Multiple sequence alignment - TraesCS2A01G529100

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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 TraesCS2A01G529100 chr2A 100.000 2680 0 0 1 2680 747698693 747696014 0.000000e+00 4950
1 TraesCS2A01G529100 chr2A 93.114 1249 86 0 724 1972 747842408 747841160 0.000000e+00 1831
2 TraesCS2A01G529100 chr2A 92.794 1249 88 1 724 1972 747727852 747726606 0.000000e+00 1807
3 TraesCS2A01G529100 chr2A 92.794 1249 88 1 724 1972 747780961 747779715 0.000000e+00 1807
4 TraesCS2A01G529100 chr2A 92.634 1249 90 1 724 1972 747734178 747732932 0.000000e+00 1796
5 TraesCS2A01G529100 chr2A 92.634 1249 90 1 724 1972 747747342 747746096 0.000000e+00 1796
6 TraesCS2A01G529100 chr2A 92.554 1249 91 1 724 1972 747817131 747815885 0.000000e+00 1790
7 TraesCS2A01G529100 chr2A 92.554 1249 91 1 724 1972 747820269 747819023 0.000000e+00 1790
8 TraesCS2A01G529100 chr2A 92.486 1251 90 3 724 1972 747839321 747838073 0.000000e+00 1786
9 TraesCS2A01G529100 chr2A 92.474 1249 92 1 724 1972 747743691 747742445 0.000000e+00 1784
10 TraesCS2A01G529100 chr2A 88.469 1058 91 13 1651 2680 747844601 747843547 0.000000e+00 1249
11 TraesCS2A01G529100 chr2A 91.561 711 57 3 1972 2680 747732905 747732196 0.000000e+00 977
12 TraesCS2A01G529100 chr2A 91.561 711 57 3 1972 2680 747815858 747815149 0.000000e+00 977
13 TraesCS2A01G529100 chr2A 91.421 711 58 3 1972 2680 747723442 747722733 0.000000e+00 972
14 TraesCS2A01G529100 chr2A 91.421 711 56 5 1972 2680 747776499 747775792 0.000000e+00 970
15 TraesCS2A01G529100 chr2A 91.280 711 58 4 1972 2680 747720252 747719544 0.000000e+00 966
16 TraesCS2A01G529100 chr2A 91.139 711 59 4 1972 2680 747779688 747778980 0.000000e+00 961
17 TraesCS2A01G529100 chr2A 91.139 711 59 4 1972 2680 747812668 747811960 0.000000e+00 961
18 TraesCS2A01G529100 chr2A 93.731 335 18 3 1 333 86722592 86722259 1.430000e-137 499
19 TraesCS2A01G529100 chrUn 91.421 711 58 3 1972 2680 420896076 420896785 0.000000e+00 972
20 TraesCS2A01G529100 chr1A 88.646 687 58 14 1 684 232154815 232154146 0.000000e+00 819
21 TraesCS2A01G529100 chr1D 86.880 686 74 12 21 694 316258556 316259237 0.000000e+00 754
22 TraesCS2A01G529100 chr1D 86.319 709 75 19 2 694 151117894 151118596 0.000000e+00 752
23 TraesCS2A01G529100 chr1D 85.755 695 78 19 2 681 151112056 151112744 0.000000e+00 715
24 TraesCS2A01G529100 chr3A 85.406 603 72 16 98 688 282036355 282036953 1.760000e-171 612
25 TraesCS2A01G529100 chr3A 95.031 322 15 1 1 322 694122885 694122565 3.080000e-139 505
26 TraesCS2A01G529100 chr6A 93.300 403 26 1 323 725 201345272 201345673 6.390000e-166 593
27 TraesCS2A01G529100 chr6A 93.994 333 17 3 1 333 458671061 458671390 3.980000e-138 501
28 TraesCS2A01G529100 chr5A 93.284 402 26 1 323 724 312357339 312356939 2.300000e-165 592
29 TraesCS2A01G529100 chr4D 93.069 404 28 0 323 726 453951882 453951479 2.300000e-165 592
30 TraesCS2A01G529100 chr4A 93.284 402 25 2 323 724 165099182 165099581 2.300000e-165 592
31 TraesCS2A01G529100 chr6B 81.848 617 85 24 21 621 449526345 449526950 6.670000e-136 494


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 TraesCS2A01G529100 chr2A 747696014 747698693 2679 True 4950.000000 4950 100.000000 1 2680 1 chr2A.!!$R2 2679
1 TraesCS2A01G529100 chr2A 747742445 747747342 4897 True 1790.000000 1796 92.554000 724 1972 2 chr2A.!!$R5 1248
2 TraesCS2A01G529100 chr2A 747838073 747844601 6528 True 1622.000000 1831 91.356333 724 2680 3 chr2A.!!$R8 1956
3 TraesCS2A01G529100 chr2A 747732196 747734178 1982 True 1386.500000 1796 92.097500 724 2680 2 chr2A.!!$R4 1956
4 TraesCS2A01G529100 chr2A 747811960 747820269 8309 True 1379.500000 1790 91.952000 724 2680 4 chr2A.!!$R7 1956
5 TraesCS2A01G529100 chr2A 747719544 747727852 8308 True 1248.333333 1807 91.831667 724 2680 3 chr2A.!!$R3 1956
6 TraesCS2A01G529100 chr2A 747775792 747780961 5169 True 1246.000000 1807 91.784667 724 2680 3 chr2A.!!$R6 1956
7 TraesCS2A01G529100 chrUn 420896076 420896785 709 False 972.000000 972 91.421000 1972 2680 1 chrUn.!!$F1 708
8 TraesCS2A01G529100 chr1A 232154146 232154815 669 True 819.000000 819 88.646000 1 684 1 chr1A.!!$R1 683
9 TraesCS2A01G529100 chr1D 316258556 316259237 681 False 754.000000 754 86.880000 21 694 1 chr1D.!!$F3 673
10 TraesCS2A01G529100 chr1D 151117894 151118596 702 False 752.000000 752 86.319000 2 694 1 chr1D.!!$F2 692
11 TraesCS2A01G529100 chr1D 151112056 151112744 688 False 715.000000 715 85.755000 2 681 1 chr1D.!!$F1 679
12 TraesCS2A01G529100 chr3A 282036355 282036953 598 False 612.000000 612 85.406000 98 688 1 chr3A.!!$F1 590
13 TraesCS2A01G529100 chr6B 449526345 449526950 605 False 494.000000 494 81.848000 21 621 1 chr6B.!!$F1 600

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
717 737 0.317479 GGTCTATTGGGATCGGGTCG 59.683 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 13496 0.519519 TTAGCGGTGGTCATTTTGCG 59.48 50.0 0.0 0.0 0.0 4.85 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
67 69 3.659786 TCGATTGTTTCTTGACGTCCAT 58.340 40.909 14.12 0.00 0.00 3.41
72 74 3.750371 TGTTTCTTGACGTCCATTCCAT 58.250 40.909 14.12 0.00 0.00 3.41
115 117 2.745281 CCAAAAATAACGCTCCCGAAGA 59.255 45.455 0.00 0.00 38.29 2.87
164 166 6.876789 TGATATTCCTTTTCTGCGAAACACTA 59.123 34.615 3.71 0.00 0.00 2.74
176 178 5.833082 TGCGAAACACTAAAATAGGCAAAA 58.167 33.333 0.00 0.00 0.00 2.44
212 218 1.057851 TGGGCCTCCGGTTAATAGGG 61.058 60.000 4.53 0.00 35.24 3.53
341 351 1.452108 GCCTCCACCAGCCACATAC 60.452 63.158 0.00 0.00 0.00 2.39
356 366 4.558697 GCCACATACGCATGTAGTGATAGA 60.559 45.833 0.00 0.00 43.73 1.98
408 420 2.440517 TGCCAGCATATTCCATGTGT 57.559 45.000 0.00 0.00 0.00 3.72
492 507 3.257375 AGGTCGTTGTTATGCACTCAGTA 59.743 43.478 0.00 0.00 0.00 2.74
493 508 4.081642 AGGTCGTTGTTATGCACTCAGTAT 60.082 41.667 0.00 0.00 0.00 2.12
500 515 1.372582 ATGCACTCAGTATTGCCGTG 58.627 50.000 0.00 4.04 38.00 4.94
503 518 1.645034 CACTCAGTATTGCCGTGGAG 58.355 55.000 0.00 0.00 0.00 3.86
504 519 1.066858 CACTCAGTATTGCCGTGGAGT 60.067 52.381 0.00 0.00 36.12 3.85
506 521 2.002586 CTCAGTATTGCCGTGGAGTTG 58.997 52.381 0.00 0.00 0.00 3.16
521 536 5.440610 GTGGAGTTGGATGGACTCATTTAT 58.559 41.667 6.59 0.00 44.15 1.40
528 543 6.425210 TGGATGGACTCATTTATCTTCGAT 57.575 37.500 0.00 0.00 32.98 3.59
553 570 6.989759 TGCTTCCGCAGTTATCATATTTAGAA 59.010 34.615 0.00 0.00 42.25 2.10
628 646 6.808008 AATAAGTGTGTGATTGAACTCTGG 57.192 37.500 0.00 0.00 0.00 3.86
660 680 2.167487 TGAGTACTGTGTGTGTCAGCAA 59.833 45.455 0.00 0.00 36.50 3.91
684 704 2.368548 CCGATCCAGGGATGACACATAA 59.631 50.000 5.35 0.00 34.60 1.90
689 709 1.935873 CAGGGATGACACATAAGCACG 59.064 52.381 0.00 0.00 0.00 5.34
694 714 2.363788 TGACACATAAGCACGGAGAC 57.636 50.000 0.00 0.00 0.00 3.36
697 717 3.119602 TGACACATAAGCACGGAGACTAC 60.120 47.826 0.00 0.00 0.00 2.73
698 718 2.159421 ACACATAAGCACGGAGACTACG 60.159 50.000 5.27 5.27 37.36 3.51
699 719 1.404391 ACATAAGCACGGAGACTACGG 59.596 52.381 12.67 1.50 35.23 4.02
701 721 1.089920 TAAGCACGGAGACTACGGTC 58.910 55.000 12.67 2.28 42.41 4.79
713 733 2.228343 GACTACGGTCTATTGGGATCGG 59.772 54.545 2.38 0.00 43.25 4.18
715 735 0.398098 ACGGTCTATTGGGATCGGGT 60.398 55.000 2.38 0.00 43.25 5.28
717 737 0.317479 GGTCTATTGGGATCGGGTCG 59.683 60.000 0.00 0.00 0.00 4.79
718 738 0.319641 GTCTATTGGGATCGGGTCGC 60.320 60.000 0.00 0.00 40.04 5.19
719 739 0.469331 TCTATTGGGATCGGGTCGCT 60.469 55.000 6.87 0.00 40.27 4.93
720 740 1.202964 TCTATTGGGATCGGGTCGCTA 60.203 52.381 6.87 0.00 40.27 4.26
721 741 0.963962 TATTGGGATCGGGTCGCTAC 59.036 55.000 6.87 0.00 40.27 3.58
722 742 1.046472 ATTGGGATCGGGTCGCTACA 61.046 55.000 6.87 0.00 40.27 2.74
733 2204 2.134346 GGTCGCTACAACACCGTAAAA 58.866 47.619 0.00 0.00 0.00 1.52
739 2210 6.300668 GTCGCTACAACACCGTAAAATTTTAC 59.699 38.462 24.95 24.95 39.62 2.01
741 2212 6.301372 CGCTACAACACCGTAAAATTTTACAG 59.699 38.462 30.61 24.82 42.34 2.74
843 5452 9.378551 ACAGAAGCATAATTTCTTATTGTACGA 57.621 29.630 0.00 0.00 32.75 3.43
973 5582 2.863401 ACATGCGCGAGTACTAATCA 57.137 45.000 12.10 0.00 0.00 2.57
1074 5683 2.288579 CCACACAACAAGCAAGCATCAT 60.289 45.455 0.00 0.00 0.00 2.45
1076 5685 2.029649 ACACAACAAGCAAGCATCATCC 60.030 45.455 0.00 0.00 0.00 3.51
1220 5829 3.077907 CCACTGTCATCCCCCGTT 58.922 61.111 0.00 0.00 0.00 4.44
1268 5877 1.378531 TTGCTCTCAAAGTGTGCGTT 58.621 45.000 0.00 0.00 0.00 4.84
1274 5883 2.931325 TCTCAAAGTGTGCGTTAACGTT 59.069 40.909 27.28 11.91 42.22 3.99
1283 5892 2.519826 CGTTAACGTTCGCTTGGGA 58.480 52.632 19.75 0.00 34.11 4.37
1320 5929 1.228367 AAGAACCAGTGCTGCCAGG 60.228 57.895 0.00 0.00 0.00 4.45
1365 5974 1.876799 CATACTGTTTGTGTTCCGCCA 59.123 47.619 0.00 0.00 0.00 5.69
1378 5987 2.672651 CGCCATCACCCAAGCACA 60.673 61.111 0.00 0.00 0.00 4.57
1396 6005 1.146930 ATGCCCGTGTCTATGCCAG 59.853 57.895 0.00 0.00 0.00 4.85
1397 6006 2.203070 GCCCGTGTCTATGCCAGG 60.203 66.667 0.00 0.00 0.00 4.45
1497 6106 0.685097 GTGAACACCTAGCCTCACCA 59.315 55.000 0.00 0.00 33.57 4.17
1523 6132 0.956633 CTCAATGTGTGCAAGCAGGT 59.043 50.000 0.00 0.00 0.00 4.00
1613 9359 2.692041 ACCTTCCGTACTAGCATGTACC 59.308 50.000 11.81 0.00 39.51 3.34
1640 9386 2.762327 GGACCCGACTAAACCAGTGATA 59.238 50.000 0.00 0.00 37.72 2.15
1641 9387 3.429960 GGACCCGACTAAACCAGTGATAC 60.430 52.174 0.00 0.00 37.72 2.24
1671 9419 0.897621 ATCATGTCCAGTGCGAGTGA 59.102 50.000 0.00 0.00 0.00 3.41
1692 9440 7.445121 AGTGATCATCTAAATAAGAATCCGCA 58.555 34.615 0.00 0.00 37.89 5.69
1695 9443 6.861065 TCATCTAAATAAGAATCCGCAACC 57.139 37.500 0.00 0.00 37.89 3.77
1752 9500 5.133941 TGCCTTTTTGTCTGTGTGGTAATA 58.866 37.500 0.00 0.00 0.00 0.98
1791 9539 4.398044 TCCTATGTGAAAATTTTCCCGAGC 59.602 41.667 24.51 12.02 36.36 5.03
1844 9592 0.944311 ACTCACAACGTAGCTTGCCG 60.944 55.000 0.00 0.00 0.00 5.69
1856 9604 1.956477 AGCTTGCCGAGTGAATTTGTT 59.044 42.857 0.00 0.00 0.00 2.83
1862 9610 2.161609 GCCGAGTGAATTTGTTAGGGTG 59.838 50.000 0.00 0.00 0.00 4.61
1867 9615 4.332828 AGTGAATTTGTTAGGGTGGTAGC 58.667 43.478 0.00 0.00 0.00 3.58
1895 9643 2.034878 CCATCACAGGCTCTAGTGCTA 58.965 52.381 15.85 0.00 35.76 3.49
1936 9684 4.439837 GGCATCAAAAAGCTCAAGGATCTC 60.440 45.833 0.00 0.00 0.00 2.75
2004 9806 0.973632 TAGTTCGCTCAGAAAGGCCA 59.026 50.000 5.01 0.00 41.10 5.36
2005 9807 0.108585 AGTTCGCTCAGAAAGGCCAA 59.891 50.000 5.01 0.00 41.10 4.52
2016 9818 3.129988 CAGAAAGGCCAATTGACATCTCC 59.870 47.826 5.01 0.00 0.00 3.71
2017 9819 2.905415 AAGGCCAATTGACATCTCCA 57.095 45.000 5.01 0.00 0.00 3.86
2020 9822 4.524802 AGGCCAATTGACATCTCCATAA 57.475 40.909 5.01 0.00 0.00 1.90
2021 9823 5.070823 AGGCCAATTGACATCTCCATAAT 57.929 39.130 5.01 0.00 0.00 1.28
2166 9968 2.741759 TTGAGCACTCTACAATGCGA 57.258 45.000 0.00 0.00 46.74 5.10
2246 10048 5.258051 AGGTTTAACATCCGAAAAGGCATA 58.742 37.500 0.00 0.00 40.77 3.14
2293 10097 2.093341 AGGATTGCATGTTTTGGCCATC 60.093 45.455 6.09 0.54 32.94 3.51
2296 10100 1.350071 TGCATGTTTTGGCCATCCTT 58.650 45.000 6.09 0.00 0.00 3.36
2306 10110 6.261826 TGTTTTGGCCATCCTTTGTTTATTTG 59.738 34.615 6.09 0.00 0.00 2.32
2354 10158 6.484288 TGTATTCCAGATTCCTCAACAACAT 58.516 36.000 0.00 0.00 0.00 2.71
2414 10218 0.746923 GTAACCATGAAGCCCCCGAC 60.747 60.000 0.00 0.00 0.00 4.79
2433 10237 1.167851 CGGTGACAAGCCATCACATT 58.832 50.000 12.96 0.00 46.89 2.71
2497 13489 1.985159 ACCTAGGTGCAAGATCCAACA 59.015 47.619 15.42 0.00 0.00 3.33
2504 13496 3.378427 GGTGCAAGATCCAACATAACTCC 59.622 47.826 0.00 0.00 0.00 3.85
2545 16726 9.961265 GCTAACACTTACTATTTTTCCAAAACT 57.039 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 2.912771 ACAAACGTGATCCACAAGACA 58.087 42.857 0.00 0.00 33.40 3.41
176 178 2.356022 GCCCAGCCCAAATTGCTATTTT 60.356 45.455 3.23 0.00 36.81 1.82
180 183 1.685421 GGCCCAGCCCAAATTGCTA 60.685 57.895 0.00 0.00 44.06 3.49
341 351 8.076714 ACAAATAACATCTATCACTACATGCG 57.923 34.615 0.00 0.00 0.00 4.73
356 366 8.192774 CACCATAGAGCAATGAACAAATAACAT 58.807 33.333 0.00 0.00 0.00 2.71
379 390 4.022849 GGAATATGCTGGCAAGATAACACC 60.023 45.833 0.00 0.00 0.00 4.16
408 420 0.882927 GTTGCAGCCGTGTAGGTCAA 60.883 55.000 0.00 0.00 43.70 3.18
443 458 4.691216 GCACCTTACTCTTCGTCTGAAAAT 59.309 41.667 0.00 0.00 32.66 1.82
492 507 0.680921 CCATCCAACTCCACGGCAAT 60.681 55.000 0.00 0.00 0.00 3.56
493 508 1.303236 CCATCCAACTCCACGGCAA 60.303 57.895 0.00 0.00 0.00 4.52
500 515 5.934781 AGATAAATGAGTCCATCCAACTCC 58.065 41.667 1.17 0.00 42.03 3.85
503 518 6.049149 TCGAAGATAAATGAGTCCATCCAAC 58.951 40.000 0.00 0.00 31.40 3.77
504 519 6.233905 TCGAAGATAAATGAGTCCATCCAA 57.766 37.500 0.00 0.00 31.40 3.53
506 521 5.121454 GCATCGAAGATAAATGAGTCCATCC 59.879 44.000 0.00 0.00 45.12 3.51
577 594 9.521503 CATCGAATGTCTCAGAAAGATTACTTA 57.478 33.333 0.00 0.00 36.11 2.24
578 595 8.037758 ACATCGAATGTCTCAGAAAGATTACTT 58.962 33.333 0.00 0.00 39.92 2.24
582 599 8.954950 ATTACATCGAATGTCTCAGAAAGATT 57.045 30.769 4.15 0.00 43.67 2.40
585 602 9.307121 ACTTATTACATCGAATGTCTCAGAAAG 57.693 33.333 4.15 4.82 43.67 2.62
628 646 7.817962 ACACACACAGTACTCAAGGATTTATAC 59.182 37.037 0.00 0.00 0.00 1.47
660 680 1.971357 GTGTCATCCCTGGATCGGTAT 59.029 52.381 0.00 0.00 31.62 2.73
684 704 3.588336 GACCGTAGTCTCCGTGCT 58.412 61.111 0.00 0.00 40.10 4.40
694 714 1.544691 CCCGATCCCAATAGACCGTAG 59.455 57.143 0.00 0.00 0.00 3.51
697 717 0.317479 GACCCGATCCCAATAGACCG 59.683 60.000 0.00 0.00 0.00 4.79
698 718 0.317479 CGACCCGATCCCAATAGACC 59.683 60.000 0.00 0.00 0.00 3.85
699 719 0.319641 GCGACCCGATCCCAATAGAC 60.320 60.000 0.00 0.00 0.00 2.59
701 721 1.067776 GTAGCGACCCGATCCCAATAG 60.068 57.143 0.00 0.00 0.00 1.73
702 722 0.963962 GTAGCGACCCGATCCCAATA 59.036 55.000 0.00 0.00 0.00 1.90
704 724 1.259142 TTGTAGCGACCCGATCCCAA 61.259 55.000 0.00 0.00 0.00 4.12
705 725 1.683025 TTGTAGCGACCCGATCCCA 60.683 57.895 0.00 0.00 0.00 4.37
706 726 1.227176 GTTGTAGCGACCCGATCCC 60.227 63.158 0.00 0.00 0.00 3.85
707 727 0.804933 GTGTTGTAGCGACCCGATCC 60.805 60.000 0.00 0.00 0.00 3.36
708 728 0.804933 GGTGTTGTAGCGACCCGATC 60.805 60.000 0.00 0.00 0.00 3.69
710 730 2.652530 GGTGTTGTAGCGACCCGA 59.347 61.111 0.00 0.00 0.00 5.14
717 737 7.354257 TCTGTAAAATTTTACGGTGTTGTAGC 58.646 34.615 33.51 12.42 45.68 3.58
718 738 8.553696 ACTCTGTAAAATTTTACGGTGTTGTAG 58.446 33.333 32.44 26.78 46.32 2.74
719 739 8.436046 ACTCTGTAAAATTTTACGGTGTTGTA 57.564 30.769 32.44 20.51 46.32 2.41
720 740 7.324354 ACTCTGTAAAATTTTACGGTGTTGT 57.676 32.000 32.44 26.17 46.32 3.32
739 2210 6.542852 TCGTTGTTTTCTTTGAGAAACTCTG 58.457 36.000 2.79 0.00 43.25 3.35
741 2212 7.790861 TTTCGTTGTTTTCTTTGAGAAACTC 57.209 32.000 2.79 0.00 43.25 3.01
758 2229 6.797033 GTCCACATTCTCATAGTTTTTCGTTG 59.203 38.462 0.00 0.00 0.00 4.10
759 2230 6.485313 TGTCCACATTCTCATAGTTTTTCGTT 59.515 34.615 0.00 0.00 0.00 3.85
973 5582 3.432046 CCTGTGAAATTGTTTGGCAAGGT 60.432 43.478 0.00 0.00 40.86 3.50
1074 5683 1.364317 TTGGTGGTCCCCATTGTGGA 61.364 55.000 0.00 0.00 40.96 4.02
1076 5685 0.468958 TGTTGGTGGTCCCCATTGTG 60.469 55.000 0.40 0.00 35.28 3.33
1167 5776 2.889617 CGGTAGGTCATCGCCACA 59.110 61.111 0.00 0.00 0.00 4.17
1220 5829 4.555709 AACTTGCACCGTCCGCCA 62.556 61.111 0.00 0.00 0.00 5.69
1268 5877 2.529780 TCTTTCCCAAGCGAACGTTA 57.470 45.000 0.00 0.00 0.00 3.18
1274 5883 0.392998 GGCTCATCTTTCCCAAGCGA 60.393 55.000 0.00 0.00 33.77 4.93
1283 5892 2.859165 TCTCAAACGGGCTCATCTTT 57.141 45.000 0.00 0.00 0.00 2.52
1347 5956 2.147958 GATGGCGGAACACAAACAGTA 58.852 47.619 0.00 0.00 0.00 2.74
1365 5974 1.683365 GGGCATGTGCTTGGGTGAT 60.683 57.895 4.84 0.00 41.70 3.06
1378 5987 1.146930 CTGGCATAGACACGGGCAT 59.853 57.895 0.00 0.00 36.46 4.40
1415 6024 3.521995 ACAGACTGTGAGAATGGCG 57.478 52.632 7.47 0.00 0.00 5.69
1541 6150 4.154737 GTGATGTACATGTGTTGATGCACT 59.845 41.667 14.43 0.00 39.89 4.40
1596 6205 1.311859 CCGGTACATGCTAGTACGGA 58.688 55.000 20.20 0.00 43.75 4.69
1599 6208 3.119029 TCCAAACCGGTACATGCTAGTAC 60.119 47.826 8.00 9.79 42.78 2.73
1629 9375 8.264347 TGATATACATGTGTGTATCACTGGTTT 58.736 33.333 21.30 0.00 46.06 3.27
1662 9410 7.700322 TTCTTATTTAGATGATCACTCGCAC 57.300 36.000 0.00 0.00 31.54 5.34
1671 9419 7.227156 AGGTTGCGGATTCTTATTTAGATGAT 58.773 34.615 0.00 0.00 31.54 2.45
1692 9440 8.893727 GCATCACAAATAATACAAGTAGAGGTT 58.106 33.333 0.00 0.00 0.00 3.50
1695 9443 8.131455 ACGCATCACAAATAATACAAGTAGAG 57.869 34.615 0.00 0.00 0.00 2.43
1752 9500 7.932134 TCACATAGGAGGCATATCCATAAAAT 58.068 34.615 4.85 0.00 42.26 1.82
1791 9539 3.791973 ATGAACTTCTGAGCTAGACGG 57.208 47.619 0.00 0.00 34.43 4.79
1844 9592 4.395231 GCTACCACCCTAACAAATTCACTC 59.605 45.833 0.00 0.00 0.00 3.51
1856 9604 1.631898 GGGAAAGTTGCTACCACCCTA 59.368 52.381 14.21 0.00 32.33 3.53
1862 9610 2.749621 CTGTGATGGGAAAGTTGCTACC 59.250 50.000 0.00 0.00 0.00 3.18
1867 9615 1.815003 GAGCCTGTGATGGGAAAGTTG 59.185 52.381 0.00 0.00 0.00 3.16
1936 9684 2.127271 TAGGGCATGTGTGGTCATTG 57.873 50.000 0.00 0.00 0.00 2.82
1975 9777 3.118629 TCTGAGCGAACTAATGCCATCTT 60.119 43.478 0.00 0.00 0.00 2.40
2033 9835 5.880332 GGATGCTAGTCACCATCTTGTTTTA 59.120 40.000 7.67 0.00 38.28 1.52
2130 9932 3.858238 GCTCAAATCATTTTCTGCAGCTC 59.142 43.478 9.47 0.00 0.00 4.09
2134 9936 4.521639 AGAGTGCTCAAATCATTTTCTGCA 59.478 37.500 1.82 0.00 31.65 4.41
2166 9968 7.173218 CACTACAGGTGTTTTGTCATTAGATGT 59.827 37.037 0.00 0.00 40.79 3.06
2259 10062 1.952296 GCAATCCTGGCTTGGTGATAG 59.048 52.381 11.85 0.00 0.00 2.08
2293 10097 9.658799 TCTCTCTCATAGTCAAATAAACAAAGG 57.341 33.333 0.00 0.00 0.00 3.11
2306 10110 9.399797 ACAGATATGATCATCTCTCTCATAGTC 57.600 37.037 18.11 0.00 35.85 2.59
2344 10148 6.092092 TCAAGTTTGTCACAATGTTGTTGAG 58.908 36.000 10.65 0.00 39.91 3.02
2354 10158 5.184864 AGACAATGGTTCAAGTTTGTCACAA 59.815 36.000 14.79 0.00 46.51 3.33
2414 10218 1.135603 CAATGTGATGGCTTGTCACCG 60.136 52.381 13.06 2.34 44.10 4.94
2433 10237 3.663202 TGCTCGACGTCTAGCACA 58.337 55.556 33.40 17.35 43.56 4.57
2497 13489 2.752903 GGTGGTCATTTTGCGGAGTTAT 59.247 45.455 0.00 0.00 0.00 1.89
2504 13496 0.519519 TTAGCGGTGGTCATTTTGCG 59.480 50.000 0.00 0.00 0.00 4.85
2545 16726 0.960364 GGCTCGGATTGTTGGCTTGA 60.960 55.000 0.00 0.00 0.00 3.02
2546 16727 0.962356 AGGCTCGGATTGTTGGCTTG 60.962 55.000 0.00 0.00 31.12 4.01
2547 16728 0.678048 GAGGCTCGGATTGTTGGCTT 60.678 55.000 0.00 0.00 35.46 4.35
2627 16809 6.414732 TCATAAACTTTGACGAGATCCCAAT 58.585 36.000 0.00 0.00 0.00 3.16
2628 16810 5.800296 TCATAAACTTTGACGAGATCCCAA 58.200 37.500 0.00 0.00 0.00 4.12
2629 16811 5.414789 TCATAAACTTTGACGAGATCCCA 57.585 39.130 0.00 0.00 0.00 4.37
2632 16814 7.596995 CCTAGGATCATAAACTTTGACGAGATC 59.403 40.741 1.05 0.00 0.00 2.75
2633 16815 7.287927 TCCTAGGATCATAAACTTTGACGAGAT 59.712 37.037 7.62 0.00 0.00 2.75
2634 16816 6.605995 TCCTAGGATCATAAACTTTGACGAGA 59.394 38.462 7.62 0.00 0.00 4.04
2635 16817 6.697892 GTCCTAGGATCATAAACTTTGACGAG 59.302 42.308 16.27 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.