Multiple sequence alignment - TraesCS4D01G205900

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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 TraesCS4D01G205900 chr4D 100.000 3983 0 0 1 3983 353519294 353523276 0.000000e+00 7356.0
1 TraesCS4D01G205900 chr4A 91.413 3610 141 57 410 3926 111295693 111292160 0.000000e+00 4793.0
2 TraesCS4D01G205900 chr4A 90.964 166 14 1 1 166 111296449 111296285 5.180000e-54 222.0
3 TraesCS4D01G205900 chr4A 82.456 285 17 13 152 419 111296268 111296000 6.700000e-53 219.0
4 TraesCS4D01G205900 chr4A 93.103 58 3 1 3927 3983 111292116 111292059 2.550000e-12 84.2
5 TraesCS4D01G205900 chr4B 94.095 3150 95 29 613 3725 437071342 437074437 0.000000e+00 4702.0
6 TraesCS4D01G205900 chr4B 96.689 151 4 1 3776 3926 437074557 437074706 2.380000e-62 250.0
7 TraesCS4D01G205900 chr4B 97.368 76 2 0 3804 3879 437074490 437074565 3.230000e-26 130.0
8 TraesCS4D01G205900 chr4B 100.000 36 0 0 3724 3759 437074455 437074490 2.570000e-07 67.6
9 TraesCS4D01G205900 chr5D 76.752 314 31 23 1869 2170 543634988 543634705 1.930000e-28 137.0
10 TraesCS4D01G205900 chr2D 92.308 78 5 1 2093 2170 568463671 568463747 4.210000e-20 110.0


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 TraesCS4D01G205900 chr4D 353519294 353523276 3982 False 7356.00 7356 100.000 1 3983 1 chr4D.!!$F1 3982
1 TraesCS4D01G205900 chr4A 111292059 111296449 4390 True 1329.55 4793 89.484 1 3983 4 chr4A.!!$R1 3982
2 TraesCS4D01G205900 chr4B 437071342 437074706 3364 False 1287.40 4702 97.038 613 3926 4 chr4B.!!$F1 3313

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
932 1308 0.040204 CAGCTTCCCCCACCAATTCT 59.960 55.0 0.00 0.0 0.0 2.40 F
1369 1746 0.108615 GGCAGCACGACATGTACTCT 60.109 55.0 0.00 0.0 0.0 3.24 F
1655 2035 0.679505 TTGGTCGTGCTAGCAGTCTT 59.320 50.0 20.03 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2188 2.270923 CGAATCAAATCGAGACTGCCA 58.729 47.619 0.00 0.00 45.48 4.92 R
2520 2956 2.571216 AACACGGCGAGCACCTACT 61.571 57.895 16.62 0.00 0.00 2.57 R
3569 4024 1.798626 ATCTCTCCAGCTGGCATGTA 58.201 50.000 28.91 9.57 34.44 2.29 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
65 66 6.959639 TCAATTTGAAGAGTTAGGTTGCTT 57.040 33.333 0.00 0.00 0.00 3.91
90 91 7.801104 TCATTGCATAGGTAGTTGATTCCTTA 58.199 34.615 0.00 0.00 33.34 2.69
91 92 8.439971 TCATTGCATAGGTAGTTGATTCCTTAT 58.560 33.333 0.00 0.00 33.34 1.73
100 101 7.127955 AGGTAGTTGATTCCTTATGACAATCCT 59.872 37.037 0.00 0.00 0.00 3.24
111 112 3.423539 TGACAATCCTCAACCTGAAGG 57.576 47.619 0.00 0.00 42.17 3.46
112 113 2.978978 TGACAATCCTCAACCTGAAGGA 59.021 45.455 2.62 0.00 38.94 3.36
120 121 3.556004 CCTCAACCTGAAGGAGTGAACTC 60.556 52.174 2.62 1.63 42.14 3.01
178 210 7.876936 TGTCTAGTAGGTCAATCGAACTATT 57.123 36.000 0.00 0.00 43.34 1.73
249 281 8.624776 CCGATGTTGTGCTATGATATCTATCTA 58.375 37.037 3.98 0.00 33.88 1.98
253 285 8.451748 TGTTGTGCTATGATATCTATCTACGTC 58.548 37.037 3.98 0.00 33.88 4.34
254 286 7.235430 TGTGCTATGATATCTATCTACGTCG 57.765 40.000 3.98 0.00 33.88 5.12
255 287 6.817140 TGTGCTATGATATCTATCTACGTCGT 59.183 38.462 2.21 2.21 33.88 4.34
256 288 7.333672 TGTGCTATGATATCTATCTACGTCGTT 59.666 37.037 1.78 0.00 33.88 3.85
257 289 8.176365 GTGCTATGATATCTATCTACGTCGTTT 58.824 37.037 1.78 0.00 33.88 3.60
258 290 8.727910 TGCTATGATATCTATCTACGTCGTTTT 58.272 33.333 1.78 0.00 33.88 2.43
286 318 8.800370 TTACACTGTATAAGATTGCAAATGGA 57.200 30.769 1.71 0.00 0.00 3.41
288 320 7.709947 ACACTGTATAAGATTGCAAATGGATG 58.290 34.615 1.71 0.00 0.00 3.51
289 321 7.340232 ACACTGTATAAGATTGCAAATGGATGT 59.660 33.333 1.71 0.00 0.00 3.06
290 322 8.839343 CACTGTATAAGATTGCAAATGGATGTA 58.161 33.333 1.71 0.00 0.00 2.29
294 326 3.569491 AGATTGCAAATGGATGTAGGGG 58.431 45.455 1.71 0.00 0.00 4.79
306 338 3.181434 GGATGTAGGGGTTTGGATATGCA 60.181 47.826 0.00 0.00 0.00 3.96
313 345 3.428862 GGGGTTTGGATATGCAAAAGACG 60.429 47.826 22.07 0.00 0.00 4.18
314 346 3.428862 GGGTTTGGATATGCAAAAGACGG 60.429 47.826 22.07 0.00 0.00 4.79
315 347 3.179048 GTTTGGATATGCAAAAGACGGC 58.821 45.455 22.07 6.92 0.00 5.68
318 350 1.268743 GGATATGCAAAAGACGGCTGC 60.269 52.381 0.00 0.00 36.60 5.25
331 363 2.248431 GCTGCGACCAACGAACAC 59.752 61.111 0.00 0.00 45.77 3.32
332 364 2.544359 CTGCGACCAACGAACACG 59.456 61.111 0.00 0.00 45.77 4.49
344 376 0.796312 CGAACACGGACAAATGAGGG 59.204 55.000 0.00 0.00 0.00 4.30
395 443 3.245052 GGGGCTCATATTAGTCCAATGCT 60.245 47.826 9.71 0.00 43.48 3.79
402 450 7.307632 GCTCATATTAGTCCAATGCTGTTGTAG 60.308 40.741 2.54 0.00 0.00 2.74
423 787 5.502153 AGATGGTCTAGTGTCATACGAAC 57.498 43.478 0.00 0.00 0.00 3.95
430 794 0.989890 GTGTCATACGAACGCCACTC 59.010 55.000 0.00 0.00 0.00 3.51
437 801 1.079819 CGAACGCCACTCTCATGGT 60.080 57.895 0.00 0.00 42.28 3.55
473 837 2.616842 GAGTTCAACTCGGAAAAGGCAA 59.383 45.455 0.65 0.00 35.28 4.52
494 865 0.602905 CGGAAGCCATACCCCGATTC 60.603 60.000 0.00 0.00 44.29 2.52
545 917 1.528776 TTCCGGTTGGTTTTCCCCG 60.529 57.895 0.00 0.00 42.02 5.73
558 930 1.187087 TTCCCCGCACAACAAAAAGT 58.813 45.000 0.00 0.00 0.00 2.66
562 934 2.192624 CCCGCACAACAAAAAGTTCTG 58.807 47.619 0.00 0.00 38.74 3.02
563 935 1.587946 CCGCACAACAAAAAGTTCTGC 59.412 47.619 0.00 0.00 45.27 4.26
564 936 1.587946 CGCACAACAAAAAGTTCTGCC 59.412 47.619 3.32 0.00 45.76 4.85
635 1007 9.252962 GGCATAATGATGTCAGGAAATAAAAAG 57.747 33.333 0.00 0.00 37.63 2.27
640 1012 7.214467 TGATGTCAGGAAATAAAAAGTGGTC 57.786 36.000 0.00 0.00 0.00 4.02
679 1051 0.673956 GGAAGGAAGAACGAGCCCAC 60.674 60.000 0.00 0.00 0.00 4.61
684 1056 0.955919 GAAGAACGAGCCCACCAAGG 60.956 60.000 0.00 0.00 37.03 3.61
685 1057 1.705997 AAGAACGAGCCCACCAAGGT 61.706 55.000 0.00 0.00 34.66 3.50
686 1058 0.834687 AGAACGAGCCCACCAAGGTA 60.835 55.000 0.00 0.00 34.66 3.08
769 1143 2.900167 CGTGGGTCGTGAGTCGTGA 61.900 63.158 0.00 0.00 40.80 4.35
771 1145 1.527611 TGGGTCGTGAGTCGTGAGT 60.528 57.895 0.00 0.00 40.80 3.41
772 1146 1.209640 GGGTCGTGAGTCGTGAGTC 59.790 63.158 0.00 0.00 40.80 3.36
773 1147 1.154450 GGTCGTGAGTCGTGAGTCG 60.154 63.158 0.60 0.00 40.80 4.18
774 1148 1.568514 GTCGTGAGTCGTGAGTCGT 59.431 57.895 0.60 0.00 40.80 4.34
775 1149 0.721811 GTCGTGAGTCGTGAGTCGTG 60.722 60.000 0.60 0.00 40.80 4.35
776 1150 2.075489 CGTGAGTCGTGAGTCGTGC 61.075 63.158 0.60 0.00 40.80 5.34
777 1151 1.008881 GTGAGTCGTGAGTCGTGCA 60.009 57.895 0.60 0.00 40.80 4.57
778 1152 1.008881 TGAGTCGTGAGTCGTGCAC 60.009 57.895 6.82 6.82 40.80 4.57
779 1153 1.729838 GAGTCGTGAGTCGTGCACC 60.730 63.158 12.15 0.00 40.80 5.01
780 1154 2.733593 GTCGTGAGTCGTGCACCC 60.734 66.667 12.15 1.70 40.80 4.61
781 1155 3.986006 TCGTGAGTCGTGCACCCC 61.986 66.667 12.15 1.29 40.80 4.95
783 1157 3.936203 GTGAGTCGTGCACCCCCA 61.936 66.667 12.15 1.41 0.00 4.96
847 1221 2.344025 CCCCCTACTATTTTATCGCGC 58.656 52.381 0.00 0.00 0.00 6.86
932 1308 0.040204 CAGCTTCCCCCACCAATTCT 59.960 55.000 0.00 0.00 0.00 2.40
933 1309 0.332972 AGCTTCCCCCACCAATTCTC 59.667 55.000 0.00 0.00 0.00 2.87
1369 1746 0.108615 GGCAGCACGACATGTACTCT 60.109 55.000 0.00 0.00 0.00 3.24
1537 1917 6.441093 TCATGTAATTTGGCTGCTTCTTAG 57.559 37.500 0.00 0.00 0.00 2.18
1538 1918 5.945784 TCATGTAATTTGGCTGCTTCTTAGT 59.054 36.000 0.00 0.00 0.00 2.24
1539 1919 7.109501 TCATGTAATTTGGCTGCTTCTTAGTA 58.890 34.615 0.00 0.00 0.00 1.82
1540 1920 6.737254 TGTAATTTGGCTGCTTCTTAGTAC 57.263 37.500 0.00 0.00 0.00 2.73
1570 1950 7.912056 TGGTCTCAAAGAATCTCATAGTTTG 57.088 36.000 0.00 0.00 0.00 2.93
1577 1957 5.033589 AGAATCTCATAGTTTGCCTGGAG 57.966 43.478 0.00 0.00 0.00 3.86
1578 1958 2.698855 TCTCATAGTTTGCCTGGAGC 57.301 50.000 0.00 0.00 44.14 4.70
1585 1965 2.716217 AGTTTGCCTGGAGCTTGTATC 58.284 47.619 0.00 0.00 44.23 2.24
1649 2029 1.394917 CTGTGATTTGGTCGTGCTAGC 59.605 52.381 8.10 8.10 0.00 3.42
1652 2032 1.001974 TGATTTGGTCGTGCTAGCAGT 59.998 47.619 20.03 0.00 0.00 4.40
1655 2035 0.679505 TTGGTCGTGCTAGCAGTCTT 59.320 50.000 20.03 0.00 0.00 3.01
1682 2087 7.547119 CGTTGTTGAATTTTCTTAGCTTGTTC 58.453 34.615 0.00 0.00 0.00 3.18
1762 2167 1.000506 GTGACCTCTTTACTGGCGTGA 59.999 52.381 0.00 0.00 0.00 4.35
1774 2179 4.685169 ACTGGCGTGATTATGTTTTCAG 57.315 40.909 0.00 0.00 0.00 3.02
1783 2188 3.980646 TTATGTTTTCAGTTGCGCTGT 57.019 38.095 9.73 0.00 45.23 4.40
1786 2191 1.065600 TTTTCAGTTGCGCTGTGGC 59.934 52.632 9.73 0.00 45.23 5.01
1900 2318 8.251026 TGTTATGGTCTCTCAGTTTGTATAGTG 58.749 37.037 0.00 0.00 0.00 2.74
1966 2384 8.621286 CAGTTTCTTGTTCATAAGGTACTGTTT 58.379 33.333 0.00 0.00 40.86 2.83
2326 2762 7.195374 TGCTAAGAGGTATGTTAGATTTGGT 57.805 36.000 0.00 0.00 34.89 3.67
2480 2916 3.577649 ATATATCGCAGAGGTGTTCCG 57.422 47.619 0.00 0.00 43.63 4.30
2682 3119 9.328845 GCATATTAATCATGTTCCACCATTTTT 57.671 29.630 0.00 0.00 0.00 1.94
2716 3153 8.410673 TTGAATGTTTATAGGTGCACCTTTTA 57.589 30.769 41.69 28.89 46.09 1.52
2726 3163 4.126437 GGTGCACCTTTTATTGCTTTGTT 58.874 39.130 29.12 0.00 39.62 2.83
2762 3199 1.216178 CCCACCTTACCGTACACCG 59.784 63.158 0.00 0.00 0.00 4.94
3028 3467 8.814931 TGATATTCAACATGAAATTTGAAGGGT 58.185 29.630 12.88 4.16 43.21 4.34
3301 3749 1.937546 CTCACATTCCTTTGCCGCCC 61.938 60.000 0.00 0.00 0.00 6.13
3523 3975 1.160137 GCAGGTGGTTGCTACTCTTG 58.840 55.000 0.00 0.88 40.89 3.02
3700 4155 8.566260 GTGCAAATCTAGCAATATTCTCTTCAT 58.434 33.333 0.00 0.00 44.64 2.57
3772 4246 5.817816 CAGGGGTCAATAAAGTGTCTGATAC 59.182 44.000 0.00 0.00 0.00 2.24
3798 4322 0.463833 GGTGGATTCGCTAGTTGGGG 60.464 60.000 0.00 0.00 0.00 4.96
3802 4326 1.209747 GGATTCGCTAGTTGGGGTTCT 59.790 52.381 0.00 0.00 0.00 3.01
3855 4379 3.740590 CTTTGCGATCTGCTAACAGTTG 58.259 45.455 10.16 0.00 46.63 3.16
3931 4455 2.763215 CCCCCTTGCAGCCAACTA 59.237 61.111 0.00 0.00 0.00 2.24
3932 4456 1.379044 CCCCCTTGCAGCCAACTAG 60.379 63.158 0.00 0.00 0.00 2.57
3933 4457 1.379044 CCCCTTGCAGCCAACTAGG 60.379 63.158 0.00 0.00 41.84 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 6.735694 GCAATGAAGCAACCTAACTCTTCAAA 60.736 38.462 7.48 0.00 45.20 2.69
65 66 6.252599 AGGAATCAACTACCTATGCAATGA 57.747 37.500 0.00 0.00 31.78 2.57
90 91 3.588842 TCCTTCAGGTTGAGGATTGTCAT 59.411 43.478 0.00 0.00 36.34 3.06
91 92 2.978978 TCCTTCAGGTTGAGGATTGTCA 59.021 45.455 0.00 0.00 36.34 3.58
100 101 3.753294 GAGTTCACTCCTTCAGGTTGA 57.247 47.619 0.00 0.00 37.02 3.18
111 112 5.061920 AGATAGTTTGTCGGAGTTCACTC 57.938 43.478 0.00 0.00 42.14 3.51
112 113 5.711036 ACTAGATAGTTTGTCGGAGTTCACT 59.289 40.000 0.00 0.00 31.13 3.41
120 121 6.740110 AGAAGCATACTAGATAGTTTGTCGG 58.260 40.000 0.00 0.00 37.51 4.79
124 125 8.561212 ACGACTAGAAGCATACTAGATAGTTTG 58.439 37.037 15.24 2.26 39.48 2.93
125 126 8.680039 ACGACTAGAAGCATACTAGATAGTTT 57.320 34.615 15.24 0.00 39.48 2.66
193 225 7.765307 AGCAAGTTCATCATTACAAATCGAAT 58.235 30.769 0.00 0.00 0.00 3.34
195 227 6.741992 AGCAAGTTCATCATTACAAATCGA 57.258 33.333 0.00 0.00 0.00 3.59
197 229 7.380602 GGCATAGCAAGTTCATCATTACAAATC 59.619 37.037 0.00 0.00 0.00 2.17
214 246 1.093972 CACAACATCGGGCATAGCAA 58.906 50.000 0.00 0.00 0.00 3.91
249 281 9.624697 TCTTATACAGTGTAAATAAAACGACGT 57.375 29.630 7.16 0.00 0.00 4.34
260 292 9.237187 TCCATTTGCAATCTTATACAGTGTAAA 57.763 29.630 7.16 2.86 0.00 2.01
261 293 8.800370 TCCATTTGCAATCTTATACAGTGTAA 57.200 30.769 7.16 0.00 0.00 2.41
262 294 8.839343 CATCCATTTGCAATCTTATACAGTGTA 58.161 33.333 5.24 5.24 0.00 2.90
263 295 7.340232 ACATCCATTTGCAATCTTATACAGTGT 59.660 33.333 0.00 0.00 0.00 3.55
264 296 7.709947 ACATCCATTTGCAATCTTATACAGTG 58.290 34.615 0.00 0.00 0.00 3.66
265 297 7.886629 ACATCCATTTGCAATCTTATACAGT 57.113 32.000 0.00 0.00 0.00 3.55
266 298 8.509690 CCTACATCCATTTGCAATCTTATACAG 58.490 37.037 0.00 0.00 0.00 2.74
281 313 5.644188 CATATCCAAACCCCTACATCCATT 58.356 41.667 0.00 0.00 0.00 3.16
282 314 4.509122 GCATATCCAAACCCCTACATCCAT 60.509 45.833 0.00 0.00 0.00 3.41
283 315 3.181434 GCATATCCAAACCCCTACATCCA 60.181 47.826 0.00 0.00 0.00 3.41
284 316 3.181434 TGCATATCCAAACCCCTACATCC 60.181 47.826 0.00 0.00 0.00 3.51
285 317 4.098914 TGCATATCCAAACCCCTACATC 57.901 45.455 0.00 0.00 0.00 3.06
286 318 4.534647 TTGCATATCCAAACCCCTACAT 57.465 40.909 0.00 0.00 0.00 2.29
288 320 4.953579 TCTTTTGCATATCCAAACCCCTAC 59.046 41.667 0.00 0.00 34.68 3.18
289 321 4.953579 GTCTTTTGCATATCCAAACCCCTA 59.046 41.667 0.00 0.00 34.68 3.53
290 322 3.769300 GTCTTTTGCATATCCAAACCCCT 59.231 43.478 0.00 0.00 34.68 4.79
294 326 3.119495 AGCCGTCTTTTGCATATCCAAAC 60.119 43.478 0.00 0.00 34.68 2.93
306 338 1.525077 TTGGTCGCAGCCGTCTTTT 60.525 52.632 0.00 0.00 35.54 2.27
313 345 2.970324 TGTTCGTTGGTCGCAGCC 60.970 61.111 0.00 0.00 39.67 4.85
314 346 2.248431 GTGTTCGTTGGTCGCAGC 59.752 61.111 0.00 0.00 39.67 5.25
315 347 2.544359 CGTGTTCGTTGGTCGCAG 59.456 61.111 0.00 0.00 39.67 5.18
318 350 1.146957 TTGTCCGTGTTCGTTGGTCG 61.147 55.000 0.00 0.00 41.41 4.79
331 363 1.378514 CCCACCCCTCATTTGTCCG 60.379 63.158 0.00 0.00 0.00 4.79
332 364 0.034089 CTCCCACCCCTCATTTGTCC 60.034 60.000 0.00 0.00 0.00 4.02
344 376 4.660938 AAACAGCGGCCTCCCACC 62.661 66.667 0.00 0.00 0.00 4.61
356 388 3.117888 AGCCCCTATATGTCCACAAACAG 60.118 47.826 0.00 0.00 31.50 3.16
360 392 2.770447 TGAGCCCCTATATGTCCACAA 58.230 47.619 0.00 0.00 0.00 3.33
373 421 3.084786 GCATTGGACTAATATGAGCCCC 58.915 50.000 0.00 0.00 0.00 5.80
395 443 6.183360 CGTATGACACTAGACCATCTACAACA 60.183 42.308 0.00 0.00 0.00 3.33
402 450 4.280461 CGTTCGTATGACACTAGACCATC 58.720 47.826 0.00 0.00 0.00 3.51
423 787 2.887568 GCGACCATGAGAGTGGCG 60.888 66.667 0.00 0.00 43.27 5.69
473 837 3.861797 CGGGGTATGGCTTCCGCT 61.862 66.667 0.00 0.00 35.95 5.52
513 884 6.532826 ACCAACCGGAACTACTTACAATTAA 58.467 36.000 9.46 0.00 35.59 1.40
514 885 6.112927 ACCAACCGGAACTACTTACAATTA 57.887 37.500 9.46 0.00 35.59 1.40
516 887 4.628963 ACCAACCGGAACTACTTACAAT 57.371 40.909 9.46 0.00 35.59 2.71
518 889 4.420522 AAACCAACCGGAACTACTTACA 57.579 40.909 9.46 0.00 35.59 2.41
519 890 4.214119 GGAAAACCAACCGGAACTACTTAC 59.786 45.833 9.46 0.00 35.59 2.34
520 891 4.388485 GGAAAACCAACCGGAACTACTTA 58.612 43.478 9.46 0.00 35.59 2.24
522 893 2.487805 GGGAAAACCAACCGGAACTACT 60.488 50.000 9.46 0.00 39.85 2.57
523 894 1.881973 GGGAAAACCAACCGGAACTAC 59.118 52.381 9.46 0.00 39.85 2.73
535 907 0.175989 TTTGTTGTGCGGGGAAAACC 59.824 50.000 0.00 0.00 39.11 3.27
562 934 3.715628 TGTTCTGCTCAAGAAAAAGGC 57.284 42.857 0.00 0.00 46.51 4.35
563 935 5.410067 TGTTTGTTCTGCTCAAGAAAAAGG 58.590 37.500 0.00 0.00 46.51 3.11
564 936 6.587608 ACTTGTTTGTTCTGCTCAAGAAAAAG 59.412 34.615 9.63 0.00 46.51 2.27
624 996 4.864704 TGCCAGACCACTTTTTATTTCC 57.135 40.909 0.00 0.00 0.00 3.13
625 997 7.492344 CCATTATGCCAGACCACTTTTTATTTC 59.508 37.037 0.00 0.00 0.00 2.17
627 999 6.667414 TCCATTATGCCAGACCACTTTTTATT 59.333 34.615 0.00 0.00 0.00 1.40
629 1001 5.575157 TCCATTATGCCAGACCACTTTTTA 58.425 37.500 0.00 0.00 0.00 1.52
635 1007 4.160252 ACAAATTCCATTATGCCAGACCAC 59.840 41.667 0.00 0.00 0.00 4.16
640 1012 6.239120 CCTTCCTACAAATTCCATTATGCCAG 60.239 42.308 0.00 0.00 0.00 4.85
679 1051 2.022934 GACCGGACTCTACTACCTTGG 58.977 57.143 9.46 0.00 0.00 3.61
684 1056 1.294857 GTCGGACCGGACTCTACTAC 58.705 60.000 15.25 0.00 34.09 2.73
685 1057 0.179000 GGTCGGACCGGACTCTACTA 59.821 60.000 15.25 0.00 37.12 1.82
686 1058 1.077858 GGTCGGACCGGACTCTACT 60.078 63.158 15.25 0.00 37.12 2.57
763 1137 2.733593 GGGTGCACGACTCACGAC 60.734 66.667 11.45 0.00 45.77 4.34
782 1156 3.966543 GTGAGGTGGGGTGGGGTG 61.967 72.222 0.00 0.00 0.00 4.61
830 1204 1.389106 GCGGCGCGATAAAATAGTAGG 59.611 52.381 19.09 0.00 0.00 3.18
831 1205 2.763930 GCGGCGCGATAAAATAGTAG 57.236 50.000 19.09 0.00 0.00 2.57
1263 1640 0.666577 CTCGGCGAAAACGGAAGACT 60.667 55.000 12.13 0.00 0.00 3.24
1408 1785 2.782222 GGTGCCGGTCTCGATAGCA 61.782 63.158 1.90 0.00 39.00 3.49
1537 1917 6.388278 AGATTCTTTGAGACCAACTACGTAC 58.612 40.000 0.00 0.00 30.88 3.67
1538 1918 6.208007 TGAGATTCTTTGAGACCAACTACGTA 59.792 38.462 0.00 0.00 30.88 3.57
1539 1919 5.010719 TGAGATTCTTTGAGACCAACTACGT 59.989 40.000 0.00 0.00 30.88 3.57
1540 1920 5.470368 TGAGATTCTTTGAGACCAACTACG 58.530 41.667 0.00 0.00 30.88 3.51
1570 1950 1.208052 TGACTGATACAAGCTCCAGGC 59.792 52.381 0.00 0.00 42.19 4.85
1585 1965 7.658982 TGCCAGATCTATAAAATAGCTTGACTG 59.341 37.037 0.00 0.00 0.00 3.51
1649 2029 5.036737 AGAAAATTCAACAACGCAAGACTG 58.963 37.500 0.00 0.00 43.62 3.51
1652 2032 5.685511 GCTAAGAAAATTCAACAACGCAAGA 59.314 36.000 0.00 0.00 43.62 3.02
1655 2035 5.181690 AGCTAAGAAAATTCAACAACGCA 57.818 34.783 0.00 0.00 0.00 5.24
1682 2087 6.936279 TGAGAACTAAAGTCCTATTCACAGG 58.064 40.000 0.00 0.00 37.00 4.00
1732 2137 0.969894 AAGAGGTCACACCCTTCGAG 59.030 55.000 0.00 0.00 39.75 4.04
1734 2139 2.299297 AGTAAAGAGGTCACACCCTTCG 59.701 50.000 0.00 0.00 39.75 3.79
1774 2179 2.959357 GAGACTGCCACAGCGCAAC 61.959 63.158 11.47 0.00 44.31 4.17
1783 2188 2.270923 CGAATCAAATCGAGACTGCCA 58.729 47.619 0.00 0.00 45.48 4.92
1786 2191 8.168626 TCAATTAAACGAATCAAATCGAGACTG 58.831 33.333 3.47 0.00 45.48 3.51
1900 2318 8.662781 TGGAGAGCATATCAACATTTAAGTAC 57.337 34.615 0.00 0.00 0.00 2.73
2082 2518 3.128415 CACACAGAACACACACATGGAAA 59.872 43.478 0.00 0.00 0.00 3.13
2326 2762 9.887629 AAATTGAATCCACAAATATGTAATGCA 57.112 25.926 0.00 0.00 37.82 3.96
2480 2916 8.958119 TCCTGAAATATTGGGCGATATATAAC 57.042 34.615 0.00 0.00 0.00 1.89
2520 2956 2.571216 AACACGGCGAGCACCTACT 61.571 57.895 16.62 0.00 0.00 2.57
2682 3119 8.405531 GCACCTATAAACATTCAATAAAGCAGA 58.594 33.333 0.00 0.00 0.00 4.26
2762 3199 3.243367 TGGTGCACTGTAACAAATGAAGC 60.243 43.478 17.98 0.00 0.00 3.86
3028 3467 2.937959 AAAGCGGGAACAAAGGGGCA 62.938 55.000 0.00 0.00 0.00 5.36
3301 3749 6.203145 CACATCTGAATTTCAGCCTCTAGATG 59.797 42.308 19.53 17.17 43.95 2.90
3327 3779 3.266772 AGGGTTTAGCTTGATCACCATGA 59.733 43.478 0.00 0.00 0.00 3.07
3523 3975 9.683069 AATAAAGCAATGCTAGCATAATAACAC 57.317 29.630 29.77 13.85 38.25 3.32
3569 4024 1.798626 ATCTCTCCAGCTGGCATGTA 58.201 50.000 28.91 9.57 34.44 2.29
3700 4155 0.246360 CTGGCATGTGACTCGGTACA 59.754 55.000 0.00 0.00 0.00 2.90
3772 4246 2.293677 ACTAGCGAATCCACCATACTCG 59.706 50.000 0.00 0.00 0.00 4.18
3798 4322 8.017946 CACCTTAATGCTTCTTCAGTAAAGAAC 58.982 37.037 0.00 0.00 46.64 3.01
3802 4326 5.767665 TGCACCTTAATGCTTCTTCAGTAAA 59.232 36.000 2.92 0.00 46.28 2.01
3855 4379 2.698274 ACCAAACCAATTGACAACCCTC 59.302 45.455 7.12 0.00 41.85 4.30
3926 4450 8.378172 TCCAAATAATATTTCGAGCCTAGTTG 57.622 34.615 0.00 0.00 0.00 3.16
3927 4451 8.837389 GTTCCAAATAATATTTCGAGCCTAGTT 58.163 33.333 0.00 0.00 0.00 2.24
3928 4452 7.444487 GGTTCCAAATAATATTTCGAGCCTAGT 59.556 37.037 15.18 0.00 0.00 2.57
3929 4453 7.094762 GGGTTCCAAATAATATTTCGAGCCTAG 60.095 40.741 19.36 0.00 0.00 3.02
3930 4454 6.713450 GGGTTCCAAATAATATTTCGAGCCTA 59.287 38.462 19.36 0.00 0.00 3.93
3931 4455 5.535030 GGGTTCCAAATAATATTTCGAGCCT 59.465 40.000 19.36 0.00 0.00 4.58
3932 4456 5.300792 TGGGTTCCAAATAATATTTCGAGCC 59.699 40.000 14.47 14.47 0.00 4.70
3933 4457 6.385649 TGGGTTCCAAATAATATTTCGAGC 57.614 37.500 0.00 0.00 0.00 5.03
3935 4459 7.948034 AGTTGGGTTCCAAATAATATTTCGA 57.052 32.000 0.45 0.00 45.73 3.71


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

AutoCloner maintained by Alex Coulton.