Multiple sequence alignment - TraesCS3B01G403000

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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 TraesCS3B01G403000 chr3B 100.000 3668 0 0 1 3668 637071881 637075548 0.000000e+00 6774.0
1 TraesCS3B01G403000 chr3D 95.949 2765 79 13 915 3668 477892202 477894944 0.000000e+00 4455.0
2 TraesCS3B01G403000 chr3D 90.201 1888 155 11 1042 2922 253394926 253393062 0.000000e+00 2435.0
3 TraesCS3B01G403000 chr3D 85.252 278 27 5 557 834 477890724 477890987 1.300000e-69 274.0
4 TraesCS3B01G403000 chr3D 84.232 241 23 7 3284 3522 253393052 253392825 1.710000e-53 220.0
5 TraesCS3B01G403000 chr3A 95.756 2757 93 13 926 3668 621226802 621229548 0.000000e+00 4421.0
6 TraesCS3B01G403000 chr3A 82.353 544 65 16 298 834 621226025 621226544 9.350000e-121 444.0
7 TraesCS3B01G403000 chr3A 85.185 297 36 8 1 294 621225529 621225820 7.700000e-77 298.0
8 TraesCS3B01G403000 chr7A 100.000 30 0 0 798 827 92085043 92085072 5.120000e-04 56.5
9 TraesCS3B01G403000 chr7A 100.000 29 0 0 799 827 486928473 486928501 2.000000e-03 54.7
10 TraesCS3B01G403000 chr6B 100.000 30 0 0 798 827 268718283 268718254 5.120000e-04 56.5
11 TraesCS3B01G403000 chr5A 100.000 30 0 0 798 827 535146364 535146393 5.120000e-04 56.5
12 TraesCS3B01G403000 chr7D 100.000 29 0 0 799 827 89759343 89759315 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 TraesCS3B01G403000 chr3B 637071881 637075548 3667 False 6774.0 6774 100.000000 1 3668 1 chr3B.!!$F1 3667
1 TraesCS3B01G403000 chr3D 477890724 477894944 4220 False 2364.5 4455 90.600500 557 3668 2 chr3D.!!$F1 3111
2 TraesCS3B01G403000 chr3D 253392825 253394926 2101 True 1327.5 2435 87.216500 1042 3522 2 chr3D.!!$R1 2480
3 TraesCS3B01G403000 chr3A 621225529 621229548 4019 False 1721.0 4421 87.764667 1 3668 3 chr3A.!!$F1 3667

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
718 936 0.538057 TTGCACTTGGAGCTCCCTTG 60.538 55.0 29.95 22.66 35.38 3.61 F
1570 3026 0.039618 GGAAATGTGGCTTGAGGGGA 59.960 55.0 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 3067 1.359475 GACCATCGAGTAGCCGTCC 59.641 63.158 0.0 0.0 0.00 4.79 R
2997 4461 1.207791 AGGGGATACAGGCAAGTGAG 58.792 55.000 0.0 0.0 39.74 3.51 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
157 159 5.423886 GTTTTCATGAAACCCAGTGGAAAA 58.576 37.500 20.35 3.86 41.43 2.29
158 160 5.683876 TTTCATGAAACCCAGTGGAAAAA 57.316 34.783 16.91 0.00 34.81 1.94
200 203 4.537688 TCAAAACAGAGAGGAAGGGATGAT 59.462 41.667 0.00 0.00 0.00 2.45
209 212 8.912988 CAGAGAGGAAGGGATGATAATATAGAC 58.087 40.741 0.00 0.00 0.00 2.59
213 216 8.386012 AGGAAGGGATGATAATATAGACAAGG 57.614 38.462 0.00 0.00 0.00 3.61
219 222 8.552296 GGGATGATAATATAGACAAGGTTGGAT 58.448 37.037 0.00 0.00 0.00 3.41
226 229 5.983333 ATAGACAAGGTTGGATGAAGGAT 57.017 39.130 0.00 0.00 0.00 3.24
246 249 3.701532 TTAGCGGACAACAAAACCTTG 57.298 42.857 0.00 0.00 38.61 3.61
260 263 7.913674 ACAAAACCTTGCTCAAAACAATTTA 57.086 28.000 0.00 0.00 35.84 1.40
268 271 9.643693 CCTTGCTCAAAACAATTTATTCTACAT 57.356 29.630 0.00 0.00 0.00 2.29
316 519 3.767711 AGAAAGAACCAAATGGAGGGTC 58.232 45.455 6.42 0.00 43.37 4.46
322 525 0.881118 CCAAATGGAGGGTCACAACG 59.119 55.000 0.00 0.00 37.39 4.10
325 528 1.056660 AATGGAGGGTCACAACGACT 58.943 50.000 0.00 0.00 44.70 4.18
347 550 2.814023 TTTTTGACGTGGTGGCCAT 58.186 47.368 9.72 0.00 35.28 4.40
361 564 1.849692 TGGCCATAAGCTCATAACCCA 59.150 47.619 0.00 0.00 43.05 4.51
377 580 3.594603 ACCCACGACATGTAAAGAGAG 57.405 47.619 0.00 0.00 0.00 3.20
390 597 7.833682 ACATGTAAAGAGAGAGAGATGAGAAGA 59.166 37.037 0.00 0.00 0.00 2.87
394 601 5.715439 AGAGAGAGAGATGAGAAGAAGGA 57.285 43.478 0.00 0.00 0.00 3.36
397 604 4.478317 AGAGAGAGATGAGAAGAAGGAGGA 59.522 45.833 0.00 0.00 0.00 3.71
400 607 4.882559 AGAGATGAGAAGAAGGAGGATGT 58.117 43.478 0.00 0.00 0.00 3.06
401 608 4.895297 AGAGATGAGAAGAAGGAGGATGTC 59.105 45.833 0.00 0.00 0.00 3.06
407 614 1.196012 AGAAGGAGGATGTCGGTTCC 58.804 55.000 0.00 0.00 0.00 3.62
416 623 5.174037 AGGATGTCGGTTCCTTTTGATTA 57.826 39.130 0.00 0.00 40.84 1.75
424 631 5.474189 TCGGTTCCTTTTGATTAATTCGGTT 59.526 36.000 0.00 0.00 0.00 4.44
425 632 5.571357 CGGTTCCTTTTGATTAATTCGGTTG 59.429 40.000 0.00 0.00 0.00 3.77
426 633 6.452242 GGTTCCTTTTGATTAATTCGGTTGT 58.548 36.000 0.00 0.00 0.00 3.32
433 640 6.737254 TTGATTAATTCGGTTGTCTCTTCC 57.263 37.500 0.00 0.00 0.00 3.46
437 644 3.889520 ATTCGGTTGTCTCTTCCCTAC 57.110 47.619 0.00 0.00 0.00 3.18
438 645 2.297698 TCGGTTGTCTCTTCCCTACA 57.702 50.000 0.00 0.00 0.00 2.74
440 647 1.402456 CGGTTGTCTCTTCCCTACACG 60.402 57.143 0.00 0.00 0.00 4.49
443 650 3.576648 GTTGTCTCTTCCCTACACGAAG 58.423 50.000 0.00 0.00 38.47 3.79
451 658 0.745468 CCCTACACGAAGCCCTAGTC 59.255 60.000 0.00 0.00 0.00 2.59
455 662 3.315749 CCTACACGAAGCCCTAGTCTAAG 59.684 52.174 0.00 0.00 0.00 2.18
463 670 2.969262 AGCCCTAGTCTAAGATTGGCTC 59.031 50.000 0.00 0.00 44.01 4.70
466 673 3.323403 CCCTAGTCTAAGATTGGCTCTGG 59.677 52.174 0.00 0.00 33.29 3.86
479 686 5.708736 TTGGCTCTGGGTATTATCTTTGA 57.291 39.130 0.00 0.00 0.00 2.69
500 707 8.899887 TTTGATGAATTATTTCCCCTCTTCTT 57.100 30.769 0.00 0.00 0.00 2.52
506 714 9.989296 TGAATTATTTCCCCTCTTCTTTTATGA 57.011 29.630 0.00 0.00 0.00 2.15
514 722 7.237982 TCCCCTCTTCTTTTATGAAAATCACA 58.762 34.615 0.00 0.00 0.00 3.58
523 731 8.321353 TCTTTTATGAAAATCACAGAGCTCCTA 58.679 33.333 10.93 0.00 0.00 2.94
526 734 9.466497 TTTATGAAAATCACAGAGCTCCTATTT 57.534 29.630 10.93 8.52 0.00 1.40
527 735 7.951347 ATGAAAATCACAGAGCTCCTATTTT 57.049 32.000 10.93 15.87 31.23 1.82
708 926 5.920273 CCATTACTACAAAAGTTGCACTTGG 59.080 40.000 0.00 0.00 38.66 3.61
714 932 1.322442 AAAGTTGCACTTGGAGCTCC 58.678 50.000 26.78 26.78 38.66 4.70
716 934 1.073897 GTTGCACTTGGAGCTCCCT 59.926 57.895 29.95 9.61 35.38 4.20
717 935 0.538287 GTTGCACTTGGAGCTCCCTT 60.538 55.000 29.95 11.18 35.38 3.95
718 936 0.538057 TTGCACTTGGAGCTCCCTTG 60.538 55.000 29.95 22.66 35.38 3.61
721 939 1.271379 GCACTTGGAGCTCCCTTGTTA 60.271 52.381 29.95 7.26 35.38 2.41
728 946 4.272489 TGGAGCTCCCTTGTTATCAAATG 58.728 43.478 29.95 0.00 35.38 2.32
731 949 4.284178 AGCTCCCTTGTTATCAAATGCAT 58.716 39.130 0.00 0.00 32.87 3.96
732 950 4.340381 AGCTCCCTTGTTATCAAATGCATC 59.660 41.667 0.00 0.00 32.87 3.91
733 951 4.098349 GCTCCCTTGTTATCAAATGCATCA 59.902 41.667 0.00 0.00 32.87 3.07
787 1005 5.533154 TGAACACGGATTCAATGGTACTTTT 59.467 36.000 1.47 0.00 35.65 2.27
853 1071 8.951969 CGTAAGTTCTACGTATGATTTTAGGAC 58.048 37.037 0.00 0.00 36.31 3.85
855 1073 8.928270 AAGTTCTACGTATGATTTTAGGACTG 57.072 34.615 0.00 0.00 31.81 3.51
856 1074 8.064336 AGTTCTACGTATGATTTTAGGACTGT 57.936 34.615 0.00 0.00 30.48 3.55
857 1075 9.182214 AGTTCTACGTATGATTTTAGGACTGTA 57.818 33.333 0.00 0.00 30.48 2.74
858 1076 9.962783 GTTCTACGTATGATTTTAGGACTGTAT 57.037 33.333 0.00 0.00 0.00 2.29
921 2287 6.825284 TTCTGTGATTTAAAACGTACGTCA 57.175 33.333 23.05 10.52 0.00 4.35
1146 2602 2.269529 CCTCCTCCGATCCTACGCC 61.270 68.421 0.00 0.00 0.00 5.68
1224 2680 2.202756 CCGCTCCTCTACAACGCC 60.203 66.667 0.00 0.00 0.00 5.68
1272 2728 4.154347 CTCCCCACTGCTCTCGCC 62.154 72.222 0.00 0.00 34.43 5.54
1387 2843 0.533755 CGCCAAGATCCTCCATGGTC 60.534 60.000 12.58 1.25 35.34 4.02
1394 2850 1.330655 ATCCTCCATGGTCTCGCGTT 61.331 55.000 12.58 0.00 37.07 4.84
1404 2860 0.379669 GTCTCGCGTTATCTTCCGGA 59.620 55.000 5.77 0.00 0.00 5.14
1462 2918 1.525619 GCGCGTACTCAAAGTTCTTGT 59.474 47.619 8.43 0.00 0.00 3.16
1503 2959 2.792890 CGTGTTTGATGGTTTGCGTGAA 60.793 45.455 0.00 0.00 0.00 3.18
1570 3026 0.039618 GGAAATGTGGCTTGAGGGGA 59.960 55.000 0.00 0.00 0.00 4.81
1584 3040 3.146066 TGAGGGGATTCAACTGTTTTCG 58.854 45.455 0.00 0.00 0.00 3.46
1611 3067 3.995809 TAGGGCTGGGGAGGAACCG 62.996 68.421 0.00 0.00 40.11 4.44
2041 3497 5.398603 AGACATCAAAGTCTCATCTTCGT 57.601 39.130 0.00 0.00 45.35 3.85
2109 3565 4.204012 TGGTATTCCGCCAAATTCCTAAG 58.796 43.478 3.92 0.00 36.30 2.18
2277 3733 1.066303 CATGCAGGACTCCTAGACGAC 59.934 57.143 0.00 0.00 29.64 4.34
2421 3877 1.218854 GACAATGCCAATGCCACCC 59.781 57.895 0.00 0.00 36.33 4.61
2617 4080 4.020218 TCAGGACCGAGATGTTGAAAGAAT 60.020 41.667 0.00 0.00 0.00 2.40
2623 4086 7.872993 GGACCGAGATGTTGAAAGAATATATGA 59.127 37.037 0.00 0.00 0.00 2.15
2775 4238 8.992835 ATATCTGAAATTGCTTCAAAACTTCC 57.007 30.769 0.00 0.00 43.54 3.46
2776 4239 6.469782 TCTGAAATTGCTTCAAAACTTCCT 57.530 33.333 0.00 0.00 43.54 3.36
2777 4240 7.581213 TCTGAAATTGCTTCAAAACTTCCTA 57.419 32.000 0.00 0.00 43.54 2.94
2778 4241 8.181904 TCTGAAATTGCTTCAAAACTTCCTAT 57.818 30.769 0.00 0.00 43.54 2.57
2863 4327 3.743521 TCTGCTGTTGCTGAGTACAAAT 58.256 40.909 0.00 0.00 41.21 2.32
2981 4445 3.829601 CACTCTTTCTAGTGGAGTCCTGT 59.170 47.826 11.33 0.00 42.63 4.00
2997 4461 2.825532 TCCTGTATTTTTCTTGCCTGGC 59.174 45.455 12.87 12.87 0.00 4.85
3346 4811 9.507280 CGAAATGATATAATCAGCACAACTTTT 57.493 29.630 0.00 0.00 43.53 2.27
3411 4878 4.334759 CACTTCTTAGTGCTTGGATGATGG 59.665 45.833 0.00 0.00 44.81 3.51
3486 4955 8.697507 ATCTTTTAAAGAAAGCCAAAGAGAGA 57.302 30.769 11.63 0.00 41.63 3.10
3618 5093 6.605471 TGGTAGAAGATACTTGTCATGTGT 57.395 37.500 1.71 0.00 0.00 3.72
3619 5094 6.631016 TGGTAGAAGATACTTGTCATGTGTC 58.369 40.000 7.33 7.33 0.00 3.67
3622 5097 5.728471 AGAAGATACTTGTCATGTGTCAGG 58.272 41.667 15.11 0.00 0.00 3.86
3635 5110 8.590204 TGTCATGTGTCAGGTTTATAAGAGTAA 58.410 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 9.959721 GCCCACCTTCTATTTATCTATGAAATA 57.040 33.333 0.00 0.00 0.00 1.40
103 105 8.448008 TGCCCACCTTCTATTTATCTATGAAAT 58.552 33.333 0.00 0.00 0.00 2.17
105 107 7.072454 ACTGCCCACCTTCTATTTATCTATGAA 59.928 37.037 0.00 0.00 0.00 2.57
106 108 6.558775 ACTGCCCACCTTCTATTTATCTATGA 59.441 38.462 0.00 0.00 0.00 2.15
107 109 6.773638 ACTGCCCACCTTCTATTTATCTATG 58.226 40.000 0.00 0.00 0.00 2.23
109 111 6.409234 CCAACTGCCCACCTTCTATTTATCTA 60.409 42.308 0.00 0.00 0.00 1.98
111 113 4.580580 CCAACTGCCCACCTTCTATTTATC 59.419 45.833 0.00 0.00 0.00 1.75
113 115 3.332485 ACCAACTGCCCACCTTCTATTTA 59.668 43.478 0.00 0.00 0.00 1.40
114 116 2.110011 ACCAACTGCCCACCTTCTATTT 59.890 45.455 0.00 0.00 0.00 1.40
115 117 1.710809 ACCAACTGCCCACCTTCTATT 59.289 47.619 0.00 0.00 0.00 1.73
116 118 1.372501 ACCAACTGCCCACCTTCTAT 58.627 50.000 0.00 0.00 0.00 1.98
122 124 1.047801 ATGAAAACCAACTGCCCACC 58.952 50.000 0.00 0.00 0.00 4.61
176 178 4.537688 TCATCCCTTCCTCTCTGTTTTGAT 59.462 41.667 0.00 0.00 0.00 2.57
177 179 3.909995 TCATCCCTTCCTCTCTGTTTTGA 59.090 43.478 0.00 0.00 0.00 2.69
178 180 4.292186 TCATCCCTTCCTCTCTGTTTTG 57.708 45.455 0.00 0.00 0.00 2.44
182 184 8.628281 TCTATATTATCATCCCTTCCTCTCTGT 58.372 37.037 0.00 0.00 0.00 3.41
183 185 8.912988 GTCTATATTATCATCCCTTCCTCTCTG 58.087 40.741 0.00 0.00 0.00 3.35
184 186 8.628281 TGTCTATATTATCATCCCTTCCTCTCT 58.372 37.037 0.00 0.00 0.00 3.10
185 187 8.830915 TGTCTATATTATCATCCCTTCCTCTC 57.169 38.462 0.00 0.00 0.00 3.20
190 193 9.442047 CAACCTTGTCTATATTATCATCCCTTC 57.558 37.037 0.00 0.00 0.00 3.46
200 203 8.561536 TCCTTCATCCAACCTTGTCTATATTA 57.438 34.615 0.00 0.00 0.00 0.98
209 212 3.313526 CGCTAATCCTTCATCCAACCTTG 59.686 47.826 0.00 0.00 0.00 3.61
213 216 2.872858 GTCCGCTAATCCTTCATCCAAC 59.127 50.000 0.00 0.00 0.00 3.77
219 222 3.410631 TTGTTGTCCGCTAATCCTTCA 57.589 42.857 0.00 0.00 0.00 3.02
226 229 2.223618 GCAAGGTTTTGTTGTCCGCTAA 60.224 45.455 0.00 0.00 36.65 3.09
294 297 4.152647 GACCCTCCATTTGGTTCTTTCTT 58.847 43.478 0.00 0.00 34.20 2.52
295 298 3.140144 TGACCCTCCATTTGGTTCTTTCT 59.860 43.478 0.00 0.00 34.20 2.52
296 299 3.255888 GTGACCCTCCATTTGGTTCTTTC 59.744 47.826 0.00 0.00 34.20 2.62
304 507 1.535462 GTCGTTGTGACCCTCCATTTG 59.465 52.381 0.00 0.00 42.04 2.32
332 535 0.958382 GCTTATGGCCACCACGTCAA 60.958 55.000 8.16 0.00 35.80 3.18
333 536 1.376683 GCTTATGGCCACCACGTCA 60.377 57.895 8.16 0.00 35.80 4.35
334 537 1.078426 AGCTTATGGCCACCACGTC 60.078 57.895 8.16 0.00 43.05 4.34
336 539 0.464373 ATGAGCTTATGGCCACCACG 60.464 55.000 8.16 0.00 43.05 4.94
338 541 2.422803 GGTTATGAGCTTATGGCCACCA 60.423 50.000 8.16 0.00 43.05 4.17
339 542 2.230660 GGTTATGAGCTTATGGCCACC 58.769 52.381 8.16 0.00 43.05 4.61
340 543 2.230660 GGGTTATGAGCTTATGGCCAC 58.769 52.381 8.16 0.00 43.05 5.01
341 544 1.849692 TGGGTTATGAGCTTATGGCCA 59.150 47.619 8.56 8.56 43.05 5.36
342 545 2.230660 GTGGGTTATGAGCTTATGGCC 58.769 52.381 0.32 0.00 43.05 5.36
343 546 1.873591 CGTGGGTTATGAGCTTATGGC 59.126 52.381 0.32 0.00 42.19 4.40
347 550 3.196901 ACATGTCGTGGGTTATGAGCTTA 59.803 43.478 0.00 0.00 0.00 3.09
361 564 5.883115 TCATCTCTCTCTCTTTACATGTCGT 59.117 40.000 0.00 0.00 0.00 4.34
377 580 4.895297 ACATCCTCCTTCTTCTCATCTCTC 59.105 45.833 0.00 0.00 0.00 3.20
390 597 1.657804 AAGGAACCGACATCCTCCTT 58.342 50.000 4.42 0.00 46.65 3.36
397 604 6.404293 CCGAATTAATCAAAAGGAACCGACAT 60.404 38.462 0.00 0.00 0.00 3.06
400 607 5.005094 ACCGAATTAATCAAAAGGAACCGA 58.995 37.500 0.00 0.00 0.00 4.69
401 608 5.305139 ACCGAATTAATCAAAAGGAACCG 57.695 39.130 0.00 0.00 0.00 4.44
407 614 7.750903 GGAAGAGACAACCGAATTAATCAAAAG 59.249 37.037 0.00 0.00 0.00 2.27
416 623 3.581332 TGTAGGGAAGAGACAACCGAATT 59.419 43.478 0.00 0.00 0.00 2.17
424 631 1.544691 GCTTCGTGTAGGGAAGAGACA 59.455 52.381 5.77 0.00 42.74 3.41
425 632 1.135053 GGCTTCGTGTAGGGAAGAGAC 60.135 57.143 5.77 0.00 42.74 3.36
426 633 1.183549 GGCTTCGTGTAGGGAAGAGA 58.816 55.000 5.77 0.00 42.74 3.10
433 640 1.765230 AGACTAGGGCTTCGTGTAGG 58.235 55.000 0.00 0.00 0.00 3.18
437 644 4.363999 CAATCTTAGACTAGGGCTTCGTG 58.636 47.826 0.00 0.00 0.00 4.35
438 645 3.385111 CCAATCTTAGACTAGGGCTTCGT 59.615 47.826 0.00 0.00 0.00 3.85
440 647 3.734463 GCCAATCTTAGACTAGGGCTTC 58.266 50.000 7.67 0.00 37.00 3.86
443 650 2.969262 AGAGCCAATCTTAGACTAGGGC 59.031 50.000 7.05 7.05 40.18 5.19
451 658 7.251321 AGATAATACCCAGAGCCAATCTTAG 57.749 40.000 0.00 0.00 35.47 2.18
455 662 6.299141 TCAAAGATAATACCCAGAGCCAATC 58.701 40.000 0.00 0.00 0.00 2.67
488 695 7.728083 TGTGATTTTCATAAAAGAAGAGGGGAA 59.272 33.333 0.00 0.00 33.22 3.97
497 704 7.170965 AGGAGCTCTGTGATTTTCATAAAAGA 58.829 34.615 14.64 0.00 33.22 2.52
500 707 9.466497 AAATAGGAGCTCTGTGATTTTCATAAA 57.534 29.630 14.64 0.00 0.00 1.40
531 739 8.499403 TTCCAAACGGATTTTCTTTTTCAAAT 57.501 26.923 0.00 0.00 30.78 2.32
534 742 6.536941 CCTTTCCAAACGGATTTTCTTTTTCA 59.463 34.615 0.00 0.00 30.78 2.69
535 743 6.759356 TCCTTTCCAAACGGATTTTCTTTTTC 59.241 34.615 0.00 0.00 30.78 2.29
537 746 6.127168 ACTCCTTTCCAAACGGATTTTCTTTT 60.127 34.615 0.00 0.00 30.78 2.27
541 750 4.848562 ACTCCTTTCCAAACGGATTTTC 57.151 40.909 0.00 0.00 30.78 2.29
544 753 6.598064 CAGTTATACTCCTTTCCAAACGGATT 59.402 38.462 0.00 0.00 30.78 3.01
548 757 6.348213 CCAACAGTTATACTCCTTTCCAAACG 60.348 42.308 0.00 0.00 0.00 3.60
553 762 6.235664 TGAACCAACAGTTATACTCCTTTCC 58.764 40.000 0.00 0.00 39.40 3.13
567 776 7.656948 ACCAAACATATCAAAATGAACCAACAG 59.343 33.333 0.00 0.00 0.00 3.16
676 894 8.296713 GCAACTTTTGTAGTAATGGAGAATCAA 58.703 33.333 0.00 0.00 35.54 2.57
708 926 3.696051 TGCATTTGATAACAAGGGAGCTC 59.304 43.478 4.71 4.71 37.32 4.09
714 932 9.752961 TTCATATTGATGCATTTGATAACAAGG 57.247 29.630 0.00 0.00 33.78 3.61
721 939 9.040939 CACATGTTTCATATTGATGCATTTGAT 57.959 29.630 0.00 0.00 32.62 2.57
728 946 8.692110 TTCTTTCACATGTTTCATATTGATGC 57.308 30.769 0.00 0.00 32.62 3.91
744 962 8.006590 CGTGTTCAAAACAAAATTTCTTTCACA 58.993 29.630 0.00 0.00 44.16 3.58
787 1005 6.876789 TGAGCGACAAATAATTCCAGACTAAA 59.123 34.615 0.00 0.00 0.00 1.85
790 1008 4.832248 TGAGCGACAAATAATTCCAGACT 58.168 39.130 0.00 0.00 0.00 3.24
898 1116 6.825284 TGACGTACGTTTTAAATCACAGAA 57.175 33.333 23.70 0.00 0.00 3.02
900 1118 6.813327 TCATGACGTACGTTTTAAATCACAG 58.187 36.000 23.70 10.01 0.00 3.66
902 1120 7.424452 GGATTCATGACGTACGTTTTAAATCAC 59.576 37.037 28.51 20.83 0.00 3.06
921 2287 3.612479 GCAGTTTCAAGCGTTGGATTCAT 60.612 43.478 0.00 0.00 0.00 2.57
973 2426 0.461961 ACTAATGACTGGCGCCTCTC 59.538 55.000 29.70 21.24 0.00 3.20
978 2431 0.940126 CATGGACTAATGACTGGCGC 59.060 55.000 0.00 0.00 0.00 6.53
979 2432 1.134401 ACCATGGACTAATGACTGGCG 60.134 52.381 21.47 0.00 0.00 5.69
1126 2582 1.528542 CGTAGGATCGGAGGAGGCA 60.529 63.158 0.00 0.00 0.00 4.75
1224 2680 2.954868 GAGTGGGCGCGTATGACG 60.955 66.667 8.43 0.00 45.88 4.35
1365 2821 3.125376 ATGGAGGATCTTGGCGGCC 62.125 63.158 13.32 13.32 33.73 6.13
1387 2843 1.409412 CATCCGGAAGATAACGCGAG 58.591 55.000 15.93 0.00 32.37 5.03
1394 2850 1.482553 GGGAGGACCATCCGGAAGATA 60.483 57.143 9.01 0.00 42.75 1.98
1449 2905 3.621268 TGTCCACGAACAAGAACTTTGAG 59.379 43.478 0.00 0.00 0.00 3.02
1462 2918 2.355837 GCGAGCACTGTCCACGAA 60.356 61.111 0.00 0.00 0.00 3.85
1481 2937 0.593773 ACGCAAACCATCAAACACGC 60.594 50.000 0.00 0.00 0.00 5.34
1482 2938 1.119635 CACGCAAACCATCAAACACG 58.880 50.000 0.00 0.00 0.00 4.49
1503 2959 1.913762 CCAGAGAACCAGGTCCGGT 60.914 63.158 0.00 0.11 42.71 5.28
1570 3026 3.059166 GCATTGCCGAAAACAGTTGAAT 58.941 40.909 0.00 0.00 0.00 2.57
1584 3040 3.211963 CCAGCCCTACGCATTGCC 61.212 66.667 2.41 0.00 41.38 4.52
1611 3067 1.359475 GACCATCGAGTAGCCGTCC 59.641 63.158 0.00 0.00 0.00 4.79
2109 3565 7.766278 ACCATATTGTACATGACTGAGTTCTTC 59.234 37.037 0.00 0.00 0.00 2.87
2277 3733 4.202245 TCTCCTAAACAACTTCCATCCG 57.798 45.455 0.00 0.00 0.00 4.18
2326 3782 5.918576 CCATGTAGACATAATGCTGCATTTG 59.081 40.000 30.35 26.16 35.68 2.32
2421 3877 3.430862 CCCCACACGCCACAATCG 61.431 66.667 0.00 0.00 0.00 3.34
2617 4080 8.768397 ACTTATCCCTGTGTTCTTGTTCATATA 58.232 33.333 0.00 0.00 0.00 0.86
2623 4086 4.827284 CCAACTTATCCCTGTGTTCTTGTT 59.173 41.667 0.00 0.00 0.00 2.83
2981 4445 3.766545 AGTGAGCCAGGCAAGAAAAATA 58.233 40.909 15.80 0.00 0.00 1.40
2997 4461 1.207791 AGGGGATACAGGCAAGTGAG 58.792 55.000 0.00 0.00 39.74 3.51
3346 4811 4.075682 TCGCCACAGAACCATAAAATGAA 58.924 39.130 0.00 0.00 0.00 2.57
3411 4878 5.047943 TGACTACTTGACTAAGCCTCAACTC 60.048 44.000 0.00 0.00 37.43 3.01
3514 4983 3.454447 TGCTGCAGCCTTTAGGATAAGTA 59.546 43.478 34.64 8.93 41.18 2.24
3635 5110 5.198965 TCAAACCGACCTAGCTAAGAGTAT 58.801 41.667 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.