Multiple sequence alignment - TraesCS3D01G481100

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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 TraesCS3D01G481100 chr3D 100.000 3390 0 0 1 3390 579397524 579400913 0.000000e+00 6261.0
1 TraesCS3D01G481100 chr3D 92.463 1977 108 14 1010 2974 579582768 579580821 0.000000e+00 2787.0
2 TraesCS3D01G481100 chr3D 92.086 417 29 3 2978 3390 579580785 579580369 4.870000e-163 584.0
3 TraesCS3D01G481100 chr3D 84.422 398 26 23 199 593 579425872 579426236 3.220000e-95 359.0
4 TraesCS3D01G481100 chr3D 77.395 522 106 11 1639 2156 567371516 567372029 1.980000e-77 300.0
5 TraesCS3D01G481100 chr3D 82.421 347 45 9 1010 1345 565641949 565642290 4.280000e-74 289.0
6 TraesCS3D01G481100 chr3D 81.132 371 52 14 2534 2893 138901770 138901407 7.160000e-72 281.0
7 TraesCS3D01G481100 chr3D 77.103 428 87 10 1684 2105 520440644 520441066 1.570000e-58 237.0
8 TraesCS3D01G481100 chr3D 84.746 236 36 0 1010 1245 565830778 565831013 1.570000e-58 237.0
9 TraesCS3D01G481100 chr3D 78.979 333 57 10 2567 2891 567930726 567931053 7.370000e-52 215.0
10 TraesCS3D01G481100 chr3D 86.294 197 23 3 193 386 579583806 579583611 9.530000e-51 211.0
11 TraesCS3D01G481100 chr3D 73.163 626 135 25 1555 2156 568111384 568112000 9.600000e-46 195.0
12 TraesCS3D01G481100 chr3D 81.579 228 33 8 2567 2788 569464726 569464502 2.690000e-41 180.0
13 TraesCS3D01G481100 chr3D 72.347 622 144 22 1553 2156 566743192 566743803 1.620000e-38 171.0
14 TraesCS3D01G481100 chr3D 87.597 129 13 3 35 161 579584015 579583888 2.730000e-31 147.0
15 TraesCS3D01G481100 chr3D 85.600 125 11 6 457 577 579583470 579583349 1.280000e-24 124.0
16 TraesCS3D01G481100 chr3D 76.887 212 37 10 1138 1338 568136871 568137081 3.580000e-20 110.0
17 TraesCS3D01G481100 chr3D 91.111 45 3 1 2864 2907 568112756 568112800 3.650000e-05 60.2
18 TraesCS3D01G481100 chr3B 91.667 1368 103 4 1010 2371 773747083 773748445 0.000000e+00 1884.0
19 TraesCS3D01G481100 chr3B 89.922 903 70 8 1888 2781 773882269 773881379 0.000000e+00 1144.0
20 TraesCS3D01G481100 chr3B 76.163 1720 281 78 1023 2698 684513956 684512322 0.000000e+00 785.0
21 TraesCS3D01G481100 chr3B 85.714 518 37 10 1021 1536 773882749 773882267 2.330000e-141 512.0
22 TraesCS3D01G481100 chr3B 84.459 444 45 17 169 593 773762578 773763016 1.880000e-112 416.0
23 TraesCS3D01G481100 chr3B 92.969 256 8 4 3144 3390 773880751 773880497 6.910000e-97 364.0
24 TraesCS3D01G481100 chr3B 80.435 414 46 21 199 596 773746225 773746619 1.990000e-72 283.0
25 TraesCS3D01G481100 chr3B 74.478 670 129 34 1459 2101 684505403 684504749 5.620000e-63 252.0
26 TraesCS3D01G481100 chr3B 81.646 316 30 15 256 551 773883579 773883272 1.570000e-58 237.0
27 TraesCS3D01G481100 chr3B 82.869 251 40 3 1014 1262 754308128 754308377 4.400000e-54 222.0
28 TraesCS3D01G481100 chr3B 73.241 725 132 39 1454 2144 754302750 754303446 1.230000e-49 207.0
29 TraesCS3D01G481100 chr3B 84.677 124 19 0 38 161 773897439 773897316 1.280000e-24 124.0
30 TraesCS3D01G481100 chr3B 88.043 92 6 1 2970 3056 773880842 773880751 1.660000e-18 104.0
31 TraesCS3D01G481100 chr3B 85.542 83 11 1 2828 2909 201999218 201999136 6.030000e-13 86.1
32 TraesCS3D01G481100 chr3A 92.554 1249 76 3 1010 2255 714595661 714596895 0.000000e+00 1775.0
33 TraesCS3D01G481100 chr3A 77.022 1719 288 69 1023 2698 655570584 655568930 0.000000e+00 887.0
34 TraesCS3D01G481100 chr3A 87.645 518 43 12 2473 2974 714597031 714597543 1.750000e-162 582.0
35 TraesCS3D01G481100 chr3A 75.145 1203 219 50 987 2156 700352297 700351142 3.040000e-135 492.0
36 TraesCS3D01G481100 chr3A 83.524 437 45 16 169 583 714603702 714604133 1.910000e-102 383.0
37 TraesCS3D01G481100 chr3A 81.892 370 52 10 2534 2893 157040009 157039645 7.110000e-77 298.0
38 TraesCS3D01G481100 chr3A 92.344 209 14 2 2970 3177 714597571 714597778 2.560000e-76 296.0
39 TraesCS3D01G481100 chr3A 82.353 340 51 6 1009 1345 702407849 702407516 1.540000e-73 287.0
40 TraesCS3D01G481100 chr3A 93.750 176 9 1 3217 3390 714597775 714597950 2.590000e-66 263.0
41 TraesCS3D01G481100 chr3A 76.099 523 111 13 1639 2156 701369970 701370483 9.330000e-66 261.0
42 TraesCS3D01G481100 chr3A 96.875 96 3 0 35 130 714603529 714603624 9.730000e-36 161.0
43 TraesCS3D01G481100 chr3A 92.857 98 6 1 2285 2381 714596879 714596976 1.270000e-29 141.0
44 TraesCS3D01G481100 chr3A 81.618 136 16 1 35 161 714625378 714625243 1.660000e-18 104.0
45 TraesCS3D01G481100 chr3A 76.882 186 30 10 1171 1344 700441703 700441519 3.600000e-15 93.5
46 TraesCS3D01G481100 chr3A 81.928 83 14 1 2828 2909 157040526 157040444 6.070000e-08 69.4
47 TraesCS3D01G481100 chr3A 97.297 37 1 0 1 37 714592985 714593021 2.820000e-06 63.9
48 TraesCS3D01G481100 chr2A 74.888 669 155 10 1455 2118 45080483 45081143 3.310000e-75 292.0
49 TraesCS3D01G481100 chrUn 85.833 240 28 5 1015 1248 41059800 41059561 2.020000e-62 250.0
50 TraesCS3D01G481100 chrUn 80.909 220 38 4 2570 2788 40930078 40929862 1.620000e-38 171.0
51 TraesCS3D01G481100 chrUn 80.672 238 22 15 345 570 230760114 230759889 2.710000e-36 163.0
52 TraesCS3D01G481100 chrUn 83.505 97 15 1 2567 2663 314513609 314513514 4.660000e-14 89.8
53 TraesCS3D01G481100 chr4A 79.456 331 35 19 255 570 714667641 714667329 1.590000e-48 204.0
54 TraesCS3D01G481100 chr4A 71.456 515 134 12 1649 2156 648794677 648794169 1.280000e-24 124.0
55 TraesCS3D01G481100 chr4B 79.217 332 34 20 255 570 430672539 430672227 7.420000e-47 198.0
56 TraesCS3D01G481100 chr7A 73.837 516 121 13 1649 2156 41048137 41047628 3.450000e-45 193.0
57 TraesCS3D01G481100 chr7D 73.477 509 118 13 1649 2147 41601215 41600714 3.480000e-40 176.0
58 TraesCS3D01G481100 chr2D 85.393 89 10 2 2994 3079 43291232 43291320 4.660000e-14 89.8


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 TraesCS3D01G481100 chr3D 579397524 579400913 3389 False 6261.00 6261 100.000000 1 3390 1 chr3D.!!$F8 3389
1 TraesCS3D01G481100 chr3D 579580369 579584015 3646 True 770.60 2787 88.808000 35 3390 5 chr3D.!!$R3 3355
2 TraesCS3D01G481100 chr3D 567371516 567372029 513 False 300.00 300 77.395000 1639 2156 1 chr3D.!!$F5 517
3 TraesCS3D01G481100 chr3B 773746225 773748445 2220 False 1083.50 1884 86.051000 199 2371 2 chr3B.!!$F4 2172
4 TraesCS3D01G481100 chr3B 684512322 684513956 1634 True 785.00 785 76.163000 1023 2698 1 chr3B.!!$R3 1675
5 TraesCS3D01G481100 chr3B 773880497 773883579 3082 True 472.20 1144 87.658800 256 3390 5 chr3B.!!$R5 3134
6 TraesCS3D01G481100 chr3B 684504749 684505403 654 True 252.00 252 74.478000 1459 2101 1 chr3B.!!$R2 642
7 TraesCS3D01G481100 chr3B 754302750 754303446 696 False 207.00 207 73.241000 1454 2144 1 chr3B.!!$F1 690
8 TraesCS3D01G481100 chr3A 655568930 655570584 1654 True 887.00 887 77.022000 1023 2698 1 chr3A.!!$R1 1675
9 TraesCS3D01G481100 chr3A 714592985 714597950 4965 False 520.15 1775 92.741167 1 3390 6 chr3A.!!$F2 3389
10 TraesCS3D01G481100 chr3A 700351142 700352297 1155 True 492.00 492 75.145000 987 2156 1 chr3A.!!$R2 1169
11 TraesCS3D01G481100 chr3A 714603529 714604133 604 False 272.00 383 90.199500 35 583 2 chr3A.!!$F3 548
12 TraesCS3D01G481100 chr3A 701369970 701370483 513 False 261.00 261 76.099000 1639 2156 1 chr3A.!!$F1 517
13 TraesCS3D01G481100 chr2A 45080483 45081143 660 False 292.00 292 74.888000 1455 2118 1 chr2A.!!$F1 663

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
599 2354 0.036164 TGCATCGTGGGCACTTAACT 59.964 50.0 0.00 0.0 36.11 2.24 F
732 2581 0.250081 GATGCCCGAGGAATGAGGTC 60.250 60.0 0.00 0.0 0.00 3.85 F
843 2723 0.250166 CTCGGCTGCATCCATCATCA 60.250 55.0 7.47 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 3972 1.822506 GGCTACCACCCAAGAACTTC 58.177 55.000 0.0 0.0 0.0 3.01 R
1941 3991 4.431131 CCATCCCAAGGCACGGCT 62.431 66.667 0.0 0.0 0.0 5.52 R
2781 5228 4.764172 AGCACAATCTAGAATCTGACCAC 58.236 43.478 0.0 0.0 0.0 4.16 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
32 33 0.602638 TCGATAACCATGATGCCCGC 60.603 55.000 0.00 0.00 0.00 6.13
44 1189 2.158769 TGATGCCCGCTACAAGATGAAT 60.159 45.455 0.00 0.00 0.00 2.57
206 1803 5.459536 TGGCATAGACAACTATAGCTCAG 57.540 43.478 0.00 0.00 37.24 3.35
221 1818 0.731417 CTCAGTTGCACAGCTATGGC 59.269 55.000 0.00 0.00 39.06 4.40
289 1887 9.838339 AAACATGACCAAAATTACCAATAACAA 57.162 25.926 0.00 0.00 0.00 2.83
332 1933 4.807304 TGAGTTAAACACGAGGTTTCAGAC 59.193 41.667 11.97 10.06 46.61 3.51
387 1997 1.315257 AAACCATGGCGATGCTCCAC 61.315 55.000 13.04 0.00 36.26 4.02
392 2002 4.148825 GGCGATGCTCCACTCCGT 62.149 66.667 0.00 0.00 0.00 4.69
432 2138 1.440893 CAGATCAGCGTGGGGAGAG 59.559 63.158 0.00 0.00 0.00 3.20
445 2151 1.296715 GGAGAGAACCACCACGCAT 59.703 57.895 0.00 0.00 0.00 4.73
525 2237 5.536554 TGAATTCATCGAAGTTCAGAAGC 57.463 39.130 3.38 2.24 0.00 3.86
526 2238 4.996758 TGAATTCATCGAAGTTCAGAAGCA 59.003 37.500 3.38 4.43 0.00 3.91
528 2240 3.942130 TCATCGAAGTTCAGAAGCAGA 57.058 42.857 3.32 0.00 0.00 4.26
529 2241 4.462508 TCATCGAAGTTCAGAAGCAGAT 57.537 40.909 3.32 0.00 0.00 2.90
530 2242 4.428209 TCATCGAAGTTCAGAAGCAGATC 58.572 43.478 3.32 0.00 0.00 2.75
533 2245 3.256879 TCGAAGTTCAGAAGCAGATCAGT 59.743 43.478 3.32 0.00 0.00 3.41
551 2274 1.135257 AGTGTAGCTCTGCTTGTAGCG 60.135 52.381 0.00 0.00 46.26 4.26
587 2310 2.223595 CGAGTACTGAATCCTGCATCGT 60.224 50.000 0.00 0.00 0.00 3.73
588 2311 3.119291 GAGTACTGAATCCTGCATCGTG 58.881 50.000 0.00 0.00 0.00 4.35
590 2313 0.107508 ACTGAATCCTGCATCGTGGG 60.108 55.000 0.00 0.00 0.00 4.61
591 2314 1.442526 CTGAATCCTGCATCGTGGGC 61.443 60.000 0.00 0.00 0.00 5.36
592 2315 1.451927 GAATCCTGCATCGTGGGCA 60.452 57.895 0.00 0.00 39.32 5.36
593 2316 1.718757 GAATCCTGCATCGTGGGCAC 61.719 60.000 0.00 0.00 36.11 5.01
599 2354 0.036164 TGCATCGTGGGCACTTAACT 59.964 50.000 0.00 0.00 36.11 2.24
622 2377 5.556355 ACACTGAATCAATGCATACACTG 57.444 39.130 0.00 0.00 0.00 3.66
624 2379 5.122869 ACACTGAATCAATGCATACACTGAC 59.877 40.000 0.00 0.00 34.34 3.51
625 2380 5.122711 CACTGAATCAATGCATACACTGACA 59.877 40.000 0.00 0.00 34.34 3.58
626 2381 5.122869 ACTGAATCAATGCATACACTGACAC 59.877 40.000 0.00 0.00 34.34 3.67
627 2382 5.002516 TGAATCAATGCATACACTGACACA 58.997 37.500 0.00 1.66 34.34 3.72
628 2383 5.472820 TGAATCAATGCATACACTGACACAA 59.527 36.000 0.00 0.00 34.34 3.33
660 2496 4.143200 TGCAGTACACGAATTCGAATGAAC 60.143 41.667 33.05 20.69 43.02 3.18
663 2499 6.359545 CAGTACACGAATTCGAATGAACAAA 58.640 36.000 33.05 5.94 43.02 2.83
666 2502 8.714179 AGTACACGAATTCGAATGAACAAAATA 58.286 29.630 33.05 6.71 43.02 1.40
667 2503 9.485591 GTACACGAATTCGAATGAACAAAATAT 57.514 29.630 33.05 3.39 43.02 1.28
677 2513 6.912591 CGAATGAACAAAATATACCTTGCTCC 59.087 38.462 0.00 0.00 0.00 4.70
701 2550 3.383825 GCTCTGGATTTCAATTGATGCCT 59.616 43.478 9.40 0.00 0.00 4.75
709 2558 4.374843 TTCAATTGATGCCTTTCGATGG 57.625 40.909 9.40 1.06 0.00 3.51
726 2575 2.423446 GCGAGATGCCCGAGGAAT 59.577 61.111 0.00 0.00 37.76 3.01
728 2577 1.742146 CGAGATGCCCGAGGAATGA 59.258 57.895 0.00 0.00 0.00 2.57
729 2578 0.319383 CGAGATGCCCGAGGAATGAG 60.319 60.000 0.00 0.00 0.00 2.90
731 2580 0.692419 AGATGCCCGAGGAATGAGGT 60.692 55.000 0.00 0.00 0.00 3.85
732 2581 0.250081 GATGCCCGAGGAATGAGGTC 60.250 60.000 0.00 0.00 0.00 3.85
744 2593 2.760385 GAGGTCCTGAGGTCGGGG 60.760 72.222 0.00 0.00 42.72 5.73
787 2665 2.652095 CCGCCGGTAGGGTTCAGAA 61.652 63.158 1.90 0.00 38.44 3.02
800 2679 0.473755 TTCAGAACTGAAGGCTGGCA 59.526 50.000 12.40 0.00 43.90 4.92
804 2683 1.228367 AACTGAAGGCTGGCACTGG 60.228 57.895 3.38 0.00 0.00 4.00
805 2684 1.708993 AACTGAAGGCTGGCACTGGA 61.709 55.000 3.38 0.00 0.00 3.86
812 2692 4.039092 CTGGCACTGGACTGGGGG 62.039 72.222 0.00 0.00 0.00 5.40
827 2707 4.883354 GGGAATGGGCTGGCCTCG 62.883 72.222 21.72 0.00 36.10 4.63
841 2721 1.072678 CCTCGGCTGCATCCATCAT 59.927 57.895 7.47 0.00 0.00 2.45
842 2722 0.954449 CCTCGGCTGCATCCATCATC 60.954 60.000 7.47 0.00 0.00 2.92
843 2723 0.250166 CTCGGCTGCATCCATCATCA 60.250 55.000 7.47 0.00 0.00 3.07
844 2724 0.250166 TCGGCTGCATCCATCATCAG 60.250 55.000 7.47 0.00 0.00 2.90
908 2805 1.268625 CCCGTTTAAGCCCAGTTCAAC 59.731 52.381 0.00 0.00 0.00 3.18
946 2869 1.628846 GAGAGCAAAACCTACCTCCCA 59.371 52.381 0.00 0.00 0.00 4.37
1187 3180 2.041819 CCCCCTCCTCTACGGCTT 60.042 66.667 0.00 0.00 0.00 4.35
1401 3418 4.752879 TGCAACCCCGCTACTCGC 62.753 66.667 0.00 0.00 36.73 5.03
1808 3855 2.287788 GCATGTCCGGCTTTAATGATGG 60.288 50.000 0.00 0.00 0.00 3.51
1851 3898 2.113433 GGCGCAGGACTACGAGAGA 61.113 63.158 10.83 0.00 0.00 3.10
1925 3972 1.862411 GCGGTTTGGAAAGTTTGACGG 60.862 52.381 0.00 0.00 0.00 4.79
1941 3991 1.426751 ACGGAAGTTCTTGGGTGGTA 58.573 50.000 2.25 0.00 46.40 3.25
2109 4159 4.618920 ACATACCTTCTTTCCGACACTT 57.381 40.909 0.00 0.00 0.00 3.16
2251 4306 5.573337 ATGAGCCTGCTAGTTTCATTTTC 57.427 39.130 0.00 0.00 0.00 2.29
2286 4342 8.097038 ACAAGTTATGATCAAGAAGCTTGACTA 58.903 33.333 25.46 5.14 36.54 2.59
2293 4354 9.842775 ATGATCAAGAAGCTTGACTATTTCATA 57.157 29.630 2.10 0.00 32.84 2.15
2344 4417 2.047274 GCTGAAGTGGCTGCCGTA 60.047 61.111 14.98 0.00 0.00 4.02
2360 4433 3.932710 TGCCGTAAGTCTTGATGCTAAAG 59.067 43.478 0.00 0.00 0.00 1.85
2383 4489 7.484035 AGTTGCAAGTCTCTGTTTACTTAAG 57.516 36.000 0.00 0.00 34.23 1.85
2538 4650 9.866655 TGAGGCAGATTATCCTGTTTTAATTAT 57.133 29.630 0.00 0.00 36.57 1.28
2700 4820 8.793592 ACTTTATCTGTGACCATTTTAAGGAAC 58.206 33.333 0.00 0.00 0.00 3.62
2737 4857 9.013229 TGTGATGTTTGATCTTAACATAAGCTT 57.987 29.630 19.80 3.48 44.05 3.74
2756 4876 9.920946 ATAAGCTTGAGAAATGGAACCTTTATA 57.079 29.630 9.86 0.00 0.00 0.98
2758 4878 8.829373 AGCTTGAGAAATGGAACCTTTATATT 57.171 30.769 0.00 0.00 0.00 1.28
2759 4879 8.689972 AGCTTGAGAAATGGAACCTTTATATTG 58.310 33.333 0.00 0.00 0.00 1.90
2789 5236 2.317040 AGAAAGGTTCTCGTGGTCAGA 58.683 47.619 0.00 0.00 34.07 3.27
2897 5357 1.413077 ACTATGAGCCGGCTAGTTTCC 59.587 52.381 32.97 16.94 0.00 3.13
2912 5372 6.315642 GGCTAGTTTCCTTTTATGTACTGACC 59.684 42.308 0.00 0.00 0.00 4.02
2915 5375 5.699458 AGTTTCCTTTTATGTACTGACCGTG 59.301 40.000 0.00 0.00 0.00 4.94
2917 5377 5.981088 TCCTTTTATGTACTGACCGTGTA 57.019 39.130 0.00 0.00 0.00 2.90
2920 5380 8.065473 TCCTTTTATGTACTGACCGTGTAATA 57.935 34.615 0.00 0.00 0.00 0.98
2961 5422 7.581213 ACTTGTGAAAAACTGTGAATATCCA 57.419 32.000 0.00 0.00 0.00 3.41
3001 5494 2.968574 TGGCCAGCTTTTGAAATGGTTA 59.031 40.909 0.00 0.00 35.17 2.85
3020 5513 4.396166 GGTTACCATTGATCTGTCTTGTGG 59.604 45.833 0.00 0.00 0.00 4.17
3024 5517 2.084610 TTGATCTGTCTTGTGGCTCG 57.915 50.000 0.00 0.00 0.00 5.03
3111 5612 7.004086 TCTTAAAGGTCATCAGTGGTTTCATT 58.996 34.615 0.00 0.00 0.00 2.57
3197 5698 5.797051 TCAAACGGCCTAGTTGTTAGTAAT 58.203 37.500 0.00 0.00 34.14 1.89
3244 5745 5.529060 GCTGCTATATAAAGTTTGAGCCTGT 59.471 40.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.514441 GCATGGACTCCATTCATCTTGTAG 59.486 45.833 7.95 0.00 42.23 2.74
44 1189 0.900421 CAGACTCAGCATGGACTCCA 59.100 55.000 0.00 0.00 38.19 3.86
115 1260 9.608617 CTGCTCATCATGTATGATAAAAATGTC 57.391 33.333 7.01 0.00 45.23 3.06
206 1803 1.167851 TTCTGCCATAGCTGTGCAAC 58.832 50.000 4.68 0.00 40.80 4.17
296 1897 8.853345 TCGTGTTTAACTCAGTTCGAATAATAC 58.147 33.333 0.00 0.00 0.00 1.89
315 1916 9.456347 AACTACAGAGTCTGAAACCTCGTGTTT 62.456 40.741 26.86 1.79 41.86 2.83
332 1933 7.444183 TCTGAAACCAACCAATTAACTACAGAG 59.556 37.037 0.00 0.00 0.00 3.35
392 2002 3.245346 TCACGATGTGGTGGCCCA 61.245 61.111 0.00 0.00 38.46 5.36
398 2014 0.969149 TCTGCTTCTCACGATGTGGT 59.031 50.000 0.00 0.00 33.87 4.16
401 2107 2.738000 GCTGATCTGCTTCTCACGATGT 60.738 50.000 16.60 0.00 0.00 3.06
407 2113 0.108472 CCACGCTGATCTGCTTCTCA 60.108 55.000 20.58 0.00 0.00 3.27
466 2172 6.985188 TCCTGTGTGTTAGATTTTATCAGC 57.015 37.500 0.00 0.00 0.00 4.26
526 2238 2.830923 ACAAGCAGAGCTACACTGATCT 59.169 45.455 5.14 0.00 38.25 2.75
528 2240 3.430098 GCTACAAGCAGAGCTACACTGAT 60.430 47.826 5.14 0.00 41.89 2.90
529 2241 2.094494 GCTACAAGCAGAGCTACACTGA 60.094 50.000 5.14 0.00 41.89 3.41
530 2242 2.266554 GCTACAAGCAGAGCTACACTG 58.733 52.381 0.00 0.00 41.89 3.66
533 2245 0.173481 CCGCTACAAGCAGAGCTACA 59.827 55.000 0.00 0.00 42.58 2.74
568 2291 2.159043 CCACGATGCAGGATTCAGTACT 60.159 50.000 0.00 0.00 0.00 2.73
587 2310 4.041075 TGATTCAGTGTAGTTAAGTGCCCA 59.959 41.667 0.00 0.00 0.00 5.36
588 2311 4.575885 TGATTCAGTGTAGTTAAGTGCCC 58.424 43.478 0.00 0.00 0.00 5.36
590 2313 6.024049 GCATTGATTCAGTGTAGTTAAGTGC 58.976 40.000 10.42 0.00 0.00 4.40
591 2314 7.132694 TGCATTGATTCAGTGTAGTTAAGTG 57.867 36.000 10.42 0.00 0.00 3.16
592 2315 7.928307 ATGCATTGATTCAGTGTAGTTAAGT 57.072 32.000 10.42 0.00 0.00 2.24
593 2316 8.882736 TGTATGCATTGATTCAGTGTAGTTAAG 58.117 33.333 3.54 0.00 0.00 1.85
599 2354 6.313658 GTCAGTGTATGCATTGATTCAGTGTA 59.686 38.462 11.90 6.71 42.07 2.90
636 2472 3.991121 TCATTCGAATTCGTGTACTGCAA 59.009 39.130 25.93 11.67 40.80 4.08
660 2496 5.008415 CAGAGCAGGAGCAAGGTATATTTTG 59.992 44.000 0.00 0.00 45.49 2.44
663 2499 3.072184 CCAGAGCAGGAGCAAGGTATATT 59.928 47.826 0.00 0.00 45.49 1.28
666 2502 0.835941 CCAGAGCAGGAGCAAGGTAT 59.164 55.000 0.00 0.00 45.49 2.73
667 2503 0.252239 TCCAGAGCAGGAGCAAGGTA 60.252 55.000 0.00 0.00 45.49 3.08
677 2513 4.360563 GCATCAATTGAAATCCAGAGCAG 58.639 43.478 13.09 0.00 0.00 4.24
709 2558 1.958205 CATTCCTCGGGCATCTCGC 60.958 63.158 0.00 0.00 41.28 5.03
710 2559 0.319383 CTCATTCCTCGGGCATCTCG 60.319 60.000 0.00 0.00 0.00 4.04
725 2574 1.381872 CCCGACCTCAGGACCTCAT 60.382 63.158 0.00 0.00 0.00 2.90
726 2575 2.037367 CCCGACCTCAGGACCTCA 59.963 66.667 0.00 0.00 0.00 3.86
787 2665 2.149383 TCCAGTGCCAGCCTTCAGT 61.149 57.895 0.00 0.00 0.00 3.41
800 2679 1.930656 CCCATTCCCCCAGTCCAGT 60.931 63.158 0.00 0.00 0.00 4.00
804 2683 2.276740 CAGCCCATTCCCCCAGTC 59.723 66.667 0.00 0.00 0.00 3.51
805 2684 3.350163 CCAGCCCATTCCCCCAGT 61.350 66.667 0.00 0.00 0.00 4.00
824 2704 0.250166 TGATGATGGATGCAGCCGAG 60.250 55.000 17.68 0.00 0.00 4.63
827 2707 0.952280 CACTGATGATGGATGCAGCC 59.048 55.000 15.83 15.83 31.74 4.85
829 2709 1.605753 CCCACTGATGATGGATGCAG 58.394 55.000 0.00 0.00 39.87 4.41
841 2721 2.528818 CCTTCCACTGGCCCACTGA 61.529 63.158 0.00 0.00 0.00 3.41
842 2722 2.034687 CCTTCCACTGGCCCACTG 59.965 66.667 0.00 0.00 0.00 3.66
843 2723 3.971702 GCCTTCCACTGGCCCACT 61.972 66.667 0.00 0.00 44.32 4.00
908 2805 2.420372 TCTCTCGTCTCGTGGATTGAAG 59.580 50.000 0.00 0.00 0.00 3.02
1339 3356 0.250295 CTGGTGTTGCGGAAGGAGAA 60.250 55.000 0.00 0.00 0.00 2.87
1401 3418 3.155167 GGGAGGGGAGCGTACTGG 61.155 72.222 0.00 0.00 0.00 4.00
1808 3855 3.490348 CAGATATCAATGGTTGTCCCCC 58.510 50.000 5.32 0.00 0.00 5.40
1925 3972 1.822506 GGCTACCACCCAAGAACTTC 58.177 55.000 0.00 0.00 0.00 3.01
1941 3991 4.431131 CCATCCCAAGGCACGGCT 62.431 66.667 0.00 0.00 0.00 5.52
2251 4306 8.374327 TCTTGATCATAACTTGTCTATGCATG 57.626 34.615 10.16 0.00 0.00 4.06
2344 4417 5.300286 ACTTGCAACTTTAGCATCAAGACTT 59.700 36.000 0.00 0.00 42.33 3.01
2360 4433 7.011109 TCACTTAAGTAAACAGAGACTTGCAAC 59.989 37.037 8.04 0.00 36.58 4.17
2485 4593 6.551736 TCTTGTCAGCTAAAACAAAACAGAC 58.448 36.000 9.10 0.00 35.13 3.51
2685 4805 7.610865 TGAATCATTGGTTCCTTAAAATGGTC 58.389 34.615 7.19 0.00 32.17 4.02
2700 4820 7.489160 AGATCAAACATCACATGAATCATTGG 58.511 34.615 0.00 0.00 0.00 3.16
2756 4876 8.968969 ACGAGAACCTTTCTACTACTTATCAAT 58.031 33.333 0.00 0.00 40.87 2.57
2758 4878 7.148120 CCACGAGAACCTTTCTACTACTTATCA 60.148 40.741 0.00 0.00 40.87 2.15
2759 4879 7.148103 ACCACGAGAACCTTTCTACTACTTATC 60.148 40.741 0.00 0.00 40.87 1.75
2778 4901 5.039984 CACAATCTAGAATCTGACCACGAG 58.960 45.833 0.00 0.00 0.00 4.18
2781 5228 4.764172 AGCACAATCTAGAATCTGACCAC 58.236 43.478 0.00 0.00 0.00 4.16
2789 5236 8.814038 ATTTAAAGTGGAGCACAATCTAGAAT 57.186 30.769 0.00 0.00 36.74 2.40
2897 5357 8.922058 ACTATTACACGGTCAGTACATAAAAG 57.078 34.615 0.00 0.00 0.00 2.27
2920 5380 9.979578 TTTCACAAGTATAAATTTCATGCAACT 57.020 25.926 0.00 0.00 0.00 3.16
2944 5404 6.013466 AGCCCAAATGGATATTCACAGTTTTT 60.013 34.615 0.00 0.00 37.39 1.94
2961 5422 2.224354 CCAAAACAGCTTCAGCCCAAAT 60.224 45.455 0.00 0.00 43.38 2.32
3001 5494 2.040813 AGCCACAAGACAGATCAATGGT 59.959 45.455 0.00 0.00 0.00 3.55
3020 5513 2.616842 TCAGTTCAAAGGAAAACCGAGC 59.383 45.455 0.00 0.00 34.13 5.03
3024 5517 7.222805 GTCAATTCTTCAGTTCAAAGGAAAACC 59.777 37.037 0.00 0.00 34.13 3.27
3083 5581 6.884280 AACCACTGATGACCTTTAAGAAAG 57.116 37.500 0.00 0.00 38.24 2.62
3218 5719 5.994668 AGGCTCAAACTTTATATAGCAGCTC 59.005 40.000 0.00 0.00 0.00 4.09
3244 5745 0.829990 TATGCATCGACAGAAGCCCA 59.170 50.000 0.19 0.00 40.09 5.36


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

AutoCloner maintained by Alex Coulton.