Multiple sequence alignment - TraesCS2D01G147600

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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 TraesCS2D01G147600 chr2D 100.000 2655 0 0 1 2655 88592777 88590123 0.000000e+00 4903.0
1 TraesCS2D01G147600 chr2D 94.465 1915 61 15 1 1880 88661120 88659216 0.000000e+00 2907.0
2 TraesCS2D01G147600 chr2D 89.180 1146 76 29 765 1880 88743653 88742526 0.000000e+00 1386.0
3 TraesCS2D01G147600 chr2D 84.818 685 73 16 1983 2655 296374470 296373805 0.000000e+00 660.0
4 TraesCS2D01G147600 chr2D 86.792 477 51 3 1984 2448 600055856 600055380 3.030000e-144 521.0
5 TraesCS2D01G147600 chr2B 90.069 1158 51 17 767 1894 141641966 141640843 0.000000e+00 1443.0
6 TraesCS2D01G147600 chr2B 84.942 684 79 15 1983 2655 366008194 366008864 0.000000e+00 671.0
7 TraesCS2D01G147600 chr2B 83.516 91 12 3 950 1040 141387615 141387528 6.090000e-12 82.4
8 TraesCS2D01G147600 chr2A 86.834 1276 80 31 765 1985 88747978 88746736 0.000000e+00 1345.0
9 TraesCS2D01G147600 chr2A 82.115 520 79 13 16 525 88748564 88748049 1.460000e-117 433.0
10 TraesCS2D01G147600 chr2A 82.548 361 38 10 2303 2655 367653408 367653065 7.190000e-76 294.0
11 TraesCS2D01G147600 chr1B 89.034 611 58 2 2053 2655 623226466 623227075 0.000000e+00 749.0
12 TraesCS2D01G147600 chr1B 81.836 512 64 12 2151 2653 133485595 133485104 1.140000e-108 403.0
13 TraesCS2D01G147600 chr7D 84.964 685 76 17 1984 2655 71621452 71622122 0.000000e+00 669.0
14 TraesCS2D01G147600 chr4B 84.795 684 65 18 1986 2655 65941031 65940373 0.000000e+00 651.0
15 TraesCS2D01G147600 chr7A 85.420 583 68 9 2083 2655 162044127 162044702 8.190000e-165 590.0
16 TraesCS2D01G147600 chr7A 84.247 584 73 12 2083 2655 162043551 162044126 3.860000e-153 551.0
17 TraesCS2D01G147600 chr3B 87.045 440 54 1 2216 2655 95846756 95847192 6.600000e-136 494.0
18 TraesCS2D01G147600 chr1D 81.818 605 81 10 1984 2572 465342810 465343401 5.140000e-132 481.0
19 TraesCS2D01G147600 chr4A 85.553 443 41 6 2212 2654 520065569 520065988 2.430000e-120 442.0
20 TraesCS2D01G147600 chr3A 84.919 431 52 2 1984 2413 171788785 171789203 8.790000e-115 424.0
21 TraesCS2D01G147600 chr3A 87.448 239 22 4 2418 2655 171790545 171790776 4.360000e-68 268.0
22 TraesCS2D01G147600 chr3A 85.714 133 19 0 1984 2116 28147257 28147125 9.910000e-30 141.0
23 TraesCS2D01G147600 chr3D 86.486 333 38 4 2323 2655 473447884 473447559 2.510000e-95 359.0
24 TraesCS2D01G147600 chr6A 74.334 413 71 23 18 409 135222732 135223130 2.750000e-30 143.0


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 TraesCS2D01G147600 chr2D 88590123 88592777 2654 True 4903.0 4903 100.0000 1 2655 1 chr2D.!!$R1 2654
1 TraesCS2D01G147600 chr2D 88659216 88661120 1904 True 2907.0 2907 94.4650 1 1880 1 chr2D.!!$R2 1879
2 TraesCS2D01G147600 chr2D 88742526 88743653 1127 True 1386.0 1386 89.1800 765 1880 1 chr2D.!!$R3 1115
3 TraesCS2D01G147600 chr2D 296373805 296374470 665 True 660.0 660 84.8180 1983 2655 1 chr2D.!!$R4 672
4 TraesCS2D01G147600 chr2B 141640843 141641966 1123 True 1443.0 1443 90.0690 767 1894 1 chr2B.!!$R2 1127
5 TraesCS2D01G147600 chr2B 366008194 366008864 670 False 671.0 671 84.9420 1983 2655 1 chr2B.!!$F1 672
6 TraesCS2D01G147600 chr2A 88746736 88748564 1828 True 889.0 1345 84.4745 16 1985 2 chr2A.!!$R2 1969
7 TraesCS2D01G147600 chr1B 623226466 623227075 609 False 749.0 749 89.0340 2053 2655 1 chr1B.!!$F1 602
8 TraesCS2D01G147600 chr7D 71621452 71622122 670 False 669.0 669 84.9640 1984 2655 1 chr7D.!!$F1 671
9 TraesCS2D01G147600 chr4B 65940373 65941031 658 True 651.0 651 84.7950 1986 2655 1 chr4B.!!$R1 669
10 TraesCS2D01G147600 chr7A 162043551 162044702 1151 False 570.5 590 84.8335 2083 2655 2 chr7A.!!$F1 572
11 TraesCS2D01G147600 chr1D 465342810 465343401 591 False 481.0 481 81.8180 1984 2572 1 chr1D.!!$F1 588
12 TraesCS2D01G147600 chr3A 171788785 171790776 1991 False 346.0 424 86.1835 1984 2655 2 chr3A.!!$F1 671

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
338 346 0.182775 AGCTGAAACTTTCACCCCGT 59.817 50.0 0.0 0.0 35.46 5.28 F
339 347 0.310854 GCTGAAACTTTCACCCCGTG 59.689 55.0 0.0 0.0 35.46 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1814 0.029035 CATCTTGCGCAATCTCTGGC 59.971 55.0 25.26 0.0 0.00 4.85 R
1895 2139 0.250553 TGGGTTCGGTTCGATGCTTT 60.251 50.0 0.00 0.0 35.23 3.51 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
338 346 0.182775 AGCTGAAACTTTCACCCCGT 59.817 50.000 0.00 0.00 35.46 5.28
339 347 0.310854 GCTGAAACTTTCACCCCGTG 59.689 55.000 0.00 0.00 35.46 4.94
386 395 2.029020 GCTAAAGAGGGGCCAAAAACTG 60.029 50.000 4.39 0.00 0.00 3.16
566 586 9.772973 AGGCGTTGTTATCATATTGTTCTATTA 57.227 29.630 0.00 0.00 0.00 0.98
612 632 7.618019 TCTATTAGGGTTGAGTGCAGATTAT 57.382 36.000 0.00 0.00 0.00 1.28
613 633 8.721133 TCTATTAGGGTTGAGTGCAGATTATA 57.279 34.615 0.00 0.00 0.00 0.98
614 634 8.807118 TCTATTAGGGTTGAGTGCAGATTATAG 58.193 37.037 0.00 0.00 0.00 1.31
615 635 7.618019 ATTAGGGTTGAGTGCAGATTATAGA 57.382 36.000 0.00 0.00 0.00 1.98
616 636 5.957771 AGGGTTGAGTGCAGATTATAGAA 57.042 39.130 0.00 0.00 0.00 2.10
617 637 5.675538 AGGGTTGAGTGCAGATTATAGAAC 58.324 41.667 0.00 0.00 0.00 3.01
618 638 5.426833 AGGGTTGAGTGCAGATTATAGAACT 59.573 40.000 0.00 0.00 0.00 3.01
619 639 6.069963 AGGGTTGAGTGCAGATTATAGAACTT 60.070 38.462 0.00 0.00 0.00 2.66
620 640 6.258947 GGGTTGAGTGCAGATTATAGAACTTC 59.741 42.308 0.00 0.00 0.00 3.01
621 641 6.258947 GGTTGAGTGCAGATTATAGAACTTCC 59.741 42.308 0.00 0.00 0.00 3.46
622 642 6.798427 TGAGTGCAGATTATAGAACTTCCT 57.202 37.500 0.00 0.00 0.00 3.36
623 643 6.810911 TGAGTGCAGATTATAGAACTTCCTC 58.189 40.000 0.00 0.00 0.00 3.71
624 644 6.381133 TGAGTGCAGATTATAGAACTTCCTCA 59.619 38.462 0.00 0.00 0.00 3.86
625 645 7.093333 TGAGTGCAGATTATAGAACTTCCTCAA 60.093 37.037 0.00 0.00 0.00 3.02
626 646 7.624549 AGTGCAGATTATAGAACTTCCTCAAA 58.375 34.615 0.00 0.00 0.00 2.69
627 647 8.103305 AGTGCAGATTATAGAACTTCCTCAAAA 58.897 33.333 0.00 0.00 0.00 2.44
628 648 8.730680 GTGCAGATTATAGAACTTCCTCAAAAA 58.269 33.333 0.00 0.00 0.00 1.94
659 679 9.563898 AAAAAGTACTCCTTTCGTTTACTTTTG 57.436 29.630 15.05 0.00 45.54 2.44
660 680 7.854557 AAGTACTCCTTTCGTTTACTTTTGT 57.145 32.000 0.00 0.00 30.48 2.83
661 681 8.947055 AAGTACTCCTTTCGTTTACTTTTGTA 57.053 30.769 0.00 0.00 30.48 2.41
662 682 8.947055 AGTACTCCTTTCGTTTACTTTTGTAA 57.053 30.769 0.00 0.00 42.54 2.41
663 683 9.038803 AGTACTCCTTTCGTTTACTTTTGTAAG 57.961 33.333 0.00 0.00 44.60 2.34
664 684 9.034544 GTACTCCTTTCGTTTACTTTTGTAAGA 57.965 33.333 0.00 0.00 44.60 2.10
665 685 7.913423 ACTCCTTTCGTTTACTTTTGTAAGAC 58.087 34.615 0.00 0.00 44.60 3.01
666 686 6.936374 TCCTTTCGTTTACTTTTGTAAGACG 58.064 36.000 12.59 12.59 44.60 4.18
667 687 6.534793 TCCTTTCGTTTACTTTTGTAAGACGT 59.465 34.615 15.51 0.00 44.60 4.34
668 688 7.064490 TCCTTTCGTTTACTTTTGTAAGACGTT 59.936 33.333 15.51 0.00 44.60 3.99
669 689 7.693536 CCTTTCGTTTACTTTTGTAAGACGTTT 59.306 33.333 15.51 0.00 44.60 3.60
670 690 8.947304 TTTCGTTTACTTTTGTAAGACGTTTT 57.053 26.923 0.00 0.00 44.60 2.43
739 759 8.867112 TTTAAGACATCACCTAGTATTAAGCG 57.133 34.615 0.00 0.00 34.25 4.68
740 760 6.710597 AAGACATCACCTAGTATTAAGCGA 57.289 37.500 0.00 0.00 0.00 4.93
741 761 6.074544 AGACATCACCTAGTATTAAGCGAC 57.925 41.667 0.00 0.00 0.00 5.19
742 762 5.828859 AGACATCACCTAGTATTAAGCGACT 59.171 40.000 0.00 0.00 0.00 4.18
743 763 6.321690 AGACATCACCTAGTATTAAGCGACTT 59.678 38.462 0.00 0.00 0.00 3.01
744 764 7.501559 AGACATCACCTAGTATTAAGCGACTTA 59.498 37.037 0.00 0.00 0.00 2.24
745 765 7.424001 ACATCACCTAGTATTAAGCGACTTAC 58.576 38.462 0.00 0.00 0.00 2.34
746 766 7.067859 ACATCACCTAGTATTAAGCGACTTACA 59.932 37.037 0.00 0.00 0.00 2.41
747 767 7.395190 TCACCTAGTATTAAGCGACTTACAA 57.605 36.000 0.00 0.00 0.00 2.41
748 768 7.829725 TCACCTAGTATTAAGCGACTTACAAA 58.170 34.615 0.00 0.00 0.00 2.83
749 769 8.306038 TCACCTAGTATTAAGCGACTTACAAAA 58.694 33.333 0.00 0.00 0.00 2.44
750 770 8.592998 CACCTAGTATTAAGCGACTTACAAAAG 58.407 37.037 0.00 0.00 38.77 2.27
752 772 8.592998 CCTAGTATTAAGCGACTTACAAAAGTG 58.407 37.037 0.00 0.00 46.09 3.16
753 773 7.360575 AGTATTAAGCGACTTACAAAAGTGG 57.639 36.000 0.00 0.00 46.09 4.00
754 774 7.156673 AGTATTAAGCGACTTACAAAAGTGGA 58.843 34.615 4.71 0.00 46.09 4.02
755 775 5.662211 TTAAGCGACTTACAAAAGTGGAC 57.338 39.130 4.71 0.00 46.09 4.02
756 776 3.188159 AGCGACTTACAAAAGTGGACA 57.812 42.857 4.71 0.00 46.09 4.02
757 777 3.131396 AGCGACTTACAAAAGTGGACAG 58.869 45.455 4.71 0.00 46.09 3.51
758 778 3.128349 GCGACTTACAAAAGTGGACAGA 58.872 45.455 4.71 0.00 46.09 3.41
759 779 3.184581 GCGACTTACAAAAGTGGACAGAG 59.815 47.826 4.71 0.00 46.09 3.35
760 780 3.741344 CGACTTACAAAAGTGGACAGAGG 59.259 47.826 0.00 0.00 46.09 3.69
761 781 4.065789 GACTTACAAAAGTGGACAGAGGG 58.934 47.826 0.00 0.00 46.09 4.30
762 782 3.714798 ACTTACAAAAGTGGACAGAGGGA 59.285 43.478 0.00 0.00 44.40 4.20
763 783 2.938956 ACAAAAGTGGACAGAGGGAG 57.061 50.000 0.00 0.00 0.00 4.30
1009 1190 0.953471 TCCGCAAATCAGGGTTGACG 60.953 55.000 0.00 0.00 35.83 4.35
1436 1662 6.334989 TGTTCGTACAAATCCGATAACTCAT 58.665 36.000 0.00 0.00 32.44 2.90
1568 1803 1.078214 CGAGGATGGGCTTCAGCAA 60.078 57.895 0.30 0.00 44.36 3.91
1577 1812 2.505407 TGGGCTTCAGCAATAGAGCTAA 59.495 45.455 0.30 0.00 44.54 3.09
1578 1813 2.875317 GGGCTTCAGCAATAGAGCTAAC 59.125 50.000 0.30 0.00 44.54 2.34
1579 1814 2.541762 GGCTTCAGCAATAGAGCTAACG 59.458 50.000 0.30 0.00 44.54 3.18
1581 1816 2.225068 TCAGCAATAGAGCTAACGCC 57.775 50.000 0.00 0.00 44.54 5.68
1582 1817 1.480545 TCAGCAATAGAGCTAACGCCA 59.519 47.619 0.00 0.00 44.54 5.69
1583 1818 1.863454 CAGCAATAGAGCTAACGCCAG 59.137 52.381 0.00 0.00 44.54 4.85
1609 1844 1.353103 GCAAGATGCAACCGATCGG 59.647 57.895 32.20 32.20 44.26 4.18
1633 1868 2.416372 CTATGCGCGCGTTGATGTCC 62.416 60.000 32.97 12.41 0.00 4.02
1763 2007 4.898265 AGCAGCAGTATTTCCTATCTCTGA 59.102 41.667 0.00 0.00 0.00 3.27
1804 2048 5.220548 GCTTGCTGTTACTGTATCATGTCTG 60.221 44.000 0.00 0.00 0.00 3.51
1854 2098 5.047847 TGTCCACTTTTACAGAGAAACTCG 58.952 41.667 0.00 0.00 35.36 4.18
1875 2119 8.206325 ACTCGTTAGAATATCAGTTAGTCGAA 57.794 34.615 0.00 0.00 30.22 3.71
1910 2158 3.322211 TCCTAAAAGCATCGAACCGAA 57.678 42.857 0.00 0.00 39.99 4.30
1912 2160 2.095372 CCTAAAAGCATCGAACCGAACC 59.905 50.000 0.00 0.00 39.99 3.62
1914 2162 0.250553 AAAGCATCGAACCGAACCCA 60.251 50.000 0.00 0.00 39.99 4.51
1920 2168 4.000988 GCATCGAACCGAACCCATATAAT 58.999 43.478 0.00 0.00 39.99 1.28
1921 2169 4.142902 GCATCGAACCGAACCCATATAATG 60.143 45.833 0.00 0.00 39.99 1.90
1922 2170 3.395639 TCGAACCGAACCCATATAATGC 58.604 45.455 0.00 0.00 31.06 3.56
1923 2171 3.070446 TCGAACCGAACCCATATAATGCT 59.930 43.478 0.00 0.00 31.06 3.79
1924 2172 3.813166 CGAACCGAACCCATATAATGCTT 59.187 43.478 0.00 0.00 0.00 3.91
1925 2173 4.274950 CGAACCGAACCCATATAATGCTTT 59.725 41.667 0.00 0.00 0.00 3.51
1926 2174 5.467399 CGAACCGAACCCATATAATGCTTTA 59.533 40.000 0.00 0.00 0.00 1.85
1927 2175 6.347402 CGAACCGAACCCATATAATGCTTTAG 60.347 42.308 0.00 0.00 0.00 1.85
1930 2178 6.485648 ACCGAACCCATATAATGCTTTAGAAC 59.514 38.462 0.00 0.00 0.00 3.01
1931 2179 6.710744 CCGAACCCATATAATGCTTTAGAACT 59.289 38.462 0.00 0.00 0.00 3.01
1932 2180 7.307989 CCGAACCCATATAATGCTTTAGAACTG 60.308 40.741 0.00 0.00 0.00 3.16
1933 2181 7.226720 CGAACCCATATAATGCTTTAGAACTGT 59.773 37.037 0.00 0.00 0.00 3.55
1934 2182 9.555727 GAACCCATATAATGCTTTAGAACTGTA 57.444 33.333 0.00 0.00 0.00 2.74
1935 2183 9.914834 AACCCATATAATGCTTTAGAACTGTAA 57.085 29.630 0.00 0.00 0.00 2.41
1936 2184 9.914834 ACCCATATAATGCTTTAGAACTGTAAA 57.085 29.630 0.00 0.00 0.00 2.01
1972 2220 4.591498 TCTCTTCTAAACTGCACCTAACCA 59.409 41.667 0.00 0.00 0.00 3.67
1981 2229 3.279434 CTGCACCTAACCAATCCCTTAC 58.721 50.000 0.00 0.00 0.00 2.34
2025 2273 4.935808 CCCTATTCTGCGAAACTGTAAACT 59.064 41.667 0.00 0.00 0.00 2.66
2026 2274 5.163854 CCCTATTCTGCGAAACTGTAAACTG 60.164 44.000 0.00 0.00 0.00 3.16
2027 2275 5.408604 CCTATTCTGCGAAACTGTAAACTGT 59.591 40.000 0.00 0.00 0.00 3.55
2033 2281 6.259167 TCTGCGAAACTGTAAACTGTGTTTAT 59.741 34.615 6.24 0.00 33.49 1.40
2047 2295 1.132834 TGTTTATAGTTCGCGCGAGGA 59.867 47.619 32.74 21.42 0.00 3.71
2068 2316 6.885922 AGGACGTCTATACAGGCTTAAAATT 58.114 36.000 16.46 0.00 0.00 1.82
2146 2397 4.331443 TGCGCGAGAAATTTAAGCAATAGA 59.669 37.500 12.10 0.00 0.00 1.98
2149 2400 6.649436 CGCGAGAAATTTAAGCAATAGATCA 58.351 36.000 0.00 0.00 0.00 2.92
2200 2462 0.598158 GGCAGGTCGTTCGTACACAA 60.598 55.000 0.00 0.00 0.00 3.33
2247 2511 2.044650 AGCTACGCCGGACCTACA 60.045 61.111 5.05 0.00 0.00 2.74
2353 3194 4.450082 TCGAGGTCGATGAAGAAATTCA 57.550 40.909 0.00 0.00 44.22 2.57
2373 3214 1.372087 CCTGCTCCGCCTTCATGAAC 61.372 60.000 3.38 0.00 0.00 3.18
2507 4693 3.195698 GTTCCAGGATGACGCGCC 61.196 66.667 5.73 0.00 39.69 6.53
2529 4717 2.042843 GAGCTCCTCCTTCCCCGA 60.043 66.667 0.87 0.00 0.00 5.14
2636 4832 0.967887 CTCCGGCTCTCTCTTCACCA 60.968 60.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 211 0.391130 TTTCCATCACTTCGGGAGCG 60.391 55.000 0.00 0.00 31.19 5.03
338 346 9.405587 CGTTTCCAAATAGCTAGAAAATTTTCA 57.594 29.630 28.00 15.37 39.61 2.69
339 347 8.860128 CCGTTTCCAAATAGCTAGAAAATTTTC 58.140 33.333 21.00 21.00 37.45 2.29
343 351 5.652452 AGCCGTTTCCAAATAGCTAGAAAAT 59.348 36.000 7.29 0.00 30.55 1.82
525 535 1.003118 ACGCCTTTGGTTAGCATCTCA 59.997 47.619 0.00 0.00 0.00 3.27
636 656 7.854557 ACAAAAGTAAACGAAAGGAGTACTT 57.145 32.000 0.00 0.00 42.52 2.24
637 657 8.947055 TTACAAAAGTAAACGAAAGGAGTACT 57.053 30.769 0.00 0.00 0.00 2.73
638 658 9.034544 TCTTACAAAAGTAAACGAAAGGAGTAC 57.965 33.333 0.00 0.00 34.13 2.73
639 659 9.034544 GTCTTACAAAAGTAAACGAAAGGAGTA 57.965 33.333 0.00 0.00 34.13 2.59
640 660 7.254218 CGTCTTACAAAAGTAAACGAAAGGAGT 60.254 37.037 12.95 0.00 34.13 3.85
641 661 7.061634 CGTCTTACAAAAGTAAACGAAAGGAG 58.938 38.462 12.95 0.00 34.13 3.69
642 662 6.534793 ACGTCTTACAAAAGTAAACGAAAGGA 59.465 34.615 19.49 1.14 34.13 3.36
643 663 6.708676 ACGTCTTACAAAAGTAAACGAAAGG 58.291 36.000 19.49 0.00 34.13 3.11
644 664 8.591698 AAACGTCTTACAAAAGTAAACGAAAG 57.408 30.769 19.49 0.96 34.13 2.62
645 665 8.947304 AAAACGTCTTACAAAAGTAAACGAAA 57.053 26.923 19.49 0.00 34.13 3.46
713 733 9.477484 CGCTTAATACTAGGTGATGTCTTAAAT 57.523 33.333 0.00 0.00 0.00 1.40
714 734 8.689061 TCGCTTAATACTAGGTGATGTCTTAAA 58.311 33.333 0.00 0.00 0.00 1.52
715 735 8.133627 GTCGCTTAATACTAGGTGATGTCTTAA 58.866 37.037 0.00 0.00 0.00 1.85
716 736 7.501559 AGTCGCTTAATACTAGGTGATGTCTTA 59.498 37.037 0.00 0.00 0.00 2.10
717 737 6.321690 AGTCGCTTAATACTAGGTGATGTCTT 59.678 38.462 0.00 0.00 0.00 3.01
718 738 5.828859 AGTCGCTTAATACTAGGTGATGTCT 59.171 40.000 0.00 0.00 0.00 3.41
719 739 6.074544 AGTCGCTTAATACTAGGTGATGTC 57.925 41.667 0.00 0.00 0.00 3.06
720 740 6.466885 AAGTCGCTTAATACTAGGTGATGT 57.533 37.500 0.00 0.00 0.00 3.06
721 741 7.423199 TGTAAGTCGCTTAATACTAGGTGATG 58.577 38.462 0.00 0.00 0.00 3.07
722 742 7.578310 TGTAAGTCGCTTAATACTAGGTGAT 57.422 36.000 0.00 0.00 0.00 3.06
723 743 7.395190 TTGTAAGTCGCTTAATACTAGGTGA 57.605 36.000 0.00 0.00 0.00 4.02
724 744 8.470040 TTTTGTAAGTCGCTTAATACTAGGTG 57.530 34.615 0.00 0.00 0.00 4.00
725 745 8.309656 ACTTTTGTAAGTCGCTTAATACTAGGT 58.690 33.333 0.00 0.00 40.60 3.08
726 746 8.592998 CACTTTTGTAAGTCGCTTAATACTAGG 58.407 37.037 0.00 0.00 42.67 3.02
727 747 8.592998 CCACTTTTGTAAGTCGCTTAATACTAG 58.407 37.037 1.67 0.00 42.67 2.57
728 748 8.306038 TCCACTTTTGTAAGTCGCTTAATACTA 58.694 33.333 1.67 0.00 42.67 1.82
729 749 7.117379 GTCCACTTTTGTAAGTCGCTTAATACT 59.883 37.037 1.67 0.00 42.67 2.12
730 750 7.095523 TGTCCACTTTTGTAAGTCGCTTAATAC 60.096 37.037 1.67 0.00 42.67 1.89
731 751 6.930164 TGTCCACTTTTGTAAGTCGCTTAATA 59.070 34.615 1.67 0.00 42.67 0.98
732 752 5.761234 TGTCCACTTTTGTAAGTCGCTTAAT 59.239 36.000 1.67 0.00 42.67 1.40
733 753 5.117584 TGTCCACTTTTGTAAGTCGCTTAA 58.882 37.500 1.67 0.00 42.67 1.85
734 754 4.695396 TGTCCACTTTTGTAAGTCGCTTA 58.305 39.130 0.00 0.00 42.67 3.09
735 755 3.537580 TGTCCACTTTTGTAAGTCGCTT 58.462 40.909 0.00 0.00 42.67 4.68
736 756 3.131396 CTGTCCACTTTTGTAAGTCGCT 58.869 45.455 0.00 0.00 42.67 4.93
737 757 3.128349 TCTGTCCACTTTTGTAAGTCGC 58.872 45.455 0.00 0.00 42.67 5.19
738 758 3.741344 CCTCTGTCCACTTTTGTAAGTCG 59.259 47.826 0.00 0.00 42.67 4.18
739 759 4.065789 CCCTCTGTCCACTTTTGTAAGTC 58.934 47.826 0.00 0.00 42.67 3.01
740 760 3.714798 TCCCTCTGTCCACTTTTGTAAGT 59.285 43.478 0.00 0.00 45.40 2.24
741 761 4.202367 ACTCCCTCTGTCCACTTTTGTAAG 60.202 45.833 0.00 0.00 37.40 2.34
742 762 3.714798 ACTCCCTCTGTCCACTTTTGTAA 59.285 43.478 0.00 0.00 0.00 2.41
743 763 3.314693 ACTCCCTCTGTCCACTTTTGTA 58.685 45.455 0.00 0.00 0.00 2.41
744 764 2.127708 ACTCCCTCTGTCCACTTTTGT 58.872 47.619 0.00 0.00 0.00 2.83
745 765 2.938956 ACTCCCTCTGTCCACTTTTG 57.061 50.000 0.00 0.00 0.00 2.44
746 766 3.858135 TCTACTCCCTCTGTCCACTTTT 58.142 45.455 0.00 0.00 0.00 2.27
747 767 3.544698 TCTACTCCCTCTGTCCACTTT 57.455 47.619 0.00 0.00 0.00 2.66
748 768 3.076182 TCTTCTACTCCCTCTGTCCACTT 59.924 47.826 0.00 0.00 0.00 3.16
749 769 2.650322 TCTTCTACTCCCTCTGTCCACT 59.350 50.000 0.00 0.00 0.00 4.00
750 770 3.088789 TCTTCTACTCCCTCTGTCCAC 57.911 52.381 0.00 0.00 0.00 4.02
751 771 3.827817 TTCTTCTACTCCCTCTGTCCA 57.172 47.619 0.00 0.00 0.00 4.02
752 772 4.959839 AGATTTCTTCTACTCCCTCTGTCC 59.040 45.833 0.00 0.00 30.96 4.02
753 773 5.654650 TGAGATTTCTTCTACTCCCTCTGTC 59.345 44.000 0.00 0.00 33.74 3.51
754 774 5.584913 TGAGATTTCTTCTACTCCCTCTGT 58.415 41.667 0.00 0.00 33.74 3.41
755 775 6.729690 ATGAGATTTCTTCTACTCCCTCTG 57.270 41.667 0.00 0.00 33.74 3.35
756 776 6.780522 GGTATGAGATTTCTTCTACTCCCTCT 59.219 42.308 0.00 0.00 33.74 3.69
757 777 6.551601 TGGTATGAGATTTCTTCTACTCCCTC 59.448 42.308 0.00 0.00 33.74 4.30
758 778 6.444704 TGGTATGAGATTTCTTCTACTCCCT 58.555 40.000 0.00 0.00 33.74 4.20
759 779 6.732896 TGGTATGAGATTTCTTCTACTCCC 57.267 41.667 0.00 0.00 33.74 4.30
760 780 8.646900 AGAATGGTATGAGATTTCTTCTACTCC 58.353 37.037 0.00 0.00 33.74 3.85
761 781 9.691362 GAGAATGGTATGAGATTTCTTCTACTC 57.309 37.037 0.00 0.00 33.74 2.59
762 782 8.356657 CGAGAATGGTATGAGATTTCTTCTACT 58.643 37.037 0.00 0.00 33.74 2.57
763 783 8.138712 ACGAGAATGGTATGAGATTTCTTCTAC 58.861 37.037 0.00 0.00 33.74 2.59
910 1087 5.499139 AAAACAGACATCTCTCGCAAAAA 57.501 34.783 0.00 0.00 0.00 1.94
911 1088 6.260050 ACTTAAAACAGACATCTCTCGCAAAA 59.740 34.615 0.00 0.00 0.00 2.44
912 1089 5.758296 ACTTAAAACAGACATCTCTCGCAAA 59.242 36.000 0.00 0.00 0.00 3.68
1009 1190 7.973388 CCAACTGATTCTATATAGAGTAGCAGC 59.027 40.741 21.53 8.88 33.21 5.25
1568 1803 3.553922 GCAATCTCTGGCGTTAGCTCTAT 60.554 47.826 0.00 0.00 44.37 1.98
1579 1814 0.029035 CATCTTGCGCAATCTCTGGC 59.971 55.000 25.26 0.00 0.00 4.85
1581 1816 3.528594 GCATCTTGCGCAATCTCTG 57.471 52.632 25.26 18.09 31.71 3.35
1609 1844 3.245315 AACGCGCGCATAGACGAC 61.245 61.111 32.58 0.00 34.06 4.34
1615 1850 2.521771 GGACATCAACGCGCGCATA 61.522 57.895 32.58 15.93 0.00 3.14
1670 1905 5.711506 TGCATGAATTCCACAAACTCTGTAT 59.288 36.000 2.27 0.00 36.10 2.29
1676 1916 4.081862 CCTGATGCATGAATTCCACAAACT 60.082 41.667 2.46 0.00 0.00 2.66
1830 2074 5.175856 CGAGTTTCTCTGTAAAAGTGGACAG 59.824 44.000 0.00 0.00 43.70 3.51
1854 2098 7.427214 AGGCTTCGACTAACTGATATTCTAAC 58.573 38.462 0.00 0.00 0.00 2.34
1875 2119 5.787380 CTTTTAGGAATCAAAAGCAAGGCT 58.213 37.500 0.00 0.00 42.56 4.58
1895 2139 0.250553 TGGGTTCGGTTCGATGCTTT 60.251 50.000 0.00 0.00 35.23 3.51
1899 2143 4.142902 GCATTATATGGGTTCGGTTCGATG 60.143 45.833 0.00 0.00 35.23 3.84
1900 2144 4.000988 GCATTATATGGGTTCGGTTCGAT 58.999 43.478 0.00 0.00 35.23 3.59
1903 2151 5.767816 AAAGCATTATATGGGTTCGGTTC 57.232 39.130 0.00 0.00 0.00 3.62
1910 2158 9.914834 TTTACAGTTCTAAAGCATTATATGGGT 57.085 29.630 0.00 0.00 0.00 4.51
1938 2186 9.651913 TGCAGTTTAGAAGAGAAAAACATTTTT 57.348 25.926 2.00 2.00 42.60 1.94
1939 2187 9.087424 GTGCAGTTTAGAAGAGAAAAACATTTT 57.913 29.630 0.00 0.00 35.93 1.82
1940 2188 7.706607 GGTGCAGTTTAGAAGAGAAAAACATTT 59.293 33.333 0.00 0.00 35.93 2.32
1941 2189 7.068716 AGGTGCAGTTTAGAAGAGAAAAACATT 59.931 33.333 0.00 0.00 35.93 2.71
1942 2190 6.547510 AGGTGCAGTTTAGAAGAGAAAAACAT 59.452 34.615 0.00 0.00 35.93 2.71
1943 2191 5.885912 AGGTGCAGTTTAGAAGAGAAAAACA 59.114 36.000 0.00 0.00 35.93 2.83
1944 2192 6.378710 AGGTGCAGTTTAGAAGAGAAAAAC 57.621 37.500 0.00 0.00 34.13 2.43
1945 2193 7.012989 GGTTAGGTGCAGTTTAGAAGAGAAAAA 59.987 37.037 0.00 0.00 0.00 1.94
1952 2200 5.123979 GGATTGGTTAGGTGCAGTTTAGAAG 59.876 44.000 0.00 0.00 0.00 2.85
1953 2201 5.007682 GGATTGGTTAGGTGCAGTTTAGAA 58.992 41.667 0.00 0.00 0.00 2.10
1961 2209 2.645297 TGTAAGGGATTGGTTAGGTGCA 59.355 45.455 0.00 0.00 0.00 4.57
1972 2220 5.221621 GCTAGAGATGCTCTTGTAAGGGATT 60.222 44.000 1.88 0.00 41.50 3.01
1981 2229 2.224018 GGGTCTGCTAGAGATGCTCTTG 60.224 54.545 1.88 2.09 41.50 3.02
2025 2273 1.915350 CTCGCGCGAACTATAAACACA 59.085 47.619 33.99 6.37 0.00 3.72
2026 2274 1.254570 CCTCGCGCGAACTATAAACAC 59.745 52.381 33.99 0.00 0.00 3.32
2027 2275 1.132834 TCCTCGCGCGAACTATAAACA 59.867 47.619 33.99 7.18 0.00 2.83
2033 2281 3.372676 GACGTCCTCGCGCGAACTA 62.373 63.158 33.99 18.60 41.18 2.24
2047 2295 6.359480 GCAATTTTAAGCCTGTATAGACGT 57.641 37.500 0.00 0.00 0.00 4.34
2113 2361 2.483583 TTCTCGCGCAAAACATGTTT 57.516 40.000 18.13 18.13 0.00 2.83
2123 2374 2.979401 TTGCTTAAATTTCTCGCGCA 57.021 40.000 8.75 0.00 0.00 6.09
2146 2397 1.621992 ACGATCTATGCTCCGGTGAT 58.378 50.000 7.92 0.99 0.00 3.06
2149 2400 1.693627 AGAACGATCTATGCTCCGGT 58.306 50.000 0.00 0.00 32.88 5.28
2247 2511 4.682778 TTTTGTCTAGTGCTGTGGTAGT 57.317 40.909 0.00 0.00 0.00 2.73
2318 3159 1.078356 CTCGACTCCTCCGACTCCA 60.078 63.158 0.00 0.00 32.18 3.86


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

AutoCloner maintained by Alex Coulton.