Multiple sequence alignment - TraesCS3D01G214900

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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 TraesCS3D01G214900 chr3D 100.000 2839 0 0 1 2839 290188114 290190952 0.000000e+00 5243
1 TraesCS3D01G214900 chr3D 80.614 619 86 24 239 827 577421230 577420616 5.580000e-122 448
2 TraesCS3D01G214900 chr3D 83.526 346 35 13 21 365 577421514 577421190 1.280000e-78 303
3 TraesCS3D01G214900 chr3A 93.325 839 47 4 938 1768 382364535 382365372 0.000000e+00 1230
4 TraesCS3D01G214900 chr3A 91.736 726 27 14 239 953 382363813 382364516 0.000000e+00 977
5 TraesCS3D01G214900 chr3A 93.252 489 30 3 1785 2271 382365357 382365844 0.000000e+00 717
6 TraesCS3D01G214900 chr3A 91.415 431 27 8 2416 2837 382367040 382367469 1.470000e-162 582
7 TraesCS3D01G214900 chr3A 94.040 151 9 0 2267 2417 382366329 382366479 2.200000e-56 230
8 TraesCS3D01G214900 chrUn 87.843 765 74 12 1019 1768 356073017 356073777 0.000000e+00 880
9 TraesCS3D01G214900 chrUn 88.290 427 31 10 1806 2224 356073786 356074201 7.070000e-136 494
10 TraesCS3D01G214900 chr2A 87.760 768 75 12 1019 1771 203787330 203786567 0.000000e+00 880
11 TraesCS3D01G214900 chr2A 87.760 768 75 12 1019 1771 203846039 203845276 0.000000e+00 880
12 TraesCS3D01G214900 chr2A 88.525 427 30 10 1806 2224 203786561 203786146 1.520000e-137 499
13 TraesCS3D01G214900 chr2A 88.290 427 31 10 1806 2224 203845270 203844855 7.070000e-136 494
14 TraesCS3D01G214900 chr4D 84.028 288 27 11 46 332 465955789 465955520 2.810000e-65 259
15 TraesCS3D01G214900 chr2D 83.681 288 28 11 46 332 629572676 629572945 1.310000e-63 254
16 TraesCS3D01G214900 chr3B 75.123 406 75 16 2442 2836 532343352 532343742 1.750000e-37 167


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 TraesCS3D01G214900 chr3D 290188114 290190952 2838 False 5243.0 5243 100.0000 1 2839 1 chr3D.!!$F1 2838
1 TraesCS3D01G214900 chr3D 577420616 577421514 898 True 375.5 448 82.0700 21 827 2 chr3D.!!$R1 806
2 TraesCS3D01G214900 chr3A 382363813 382367469 3656 False 747.2 1230 92.7536 239 2837 5 chr3A.!!$F1 2598
3 TraesCS3D01G214900 chrUn 356073017 356074201 1184 False 687.0 880 88.0665 1019 2224 2 chrUn.!!$F1 1205
4 TraesCS3D01G214900 chr2A 203786146 203787330 1184 True 689.5 880 88.1425 1019 2224 2 chr2A.!!$R1 1205
5 TraesCS3D01G214900 chr2A 203844855 203846039 1184 True 687.0 880 88.0250 1019 2224 2 chr2A.!!$R2 1205

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
630 731 0.036388 TTCCTAAGTTGCTGCCTCGG 60.036 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 3036 0.54851 GCATTAGACCTCCCAGCCTT 59.451 55.0 0.0 0.0 0.0 4.35 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
60 61 0.322322 AACGTAAACCGCCTCCATGA 59.678 50.000 0.00 0.00 41.42 3.07
61 62 0.390735 ACGTAAACCGCCTCCATGAC 60.391 55.000 0.00 0.00 41.42 3.06
62 63 1.087771 CGTAAACCGCCTCCATGACC 61.088 60.000 0.00 0.00 0.00 4.02
77 78 1.803334 TGACCACCGTTAGATGCAAC 58.197 50.000 0.00 0.00 0.00 4.17
89 90 2.474561 ATGCAACTCATCACAGCCG 58.525 52.632 0.00 0.00 0.00 5.52
91 92 1.229975 TGCAACTCATCACAGCCGTG 61.230 55.000 0.00 0.00 45.08 4.94
92 93 1.915614 GCAACTCATCACAGCCGTGG 61.916 60.000 0.00 0.00 43.79 4.94
105 106 0.960364 GCCGTGGCTTTTCTCATCCA 60.960 55.000 2.98 0.00 38.26 3.41
112 113 4.012374 TGGCTTTTCTCATCCACAGATTC 58.988 43.478 0.00 0.00 0.00 2.52
148 149 2.356793 CCTCGCTCCATCATCGGC 60.357 66.667 0.00 0.00 0.00 5.54
174 175 4.087892 CTGCTACTGCCCCGCTGT 62.088 66.667 1.76 1.76 42.86 4.40
177 178 3.127533 CTACTGCCCCGCTGTTGC 61.128 66.667 1.41 0.00 40.85 4.17
178 179 3.899981 CTACTGCCCCGCTGTTGCA 62.900 63.158 1.41 0.00 40.85 4.08
180 181 2.967507 TACTGCCCCGCTGTTGCAAA 62.968 55.000 0.00 0.00 40.85 3.68
181 182 3.562779 CTGCCCCGCTGTTGCAAAG 62.563 63.158 0.00 2.35 39.64 2.77
182 183 3.605664 GCCCCGCTGTTGCAAAGT 61.606 61.111 0.00 0.00 39.64 2.66
183 184 2.336088 CCCCGCTGTTGCAAAGTG 59.664 61.111 0.00 7.88 39.64 3.16
185 186 2.489275 CCCGCTGTTGCAAAGTGGT 61.489 57.895 25.82 0.00 42.68 4.16
186 187 1.008538 CCGCTGTTGCAAAGTGGTC 60.009 57.895 22.58 4.75 39.93 4.02
187 188 1.008538 CGCTGTTGCAAAGTGGTCC 60.009 57.895 0.00 0.00 39.64 4.46
188 189 1.723608 CGCTGTTGCAAAGTGGTCCA 61.724 55.000 0.00 0.00 39.64 4.02
189 190 0.675633 GCTGTTGCAAAGTGGTCCAT 59.324 50.000 0.00 0.00 39.41 3.41
190 191 1.336240 GCTGTTGCAAAGTGGTCCATC 60.336 52.381 0.00 0.00 39.41 3.51
191 192 1.270550 CTGTTGCAAAGTGGTCCATCC 59.729 52.381 0.00 0.00 0.00 3.51
192 193 1.327303 GTTGCAAAGTGGTCCATCCA 58.673 50.000 0.00 0.00 45.01 3.41
203 204 0.749649 GTCCATCCATGACGCTCTCT 59.250 55.000 0.00 0.00 0.00 3.10
243 328 2.588877 CGGCCCAACTATGCTCCG 60.589 66.667 0.00 0.00 34.96 4.63
245 330 1.523938 GGCCCAACTATGCTCCGTC 60.524 63.158 0.00 0.00 0.00 4.79
251 336 1.949847 AACTATGCTCCGTCGCAGCT 61.950 55.000 9.99 0.00 44.10 4.24
263 348 4.838486 GCAGCTCCGACGACCTCG 62.838 72.222 0.00 0.00 46.33 4.63
264 349 3.125573 CAGCTCCGACGACCTCGA 61.126 66.667 0.78 0.00 46.14 4.04
443 535 1.459209 CACAACTTCATCGCAACGCTA 59.541 47.619 0.00 0.00 0.00 4.26
520 612 2.433838 CAGGAGCGTGCAGTCAGG 60.434 66.667 0.00 0.00 0.00 3.86
628 729 1.079503 CGTTCCTAAGTTGCTGCCTC 58.920 55.000 0.00 0.00 0.00 4.70
630 731 0.036388 TTCCTAAGTTGCTGCCTCGG 60.036 55.000 0.00 0.00 0.00 4.63
672 773 0.912487 AGCGGTTGGGTGGATAGGAA 60.912 55.000 0.00 0.00 0.00 3.36
673 774 0.463833 GCGGTTGGGTGGATAGGAAG 60.464 60.000 0.00 0.00 0.00 3.46
690 792 7.148340 GGATAGGAAGAGACAAAGTCAACAATG 60.148 40.741 0.00 0.00 34.60 2.82
725 827 0.250553 AACGATTCAGCGGTTGGGAA 60.251 50.000 0.00 0.00 35.12 3.97
747 849 1.378514 CGGGGTGCATGTTAAGGCT 60.379 57.895 0.00 0.00 33.17 4.58
748 850 0.107410 CGGGGTGCATGTTAAGGCTA 60.107 55.000 0.00 0.00 33.17 3.93
749 851 1.680555 CGGGGTGCATGTTAAGGCTAA 60.681 52.381 0.00 0.00 33.17 3.09
750 852 2.024414 GGGGTGCATGTTAAGGCTAAG 58.976 52.381 0.00 0.00 33.17 2.18
751 853 2.024414 GGGTGCATGTTAAGGCTAAGG 58.976 52.381 0.00 0.00 33.17 2.69
752 854 1.405463 GGTGCATGTTAAGGCTAAGGC 59.595 52.381 0.00 0.00 33.17 4.35
753 855 1.064060 GTGCATGTTAAGGCTAAGGCG 59.936 52.381 0.00 0.00 39.81 5.52
754 856 0.663153 GCATGTTAAGGCTAAGGCGG 59.337 55.000 0.00 0.00 39.81 6.13
755 857 1.308998 CATGTTAAGGCTAAGGCGGG 58.691 55.000 0.00 0.00 39.81 6.13
756 858 0.465642 ATGTTAAGGCTAAGGCGGGC 60.466 55.000 0.00 0.00 39.81 6.13
757 859 2.178235 GTTAAGGCTAAGGCGGGCG 61.178 63.158 0.00 0.00 39.81 6.13
758 860 4.540735 TAAGGCTAAGGCGGGCGC 62.541 66.667 0.00 0.00 39.81 6.53
858 960 8.825745 GTTTTCCAAACAGAAAATAAGCATTGA 58.174 29.630 3.07 0.00 44.96 2.57
875 977 3.708403 TTGAAGAGGACATGATGCTGT 57.292 42.857 0.00 0.00 0.00 4.40
912 1014 1.079543 CAGCCTTGGACAGACTCCG 60.080 63.158 0.00 0.00 43.03 4.63
935 1037 5.582269 CGGATCAAAGTACATCATGTGACTT 59.418 40.000 0.00 3.92 30.90 3.01
936 1038 6.456047 CGGATCAAAGTACATCATGTGACTTG 60.456 42.308 0.00 1.16 30.47 3.16
1006 1144 4.022068 TGGGTCAAGAAACAATCAATCTGC 60.022 41.667 0.00 0.00 0.00 4.26
1426 1602 1.958205 GGGCGAGATGGAAGCATCG 60.958 63.158 0.00 0.00 36.73 3.84
1535 1723 0.803380 GGTACCACCGTCGGAAATCG 60.803 60.000 20.51 2.35 40.90 3.34
1562 1750 0.033991 ACTCGGGAAGCTGCTAGAGA 60.034 55.000 22.18 11.84 0.00 3.10
1594 1782 1.560923 CGGATGTGACATTCGAGGTC 58.439 55.000 21.09 11.20 35.83 3.85
1722 1910 1.829970 TTGCCAACATGCAACCCGA 60.830 52.632 0.00 0.00 45.77 5.14
1772 1961 2.551644 ACGATTCGTTGCCTTTCCC 58.448 52.632 5.75 0.00 36.35 3.97
1773 1962 0.036306 ACGATTCGTTGCCTTTCCCT 59.964 50.000 5.75 0.00 36.35 4.20
1774 1963 0.727398 CGATTCGTTGCCTTTCCCTC 59.273 55.000 0.00 0.00 0.00 4.30
1775 1964 1.821216 GATTCGTTGCCTTTCCCTCA 58.179 50.000 0.00 0.00 0.00 3.86
1776 1965 2.159382 GATTCGTTGCCTTTCCCTCAA 58.841 47.619 0.00 0.00 0.00 3.02
1777 1966 2.060050 TTCGTTGCCTTTCCCTCAAA 57.940 45.000 0.00 0.00 0.00 2.69
1778 1967 2.060050 TCGTTGCCTTTCCCTCAAAA 57.940 45.000 0.00 0.00 0.00 2.44
1779 1968 2.379972 TCGTTGCCTTTCCCTCAAAAA 58.620 42.857 0.00 0.00 0.00 1.94
1820 2012 1.131218 CGACGACGACGACTTGCTA 59.869 57.895 15.32 0.00 42.66 3.49
2005 2197 2.424601 GGCTACAAGATGCTTGCATTCA 59.575 45.455 9.59 0.00 0.00 2.57
2014 2206 7.604927 ACAAGATGCTTGCATTCAATTTATTGT 59.395 29.630 9.59 3.85 38.84 2.71
2020 2212 9.036671 TGCTTGCATTCAATTTATTGTATCATG 57.963 29.630 2.66 0.00 38.84 3.07
2068 2262 1.009829 CAAGCAGAGGGTACAATCGC 58.990 55.000 0.00 0.91 0.00 4.58
2091 2285 4.631813 CCTCAAAAGAACTTGTCCGGATAG 59.368 45.833 7.81 11.38 0.00 2.08
2186 2382 9.732130 ATCTTAACCAATCATCCTATAAAGAGC 57.268 33.333 0.00 0.00 0.00 4.09
2193 2389 5.961396 TCATCCTATAAAGAGCGGACTAC 57.039 43.478 0.00 0.00 0.00 2.73
2194 2390 5.632118 TCATCCTATAAAGAGCGGACTACT 58.368 41.667 0.00 0.00 0.00 2.57
2226 2422 5.361857 CCAATAATTCTCTGTGGCCTTCAAT 59.638 40.000 3.32 0.00 0.00 2.57
2231 2427 2.507058 TCTCTGTGGCCTTCAATAGCAT 59.493 45.455 3.32 0.00 0.00 3.79
2232 2428 2.617308 CTCTGTGGCCTTCAATAGCATG 59.383 50.000 3.32 0.00 0.00 4.06
2252 2448 1.891150 GCCCTGCCATATCTTCAATGG 59.109 52.381 0.00 0.00 45.68 3.16
2312 2997 5.694006 AGATAGCTTGAAATGATACGTCAGC 59.306 40.000 0.00 0.00 37.87 4.26
2330 3015 1.521681 CCGAGAAGATGGCCGTTCC 60.522 63.158 0.00 0.00 0.00 3.62
2351 3036 0.547553 TGGCTCTGCATATTCAGGCA 59.452 50.000 14.25 3.36 39.59 4.75
2401 3086 4.795278 GCCTTTGCATATTCAGAGAAAACG 59.205 41.667 0.00 0.00 37.47 3.60
2471 3718 1.731613 TACCGTGCTTTCGAGCGTG 60.732 57.895 0.00 0.00 37.69 5.34
2497 3744 4.637483 TGCAACCAATTAATAGCAGCTC 57.363 40.909 0.00 0.00 0.00 4.09
2502 3749 4.261801 ACCAATTAATAGCAGCTCAACGT 58.738 39.130 0.00 0.00 0.00 3.99
2541 3788 5.474876 GCCTTGGAGAGAGAATCAAGAAAAA 59.525 40.000 0.00 0.00 38.96 1.94
2573 3820 7.042523 CGCTGAAAAAGAAAAACCAAAGATCAT 60.043 33.333 0.00 0.00 0.00 2.45
2579 3826 4.347583 AGAAAAACCAAAGATCATGGCCAA 59.652 37.500 10.96 0.00 41.89 4.52
2600 3847 8.575589 GGCCAACAAATTATTTCCTTTTTCAAT 58.424 29.630 0.00 0.00 0.00 2.57
2666 3916 7.168219 ACCATGTGTTAATCTACAGACAACAT 58.832 34.615 10.00 0.00 35.86 2.71
2686 3936 7.926018 ACAACATGACTCCAAAGAAAAATAACC 59.074 33.333 0.00 0.00 0.00 2.85
2812 4068 5.047377 TCAACTTTTTGCAGTGAAAGGTTCT 60.047 36.000 17.84 1.51 35.11 3.01
2837 4093 3.119637 CCAATGCTAACCACGGTTTTAGG 60.120 47.826 6.80 0.00 39.31 2.69
2838 4094 2.188062 TGCTAACCACGGTTTTAGGG 57.812 50.000 6.80 0.00 39.31 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.692367 GATGATCCGGCGTTCGCG 61.692 66.667 6.01 0.00 44.73 5.87
8 9 3.338676 GGATGATCCGGCGTTCGC 61.339 66.667 6.01 8.75 37.59 4.70
32 33 1.062258 CGGTTTACGTTAGCTTCGCA 58.938 50.000 10.18 0.00 37.93 5.10
38 39 0.390209 TGGAGGCGGTTTACGTTAGC 60.390 55.000 0.00 0.00 46.52 3.09
60 61 1.346395 TGAGTTGCATCTAACGGTGGT 59.654 47.619 0.00 0.00 35.73 4.16
61 62 2.093306 TGAGTTGCATCTAACGGTGG 57.907 50.000 0.00 0.00 35.73 4.61
91 92 3.379688 GGAATCTGTGGATGAGAAAAGCC 59.620 47.826 0.00 0.00 31.75 4.35
92 93 3.064545 CGGAATCTGTGGATGAGAAAAGC 59.935 47.826 0.00 0.00 31.75 3.51
101 102 1.417517 TGCTATGCGGAATCTGTGGAT 59.582 47.619 0.00 0.00 0.00 3.41
105 106 2.555199 GAAGTGCTATGCGGAATCTGT 58.445 47.619 0.00 0.00 0.00 3.41
112 113 2.511373 TGCGGAAGTGCTATGCGG 60.511 61.111 0.98 0.00 35.36 5.69
169 170 1.008538 GGACCACTTTGCAACAGCG 60.009 57.895 0.00 0.00 0.00 5.18
170 171 0.675633 ATGGACCACTTTGCAACAGC 59.324 50.000 0.00 0.00 0.00 4.40
171 172 1.270550 GGATGGACCACTTTGCAACAG 59.729 52.381 0.00 2.74 38.79 3.16
172 173 1.327303 GGATGGACCACTTTGCAACA 58.673 50.000 0.00 0.00 38.79 3.33
173 174 1.327303 TGGATGGACCACTTTGCAAC 58.673 50.000 0.00 0.00 44.64 4.17
174 175 3.837893 TGGATGGACCACTTTGCAA 57.162 47.368 0.00 0.00 44.64 4.08
183 184 0.249657 GAGAGCGTCATGGATGGACC 60.250 60.000 0.00 0.00 39.54 4.46
185 186 1.137675 CAAGAGAGCGTCATGGATGGA 59.862 52.381 0.00 0.00 0.00 3.41
186 187 1.134580 ACAAGAGAGCGTCATGGATGG 60.135 52.381 0.00 0.00 0.00 3.51
187 188 2.200067 GACAAGAGAGCGTCATGGATG 58.800 52.381 0.00 0.00 32.24 3.51
188 189 1.202348 CGACAAGAGAGCGTCATGGAT 60.202 52.381 0.00 0.00 32.24 3.41
189 190 0.171231 CGACAAGAGAGCGTCATGGA 59.829 55.000 0.00 0.00 32.24 3.41
190 191 1.416813 GCGACAAGAGAGCGTCATGG 61.417 60.000 0.00 0.00 32.24 3.66
191 192 0.457509 AGCGACAAGAGAGCGTCATG 60.458 55.000 0.00 0.00 35.78 3.07
192 193 0.179150 GAGCGACAAGAGAGCGTCAT 60.179 55.000 0.00 0.00 35.78 3.06
193 194 1.210413 GAGCGACAAGAGAGCGTCA 59.790 57.895 0.00 0.00 35.78 4.35
194 195 1.515304 GGAGCGACAAGAGAGCGTC 60.515 63.158 0.00 0.00 35.78 5.19
195 196 2.268802 TGGAGCGACAAGAGAGCGT 61.269 57.895 0.00 0.00 35.78 5.07
196 197 1.803519 GTGGAGCGACAAGAGAGCG 60.804 63.158 0.00 0.00 35.78 5.03
197 198 0.735632 CAGTGGAGCGACAAGAGAGC 60.736 60.000 0.00 0.00 0.00 4.09
198 199 0.735632 GCAGTGGAGCGACAAGAGAG 60.736 60.000 0.00 0.00 0.00 3.20
203 204 2.666190 GCTGCAGTGGAGCGACAA 60.666 61.111 21.42 0.00 37.31 3.18
227 228 1.523938 GACGGAGCATAGTTGGGCC 60.524 63.158 0.00 0.00 0.00 5.80
233 234 2.105128 GCTGCGACGGAGCATAGT 59.895 61.111 32.72 0.00 46.97 2.12
234 235 1.659954 GAGCTGCGACGGAGCATAG 60.660 63.158 37.14 6.15 46.97 2.23
235 236 2.413351 GAGCTGCGACGGAGCATA 59.587 61.111 37.14 0.00 46.97 3.14
261 346 1.999735 GTTTCAATGGAGCATCGTCGA 59.000 47.619 0.00 0.00 34.37 4.20
263 348 2.352960 GAGGTTTCAATGGAGCATCGTC 59.647 50.000 0.00 0.00 34.37 4.20
264 349 2.290260 TGAGGTTTCAATGGAGCATCGT 60.290 45.455 0.00 0.00 34.37 3.73
451 543 2.105930 CTCGACTGCTGCTAGCCC 59.894 66.667 13.29 3.74 41.51 5.19
672 773 5.070981 TCTCCTCATTGTTGACTTTGTCTCT 59.929 40.000 0.00 0.00 33.15 3.10
673 774 5.178438 GTCTCCTCATTGTTGACTTTGTCTC 59.822 44.000 0.00 0.00 33.15 3.36
690 792 2.836262 TCGTTATCCTCTCGTCTCCTC 58.164 52.381 0.00 0.00 0.00 3.71
725 827 0.672401 CTTAACATGCACCCCGTCGT 60.672 55.000 0.00 0.00 0.00 4.34
858 960 2.234661 TCGAACAGCATCATGTCCTCTT 59.765 45.455 0.00 0.00 31.50 2.85
875 977 1.098050 GGCTCCGTAACCTAGTCGAA 58.902 55.000 0.00 0.00 0.00 3.71
912 1014 6.595326 TCAAGTCACATGATGTACTTTGATCC 59.405 38.462 13.80 0.00 28.81 3.36
935 1037 6.983474 TTGATCGAATCAAATTAGCAGTCA 57.017 33.333 7.53 0.00 45.57 3.41
970 1101 9.209048 TGTTTCTTGACCCATAGTATGTAGTAT 57.791 33.333 9.28 0.00 0.00 2.12
971 1102 8.598202 TGTTTCTTGACCCATAGTATGTAGTA 57.402 34.615 9.28 0.00 0.00 1.82
972 1103 7.490657 TGTTTCTTGACCCATAGTATGTAGT 57.509 36.000 9.28 6.13 0.00 2.73
973 1104 8.964476 ATTGTTTCTTGACCCATAGTATGTAG 57.036 34.615 9.28 3.04 0.00 2.74
976 1107 7.864108 TGATTGTTTCTTGACCCATAGTATG 57.136 36.000 2.90 2.90 0.00 2.39
984 1122 4.022068 TGCAGATTGATTGTTTCTTGACCC 60.022 41.667 0.00 0.00 0.00 4.46
994 1132 2.224843 TGTCCTGGTGCAGATTGATTGT 60.225 45.455 0.00 0.00 32.44 2.71
1006 1144 0.764890 TTCTTGGTCCTGTCCTGGTG 59.235 55.000 0.00 0.00 0.00 4.17
1030 1168 5.557893 GCTCAGCAAGATCGACATTACATTC 60.558 44.000 0.00 0.00 0.00 2.67
1060 1199 2.661866 GACTCCGCTGTGCACGTT 60.662 61.111 13.13 0.00 0.00 3.99
1283 1456 2.040009 ATTGTGGAGGATACCCGCGG 62.040 60.000 21.04 21.04 39.44 6.46
1331 1504 2.475487 CCACCGACGAAGAAAGAGAAAC 59.525 50.000 0.00 0.00 0.00 2.78
1426 1602 1.593006 CGATCGTCAACAACATAGCCC 59.407 52.381 7.03 0.00 0.00 5.19
1519 1695 2.433664 GCGATTTCCGACGGTGGT 60.434 61.111 14.79 0.23 41.76 4.16
1539 1727 2.521958 TAGCAGCTTCCCGAGTTGGC 62.522 60.000 0.00 0.00 37.11 4.52
1562 1750 3.717294 ATCCGCGCCCTCCTTTGT 61.717 61.111 0.00 0.00 0.00 2.83
1594 1782 2.019156 GCCGGGAATTTCTCTCCTTGG 61.019 57.143 2.18 0.00 33.88 3.61
1722 1910 7.957002 TGAAGTAGAGAGAAACTTGAAGACAT 58.043 34.615 0.00 0.00 36.10 3.06
1786 1975 3.143712 CGTCACGCAACGAATCGT 58.856 55.556 0.96 0.96 45.37 3.73
1792 1981 4.087079 CGTCGTCGTCACGCAACG 62.087 66.667 5.13 5.13 46.28 4.10
1793 1982 2.723271 TCGTCGTCGTCACGCAAC 60.723 61.111 1.33 0.00 46.28 4.17
1794 1983 2.723271 GTCGTCGTCGTCACGCAA 60.723 61.111 1.33 0.00 46.28 4.85
1795 1984 4.999532 CGTCGTCGTCGTCACGCA 63.000 66.667 3.67 0.00 46.28 5.24
1796 1985 4.707840 TCGTCGTCGTCGTCACGC 62.708 66.667 11.41 0.00 46.28 5.34
1798 1987 1.083144 AAGTCGTCGTCGTCGTCAC 60.083 57.895 11.41 4.02 38.33 3.67
1820 2012 5.068460 CACCTCTTTCTTATCGTCTCCATCT 59.932 44.000 0.00 0.00 0.00 2.90
2020 2212 7.928706 ACCACATCATCTAGCATTTTAGTAGAC 59.071 37.037 0.00 0.00 0.00 2.59
2033 2226 1.945394 GCTTGCCACCACATCATCTAG 59.055 52.381 0.00 0.00 0.00 2.43
2068 2262 2.846193 TCCGGACAAGTTCTTTTGAGG 58.154 47.619 0.00 0.00 0.00 3.86
2091 2285 5.622233 GCTTTTTCCCACATCTCCATTACAC 60.622 44.000 0.00 0.00 0.00 2.90
2211 2407 2.408271 TGCTATTGAAGGCCACAGAG 57.592 50.000 5.01 7.45 0.00 3.35
2231 2427 2.589720 CATTGAAGATATGGCAGGGCA 58.410 47.619 0.00 0.00 0.00 5.36
2232 2428 1.891150 CCATTGAAGATATGGCAGGGC 59.109 52.381 0.00 0.00 36.43 5.19
2238 2434 3.312421 ACGTTTCGCCATTGAAGATATGG 59.688 43.478 0.00 0.00 44.40 2.74
2252 2448 4.625135 CTGTTAACAGTATCACGTTTCGC 58.375 43.478 24.70 0.00 39.09 4.70
2274 2959 7.469537 TCAAGCTATCTCCTAAGGCTATTAC 57.530 40.000 0.00 0.00 32.64 1.89
2281 2966 7.543868 CGTATCATTTCAAGCTATCTCCTAAGG 59.456 40.741 0.00 0.00 0.00 2.69
2312 2997 1.521681 GGAACGGCCATCTTCTCGG 60.522 63.158 2.24 0.00 36.34 4.63
2330 3015 1.224075 CCTGAATATGCAGAGCCACG 58.776 55.000 12.76 0.00 38.14 4.94
2351 3036 0.548510 GCATTAGACCTCCCAGCCTT 59.451 55.000 0.00 0.00 0.00 4.35
2444 3691 2.603953 GAAAGCACGGTACTGACCTAC 58.396 52.381 9.17 0.00 44.46 3.18
2464 3711 2.476051 GTTGCATCCACACGCTCG 59.524 61.111 0.00 0.00 0.00 5.03
2471 3718 5.261209 TGCTATTAATTGGTTGCATCCAC 57.739 39.130 16.21 3.21 37.20 4.02
2497 3744 2.201732 CCAATACGGAGGATCACGTTG 58.798 52.381 13.24 7.72 41.12 4.10
2502 3749 1.140852 CAAGGCCAATACGGAGGATCA 59.859 52.381 5.01 0.00 36.25 2.92
2541 3788 5.988561 TGGTTTTTCTTTTTCAGCGCATATT 59.011 32.000 11.47 0.00 0.00 1.28
2573 3820 7.056635 TGAAAAAGGAAATAATTTGTTGGCCA 58.943 30.769 0.00 0.00 0.00 5.36
2641 3891 6.530120 TGTTGTCTGTAGATTAACACATGGT 58.470 36.000 0.00 0.00 32.76 3.55
2660 3910 7.926018 GGTTATTTTTCTTTGGAGTCATGTTGT 59.074 33.333 0.00 0.00 0.00 3.32
2666 3916 7.066781 AGAAGGGTTATTTTTCTTTGGAGTCA 58.933 34.615 0.00 0.00 0.00 3.41
2686 3936 5.452078 TTGCCAATCACAAACTTAGAAGG 57.548 39.130 0.00 0.00 0.00 3.46
2777 4033 7.648908 CACTGCAAAAAGTTGAAATAGTGATGA 59.351 33.333 0.00 0.00 36.80 2.92
2792 4048 4.978580 GCTAGAACCTTTCACTGCAAAAAG 59.021 41.667 0.00 8.29 33.26 2.27
2793 4049 4.202111 GGCTAGAACCTTTCACTGCAAAAA 60.202 41.667 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.