Multiple sequence alignment - TraesCS2A01G269500

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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 TraesCS2A01G269500 chr2A 100.000 2764 0 0 1 2764 435577368 435580131 0.000000e+00 5105
1 TraesCS2A01G269500 chr2B 92.484 2661 186 11 1 2656 397918810 397921461 0.000000e+00 3794
2 TraesCS2A01G269500 chr2D 93.189 2496 132 18 272 2756 329147848 329150316 0.000000e+00 3633
3 TraesCS2A01G269500 chr2D 86.429 280 38 0 1 280 329139370 329139649 9.620000e-80 307
4 TraesCS2A01G269500 chr7D 84.348 345 46 7 187 528 538241312 538241651 5.710000e-87 331
5 TraesCS2A01G269500 chr1D 84.058 345 50 5 174 515 36531888 36532230 7.380000e-86 327
6 TraesCS2A01G269500 chr7B 86.689 293 36 3 189 479 205365469 205365760 3.430000e-84 322
7 TraesCS2A01G269500 chr4A 83.768 345 49 7 173 515 645306192 645306531 1.240000e-83 320
8 TraesCS2A01G269500 chr6B 83.099 355 50 9 166 515 656290735 656291084 5.750000e-82 315
9 TraesCS2A01G269500 chr5D 83.673 343 47 8 180 516 554573251 554572912 5.750000e-82 315
10 TraesCS2A01G269500 chr5D 82.849 344 49 9 174 513 355098219 355098556 1.610000e-77 300


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 TraesCS2A01G269500 chr2A 435577368 435580131 2763 False 5105 5105 100.000 1 2764 1 chr2A.!!$F1 2763
1 TraesCS2A01G269500 chr2B 397918810 397921461 2651 False 3794 3794 92.484 1 2656 1 chr2B.!!$F1 2655
2 TraesCS2A01G269500 chr2D 329147848 329150316 2468 False 3633 3633 93.189 272 2756 1 chr2D.!!$F2 2484


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
247 248 0.109342 ACGGGATGATGGAAGATGGC 59.891 55.0 0.0 0.0 0.0 4.40 F
250 251 0.109342 GGATGATGGAAGATGGCGGT 59.891 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1288 0.174389 CAGGTCCTCATCGGTCACAG 59.826 60.0 0.0 0.0 0.0 3.66 R
1826 1832 0.323542 ATGTCCTCTCCCTCGTCGTT 60.324 55.0 0.0 0.0 0.0 3.85 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
25 26 1.590591 TGGTGCTATGTGTGGGGTAT 58.409 50.000 0.00 0.00 0.00 2.73
37 38 4.042311 TGTGTGGGGTATGAGTTGTACAAT 59.958 41.667 12.26 0.85 0.00 2.71
39 40 5.007034 TGTGGGGTATGAGTTGTACAATTG 58.993 41.667 12.26 3.24 0.00 2.32
63 64 6.021596 GTGCAGTTTGTGTACATGTATTAGC 58.978 40.000 9.18 6.05 41.23 3.09
67 68 3.528597 TGTGTACATGTATTAGCCGCA 57.471 42.857 9.18 5.75 0.00 5.69
83 84 1.269726 CCGCATTGAGCAAAGGTTGTT 60.270 47.619 0.00 0.00 46.13 2.83
84 85 2.030363 CCGCATTGAGCAAAGGTTGTTA 60.030 45.455 0.00 0.00 46.13 2.41
95 96 7.831690 TGAGCAAAGGTTGTTATATACATGGAA 59.168 33.333 0.00 0.00 36.44 3.53
97 98 9.860650 AGCAAAGGTTGTTATATACATGGAATA 57.139 29.630 0.00 0.00 36.44 1.75
119 120 3.310501 ACAAGTTACAACACGCTTGTACC 59.689 43.478 6.95 0.60 46.39 3.34
127 128 0.537188 CACGCTTGTACCCTGATCCT 59.463 55.000 0.00 0.00 0.00 3.24
137 138 5.525484 TGTACCCTGATCCTTAGTGTGTAT 58.475 41.667 0.00 0.00 0.00 2.29
144 145 6.121776 TGATCCTTAGTGTGTATGTGGTTT 57.878 37.500 0.00 0.00 0.00 3.27
148 149 5.761234 TCCTTAGTGTGTATGTGGTTTTGAC 59.239 40.000 0.00 0.00 0.00 3.18
154 155 6.093771 AGTGTGTATGTGGTTTTGACGTTAAA 59.906 34.615 0.73 0.73 0.00 1.52
156 157 8.068977 GTGTGTATGTGGTTTTGACGTTAAATA 58.931 33.333 6.31 0.00 0.00 1.40
165 166 9.420551 TGGTTTTGACGTTAAATAACAACTTTT 57.579 25.926 6.31 0.00 35.99 2.27
183 184 1.295792 TTTGTGGCTTGACTGTCGAC 58.704 50.000 9.11 9.11 0.00 4.20
185 186 1.007734 GTGGCTTGACTGTCGACGA 60.008 57.895 11.62 0.00 0.00 4.20
199 200 1.732809 TCGACGACAGATGAGACTGAC 59.267 52.381 0.00 0.00 40.63 3.51
210 211 5.921976 CAGATGAGACTGACAAGATCTATGC 59.078 44.000 0.00 0.00 39.94 3.14
219 220 7.559486 ACTGACAAGATCTATGCAGTGATTTA 58.441 34.615 18.12 0.00 35.41 1.40
227 228 8.435187 AGATCTATGCAGTGATTTATCCTGAAA 58.565 33.333 0.00 0.00 31.15 2.69
229 230 8.213518 TCTATGCAGTGATTTATCCTGAAAAC 57.786 34.615 0.00 0.00 31.15 2.43
237 238 6.263168 GTGATTTATCCTGAAAACGGGATGAT 59.737 38.462 17.58 12.24 41.78 2.45
247 248 0.109342 ACGGGATGATGGAAGATGGC 59.891 55.000 0.00 0.00 0.00 4.40
250 251 0.109342 GGATGATGGAAGATGGCGGT 59.891 55.000 0.00 0.00 0.00 5.68
251 252 1.477558 GGATGATGGAAGATGGCGGTT 60.478 52.381 0.00 0.00 0.00 4.44
260 261 1.224592 GATGGCGGTTGTGGATCCT 59.775 57.895 14.23 0.00 0.00 3.24
266 267 1.685224 GGTTGTGGATCCTGGAGCA 59.315 57.895 14.71 1.84 0.00 4.26
270 271 1.225426 GTGGATCCTGGAGCATGCA 59.775 57.895 21.98 0.00 33.07 3.96
302 303 2.770447 TGTTATGGGATGCCTAGACCA 58.230 47.619 4.35 0.00 37.41 4.02
321 322 2.771943 CCAGATGGTCTTAAGGCCACTA 59.228 50.000 30.58 9.15 37.62 2.74
342 343 9.254133 CCACTAGATTAGATTGTGTCTGTTATG 57.746 37.037 0.00 0.00 37.83 1.90
345 346 6.573434 AGATTAGATTGTGTCTGTTATGCGA 58.427 36.000 0.00 0.00 37.83 5.10
349 350 4.389992 AGATTGTGTCTGTTATGCGAACAG 59.610 41.667 20.07 20.07 46.67 3.16
359 360 0.541392 ATGCGAACAGGGCACATCTA 59.459 50.000 0.00 0.00 44.23 1.98
385 386 4.134563 ACTTGTAGGTGTAGCAACTTTGG 58.865 43.478 0.00 0.00 31.86 3.28
398 399 4.644685 AGCAACTTTGGTTTGCTTAGAAGA 59.355 37.500 3.75 0.00 36.88 2.87
408 409 3.719268 TGCTTAGAAGATGGCTTTGGA 57.281 42.857 0.00 0.00 33.61 3.53
432 434 9.342308 GGATTGATCCTTGTATTATTTGTCAGA 57.658 33.333 2.72 0.00 43.73 3.27
498 500 2.076803 GGAGGCCGGGGTAATCCTT 61.077 63.158 2.18 0.00 35.33 3.36
500 502 2.053259 GAGGCCGGGGTAATCCTTCC 62.053 65.000 2.18 0.00 35.33 3.46
502 504 1.642513 GGCCGGGGTAATCCTTCCTT 61.643 60.000 2.18 0.00 35.33 3.36
509 511 4.533815 GGGGTAATCCTTCCTTTCGAAAT 58.466 43.478 11.70 0.00 35.33 2.17
510 512 5.685599 CGGGGTAATCCTTCCTTTCGAAATA 60.686 44.000 11.70 0.00 35.33 1.40
515 517 9.569167 GGTAATCCTTCCTTTCGAAATAAAAAG 57.431 33.333 11.70 11.66 33.26 2.27
519 521 9.860898 ATCCTTCCTTTCGAAATAAAAAGAATG 57.139 29.630 11.70 5.72 35.02 2.67
577 582 3.270027 TGAGTTAGATTTCACCCATGCG 58.730 45.455 0.00 0.00 0.00 4.73
587 592 0.248661 CACCCATGCGTACTCGAGAG 60.249 60.000 21.68 11.01 39.71 3.20
660 665 2.895404 ACCTGTAAGTAGTCAAGCCGAA 59.105 45.455 0.00 0.00 0.00 4.30
683 688 0.391597 CGCGGGTGTCCTATGGTTAT 59.608 55.000 0.00 0.00 0.00 1.89
928 933 1.490490 CATCCATTCGGAGGAGGGAAA 59.510 52.381 0.00 0.00 46.44 3.13
967 972 2.095853 CCATTCGATAGCCAACACACAC 59.904 50.000 0.00 0.00 0.00 3.82
972 977 3.194755 TCGATAGCCAACACACACTACAT 59.805 43.478 0.00 0.00 0.00 2.29
1016 1021 1.368209 CAATGGCCAACAGCTGCAA 59.632 52.632 10.96 0.00 43.05 4.08
1293 1298 2.809601 GCGAACGCTGTGACCGAT 60.810 61.111 11.97 0.00 38.26 4.18
1401 1406 2.618045 CCCTGCCCTCGACTTGTATTTT 60.618 50.000 0.00 0.00 0.00 1.82
1584 1589 0.877071 GTCCAGGTCAGTAACGTCGA 59.123 55.000 0.00 0.00 0.00 4.20
1634 1640 7.967908 AGTATAGATTCCGAAAGAACCATCAT 58.032 34.615 0.00 0.00 37.29 2.45
1668 1674 1.129917 TGGTCGGTTGTTTGGTCCTA 58.870 50.000 0.00 0.00 0.00 2.94
1682 1688 1.415659 GGTCCTATGACTCATGCAGCT 59.584 52.381 1.42 0.00 41.47 4.24
1760 1766 1.486310 TGTTCAGTGAAGCACTCCAGT 59.514 47.619 5.62 0.00 43.43 4.00
1769 1775 1.005630 GCACTCCAGTTGAGAGCGT 60.006 57.895 0.00 0.00 45.60 5.07
1794 1800 1.638070 TGCAATGAACCACCCATCCTA 59.362 47.619 0.00 0.00 0.00 2.94
1797 1803 3.696045 CAATGAACCACCCATCCTACAA 58.304 45.455 0.00 0.00 0.00 2.41
1826 1832 5.408880 TGTACATCCGAGTGTTCCATTAA 57.591 39.130 0.00 0.00 33.62 1.40
1849 1855 0.333312 ACGAGGGAGAGGACATGACT 59.667 55.000 0.00 0.00 0.00 3.41
1889 1896 2.102588 ACGTCTAACCTTGTTGCTCTGT 59.897 45.455 0.00 0.00 0.00 3.41
1890 1897 3.319972 ACGTCTAACCTTGTTGCTCTGTA 59.680 43.478 0.00 0.00 0.00 2.74
1958 1965 0.324275 AACATTAATGCACCGCCCCT 60.324 50.000 15.48 0.00 0.00 4.79
2039 2046 8.500753 TTAGAAACACTAACTCTTGCTGAAAA 57.499 30.769 0.00 0.00 36.33 2.29
2168 2177 4.601857 AGATTGTAGGGGAGAAAAGTTGGA 59.398 41.667 0.00 0.00 0.00 3.53
2210 2219 5.059161 TGAATCAGAGATTTTAGATGGGCG 58.941 41.667 0.00 0.00 0.00 6.13
2250 2259 7.002250 TGAATGTCTGAAATTAAATTGGGCA 57.998 32.000 0.00 0.00 0.00 5.36
2256 2265 4.764172 TGAAATTAAATTGGGCATTCCGG 58.236 39.130 0.00 0.00 38.76 5.14
2399 2408 2.351418 TGATTGGACTTAGCGCAAATCG 59.649 45.455 11.47 0.00 42.12 3.34
2415 2424 5.616204 CGCAAATCGCTCATGTGAATATCAT 60.616 40.000 0.00 0.00 39.08 2.45
2450 2459 4.100653 TGGATTCTCAAGCCTCAGATACAG 59.899 45.833 0.00 0.00 37.96 2.74
2452 2461 4.727507 TTCTCAAGCCTCAGATACAGAC 57.272 45.455 0.00 0.00 0.00 3.51
2453 2462 3.701664 TCTCAAGCCTCAGATACAGACA 58.298 45.455 0.00 0.00 0.00 3.41
2461 2471 4.626042 CCTCAGATACAGACATGGCTTAC 58.374 47.826 0.00 0.00 0.00 2.34
2477 2487 2.879756 GCTTACTGGGCATCTCCAAACA 60.880 50.000 0.00 0.00 36.21 2.83
2498 2508 5.113383 ACATTGACGTTAAACAGACACTCA 58.887 37.500 0.00 0.00 0.00 3.41
2527 2537 0.535335 GTGGACATCTAACCTGGCGA 59.465 55.000 0.00 0.00 0.00 5.54
2565 2575 7.447238 CACTATCCTTTGAACCTTTTCCAGTTA 59.553 37.037 0.00 0.00 0.00 2.24
2571 2581 7.604545 CCTTTGAACCTTTTCCAGTTAAAACAA 59.395 33.333 0.00 0.00 0.00 2.83
2572 2582 8.904099 TTTGAACCTTTTCCAGTTAAAACAAA 57.096 26.923 0.00 0.00 0.00 2.83
2681 2691 8.823220 ATTAAACTAAACTAATGCTGGATGGT 57.177 30.769 0.00 0.00 0.00 3.55
2691 2701 4.630644 ATGCTGGATGGTAACCTCATAG 57.369 45.455 0.00 0.00 32.06 2.23
2694 2704 1.691976 TGGATGGTAACCTCATAGGCG 59.308 52.381 0.00 0.00 39.63 5.52
2698 2708 0.828677 GGTAACCTCATAGGCGTGGT 59.171 55.000 0.00 0.00 39.63 4.16
2699 2709 1.208776 GGTAACCTCATAGGCGTGGTT 59.791 52.381 4.55 4.55 44.03 3.67
2716 2726 0.108281 GTTTCCGAGGCCACTAGGAC 60.108 60.000 5.01 0.00 46.46 3.85
2727 2737 1.202463 CCACTAGGACTGCAATCCTCG 60.202 57.143 22.15 17.45 46.92 4.63
2730 2740 1.751351 CTAGGACTGCAATCCTCGTCA 59.249 52.381 22.15 1.51 46.92 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.297701 CCCCACACATAGCACCATAAC 58.702 52.381 0.00 0.00 0.00 1.89
7 8 1.488812 TCATACCCCACACATAGCACC 59.511 52.381 0.00 0.00 0.00 5.01
15 16 3.688694 TGTACAACTCATACCCCACAC 57.311 47.619 0.00 0.00 0.00 3.82
25 26 5.105957 ACAAACTGCACAATTGTACAACTCA 60.106 36.000 11.22 3.99 35.63 3.41
37 38 6.384258 AATACATGTACACAAACTGCACAA 57.616 33.333 7.96 0.00 0.00 3.33
39 40 6.021596 GCTAATACATGTACACAAACTGCAC 58.978 40.000 7.96 0.00 0.00 4.57
59 60 0.810648 CCTTTGCTCAATGCGGCTAA 59.189 50.000 0.00 0.00 46.63 3.09
63 64 0.314935 ACAACCTTTGCTCAATGCGG 59.685 50.000 0.00 0.00 46.63 5.69
67 68 8.632679 CCATGTATATAACAACCTTTGCTCAAT 58.367 33.333 0.00 0.00 42.70 2.57
101 102 2.222445 CAGGGTACAAGCGTGTTGTAAC 59.778 50.000 11.38 15.58 40.78 2.50
107 108 0.249398 GGATCAGGGTACAAGCGTGT 59.751 55.000 10.83 10.83 42.09 4.49
108 109 0.537188 AGGATCAGGGTACAAGCGTG 59.463 55.000 0.00 0.00 33.30 5.34
109 110 1.276622 AAGGATCAGGGTACAAGCGT 58.723 50.000 0.00 0.00 0.00 5.07
116 117 5.362717 CACATACACACTAAGGATCAGGGTA 59.637 44.000 0.00 0.00 0.00 3.69
119 120 4.162320 ACCACATACACACTAAGGATCAGG 59.838 45.833 0.00 0.00 0.00 3.86
127 128 5.117584 ACGTCAAAACCACATACACACTAA 58.882 37.500 0.00 0.00 0.00 2.24
137 138 7.536855 AGTTGTTATTTAACGTCAAAACCACA 58.463 30.769 0.00 0.00 39.00 4.17
144 145 8.861101 CCACAAAAAGTTGTTATTTAACGTCAA 58.139 29.630 0.00 0.00 46.01 3.18
148 149 7.458038 AGCCACAAAAAGTTGTTATTTAACG 57.542 32.000 0.00 0.00 46.01 3.18
154 155 6.042143 CAGTCAAGCCACAAAAAGTTGTTAT 58.958 36.000 0.00 0.00 46.01 1.89
156 157 4.244862 CAGTCAAGCCACAAAAAGTTGTT 58.755 39.130 0.00 0.00 46.01 2.83
165 166 0.874175 CGTCGACAGTCAAGCCACAA 60.874 55.000 17.16 0.00 0.00 3.33
168 169 1.007734 GTCGTCGACAGTCAAGCCA 60.008 57.895 20.28 0.00 32.09 4.75
169 170 1.007734 TGTCGTCGACAGTCAAGCC 60.008 57.895 23.70 0.00 37.67 4.35
183 184 3.839051 TCTTGTCAGTCTCATCTGTCG 57.161 47.619 0.00 0.00 36.85 4.35
185 186 6.461370 GCATAGATCTTGTCAGTCTCATCTGT 60.461 42.308 0.00 0.00 36.85 3.41
192 193 4.708909 TCACTGCATAGATCTTGTCAGTCT 59.291 41.667 15.92 0.00 32.76 3.24
199 200 7.876582 TCAGGATAAATCACTGCATAGATCTTG 59.123 37.037 0.00 0.32 32.42 3.02
210 211 4.941263 TCCCGTTTTCAGGATAAATCACTG 59.059 41.667 0.00 0.00 0.00 3.66
219 220 2.509548 TCCATCATCCCGTTTTCAGGAT 59.490 45.455 0.00 0.00 43.89 3.24
227 228 1.477558 GCCATCTTCCATCATCCCGTT 60.478 52.381 0.00 0.00 0.00 4.44
229 230 0.952497 CGCCATCTTCCATCATCCCG 60.952 60.000 0.00 0.00 0.00 5.14
237 238 1.303236 CCACAACCGCCATCTTCCA 60.303 57.895 0.00 0.00 0.00 3.53
247 248 1.450312 GCTCCAGGATCCACAACCG 60.450 63.158 15.82 0.00 0.00 4.44
250 251 0.394762 GCATGCTCCAGGATCCACAA 60.395 55.000 15.82 0.00 0.00 3.33
251 252 1.225426 GCATGCTCCAGGATCCACA 59.775 57.895 15.82 4.22 0.00 4.17
260 261 2.111669 CCGCCTATGCATGCTCCA 59.888 61.111 20.33 0.00 37.32 3.86
270 271 1.545428 CCCATAACATGCACCGCCTAT 60.545 52.381 0.00 0.00 0.00 2.57
282 283 2.705658 CTGGTCTAGGCATCCCATAACA 59.294 50.000 0.00 0.00 0.00 2.41
302 303 3.995636 TCTAGTGGCCTTAAGACCATCT 58.004 45.455 14.10 14.11 38.46 2.90
321 322 6.573434 TCGCATAACAGACACAATCTAATCT 58.427 36.000 0.00 0.00 35.15 2.40
342 343 2.526304 TATAGATGTGCCCTGTTCGC 57.474 50.000 0.00 0.00 0.00 4.70
345 346 6.500589 ACAAGTATATAGATGTGCCCTGTT 57.499 37.500 0.66 0.00 0.00 3.16
349 350 6.014499 ACACCTACAAGTATATAGATGTGCCC 60.014 42.308 9.55 0.00 0.00 5.36
359 360 7.769044 CCAAAGTTGCTACACCTACAAGTATAT 59.231 37.037 0.13 0.00 0.00 0.86
385 386 4.218417 TCCAAAGCCATCTTCTAAGCAAAC 59.782 41.667 0.00 0.00 0.00 2.93
408 409 9.911788 AGTCTGACAAATAATACAAGGATCAAT 57.088 29.630 10.88 0.00 0.00 2.57
515 517 8.519526 TGTGTGTATGGGTAAGAAAAATCATTC 58.480 33.333 0.00 0.00 0.00 2.67
518 520 7.001674 AGTGTGTGTATGGGTAAGAAAAATCA 58.998 34.615 0.00 0.00 0.00 2.57
519 521 7.448748 AGTGTGTGTATGGGTAAGAAAAATC 57.551 36.000 0.00 0.00 0.00 2.17
558 563 3.350219 ACGCATGGGTGAAATCTAACT 57.650 42.857 15.49 0.00 0.00 2.24
577 582 9.018716 GCTATTTTAAGGTTTACTCTCGAGTAC 57.981 37.037 13.13 4.37 43.02 2.73
587 592 8.678593 AGGATGCTAGCTATTTTAAGGTTTAC 57.321 34.615 17.23 0.00 0.00 2.01
660 665 3.161450 ATAGGACACCCGCGCCAT 61.161 61.111 0.00 0.00 37.58 4.40
665 670 2.632987 AATAACCATAGGACACCCGC 57.367 50.000 0.00 0.00 37.58 6.13
683 688 1.468985 CCATGCCGGATGGTTGTTAA 58.531 50.000 19.26 0.00 46.20 2.01
946 951 2.095853 GTGTGTGTTGGCTATCGAATGG 59.904 50.000 0.00 0.00 0.00 3.16
967 972 6.455646 GCAATGGTTTCTCTGTAACGATGTAG 60.456 42.308 0.00 0.00 0.00 2.74
972 977 3.496884 GTGCAATGGTTTCTCTGTAACGA 59.503 43.478 0.00 0.00 0.00 3.85
1016 1021 4.012895 CGCCGCGCTTGTGTTCTT 62.013 61.111 5.56 0.00 0.00 2.52
1231 1236 2.431260 GCGGTCGGCTTCGTACAA 60.431 61.111 0.00 0.00 39.11 2.41
1283 1288 0.174389 CAGGTCCTCATCGGTCACAG 59.826 60.000 0.00 0.00 0.00 3.66
1293 1298 2.907703 GAGCTCATCCAGGTCCTCA 58.092 57.895 9.40 0.00 42.98 3.86
1393 1398 2.690173 CGGTTGACGGCAAAATACAA 57.310 45.000 4.55 0.00 39.42 2.41
1419 1424 2.656651 CGCATCTTCGGCTCGGAG 60.657 66.667 0.00 0.00 33.10 4.63
1584 1589 7.342769 AGGAAGAAATTAACAAGGAAACGTT 57.657 32.000 0.00 0.00 0.00 3.99
1634 1640 7.332557 ACAACCGACCACATAATAACATAAGA 58.667 34.615 0.00 0.00 0.00 2.10
1668 1674 1.818363 CGCCAGCTGCATGAGTCAT 60.818 57.895 8.66 0.00 41.33 3.06
1682 1688 1.476845 TAAGCTGTGGGTTCTCGCCA 61.477 55.000 0.00 0.00 34.76 5.69
1760 1766 0.890542 ATTGCAGCCAACGCTCTCAA 60.891 50.000 0.00 0.00 43.95 3.02
1769 1775 1.470996 GGGTGGTTCATTGCAGCCAA 61.471 55.000 0.00 0.00 35.49 4.52
1794 1800 2.803956 CTCGGATGTACAACGGTTTTGT 59.196 45.455 19.10 0.00 36.49 2.83
1797 1803 2.224113 ACACTCGGATGTACAACGGTTT 60.224 45.455 19.10 9.35 0.00 3.27
1826 1832 0.323542 ATGTCCTCTCCCTCGTCGTT 60.324 55.000 0.00 0.00 0.00 3.85
1849 1855 2.223595 CGTTGTGTTAATTGCACCACCA 60.224 45.455 10.96 0.00 36.11 4.17
1889 1896 0.398696 ACAACAACCATGGGCGTCTA 59.601 50.000 18.09 0.00 0.00 2.59
1890 1897 1.150536 ACAACAACCATGGGCGTCT 59.849 52.632 18.09 1.24 0.00 4.18
1958 1965 6.951062 TCAAATGTTGTCCTGTCAATACAA 57.049 33.333 0.00 0.00 34.49 2.41
2039 2046 6.818142 GTGCATGCCTAGTTTTTATGGAAATT 59.182 34.615 16.68 0.00 0.00 1.82
2079 2087 4.304110 TGGATGAGTGTGTTTTAGTCGAC 58.696 43.478 7.70 7.70 0.00 4.20
2210 2219 9.366216 TCAGACATTCAGTGTTGTATTACATAC 57.634 33.333 0.00 1.10 42.36 2.39
2250 2259 2.968675 GTGCAAGTACTGTACCGGAAT 58.031 47.619 9.46 0.00 34.78 3.01
2256 2265 3.256136 AGTCAGAGGTGCAAGTACTGTAC 59.744 47.826 9.93 9.93 39.75 2.90
2310 2319 4.451096 GTGTCGTGGACAAGTAATTCACAT 59.549 41.667 0.00 0.00 44.49 3.21
2415 2424 8.497745 AGGCTTGAGAATCCATAGAAGAAATTA 58.502 33.333 0.00 0.00 0.00 1.40
2450 2459 1.133976 AGATGCCCAGTAAGCCATGTC 60.134 52.381 0.00 0.00 0.00 3.06
2452 2461 1.602311 GAGATGCCCAGTAAGCCATG 58.398 55.000 0.00 0.00 0.00 3.66
2453 2462 0.475906 GGAGATGCCCAGTAAGCCAT 59.524 55.000 0.00 0.00 0.00 4.40
2461 2471 2.165030 GTCAATGTTTGGAGATGCCCAG 59.835 50.000 0.00 0.00 37.53 4.45
2477 2487 5.113383 TGTGAGTGTCTGTTTAACGTCAAT 58.887 37.500 0.00 0.00 0.00 2.57
2518 2528 0.179004 TTGATGGTGTTCGCCAGGTT 60.179 50.000 10.79 0.00 42.47 3.50
2522 2532 0.665835 GTGTTTGATGGTGTTCGCCA 59.334 50.000 7.56 7.56 43.48 5.69
2527 2537 6.068010 TCAAAGGATAGTGTTTGATGGTGTT 58.932 36.000 0.00 0.00 37.67 3.32
2681 2691 2.093341 GGAAACCACGCCTATGAGGTTA 60.093 50.000 0.00 0.00 43.17 2.85
2698 2708 0.252103 AGTCCTAGTGGCCTCGGAAA 60.252 55.000 3.32 0.00 34.57 3.13
2699 2709 0.970937 CAGTCCTAGTGGCCTCGGAA 60.971 60.000 3.32 0.00 34.57 4.30
2716 2726 2.363807 GTCGTGACGAGGATTGCAG 58.636 57.895 8.41 0.00 36.23 4.41
2727 2737 2.027625 CTTCCCCAAGCGTCGTGAC 61.028 63.158 0.00 0.00 0.00 3.67
2730 2740 2.342648 GACTTCCCCAAGCGTCGT 59.657 61.111 0.00 0.00 32.09 4.34



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

AutoCloner maintained by Alex Coulton.