Multiple sequence alignment - TraesCS7D01G182900

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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 TraesCS7D01G182900 chr7D 100.000 2666 0 0 1 2666 136254664 136251999 0.000000e+00 4924.0
1 TraesCS7D01G182900 chr7D 83.600 250 37 4 75 321 234793399 234793151 5.740000e-57 231.0
2 TraesCS7D01G182900 chr7B 93.513 1896 80 23 772 2634 99131347 99129462 0.000000e+00 2780.0
3 TraesCS7D01G182900 chr7B 83.150 273 41 5 38 308 511962814 511963083 7.370000e-61 244.0
4 TraesCS7D01G182900 chr7A 91.645 1939 94 16 1 1910 135902804 135900905 0.000000e+00 2621.0
5 TraesCS7D01G182900 chr7A 94.614 687 31 4 1902 2583 135900802 135900117 0.000000e+00 1059.0
6 TraesCS7D01G182900 chr7A 84.247 292 43 3 32 321 33030188 33029898 5.620000e-72 281.0
7 TraesCS7D01G182900 chr5B 84.420 276 41 2 1310 1584 430680028 430679754 1.220000e-68 270.0
8 TraesCS7D01G182900 chr5B 81.944 144 23 2 538 678 485896899 485896756 4.660000e-23 119.0
9 TraesCS7D01G182900 chr5B 82.927 82 12 2 1343 1423 123760773 123760693 3.680000e-09 73.1
10 TraesCS7D01G182900 chr5D 81.988 322 47 9 1 320 519451392 519451704 2.040000e-66 263.0
11 TraesCS7D01G182900 chr5D 85.317 252 37 0 1310 1561 364670755 364670504 7.320000e-66 261.0
12 TraesCS7D01G182900 chr5D 80.282 142 27 1 320 461 238134030 238134170 3.630000e-19 106.0
13 TraesCS7D01G182900 chr5D 88.333 60 7 0 1343 1402 113391589 113391530 3.680000e-09 73.1
14 TraesCS7D01G182900 chr5A 82.492 297 44 7 29 321 409330644 409330936 1.220000e-63 254.0
15 TraesCS7D01G182900 chr5A 82.609 276 46 2 1310 1584 465996825 465996551 2.650000e-60 243.0
16 TraesCS7D01G182900 chr3B 84.825 257 33 4 65 316 469675538 469675793 1.220000e-63 254.0
17 TraesCS7D01G182900 chr4D 81.570 293 44 7 32 321 502022332 502022617 1.600000e-57 233.0
18 TraesCS7D01G182900 chr4D 80.822 292 51 5 28 316 35593292 35593003 9.600000e-55 224.0
19 TraesCS7D01G182900 chr6A 82.773 238 33 6 1315 1548 520869896 520870129 3.480000e-49 206.0
20 TraesCS7D01G182900 chr6B 85.714 175 23 2 1293 1466 566535475 566535648 1.630000e-42 183.0
21 TraesCS7D01G182900 chr6B 76.498 217 42 8 537 747 192356886 192357099 2.810000e-20 110.0
22 TraesCS7D01G182900 chr6D 88.235 153 17 1 1315 1466 379724015 379723863 5.860000e-42 182.0
23 TraesCS7D01G182900 chr3A 80.162 247 45 4 73 316 743861932 743862177 5.860000e-42 182.0
24 TraesCS7D01G182900 chr3A 78.125 192 33 8 538 723 485944051 485943863 2.170000e-21 113.0
25 TraesCS7D01G182900 chr3A 91.667 72 6 0 319 390 239967886 239967957 1.690000e-17 100.0
26 TraesCS7D01G182900 chr2A 80.102 196 30 7 538 726 207480391 207480198 1.290000e-28 137.0
27 TraesCS7D01G182900 chr2A 81.507 146 24 3 326 469 382325995 382326139 1.680000e-22 117.0
28 TraesCS7D01G182900 chr3D 82.000 150 26 1 320 469 477915005 477915153 2.790000e-25 126.0
29 TraesCS7D01G182900 chr1B 76.569 239 47 7 514 745 515520868 515520632 3.600000e-24 122.0
30 TraesCS7D01G182900 chr2D 85.586 111 15 1 323 432 304268284 304268394 6.030000e-22 115.0
31 TraesCS7D01G182900 chr2D 91.781 73 4 2 319 390 481061743 481061814 1.690000e-17 100.0
32 TraesCS7D01G182900 chr2D 76.500 200 36 9 537 728 527641120 527640924 6.070000e-17 99.0
33 TraesCS7D01G182900 chr1A 81.618 136 25 0 327 462 579161679 579161544 2.170000e-21 113.0
34 TraesCS7D01G182900 chr4B 80.000 150 30 0 319 468 142543505 142543356 7.800000e-21 111.0
35 TraesCS7D01G182900 chr4B 74.779 226 45 12 534 753 645307890 645307671 1.020000e-14 91.6
36 TraesCS7D01G182900 chr1D 75.455 220 47 5 539 753 371064036 371063819 1.690000e-17 100.0


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 TraesCS7D01G182900 chr7D 136251999 136254664 2665 True 4924 4924 100.0000 1 2666 1 chr7D.!!$R1 2665
1 TraesCS7D01G182900 chr7B 99129462 99131347 1885 True 2780 2780 93.5130 772 2634 1 chr7B.!!$R1 1862
2 TraesCS7D01G182900 chr7A 135900117 135902804 2687 True 1840 2621 93.1295 1 2583 2 chr7A.!!$R2 2582

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
40 41 0.040646 TCCAGTACCTGTCCACGGAT 59.959 55.0 0.00 0.0 0.0 4.18 F
1609 1651 0.175760 GGCCTCGAGCAATCACAGTA 59.824 55.0 6.99 0.0 46.5 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1662 0.251033 TGCTGTTCTTGCATGGCTCT 60.251 50.000 0.0 0.0 35.31 4.09 R
2634 2809 1.875514 TGTGTCTGATTCTGCTTGCAC 59.124 47.619 0.0 0.0 0.00 4.57 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
26 27 5.250200 TGTAAATTTTCTACCGCATCCAGT 58.750 37.500 0.00 0.00 0.00 4.00
30 31 2.154567 TTCTACCGCATCCAGTACCT 57.845 50.000 0.00 0.00 0.00 3.08
37 38 0.460284 GCATCCAGTACCTGTCCACG 60.460 60.000 0.00 0.00 0.00 4.94
40 41 0.040646 TCCAGTACCTGTCCACGGAT 59.959 55.000 0.00 0.00 0.00 4.18
45 46 2.091499 AGTACCTGTCCACGGATATGGA 60.091 50.000 8.36 0.00 46.92 3.41
57 58 2.338809 GGATATGGATGTGGGAGGACA 58.661 52.381 0.00 0.00 0.00 4.02
72 73 2.672996 ACACCATCCAACCGCAGC 60.673 61.111 0.00 0.00 0.00 5.25
103 104 7.309920 ACATTTCGAACCGCATTTTAACTAAT 58.690 30.769 0.00 0.00 0.00 1.73
104 105 7.810759 ACATTTCGAACCGCATTTTAACTAATT 59.189 29.630 0.00 0.00 0.00 1.40
139 140 2.217750 CAAACCGGCCGATATTCATCA 58.782 47.619 30.73 0.00 0.00 3.07
169 170 8.761575 TTGGATAAAAAGAAGCACAAATCATC 57.238 30.769 0.00 0.00 0.00 2.92
170 171 8.125978 TGGATAAAAAGAAGCACAAATCATCT 57.874 30.769 0.00 0.00 0.00 2.90
182 183 7.602753 AGCACAAATCATCTATACGTAGCATA 58.397 34.615 0.08 0.00 0.00 3.14
235 236 8.892723 CAAATTTGACTACATTAGCCAGATGTA 58.107 33.333 13.08 4.86 38.58 2.29
236 237 8.438676 AATTTGACTACATTAGCCAGATGTAC 57.561 34.615 1.53 0.00 38.58 2.90
237 238 6.538945 TTGACTACATTAGCCAGATGTACA 57.461 37.500 0.00 0.00 38.58 2.90
268 269 1.860950 CATCAACGGATCATGTCGTCC 59.139 52.381 10.64 7.83 38.78 4.79
288 289 3.461458 TCCCATACATACTGCCCATTCAA 59.539 43.478 0.00 0.00 0.00 2.69
324 326 0.822811 TGTACGTAAATAGCCGGGCA 59.177 50.000 23.09 7.74 0.00 5.36
325 327 1.211743 GTACGTAAATAGCCGGGCAC 58.788 55.000 23.09 9.14 0.00 5.01
347 349 2.378038 CCCATATCCGCCCCATATTTG 58.622 52.381 0.00 0.00 0.00 2.32
348 350 2.025416 CCCATATCCGCCCCATATTTGA 60.025 50.000 0.00 0.00 0.00 2.69
381 384 3.971453 ATGTCTGTCAGTCCGCGCG 62.971 63.158 25.67 25.67 0.00 6.86
387 390 2.733218 TCAGTCCGCGCGTTTGAG 60.733 61.111 29.95 13.21 0.00 3.02
411 414 2.095919 GTCCGTCAGGGTCAAAATTTCG 60.096 50.000 0.00 0.00 38.33 3.46
437 440 3.066190 CAGTGACCGGGCCGTCTA 61.066 66.667 26.32 7.20 33.70 2.59
438 441 2.043248 AGTGACCGGGCCGTCTAT 60.043 61.111 26.32 7.10 33.70 1.98
439 442 2.125961 AGTGACCGGGCCGTCTATC 61.126 63.158 26.32 16.43 33.70 2.08
440 443 2.125961 GTGACCGGGCCGTCTATCT 61.126 63.158 26.32 0.00 33.70 1.98
441 444 2.125326 TGACCGGGCCGTCTATCTG 61.125 63.158 26.32 10.01 33.70 2.90
442 445 2.838225 ACCGGGCCGTCTATCTGG 60.838 66.667 26.32 9.20 0.00 3.86
443 446 2.520982 CCGGGCCGTCTATCTGGA 60.521 66.667 26.32 0.00 0.00 3.86
444 447 2.728817 CGGGCCGTCTATCTGGAC 59.271 66.667 19.97 0.00 0.00 4.02
454 457 2.094182 GTCTATCTGGACGTTTGAGGCA 60.094 50.000 0.00 0.00 0.00 4.75
462 465 1.106944 ACGTTTGAGGCAGGTTTGGG 61.107 55.000 0.00 0.00 0.00 4.12
463 466 1.805428 CGTTTGAGGCAGGTTTGGGG 61.805 60.000 0.00 0.00 0.00 4.96
510 513 8.948401 AACTCTAGCTCCATATAAGATCTCAA 57.052 34.615 0.00 0.00 0.00 3.02
531 534 9.667107 TCTCAACATAGTTTTACCTTAATCCAG 57.333 33.333 0.00 0.00 0.00 3.86
614 617 4.582656 TCATCCGGTTTCAATGAAGTTTGT 59.417 37.500 0.00 0.00 0.00 2.83
618 621 3.638484 GGTTTCAATGAAGTTTGTCCGG 58.362 45.455 0.00 0.00 0.00 5.14
619 622 3.067601 GGTTTCAATGAAGTTTGTCCGGT 59.932 43.478 0.00 0.00 0.00 5.28
651 654 4.870123 TTTTGAATTGTATGCTGGCAGT 57.130 36.364 17.16 0.00 0.00 4.40
689 709 2.126071 ATCCGTGTCCGCGAACTG 60.126 61.111 8.23 0.00 0.00 3.16
718 738 4.873129 CGTGGACGGATGCGGGAG 62.873 72.222 12.44 0.00 35.37 4.30
729 749 1.952296 GATGCGGGAGAGAATTTGCAT 59.048 47.619 0.00 0.00 44.95 3.96
734 754 2.353889 CGGGAGAGAATTTGCATGTCAG 59.646 50.000 0.00 0.00 0.00 3.51
735 755 2.098770 GGGAGAGAATTTGCATGTCAGC 59.901 50.000 0.00 0.00 0.00 4.26
752 772 2.736721 TCAGCGTTGAAGATGCACTAAC 59.263 45.455 0.00 0.00 42.96 2.34
901 934 2.163613 GTGCCACACTATAAAAGGCCAC 59.836 50.000 5.01 0.00 44.60 5.01
916 949 1.975327 CCACGGCTTCTTCTCCTCA 59.025 57.895 0.00 0.00 0.00 3.86
969 1002 3.129638 GTGCTACTACACTAGAAGCTGCT 59.870 47.826 0.00 0.00 37.58 4.24
1016 1049 3.199946 AGGACCATGTACCACCATAACAG 59.800 47.826 7.89 0.00 0.00 3.16
1189 1222 1.677576 CAGCAGCCTTTGAGTTTGACA 59.322 47.619 0.00 0.00 0.00 3.58
1191 1224 1.269257 GCAGCCTTTGAGTTTGACACC 60.269 52.381 0.00 0.00 0.00 4.16
1200 1233 4.271696 TGAGTTTGACACCATCCTACTG 57.728 45.455 0.00 0.00 0.00 2.74
1273 1309 2.660802 CCGGTGGCGGAAACTACT 59.339 61.111 0.00 0.00 0.00 2.57
1274 1310 1.740296 CCGGTGGCGGAAACTACTG 60.740 63.158 0.00 0.00 0.00 2.74
1609 1651 0.175760 GGCCTCGAGCAATCACAGTA 59.824 55.000 6.99 0.00 46.50 2.74
1612 1654 1.134995 CCTCGAGCAATCACAGTAGCA 60.135 52.381 6.99 0.00 0.00 3.49
1620 1662 1.857965 ATCACAGTAGCAGCTCCTCA 58.142 50.000 0.00 0.00 0.00 3.86
1945 2109 6.860080 AGCTTGTGATGAATGAAACCAATAG 58.140 36.000 0.00 0.00 0.00 1.73
2047 2212 4.580868 TCCATAATGCGGTGAACTACAAA 58.419 39.130 0.00 0.00 0.00 2.83
2190 2356 5.556355 TGTATCGTCTACTTCGTTGATGT 57.444 39.130 0.00 0.00 0.00 3.06
2206 2372 5.008415 CGTTGATGTCGACTTACCTACCTAT 59.992 44.000 17.92 0.00 0.00 2.57
2234 2400 3.254411 GCTTTTCTTTGGCAGCTAAGTCT 59.746 43.478 0.00 0.00 0.00 3.24
2366 2534 1.059098 TCACTGAGATGCTTGTGGGT 58.941 50.000 0.00 0.00 0.00 4.51
2503 2678 6.668323 AGACGTGAATGTTTTGTTAATCCAG 58.332 36.000 0.00 0.00 0.00 3.86
2526 2701 3.679389 TGGAAAATGAGCTTCAGGAGTC 58.321 45.455 0.00 0.00 0.00 3.36
2529 2704 1.561643 AATGAGCTTCAGGAGTCGGA 58.438 50.000 0.00 0.00 0.00 4.55
2530 2705 1.786937 ATGAGCTTCAGGAGTCGGAT 58.213 50.000 0.00 0.00 0.00 4.18
2552 2727 5.860941 TTTACAGCATGGAAACCTTCAAA 57.139 34.783 0.00 0.00 42.26 2.69
2610 2785 7.290813 CCTAAAAACTAGGAGGAGGCATATTT 58.709 38.462 0.00 0.00 36.85 1.40
2611 2786 7.229506 CCTAAAAACTAGGAGGAGGCATATTTG 59.770 40.741 0.00 0.00 36.85 2.32
2634 2809 6.222389 TGCTATTCAAATGGTTGTGGAAAAG 58.778 36.000 0.00 0.00 36.07 2.27
2635 2810 6.183360 TGCTATTCAAATGGTTGTGGAAAAGT 60.183 34.615 0.00 0.00 36.07 2.66
2636 2811 6.146021 GCTATTCAAATGGTTGTGGAAAAGTG 59.854 38.462 0.00 0.00 36.07 3.16
2637 2812 3.791245 TCAAATGGTTGTGGAAAAGTGC 58.209 40.909 0.00 0.00 36.07 4.40
2638 2813 3.196469 TCAAATGGTTGTGGAAAAGTGCA 59.804 39.130 0.00 0.00 36.07 4.57
2639 2814 3.902881 AATGGTTGTGGAAAAGTGCAA 57.097 38.095 0.00 0.00 0.00 4.08
2640 2815 2.957491 TGGTTGTGGAAAAGTGCAAG 57.043 45.000 0.00 0.00 0.00 4.01
2641 2816 1.134848 TGGTTGTGGAAAAGTGCAAGC 60.135 47.619 0.00 0.00 0.00 4.01
2642 2817 1.134848 GGTTGTGGAAAAGTGCAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
2643 2818 2.195922 GTTGTGGAAAAGTGCAAGCAG 58.804 47.619 0.00 0.00 0.00 4.24
2644 2819 1.761449 TGTGGAAAAGTGCAAGCAGA 58.239 45.000 0.00 0.00 0.00 4.26
2645 2820 2.098614 TGTGGAAAAGTGCAAGCAGAA 58.901 42.857 0.00 0.00 0.00 3.02
2646 2821 2.694628 TGTGGAAAAGTGCAAGCAGAAT 59.305 40.909 0.00 0.00 0.00 2.40
2647 2822 3.243501 TGTGGAAAAGTGCAAGCAGAATC 60.244 43.478 0.00 0.00 0.00 2.52
2648 2823 2.957680 TGGAAAAGTGCAAGCAGAATCA 59.042 40.909 0.00 0.00 0.00 2.57
2649 2824 3.005050 TGGAAAAGTGCAAGCAGAATCAG 59.995 43.478 0.00 0.00 0.00 2.90
2650 2825 3.254166 GGAAAAGTGCAAGCAGAATCAGA 59.746 43.478 0.00 0.00 0.00 3.27
2651 2826 3.911661 AAAGTGCAAGCAGAATCAGAC 57.088 42.857 0.00 0.00 0.00 3.51
2652 2827 2.556144 AGTGCAAGCAGAATCAGACA 57.444 45.000 0.00 0.00 0.00 3.41
2653 2828 2.149578 AGTGCAAGCAGAATCAGACAC 58.850 47.619 0.00 0.00 0.00 3.67
2654 2829 1.875514 GTGCAAGCAGAATCAGACACA 59.124 47.619 0.00 0.00 0.00 3.72
2655 2830 2.291465 GTGCAAGCAGAATCAGACACAA 59.709 45.455 0.00 0.00 0.00 3.33
2656 2831 2.950975 TGCAAGCAGAATCAGACACAAA 59.049 40.909 0.00 0.00 0.00 2.83
2657 2832 3.570975 TGCAAGCAGAATCAGACACAAAT 59.429 39.130 0.00 0.00 0.00 2.32
2658 2833 4.038282 TGCAAGCAGAATCAGACACAAATT 59.962 37.500 0.00 0.00 0.00 1.82
2659 2834 5.241285 TGCAAGCAGAATCAGACACAAATTA 59.759 36.000 0.00 0.00 0.00 1.40
2660 2835 6.071784 TGCAAGCAGAATCAGACACAAATTAT 60.072 34.615 0.00 0.00 0.00 1.28
2661 2836 6.810182 GCAAGCAGAATCAGACACAAATTATT 59.190 34.615 0.00 0.00 0.00 1.40
2662 2837 7.970061 GCAAGCAGAATCAGACACAAATTATTA 59.030 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.818857 GGTACTGGATGCGGTAGAAAATTTA 59.181 40.000 6.09 0.00 0.00 1.40
26 27 2.759839 TCCATATCCGTGGACAGGTA 57.240 50.000 0.00 0.00 43.20 3.08
37 38 2.039084 GTGTCCTCCCACATCCATATCC 59.961 54.545 0.00 0.00 35.38 2.59
40 41 1.274126 TGGTGTCCTCCCACATCCATA 60.274 52.381 0.00 0.00 37.06 2.74
45 46 2.311287 GGATGGTGTCCTCCCACAT 58.689 57.895 0.00 0.00 44.16 3.21
72 73 0.315869 GCGGTTCGAAATGTATGCGG 60.316 55.000 0.00 0.00 0.00 5.69
103 104 3.304559 CGGTTTGCGTGAATTTTGTTCAA 59.695 39.130 0.00 0.00 0.00 2.69
104 105 2.854777 CGGTTTGCGTGAATTTTGTTCA 59.145 40.909 0.00 0.00 0.00 3.18
118 119 0.951558 ATGAATATCGGCCGGTTTGC 59.048 50.000 27.83 13.49 0.00 3.68
139 140 8.785329 TTTGTGCTTCTTTTTATCCAAACTTT 57.215 26.923 0.00 0.00 0.00 2.66
154 155 6.642950 GCTACGTATAGATGATTTGTGCTTCT 59.357 38.462 0.00 0.00 0.00 2.85
209 210 7.765307 ACATCTGGCTAATGTAGTCAAATTTG 58.235 34.615 12.15 12.15 40.35 2.32
226 227 5.587289 TGAAAAACTTGTTGTACATCTGGC 58.413 37.500 0.00 0.00 0.00 4.85
235 236 5.317733 TCCGTTGATGAAAAACTTGTTGT 57.682 34.783 0.00 0.00 0.00 3.32
236 237 5.976534 TGATCCGTTGATGAAAAACTTGTTG 59.023 36.000 0.00 0.00 0.00 3.33
237 238 6.142818 TGATCCGTTGATGAAAAACTTGTT 57.857 33.333 0.00 0.00 0.00 2.83
268 269 6.040729 TGAAATTGAATGGGCAGTATGTATGG 59.959 38.462 0.00 0.00 39.31 2.74
288 289 6.854496 ACGTACACACACTGTTTATGAAAT 57.146 33.333 0.00 0.00 33.91 2.17
324 326 2.424989 TATGGGGCGGATATGGGGGT 62.425 60.000 0.00 0.00 0.00 4.95
325 327 0.993509 ATATGGGGCGGATATGGGGG 60.994 60.000 0.00 0.00 0.00 5.40
347 349 3.055963 CAGACATCCCTCATATCCAGCTC 60.056 52.174 0.00 0.00 0.00 4.09
348 350 2.905085 CAGACATCCCTCATATCCAGCT 59.095 50.000 0.00 0.00 0.00 4.24
381 384 2.027625 CCTGACGGACGCCTCAAAC 61.028 63.158 0.00 0.00 0.00 2.93
387 390 2.999739 TTTTGACCCTGACGGACGCC 63.000 60.000 0.00 0.00 34.64 5.68
391 394 2.147958 CGAAATTTTGACCCTGACGGA 58.852 47.619 0.00 0.00 34.64 4.69
411 414 2.357517 CGGTCACTGGCAGGTCAC 60.358 66.667 20.34 11.46 0.00 3.67
433 436 2.094182 TGCCTCAAACGTCCAGATAGAC 60.094 50.000 0.00 0.00 0.00 2.59
434 437 2.166459 CTGCCTCAAACGTCCAGATAGA 59.834 50.000 0.00 0.00 0.00 1.98
435 438 2.544685 CTGCCTCAAACGTCCAGATAG 58.455 52.381 0.00 0.00 0.00 2.08
436 439 1.207089 CCTGCCTCAAACGTCCAGATA 59.793 52.381 0.00 0.00 0.00 1.98
437 440 0.036010 CCTGCCTCAAACGTCCAGAT 60.036 55.000 0.00 0.00 0.00 2.90
438 441 1.371183 CCTGCCTCAAACGTCCAGA 59.629 57.895 0.00 0.00 0.00 3.86
439 442 0.535102 AACCTGCCTCAAACGTCCAG 60.535 55.000 0.00 0.00 0.00 3.86
440 443 0.106918 AAACCTGCCTCAAACGTCCA 60.107 50.000 0.00 0.00 0.00 4.02
441 444 0.310854 CAAACCTGCCTCAAACGTCC 59.689 55.000 0.00 0.00 0.00 4.79
442 445 0.310854 CCAAACCTGCCTCAAACGTC 59.689 55.000 0.00 0.00 0.00 4.34
443 446 1.106944 CCCAAACCTGCCTCAAACGT 61.107 55.000 0.00 0.00 0.00 3.99
444 447 1.659794 CCCAAACCTGCCTCAAACG 59.340 57.895 0.00 0.00 0.00 3.60
463 466 1.407025 GGTAGCTTAGAGTTGGGGCAC 60.407 57.143 0.00 0.00 0.00 5.01
469 472 4.705337 AGAGTTCGGTAGCTTAGAGTTG 57.295 45.455 0.00 0.00 0.00 3.16
470 473 4.336153 GCTAGAGTTCGGTAGCTTAGAGTT 59.664 45.833 0.00 0.00 38.92 3.01
575 578 9.753674 AAACCGGATGATATTCATATAAACCAT 57.246 29.630 9.46 0.00 37.20 3.55
614 617 7.982354 ACAATTCAAAATTTTAGACAAACCGGA 59.018 29.630 9.46 0.00 0.00 5.14
651 654 1.529796 GGGATACGGGCATCCAACA 59.470 57.895 13.09 0.00 45.52 3.33
718 738 2.907910 ACGCTGACATGCAAATTCTC 57.092 45.000 0.00 0.00 0.00 2.87
729 749 0.867746 GTGCATCTTCAACGCTGACA 59.132 50.000 0.00 0.00 0.00 3.58
734 754 2.076863 AGGTTAGTGCATCTTCAACGC 58.923 47.619 0.00 0.00 0.00 4.84
735 755 3.667960 GCAAGGTTAGTGCATCTTCAACG 60.668 47.826 0.00 0.00 41.80 4.10
752 772 4.278419 GGTAGCTTACAAATATGGGCAAGG 59.722 45.833 0.00 0.00 0.00 3.61
818 838 8.645814 TCTTCTCTCTCTCTCTCGTATAGTAT 57.354 38.462 0.00 0.00 0.00 2.12
819 839 7.940688 TCTCTTCTCTCTCTCTCTCGTATAGTA 59.059 40.741 0.00 0.00 0.00 1.82
820 840 6.776116 TCTCTTCTCTCTCTCTCTCGTATAGT 59.224 42.308 0.00 0.00 0.00 2.12
821 841 7.215719 TCTCTTCTCTCTCTCTCTCGTATAG 57.784 44.000 0.00 0.00 0.00 1.31
822 842 7.591421 TTCTCTTCTCTCTCTCTCTCGTATA 57.409 40.000 0.00 0.00 0.00 1.47
823 843 6.479972 TTCTCTTCTCTCTCTCTCTCGTAT 57.520 41.667 0.00 0.00 0.00 3.06
824 844 5.925506 TTCTCTTCTCTCTCTCTCTCGTA 57.074 43.478 0.00 0.00 0.00 3.43
825 845 4.819105 TTCTCTTCTCTCTCTCTCTCGT 57.181 45.455 0.00 0.00 0.00 4.18
826 846 4.332819 GGTTTCTCTTCTCTCTCTCTCTCG 59.667 50.000 0.00 0.00 0.00 4.04
827 847 5.253330 TGGTTTCTCTTCTCTCTCTCTCTC 58.747 45.833 0.00 0.00 0.00 3.20
828 848 5.255397 TGGTTTCTCTTCTCTCTCTCTCT 57.745 43.478 0.00 0.00 0.00 3.10
829 849 6.152661 TCAATGGTTTCTCTTCTCTCTCTCTC 59.847 42.308 0.00 0.00 0.00 3.20
830 850 6.015918 TCAATGGTTTCTCTTCTCTCTCTCT 58.984 40.000 0.00 0.00 0.00 3.10
901 934 1.805871 GCAGATGAGGAGAAGAAGCCG 60.806 57.143 0.00 0.00 0.00 5.52
916 949 2.806434 TGTTTGTTGGCTATGGCAGAT 58.194 42.857 2.58 0.00 39.75 2.90
969 1002 8.902540 TGTTTCTTGTCTCTTCTTTGCTTATA 57.097 30.769 0.00 0.00 0.00 0.98
1189 1222 1.482593 CGCTTCTTCCAGTAGGATGGT 59.517 52.381 0.00 0.00 45.26 3.55
1191 1224 1.808133 GCCGCTTCTTCCAGTAGGATG 60.808 57.143 0.00 0.00 45.26 3.51
1200 1233 1.448717 GAGGTGAGCCGCTTCTTCC 60.449 63.158 0.00 0.00 40.50 3.46
1501 1537 1.893919 GCCTTCTCGTCCCTGAGCTT 61.894 60.000 0.00 0.00 35.90 3.74
1560 1596 2.665603 GCCTTCTTCTCCGGTGCT 59.334 61.111 0.00 0.00 0.00 4.40
1620 1662 0.251033 TGCTGTTCTTGCATGGCTCT 60.251 50.000 0.00 0.00 35.31 4.09
1781 1830 1.456892 ATGCATGACCCCAGCCATG 60.457 57.895 0.00 0.00 42.13 3.66
1945 2109 5.932303 TCATACTTTGGTCTTGCTACTGTTC 59.068 40.000 0.00 0.00 0.00 3.18
2102 2268 2.846193 TCAAGTGGAGGAAAAGGTTCG 58.154 47.619 0.00 0.00 34.28 3.95
2107 2273 5.005740 TGACATCATCAAGTGGAGGAAAAG 58.994 41.667 0.00 0.00 40.14 2.27
2190 2356 4.135306 CAGCTGATAGGTAGGTAAGTCGA 58.865 47.826 8.42 0.00 0.00 4.20
2206 2372 1.338973 CTGCCAAAGAAAAGCAGCTGA 59.661 47.619 20.43 0.00 46.60 4.26
2234 2400 3.381272 GCAAAAACTATAGCATGCTGGGA 59.619 43.478 30.42 11.15 0.00 4.37
2366 2534 6.899089 TGCTCAAGATTCTTGGGAACATATA 58.101 36.000 26.87 4.77 42.32 0.86
2480 2651 6.664515 TCTGGATTAACAAAACATTCACGTC 58.335 36.000 0.00 0.00 0.00 4.34
2503 2678 4.268359 ACTCCTGAAGCTCATTTTCCATC 58.732 43.478 0.00 0.00 0.00 3.51
2509 2684 1.902508 TCCGACTCCTGAAGCTCATTT 59.097 47.619 0.00 0.00 0.00 2.32
2526 2701 3.016736 AGGTTTCCATGCTGTAAATCCG 58.983 45.455 0.00 0.00 0.00 4.18
2529 2704 6.183360 TGTTTGAAGGTTTCCATGCTGTAAAT 60.183 34.615 0.00 0.00 0.00 1.40
2530 2705 5.127845 TGTTTGAAGGTTTCCATGCTGTAAA 59.872 36.000 0.00 0.00 0.00 2.01
2552 2727 1.956477 GCAAATCCACTTGTCCTGTGT 59.044 47.619 0.00 0.00 33.92 3.72
2577 2752 7.614192 CCTCCTCCTAGTTTTTAGGCATTTTAA 59.386 37.037 0.00 0.00 34.74 1.52
2578 2753 7.116736 CCTCCTCCTAGTTTTTAGGCATTTTA 58.883 38.462 0.00 0.00 34.74 1.52
2610 2785 5.798125 TTTCCACAACCATTTGAATAGCA 57.202 34.783 0.00 0.00 36.48 3.49
2611 2786 6.146021 CACTTTTCCACAACCATTTGAATAGC 59.854 38.462 0.00 0.00 36.48 2.97
2634 2809 1.875514 TGTGTCTGATTCTGCTTGCAC 59.124 47.619 0.00 0.00 0.00 4.57
2635 2810 2.259266 TGTGTCTGATTCTGCTTGCA 57.741 45.000 0.00 0.00 0.00 4.08
2636 2811 3.631145 TTTGTGTCTGATTCTGCTTGC 57.369 42.857 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.