Multiple sequence alignment - TraesCS3A01G356200

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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 TraesCS3A01G356200 chr3A 100.000 2750 0 0 1 2750 603848322 603845573 0.000000e+00 5079.0
1 TraesCS3A01G356200 chr3A 81.215 1070 124 43 561 1581 603814546 603813505 0.000000e+00 791.0
2 TraesCS3A01G356200 chr3A 83.710 841 80 31 931 1742 603895921 603895109 0.000000e+00 741.0
3 TraesCS3A01G356200 chr3A 84.946 186 26 2 1770 1954 136035589 136035405 1.300000e-43 187.0
4 TraesCS3A01G356200 chr3A 97.059 34 1 0 201 234 169231569 169231536 1.060000e-04 58.4
5 TraesCS3A01G356200 chr3A 100.000 29 0 0 869 897 603895999 603895971 1.000000e-03 54.7
6 TraesCS3A01G356200 chr3D 92.851 1203 58 6 1562 2749 461371557 461370368 0.000000e+00 1720.0
7 TraesCS3A01G356200 chr3D 90.888 1306 69 13 1471 2749 461426375 461425093 0.000000e+00 1707.0
8 TraesCS3A01G356200 chr3D 84.367 774 85 16 937 1682 461589600 461588835 0.000000e+00 726.0
9 TraesCS3A01G356200 chr3D 84.225 748 66 24 844 1569 461373200 461372483 0.000000e+00 680.0
10 TraesCS3A01G356200 chr3D 88.226 603 26 19 844 1426 461426948 461426371 0.000000e+00 678.0
11 TraesCS3A01G356200 chr3D 82.982 758 82 29 844 1581 461313866 461313136 2.310000e-180 641.0
12 TraesCS3A01G356200 chr3D 87.812 320 21 11 263 567 461427604 461427288 2.600000e-95 359.0
13 TraesCS3A01G356200 chr3D 88.496 226 8 8 565 773 461427259 461427035 9.770000e-65 257.0
14 TraesCS3A01G356200 chr3D 84.305 223 16 9 561 771 461373508 461373293 1.670000e-47 200.0
15 TraesCS3A01G356200 chr3D 90.698 129 10 2 43 169 461428643 461428515 1.310000e-38 171.0
16 TraesCS3A01G356200 chr3D 97.297 37 1 0 55 91 461404903 461404867 2.290000e-06 63.9
17 TraesCS3A01G356200 chr3D 100.000 30 0 0 868 897 461589688 461589659 3.830000e-04 56.5
18 TraesCS3A01G356200 chr3B 86.251 931 64 25 674 1577 612296345 612295452 0.000000e+00 952.0
19 TraesCS3A01G356200 chr3B 82.331 1064 135 21 1577 2608 612294046 612293004 0.000000e+00 874.0
20 TraesCS3A01G356200 chr3B 81.693 945 106 31 868 1759 612360464 612359534 0.000000e+00 725.0
21 TraesCS3A01G356200 chr3B 83.703 767 78 30 844 1581 612104476 612103728 0.000000e+00 680.0
22 TraesCS3A01G356200 chr3B 89.369 301 16 4 273 567 612297231 612296941 5.600000e-97 364.0
23 TraesCS3A01G356200 chr3B 82.407 216 15 13 569 771 612104764 612104559 1.690000e-37 167.0
24 TraesCS3A01G356200 chr1D 87.692 195 23 1 1770 1964 339738523 339738330 2.760000e-55 226.0
25 TraesCS3A01G356200 chr2B 88.235 119 14 0 1770 1888 756998987 756999105 2.850000e-30 143.0
26 TraesCS3A01G356200 chr1B 83.217 143 24 0 1770 1912 99078933 99078791 6.180000e-27 132.0
27 TraesCS3A01G356200 chr1B 97.222 36 1 0 201 236 623998446 623998411 8.220000e-06 62.1
28 TraesCS3A01G356200 chr2A 80.667 150 29 0 1770 1919 16018111 16018260 1.730000e-22 117.0
29 TraesCS3A01G356200 chr7A 82.645 121 21 0 1786 1906 678962262 678962142 1.040000e-19 108.0
30 TraesCS3A01G356200 chr7B 100.000 29 0 0 238 266 245218041 245218069 1.000000e-03 54.7


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 TraesCS3A01G356200 chr3A 603845573 603848322 2749 True 5079.000000 5079 100.000000 1 2750 1 chr3A.!!$R4 2749
1 TraesCS3A01G356200 chr3A 603813505 603814546 1041 True 791.000000 791 81.215000 561 1581 1 chr3A.!!$R3 1020
2 TraesCS3A01G356200 chr3A 603895109 603895999 890 True 397.850000 741 91.855000 869 1742 2 chr3A.!!$R5 873
3 TraesCS3A01G356200 chr3D 461370368 461373508 3140 True 866.666667 1720 87.127000 561 2749 3 chr3D.!!$R3 2188
4 TraesCS3A01G356200 chr3D 461313136 461313866 730 True 641.000000 641 82.982000 844 1581 1 chr3D.!!$R1 737
5 TraesCS3A01G356200 chr3D 461425093 461428643 3550 True 634.400000 1707 89.224000 43 2749 5 chr3D.!!$R4 2706
6 TraesCS3A01G356200 chr3D 461588835 461589688 853 True 391.250000 726 92.183500 868 1682 2 chr3D.!!$R5 814
7 TraesCS3A01G356200 chr3B 612293004 612297231 4227 True 730.000000 952 85.983667 273 2608 3 chr3B.!!$R3 2335
8 TraesCS3A01G356200 chr3B 612359534 612360464 930 True 725.000000 725 81.693000 868 1759 1 chr3B.!!$R1 891
9 TraesCS3A01G356200 chr3B 612103728 612104764 1036 True 423.500000 680 83.055000 569 1581 2 chr3B.!!$R2 1012

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
911 2378 0.038251 TGCAGCCGATAGATTAGCCG 60.038 55.0 0.0 0.0 39.76 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 6095 0.52218 GCTCCTCGTCGAGAACTGAA 59.478 55.0 23.74 1.25 30.97 3.02 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 2.827604 AAACATCGCTGGTCAGACG 58.172 52.632 1.65 5.48 0.00 4.18
19 20 1.291877 AAACATCGCTGGTCAGACGC 61.292 55.000 1.65 0.00 0.00 5.19
20 21 2.125952 CATCGCTGGTCAGACGCA 60.126 61.111 1.65 0.00 0.00 5.24
21 22 1.520120 CATCGCTGGTCAGACGCAT 60.520 57.895 1.65 0.08 0.00 4.73
22 23 1.227089 ATCGCTGGTCAGACGCATC 60.227 57.895 1.65 0.00 0.00 3.91
23 24 1.948721 ATCGCTGGTCAGACGCATCA 61.949 55.000 1.65 0.00 0.00 3.07
24 25 1.737735 CGCTGGTCAGACGCATCAA 60.738 57.895 1.65 0.00 0.00 2.57
25 26 1.086067 CGCTGGTCAGACGCATCAAT 61.086 55.000 1.65 0.00 0.00 2.57
26 27 1.089920 GCTGGTCAGACGCATCAATT 58.910 50.000 1.65 0.00 0.00 2.32
27 28 2.279741 GCTGGTCAGACGCATCAATTA 58.720 47.619 1.65 0.00 0.00 1.40
28 29 2.286294 GCTGGTCAGACGCATCAATTAG 59.714 50.000 1.65 0.00 0.00 1.73
29 30 2.279741 TGGTCAGACGCATCAATTAGC 58.720 47.619 0.00 0.00 0.00 3.09
30 31 2.279741 GGTCAGACGCATCAATTAGCA 58.720 47.619 0.00 0.00 0.00 3.49
31 32 2.286294 GGTCAGACGCATCAATTAGCAG 59.714 50.000 0.00 0.00 0.00 4.24
32 33 1.935873 TCAGACGCATCAATTAGCAGC 59.064 47.619 0.00 0.00 0.00 5.25
33 34 1.003116 CAGACGCATCAATTAGCAGCC 60.003 52.381 0.00 0.00 0.00 4.85
34 35 0.308993 GACGCATCAATTAGCAGCCC 59.691 55.000 0.00 0.00 0.00 5.19
35 36 1.280746 CGCATCAATTAGCAGCCCG 59.719 57.895 0.00 0.00 0.00 6.13
36 37 1.656441 GCATCAATTAGCAGCCCGG 59.344 57.895 0.00 0.00 0.00 5.73
37 38 0.819259 GCATCAATTAGCAGCCCGGA 60.819 55.000 0.73 0.00 0.00 5.14
38 39 1.679139 CATCAATTAGCAGCCCGGAA 58.321 50.000 0.73 0.00 0.00 4.30
39 40 2.023673 CATCAATTAGCAGCCCGGAAA 58.976 47.619 0.73 0.00 0.00 3.13
40 41 2.208132 TCAATTAGCAGCCCGGAAAA 57.792 45.000 0.73 0.00 0.00 2.29
41 42 2.520069 TCAATTAGCAGCCCGGAAAAA 58.480 42.857 0.73 0.00 0.00 1.94
94 95 2.899900 TGTTCAGCACACTCCTATCAGT 59.100 45.455 0.00 0.00 0.00 3.41
103 104 1.899814 ACTCCTATCAGTTGTCCGCAA 59.100 47.619 0.00 0.00 0.00 4.85
111 113 4.693532 TTGTCCGCAACTGCTAGG 57.306 55.556 0.00 0.00 39.32 3.02
145 147 4.013728 CCGGTCAAGGGATAAATCAACAA 58.986 43.478 0.00 0.00 0.00 2.83
163 165 6.237901 TCAACAATAACTTGGACTGCTATGT 58.762 36.000 0.00 0.00 36.64 2.29
164 166 7.390823 TCAACAATAACTTGGACTGCTATGTA 58.609 34.615 0.00 0.00 36.64 2.29
174 176 9.090103 ACTTGGACTGCTATGTATAATAAGCTA 57.910 33.333 0.00 0.00 35.95 3.32
200 202 5.532025 AATAACGAAGACAACTTGCTAGC 57.468 39.130 8.10 8.10 36.39 3.42
201 203 2.821991 ACGAAGACAACTTGCTAGCT 57.178 45.000 17.23 0.00 36.39 3.32
208 210 2.163815 GACAACTTGCTAGCTCTCCGTA 59.836 50.000 17.23 0.00 0.00 4.02
209 211 2.561419 ACAACTTGCTAGCTCTCCGTAA 59.439 45.455 17.23 0.00 0.00 3.18
210 212 3.006537 ACAACTTGCTAGCTCTCCGTAAA 59.993 43.478 17.23 0.00 0.00 2.01
211 213 3.512033 ACTTGCTAGCTCTCCGTAAAG 57.488 47.619 17.23 10.64 0.00 1.85
218 220 7.520451 TGCTAGCTCTCCGTAAAGAAATATA 57.480 36.000 17.23 0.00 0.00 0.86
219 221 7.948357 TGCTAGCTCTCCGTAAAGAAATATAA 58.052 34.615 17.23 0.00 0.00 0.98
221 223 8.298140 GCTAGCTCTCCGTAAAGAAATATAAGA 58.702 37.037 7.70 0.00 0.00 2.10
224 226 8.861086 AGCTCTCCGTAAAGAAATATAAGATCA 58.139 33.333 0.00 0.00 0.00 2.92
267 1100 6.743575 AATACTCCTTCCGTCTCAAAATTG 57.256 37.500 0.00 0.00 0.00 2.32
271 1104 2.351738 CCTTCCGTCTCAAAATTGCACC 60.352 50.000 0.00 0.00 0.00 5.01
339 1172 2.431057 TCTAGAGGATTTGAACCGAGCC 59.569 50.000 0.00 0.00 0.00 4.70
355 1188 1.583967 GCCAGTCGTGTCGATCTCG 60.584 63.158 0.00 0.00 38.42 4.04
381 1214 3.345508 AACTATCGGTTTGACCCTTCC 57.654 47.619 0.00 0.00 33.75 3.46
431 1264 2.290641 GCAACAAGACAAGGTACACCAG 59.709 50.000 0.38 0.00 38.89 4.00
444 1277 1.961277 CACCAGCGGGAGTGTGAAC 60.961 63.158 10.86 0.00 38.05 3.18
445 1278 2.425592 CCAGCGGGAGTGTGAACA 59.574 61.111 0.00 0.00 35.59 3.18
506 1360 1.494189 CGCGGAAGTAAAACACCCG 59.506 57.895 0.00 0.00 38.02 5.28
508 1362 1.494189 CGGAAGTAAAACACCCGCG 59.506 57.895 0.00 0.00 31.08 6.46
510 1364 1.508808 GGAAGTAAAACACCCGCGCA 61.509 55.000 8.75 0.00 0.00 6.09
618 1509 7.789273 TGTTGACTAGACTAGATACTGCTAC 57.211 40.000 16.55 5.93 0.00 3.58
689 2062 6.546428 ACTGTAGTAGACTAGTACCGGTAA 57.454 41.667 17.78 0.00 34.43 2.85
690 2063 6.342111 ACTGTAGTAGACTAGTACCGGTAAC 58.658 44.000 17.78 9.12 34.43 2.50
691 2064 6.155393 ACTGTAGTAGACTAGTACCGGTAACT 59.845 42.308 17.78 16.22 34.43 2.24
692 2065 7.342284 ACTGTAGTAGACTAGTACCGGTAACTA 59.658 40.741 17.78 15.17 34.43 2.24
693 2066 8.074613 TGTAGTAGACTAGTACCGGTAACTAA 57.925 38.462 17.78 6.94 34.43 2.24
734 2107 4.037565 GTCAAACTTCCCCATCGAAAAGTT 59.962 41.667 0.00 0.00 42.20 2.66
766 2139 0.251653 TCCACGTCTAGAACCCAGCT 60.252 55.000 0.00 0.00 0.00 4.24
773 2146 4.202284 ACGTCTAGAACCCAGCTAACAAAA 60.202 41.667 0.00 0.00 0.00 2.44
774 2147 4.389077 CGTCTAGAACCCAGCTAACAAAAG 59.611 45.833 0.00 0.00 0.00 2.27
775 2148 5.548406 GTCTAGAACCCAGCTAACAAAAGA 58.452 41.667 0.00 0.00 0.00 2.52
776 2149 6.174049 GTCTAGAACCCAGCTAACAAAAGAT 58.826 40.000 0.00 0.00 0.00 2.40
777 2150 6.655425 GTCTAGAACCCAGCTAACAAAAGATT 59.345 38.462 0.00 0.00 0.00 2.40
778 2151 7.175119 GTCTAGAACCCAGCTAACAAAAGATTT 59.825 37.037 0.00 0.00 0.00 2.17
779 2152 6.332735 AGAACCCAGCTAACAAAAGATTTC 57.667 37.500 0.00 0.00 0.00 2.17
780 2153 5.833131 AGAACCCAGCTAACAAAAGATTTCA 59.167 36.000 0.00 0.00 0.00 2.69
781 2154 6.323739 AGAACCCAGCTAACAAAAGATTTCAA 59.676 34.615 0.00 0.00 0.00 2.69
782 2155 6.478512 ACCCAGCTAACAAAAGATTTCAAA 57.521 33.333 0.00 0.00 0.00 2.69
783 2156 6.883744 ACCCAGCTAACAAAAGATTTCAAAA 58.116 32.000 0.00 0.00 0.00 2.44
784 2157 7.334858 ACCCAGCTAACAAAAGATTTCAAAAA 58.665 30.769 0.00 0.00 0.00 1.94
902 2369 2.549926 CATTACACAGTGCAGCCGATA 58.450 47.619 0.00 0.00 0.00 2.92
910 2377 1.001406 AGTGCAGCCGATAGATTAGCC 59.999 52.381 0.00 0.00 39.76 3.93
911 2378 0.038251 TGCAGCCGATAGATTAGCCG 60.038 55.000 0.00 0.00 39.76 5.52
914 2381 1.813178 CAGCCGATAGATTAGCCGAGA 59.187 52.381 0.00 0.00 39.76 4.04
915 2382 2.088423 AGCCGATAGATTAGCCGAGAG 58.912 52.381 0.00 0.00 39.76 3.20
916 2383 1.468395 GCCGATAGATTAGCCGAGAGC 60.468 57.143 0.00 0.00 40.01 4.09
917 2384 1.202087 CCGATAGATTAGCCGAGAGCG 60.202 57.143 0.00 0.00 44.18 5.03
918 2385 1.732809 CGATAGATTAGCCGAGAGCGA 59.267 52.381 0.00 0.00 44.18 4.93
919 2386 2.353269 CGATAGATTAGCCGAGAGCGAT 59.647 50.000 0.00 0.00 44.18 4.58
920 2387 3.556365 CGATAGATTAGCCGAGAGCGATA 59.444 47.826 0.00 0.00 44.18 2.92
921 2388 4.551217 CGATAGATTAGCCGAGAGCGATAC 60.551 50.000 0.00 0.00 44.18 2.24
922 2389 6.919684 CGATAGATTAGCCGAGAGCGATACA 61.920 48.000 0.00 0.00 44.18 2.29
923 2390 8.824157 CGATAGATTAGCCGAGAGCGATACAC 62.824 50.000 0.00 0.00 44.18 2.90
925 2392 2.713770 GCCGAGAGCGATACACGA 59.286 61.111 0.00 0.00 45.77 4.35
926 2393 1.654743 GCCGAGAGCGATACACGAC 60.655 63.158 0.00 0.00 45.77 4.34
927 2394 1.009900 CCGAGAGCGATACACGACC 60.010 63.158 0.00 0.00 45.77 4.79
928 2395 1.367782 CGAGAGCGATACACGACCG 60.368 63.158 0.00 0.00 45.77 4.79
929 2396 1.759293 CGAGAGCGATACACGACCGA 61.759 60.000 0.00 0.00 45.77 4.69
1532 3098 0.107831 AACTGCGCCAAGTGTAGGAA 59.892 50.000 4.18 0.00 30.40 3.36
1825 5762 6.365520 AGTCCCTGAACTTGAAAAATACACT 58.634 36.000 0.00 0.00 0.00 3.55
1828 5765 6.486657 TCCCTGAACTTGAAAAATACACTGAG 59.513 38.462 0.00 0.00 0.00 3.35
1895 5832 5.417894 TCTCATCCATAGACGTAAAGTGTGT 59.582 40.000 0.00 0.00 0.00 3.72
1906 5843 0.531974 AAAGTGTGTCGACGTGGCAT 60.532 50.000 11.62 0.00 0.00 4.40
1922 5859 1.350193 GCATCGTATATGGCTGACGG 58.650 55.000 0.00 0.00 37.20 4.79
2004 5950 7.475015 TGCAAGAGATTCGGATTAAAATTCAG 58.525 34.615 0.00 0.00 0.00 3.02
2017 5963 4.605640 AAAATTCAGTTCCATGTGTGGG 57.394 40.909 0.00 0.00 46.06 4.61
2110 6057 2.033141 AGCTCATGGCACTTGCGT 59.967 55.556 8.58 0.00 44.79 5.24
2140 6087 0.741326 GCTCGTGCTCTATGGACTCA 59.259 55.000 1.41 0.00 34.66 3.41
2148 6095 5.181748 GTGCTCTATGGACTCAAAGAATGT 58.818 41.667 0.00 0.00 33.97 2.71
2187 6137 1.006813 AGCTCCTCCAGGAAGAGAGA 58.993 55.000 18.27 0.00 44.91 3.10
2238 6188 0.820891 ACAAGTTGCACCTCAGCCAG 60.821 55.000 1.81 0.00 0.00 4.85
2261 6211 1.229209 TGTTCCCTCTCCTCGGCTT 60.229 57.895 0.00 0.00 0.00 4.35
2416 6369 1.510383 GTGCCAAGCAACACACACA 59.490 52.632 0.00 0.00 41.47 3.72
2420 6373 1.318886 CCAAGCAACACACACACCCA 61.319 55.000 0.00 0.00 0.00 4.51
2511 6465 2.425312 ACGGCAACTTCAACATGTTCAA 59.575 40.909 8.48 0.26 0.00 2.69
2521 6475 4.468713 TCAACATGTTCAAGGATGGTGAA 58.531 39.130 8.48 0.00 42.10 3.18
2593 6547 0.250901 GGTCTGGTGATGTGGTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
2599 6553 1.538047 GTGATGTGGTGCTTGTGGAT 58.462 50.000 0.00 0.00 0.00 3.41
2638 6592 0.665068 CGGATTCAACGACGTGGTGA 60.665 55.000 3.24 2.63 0.00 4.02
2706 6660 6.864421 TCATAGACACCATCTATCCTTACCT 58.136 40.000 0.00 0.00 46.04 3.08
2749 6703 4.857588 CCGTGCTAGACAACTAACTTACTG 59.142 45.833 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.291877 GCGTCTGACCAGCGATGTTT 61.292 55.000 14.56 0.00 32.49 2.83
1 2 1.738099 GCGTCTGACCAGCGATGTT 60.738 57.895 14.56 0.00 32.49 2.71
2 3 2.125912 GCGTCTGACCAGCGATGT 60.126 61.111 14.56 0.00 32.49 3.06
3 4 1.485838 GATGCGTCTGACCAGCGATG 61.486 60.000 14.56 0.00 32.49 3.84
4 5 1.227089 GATGCGTCTGACCAGCGAT 60.227 57.895 14.56 0.00 32.49 4.58
5 6 2.153547 TTGATGCGTCTGACCAGCGA 62.154 55.000 7.58 1.73 32.49 4.93
6 7 1.086067 ATTGATGCGTCTGACCAGCG 61.086 55.000 7.58 8.66 0.00 5.18
7 8 1.089920 AATTGATGCGTCTGACCAGC 58.910 50.000 7.58 5.06 0.00 4.85
8 9 2.286294 GCTAATTGATGCGTCTGACCAG 59.714 50.000 7.58 0.00 0.00 4.00
9 10 2.279741 GCTAATTGATGCGTCTGACCA 58.720 47.619 7.58 1.96 0.00 4.02
10 11 2.279741 TGCTAATTGATGCGTCTGACC 58.720 47.619 7.58 0.00 0.00 4.02
11 12 2.286067 GCTGCTAATTGATGCGTCTGAC 60.286 50.000 7.58 0.00 0.00 3.51
12 13 1.935873 GCTGCTAATTGATGCGTCTGA 59.064 47.619 7.58 0.00 0.00 3.27
13 14 1.003116 GGCTGCTAATTGATGCGTCTG 60.003 52.381 7.58 0.00 0.00 3.51
14 15 1.303309 GGCTGCTAATTGATGCGTCT 58.697 50.000 7.58 0.00 0.00 4.18
15 16 0.308993 GGGCTGCTAATTGATGCGTC 59.691 55.000 0.00 0.00 0.00 5.19
16 17 1.439353 CGGGCTGCTAATTGATGCGT 61.439 55.000 0.00 0.00 0.00 5.24
17 18 1.280746 CGGGCTGCTAATTGATGCG 59.719 57.895 0.00 0.00 0.00 4.73
18 19 0.819259 TCCGGGCTGCTAATTGATGC 60.819 55.000 0.00 0.00 0.00 3.91
19 20 1.679139 TTCCGGGCTGCTAATTGATG 58.321 50.000 0.00 0.00 0.00 3.07
20 21 2.435372 TTTCCGGGCTGCTAATTGAT 57.565 45.000 0.00 0.00 0.00 2.57
21 22 2.208132 TTTTCCGGGCTGCTAATTGA 57.792 45.000 0.00 0.00 0.00 2.57
38 39 2.034812 TGCTCGGCCGTTAATTGTTTTT 59.965 40.909 27.15 0.00 0.00 1.94
39 40 1.609555 TGCTCGGCCGTTAATTGTTTT 59.390 42.857 27.15 0.00 0.00 2.43
40 41 1.199097 CTGCTCGGCCGTTAATTGTTT 59.801 47.619 27.15 0.00 0.00 2.83
41 42 0.802494 CTGCTCGGCCGTTAATTGTT 59.198 50.000 27.15 0.00 0.00 2.83
111 113 0.035739 TTGACCGGGGTTAACTGCTC 59.964 55.000 6.32 0.00 0.00 4.26
115 117 0.474273 TCCCTTGACCGGGGTTAACT 60.474 55.000 6.32 0.00 44.78 2.24
121 123 1.493022 TGATTTATCCCTTGACCGGGG 59.507 52.381 6.32 0.00 44.78 5.73
122 124 2.949644 GTTGATTTATCCCTTGACCGGG 59.050 50.000 6.32 0.00 46.13 5.73
136 138 6.655078 AGCAGTCCAAGTTATTGTTGATTT 57.345 33.333 0.00 0.00 34.39 2.17
179 181 4.822026 AGCTAGCAAGTTGTCTTCGTTAT 58.178 39.130 18.83 0.00 0.00 1.89
180 182 4.022242 AGAGCTAGCAAGTTGTCTTCGTTA 60.022 41.667 18.83 0.00 0.00 3.18
181 183 3.060602 GAGCTAGCAAGTTGTCTTCGTT 58.939 45.455 18.83 0.00 0.00 3.85
183 185 2.920490 GAGAGCTAGCAAGTTGTCTTCG 59.080 50.000 18.83 0.00 0.00 3.79
184 186 3.258228 GGAGAGCTAGCAAGTTGTCTTC 58.742 50.000 18.83 4.66 0.00 2.87
185 187 2.353208 CGGAGAGCTAGCAAGTTGTCTT 60.353 50.000 18.83 0.00 0.00 3.01
187 189 1.067495 ACGGAGAGCTAGCAAGTTGTC 60.067 52.381 18.83 4.25 0.00 3.18
188 190 0.969894 ACGGAGAGCTAGCAAGTTGT 59.030 50.000 18.83 6.80 0.00 3.32
189 191 2.941453 TACGGAGAGCTAGCAAGTTG 57.059 50.000 18.83 6.12 0.00 3.16
190 192 3.510360 TCTTTACGGAGAGCTAGCAAGTT 59.490 43.478 18.83 0.00 0.00 2.66
191 193 3.090037 TCTTTACGGAGAGCTAGCAAGT 58.910 45.455 18.83 11.10 0.00 3.16
192 194 3.784701 TCTTTACGGAGAGCTAGCAAG 57.215 47.619 18.83 9.07 0.00 4.01
193 195 4.530710 TTTCTTTACGGAGAGCTAGCAA 57.469 40.909 18.83 0.00 0.00 3.91
194 196 4.737855 ATTTCTTTACGGAGAGCTAGCA 57.262 40.909 18.83 0.00 0.00 3.49
195 197 8.298140 TCTTATATTTCTTTACGGAGAGCTAGC 58.702 37.037 6.62 6.62 0.00 3.42
198 200 8.861086 TGATCTTATATTTCTTTACGGAGAGCT 58.139 33.333 0.00 0.00 0.00 4.09
199 201 9.646427 ATGATCTTATATTTCTTTACGGAGAGC 57.354 33.333 0.00 0.00 0.00 4.09
247 936 2.814336 GCAATTTTGAGACGGAAGGAGT 59.186 45.455 0.00 0.00 0.00 3.85
255 944 1.135972 CCTCGGTGCAATTTTGAGACG 60.136 52.381 0.00 0.00 0.00 4.18
258 1091 3.666902 CGTAACCTCGGTGCAATTTTGAG 60.667 47.826 0.00 0.00 0.00 3.02
261 1094 1.538075 CCGTAACCTCGGTGCAATTTT 59.462 47.619 0.00 0.00 44.77 1.82
292 1125 2.815211 CGTGACGTCCATGCCCAG 60.815 66.667 14.12 0.00 0.00 4.45
339 1172 0.722282 AGACGAGATCGACACGACTG 59.278 55.000 9.58 0.00 43.02 3.51
378 1211 4.157656 CCAAATTTATTGTCTCGGCTGGAA 59.842 41.667 0.00 0.00 0.00 3.53
381 1214 4.155826 TCACCAAATTTATTGTCTCGGCTG 59.844 41.667 0.00 0.00 0.00 4.85
431 1264 2.604174 CGGTTGTTCACACTCCCGC 61.604 63.158 0.00 0.00 32.53 6.13
444 1277 3.880162 TACGGGTTTCGGCCGGTTG 62.880 63.158 27.83 11.99 44.45 3.77
445 1278 3.624872 TACGGGTTTCGGCCGGTT 61.625 61.111 27.83 4.30 44.45 4.44
618 1509 5.970592 TCAATCTTGTCATGTGAGTCTAGG 58.029 41.667 0.00 0.00 0.00 3.02
683 2056 3.488721 CGGTGTGAGAGATTAGTTACCGG 60.489 52.174 0.00 0.00 44.26 5.28
685 2058 3.445857 GCGGTGTGAGAGATTAGTTACC 58.554 50.000 0.00 0.00 0.00 2.85
686 2059 3.106672 CGCGGTGTGAGAGATTAGTTAC 58.893 50.000 0.00 0.00 0.00 2.50
687 2060 2.479049 GCGCGGTGTGAGAGATTAGTTA 60.479 50.000 8.83 0.00 0.00 2.24
688 2061 1.736032 GCGCGGTGTGAGAGATTAGTT 60.736 52.381 8.83 0.00 0.00 2.24
689 2062 0.179134 GCGCGGTGTGAGAGATTAGT 60.179 55.000 8.83 0.00 0.00 2.24
690 2063 0.872021 GGCGCGGTGTGAGAGATTAG 60.872 60.000 8.83 0.00 0.00 1.73
691 2064 1.141019 GGCGCGGTGTGAGAGATTA 59.859 57.895 8.83 0.00 0.00 1.75
692 2065 2.125512 GGCGCGGTGTGAGAGATT 60.126 61.111 8.83 0.00 0.00 2.40
693 2066 4.498520 CGGCGCGGTGTGAGAGAT 62.499 66.667 8.83 0.00 0.00 2.75
787 2160 5.175127 CAAGTGTTTGTTAGCTGGGTTTTT 58.825 37.500 0.00 0.00 0.00 1.94
788 2161 4.754322 CAAGTGTTTGTTAGCTGGGTTTT 58.246 39.130 0.00 0.00 0.00 2.43
789 2162 3.430236 GCAAGTGTTTGTTAGCTGGGTTT 60.430 43.478 0.00 0.00 36.65 3.27
790 2163 2.100749 GCAAGTGTTTGTTAGCTGGGTT 59.899 45.455 0.00 0.00 36.65 4.11
791 2164 1.681264 GCAAGTGTTTGTTAGCTGGGT 59.319 47.619 0.00 0.00 36.65 4.51
792 2165 1.334960 CGCAAGTGTTTGTTAGCTGGG 60.335 52.381 0.00 0.00 36.65 4.45
793 2166 1.601903 TCGCAAGTGTTTGTTAGCTGG 59.398 47.619 0.00 0.00 36.65 4.85
794 2167 2.908634 CTCGCAAGTGTTTGTTAGCTG 58.091 47.619 0.00 0.00 36.65 4.24
795 2168 1.264288 GCTCGCAAGTGTTTGTTAGCT 59.736 47.619 0.00 0.00 39.26 3.32
796 2169 1.663161 GGCTCGCAAGTGTTTGTTAGC 60.663 52.381 7.17 7.17 40.45 3.09
797 2170 1.601903 TGGCTCGCAAGTGTTTGTTAG 59.398 47.619 0.00 0.00 36.65 2.34
798 2171 1.669604 TGGCTCGCAAGTGTTTGTTA 58.330 45.000 0.00 0.00 36.65 2.41
799 2172 0.814457 TTGGCTCGCAAGTGTTTGTT 59.186 45.000 0.00 0.00 36.65 2.83
800 2173 0.814457 TTTGGCTCGCAAGTGTTTGT 59.186 45.000 0.00 0.00 36.65 2.83
801 2174 1.199624 GTTTGGCTCGCAAGTGTTTG 58.800 50.000 0.00 0.00 37.36 2.93
802 2175 0.102300 GGTTTGGCTCGCAAGTGTTT 59.898 50.000 0.00 0.00 39.48 2.83
803 2176 1.733526 GGTTTGGCTCGCAAGTGTT 59.266 52.632 0.00 0.00 39.48 3.32
804 2177 2.193536 GGGTTTGGCTCGCAAGTGT 61.194 57.895 0.00 0.00 39.48 3.55
834 2266 2.158943 GGTGGCTCTTATAGTGTGTCCC 60.159 54.545 0.00 0.00 0.00 4.46
835 2267 2.500098 TGGTGGCTCTTATAGTGTGTCC 59.500 50.000 0.00 0.00 0.00 4.02
836 2268 3.786635 CTGGTGGCTCTTATAGTGTGTC 58.213 50.000 0.00 0.00 0.00 3.67
841 2273 1.879575 TGGCTGGTGGCTCTTATAGT 58.120 50.000 0.00 0.00 41.46 2.12
842 2274 3.615110 CGTATGGCTGGTGGCTCTTATAG 60.615 52.174 0.00 0.00 41.46 1.31
902 2369 2.226912 GTGTATCGCTCTCGGCTAATCT 59.773 50.000 0.00 0.00 39.13 2.40
910 2377 1.367782 CGGTCGTGTATCGCTCTCG 60.368 63.158 0.00 0.00 39.67 4.04
911 2378 0.042013 CTCGGTCGTGTATCGCTCTC 60.042 60.000 0.00 0.00 39.67 3.20
914 2381 2.408022 GCTCGGTCGTGTATCGCT 59.592 61.111 0.00 0.00 39.67 4.93
915 2382 3.017314 CGCTCGGTCGTGTATCGC 61.017 66.667 0.00 0.00 39.67 4.58
916 2383 1.650536 GTCGCTCGGTCGTGTATCG 60.651 63.158 0.00 0.00 41.41 2.92
917 2384 0.098376 AAGTCGCTCGGTCGTGTATC 59.902 55.000 0.00 0.00 0.00 2.24
918 2385 0.524862 AAAGTCGCTCGGTCGTGTAT 59.475 50.000 0.00 0.00 0.00 2.29
919 2386 0.311790 AAAAGTCGCTCGGTCGTGTA 59.688 50.000 0.00 0.00 0.00 2.90
920 2387 0.529119 AAAAAGTCGCTCGGTCGTGT 60.529 50.000 0.00 0.00 0.00 4.49
921 2388 0.111266 CAAAAAGTCGCTCGGTCGTG 60.111 55.000 0.00 0.00 0.00 4.35
922 2389 0.249155 TCAAAAAGTCGCTCGGTCGT 60.249 50.000 0.00 0.00 0.00 4.34
923 2390 1.059264 GATCAAAAAGTCGCTCGGTCG 59.941 52.381 0.00 0.00 0.00 4.79
924 2391 1.059264 CGATCAAAAAGTCGCTCGGTC 59.941 52.381 0.00 0.00 0.00 4.79
925 2392 1.068474 CGATCAAAAAGTCGCTCGGT 58.932 50.000 0.00 0.00 0.00 4.69
926 2393 0.370273 CCGATCAAAAAGTCGCTCGG 59.630 55.000 0.00 0.00 39.58 4.63
927 2394 0.370273 CCCGATCAAAAAGTCGCTCG 59.630 55.000 0.00 0.00 36.57 5.03
928 2395 0.727398 CCCCGATCAAAAAGTCGCTC 59.273 55.000 0.00 0.00 36.57 5.03
929 2396 0.676782 CCCCCGATCAAAAAGTCGCT 60.677 55.000 0.00 0.00 36.57 4.93
1227 2743 4.389576 CCAACCGCGTGCAGCTTC 62.390 66.667 4.92 0.00 45.59 3.86
1344 2893 4.796231 CCGACGGCGAACTGGAGG 62.796 72.222 15.16 1.65 40.82 4.30
1449 3007 3.403057 CACGACGCCAACTCCGTG 61.403 66.667 0.00 0.00 44.66 4.94
1825 5762 2.884639 GCCAAGTTTTAGAACCAGCTCA 59.115 45.455 0.00 0.00 36.39 4.26
1828 5765 2.360801 TGTGCCAAGTTTTAGAACCAGC 59.639 45.455 0.00 0.00 36.39 4.85
1895 5832 1.068816 CCATATACGATGCCACGTCGA 60.069 52.381 15.47 0.86 45.32 4.20
1906 5843 1.663739 GCCCGTCAGCCATATACGA 59.336 57.895 0.00 0.00 38.89 3.43
2017 5963 3.119463 CGATGAATTTGGTGTTTGCGTTC 59.881 43.478 0.00 0.00 0.00 3.95
2140 6087 4.617959 TCGTCGAGAACTGAACATTCTTT 58.382 39.130 0.00 0.00 36.53 2.52
2148 6095 0.522180 GCTCCTCGTCGAGAACTGAA 59.478 55.000 23.74 1.25 30.97 3.02
2187 6137 2.173519 CCAATGACACCTTCATGGCTT 58.826 47.619 0.00 0.00 44.86 4.35
2238 6188 3.003763 AGGAGAGGGAACACCGCC 61.004 66.667 0.00 0.00 46.96 6.13
2261 6211 1.174078 TGTGTTAGCGTCGTCTCCCA 61.174 55.000 0.00 0.00 0.00 4.37
2357 6310 1.224069 GGCATGCATCTACGACGCAT 61.224 55.000 21.36 0.00 42.25 4.73
2358 6311 1.882625 GGCATGCATCTACGACGCA 60.883 57.895 21.36 0.00 34.65 5.24
2416 6369 4.822896 GTGATCTCTATCTAGAACGTGGGT 59.177 45.833 0.00 0.00 32.93 4.51
2420 6373 5.686753 AGTGGTGATCTCTATCTAGAACGT 58.313 41.667 0.00 0.00 32.93 3.99
2511 6465 0.839946 CCGGATTCCTTCACCATCCT 59.160 55.000 0.00 0.00 35.23 3.24
2549 6503 2.669569 GAGCTTCCAGCCGTGCAA 60.670 61.111 0.00 0.00 43.77 4.08
2550 6504 3.474486 TTGAGCTTCCAGCCGTGCA 62.474 57.895 0.00 0.00 43.77 4.57
2686 6640 5.964477 TGAAAGGTAAGGATAGATGGTGTCT 59.036 40.000 0.00 0.00 41.11 3.41
2717 6671 5.003804 AGTTGTCTAGCACGGATTTCAAAT 58.996 37.500 0.00 0.00 0.00 2.32
2723 6677 4.803098 AGTTAGTTGTCTAGCACGGATT 57.197 40.909 0.00 0.00 31.27 3.01
2727 6681 5.994235 CAGTAAGTTAGTTGTCTAGCACG 57.006 43.478 0.00 0.00 31.27 5.34


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

AutoCloner maintained by Alex Coulton.