Multiple sequence alignment - TraesCS2A01G371700

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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 TraesCS2A01G371700 chr2A 100.000 4034 0 0 1 4034 613990447 613994480 0.000000e+00 7450.0
1 TraesCS2A01G371700 chr2A 76.955 1931 365 48 1066 2974 613989728 613987856 0.000000e+00 1027.0
2 TraesCS2A01G371700 chr2D 94.954 3072 96 25 995 4034 472470442 472473486 0.000000e+00 4759.0
3 TraesCS2A01G371700 chr2D 76.729 1938 385 40 1052 2974 472468946 472467060 0.000000e+00 1020.0
4 TraesCS2A01G371700 chr2D 81.232 1055 74 50 1 976 472469365 472470374 0.000000e+00 737.0
5 TraesCS2A01G371700 chr2B 93.883 3057 103 29 995 4034 551637813 551640802 0.000000e+00 4532.0
6 TraesCS2A01G371700 chr2B 76.489 1948 385 47 1047 2974 551635263 551633369 0.000000e+00 992.0
7 TraesCS2A01G371700 chr2B 88.451 381 17 7 563 921 551637108 551637483 6.190000e-118 435.0
8 TraesCS2A01G371700 chr2B 76.482 523 56 24 1 480 551635654 551636152 5.250000e-54 222.0
9 TraesCS2A01G371700 chr2B 81.319 182 34 0 2112 2293 132510624 132510443 9.030000e-32 148.0
10 TraesCS2A01G371700 chr5B 76.745 1948 373 64 1052 2967 586359938 586358039 0.000000e+00 1014.0
11 TraesCS2A01G371700 chr5B 78.215 661 115 17 2006 2665 664683957 664683325 2.920000e-106 396.0
12 TraesCS2A01G371700 chr5A 76.337 1944 392 53 1050 2967 597688203 597686302 0.000000e+00 979.0
13 TraesCS2A01G371700 chr5A 77.912 661 117 17 2006 2665 655462796 655462164 6.320000e-103 385.0
14 TraesCS2A01G371700 chr5A 78.347 605 106 13 2062 2664 655991188 655991769 6.370000e-98 368.0
15 TraesCS2A01G371700 chr5D 79.646 1130 206 17 1845 2967 478594582 478595694 0.000000e+00 791.0
16 TraesCS2A01G371700 chr5D 74.338 491 105 17 1138 1622 478590724 478591199 5.320000e-44 189.0
17 TraesCS2A01G371700 chr5D 77.333 300 57 9 1236 1531 478560242 478560534 2.490000e-37 167.0
18 TraesCS2A01G371700 chr1B 74.153 1888 400 60 1112 2961 266109660 266111497 0.000000e+00 702.0
19 TraesCS2A01G371700 chr1A 73.728 1945 424 61 1053 2961 238671710 238673603 0.000000e+00 680.0
20 TraesCS2A01G371700 chr7D 73.368 1716 368 70 1039 2721 47454070 47455729 4.560000e-154 555.0
21 TraesCS2A01G371700 chr4A 73.430 1513 343 47 1237 2721 662202219 662200738 2.780000e-141 512.0
22 TraesCS2A01G371700 chr4B 80.769 182 34 1 2112 2293 281901881 281901701 1.510000e-29 141.0
23 TraesCS2A01G371700 chr4B 80.469 128 23 2 1360 1486 574169729 574169855 3.320000e-16 97.1
24 TraesCS2A01G371700 chr4D 79.845 129 22 4 1360 1486 459383716 459383842 1.540000e-14 91.6


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 TraesCS2A01G371700 chr2A 613990447 613994480 4033 False 7450.000000 7450 100.000 1 4034 1 chr2A.!!$F1 4033
1 TraesCS2A01G371700 chr2A 613987856 613989728 1872 True 1027.000000 1027 76.955 1066 2974 1 chr2A.!!$R1 1908
2 TraesCS2A01G371700 chr2D 472469365 472473486 4121 False 2748.000000 4759 88.093 1 4034 2 chr2D.!!$F1 4033
3 TraesCS2A01G371700 chr2D 472467060 472468946 1886 True 1020.000000 1020 76.729 1052 2974 1 chr2D.!!$R1 1922
4 TraesCS2A01G371700 chr2B 551635654 551640802 5148 False 1729.666667 4532 86.272 1 4034 3 chr2B.!!$F1 4033
5 TraesCS2A01G371700 chr2B 551633369 551635263 1894 True 992.000000 992 76.489 1047 2974 1 chr2B.!!$R2 1927
6 TraesCS2A01G371700 chr5B 586358039 586359938 1899 True 1014.000000 1014 76.745 1052 2967 1 chr5B.!!$R1 1915
7 TraesCS2A01G371700 chr5B 664683325 664683957 632 True 396.000000 396 78.215 2006 2665 1 chr5B.!!$R2 659
8 TraesCS2A01G371700 chr5A 597686302 597688203 1901 True 979.000000 979 76.337 1050 2967 1 chr5A.!!$R1 1917
9 TraesCS2A01G371700 chr5A 655462164 655462796 632 True 385.000000 385 77.912 2006 2665 1 chr5A.!!$R2 659
10 TraesCS2A01G371700 chr5A 655991188 655991769 581 False 368.000000 368 78.347 2062 2664 1 chr5A.!!$F1 602
11 TraesCS2A01G371700 chr5D 478590724 478595694 4970 False 490.000000 791 76.992 1138 2967 2 chr5D.!!$F2 1829
12 TraesCS2A01G371700 chr1B 266109660 266111497 1837 False 702.000000 702 74.153 1112 2961 1 chr1B.!!$F1 1849
13 TraesCS2A01G371700 chr1A 238671710 238673603 1893 False 680.000000 680 73.728 1053 2961 1 chr1A.!!$F1 1908
14 TraesCS2A01G371700 chr7D 47454070 47455729 1659 False 555.000000 555 73.368 1039 2721 1 chr7D.!!$F1 1682
15 TraesCS2A01G371700 chr4A 662200738 662202219 1481 True 512.000000 512 73.430 1237 2721 1 chr4A.!!$R1 1484

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
170 177 0.102481 ACCGCAACGCTGTATCCTAG 59.898 55.0 0.00 0.00 0.00 3.02 F
173 180 0.105039 GCAACGCTGTATCCTAGCCT 59.895 55.0 0.00 0.00 37.90 4.58 F
757 1721 0.108709 CCATCGCCCACAATTTGGTG 60.109 55.0 0.78 0.00 45.25 4.17 F
1525 2763 0.927083 CGACAACGCGGGATACTACG 60.927 60.0 12.47 1.19 40.05 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 2753 0.230769 CGTCGTCGTCGTAGTATCCC 59.769 60.000 3.67 0.00 38.33 3.85 R
1679 6123 0.959372 GACGGAGGAGAGGTTGACGA 60.959 60.000 0.00 0.00 0.00 4.20 R
2308 6770 2.881352 CGCCGTCTTCTTCTCGCC 60.881 66.667 0.00 0.00 0.00 5.54 R
3093 7580 0.106149 ACTCACCCGGTTCTGAACAC 59.894 55.000 21.01 10.18 0.00 3.32 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
78 79 6.625081 CGGGAGTCAAAGTCAAAAAGAAGTTT 60.625 38.462 0.00 0.00 0.00 2.66
114 115 6.561070 ACATATCTTATTAGGTTAGGTGGGCA 59.439 38.462 0.00 0.00 0.00 5.36
118 119 5.430417 TCTTATTAGGTTAGGTGGGCAATGA 59.570 40.000 0.00 0.00 0.00 2.57
150 157 0.681733 AGTGAGTGGTTGAGCGTCAT 59.318 50.000 0.00 0.00 0.00 3.06
162 169 2.695055 CGTCATACCGCAACGCTG 59.305 61.111 0.00 0.00 0.00 5.18
163 170 2.092291 CGTCATACCGCAACGCTGT 61.092 57.895 0.00 0.00 0.00 4.40
164 171 0.799152 CGTCATACCGCAACGCTGTA 60.799 55.000 0.00 0.00 33.29 2.74
165 172 1.567504 GTCATACCGCAACGCTGTAT 58.432 50.000 0.00 0.00 38.98 2.29
166 173 1.521423 GTCATACCGCAACGCTGTATC 59.479 52.381 0.72 0.00 36.97 2.24
168 175 0.750850 ATACCGCAACGCTGTATCCT 59.249 50.000 0.00 0.00 34.77 3.24
169 176 1.391577 TACCGCAACGCTGTATCCTA 58.608 50.000 0.00 0.00 0.00 2.94
170 177 0.102481 ACCGCAACGCTGTATCCTAG 59.898 55.000 0.00 0.00 0.00 3.02
171 178 1.215655 CCGCAACGCTGTATCCTAGC 61.216 60.000 0.00 0.00 37.80 3.42
172 179 1.215655 CGCAACGCTGTATCCTAGCC 61.216 60.000 0.00 0.00 37.90 3.93
173 180 0.105039 GCAACGCTGTATCCTAGCCT 59.895 55.000 0.00 0.00 37.90 4.58
174 181 1.858091 CAACGCTGTATCCTAGCCTG 58.142 55.000 0.00 0.00 37.90 4.85
176 183 2.002505 ACGCTGTATCCTAGCCTGAT 57.997 50.000 0.00 0.00 37.90 2.90
177 184 3.156288 ACGCTGTATCCTAGCCTGATA 57.844 47.619 0.00 0.00 37.90 2.15
178 185 3.085533 ACGCTGTATCCTAGCCTGATAG 58.914 50.000 0.00 0.00 37.90 2.08
181 188 5.126779 CGCTGTATCCTAGCCTGATAGATA 58.873 45.833 0.00 0.00 37.90 1.98
182 189 5.008217 CGCTGTATCCTAGCCTGATAGATAC 59.992 48.000 0.00 0.00 37.90 2.24
185 192 6.901300 TGTATCCTAGCCTGATAGATACGAT 58.099 40.000 0.00 0.00 0.00 3.73
187 194 7.932491 TGTATCCTAGCCTGATAGATACGATAC 59.068 40.741 0.00 0.00 31.13 2.24
188 195 5.358090 TCCTAGCCTGATAGATACGATACG 58.642 45.833 0.00 0.00 0.00 3.06
212 219 0.319555 AGCTGCTAACTGCGACGAAA 60.320 50.000 0.00 0.00 46.63 3.46
222 229 0.237235 TGCGACGAAATTGAGTTGGC 59.763 50.000 0.00 4.25 0.00 4.52
223 230 0.789383 GCGACGAAATTGAGTTGGCG 60.789 55.000 0.00 0.00 0.00 5.69
224 231 0.789383 CGACGAAATTGAGTTGGCGC 60.789 55.000 0.00 0.00 0.00 6.53
251 258 0.243907 TCTTTGACTTCTCCTCGGCG 59.756 55.000 0.00 0.00 0.00 6.46
255 262 1.590259 GACTTCTCCTCGGCGCATC 60.590 63.158 10.83 0.00 0.00 3.91
256 263 2.284798 GACTTCTCCTCGGCGCATCA 62.285 60.000 10.83 0.00 0.00 3.07
258 265 2.563050 CTTCTCCTCGGCGCATCACA 62.563 60.000 10.83 0.00 0.00 3.58
267 280 1.665679 CGGCGCATCACATTTCTTACT 59.334 47.619 10.83 0.00 0.00 2.24
285 298 5.527951 TCTTACTACTCGTGTCAGGATCATC 59.472 44.000 0.00 0.00 0.00 2.92
286 299 3.892284 ACTACTCGTGTCAGGATCATCT 58.108 45.455 0.00 0.00 0.00 2.90
292 305 4.023980 TCGTGTCAGGATCATCTAAGGTT 58.976 43.478 0.00 0.00 0.00 3.50
293 306 5.198207 TCGTGTCAGGATCATCTAAGGTTA 58.802 41.667 0.00 0.00 0.00 2.85
296 309 6.276847 GTGTCAGGATCATCTAAGGTTACAG 58.723 44.000 0.00 0.00 0.00 2.74
301 314 7.786943 TCAGGATCATCTAAGGTTACAGAGAAT 59.213 37.037 0.00 0.00 0.00 2.40
303 316 8.428063 AGGATCATCTAAGGTTACAGAGAATTG 58.572 37.037 0.00 0.00 0.00 2.32
315 328 2.945668 CAGAGAATTGGACCCGGAAATC 59.054 50.000 0.73 0.00 0.00 2.17
318 331 1.035385 AATTGGACCCGGAAATCGCC 61.035 55.000 0.73 0.00 37.59 5.54
321 334 2.267961 GACCCGGAAATCGCCAGT 59.732 61.111 0.73 0.00 37.59 4.00
322 335 1.814169 GACCCGGAAATCGCCAGTC 60.814 63.158 0.73 0.00 37.59 3.51
332 355 4.467735 GAAATCGCCAGTCTCAAAAGAAC 58.532 43.478 0.00 0.00 31.93 3.01
333 356 1.878953 TCGCCAGTCTCAAAAGAACC 58.121 50.000 0.00 0.00 31.93 3.62
339 362 0.511653 GTCTCAAAAGAACCGGCGTC 59.488 55.000 6.01 0.00 31.93 5.19
362 386 5.518847 TCGTATTAAAACCTCGAAGCAGATG 59.481 40.000 0.00 0.00 0.00 2.90
366 390 2.611225 AACCTCGAAGCAGATGGATC 57.389 50.000 0.00 0.00 0.00 3.36
396 438 1.382629 CCACCGGGGAAAATGAGGT 59.617 57.895 4.41 0.00 40.01 3.85
405 447 3.282885 GGGAAAATGAGGTGAGTGGATC 58.717 50.000 0.00 0.00 0.00 3.36
414 456 1.656652 GTGAGTGGATCGGTCAATGG 58.343 55.000 0.00 0.00 0.00 3.16
415 457 1.207089 GTGAGTGGATCGGTCAATGGA 59.793 52.381 0.00 0.00 0.00 3.41
416 458 1.482182 TGAGTGGATCGGTCAATGGAG 59.518 52.381 0.00 0.00 0.00 3.86
417 459 1.482593 GAGTGGATCGGTCAATGGAGT 59.517 52.381 0.00 0.00 0.00 3.85
469 517 2.355837 GCACACGAGACGAGCCAA 60.356 61.111 0.00 0.00 0.00 4.52
561 651 1.270199 CCTGCATGCAGCCTCTAGTAG 60.270 57.143 37.11 19.15 44.83 2.57
668 1628 4.681978 GAACGGGCAGCGGACAGT 62.682 66.667 0.00 0.00 28.63 3.55
686 1646 1.600636 TGACAAAGCCAAGAGCCCG 60.601 57.895 0.00 0.00 45.47 6.13
737 1701 1.205820 CACATGTGCAGTCGCTGTG 59.794 57.895 13.94 0.00 39.64 3.66
753 1717 1.184322 TGTGCCATCGCCCACAATTT 61.184 50.000 0.00 0.00 38.87 1.82
757 1721 0.108709 CCATCGCCCACAATTTGGTG 60.109 55.000 0.78 0.00 45.25 4.17
785 1749 5.095490 CGACCAAACATTAGATTTTGCCTC 58.905 41.667 0.00 0.00 32.34 4.70
838 1802 2.703007 ACCAGGATCTGTGCTAATCTCC 59.297 50.000 0.00 0.00 0.00 3.71
851 1815 5.232414 GTGCTAATCTCCACGTTTACATCTC 59.768 44.000 0.00 0.00 0.00 2.75
867 1831 2.509052 TCTCGGTCAACTTCACACTG 57.491 50.000 0.00 0.00 0.00 3.66
978 2159 4.393155 AGCCACGGCATTCGCAGA 62.393 61.111 11.35 0.00 44.88 4.26
996 2206 2.359848 CAGACTGCAGAGATCCAGAGAG 59.640 54.545 23.35 0.00 33.40 3.20
997 2207 2.241941 AGACTGCAGAGATCCAGAGAGA 59.758 50.000 23.35 0.00 33.40 3.10
1024 2253 1.685355 GCTCCTTCTCCTGCTCCTCC 61.685 65.000 0.00 0.00 0.00 4.30
1026 2255 1.216678 CTCCTTCTCCTGCTCCTCCTA 59.783 57.143 0.00 0.00 0.00 2.94
1525 2763 0.927083 CGACAACGCGGGATACTACG 60.927 60.000 12.47 1.19 40.05 3.51
2190 6652 2.291043 GGAGGTGGTGACCATCGGT 61.291 63.158 7.94 0.00 45.98 4.69
2308 6770 1.081641 AAGCACCTGTACGACGACG 60.082 57.895 5.58 5.58 45.75 5.12
2309 6771 2.467946 AAGCACCTGTACGACGACGG 62.468 60.000 12.58 0.43 44.46 4.79
2310 6772 2.503375 CACCTGTACGACGACGGC 60.503 66.667 12.58 0.00 44.46 5.68
2311 6773 4.093952 ACCTGTACGACGACGGCG 62.094 66.667 23.84 23.84 44.46 6.46
2321 6783 0.793853 GACGACGGCGAGAAGAAGAC 60.794 60.000 22.49 0.00 41.64 3.01
2323 6785 1.514443 GACGGCGAGAAGAAGACGG 60.514 63.158 16.62 0.00 0.00 4.79
3083 7570 2.203401 GCTGTCTGCTAGCATCTTCAG 58.797 52.381 19.72 21.57 40.81 3.02
3088 7575 5.114780 TGTCTGCTAGCATCTTCAGATTTC 58.885 41.667 19.72 0.06 37.81 2.17
3091 7578 4.507710 TGCTAGCATCTTCAGATTTCGTT 58.492 39.130 14.93 0.00 31.21 3.85
3093 7580 5.163824 TGCTAGCATCTTCAGATTTCGTTTG 60.164 40.000 14.93 0.00 31.21 2.93
3124 7611 1.333619 CGGGTGAGTTTCTTTGTGTGG 59.666 52.381 0.00 0.00 0.00 4.17
3125 7612 2.375146 GGGTGAGTTTCTTTGTGTGGT 58.625 47.619 0.00 0.00 0.00 4.16
3126 7613 3.547746 GGGTGAGTTTCTTTGTGTGGTA 58.452 45.455 0.00 0.00 0.00 3.25
3127 7614 3.314357 GGGTGAGTTTCTTTGTGTGGTAC 59.686 47.826 0.00 0.00 0.00 3.34
3167 7654 3.003275 ACCTGAATGTAAAGTGTTGTGCG 59.997 43.478 0.00 0.00 0.00 5.34
3208 7695 9.330063 GGTTTGATGTTCAGATGAGATATTACA 57.670 33.333 0.00 0.00 0.00 2.41
3251 7739 0.681243 GTTTGATCTCCCACCCCAGC 60.681 60.000 0.00 0.00 0.00 4.85
3255 7743 0.394899 GATCTCCCACCCCAGCTTTG 60.395 60.000 0.00 0.00 0.00 2.77
3257 7745 0.474854 TCTCCCACCCCAGCTTTGTA 60.475 55.000 0.00 0.00 0.00 2.41
3339 7841 9.778741 AATCTGAATATTTCGTTTATGCTAGGA 57.221 29.630 0.00 0.00 0.00 2.94
3340 7842 8.818141 TCTGAATATTTCGTTTATGCTAGGAG 57.182 34.615 0.00 0.00 0.00 3.69
3341 7843 8.421784 TCTGAATATTTCGTTTATGCTAGGAGT 58.578 33.333 0.00 0.00 0.00 3.85
3342 7844 9.692749 CTGAATATTTCGTTTATGCTAGGAGTA 57.307 33.333 0.00 0.00 0.00 2.59
3343 7845 9.692749 TGAATATTTCGTTTATGCTAGGAGTAG 57.307 33.333 0.00 0.00 0.00 2.57
3438 7966 8.941977 AGCGTGTTGAACATATTTTTACAGATA 58.058 29.630 0.00 0.00 0.00 1.98
3540 8068 9.590451 CATATTGCTCAGTAAAATTGGTTTGAT 57.410 29.630 0.00 0.00 0.00 2.57
3554 8087 5.799827 TGGTTTGATTTACCCCAAAGAAG 57.200 39.130 0.00 0.00 33.52 2.85
3558 8091 6.929049 GGTTTGATTTACCCCAAAGAAGAAAG 59.071 38.462 0.00 0.00 33.52 2.62
3585 8118 1.063942 TCTGGGCATCTAGAAGACGGA 60.064 52.381 0.00 0.00 0.00 4.69
3615 8148 3.508744 AAATAATTGGTCCGCTGCAAG 57.491 42.857 0.00 0.00 0.00 4.01
3690 8224 5.065731 CCTTCCAGAAGAAATAGCATGTGAC 59.934 44.000 9.00 0.00 40.79 3.67
3747 8281 5.513233 ACTTTGTGCTTCCAGAATCCATAT 58.487 37.500 0.00 0.00 0.00 1.78
3748 8282 6.662755 ACTTTGTGCTTCCAGAATCCATATA 58.337 36.000 0.00 0.00 0.00 0.86
3749 8283 6.543831 ACTTTGTGCTTCCAGAATCCATATAC 59.456 38.462 0.00 0.00 0.00 1.47
3786 8324 2.082231 CTGTCAGAGCAACCAGATTGG 58.918 52.381 0.00 0.00 45.02 3.16
3812 8350 4.371855 CATCATATGCATGGGATGAAGC 57.628 45.455 26.09 0.00 39.52 3.86
3816 8354 1.868713 ATGCATGGGATGAAGCCAAA 58.131 45.000 0.00 0.00 0.00 3.28
3834 8372 1.480789 AAGAACAAAACCAAGGCCGT 58.519 45.000 0.00 0.00 0.00 5.68
3877 8415 8.325421 TCTACGCAATAACAAATCCTACAAAA 57.675 30.769 0.00 0.00 0.00 2.44
3921 8459 6.309737 ACACAACGATCGTTTCTAAGGAATAC 59.690 38.462 29.89 0.00 36.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 7.016153 TGCCCACCTAACCTAATAAGATATG 57.984 40.000 0.00 0.00 0.00 1.78
91 92 7.642094 TTGCCCACCTAACCTAATAAGATAT 57.358 36.000 0.00 0.00 0.00 1.63
92 93 7.293771 TCATTGCCCACCTAACCTAATAAGATA 59.706 37.037 0.00 0.00 0.00 1.98
93 94 5.987019 TTGCCCACCTAACCTAATAAGAT 57.013 39.130 0.00 0.00 0.00 2.40
94 95 5.430417 TCATTGCCCACCTAACCTAATAAGA 59.570 40.000 0.00 0.00 0.00 2.10
95 96 5.531287 GTCATTGCCCACCTAACCTAATAAG 59.469 44.000 0.00 0.00 0.00 1.73
96 97 5.044772 TGTCATTGCCCACCTAACCTAATAA 60.045 40.000 0.00 0.00 0.00 1.40
97 98 4.475381 TGTCATTGCCCACCTAACCTAATA 59.525 41.667 0.00 0.00 0.00 0.98
98 99 3.268334 TGTCATTGCCCACCTAACCTAAT 59.732 43.478 0.00 0.00 0.00 1.73
99 100 2.645297 TGTCATTGCCCACCTAACCTAA 59.355 45.455 0.00 0.00 0.00 2.69
100 101 2.270858 TGTCATTGCCCACCTAACCTA 58.729 47.619 0.00 0.00 0.00 3.08
101 102 1.072266 TGTCATTGCCCACCTAACCT 58.928 50.000 0.00 0.00 0.00 3.50
102 103 2.143876 ATGTCATTGCCCACCTAACC 57.856 50.000 0.00 0.00 0.00 2.85
114 115 6.111382 CACTCACTCCTGTCATAATGTCATT 58.889 40.000 3.06 3.06 0.00 2.57
118 119 3.840666 ACCACTCACTCCTGTCATAATGT 59.159 43.478 0.00 0.00 0.00 2.71
150 157 1.335810 CTAGGATACAGCGTTGCGGTA 59.664 52.381 0.00 4.37 42.50 4.02
159 166 5.008217 CGTATCTATCAGGCTAGGATACAGC 59.992 48.000 18.84 0.00 41.41 4.40
160 167 6.350103 TCGTATCTATCAGGCTAGGATACAG 58.650 44.000 18.84 14.28 41.41 2.74
161 168 6.309389 TCGTATCTATCAGGCTAGGATACA 57.691 41.667 18.84 2.45 41.41 2.29
162 169 7.116662 CGTATCGTATCTATCAGGCTAGGATAC 59.883 44.444 11.33 11.33 37.95 2.24
163 170 7.015001 TCGTATCGTATCTATCAGGCTAGGATA 59.985 40.741 0.00 0.00 0.00 2.59
164 171 5.992829 CGTATCGTATCTATCAGGCTAGGAT 59.007 44.000 0.00 0.00 0.00 3.24
165 172 5.128335 TCGTATCGTATCTATCAGGCTAGGA 59.872 44.000 0.00 0.00 0.00 2.94
166 173 5.358090 TCGTATCGTATCTATCAGGCTAGG 58.642 45.833 0.00 0.00 0.00 3.02
168 175 5.358090 CCTCGTATCGTATCTATCAGGCTA 58.642 45.833 0.00 0.00 0.00 3.93
169 176 4.193090 CCTCGTATCGTATCTATCAGGCT 58.807 47.826 0.00 0.00 0.00 4.58
170 177 3.242804 GCCTCGTATCGTATCTATCAGGC 60.243 52.174 0.00 0.00 37.35 4.85
171 178 3.939592 TGCCTCGTATCGTATCTATCAGG 59.060 47.826 0.00 0.00 0.00 3.86
172 179 4.495019 GCTGCCTCGTATCGTATCTATCAG 60.495 50.000 0.00 0.00 0.00 2.90
173 180 3.374367 GCTGCCTCGTATCGTATCTATCA 59.626 47.826 0.00 0.00 0.00 2.15
174 181 3.623960 AGCTGCCTCGTATCGTATCTATC 59.376 47.826 0.00 0.00 0.00 2.08
176 183 2.742589 CAGCTGCCTCGTATCGTATCTA 59.257 50.000 0.00 0.00 0.00 1.98
177 184 1.537638 CAGCTGCCTCGTATCGTATCT 59.462 52.381 0.00 0.00 0.00 1.98
178 185 1.970447 CAGCTGCCTCGTATCGTATC 58.030 55.000 0.00 0.00 0.00 2.24
181 188 1.101635 TAGCAGCTGCCTCGTATCGT 61.102 55.000 34.39 15.49 43.38 3.73
182 189 0.030773 TTAGCAGCTGCCTCGTATCG 59.969 55.000 34.39 0.00 43.38 2.92
185 192 0.173481 CAGTTAGCAGCTGCCTCGTA 59.827 55.000 34.39 17.83 43.38 3.43
187 194 3.791539 CAGTTAGCAGCTGCCTCG 58.208 61.111 34.39 15.27 43.38 4.63
222 229 4.520846 GTCAAAGATGGGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
223 230 2.583685 GAAGTCAAAGATGGGCGCGC 62.584 60.000 25.94 25.94 0.00 6.86
224 231 1.021390 AGAAGTCAAAGATGGGCGCG 61.021 55.000 0.00 0.00 0.00 6.86
231 238 1.134965 CGCCGAGGAGAAGTCAAAGAT 60.135 52.381 0.00 0.00 0.00 2.40
251 258 5.577164 ACACGAGTAGTAAGAAATGTGATGC 59.423 40.000 0.00 0.00 0.00 3.91
255 262 5.573282 CCTGACACGAGTAGTAAGAAATGTG 59.427 44.000 0.00 0.00 0.00 3.21
256 263 5.475909 TCCTGACACGAGTAGTAAGAAATGT 59.524 40.000 0.00 0.00 0.00 2.71
258 265 6.377429 TGATCCTGACACGAGTAGTAAGAAAT 59.623 38.462 0.00 0.00 0.00 2.17
267 280 4.822350 CCTTAGATGATCCTGACACGAGTA 59.178 45.833 0.00 0.00 0.00 2.59
285 298 5.429130 GGGTCCAATTCTCTGTAACCTTAG 58.571 45.833 0.00 0.00 0.00 2.18
286 299 4.081309 CGGGTCCAATTCTCTGTAACCTTA 60.081 45.833 0.00 0.00 0.00 2.69
292 305 2.241281 TCCGGGTCCAATTCTCTGTA 57.759 50.000 0.00 0.00 0.00 2.74
293 306 1.358152 TTCCGGGTCCAATTCTCTGT 58.642 50.000 0.00 0.00 0.00 3.41
296 309 1.940613 CGATTTCCGGGTCCAATTCTC 59.059 52.381 0.00 0.00 33.91 2.87
301 314 2.045731 GGCGATTTCCGGGTCCAA 60.046 61.111 0.00 0.00 39.04 3.53
303 316 2.513897 CTGGCGATTTCCGGGTCC 60.514 66.667 0.00 0.00 39.04 4.46
315 328 0.512952 CGGTTCTTTTGAGACTGGCG 59.487 55.000 0.00 0.00 0.00 5.69
318 331 0.512952 CGCCGGTTCTTTTGAGACTG 59.487 55.000 1.90 0.00 0.00 3.51
321 334 0.942410 CGACGCCGGTTCTTTTGAGA 60.942 55.000 1.90 0.00 0.00 3.27
322 335 1.219522 ACGACGCCGGTTCTTTTGAG 61.220 55.000 1.90 0.00 40.78 3.02
332 355 1.589779 GAGGTTTTAATACGACGCCGG 59.410 52.381 0.00 0.00 40.78 6.13
333 356 1.253545 CGAGGTTTTAATACGACGCCG 59.746 52.381 0.00 0.00 42.50 6.46
339 362 5.276868 CCATCTGCTTCGAGGTTTTAATACG 60.277 44.000 0.00 0.00 0.00 3.06
366 390 0.965363 CCCGGTGGTTGAGGATTTGG 60.965 60.000 0.00 0.00 0.00 3.28
396 438 1.482182 CTCCATTGACCGATCCACTCA 59.518 52.381 0.00 0.00 0.00 3.41
405 447 1.273606 ACTCACTCACTCCATTGACCG 59.726 52.381 0.00 0.00 0.00 4.79
414 456 0.952984 GGCTTGCCACTCACTCACTC 60.953 60.000 6.79 0.00 0.00 3.51
415 457 1.072159 GGCTTGCCACTCACTCACT 59.928 57.895 6.79 0.00 0.00 3.41
416 458 1.968540 GGGCTTGCCACTCACTCAC 60.969 63.158 14.04 0.00 0.00 3.51
417 459 2.431683 GGGCTTGCCACTCACTCA 59.568 61.111 14.04 0.00 0.00 3.41
450 498 2.505118 GGCTCGTCTCGTGTGCTC 60.505 66.667 0.00 0.00 0.00 4.26
455 503 0.734253 CTTCCTTGGCTCGTCTCGTG 60.734 60.000 0.00 0.00 0.00 4.35
457 505 1.153745 CCTTCCTTGGCTCGTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
526 616 4.320456 AGGTGCAGCCCACTCACG 62.320 66.667 13.29 0.00 44.08 4.35
528 618 4.648626 GCAGGTGCAGCCCACTCA 62.649 66.667 13.29 0.00 44.08 3.41
538 628 2.881539 TAGAGGCTGCATGCAGGTGC 62.882 60.000 40.59 30.15 45.15 5.01
539 629 0.814410 CTAGAGGCTGCATGCAGGTG 60.814 60.000 40.59 23.00 45.15 4.00
540 630 1.270414 ACTAGAGGCTGCATGCAGGT 61.270 55.000 40.59 28.34 45.15 4.00
541 631 0.755079 TACTAGAGGCTGCATGCAGG 59.245 55.000 40.59 27.74 45.15 4.85
542 632 1.411977 ACTACTAGAGGCTGCATGCAG 59.588 52.381 37.81 37.81 45.15 4.41
599 1538 4.789075 CGAATGGACGCGACCGGT 62.789 66.667 22.04 6.92 39.22 5.28
668 1628 1.600636 CGGGCTCTTGGCTTTGTCA 60.601 57.895 0.00 0.00 41.46 3.58
686 1646 2.107953 GGAGCCGTGATGCCTCTC 59.892 66.667 0.00 0.00 0.00 3.20
717 1681 0.033366 ACAGCGACTGCACATGTGTA 59.967 50.000 26.01 21.19 46.23 2.90
737 1701 1.153588 CCAAATTGTGGGCGATGGC 60.154 57.895 0.00 0.00 44.64 4.40
749 1713 3.370231 GGTCGCGCCCACCAAATT 61.370 61.111 16.58 0.00 33.63 1.82
757 1721 1.022451 TCTAATGTTTGGTCGCGCCC 61.022 55.000 15.40 8.30 36.04 6.13
770 1734 3.209410 AGGAGCGAGGCAAAATCTAATG 58.791 45.455 0.00 0.00 0.00 1.90
785 1749 0.451383 CTGTGAGAGTGAGAGGAGCG 59.549 60.000 0.00 0.00 0.00 5.03
838 1802 3.314553 AGTTGACCGAGATGTAAACGTG 58.685 45.455 0.00 0.00 35.16 4.49
851 1815 1.299541 AAGCAGTGTGAAGTTGACCG 58.700 50.000 0.00 0.00 0.00 4.79
867 1831 2.894765 TGGGTGGCTTAACCTTAAAAGC 59.105 45.455 1.67 1.67 45.88 3.51
921 1885 3.054139 ACTGATACTACTCCCGGTGTGTA 60.054 47.826 0.00 2.85 0.00 2.90
922 1886 2.291411 ACTGATACTACTCCCGGTGTGT 60.291 50.000 0.00 1.69 0.00 3.72
923 1887 2.099263 CACTGATACTACTCCCGGTGTG 59.901 54.545 0.00 0.00 0.00 3.82
976 2157 2.241941 TCTCTCTGGATCTCTGCAGTCT 59.758 50.000 14.67 0.00 41.30 3.24
978 2159 2.378038 GTCTCTCTGGATCTCTGCAGT 58.622 52.381 14.67 0.00 41.30 4.40
982 2192 2.036217 GCATGGTCTCTCTGGATCTCTG 59.964 54.545 0.00 0.00 0.00 3.35
996 2206 1.522580 GAGAAGGAGCGGCATGGTC 60.523 63.158 1.45 0.00 44.49 4.02
997 2207 2.586792 GAGAAGGAGCGGCATGGT 59.413 61.111 1.45 0.00 0.00 3.55
1515 2753 0.230769 CGTCGTCGTCGTAGTATCCC 59.769 60.000 3.67 0.00 38.33 3.85
1518 2756 1.083806 TGCCGTCGTCGTCGTAGTAT 61.084 55.000 10.76 0.00 38.33 2.12
1519 2757 1.736282 TGCCGTCGTCGTCGTAGTA 60.736 57.895 10.76 0.00 38.33 1.82
1520 2758 3.043713 TGCCGTCGTCGTCGTAGT 61.044 61.111 10.76 0.00 38.33 2.73
1679 6123 0.959372 GACGGAGGAGAGGTTGACGA 60.959 60.000 0.00 0.00 0.00 4.20
2308 6770 2.881352 CGCCGTCTTCTTCTCGCC 60.881 66.667 0.00 0.00 0.00 5.54
2309 6771 2.881352 CCGCCGTCTTCTTCTCGC 60.881 66.667 0.00 0.00 0.00 5.03
2310 6772 2.881352 GCCGCCGTCTTCTTCTCG 60.881 66.667 0.00 0.00 0.00 4.04
2311 6773 2.881352 CGCCGCCGTCTTCTTCTC 60.881 66.667 0.00 0.00 0.00 2.87
2616 7097 3.011517 AGCATGAAGGCCCCGAGT 61.012 61.111 0.00 0.00 0.00 4.18
3050 7537 2.917971 GCAGACAGCAGTTCTAGTTACG 59.082 50.000 0.00 0.00 44.79 3.18
3083 7570 3.966218 CGGTTCTGAACACAAACGAAATC 59.034 43.478 21.01 0.00 0.00 2.17
3088 7575 0.306533 CCCGGTTCTGAACACAAACG 59.693 55.000 21.01 14.24 0.00 3.60
3091 7578 0.542333 TCACCCGGTTCTGAACACAA 59.458 50.000 21.01 0.00 0.00 3.33
3093 7580 0.106149 ACTCACCCGGTTCTGAACAC 59.894 55.000 21.01 10.18 0.00 3.32
3124 7611 7.389884 TCAGGTTATCGATCCATGTACTAGTAC 59.610 40.741 23.58 23.58 36.63 2.73
3125 7612 7.455891 TCAGGTTATCGATCCATGTACTAGTA 58.544 38.462 0.00 0.00 0.00 1.82
3126 7613 6.304624 TCAGGTTATCGATCCATGTACTAGT 58.695 40.000 0.00 0.00 0.00 2.57
3127 7614 6.819397 TCAGGTTATCGATCCATGTACTAG 57.181 41.667 0.00 0.00 0.00 2.57
3187 7674 8.363390 TGGTCTGTAATATCTCATCTGAACATC 58.637 37.037 0.00 0.00 0.00 3.06
3220 7708 4.972514 GAGATCAAACACCCAAATCTCC 57.027 45.455 0.00 0.00 37.47 3.71
3251 7739 8.997621 TCCTAGCACTACATTAGTTTACAAAG 57.002 34.615 0.00 0.00 36.76 2.77
3255 7743 8.999220 AAACTCCTAGCACTACATTAGTTTAC 57.001 34.615 0.00 0.00 36.76 2.01
3257 7745 7.819900 CAGAAACTCCTAGCACTACATTAGTTT 59.180 37.037 0.00 0.00 38.31 2.66
3338 7840 2.809696 GCCGTCAGGATCTCTACTACTC 59.190 54.545 0.00 0.00 41.02 2.59
3339 7841 2.440253 AGCCGTCAGGATCTCTACTACT 59.560 50.000 0.00 0.00 41.02 2.57
3340 7842 2.550606 CAGCCGTCAGGATCTCTACTAC 59.449 54.545 0.00 0.00 41.02 2.73
3341 7843 2.438392 TCAGCCGTCAGGATCTCTACTA 59.562 50.000 0.00 0.00 41.02 1.82
3342 7844 1.213182 TCAGCCGTCAGGATCTCTACT 59.787 52.381 0.00 0.00 41.02 2.57
3343 7845 1.335496 GTCAGCCGTCAGGATCTCTAC 59.665 57.143 0.00 0.00 41.02 2.59
3373 7875 1.212688 CTGGATCTTGTGGCATGGGTA 59.787 52.381 0.00 0.00 0.00 3.69
3455 7983 9.939802 AGAAAGAGAGTAAACCATATTTACGTT 57.060 29.630 0.00 0.00 39.25 3.99
3498 8026 9.932207 TGAGCAATATGTTTTTCATCAAAAGAT 57.068 25.926 0.00 0.00 40.54 2.40
3514 8042 8.984891 TCAAACCAATTTTACTGAGCAATATG 57.015 30.769 0.00 0.00 0.00 1.78
3540 8068 5.741673 GCAATGCTTTCTTCTTTGGGGTAAA 60.742 40.000 0.00 0.00 0.00 2.01
3654 8188 9.620259 ATTTCTTCTGGAAGGACTTATTGATAC 57.380 33.333 10.01 0.00 38.88 2.24
3661 8195 6.620877 TGCTATTTCTTCTGGAAGGACTTA 57.379 37.500 10.01 0.00 38.88 2.24
3690 8224 5.405797 CGTGACATCATAGACCATATGAGG 58.594 45.833 3.65 7.72 40.38 3.86
3812 8350 2.560504 GGCCTTGGTTTTGTTCTTTGG 58.439 47.619 0.00 0.00 0.00 3.28
3816 8354 2.227194 CTACGGCCTTGGTTTTGTTCT 58.773 47.619 0.00 0.00 0.00 3.01
3877 8415 5.194432 TGTGTGGGTTTGTACTTTGTACAT 58.806 37.500 10.75 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.