Multiple sequence alignment - TraesCS2A01G535200

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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 TraesCS2A01G535200 chr2A 100.000 2999 0 0 1 2999 750225834 750222836 0.000000e+00 5539
1 TraesCS2A01G535200 chr2A 89.234 1319 123 10 938 2250 749968503 749969808 0.000000e+00 1631
2 TraesCS2A01G535200 chr2A 97.884 567 8 3 2436 2999 93467086 93467651 0.000000e+00 977
3 TraesCS2A01G535200 chr2A 80.934 257 20 9 499 746 749968215 749968451 3.070000e-40 176
4 TraesCS2A01G535200 chr2A 92.000 100 7 1 2337 2435 749969999 749970098 4.030000e-29 139
5 TraesCS2A01G535200 chr2D 93.129 1339 81 2 998 2333 619144983 619146313 0.000000e+00 1953
6 TraesCS2A01G535200 chr2D 89.082 806 35 22 15 815 619144183 619144940 0.000000e+00 952
7 TraesCS2A01G535200 chr2D 79.317 556 99 5 998 1551 586265511 586264970 2.820000e-100 375
8 TraesCS2A01G535200 chr2D 81.622 370 50 16 17 380 152739213 152739570 1.050000e-74 291
9 TraesCS2A01G535200 chr2D 93.233 133 7 2 812 943 294595935 294595804 8.480000e-46 195
10 TraesCS2A01G535200 chr2D 97.959 98 2 0 2338 2435 619146368 619146465 1.430000e-38 171
11 TraesCS2A01G535200 chr2B 92.191 1383 90 7 958 2333 756966629 756968000 0.000000e+00 1940
12 TraesCS2A01G535200 chr2B 89.166 1403 124 9 938 2333 756703694 756705075 0.000000e+00 1724
13 TraesCS2A01G535200 chr2B 89.294 1345 127 4 998 2333 756634704 756636040 0.000000e+00 1670
14 TraesCS2A01G535200 chr2B 90.975 554 37 8 244 790 756966083 756966630 0.000000e+00 734
15 TraesCS2A01G535200 chr2B 86.799 606 80 0 998 1603 757879878 757880483 0.000000e+00 676
16 TraesCS2A01G535200 chr2B 81.989 372 55 9 34 401 210698794 210699157 3.760000e-79 305
17 TraesCS2A01G535200 chr2B 87.500 176 22 0 1000 1175 707715330 707715155 1.410000e-48 204
18 TraesCS2A01G535200 chr2B 93.233 133 7 2 812 943 40675123 40674992 8.480000e-46 195
19 TraesCS2A01G535200 chr2B 93.233 133 7 2 812 943 40701967 40701836 8.480000e-46 195
20 TraesCS2A01G535200 chr2B 79.814 322 22 11 499 817 756703417 756703698 8.480000e-46 195
21 TraesCS2A01G535200 chr2B 96.040 101 4 0 2335 2435 756636091 756636191 6.650000e-37 165
22 TraesCS2A01G535200 chr2B 96.000 100 3 1 2337 2435 756705124 756705223 8.600000e-36 161
23 TraesCS2A01G535200 chr2B 94.118 102 5 1 2335 2435 756968050 756968151 1.440000e-33 154
24 TraesCS2A01G535200 chr3A 98.404 564 7 1 2436 2999 735573321 735572760 0.000000e+00 990
25 TraesCS2A01G535200 chr3A 98.060 567 8 2 2436 2999 3570352 3570918 0.000000e+00 983
26 TraesCS2A01G535200 chr3A 97.884 567 9 2 2435 2999 55870107 55870672 0.000000e+00 977
27 TraesCS2A01G535200 chr3A 77.368 380 66 16 10 383 180812442 180812077 1.090000e-49 207
28 TraesCS2A01G535200 chr7A 98.227 564 9 1 2436 2999 648587350 648587912 0.000000e+00 985
29 TraesCS2A01G535200 chr7A 97.884 567 8 2 2436 2999 69443501 69444066 0.000000e+00 977
30 TraesCS2A01G535200 chr1A 98.050 564 11 0 2436 2999 99510632 99510069 0.000000e+00 981
31 TraesCS2A01G535200 chr1A 96.063 127 4 1 816 942 36767311 36767186 3.920000e-49 206
32 TraesCS2A01G535200 chr6A 97.884 567 9 3 2436 2999 581314342 581314908 0.000000e+00 977
33 TraesCS2A01G535200 chr6A 79.507 527 106 2 1002 1527 593442537 593442012 1.020000e-99 374
34 TraesCS2A01G535200 chr4A 97.217 575 11 4 2428 2999 612940493 612941065 0.000000e+00 968
35 TraesCS2A01G535200 chr4A 89.865 148 14 1 799 945 623322247 623322100 3.950000e-44 189
36 TraesCS2A01G535200 chr3B 80.270 370 51 19 21 380 222191063 222191420 2.970000e-65 259
37 TraesCS2A01G535200 chr3B 91.912 136 11 0 808 943 184611441 184611576 1.100000e-44 191
38 TraesCS2A01G535200 chr3B 93.023 129 8 1 816 944 637085501 637085374 1.420000e-43 187
39 TraesCS2A01G535200 chr5B 80.743 296 40 14 25 313 307401277 307401562 6.510000e-52 215
40 TraesCS2A01G535200 chr5A 77.867 375 57 18 26 395 438151776 438151423 3.030000e-50 209
41 TraesCS2A01G535200 chr5A 78.896 308 42 20 16 314 442356908 442357201 1.420000e-43 187
42 TraesCS2A01G535200 chr5A 78.983 295 41 12 92 383 381307425 381307149 6.600000e-42 182
43 TraesCS2A01G535200 chr3D 93.233 133 7 2 812 943 530632355 530632486 8.480000e-46 195
44 TraesCS2A01G535200 chr6B 91.367 139 10 2 805 942 495435709 495435572 3.950000e-44 189
45 TraesCS2A01G535200 chr1D 84.211 114 13 5 260 371 332402837 332402727 4.090000e-19 106


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 TraesCS2A01G535200 chr2A 750222836 750225834 2998 True 5539.000000 5539 100.000000 1 2999 1 chr2A.!!$R1 2998
1 TraesCS2A01G535200 chr2A 93467086 93467651 565 False 977.000000 977 97.884000 2436 2999 1 chr2A.!!$F1 563
2 TraesCS2A01G535200 chr2A 749968215 749970098 1883 False 648.666667 1631 87.389333 499 2435 3 chr2A.!!$F2 1936
3 TraesCS2A01G535200 chr2D 619144183 619146465 2282 False 1025.333333 1953 93.390000 15 2435 3 chr2D.!!$F2 2420
4 TraesCS2A01G535200 chr2D 586264970 586265511 541 True 375.000000 375 79.317000 998 1551 1 chr2D.!!$R2 553
5 TraesCS2A01G535200 chr2B 756966083 756968151 2068 False 942.666667 1940 92.428000 244 2435 3 chr2B.!!$F5 2191
6 TraesCS2A01G535200 chr2B 756634704 756636191 1487 False 917.500000 1670 92.667000 998 2435 2 chr2B.!!$F3 1437
7 TraesCS2A01G535200 chr2B 756703417 756705223 1806 False 693.333333 1724 88.326667 499 2435 3 chr2B.!!$F4 1936
8 TraesCS2A01G535200 chr2B 757879878 757880483 605 False 676.000000 676 86.799000 998 1603 1 chr2B.!!$F2 605
9 TraesCS2A01G535200 chr3A 735572760 735573321 561 True 990.000000 990 98.404000 2436 2999 1 chr3A.!!$R2 563
10 TraesCS2A01G535200 chr3A 3570352 3570918 566 False 983.000000 983 98.060000 2436 2999 1 chr3A.!!$F1 563
11 TraesCS2A01G535200 chr3A 55870107 55870672 565 False 977.000000 977 97.884000 2435 2999 1 chr3A.!!$F2 564
12 TraesCS2A01G535200 chr7A 648587350 648587912 562 False 985.000000 985 98.227000 2436 2999 1 chr7A.!!$F2 563
13 TraesCS2A01G535200 chr7A 69443501 69444066 565 False 977.000000 977 97.884000 2436 2999 1 chr7A.!!$F1 563
14 TraesCS2A01G535200 chr1A 99510069 99510632 563 True 981.000000 981 98.050000 2436 2999 1 chr1A.!!$R2 563
15 TraesCS2A01G535200 chr6A 581314342 581314908 566 False 977.000000 977 97.884000 2436 2999 1 chr6A.!!$F1 563
16 TraesCS2A01G535200 chr6A 593442012 593442537 525 True 374.000000 374 79.507000 1002 1527 1 chr6A.!!$R1 525
17 TraesCS2A01G535200 chr4A 612940493 612941065 572 False 968.000000 968 97.217000 2428 2999 1 chr4A.!!$F1 571

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
215 217 0.189574 TCCTGTTGATTTTGGGGCCA 59.810 50.0 4.39 0.0 0.00 5.36 F
835 857 0.754472 ACTCCCTTCGTCCGAAAACA 59.246 50.0 3.52 0.0 33.34 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1155 0.836400 TTGTCGGGGAGAAGAAGCCT 60.836 55.0 0.00 0.0 0.0 4.58 R
2789 2955 0.455464 CGTATCGTCGACCAAGCACA 60.455 55.0 10.58 0.0 0.0 4.57 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
22 23 2.791383 TTTTGCGGGTGAACATTGAG 57.209 45.000 0.00 0.00 0.00 3.02
106 107 5.838529 ACACGCATGTATAGCAATGTAGTA 58.161 37.500 0.00 0.00 37.26 1.82
107 108 5.920840 ACACGCATGTATAGCAATGTAGTAG 59.079 40.000 0.00 0.00 37.26 2.57
108 109 5.920840 CACGCATGTATAGCAATGTAGTAGT 59.079 40.000 0.00 0.00 0.00 2.73
109 110 7.081976 CACGCATGTATAGCAATGTAGTAGTA 58.918 38.462 0.00 0.00 0.00 1.82
110 111 7.755373 CACGCATGTATAGCAATGTAGTAGTAT 59.245 37.037 0.00 0.00 0.00 2.12
111 112 8.953313 ACGCATGTATAGCAATGTAGTAGTATA 58.047 33.333 0.00 0.00 0.00 1.47
112 113 9.952188 CGCATGTATAGCAATGTAGTAGTATAT 57.048 33.333 0.00 0.00 0.00 0.86
116 117 9.117183 TGTATAGCAATGTAGTAGTATATCGGG 57.883 37.037 0.00 0.00 0.00 5.14
117 118 9.118300 GTATAGCAATGTAGTAGTATATCGGGT 57.882 37.037 0.00 0.00 0.00 5.28
118 119 6.512342 AGCAATGTAGTAGTATATCGGGTC 57.488 41.667 0.00 0.00 0.00 4.46
121 122 7.178628 AGCAATGTAGTAGTATATCGGGTCAAT 59.821 37.037 0.00 0.00 0.00 2.57
215 217 0.189574 TCCTGTTGATTTTGGGGCCA 59.810 50.000 4.39 0.00 0.00 5.36
228 230 1.760029 TGGGGCCAAAACTTTGTCTTC 59.240 47.619 4.39 0.00 36.45 2.87
238 240 3.427161 ACTTTGTCTTCTTTGTGCAGC 57.573 42.857 0.00 0.00 0.00 5.25
395 398 1.826054 CCCGTGCACCAAAAGTCCA 60.826 57.895 12.15 0.00 0.00 4.02
468 471 2.224548 ACACCAGCTTACCTTTCTCCAC 60.225 50.000 0.00 0.00 0.00 4.02
532 541 1.747145 CAAGCAAACCCACATGCCA 59.253 52.632 0.00 0.00 43.57 4.92
559 568 1.774110 TCTCCTGTCATCCTCTCAGC 58.226 55.000 0.00 0.00 0.00 4.26
645 654 2.050144 TGGACTTTTGAGTCTCCAGCT 58.950 47.619 6.53 0.00 38.74 4.24
680 692 6.040955 TCTGGCCATATGTGCTAGCTATATAC 59.959 42.308 17.23 13.60 37.26 1.47
751 766 1.521616 CTGCTCTGCTCTCTTCCCC 59.478 63.158 0.00 0.00 0.00 4.81
815 837 9.533831 ACCTTGATGTTTTTATCCTTATCAACT 57.466 29.630 0.00 0.00 32.83 3.16
821 843 9.628500 ATGTTTTTATCCTTATCAACTACTCCC 57.372 33.333 0.00 0.00 0.00 4.30
822 844 8.832735 TGTTTTTATCCTTATCAACTACTCCCT 58.167 33.333 0.00 0.00 0.00 4.20
823 845 9.682465 GTTTTTATCCTTATCAACTACTCCCTT 57.318 33.333 0.00 0.00 0.00 3.95
824 846 9.901172 TTTTTATCCTTATCAACTACTCCCTTC 57.099 33.333 0.00 0.00 0.00 3.46
825 847 5.793030 ATCCTTATCAACTACTCCCTTCG 57.207 43.478 0.00 0.00 0.00 3.79
826 848 4.607239 TCCTTATCAACTACTCCCTTCGT 58.393 43.478 0.00 0.00 0.00 3.85
827 849 4.643784 TCCTTATCAACTACTCCCTTCGTC 59.356 45.833 0.00 0.00 0.00 4.20
828 850 4.202131 CCTTATCAACTACTCCCTTCGTCC 60.202 50.000 0.00 0.00 0.00 4.79
829 851 1.171308 TCAACTACTCCCTTCGTCCG 58.829 55.000 0.00 0.00 0.00 4.79
830 852 1.171308 CAACTACTCCCTTCGTCCGA 58.829 55.000 0.00 0.00 0.00 4.55
831 853 1.542915 CAACTACTCCCTTCGTCCGAA 59.457 52.381 1.81 1.81 0.00 4.30
832 854 1.915141 ACTACTCCCTTCGTCCGAAA 58.085 50.000 3.52 0.00 33.34 3.46
833 855 2.242043 ACTACTCCCTTCGTCCGAAAA 58.758 47.619 3.52 0.00 33.34 2.29
834 856 2.029560 ACTACTCCCTTCGTCCGAAAAC 60.030 50.000 3.52 0.00 33.34 2.43
835 857 0.754472 ACTCCCTTCGTCCGAAAACA 59.246 50.000 3.52 0.00 33.34 2.83
836 858 1.145803 CTCCCTTCGTCCGAAAACAC 58.854 55.000 3.52 0.00 33.34 3.32
837 859 0.754472 TCCCTTCGTCCGAAAACACT 59.246 50.000 3.52 0.00 33.34 3.55
838 860 1.139455 TCCCTTCGTCCGAAAACACTT 59.861 47.619 3.52 0.00 33.34 3.16
839 861 1.263217 CCCTTCGTCCGAAAACACTTG 59.737 52.381 3.52 0.00 33.34 3.16
840 862 1.937899 CCTTCGTCCGAAAACACTTGT 59.062 47.619 3.52 0.00 33.34 3.16
841 863 2.033151 CCTTCGTCCGAAAACACTTGTC 60.033 50.000 3.52 0.00 33.34 3.18
842 864 2.296831 TCGTCCGAAAACACTTGTCA 57.703 45.000 0.00 0.00 0.00 3.58
843 865 2.828877 TCGTCCGAAAACACTTGTCAT 58.171 42.857 0.00 0.00 0.00 3.06
844 866 2.798283 TCGTCCGAAAACACTTGTCATC 59.202 45.455 0.00 0.00 0.00 2.92
845 867 2.542178 CGTCCGAAAACACTTGTCATCA 59.458 45.455 0.00 0.00 0.00 3.07
846 868 3.001838 CGTCCGAAAACACTTGTCATCAA 59.998 43.478 0.00 0.00 0.00 2.57
847 869 4.495019 CGTCCGAAAACACTTGTCATCAAA 60.495 41.667 0.00 0.00 32.87 2.69
848 870 5.336744 GTCCGAAAACACTTGTCATCAAAA 58.663 37.500 0.00 0.00 32.87 2.44
849 871 5.977129 GTCCGAAAACACTTGTCATCAAAAT 59.023 36.000 0.00 0.00 32.87 1.82
850 872 5.976534 TCCGAAAACACTTGTCATCAAAATG 59.023 36.000 0.00 0.00 32.87 2.32
851 873 5.175491 CCGAAAACACTTGTCATCAAAATGG 59.825 40.000 0.00 0.00 33.42 3.16
852 874 5.976534 CGAAAACACTTGTCATCAAAATGGA 59.023 36.000 0.00 0.00 33.42 3.41
853 875 6.642131 CGAAAACACTTGTCATCAAAATGGAT 59.358 34.615 0.00 0.00 33.42 3.41
854 876 7.807433 CGAAAACACTTGTCATCAAAATGGATA 59.193 33.333 0.00 0.00 33.42 2.59
855 877 9.474920 GAAAACACTTGTCATCAAAATGGATAA 57.525 29.630 0.00 0.00 33.42 1.75
856 878 9.829507 AAAACACTTGTCATCAAAATGGATAAA 57.170 25.926 0.00 0.00 33.42 1.40
857 879 9.829507 AAACACTTGTCATCAAAATGGATAAAA 57.170 25.926 0.00 0.00 33.42 1.52
858 880 9.480053 AACACTTGTCATCAAAATGGATAAAAG 57.520 29.630 0.00 0.00 33.42 2.27
859 881 8.090214 ACACTTGTCATCAAAATGGATAAAAGG 58.910 33.333 0.00 0.00 33.42 3.11
860 882 8.306038 CACTTGTCATCAAAATGGATAAAAGGA 58.694 33.333 0.00 0.00 33.42 3.36
861 883 8.526147 ACTTGTCATCAAAATGGATAAAAGGAG 58.474 33.333 0.00 0.00 33.42 3.69
862 884 8.648698 TTGTCATCAAAATGGATAAAAGGAGA 57.351 30.769 0.00 0.00 33.42 3.71
863 885 8.827832 TGTCATCAAAATGGATAAAAGGAGAT 57.172 30.769 0.00 0.00 33.42 2.75
864 886 8.689061 TGTCATCAAAATGGATAAAAGGAGATG 58.311 33.333 0.00 0.00 33.42 2.90
865 887 8.689972 GTCATCAAAATGGATAAAAGGAGATGT 58.310 33.333 0.00 0.00 33.42 3.06
866 888 9.919416 TCATCAAAATGGATAAAAGGAGATGTA 57.081 29.630 0.00 0.00 33.42 2.29
874 896 9.607333 ATGGATAAAAGGAGATGTATCTAGACA 57.393 33.333 0.00 0.00 37.25 3.41
875 897 9.607333 TGGATAAAAGGAGATGTATCTAGACAT 57.393 33.333 0.00 0.00 42.82 3.06
929 951 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
930 952 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
931 953 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
932 954 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
933 955 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
934 956 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
935 957 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
936 958 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
937 959 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
938 960 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
939 961 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
964 986 6.655078 AGTTCCATTAATTGCAGACTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
985 1012 8.675705 TTTGTCAACTTTCATCTAATCTGTGA 57.324 30.769 0.00 0.00 0.00 3.58
1264 1293 0.816825 CCCTTGGTCCATGATGCTCG 60.817 60.000 6.33 0.00 0.00 5.03
1426 1455 2.658285 ACAACATGGACATATGGCAGG 58.342 47.619 11.56 1.16 32.32 4.85
1470 1499 6.375455 ACACAATACTTCCAACCATGAGATTC 59.625 38.462 0.00 0.00 0.00 2.52
1485 1514 5.227569 TGAGATTCTTGGTGAGCTACAAA 57.772 39.130 0.00 0.00 0.00 2.83
1503 1532 0.454957 AAGCACAAATCATCGCACGC 60.455 50.000 0.00 0.00 0.00 5.34
1688 1720 1.264557 CACTAGCTCCATCTCGTACCG 59.735 57.143 0.00 0.00 0.00 4.02
1724 1756 3.502595 TCTGGAGACGAGTTCAGTTACAG 59.497 47.826 0.00 0.00 0.00 2.74
1832 1864 1.474879 TGCGTCGTGGATAGTCATCAA 59.525 47.619 0.00 0.00 32.32 2.57
1833 1865 2.100749 TGCGTCGTGGATAGTCATCAAT 59.899 45.455 0.00 0.00 32.32 2.57
1834 1866 2.472861 GCGTCGTGGATAGTCATCAATG 59.527 50.000 0.00 0.00 32.32 2.82
1835 1867 3.795488 GCGTCGTGGATAGTCATCAATGA 60.795 47.826 0.00 0.00 32.32 2.57
1836 1868 3.977579 CGTCGTGGATAGTCATCAATGAG 59.022 47.826 0.00 0.00 37.51 2.90
1837 1869 3.738282 GTCGTGGATAGTCATCAATGAGC 59.262 47.826 0.00 0.00 37.51 4.26
1838 1870 3.638627 TCGTGGATAGTCATCAATGAGCT 59.361 43.478 0.00 0.00 37.51 4.09
1839 1871 4.100035 TCGTGGATAGTCATCAATGAGCTT 59.900 41.667 0.00 0.00 37.51 3.74
1907 1939 3.467803 GTTTGGCTACTGTGACTTCACT 58.532 45.455 10.63 0.00 46.55 3.41
2284 2381 3.497942 GGTATTCGGTATTCCATGCCCTT 60.498 47.826 0.00 0.00 0.00 3.95
2371 2525 6.808008 AGCATACCATTTTCAAGATATCCG 57.192 37.500 0.00 0.00 0.00 4.18
2789 2955 5.329399 AGAGAAGTGTCCTCTGTTATGTCT 58.671 41.667 0.00 0.00 39.36 3.41
2804 2970 1.007734 GTCTGTGCTTGGTCGACGA 60.008 57.895 9.92 1.86 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.269517 GCTCAATGTTCACCCGCAAAA 60.270 47.619 0.00 0.00 0.00 2.44
6 7 1.971167 GGCTCAATGTTCACCCGCA 60.971 57.895 0.00 0.00 0.00 5.69
7 8 1.244019 AAGGCTCAATGTTCACCCGC 61.244 55.000 0.00 0.00 0.00 6.13
8 9 1.247567 AAAGGCTCAATGTTCACCCG 58.752 50.000 0.00 0.00 0.00 5.28
9 10 2.893489 AGAAAAGGCTCAATGTTCACCC 59.107 45.455 0.00 0.00 0.00 4.61
10 11 4.590850 AAGAAAAGGCTCAATGTTCACC 57.409 40.909 0.00 0.00 0.00 4.02
11 12 7.203218 ACTTAAAGAAAAGGCTCAATGTTCAC 58.797 34.615 0.00 0.00 0.00 3.18
12 13 7.346751 ACTTAAAGAAAAGGCTCAATGTTCA 57.653 32.000 0.00 0.00 0.00 3.18
13 14 7.920682 TGAACTTAAAGAAAAGGCTCAATGTTC 59.079 33.333 0.00 0.00 0.00 3.18
14 15 7.781056 TGAACTTAAAGAAAAGGCTCAATGTT 58.219 30.769 0.00 0.00 0.00 2.71
15 16 7.346751 TGAACTTAAAGAAAAGGCTCAATGT 57.653 32.000 0.00 0.00 0.00 2.71
16 17 8.647143 TTTGAACTTAAAGAAAAGGCTCAATG 57.353 30.769 0.00 0.00 34.81 2.82
17 18 9.665719 TTTTTGAACTTAAAGAAAAGGCTCAAT 57.334 25.926 0.00 0.00 34.81 2.57
106 107 8.746052 TTGATGAAAAATTGACCCGATATACT 57.254 30.769 0.00 0.00 0.00 2.12
111 112 8.289618 CGTATATTGATGAAAAATTGACCCGAT 58.710 33.333 0.00 0.00 0.00 4.18
112 113 7.281324 ACGTATATTGATGAAAAATTGACCCGA 59.719 33.333 0.00 0.00 0.00 5.14
113 114 7.375808 CACGTATATTGATGAAAAATTGACCCG 59.624 37.037 0.00 0.00 0.00 5.28
114 115 7.167468 GCACGTATATTGATGAAAAATTGACCC 59.833 37.037 0.00 0.00 0.00 4.46
115 116 7.915397 AGCACGTATATTGATGAAAAATTGACC 59.085 33.333 0.00 0.00 0.00 4.02
116 117 8.841444 AGCACGTATATTGATGAAAAATTGAC 57.159 30.769 0.00 0.00 0.00 3.18
117 118 9.288124 CAAGCACGTATATTGATGAAAAATTGA 57.712 29.630 0.00 0.00 0.00 2.57
118 119 8.051909 GCAAGCACGTATATTGATGAAAAATTG 58.948 33.333 9.90 0.00 0.00 2.32
121 122 6.616017 TGCAAGCACGTATATTGATGAAAAA 58.384 32.000 9.90 0.00 0.00 1.94
133 134 2.094026 TCTCTCACATGCAAGCACGTAT 60.094 45.455 0.00 0.00 0.00 3.06
197 199 1.055040 TTGGCCCCAAAATCAACAGG 58.945 50.000 0.00 0.00 32.44 4.00
198 200 2.926778 TTTGGCCCCAAAATCAACAG 57.073 45.000 9.92 0.00 42.16 3.16
215 217 4.627035 GCTGCACAAAGAAGACAAAGTTTT 59.373 37.500 0.00 0.00 0.00 2.43
228 230 5.863898 TGTTGTATTATACGCTGCACAAAG 58.136 37.500 0.00 0.00 0.00 2.77
262 264 9.485206 GTGGTCTAAGTACTTAGTGAAATTTCA 57.515 33.333 31.98 16.91 42.29 2.69
395 398 5.428184 AAAGAGCCAGCTATGAGTAAAGT 57.572 39.130 0.00 0.00 0.00 2.66
468 471 5.911378 TCGGATGAATATCTCCAGAGATG 57.089 43.478 18.40 1.59 46.80 2.90
532 541 4.712337 AGAGGATGACAGGAGAAACGTAAT 59.288 41.667 0.00 0.00 0.00 1.89
680 692 4.253685 AGGTTGACAATTGACATAGACCG 58.746 43.478 13.59 0.00 0.00 4.79
732 747 1.153389 GGGAAGAGAGCAGAGCAGC 60.153 63.158 0.00 0.00 0.00 5.25
751 766 0.811616 GCACAGATGGCCTACCTTCG 60.812 60.000 3.32 0.00 43.36 3.79
815 837 1.962807 TGTTTTCGGACGAAGGGAGTA 59.037 47.619 7.25 0.00 35.38 2.59
816 838 0.754472 TGTTTTCGGACGAAGGGAGT 59.246 50.000 7.25 0.00 35.38 3.85
817 839 1.145803 GTGTTTTCGGACGAAGGGAG 58.854 55.000 7.25 0.00 35.38 4.30
818 840 0.754472 AGTGTTTTCGGACGAAGGGA 59.246 50.000 7.25 0.00 35.38 4.20
819 841 1.263217 CAAGTGTTTTCGGACGAAGGG 59.737 52.381 7.25 0.00 35.38 3.95
820 842 1.937899 ACAAGTGTTTTCGGACGAAGG 59.062 47.619 7.25 0.00 35.38 3.46
821 843 2.605818 TGACAAGTGTTTTCGGACGAAG 59.394 45.455 7.25 0.00 35.38 3.79
822 844 2.619147 TGACAAGTGTTTTCGGACGAA 58.381 42.857 2.62 2.62 0.00 3.85
823 845 2.296831 TGACAAGTGTTTTCGGACGA 57.703 45.000 0.00 0.00 0.00 4.20
824 846 2.542178 TGATGACAAGTGTTTTCGGACG 59.458 45.455 0.00 0.00 0.00 4.79
825 847 4.545823 TTGATGACAAGTGTTTTCGGAC 57.454 40.909 0.00 0.00 0.00 4.79
826 848 5.568685 TTTTGATGACAAGTGTTTTCGGA 57.431 34.783 0.00 0.00 37.32 4.55
827 849 5.175491 CCATTTTGATGACAAGTGTTTTCGG 59.825 40.000 0.00 0.00 37.32 4.30
828 850 5.976534 TCCATTTTGATGACAAGTGTTTTCG 59.023 36.000 0.00 0.00 37.32 3.46
829 851 7.951530 ATCCATTTTGATGACAAGTGTTTTC 57.048 32.000 0.00 0.00 37.32 2.29
830 852 9.829507 TTTATCCATTTTGATGACAAGTGTTTT 57.170 25.926 0.00 0.00 37.32 2.43
831 853 9.829507 TTTTATCCATTTTGATGACAAGTGTTT 57.170 25.926 0.00 0.00 37.32 2.83
832 854 9.480053 CTTTTATCCATTTTGATGACAAGTGTT 57.520 29.630 0.00 0.00 37.32 3.32
833 855 8.090214 CCTTTTATCCATTTTGATGACAAGTGT 58.910 33.333 0.00 0.00 37.32 3.55
834 856 8.306038 TCCTTTTATCCATTTTGATGACAAGTG 58.694 33.333 0.00 0.00 37.32 3.16
835 857 8.421249 TCCTTTTATCCATTTTGATGACAAGT 57.579 30.769 0.00 0.00 37.32 3.16
836 858 8.742777 TCTCCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
837 859 8.648698 TCTCCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
838 860 8.689061 CATCTCCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 32.05 3.58
839 861 8.689972 ACATCTCCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 33.85 3.06
840 862 8.827832 ACATCTCCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 33.85 2.92
848 870 9.607333 TGTCTAGATACATCTCCTTTTATCCAT 57.393 33.333 0.00 0.00 38.32 3.41
849 871 9.607333 ATGTCTAGATACATCTCCTTTTATCCA 57.393 33.333 0.00 0.00 35.08 3.41
903 925 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
904 926 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
905 927 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
906 928 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
907 929 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
908 930 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
909 931 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
910 932 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
911 933 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
912 934 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
913 935 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
914 936 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
915 937 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
916 938 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
917 939 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
918 940 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
919 941 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
920 942 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
921 943 4.019174 ACTACTTCCTCCGTCCGAAAATA 58.981 43.478 0.00 0.00 0.00 1.40
922 944 2.830321 ACTACTTCCTCCGTCCGAAAAT 59.170 45.455 0.00 0.00 0.00 1.82
923 945 2.242043 ACTACTTCCTCCGTCCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
924 946 1.915141 ACTACTTCCTCCGTCCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
925 947 1.815003 GAACTACTTCCTCCGTCCGAA 59.185 52.381 0.00 0.00 0.00 4.30
926 948 1.457346 GAACTACTTCCTCCGTCCGA 58.543 55.000 0.00 0.00 0.00 4.55
927 949 0.455005 GGAACTACTTCCTCCGTCCG 59.545 60.000 0.00 0.00 42.72 4.79
928 950 1.553706 TGGAACTACTTCCTCCGTCC 58.446 55.000 3.23 0.00 45.87 4.79
929 951 3.889520 AATGGAACTACTTCCTCCGTC 57.110 47.619 3.23 0.00 45.87 4.79
930 952 5.952347 ATTAATGGAACTACTTCCTCCGT 57.048 39.130 3.23 0.00 45.87 4.69
931 953 5.007724 GCAATTAATGGAACTACTTCCTCCG 59.992 44.000 0.00 0.00 45.87 4.63
932 954 5.885912 TGCAATTAATGGAACTACTTCCTCC 59.114 40.000 0.00 0.00 45.87 4.30
933 955 6.823689 TCTGCAATTAATGGAACTACTTCCTC 59.176 38.462 0.00 0.00 45.87 3.71
934 956 6.599638 GTCTGCAATTAATGGAACTACTTCCT 59.400 38.462 0.00 0.00 45.87 3.36
935 957 6.599638 AGTCTGCAATTAATGGAACTACTTCC 59.400 38.462 0.00 0.00 45.89 3.46
936 958 7.617041 AGTCTGCAATTAATGGAACTACTTC 57.383 36.000 0.00 0.00 0.00 3.01
937 959 8.299570 CAAAGTCTGCAATTAATGGAACTACTT 58.700 33.333 0.00 0.00 0.00 2.24
938 960 7.448469 ACAAAGTCTGCAATTAATGGAACTACT 59.552 33.333 0.00 0.00 0.00 2.57
939 961 7.593825 ACAAAGTCTGCAATTAATGGAACTAC 58.406 34.615 0.00 0.00 0.00 2.73
951 973 5.581126 TGAAAGTTGACAAAGTCTGCAAT 57.419 34.783 0.00 0.00 33.15 3.56
964 986 5.869344 CCGTCACAGATTAGATGAAAGTTGA 59.131 40.000 0.00 0.00 0.00 3.18
1128 1155 0.836400 TTGTCGGGGAGAAGAAGCCT 60.836 55.000 0.00 0.00 0.00 4.58
1208 1235 3.124921 GGTTGGCGATCCACACGG 61.125 66.667 0.00 0.00 43.33 4.94
1264 1293 2.669434 TGCGAGAATTGTTAGTTACCGC 59.331 45.455 0.00 0.00 40.40 5.68
1426 1455 2.817258 TGTCGGTTGGATGATCAAAACC 59.183 45.455 20.50 20.50 38.96 3.27
1485 1514 1.135315 GCGTGCGATGATTTGTGCT 59.865 52.632 0.00 0.00 0.00 4.40
1503 1532 1.667722 GCCCTTCCAAGCAACAAGG 59.332 57.895 0.00 0.00 37.09 3.61
1688 1720 3.748568 GTCTCCAGAGGTGACAATTGTTC 59.251 47.826 13.36 6.21 43.28 3.18
1724 1756 2.285977 AGTTGTCGGAAACAGTGAACC 58.714 47.619 0.00 0.00 39.58 3.62
1734 1766 2.549992 CCTGAATGGTGAGTTGTCGGAA 60.550 50.000 0.00 0.00 0.00 4.30
1907 1939 1.075212 TGACATGTTGGAATGGCCTCA 59.925 47.619 3.32 0.00 34.38 3.86
1950 1982 8.800332 TCCTTTAAAAGAGTTACTACTGTCGAT 58.200 33.333 0.00 0.00 33.84 3.59
2025 2057 3.511540 GGAACCTTCATTCCAGGAAAAGG 59.488 47.826 23.61 23.61 46.49 3.11
2529 2683 2.907696 TGGATTGAACCGGGACTAAAGA 59.092 45.455 6.32 0.00 0.00 2.52
2556 2710 1.265454 CGTGGAGGGCCTTTAGTCCT 61.265 60.000 7.89 0.00 34.31 3.85
2789 2955 0.455464 CGTATCGTCGACCAAGCACA 60.455 55.000 10.58 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.