Multiple sequence alignment - TraesCS5D01G423700

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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 TraesCS5D01G423700 chr5D 100.000 1614 0 0 612 2225 483643969 483642356 0.000000e+00 2981
1 TraesCS5D01G423700 chr5D 100.000 214 0 0 1 214 483644580 483644367 1.600000e-106 396
2 TraesCS5D01G423700 chr5A 90.148 812 43 14 935 1724 605098708 605097912 0.000000e+00 1022
3 TraesCS5D01G423700 chr5A 90.196 204 7 7 2024 2225 605097614 605097422 1.020000e-63 254
4 TraesCS5D01G423700 chr5B 85.098 765 57 38 987 1722 594735551 594734815 0.000000e+00 728
5 TraesCS5D01G423700 chr5B 93.333 270 11 5 612 877 594736436 594736170 2.070000e-105 392
6 TraesCS5D01G423700 chr5B 85.393 356 24 13 1862 2214 594734502 594734172 5.880000e-91 344
7 TraesCS5D01G423700 chr5B 87.736 106 11 2 41 145 594738635 594738531 3.000000e-24 122


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 TraesCS5D01G423700 chr5D 483642356 483644580 2224 True 1688.5 2981 100.000 1 2225 2 chr5D.!!$R1 2224
1 TraesCS5D01G423700 chr5A 605097422 605098708 1286 True 638.0 1022 90.172 935 2225 2 chr5A.!!$R1 1290
2 TraesCS5D01G423700 chr5B 594734172 594738635 4463 True 396.5 728 87.890 41 2214 4 chr5B.!!$R1 2173

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
886 2519 0.028505 CGCAGCAATTCGATCCCAAG 59.971 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 3998 0.108945 GCCCATGCTGTCAGCTTTTC 60.109 55.0 24.76 7.5 42.97 2.29 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
18 19 3.181367 CAGAATGTCTGGCCACGC 58.819 61.111 0.00 0.00 40.71 5.34
30 31 4.052229 CCACGCCGTCTCCGTCTT 62.052 66.667 0.00 0.00 36.69 3.01
31 32 2.049433 CACGCCGTCTCCGTCTTT 60.049 61.111 0.00 0.00 36.69 2.52
32 33 2.049433 ACGCCGTCTCCGTCTTTG 60.049 61.111 0.00 0.00 32.83 2.77
33 34 2.809601 CGCCGTCTCCGTCTTTGG 60.810 66.667 0.00 0.00 0.00 3.28
34 35 3.119096 GCCGTCTCCGTCTTTGGC 61.119 66.667 0.00 0.00 35.04 4.52
35 36 2.657237 CCGTCTCCGTCTTTGGCT 59.343 61.111 0.00 0.00 0.00 4.75
36 37 1.004918 CCGTCTCCGTCTTTGGCTT 60.005 57.895 0.00 0.00 0.00 4.35
37 38 1.291877 CCGTCTCCGTCTTTGGCTTG 61.292 60.000 0.00 0.00 0.00 4.01
38 39 1.869690 GTCTCCGTCTTTGGCTTGC 59.130 57.895 0.00 0.00 0.00 4.01
39 40 1.302511 TCTCCGTCTTTGGCTTGCC 60.303 57.895 4.43 4.43 0.00 4.52
40 41 2.282180 TCCGTCTTTGGCTTGCCC 60.282 61.111 9.35 0.00 0.00 5.36
41 42 2.282462 CCGTCTTTGGCTTGCCCT 60.282 61.111 9.35 0.00 0.00 5.19
42 43 1.903404 CCGTCTTTGGCTTGCCCTT 60.903 57.895 9.35 0.00 0.00 3.95
43 44 0.608035 CCGTCTTTGGCTTGCCCTTA 60.608 55.000 9.35 0.00 0.00 2.69
44 45 0.521735 CGTCTTTGGCTTGCCCTTAC 59.478 55.000 9.35 1.91 0.00 2.34
45 46 1.882352 CGTCTTTGGCTTGCCCTTACT 60.882 52.381 9.35 0.00 0.00 2.24
50 51 0.324943 TGGCTTGCCCTTACTCTGAC 59.675 55.000 9.35 0.00 0.00 3.51
53 54 1.737363 GCTTGCCCTTACTCTGACGAG 60.737 57.143 0.00 0.00 43.10 4.18
55 56 1.142097 GCCCTTACTCTGACGAGCC 59.858 63.158 0.00 0.00 41.09 4.70
59 60 0.528017 CTTACTCTGACGAGCCTGCA 59.472 55.000 0.00 0.00 41.09 4.41
60 61 0.966179 TTACTCTGACGAGCCTGCAA 59.034 50.000 0.00 0.00 41.09 4.08
73 74 1.672030 CTGCAACATCACCTCCGCA 60.672 57.895 0.00 0.00 0.00 5.69
75 76 0.821301 TGCAACATCACCTCCGCAAA 60.821 50.000 0.00 0.00 0.00 3.68
76 77 0.527565 GCAACATCACCTCCGCAAAT 59.472 50.000 0.00 0.00 0.00 2.32
77 78 1.468054 GCAACATCACCTCCGCAAATC 60.468 52.381 0.00 0.00 0.00 2.17
79 80 0.249120 ACATCACCTCCGCAAATCGA 59.751 50.000 0.00 0.00 41.67 3.59
115 116 4.700365 CGGCTCGTCGACAGCACA 62.700 66.667 28.66 5.48 38.77 4.57
122 123 2.964925 TCGACAGCACAACACGGC 60.965 61.111 0.00 0.00 0.00 5.68
137 138 0.953960 ACGGCCGACCATGTTTTCTC 60.954 55.000 35.90 0.00 34.57 2.87
154 441 1.133199 TCTCTTGGCCACCATGGTTTT 60.133 47.619 16.84 0.00 40.46 2.43
180 467 1.092921 GTCAGGCCGACAACACAACA 61.093 55.000 18.80 0.00 44.69 3.33
181 468 1.092921 TCAGGCCGACAACACAACAC 61.093 55.000 0.00 0.00 0.00 3.32
191 478 0.722848 AACACAACACGTTCGACCAC 59.277 50.000 0.00 0.00 0.00 4.16
192 479 0.390078 ACACAACACGTTCGACCACA 60.390 50.000 0.00 0.00 0.00 4.17
195 482 1.282817 CAACACGTTCGACCACAAGA 58.717 50.000 0.00 0.00 0.00 3.02
200 487 2.031420 CACGTTCGACCACAAGAGAGTA 60.031 50.000 0.00 0.00 0.00 2.59
203 490 3.852536 CGTTCGACCACAAGAGAGTAATC 59.147 47.826 0.00 0.00 0.00 1.75
208 495 1.473434 CCACAAGAGAGTAATCCCGGC 60.473 57.143 0.00 0.00 0.00 6.13
696 2325 1.265236 CCAAATTAAGCACCAGGCCA 58.735 50.000 5.01 0.00 46.50 5.36
708 2337 3.494254 AGGCCAAACGGTCACCCA 61.494 61.111 5.01 0.00 0.00 4.51
771 2403 4.033776 CCCAGCCGCCTTCTTCCA 62.034 66.667 0.00 0.00 0.00 3.53
775 2407 3.423154 GCCGCCTTCTTCCACACG 61.423 66.667 0.00 0.00 0.00 4.49
779 2411 1.084370 CGCCTTCTTCCACACGATCC 61.084 60.000 0.00 0.00 0.00 3.36
817 2449 1.615124 TCATCCATGTCCCCCGTGT 60.615 57.895 0.00 0.00 0.00 4.49
825 2457 4.040706 TCCATGTCCCCCGTGTATATAAAC 59.959 45.833 0.00 0.00 0.00 2.01
827 2459 2.705127 TGTCCCCCGTGTATATAAACCC 59.295 50.000 0.00 0.00 0.00 4.11
877 2510 1.136147 CAGAGCACCGCAGCAATTC 59.864 57.895 0.00 0.00 36.85 2.17
878 2511 2.099062 GAGCACCGCAGCAATTCG 59.901 61.111 0.00 0.00 36.85 3.34
879 2512 2.358615 AGCACCGCAGCAATTCGA 60.359 55.556 0.00 0.00 36.85 3.71
880 2513 1.709147 GAGCACCGCAGCAATTCGAT 61.709 55.000 0.00 0.00 36.85 3.59
881 2514 1.297893 GCACCGCAGCAATTCGATC 60.298 57.895 0.00 0.00 0.00 3.69
882 2515 1.353103 CACCGCAGCAATTCGATCC 59.647 57.895 0.00 0.00 0.00 3.36
883 2516 1.819632 ACCGCAGCAATTCGATCCC 60.820 57.895 0.00 0.00 0.00 3.85
884 2517 1.819208 CCGCAGCAATTCGATCCCA 60.819 57.895 0.00 0.00 0.00 4.37
885 2518 1.375853 CCGCAGCAATTCGATCCCAA 61.376 55.000 0.00 0.00 0.00 4.12
886 2519 0.028505 CGCAGCAATTCGATCCCAAG 59.971 55.000 0.00 0.00 0.00 3.61
887 2520 0.248784 GCAGCAATTCGATCCCAAGC 60.249 55.000 0.00 0.00 0.00 4.01
888 2521 1.097232 CAGCAATTCGATCCCAAGCA 58.903 50.000 0.00 0.00 0.00 3.91
889 2522 1.679680 CAGCAATTCGATCCCAAGCAT 59.320 47.619 0.00 0.00 0.00 3.79
890 2523 1.952296 AGCAATTCGATCCCAAGCATC 59.048 47.619 0.00 0.00 0.00 3.91
891 2524 1.000938 GCAATTCGATCCCAAGCATCC 60.001 52.381 0.00 0.00 0.00 3.51
892 2525 1.610522 CAATTCGATCCCAAGCATCCC 59.389 52.381 0.00 0.00 0.00 3.85
893 2526 0.111253 ATTCGATCCCAAGCATCCCC 59.889 55.000 0.00 0.00 0.00 4.81
894 2527 1.994885 TTCGATCCCAAGCATCCCCC 61.995 60.000 0.00 0.00 0.00 5.40
908 2541 3.182263 CCCCCACCAACCTCACCA 61.182 66.667 0.00 0.00 0.00 4.17
909 2542 2.547595 CCCCCACCAACCTCACCAT 61.548 63.158 0.00 0.00 0.00 3.55
910 2543 1.000896 CCCCACCAACCTCACCATC 60.001 63.158 0.00 0.00 0.00 3.51
911 2544 1.000896 CCCACCAACCTCACCATCC 60.001 63.158 0.00 0.00 0.00 3.51
912 2545 1.500783 CCCACCAACCTCACCATCCT 61.501 60.000 0.00 0.00 0.00 3.24
913 2546 0.035056 CCACCAACCTCACCATCCTC 60.035 60.000 0.00 0.00 0.00 3.71
914 2547 0.391661 CACCAACCTCACCATCCTCG 60.392 60.000 0.00 0.00 0.00 4.63
915 2548 0.836400 ACCAACCTCACCATCCTCGT 60.836 55.000 0.00 0.00 0.00 4.18
916 2549 1.191535 CCAACCTCACCATCCTCGTA 58.808 55.000 0.00 0.00 0.00 3.43
917 2550 1.134788 CCAACCTCACCATCCTCGTAC 60.135 57.143 0.00 0.00 0.00 3.67
918 2551 1.134788 CAACCTCACCATCCTCGTACC 60.135 57.143 0.00 0.00 0.00 3.34
919 2552 1.035932 ACCTCACCATCCTCGTACCG 61.036 60.000 0.00 0.00 0.00 4.02
920 2553 1.065928 CTCACCATCCTCGTACCGC 59.934 63.158 0.00 0.00 0.00 5.68
967 3136 4.496336 AGCATCCAAGCCGGCCTC 62.496 66.667 26.15 4.36 34.23 4.70
1236 3409 1.429825 CGTCTGATCGGTCGAGCTT 59.570 57.895 14.92 0.00 0.00 3.74
1249 3422 1.106944 CGAGCTTCCTCCTCCTCCTC 61.107 65.000 0.00 0.00 34.49 3.71
1250 3423 1.076339 AGCTTCCTCCTCCTCCTCG 60.076 63.158 0.00 0.00 0.00 4.63
1286 3459 5.471257 GTGTTGTTTGTTTACTGGGTTTGA 58.529 37.500 0.00 0.00 0.00 2.69
1308 3505 6.509656 TGATTATTACCGTGTACATGGAGTC 58.490 40.000 35.58 20.74 39.90 3.36
1352 3552 3.456644 TGGTGTTTACTGTGAAGGAGGAA 59.543 43.478 0.00 0.00 0.00 3.36
1472 3691 3.316283 CGTTGCTTGGTTTGTATGCAAT 58.684 40.909 0.00 0.00 43.87 3.56
1500 3720 2.866028 CAGGCTTGCGTCTGAAGC 59.134 61.111 8.69 8.69 45.75 3.86
1505 3725 1.786582 CTTGCGTCTGAAGCTGAGC 59.213 57.895 16.17 0.00 35.28 4.26
1526 3746 2.164219 CGGAATTGGGTTTCTGATGTGG 59.836 50.000 0.00 0.00 34.50 4.17
1584 3806 4.468153 GGAGGAGTACAGATTCAGGAACTT 59.532 45.833 0.00 0.00 34.60 2.66
1597 3819 5.078411 TCAGGAACTTGATAGAGTTGAGC 57.922 43.478 0.00 0.00 39.84 4.26
1630 3852 3.426525 CGCAAAAGTTCCTTGAAGAATGC 59.573 43.478 0.00 0.00 0.00 3.56
1646 3868 0.174162 ATGCTTTTCGATGCAAGGCC 59.826 50.000 11.27 0.00 42.74 5.19
1648 3870 0.457337 GCTTTTCGATGCAAGGCCAG 60.457 55.000 5.01 0.00 0.00 4.85
1653 3875 1.675310 CGATGCAAGGCCAGTTGGA 60.675 57.895 5.01 2.84 37.39 3.53
1654 3876 1.033746 CGATGCAAGGCCAGTTGGAT 61.034 55.000 10.92 10.92 40.80 3.41
1655 3877 1.746861 CGATGCAAGGCCAGTTGGATA 60.747 52.381 11.07 0.00 38.47 2.59
1656 3878 2.378038 GATGCAAGGCCAGTTGGATAA 58.622 47.619 11.07 0.00 38.47 1.75
1657 3879 2.300956 TGCAAGGCCAGTTGGATAAA 57.699 45.000 5.01 0.00 37.39 1.40
1658 3880 2.818921 TGCAAGGCCAGTTGGATAAAT 58.181 42.857 5.01 0.00 37.39 1.40
1659 3881 3.974719 TGCAAGGCCAGTTGGATAAATA 58.025 40.909 5.01 0.00 37.39 1.40
1660 3882 4.348486 TGCAAGGCCAGTTGGATAAATAA 58.652 39.130 5.01 0.00 37.39 1.40
1661 3883 4.774726 TGCAAGGCCAGTTGGATAAATAAA 59.225 37.500 5.01 0.00 37.39 1.40
1662 3884 5.424895 TGCAAGGCCAGTTGGATAAATAAAT 59.575 36.000 5.01 0.00 37.39 1.40
1663 3885 6.609212 TGCAAGGCCAGTTGGATAAATAAATA 59.391 34.615 5.01 0.00 37.39 1.40
1664 3886 7.124901 TGCAAGGCCAGTTGGATAAATAAATAA 59.875 33.333 5.01 0.00 37.39 1.40
1665 3887 7.984617 GCAAGGCCAGTTGGATAAATAAATAAA 59.015 33.333 5.01 0.00 37.39 1.40
1724 3969 2.524306 TCCAAAAATAGCACCAGGTGG 58.476 47.619 21.77 0.00 42.17 4.61
1725 3970 1.066929 CCAAAAATAGCACCAGGTGGC 60.067 52.381 21.77 13.20 39.32 5.01
1726 3971 1.895131 CAAAAATAGCACCAGGTGGCT 59.105 47.619 21.77 19.24 43.94 4.75
1727 3972 2.299867 CAAAAATAGCACCAGGTGGCTT 59.700 45.455 21.77 7.16 41.41 4.35
1728 3973 1.549203 AAATAGCACCAGGTGGCTTG 58.451 50.000 21.77 0.00 41.41 4.01
1729 3974 0.698238 AATAGCACCAGGTGGCTTGA 59.302 50.000 21.77 5.48 41.41 3.02
1730 3975 0.254178 ATAGCACCAGGTGGCTTGAG 59.746 55.000 21.77 0.00 41.41 3.02
1731 3976 0.835971 TAGCACCAGGTGGCTTGAGA 60.836 55.000 21.77 1.45 41.41 3.27
1732 3977 1.001641 GCACCAGGTGGCTTGAGAT 60.002 57.895 21.77 0.00 39.32 2.75
1733 3978 1.028868 GCACCAGGTGGCTTGAGATC 61.029 60.000 21.77 0.00 39.32 2.75
1734 3979 0.325933 CACCAGGTGGCTTGAGATCA 59.674 55.000 12.40 0.00 39.32 2.92
1735 3980 0.617413 ACCAGGTGGCTTGAGATCAG 59.383 55.000 0.00 0.00 39.32 2.90
1736 3981 0.107312 CCAGGTGGCTTGAGATCAGG 60.107 60.000 0.00 0.00 0.00 3.86
1737 3982 0.107312 CAGGTGGCTTGAGATCAGGG 60.107 60.000 0.00 0.00 0.00 4.45
1738 3983 0.252881 AGGTGGCTTGAGATCAGGGA 60.253 55.000 0.00 0.00 0.00 4.20
1739 3984 0.620556 GGTGGCTTGAGATCAGGGAA 59.379 55.000 0.00 0.00 0.00 3.97
1740 3985 1.004745 GGTGGCTTGAGATCAGGGAAA 59.995 52.381 0.00 0.00 0.00 3.13
1741 3986 2.357569 GGTGGCTTGAGATCAGGGAAAT 60.358 50.000 0.00 0.00 0.00 2.17
1742 3987 3.359950 GTGGCTTGAGATCAGGGAAATT 58.640 45.455 0.00 0.00 0.00 1.82
1743 3988 3.129988 GTGGCTTGAGATCAGGGAAATTG 59.870 47.826 0.00 0.00 0.00 2.32
1744 3989 3.010472 TGGCTTGAGATCAGGGAAATTGA 59.990 43.478 0.00 0.00 0.00 2.57
1745 3990 4.213513 GGCTTGAGATCAGGGAAATTGAT 58.786 43.478 0.00 0.00 37.96 2.57
1750 3995 3.492102 GATCAGGGAAATTGATCCGGA 57.508 47.619 6.61 6.61 43.20 5.14
1751 3996 4.026356 GATCAGGGAAATTGATCCGGAT 57.974 45.455 19.21 19.21 43.20 4.18
1752 3997 3.213206 TCAGGGAAATTGATCCGGATG 57.787 47.619 24.82 4.64 40.62 3.51
1753 3998 2.158623 TCAGGGAAATTGATCCGGATGG 60.159 50.000 24.82 0.00 40.62 3.51
1766 4011 0.449388 CGGATGGAAAAGCTGACAGC 59.551 55.000 20.12 20.12 42.84 4.40
1807 4101 5.753438 TGTAATACTCATAAGCAAGAAGGCG 59.247 40.000 0.00 0.00 39.27 5.52
1827 4121 5.248477 AGGCGGAACTATATCAATGTATGGT 59.752 40.000 0.00 0.00 0.00 3.55
1858 4321 2.059756 TGGAGGTTTGAGAGGGGATT 57.940 50.000 0.00 0.00 0.00 3.01
1887 4350 3.565063 GCACATGTTTTGATTTTGCCCTT 59.435 39.130 0.00 0.00 0.00 3.95
1926 4396 3.598019 AAACCAACACATCATCATGGC 57.402 42.857 0.00 0.00 34.45 4.40
1936 4406 5.181811 ACACATCATCATGGCAATAATACCG 59.818 40.000 0.00 0.00 33.82 4.02
1956 4426 9.615295 AATACCGTGATAATTTTGTAAACACAC 57.385 29.630 0.00 0.00 0.00 3.82
2005 4477 1.265236 TCCATGGTGGAATGGTTTGC 58.735 50.000 12.58 0.00 45.00 3.68
2006 4478 0.108709 CCATGGTGGAATGGTTTGCG 60.109 55.000 2.57 0.00 40.96 4.85
2007 4479 0.108709 CATGGTGGAATGGTTTGCGG 60.109 55.000 0.00 0.00 0.00 5.69
2008 4480 0.541764 ATGGTGGAATGGTTTGCGGT 60.542 50.000 0.00 0.00 0.00 5.68
2009 4481 1.288752 GGTGGAATGGTTTGCGGTG 59.711 57.895 0.00 0.00 0.00 4.94
2010 4482 1.175983 GGTGGAATGGTTTGCGGTGA 61.176 55.000 0.00 0.00 0.00 4.02
2011 4483 0.887933 GTGGAATGGTTTGCGGTGAT 59.112 50.000 0.00 0.00 0.00 3.06
2012 4484 1.272212 GTGGAATGGTTTGCGGTGATT 59.728 47.619 0.00 0.00 0.00 2.57
2013 4485 2.490115 GTGGAATGGTTTGCGGTGATTA 59.510 45.455 0.00 0.00 0.00 1.75
2014 4486 3.057174 GTGGAATGGTTTGCGGTGATTAA 60.057 43.478 0.00 0.00 0.00 1.40
2015 4487 3.057174 TGGAATGGTTTGCGGTGATTAAC 60.057 43.478 0.00 0.00 0.00 2.01
2016 4488 3.507786 GAATGGTTTGCGGTGATTAACC 58.492 45.455 0.00 0.00 46.60 2.85
2026 4498 3.994204 GGTGATTAACCGTTGTTTGGT 57.006 42.857 0.00 0.00 39.81 3.67
2054 4526 3.338249 TGCAATCAGCTAACCACTTCTC 58.662 45.455 0.00 0.00 45.94 2.87
2059 4531 4.527509 TCAGCTAACCACTTCTCAAGAG 57.472 45.455 0.00 0.00 0.00 2.85
2060 4532 3.259374 TCAGCTAACCACTTCTCAAGAGG 59.741 47.826 0.00 0.00 43.87 3.69
2083 4555 5.007626 GGTTTCTTGGTTTGCAATTTCCTTC 59.992 40.000 0.00 0.00 0.00 3.46
2196 4669 0.898320 TAGAGAGTTGAGCTGGCACC 59.102 55.000 0.00 0.00 0.00 5.01
2208 4681 1.134670 GCTGGCACCGTCTCTTCTAAT 60.135 52.381 0.00 0.00 0.00 1.73
2219 4692 8.784994 CACCGTCTCTTCTAATATACATACACT 58.215 37.037 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.672356 GCGTGGCCAGACATTCTGT 60.672 57.895 5.11 0.00 42.80 3.41
1 2 3.181367 GCGTGGCCAGACATTCTG 58.819 61.111 5.11 0.00 43.91 3.02
20 21 1.578206 GGCAAGCCAAAGACGGAGAC 61.578 60.000 6.14 0.00 35.81 3.36
21 22 1.302511 GGCAAGCCAAAGACGGAGA 60.303 57.895 6.14 0.00 35.81 3.71
22 23 2.335712 GGGCAAGCCAAAGACGGAG 61.336 63.158 13.87 0.00 37.98 4.63
23 24 2.282180 GGGCAAGCCAAAGACGGA 60.282 61.111 13.87 0.00 37.98 4.69
24 25 0.608035 TAAGGGCAAGCCAAAGACGG 60.608 55.000 13.87 0.00 37.98 4.79
25 26 0.521735 GTAAGGGCAAGCCAAAGACG 59.478 55.000 13.87 0.00 37.98 4.18
26 27 1.813178 GAGTAAGGGCAAGCCAAAGAC 59.187 52.381 13.87 5.12 37.98 3.01
27 28 1.705186 AGAGTAAGGGCAAGCCAAAGA 59.295 47.619 13.87 0.00 37.98 2.52
28 29 1.815003 CAGAGTAAGGGCAAGCCAAAG 59.185 52.381 13.87 0.00 37.98 2.77
29 30 1.423541 TCAGAGTAAGGGCAAGCCAAA 59.576 47.619 13.87 0.00 37.98 3.28
30 31 1.064003 TCAGAGTAAGGGCAAGCCAA 58.936 50.000 13.87 0.00 37.98 4.52
31 32 0.324943 GTCAGAGTAAGGGCAAGCCA 59.675 55.000 13.87 0.00 37.98 4.75
32 33 0.741221 CGTCAGAGTAAGGGCAAGCC 60.741 60.000 1.52 1.52 0.00 4.35
33 34 0.246635 TCGTCAGAGTAAGGGCAAGC 59.753 55.000 0.00 0.00 0.00 4.01
34 35 1.737363 GCTCGTCAGAGTAAGGGCAAG 60.737 57.143 0.00 0.00 46.03 4.01
35 36 0.246635 GCTCGTCAGAGTAAGGGCAA 59.753 55.000 0.00 0.00 46.03 4.52
36 37 1.605058 GGCTCGTCAGAGTAAGGGCA 61.605 60.000 0.00 0.00 46.03 5.36
37 38 1.142097 GGCTCGTCAGAGTAAGGGC 59.858 63.158 0.00 0.00 46.03 5.19
38 39 0.457851 CAGGCTCGTCAGAGTAAGGG 59.542 60.000 0.00 0.00 46.03 3.95
39 40 0.179124 GCAGGCTCGTCAGAGTAAGG 60.179 60.000 0.00 0.00 46.03 2.69
40 41 0.528017 TGCAGGCTCGTCAGAGTAAG 59.472 55.000 0.00 0.00 46.03 2.34
41 42 0.966179 TTGCAGGCTCGTCAGAGTAA 59.034 50.000 0.00 0.00 46.03 2.24
42 43 0.243907 GTTGCAGGCTCGTCAGAGTA 59.756 55.000 0.00 0.00 46.03 2.59
43 44 1.005630 GTTGCAGGCTCGTCAGAGT 60.006 57.895 0.00 0.00 46.03 3.24
45 46 0.390340 GATGTTGCAGGCTCGTCAGA 60.390 55.000 0.00 0.00 0.00 3.27
50 51 1.364626 GAGGTGATGTTGCAGGCTCG 61.365 60.000 0.00 0.00 0.00 5.03
53 54 2.401766 CGGAGGTGATGTTGCAGGC 61.402 63.158 0.00 0.00 0.00 4.85
55 56 1.236616 TTGCGGAGGTGATGTTGCAG 61.237 55.000 0.00 0.00 33.41 4.41
59 60 1.086696 CGATTTGCGGAGGTGATGTT 58.913 50.000 0.00 0.00 36.03 2.71
60 61 0.249120 TCGATTTGCGGAGGTGATGT 59.751 50.000 0.00 0.00 41.33 3.06
73 74 2.346803 CGGAGACAACATGGTCGATTT 58.653 47.619 0.00 0.00 42.62 2.17
75 76 0.175760 CCGGAGACAACATGGTCGAT 59.824 55.000 0.00 0.00 42.62 3.59
76 77 1.589630 CCGGAGACAACATGGTCGA 59.410 57.895 0.00 0.00 42.62 4.20
77 78 2.100631 GCCGGAGACAACATGGTCG 61.101 63.158 5.05 0.00 42.62 4.79
79 80 0.321653 GAAGCCGGAGACAACATGGT 60.322 55.000 5.05 0.00 0.00 3.55
122 123 1.200020 GCCAAGAGAAAACATGGTCGG 59.800 52.381 0.00 0.00 35.34 4.79
137 138 1.273327 GAGAAAACCATGGTGGCCAAG 59.727 52.381 20.60 0.00 42.67 3.61
154 441 3.298958 GTCGGCCTGACCATGAGA 58.701 61.111 14.46 0.00 42.04 3.27
164 451 2.177580 CGTGTTGTGTTGTCGGCCT 61.178 57.895 0.00 0.00 0.00 5.19
177 464 1.135527 TCTCTTGTGGTCGAACGTGTT 59.864 47.619 0.00 0.00 0.00 3.32
180 467 1.030457 ACTCTCTTGTGGTCGAACGT 58.970 50.000 0.00 0.00 0.00 3.99
181 468 2.983402 TACTCTCTTGTGGTCGAACG 57.017 50.000 0.00 0.00 0.00 3.95
191 478 0.830648 TGGCCGGGATTACTCTCTTG 59.169 55.000 2.18 0.00 0.00 3.02
192 479 0.831307 GTGGCCGGGATTACTCTCTT 59.169 55.000 2.18 0.00 0.00 2.85
195 482 1.306654 TGGTGGCCGGGATTACTCT 60.307 57.895 2.18 0.00 0.00 3.24
623 2252 2.946762 GTGGAGCGTGTTTCAGCC 59.053 61.111 0.00 0.00 0.00 4.85
678 2307 3.066380 GTTTGGCCTGGTGCTTAATTTG 58.934 45.455 3.32 0.00 40.92 2.32
688 2317 2.203294 GTGACCGTTTGGCCTGGT 60.203 61.111 3.32 6.79 39.70 4.00
771 2403 1.668101 GCGGAGGAGAAGGATCGTGT 61.668 60.000 0.00 0.00 0.00 4.49
775 2407 2.731374 CGGCGGAGGAGAAGGATC 59.269 66.667 0.00 0.00 0.00 3.36
779 2411 2.202810 GAAGCGGCGGAGGAGAAG 60.203 66.667 9.78 0.00 0.00 2.85
799 2431 0.325765 TACACGGGGGACATGGATGA 60.326 55.000 0.00 0.00 0.00 2.92
831 2463 4.796495 GGAAGCCGCGTGGGGATT 62.796 66.667 18.41 6.13 38.66 3.01
877 2510 2.113986 GGGGGATGCTTGGGATCG 59.886 66.667 0.00 0.00 0.00 3.69
891 2524 2.499303 GATGGTGAGGTTGGTGGGGG 62.499 65.000 0.00 0.00 0.00 5.40
892 2525 1.000896 GATGGTGAGGTTGGTGGGG 60.001 63.158 0.00 0.00 0.00 4.96
893 2526 1.000896 GGATGGTGAGGTTGGTGGG 60.001 63.158 0.00 0.00 0.00 4.61
894 2527 0.035056 GAGGATGGTGAGGTTGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
895 2528 0.391661 CGAGGATGGTGAGGTTGGTG 60.392 60.000 0.00 0.00 0.00 4.17
896 2529 0.836400 ACGAGGATGGTGAGGTTGGT 60.836 55.000 0.00 0.00 0.00 3.67
897 2530 1.134788 GTACGAGGATGGTGAGGTTGG 60.135 57.143 0.00 0.00 0.00 3.77
898 2531 1.134788 GGTACGAGGATGGTGAGGTTG 60.135 57.143 0.00 0.00 0.00 3.77
899 2532 1.192428 GGTACGAGGATGGTGAGGTT 58.808 55.000 0.00 0.00 0.00 3.50
900 2533 2.897699 GGTACGAGGATGGTGAGGT 58.102 57.895 0.00 0.00 0.00 3.85
914 2547 4.367023 TGCCTGGACGTGCGGTAC 62.367 66.667 15.23 7.15 0.00 3.34
915 2548 4.063967 CTGCCTGGACGTGCGGTA 62.064 66.667 15.23 11.19 0.00 4.02
918 2551 3.932580 TTAGCTGCCTGGACGTGCG 62.933 63.158 1.60 0.00 0.00 5.34
919 2552 1.432270 GATTAGCTGCCTGGACGTGC 61.432 60.000 0.00 0.00 0.00 5.34
920 2553 0.108186 TGATTAGCTGCCTGGACGTG 60.108 55.000 0.00 0.00 0.00 4.49
933 3102 4.272991 GGATGCTTGAGCTTGACTGATTAG 59.727 45.833 4.44 0.00 42.66 1.73
967 3136 1.242076 GGATGGATGCCTTCAATCCG 58.758 55.000 4.79 0.00 43.63 4.18
979 3148 2.205462 CCTCCCTCCCGGATGGAT 59.795 66.667 11.56 0.00 44.07 3.41
1184 3357 1.305465 TTCTTCATCGGGACCGGGA 60.305 57.895 6.32 6.43 40.25 5.14
1195 3368 2.378634 CGGGGCCCTCCTTCTTCAT 61.379 63.158 24.38 0.00 35.33 2.57
1236 3409 3.024356 AGCCGAGGAGGAGGAGGA 61.024 66.667 0.00 0.00 45.00 3.71
1249 3422 4.988598 ACACCAACGCTCCAGCCG 62.989 66.667 0.00 0.00 37.91 5.52
1250 3423 2.594592 AACACCAACGCTCCAGCC 60.595 61.111 0.00 0.00 37.91 4.85
1286 3459 6.474140 TGACTCCATGTACACGGTAATAAT 57.526 37.500 8.01 0.00 0.00 1.28
1308 3505 4.027458 CACACAAGAAACGAGCAACAAATG 60.027 41.667 0.00 0.00 0.00 2.32
1352 3552 0.253044 CACACCGGATCAACATCCCT 59.747 55.000 9.46 0.00 45.67 4.20
1472 3691 1.269206 CGCAAGCCTGAGAAAGCAAAA 60.269 47.619 0.00 0.00 0.00 2.44
1500 3720 1.470098 CAGAAACCCAATTCCGCTCAG 59.530 52.381 0.00 0.00 0.00 3.35
1505 3725 2.164219 CCACATCAGAAACCCAATTCCG 59.836 50.000 0.00 0.00 0.00 4.30
1526 3746 3.194005 TGACACCTGAAACTCTTCCAC 57.806 47.619 0.00 0.00 0.00 4.02
1584 3806 2.093816 CAGTGCCAGCTCAACTCTATCA 60.094 50.000 0.00 0.00 0.00 2.15
1630 3852 0.883833 ACTGGCCTTGCATCGAAAAG 59.116 50.000 3.32 0.00 0.00 2.27
1659 3881 9.118300 TGCAAAATCAGATTTGGTGTTTTATTT 57.882 25.926 9.24 0.00 39.99 1.40
1660 3882 8.558700 GTGCAAAATCAGATTTGGTGTTTTATT 58.441 29.630 9.24 0.00 39.99 1.40
1661 3883 7.714377 TGTGCAAAATCAGATTTGGTGTTTTAT 59.286 29.630 9.24 0.00 39.99 1.40
1662 3884 7.044181 TGTGCAAAATCAGATTTGGTGTTTTA 58.956 30.769 9.24 0.00 39.99 1.52
1663 3885 5.879223 TGTGCAAAATCAGATTTGGTGTTTT 59.121 32.000 9.24 0.00 39.99 2.43
1664 3886 5.426504 TGTGCAAAATCAGATTTGGTGTTT 58.573 33.333 9.24 0.00 39.99 2.83
1665 3887 5.021033 TGTGCAAAATCAGATTTGGTGTT 57.979 34.783 9.24 0.00 39.99 3.32
1724 3969 4.277921 GGATCAATTTCCCTGATCTCAAGC 59.722 45.833 11.46 0.00 45.67 4.01
1725 3970 4.514441 CGGATCAATTTCCCTGATCTCAAG 59.486 45.833 11.46 0.54 45.67 3.02
1726 3971 4.454678 CGGATCAATTTCCCTGATCTCAA 58.545 43.478 11.46 0.00 45.67 3.02
1727 3972 3.181451 CCGGATCAATTTCCCTGATCTCA 60.181 47.826 0.00 0.00 45.67 3.27
1728 3973 3.071602 TCCGGATCAATTTCCCTGATCTC 59.928 47.826 0.00 3.20 45.67 2.75
1729 3974 3.048600 TCCGGATCAATTTCCCTGATCT 58.951 45.455 0.00 0.00 45.67 2.75
1730 3975 3.492102 TCCGGATCAATTTCCCTGATC 57.508 47.619 0.00 4.56 45.66 2.92
1731 3976 3.499202 CCATCCGGATCAATTTCCCTGAT 60.499 47.826 15.88 0.00 36.21 2.90
1732 3977 2.158623 CCATCCGGATCAATTTCCCTGA 60.159 50.000 15.88 0.00 31.61 3.86
1733 3978 2.158623 TCCATCCGGATCAATTTCCCTG 60.159 50.000 15.88 0.00 35.91 4.45
1734 3979 2.135189 TCCATCCGGATCAATTTCCCT 58.865 47.619 15.88 0.00 35.91 4.20
1735 3980 2.656947 TCCATCCGGATCAATTTCCC 57.343 50.000 15.88 0.00 35.91 3.97
1736 3981 4.737649 GCTTTTCCATCCGGATCAATTTCC 60.738 45.833 15.88 0.00 42.41 3.13
1737 3982 4.098501 AGCTTTTCCATCCGGATCAATTTC 59.901 41.667 15.88 1.45 42.41 2.17
1738 3983 4.026052 AGCTTTTCCATCCGGATCAATTT 58.974 39.130 15.88 0.00 42.41 1.82
1739 3984 3.382546 CAGCTTTTCCATCCGGATCAATT 59.617 43.478 15.88 0.00 42.41 2.32
1740 3985 2.954318 CAGCTTTTCCATCCGGATCAAT 59.046 45.455 15.88 0.00 42.41 2.57
1741 3986 2.026356 TCAGCTTTTCCATCCGGATCAA 60.026 45.455 15.88 7.67 42.41 2.57
1742 3987 1.559219 TCAGCTTTTCCATCCGGATCA 59.441 47.619 15.88 0.30 42.41 2.92
1743 3988 1.943340 GTCAGCTTTTCCATCCGGATC 59.057 52.381 15.88 0.79 42.41 3.36
1744 3989 1.281867 TGTCAGCTTTTCCATCCGGAT 59.718 47.619 12.38 12.38 42.41 4.18
1745 3990 0.690192 TGTCAGCTTTTCCATCCGGA 59.310 50.000 6.61 6.61 40.60 5.14
1746 3991 1.089920 CTGTCAGCTTTTCCATCCGG 58.910 55.000 0.00 0.00 0.00 5.14
1747 3992 0.449388 GCTGTCAGCTTTTCCATCCG 59.551 55.000 17.89 0.00 38.45 4.18
1748 3993 1.538047 TGCTGTCAGCTTTTCCATCC 58.462 50.000 24.76 0.00 42.97 3.51
1749 3994 2.159282 CCATGCTGTCAGCTTTTCCATC 60.159 50.000 24.76 0.00 42.97 3.51
1750 3995 1.822990 CCATGCTGTCAGCTTTTCCAT 59.177 47.619 24.76 6.81 42.97 3.41
1751 3996 1.250328 CCATGCTGTCAGCTTTTCCA 58.750 50.000 24.76 4.55 42.97 3.53
1752 3997 0.529378 CCCATGCTGTCAGCTTTTCC 59.471 55.000 24.76 0.00 42.97 3.13
1753 3998 0.108945 GCCCATGCTGTCAGCTTTTC 60.109 55.000 24.76 7.50 42.97 2.29
1754 3999 1.969862 GCCCATGCTGTCAGCTTTT 59.030 52.632 24.76 7.91 42.97 2.27
1766 4011 7.775120 AGTATTACAAAAGAATTCAGCCCATG 58.225 34.615 8.44 0.76 0.00 3.66
1782 4047 6.257849 CGCCTTCTTGCTTATGAGTATTACAA 59.742 38.462 0.00 0.00 0.00 2.41
1783 4048 5.753438 CGCCTTCTTGCTTATGAGTATTACA 59.247 40.000 0.00 0.00 0.00 2.41
1827 4121 9.627123 CCTCTCAAACCTCCATACAATTAATTA 57.373 33.333 0.00 0.00 0.00 1.40
1843 4306 2.879103 TCACAATCCCCTCTCAAACC 57.121 50.000 0.00 0.00 0.00 3.27
1844 4307 3.119352 GCAATCACAATCCCCTCTCAAAC 60.119 47.826 0.00 0.00 0.00 2.93
1845 4308 3.091545 GCAATCACAATCCCCTCTCAAA 58.908 45.455 0.00 0.00 0.00 2.69
1846 4309 2.041485 TGCAATCACAATCCCCTCTCAA 59.959 45.455 0.00 0.00 0.00 3.02
1847 4310 1.634973 TGCAATCACAATCCCCTCTCA 59.365 47.619 0.00 0.00 0.00 3.27
1871 4334 5.119694 TGTACCAAAGGGCAAAATCAAAAC 58.880 37.500 0.00 0.00 37.90 2.43
1887 4350 4.691216 GGTTTTTGTTTGTGCTTGTACCAA 59.309 37.500 0.00 0.00 0.00 3.67
1956 4426 8.216453 GCACTTACTGCAATTAAAAACATGAAG 58.784 33.333 0.00 0.00 46.29 3.02
1972 4442 6.693626 CCACCATGGATTTGCACTTACTGC 62.694 50.000 21.47 0.00 42.98 4.40
2006 4478 3.994204 ACCAAACAACGGTTAATCACC 57.006 42.857 0.00 0.00 43.16 4.02
2007 4479 4.438471 CGAAACCAAACAACGGTTAATCAC 59.562 41.667 0.00 0.00 46.12 3.06
2008 4480 4.334759 TCGAAACCAAACAACGGTTAATCA 59.665 37.500 0.00 0.00 46.12 2.57
2009 4481 4.846509 TCGAAACCAAACAACGGTTAATC 58.153 39.130 0.00 0.00 46.12 1.75
2010 4482 4.897025 TCGAAACCAAACAACGGTTAAT 57.103 36.364 0.00 0.00 46.12 1.40
2011 4483 4.897025 ATCGAAACCAAACAACGGTTAA 57.103 36.364 0.00 0.00 46.12 2.01
2012 4484 4.599047 CAATCGAAACCAAACAACGGTTA 58.401 39.130 0.00 0.00 46.12 2.85
2014 4486 2.796735 GCAATCGAAACCAAACAACGGT 60.797 45.455 0.00 0.00 38.85 4.83
2015 4487 1.784283 GCAATCGAAACCAAACAACGG 59.216 47.619 0.00 0.00 0.00 4.44
2016 4488 2.455032 TGCAATCGAAACCAAACAACG 58.545 42.857 0.00 0.00 0.00 4.10
2017 4489 4.505922 TGATTGCAATCGAAACCAAACAAC 59.494 37.500 29.23 6.51 38.26 3.32
2018 4490 4.686972 TGATTGCAATCGAAACCAAACAA 58.313 34.783 29.23 8.91 38.26 2.83
2019 4491 4.297510 CTGATTGCAATCGAAACCAAACA 58.702 39.130 29.23 11.44 38.26 2.83
2020 4492 3.121778 GCTGATTGCAATCGAAACCAAAC 59.878 43.478 29.23 7.58 42.31 2.93
2021 4493 3.005684 AGCTGATTGCAATCGAAACCAAA 59.994 39.130 29.23 12.17 45.94 3.28
2022 4494 2.557924 AGCTGATTGCAATCGAAACCAA 59.442 40.909 29.23 12.83 45.94 3.67
2023 4495 2.161855 AGCTGATTGCAATCGAAACCA 58.838 42.857 29.23 14.03 45.94 3.67
2024 4496 2.927553 AGCTGATTGCAATCGAAACC 57.072 45.000 29.23 17.04 45.94 3.27
2025 4497 4.098416 GGTTAGCTGATTGCAATCGAAAC 58.902 43.478 29.23 25.99 45.94 2.78
2026 4498 3.755905 TGGTTAGCTGATTGCAATCGAAA 59.244 39.130 29.23 18.87 45.94 3.46
2027 4499 3.126858 GTGGTTAGCTGATTGCAATCGAA 59.873 43.478 29.23 19.06 45.94 3.71
2028 4500 2.677836 GTGGTTAGCTGATTGCAATCGA 59.322 45.455 29.23 19.07 45.94 3.59
2059 4531 4.450976 AGGAAATTGCAAACCAAGAAACC 58.549 39.130 18.22 7.11 36.76 3.27
2060 4532 5.584251 TGAAGGAAATTGCAAACCAAGAAAC 59.416 36.000 18.22 2.74 36.76 2.78
2062 4534 5.350504 TGAAGGAAATTGCAAACCAAGAA 57.649 34.783 18.22 3.68 36.76 2.52
2083 4555 1.065701 GCTTCAGATGCAAGCCTGATG 59.934 52.381 14.75 16.42 40.45 3.07
2196 4669 9.613957 CCAAGTGTATGTATATTAGAAGAGACG 57.386 37.037 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.