Multiple sequence alignment - TraesCS3D01G269300

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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 TraesCS3D01G269300 chr3D 100.000 3747 0 0 1 3747 374011196 374014942 0.000000e+00 6920.0
1 TraesCS3D01G269300 chr3D 92.000 50 4 0 2251 2300 374013405 374013454 1.870000e-08 71.3
2 TraesCS3D01G269300 chr3D 92.000 50 4 0 2210 2259 374013446 374013495 1.870000e-08 71.3
3 TraesCS3D01G269300 chr3B 95.227 3394 122 26 4 3378 487767006 487770378 0.000000e+00 5334.0
4 TraesCS3D01G269300 chr3B 95.887 389 9 5 3363 3747 487773290 487773675 1.140000e-174 623.0
5 TraesCS3D01G269300 chr3B 78.889 270 41 9 5 262 117919515 117919780 6.440000e-38 169.0
6 TraesCS3D01G269300 chr3B 92.000 50 4 0 2210 2259 487769247 487769296 1.870000e-08 71.3
7 TraesCS3D01G269300 chr3B 90.196 51 4 1 2251 2300 487769205 487769255 8.690000e-07 65.8
8 TraesCS3D01G269300 chr3A 96.424 1510 38 8 2251 3747 496038007 496039513 0.000000e+00 2475.0
9 TraesCS3D01G269300 chr3A 90.767 1852 81 29 3 1824 496035738 496037529 0.000000e+00 2390.0
10 TraesCS3D01G269300 chr3A 89.670 455 29 7 1821 2259 496037604 496038056 7.030000e-157 564.0
11 TraesCS3D01G269300 chr4D 82.283 254 41 3 5 256 430831748 430831999 2.270000e-52 217.0
12 TraesCS3D01G269300 chr4D 80.351 285 42 8 2 274 111131850 111132132 1.760000e-48 204.0
13 TraesCS3D01G269300 chr4D 90.110 91 6 2 3467 3557 337520668 337520755 8.500000e-22 115.0
14 TraesCS3D01G269300 chr6B 79.924 264 43 8 1 262 707218090 707218345 6.390000e-43 185.0
15 TraesCS3D01G269300 chr1A 80.000 270 39 6 5 262 15780040 15779774 6.390000e-43 185.0
16 TraesCS3D01G269300 chr1A 78.598 271 42 7 5 262 15690986 15690719 8.330000e-37 165.0
17 TraesCS3D01G269300 chr1A 78.327 263 42 9 5 256 251580646 251580388 5.010000e-34 156.0
18 TraesCS3D01G269300 chr6A 76.652 227 40 10 4 220 523938348 523938125 3.060000e-21 113.0
19 TraesCS3D01G269300 chr2B 88.636 88 8 2 3470 3557 4837548 4837463 5.120000e-19 106.0
20 TraesCS3D01G269300 chr5A 75.610 205 46 3 427 629 558344765 558344967 8.560000e-17 99.0
21 TraesCS3D01G269300 chr5B 86.517 89 8 3 3469 3557 654756632 654756548 1.110000e-15 95.3
22 TraesCS3D01G269300 chr7D 85.714 91 10 3 3470 3560 549516522 549516435 3.980000e-15 93.5
23 TraesCS3D01G269300 chr7D 83.117 77 10 2 559 632 457437634 457437558 2.420000e-07 67.6
24 TraesCS3D01G269300 chr6D 85.393 89 9 3 3470 3558 330111495 330111411 5.150000e-14 89.8
25 TraesCS3D01G269300 chr2D 86.747 83 8 3 3470 3552 86080913 86080992 5.150000e-14 89.8
26 TraesCS3D01G269300 chr4B 84.783 92 9 4 3467 3557 416642527 416642614 1.850000e-13 87.9


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 TraesCS3D01G269300 chr3D 374011196 374014942 3746 False 2354.200000 6920 94.666667 1 3747 3 chr3D.!!$F1 3746
1 TraesCS3D01G269300 chr3B 487767006 487773675 6669 False 1523.525000 5334 93.327500 4 3747 4 chr3B.!!$F2 3743
2 TraesCS3D01G269300 chr3A 496035738 496039513 3775 False 1809.666667 2475 92.287000 3 3747 3 chr3A.!!$F1 3744

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
222 234 0.179081 GCTAGAATCACCACCGGGAC 60.179 60.000 6.32 0.0 38.05 4.46 F
356 369 1.684450 TCTACTTGTGTTCACGCCAGA 59.316 47.619 0.00 0.0 0.00 3.86 F
1035 1051 2.101783 TGTGCATCATCCAATCAACCC 58.898 47.619 0.00 0.0 0.00 4.11 F
1036 1052 2.291735 TGTGCATCATCCAATCAACCCT 60.292 45.455 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1993 0.799393 GGGAAGAAGCAAGAGAACGC 59.201 55.000 0.00 0.00 0.00 4.84 R
2233 2374 3.008704 AGTTGTAGCTTGTTATTCCGGGT 59.991 43.478 0.00 0.00 0.00 5.28 R
2380 2562 1.538047 GCAATGTGACACCAGGATGT 58.462 50.000 2.45 0.00 34.78 3.06 R
2942 3130 3.624410 TGTATGCTAGCATGCAGTTTCAG 59.376 43.478 35.52 7.67 46.71 3.02 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
28 29 2.159156 TCGTCGTGCTAAAGCCACATAT 60.159 45.455 0.00 0.00 41.18 1.78
29 30 3.067040 TCGTCGTGCTAAAGCCACATATA 59.933 43.478 0.00 0.00 41.18 0.86
41 42 2.560504 CCACATATAAGACCAGCGCAA 58.439 47.619 11.47 0.00 0.00 4.85
55 56 1.061799 GCGCAACAGAACAGCAATCG 61.062 55.000 0.30 0.00 0.00 3.34
56 57 0.453282 CGCAACAGAACAGCAATCGG 60.453 55.000 0.00 0.00 0.00 4.18
72 73 2.233654 CGGCGCCGATGAAGAGAAG 61.234 63.158 44.86 9.41 42.83 2.85
82 83 4.261405 CCGATGAAGAGAAGCTTAGATCGT 60.261 45.833 0.00 0.00 42.20 3.73
105 106 6.309737 CGTAAGGATCAAACCTGTAGTTACAC 59.690 42.308 0.00 0.00 40.49 2.90
111 112 4.805192 TCAAACCTGTAGTTACACGAACAC 59.195 41.667 0.00 0.00 40.86 3.32
112 113 4.389890 AACCTGTAGTTACACGAACACA 57.610 40.909 0.00 0.00 40.86 3.72
113 114 3.973657 ACCTGTAGTTACACGAACACAG 58.026 45.455 0.00 0.78 41.68 3.66
114 115 3.633525 ACCTGTAGTTACACGAACACAGA 59.366 43.478 15.42 0.00 43.03 3.41
115 116 4.280174 ACCTGTAGTTACACGAACACAGAT 59.720 41.667 15.42 3.05 43.03 2.90
116 117 4.621460 CCTGTAGTTACACGAACACAGATG 59.379 45.833 15.42 0.00 43.03 2.90
117 118 5.441709 TGTAGTTACACGAACACAGATGA 57.558 39.130 0.00 0.00 40.86 2.92
118 119 5.834169 TGTAGTTACACGAACACAGATGAA 58.166 37.500 0.00 0.00 40.86 2.57
119 120 5.688621 TGTAGTTACACGAACACAGATGAAC 59.311 40.000 0.00 0.00 40.86 3.18
120 121 3.734231 AGTTACACGAACACAGATGAACG 59.266 43.478 0.00 0.00 40.86 3.95
149 160 1.890041 CCACCGAAGACAAACGCCA 60.890 57.895 0.00 0.00 0.00 5.69
159 170 3.157087 AGACAAACGCCAATTGAATCCT 58.843 40.909 7.12 0.00 0.00 3.24
170 181 5.138276 CCAATTGAATCCTGTGAGATCCAT 58.862 41.667 7.12 0.00 0.00 3.41
171 182 5.597182 CCAATTGAATCCTGTGAGATCCATT 59.403 40.000 7.12 0.00 0.00 3.16
220 232 0.469917 ATGCTAGAATCACCACCGGG 59.530 55.000 6.32 0.00 41.29 5.73
221 233 0.616395 TGCTAGAATCACCACCGGGA 60.616 55.000 6.32 0.00 38.05 5.14
222 234 0.179081 GCTAGAATCACCACCGGGAC 60.179 60.000 6.32 0.00 38.05 4.46
312 325 7.986889 TGTTGATTCCAAATGATATCGAGAGAA 59.013 33.333 0.00 0.00 37.62 2.87
348 361 5.500645 AAAAACTGCCTCTACTTGTGTTC 57.499 39.130 0.00 0.00 0.00 3.18
350 363 3.113260 ACTGCCTCTACTTGTGTTCAC 57.887 47.619 0.00 0.00 0.00 3.18
356 369 1.684450 TCTACTTGTGTTCACGCCAGA 59.316 47.619 0.00 0.00 0.00 3.86
449 463 7.820648 AGATTTTTAAGCACGACAAATCTGAT 58.179 30.769 7.80 0.00 40.86 2.90
557 571 8.223100 GTCAAAAATTTACCATGCTTGCTAAAG 58.777 33.333 6.34 0.00 36.41 1.85
561 575 8.900983 AAATTTACCATGCTTGCTAAAGAAAA 57.099 26.923 6.34 0.00 35.19 2.29
564 578 8.900983 TTTACCATGCTTGCTAAAGAAAATTT 57.099 26.923 0.00 0.00 35.19 1.82
574 588 6.890558 TGCTAAAGAAAATTTTCATGCTTGC 58.109 32.000 28.00 22.20 39.61 4.01
577 591 6.601741 AAAGAAAATTTTCATGCTTGCGAA 57.398 29.167 28.00 0.00 39.61 4.70
637 651 9.079833 CATGCTTAAAAATCTGACATTTGTAGG 57.920 33.333 0.00 0.00 0.00 3.18
679 693 5.895636 TTCCTGCTATATTTGTTGTGGTG 57.104 39.130 0.00 0.00 0.00 4.17
774 788 3.645212 TGGCAAAGATCCTAGGAGATCAG 59.355 47.826 18.34 8.16 44.32 2.90
902 916 5.047021 GCCATGCCACTAGAATACTAGATGA 60.047 44.000 10.60 0.00 46.34 2.92
963 978 8.603304 AGCAAGTCTCCCTTTTAATAAAGAGTA 58.397 33.333 0.00 0.00 42.78 2.59
1035 1051 2.101783 TGTGCATCATCCAATCAACCC 58.898 47.619 0.00 0.00 0.00 4.11
1036 1052 2.291735 TGTGCATCATCCAATCAACCCT 60.292 45.455 0.00 0.00 0.00 4.34
1385 1401 2.954318 ACACATCTTGCAAAGCTGAAGT 59.046 40.909 0.00 0.00 42.40 3.01
1695 1725 6.743575 ATATGTGGAAGCAGTAGAAACAAC 57.256 37.500 0.00 0.00 0.00 3.32
1697 1727 3.876914 TGTGGAAGCAGTAGAAACAACTG 59.123 43.478 0.00 0.00 45.80 3.16
1868 1993 2.683867 AGTTAGGTGTGCTAGCTCTACG 59.316 50.000 17.23 0.00 38.31 3.51
2218 2359 3.492102 AGGTACTGCACACAACTTCAT 57.508 42.857 0.00 0.00 37.18 2.57
2219 2360 3.820557 AGGTACTGCACACAACTTCATT 58.179 40.909 0.00 0.00 37.18 2.57
2220 2361 4.968259 AGGTACTGCACACAACTTCATTA 58.032 39.130 0.00 0.00 37.18 1.90
2221 2362 5.373222 AGGTACTGCACACAACTTCATTAA 58.627 37.500 0.00 0.00 37.18 1.40
2222 2363 6.003950 AGGTACTGCACACAACTTCATTAAT 58.996 36.000 0.00 0.00 37.18 1.40
2223 2364 6.149474 AGGTACTGCACACAACTTCATTAATC 59.851 38.462 0.00 0.00 37.18 1.75
2224 2365 5.376854 ACTGCACACAACTTCATTAATCC 57.623 39.130 0.00 0.00 0.00 3.01
2225 2366 5.072741 ACTGCACACAACTTCATTAATCCT 58.927 37.500 0.00 0.00 0.00 3.24
2226 2367 5.536161 ACTGCACACAACTTCATTAATCCTT 59.464 36.000 0.00 0.00 0.00 3.36
2227 2368 5.771469 TGCACACAACTTCATTAATCCTTG 58.229 37.500 0.00 0.00 0.00 3.61
2228 2369 5.534278 TGCACACAACTTCATTAATCCTTGA 59.466 36.000 0.00 0.00 0.00 3.02
2229 2370 6.040278 TGCACACAACTTCATTAATCCTTGAA 59.960 34.615 0.00 0.00 0.00 2.69
2230 2371 7.092716 GCACACAACTTCATTAATCCTTGAAT 58.907 34.615 0.00 0.00 31.83 2.57
2231 2372 7.599998 GCACACAACTTCATTAATCCTTGAATT 59.400 33.333 0.00 0.00 31.83 2.17
2232 2373 9.480053 CACACAACTTCATTAATCCTTGAATTT 57.520 29.630 0.00 0.00 31.83 1.82
2236 2377 9.586435 CAACTTCATTAATCCTTGAATTTACCC 57.414 33.333 0.00 0.00 31.83 3.69
2237 2378 7.996385 ACTTCATTAATCCTTGAATTTACCCG 58.004 34.615 0.00 0.00 31.83 5.28
2238 2379 6.952773 TCATTAATCCTTGAATTTACCCGG 57.047 37.500 0.00 0.00 0.00 5.73
2239 2380 6.664714 TCATTAATCCTTGAATTTACCCGGA 58.335 36.000 0.73 0.00 0.00 5.14
2240 2381 7.120051 TCATTAATCCTTGAATTTACCCGGAA 58.880 34.615 0.73 0.00 0.00 4.30
2241 2382 7.782644 TCATTAATCCTTGAATTTACCCGGAAT 59.217 33.333 0.73 0.00 0.00 3.01
2242 2383 9.073475 CATTAATCCTTGAATTTACCCGGAATA 57.927 33.333 0.73 0.00 0.00 1.75
2243 2384 9.649316 ATTAATCCTTGAATTTACCCGGAATAA 57.351 29.630 0.73 0.00 0.00 1.40
2244 2385 6.954487 ATCCTTGAATTTACCCGGAATAAC 57.046 37.500 0.73 0.00 0.00 1.89
2245 2386 5.817784 TCCTTGAATTTACCCGGAATAACA 58.182 37.500 0.73 0.00 0.00 2.41
2246 2387 6.246919 TCCTTGAATTTACCCGGAATAACAA 58.753 36.000 0.73 5.08 0.00 2.83
2247 2388 6.376018 TCCTTGAATTTACCCGGAATAACAAG 59.624 38.462 0.73 13.40 34.55 3.16
2248 2389 5.570234 TGAATTTACCCGGAATAACAAGC 57.430 39.130 0.73 0.00 0.00 4.01
2249 2390 5.258051 TGAATTTACCCGGAATAACAAGCT 58.742 37.500 0.73 0.00 0.00 3.74
2250 2391 6.416415 TGAATTTACCCGGAATAACAAGCTA 58.584 36.000 0.73 0.00 0.00 3.32
2251 2392 6.316890 TGAATTTACCCGGAATAACAAGCTAC 59.683 38.462 0.73 0.00 0.00 3.58
2252 2393 4.822685 TTACCCGGAATAACAAGCTACA 57.177 40.909 0.73 0.00 0.00 2.74
2253 2394 3.706600 ACCCGGAATAACAAGCTACAA 57.293 42.857 0.73 0.00 0.00 2.41
2254 2395 3.340928 ACCCGGAATAACAAGCTACAAC 58.659 45.455 0.73 0.00 0.00 3.32
2255 2396 3.008704 ACCCGGAATAACAAGCTACAACT 59.991 43.478 0.73 0.00 0.00 3.16
2256 2397 3.621715 CCCGGAATAACAAGCTACAACTC 59.378 47.826 0.73 0.00 0.00 3.01
2257 2398 3.621715 CCGGAATAACAAGCTACAACTCC 59.378 47.826 0.00 0.00 0.00 3.85
2258 2399 4.250464 CGGAATAACAAGCTACAACTCCA 58.750 43.478 0.00 0.00 0.00 3.86
2262 2403 7.465513 CGGAATAACAAGCTACAACTCCATTAC 60.466 40.741 0.00 0.00 0.00 1.89
2292 2433 7.057894 TGAATTTACCCGGAATAACAAGCTAT 58.942 34.615 0.73 0.00 0.00 2.97
2380 2562 2.360600 GGGCCACCACATTACGCA 60.361 61.111 4.39 0.00 36.50 5.24
2460 2642 1.177401 TGGAGACAGATGGACGAGTG 58.823 55.000 0.00 0.00 35.01 3.51
2461 2643 1.178276 GGAGACAGATGGACGAGTGT 58.822 55.000 0.00 0.00 0.00 3.55
2563 2745 3.383698 AGGAATCTACCCGTCTGAGAA 57.616 47.619 0.00 0.00 0.00 2.87
2613 2795 4.563337 TTCGACGAGTATGAATTCCGAT 57.437 40.909 2.27 0.00 0.00 4.18
2667 2855 5.752955 GCTATGATCCTCAAGTGTTCTTCTC 59.247 44.000 0.00 0.00 0.00 2.87
2942 3130 2.191128 AGATGTGTTGACTCTTGCCC 57.809 50.000 0.00 0.00 0.00 5.36
3444 6565 9.967346 TCTCTGTATAGTGTACATTTAATCTGC 57.033 33.333 0.00 0.00 0.00 4.26
3586 6714 6.462347 GGAAAAAGCAAACTGATAAAGGGTCA 60.462 38.462 0.00 0.00 0.00 4.02
3587 6715 6.670695 AAAAGCAAACTGATAAAGGGTCAT 57.329 33.333 0.00 0.00 0.00 3.06
3598 6726 3.726291 AAAGGGTCATGGTTTCAAACG 57.274 42.857 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.220133 GCTTTAGCACGACGACTTTTCA 59.780 45.455 0.00 0.00 41.59 2.69
1 2 2.411160 GGCTTTAGCACGACGACTTTTC 60.411 50.000 0.00 0.00 44.36 2.29
19 20 1.541233 GCGCTGGTCTTATATGTGGCT 60.541 52.381 0.00 0.00 0.00 4.75
28 29 1.202592 TGTTCTGTTGCGCTGGTCTTA 60.203 47.619 9.73 0.00 0.00 2.10
29 30 0.463654 TGTTCTGTTGCGCTGGTCTT 60.464 50.000 9.73 0.00 0.00 3.01
41 42 2.680913 GCGCCGATTGCTGTTCTGT 61.681 57.895 0.00 0.00 38.05 3.41
55 56 2.529619 GCTTCTCTTCATCGGCGCC 61.530 63.158 19.07 19.07 0.00 6.53
56 57 1.086634 AAGCTTCTCTTCATCGGCGC 61.087 55.000 0.00 0.00 0.00 6.53
72 73 5.908916 GGTTTGATCCTTACGATCTAAGC 57.091 43.478 9.24 9.24 46.35 3.09
82 83 6.209192 TCGTGTAACTACAGGTTTGATCCTTA 59.791 38.462 8.87 0.00 41.41 2.69
94 95 5.458015 TCATCTGTGTTCGTGTAACTACAG 58.542 41.667 0.00 0.00 42.42 2.74
105 106 3.049912 TGTCTTCGTTCATCTGTGTTCG 58.950 45.455 0.00 0.00 0.00 3.95
111 112 3.118992 TGGATCCTGTCTTCGTTCATCTG 60.119 47.826 14.23 0.00 0.00 2.90
112 113 3.099905 TGGATCCTGTCTTCGTTCATCT 58.900 45.455 14.23 0.00 0.00 2.90
113 114 3.190874 GTGGATCCTGTCTTCGTTCATC 58.809 50.000 14.23 0.00 0.00 2.92
114 115 2.093447 GGTGGATCCTGTCTTCGTTCAT 60.093 50.000 14.23 0.00 0.00 2.57
115 116 1.275291 GGTGGATCCTGTCTTCGTTCA 59.725 52.381 14.23 0.00 0.00 3.18
116 117 1.736032 CGGTGGATCCTGTCTTCGTTC 60.736 57.143 14.23 0.00 0.00 3.95
117 118 0.246635 CGGTGGATCCTGTCTTCGTT 59.753 55.000 14.23 0.00 0.00 3.85
118 119 0.611062 TCGGTGGATCCTGTCTTCGT 60.611 55.000 14.23 0.00 0.00 3.85
119 120 0.530744 TTCGGTGGATCCTGTCTTCG 59.469 55.000 14.23 7.79 0.00 3.79
120 121 1.825474 TCTTCGGTGGATCCTGTCTTC 59.175 52.381 14.23 0.00 0.00 2.87
149 160 5.597182 CCAATGGATCTCACAGGATTCAATT 59.403 40.000 0.00 0.00 35.18 2.32
159 170 4.326826 GTTTGTCTCCAATGGATCTCACA 58.673 43.478 0.87 0.91 0.00 3.58
220 232 2.140839 TCTTCCCTCTTAGTCCCGTC 57.859 55.000 0.00 0.00 0.00 4.79
221 233 2.617840 TTCTTCCCTCTTAGTCCCGT 57.382 50.000 0.00 0.00 0.00 5.28
222 234 4.489306 AAATTCTTCCCTCTTAGTCCCG 57.511 45.455 0.00 0.00 0.00 5.14
232 244 8.899887 TTTGAAGATGGAATAAATTCTTCCCT 57.100 30.769 14.16 7.10 42.09 4.20
233 245 8.971073 TCTTTGAAGATGGAATAAATTCTTCCC 58.029 33.333 14.16 3.76 42.09 3.97
256 269 0.677098 TAGAGGCGACGACAGCTCTT 60.677 55.000 2.19 0.00 34.52 2.85
304 317 4.036567 TGTTGACTTTTCGTTCTCTCGA 57.963 40.909 0.00 0.00 38.08 4.04
348 361 0.385849 TACGTACGTGTTCTGGCGTG 60.386 55.000 30.25 0.00 41.68 5.34
350 363 1.400990 GCTACGTACGTGTTCTGGCG 61.401 60.000 30.25 9.23 0.00 5.69
356 369 7.119605 TCATAAATTTTGCTACGTACGTGTT 57.880 32.000 30.25 6.64 0.00 3.32
544 558 7.480542 GCATGAAAATTTTCTTTAGCAAGCATG 59.519 33.333 26.73 19.34 38.02 4.06
557 571 6.190962 TGTTTTCGCAAGCATGAAAATTTTC 58.809 32.000 21.60 21.60 43.57 2.29
561 575 7.599630 ATTATGTTTTCGCAAGCATGAAAAT 57.400 28.000 7.35 0.00 43.57 1.82
564 578 7.062839 GGTAAATTATGTTTTCGCAAGCATGAA 59.937 33.333 7.35 0.00 34.89 2.57
574 588 9.197694 TGTTTTGGATGGTAAATTATGTTTTCG 57.802 29.630 0.00 0.00 0.00 3.46
712 726 7.104290 GGTTACTTAGGAGAGTAATTTGCACT 58.896 38.462 0.00 0.00 42.31 4.40
774 788 7.254421 GGCAATGCATTTTAATTAGTTAGGTGC 60.254 37.037 9.83 4.74 0.00 5.01
963 978 2.988859 TCTTGCAGGCCAATATATCCCT 59.011 45.455 5.01 0.00 31.91 4.20
1035 1051 2.975489 AGCTAGGAGGAGAGAGAGAGAG 59.025 54.545 0.00 0.00 0.00 3.20
1036 1052 3.060479 AGCTAGGAGGAGAGAGAGAGA 57.940 52.381 0.00 0.00 0.00 3.10
1739 1779 6.889301 TCACAAAGAAGCTCAAAATCTCAT 57.111 33.333 0.00 0.00 0.00 2.90
1803 1849 6.991485 TTCAAGAATGATTGCTCGTTTTTC 57.009 33.333 0.00 0.00 34.96 2.29
1809 1856 9.292846 TCAAATTAATTCAAGAATGATTGCTCG 57.707 29.630 0.10 0.00 34.96 5.03
1868 1993 0.799393 GGGAAGAAGCAAGAGAACGC 59.201 55.000 0.00 0.00 0.00 4.84
2218 2359 8.905850 GTTATTCCGGGTAAATTCAAGGATTAA 58.094 33.333 0.00 0.00 0.00 1.40
2219 2360 8.053963 TGTTATTCCGGGTAAATTCAAGGATTA 58.946 33.333 0.00 0.00 0.00 1.75
2220 2361 6.893005 TGTTATTCCGGGTAAATTCAAGGATT 59.107 34.615 0.00 0.00 0.00 3.01
2221 2362 6.428295 TGTTATTCCGGGTAAATTCAAGGAT 58.572 36.000 0.00 0.00 0.00 3.24
2222 2363 5.817784 TGTTATTCCGGGTAAATTCAAGGA 58.182 37.500 0.00 0.00 0.00 3.36
2223 2364 6.518208 TTGTTATTCCGGGTAAATTCAAGG 57.482 37.500 0.00 0.00 0.00 3.61
2224 2365 6.033966 GCTTGTTATTCCGGGTAAATTCAAG 58.966 40.000 0.00 12.81 34.18 3.02
2225 2366 5.712917 AGCTTGTTATTCCGGGTAAATTCAA 59.287 36.000 0.00 3.56 0.00 2.69
2226 2367 5.258051 AGCTTGTTATTCCGGGTAAATTCA 58.742 37.500 0.00 0.00 0.00 2.57
2227 2368 5.830000 AGCTTGTTATTCCGGGTAAATTC 57.170 39.130 0.00 0.00 0.00 2.17
2228 2369 6.181908 TGTAGCTTGTTATTCCGGGTAAATT 58.818 36.000 0.00 0.00 0.00 1.82
2229 2370 5.747342 TGTAGCTTGTTATTCCGGGTAAAT 58.253 37.500 0.00 0.00 0.00 1.40
2230 2371 5.163281 TGTAGCTTGTTATTCCGGGTAAA 57.837 39.130 0.00 0.00 0.00 2.01
2231 2372 4.822685 TGTAGCTTGTTATTCCGGGTAA 57.177 40.909 0.00 0.00 0.00 2.85
2232 2373 4.223477 AGTTGTAGCTTGTTATTCCGGGTA 59.777 41.667 0.00 0.00 0.00 3.69
2233 2374 3.008704 AGTTGTAGCTTGTTATTCCGGGT 59.991 43.478 0.00 0.00 0.00 5.28
2234 2375 3.606687 AGTTGTAGCTTGTTATTCCGGG 58.393 45.455 0.00 0.00 0.00 5.73
2235 2376 3.621715 GGAGTTGTAGCTTGTTATTCCGG 59.378 47.826 0.00 0.00 0.00 5.14
2236 2377 4.250464 TGGAGTTGTAGCTTGTTATTCCG 58.750 43.478 0.00 0.00 0.00 4.30
2237 2378 6.759497 AATGGAGTTGTAGCTTGTTATTCC 57.241 37.500 0.00 0.00 0.00 3.01
2238 2379 8.494016 AGTAATGGAGTTGTAGCTTGTTATTC 57.506 34.615 0.00 0.00 0.00 1.75
2239 2380 7.553044 GGAGTAATGGAGTTGTAGCTTGTTATT 59.447 37.037 0.00 0.00 0.00 1.40
2240 2381 7.048512 GGAGTAATGGAGTTGTAGCTTGTTAT 58.951 38.462 0.00 0.00 0.00 1.89
2241 2382 6.212791 AGGAGTAATGGAGTTGTAGCTTGTTA 59.787 38.462 0.00 0.00 0.00 2.41
2242 2383 5.013183 AGGAGTAATGGAGTTGTAGCTTGTT 59.987 40.000 0.00 0.00 0.00 2.83
2243 2384 4.532521 AGGAGTAATGGAGTTGTAGCTTGT 59.467 41.667 0.00 0.00 0.00 3.16
2244 2385 5.091261 AGGAGTAATGGAGTTGTAGCTTG 57.909 43.478 0.00 0.00 0.00 4.01
2245 2386 5.248477 TCAAGGAGTAATGGAGTTGTAGCTT 59.752 40.000 0.00 0.00 0.00 3.74
2246 2387 4.777896 TCAAGGAGTAATGGAGTTGTAGCT 59.222 41.667 0.00 0.00 0.00 3.32
2247 2388 5.086104 TCAAGGAGTAATGGAGTTGTAGC 57.914 43.478 0.00 0.00 0.00 3.58
2248 2389 8.567285 AAATTCAAGGAGTAATGGAGTTGTAG 57.433 34.615 0.00 0.00 0.00 2.74
2249 2390 9.444600 GTAAATTCAAGGAGTAATGGAGTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
2250 2391 7.393515 GGTAAATTCAAGGAGTAATGGAGTTGT 59.606 37.037 0.00 0.00 0.00 3.32
2251 2392 7.148069 GGGTAAATTCAAGGAGTAATGGAGTTG 60.148 40.741 0.00 0.00 0.00 3.16
2252 2393 6.890268 GGGTAAATTCAAGGAGTAATGGAGTT 59.110 38.462 0.00 0.00 0.00 3.01
2253 2394 6.424032 GGGTAAATTCAAGGAGTAATGGAGT 58.576 40.000 0.00 0.00 0.00 3.85
2254 2395 5.527582 CGGGTAAATTCAAGGAGTAATGGAG 59.472 44.000 0.00 0.00 0.00 3.86
2255 2396 5.433526 CGGGTAAATTCAAGGAGTAATGGA 58.566 41.667 0.00 0.00 0.00 3.41
2256 2397 4.578928 CCGGGTAAATTCAAGGAGTAATGG 59.421 45.833 0.00 0.00 0.00 3.16
2257 2398 5.433526 TCCGGGTAAATTCAAGGAGTAATG 58.566 41.667 0.00 0.00 0.00 1.90
2258 2399 5.703730 TCCGGGTAAATTCAAGGAGTAAT 57.296 39.130 0.00 0.00 0.00 1.89
2262 2403 5.883673 TGTTATTCCGGGTAAATTCAAGGAG 59.116 40.000 0.00 0.00 0.00 3.69
2292 2433 3.762407 TGCAGTTGTTAGTTGGAGCTA 57.238 42.857 0.00 0.00 0.00 3.32
2380 2562 1.538047 GCAATGTGACACCAGGATGT 58.462 50.000 2.45 0.00 34.78 3.06
2460 2642 4.309099 TGCTTTTTGATCAGCCATTCAAC 58.691 39.130 0.00 0.00 34.91 3.18
2461 2643 4.603989 TGCTTTTTGATCAGCCATTCAA 57.396 36.364 0.00 0.00 34.91 2.69
2563 2745 4.101448 GCTCCGGTCATGGTGCCT 62.101 66.667 0.00 0.00 41.52 4.75
2586 2768 4.576216 ATTCATACTCGTCGAATCAGCT 57.424 40.909 0.00 0.00 0.00 4.24
2657 2839 5.471257 AGATGAACGTAAGGAGAAGAACAC 58.529 41.667 0.00 0.00 46.39 3.32
2667 2855 3.948473 TCAGAGGAGAGATGAACGTAAGG 59.052 47.826 0.00 0.00 46.39 2.69
2942 3130 3.624410 TGTATGCTAGCATGCAGTTTCAG 59.376 43.478 35.52 7.67 46.71 3.02
3542 6668 9.603921 CTTTTTCCAAAGTATTACCTCCGTATA 57.396 33.333 0.00 0.00 35.53 1.47


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

AutoCloner maintained by Alex Coulton.