Multiple sequence alignment - TraesCS3A01G030400

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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 TraesCS3A01G030400 chr3A 100.000 5824 0 0 1 5824 16007968 16013791 0.000000e+00 10756.0
1 TraesCS3A01G030400 chr3A 85.581 2136 224 32 1247 3344 15835636 15837725 0.000000e+00 2161.0
2 TraesCS3A01G030400 chr3A 87.373 1869 170 29 3042 4870 17333230 17335072 0.000000e+00 2084.0
3 TraesCS3A01G030400 chr3A 86.510 1868 183 31 3045 4870 17378092 17376252 0.000000e+00 1989.0
4 TraesCS3A01G030400 chr3A 88.590 1560 161 11 3318 4870 15837769 15839318 0.000000e+00 1879.0
5 TraesCS3A01G030400 chr3A 83.695 1938 245 32 1141 3021 17331250 17333173 0.000000e+00 1762.0
6 TraesCS3A01G030400 chr3A 84.387 1787 253 12 1263 3036 17379908 17378135 0.000000e+00 1731.0
7 TraesCS3A01G030400 chr3A 84.111 1800 255 16 1263 3036 16234688 16232894 0.000000e+00 1711.0
8 TraesCS3A01G030400 chr3A 94.830 619 25 2 5117 5735 16334935 16335546 0.000000e+00 959.0
9 TraesCS3A01G030400 chr3A 97.007 401 6 3 4725 5122 16321339 16321736 0.000000e+00 669.0
10 TraesCS3A01G030400 chr3A 81.414 382 53 10 639 1016 15833822 15834189 4.410000e-76 296.0
11 TraesCS3A01G030400 chr3A 86.957 92 9 3 4934 5022 16231004 16230913 3.710000e-17 100.0
12 TraesCS3A01G030400 chr3A 85.870 92 10 3 4934 5022 17376245 17376154 1.730000e-15 95.3
13 TraesCS3A01G030400 chr3A 94.872 39 1 1 1009 1047 15835445 15835482 6.300000e-05 60.2
14 TraesCS3A01G030400 chr3B 93.422 4728 216 35 1072 5745 12933216 12937902 0.000000e+00 6920.0
15 TraesCS3A01G030400 chr3B 89.983 4073 278 43 1047 5021 13245800 13249840 0.000000e+00 5142.0
16 TraesCS3A01G030400 chr3B 87.506 2113 184 49 3232 5300 13414906 13416982 0.000000e+00 2366.0
17 TraesCS3A01G030400 chr3B 85.000 2340 248 41 1047 3344 12472276 12474554 0.000000e+00 2281.0
18 TraesCS3A01G030400 chr3B 85.934 2147 221 28 1247 3344 12843126 12841012 0.000000e+00 2217.0
19 TraesCS3A01G030400 chr3B 88.292 1563 164 12 3318 4870 12840968 12839415 0.000000e+00 1855.0
20 TraesCS3A01G030400 chr3B 87.011 1586 173 19 3318 4896 12474598 12476157 0.000000e+00 1757.0
21 TraesCS3A01G030400 chr3B 91.639 909 53 7 145 1048 12547302 12546412 0.000000e+00 1236.0
22 TraesCS3A01G030400 chr3B 85.930 1059 130 12 1990 3036 13413562 13414613 0.000000e+00 1112.0
23 TraesCS3A01G030400 chr3B 86.009 1065 93 18 5 1047 13409044 13410074 0.000000e+00 1090.0
24 TraesCS3A01G030400 chr3B 89.085 623 54 7 193 810 13245013 13245626 0.000000e+00 761.0
25 TraesCS3A01G030400 chr3B 85.913 575 47 12 6 561 13241019 13241578 3.020000e-162 582.0
26 TraesCS3A01G030400 chr3B 85.377 424 23 6 5354 5738 13419506 13419929 2.530000e-108 403.0
27 TraesCS3A01G030400 chr3B 78.594 626 101 21 28 627 238825991 238826609 3.290000e-102 383.0
28 TraesCS3A01G030400 chr3B 80.840 381 57 10 639 1016 12470145 12470512 9.550000e-73 285.0
29 TraesCS3A01G030400 chr3B 91.919 198 13 1 1 195 13244530 13244727 2.070000e-69 274.0
30 TraesCS3A01G030400 chr3B 80.541 370 53 11 639 1003 12902539 12902184 3.460000e-67 267.0
31 TraesCS3A01G030400 chr3B 88.679 106 12 0 4916 5021 12476259 12476364 4.740000e-26 130.0
32 TraesCS3A01G030400 chr3B 91.860 86 6 1 5740 5824 13420465 13420550 1.030000e-22 119.0
33 TraesCS3A01G030400 chr3B 95.745 47 1 1 5321 5367 13416981 13417026 2.250000e-09 75.0
34 TraesCS3A01G030400 chr3B 93.023 43 2 1 1005 1047 12843358 12843317 1.750000e-05 62.1
35 TraesCS3A01G030400 chr3B 100.000 30 0 0 5594 5623 12478922 12478951 8.150000e-04 56.5
36 TraesCS3A01G030400 chr3D 88.893 2575 189 38 3243 5738 5408131 5405575 0.000000e+00 3081.0
37 TraesCS3A01G030400 chr3D 84.285 2768 303 60 644 3344 41427652 41424950 0.000000e+00 2580.0
38 TraesCS3A01G030400 chr3D 88.299 2034 176 24 1047 3036 5410448 5408433 0.000000e+00 2381.0
39 TraesCS3A01G030400 chr3D 84.806 2343 244 50 1047 3344 41596936 41594661 0.000000e+00 2252.0
40 TraesCS3A01G030400 chr3D 86.617 1868 181 33 3045 4870 5374756 5372916 0.000000e+00 2001.0
41 TraesCS3A01G030400 chr3D 87.047 1737 183 22 3318 5021 41594617 41592890 0.000000e+00 1923.0
42 TraesCS3A01G030400 chr3D 88.476 1588 167 10 3317 4896 41424899 41423320 0.000000e+00 1905.0
43 TraesCS3A01G030400 chr3D 84.403 1808 259 11 1248 3036 5376602 5374799 0.000000e+00 1755.0
44 TraesCS3A01G030400 chr3D 84.754 1771 244 7 1263 3021 5328621 5330377 0.000000e+00 1751.0
45 TraesCS3A01G030400 chr3D 88.669 1059 83 17 1 1048 5411506 5410474 0.000000e+00 1256.0
46 TraesCS3A01G030400 chr3D 82.199 382 50 10 639 1016 41598616 41598249 4.380000e-81 313.0
47 TraesCS3A01G030400 chr3D 85.556 180 21 3 31 207 507768891 507769068 3.580000e-42 183.0
48 TraesCS3A01G030400 chr3D 88.172 93 7 4 4934 5022 5372909 5372817 2.220000e-19 108.0
49 TraesCS3A01G030400 chr3D 90.196 51 1 1 5595 5641 41589884 41589834 4.870000e-06 63.9
50 TraesCS3A01G030400 chr2A 78.675 619 109 13 28 627 726280577 726281191 1.970000e-104 390.0
51 TraesCS3A01G030400 chr1D 78.768 617 103 18 31 627 112479118 112478510 7.080000e-104 388.0
52 TraesCS3A01G030400 chr4D 78.675 619 105 12 28 627 96586144 96586754 2.550000e-103 387.0
53 TraesCS3A01G030400 chr7D 79.002 481 78 10 164 627 54927697 54928171 2.040000e-79 307.0
54 TraesCS3A01G030400 chr7D 76.200 500 84 18 30 502 29040538 29040047 1.260000e-56 231.0
55 TraesCS3A01G030400 chr6B 77.951 449 88 7 185 627 49380512 49380069 2.670000e-68 270.0
56 TraesCS3A01G030400 chr5B 80.102 392 48 21 30 400 400091174 400090792 1.240000e-66 265.0


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 TraesCS3A01G030400 chr3A 16007968 16013791 5823 False 10756.000000 10756 100.000000 1 5824 1 chr3A.!!$F1 5823
1 TraesCS3A01G030400 chr3A 17331250 17335072 3822 False 1923.000000 2084 85.534000 1141 4870 2 chr3A.!!$F5 3729
2 TraesCS3A01G030400 chr3A 17376154 17379908 3754 True 1271.766667 1989 85.589000 1263 5022 3 chr3A.!!$R2 3759
3 TraesCS3A01G030400 chr3A 15833822 15839318 5496 False 1099.050000 2161 87.614250 639 4870 4 chr3A.!!$F4 4231
4 TraesCS3A01G030400 chr3A 16334935 16335546 611 False 959.000000 959 94.830000 5117 5735 1 chr3A.!!$F3 618
5 TraesCS3A01G030400 chr3A 16230913 16234688 3775 True 905.500000 1711 85.534000 1263 5022 2 chr3A.!!$R1 3759
6 TraesCS3A01G030400 chr3B 12933216 12937902 4686 False 6920.000000 6920 93.422000 1072 5745 1 chr3B.!!$F1 4673
7 TraesCS3A01G030400 chr3B 13241019 13249840 8821 False 1689.750000 5142 89.225000 1 5021 4 chr3B.!!$F4 5020
8 TraesCS3A01G030400 chr3B 12839415 12843358 3943 True 1378.033333 2217 89.083000 1005 4870 3 chr3B.!!$R3 3865
9 TraesCS3A01G030400 chr3B 12546412 12547302 890 True 1236.000000 1236 91.639000 145 1048 1 chr3B.!!$R1 903
10 TraesCS3A01G030400 chr3B 12470145 12478951 8806 False 901.900000 2281 88.306000 639 5623 5 chr3B.!!$F3 4984
11 TraesCS3A01G030400 chr3B 13409044 13420550 11506 False 860.833333 2366 88.737833 5 5824 6 chr3B.!!$F5 5819
12 TraesCS3A01G030400 chr3B 238825991 238826609 618 False 383.000000 383 78.594000 28 627 1 chr3B.!!$F2 599
13 TraesCS3A01G030400 chr3D 41423320 41427652 4332 True 2242.500000 2580 86.380500 644 4896 2 chr3D.!!$R3 4252
14 TraesCS3A01G030400 chr3D 5405575 5411506 5931 True 2239.333333 3081 88.620333 1 5738 3 chr3D.!!$R2 5737
15 TraesCS3A01G030400 chr3D 5328621 5330377 1756 False 1751.000000 1751 84.754000 1263 3021 1 chr3D.!!$F1 1758
16 TraesCS3A01G030400 chr3D 5372817 5376602 3785 True 1288.000000 2001 86.397333 1248 5022 3 chr3D.!!$R1 3774
17 TraesCS3A01G030400 chr3D 41589834 41598616 8782 True 1137.975000 2252 86.062000 639 5641 4 chr3D.!!$R4 5002
18 TraesCS3A01G030400 chr2A 726280577 726281191 614 False 390.000000 390 78.675000 28 627 1 chr2A.!!$F1 599
19 TraesCS3A01G030400 chr1D 112478510 112479118 608 True 388.000000 388 78.768000 31 627 1 chr1D.!!$R1 596
20 TraesCS3A01G030400 chr4D 96586144 96586754 610 False 387.000000 387 78.675000 28 627 1 chr4D.!!$F1 599

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
220 4025 0.108945 GCCTCATCTTGCAACTTGCC 60.109 55.0 11.29 0.00 44.23 4.52 F
1199 8133 0.316841 GAGATCTAGCAAGCCTCCGG 59.683 60.0 0.00 0.00 0.00 5.14 F
1829 9851 0.107066 TGCATCGCCACCAGATGAAT 60.107 50.0 10.01 0.00 46.09 2.57 F
2753 11108 0.261991 ATGAGGCTAGGGAGGTCGAA 59.738 55.0 0.00 0.00 0.00 3.71 F
3625 12208 1.745232 TGACTTGTCACGGTTTTGCT 58.255 45.0 0.00 0.00 0.00 3.91 F
4355 12983 0.949588 CAGTGTGTCTCAGCCTGCTG 60.950 60.0 12.91 12.91 44.86 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 9851 0.623723 GCCCCTGGTGGAATTGACTA 59.376 55.000 5.51 0.0 35.39 2.59 R
2927 11282 0.035739 GAAGTTCAACTACCCGCCCA 59.964 55.000 0.00 0.0 0.00 5.36 R
3457 12029 0.388649 GAGCTACCACGTCACTGGTG 60.389 60.000 5.72 0.0 44.76 4.17 R
3644 12236 0.534873 TCGCAGCAACAGGTAGCATA 59.465 50.000 0.00 0.0 0.00 3.14 R
4795 13423 0.764890 CTGGAACTCTTCACACCCCA 59.235 55.000 0.00 0.0 0.00 4.96 R
5738 19641 1.303317 GCGTTCCCCACTTCCATGT 60.303 57.895 0.00 0.0 0.00 3.21 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
195 4000 6.594159 CCAAAGATACATCGAAAACACCTAGT 59.406 38.462 0.00 0.00 0.00 2.57
220 4025 0.108945 GCCTCATCTTGCAACTTGCC 60.109 55.000 11.29 0.00 44.23 4.52
291 4130 2.159627 GTGTCCGAATTCGTTCTTGCAT 59.840 45.455 25.10 0.00 37.74 3.96
292 4131 3.369756 GTGTCCGAATTCGTTCTTGCATA 59.630 43.478 25.10 0.07 37.74 3.14
294 4133 3.617263 GTCCGAATTCGTTCTTGCATACT 59.383 43.478 25.10 0.00 37.74 2.12
322 4163 4.943705 TCAGGTGAGCATGAATTAGGTTTC 59.056 41.667 0.00 0.00 32.01 2.78
337 4178 1.338769 GGTTTCTTGGGAAGCGCTCTA 60.339 52.381 12.06 0.00 34.22 2.43
368 4209 2.493278 CCAAGTTTGTCATCATGGGTCC 59.507 50.000 0.00 0.00 0.00 4.46
521 4374 9.649167 GTGTCTACCTATAGTTGTTGTTACATT 57.351 33.333 0.00 0.00 33.44 2.71
522 4375 9.865321 TGTCTACCTATAGTTGTTGTTACATTC 57.135 33.333 0.00 0.00 33.44 2.67
592 4447 7.642669 TGTTGCATGCTATTTTCTATTAGAGC 58.357 34.615 20.33 0.00 0.00 4.09
774 4638 1.345415 GGTCACCGGTAAAGTCTGGAA 59.655 52.381 6.87 0.00 37.31 3.53
849 4734 0.391661 TGCATCTCCGGAAAGAGTGC 60.392 55.000 5.23 11.93 39.38 4.40
945 4832 1.061485 GACGAGGAGACAAACGCTTC 58.939 55.000 0.00 0.00 0.00 3.86
1048 6671 1.439644 GGCTAGAACTCAGGAGCCG 59.560 63.158 0.00 0.00 44.72 5.52
1050 6673 1.390565 GCTAGAACTCAGGAGCCGTA 58.609 55.000 0.00 0.00 0.00 4.02
1051 6674 1.335496 GCTAGAACTCAGGAGCCGTAG 59.665 57.143 0.00 0.00 0.00 3.51
1060 6725 1.038130 AGGAGCCGTAGTTGCGATCT 61.038 55.000 0.00 0.00 0.00 2.75
1103 7892 0.881600 GCCGTGGTACTTTTGTCCGT 60.882 55.000 0.00 0.00 0.00 4.69
1122 7915 7.587629 TGTCCGTGTAGTATTATAGGAATTCG 58.412 38.462 0.00 0.00 0.00 3.34
1152 7988 3.119743 TCCGTACGTGGCATAGCATATAC 60.120 47.826 15.21 0.00 0.00 1.47
1153 7989 3.176708 CGTACGTGGCATAGCATATACC 58.823 50.000 7.22 0.00 0.00 2.73
1158 8087 0.999406 GGCATAGCATATACCGCACG 59.001 55.000 0.00 0.00 0.00 5.34
1199 8133 0.316841 GAGATCTAGCAAGCCTCCGG 59.683 60.000 0.00 0.00 0.00 5.14
1322 8882 3.372206 CCAATCTTTACTTGCTCGACCTG 59.628 47.826 0.00 0.00 0.00 4.00
1778 9800 2.047179 GAGTCCACGAACCTGGCC 60.047 66.667 0.00 0.00 0.00 5.36
1829 9851 0.107066 TGCATCGCCACCAGATGAAT 60.107 50.000 10.01 0.00 46.09 2.57
2167 10420 0.320683 TGTGCTCCTGATCAACACGG 60.321 55.000 0.00 0.00 33.96 4.94
2188 10474 4.562963 CGGTGATGATGATGATGATGAGGT 60.563 45.833 0.00 0.00 0.00 3.85
2191 10477 4.349930 TGATGATGATGATGATGAGGTGGT 59.650 41.667 0.00 0.00 0.00 4.16
2201 10487 0.618968 ATGAGGTGGTGGAGGAGGAC 60.619 60.000 0.00 0.00 0.00 3.85
2213 10508 1.378250 GGAGGACGAGGACGAGGAA 60.378 63.158 0.00 0.00 42.66 3.36
2234 10562 4.065321 AGAGGAAGAGGAATACAATGCG 57.935 45.455 0.00 0.00 0.00 4.73
2279 10611 3.244665 TGTGTGAAGCATCAACCTCTCAT 60.245 43.478 0.00 0.00 37.30 2.90
2284 10619 1.064906 AGCATCAACCTCTCATGTGGG 60.065 52.381 0.00 0.00 0.00 4.61
2600 10955 3.726557 ACTGGTGACCATGATGATGTT 57.273 42.857 4.03 0.00 30.82 2.71
2753 11108 0.261991 ATGAGGCTAGGGAGGTCGAA 59.738 55.000 0.00 0.00 0.00 3.71
2781 11136 3.067106 CAAACCATCAGTGCTTACGACT 58.933 45.455 0.00 0.00 0.00 4.18
2911 11266 3.222603 AGAAGAAAAATGCCGTTCCTGT 58.777 40.909 0.00 0.00 0.00 4.00
2927 11282 2.571653 TCCTGTCGATCTTTCATGGGTT 59.428 45.455 0.00 0.00 0.00 4.11
3090 11485 2.537560 CGCCCCATGAGATCGTTGC 61.538 63.158 0.00 0.00 0.00 4.17
3397 11969 6.504398 TCTAGATAATGATGTCGAAAGCGTT 58.496 36.000 3.43 3.43 38.98 4.84
3457 12029 1.821216 TCCGGTCTTTGCTCCAATTC 58.179 50.000 0.00 0.00 0.00 2.17
3625 12208 1.745232 TGACTTGTCACGGTTTTGCT 58.255 45.000 0.00 0.00 0.00 3.91
3644 12236 4.115199 GGGGGACGAAGGCTGCAT 62.115 66.667 0.50 0.00 0.00 3.96
3689 12281 3.145286 TCGTCATGCTTTCCACATTTCA 58.855 40.909 0.00 0.00 0.00 2.69
4097 12725 3.126858 CACCTGAAAATACACGGTCCATG 59.873 47.826 0.00 0.00 0.00 3.66
4355 12983 0.949588 CAGTGTGTCTCAGCCTGCTG 60.950 60.000 12.91 12.91 44.86 4.41
4565 13193 1.622607 TAACCCTCCGGACCATGCAG 61.623 60.000 0.00 0.00 0.00 4.41
4696 13324 2.592574 CGACGATGCCCATGCCAT 60.593 61.111 0.00 0.00 36.33 4.40
5237 13976 1.588239 TGGATCCAGCTCAATCCAGT 58.412 50.000 18.57 0.00 45.05 4.00
5259 13998 7.371159 CAGTTAGCAATAATAGACGGAGATGA 58.629 38.462 0.00 0.00 0.00 2.92
5304 14043 1.681166 GCATGCACTTCCAGATGACCT 60.681 52.381 14.21 0.00 0.00 3.85
5340 14102 9.787435 CCCCATATATAGTAGTTACTGCAAAAA 57.213 33.333 2.94 0.00 37.10 1.94
5430 16702 6.951198 TGGTTATCATCACCATTTGTTTAGGT 59.049 34.615 0.00 0.00 39.53 3.08
5558 19457 6.373759 TCTGTAGACAAGATAGGAGGCAATA 58.626 40.000 0.00 0.00 0.00 1.90
5570 19469 9.018582 AGATAGGAGGCAATATTTATTCTTTGC 57.981 33.333 0.00 0.00 42.81 3.68
5666 19569 4.475944 GCACACTAAAAGCAACATTCGAT 58.524 39.130 0.00 0.00 0.00 3.59
5738 19641 6.296026 ACAGCAAACTAGTTCATAGACCAAA 58.704 36.000 8.95 0.00 35.30 3.28
5753 20190 1.219213 ACCAAACATGGAAGTGGGGAA 59.781 47.619 1.10 0.00 35.32 3.97
5795 20232 3.253230 CACACGCATGATACAGTCTTGA 58.747 45.455 0.00 0.00 34.74 3.02
5801 20238 4.063689 GCATGATACAGTCTTGATGAGGG 58.936 47.826 0.00 0.00 34.74 4.30
5802 20239 4.202295 GCATGATACAGTCTTGATGAGGGA 60.202 45.833 0.00 0.00 34.74 4.20
5808 20246 5.762179 ACAGTCTTGATGAGGGATAACAA 57.238 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 4025 2.933573 AGAGTAGACTATGGTGACGGG 58.066 52.381 0.00 0.00 0.00 5.28
267 4102 2.806244 CAAGAACGAATTCGGACACCTT 59.194 45.455 29.79 19.98 44.95 3.50
291 4130 5.675684 TTCATGCTCACCTGATGTAAGTA 57.324 39.130 0.00 0.00 0.00 2.24
292 4131 4.558226 TTCATGCTCACCTGATGTAAGT 57.442 40.909 0.00 0.00 0.00 2.24
294 4133 6.057533 CCTAATTCATGCTCACCTGATGTAA 58.942 40.000 0.00 0.00 0.00 2.41
322 4163 4.094684 CGTAGAGCGCTTCCCAAG 57.905 61.111 13.26 0.00 0.00 3.61
337 4178 0.105408 ACAAACTTGGGTAGTCGCGT 59.895 50.000 5.77 0.00 35.54 6.01
446 4299 0.532862 ATTAGTTGCTGCGGGATCGG 60.533 55.000 0.00 0.00 36.79 4.18
521 4374 3.815856 AACATGCACAACAACATTGGA 57.184 38.095 0.00 0.00 0.00 3.53
522 4375 4.879104 AAAACATGCACAACAACATTGG 57.121 36.364 0.00 0.00 0.00 3.16
639 4496 3.547054 ACGGTTGTTTAGTCCTTGTCA 57.453 42.857 0.00 0.00 0.00 3.58
774 4638 1.537202 GCGGTCAAAGCAAACTCTCAT 59.463 47.619 0.00 0.00 34.19 2.90
804 4689 6.910259 ACCCATCTTAATAGTTTCTTCCCT 57.090 37.500 0.00 0.00 0.00 4.20
849 4734 5.867903 ATGTAGATGGAGAGAAGGAAGTG 57.132 43.478 0.00 0.00 0.00 3.16
892 4777 2.124612 CCACCGCCTCATGCATCA 60.125 61.111 0.00 0.00 41.33 3.07
894 4779 2.288642 ATTCCCACCGCCTCATGCAT 62.289 55.000 0.00 0.00 41.33 3.96
895 4780 2.497792 AATTCCCACCGCCTCATGCA 62.498 55.000 0.00 0.00 41.33 3.96
937 4824 1.870055 TAGGCGTCTCGGAAGCGTTT 61.870 55.000 0.00 0.00 37.89 3.60
945 4832 0.955178 ACAGATCATAGGCGTCTCGG 59.045 55.000 0.00 0.00 0.00 4.63
1048 6671 4.933330 TCCAACAGATAGATCGCAACTAC 58.067 43.478 0.00 0.00 0.00 2.73
1050 6673 4.471904 TTCCAACAGATAGATCGCAACT 57.528 40.909 0.00 0.00 0.00 3.16
1051 6674 5.741388 AATTCCAACAGATAGATCGCAAC 57.259 39.130 0.00 0.00 0.00 4.17
1060 6725 7.014230 GGCCTGCTTAATTAATTCCAACAGATA 59.986 37.037 3.39 0.00 0.00 1.98
1122 7915 0.935196 GCCACGTACGGATTGGATTC 59.065 55.000 23.28 5.84 31.39 2.52
1158 8087 3.723348 GGCTGGAAACGCACGGTC 61.723 66.667 0.00 0.00 0.00 4.79
1199 8133 3.889044 TCGACTGATCTCGCCGGC 61.889 66.667 19.07 19.07 33.47 6.13
1200 8134 2.024871 GTCGACTGATCTCGCCGG 59.975 66.667 8.70 0.00 33.47 6.13
1201 8135 1.583967 GTGTCGACTGATCTCGCCG 60.584 63.158 17.92 0.00 33.47 6.46
1202 8136 1.226717 GGTGTCGACTGATCTCGCC 60.227 63.158 17.92 0.00 33.47 5.54
1322 8882 2.828549 ATGCGGCCGGATTTCACC 60.829 61.111 27.97 7.31 0.00 4.02
1778 9800 1.291184 TGCCGATTTCACGCACTCTG 61.291 55.000 0.00 0.00 0.00 3.35
1829 9851 0.623723 GCCCCTGGTGGAATTGACTA 59.376 55.000 5.51 0.00 35.39 2.59
1919 9941 0.892755 TGGTGCCTACTTGTCGGTAG 59.107 55.000 0.00 0.00 38.95 3.18
2123 10376 2.158475 TGCATCCTCTTTGGTGGAACTT 60.158 45.455 0.00 0.00 38.41 2.66
2167 10420 4.695928 CCACCTCATCATCATCATCATCAC 59.304 45.833 0.00 0.00 0.00 3.06
2188 10474 2.037367 CCTCGTCCTCCTCCACCA 59.963 66.667 0.00 0.00 0.00 4.17
2191 10477 2.045242 CGTCCTCGTCCTCCTCCA 60.045 66.667 0.00 0.00 0.00 3.86
2201 10487 0.736053 CTTCCTCTTCCTCGTCCTCG 59.264 60.000 0.00 0.00 38.55 4.63
2213 10508 3.452627 ACGCATTGTATTCCTCTTCCTCT 59.547 43.478 0.00 0.00 0.00 3.69
2234 10562 2.288666 TCTTGGTTGTCTTGTGAGCAC 58.711 47.619 0.00 0.00 0.00 4.40
2284 10619 0.890996 CTTCTGCTTGGTGGGTGGTC 60.891 60.000 0.00 0.00 0.00 4.02
2753 11108 1.167851 CACTGATGGTTTGGTCGCAT 58.832 50.000 0.00 0.00 0.00 4.73
2781 11136 6.430000 GCAGAGTGGTTAGAGTCCAATTTTAA 59.570 38.462 0.00 0.00 36.68 1.52
2858 11213 0.395586 ACAAGGGTGCACTTTCAGCA 60.396 50.000 17.98 0.00 40.19 4.41
2860 11215 3.120199 CGATAACAAGGGTGCACTTTCAG 60.120 47.826 17.98 6.08 0.00 3.02
2911 11266 1.681780 GCCCAACCCATGAAAGATCGA 60.682 52.381 0.00 0.00 0.00 3.59
2927 11282 0.035739 GAAGTTCAACTACCCGCCCA 59.964 55.000 0.00 0.00 0.00 5.36
3090 11485 1.270094 TGTAGTGCTTGTCCTTGACGG 60.270 52.381 0.00 0.00 34.95 4.79
3234 11663 4.542525 ACCAAAATAGTCCCCACCTCATTA 59.457 41.667 0.00 0.00 0.00 1.90
3397 11969 1.077787 CCTTGACATTGCCGGGCTA 60.078 57.895 21.46 13.84 0.00 3.93
3457 12029 0.388649 GAGCTACCACGTCACTGGTG 60.389 60.000 5.72 0.00 44.76 4.17
3644 12236 0.534873 TCGCAGCAACAGGTAGCATA 59.465 50.000 0.00 0.00 0.00 3.14
3689 12281 1.842562 AGGGCTCATCTGCAGTACATT 59.157 47.619 14.67 0.00 34.04 2.71
4097 12725 5.043248 GGCTATTCATTTGTAACCATGCAC 58.957 41.667 0.00 0.00 0.00 4.57
4355 12983 1.635663 CCTCGCCACCGAATGTGTTC 61.636 60.000 0.00 0.00 43.87 3.18
4565 13193 1.962306 TGGCCGACGTAAAAGGTGC 60.962 57.895 0.00 0.00 0.00 5.01
4658 13286 2.827921 GACAACATTTCCCTGAAGCCAT 59.172 45.455 0.00 0.00 0.00 4.40
4696 13324 0.885879 TCGCTTCCTAGTCGCTTCAA 59.114 50.000 0.00 0.00 0.00 2.69
4795 13423 0.764890 CTGGAACTCTTCACACCCCA 59.235 55.000 0.00 0.00 0.00 4.96
5237 13976 6.493802 AGGTCATCTCCGTCTATTATTGCTAA 59.506 38.462 0.00 0.00 0.00 3.09
5430 16702 7.587629 CAAGTAGCAGATTGAATTCTGAAACA 58.412 34.615 7.05 0.00 44.88 2.83
5469 19266 3.769739 AGCAAGATCAACTGTACACCA 57.230 42.857 0.00 0.00 0.00 4.17
5558 19457 8.379428 AGATTTGGGGTAAGCAAAGAATAAAT 57.621 30.769 0.00 0.00 0.00 1.40
5570 19469 4.781934 CCCTCTACAAGATTTGGGGTAAG 58.218 47.826 0.00 0.00 34.12 2.34
5738 19641 1.303317 GCGTTCCCCACTTCCATGT 60.303 57.895 0.00 0.00 0.00 3.21
5753 20190 3.115554 GCTTCTTTTGTTGAACATGCGT 58.884 40.909 0.00 0.00 0.00 5.24
5760 20197 2.095008 TGCGTGTGCTTCTTTTGTTGAA 60.095 40.909 0.00 0.00 43.34 2.69
5761 20198 1.470494 TGCGTGTGCTTCTTTTGTTGA 59.530 42.857 0.00 0.00 43.34 3.18
5795 20232 7.893302 TGTCCTGTAAATTTTGTTATCCCTCAT 59.107 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.