Multiple sequence alignment - TraesCS3D01G292000

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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 TraesCS3D01G292000 chr3D 100.000 3170 0 0 1 3170 401887029 401890198 0.000000e+00 5854.0
1 TraesCS3D01G292000 chr3A 94.010 2404 86 26 775 3168 522240999 522243354 0.000000e+00 3589.0
2 TraesCS3D01G292000 chr3A 89.792 578 50 4 3 572 65871263 65871839 0.000000e+00 732.0
3 TraesCS3D01G292000 chr3A 80.000 375 70 4 2794 3166 75156426 75156055 4.030000e-69 272.0
4 TraesCS3D01G292000 chr3A 91.558 154 13 0 572 725 522240836 522240989 2.480000e-51 213.0
5 TraesCS3D01G292000 chr3B 96.316 1303 44 2 873 2175 527375664 527376962 0.000000e+00 2137.0
6 TraesCS3D01G292000 chr3B 92.887 239 8 4 637 873 527373832 527374063 3.920000e-89 339.0
7 TraesCS3D01G292000 chr3B 83.562 219 22 7 2292 2504 527377045 527377255 3.230000e-45 193.0
8 TraesCS3D01G292000 chr3B 87.778 90 8 2 2533 2619 527377253 527377342 5.590000e-18 102.0
9 TraesCS3D01G292000 chr3B 95.745 47 1 1 2250 2295 527376984 527377030 1.220000e-09 75.0
10 TraesCS3D01G292000 chr2D 89.913 575 48 8 1 568 498110922 498110351 0.000000e+00 732.0
11 TraesCS3D01G292000 chr1B 89.619 578 52 4 3 572 531383313 531382736 0.000000e+00 728.0
12 TraesCS3D01G292000 chr1B 89.354 573 51 3 1 563 639061375 639060803 0.000000e+00 712.0
13 TraesCS3D01G292000 chr1B 89.005 573 57 1 1 567 206422576 206422004 0.000000e+00 704.0
14 TraesCS3D01G292000 chr1B 88.696 575 58 2 1 568 8705545 8706119 0.000000e+00 695.0
15 TraesCS3D01G292000 chr1B 81.150 313 56 2 2789 3101 670277482 670277791 6.790000e-62 248.0
16 TraesCS3D01G292000 chr5B 89.807 569 52 1 1 563 412283832 412284400 0.000000e+00 725.0
17 TraesCS3D01G292000 chr5B 88.699 584 52 8 1 571 356369484 356370066 0.000000e+00 701.0
18 TraesCS3D01G292000 chr5B 82.822 326 52 4 2781 3104 271098776 271098453 4.000000e-74 289.0
19 TraesCS3D01G292000 chr5B 82.019 317 54 3 2789 3105 348444609 348444296 1.870000e-67 267.0
20 TraesCS3D01G292000 chr5D 88.601 579 55 5 1 568 450384399 450383821 0.000000e+00 693.0
21 TraesCS3D01G292000 chr5D 81.651 327 49 10 2785 3107 489771820 489772139 8.720000e-66 261.0
22 TraesCS3D01G292000 chr6B 82.075 318 51 6 2788 3103 529402902 529403215 1.870000e-67 267.0
23 TraesCS3D01G292000 chr7D 81.505 319 56 3 2789 3105 473107101 473107418 3.140000e-65 259.0
24 TraesCS3D01G292000 chr7D 80.878 319 55 5 2788 3105 29756087 29755774 2.440000e-61 246.0
25 TraesCS3D01G292000 chr2B 90.244 41 4 0 2645 2685 3421101 3421141 2.000000e-03 54.7


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 TraesCS3D01G292000 chr3D 401887029 401890198 3169 False 5854.0 5854 100.0000 1 3170 1 chr3D.!!$F1 3169
1 TraesCS3D01G292000 chr3A 522240836 522243354 2518 False 1901.0 3589 92.7840 572 3168 2 chr3A.!!$F2 2596
2 TraesCS3D01G292000 chr3A 65871263 65871839 576 False 732.0 732 89.7920 3 572 1 chr3A.!!$F1 569
3 TraesCS3D01G292000 chr3B 527373832 527377342 3510 False 569.2 2137 91.2576 637 2619 5 chr3B.!!$F1 1982
4 TraesCS3D01G292000 chr2D 498110351 498110922 571 True 732.0 732 89.9130 1 568 1 chr2D.!!$R1 567
5 TraesCS3D01G292000 chr1B 531382736 531383313 577 True 728.0 728 89.6190 3 572 1 chr1B.!!$R2 569
6 TraesCS3D01G292000 chr1B 639060803 639061375 572 True 712.0 712 89.3540 1 563 1 chr1B.!!$R3 562
7 TraesCS3D01G292000 chr1B 206422004 206422576 572 True 704.0 704 89.0050 1 567 1 chr1B.!!$R1 566
8 TraesCS3D01G292000 chr1B 8705545 8706119 574 False 695.0 695 88.6960 1 568 1 chr1B.!!$F1 567
9 TraesCS3D01G292000 chr5B 412283832 412284400 568 False 725.0 725 89.8070 1 563 1 chr5B.!!$F2 562
10 TraesCS3D01G292000 chr5B 356369484 356370066 582 False 701.0 701 88.6990 1 571 1 chr5B.!!$F1 570
11 TraesCS3D01G292000 chr5D 450383821 450384399 578 True 693.0 693 88.6010 1 568 1 chr5D.!!$R1 567

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
512 526 0.032678 CCGGTGGAGATCGATGGAAG 59.967 60.0 0.54 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2380 4022 0.029834 GAAATGCCATGTAGCCGCTG 59.97 55.0 2.16 0.0 0.0 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
154 155 1.668826 AACCTTCCTGCTCCACCATA 58.331 50.000 0.00 0.00 0.00 2.74
155 156 1.207791 ACCTTCCTGCTCCACCATAG 58.792 55.000 0.00 0.00 0.00 2.23
195 196 1.028905 CAACGGGGACAAAGCAGAAA 58.971 50.000 0.00 0.00 0.00 2.52
209 210 3.501349 AGCAGAAAGAGAGACACACCTA 58.499 45.455 0.00 0.00 0.00 3.08
263 264 2.961893 ATGAACCCTAACGCCGCCA 61.962 57.895 0.00 0.00 0.00 5.69
294 295 1.351430 CGACGAACACACGATGCCAT 61.351 55.000 0.00 0.00 37.03 4.40
309 310 1.513158 CCATCAACTCCGAGACGCT 59.487 57.895 1.33 0.00 0.00 5.07
324 325 0.250467 ACGCTGCCATGAAGAACACT 60.250 50.000 0.00 0.00 0.00 3.55
360 361 7.009179 AGTGGAGTTGAGACAGATTTATTCA 57.991 36.000 0.00 0.00 0.00 2.57
413 414 2.742053 CACCACGACCTACAAATCCAAG 59.258 50.000 0.00 0.00 0.00 3.61
436 443 0.602905 CAGAGCGAAGAAACGGGGTT 60.603 55.000 0.00 0.00 0.00 4.11
449 458 1.083141 GGGGTTCCCCTCTCTCCTT 59.917 63.158 18.94 0.00 44.66 3.36
512 526 0.032678 CCGGTGGAGATCGATGGAAG 59.967 60.000 0.54 0.00 0.00 3.46
591 608 9.965824 CTTGATACCACAAGAAAACTAACAATT 57.034 29.630 0.00 0.00 46.85 2.32
594 611 9.113876 GATACCACAAGAAAACTAACAATTTCG 57.886 33.333 0.00 0.00 39.83 3.46
599 616 6.695713 ACAAGAAAACTAACAATTTCGGCTTC 59.304 34.615 0.00 0.00 39.83 3.86
616 633 2.811873 GCTTCTTGTCAGCTGAAAGGGA 60.812 50.000 20.19 7.53 34.15 4.20
620 637 5.441718 TCTTGTCAGCTGAAAGGGATATT 57.558 39.130 20.19 0.00 0.00 1.28
622 639 5.649395 TCTTGTCAGCTGAAAGGGATATTTG 59.351 40.000 20.19 1.14 0.00 2.32
623 640 4.272489 TGTCAGCTGAAAGGGATATTTGG 58.728 43.478 20.19 0.00 0.00 3.28
639 656 7.728532 GGGATATTTGGGTAATTACATCACCTT 59.271 37.037 17.16 5.39 32.66 3.50
740 758 5.416947 GTCAACGACTGTAACCCTGATATT 58.583 41.667 0.00 0.00 0.00 1.28
745 763 8.548721 CAACGACTGTAACCCTGATATTTAATC 58.451 37.037 0.00 0.00 0.00 1.75
805 823 0.902516 AGGAGGTCAGTGGAGAGTGC 60.903 60.000 0.00 0.00 0.00 4.40
820 838 2.117423 TGCAGACTGGAGGGTCGA 59.883 61.111 4.26 0.00 40.76 4.20
930 2550 4.448210 GGACGGCAATTCATAGTTAAGGA 58.552 43.478 0.00 0.00 0.00 3.36
936 2556 4.495844 GCAATTCATAGTTAAGGACGTGGC 60.496 45.833 0.00 0.00 0.00 5.01
978 2598 1.011595 TCTAGCTCTCCCAAGTCCCT 58.988 55.000 0.00 0.00 0.00 4.20
1107 2727 0.105039 CCAAGTCTATGTCCCTCCGC 59.895 60.000 0.00 0.00 0.00 5.54
1169 2789 2.267006 CGGCTCCATCACTGTGCT 59.733 61.111 2.12 0.00 0.00 4.40
1267 2887 2.356673 GTTTCTTCGACGCCGGGT 60.357 61.111 2.18 0.00 36.24 5.28
1375 2995 3.214123 CCATGCTGCACCCCATCG 61.214 66.667 3.57 0.00 0.00 3.84
1527 3147 2.281139 TTCAACGACGCCATGGCA 60.281 55.556 34.93 12.24 42.06 4.92
1836 3456 2.347697 TGGACGAACTTGACTGATCG 57.652 50.000 0.00 0.00 40.90 3.69
1839 3459 3.109619 GGACGAACTTGACTGATCGATC 58.890 50.000 18.72 18.72 38.59 3.69
1842 3462 3.057526 ACGAACTTGACTGATCGATCACA 60.058 43.478 23.99 18.02 38.59 3.58
1848 3468 2.196749 GACTGATCGATCACATTGCGT 58.803 47.619 23.99 18.24 32.50 5.24
1849 3469 2.604914 GACTGATCGATCACATTGCGTT 59.395 45.455 23.99 4.77 32.50 4.84
1850 3470 3.002791 ACTGATCGATCACATTGCGTTT 58.997 40.909 23.99 0.00 32.50 3.60
1965 3585 4.778143 GGCGGCAGGGTGATCGTT 62.778 66.667 3.07 0.00 0.00 3.85
2046 3666 0.469917 GGGACGTGATGATGATGGGT 59.530 55.000 0.00 0.00 0.00 4.51
2175 3795 6.383147 TGATCGAGGTTTACCCTTAGATTTCT 59.617 38.462 0.00 0.00 46.51 2.52
2176 3796 6.218108 TCGAGGTTTACCCTTAGATTTCTC 57.782 41.667 0.00 0.00 46.51 2.87
2186 3806 6.365520 ACCCTTAGATTTCTCTCTCTCTCTC 58.634 44.000 0.00 0.00 32.66 3.20
2188 3808 6.712547 CCCTTAGATTTCTCTCTCTCTCTCTC 59.287 46.154 0.00 0.00 32.66 3.20
2190 3810 7.659390 CCTTAGATTTCTCTCTCTCTCTCTCTC 59.341 44.444 0.00 0.00 32.66 3.20
2191 3811 6.821616 AGATTTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
2192 3812 6.825610 AGATTTCTCTCTCTCTCTCTCTCTC 58.174 44.000 0.00 0.00 0.00 3.20
2193 3813 6.614906 AGATTTCTCTCTCTCTCTCTCTCTCT 59.385 42.308 0.00 0.00 0.00 3.10
2196 3816 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2197 3817 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2198 3818 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2199 3819 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2200 3820 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2201 3821 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2202 3822 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2203 3823 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2204 3824 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2205 3825 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2206 3826 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2207 3827 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2208 3828 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2209 3829 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2210 3830 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2211 3831 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2212 3832 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2213 3833 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2214 3834 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2225 3845 2.088423 TCTCTCTCTCTTGCGAGGAAC 58.912 52.381 0.00 0.00 37.86 3.62
2230 3850 1.825474 CTCTCTTGCGAGGAACCCTTA 59.175 52.381 0.00 0.00 37.86 2.69
2231 3851 1.825474 TCTCTTGCGAGGAACCCTTAG 59.175 52.381 0.00 0.00 37.86 2.18
2232 3852 0.902531 TCTTGCGAGGAACCCTTAGG 59.097 55.000 0.00 0.00 31.76 2.69
2305 3944 0.919710 AAGGGGTCTATGGTGGCTTC 59.080 55.000 0.00 0.00 0.00 3.86
2322 3961 2.288457 GCTTCTGGCCTTTTCTTTGACC 60.288 50.000 3.32 0.00 34.27 4.02
2335 3977 4.461992 TCTTTGACCAAAAATCGACGAC 57.538 40.909 0.00 0.00 0.00 4.34
2350 3992 5.646467 TCGACGACGAAAAGAAAAAGAAT 57.354 34.783 7.68 0.00 45.74 2.40
2351 3993 5.663292 TCGACGACGAAAAGAAAAAGAATC 58.337 37.500 7.68 0.00 45.74 2.52
2352 3994 5.232626 TCGACGACGAAAAGAAAAAGAATCA 59.767 36.000 7.68 0.00 45.74 2.57
2353 3995 5.899696 CGACGACGAAAAGAAAAAGAATCAA 59.100 36.000 0.00 0.00 42.66 2.57
2380 4022 4.147449 GATGGCAAAAGGGGCGCC 62.147 66.667 21.18 21.18 46.43 6.53
2454 4101 2.034558 CGTTCCAGTGTTCCAGCAAAAT 59.965 45.455 0.00 0.00 0.00 1.82
2455 4102 3.490761 CGTTCCAGTGTTCCAGCAAAATT 60.491 43.478 0.00 0.00 0.00 1.82
2509 4161 7.584123 GTCATCATCGTGAGTATATGCAAAAAC 59.416 37.037 0.00 0.00 0.00 2.43
2575 4227 9.920946 AGGAGCTGATCAAATTAACCTTTTATA 57.079 29.630 0.00 0.00 0.00 0.98
2613 4268 9.091784 CAAATACTGATATTCGATGTCCCTATG 57.908 37.037 0.00 0.00 30.27 2.23
2651 4307 4.332819 AGACTTGTTGAAGGTCAAGAAACG 59.667 41.667 11.07 0.00 38.82 3.60
2658 4314 1.583054 AGGTCAAGAAACGTGAGCAC 58.417 50.000 15.90 0.00 44.19 4.40
2684 4340 6.655078 ATGTCAAATTTAGCACTTGAACCT 57.345 33.333 0.00 0.00 31.21 3.50
2685 4341 7.759489 ATGTCAAATTTAGCACTTGAACCTA 57.241 32.000 0.00 0.00 31.21 3.08
2692 4349 0.875059 GCACTTGAACCTAGTGGCAC 59.125 55.000 10.29 10.29 42.53 5.01
2724 4381 2.508300 TGAACCAAGTATAAGAGGGGGC 59.492 50.000 0.00 0.00 0.00 5.80
2780 4437 3.055891 GCCTTTGCTAACCCATGAAACAT 60.056 43.478 0.00 0.00 33.53 2.71
2792 4449 4.339247 CCCATGAAACATGGCTAACTAAGG 59.661 45.833 21.09 4.87 37.85 2.69
2802 4459 3.388024 TGGCTAACTAAGGGCATCTACAG 59.612 47.826 0.00 0.00 33.16 2.74
2810 4467 4.530857 GCATCTACAGCCGGGCGT 62.531 66.667 14.39 16.48 0.00 5.68
2829 4486 2.650322 GTCCCAAACACTCCTCAAACA 58.350 47.619 0.00 0.00 0.00 2.83
2831 4488 1.681264 CCCAAACACTCCTCAAACACC 59.319 52.381 0.00 0.00 0.00 4.16
2934 4591 1.372683 CGGCACCCCTCATATCCAG 59.627 63.158 0.00 0.00 0.00 3.86
2959 4616 1.612035 ATATGGGGCAGATATGGGGG 58.388 55.000 0.00 0.00 0.00 5.40
2960 4617 0.198437 TATGGGGCAGATATGGGGGT 59.802 55.000 0.00 0.00 0.00 4.95
2961 4618 1.437849 ATGGGGCAGATATGGGGGTG 61.438 60.000 0.00 0.00 0.00 4.61
2962 4619 2.116125 GGGCAGATATGGGGGTGC 59.884 66.667 0.00 0.00 35.07 5.01
2963 4620 2.766925 GGGCAGATATGGGGGTGCA 61.767 63.158 0.00 0.00 37.68 4.57
2964 4621 1.529244 GGCAGATATGGGGGTGCAC 60.529 63.158 8.80 8.80 37.68 4.57
2965 4622 1.893808 GCAGATATGGGGGTGCACG 60.894 63.158 11.45 0.00 35.91 5.34
2966 4623 1.227943 CAGATATGGGGGTGCACGG 60.228 63.158 11.45 0.00 0.00 4.94
2967 4624 2.113139 GATATGGGGGTGCACGGG 59.887 66.667 11.45 0.00 0.00 5.28
2968 4625 4.204028 ATATGGGGGTGCACGGGC 62.204 66.667 11.45 0.34 41.68 6.13
2998 4655 1.668151 GTCGGATCCAATAGCCCGC 60.668 63.158 13.41 0.00 41.55 6.13
3035 4692 0.394899 CCAAATCCACCCTCCAGAGC 60.395 60.000 0.00 0.00 0.00 4.09
3075 4732 2.243736 TCTCCTCTCTTCTTCCTCCTCC 59.756 54.545 0.00 0.00 0.00 4.30
3079 4736 2.202810 CTTCTTCCTCCTCCGCGC 60.203 66.667 0.00 0.00 0.00 6.86
3140 4797 3.134792 GCTCTCTCGTCCTCGGCA 61.135 66.667 0.00 0.00 37.69 5.69
3154 4811 2.202756 GGCATGGAGGACGTCGTC 60.203 66.667 26.08 26.08 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.859427 TTTCCTCCTCCGACGTCGTG 61.859 60.000 33.49 24.72 37.74 4.35
195 196 4.020543 GACTCCATTAGGTGTGTCTCTCT 58.979 47.826 0.00 0.00 41.49 3.10
209 210 4.778143 GGCGGCGGTGACTCCATT 62.778 66.667 9.78 0.00 35.57 3.16
263 264 4.863131 GTGTGTTCGTCGATCCTTTAGATT 59.137 41.667 0.00 0.00 34.42 2.40
294 295 2.258591 GCAGCGTCTCGGAGTTGA 59.741 61.111 4.69 0.00 0.00 3.18
309 310 0.178995 TGGCAGTGTTCTTCATGGCA 60.179 50.000 0.00 0.00 44.77 4.92
324 325 0.178932 ACTCCACTCCTACACTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
333 334 2.685106 TCTGTCTCAACTCCACTCCT 57.315 50.000 0.00 0.00 0.00 3.69
413 414 0.992802 CCGTTTCTTCGCTCTGTAGC 59.007 55.000 0.00 0.00 45.86 3.58
436 443 2.042843 GCGGAAGGAGAGAGGGGA 60.043 66.667 0.00 0.00 0.00 4.81
546 563 1.755783 CGTTCCCTACCCTAGCCGT 60.756 63.158 0.00 0.00 0.00 5.68
568 585 9.113876 CGAAATTGTTAGTTTTCTTGTGGTATC 57.886 33.333 0.00 0.00 31.20 2.24
591 608 0.392706 TCAGCTGACAAGAAGCCGAA 59.607 50.000 13.74 0.00 41.82 4.30
594 611 1.538950 CCTTTCAGCTGACAAGAAGCC 59.461 52.381 26.63 0.00 41.82 4.35
599 616 5.163581 CCAAATATCCCTTTCAGCTGACAAG 60.164 44.000 18.03 20.57 0.00 3.16
639 656 2.857748 CTGACATCGCGTTACATAAGCA 59.142 45.455 5.77 0.00 0.00 3.91
740 758 7.848223 TGCGAGAAAGAGAATCATTGATTAA 57.152 32.000 11.79 0.00 37.82 1.40
782 800 0.612174 TCTCCACTGACCTCCTTCCG 60.612 60.000 0.00 0.00 0.00 4.30
805 823 2.055042 CCCTCGACCCTCCAGTCTG 61.055 68.421 0.00 0.00 34.46 3.51
820 838 1.359168 ACGAAGGTTCCTAAAGCCCT 58.641 50.000 0.00 0.00 33.23 5.19
936 2556 1.658994 TGGTTAATTTAGAGGCGCCG 58.341 50.000 23.20 0.00 0.00 6.46
978 2598 4.140536 TGACAATGTGCTTGATTGGTGTA 58.859 39.130 0.00 0.00 38.29 2.90
1034 2654 2.202676 CTTGGAGGAGCTCGTCGC 60.203 66.667 25.58 19.49 39.57 5.19
1267 2887 2.970639 GTAGGTGTCTGGCGCTGA 59.029 61.111 7.64 3.05 0.00 4.26
1375 2995 2.125673 CATGGACGGGGACACGAC 60.126 66.667 0.00 0.00 37.61 4.34
1661 3281 4.077188 GGACGCTGCACTTGACGC 62.077 66.667 0.00 0.00 0.00 5.19
1849 3469 5.449451 GCGAACAGAAGTCCCAAAGTAAAAA 60.449 40.000 0.00 0.00 0.00 1.94
1850 3470 4.035909 GCGAACAGAAGTCCCAAAGTAAAA 59.964 41.667 0.00 0.00 0.00 1.52
2160 3780 7.878495 AGAGAGAGAGAGAAATCTAAGGGTAA 58.122 38.462 0.00 0.00 0.00 2.85
2175 3795 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2176 3796 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2186 3806 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2188 3808 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2190 3810 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2191 3811 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2192 3812 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2193 3813 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2196 3816 4.125703 GCAAGAGAGAGAGAGAGAGAGAG 58.874 52.174 0.00 0.00 0.00 3.20
2197 3817 3.430790 CGCAAGAGAGAGAGAGAGAGAGA 60.431 52.174 0.00 0.00 43.02 3.10
2198 3818 2.868583 CGCAAGAGAGAGAGAGAGAGAG 59.131 54.545 0.00 0.00 43.02 3.20
2199 3819 2.499693 TCGCAAGAGAGAGAGAGAGAGA 59.500 50.000 0.00 0.00 45.01 3.10
2200 3820 2.905075 TCGCAAGAGAGAGAGAGAGAG 58.095 52.381 0.00 0.00 45.01 3.20
2213 3833 1.830071 ACCTAAGGGTTCCTCGCAAGA 60.830 52.381 0.00 0.00 44.73 3.02
2214 3834 0.613777 ACCTAAGGGTTCCTCGCAAG 59.386 55.000 0.00 0.00 44.73 4.01
2225 3845 4.762251 CAGAGACAAAAGGAAACCTAAGGG 59.238 45.833 0.00 0.00 31.13 3.95
2230 3850 3.953542 ACCAGAGACAAAAGGAAACCT 57.046 42.857 0.00 0.00 33.87 3.50
2231 3851 5.535030 ACAATACCAGAGACAAAAGGAAACC 59.465 40.000 0.00 0.00 0.00 3.27
2232 3852 6.438763 CACAATACCAGAGACAAAAGGAAAC 58.561 40.000 0.00 0.00 0.00 2.78
2305 3944 3.817709 TTTGGTCAAAGAAAAGGCCAG 57.182 42.857 5.01 0.00 0.00 4.85
2310 3949 5.968848 TCGTCGATTTTTGGTCAAAGAAAAG 59.031 36.000 0.00 0.00 0.00 2.27
2322 3961 6.471298 TTTTCTTTTCGTCGTCGATTTTTG 57.529 33.333 5.44 0.00 45.65 2.44
2350 3992 6.041182 CCCTTTTGCCATCATAGATTGATTGA 59.959 38.462 0.00 0.00 42.62 2.57
2351 3993 6.220930 CCCTTTTGCCATCATAGATTGATTG 58.779 40.000 0.00 0.00 42.62 2.67
2352 3994 5.306160 CCCCTTTTGCCATCATAGATTGATT 59.694 40.000 0.00 0.00 42.62 2.57
2353 3995 4.836736 CCCCTTTTGCCATCATAGATTGAT 59.163 41.667 0.00 0.00 46.27 2.57
2380 4022 0.029834 GAAATGCCATGTAGCCGCTG 59.970 55.000 2.16 0.00 0.00 5.18
2381 4023 0.394216 TGAAATGCCATGTAGCCGCT 60.394 50.000 0.00 0.00 0.00 5.52
2454 4101 6.516739 TGGTAAACACAGACAAATGACAAA 57.483 33.333 0.00 0.00 0.00 2.83
2455 4102 6.516739 TTGGTAAACACAGACAAATGACAA 57.483 33.333 0.00 0.00 0.00 3.18
2509 4161 1.141254 AGCAGGAGAAGATGATGGCAG 59.859 52.381 0.00 0.00 0.00 4.85
2575 4227 3.016031 TCAGTATTTGTTCGCATGGCAT 58.984 40.909 0.00 0.00 0.00 4.40
2613 4268 6.257849 TCAACAAGTCTAATCAATACCGCATC 59.742 38.462 0.00 0.00 0.00 3.91
2651 4307 4.622740 GCTAAATTTGACATTGGTGCTCAC 59.377 41.667 0.00 0.00 0.00 3.51
2658 4314 6.146021 GGTTCAAGTGCTAAATTTGACATTGG 59.854 38.462 0.00 0.00 31.11 3.16
2684 4340 4.236527 TCACTCTCTATCAGTGCCACTA 57.763 45.455 0.00 0.00 41.04 2.74
2685 4341 3.093057 TCACTCTCTATCAGTGCCACT 57.907 47.619 0.00 0.00 41.04 4.00
2692 4349 9.126151 TCTTATACTTGGTTCACTCTCTATCAG 57.874 37.037 0.00 0.00 0.00 2.90
2724 4381 7.601856 TGTTTCTTAACTAATTGGGCAATCAG 58.398 34.615 0.00 0.00 35.24 2.90
2780 4437 3.380393 TGTAGATGCCCTTAGTTAGCCA 58.620 45.455 0.00 0.00 0.00 4.75
2810 4467 2.650322 GTGTTTGAGGAGTGTTTGGGA 58.350 47.619 0.00 0.00 0.00 4.37
2858 4515 4.143179 CCGACTAGGTTGAAATTTCGTGAC 60.143 45.833 13.34 11.11 34.51 3.67
2899 4556 4.131088 GGTCAGCCCGGTCGTCTC 62.131 72.222 0.00 0.00 0.00 3.36
2918 4575 1.073897 GGCTGGATATGAGGGGTGC 59.926 63.158 0.00 0.00 0.00 5.01
2947 4604 1.893808 CGTGCACCCCCATATCTGC 60.894 63.158 12.15 0.00 0.00 4.26
2949 4606 2.452064 CCCGTGCACCCCCATATCT 61.452 63.158 12.15 0.00 0.00 1.98
2976 4633 0.387929 GGCTATTGGATCCGACGTGA 59.612 55.000 2.95 0.00 0.00 4.35
2998 4655 1.625417 GGTGCAATTTGGGATGGGGG 61.625 60.000 0.00 0.00 0.00 5.40
3007 4664 2.038820 AGGGTGGATTTGGTGCAATTTG 59.961 45.455 0.00 0.00 0.00 2.32
3035 4692 3.999663 GAGAGATTAAATGGATCCGGCAG 59.000 47.826 7.39 0.00 0.00 4.85
3079 4736 4.421479 AAGCTGCGAGACGGACGG 62.421 66.667 0.00 0.00 0.00 4.79
3126 4783 2.069465 CTCCATGCCGAGGACGAGAG 62.069 65.000 0.00 0.00 42.66 3.20
3140 4797 3.823330 GGCGACGACGTCCTCCAT 61.823 66.667 21.63 0.00 41.98 3.41


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

AutoCloner maintained by Alex Coulton.