Multiple sequence alignment - TraesCS6B01G021300

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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 TraesCS6B01G021300 chr6B 100.000 6347 0 0 1 6347 12954761 12961107 0.000000e+00 11721.0
1 TraesCS6B01G021300 chr6B 94.048 84 5 0 314 397 200777247 200777330 1.860000e-25 128.0
2 TraesCS6B01G021300 chr6B 81.437 167 21 5 4864 5020 394652740 394652574 1.860000e-25 128.0
3 TraesCS6B01G021300 chrUn 97.359 2575 38 6 3 2548 79951494 79954067 0.000000e+00 4351.0
4 TraesCS6B01G021300 chrUn 96.117 2575 85 2 2545 5111 79954156 79956723 0.000000e+00 4187.0
5 TraesCS6B01G021300 chrUn 96.940 1242 30 3 5109 6347 79957322 79958558 0.000000e+00 2076.0
6 TraesCS6B01G021300 chrUn 100.000 408 0 0 878 1285 477903133 477902726 0.000000e+00 754.0
7 TraesCS6B01G021300 chr6A 91.838 1703 118 7 3136 4836 7163452 7161769 0.000000e+00 2355.0
8 TraesCS6B01G021300 chr6A 86.725 1612 167 29 799 2377 7165972 7164375 0.000000e+00 1748.0
9 TraesCS6B01G021300 chr6A 87.973 449 48 4 2545 2989 7163979 7163533 5.640000e-145 525.0
10 TraesCS6B01G021300 chr6A 97.333 75 2 0 3019 3093 7163533 7163459 1.860000e-25 128.0
11 TraesCS6B01G021300 chr6A 93.827 81 5 0 314 394 155803833 155803753 8.640000e-24 122.0
12 TraesCS6B01G021300 chr2B 81.988 1871 294 32 2795 4646 9889453 9891299 0.000000e+00 1548.0
13 TraesCS6B01G021300 chr2B 81.937 1766 282 32 2841 4586 9620338 9622086 0.000000e+00 1459.0
14 TraesCS6B01G021300 chr2B 75.909 880 159 31 1001 1864 9887760 9888602 9.910000e-108 401.0
15 TraesCS6B01G021300 chr2B 85.714 224 27 3 4892 5111 195196174 195195952 1.380000e-56 231.0
16 TraesCS6B01G021300 chr2B 84.932 219 30 3 4895 5110 750007815 750007597 1.070000e-52 219.0
17 TraesCS6B01G021300 chr2B 85.849 106 13 1 314 417 90381094 90381199 1.870000e-20 111.0
18 TraesCS6B01G021300 chr2B 77.976 168 21 8 4867 5021 46815601 46815765 2.440000e-14 91.6
19 TraesCS6B01G021300 chr2A 82.253 1820 294 24 2853 4655 1208405 1210212 0.000000e+00 1544.0
20 TraesCS6B01G021300 chr2A 74.947 1409 294 43 3035 4415 17001572 17000195 5.480000e-165 592.0
21 TraesCS6B01G021300 chr2A 74.196 1275 272 36 2866 4109 768732856 768731608 4.450000e-131 479.0
22 TraesCS6B01G021300 chr2A 83.197 244 29 5 4866 5099 164870588 164870829 4.980000e-51 213.0
23 TraesCS6B01G021300 chr2A 82.895 228 38 1 2603 2829 1203182 1203409 3.000000e-48 204.0
24 TraesCS6B01G021300 chr7D 74.016 1143 247 34 3032 4155 634110264 634109153 2.740000e-113 420.0
25 TraesCS6B01G021300 chr7D 84.496 258 29 2 4865 5111 175442728 175442985 1.770000e-60 244.0
26 TraesCS6B01G021300 chr7D 75.952 420 78 20 1001 1410 3581724 3582130 1.810000e-45 195.0
27 TraesCS6B01G021300 chr7B 73.758 1147 255 26 3023 4155 742554275 742553161 5.920000e-110 409.0
28 TraesCS6B01G021300 chr7B 92.857 84 6 0 314 397 747370650 747370733 8.640000e-24 122.0
29 TraesCS6B01G021300 chr4A 90.323 217 20 1 4895 5111 63800120 63799905 3.750000e-72 283.0
30 TraesCS6B01G021300 chr4A 74.634 410 87 15 1001 1403 742271664 742271265 1.420000e-36 165.0
31 TraesCS6B01G021300 chr4A 80.120 166 22 6 1001 1165 733929095 733928940 5.200000e-21 113.0
32 TraesCS6B01G021300 chr3B 86.667 255 26 3 4865 5111 794589772 794589518 6.270000e-70 276.0
33 TraesCS6B01G021300 chr4D 84.252 254 29 3 4866 5111 406201063 406200813 2.960000e-58 237.0
34 TraesCS6B01G021300 chr4D 85.185 216 30 2 4898 5111 359225183 359224968 2.980000e-53 220.0
35 TraesCS6B01G021300 chr3A 87.374 198 22 2 4895 5089 724015988 724015791 2.300000e-54 224.0
36 TraesCS6B01G021300 chr3A 77.536 138 21 4 4866 4994 646458339 646458475 2.450000e-09 75.0
37 TraesCS6B01G021300 chr3D 82.625 259 28 7 4866 5111 108588886 108589140 4.980000e-51 213.0
38 TraesCS6B01G021300 chr7A 75.714 420 85 13 1001 1413 3379609 3380018 1.810000e-45 195.0
39 TraesCS6B01G021300 chr7A 79.286 140 19 6 4864 4994 573933589 573933727 8.760000e-14 89.8
40 TraesCS6B01G021300 chr2D 78.472 288 53 7 1000 1284 16495170 16494889 5.060000e-41 180.0
41 TraesCS6B01G021300 chr5D 95.000 80 4 0 314 393 65990509 65990588 6.680000e-25 126.0
42 TraesCS6B01G021300 chr6D 93.902 82 5 0 314 395 91559612 91559531 2.400000e-24 124.0
43 TraesCS6B01G021300 chr1B 94.937 79 4 0 314 392 555629470 555629392 2.400000e-24 124.0
44 TraesCS6B01G021300 chr1A 94.937 79 4 0 314 392 508633102 508633024 2.400000e-24 124.0


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 TraesCS6B01G021300 chr6B 12954761 12961107 6346 False 11721.0 11721 100.000000 1 6347 1 chr6B.!!$F1 6346
1 TraesCS6B01G021300 chrUn 79951494 79958558 7064 False 3538.0 4351 96.805333 3 6347 3 chrUn.!!$F1 6344
2 TraesCS6B01G021300 chr6A 7161769 7165972 4203 True 1189.0 2355 90.967250 799 4836 4 chr6A.!!$R2 4037
3 TraesCS6B01G021300 chr2B 9620338 9622086 1748 False 1459.0 1459 81.937000 2841 4586 1 chr2B.!!$F1 1745
4 TraesCS6B01G021300 chr2B 9887760 9891299 3539 False 974.5 1548 78.948500 1001 4646 2 chr2B.!!$F4 3645
5 TraesCS6B01G021300 chr2A 1208405 1210212 1807 False 1544.0 1544 82.253000 2853 4655 1 chr2A.!!$F2 1802
6 TraesCS6B01G021300 chr2A 17000195 17001572 1377 True 592.0 592 74.947000 3035 4415 1 chr2A.!!$R1 1380
7 TraesCS6B01G021300 chr2A 768731608 768732856 1248 True 479.0 479 74.196000 2866 4109 1 chr2A.!!$R2 1243
8 TraesCS6B01G021300 chr7D 634109153 634110264 1111 True 420.0 420 74.016000 3032 4155 1 chr7D.!!$R1 1123
9 TraesCS6B01G021300 chr7B 742553161 742554275 1114 True 409.0 409 73.758000 3023 4155 1 chr7B.!!$R1 1132

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
205 206 2.452600 AAAACTGGGCCTTTGTCTCA 57.547 45.000 4.53 0.0 0.00 3.27 F
1707 1767 2.603473 GGAGGGGTGGGCAAAACC 60.603 66.667 0.00 0.0 36.94 3.27 F
3270 3695 0.250338 GCAACGGGAAGGTGAAGAGT 60.250 55.000 0.00 0.0 40.93 3.24 F
4280 4717 0.469892 ACAGGGGAAAACAAGGCTGG 60.470 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1801 0.532115 GCCCGGCAGTCAAATTGATT 59.468 50.0 3.91 0.0 0.0 2.57 R
3364 3789 0.949105 CGGACTTTGTTGCTAGGCGT 60.949 55.0 0.00 0.0 0.0 5.68 R
4299 4736 0.179073 GCTCCTCAAATCCGCTAGCA 60.179 55.0 16.45 0.0 0.0 3.49 R
5387 6443 0.310854 GACCAAAACAGCCCGAAGTG 59.689 55.0 0.00 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
40 41 2.971330 CAGATGCTTATCCAGGGAGAGT 59.029 50.000 0.00 0.00 0.00 3.24
69 70 3.050089 GGCAGGACCAACATGGAAA 57.950 52.632 2.85 0.00 40.96 3.13
117 118 4.351131 AACTTGGTTGTTTGAACGAGAC 57.649 40.909 0.00 0.00 0.00 3.36
120 121 4.035208 ACTTGGTTGTTTGAACGAGACATC 59.965 41.667 0.00 0.00 0.00 3.06
205 206 2.452600 AAAACTGGGCCTTTGTCTCA 57.547 45.000 4.53 0.00 0.00 3.27
218 219 4.874966 CCTTTGTCTCAGGTCATGATTCTC 59.125 45.833 0.00 0.00 37.28 2.87
243 244 6.884295 CCCTTCTGACATACTGGATTTGTTAA 59.116 38.462 0.00 0.00 0.00 2.01
336 356 9.862371 ATGATAAGTGTCTCAACTTTGTACTAG 57.138 33.333 0.00 0.00 40.77 2.57
382 402 4.755123 ACTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
402 422 3.149981 CGGAGTGAGTATGATAGAGCCA 58.850 50.000 0.00 0.00 0.00 4.75
406 426 5.278758 GGAGTGAGTATGATAGAGCCAGAAC 60.279 48.000 0.00 0.00 0.00 3.01
494 514 6.766467 GCAACAGGTAATAGCTAACCTAACAT 59.234 38.462 15.35 1.66 44.43 2.71
605 625 6.000219 GCTAGTATGATGGACAATTGGACAT 59.000 40.000 10.83 13.02 0.00 3.06
675 695 6.833416 AGATGCTCTTATCTGTATAGGCCTAG 59.167 42.308 19.33 6.24 36.12 3.02
1491 1551 3.329093 GGAGGATTCCAGGCTGCT 58.671 61.111 9.56 0.00 43.45 4.24
1707 1767 2.603473 GGAGGGGTGGGCAAAACC 60.603 66.667 0.00 0.00 36.94 3.27
1741 1801 6.268825 TGGCGTTATACCAAAAATTTGCTA 57.731 33.333 0.29 0.00 36.86 3.49
2138 2201 2.609427 TGCATAGTGCTCTCCATGTC 57.391 50.000 3.41 0.00 45.31 3.06
2141 2204 2.611292 GCATAGTGCTCTCCATGTCAAC 59.389 50.000 0.00 0.00 40.96 3.18
2390 2610 2.018542 TTAACAGGTATGCACGCCTC 57.981 50.000 7.84 0.00 31.73 4.70
2536 2762 8.915654 CATGTGAAAGTTATTTAAGCTGTTTCC 58.084 33.333 0.00 0.00 0.00 3.13
2700 3020 4.838986 TCACTGCCTAAAAGTAAGAGAGGT 59.161 41.667 0.00 0.00 0.00 3.85
2733 3053 0.393132 TCACCACACGGTTTCAAGCA 60.393 50.000 0.00 0.00 46.31 3.91
2775 3098 9.829507 ATAAGAGATAAAGGAGTTCATGTTCAG 57.170 33.333 0.00 0.00 0.00 3.02
2971 3384 0.804989 GGACTGGATGGAAGTTTGCG 59.195 55.000 0.00 0.00 0.00 4.85
3116 3541 1.244019 AAGGGGCGAAACATCAGCAC 61.244 55.000 0.00 0.00 0.00 4.40
3117 3542 2.877691 GGGCGAAACATCAGCACC 59.122 61.111 0.00 0.00 0.00 5.01
3270 3695 0.250338 GCAACGGGAAGGTGAAGAGT 60.250 55.000 0.00 0.00 40.93 3.24
3820 4251 0.532115 AACAATGAAATCCCTGCGCC 59.468 50.000 4.18 0.00 0.00 6.53
3957 4388 8.713271 AGTAAACTTTTCAGAGAATTAAGCTCG 58.287 33.333 0.00 0.00 37.46 5.03
4092 4523 4.380531 CTCTTGAACTGTCTGGCAAGTTA 58.619 43.478 3.17 0.00 38.95 2.24
4280 4717 0.469892 ACAGGGGAAAACAAGGCTGG 60.470 55.000 0.00 0.00 0.00 4.85
4299 4736 3.713764 CTGGTGGGAAGATCATAGTTCCT 59.286 47.826 10.38 0.00 41.84 3.36
4533 4973 2.019249 GAGAATATGGCAACTGCAGCA 58.981 47.619 15.27 3.58 44.36 4.41
4703 5149 8.775527 CAGAGCAGTATTTACTCGATCTACTTA 58.224 37.037 0.00 0.00 32.50 2.24
4862 5309 5.954335 AGCTTGCCTTAACAAATGATACAC 58.046 37.500 0.00 0.00 0.00 2.90
4887 5334 3.120095 CGTATGTGGTCGTTACTCACTCA 60.120 47.826 0.00 0.00 31.73 3.41
4938 5393 0.833834 ATGGGAGATGGTAGCTCGGG 60.834 60.000 0.00 0.00 33.19 5.14
4946 5401 4.528920 AGATGGTAGCTCGGGATATCTAC 58.471 47.826 2.05 0.00 0.00 2.59
4962 5417 1.700739 TCTACAACCGGTTTGGATGGT 59.299 47.619 19.55 13.96 44.51 3.55
4964 5419 0.825840 ACAACCGGTTTGGATGGTGG 60.826 55.000 19.55 5.46 44.51 4.61
5010 5465 4.636206 AGTCATCAAGTTCTATTTTCGCCC 59.364 41.667 0.00 0.00 0.00 6.13
5011 5466 3.621268 TCATCAAGTTCTATTTTCGCCCG 59.379 43.478 0.00 0.00 0.00 6.13
5012 5467 1.735571 TCAAGTTCTATTTTCGCCCGC 59.264 47.619 0.00 0.00 0.00 6.13
5013 5468 1.737793 CAAGTTCTATTTTCGCCCGCT 59.262 47.619 0.00 0.00 0.00 5.52
5014 5469 2.933906 CAAGTTCTATTTTCGCCCGCTA 59.066 45.455 0.00 0.00 0.00 4.26
5072 5527 1.338200 GCGAGGTTGTTCTGGATCACT 60.338 52.381 0.00 0.00 0.00 3.41
5098 5553 7.012515 TGACTTTTCGGTCACTTTGCTTAATAA 59.987 33.333 0.00 0.00 40.72 1.40
5099 5554 7.136772 ACTTTTCGGTCACTTTGCTTAATAAC 58.863 34.615 0.00 0.00 0.00 1.89
5153 6209 7.156673 ACTTGATCAAATCACAATCCCTTTTG 58.843 34.615 9.88 0.00 39.39 2.44
5157 6213 5.481105 TCAAATCACAATCCCTTTTGATGC 58.519 37.500 0.00 0.00 32.88 3.91
5195 6251 3.441163 CATCATGCTCCAACCGAAAATG 58.559 45.455 0.00 0.00 0.00 2.32
5201 6257 2.094545 GCTCCAACCGAAAATGCATCTT 60.095 45.455 0.00 0.00 0.00 2.40
5202 6258 3.614870 GCTCCAACCGAAAATGCATCTTT 60.615 43.478 0.00 3.05 0.00 2.52
5208 6264 6.368516 CCAACCGAAAATGCATCTTTTACATT 59.631 34.615 0.00 0.00 35.59 2.71
5209 6265 7.095271 CCAACCGAAAATGCATCTTTTACATTT 60.095 33.333 0.00 0.00 43.84 2.32
5210 6266 7.581011 ACCGAAAATGCATCTTTTACATTTC 57.419 32.000 0.00 2.90 41.78 2.17
5211 6267 7.151308 ACCGAAAATGCATCTTTTACATTTCA 58.849 30.769 0.00 0.00 41.78 2.69
5259 6315 5.181690 TGCATCCTTACAACTCAAACAAC 57.818 39.130 0.00 0.00 0.00 3.32
5278 6334 5.736338 ACAACAGCACAAATTTTAATTGCG 58.264 33.333 0.00 0.00 0.00 4.85
5336 6392 5.791336 AGTACGCATTCAGATCAAGGATA 57.209 39.130 0.00 0.00 0.00 2.59
5383 6439 5.242393 AGTCAAATAAAGCAGCATGTCAGTT 59.758 36.000 0.00 0.00 39.31 3.16
5387 6443 8.397906 TCAAATAAAGCAGCATGTCAGTTATAC 58.602 33.333 0.00 0.00 39.31 1.47
5448 6504 2.574450 TGGGTCTGTTTTAAACCGGTC 58.426 47.619 8.04 0.00 33.69 4.79
5467 6523 2.286294 GTCTGTGATAAGCATTCTGCCG 59.714 50.000 0.00 0.00 46.52 5.69
5503 6559 2.595124 TCACTGACACGCTTGAAGAA 57.405 45.000 0.00 0.00 0.00 2.52
5563 6619 1.323271 GCCGGTCAGTGATGAGAGGA 61.323 60.000 1.90 0.00 0.00 3.71
5607 6663 6.682537 AGAGGTGAAAGATCCTTCTCTCTAT 58.317 40.000 19.56 7.06 36.18 1.98
5621 6677 9.058174 TCCTTCTCTCTATTCTACAAGTATTCG 57.942 37.037 0.00 0.00 0.00 3.34
5663 6719 8.828751 ACCTGTTATACCTGAAATAACCTTACA 58.171 33.333 4.11 0.00 38.49 2.41
5664 6720 9.847224 CCTGTTATACCTGAAATAACCTTACAT 57.153 33.333 4.11 0.00 38.49 2.29
5677 6733 4.396357 ACCTTACATTTCCCCATGACAA 57.604 40.909 0.00 0.00 0.00 3.18
5680 6736 4.526262 CCTTACATTTCCCCATGACAACAA 59.474 41.667 0.00 0.00 0.00 2.83
5745 6801 0.109132 CCGGTTTTCTGCATTCAGCC 60.109 55.000 0.00 0.00 44.83 4.85
5924 6980 1.015109 TGTTGCAACTCGCCGTAAAA 58.985 45.000 28.61 2.96 41.33 1.52
5939 6995 5.387342 CGCCGTAAAATTTTGCTGAGAAAAG 60.387 40.000 13.76 0.00 0.00 2.27
6150 7209 3.644966 TCGGGTTTTCTATTGATGCCT 57.355 42.857 0.00 0.00 0.00 4.75
6276 7335 9.803315 TTCCTGATATTATGATAAGCATCGTAC 57.197 33.333 0.00 0.00 38.44 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.825836 GTCAGGAATGCCGGGCAG 60.826 66.667 27.62 13.25 43.65 4.85
1 2 3.645660 TGTCAGGAATGCCGGGCA 61.646 61.111 26.11 26.11 41.78 5.36
6 7 0.737219 GCATCTGTGTCAGGAATGCC 59.263 55.000 10.36 0.00 36.41 4.40
69 70 6.775594 AAACTCAAAACTAACAGGAAAGCT 57.224 33.333 0.00 0.00 0.00 3.74
117 118 2.370281 ACTCGTGTTGCACTAGGATG 57.630 50.000 0.00 0.00 32.50 3.51
120 121 3.021269 TGTAACTCGTGTTGCACTAGG 57.979 47.619 15.61 0.00 42.31 3.02
141 142 4.217118 CAGGAGAAAGGGTTGATCTGTTTG 59.783 45.833 0.00 0.00 0.00 2.93
205 206 3.454082 GTCAGAAGGGAGAATCATGACCT 59.546 47.826 0.00 0.00 36.25 3.85
218 219 4.848357 ACAAATCCAGTATGTCAGAAGGG 58.152 43.478 0.00 0.00 0.00 3.95
243 244 6.074648 TCCAAAAACACCAATAAGTCCATCT 58.925 36.000 0.00 0.00 0.00 2.90
336 356 8.599055 AGTTTACTACACCTTTGTACTAAAGC 57.401 34.615 10.51 0.00 37.15 3.51
382 402 4.402829 TCTGGCTCTATCATACTCACTCC 58.597 47.826 0.00 0.00 0.00 3.85
392 412 0.179100 GCTGCGTTCTGGCTCTATCA 60.179 55.000 0.00 0.00 0.00 2.15
402 422 3.334583 TGAATTAGGAAGCTGCGTTCT 57.665 42.857 1.18 1.18 0.00 3.01
406 426 2.540361 GCACATGAATTAGGAAGCTGCG 60.540 50.000 0.00 0.00 0.00 5.18
476 496 6.204882 CCTTGGCATGTTAGGTTAGCTATTAC 59.795 42.308 0.00 0.00 0.00 1.89
494 514 0.038599 ATCATGCTGACACCTTGGCA 59.961 50.000 0.00 0.00 39.06 4.92
605 625 3.282021 GCTGGACTTGGCATCTATGAAA 58.718 45.455 0.00 0.00 0.00 2.69
675 695 6.371548 TCAGTCAACTCTTACCATTATTGCAC 59.628 38.462 0.00 0.00 0.00 4.57
876 905 4.984785 GCTTTGAGGGACTGTTGATTTTTC 59.015 41.667 0.00 0.00 41.55 2.29
1285 1335 2.358003 GCAGCAGACTTCGCCACT 60.358 61.111 0.00 0.00 0.00 4.00
1491 1551 1.980765 AGGCTCATCTGTTGGTTCTCA 59.019 47.619 0.00 0.00 0.00 3.27
1707 1767 0.746063 ATAACGCCATGGCCATTGTG 59.254 50.000 30.79 24.72 37.98 3.33
1741 1801 0.532115 GCCCGGCAGTCAAATTGATT 59.468 50.000 3.91 0.00 0.00 2.57
2138 2201 7.122650 TCCCTTTTTAATGAGAGCTAATGGTTG 59.877 37.037 0.00 0.00 0.00 3.77
2141 2204 7.645058 TTCCCTTTTTAATGAGAGCTAATGG 57.355 36.000 0.00 0.00 0.00 3.16
2474 2699 9.203421 TGTGTCCTACATATATGCGAAATTTAG 57.797 33.333 12.79 5.20 33.42 1.85
2522 2748 8.958119 TTATATGTCTCGGAAACAGCTTAAAT 57.042 30.769 0.00 0.00 0.00 1.40
2700 3020 2.238395 TGTGGTGAGTATTATGCTGCCA 59.762 45.455 0.00 0.00 0.00 4.92
2733 3053 2.002586 CTTATGCACGCACTAGCAACT 58.997 47.619 0.00 0.00 44.88 3.16
2775 3098 1.551883 TCCCTAAGTACGCCCACTTTC 59.448 52.381 3.17 0.00 39.45 2.62
2971 3384 2.046604 GTCCGGTACCAACCTGGC 60.047 66.667 13.54 0.00 42.67 4.85
2989 3402 1.304464 GGCCAAGAGGTTTCCCAGG 60.304 63.158 0.00 0.00 37.19 4.45
3270 3695 6.599244 GGAGAACCATGTCATGAACTTGATAA 59.401 38.462 14.67 0.00 35.55 1.75
3364 3789 0.949105 CGGACTTTGTTGCTAGGCGT 60.949 55.000 0.00 0.00 0.00 5.68
3820 4251 4.308265 TCGATCTCGATACCTGACAGTAG 58.692 47.826 0.93 0.00 44.22 2.57
3957 4388 4.265073 AGCCACCAAGATACTCAATTGAC 58.735 43.478 3.38 0.00 0.00 3.18
4092 4523 1.067295 TCCATTGTGGGAGCTCAACT 58.933 50.000 17.19 0.00 38.32 3.16
4128 4559 2.352814 CGAGAGGGTCAACTTCGTCAAT 60.353 50.000 0.00 0.00 0.00 2.57
4280 4717 3.135530 AGCAGGAACTATGATCTTCCCAC 59.864 47.826 7.63 1.86 37.27 4.61
4299 4736 0.179073 GCTCCTCAAATCCGCTAGCA 60.179 55.000 16.45 0.00 0.00 3.49
4515 4952 2.480759 CCTTGCTGCAGTTGCCATATTC 60.481 50.000 16.64 0.00 41.18 1.75
4533 4973 1.272704 GGGCCTTTGTCATCTTCCCTT 60.273 52.381 0.84 0.00 0.00 3.95
4657 5103 6.620303 GCTCTGAACTTGCACAAAGAATAGAG 60.620 42.308 0.00 0.00 39.57 2.43
4785 5232 7.962441 TGGATTCTGCTATGCTACTGTAAATA 58.038 34.615 0.00 0.00 0.00 1.40
4862 5309 3.789756 GTGAGTAACGACCACATACGATG 59.210 47.826 0.00 0.00 31.06 3.84
4887 5334 3.157087 CAGTAACCAAAGGCTTCCACAT 58.843 45.455 0.00 0.00 0.00 3.21
4923 5378 3.626930 AGATATCCCGAGCTACCATCTC 58.373 50.000 0.00 0.00 0.00 2.75
4924 5379 3.748645 AGATATCCCGAGCTACCATCT 57.251 47.619 0.00 0.00 0.00 2.90
4925 5380 4.270834 TGTAGATATCCCGAGCTACCATC 58.729 47.826 0.00 0.00 33.92 3.51
4926 5381 4.317530 TGTAGATATCCCGAGCTACCAT 57.682 45.455 0.00 0.00 33.92 3.55
4927 5382 3.801307 TGTAGATATCCCGAGCTACCA 57.199 47.619 0.00 0.00 33.92 3.25
4928 5383 3.193056 GGTTGTAGATATCCCGAGCTACC 59.807 52.174 0.00 0.00 33.92 3.18
4929 5384 3.119919 CGGTTGTAGATATCCCGAGCTAC 60.120 52.174 10.76 1.92 41.08 3.58
4930 5385 3.079578 CGGTTGTAGATATCCCGAGCTA 58.920 50.000 10.76 0.00 41.08 3.32
4938 5393 4.755123 CCATCCAAACCGGTTGTAGATATC 59.245 45.833 23.08 0.00 35.23 1.63
4946 5401 0.825840 ACCACCATCCAAACCGGTTG 60.826 55.000 23.08 14.70 36.94 3.77
4962 5417 7.460214 AAACACCTATCCTATTATTGGACCA 57.540 36.000 0.00 0.00 36.30 4.02
4964 5419 9.708092 GACTAAACACCTATCCTATTATTGGAC 57.292 37.037 0.00 0.00 36.30 4.02
4994 5449 2.109425 AGCGGGCGAAAATAGAACTT 57.891 45.000 0.00 0.00 0.00 2.66
4995 5450 2.973694 TAGCGGGCGAAAATAGAACT 57.026 45.000 0.00 0.00 0.00 3.01
5031 5486 5.700832 TCGCTCAGAGCTGAAGAAAAATTAA 59.299 36.000 20.39 0.00 39.60 1.40
5057 5512 5.559035 CGAAAAGTCAGTGATCCAGAACAAC 60.559 44.000 0.00 0.00 0.00 3.32
5072 5527 2.639065 AGCAAAGTGACCGAAAAGTCA 58.361 42.857 0.00 0.00 44.38 3.41
5098 5553 3.490031 TTGACACATGCAGCCCCGT 62.490 57.895 0.00 0.00 0.00 5.28
5099 5554 2.672651 TTGACACATGCAGCCCCG 60.673 61.111 0.00 0.00 0.00 5.73
5153 6209 3.066203 TGCTCATCATGATTGTGTGCATC 59.934 43.478 16.54 0.00 37.42 3.91
5157 6213 4.893424 TGATGCTCATCATGATTGTGTG 57.107 40.909 5.16 0.00 42.42 3.82
5181 6237 3.855689 AAGATGCATTTTCGGTTGGAG 57.144 42.857 0.00 0.00 0.00 3.86
5259 6315 5.401972 TGAGTCGCAATTAAAATTTGTGCTG 59.598 36.000 12.03 7.70 0.00 4.41
5278 6334 4.189639 ACCCGAGTAAAAGATGTGAGTC 57.810 45.455 0.00 0.00 0.00 3.36
5336 6392 5.028549 AGTCTGAGTTGATCACTTTGTGT 57.971 39.130 0.00 0.00 35.01 3.72
5383 6439 3.244630 ACCAAAACAGCCCGAAGTGTATA 60.245 43.478 0.00 0.00 0.00 1.47
5387 6443 0.310854 GACCAAAACAGCCCGAAGTG 59.689 55.000 0.00 0.00 0.00 3.16
5467 6523 3.092301 AGTGATAAGCTTTTTGGGGCTC 58.908 45.455 3.20 0.00 37.87 4.70
5563 6619 6.722129 ACCTCTACAGATCAAAACACTACTCT 59.278 38.462 0.00 0.00 0.00 3.24
5663 6719 3.255642 CGTTCTTGTTGTCATGGGGAAAT 59.744 43.478 0.00 0.00 0.00 2.17
5664 6720 2.621055 CGTTCTTGTTGTCATGGGGAAA 59.379 45.455 0.00 0.00 0.00 3.13
5665 6721 2.226330 CGTTCTTGTTGTCATGGGGAA 58.774 47.619 0.00 0.00 0.00 3.97
5677 6733 3.143728 GGTAAACATCCACCGTTCTTGT 58.856 45.455 0.00 0.00 0.00 3.16
5745 6801 0.670239 GCCCGCAAGACAATTTTGGG 60.670 55.000 0.00 0.00 43.02 4.12
5881 6937 9.499479 ACACATATTAATGTTCATTGCCAAAAA 57.501 25.926 8.11 0.00 44.07 1.94
5924 6980 8.370182 ACCACATATTTCTTTTCTCAGCAAAAT 58.630 29.630 0.00 0.00 0.00 1.82
5939 6995 7.335422 AGAGAATCACAGACAACCACATATTTC 59.665 37.037 0.00 0.00 37.82 2.17
6083 7142 7.812690 TTCATTGGTTTCAGATGATATCCTG 57.187 36.000 0.00 1.51 30.59 3.86
6276 7335 4.149221 TGTGTCATTTTCGTAACGCTACAG 59.851 41.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.