Multiple sequence alignment - TraesCS2A01G429800

Loading Multiple Alignment...

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 TraesCS2A01G429800 chr2A 100.000 4702 0 0 1 4702 683015787 683011086 0.000000e+00 8684.0
1 TraesCS2A01G429800 chr2D 96.988 3187 65 17 679 3843 539430563 539427386 0.000000e+00 5325.0
2 TraesCS2A01G429800 chr2D 87.473 455 24 8 3839 4263 635948127 635947676 1.180000e-135 494.0
3 TraesCS2A01G429800 chr2D 88.341 223 23 3 4482 4702 539426439 539426218 1.000000e-66 265.0
4 TraesCS2A01G429800 chr2D 96.552 116 4 0 4258 4373 635947652 635947537 4.800000e-45 193.0
5 TraesCS2A01G429800 chr2D 90.000 70 3 1 4395 4460 263506211 263506142 2.330000e-13 87.9
6 TraesCS2A01G429800 chr2D 92.063 63 4 1 4406 4468 635947441 635947380 2.330000e-13 87.9
7 TraesCS2A01G429800 chr2D 88.000 75 5 1 4395 4465 78382740 78382666 8.380000e-13 86.1
8 TraesCS2A01G429800 chr2B 93.680 3133 119 31 734 3843 643686210 643683134 0.000000e+00 4615.0
9 TraesCS2A01G429800 chr2B 91.587 416 30 4 268 679 36804133 36804547 1.900000e-158 569.0
10 TraesCS2A01G429800 chr2B 94.922 256 13 0 1 256 36803456 36803711 7.330000e-108 401.0
11 TraesCS2A01G429800 chr2B 84.167 360 29 11 3962 4296 468738016 468737660 1.630000e-84 324.0
12 TraesCS2A01G429800 chr2B 90.688 247 16 4 4460 4701 643683141 643682897 5.870000e-84 322.0
13 TraesCS2A01G429800 chr2B 94.068 118 7 0 3844 3961 468738168 468738051 3.740000e-41 180.0
14 TraesCS2A01G429800 chr3A 96.486 683 13 3 1 679 611714641 611715316 0.000000e+00 1118.0
15 TraesCS2A01G429800 chr3A 85.836 353 18 15 3959 4284 533076968 533076621 3.480000e-91 346.0
16 TraesCS2A01G429800 chr3A 95.000 120 5 1 3844 3962 533077113 533076994 2.230000e-43 187.0
17 TraesCS2A01G429800 chr3A 83.092 207 22 7 4059 4258 739736528 739736728 4.840000e-40 176.0
18 TraesCS2A01G429800 chr3A 93.913 115 7 0 4258 4372 533076600 533076486 1.740000e-39 174.0
19 TraesCS2A01G429800 chr3A 89.344 122 8 4 3844 3961 264030347 264030467 1.050000e-31 148.0
20 TraesCS2A01G429800 chr7A 96.182 681 14 5 1 679 698692780 698693450 0.000000e+00 1103.0
21 TraesCS2A01G429800 chr7A 80.597 201 33 3 35 229 36100629 36100429 2.930000e-32 150.0
22 TraesCS2A01G429800 chr3B 91.387 685 41 7 1 679 356866972 356867644 0.000000e+00 922.0
23 TraesCS2A01G429800 chr3B 81.095 201 32 3 35 229 765607709 765607909 6.300000e-34 156.0
24 TraesCS2A01G429800 chr3B 90.000 120 9 3 3844 3961 299139126 299139008 8.150000e-33 152.0
25 TraesCS2A01G429800 chr1D 91.014 690 34 11 1 679 483447323 483447995 0.000000e+00 905.0
26 TraesCS2A01G429800 chr5D 90.200 449 14 5 3844 4263 261388625 261389072 4.110000e-155 558.0
27 TraesCS2A01G429800 chr5D 82.249 507 52 24 1696 2188 530873539 530873057 2.040000e-108 403.0
28 TraesCS2A01G429800 chr5D 87.147 319 23 13 994 1312 530874122 530873822 3.480000e-91 346.0
29 TraesCS2A01G429800 chr5D 96.552 116 4 0 4258 4373 261389111 261389226 4.800000e-45 193.0
30 TraesCS2A01G429800 chr5D 96.296 54 2 0 4406 4459 261389350 261389403 6.480000e-14 89.8
31 TraesCS2A01G429800 chr5D 90.164 61 6 0 4406 4466 274767970 274767910 3.900000e-11 80.5
32 TraesCS2A01G429800 chr5A 92.717 357 14 7 336 683 241188774 241188421 5.430000e-139 505.0
33 TraesCS2A01G429800 chr5A 97.297 37 1 0 649 685 558114949 558114913 3.930000e-06 63.9
34 TraesCS2A01G429800 chr5A 97.297 37 1 0 649 685 558115438 558115402 3.930000e-06 63.9
35 TraesCS2A01G429800 chr4A 80.115 694 74 38 1517 2188 641401326 641401977 4.290000e-125 459.0
36 TraesCS2A01G429800 chr4A 87.346 324 23 10 994 1314 641400892 641401200 5.790000e-94 355.0
37 TraesCS2A01G429800 chr4A 80.597 201 33 3 35 229 34548529 34548729 2.930000e-32 150.0
38 TraesCS2A01G429800 chr6D 89.820 334 22 11 3958 4284 402347966 402347638 7.280000e-113 418.0
39 TraesCS2A01G429800 chr6D 79.357 373 50 14 849 1217 439114499 439114848 2.190000e-58 237.0
40 TraesCS2A01G429800 chr6D 95.798 119 5 0 3844 3962 402348113 402347995 4.800000e-45 193.0
41 TraesCS2A01G429800 chr6D 93.966 116 7 0 4258 4373 402347617 402347502 4.840000e-40 176.0
42 TraesCS2A01G429800 chr6D 95.000 60 3 0 4406 4465 402347376 402347317 1.390000e-15 95.3
43 TraesCS2A01G429800 chr5B 88.991 327 18 10 994 1317 670118217 670117906 5.710000e-104 388.0
44 TraesCS2A01G429800 chr4B 89.683 126 12 1 3837 3961 22848331 22848206 4.870000e-35 159.0
45 TraesCS2A01G429800 chr4B 91.935 62 4 1 4406 4467 22847557 22847497 8.380000e-13 86.1
46 TraesCS2A01G429800 chr4D 90.756 119 10 1 3844 3961 10977814 10977932 1.750000e-34 158.0
47 TraesCS2A01G429800 chr4D 90.141 71 3 1 4395 4461 10978264 10978334 6.480000e-14 89.8
48 TraesCS2A01G429800 chr6B 94.444 54 3 0 4406 4459 98852179 98852126 3.020000e-12 84.2
49 TraesCS2A01G429800 chr3D 96.970 33 1 0 4230 4262 545332539 545332507 6.570000e-04 56.5


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 TraesCS2A01G429800 chr2A 683011086 683015787 4701 True 8684.000000 8684 100.000000 1 4702 1 chr2A.!!$R1 4701
1 TraesCS2A01G429800 chr2D 539426218 539430563 4345 True 2795.000000 5325 92.664500 679 4702 2 chr2D.!!$R3 4023
2 TraesCS2A01G429800 chr2D 635947380 635948127 747 True 258.300000 494 92.029333 3839 4468 3 chr2D.!!$R4 629
3 TraesCS2A01G429800 chr2B 643682897 643686210 3313 True 2468.500000 4615 92.184000 734 4701 2 chr2B.!!$R2 3967
4 TraesCS2A01G429800 chr2B 36803456 36804547 1091 False 485.000000 569 93.254500 1 679 2 chr2B.!!$F1 678
5 TraesCS2A01G429800 chr2B 468737660 468738168 508 True 252.000000 324 89.117500 3844 4296 2 chr2B.!!$R1 452
6 TraesCS2A01G429800 chr3A 611714641 611715316 675 False 1118.000000 1118 96.486000 1 679 1 chr3A.!!$F2 678
7 TraesCS2A01G429800 chr3A 533076486 533077113 627 True 235.666667 346 91.583000 3844 4372 3 chr3A.!!$R1 528
8 TraesCS2A01G429800 chr7A 698692780 698693450 670 False 1103.000000 1103 96.182000 1 679 1 chr7A.!!$F1 678
9 TraesCS2A01G429800 chr3B 356866972 356867644 672 False 922.000000 922 91.387000 1 679 1 chr3B.!!$F1 678
10 TraesCS2A01G429800 chr1D 483447323 483447995 672 False 905.000000 905 91.014000 1 679 1 chr1D.!!$F1 678
11 TraesCS2A01G429800 chr5D 530873057 530874122 1065 True 374.500000 403 84.698000 994 2188 2 chr5D.!!$R2 1194
12 TraesCS2A01G429800 chr5D 261388625 261389403 778 False 280.266667 558 94.349333 3844 4459 3 chr5D.!!$F1 615
13 TraesCS2A01G429800 chr4A 641400892 641401977 1085 False 407.000000 459 83.730500 994 2188 2 chr4A.!!$F2 1194
14 TraesCS2A01G429800 chr6D 402347317 402348113 796 True 220.575000 418 93.646000 3844 4465 4 chr6D.!!$R1 621

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
843 1300 0.335019 GGGGTAAAATCAGGCCCACT 59.665 55.000 0.0 0.0 42.79 4.00 F
845 1302 1.005450 GGGTAAAATCAGGCCCACTCA 59.995 52.381 0.0 0.0 40.76 3.41 F
1125 1588 1.153628 GCCGCTCCACAACTACGAT 60.154 57.895 0.0 0.0 0.00 3.73 F
1904 2444 2.164422 CGCTGAAGTAGACAGTGATCCA 59.836 50.000 0.0 0.0 45.17 3.41 F
3324 3893 0.827368 GGCGAAGGAGGAAGAGACAT 59.173 55.000 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2195 1.073722 CAAGCAGGAGCAGGAACCA 59.926 57.895 0.00 0.00 45.49 3.67 R
1904 2444 1.562783 GTACAAGCTCCCCAGACTCT 58.437 55.000 0.00 0.00 0.00 3.24 R
2195 2755 2.559668 AGAATCATGGTGTGTGCCTTTG 59.440 45.455 0.00 0.00 0.00 2.77 R
3635 4207 1.211212 TCGTAATCCCTCCTCGAGTGA 59.789 52.381 12.31 7.52 0.00 3.41 R
4163 5027 0.247736 CCTCGCTACAGTTCTTGGCT 59.752 55.000 0.00 0.00 0.00 4.75 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
153 154 8.718102 TGAAGCTATGGTTCAAGATTAGTAAC 57.282 34.615 9.34 0.00 45.12 2.50
371 790 5.357742 AGATCCCTTTTTGCACACTTTTT 57.642 34.783 0.00 0.00 0.00 1.94
502 921 3.813166 CCCCATTCATTACGTATGTCACC 59.187 47.826 0.00 0.00 35.64 4.02
681 1118 4.421948 GCACGTGCATACTTACTAGTCTT 58.578 43.478 34.52 0.00 41.59 3.01
761 1198 2.125673 ATACACGTGCACGGCCTC 60.126 61.111 39.21 1.35 44.95 4.70
835 1292 2.820479 CGCCGCGGGGTAAAATCA 60.820 61.111 32.15 0.00 34.97 2.57
836 1293 2.819552 CGCCGCGGGGTAAAATCAG 61.820 63.158 32.15 0.00 34.97 2.90
837 1294 2.478033 GCCGCGGGGTAAAATCAGG 61.478 63.158 29.38 0.00 34.97 3.86
838 1295 2.478033 CCGCGGGGTAAAATCAGGC 61.478 63.158 20.10 0.00 0.00 4.85
839 1296 2.478033 CGCGGGGTAAAATCAGGCC 61.478 63.158 0.00 0.00 0.00 5.19
840 1297 2.125326 GCGGGGTAAAATCAGGCCC 61.125 63.158 0.00 0.00 40.35 5.80
841 1298 1.304952 CGGGGTAAAATCAGGCCCA 59.695 57.895 0.00 0.00 42.79 5.36
842 1299 1.035385 CGGGGTAAAATCAGGCCCAC 61.035 60.000 0.00 0.00 42.79 4.61
843 1300 0.335019 GGGGTAAAATCAGGCCCACT 59.665 55.000 0.00 0.00 42.79 4.00
844 1301 1.685180 GGGGTAAAATCAGGCCCACTC 60.685 57.143 0.00 0.00 42.79 3.51
845 1302 1.005450 GGGTAAAATCAGGCCCACTCA 59.995 52.381 0.00 0.00 40.76 3.41
846 1303 2.358195 GGGTAAAATCAGGCCCACTCAT 60.358 50.000 0.00 0.00 40.76 2.90
847 1304 2.952310 GGTAAAATCAGGCCCACTCATC 59.048 50.000 0.00 0.00 0.00 2.92
848 1305 2.149973 AAAATCAGGCCCACTCATCC 57.850 50.000 0.00 0.00 0.00 3.51
849 1306 1.302907 AAATCAGGCCCACTCATCCT 58.697 50.000 0.00 0.00 0.00 3.24
859 1316 1.703411 CACTCATCCTCTCCTCCTCC 58.297 60.000 0.00 0.00 0.00 4.30
863 1320 1.630333 ATCCTCTCCTCCTCCCCCA 60.630 63.158 0.00 0.00 0.00 4.96
1125 1588 1.153628 GCCGCTCCACAACTACGAT 60.154 57.895 0.00 0.00 0.00 3.73
1445 1919 8.253810 TCTGTTTATTTCTCTGTATCTGTGAGG 58.746 37.037 0.00 0.00 0.00 3.86
1448 1922 9.303537 GTTTATTTCTCTGTATCTGTGAGGTAC 57.696 37.037 0.00 0.00 0.00 3.34
1468 1942 5.010213 GGTACCCTTTTGCTATGTGAAAACA 59.990 40.000 0.00 0.00 0.00 2.83
1655 2184 6.034683 GCTTATGTTGTTCCTAGTGAAGTACG 59.965 42.308 0.00 0.00 32.37 3.67
1656 2185 4.924305 TGTTGTTCCTAGTGAAGTACGT 57.076 40.909 0.00 0.00 32.37 3.57
1666 2195 6.891908 TCCTAGTGAAGTACGTATAAAACCCT 59.108 38.462 0.00 0.00 0.00 4.34
1759 2295 9.167311 GTTGGTAGATTGTCAATAGTTTCTGAT 57.833 33.333 0.00 0.00 0.00 2.90
1880 2417 2.975489 AGAAGCTGAGGTTGGAGAGAAA 59.025 45.455 0.00 0.00 0.00 2.52
1904 2444 2.164422 CGCTGAAGTAGACAGTGATCCA 59.836 50.000 0.00 0.00 45.17 3.41
1946 2494 4.541705 CTGGGAAGGAGTCTGAAGAGATA 58.458 47.826 0.00 0.00 0.00 1.98
1973 2521 6.227522 TGTTGATGTTCAGAACGATAGGAAA 58.772 36.000 8.80 0.00 43.77 3.13
2195 2755 2.825532 TCATAAGAAGGCAAAACAGGGC 59.174 45.455 0.00 0.00 0.00 5.19
2261 2821 1.134848 GGCAAGAAGGCAAAACACACA 60.135 47.619 0.00 0.00 43.51 3.72
2360 2920 6.059787 AGAAGCAAGTACAAGGATGATTCT 57.940 37.500 0.00 3.33 41.99 2.40
2409 2969 1.203523 ACAGTGATTCAGAGAGCGACC 59.796 52.381 0.00 0.00 0.00 4.79
2783 3343 4.942761 AAAGAAGAAGCCTGCAAAATCA 57.057 36.364 0.00 0.00 0.00 2.57
2921 3487 1.212688 TCGGATGGATGGCAAAGACAT 59.787 47.619 0.00 0.00 31.76 3.06
2922 3488 1.335810 CGGATGGATGGCAAAGACATG 59.664 52.381 0.00 0.00 27.61 3.21
2923 3489 2.381911 GGATGGATGGCAAAGACATGT 58.618 47.619 0.00 0.00 27.61 3.21
3324 3893 0.827368 GGCGAAGGAGGAAGAGACAT 59.173 55.000 0.00 0.00 0.00 3.06
3376 3945 0.967380 GAGCATGGTGTGGAAAGGGG 60.967 60.000 0.00 0.00 0.00 4.79
3405 3974 4.495690 AGAAAGGTTGGAGAAGATAGGC 57.504 45.455 0.00 0.00 0.00 3.93
3604 4176 8.770322 AGCTAGATATTCAGATAGCCATGATTT 58.230 33.333 0.00 0.00 41.23 2.17
3703 4275 1.079503 GACAGGAGGCATCGTTGAAC 58.920 55.000 8.25 0.00 0.00 3.18
3766 4338 3.004629 TGCTTGTTAGTTTGCATCACTGG 59.995 43.478 8.93 0.00 0.00 4.00
3791 4364 7.143340 GGAAGGAGTAAACACACATTTTTACC 58.857 38.462 0.00 0.00 38.45 2.85
3798 4371 6.635166 AAACACACATTTTTACCGTTTGTC 57.365 33.333 0.00 0.00 0.00 3.18
3946 4519 1.407979 CGGGGATACGGCAGGATATAC 59.592 57.143 0.00 0.00 37.60 1.47
4006 4614 5.605534 AGTACTGACATATGTTGCCTCATC 58.394 41.667 10.30 0.00 0.00 2.92
4010 4618 5.356190 ACTGACATATGTTGCCTCATCTTTG 59.644 40.000 10.30 0.00 0.00 2.77
4055 4896 3.513912 TGAGGATCACACGGTCACTTTAT 59.486 43.478 0.00 0.00 42.56 1.40
4057 4898 5.362717 TGAGGATCACACGGTCACTTTATAT 59.637 40.000 0.00 0.00 42.56 0.86
4191 5055 3.222173 ACTGTAGCGAGGAGATGAGAT 57.778 47.619 0.00 0.00 0.00 2.75
4195 5059 2.363306 AGCGAGGAGATGAGATGACT 57.637 50.000 0.00 0.00 0.00 3.41
4265 5628 3.686726 CACCCAAATCTTCTTTCTCCTCG 59.313 47.826 0.00 0.00 0.00 4.63
4313 5676 2.343758 GTCGAGGTTGCCAGCTCA 59.656 61.111 16.27 2.15 46.39 4.26
4339 5702 2.902846 ATCCGTCGGAGGAGAGCG 60.903 66.667 20.50 0.00 44.55 5.03
4575 6032 9.730705 TTGTTCTTCATTCTAATGATTCTCTGT 57.269 29.630 6.24 0.00 44.27 3.41
4616 6073 3.623060 TCATTTCTATGAAGCGAAGTGCC 59.377 43.478 0.00 0.00 39.09 5.01
4617 6074 3.374988 CATTTCTATGAAGCGAAGTGCCA 59.625 43.478 0.00 0.00 37.99 4.92
4632 6089 0.899019 TGCCACGCTGGTACATCTTA 59.101 50.000 0.00 0.00 40.46 2.10
4678 6137 2.877300 GCCATTGAAGAAGGCTCAGTCA 60.877 50.000 0.00 0.00 44.92 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 8.682936 AGGAATTGTATGCTTAGACCAAATAG 57.317 34.615 0.00 0.00 0.00 1.73
254 255 8.833734 AGCATCCATTAGCTGCCATATATATAT 58.166 33.333 0.00 0.00 40.13 0.86
255 256 8.211030 AGCATCCATTAGCTGCCATATATATA 57.789 34.615 0.00 0.00 40.13 0.86
256 257 7.087895 AGCATCCATTAGCTGCCATATATAT 57.912 36.000 0.00 0.00 40.13 0.86
257 258 6.505048 AGCATCCATTAGCTGCCATATATA 57.495 37.500 0.00 0.00 40.13 0.86
258 259 5.384145 AGCATCCATTAGCTGCCATATAT 57.616 39.130 0.00 0.00 40.13 0.86
635 1072 2.878406 CGCCCGTCTCCATAATTCAATT 59.122 45.455 0.00 0.00 0.00 2.32
644 1081 4.015406 TGCAACGCCCGTCTCCAT 62.015 61.111 0.00 0.00 0.00 3.41
737 1174 1.202371 CCGTGCACGTGTATGTCCTAT 60.202 52.381 34.81 0.00 37.74 2.57
738 1175 0.171679 CCGTGCACGTGTATGTCCTA 59.828 55.000 34.81 0.00 37.74 2.94
761 1198 0.608130 TGTCGGTGTCTGATTCTGGG 59.392 55.000 0.00 0.00 0.00 4.45
835 1292 1.383803 GGAGAGGATGAGTGGGCCT 60.384 63.158 4.53 0.00 33.97 5.19
836 1293 1.383803 AGGAGAGGATGAGTGGGCC 60.384 63.158 0.00 0.00 0.00 5.80
837 1294 1.406860 GGAGGAGAGGATGAGTGGGC 61.407 65.000 0.00 0.00 0.00 5.36
838 1295 0.264359 AGGAGGAGAGGATGAGTGGG 59.736 60.000 0.00 0.00 0.00 4.61
839 1296 1.703411 GAGGAGGAGAGGATGAGTGG 58.297 60.000 0.00 0.00 0.00 4.00
840 1297 1.703411 GGAGGAGGAGAGGATGAGTG 58.297 60.000 0.00 0.00 0.00 3.51
841 1298 0.560688 GGGAGGAGGAGAGGATGAGT 59.439 60.000 0.00 0.00 0.00 3.41
842 1299 0.178935 GGGGAGGAGGAGAGGATGAG 60.179 65.000 0.00 0.00 0.00 2.90
843 1300 1.669927 GGGGGAGGAGGAGAGGATGA 61.670 65.000 0.00 0.00 0.00 2.92
844 1301 1.152139 GGGGGAGGAGGAGAGGATG 60.152 68.421 0.00 0.00 0.00 3.51
845 1302 1.015131 ATGGGGGAGGAGGAGAGGAT 61.015 60.000 0.00 0.00 0.00 3.24
846 1303 1.630333 ATGGGGGAGGAGGAGAGGA 60.630 63.158 0.00 0.00 0.00 3.71
847 1304 1.152139 GATGGGGGAGGAGGAGAGG 60.152 68.421 0.00 0.00 0.00 3.69
848 1305 1.532794 CGATGGGGGAGGAGGAGAG 60.533 68.421 0.00 0.00 0.00 3.20
849 1306 2.299727 GACGATGGGGGAGGAGGAGA 62.300 65.000 0.00 0.00 0.00 3.71
1141 1607 2.892425 CATCCCGCCGAGCTTGTC 60.892 66.667 0.00 0.00 0.00 3.18
1445 1919 6.079424 TGTTTTCACATAGCAAAAGGGTAC 57.921 37.500 0.00 0.00 31.13 3.34
1448 1922 5.200368 ACTGTTTTCACATAGCAAAAGGG 57.800 39.130 0.00 0.00 30.39 3.95
1468 1942 5.882557 CCACATAGCAAAAGGATAACTGACT 59.117 40.000 0.00 0.00 0.00 3.41
1558 2054 7.864108 TTCAATGTGAAATATCCTCGAACAT 57.136 32.000 0.00 0.00 32.71 2.71
1655 2184 3.945921 GAGCAGGAACCAGGGTTTTATAC 59.054 47.826 4.99 0.00 38.60 1.47
1656 2185 3.053917 GGAGCAGGAACCAGGGTTTTATA 60.054 47.826 4.99 0.00 38.60 0.98
1666 2195 1.073722 CAAGCAGGAGCAGGAACCA 59.926 57.895 0.00 0.00 45.49 3.67
1718 2250 5.492895 TCTACCAACAGAACAAACAACTGA 58.507 37.500 0.00 0.00 35.85 3.41
1759 2295 6.611613 ACCTGAGAAGATTCACATGTCTTA 57.388 37.500 0.00 0.00 34.97 2.10
1880 2417 3.728076 TCACTGTCTACTTCAGCGTTT 57.272 42.857 0.00 0.00 36.50 3.60
1904 2444 1.562783 GTACAAGCTCCCCAGACTCT 58.437 55.000 0.00 0.00 0.00 3.24
1946 2494 6.045318 CCTATCGTTCTGAACATCAACATCT 58.955 40.000 19.56 0.00 0.00 2.90
2195 2755 2.559668 AGAATCATGGTGTGTGCCTTTG 59.440 45.455 0.00 0.00 0.00 2.77
2206 2766 3.201487 TGAATCAGCCTCAGAATCATGGT 59.799 43.478 0.00 0.00 0.00 3.55
2261 2821 3.420893 TCCCTCATCACGATTGCTTTTT 58.579 40.909 0.00 0.00 0.00 1.94
2360 2920 3.136009 TCACTCTCCGAGTCACTGTAA 57.864 47.619 0.00 0.00 41.37 2.41
2632 3192 7.870445 TCACAGGCCTTTTGTTTTTATATTCAC 59.130 33.333 0.00 0.00 0.00 3.18
2783 3343 9.739276 TTATCAACTTTAGAAACATGGACAGAT 57.261 29.630 0.00 0.00 0.00 2.90
3324 3893 3.748048 CGCTCATGTTCCTTCTCTTTCAA 59.252 43.478 0.00 0.00 0.00 2.69
3376 3945 2.362077 TCTCCAACCTTTCTTTTGCTGC 59.638 45.455 0.00 0.00 0.00 5.25
3405 3974 3.315191 AGTCTGTTTGAATTTGGGTCGTG 59.685 43.478 0.00 0.00 0.00 4.35
3635 4207 1.211212 TCGTAATCCCTCCTCGAGTGA 59.789 52.381 12.31 7.52 0.00 3.41
3653 4225 4.153296 TCATCTCTAGAATAGCGCTCTTCG 59.847 45.833 24.46 14.56 38.99 3.79
3703 4275 9.690434 GACTTACATTTTAAGATAACTTCTGCG 57.310 33.333 0.00 0.00 37.53 5.18
3731 4303 6.472686 ACTAACAAGCAATGGTAAAAACCA 57.527 33.333 0.00 0.00 44.85 3.67
3732 4304 7.626446 CAAACTAACAAGCAATGGTAAAAACC 58.374 34.615 0.00 0.00 28.65 3.27
3766 4338 7.143340 GGTAAAAATGTGTGTTTACTCCTTCC 58.857 38.462 6.33 0.00 39.25 3.46
3791 4364 9.490663 CCTAAAAGATTAGCATTAAGACAAACG 57.509 33.333 0.00 0.00 37.74 3.60
3798 4371 9.573133 CAAACCACCTAAAAGATTAGCATTAAG 57.427 33.333 0.00 0.00 37.74 1.85
3920 4493 2.040009 CTGCCGTATCCCCGAATGGT 62.040 60.000 0.00 0.00 0.00 3.55
4055 4896 0.826715 GCTCTGAGTGCAGGGTCATA 59.173 55.000 6.53 0.00 44.79 2.15
4057 4898 2.587247 GGCTCTGAGTGCAGGGTCA 61.587 63.158 8.86 0.00 46.64 4.02
4064 4928 1.661341 CTTATGTGGGCTCTGAGTGC 58.339 55.000 6.53 0.00 0.00 4.40
4163 5027 0.247736 CCTCGCTACAGTTCTTGGCT 59.752 55.000 0.00 0.00 0.00 4.75
4265 5628 1.488393 AGGGAAGAAGATACAGGCAGC 59.512 52.381 0.00 0.00 0.00 5.25
4339 5702 3.470567 CGACCACGACGCTGCTTC 61.471 66.667 0.00 0.00 42.66 3.86
4411 5867 2.223641 TGCCGTATTGCCGTTCTAGTAG 60.224 50.000 0.00 0.00 0.00 2.57
4477 5933 6.627087 ACCCAAGTGAAATAATCTGAGAGA 57.373 37.500 0.00 0.00 0.00 3.10
4499 5955 6.749118 CCAAAAGCTGCTATGAAGTTTATCAC 59.251 38.462 14.75 0.00 30.82 3.06
4537 5993 4.916983 TGAAGAACAATGAACACAAGGG 57.083 40.909 0.00 0.00 0.00 3.95
4539 5995 9.903682 ATTAGAATGAAGAACAATGAACACAAG 57.096 29.630 0.00 0.00 0.00 3.16
4569 6026 0.972134 CTGCAGAGGGACAACAGAGA 59.028 55.000 8.42 0.00 0.00 3.10
4575 6032 1.203441 AGATGCCTGCAGAGGGACAA 61.203 55.000 17.39 0.00 43.63 3.18
4616 6073 3.246226 GCTCAATAAGATGTACCAGCGTG 59.754 47.826 0.00 0.00 0.00 5.34
4617 6074 3.118775 TGCTCAATAAGATGTACCAGCGT 60.119 43.478 0.00 0.00 0.00 5.07
4632 6089 4.460382 CCAATGTTACTGTCCTTGCTCAAT 59.540 41.667 0.00 0.00 0.00 2.57
4678 6137 1.090052 GCCGAAATCTTGCGCTAGGT 61.090 55.000 18.64 9.16 0.00 3.08


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

AutoCloner maintained by Alex Coulton.