0.00 0.00 40.45 3.16
3386 3715 0.533032 GGAAGTTCCCGAGGAGTGAG 59.467 60.000 11.17 0.00 31.21 3.51
3479 3808 5.711506 TGTAAACTCAACCATCATGAATGCT 59.288 36.000 0.00 0.00 33.71 3.79
3847 4176 1.171308 CCATGCTGAACCACTTGAGG 58.829 55.000 0.00 0.00 0.00 3.86
4123 4452 7.398024 AGCAGTGGAAGAACAAAGATATTACT 58.602 34.615 0.00 0.00 0.00 2.24
4160 4489 3.772387 TGGCAAACCATGGTGAGATTAA 58.228 40.909 20.60 0.00 42.67 1.40
4166 4495 6.751888 GCAAACCATGGTGAGATTAATAACAC 59.248 38.462 20.60 12.99 0.00 3.32
4194 4523 9.334947 ACTGTAGGATTTCATATCATTGTTCAG 57.665 33.333 0.00 0.00 0.00 3.02
4221 4550 8.371571 TGCATCATATCTCACATTATCCTACT 57.628 34.615 0.00 0.00 0.00 2.57
4232 4561 9.442047 CTCACATTATCCTACTGTTTTCTTCTT 57.558 33.333 0.00 0.00 0.00 2.52
4263 4592 2.175715 AGACAGGGTTCTTTGGAAGCTT 59.824 45.455 0.00 0.00 45.85 3.74
4317 4646 2.358737 CTGACGCACCCCCTTGAC 60.359 66.667 0.00 0.00 0.00 3.18
4339 4668 0.548031 ATCGTGGCATGTCCTTGGAT 59.452 50.000 6.60 0.00 35.26 3.41
4359 4688 5.371176 TGGATTAGGATACAACCCAAGCATA 59.629 40.000 0.00 0.00 41.41 3.14
4368 4697 1.592669 CCCAAGCATAGACCGCTCG 60.593 63.158 0.00 0.00 39.29 5.03
4527 4856 6.095432 AGTGAGTAGATGTGATATGAAGCC 57.905 41.667 0.00 0.00 0.00 4.35
4530 4859 2.175878 AGATGTGATATGAAGCCGCC 57.824 50.000 0.00 0.00 0.00 6.13
4658 4987 2.417787 GCACCCTGGAAATTTCTGATGC 60.418 50.000 17.42 15.08 0.00 3.91
4789 5118 1.394618 GTGCCTGTGGTTGGTGTTAA 58.605 50.000 0.00 0.00 0.00 2.01
4802 5131 5.009210 GGTTGGTGTTAATGTGTTGCTTAGA 59.991 40.000 0.00 0.00 0.00 2.10
4831 5160 8.484214 ACTATAGCAGAATTTCTGGAGTGATA 57.516 34.615 24.09 5.91 44.43 2.15
4872 5244 2.845363 TCTTGCTGTTGCTCAGATGA 57.155 45.000 12.29 5.14 46.27 2.92
4873 5245 3.345508 TCTTGCTGTTGCTCAGATGAT 57.654 42.857 12.29 0.00 46.27 2.45
4874 5246 3.682696 TCTTGCTGTTGCTCAGATGATT 58.317 40.909 12.29 0.00 46.27 2.57
4875 5247 4.077108 TCTTGCTGTTGCTCAGATGATTT 58.923 39.130 12.29 0.00 46.27 2.17
4876 5248 5.247862 TCTTGCTGTTGCTCAGATGATTTA 58.752 37.500 12.29 0.00 46.27 1.40
4877 5249 5.706833 TCTTGCTGTTGCTCAGATGATTTAA 59.293 36.000 12.29 0.00 46.27 1.52
4878 5250 5.556355 TGCTGTTGCTCAGATGATTTAAG 57.444 39.130 12.29 0.00 46.27 1.85
4879 5251 5.005740 TGCTGTTGCTCAGATGATTTAAGT 58.994 37.500 12.29 0.00 46.27 2.24
4880 5252 5.106436 TGCTGTTGCTCAGATGATTTAAGTG 60.106 40.000 12.29 0.00 46.27 3.16
4881 5253 5.675575 GCTGTTGCTCAGATGATTTAAGTGG 60.676 44.000 12.29 0.00 46.27 4.00
4882 5254 5.559770 TGTTGCTCAGATGATTTAAGTGGA 58.440 37.500 0.00 0.00 0.00 4.02
4883 5255 6.003326 TGTTGCTCAGATGATTTAAGTGGAA 58.997 36.000 0.00 0.00 0.00 3.53
4884 5256 6.660521 TGTTGCTCAGATGATTTAAGTGGAAT 59.339 34.615 0.00 0.00 0.00 3.01
4885 5257 7.177216 TGTTGCTCAGATGATTTAAGTGGAATT 59.823 33.333 0.00 0.00 0.00 2.17
4886 5258 7.325660 TGCTCAGATGATTTAAGTGGAATTC 57.674 36.000 0.00 0.00 0.00 2.17
4887 5259 6.885918 TGCTCAGATGATTTAAGTGGAATTCA 59.114 34.615 7.93 0.00 0.00 2.57
4888 5260 7.066645 TGCTCAGATGATTTAAGTGGAATTCAG 59.933 37.037 7.93 0.00 0.00 3.02
4889 5261 7.281774 GCTCAGATGATTTAAGTGGAATTCAGA 59.718 37.037 7.93 0.00 0.00 3.27
4890 5262 9.170734 CTCAGATGATTTAAGTGGAATTCAGAA 57.829 33.333 7.93 0.00 0.00 3.02
4891 5263 9.690913 TCAGATGATTTAAGTGGAATTCAGAAT 57.309 29.630 7.93 0.00 0.00 2.40
4892 5264 9.947669 CAGATGATTTAAGTGGAATTCAGAATC 57.052 33.333 7.93 7.51 0.00 2.52
4893 5265 9.690913 AGATGATTTAAGTGGAATTCAGAATCA 57.309 29.630 7.93 12.05 0.00 2.57
4911 5283 9.091784 TCAGAATCAAAATTATGAGAGAAGACG 57.908 33.333 0.00 0.00 38.00 4.18
4917 5289 7.441157 TCAAAATTATGAGAGAAGACGTGTTGT 59.559 33.333 1.19 0.00 0.00 3.32
4949 5321 8.652810 ATTGTAAGAATTGCATTATCTTTGCC 57.347 30.769 12.57 4.93 41.29 4.52
4951 5323 3.709987 AGAATTGCATTATCTTTGCCGC 58.290 40.909 0.00 0.00 39.39 6.53
5079 5451 3.305608 CCACTGGTTTCTGCCTTTGATTC 60.306 47.826 0.00 0.00 0.00 2.52
5097 5469 1.352083 TCTAGTTTGTGCAGGCCTCT 58.648 50.000 0.00 0.00 0.00 3.69
5176 5549 1.317613 AACGTTCTTGCATTGCCTGA 58.682 45.000 6.12 1.37 0.00 3.86
5242 5624 2.671963 GAACAACCTGGGCGTCCC 60.672 66.667 2.12 5.67 45.71 4.46
5293 5675 4.247380 CATGGCCGGCTCCTCCTC 62.247 72.222 28.56 8.18 0.00 3.71
5299 5681 4.504916 CGGCTCCTCCTCGTGCTG 62.505 72.222 0.00 0.00 0.00 4.41
5300 5682 4.154347 GGCTCCTCCTCGTGCTGG 62.154 72.222 0.00 0.00 0.00 4.85
5301 5683 4.828925 GCTCCTCCTCGTGCTGGC 62.829 72.222 0.00 0.00 0.00 4.85
5302 5684 3.073735 CTCCTCCTCGTGCTGGCT 61.074 66.667 0.00 0.00 0.00 4.75
5303 5685 3.368190 CTCCTCCTCGTGCTGGCTG 62.368 68.421 0.00 0.00 0.00 4.85
5305 5687 4.079850 CTCCTCGTGCTGGCTGCT 62.080 66.667 17.45 0.00 43.37 4.24
5306 5688 4.074526 TCCTCGTGCTGGCTGCTC 62.075 66.667 17.45 12.67 43.37 4.26
5311 5693 4.724602 GTGCTGGCTGCTCGACGA 62.725 66.667 17.45 0.00 43.37 4.20
5312 5694 4.426112 TGCTGGCTGCTCGACGAG 62.426 66.667 20.56 20.56 43.37 4.18
5321 5703 3.169198 CTCGACGAGCTTTTGGCC 58.831 61.111 12.67 0.00 43.05 5.36
5322 5704 1.667830 CTCGACGAGCTTTTGGCCA 60.668 57.895 12.67 0.00 43.05 5.36
5323 5705 1.003839 TCGACGAGCTTTTGGCCAT 60.004 52.632 6.09 0.00 43.05 4.40
5324 5706 1.135315 CGACGAGCTTTTGGCCATG 59.865 57.895 6.09 0.65 43.05 3.66
5325 5707 1.508088 GACGAGCTTTTGGCCATGG 59.492 57.895 6.09 7.63 43.05 3.66
5326 5708 2.182537 CGAGCTTTTGGCCATGGC 59.817 61.111 29.47 29.47 43.05 4.40
5340 5722 3.642741 ATGGCCGGTTCCTCCTCCT 62.643 63.158 1.90 0.00 0.00 3.69
5345 5727 2.677848 GGTTCCTCCTCCTTGCCC 59.322 66.667 0.00 0.00 0.00 5.36
5378 5760 2.780924 TTCCCCAAGCCCACACCT 60.781 61.111 0.00 0.00 0.00 4.00
5391 5773 0.817634 CACACCTTTCCTCAACGGCA 60.818 55.000 0.00 0.00 0.00 5.69
5412 5794 0.535335 AATCGGGTGAGCGTACATGT 59.465 50.000 2.69 2.69 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.730680 GCATTCTTGAAAGTGTCTAATTCCTAA 58.269 33.333 0.00 0.00 0.00 2.69
3 4 7.064609 CGCATTCTTGAAAGTGTCTAATTCCTA 59.935 37.037 0.00 0.00 0.00 2.94
4 5 6.128172 CGCATTCTTGAAAGTGTCTAATTCCT 60.128 38.462 0.00 0.00 0.00 3.36
9 10 4.152402 GCTCGCATTCTTGAAAGTGTCTAA 59.848 41.667 0.30 0.00 0.00 2.10
36 37 2.258109 GTCCAACTACCTGAGTCCCTT 58.742 52.381 0.00 0.00 37.44 3.95
126 127 2.498644 TGACACAACCCAAAGTGACA 57.501 45.000 0.00 0.00 39.03 3.58
127 128 4.156008 GGATATGACACAACCCAAAGTGAC 59.844 45.833 0.00 0.00 39.03 3.67
130 131 4.567747 GGAGGATATGACACAACCCAAAGT 60.568 45.833 0.00 0.00 0.00 2.66
152 153 0.394899 GCCAATCTGGGTCTCTTGGG 60.395 60.000 0.00 0.00 38.84 4.12
200 201 9.574516 ACTTAAACATGTTGATAAGGAAACTCT 57.425 29.630 24.08 7.62 42.68 3.24
259 260 1.963515 GGTGCCAGTCTTTTCCATGTT 59.036 47.619 0.00 0.00 0.00 2.71
287 288 7.404671 AAAGAAGTCTTGGTTACATTTGTGT 57.595 32.000 0.00 0.00 36.12 3.72
292 293 5.077564 GGGGAAAGAAGTCTTGGTTACATT 58.922 41.667 0.00 0.00 36.12 2.71
295 296 3.072211 CGGGGAAAGAAGTCTTGGTTAC 58.928 50.000 0.00 0.00 36.12 2.50
301 302 0.765510 ACTGCGGGGAAAGAAGTCTT 59.234 50.000 0.00 0.00 37.91 3.01
422 424 7.040062 ACCAAACACCGAATGAGAAATATTTGA 60.040 33.333 5.17 0.00 0.00 2.69
439 441 1.684450 CCAAGTACCCAACCAAACACC 59.316 52.381 0.00 0.00 0.00 4.16
446 448 2.501261 GTTGTCTCCAAGTACCCAACC 58.499 52.381 0.00 0.00 0.00 3.77
462 464 3.476552 TCGAGCTGAAATCAAAGGTTGT 58.523 40.909 0.00 0.00 0.00 3.32
463 465 4.488126 TTCGAGCTGAAATCAAAGGTTG 57.512 40.909 0.00 0.00 32.37 3.77
515 517 1.506262 CAACGGGGCAAATCTTCCG 59.494 57.895 0.00 0.00 46.95 4.30
528 693 4.341502 CAAGCAACGGGGCAACGG 62.342 66.667 5.83 0.00 38.39 4.44
540 714 4.036262 GTGCCCGATATTTATTGTCAAGCA 59.964 41.667 0.00 0.00 0.00 3.91
558 732 4.416738 GAGGTCAGCCAGGTGCCC 62.417 72.222 6.67 0.00 42.71 5.36
559 797 2.490270 AATGAGGTCAGCCAGGTGCC 62.490 60.000 0.00 0.00 42.71 5.01
568 806 0.883833 GTGGGTGCAAATGAGGTCAG 59.116 55.000 0.00 0.00 0.00 3.51
782 1021 1.816183 CGCTTTGGTTTGGTCTGGGTA 60.816 52.381 0.00 0.00 0.00 3.69
783 1022 1.106944 CGCTTTGGTTTGGTCTGGGT 61.107 55.000 0.00 0.00 0.00 4.51
786 1025 2.159707 CGTATCGCTTTGGTTTGGTCTG 60.160 50.000 0.00 0.00 0.00 3.51
813 1052 2.363683 GCAATGGAGGAGTTCAGGAAG 58.636 52.381 0.00 0.00 0.00 3.46
822 1061 1.019673 CACGAATGGCAATGGAGGAG 58.980 55.000 0.00 0.00 0.00 3.69
897 1136 3.491652 GTGCGCTCGCCTCCTTTC 61.492 66.667 9.73 0.00 41.09 2.62
1184 1430 1.423541 TCTAGCAAAAGTGGCCTGGAA 59.576 47.619 3.32 0.00 0.00 3.53
1185 1431 1.003580 CTCTAGCAAAAGTGGCCTGGA 59.996 52.381 3.32 0.00 0.00 3.86
1207 1453 0.109342 CCATGGCATAGGGAGTGGTC 59.891 60.000 0.00 0.00 29.57 4.02
1214 1462 2.276732 ACGAAATCCATGGCATAGGG 57.723 50.000 6.96 0.00 0.00 3.53
1278 1526 2.114670 CAAGCGCGGATGGACCAAT 61.115 57.895 8.83 0.00 38.90 3.16
1365 1614 2.225068 ATCAAATCTACACGGCGGAG 57.775 50.000 13.24 5.87 0.00 4.63
1387 1636 5.880332 GCTGAATAACAATCCTGAACCACTA 59.120 40.000 0.00 0.00 0.00 2.74
1412 1661 1.557371 TGAGGCCAAACCACATCGATA 59.443 47.619 5.01 0.00 43.14 2.92
1415 1664 1.926511 GCTGAGGCCAAACCACATCG 61.927 60.000 5.01 0.00 43.14 3.84
1543 1792 1.069978 TGAATCAGAACGTCCACTGCA 59.930 47.619 10.94 0.00 34.57 4.41
1577 1826 5.335191 CCAAGAGAGCAAAACAGGATAACAC 60.335 44.000 0.00 0.00 0.00 3.32
1578 1827 4.761739 CCAAGAGAGCAAAACAGGATAACA 59.238 41.667 0.00 0.00 0.00 2.41
1579 1828 4.762251 ACCAAGAGAGCAAAACAGGATAAC 59.238 41.667 0.00 0.00 0.00 1.89
1582 1831 3.152341 CACCAAGAGAGCAAAACAGGAT 58.848 45.455 0.00 0.00 0.00 3.24
1611 1860 5.357257 ACATCCAACCTACGAATGACATAC 58.643 41.667 0.00 0.00 0.00 2.39
1619 1868 2.769663 AGCCATACATCCAACCTACGAA 59.230 45.455 0.00 0.00 0.00 3.85
1697 1946 5.701290 AGTTTGCACAGATAAGTGTAGGTTC 59.299 40.000 0.00 0.00 41.52 3.62
1764 2013 4.783242 TGATAAAGCAAAAGACAACTCGC 58.217 39.130 0.00 0.00 0.00 5.03
1814 2063 9.211485 GTTCCTAAATACTAACAGCTAACAACA 57.789 33.333 0.00 0.00 0.00 3.33
2001 2327 3.002791 GGCTTCAATGTGAGACGAATCA 58.997 45.455 0.00 0.00 0.00 2.57
2289 2615 3.877508 GTGCCTGTTTCTTGTTGACTAGT 59.122 43.478 0.00 0.00 0.00 2.57
2460 2786 0.698238 CCTGAACCATCCTTGGGTGA 59.302 55.000 0.74 0.00 45.49 4.02
2670 2999 6.423905 CCAAATAGTACCAAGACGTCATATGG 59.576 42.308 24.80 24.80 38.91 2.74
3001 3330 1.285078 TCTGCAGTAGCCTCTCCTACA 59.715 52.381 14.67 0.00 40.07 2.74
3109 3438 4.330074 CAGGTGCACTGTAAAGTAGCATAC 59.670 45.833 17.98 8.99 42.42 2.39
4123 4452 0.618458 GCCACTTGTGGTAGATCCCA 59.382 55.000 19.47 0.00 34.77 4.37
4160 4489 8.713971 TGATATGAAATCCTACAGTGGTGTTAT 58.286 33.333 0.00 0.00 38.19 1.89
4166 4495 8.455903 AACAATGATATGAAATCCTACAGTGG 57.544 34.615 0.00 0.00 0.00 4.00
4194 4523 9.258826 GTAGGATAATGTGAGATATGATGCATC 57.741 37.037 20.14 20.14 0.00 3.91
4232 4561 6.490040 CCAAAGAACCCTGTCTTCATTCTAAA 59.510 38.462 0.00 0.00 36.84 1.85
4263 4592 2.153401 CCCAGGTGGAAGTGTCCCA 61.153 63.158 0.00 0.00 44.23 4.37
4317 4646 1.135315 CCAAGGACATGCCACGATTTG 60.135 52.381 8.58 4.31 40.02 2.32
4339 4668 5.163237 GGTCTATGCTTGGGTTGTATCCTAA 60.163 44.000 0.00 0.00 0.00 2.69
4359 4688 0.180642 TGTCTATCTCCGAGCGGTCT 59.819 55.000 13.48 0.00 36.47 3.85
4368 4697 3.129871 GACAGCAGCATTGTCTATCTCC 58.870 50.000 7.40 0.00 41.29 3.71
4527 4856 2.432628 GTGTGACCTTCTCCGGCG 60.433 66.667 0.00 0.00 0.00 6.46
4530 4859 1.546029 TCAGATGTGTGACCTTCTCCG 59.454 52.381 0.00 0.00 0.00 4.63
4658 4987 1.931841 CACATCAATCCTGAGAGCGTG 59.068 52.381 0.00 0.00 34.23 5.34
4755 5084 1.368850 GCACGCGTTCAACAGGTTC 60.369 57.895 10.22 0.00 0.00 3.62
4813 5142 9.388506 ACAATTACTATCACTCCAGAAATTCTG 57.611 33.333 15.64 15.64 43.91 3.02
4885 5257 9.091784 CGTCTTCTCTCATAATTTTGATTCTGA 57.908 33.333 0.00 0.00 0.00 3.27
4886 5258 8.877779 ACGTCTTCTCTCATAATTTTGATTCTG 58.122 33.333 0.00 0.00 0.00 3.02
4887 5259 8.877779 CACGTCTTCTCTCATAATTTTGATTCT 58.122 33.333 0.00 0.00 0.00 2.40
4888 5260 8.660373 ACACGTCTTCTCTCATAATTTTGATTC 58.340 33.333 0.00 0.00 0.00 2.52
4889 5261 8.553459 ACACGTCTTCTCTCATAATTTTGATT 57.447 30.769 0.00 0.00 0.00 2.57
4890 5262 8.446273 CAACACGTCTTCTCTCATAATTTTGAT 58.554 33.333 0.00 0.00 0.00 2.57
4891 5263 7.441157 ACAACACGTCTTCTCTCATAATTTTGA 59.559 33.333 0.00 0.00 0.00 2.69
4892 5264 7.531871 CACAACACGTCTTCTCTCATAATTTTG 59.468 37.037 0.00 0.00 0.00 2.44
4893 5265 7.307989 CCACAACACGTCTTCTCTCATAATTTT 60.308 37.037 0.00 0.00 0.00 1.82
4894 5266 6.147821 CCACAACACGTCTTCTCTCATAATTT 59.852 38.462 0.00 0.00 0.00 1.82
4895 5267 5.639506 CCACAACACGTCTTCTCTCATAATT 59.360 40.000 0.00 0.00 0.00 1.40
4896 5268 5.171476 CCACAACACGTCTTCTCTCATAAT 58.829 41.667 0.00 0.00 0.00 1.28
4897 5269 4.556233 CCACAACACGTCTTCTCTCATAA 58.444 43.478 0.00 0.00 0.00 1.90
4898 5270 3.056821 CCCACAACACGTCTTCTCTCATA 60.057 47.826 0.00 0.00 0.00 2.15
4899 5271 2.289072 CCCACAACACGTCTTCTCTCAT 60.289 50.000 0.00 0.00 0.00 2.90
4900 5272 1.068588 CCCACAACACGTCTTCTCTCA 59.931 52.381 0.00 0.00 0.00 3.27
4901 5273 1.340248 TCCCACAACACGTCTTCTCTC 59.660 52.381 0.00 0.00 0.00 3.20
4902 5274 1.410004 TCCCACAACACGTCTTCTCT 58.590 50.000 0.00 0.00 0.00 3.10
4903 5275 2.457366 ATCCCACAACACGTCTTCTC 57.543 50.000 0.00 0.00 0.00 2.87
4904 5276 4.553330 ATTATCCCACAACACGTCTTCT 57.447 40.909 0.00 0.00 0.00 2.85
4905 5277 4.454504 ACAATTATCCCACAACACGTCTTC 59.545 41.667 0.00 0.00 0.00 2.87
4906 5278 4.394729 ACAATTATCCCACAACACGTCTT 58.605 39.130 0.00 0.00 0.00 3.01
4907 5279 4.015872 ACAATTATCCCACAACACGTCT 57.984 40.909 0.00 0.00 0.00 4.18
4908 5280 5.640357 TCTTACAATTATCCCACAACACGTC 59.360 40.000 0.00 0.00 0.00 4.34
4909 5281 5.553123 TCTTACAATTATCCCACAACACGT 58.447 37.500 0.00 0.00 0.00 4.49
4910 5282 6.489127 TTCTTACAATTATCCCACAACACG 57.511 37.500 0.00 0.00 0.00 4.49
4911 5283 7.275560 GCAATTCTTACAATTATCCCACAACAC 59.724 37.037 0.00 0.00 0.00 3.32
4949 5321 0.179111 TCGAATACTCCCAAGCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
4951 5323 2.544685 CACTCGAATACTCCCAAGCAG 58.455 52.381 0.00 0.00 0.00 4.24
5079 5451 1.271054 ACAGAGGCCTGCACAAACTAG 60.271 52.381 12.00 0.00 44.16 2.57
5097 5469 2.104792 ACTACTTTGGCAAGCTCTGACA 59.895 45.455 0.00 0.88 43.31 3.58
5176 5549 2.514592 CCCGAGCGCCACATGAAT 60.515 61.111 2.29 0.00 0.00 2.57
5304 5686 1.021390 ATGGCCAAAAGCTCGTCGAG 61.021 55.000 18.08 18.08 43.05 4.04
5305 5687 1.003839 ATGGCCAAAAGCTCGTCGA 60.004 52.632 10.96 0.00 43.05 4.20
5306 5688 1.135315 CATGGCCAAAAGCTCGTCG 59.865 57.895 10.96 0.00 43.05 5.12
5307 5689 1.508088 CCATGGCCAAAAGCTCGTC 59.492 57.895 10.96 0.00 43.05 4.20
5308 5690 2.639327 GCCATGGCCAAAAGCTCGT 61.639 57.895 27.24 0.00 43.05 4.18
5309 5691 2.182537 GCCATGGCCAAAAGCTCG 59.817 61.111 27.24 0.00 43.05 5.03
5320 5702 3.406595 GAGGAGGAACCGGCCATGG 62.407 68.421 7.63 7.63 44.74 3.66
5321 5703 2.190578 GAGGAGGAACCGGCCATG 59.809 66.667 0.00 0.00 44.74 3.66
5322 5704 3.090532 GGAGGAGGAACCGGCCAT 61.091 66.667 0.00 0.00 44.74 4.40
5323 5705 3.864983 AAGGAGGAGGAACCGGCCA 62.865 63.158 0.00 0.00 44.74 5.36
5324 5706 3.009714 AAGGAGGAGGAACCGGCC 61.010 66.667 0.00 0.00 44.74 6.13
5325 5707 2.269241 CAAGGAGGAGGAACCGGC 59.731 66.667 0.00 0.00 44.74 6.13
5326 5708 2.269241 GCAAGGAGGAGGAACCGG 59.731 66.667 0.00 0.00 44.74 5.28
5327 5709 2.269241 GGCAAGGAGGAGGAACCG 59.731 66.667 0.00 0.00 44.74 4.44
5328 5710 1.575447 ATGGGCAAGGAGGAGGAACC 61.575 60.000 0.00 0.00 39.35 3.62
5329 5711 0.106967 GATGGGCAAGGAGGAGGAAC 60.107 60.000 0.00 0.00 0.00 3.62
5330 5712 0.253347 AGATGGGCAAGGAGGAGGAA 60.253 55.000 0.00 0.00 0.00 3.36
5378 5760 0.871722 CGATTGTGCCGTTGAGGAAA 59.128 50.000 0.00 0.00 45.00 3.13
5391 5773 0.535335 ATGTACGCTCACCCGATTGT 59.465 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.