Multiple sequence alignment - TraesCS2D01G148000

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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 TraesCS2D01G148000 chr2D 100.000 5972 0 0 1 5972 89264557 89258586 0.000000e+00 11029
1 TraesCS2D01G148000 chr2D 90.446 157 14 1 5817 5972 471013083 471012927 7.850000e-49 206
2 TraesCS2D01G148000 chr2D 90.446 157 13 2 5818 5972 535733323 535733167 7.850000e-49 206
3 TraesCS2D01G148000 chr2A 93.288 3069 152 20 2516 5548 88986338 88983288 0.000000e+00 4477
4 TraesCS2D01G148000 chr2A 94.121 2058 81 21 494 2522 88988412 88986366 0.000000e+00 3094
5 TraesCS2D01G148000 chr2A 87.221 493 52 5 1 490 88989290 88988806 8.750000e-153 551
6 TraesCS2D01G148000 chr2A 92.357 157 11 1 5817 5972 84005223 84005067 7.790000e-54 222
7 TraesCS2D01G148000 chr2B 94.437 1582 47 18 3673 5222 141838120 141836548 0.000000e+00 2396
8 TraesCS2D01G148000 chr2B 90.335 1821 115 28 1 1805 141842511 141840736 0.000000e+00 2331
9 TraesCS2D01G148000 chr2B 94.859 1167 51 5 2516 3675 141839933 141838769 0.000000e+00 1814
10 TraesCS2D01G148000 chr2B 91.995 787 41 10 5204 5972 141836527 141835745 0.000000e+00 1085
11 TraesCS2D01G148000 chr2B 94.815 675 25 5 1853 2522 141840630 141839961 0.000000e+00 1044
12 TraesCS2D01G148000 chr2B 88.976 381 38 4 7 384 141907174 141906795 9.060000e-128 468
13 TraesCS2D01G148000 chr2B 88.714 381 39 4 7 384 141868612 141868233 4.220000e-126 462
14 TraesCS2D01G148000 chr2B 86.452 155 9 4 400 554 141860356 141860214 6.200000e-35 159
15 TraesCS2D01G148000 chr2B 95.714 70 3 0 1805 1874 141840712 141840643 4.890000e-21 113
16 TraesCS2D01G148000 chr3D 89.502 1286 119 11 3093 4362 136724317 136725602 0.000000e+00 1613
17 TraesCS2D01G148000 chr3D 81.477 907 96 35 952 1806 136721799 136722685 0.000000e+00 678
18 TraesCS2D01G148000 chr3D 86.275 255 24 10 2829 3081 136723980 136724225 3.550000e-67 267
19 TraesCS2D01G148000 chr3B 89.191 1286 122 12 3093 4362 199529387 199530671 0.000000e+00 1589
20 TraesCS2D01G148000 chr3B 82.726 1152 123 37 641 1744 199526465 199527588 0.000000e+00 955
21 TraesCS2D01G148000 chr3B 85.408 233 26 7 2795 3027 199528630 199528854 1.000000e-57 235
22 TraesCS2D01G148000 chr3B 90.446 157 14 1 5817 5972 712185963 712185807 7.850000e-49 206
23 TraesCS2D01G148000 chr3B 76.730 318 29 19 5160 5461 199532092 199532380 1.040000e-27 135
24 TraesCS2D01G148000 chr3A 88.578 1287 122 14 3093 4362 154661293 154662571 0.000000e+00 1539
25 TraesCS2D01G148000 chr3A 83.181 767 81 29 1075 1806 154658777 154659530 0.000000e+00 658
26 TraesCS2D01G148000 chr3A 84.451 701 70 17 1831 2522 154659651 154660321 0.000000e+00 654
27 TraesCS2D01G148000 chr3A 83.146 445 56 13 641 1079 154658310 154658741 7.260000e-104 388
28 TraesCS2D01G148000 chr3A 87.500 288 25 8 2795 3081 154660933 154661210 7.470000e-84 322
29 TraesCS2D01G148000 chr3A 80.636 346 43 14 5132 5461 154663766 154664103 4.620000e-61 246
30 TraesCS2D01G148000 chr3A 91.026 156 13 1 5818 5972 732874597 732874442 6.060000e-50 209
31 TraesCS2D01G148000 chr3A 91.026 156 13 1 5818 5972 738233752 738233597 6.060000e-50 209
32 TraesCS2D01G148000 chr7D 90.506 158 13 1 5817 5972 474700650 474700493 2.180000e-49 207
33 TraesCS2D01G148000 chr5D 90.968 155 13 1 5818 5972 519337992 519338145 2.180000e-49 207


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 TraesCS2D01G148000 chr2D 89258586 89264557 5971 True 11029.000000 11029 100.000000 1 5972 1 chr2D.!!$R1 5971
1 TraesCS2D01G148000 chr2A 88983288 88989290 6002 True 2707.333333 4477 91.543333 1 5548 3 chr2A.!!$R2 5547
2 TraesCS2D01G148000 chr2B 141835745 141842511 6766 True 1463.833333 2396 93.692500 1 5972 6 chr2B.!!$R4 5971
3 TraesCS2D01G148000 chr3D 136721799 136725602 3803 False 852.666667 1613 85.751333 952 4362 3 chr3D.!!$F1 3410
4 TraesCS2D01G148000 chr3B 199526465 199532380 5915 False 728.500000 1589 83.513750 641 5461 4 chr3B.!!$F1 4820
5 TraesCS2D01G148000 chr3A 154658310 154664103 5793 False 634.500000 1539 84.582000 641 5461 6 chr3A.!!$F1 4820

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
870 1283 0.402861 ACTGTTCCTTTCCCCCTCCA 60.403 55.0 0.00 0.00 0.00 3.86 F
1484 1966 0.179065 TCATGGAGCAGAAGATGGCG 60.179 55.0 0.00 0.00 34.54 5.69 F
2349 3036 0.834612 ACGGAGGTTGGACAGTGAAA 59.165 50.0 0.00 0.00 0.00 2.69 F
3129 4634 0.321671 TGACTTGACAGGTAGCTGCC 59.678 55.0 21.58 13.81 0.00 4.85 F
4542 7438 0.317160 CTGACCACCTACGCAAGACA 59.683 55.0 0.00 0.00 43.62 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3311 0.695347 CCTTGACAAGCCTCCCTCTT 59.305 55.000 9.85 0.0 0.00 2.85 R
2708 3433 2.124570 GCCTCACCATCGGCACAT 60.125 61.111 0.00 0.0 45.59 3.21 R
3786 5952 0.036010 CGTCCTGCTTTGGGAGATGT 60.036 55.000 0.00 0.0 33.04 3.06 R
4800 7696 0.252479 CATGCTCAGCAGGGTCTCTT 59.748 55.000 5.13 0.0 43.65 2.85 R
5645 8693 0.872881 CGGCCACGGGTAAATAGTCG 60.873 60.000 2.24 0.0 36.18 4.18 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
54 55 6.782986 TGGTCATTGCCTTATCTATAATGCT 58.217 36.000 10.15 0.00 35.69 3.79
56 57 6.404074 GGTCATTGCCTTATCTATAATGCTGC 60.404 42.308 10.15 0.00 35.69 5.25
57 58 6.149973 GTCATTGCCTTATCTATAATGCTGCA 59.850 38.462 4.13 4.13 35.69 4.41
63 64 6.293407 GCCTTATCTATAATGCTGCACGAAAA 60.293 38.462 3.57 0.00 33.10 2.29
98 99 1.207089 TCAAATCCATCGACCTCGCTT 59.793 47.619 0.00 0.00 39.60 4.68
171 172 1.895131 GTTCTCCGGGTAGGTGTGTTA 59.105 52.381 0.00 0.00 41.99 2.41
175 176 1.619827 TCCGGGTAGGTGTGTTACTTG 59.380 52.381 0.00 0.00 41.99 3.16
180 182 2.289882 GGTAGGTGTGTTACTTGTCCCC 60.290 54.545 0.00 0.00 0.00 4.81
211 213 0.940126 CACATAGCGCCAAGACATCC 59.060 55.000 2.29 0.00 0.00 3.51
219 221 1.066143 CGCCAAGACATCCTACAAGGT 60.066 52.381 0.00 0.00 36.53 3.50
257 259 5.243730 CACCAATTCATCCTTGTGTAAAGGT 59.756 40.000 4.14 0.00 38.55 3.50
312 315 8.465273 AAATAAAACACTAGAAGCAGAAAGGT 57.535 30.769 0.00 0.00 0.00 3.50
323 326 4.039603 AGCAGAAAGGTAAAAGGCTCAT 57.960 40.909 0.00 0.00 0.00 2.90
337 340 3.499338 AGGCTCATGGACAAAAATGACA 58.501 40.909 0.00 0.00 0.00 3.58
340 343 4.501229 GGCTCATGGACAAAAATGACAACA 60.501 41.667 0.00 0.00 0.00 3.33
382 391 9.396022 GATAAATACAGATGAGAGGAAAAACCA 57.604 33.333 0.00 0.00 42.04 3.67
383 392 9.753674 ATAAATACAGATGAGAGGAAAAACCAA 57.246 29.630 0.00 0.00 42.04 3.67
385 394 8.477419 AATACAGATGAGAGGAAAAACCAAAA 57.523 30.769 0.00 0.00 42.04 2.44
426 435 4.521256 ACTAAATGTTGCATACCAAACGGT 59.479 37.500 0.00 0.00 40.86 4.83
436 445 2.047002 ACCAAACGGTACAGCAAAGT 57.953 45.000 0.00 0.00 33.92 2.66
437 446 1.673920 ACCAAACGGTACAGCAAAGTG 59.326 47.619 0.00 0.00 33.92 3.16
442 452 1.599797 GGTACAGCAAAGTGGGCGT 60.600 57.895 0.00 0.00 36.08 5.68
530 930 1.067354 ACGTCGTGACCCTACATTTCC 60.067 52.381 0.00 0.00 0.00 3.13
618 1022 3.131223 TGTTTTGCATTCCGTTGGAGAAA 59.869 39.130 0.00 0.00 31.21 2.52
762 1175 2.388106 CGGTAAAAACCAACGGACAC 57.612 50.000 0.00 0.00 0.00 3.67
770 1183 2.892914 CAACGGACACACACGGCA 60.893 61.111 0.00 0.00 0.00 5.69
790 1203 3.812262 CATCCATCAATCACTGTAGCCA 58.188 45.455 0.00 0.00 0.00 4.75
861 1274 1.972872 CAGTCCAGCACTGTTCCTTT 58.027 50.000 0.00 0.00 46.81 3.11
870 1283 0.402861 ACTGTTCCTTTCCCCCTCCA 60.403 55.000 0.00 0.00 0.00 3.86
886 1299 0.999712 TCCATCTTTCACCCCCTTCC 59.000 55.000 0.00 0.00 0.00 3.46
1020 1436 0.758734 TGGCGATCGATCAATCCCTT 59.241 50.000 24.40 0.00 0.00 3.95
1044 1460 1.680249 GCAAGTTCATCCCCTCCACTC 60.680 57.143 0.00 0.00 0.00 3.51
1076 1532 0.453782 GCGGCTGCGATTTAAACGTT 60.454 50.000 0.00 0.00 0.00 3.99
1117 1573 6.025749 TCTTGATTTCTCAGCGTTCTCTTA 57.974 37.500 0.00 0.00 31.68 2.10
1145 1601 8.330466 TCTTCGATTAATGGAGCTTTTTACAA 57.670 30.769 0.00 0.00 0.00 2.41
1170 1633 0.544357 TCCCGTGACATCTTGAGGGT 60.544 55.000 0.00 0.00 39.78 4.34
1307 1787 7.760340 ACAGATTTTGTTTCTCTACGGACTATC 59.240 37.037 0.00 0.00 36.31 2.08
1420 1902 3.478274 GAGGCCAGCAGGAGGAGG 61.478 72.222 5.01 0.00 36.89 4.30
1421 1903 3.991924 GAGGCCAGCAGGAGGAGGA 62.992 68.421 5.01 0.00 36.89 3.71
1422 1904 3.478274 GGCCAGCAGGAGGAGGAG 61.478 72.222 0.00 0.00 36.89 3.69
1438 1920 3.003763 AGGAGGTTCCCCGTCTGC 61.004 66.667 0.00 0.00 37.19 4.26
1484 1966 0.179065 TCATGGAGCAGAAGATGGCG 60.179 55.000 0.00 0.00 34.54 5.69
1601 2083 1.361668 CGACTCGGATTGTTGGCCAG 61.362 60.000 5.11 0.00 0.00 4.85
1681 2194 6.234177 GCTGCCTCTGATAAACTATAATGGT 58.766 40.000 0.00 0.00 0.00 3.55
1954 2636 8.749354 ACCGTATGCATTCTATGTTATCAGATA 58.251 33.333 3.54 0.00 0.00 1.98
1955 2637 9.025020 CCGTATGCATTCTATGTTATCAGATAC 57.975 37.037 3.54 0.00 0.00 2.24
2349 3036 0.834612 ACGGAGGTTGGACAGTGAAA 59.165 50.000 0.00 0.00 0.00 2.69
2426 3113 7.652507 ACCGCTAAAGTAAGATAATTCAGTAGC 59.347 37.037 0.00 0.00 0.00 3.58
2586 3311 3.449377 GGTTGGTTGGGTTTCAGAAGAAA 59.551 43.478 0.00 0.00 41.26 2.52
2708 3433 5.527033 CAAGAGCGACATAGATGAAGATCA 58.473 41.667 0.00 0.00 0.00 2.92
2784 3509 7.791880 ACACTCTTGTTGTTCAAAGCTTGAAAT 60.792 33.333 0.00 0.00 41.42 2.17
2931 4354 4.096081 GGATTCAGATGACTGGCTCAAAAG 59.904 45.833 0.00 0.00 43.60 2.27
3129 4634 0.321671 TGACTTGACAGGTAGCTGCC 59.678 55.000 21.58 13.81 0.00 4.85
3151 4656 5.050431 GCCGTTAATTGCAAAAAGACATGTT 60.050 36.000 1.71 0.00 0.00 2.71
3462 4974 1.774254 ACAACATGTGGACCCAAGAGA 59.226 47.619 7.39 0.00 0.00 3.10
3593 5106 4.523943 TGGAAACTGCACAATTTAGAGCAT 59.476 37.500 0.00 0.00 34.68 3.79
3638 5151 6.211584 AGTTTCAGGTAGAGCAGTCTCATAAA 59.788 38.462 0.00 0.00 41.81 1.40
3663 5176 4.357918 AGTATATGTGTGGATGCTTCCC 57.642 45.455 15.62 7.94 41.83 3.97
3678 5843 0.531974 TTCCCGAGTGTCACTTGTGC 60.532 55.000 17.37 0.00 0.00 4.57
3786 5952 0.662619 CGTCTGGCTTCTGCAACAAA 59.337 50.000 0.00 0.00 41.91 2.83
3799 5965 2.224018 TGCAACAAACATCTCCCAAAGC 60.224 45.455 0.00 0.00 0.00 3.51
3822 5988 3.566322 AGGACGCTACTATTGTGCTAGAG 59.434 47.826 0.00 0.00 32.20 2.43
3951 6117 5.584649 TGTTGTAGTCTTTCAACTTGTCAGG 59.415 40.000 16.19 0.00 42.71 3.86
4342 7235 2.918571 TGCAACGCAGAGGAAGAAG 58.081 52.632 0.00 0.00 33.32 2.85
4542 7438 0.317160 CTGACCACCTACGCAAGACA 59.683 55.000 0.00 0.00 43.62 3.41
4640 7536 3.068873 GTGGGAGTGATCATGGAGACTAC 59.931 52.174 0.00 0.00 0.00 2.73
4800 7696 1.004560 CAGCCTTTCTGCTCGACCA 60.005 57.895 0.00 0.00 40.32 4.02
5198 8166 5.473066 AGGTAGGTTTTACGCTTCTTGTA 57.527 39.130 0.00 0.00 0.00 2.41
5352 8373 4.273480 CAGTCTGGTTTGAGTAGTTGTTGG 59.727 45.833 0.00 0.00 0.00 3.77
5358 8379 2.254546 TGAGTAGTTGTTGGGTGCAG 57.745 50.000 0.00 0.00 0.00 4.41
5366 8387 1.360192 GTTGGGTGCAGTTCAGTGC 59.640 57.895 0.00 0.00 44.27 4.40
5402 8438 1.303309 CTAGTATTGTGCAGGCAGCC 58.697 55.000 1.84 1.84 44.83 4.85
5409 8445 1.210155 GTGCAGGCAGCCGTTTTAG 59.790 57.895 5.55 0.00 44.83 1.85
5507 8543 0.727398 GGCGTTCCTATGCACTCAAC 59.273 55.000 0.00 0.00 38.06 3.18
5511 8547 3.304391 GCGTTCCTATGCACTCAACAAAA 60.304 43.478 0.00 0.00 36.27 2.44
5534 8570 1.680522 ATAGGCCCTGACTGACTGCG 61.681 60.000 0.00 0.00 0.00 5.18
5741 8789 1.374758 GGACACAAGCCCTCTGACG 60.375 63.158 0.00 0.00 0.00 4.35
5763 8811 3.114606 TGGAGACAGGCCTGATATTTCA 58.885 45.455 39.19 23.04 35.01 2.69
5805 8855 4.648651 TCTCTTTTCCTTTTAAGACCCCG 58.351 43.478 0.00 0.00 0.00 5.73
5807 8857 1.913778 TTTCCTTTTAAGACCCCGCC 58.086 50.000 0.00 0.00 0.00 6.13
5809 8859 0.326927 TCCTTTTAAGACCCCGCCAG 59.673 55.000 0.00 0.00 0.00 4.85
5810 8860 1.313091 CCTTTTAAGACCCCGCCAGC 61.313 60.000 0.00 0.00 0.00 4.85
5811 8861 0.322546 CTTTTAAGACCCCGCCAGCT 60.323 55.000 0.00 0.00 0.00 4.24
5813 8863 0.111639 TTTAAGACCCCGCCAGCTTT 59.888 50.000 0.00 0.00 0.00 3.51
5814 8864 0.985760 TTAAGACCCCGCCAGCTTTA 59.014 50.000 0.00 0.00 0.00 1.85
5839 8889 2.737252 AGCAACTAGTTAACAAGCGCTC 59.263 45.455 12.06 0.00 0.00 5.03
5840 8890 2.159693 GCAACTAGTTAACAAGCGCTCC 60.160 50.000 12.06 0.00 0.00 4.70
5843 8893 3.586892 ACTAGTTAACAAGCGCTCCTTC 58.413 45.455 12.06 0.00 0.00 3.46
5844 8894 2.543777 AGTTAACAAGCGCTCCTTCA 57.456 45.000 12.06 0.00 0.00 3.02
5846 8896 1.464997 GTTAACAAGCGCTCCTTCAGG 59.535 52.381 12.06 0.00 0.00 3.86
5863 8913 2.573009 TCAGGAGCCTCACAATGATCAA 59.427 45.455 0.00 0.00 0.00 2.57
5865 8915 2.306805 AGGAGCCTCACAATGATCAACA 59.693 45.455 0.00 0.00 0.00 3.33
5866 8916 2.421424 GGAGCCTCACAATGATCAACAC 59.579 50.000 0.00 0.00 0.00 3.32
5919 8969 3.764466 CGCTCTGGACGCTCCCTT 61.764 66.667 2.23 0.00 35.03 3.95
5922 8972 3.708220 CTCTGGACGCTCCCTTCGC 62.708 68.421 2.23 0.00 35.03 4.70
5928 8978 0.179189 GACGCTCCCTTCGCATTTTG 60.179 55.000 0.00 0.00 0.00 2.44
5955 9006 0.308068 TTTTTCCGCGCACGATTTCA 59.692 45.000 8.75 0.00 43.93 2.69
5968 9019 5.443170 CGCACGATTTCAGCTTTTTAAATGG 60.443 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.603131 AGGCAATGACCAACATACAATCT 58.397 39.130 0.00 0.00 38.38 2.40
51 52 2.535331 GAAAAAGGTTTTCGTGCAGCA 58.465 42.857 0.00 0.00 0.00 4.41
54 55 1.473278 ACCGAAAAAGGTTTTCGTGCA 59.527 42.857 25.53 0.00 46.85 4.57
56 57 5.972382 TGAATTACCGAAAAAGGTTTTCGTG 59.028 36.000 25.53 20.47 46.85 4.35
57 58 6.134040 TGAATTACCGAAAAAGGTTTTCGT 57.866 33.333 25.53 18.47 46.85 3.85
98 99 7.201702 TGTACCATTACCATTAGTCCAATGA 57.798 36.000 0.00 0.00 45.99 2.57
135 136 4.464008 GGAGAACTAATGGGCAATCATCA 58.536 43.478 0.00 0.00 0.00 3.07
171 172 2.185310 GATGCACTCGGGGGACAAGT 62.185 60.000 0.00 0.00 0.00 3.16
175 176 2.125106 GTGATGCACTCGGGGGAC 60.125 66.667 0.00 0.00 0.00 4.46
211 213 0.732880 CGTCACCTGCGACCTTGTAG 60.733 60.000 0.00 0.00 31.91 2.74
237 239 7.121315 GCTAGAACCTTTACACAAGGATGAATT 59.879 37.037 7.64 0.00 39.81 2.17
257 259 0.536724 TGCTGGCAGATTCGCTAGAA 59.463 50.000 20.86 4.82 42.69 2.10
312 315 6.041409 TGTCATTTTTGTCCATGAGCCTTTTA 59.959 34.615 0.00 0.00 29.85 1.52
323 326 5.413309 AAGGTTGTTGTCATTTTTGTCCA 57.587 34.783 0.00 0.00 0.00 4.02
356 365 9.396022 TGGTTTTTCCTCTCATCTGTATTTATC 57.604 33.333 0.00 0.00 37.07 1.75
357 366 9.753674 TTGGTTTTTCCTCTCATCTGTATTTAT 57.246 29.630 0.00 0.00 37.07 1.40
358 367 9.581289 TTTGGTTTTTCCTCTCATCTGTATTTA 57.419 29.630 0.00 0.00 37.07 1.40
359 368 8.477419 TTTGGTTTTTCCTCTCATCTGTATTT 57.523 30.769 0.00 0.00 37.07 1.40
426 435 0.602638 CAGACGCCCACTTTGCTGTA 60.603 55.000 0.00 0.00 0.00 2.74
436 445 5.128827 AGAATTTACTAGAATCAGACGCCCA 59.871 40.000 0.00 0.00 0.00 5.36
437 446 5.463724 CAGAATTTACTAGAATCAGACGCCC 59.536 44.000 0.00 0.00 0.00 6.13
442 452 8.630037 TCATACGCAGAATTTACTAGAATCAGA 58.370 33.333 0.00 0.00 0.00 3.27
484 494 8.335256 ACACGAACATATTTTGAGTTTTTGAC 57.665 30.769 0.00 0.00 0.00 3.18
490 500 6.399249 CGACGTACACGAACATATTTTGAGTT 60.399 38.462 9.04 0.00 43.02 3.01
492 502 5.060077 ACGACGTACACGAACATATTTTGAG 59.940 40.000 9.04 0.00 43.02 3.02
568 972 2.210116 GAAAAAGCTCACCACTCGTCA 58.790 47.619 0.00 0.00 0.00 4.35
618 1022 5.296035 GGATTAACGGAATGAACCTCGAAAT 59.704 40.000 0.00 0.00 0.00 2.17
679 1088 8.151596 ACCGTATTTACCATTTTCCATGTTTTT 58.848 29.630 0.00 0.00 0.00 1.94
680 1089 7.672240 ACCGTATTTACCATTTTCCATGTTTT 58.328 30.769 0.00 0.00 0.00 2.43
762 1175 1.064505 GTGATTGATGGATGCCGTGTG 59.935 52.381 0.00 0.00 0.00 3.82
770 1183 4.508551 TTGGCTACAGTGATTGATGGAT 57.491 40.909 0.00 0.00 0.00 3.41
790 1203 2.851195 AGCAGAAACAGATGACCGTTT 58.149 42.857 0.00 0.00 38.02 3.60
861 1274 0.919289 GGGTGAAAGATGGAGGGGGA 60.919 60.000 0.00 0.00 0.00 4.81
870 1283 1.221909 GGGGGAAGGGGGTGAAAGAT 61.222 60.000 0.00 0.00 0.00 2.40
886 1299 3.093172 GGCAGAGAGGGAAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
892 1305 1.979155 CACAGACGGCAGAGAGGGA 60.979 63.158 0.00 0.00 0.00 4.20
1020 1436 1.564348 GGAGGGGATGAACTTGCCTTA 59.436 52.381 0.00 0.00 0.00 2.69
1044 1460 1.517257 AGCCGCACGAATCGAAGAG 60.517 57.895 10.55 3.11 43.63 2.85
1117 1573 9.788960 GTAAAAAGCTCCATTAATCGAAGATTT 57.211 29.630 0.34 0.00 45.12 2.17
1145 1601 2.019249 CAAGATGTCACGGGATTGCAT 58.981 47.619 0.00 0.00 0.00 3.96
1170 1633 6.488683 AGGATGACGAAATAAACACAAAGGAA 59.511 34.615 0.00 0.00 0.00 3.36
1302 1782 3.511477 ACCAATCCCATCTAGCGATAGT 58.489 45.455 7.70 0.00 39.35 2.12
1307 1787 2.744202 GCATTACCAATCCCATCTAGCG 59.256 50.000 0.00 0.00 0.00 4.26
1438 1920 0.392193 ATCTCGCTGGCTCTTGTTGG 60.392 55.000 0.00 0.00 0.00 3.77
1484 1966 1.509923 GAGCCTTTGATGCACCAGC 59.490 57.895 0.00 0.00 42.57 4.85
1908 2588 3.366679 GGTCATGAGAATTGGTTGCACTG 60.367 47.826 0.00 0.00 0.00 3.66
2197 2881 2.751259 AGAGCCACAAATGCACATGTAG 59.249 45.455 0.00 0.92 0.00 2.74
2349 3036 5.910614 AGAAACATCAAGCAGCTTTTCTTT 58.089 33.333 4.38 0.91 0.00 2.52
2426 3113 1.469703 TGCGCAATGACAAGAATGGAG 59.530 47.619 8.16 0.00 0.00 3.86
2586 3311 0.695347 CCTTGACAAGCCTCCCTCTT 59.305 55.000 9.85 0.00 0.00 2.85
2708 3433 2.124570 GCCTCACCATCGGCACAT 60.125 61.111 0.00 0.00 45.59 3.21
2749 3474 7.624360 TGAACAACAAGAGTGTCTTAAATGT 57.376 32.000 0.00 0.00 36.80 2.71
2931 4354 5.418840 TCCAGAAATTCAGCCCATTAAGAAC 59.581 40.000 0.00 0.00 0.00 3.01
3129 4634 7.159437 TGAACATGTCTTTTTGCAATTAACG 57.841 32.000 0.00 0.00 0.00 3.18
3151 4656 7.696992 ACAAGAAAAGTTTGAAGTACCTTGA 57.303 32.000 0.00 0.00 34.37 3.02
3462 4974 6.408434 GCATTTCCTCCCATTCAATATTTGGT 60.408 38.462 4.37 0.00 0.00 3.67
3638 5151 6.525629 GGAAGCATCCACACATATACTAAGT 58.474 40.000 2.32 0.00 45.79 2.24
3656 5169 0.249868 CAAGTGACACTCGGGAAGCA 60.250 55.000 8.93 0.00 0.00 3.91
3663 5176 1.070376 CATGTGCACAAGTGACACTCG 60.070 52.381 25.72 0.00 37.97 4.18
3678 5843 6.127111 TGTTTTCATTAATCCCATCCCATGTG 60.127 38.462 0.00 0.00 0.00 3.21
3786 5952 0.036010 CGTCCTGCTTTGGGAGATGT 60.036 55.000 0.00 0.00 33.04 3.06
3799 5965 2.586258 AGCACAATAGTAGCGTCCTG 57.414 50.000 0.00 0.00 0.00 3.86
3822 5988 5.759059 TCATAATTATGCCCATCCTCATCC 58.241 41.667 18.89 0.00 33.76 3.51
3951 6117 4.044426 CACTTGCCTTAAACTTTGCTGAC 58.956 43.478 0.00 0.00 0.00 3.51
4083 6251 0.546122 TGGATAAGTGCGGGCAGAAT 59.454 50.000 0.00 0.00 0.00 2.40
4129 6299 8.217111 TCAATATATACACCTGAATGGAAAGCA 58.783 33.333 0.00 0.00 39.71 3.91
4145 6315 8.480853 GTGAAGTTGTTCGCTCTCAATATATAC 58.519 37.037 0.00 0.00 39.68 1.47
4289 7180 7.554118 ACATGATTCAGAAGATTCAACGGTTAT 59.446 33.333 0.00 0.00 37.59 1.89
4342 7235 5.870978 CCTTTGATTTGACATCATTGGAACC 59.129 40.000 0.00 0.00 0.00 3.62
4542 7438 1.469940 GCACAGCACAGCTCGTAGTAT 60.470 52.381 0.00 0.00 36.40 2.12
4640 7536 0.600255 GATACCCTCCGCGATGTTGG 60.600 60.000 8.23 2.81 0.00 3.77
4800 7696 0.252479 CATGCTCAGCAGGGTCTCTT 59.748 55.000 5.13 0.00 43.65 2.85
5006 7932 1.131826 GTCGCCCAAAACATCGTCG 59.868 57.895 0.00 0.00 0.00 5.12
5352 8373 1.714899 AACACGCACTGAACTGCACC 61.715 55.000 0.00 0.00 36.94 5.01
5358 8379 1.941812 CAGGGAACACGCACTGAAC 59.058 57.895 0.00 0.00 32.86 3.18
5366 8387 1.225376 TAGCAAACGCAGGGAACACG 61.225 55.000 0.00 0.00 38.05 4.49
5402 8438 7.163682 CGACCAAGAAAGAAAAGAACTAAAACG 59.836 37.037 0.00 0.00 0.00 3.60
5409 8445 4.282873 CAGCGACCAAGAAAGAAAAGAAC 58.717 43.478 0.00 0.00 0.00 3.01
5511 8547 3.690460 CAGTCAGTCAGGGCCTATTTTT 58.310 45.455 5.28 0.00 0.00 1.94
5516 8552 2.351244 CGCAGTCAGTCAGGGCCTA 61.351 63.158 5.28 0.00 0.00 3.93
5518 8554 3.537206 AACGCAGTCAGTCAGGGCC 62.537 63.158 0.00 0.00 45.00 5.80
5645 8693 0.872881 CGGCCACGGGTAAATAGTCG 60.873 60.000 2.24 0.00 36.18 4.18
5723 8771 1.374758 CGTCAGAGGGCTTGTGTCC 60.375 63.158 0.00 0.00 38.50 4.02
5741 8789 3.118261 TGAAATATCAGGCCTGTCTCCAC 60.118 47.826 31.58 19.40 0.00 4.02
5763 8811 2.438800 AGTCTAGCAGTACCCGACAT 57.561 50.000 0.00 0.00 0.00 3.06
5805 8855 4.698575 ACTAGTTGCTCTATAAAGCTGGC 58.301 43.478 0.00 0.00 42.94 4.85
5807 8857 8.703604 TGTTAACTAGTTGCTCTATAAAGCTG 57.296 34.615 18.56 0.00 42.94 4.24
5809 8859 8.117370 GCTTGTTAACTAGTTGCTCTATAAAGC 58.883 37.037 18.56 15.36 42.82 3.51
5810 8860 8.321716 CGCTTGTTAACTAGTTGCTCTATAAAG 58.678 37.037 18.56 10.54 0.00 1.85
5811 8861 7.201496 GCGCTTGTTAACTAGTTGCTCTATAAA 60.201 37.037 18.56 0.00 0.00 1.40
5813 8863 5.747197 GCGCTTGTTAACTAGTTGCTCTATA 59.253 40.000 18.56 0.00 0.00 1.31
5814 8864 4.567159 GCGCTTGTTAACTAGTTGCTCTAT 59.433 41.667 18.56 0.00 0.00 1.98
5839 8889 1.280133 TCATTGTGAGGCTCCTGAAGG 59.720 52.381 12.86 3.95 0.00 3.46
5840 8890 2.775911 TCATTGTGAGGCTCCTGAAG 57.224 50.000 12.86 0.00 0.00 3.02
5843 8893 2.681848 GTTGATCATTGTGAGGCTCCTG 59.318 50.000 12.86 4.70 0.00 3.86
5844 8894 2.306805 TGTTGATCATTGTGAGGCTCCT 59.693 45.455 12.86 0.00 0.00 3.69
5846 8896 2.421424 GGTGTTGATCATTGTGAGGCTC 59.579 50.000 7.79 7.79 0.00 4.70
5854 8904 2.669113 CGCCAAGTGGTGTTGATCATTG 60.669 50.000 0.00 0.00 40.69 2.82
5907 8957 2.463589 AAATGCGAAGGGAGCGTCCA 62.464 55.000 6.41 0.00 38.64 4.02
5943 8994 1.408422 AAAAAGCTGAAATCGTGCGC 58.592 45.000 0.00 0.00 0.00 6.09
5944 8995 5.443170 CCATTTAAAAAGCTGAAATCGTGCG 60.443 40.000 0.00 0.00 0.00 5.34
5946 8997 7.406799 AACCATTTAAAAAGCTGAAATCGTG 57.593 32.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.