Multiple sequence alignment - TraesCS5A01G552500

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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 TraesCS5A01G552500 chr5A 100.000 2708 0 0 1 2708 705406880 705409587 0.000000e+00 5001.0
1 TraesCS5A01G552500 chr5A 91.547 556 32 12 2064 2607 705382175 705381623 0.000000e+00 752.0
2 TraesCS5A01G552500 chr5A 82.435 575 87 11 1142 1710 705395169 705394603 8.710000e-135 490.0
3 TraesCS5A01G552500 chr5A 80.856 444 70 11 1273 1710 705322831 705323265 4.320000e-88 335.0
4 TraesCS5A01G552500 chr4B 92.783 1926 102 18 811 2708 665435533 665437449 0.000000e+00 2752.0
5 TraesCS5A01G552500 chr4B 91.757 1929 107 24 813 2706 665382167 665380256 0.000000e+00 2634.0
6 TraesCS5A01G552500 chr4B 93.287 1162 71 2 813 1967 665383497 665382336 0.000000e+00 1707.0
7 TraesCS5A01G552500 chr4B 93.213 1164 72 2 811 1967 665384829 665383666 0.000000e+00 1705.0
8 TraesCS5A01G552500 chrUn 95.521 1027 44 2 812 1837 108608076 108609101 0.000000e+00 1640.0
9 TraesCS5A01G552500 chrUn 92.308 429 27 5 63 488 108606931 108607356 2.980000e-169 604.0
10 TraesCS5A01G552500 chrUn 77.644 917 168 27 1115 2013 351552592 351553489 8.590000e-145 523.0
11 TraesCS5A01G552500 chrUn 82.203 590 91 11 1127 1710 108604181 108604762 1.870000e-136 496.0
12 TraesCS5A01G552500 chrUn 92.857 84 6 0 160 243 108606608 108606691 3.660000e-24 122.0
13 TraesCS5A01G552500 chrUn 91.176 68 3 3 749 814 108607348 108607414 3.710000e-14 89.8
14 TraesCS5A01G552500 chr7B 88.703 717 38 20 2000 2708 742235636 742236317 0.000000e+00 835.0
15 TraesCS5A01G552500 chr7A 90.870 460 34 6 29 488 617182222 617182673 6.410000e-171 610.0
16 TraesCS5A01G552500 chr2B 80.220 728 118 12 1019 1727 695116447 695115727 8.590000e-145 523.0
17 TraesCS5A01G552500 chr1D 87.226 274 32 3 483 753 203155107 203155380 2.620000e-80 309.0
18 TraesCS5A01G552500 chr2A 82.090 134 16 4 98 224 761293046 761292914 1.030000e-19 108.0
19 TraesCS5A01G552500 chr5B 89.474 57 2 4 2341 2395 15334174 15334228 4.840000e-08 69.4


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 TraesCS5A01G552500 chr5A 705406880 705409587 2707 False 5001.000000 5001 100.000000 1 2708 1 chr5A.!!$F2 2707
1 TraesCS5A01G552500 chr5A 705381623 705382175 552 True 752.000000 752 91.547000 2064 2607 1 chr5A.!!$R1 543
2 TraesCS5A01G552500 chr5A 705394603 705395169 566 True 490.000000 490 82.435000 1142 1710 1 chr5A.!!$R2 568
3 TraesCS5A01G552500 chr4B 665435533 665437449 1916 False 2752.000000 2752 92.783000 811 2708 1 chr4B.!!$F1 1897
4 TraesCS5A01G552500 chr4B 665380256 665384829 4573 True 2015.333333 2634 92.752333 811 2706 3 chr4B.!!$R1 1895
5 TraesCS5A01G552500 chrUn 108604181 108609101 4920 False 590.360000 1640 90.813000 63 1837 5 chrUn.!!$F2 1774
6 TraesCS5A01G552500 chrUn 351552592 351553489 897 False 523.000000 523 77.644000 1115 2013 1 chrUn.!!$F1 898
7 TraesCS5A01G552500 chr7B 742235636 742236317 681 False 835.000000 835 88.703000 2000 2708 1 chr7B.!!$F1 708
8 TraesCS5A01G552500 chr2B 695115727 695116447 720 True 523.000000 523 80.220000 1019 1727 1 chr2B.!!$R1 708

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
47 48 0.108992 ACAGCCATTGATGCGCTTTG 60.109 50.0 9.73 0.0 33.87 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 7918 1.481772 AGCACAAGGAAGCAAGCAAAA 59.518 42.857 0.0 0.0 0.0 2.44 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
17 18 3.083997 ATGCACGGGAGGAGGTCC 61.084 66.667 0.00 0.00 46.10 4.46
24 25 3.083997 GGAGGAGGTCCCGTGCAT 61.084 66.667 0.00 0.00 39.88 3.96
26 27 3.391665 GAGGAGGTCCCGTGCATGG 62.392 68.421 18.73 18.73 40.87 3.66
44 45 2.117156 GGACAGCCATTGATGCGCT 61.117 57.895 9.73 0.00 35.61 5.92
45 46 1.660560 GGACAGCCATTGATGCGCTT 61.661 55.000 9.73 0.55 33.87 4.68
46 47 0.171903 GACAGCCATTGATGCGCTTT 59.828 50.000 9.73 0.00 33.87 3.51
47 48 0.108992 ACAGCCATTGATGCGCTTTG 60.109 50.000 9.73 0.00 33.87 2.77
48 49 0.171679 CAGCCATTGATGCGCTTTGA 59.828 50.000 9.73 0.00 33.87 2.69
49 50 0.454600 AGCCATTGATGCGCTTTGAG 59.545 50.000 9.73 0.00 32.79 3.02
50 51 0.452987 GCCATTGATGCGCTTTGAGA 59.547 50.000 9.73 0.00 0.00 3.27
51 52 1.066605 GCCATTGATGCGCTTTGAGAT 59.933 47.619 9.73 0.00 0.00 2.75
52 53 2.480759 GCCATTGATGCGCTTTGAGATT 60.481 45.455 9.73 0.00 0.00 2.40
55 56 1.009078 TGATGCGCTTTGAGATTCGG 58.991 50.000 9.73 0.00 0.00 4.30
56 57 1.290203 GATGCGCTTTGAGATTCGGA 58.710 50.000 9.73 0.00 0.00 4.55
58 59 1.349973 GCGCTTTGAGATTCGGAGC 59.650 57.895 0.00 0.00 0.00 4.70
61 62 1.673168 GCTTTGAGATTCGGAGCCAT 58.327 50.000 0.00 0.00 0.00 4.40
62 63 1.332997 GCTTTGAGATTCGGAGCCATG 59.667 52.381 0.00 0.00 0.00 3.66
63 64 1.332997 CTTTGAGATTCGGAGCCATGC 59.667 52.381 0.00 0.00 0.00 4.06
64 65 0.252761 TTGAGATTCGGAGCCATGCA 59.747 50.000 0.00 0.00 0.00 3.96
65 66 0.471191 TGAGATTCGGAGCCATGCAT 59.529 50.000 0.00 0.00 0.00 3.96
66 67 1.693606 TGAGATTCGGAGCCATGCATA 59.306 47.619 0.00 0.00 0.00 3.14
79 2768 3.631686 GCCATGCATATGTACTTTCACCA 59.368 43.478 0.00 0.00 32.21 4.17
223 2912 9.138062 GTTTGCATATTTGTGTTTATGATGACA 57.862 29.630 0.00 0.00 0.00 3.58
231 2920 9.850628 ATTTGTGTTTATGATGACAAGATCTTG 57.149 29.630 29.74 29.74 45.58 3.02
257 2946 7.972832 AAACGAGACCACTTTTGAATATACA 57.027 32.000 0.00 0.00 0.00 2.29
262 2951 8.664798 CGAGACCACTTTTGAATATACATTGAA 58.335 33.333 0.00 0.00 0.00 2.69
325 3017 7.346208 TGTGAAACACGATGAAACACTATAG 57.654 36.000 0.00 0.00 45.67 1.31
332 3024 9.701098 AACACGATGAAACACTATAGAAAACTA 57.299 29.630 6.78 0.00 0.00 2.24
333 3025 9.871238 ACACGATGAAACACTATAGAAAACTAT 57.129 29.630 6.78 0.00 0.00 2.12
408 3100 9.617523 GGAATTAATGAATTTGGATGGTGATTT 57.382 29.630 0.00 0.00 35.33 2.17
420 3112 7.537596 TGGATGGTGATTTAGTTGTCAAAAT 57.462 32.000 0.00 0.00 0.00 1.82
519 3211 9.897744 TTGTTTGCATTTTTAATTTTGTTCACA 57.102 22.222 0.00 0.00 0.00 3.58
520 3212 9.897744 TGTTTGCATTTTTAATTTTGTTCACAA 57.102 22.222 0.00 0.00 0.00 3.33
566 3258 9.800433 AATGTTCCCATTTTCAAAATTTTGTTC 57.200 25.926 25.98 9.35 38.10 3.18
567 3259 8.340618 TGTTCCCATTTTCAAAATTTTGTTCA 57.659 26.923 25.98 13.77 39.18 3.18
568 3260 8.239998 TGTTCCCATTTTCAAAATTTTGTTCAC 58.760 29.630 25.98 13.25 39.18 3.18
569 3261 7.928307 TCCCATTTTCAAAATTTTGTTCACA 57.072 28.000 25.98 7.82 39.18 3.58
570 3262 8.340618 TCCCATTTTCAAAATTTTGTTCACAA 57.659 26.923 25.98 12.88 39.18 3.33
571 3263 8.796475 TCCCATTTTCAAAATTTTGTTCACAAA 58.204 25.926 25.98 17.21 43.36 2.83
572 3264 9.583765 CCCATTTTCAAAATTTTGTTCACAAAT 57.416 25.926 25.98 19.16 44.30 2.32
608 3300 9.775854 ATTCATGTTTTGGATATTTGTTCACAA 57.224 25.926 0.00 0.00 0.00 3.33
623 3315 8.939201 TTTGTTCACAAATTCTAAAATGCTCA 57.061 26.923 0.79 0.00 40.55 4.26
624 3316 8.578308 TTGTTCACAAATTCTAAAATGCTCAG 57.422 30.769 0.00 0.00 32.11 3.35
625 3317 7.939782 TGTTCACAAATTCTAAAATGCTCAGA 58.060 30.769 0.00 0.00 0.00 3.27
626 3318 8.412456 TGTTCACAAATTCTAAAATGCTCAGAA 58.588 29.630 0.00 0.00 33.12 3.02
627 3319 9.248291 GTTCACAAATTCTAAAATGCTCAGAAA 57.752 29.630 0.00 0.00 32.38 2.52
628 3320 8.801715 TCACAAATTCTAAAATGCTCAGAAAC 57.198 30.769 0.00 0.00 32.38 2.78
629 3321 8.632679 TCACAAATTCTAAAATGCTCAGAAACT 58.367 29.630 0.00 0.00 32.38 2.66
630 3322 9.252962 CACAAATTCTAAAATGCTCAGAAACTT 57.747 29.630 0.00 0.00 32.38 2.66
631 3323 9.468532 ACAAATTCTAAAATGCTCAGAAACTTC 57.531 29.630 0.00 0.00 32.38 3.01
632 3324 9.467258 CAAATTCTAAAATGCTCAGAAACTTCA 57.533 29.630 0.00 0.00 32.38 3.02
636 3328 9.868277 TTCTAAAATGCTCAGAAACTTCAAAAA 57.132 25.926 0.00 0.00 0.00 1.94
655 3347 5.722021 AAAAATGTTCCCGCACTAGATTT 57.278 34.783 0.00 0.00 0.00 2.17
656 3348 4.701956 AAATGTTCCCGCACTAGATTTG 57.298 40.909 0.00 0.00 0.00 2.32
657 3349 2.851263 TGTTCCCGCACTAGATTTGT 57.149 45.000 0.00 0.00 0.00 2.83
658 3350 3.134574 TGTTCCCGCACTAGATTTGTT 57.865 42.857 0.00 0.00 0.00 2.83
659 3351 3.071479 TGTTCCCGCACTAGATTTGTTC 58.929 45.455 0.00 0.00 0.00 3.18
660 3352 3.071479 GTTCCCGCACTAGATTTGTTCA 58.929 45.455 0.00 0.00 0.00 3.18
661 3353 2.695359 TCCCGCACTAGATTTGTTCAC 58.305 47.619 0.00 0.00 0.00 3.18
662 3354 1.393539 CCCGCACTAGATTTGTTCACG 59.606 52.381 0.00 0.00 0.00 4.35
663 3355 2.333926 CCGCACTAGATTTGTTCACGA 58.666 47.619 0.00 0.00 0.00 4.35
664 3356 2.734606 CCGCACTAGATTTGTTCACGAA 59.265 45.455 0.00 0.00 0.00 3.85
665 3357 3.370978 CCGCACTAGATTTGTTCACGAAT 59.629 43.478 0.00 0.00 32.83 3.34
666 3358 4.142902 CCGCACTAGATTTGTTCACGAATT 60.143 41.667 0.00 0.00 30.40 2.17
667 3359 5.382303 CGCACTAGATTTGTTCACGAATTT 58.618 37.500 0.00 0.00 30.40 1.82
668 3360 6.401688 CCGCACTAGATTTGTTCACGAATTTA 60.402 38.462 0.00 0.00 30.40 1.40
669 3361 7.012943 CGCACTAGATTTGTTCACGAATTTAA 58.987 34.615 0.00 0.00 30.40 1.52
670 3362 7.532546 CGCACTAGATTTGTTCACGAATTTAAA 59.467 33.333 0.00 0.00 30.40 1.52
671 3363 9.176181 GCACTAGATTTGTTCACGAATTTAAAA 57.824 29.630 0.00 0.00 30.40 1.52
837 4194 2.584418 CAGCCGCCTCGTCTGATG 60.584 66.667 0.00 0.00 0.00 3.07
838 4195 2.755876 AGCCGCCTCGTCTGATGA 60.756 61.111 0.00 0.00 0.00 2.92
852 4209 4.384247 CGTCTGATGAGTGTCACTCTTTTC 59.616 45.833 28.67 22.22 45.27 2.29
995 4358 3.864983 ATGGACCGACCCACCCAGT 62.865 63.158 0.00 0.00 39.34 4.00
1003 4366 1.229820 ACCCACCCAGTAGCCATGA 60.230 57.895 0.00 0.00 0.00 3.07
1004 4367 0.624500 ACCCACCCAGTAGCCATGAT 60.625 55.000 0.00 0.00 0.00 2.45
1245 4612 4.722700 CCCACGTCCAAGCCCCTG 62.723 72.222 0.00 0.00 0.00 4.45
1384 4751 1.005630 GACGCAGAGCCAGTCAAGT 60.006 57.895 0.00 0.00 35.19 3.16
1452 7491 1.142748 GCCCATCAGAGAGACCGTG 59.857 63.158 0.00 0.00 0.00 4.94
1647 7686 1.026182 TGGCGGTGATGAACATGCTC 61.026 55.000 0.00 0.00 34.63 4.26
1698 7741 0.250038 CTCACGCCATCCCGATCAAT 60.250 55.000 0.00 0.00 0.00 2.57
1757 7800 7.413767 GCTGGTTTTAGACTTTATTTAGGTCCG 60.414 40.741 0.00 0.00 0.00 4.79
1763 7812 5.021458 AGACTTTATTTAGGTCCGTCTCCA 58.979 41.667 0.00 0.00 0.00 3.86
1764 7813 5.082251 ACTTTATTTAGGTCCGTCTCCAC 57.918 43.478 0.00 0.00 0.00 4.02
1798 7876 3.064207 TCATGTCCGTCTAGTTTGTTGC 58.936 45.455 0.00 0.00 0.00 4.17
1832 7918 1.414919 TGGAACACGTAGGCTTTCAGT 59.585 47.619 0.00 0.00 0.00 3.41
1855 7942 1.202806 TGCTTGCTTCCTTGTGCTAGT 60.203 47.619 0.00 0.00 35.21 2.57
2029 8119 2.887151 ATGACCCCTCAACTCCAAAG 57.113 50.000 0.00 0.00 0.00 2.77
2032 8122 1.304464 CCCCTCAACTCCAAAGCCC 60.304 63.158 0.00 0.00 0.00 5.19
2037 8128 2.500229 CTCAACTCCAAAGCCCGTAAA 58.500 47.619 0.00 0.00 0.00 2.01
2094 8185 3.442076 TCCTCTCAAACCTTCTCCCTAC 58.558 50.000 0.00 0.00 0.00 3.18
2158 8253 4.969359 AGCTAGAGGATGCCCTAACTTAAA 59.031 41.667 0.00 0.00 44.53 1.52
2258 8356 4.640805 TTCGACAACGCTTTCTCATTAC 57.359 40.909 0.00 0.00 39.58 1.89
2294 8392 6.885922 ACATAAGTAACAGTCCATTCCTACC 58.114 40.000 0.00 0.00 0.00 3.18
2301 8399 3.000727 CAGTCCATTCCTACCACGTTTC 58.999 50.000 0.00 0.00 0.00 2.78
2320 8418 6.650807 ACGTTTCCCTCATACATAGCATAATG 59.349 38.462 0.00 0.00 0.00 1.90
2455 8554 9.461312 ACACATTGTACATTTCTGGTATACATT 57.539 29.630 5.01 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.083997 GGACCTCCTCCCGTGCAT 61.084 66.667 0.00 0.00 31.83 3.96
7 8 3.083997 ATGCACGGGACCTCCTCC 61.084 66.667 0.00 0.00 38.55 4.30
8 9 2.187946 CATGCACGGGACCTCCTC 59.812 66.667 0.00 0.00 35.95 3.71
17 18 4.720902 TGGCTGTCCCATGCACGG 62.721 66.667 0.00 0.00 39.18 4.94
26 27 1.660560 AAGCGCATCAATGGCTGTCC 61.661 55.000 11.47 0.00 35.49 4.02
27 28 0.171903 AAAGCGCATCAATGGCTGTC 59.828 50.000 11.47 0.00 35.49 3.51
30 31 0.454600 CTCAAAGCGCATCAATGGCT 59.545 50.000 11.47 1.59 36.38 4.75
31 32 0.452987 TCTCAAAGCGCATCAATGGC 59.547 50.000 11.47 0.00 0.00 4.40
34 35 2.032550 CCGAATCTCAAAGCGCATCAAT 59.967 45.455 11.47 0.00 0.00 2.57
35 36 1.398041 CCGAATCTCAAAGCGCATCAA 59.602 47.619 11.47 0.00 0.00 2.57
37 38 1.260033 CTCCGAATCTCAAAGCGCATC 59.740 52.381 11.47 0.00 0.00 3.91
38 39 1.293924 CTCCGAATCTCAAAGCGCAT 58.706 50.000 11.47 0.00 0.00 4.73
40 41 1.349973 GCTCCGAATCTCAAAGCGC 59.650 57.895 0.00 0.00 0.00 5.92
44 45 1.339920 TGCATGGCTCCGAATCTCAAA 60.340 47.619 0.00 0.00 0.00 2.69
45 46 0.252761 TGCATGGCTCCGAATCTCAA 59.747 50.000 0.00 0.00 0.00 3.02
46 47 0.471191 ATGCATGGCTCCGAATCTCA 59.529 50.000 0.00 0.00 0.00 3.27
47 48 2.462456 TATGCATGGCTCCGAATCTC 57.538 50.000 10.16 0.00 0.00 2.75
48 49 2.039480 ACATATGCATGGCTCCGAATCT 59.961 45.455 10.16 0.00 36.39 2.40
49 50 2.430465 ACATATGCATGGCTCCGAATC 58.570 47.619 10.16 0.00 36.39 2.52
50 51 2.574006 ACATATGCATGGCTCCGAAT 57.426 45.000 10.16 0.00 36.39 3.34
51 52 2.368548 AGTACATATGCATGGCTCCGAA 59.631 45.455 10.16 0.00 36.39 4.30
52 53 1.970640 AGTACATATGCATGGCTCCGA 59.029 47.619 10.16 0.00 36.39 4.55
55 56 4.023707 GGTGAAAGTACATATGCATGGCTC 60.024 45.833 10.16 0.00 36.39 4.70
56 57 3.885297 GGTGAAAGTACATATGCATGGCT 59.115 43.478 10.16 0.00 36.39 4.75
58 59 4.639755 TGTGGTGAAAGTACATATGCATGG 59.360 41.667 10.16 3.88 36.39 3.66
61 62 5.816449 CATGTGGTGAAAGTACATATGCA 57.184 39.130 1.58 0.00 33.57 3.96
62 63 4.601019 GCATGTGGTGAAAGTACATATGC 58.399 43.478 1.58 9.24 46.82 3.14
63 64 5.816449 TGCATGTGGTGAAAGTACATATG 57.184 39.130 0.00 0.00 36.97 1.78
64 65 5.221106 GCATGCATGTGGTGAAAGTACATAT 60.221 40.000 26.79 0.00 33.57 1.78
65 66 4.096231 GCATGCATGTGGTGAAAGTACATA 59.904 41.667 26.79 0.00 33.57 2.29
66 67 3.119388 GCATGCATGTGGTGAAAGTACAT 60.119 43.478 26.79 0.00 35.56 2.29
79 2768 0.604578 GGAACAGTTGGCATGCATGT 59.395 50.000 26.79 14.85 0.00 3.21
223 2912 4.962155 AGTGGTCTCGTTTTCAAGATCTT 58.038 39.130 0.88 0.88 0.00 2.40
231 2920 8.500773 TGTATATTCAAAAGTGGTCTCGTTTTC 58.499 33.333 0.00 0.00 0.00 2.29
291 2982 8.958175 TTCATCGTGTTTCACATATTTTTACC 57.042 30.769 1.00 0.00 33.40 2.85
293 2984 9.952188 TGTTTCATCGTGTTTCACATATTTTTA 57.048 25.926 1.00 0.00 33.40 1.52
296 2988 7.648142 AGTGTTTCATCGTGTTTCACATATTT 58.352 30.769 1.00 0.00 33.40 1.40
299 2991 7.899178 ATAGTGTTTCATCGTGTTTCACATA 57.101 32.000 1.00 0.00 33.40 2.29
301 2993 7.149307 TCTATAGTGTTTCATCGTGTTTCACA 58.851 34.615 0.00 0.00 33.40 3.58
377 3069 6.146510 CCATCCAAATTCATTAATTCCATGCG 59.853 38.462 0.00 0.00 34.12 4.73
493 3185 9.897744 TGTGAACAAAATTAAAAATGCAAACAA 57.102 22.222 0.00 0.00 0.00 2.83
494 3186 9.897744 TTGTGAACAAAATTAAAAATGCAAACA 57.102 22.222 0.00 0.00 32.11 2.83
541 3233 8.964772 TGAACAAAATTTTGAAAATGGGAACAT 58.035 25.926 32.20 6.92 46.83 2.71
542 3234 8.239998 GTGAACAAAATTTTGAAAATGGGAACA 58.760 29.630 32.20 14.88 42.49 3.18
543 3235 8.239998 TGTGAACAAAATTTTGAAAATGGGAAC 58.760 29.630 32.20 17.38 40.55 3.62
544 3236 8.340618 TGTGAACAAAATTTTGAAAATGGGAA 57.659 26.923 32.20 9.63 40.55 3.97
545 3237 7.928307 TGTGAACAAAATTTTGAAAATGGGA 57.072 28.000 32.20 9.38 40.55 4.37
546 3238 8.976986 TTTGTGAACAAAATTTTGAAAATGGG 57.023 26.923 32.20 8.27 42.26 4.00
582 3274 9.775854 TTGTGAACAAATATCCAAAACATGAAT 57.224 25.926 0.00 0.00 32.11 2.57
583 3275 9.605275 TTTGTGAACAAATATCCAAAACATGAA 57.395 25.926 0.00 0.00 40.55 2.57
599 3291 8.412456 TCTGAGCATTTTAGAATTTGTGAACAA 58.588 29.630 0.00 0.00 0.00 2.83
600 3292 7.939782 TCTGAGCATTTTAGAATTTGTGAACA 58.060 30.769 0.00 0.00 0.00 3.18
601 3293 8.801715 TTCTGAGCATTTTAGAATTTGTGAAC 57.198 30.769 0.00 0.00 0.00 3.18
602 3294 9.248291 GTTTCTGAGCATTTTAGAATTTGTGAA 57.752 29.630 0.00 0.00 31.21 3.18
603 3295 8.632679 AGTTTCTGAGCATTTTAGAATTTGTGA 58.367 29.630 0.00 0.00 31.21 3.58
604 3296 8.807667 AGTTTCTGAGCATTTTAGAATTTGTG 57.192 30.769 0.00 0.00 31.21 3.33
605 3297 9.468532 GAAGTTTCTGAGCATTTTAGAATTTGT 57.531 29.630 0.00 0.00 31.21 2.83
606 3298 9.467258 TGAAGTTTCTGAGCATTTTAGAATTTG 57.533 29.630 0.00 0.00 31.21 2.32
610 3302 9.868277 TTTTTGAAGTTTCTGAGCATTTTAGAA 57.132 25.926 0.00 0.00 0.00 2.10
633 3325 5.010617 ACAAATCTAGTGCGGGAACATTTTT 59.989 36.000 0.00 0.00 0.00 1.94
634 3326 4.522789 ACAAATCTAGTGCGGGAACATTTT 59.477 37.500 0.00 0.00 0.00 1.82
635 3327 4.079253 ACAAATCTAGTGCGGGAACATTT 58.921 39.130 0.00 0.00 0.00 2.32
636 3328 3.686016 ACAAATCTAGTGCGGGAACATT 58.314 40.909 0.00 0.00 0.00 2.71
637 3329 3.350219 ACAAATCTAGTGCGGGAACAT 57.650 42.857 0.00 0.00 0.00 2.71
638 3330 2.851263 ACAAATCTAGTGCGGGAACA 57.149 45.000 0.00 0.00 0.00 3.18
639 3331 3.071479 TGAACAAATCTAGTGCGGGAAC 58.929 45.455 0.00 0.00 0.00 3.62
640 3332 3.071479 GTGAACAAATCTAGTGCGGGAA 58.929 45.455 0.00 0.00 0.00 3.97
641 3333 2.695359 GTGAACAAATCTAGTGCGGGA 58.305 47.619 0.00 0.00 0.00 5.14
642 3334 1.393539 CGTGAACAAATCTAGTGCGGG 59.606 52.381 0.00 0.00 0.00 6.13
643 3335 2.333926 TCGTGAACAAATCTAGTGCGG 58.666 47.619 0.00 0.00 0.00 5.69
644 3336 4.584029 ATTCGTGAACAAATCTAGTGCG 57.416 40.909 0.00 0.00 0.00 5.34
645 3337 8.722342 TTTAAATTCGTGAACAAATCTAGTGC 57.278 30.769 0.00 0.00 0.00 4.40
742 3434 9.862371 ACACTGTGTGTTTAAATTTGTGAATAA 57.138 25.926 13.50 0.00 45.08 1.40
744 3436 9.862371 TTACACTGTGTGTTTAAATTTGTGAAT 57.138 25.926 22.97 0.00 45.08 2.57
745 3437 9.862371 ATTACACTGTGTGTTTAAATTTGTGAA 57.138 25.926 22.97 4.73 45.08 3.18
746 3438 9.509855 GATTACACTGTGTGTTTAAATTTGTGA 57.490 29.630 22.97 0.00 45.08 3.58
747 3439 9.295214 TGATTACACTGTGTGTTTAAATTTGTG 57.705 29.630 22.97 0.00 45.08 3.33
748 3440 9.862371 TTGATTACACTGTGTGTTTAAATTTGT 57.138 25.926 22.97 0.00 45.08 2.83
753 3445 9.915629 AAAGTTTGATTACACTGTGTGTTTAAA 57.084 25.926 22.97 14.82 45.08 1.52
754 3446 9.915629 AAAAGTTTGATTACACTGTGTGTTTAA 57.084 25.926 22.97 9.81 45.08 1.52
801 3494 6.092670 GCGGCTGCTTTGATCAGATAAATATA 59.907 38.462 11.21 0.00 38.39 0.86
802 3495 5.106396 GCGGCTGCTTTGATCAGATAAATAT 60.106 40.000 11.21 0.00 38.39 1.28
837 4194 3.873952 AGCACAAGAAAAGAGTGACACTC 59.126 43.478 25.27 25.27 45.38 3.51
838 4195 3.878778 AGCACAAGAAAAGAGTGACACT 58.121 40.909 8.12 8.12 35.33 3.55
940 4297 7.176865 TCAAGTACTCCAGTATATATGGACTGC 59.823 40.741 9.34 2.54 41.96 4.40
995 4358 1.618837 GGAGGAACGCTATCATGGCTA 59.381 52.381 0.00 0.00 0.00 3.93
1003 4366 4.120946 AGAGGAATAGGAGGAACGCTAT 57.879 45.455 0.00 0.00 0.00 2.97
1004 4367 3.596940 AGAGGAATAGGAGGAACGCTA 57.403 47.619 0.00 0.00 0.00 4.26
1377 4744 2.753029 GCCAGAGCCCACTTGACT 59.247 61.111 0.00 0.00 0.00 3.41
1452 7491 1.522580 GCTGTCCCATCCGCTTCTC 60.523 63.158 0.00 0.00 0.00 2.87
1647 7686 1.493950 GCTCGAAGTCCGCATCCATG 61.494 60.000 0.00 0.00 38.37 3.66
1698 7741 4.968626 CATGCATGCACGTTTACTCTAAA 58.031 39.130 25.37 0.00 0.00 1.85
1757 7800 4.307432 TGAAAGAAACATCGAGTGGAGAC 58.693 43.478 0.00 0.00 0.00 3.36
1763 7812 3.679980 CGGACATGAAAGAAACATCGAGT 59.320 43.478 0.00 0.00 0.00 4.18
1764 7813 3.679980 ACGGACATGAAAGAAACATCGAG 59.320 43.478 0.00 0.00 0.00 4.04
1798 7876 4.142359 ACGTGTTCCAACTAGCTAGATGAG 60.142 45.833 27.41 18.51 0.00 2.90
1809 7887 2.158871 TGAAAGCCTACGTGTTCCAACT 60.159 45.455 0.00 0.00 0.00 3.16
1832 7918 1.481772 AGCACAAGGAAGCAAGCAAAA 59.518 42.857 0.00 0.00 0.00 2.44
2029 8119 3.124560 GAGATGCTCTAAGTTTACGGGC 58.875 50.000 0.00 0.00 0.00 6.13
2032 8122 7.866729 TCTGATAGAGATGCTCTAAGTTTACG 58.133 38.462 8.11 0.00 44.76 3.18
2094 8185 6.650390 CACCCCAAATATTTGACTTTTTGAGG 59.350 38.462 26.32 15.77 40.55 3.86
2294 8392 3.792401 TGCTATGTATGAGGGAAACGTG 58.208 45.455 0.00 0.00 0.00 4.49
2301 8399 7.984422 TTTGACATTATGCTATGTATGAGGG 57.016 36.000 0.00 0.00 38.80 4.30
2320 8418 9.974750 GTTCTTGACTTAAGCTATGTATTTGAC 57.025 33.333 1.29 0.00 36.31 3.18
2572 8680 5.049543 TCCGGTGTTTAAGAAAAATGTACGG 60.050 40.000 0.00 0.00 36.66 4.02
2604 8716 9.491675 AATTCAGAAAAATGTTCAACATGCATA 57.508 25.926 3.07 0.00 37.97 3.14
2607 8719 8.763356 TGTAATTCAGAAAAATGTTCAACATGC 58.237 29.630 3.07 0.00 37.97 4.06


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

AutoCloner maintained by Alex Coulton.