Multiple sequence alignment - TraesCS4A01G262000

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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 TraesCS4A01G262000 chr4A 100.000 3011 0 0 1 3011 574381652 574384662 0.000000e+00 5561.0
1 TraesCS4A01G262000 chr4A 89.602 327 27 6 264 590 601013458 601013139 2.790000e-110 409.0
2 TraesCS4A01G262000 chr4D 96.198 1762 53 7 740 2497 29179642 29177891 0.000000e+00 2870.0
3 TraesCS4A01G262000 chr4D 82.883 555 38 34 2506 3011 29177840 29177294 2.130000e-121 446.0
4 TraesCS4A01G262000 chr4B 93.333 1530 63 7 716 2222 41746543 41745030 0.000000e+00 2224.0
5 TraesCS4A01G262000 chr4B 90.064 312 21 6 2690 2993 41744593 41744284 2.180000e-106 396.0
6 TraesCS4A01G262000 chr4B 94.805 77 4 0 2285 2361 41745030 41744954 1.470000e-23 121.0
7 TraesCS4A01G262000 chr4B 100.000 31 0 0 675 705 41746568 41746538 1.170000e-04 58.4
8 TraesCS4A01G262000 chr2A 97.494 399 10 0 190 588 589658509 589658111 0.000000e+00 682.0
9 TraesCS4A01G262000 chr2A 98.438 192 3 0 1 192 589659590 589659399 3.720000e-89 339.0
10 TraesCS4A01G262000 chr5A 93.846 390 15 4 190 579 433548022 433548402 2.010000e-161 579.0
11 TraesCS4A01G262000 chr5A 93.750 192 12 0 1 192 433543777 433543968 3.800000e-74 289.0
12 TraesCS4A01G262000 chr3A 93.233 399 18 1 190 588 741742222 741741833 2.010000e-161 579.0
13 TraesCS4A01G262000 chr3A 94.792 192 10 0 1 192 741743327 741743136 1.750000e-77 300.0
14 TraesCS4A01G262000 chr6A 92.481 399 10 4 190 588 60000856 60000478 1.220000e-153 553.0
15 TraesCS4A01G262000 chr6A 96.503 143 4 1 50 192 60002140 60001999 5.020000e-58 235.0
16 TraesCS4A01G262000 chr7B 90.511 274 20 3 321 589 104302772 104302500 1.030000e-94 357.0
17 TraesCS4A01G262000 chr5D 89.655 174 12 3 264 437 482600993 482600826 1.820000e-52 217.0
18 TraesCS4A01G262000 chr5D 94.215 121 6 1 469 589 482600829 482600710 1.840000e-42 183.0
19 TraesCS4A01G262000 chr1D 90.476 105 9 1 473 576 198524080 198523976 1.460000e-28 137.0


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 TraesCS4A01G262000 chr4A 574381652 574384662 3010 False 5561.00 5561 100.0000 1 3011 1 chr4A.!!$F1 3010
1 TraesCS4A01G262000 chr4D 29177294 29179642 2348 True 1658.00 2870 89.5405 740 3011 2 chr4D.!!$R1 2271
2 TraesCS4A01G262000 chr4B 41744284 41746568 2284 True 699.85 2224 94.5505 675 2993 4 chr4B.!!$R1 2318
3 TraesCS4A01G262000 chr2A 589658111 589659590 1479 True 510.50 682 97.9660 1 588 2 chr2A.!!$R1 587
4 TraesCS4A01G262000 chr3A 741741833 741743327 1494 True 439.50 579 94.0125 1 588 2 chr3A.!!$R1 587
5 TraesCS4A01G262000 chr6A 60000478 60002140 1662 True 394.00 553 94.4920 50 588 2 chr6A.!!$R1 538

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
709 1900 0.034337 TCCAAAGGAGTTCCCGTTCG 59.966 55.0 0.0 0.0 40.87 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 3477 0.251832 TCCCTCTCCCAGATATCCGC 60.252 60.0 0.0 0.0 0.0 5.54 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
27 28 2.289820 GGGTTCGGTTGAGTCAACTTTC 59.710 50.000 29.89 18.87 43.14 2.62
141 142 6.932356 TCTTAGCCATGATTTAGAAGCAAG 57.068 37.500 0.00 0.00 0.00 4.01
192 193 2.234913 ATTGTAGTCCGGGCCGTGTC 62.235 60.000 26.32 14.20 0.00 3.67
193 194 4.487412 GTAGTCCGGGCCGTGTCG 62.487 72.222 26.32 9.60 0.00 4.35
370 1543 4.018484 AGGAGTACTACTCACGAACAGT 57.982 45.455 16.49 0.00 46.79 3.55
389 1562 1.191489 TCCACCCAGATGTTCGCTGA 61.191 55.000 0.00 0.00 35.39 4.26
438 1629 0.974010 TATCCAGGCCGTCGTTTCCT 60.974 55.000 0.00 0.00 0.00 3.36
452 1643 2.246761 TTTCCTCATACGGCCCCACG 62.247 60.000 0.00 0.00 40.31 4.94
500 1691 1.166531 AACTCACCTGCGTTTCTGCC 61.167 55.000 0.00 0.00 0.00 4.85
545 1736 1.077501 CGCTGTCCCATTGGTCCAT 60.078 57.895 1.20 0.00 0.00 3.41
588 1779 1.040646 TCACCATATCGCCACTCTCC 58.959 55.000 0.00 0.00 0.00 3.71
589 1780 1.043816 CACCATATCGCCACTCTCCT 58.956 55.000 0.00 0.00 0.00 3.69
590 1781 1.414181 CACCATATCGCCACTCTCCTT 59.586 52.381 0.00 0.00 0.00 3.36
591 1782 2.628178 CACCATATCGCCACTCTCCTTA 59.372 50.000 0.00 0.00 0.00 2.69
592 1783 2.894126 ACCATATCGCCACTCTCCTTAG 59.106 50.000 0.00 0.00 0.00 2.18
593 1784 3.157881 CCATATCGCCACTCTCCTTAGA 58.842 50.000 0.00 0.00 0.00 2.10
594 1785 3.574396 CCATATCGCCACTCTCCTTAGAA 59.426 47.826 0.00 0.00 0.00 2.10
595 1786 4.039245 CCATATCGCCACTCTCCTTAGAAA 59.961 45.833 0.00 0.00 0.00 2.52
596 1787 5.279708 CCATATCGCCACTCTCCTTAGAAAT 60.280 44.000 0.00 0.00 0.00 2.17
597 1788 3.526931 TCGCCACTCTCCTTAGAAATG 57.473 47.619 0.00 0.00 0.00 2.32
598 1789 1.936547 CGCCACTCTCCTTAGAAATGC 59.063 52.381 0.00 0.00 0.00 3.56
599 1790 1.936547 GCCACTCTCCTTAGAAATGCG 59.063 52.381 0.00 0.00 0.00 4.73
600 1791 1.936547 CCACTCTCCTTAGAAATGCGC 59.063 52.381 0.00 0.00 0.00 6.09
601 1792 2.621338 CACTCTCCTTAGAAATGCGCA 58.379 47.619 14.96 14.96 0.00 6.09
602 1793 3.002791 CACTCTCCTTAGAAATGCGCAA 58.997 45.455 17.11 0.00 0.00 4.85
603 1794 3.003480 ACTCTCCTTAGAAATGCGCAAC 58.997 45.455 17.11 9.50 0.00 4.17
604 1795 3.002791 CTCTCCTTAGAAATGCGCAACA 58.997 45.455 17.11 0.00 0.00 3.33
605 1796 3.407698 TCTCCTTAGAAATGCGCAACAA 58.592 40.909 17.11 3.16 0.00 2.83
606 1797 3.818210 TCTCCTTAGAAATGCGCAACAAA 59.182 39.130 17.11 3.94 0.00 2.83
607 1798 4.277174 TCTCCTTAGAAATGCGCAACAAAA 59.723 37.500 17.11 4.73 0.00 2.44
608 1799 4.938080 TCCTTAGAAATGCGCAACAAAAA 58.062 34.783 17.11 5.91 0.00 1.94
609 1800 4.981674 TCCTTAGAAATGCGCAACAAAAAG 59.018 37.500 17.11 15.43 0.00 2.27
610 1801 4.744631 CCTTAGAAATGCGCAACAAAAAGT 59.255 37.500 17.11 0.00 0.00 2.66
611 1802 5.332506 CCTTAGAAATGCGCAACAAAAAGTG 60.333 40.000 17.11 6.70 0.00 3.16
612 1803 3.520569 AGAAATGCGCAACAAAAAGTGT 58.479 36.364 17.11 0.00 44.64 3.55
613 1804 4.677584 AGAAATGCGCAACAAAAAGTGTA 58.322 34.783 17.11 0.00 40.60 2.90
614 1805 4.739716 AGAAATGCGCAACAAAAAGTGTAG 59.260 37.500 17.11 0.00 40.60 2.74
615 1806 3.708563 ATGCGCAACAAAAAGTGTAGT 57.291 38.095 17.11 0.00 40.60 2.73
616 1807 4.822036 ATGCGCAACAAAAAGTGTAGTA 57.178 36.364 17.11 0.00 40.60 1.82
617 1808 4.617808 TGCGCAACAAAAAGTGTAGTAA 57.382 36.364 8.16 0.00 40.60 2.24
618 1809 5.176407 TGCGCAACAAAAAGTGTAGTAAT 57.824 34.783 8.16 0.00 40.60 1.89
619 1810 4.973051 TGCGCAACAAAAAGTGTAGTAATG 59.027 37.500 8.16 0.00 40.60 1.90
620 1811 4.143618 GCGCAACAAAAAGTGTAGTAATGC 60.144 41.667 0.30 0.00 40.60 3.56
621 1812 4.381566 CGCAACAAAAAGTGTAGTAATGCC 59.618 41.667 0.00 0.00 40.60 4.40
622 1813 4.684242 GCAACAAAAAGTGTAGTAATGCCC 59.316 41.667 0.00 0.00 40.60 5.36
623 1814 5.227152 CAACAAAAAGTGTAGTAATGCCCC 58.773 41.667 0.00 0.00 40.60 5.80
624 1815 3.830178 ACAAAAAGTGTAGTAATGCCCCC 59.170 43.478 0.00 0.00 39.29 5.40
673 1864 8.816640 TCTTTTTCTAAAGAATGTGCATTTCC 57.183 30.769 8.30 0.00 45.08 3.13
705 1896 1.751437 GGATTCCAAAGGAGTTCCCG 58.249 55.000 0.00 0.00 40.87 5.14
706 1897 1.004394 GGATTCCAAAGGAGTTCCCGT 59.996 52.381 0.00 0.00 40.87 5.28
707 1898 2.554564 GGATTCCAAAGGAGTTCCCGTT 60.555 50.000 0.00 0.00 40.87 4.44
708 1899 2.265589 TTCCAAAGGAGTTCCCGTTC 57.734 50.000 0.00 0.00 40.87 3.95
709 1900 0.034337 TCCAAAGGAGTTCCCGTTCG 59.966 55.000 0.00 0.00 40.87 3.95
710 1901 0.250166 CCAAAGGAGTTCCCGTTCGT 60.250 55.000 0.00 0.00 40.87 3.85
711 1902 0.865769 CAAAGGAGTTCCCGTTCGTG 59.134 55.000 0.00 0.00 40.87 4.35
712 1903 0.466963 AAAGGAGTTCCCGTTCGTGT 59.533 50.000 0.00 0.00 40.87 4.49
713 1904 1.331214 AAGGAGTTCCCGTTCGTGTA 58.669 50.000 0.00 0.00 40.87 2.90
714 1905 0.600057 AGGAGTTCCCGTTCGTGTAC 59.400 55.000 0.00 0.00 40.87 2.90
715 1906 0.730494 GGAGTTCCCGTTCGTGTACG 60.730 60.000 0.00 0.00 41.06 3.67
716 1907 0.040067 GAGTTCCCGTTCGTGTACGT 60.040 55.000 4.20 0.00 39.81 3.57
717 1908 0.385390 AGTTCCCGTTCGTGTACGTT 59.615 50.000 0.00 0.00 39.81 3.99
718 1909 0.778223 GTTCCCGTTCGTGTACGTTC 59.222 55.000 0.00 0.00 39.81 3.95
719 1910 0.318614 TTCCCGTTCGTGTACGTTCC 60.319 55.000 0.00 0.00 39.81 3.62
720 1911 1.734117 CCCGTTCGTGTACGTTCCC 60.734 63.158 0.00 0.00 39.81 3.97
888 2096 0.105964 CTCCTCCTCCTCCGATCCAA 60.106 60.000 0.00 0.00 0.00 3.53
921 2129 2.193248 GCCCTTCCCTTCCATCGG 59.807 66.667 0.00 0.00 0.00 4.18
981 2190 0.263172 TCCTCCTCATCCTCCTGTCC 59.737 60.000 0.00 0.00 0.00 4.02
985 2194 1.142748 CTCATCCTCCTGTCCGCAC 59.857 63.158 0.00 0.00 0.00 5.34
986 2195 2.187946 CATCCTCCTGTCCGCACC 59.812 66.667 0.00 0.00 0.00 5.01
1398 2613 2.049063 GCCGAGACAGTGACGCTT 60.049 61.111 0.00 0.00 0.00 4.68
1408 2623 0.396435 AGTGACGCTTCCCAACATGA 59.604 50.000 0.00 0.00 0.00 3.07
1409 2624 1.202758 AGTGACGCTTCCCAACATGAA 60.203 47.619 0.00 0.00 0.00 2.57
1585 2800 1.261238 GGTGCTGGAGCTCTACCACT 61.261 60.000 20.81 0.00 42.66 4.00
1856 3071 0.268869 TACCTGAGGGCCATGGAGAT 59.731 55.000 18.40 0.00 35.63 2.75
2056 3271 0.518636 GCAGCAAGCAAGTCGATTCA 59.481 50.000 0.00 0.00 44.79 2.57
2070 3285 3.743396 GTCGATTCATTACTGATCAGGGC 59.257 47.826 26.08 3.28 0.00 5.19
2101 3316 1.669440 CATTGCAGGCAAGGCTGTT 59.331 52.632 22.29 7.57 39.47 3.16
2102 3317 0.669318 CATTGCAGGCAAGGCTGTTG 60.669 55.000 22.29 14.51 39.47 3.33
2103 3318 0.828762 ATTGCAGGCAAGGCTGTTGA 60.829 50.000 22.29 10.75 39.47 3.18
2106 3321 1.530013 GCAGGCAAGGCTGTTGATGT 61.530 55.000 22.29 0.00 0.00 3.06
2115 3330 3.198068 AGGCTGTTGATGTTGTATAGCG 58.802 45.455 0.00 0.00 0.00 4.26
2133 3348 9.320406 TGTATAGCGTTTTTGTAATCTTTTTCG 57.680 29.630 0.00 0.00 0.00 3.46
2225 3440 0.952984 GCAGAGAAGTCACTGGCACC 60.953 60.000 7.69 0.00 35.53 5.01
2238 3453 0.105760 TGGCACCTGTGGATTTTGGT 60.106 50.000 0.00 0.00 0.00 3.67
2268 3483 4.881273 ACTGCAGAATAATGTTTGCGGATA 59.119 37.500 23.35 0.00 43.81 2.59
2320 3535 0.944386 AACATTCGTTCGTGCAAGCT 59.056 45.000 0.00 0.00 0.00 3.74
2401 3616 2.263077 GATCTCTTCGACAACACGCAT 58.737 47.619 0.00 0.00 0.00 4.73
2404 3619 1.792367 CTCTTCGACAACACGCATTCA 59.208 47.619 0.00 0.00 0.00 2.57
2447 3662 6.410540 ACAGAGTAATCAGATTCAGGAAACC 58.589 40.000 0.00 0.00 0.00 3.27
2453 3668 2.441375 TCAGATTCAGGAAACCACACCA 59.559 45.455 0.00 0.00 0.00 4.17
2456 3671 0.923358 TTCAGGAAACCACACCACCT 59.077 50.000 0.00 0.00 0.00 4.00
2503 3718 7.898918 TGATCAAACCAAACTGAATCATCAAT 58.101 30.769 0.00 0.00 34.49 2.57
2535 3799 2.551459 CAAGCAAGCAAGCTCAGTAACT 59.449 45.455 3.26 0.00 45.89 2.24
2727 4103 5.523188 GCGAGATGATCATTTCTTTCAGACT 59.477 40.000 20.48 5.49 0.00 3.24
2785 4161 7.491372 CACAGGGAATTCATTCAATCATTCAAG 59.509 37.037 7.93 0.00 38.53 3.02
2791 4167 5.725325 TCATTCAATCATTCAAGCAACCA 57.275 34.783 0.00 0.00 0.00 3.67
2811 4187 9.213799 GCAACCAAACCATATCAATCTTAAAAA 57.786 29.630 0.00 0.00 0.00 1.94
2877 4258 6.507568 AGGAGTATATATTCCTCCCCTCTTG 58.492 44.000 18.62 0.00 44.85 3.02
2965 4349 3.347216 CCATTTCAGACTCCCGAAACAT 58.653 45.455 0.00 0.00 34.16 2.71
2967 4351 3.762407 TTTCAGACTCCCGAAACATCA 57.238 42.857 0.00 0.00 0.00 3.07
2981 4365 3.799281 AACATCACAACCCACAACTTG 57.201 42.857 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.135141 CCGGACAGAAGAGAGAAGCAG 60.135 57.143 0.00 0.00 0.00 4.24
141 142 7.945134 ACCATACTTCCAAAGATATGCAAATC 58.055 34.615 0.00 0.00 0.00 2.17
192 193 7.468922 TGCTCAACACATAGAAAGATATTCG 57.531 36.000 0.00 0.00 0.00 3.34
193 194 9.661187 CAATGCTCAACACATAGAAAGATATTC 57.339 33.333 0.00 0.00 0.00 1.75
370 1543 1.191489 TCAGCGAACATCTGGGTGGA 61.191 55.000 0.00 0.00 32.58 4.02
420 1611 2.240162 GAGGAAACGACGGCCTGGAT 62.240 60.000 10.34 0.00 30.70 3.41
452 1643 0.865639 GAAAACGCATGCATACGGGC 60.866 55.000 22.58 10.26 0.00 6.13
545 1736 1.219124 CTCGCCTGCTCCTGCTTTA 59.781 57.895 0.00 0.00 40.48 1.85
588 1779 5.231991 ACACTTTTTGTTGCGCATTTCTAAG 59.768 36.000 12.75 14.90 33.09 2.18
589 1780 5.105752 ACACTTTTTGTTGCGCATTTCTAA 58.894 33.333 12.75 5.75 33.09 2.10
590 1781 4.677584 ACACTTTTTGTTGCGCATTTCTA 58.322 34.783 12.75 0.00 33.09 2.10
591 1782 3.520569 ACACTTTTTGTTGCGCATTTCT 58.479 36.364 12.75 0.00 33.09 2.52
592 1783 3.923827 ACACTTTTTGTTGCGCATTTC 57.076 38.095 12.75 5.82 33.09 2.17
593 1784 4.429108 ACTACACTTTTTGTTGCGCATTT 58.571 34.783 12.75 0.00 39.91 2.32
594 1785 4.040445 ACTACACTTTTTGTTGCGCATT 57.960 36.364 12.75 0.00 39.91 3.56
595 1786 3.708563 ACTACACTTTTTGTTGCGCAT 57.291 38.095 12.75 0.00 39.91 4.73
596 1787 4.617808 TTACTACACTTTTTGTTGCGCA 57.382 36.364 5.66 5.66 39.91 6.09
597 1788 4.143618 GCATTACTACACTTTTTGTTGCGC 60.144 41.667 0.00 0.00 39.91 6.09
598 1789 4.381566 GGCATTACTACACTTTTTGTTGCG 59.618 41.667 0.00 0.00 37.69 4.85
599 1790 4.684242 GGGCATTACTACACTTTTTGTTGC 59.316 41.667 0.00 0.00 39.91 4.17
600 1791 5.227152 GGGGCATTACTACACTTTTTGTTG 58.773 41.667 0.00 0.00 39.91 3.33
601 1792 4.282449 GGGGGCATTACTACACTTTTTGTT 59.718 41.667 0.00 0.00 39.91 2.83
602 1793 3.830178 GGGGGCATTACTACACTTTTTGT 59.170 43.478 0.00 0.00 42.84 2.83
603 1794 4.450082 GGGGGCATTACTACACTTTTTG 57.550 45.455 0.00 0.00 0.00 2.44
649 1840 8.822652 AGGAAATGCACATTCTTTAGAAAAAG 57.177 30.769 12.37 0.00 42.99 2.27
650 1841 9.912634 CTAGGAAATGCACATTCTTTAGAAAAA 57.087 29.630 12.37 0.00 37.61 1.94
651 1842 8.522830 CCTAGGAAATGCACATTCTTTAGAAAA 58.477 33.333 1.05 0.00 37.61 2.29
652 1843 7.669722 ACCTAGGAAATGCACATTCTTTAGAAA 59.330 33.333 17.98 0.00 37.61 2.52
653 1844 7.175104 ACCTAGGAAATGCACATTCTTTAGAA 58.825 34.615 17.98 0.00 38.56 2.10
654 1845 6.721318 ACCTAGGAAATGCACATTCTTTAGA 58.279 36.000 17.98 0.00 0.00 2.10
655 1846 7.253422 CAACCTAGGAAATGCACATTCTTTAG 58.747 38.462 17.98 12.92 0.00 1.85
656 1847 6.350110 GCAACCTAGGAAATGCACATTCTTTA 60.350 38.462 24.27 6.43 38.63 1.85
657 1848 5.567423 GCAACCTAGGAAATGCACATTCTTT 60.567 40.000 24.27 0.00 38.63 2.52
658 1849 4.082026 GCAACCTAGGAAATGCACATTCTT 60.082 41.667 24.27 8.48 38.63 2.52
659 1850 3.445096 GCAACCTAGGAAATGCACATTCT 59.555 43.478 24.27 0.96 38.63 2.40
660 1851 3.193267 TGCAACCTAGGAAATGCACATTC 59.807 43.478 26.51 5.67 43.32 2.67
661 1852 3.164268 TGCAACCTAGGAAATGCACATT 58.836 40.909 26.51 4.08 43.32 2.71
662 1853 2.806434 TGCAACCTAGGAAATGCACAT 58.194 42.857 26.51 0.00 43.32 3.21
663 1854 2.284754 TGCAACCTAGGAAATGCACA 57.715 45.000 26.51 13.15 43.32 4.57
665 1856 2.030363 CGTTTGCAACCTAGGAAATGCA 60.030 45.455 26.51 26.51 46.21 3.96
666 1857 2.595386 CGTTTGCAACCTAGGAAATGC 58.405 47.619 17.98 21.39 39.22 3.56
667 1858 2.817258 TCCGTTTGCAACCTAGGAAATG 59.183 45.455 17.98 12.33 36.12 2.32
668 1859 3.149005 TCCGTTTGCAACCTAGGAAAT 57.851 42.857 17.98 0.00 31.50 2.17
669 1860 2.642154 TCCGTTTGCAACCTAGGAAA 57.358 45.000 17.98 2.07 0.00 3.13
670 1861 2.871096 ATCCGTTTGCAACCTAGGAA 57.129 45.000 17.98 0.00 0.00 3.36
671 1862 2.617021 GGAATCCGTTTGCAACCTAGGA 60.617 50.000 17.98 6.23 0.00 2.94
672 1863 1.743394 GGAATCCGTTTGCAACCTAGG 59.257 52.381 7.41 7.41 0.00 3.02
673 1864 2.432444 TGGAATCCGTTTGCAACCTAG 58.568 47.619 0.00 0.00 32.09 3.02
705 1896 0.314935 TGGAGGGAACGTACACGAAC 59.685 55.000 9.04 1.99 43.02 3.95
706 1897 1.039068 TTGGAGGGAACGTACACGAA 58.961 50.000 9.04 0.00 36.47 3.85
707 1898 1.039068 TTTGGAGGGAACGTACACGA 58.961 50.000 9.04 0.00 36.47 4.35
708 1899 1.868469 TTTTGGAGGGAACGTACACG 58.132 50.000 0.00 0.00 36.47 4.49
709 1900 4.517832 AGAAATTTTGGAGGGAACGTACAC 59.482 41.667 0.00 0.00 36.47 2.90
710 1901 4.517453 CAGAAATTTTGGAGGGAACGTACA 59.483 41.667 0.00 0.00 34.01 2.90
711 1902 4.615223 GCAGAAATTTTGGAGGGAACGTAC 60.615 45.833 0.00 0.00 0.00 3.67
712 1903 3.504520 GCAGAAATTTTGGAGGGAACGTA 59.495 43.478 0.00 0.00 0.00 3.57
713 1904 2.296190 GCAGAAATTTTGGAGGGAACGT 59.704 45.455 0.00 0.00 0.00 3.99
714 1905 2.668279 CGCAGAAATTTTGGAGGGAACG 60.668 50.000 0.00 0.00 0.00 3.95
715 1906 2.296190 ACGCAGAAATTTTGGAGGGAAC 59.704 45.455 0.00 0.00 0.00 3.62
716 1907 2.593026 ACGCAGAAATTTTGGAGGGAA 58.407 42.857 0.00 0.00 0.00 3.97
717 1908 2.286365 ACGCAGAAATTTTGGAGGGA 57.714 45.000 0.00 0.00 0.00 4.20
718 1909 2.676076 CAACGCAGAAATTTTGGAGGG 58.324 47.619 0.00 0.00 0.00 4.30
719 1910 2.061028 GCAACGCAGAAATTTTGGAGG 58.939 47.619 0.00 0.00 0.00 4.30
720 1911 2.741612 TGCAACGCAGAAATTTTGGAG 58.258 42.857 0.00 0.00 33.32 3.86
921 2129 2.356673 GGGACGTGTGGTTCGGTC 60.357 66.667 0.00 0.00 0.00 4.79
1213 2428 4.475135 GAGGCCGGACTGGAAGGC 62.475 72.222 19.29 0.00 46.31 4.35
1398 2613 0.187117 TGGGCTTGTTCATGTTGGGA 59.813 50.000 0.00 0.00 0.00 4.37
1408 2623 1.599797 GGTACACGCTGGGCTTGTT 60.600 57.895 6.94 0.00 37.78 2.83
1409 2624 2.032071 GGTACACGCTGGGCTTGT 59.968 61.111 6.85 6.85 43.23 3.16
1585 2800 1.146930 GCATGAGCCCGATCTTGGA 59.853 57.895 0.00 0.00 33.58 3.53
1755 2970 2.901840 CAATGCCCCACGATCCGG 60.902 66.667 0.00 0.00 0.00 5.14
2050 3265 2.733552 CGCCCTGATCAGTAATGAATCG 59.266 50.000 21.11 8.41 0.00 3.34
2056 3271 4.689612 ATTACACGCCCTGATCAGTAAT 57.310 40.909 21.11 14.23 0.00 1.89
2070 3285 2.478370 CCTGCAATGCCTGAATTACACG 60.478 50.000 1.53 0.00 0.00 4.49
2101 3316 8.941977 AGATTACAAAAACGCTATACAACATCA 58.058 29.630 0.00 0.00 0.00 3.07
2102 3317 9.769093 AAGATTACAAAAACGCTATACAACATC 57.231 29.630 0.00 0.00 0.00 3.06
2209 3424 0.394565 ACAGGTGCCAGTGACTTCTC 59.605 55.000 0.00 0.00 0.00 2.87
2225 3440 3.068590 AGTTGCAGAACCAAAATCCACAG 59.931 43.478 0.00 0.00 31.81 3.66
2253 3468 5.013079 TCTCCCAGATATCCGCAAACATTAT 59.987 40.000 0.00 0.00 0.00 1.28
2262 3477 0.251832 TCCCTCTCCCAGATATCCGC 60.252 60.000 0.00 0.00 0.00 5.54
2268 3483 1.217689 CTCTCTGTCCCTCTCCCAGAT 59.782 57.143 0.00 0.00 34.90 2.90
2401 3616 7.231519 TCTGTCTCTACTCTTGTCTGAAATGAA 59.768 37.037 0.00 0.00 0.00 2.57
2404 3619 6.719370 ACTCTGTCTCTACTCTTGTCTGAAAT 59.281 38.462 0.00 0.00 0.00 2.17
2447 3662 1.073763 TGAATTCCCAGAGGTGGTGTG 59.926 52.381 2.27 0.00 43.23 3.82
2453 3668 4.202441 CGAATGAATGAATTCCCAGAGGT 58.798 43.478 2.27 0.00 35.97 3.85
2456 3671 4.502105 TCCGAATGAATGAATTCCCAGA 57.498 40.909 2.27 0.00 35.97 3.86
2503 3718 2.969990 TGCTTGCTTGTTGCTTTTTGA 58.030 38.095 0.00 0.00 43.37 2.69
2562 3851 8.560355 ACAAAATGCTATTCATGTACTGTACA 57.440 30.769 21.68 21.68 43.80 2.90
2563 3852 8.883731 AGACAAAATGCTATTCATGTACTGTAC 58.116 33.333 10.98 10.98 35.13 2.90
2564 3853 8.882736 CAGACAAAATGCTATTCATGTACTGTA 58.117 33.333 0.00 0.00 35.13 2.74
2565 3854 7.627088 GCAGACAAAATGCTATTCATGTACTGT 60.627 37.037 0.00 0.00 40.59 3.55
2566 3855 6.690098 GCAGACAAAATGCTATTCATGTACTG 59.310 38.462 0.00 0.00 40.59 2.74
2567 3856 6.375174 TGCAGACAAAATGCTATTCATGTACT 59.625 34.615 0.00 0.00 44.17 2.73
2568 3857 6.554419 TGCAGACAAAATGCTATTCATGTAC 58.446 36.000 0.00 0.00 44.17 2.90
2758 4134 6.438108 TGAATGATTGAATGAATTCCCTGTGT 59.562 34.615 2.27 0.00 35.97 3.72
2785 4161 8.770438 TTTTAAGATTGATATGGTTTGGTTGC 57.230 30.769 0.00 0.00 0.00 4.17
2811 4187 2.094182 ACATATGTTGCTCGGTCGTCTT 60.094 45.455 1.41 0.00 0.00 3.01
2812 4188 1.476891 ACATATGTTGCTCGGTCGTCT 59.523 47.619 1.41 0.00 0.00 4.18
2816 4192 1.004927 GCGAACATATGTTGCTCGGTC 60.005 52.381 25.42 8.46 42.73 4.79
2819 4195 4.652175 ATATGCGAACATATGTTGCTCG 57.348 40.909 25.42 21.98 45.74 5.03
2877 4258 5.096954 TGAATGAGTCGATCGATCAGTAC 57.903 43.478 22.50 17.73 0.00 2.73
2939 4320 1.396653 GGGAGTCTGAAATGGCATGG 58.603 55.000 0.00 0.00 0.00 3.66
2941 4322 0.911769 TCGGGAGTCTGAAATGGCAT 59.088 50.000 0.00 0.00 0.00 4.40
2942 4323 0.690192 TTCGGGAGTCTGAAATGGCA 59.310 50.000 0.00 0.00 35.50 4.92
2943 4324 1.468914 GTTTCGGGAGTCTGAAATGGC 59.531 52.381 12.18 0.49 46.30 4.40
2946 4327 4.003648 GTGATGTTTCGGGAGTCTGAAAT 58.996 43.478 12.18 1.16 46.30 2.17
2965 4349 3.118075 TCATCTCAAGTTGTGGGTTGTGA 60.118 43.478 2.11 0.00 30.50 3.58
2967 4351 3.576078 TCATCTCAAGTTGTGGGTTGT 57.424 42.857 2.11 0.00 30.50 3.32
2981 4365 2.455032 CCTGACGACGATGTTCATCTC 58.545 52.381 0.00 6.68 0.00 2.75


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

AutoCloner maintained by Alex Coulton.