Multiple sequence alignment - TraesCS7D01G500600

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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 TraesCS7D01G500600 chr7D 100.000 6312 0 0 1 6312 606698935 606705246 0.000000e+00 11657.0
1 TraesCS7D01G500600 chr7D 87.826 460 43 5 1414 1861 607504922 607504464 1.560000e-145 527.0
2 TraesCS7D01G500600 chr7D 87.556 450 34 8 5884 6312 37925032 37925480 9.450000e-138 501.0
3 TraesCS7D01G500600 chr7D 87.566 378 32 6 5793 6170 141230795 141230433 2.100000e-114 424.0
4 TraesCS7D01G500600 chr7D 76.207 290 34 19 487 767 606180510 606180773 3.090000e-23 121.0
5 TraesCS7D01G500600 chr7D 83.594 128 12 5 487 614 606301354 606301472 1.860000e-20 111.0
6 TraesCS7D01G500600 chr7D 90.164 61 3 3 487 546 606010452 606010510 6.790000e-10 76.8
7 TraesCS7D01G500600 chr7A 93.313 4965 254 27 1414 6312 698762810 698767762 0.000000e+00 7258.0
8 TraesCS7D01G500600 chr7A 92.975 4868 271 18 1503 6312 698849935 698854789 0.000000e+00 7029.0
9 TraesCS7D01G500600 chr7A 93.605 3972 193 22 2396 6312 699020776 699024741 0.000000e+00 5871.0
10 TraesCS7D01G500600 chr7A 92.277 997 65 2 1414 2398 699019543 699020539 0.000000e+00 1404.0
11 TraesCS7D01G500600 chr7A 95.977 522 20 1 9 529 699016290 699016811 0.000000e+00 846.0
12 TraesCS7D01G500600 chr7A 95.402 522 23 1 9 529 698846279 698846800 0.000000e+00 830.0
13 TraesCS7D01G500600 chr7A 95.211 522 24 1 9 529 698759540 698760061 0.000000e+00 824.0
14 TraesCS7D01G500600 chr7A 98.913 92 1 0 1414 1505 698849539 698849630 1.410000e-36 165.0
15 TraesCS7D01G500600 chrUn 94.079 4594 209 26 1776 6312 92707977 92703390 0.000000e+00 6918.0
16 TraesCS7D01G500600 chrUn 90.903 4199 324 26 1620 5788 33119428 33123598 0.000000e+00 5585.0
17 TraesCS7D01G500600 chrUn 90.466 1416 76 22 12 1416 33117570 33118937 0.000000e+00 1812.0
18 TraesCS7D01G500600 chrUn 91.794 914 53 13 276 1177 92708955 92708052 0.000000e+00 1253.0
19 TraesCS7D01G500600 chrUn 88.197 466 39 4 1414 1868 33118986 33119446 5.570000e-150 542.0
20 TraesCS7D01G500600 chr7B 93.149 4671 250 22 1711 6312 691022456 691027125 0.000000e+00 6789.0
21 TraesCS7D01G500600 chr7B 89.884 2412 206 19 2416 4798 690950108 690952510 0.000000e+00 3068.0
22 TraesCS7D01G500600 chr7B 87.385 1197 73 37 264 1417 691021063 691022224 0.000000e+00 1303.0
23 TraesCS7D01G500600 chr7B 90.138 943 63 15 487 1417 690915265 690916189 0.000000e+00 1199.0
24 TraesCS7D01G500600 chr7B 88.006 717 65 7 2416 3112 690916685 690917400 0.000000e+00 828.0
25 TraesCS7D01G500600 chr7B 87.061 541 34 15 5793 6312 650132207 650131682 4.240000e-161 579.0
26 TraesCS7D01G500600 chr7B 89.302 430 30 3 1414 1832 690916230 690916654 5.610000e-145 525.0
27 TraesCS7D01G500600 chr7B 88.366 404 36 1 1440 1832 690949674 690950077 5.730000e-130 475.0
28 TraesCS7D01G500600 chr7B 90.652 353 18 3 1414 1751 691022265 691022617 7.460000e-124 455.0
29 TraesCS7D01G500600 chr7B 78.088 251 30 13 380 615 690198911 690199151 1.100000e-27 135.0
30 TraesCS7D01G500600 chr3B 90.336 4429 352 31 1414 5797 760055363 760050966 0.000000e+00 5738.0
31 TraesCS7D01G500600 chr3B 91.018 1414 70 25 19 1417 760056775 760055404 0.000000e+00 1855.0
32 TraesCS7D01G500600 chr3B 87.246 541 34 10 5793 6312 543720622 543720096 9.120000e-163 584.0
33 TraesCS7D01G500600 chr3B 87.061 541 35 14 5793 6312 661541389 661541915 4.240000e-161 579.0
34 TraesCS7D01G500600 chr3B 86.506 541 42 10 5793 6312 436511338 436511868 3.300000e-157 566.0
35 TraesCS7D01G500600 chr3A 90.533 3961 323 28 1620 5548 704694760 704690820 0.000000e+00 5190.0
36 TraesCS7D01G500600 chr3A 90.455 3960 328 21 1620 5548 704780524 704776584 0.000000e+00 5173.0
37 TraesCS7D01G500600 chr3A 89.720 3959 338 29 1620 5548 704840580 704836661 0.000000e+00 4992.0
38 TraesCS7D01G500600 chr3A 90.723 3374 274 21 2445 5788 704578363 704581727 0.000000e+00 4460.0
39 TraesCS7D01G500600 chr3A 90.960 1427 74 21 9 1417 704570346 704571735 0.000000e+00 1869.0
40 TraesCS7D01G500600 chr3A 88.710 1426 72 34 12 1417 704782485 704781129 0.000000e+00 1659.0
41 TraesCS7D01G500600 chr3A 88.577 1427 76 32 12 1417 704842433 704841073 0.000000e+00 1652.0
42 TraesCS7D01G500600 chr3A 93.495 661 28 6 767 1418 704695905 704695251 0.000000e+00 968.0
43 TraesCS7D01G500600 chr3A 89.136 718 42 17 12 718 704696612 704695920 0.000000e+00 861.0
44 TraesCS7D01G500600 chr3A 85.944 498 47 4 1417 1895 704695208 704694715 1.570000e-140 510.0
45 TraesCS7D01G500600 chr3A 86.076 474 43 4 1414 1868 704571776 704572245 7.350000e-134 488.0
46 TraesCS7D01G500600 chr3A 85.714 483 46 6 1414 1877 704781088 704780610 7.350000e-134 488.0
47 TraesCS7D01G500600 chr3A 85.124 484 48 5 1414 1877 704841032 704840553 2.060000e-129 473.0
48 TraesCS7D01G500600 chr3A 88.172 372 32 6 5793 6164 120812174 120812533 3.500000e-117 433.0
49 TraesCS7D01G500600 chr1B 87.222 540 46 5 5793 6312 266112517 266113053 1.520000e-165 593.0
50 TraesCS7D01G500600 chr2A 86.949 544 46 12 5793 6311 694758322 694758865 7.050000e-164 588.0
51 TraesCS7D01G500600 chr5B 86.876 541 36 13 5793 6312 532316274 532315748 1.970000e-159 573.0
52 TraesCS7D01G500600 chr6B 86.506 541 38 11 5793 6312 184810356 184809830 4.270000e-156 562.0
53 TraesCS7D01G500600 chr6B 83.503 491 44 10 5793 6262 30164675 30165149 2.100000e-114 424.0
54 TraesCS7D01G500600 chr4A 88.305 419 28 4 5915 6312 640151698 640152116 3.420000e-132 483.0
55 TraesCS7D01G500600 chr1A 91.971 137 11 0 6176 6312 491997196 491997332 6.460000e-45 193.0
56 TraesCS7D01G500600 chr5D 93.443 61 4 0 5793 5853 430449983 430449923 2.420000e-14 91.6


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 TraesCS7D01G500600 chr7D 606698935 606705246 6311 False 11657.000000 11657 100.000000 1 6312 1 chr7D.!!$F5 6311
1 TraesCS7D01G500600 chr7A 698759540 698767762 8222 False 4041.000000 7258 94.262000 9 6312 2 chr7A.!!$F1 6303
2 TraesCS7D01G500600 chr7A 699016290 699024741 8451 False 2707.000000 5871 93.953000 9 6312 3 chr7A.!!$F3 6303
3 TraesCS7D01G500600 chr7A 698846279 698854789 8510 False 2674.666667 7029 95.763333 9 6312 3 chr7A.!!$F2 6303
4 TraesCS7D01G500600 chrUn 92703390 92708955 5565 True 4085.500000 6918 92.936500 276 6312 2 chrUn.!!$R1 6036
5 TraesCS7D01G500600 chrUn 33117570 33123598 6028 False 2646.333333 5585 89.855333 12 5788 3 chrUn.!!$F1 5776
6 TraesCS7D01G500600 chr7B 691021063 691027125 6062 False 2849.000000 6789 90.395333 264 6312 3 chr7B.!!$F4 6048
7 TraesCS7D01G500600 chr7B 690949674 690952510 2836 False 1771.500000 3068 89.125000 1440 4798 2 chr7B.!!$F3 3358
8 TraesCS7D01G500600 chr7B 690915265 690917400 2135 False 850.666667 1199 89.148667 487 3112 3 chr7B.!!$F2 2625
9 TraesCS7D01G500600 chr7B 650131682 650132207 525 True 579.000000 579 87.061000 5793 6312 1 chr7B.!!$R1 519
10 TraesCS7D01G500600 chr3B 760050966 760056775 5809 True 3796.500000 5738 90.677000 19 5797 2 chr3B.!!$R2 5778
11 TraesCS7D01G500600 chr3B 543720096 543720622 526 True 584.000000 584 87.246000 5793 6312 1 chr3B.!!$R1 519
12 TraesCS7D01G500600 chr3B 661541389 661541915 526 False 579.000000 579 87.061000 5793 6312 1 chr3B.!!$F2 519
13 TraesCS7D01G500600 chr3B 436511338 436511868 530 False 566.000000 566 86.506000 5793 6312 1 chr3B.!!$F1 519
14 TraesCS7D01G500600 chr3A 704578363 704581727 3364 False 4460.000000 4460 90.723000 2445 5788 1 chr3A.!!$F2 3343
15 TraesCS7D01G500600 chr3A 704776584 704782485 5901 True 2440.000000 5173 88.293000 12 5548 3 chr3A.!!$R2 5536
16 TraesCS7D01G500600 chr3A 704836661 704842433 5772 True 2372.333333 4992 87.807000 12 5548 3 chr3A.!!$R3 5536
17 TraesCS7D01G500600 chr3A 704690820 704696612 5792 True 1882.250000 5190 89.777000 12 5548 4 chr3A.!!$R1 5536
18 TraesCS7D01G500600 chr3A 704570346 704572245 1899 False 1178.500000 1869 88.518000 9 1868 2 chr3A.!!$F3 1859
19 TraesCS7D01G500600 chr1B 266112517 266113053 536 False 593.000000 593 87.222000 5793 6312 1 chr1B.!!$F1 519
20 TraesCS7D01G500600 chr2A 694758322 694758865 543 False 588.000000 588 86.949000 5793 6311 1 chr2A.!!$F1 518
21 TraesCS7D01G500600 chr5B 532315748 532316274 526 True 573.000000 573 86.876000 5793 6312 1 chr5B.!!$R1 519
22 TraesCS7D01G500600 chr6B 184809830 184810356 526 True 562.000000 562 86.506000 5793 6312 1 chr6B.!!$R1 519

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
173 175 1.843206 TGAATACATAGGCCTGGCACA 59.157 47.619 22.05 7.52 0.00 4.57 F
1272 3203 0.617935 TGATGGATGGAAAGACGGCA 59.382 50.000 0.00 0.00 0.00 5.69 F
2809 6065 0.608130 CATTGGACGAGAGGACCACA 59.392 55.000 0.00 0.00 40.26 4.17 F
4397 7688 1.078848 GCGACACTGCCTCTTGGAT 60.079 57.895 0.00 0.00 34.57 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 3981 1.480954 CCCTACTAACTCATGTGCCGT 59.519 52.381 0.0 0.0 0.0 5.68 R
2865 6121 1.043673 GTCCTCCCGTCCAGTGCTAT 61.044 60.000 0.0 0.0 0.0 2.97 R
4781 8072 1.314534 CCGGCCAGATGACATTGCAA 61.315 55.000 0.0 0.0 0.0 4.08 R
5951 9262 0.037303 ATTGCCCCGCTCATCTATGG 59.963 55.000 0.0 0.0 0.0 2.74 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
70 71 2.271800 GGCAGAAACTACAGACATCCG 58.728 52.381 0.00 0.00 0.00 4.18
74 75 2.897969 AGAAACTACAGACATCCGTGGT 59.102 45.455 0.00 0.00 0.00 4.16
169 171 5.192927 TCTTTGTTGAATACATAGGCCTGG 58.807 41.667 17.99 10.42 36.71 4.45
173 175 1.843206 TGAATACATAGGCCTGGCACA 59.157 47.619 22.05 7.52 0.00 4.57
203 205 4.825546 AGGATCAAAGCATAAGCAATCG 57.174 40.909 0.00 0.00 45.49 3.34
221 223 2.722071 TCGTTTGGTTCGAATTTGTGC 58.278 42.857 0.00 0.00 34.36 4.57
450 471 2.229062 TCTGACGACTGAGACATGAACC 59.771 50.000 0.00 0.00 0.00 3.62
614 2483 2.297701 GTGGTTTTGCTCACCTCTCAA 58.702 47.619 1.90 0.00 35.07 3.02
891 2809 5.068067 AGACGAGGAAGCTAATAGAGGTTTC 59.932 44.000 0.00 0.00 45.96 2.78
892 2810 4.099727 ACGAGGAAGCTAATAGAGGTTTCC 59.900 45.833 0.00 0.00 45.96 3.13
893 2811 4.342665 CGAGGAAGCTAATAGAGGTTTCCT 59.657 45.833 10.05 10.05 45.96 3.36
894 2812 5.163395 CGAGGAAGCTAATAGAGGTTTCCTT 60.163 44.000 11.22 0.00 45.96 3.36
895 2813 6.630638 CGAGGAAGCTAATAGAGGTTTCCTTT 60.631 42.308 11.22 0.00 45.96 3.11
1272 3203 0.617935 TGATGGATGGAAAGACGGCA 59.382 50.000 0.00 0.00 0.00 5.69
1665 3981 0.683504 GTAGGAGAGCGGAGGTGGAA 60.684 60.000 0.00 0.00 39.88 3.53
1757 4073 1.070445 CTGATCGGATGGGGACTGC 59.930 63.158 0.00 0.00 0.00 4.40
1821 4590 1.739067 GCATTGTCGGTTTCTAGCCT 58.261 50.000 0.00 0.00 0.00 4.58
1838 4804 4.337264 AGCCTAAAACAATGGGATCCTT 57.663 40.909 12.58 0.00 0.00 3.36
1846 4812 3.886123 ACAATGGGATCCTTTCTAACCG 58.114 45.455 12.58 0.00 0.00 4.44
1853 4819 3.388350 GGATCCTTTCTAACCGTCCATCT 59.612 47.826 3.84 0.00 0.00 2.90
1896 4862 1.472480 GATGGGGAACAAACGTGGATG 59.528 52.381 0.00 0.00 0.00 3.51
1961 4927 5.724854 AGGTTGATAGTGTTTAGGAGGCTAA 59.275 40.000 0.00 0.00 0.00 3.09
1989 4955 5.186256 TGGTCACTCCAATGGCTAATTTA 57.814 39.130 0.00 0.00 44.12 1.40
2173 5143 5.503357 CGTGTTCGATGGTTGTATTTATGGG 60.503 44.000 0.00 0.00 39.71 4.00
2183 5153 8.367660 TGGTTGTATTTATGGGCAATTAGAAA 57.632 30.769 0.00 0.00 0.00 2.52
2340 5319 5.584649 CCAATCACACAAGGTATACGATTGT 59.415 40.000 15.60 15.60 35.77 2.71
2374 5355 8.856153 TGTTTTCTAGGTTGCATGAATACTAA 57.144 30.769 0.00 0.00 0.00 2.24
2539 5782 5.235831 GCCCCTTTTAAGTACATACATCGAC 59.764 44.000 0.00 0.00 0.00 4.20
2675 5918 8.818141 TTTCCTGAATCTCTACTATTAATGCG 57.182 34.615 0.00 0.00 0.00 4.73
2736 5979 1.878948 GCCCACAACTGCATGCAATTT 60.879 47.619 22.88 14.72 0.00 1.82
2809 6065 0.608130 CATTGGACGAGAGGACCACA 59.392 55.000 0.00 0.00 40.26 4.17
2904 6166 7.201821 GGAGGACCACATTAAGTATGGAAATTG 60.202 40.741 8.92 0.00 38.64 2.32
3005 6269 9.054191 GTGGTTAACGTTTACAAACTAATATGC 57.946 33.333 18.12 0.00 36.77 3.14
3017 6281 7.039270 ACAAACTAATATGCGTGTGATCACTA 58.961 34.615 25.55 10.46 41.89 2.74
3046 6310 2.125269 AGCATTACGTGGGCCGAC 60.125 61.111 8.02 8.02 40.70 4.79
3120 6388 5.940470 ACTTGATCTTCAGGTTCACCAATAC 59.060 40.000 0.00 0.00 32.42 1.89
3218 6486 8.691797 TGTTTTAGCCTTTGTTTCTGTATCTTT 58.308 29.630 0.00 0.00 0.00 2.52
3622 6895 5.897824 AGTACTCGGGGAATAAGAGAAATGA 59.102 40.000 0.00 0.00 36.03 2.57
3704 6977 2.100252 CAGGATGACATGGACAATTGCC 59.900 50.000 5.05 8.58 39.69 4.52
3705 6978 2.024655 AGGATGACATGGACAATTGCCT 60.025 45.455 16.52 4.73 0.00 4.75
3758 7031 4.985409 CAGATCGGCCTTGATAGTAAGAAC 59.015 45.833 0.00 0.00 0.00 3.01
3848 7126 2.702592 TAATTGTAGGGGCTGTTCCG 57.297 50.000 0.00 0.00 34.94 4.30
4024 7305 8.424133 GCTTTTATTTTCTGGGGAACATATCAT 58.576 33.333 0.00 0.00 28.27 2.45
4134 7416 7.418483 GCATGCCCCATATTTTTAGGAGTTTTA 60.418 37.037 6.36 0.00 0.00 1.52
4212 7502 4.928020 CGATGAACATCCATCTCATACCTG 59.072 45.833 8.87 0.00 40.46 4.00
4287 7577 3.077359 CAAGTCAAATCCCTCTGGTGAC 58.923 50.000 0.00 0.00 36.10 3.67
4304 7594 3.248602 GGTGACGCATATGAAAGATGGAC 59.751 47.826 6.97 0.00 0.00 4.02
4335 7625 2.865551 CAACATGAACAACAAGGGCAAC 59.134 45.455 0.00 0.00 0.00 4.17
4397 7688 1.078848 GCGACACTGCCTCTTGGAT 60.079 57.895 0.00 0.00 34.57 3.41
4515 7806 5.074115 CCAAAGTATGTTGGGAAACTACCA 58.926 41.667 0.00 0.00 43.79 3.25
4544 7835 3.251004 GCGAGAAGATTCACAGGTTTTGT 59.749 43.478 0.00 0.00 41.94 2.83
4615 7906 8.410912 TGTCAGATGAATTTCCATCATTCAATC 58.589 33.333 9.18 0.23 42.53 2.67
4671 7962 6.488006 GCAAGATAATGGAGATAAGCAAAGGA 59.512 38.462 0.00 0.00 0.00 3.36
4749 8040 1.344438 TCTCTTGTCGCATCACAGGTT 59.656 47.619 0.00 0.00 0.00 3.50
4781 8072 4.223923 ACATAGCAACCAACTAGAGAGCTT 59.776 41.667 0.00 0.00 32.49 3.74
4862 8153 1.487976 CACATCAGTGGGAGGCTACAT 59.512 52.381 0.00 0.00 42.13 2.29
5028 8319 6.064060 TCACAACCTTCAGACAGATGATTTT 58.936 36.000 0.00 0.00 0.00 1.82
5173 8464 6.262944 GGATGATATACTTTCCAACATGCACA 59.737 38.462 0.00 0.00 0.00 4.57
5188 8479 4.697352 ACATGCACATGGAAGTAAGAACTC 59.303 41.667 14.73 0.00 42.91 3.01
5203 8494 7.091443 AGTAAGAACTCTTCTCATTTGTACGG 58.909 38.462 0.00 0.00 39.61 4.02
5295 8587 4.996122 GGATTTCACTGGAGATGATGCTAG 59.004 45.833 0.00 0.00 0.00 3.42
5339 8631 0.548989 TATGTTAGGCCGCCCAATGT 59.451 50.000 5.55 0.00 0.00 2.71
5373 8665 4.582240 TGATCAAGAGTATCATGCTCGAGT 59.418 41.667 15.13 0.00 32.22 4.18
5464 8756 8.988060 TCATATACCAGTGGTTCTTTGAGATAA 58.012 33.333 22.49 0.00 37.09 1.75
5688 8981 3.181500 GCCCATCATGTTTTTACCTCGAC 60.181 47.826 0.00 0.00 0.00 4.20
5690 8983 3.063452 CCATCATGTTTTTACCTCGACGG 59.937 47.826 0.00 0.03 39.35 4.79
5692 8985 2.299582 TCATGTTTTTACCTCGACGGGA 59.700 45.455 0.00 0.00 36.97 5.14
5803 9097 8.431910 ACTAAAGACAACTAAAGATGGACCTA 57.568 34.615 0.00 0.00 0.00 3.08
5835 9129 2.838736 TCCATAGAGCGAAGAATTGCC 58.161 47.619 0.00 0.00 0.00 4.52
5848 9142 1.945394 GAATTGCCTGATGTGCTCGAT 59.055 47.619 0.00 0.00 0.00 3.59
5853 9147 0.249784 CCTGATGTGCTCGATGGAGG 60.250 60.000 6.88 0.00 40.80 4.30
5951 9262 5.006386 TCCAATTCTTTCTCTTGGAAGCTC 58.994 41.667 0.91 0.00 44.06 4.09
6002 9313 1.379044 CGCCCAAGAAGCCAAGGAT 60.379 57.895 0.00 0.00 0.00 3.24
6173 9484 2.633481 AGAGCCCTCGTAAACTTGTCTT 59.367 45.455 0.00 0.00 34.09 3.01
6208 9540 3.676873 GCTGGCAAACATACTCCCAATTG 60.677 47.826 0.00 0.00 0.00 2.32
6221 9553 2.971330 TCCCAATTGACCTTGCATTTGT 59.029 40.909 7.12 0.00 30.93 2.83
6262 9595 1.278127 CCGGACCAAAGGAAAGCTCTA 59.722 52.381 0.00 0.00 0.00 2.43
6296 9629 3.157087 ACATTGTGAAGGATGGTTGGTC 58.843 45.455 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.911651 TCTGCCATTTTTATTTTCATTACCCA 58.088 30.769 0.00 0.00 0.00 4.51
74 75 4.536090 AGAGTGGATTTATTGTGGTCCAGA 59.464 41.667 0.00 0.00 41.14 3.86
86 87 8.798975 AATACAGGGATAGAAGAGTGGATTTA 57.201 34.615 0.00 0.00 0.00 1.40
89 90 7.079048 AGAAATACAGGGATAGAAGAGTGGAT 58.921 38.462 0.00 0.00 0.00 3.41
169 171 6.973843 TGCTTTGATCCTTATTATGATGTGC 58.026 36.000 0.00 0.00 0.00 4.57
173 175 9.524496 TGCTTATGCTTTGATCCTTATTATGAT 57.476 29.630 1.96 0.00 40.48 2.45
203 205 2.456010 ACGCACAAATTCGAACCAAAC 58.544 42.857 0.00 0.00 0.00 2.93
221 223 2.477525 GGGCGAGAGTAAGTGAGTAACG 60.478 54.545 0.00 0.00 0.00 3.18
450 471 0.612174 TGACCGGGAACAGAGAGAGG 60.612 60.000 6.32 0.00 0.00 3.69
614 2483 1.000896 CGGCCCATGGTTTCTTCCT 60.001 57.895 11.73 0.00 0.00 3.36
891 2809 5.278957 CCATCTAAGAACACAACCCAAAAGG 60.279 44.000 0.00 0.00 43.78 3.11
892 2810 5.772521 CCATCTAAGAACACAACCCAAAAG 58.227 41.667 0.00 0.00 0.00 2.27
893 2811 4.038642 GCCATCTAAGAACACAACCCAAAA 59.961 41.667 0.00 0.00 0.00 2.44
894 2812 3.572255 GCCATCTAAGAACACAACCCAAA 59.428 43.478 0.00 0.00 0.00 3.28
895 2813 3.153919 GCCATCTAAGAACACAACCCAA 58.846 45.455 0.00 0.00 0.00 4.12
957 2881 2.468831 TGAAAAAGCAAACGCCATCAC 58.531 42.857 0.00 0.00 0.00 3.06
1517 3806 7.761409 AGTGCATGTGTATGTGGTTTAATAAG 58.239 34.615 0.00 0.00 36.65 1.73
1522 3811 4.905429 AGAGTGCATGTGTATGTGGTTTA 58.095 39.130 0.00 0.00 36.65 2.01
1665 3981 1.480954 CCCTACTAACTCATGTGCCGT 59.519 52.381 0.00 0.00 0.00 5.68
1715 4031 3.195825 CGGATGGTTAGATAGGATCCCAC 59.804 52.174 8.55 0.00 30.55 4.61
1751 4067 2.809010 GCTCTCCTACCGCAGTCC 59.191 66.667 0.00 0.00 0.00 3.85
1757 4073 2.124236 ACCTCCGCTCTCCTACCG 60.124 66.667 0.00 0.00 0.00 4.02
1821 4590 6.376018 CGGTTAGAAAGGATCCCATTGTTTTA 59.624 38.462 8.55 0.00 0.00 1.52
1838 4804 5.181433 CGATCTGATAGATGGACGGTTAGAA 59.819 44.000 0.00 0.00 34.53 2.10
1853 4819 2.833943 CCACCATCCATCCGATCTGATA 59.166 50.000 0.00 0.00 0.00 2.15
1896 4862 2.224281 TGGGATCTCATAATCACGTGCC 60.224 50.000 11.67 1.52 31.31 5.01
1954 4920 3.526534 GAGTGACCATGTCTTTAGCCTC 58.473 50.000 0.00 0.00 33.15 4.70
1989 4955 2.224892 TGACACAGACTCTCACTAGGCT 60.225 50.000 0.00 0.00 34.10 4.58
2340 5319 3.788227 ACCTAGAAAACAGATGTGGCA 57.212 42.857 0.00 0.00 0.00 4.92
2453 5696 6.882678 TCATAAGGAGTAACAACTTTAAGGGC 59.117 38.462 0.00 0.00 0.00 5.19
2507 5750 4.786454 TGTACTTAAAAGGGGCACTCCTAT 59.214 41.667 0.00 0.00 35.80 2.57
2539 5782 6.758806 AGGTATTACCCATGGTTAACCTAG 57.241 41.667 24.78 16.33 39.75 3.02
2675 5918 6.049263 AGAATTATCTCGGACGATTTTTGC 57.951 37.500 0.00 0.00 0.00 3.68
2831 6087 2.317040 ACATGATACTCCCGTCCGAAT 58.683 47.619 0.00 0.00 0.00 3.34
2834 6090 3.720949 TTAACATGATACTCCCGTCCG 57.279 47.619 0.00 0.00 0.00 4.79
2849 6105 9.679661 TCCAGTGCTATCTTTTCATAATTAACA 57.320 29.630 0.00 0.00 0.00 2.41
2865 6121 1.043673 GTCCTCCCGTCCAGTGCTAT 61.044 60.000 0.00 0.00 0.00 2.97
2866 6122 1.681327 GTCCTCCCGTCCAGTGCTA 60.681 63.158 0.00 0.00 0.00 3.49
2904 6166 5.807520 CGAGGGCATACATATTCTACATGAC 59.192 44.000 0.00 0.00 0.00 3.06
2968 6232 5.523438 AACGTTAACCACCATTGTCAATT 57.477 34.783 0.00 0.00 0.00 2.32
3005 6269 8.141641 GCTCTAAGCATTTTTAGTGATCACACG 61.142 40.741 27.02 8.37 45.17 4.49
3046 6310 7.987750 TCTCTAGCATACTAGGTAACATCTG 57.012 40.000 0.00 0.00 45.20 2.90
3120 6388 6.996879 AGGGAAATCACATCATCATGTCTAAG 59.003 38.462 0.00 0.00 41.69 2.18
3218 6486 8.637099 TGTGAAAAATTCCACACATTCAATAGA 58.363 29.630 0.00 0.00 38.26 1.98
3359 6631 8.201464 TGCGTAGGATCAATGACTTAGATTTAA 58.799 33.333 0.00 0.00 0.00 1.52
3376 6648 4.131376 GCACTGCATGCGTAGGAT 57.869 55.556 14.09 0.00 46.55 3.24
3622 6895 4.586421 TGTTCTCGCTAGAATCATCTCCAT 59.414 41.667 3.75 0.00 43.50 3.41
3705 6978 8.792830 ATAGCTTCTAGAAACTTGTTATGCAA 57.207 30.769 13.39 0.00 35.50 4.08
3825 7102 3.883489 GGAACAGCCCCTACAATTATGTC 59.117 47.826 0.00 0.00 41.05 3.06
3848 7126 6.515272 TTCATCAGCTCCAATACCTTTTTC 57.485 37.500 0.00 0.00 0.00 2.29
4024 7305 3.822735 AGTTGCATTGCTAGAGCTTTGAA 59.177 39.130 10.49 0.00 42.66 2.69
4134 7416 3.377253 ACTGAAGATGTTGCATGGGAT 57.623 42.857 0.00 0.00 0.00 3.85
4195 7485 6.770286 AATAACCAGGTATGAGATGGATGT 57.230 37.500 0.00 0.00 37.54 3.06
4287 7577 3.732212 TGAGGTCCATCTTTCATATGCG 58.268 45.455 0.00 0.00 0.00 4.73
4304 7594 4.450757 TGTTGTTCATGTTGTACGATGAGG 59.549 41.667 0.00 0.00 30.39 3.86
4335 7625 5.007921 TCCATGTTCGTGATTATGCATGAAG 59.992 40.000 10.16 0.00 42.58 3.02
4397 7688 5.008811 CCCGTTGAACCATACTTGTTTGTAA 59.991 40.000 0.00 0.00 0.00 2.41
4438 7729 4.574599 AGAAGTTGCTTTGGATGTTCAC 57.425 40.909 0.00 0.00 0.00 3.18
4515 7806 2.101415 TGTGAATCTTCTCGCATCCGAT 59.899 45.455 0.00 0.00 43.47 4.18
4544 7835 2.449967 TAGGCTGACGGGAGGGTCAA 62.450 60.000 0.00 0.00 45.59 3.18
4615 7906 6.051074 TGATGTCAGCACAGGAATTACTATG 58.949 40.000 0.00 0.00 35.41 2.23
4671 7962 5.428457 ACTTTGAAGAATGGAAGGGGTTTTT 59.572 36.000 0.00 0.00 0.00 1.94
4749 8040 4.076394 GTTGGTTGCTATGTGGGAAGTTA 58.924 43.478 0.00 0.00 0.00 2.24
4781 8072 1.314534 CCGGCCAGATGACATTGCAA 61.315 55.000 0.00 0.00 0.00 4.08
4859 8150 0.038599 TGGTGCCATCTGCTCAATGT 59.961 50.000 0.00 0.00 42.00 2.71
4862 8153 1.272037 TGAATGGTGCCATCTGCTCAA 60.272 47.619 3.96 0.00 42.00 3.02
5173 8464 8.160106 ACAAATGAGAAGAGTTCTTACTTCCAT 58.840 33.333 0.00 0.00 42.09 3.41
5188 8479 6.980978 ACACATAGATCCGTACAAATGAGAAG 59.019 38.462 0.00 0.00 0.00 2.85
5203 8494 9.177304 CAACAATTCATATGCAACACATAGATC 57.823 33.333 0.00 0.00 44.40 2.75
5295 8587 2.555199 ACTATCATGCTTCTTCCACGC 58.445 47.619 0.00 0.00 0.00 5.34
5339 8631 4.897509 ACTCTTGATCAACCATCTCACA 57.102 40.909 3.38 0.00 31.92 3.58
5373 8665 3.523564 ACTCTATTGCCTTAAAGAGCCCA 59.476 43.478 0.00 0.00 39.26 5.36
5464 8756 6.240894 TCTCAATGTTATGCAAGAGGAAGTT 58.759 36.000 0.00 0.00 35.40 2.66
5618 8911 1.557832 GTGTGCCCTGTTACCATAGGA 59.442 52.381 0.00 0.00 36.11 2.94
5631 8924 1.562475 TCCCAGGTATAAAGTGTGCCC 59.438 52.381 0.00 0.00 0.00 5.36
5688 8981 2.093658 ACATGGCACTTAGTACTTCCCG 60.094 50.000 0.00 0.00 0.00 5.14
5690 8983 3.939066 ACACATGGCACTTAGTACTTCC 58.061 45.455 0.00 0.00 0.00 3.46
5692 8985 6.014499 AGAGTAACACATGGCACTTAGTACTT 60.014 38.462 0.00 0.00 0.00 2.24
5803 9097 8.807118 TCTTCGCTCTATGGATGATACTAAATT 58.193 33.333 0.00 0.00 0.00 1.82
5835 9129 0.879400 GCCTCCATCGAGCACATCAG 60.879 60.000 0.00 0.00 34.49 2.90
5848 9142 2.440147 CCACCACCAATGCCTCCA 59.560 61.111 0.00 0.00 0.00 3.86
5853 9147 2.573083 CCACCACCACCACCAATGC 61.573 63.158 0.00 0.00 0.00 3.56
5951 9262 0.037303 ATTGCCCCGCTCATCTATGG 59.963 55.000 0.00 0.00 0.00 2.74
6119 9430 3.140707 TGGCCATGATATGAATGGAAGGT 59.859 43.478 15.36 0.00 46.44 3.50
6133 9444 2.823593 CGGTTGCGATGGCCATGA 60.824 61.111 26.56 3.40 38.85 3.07
6173 9484 0.472044 TGCCAGCCACTTGAGTACAA 59.528 50.000 0.00 0.00 34.65 2.41
6208 9540 0.243636 CGGGGAACAAATGCAAGGTC 59.756 55.000 0.00 0.00 0.00 3.85
6221 9553 1.070105 CGGACAAGACAACGGGGAA 59.930 57.895 0.00 0.00 0.00 3.97
6262 9595 3.402110 TCACAATGTCAACAAGCTCGAT 58.598 40.909 0.00 0.00 0.00 3.59
6277 9610 2.436417 CGACCAACCATCCTTCACAAT 58.564 47.619 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.