Multiple sequence alignment - TraesCS3B01G612200

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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 TraesCS3B01G612200 chr3B 100.000 2975 0 0 1 2975 829543481 829540507 0.000000e+00 5494.0
1 TraesCS3B01G612200 chr3D 94.350 1947 50 17 1032 2975 611919316 611917427 0.000000e+00 2931.0
2 TraesCS3B01G612200 chr3D 83.333 648 30 28 300 925 611919993 611919402 7.300000e-146 527.0
3 TraesCS3B01G612200 chr3D 87.425 167 18 3 79 244 611923361 611923197 3.910000e-44 189.0
4 TraesCS3B01G612200 chr3D 97.590 83 2 0 1 83 611924937 611924855 3.090000e-30 143.0
5 TraesCS3B01G612200 chr3D 92.537 67 1 2 240 304 611922957 611922893 3.160000e-15 93.5
6 TraesCS3B01G612200 chr3A 89.039 2363 115 55 193 2485 746635343 746633055 0.000000e+00 2796.0
7 TraesCS3B01G612200 chr3A 92.702 507 18 12 2482 2975 746632868 746632368 0.000000e+00 713.0
8 TraesCS3B01G612200 chr3A 89.848 197 16 4 2 196 746635737 746635543 1.770000e-62 250.0
9 TraesCS3B01G612200 chr1B 82.439 205 34 2 1356 1559 37799453 37799656 8.470000e-41 178.0
10 TraesCS3B01G612200 chr4A 80.189 212 39 3 1345 1554 159294867 159294657 3.970000e-34 156.0
11 TraesCS3B01G612200 chr4A 95.349 43 2 0 102 144 500146179 500146221 5.320000e-08 69.4
12 TraesCS3B01G612200 chr1D 80.488 205 38 2 1356 1559 22437243 22437040 3.970000e-34 156.0
13 TraesCS3B01G612200 chr4D 79.812 213 39 4 1345 1554 315597308 315597519 5.140000e-33 152.0
14 TraesCS3B01G612200 chr1A 79.512 205 40 2 1356 1559 23339861 23340064 8.590000e-31 145.0
15 TraesCS3B01G612200 chr4B 79.327 208 40 3 1349 1554 393406260 393406466 3.090000e-30 143.0
16 TraesCS3B01G612200 chr2D 79.897 194 39 0 1358 1551 48133243 48133436 3.090000e-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 TraesCS3B01G612200 chr3B 829540507 829543481 2974 True 5494.0 5494 100.000000 1 2975 1 chr3B.!!$R1 2974
1 TraesCS3B01G612200 chr3D 611917427 611924937 7510 True 776.7 2931 91.047000 1 2975 5 chr3D.!!$R1 2974
2 TraesCS3B01G612200 chr3A 746632368 746635737 3369 True 1253.0 2796 90.529667 2 2975 3 chr3A.!!$R1 2973

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
393 5250 0.096976 GTGTGCGTGCATGTGGTATC 59.903 55.0 7.93 0.00 0.00 2.24 F
858 5779 0.104409 ACCTCCCAAGTGGACTCCTT 60.104 55.0 0.00 0.00 38.61 3.36 F
977 5914 0.250081 GCCTGCAGGTGGTAGCTATC 60.250 60.0 32.81 9.23 37.57 2.08 F
1685 6631 0.408309 TCCTCCTCCTCCTCAACGAA 59.592 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 6621 0.381445 TCGTTGTCGTTCGTTGAGGA 59.619 50.000 0.00 0.0 38.33 3.71 R
1847 6793 0.729478 CGGCACTATCATAGACGGCG 60.729 60.000 16.20 16.2 41.24 6.46 R
1854 6800 1.754380 AAGGCGGCGGCACTATCATA 61.754 55.000 34.87 0.0 42.47 2.15 R
2851 8002 4.082300 GGAGTACTGCAGATCATCGATCAT 60.082 45.833 23.35 0.0 41.12 2.45 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
141 1641 3.526931 TGAGATTTAGCCAAGTCTCGG 57.473 47.619 11.59 0.00 45.70 4.63
159 1659 9.498176 AAGTCTCGGTTAAAGTAACATAACATT 57.502 29.630 0.96 0.00 40.39 2.71
162 1662 9.146984 TCTCGGTTAAAGTAACATAACATTCAG 57.853 33.333 0.96 0.00 40.39 3.02
163 1663 8.259049 TCGGTTAAAGTAACATAACATTCAGG 57.741 34.615 0.96 0.00 40.39 3.86
180 1681 8.243289 ACATTCAGGCGAGAAAAATAAAATTG 57.757 30.769 0.00 0.00 0.00 2.32
228 1932 7.975058 TCTTACAGATATAGTATCGACCGAGAG 59.025 40.741 0.00 0.00 0.00 3.20
370 5227 3.349006 GTGTCCCGCACTGCTGTG 61.349 66.667 18.54 18.54 44.41 3.66
371 5228 3.545574 TGTCCCGCACTGCTGTGA 61.546 61.111 25.94 3.38 46.55 3.58
372 5229 2.740055 GTCCCGCACTGCTGTGAG 60.740 66.667 25.94 22.01 46.55 3.51
373 5230 3.233980 TCCCGCACTGCTGTGAGT 61.234 61.111 25.94 0.00 46.55 3.41
384 5241 2.125350 TGTGAGTGTGTGCGTGCA 60.125 55.556 0.00 0.00 0.00 4.57
385 5242 1.501337 CTGTGAGTGTGTGCGTGCAT 61.501 55.000 0.00 0.00 0.00 3.96
386 5243 1.082561 GTGAGTGTGTGCGTGCATG 60.083 57.895 0.09 0.09 0.00 4.06
387 5244 1.523484 TGAGTGTGTGCGTGCATGT 60.523 52.632 7.93 0.00 0.00 3.21
388 5245 1.082561 GAGTGTGTGCGTGCATGTG 60.083 57.895 7.93 0.00 0.00 3.21
390 5247 2.515757 TGTGTGCGTGCATGTGGT 60.516 55.556 7.93 0.00 0.00 4.16
393 5250 0.096976 GTGTGCGTGCATGTGGTATC 59.903 55.000 7.93 0.00 0.00 2.24
394 5251 0.321122 TGTGCGTGCATGTGGTATCA 60.321 50.000 7.93 0.00 0.00 2.15
424 5290 9.038803 GTGATGGTGTGCATATATGATATGTAG 57.961 37.037 17.10 0.00 0.00 2.74
507 5391 0.670546 CAGCACGGATGGACGAAACT 60.671 55.000 0.00 0.00 37.61 2.66
527 5411 7.513660 CGAAACTAATATATGATCGGTGATGCG 60.514 40.741 0.00 0.00 0.00 4.73
619 5520 1.002921 ATGGATCCGTCCTGGTGGA 59.997 57.895 7.39 11.76 45.32 4.02
627 5528 3.716195 TCCTGGTGGATGGTGCGG 61.716 66.667 0.00 0.00 37.46 5.69
634 5535 1.299541 GTGGATGGTGCGGTTGATAG 58.700 55.000 0.00 0.00 0.00 2.08
636 5537 1.768275 TGGATGGTGCGGTTGATAGAT 59.232 47.619 0.00 0.00 0.00 1.98
637 5538 2.969262 TGGATGGTGCGGTTGATAGATA 59.031 45.455 0.00 0.00 0.00 1.98
638 5539 3.006859 TGGATGGTGCGGTTGATAGATAG 59.993 47.826 0.00 0.00 0.00 2.08
639 5540 3.258372 GGATGGTGCGGTTGATAGATAGA 59.742 47.826 0.00 0.00 0.00 1.98
640 5541 4.081420 GGATGGTGCGGTTGATAGATAGAT 60.081 45.833 0.00 0.00 0.00 1.98
641 5542 5.127194 GGATGGTGCGGTTGATAGATAGATA 59.873 44.000 0.00 0.00 0.00 1.98
642 5543 6.183360 GGATGGTGCGGTTGATAGATAGATAT 60.183 42.308 0.00 0.00 0.00 1.63
643 5544 7.014326 GGATGGTGCGGTTGATAGATAGATATA 59.986 40.741 0.00 0.00 0.00 0.86
644 5545 7.898014 TGGTGCGGTTGATAGATAGATATAT 57.102 36.000 0.00 0.00 0.00 0.86
722 5628 3.601435 TCGCTATCTTCCTCCTCTATCG 58.399 50.000 0.00 0.00 0.00 2.92
723 5629 3.261137 TCGCTATCTTCCTCCTCTATCGA 59.739 47.826 0.00 0.00 0.00 3.59
724 5630 4.080807 TCGCTATCTTCCTCCTCTATCGAT 60.081 45.833 2.16 2.16 0.00 3.59
725 5631 4.272504 CGCTATCTTCCTCCTCTATCGATC 59.727 50.000 0.00 0.00 0.00 3.69
726 5632 4.578928 GCTATCTTCCTCCTCTATCGATCC 59.421 50.000 0.00 0.00 0.00 3.36
727 5633 3.443145 TCTTCCTCCTCTATCGATCCC 57.557 52.381 0.00 0.00 0.00 3.85
728 5634 2.990284 TCTTCCTCCTCTATCGATCCCT 59.010 50.000 0.00 0.00 0.00 4.20
729 5635 2.889170 TCCTCCTCTATCGATCCCTG 57.111 55.000 0.00 0.00 0.00 4.45
820 5738 2.151388 GCCCCCTCCCGCCTATAAA 61.151 63.158 0.00 0.00 0.00 1.40
821 5739 1.759236 CCCCCTCCCGCCTATAAAC 59.241 63.158 0.00 0.00 0.00 2.01
823 5741 0.767060 CCCCTCCCGCCTATAAACCT 60.767 60.000 0.00 0.00 0.00 3.50
857 5778 0.838122 CACCTCCCAAGTGGACTCCT 60.838 60.000 0.00 0.00 38.61 3.69
858 5779 0.104409 ACCTCCCAAGTGGACTCCTT 60.104 55.000 0.00 0.00 38.61 3.36
859 5780 0.615850 CCTCCCAAGTGGACTCCTTC 59.384 60.000 0.00 0.00 38.61 3.46
896 5817 4.941263 CCATTTCCATACGTTTCTTCCTCA 59.059 41.667 0.00 0.00 0.00 3.86
911 5832 1.620819 TCCTCAAGTCAAGTGGCTCTC 59.379 52.381 0.00 0.00 0.00 3.20
915 5836 2.094494 TCAAGTCAAGTGGCTCTCGATC 60.094 50.000 0.00 0.00 0.00 3.69
916 5837 0.820871 AGTCAAGTGGCTCTCGATCC 59.179 55.000 0.00 0.00 0.00 3.36
942 5879 3.056821 CACCAACATCTTCTGTCCGTAGA 60.057 47.826 0.00 0.00 36.98 2.59
943 5880 3.056749 ACCAACATCTTCTGTCCGTAGAC 60.057 47.826 0.00 0.00 43.83 2.59
945 5882 1.743958 ACATCTTCTGTCCGTAGACCG 59.256 52.381 0.00 0.00 42.81 4.79
947 5884 2.768253 TCTTCTGTCCGTAGACCGTA 57.232 50.000 0.00 0.00 42.81 4.02
949 5886 1.063764 CTTCTGTCCGTAGACCGTAGC 59.936 57.143 0.00 0.00 42.81 3.58
951 5888 1.093159 CTGTCCGTAGACCGTAGCTT 58.907 55.000 0.00 0.00 42.81 3.74
955 5892 0.381089 CCGTAGACCGTAGCTTCCTG 59.619 60.000 0.00 0.00 33.66 3.86
957 5894 1.472188 GTAGACCGTAGCTTCCTGGT 58.528 55.000 0.00 0.00 37.44 4.00
958 5895 1.134560 GTAGACCGTAGCTTCCTGGTG 59.865 57.143 0.00 0.00 34.12 4.17
959 5896 1.448013 GACCGTAGCTTCCTGGTGC 60.448 63.158 0.00 6.38 34.12 5.01
963 5900 1.746991 GTAGCTTCCTGGTGCCTGC 60.747 63.158 0.00 2.13 0.00 4.85
964 5901 2.223443 TAGCTTCCTGGTGCCTGCA 61.223 57.895 0.00 0.00 0.00 4.41
965 5902 2.189191 TAGCTTCCTGGTGCCTGCAG 62.189 60.000 6.78 6.78 0.00 4.41
966 5903 2.360852 CTTCCTGGTGCCTGCAGG 60.361 66.667 29.34 29.34 37.45 4.85
967 5904 3.177884 TTCCTGGTGCCTGCAGGT 61.178 61.111 32.81 0.00 37.38 4.00
968 5905 3.496309 TTCCTGGTGCCTGCAGGTG 62.496 63.158 32.81 17.31 37.38 4.00
970 5907 4.275508 CTGGTGCCTGCAGGTGGT 62.276 66.667 32.81 0.00 37.57 4.16
971 5908 2.851588 TGGTGCCTGCAGGTGGTA 60.852 61.111 32.81 15.29 37.57 3.25
972 5909 2.045926 GGTGCCTGCAGGTGGTAG 60.046 66.667 32.81 7.85 37.57 3.18
973 5910 2.747855 GTGCCTGCAGGTGGTAGC 60.748 66.667 32.81 18.08 37.57 3.58
974 5911 2.930019 TGCCTGCAGGTGGTAGCT 60.930 61.111 32.81 0.00 37.57 3.32
975 5912 1.612146 TGCCTGCAGGTGGTAGCTA 60.612 57.895 32.81 7.66 37.57 3.32
976 5913 0.982852 TGCCTGCAGGTGGTAGCTAT 60.983 55.000 32.81 0.00 37.57 2.97
977 5914 0.250081 GCCTGCAGGTGGTAGCTATC 60.250 60.000 32.81 9.23 37.57 2.08
978 5915 1.418334 CCTGCAGGTGGTAGCTATCT 58.582 55.000 25.53 0.00 0.00 1.98
1217 6162 3.588906 CATGCCGTGCCATGCGAT 61.589 61.111 0.00 0.00 36.52 4.58
1218 6163 3.588906 ATGCCGTGCCATGCGATG 61.589 61.111 0.00 0.00 0.00 3.84
1222 6167 3.588906 CGTGCCATGCGATGCCAT 61.589 61.111 0.00 0.00 0.00 4.40
1223 6168 2.027024 GTGCCATGCGATGCCATG 59.973 61.111 0.00 0.00 41.71 3.66
1224 6169 3.906879 TGCCATGCGATGCCATGC 61.907 61.111 0.00 0.00 40.92 4.06
1225 6170 4.994201 GCCATGCGATGCCATGCG 62.994 66.667 0.00 0.00 40.92 4.73
1226 6171 3.588906 CCATGCGATGCCATGCGT 61.589 61.111 0.00 0.00 40.92 5.24
1227 6172 2.353030 CATGCGATGCCATGCGTG 60.353 61.111 0.00 0.00 41.23 5.34
1228 6173 4.260355 ATGCGATGCCATGCGTGC 62.260 61.111 0.00 0.00 0.00 5.34
1310 6256 1.282248 TTGTGTGCTAACGCTCTCGC 61.282 55.000 0.00 0.00 39.84 5.03
1351 6297 1.578423 GCTCTTGTGTCTGCCTTGC 59.422 57.895 0.00 0.00 0.00 4.01
1608 6554 4.087892 TCTGCTGCTTCGGCCTCC 62.088 66.667 0.00 0.00 40.91 4.30
1609 6555 4.399395 CTGCTGCTTCGGCCTCCA 62.399 66.667 0.00 0.00 40.91 3.86
1610 6556 4.704833 TGCTGCTTCGGCCTCCAC 62.705 66.667 0.00 0.00 40.91 4.02
1612 6558 4.069232 CTGCTTCGGCCTCCACGA 62.069 66.667 0.00 0.00 40.91 4.35
1613 6559 4.373116 TGCTTCGGCCTCCACGAC 62.373 66.667 0.00 0.00 40.45 4.34
1674 6620 2.363147 ACGTCCAGCTCCTCCTCC 60.363 66.667 0.00 0.00 0.00 4.30
1675 6621 2.043450 CGTCCAGCTCCTCCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
1676 6622 2.124693 CGTCCAGCTCCTCCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
1677 6623 1.760480 GTCCAGCTCCTCCTCCTCC 60.760 68.421 0.00 0.00 0.00 4.30
1685 6631 0.408309 TCCTCCTCCTCCTCAACGAA 59.592 55.000 0.00 0.00 0.00 3.85
1695 6641 1.001048 TCCTCAACGAACGACAACGAT 60.001 47.619 0.14 0.00 42.66 3.73
1699 6645 2.725723 TCAACGAACGACAACGATAACC 59.274 45.455 0.14 0.00 42.66 2.85
1752 6698 2.598394 GCCAGCCAGGAACAAGCA 60.598 61.111 0.00 0.00 41.22 3.91
1774 6720 0.542938 TCACCAGCTGCTCTACACCT 60.543 55.000 8.66 0.00 0.00 4.00
1816 6762 2.031465 TCCTTTGGAACGACGCCC 59.969 61.111 0.00 0.00 0.00 6.13
1917 6863 2.043349 TCGGATTCGCTCTGGGGA 60.043 61.111 0.00 0.00 36.13 4.81
1923 6869 3.317280 TTCGCTCTGGGGAATAGGT 57.683 52.632 0.00 0.00 39.05 3.08
1981 6927 2.870175 CCGGTGCCCCATGATATTTTA 58.130 47.619 0.00 0.00 0.00 1.52
2099 7046 7.085116 CGAGACTTAATATGTACCAGTGATCC 58.915 42.308 0.00 0.00 0.00 3.36
2145 7093 9.463443 GGGATTTATGCTTTTGTACATGTAATC 57.537 33.333 7.25 4.26 33.01 1.75
2405 7362 8.024865 ACACACACAATATGTTCATTCATTCAG 58.975 33.333 0.00 0.00 40.64 3.02
2441 7398 5.506708 GAAGTAGGCCCTTCTTTAATTCCA 58.493 41.667 12.97 0.00 38.24 3.53
2526 7673 7.178712 ACTTCATAATTAAAGAGAATCCGCG 57.821 36.000 0.00 0.00 33.66 6.46
2548 7695 5.164177 GCGTAAGAAATGTATTCCGAGATCG 60.164 44.000 0.00 0.00 43.02 3.69
2560 7707 4.853924 TCCGAGATCGATCAATCAATCA 57.146 40.909 26.47 0.06 43.02 2.57
2561 7708 5.200368 TCCGAGATCGATCAATCAATCAA 57.800 39.130 26.47 3.62 43.02 2.57
2562 7709 5.787380 TCCGAGATCGATCAATCAATCAAT 58.213 37.500 26.47 2.11 43.02 2.57
2563 7710 5.866092 TCCGAGATCGATCAATCAATCAATC 59.134 40.000 26.47 10.45 43.02 2.67
2803 7954 3.385314 TCATGCCCCAATCTCAATCAA 57.615 42.857 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.957759 ACAAGACGCAAAGTAACAAACT 57.042 36.364 0.00 0.00 41.49 2.66
95 1595 3.034635 ACTGAGACCTAGCAATACCCAG 58.965 50.000 0.00 0.00 0.00 4.45
96 1596 3.031736 GACTGAGACCTAGCAATACCCA 58.968 50.000 0.00 0.00 0.00 4.51
101 1601 3.701542 TCAATCGACTGAGACCTAGCAAT 59.298 43.478 0.00 0.00 0.00 3.56
103 1603 2.685388 CTCAATCGACTGAGACCTAGCA 59.315 50.000 18.76 0.00 44.82 3.49
141 1641 7.745015 TCGCCTGAATGTTATGTTACTTTAAC 58.255 34.615 3.14 3.14 39.11 2.01
159 1659 5.633182 GCACAATTTTATTTTTCTCGCCTGA 59.367 36.000 0.00 0.00 0.00 3.86
162 1662 5.608146 GTGCACAATTTTATTTTTCTCGCC 58.392 37.500 13.17 0.00 0.00 5.54
163 1663 5.297314 CGTGCACAATTTTATTTTTCTCGC 58.703 37.500 18.64 0.00 0.00 5.03
208 1912 5.875910 CCAACTCTCGGTCGATACTATATCT 59.124 44.000 0.00 0.00 0.00 1.98
228 1932 3.500680 TGGTCGACTAAGATTTTGCCAAC 59.499 43.478 16.46 0.00 0.00 3.77
278 2226 1.592400 TAAGGTGACGTCCCAGCGAG 61.592 60.000 20.68 0.00 39.35 5.03
279 2227 0.968901 ATAAGGTGACGTCCCAGCGA 60.969 55.000 20.68 6.29 39.35 4.93
334 5191 8.794553 CGGGACACTATATATAGTTGAAGAGTT 58.205 37.037 20.59 2.85 41.44 3.01
366 5223 1.501337 ATGCACGCACACACTCACAG 61.501 55.000 0.00 0.00 0.00 3.66
367 5224 1.523484 ATGCACGCACACACTCACA 60.523 52.632 0.00 0.00 0.00 3.58
368 5225 1.082561 CATGCACGCACACACTCAC 60.083 57.895 0.00 0.00 0.00 3.51
369 5226 1.523484 ACATGCACGCACACACTCA 60.523 52.632 0.00 0.00 0.00 3.41
370 5227 1.082561 CACATGCACGCACACACTC 60.083 57.895 0.00 0.00 0.00 3.51
371 5228 2.545596 CCACATGCACGCACACACT 61.546 57.895 0.00 0.00 0.00 3.55
372 5229 1.502990 TACCACATGCACGCACACAC 61.503 55.000 0.00 0.00 0.00 3.82
373 5230 0.605050 ATACCACATGCACGCACACA 60.605 50.000 0.00 0.00 0.00 3.72
384 5241 2.846206 ACCATCACCACTGATACCACAT 59.154 45.455 0.00 0.00 35.17 3.21
385 5242 2.027285 CACCATCACCACTGATACCACA 60.027 50.000 0.00 0.00 35.17 4.17
386 5243 2.027192 ACACCATCACCACTGATACCAC 60.027 50.000 0.00 0.00 35.17 4.16
387 5244 2.027285 CACACCATCACCACTGATACCA 60.027 50.000 0.00 0.00 35.17 3.25
388 5245 2.632377 CACACCATCACCACTGATACC 58.368 52.381 0.00 0.00 35.17 2.73
390 5247 1.627834 TGCACACCATCACCACTGATA 59.372 47.619 0.00 0.00 35.17 2.15
393 5250 2.112380 TATGCACACCATCACCACTG 57.888 50.000 0.00 0.00 35.34 3.66
394 5251 4.102996 TCATATATGCACACCATCACCACT 59.897 41.667 7.92 0.00 35.34 4.00
424 5290 1.405821 AGTGAGTACAGCATAGACGCC 59.594 52.381 0.00 0.00 0.00 5.68
498 5382 7.310664 TCACCGATCATATATTAGTTTCGTCC 58.689 38.462 0.00 0.00 0.00 4.79
507 5391 5.592104 ACCGCATCACCGATCATATATTA 57.408 39.130 0.00 0.00 0.00 0.98
527 5411 5.475564 TGATTGCCTCTTTTTACCAAGTACC 59.524 40.000 0.00 0.00 0.00 3.34
619 5520 6.798427 ATATCTATCTATCAACCGCACCAT 57.202 37.500 0.00 0.00 0.00 3.55
641 5542 9.955102 ATGTCAATGCACATCTATCACTAATAT 57.045 29.630 0.00 0.00 30.76 1.28
642 5543 9.428097 GATGTCAATGCACATCTATCACTAATA 57.572 33.333 14.28 0.00 46.37 0.98
643 5544 8.320396 GATGTCAATGCACATCTATCACTAAT 57.680 34.615 14.28 0.00 46.37 1.73
644 5545 7.719778 GATGTCAATGCACATCTATCACTAA 57.280 36.000 14.28 0.00 46.37 2.24
722 5628 4.708177 TGATTTCCTTTCGATCAGGGATC 58.292 43.478 10.54 13.10 35.88 3.36
723 5629 4.778213 TGATTTCCTTTCGATCAGGGAT 57.222 40.909 10.54 6.15 31.50 3.85
724 5630 4.568072 TTGATTTCCTTTCGATCAGGGA 57.432 40.909 10.54 0.08 32.00 4.20
725 5631 5.643379 TTTTGATTTCCTTTCGATCAGGG 57.357 39.130 10.54 0.00 32.00 4.45
726 5632 5.098211 GCTTTTGATTTCCTTTCGATCAGG 58.902 41.667 5.00 5.00 32.00 3.86
727 5633 5.702865 TGCTTTTGATTTCCTTTCGATCAG 58.297 37.500 0.00 0.00 32.00 2.90
728 5634 5.703978 TGCTTTTGATTTCCTTTCGATCA 57.296 34.783 0.00 0.00 0.00 2.92
729 5635 5.061435 GCTTGCTTTTGATTTCCTTTCGATC 59.939 40.000 0.00 0.00 0.00 3.69
742 5648 3.181473 ACATGCTCTTTGCTTGCTTTTGA 60.181 39.130 0.00 0.00 46.78 2.69
807 5713 0.250338 GGCAGGTTTATAGGCGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
808 5714 1.834301 GGCAGGTTTATAGGCGGGA 59.166 57.895 0.00 0.00 0.00 5.14
820 5738 4.295119 GTGTGGTCGACGGCAGGT 62.295 66.667 9.92 0.00 0.00 4.00
823 5741 4.595538 GTGGTGTGGTCGACGGCA 62.596 66.667 9.92 8.02 0.00 5.69
857 5778 4.159506 GGAAATGGAACGGAATGGAATGAA 59.840 41.667 0.00 0.00 0.00 2.57
858 5779 3.699038 GGAAATGGAACGGAATGGAATGA 59.301 43.478 0.00 0.00 0.00 2.57
859 5780 3.446873 TGGAAATGGAACGGAATGGAATG 59.553 43.478 0.00 0.00 0.00 2.67
896 5817 1.205893 GGATCGAGAGCCACTTGACTT 59.794 52.381 2.07 0.00 41.26 3.01
911 5832 0.253044 AGATGTTGGTGGTGGGATCG 59.747 55.000 0.00 0.00 0.00 3.69
915 5836 1.202927 ACAGAAGATGTTGGTGGTGGG 60.203 52.381 0.00 0.00 39.96 4.61
916 5837 2.154462 GACAGAAGATGTTGGTGGTGG 58.846 52.381 0.00 0.00 44.17 4.61
942 5879 2.663196 GCACCAGGAAGCTACGGT 59.337 61.111 0.00 0.00 0.00 4.83
943 5880 2.125106 GGCACCAGGAAGCTACGG 60.125 66.667 0.00 0.00 0.00 4.02
945 5882 1.746991 GCAGGCACCAGGAAGCTAC 60.747 63.158 0.00 0.00 0.00 3.58
947 5884 3.564345 CTGCAGGCACCAGGAAGCT 62.564 63.158 5.57 0.00 0.00 3.74
955 5892 2.045926 CTACCACCTGCAGGCACC 60.046 66.667 33.06 0.00 39.32 5.01
957 5894 0.982852 ATAGCTACCACCTGCAGGCA 60.983 55.000 33.06 14.24 39.32 4.75
958 5895 0.250081 GATAGCTACCACCTGCAGGC 60.250 60.000 33.06 17.21 39.32 4.85
959 5896 1.418334 AGATAGCTACCACCTGCAGG 58.582 55.000 31.60 31.60 42.17 4.85
963 5900 2.032620 ACGGAAGATAGCTACCACCTG 58.967 52.381 0.00 0.00 0.00 4.00
964 5901 2.032620 CACGGAAGATAGCTACCACCT 58.967 52.381 0.00 0.00 0.00 4.00
965 5902 1.755380 ACACGGAAGATAGCTACCACC 59.245 52.381 0.00 0.00 0.00 4.61
966 5903 3.119245 TGAACACGGAAGATAGCTACCAC 60.119 47.826 0.00 0.00 0.00 4.16
967 5904 3.093814 TGAACACGGAAGATAGCTACCA 58.906 45.455 0.00 0.00 0.00 3.25
968 5905 3.119245 TGTGAACACGGAAGATAGCTACC 60.119 47.826 0.00 0.00 0.00 3.18
969 5906 4.106029 TGTGAACACGGAAGATAGCTAC 57.894 45.455 0.00 0.00 0.00 3.58
970 5907 4.645136 AGATGTGAACACGGAAGATAGCTA 59.355 41.667 0.00 0.00 0.00 3.32
971 5908 3.449018 AGATGTGAACACGGAAGATAGCT 59.551 43.478 0.00 0.00 0.00 3.32
972 5909 3.786635 AGATGTGAACACGGAAGATAGC 58.213 45.455 0.57 0.00 0.00 2.97
973 5910 4.142160 TGGAGATGTGAACACGGAAGATAG 60.142 45.833 0.57 0.00 0.00 2.08
974 5911 3.767131 TGGAGATGTGAACACGGAAGATA 59.233 43.478 0.57 0.00 0.00 1.98
975 5912 2.567169 TGGAGATGTGAACACGGAAGAT 59.433 45.455 0.57 0.00 0.00 2.40
976 5913 1.967779 TGGAGATGTGAACACGGAAGA 59.032 47.619 0.57 0.00 0.00 2.87
977 5914 2.455674 TGGAGATGTGAACACGGAAG 57.544 50.000 0.57 0.00 0.00 3.46
978 5915 2.673893 CGATGGAGATGTGAACACGGAA 60.674 50.000 0.57 0.00 0.00 4.30
1089 6034 2.284625 TCCTGCTCCGTCCATGGT 60.285 61.111 12.58 0.00 0.00 3.55
1228 6173 4.246206 CATGCATGCGTGGAGGCG 62.246 66.667 28.79 5.17 35.06 5.52
1229 6174 4.564116 GCATGCATGCGTGGAGGC 62.564 66.667 34.64 20.99 45.64 4.70
1252 6198 0.542805 ATTTTGGTCCCATGCATGCC 59.457 50.000 21.69 16.96 0.00 4.40
1258 6204 5.047802 GGCTACATCATATTTTGGTCCCATG 60.048 44.000 0.00 0.00 0.00 3.66
1259 6205 5.079643 GGCTACATCATATTTTGGTCCCAT 58.920 41.667 0.00 0.00 0.00 4.00
1331 6277 1.302033 AAGGCAGACACAAGAGCGG 60.302 57.895 0.00 0.00 0.00 5.52
1332 6278 1.864862 CAAGGCAGACACAAGAGCG 59.135 57.895 0.00 0.00 0.00 5.03
1351 6297 0.531200 GTCCGGTTGAGACCTGTAGG 59.469 60.000 0.00 0.00 44.20 3.18
1518 6464 2.126071 ATCTCGTTGTCGGTGCGG 60.126 61.111 0.00 0.00 37.69 5.69
1674 6620 0.776451 CGTTGTCGTTCGTTGAGGAG 59.224 55.000 0.00 0.00 0.00 3.69
1675 6621 0.381445 TCGTTGTCGTTCGTTGAGGA 59.619 50.000 0.00 0.00 38.33 3.71
1676 6622 1.415374 ATCGTTGTCGTTCGTTGAGG 58.585 50.000 0.00 0.00 38.33 3.86
1677 6623 3.181546 GGTTATCGTTGTCGTTCGTTGAG 60.182 47.826 0.00 0.00 38.33 3.02
1685 6631 1.973138 CGAGTGGTTATCGTTGTCGT 58.027 50.000 0.00 0.00 38.33 4.34
1695 6641 1.447140 GCCGTGATGCGAGTGGTTA 60.447 57.895 0.00 0.00 44.77 2.85
1699 6645 3.490759 GTGGCCGTGATGCGAGTG 61.491 66.667 0.00 0.00 44.77 3.51
1816 6762 1.269988 CCATGCGTAGGAGTCCATGAG 60.270 57.143 12.86 0.65 37.78 2.90
1847 6793 0.729478 CGGCACTATCATAGACGGCG 60.729 60.000 16.20 16.20 41.24 6.46
1854 6800 1.754380 AAGGCGGCGGCACTATCATA 61.754 55.000 34.87 0.00 42.47 2.15
1981 6927 8.811017 ACTAAGGAAAGATCGATGATGTATGAT 58.189 33.333 0.54 0.00 0.00 2.45
2017 6964 2.092538 AGCATCTTCAGCTAGTTGGCAT 60.093 45.455 6.75 0.00 41.32 4.40
2145 7093 8.286191 TCTATCATACATACACATGGAGCTAG 57.714 38.462 0.00 0.00 36.39 3.42
2146 7094 7.890655 ACTCTATCATACATACACATGGAGCTA 59.109 37.037 0.00 0.00 36.39 3.32
2147 7095 6.723515 ACTCTATCATACATACACATGGAGCT 59.276 38.462 0.00 0.00 36.39 4.09
2148 7096 6.929625 ACTCTATCATACATACACATGGAGC 58.070 40.000 0.00 0.00 36.39 4.70
2269 7219 9.689976 CTGAATTCTCAAGGACTAGTATATGTG 57.310 37.037 7.05 0.00 0.00 3.21
2405 7362 2.213499 CCTACTTCGGCATCAACATCC 58.787 52.381 0.00 0.00 0.00 3.51
2441 7398 4.381411 GCCAGCCTTTAGTTTCGATATCT 58.619 43.478 0.34 0.00 0.00 1.98
2526 7673 7.808381 TGATCGATCTCGGAATACATTTCTTAC 59.192 37.037 25.02 0.00 40.29 2.34
2851 8002 4.082300 GGAGTACTGCAGATCATCGATCAT 60.082 45.833 23.35 0.00 41.12 2.45


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

AutoCloner maintained by Alex Coulton.