Multiple sequence alignment - TraesCS2B01G310300

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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 TraesCS2B01G310300 chr2B 100.000 2831 0 0 1 2831 443159439 443162269 0.000000e+00 5228.0
1 TraesCS2B01G310300 chr2D 92.069 1324 58 13 2 1321 373678511 373679791 0.000000e+00 1820.0
2 TraesCS2B01G310300 chr2D 92.720 989 26 17 1350 2319 373679791 373680752 0.000000e+00 1386.0
3 TraesCS2B01G310300 chr2D 85.167 209 13 4 2641 2831 373681314 373681522 6.190000e-47 198.0
4 TraesCS2B01G310300 chr2D 80.087 231 18 16 2318 2530 373680786 373681006 2.270000e-31 147.0
5 TraesCS2B01G310300 chr2D 92.683 41 3 0 2270 2310 373680633 373680673 3.050000e-05 60.2
6 TraesCS2B01G310300 chr2A 90.167 1261 101 16 938 2189 505086339 505087585 0.000000e+00 1620.0
7 TraesCS2B01G310300 chr2A 88.022 910 57 21 1 879 505085438 505086326 0.000000e+00 1029.0


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 TraesCS2B01G310300 chr2B 443159439 443162269 2830 False 5228.00 5228 100.0000 1 2831 1 chr2B.!!$F1 2830
1 TraesCS2B01G310300 chr2D 373678511 373681522 3011 False 722.24 1820 88.5452 2 2831 5 chr2D.!!$F1 2829
2 TraesCS2B01G310300 chr2A 505085438 505087585 2147 False 1324.50 1620 89.0945 1 2189 2 chr2A.!!$F1 2188

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
19 20 0.625849 AGGGGGTTTATGCCTCAGTG 59.374 55.000 0.0 0.0 0.00 3.66 F
497 505 1.336980 TGTTGTTCGTATGCCGCACTA 60.337 47.619 0.0 0.0 33.64 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1444 2.034432 CACAACCAACTGCAACATAGCA 59.966 45.455 0.0 0.0 43.35 3.49 R
2219 2277 0.035915 GTGAGACAAGGGAAGGAGCC 60.036 60.000 0.0 0.0 0.00 4.70 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
19 20 0.625849 AGGGGGTTTATGCCTCAGTG 59.374 55.000 0.00 0.00 0.00 3.66
23 24 2.357154 GGGGTTTATGCCTCAGTGACAT 60.357 50.000 2.20 2.20 0.00 3.06
26 27 4.009675 GGTTTATGCCTCAGTGACATTCA 58.990 43.478 1.92 0.00 0.00 2.57
51 52 3.555518 GCTTTCTCATTGAAACACGGAC 58.444 45.455 0.00 0.00 39.50 4.79
90 91 5.575995 CCTAGTAAACGACTCAAAAGCCTAC 59.424 44.000 0.00 0.00 39.81 3.18
95 98 4.547406 ACGACTCAAAAGCCTACAAAAC 57.453 40.909 0.00 0.00 0.00 2.43
98 101 5.124936 ACGACTCAAAAGCCTACAAAACTTT 59.875 36.000 0.00 0.00 35.20 2.66
102 105 9.361315 GACTCAAAAGCCTACAAAACTTTTAAA 57.639 29.630 0.00 0.00 40.63 1.52
103 106 9.146984 ACTCAAAAGCCTACAAAACTTTTAAAC 57.853 29.630 0.00 0.00 40.63 2.01
104 107 9.366216 CTCAAAAGCCTACAAAACTTTTAAACT 57.634 29.630 0.00 0.00 40.63 2.66
107 110 6.156748 AGCCTACAAAACTTTTAAACTGGG 57.843 37.500 0.00 0.00 0.00 4.45
109 112 5.452776 GCCTACAAAACTTTTAAACTGGGCT 60.453 40.000 0.00 0.00 0.00 5.19
110 113 5.983118 CCTACAAAACTTTTAAACTGGGCTG 59.017 40.000 0.00 0.00 0.00 4.85
337 345 1.808133 GCAGAAACCCTAGCAGATCGG 60.808 57.143 0.00 0.00 0.00 4.18
491 499 2.343101 TGCTAGTGTTGTTCGTATGCC 58.657 47.619 0.00 0.00 0.00 4.40
497 505 1.336980 TGTTGTTCGTATGCCGCACTA 60.337 47.619 0.00 0.00 33.64 2.74
521 529 5.354234 ACGTTAGATGTTGATGAAATGGGAC 59.646 40.000 0.00 0.00 0.00 4.46
631 663 8.263940 TCAGTAAAACATCTTGGTATAGTTGC 57.736 34.615 0.00 0.00 0.00 4.17
632 664 8.100791 TCAGTAAAACATCTTGGTATAGTTGCT 58.899 33.333 0.00 0.00 0.00 3.91
633 665 8.177663 CAGTAAAACATCTTGGTATAGTTGCTG 58.822 37.037 0.00 0.00 0.00 4.41
770 806 8.883731 CATTGTCCTCGTGAAAGTAATTTATCT 58.116 33.333 0.00 0.00 0.00 1.98
772 808 8.842358 TGTCCTCGTGAAAGTAATTTATCTTT 57.158 30.769 0.00 0.00 36.72 2.52
886 923 7.478322 ACTGATGCTTTGTTAATTATGCTCTG 58.522 34.615 0.00 0.00 0.00 3.35
896 933 7.475015 TGTTAATTATGCTCTGAGTTGATTGC 58.525 34.615 6.53 0.00 0.00 3.56
908 945 5.406649 TGAGTTGATTGCGACTTTTGTTTT 58.593 33.333 0.00 0.00 38.89 2.43
922 959 7.746475 CGACTTTTGTTTTCTGTCAGATATTCC 59.254 37.037 2.68 0.00 0.00 3.01
924 961 8.912988 ACTTTTGTTTTCTGTCAGATATTCCAA 58.087 29.630 2.68 0.85 0.00 3.53
994 1031 7.027161 GCTTATTTTGTTCCTTCGCTATTTGA 58.973 34.615 0.00 0.00 0.00 2.69
1086 1123 3.843027 ACCTGACATCCATTCTTGAGTCT 59.157 43.478 0.00 0.00 0.00 3.24
1093 1130 6.118170 ACATCCATTCTTGAGTCTGGTAATG 58.882 40.000 0.00 0.00 0.00 1.90
1109 1146 3.439129 GGTAATGTTGTCTTACTGGGTGC 59.561 47.826 0.00 0.00 31.26 5.01
1147 1184 4.503296 GGTCCTGCTGTTTTCTTCTACTGA 60.503 45.833 0.00 0.00 0.00 3.41
1178 1215 5.762179 TCTTTGGATCCTACAGTTGATGT 57.238 39.130 14.23 0.00 46.45 3.06
1185 1222 5.760253 GGATCCTACAGTTGATGTTACCATG 59.240 44.000 3.84 0.00 39.96 3.66
1186 1223 5.755409 TCCTACAGTTGATGTTACCATGT 57.245 39.130 0.00 0.00 39.96 3.21
1187 1224 6.121776 TCCTACAGTTGATGTTACCATGTT 57.878 37.500 0.00 0.00 39.96 2.71
1188 1225 7.247456 TCCTACAGTTGATGTTACCATGTTA 57.753 36.000 0.00 0.00 39.96 2.41
1189 1226 7.101054 TCCTACAGTTGATGTTACCATGTTAC 58.899 38.462 0.00 0.00 39.96 2.50
1190 1227 6.315393 CCTACAGTTGATGTTACCATGTTACC 59.685 42.308 0.00 0.00 39.96 2.85
1191 1228 4.693566 ACAGTTGATGTTACCATGTTACCG 59.306 41.667 0.00 0.00 39.96 4.02
1247 1287 3.569701 ACCTACACTTGAAATGTGGCTTG 59.430 43.478 0.00 0.00 45.37 4.01
1264 1304 3.205338 GCTTGCCAATGAAAACAACCTT 58.795 40.909 0.00 0.00 0.00 3.50
1329 1369 5.392380 GCTTTGACACAAGGGAGATTGTATG 60.392 44.000 0.00 0.00 41.41 2.39
1331 1371 5.241403 TGACACAAGGGAGATTGTATGTT 57.759 39.130 0.00 0.00 41.41 2.71
1334 1374 7.402054 TGACACAAGGGAGATTGTATGTTTAT 58.598 34.615 0.00 0.00 41.41 1.40
1363 1406 6.426937 AGGTCACTTGTATGTAATGTGTTGTC 59.573 38.462 0.00 0.00 0.00 3.18
1673 1716 0.187361 TCCCACCTTTCCCCTTGTTG 59.813 55.000 0.00 0.00 0.00 3.33
1787 1831 7.359595 TGATAATGTTCTAACTGTTTGTGTGC 58.640 34.615 0.00 0.00 0.00 4.57
1842 1886 0.034337 TCGACTAAGTTGTGGGGCAC 59.966 55.000 0.00 0.00 34.56 5.01
2025 2069 5.107143 CCAATTTTGGTCCTTTAACAATGCG 60.107 40.000 0.95 0.00 43.43 4.73
2059 2105 2.846206 TCTGCCTGTTCCATGTATCCTT 59.154 45.455 0.00 0.00 0.00 3.36
2060 2106 4.037222 TCTGCCTGTTCCATGTATCCTTA 58.963 43.478 0.00 0.00 0.00 2.69
2069 2115 5.290493 TCCATGTATCCTTAAATCGCTGT 57.710 39.130 0.00 0.00 0.00 4.40
2087 2133 3.119708 GCTGTCCCATTTTTCTGCTAGTG 60.120 47.826 0.00 0.00 0.00 2.74
2104 2150 6.535540 TGCTAGTGTTTTGGTGAACCTAATA 58.464 36.000 0.37 0.00 36.82 0.98
2109 2155 7.057894 AGTGTTTTGGTGAACCTAATACAGAA 58.942 34.615 0.37 0.00 36.82 3.02
2140 2186 0.888736 TTGGCACATCGTTGAGTGGG 60.889 55.000 0.00 0.00 39.30 4.61
2189 2235 5.986135 GCAAATCTCATTCCGACTAGTACAT 59.014 40.000 0.00 0.00 0.00 2.29
2191 2237 6.961360 AATCTCATTCCGACTAGTACATGA 57.039 37.500 0.00 0.75 0.00 3.07
2192 2238 7.531857 AATCTCATTCCGACTAGTACATGAT 57.468 36.000 0.00 0.00 0.00 2.45
2193 2239 6.561737 TCTCATTCCGACTAGTACATGATC 57.438 41.667 0.00 0.00 0.00 2.92
2195 2241 4.523173 TCATTCCGACTAGTACATGATCCC 59.477 45.833 0.00 0.00 0.00 3.85
2196 2242 2.501261 TCCGACTAGTACATGATCCCG 58.499 52.381 0.00 0.00 0.00 5.14
2197 2243 2.105306 TCCGACTAGTACATGATCCCGA 59.895 50.000 0.00 0.00 0.00 5.14
2198 2244 3.082548 CCGACTAGTACATGATCCCGAT 58.917 50.000 0.00 0.00 0.00 4.18
2200 2246 4.022242 CCGACTAGTACATGATCCCGATTT 60.022 45.833 0.00 0.00 0.00 2.17
2201 2247 4.917998 CGACTAGTACATGATCCCGATTTG 59.082 45.833 0.00 0.00 0.00 2.32
2202 2248 5.215252 ACTAGTACATGATCCCGATTTGG 57.785 43.478 0.00 0.00 37.55 3.28
2205 2251 4.855340 AGTACATGATCCCGATTTGGTTT 58.145 39.130 0.00 0.00 35.15 3.27
2232 2290 0.833949 GTAGGAGGCTCCTTCCCTTG 59.166 60.000 39.04 0.00 46.91 3.61
2233 2291 0.417841 TAGGAGGCTCCTTCCCTTGT 59.582 55.000 39.04 16.63 46.91 3.16
2235 2293 0.912006 GGAGGCTCCTTCCCTTGTCT 60.912 60.000 26.44 0.00 32.53 3.41
2236 2294 0.539518 GAGGCTCCTTCCCTTGTCTC 59.460 60.000 2.15 0.00 31.41 3.36
2237 2295 0.178891 AGGCTCCTTCCCTTGTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
2238 2296 0.035915 GGCTCCTTCCCTTGTCTCAC 60.036 60.000 0.00 0.00 0.00 3.51
2239 2297 0.980423 GCTCCTTCCCTTGTCTCACT 59.020 55.000 0.00 0.00 0.00 3.41
2247 2310 1.827969 CCCTTGTCTCACTGAGTAGGG 59.172 57.143 19.94 19.94 37.50 3.53
2269 2332 3.810743 GCTGGTGATTTGGTTACTGAGGT 60.811 47.826 0.00 0.00 0.00 3.85
2270 2333 4.564821 GCTGGTGATTTGGTTACTGAGGTA 60.565 45.833 0.00 0.00 0.00 3.08
2271 2334 5.160607 TGGTGATTTGGTTACTGAGGTAG 57.839 43.478 0.00 0.00 0.00 3.18
2272 2335 4.595781 TGGTGATTTGGTTACTGAGGTAGT 59.404 41.667 0.00 0.00 43.56 2.73
2273 2336 4.935808 GGTGATTTGGTTACTGAGGTAGTG 59.064 45.833 0.00 0.00 40.65 2.74
2274 2337 5.279809 GGTGATTTGGTTACTGAGGTAGTGA 60.280 44.000 0.00 0.00 40.65 3.41
2275 2338 5.869888 GTGATTTGGTTACTGAGGTAGTGAG 59.130 44.000 0.00 0.00 40.65 3.51
2276 2339 5.542635 TGATTTGGTTACTGAGGTAGTGAGT 59.457 40.000 0.00 0.00 40.65 3.41
2337 2435 5.565592 CAGATAAGCTGCCACACAAAATA 57.434 39.130 0.00 0.00 37.90 1.40
2338 2436 6.140303 CAGATAAGCTGCCACACAAAATAT 57.860 37.500 0.00 0.00 37.90 1.28
2342 2440 3.156293 AGCTGCCACACAAAATATGTCA 58.844 40.909 0.00 0.00 41.46 3.58
2365 2463 1.002430 AGTCATGACGTGCACCTTGAT 59.998 47.619 19.85 0.00 36.20 2.57
2377 2481 1.593006 CACCTTGATATTCGTGCGTCC 59.407 52.381 0.00 0.00 0.00 4.79
2385 2489 1.863662 ATTCGTGCGTCCGTCAGTCT 61.864 55.000 0.00 0.00 0.00 3.24
2399 2503 2.093783 GTCAGTCTTAATTTCGTGCGGG 59.906 50.000 0.00 0.00 0.00 6.13
2400 2504 2.028839 TCAGTCTTAATTTCGTGCGGGA 60.029 45.455 0.00 0.00 0.00 5.14
2401 2505 2.348666 CAGTCTTAATTTCGTGCGGGAG 59.651 50.000 0.00 0.00 0.00 4.30
2403 2507 2.347755 GTCTTAATTTCGTGCGGGAGTC 59.652 50.000 0.00 0.00 0.00 3.36
2404 2508 2.028839 TCTTAATTTCGTGCGGGAGTCA 60.029 45.455 0.00 0.00 0.00 3.41
2407 2511 0.806102 ATTTCGTGCGGGAGTCATCG 60.806 55.000 0.00 0.00 0.00 3.84
2415 2519 1.517257 GGGAGTCATCGCACGAGTG 60.517 63.158 0.00 0.00 38.25 3.51
2428 2532 3.303605 GAGTGCTATGCTCGCGTG 58.696 61.111 5.77 4.44 0.00 5.34
2429 2533 2.864931 GAGTGCTATGCTCGCGTGC 61.865 63.158 25.10 25.10 0.00 5.34
2430 2534 4.271170 GTGCTATGCTCGCGTGCG 62.271 66.667 25.83 14.27 41.35 5.34
2433 2537 4.569023 CTATGCTCGCGTGCGGGA 62.569 66.667 25.83 12.38 43.62 5.14
2446 2550 0.828022 TGCGGGAGTCATTATCGGTT 59.172 50.000 0.00 0.00 0.00 4.44
2484 2596 7.043458 CGATGTTTTTAAGCTGTCAAATTGTGT 60.043 33.333 0.00 0.00 0.00 3.72
2499 2611 1.080638 TGTGTTTGGGCTAAGGGGAT 58.919 50.000 0.00 0.00 0.00 3.85
2552 2842 6.415573 GGTACATGTTTAAATCAGGAGGACT 58.584 40.000 2.30 0.00 0.00 3.85
2553 2843 6.539103 GGTACATGTTTAAATCAGGAGGACTC 59.461 42.308 2.30 0.00 0.00 3.36
2562 2852 3.063084 GGAGGACTCCGCACGTCT 61.063 66.667 2.05 0.00 40.36 4.18
2563 2853 2.179517 GAGGACTCCGCACGTCTG 59.820 66.667 0.00 0.00 0.00 3.51
2564 2854 2.597805 AGGACTCCGCACGTCTGT 60.598 61.111 0.00 0.00 0.00 3.41
2565 2855 1.303074 AGGACTCCGCACGTCTGTA 60.303 57.895 0.00 0.00 0.00 2.74
2566 2856 0.680280 AGGACTCCGCACGTCTGTAT 60.680 55.000 0.00 0.00 0.00 2.29
2567 2857 1.019673 GGACTCCGCACGTCTGTATA 58.980 55.000 0.00 0.00 0.00 1.47
2568 2858 1.402968 GGACTCCGCACGTCTGTATAA 59.597 52.381 0.00 0.00 0.00 0.98
2569 2859 2.159338 GGACTCCGCACGTCTGTATAAA 60.159 50.000 0.00 0.00 0.00 1.40
2570 2860 2.850647 GACTCCGCACGTCTGTATAAAC 59.149 50.000 0.00 0.00 0.00 2.01
2571 2861 2.229543 ACTCCGCACGTCTGTATAAACA 59.770 45.455 0.00 0.00 0.00 2.83
2592 2882 4.141111 ACAGGGGTACATGTTTAGTTGGTT 60.141 41.667 2.30 0.00 0.00 3.67
2595 2885 5.311385 AGGGGTACATGTTTAGTTGGTTAGT 59.689 40.000 2.30 0.00 0.00 2.24
2596 2886 6.005823 GGGGTACATGTTTAGTTGGTTAGTT 58.994 40.000 2.30 0.00 0.00 2.24
2610 2900 4.680407 TGGTTAGTTAGGAGCCTGTAGAA 58.320 43.478 0.00 0.00 0.00 2.10
2611 2901 5.088730 TGGTTAGTTAGGAGCCTGTAGAAA 58.911 41.667 0.00 0.00 0.00 2.52
2612 2902 5.046807 TGGTTAGTTAGGAGCCTGTAGAAAC 60.047 44.000 0.00 0.00 0.00 2.78
2630 2920 2.902705 ACAGTTTGTAAGACTCCGCA 57.097 45.000 0.00 0.00 0.00 5.69
2674 3012 6.403333 TTTGTAGTTTATCTCATCGTGTGC 57.597 37.500 0.00 0.00 0.00 4.57
2692 3030 4.574828 GTGTGCTTTTCTCTTCCAACACTA 59.425 41.667 0.00 0.00 0.00 2.74
2704 3060 4.411256 TCCAACACTACTCGGAGTTTTT 57.589 40.909 16.95 2.04 0.00 1.94
2720 3076 2.727103 TTTTTCAAGGAGGCCCGTG 58.273 52.632 0.00 0.00 42.33 4.94
2740 3096 5.460748 CCGTGTTTTTGTGGGTTTAGATTTC 59.539 40.000 0.00 0.00 0.00 2.17
2743 3099 6.700081 GTGTTTTTGTGGGTTTAGATTTCTCC 59.300 38.462 0.00 0.00 0.00 3.71
2752 3108 7.418378 TGGGTTTAGATTTCTCCCATTTGTAT 58.582 34.615 2.22 0.00 42.52 2.29
2825 3181 6.682861 GCAAATTTGGCCTCTTAAATATCCGT 60.683 38.462 19.47 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.400251 TCAATGAGAAAGCCCATGAATGTC 59.600 41.667 0.00 0.00 0.00 3.06
23 24 4.588106 TGTTTCAATGAGAAAGCCCATGAA 59.412 37.500 0.00 0.00 46.34 2.57
26 27 3.057315 CGTGTTTCAATGAGAAAGCCCAT 60.057 43.478 0.00 0.00 46.34 4.00
51 52 0.462047 CTAGGCCCAGCAACCGTTAG 60.462 60.000 0.00 0.00 0.00 2.34
90 91 8.831715 AATATCAGCCCAGTTTAAAAGTTTTG 57.168 30.769 11.18 0.00 0.00 2.44
98 101 9.609346 GTCTACTAAAATATCAGCCCAGTTTAA 57.391 33.333 0.00 0.00 0.00 1.52
102 105 5.597182 TCGTCTACTAAAATATCAGCCCAGT 59.403 40.000 0.00 0.00 0.00 4.00
103 106 6.085555 TCGTCTACTAAAATATCAGCCCAG 57.914 41.667 0.00 0.00 0.00 4.45
104 107 5.010719 CCTCGTCTACTAAAATATCAGCCCA 59.989 44.000 0.00 0.00 0.00 5.36
107 110 6.802834 GCTACCTCGTCTACTAAAATATCAGC 59.197 42.308 0.00 0.00 0.00 4.26
109 112 7.521748 GCTGCTACCTCGTCTACTAAAATATCA 60.522 40.741 0.00 0.00 0.00 2.15
110 113 6.802834 GCTGCTACCTCGTCTACTAAAATATC 59.197 42.308 0.00 0.00 0.00 1.63
300 308 3.015312 GCGAGTAAGGGGCTCCGTT 62.015 63.158 0.00 0.00 38.33 4.44
491 499 4.102649 TCATCAACATCTAACGTAGTGCG 58.897 43.478 0.00 0.00 45.00 5.34
497 505 5.354234 GTCCCATTTCATCAACATCTAACGT 59.646 40.000 0.00 0.00 0.00 3.99
521 529 1.453155 AGCACATGGCCGAACTAAAG 58.547 50.000 0.00 0.00 46.50 1.85
631 663 4.492570 CGAAACCGAATAGCTAACTTGCAG 60.493 45.833 0.00 0.00 34.99 4.41
632 664 3.369756 CGAAACCGAATAGCTAACTTGCA 59.630 43.478 0.00 0.00 34.99 4.08
633 665 3.370061 ACGAAACCGAATAGCTAACTTGC 59.630 43.478 0.00 0.00 0.00 4.01
708 740 5.534207 TTCCAGTAAGAACCACGTAGAAA 57.466 39.130 0.00 0.00 0.00 2.52
710 742 4.525487 ACATTCCAGTAAGAACCACGTAGA 59.475 41.667 0.00 0.00 0.00 2.59
770 806 9.757227 GGGCATTTATGTGCTACAATAATAAAA 57.243 29.630 0.00 0.00 44.45 1.52
772 808 8.704849 AGGGCATTTATGTGCTACAATAATAA 57.295 30.769 0.00 0.00 44.45 1.40
782 818 5.658190 AGACAAATAAGGGCATTTATGTGCT 59.342 36.000 9.72 6.65 44.45 4.40
787 823 9.603921 CAAATCAAGACAAATAAGGGCATTTAT 57.396 29.630 0.00 0.00 0.00 1.40
859 896 8.186821 AGAGCATAATTAACAAAGCATCAGTTC 58.813 33.333 0.00 0.00 0.00 3.01
886 923 5.743872 AGAAAACAAAAGTCGCAATCAACTC 59.256 36.000 0.00 0.00 0.00 3.01
896 933 7.746475 GGAATATCTGACAGAAAACAAAAGTCG 59.254 37.037 9.70 0.00 32.08 4.18
924 961 9.933723 ACGGTCAACTAAATAACTGTAAATACT 57.066 29.630 0.00 0.00 29.67 2.12
946 983 2.367567 AGTGTGACCTCAACATTACGGT 59.632 45.455 0.00 0.00 0.00 4.83
994 1031 3.087031 CAGCAATGAACTTCATCCTGGT 58.913 45.455 17.08 11.12 35.76 4.00
1086 1123 4.647611 CACCCAGTAAGACAACATTACCA 58.352 43.478 0.00 0.00 34.34 3.25
1109 1146 3.694566 GCAGGACCAAAACTAATGTAGGG 59.305 47.826 0.00 0.00 0.00 3.53
1247 1287 4.154015 GGCATAAAGGTTGTTTTCATTGGC 59.846 41.667 0.00 0.00 0.00 4.52
1289 1329 7.770433 TGTGTCAAAGCTAAGCATATTCTACAT 59.230 33.333 0.00 0.00 0.00 2.29
1306 1346 5.707298 ACATACAATCTCCCTTGTGTCAAAG 59.293 40.000 0.00 0.00 39.60 2.77
1334 1374 8.911918 ACACATTACATACAAGTGACCTTTAA 57.088 30.769 0.00 0.00 34.47 1.52
1338 1378 6.296026 ACAACACATTACATACAAGTGACCT 58.704 36.000 0.00 0.00 34.47 3.85
1346 1386 7.575414 AACAAAGGACAACACATTACATACA 57.425 32.000 0.00 0.00 0.00 2.29
1401 1444 2.034432 CACAACCAACTGCAACATAGCA 59.966 45.455 0.00 0.00 43.35 3.49
1787 1831 2.127118 CCTGCAAGTTGAAGCGCG 60.127 61.111 7.16 0.00 0.00 6.86
1842 1886 6.723298 AGGATAGATACTTCAGACACAAGG 57.277 41.667 0.00 0.00 0.00 3.61
1923 1967 4.942761 ATCAAAACATTGTCTTGCCAGT 57.057 36.364 0.00 0.00 0.00 4.00
2025 2069 4.045636 ACAGGCAGAACATCAAAACAAC 57.954 40.909 0.00 0.00 0.00 3.32
2069 2115 5.221422 CCAAAACACTAGCAGAAAAATGGGA 60.221 40.000 0.00 0.00 0.00 4.37
2087 2133 8.793592 AGAATTCTGTATTAGGTTCACCAAAAC 58.206 33.333 7.30 0.00 38.89 2.43
2104 2150 6.815089 TGTGCCAATTTACAAAGAATTCTGT 58.185 32.000 9.17 7.15 0.00 3.41
2109 2155 6.024552 ACGATGTGCCAATTTACAAAGAAT 57.975 33.333 0.00 0.00 0.00 2.40
2140 2186 2.351738 GCTGTAACAACCATGGCACTTC 60.352 50.000 13.04 0.00 0.00 3.01
2219 2277 0.035915 GTGAGACAAGGGAAGGAGCC 60.036 60.000 0.00 0.00 0.00 4.70
2232 2290 0.820871 CCAGCCCTACTCAGTGAGAC 59.179 60.000 26.86 9.89 33.32 3.36
2233 2291 0.409876 ACCAGCCCTACTCAGTGAGA 59.590 55.000 26.86 9.35 33.32 3.27
2235 2293 0.114364 TCACCAGCCCTACTCAGTGA 59.886 55.000 0.00 0.00 36.70 3.41
2236 2294 1.198713 ATCACCAGCCCTACTCAGTG 58.801 55.000 0.00 0.00 32.97 3.66
2237 2295 1.958288 AATCACCAGCCCTACTCAGT 58.042 50.000 0.00 0.00 0.00 3.41
2238 2296 2.636830 CAAATCACCAGCCCTACTCAG 58.363 52.381 0.00 0.00 0.00 3.35
2239 2297 1.281867 CCAAATCACCAGCCCTACTCA 59.718 52.381 0.00 0.00 0.00 3.41
2247 2310 2.749621 CCTCAGTAACCAAATCACCAGC 59.250 50.000 0.00 0.00 0.00 4.85
2269 2332 6.426937 GCTTCCTACAATCAAACAACTCACTA 59.573 38.462 0.00 0.00 0.00 2.74
2270 2333 5.239525 GCTTCCTACAATCAAACAACTCACT 59.760 40.000 0.00 0.00 0.00 3.41
2271 2334 5.239525 AGCTTCCTACAATCAAACAACTCAC 59.760 40.000 0.00 0.00 0.00 3.51
2272 2335 5.376625 AGCTTCCTACAATCAAACAACTCA 58.623 37.500 0.00 0.00 0.00 3.41
2273 2336 5.106515 GGAGCTTCCTACAATCAAACAACTC 60.107 44.000 0.00 0.00 32.53 3.01
2274 2337 4.762251 GGAGCTTCCTACAATCAAACAACT 59.238 41.667 0.00 0.00 32.53 3.16
2275 2338 5.048153 GGAGCTTCCTACAATCAAACAAC 57.952 43.478 0.00 0.00 32.53 3.32
2342 2440 0.610174 AGGTGCACGTCATGACTCAT 59.390 50.000 22.95 6.31 0.00 2.90
2365 2463 0.179181 GACTGACGGACGCACGAATA 60.179 55.000 6.34 0.00 37.61 1.75
2373 2477 3.059044 CACGAAATTAAGACTGACGGACG 59.941 47.826 0.00 0.00 0.00 4.79
2377 2481 2.222508 CCGCACGAAATTAAGACTGACG 60.223 50.000 0.00 0.00 0.00 4.35
2385 2489 2.459060 TGACTCCCGCACGAAATTAA 57.541 45.000 0.00 0.00 0.00 1.40
2411 2515 2.864931 GCACGCGAGCATAGCACTC 61.865 63.158 23.72 0.00 36.06 3.51
2412 2516 2.887568 GCACGCGAGCATAGCACT 60.888 61.111 23.72 0.00 36.06 4.40
2416 2520 4.569023 TCCCGCACGCGAGCATAG 62.569 66.667 27.33 15.08 42.83 2.23
2421 2525 2.607668 TAATGACTCCCGCACGCGAG 62.608 60.000 15.93 5.97 42.83 5.03
2422 2526 2.011741 ATAATGACTCCCGCACGCGA 62.012 55.000 15.93 0.00 42.83 5.87
2423 2527 1.548973 GATAATGACTCCCGCACGCG 61.549 60.000 3.53 3.53 39.44 6.01
2424 2528 1.548973 CGATAATGACTCCCGCACGC 61.549 60.000 0.00 0.00 0.00 5.34
2425 2529 0.939577 CCGATAATGACTCCCGCACG 60.940 60.000 0.00 0.00 0.00 5.34
2426 2530 0.104304 ACCGATAATGACTCCCGCAC 59.896 55.000 0.00 0.00 0.00 5.34
2427 2531 0.828022 AACCGATAATGACTCCCGCA 59.172 50.000 0.00 0.00 0.00 5.69
2428 2532 1.217882 CAACCGATAATGACTCCCGC 58.782 55.000 0.00 0.00 0.00 6.13
2429 2533 1.540363 CCCAACCGATAATGACTCCCG 60.540 57.143 0.00 0.00 0.00 5.14
2430 2534 1.202770 CCCCAACCGATAATGACTCCC 60.203 57.143 0.00 0.00 0.00 4.30
2431 2535 1.489230 ACCCCAACCGATAATGACTCC 59.511 52.381 0.00 0.00 0.00 3.85
2433 2537 3.732048 AAACCCCAACCGATAATGACT 57.268 42.857 0.00 0.00 0.00 3.41
2434 2538 4.701171 TGTAAAACCCCAACCGATAATGAC 59.299 41.667 0.00 0.00 0.00 3.06
2435 2539 4.701171 GTGTAAAACCCCAACCGATAATGA 59.299 41.667 0.00 0.00 0.00 2.57
2436 2540 4.437659 CGTGTAAAACCCCAACCGATAATG 60.438 45.833 0.00 0.00 0.00 1.90
2446 2550 6.461110 TTAAAAACATCGTGTAAAACCCCA 57.539 33.333 0.00 0.00 0.00 4.96
2484 2596 1.272985 CCAACATCCCCTTAGCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
2530 2819 6.650120 GGAGTCCTCCTGATTTAAACATGTA 58.350 40.000 0.41 0.00 46.16 2.29
2562 2852 7.920227 ACTAAACATGTACCCCTGTTTATACA 58.080 34.615 18.21 6.16 43.26 2.29
2563 2853 8.671028 CAACTAAACATGTACCCCTGTTTATAC 58.329 37.037 18.21 0.00 43.26 1.47
2564 2854 7.830201 CCAACTAAACATGTACCCCTGTTTATA 59.170 37.037 18.21 6.88 43.26 0.98
2565 2855 6.661805 CCAACTAAACATGTACCCCTGTTTAT 59.338 38.462 18.21 8.41 43.26 1.40
2566 2856 6.005198 CCAACTAAACATGTACCCCTGTTTA 58.995 40.000 17.46 17.46 42.23 2.01
2567 2857 4.830600 CCAACTAAACATGTACCCCTGTTT 59.169 41.667 17.19 17.19 45.07 2.83
2568 2858 4.141111 ACCAACTAAACATGTACCCCTGTT 60.141 41.667 0.00 0.00 37.19 3.16
2569 2859 3.396611 ACCAACTAAACATGTACCCCTGT 59.603 43.478 0.00 0.00 0.00 4.00
2570 2860 4.028993 ACCAACTAAACATGTACCCCTG 57.971 45.455 0.00 0.00 0.00 4.45
2571 2861 4.734843 AACCAACTAAACATGTACCCCT 57.265 40.909 0.00 0.00 0.00 4.79
2572 2862 5.563592 ACTAACCAACTAAACATGTACCCC 58.436 41.667 0.00 0.00 0.00 4.95
2573 2863 7.335171 CCTAACTAACCAACTAAACATGTACCC 59.665 40.741 0.00 0.00 0.00 3.69
2574 2864 8.096414 TCCTAACTAACCAACTAAACATGTACC 58.904 37.037 0.00 0.00 0.00 3.34
2575 2865 9.148104 CTCCTAACTAACCAACTAAACATGTAC 57.852 37.037 0.00 0.00 0.00 2.90
2576 2866 7.820872 GCTCCTAACTAACCAACTAAACATGTA 59.179 37.037 0.00 0.00 0.00 2.29
2577 2867 6.653740 GCTCCTAACTAACCAACTAAACATGT 59.346 38.462 0.00 0.00 0.00 3.21
2578 2868 6.093633 GGCTCCTAACTAACCAACTAAACATG 59.906 42.308 0.00 0.00 0.00 3.21
2589 2879 5.046807 TGTTTCTACAGGCTCCTAACTAACC 60.047 44.000 0.00 0.00 0.00 2.85
2592 2882 5.916661 CTGTTTCTACAGGCTCCTAACTA 57.083 43.478 0.00 0.00 46.52 2.24
2610 2900 2.870411 GTGCGGAGTCTTACAAACTGTT 59.130 45.455 0.00 0.00 0.00 3.16
2611 2901 2.480845 GTGCGGAGTCTTACAAACTGT 58.519 47.619 0.00 0.00 0.00 3.55
2612 2902 1.455786 CGTGCGGAGTCTTACAAACTG 59.544 52.381 0.00 0.00 0.00 3.16
2630 2920 8.193250 ACAAATTTATTACGAATGCTAGACGT 57.807 30.769 0.00 0.00 42.70 4.34
2674 3012 4.686554 CCGAGTAGTGTTGGAAGAGAAAAG 59.313 45.833 0.00 0.00 0.00 2.27
2704 3060 0.106419 AAACACGGGCCTCCTTGAAA 60.106 50.000 0.84 0.00 36.00 2.69
2720 3076 6.183360 TGGGAGAAATCTAAACCCACAAAAAC 60.183 38.462 0.00 0.00 44.50 2.43
2740 3096 9.454859 AGAGTAGAAAGAAAATACAAATGGGAG 57.545 33.333 0.00 0.00 0.00 4.30
2776 3132 2.116238 GTCCAACTGTAGGATGCCCTA 58.884 52.381 0.00 0.00 43.97 3.53


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

AutoCloner maintained by Alex Coulton.