Multiple sequence alignment - TraesCS2D01G556000

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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 TraesCS2D01G556000 chr2D 100.000 3809 0 0 1 3809 629736661 629732853 0.000000e+00 7035.0
1 TraesCS2D01G556000 chr2D 90.649 2620 188 28 276 2866 630065566 630068157 0.000000e+00 3428.0
2 TraesCS2D01G556000 chr2D 87.834 2244 211 31 1532 3759 629975379 629977576 0.000000e+00 2575.0
3 TraesCS2D01G556000 chr2D 87.150 1891 188 31 773 2628 630033485 630035355 0.000000e+00 2095.0
4 TraesCS2D01G556000 chr2D 86.774 1807 199 30 1013 2787 630098897 630097099 0.000000e+00 1977.0
5 TraesCS2D01G556000 chr2D 86.663 1807 199 31 1013 2787 630621053 630622849 0.000000e+00 1964.0
6 TraesCS2D01G556000 chr2D 95.488 953 38 4 2861 3809 630082870 630083821 0.000000e+00 1517.0
7 TraesCS2D01G556000 chr2D 85.167 1200 133 20 2624 3809 630044200 630045368 0.000000e+00 1188.0
8 TraesCS2D01G556000 chr2D 83.518 722 57 28 751 1448 629974698 629975381 5.410000e-173 617.0
9 TraesCS2D01G556000 chr2D 85.625 160 16 5 3040 3193 600425379 600425221 1.100000e-35 161.0
10 TraesCS2D01G556000 chr2D 95.745 47 2 0 1215 1261 630638195 630638149 4.080000e-10 76.8
11 TraesCS2D01G556000 chr2B 90.217 2494 198 28 954 3416 773004296 773006774 0.000000e+00 3212.0
12 TraesCS2D01G556000 chr2B 86.166 1836 204 36 1013 2809 773722822 773724646 0.000000e+00 1938.0
13 TraesCS2D01G556000 chr2B 83.397 789 107 9 2930 3704 773020057 773020835 0.000000e+00 710.0
14 TraesCS2D01G556000 chr2B 86.047 559 36 15 387 922 773003756 773004295 2.570000e-156 562.0
15 TraesCS2D01G556000 chr2B 82.609 184 29 3 81 263 166880028 166880209 3.940000e-35 159.0
16 TraesCS2D01G556000 chr2A 91.500 2106 129 21 727 2809 760776729 760774651 0.000000e+00 2852.0
17 TraesCS2D01G556000 chr2A 87.769 1488 167 12 1331 2809 760762036 760763517 0.000000e+00 1725.0
18 TraesCS2D01G556000 chr2A 87.778 360 41 3 83 440 760777757 760777399 5.890000e-113 418.0
19 TraesCS2D01G556000 chr2A 93.243 222 15 0 1013 1234 760761696 760761917 1.020000e-85 327.0
20 TraesCS2D01G556000 chr2A 83.983 231 30 6 2965 3193 43142800 43143025 8.290000e-52 215.0
21 TraesCS2D01G556000 chr2A 82.759 261 21 4 433 686 760776976 760776733 1.070000e-50 211.0
22 TraesCS2D01G556000 chr6A 80.764 1466 244 30 1342 2782 15628586 15627134 0.000000e+00 1110.0
23 TraesCS2D01G556000 chr7D 86.555 238 27 5 2964 3198 449463604 449463839 1.360000e-64 257.0
24 TraesCS2D01G556000 chr7D 82.781 151 19 7 85 230 233215174 233215322 1.110000e-25 128.0
25 TraesCS2D01G556000 chr7D 83.019 106 12 5 3653 3757 291512116 291512016 1.460000e-14 91.6
26 TraesCS2D01G556000 chr7B 85.294 238 30 5 2964 3198 467448607 467448842 1.370000e-59 241.0
27 TraesCS2D01G556000 chr7B 89.855 69 5 2 3653 3720 361162491 361162558 1.880000e-13 87.9
28 TraesCS2D01G556000 chr5D 86.127 173 17 6 80 250 115026848 115026681 3.020000e-41 180.0
29 TraesCS2D01G556000 chr3B 80.952 231 39 5 2964 3193 123600521 123600747 1.090000e-40 178.0
30 TraesCS2D01G556000 chrUn 85.799 169 20 3 81 249 92809767 92809603 3.910000e-40 176.0
31 TraesCS2D01G556000 chr1B 96.364 55 0 2 195 248 598426283 598426230 5.240000e-14 89.8
32 TraesCS2D01G556000 chr7A 82.955 88 13 2 3653 3739 326032141 326032055 1.130000e-10 78.7


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 TraesCS2D01G556000 chr2D 629732853 629736661 3808 True 7035.000000 7035 100.000000 1 3809 1 chr2D.!!$R2 3808
1 TraesCS2D01G556000 chr2D 630065566 630068157 2591 False 3428.000000 3428 90.649000 276 2866 1 chr2D.!!$F3 2590
2 TraesCS2D01G556000 chr2D 630033485 630035355 1870 False 2095.000000 2095 87.150000 773 2628 1 chr2D.!!$F1 1855
3 TraesCS2D01G556000 chr2D 630097099 630098897 1798 True 1977.000000 1977 86.774000 1013 2787 1 chr2D.!!$R3 1774
4 TraesCS2D01G556000 chr2D 630621053 630622849 1796 False 1964.000000 1964 86.663000 1013 2787 1 chr2D.!!$F5 1774
5 TraesCS2D01G556000 chr2D 629974698 629977576 2878 False 1596.000000 2575 85.676000 751 3759 2 chr2D.!!$F6 3008
6 TraesCS2D01G556000 chr2D 630082870 630083821 951 False 1517.000000 1517 95.488000 2861 3809 1 chr2D.!!$F4 948
7 TraesCS2D01G556000 chr2D 630044200 630045368 1168 False 1188.000000 1188 85.167000 2624 3809 1 chr2D.!!$F2 1185
8 TraesCS2D01G556000 chr2B 773722822 773724646 1824 False 1938.000000 1938 86.166000 1013 2809 1 chr2B.!!$F3 1796
9 TraesCS2D01G556000 chr2B 773003756 773006774 3018 False 1887.000000 3212 88.132000 387 3416 2 chr2B.!!$F4 3029
10 TraesCS2D01G556000 chr2B 773020057 773020835 778 False 710.000000 710 83.397000 2930 3704 1 chr2B.!!$F2 774
11 TraesCS2D01G556000 chr2A 760774651 760777757 3106 True 1160.333333 2852 87.345667 83 2809 3 chr2A.!!$R1 2726
12 TraesCS2D01G556000 chr2A 760761696 760763517 1821 False 1026.000000 1725 90.506000 1013 2809 2 chr2A.!!$F2 1796
13 TraesCS2D01G556000 chr6A 15627134 15628586 1452 True 1110.000000 1110 80.764000 1342 2782 1 chr6A.!!$R1 1440

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
848 1316 0.035152 AATGGCGTGGCATCTTCTGA 60.035 50.0 9.50 0.0 0.00 3.27 F
984 1490 0.166597 CTTTTCTTGCAGCGCATCGA 59.833 50.0 11.47 0.0 38.76 3.59 F
1695 2362 0.462047 GCGAGTGGAACCCGATGATT 60.462 55.0 0.00 0.0 37.80 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2911 1.139095 GTCCACGATGTCGACCTCC 59.861 63.158 14.12 0.86 43.02 4.30 R
2247 2917 1.514228 CTCCACGTCCACGATGTCG 60.514 63.158 6.03 0.11 43.02 4.35 R
3575 4297 0.820891 GGATCGGCCATTGTGCAGAT 60.821 55.000 2.24 10.71 46.57 2.90 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
20 21 2.953020 CCGAGCCAGTATCTATCTTGC 58.047 52.381 0.00 0.00 0.00 4.01
21 22 2.297315 CCGAGCCAGTATCTATCTTGCA 59.703 50.000 0.00 0.00 0.00 4.08
22 23 3.243873 CCGAGCCAGTATCTATCTTGCAA 60.244 47.826 0.00 0.00 0.00 4.08
23 24 3.738282 CGAGCCAGTATCTATCTTGCAAC 59.262 47.826 0.00 0.00 0.00 4.17
24 25 3.722147 AGCCAGTATCTATCTTGCAACG 58.278 45.455 0.00 0.00 0.00 4.10
25 26 2.802816 GCCAGTATCTATCTTGCAACGG 59.197 50.000 0.00 0.00 0.00 4.44
26 27 3.393800 CCAGTATCTATCTTGCAACGGG 58.606 50.000 0.00 0.00 0.00 5.28
27 28 3.181465 CCAGTATCTATCTTGCAACGGGT 60.181 47.826 0.00 0.00 0.00 5.28
28 29 4.442706 CAGTATCTATCTTGCAACGGGTT 58.557 43.478 0.00 0.00 0.00 4.11
29 30 4.876107 CAGTATCTATCTTGCAACGGGTTT 59.124 41.667 0.00 0.00 0.00 3.27
30 31 4.876107 AGTATCTATCTTGCAACGGGTTTG 59.124 41.667 0.00 0.00 38.37 2.93
31 32 3.134574 TCTATCTTGCAACGGGTTTGT 57.865 42.857 0.00 0.00 37.54 2.83
32 33 3.482436 TCTATCTTGCAACGGGTTTGTT 58.518 40.909 0.00 0.00 37.54 2.83
38 39 1.298788 CAACGGGTTTGTTGTCGGC 60.299 57.895 0.00 0.00 43.28 5.54
39 40 1.452470 AACGGGTTTGTTGTCGGCT 60.452 52.632 0.00 0.00 0.00 5.52
40 41 0.179051 AACGGGTTTGTTGTCGGCTA 60.179 50.000 0.00 0.00 0.00 3.93
41 42 0.881600 ACGGGTTTGTTGTCGGCTAC 60.882 55.000 0.00 0.00 0.00 3.58
42 43 0.881159 CGGGTTTGTTGTCGGCTACA 60.881 55.000 0.00 0.00 35.88 2.74
43 44 1.310904 GGGTTTGTTGTCGGCTACAA 58.689 50.000 12.95 12.95 45.90 2.41
53 54 4.735662 TGTCGGCTACAATGTGTTTAAC 57.264 40.909 0.00 0.00 34.29 2.01
54 55 4.127907 TGTCGGCTACAATGTGTTTAACA 58.872 39.130 0.00 0.00 36.74 2.41
55 56 4.575236 TGTCGGCTACAATGTGTTTAACAA 59.425 37.500 0.00 0.00 36.18 2.83
56 57 5.239744 TGTCGGCTACAATGTGTTTAACAAT 59.760 36.000 0.00 0.00 36.18 2.71
57 58 5.793457 GTCGGCTACAATGTGTTTAACAATC 59.207 40.000 0.00 0.00 43.61 2.67
58 59 5.703592 TCGGCTACAATGTGTTTAACAATCT 59.296 36.000 0.00 0.00 43.61 2.40
59 60 6.205853 TCGGCTACAATGTGTTTAACAATCTT 59.794 34.615 0.00 0.00 43.61 2.40
60 61 7.388224 TCGGCTACAATGTGTTTAACAATCTTA 59.612 33.333 0.00 0.00 43.61 2.10
61 62 8.181573 CGGCTACAATGTGTTTAACAATCTTAT 58.818 33.333 0.00 0.00 43.61 1.73
87 88 2.571216 CCCAGTATCTACCGCCCCG 61.571 68.421 0.00 0.00 0.00 5.73
92 93 3.761690 TATCTACCGCCCCGCCCTT 62.762 63.158 0.00 0.00 0.00 3.95
123 124 4.954970 CCCACTGCCGTTGCTGGT 62.955 66.667 0.00 0.00 40.45 4.00
128 129 3.832237 CTGCCGTTGCTGGTCACCT 62.832 63.158 0.00 0.00 38.71 4.00
139 140 4.176752 GTCACCTCCCCGGCCATC 62.177 72.222 2.24 0.00 35.61 3.51
151 152 1.772156 GGCCATCCCTCTAAGCCCT 60.772 63.158 0.00 0.00 37.66 5.19
154 155 2.040144 GCCATCCCTCTAAGCCCTACA 61.040 57.143 0.00 0.00 0.00 2.74
169 171 2.167662 CCTACACCACCCATGAAAACC 58.832 52.381 0.00 0.00 0.00 3.27
175 177 1.340991 CCACCCATGAAAACCTCCGAT 60.341 52.381 0.00 0.00 0.00 4.18
180 182 2.880890 CCATGAAAACCTCCGATGATCC 59.119 50.000 0.00 0.00 0.00 3.36
190 192 2.446848 CGATGATCCCCTGCACCCT 61.447 63.158 0.00 0.00 0.00 4.34
191 193 1.453669 GATGATCCCCTGCACCCTC 59.546 63.158 0.00 0.00 0.00 4.30
215 218 5.044846 CCCCACCCTTAAGATAGATAATGGG 60.045 48.000 3.36 8.33 42.33 4.00
240 243 3.252351 GTGGCTTCCCCCTAAGATAGAT 58.748 50.000 0.00 0.00 0.00 1.98
250 253 4.164988 CCCCTAAGATAGATAATGGGGCTG 59.835 50.000 0.00 0.00 45.14 4.85
258 261 2.782341 AGATAATGGGGCTGCTTCTTCT 59.218 45.455 0.00 0.00 0.00 2.85
262 265 2.124942 GGGCTGCTTCTTCTCCGG 60.125 66.667 0.00 0.00 0.00 5.14
263 266 2.124942 GGCTGCTTCTTCTCCGGG 60.125 66.667 0.00 0.00 0.00 5.73
264 267 2.660064 GGCTGCTTCTTCTCCGGGA 61.660 63.158 0.00 0.00 0.00 5.14
279 282 2.152016 CCGGGAAGGTTGTTTCTTCTC 58.848 52.381 0.00 0.00 40.17 2.87
318 321 6.212187 CCAAGATGAAAGGAAGAAGGGAAAAT 59.788 38.462 0.00 0.00 0.00 1.82
338 341 2.531206 TGTAACTGGCGCAAAACAAAC 58.469 42.857 10.83 0.00 0.00 2.93
368 371 3.744660 ACCTGAGAAGTAGCAAAACTGG 58.255 45.455 0.00 0.00 0.00 4.00
451 884 4.427312 GAATGCATGCTTCCTTTTACTGG 58.573 43.478 20.33 0.00 0.00 4.00
458 891 0.037160 TTCCTTTTACTGGTCCCGGC 59.963 55.000 0.00 0.00 0.00 6.13
465 898 2.458969 TACTGGTCCCGGCCCAACTA 62.459 60.000 11.72 2.92 0.00 2.24
552 987 2.795231 AGTAGACATGCACAGCCAAT 57.205 45.000 0.00 0.00 0.00 3.16
593 1035 2.322081 TGACCTTTAGCAACCGCGC 61.322 57.895 0.00 0.00 45.49 6.86
648 1101 4.400529 TGGAGGCCTTTGAAAAAGAAAC 57.599 40.909 6.77 0.00 0.00 2.78
680 1133 2.271800 CCGTGCCAACTCTACATCTTC 58.728 52.381 0.00 0.00 0.00 2.87
692 1145 6.559810 ACTCTACATCTTCGTTTCATCTCTG 58.440 40.000 0.00 0.00 0.00 3.35
701 1154 0.321346 TTTCATCTCTGGCAGCACGA 59.679 50.000 10.34 6.53 0.00 4.35
722 1175 7.234384 CACGAACGCTAGAAAACAAGAATAAT 58.766 34.615 0.00 0.00 0.00 1.28
848 1316 0.035152 AATGGCGTGGCATCTTCTGA 60.035 50.000 9.50 0.00 0.00 3.27
884 1358 3.470709 CGATCCAGCATTTATCACCAGT 58.529 45.455 0.00 0.00 0.00 4.00
969 1465 1.282157 CCACCTAGCTACCTGGCTTTT 59.718 52.381 0.00 0.00 42.97 2.27
976 1482 1.200948 GCTACCTGGCTTTTCTTGCAG 59.799 52.381 0.00 0.00 0.00 4.41
981 1487 1.080298 GGCTTTTCTTGCAGCGCAT 60.080 52.632 11.47 0.00 38.76 4.73
984 1490 0.166597 CTTTTCTTGCAGCGCATCGA 59.833 50.000 11.47 0.00 38.76 3.59
994 1500 2.961721 CGCATCGACCATCCACGG 60.962 66.667 0.00 0.00 0.00 4.94
996 1502 2.900273 CATCGACCATCCACGGGT 59.100 61.111 0.00 0.00 42.61 5.28
1198 1704 4.082523 CGCTTTCCTCCCTCGGCA 62.083 66.667 0.00 0.00 0.00 5.69
1261 1801 0.601046 TTCGCAAGCTCCTCTGTGTG 60.601 55.000 0.00 0.00 37.18 3.82
1490 2136 3.429141 GCTCGTCCTCGTCGACCA 61.429 66.667 10.58 0.00 38.33 4.02
1494 2140 3.063084 GTCCTCGTCGACCAGGCT 61.063 66.667 22.96 0.00 0.00 4.58
1695 2362 0.462047 GCGAGTGGAACCCGATGATT 60.462 55.000 0.00 0.00 37.80 2.57
1905 2572 4.473520 AATGTCTGCCTCCGCCGG 62.474 66.667 0.00 0.00 0.00 6.13
1929 2596 2.829458 GCCCCGAGCGTCTACTCT 60.829 66.667 0.00 0.00 34.35 3.24
2247 2917 4.864334 CCTGGCATGGCGGAGGTC 62.864 72.222 28.56 0.00 0.00 3.85
2261 2931 1.919956 GAGGTCGACATCGTGGACGT 61.920 60.000 18.91 4.50 41.12 4.34
2262 2932 1.800315 GGTCGACATCGTGGACGTG 60.800 63.158 18.91 0.33 41.12 4.49
2272 2942 4.988716 TGGACGTGGAGACCGGCT 62.989 66.667 0.00 0.00 37.49 5.52
2437 3107 2.681421 ACCCGGACGGTTACCTCC 60.681 66.667 0.73 4.92 45.36 4.30
2529 3199 3.390521 CTCTACGGCCACCCAGCA 61.391 66.667 2.24 0.00 0.00 4.41
2809 3488 1.015109 CAGCAGCAGCAAGATGTAGG 58.985 55.000 3.17 0.00 45.49 3.18
2957 3637 0.112995 TGGACTGCTTTTCATGCCCT 59.887 50.000 0.00 0.00 0.00 5.19
3062 3745 4.839668 TTTTACATCACCAAAACCTCCG 57.160 40.909 0.00 0.00 0.00 4.63
3079 3762 1.134699 TCCGACTCCAACAGATGATGC 60.135 52.381 0.00 0.00 0.00 3.91
3420 4141 2.357034 AAGCAACGCCGACGATGT 60.357 55.556 0.00 0.00 43.33 3.06
3421 4142 1.897398 GAAGCAACGCCGACGATGTT 61.897 55.000 0.00 0.00 43.33 2.71
3557 4279 3.446570 GCTGCTGCTTCGGCCAAT 61.447 61.111 8.53 0.00 40.91 3.16
3559 4281 2.020131 CTGCTGCTTCGGCCAATAG 58.980 57.895 2.24 0.00 40.91 1.73
3575 4297 3.304794 CCAATAGCCGAAACGACCAAAAA 60.305 43.478 0.00 0.00 0.00 1.94
3793 4524 1.422531 TTGCTTGAATGGCCCAAGTT 58.577 45.000 18.05 1.43 42.11 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.297315 TGCAAGATAGATACTGGCTCGG 59.703 50.000 0.00 0.00 35.55 4.63
1 2 3.650070 TGCAAGATAGATACTGGCTCG 57.350 47.619 0.00 0.00 35.55 5.03
2 3 3.738282 CGTTGCAAGATAGATACTGGCTC 59.262 47.826 0.00 0.00 35.55 4.70
3 4 3.493350 CCGTTGCAAGATAGATACTGGCT 60.493 47.826 0.00 0.00 35.55 4.75
4 5 2.802816 CCGTTGCAAGATAGATACTGGC 59.197 50.000 0.00 0.00 35.14 4.85
5 6 3.181465 ACCCGTTGCAAGATAGATACTGG 60.181 47.826 0.00 0.00 0.00 4.00
6 7 4.060038 ACCCGTTGCAAGATAGATACTG 57.940 45.455 0.00 0.00 0.00 2.74
7 8 4.755266 AACCCGTTGCAAGATAGATACT 57.245 40.909 0.00 0.00 0.00 2.12
8 9 4.634443 ACAAACCCGTTGCAAGATAGATAC 59.366 41.667 0.00 0.00 41.31 2.24
9 10 4.839121 ACAAACCCGTTGCAAGATAGATA 58.161 39.130 0.00 0.00 41.31 1.98
10 11 3.686016 ACAAACCCGTTGCAAGATAGAT 58.314 40.909 0.00 0.00 41.31 1.98
11 12 3.134574 ACAAACCCGTTGCAAGATAGA 57.865 42.857 0.00 0.00 41.31 1.98
12 13 3.564511 CAACAAACCCGTTGCAAGATAG 58.435 45.455 0.00 0.00 41.31 2.08
13 14 3.634568 CAACAAACCCGTTGCAAGATA 57.365 42.857 0.00 0.00 41.31 1.98
14 15 2.507339 CAACAAACCCGTTGCAAGAT 57.493 45.000 0.00 0.00 41.31 2.40
21 22 0.179051 TAGCCGACAACAAACCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
22 23 0.881600 GTAGCCGACAACAAACCCGT 60.882 55.000 0.00 0.00 0.00 5.28
23 24 0.881159 TGTAGCCGACAACAAACCCG 60.881 55.000 0.00 0.00 34.15 5.28
24 25 1.310904 TTGTAGCCGACAACAAACCC 58.689 50.000 0.00 0.00 43.30 4.11
32 33 4.127907 TGTTAAACACATTGTAGCCGACA 58.872 39.130 0.00 0.00 35.78 4.35
33 34 4.735662 TGTTAAACACATTGTAGCCGAC 57.264 40.909 0.00 0.00 0.00 4.79
34 35 5.703592 AGATTGTTAAACACATTGTAGCCGA 59.296 36.000 0.00 0.00 34.43 5.54
35 36 5.938322 AGATTGTTAAACACATTGTAGCCG 58.062 37.500 0.00 0.00 34.43 5.52
56 57 8.582437 CGGTAGATACTGGGTGAAAATATAAGA 58.418 37.037 0.00 0.00 0.00 2.10
57 58 7.331193 GCGGTAGATACTGGGTGAAAATATAAG 59.669 40.741 1.21 0.00 33.20 1.73
58 59 7.156673 GCGGTAGATACTGGGTGAAAATATAA 58.843 38.462 1.21 0.00 33.20 0.98
59 60 6.295462 GGCGGTAGATACTGGGTGAAAATATA 60.295 42.308 1.21 0.00 33.20 0.86
60 61 5.512576 GGCGGTAGATACTGGGTGAAAATAT 60.513 44.000 1.21 0.00 33.20 1.28
61 62 4.202284 GGCGGTAGATACTGGGTGAAAATA 60.202 45.833 1.21 0.00 33.20 1.40
62 63 3.433173 GGCGGTAGATACTGGGTGAAAAT 60.433 47.826 1.21 0.00 33.20 1.82
63 64 2.093341 GGCGGTAGATACTGGGTGAAAA 60.093 50.000 1.21 0.00 33.20 2.29
64 65 1.483415 GGCGGTAGATACTGGGTGAAA 59.517 52.381 1.21 0.00 33.20 2.69
65 66 1.117150 GGCGGTAGATACTGGGTGAA 58.883 55.000 1.21 0.00 33.20 3.18
66 67 0.757935 GGGCGGTAGATACTGGGTGA 60.758 60.000 1.21 0.00 33.20 4.02
67 68 1.746517 GGGCGGTAGATACTGGGTG 59.253 63.158 1.21 0.00 33.20 4.61
68 69 1.458967 GGGGCGGTAGATACTGGGT 60.459 63.158 1.21 0.00 33.20 4.51
69 70 2.571216 CGGGGCGGTAGATACTGGG 61.571 68.421 1.21 0.00 33.20 4.45
70 71 3.048602 CGGGGCGGTAGATACTGG 58.951 66.667 1.21 0.00 33.20 4.00
71 72 2.338984 GCGGGGCGGTAGATACTG 59.661 66.667 0.00 0.00 35.68 2.74
72 73 2.916181 GGCGGGGCGGTAGATACT 60.916 66.667 0.00 0.00 0.00 2.12
73 74 3.999948 GGGCGGGGCGGTAGATAC 62.000 72.222 0.00 0.00 0.00 2.24
74 75 3.761690 AAGGGCGGGGCGGTAGATA 62.762 63.158 0.00 0.00 0.00 1.98
77 78 4.851179 GAAAGGGCGGGGCGGTAG 62.851 72.222 0.00 0.00 0.00 3.18
87 88 1.000771 GGGAGGTTGAGGAAAGGGC 60.001 63.158 0.00 0.00 0.00 5.19
108 109 2.591429 TGACCAGCAACGGCAGTG 60.591 61.111 0.00 0.00 44.61 3.66
111 112 3.825160 GAGGTGACCAGCAACGGCA 62.825 63.158 3.63 0.00 44.61 5.69
112 113 3.050275 GAGGTGACCAGCAACGGC 61.050 66.667 3.63 0.00 39.91 5.68
114 115 2.358737 GGGAGGTGACCAGCAACG 60.359 66.667 3.63 0.00 39.91 4.10
128 129 2.965226 CTTAGAGGGATGGCCGGGGA 62.965 65.000 2.18 0.00 33.83 4.81
134 135 0.687920 GTAGGGCTTAGAGGGATGGC 59.312 60.000 0.00 0.00 0.00 4.40
139 140 0.831307 GTGGTGTAGGGCTTAGAGGG 59.169 60.000 0.00 0.00 0.00 4.30
151 152 2.224917 GGAGGTTTTCATGGGTGGTGTA 60.225 50.000 0.00 0.00 0.00 2.90
154 155 0.251165 CGGAGGTTTTCATGGGTGGT 60.251 55.000 0.00 0.00 0.00 4.16
169 171 1.070445 GTGCAGGGGATCATCGGAG 59.930 63.158 0.00 0.00 0.00 4.63
175 177 2.692368 GGAGGGTGCAGGGGATCA 60.692 66.667 0.00 0.00 0.00 2.92
190 192 5.790618 CCATTATCTATCTTAAGGGTGGGGA 59.209 44.000 1.85 0.00 0.00 4.81
191 193 5.044846 CCCATTATCTATCTTAAGGGTGGGG 60.045 48.000 1.85 0.00 39.05 4.96
196 198 6.942576 CACAACCCCATTATCTATCTTAAGGG 59.057 42.308 1.85 0.00 38.04 3.95
198 200 6.431234 GCCACAACCCCATTATCTATCTTAAG 59.569 42.308 0.00 0.00 0.00 1.85
199 201 6.102615 AGCCACAACCCCATTATCTATCTTAA 59.897 38.462 0.00 0.00 0.00 1.85
215 218 0.323451 CTTAGGGGGAAGCCACAACC 60.323 60.000 0.00 0.00 0.00 3.77
229 232 4.472833 AGCAGCCCCATTATCTATCTTAGG 59.527 45.833 0.00 0.00 0.00 2.69
240 243 1.212935 GGAGAAGAAGCAGCCCCATTA 59.787 52.381 0.00 0.00 0.00 1.90
258 261 1.772453 AGAAGAAACAACCTTCCCGGA 59.228 47.619 0.73 0.00 40.54 5.14
262 265 2.152016 CCGGAGAAGAAACAACCTTCC 58.848 52.381 0.00 0.00 40.54 3.46
263 266 1.535896 GCCGGAGAAGAAACAACCTTC 59.464 52.381 5.05 0.00 40.10 3.46
264 267 1.605753 GCCGGAGAAGAAACAACCTT 58.394 50.000 5.05 0.00 0.00 3.50
292 295 3.657727 TCCCTTCTTCCTTTCATCTTGGT 59.342 43.478 0.00 0.00 0.00 3.67
318 321 2.164624 AGTTTGTTTTGCGCCAGTTACA 59.835 40.909 4.18 0.00 0.00 2.41
394 397 9.886132 TTATCCTAAATCCTCTAAACACAACTC 57.114 33.333 0.00 0.00 0.00 3.01
431 434 3.434309 ACCAGTAAAAGGAAGCATGCAT 58.566 40.909 21.98 8.13 0.00 3.96
451 884 1.579964 CGTTTTAGTTGGGCCGGGAC 61.580 60.000 2.18 0.00 0.00 4.46
458 891 7.250445 AGTAGTAACAAACGTTTTAGTTGGG 57.750 36.000 20.82 8.41 34.14 4.12
465 898 8.014517 TCGAAACAAAGTAGTAACAAACGTTTT 58.985 29.630 11.66 0.00 0.00 2.43
552 987 1.340502 TGTCAGTTGGTTGGTCTTGCA 60.341 47.619 0.00 0.00 0.00 4.08
593 1035 1.511850 TTCTGCAATGGAGTGTGACG 58.488 50.000 0.85 0.00 0.00 4.35
680 1133 0.445436 GTGCTGCCAGAGATGAAACG 59.555 55.000 0.00 0.00 0.00 3.60
692 1145 1.289109 TTTCTAGCGTTCGTGCTGCC 61.289 55.000 9.27 0.00 46.70 4.85
722 1175 1.448985 GCGGGCATGTTCTTCTTGTA 58.551 50.000 0.00 0.00 0.00 2.41
762 1220 1.732259 AGGCGACGTGCTAAATCTTTG 59.268 47.619 0.00 0.00 45.43 2.77
769 1228 0.942410 GTTCACAGGCGACGTGCTAA 60.942 55.000 8.16 0.00 45.43 3.09
770 1229 1.372499 GTTCACAGGCGACGTGCTA 60.372 57.895 8.16 0.00 45.43 3.49
848 1316 4.792057 GCTGGATCGCTACTACGTTTACAT 60.792 45.833 0.00 0.00 0.00 2.29
884 1358 2.063015 ATGGGACGGTCAGGCAAACA 62.063 55.000 10.76 0.00 0.00 2.83
969 1465 2.815211 GGTCGATGCGCTGCAAGA 60.815 61.111 9.73 7.43 43.62 3.02
976 1482 3.630148 CGTGGATGGTCGATGCGC 61.630 66.667 0.00 0.00 0.00 6.09
981 1487 2.660206 CAACCCGTGGATGGTCGA 59.340 61.111 0.00 0.00 34.15 4.20
984 1490 2.763215 ATGCAACCCGTGGATGGT 59.237 55.556 0.00 0.00 36.83 3.55
1185 1691 1.762460 GGAGATGCCGAGGGAGGAA 60.762 63.158 0.00 0.00 0.00 3.36
1198 1704 3.210528 GACGTCGAGGCGGGAGAT 61.211 66.667 4.75 0.00 35.98 2.75
1261 1801 5.964958 TTCATGAATTCAGTTTCACTCCC 57.035 39.130 14.54 0.00 38.37 4.30
1287 1843 3.302161 CATGGATCATCACCCACCAATT 58.698 45.455 0.00 0.00 34.92 2.32
1755 2422 5.674525 GACATCATGGTCACCAAGAAGATA 58.325 41.667 11.14 0.00 34.85 1.98
1815 2482 3.321648 ATGGGCAGCGTCCACAGA 61.322 61.111 4.02 0.00 41.42 3.41
1876 2543 3.499737 GACATTCGTGCCGCCCAG 61.500 66.667 0.00 0.00 0.00 4.45
1915 2582 1.729470 ATGGCAGAGTAGACGCTCGG 61.729 60.000 0.00 0.00 40.26 4.63
1919 2586 2.009888 GCAATGGCAGAGTAGACGC 58.990 57.895 0.00 0.00 40.72 5.19
2241 2911 1.139095 GTCCACGATGTCGACCTCC 59.861 63.158 14.12 0.86 43.02 4.30
2247 2917 1.514228 CTCCACGTCCACGATGTCG 60.514 63.158 6.03 0.11 43.02 4.35
2337 3007 2.288025 GCCGTCCTTGAGGTACCCA 61.288 63.158 8.74 3.39 36.34 4.51
2437 3107 4.570663 GGACCGGTCGCGGATCTG 62.571 72.222 27.68 0.00 0.00 2.90
2777 3447 3.315142 CTGCTGCTACCCCTGCGAA 62.315 63.158 0.00 0.00 33.01 4.70
2809 3488 2.489275 CCCATTGCCATGCCGTACC 61.489 63.158 0.00 0.00 0.00 3.34
2957 3637 3.708121 TCTATTGAAGATGCTCTGAGGCA 59.292 43.478 6.83 5.59 46.63 4.75
2994 3677 8.816640 ATTTTACTCAAAGCACAATTTAGTGG 57.183 30.769 0.00 0.00 39.87 4.00
3062 3745 4.771590 TTTTGCATCATCTGTTGGAGTC 57.228 40.909 0.00 0.00 0.00 3.36
3079 3762 1.940613 GAGCACTACCGCCCTATTTTG 59.059 52.381 0.00 0.00 0.00 2.44
3416 4137 1.136336 GTCGTTGCTTCGGTCAACATC 60.136 52.381 13.00 4.65 42.78 3.06
3420 4141 1.952133 CGGTCGTTGCTTCGGTCAA 60.952 57.895 1.90 0.00 0.00 3.18
3421 4142 2.355363 CGGTCGTTGCTTCGGTCA 60.355 61.111 1.90 0.00 0.00 4.02
3493 4215 1.091771 TCATCGTCCGACGTAGGTCC 61.092 60.000 19.89 5.90 43.14 4.46
3557 4279 3.187637 CAGATTTTTGGTCGTTTCGGCTA 59.812 43.478 0.00 0.00 0.00 3.93
3559 4281 2.315901 CAGATTTTTGGTCGTTTCGGC 58.684 47.619 0.00 0.00 0.00 5.54
3568 4290 2.550639 GGCCATTGTGCAGATTTTTGGT 60.551 45.455 0.00 0.00 0.00 3.67
3575 4297 0.820891 GGATCGGCCATTGTGCAGAT 60.821 55.000 2.24 10.71 46.57 2.90


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

AutoCloner maintained by Alex Coulton.