Multiple sequence alignment - TraesCS3D01G457100

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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 TraesCS3D01G457100 chr3D 100.000 3749 0 0 1 3749 562544158 562547906 0.000000e+00 6924.0
1 TraesCS3D01G457100 chr3D 81.087 1380 196 40 933 2267 562538185 562539544 0.000000e+00 1042.0
2 TraesCS3D01G457100 chr3D 80.974 1314 197 39 992 2267 562504180 562505478 0.000000e+00 992.0
3 TraesCS3D01G457100 chr3D 80.694 1326 185 44 992 2267 561462583 561461279 0.000000e+00 965.0
4 TraesCS3D01G457100 chr3D 78.902 1275 227 26 1020 2266 561456374 561455114 0.000000e+00 826.0
5 TraesCS3D01G457100 chr3D 76.491 1442 260 49 958 2346 561711698 561710283 0.000000e+00 712.0
6 TraesCS3D01G457100 chr3D 88.060 134 16 0 2133 2266 562565630 562565763 3.880000e-35 159.0
7 TraesCS3D01G457100 chr3A 93.981 1894 84 11 560 2436 697679500 697681380 0.000000e+00 2839.0
8 TraesCS3D01G457100 chr3A 81.172 1365 199 34 945 2267 697673423 697674771 0.000000e+00 1044.0
9 TraesCS3D01G457100 chr3A 93.432 472 14 9 99 557 697678976 697679443 0.000000e+00 684.0
10 TraesCS3D01G457100 chr3A 80.000 940 151 27 1187 2103 697617717 697618642 0.000000e+00 660.0
11 TraesCS3D01G457100 chr3A 87.218 133 16 1 2133 2265 697681995 697682126 2.330000e-32 150.0
12 TraesCS3D01G457100 chr3B 91.146 1841 92 28 645 2436 749978959 749980777 0.000000e+00 2431.0
13 TraesCS3D01G457100 chr3B 81.149 1358 203 36 946 2267 749725723 749727063 0.000000e+00 1040.0
14 TraesCS3D01G457100 chr3B 80.848 1368 197 40 946 2267 749859870 749861218 0.000000e+00 1014.0
15 TraesCS3D01G457100 chr3B 80.503 1154 165 29 992 2095 748787192 748786049 0.000000e+00 830.0
16 TraesCS3D01G457100 chr3B 77.031 1354 235 57 946 2245 749648213 749649544 0.000000e+00 708.0
17 TraesCS3D01G457100 chr3B 86.131 137 16 1 2133 2266 749981696 749981832 1.090000e-30 145.0
18 TraesCS3D01G457100 chr4A 95.375 1319 49 7 2436 3749 15933926 15932615 0.000000e+00 2087.0
19 TraesCS3D01G457100 chr4A 95.307 1321 46 8 2436 3749 682743932 682745243 0.000000e+00 2082.0
20 TraesCS3D01G457100 chr4D 95.238 987 38 4 2767 3749 451030008 451030989 0.000000e+00 1554.0
21 TraesCS3D01G457100 chr4B 91.436 1121 45 15 2436 3553 564143418 564144490 0.000000e+00 1491.0
22 TraesCS3D01G457100 chr4B 96.667 120 3 1 3630 3749 564144488 564144606 8.210000e-47 198.0
23 TraesCS3D01G457100 chr6D 92.832 558 29 4 3135 3681 28322287 28321730 0.000000e+00 798.0
24 TraesCS3D01G457100 chr6D 86.648 719 63 25 2832 3542 185189997 185189304 0.000000e+00 765.0
25 TraesCS3D01G457100 chr6D 89.303 402 35 4 2436 2829 185191649 185191248 7.230000e-137 497.0
26 TraesCS3D01G457100 chr5D 92.652 558 33 3 3132 3681 490447874 490447317 0.000000e+00 797.0
27 TraesCS3D01G457100 chr5D 95.949 395 14 2 2437 2829 490449671 490449277 1.140000e-179 640.0
28 TraesCS3D01G457100 chr5D 94.684 395 17 3 2437 2829 441584123 441583731 8.900000e-171 610.0
29 TraesCS3D01G457100 chr5D 93.156 263 11 4 2826 3086 490448129 490447872 2.730000e-101 379.0
30 TraesCS3D01G457100 chr5D 93.056 72 4 1 3679 3749 441579319 441579248 1.840000e-18 104.0
31 TraesCS3D01G457100 chr5D 93.056 72 4 1 3679 3749 490446153 490446082 1.840000e-18 104.0
32 TraesCS3D01G457100 chr6B 86.951 728 68 18 2826 3542 297303037 297302326 0.000000e+00 793.0
33 TraesCS3D01G457100 chr6B 92.473 558 33 6 3132 3681 52366059 52365503 0.000000e+00 789.0
34 TraesCS3D01G457100 chr6B 82.323 396 35 17 11 400 600783220 600782854 1.010000e-80 311.0
35 TraesCS3D01G457100 chr6A 89.048 557 33 3 3132 3681 29565857 29566392 0.000000e+00 665.0
36 TraesCS3D01G457100 chr5B 95.455 396 16 2 2436 2829 604878266 604877871 6.830000e-177 630.0
37 TraesCS3D01G457100 chr1A 94.192 396 19 3 2436 2829 538672307 538672700 5.360000e-168 601.0
38 TraesCS3D01G457100 chr2B 93.812 404 15 6 2436 2829 733149831 733150234 1.930000e-167 599.0
39 TraesCS3D01G457100 chr2B 92.803 264 12 4 2826 3087 733151435 733151693 3.540000e-100 375.0
40 TraesCS3D01G457100 chrUn 92.191 397 21 6 2436 2829 991294 990905 1.520000e-153 553.0
41 TraesCS3D01G457100 chr7D 92.045 264 13 5 2826 3086 44729813 44729555 7.650000e-97 364.0
42 TraesCS3D01G457100 chr7A 95.349 43 2 0 3679 3721 47305048 47305006 6.720000e-08 69.4


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 TraesCS3D01G457100 chr3D 562544158 562547906 3748 False 6924.000000 6924 100.000000 1 3749 1 chr3D.!!$F3 3748
1 TraesCS3D01G457100 chr3D 562538185 562539544 1359 False 1042.000000 1042 81.087000 933 2267 1 chr3D.!!$F2 1334
2 TraesCS3D01G457100 chr3D 562504180 562505478 1298 False 992.000000 992 80.974000 992 2267 1 chr3D.!!$F1 1275
3 TraesCS3D01G457100 chr3D 561461279 561462583 1304 True 965.000000 965 80.694000 992 2267 1 chr3D.!!$R2 1275
4 TraesCS3D01G457100 chr3D 561455114 561456374 1260 True 826.000000 826 78.902000 1020 2266 1 chr3D.!!$R1 1246
5 TraesCS3D01G457100 chr3D 561710283 561711698 1415 True 712.000000 712 76.491000 958 2346 1 chr3D.!!$R3 1388
6 TraesCS3D01G457100 chr3A 697678976 697682126 3150 False 1224.333333 2839 91.543667 99 2436 3 chr3A.!!$F3 2337
7 TraesCS3D01G457100 chr3A 697673423 697674771 1348 False 1044.000000 1044 81.172000 945 2267 1 chr3A.!!$F2 1322
8 TraesCS3D01G457100 chr3A 697617717 697618642 925 False 660.000000 660 80.000000 1187 2103 1 chr3A.!!$F1 916
9 TraesCS3D01G457100 chr3B 749978959 749981832 2873 False 1288.000000 2431 88.638500 645 2436 2 chr3B.!!$F4 1791
10 TraesCS3D01G457100 chr3B 749725723 749727063 1340 False 1040.000000 1040 81.149000 946 2267 1 chr3B.!!$F2 1321
11 TraesCS3D01G457100 chr3B 749859870 749861218 1348 False 1014.000000 1014 80.848000 946 2267 1 chr3B.!!$F3 1321
12 TraesCS3D01G457100 chr3B 748786049 748787192 1143 True 830.000000 830 80.503000 992 2095 1 chr3B.!!$R1 1103
13 TraesCS3D01G457100 chr3B 749648213 749649544 1331 False 708.000000 708 77.031000 946 2245 1 chr3B.!!$F1 1299
14 TraesCS3D01G457100 chr4A 15932615 15933926 1311 True 2087.000000 2087 95.375000 2436 3749 1 chr4A.!!$R1 1313
15 TraesCS3D01G457100 chr4A 682743932 682745243 1311 False 2082.000000 2082 95.307000 2436 3749 1 chr4A.!!$F1 1313
16 TraesCS3D01G457100 chr4D 451030008 451030989 981 False 1554.000000 1554 95.238000 2767 3749 1 chr4D.!!$F1 982
17 TraesCS3D01G457100 chr4B 564143418 564144606 1188 False 844.500000 1491 94.051500 2436 3749 2 chr4B.!!$F1 1313
18 TraesCS3D01G457100 chr6D 28321730 28322287 557 True 798.000000 798 92.832000 3135 3681 1 chr6D.!!$R1 546
19 TraesCS3D01G457100 chr6D 185189304 185191649 2345 True 631.000000 765 87.975500 2436 3542 2 chr6D.!!$R2 1106
20 TraesCS3D01G457100 chr5D 490446082 490449671 3589 True 480.000000 797 93.703250 2437 3749 4 chr5D.!!$R3 1312
21 TraesCS3D01G457100 chr6B 297302326 297303037 711 True 793.000000 793 86.951000 2826 3542 1 chr6B.!!$R2 716
22 TraesCS3D01G457100 chr6B 52365503 52366059 556 True 789.000000 789 92.473000 3132 3681 1 chr6B.!!$R1 549
23 TraesCS3D01G457100 chr6A 29565857 29566392 535 False 665.000000 665 89.048000 3132 3681 1 chr6A.!!$F1 549
24 TraesCS3D01G457100 chr2B 733149831 733151693 1862 False 487.000000 599 93.307500 2436 3087 2 chr2B.!!$F1 651

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
746 814 0.179032 TGTCACCGACAACAAGGCAT 60.179 50.0 0.00 0.00 39.78 4.40 F
931 1021 0.315251 TCGATTCAGCTGGCCTATCG 59.685 55.0 23.22 23.22 39.40 2.92 F
1696 1910 0.321564 CCATGGCAAGGTCTTCGTGA 60.322 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1957 0.321122 CAAGGGTGAAGAAGCTCGCT 60.321 55.000 0.00 0.0 0.00 4.93 R
1794 2014 1.153289 CCTGGAATCCTCCGCACAG 60.153 63.158 0.00 0.0 45.85 3.66 R
3292 5069 0.321298 ACCACAAGCACCGGTATGAC 60.321 55.000 6.87 0.0 0.00 3.06 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
38 39 9.657419 AAAAGACATAATAAGCCCAATTTTCTG 57.343 29.630 0.00 0.00 0.00 3.02
39 40 6.809869 AGACATAATAAGCCCAATTTTCTGC 58.190 36.000 0.00 0.00 0.00 4.26
40 41 6.608808 AGACATAATAAGCCCAATTTTCTGCT 59.391 34.615 0.00 0.00 35.08 4.24
41 42 6.809869 ACATAATAAGCCCAATTTTCTGCTC 58.190 36.000 0.00 0.00 32.62 4.26
42 43 6.380846 ACATAATAAGCCCAATTTTCTGCTCA 59.619 34.615 0.00 0.00 32.62 4.26
43 44 4.725790 ATAAGCCCAATTTTCTGCTCAC 57.274 40.909 0.00 0.00 32.62 3.51
44 45 2.299326 AGCCCAATTTTCTGCTCACT 57.701 45.000 0.00 0.00 0.00 3.41
45 46 3.439857 AGCCCAATTTTCTGCTCACTA 57.560 42.857 0.00 0.00 0.00 2.74
46 47 3.084786 AGCCCAATTTTCTGCTCACTAC 58.915 45.455 0.00 0.00 0.00 2.73
47 48 2.164422 GCCCAATTTTCTGCTCACTACC 59.836 50.000 0.00 0.00 0.00 3.18
48 49 3.420893 CCCAATTTTCTGCTCACTACCA 58.579 45.455 0.00 0.00 0.00 3.25
49 50 4.019174 CCCAATTTTCTGCTCACTACCAT 58.981 43.478 0.00 0.00 0.00 3.55
50 51 4.096984 CCCAATTTTCTGCTCACTACCATC 59.903 45.833 0.00 0.00 0.00 3.51
51 52 4.701651 CCAATTTTCTGCTCACTACCATCA 59.298 41.667 0.00 0.00 0.00 3.07
52 53 5.183713 CCAATTTTCTGCTCACTACCATCAA 59.816 40.000 0.00 0.00 0.00 2.57
53 54 6.320171 CAATTTTCTGCTCACTACCATCAAG 58.680 40.000 0.00 0.00 0.00 3.02
54 55 4.623932 TTTCTGCTCACTACCATCAAGT 57.376 40.909 0.00 0.00 0.00 3.16
55 56 3.876274 TCTGCTCACTACCATCAAGTC 57.124 47.619 0.00 0.00 0.00 3.01
56 57 3.435275 TCTGCTCACTACCATCAAGTCT 58.565 45.455 0.00 0.00 0.00 3.24
57 58 3.834813 TCTGCTCACTACCATCAAGTCTT 59.165 43.478 0.00 0.00 0.00 3.01
58 59 3.930336 TGCTCACTACCATCAAGTCTTG 58.070 45.455 6.21 6.21 0.00 3.02
59 60 3.578282 TGCTCACTACCATCAAGTCTTGA 59.422 43.478 17.46 17.46 45.01 3.02
60 61 4.040339 TGCTCACTACCATCAAGTCTTGAA 59.960 41.667 18.93 2.13 43.95 2.69
61 62 4.629200 GCTCACTACCATCAAGTCTTGAAG 59.371 45.833 18.93 14.37 43.95 3.02
62 63 4.569943 TCACTACCATCAAGTCTTGAAGC 58.430 43.478 18.93 0.00 43.95 3.86
63 64 4.284490 TCACTACCATCAAGTCTTGAAGCT 59.716 41.667 18.93 5.23 43.95 3.74
64 65 4.391216 CACTACCATCAAGTCTTGAAGCTG 59.609 45.833 18.93 12.54 43.95 4.24
65 66 2.787994 ACCATCAAGTCTTGAAGCTGG 58.212 47.619 23.52 23.52 43.95 4.85
66 67 2.373169 ACCATCAAGTCTTGAAGCTGGA 59.627 45.455 28.69 5.71 43.95 3.86
67 68 2.746362 CCATCAAGTCTTGAAGCTGGAC 59.254 50.000 21.80 0.00 43.95 4.02
68 69 3.558746 CCATCAAGTCTTGAAGCTGGACT 60.559 47.826 21.80 2.31 43.95 3.85
69 70 3.117491 TCAAGTCTTGAAGCTGGACTG 57.883 47.619 13.00 7.23 39.80 3.51
70 71 2.700371 TCAAGTCTTGAAGCTGGACTGA 59.300 45.455 13.00 8.76 39.80 3.41
71 72 3.134623 TCAAGTCTTGAAGCTGGACTGAA 59.865 43.478 13.00 2.96 39.80 3.02
72 73 3.118905 AGTCTTGAAGCTGGACTGAAC 57.881 47.619 9.92 0.00 38.65 3.18
73 74 2.147150 GTCTTGAAGCTGGACTGAACC 58.853 52.381 0.00 0.00 0.00 3.62
74 75 1.768275 TCTTGAAGCTGGACTGAACCA 59.232 47.619 0.00 0.00 38.33 3.67
88 89 8.033178 TGGACTGAACCAGATTATGAATATCA 57.967 34.615 0.45 0.00 34.77 2.15
89 90 8.663167 TGGACTGAACCAGATTATGAATATCAT 58.337 33.333 0.45 0.00 36.65 2.45
207 208 4.767409 AGAAAACATAGAAGAAACCCTGGC 59.233 41.667 0.00 0.00 0.00 4.85
373 374 7.218614 GGATTTGCCATGATCCAAATAATGAA 58.781 34.615 14.62 0.00 40.60 2.57
378 379 8.665643 TGCCATGATCCAAATAATGAATTTTC 57.334 30.769 0.00 0.00 35.54 2.29
484 485 6.252233 TGAGGTATGAATTTTCCATTGTCCA 58.748 36.000 0.00 0.00 0.00 4.02
541 553 6.252995 ACCTACATCTTTTCCATAGGCAAAA 58.747 36.000 0.00 0.00 36.63 2.44
548 560 9.603921 CATCTTTTCCATAGGCAAAACAATAAT 57.396 29.630 0.00 0.00 0.00 1.28
556 568 9.176460 CCATAGGCAAAACAATAATTTTTCCAT 57.824 29.630 3.17 0.00 37.33 3.41
557 569 9.991388 CATAGGCAAAACAATAATTTTTCCATG 57.009 29.630 3.17 0.00 37.33 3.66
558 570 9.956640 ATAGGCAAAACAATAATTTTTCCATGA 57.043 25.926 0.00 0.00 37.33 3.07
559 571 8.688747 AGGCAAAACAATAATTTTTCCATGAA 57.311 26.923 0.00 0.00 37.33 2.57
560 572 8.567104 AGGCAAAACAATAATTTTTCCATGAAC 58.433 29.630 0.00 0.00 37.33 3.18
561 573 8.348507 GGCAAAACAATAATTTTTCCATGAACA 58.651 29.630 0.00 0.00 35.61 3.18
608 676 4.830765 GGTGCTACCGCCGCATGA 62.831 66.667 0.00 0.00 39.89 3.07
619 687 1.153568 CCGCATGACCTCGATGTGT 60.154 57.895 0.00 0.00 30.70 3.72
625 693 1.257750 TGACCTCGATGTGTCTGGGG 61.258 60.000 0.00 0.00 32.67 4.96
695 763 0.179108 GAATAAGCGAGTGGGCGACT 60.179 55.000 0.31 0.31 37.76 4.18
712 780 0.616111 ACTGAGCGAGGGGAAGATGT 60.616 55.000 0.00 0.00 0.00 3.06
740 808 5.180492 GGATTCTAAAATGTCACCGACAACA 59.820 40.000 0.22 0.00 45.96 3.33
746 814 0.179032 TGTCACCGACAACAAGGCAT 60.179 50.000 0.00 0.00 39.78 4.40
803 873 2.794981 CGATAGGAAGCACGTTCGTGAT 60.795 50.000 25.87 18.67 38.30 3.06
931 1021 0.315251 TCGATTCAGCTGGCCTATCG 59.685 55.000 23.22 23.22 39.40 2.92
977 1076 2.313427 CCCCTCCGGAAAATCCCCA 61.313 63.158 5.23 0.00 31.13 4.96
1068 1188 1.659335 GGTGCTTGACGACGACGAA 60.659 57.895 15.32 0.00 42.66 3.85
1660 1874 1.332904 CGTTTGACGCACACTTCCTTC 60.333 52.381 0.00 0.00 33.65 3.46
1696 1910 0.321564 CCATGGCAAGGTCTTCGTGA 60.322 55.000 0.00 0.00 0.00 4.35
1737 1957 0.991146 TGGGTCTAGATTTGGCAGCA 59.009 50.000 0.00 0.00 0.00 4.41
1794 2014 1.398390 CGCCACAATTACAAGCTCTCC 59.602 52.381 0.00 0.00 0.00 3.71
1810 2030 1.612146 TCCTGTGCGGAGGATTCCA 60.612 57.895 5.29 0.00 44.26 3.53
1862 2082 0.612229 CTCAGTGTGTGGCTCCATCT 59.388 55.000 0.00 0.00 0.00 2.90
2278 2529 3.929610 GAGAGGTATGTTTCTGACTGTGC 59.070 47.826 0.00 0.00 0.00 4.57
2612 2880 4.763793 CCACATGAAGGTTGTTCTTCTCAT 59.236 41.667 0.00 0.00 42.54 2.90
2712 2982 4.389374 TCTTCTCAAGGAAACACACATCC 58.611 43.478 0.00 0.00 33.07 3.51
2713 2983 3.855255 TCTCAAGGAAACACACATCCA 57.145 42.857 0.00 0.00 38.23 3.41
2719 2989 5.652014 TCAAGGAAACACACATCCATATTCC 59.348 40.000 0.00 0.00 38.23 3.01
2788 3059 2.452600 TCCCAAATGGAAGGTATGCC 57.547 50.000 0.00 0.00 41.40 4.40
2804 3075 3.525800 ATGCCACTTGGGAGTTTACTT 57.474 42.857 0.00 0.00 39.50 2.24
3013 4726 4.370049 TGTCCAAAACGTTATCTCAACGA 58.630 39.130 15.63 0.00 45.64 3.85
3048 4762 4.651867 GTGGTCATGGAGCAGCAT 57.348 55.556 0.00 0.00 40.79 3.79
3292 5069 3.132289 ACCCTATACGTCTTCACCACATG 59.868 47.826 0.00 0.00 0.00 3.21
3414 5191 0.966875 GGCTGCACACATCAATCCCA 60.967 55.000 0.50 0.00 0.00 4.37
3489 5291 9.241919 TGAAAGATAAAATTATGAACTGCTCCA 57.758 29.630 0.00 0.00 0.00 3.86
3595 5464 7.222999 GGTCTTATATCGAAACAGAAGGAACTG 59.777 40.741 0.00 0.00 40.86 3.16
3656 5741 4.340950 TGGTCTTGTCCTGTCAAATTTTCC 59.659 41.667 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.657419 CAGAAAATTGGGCTTATTATGTCTTTT 57.343 29.630 0.00 0.00 0.00 2.27
13 14 7.765819 GCAGAAAATTGGGCTTATTATGTCTTT 59.234 33.333 0.00 0.00 0.00 2.52
14 15 7.124750 AGCAGAAAATTGGGCTTATTATGTCTT 59.875 33.333 0.00 0.00 31.34 3.01
15 16 6.608808 AGCAGAAAATTGGGCTTATTATGTCT 59.391 34.615 0.00 0.00 31.34 3.41
16 17 6.809869 AGCAGAAAATTGGGCTTATTATGTC 58.190 36.000 0.00 0.00 31.34 3.06
17 18 6.380846 TGAGCAGAAAATTGGGCTTATTATGT 59.619 34.615 0.00 0.00 36.59 2.29
18 19 6.698766 GTGAGCAGAAAATTGGGCTTATTATG 59.301 38.462 0.00 0.00 36.59 1.90
19 20 6.608808 AGTGAGCAGAAAATTGGGCTTATTAT 59.391 34.615 0.00 0.00 36.59 1.28
20 21 5.951747 AGTGAGCAGAAAATTGGGCTTATTA 59.048 36.000 0.00 0.00 36.59 0.98
21 22 4.774200 AGTGAGCAGAAAATTGGGCTTATT 59.226 37.500 0.00 0.00 36.59 1.40
22 23 4.347607 AGTGAGCAGAAAATTGGGCTTAT 58.652 39.130 0.00 0.00 36.59 1.73
23 24 3.766545 AGTGAGCAGAAAATTGGGCTTA 58.233 40.909 0.00 0.00 36.59 3.09
24 25 2.601905 AGTGAGCAGAAAATTGGGCTT 58.398 42.857 0.00 0.00 36.59 4.35
25 26 2.299326 AGTGAGCAGAAAATTGGGCT 57.701 45.000 0.00 0.00 39.75 5.19
26 27 2.164422 GGTAGTGAGCAGAAAATTGGGC 59.836 50.000 0.00 0.00 0.00 5.36
27 28 3.420893 TGGTAGTGAGCAGAAAATTGGG 58.579 45.455 0.00 0.00 0.00 4.12
28 29 4.701651 TGATGGTAGTGAGCAGAAAATTGG 59.298 41.667 0.00 0.00 36.28 3.16
29 30 5.885230 TGATGGTAGTGAGCAGAAAATTG 57.115 39.130 0.00 0.00 36.28 2.32
30 31 6.006449 ACTTGATGGTAGTGAGCAGAAAATT 58.994 36.000 0.00 0.00 36.28 1.82
31 32 5.564550 ACTTGATGGTAGTGAGCAGAAAAT 58.435 37.500 0.00 0.00 36.28 1.82
32 33 4.973168 ACTTGATGGTAGTGAGCAGAAAA 58.027 39.130 0.00 0.00 36.28 2.29
33 34 4.284490 AGACTTGATGGTAGTGAGCAGAAA 59.716 41.667 0.00 0.00 36.28 2.52
34 35 3.834813 AGACTTGATGGTAGTGAGCAGAA 59.165 43.478 0.00 0.00 36.28 3.02
35 36 3.435275 AGACTTGATGGTAGTGAGCAGA 58.565 45.455 0.00 0.00 36.28 4.26
36 37 3.883830 AGACTTGATGGTAGTGAGCAG 57.116 47.619 0.00 0.00 36.28 4.24
37 38 3.578282 TCAAGACTTGATGGTAGTGAGCA 59.422 43.478 13.99 0.00 37.51 4.26
38 39 4.193826 TCAAGACTTGATGGTAGTGAGC 57.806 45.455 13.99 0.00 34.08 4.26
39 40 4.629200 GCTTCAAGACTTGATGGTAGTGAG 59.371 45.833 24.63 15.48 39.84 3.51
40 41 4.284490 AGCTTCAAGACTTGATGGTAGTGA 59.716 41.667 25.74 7.63 41.74 3.41
41 42 4.391216 CAGCTTCAAGACTTGATGGTAGTG 59.609 45.833 26.18 15.62 41.66 2.74
42 43 4.564406 CCAGCTTCAAGACTTGATGGTAGT 60.564 45.833 26.18 8.72 41.66 2.73
43 44 3.937706 CCAGCTTCAAGACTTGATGGTAG 59.062 47.826 26.18 19.21 41.66 3.18
44 45 3.582647 TCCAGCTTCAAGACTTGATGGTA 59.417 43.478 26.18 14.94 41.66 3.25
45 46 2.373169 TCCAGCTTCAAGACTTGATGGT 59.627 45.455 25.33 24.22 43.52 3.55
46 47 2.746362 GTCCAGCTTCAAGACTTGATGG 59.254 50.000 22.50 22.50 39.84 3.51
47 48 3.436015 CAGTCCAGCTTCAAGACTTGATG 59.564 47.826 18.38 19.98 38.80 3.07
48 49 3.326006 TCAGTCCAGCTTCAAGACTTGAT 59.674 43.478 18.38 1.28 38.80 2.57
49 50 2.700371 TCAGTCCAGCTTCAAGACTTGA 59.300 45.455 13.99 13.99 38.80 3.02
50 51 3.117491 TCAGTCCAGCTTCAAGACTTG 57.883 47.619 9.03 9.03 38.80 3.16
51 52 3.471680 GTTCAGTCCAGCTTCAAGACTT 58.528 45.455 3.36 0.00 38.80 3.01
52 53 2.224402 GGTTCAGTCCAGCTTCAAGACT 60.224 50.000 0.00 0.00 41.49 3.24
53 54 2.147150 GGTTCAGTCCAGCTTCAAGAC 58.853 52.381 0.00 0.00 0.00 3.01
54 55 1.768275 TGGTTCAGTCCAGCTTCAAGA 59.232 47.619 0.00 0.00 33.19 3.02
55 56 2.149578 CTGGTTCAGTCCAGCTTCAAG 58.850 52.381 0.00 0.00 46.53 3.02
56 57 2.260844 CTGGTTCAGTCCAGCTTCAA 57.739 50.000 0.00 0.00 46.53 2.69
63 64 8.033178 TGATATTCATAATCTGGTTCAGTCCA 57.967 34.615 0.00 0.00 36.00 4.02
256 257 2.497273 ACTAATTGCTTTGGACCATGGC 59.503 45.455 13.04 4.47 0.00 4.40
402 403 9.861138 CAAATTGACTTTTTATCGAATGCAAAA 57.139 25.926 0.00 0.00 0.00 2.44
420 421 9.727627 TTTTATTTTTCAACATGGCAAATTGAC 57.272 25.926 14.31 0.00 32.21 3.18
449 450 9.075678 GAAAATTCATACCTCAGATCATGGAAT 57.924 33.333 0.00 0.00 0.00 3.01
460 461 6.252233 TGGACAATGGAAAATTCATACCTCA 58.748 36.000 0.00 0.00 0.00 3.86
491 492 5.708230 AGACCATCGCTTTAACCAATAACAA 59.292 36.000 0.00 0.00 0.00 2.83
506 507 4.323553 AAGATGTAGGTTAGACCATCGC 57.676 45.455 0.00 0.00 41.95 4.58
507 508 5.753921 GGAAAAGATGTAGGTTAGACCATCG 59.246 44.000 0.00 0.00 41.95 3.84
541 553 9.401058 TGGTTTTGTTCATGGAAAAATTATTGT 57.599 25.926 0.00 0.00 0.00 2.71
548 560 6.096001 CCCAAATGGTTTTGTTCATGGAAAAA 59.904 34.615 0.00 0.00 40.55 1.94
553 565 4.348863 TCCCAAATGGTTTTGTTCATGG 57.651 40.909 0.00 0.00 40.55 3.66
556 568 3.777522 AGGTTCCCAAATGGTTTTGTTCA 59.222 39.130 0.00 0.00 40.55 3.18
557 569 4.415881 AGGTTCCCAAATGGTTTTGTTC 57.584 40.909 0.00 0.00 40.55 3.18
558 570 4.202172 CGTAGGTTCCCAAATGGTTTTGTT 60.202 41.667 0.00 0.00 40.55 2.83
559 571 3.319689 CGTAGGTTCCCAAATGGTTTTGT 59.680 43.478 0.00 0.00 40.55 2.83
560 572 3.908213 CGTAGGTTCCCAAATGGTTTTG 58.092 45.455 0.00 0.00 41.59 2.44
578 646 0.038599 TAGCACCAGTGACTCCCGTA 59.961 55.000 0.99 0.00 0.00 4.02
583 651 1.446272 GCGGTAGCACCAGTGACTC 60.446 63.158 0.99 0.00 44.35 3.36
608 676 1.990060 CCCCCAGACACATCGAGGT 60.990 63.158 0.00 0.00 0.00 3.85
625 693 1.961277 CCAACTCACAGCGACACCC 60.961 63.158 0.00 0.00 0.00 4.61
628 696 1.227527 CCACCAACTCACAGCGACA 60.228 57.895 0.00 0.00 0.00 4.35
633 701 1.228245 CCCACCCACCAACTCACAG 60.228 63.158 0.00 0.00 0.00 3.66
695 763 0.614697 TCACATCTTCCCCTCGCTCA 60.615 55.000 0.00 0.00 0.00 4.26
699 767 1.195115 TCCTTCACATCTTCCCCTCG 58.805 55.000 0.00 0.00 0.00 4.63
712 780 5.642063 GTCGGTGACATTTTAGAATCCTTCA 59.358 40.000 0.00 0.00 32.09 3.02
723 791 2.223711 GCCTTGTTGTCGGTGACATTTT 60.224 45.455 0.00 0.00 42.40 1.82
731 799 4.864704 ATTTTTATGCCTTGTTGTCGGT 57.135 36.364 0.00 0.00 0.00 4.69
733 801 5.177327 AGCAAATTTTTATGCCTTGTTGTCG 59.823 36.000 0.00 0.00 43.57 4.35
740 808 4.244862 CACGGAGCAAATTTTTATGCCTT 58.755 39.130 0.00 0.00 43.57 4.35
746 814 3.891324 CGAACCACGGAGCAAATTTTTA 58.109 40.909 0.00 0.00 38.46 1.52
822 892 8.771521 ATCATGGAATCCATTAAAATCTGACA 57.228 30.769 12.91 0.00 42.23 3.58
882 972 7.989947 TCCTTCCTTTTTCTTCTAGGCTATA 57.010 36.000 0.00 0.00 0.00 1.31
889 979 6.367969 CGATCGTTTCCTTCCTTTTTCTTCTA 59.632 38.462 7.03 0.00 0.00 2.10
895 985 5.472137 TGAATCGATCGTTTCCTTCCTTTTT 59.528 36.000 27.46 0.00 0.00 1.94
931 1021 0.467804 GGTGGGAGAGGAGCAGAATC 59.532 60.000 0.00 0.00 0.00 2.52
989 1088 1.818060 CTCCGTCCATGATTTTTGGCA 59.182 47.619 0.00 0.00 34.06 4.92
993 1092 3.871594 GTCGATCTCCGTCCATGATTTTT 59.128 43.478 0.00 0.00 39.75 1.94
1068 1188 1.527380 GAGGATCTCGCGGAGGAGT 60.527 63.158 6.13 0.00 35.52 3.85
1365 1498 3.251571 GCCGTCGTTGAAGAACTCTATT 58.748 45.455 0.00 0.00 0.00 1.73
1521 1699 2.031919 AAGGTGATGCCGTTGCGA 59.968 55.556 0.00 0.00 43.70 5.10
1660 1874 3.638160 CCATGGATGGGTGGTAGAATTTG 59.362 47.826 5.56 0.00 44.31 2.32
1737 1957 0.321122 CAAGGGTGAAGAAGCTCGCT 60.321 55.000 0.00 0.00 0.00 4.93
1794 2014 1.153289 CCTGGAATCCTCCGCACAG 60.153 63.158 0.00 0.00 45.85 3.66
1810 2030 2.168106 CTGCACTGACAAGATAGAGCCT 59.832 50.000 0.00 0.00 30.83 4.58
2525 2787 8.918202 ACAAACTAATAACATTCAGAGGTGAA 57.082 30.769 0.00 0.00 46.81 3.18
2612 2880 4.081254 ACTGATAGCTGCAGATCTGTTGAA 60.081 41.667 23.38 6.94 36.86 2.69
2712 2982 5.503634 TCCACCACCATATGAGGAATATG 57.496 43.478 17.74 7.86 45.40 1.78
2713 2983 6.158695 GGTATCCACCACCATATGAGGAATAT 59.841 42.308 17.74 10.83 45.04 1.28
2788 3059 4.401202 ACCAAACAAGTAAACTCCCAAGTG 59.599 41.667 0.00 0.00 35.36 3.16
2890 4600 7.039882 GGTCAAGTAGAGAAATACAAATCCGA 58.960 38.462 0.00 0.00 0.00 4.55
2891 4601 7.042335 AGGTCAAGTAGAGAAATACAAATCCG 58.958 38.462 0.00 0.00 0.00 4.18
2892 4602 8.794335 AAGGTCAAGTAGAGAAATACAAATCC 57.206 34.615 0.00 0.00 0.00 3.01
2893 4603 8.884726 GGAAGGTCAAGTAGAGAAATACAAATC 58.115 37.037 0.00 0.00 0.00 2.17
2898 4608 8.850007 AAAAGGAAGGTCAAGTAGAGAAATAC 57.150 34.615 0.00 0.00 0.00 1.89
3048 4762 5.255687 ACAATCATGTCAAAGCCATACTGA 58.744 37.500 0.00 0.00 33.41 3.41
3235 5008 5.598005 CCTAATGGAAGTATGGATTTGCCAA 59.402 40.000 0.00 0.00 42.99 4.52
3292 5069 0.321298 ACCACAAGCACCGGTATGAC 60.321 55.000 6.87 0.00 0.00 3.06
3414 5191 6.869206 TTAGGTAGTAACAAATCTGCCTCT 57.131 37.500 5.21 0.00 43.60 3.69
3489 5291 9.520515 ACATGAGACTTTTATACCAAAACAGAT 57.479 29.630 0.00 0.00 0.00 2.90
3556 5422 5.625150 GATATAAGACCAGGCATGTTCCTT 58.375 41.667 0.00 0.20 33.25 3.36
3628 5498 1.968493 TGACAGGACAAGACCAGGTAC 59.032 52.381 0.00 0.00 0.00 3.34
3656 5741 8.078596 GGCCAAAGATGTATAGAAATAGCAAAG 58.921 37.037 0.00 0.00 0.00 2.77
3711 6962 5.032846 AGATGAATTCTGGAAGTACCCTGA 58.967 41.667 7.05 0.00 38.00 3.86


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

AutoCloner maintained by Alex Coulton.