Multiple sequence alignment - TraesCS2D01G290400

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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 TraesCS2D01G290400 chr2D 100.000 2809 0 0 1 2809 372697384 372694576 0.000000e+00 5188
1 TraesCS2D01G290400 chr2B 93.433 1203 42 17 1328 2519 442307760 442306584 0.000000e+00 1749
2 TraesCS2D01G290400 chr2B 87.512 1017 50 32 281 1255 442308891 442307910 0.000000e+00 1103
3 TraesCS2D01G290400 chr2B 90.610 213 3 3 1 208 442309226 442309026 1.660000e-67 267
4 TraesCS2D01G290400 chr2B 81.505 319 13 14 2517 2809 442306502 442306204 1.310000e-53 220
5 TraesCS2D01G290400 chr2A 88.823 1181 61 33 1671 2795 504071600 504070435 0.000000e+00 1384
6 TraesCS2D01G290400 chr2A 85.714 1295 57 57 3 1246 504073435 504072218 0.000000e+00 1249
7 TraesCS2D01G290400 chr2A 95.122 328 9 4 1336 1660 504072007 504071684 6.940000e-141 510


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 TraesCS2D01G290400 chr2D 372694576 372697384 2808 True 5188.000000 5188 100.000000 1 2809 1 chr2D.!!$R1 2808
1 TraesCS2D01G290400 chr2B 442306204 442309226 3022 True 834.750000 1749 88.265000 1 2809 4 chr2B.!!$R1 2808
2 TraesCS2D01G290400 chr2A 504070435 504073435 3000 True 1047.666667 1384 89.886333 3 2795 3 chr2A.!!$R1 2792

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
450 567 0.391661 ATGGCAGCTCACCTAACACG 60.392 55.0 4.01 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2261 0.305009 GCGAAATTAAGCTCTCGGGC 59.695 55.0 0.0 0.0 0.0 6.13 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
94 95 1.153066 ACAACACGCATCCACCACA 60.153 52.632 0.00 0.00 0.00 4.17
99 100 0.749091 CACGCATCCACCACATCCAT 60.749 55.000 0.00 0.00 0.00 3.41
107 108 1.382522 CACCACATCCATACCACAGC 58.617 55.000 0.00 0.00 0.00 4.40
208 214 4.704965 CAACCCAAAGCTACCTATCTACC 58.295 47.826 0.00 0.00 0.00 3.18
209 215 4.003584 ACCCAAAGCTACCTATCTACCA 57.996 45.455 0.00 0.00 0.00 3.25
210 216 3.967987 ACCCAAAGCTACCTATCTACCAG 59.032 47.826 0.00 0.00 0.00 4.00
212 218 5.145564 CCCAAAGCTACCTATCTACCAGTA 58.854 45.833 0.00 0.00 0.00 2.74
213 219 5.010820 CCCAAAGCTACCTATCTACCAGTAC 59.989 48.000 0.00 0.00 0.00 2.73
214 220 5.834204 CCAAAGCTACCTATCTACCAGTACT 59.166 44.000 0.00 0.00 0.00 2.73
215 221 7.002879 CCAAAGCTACCTATCTACCAGTACTA 58.997 42.308 0.00 0.00 0.00 1.82
216 222 7.040548 CCAAAGCTACCTATCTACCAGTACTAC 60.041 44.444 0.00 0.00 0.00 2.73
217 223 5.792741 AGCTACCTATCTACCAGTACTACG 58.207 45.833 0.00 0.00 0.00 3.51
218 224 5.306678 AGCTACCTATCTACCAGTACTACGT 59.693 44.000 0.00 0.00 0.00 3.57
219 225 6.495181 AGCTACCTATCTACCAGTACTACGTA 59.505 42.308 0.00 0.00 0.00 3.57
220 226 7.180051 AGCTACCTATCTACCAGTACTACGTAT 59.820 40.741 0.00 0.00 0.00 3.06
221 227 7.277539 GCTACCTATCTACCAGTACTACGTATG 59.722 44.444 0.00 0.00 0.00 2.39
222 228 7.072263 ACCTATCTACCAGTACTACGTATGT 57.928 40.000 0.00 0.00 0.00 2.29
272 360 2.297701 CAAAGTGCAAGTGGTGGTACT 58.702 47.619 0.00 0.00 0.00 2.73
273 361 3.472652 CAAAGTGCAAGTGGTGGTACTA 58.527 45.455 0.00 0.00 29.56 1.82
274 362 2.833631 AGTGCAAGTGGTGGTACTAC 57.166 50.000 0.00 0.00 0.00 2.73
275 363 1.346722 AGTGCAAGTGGTGGTACTACC 59.653 52.381 20.88 20.88 41.24 3.18
276 364 1.346722 GTGCAAGTGGTGGTACTACCT 59.653 52.381 26.61 7.13 41.43 3.08
450 567 0.391661 ATGGCAGCTCACCTAACACG 60.392 55.000 4.01 0.00 0.00 4.49
559 679 2.877582 GTTCGGCGCACGTACGAT 60.878 61.111 24.41 3.10 44.69 3.73
601 732 2.629137 TGCAAACCACTGAAATGATGCT 59.371 40.909 0.00 0.00 0.00 3.79
604 738 4.084223 GCAAACCACTGAAATGATGCTTTG 60.084 41.667 0.00 0.00 0.00 2.77
608 742 3.311106 CACTGAAATGATGCTTTGCGTT 58.689 40.909 0.00 0.00 0.00 4.84
623 757 6.036953 TGCTTTGCGTTCTTTGATTTGAATTT 59.963 30.769 0.00 0.00 0.00 1.82
691 840 2.617274 GCAGCCGTTTCACCTCACC 61.617 63.158 0.00 0.00 0.00 4.02
692 841 1.966451 CAGCCGTTTCACCTCACCC 60.966 63.158 0.00 0.00 0.00 4.61
693 842 3.047877 GCCGTTTCACCTCACCCG 61.048 66.667 0.00 0.00 0.00 5.28
694 843 2.738480 CCGTTTCACCTCACCCGA 59.262 61.111 0.00 0.00 0.00 5.14
695 844 1.666872 CCGTTTCACCTCACCCGAC 60.667 63.158 0.00 0.00 0.00 4.79
696 845 1.666872 CGTTTCACCTCACCCGACC 60.667 63.158 0.00 0.00 0.00 4.79
716 865 5.105228 CGACCTCCCCTTTTATACTGTACAA 60.105 44.000 0.00 0.00 0.00 2.41
744 893 1.979469 GACGGATCGATCGCATTACTG 59.021 52.381 18.81 7.11 0.00 2.74
745 894 0.710567 CGGATCGATCGCATTACTGC 59.289 55.000 18.81 1.21 45.31 4.40
758 907 1.962321 TTACTGCTTCCGCGGCCATA 61.962 55.000 23.51 0.00 46.69 2.74
801 950 1.951130 CGATAAGCATGCGACGGCT 60.951 57.895 13.01 0.00 43.46 5.52
850 1004 1.968493 GTGATATAAGTGGCGGGGAGA 59.032 52.381 0.00 0.00 0.00 3.71
872 1026 2.742372 CCGGCCGTGAAGACAAGG 60.742 66.667 26.12 0.00 45.85 3.61
894 1048 8.581578 CAAGGTATAGGAAGAAGAGAGAATACC 58.418 40.741 0.00 0.00 38.46 2.73
898 1052 5.930837 AGGAAGAAGAGAGAATACCACTG 57.069 43.478 0.00 0.00 0.00 3.66
944 1098 5.393124 AGTCGATTGATTACGTTACGTGAA 58.607 37.500 21.22 10.87 41.39 3.18
961 1128 0.935366 GAAGTGCGTCGATCGATCCC 60.935 60.000 22.50 12.73 42.86 3.85
981 1148 3.552132 CTAGGAAGGAAGGAAGGAAGC 57.448 52.381 0.00 0.00 0.00 3.86
985 1152 1.815613 GAAGGAAGGAAGGAAGCAAGC 59.184 52.381 0.00 0.00 0.00 4.01
986 1153 0.773644 AGGAAGGAAGGAAGCAAGCA 59.226 50.000 0.00 0.00 0.00 3.91
991 1158 1.357079 AGGAAGGAAGCAAGCAAGGAT 59.643 47.619 0.00 0.00 0.00 3.24
992 1159 2.578021 AGGAAGGAAGCAAGCAAGGATA 59.422 45.455 0.00 0.00 0.00 2.59
994 1161 2.725221 AGGAAGCAAGCAAGGATAGG 57.275 50.000 0.00 0.00 0.00 2.57
995 1162 2.200081 AGGAAGCAAGCAAGGATAGGA 58.800 47.619 0.00 0.00 0.00 2.94
998 1167 4.041444 AGGAAGCAAGCAAGGATAGGATAG 59.959 45.833 0.00 0.00 0.00 2.08
1008 1177 1.488393 GGATAGGATAGGATGCAGGGC 59.512 57.143 0.00 0.00 0.00 5.19
1011 1180 0.764369 AGGATAGGATGCAGGGCGAA 60.764 55.000 0.00 0.00 0.00 4.70
1246 1421 4.547532 CCTAGCATTCATACGACAGGTAC 58.452 47.826 0.00 0.00 32.95 3.34
1247 1422 3.454371 AGCATTCATACGACAGGTACC 57.546 47.619 2.73 2.73 32.95 3.34
1248 1423 3.031736 AGCATTCATACGACAGGTACCT 58.968 45.455 9.21 9.21 32.95 3.08
1249 1424 4.212716 AGCATTCATACGACAGGTACCTA 58.787 43.478 15.80 0.00 32.95 3.08
1250 1425 4.037684 AGCATTCATACGACAGGTACCTAC 59.962 45.833 15.80 10.98 32.95 3.18
1251 1426 4.795308 GCATTCATACGACAGGTACCTACC 60.795 50.000 15.80 8.37 46.82 3.18
1267 1442 6.271159 GGTACCTACCTAGTACTCCTAGCTAA 59.729 46.154 4.06 0.00 41.68 3.09
1268 1443 7.037658 GGTACCTACCTAGTACTCCTAGCTAAT 60.038 44.444 4.06 0.00 41.68 1.73
1294 1469 5.275974 GTAGTACTACTCTTCGGTTACGACG 60.276 48.000 23.17 0.00 39.73 5.12
1308 1646 4.202010 GGTTACGACGTAGCCTAAACCATA 60.202 45.833 27.66 0.00 36.64 2.74
1309 1647 3.427161 ACGACGTAGCCTAAACCATAC 57.573 47.619 0.00 0.00 0.00 2.39
1310 1648 2.754552 ACGACGTAGCCTAAACCATACA 59.245 45.455 0.00 0.00 0.00 2.29
1311 1649 3.181493 ACGACGTAGCCTAAACCATACAG 60.181 47.826 0.00 0.00 0.00 2.74
1312 1650 3.121544 GACGTAGCCTAAACCATACAGC 58.878 50.000 0.00 0.00 0.00 4.40
1313 1651 2.764572 ACGTAGCCTAAACCATACAGCT 59.235 45.455 0.00 0.00 0.00 4.24
1314 1652 3.181478 ACGTAGCCTAAACCATACAGCTC 60.181 47.826 0.00 0.00 0.00 4.09
1315 1653 3.181479 CGTAGCCTAAACCATACAGCTCA 60.181 47.826 0.00 0.00 0.00 4.26
1316 1654 4.679639 CGTAGCCTAAACCATACAGCTCAA 60.680 45.833 0.00 0.00 0.00 3.02
1317 1655 4.301072 AGCCTAAACCATACAGCTCAAA 57.699 40.909 0.00 0.00 0.00 2.69
1318 1656 4.010349 AGCCTAAACCATACAGCTCAAAC 58.990 43.478 0.00 0.00 0.00 2.93
1320 1658 4.250464 CCTAAACCATACAGCTCAAACGA 58.750 43.478 0.00 0.00 0.00 3.85
1321 1659 4.693566 CCTAAACCATACAGCTCAAACGAA 59.306 41.667 0.00 0.00 0.00 3.85
1322 1660 5.180492 CCTAAACCATACAGCTCAAACGAAA 59.820 40.000 0.00 0.00 0.00 3.46
1323 1661 5.508200 AAACCATACAGCTCAAACGAAAA 57.492 34.783 0.00 0.00 0.00 2.29
1326 1664 4.759693 ACCATACAGCTCAAACGAAAATGA 59.240 37.500 0.00 0.00 0.00 2.57
1327 1665 5.415701 ACCATACAGCTCAAACGAAAATGAT 59.584 36.000 0.00 0.00 0.00 2.45
1328 1666 5.740569 CCATACAGCTCAAACGAAAATGATG 59.259 40.000 0.00 0.00 0.00 3.07
1329 1667 4.836125 ACAGCTCAAACGAAAATGATGT 57.164 36.364 0.00 0.00 0.00 3.06
1330 1668 4.539870 ACAGCTCAAACGAAAATGATGTG 58.460 39.130 0.00 0.00 0.00 3.21
1473 1811 2.352817 AGGACTTCCTGGACGTGAC 58.647 57.895 10.91 3.76 46.55 3.67
1474 1812 0.469331 AGGACTTCCTGGACGTGACA 60.469 55.000 10.91 0.00 46.55 3.58
1484 1826 4.466370 TCCTGGACGTGACATAGAAATTCT 59.534 41.667 0.00 0.00 0.00 2.40
1485 1827 5.655090 TCCTGGACGTGACATAGAAATTCTA 59.345 40.000 5.07 5.07 32.87 2.10
1486 1828 5.749109 CCTGGACGTGACATAGAAATTCTAC 59.251 44.000 4.66 0.00 30.79 2.59
1487 1829 6.405953 CCTGGACGTGACATAGAAATTCTACT 60.406 42.308 4.66 0.00 30.79 2.57
1546 1891 8.364129 ACATGTGGATTTTATTGTTGTTGAAC 57.636 30.769 0.00 0.00 0.00 3.18
2170 2613 4.633175 TCCATTGTTGTCGTTGTTAGCTA 58.367 39.130 0.00 0.00 0.00 3.32
2171 2614 4.688879 TCCATTGTTGTCGTTGTTAGCTAG 59.311 41.667 0.00 0.00 0.00 3.42
2172 2615 4.394795 CATTGTTGTCGTTGTTAGCTAGC 58.605 43.478 6.62 6.62 0.00 3.42
2173 2616 2.055838 TGTTGTCGTTGTTAGCTAGCG 58.944 47.619 9.55 3.40 0.00 4.26
2234 2683 4.396166 CCATTGATTCTTCCGTTAGTGCTT 59.604 41.667 0.00 0.00 0.00 3.91
2235 2684 5.584649 CCATTGATTCTTCCGTTAGTGCTTA 59.415 40.000 0.00 0.00 0.00 3.09
2261 2710 1.673808 GCCCACCTAGTACTGTCCCG 61.674 65.000 5.39 0.00 0.00 5.14
2288 2737 2.616969 TGCTCTTGCAGTTTCCGAC 58.383 52.632 0.00 0.00 45.31 4.79
2338 2787 0.956633 CTTGCAACACCATCAGCACT 59.043 50.000 0.00 0.00 36.62 4.40
2442 2897 3.534160 ACGTCACGTTTAGCAGCG 58.466 55.556 0.00 0.00 36.35 5.18
2482 2937 7.712205 TCGACCTAGGTAACATTTAATTAAGCC 59.288 37.037 16.29 0.00 41.41 4.35
2599 3155 4.019231 AGCCATGACTCATGATGCTGATAT 60.019 41.667 19.04 0.00 43.81 1.63
2603 3159 7.385478 GCCATGACTCATGATGCTGATATATAG 59.615 40.741 19.04 0.33 43.81 1.31
2604 3160 7.873505 CCATGACTCATGATGCTGATATATAGG 59.126 40.741 19.04 0.00 43.81 2.57
2610 3168 5.774498 TGATGCTGATATATAGGTAGGCG 57.226 43.478 0.00 0.00 0.00 5.52
2725 3288 0.534427 CGGAGCATGCATGGACTGAT 60.534 55.000 27.34 0.97 0.00 2.90
2726 3289 0.952280 GGAGCATGCATGGACTGATG 59.048 55.000 27.34 1.74 0.00 3.07
2727 3290 1.476291 GGAGCATGCATGGACTGATGA 60.476 52.381 27.34 0.00 0.00 2.92
2728 3291 1.874231 GAGCATGCATGGACTGATGAG 59.126 52.381 27.34 0.00 0.00 2.90
2759 3322 3.402628 CCAGCTGGTATGTATGGTACC 57.597 52.381 25.53 4.43 41.59 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 2.624838 AGGCTTGGAAGACACACAAATG 59.375 45.455 0.00 0.00 36.14 2.32
214 220 7.164122 AGTGGCTAAGCTATACTACATACGTA 58.836 38.462 0.00 0.00 0.00 3.57
215 221 6.002704 AGTGGCTAAGCTATACTACATACGT 58.997 40.000 0.00 0.00 0.00 3.57
216 222 6.148976 TGAGTGGCTAAGCTATACTACATACG 59.851 42.308 0.00 0.00 0.00 3.06
217 223 7.450124 TGAGTGGCTAAGCTATACTACATAC 57.550 40.000 0.00 0.00 0.00 2.39
218 224 8.473358 TTTGAGTGGCTAAGCTATACTACATA 57.527 34.615 0.00 0.00 0.00 2.29
219 225 6.978674 TTGAGTGGCTAAGCTATACTACAT 57.021 37.500 0.00 0.00 0.00 2.29
220 226 6.785337 TTTGAGTGGCTAAGCTATACTACA 57.215 37.500 0.00 0.00 0.00 2.74
221 227 6.201234 GCTTTTGAGTGGCTAAGCTATACTAC 59.799 42.308 0.00 0.00 39.79 2.73
222 228 6.281405 GCTTTTGAGTGGCTAAGCTATACTA 58.719 40.000 0.00 0.00 39.79 1.82
249 337 1.674764 CCACCACTTGCACTTTGGCA 61.675 55.000 7.24 0.00 43.19 4.92
273 361 9.003658 CATTGTGTATGTCTTTCTTTCTTAGGT 57.996 33.333 0.00 0.00 0.00 3.08
274 362 9.219603 TCATTGTGTATGTCTTTCTTTCTTAGG 57.780 33.333 0.00 0.00 35.64 2.69
276 364 9.996554 TCTCATTGTGTATGTCTTTCTTTCTTA 57.003 29.630 0.00 0.00 35.64 2.10
298 399 3.197092 CGGCGCATGCATGTCTCA 61.197 61.111 26.79 0.00 45.35 3.27
349 454 2.512515 GGATCGGACTGTGCAGCC 60.513 66.667 0.00 1.46 0.00 4.85
450 567 1.675641 CTGCACCTGTAGTTGGCCC 60.676 63.158 0.00 0.00 0.00 5.80
494 614 4.880120 AGAGAAACCATGTCGATCGTAGTA 59.120 41.667 15.94 0.45 0.00 1.82
495 615 3.695060 AGAGAAACCATGTCGATCGTAGT 59.305 43.478 15.94 3.88 0.00 2.73
496 616 4.294416 AGAGAAACCATGTCGATCGTAG 57.706 45.455 15.94 3.61 0.00 3.51
559 679 3.080765 ATGTGGCCGGGTGATCGA 61.081 61.111 2.18 0.00 0.00 3.59
601 732 6.760770 AGGAAATTCAAATCAAAGAACGCAAA 59.239 30.769 0.00 0.00 0.00 3.68
604 738 5.346011 GGAGGAAATTCAAATCAAAGAACGC 59.654 40.000 0.00 0.00 0.00 4.84
608 742 4.766891 AGCGGAGGAAATTCAAATCAAAGA 59.233 37.500 0.00 0.00 0.00 2.52
623 757 3.429684 GGAAACAAAACAAAAGCGGAGGA 60.430 43.478 0.00 0.00 0.00 3.71
691 840 2.770232 ACAGTATAAAAGGGGAGGTCGG 59.230 50.000 0.00 0.00 0.00 4.79
692 841 4.403432 TGTACAGTATAAAAGGGGAGGTCG 59.597 45.833 0.00 0.00 0.00 4.79
693 842 5.945144 TGTACAGTATAAAAGGGGAGGTC 57.055 43.478 0.00 0.00 0.00 3.85
694 843 5.548836 TGTTGTACAGTATAAAAGGGGAGGT 59.451 40.000 0.00 0.00 0.00 3.85
695 844 6.057321 TGTTGTACAGTATAAAAGGGGAGG 57.943 41.667 0.00 0.00 0.00 4.30
696 845 6.942976 TCTGTTGTACAGTATAAAAGGGGAG 58.057 40.000 7.27 0.00 46.03 4.30
726 875 0.710567 GCAGTAATGCGATCGATCCG 59.289 55.000 21.57 14.91 0.00 4.18
727 876 2.071688 AGCAGTAATGCGATCGATCC 57.928 50.000 21.57 12.54 40.27 3.36
745 894 2.823829 GCAACTATGGCCGCGGAAG 61.824 63.158 33.48 21.37 0.00 3.46
872 1026 8.573035 CAGTGGTATTCTCTCTTCTTCCTATAC 58.427 40.741 0.00 0.00 0.00 1.47
894 1048 0.389817 TGCTACTAGTTGGCGCAGTG 60.390 55.000 10.83 0.11 0.00 3.66
898 1052 1.000145 GAGTTGCTACTAGTTGGCGC 59.000 55.000 0.00 0.00 33.84 6.53
944 1098 0.534427 TAGGGATCGATCGACGCACT 60.534 55.000 22.06 22.68 42.26 4.40
961 1128 2.840651 TGCTTCCTTCCTTCCTTCCTAG 59.159 50.000 0.00 0.00 0.00 3.02
981 1148 4.260170 GCATCCTATCCTATCCTTGCTTG 58.740 47.826 0.00 0.00 0.00 4.01
985 1152 3.199508 CCCTGCATCCTATCCTATCCTTG 59.800 52.174 0.00 0.00 0.00 3.61
986 1153 3.458831 CCCTGCATCCTATCCTATCCTT 58.541 50.000 0.00 0.00 0.00 3.36
991 1158 0.114364 TCGCCCTGCATCCTATCCTA 59.886 55.000 0.00 0.00 0.00 2.94
992 1159 0.764369 TTCGCCCTGCATCCTATCCT 60.764 55.000 0.00 0.00 0.00 3.24
994 1161 0.394565 ACTTCGCCCTGCATCCTATC 59.605 55.000 0.00 0.00 0.00 2.08
995 1162 0.107456 CACTTCGCCCTGCATCCTAT 59.893 55.000 0.00 0.00 0.00 2.57
998 1167 2.825836 CCACTTCGCCCTGCATCC 60.826 66.667 0.00 0.00 0.00 3.51
1008 1177 3.123620 GCCTGCTGCTCCACTTCG 61.124 66.667 0.00 0.00 36.87 3.79
1259 1434 9.357652 CGAAGAGTAGTACTACTATTAGCTAGG 57.642 40.741 32.37 18.23 44.65 3.02
1260 1435 9.357652 CCGAAGAGTAGTACTACTATTAGCTAG 57.642 40.741 32.37 22.50 44.65 3.42
1263 1438 7.961325 ACCGAAGAGTAGTACTACTATTAGC 57.039 40.000 32.37 23.05 44.65 3.09
1267 1442 7.650104 GTCGTAACCGAAGAGTAGTACTACTAT 59.350 40.741 30.80 26.30 44.55 2.12
1268 1443 6.973474 GTCGTAACCGAAGAGTAGTACTACTA 59.027 42.308 30.80 13.47 44.55 1.82
1290 1465 3.369385 CTGTATGGTTTAGGCTACGTCG 58.631 50.000 0.00 0.00 0.00 5.12
1294 1469 4.402056 TGAGCTGTATGGTTTAGGCTAC 57.598 45.455 0.00 0.00 0.00 3.58
1308 1646 4.036734 ACACATCATTTTCGTTTGAGCTGT 59.963 37.500 0.00 0.00 0.00 4.40
1309 1647 4.539870 ACACATCATTTTCGTTTGAGCTG 58.460 39.130 0.00 0.00 0.00 4.24
1310 1648 4.836125 ACACATCATTTTCGTTTGAGCT 57.164 36.364 0.00 0.00 0.00 4.09
1311 1649 5.231991 ACAAACACATCATTTTCGTTTGAGC 59.768 36.000 17.39 0.00 45.82 4.26
1312 1650 6.810888 ACAAACACATCATTTTCGTTTGAG 57.189 33.333 17.39 0.00 45.82 3.02
1313 1651 6.915300 CCTACAAACACATCATTTTCGTTTGA 59.085 34.615 17.39 3.81 45.82 2.69
1315 1653 7.033530 TCCTACAAACACATCATTTTCGTTT 57.966 32.000 0.00 0.00 0.00 3.60
1316 1654 6.627395 TCCTACAAACACATCATTTTCGTT 57.373 33.333 0.00 0.00 0.00 3.85
1317 1655 5.334879 GCTCCTACAAACACATCATTTTCGT 60.335 40.000 0.00 0.00 0.00 3.85
1318 1656 5.088739 GCTCCTACAAACACATCATTTTCG 58.911 41.667 0.00 0.00 0.00 3.46
1320 1658 5.047802 CCAGCTCCTACAAACACATCATTTT 60.048 40.000 0.00 0.00 0.00 1.82
1321 1659 4.460382 CCAGCTCCTACAAACACATCATTT 59.540 41.667 0.00 0.00 0.00 2.32
1322 1660 4.012374 CCAGCTCCTACAAACACATCATT 58.988 43.478 0.00 0.00 0.00 2.57
1323 1661 3.264193 TCCAGCTCCTACAAACACATCAT 59.736 43.478 0.00 0.00 0.00 2.45
1326 1664 3.560025 CCTTCCAGCTCCTACAAACACAT 60.560 47.826 0.00 0.00 0.00 3.21
1327 1665 2.224523 CCTTCCAGCTCCTACAAACACA 60.225 50.000 0.00 0.00 0.00 3.72
1328 1666 2.427506 CCTTCCAGCTCCTACAAACAC 58.572 52.381 0.00 0.00 0.00 3.32
1329 1667 1.351017 CCCTTCCAGCTCCTACAAACA 59.649 52.381 0.00 0.00 0.00 2.83
1330 1668 1.628846 TCCCTTCCAGCTCCTACAAAC 59.371 52.381 0.00 0.00 0.00 2.93
1484 1826 9.502091 AATGAATGCAGTGAAAGTAAGTAAGTA 57.498 29.630 0.00 0.00 0.00 2.24
1485 1827 7.986085 ATGAATGCAGTGAAAGTAAGTAAGT 57.014 32.000 0.00 0.00 0.00 2.24
1540 1885 3.768468 TGTTCGTTTTCCCAGTTCAAC 57.232 42.857 0.00 0.00 0.00 3.18
1546 1891 3.129638 TCCTGTTTTGTTCGTTTTCCCAG 59.870 43.478 0.00 0.00 0.00 4.45
1703 2122 3.512033 AGAGCGGAGTAAAGTGATCAC 57.488 47.619 18.47 18.47 0.00 3.06
1718 2137 1.424240 CAGCTGCACATGAAGAGCG 59.576 57.895 0.00 0.00 36.53 5.03
1838 2261 0.305009 GCGAAATTAAGCTCTCGGGC 59.695 55.000 0.00 0.00 0.00 6.13
2171 2614 2.094494 TCTCTAGCATATTAGCTGCCGC 60.094 50.000 0.00 0.00 46.11 6.53
2172 2615 3.441922 TCTCTCTAGCATATTAGCTGCCG 59.558 47.826 0.00 0.00 46.11 5.69
2173 2616 4.142182 CCTCTCTCTAGCATATTAGCTGCC 60.142 50.000 0.00 0.00 46.11 4.85
2234 2683 6.271585 ACAGTACTAGGTGGGCTACTTATA 57.728 41.667 0.00 0.00 0.00 0.98
2235 2684 5.139001 GACAGTACTAGGTGGGCTACTTAT 58.861 45.833 0.00 0.00 0.00 1.73
2288 2737 1.805345 CTGAGCTGCTGACCTTTCAAG 59.195 52.381 7.01 0.00 0.00 3.02
2363 2817 2.993899 CAGTTCGTTATGGGTGTCAGTC 59.006 50.000 0.00 0.00 0.00 3.51
2482 2937 2.692041 GCTCATCATTTCCTTTCCTGGG 59.308 50.000 0.00 0.00 0.00 4.45
2599 3155 2.232208 TCTCGTCGATCGCCTACCTATA 59.768 50.000 11.09 0.00 39.67 1.31
2603 3159 1.279238 GTCTCGTCGATCGCCTACC 59.721 63.158 11.09 0.00 39.67 3.18
2604 3160 0.042013 CTGTCTCGTCGATCGCCTAC 60.042 60.000 11.09 2.46 39.67 3.18
2610 3168 1.226717 GTGGCCTGTCTCGTCGATC 60.227 63.158 3.32 0.00 0.00 3.69
2725 3288 1.827344 CAGCTGGTCCATACTCACTCA 59.173 52.381 5.57 0.00 0.00 3.41
2726 3289 1.137872 CCAGCTGGTCCATACTCACTC 59.862 57.143 25.53 0.00 0.00 3.51
2727 3290 1.198713 CCAGCTGGTCCATACTCACT 58.801 55.000 25.53 0.00 0.00 3.41
2728 3291 3.768633 CCAGCTGGTCCATACTCAC 57.231 57.895 25.53 0.00 0.00 3.51
2751 3314 4.650131 TCGGTGATGTAATGTGGTACCATA 59.350 41.667 19.72 16.90 0.00 2.74
2752 3315 3.452990 TCGGTGATGTAATGTGGTACCAT 59.547 43.478 19.72 4.58 0.00 3.55
2753 3316 2.832733 TCGGTGATGTAATGTGGTACCA 59.167 45.455 11.60 11.60 0.00 3.25
2754 3317 3.530265 TCGGTGATGTAATGTGGTACC 57.470 47.619 4.43 4.43 0.00 3.34
2757 3320 4.703897 CCTATTCGGTGATGTAATGTGGT 58.296 43.478 0.00 0.00 0.00 4.16
2758 3321 3.498397 GCCTATTCGGTGATGTAATGTGG 59.502 47.826 0.00 0.00 34.25 4.17
2759 3322 3.184379 CGCCTATTCGGTGATGTAATGTG 59.816 47.826 0.00 0.00 46.58 3.21


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

AutoCloner maintained by Alex Coulton.