Multiple sequence alignment - TraesCS2B01G572700

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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 TraesCS2B01G572700 chr2B 100.000 2720 0 0 1 2720 762428766 762431485 0.000000e+00 5024
1 TraesCS2B01G572700 chr2D 85.638 2444 149 92 1 2336 621495155 621497504 0.000000e+00 2383
2 TraesCS2B01G572700 chr2D 82.776 389 25 21 2344 2719 621497542 621497901 2.630000e-80 309
3 TraesCS2B01G572700 chr2D 79.167 312 34 17 2332 2640 621502647 621502930 1.290000e-43 187
4 TraesCS2B01G572700 chr2D 77.830 212 28 12 2107 2305 621502075 621502280 2.210000e-21 113
5 TraesCS2B01G572700 chr2A 85.563 1704 112 57 163 1770 753228235 753229900 0.000000e+00 1661
6 TraesCS2B01G572700 chr2A 88.109 513 22 18 1840 2326 753229921 753230420 8.450000e-160 573
7 TraesCS2B01G572700 chr2A 81.481 135 19 4 2574 2706 753230628 753230758 3.700000e-19 106
8 TraesCS2B01G572700 chr3D 91.209 182 15 1 1178 1359 554140222 554140402 2.090000e-61 246


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 TraesCS2B01G572700 chr2B 762428766 762431485 2719 False 5024 5024 100.000 1 2720 1 chr2B.!!$F1 2719
1 TraesCS2B01G572700 chr2D 621495155 621497901 2746 False 1346 2383 84.207 1 2719 2 chr2D.!!$F1 2718
2 TraesCS2B01G572700 chr2A 753228235 753230758 2523 False 780 1661 85.051 163 2706 3 chr2A.!!$F1 2543

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
751 845 0.108396 CTCCACACCACACCACATCA 59.892 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2650 0.036765 AGCTTTATCGGTGTGGCGAA 60.037 50.0 0.0 0.0 0.0 4.7 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
44 45 0.907486 CTCTTGAGCCTCATCCACCA 59.093 55.000 0.00 0.00 0.00 4.17
85 86 1.527844 GGAGATGACATGCTGGCCC 60.528 63.158 0.00 0.00 0.00 5.80
129 132 1.227089 CCTCGATCAAGCCGTCCAG 60.227 63.158 0.00 0.00 0.00 3.86
130 133 1.227089 CTCGATCAAGCCGTCCAGG 60.227 63.158 0.00 0.00 44.97 4.45
131 134 1.667154 CTCGATCAAGCCGTCCAGGA 61.667 60.000 0.00 0.00 45.00 3.86
132 135 1.043116 TCGATCAAGCCGTCCAGGAT 61.043 55.000 0.00 0.00 45.00 3.24
171 174 0.883370 AGTCGCCGTTGAAAGGAACC 60.883 55.000 0.07 0.00 0.00 3.62
235 252 2.304092 CCCATCCACATCCACATCAAG 58.696 52.381 0.00 0.00 0.00 3.02
240 257 1.676916 CCACATCCACATCAAGCTCGT 60.677 52.381 0.00 0.00 0.00 4.18
241 258 1.662629 CACATCCACATCAAGCTCGTC 59.337 52.381 0.00 0.00 0.00 4.20
267 297 3.760035 CCGTCGGGGACACCAGAG 61.760 72.222 2.34 0.00 41.78 3.35
270 300 1.292541 GTCGGGGACACCAGAGTTC 59.707 63.158 0.00 0.00 41.78 3.01
348 405 1.821759 CACGGCACCACCACAGAAA 60.822 57.895 0.00 0.00 39.03 2.52
377 434 2.203294 GGGACGGCACTTGGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
397 458 4.057428 GACGTCGAGCCAGCAGGT 62.057 66.667 0.00 0.00 37.19 4.00
398 459 4.363990 ACGTCGAGCCAGCAGGTG 62.364 66.667 0.00 0.00 37.19 4.00
412 475 3.647771 GGTGGTGACCTGACCCCC 61.648 72.222 2.11 0.00 39.47 5.40
413 476 2.529389 GTGGTGACCTGACCCCCT 60.529 66.667 2.11 0.00 34.79 4.79
414 477 1.229400 GTGGTGACCTGACCCCCTA 60.229 63.158 2.11 0.00 34.79 3.53
416 479 1.080538 GGTGACCTGACCCCCTACT 59.919 63.158 0.00 0.00 0.00 2.57
425 488 2.973406 CTGACCCCCTACTAATTCTCCC 59.027 54.545 0.00 0.00 0.00 4.30
442 505 3.202151 TCTCCCAAAAGGTCTGAACTTGT 59.798 43.478 9.03 0.00 36.75 3.16
574 656 1.153706 CGACCCGACCATACACACC 60.154 63.158 0.00 0.00 0.00 4.16
579 661 1.078708 CGACCATACACACCCCACC 60.079 63.158 0.00 0.00 0.00 4.61
580 662 1.832719 CGACCATACACACCCCACCA 61.833 60.000 0.00 0.00 0.00 4.17
581 663 0.322187 GACCATACACACCCCACCAC 60.322 60.000 0.00 0.00 0.00 4.16
584 666 0.953471 CATACACACCCCACCACACG 60.953 60.000 0.00 0.00 0.00 4.49
590 672 4.885270 CCCCACCACACGCCACAA 62.885 66.667 0.00 0.00 0.00 3.33
597 679 1.269936 ACCACACGCCACAAGTAGTAC 60.270 52.381 0.00 0.00 0.00 2.73
598 680 1.269883 CCACACGCCACAAGTAGTACA 60.270 52.381 2.52 0.00 0.00 2.90
602 684 1.270465 ACGCCACAAGTAGTACAACCC 60.270 52.381 2.52 0.00 0.00 4.11
603 685 1.270412 CGCCACAAGTAGTACAACCCA 60.270 52.381 2.52 0.00 0.00 4.51
604 686 2.807472 CGCCACAAGTAGTACAACCCAA 60.807 50.000 2.52 0.00 0.00 4.12
607 689 3.566742 CCACAAGTAGTACAACCCAAACC 59.433 47.826 2.52 0.00 0.00 3.27
609 691 4.641094 CACAAGTAGTACAACCCAAACCAA 59.359 41.667 2.52 0.00 0.00 3.67
668 752 3.181967 CGTCGCCTTGGCTTCTCG 61.182 66.667 10.12 5.40 0.00 4.04
733 822 2.038762 ACCAGACCCAACCCACCT 60.039 61.111 0.00 0.00 0.00 4.00
744 838 2.113139 CCCACCTCCACACCACAC 59.887 66.667 0.00 0.00 0.00 3.82
748 842 1.998438 ACCTCCACACCACACCACA 60.998 57.895 0.00 0.00 0.00 4.17
749 843 1.352622 ACCTCCACACCACACCACAT 61.353 55.000 0.00 0.00 0.00 3.21
751 845 0.108396 CTCCACACCACACCACATCA 59.892 55.000 0.00 0.00 0.00 3.07
753 847 1.172180 CCACACCACACCACATCACC 61.172 60.000 0.00 0.00 0.00 4.02
754 848 0.179020 CACACCACACCACATCACCT 60.179 55.000 0.00 0.00 0.00 4.00
755 849 0.108585 ACACCACACCACATCACCTC 59.891 55.000 0.00 0.00 0.00 3.85
756 850 0.108396 CACCACACCACATCACCTCA 59.892 55.000 0.00 0.00 0.00 3.86
830 937 1.377856 GCCCCCAAGAAGCTGAGAC 60.378 63.158 0.00 0.00 0.00 3.36
973 1080 2.185350 CCGCCAGCCAGTGAGTAG 59.815 66.667 0.00 0.00 0.00 2.57
981 1088 4.778579 CCAGCCAGTGAGTAGTACTACTA 58.221 47.826 30.80 18.11 45.63 1.82
982 1089 5.378332 CCAGCCAGTGAGTAGTACTACTAT 58.622 45.833 30.80 18.86 45.63 2.12
987 1094 7.835181 AGCCAGTGAGTAGTACTACTATTTCTT 59.165 37.037 30.80 11.42 45.63 2.52
988 1095 8.468399 GCCAGTGAGTAGTACTACTATTTCTTT 58.532 37.037 30.80 10.72 45.63 2.52
989 1096 9.790389 CCAGTGAGTAGTACTACTATTTCTTTG 57.210 37.037 30.80 20.77 45.63 2.77
1026 1139 1.615424 GCTGTACCAGGGGAAGGGA 60.615 63.158 0.00 0.00 31.21 4.20
1167 1280 2.185350 CTGGCCTACCTGCTGTCG 59.815 66.667 3.32 0.00 36.63 4.35
1378 1494 1.611965 GAGGGAGCAGCCAAAGGAT 59.388 57.895 0.00 0.00 38.95 3.24
1382 1498 2.439156 AGCAGCCAAAGGATCCGC 60.439 61.111 5.98 3.41 0.00 5.54
1770 1894 5.236911 CGCTAGAACTTCTCGTAGATTAGGT 59.763 44.000 0.00 0.00 33.89 3.08
1771 1895 6.238429 CGCTAGAACTTCTCGTAGATTAGGTT 60.238 42.308 0.00 0.00 33.89 3.50
1775 1899 7.540299 AGAACTTCTCGTAGATTAGGTTGAAG 58.460 38.462 0.00 0.00 33.89 3.02
1788 1912 3.683802 AGGTTGAAGCAAGAATGGAGAG 58.316 45.455 0.00 0.00 0.00 3.20
1789 1913 3.328931 AGGTTGAAGCAAGAATGGAGAGA 59.671 43.478 0.00 0.00 0.00 3.10
1790 1914 3.438434 GGTTGAAGCAAGAATGGAGAGAC 59.562 47.826 0.00 0.00 0.00 3.36
1792 1916 2.275318 GAAGCAAGAATGGAGAGACCG 58.725 52.381 0.00 0.00 42.61 4.79
1793 1917 0.107945 AGCAAGAATGGAGAGACCGC 60.108 55.000 0.00 0.00 42.61 5.68
1794 1918 1.092345 GCAAGAATGGAGAGACCGCC 61.092 60.000 0.00 0.00 42.61 6.13
1795 1919 0.250234 CAAGAATGGAGAGACCGCCA 59.750 55.000 0.00 0.00 46.23 5.69
1797 1921 0.539051 AGAATGGAGAGACCGCCAAG 59.461 55.000 0.00 0.00 45.33 3.61
1798 1922 0.537188 GAATGGAGAGACCGCCAAGA 59.463 55.000 0.00 0.00 45.33 3.02
1799 1923 1.139853 GAATGGAGAGACCGCCAAGAT 59.860 52.381 0.00 0.00 45.33 2.40
1800 1924 0.467384 ATGGAGAGACCGCCAAGATG 59.533 55.000 0.00 0.00 45.33 2.90
1801 1925 1.144936 GGAGAGACCGCCAAGATGG 59.855 63.158 0.00 0.00 41.55 3.51
1802 1926 1.617947 GGAGAGACCGCCAAGATGGT 61.618 60.000 0.00 0.00 40.46 3.55
1806 1930 2.671070 ACCGCCAAGATGGTCAGG 59.329 61.111 0.00 2.76 40.46 3.86
1807 1931 2.224159 ACCGCCAAGATGGTCAGGT 61.224 57.895 7.26 7.26 40.46 4.00
1808 1932 1.450312 CCGCCAAGATGGTCAGGTC 60.450 63.158 0.00 0.00 40.46 3.85
1809 1933 1.296392 CGCCAAGATGGTCAGGTCA 59.704 57.895 0.00 0.00 40.46 4.02
1810 1934 0.742281 CGCCAAGATGGTCAGGTCAG 60.742 60.000 0.00 0.00 40.46 3.51
1811 1935 0.393537 GCCAAGATGGTCAGGTCAGG 60.394 60.000 0.00 0.00 40.46 3.86
1812 1936 0.987294 CCAAGATGGTCAGGTCAGGT 59.013 55.000 0.00 0.00 31.35 4.00
1813 1937 1.065854 CCAAGATGGTCAGGTCAGGTC 60.066 57.143 0.00 0.00 31.35 3.85
1814 1938 1.625315 CAAGATGGTCAGGTCAGGTCA 59.375 52.381 0.00 0.00 0.00 4.02
1815 1939 1.566211 AGATGGTCAGGTCAGGTCAG 58.434 55.000 0.00 0.00 0.00 3.51
1816 1940 0.539051 GATGGTCAGGTCAGGTCAGG 59.461 60.000 0.00 0.00 0.00 3.86
1817 1941 0.178891 ATGGTCAGGTCAGGTCAGGT 60.179 55.000 0.00 0.00 0.00 4.00
1818 1942 0.832135 TGGTCAGGTCAGGTCAGGTC 60.832 60.000 0.00 0.00 0.00 3.85
1855 1979 1.230324 GTCAGGTCAGTGAAACCAGC 58.770 55.000 0.00 0.00 39.39 4.85
1896 2027 0.466007 TGTCCAAGCAAGCAAGAGCA 60.466 50.000 0.00 0.00 45.49 4.26
1897 2028 0.886563 GTCCAAGCAAGCAAGAGCAT 59.113 50.000 0.00 0.00 45.49 3.79
1968 2115 2.770904 GGCTCCGGGTGGGGATTA 60.771 66.667 0.00 0.00 38.40 1.75
1969 2116 2.380285 GGCTCCGGGTGGGGATTAA 61.380 63.158 0.00 0.00 38.40 1.40
1972 2119 0.759346 CTCCGGGTGGGGATTAAGAG 59.241 60.000 0.00 0.00 38.40 2.85
1973 2120 0.043637 TCCGGGTGGGGATTAAGAGT 59.956 55.000 0.00 0.00 36.01 3.24
1974 2121 0.468648 CCGGGTGGGGATTAAGAGTC 59.531 60.000 0.00 0.00 0.00 3.36
1975 2122 0.468648 CGGGTGGGGATTAAGAGTCC 59.531 60.000 0.00 0.00 34.92 3.85
2059 2218 2.919772 TTCCCCATTTCCCCTTTCTC 57.080 50.000 0.00 0.00 0.00 2.87
2073 2236 2.158842 CCTTTCTCTCCTCGCCATTGAT 60.159 50.000 0.00 0.00 0.00 2.57
2078 2241 0.106335 CTCCTCGCCATTGATGAGCT 59.894 55.000 0.00 0.00 0.00 4.09
2079 2242 0.179065 TCCTCGCCATTGATGAGCTG 60.179 55.000 0.00 0.00 0.00 4.24
2080 2243 1.647629 CTCGCCATTGATGAGCTGC 59.352 57.895 0.00 0.00 0.00 5.25
2081 2244 0.814410 CTCGCCATTGATGAGCTGCT 60.814 55.000 0.00 0.00 0.00 4.24
2082 2245 0.393402 TCGCCATTGATGAGCTGCTT 60.393 50.000 2.53 0.00 0.00 3.91
2083 2246 0.029035 CGCCATTGATGAGCTGCTTC 59.971 55.000 2.53 0.00 0.00 3.86
2084 2247 1.100510 GCCATTGATGAGCTGCTTCA 58.899 50.000 2.53 1.07 0.00 3.02
2085 2248 1.065701 GCCATTGATGAGCTGCTTCAG 59.934 52.381 2.53 0.00 32.92 3.02
2151 2319 3.340814 TGCAGGACCAAGAATCTCTTC 57.659 47.619 0.00 0.00 33.78 2.87
2210 2379 2.970324 TGCCAACCTCGTTGTCGC 60.970 61.111 4.00 2.13 41.41 5.19
2293 2462 1.221021 CCCTCGCTAACCCTGTTCC 59.779 63.158 0.00 0.00 0.00 3.62
2294 2463 1.221021 CCTCGCTAACCCTGTTCCC 59.779 63.158 0.00 0.00 0.00 3.97
2295 2464 1.221021 CTCGCTAACCCTGTTCCCC 59.779 63.158 0.00 0.00 0.00 4.81
2296 2465 1.229400 TCGCTAACCCTGTTCCCCT 60.229 57.895 0.00 0.00 0.00 4.79
2297 2466 1.078426 CGCTAACCCTGTTCCCCTG 60.078 63.158 0.00 0.00 0.00 4.45
2299 2468 1.853250 GCTAACCCTGTTCCCCTGCT 61.853 60.000 0.00 0.00 0.00 4.24
2300 2469 0.035056 CTAACCCTGTTCCCCTGCTG 60.035 60.000 0.00 0.00 0.00 4.41
2319 2496 3.165606 CTCACTCATGGTGGGCTTC 57.834 57.895 12.53 0.00 45.38 3.86
2327 2504 2.668550 GGTGGGCTTCGGTGACAC 60.669 66.667 0.00 0.00 0.00 3.67
2329 2506 1.302511 GTGGGCTTCGGTGACACAT 60.303 57.895 8.08 0.00 32.58 3.21
2330 2507 1.003839 TGGGCTTCGGTGACACATC 60.004 57.895 8.08 0.00 0.00 3.06
2332 2509 1.003839 GGCTTCGGTGACACATCCA 60.004 57.895 8.08 0.00 0.00 3.41
2333 2510 0.392998 GGCTTCGGTGACACATCCAT 60.393 55.000 8.08 0.00 0.00 3.41
2334 2511 0.729116 GCTTCGGTGACACATCCATG 59.271 55.000 8.08 0.00 0.00 3.66
2335 2512 0.729116 CTTCGGTGACACATCCATGC 59.271 55.000 8.08 0.00 0.00 4.06
2337 2514 1.447663 CGGTGACACATCCATGCGA 60.448 57.895 8.08 0.00 0.00 5.10
2339 2516 1.164411 GGTGACACATCCATGCGAAA 58.836 50.000 8.08 0.00 0.00 3.46
2341 2518 2.942376 GGTGACACATCCATGCGAAATA 59.058 45.455 8.08 0.00 0.00 1.40
2342 2519 3.565482 GGTGACACATCCATGCGAAATAT 59.435 43.478 8.08 0.00 0.00 1.28
2368 2584 7.568199 AGTAGCAAGTACAATCTTTGTTGTT 57.432 32.000 0.00 0.00 42.22 2.83
2377 2593 6.704512 ACAATCTTTGTTGTTGTTGTTGTC 57.295 33.333 0.00 0.00 42.22 3.18
2398 2620 6.148948 TGTCGTTGGTTGATTGATTTGATTC 58.851 36.000 0.00 0.00 0.00 2.52
2404 2626 5.879777 TGGTTGATTGATTTGATTCGAGCTA 59.120 36.000 0.00 0.00 0.00 3.32
2423 2650 2.123409 GCTAGCTAGCTGGAGCAGT 58.877 57.895 33.71 3.04 45.43 4.40
2424 2651 0.463620 GCTAGCTAGCTGGAGCAGTT 59.536 55.000 33.71 2.26 45.43 3.16
2425 2652 1.537990 GCTAGCTAGCTGGAGCAGTTC 60.538 57.143 33.71 7.98 45.43 3.01
2426 2653 0.741326 TAGCTAGCTGGAGCAGTTCG 59.259 55.000 27.68 0.00 45.43 3.95
2427 2654 2.170434 GCTAGCTGGAGCAGTTCGC 61.170 63.158 7.70 0.00 45.16 4.70
2428 2655 1.520342 CTAGCTGGAGCAGTTCGCC 60.520 63.158 0.00 0.00 45.16 5.54
2429 2656 2.230994 CTAGCTGGAGCAGTTCGCCA 62.231 60.000 0.00 0.00 45.16 5.69
2477 2704 7.426929 AACAGGAATTAATCATCGTATCTGC 57.573 36.000 0.00 0.00 0.00 4.26
2478 2705 6.524734 ACAGGAATTAATCATCGTATCTGCA 58.475 36.000 0.00 0.00 0.00 4.41
2479 2706 6.648310 ACAGGAATTAATCATCGTATCTGCAG 59.352 38.462 7.63 7.63 0.00 4.41
2480 2707 6.870439 CAGGAATTAATCATCGTATCTGCAGA 59.130 38.462 20.79 20.79 0.00 4.26
2512 2739 3.414700 GACGTGGCGGCAGAACTG 61.415 66.667 13.91 2.50 33.63 3.16
2513 2740 4.988598 ACGTGGCGGCAGAACTGG 62.989 66.667 13.91 0.00 0.00 4.00
2517 2744 4.344865 GGCGGCAGAACTGGGGAA 62.345 66.667 3.07 0.00 0.00 3.97
2518 2745 3.056328 GCGGCAGAACTGGGGAAC 61.056 66.667 0.00 0.00 0.00 3.62
2519 2746 2.750350 CGGCAGAACTGGGGAACT 59.250 61.111 3.99 0.00 0.00 3.01
2541 2768 0.239879 TGCGAATTTGACCCGAAAGC 59.760 50.000 0.00 0.00 0.00 3.51
2632 2864 9.090692 CATCTTTTGAACCATGCCTTTTATTAG 57.909 33.333 0.00 0.00 0.00 1.73
2634 2866 8.087750 TCTTTTGAACCATGCCTTTTATTAGTG 58.912 33.333 0.00 0.00 0.00 2.74
2635 2867 6.909550 TTGAACCATGCCTTTTATTAGTGT 57.090 33.333 0.00 0.00 0.00 3.55
2637 2869 7.296628 TGAACCATGCCTTTTATTAGTGTTT 57.703 32.000 0.00 0.00 0.00 2.83
2638 2870 7.375053 TGAACCATGCCTTTTATTAGTGTTTC 58.625 34.615 0.00 0.00 0.00 2.78
2641 2873 8.823220 ACCATGCCTTTTATTAGTGTTTCTAT 57.177 30.769 0.00 0.00 0.00 1.98
2706 2942 2.097825 CATTGGAGGAGGCAAAAGGAG 58.902 52.381 0.00 0.00 0.00 3.69
2719 2955 7.175816 GGAGGCAAAAGGAGGATTAGATATTTC 59.824 40.741 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.512515 GCGTGGTGGATGAGGCTC 60.513 66.667 7.79 7.79 0.00 4.70
31 32 3.005539 AGCGTGGTGGATGAGGCT 61.006 61.111 0.00 0.00 0.00 4.58
44 45 4.271816 CGAGCATAGCCCGAGCGT 62.272 66.667 0.00 0.00 46.67 5.07
99 100 3.765257 ATCGAGGGAGGAGGCAGGG 62.765 68.421 0.00 0.00 0.00 4.45
110 113 2.107141 GGACGGCTTGATCGAGGG 59.893 66.667 12.06 0.00 0.00 4.30
130 133 0.959553 TCGCTCGTAGGGAATCCATC 59.040 55.000 0.09 0.00 34.02 3.51
131 134 0.962489 CTCGCTCGTAGGGAATCCAT 59.038 55.000 0.09 0.00 36.71 3.41
132 135 1.735376 GCTCGCTCGTAGGGAATCCA 61.735 60.000 0.09 0.00 36.71 3.41
235 252 2.202756 CGGGGTTAGCTGACGAGC 60.203 66.667 2.14 0.00 46.64 5.03
309 340 2.104331 GTGGTCGGTCGATGCGAT 59.896 61.111 0.00 0.00 38.42 4.58
310 341 4.124351 GGTGGTCGGTCGATGCGA 62.124 66.667 0.00 0.00 0.00 5.10
344 401 1.886542 GTCCCGCTGGTGAAAATTTCT 59.113 47.619 7.29 0.00 0.00 2.52
345 402 1.401018 CGTCCCGCTGGTGAAAATTTC 60.401 52.381 0.00 0.00 0.00 2.17
348 405 1.674322 CCGTCCCGCTGGTGAAAAT 60.674 57.895 0.00 0.00 0.00 1.82
375 432 2.865308 CTGGCTCGACGTCGTACA 59.135 61.111 34.40 27.56 40.80 2.90
376 433 2.576317 GCTGGCTCGACGTCGTAC 60.576 66.667 34.40 26.38 40.80 3.67
377 434 3.035576 CTGCTGGCTCGACGTCGTA 62.036 63.158 34.40 21.01 40.80 3.43
397 458 1.229400 GTAGGGGGTCAGGTCACCA 60.229 63.158 0.00 0.00 38.32 4.17
398 459 0.337428 TAGTAGGGGGTCAGGTCACC 59.663 60.000 0.00 0.00 35.42 4.02
400 461 3.013648 AGAATTAGTAGGGGGTCAGGTCA 59.986 47.826 0.00 0.00 0.00 4.02
401 462 3.642377 GAGAATTAGTAGGGGGTCAGGTC 59.358 52.174 0.00 0.00 0.00 3.85
402 463 3.632906 GGAGAATTAGTAGGGGGTCAGGT 60.633 52.174 0.00 0.00 0.00 4.00
412 475 6.947464 TCAGACCTTTTGGGAGAATTAGTAG 58.053 40.000 0.00 0.00 46.08 2.57
413 476 6.945636 TCAGACCTTTTGGGAGAATTAGTA 57.054 37.500 0.00 0.00 46.08 1.82
414 477 5.843019 TCAGACCTTTTGGGAGAATTAGT 57.157 39.130 0.00 0.00 46.08 2.24
416 479 6.200878 AGTTCAGACCTTTTGGGAGAATTA 57.799 37.500 0.00 0.00 46.08 1.40
560 642 1.078708 GTGGGGTGTGTATGGTCGG 60.079 63.158 0.00 0.00 0.00 4.79
562 644 0.322187 GTGGTGGGGTGTGTATGGTC 60.322 60.000 0.00 0.00 0.00 4.02
567 649 2.823114 CGTGTGGTGGGGTGTGTA 59.177 61.111 0.00 0.00 0.00 2.90
574 656 2.668185 TACTTGTGGCGTGTGGTGGG 62.668 60.000 0.00 0.00 0.00 4.61
579 661 2.143008 TGTACTACTTGTGGCGTGTG 57.857 50.000 0.00 0.00 0.00 3.82
580 662 2.476821 GTTGTACTACTTGTGGCGTGT 58.523 47.619 0.00 0.00 0.00 4.49
581 663 1.796459 GGTTGTACTACTTGTGGCGTG 59.204 52.381 7.38 0.00 0.00 5.34
584 666 2.554370 TGGGTTGTACTACTTGTGGC 57.446 50.000 7.38 0.00 0.00 5.01
590 672 5.127519 GGTTTTTGGTTTGGGTTGTACTACT 59.872 40.000 7.38 0.00 0.00 2.57
597 679 4.155099 GTCTTTGGTTTTTGGTTTGGGTTG 59.845 41.667 0.00 0.00 0.00 3.77
598 680 4.328536 GTCTTTGGTTTTTGGTTTGGGTT 58.671 39.130 0.00 0.00 0.00 4.11
602 684 4.926832 ACTTCGTCTTTGGTTTTTGGTTTG 59.073 37.500 0.00 0.00 0.00 2.93
603 685 5.142061 ACTTCGTCTTTGGTTTTTGGTTT 57.858 34.783 0.00 0.00 0.00 3.27
604 686 4.794278 ACTTCGTCTTTGGTTTTTGGTT 57.206 36.364 0.00 0.00 0.00 3.67
607 689 4.561213 GTCCAACTTCGTCTTTGGTTTTTG 59.439 41.667 10.19 0.00 42.62 2.44
609 691 3.129813 GGTCCAACTTCGTCTTTGGTTTT 59.870 43.478 10.19 0.00 42.62 2.43
668 752 1.866853 GCCCTATTATTGCAGCCGGC 61.867 60.000 21.89 21.89 45.13 6.13
670 754 2.257353 GGCCCTATTATTGCAGCCG 58.743 57.895 0.00 0.00 0.00 5.52
733 822 0.179032 GTGATGTGGTGTGGTGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
744 838 1.002134 GGGGTGTGAGGTGATGTGG 60.002 63.158 0.00 0.00 0.00 4.17
748 842 1.500783 CCCTTGGGGTGTGAGGTGAT 61.501 60.000 0.00 0.00 38.25 3.06
749 843 2.153401 CCCTTGGGGTGTGAGGTGA 61.153 63.158 0.00 0.00 38.25 4.02
848 955 3.649986 GGCTGCGACGTTGCTGTT 61.650 61.111 28.67 0.00 36.33 3.16
973 1080 6.570690 CGCAGGTCAAAGAAATAGTAGTAC 57.429 41.667 0.00 0.00 0.00 2.73
1743 1867 0.376152 TACGAGAAGTTCTAGCGGCG 59.624 55.000 15.84 0.51 0.00 6.46
1744 1868 1.669779 TCTACGAGAAGTTCTAGCGGC 59.330 52.381 15.84 0.00 0.00 6.53
1745 1869 4.555348 AATCTACGAGAAGTTCTAGCGG 57.445 45.455 15.84 8.53 0.00 5.52
1746 1870 5.236911 ACCTAATCTACGAGAAGTTCTAGCG 59.763 44.000 12.39 11.82 0.00 4.26
1747 1871 6.622833 ACCTAATCTACGAGAAGTTCTAGC 57.377 41.667 12.39 0.00 0.00 3.42
1748 1872 8.211116 TCAACCTAATCTACGAGAAGTTCTAG 57.789 38.462 5.09 8.51 0.00 2.43
1770 1894 3.679389 GGTCTCTCCATTCTTGCTTCAA 58.321 45.455 0.00 0.00 35.97 2.69
1771 1895 2.354103 CGGTCTCTCCATTCTTGCTTCA 60.354 50.000 0.00 0.00 35.57 3.02
1775 1899 1.092345 GGCGGTCTCTCCATTCTTGC 61.092 60.000 0.00 0.00 35.57 4.01
1789 1913 2.185310 GACCTGACCATCTTGGCGGT 62.185 60.000 3.33 3.33 42.67 5.68
1790 1914 1.450312 GACCTGACCATCTTGGCGG 60.450 63.158 0.00 0.00 42.67 6.13
1792 1916 0.393537 CCTGACCTGACCATCTTGGC 60.394 60.000 0.00 0.00 42.67 4.52
1793 1917 0.987294 ACCTGACCTGACCATCTTGG 59.013 55.000 0.00 0.00 45.02 3.61
1794 1918 1.625315 TGACCTGACCTGACCATCTTG 59.375 52.381 0.00 0.00 0.00 3.02
1795 1919 1.905215 CTGACCTGACCTGACCATCTT 59.095 52.381 0.00 0.00 0.00 2.40
1797 1921 0.539051 CCTGACCTGACCTGACCATC 59.461 60.000 0.00 0.00 0.00 3.51
1798 1922 0.178891 ACCTGACCTGACCTGACCAT 60.179 55.000 0.00 0.00 0.00 3.55
1799 1923 0.832135 GACCTGACCTGACCTGACCA 60.832 60.000 0.00 0.00 0.00 4.02
1800 1924 0.832135 TGACCTGACCTGACCTGACC 60.832 60.000 0.00 0.00 0.00 4.02
1801 1925 0.605589 CTGACCTGACCTGACCTGAC 59.394 60.000 0.00 0.00 0.00 3.51
1802 1926 0.542938 CCTGACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
1803 1927 0.833834 ACCTGACCTGACCTGACCTG 60.834 60.000 0.00 0.00 0.00 4.00
1804 1928 0.543174 GACCTGACCTGACCTGACCT 60.543 60.000 0.00 0.00 0.00 3.85
1805 1929 0.832135 TGACCTGACCTGACCTGACC 60.832 60.000 0.00 0.00 0.00 4.02
1806 1930 0.605589 CTGACCTGACCTGACCTGAC 59.394 60.000 0.00 0.00 0.00 3.51
1807 1931 0.542938 CCTGACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
1808 1932 0.833834 ACCTGACCTGACCTGACCTG 60.834 60.000 0.00 0.00 0.00 4.00
1809 1933 0.543174 GACCTGACCTGACCTGACCT 60.543 60.000 0.00 0.00 0.00 3.85
1810 1934 0.832135 TGACCTGACCTGACCTGACC 60.832 60.000 0.00 0.00 0.00 4.02
1811 1935 0.605589 CTGACCTGACCTGACCTGAC 59.394 60.000 0.00 0.00 0.00 3.51
1812 1936 0.542938 CCTGACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
1813 1937 0.833834 ACCTGACCTGACCTGACCTG 60.834 60.000 0.00 0.00 0.00 4.00
1814 1938 0.543174 GACCTGACCTGACCTGACCT 60.543 60.000 0.00 0.00 0.00 3.85
1815 1939 0.832135 TGACCTGACCTGACCTGACC 60.832 60.000 0.00 0.00 0.00 4.02
1816 1940 0.605589 CTGACCTGACCTGACCTGAC 59.394 60.000 0.00 0.00 0.00 3.51
1817 1941 0.542938 CCTGACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
1818 1942 0.833834 ACCTGACCTGACCTGACCTG 60.834 60.000 0.00 0.00 0.00 4.00
1855 1979 5.989777 ACAAAACCAACTGCTAGTACTACTG 59.010 40.000 0.00 3.66 0.00 2.74
1968 2115 2.348472 TGTGGGGAGATTTGGACTCTT 58.652 47.619 0.00 0.00 35.10 2.85
1969 2116 2.044793 TGTGGGGAGATTTGGACTCT 57.955 50.000 0.00 0.00 35.10 3.24
1972 2119 1.284785 TGGATGTGGGGAGATTTGGAC 59.715 52.381 0.00 0.00 0.00 4.02
1973 2120 1.565759 CTGGATGTGGGGAGATTTGGA 59.434 52.381 0.00 0.00 0.00 3.53
1974 2121 1.410648 CCTGGATGTGGGGAGATTTGG 60.411 57.143 0.00 0.00 0.00 3.28
1975 2122 2.025863 GCCTGGATGTGGGGAGATTTG 61.026 57.143 0.00 0.00 0.00 2.32
2059 2218 0.106335 AGCTCATCAATGGCGAGGAG 59.894 55.000 0.00 0.00 44.64 3.69
2079 2242 7.978982 TCAGATTACTAAGATTTTGCTGAAGC 58.021 34.615 0.00 0.00 42.50 3.86
2080 2243 9.766277 GTTCAGATTACTAAGATTTTGCTGAAG 57.234 33.333 0.00 0.00 39.59 3.02
2081 2244 9.507329 AGTTCAGATTACTAAGATTTTGCTGAA 57.493 29.630 0.00 0.00 37.47 3.02
2082 2245 8.939929 CAGTTCAGATTACTAAGATTTTGCTGA 58.060 33.333 0.00 0.00 0.00 4.26
2083 2246 8.725148 ACAGTTCAGATTACTAAGATTTTGCTG 58.275 33.333 0.00 0.00 0.00 4.41
2084 2247 8.854614 ACAGTTCAGATTACTAAGATTTTGCT 57.145 30.769 0.00 0.00 0.00 3.91
2085 2248 7.900352 CGACAGTTCAGATTACTAAGATTTTGC 59.100 37.037 0.00 0.00 0.00 3.68
2086 2249 9.140286 TCGACAGTTCAGATTACTAAGATTTTG 57.860 33.333 0.00 0.00 0.00 2.44
2095 2258 6.758886 GGAATCAATCGACAGTTCAGATTACT 59.241 38.462 0.00 0.00 33.75 2.24
2096 2259 6.758886 AGGAATCAATCGACAGTTCAGATTAC 59.241 38.462 0.00 0.00 33.75 1.89
2098 2261 5.583854 CAGGAATCAATCGACAGTTCAGATT 59.416 40.000 0.00 0.00 35.24 2.40
2099 2262 5.114780 CAGGAATCAATCGACAGTTCAGAT 58.885 41.667 0.00 0.00 0.00 2.90
2101 2264 3.063180 GCAGGAATCAATCGACAGTTCAG 59.937 47.826 0.00 0.00 0.00 3.02
2155 2323 9.654663 CTACAGGCTTTAATAACAAGAACTAGT 57.345 33.333 0.00 0.00 0.00 2.57
2156 2324 9.871238 TCTACAGGCTTTAATAACAAGAACTAG 57.129 33.333 0.00 0.00 0.00 2.57
2178 2347 6.456988 CGAGGTTGGCACTTAATCATTTCTAC 60.457 42.308 0.00 0.00 0.00 2.59
2180 2349 4.396166 CGAGGTTGGCACTTAATCATTTCT 59.604 41.667 0.00 0.00 0.00 2.52
2293 2462 1.451567 CCATGAGTGAGCAGCAGGG 60.452 63.158 0.00 0.00 0.00 4.45
2294 2463 1.298993 ACCATGAGTGAGCAGCAGG 59.701 57.895 0.00 0.00 0.00 4.85
2319 2496 1.018752 TTCGCATGGATGTGTCACCG 61.019 55.000 0.00 0.00 39.25 4.94
2327 2504 6.726258 TGCTACTAATATTTCGCATGGATG 57.274 37.500 0.00 0.00 0.00 3.51
2329 2506 6.288294 ACTTGCTACTAATATTTCGCATGGA 58.712 36.000 0.00 0.00 0.00 3.41
2330 2507 6.545504 ACTTGCTACTAATATTTCGCATGG 57.454 37.500 0.00 0.00 0.00 3.66
2332 2509 8.657074 TTGTACTTGCTACTAATATTTCGCAT 57.343 30.769 0.00 0.00 0.00 4.73
2333 2510 8.657074 ATTGTACTTGCTACTAATATTTCGCA 57.343 30.769 0.00 0.00 0.00 5.10
2334 2511 8.979574 AGATTGTACTTGCTACTAATATTTCGC 58.020 33.333 0.00 0.00 0.00 4.70
2341 2518 9.284968 ACAACAAAGATTGTACTTGCTACTAAT 57.715 29.630 0.00 0.00 44.59 1.73
2342 2519 8.671384 ACAACAAAGATTGTACTTGCTACTAA 57.329 30.769 0.00 0.00 44.59 2.24
2362 2578 2.293677 ACCAACGACAACAACAACAACA 59.706 40.909 0.00 0.00 0.00 3.33
2365 2581 2.552743 TCAACCAACGACAACAACAACA 59.447 40.909 0.00 0.00 0.00 3.33
2368 2584 3.440522 TCAATCAACCAACGACAACAACA 59.559 39.130 0.00 0.00 0.00 3.33
2377 2593 5.389778 TCGAATCAAATCAATCAACCAACG 58.610 37.500 0.00 0.00 0.00 4.10
2410 2637 1.520342 GGCGAACTGCTCCAGCTAG 60.520 63.158 0.00 0.00 45.43 3.42
2411 2638 2.282783 TGGCGAACTGCTCCAGCTA 61.283 57.895 0.00 0.00 45.43 3.32
2412 2639 3.630013 TGGCGAACTGCTCCAGCT 61.630 61.111 0.00 0.00 45.43 4.24
2413 2640 3.426568 GTGGCGAACTGCTCCAGC 61.427 66.667 0.00 0.00 45.43 4.85
2414 2641 2.031012 TGTGGCGAACTGCTCCAG 59.969 61.111 0.00 0.00 45.43 3.86
2416 2643 3.050275 GGTGTGGCGAACTGCTCC 61.050 66.667 0.00 0.00 45.43 4.70
2417 2644 3.414700 CGGTGTGGCGAACTGCTC 61.415 66.667 0.00 0.00 45.43 4.26
2418 2645 1.884075 TATCGGTGTGGCGAACTGCT 61.884 55.000 0.00 0.00 45.43 4.24
2419 2646 1.017177 TTATCGGTGTGGCGAACTGC 61.017 55.000 0.00 0.00 45.38 4.40
2420 2647 1.393539 CTTTATCGGTGTGGCGAACTG 59.606 52.381 0.00 0.00 0.00 3.16
2421 2648 1.722011 CTTTATCGGTGTGGCGAACT 58.278 50.000 0.00 0.00 0.00 3.01
2422 2649 0.096454 GCTTTATCGGTGTGGCGAAC 59.904 55.000 0.00 0.00 0.00 3.95
2423 2650 0.036765 AGCTTTATCGGTGTGGCGAA 60.037 50.000 0.00 0.00 0.00 4.70
2424 2651 0.459585 GAGCTTTATCGGTGTGGCGA 60.460 55.000 0.00 0.00 0.00 5.54
2425 2652 1.752501 CGAGCTTTATCGGTGTGGCG 61.753 60.000 0.00 0.00 39.04 5.69
2426 2653 0.459585 TCGAGCTTTATCGGTGTGGC 60.460 55.000 0.00 0.00 42.93 5.01
2427 2654 1.560923 CTCGAGCTTTATCGGTGTGG 58.439 55.000 0.00 0.00 42.93 4.17
2428 2655 0.924090 GCTCGAGCTTTATCGGTGTG 59.076 55.000 29.88 0.00 42.93 3.82
2429 2656 3.347411 GCTCGAGCTTTATCGGTGT 57.653 52.632 29.88 0.00 42.93 4.16
2476 2703 2.639286 CGGTGGTTGTTGCTCTGC 59.361 61.111 0.00 0.00 0.00 4.26
2477 2704 2.639286 GCGGTGGTTGTTGCTCTG 59.361 61.111 0.00 0.00 0.00 3.35
2478 2705 2.972505 CGCGGTGGTTGTTGCTCT 60.973 61.111 0.00 0.00 0.00 4.09
2479 2706 2.970324 TCGCGGTGGTTGTTGCTC 60.970 61.111 6.13 0.00 0.00 4.26
2480 2707 3.276846 GTCGCGGTGGTTGTTGCT 61.277 61.111 6.13 0.00 0.00 3.91
2503 2730 1.303643 CCAGTTCCCCAGTTCTGCC 60.304 63.158 0.00 0.00 0.00 4.85
2506 2733 1.456287 GCACCAGTTCCCCAGTTCT 59.544 57.895 0.00 0.00 0.00 3.01
2508 2735 1.990160 TTCGCACCAGTTCCCCAGTT 61.990 55.000 0.00 0.00 0.00 3.16
2509 2736 1.779061 ATTCGCACCAGTTCCCCAGT 61.779 55.000 0.00 0.00 0.00 4.00
2511 2738 0.178975 AAATTCGCACCAGTTCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
2512 2739 0.243636 CAAATTCGCACCAGTTCCCC 59.756 55.000 0.00 0.00 0.00 4.81
2513 2740 1.068541 GTCAAATTCGCACCAGTTCCC 60.069 52.381 0.00 0.00 0.00 3.97
2514 2741 1.068541 GGTCAAATTCGCACCAGTTCC 60.069 52.381 0.00 0.00 0.00 3.62
2515 2742 1.068541 GGGTCAAATTCGCACCAGTTC 60.069 52.381 3.53 0.00 31.06 3.01
2516 2743 0.958822 GGGTCAAATTCGCACCAGTT 59.041 50.000 3.53 0.00 31.06 3.16
2517 2744 1.234615 CGGGTCAAATTCGCACCAGT 61.235 55.000 3.53 0.00 31.06 4.00
2518 2745 0.953471 TCGGGTCAAATTCGCACCAG 60.953 55.000 3.53 0.13 31.06 4.00
2519 2746 0.535328 TTCGGGTCAAATTCGCACCA 60.535 50.000 3.53 0.00 31.06 4.17
2568 2795 1.203237 AGAAAGAGAGAGGTGGGAGCA 60.203 52.381 0.00 0.00 0.00 4.26
2634 2866 9.213799 CCCTCTCAAAGCATAGATAATAGAAAC 57.786 37.037 0.00 0.00 0.00 2.78
2635 2867 8.378565 CCCCTCTCAAAGCATAGATAATAGAAA 58.621 37.037 0.00 0.00 0.00 2.52
2637 2869 7.019388 ACCCCTCTCAAAGCATAGATAATAGA 58.981 38.462 0.00 0.00 0.00 1.98
2638 2870 7.251321 ACCCCTCTCAAAGCATAGATAATAG 57.749 40.000 0.00 0.00 0.00 1.73
2641 2873 7.633018 AATACCCCTCTCAAAGCATAGATAA 57.367 36.000 0.00 0.00 0.00 1.75
2669 2901 4.525874 TCCAATGCCACAATTGAATACACA 59.474 37.500 13.59 1.90 39.46 3.72


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

AutoCloner maintained by Alex Coulton.