Multiple sequence alignment - TraesCS1B01G113500

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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 TraesCS1B01G113500 chr1B 100.000 2762 0 0 1 2762 132937251 132940012 0.000000e+00 5101.0
1 TraesCS1B01G113500 chr1B 89.095 807 76 8 989 1795 133032480 133033274 0.000000e+00 992.0
2 TraesCS1B01G113500 chr1B 84.518 788 107 12 990 1769 133075666 133076446 0.000000e+00 765.0
3 TraesCS1B01G113500 chr1B 87.263 581 67 6 2181 2757 54024968 54024391 0.000000e+00 656.0
4 TraesCS1B01G113500 chr1B 86.964 583 70 6 2180 2757 54018575 54017994 0.000000e+00 651.0
5 TraesCS1B01G113500 chr1D 91.779 2080 98 41 1 2068 80447324 80449342 0.000000e+00 2826.0
6 TraesCS1B01G113500 chr1D 86.439 848 86 18 974 1795 80537065 80537909 0.000000e+00 902.0
7 TraesCS1B01G113500 chr1D 83.718 866 110 22 914 1769 80540915 80541759 0.000000e+00 789.0
8 TraesCS1B01G113500 chr1D 83.420 772 111 14 1000 1766 80817018 80817777 0.000000e+00 701.0
9 TraesCS1B01G113500 chr1D 87.091 581 70 4 2181 2757 79928210 79928789 0.000000e+00 652.0
10 TraesCS1B01G113500 chr1D 77.778 108 21 3 1936 2042 19263739 19263634 2.300000e-06 63.9
11 TraesCS1B01G113500 chr1A 90.734 2126 113 34 1 2088 99017610 99019689 0.000000e+00 2758.0
12 TraesCS1B01G113500 chr1A 86.594 828 88 12 974 1795 99048751 99049561 0.000000e+00 893.0
13 TraesCS1B01G113500 chr1A 83.141 866 118 18 916 1769 99071033 99071882 0.000000e+00 765.0
14 TraesCS1B01G113500 chr1A 83.355 775 105 20 1000 1766 99234402 99235160 0.000000e+00 695.0
15 TraesCS1B01G113500 chr1A 78.704 108 20 3 1936 2042 21039721 21039616 4.940000e-08 69.4
16 TraesCS1B01G113500 chr3B 87.973 582 64 5 2181 2757 629810786 629811366 0.000000e+00 682.0
17 TraesCS1B01G113500 chr3B 87.713 586 65 6 2175 2754 407543060 407543644 0.000000e+00 676.0
18 TraesCS1B01G113500 chr3D 87.826 575 64 5 2180 2749 276399201 276398628 0.000000e+00 669.0
19 TraesCS1B01G113500 chr7B 82.391 778 121 15 1000 1767 95337271 95338042 0.000000e+00 664.0
20 TraesCS1B01G113500 chr7B 87.414 580 65 7 2181 2754 292639832 292640409 0.000000e+00 660.0
21 TraesCS1B01G113500 chr5B 87.091 581 70 5 2181 2757 31067688 31067109 0.000000e+00 652.0
22 TraesCS1B01G113500 chr4A 87.069 580 69 6 2180 2754 710617564 710618142 0.000000e+00 651.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G113500 chr1B 132937251 132940012 2761 False 5101.0 5101 100.0000 1 2762 1 chr1B.!!$F1 2761
1 TraesCS1B01G113500 chr1B 133032480 133033274 794 False 992.0 992 89.0950 989 1795 1 chr1B.!!$F2 806
2 TraesCS1B01G113500 chr1B 133075666 133076446 780 False 765.0 765 84.5180 990 1769 1 chr1B.!!$F3 779
3 TraesCS1B01G113500 chr1B 54024391 54024968 577 True 656.0 656 87.2630 2181 2757 1 chr1B.!!$R2 576
4 TraesCS1B01G113500 chr1B 54017994 54018575 581 True 651.0 651 86.9640 2180 2757 1 chr1B.!!$R1 577
5 TraesCS1B01G113500 chr1D 80447324 80449342 2018 False 2826.0 2826 91.7790 1 2068 1 chr1D.!!$F2 2067
6 TraesCS1B01G113500 chr1D 80537065 80541759 4694 False 845.5 902 85.0785 914 1795 2 chr1D.!!$F4 881
7 TraesCS1B01G113500 chr1D 80817018 80817777 759 False 701.0 701 83.4200 1000 1766 1 chr1D.!!$F3 766
8 TraesCS1B01G113500 chr1D 79928210 79928789 579 False 652.0 652 87.0910 2181 2757 1 chr1D.!!$F1 576
9 TraesCS1B01G113500 chr1A 99017610 99019689 2079 False 2758.0 2758 90.7340 1 2088 1 chr1A.!!$F1 2087
10 TraesCS1B01G113500 chr1A 99048751 99049561 810 False 893.0 893 86.5940 974 1795 1 chr1A.!!$F2 821
11 TraesCS1B01G113500 chr1A 99071033 99071882 849 False 765.0 765 83.1410 916 1769 1 chr1A.!!$F3 853
12 TraesCS1B01G113500 chr1A 99234402 99235160 758 False 695.0 695 83.3550 1000 1766 1 chr1A.!!$F4 766
13 TraesCS1B01G113500 chr3B 629810786 629811366 580 False 682.0 682 87.9730 2181 2757 1 chr3B.!!$F2 576
14 TraesCS1B01G113500 chr3B 407543060 407543644 584 False 676.0 676 87.7130 2175 2754 1 chr3B.!!$F1 579
15 TraesCS1B01G113500 chr3D 276398628 276399201 573 True 669.0 669 87.8260 2180 2749 1 chr3D.!!$R1 569
16 TraesCS1B01G113500 chr7B 95337271 95338042 771 False 664.0 664 82.3910 1000 1767 1 chr7B.!!$F1 767
17 TraesCS1B01G113500 chr7B 292639832 292640409 577 False 660.0 660 87.4140 2181 2754 1 chr7B.!!$F2 573
18 TraesCS1B01G113500 chr5B 31067109 31067688 579 True 652.0 652 87.0910 2181 2757 1 chr5B.!!$R1 576
19 TraesCS1B01G113500 chr4A 710617564 710618142 578 False 651.0 651 87.0690 2180 2754 1 chr4A.!!$F1 574

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
964 993 0.173481 CGTCCATCTCCAAGAAGCGA 59.827 55.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2335 0.040425 GGCACAAAGATTGTTCGCGT 60.04 50.0 5.77 0.0 43.23 6.01 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
129 131 6.882610 TGTTTCTTTATGACATGTGAGCTT 57.117 33.333 1.15 0.00 0.00 3.74
149 151 4.435651 GCTTACTGCGTAACATCTTGTTCC 60.436 45.833 0.00 0.00 40.22 3.62
187 189 1.338655 GATCTTCCTCTGGAGCCGTAC 59.661 57.143 0.00 0.00 31.21 3.67
274 276 0.657840 GGATGATCCTTTTCGCCACG 59.342 55.000 3.71 0.00 32.53 4.94
301 303 5.396548 CCTGGAGAACATCAGAGATGTCATT 60.397 44.000 12.53 0.00 33.11 2.57
473 475 8.978564 ATATCATTTGATATGTCTCGTGTCTC 57.021 34.615 11.36 0.00 43.85 3.36
482 484 1.068748 GTCTCGTGTCTCGGCTTGTTA 60.069 52.381 0.00 0.00 40.32 2.41
556 558 9.717942 AGTATTATTGGTCATTAGCATCTTCTC 57.282 33.333 0.00 0.00 32.06 2.87
605 608 4.457603 TGTTTGTATCTTATGCCGCAAACT 59.542 37.500 15.66 0.00 43.24 2.66
634 637 6.715347 ACTGTTTTGAAGATGCCTTAGTTT 57.285 33.333 0.00 0.00 31.62 2.66
681 688 0.679640 TTCGCCCACAATAGCCCAAG 60.680 55.000 0.00 0.00 0.00 3.61
683 690 1.758122 GCCCACAATAGCCCAAGGG 60.758 63.158 0.00 0.00 39.33 3.95
686 693 0.748005 CCACAATAGCCCAAGGGTCG 60.748 60.000 7.05 0.00 37.65 4.79
834 863 4.386711 TCATAGTACGACGATGTGGATCT 58.613 43.478 0.00 0.00 33.69 2.75
881 910 4.280494 AAGCAGTGACGCGTCGGT 62.280 61.111 31.88 21.14 36.85 4.69
913 942 3.454371 ACCAACTCCGCTATGTGTATC 57.546 47.619 0.00 0.00 0.00 2.24
964 993 0.173481 CGTCCATCTCCAAGAAGCGA 59.827 55.000 0.00 0.00 0.00 4.93
1240 1273 3.891422 ACCTCTCTTCTCTTCTGCATG 57.109 47.619 0.00 0.00 0.00 4.06
1250 1317 4.464008 TCTCTTCTGCATGGAAAACTTGT 58.536 39.130 0.00 0.00 0.00 3.16
1252 1319 6.240894 TCTCTTCTGCATGGAAAACTTGTAT 58.759 36.000 0.00 0.00 0.00 2.29
1253 1320 7.394016 TCTCTTCTGCATGGAAAACTTGTATA 58.606 34.615 0.00 0.00 0.00 1.47
1254 1321 7.334421 TCTCTTCTGCATGGAAAACTTGTATAC 59.666 37.037 0.00 0.00 0.00 1.47
1256 1323 5.242434 TCTGCATGGAAAACTTGTATACGT 58.758 37.500 0.00 0.00 0.00 3.57
1257 1324 6.399743 TCTGCATGGAAAACTTGTATACGTA 58.600 36.000 0.00 0.00 0.00 3.57
1258 1325 6.311935 TCTGCATGGAAAACTTGTATACGTAC 59.688 38.462 0.00 0.00 0.00 3.67
1691 1786 2.936032 GTGGGAGGGGCTCAAGGT 60.936 66.667 0.00 0.00 31.08 3.50
1734 1829 4.615815 GAGCTCATGCCGCCGGAT 62.616 66.667 7.68 0.00 40.80 4.18
1769 1864 4.464069 AGAAAGCAGAGTAGTGATGACC 57.536 45.455 0.00 0.00 0.00 4.02
1816 1911 2.139917 CCACGTTCACCAAAATCGAGA 58.860 47.619 0.00 0.00 0.00 4.04
1835 1947 0.597072 AACTGTCGAGTCTCCGGTTC 59.403 55.000 0.00 0.00 0.00 3.62
1842 1954 0.524862 GAGTCTCCGGTTCTGCGTTA 59.475 55.000 0.00 0.00 0.00 3.18
1880 1992 2.549633 GCATGTATGTTCTGTGCCAC 57.450 50.000 0.00 0.00 0.00 5.01
1984 2194 6.017109 TGAGTTTATTCCAAGTCAAGCTTCAC 60.017 38.462 0.00 0.00 33.90 3.18
2089 2311 4.350368 TGATAATGACACACACACACCT 57.650 40.909 0.00 0.00 0.00 4.00
2090 2312 4.064388 TGATAATGACACACACACACCTG 58.936 43.478 0.00 0.00 0.00 4.00
2091 2313 2.708216 AATGACACACACACACCTGA 57.292 45.000 0.00 0.00 0.00 3.86
2092 2314 1.953559 ATGACACACACACACCTGAC 58.046 50.000 0.00 0.00 0.00 3.51
2094 2316 1.762222 GACACACACACACCTGACGC 61.762 60.000 0.00 0.00 0.00 5.19
2095 2317 1.521457 CACACACACACCTGACGCT 60.521 57.895 0.00 0.00 0.00 5.07
2096 2318 1.227263 ACACACACACCTGACGCTC 60.227 57.895 0.00 0.00 0.00 5.03
2097 2319 1.956170 CACACACACCTGACGCTCC 60.956 63.158 0.00 0.00 0.00 4.70
2098 2320 2.134287 ACACACACCTGACGCTCCT 61.134 57.895 0.00 0.00 0.00 3.69
2099 2321 1.069765 CACACACCTGACGCTCCTT 59.930 57.895 0.00 0.00 0.00 3.36
2102 2324 0.389948 CACACCTGACGCTCCTTACC 60.390 60.000 0.00 0.00 0.00 2.85
2103 2325 1.218316 CACCTGACGCTCCTTACCC 59.782 63.158 0.00 0.00 0.00 3.69
2104 2326 1.229082 ACCTGACGCTCCTTACCCA 60.229 57.895 0.00 0.00 0.00 4.51
2105 2327 1.218316 CCTGACGCTCCTTACCCAC 59.782 63.158 0.00 0.00 0.00 4.61
2106 2328 1.258445 CCTGACGCTCCTTACCCACT 61.258 60.000 0.00 0.00 0.00 4.00
2107 2329 0.108615 CTGACGCTCCTTACCCACTG 60.109 60.000 0.00 0.00 0.00 3.66
2108 2330 0.830444 TGACGCTCCTTACCCACTGT 60.830 55.000 0.00 0.00 0.00 3.55
2109 2331 0.320697 GACGCTCCTTACCCACTGTT 59.679 55.000 0.00 0.00 0.00 3.16
2110 2332 0.763035 ACGCTCCTTACCCACTGTTT 59.237 50.000 0.00 0.00 0.00 2.83
2111 2333 1.142262 ACGCTCCTTACCCACTGTTTT 59.858 47.619 0.00 0.00 0.00 2.43
2112 2334 1.804748 CGCTCCTTACCCACTGTTTTC 59.195 52.381 0.00 0.00 0.00 2.29
2113 2335 2.808933 CGCTCCTTACCCACTGTTTTCA 60.809 50.000 0.00 0.00 0.00 2.69
2114 2336 2.552743 GCTCCTTACCCACTGTTTTCAC 59.447 50.000 0.00 0.00 0.00 3.18
2115 2337 2.806244 CTCCTTACCCACTGTTTTCACG 59.194 50.000 0.00 0.00 0.00 4.35
2116 2338 1.265905 CCTTACCCACTGTTTTCACGC 59.734 52.381 0.00 0.00 0.00 5.34
2117 2339 0.938713 TTACCCACTGTTTTCACGCG 59.061 50.000 3.53 3.53 0.00 6.01
2118 2340 0.104487 TACCCACTGTTTTCACGCGA 59.896 50.000 15.93 0.00 0.00 5.87
2119 2341 0.745128 ACCCACTGTTTTCACGCGAA 60.745 50.000 15.93 0.00 0.00 4.70
2120 2342 0.316689 CCCACTGTTTTCACGCGAAC 60.317 55.000 15.93 7.38 0.00 3.95
2121 2343 0.375454 CCACTGTTTTCACGCGAACA 59.625 50.000 15.93 12.33 34.80 3.18
2122 2344 1.202087 CCACTGTTTTCACGCGAACAA 60.202 47.619 15.93 0.00 35.54 2.83
2123 2345 2.540769 CCACTGTTTTCACGCGAACAAT 60.541 45.455 15.93 0.00 35.54 2.71
2124 2346 2.713976 CACTGTTTTCACGCGAACAATC 59.286 45.455 15.93 1.63 35.54 2.67
2125 2347 2.612212 ACTGTTTTCACGCGAACAATCT 59.388 40.909 15.93 0.00 35.54 2.40
2126 2348 3.064820 ACTGTTTTCACGCGAACAATCTT 59.935 39.130 15.93 0.00 35.54 2.40
2127 2349 4.022464 TGTTTTCACGCGAACAATCTTT 57.978 36.364 15.93 0.00 33.19 2.52
2128 2350 3.788694 TGTTTTCACGCGAACAATCTTTG 59.211 39.130 15.93 0.00 33.19 2.77
2130 2352 2.661504 TCACGCGAACAATCTTTGTG 57.338 45.000 15.93 0.00 44.59 3.33
2131 2353 1.044725 CACGCGAACAATCTTTGTGC 58.955 50.000 15.93 0.00 44.59 4.57
2132 2354 0.040425 ACGCGAACAATCTTTGTGCC 60.040 50.000 15.93 0.00 44.59 5.01
2133 2355 0.040514 CGCGAACAATCTTTGTGCCA 60.041 50.000 0.00 0.00 44.59 4.92
2134 2356 1.401409 CGCGAACAATCTTTGTGCCAT 60.401 47.619 0.00 0.00 44.59 4.40
2135 2357 2.253603 GCGAACAATCTTTGTGCCATC 58.746 47.619 0.00 0.00 44.59 3.51
2136 2358 2.508867 CGAACAATCTTTGTGCCATCG 58.491 47.619 0.00 0.00 44.59 3.84
2137 2359 2.728846 CGAACAATCTTTGTGCCATCGG 60.729 50.000 4.94 0.00 44.59 4.18
2138 2360 2.198827 ACAATCTTTGTGCCATCGGA 57.801 45.000 0.00 0.00 43.48 4.55
2139 2361 2.726821 ACAATCTTTGTGCCATCGGAT 58.273 42.857 0.00 0.00 43.48 4.18
2140 2362 3.884895 ACAATCTTTGTGCCATCGGATA 58.115 40.909 0.00 0.00 43.48 2.59
2141 2363 3.627577 ACAATCTTTGTGCCATCGGATAC 59.372 43.478 0.00 0.00 43.48 2.24
2142 2364 3.845781 ATCTTTGTGCCATCGGATACT 57.154 42.857 0.00 0.00 0.00 2.12
2143 2365 2.905075 TCTTTGTGCCATCGGATACTG 58.095 47.619 0.00 0.00 0.00 2.74
2144 2366 1.331756 CTTTGTGCCATCGGATACTGC 59.668 52.381 0.00 0.00 0.00 4.40
2145 2367 0.251634 TTGTGCCATCGGATACTGCA 59.748 50.000 5.28 5.28 0.00 4.41
2148 2370 0.251634 TGCCATCGGATACTGCACAA 59.748 50.000 5.28 0.00 0.00 3.33
2156 2378 2.282555 CGGATACTGCACAAGAATCACG 59.717 50.000 0.00 0.00 0.00 4.35
2157 2379 3.521560 GGATACTGCACAAGAATCACGA 58.478 45.455 0.00 0.00 0.00 4.35
2158 2380 3.307242 GGATACTGCACAAGAATCACGAC 59.693 47.826 0.00 0.00 0.00 4.34
2160 2382 0.179240 CTGCACAAGAATCACGACGC 60.179 55.000 0.00 0.00 0.00 5.19
2161 2383 0.878086 TGCACAAGAATCACGACGCA 60.878 50.000 0.00 0.00 0.00 5.24
2162 2384 0.451135 GCACAAGAATCACGACGCAC 60.451 55.000 0.00 0.00 0.00 5.34
2163 2385 1.139989 CACAAGAATCACGACGCACT 58.860 50.000 0.00 0.00 0.00 4.40
2164 2386 1.136529 CACAAGAATCACGACGCACTG 60.137 52.381 0.00 0.00 0.00 3.66
2189 2411 0.870393 CACCGCATCATGATAGGTGC 59.130 55.000 32.07 22.60 39.84 5.01
2194 2608 2.615447 CGCATCATGATAGGTGCAAACT 59.385 45.455 16.89 0.00 37.44 2.66
2195 2609 3.547413 CGCATCATGATAGGTGCAAACTG 60.547 47.826 16.89 0.78 37.44 3.16
2196 2610 3.379372 GCATCATGATAGGTGCAAACTGT 59.621 43.478 8.15 0.00 37.52 3.55
2207 2622 3.498082 GTGCAAACTGTTGAACGAGTTT 58.502 40.909 15.27 15.27 41.96 2.66
2236 4900 1.021390 GGTGGCCTGATCTTCACGTG 61.021 60.000 9.94 9.94 0.00 4.49
2240 4904 1.139058 GGCCTGATCTTCACGTGGTAT 59.861 52.381 17.00 6.81 0.00 2.73
2326 4996 0.671163 GGATGCAACCCGTACGTTGA 60.671 55.000 19.34 7.64 44.88 3.18
2332 5002 2.612604 CAACCCGTACGTTGATGATGA 58.387 47.619 15.21 0.00 44.88 2.92
2335 5005 3.018856 ACCCGTACGTTGATGATGACTA 58.981 45.455 15.21 0.00 0.00 2.59
2338 5008 4.439700 CCCGTACGTTGATGATGACTAACT 60.440 45.833 15.21 0.00 0.00 2.24
2340 5010 4.499399 CGTACGTTGATGATGACTAACTGG 59.501 45.833 7.22 0.00 0.00 4.00
2346 5016 6.520272 GTTGATGATGACTAACTGGAGCTAT 58.480 40.000 0.00 0.00 0.00 2.97
2371 5041 4.878397 AGAACTCCAACTTGTTGTCTGAAG 59.122 41.667 11.82 4.81 0.00 3.02
2382 5052 7.155328 ACTTGTTGTCTGAAGAATCGTAGAAT 58.845 34.615 0.00 0.00 43.58 2.40
2391 5061 5.642063 TGAAGAATCGTAGAATCACAAACCC 59.358 40.000 0.00 0.00 43.58 4.11
2399 5069 5.164022 CGTAGAATCACAAACCCGAACTAAC 60.164 44.000 0.00 0.00 0.00 2.34
2405 5075 2.158579 ACAAACCCGAACTAACCCACAT 60.159 45.455 0.00 0.00 0.00 3.21
2412 5082 4.703093 CCCGAACTAACCCACATAAAACAT 59.297 41.667 0.00 0.00 0.00 2.71
2416 5086 6.370442 CGAACTAACCCACATAAAACATCTGA 59.630 38.462 0.00 0.00 0.00 3.27
2458 5128 1.760029 GGGAACTAGAGGCTCCTTCTG 59.240 57.143 11.71 0.00 0.00 3.02
2468 5138 0.462759 GCTCCTTCTGGTGAATCCGG 60.463 60.000 0.00 0.00 43.70 5.14
2629 5598 6.657541 CCCTTAGCTAGGTGTGAAAATGTTTA 59.342 38.462 4.27 0.00 43.07 2.01
2662 5631 1.002315 CTTTGCATGGTTTCCTTGGGG 59.998 52.381 0.00 0.00 0.00 4.96
2683 5652 3.078837 GGAATAAGCCGTCAACTTTGGA 58.921 45.455 0.00 0.00 0.00 3.53
2749 5719 1.676014 GGACACCTTCCACGAGAATGG 60.676 57.143 0.00 0.00 45.10 3.16
2757 5727 1.134367 TCCACGAGAATGGCTAGAACG 59.866 52.381 0.00 0.00 39.85 3.95
2758 5728 0.924090 CACGAGAATGGCTAGAACGC 59.076 55.000 0.00 0.00 0.00 4.84
2759 5729 0.818296 ACGAGAATGGCTAGAACGCT 59.182 50.000 0.00 0.00 0.00 5.07
2760 5730 1.204941 ACGAGAATGGCTAGAACGCTT 59.795 47.619 0.00 0.00 0.00 4.68
2761 5731 1.590238 CGAGAATGGCTAGAACGCTTG 59.410 52.381 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 131 4.260139 TGGAACAAGATGTTACGCAGTA 57.740 40.909 1.34 0.00 44.06 2.74
149 151 1.244816 TCGGCGTCCAGTATCCTATG 58.755 55.000 6.85 0.00 0.00 2.23
166 168 1.361993 CGGCTCCAGAGGAAGATCG 59.638 63.158 0.00 0.00 0.00 3.69
187 189 1.321074 GGAGGTCCAGGTACCACTCG 61.321 65.000 15.94 0.00 42.40 4.18
254 256 0.657840 GTGGCGAAAAGGATCATCCG 59.342 55.000 0.00 0.00 42.75 4.18
274 276 0.179936 CTCTGATGTTCTCCAGGCCC 59.820 60.000 0.00 0.00 0.00 5.80
301 303 2.135189 CCAGGGTATCTTGGGAATGGA 58.865 52.381 0.00 0.00 0.00 3.41
588 590 4.185394 TCGAAAGTTTGCGGCATAAGATA 58.815 39.130 2.28 0.00 0.00 1.98
605 608 4.338118 AGGCATCTTCAAAACAGTTCGAAA 59.662 37.500 0.00 0.00 0.00 3.46
634 637 4.080582 ACACCGATTTAACATCCTCCATGA 60.081 41.667 0.00 0.00 36.21 3.07
683 690 0.591659 GAAAGAAACTGGGGCACGAC 59.408 55.000 0.00 0.00 0.00 4.34
686 693 4.341235 ACTTTAAGAAAGAAACTGGGGCAC 59.659 41.667 5.98 0.00 41.02 5.01
834 863 2.212900 CTGACCGACGATGCAGTCCA 62.213 60.000 0.00 0.00 37.85 4.02
876 905 3.255969 TGGTTAAATAGGCAGACCGAC 57.744 47.619 0.00 0.00 42.76 4.79
881 910 3.869065 CGGAGTTGGTTAAATAGGCAGA 58.131 45.455 0.00 0.00 0.00 4.26
913 942 1.071019 CTGCTTGCTTGATTGCGCTG 61.071 55.000 9.73 0.00 35.36 5.18
964 993 3.492102 TTGCTCTGTTCTACTGGCTTT 57.508 42.857 0.00 0.00 0.00 3.51
969 998 3.058639 GCTTGGTTTGCTCTGTTCTACTG 60.059 47.826 0.00 0.00 0.00 2.74
976 1006 1.035139 CCTTGCTTGGTTTGCTCTGT 58.965 50.000 0.00 0.00 0.00 3.41
1240 1273 5.764862 CGTTCGTACGTATACAAGTTTTCC 58.235 41.667 16.05 0.00 42.72 3.13
1256 1323 8.969121 TTGAGATTGTTAATAACTCGTTCGTA 57.031 30.769 4.67 0.00 0.00 3.43
1257 1324 7.878477 TTGAGATTGTTAATAACTCGTTCGT 57.122 32.000 4.67 0.00 0.00 3.85
1258 1325 9.755064 AATTTGAGATTGTTAATAACTCGTTCG 57.245 29.630 4.67 0.00 0.00 3.95
1734 1829 1.963515 GCTTTCTTTCCAAGCCCAAGA 59.036 47.619 0.00 0.00 40.79 3.02
1769 1864 2.701006 CGGCGTAATTGTCAGGCG 59.299 61.111 0.00 6.04 45.35 5.52
1808 1903 3.119779 GGAGACTCGACAGTTCTCGATTT 60.120 47.826 0.00 0.00 41.71 2.17
1816 1911 0.597072 GAACCGGAGACTCGACAGTT 59.403 55.000 9.46 0.00 30.63 3.16
1853 1965 2.047151 GAACATACATGCCGGTGCCG 62.047 60.000 1.90 3.25 36.33 5.69
1887 1999 5.277828 GCGTGAGACTAAAACCTCAAAACAT 60.278 40.000 0.00 0.00 40.64 2.71
1896 2008 6.476243 TTATTCAAGCGTGAGACTAAAACC 57.524 37.500 1.81 0.00 34.49 3.27
1960 2170 6.205658 AGTGAAGCTTGACTTGGAATAAACTC 59.794 38.462 13.24 0.00 39.29 3.01
1961 2171 6.064717 AGTGAAGCTTGACTTGGAATAAACT 58.935 36.000 13.24 0.00 39.29 2.66
1970 2180 8.077991 TGATCAAATTTAGTGAAGCTTGACTTG 58.922 33.333 23.76 15.02 39.29 3.16
2026 2236 9.961265 ATATCATAATGAGCAAGTTTGATGTTG 57.039 29.630 0.00 0.00 0.00 3.33
2077 2299 1.490693 GAGCGTCAGGTGTGTGTGTG 61.491 60.000 0.00 0.00 0.00 3.82
2089 2311 0.830444 ACAGTGGGTAAGGAGCGTCA 60.830 55.000 0.00 0.00 0.00 4.35
2090 2312 0.320697 AACAGTGGGTAAGGAGCGTC 59.679 55.000 0.00 0.00 0.00 5.19
2091 2313 0.763035 AAACAGTGGGTAAGGAGCGT 59.237 50.000 0.00 0.00 0.00 5.07
2092 2314 1.804748 GAAAACAGTGGGTAAGGAGCG 59.195 52.381 0.00 0.00 0.00 5.03
2094 2316 2.806244 CGTGAAAACAGTGGGTAAGGAG 59.194 50.000 0.00 0.00 0.00 3.69
2095 2317 2.841215 CGTGAAAACAGTGGGTAAGGA 58.159 47.619 0.00 0.00 0.00 3.36
2096 2318 1.265905 GCGTGAAAACAGTGGGTAAGG 59.734 52.381 0.00 0.00 0.00 2.69
2097 2319 1.070175 CGCGTGAAAACAGTGGGTAAG 60.070 52.381 0.00 0.00 0.00 2.34
2098 2320 0.938713 CGCGTGAAAACAGTGGGTAA 59.061 50.000 0.00 0.00 0.00 2.85
2099 2321 0.104487 TCGCGTGAAAACAGTGGGTA 59.896 50.000 5.77 0.00 0.00 3.69
2102 2324 0.375454 TGTTCGCGTGAAAACAGTGG 59.625 50.000 13.92 0.00 35.46 4.00
2103 2325 2.166741 TTGTTCGCGTGAAAACAGTG 57.833 45.000 13.92 0.00 36.78 3.66
2104 2326 2.612212 AGATTGTTCGCGTGAAAACAGT 59.388 40.909 13.92 5.73 36.78 3.55
2105 2327 3.253371 AGATTGTTCGCGTGAAAACAG 57.747 42.857 13.92 0.00 36.78 3.16
2106 2328 3.684103 AAGATTGTTCGCGTGAAAACA 57.316 38.095 13.92 6.16 35.46 2.83
2107 2329 3.789224 ACAAAGATTGTTCGCGTGAAAAC 59.211 39.130 13.92 3.15 42.22 2.43
2108 2330 3.788694 CACAAAGATTGTTCGCGTGAAAA 59.211 39.130 13.92 4.96 43.23 2.29
2109 2331 3.358775 CACAAAGATTGTTCGCGTGAAA 58.641 40.909 13.92 0.00 43.23 2.69
2110 2332 2.852901 GCACAAAGATTGTTCGCGTGAA 60.853 45.455 7.45 7.45 43.23 3.18
2111 2333 1.333702 GCACAAAGATTGTTCGCGTGA 60.334 47.619 5.77 0.00 43.23 4.35
2112 2334 1.044725 GCACAAAGATTGTTCGCGTG 58.955 50.000 5.77 0.00 43.23 5.34
2113 2335 0.040425 GGCACAAAGATTGTTCGCGT 60.040 50.000 5.77 0.00 43.23 6.01
2114 2336 0.040514 TGGCACAAAGATTGTTCGCG 60.041 50.000 0.00 0.00 43.23 5.87
2115 2337 3.863681 TGGCACAAAGATTGTTCGC 57.136 47.368 0.00 0.00 43.23 4.70
2128 2350 2.311294 GTGCAGTATCCGATGGCAC 58.689 57.895 14.74 14.74 46.53 5.01
2129 2351 0.251634 TTGTGCAGTATCCGATGGCA 59.748 50.000 0.00 0.00 0.00 4.92
2130 2352 0.940126 CTTGTGCAGTATCCGATGGC 59.060 55.000 0.00 0.00 0.00 4.40
2131 2353 2.602257 TCTTGTGCAGTATCCGATGG 57.398 50.000 0.00 0.00 0.00 3.51
2132 2354 4.025396 GTGATTCTTGTGCAGTATCCGATG 60.025 45.833 0.00 0.00 29.97 3.84
2133 2355 4.122776 GTGATTCTTGTGCAGTATCCGAT 58.877 43.478 0.00 0.00 29.97 4.18
2134 2356 3.521560 GTGATTCTTGTGCAGTATCCGA 58.478 45.455 0.00 0.00 29.97 4.55
2135 2357 2.282555 CGTGATTCTTGTGCAGTATCCG 59.717 50.000 0.00 0.00 29.97 4.18
2136 2358 3.307242 GTCGTGATTCTTGTGCAGTATCC 59.693 47.826 0.00 0.00 29.97 2.59
2137 2359 3.000674 CGTCGTGATTCTTGTGCAGTATC 60.001 47.826 0.00 0.00 31.39 2.24
2138 2360 2.923655 CGTCGTGATTCTTGTGCAGTAT 59.076 45.455 0.00 0.00 0.00 2.12
2139 2361 2.324860 CGTCGTGATTCTTGTGCAGTA 58.675 47.619 0.00 0.00 0.00 2.74
2140 2362 1.139989 CGTCGTGATTCTTGTGCAGT 58.860 50.000 0.00 0.00 0.00 4.40
2141 2363 0.179240 GCGTCGTGATTCTTGTGCAG 60.179 55.000 0.00 0.00 0.00 4.41
2142 2364 0.878086 TGCGTCGTGATTCTTGTGCA 60.878 50.000 0.00 0.00 0.00 4.57
2143 2365 0.451135 GTGCGTCGTGATTCTTGTGC 60.451 55.000 0.00 0.00 0.00 4.57
2144 2366 1.136529 CAGTGCGTCGTGATTCTTGTG 60.137 52.381 0.00 0.00 0.00 3.33
2145 2367 1.139989 CAGTGCGTCGTGATTCTTGT 58.860 50.000 0.00 0.00 0.00 3.16
2148 2370 3.862124 GCAGTGCGTCGTGATTCT 58.138 55.556 0.00 0.00 0.00 2.40
2167 2389 1.762370 ACCTATCATGATGCGGTGACA 59.238 47.619 23.13 1.42 0.00 3.58
2189 2411 4.889241 ACGTAAACTCGTTCAACAGTTTG 58.111 39.130 19.83 11.59 41.80 2.93
2194 2608 2.118683 CGGACGTAAACTCGTTCAACA 58.881 47.619 0.00 0.00 44.21 3.33
2195 2609 2.384382 TCGGACGTAAACTCGTTCAAC 58.616 47.619 0.00 0.00 44.21 3.18
2196 2610 2.605338 CCTCGGACGTAAACTCGTTCAA 60.605 50.000 0.00 0.00 44.21 2.69
2207 2622 4.371417 AGGCCACCCTCGGACGTA 62.371 66.667 5.01 0.00 40.05 3.57
2236 4900 8.160106 AGTTATCCCTTCTGATTCAATCATACC 58.840 37.037 0.00 0.00 38.85 2.73
2240 4904 7.071698 AGCTAGTTATCCCTTCTGATTCAATCA 59.928 37.037 0.00 0.00 37.76 2.57
2274 4944 6.702329 CAGGTATAAAGCTAGTTATCCCAGG 58.298 44.000 3.42 0.00 0.00 4.45
2326 4996 8.364142 GTTCTTATAGCTCCAGTTAGTCATCAT 58.636 37.037 0.00 0.00 0.00 2.45
2340 5010 6.651225 ACAACAAGTTGGAGTTCTTATAGCTC 59.349 38.462 16.45 0.00 44.45 4.09
2346 5016 5.984725 TCAGACAACAAGTTGGAGTTCTTA 58.015 37.500 16.45 0.67 44.45 2.10
2359 5029 7.116376 GTGATTCTACGATTCTTCAGACAACAA 59.884 37.037 0.00 0.00 0.00 2.83
2371 5041 4.178540 TCGGGTTTGTGATTCTACGATTC 58.821 43.478 0.00 0.00 0.00 2.52
2382 5052 1.489649 TGGGTTAGTTCGGGTTTGTGA 59.510 47.619 0.00 0.00 0.00 3.58
2391 5061 6.370442 TCAGATGTTTTATGTGGGTTAGTTCG 59.630 38.462 0.00 0.00 0.00 3.95
2399 5069 4.217550 ACGGTTTCAGATGTTTTATGTGGG 59.782 41.667 0.00 0.00 0.00 4.61
2405 5075 5.407387 GTGCTCTACGGTTTCAGATGTTTTA 59.593 40.000 0.00 0.00 0.00 1.52
2433 5103 1.062352 GGAGCCTCTAGTTCCCCCTAA 60.062 57.143 0.00 0.00 0.00 2.69
2458 5128 2.280628 GTGAGTTCATCCGGATTCACC 58.719 52.381 26.45 15.46 35.81 4.02
2468 5138 3.817647 ACCTTTGCTCTTGTGAGTTCATC 59.182 43.478 0.00 0.00 42.13 2.92
2573 5538 6.104094 TCCTTGCTATAAAACCCCATATCCTT 59.896 38.462 0.00 0.00 0.00 3.36
2578 5543 5.718801 TGTCCTTGCTATAAAACCCCATA 57.281 39.130 0.00 0.00 0.00 2.74
2662 5631 3.078837 TCCAAAGTTGACGGCTTATTCC 58.921 45.455 0.00 0.00 0.00 3.01
2683 5652 2.698797 TCGAGGAGTTCTCCAACAACTT 59.301 45.455 19.28 0.00 39.30 2.66


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

AutoCloner maintained by Alex Coulton.