Multiple sequence alignment - TraesCS5B01G076100

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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 TraesCS5B01G076100 chr5B 100.000 2318 0 0 1 2318 91107881 91110198 0.000000e+00 4281
1 TraesCS5B01G076100 chr5B 83.839 1219 130 30 407 1601 90987751 90988926 0.000000e+00 1098
2 TraesCS5B01G076100 chr5A 86.354 2257 186 63 1 2223 78473502 78475670 0.000000e+00 2350
3 TraesCS5B01G076100 chr5A 85.177 1329 157 21 313 1616 78425872 78427185 0.000000e+00 1327
4 TraesCS5B01G076100 chr5A 85.618 890 103 12 724 1605 78368722 78369594 0.000000e+00 911
5 TraesCS5B01G076100 chr5A 84.459 444 43 13 283 701 78368158 78368600 4.610000e-112 414
6 TraesCS5B01G076100 chr5D 87.357 1487 128 28 745 2223 84178047 84179481 0.000000e+00 1650
7 TraesCS5B01G076100 chr5D 82.835 769 74 27 2 746 84011063 84011797 9.030000e-179 636
8 TraesCS5B01G076100 chr5D 77.287 973 162 37 469 1413 84185156 84186097 3.410000e-143 518
9 TraesCS5B01G076100 chr2D 79.956 918 143 33 723 1615 547952151 547951250 2.510000e-179 638
10 TraesCS5B01G076100 chr2D 80.272 882 134 23 699 1551 547791560 547790690 1.510000e-176 628
11 TraesCS5B01G076100 chr2D 79.457 920 148 32 723 1616 547806714 547805810 4.230000e-172 614
12 TraesCS5B01G076100 chr2B 82.930 703 98 19 726 1411 654727094 654726397 4.230000e-172 614


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 TraesCS5B01G076100 chr5B 91107881 91110198 2317 False 4281.0 4281 100.0000 1 2318 1 chr5B.!!$F2 2317
1 TraesCS5B01G076100 chr5B 90987751 90988926 1175 False 1098.0 1098 83.8390 407 1601 1 chr5B.!!$F1 1194
2 TraesCS5B01G076100 chr5A 78473502 78475670 2168 False 2350.0 2350 86.3540 1 2223 1 chr5A.!!$F2 2222
3 TraesCS5B01G076100 chr5A 78425872 78427185 1313 False 1327.0 1327 85.1770 313 1616 1 chr5A.!!$F1 1303
4 TraesCS5B01G076100 chr5A 78368158 78369594 1436 False 662.5 911 85.0385 283 1605 2 chr5A.!!$F3 1322
5 TraesCS5B01G076100 chr5D 84178047 84179481 1434 False 1650.0 1650 87.3570 745 2223 1 chr5D.!!$F2 1478
6 TraesCS5B01G076100 chr5D 84011063 84011797 734 False 636.0 636 82.8350 2 746 1 chr5D.!!$F1 744
7 TraesCS5B01G076100 chr5D 84185156 84186097 941 False 518.0 518 77.2870 469 1413 1 chr5D.!!$F3 944
8 TraesCS5B01G076100 chr2D 547951250 547952151 901 True 638.0 638 79.9560 723 1615 1 chr2D.!!$R3 892
9 TraesCS5B01G076100 chr2D 547790690 547791560 870 True 628.0 628 80.2720 699 1551 1 chr2D.!!$R1 852
10 TraesCS5B01G076100 chr2D 547805810 547806714 904 True 614.0 614 79.4570 723 1616 1 chr2D.!!$R2 893
11 TraesCS5B01G076100 chr2B 654726397 654727094 697 True 614.0 614 82.9300 726 1411 1 chr2B.!!$R1 685

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
467 497 0.454600 ATTGCTCTGCCAATGAAGCG 59.545 50.0 0.00 0.00 34.32 4.68 F
1009 1221 0.466922 ACCAGCATCCATGGCTAAGC 60.467 55.0 6.96 8.12 41.87 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1518 0.172578 CCGGTCATCACGAGCAGTTA 59.827 55.0 0.0 0.0 42.55 2.24 R
1877 2134 0.541863 TGGAATCGAAGAGGGGAAGC 59.458 55.0 0.0 0.0 43.63 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
82 89 6.621596 GCATTACTGAGCTAAAGTCCACAAAG 60.622 42.308 4.85 0.00 0.00 2.77
100 108 4.041198 ACAAAGGCTACTAGCACCTAACAA 59.959 41.667 10.27 0.00 44.75 2.83
122 130 6.472163 ACAACAAACGTCAAATGTGAATTCTC 59.528 34.615 7.05 3.61 34.87 2.87
154 162 3.070159 TCTCAAGCTATAGTGGGTGCATC 59.930 47.826 0.84 0.00 0.00 3.91
177 185 2.857152 GTCAAATGTGAAACGCTGCAAA 59.143 40.909 0.00 0.00 42.39 3.68
178 186 3.305629 GTCAAATGTGAAACGCTGCAAAA 59.694 39.130 0.00 0.00 42.39 2.44
179 187 3.928992 TCAAATGTGAAACGCTGCAAAAA 59.071 34.783 0.00 0.00 42.39 1.94
398 422 7.108847 AGAAAACATGATCCTCTTTCTCGAAT 58.891 34.615 0.00 0.00 32.25 3.34
411 435 7.905493 CCTCTTTCTCGAATACAAAATAACTGC 59.095 37.037 0.00 0.00 0.00 4.40
418 442 7.644490 TCGAATACAAAATAACTGCAAACACT 58.356 30.769 0.00 0.00 0.00 3.55
439 463 6.320164 ACACTTGATACAAGGCAAAACACTTA 59.680 34.615 14.51 0.00 0.00 2.24
452 476 6.796552 GGCAAAACACTTATTTAGCAAATTGC 59.203 34.615 10.41 10.41 45.46 3.56
467 497 0.454600 ATTGCTCTGCCAATGAAGCG 59.545 50.000 0.00 0.00 34.32 4.68
484 514 5.376625 TGAAGCGATTCCTATAATTTGGCT 58.623 37.500 11.45 0.00 0.00 4.75
494 524 4.096382 CCTATAATTTGGCTGCGAAACACT 59.904 41.667 12.01 3.23 0.00 3.55
519 550 3.440173 ACACAGAGTTTTCAGTGGTTGTG 59.560 43.478 5.32 0.00 43.04 3.33
571 602 8.777865 TCAATCTTCAAAATGTTATCTCGAGT 57.222 30.769 13.13 2.46 0.00 4.18
593 641 6.507023 AGTCGTCTTTCTTCAATGCAAAAAT 58.493 32.000 0.00 0.00 0.00 1.82
594 642 6.638468 AGTCGTCTTTCTTCAATGCAAAAATC 59.362 34.615 0.00 0.00 0.00 2.17
595 643 6.417635 GTCGTCTTTCTTCAATGCAAAAATCA 59.582 34.615 0.00 0.00 0.00 2.57
596 644 6.977502 TCGTCTTTCTTCAATGCAAAAATCAA 59.022 30.769 0.00 0.00 0.00 2.57
598 646 7.790673 CGTCTTTCTTCAATGCAAAAATCAAAG 59.209 33.333 0.00 0.00 0.00 2.77
600 648 9.381033 TCTTTCTTCAATGCAAAAATCAAAGAA 57.619 25.926 0.00 0.00 31.62 2.52
614 662 9.942850 AAAAATCAAAGAATTATTGGAATCGGT 57.057 25.926 0.00 0.00 0.00 4.69
627 675 4.002982 TGGAATCGGTGAATCACTTTCTG 58.997 43.478 13.53 0.00 35.23 3.02
682 738 6.043590 ACTCCTGATGTTGCATTATGGAGATA 59.956 38.462 20.27 0.00 41.50 1.98
693 749 6.430925 TGCATTATGGAGATATTTGCACCTAC 59.569 38.462 0.00 0.00 32.60 3.18
741 904 7.995289 TGGTATATATCTTTTTGTGGCAACTG 58.005 34.615 0.00 0.00 37.61 3.16
846 1016 3.338249 TGGTGAGTCTAATTGCTTGCTC 58.662 45.455 0.00 0.00 0.00 4.26
928 1101 3.490439 ACATTCATCTCACACACCACA 57.510 42.857 0.00 0.00 0.00 4.17
963 1136 6.603201 CCTAGCCAAGACAAAAATCTCCAATA 59.397 38.462 0.00 0.00 0.00 1.90
971 1144 6.664816 AGACAAAAATCTCCAATAGCAATCCA 59.335 34.615 0.00 0.00 0.00 3.41
1009 1221 0.466922 ACCAGCATCCATGGCTAAGC 60.467 55.000 6.96 8.12 41.87 3.09
1047 1259 1.134946 GCACTGTTGCTTGTTCTGGTT 59.865 47.619 0.00 0.00 46.17 3.67
1075 1287 1.086696 CACGGCAATAGAGGGTGTTG 58.913 55.000 0.00 0.00 0.00 3.33
1192 1404 2.597217 CGCTTGGGAAGGCCAACA 60.597 61.111 5.01 0.00 35.15 3.33
1226 1439 0.739462 CGCTACAAAGGCATCACCGA 60.739 55.000 0.00 0.00 46.52 4.69
1305 1518 4.052518 GGCCTCACCATGCCCAGT 62.053 66.667 0.00 0.00 41.97 4.00
1321 1534 2.263077 CCAGTAACTGCTCGTGATGAC 58.737 52.381 0.00 0.00 0.00 3.06
1424 1676 5.010012 AGCACTTGAAAGGTCTTATTGTTGG 59.990 40.000 0.00 0.00 0.00 3.77
1457 1709 8.899427 TTTGAATTCTCTGCCTATCTCATTAG 57.101 34.615 7.05 0.00 0.00 1.73
1459 1711 8.027524 TGAATTCTCTGCCTATCTCATTAGTT 57.972 34.615 7.05 0.00 0.00 2.24
1514 1767 4.319177 CTGGAAGTGTAAGGAGGACAAAG 58.681 47.826 0.00 0.00 0.00 2.77
1518 1771 2.372172 AGTGTAAGGAGGACAAAGGTGG 59.628 50.000 0.00 0.00 0.00 4.61
1551 1805 9.288576 TGCAGTCCCATGAATTTAATATCTTAG 57.711 33.333 0.00 0.00 0.00 2.18
1569 1823 6.614694 TCTTAGGTGGTGAGCTTGTTATTA 57.385 37.500 0.00 0.00 0.00 0.98
1589 1845 6.976636 ATTACCCAAAAGTTGTGTGTTTTG 57.023 33.333 0.00 0.00 41.39 2.44
1632 1889 8.690840 GCGATCACAAGGTAATTTAAATATTGC 58.309 33.333 0.01 0.35 0.00 3.56
1679 1936 9.149225 CATAGACATCCTTATAGTTGATTCTGC 57.851 37.037 0.00 0.00 0.00 4.26
1691 1948 6.949352 AGTTGATTCTGCTTTCTCTTCAAA 57.051 33.333 0.00 0.00 0.00 2.69
1708 1965 9.155975 TCTCTTCAAATTATTAAGTCTCACAGC 57.844 33.333 0.00 0.00 0.00 4.40
1737 1994 5.431420 TTGTTGCAAATATATGCCCTACG 57.569 39.130 0.00 0.00 45.83 3.51
1755 2012 4.747108 CCTACGAAGACATGAATCCACATC 59.253 45.833 0.00 0.00 0.00 3.06
1780 2037 6.034898 CGGTTGAAATATTTCCATTGAAGTGC 59.965 38.462 22.42 0.92 36.36 4.40
1782 2039 7.550196 GGTTGAAATATTTCCATTGAAGTGCAT 59.450 33.333 22.42 0.00 36.36 3.96
1784 2041 8.481974 TGAAATATTTCCATTGAAGTGCATTG 57.518 30.769 22.42 0.00 36.36 2.82
1802 2059 6.095440 GTGCATTGGATTGTTGGTAAGTATCT 59.905 38.462 0.00 0.00 0.00 1.98
1812 2069 7.956420 TGTTGGTAAGTATCTACAACAACAG 57.044 36.000 6.12 0.00 0.00 3.16
1818 2075 8.086522 GGTAAGTATCTACAACAACAGAAGACA 58.913 37.037 0.00 0.00 0.00 3.41
1827 2084 2.169352 ACAACAGAAGACAGACTGCACT 59.831 45.455 1.25 0.00 37.61 4.40
1836 2093 4.960938 AGACAGACTGCACTGAAACATAA 58.039 39.130 11.03 0.00 40.63 1.90
1843 2100 2.295909 TGCACTGAAACATAAGGTTGGC 59.704 45.455 0.00 0.00 40.35 4.52
1846 2103 4.379499 GCACTGAAACATAAGGTTGGCTAC 60.379 45.833 0.00 0.00 40.35 3.58
1877 2134 6.547141 ACCATGGTCATTACATTTATCACCAG 59.453 38.462 13.00 0.00 35.93 4.00
1881 2138 6.318648 TGGTCATTACATTTATCACCAGCTTC 59.681 38.462 0.00 0.00 0.00 3.86
1890 2147 1.078848 CACCAGCTTCCCCTCTTCG 60.079 63.158 0.00 0.00 0.00 3.79
1892 2149 0.618968 ACCAGCTTCCCCTCTTCGAT 60.619 55.000 0.00 0.00 0.00 3.59
1902 2159 2.945668 CCCCTCTTCGATTCCATGAAAC 59.054 50.000 0.00 0.00 0.00 2.78
1903 2160 3.370953 CCCCTCTTCGATTCCATGAAACT 60.371 47.826 0.00 0.00 0.00 2.66
1936 2193 5.582269 TCTTCGCACCAATAATCTTTGAGAG 59.418 40.000 0.00 0.00 0.00 3.20
1937 2194 5.084818 TCGCACCAATAATCTTTGAGAGA 57.915 39.130 0.00 0.00 39.13 3.10
1938 2195 5.111989 TCGCACCAATAATCTTTGAGAGAG 58.888 41.667 0.00 0.00 37.93 3.20
1942 2199 7.361201 CGCACCAATAATCTTTGAGAGAGAAAA 60.361 37.037 0.00 0.00 37.93 2.29
1987 2244 5.534407 TGAGAGCTTGTACGTGAACAAATA 58.466 37.500 0.00 0.00 38.81 1.40
2042 2299 3.378112 CGATTGGTACATTGTCATGCCTT 59.622 43.478 0.00 0.00 39.30 4.35
2044 2301 4.517952 TTGGTACATTGTCATGCCTTTG 57.482 40.909 0.00 0.00 39.30 2.77
2078 2335 6.103997 CCGCCTTATATATTACGTGACCATT 58.896 40.000 0.00 0.00 0.00 3.16
2093 2350 6.094742 ACGTGACCATTAATTGATGTAATGCA 59.905 34.615 9.16 0.00 37.54 3.96
2107 2364 4.804108 TGTAATGCAGTGCAAATACCAAC 58.196 39.130 27.87 17.30 43.62 3.77
2114 2371 4.402583 CAGTGCAAATACCAACATGTACG 58.597 43.478 0.00 0.00 34.23 3.67
2119 2376 6.256975 GTGCAAATACCAACATGTACGATCTA 59.743 38.462 0.00 0.00 0.00 1.98
2163 2422 6.925718 CACTCATGTCGTCATATATGTCCTTT 59.074 38.462 12.42 0.00 32.47 3.11
2183 2442 7.337942 GTCCTTTCTGATCATGTTCCTATTGTT 59.662 37.037 0.00 0.00 0.00 2.83
2186 2445 9.565213 CTTTCTGATCATGTTCCTATTGTTTTC 57.435 33.333 0.00 0.00 0.00 2.29
2194 2453 8.286800 TCATGTTCCTATTGTTTTCGTGTTTAG 58.713 33.333 0.00 0.00 0.00 1.85
2237 2498 9.135843 TGAATAAGATGTTTAACTACACACTCG 57.864 33.333 0.00 0.00 0.00 4.18
2238 2499 8.475331 AATAAGATGTTTAACTACACACTCGG 57.525 34.615 0.00 0.00 0.00 4.63
2239 2500 5.717078 AGATGTTTAACTACACACTCGGA 57.283 39.130 0.00 0.00 0.00 4.55
2240 2501 6.092955 AGATGTTTAACTACACACTCGGAA 57.907 37.500 0.00 0.00 0.00 4.30
2241 2502 6.157211 AGATGTTTAACTACACACTCGGAAG 58.843 40.000 0.00 0.00 0.00 3.46
2242 2503 4.624015 TGTTTAACTACACACTCGGAAGG 58.376 43.478 0.00 0.00 0.00 3.46
2243 2504 3.947910 TTAACTACACACTCGGAAGGG 57.052 47.619 0.00 0.00 37.84 3.95
2244 2505 2.005370 AACTACACACTCGGAAGGGA 57.995 50.000 0.00 0.00 33.92 4.20
2245 2506 2.005370 ACTACACACTCGGAAGGGAA 57.995 50.000 0.00 0.00 33.92 3.97
2246 2507 2.537143 ACTACACACTCGGAAGGGAAT 58.463 47.619 0.00 0.00 33.92 3.01
2247 2508 2.233922 ACTACACACTCGGAAGGGAATG 59.766 50.000 0.00 0.00 33.92 2.67
2248 2509 1.056660 ACACACTCGGAAGGGAATGT 58.943 50.000 0.00 0.00 33.92 2.71
2249 2510 1.420138 ACACACTCGGAAGGGAATGTT 59.580 47.619 0.00 0.00 30.92 2.71
2250 2511 1.806542 CACACTCGGAAGGGAATGTTG 59.193 52.381 0.00 0.00 33.92 3.33
2251 2512 0.804989 CACTCGGAAGGGAATGTTGC 59.195 55.000 0.00 0.00 33.92 4.17
2252 2513 0.693049 ACTCGGAAGGGAATGTTGCT 59.307 50.000 0.00 0.00 33.92 3.91
2253 2514 1.073923 ACTCGGAAGGGAATGTTGCTT 59.926 47.619 0.00 0.00 33.92 3.91
2254 2515 2.304761 ACTCGGAAGGGAATGTTGCTTA 59.695 45.455 0.00 0.00 33.92 3.09
2255 2516 3.054361 ACTCGGAAGGGAATGTTGCTTAT 60.054 43.478 0.00 0.00 33.92 1.73
2256 2517 4.163458 ACTCGGAAGGGAATGTTGCTTATA 59.837 41.667 0.00 0.00 33.92 0.98
2257 2518 5.105567 TCGGAAGGGAATGTTGCTTATAA 57.894 39.130 0.00 0.00 0.00 0.98
2258 2519 5.690865 TCGGAAGGGAATGTTGCTTATAAT 58.309 37.500 0.00 0.00 0.00 1.28
2259 2520 6.126409 TCGGAAGGGAATGTTGCTTATAATT 58.874 36.000 0.00 0.00 0.00 1.40
2260 2521 6.605594 TCGGAAGGGAATGTTGCTTATAATTT 59.394 34.615 0.00 0.00 0.00 1.82
2261 2522 7.776030 TCGGAAGGGAATGTTGCTTATAATTTA 59.224 33.333 0.00 0.00 0.00 1.40
2262 2523 8.576442 CGGAAGGGAATGTTGCTTATAATTTAT 58.424 33.333 0.00 0.00 0.00 1.40
2291 2552 9.956640 ACTAAATCATTCTCTCTTTGTCATTCT 57.043 29.630 0.00 0.00 0.00 2.40
2296 2557 8.640091 TCATTCTCTCTTTGTCATTCTTATCG 57.360 34.615 0.00 0.00 0.00 2.92
2297 2558 7.708322 TCATTCTCTCTTTGTCATTCTTATCGG 59.292 37.037 0.00 0.00 0.00 4.18
2298 2559 6.531503 TCTCTCTTTGTCATTCTTATCGGT 57.468 37.500 0.00 0.00 0.00 4.69
2299 2560 6.333416 TCTCTCTTTGTCATTCTTATCGGTG 58.667 40.000 0.00 0.00 0.00 4.94
2300 2561 5.419542 TCTCTTTGTCATTCTTATCGGTGG 58.580 41.667 0.00 0.00 0.00 4.61
2301 2562 5.046591 TCTCTTTGTCATTCTTATCGGTGGT 60.047 40.000 0.00 0.00 0.00 4.16
2302 2563 5.556915 TCTTTGTCATTCTTATCGGTGGTT 58.443 37.500 0.00 0.00 0.00 3.67
2303 2564 6.703319 TCTTTGTCATTCTTATCGGTGGTTA 58.297 36.000 0.00 0.00 0.00 2.85
2304 2565 7.335627 TCTTTGTCATTCTTATCGGTGGTTAT 58.664 34.615 0.00 0.00 0.00 1.89
2305 2566 7.827236 TCTTTGTCATTCTTATCGGTGGTTATT 59.173 33.333 0.00 0.00 0.00 1.40
2306 2567 7.931578 TTGTCATTCTTATCGGTGGTTATTT 57.068 32.000 0.00 0.00 0.00 1.40
2307 2568 7.931578 TGTCATTCTTATCGGTGGTTATTTT 57.068 32.000 0.00 0.00 0.00 1.82
2308 2569 8.343168 TGTCATTCTTATCGGTGGTTATTTTT 57.657 30.769 0.00 0.00 0.00 1.94
2309 2570 8.455682 TGTCATTCTTATCGGTGGTTATTTTTC 58.544 33.333 0.00 0.00 0.00 2.29
2310 2571 8.455682 GTCATTCTTATCGGTGGTTATTTTTCA 58.544 33.333 0.00 0.00 0.00 2.69
2311 2572 9.184523 TCATTCTTATCGGTGGTTATTTTTCAT 57.815 29.630 0.00 0.00 0.00 2.57
2312 2573 9.236691 CATTCTTATCGGTGGTTATTTTTCATG 57.763 33.333 0.00 0.00 0.00 3.07
2313 2574 6.791303 TCTTATCGGTGGTTATTTTTCATGC 58.209 36.000 0.00 0.00 0.00 4.06
2314 2575 6.601613 TCTTATCGGTGGTTATTTTTCATGCT 59.398 34.615 0.00 0.00 0.00 3.79
2315 2576 4.695217 TCGGTGGTTATTTTTCATGCTC 57.305 40.909 0.00 0.00 0.00 4.26
2316 2577 4.075682 TCGGTGGTTATTTTTCATGCTCA 58.924 39.130 0.00 0.00 0.00 4.26
2317 2578 4.155826 TCGGTGGTTATTTTTCATGCTCAG 59.844 41.667 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 89 3.604875 TGTTGTTAGGTGCTAGTAGCC 57.395 47.619 19.41 10.43 41.51 3.93
100 108 6.130298 TGAGAATTCACATTTGACGTTTGT 57.870 33.333 8.44 0.00 0.00 2.83
122 130 7.655328 CCCACTATAGCTTGAGATACTTTCTTG 59.345 40.741 0.00 0.00 33.74 3.02
154 162 1.673760 CAGCGTTTCACATTTGACGG 58.326 50.000 0.00 0.00 0.00 4.79
195 203 7.608761 TGGCCTGTTTCTCGTTAATTAATTAGT 59.391 33.333 3.32 0.00 0.00 2.24
214 222 1.073025 TTCTGCGACATTGGCCTGT 59.927 52.632 3.32 0.00 0.00 4.00
384 408 9.151471 CAGTTATTTTGTATTCGAGAAAGAGGA 57.849 33.333 0.00 0.00 0.00 3.71
398 422 9.672086 GTATCAAGTGTTTGCAGTTATTTTGTA 57.328 29.630 0.00 0.00 36.56 2.41
411 435 5.809562 TGTTTTGCCTTGTATCAAGTGTTTG 59.190 36.000 8.37 0.00 35.57 2.93
418 442 9.906660 CTAAATAAGTGTTTTGCCTTGTATCAA 57.093 29.630 0.00 0.00 0.00 2.57
452 476 1.332997 GGAATCGCTTCATTGGCAGAG 59.667 52.381 0.92 0.00 32.70 3.35
458 482 6.583806 GCCAAATTATAGGAATCGCTTCATTG 59.416 38.462 0.92 0.00 32.70 2.82
467 497 5.689383 TTCGCAGCCAAATTATAGGAATC 57.311 39.130 0.00 0.00 0.00 2.52
494 524 2.167693 ACCACTGAAAACTCTGTGTCGA 59.832 45.455 10.14 0.00 37.71 4.20
496 526 3.689649 ACAACCACTGAAAACTCTGTGTC 59.310 43.478 10.14 0.00 37.71 3.67
501 531 6.828785 AGATTAACACAACCACTGAAAACTCT 59.171 34.615 0.00 0.00 0.00 3.24
567 598 2.731451 TGCATTGAAGAAAGACGACTCG 59.269 45.455 0.00 0.00 0.00 4.18
571 602 6.502652 TGATTTTTGCATTGAAGAAAGACGA 58.497 32.000 0.00 0.00 0.00 4.20
593 641 7.695480 TTCACCGATTCCAATAATTCTTTGA 57.305 32.000 3.29 0.00 0.00 2.69
594 642 8.190122 TGATTCACCGATTCCAATAATTCTTTG 58.810 33.333 0.00 0.00 0.00 2.77
595 643 8.190784 GTGATTCACCGATTCCAATAATTCTTT 58.809 33.333 5.44 0.00 0.00 2.52
596 644 7.557719 AGTGATTCACCGATTCCAATAATTCTT 59.442 33.333 13.14 0.00 34.49 2.52
598 646 7.264373 AGTGATTCACCGATTCCAATAATTC 57.736 36.000 13.14 0.00 34.49 2.17
600 648 7.557719 AGAAAGTGATTCACCGATTCCAATAAT 59.442 33.333 13.14 0.00 40.72 1.28
601 649 6.884295 AGAAAGTGATTCACCGATTCCAATAA 59.116 34.615 13.14 0.00 40.72 1.40
602 650 6.316140 CAGAAAGTGATTCACCGATTCCAATA 59.684 38.462 13.14 0.00 40.72 1.90
603 651 5.124457 CAGAAAGTGATTCACCGATTCCAAT 59.876 40.000 13.14 0.00 40.72 3.16
604 652 4.455533 CAGAAAGTGATTCACCGATTCCAA 59.544 41.667 13.14 0.00 40.72 3.53
605 653 4.002982 CAGAAAGTGATTCACCGATTCCA 58.997 43.478 13.14 0.00 40.72 3.53
606 654 4.003648 ACAGAAAGTGATTCACCGATTCC 58.996 43.478 13.14 0.00 40.72 3.01
607 655 4.690748 TGACAGAAAGTGATTCACCGATTC 59.309 41.667 13.14 14.16 40.72 2.52
611 659 4.715896 CAATGACAGAAAGTGATTCACCG 58.284 43.478 13.14 0.52 40.72 4.94
613 661 4.083855 TCGCAATGACAGAAAGTGATTCAC 60.084 41.667 8.82 8.82 40.72 3.18
614 662 4.064388 TCGCAATGACAGAAAGTGATTCA 58.936 39.130 0.00 0.00 40.72 2.57
627 675 1.732259 AGACCAATTCGTCGCAATGAC 59.268 47.619 0.00 0.00 44.53 3.06
718 779 7.915397 CCACAGTTGCCACAAAAAGATATATAC 59.085 37.037 0.00 0.00 0.00 1.47
732 895 0.249741 ACGACTACCACAGTTGCCAC 60.250 55.000 0.00 0.00 41.83 5.01
741 904 5.063060 GGTGTTGAATGATAACGACTACCAC 59.937 44.000 0.00 0.00 0.00 4.16
830 1000 2.005451 CAGCGAGCAAGCAATTAGACT 58.995 47.619 6.21 0.00 40.15 3.24
846 1016 6.232139 TCATGAAATGTATATTCTGCAGCG 57.768 37.500 9.47 0.00 46.80 5.18
858 1028 5.754782 AGGCACCTATGTTCATGAAATGTA 58.245 37.500 10.35 2.92 46.80 2.29
936 1109 4.396478 GGAGATTTTTGTCTTGGCTAGGTC 59.604 45.833 0.00 0.00 0.00 3.85
944 1117 7.490402 GGATTGCTATTGGAGATTTTTGTCTTG 59.510 37.037 0.00 0.00 0.00 3.02
948 1121 6.438425 AGTGGATTGCTATTGGAGATTTTTGT 59.562 34.615 0.00 0.00 0.00 2.83
950 1123 8.055181 TCTAGTGGATTGCTATTGGAGATTTTT 58.945 33.333 0.00 0.00 0.00 1.94
1059 1271 2.301346 CCATCAACACCCTCTATTGCC 58.699 52.381 0.00 0.00 0.00 4.52
1075 1287 0.666913 GACATGCCACAGATGCCATC 59.333 55.000 0.00 0.00 0.00 3.51
1134 1346 2.650322 GGACTGTCTGTTGGGTTTTCA 58.350 47.619 7.85 0.00 0.00 2.69
1192 1404 3.009026 TGTAGCGACAAATGCATGACAT 58.991 40.909 0.00 0.00 42.30 3.06
1226 1439 3.071602 GTGGTACATCCTCAGCCATATGT 59.928 47.826 1.24 0.00 44.52 2.29
1305 1518 0.172578 CCGGTCATCACGAGCAGTTA 59.827 55.000 0.00 0.00 42.55 2.24
1321 1534 0.320771 GCTATGGATAGTGCACCCGG 60.321 60.000 14.63 0.00 32.96 5.73
1424 1676 4.217118 AGGCAGAGAATTCAAATCACACAC 59.783 41.667 8.44 0.00 0.00 3.82
1482 1734 9.529823 CCTCCTTACACTTCCAGTATACATATA 57.470 37.037 5.50 0.00 0.00 0.86
1483 1735 8.232412 TCCTCCTTACACTTCCAGTATACATAT 58.768 37.037 5.50 0.00 0.00 1.78
1514 1767 2.570181 GACTGCATGCAAGCCACC 59.430 61.111 22.88 3.56 0.00 4.61
1518 1771 1.141019 CATGGGACTGCATGCAAGC 59.859 57.895 22.88 15.75 0.00 4.01
1551 1805 3.014623 GGGTAATAACAAGCTCACCACC 58.985 50.000 0.00 0.00 0.00 4.61
1589 1845 6.855914 TGTGATCGCTTTTTACTTGTTCATTC 59.144 34.615 7.94 0.00 0.00 2.67
1632 1889 1.869767 GGCCGCTCTGATAGTTGATTG 59.130 52.381 0.00 0.00 0.00 2.67
1646 1903 1.056700 AAGGATGTCTATGGGCCGCT 61.057 55.000 0.00 0.00 0.00 5.52
1691 1948 9.113838 CAATAGGTTGCTGTGAGACTTAATAAT 57.886 33.333 0.00 0.00 0.00 1.28
1720 1977 4.994852 TGTCTTCGTAGGGCATATATTTGC 59.005 41.667 9.42 9.42 42.01 3.68
1737 1994 3.535561 ACCGATGTGGATTCATGTCTTC 58.464 45.455 0.00 0.00 42.00 2.87
1755 2012 6.034898 GCACTTCAATGGAAATATTTCAACCG 59.965 38.462 25.55 12.15 38.92 4.44
1780 2037 8.731275 TGTAGATACTTACCAACAATCCAATG 57.269 34.615 0.00 0.00 0.00 2.82
1782 2039 8.158132 TGTTGTAGATACTTACCAACAATCCAA 58.842 33.333 0.00 0.00 29.78 3.53
1784 2041 8.448615 GTTGTTGTAGATACTTACCAACAATCC 58.551 37.037 16.33 4.63 37.17 3.01
1802 2059 4.119862 GCAGTCTGTCTTCTGTTGTTGTA 58.880 43.478 0.93 0.00 34.57 2.41
1812 2069 3.198068 TGTTTCAGTGCAGTCTGTCTTC 58.802 45.455 0.93 0.00 36.85 2.87
1818 2075 4.357918 ACCTTATGTTTCAGTGCAGTCT 57.642 40.909 0.00 0.00 0.00 3.24
1827 2084 4.720046 TGTGTAGCCAACCTTATGTTTCA 58.280 39.130 0.00 0.00 34.00 2.69
1836 2093 1.064003 TGGTCATGTGTAGCCAACCT 58.936 50.000 0.00 0.00 0.00 3.50
1869 2126 2.119495 GAAGAGGGGAAGCTGGTGATA 58.881 52.381 0.00 0.00 0.00 2.15
1877 2134 0.541863 TGGAATCGAAGAGGGGAAGC 59.458 55.000 0.00 0.00 43.63 3.86
1881 2138 2.945668 GTTTCATGGAATCGAAGAGGGG 59.054 50.000 0.00 0.00 43.63 4.79
1890 2147 3.334691 TGACACCGAGTTTCATGGAATC 58.665 45.455 0.00 0.00 0.00 2.52
1892 2149 2.920724 TGACACCGAGTTTCATGGAA 57.079 45.000 0.00 0.00 0.00 3.53
1902 2159 1.078759 GGTGCGAAGATGACACCGAG 61.079 60.000 0.00 0.00 44.02 4.63
1903 2160 1.080093 GGTGCGAAGATGACACCGA 60.080 57.895 0.00 0.00 44.02 4.69
2000 2257 2.084546 GAGGAACGCCAATAAACTGCT 58.915 47.619 0.00 0.00 36.29 4.24
2001 2258 1.202031 CGAGGAACGCCAATAAACTGC 60.202 52.381 0.00 0.00 36.29 4.40
2044 2301 9.443283 CGTAATATATAAGGCGGTGAAGTATAC 57.557 37.037 0.00 0.00 0.00 1.47
2069 2326 6.493978 TGCATTACATCAATTAATGGTCACG 58.506 36.000 0.00 0.00 37.39 4.35
2078 2335 7.920151 GGTATTTGCACTGCATTACATCAATTA 59.080 33.333 18.94 0.00 38.76 1.40
2082 2339 4.704057 TGGTATTTGCACTGCATTACATCA 59.296 37.500 18.94 10.63 38.76 3.07
2083 2340 5.247507 TGGTATTTGCACTGCATTACATC 57.752 39.130 18.94 8.96 38.76 3.06
2084 2341 5.047448 TGTTGGTATTTGCACTGCATTACAT 60.047 36.000 18.94 8.12 38.76 2.29
2085 2342 4.279420 TGTTGGTATTTGCACTGCATTACA 59.721 37.500 18.94 8.00 38.76 2.41
2086 2343 4.804108 TGTTGGTATTTGCACTGCATTAC 58.196 39.130 4.10 9.79 38.76 1.89
2090 2347 2.627221 ACATGTTGGTATTTGCACTGCA 59.373 40.909 0.00 0.00 36.47 4.41
2093 2350 4.320023 TCGTACATGTTGGTATTTGCACT 58.680 39.130 2.30 0.00 0.00 4.40
2124 2381 8.178313 ACGACATGAGTGATAATCTATTGGTA 57.822 34.615 0.00 0.00 0.00 3.25
2136 2393 6.435591 AGGACATATATGACGACATGAGTGAT 59.564 38.462 19.63 1.39 37.87 3.06
2137 2394 5.770162 AGGACATATATGACGACATGAGTGA 59.230 40.000 19.63 0.00 37.87 3.41
2139 2396 6.656632 AAGGACATATATGACGACATGAGT 57.343 37.500 19.63 0.00 37.87 3.41
2163 2422 6.878923 ACGAAAACAATAGGAACATGATCAGA 59.121 34.615 0.00 0.00 0.00 3.27
2223 2484 3.499338 TCCCTTCCGAGTGTGTAGTTAA 58.501 45.455 0.00 0.00 0.00 2.01
2224 2485 3.159213 TCCCTTCCGAGTGTGTAGTTA 57.841 47.619 0.00 0.00 0.00 2.24
2225 2486 2.005370 TCCCTTCCGAGTGTGTAGTT 57.995 50.000 0.00 0.00 0.00 2.24
2226 2487 2.005370 TTCCCTTCCGAGTGTGTAGT 57.995 50.000 0.00 0.00 0.00 2.73
2227 2488 2.233922 ACATTCCCTTCCGAGTGTGTAG 59.766 50.000 0.00 0.00 32.11 2.74
2228 2489 2.253610 ACATTCCCTTCCGAGTGTGTA 58.746 47.619 0.00 0.00 32.11 2.90
2229 2490 1.056660 ACATTCCCTTCCGAGTGTGT 58.943 50.000 0.00 0.00 32.11 3.72
2230 2491 1.806542 CAACATTCCCTTCCGAGTGTG 59.193 52.381 0.00 0.00 33.47 3.82
2231 2492 1.882352 GCAACATTCCCTTCCGAGTGT 60.882 52.381 0.00 0.00 34.50 3.55
2232 2493 0.804989 GCAACATTCCCTTCCGAGTG 59.195 55.000 0.00 0.00 0.00 3.51
2233 2494 0.693049 AGCAACATTCCCTTCCGAGT 59.307 50.000 0.00 0.00 0.00 4.18
2234 2495 1.826385 AAGCAACATTCCCTTCCGAG 58.174 50.000 0.00 0.00 0.00 4.63
2235 2496 3.644966 ATAAGCAACATTCCCTTCCGA 57.355 42.857 0.00 0.00 0.00 4.55
2236 2497 6.391227 AATTATAAGCAACATTCCCTTCCG 57.609 37.500 0.00 0.00 0.00 4.30
2265 2526 9.956640 AGAATGACAAAGAGAGAATGATTTAGT 57.043 29.630 0.00 0.00 0.00 2.24
2270 2531 9.258826 CGATAAGAATGACAAAGAGAGAATGAT 57.741 33.333 0.00 0.00 0.00 2.45
2271 2532 7.708322 CCGATAAGAATGACAAAGAGAGAATGA 59.292 37.037 0.00 0.00 0.00 2.57
2272 2533 7.493971 ACCGATAAGAATGACAAAGAGAGAATG 59.506 37.037 0.00 0.00 0.00 2.67
2273 2534 7.493971 CACCGATAAGAATGACAAAGAGAGAAT 59.506 37.037 0.00 0.00 0.00 2.40
2274 2535 6.813649 CACCGATAAGAATGACAAAGAGAGAA 59.186 38.462 0.00 0.00 0.00 2.87
2275 2536 6.333416 CACCGATAAGAATGACAAAGAGAGA 58.667 40.000 0.00 0.00 0.00 3.10
2276 2537 5.521735 CCACCGATAAGAATGACAAAGAGAG 59.478 44.000 0.00 0.00 0.00 3.20
2277 2538 5.046591 ACCACCGATAAGAATGACAAAGAGA 60.047 40.000 0.00 0.00 0.00 3.10
2278 2539 5.178797 ACCACCGATAAGAATGACAAAGAG 58.821 41.667 0.00 0.00 0.00 2.85
2279 2540 5.160607 ACCACCGATAAGAATGACAAAGA 57.839 39.130 0.00 0.00 0.00 2.52
2280 2541 5.880054 AACCACCGATAAGAATGACAAAG 57.120 39.130 0.00 0.00 0.00 2.77
2281 2542 7.931578 AATAACCACCGATAAGAATGACAAA 57.068 32.000 0.00 0.00 0.00 2.83
2282 2543 7.931578 AAATAACCACCGATAAGAATGACAA 57.068 32.000 0.00 0.00 0.00 3.18
2283 2544 7.931578 AAAATAACCACCGATAAGAATGACA 57.068 32.000 0.00 0.00 0.00 3.58
2284 2545 8.455682 TGAAAAATAACCACCGATAAGAATGAC 58.544 33.333 0.00 0.00 0.00 3.06
2285 2546 8.568676 TGAAAAATAACCACCGATAAGAATGA 57.431 30.769 0.00 0.00 0.00 2.57
2286 2547 9.236691 CATGAAAAATAACCACCGATAAGAATG 57.763 33.333 0.00 0.00 0.00 2.67
2287 2548 7.920682 GCATGAAAAATAACCACCGATAAGAAT 59.079 33.333 0.00 0.00 0.00 2.40
2288 2549 7.122055 AGCATGAAAAATAACCACCGATAAGAA 59.878 33.333 0.00 0.00 0.00 2.52
2289 2550 6.601613 AGCATGAAAAATAACCACCGATAAGA 59.398 34.615 0.00 0.00 0.00 2.10
2290 2551 6.795399 AGCATGAAAAATAACCACCGATAAG 58.205 36.000 0.00 0.00 0.00 1.73
2291 2552 6.375736 TGAGCATGAAAAATAACCACCGATAA 59.624 34.615 0.00 0.00 0.00 1.75
2292 2553 5.883115 TGAGCATGAAAAATAACCACCGATA 59.117 36.000 0.00 0.00 0.00 2.92
2293 2554 4.704540 TGAGCATGAAAAATAACCACCGAT 59.295 37.500 0.00 0.00 0.00 4.18
2294 2555 4.075682 TGAGCATGAAAAATAACCACCGA 58.924 39.130 0.00 0.00 0.00 4.69
2295 2556 4.414852 CTGAGCATGAAAAATAACCACCG 58.585 43.478 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.