Multiple sequence alignment - TraesCS7A01G550900

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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 TraesCS7A01G550900 chr7A 100.000 3740 0 0 1 3740 724651926 724655665 0.000000e+00 6907.0
1 TraesCS7A01G550900 chr7A 83.333 78 10 3 2957 3034 724668992 724669066 6.700000e-08 69.4
2 TraesCS7A01G550900 chr7D 92.467 2894 143 27 579 3436 628522532 628519678 0.000000e+00 4067.0
3 TraesCS7A01G550900 chr7D 85.913 646 62 11 3045 3689 628512927 628512310 0.000000e+00 662.0
4 TraesCS7A01G550900 chr7D 90.860 372 31 1 2340 2711 628517849 628517481 2.590000e-136 496.0
5 TraesCS7A01G550900 chr7D 84.795 342 36 11 201 532 628522986 628522651 2.780000e-86 329.0
6 TraesCS7A01G550900 chr7D 97.159 176 5 0 2870 3045 628517466 628517291 7.850000e-77 298.0
7 TraesCS7A01G550900 chr7D 85.366 205 29 1 1 205 628523239 628523036 1.050000e-50 211.0
8 TraesCS7A01G550900 chr7B 91.422 2891 180 26 646 3496 730400123 730397261 0.000000e+00 3903.0
9 TraesCS7A01G550900 chr7B 86.308 1154 88 30 2405 3518 730485294 730486417 0.000000e+00 1192.0
10 TraesCS7A01G550900 chr7B 88.542 384 44 0 1934 2317 730484910 730485293 2.030000e-127 466.0
11 TraesCS7A01G550900 chr7B 86.723 354 36 5 214 567 730400525 730400183 2.110000e-102 383.0
12 TraesCS7A01G550900 chr7B 83.618 293 32 12 2750 3034 730508944 730509228 1.030000e-65 261.0
13 TraesCS7A01G550900 chr7B 86.598 194 24 2 1 193 730400789 730400597 2.930000e-51 213.0
14 TraesCS7A01G550900 chr6B 75.710 1478 298 42 1255 2706 619032415 619030973 0.000000e+00 684.0
15 TraesCS7A01G550900 chr6A 75.084 1485 303 42 1252 2706 556558602 556557155 6.820000e-177 630.0
16 TraesCS7A01G550900 chr6D 75.035 1418 273 51 1331 2706 411673735 411672357 1.940000e-162 582.0
17 TraesCS7A01G550900 chr1B 80.080 251 44 4 1044 1293 4602253 4602498 8.250000e-42 182.0
18 TraesCS7A01G550900 chr3D 82.222 135 17 5 202 332 26300096 26300227 3.950000e-20 110.0
19 TraesCS7A01G550900 chr1D 81.356 118 21 1 216 332 365800823 365800706 1.110000e-15 95.3
20 TraesCS7A01G550900 chr3B 85.294 68 9 1 265 332 43925422 43925488 6.700000e-08 69.4
21 TraesCS7A01G550900 chr3B 85.294 68 9 1 265 332 44031236 44031302 6.700000e-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 TraesCS7A01G550900 chr7A 724651926 724655665 3739 False 6907.000000 6907 100.000000 1 3740 1 chr7A.!!$F1 3739
1 TraesCS7A01G550900 chr7D 628517291 628523239 5948 True 1080.200000 4067 90.129400 1 3436 5 chr7D.!!$R2 3435
2 TraesCS7A01G550900 chr7D 628512310 628512927 617 True 662.000000 662 85.913000 3045 3689 1 chr7D.!!$R1 644
3 TraesCS7A01G550900 chr7B 730397261 730400789 3528 True 1499.666667 3903 88.247667 1 3496 3 chr7B.!!$R1 3495
4 TraesCS7A01G550900 chr7B 730484910 730486417 1507 False 829.000000 1192 87.425000 1934 3518 2 chr7B.!!$F2 1584
5 TraesCS7A01G550900 chr6B 619030973 619032415 1442 True 684.000000 684 75.710000 1255 2706 1 chr6B.!!$R1 1451
6 TraesCS7A01G550900 chr6A 556557155 556558602 1447 True 630.000000 630 75.084000 1252 2706 1 chr6A.!!$R1 1454
7 TraesCS7A01G550900 chr6D 411672357 411673735 1378 True 582.000000 582 75.035000 1331 2706 1 chr6D.!!$R1 1375

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
293 346 0.242017 AGCAAAGATGGTTCGCTTGC 59.758 50.0 0.00 0.0 41.81 4.01 F
332 385 0.903942 TTCGCCGGGTACAATTACCT 59.096 50.0 2.18 0.0 46.56 3.08 F
2056 2247 0.249120 CTCAGCCGGGTACAACATCA 59.751 55.0 5.47 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2154 0.396139 TAGAACCGGTCCACGCCTAT 60.396 55.000 8.04 0.00 42.52 2.57 R
2295 2486 0.734942 CTTCTTTCGGGTTCGCGCTA 60.735 55.000 5.56 0.00 36.13 4.26 R
3419 3659 1.347707 TCTTAGAACCTGGCACCAGTG 59.652 52.381 15.39 9.32 42.15 3.66 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
47 48 9.796120 TTGTAATTCAAACTACTTCAACCAAAG 57.204 29.630 0.00 0.00 32.64 2.77
48 49 8.962679 TGTAATTCAAACTACTTCAACCAAAGT 58.037 29.630 0.00 0.00 42.10 2.66
50 51 7.639113 ATTCAAACTACTTCAACCAAAGTCA 57.361 32.000 0.00 0.00 40.01 3.41
86 87 8.677148 TGATAGTGGATTAATTAAGCAACTCC 57.323 34.615 23.41 17.28 37.14 3.85
89 90 7.396540 AGTGGATTAATTAAGCAACTCCAAG 57.603 36.000 16.18 0.00 30.49 3.61
100 101 6.749923 AAGCAACTCCAAGATATTCTCAAC 57.250 37.500 0.00 0.00 0.00 3.18
164 165 1.359459 CCCTTAGCTGGCGAACGTTC 61.359 60.000 18.47 18.47 0.00 3.95
165 166 0.669318 CCTTAGCTGGCGAACGTTCA 60.669 55.000 26.71 8.47 0.00 3.18
166 167 0.438830 CTTAGCTGGCGAACGTTCAC 59.561 55.000 26.71 17.89 0.00 3.18
185 186 1.077265 CAGGGAGGGTGGCATTTGT 59.923 57.895 0.00 0.00 0.00 2.83
189 190 1.560505 GGAGGGTGGCATTTGTGAAT 58.439 50.000 0.00 0.00 0.00 2.57
193 194 3.953612 GAGGGTGGCATTTGTGAATGATA 59.046 43.478 3.47 0.00 44.37 2.15
200 201 4.520492 GGCATTTGTGAATGATACCCTAGG 59.480 45.833 0.06 0.06 44.37 3.02
205 206 7.201821 CATTTGTGAATGATACCCTAGGGTTTC 60.202 40.741 38.11 35.31 44.49 2.78
244 297 6.673316 GCAAATTTTGTTTAAAACTGCCGTCA 60.673 34.615 10.65 0.00 39.59 4.35
254 307 2.768253 ACTGCCGTCATTTGATCTCA 57.232 45.000 0.00 0.00 0.00 3.27
293 346 0.242017 AGCAAAGATGGTTCGCTTGC 59.758 50.000 0.00 0.00 41.81 4.01
305 358 2.750237 GCTTGCCACCCCCTTACG 60.750 66.667 0.00 0.00 0.00 3.18
306 359 3.074281 CTTGCCACCCCCTTACGA 58.926 61.111 0.00 0.00 0.00 3.43
332 385 0.903942 TTCGCCGGGTACAATTACCT 59.096 50.000 2.18 0.00 46.56 3.08
336 389 2.418471 CGCCGGGTACAATTACCTTACA 60.418 50.000 2.18 0.00 46.56 2.41
340 393 5.125900 GCCGGGTACAATTACCTTACATTTT 59.874 40.000 2.18 0.00 46.56 1.82
341 394 6.557110 CCGGGTACAATTACCTTACATTTTG 58.443 40.000 0.00 0.00 46.56 2.44
342 395 6.374894 CCGGGTACAATTACCTTACATTTTGA 59.625 38.462 0.00 0.00 46.56 2.69
343 396 7.067737 CCGGGTACAATTACCTTACATTTTGAT 59.932 37.037 0.00 0.00 46.56 2.57
344 397 7.913297 CGGGTACAATTACCTTACATTTTGATG 59.087 37.037 0.00 0.00 46.56 3.07
345 398 8.745590 GGGTACAATTACCTTACATTTTGATGT 58.254 33.333 0.00 0.00 46.56 3.06
377 430 7.553881 TCTTTTGTTTAGAGTCACTCAAAGG 57.446 36.000 7.77 0.00 32.06 3.11
395 448 6.908825 TCAAAGGCATGTGTTATTGAACTAC 58.091 36.000 0.00 0.00 36.45 2.73
466 526 5.181748 ACAAAGCCAACATCTAGATCAGTC 58.818 41.667 1.03 0.00 0.00 3.51
467 527 5.181009 CAAAGCCAACATCTAGATCAGTCA 58.819 41.667 1.03 0.00 0.00 3.41
469 529 5.426689 AGCCAACATCTAGATCAGTCAAA 57.573 39.130 1.03 0.00 0.00 2.69
471 531 5.879223 AGCCAACATCTAGATCAGTCAAAAG 59.121 40.000 1.03 0.00 0.00 2.27
475 535 7.012138 CCAACATCTAGATCAGTCAAAAGATGG 59.988 40.741 1.03 0.00 39.80 3.51
503 565 4.653868 ACGAGGAAGAAGAGTACAAGAGA 58.346 43.478 0.00 0.00 0.00 3.10
527 589 8.197439 AGACAGCTTGTAAATTTTAAAAGCACT 58.803 29.630 31.41 25.29 44.45 4.40
528 590 8.352752 ACAGCTTGTAAATTTTAAAAGCACTC 57.647 30.769 31.41 13.29 44.45 3.51
532 594 5.774630 TGTAAATTTTAAAAGCACTCCCCG 58.225 37.500 6.79 0.00 0.00 5.73
575 641 8.375608 TGGATTTGTTTTATTCACACAAATGG 57.624 30.769 12.88 0.00 46.36 3.16
577 643 8.711457 GGATTTGTTTTATTCACACAAATGGAG 58.289 33.333 12.88 0.00 46.36 3.86
578 644 9.260002 GATTTGTTTTATTCACACAAATGGAGT 57.740 29.630 12.88 0.00 46.36 3.85
582 648 9.906660 TGTTTTATTCACACAAATGGAGTAATC 57.093 29.630 0.00 0.00 0.00 1.75
736 879 6.649973 TCCTCCTTTATCTACGTCTTATCTCG 59.350 42.308 0.00 0.00 0.00 4.04
737 880 6.427547 CCTCCTTTATCTACGTCTTATCTCGT 59.572 42.308 0.00 0.00 42.82 4.18
848 1001 4.473520 CGGCGCCCTCCAGTCAAT 62.474 66.667 23.46 0.00 0.00 2.57
1104 1265 2.125350 GTCCTCTGCTTCAGCCGG 60.125 66.667 0.00 0.00 41.18 6.13
1294 1455 1.979693 GACTGGGAGGTGCTCGTCT 60.980 63.158 8.23 0.00 0.00 4.18
1482 1646 2.351322 CGGCTCGTGATCTCGTCG 60.351 66.667 16.03 13.97 0.00 5.12
1483 1647 2.792599 GGCTCGTGATCTCGTCGT 59.207 61.111 16.03 0.00 0.00 4.34
1484 1648 1.297745 GGCTCGTGATCTCGTCGTC 60.298 63.158 16.03 7.41 0.00 4.20
1485 1649 1.648756 GCTCGTGATCTCGTCGTCG 60.649 63.158 16.03 0.00 38.55 5.12
1659 1823 2.626780 CGCGGCCTCTGATATCCGA 61.627 63.158 13.93 0.00 44.23 4.55
1844 2011 2.893398 GTCCCTGGCCGTCTACAG 59.107 66.667 0.00 0.00 34.54 2.74
1965 2156 2.184836 GTGTACCACGCGGCCATA 59.815 61.111 12.47 0.00 34.57 2.74
2056 2247 0.249120 CTCAGCCGGGTACAACATCA 59.751 55.000 5.47 0.00 0.00 3.07
2129 2320 3.624300 CGCAGCGCTCCGAGATTG 61.624 66.667 17.63 0.00 0.00 2.67
2190 2381 0.687757 TCTCCCCGAGATGGAACCAG 60.688 60.000 0.00 0.00 42.00 4.00
2286 2477 2.033448 TGCGCCGATTTTGGACCT 59.967 55.556 4.18 0.00 0.00 3.85
2682 2879 1.740296 CGCGACCCGAAGATGGTTT 60.740 57.895 0.00 0.00 40.02 3.27
2767 2966 3.243367 GCATTGCAGTGTACAAACCAAGA 60.243 43.478 11.18 0.00 0.00 3.02
2768 2967 4.736168 GCATTGCAGTGTACAAACCAAGAA 60.736 41.667 11.18 0.00 0.00 2.52
2769 2968 4.630894 TTGCAGTGTACAAACCAAGAAG 57.369 40.909 0.00 0.00 0.00 2.85
2787 2986 6.705381 CCAAGAAGAAGATTAGGATACAGCAG 59.295 42.308 0.00 0.00 41.41 4.24
2788 2987 7.418368 CCAAGAAGAAGATTAGGATACAGCAGA 60.418 40.741 0.00 0.00 41.41 4.26
2789 2988 7.667575 AGAAGAAGATTAGGATACAGCAGAA 57.332 36.000 0.00 0.00 41.41 3.02
2790 2989 7.496747 AGAAGAAGATTAGGATACAGCAGAAC 58.503 38.462 0.00 0.00 41.41 3.01
2791 2990 6.798427 AGAAGATTAGGATACAGCAGAACA 57.202 37.500 0.00 0.00 41.41 3.18
2849 3056 5.703730 TTGTTGGGTTAGGAACTATAGGG 57.296 43.478 4.43 0.00 42.38 3.53
3056 3296 9.692749 TTGTCAAAAACAATACTGTGTTAACAA 57.307 25.926 10.51 4.76 42.95 2.83
3125 3365 2.677199 GCATCACGACTTCTTCTGTCA 58.323 47.619 0.00 0.00 34.37 3.58
3139 3379 4.096382 TCTTCTGTCACTTTTCTTGGCAAC 59.904 41.667 0.00 0.00 0.00 4.17
3276 3516 6.215845 TCTATGCCAAAAAGAAACTGCTTTC 58.784 36.000 0.00 0.00 37.12 2.62
3359 3599 7.910162 GTGCATATTGGTATGTAACTTGAAGTG 59.090 37.037 0.00 0.00 39.90 3.16
3419 3659 0.596082 TTGCAGCTTAAAAGGGTCGC 59.404 50.000 0.00 0.00 0.00 5.19
3442 3682 3.690460 CTGGTGCCAGGTTCTAAGAATT 58.310 45.455 10.28 0.00 40.17 2.17
3485 3725 7.346751 TGAAAGAAAGCAACCTTTATTGACT 57.653 32.000 0.00 0.00 40.51 3.41
3550 3790 8.310382 TGATGAAACTTATTTGGGGTTATGTTG 58.690 33.333 0.00 0.00 0.00 3.33
3588 3828 8.924511 ATGGACTCAGTCAAATCTAAAAAGAA 57.075 30.769 7.24 0.00 33.68 2.52
3628 3868 6.364435 GCTAAAGCTTGAGTTGATTTGAAAGG 59.636 38.462 12.62 0.00 38.21 3.11
3640 3880 4.949856 TGATTTGAAAGGGAGGAAGTATGC 59.050 41.667 0.00 0.00 0.00 3.14
3642 3882 4.380843 TTGAAAGGGAGGAAGTATGCAA 57.619 40.909 0.00 0.00 0.00 4.08
3694 3936 3.878160 ACAACAATGTGAAAAACGGGT 57.122 38.095 0.00 0.00 38.69 5.28
3696 3938 4.570930 ACAACAATGTGAAAAACGGGTTT 58.429 34.783 0.00 0.00 38.69 3.27
3697 3939 4.998033 ACAACAATGTGAAAAACGGGTTTT 59.002 33.333 2.88 2.88 40.30 2.43
3698 3940 5.106908 ACAACAATGTGAAAAACGGGTTTTG 60.107 36.000 8.75 0.00 39.36 2.44
3699 3941 3.372514 ACAATGTGAAAAACGGGTTTTGC 59.627 39.130 8.75 8.91 41.45 3.68
3703 3961 4.755411 TGTGAAAAACGGGTTTTGCATTA 58.245 34.783 18.04 9.78 46.38 1.90
3705 3963 5.642063 TGTGAAAAACGGGTTTTGCATTAAA 59.358 32.000 18.04 5.24 46.38 1.52
3709 3967 5.915812 AAACGGGTTTTGCATTAAACATC 57.084 34.783 14.30 6.48 39.27 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.447040 GACTTTGGTTGAAGTAGTTTGAATTAC 57.553 33.333 0.00 0.00 39.84 1.89
25 26 8.062065 TGACTTTGGTTGAAGTAGTTTGAATT 57.938 30.769 0.00 0.00 39.84 2.17
86 87 8.654215 CATCACCGATATGTTGAGAATATCTTG 58.346 37.037 0.00 0.00 35.65 3.02
89 90 6.536582 CCCATCACCGATATGTTGAGAATATC 59.463 42.308 0.00 0.00 34.84 1.63
100 101 2.146342 GTTGCTCCCATCACCGATATG 58.854 52.381 0.00 0.00 0.00 1.78
165 166 2.169810 AAATGCCACCCTCCCTGGT 61.170 57.895 0.00 0.00 39.96 4.00
166 167 1.683365 CAAATGCCACCCTCCCTGG 60.683 63.158 0.00 0.00 0.00 4.45
193 194 6.109253 TCTCTCGAGAAGAAACCCTAGGGT 62.109 50.000 28.99 28.99 41.82 4.34
206 207 4.821805 ACAAAATTTGCCTTCTCTCGAGAA 59.178 37.500 17.36 8.88 44.47 2.87
207 208 4.389374 ACAAAATTTGCCTTCTCTCGAGA 58.611 39.130 15.70 15.70 35.27 4.04
208 209 4.756084 ACAAAATTTGCCTTCTCTCGAG 57.244 40.909 5.93 5.93 0.00 4.04
210 211 7.692908 TTTAAACAAAATTTGCCTTCTCTCG 57.307 32.000 5.52 0.00 0.00 4.04
211 212 9.098355 AGTTTTAAACAAAATTTGCCTTCTCTC 57.902 29.630 10.60 0.00 0.00 3.20
212 213 8.882736 CAGTTTTAAACAAAATTTGCCTTCTCT 58.117 29.630 10.60 0.00 0.00 3.10
223 276 7.278868 TCAAATGACGGCAGTTTTAAACAAAAT 59.721 29.630 0.00 0.00 28.37 1.82
254 307 9.846248 CTTTGCTGACAGCTTTAGTTATAAAAT 57.154 29.630 26.94 0.00 42.97 1.82
268 321 1.135859 CGAACCATCTTTGCTGACAGC 60.136 52.381 20.86 20.86 42.82 4.40
272 325 1.536766 CAAGCGAACCATCTTTGCTGA 59.463 47.619 0.00 0.00 35.77 4.26
293 346 1.079612 GTTCGTCGTAAGGGGGTGG 60.080 63.158 0.00 0.00 38.47 4.61
319 372 8.745590 ACATCAAAATGTAAGGTAATTGTACCC 58.254 33.333 0.00 0.00 46.03 3.69
361 414 4.202357 ACACATGCCTTTGAGTGACTCTAA 60.202 41.667 14.42 11.52 35.97 2.10
395 448 6.978659 TCACTCACGCCATTTAGAGTATAAAG 59.021 38.462 0.00 0.00 39.17 1.85
412 465 2.455674 TGGTTCTTGGATCACTCACG 57.544 50.000 0.00 0.00 0.00 4.35
466 526 4.829064 TCCTCGTTTCAACCATCTTTTG 57.171 40.909 0.00 0.00 0.00 2.44
467 527 5.130350 TCTTCCTCGTTTCAACCATCTTTT 58.870 37.500 0.00 0.00 0.00 2.27
469 529 4.351874 TCTTCCTCGTTTCAACCATCTT 57.648 40.909 0.00 0.00 0.00 2.40
471 531 4.315803 TCTTCTTCCTCGTTTCAACCATC 58.684 43.478 0.00 0.00 0.00 3.51
475 535 5.287226 TGTACTCTTCTTCCTCGTTTCAAC 58.713 41.667 0.00 0.00 0.00 3.18
503 565 7.438160 GGAGTGCTTTTAAAATTTACAAGCTGT 59.562 33.333 26.70 18.14 40.48 4.40
518 580 1.681076 GGGACGGGGAGTGCTTTTA 59.319 57.895 0.00 0.00 41.32 1.52
527 589 2.361771 GTGACTAGGGGACGGGGA 59.638 66.667 0.00 0.00 0.00 4.81
528 590 2.038329 TGTGACTAGGGGACGGGG 59.962 66.667 0.00 0.00 0.00 5.73
532 594 2.304761 TCCATTTGTGTGACTAGGGGAC 59.695 50.000 0.00 0.00 0.00 4.46
625 761 9.969001 TTGCCTAGGAGTATTTATTTACAAACT 57.031 29.630 14.75 0.00 0.00 2.66
626 762 9.999009 GTTGCCTAGGAGTATTTATTTACAAAC 57.001 33.333 14.75 0.00 0.00 2.93
627 763 9.969001 AGTTGCCTAGGAGTATTTATTTACAAA 57.031 29.630 14.75 0.00 0.00 2.83
628 764 9.391006 CAGTTGCCTAGGAGTATTTATTTACAA 57.609 33.333 14.75 0.00 0.00 2.41
630 766 7.497909 TGCAGTTGCCTAGGAGTATTTATTTAC 59.502 37.037 14.75 0.00 41.18 2.01
631 767 7.570132 TGCAGTTGCCTAGGAGTATTTATTTA 58.430 34.615 14.75 0.00 41.18 1.40
632 768 6.423182 TGCAGTTGCCTAGGAGTATTTATTT 58.577 36.000 14.75 0.00 41.18 1.40
634 770 5.630415 TGCAGTTGCCTAGGAGTATTTAT 57.370 39.130 14.75 0.00 41.18 1.40
635 771 5.429681 TTGCAGTTGCCTAGGAGTATTTA 57.570 39.130 14.75 0.00 41.18 1.40
638 774 4.510167 AATTGCAGTTGCCTAGGAGTAT 57.490 40.909 14.75 0.00 41.18 2.12
639 775 4.301072 AAATTGCAGTTGCCTAGGAGTA 57.699 40.909 14.75 0.00 41.18 2.59
641 777 4.525912 AAAAATTGCAGTTGCCTAGGAG 57.474 40.909 14.75 0.00 41.18 3.69
662 805 2.096819 GCGACCACACTCTGTTTTGAAA 59.903 45.455 0.00 0.00 0.00 2.69
663 806 1.668751 GCGACCACACTCTGTTTTGAA 59.331 47.619 0.00 0.00 0.00 2.69
664 807 1.295792 GCGACCACACTCTGTTTTGA 58.704 50.000 0.00 0.00 0.00 2.69
678 821 1.874345 TTTGAGAGTCCTCCGCGACC 61.874 60.000 8.23 0.00 38.66 4.79
736 879 0.040425 ACAAACGCTGCGATGGAAAC 60.040 50.000 30.47 0.00 0.00 2.78
737 880 0.665835 AACAAACGCTGCGATGGAAA 59.334 45.000 30.47 0.00 0.00 3.13
767 910 2.165845 GGAAAGCTCGACTAAGCCTACA 59.834 50.000 0.00 0.00 43.56 2.74
834 987 2.825836 GGCATTGACTGGAGGGCG 60.826 66.667 0.00 0.00 0.00 6.13
835 988 2.048603 GTGGCATTGACTGGAGGGC 61.049 63.158 0.00 0.00 0.00 5.19
836 989 1.746615 CGTGGCATTGACTGGAGGG 60.747 63.158 0.00 0.00 0.00 4.30
837 990 0.249120 TACGTGGCATTGACTGGAGG 59.751 55.000 0.00 0.00 0.00 4.30
838 991 2.315925 ATACGTGGCATTGACTGGAG 57.684 50.000 0.00 0.00 0.00 3.86
839 992 5.294356 GTTATATACGTGGCATTGACTGGA 58.706 41.667 0.00 0.00 0.00 3.86
840 993 4.451096 GGTTATATACGTGGCATTGACTGG 59.549 45.833 0.00 0.00 0.00 4.00
841 994 4.451096 GGGTTATATACGTGGCATTGACTG 59.549 45.833 0.00 0.00 0.00 3.51
848 1001 1.614903 CCTCGGGTTATATACGTGGCA 59.385 52.381 0.00 0.00 35.02 4.92
1322 1486 3.608662 ACGTCGCGTTCCCTCCAA 61.609 61.111 5.77 0.00 36.35 3.53
1464 1628 2.792599 GACGAGATCACGAGCCGT 59.207 61.111 19.57 6.31 42.36 5.68
1607 1771 3.056328 GCGGGTTGACTCCCTTGC 61.056 66.667 0.25 0.00 44.95 4.01
1886 2077 2.178890 CAGGCGCAGATCAGCTTCC 61.179 63.158 10.83 8.99 0.00 3.46
1963 2154 0.396139 TAGAACCGGTCCACGCCTAT 60.396 55.000 8.04 0.00 42.52 2.57
1965 2156 2.283388 TAGAACCGGTCCACGCCT 60.283 61.111 8.04 1.11 42.52 5.52
2056 2247 4.697756 CGGCCATGTCACGGTGGT 62.698 66.667 8.50 0.00 37.81 4.16
2115 2306 2.185350 CACCAATCTCGGAGCGCT 59.815 61.111 11.27 11.27 0.00 5.92
2286 2477 1.517694 GTTCGCGCTATGACCGGAA 60.518 57.895 9.46 0.00 0.00 4.30
2292 2483 0.804544 CTTTCGGGTTCGCGCTATGA 60.805 55.000 5.56 0.00 36.13 2.15
2295 2486 0.734942 CTTCTTTCGGGTTCGCGCTA 60.735 55.000 5.56 0.00 36.13 4.26
2297 2488 2.474712 CTTCTTTCGGGTTCGCGC 59.525 61.111 0.00 0.00 36.13 6.86
2395 2586 1.153745 GGATCGAGTTGAGCAGCGT 60.154 57.895 0.00 0.00 33.60 5.07
2626 2818 3.882888 TCATTCACCTCGCAAAACTTCTT 59.117 39.130 0.00 0.00 0.00 2.52
2673 2870 0.469144 ACCCAACGCCAAACCATCTT 60.469 50.000 0.00 0.00 0.00 2.40
2682 2879 3.875023 TTCCCGAACCCAACGCCA 61.875 61.111 0.00 0.00 0.00 5.69
2767 2966 7.187824 TGTTCTGCTGTATCCTAATCTTCTT 57.812 36.000 0.00 0.00 0.00 2.52
2768 2967 6.798427 TGTTCTGCTGTATCCTAATCTTCT 57.202 37.500 0.00 0.00 0.00 2.85
2769 2968 7.334421 TGTTTGTTCTGCTGTATCCTAATCTTC 59.666 37.037 0.00 0.00 0.00 2.87
2787 2986 7.250569 TGTCTTGAAAGAATCAGTGTTTGTTC 58.749 34.615 0.00 0.19 39.77 3.18
2788 2987 7.156876 TGTCTTGAAAGAATCAGTGTTTGTT 57.843 32.000 0.00 0.00 39.77 2.83
2789 2988 6.757897 TGTCTTGAAAGAATCAGTGTTTGT 57.242 33.333 0.00 0.00 39.77 2.83
2790 2989 9.903682 ATTATGTCTTGAAAGAATCAGTGTTTG 57.096 29.630 0.00 0.00 39.77 2.93
2821 3023 5.529581 AGTTCCTAACCCAACAATGTTTG 57.470 39.130 0.00 0.00 0.00 2.93
2849 3056 1.154197 GTACAAGAAAGGGACCGTGC 58.846 55.000 0.00 0.00 0.00 5.34
3073 3313 5.071250 ACCAGGACACACTTTGTATCTTGTA 59.929 40.000 0.00 0.00 39.17 2.41
3074 3314 4.141482 ACCAGGACACACTTTGTATCTTGT 60.141 41.667 0.00 0.00 39.17 3.16
3120 3360 3.781079 TGTTGCCAAGAAAAGTGACAG 57.219 42.857 0.00 0.00 0.00 3.51
3191 3431 3.252554 AGGATGCCCTCTCTAACTAGG 57.747 52.381 0.00 0.00 38.86 3.02
3204 3444 2.802719 TGGTGGAAAGTTAAGGATGCC 58.197 47.619 0.00 0.00 0.00 4.40
3257 3497 3.530535 TGGAAAGCAGTTTCTTTTTGGC 58.469 40.909 0.00 0.00 41.72 4.52
3330 3570 8.341892 TCAAGTTACATACCAATATGCACAAA 57.658 30.769 0.00 0.00 41.83 2.83
3419 3659 1.347707 TCTTAGAACCTGGCACCAGTG 59.652 52.381 15.39 9.32 42.15 3.66
3433 3673 9.516546 TCTCATCTAGCCGTTATAATTCTTAGA 57.483 33.333 0.00 0.00 0.00 2.10
3442 3682 8.178313 TCTTTCATTCTCATCTAGCCGTTATA 57.822 34.615 0.00 0.00 0.00 0.98
3519 3759 6.074648 ACCCCAAATAAGTTTCATCAACAGA 58.925 36.000 0.00 0.00 37.93 3.41
3520 3760 6.345096 ACCCCAAATAAGTTTCATCAACAG 57.655 37.500 0.00 0.00 37.93 3.16
3521 3761 6.739331 AACCCCAAATAAGTTTCATCAACA 57.261 33.333 0.00 0.00 37.93 3.33
3522 3762 8.311109 ACATAACCCCAAATAAGTTTCATCAAC 58.689 33.333 0.00 0.00 35.32 3.18
3523 3763 8.429237 ACATAACCCCAAATAAGTTTCATCAA 57.571 30.769 0.00 0.00 0.00 2.57
3524 3764 8.310382 CAACATAACCCCAAATAAGTTTCATCA 58.690 33.333 0.00 0.00 0.00 3.07
3525 3765 8.527810 TCAACATAACCCCAAATAAGTTTCATC 58.472 33.333 0.00 0.00 0.00 2.92
3563 3803 8.924511 TTCTTTTTAGATTTGACTGAGTCCAT 57.075 30.769 10.52 1.97 0.00 3.41
3566 3806 9.980780 GCTATTCTTTTTAGATTTGACTGAGTC 57.019 33.333 5.47 5.47 0.00 3.36
3578 3818 8.947115 GCTTTGTCCTAAGCTATTCTTTTTAGA 58.053 33.333 6.27 0.00 45.50 2.10
3613 3853 5.073428 ACTTCCTCCCTTTCAAATCAACTC 58.927 41.667 0.00 0.00 0.00 3.01
3628 3868 3.060602 GCTCGTATTGCATACTTCCTCC 58.939 50.000 0.00 0.00 33.59 4.30
3640 3880 4.715520 ATTGCGATAGTTGCTCGTATTG 57.284 40.909 0.00 0.00 38.37 1.90
3642 3882 8.703604 ATATTTATTGCGATAGTTGCTCGTAT 57.296 30.769 0.00 0.00 38.37 3.06
3673 3913 5.106908 AAAACCCGTTTTTCACATTGTTGTG 60.107 36.000 0.00 0.00 43.03 3.33
3690 3932 7.826260 ATTAAGATGTTTAATGCAAAACCCG 57.174 32.000 10.68 0.00 38.35 5.28


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

AutoCloner maintained by Alex Coulton.