Multiple sequence alignment - TraesCS2B01G026700

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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 TraesCS2B01G026700 chr2B 100.000 3482 0 0 1 3482 12421314 12424795 0.000000e+00 6431.0
1 TraesCS2B01G026700 chr2B 91.738 3159 194 32 377 3482 11518949 11515805 0.000000e+00 4325.0
2 TraesCS2B01G026700 chr2B 85.647 1707 237 7 815 2520 768807185 768805486 0.000000e+00 1788.0
3 TraesCS2B01G026700 chr2B 83.798 1901 269 23 628 2520 138993653 138991784 0.000000e+00 1768.0
4 TraesCS2B01G026700 chr2B 84.534 1707 255 8 815 2520 768929605 768927907 0.000000e+00 1681.0
5 TraesCS2B01G026700 chr2B 82.644 1498 233 16 1031 2518 13058749 13057269 0.000000e+00 1301.0
6 TraesCS2B01G026700 chr2B 80.289 1522 245 28 1001 2520 11226425 11224957 0.000000e+00 1098.0
7 TraesCS2B01G026700 chr2B 98.006 351 5 2 1 350 11519294 11518945 2.970000e-170 608.0
8 TraesCS2B01G026700 chr2B 75.776 322 47 18 649 956 13347811 13347507 2.180000e-27 134.0
9 TraesCS2B01G026700 chr2D 89.614 2956 244 34 576 3482 9604325 9607266 0.000000e+00 3699.0
10 TraesCS2B01G026700 chr2D 85.375 1894 253 17 623 2508 19586638 19588515 0.000000e+00 1941.0
11 TraesCS2B01G026700 chr2D 83.667 1898 282 26 641 2520 8695302 8697189 0.000000e+00 1762.0
12 TraesCS2B01G026700 chr2D 83.481 1925 274 26 640 2556 85929932 85928044 0.000000e+00 1753.0
13 TraesCS2B01G026700 chr2D 83.938 193 29 2 7 198 9384473 9384664 2.130000e-42 183.0
14 TraesCS2B01G026700 chr2A 90.713 2455 170 26 374 2794 8706773 8709203 0.000000e+00 3217.0
15 TraesCS2B01G026700 chr2A 83.784 370 36 13 3 355 8706299 8706661 2.590000e-86 329.0
16 TraesCS2B01G026700 chr2A 94.872 39 2 0 216 254 45481614 45481652 1.040000e-05 62.1
17 TraesCS2B01G026700 chr2A 94.872 39 2 0 216 254 360748914 360748952 1.040000e-05 62.1
18 TraesCS2B01G026700 chr1B 97.500 40 0 1 215 253 39519036 39519075 2.240000e-07 67.6
19 TraesCS2B01G026700 chr5D 97.368 38 1 0 216 253 387683608 387683645 8.070000e-07 65.8
20 TraesCS2B01G026700 chr3A 100.000 35 0 0 219 253 41365287 41365253 8.070000e-07 65.8
21 TraesCS2B01G026700 chr3D 95.000 40 2 0 216 255 132507669 132507630 2.900000e-06 63.9
22 TraesCS2B01G026700 chr6D 97.143 35 1 0 219 253 58245413 58245379 3.750000e-05 60.2
23 TraesCS2B01G026700 chr6A 97.143 35 1 0 219 253 73562030 73561996 3.750000e-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 TraesCS2B01G026700 chr2B 12421314 12424795 3481 False 6431.0 6431 100.0000 1 3482 1 chr2B.!!$F1 3481
1 TraesCS2B01G026700 chr2B 11515805 11519294 3489 True 2466.5 4325 94.8720 1 3482 2 chr2B.!!$R7 3481
2 TraesCS2B01G026700 chr2B 768805486 768807185 1699 True 1788.0 1788 85.6470 815 2520 1 chr2B.!!$R5 1705
3 TraesCS2B01G026700 chr2B 138991784 138993653 1869 True 1768.0 1768 83.7980 628 2520 1 chr2B.!!$R4 1892
4 TraesCS2B01G026700 chr2B 768927907 768929605 1698 True 1681.0 1681 84.5340 815 2520 1 chr2B.!!$R6 1705
5 TraesCS2B01G026700 chr2B 13057269 13058749 1480 True 1301.0 1301 82.6440 1031 2518 1 chr2B.!!$R2 1487
6 TraesCS2B01G026700 chr2B 11224957 11226425 1468 True 1098.0 1098 80.2890 1001 2520 1 chr2B.!!$R1 1519
7 TraesCS2B01G026700 chr2D 9604325 9607266 2941 False 3699.0 3699 89.6140 576 3482 1 chr2D.!!$F3 2906
8 TraesCS2B01G026700 chr2D 19586638 19588515 1877 False 1941.0 1941 85.3750 623 2508 1 chr2D.!!$F4 1885
9 TraesCS2B01G026700 chr2D 8695302 8697189 1887 False 1762.0 1762 83.6670 641 2520 1 chr2D.!!$F1 1879
10 TraesCS2B01G026700 chr2D 85928044 85929932 1888 True 1753.0 1753 83.4810 640 2556 1 chr2D.!!$R1 1916
11 TraesCS2B01G026700 chr2A 8706299 8709203 2904 False 1773.0 3217 87.2485 3 2794 2 chr2A.!!$F3 2791

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
362 377 0.107459 GAGGGAGAACCATGGCAGAC 60.107 60.0 13.04 1.08 43.89 3.51 F
364 379 0.393537 GGGAGAACCATGGCAGACTG 60.394 60.0 13.04 0.00 39.85 3.51 F
1632 1807 0.899720 TTCCGGTCATAGGTGGTGTC 59.100 55.0 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2200 0.459489 GTGCAACTCCTTGGCAAACA 59.541 50.000 0.00 0.0 39.57 2.83 R
2206 2382 1.002773 GTCCGTTATGTCCACTGGGTT 59.997 52.381 0.00 0.0 34.93 4.11 R
3393 3639 0.100503 GGTGCAGTTGGTGAACACAC 59.899 55.000 7.25 0.0 36.19 3.82 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
164 173 8.871125 AGAGAGAAAGTGGAAGTATCTAAAACA 58.129 33.333 0.00 0.00 0.00 2.83
324 339 1.823899 GACCATGGCGATTGTCCCC 60.824 63.158 13.04 0.00 0.00 4.81
347 362 2.257207 TGTCAAGTTACAGAGGGAGGG 58.743 52.381 0.00 0.00 0.00 4.30
348 363 2.158219 TGTCAAGTTACAGAGGGAGGGA 60.158 50.000 0.00 0.00 0.00 4.20
349 364 2.498078 GTCAAGTTACAGAGGGAGGGAG 59.502 54.545 0.00 0.00 0.00 4.30
350 365 2.382305 TCAAGTTACAGAGGGAGGGAGA 59.618 50.000 0.00 0.00 0.00 3.71
351 366 3.173965 CAAGTTACAGAGGGAGGGAGAA 58.826 50.000 0.00 0.00 0.00 2.87
352 367 2.822697 AGTTACAGAGGGAGGGAGAAC 58.177 52.381 0.00 0.00 0.00 3.01
353 368 1.832366 GTTACAGAGGGAGGGAGAACC 59.168 57.143 0.00 0.00 40.67 3.62
354 369 1.089978 TACAGAGGGAGGGAGAACCA 58.910 55.000 0.00 0.00 43.89 3.67
355 370 0.419459 ACAGAGGGAGGGAGAACCAT 59.581 55.000 0.00 0.00 43.89 3.55
356 371 0.835941 CAGAGGGAGGGAGAACCATG 59.164 60.000 0.00 0.00 43.89 3.66
357 372 0.327000 AGAGGGAGGGAGAACCATGG 60.327 60.000 11.19 11.19 43.89 3.66
358 373 1.988982 GAGGGAGGGAGAACCATGGC 61.989 65.000 13.04 0.00 43.89 4.40
359 374 2.308722 GGGAGGGAGAACCATGGCA 61.309 63.158 13.04 0.00 43.89 4.92
360 375 1.225704 GGAGGGAGAACCATGGCAG 59.774 63.158 13.04 0.00 43.89 4.85
361 376 1.274703 GGAGGGAGAACCATGGCAGA 61.275 60.000 13.04 0.00 43.89 4.26
362 377 0.107459 GAGGGAGAACCATGGCAGAC 60.107 60.000 13.04 1.08 43.89 3.51
363 378 0.548682 AGGGAGAACCATGGCAGACT 60.549 55.000 13.04 5.96 43.89 3.24
364 379 0.393537 GGGAGAACCATGGCAGACTG 60.394 60.000 13.04 0.00 39.85 3.51
365 380 1.028868 GGAGAACCATGGCAGACTGC 61.029 60.000 19.55 19.55 38.24 4.40
374 389 3.978272 GCAGACTGCCAGAAGGTG 58.022 61.111 17.01 0.00 37.42 4.00
1072 1244 4.022242 TCTCCTTCCTGAAGAACAAGTACG 60.022 45.833 8.46 0.00 40.79 3.67
1093 1265 1.002069 ATCCTCCTTGAACCATGCCA 58.998 50.000 0.00 0.00 0.00 4.92
1108 1280 0.984230 TGCCAAATCCGAGGAGAAGT 59.016 50.000 0.00 0.00 0.00 3.01
1435 1608 8.141268 CCTTGGAAAGCTTAGAAATTGTTGTTA 58.859 33.333 0.00 0.00 44.44 2.41
1632 1807 0.899720 TTCCGGTCATAGGTGGTGTC 59.100 55.000 0.00 0.00 0.00 3.67
2024 2200 6.045318 CACAGCTAGTACAAATAGCAGATGT 58.955 40.000 13.34 7.46 46.57 3.06
2196 2372 2.949106 CACCCAAGCACGCTTCTG 59.051 61.111 0.16 0.00 33.42 3.02
2206 2382 1.148273 ACGCTTCTGGAACAAGGCA 59.852 52.632 0.00 0.00 38.70 4.75
2331 2525 2.016393 TTCTGGCCGATCCTAGCGTG 62.016 60.000 0.00 0.00 35.26 5.34
2355 2549 7.006509 TGAGACCCAAAGAAGATTTCATTCTT 58.993 34.615 0.00 0.00 46.37 2.52
2448 2648 5.295787 CACAAGTGAAGGTAGTGCTTTACAA 59.704 40.000 0.00 0.00 0.00 2.41
2452 2652 3.136809 TGAAGGTAGTGCTTTACAACCCA 59.863 43.478 0.00 0.00 30.46 4.51
2566 2769 6.971602 AGATGTGTTCATGTATACGGAGTAG 58.028 40.000 0.00 0.00 39.57 2.57
2602 2805 9.754382 AAATGTATTTTGGATCTCATGTAATGC 57.246 29.630 0.00 0.00 46.21 3.56
2604 2807 7.933396 TGTATTTTGGATCTCATGTAATGCAG 58.067 34.615 0.00 0.00 46.21 4.41
2605 2808 5.840243 TTTTGGATCTCATGTAATGCAGG 57.160 39.130 0.00 0.00 46.21 4.85
2606 2809 4.508551 TTGGATCTCATGTAATGCAGGT 57.491 40.909 0.00 0.00 46.21 4.00
2607 2810 5.628797 TTGGATCTCATGTAATGCAGGTA 57.371 39.130 0.00 0.00 46.21 3.08
2610 2813 5.822519 TGGATCTCATGTAATGCAGGTAAAC 59.177 40.000 0.00 0.00 46.21 2.01
2651 2856 3.272574 ACTATCCACCACATGCTCTTG 57.727 47.619 0.00 0.00 0.00 3.02
2659 2864 3.681897 CACCACATGCTCTTGTAGTCTTC 59.318 47.826 0.00 0.00 0.00 2.87
2690 2895 7.426929 AGTTGTCTCAGTAATGTTGCTTTAG 57.573 36.000 0.00 0.00 0.00 1.85
2692 2897 7.386299 AGTTGTCTCAGTAATGTTGCTTTAGAG 59.614 37.037 0.00 0.00 0.00 2.43
2713 2924 4.458397 AGGAAAGAGGTACATGCATCATG 58.542 43.478 0.00 5.35 46.18 3.07
2720 2946 6.594744 AGAGGTACATGCATCATGACATTTA 58.405 36.000 13.11 0.00 43.81 1.40
2748 2978 5.824904 AGTTGATACCAATGATGAAGTGC 57.175 39.130 0.00 0.00 34.39 4.40
2756 2994 2.105006 ATGATGAAGTGCGAGCTGTT 57.895 45.000 0.00 0.00 0.00 3.16
2773 3011 2.489329 CTGTTGTGTGGATGTGGATTCC 59.511 50.000 0.00 0.00 0.00 3.01
2788 3026 4.626172 GTGGATTCCACGAAGAACTTAGAC 59.374 45.833 19.65 0.00 44.95 2.59
2807 3045 7.506261 ACTTAGACCGGATCAGATTATAGTTGT 59.494 37.037 9.46 0.00 0.00 3.32
2808 3046 6.334102 AGACCGGATCAGATTATAGTTGTC 57.666 41.667 9.46 0.00 0.00 3.18
2847 3085 5.012328 AGATTAAGAAACTGACTAGGCGG 57.988 43.478 1.68 1.68 0.00 6.13
2869 3107 0.886490 GGATCCAACATAGGCCAGCG 60.886 60.000 6.95 0.00 0.00 5.18
2885 3123 0.539438 AGCGCCTCCCACAAAATCAA 60.539 50.000 2.29 0.00 0.00 2.57
2939 3178 6.145371 CCAGTTCAATTTCAAATTACCAACGG 59.855 38.462 0.00 1.00 0.00 4.44
2944 3183 6.488683 TCAATTTCAAATTACCAACGGACTCT 59.511 34.615 0.00 0.00 0.00 3.24
2947 3186 4.710324 TCAAATTACCAACGGACTCTGTT 58.290 39.130 0.00 0.00 0.00 3.16
2975 3214 1.005097 AGGTGATGAGATTGCCTTGCA 59.995 47.619 0.00 0.00 36.47 4.08
2977 3216 1.089112 TGATGAGATTGCCTTGCACG 58.911 50.000 0.00 0.00 38.71 5.34
2989 3228 4.577677 TGCACGGCAAGGCTTGGA 62.578 61.111 27.25 0.81 34.76 3.53
2998 3237 1.000866 AAGGCTTGGAATGGGAGGC 59.999 57.895 0.00 0.00 36.33 4.70
3003 3242 0.609131 CTTGGAATGGGAGGCGTTGT 60.609 55.000 0.00 0.00 0.00 3.32
3007 3246 0.250513 GAATGGGAGGCGTTGTCTCT 59.749 55.000 0.00 0.00 34.33 3.10
3008 3247 0.250513 AATGGGAGGCGTTGTCTCTC 59.749 55.000 0.00 0.00 34.97 3.20
3009 3248 1.533033 TGGGAGGCGTTGTCTCTCA 60.533 57.895 0.00 0.00 42.96 3.27
3011 3250 1.536943 GGGAGGCGTTGTCTCTCACT 61.537 60.000 0.00 0.00 34.47 3.41
3027 3266 2.295349 CTCACTTTCAAGCAAGCCATGT 59.705 45.455 0.00 0.00 0.00 3.21
3038 3277 0.251341 AAGCCATGTGGAGGTGGAAC 60.251 55.000 2.55 0.00 37.72 3.62
3063 3303 2.312741 AGAGGAAATTCAAGGCCATCCA 59.687 45.455 5.01 0.00 33.74 3.41
3094 3334 7.333174 GGAAACAAAAACATGAAGTTCTTCCAA 59.667 33.333 0.00 0.00 40.26 3.53
3108 3348 4.174704 TCTTCCAATGCTATTGCCTCAT 57.825 40.909 0.00 0.00 38.71 2.90
3117 3357 4.431661 GCTATTGCCTCATAGCATTTCC 57.568 45.455 12.52 0.00 43.64 3.13
3119 3359 4.279169 GCTATTGCCTCATAGCATTTCCAA 59.721 41.667 12.52 0.00 43.64 3.53
3145 3385 0.683973 ATGATCCACTCCCTCGATGC 59.316 55.000 0.00 0.00 0.00 3.91
3166 3406 1.738099 GCTGCGACTTCGTGGTCAT 60.738 57.895 0.00 0.00 42.22 3.06
3168 3408 0.388520 CTGCGACTTCGTGGTCATGA 60.389 55.000 0.00 0.00 42.22 3.07
3190 3435 3.234630 AAAGCCTACGCGCTCCACA 62.235 57.895 5.73 0.00 38.44 4.17
3199 3444 0.179137 CGCGCTCCACATCTTCTACA 60.179 55.000 5.56 0.00 0.00 2.74
3208 3453 0.585357 CATCTTCTACAGCGGCATGC 59.415 55.000 9.90 9.90 46.98 4.06
3220 3465 0.527113 CGGCATGCTTGACCAATCAA 59.473 50.000 18.92 0.00 42.73 2.57
3235 3480 0.916358 ATCAAGGGCCACCAGCTAGT 60.916 55.000 6.18 0.00 43.05 2.57
3271 3516 3.239026 CGCGCATCAATCAATTCTTTGAC 59.761 43.478 8.75 0.00 44.36 3.18
3279 3524 7.202016 TCAATCAATTCTTTGACACCTACAC 57.798 36.000 0.00 0.00 44.36 2.90
3326 3572 3.879892 GAGCAAGTGGAGTAATGGATTCC 59.120 47.826 0.00 0.00 34.46 3.01
3327 3573 3.266772 AGCAAGTGGAGTAATGGATTCCA 59.733 43.478 8.08 8.08 41.48 3.53
3328 3574 4.016444 GCAAGTGGAGTAATGGATTCCAA 58.984 43.478 9.98 0.00 44.97 3.53
3331 3577 5.715439 AGTGGAGTAATGGATTCCAATGA 57.285 39.130 9.98 0.00 44.97 2.57
3339 3585 9.342308 GAGTAATGGATTCCAATGATTGAGTTA 57.658 33.333 9.98 0.00 36.95 2.24
3389 3635 4.209452 TCAAGACAATGTTGTTTCTCGC 57.791 40.909 0.00 0.00 42.43 5.03
3391 3637 2.479837 AGACAATGTTGTTTCTCGCGA 58.520 42.857 9.26 9.26 42.43 5.87
3393 3639 3.120546 AGACAATGTTGTTTCTCGCGATG 60.121 43.478 10.36 2.95 42.43 3.84
3398 3644 1.260561 GTTGTTTCTCGCGATGTGTGT 59.739 47.619 10.36 0.00 0.00 3.72
3407 3653 0.944386 GCGATGTGTGTTCACCAACT 59.056 50.000 0.37 0.00 43.26 3.16
3432 3678 1.227089 CTTCGGCATCTCCACGGAG 60.227 63.158 6.77 6.77 43.21 4.63
3434 3680 1.541310 TTCGGCATCTCCACGGAGTT 61.541 55.000 12.77 1.85 41.61 3.01
3439 3690 1.927895 CATCTCCACGGAGTTAGTGC 58.072 55.000 12.77 0.00 41.61 4.40
3445 3696 0.317160 CACGGAGTTAGTGCCAGTGA 59.683 55.000 0.00 0.00 41.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.568538 CTGCAAGTGGACTTTACAATGC 58.431 45.455 0.00 0.00 33.11 3.56
164 173 6.560253 AGTTATTCACTTGAACGAGCAAAT 57.440 33.333 0.00 0.00 36.80 2.32
324 339 3.306364 CCTCCCTCTGTAACTTGACAGTG 60.306 52.174 3.66 1.68 45.88 3.66
345 360 0.393537 CAGTCTGCCATGGTTCTCCC 60.394 60.000 14.67 0.00 0.00 4.30
346 361 1.028868 GCAGTCTGCCATGGTTCTCC 61.029 60.000 14.27 0.00 37.42 3.71
347 362 2.475666 GCAGTCTGCCATGGTTCTC 58.524 57.895 14.27 2.41 37.42 2.87
348 363 4.730487 GCAGTCTGCCATGGTTCT 57.270 55.556 14.27 4.07 37.42 3.01
357 372 1.673665 CCACCTTCTGGCAGTCTGC 60.674 63.158 16.93 16.93 44.08 4.26
358 373 1.002868 CCCACCTTCTGGCAGTCTG 60.003 63.158 15.27 6.39 39.01 3.51
359 374 2.227036 CCCCACCTTCTGGCAGTCT 61.227 63.158 15.27 0.00 39.01 3.24
360 375 2.352805 CCCCACCTTCTGGCAGTC 59.647 66.667 15.27 0.00 39.01 3.51
361 376 3.260100 CCCCCACCTTCTGGCAGT 61.260 66.667 15.27 0.00 39.01 4.40
362 377 2.935481 TCCCCCACCTTCTGGCAG 60.935 66.667 8.58 8.58 39.01 4.85
363 378 2.935481 CTCCCCCACCTTCTGGCA 60.935 66.667 0.00 0.00 39.01 4.92
364 379 4.432741 GCTCCCCCACCTTCTGGC 62.433 72.222 0.00 0.00 39.01 4.85
365 380 3.732849 GGCTCCCCCACCTTCTGG 61.733 72.222 0.00 0.00 40.26 3.86
366 381 4.101448 CGGCTCCCCCACCTTCTG 62.101 72.222 0.00 0.00 0.00 3.02
367 382 4.658786 ACGGCTCCCCCACCTTCT 62.659 66.667 0.00 0.00 0.00 2.85
368 383 4.097361 GACGGCTCCCCCACCTTC 62.097 72.222 0.00 0.00 0.00 3.46
372 387 4.717313 GTTGGACGGCTCCCCCAC 62.717 72.222 0.00 0.00 35.34 4.61
373 388 4.974438 AGTTGGACGGCTCCCCCA 62.974 66.667 0.00 0.00 35.34 4.96
374 389 4.097361 GAGTTGGACGGCTCCCCC 62.097 72.222 0.00 0.00 35.34 5.40
375 390 4.452733 CGAGTTGGACGGCTCCCC 62.453 72.222 0.00 0.00 35.34 4.81
443 585 4.290711 TGTTCATGCTCAATCTCTCCAA 57.709 40.909 0.00 0.00 0.00 3.53
824 992 0.673333 CGGCTGCTAACATGTGTCCA 60.673 55.000 0.00 0.00 0.00 4.02
1072 1244 2.027385 GGCATGGTTCAAGGAGGATTC 58.973 52.381 0.00 0.00 0.00 2.52
1093 1265 2.237392 CCCTCAACTTCTCCTCGGATTT 59.763 50.000 0.00 0.00 0.00 2.17
1108 1280 0.843309 TGTTGCAACCTCTCCCTCAA 59.157 50.000 26.14 0.76 0.00 3.02
1339 1511 2.132762 TCGAGAACGCTTGAAAGGAAC 58.867 47.619 0.00 0.00 39.58 3.62
1435 1608 3.638160 ACAACAAATTCTGCCATGTGAGT 59.362 39.130 0.00 0.00 0.00 3.41
1632 1807 3.305335 CCAATGTTTTCTTCCCAACTCCG 60.305 47.826 0.00 0.00 0.00 4.63
2024 2200 0.459489 GTGCAACTCCTTGGCAAACA 59.541 50.000 0.00 0.00 39.57 2.83
2196 2372 1.463553 CCACTGGGTTGCCTTGTTCC 61.464 60.000 0.00 0.00 0.00 3.62
2206 2382 1.002773 GTCCGTTATGTCCACTGGGTT 59.997 52.381 0.00 0.00 34.93 4.11
2331 2525 7.459795 AAGAATGAAATCTTCTTTGGGTCTC 57.540 36.000 0.00 0.00 39.34 3.36
2355 2549 6.468651 GGGGTATCCTTGATTCCCATGAAATA 60.469 42.308 17.35 0.00 47.00 1.40
2448 2648 1.532316 TCGTCGTTTCCTCCTGGGT 60.532 57.895 0.00 0.00 36.25 4.51
2452 2652 0.251253 ACTCCTCGTCGTTTCCTCCT 60.251 55.000 0.00 0.00 0.00 3.69
2541 2744 5.833082 ACTCCGTATACATGAACACATCTC 58.167 41.667 0.00 0.00 0.00 2.75
2585 2788 4.508551 ACCTGCATTACATGAGATCCAA 57.491 40.909 0.00 0.00 0.00 3.53
2586 2789 5.628797 TTACCTGCATTACATGAGATCCA 57.371 39.130 0.00 0.00 0.00 3.41
2600 2803 9.781633 TCTAGTAAAAATACAAGTTTACCTGCA 57.218 29.630 0.00 0.00 39.83 4.41
2651 2856 8.301002 ACTGAGACAACTAGAAATGAAGACTAC 58.699 37.037 0.00 0.00 0.00 2.73
2659 2864 7.959651 GCAACATTACTGAGACAACTAGAAATG 59.040 37.037 0.00 0.00 0.00 2.32
2690 2895 4.142609 TGATGCATGTACCTCTTTCCTC 57.857 45.455 2.46 0.00 0.00 3.71
2692 2897 4.274459 GTCATGATGCATGTACCTCTTTCC 59.726 45.833 2.46 0.00 41.98 3.13
2720 2946 9.520515 ACTTCATCATTGGTATCAACTTTAGTT 57.479 29.630 0.00 0.00 39.12 2.24
2748 2978 0.514255 CACATCCACACAACAGCTCG 59.486 55.000 0.00 0.00 0.00 5.03
2773 3011 3.119602 TGATCCGGTCTAAGTTCTTCGTG 60.120 47.826 0.00 0.00 0.00 4.35
2776 3014 4.985538 TCTGATCCGGTCTAAGTTCTTC 57.014 45.455 0.00 0.00 0.00 2.87
2788 3026 8.088365 TGTAATGACAACTATAATCTGATCCGG 58.912 37.037 0.00 0.00 30.68 5.14
2837 3075 3.224324 GATCCGGCCGCCTAGTCA 61.224 66.667 22.85 0.00 0.00 3.41
2847 3085 1.600916 GGCCTATGTTGGATCCGGC 60.601 63.158 15.61 15.61 36.83 6.13
2869 3107 7.011389 GCTAAATTTATTGATTTTGTGGGAGGC 59.989 37.037 0.00 0.00 31.96 4.70
2913 3151 6.145371 CGTTGGTAATTTGAAATTGAACTGGG 59.855 38.462 13.08 0.00 0.00 4.45
2939 3178 4.592485 TCACCTGAAAGAGAACAGAGTC 57.408 45.455 0.00 0.00 36.38 3.36
2944 3183 5.752036 ATCTCATCACCTGAAAGAGAACA 57.248 39.130 12.26 0.00 40.30 3.18
2947 3186 4.511527 GCAATCTCATCACCTGAAAGAGA 58.488 43.478 11.18 11.18 40.78 3.10
2975 3214 1.978617 CCATTCCAAGCCTTGCCGT 60.979 57.895 0.00 0.00 0.00 5.68
2977 3216 1.305213 TCCCATTCCAAGCCTTGCC 60.305 57.895 0.00 0.00 0.00 4.52
2989 3228 0.250513 GAGAGACAACGCCTCCCATT 59.749 55.000 0.00 0.00 0.00 3.16
2998 3237 2.866156 TGCTTGAAAGTGAGAGACAACG 59.134 45.455 0.00 0.00 0.00 4.10
3003 3242 2.158769 TGGCTTGCTTGAAAGTGAGAGA 60.159 45.455 0.00 0.00 0.00 3.10
3007 3246 2.034939 CACATGGCTTGCTTGAAAGTGA 59.965 45.455 0.00 0.00 0.00 3.41
3008 3247 2.400399 CACATGGCTTGCTTGAAAGTG 58.600 47.619 0.00 0.00 0.00 3.16
3009 3248 1.342174 CCACATGGCTTGCTTGAAAGT 59.658 47.619 0.00 0.00 0.00 2.66
3011 3250 1.614903 CTCCACATGGCTTGCTTGAAA 59.385 47.619 0.00 0.00 34.44 2.69
3027 3266 0.771127 CCTCTTTGGTTCCACCTCCA 59.229 55.000 0.00 0.00 39.58 3.86
3038 3277 2.899256 TGGCCTTGAATTTCCTCTTTGG 59.101 45.455 3.32 0.00 37.10 3.28
3050 3289 1.299648 CCTCGTGGATGGCCTTGAA 59.700 57.895 3.32 0.00 34.57 2.69
3052 3291 2.124570 CCCTCGTGGATGGCCTTG 60.125 66.667 3.32 0.00 35.39 3.61
3063 3303 4.401202 ACTTCATGTTTTTGTTTCCCTCGT 59.599 37.500 0.00 0.00 0.00 4.18
3074 3314 6.585416 AGCATTGGAAGAACTTCATGTTTTT 58.415 32.000 15.02 0.00 41.20 1.94
3108 3348 6.436847 TGGATCATGTTTCTTTGGAAATGCTA 59.563 34.615 0.00 0.00 42.45 3.49
3117 3357 4.338879 AGGGAGTGGATCATGTTTCTTTG 58.661 43.478 0.00 0.00 0.00 2.77
3119 3359 3.369892 CGAGGGAGTGGATCATGTTTCTT 60.370 47.826 0.00 0.00 0.00 2.52
3166 3406 2.677003 GCGCGTAGGCTTTGCTTCA 61.677 57.895 8.43 0.00 36.88 3.02
3168 3408 2.358737 AGCGCGTAGGCTTTGCTT 60.359 55.556 8.43 0.00 41.39 3.91
3190 3435 2.997899 GCATGCCGCTGTAGAAGAT 58.002 52.632 6.36 0.00 37.77 2.40
3210 3455 1.076549 GGTGGCCCTTGATTGGTCA 59.923 57.895 0.00 0.00 34.43 4.02
3212 3457 1.077265 CTGGTGGCCCTTGATTGGT 59.923 57.895 0.00 0.00 0.00 3.67
3220 3465 3.721706 GCACTAGCTGGTGGCCCT 61.722 66.667 28.76 0.00 43.05 5.19
3242 3487 4.488136 ATTGATGCGCGGCCAGGA 62.488 61.111 8.83 0.00 0.00 3.86
3252 3497 5.717119 AGGTGTCAAAGAATTGATTGATGC 58.283 37.500 5.95 3.37 46.67 3.91
3254 3499 7.667219 AGTGTAGGTGTCAAAGAATTGATTGAT 59.333 33.333 5.95 0.00 46.67 2.57
3271 3516 4.494484 TGATGAAACATCGAGTGTAGGTG 58.506 43.478 7.14 0.00 41.14 4.00
3279 3524 4.265556 GGTACGAACTGATGAAACATCGAG 59.734 45.833 7.14 7.90 34.62 4.04
3326 3572 7.750458 GTGTGTTGTACCATAACTCAATCATTG 59.250 37.037 0.00 0.00 34.54 2.82
3327 3573 7.094377 GGTGTGTTGTACCATAACTCAATCATT 60.094 37.037 2.12 0.00 38.12 2.57
3328 3574 6.374333 GGTGTGTTGTACCATAACTCAATCAT 59.626 38.462 2.12 0.00 38.12 2.45
3331 3577 5.626142 TGGTGTGTTGTACCATAACTCAAT 58.374 37.500 0.00 0.00 43.00 2.57
3348 3594 2.779755 TAGCCAAGTGGTATGGTGTG 57.220 50.000 0.00 0.00 40.23 3.82
3389 3635 1.334059 GCAGTTGGTGAACACACATCG 60.334 52.381 7.25 0.00 36.39 3.84
3391 3637 1.405105 GTGCAGTTGGTGAACACACAT 59.595 47.619 7.25 0.00 39.46 3.21
3393 3639 0.100503 GGTGCAGTTGGTGAACACAC 59.899 55.000 7.25 0.00 36.19 3.82
3398 3644 1.388547 GAAGTGGTGCAGTTGGTGAA 58.611 50.000 0.00 0.00 0.00 3.18
3407 3653 1.375908 GAGATGCCGAAGTGGTGCA 60.376 57.895 0.00 0.00 41.21 4.57
3432 3678 3.936372 TCTAGTGTCACTGGCACTAAC 57.064 47.619 21.16 0.00 45.34 2.34
3434 3680 5.479027 TGTAAATCTAGTGTCACTGGCACTA 59.521 40.000 19.96 19.96 44.41 2.74
3439 3690 5.869888 GGACTTGTAAATCTAGTGTCACTGG 59.130 44.000 16.03 12.95 32.78 4.00
3445 3696 5.979288 AGTCGGACTTGTAAATCTAGTGT 57.021 39.130 4.45 0.00 32.78 3.55


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

AutoCloner maintained by Alex Coulton.