Multiple sequence alignment - TraesCS6A01G037200

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 TraesCS6A01G037200 chr6A 100.000 2416 0 0 1 2416 18438492 18440907 0.000000e+00 4462.0
1 TraesCS6A01G037200 chr6B 93.362 693 44 2 1726 2416 632307493 632308185 0.000000e+00 1024.0
2 TraesCS6A01G037200 chr6B 92.775 692 48 2 1726 2416 646264310 646263620 0.000000e+00 1000.0
3 TraesCS6A01G037200 chr6B 81.494 897 100 28 827 1718 31714288 31713453 0.000000e+00 676.0
4 TraesCS6A01G037200 chr6B 81.161 844 94 31 870 1699 31395879 31396671 3.410000e-173 617.0
5 TraesCS6A01G037200 chr6B 82.162 740 88 24 974 1699 30877556 30878265 1.600000e-166 595.0
6 TraesCS6A01G037200 chr6B 80.427 843 101 27 871 1699 31361579 31362371 3.460000e-163 584.0
7 TraesCS6A01G037200 chr6B 80.387 775 81 24 84 818 30734661 30735404 7.650000e-145 523.0
8 TraesCS6A01G037200 chr6B 80.438 777 77 28 84 818 30813321 30814064 7.650000e-145 523.0
9 TraesCS6A01G037200 chr6B 79.742 775 86 28 84 818 30876643 30877386 1.670000e-136 496.0
10 TraesCS6A01G037200 chr6B 80.447 716 71 22 1 675 30862080 30862767 1.300000e-132 483.0
11 TraesCS6A01G037200 chr6B 80.307 716 72 22 1 675 30797245 30797932 6.040000e-131 477.0
12 TraesCS6A01G037200 chr6B 80.028 716 74 22 1 675 30718239 30718926 1.310000e-127 466.0
13 TraesCS6A01G037200 chr6B 79.398 665 95 23 995 1658 31717380 31716757 4.770000e-117 431.0
14 TraesCS6A01G037200 chr6B 81.122 588 65 13 7 576 31715090 31714531 1.720000e-116 429.0
15 TraesCS6A01G037200 chr6B 81.404 527 73 13 1179 1699 30718924 30719431 8.040000e-110 407.0
16 TraesCS6A01G037200 chr6B 81.391 532 67 16 1179 1699 30797930 30798440 2.890000e-109 405.0
17 TraesCS6A01G037200 chr6B 81.426 533 65 17 1179 1699 30862765 30863275 2.890000e-109 405.0
18 TraesCS6A01G037200 chr6B 84.712 399 34 13 442 818 30655736 30656129 8.160000e-100 374.0
19 TraesCS6A01G037200 chr6B 84.461 399 35 13 442 818 30651823 30652216 3.790000e-98 368.0
20 TraesCS6A01G037200 chr6B 84.461 399 35 13 442 818 30653915 30654308 3.790000e-98 368.0
21 TraesCS6A01G037200 chr6B 76.056 710 121 35 905 1602 31278516 31279188 8.330000e-85 324.0
22 TraesCS6A01G037200 chr6B 80.214 187 30 5 905 1090 30872866 30873046 1.510000e-27 134.0
23 TraesCS6A01G037200 chr6B 95.181 83 3 1 736 818 31714415 31714334 1.950000e-26 130.0
24 TraesCS6A01G037200 chr6B 94.595 74 4 0 1 74 30734533 30734606 5.460000e-22 115.0
25 TraesCS6A01G037200 chr6B 94.595 74 4 0 1 74 30813193 30813266 5.460000e-22 115.0
26 TraesCS6A01G037200 chr6B 94.595 74 4 0 1 74 30876515 30876588 5.460000e-22 115.0
27 TraesCS6A01G037200 chr6B 91.892 74 6 0 1 74 31319742 31319815 1.180000e-18 104.0
28 TraesCS6A01G037200 chr6B 91.892 74 6 0 1 74 31333551 31333624 1.180000e-18 104.0
29 TraesCS6A01G037200 chr6B 83.951 81 13 0 1010 1090 30728964 30729044 7.160000e-11 78.7
30 TraesCS6A01G037200 chr6B 83.951 81 13 0 1010 1090 30807933 30808013 7.160000e-11 78.7
31 TraesCS6A01G037200 chr6B 82.927 82 10 3 1010 1089 30641202 30641281 1.200000e-08 71.3
32 TraesCS6A01G037200 chr6D 86.621 882 101 12 827 1699 17821946 17822819 0.000000e+00 959.0
33 TraesCS6A01G037200 chr6D 89.868 760 46 4 827 1586 17491579 17492307 0.000000e+00 948.0
34 TraesCS6A01G037200 chr6D 77.699 704 112 29 957 1658 17485727 17486387 2.910000e-104 388.0
35 TraesCS6A01G037200 chr6D 88.048 251 24 4 571 818 17821653 17821900 2.350000e-75 292.0
36 TraesCS6A01G037200 chr6D 86.235 247 24 8 570 815 17491293 17491530 2.380000e-65 259.0
37 TraesCS6A01G037200 chr6D 88.108 185 19 3 385 566 17821433 17821617 1.450000e-52 217.0
38 TraesCS6A01G037200 chrUn 93.058 605 40 2 1814 2416 85423312 85422708 0.000000e+00 883.0
39 TraesCS6A01G037200 chrUn 93.058 605 40 2 1814 2416 85973186 85973790 0.000000e+00 883.0
40 TraesCS6A01G037200 chrUn 78.757 692 142 5 1727 2416 41471240 41470552 2.190000e-125 459.0
41 TraesCS6A01G037200 chr2D 92.105 532 41 1 1881 2411 378347830 378347299 0.000000e+00 749.0
42 TraesCS6A01G037200 chr2D 93.902 164 9 1 1727 1890 378356587 378356425 1.860000e-61 246.0
43 TraesCS6A01G037200 chr7A 91.912 408 32 1 1726 2133 728888811 728888405 9.690000e-159 569.0
44 TraesCS6A01G037200 chr7A 78.143 700 142 7 1726 2416 685022724 685022027 3.690000e-118 435.0
45 TraesCS6A01G037200 chr7A 91.903 247 19 1 2166 2411 728888409 728888163 6.390000e-91 344.0
46 TraesCS6A01G037200 chr3D 78.009 673 136 12 1728 2394 582776086 582775420 1.730000e-111 412.0
47 TraesCS6A01G037200 chr1A 97.059 102 2 1 1727 1828 535703569 535703469 1.150000e-38 171.0


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 TraesCS6A01G037200 chr6A 18438492 18440907 2415 False 4462.000000 4462 100.000000 1 2416 1 chr6A.!!$F1 2415
1 TraesCS6A01G037200 chr6B 632307493 632308185 692 False 1024.000000 1024 93.362000 1726 2416 1 chr6B.!!$F9 690
2 TraesCS6A01G037200 chr6B 646263620 646264310 690 True 1000.000000 1000 92.775000 1726 2416 1 chr6B.!!$R1 690
3 TraesCS6A01G037200 chr6B 31395879 31396671 792 False 617.000000 617 81.161000 870 1699 1 chr6B.!!$F8 829
4 TraesCS6A01G037200 chr6B 31361579 31362371 792 False 584.000000 584 80.427000 871 1699 1 chr6B.!!$F7 828
5 TraesCS6A01G037200 chr6B 30862080 30863275 1195 False 444.000000 483 80.936500 1 1699 2 chr6B.!!$F15 1698
6 TraesCS6A01G037200 chr6B 30797245 30798440 1195 False 441.000000 477 80.849000 1 1699 2 chr6B.!!$F13 1698
7 TraesCS6A01G037200 chr6B 30718239 30719431 1192 False 436.500000 466 80.716000 1 1699 2 chr6B.!!$F11 1698
8 TraesCS6A01G037200 chr6B 31713453 31717380 3927 True 416.500000 676 84.298750 7 1718 4 chr6B.!!$R2 1711
9 TraesCS6A01G037200 chr6B 30651823 30656129 4306 False 370.000000 374 84.544667 442 818 3 chr6B.!!$F10 376
10 TraesCS6A01G037200 chr6B 30872866 30878265 5399 False 335.000000 595 84.178250 1 1699 4 chr6B.!!$F16 1698
11 TraesCS6A01G037200 chr6B 31278516 31279188 672 False 324.000000 324 76.056000 905 1602 1 chr6B.!!$F4 697
12 TraesCS6A01G037200 chr6B 30734533 30735404 871 False 319.000000 523 87.491000 1 818 2 chr6B.!!$F12 817
13 TraesCS6A01G037200 chr6B 30813193 30814064 871 False 319.000000 523 87.516500 1 818 2 chr6B.!!$F14 817
14 TraesCS6A01G037200 chr6D 17491293 17492307 1014 False 603.500000 948 88.051500 570 1586 2 chr6D.!!$F2 1016
15 TraesCS6A01G037200 chr6D 17821433 17822819 1386 False 489.333333 959 87.592333 385 1699 3 chr6D.!!$F3 1314
16 TraesCS6A01G037200 chr6D 17485727 17486387 660 False 388.000000 388 77.699000 957 1658 1 chr6D.!!$F1 701
17 TraesCS6A01G037200 chrUn 85422708 85423312 604 True 883.000000 883 93.058000 1814 2416 1 chrUn.!!$R2 602
18 TraesCS6A01G037200 chrUn 85973186 85973790 604 False 883.000000 883 93.058000 1814 2416 1 chrUn.!!$F1 602
19 TraesCS6A01G037200 chrUn 41470552 41471240 688 True 459.000000 459 78.757000 1727 2416 1 chrUn.!!$R1 689
20 TraesCS6A01G037200 chr2D 378347299 378347830 531 True 749.000000 749 92.105000 1881 2411 1 chr2D.!!$R1 530
21 TraesCS6A01G037200 chr7A 728888163 728888811 648 True 456.500000 569 91.907500 1726 2411 2 chr7A.!!$R2 685
22 TraesCS6A01G037200 chr7A 685022027 685022724 697 True 435.000000 435 78.143000 1726 2416 1 chr7A.!!$R1 690
23 TraesCS6A01G037200 chr3D 582775420 582776086 666 True 412.000000 412 78.009000 1728 2394 1 chr3D.!!$R1 666

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
417 4130 0.034896 TTGCCGAGTCCCTGTCTTTC 59.965 55.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 8275 0.31716 CCGGTGACTACAGCAAGACA 59.683 55.0 0.0 0.0 43.66 3.41 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
26 3676 1.183549 TTTCCCGAGCTCTAGGTGTC 58.816 55.000 12.85 0.00 0.00 3.67
88 3783 6.643388 ACATAGCTATTTGTGAGTGTCATCA 58.357 36.000 2.64 0.00 0.00 3.07
135 3830 6.182627 GGCAATACATGGGATCATCATAAGA 58.817 40.000 0.00 0.00 0.00 2.10
142 3837 4.464008 TGGGATCATCATAAGACCTTTGC 58.536 43.478 0.00 0.00 0.00 3.68
154 3849 2.042831 CCTTTGCCGAGAGCCTTGG 61.043 63.158 4.52 4.52 42.71 3.61
183 3878 3.053831 ACTCGGTAAATGGTTCCTGTG 57.946 47.619 0.00 0.00 0.00 3.66
200 3913 5.597806 TCCTGTGTTAAAGTATATGCCGAG 58.402 41.667 0.00 0.00 0.00 4.63
204 3917 3.799963 TGTTAAAGTATATGCCGAGCGTG 59.200 43.478 1.42 0.00 0.00 5.34
208 3921 1.066752 TATATGCCGAGCGTGCGTT 59.933 52.632 1.42 0.00 0.00 4.84
210 3923 3.801850 TATATGCCGAGCGTGCGTTGT 62.802 52.381 1.42 0.00 0.00 3.32
227 3940 2.112928 TGGCACACTCGGCACAAT 59.887 55.556 0.00 0.00 36.38 2.71
231 3944 1.868997 CACACTCGGCACAATGGAC 59.131 57.895 0.00 0.00 0.00 4.02
233 3946 2.040544 CACTCGGCACAATGGACCC 61.041 63.158 0.00 0.00 0.00 4.46
234 3947 2.438434 CTCGGCACAATGGACCCC 60.438 66.667 0.00 0.00 0.00 4.95
235 3948 3.253061 TCGGCACAATGGACCCCA 61.253 61.111 0.00 0.00 38.19 4.96
237 3950 2.679996 GGCACAATGGACCCCACC 60.680 66.667 0.00 0.00 35.80 4.61
238 3951 2.117206 GCACAATGGACCCCACCA 59.883 61.111 0.00 0.00 44.41 4.17
254 3967 2.684881 CCACCATTACAGAGCCATCAAC 59.315 50.000 0.00 0.00 0.00 3.18
287 4000 3.389741 GCATGTGGCGTCTTCTTTG 57.610 52.632 0.00 0.00 0.00 2.77
289 4002 1.400242 GCATGTGGCGTCTTCTTTGTC 60.400 52.381 0.00 0.00 0.00 3.18
290 4003 1.872952 CATGTGGCGTCTTCTTTGTCA 59.127 47.619 0.00 0.00 0.00 3.58
292 4005 2.571212 TGTGGCGTCTTCTTTGTCAAT 58.429 42.857 0.00 0.00 0.00 2.57
299 4012 0.454957 CTTCTTTGTCAATGGCCGCG 60.455 55.000 0.00 0.00 0.00 6.46
301 4014 2.981560 CTTTGTCAATGGCCGCGCT 61.982 57.895 5.56 0.00 0.00 5.92
312 4025 3.184683 CCGCGCTTGAGCTCTCAC 61.185 66.667 16.19 2.82 39.66 3.51
313 4026 2.126149 CGCGCTTGAGCTCTCACT 60.126 61.111 16.19 0.00 39.66 3.41
314 4027 1.735920 CGCGCTTGAGCTCTCACTT 60.736 57.895 16.19 0.00 39.66 3.16
315 4028 1.681945 CGCGCTTGAGCTCTCACTTC 61.682 60.000 16.19 0.00 39.66 3.01
316 4029 0.389687 GCGCTTGAGCTCTCACTTCT 60.390 55.000 16.19 0.00 39.66 2.85
317 4030 1.627879 CGCTTGAGCTCTCACTTCTC 58.372 55.000 16.19 0.00 39.66 2.87
318 4031 1.627879 GCTTGAGCTCTCACTTCTCG 58.372 55.000 16.19 0.00 39.66 4.04
319 4032 1.735369 GCTTGAGCTCTCACTTCTCGG 60.735 57.143 16.19 0.00 39.66 4.63
320 4033 1.543802 CTTGAGCTCTCACTTCTCGGT 59.456 52.381 16.19 0.00 39.66 4.69
321 4034 2.491675 TGAGCTCTCACTTCTCGGTA 57.508 50.000 16.19 0.00 34.14 4.02
322 4035 2.791655 TGAGCTCTCACTTCTCGGTAA 58.208 47.619 16.19 0.00 34.14 2.85
323 4036 3.154710 TGAGCTCTCACTTCTCGGTAAA 58.845 45.455 16.19 0.00 34.14 2.01
324 4037 3.572682 TGAGCTCTCACTTCTCGGTAAAA 59.427 43.478 16.19 0.00 34.14 1.52
330 4043 6.409524 TCTCACTTCTCGGTAAAAGGTAAA 57.590 37.500 0.00 0.00 0.00 2.01
335 4048 5.994054 ACTTCTCGGTAAAAGGTAAAAGGTC 59.006 40.000 0.00 0.00 0.00 3.85
341 4054 7.278875 TCGGTAAAAGGTAAAAGGTCTGTAAA 58.721 34.615 0.00 0.00 0.00 2.01
348 4061 4.450080 GGTAAAAGGTCTGTAAACCGAGTG 59.550 45.833 0.00 0.00 44.49 3.51
349 4062 3.832615 AAAGGTCTGTAAACCGAGTGT 57.167 42.857 0.00 0.00 44.49 3.55
417 4130 0.034896 TTGCCGAGTCCCTGTCTTTC 59.965 55.000 0.00 0.00 0.00 2.62
427 4140 2.176889 CCCTGTCTTTCCCGAGAGTTA 58.823 52.381 0.00 0.00 0.00 2.24
433 4146 4.401519 TGTCTTTCCCGAGAGTTATACTGG 59.598 45.833 0.00 0.00 0.00 4.00
450 4163 3.299503 ACTGGGCAAAGAAGTGATTTGT 58.700 40.909 0.96 0.00 39.36 2.83
465 4178 3.442273 TGATTTGTTACGGATTTCCCAGC 59.558 43.478 0.00 0.00 34.14 4.85
521 6330 4.390603 TCAACTGTTAGCGTCGCATTATTT 59.609 37.500 21.09 0.00 0.00 1.40
531 6340 6.375377 AGCGTCGCATTATTTTAGAACAAAA 58.625 32.000 21.09 0.00 0.00 2.44
556 6365 4.603131 AGAACAATCATACAGTTGGCCAT 58.397 39.130 6.09 0.00 0.00 4.40
581 6415 4.275936 ACCTGCATGTTAGAGTCAAACAAC 59.724 41.667 0.00 0.00 40.05 3.32
629 6468 5.560966 AGCGATCAACCGAATAAATTTGT 57.439 34.783 0.00 0.00 0.00 2.83
653 6492 1.890041 GCACCACGGCGGCATAATA 60.890 57.895 13.24 0.00 39.03 0.98
663 6502 3.367932 CGGCGGCATAATACACTATCAAG 59.632 47.826 10.53 0.00 0.00 3.02
667 6506 5.615544 GCGGCATAATACACTATCAAGCAAG 60.616 44.000 0.00 0.00 0.00 4.01
695 6534 6.319152 TGATGAGCTTGACTAACTACTCCTAC 59.681 42.308 0.00 0.00 0.00 3.18
696 6535 5.817784 TGAGCTTGACTAACTACTCCTACT 58.182 41.667 0.00 0.00 0.00 2.57
697 6536 6.955364 TGAGCTTGACTAACTACTCCTACTA 58.045 40.000 0.00 0.00 0.00 1.82
698 6537 7.400439 TGAGCTTGACTAACTACTCCTACTAA 58.600 38.462 0.00 0.00 0.00 2.24
699 6538 7.553402 TGAGCTTGACTAACTACTCCTACTAAG 59.447 40.741 0.00 0.00 0.00 2.18
788 6628 1.001378 ACAACGTCAGCATTTTGAGCC 60.001 47.619 0.00 0.00 0.00 4.70
789 6629 1.001487 CAACGTCAGCATTTTGAGCCA 60.001 47.619 0.00 0.00 0.00 4.75
860 6737 5.082059 CGTCTGACAAAGAATCATTTTCCG 58.918 41.667 8.73 0.00 36.40 4.30
874 6751 6.978343 TCATTTTCCGTTATAGTCACCAAG 57.022 37.500 0.00 0.00 0.00 3.61
900 6783 1.216710 GCTCGGTCAGGAGGAGTTG 59.783 63.158 0.00 0.00 34.56 3.16
954 6837 3.378427 ACAAGAACAAGAAGCAACTGACC 59.622 43.478 0.00 0.00 0.00 4.02
1011 6899 3.572539 GATTTGATGGCGCGCGGA 61.573 61.111 33.06 15.07 0.00 5.54
1193 7111 4.166011 GAATGCGGCCGTGAGCAC 62.166 66.667 28.70 9.35 46.83 4.40
1249 7185 2.361104 GGCGCATTCCAAGTCCCA 60.361 61.111 10.83 0.00 0.00 4.37
1319 7255 4.722700 ATGGCCGTGCTGTGGGAC 62.723 66.667 0.00 0.00 0.00 4.46
1401 7337 4.838152 TCCTCATGCGCTTCGGCC 62.838 66.667 9.73 0.00 37.76 6.13
1474 7410 2.769095 GAGGACATAGAAGGAGGTTGCT 59.231 50.000 0.00 0.00 0.00 3.91
1475 7411 2.503356 AGGACATAGAAGGAGGTTGCTG 59.497 50.000 0.00 0.00 0.00 4.41
1540 7487 1.209383 GCCGTTTTCCGAGGCTTTC 59.791 57.895 0.00 0.00 46.83 2.62
1590 7538 3.055385 TCAAGCCCCACTCTTGTGTATAC 60.055 47.826 0.00 0.00 42.34 1.47
1633 7582 7.206789 TCCAGGTAAATGGAAATGTCTCATA 57.793 36.000 0.00 0.00 46.45 2.15
1672 7621 8.696374 TCTGGTATTTCTACTTTCAGTCTATGG 58.304 37.037 0.00 0.00 0.00 2.74
1685 7634 5.277250 TCAGTCTATGGAACTTGGGATACA 58.723 41.667 0.00 0.00 39.74 2.29
1699 7648 1.751924 GGATACACTCGCTCAACTCCT 59.248 52.381 0.00 0.00 0.00 3.69
1700 7649 2.480416 GGATACACTCGCTCAACTCCTG 60.480 54.545 0.00 0.00 0.00 3.86
1710 7659 1.107114 TCAACTCCTGAGATCGGCTC 58.893 55.000 0.22 0.00 44.21 4.70
1792 7741 1.895798 CTAGGACAGTCAGCCAACAGA 59.104 52.381 2.17 0.00 0.00 3.41
1852 7801 3.562973 ACTCAGTCACATTCAAAGTGCAG 59.437 43.478 0.00 0.00 36.93 4.41
1856 7805 2.029649 GTCACATTCAAAGTGCAGGCAT 60.030 45.455 0.00 0.00 36.93 4.40
1974 7924 8.402798 TCTAAAATAGAAGCCACAATTGAACA 57.597 30.769 13.59 0.00 0.00 3.18
2025 7975 5.542635 ACACCACCTCTAGACAATCAGTTTA 59.457 40.000 0.00 0.00 0.00 2.01
2199 8157 3.142174 CTCCTCGCCTTCTTCAAAGTTT 58.858 45.455 0.00 0.00 0.00 2.66
2250 8208 4.980805 TGTTCCAGCGGTCGCCAC 62.981 66.667 11.95 4.92 43.17 5.01
2317 8275 5.772672 AGGATTGCTATCACTTCTCTCGTAT 59.227 40.000 10.33 0.00 32.09 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.366916 CACCTAGAGCTCGGGAAATGAT 59.633 50.000 27.39 8.16 0.00 2.45
26 3676 1.508088 GAAATCTGCCAAGTGCCCG 59.492 57.895 0.00 0.00 40.16 6.13
88 3783 2.331265 GGCTTGTTTTGCCGAGAGT 58.669 52.632 0.00 0.00 41.03 3.24
112 3807 6.094603 GGTCTTATGATGATCCCATGTATTGC 59.905 42.308 7.67 0.00 32.09 3.56
119 3814 5.075493 GCAAAGGTCTTATGATGATCCCAT 58.925 41.667 0.00 0.00 35.29 4.00
135 3830 1.302832 CAAGGCTCTCGGCAAAGGT 60.303 57.895 0.00 0.00 44.01 3.50
142 3837 2.340427 TTTTTGCCAAGGCTCTCGG 58.660 52.632 12.96 0.00 42.51 4.63
179 3874 4.085055 CGCTCGGCATATACTTTAACACAG 60.085 45.833 0.00 0.00 0.00 3.66
183 3878 3.362693 GCACGCTCGGCATATACTTTAAC 60.363 47.826 0.00 0.00 0.00 2.01
204 3917 4.012895 CCGAGTGTGCCACAACGC 62.013 66.667 16.51 5.85 36.74 4.84
208 3921 2.956799 ATTGTGCCGAGTGTGCCACA 62.957 55.000 0.00 0.00 36.74 4.17
210 3923 2.112928 ATTGTGCCGAGTGTGCCA 59.887 55.556 0.00 0.00 0.00 4.92
213 3926 1.577328 GGTCCATTGTGCCGAGTGTG 61.577 60.000 0.00 0.00 0.00 3.82
217 3930 2.438434 GGGGTCCATTGTGCCGAG 60.438 66.667 0.00 0.00 0.00 4.63
227 3940 1.285280 CTCTGTAATGGTGGGGTCCA 58.715 55.000 0.00 0.00 42.01 4.02
231 3944 0.552848 ATGGCTCTGTAATGGTGGGG 59.447 55.000 0.00 0.00 0.00 4.96
233 3946 2.684881 GTTGATGGCTCTGTAATGGTGG 59.315 50.000 0.00 0.00 0.00 4.61
234 3947 2.684881 GGTTGATGGCTCTGTAATGGTG 59.315 50.000 0.00 0.00 0.00 4.17
235 3948 2.680805 CGGTTGATGGCTCTGTAATGGT 60.681 50.000 0.00 0.00 0.00 3.55
237 3950 1.331756 GCGGTTGATGGCTCTGTAATG 59.668 52.381 0.00 0.00 0.00 1.90
238 3951 1.668419 GCGGTTGATGGCTCTGTAAT 58.332 50.000 0.00 0.00 0.00 1.89
239 3952 0.739462 CGCGGTTGATGGCTCTGTAA 60.739 55.000 0.00 0.00 0.00 2.41
240 3953 1.153647 CGCGGTTGATGGCTCTGTA 60.154 57.895 0.00 0.00 0.00 2.74
243 3956 4.473520 CCCGCGGTTGATGGCTCT 62.474 66.667 26.12 0.00 0.00 4.09
264 3977 1.228245 AAGACGCCACATGCACCTT 60.228 52.632 0.00 0.00 41.33 3.50
266 3979 1.237285 AAGAAGACGCCACATGCACC 61.237 55.000 0.00 0.00 41.33 5.01
272 3985 2.031258 TTGACAAAGAAGACGCCACA 57.969 45.000 0.00 0.00 0.00 4.17
287 4000 3.386867 CTCAAGCGCGGCCATTGAC 62.387 63.158 8.83 0.00 0.00 3.18
289 4002 4.842091 GCTCAAGCGCGGCCATTG 62.842 66.667 8.83 0.00 0.00 2.82
299 4012 1.627879 CGAGAAGTGAGAGCTCAAGC 58.372 55.000 17.77 5.38 41.85 4.01
301 4014 1.621992 ACCGAGAAGTGAGAGCTCAA 58.378 50.000 17.77 0.00 41.85 3.02
311 4024 5.933617 ACCTTTTACCTTTTACCGAGAAGT 58.066 37.500 0.00 0.00 0.00 3.01
312 4025 6.147328 CAGACCTTTTACCTTTTACCGAGAAG 59.853 42.308 0.00 0.00 0.00 2.85
313 4026 5.993441 CAGACCTTTTACCTTTTACCGAGAA 59.007 40.000 0.00 0.00 0.00 2.87
314 4027 5.070847 ACAGACCTTTTACCTTTTACCGAGA 59.929 40.000 0.00 0.00 0.00 4.04
315 4028 5.303165 ACAGACCTTTTACCTTTTACCGAG 58.697 41.667 0.00 0.00 0.00 4.63
316 4029 5.294734 ACAGACCTTTTACCTTTTACCGA 57.705 39.130 0.00 0.00 0.00 4.69
317 4030 7.355017 GTTTACAGACCTTTTACCTTTTACCG 58.645 38.462 0.00 0.00 0.00 4.02
318 4031 7.520453 CGGTTTACAGACCTTTTACCTTTTACC 60.520 40.741 0.00 0.00 37.56 2.85
319 4032 7.226523 TCGGTTTACAGACCTTTTACCTTTTAC 59.773 37.037 0.00 0.00 37.56 2.01
320 4033 7.278875 TCGGTTTACAGACCTTTTACCTTTTA 58.721 34.615 0.00 0.00 37.56 1.52
321 4034 6.121590 TCGGTTTACAGACCTTTTACCTTTT 58.878 36.000 0.00 0.00 37.56 2.27
322 4035 5.683681 TCGGTTTACAGACCTTTTACCTTT 58.316 37.500 0.00 0.00 37.56 3.11
323 4036 5.163269 ACTCGGTTTACAGACCTTTTACCTT 60.163 40.000 0.00 0.00 37.56 3.50
324 4037 4.346127 ACTCGGTTTACAGACCTTTTACCT 59.654 41.667 0.00 0.00 37.56 3.08
330 4043 3.832615 AACACTCGGTTTACAGACCTT 57.167 42.857 0.00 0.00 35.82 3.50
373 4086 2.304761 TCACCCATTACCGAGAAAGCTT 59.695 45.455 0.00 0.00 0.00 3.74
380 4093 2.097466 GCAATTGTCACCCATTACCGAG 59.903 50.000 7.40 0.00 0.00 4.63
381 4094 2.088423 GCAATTGTCACCCATTACCGA 58.912 47.619 7.40 0.00 0.00 4.69
382 4095 1.134175 GGCAATTGTCACCCATTACCG 59.866 52.381 4.85 0.00 0.00 4.02
388 4101 0.605319 GACTCGGCAATTGTCACCCA 60.605 55.000 11.22 0.00 0.00 4.51
417 4130 1.410004 TGCCCAGTATAACTCTCGGG 58.590 55.000 0.00 0.00 36.71 5.14
427 4140 5.079643 ACAAATCACTTCTTTGCCCAGTAT 58.920 37.500 0.00 0.00 37.15 2.12
433 4146 4.023536 TCCGTAACAAATCACTTCTTTGCC 60.024 41.667 0.00 0.00 37.15 4.52
450 4163 1.626321 TCACTGCTGGGAAATCCGTAA 59.374 47.619 0.00 0.00 38.76 3.18
465 4178 3.947868 AGGACACTCCATTGAATCACTG 58.052 45.455 0.00 0.00 39.61 3.66
494 4207 4.295857 TGCGACGCTAACAGTTGATATA 57.704 40.909 22.08 0.00 0.00 0.86
499 6308 3.925688 ATAATGCGACGCTAACAGTTG 57.074 42.857 22.08 0.00 0.00 3.16
504 6313 6.471839 TGTTCTAAAATAATGCGACGCTAAC 58.528 36.000 22.08 9.47 0.00 2.34
505 6314 6.650239 TGTTCTAAAATAATGCGACGCTAA 57.350 33.333 22.08 6.60 0.00 3.09
531 6340 5.304101 TGGCCAACTGTATGATTGTTCTTTT 59.696 36.000 0.61 0.00 0.00 2.27
535 6344 4.398988 TGATGGCCAACTGTATGATTGTTC 59.601 41.667 10.96 0.00 0.00 3.18
542 6351 2.425143 AGGTGATGGCCAACTGTATG 57.575 50.000 10.96 0.00 42.30 2.39
551 6360 1.027357 CTAACATGCAGGTGATGGCC 58.973 55.000 4.03 0.00 0.00 5.36
556 6365 4.065088 GTTTGACTCTAACATGCAGGTGA 58.935 43.478 4.03 0.00 0.00 4.02
581 6415 2.159920 CGTCTCTCATGTCTGCAAAACG 60.160 50.000 0.00 0.00 0.00 3.60
629 6468 4.680237 CCGCCGTGGTGCTCAAGA 62.680 66.667 0.00 0.00 0.00 3.02
653 6492 5.296283 GCTCATCATTCTTGCTTGATAGTGT 59.704 40.000 0.00 0.00 31.50 3.55
663 6502 5.353678 AGTTAGTCAAGCTCATCATTCTTGC 59.646 40.000 0.00 0.00 37.64 4.01
667 6506 6.699642 GGAGTAGTTAGTCAAGCTCATCATTC 59.300 42.308 0.00 0.00 0.00 2.67
732 6571 2.770164 AGTGGATCGGAGAAGTTTGG 57.230 50.000 0.00 0.00 43.58 3.28
788 6628 1.202463 AGATTCCGACCTGAAGCGATG 60.202 52.381 0.00 0.00 35.84 3.84
789 6629 1.115467 AGATTCCGACCTGAAGCGAT 58.885 50.000 0.00 0.00 35.84 4.58
860 6737 8.753175 CGAGCTTTATAACTTGGTGACTATAAC 58.247 37.037 0.00 0.00 0.00 1.89
874 6751 3.383825 TCCTCCTGACCGAGCTTTATAAC 59.616 47.826 0.00 0.00 0.00 1.89
900 6783 1.807573 GCTACAGCTCTGCACGTCC 60.808 63.158 0.00 0.00 38.21 4.79
1011 6899 0.252197 GTATCCACTCGGCCACCTTT 59.748 55.000 2.24 0.00 0.00 3.11
1192 7110 4.096003 CACCATTCCCGCTCCCGT 62.096 66.667 0.00 0.00 0.00 5.28
1261 7197 1.592669 CTCATAAGCGCCGACAGGG 60.593 63.158 2.29 0.00 38.20 4.45
1293 7229 2.398554 GCACGGCCATCACGTTCAT 61.399 57.895 2.24 0.00 43.58 2.57
1337 7273 1.377725 GGACTCCACCAGCCACATG 60.378 63.158 0.00 0.00 0.00 3.21
1401 7337 2.452295 TGAAGTCAGAGCTGCTTGAG 57.548 50.000 2.53 0.00 30.92 3.02
1474 7410 2.582052 AGAAAACGAAATCCAGCCACA 58.418 42.857 0.00 0.00 0.00 4.17
1475 7411 3.643159 AAGAAAACGAAATCCAGCCAC 57.357 42.857 0.00 0.00 0.00 5.01
1540 7487 6.461698 GCATTTACACAACTTCTTACGAATCG 59.538 38.462 0.00 0.00 0.00 3.34
1544 7491 4.453136 GGGCATTTACACAACTTCTTACGA 59.547 41.667 0.00 0.00 0.00 3.43
1590 7538 5.924825 CCTGGAAGCAAGAAAGAAATTTCTG 59.075 40.000 21.15 10.32 40.81 3.02
1663 7612 5.129485 AGTGTATCCCAAGTTCCATAGACTG 59.871 44.000 0.00 0.00 0.00 3.51
1672 7621 2.094182 TGAGCGAGTGTATCCCAAGTTC 60.094 50.000 0.00 0.00 0.00 3.01
1736 7685 7.886629 ATGAATAAAGCTCTCTAAATTGCCA 57.113 32.000 0.00 0.00 0.00 4.92
1792 7741 1.625818 CCAAGCTTCCTAGTGACCAGT 59.374 52.381 0.00 0.00 0.00 4.00
1852 7801 1.602851 CATCTCTGTGCTAAGCATGCC 59.397 52.381 15.66 0.00 41.91 4.40
1856 7805 2.306341 GCTCATCTCTGTGCTAAGCA 57.694 50.000 0.00 0.00 38.53 3.91
1959 7909 6.100404 ACAATACATGTTCAATTGTGGCTT 57.900 33.333 19.78 0.93 41.14 4.35
1969 7919 2.741517 CACTCGCCACAATACATGTTCA 59.258 45.455 2.30 0.00 41.46 3.18
1974 7924 2.290008 TGGAACACTCGCCACAATACAT 60.290 45.455 0.00 0.00 0.00 2.29
2025 7975 4.097286 GGGGTTTTACGCATGTGATAATGT 59.903 41.667 14.43 0.00 32.03 2.71
2199 8157 0.541063 TCTCAACTGACGGGGCACTA 60.541 55.000 0.00 0.00 0.00 2.74
2301 8259 5.590663 AGCAAGACATACGAGAGAAGTGATA 59.409 40.000 0.00 0.00 0.00 2.15
2317 8275 0.317160 CCGGTGACTACAGCAAGACA 59.683 55.000 0.00 0.00 43.66 3.41


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

AutoCloner maintained by Alex Coulton.