Multiple sequence alignment - TraesCS2A01G198900

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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 TraesCS2A01G198900 chr2A 100.000 2178 0 0 766 2943 171085166 171082989 0.000000e+00 4023.0
1 TraesCS2A01G198900 chr2A 100.000 454 0 0 1 454 171085931 171085478 0.000000e+00 839.0
2 TraesCS2A01G198900 chr2B 94.467 1211 48 8 815 2025 216947509 216946318 0.000000e+00 1847.0
3 TraesCS2A01G198900 chr2B 81.421 366 53 11 2259 2617 52634850 52635207 4.800000e-73 285.0
4 TraesCS2A01G198900 chr2B 87.156 218 9 6 845 1054 216952542 216952336 2.280000e-56 230.0
5 TraesCS2A01G198900 chr2B 94.161 137 8 0 277 413 216948106 216947970 2.970000e-50 209.0
6 TraesCS2A01G198900 chr2B 93.846 130 3 4 173 298 216948242 216948114 1.080000e-44 191.0
7 TraesCS2A01G198900 chr2B 85.792 183 14 7 276 454 216952777 216952603 1.800000e-42 183.0
8 TraesCS2A01G198900 chr2B 92.857 126 6 2 1 126 216951139 216951017 2.330000e-41 180.0
9 TraesCS2A01G198900 chr2D 96.104 1001 30 4 832 1832 159861974 159860983 0.000000e+00 1624.0
10 TraesCS2A01G198900 chr2D 77.188 640 94 31 2022 2618 32042661 32043291 2.830000e-85 326.0
11 TraesCS2A01G198900 chr2D 94.472 199 7 3 1828 2025 159855622 159855427 1.330000e-78 303.0
12 TraesCS2A01G198900 chr2D 86.758 219 19 4 193 401 159862266 159862048 4.900000e-58 235.0
13 TraesCS2A01G198900 chr1B 86.885 854 68 14 2022 2863 181436180 181435359 0.000000e+00 917.0
14 TraesCS2A01G198900 chr5D 91.345 647 44 5 2022 2665 560183462 560184099 0.000000e+00 874.0
15 TraesCS2A01G198900 chr5D 96.667 60 2 0 2884 2943 560185713 560185772 1.870000e-17 100.0
16 TraesCS2A01G198900 chr7D 82.911 474 53 17 2023 2479 179519949 179519487 4.570000e-108 401.0
17 TraesCS2A01G198900 chr3B 81.230 309 37 13 2320 2618 725703854 725703557 2.280000e-56 230.0
18 TraesCS2A01G198900 chr3D 94.737 38 2 0 2020 2057 562206738 562206701 3.170000e-05 60.2
19 TraesCS2A01G198900 chr6D 100.000 28 0 0 2020 2047 38227030 38227057 5.000000e-03 52.8


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 TraesCS2A01G198900 chr2A 171082989 171085931 2942 True 2431.000000 4023 100.000000 1 2943 2 chr2A.!!$R1 2942
1 TraesCS2A01G198900 chr2B 216946318 216952777 6459 True 473.333333 1847 91.379833 1 2025 6 chr2B.!!$R1 2024
2 TraesCS2A01G198900 chr2D 159860983 159862266 1283 True 929.500000 1624 91.431000 193 1832 2 chr2D.!!$R2 1639
3 TraesCS2A01G198900 chr2D 32042661 32043291 630 False 326.000000 326 77.188000 2022 2618 1 chr2D.!!$F1 596
4 TraesCS2A01G198900 chr1B 181435359 181436180 821 True 917.000000 917 86.885000 2022 2863 1 chr1B.!!$R1 841
5 TraesCS2A01G198900 chr5D 560183462 560185772 2310 False 487.000000 874 94.006000 2022 2943 2 chr5D.!!$F1 921

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
98 1737 0.107654 AGTTGGATGCCCTTCGTAGC 60.108 55.0 0.0 0.0 0.0 3.58 F
818 5587 0.321653 AACGCATCTCCCTCCAACAC 60.322 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 6159 0.101399 AACCGCAGCGTCTCTATCAG 59.899 55.0 15.05 0.0 0.00 2.90 R
2404 7213 0.100325 TTTGCTTGACCTTGTGCACG 59.900 50.0 13.13 0.0 35.01 5.34 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
24 1663 5.012148 TCGATCTCCTTGGTTCTCTCTTTTT 59.988 40.000 0.00 0.00 0.00 1.94
45 1684 7.921786 TTTTTCCTTGTCGATGTATCAATCT 57.078 32.000 0.00 0.00 0.00 2.40
91 1730 1.135094 ATCGATCAGTTGGATGCCCT 58.865 50.000 0.00 0.00 36.00 5.19
94 1733 1.303309 GATCAGTTGGATGCCCTTCG 58.697 55.000 0.00 0.00 36.00 3.79
98 1737 0.107654 AGTTGGATGCCCTTCGTAGC 60.108 55.000 0.00 0.00 0.00 3.58
105 1744 2.167861 GCCCTTCGTAGCTCGCTTG 61.168 63.158 0.00 0.00 39.67 4.01
127 1766 2.202730 GCTGCAGCTCGACTCCTC 60.203 66.667 31.33 0.00 38.21 3.71
128 1767 2.493973 CTGCAGCTCGACTCCTCC 59.506 66.667 0.00 0.00 0.00 4.30
129 1768 2.036414 TGCAGCTCGACTCCTCCT 59.964 61.111 0.00 0.00 0.00 3.69
130 1769 2.282147 CTGCAGCTCGACTCCTCCTG 62.282 65.000 0.00 0.00 0.00 3.86
131 1770 2.493973 CAGCTCGACTCCTCCTGC 59.506 66.667 0.00 0.00 0.00 4.85
156 4545 7.066284 GCATATATATTGTGCAGGTAAAGAGGG 59.934 40.741 14.47 0.00 38.68 4.30
157 4546 4.862641 ATATTGTGCAGGTAAAGAGGGT 57.137 40.909 0.00 0.00 0.00 4.34
158 4547 3.525800 ATTGTGCAGGTAAAGAGGGTT 57.474 42.857 0.00 0.00 0.00 4.11
159 4548 4.650972 ATTGTGCAGGTAAAGAGGGTTA 57.349 40.909 0.00 0.00 0.00 2.85
160 4549 3.695830 TGTGCAGGTAAAGAGGGTTAG 57.304 47.619 0.00 0.00 0.00 2.34
161 4550 3.244582 TGTGCAGGTAAAGAGGGTTAGA 58.755 45.455 0.00 0.00 0.00 2.10
162 4551 3.007614 TGTGCAGGTAAAGAGGGTTAGAC 59.992 47.826 0.00 0.00 0.00 2.59
163 4552 3.261137 GTGCAGGTAAAGAGGGTTAGACT 59.739 47.826 0.00 0.00 0.00 3.24
164 4553 3.908103 TGCAGGTAAAGAGGGTTAGACTT 59.092 43.478 0.00 0.00 0.00 3.01
165 4554 4.254492 GCAGGTAAAGAGGGTTAGACTTG 58.746 47.826 0.00 0.00 0.00 3.16
166 4555 4.020485 GCAGGTAAAGAGGGTTAGACTTGA 60.020 45.833 0.00 0.00 0.00 3.02
167 4556 5.480205 CAGGTAAAGAGGGTTAGACTTGAC 58.520 45.833 0.00 0.00 0.00 3.18
168 4557 4.531339 AGGTAAAGAGGGTTAGACTTGACC 59.469 45.833 0.00 0.00 42.44 4.02
169 4558 3.679824 AAAGAGGGTTAGACTTGACCG 57.320 47.619 2.64 0.00 36.78 4.79
170 4559 2.599408 AGAGGGTTAGACTTGACCGA 57.401 50.000 0.00 0.00 36.78 4.69
171 4560 2.169330 AGAGGGTTAGACTTGACCGAC 58.831 52.381 0.00 0.54 36.78 4.79
172 4561 1.891150 GAGGGTTAGACTTGACCGACA 59.109 52.381 0.00 0.00 36.78 4.35
173 4562 2.496470 GAGGGTTAGACTTGACCGACAT 59.504 50.000 0.00 0.00 36.78 3.06
174 4563 2.496470 AGGGTTAGACTTGACCGACATC 59.504 50.000 0.00 0.00 36.78 3.06
175 4564 2.496470 GGGTTAGACTTGACCGACATCT 59.504 50.000 0.00 0.00 36.78 2.90
176 4565 3.512680 GGTTAGACTTGACCGACATCTG 58.487 50.000 0.00 0.00 0.00 2.90
177 4566 3.512680 GTTAGACTTGACCGACATCTGG 58.487 50.000 0.00 0.00 0.00 3.86
178 4567 1.924731 AGACTTGACCGACATCTGGA 58.075 50.000 0.00 0.00 0.00 3.86
179 4568 1.821753 AGACTTGACCGACATCTGGAG 59.178 52.381 0.00 0.00 0.00 3.86
189 4578 3.024547 CGACATCTGGAGGGTTAGAGAA 58.975 50.000 0.00 0.00 0.00 2.87
233 4624 3.371063 GACACGACGGGAGGCTGA 61.371 66.667 2.90 0.00 33.72 4.26
331 4754 3.343972 GCAACCTGCACACATCGT 58.656 55.556 0.00 0.00 44.26 3.73
355 4778 7.485913 CGTGATGCTATTTATTAATCCAATGGC 59.514 37.037 16.05 16.05 35.55 4.40
411 4834 2.809446 GGCAACCAACAAACTCTGTTC 58.191 47.619 0.00 0.00 45.50 3.18
412 4835 2.450160 GCAACCAACAAACTCTGTTCG 58.550 47.619 0.00 0.00 45.50 3.95
413 4836 2.450160 CAACCAACAAACTCTGTTCGC 58.550 47.619 0.00 0.00 45.50 4.70
414 4837 1.745232 ACCAACAAACTCTGTTCGCA 58.255 45.000 0.00 0.00 45.50 5.10
415 4838 2.297701 ACCAACAAACTCTGTTCGCAT 58.702 42.857 0.00 0.00 45.50 4.73
416 4839 2.687935 ACCAACAAACTCTGTTCGCATT 59.312 40.909 0.00 0.00 45.50 3.56
417 4840 3.130340 ACCAACAAACTCTGTTCGCATTT 59.870 39.130 0.00 0.00 45.50 2.32
418 4841 3.730715 CCAACAAACTCTGTTCGCATTTC 59.269 43.478 0.00 0.00 45.50 2.17
419 4842 4.350346 CAACAAACTCTGTTCGCATTTCA 58.650 39.130 0.00 0.00 45.50 2.69
420 4843 4.630894 ACAAACTCTGTTCGCATTTCAA 57.369 36.364 0.00 0.00 32.99 2.69
421 4844 4.992688 ACAAACTCTGTTCGCATTTCAAA 58.007 34.783 0.00 0.00 32.99 2.69
422 4845 5.406649 ACAAACTCTGTTCGCATTTCAAAA 58.593 33.333 0.00 0.00 32.99 2.44
423 4846 5.866633 ACAAACTCTGTTCGCATTTCAAAAA 59.133 32.000 0.00 0.00 32.99 1.94
790 5213 1.137513 GTCCAACGTCTCTGTTTCCG 58.862 55.000 0.00 0.00 0.00 4.30
791 5214 1.034356 TCCAACGTCTCTGTTTCCGA 58.966 50.000 0.00 0.00 0.00 4.55
792 5215 1.137513 CCAACGTCTCTGTTTCCGAC 58.862 55.000 0.00 0.00 0.00 4.79
794 5217 3.449042 CGTCTCTGTTTCCGACGC 58.551 61.111 0.00 0.00 43.02 5.19
795 5218 2.087009 CGTCTCTGTTTCCGACGCC 61.087 63.158 0.00 0.00 43.02 5.68
796 5219 1.006571 GTCTCTGTTTCCGACGCCA 60.007 57.895 0.00 0.00 0.00 5.69
797 5220 1.006571 TCTCTGTTTCCGACGCCAC 60.007 57.895 0.00 0.00 0.00 5.01
798 5221 2.027625 CTCTGTTTCCGACGCCACC 61.028 63.158 0.00 0.00 0.00 4.61
799 5222 2.280524 CTGTTTCCGACGCCACCA 60.281 61.111 0.00 0.00 0.00 4.17
800 5223 1.890041 CTGTTTCCGACGCCACCAA 60.890 57.895 0.00 0.00 0.00 3.67
801 5224 2.113131 CTGTTTCCGACGCCACCAAC 62.113 60.000 0.00 0.00 0.00 3.77
802 5225 2.968156 TTTCCGACGCCACCAACG 60.968 61.111 0.00 0.00 0.00 4.10
806 5229 4.147322 CGACGCCACCAACGCATC 62.147 66.667 0.00 0.00 0.00 3.91
807 5230 2.742372 GACGCCACCAACGCATCT 60.742 61.111 0.00 0.00 0.00 2.90
808 5231 2.740714 GACGCCACCAACGCATCTC 61.741 63.158 0.00 0.00 0.00 2.75
809 5232 3.499737 CGCCACCAACGCATCTCC 61.500 66.667 0.00 0.00 0.00 3.71
810 5233 3.134127 GCCACCAACGCATCTCCC 61.134 66.667 0.00 0.00 0.00 4.30
811 5234 2.671070 CCACCAACGCATCTCCCT 59.329 61.111 0.00 0.00 0.00 4.20
812 5235 1.450312 CCACCAACGCATCTCCCTC 60.450 63.158 0.00 0.00 0.00 4.30
813 5236 1.450312 CACCAACGCATCTCCCTCC 60.450 63.158 0.00 0.00 0.00 4.30
818 5587 0.321653 AACGCATCTCCCTCCAACAC 60.322 55.000 0.00 0.00 0.00 3.32
897 5666 3.330720 CCAAACCTCCTCCCCGCT 61.331 66.667 0.00 0.00 0.00 5.52
899 5668 1.377333 CAAACCTCCTCCCCGCTTC 60.377 63.158 0.00 0.00 0.00 3.86
900 5669 2.603652 AAACCTCCTCCCCGCTTCC 61.604 63.158 0.00 0.00 0.00 3.46
1108 5877 3.709633 ACTGCCCGCTCAGCATCA 61.710 61.111 0.00 0.00 40.04 3.07
1390 6159 2.606826 AGGAGTTGGTCGACCCCC 60.607 66.667 31.19 24.04 34.29 5.40
1515 6284 2.930826 AGGTGTTCGACATTGAGGTT 57.069 45.000 0.00 0.00 0.00 3.50
1577 6346 1.014564 GTGGTCTACCGCTTCACAGC 61.015 60.000 5.44 0.00 43.02 4.40
1604 6373 1.330521 GCAGCGTGACAAGAAGTGAAA 59.669 47.619 0.00 0.00 0.00 2.69
1614 6383 3.950395 ACAAGAAGTGAAAGAAGCAGCTT 59.050 39.130 7.60 7.60 0.00 3.74
1615 6384 4.036144 ACAAGAAGTGAAAGAAGCAGCTTC 59.964 41.667 25.46 25.46 40.45 3.86
1640 6409 7.893302 TCTCCAAAAGGTAATGGATGTAATGTT 59.107 33.333 0.00 0.00 44.41 2.71
1671 6440 1.561076 TGCCCATGCTGATTCTACTGT 59.439 47.619 0.00 0.00 38.71 3.55
1672 6441 2.771372 TGCCCATGCTGATTCTACTGTA 59.229 45.455 0.00 0.00 38.71 2.74
1673 6442 3.134458 GCCCATGCTGATTCTACTGTAC 58.866 50.000 0.00 0.00 33.53 2.90
1674 6443 3.181461 GCCCATGCTGATTCTACTGTACT 60.181 47.826 0.00 0.00 33.53 2.73
1675 6444 4.375272 CCCATGCTGATTCTACTGTACTG 58.625 47.826 0.00 0.00 0.00 2.74
1726 6500 1.266718 ACGATGTGACATTGTGCAACC 59.733 47.619 17.24 0.00 34.36 3.77
1729 6503 1.383523 TGTGACATTGTGCAACCGAA 58.616 45.000 0.00 0.00 34.36 4.30
1764 6538 4.006319 CAGGAAATCTTTCTTCCGAGCTT 58.994 43.478 2.93 0.00 45.97 3.74
1819 6593 6.961554 CGAGAATTTAGTTGTATGCTGGTTTC 59.038 38.462 0.00 0.00 0.00 2.78
1826 6600 4.518970 AGTTGTATGCTGGTTTCGATTGTT 59.481 37.500 0.00 0.00 0.00 2.83
1897 6671 5.441500 TCAAAGTGTTGGATTGTAGTTCCA 58.558 37.500 0.00 0.00 41.50 3.53
1910 6684 7.545615 GGATTGTAGTTCCAAATTTCATGAACC 59.454 37.037 7.89 0.00 38.24 3.62
1914 6688 4.218417 AGTTCCAAATTTCATGAACCCTCG 59.782 41.667 7.89 0.00 38.24 4.63
1954 6728 4.641396 CCTGAACTCTATGGTTGTTGACA 58.359 43.478 0.00 0.00 0.00 3.58
1960 6734 8.564574 TGAACTCTATGGTTGTTGACATTTTAC 58.435 33.333 0.00 0.00 0.00 2.01
1964 6738 7.870826 TCTATGGTTGTTGACATTTTACACAG 58.129 34.615 0.00 0.00 0.00 3.66
1965 6739 5.906113 TGGTTGTTGACATTTTACACAGT 57.094 34.783 0.00 0.00 0.00 3.55
1972 6746 4.843147 TGACATTTTACACAGTTGCTTCG 58.157 39.130 0.00 0.00 0.00 3.79
1975 6749 3.766676 TTTTACACAGTTGCTTCGCAA 57.233 38.095 0.00 0.00 46.80 4.85
1988 6762 3.130819 CGCAAGCAACGGGGCATA 61.131 61.111 3.39 0.00 35.83 3.14
2124 6899 5.535406 ACCCTCAAAGTACCTCATATCTACG 59.465 44.000 0.00 0.00 0.00 3.51
2186 6983 7.412063 TCAATTGCACAATCGATCTAGAATTG 58.588 34.615 12.21 12.21 32.19 2.32
2217 7014 7.232127 CCAATGCTTATGGATCCTTAAATCTGT 59.768 37.037 18.05 3.94 40.56 3.41
2295 7104 8.003784 GTCAAAAGAAAACAAACTTCACTTGTG 58.996 33.333 0.00 0.00 37.10 3.33
2404 7213 0.673437 TGCTGCAGCTTTTTGGTACC 59.327 50.000 36.61 4.43 42.66 3.34
2518 7330 3.791887 CGGATCTTAGACATCGTTGTGTC 59.208 47.826 3.34 7.01 46.90 3.67
2529 7341 2.912771 TCGTTGTGTCCACATCAGTTT 58.087 42.857 0.20 0.00 41.52 2.66
2530 7342 2.611751 TCGTTGTGTCCACATCAGTTTG 59.388 45.455 0.20 0.00 41.52 2.93
2531 7343 2.611751 CGTTGTGTCCACATCAGTTTGA 59.388 45.455 0.20 0.00 41.52 2.69
2532 7344 3.064682 CGTTGTGTCCACATCAGTTTGAA 59.935 43.478 0.20 0.00 41.52 2.69
2533 7345 4.601019 GTTGTGTCCACATCAGTTTGAAG 58.399 43.478 0.20 0.00 41.52 3.02
2534 7346 3.884895 TGTGTCCACATCAGTTTGAAGT 58.115 40.909 0.00 0.00 36.21 3.01
2535 7347 3.876914 TGTGTCCACATCAGTTTGAAGTC 59.123 43.478 0.00 0.00 36.21 3.01
2632 7453 4.509970 TCAAACTGGTCAACACAATAGTCG 59.490 41.667 0.00 0.00 0.00 4.18
2792 7624 2.359169 CCGGGAAGCAGTAGAGCCA 61.359 63.158 0.00 0.00 34.23 4.75
2799 7631 1.079819 GCAGTAGAGCCAGTTCGCA 60.080 57.895 0.00 0.00 0.00 5.10
2809 7641 4.664677 AGTTCGCAGCCGCTCGTT 62.665 61.111 10.60 0.00 35.30 3.85
2866 7698 1.597461 GAAACTGGGAGGACGGAGG 59.403 63.158 0.00 0.00 0.00 4.30
2879 7711 3.605895 GGAGGACGAGACCACCTC 58.394 66.667 0.00 0.00 46.44 3.85
2880 7712 1.000646 GGAGGACGAGACCACCTCT 60.001 63.158 0.00 0.00 46.39 3.69
2881 7713 0.612453 GGAGGACGAGACCACCTCTT 60.612 60.000 0.00 0.00 46.39 2.85
2882 7714 0.812549 GAGGACGAGACCACCTCTTC 59.187 60.000 0.00 0.00 44.54 2.87
2894 9249 1.290955 CCTCTTCCGTGGTTGCGTA 59.709 57.895 0.00 0.00 0.00 4.42
2904 9259 1.082104 GGTTGCGTACAGTGCTTGC 60.082 57.895 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.374042 AGAGAGAACCAAGGAGATCGA 57.626 47.619 0.00 0.00 0.00 3.59
1 2 4.464069 AAAGAGAGAACCAAGGAGATCG 57.536 45.455 0.00 0.00 0.00 3.69
24 1663 5.977635 ACAGATTGATACATCGACAAGGAA 58.022 37.500 0.00 0.00 0.00 3.36
25 1664 5.598416 ACAGATTGATACATCGACAAGGA 57.402 39.130 0.00 0.00 0.00 3.36
26 1665 5.503031 GCAACAGATTGATACATCGACAAGG 60.503 44.000 0.00 0.00 38.15 3.61
27 1666 5.496387 GCAACAGATTGATACATCGACAAG 58.504 41.667 0.00 0.00 38.15 3.16
28 1667 4.332543 GGCAACAGATTGATACATCGACAA 59.667 41.667 0.00 0.00 38.15 3.18
91 1730 0.452184 CTCTCCAAGCGAGCTACGAA 59.548 55.000 9.32 0.00 45.77 3.85
129 1768 7.607607 CCTCTTTACCTGCACAATATATATGCA 59.392 37.037 18.65 18.65 46.73 3.96
130 1769 7.066284 CCCTCTTTACCTGCACAATATATATGC 59.934 40.741 12.80 12.80 39.88 3.14
131 1770 8.103305 ACCCTCTTTACCTGCACAATATATATG 58.897 37.037 0.00 0.00 0.00 1.78
151 4540 2.169330 GTCGGTCAAGTCTAACCCTCT 58.831 52.381 0.00 0.00 31.49 3.69
152 4541 1.891150 TGTCGGTCAAGTCTAACCCTC 59.109 52.381 0.00 0.00 31.49 4.30
153 4542 2.005370 TGTCGGTCAAGTCTAACCCT 57.995 50.000 0.00 0.00 31.49 4.34
156 4545 3.192844 TCCAGATGTCGGTCAAGTCTAAC 59.807 47.826 0.00 0.00 0.00 2.34
157 4546 3.427573 TCCAGATGTCGGTCAAGTCTAA 58.572 45.455 0.00 0.00 0.00 2.10
158 4547 3.017442 CTCCAGATGTCGGTCAAGTCTA 58.983 50.000 0.00 0.00 0.00 2.59
159 4548 1.821753 CTCCAGATGTCGGTCAAGTCT 59.178 52.381 0.00 0.00 0.00 3.24
160 4549 1.134965 CCTCCAGATGTCGGTCAAGTC 60.135 57.143 0.00 0.00 0.00 3.01
161 4550 0.898320 CCTCCAGATGTCGGTCAAGT 59.102 55.000 0.00 0.00 0.00 3.16
162 4551 0.176680 CCCTCCAGATGTCGGTCAAG 59.823 60.000 0.00 0.00 0.00 3.02
163 4552 0.544357 ACCCTCCAGATGTCGGTCAA 60.544 55.000 0.00 0.00 0.00 3.18
164 4553 0.544357 AACCCTCCAGATGTCGGTCA 60.544 55.000 0.00 0.00 0.00 4.02
165 4554 1.409427 CTAACCCTCCAGATGTCGGTC 59.591 57.143 0.00 0.00 0.00 4.79
166 4555 1.006758 TCTAACCCTCCAGATGTCGGT 59.993 52.381 0.00 0.00 0.00 4.69
167 4556 1.683917 CTCTAACCCTCCAGATGTCGG 59.316 57.143 0.00 0.00 0.00 4.79
168 4557 2.656002 TCTCTAACCCTCCAGATGTCG 58.344 52.381 0.00 0.00 0.00 4.35
169 4558 4.039852 GGATTCTCTAACCCTCCAGATGTC 59.960 50.000 0.00 0.00 0.00 3.06
170 4559 3.970640 GGATTCTCTAACCCTCCAGATGT 59.029 47.826 0.00 0.00 0.00 3.06
171 4560 3.006323 CGGATTCTCTAACCCTCCAGATG 59.994 52.174 0.00 0.00 0.00 2.90
172 4561 3.235200 CGGATTCTCTAACCCTCCAGAT 58.765 50.000 0.00 0.00 0.00 2.90
173 4562 2.667470 CGGATTCTCTAACCCTCCAGA 58.333 52.381 0.00 0.00 0.00 3.86
174 4563 1.689273 CCGGATTCTCTAACCCTCCAG 59.311 57.143 0.00 0.00 0.00 3.86
175 4564 1.289830 TCCGGATTCTCTAACCCTCCA 59.710 52.381 0.00 0.00 0.00 3.86
176 4565 1.687660 GTCCGGATTCTCTAACCCTCC 59.312 57.143 7.81 0.00 0.00 4.30
177 4566 1.687660 GGTCCGGATTCTCTAACCCTC 59.312 57.143 7.81 0.00 0.00 4.30
178 4567 1.291335 AGGTCCGGATTCTCTAACCCT 59.709 52.381 7.81 2.42 0.00 4.34
179 4568 1.790818 AGGTCCGGATTCTCTAACCC 58.209 55.000 7.81 0.00 0.00 4.11
189 4578 3.758554 CTGAAATCAAACAAGGTCCGGAT 59.241 43.478 7.81 0.00 0.00 4.18
256 4647 6.587990 TGTTTTGTTCATTGTTTGACACGATT 59.412 30.769 0.00 0.00 32.84 3.34
268 4659 7.505646 TGTTTCGTCTTTTGTTTTGTTCATTG 58.494 30.769 0.00 0.00 0.00 2.82
272 4663 5.444087 GCCTGTTTCGTCTTTTGTTTTGTTC 60.444 40.000 0.00 0.00 0.00 3.18
331 4754 8.525316 CAGCCATTGGATTAATAAATAGCATCA 58.475 33.333 6.95 0.00 0.00 3.07
342 4765 5.972107 GCTATCACAGCCATTGGATTAAT 57.028 39.130 6.95 0.00 45.23 1.40
355 4778 6.486253 TTTGCTAAAACTCAGCTATCACAG 57.514 37.500 0.00 0.00 39.83 3.66
425 4848 7.119262 CCATTATAGTGGTCGAACAGAGTTTTT 59.881 37.037 1.63 0.00 34.46 1.94
426 4849 6.594159 CCATTATAGTGGTCGAACAGAGTTTT 59.406 38.462 1.63 0.00 34.46 2.43
427 4850 6.106673 CCATTATAGTGGTCGAACAGAGTTT 58.893 40.000 1.63 0.00 34.46 2.66
790 5213 2.740714 GAGATGCGTTGGTGGCGTC 61.741 63.158 0.00 0.00 44.76 5.19
791 5214 2.742372 GAGATGCGTTGGTGGCGT 60.742 61.111 0.00 0.00 0.00 5.68
792 5215 3.499737 GGAGATGCGTTGGTGGCG 61.500 66.667 0.00 0.00 0.00 5.69
793 5216 3.134127 GGGAGATGCGTTGGTGGC 61.134 66.667 0.00 0.00 0.00 5.01
794 5217 1.450312 GAGGGAGATGCGTTGGTGG 60.450 63.158 0.00 0.00 0.00 4.61
795 5218 1.450312 GGAGGGAGATGCGTTGGTG 60.450 63.158 0.00 0.00 0.00 4.17
796 5219 1.488705 TTGGAGGGAGATGCGTTGGT 61.489 55.000 0.00 0.00 0.00 3.67
797 5220 1.026718 GTTGGAGGGAGATGCGTTGG 61.027 60.000 0.00 0.00 0.00 3.77
798 5221 0.321564 TGTTGGAGGGAGATGCGTTG 60.322 55.000 0.00 0.00 0.00 4.10
799 5222 0.321653 GTGTTGGAGGGAGATGCGTT 60.322 55.000 0.00 0.00 0.00 4.84
800 5223 1.296715 GTGTTGGAGGGAGATGCGT 59.703 57.895 0.00 0.00 0.00 5.24
801 5224 1.021390 GTGTGTTGGAGGGAGATGCG 61.021 60.000 0.00 0.00 0.00 4.73
802 5225 0.678048 GGTGTGTTGGAGGGAGATGC 60.678 60.000 0.00 0.00 0.00 3.91
803 5226 0.035056 GGGTGTGTTGGAGGGAGATG 60.035 60.000 0.00 0.00 0.00 2.90
804 5227 1.553690 CGGGTGTGTTGGAGGGAGAT 61.554 60.000 0.00 0.00 0.00 2.75
805 5228 2.214216 CGGGTGTGTTGGAGGGAGA 61.214 63.158 0.00 0.00 0.00 3.71
806 5229 2.347490 CGGGTGTGTTGGAGGGAG 59.653 66.667 0.00 0.00 0.00 4.30
807 5230 3.948719 GCGGGTGTGTTGGAGGGA 61.949 66.667 0.00 0.00 0.00 4.20
809 5232 2.191786 TATGGCGGGTGTGTTGGAGG 62.192 60.000 0.00 0.00 0.00 4.30
810 5233 0.107214 ATATGGCGGGTGTGTTGGAG 60.107 55.000 0.00 0.00 0.00 3.86
811 5234 0.107410 GATATGGCGGGTGTGTTGGA 60.107 55.000 0.00 0.00 0.00 3.53
812 5235 1.101049 GGATATGGCGGGTGTGTTGG 61.101 60.000 0.00 0.00 0.00 3.77
813 5236 0.107214 AGGATATGGCGGGTGTGTTG 60.107 55.000 0.00 0.00 0.00 3.33
818 5587 1.302033 GCAGAGGATATGGCGGGTG 60.302 63.158 0.00 0.00 0.00 4.61
932 5701 1.304381 TGGAATTGGTGGAGCTGCC 60.304 57.895 1.53 0.00 37.10 4.85
1089 5858 4.790962 ATGCTGAGCGGGCAGTGG 62.791 66.667 0.00 0.00 43.15 4.00
1390 6159 0.101399 AACCGCAGCGTCTCTATCAG 59.899 55.000 15.05 0.00 0.00 2.90
1515 6284 0.541764 GGGGTGGATCCTTGTGCAAA 60.542 55.000 14.23 0.00 36.25 3.68
1577 6346 0.162507 CTTGTCACGCTGCTTCTTCG 59.837 55.000 0.00 0.00 0.00 3.79
1614 6383 7.410174 ACATTACATCCATTACCTTTTGGAGA 58.590 34.615 0.00 0.00 44.87 3.71
1615 6384 7.645058 ACATTACATCCATTACCTTTTGGAG 57.355 36.000 0.00 0.00 44.87 3.86
1640 6409 0.176219 GCATGGGCATAAGCAAGCAA 59.824 50.000 0.00 0.00 44.61 3.91
1671 6440 8.671384 ACATTTTGTGTTTAACTCTAGCAGTA 57.329 30.769 0.00 0.00 38.01 2.74
1672 6441 7.568199 ACATTTTGTGTTTAACTCTAGCAGT 57.432 32.000 0.00 0.00 38.01 4.40
1700 6474 3.370276 CACAATGTCACATCGTTTGCAA 58.630 40.909 0.00 0.00 0.00 4.08
1726 6500 9.463443 AAGATTTCCTGTTTAATTTTGTCTTCG 57.537 29.630 0.00 0.00 0.00 3.79
1764 6538 3.749226 TGCACAATGTGATACTGTTCCA 58.251 40.909 18.66 0.00 35.23 3.53
1819 6593 3.439241 GCAGAAGCACCCGAACAATCG 62.439 57.143 0.00 0.00 44.07 3.34
1826 6600 4.704833 GCCAGCAGAAGCACCCGA 62.705 66.667 0.00 0.00 45.49 5.14
1897 6671 2.807676 AGGCGAGGGTTCATGAAATTT 58.192 42.857 10.35 0.00 0.00 1.82
1910 6684 5.473504 AGGCAATGTATTATTTTAGGCGAGG 59.526 40.000 0.00 0.00 0.00 4.63
1914 6688 7.716612 AGTTCAGGCAATGTATTATTTTAGGC 58.283 34.615 0.00 0.00 0.00 3.93
1972 6746 2.800736 CTATGCCCCGTTGCTTGC 59.199 61.111 0.00 0.00 0.00 4.01
1975 6749 0.684153 ATTTGCTATGCCCCGTTGCT 60.684 50.000 0.00 0.00 0.00 3.91
1978 6752 2.301583 ACAAAATTTGCTATGCCCCGTT 59.698 40.909 5.52 0.00 0.00 4.44
1980 6754 2.671130 ACAAAATTTGCTATGCCCCG 57.329 45.000 5.52 0.00 0.00 5.73
1981 6755 4.736126 ACTACAAAATTTGCTATGCCCC 57.264 40.909 5.52 0.00 0.00 5.80
1983 6757 6.183360 GCTCAAACTACAAAATTTGCTATGCC 60.183 38.462 5.52 0.00 36.06 4.40
1984 6758 6.587608 AGCTCAAACTACAAAATTTGCTATGC 59.412 34.615 5.52 0.79 36.06 3.14
1988 6762 6.258507 CCAAAGCTCAAACTACAAAATTTGCT 59.741 34.615 5.52 0.00 36.06 3.91
2142 6917 6.964807 ATTGAGCCATATTGTATGCTTTCA 57.035 33.333 0.00 0.00 33.41 2.69
2147 6922 4.682860 GTGCAATTGAGCCATATTGTATGC 59.317 41.667 10.34 0.00 34.88 3.14
2148 6923 5.834169 TGTGCAATTGAGCCATATTGTATG 58.166 37.500 10.34 0.00 34.88 2.39
2186 6983 4.218312 AGGATCCATAAGCATTGGGTTTC 58.782 43.478 15.82 0.00 35.99 2.78
2404 7213 0.100325 TTTGCTTGACCTTGTGCACG 59.900 50.000 13.13 0.00 35.01 5.34
2479 7291 3.559238 TCCGCTCAATTTTTCTGCTTC 57.441 42.857 0.00 0.00 0.00 3.86
2486 7298 6.238211 CGATGTCTAAGATCCGCTCAATTTTT 60.238 38.462 0.00 0.00 0.00 1.94
2491 7303 2.688446 ACGATGTCTAAGATCCGCTCAA 59.312 45.455 0.00 0.00 0.00 3.02
2518 7330 4.023707 GGTTCAGACTTCAAACTGATGTGG 60.024 45.833 0.00 0.00 41.71 4.17
2529 7341 2.294233 GCATTTGCTGGTTCAGACTTCA 59.706 45.455 0.00 0.00 38.21 3.02
2530 7342 2.294233 TGCATTTGCTGGTTCAGACTTC 59.706 45.455 3.94 0.00 42.66 3.01
2531 7343 2.309613 TGCATTTGCTGGTTCAGACTT 58.690 42.857 3.94 0.00 42.66 3.01
2532 7344 1.985473 TGCATTTGCTGGTTCAGACT 58.015 45.000 3.94 0.00 42.66 3.24
2533 7345 2.991190 CAATGCATTTGCTGGTTCAGAC 59.009 45.455 9.83 0.00 42.66 3.51
2534 7346 2.892215 TCAATGCATTTGCTGGTTCAGA 59.108 40.909 9.83 0.00 42.66 3.27
2535 7347 3.306917 TCAATGCATTTGCTGGTTCAG 57.693 42.857 9.83 0.00 42.66 3.02
2632 7453 2.514824 GGACAGATTGCTCCGGGC 60.515 66.667 0.00 4.52 42.22 6.13
2774 7606 2.303549 CTGGCTCTACTGCTTCCCGG 62.304 65.000 0.00 0.00 0.00 5.73
2775 7607 1.142748 CTGGCTCTACTGCTTCCCG 59.857 63.158 0.00 0.00 0.00 5.14
2779 7611 0.390472 GCGAACTGGCTCTACTGCTT 60.390 55.000 0.00 0.00 0.00 3.91
2809 7641 1.880894 CCTCGACCTAACTCGTGCA 59.119 57.895 0.00 0.00 35.10 4.57
2837 7669 2.033194 CCAGTTTCCTTCGACCCGC 61.033 63.158 0.00 0.00 0.00 6.13
2843 7675 0.389948 CGTCCTCCCAGTTTCCTTCG 60.390 60.000 0.00 0.00 0.00 3.79
2866 7698 1.242665 ACGGAAGAGGTGGTCTCGTC 61.243 60.000 0.00 0.00 46.82 4.20
2877 7709 0.319211 TGTACGCAACCACGGAAGAG 60.319 55.000 0.00 0.00 37.37 2.85
2878 7710 0.319211 CTGTACGCAACCACGGAAGA 60.319 55.000 0.00 0.00 37.37 2.87
2879 7711 0.599204 ACTGTACGCAACCACGGAAG 60.599 55.000 0.00 0.00 37.37 3.46
2880 7712 0.876777 CACTGTACGCAACCACGGAA 60.877 55.000 0.00 0.00 37.37 4.30
2881 7713 1.300311 CACTGTACGCAACCACGGA 60.300 57.895 0.00 0.00 37.37 4.69
2882 7714 2.950172 GCACTGTACGCAACCACGG 61.950 63.158 0.00 0.00 37.37 4.94
2894 9249 1.002868 CTAGCCCAGCAAGCACTGT 60.003 57.895 0.00 0.00 35.83 3.55


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

AutoCloner maintained by Alex Coulton.