Multiple sequence alignment - TraesCS1B01G187500

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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 TraesCS1B01G187500 chr1B 100.000 4142 0 0 1 4142 335731739 335735880 0.000000e+00 7649.0
1 TraesCS1B01G187500 chr1D 91.729 2261 121 32 262 2484 238471439 238469207 0.000000e+00 3079.0
2 TraesCS1B01G187500 chr1D 92.863 1289 61 13 2879 4142 238468823 238467541 0.000000e+00 1842.0
3 TraesCS1B01G187500 chr1D 92.727 385 23 4 2469 2853 238469192 238468813 6.050000e-153 551.0
4 TraesCS1B01G187500 chr1D 80.657 274 23 18 1 268 238471710 238471461 7.070000e-43 185.0
5 TraesCS1B01G187500 chr1D 81.720 93 9 6 3976 4064 238467758 238467670 2.070000e-08 71.3
6 TraesCS1B01G187500 chr1A 91.924 1263 75 17 2880 4123 302198652 302197398 0.000000e+00 1742.0
7 TraesCS1B01G187500 chr1A 88.576 1383 79 40 783 2127 302200854 302199513 0.000000e+00 1605.0
8 TraesCS1B01G187500 chr1A 84.154 833 52 34 1 786 302201710 302200911 0.000000e+00 734.0
9 TraesCS1B01G187500 chr1A 92.713 247 17 1 2139 2385 302199476 302199231 5.090000e-94 355.0
10 TraesCS1B01G187500 chr1A 87.726 277 26 5 2384 2654 302199177 302198903 2.400000e-82 316.0
11 TraesCS1B01G187500 chr1A 94.972 179 6 1 2680 2855 302198821 302198643 1.130000e-70 278.0
12 TraesCS1B01G187500 chr3B 92.593 54 3 1 1 53 4693348 4693295 4.440000e-10 76.8


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 TraesCS1B01G187500 chr1B 335731739 335735880 4141 False 7649.000000 7649 100.000000 1 4142 1 chr1B.!!$F1 4141
1 TraesCS1B01G187500 chr1D 238467541 238471710 4169 True 1145.660000 3079 87.939200 1 4142 5 chr1D.!!$R1 4141
2 TraesCS1B01G187500 chr1A 302197398 302201710 4312 True 838.333333 1742 90.010833 1 4123 6 chr1A.!!$R1 4122

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
214 237 0.035739 GGTTGGGTCGAGCAAGGTTA 59.964 55.0 17.59 0.0 0.0 2.85 F
321 372 0.172578 GTGGGGGCAAACGATTAAGC 59.827 55.0 0.00 0.0 0.0 3.09 F
2088 2295 0.391130 GCGGCATTCTCACAGGTACA 60.391 55.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2055 0.450983 GGACAGCAAATCAGCAGAGC 59.549 55.0 0.00 0.0 36.85 4.09 R
2261 2494 0.387565 GAGGCCTCCTTGATCTCGAC 59.612 60.0 23.19 0.0 31.76 4.20 R
3642 4068 0.678048 GGAACTTCCTTGCATCGCCT 60.678 55.0 0.00 0.0 32.53 5.52 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
83 104 2.610374 GTGTGGTGTTGTGTTGTATCGT 59.390 45.455 0.00 0.00 0.00 3.73
85 106 3.690139 TGTGGTGTTGTGTTGTATCGTTT 59.310 39.130 0.00 0.00 0.00 3.60
106 127 9.228949 TCGTTTGTTGTAAGGGCTTTATTAATA 57.771 29.630 0.00 0.00 0.00 0.98
134 157 4.238514 CAGGACGACAACCTTCTTTCTAG 58.761 47.826 0.00 0.00 35.35 2.43
135 158 3.258622 AGGACGACAACCTTCTTTCTAGG 59.741 47.826 0.00 0.00 38.79 3.02
185 208 4.939948 GACGAAATAGATCAAGCTCGTC 57.060 45.455 18.33 18.33 45.49 4.20
186 209 3.364062 ACGAAATAGATCAAGCTCGTCG 58.636 45.455 7.00 3.74 34.68 5.12
187 210 2.721603 CGAAATAGATCAAGCTCGTCGG 59.278 50.000 0.00 0.00 0.00 4.79
188 211 2.802787 AATAGATCAAGCTCGTCGGG 57.197 50.000 0.00 0.00 0.00 5.14
189 212 1.693627 ATAGATCAAGCTCGTCGGGT 58.306 50.000 0.00 0.00 0.00 5.28
190 213 2.336945 TAGATCAAGCTCGTCGGGTA 57.663 50.000 0.00 0.00 0.00 3.69
191 214 0.739561 AGATCAAGCTCGTCGGGTAC 59.260 55.000 0.00 0.00 0.00 3.34
192 215 0.739561 GATCAAGCTCGTCGGGTACT 59.260 55.000 0.00 0.00 0.00 2.73
193 216 0.739561 ATCAAGCTCGTCGGGTACTC 59.260 55.000 0.00 0.00 0.00 2.59
204 227 2.575461 GGTACTCGGGTTGGGTCG 59.425 66.667 0.00 0.00 0.00 4.79
214 237 0.035739 GGTTGGGTCGAGCAAGGTTA 59.964 55.000 17.59 0.00 0.00 2.85
224 247 6.049790 GGTCGAGCAAGGTTAATAGAAGATT 58.950 40.000 10.30 0.00 0.00 2.40
228 251 8.861086 TCGAGCAAGGTTAATAGAAGATTAGAT 58.139 33.333 0.00 0.00 0.00 1.98
229 252 9.482627 CGAGCAAGGTTAATAGAAGATTAGATT 57.517 33.333 0.00 0.00 0.00 2.40
269 320 0.394216 TGCCACAGTGGTATCCATGC 60.394 55.000 21.26 4.40 40.46 4.06
277 328 3.567164 CAGTGGTATCCATGCCATTTCTC 59.433 47.826 0.00 0.00 44.38 2.87
278 329 3.461085 AGTGGTATCCATGCCATTTCTCT 59.539 43.478 0.00 0.00 44.38 3.10
285 336 7.014615 GGTATCCATGCCATTTCTCTGTTTATT 59.985 37.037 0.00 0.00 32.29 1.40
308 359 4.586841 TGAGAAAACAAAGTAATGTGGGGG 59.413 41.667 0.00 0.00 32.81 5.40
314 365 1.253100 AAGTAATGTGGGGGCAAACG 58.747 50.000 0.00 0.00 0.00 3.60
317 368 1.822371 GTAATGTGGGGGCAAACGATT 59.178 47.619 0.00 0.00 0.00 3.34
321 372 0.172578 GTGGGGGCAAACGATTAAGC 59.827 55.000 0.00 0.00 0.00 3.09
329 380 1.068885 CAAACGATTAAGCGCCCAACA 60.069 47.619 13.91 0.00 33.86 3.33
334 385 3.630312 ACGATTAAGCGCCCAACAAATAT 59.370 39.130 13.91 0.00 33.86 1.28
335 386 4.219033 CGATTAAGCGCCCAACAAATATC 58.781 43.478 2.29 0.00 0.00 1.63
336 387 3.684103 TTAAGCGCCCAACAAATATCG 57.316 42.857 2.29 0.00 0.00 2.92
416 473 6.038936 TGAAAATCTACTGCACATGGATCATG 59.961 38.462 6.37 6.37 46.18 3.07
587 676 3.961414 GTGCCGTCCCTTTCCCCA 61.961 66.667 0.00 0.00 0.00 4.96
670 759 0.759346 ACCTCCGGTATCAATCAGGC 59.241 55.000 0.00 0.00 32.11 4.85
693 782 3.083997 GTCAGTCGATGGGGCCCT 61.084 66.667 25.93 9.44 0.00 5.19
695 784 2.190578 CAGTCGATGGGGCCCTTC 59.809 66.667 25.93 25.37 0.00 3.46
716 805 3.067011 TGGATCTCCACGGTGAAGT 57.933 52.632 10.28 0.00 42.01 3.01
719 808 1.482593 GGATCTCCACGGTGAAGTGAT 59.517 52.381 10.28 5.75 44.43 3.06
780 873 2.032620 CTCTGTACACCGGATAAGGCT 58.967 52.381 9.46 0.00 33.69 4.58
826 979 5.692115 TCCCAAGCATCACTTCATTACTA 57.308 39.130 0.00 0.00 36.04 1.82
827 980 6.061022 TCCCAAGCATCACTTCATTACTAA 57.939 37.500 0.00 0.00 36.04 2.24
828 981 6.480763 TCCCAAGCATCACTTCATTACTAAA 58.519 36.000 0.00 0.00 36.04 1.85
829 982 6.945435 TCCCAAGCATCACTTCATTACTAAAA 59.055 34.615 0.00 0.00 36.04 1.52
947 1100 0.881118 TTCAGCCGCTTGATCAAACC 59.119 50.000 9.88 2.82 0.00 3.27
971 1124 2.210013 TCAGTGCCTGGCTTCTCGT 61.210 57.895 21.03 0.00 31.51 4.18
972 1125 1.302033 CAGTGCCTGGCTTCTCGTT 60.302 57.895 21.03 0.00 0.00 3.85
973 1126 1.004440 AGTGCCTGGCTTCTCGTTC 60.004 57.895 21.03 0.66 0.00 3.95
974 1127 1.004440 GTGCCTGGCTTCTCGTTCT 60.004 57.895 21.03 0.00 0.00 3.01
975 1128 1.016653 GTGCCTGGCTTCTCGTTCTC 61.017 60.000 21.03 0.00 0.00 2.87
976 1129 1.807573 GCCTGGCTTCTCGTTCTCG 60.808 63.158 12.43 0.00 38.55 4.04
1097 1258 1.550976 TCCTCTTCTTTTCTCTCCCGC 59.449 52.381 0.00 0.00 0.00 6.13
1328 1489 1.467713 GGACAGTTCGACGAGGTCATC 60.468 57.143 20.52 8.44 32.09 2.92
1329 1490 1.199327 GACAGTTCGACGAGGTCATCA 59.801 52.381 16.56 0.00 32.09 3.07
1391 1569 3.338818 TTTTCTGACGAGCTTTGCTTG 57.661 42.857 5.35 5.35 44.94 4.01
1398 1576 2.524636 CGAGCTTTGCTTGGCAGCTC 62.525 60.000 17.80 17.80 46.36 4.09
1452 1630 1.835483 CTTCTTGCGCGTGAGTTGCT 61.835 55.000 8.43 0.00 35.96 3.91
1453 1631 1.831389 TTCTTGCGCGTGAGTTGCTC 61.831 55.000 8.43 0.00 35.96 4.26
1454 1632 2.280119 TTGCGCGTGAGTTGCTCT 60.280 55.556 8.43 0.00 35.96 4.09
1760 1959 1.558233 AACCCTCTGACTTACCCGAG 58.442 55.000 0.00 0.00 0.00 4.63
1851 2055 1.554042 AAAGCGGTCGTAGTTGTGCG 61.554 55.000 0.00 0.00 0.00 5.34
2005 2209 1.743958 CAGGCCAATTCTTCTCTGCTG 59.256 52.381 5.01 0.00 0.00 4.41
2022 2229 7.727181 TCTCTGCTGGTACTATTTTCCTAATC 58.273 38.462 0.00 0.00 0.00 1.75
2024 2231 7.857456 TCTGCTGGTACTATTTTCCTAATCAA 58.143 34.615 0.00 0.00 0.00 2.57
2088 2295 0.391130 GCGGCATTCTCACAGGTACA 60.391 55.000 0.00 0.00 0.00 2.90
2091 2298 2.677902 CGGCATTCTCACAGGTACACAT 60.678 50.000 0.00 0.00 0.00 3.21
2101 2308 6.014925 TCTCACAGGTACACATAGCACTTTTA 60.015 38.462 0.00 0.00 0.00 1.52
2102 2309 6.526526 TCACAGGTACACATAGCACTTTTAA 58.473 36.000 0.00 0.00 0.00 1.52
2104 2311 7.663905 TCACAGGTACACATAGCACTTTTAATT 59.336 33.333 0.00 0.00 0.00 1.40
2105 2312 8.941977 CACAGGTACACATAGCACTTTTAATTA 58.058 33.333 0.00 0.00 0.00 1.40
2106 2313 8.943002 ACAGGTACACATAGCACTTTTAATTAC 58.057 33.333 0.00 0.00 0.00 1.89
2181 2414 2.691011 GAGGATAGACCGAAGCTTCTGT 59.309 50.000 21.71 21.71 44.74 3.41
2258 2491 2.083774 CCAAGCAAGAGAATTACCGCA 58.916 47.619 0.00 0.00 0.00 5.69
2284 2517 1.762460 GATCAAGGAGGCCTCGGGA 60.762 63.158 26.36 21.83 30.89 5.14
2287 2520 2.840102 AAGGAGGCCTCGGGATCG 60.840 66.667 26.36 0.00 30.89 3.69
2380 2615 6.552725 TGCATCAACTCTTATGATCTACTCCT 59.447 38.462 0.00 0.00 35.38 3.69
2381 2616 7.090173 GCATCAACTCTTATGATCTACTCCTC 58.910 42.308 0.00 0.00 35.38 3.71
2461 2750 4.504858 AGGTCAAGTTACAAGCCTTATCG 58.495 43.478 0.00 0.00 0.00 2.92
2501 2831 9.987272 AAGAATTTCAACTTTAAAATCTCTGGG 57.013 29.630 0.00 0.00 28.33 4.45
2502 2832 9.147732 AGAATTTCAACTTTAAAATCTCTGGGT 57.852 29.630 0.00 0.00 0.00 4.51
2503 2833 9.764363 GAATTTCAACTTTAAAATCTCTGGGTT 57.236 29.630 0.00 0.00 0.00 4.11
2506 2836 9.594478 TTTCAACTTTAAAATCTCTGGGTTTTC 57.406 29.630 0.00 0.00 0.00 2.29
2507 2837 8.533569 TCAACTTTAAAATCTCTGGGTTTTCT 57.466 30.769 0.00 0.00 0.00 2.52
2549 2880 4.510038 AATTCAGTGCCATGTTTCACTC 57.490 40.909 8.87 0.00 41.19 3.51
2671 3002 1.538047 CACAGTGGTTCCTTCCATGG 58.462 55.000 4.97 4.97 39.81 3.66
2792 3180 3.826729 GGTGGTTGCACTCCTAAATTCTT 59.173 43.478 8.33 0.00 0.00 2.52
2806 3194 6.044287 TCCTAAATTCTTAGCATATGCCCTCA 59.956 38.462 23.96 5.41 43.38 3.86
2842 3233 6.127619 GCTCTTTTATGTGCCTTTCTAACCAT 60.128 38.462 0.00 0.00 0.00 3.55
2843 3234 7.156876 TCTTTTATGTGCCTTTCTAACCATG 57.843 36.000 0.00 0.00 0.00 3.66
2845 3236 5.895636 TTATGTGCCTTTCTAACCATGTG 57.104 39.130 0.00 0.00 0.00 3.21
2846 3237 3.222173 TGTGCCTTTCTAACCATGTGT 57.778 42.857 0.00 0.00 0.00 3.72
2847 3238 2.884012 TGTGCCTTTCTAACCATGTGTG 59.116 45.455 0.00 0.00 0.00 3.82
2848 3239 2.884639 GTGCCTTTCTAACCATGTGTGT 59.115 45.455 0.00 0.00 0.00 3.72
2849 3240 2.884012 TGCCTTTCTAACCATGTGTGTG 59.116 45.455 0.00 0.00 0.00 3.82
2850 3241 2.884639 GCCTTTCTAACCATGTGTGTGT 59.115 45.455 0.00 0.00 0.00 3.72
2851 3242 3.304659 GCCTTTCTAACCATGTGTGTGTG 60.305 47.826 0.00 0.00 0.00 3.82
2852 3243 3.882888 CCTTTCTAACCATGTGTGTGTGT 59.117 43.478 0.00 0.00 0.00 3.72
2853 3244 4.261155 CCTTTCTAACCATGTGTGTGTGTG 60.261 45.833 0.00 0.00 0.00 3.82
2854 3245 3.552132 TCTAACCATGTGTGTGTGTGT 57.448 42.857 0.00 0.00 0.00 3.72
2855 3246 3.202097 TCTAACCATGTGTGTGTGTGTG 58.798 45.455 0.00 0.00 0.00 3.82
2856 3247 1.832883 AACCATGTGTGTGTGTGTGT 58.167 45.000 0.00 0.00 0.00 3.72
2857 3248 1.093972 ACCATGTGTGTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
2858 3249 1.093972 CCATGTGTGTGTGTGTGTGT 58.906 50.000 0.00 0.00 0.00 3.72
2859 3250 1.202166 CCATGTGTGTGTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
2860 3251 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
2861 3252 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2862 3253 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2863 3254 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2864 3255 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2865 3256 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2866 3257 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2867 3258 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2868 3259 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2869 3260 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2870 3261 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2871 3262 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2872 3263 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2873 3264 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2874 3265 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2875 3266 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2876 3267 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2877 3268 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2878 3269 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3091 3485 3.179265 ACGTCGATGCGCCGAAAG 61.179 61.111 10.32 10.04 40.51 2.62
3108 3502 4.025401 GTTGTTGCTCCGCACCCG 62.025 66.667 0.00 0.00 38.71 5.28
3123 3517 2.810767 GCACCCGAAGAAGAAGGAAGTT 60.811 50.000 0.00 0.00 0.00 2.66
3132 3526 6.908284 CGAAGAAGAAGGAAGTTAGATACTCG 59.092 42.308 0.00 0.00 35.54 4.18
3194 3599 4.019858 CTGATCTGACCAGTAGACTTGGA 58.980 47.826 0.00 0.00 0.00 3.53
3196 3601 2.160205 TCTGACCAGTAGACTTGGACG 58.840 52.381 0.00 0.00 0.00 4.79
3247 3652 6.801539 TTGTTCATAGGTTGCAAGTAAGAG 57.198 37.500 0.00 0.00 0.00 2.85
3365 3770 9.719355 TTTATCAGAACATTTGCAGTTACTAGA 57.281 29.630 0.00 0.00 0.00 2.43
3366 3771 9.890629 TTATCAGAACATTTGCAGTTACTAGAT 57.109 29.630 0.00 0.00 0.00 1.98
3373 3778 8.575565 ACATTTGCAGTTACTAGATATACACG 57.424 34.615 0.00 0.00 0.00 4.49
3391 3796 4.268522 ACACGAAAATATGCGCGAATTAC 58.731 39.130 12.10 3.70 0.00 1.89
3482 3892 0.973632 TCACTCATGTACCCAACGCT 59.026 50.000 0.00 0.00 0.00 5.07
3604 4030 3.627747 GGTCAAAGTAGGAGAGGAGGCTA 60.628 52.174 0.00 0.00 0.00 3.93
3642 4068 1.466856 GCAATGTGAGGCAGATCCAA 58.533 50.000 0.00 0.00 37.29 3.53
3664 4093 1.803289 GATGCAAGGAAGTTCCGGC 59.197 57.895 25.75 25.75 42.75 6.13
3665 4094 2.513395 TGCAAGGAAGTTCCGGCA 59.487 55.556 29.18 29.18 45.02 5.69
3666 4095 1.600636 TGCAAGGAAGTTCCGGCAG 60.601 57.895 29.18 16.83 43.34 4.85
3707 4136 2.827642 GAGACATGGGGCAGCAGC 60.828 66.667 0.00 0.00 41.10 5.25
4030 4465 1.369839 CGCTAGTGCTCTCCTCGTCA 61.370 60.000 0.00 0.00 36.97 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.012673 GCAAGATACAAGGGTGCTCAG 58.987 52.381 0.00 0.00 32.43 3.35
37 38 9.853177 ACAATAAAGAGAAAAGGAGAAGAAGAA 57.147 29.630 0.00 0.00 0.00 2.52
38 39 9.277783 CACAATAAAGAGAAAAGGAGAAGAAGA 57.722 33.333 0.00 0.00 0.00 2.87
39 40 9.061435 ACACAATAAAGAGAAAAGGAGAAGAAG 57.939 33.333 0.00 0.00 0.00 2.85
40 41 8.840321 CACACAATAAAGAGAAAAGGAGAAGAA 58.160 33.333 0.00 0.00 0.00 2.52
41 42 7.445402 CCACACAATAAAGAGAAAAGGAGAAGA 59.555 37.037 0.00 0.00 0.00 2.87
42 43 7.229506 ACCACACAATAAAGAGAAAAGGAGAAG 59.770 37.037 0.00 0.00 0.00 2.85
43 44 7.013274 CACCACACAATAAAGAGAAAAGGAGAA 59.987 37.037 0.00 0.00 0.00 2.87
48 49 7.220683 CACAACACCACACAATAAAGAGAAAAG 59.779 37.037 0.00 0.00 0.00 2.27
106 127 3.008049 AGAAGGTTGTCGTCCTGCTTTAT 59.992 43.478 0.00 0.00 37.69 1.40
113 134 3.258622 CCTAGAAAGAAGGTTGTCGTCCT 59.741 47.826 0.00 0.00 36.81 3.85
116 137 4.950205 TTCCTAGAAAGAAGGTTGTCGT 57.050 40.909 0.00 0.00 35.48 4.34
142 165 2.095252 GCTCGTTCGTTCCTGCTCC 61.095 63.158 0.00 0.00 0.00 4.70
185 208 2.999063 ACCCAACCCGAGTACCCG 60.999 66.667 0.00 0.00 0.00 5.28
186 209 2.984623 GACCCAACCCGAGTACCC 59.015 66.667 0.00 0.00 0.00 3.69
187 210 1.941999 CTCGACCCAACCCGAGTACC 61.942 65.000 0.00 0.00 44.99 3.34
188 211 1.509923 CTCGACCCAACCCGAGTAC 59.490 63.158 0.00 0.00 44.99 2.73
189 212 4.007457 CTCGACCCAACCCGAGTA 57.993 61.111 0.00 0.00 44.99 2.59
192 215 3.234630 CTTGCTCGACCCAACCCGA 62.235 63.158 0.00 0.00 0.00 5.14
193 216 2.742372 CTTGCTCGACCCAACCCG 60.742 66.667 0.00 0.00 0.00 5.28
238 261 3.128242 CCACTGTGGCATTTTTGCAAAAA 59.872 39.130 32.91 32.91 41.59 1.94
239 262 2.681848 CCACTGTGGCATTTTTGCAAAA 59.318 40.909 20.46 20.46 36.33 2.44
240 263 2.286872 CCACTGTGGCATTTTTGCAAA 58.713 42.857 14.87 8.05 36.33 3.68
256 279 3.461085 AGAGAAATGGCATGGATACCACT 59.539 43.478 0.00 0.00 39.19 4.00
269 320 9.748708 TTGTTTTCTCAATAAACAGAGAAATGG 57.251 29.630 15.69 0.00 43.85 3.16
285 336 4.586841 CCCCCACATTACTTTGTTTTCTCA 59.413 41.667 0.00 0.00 0.00 3.27
308 359 0.109504 TTGGGCGCTTAATCGTTTGC 60.110 50.000 7.64 0.00 0.00 3.68
314 365 4.219033 CGATATTTGTTGGGCGCTTAATC 58.781 43.478 7.64 0.00 0.00 1.75
317 368 1.944024 CCGATATTTGTTGGGCGCTTA 59.056 47.619 7.64 0.00 0.00 3.09
329 380 4.221703 TGTTTGGTCATTTGCCCGATATTT 59.778 37.500 0.00 0.00 0.00 1.40
334 385 0.671251 GTGTTTGGTCATTTGCCCGA 59.329 50.000 0.00 0.00 0.00 5.14
335 386 0.319469 GGTGTTTGGTCATTTGCCCG 60.319 55.000 0.00 0.00 0.00 6.13
336 387 0.034756 GGGTGTTTGGTCATTTGCCC 59.965 55.000 0.00 0.00 0.00 5.36
395 452 4.141321 ACCATGATCCATGTGCAGTAGATT 60.141 41.667 0.00 0.00 39.94 2.40
398 455 3.204306 ACCATGATCCATGTGCAGTAG 57.796 47.619 0.00 0.00 39.94 2.57
416 473 4.816385 TGATTGATTTCTCTGCGGATAACC 59.184 41.667 0.00 0.00 0.00 2.85
587 676 2.227626 CGAGTGAGAGTGACAGTGACAT 59.772 50.000 0.00 0.00 0.00 3.06
670 759 1.226802 CCCATCGACTGACTGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
719 808 0.179048 GGGCGATGGTGATGTCATCA 60.179 55.000 11.62 11.62 41.79 3.07
742 831 2.269241 GGCGCTGGTTTAGAGGCT 59.731 61.111 7.64 0.00 46.09 4.58
780 873 2.764128 GGGTGCAGGGGATCTCGA 60.764 66.667 0.00 0.00 0.00 4.04
826 979 2.756760 AGCTGGCGATGAATGATGTTTT 59.243 40.909 0.00 0.00 0.00 2.43
827 980 2.372264 AGCTGGCGATGAATGATGTTT 58.628 42.857 0.00 0.00 0.00 2.83
828 981 2.048444 AGCTGGCGATGAATGATGTT 57.952 45.000 0.00 0.00 0.00 2.71
829 982 1.945394 GAAGCTGGCGATGAATGATGT 59.055 47.619 0.00 0.00 0.00 3.06
1328 1489 2.040012 CAGGGAGGGGATGAAGATGATG 59.960 54.545 0.00 0.00 0.00 3.07
1329 1490 2.346529 CAGGGAGGGGATGAAGATGAT 58.653 52.381 0.00 0.00 0.00 2.45
1391 1569 2.887568 CGATCACCACGAGCTGCC 60.888 66.667 0.00 0.00 0.00 4.85
1739 1938 2.688958 CTCGGGTAAGTCAGAGGGTTAG 59.311 54.545 0.00 0.00 0.00 2.34
1760 1959 3.134458 AGCAAGTTATCTTAGGCATCGC 58.866 45.455 0.00 0.00 32.07 4.58
1827 2031 2.798847 ACAACTACGACCGCTTTCTTTC 59.201 45.455 0.00 0.00 0.00 2.62
1851 2055 0.450983 GGACAGCAAATCAGCAGAGC 59.549 55.000 0.00 0.00 36.85 4.09
2005 2209 9.614792 AGTGACATTGATTAGGAAAATAGTACC 57.385 33.333 0.00 0.00 0.00 3.34
2022 2229 2.416202 TGCATTAGCGACAGTGACATTG 59.584 45.455 0.00 0.00 46.23 2.82
2024 2231 2.274437 CTGCATTAGCGACAGTGACAT 58.726 47.619 0.00 0.00 46.23 3.06
2088 2295 9.408648 AGCTAATGGTAATTAAAAGTGCTATGT 57.591 29.630 0.00 0.00 28.38 2.29
2137 2370 5.048782 TCCATGTGAGCAAAGTTCATGTTAC 60.049 40.000 0.00 0.00 35.54 2.50
2181 2414 6.463995 AGTTGTTTGGTTTATTTCTGAGCA 57.536 33.333 0.00 0.00 0.00 4.26
2258 2491 1.045911 GCCTCCTTGATCTCGACCCT 61.046 60.000 0.00 0.00 0.00 4.34
2260 2493 1.045911 AGGCCTCCTTGATCTCGACC 61.046 60.000 0.00 0.00 0.00 4.79
2261 2494 0.387565 GAGGCCTCCTTGATCTCGAC 59.612 60.000 23.19 0.00 31.76 4.20
2284 2517 2.159338 GCACAAATGCCTTGATGACGAT 60.159 45.455 2.85 0.00 46.97 3.73
2380 2615 9.965824 GACTTCAAAATCATTCCAGTAAAAAGA 57.034 29.630 0.00 0.00 0.00 2.52
2381 2616 9.971922 AGACTTCAAAATCATTCCAGTAAAAAG 57.028 29.630 0.00 0.00 0.00 2.27
2488 2811 8.763601 TCCAAAAAGAAAACCCAGAGATTTTAA 58.236 29.630 0.00 0.00 0.00 1.52
2494 2824 5.269189 AGTTCCAAAAAGAAAACCCAGAGA 58.731 37.500 0.00 0.00 0.00 3.10
2495 2825 5.598416 AGTTCCAAAAAGAAAACCCAGAG 57.402 39.130 0.00 0.00 0.00 3.35
2496 2826 5.482175 TGAAGTTCCAAAAAGAAAACCCAGA 59.518 36.000 0.00 0.00 0.00 3.86
2497 2827 5.580691 GTGAAGTTCCAAAAAGAAAACCCAG 59.419 40.000 0.00 0.00 0.00 4.45
2498 2828 5.483811 GTGAAGTTCCAAAAAGAAAACCCA 58.516 37.500 0.00 0.00 0.00 4.51
2500 2830 5.730550 AGGTGAAGTTCCAAAAAGAAAACC 58.269 37.500 0.00 0.00 0.00 3.27
2501 2831 7.667043 AAAGGTGAAGTTCCAAAAAGAAAAC 57.333 32.000 0.00 0.00 0.00 2.43
2502 2832 8.684386 AAAAAGGTGAAGTTCCAAAAAGAAAA 57.316 26.923 0.00 0.00 0.00 2.29
2503 2833 9.780186 TTAAAAAGGTGAAGTTCCAAAAAGAAA 57.220 25.926 0.00 0.00 0.00 2.52
2504 2834 9.952030 ATTAAAAAGGTGAAGTTCCAAAAAGAA 57.048 25.926 0.00 0.00 0.00 2.52
2505 2835 9.952030 AATTAAAAAGGTGAAGTTCCAAAAAGA 57.048 25.926 0.00 0.00 0.00 2.52
2507 2837 9.726438 TGAATTAAAAAGGTGAAGTTCCAAAAA 57.274 25.926 0.00 0.00 0.00 1.94
2510 2840 7.978975 CACTGAATTAAAAAGGTGAAGTTCCAA 59.021 33.333 0.00 0.00 0.00 3.53
2512 2842 6.420903 GCACTGAATTAAAAAGGTGAAGTTCC 59.579 38.462 0.00 0.00 0.00 3.62
2549 2880 5.291858 TCTTGACGCTTCTGCATAATTAGTG 59.708 40.000 0.00 0.00 39.64 2.74
2671 3002 4.743493 TCAGTTCAGGTTTTGTTTTGAGC 58.257 39.130 0.00 0.00 0.00 4.26
2792 3180 2.775911 GCATCTGAGGGCATATGCTA 57.224 50.000 26.12 10.29 45.75 3.49
2842 3233 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2843 3234 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2845 3236 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2846 3237 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2847 3238 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2848 3239 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2849 3240 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2850 3241 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2851 3242 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2852 3243 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2853 3244 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2854 3245 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2855 3246 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2856 3247 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2857 3248 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2858 3249 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2859 3250 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2860 3251 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2861 3252 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2862 3253 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2863 3254 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2864 3255 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2865 3256 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2866 3257 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2867 3258 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2868 3259 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2869 3260 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2870 3261 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
2871 3262 1.804151 AGAACACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
2872 3263 2.073056 GAGAACACACACACACACACA 58.927 47.619 0.00 0.00 0.00 3.72
2873 3264 2.346803 AGAGAACACACACACACACAC 58.653 47.619 0.00 0.00 0.00 3.82
2874 3265 2.741517 CAAGAGAACACACACACACACA 59.258 45.455 0.00 0.00 0.00 3.72
2875 3266 2.476185 GCAAGAGAACACACACACACAC 60.476 50.000 0.00 0.00 0.00 3.82
2876 3267 1.737236 GCAAGAGAACACACACACACA 59.263 47.619 0.00 0.00 0.00 3.72
2877 3268 1.737236 TGCAAGAGAACACACACACAC 59.263 47.619 0.00 0.00 0.00 3.82
2878 3269 2.106477 TGCAAGAGAACACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
3108 3502 7.987649 TCGAGTATCTAACTTCCTTCTTCTTC 58.012 38.462 0.00 0.00 39.07 2.87
3123 3517 4.720046 AGATTCAGGTGCTCGAGTATCTA 58.280 43.478 16.37 2.13 0.00 1.98
3132 3526 4.953667 TGACATATGAGATTCAGGTGCTC 58.046 43.478 10.38 0.00 0.00 4.26
3194 3599 1.935873 CAACAGATCGATGAATGGCGT 59.064 47.619 0.54 0.00 0.00 5.68
3196 3601 3.624861 AGAACAACAGATCGATGAATGGC 59.375 43.478 0.54 0.00 0.00 4.40
3247 3652 4.629200 GCTTCATAGTATCCAGCTGCATAC 59.371 45.833 18.48 18.48 0.00 2.39
3365 3770 5.832568 TTCGCGCATATTTTCGTGTATAT 57.167 34.783 8.75 0.00 37.46 0.86
3366 3771 5.832568 ATTCGCGCATATTTTCGTGTATA 57.167 34.783 8.75 0.00 37.46 1.47
3367 3772 4.725556 ATTCGCGCATATTTTCGTGTAT 57.274 36.364 8.75 0.00 37.46 2.29
3370 3775 4.514506 AGTAATTCGCGCATATTTTCGTG 58.485 39.130 8.75 0.00 37.53 4.35
3371 3776 4.789095 AGTAATTCGCGCATATTTTCGT 57.211 36.364 8.75 0.00 0.00 3.85
3372 3777 6.136007 TCTAGTAATTCGCGCATATTTTCG 57.864 37.500 8.75 0.00 0.00 3.46
3391 3796 5.980116 ACAGCTGCTTTTCGTGTATATCTAG 59.020 40.000 15.27 0.00 0.00 2.43
3482 3892 7.959175 ACACTTACTGTAGTTGTTAGGATTGA 58.041 34.615 0.00 0.00 0.00 2.57
3521 3931 5.509163 GCCGATTCAGGAGTAGCTGTATTTA 60.509 44.000 0.00 0.00 0.00 1.40
3525 3935 1.681793 GCCGATTCAGGAGTAGCTGTA 59.318 52.381 0.00 0.00 0.00 2.74
3642 4068 0.678048 GGAACTTCCTTGCATCGCCT 60.678 55.000 0.00 0.00 32.53 5.52
3707 4136 2.808315 CGAGGAGATGGACGTGGG 59.192 66.667 0.00 0.00 0.00 4.61
3709 4138 1.226802 CAGCGAGGAGATGGACGTG 60.227 63.158 0.00 0.00 31.47 4.49
4015 4450 2.294074 GTCTATGACGAGGAGAGCACT 58.706 52.381 0.00 0.00 0.00 4.40
4030 4465 2.716244 CTCGCGCTGGTCGTCTAT 59.284 61.111 5.56 0.00 41.07 1.98


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

AutoCloner maintained by Alex Coulton.