Multiple sequence alignment - TraesCS3B01G416000

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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 TraesCS3B01G416000 chr3B 100.000 3949 0 0 1 3949 652733724 652737672 0.000000e+00 7293.0
1 TraesCS3B01G416000 chr3B 87.826 575 56 7 1249 1811 304807207 304806635 0.000000e+00 662.0
2 TraesCS3B01G416000 chr3B 77.326 172 25 9 329 495 810285429 810285591 5.440000e-14 89.8
3 TraesCS3B01G416000 chr3B 92.500 40 3 0 505 544 426999786 426999825 1.530000e-04 58.4
4 TraesCS3B01G416000 chr3D 93.476 3265 149 35 211 3434 490833594 490836835 0.000000e+00 4791.0
5 TraesCS3B01G416000 chr3D 84.760 479 33 5 3476 3936 490837089 490837545 1.010000e-120 444.0
6 TraesCS3B01G416000 chr3D 78.017 232 18 15 1 201 490832975 490833204 8.970000e-22 115.0
7 TraesCS3B01G416000 chr3A 92.912 2624 111 29 865 3434 633052725 633055327 0.000000e+00 3746.0
8 TraesCS3B01G416000 chr3A 87.377 713 50 19 127 819 633051610 633052302 0.000000e+00 782.0
9 TraesCS3B01G416000 chr3A 87.449 494 25 9 3476 3949 633055610 633056086 5.810000e-148 534.0
10 TraesCS3B01G416000 chr3A 81.250 192 28 7 308 495 51283552 51283365 8.840000e-32 148.0
11 TraesCS3B01G416000 chr7B 78.000 300 45 18 193 484 24416379 24416665 6.790000e-38 169.0
12 TraesCS3B01G416000 chr7B 79.235 183 29 6 326 504 252682329 252682152 6.930000e-23 119.0
13 TraesCS3B01G416000 chr7B 77.368 190 23 12 321 506 72507481 72507654 1.170000e-15 95.3
14 TraesCS3B01G416000 chr7B 95.122 41 2 0 504 544 506757951 506757911 9.160000e-07 65.8
15 TraesCS3B01G416000 chr2D 79.528 254 34 9 247 495 336965914 336965674 8.780000e-37 165.0
16 TraesCS3B01G416000 chr2D 80.435 184 29 3 324 505 126144484 126144306 2.480000e-27 134.0
17 TraesCS3B01G416000 chr2D 78.641 103 12 7 263 356 580189546 580189445 4.260000e-05 60.2
18 TraesCS3B01G416000 chr7D 79.116 249 36 13 241 484 77494737 77494974 1.470000e-34 158.0
19 TraesCS3B01G416000 chr7D 95.122 41 2 0 504 544 481179873 481179833 9.160000e-07 65.8
20 TraesCS3B01G416000 chr5D 77.778 288 41 18 213 495 254833833 254834102 5.280000e-34 156.0
21 TraesCS3B01G416000 chr5A 77.352 287 49 8 213 495 338233357 338233631 5.280000e-34 156.0
22 TraesCS3B01G416000 chr2A 78.431 255 36 10 246 495 447145754 447145514 8.840000e-32 148.0
23 TraesCS3B01G416000 chr4D 76.226 265 42 14 232 487 501046344 501046092 1.930000e-23 121.0
24 TraesCS3B01G416000 chr4D 83.333 78 8 4 397 471 10100747 10100822 2.550000e-07 67.6
25 TraesCS3B01G416000 chr7A 79.058 191 18 16 313 499 715708973 715709145 1.160000e-20 111.0
26 TraesCS3B01G416000 chr1D 78.344 157 24 6 326 479 156123362 156123213 4.200000e-15 93.5
27 TraesCS3B01G416000 chr1D 79.231 130 22 5 1045 1170 360481297 360481169 7.030000e-13 86.1
28 TraesCS3B01G416000 chr1D 91.111 45 3 1 502 546 22626868 22626911 4.260000e-05 60.2
29 TraesCS3B01G416000 chr1A 80.508 118 21 2 1040 1156 460334235 460334119 5.440000e-14 89.8
30 TraesCS3B01G416000 chr1B 83.544 79 13 0 1045 1123 482716644 482716566 1.520000e-09 75.0
31 TraesCS3B01G416000 chr1B 97.561 41 1 0 505 545 4789427 4789387 1.970000e-08 71.3
32 TraesCS3B01G416000 chr1B 92.857 42 2 1 505 546 38831152 38831112 4.260000e-05 60.2


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 TraesCS3B01G416000 chr3B 652733724 652737672 3948 False 7293.000000 7293 100.000000 1 3949 1 chr3B.!!$F2 3948
1 TraesCS3B01G416000 chr3B 304806635 304807207 572 True 662.000000 662 87.826000 1249 1811 1 chr3B.!!$R1 562
2 TraesCS3B01G416000 chr3D 490832975 490837545 4570 False 1783.333333 4791 85.417667 1 3936 3 chr3D.!!$F1 3935
3 TraesCS3B01G416000 chr3A 633051610 633056086 4476 False 1687.333333 3746 89.246000 127 3949 3 chr3A.!!$F1 3822

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
862 1387 1.094073 TCTCCCTCCGTCGTTCGATC 61.094 60.0 0.00 0.00 42.86 3.69 F
1281 2112 0.104120 TCTGTGGTGACGTGACCTTG 59.896 55.0 24.85 14.18 36.88 3.61 F
1755 2606 0.397675 TGATCATCCTCCACGCTCCT 60.398 55.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2950 1.623811 ACCTAACAAGACACGGCATCT 59.376 47.619 0.00 0.0 0.00 2.90 R
2888 3744 0.406361 AGGGAAGTGAGTCGTCCTCT 59.594 55.000 7.13 1.7 42.82 3.69 R
3552 4664 0.035915 GACTTCTTCAGCCACCTCCC 60.036 60.000 0.00 0.0 0.00 4.30 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
24 25 3.042059 TCTCCCTAATAAAGACCGGCT 57.958 47.619 0.00 0.00 0.00 5.52
25 26 2.963782 TCTCCCTAATAAAGACCGGCTC 59.036 50.000 0.00 0.00 0.00 4.70
26 27 2.966516 CTCCCTAATAAAGACCGGCTCT 59.033 50.000 0.00 0.10 0.00 4.09
36 37 2.045926 CCGGCTCTGTCCCTTTGG 60.046 66.667 0.00 0.00 0.00 3.28
47 48 3.028130 TGTCCCTTTGGAAAACAAGGTC 58.972 45.455 0.00 0.00 44.07 3.85
48 49 3.296854 GTCCCTTTGGAAAACAAGGTCT 58.703 45.455 0.00 0.00 44.07 3.85
50 51 4.161565 GTCCCTTTGGAAAACAAGGTCTTT 59.838 41.667 0.00 0.00 44.07 2.52
51 52 4.404394 TCCCTTTGGAAAACAAGGTCTTTC 59.596 41.667 0.00 0.00 40.82 2.62
67 68 6.890293 AGGTCTTTCCTATGATAGAACCAAC 58.110 40.000 0.00 0.00 46.10 3.77
69 70 6.987404 GGTCTTTCCTATGATAGAACCAACTC 59.013 42.308 0.00 0.00 32.07 3.01
70 71 6.987404 GTCTTTCCTATGATAGAACCAACTCC 59.013 42.308 0.00 0.00 31.56 3.85
79 80 1.202651 AGAACCAACTCCAAGACCACG 60.203 52.381 0.00 0.00 0.00 4.94
84 85 2.032924 CCAACTCCAAGACCACGAAAAC 59.967 50.000 0.00 0.00 0.00 2.43
86 87 2.993937 ACTCCAAGACCACGAAAACAA 58.006 42.857 0.00 0.00 0.00 2.83
100 101 8.573035 ACCACGAAAACAATAGACAACATTTAT 58.427 29.630 0.00 0.00 0.00 1.40
157 187 9.935241 ATGCCATGTATTTATCTCTACTACAAG 57.065 33.333 0.00 0.00 0.00 3.16
177 207 5.222130 ACAAGAGGGGAGTTGATGTTTGTAT 60.222 40.000 0.00 0.00 0.00 2.29
179 209 4.536090 AGAGGGGAGTTGATGTTTGTATGA 59.464 41.667 0.00 0.00 0.00 2.15
180 210 4.848357 AGGGGAGTTGATGTTTGTATGAG 58.152 43.478 0.00 0.00 0.00 2.90
201 231 5.014123 TGAGATCAAATGTAGTTTCACCCCT 59.986 40.000 0.00 0.00 0.00 4.79
203 233 4.715534 TCAAATGTAGTTTCACCCCTCA 57.284 40.909 0.00 0.00 0.00 3.86
261 671 6.434340 GTGTTTTCCTTTCCTCATCCTTATGT 59.566 38.462 0.00 0.00 34.50 2.29
286 696 3.065786 ACCATGTTCTGCGCTAATCAATG 59.934 43.478 9.73 5.80 0.00 2.82
308 718 9.806203 CAATGAAATCTTACTAAAATCATGCCA 57.194 29.630 0.00 0.00 0.00 4.92
360 773 5.359860 ACCAAAACCTCAACTAAGTCCAAAG 59.640 40.000 0.00 0.00 0.00 2.77
387 800 9.981460 AAAAATCTTGACTTTCTCTACCCATAT 57.019 29.630 0.00 0.00 0.00 1.78
388 801 9.620259 AAAATCTTGACTTTCTCTACCCATATC 57.380 33.333 0.00 0.00 0.00 1.63
389 802 6.732896 TCTTGACTTTCTCTACCCATATCC 57.267 41.667 0.00 0.00 0.00 2.59
392 805 8.010697 TCTTGACTTTCTCTACCCATATCCATA 58.989 37.037 0.00 0.00 0.00 2.74
395 808 6.635021 ACTTTCTCTACCCATATCCATACCT 58.365 40.000 0.00 0.00 0.00 3.08
457 872 3.280938 TTCCCTTCCCGCACCCATG 62.281 63.158 0.00 0.00 0.00 3.66
537 953 3.587506 ACCACTAGAATATGTATGCCCCC 59.412 47.826 0.00 0.00 0.00 5.40
538 954 3.587061 CCACTAGAATATGTATGCCCCCA 59.413 47.826 0.00 0.00 0.00 4.96
825 1350 7.407337 GCGTATAAGTTCGAAAAATTCTCCAT 58.593 34.615 0.00 0.00 0.00 3.41
862 1387 1.094073 TCTCCCTCCGTCGTTCGATC 61.094 60.000 0.00 0.00 42.86 3.69
911 1718 3.470709 CAGGACAAGGCATACATACAGG 58.529 50.000 0.00 0.00 0.00 4.00
912 1719 3.115390 AGGACAAGGCATACATACAGGT 58.885 45.455 0.00 0.00 0.00 4.00
1225 2055 3.511477 AGCTCTAGGTCTTTCTGGTTCA 58.489 45.455 0.00 0.00 0.00 3.18
1281 2112 0.104120 TCTGTGGTGACGTGACCTTG 59.896 55.000 24.85 14.18 36.88 3.61
1366 2197 0.618458 GGGATGGTCACCAGTAAGCA 59.382 55.000 1.19 0.00 36.75 3.91
1371 2202 1.204704 TGGTCACCAGTAAGCATCTCG 59.795 52.381 0.00 0.00 0.00 4.04
1373 2204 2.263077 GTCACCAGTAAGCATCTCGTG 58.737 52.381 0.00 0.00 0.00 4.35
1401 2236 1.695242 TGCCCTTCGTCTGTTCCTTAA 59.305 47.619 0.00 0.00 0.00 1.85
1419 2254 8.689972 GTTCCTTAATCATGTGAGAATTGGATT 58.310 33.333 0.00 0.00 0.00 3.01
1582 2426 7.223193 ACGTTTTAGCTCGCATGTATAACATTA 59.777 33.333 0.00 0.00 36.53 1.90
1755 2606 0.397675 TGATCATCCTCCACGCTCCT 60.398 55.000 0.00 0.00 0.00 3.69
1834 2685 1.629353 AGCTCCCATGCTATCTCCATG 59.371 52.381 0.00 0.00 42.10 3.66
2008 2859 6.741992 TCTATGTTGGTATTTGCTCTGTTG 57.258 37.500 0.00 0.00 0.00 3.33
2063 2914 3.055385 TGCGCCTCTGGTTTCTTATAGTT 60.055 43.478 4.18 0.00 0.00 2.24
2068 2919 5.354513 GCCTCTGGTTTCTTATAGTTGGTTC 59.645 44.000 0.00 0.00 0.00 3.62
2072 2923 6.993902 TCTGGTTTCTTATAGTTGGTTCGTTT 59.006 34.615 0.00 0.00 0.00 3.60
2170 3021 2.871096 AAACTTACCATTCAGGGCGA 57.129 45.000 0.00 0.00 43.89 5.54
2450 3305 5.527214 TCAGGCATTGGATACTTTCAATACG 59.473 40.000 0.00 0.00 32.92 3.06
2555 3411 2.885135 ACATCAGGCATTCTTGACCA 57.115 45.000 0.00 0.00 0.00 4.02
2556 3412 3.377253 ACATCAGGCATTCTTGACCAT 57.623 42.857 0.00 0.00 0.00 3.55
2566 3422 6.014327 AGGCATTCTTGACCATTGTGTTAATT 60.014 34.615 0.00 0.00 0.00 1.40
2572 3428 8.415950 TCTTGACCATTGTGTTAATTGGTTAT 57.584 30.769 0.00 0.00 0.00 1.89
2575 3431 7.825681 TGACCATTGTGTTAATTGGTTATCTG 58.174 34.615 0.00 0.00 0.00 2.90
2580 3436 9.559958 CATTGTGTTAATTGGTTATCTGACTTC 57.440 33.333 0.00 0.00 0.00 3.01
2760 3616 4.452455 GGTACAATGGCAGGAGAAATATCG 59.548 45.833 0.00 0.00 0.00 2.92
2767 3623 4.346709 TGGCAGGAGAAATATCGTATTCCA 59.653 41.667 0.00 0.00 0.00 3.53
2771 3627 4.989168 AGGAGAAATATCGTATTCCAACGC 59.011 41.667 0.00 0.00 42.56 4.84
2772 3628 4.748102 GGAGAAATATCGTATTCCAACGCA 59.252 41.667 0.00 0.00 42.56 5.24
2775 3631 5.462398 AGAAATATCGTATTCCAACGCACTC 59.538 40.000 0.00 0.00 42.56 3.51
2784 3640 3.829886 TCCAACGCACTCATCATTTTC 57.170 42.857 0.00 0.00 0.00 2.29
2866 3722 0.893270 TGGCACATCCAAGGAAACGG 60.893 55.000 0.00 0.00 43.21 4.44
2867 3723 1.212751 GCACATCCAAGGAAACGGC 59.787 57.895 0.00 0.00 0.00 5.68
2868 3724 1.501741 CACATCCAAGGAAACGGCG 59.498 57.895 4.80 4.80 0.00 6.46
2888 3744 0.869730 GCGACGTAGGGAAGCAAAAA 59.130 50.000 0.00 0.00 0.00 1.94
2897 3753 1.535896 GGGAAGCAAAAAGAGGACGAC 59.464 52.381 0.00 0.00 0.00 4.34
3011 3867 1.457346 CCTCAAGACCTTCATGTGGC 58.543 55.000 7.28 2.14 0.00 5.01
3022 3878 3.717294 ATGTGGCGAGGGTGGACC 61.717 66.667 0.00 0.00 40.67 4.46
3058 3924 1.153168 CGGTACAAGGCCATCCTGG 60.153 63.158 5.01 0.00 43.40 4.45
3143 4009 1.467035 CGTCGGAGCTAGGTGTTGTAC 60.467 57.143 0.00 0.00 0.00 2.90
3144 4010 0.806868 TCGGAGCTAGGTGTTGTACG 59.193 55.000 0.00 0.00 0.00 3.67
3145 4011 0.806868 CGGAGCTAGGTGTTGTACGA 59.193 55.000 0.00 0.00 0.00 3.43
3146 4012 1.404391 CGGAGCTAGGTGTTGTACGAT 59.596 52.381 0.00 0.00 0.00 3.73
3150 4016 4.357996 GAGCTAGGTGTTGTACGATTACC 58.642 47.826 0.00 10.18 0.00 2.85
3155 4021 3.322828 AGGTGTTGTACGATTACCTGTGT 59.677 43.478 16.97 0.00 40.11 3.72
3166 4032 7.166691 ACGATTACCTGTGTACTGTAGAAAT 57.833 36.000 0.00 0.00 0.00 2.17
3182 4051 3.989698 AATCGCGCCGTGTGAGGAG 62.990 63.158 0.00 0.00 41.19 3.69
3223 4092 4.908601 TTGTGAGGGATGTTGTAGATGT 57.091 40.909 0.00 0.00 0.00 3.06
3321 4190 1.084370 CCTCGGGATGTTTCAGTCGC 61.084 60.000 0.00 0.00 0.00 5.19
3340 4209 4.615541 GTCGCTGTATTGTTTGTTTTAGGC 59.384 41.667 0.00 0.00 0.00 3.93
3361 4230 2.248280 TGCATTGTACACTCCGTTGT 57.752 45.000 0.00 0.00 0.00 3.32
3391 4260 3.243359 TGGAGAAGCAATTCCACCTTT 57.757 42.857 0.00 0.00 38.53 3.11
3441 4310 3.676291 AGAAGGTTCTCTGCTGAGTTC 57.324 47.619 18.82 14.70 40.98 3.01
3447 4330 1.261480 TCTCTGCTGAGTTCCAGGTC 58.739 55.000 18.82 0.00 43.13 3.85
3489 4600 5.457140 ACCAAGCATTGTGTTGTAATAACG 58.543 37.500 0.00 0.00 46.99 3.18
3494 4605 2.865556 TGTGTTGTAATAACGCAGCG 57.134 45.000 14.82 14.82 35.94 5.18
3552 4664 3.989705 TGTGCAATATCTTCACGAACG 57.010 42.857 0.00 0.00 33.69 3.95
3604 4733 0.250338 GGAAACGTTCTGCAGGGTCT 60.250 55.000 15.13 0.00 0.00 3.85
3613 4742 1.160137 CTGCAGGGTCTTTTTCCTCG 58.840 55.000 5.57 0.00 0.00 4.63
3617 4746 0.602905 AGGGTCTTTTTCCTCGTGCG 60.603 55.000 0.00 0.00 0.00 5.34
3712 4846 1.043022 AAGGTGCAAAAGCCAAGGAG 58.957 50.000 0.00 0.00 0.00 3.69
3746 4880 1.130373 CGTATGAACTGCCGTGCAATT 59.870 47.619 0.00 0.00 38.41 2.32
3807 4941 3.978687 TCCGAACAGTGAGAAGTTCTTC 58.021 45.455 6.88 4.05 41.40 2.87
3813 4947 4.954875 ACAGTGAGAAGTTCTTCCTCTTG 58.045 43.478 6.88 3.56 0.00 3.02
3814 4948 3.745458 CAGTGAGAAGTTCTTCCTCTTGC 59.255 47.826 6.88 0.00 0.00 4.01
3815 4949 3.070748 GTGAGAAGTTCTTCCTCTTGCC 58.929 50.000 6.88 0.00 0.00 4.52
3816 4950 2.289072 TGAGAAGTTCTTCCTCTTGCCG 60.289 50.000 6.88 0.00 0.00 5.69
3817 4951 0.799393 GAAGTTCTTCCTCTTGCCGC 59.201 55.000 0.00 0.00 0.00 6.53
3818 4952 0.108585 AAGTTCTTCCTCTTGCCGCA 59.891 50.000 0.00 0.00 0.00 5.69
3819 4953 0.108585 AGTTCTTCCTCTTGCCGCAA 59.891 50.000 5.52 5.52 0.00 4.85
3820 4954 0.238553 GTTCTTCCTCTTGCCGCAAC 59.761 55.000 0.38 0.00 0.00 4.17
3821 4955 0.179032 TTCTTCCTCTTGCCGCAACA 60.179 50.000 0.38 0.00 0.00 3.33
3822 4956 0.603707 TCTTCCTCTTGCCGCAACAG 60.604 55.000 0.38 1.07 0.00 3.16
3823 4957 1.580845 CTTCCTCTTGCCGCAACAGG 61.581 60.000 18.67 18.67 32.09 4.00
3824 4958 2.032528 CCTCTTGCCGCAACAGGA 59.967 61.111 19.74 7.37 32.46 3.86
3825 4959 2.328099 CCTCTTGCCGCAACAGGAC 61.328 63.158 19.74 0.00 32.46 3.85
3836 4970 1.813513 CAACAGGACGGATGCTTTCT 58.186 50.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.966516 AGAGCCGGTCTTTATTAGGGAG 59.033 50.000 1.90 0.00 27.07 4.30
20 21 0.250727 TTTCCAAAGGGACAGAGCCG 60.251 55.000 0.00 0.00 44.89 5.52
24 25 3.295973 CCTTGTTTTCCAAAGGGACAGA 58.704 45.455 0.00 0.00 44.89 3.41
25 26 3.031013 ACCTTGTTTTCCAAAGGGACAG 58.969 45.455 6.42 0.00 44.89 3.51
26 27 3.028130 GACCTTGTTTTCCAAAGGGACA 58.972 45.455 6.42 0.00 44.89 4.02
47 48 6.889198 TGGAGTTGGTTCTATCATAGGAAAG 58.111 40.000 0.00 0.00 0.00 2.62
48 49 6.884472 TGGAGTTGGTTCTATCATAGGAAA 57.116 37.500 0.00 0.00 0.00 3.13
50 51 6.098409 GTCTTGGAGTTGGTTCTATCATAGGA 59.902 42.308 0.00 0.00 0.00 2.94
51 52 6.284459 GTCTTGGAGTTGGTTCTATCATAGG 58.716 44.000 0.00 0.00 0.00 2.57
67 68 4.994852 TCTATTGTTTTCGTGGTCTTGGAG 59.005 41.667 0.00 0.00 0.00 3.86
69 70 4.513692 TGTCTATTGTTTTCGTGGTCTTGG 59.486 41.667 0.00 0.00 0.00 3.61
70 71 5.666969 TGTCTATTGTTTTCGTGGTCTTG 57.333 39.130 0.00 0.00 0.00 3.02
125 126 9.236006 GTAGAGATAAATACATGGCATTTGGAT 57.764 33.333 14.49 0.00 0.00 3.41
155 185 3.884037 ACAAACATCAACTCCCCTCTT 57.116 42.857 0.00 0.00 0.00 2.85
157 187 4.843728 TCATACAAACATCAACTCCCCTC 58.156 43.478 0.00 0.00 0.00 4.30
177 207 5.014123 AGGGGTGAAACTACATTTGATCTCA 59.986 40.000 0.00 0.00 36.74 3.27
179 209 5.014123 TGAGGGGTGAAACTACATTTGATCT 59.986 40.000 0.00 0.00 36.74 2.75
180 210 5.123979 GTGAGGGGTGAAACTACATTTGATC 59.876 44.000 0.00 0.00 36.74 2.92
234 644 5.066913 AGGATGAGGAAAGGAAAACACTT 57.933 39.130 0.00 0.00 0.00 3.16
239 649 9.020731 GTTTACATAAGGATGAGGAAAGGAAAA 57.979 33.333 0.00 0.00 36.48 2.29
248 658 7.012704 CAGAACATGGTTTACATAAGGATGAGG 59.987 40.741 0.00 0.00 37.84 3.86
251 661 6.498304 GCAGAACATGGTTTACATAAGGATG 58.502 40.000 0.00 0.00 37.84 3.51
252 662 5.296780 CGCAGAACATGGTTTACATAAGGAT 59.703 40.000 0.00 0.00 37.84 3.24
261 671 4.257731 TGATTAGCGCAGAACATGGTTTA 58.742 39.130 11.47 0.00 0.00 2.01
286 696 7.922278 TGCATGGCATGATTTTAGTAAGATTTC 59.078 33.333 30.69 7.19 31.71 2.17
306 716 8.481974 TTTGATTTGATTGAGTTAATGCATGG 57.518 30.769 0.00 0.00 0.00 3.66
360 773 7.745620 TGGGTAGAGAAAGTCAAGATTTTTC 57.254 36.000 0.00 0.00 0.00 2.29
413 826 9.868277 ACACAATTTGATTTAGTTGAGTTTTGA 57.132 25.926 2.79 0.00 0.00 2.69
420 834 7.595819 AGGGAACACAATTTGATTTAGTTGA 57.404 32.000 2.79 0.00 0.00 3.18
436 851 2.671963 GGTGCGGGAAGGGAACAC 60.672 66.667 0.00 0.00 0.00 3.32
833 1358 1.128200 CGGAGGGAGAGAGAGAGAGA 58.872 60.000 0.00 0.00 0.00 3.10
834 1359 0.837272 ACGGAGGGAGAGAGAGAGAG 59.163 60.000 0.00 0.00 0.00 3.20
845 1370 2.117156 GGATCGAACGACGGAGGGA 61.117 63.158 0.00 0.00 42.82 4.20
911 1718 3.135056 CTACGAGGGGCCGCTGTAC 62.135 68.421 29.42 12.16 0.00 2.90
912 1719 2.831742 CTACGAGGGGCCGCTGTA 60.832 66.667 29.42 24.58 0.00 2.74
1178 1987 2.563427 GGGCAAGAAAGCGACAGC 59.437 61.111 0.00 0.00 45.58 4.40
1190 2019 0.687757 AGAGCTACATCGAGGGGCAA 60.688 55.000 16.75 0.00 0.00 4.52
1281 2112 1.888512 TGCAATTTTCAGAGGACAGCC 59.111 47.619 0.00 0.00 0.00 4.85
1366 2197 0.755686 GGGCAAGAGGATCACGAGAT 59.244 55.000 0.00 0.00 37.82 2.75
1371 2202 0.250513 ACGAAGGGCAAGAGGATCAC 59.749 55.000 0.00 0.00 37.82 3.06
1373 2204 0.827368 AGACGAAGGGCAAGAGGATC 59.173 55.000 0.00 0.00 0.00 3.36
1401 2236 7.061054 ACATCTGAATCCAATTCTCACATGAT 58.939 34.615 0.00 0.00 39.96 2.45
1419 2254 3.008266 TCAGGTTGCAATGAGACATCTGA 59.992 43.478 0.59 0.00 0.00 3.27
1582 2426 3.678072 ACGAACACGACAATCGAATTCAT 59.322 39.130 6.22 0.00 43.74 2.57
1598 2445 3.894782 CATGGACATGTCAAACGAACA 57.105 42.857 26.47 13.78 34.23 3.18
1850 2701 5.922544 CCATGTCAAAAGACAAGTCCATTTC 59.077 40.000 2.13 0.00 38.69 2.17
1874 2725 2.919229 GCTGCAACAACATTACAGATGC 59.081 45.455 0.00 0.00 0.00 3.91
1929 2780 7.536622 GCACAATATAGCATAAGAAGCAATGAC 59.463 37.037 0.00 0.00 0.00 3.06
2063 2914 9.476202 CAATACTCATCATATAGAAACGAACCA 57.524 33.333 0.00 0.00 0.00 3.67
2077 2928 9.708092 CATCTAACAGATGTCAATACTCATCAT 57.292 33.333 7.81 0.00 45.33 2.45
2095 2946 2.831685 ACAAGACACGGCATCTAACA 57.168 45.000 0.00 0.00 0.00 2.41
2099 2950 1.623811 ACCTAACAAGACACGGCATCT 59.376 47.619 0.00 0.00 0.00 2.90
2170 3021 2.158234 TGGAAATACCCAGCCTGGTTTT 60.158 45.455 10.47 6.63 39.91 2.43
2229 3080 7.681939 TGTTCAGGTAAACTAATTGGATGAC 57.318 36.000 0.00 0.00 0.00 3.06
2264 3115 4.981806 TTTTACATATCAAGGCAGGCAC 57.018 40.909 0.00 0.00 0.00 5.01
2271 3122 9.423061 CAAAAGTTCCCTTTTTACATATCAAGG 57.577 33.333 0.00 0.00 46.27 3.61
2387 3242 8.366401 ACAAGTGATGTAGAGATGAGGATATTG 58.634 37.037 0.00 0.00 41.63 1.90
2450 3305 2.044946 ATGGGAGAAACCAGCGCC 60.045 61.111 2.29 0.00 45.20 6.53
2555 3411 9.520515 AGAAGTCAGATAACCAATTAACACAAT 57.479 29.630 0.00 0.00 0.00 2.71
2556 3412 8.783093 CAGAAGTCAGATAACCAATTAACACAA 58.217 33.333 0.00 0.00 0.00 3.33
2566 3422 6.269077 TCAGGTAAACAGAAGTCAGATAACCA 59.731 38.462 0.00 0.00 0.00 3.67
2572 3428 6.153000 GGATAGTCAGGTAAACAGAAGTCAGA 59.847 42.308 0.00 0.00 0.00 3.27
2575 3431 6.282199 TGGATAGTCAGGTAAACAGAAGTC 57.718 41.667 0.00 0.00 0.00 3.01
2760 3616 4.882671 AATGATGAGTGCGTTGGAATAC 57.117 40.909 0.00 0.00 0.00 1.89
2767 3623 3.679389 AGAGGAAAATGATGAGTGCGTT 58.321 40.909 0.00 0.00 0.00 4.84
2771 3627 7.172875 GTCATATGGAGAGGAAAATGATGAGTG 59.827 40.741 2.13 0.00 0.00 3.51
2772 3628 7.072202 AGTCATATGGAGAGGAAAATGATGAGT 59.928 37.037 2.13 0.00 0.00 3.41
2775 3631 6.072618 GCAGTCATATGGAGAGGAAAATGATG 60.073 42.308 2.13 0.00 0.00 3.07
2784 3640 2.036992 GGTCTGCAGTCATATGGAGAGG 59.963 54.545 14.67 0.00 46.63 3.69
2825 3681 2.918774 ATATCTTTGGAGGGAGGGGT 57.081 50.000 0.00 0.00 0.00 4.95
2867 3723 3.636313 TTGCTTCCCTACGTCGCCG 62.636 63.158 0.00 0.00 40.83 6.46
2868 3724 0.952010 TTTTGCTTCCCTACGTCGCC 60.952 55.000 0.00 0.00 0.00 5.54
2888 3744 0.406361 AGGGAAGTGAGTCGTCCTCT 59.594 55.000 7.13 1.70 42.82 3.69
2897 3753 2.099141 TGAAATCGCAGGGAAGTGAG 57.901 50.000 0.00 0.00 0.00 3.51
3022 3878 3.006728 TCGGTAACAGGCCCTGGG 61.007 66.667 16.70 8.86 35.51 4.45
3025 3881 2.786512 TACCGTCGGTAACAGGCCCT 62.787 60.000 21.75 0.00 34.97 5.19
3128 3994 4.097589 AGGTAATCGTACAACACCTAGCTC 59.902 45.833 0.00 0.00 37.85 4.09
3143 4009 6.414109 CGATTTCTACAGTACACAGGTAATCG 59.586 42.308 12.38 12.38 0.00 3.34
3144 4010 6.198591 GCGATTTCTACAGTACACAGGTAATC 59.801 42.308 0.00 0.00 0.00 1.75
3145 4011 6.040878 GCGATTTCTACAGTACACAGGTAAT 58.959 40.000 0.00 0.00 0.00 1.89
3146 4012 5.404946 GCGATTTCTACAGTACACAGGTAA 58.595 41.667 0.00 0.00 0.00 2.85
3150 4016 2.279136 GCGCGATTTCTACAGTACACAG 59.721 50.000 12.10 0.00 0.00 3.66
3155 4021 0.452987 ACGGCGCGATTTCTACAGTA 59.547 50.000 12.10 0.00 0.00 2.74
3200 4069 5.003804 ACATCTACAACATCCCTCACAAAC 58.996 41.667 0.00 0.00 0.00 2.93
3223 4092 2.636647 TCACATCAGACAGGCAACAA 57.363 45.000 0.00 0.00 41.41 2.83
3321 4190 5.982516 TGCAAGCCTAAAACAAACAATACAG 59.017 36.000 0.00 0.00 0.00 2.74
3340 4209 2.548057 ACAACGGAGTGTACAATGCAAG 59.452 45.455 15.13 6.18 45.00 4.01
3361 4230 2.708216 TGCTTCTCCACAGACACAAA 57.292 45.000 0.00 0.00 0.00 2.83
3391 4260 1.327303 GCAAAACAGGATGACCACCA 58.673 50.000 0.00 0.00 39.69 4.17
3464 4347 6.129221 CGTTATTACAACACAATGCTTGGTTG 60.129 38.462 17.75 17.75 42.40 3.77
3468 4351 4.914504 TGCGTTATTACAACACAATGCTTG 59.085 37.500 0.00 0.00 34.68 4.01
3469 4352 5.114785 TGCGTTATTACAACACAATGCTT 57.885 34.783 0.00 0.00 34.68 3.91
3489 4600 4.083581 ACTTATTCAACACAATCGCTGC 57.916 40.909 0.00 0.00 0.00 5.25
3552 4664 0.035915 GACTTCTTCAGCCACCTCCC 60.036 60.000 0.00 0.00 0.00 4.30
3604 4733 1.868498 CAACTACCGCACGAGGAAAAA 59.132 47.619 0.00 0.00 34.73 1.94
3649 4781 8.021159 AGCTCCTATTTAGGGGATTTCGTTTTT 61.021 37.037 7.73 0.00 40.28 1.94
3652 4784 4.412528 AGCTCCTATTTAGGGGATTTCGTT 59.587 41.667 7.73 0.00 40.28 3.85
3653 4785 3.974642 AGCTCCTATTTAGGGGATTTCGT 59.025 43.478 7.73 0.00 40.28 3.85
3712 4846 2.156098 TCATACGTTTGGTTGGGCTTC 58.844 47.619 6.15 0.00 0.00 3.86
3746 4880 2.182284 CGCCGGTCCACATACGAA 59.818 61.111 1.90 0.00 0.00 3.85
3766 4900 3.244387 GGAGTCCATATCCAAGAAGGCTC 60.244 52.174 3.60 0.00 36.79 4.70
3813 4947 3.499737 CATCCGTCCTGTTGCGGC 61.500 66.667 0.00 0.00 46.79 6.53
3815 4949 1.577328 AAAGCATCCGTCCTGTTGCG 61.577 55.000 0.00 0.00 40.00 4.85
3816 4950 0.169009 GAAAGCATCCGTCCTGTTGC 59.831 55.000 0.00 0.00 35.34 4.17
3817 4951 1.813513 AGAAAGCATCCGTCCTGTTG 58.186 50.000 0.00 0.00 0.00 3.33
3818 4952 2.093447 CCTAGAAAGCATCCGTCCTGTT 60.093 50.000 0.00 0.00 0.00 3.16
3819 4953 1.482593 CCTAGAAAGCATCCGTCCTGT 59.517 52.381 0.00 0.00 0.00 4.00
3820 4954 1.757118 TCCTAGAAAGCATCCGTCCTG 59.243 52.381 0.00 0.00 0.00 3.86
3821 4955 2.160721 TCCTAGAAAGCATCCGTCCT 57.839 50.000 0.00 0.00 0.00 3.85
3822 4956 3.615351 GCTATCCTAGAAAGCATCCGTCC 60.615 52.174 0.00 0.00 36.26 4.79
3823 4957 3.580731 GCTATCCTAGAAAGCATCCGTC 58.419 50.000 0.00 0.00 36.26 4.79
3824 4958 2.029828 CGCTATCCTAGAAAGCATCCGT 60.030 50.000 10.32 0.00 35.98 4.69
3825 4959 2.600731 CGCTATCCTAGAAAGCATCCG 58.399 52.381 10.32 0.00 35.98 4.18
3836 4970 1.096967 TGAACGCGTCCGCTATCCTA 61.097 55.000 14.44 0.00 39.32 2.94


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

AutoCloner maintained by Alex Coulton.