Multiple sequence alignment - TraesCS2D01G261000

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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 TraesCS2D01G261000 chr2D 100.000 3282 0 0 1 3282 317875066 317878347 0.000000e+00 6061.0
1 TraesCS2D01G261000 chr2D 87.013 462 48 6 507 956 317875335 317875796 8.120000e-141 510.0
2 TraesCS2D01G261000 chr2D 87.013 462 48 6 270 731 317875572 317876021 8.120000e-141 510.0
3 TraesCS2D01G261000 chr2D 85.849 106 15 0 2290 2395 477833339 477833444 2.680000e-21 113.0
4 TraesCS2D01G261000 chr2A 95.668 1662 52 7 1632 3282 415264538 415262886 0.000000e+00 2652.0
5 TraesCS2D01G261000 chr2A 96.431 1597 52 3 1 1596 415266130 415264538 0.000000e+00 2628.0
6 TraesCS2D01G261000 chr2A 86.304 460 51 6 507 956 415265861 415265404 1.060000e-134 490.0
7 TraesCS2D01G261000 chr2A 85.931 462 52 5 270 731 415265627 415265179 6.370000e-132 481.0
8 TraesCS2D01G261000 chr3A 77.823 248 48 4 2006 2250 49824183 49824426 2.640000e-31 147.0
9 TraesCS2D01G261000 chr2B 83.516 91 14 1 2291 2380 559912382 559912472 2.100000e-12 84.2


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 TraesCS2D01G261000 chr2D 317875066 317878347 3281 False 2360.333333 6061 91.3420 1 3282 3 chr2D.!!$F2 3281
1 TraesCS2D01G261000 chr2A 415262886 415266130 3244 True 1562.750000 2652 91.0835 1 3282 4 chr2A.!!$R1 3281

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
87 88 0.114560 AGGAAAGGGACGAGGTCTCA 59.885 55.0 0.0 0.0 35.11 3.27 F
1352 1354 0.895530 TTGGAGTGTCTAAGGGAGCG 59.104 55.0 0.0 0.0 0.00 5.03 F
2101 2107 0.108585 AGCTGCGGAAGTTGAAGGAA 59.891 50.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1482 0.881118 CCGGACATTGTTGGAACCAG 59.119 55.0 0.0 0.0 0.00 4.00 R
2224 2230 0.107945 ACTCGATGCCTTCTTCCAGC 60.108 55.0 0.0 0.0 0.00 4.85 R
3022 3035 0.457443 GTAATGCAAGCCTGAAGCCC 59.543 55.0 0.0 0.0 45.47 5.19 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
31 32 0.669318 CTTTTGACTGGACCGCGCTA 60.669 55.000 5.56 0.00 0.00 4.26
61 62 2.886081 CTCGTGGAGGAAGAGATGTTG 58.114 52.381 0.00 0.00 32.22 3.33
85 86 2.458620 CTTAGGAAAGGGACGAGGTCT 58.541 52.381 0.00 0.00 32.47 3.85
87 88 0.114560 AGGAAAGGGACGAGGTCTCA 59.885 55.000 0.00 0.00 35.11 3.27
181 182 1.497278 CAAGTCGTCATTGGGTGCG 59.503 57.895 0.00 0.00 0.00 5.34
220 221 1.401539 GCAATCAGCGGGAGAAACAAC 60.402 52.381 0.00 0.00 0.00 3.32
252 253 2.354259 CAGTGAGCTGGATTCCAAGTC 58.646 52.381 6.88 6.90 39.01 3.01
263 264 3.511146 GGATTCCAAGTCCAAGATGCAAA 59.489 43.478 0.00 0.00 35.76 3.68
293 294 2.392821 GTGCGAGATCTATGCAGACAG 58.607 52.381 19.41 0.00 39.67 3.51
299 300 4.083855 CGAGATCTATGCAGACAGAGACTC 60.084 50.000 0.00 15.07 46.36 3.36
331 332 6.712276 AGCTACCTTAAACAAGCTTGATAGT 58.288 36.000 32.50 19.95 42.52 2.12
332 333 7.848128 AGCTACCTTAAACAAGCTTGATAGTA 58.152 34.615 32.50 19.99 42.52 1.82
333 334 7.764901 AGCTACCTTAAACAAGCTTGATAGTAC 59.235 37.037 32.50 15.90 42.52 2.73
366 367 3.438360 AGCAAGACAAAGAAAAGTTGCG 58.562 40.909 0.00 0.00 43.94 4.85
373 374 2.362668 AAGAAAAGTTGCGTTCGACG 57.637 45.000 0.00 3.50 45.88 5.12
403 404 1.563924 ACGATGCTGTAGTTACCCCA 58.436 50.000 0.00 0.00 0.00 4.96
409 410 4.440826 TGCTGTAGTTACCCCAAAAAGA 57.559 40.909 0.00 0.00 0.00 2.52
476 477 6.271488 TGAAAAAGGATCTCGATGCAAAAT 57.729 33.333 0.00 0.00 0.00 1.82
571 572 3.634448 CCCTGAAAGAGCTCGATAGAAGA 59.366 47.826 8.37 0.00 40.98 2.87
596 597 4.646492 ACCTTGAGCAAGACAATGAAAACT 59.354 37.500 11.61 0.00 40.79 2.66
607 608 6.339730 AGACAATGAAAACTTGCATTCAACA 58.660 32.000 4.67 0.00 38.88 3.33
608 609 6.817641 AGACAATGAAAACTTGCATTCAACAA 59.182 30.769 4.67 0.00 38.88 2.83
621 622 3.673746 TTCAACAAAGTCGCTCAACAG 57.326 42.857 0.00 0.00 0.00 3.16
760 761 2.118313 TTGATGTGAGACCCATGCAG 57.882 50.000 0.00 0.00 0.00 4.41
790 791 3.754965 TGCACCACTAAAAGAGCTTGAT 58.245 40.909 0.00 0.00 0.00 2.57
857 858 2.649331 GCTCAACGAGGCTGTAGTTA 57.351 50.000 0.00 0.00 0.00 2.24
899 900 2.245159 TGAGTTGCAACACTCAGAGG 57.755 50.000 30.11 0.00 46.76 3.69
918 919 4.231426 AGAGGTGGATCCCAAGATGAAAAT 59.769 41.667 9.90 0.00 34.18 1.82
971 972 3.003689 AGCAAGATCCAAACAACTTGACG 59.996 43.478 0.00 0.00 41.16 4.35
1055 1057 5.879237 TGTAAAATCCAAGATGATTGACGC 58.121 37.500 0.00 0.00 35.21 5.19
1072 1074 1.662629 ACGCGAGATGCAAGAAGATTG 59.337 47.619 15.93 0.00 46.97 2.67
1133 1135 1.242076 GATGCCAGACACTTGCAGTT 58.758 50.000 0.00 0.00 35.66 3.16
1160 1162 4.283212 GGCAAGATCTATGGAGCTAGAAGT 59.717 45.833 0.00 0.00 37.20 3.01
1188 1190 1.902508 AGGAGGCTTGAAACGAGATCA 59.097 47.619 0.00 0.00 0.00 2.92
1299 1301 4.137543 CAGTTGAGTCTTTTAACCAGGCT 58.862 43.478 0.00 0.00 0.00 4.58
1302 1304 6.262273 CAGTTGAGTCTTTTAACCAGGCTTTA 59.738 38.462 0.00 0.00 0.00 1.85
1339 1341 6.310149 AGAAAAGGAAATGATGAGTTGGAGT 58.690 36.000 0.00 0.00 0.00 3.85
1352 1354 0.895530 TTGGAGTGTCTAAGGGAGCG 59.104 55.000 0.00 0.00 0.00 5.03
1420 1422 5.130292 TCGTGTTCTACTAACCAAGGAAG 57.870 43.478 0.00 0.00 0.00 3.46
1461 1463 2.406452 AAGTTGCGCGGAAAAGGCTG 62.406 55.000 16.61 0.00 0.00 4.85
1478 1480 3.840666 AGGCTGAAAGATGTAAGTGAGGA 59.159 43.478 0.00 0.00 34.07 3.71
1480 1482 3.620821 GCTGAAAGATGTAAGTGAGGAGC 59.379 47.826 0.00 0.00 34.07 4.70
1488 1490 1.623811 GTAAGTGAGGAGCTGGTTCCA 59.376 52.381 0.00 0.00 39.84 3.53
1566 1568 3.435671 GTCACCACTAATTGCCACTGTAC 59.564 47.826 0.00 0.00 0.00 2.90
1579 1581 4.041075 TGCCACTGTACTTTATCTGTTCCA 59.959 41.667 0.00 0.00 0.00 3.53
1586 1588 7.441458 ACTGTACTTTATCTGTTCCAACACTTC 59.559 37.037 0.00 0.00 34.70 3.01
1596 1598 1.702401 TCCAACACTTCCTGGCATGTA 59.298 47.619 0.00 0.00 32.33 2.29
1597 1599 2.308570 TCCAACACTTCCTGGCATGTAT 59.691 45.455 0.00 0.00 32.33 2.29
1598 1600 3.091545 CCAACACTTCCTGGCATGTATT 58.908 45.455 0.00 0.00 0.00 1.89
1599 1601 3.129287 CCAACACTTCCTGGCATGTATTC 59.871 47.826 0.00 0.00 0.00 1.75
1600 1602 2.632377 ACACTTCCTGGCATGTATTCG 58.368 47.619 0.00 0.00 0.00 3.34
1601 1603 2.027192 ACACTTCCTGGCATGTATTCGT 60.027 45.455 0.00 0.00 0.00 3.85
1602 1604 2.352651 CACTTCCTGGCATGTATTCGTG 59.647 50.000 0.00 0.00 0.00 4.35
1603 1605 2.027192 ACTTCCTGGCATGTATTCGTGT 60.027 45.455 0.00 0.00 33.51 4.49
1604 1606 2.022764 TCCTGGCATGTATTCGTGTG 57.977 50.000 0.00 0.00 33.51 3.82
1605 1607 1.016627 CCTGGCATGTATTCGTGTGG 58.983 55.000 0.00 0.00 33.51 4.17
1606 1608 1.678728 CCTGGCATGTATTCGTGTGGT 60.679 52.381 0.00 0.00 33.51 4.16
1607 1609 2.419436 CCTGGCATGTATTCGTGTGGTA 60.419 50.000 0.00 0.00 33.51 3.25
1608 1610 2.607635 CTGGCATGTATTCGTGTGGTAC 59.392 50.000 0.00 0.00 33.51 3.34
1609 1611 2.235155 TGGCATGTATTCGTGTGGTACT 59.765 45.455 0.00 0.00 33.51 2.73
1610 1612 3.267483 GGCATGTATTCGTGTGGTACTT 58.733 45.455 0.00 0.00 33.51 2.24
1611 1613 3.687698 GGCATGTATTCGTGTGGTACTTT 59.312 43.478 0.00 0.00 33.51 2.66
1612 1614 4.155280 GGCATGTATTCGTGTGGTACTTTT 59.845 41.667 0.00 0.00 33.51 2.27
1613 1615 5.086058 GCATGTATTCGTGTGGTACTTTTG 58.914 41.667 0.00 0.00 33.51 2.44
1614 1616 4.735662 TGTATTCGTGTGGTACTTTTGC 57.264 40.909 0.00 0.00 0.00 3.68
1615 1617 4.127907 TGTATTCGTGTGGTACTTTTGCA 58.872 39.130 0.00 0.00 0.00 4.08
1616 1618 4.757657 TGTATTCGTGTGGTACTTTTGCAT 59.242 37.500 0.00 0.00 0.00 3.96
1617 1619 5.932883 TGTATTCGTGTGGTACTTTTGCATA 59.067 36.000 0.00 0.00 0.00 3.14
1618 1620 6.596106 TGTATTCGTGTGGTACTTTTGCATAT 59.404 34.615 0.00 0.00 0.00 1.78
1619 1621 7.764901 TGTATTCGTGTGGTACTTTTGCATATA 59.235 33.333 0.00 0.00 0.00 0.86
1620 1622 7.801716 ATTCGTGTGGTACTTTTGCATATAT 57.198 32.000 0.00 0.00 0.00 0.86
1621 1623 6.597262 TCGTGTGGTACTTTTGCATATATG 57.403 37.500 8.45 8.45 0.00 1.78
1622 1624 5.525745 TCGTGTGGTACTTTTGCATATATGG 59.474 40.000 14.51 0.00 0.00 2.74
1623 1625 5.295787 CGTGTGGTACTTTTGCATATATGGT 59.704 40.000 14.51 5.92 0.00 3.55
1624 1626 6.183360 CGTGTGGTACTTTTGCATATATGGTT 60.183 38.462 14.51 0.00 0.00 3.67
1625 1627 7.011576 CGTGTGGTACTTTTGCATATATGGTTA 59.988 37.037 14.51 0.00 0.00 2.85
1626 1628 8.846211 GTGTGGTACTTTTGCATATATGGTTAT 58.154 33.333 14.51 0.00 0.00 1.89
1698 1701 1.161843 AGTTTACAAATGGACGGGCG 58.838 50.000 0.00 0.00 0.00 6.13
1837 1840 4.919754 GGCAAGCTGAAATTACAAACTCAG 59.080 41.667 0.00 0.00 38.66 3.35
1971 1977 0.111061 TCTTGCAGCTGAATGGTGGT 59.889 50.000 20.43 0.00 43.78 4.16
1973 1979 0.467844 TTGCAGCTGAATGGTGGTGT 60.468 50.000 20.43 0.00 43.78 4.16
2003 2009 6.662414 TCCTATCTTTTTACAAGCATCACG 57.338 37.500 0.00 0.00 0.00 4.35
2028 2034 2.179427 TCCGTGATTCCATCTGACAGT 58.821 47.619 1.59 0.00 0.00 3.55
2088 2094 0.935898 GAGGATGATGACAAGCTGCG 59.064 55.000 0.00 0.00 0.00 5.18
2101 2107 0.108585 AGCTGCGGAAGTTGAAGGAA 59.891 50.000 0.00 0.00 0.00 3.36
2191 2197 2.038689 TGGCCGTTATGTTGTACCAGAA 59.961 45.455 0.00 0.00 0.00 3.02
2224 2230 2.485122 GATGGCCGGAAAGCAACG 59.515 61.111 5.05 0.00 0.00 4.10
2278 2287 1.401552 TGGCAATCACATAAGAAGCGC 59.598 47.619 0.00 0.00 0.00 5.92
2302 2314 3.677963 CTGGGAAGCCAGGTTTCAT 57.322 52.632 17.19 0.00 34.47 2.57
2360 2372 5.047519 CCAAGCTTTCATGGAGTGAGAAAAT 60.048 40.000 0.00 0.00 39.12 1.82
2429 2441 3.842925 TTGTCCCTGCGCTGAACCC 62.843 63.158 16.65 1.43 0.00 4.11
2530 2542 9.886132 ATGTTTTAGTGTATTAGGTAGAGGTTG 57.114 33.333 0.00 0.00 0.00 3.77
2560 2572 5.822519 GGCTCATTGGTTGATACTGATTGTA 59.177 40.000 0.00 0.00 32.72 2.41
2581 2593 8.564648 TTGTACAACTATATTAACCGTCATCG 57.435 34.615 3.59 0.00 0.00 3.84
2600 2612 8.376203 CGTCATCGCCTTTCATCTTATTATTAG 58.624 37.037 0.00 0.00 0.00 1.73
2630 2642 6.662755 TCCTCTTATTGTAGAATTGGCATGT 58.337 36.000 0.00 0.00 0.00 3.21
2634 2646 9.764363 CTCTTATTGTAGAATTGGCATGTACTA 57.236 33.333 0.00 0.00 0.00 1.82
2657 2669 9.203163 ACTACTAGTCTAAAATGTAGATTGCCT 57.797 33.333 0.00 0.00 35.78 4.75
2658 2670 9.685828 CTACTAGTCTAAAATGTAGATTGCCTC 57.314 37.037 0.00 0.00 34.28 4.70
2659 2671 8.312669 ACTAGTCTAAAATGTAGATTGCCTCT 57.687 34.615 0.00 0.00 38.06 3.69
2660 2672 8.763601 ACTAGTCTAAAATGTAGATTGCCTCTT 58.236 33.333 0.00 0.00 35.28 2.85
2663 2675 9.771534 AGTCTAAAATGTAGATTGCCTCTTATC 57.228 33.333 0.00 0.00 35.28 1.75
2664 2676 9.771534 GTCTAAAATGTAGATTGCCTCTTATCT 57.228 33.333 0.00 0.00 35.28 1.98
2726 2738 2.146342 GCTCTTGTGTGTATGTGTGCT 58.854 47.619 0.00 0.00 0.00 4.40
2743 2756 1.322442 GCTTGTGGTGGAAAGCTTCT 58.678 50.000 0.00 0.00 44.33 2.85
2750 2763 3.630312 GTGGTGGAAAGCTTCTGTGTTAA 59.370 43.478 0.00 0.00 0.00 2.01
2854 2867 5.742453 GCACATGAGCTTGATGTAGAAATTG 59.258 40.000 7.97 1.18 32.64 2.32
2876 2889 0.661020 GTGTGGTGGAAGTGAAACCG 59.339 55.000 0.00 0.00 37.80 4.44
2880 2893 3.618171 GTGGAAGTGAAACCGCCTA 57.382 52.632 0.00 0.00 37.80 3.93
2929 2942 7.748031 TGTTTTGTACAGCTAAAACATTGTG 57.252 32.000 17.31 0.00 46.12 3.33
2952 2965 0.930310 TGATCTGCGCGTTCTTATGC 59.070 50.000 8.43 0.00 0.00 3.14
2989 3002 5.006386 ACTGCTGCAAGTATAAGCTTTTCT 58.994 37.500 3.20 0.00 37.82 2.52
2990 3003 5.106396 ACTGCTGCAAGTATAAGCTTTTCTG 60.106 40.000 3.20 0.00 37.82 3.02
3006 3019 2.787473 TCTGGTTCCTGCTAATGTGG 57.213 50.000 0.00 0.00 0.00 4.17
3007 3020 1.985159 TCTGGTTCCTGCTAATGTGGT 59.015 47.619 0.00 0.00 0.00 4.16
3012 3025 2.672961 TCCTGCTAATGTGGTTCTCG 57.327 50.000 0.00 0.00 0.00 4.04
3018 3031 4.183865 TGCTAATGTGGTTCTCGAATCAG 58.816 43.478 0.00 0.00 31.11 2.90
3022 3035 2.766313 TGTGGTTCTCGAATCAGTTGG 58.234 47.619 0.00 0.00 31.11 3.77
3049 3062 3.455910 TCAGGCTTGCATTACAGGTATCT 59.544 43.478 0.00 0.00 0.00 1.98
3052 3065 6.000219 CAGGCTTGCATTACAGGTATCTATT 59.000 40.000 0.00 0.00 0.00 1.73
3170 3183 9.562408 CTGTCTAACTAACATGGAGAGTAGATA 57.438 37.037 0.00 5.12 0.00 1.98
3188 3201 7.067421 AGTAGATAGTACACCAGGAGCATTTA 58.933 38.462 0.00 0.00 0.00 1.40
3213 3226 2.565391 TCGAGCTGATAGGAAACCAACA 59.435 45.455 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.422597 CGGTCCAGTCAAAAGTATGCA 58.577 47.619 0.00 0.00 0.00 3.96
31 32 1.333636 CCTCCACGAGGCTCCAGATT 61.334 60.000 9.32 0.00 43.29 2.40
61 62 1.137282 CTCGTCCCTTTCCTAAGCTCC 59.863 57.143 0.00 0.00 0.00 4.70
85 86 0.380733 CGTAGTAGCATGCCGAGTGA 59.619 55.000 15.66 0.00 0.00 3.41
87 88 1.734137 CCGTAGTAGCATGCCGAGT 59.266 57.895 15.66 8.45 0.00 4.18
181 182 1.856265 CGGAGGGCTTCTTGTGTTGC 61.856 60.000 0.00 0.00 0.00 4.17
212 213 4.885325 ACTGGTTGTTAATCGGTTGTTTCT 59.115 37.500 0.00 0.00 0.00 2.52
220 221 2.416547 CAGCTCACTGGTTGTTAATCGG 59.583 50.000 0.00 0.00 40.48 4.18
252 253 5.571277 CACCAAAAAGTTTTTGCATCTTGG 58.429 37.500 28.19 19.16 30.67 3.61
263 264 5.619981 GCATAGATCTCGCACCAAAAAGTTT 60.620 40.000 0.00 0.00 0.00 2.66
293 294 3.520402 AGCTAGCGCTGGAGTCTC 58.480 61.111 26.32 6.06 46.86 3.36
331 332 4.776349 TGTCTTGCTCAAGGTTCTTTGTA 58.224 39.130 9.48 0.00 38.88 2.41
332 333 3.620488 TGTCTTGCTCAAGGTTCTTTGT 58.380 40.909 9.48 0.00 38.88 2.83
333 334 4.637483 TTGTCTTGCTCAAGGTTCTTTG 57.363 40.909 9.48 0.00 38.88 2.77
366 367 1.447201 CGTTGAGTGACTTCGTCGAAC 59.553 52.381 2.90 0.00 34.95 3.95
373 374 2.408050 ACAGCATCGTTGAGTGACTTC 58.592 47.619 0.00 0.00 0.00 3.01
476 477 1.588824 CTTGCTTCGGGCTGCATTGA 61.589 55.000 0.50 0.00 42.39 2.57
571 572 5.596836 TTTCATTGTCTTGCTCAAGGTTT 57.403 34.783 9.48 0.00 38.88 3.27
596 597 2.357323 TGAGCGACTTTGTTGAATGCAA 59.643 40.909 0.00 0.00 0.00 4.08
599 600 3.951306 TGTTGAGCGACTTTGTTGAATG 58.049 40.909 0.00 0.00 0.00 2.67
607 608 0.886490 CAGCCCTGTTGAGCGACTTT 60.886 55.000 0.00 0.00 0.00 2.66
608 609 1.302033 CAGCCCTGTTGAGCGACTT 60.302 57.895 0.00 0.00 0.00 3.01
674 675 5.310409 TCCTTATTCATCTTGGGATCCAC 57.690 43.478 15.23 3.53 30.78 4.02
760 761 2.169832 TTAGTGGTGCAAGCTCTGTC 57.830 50.000 0.00 0.00 38.74 3.51
899 900 4.280819 TCCATTTTCATCTTGGGATCCAC 58.719 43.478 15.23 3.53 30.78 4.02
971 972 2.883267 CTAGGCTGCTTGTCCCTGGC 62.883 65.000 0.00 0.00 0.00 4.85
1055 1057 3.373130 TGCTTCAATCTTCTTGCATCTCG 59.627 43.478 0.00 0.00 0.00 4.04
1072 1074 3.750130 TCAAACTCTGCTGATCTTGCTTC 59.250 43.478 11.38 0.00 0.00 3.86
1133 1135 3.044156 AGCTCCATAGATCTTGCCTCAA 58.956 45.455 0.00 0.00 0.00 3.02
1160 1162 3.157087 GTTTCAAGCCTCCTGGATTTCA 58.843 45.455 0.00 0.00 40.42 2.69
1299 1301 6.130569 TCCTTTTCTTTGCTGGGTTACTAAA 58.869 36.000 0.00 0.00 0.00 1.85
1302 1304 4.178956 TCCTTTTCTTTGCTGGGTTACT 57.821 40.909 0.00 0.00 0.00 2.24
1339 1341 1.340697 TGCTACTCGCTCCCTTAGACA 60.341 52.381 0.00 0.00 40.11 3.41
1352 1354 6.090088 CAGTTCATTCTGTAACTGTGCTACTC 59.910 42.308 6.97 0.00 44.83 2.59
1449 1451 1.541588 ACATCTTTCAGCCTTTTCCGC 59.458 47.619 0.00 0.00 0.00 5.54
1461 1463 4.187694 CCAGCTCCTCACTTACATCTTTC 58.812 47.826 0.00 0.00 0.00 2.62
1478 1480 1.620822 GGACATTGTTGGAACCAGCT 58.379 50.000 8.93 0.00 0.00 4.24
1480 1482 0.881118 CCGGACATTGTTGGAACCAG 59.119 55.000 0.00 0.00 0.00 4.00
1488 1490 8.087750 CCAAATTTATATATGCCGGACATTGTT 58.912 33.333 5.05 0.24 40.38 2.83
1566 1568 5.182001 CCAGGAAGTGTTGGAACAGATAAAG 59.818 44.000 0.00 0.00 42.39 1.85
1579 1581 3.009723 CGAATACATGCCAGGAAGTGTT 58.990 45.455 0.00 0.00 0.00 3.32
1586 1588 1.016627 CCACACGAATACATGCCAGG 58.983 55.000 0.00 0.00 0.00 4.45
1596 1598 7.255104 CCATATATGCAAAAGTACCACACGAAT 60.255 37.037 7.24 0.00 0.00 3.34
1597 1599 6.037720 CCATATATGCAAAAGTACCACACGAA 59.962 38.462 7.24 0.00 0.00 3.85
1598 1600 5.525745 CCATATATGCAAAAGTACCACACGA 59.474 40.000 7.24 0.00 0.00 4.35
1599 1601 5.295787 ACCATATATGCAAAAGTACCACACG 59.704 40.000 7.24 0.00 0.00 4.49
1600 1602 6.693315 ACCATATATGCAAAAGTACCACAC 57.307 37.500 7.24 0.00 0.00 3.82
1601 1603 8.988546 ATAACCATATATGCAAAAGTACCACA 57.011 30.769 7.24 0.00 0.00 4.17
1631 1633 6.789457 AGATGGGATCACAAGGATAATAGTGA 59.211 38.462 0.00 0.00 44.16 3.41
1651 1654 2.356135 CCCCTACAAACACGAAGATGG 58.644 52.381 0.00 0.00 0.00 3.51
1652 1655 1.737793 GCCCCTACAAACACGAAGATG 59.262 52.381 0.00 0.00 0.00 2.90
1698 1701 5.804771 GCCCATTCTCTTGACCCCTATATTC 60.805 48.000 0.00 0.00 0.00 1.75
1765 1768 4.922206 ACTTGGGCATCTTCTTGTGATAA 58.078 39.130 0.00 0.00 0.00 1.75
1837 1840 2.678336 CGATCTTAAAAGGGTGCCACTC 59.322 50.000 0.00 0.00 0.00 3.51
1971 1977 7.362056 GCTTGTAAAAAGATAGGAATGCTCACA 60.362 37.037 0.00 0.00 0.00 3.58
1973 1979 6.658816 TGCTTGTAAAAAGATAGGAATGCTCA 59.341 34.615 0.00 0.00 0.00 4.26
2028 2034 8.704668 ACACCAAATAGTGAGATCATGTATGTA 58.295 33.333 0.00 0.00 40.34 2.29
2088 2094 4.022849 CACCATGTTCTTCCTTCAACTTCC 60.023 45.833 0.00 0.00 0.00 3.46
2101 2107 5.948162 AGTGCATATTTCTTCACCATGTTCT 59.052 36.000 0.00 0.00 0.00 3.01
2191 2197 3.136626 GGCCATCCTTATAGTTCCACAGT 59.863 47.826 0.00 0.00 0.00 3.55
2224 2230 0.107945 ACTCGATGCCTTCTTCCAGC 60.108 55.000 0.00 0.00 0.00 4.85
2249 2255 3.648339 ATGTGATTGCCACTGTTTCAC 57.352 42.857 0.00 0.00 45.86 3.18
2302 2314 1.271840 AAACTCGCCCCCTCTATGCA 61.272 55.000 0.00 0.00 0.00 3.96
2412 2424 4.329545 GGGTTCAGCGCAGGGACA 62.330 66.667 11.47 0.00 0.00 4.02
2429 2441 2.032550 CACGAAGCCTGCAGATAAATGG 59.967 50.000 17.39 0.00 0.00 3.16
2504 2516 9.886132 CAACCTCTACCTAATACACTAAAACAT 57.114 33.333 0.00 0.00 0.00 2.71
2530 2542 2.489938 TCAACCAATGAGCCACTACC 57.510 50.000 0.00 0.00 33.04 3.18
2560 2572 4.986659 GGCGATGACGGTTAATATAGTTGT 59.013 41.667 0.00 0.00 40.15 3.32
2634 2646 8.312669 AGAGGCAATCTACATTTTAGACTAGT 57.687 34.615 0.00 0.00 36.10 2.57
2638 2650 9.771534 AGATAAGAGGCAATCTACATTTTAGAC 57.228 33.333 0.00 0.00 37.23 2.59
2726 2738 2.023673 CACAGAAGCTTTCCACCACAA 58.976 47.619 0.00 0.00 0.00 3.33
2739 2752 6.192360 CAGTTCGACCTTTTTAACACAGAAG 58.808 40.000 0.00 0.00 0.00 2.85
2743 2756 3.065648 GGCAGTTCGACCTTTTTAACACA 59.934 43.478 0.00 0.00 0.00 3.72
2750 2763 2.154462 CATGAGGCAGTTCGACCTTTT 58.846 47.619 0.00 0.00 36.05 2.27
2836 2849 5.106396 ACACTGCAATTTCTACATCAAGCTC 60.106 40.000 0.00 0.00 0.00 4.09
2854 2867 1.065551 GTTTCACTTCCACCACACTGC 59.934 52.381 0.00 0.00 0.00 4.40
2929 2942 1.565305 AAGAACGCGCAGATCATCTC 58.435 50.000 5.73 0.00 0.00 2.75
2989 3002 2.375174 AGAACCACATTAGCAGGAACCA 59.625 45.455 0.00 0.00 0.00 3.67
2990 3003 3.010420 GAGAACCACATTAGCAGGAACC 58.990 50.000 0.00 0.00 0.00 3.62
3006 3019 1.087501 GCCCCAACTGATTCGAGAAC 58.912 55.000 0.00 0.00 0.00 3.01
3007 3020 0.984230 AGCCCCAACTGATTCGAGAA 59.016 50.000 0.00 0.00 0.00 2.87
3012 3025 1.467920 CCTGAAGCCCCAACTGATTC 58.532 55.000 0.00 0.00 0.00 2.52
3018 3031 2.935740 GCAAGCCTGAAGCCCCAAC 61.936 63.158 0.00 0.00 45.47 3.77
3022 3035 0.457443 GTAATGCAAGCCTGAAGCCC 59.543 55.000 0.00 0.00 45.47 5.19
3052 3065 8.384607 TCTGTACAAAAGCACATATACACAAA 57.615 30.769 0.00 0.00 0.00 2.83
3170 3183 3.264450 AGCTTAAATGCTCCTGGTGTACT 59.736 43.478 0.00 0.00 39.34 2.73
3213 3226 6.182627 TGTGATGGCATCTACTTCAATTTCT 58.817 36.000 26.49 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.