Multiple sequence alignment - TraesCS3D01G102500

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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 TraesCS3D01G102500 chr3D 100.000 2702 0 0 1 2702 55155503 55158204 0.000000e+00 4990
1 TraesCS3D01G102500 chr3D 84.314 204 20 5 2498 2698 55165696 55165890 3.550000e-44 189
2 TraesCS3D01G102500 chr3D 93.617 94 6 0 1958 2051 55157345 55157438 1.010000e-29 141
3 TraesCS3D01G102500 chr3D 93.617 94 6 0 1843 1936 55157460 55157553 1.010000e-29 141
4 TraesCS3D01G102500 chr7A 91.319 2419 141 28 1 2356 670166430 670168842 0.000000e+00 3240
5 TraesCS3D01G102500 chr7A 81.611 571 87 12 1045 1601 670342225 670341659 8.820000e-125 457
6 TraesCS3D01G102500 chr7A 79.123 570 104 9 1041 1601 670536793 670537356 1.960000e-101 379
7 TraesCS3D01G102500 chr7A 78.622 421 42 22 475 850 670342841 670342424 4.500000e-58 235
8 TraesCS3D01G102500 chr7A 92.308 91 4 1 1843 1933 670168415 670168502 2.820000e-25 126
9 TraesCS3D01G102500 chr7D 94.638 2070 80 11 1 2039 577920974 577923043 0.000000e+00 3179
10 TraesCS3D01G102500 chr7D 79.128 872 107 36 19 842 577962448 577963292 1.420000e-147 532
11 TraesCS3D01G102500 chr7D 81.961 571 92 7 1041 1601 577963504 577964073 8.760000e-130 473
12 TraesCS3D01G102500 chr7D 79.298 570 103 9 1041 1601 578465261 578465824 4.220000e-103 385
13 TraesCS3D01G102500 chr7D 77.589 647 71 32 251 848 578164349 578163728 9.330000e-85 324
14 TraesCS3D01G102500 chr7D 90.129 233 19 3 155 387 577884852 577885080 1.570000e-77 300
15 TraesCS3D01G102500 chr7D 84.926 272 28 11 2431 2698 577923767 577924029 2.060000e-66 263
16 TraesCS3D01G102500 chr7D 95.804 143 3 2 19 160 577882980 577883120 7.530000e-56 228
17 TraesCS3D01G102500 chr7D 90.964 166 15 0 2067 2232 577923390 577923555 9.740000e-55 224
18 TraesCS3D01G102500 chr7D 84.524 168 19 2 2497 2664 577937509 577937669 2.780000e-35 159
19 TraesCS3D01G102500 chr7D 95.556 90 3 1 427 516 577885265 577885353 2.800000e-30 143
20 TraesCS3D01G102500 chr7D 92.683 82 6 0 1843 1924 577922962 577923043 4.730000e-23 119
21 TraesCS3D01G102500 chr7B 94.719 1761 73 12 58 1804 641742986 641741232 0.000000e+00 2719
22 TraesCS3D01G102500 chr7B 92.885 1827 75 16 1 1804 641367958 641369752 0.000000e+00 2603
23 TraesCS3D01G102500 chr7B 87.772 597 56 9 1807 2387 641369790 641370385 0.000000e+00 682
24 TraesCS3D01G102500 chr7B 82.011 567 96 4 1041 1601 642076924 642076358 6.770000e-131 477
25 TraesCS3D01G102500 chr7B 76.184 781 88 43 19 744 641459786 641460523 3.360000e-84 322
26 TraesCS3D01G102500 chr7B 76.984 378 47 21 475 823 642077476 642077110 2.140000e-41 180
27 TraesCS3D01G102500 chr7B 93.407 91 6 0 1846 1936 641369950 641370040 4.690000e-28 135
28 TraesCS3D01G102500 chr7B 100.000 55 0 0 1 55 641743020 641742966 4.760000e-18 102


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 TraesCS3D01G102500 chr3D 55155503 55158204 2701 False 1757.333333 4990 95.744667 1 2702 3 chr3D.!!$F2 2701
1 TraesCS3D01G102500 chr7A 670166430 670168842 2412 False 1683.000000 3240 91.813500 1 2356 2 chr7A.!!$F2 2355
2 TraesCS3D01G102500 chr7A 670536793 670537356 563 False 379.000000 379 79.123000 1041 1601 1 chr7A.!!$F1 560
3 TraesCS3D01G102500 chr7A 670341659 670342841 1182 True 346.000000 457 80.116500 475 1601 2 chr7A.!!$R1 1126
4 TraesCS3D01G102500 chr7D 577920974 577924029 3055 False 946.250000 3179 90.802750 1 2698 4 chr7D.!!$F4 2697
5 TraesCS3D01G102500 chr7D 577962448 577964073 1625 False 502.500000 532 80.544500 19 1601 2 chr7D.!!$F5 1582
6 TraesCS3D01G102500 chr7D 578465261 578465824 563 False 385.000000 385 79.298000 1041 1601 1 chr7D.!!$F2 560
7 TraesCS3D01G102500 chr7D 578163728 578164349 621 True 324.000000 324 77.589000 251 848 1 chr7D.!!$R1 597
8 TraesCS3D01G102500 chr7D 577882980 577885353 2373 False 223.666667 300 93.829667 19 516 3 chr7D.!!$F3 497
9 TraesCS3D01G102500 chr7B 641741232 641743020 1788 True 1410.500000 2719 97.359500 1 1804 2 chr7B.!!$R1 1803
10 TraesCS3D01G102500 chr7B 641367958 641370385 2427 False 1140.000000 2603 91.354667 1 2387 3 chr7B.!!$F2 2386
11 TraesCS3D01G102500 chr7B 642076358 642077476 1118 True 328.500000 477 79.497500 475 1601 2 chr7B.!!$R2 1126
12 TraesCS3D01G102500 chr7B 641459786 641460523 737 False 322.000000 322 76.184000 19 744 1 chr7B.!!$F1 725

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
276 2016 2.39659 TGTCGCCATCTACTTTTCCC 57.603 50.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 4085 0.109781 GCCACACGCAAACATACCAG 60.11 55.0 0.0 0.0 37.47 4.0 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
275 2015 2.678336 CCTTGTCGCCATCTACTTTTCC 59.322 50.000 0.00 0.00 0.00 3.13
276 2016 2.396590 TGTCGCCATCTACTTTTCCC 57.603 50.000 0.00 0.00 0.00 3.97
419 2249 6.851222 ATCGATTACTTGTGCAATCTAAGG 57.149 37.500 0.00 0.00 0.00 2.69
543 2434 2.939103 GGTGGCTTACATTGCTGTAGAG 59.061 50.000 0.00 0.00 39.00 2.43
791 2738 3.144506 AGAGAGGCACAAATGTTCACAG 58.855 45.455 0.00 0.00 0.00 3.66
1389 3470 1.118965 TCACCAAGGAGGACAAGCGA 61.119 55.000 0.00 0.00 41.22 4.93
1392 3473 1.006102 CAAGGAGGACAAGCGACGT 60.006 57.895 0.00 0.00 0.00 4.34
1393 3474 1.009389 CAAGGAGGACAAGCGACGTC 61.009 60.000 5.18 5.18 0.00 4.34
1674 3779 0.882927 GCACCTACGTGTGGCAAGAA 60.883 55.000 7.98 0.00 42.39 2.52
1683 3788 0.535780 TGTGGCAAGAACCTCAGCAG 60.536 55.000 0.00 0.00 0.00 4.24
1726 3831 4.100808 GCTATCACCAGATTCAGAGTCCTT 59.899 45.833 0.00 0.00 35.67 3.36
1728 3833 2.027745 TCACCAGATTCAGAGTCCTTGC 60.028 50.000 0.00 0.00 0.00 4.01
1731 3836 3.073650 ACCAGATTCAGAGTCCTTGCTTT 59.926 43.478 0.00 0.00 0.00 3.51
1745 3854 3.259123 CCTTGCTTTAGCCTGGACATTTT 59.741 43.478 0.00 0.00 41.18 1.82
1746 3855 4.488879 CTTGCTTTAGCCTGGACATTTTC 58.511 43.478 0.00 0.00 41.18 2.29
1781 3893 6.751888 GGTTTTGCGTTAGCTTTCATATGATT 59.248 34.615 6.17 0.00 45.42 2.57
1788 3900 9.450807 GCGTTAGCTTTCATATGATTGTTATTT 57.549 29.630 6.17 0.00 41.01 1.40
1837 3985 1.842720 CTGTTGTCGTGGTGTCGTTA 58.157 50.000 0.00 0.00 0.00 3.18
1844 3992 1.068748 TCGTGGTGTCGTTAGAGAAGC 60.069 52.381 0.00 0.00 0.00 3.86
1876 4024 9.696917 GAATTTGTGATTTGAGACTAATTGGTT 57.303 29.630 0.00 0.00 30.83 3.67
1933 4081 6.454795 TCTGGTGATGCCTTGTTTTTATTTC 58.545 36.000 0.00 0.00 38.35 2.17
1934 4082 6.267471 TCTGGTGATGCCTTGTTTTTATTTCT 59.733 34.615 0.00 0.00 38.35 2.52
1935 4083 7.450014 TCTGGTGATGCCTTGTTTTTATTTCTA 59.550 33.333 0.00 0.00 38.35 2.10
1936 4084 8.133024 TGGTGATGCCTTGTTTTTATTTCTAT 57.867 30.769 0.00 0.00 38.35 1.98
1937 4085 8.250332 TGGTGATGCCTTGTTTTTATTTCTATC 58.750 33.333 0.00 0.00 38.35 2.08
1938 4086 8.470002 GGTGATGCCTTGTTTTTATTTCTATCT 58.530 33.333 0.00 0.00 0.00 1.98
1939 4087 9.294030 GTGATGCCTTGTTTTTATTTCTATCTG 57.706 33.333 0.00 0.00 0.00 2.90
1940 4088 8.469200 TGATGCCTTGTTTTTATTTCTATCTGG 58.531 33.333 0.00 0.00 0.00 3.86
1981 4136 7.031372 CAGTACCATGAATTTGTGATTTGAGG 58.969 38.462 0.00 0.00 0.00 3.86
2079 4553 7.475771 TTTATGAAATGTTTGCTTGTGGTTC 57.524 32.000 0.00 0.00 0.00 3.62
2099 4579 3.011818 TCAGCTGTATTGTCTTGCATGG 58.988 45.455 14.67 0.00 0.00 3.66
2138 4620 1.471684 GCTCCAGCTGAATTTGTCTGG 59.528 52.381 17.39 12.10 45.59 3.86
2169 4651 4.157289 TGTGCATTGGTGTTTTGCAAAATT 59.843 33.333 26.24 6.31 46.91 1.82
2176 4658 6.654793 TGGTGTTTTGCAAAATTAACAGTC 57.345 33.333 26.24 15.05 31.75 3.51
2179 4661 6.399626 GTGTTTTGCAAAATTAACAGTCGAC 58.600 36.000 26.24 7.70 31.75 4.20
2185 4667 4.433805 GCAAAATTAACAGTCGACGATCGT 60.434 41.667 22.97 22.97 41.35 3.73
2252 4739 2.975732 TCTGTAGAGCAGCATCAAGG 57.024 50.000 0.00 0.00 44.66 3.61
2266 4774 1.722034 TCAAGGCTCTGTTCCTCACT 58.278 50.000 0.00 0.00 32.45 3.41
2269 4777 1.949799 AGGCTCTGTTCCTCACTGAT 58.050 50.000 0.00 0.00 33.21 2.90
2273 4781 1.821753 CTCTGTTCCTCACTGATCCGT 59.178 52.381 0.00 0.00 33.21 4.69
2297 4805 2.093500 TGTCACTGGGTGATGCAGATAC 60.093 50.000 3.67 0.00 44.63 2.24
2356 4864 0.391130 GTCCACGCCTGCTATCACAA 60.391 55.000 0.00 0.00 0.00 3.33
2359 4867 0.742281 CACGCCTGCTATCACAAGCT 60.742 55.000 0.00 0.00 43.19 3.74
2360 4868 0.824109 ACGCCTGCTATCACAAGCTA 59.176 50.000 0.00 0.00 43.19 3.32
2380 4888 0.878961 GTCGGCTCCGTTTTGTGAGT 60.879 55.000 8.28 0.00 40.74 3.41
2387 4895 3.614390 GCTCCGTTTTGTGAGTAGCTAGT 60.614 47.826 0.00 0.00 0.00 2.57
2396 4904 4.200092 TGTGAGTAGCTAGTCATCGATGT 58.800 43.478 29.27 9.42 37.90 3.06
2402 4910 1.539065 GCTAGTCATCGATGTGGGGTG 60.539 57.143 24.09 11.98 0.00 4.61
2404 4912 0.984230 AGTCATCGATGTGGGGTGTT 59.016 50.000 24.09 0.99 0.00 3.32
2405 4913 1.066143 AGTCATCGATGTGGGGTGTTC 60.066 52.381 24.09 5.94 0.00 3.18
2406 4914 0.108377 TCATCGATGTGGGGTGTTCG 60.108 55.000 24.09 0.00 0.00 3.95
2407 4915 0.108377 CATCGATGTGGGGTGTTCGA 60.108 55.000 17.50 0.00 43.82 3.71
2409 4917 0.037697 TCGATGTGGGGTGTTCGAAG 60.038 55.000 0.00 0.00 37.64 3.79
2411 4919 1.303317 ATGTGGGGTGTTCGAAGCC 60.303 57.895 0.00 3.92 36.97 4.35
2415 4923 4.415783 GGGTGTTCGAAGCCCAAT 57.584 55.556 25.00 0.00 41.93 3.16
2416 4924 2.653557 GGGTGTTCGAAGCCCAATT 58.346 52.632 25.00 0.00 41.93 2.32
2418 4926 2.164338 GGGTGTTCGAAGCCCAATTTA 58.836 47.619 25.00 0.00 41.93 1.40
2419 4927 2.094906 GGGTGTTCGAAGCCCAATTTAC 60.095 50.000 25.00 1.79 41.93 2.01
2420 4928 2.554893 GGTGTTCGAAGCCCAATTTACA 59.445 45.455 0.00 0.00 0.00 2.41
2421 4929 3.561503 GTGTTCGAAGCCCAATTTACAC 58.438 45.455 0.00 0.00 0.00 2.90
2422 4930 2.554893 TGTTCGAAGCCCAATTTACACC 59.445 45.455 0.00 0.00 0.00 4.16
2424 4932 0.450184 CGAAGCCCAATTTACACCGG 59.550 55.000 0.00 0.00 0.00 5.28
2426 4934 0.540830 AAGCCCAATTTACACCGGCA 60.541 50.000 0.00 0.00 42.28 5.69
2429 4937 0.525761 CCCAATTTACACCGGCACAG 59.474 55.000 0.00 0.00 0.00 3.66
2433 4941 2.809119 CAATTTACACCGGCACAGTGTA 59.191 45.455 0.00 0.00 46.37 2.90
2436 4944 2.373540 TACACCGGCACAGTGTAATC 57.626 50.000 0.00 0.00 46.37 1.75
2437 4945 0.394938 ACACCGGCACAGTGTAATCA 59.605 50.000 0.00 0.00 46.37 2.57
2438 4946 1.202710 ACACCGGCACAGTGTAATCAA 60.203 47.619 0.00 0.00 46.37 2.57
2439 4947 2.083774 CACCGGCACAGTGTAATCAAT 58.916 47.619 0.00 0.00 0.00 2.57
2440 4948 3.266636 CACCGGCACAGTGTAATCAATA 58.733 45.455 0.00 0.00 0.00 1.90
2441 4949 3.687212 CACCGGCACAGTGTAATCAATAA 59.313 43.478 0.00 0.00 0.00 1.40
2442 4950 3.687698 ACCGGCACAGTGTAATCAATAAC 59.312 43.478 0.00 0.00 0.00 1.89
2448 5027 5.163622 GCACAGTGTAATCAATAACATGGCT 60.164 40.000 1.61 0.00 0.00 4.75
2459 5038 0.106519 AACATGGCTGGACCTATGGC 60.107 55.000 0.00 0.00 40.22 4.40
2460 5039 1.281199 ACATGGCTGGACCTATGGCA 61.281 55.000 10.25 10.25 40.22 4.92
2461 5040 0.106569 CATGGCTGGACCTATGGCAA 60.107 55.000 11.45 0.00 39.59 4.52
2465 5044 2.125310 TGGACCTATGGCAACGCG 60.125 61.111 3.53 3.53 42.51 6.01
2487 5076 1.583967 CGAGCAGTCCGTCGATCAC 60.584 63.158 0.00 0.00 38.50 3.06
2518 5107 4.039357 CGTGCCGGTCGTGTCTCT 62.039 66.667 1.90 0.00 0.00 3.10
2519 5108 2.430921 GTGCCGGTCGTGTCTCTG 60.431 66.667 1.90 0.00 0.00 3.35
2520 5109 2.910479 TGCCGGTCGTGTCTCTGT 60.910 61.111 1.90 0.00 0.00 3.41
2521 5110 2.126424 GCCGGTCGTGTCTCTGTC 60.126 66.667 1.90 0.00 0.00 3.51
2522 5111 2.916052 GCCGGTCGTGTCTCTGTCA 61.916 63.158 1.90 0.00 0.00 3.58
2523 5112 1.883732 CCGGTCGTGTCTCTGTCAT 59.116 57.895 0.00 0.00 0.00 3.06
2524 5113 0.456824 CCGGTCGTGTCTCTGTCATG 60.457 60.000 0.00 0.00 0.00 3.07
2525 5114 1.073216 CGGTCGTGTCTCTGTCATGC 61.073 60.000 0.00 0.00 0.00 4.06
2526 5115 1.073216 GGTCGTGTCTCTGTCATGCG 61.073 60.000 0.00 0.00 0.00 4.73
2551 5140 4.760047 CGGCAACCTGAGACGGGG 62.760 72.222 0.00 0.00 33.40 5.73
2608 5197 3.512516 GATTGCAGCACGGGAGGC 61.513 66.667 0.00 0.00 0.00 4.70
2631 5220 3.711704 GGATCAGATTACTCTCCACCCAA 59.288 47.826 0.00 0.00 0.00 4.12
2655 5244 2.480419 GCAGTGCGTTTTGTCACTAGAT 59.520 45.455 0.00 0.00 41.19 1.98
2659 5248 5.061064 CAGTGCGTTTTGTCACTAGATAGAC 59.939 44.000 0.00 2.25 41.19 2.59
2663 5252 7.435488 GTGCGTTTTGTCACTAGATAGACATAT 59.565 37.037 14.71 0.00 43.57 1.78
2684 5273 3.429492 TGCACCTGAAATTTAGATGCCA 58.571 40.909 1.44 0.00 0.00 4.92
2686 5275 4.282957 TGCACCTGAAATTTAGATGCCAAA 59.717 37.500 1.44 0.00 0.00 3.28
2687 5276 4.866486 GCACCTGAAATTTAGATGCCAAAG 59.134 41.667 0.00 0.00 0.00 2.77
2698 5287 8.593492 ATTTAGATGCCAAAGTGTTTTCTTTC 57.407 30.769 0.00 0.00 35.77 2.62
2699 5288 4.610945 AGATGCCAAAGTGTTTTCTTTCG 58.389 39.130 0.00 0.00 35.77 3.46
2700 5289 3.859411 TGCCAAAGTGTTTTCTTTCGT 57.141 38.095 0.00 0.00 35.77 3.85
2701 5290 3.506810 TGCCAAAGTGTTTTCTTTCGTG 58.493 40.909 0.00 0.00 35.77 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 2015 7.201635 CCAGATGGTTTCAAACAAAGAAAAAGG 60.202 37.037 1.93 0.00 36.80 3.11
276 2016 7.687445 CCAGATGGTTTCAAACAAAGAAAAAG 58.313 34.615 1.93 0.00 36.80 2.27
403 2151 6.490040 ACATAAACACCTTAGATTGCACAAGT 59.510 34.615 0.00 0.00 0.00 3.16
791 2738 2.977914 TGTGCAGAGCCTTTAGATGAC 58.022 47.619 0.00 0.00 0.00 3.06
834 2790 7.595819 ATCTTTAAGACAGATAGTGCTAGCT 57.404 36.000 17.23 0.00 31.01 3.32
949 2948 1.202879 TCAATGGTCTTTCCGGCACTT 60.203 47.619 0.00 0.00 39.52 3.16
1320 3401 2.095617 TGTGAACATCTCGCATGCTTTG 60.096 45.455 17.13 9.95 39.68 2.77
1674 3779 1.374190 CTCCTGTTGCTGCTGAGGT 59.626 57.895 0.00 0.00 0.00 3.85
1683 3788 4.748144 CAGGGCCCCTCCTGTTGC 62.748 72.222 21.43 0.00 46.89 4.17
1726 3831 3.495331 TGAAAATGTCCAGGCTAAAGCA 58.505 40.909 4.07 0.00 44.36 3.91
1728 3833 6.515832 AGTTTTGAAAATGTCCAGGCTAAAG 58.484 36.000 0.00 0.00 0.00 1.85
1731 3836 6.279882 CAAAGTTTTGAAAATGTCCAGGCTA 58.720 36.000 0.00 0.00 40.55 3.93
1761 3870 6.435430 AACAATCATATGAAAGCTAACGCA 57.565 33.333 9.99 0.00 39.10 5.24
1781 3893 4.641094 ACCTGTTTCAACCGACAAATAACA 59.359 37.500 0.00 0.00 0.00 2.41
1788 3900 0.460722 TCGACCTGTTTCAACCGACA 59.539 50.000 0.00 0.00 0.00 4.35
1837 3985 7.934855 AATCACAAATTCATAGTGCTTCTCT 57.065 32.000 0.00 0.00 33.44 3.10
1876 4024 6.500589 TTGGGTTTGGAATGGTAAAATTCA 57.499 33.333 0.00 0.00 38.14 2.57
1933 4081 3.309682 CCACACGCAAACATACCAGATAG 59.690 47.826 0.00 0.00 0.00 2.08
1934 4082 3.266636 CCACACGCAAACATACCAGATA 58.733 45.455 0.00 0.00 0.00 1.98
1935 4083 2.083774 CCACACGCAAACATACCAGAT 58.916 47.619 0.00 0.00 0.00 2.90
1936 4084 1.518325 CCACACGCAAACATACCAGA 58.482 50.000 0.00 0.00 0.00 3.86
1937 4085 0.109781 GCCACACGCAAACATACCAG 60.110 55.000 0.00 0.00 37.47 4.00
1938 4086 1.953017 GCCACACGCAAACATACCA 59.047 52.632 0.00 0.00 37.47 3.25
1939 4087 4.859784 GCCACACGCAAACATACC 57.140 55.556 0.00 0.00 37.47 2.73
1981 4136 6.309494 GGAACGGTAAAATTTGACCAATTAGC 59.691 38.462 22.35 7.05 33.60 3.09
2056 4218 6.577103 TGAACCACAAGCAAACATTTCATAA 58.423 32.000 0.00 0.00 0.00 1.90
2062 4224 2.431782 AGCTGAACCACAAGCAAACATT 59.568 40.909 0.00 0.00 0.00 2.71
2079 4553 3.011818 TCCATGCAAGACAATACAGCTG 58.988 45.455 13.48 13.48 0.00 4.24
2138 4620 1.269448 ACACCAATGCACATTCGGTTC 59.731 47.619 12.08 0.00 0.00 3.62
2169 4651 3.752412 ATGAACGATCGTCGACTGTTA 57.248 42.857 22.98 1.34 43.74 2.41
2176 4658 1.253800 CAGCAGAATGAACGATCGTCG 59.746 52.381 22.98 6.33 42.67 5.12
2179 4661 2.285486 GCTTCAGCAGAATGAACGATCG 60.285 50.000 14.88 14.88 39.69 3.69
2212 4697 5.413833 CAGATCCTTGTGCATTCAGTTACTT 59.586 40.000 0.00 0.00 0.00 2.24
2252 4739 1.470632 CGGATCAGTGAGGAACAGAGC 60.471 57.143 0.00 0.00 30.46 4.09
2266 4774 0.608130 CCCAGTGACAAGACGGATCA 59.392 55.000 0.00 0.00 0.00 2.92
2269 4777 0.757561 TCACCCAGTGACAAGACGGA 60.758 55.000 0.00 0.00 37.67 4.69
2273 4781 0.764271 TGCATCACCCAGTGACAAGA 59.236 50.000 0.00 0.00 45.65 3.02
2297 4805 1.351076 AAATGCCACCCCCTTTTGAG 58.649 50.000 0.00 0.00 0.00 3.02
2359 4867 0.675083 TCACAAAACGGAGCCGACTA 59.325 50.000 16.83 0.00 42.83 2.59
2360 4868 0.600255 CTCACAAAACGGAGCCGACT 60.600 55.000 16.83 0.00 42.83 4.18
2380 4888 2.239400 CCCCACATCGATGACTAGCTA 58.761 52.381 31.33 0.00 0.00 3.32
2387 4895 0.108377 CGAACACCCCACATCGATGA 60.108 55.000 31.33 0.00 37.48 2.92
2396 4904 2.075355 ATTGGGCTTCGAACACCCCA 62.075 55.000 22.91 20.44 45.45 4.96
2402 4910 2.413634 CGGTGTAAATTGGGCTTCGAAC 60.414 50.000 0.00 0.00 0.00 3.95
2404 4912 1.444836 CGGTGTAAATTGGGCTTCGA 58.555 50.000 0.00 0.00 0.00 3.71
2405 4913 0.450184 CCGGTGTAAATTGGGCTTCG 59.550 55.000 0.00 0.00 0.00 3.79
2406 4914 0.172578 GCCGGTGTAAATTGGGCTTC 59.827 55.000 1.90 0.00 40.59 3.86
2407 4915 0.540830 TGCCGGTGTAAATTGGGCTT 60.541 50.000 1.90 0.00 44.07 4.35
2409 4917 1.214325 GTGCCGGTGTAAATTGGGC 59.786 57.895 1.90 0.00 44.00 5.36
2411 4919 1.068610 CACTGTGCCGGTGTAAATTGG 60.069 52.381 1.90 0.00 36.14 3.16
2412 4920 2.330231 CACTGTGCCGGTGTAAATTG 57.670 50.000 1.90 0.00 36.14 2.32
2419 4927 1.518325 TTGATTACACTGTGCCGGTG 58.482 50.000 7.90 11.30 45.33 4.94
2420 4928 2.489938 ATTGATTACACTGTGCCGGT 57.510 45.000 7.90 0.00 0.00 5.28
2421 4929 3.687212 TGTTATTGATTACACTGTGCCGG 59.313 43.478 7.90 0.00 0.00 6.13
2422 4930 4.937696 TGTTATTGATTACACTGTGCCG 57.062 40.909 7.90 0.00 0.00 5.69
2424 4932 5.036737 GCCATGTTATTGATTACACTGTGC 58.963 41.667 7.90 0.00 0.00 4.57
2426 4934 5.357878 CCAGCCATGTTATTGATTACACTGT 59.642 40.000 0.00 0.00 0.00 3.55
2429 4937 5.221048 GGTCCAGCCATGTTATTGATTACAC 60.221 44.000 0.00 0.00 37.17 2.90
2432 4940 5.387113 AGGTCCAGCCATGTTATTGATTA 57.613 39.130 0.00 0.00 40.61 1.75
2433 4941 4.255510 AGGTCCAGCCATGTTATTGATT 57.744 40.909 0.00 0.00 40.61 2.57
2434 4942 3.959495 AGGTCCAGCCATGTTATTGAT 57.041 42.857 0.00 0.00 40.61 2.57
2436 4944 3.822735 CCATAGGTCCAGCCATGTTATTG 59.177 47.826 0.00 0.00 40.61 1.90
2437 4945 3.751893 GCCATAGGTCCAGCCATGTTATT 60.752 47.826 0.00 0.00 40.61 1.40
2438 4946 2.224867 GCCATAGGTCCAGCCATGTTAT 60.225 50.000 0.00 0.00 40.61 1.89
2439 4947 1.142870 GCCATAGGTCCAGCCATGTTA 59.857 52.381 0.00 0.00 40.61 2.41
2440 4948 0.106519 GCCATAGGTCCAGCCATGTT 60.107 55.000 0.00 0.00 40.61 2.71
2441 4949 1.281199 TGCCATAGGTCCAGCCATGT 61.281 55.000 0.00 0.00 40.61 3.21
2442 4950 0.106569 TTGCCATAGGTCCAGCCATG 60.107 55.000 0.00 0.00 40.61 3.66
2448 5027 2.125310 CGCGTTGCCATAGGTCCA 60.125 61.111 0.00 0.00 0.00 4.02
2465 5044 4.838486 CGACGGACTGCTCGAGCC 62.838 72.222 33.23 18.49 41.18 4.70
2514 5103 3.059099 TGTGGCGCATGACAGAGA 58.941 55.556 10.83 0.00 29.71 3.10
2515 5104 1.079612 TCTGTGGCGCATGACAGAG 60.080 57.895 24.22 14.78 45.80 3.35
2516 5105 1.374631 GTCTGTGGCGCATGACAGA 60.375 57.895 24.22 24.22 44.99 3.41
2517 5106 2.733671 CGTCTGTGGCGCATGACAG 61.734 63.158 21.24 21.24 40.89 3.51
2518 5107 2.738139 CGTCTGTGGCGCATGACA 60.738 61.111 21.72 7.90 0.00 3.58
2519 5108 3.490759 CCGTCTGTGGCGCATGAC 61.491 66.667 10.83 15.89 0.00 3.06
2538 5127 2.671070 CATGCCCCGTCTCAGGTT 59.329 61.111 0.00 0.00 0.00 3.50
2551 5140 4.828296 CCCTGGGCTGGACCATGC 62.828 72.222 0.00 0.60 40.36 4.06
2608 5197 2.297597 GGGTGGAGAGTAATCTGATCCG 59.702 54.545 0.00 0.00 32.07 4.18
2631 5220 2.109739 TGACAAAACGCACTGCCGT 61.110 52.632 0.00 0.00 44.41 5.68
2655 5244 9.276590 CATCTAAATTTCAGGTGCATATGTCTA 57.723 33.333 4.29 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.