Multiple sequence alignment - TraesCS1A01G043300

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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 TraesCS1A01G043300 chr1A 100.000 2816 0 0 1 2816 24076253 24079068 0.000000e+00 5201
1 TraesCS1A01G043300 chr1A 87.006 177 15 5 2309 2480 23965651 23965824 2.860000e-45 193
2 TraesCS1A01G043300 chr1A 91.241 137 10 2 2561 2696 24078661 24078796 4.790000e-43 185
3 TraesCS1A01G043300 chr1A 91.241 137 10 2 2409 2544 24078813 24078948 4.790000e-43 185
4 TraesCS1A01G043300 chr1A 95.370 108 4 1 2317 2423 23970250 23970357 1.340000e-38 171
5 TraesCS1A01G043300 chr1A 85.057 174 19 6 2325 2498 24311651 24311817 1.340000e-38 171
6 TraesCS1A01G043300 chr1B 82.004 2495 196 125 80 2469 39310112 39312458 0.000000e+00 1886
7 TraesCS1A01G043300 chr1B 89.922 258 26 0 2557 2814 38920533 38920276 1.620000e-87 333
8 TraesCS1A01G043300 chr1B 86.486 259 25 7 2296 2551 38915113 38914862 2.760000e-70 276
9 TraesCS1A01G043300 chr1B 87.391 230 17 3 2390 2617 38920768 38920549 1.290000e-63 254
10 TraesCS1A01G043300 chr1B 93.421 152 9 1 2552 2702 38920760 38920609 1.020000e-54 224
11 TraesCS1A01G043300 chr1B 84.762 210 11 9 2609 2816 39391312 39391502 1.030000e-44 191
12 TraesCS1A01G043300 chr1B 83.824 204 26 6 2296 2498 38911902 38911705 1.330000e-43 187
13 TraesCS1A01G043300 chr1B 86.667 165 12 6 2390 2550 39312535 39312693 1.040000e-39 174
14 TraesCS1A01G043300 chr1D 88.429 1426 78 45 718 2098 22902773 22904156 0.000000e+00 1639
15 TraesCS1A01G043300 chr1D 86.135 577 39 23 75 635 22902151 22902702 4.040000e-163 584
16 TraesCS1A01G043300 chr1D 90.930 430 36 3 2389 2816 22904545 22904973 2.430000e-160 575
17 TraesCS1A01G043300 chr1D 87.059 340 22 11 2139 2470 22904155 22904480 5.730000e-97 364
18 TraesCS1A01G043300 chr1D 86.058 208 24 4 2293 2498 22883017 22883221 4.720000e-53 219
19 TraesCS1A01G043300 chr1D 90.625 128 10 2 2295 2422 22977764 22977889 4.820000e-38 169


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 TraesCS1A01G043300 chr1A 24076253 24079068 2815 False 1857.0 5201 94.160667 1 2816 3 chr1A.!!$F4 2815
1 TraesCS1A01G043300 chr1B 39310112 39312693 2581 False 1030.0 1886 84.335500 80 2550 2 chr1B.!!$F2 2470
2 TraesCS1A01G043300 chr1B 38911705 38915113 3408 True 231.5 276 85.155000 2296 2551 2 chr1B.!!$R1 255
3 TraesCS1A01G043300 chr1D 22902151 22904973 2822 False 790.5 1639 88.138250 75 2816 4 chr1D.!!$F3 2741

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
898 1004 0.038166 GAGTCCCATGGAAGCAACCA 59.962 55.0 15.22 4.45 44.41 3.67 F
1100 1233 0.178903 TACCTTGTCCTCCTGTGGCT 60.179 55.0 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1973 0.110056 GCAAATGTCACCTGCAGTCG 60.110 55.0 13.81 2.86 36.09 4.18 R
1909 2075 0.861837 CACACTTGACGACCAGAAGC 59.138 55.0 0.00 0.00 0.00 3.86 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
52 53 9.828852 GACAAGTCTCTACATATATAAGAACCG 57.171 37.037 0.00 0.00 0.00 4.44
53 54 9.570468 ACAAGTCTCTACATATATAAGAACCGA 57.430 33.333 0.00 0.00 0.00 4.69
56 57 9.179909 AGTCTCTACATATATAAGAACCGATGG 57.820 37.037 0.00 0.00 0.00 3.51
57 58 7.916450 GTCTCTACATATATAAGAACCGATGGC 59.084 40.741 0.00 0.00 0.00 4.40
58 59 6.792326 TCTACATATATAAGAACCGATGGCG 58.208 40.000 0.00 0.00 37.24 5.69
59 60 5.654603 ACATATATAAGAACCGATGGCGA 57.345 39.130 0.00 0.00 40.82 5.54
60 61 5.408356 ACATATATAAGAACCGATGGCGAC 58.592 41.667 0.00 0.00 40.82 5.19
61 62 2.410785 TATAAGAACCGATGGCGACG 57.589 50.000 0.00 0.00 40.82 5.12
68 69 4.147322 CGATGGCGACGGCAACAC 62.147 66.667 28.50 19.55 42.43 3.32
69 70 3.799755 GATGGCGACGGCAACACC 61.800 66.667 28.50 13.49 42.43 4.16
78 79 3.964875 GGCAACACCGTGTGCCAG 61.965 66.667 26.83 12.26 41.20 4.85
111 112 3.247648 GCATCGACCCATGTAACATGTAC 59.752 47.826 0.00 0.00 0.00 2.90
112 113 4.438148 CATCGACCCATGTAACATGTACA 58.562 43.478 0.00 0.00 0.00 2.90
113 114 4.746535 TCGACCCATGTAACATGTACAT 57.253 40.909 1.41 1.41 38.57 2.29
141 142 1.904865 ACCACATGTTGCCAGCCTG 60.905 57.895 0.00 0.00 0.00 4.85
158 159 2.704572 CCTGAACTCATTGACCTCCAC 58.295 52.381 0.00 0.00 0.00 4.02
172 173 6.817765 TGACCTCCACTAATCAAATCAAAC 57.182 37.500 0.00 0.00 0.00 2.93
189 215 8.828644 CAAATCAAACCAAAGATCAATCACAAA 58.171 29.630 0.00 0.00 0.00 2.83
190 216 8.597662 AATCAAACCAAAGATCAATCACAAAG 57.402 30.769 0.00 0.00 0.00 2.77
191 217 5.984926 TCAAACCAAAGATCAATCACAAAGC 59.015 36.000 0.00 0.00 0.00 3.51
192 218 4.164822 ACCAAAGATCAATCACAAAGCG 57.835 40.909 0.00 0.00 0.00 4.68
193 219 2.919229 CCAAAGATCAATCACAAAGCGC 59.081 45.455 0.00 0.00 0.00 5.92
194 220 2.532531 AAGATCAATCACAAAGCGCG 57.467 45.000 0.00 0.00 0.00 6.86
196 222 2.076100 AGATCAATCACAAAGCGCGAA 58.924 42.857 12.10 0.00 0.00 4.70
197 223 2.094894 AGATCAATCACAAAGCGCGAAG 59.905 45.455 12.10 0.00 0.00 3.79
232 259 3.409026 AGTTCTGACTTGTCATCACCC 57.591 47.619 3.79 0.00 29.87 4.61
244 271 3.625632 ATCACCCCCGCTCTGACCT 62.626 63.158 0.00 0.00 0.00 3.85
250 277 1.604378 CCCGCTCTGACCTTTCCAT 59.396 57.895 0.00 0.00 0.00 3.41
264 291 3.181510 CCTTTCCATTTTCGATGTCGTCC 60.182 47.826 2.04 0.00 40.80 4.79
280 307 2.428403 CCCGCAAAAGAAACCGCG 60.428 61.111 0.00 0.00 46.96 6.46
294 321 6.115450 AGAAACCGCGGATTAATTAAGAAC 57.885 37.500 35.90 10.91 0.00 3.01
314 341 1.336877 GAAAGCCGCGAAAATTGGTC 58.663 50.000 8.23 0.00 0.00 4.02
324 351 1.874872 GAAAATTGGTCCGTTCGGTCA 59.125 47.619 11.04 8.22 0.00 4.02
378 430 0.187117 TGAACATGGCACCTCCCAAA 59.813 50.000 0.00 0.00 38.61 3.28
379 431 1.203162 TGAACATGGCACCTCCCAAAT 60.203 47.619 0.00 0.00 38.61 2.32
380 432 1.478105 GAACATGGCACCTCCCAAATC 59.522 52.381 0.00 0.00 38.61 2.17
381 433 0.706433 ACATGGCACCTCCCAAATCT 59.294 50.000 0.00 0.00 38.61 2.40
474 547 1.139058 ACAGCACGTTCCTTCAAGAGT 59.861 47.619 0.00 0.00 0.00 3.24
513 586 5.239306 TGAATCTCACCTTTTTGTACTGCTG 59.761 40.000 0.00 0.00 0.00 4.41
514 587 4.415881 TCTCACCTTTTTGTACTGCTGA 57.584 40.909 0.00 0.00 0.00 4.26
515 588 4.380531 TCTCACCTTTTTGTACTGCTGAG 58.619 43.478 0.00 0.00 0.00 3.35
516 589 4.130118 CTCACCTTTTTGTACTGCTGAGT 58.870 43.478 0.00 0.00 36.07 3.41
519 592 2.880890 CCTTTTTGTACTGCTGAGTGCT 59.119 45.455 0.00 0.00 43.37 4.40
523 596 2.662006 TGTACTGCTGAGTGCTGATC 57.338 50.000 0.00 0.00 42.27 2.92
526 604 3.379688 TGTACTGCTGAGTGCTGATCTAG 59.620 47.826 0.00 0.00 42.27 2.43
593 671 3.378602 TCTCGTGCCTGCCGCTAA 61.379 61.111 0.00 0.00 38.78 3.09
596 674 3.799755 CGTGCCTGCCGCTAAACC 61.800 66.667 0.00 0.00 38.78 3.27
635 713 0.984230 CCAACAACCTGGAGGCTAGA 59.016 55.000 0.00 0.00 38.96 2.43
662 743 4.382577 CCCCCAGAAAATCAAAATAACCCG 60.383 45.833 0.00 0.00 0.00 5.28
667 748 5.519927 CAGAAAATCAAAATAACCCGCCATC 59.480 40.000 0.00 0.00 0.00 3.51
676 757 1.324740 AACCCGCCATCTACGTAGCA 61.325 55.000 18.00 7.40 0.00 3.49
692 773 2.764314 GCACATACGCAAGCCCCAG 61.764 63.158 0.00 0.00 45.62 4.45
709 790 6.189133 AGCCCCAGTTTTTAACCGAATAATA 58.811 36.000 0.00 0.00 0.00 0.98
774 871 1.410517 GTGTGCATCCAGCTAGCTAGA 59.589 52.381 25.15 16.98 45.94 2.43
775 872 1.685517 TGTGCATCCAGCTAGCTAGAG 59.314 52.381 25.15 14.89 45.94 2.43
776 873 1.000731 GTGCATCCAGCTAGCTAGAGG 59.999 57.143 25.15 22.61 45.94 3.69
777 874 1.337118 GCATCCAGCTAGCTAGAGGT 58.663 55.000 25.15 3.27 41.15 3.85
778 875 2.158460 TGCATCCAGCTAGCTAGAGGTA 60.158 50.000 25.15 17.20 45.94 3.08
780 877 3.812524 GCATCCAGCTAGCTAGAGGTAGA 60.813 52.174 25.15 12.45 46.05 2.59
782 879 2.159382 CCAGCTAGCTAGAGGTAGAGC 58.841 57.143 25.15 8.92 46.05 4.09
855 961 2.978010 CCGGCCCATTCCATACGC 60.978 66.667 0.00 0.00 0.00 4.42
861 967 0.317160 CCCATTCCATACGCTCGCTA 59.683 55.000 0.00 0.00 0.00 4.26
898 1004 0.038166 GAGTCCCATGGAAGCAACCA 59.962 55.000 15.22 4.45 44.41 3.67
900 1006 0.251341 GTCCCATGGAAGCAACCACT 60.251 55.000 15.22 0.00 43.03 4.00
980 1094 0.681733 CTCCACCATACGCCATAGCT 59.318 55.000 0.00 0.00 36.60 3.32
998 1112 0.744771 CTAACCCCGCAAGCTTCCTC 60.745 60.000 0.00 0.00 0.00 3.71
999 1113 2.515996 TAACCCCGCAAGCTTCCTCG 62.516 60.000 0.00 0.21 0.00 4.63
1000 1114 4.082523 CCCCGCAAGCTTCCTCGA 62.083 66.667 12.26 0.00 0.00 4.04
1001 1115 2.815647 CCCGCAAGCTTCCTCGAC 60.816 66.667 12.26 0.00 0.00 4.20
1093 1226 2.162264 AGCTACCTACCTTGTCCTCC 57.838 55.000 0.00 0.00 0.00 4.30
1094 1227 1.646977 AGCTACCTACCTTGTCCTCCT 59.353 52.381 0.00 0.00 0.00 3.69
1095 1228 1.757699 GCTACCTACCTTGTCCTCCTG 59.242 57.143 0.00 0.00 0.00 3.86
1097 1230 1.645710 ACCTACCTTGTCCTCCTGTG 58.354 55.000 0.00 0.00 0.00 3.66
1098 1231 0.905357 CCTACCTTGTCCTCCTGTGG 59.095 60.000 0.00 0.00 0.00 4.17
1099 1232 0.250513 CTACCTTGTCCTCCTGTGGC 59.749 60.000 0.00 0.00 0.00 5.01
1100 1233 0.178903 TACCTTGTCCTCCTGTGGCT 60.179 55.000 0.00 0.00 0.00 4.75
1101 1234 1.298014 CCTTGTCCTCCTGTGGCTC 59.702 63.158 0.00 0.00 0.00 4.70
1102 1235 1.079543 CTTGTCCTCCTGTGGCTCG 60.080 63.158 0.00 0.00 0.00 5.03
1103 1236 3.240134 TTGTCCTCCTGTGGCTCGC 62.240 63.158 0.00 0.00 0.00 5.03
1308 1447 2.795231 TTCCCAGGAAGATGCTTCTG 57.205 50.000 2.39 4.16 30.72 3.02
1383 1522 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
1386 1525 2.906897 CACCACCACCACCAGCAC 60.907 66.667 0.00 0.00 0.00 4.40
1403 1542 0.659427 CACCACCATCATCATCGTGC 59.341 55.000 0.00 0.00 0.00 5.34
1525 1664 2.508663 GGTACGGCGTGGAGAAGC 60.509 66.667 24.86 8.12 0.00 3.86
1566 1705 1.746615 CCCGTTGCATCACTGAGGG 60.747 63.158 0.00 0.00 0.00 4.30
1639 1797 4.289312 GCAAAAGCATGCAAGGGG 57.711 55.556 21.98 6.25 45.70 4.79
1732 1891 4.142359 TGAGTATGCGTCTCTTCCTCTTTC 60.142 45.833 6.85 0.00 33.59 2.62
1733 1892 3.764434 AGTATGCGTCTCTTCCTCTTTCA 59.236 43.478 0.00 0.00 0.00 2.69
1735 1894 1.686587 TGCGTCTCTTCCTCTTTCACA 59.313 47.619 0.00 0.00 0.00 3.58
1739 1898 4.377841 GCGTCTCTTCCTCTTTCACATTTG 60.378 45.833 0.00 0.00 0.00 2.32
1743 1902 6.931840 GTCTCTTCCTCTTTCACATTTGTAGT 59.068 38.462 0.00 0.00 0.00 2.73
1771 1935 7.120285 TGTCCATTCTTTGATTTTCTCTGCTAG 59.880 37.037 0.00 0.00 0.00 3.42
1772 1936 6.094603 TCCATTCTTTGATTTTCTCTGCTAGC 59.905 38.462 8.10 8.10 0.00 3.42
1773 1937 6.095160 CCATTCTTTGATTTTCTCTGCTAGCT 59.905 38.462 17.23 0.00 0.00 3.32
1774 1938 6.492007 TTCTTTGATTTTCTCTGCTAGCTG 57.508 37.500 17.23 16.05 0.00 4.24
1803 1967 8.920174 TGATCAAAATCTTGGCATGAATAAGAT 58.080 29.630 7.20 5.35 41.53 2.40
1808 1972 8.985315 AAATCTTGGCATGAATAAGATGAGTA 57.015 30.769 15.66 0.00 40.12 2.59
1809 1973 7.976135 ATCTTGGCATGAATAAGATGAGTAC 57.024 36.000 14.73 0.00 39.12 2.73
1810 1974 5.985530 TCTTGGCATGAATAAGATGAGTACG 59.014 40.000 0.00 0.00 0.00 3.67
1811 1975 5.529581 TGGCATGAATAAGATGAGTACGA 57.470 39.130 0.00 0.00 0.00 3.43
1878 2042 8.201554 TGCAGTGATCTGTAATTATTTCACTC 57.798 34.615 14.49 11.64 41.22 3.51
1899 2065 4.326826 TCTGTGCTTTACTGATTGGGAAG 58.673 43.478 0.00 0.00 33.00 3.46
1909 2075 2.810274 CTGATTGGGAAGCCGATGTATG 59.190 50.000 0.00 0.00 0.00 2.39
1910 2076 1.537202 GATTGGGAAGCCGATGTATGC 59.463 52.381 0.00 0.00 0.00 3.14
1911 2077 0.546122 TTGGGAAGCCGATGTATGCT 59.454 50.000 0.00 0.00 40.17 3.79
1921 2089 2.120232 CGATGTATGCTTCTGGTCGTC 58.880 52.381 0.00 0.00 0.00 4.20
1928 2096 0.861837 GCTTCTGGTCGTCAAGTGTG 59.138 55.000 0.00 0.00 0.00 3.82
1937 2105 2.013400 TCGTCAAGTGTGTTGCATTGT 58.987 42.857 0.00 0.00 0.00 2.71
2030 2211 3.958018 TGGGCCTTATAAACACGAACAT 58.042 40.909 4.53 0.00 0.00 2.71
2031 2212 5.100344 TGGGCCTTATAAACACGAACATA 57.900 39.130 4.53 0.00 0.00 2.29
2048 2229 5.238650 CGAACATAAAGGAGTGAACCTGTTT 59.761 40.000 0.00 0.00 40.49 2.83
2105 2286 1.140312 TAACATCCAGGCCAGGATCC 58.860 55.000 26.05 2.48 45.16 3.36
2127 2308 3.448340 CCCCGTTTCCGCCCAATG 61.448 66.667 0.00 0.00 0.00 2.82
2130 2314 3.369400 CGTTTCCGCCCAATGCCA 61.369 61.111 0.00 0.00 36.24 4.92
2207 2398 6.790232 ATTTGTATACCCCCAAAATGACTG 57.210 37.500 0.00 0.00 34.52 3.51
2250 2443 8.923838 ACCATGACCAAATATATCTCCTAGAT 57.076 34.615 0.00 0.00 38.70 1.98
2279 2472 4.184629 GACCGAGTAGCAAAACATCTCAT 58.815 43.478 0.00 0.00 0.00 2.90
2294 2487 9.685276 AAAACATCTCATGTAGTTTGGATATCA 57.315 29.630 4.83 0.00 44.07 2.15
2466 2812 8.175716 GCTGCGTTTTATTCTGAATATATACCC 58.824 37.037 10.68 3.82 0.00 3.69
2511 2857 9.830975 AGCTAAATAAAAATGGTTTGAACTTGT 57.169 25.926 0.00 0.00 0.00 3.16
2523 2869 6.183360 TGGTTTGAACTTGTTACTTGTACGAC 60.183 38.462 0.00 0.00 0.00 4.34
2532 2878 8.382875 ACTTGTTACTTGTACGACAAAACTTAC 58.617 33.333 0.00 0.00 37.69 2.34
2545 2891 7.698970 ACGACAAAACTTACATGGTTTAAACTG 59.301 33.333 17.50 11.45 36.09 3.16
2553 2899 9.192642 ACTTACATGGTTTAAACTGGTTAAAGT 57.807 29.630 17.50 15.45 41.33 2.66
2555 2901 6.277605 ACATGGTTTAAACTGGTTAAAGTGC 58.722 36.000 17.50 0.43 41.33 4.40
2558 2904 4.743151 GGTTTAAACTGGTTAAAGTGCAGC 59.257 41.667 17.50 0.00 41.33 5.25
2589 2935 5.890334 TCCTTTTTGTAAACTTCTGCAGTG 58.110 37.500 14.67 10.57 35.12 3.66
2592 2938 5.637006 TTTTGTAAACTTCTGCAGTGTGT 57.363 34.783 14.67 11.52 35.12 3.72
2606 2952 3.421888 GCAGTGTGTTGCGTTTTATTCTG 59.578 43.478 0.00 0.00 33.90 3.02
2729 3099 8.149973 TGTACGAGAAAACTTAGCTGATTTTT 57.850 30.769 6.31 6.31 0.00 1.94
2810 3180 8.939929 TCTCGTTCATATAGTTATAACGTAGGG 58.060 37.037 9.91 2.28 42.49 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.828852 CGGTTCTTATATATGTAGAGACTTGTC 57.171 37.037 0.00 0.00 0.00 3.18
27 28 9.570468 TCGGTTCTTATATATGTAGAGACTTGT 57.430 33.333 0.00 0.00 0.00 3.16
30 31 9.179909 CCATCGGTTCTTATATATGTAGAGACT 57.820 37.037 0.00 0.00 0.00 3.24
31 32 7.916450 GCCATCGGTTCTTATATATGTAGAGAC 59.084 40.741 0.00 1.20 0.00 3.36
32 33 7.201705 CGCCATCGGTTCTTATATATGTAGAGA 60.202 40.741 0.00 0.00 0.00 3.10
33 34 6.913132 CGCCATCGGTTCTTATATATGTAGAG 59.087 42.308 0.00 0.00 0.00 2.43
34 35 6.600427 TCGCCATCGGTTCTTATATATGTAGA 59.400 38.462 0.00 0.00 36.13 2.59
35 36 6.691818 GTCGCCATCGGTTCTTATATATGTAG 59.308 42.308 0.00 0.00 36.13 2.74
36 37 6.558009 GTCGCCATCGGTTCTTATATATGTA 58.442 40.000 0.00 0.00 36.13 2.29
37 38 5.408356 GTCGCCATCGGTTCTTATATATGT 58.592 41.667 0.00 0.00 36.13 2.29
38 39 4.499399 CGTCGCCATCGGTTCTTATATATG 59.501 45.833 0.00 0.00 36.13 1.78
39 40 4.439700 CCGTCGCCATCGGTTCTTATATAT 60.440 45.833 0.00 0.00 42.62 0.86
40 41 3.119743 CCGTCGCCATCGGTTCTTATATA 60.120 47.826 0.00 0.00 42.62 0.86
41 42 2.352421 CCGTCGCCATCGGTTCTTATAT 60.352 50.000 0.00 0.00 42.62 0.86
42 43 1.001048 CCGTCGCCATCGGTTCTTATA 60.001 52.381 0.00 0.00 42.62 0.98
43 44 0.249322 CCGTCGCCATCGGTTCTTAT 60.249 55.000 0.00 0.00 42.62 1.73
44 45 1.140161 CCGTCGCCATCGGTTCTTA 59.860 57.895 0.00 0.00 42.62 2.10
45 46 2.125673 CCGTCGCCATCGGTTCTT 60.126 61.111 0.00 0.00 42.62 2.52
51 52 4.147322 GTGTTGCCGTCGCCATCG 62.147 66.667 0.00 0.00 0.00 3.84
52 53 3.799755 GGTGTTGCCGTCGCCATC 61.800 66.667 0.00 0.00 35.75 3.51
61 62 3.964875 CTGGCACACGGTGTTGCC 61.965 66.667 30.69 30.69 41.59 4.52
62 63 4.629115 GCTGGCACACGGTGTTGC 62.629 66.667 11.82 17.19 35.75 4.17
63 64 4.312231 CGCTGGCACACGGTGTTG 62.312 66.667 11.82 8.53 35.75 3.33
112 113 3.000041 CAACATGTGGTGTACGCTACAT 59.000 45.455 26.97 26.97 41.14 2.29
113 114 2.409012 CAACATGTGGTGTACGCTACA 58.591 47.619 25.08 25.08 41.14 2.74
114 115 1.127951 GCAACATGTGGTGTACGCTAC 59.872 52.381 15.32 15.32 41.14 3.58
115 116 1.434555 GCAACATGTGGTGTACGCTA 58.565 50.000 0.00 0.00 41.14 4.26
116 117 1.234615 GGCAACATGTGGTGTACGCT 61.235 55.000 0.00 0.00 41.14 5.07
117 118 1.209127 GGCAACATGTGGTGTACGC 59.791 57.895 0.00 0.00 41.14 4.42
141 142 5.734720 TGATTAGTGGAGGTCAATGAGTTC 58.265 41.667 0.00 0.00 0.00 3.01
172 173 2.919229 GCGCTTTGTGATTGATCTTTGG 59.081 45.455 0.00 0.00 0.00 3.28
189 215 1.965930 TGGATTGTTGCTTCGCGCT 60.966 52.632 5.56 0.00 40.11 5.92
190 216 1.797537 GTGGATTGTTGCTTCGCGC 60.798 57.895 0.00 0.00 39.77 6.86
191 217 0.725784 GTGTGGATTGTTGCTTCGCG 60.726 55.000 0.00 0.00 0.00 5.87
192 218 0.310543 TGTGTGGATTGTTGCTTCGC 59.689 50.000 0.00 0.00 0.00 4.70
193 219 2.033299 ACTTGTGTGGATTGTTGCTTCG 59.967 45.455 0.00 0.00 0.00 3.79
194 220 3.715628 ACTTGTGTGGATTGTTGCTTC 57.284 42.857 0.00 0.00 0.00 3.86
196 222 3.067180 CAGAACTTGTGTGGATTGTTGCT 59.933 43.478 0.00 0.00 0.00 3.91
197 223 3.066621 TCAGAACTTGTGTGGATTGTTGC 59.933 43.478 0.00 0.00 0.00 4.17
198 224 4.336433 AGTCAGAACTTGTGTGGATTGTTG 59.664 41.667 0.00 0.00 28.74 3.33
199 225 4.526970 AGTCAGAACTTGTGTGGATTGTT 58.473 39.130 0.00 0.00 28.74 2.83
200 226 4.156455 AGTCAGAACTTGTGTGGATTGT 57.844 40.909 0.00 0.00 28.74 2.71
227 254 3.846405 AAGGTCAGAGCGGGGGTGA 62.846 63.158 0.00 0.00 0.00 4.02
230 257 2.269241 GAAAGGTCAGAGCGGGGG 59.731 66.667 0.00 0.00 0.00 5.40
232 259 0.035056 AATGGAAAGGTCAGAGCGGG 60.035 55.000 0.00 0.00 0.00 6.13
244 271 2.745281 GGGACGACATCGAAAATGGAAA 59.255 45.455 8.54 0.00 43.02 3.13
280 307 4.968181 GCGGCTTTCGTTCTTAATTAATCC 59.032 41.667 0.00 0.00 41.72 3.01
294 321 0.386731 ACCAATTTTCGCGGCTTTCG 60.387 50.000 6.13 0.00 42.76 3.46
314 341 3.403057 CACGCACTGACCGAACGG 61.403 66.667 11.83 11.83 42.03 4.44
324 351 0.443869 GCGATTCATTCACACGCACT 59.556 50.000 0.00 0.00 46.75 4.40
344 387 1.032114 GTTCAAGCCCGCCAGCTATT 61.032 55.000 0.00 0.00 44.11 1.73
346 389 2.046314 GTTCAAGCCCGCCAGCTA 60.046 61.111 0.00 0.00 44.11 3.32
348 391 3.064324 ATGTTCAAGCCCGCCAGC 61.064 61.111 0.00 0.00 0.00 4.85
354 397 1.598701 GAGGTGCCATGTTCAAGCCC 61.599 60.000 0.00 0.00 0.00 5.19
378 430 3.897239 TGTTGCGGAATTTGGGATAGAT 58.103 40.909 0.00 0.00 0.00 1.98
379 431 3.358111 TGTTGCGGAATTTGGGATAGA 57.642 42.857 0.00 0.00 0.00 1.98
380 432 3.443681 ACTTGTTGCGGAATTTGGGATAG 59.556 43.478 0.00 0.00 0.00 2.08
381 433 3.192422 CACTTGTTGCGGAATTTGGGATA 59.808 43.478 0.00 0.00 0.00 2.59
474 547 1.806542 GATTCAGAAAACGCTGGCTCA 59.193 47.619 0.00 0.00 36.55 4.26
519 592 5.255687 TGCAAGGAAATTCAAGCTAGATCA 58.744 37.500 0.00 0.00 0.00 2.92
523 596 4.400251 TCCATGCAAGGAAATTCAAGCTAG 59.600 41.667 8.54 0.00 33.93 3.42
526 604 3.598019 TCCATGCAAGGAAATTCAAGC 57.402 42.857 8.54 0.00 33.93 4.01
593 671 1.886655 GCCGGGTCAAATTCTCAGGTT 60.887 52.381 2.18 0.00 0.00 3.50
596 674 0.035056 AGGCCGGGTCAAATTCTCAG 60.035 55.000 2.18 0.00 0.00 3.35
640 718 4.754322 CGGGTTATTTTGATTTTCTGGGG 58.246 43.478 0.00 0.00 0.00 4.96
641 719 4.180817 GCGGGTTATTTTGATTTTCTGGG 58.819 43.478 0.00 0.00 0.00 4.45
642 720 4.180817 GGCGGGTTATTTTGATTTTCTGG 58.819 43.478 0.00 0.00 0.00 3.86
647 728 5.220970 CGTAGATGGCGGGTTATTTTGATTT 60.221 40.000 0.00 0.00 0.00 2.17
649 730 3.813166 CGTAGATGGCGGGTTATTTTGAT 59.187 43.478 0.00 0.00 0.00 2.57
659 740 1.299926 GTGCTACGTAGATGGCGGG 60.300 63.158 26.53 0.00 0.00 6.13
662 743 2.316792 CGTATGTGCTACGTAGATGGC 58.683 52.381 26.53 12.04 46.46 4.40
676 757 0.251165 AAACTGGGGCTTGCGTATGT 60.251 50.000 0.00 0.00 0.00 2.29
709 790 0.253327 GAAGCCGGGAAATGAGGAGT 59.747 55.000 2.18 0.00 0.00 3.85
774 871 1.215140 ACTCCTCCTACGCTCTACCT 58.785 55.000 0.00 0.00 0.00 3.08
775 872 2.104622 ACTACTCCTCCTACGCTCTACC 59.895 54.545 0.00 0.00 0.00 3.18
776 873 3.473923 ACTACTCCTCCTACGCTCTAC 57.526 52.381 0.00 0.00 0.00 2.59
777 874 5.620738 TTTACTACTCCTCCTACGCTCTA 57.379 43.478 0.00 0.00 0.00 2.43
778 875 4.500499 TTTACTACTCCTCCTACGCTCT 57.500 45.455 0.00 0.00 0.00 4.09
780 877 4.398673 CAGTTTTACTACTCCTCCTACGCT 59.601 45.833 0.00 0.00 0.00 5.07
782 879 4.704057 ACCAGTTTTACTACTCCTCCTACG 59.296 45.833 0.00 0.00 0.00 3.51
837 943 2.978010 CGTATGGAATGGGCCGGC 60.978 66.667 21.18 21.18 0.00 6.13
875 981 1.225704 GCTTCCATGGGACTCCTGG 59.774 63.158 13.02 0.00 34.62 4.45
898 1004 0.834687 TGTGGCGTTAAGAGGGGAGT 60.835 55.000 0.00 0.00 0.00 3.85
900 1006 0.988832 AATGTGGCGTTAAGAGGGGA 59.011 50.000 0.00 0.00 0.00 4.81
952 1060 1.382146 TATGGTGGAGGGGACGGAC 60.382 63.158 0.00 0.00 0.00 4.79
953 1061 1.382146 GTATGGTGGAGGGGACGGA 60.382 63.158 0.00 0.00 0.00 4.69
965 1073 1.346722 GGGTTAGCTATGGCGTATGGT 59.653 52.381 0.00 0.00 44.37 3.55
980 1094 1.298667 GAGGAAGCTTGCGGGGTTA 59.701 57.895 12.66 0.00 0.00 2.85
1079 1205 0.905357 CCACAGGAGGACAAGGTAGG 59.095 60.000 0.00 0.00 0.00 3.18
1103 1236 4.899239 GGGAGTCATGGAGCGCGG 62.899 72.222 8.83 0.00 0.00 6.46
1109 1242 2.692368 GGCCTGGGGAGTCATGGA 60.692 66.667 0.00 0.00 0.00 3.41
1261 1400 1.872679 GACGACGATCCCGCTCAAC 60.873 63.158 0.00 0.00 39.95 3.18
1263 1402 3.515286 GGACGACGATCCCGCTCA 61.515 66.667 0.00 0.00 39.95 4.26
1359 1498 0.110486 GGTGGTGGTGGTGTTGATCT 59.890 55.000 0.00 0.00 0.00 2.75
1383 1522 0.659427 CACGATGATGATGGTGGTGC 59.341 55.000 0.00 0.00 35.30 5.01
1386 1525 0.942252 CAGCACGATGATGATGGTGG 59.058 55.000 9.17 0.00 38.42 4.61
1594 1748 7.384660 GCTTCTGATCAGGATAAGTACATGAAG 59.615 40.741 22.42 13.88 32.15 3.02
1630 1787 0.850883 TTTCTCCCTCCCCCTTGCAT 60.851 55.000 0.00 0.00 0.00 3.96
1639 1797 2.853235 TCGGTTCTTTTTCTCCCTCC 57.147 50.000 0.00 0.00 0.00 4.30
1694 1853 5.560760 CGCATACTCAACAACAAGACAACAT 60.561 40.000 0.00 0.00 0.00 2.71
1700 1859 3.987868 GAGACGCATACTCAACAACAAGA 59.012 43.478 0.00 0.00 34.87 3.02
1701 1860 3.990469 AGAGACGCATACTCAACAACAAG 59.010 43.478 0.00 0.00 36.91 3.16
1732 1891 7.920151 TCAAAGAATGGACAAACTACAAATGTG 59.080 33.333 0.00 0.00 0.00 3.21
1733 1892 8.006298 TCAAAGAATGGACAAACTACAAATGT 57.994 30.769 0.00 0.00 0.00 2.71
1739 1898 9.399403 GAGAAAATCAAAGAATGGACAAACTAC 57.601 33.333 0.00 0.00 0.00 2.73
1743 1902 6.925165 GCAGAGAAAATCAAAGAATGGACAAA 59.075 34.615 0.00 0.00 0.00 2.83
1771 1935 2.864343 GCCAAGATTTTGATCATGCAGC 59.136 45.455 0.00 0.00 36.36 5.25
1772 1936 4.118093 TGCCAAGATTTTGATCATGCAG 57.882 40.909 0.00 0.00 36.36 4.41
1773 1937 4.160626 TCATGCCAAGATTTTGATCATGCA 59.839 37.500 18.04 10.83 40.64 3.96
1774 1938 4.689071 TCATGCCAAGATTTTGATCATGC 58.311 39.130 18.04 6.72 40.64 4.06
1803 1967 0.596577 GTCACCTGCAGTCGTACTCA 59.403 55.000 13.81 0.00 0.00 3.41
1808 1972 1.229428 CAAATGTCACCTGCAGTCGT 58.771 50.000 13.81 0.70 0.00 4.34
1809 1973 0.110056 GCAAATGTCACCTGCAGTCG 60.110 55.000 13.81 2.86 36.09 4.18
1810 1974 0.953727 TGCAAATGTCACCTGCAGTC 59.046 50.000 13.81 0.88 41.01 3.51
1811 1975 3.114527 TGCAAATGTCACCTGCAGT 57.885 47.368 13.81 0.00 41.01 4.40
1878 2042 3.119708 GCTTCCCAATCAGTAAAGCACAG 60.120 47.826 0.00 0.00 41.46 3.66
1899 2065 1.221414 GACCAGAAGCATACATCGGC 58.779 55.000 0.00 0.00 0.00 5.54
1909 2075 0.861837 CACACTTGACGACCAGAAGC 59.138 55.000 0.00 0.00 0.00 3.86
1910 2076 2.225068 ACACACTTGACGACCAGAAG 57.775 50.000 0.00 0.00 0.00 2.85
1911 2077 2.276201 CAACACACTTGACGACCAGAA 58.724 47.619 0.00 0.00 0.00 3.02
1912 2078 1.934589 CAACACACTTGACGACCAGA 58.065 50.000 0.00 0.00 0.00 3.86
1921 2089 2.159128 TGGGAACAATGCAACACACTTG 60.159 45.455 0.00 0.00 37.44 3.16
1937 2105 6.009589 TCAATCTATTGCAAGTTCTTGGGAA 58.990 36.000 4.94 3.86 37.68 3.97
2030 2211 6.183361 TGTCCATAAACAGGTTCACTCCTTTA 60.183 38.462 0.00 0.00 35.37 1.85
2031 2212 5.070685 GTCCATAAACAGGTTCACTCCTTT 58.929 41.667 0.00 0.00 35.37 3.11
2048 2229 1.281867 CTTTGGGCCAGTCTGTCCATA 59.718 52.381 6.23 2.99 0.00 2.74
2083 2264 1.965414 TCCTGGCCTGGATGTTAAGA 58.035 50.000 26.46 2.68 0.00 2.10
2085 2266 1.494721 GGATCCTGGCCTGGATGTTAA 59.505 52.381 40.08 17.26 46.00 2.01
2127 2308 3.213249 CAGATTTTGCTCACTTCTGGC 57.787 47.619 0.00 0.00 32.14 4.85
2178 2362 8.700051 TCATTTTGGGGGTATACAAATACAATG 58.300 33.333 5.01 6.47 39.90 2.82
2220 2413 7.294720 AGGAGATATATTTGGTCATGGTTACCA 59.705 37.037 6.53 6.53 45.26 3.25
2221 2414 7.690256 AGGAGATATATTTGGTCATGGTTACC 58.310 38.462 0.00 0.00 37.53 2.85
2222 2415 9.877178 CTAGGAGATATATTTGGTCATGGTTAC 57.123 37.037 0.00 0.00 0.00 2.50
2223 2416 9.837681 TCTAGGAGATATATTTGGTCATGGTTA 57.162 33.333 0.00 0.00 0.00 2.85
2233 2426 7.976734 GTCCGTGGAATCTAGGAGATATATTTG 59.023 40.741 0.00 0.00 32.89 2.32
2250 2443 1.180456 TTGCTACTCGGTCCGTGGAA 61.180 55.000 17.11 8.32 0.00 3.53
2304 2497 8.835467 TTCGTGTTTTGTTTTAAGATTCTCTG 57.165 30.769 0.00 0.00 0.00 3.35
2417 2757 7.744715 CAGCACACCGTAGAAGTTTATAAAAAG 59.255 37.037 0.00 0.00 0.00 2.27
2418 2758 7.577979 CAGCACACCGTAGAAGTTTATAAAAA 58.422 34.615 0.00 0.00 0.00 1.94
2433 2779 0.948678 AATAAAACGCAGCACACCGT 59.051 45.000 0.00 0.00 39.70 4.83
2492 2838 9.930693 ACAAGTAACAAGTTCAAACCATTTTTA 57.069 25.926 0.00 0.00 0.00 1.52
2496 2842 7.066043 TCGTACAAGTAACAAGTTCAAACCATT 59.934 33.333 0.00 0.00 0.00 3.16
2511 2857 7.495279 ACCATGTAAGTTTTGTCGTACAAGTAA 59.505 33.333 0.00 0.00 39.53 2.24
2523 2869 8.710835 AACCAGTTTAAACCATGTAAGTTTTG 57.289 30.769 14.72 2.27 38.37 2.44
2532 2878 6.276847 TGCACTTTAACCAGTTTAAACCATG 58.723 36.000 14.72 7.58 35.17 3.66
2567 2913 5.516339 CACACTGCAGAAGTTTACAAAAAGG 59.484 40.000 23.35 0.00 36.83 3.11
2574 2920 3.363178 GCAACACACTGCAGAAGTTTAC 58.637 45.455 23.35 11.55 42.17 2.01
2576 2922 1.202177 CGCAACACACTGCAGAAGTTT 60.202 47.619 23.35 8.78 42.77 2.66
2592 2938 9.562408 TGGGTATATATTCAGAATAAAACGCAA 57.438 29.630 19.54 10.61 30.67 4.85
2696 3043 8.709646 AGCTAAGTTTTCTCGTACAAATAACAG 58.290 33.333 0.00 0.00 0.00 3.16
2729 3099 7.933396 TGCACGTATAAGCTTACTAGTCAATA 58.067 34.615 8.70 0.00 0.00 1.90
2747 3117 1.322040 CGTTATCATGCGTTGCACGTA 59.678 47.619 9.76 6.30 44.73 3.57
2788 3158 9.298774 GATGCCCTACGTTATAACTATATGAAC 57.701 37.037 13.56 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.