Multiple sequence alignment - TraesCS1D01G228800

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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 TraesCS1D01G228800 chr1D 100.000 6040 0 0 1 6040 316686487 316680448 0.000000e+00 11154.0
1 TraesCS1D01G228800 chr1D 98.160 326 4 1 3036 3361 316683127 316682804 8.790000e-158 568.0
2 TraesCS1D01G228800 chr1D 98.160 326 4 1 3361 3684 316683452 316683127 8.790000e-158 568.0
3 TraesCS1D01G228800 chr1D 100.000 39 0 0 5745 5783 316680703 316680665 8.400000e-09 73.1
4 TraesCS1D01G228800 chr1D 100.000 39 0 0 5785 5823 316680743 316680705 8.400000e-09 73.1
5 TraesCS1D01G228800 chr1B 93.875 2857 115 24 551 3359 428813714 428810870 0.000000e+00 4252.0
6 TraesCS1D01G228800 chr1B 94.585 1939 68 15 3695 5605 428810696 428808767 0.000000e+00 2964.0
7 TraesCS1D01G228800 chr1B 95.308 341 14 2 3361 3699 428811193 428810853 1.920000e-149 540.0
8 TraesCS1D01G228800 chr1B 92.308 325 24 1 1 325 428816537 428816214 1.530000e-125 460.0
9 TraesCS1D01G228800 chr1B 91.440 257 16 4 5785 6040 428808581 428808330 1.250000e-91 348.0
10 TraesCS1D01G228800 chr1B 91.057 246 18 4 320 564 428816162 428815920 4.510000e-86 329.0
11 TraesCS1D01G228800 chr1B 94.149 188 10 1 5595 5781 428808732 428808545 9.910000e-73 285.0
12 TraesCS1D01G228800 chr1A 92.344 1933 116 20 3695 5605 397773763 397771841 0.000000e+00 2721.0
13 TraesCS1D01G228800 chr1A 89.731 2084 119 38 318 2395 397776737 397774743 0.000000e+00 2575.0
14 TraesCS1D01G228800 chr1A 90.670 911 55 9 2456 3359 397774713 397773826 0.000000e+00 1184.0
15 TraesCS1D01G228800 chr1A 93.846 325 19 1 1 325 397777110 397776787 7.040000e-134 488.0
16 TraesCS1D01G228800 chr1A 91.586 309 19 5 3391 3696 397774115 397773811 2.600000e-113 420.0
17 TraesCS1D01G228800 chr1A 90.698 258 15 5 5785 6040 397771655 397771405 9.700000e-88 335.0
18 TraesCS1D01G228800 chr1A 92.632 190 10 2 5595 5783 397771806 397771620 2.770000e-68 270.0
19 TraesCS1D01G228800 chr7D 96.296 54 2 0 2393 2446 22262964 22263017 8.340000e-14 89.8
20 TraesCS1D01G228800 chr2B 93.333 60 4 0 2388 2447 572791052 572791111 8.340000e-14 89.8
21 TraesCS1D01G228800 chr3A 93.220 59 4 0 2388 2446 659015378 659015436 3.000000e-13 87.9
22 TraesCS1D01G228800 chr7B 91.935 62 4 1 2386 2446 740050286 740050347 1.080000e-12 86.1
23 TraesCS1D01G228800 chr2A 94.545 55 3 0 2388 2442 632952299 632952353 1.080000e-12 86.1
24 TraesCS1D01G228800 chr4A 91.667 60 5 0 2387 2446 132999997 133000056 3.880000e-12 84.2
25 TraesCS1D01G228800 chr4A 83.824 68 9 2 2 68 646975291 646975225 5.050000e-06 63.9
26 TraesCS1D01G228800 chr3D 91.667 60 5 0 2387 2446 47480281 47480222 3.880000e-12 84.2
27 TraesCS1D01G228800 chr3B 91.803 61 4 1 2387 2446 111680837 111680777 3.880000e-12 84.2


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 TraesCS1D01G228800 chr1D 316680448 316686487 6039 True 11154.000000 11154 100.000000 1 6040 1 chr1D.!!$R1 6039
1 TraesCS1D01G228800 chr1D 316680665 316683452 2787 True 320.550000 568 99.080000 3036 5823 4 chr1D.!!$R2 2787
2 TraesCS1D01G228800 chr1B 428808330 428816537 8207 True 1311.142857 4252 93.246000 1 6040 7 chr1B.!!$R1 6039
3 TraesCS1D01G228800 chr1A 397771405 397777110 5705 True 1141.857143 2721 91.643857 1 6040 7 chr1A.!!$R1 6039

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
780 3061 0.840722 CCACCAACTACCACCCTCCT 60.841 60.0 0.0 0.0 0.0 3.69 F
2597 4922 0.238817 ACACGAGACGACAAGAGAGC 59.761 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2773 5103 0.249073 CTATCAGGTGGGCTTCGACG 60.249 60.0 0.00 0.0 0.0 5.12 R
5766 8397 2.048444 AGCGCACATCATTCTCCATT 57.952 45.0 11.47 0.0 0.0 3.16 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
81 82 2.357637 CACACCCTTAATTGGCATACCG 59.642 50.000 0.00 0.00 39.70 4.02
105 106 2.163818 TTGACGCAAACCCTAGACTG 57.836 50.000 0.00 0.00 0.00 3.51
255 256 7.288560 AGATCTAGAAACATGCAAGATGGAAT 58.711 34.615 0.00 0.00 0.00 3.01
264 265 6.554784 ACATGCAAGATGGAATATGGGAATA 58.445 36.000 0.00 0.00 0.00 1.75
265 266 7.186972 ACATGCAAGATGGAATATGGGAATAT 58.813 34.615 0.00 0.00 0.00 1.28
273 274 4.294435 TGGAATATGGGAATATGGCATCCA 59.706 41.667 1.65 5.56 37.46 3.41
276 277 3.839323 ATGGGAATATGGCATCCATGT 57.161 42.857 15.44 0.00 44.84 3.21
313 314 3.700038 GCTTAGGTAGACTCTGGCAACTA 59.300 47.826 0.00 0.00 37.61 2.24
316 317 1.757699 GGTAGACTCTGGCAACTAGGG 59.242 57.143 0.00 0.00 37.61 3.53
326 383 1.004394 GGCAACTAGGGTGGCTAAGTT 59.996 52.381 13.12 0.00 41.86 2.66
339 396 1.336609 GCTAAGTTGGTTCGACTCGGT 60.337 52.381 0.00 0.00 0.00 4.69
350 407 3.380479 TCGACTCGGTTTGATTCAACT 57.620 42.857 0.00 0.00 0.00 3.16
384 441 1.228003 TGCCATCCGTCACCGTTTT 60.228 52.632 0.00 0.00 0.00 2.43
386 443 1.339247 TGCCATCCGTCACCGTTTTAT 60.339 47.619 0.00 0.00 0.00 1.40
387 444 1.741145 GCCATCCGTCACCGTTTTATT 59.259 47.619 0.00 0.00 0.00 1.40
409 466 3.261643 TGCTTCTTCTGCCTTCTGTATCA 59.738 43.478 0.00 0.00 0.00 2.15
418 475 4.973168 TGCCTTCTGTATCAAGTCACTTT 58.027 39.130 0.00 0.00 0.00 2.66
436 493 6.039829 GTCACTTTTTCCTTCTCCTTCACAAT 59.960 38.462 0.00 0.00 0.00 2.71
438 495 6.264067 CACTTTTTCCTTCTCCTTCACAATCT 59.736 38.462 0.00 0.00 0.00 2.40
459 516 4.100808 TCTCAATCCTTTTTGTTGGGTTGG 59.899 41.667 5.35 0.00 42.86 3.77
485 542 7.148540 GGTGTACGTGAATGTGTATGTTTGTAT 60.149 37.037 0.00 0.00 0.00 2.29
577 2853 9.575783 GGAAATACTTCTTCTCAAGTACTACTG 57.424 37.037 0.00 0.00 40.80 2.74
617 2893 6.309389 TCCCACTCTTCTAACCCTTTAATC 57.691 41.667 0.00 0.00 0.00 1.75
780 3061 0.840722 CCACCAACTACCACCCTCCT 60.841 60.000 0.00 0.00 0.00 3.69
861 3142 3.893763 CGGCCAACAAACACCGCA 61.894 61.111 2.24 0.00 39.08 5.69
862 3143 2.279186 GGCCAACAAACACCGCAC 60.279 61.111 0.00 0.00 0.00 5.34
863 3144 2.653766 GCCAACAAACACCGCACG 60.654 61.111 0.00 0.00 0.00 5.34
864 3145 2.653766 CCAACAAACACCGCACGC 60.654 61.111 0.00 0.00 0.00 5.34
892 3177 3.357079 GCACACCGAAGCAGTGGG 61.357 66.667 0.00 0.00 41.76 4.61
1045 3332 2.443016 CCTCCTCCACCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
1046 3333 3.151022 CTCCTCCACCTCCTCCGC 61.151 72.222 0.00 0.00 0.00 5.54
1047 3334 4.779733 TCCTCCACCTCCTCCGCC 62.780 72.222 0.00 0.00 0.00 6.13
1114 3401 1.592669 CGATCGGCTGATTTCGCCT 60.593 57.895 9.98 0.00 45.37 5.52
1145 3452 3.443045 GTTGGGGCTGATGCGTGG 61.443 66.667 0.00 0.00 40.82 4.94
1264 3572 1.515521 CCTTTTGCGGCGAGGACTTT 61.516 55.000 12.98 0.00 32.11 2.66
1418 3741 3.117657 TGGGACATTTCACGCCAAA 57.882 47.368 0.00 0.00 0.00 3.28
1460 3783 2.679837 CCTGAGGACGGAAATGTTGATG 59.320 50.000 0.00 0.00 0.00 3.07
1485 3808 2.421073 GTGCAATTAAGGAACCCGTACC 59.579 50.000 0.00 0.00 0.00 3.34
1513 3836 4.343814 AGTGGTTCGGAAAATCCATTGTTT 59.656 37.500 2.36 0.00 35.91 2.83
1559 3882 5.289434 GGTTTATTGCTTTGTAGATTGCTGC 59.711 40.000 0.00 0.00 0.00 5.25
1606 3929 4.889409 TGCTGGAGAATTCTTGTTTGTCTT 59.111 37.500 9.87 0.00 0.00 3.01
1625 3948 2.554370 TTGGTAGTTCGGGTTGGAAG 57.446 50.000 0.00 0.00 0.00 3.46
1648 3971 8.990163 AAGTGTAGAAATCAAGTTCCCTTTTA 57.010 30.769 0.00 0.00 0.00 1.52
1661 3984 0.958822 CCTTTTAGGTGGCTGCGTTT 59.041 50.000 0.00 0.00 0.00 3.60
1687 4010 7.780745 TGAACATTTTAGGAACCAACTCCTTTA 59.219 33.333 0.00 0.00 43.76 1.85
1728 4051 1.112315 TTGCTGGTTGGAATTGCGGT 61.112 50.000 0.00 0.00 0.00 5.68
1742 4065 1.677633 GCGGTATGTGGTTGGCCTT 60.678 57.895 3.32 0.00 35.27 4.35
1744 4067 1.951424 GCGGTATGTGGTTGGCCTTTA 60.951 52.381 3.32 0.00 35.27 1.85
1772 4095 7.416890 CGTTCCTACAGGAGTCTTTATGAATCT 60.417 40.741 0.00 0.00 46.36 2.40
1877 4200 3.358111 TTGTTGGTTCTGGAGTGAACA 57.642 42.857 9.18 0.00 45.74 3.18
1913 4236 5.884771 AGCTGAAAGTCTGAAACAGTTTTC 58.115 37.500 0.00 16.23 38.07 2.29
1938 4261 6.600388 TGTTATAGCTGGCCAATAAGATTGA 58.400 36.000 7.01 0.00 0.00 2.57
1941 4264 3.549794 AGCTGGCCAATAAGATTGACTC 58.450 45.455 7.01 0.00 0.00 3.36
1953 4276 2.094494 AGATTGACTCTACACAGTGGCG 60.094 50.000 5.31 0.00 30.26 5.69
1961 4284 2.002586 CTACACAGTGGCGAATTGAGG 58.997 52.381 5.31 0.00 0.00 3.86
1981 4304 3.070018 GGATGAAAGTGGAGGATATGCG 58.930 50.000 0.00 0.00 0.00 4.73
2207 4531 3.805971 GTCTAAAATATAAGGCGCACCGT 59.194 43.478 10.83 0.00 42.76 4.83
2270 4595 5.572126 GTGGACTATCTTATACGAAATCGGC 59.428 44.000 7.81 0.00 44.95 5.54
2318 4643 7.594758 ACACGAATCCAACAATGTCATTTTTAG 59.405 33.333 0.00 0.00 0.00 1.85
2330 4655 9.628746 CAATGTCATTTTTAGATCACACAATCA 57.371 29.630 0.00 0.00 0.00 2.57
2402 4727 5.989777 ACATGTGCTATATTTTACCTCCGTC 59.010 40.000 0.00 0.00 0.00 4.79
2437 4762 6.338146 TGTCTTAGATTTGTCTTGATACGGG 58.662 40.000 0.00 0.00 0.00 5.28
2459 4784 5.339861 GGGTGTATCTACGGAGGGAGTATAT 60.340 48.000 0.00 0.00 0.00 0.86
2462 4787 7.831193 GGTGTATCTACGGAGGGAGTATATTTA 59.169 40.741 0.00 0.00 0.00 1.40
2464 4789 9.624373 TGTATCTACGGAGGGAGTATATTTATC 57.376 37.037 0.00 0.00 0.00 1.75
2469 4794 7.941431 ACGGAGGGAGTATATTTATCAGTAG 57.059 40.000 0.00 0.00 0.00 2.57
2550 4875 2.041922 TCGCCTCCCCTGCTACAT 60.042 61.111 0.00 0.00 0.00 2.29
2590 4915 2.051614 GTGCGACACGAGACGACA 60.052 61.111 8.95 3.71 34.91 4.35
2597 4922 0.238817 ACACGAGACGACAAGAGAGC 59.761 55.000 0.00 0.00 0.00 4.09
2651 4976 2.359850 CACTAAGGCCCAAGCGCA 60.360 61.111 11.47 0.00 41.24 6.09
2798 5128 1.794714 AGCCCACCTGATAGATTCGT 58.205 50.000 0.00 0.00 0.00 3.85
2915 5246 2.550180 GCTCTTCAGTTTGAGTCCCAAC 59.450 50.000 0.00 0.00 33.85 3.77
2916 5247 3.142174 CTCTTCAGTTTGAGTCCCAACC 58.858 50.000 0.00 0.00 33.85 3.77
5761 8392 3.887621 TCACTACCAAGTCTATGCACC 57.112 47.619 0.00 0.00 31.97 5.01
5762 8393 3.169908 TCACTACCAAGTCTATGCACCA 58.830 45.455 0.00 0.00 31.97 4.17
5763 8394 3.195610 TCACTACCAAGTCTATGCACCAG 59.804 47.826 0.00 0.00 31.97 4.00
5764 8395 3.195610 CACTACCAAGTCTATGCACCAGA 59.804 47.826 0.00 0.00 31.97 3.86
5765 8396 4.033709 ACTACCAAGTCTATGCACCAGAT 58.966 43.478 3.34 0.00 0.00 2.90
5766 8397 5.069119 CACTACCAAGTCTATGCACCAGATA 59.931 44.000 3.34 0.00 31.97 1.98
5767 8398 5.661312 ACTACCAAGTCTATGCACCAGATAA 59.339 40.000 3.34 0.00 0.00 1.75
5768 8399 5.636903 ACCAAGTCTATGCACCAGATAAT 57.363 39.130 3.34 0.00 0.00 1.28
5769 8400 5.371526 ACCAAGTCTATGCACCAGATAATG 58.628 41.667 3.34 3.89 0.00 1.90
5783 8414 5.278964 CAGATAATGGAGAATGATGTGCG 57.721 43.478 0.00 0.00 0.00 5.34
5784 8415 3.750130 AGATAATGGAGAATGATGTGCGC 59.250 43.478 0.00 0.00 0.00 6.09
5785 8416 2.048444 AATGGAGAATGATGTGCGCT 57.952 45.000 9.73 0.00 0.00 5.92
5786 8417 2.916702 ATGGAGAATGATGTGCGCTA 57.083 45.000 9.73 0.00 0.00 4.26
5787 8418 1.939974 TGGAGAATGATGTGCGCTAC 58.060 50.000 9.73 5.95 0.00 3.58
5788 8419 1.221414 GGAGAATGATGTGCGCTACC 58.779 55.000 9.73 0.00 0.00 3.18
5789 8420 1.473257 GGAGAATGATGTGCGCTACCA 60.473 52.381 9.73 2.81 0.00 3.25
5790 8421 2.279741 GAGAATGATGTGCGCTACCAA 58.720 47.619 9.73 0.00 0.00 3.67
5791 8422 2.283298 AGAATGATGTGCGCTACCAAG 58.717 47.619 9.73 0.00 0.00 3.61
5792 8423 2.009774 GAATGATGTGCGCTACCAAGT 58.990 47.619 9.73 0.00 0.00 3.16
5793 8424 1.656652 ATGATGTGCGCTACCAAGTC 58.343 50.000 9.73 0.00 0.00 3.01
5794 8425 0.608130 TGATGTGCGCTACCAAGTCT 59.392 50.000 9.73 0.00 0.00 3.24
5795 8426 1.822371 TGATGTGCGCTACCAAGTCTA 59.178 47.619 9.73 0.00 0.00 2.59
5796 8427 2.430694 TGATGTGCGCTACCAAGTCTAT 59.569 45.455 9.73 0.00 0.00 1.98
5797 8428 2.293677 TGTGCGCTACCAAGTCTATG 57.706 50.000 9.73 0.00 0.00 2.23
5798 8429 0.931005 GTGCGCTACCAAGTCTATGC 59.069 55.000 9.73 0.00 0.00 3.14
5799 8430 0.534873 TGCGCTACCAAGTCTATGCA 59.465 50.000 9.73 0.00 0.00 3.96
5800 8431 0.931005 GCGCTACCAAGTCTATGCAC 59.069 55.000 0.00 0.00 0.00 4.57
5832 8464 1.884579 GAATGATGTGCATGGGGCTAG 59.115 52.381 0.00 0.00 45.15 3.42
5962 8595 3.002102 GGCCTGGCAATAATGTTTGTTG 58.998 45.455 22.05 0.00 35.21 3.33
5974 8607 5.964887 AATGTTTGTTGGTTTTGTGATCG 57.035 34.783 0.00 0.00 0.00 3.69
5999 8632 2.423185 TGAGTCAGTGCAACACCTTTTG 59.577 45.455 0.00 0.00 41.43 2.44
6018 8651 1.619363 TTCCCATGCCCTGTAGCCT 60.619 57.895 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.271325 TGTCATCAAGTGGAACGGCAT 60.271 47.619 0.00 0.00 45.86 4.40
81 82 2.093658 TCTAGGGTTTGCGTCAATCTCC 60.094 50.000 0.00 0.00 0.00 3.71
105 106 6.019156 GCAAAGTAGCAGTCTTATGATGAGAC 60.019 42.308 9.13 9.13 42.99 3.36
230 231 6.244552 TCCATCTTGCATGTTTCTAGATCT 57.755 37.500 0.00 0.00 0.00 2.75
235 236 6.491062 CCCATATTCCATCTTGCATGTTTCTA 59.509 38.462 0.00 0.00 0.00 2.10
255 256 4.951873 ACATGGATGCCATATTCCCATA 57.048 40.909 0.00 0.00 43.15 2.74
264 265 4.795469 TCATGAACTTACATGGATGCCAT 58.205 39.130 0.00 0.00 46.37 4.40
265 266 4.201657 CTCATGAACTTACATGGATGCCA 58.798 43.478 0.00 0.00 45.10 4.92
273 274 4.307032 AAGCCACCTCATGAACTTACAT 57.693 40.909 0.00 0.00 0.00 2.29
276 277 3.844211 ACCTAAGCCACCTCATGAACTTA 59.156 43.478 0.00 0.06 0.00 2.24
313 314 0.036306 CGAACCAACTTAGCCACCCT 59.964 55.000 0.00 0.00 0.00 4.34
316 317 2.067013 GAGTCGAACCAACTTAGCCAC 58.933 52.381 0.00 0.00 0.00 5.01
326 383 2.224090 TGAATCAAACCGAGTCGAACCA 60.224 45.455 15.64 0.00 41.73 3.67
339 396 2.582052 ACCGGCAAGAGTTGAATCAAA 58.418 42.857 0.00 0.00 0.00 2.69
350 407 2.485795 GCACCAACAACCGGCAAGA 61.486 57.895 0.00 0.00 0.00 3.02
384 441 4.292186 ACAGAAGGCAGAAGAAGCAATA 57.708 40.909 0.00 0.00 0.00 1.90
386 443 2.645838 ACAGAAGGCAGAAGAAGCAA 57.354 45.000 0.00 0.00 0.00 3.91
387 444 3.261643 TGATACAGAAGGCAGAAGAAGCA 59.738 43.478 0.00 0.00 0.00 3.91
409 466 5.590663 GTGAAGGAGAAGGAAAAAGTGACTT 59.409 40.000 0.00 0.00 0.00 3.01
418 475 5.567037 TGAGATTGTGAAGGAGAAGGAAA 57.433 39.130 0.00 0.00 0.00 3.13
436 493 4.100808 CCAACCCAACAAAAAGGATTGAGA 59.899 41.667 0.00 0.00 34.38 3.27
438 495 3.135530 CCCAACCCAACAAAAAGGATTGA 59.864 43.478 0.00 0.00 34.38 2.57
459 516 5.049954 ACAAACATACACATTCACGTACACC 60.050 40.000 0.00 0.00 0.00 4.16
577 2853 3.315470 GTGGGAAATCGGAATTTCTAGGC 59.685 47.826 9.90 0.00 46.65 3.93
780 3061 0.252789 TATGGGACGGAAAGGTGGGA 60.253 55.000 0.00 0.00 0.00 4.37
892 3177 1.178276 TTCTGTCCGCTCCTCTCTTC 58.822 55.000 0.00 0.00 0.00 2.87
935 3220 0.178975 TTCCCCTTTGCGTTGGTGAT 60.179 50.000 0.00 0.00 0.00 3.06
942 3227 0.036875 CTCTCCTTTCCCCTTTGCGT 59.963 55.000 0.00 0.00 0.00 5.24
944 3229 1.630878 TCTCTCTCCTTTCCCCTTTGC 59.369 52.381 0.00 0.00 0.00 3.68
1145 3452 1.332882 GACGTACGACCACAGCGAAC 61.333 60.000 24.41 0.00 0.00 3.95
1375 3698 5.623956 TCGGCTAAAATTATCTCAAGGGA 57.376 39.130 0.00 0.00 0.00 4.20
1410 3733 3.363970 GCATCCTAACGATATTTGGCGTG 60.364 47.826 0.00 0.00 41.06 5.34
1418 3741 2.929960 CGTGACGCATCCTAACGATAT 58.070 47.619 0.00 0.00 36.38 1.63
1440 3763 3.599343 TCATCAACATTTCCGTCCTCAG 58.401 45.455 0.00 0.00 0.00 3.35
1460 3783 2.099098 CGGGTTCCTTAATTGCACCATC 59.901 50.000 0.00 0.00 0.00 3.51
1485 3808 5.699097 TGGATTTTCCGAACCACTAAAAG 57.301 39.130 0.00 0.00 40.17 2.27
1559 3882 7.519843 CAGAACATTCAAGAGTCTCATCTTTG 58.480 38.462 1.94 0.00 37.43 2.77
1606 3929 1.770061 ACTTCCAACCCGAACTACCAA 59.230 47.619 0.00 0.00 0.00 3.67
1648 3971 0.823356 ATGTTCAAACGCAGCCACCT 60.823 50.000 0.00 0.00 0.00 4.00
1661 3984 5.701224 AGGAGTTGGTTCCTAAAATGTTCA 58.299 37.500 0.00 0.00 45.76 3.18
1728 4051 1.003812 ACGCTAAAGGCCAACCACATA 59.996 47.619 5.01 0.00 39.06 2.29
1742 4065 3.083122 AGACTCCTGTAGGAACGCTAA 57.917 47.619 1.74 0.00 44.91 3.09
1744 4067 1.926108 AAGACTCCTGTAGGAACGCT 58.074 50.000 1.74 0.00 44.91 5.07
1877 4200 2.638480 TTCAGCTAGTTGCACCAGTT 57.362 45.000 0.97 0.00 45.94 3.16
1892 4215 6.846350 ACAGAAAACTGTTTCAGACTTTCAG 58.154 36.000 6.20 16.60 44.82 3.02
1913 4236 6.712095 TCAATCTTATTGGCCAGCTATAACAG 59.288 38.462 5.11 0.00 0.00 3.16
1938 4261 2.299013 TCAATTCGCCACTGTGTAGAGT 59.701 45.455 7.08 0.00 0.00 3.24
1941 4264 2.002586 CCTCAATTCGCCACTGTGTAG 58.997 52.381 7.08 0.31 0.00 2.74
1953 4276 4.848357 TCCTCCACTTTCATCCTCAATTC 58.152 43.478 0.00 0.00 0.00 2.17
1961 4284 2.481952 GCGCATATCCTCCACTTTCATC 59.518 50.000 0.30 0.00 0.00 2.92
1981 4304 9.657121 GATTCAGATTAGTGTATTAAGCTTTGC 57.343 33.333 3.20 0.00 27.39 3.68
2270 4595 8.427012 CGTGTTGGAATGAACTTTTGAATAATG 58.573 33.333 0.00 0.00 0.00 1.90
2402 4727 9.014297 AGACAAATCTAAGACAACTAATTTGGG 57.986 33.333 9.60 0.00 36.32 4.12
2437 4762 7.700022 AAATATACTCCCTCCGTAGATACAC 57.300 40.000 0.00 0.00 0.00 2.90
2462 4787 9.354673 TCTTTTCTTTCCAAATTCACTACTGAT 57.645 29.630 0.00 0.00 0.00 2.90
2464 4789 9.455847 CTTCTTTTCTTTCCAAATTCACTACTG 57.544 33.333 0.00 0.00 0.00 2.74
2469 4794 7.278646 AGCAACTTCTTTTCTTTCCAAATTCAC 59.721 33.333 0.00 0.00 0.00 3.18
2550 4875 1.227823 CGTTGGCAACCAGAGACCA 60.228 57.895 23.68 0.00 33.81 4.02
2590 4915 1.541233 CCTGTGTTGAACCGCTCTCTT 60.541 52.381 0.00 0.00 0.00 2.85
2597 4922 0.320771 AGCTAGCCTGTGTTGAACCG 60.321 55.000 12.13 0.00 0.00 4.44
2651 4976 1.322442 GGTTCTGGACAAAGCAAGCT 58.678 50.000 0.00 0.00 0.00 3.74
2750 5080 1.674962 CTAGCCTCTGATTTTGCCAGC 59.325 52.381 0.00 0.00 0.00 4.85
2773 5103 0.249073 CTATCAGGTGGGCTTCGACG 60.249 60.000 0.00 0.00 0.00 5.12
2798 5128 7.399245 AAAAAGAAACTTGTACAGCCAGTAA 57.601 32.000 0.00 0.00 33.72 2.24
2938 5276 5.777802 TCAGAGAGCTTAGAACTTGAGTTG 58.222 41.667 0.30 0.00 38.56 3.16
5761 8392 4.378149 GCGCACATCATTCTCCATTATCTG 60.378 45.833 0.30 0.00 0.00 2.90
5762 8393 3.750130 GCGCACATCATTCTCCATTATCT 59.250 43.478 0.30 0.00 0.00 1.98
5763 8394 3.750130 AGCGCACATCATTCTCCATTATC 59.250 43.478 11.47 0.00 0.00 1.75
5764 8395 3.748083 AGCGCACATCATTCTCCATTAT 58.252 40.909 11.47 0.00 0.00 1.28
5765 8396 3.198409 AGCGCACATCATTCTCCATTA 57.802 42.857 11.47 0.00 0.00 1.90
5766 8397 2.048444 AGCGCACATCATTCTCCATT 57.952 45.000 11.47 0.00 0.00 3.16
5767 8398 2.487934 GTAGCGCACATCATTCTCCAT 58.512 47.619 11.47 0.00 0.00 3.41
5768 8399 1.473257 GGTAGCGCACATCATTCTCCA 60.473 52.381 11.47 0.00 0.00 3.86
5769 8400 1.221414 GGTAGCGCACATCATTCTCC 58.779 55.000 11.47 0.00 0.00 3.71
5770 8401 1.939974 TGGTAGCGCACATCATTCTC 58.060 50.000 11.47 0.00 0.00 2.87
5771 8402 2.283298 CTTGGTAGCGCACATCATTCT 58.717 47.619 11.47 0.00 0.00 2.40
5772 8403 2.009774 ACTTGGTAGCGCACATCATTC 58.990 47.619 11.47 0.00 0.00 2.67
5773 8404 2.009774 GACTTGGTAGCGCACATCATT 58.990 47.619 11.47 0.00 0.00 2.57
5774 8405 1.208052 AGACTTGGTAGCGCACATCAT 59.792 47.619 11.47 0.00 0.00 2.45
5775 8406 0.608130 AGACTTGGTAGCGCACATCA 59.392 50.000 11.47 0.00 0.00 3.07
5776 8407 2.579207 TAGACTTGGTAGCGCACATC 57.421 50.000 11.47 0.00 0.00 3.06
5777 8408 2.826428 CATAGACTTGGTAGCGCACAT 58.174 47.619 11.47 0.00 0.00 3.21
5778 8409 1.739035 GCATAGACTTGGTAGCGCACA 60.739 52.381 11.47 2.05 0.00 4.57
5779 8410 0.931005 GCATAGACTTGGTAGCGCAC 59.069 55.000 11.47 5.73 0.00 5.34
5780 8411 0.534873 TGCATAGACTTGGTAGCGCA 59.465 50.000 11.47 0.00 0.00 6.09
5781 8412 0.931005 GTGCATAGACTTGGTAGCGC 59.069 55.000 0.00 0.00 0.00 5.92
5782 8413 1.134818 TGGTGCATAGACTTGGTAGCG 60.135 52.381 0.00 0.00 0.00 4.26
5783 8414 2.168521 TCTGGTGCATAGACTTGGTAGC 59.831 50.000 0.00 0.00 0.00 3.58
5784 8415 4.679373 ATCTGGTGCATAGACTTGGTAG 57.321 45.455 5.86 0.00 0.00 3.18
5785 8416 6.464322 CCATTATCTGGTGCATAGACTTGGTA 60.464 42.308 5.86 0.00 40.49 3.25
5786 8417 5.371526 CATTATCTGGTGCATAGACTTGGT 58.628 41.667 5.86 0.00 0.00 3.67
5787 8418 4.758674 CCATTATCTGGTGCATAGACTTGG 59.241 45.833 5.86 9.03 40.49 3.61
5788 8419 5.614308 TCCATTATCTGGTGCATAGACTTG 58.386 41.667 5.86 4.85 46.08 3.16
5789 8420 5.604231 TCTCCATTATCTGGTGCATAGACTT 59.396 40.000 5.86 0.00 46.08 3.01
5790 8421 5.150715 TCTCCATTATCTGGTGCATAGACT 58.849 41.667 5.86 0.40 46.08 3.24
5791 8422 5.474578 TCTCCATTATCTGGTGCATAGAC 57.525 43.478 5.86 0.00 46.08 2.59
5792 8423 6.270695 TCATTCTCCATTATCTGGTGCATAGA 59.729 38.462 6.15 6.15 46.08 1.98
5793 8424 6.470278 TCATTCTCCATTATCTGGTGCATAG 58.530 40.000 0.00 0.00 46.08 2.23
5794 8425 6.438186 TCATTCTCCATTATCTGGTGCATA 57.562 37.500 0.00 0.00 46.08 3.14
5795 8426 5.314718 TCATTCTCCATTATCTGGTGCAT 57.685 39.130 0.00 0.00 46.08 3.96
5796 8427 4.776435 TCATTCTCCATTATCTGGTGCA 57.224 40.909 0.00 0.00 46.08 4.57
5797 8428 5.048921 CACATCATTCTCCATTATCTGGTGC 60.049 44.000 0.00 0.00 46.08 5.01
5798 8429 5.048921 GCACATCATTCTCCATTATCTGGTG 60.049 44.000 0.00 0.00 46.08 4.17
5799 8430 5.068636 GCACATCATTCTCCATTATCTGGT 58.931 41.667 0.00 0.00 46.08 4.00
5800 8431 5.710567 ATGCACATCATTCTCCATTATCTGG 59.289 40.000 0.00 0.00 38.12 3.86
5832 8464 1.203287 GCCCTCCAAATCACTGAAAGC 59.797 52.381 0.00 0.00 37.60 3.51
5878 8511 5.240013 TGAAAGGGCTGCCATTTTATTTT 57.760 34.783 29.21 9.04 37.65 1.82
5879 8512 4.906747 TGAAAGGGCTGCCATTTTATTT 57.093 36.364 29.21 9.79 37.65 1.40
5880 8513 4.906747 TTGAAAGGGCTGCCATTTTATT 57.093 36.364 29.21 10.18 37.65 1.40
5881 8514 4.906747 TTTGAAAGGGCTGCCATTTTAT 57.093 36.364 29.21 10.56 37.65 1.40
5883 8516 3.574354 TTTTGAAAGGGCTGCCATTTT 57.426 38.095 29.21 22.75 37.65 1.82
5884 8517 3.414269 CATTTTGAAAGGGCTGCCATTT 58.586 40.909 29.05 29.05 40.34 2.32
5885 8518 2.876892 GCATTTTGAAAGGGCTGCCATT 60.877 45.455 22.05 17.94 0.00 3.16
5886 8519 1.339342 GCATTTTGAAAGGGCTGCCAT 60.339 47.619 22.05 11.43 0.00 4.40
5962 8595 1.812571 ACTCATGGCGATCACAAAACC 59.187 47.619 0.00 0.00 0.00 3.27
5974 8607 0.239347 GTGTTGCACTGACTCATGGC 59.761 55.000 0.00 0.00 0.00 4.40
5999 8632 1.453928 GGCTACAGGGCATGGGAAC 60.454 63.158 3.46 0.00 40.53 3.62


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

AutoCloner maintained by Alex Coulton.