Multiple sequence alignment - TraesCS3D01G069200

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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 TraesCS3D01G069200 chr3D 100.000 2954 0 0 1 2954 30375766 30372813 0.000000e+00 5456.0
1 TraesCS3D01G069200 chr3D 85.623 939 104 24 930 1849 29607862 29608788 0.000000e+00 957.0
2 TraesCS3D01G069200 chr3D 81.975 871 121 23 1137 1988 29410463 29411316 0.000000e+00 706.0
3 TraesCS3D01G069200 chr3D 76.444 883 125 46 1139 1988 29617060 29617892 4.590000e-108 401.0
4 TraesCS3D01G069200 chr3D 74.811 925 197 21 2044 2951 588129179 588130084 4.620000e-103 385.0
5 TraesCS3D01G069200 chr3D 82.819 227 26 11 930 1147 29615353 29615575 1.080000e-44 191.0
6 TraesCS3D01G069200 chr3D 80.000 250 29 13 967 1202 29361795 29362037 6.550000e-37 165.0
7 TraesCS3D01G069200 chr3D 84.472 161 20 5 996 1154 29623805 29623962 1.420000e-33 154.0
8 TraesCS3D01G069200 chr3D 88.095 126 10 4 1019 1141 29620264 29620387 8.530000e-31 145.0
9 TraesCS3D01G069200 chr3D 94.444 90 4 1 826 914 29615215 29615304 1.430000e-28 137.0
10 TraesCS3D01G069200 chr3A 92.486 1464 71 18 930 2379 42320410 42318972 0.000000e+00 2058.0
11 TraesCS3D01G069200 chr3A 86.457 827 90 17 1195 2006 42389985 42389166 0.000000e+00 887.0
12 TraesCS3D01G069200 chr3A 85.181 803 88 16 1062 1849 40173113 40173899 0.000000e+00 795.0
13 TraesCS3D01G069200 chr3A 78.710 1085 152 49 930 1988 40185536 40186567 0.000000e+00 651.0
14 TraesCS3D01G069200 chr3A 89.709 515 22 10 410 909 42320992 42320494 1.930000e-176 628.0
15 TraesCS3D01G069200 chr3A 90.850 306 26 2 2 306 42325248 42324944 2.740000e-110 409.0
16 TraesCS3D01G069200 chr3A 83.333 72 12 0 219 290 425970268 425970339 1.900000e-07 67.6
17 TraesCS3D01G069200 chr3B 86.749 1215 132 17 1745 2951 53198983 53197790 0.000000e+00 1325.0
18 TraesCS3D01G069200 chr3B 89.217 779 64 16 936 1700 53199747 53198975 0.000000e+00 955.0
19 TraesCS3D01G069200 chr3B 81.567 868 127 22 1139 1988 50240065 50240917 0.000000e+00 686.0
20 TraesCS3D01G069200 chr3B 77.285 1083 167 48 930 1988 50413716 50414743 5.530000e-157 564.0
21 TraesCS3D01G069200 chr3B 87.398 492 43 13 430 914 53200276 53199797 5.570000e-152 547.0
22 TraesCS3D01G069200 chr3B 84.165 581 62 16 930 1500 50397916 50398476 1.200000e-148 536.0
23 TraesCS3D01G069200 chr3B 77.093 227 39 12 1990 2210 450849281 450849500 5.170000e-23 119.0
24 TraesCS3D01G069200 chr3B 93.651 63 2 1 826 888 50424141 50424201 3.130000e-15 93.5
25 TraesCS3D01G069200 chr5D 83.232 990 123 18 1990 2951 412623221 412624195 0.000000e+00 869.0
26 TraesCS3D01G069200 chr6B 82.431 979 142 22 1990 2951 133689863 133688898 0.000000e+00 828.0
27 TraesCS3D01G069200 chr6B 78.128 919 175 21 2051 2954 35644036 35643129 7.150000e-156 560.0
28 TraesCS3D01G069200 chr6B 78.271 902 171 19 2053 2936 56091406 56092300 9.250000e-155 556.0
29 TraesCS3D01G069200 chr2A 80.624 929 144 16 1990 2909 641603863 641604764 0.000000e+00 686.0
30 TraesCS3D01G069200 chr2A 75.634 907 186 29 2044 2925 759330264 759331160 4.550000e-113 418.0
31 TraesCS3D01G069200 chr2A 84.211 114 8 5 2791 2895 433380566 433380678 5.210000e-18 102.0
32 TraesCS3D01G069200 chr2B 79.276 912 168 18 2045 2951 583534785 583535680 4.180000e-173 617.0
33 TraesCS3D01G069200 chr2B 78.078 333 67 5 1990 2321 233203710 233204037 3.860000e-49 206.0
34 TraesCS3D01G069200 chr5A 78.396 935 179 11 1996 2917 536999829 537000753 1.180000e-163 586.0
35 TraesCS3D01G069200 chr5A 77.861 935 184 10 1996 2917 536991886 536992810 2.570000e-155 558.0
36 TraesCS3D01G069200 chr5A 91.837 49 3 1 722 769 239409062 239409014 1.900000e-07 67.6
37 TraesCS3D01G069200 chr1D 81.818 671 98 13 2298 2951 485329066 485329729 2.590000e-150 542.0
38 TraesCS3D01G069200 chr7A 77.081 973 197 15 1996 2951 192372450 192373413 3.350000e-149 538.0
39 TraesCS3D01G069200 chr7A 90.698 43 3 1 1990 2032 628387798 628387839 4.110000e-04 56.5
40 TraesCS3D01G069200 chr6A 79.076 736 132 17 2216 2936 559338290 559339018 1.230000e-133 486.0
41 TraesCS3D01G069200 chr4A 73.405 925 211 17 2045 2951 470102881 470101974 2.210000e-81 313.0
42 TraesCS3D01G069200 chr5B 75.309 648 139 14 2318 2951 450413600 450412960 1.040000e-74 291.0


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 TraesCS3D01G069200 chr3D 30372813 30375766 2953 True 5456.000000 5456 100.0000 1 2954 1 chr3D.!!$R1 2953
1 TraesCS3D01G069200 chr3D 29607862 29608788 926 False 957.000000 957 85.6230 930 1849 1 chr3D.!!$F3 919
2 TraesCS3D01G069200 chr3D 29410463 29411316 853 False 706.000000 706 81.9750 1137 1988 1 chr3D.!!$F2 851
3 TraesCS3D01G069200 chr3D 588129179 588130084 905 False 385.000000 385 74.8110 2044 2951 1 chr3D.!!$F4 907
4 TraesCS3D01G069200 chr3D 29615215 29623962 8747 False 205.600000 401 85.2548 826 1988 5 chr3D.!!$F5 1162
5 TraesCS3D01G069200 chr3A 42318972 42325248 6276 True 1031.666667 2058 91.0150 2 2379 3 chr3A.!!$R2 2377
6 TraesCS3D01G069200 chr3A 42389166 42389985 819 True 887.000000 887 86.4570 1195 2006 1 chr3A.!!$R1 811
7 TraesCS3D01G069200 chr3A 40173113 40173899 786 False 795.000000 795 85.1810 1062 1849 1 chr3A.!!$F1 787
8 TraesCS3D01G069200 chr3A 40185536 40186567 1031 False 651.000000 651 78.7100 930 1988 1 chr3A.!!$F2 1058
9 TraesCS3D01G069200 chr3B 53197790 53200276 2486 True 942.333333 1325 87.7880 430 2951 3 chr3B.!!$R1 2521
10 TraesCS3D01G069200 chr3B 50240065 50240917 852 False 686.000000 686 81.5670 1139 1988 1 chr3B.!!$F1 849
11 TraesCS3D01G069200 chr3B 50413716 50414743 1027 False 564.000000 564 77.2850 930 1988 1 chr3B.!!$F3 1058
12 TraesCS3D01G069200 chr3B 50397916 50398476 560 False 536.000000 536 84.1650 930 1500 1 chr3B.!!$F2 570
13 TraesCS3D01G069200 chr5D 412623221 412624195 974 False 869.000000 869 83.2320 1990 2951 1 chr5D.!!$F1 961
14 TraesCS3D01G069200 chr6B 133688898 133689863 965 True 828.000000 828 82.4310 1990 2951 1 chr6B.!!$R2 961
15 TraesCS3D01G069200 chr6B 35643129 35644036 907 True 560.000000 560 78.1280 2051 2954 1 chr6B.!!$R1 903
16 TraesCS3D01G069200 chr6B 56091406 56092300 894 False 556.000000 556 78.2710 2053 2936 1 chr6B.!!$F1 883
17 TraesCS3D01G069200 chr2A 641603863 641604764 901 False 686.000000 686 80.6240 1990 2909 1 chr2A.!!$F2 919
18 TraesCS3D01G069200 chr2A 759330264 759331160 896 False 418.000000 418 75.6340 2044 2925 1 chr2A.!!$F3 881
19 TraesCS3D01G069200 chr2B 583534785 583535680 895 False 617.000000 617 79.2760 2045 2951 1 chr2B.!!$F2 906
20 TraesCS3D01G069200 chr5A 536999829 537000753 924 False 586.000000 586 78.3960 1996 2917 1 chr5A.!!$F2 921
21 TraesCS3D01G069200 chr5A 536991886 536992810 924 False 558.000000 558 77.8610 1996 2917 1 chr5A.!!$F1 921
22 TraesCS3D01G069200 chr1D 485329066 485329729 663 False 542.000000 542 81.8180 2298 2951 1 chr1D.!!$F1 653
23 TraesCS3D01G069200 chr7A 192372450 192373413 963 False 538.000000 538 77.0810 1996 2951 1 chr7A.!!$F1 955
24 TraesCS3D01G069200 chr6A 559338290 559339018 728 False 486.000000 486 79.0760 2216 2936 1 chr6A.!!$F1 720
25 TraesCS3D01G069200 chr4A 470101974 470102881 907 True 313.000000 313 73.4050 2045 2951 1 chr4A.!!$R1 906
26 TraesCS3D01G069200 chr5B 450412960 450413600 640 True 291.000000 291 75.3090 2318 2951 1 chr5B.!!$R1 633

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
333 3319 0.036388 CGGTGGGTAGAATGCACAGT 60.036 55.0 0.00 0.0 31.85 3.55 F
361 3347 2.153817 CGTTCTAATCCGCGATCACATG 59.846 50.0 8.23 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 6595 2.554893 TGATTAACCTTTTCGTGGGCAC 59.445 45.455 0.0 0.0 0.0 5.01 R
2354 7866 2.103373 TGGACTCACTCATCTAGGCAC 58.897 52.381 0.0 0.0 0.0 5.01 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
35 36 3.036075 ACCTAGCTTACAACGGTGTTC 57.964 47.619 13.38 1.18 39.30 3.18
69 70 1.442769 TGTTCTTCCTGCGAATGCTC 58.557 50.000 0.00 0.00 43.34 4.26
71 72 0.324614 TTCTTCCTGCGAATGCTCCA 59.675 50.000 0.00 0.00 43.34 3.86
72 73 0.543277 TCTTCCTGCGAATGCTCCAT 59.457 50.000 0.00 0.00 43.34 3.41
92 93 3.900966 TCCATCTGTTGTCTCCATGAG 57.099 47.619 0.00 0.00 0.00 2.90
132 133 1.207329 GAAGTGAAGGTATGGTCGCCT 59.793 52.381 0.00 0.00 36.51 5.52
134 135 1.090052 GTGAAGGTATGGTCGCCTGC 61.090 60.000 0.00 0.00 34.90 4.85
153 154 2.166459 TGCGAGGAGAAGTAGAACATGG 59.834 50.000 0.00 0.00 0.00 3.66
157 158 3.379452 AGGAGAAGTAGAACATGGGAGG 58.621 50.000 0.00 0.00 0.00 4.30
165 166 2.876368 GAACATGGGAGGCGGACCAG 62.876 65.000 0.00 0.46 40.67 4.00
190 191 4.012374 CAGTTGGGACACAATGCTCTATT 58.988 43.478 0.00 0.00 41.95 1.73
202 203 0.892814 GCTCTATTGCTCCCATGCCC 60.893 60.000 0.00 0.00 0.00 5.36
209 210 1.147153 GCTCCCATGCCCTACTCAC 59.853 63.158 0.00 0.00 0.00 3.51
224 225 0.101399 CTCACCCTCATCGGAGTTCG 59.899 60.000 0.00 0.00 39.64 3.95
225 226 1.519455 CACCCTCATCGGAGTTCGC 60.519 63.158 0.00 0.00 39.64 4.70
234 235 1.008767 CGGAGTTCGCGACCTATCC 60.009 63.158 9.15 12.97 0.00 2.59
239 240 3.420214 TTCGCGACCTATCCGTGGC 62.420 63.158 9.15 0.00 38.01 5.01
276 277 3.412408 GAGGGAAGTGGAGGGGCC 61.412 72.222 0.00 0.00 37.10 5.80
277 278 4.285790 AGGGAAGTGGAGGGGCCA 62.286 66.667 4.39 0.00 46.96 5.36
308 309 1.586028 CCGGAGTGGCCAAACAATG 59.414 57.895 7.24 0.00 35.94 2.82
309 310 1.178534 CCGGAGTGGCCAAACAATGT 61.179 55.000 7.24 0.00 35.94 2.71
311 312 1.068434 CGGAGTGGCCAAACAATGTTT 59.932 47.619 7.24 5.41 35.94 2.83
317 318 3.677002 CCAAACAATGTTTGGCGGT 57.323 47.368 35.66 2.43 41.95 5.68
318 319 1.216122 CCAAACAATGTTTGGCGGTG 58.784 50.000 35.66 18.09 41.95 4.94
319 320 1.216122 CAAACAATGTTTGGCGGTGG 58.784 50.000 26.25 3.68 34.12 4.61
326 3312 0.402504 TGTTTGGCGGTGGGTAGAAT 59.597 50.000 0.00 0.00 0.00 2.40
332 3318 1.369091 GCGGTGGGTAGAATGCACAG 61.369 60.000 0.00 0.00 31.85 3.66
333 3319 0.036388 CGGTGGGTAGAATGCACAGT 60.036 55.000 0.00 0.00 31.85 3.55
346 3332 3.299050 CACAGTTGGTGGCGTTCTA 57.701 52.632 0.00 0.00 44.04 2.10
361 3347 2.153817 CGTTCTAATCCGCGATCACATG 59.846 50.000 8.23 0.00 0.00 3.21
400 3390 3.726517 CGTCTGTGCTTTGCGGGG 61.727 66.667 0.00 0.00 0.00 5.73
401 3391 4.043200 GTCTGTGCTTTGCGGGGC 62.043 66.667 0.00 0.00 0.00 5.80
555 4405 9.297037 ACAAAAGAAACATAACTATACTGGCTT 57.703 29.630 0.00 0.00 0.00 4.35
560 4410 4.130118 ACATAACTATACTGGCTTGCTGC 58.870 43.478 0.00 0.00 41.94 5.25
649 4505 2.231235 GGTTAACCCATGAGGCAACAAG 59.769 50.000 14.16 0.00 40.58 3.16
1154 6594 1.140652 CCCTTCTTCTCTCCTCATGCC 59.859 57.143 0.00 0.00 0.00 4.40
1155 6595 1.202510 CCTTCTTCTCTCCTCATGCCG 60.203 57.143 0.00 0.00 0.00 5.69
1177 6617 3.192633 GTGCCCACGAAAAGGTTAATCAT 59.807 43.478 0.00 0.00 0.00 2.45
1365 6819 2.102925 CCAAACACTTCCCAAACTGCAT 59.897 45.455 0.00 0.00 0.00 3.96
1500 6964 4.451900 TCTGAAGTGTTCCAGGAAGAAAC 58.548 43.478 0.54 1.77 0.00 2.78
1587 7056 7.577979 TCAGCGATTTTTGTAGTAACGATTTT 58.422 30.769 0.00 0.00 0.00 1.82
1588 7057 8.710551 TCAGCGATTTTTGTAGTAACGATTTTA 58.289 29.630 0.00 0.00 0.00 1.52
1589 7058 9.485591 CAGCGATTTTTGTAGTAACGATTTTAT 57.514 29.630 0.00 0.00 0.00 1.40
1590 7059 9.698617 AGCGATTTTTGTAGTAACGATTTTATC 57.301 29.630 0.00 0.00 0.00 1.75
1591 7060 9.480538 GCGATTTTTGTAGTAACGATTTTATCA 57.519 29.630 0.00 0.00 0.00 2.15
1648 7129 8.807667 AATGACTAATGAAGCTTGAACAAAAG 57.192 30.769 2.10 0.64 0.00 2.27
1783 7272 6.820656 CCAAATGCAAGTCTATCTACACTTCT 59.179 38.462 0.00 0.00 30.06 2.85
2032 7535 2.884012 TGGTCGTCAATGAGCACATTTT 59.116 40.909 6.64 0.00 43.17 1.82
2034 7537 3.670055 GGTCGTCAATGAGCACATTTTTG 59.330 43.478 6.64 0.00 43.17 2.44
2035 7538 4.290155 GTCGTCAATGAGCACATTTTTGT 58.710 39.130 6.64 0.00 43.17 2.83
2037 7540 5.565259 GTCGTCAATGAGCACATTTTTGTAG 59.435 40.000 6.64 0.00 43.17 2.74
2039 7542 6.017523 TCGTCAATGAGCACATTTTTGTAGAA 60.018 34.615 6.64 0.00 43.17 2.10
2041 7544 7.326789 CGTCAATGAGCACATTTTTGTAGAATT 59.673 33.333 6.64 0.00 43.17 2.17
2042 7545 8.981647 GTCAATGAGCACATTTTTGTAGAATTT 58.018 29.630 6.64 0.00 43.17 1.82
2327 7839 2.574006 ATCCGGATGCTTGCATACAT 57.426 45.000 18.33 1.83 0.00 2.29
2354 7866 1.293924 GGTGATCTTCTGGATGCGTG 58.706 55.000 0.00 0.00 34.33 5.34
2405 7931 7.065085 CCTTGAATCATTGTACAGGTTCTACAG 59.935 40.741 8.95 3.89 0.00 2.74
2426 7952 3.509575 AGAGCTTTGGTTGTTGTGTTTGA 59.490 39.130 0.00 0.00 0.00 2.69
2439 7965 3.460103 TGTGTTTGACCCGAAGTACTTC 58.540 45.455 23.25 23.25 36.29 3.01
2460 7986 8.316640 ACTTCAGAGAATCAAATGTTGTAGAC 57.683 34.615 0.00 0.00 37.82 2.59
2495 8025 5.363101 TGCTGGTGATCAATGAATCTAGAC 58.637 41.667 0.00 0.00 0.00 2.59
2504 8035 5.965922 TCAATGAATCTAGACGCTTTCTGA 58.034 37.500 0.00 0.00 35.55 3.27
2508 8039 6.467723 TGAATCTAGACGCTTTCTGAAAAC 57.532 37.500 4.18 0.00 35.55 2.43
2514 8045 1.194772 ACGCTTTCTGAAAACGCTAGC 59.805 47.619 21.69 4.06 0.00 3.42
2651 9839 2.417933 CTCTGGATTTGGCACTCTTTCG 59.582 50.000 0.00 0.00 0.00 3.46
2689 10011 4.393990 TCTCACAATGACATCAACATGCTC 59.606 41.667 0.00 0.00 32.57 4.26
2700 10026 0.674895 AACATGCTCCAGCGGTCTTC 60.675 55.000 0.00 0.00 45.83 2.87
2701 10027 1.078918 CATGCTCCAGCGGTCTTCA 60.079 57.895 0.00 0.00 45.83 3.02
2702 10028 1.088340 CATGCTCCAGCGGTCTTCAG 61.088 60.000 0.00 0.00 45.83 3.02
2785 10124 8.019656 ACCACTACAATAAGGGATACTACTTG 57.980 38.462 0.00 0.00 0.00 3.16
2786 10125 7.842743 ACCACTACAATAAGGGATACTACTTGA 59.157 37.037 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.137513 GAACAAGGACTTGGACGACG 58.862 55.000 15.72 0.00 44.45 5.12
92 93 1.974343 TGGGTGTTATTGCCGCCAC 60.974 57.895 0.00 0.00 34.05 5.01
132 133 2.166459 CCATGTTCTACTTCTCCTCGCA 59.834 50.000 0.00 0.00 0.00 5.10
134 135 3.024547 TCCCATGTTCTACTTCTCCTCG 58.975 50.000 0.00 0.00 0.00 4.63
140 141 1.473434 CCGCCTCCCATGTTCTACTTC 60.473 57.143 0.00 0.00 0.00 3.01
141 142 0.541863 CCGCCTCCCATGTTCTACTT 59.458 55.000 0.00 0.00 0.00 2.24
190 191 1.306911 TGAGTAGGGCATGGGAGCA 60.307 57.895 0.00 0.00 35.83 4.26
202 203 2.060050 ACTCCGATGAGGGTGAGTAG 57.940 55.000 0.00 0.00 43.29 2.57
209 210 2.278857 CGCGAACTCCGATGAGGG 60.279 66.667 0.00 0.00 43.29 4.30
258 259 2.610859 GCCCCTCCACTTCCCTCA 60.611 66.667 0.00 0.00 0.00 3.86
261 262 3.732849 CTGGCCCCTCCACTTCCC 61.733 72.222 0.00 0.00 40.72 3.97
292 293 2.482864 CAAACATTGTTTGGCCACTCC 58.517 47.619 27.24 0.00 0.00 3.85
294 295 2.618442 CCAAACATTGTTTGGCCACT 57.382 45.000 35.90 5.24 41.95 4.00
306 307 0.402504 TTCTACCCACCGCCAAACAT 59.597 50.000 0.00 0.00 0.00 2.71
308 309 0.808755 CATTCTACCCACCGCCAAAC 59.191 55.000 0.00 0.00 0.00 2.93
309 310 0.963355 GCATTCTACCCACCGCCAAA 60.963 55.000 0.00 0.00 0.00 3.28
311 312 2.270850 GCATTCTACCCACCGCCA 59.729 61.111 0.00 0.00 0.00 5.69
314 315 0.036388 ACTGTGCATTCTACCCACCG 60.036 55.000 0.00 0.00 0.00 4.94
315 316 1.812571 CAACTGTGCATTCTACCCACC 59.187 52.381 0.00 0.00 0.00 4.61
316 317 1.812571 CCAACTGTGCATTCTACCCAC 59.187 52.381 0.00 0.00 0.00 4.61
317 318 1.423541 ACCAACTGTGCATTCTACCCA 59.576 47.619 0.00 0.00 0.00 4.51
318 319 1.812571 CACCAACTGTGCATTCTACCC 59.187 52.381 0.00 0.00 38.34 3.69
319 320 1.812571 CCACCAACTGTGCATTCTACC 59.187 52.381 0.00 0.00 44.01 3.18
326 3312 2.439338 AACGCCACCAACTGTGCA 60.439 55.556 0.00 0.00 44.01 4.57
332 3318 0.725117 CGGATTAGAACGCCACCAAC 59.275 55.000 0.00 0.00 0.00 3.77
333 3319 3.146783 CGGATTAGAACGCCACCAA 57.853 52.632 0.00 0.00 0.00 3.67
346 3332 1.439353 GGCACATGTGATCGCGGATT 61.439 55.000 29.80 0.00 0.00 3.01
352 3338 2.528743 GCGGAGGCACATGTGATCG 61.529 63.158 29.80 23.19 39.62 3.69
361 3347 4.681978 AACTGGACGCGGAGGCAC 62.682 66.667 12.47 0.00 39.92 5.01
400 3390 2.504681 CAATGCTCAAACCGCCGC 60.505 61.111 0.00 0.00 0.00 6.53
401 3391 0.318614 AAACAATGCTCAAACCGCCG 60.319 50.000 0.00 0.00 0.00 6.46
505 4353 7.506938 TGTCAATTCTTTTCTTTGATCCCTCTT 59.493 33.333 0.00 0.00 32.48 2.85
540 4388 3.069586 TCGCAGCAAGCCAGTATAGTTAT 59.930 43.478 0.00 0.00 41.38 1.89
555 4405 4.783621 GATGGGCCTGTCGCAGCA 62.784 66.667 4.53 0.00 42.68 4.41
649 4505 4.952262 TGAGAATCATTACTGCTTGCAC 57.048 40.909 0.00 0.00 42.56 4.57
712 4568 7.786030 ACAGAGAGAGTATATTTTTAGCTGCA 58.214 34.615 1.02 0.00 0.00 4.41
919 4820 9.944376 CTGCCTAGCTAATTATATCCTGTTTTA 57.056 33.333 0.00 0.00 0.00 1.52
920 4821 7.885399 CCTGCCTAGCTAATTATATCCTGTTTT 59.115 37.037 0.00 0.00 0.00 2.43
921 4822 7.398024 CCTGCCTAGCTAATTATATCCTGTTT 58.602 38.462 0.00 0.00 0.00 2.83
923 4824 5.104735 GCCTGCCTAGCTAATTATATCCTGT 60.105 44.000 0.00 0.00 0.00 4.00
924 4825 5.104776 TGCCTGCCTAGCTAATTATATCCTG 60.105 44.000 0.00 0.00 0.00 3.86
925 4826 5.032846 TGCCTGCCTAGCTAATTATATCCT 58.967 41.667 0.00 0.00 0.00 3.24
1155 6595 2.554893 TGATTAACCTTTTCGTGGGCAC 59.445 45.455 0.00 0.00 0.00 5.01
1271 6721 4.336153 ACGGGTGTAAAGAAACAAACGATT 59.664 37.500 0.00 0.00 35.76 3.34
1365 6819 3.202216 TTCTTGCACCGCTCGTCGA 62.202 57.895 0.00 0.00 41.67 4.20
1412 6866 4.129148 GCAGAAAGCCCCGGGGAT 62.129 66.667 44.86 37.78 37.50 3.85
1500 6964 6.595326 TCTTGCTTATATTATTGGCATCTCCG 59.405 38.462 0.00 0.00 37.80 4.63
1587 7056 7.940178 GTGTCCATATACACGAACAATGATA 57.060 36.000 0.00 0.00 40.31 2.15
1588 7057 6.844696 GTGTCCATATACACGAACAATGAT 57.155 37.500 0.00 0.00 40.31 2.45
1604 7085 6.323739 AGTCATTACTTTTGGTTTGTGTCCAT 59.676 34.615 0.00 0.00 31.01 3.41
1648 7129 4.367386 ACACGCAGGTATCAACTACTAC 57.633 45.455 0.00 0.00 0.00 2.73
1783 7272 9.607988 AGGAATATCGTTAACAAATGTGTATCA 57.392 29.630 6.39 0.00 36.80 2.15
2032 7535 7.123547 CCCCTAAACATTGGCTAAATTCTACAA 59.876 37.037 0.00 0.00 0.00 2.41
2034 7537 6.040504 CCCCCTAAACATTGGCTAAATTCTAC 59.959 42.308 0.00 0.00 0.00 2.59
2035 7538 6.133356 CCCCCTAAACATTGGCTAAATTCTA 58.867 40.000 0.00 0.00 0.00 2.10
2037 7540 4.714802 ACCCCCTAAACATTGGCTAAATTC 59.285 41.667 0.00 0.00 0.00 2.17
2039 7542 4.346478 ACCCCCTAAACATTGGCTAAAT 57.654 40.909 0.00 0.00 0.00 1.40
2041 7544 3.076182 TCAACCCCCTAAACATTGGCTAA 59.924 43.478 0.00 0.00 0.00 3.09
2042 7545 2.650322 TCAACCCCCTAAACATTGGCTA 59.350 45.455 0.00 0.00 0.00 3.93
2327 7839 5.688500 GCATCCAGAAGATCACCAGGAATTA 60.689 44.000 0.00 0.00 30.59 1.40
2354 7866 2.103373 TGGACTCACTCATCTAGGCAC 58.897 52.381 0.00 0.00 0.00 5.01
2405 7931 3.612423 GTCAAACACAACAACCAAAGCTC 59.388 43.478 0.00 0.00 0.00 4.09
2426 7952 4.087182 TGATTCTCTGAAGTACTTCGGGT 58.913 43.478 33.81 21.58 44.10 5.28
2439 7965 7.425577 TGTGTCTACAACATTTGATTCTCTG 57.574 36.000 0.00 0.00 40.80 3.35
2468 7994 5.014858 AGATTCATTGATCACCAGCAACTT 58.985 37.500 0.00 0.00 0.00 2.66
2495 8025 1.464189 GGCTAGCGTTTTCAGAAAGCG 60.464 52.381 23.49 23.49 45.98 4.68
2504 8035 5.671493 ACAATCTATACTGGCTAGCGTTTT 58.329 37.500 9.00 0.00 0.00 2.43
2508 8039 4.800993 GCATACAATCTATACTGGCTAGCG 59.199 45.833 9.00 0.00 0.00 4.26
2514 8045 7.712639 ACTTTCAGTGCATACAATCTATACTGG 59.287 37.037 0.00 0.00 35.87 4.00
2651 9839 2.029844 GAGAACCTGCCACGCTGAC 61.030 63.158 0.00 0.00 0.00 3.51
2689 10011 1.374758 GGACACTGAAGACCGCTGG 60.375 63.158 0.00 0.00 0.00 4.85
2700 10026 3.716006 CAAGCCGTGCGGACACTG 61.716 66.667 15.45 1.49 45.10 3.66
2743 10082 2.488153 GTGGTAGCCATTGACCTCAAAC 59.512 50.000 0.00 0.00 39.55 2.93
2785 10124 5.133941 TGACCACTGAGGATAGATACTGTC 58.866 45.833 0.00 0.00 41.22 3.51
2786 10125 5.130705 TGACCACTGAGGATAGATACTGT 57.869 43.478 0.00 0.00 41.22 3.55


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

AutoCloner maintained by Alex Coulton.