Multiple sequence alignment - TraesCS5D01G085200

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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 TraesCS5D01G085200 chr5D 100.000 4630 0 0 1 4630 90002778 89998149 0.000000e+00 8551
1 TraesCS5D01G085200 chr5D 95.858 169 7 0 103 271 35164269 35164437 1.640000e-69 274
2 TraesCS5D01G085200 chr5A 91.946 4408 210 62 273 4624 83633359 83629041 0.000000e+00 6039
3 TraesCS5D01G085200 chr5A 93.506 77 5 0 30 106 83633438 83633362 1.050000e-21 115
4 TraesCS5D01G085200 chr5B 95.557 1733 68 4 2543 4269 94387647 94389376 0.000000e+00 2765
5 TraesCS5D01G085200 chr5B 94.052 1160 41 8 327 1471 94385202 94386348 0.000000e+00 1735
6 TraesCS5D01G085200 chr5B 96.680 994 26 2 1520 2511 94386663 94387651 0.000000e+00 1646
7 TraesCS5D01G085200 chr5B 85.274 292 33 4 4297 4578 94389455 94389746 4.530000e-75 292
8 TraesCS5D01G085200 chr5B 92.453 106 8 0 1 106 94384747 94384852 8.020000e-33 152
9 TraesCS5D01G085200 chr1A 97.590 166 4 0 107 272 11628172 11628337 7.580000e-73 285
10 TraesCS5D01G085200 chr6B 96.407 167 6 0 105 271 147089606 147089440 4.560000e-70 276
11 TraesCS5D01G085200 chr7D 96.386 166 6 0 106 271 5492044 5492209 1.640000e-69 274
12 TraesCS5D01G085200 chr4A 94.828 174 8 1 101 274 665604291 665604119 2.120000e-68 270
13 TraesCS5D01G085200 chr7B 92.593 189 10 4 100 285 281384498 281384685 7.640000e-68 268
14 TraesCS5D01G085200 chr3B 93.785 177 9 2 96 271 755167385 755167560 9.880000e-67 265
15 TraesCS5D01G085200 chr3A 92.473 186 11 2 106 288 275568821 275569006 3.550000e-66 263
16 TraesCS5D01G085200 chr4B 89.447 199 20 1 75 273 9545319 9545122 2.770000e-62 250


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 TraesCS5D01G085200 chr5D 89998149 90002778 4629 True 8551 8551 100.0000 1 4630 1 chr5D.!!$R1 4629
1 TraesCS5D01G085200 chr5A 83629041 83633438 4397 True 3077 6039 92.7260 30 4624 2 chr5A.!!$R1 4594
2 TraesCS5D01G085200 chr5B 94384747 94389746 4999 False 1318 2765 92.8032 1 4578 5 chr5B.!!$F1 4577

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
895 1093 0.801836 CATCGAATTTTGGTGGCGGC 60.802 55.0 0.00 0.0 0.0 6.53 F
1305 1510 0.804544 GTGAGTGCGCCGCTGTATAA 60.805 55.0 11.67 0.0 0.0 0.98 F
2050 2545 0.330604 TAGTCGTCTACAGCAGGGGT 59.669 55.0 0.00 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2545 0.251386 TGCCCTTAATCCGCCAAACA 60.251 50.000 0.0 0.0 0.00 2.83 R
2617 3114 1.135333 GAAACCAAGGCAACGTCCAAA 59.865 47.619 0.0 0.0 46.39 3.28 R
3948 4452 0.892755 GGACCCACGTATCACAGTGA 59.107 55.000 5.5 5.5 40.56 3.41 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
46 47 2.507407 TGAACCAAAGATGCCCCTAC 57.493 50.000 0.00 0.00 0.00 3.18
53 54 3.962718 CCAAAGATGCCCCTACAATGAAT 59.037 43.478 0.00 0.00 0.00 2.57
121 309 1.718280 ATGATACTCCCTCCGTTCCC 58.282 55.000 0.00 0.00 0.00 3.97
128 316 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
129 317 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
136 324 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
139 327 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
163 351 7.331791 AGAGATTTCAACAAGGGACTACATAC 58.668 38.462 0.00 0.00 38.49 2.39
181 369 4.154195 ACATACGGAGCAAAATGAGTGAAC 59.846 41.667 0.00 0.00 0.00 3.18
234 422 8.050778 TCCATATGTTGTAGTCCATTTGAAAC 57.949 34.615 1.24 0.00 0.00 2.78
247 435 7.780271 AGTCCATTTGAAACCTCTAAAAAGACT 59.220 33.333 0.00 0.00 0.00 3.24
248 436 8.414003 GTCCATTTGAAACCTCTAAAAAGACTT 58.586 33.333 0.00 0.00 0.00 3.01
269 457 8.068733 AGACTTATATTTAGGAACAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
270 458 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
271 459 9.369672 ACTTATATTTAGGAACAGAGGGAGTAG 57.630 37.037 0.00 0.00 0.00 2.57
272 460 9.589461 CTTATATTTAGGAACAGAGGGAGTAGA 57.411 37.037 0.00 0.00 0.00 2.59
273 461 9.947189 TTATATTTAGGAACAGAGGGAGTAGAA 57.053 33.333 0.00 0.00 0.00 2.10
274 462 8.855804 ATATTTAGGAACAGAGGGAGTAGAAA 57.144 34.615 0.00 0.00 0.00 2.52
275 463 7.569599 ATTTAGGAACAGAGGGAGTAGAAAA 57.430 36.000 0.00 0.00 0.00 2.29
276 464 7.383156 TTTAGGAACAGAGGGAGTAGAAAAA 57.617 36.000 0.00 0.00 0.00 1.94
320 508 7.347508 ACGCAAGATAAATATACTAAAGCCG 57.652 36.000 0.00 0.00 43.62 5.52
321 509 6.927381 ACGCAAGATAAATATACTAAAGCCGT 59.073 34.615 0.00 0.00 43.62 5.68
322 510 7.440255 ACGCAAGATAAATATACTAAAGCCGTT 59.560 33.333 0.00 0.00 43.62 4.44
323 511 7.740346 CGCAAGATAAATATACTAAAGCCGTTG 59.260 37.037 0.00 0.00 43.02 4.10
324 512 8.557029 GCAAGATAAATATACTAAAGCCGTTGT 58.443 33.333 0.00 0.00 0.00 3.32
365 553 1.401018 GCACGTAATGGTGGTCAAAGC 60.401 52.381 0.00 0.00 38.36 3.51
585 781 4.436998 CCAGTCAGCGTCCGGTCC 62.437 72.222 0.00 0.00 0.00 4.46
610 808 2.349755 GCAAGGGTAGCCGTCCAA 59.650 61.111 5.06 0.00 0.00 3.53
880 1078 1.267532 CCGTGCGGAGAAATTTCATCG 60.268 52.381 19.99 20.65 37.50 3.84
895 1093 0.801836 CATCGAATTTTGGTGGCGGC 60.802 55.000 0.00 0.00 0.00 6.53
929 1127 2.159531 TGCGATCTTGGCGAGAATTTTG 60.160 45.455 8.86 0.00 38.06 2.44
958 1163 2.329379 CGACTATATTGCCGAGGAAGC 58.671 52.381 0.00 0.00 0.00 3.86
1137 1342 2.439883 GCGTCCGGGGAGTACTCT 60.440 66.667 21.88 0.00 0.00 3.24
1302 1507 3.680786 AGTGAGTGCGCCGCTGTA 61.681 61.111 11.67 0.00 0.00 2.74
1303 1508 2.509336 GTGAGTGCGCCGCTGTAT 60.509 61.111 11.67 0.00 0.00 2.29
1304 1509 1.226859 GTGAGTGCGCCGCTGTATA 60.227 57.895 11.67 0.00 0.00 1.47
1305 1510 0.804544 GTGAGTGCGCCGCTGTATAA 60.805 55.000 11.67 0.00 0.00 0.98
1402 1624 8.321353 TGGACTACATGACTAAATTCTTGATGT 58.679 33.333 0.00 0.00 0.00 3.06
1403 1625 9.817809 GGACTACATGACTAAATTCTTGATGTA 57.182 33.333 0.00 0.00 0.00 2.29
1408 1630 9.507329 ACATGACTAAATTCTTGATGTACTTGT 57.493 29.630 0.00 0.00 0.00 3.16
1435 1657 9.692749 TTCTACACATGTTTCTCAAAGTAGTAG 57.307 33.333 12.68 9.27 34.02 2.57
1481 1707 8.739039 TCATGGTGGTTTGTTTCTATAATTCTG 58.261 33.333 0.00 0.00 0.00 3.02
1482 1708 8.522830 CATGGTGGTTTGTTTCTATAATTCTGT 58.477 33.333 0.00 0.00 0.00 3.41
1486 1712 9.180678 GTGGTTTGTTTCTATAATTCTGTTGTG 57.819 33.333 0.00 0.00 0.00 3.33
1507 1733 6.457355 TGTGATACTTCATTTTGCATGCTTT 58.543 32.000 20.33 0.00 33.56 3.51
1509 1735 6.366877 GTGATACTTCATTTTGCATGCTTTGT 59.633 34.615 20.33 8.67 33.56 2.83
1683 2178 8.916654 CCGAGTTTACACATTCATATAGCTAAG 58.083 37.037 0.00 0.00 0.00 2.18
1894 2389 4.216411 ACTGTATGTCGCCAATTTAGGT 57.784 40.909 0.00 0.00 0.00 3.08
2050 2545 0.330604 TAGTCGTCTACAGCAGGGGT 59.669 55.000 0.00 0.00 0.00 4.95
2185 2680 1.813513 ATGTGACAGTTGGCTGCTAC 58.186 50.000 0.00 0.00 46.30 3.58
2278 2775 2.293122 GCATGCCCGCAAGACATAAATA 59.707 45.455 6.36 0.00 43.02 1.40
2302 2799 6.446659 GCGTACTGCAAAACAAAATTACAT 57.553 33.333 5.07 0.00 45.45 2.29
2303 2800 6.513317 GCGTACTGCAAAACAAAATTACATC 58.487 36.000 5.07 0.00 45.45 3.06
2304 2801 6.362283 GCGTACTGCAAAACAAAATTACATCT 59.638 34.615 5.07 0.00 45.45 2.90
2305 2802 7.617122 GCGTACTGCAAAACAAAATTACATCTG 60.617 37.037 5.07 0.00 45.45 2.90
2306 2803 7.589587 CGTACTGCAAAACAAAATTACATCTGA 59.410 33.333 0.00 0.00 0.00 3.27
2334 2831 3.375699 CATAGGTGACCTGGTCCTAGTT 58.624 50.000 23.42 7.81 37.27 2.24
2417 2914 1.215647 GAACGCCGAGTCCATGAGT 59.784 57.895 0.00 0.00 0.00 3.41
2464 2961 5.593679 TGGGAGGATTTTACTACTCTTCG 57.406 43.478 0.00 0.00 0.00 3.79
2469 2966 7.266400 GGAGGATTTTACTACTCTTCGTGAAT 58.734 38.462 0.00 0.00 0.00 2.57
2553 3050 7.880195 AGCAAAGTTACATACTGATATCCCATC 59.120 37.037 0.00 0.00 37.12 3.51
2617 3114 9.553064 CAGATAAAGGCAACAGTCTAATTCTAT 57.447 33.333 0.00 0.00 41.41 1.98
2726 3230 4.215908 AGCACTCCTCGATCTAATACCAA 58.784 43.478 0.00 0.00 0.00 3.67
3225 3729 0.394565 GTCTGTGGGAGCAGTTGACT 59.605 55.000 0.00 0.00 37.70 3.41
3322 3826 4.216411 ACACCTATACGCTGTTCCATTT 57.784 40.909 0.00 0.00 0.00 2.32
3347 3851 4.735985 TGCAGAATATGATGTGTTGTTGC 58.264 39.130 0.00 0.00 0.00 4.17
3348 3852 4.217983 TGCAGAATATGATGTGTTGTTGCA 59.782 37.500 0.00 0.00 0.00 4.08
3386 3890 0.178998 AGGGAATAGCGAGGCGACTA 60.179 55.000 0.00 0.00 44.43 2.59
3534 4038 0.041400 TCACAAACACGATGCGCAAG 60.041 50.000 17.11 14.98 43.44 4.01
3646 4150 4.929819 TGTGAGCTAGTGTTGTGTCTTA 57.070 40.909 0.00 0.00 0.00 2.10
3664 4168 8.651389 TGTGTCTTAAGAAGGGATAATAGATGG 58.349 37.037 6.78 0.00 0.00 3.51
3694 4198 3.897505 AGGAAAAGGAACAAACCAGATGG 59.102 43.478 0.00 0.00 42.17 3.51
3789 4293 6.017440 CACTCTAGGTAAGCTGATGTCTCTAC 60.017 46.154 0.00 0.00 0.00 2.59
3816 4320 1.522668 TTCCATTGCAGTTGGAGACG 58.477 50.000 17.06 0.00 43.87 4.18
3852 4356 5.474876 GGTTATGCAAGATTAGATTCCCCAG 59.525 44.000 0.00 0.00 0.00 4.45
3868 4372 4.729868 TCCCCAGAAAAAGAGAAAAGGAG 58.270 43.478 0.00 0.00 0.00 3.69
3948 4452 5.215160 GTTTGATCATGAAGCTTTGTTCGT 58.785 37.500 0.00 0.00 0.00 3.85
3958 4462 3.990092 AGCTTTGTTCGTCACTGTGATA 58.010 40.909 14.37 2.74 0.00 2.15
4016 4529 5.557891 AGATTGCTTAGATTTGTGTGAGC 57.442 39.130 0.00 0.00 0.00 4.26
4083 4597 0.891373 GCAAAAGAAGAGCCTTCCCC 59.109 55.000 10.27 0.00 0.00 4.81
4141 4655 1.005097 TCTCCTTGTTGCATCATGGCT 59.995 47.619 19.92 0.00 34.12 4.75
4212 4729 6.314896 AGTGCTGCTGATATTGTAGTCTTTTC 59.685 38.462 0.00 0.00 0.00 2.29
4269 4786 0.099259 CATATTGCGGCCTGTGTGTG 59.901 55.000 0.00 0.00 0.00 3.82
4276 4852 0.606401 CGGCCTGTGTGTGGATTTCT 60.606 55.000 0.00 0.00 0.00 2.52
4323 4899 5.957771 ATAGGGTGAAATTGCTGAGTCTA 57.042 39.130 0.00 0.00 0.00 2.59
4324 4900 4.213564 AGGGTGAAATTGCTGAGTCTAG 57.786 45.455 0.00 0.00 0.00 2.43
4348 4924 2.443887 GCACAGCCATGAACAATTGT 57.556 45.000 4.92 4.92 0.00 2.71
4349 4925 3.574284 GCACAGCCATGAACAATTGTA 57.426 42.857 12.39 0.00 0.00 2.41
4351 4927 4.497300 GCACAGCCATGAACAATTGTAAT 58.503 39.130 12.39 6.20 0.00 1.89
4356 4940 3.618150 GCCATGAACAATTGTAATGTGGC 59.382 43.478 26.97 26.97 31.61 5.01
4382 4966 6.058833 TCATAGCGGGCATTGTTTTAGATAA 58.941 36.000 0.00 0.00 0.00 1.75
4383 4967 6.714810 TCATAGCGGGCATTGTTTTAGATAAT 59.285 34.615 0.00 0.00 0.00 1.28
4389 4974 6.072673 CGGGCATTGTTTTAGATAATACTCCC 60.073 42.308 0.00 0.00 0.00 4.30
4392 4977 7.363431 GCATTGTTTTAGATAATACTCCCAGC 58.637 38.462 0.00 0.00 0.00 4.85
4412 4997 5.112686 CAGCAGGTCTACTTTTCCATCTAC 58.887 45.833 0.00 0.00 0.00 2.59
4470 5055 6.039382 ACAAAGTATCAACAGTTTTGGAGGAC 59.961 38.462 0.00 0.00 34.07 3.85
4472 5057 2.358322 TCAACAGTTTTGGAGGACCC 57.642 50.000 0.00 0.00 34.81 4.46
4572 5159 1.321743 CGCGTGTACAAGATCTGAAGC 59.678 52.381 13.30 0.00 0.00 3.86
4578 5165 0.901124 ACAAGATCTGAAGCCGCTCT 59.099 50.000 0.00 0.00 0.00 4.09
4579 5166 1.277557 ACAAGATCTGAAGCCGCTCTT 59.722 47.619 0.00 0.00 37.83 2.85
4580 5167 2.289945 ACAAGATCTGAAGCCGCTCTTT 60.290 45.455 0.00 0.00 34.56 2.52
4581 5168 3.055819 ACAAGATCTGAAGCCGCTCTTTA 60.056 43.478 0.00 0.00 34.56 1.85
4582 5169 3.172229 AGATCTGAAGCCGCTCTTTAC 57.828 47.619 0.00 0.00 34.56 2.01
4583 5170 2.497675 AGATCTGAAGCCGCTCTTTACA 59.502 45.455 0.00 0.00 34.56 2.41
4584 5171 3.133721 AGATCTGAAGCCGCTCTTTACAT 59.866 43.478 0.00 0.00 34.56 2.29
4585 5172 4.342378 AGATCTGAAGCCGCTCTTTACATA 59.658 41.667 0.00 0.00 34.56 2.29
4586 5173 4.672587 TCTGAAGCCGCTCTTTACATAT 57.327 40.909 0.00 0.00 34.56 1.78
4587 5174 5.784578 TCTGAAGCCGCTCTTTACATATA 57.215 39.130 0.00 0.00 34.56 0.86
4625 5212 2.542020 TCAGAATGAAACAGCACCGA 57.458 45.000 0.00 0.00 45.97 4.69
4626 5213 2.143122 TCAGAATGAAACAGCACCGAC 58.857 47.619 0.00 0.00 45.97 4.79
4627 5214 1.136252 CAGAATGAAACAGCACCGACG 60.136 52.381 0.00 0.00 39.69 5.12
4628 5215 1.144969 GAATGAAACAGCACCGACGA 58.855 50.000 0.00 0.00 0.00 4.20
4629 5216 1.529438 GAATGAAACAGCACCGACGAA 59.471 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.686683 AAATATACTATTCATTGTAGGGGCATC 57.313 33.333 0.00 0.00 0.00 3.91
128 316 8.633561 CCCTTGTTGAAATCTCTAAAAAGACTT 58.366 33.333 0.00 0.00 0.00 3.01
129 317 7.998964 TCCCTTGTTGAAATCTCTAAAAAGACT 59.001 33.333 0.00 0.00 0.00 3.24
136 324 7.311092 TGTAGTCCCTTGTTGAAATCTCTAA 57.689 36.000 0.00 0.00 0.00 2.10
139 327 6.255887 CGTATGTAGTCCCTTGTTGAAATCTC 59.744 42.308 0.00 0.00 0.00 2.75
146 334 3.782046 CTCCGTATGTAGTCCCTTGTTG 58.218 50.000 0.00 0.00 0.00 3.33
153 341 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
163 351 2.154462 AGGTTCACTCATTTTGCTCCG 58.846 47.619 0.00 0.00 0.00 4.63
207 395 7.806409 TCAAATGGACTACAACATATGGATG 57.194 36.000 7.80 8.32 39.16 3.51
212 400 8.109634 AGAGGTTTCAAATGGACTACAACATAT 58.890 33.333 0.00 0.00 0.00 1.78
218 406 8.754991 TTTTTAGAGGTTTCAAATGGACTACA 57.245 30.769 0.00 0.00 0.00 2.74
221 409 7.780271 AGTCTTTTTAGAGGTTTCAAATGGACT 59.220 33.333 0.00 0.00 0.00 3.85
247 435 9.947189 TTCTACTCCCTCTGTTCCTAAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
248 436 9.947189 TTTCTACTCCCTCTGTTCCTAAATATA 57.053 33.333 0.00 0.00 0.00 0.86
294 482 8.918658 CGGCTTTAGTATATTTATCTTGCGTTA 58.081 33.333 0.00 0.00 0.00 3.18
295 483 7.440255 ACGGCTTTAGTATATTTATCTTGCGTT 59.560 33.333 0.00 0.00 0.00 4.84
296 484 6.927381 ACGGCTTTAGTATATTTATCTTGCGT 59.073 34.615 0.00 0.00 0.00 5.24
297 485 7.347508 ACGGCTTTAGTATATTTATCTTGCG 57.652 36.000 0.00 0.00 0.00 4.85
298 486 8.557029 ACAACGGCTTTAGTATATTTATCTTGC 58.443 33.333 0.00 0.00 0.00 4.01
305 493 9.998106 ATCATAGACAACGGCTTTAGTATATTT 57.002 29.630 0.00 0.00 0.00 1.40
306 494 9.998106 AATCATAGACAACGGCTTTAGTATATT 57.002 29.630 0.00 0.00 0.00 1.28
307 495 9.640963 GAATCATAGACAACGGCTTTAGTATAT 57.359 33.333 0.00 0.00 0.00 0.86
308 496 8.857098 AGAATCATAGACAACGGCTTTAGTATA 58.143 33.333 0.00 0.00 0.00 1.47
309 497 7.727181 AGAATCATAGACAACGGCTTTAGTAT 58.273 34.615 0.00 0.00 0.00 2.12
310 498 7.108841 AGAATCATAGACAACGGCTTTAGTA 57.891 36.000 0.00 0.00 0.00 1.82
311 499 5.978814 AGAATCATAGACAACGGCTTTAGT 58.021 37.500 0.00 0.00 0.00 2.24
312 500 6.709643 CAAGAATCATAGACAACGGCTTTAG 58.290 40.000 0.00 0.00 0.00 1.85
313 501 5.064707 GCAAGAATCATAGACAACGGCTTTA 59.935 40.000 0.00 0.00 0.00 1.85
314 502 4.142600 GCAAGAATCATAGACAACGGCTTT 60.143 41.667 0.00 0.00 0.00 3.51
315 503 3.375299 GCAAGAATCATAGACAACGGCTT 59.625 43.478 0.00 0.00 0.00 4.35
316 504 2.939103 GCAAGAATCATAGACAACGGCT 59.061 45.455 0.00 0.00 0.00 5.52
317 505 2.677836 TGCAAGAATCATAGACAACGGC 59.322 45.455 0.00 0.00 0.00 5.68
318 506 4.787563 GCATGCAAGAATCATAGACAACGG 60.788 45.833 14.21 0.00 0.00 4.44
319 507 4.277258 GCATGCAAGAATCATAGACAACG 58.723 43.478 14.21 0.00 0.00 4.10
320 508 4.604976 GGCATGCAAGAATCATAGACAAC 58.395 43.478 21.36 0.00 0.00 3.32
321 509 3.313249 CGGCATGCAAGAATCATAGACAA 59.687 43.478 21.36 0.00 0.00 3.18
322 510 2.874086 CGGCATGCAAGAATCATAGACA 59.126 45.455 21.36 0.00 0.00 3.41
323 511 2.874701 ACGGCATGCAAGAATCATAGAC 59.125 45.455 21.36 0.00 0.00 2.59
324 512 2.874086 CACGGCATGCAAGAATCATAGA 59.126 45.455 21.36 0.00 0.00 1.98
325 513 3.263602 CACGGCATGCAAGAATCATAG 57.736 47.619 21.36 0.00 0.00 2.23
365 553 5.469373 TGCGTGCTATCAGTATTTTCAAG 57.531 39.130 0.00 0.00 0.00 3.02
547 740 0.393537 CAAGTCCTCATCTGGTGGGC 60.394 60.000 0.00 0.00 34.95 5.36
585 781 3.480133 CTACCCTTGCCCCCGGAG 61.480 72.222 0.73 0.00 0.00 4.63
880 1078 2.126110 CCGCCGCCACCAAAATTC 60.126 61.111 0.00 0.00 0.00 2.17
895 1093 2.691674 GATCGCAGCTTCCTCCTCCG 62.692 65.000 0.00 0.00 0.00 4.63
929 1127 1.941668 GCAATATAGTCGCAGCCTCCC 60.942 57.143 0.00 0.00 0.00 4.30
958 1163 3.090532 CTCCCTTCCTTCCCCGGG 61.091 72.222 15.80 15.80 38.07 5.73
964 1169 0.692756 CCCTCCTCCTCCCTTCCTTC 60.693 65.000 0.00 0.00 0.00 3.46
1301 1506 9.079833 GCGCTCGTAAATGGAGTTTATATTATA 57.920 33.333 0.00 0.00 34.93 0.98
1302 1507 7.817962 AGCGCTCGTAAATGGAGTTTATATTAT 59.182 33.333 2.64 0.00 34.93 1.28
1303 1508 7.149973 AGCGCTCGTAAATGGAGTTTATATTA 58.850 34.615 2.64 0.00 34.93 0.98
1304 1509 5.989777 AGCGCTCGTAAATGGAGTTTATATT 59.010 36.000 2.64 0.00 34.93 1.28
1305 1510 5.539048 AGCGCTCGTAAATGGAGTTTATAT 58.461 37.500 2.64 0.00 34.93 0.86
1402 1624 8.725405 TTGAGAAACATGTGTAGAAACAAGTA 57.275 30.769 0.00 0.00 37.36 2.24
1403 1625 7.624360 TTGAGAAACATGTGTAGAAACAAGT 57.376 32.000 0.00 0.00 37.36 3.16
1404 1626 8.184192 ACTTTGAGAAACATGTGTAGAAACAAG 58.816 33.333 0.00 0.00 37.36 3.16
1405 1627 8.050778 ACTTTGAGAAACATGTGTAGAAACAA 57.949 30.769 0.00 0.00 37.36 2.83
1406 1628 7.624360 ACTTTGAGAAACATGTGTAGAAACA 57.376 32.000 0.00 0.00 0.00 2.83
1407 1629 8.827677 ACTACTTTGAGAAACATGTGTAGAAAC 58.172 33.333 17.67 0.00 34.00 2.78
1408 1630 8.958119 ACTACTTTGAGAAACATGTGTAGAAA 57.042 30.769 17.67 5.10 34.00 2.52
1435 1657 4.992688 TGACATTTGGTTCAAACTCACAC 58.007 39.130 0.00 0.00 36.13 3.82
1481 1707 5.865552 AGCATGCAAAATGAAGTATCACAAC 59.134 36.000 21.98 0.00 38.69 3.32
1482 1708 6.028146 AGCATGCAAAATGAAGTATCACAA 57.972 33.333 21.98 0.00 38.69 3.33
1486 1712 6.956299 ACAAAGCATGCAAAATGAAGTATC 57.044 33.333 21.98 0.00 0.00 2.24
1489 1715 6.774354 CTAACAAAGCATGCAAAATGAAGT 57.226 33.333 21.98 3.70 0.00 3.01
1507 1733 0.973632 ACATGAGGACGTGGCTAACA 59.026 50.000 0.00 0.00 37.35 2.41
1509 1735 2.730382 TCTACATGAGGACGTGGCTAA 58.270 47.619 0.00 0.00 37.35 3.09
1516 1742 7.133891 AGAAAACAAAATCTACATGAGGACG 57.866 36.000 0.00 0.00 0.00 4.79
1517 1743 9.750125 AAAAGAAAACAAAATCTACATGAGGAC 57.250 29.630 0.00 0.00 0.00 3.85
1518 1744 9.748708 CAAAAGAAAACAAAATCTACATGAGGA 57.251 29.630 0.00 0.00 0.00 3.71
1570 2062 9.311916 GATAGAGCTAACATCATCCATCATTAC 57.688 37.037 0.00 0.00 0.00 1.89
1683 2178 1.230324 GGTTCAGACCACAAGACTGC 58.770 55.000 0.00 0.00 45.77 4.40
1894 2389 0.972134 CAAGGACAGCTCTGGAGTCA 59.028 55.000 3.82 0.00 34.04 3.41
2050 2545 0.251386 TGCCCTTAATCCGCCAAACA 60.251 50.000 0.00 0.00 0.00 2.83
2200 2695 1.247567 ATTTTGGAGACCACCTTGCG 58.752 50.000 0.00 0.00 30.78 4.85
2278 2775 5.583495 TGTAATTTTGTTTTGCAGTACGCT 58.417 33.333 10.27 0.00 43.06 5.07
2294 2791 7.660617 CACCTATGCTGAGATCAGATGTAATTT 59.339 37.037 13.98 0.00 46.59 1.82
2302 2799 2.961741 GGTCACCTATGCTGAGATCAGA 59.038 50.000 13.98 0.00 46.59 3.27
2303 2800 2.964464 AGGTCACCTATGCTGAGATCAG 59.036 50.000 0.00 5.45 38.46 2.90
2304 2801 2.697229 CAGGTCACCTATGCTGAGATCA 59.303 50.000 0.00 0.00 29.64 2.92
2305 2802 2.036992 CCAGGTCACCTATGCTGAGATC 59.963 54.545 0.00 0.00 29.64 2.75
2306 2803 2.045524 CCAGGTCACCTATGCTGAGAT 58.954 52.381 0.00 0.00 29.64 2.75
2334 2831 8.031864 TCTGCAAACACTTTTGAATTACAAGAA 58.968 29.630 1.29 0.00 44.38 2.52
2417 2914 3.954200 TCTAAACTGAATGAGGCATGCA 58.046 40.909 21.36 0.00 0.00 3.96
2464 2961 9.897744 TTAATGTTTTCATCAAGTGAGATTCAC 57.102 29.630 1.02 1.02 42.59 3.18
2469 2966 8.567948 GGAGTTTAATGTTTTCATCAAGTGAGA 58.432 33.333 0.00 0.00 39.94 3.27
2521 3018 9.765795 ATATCAGTATGTAACTTTGCTAGAACC 57.234 33.333 0.00 0.00 35.76 3.62
2553 3050 5.394005 GGGCATCATGACATAGAGCTAGTAG 60.394 48.000 0.00 0.00 0.00 2.57
2617 3114 1.135333 GAAACCAAGGCAACGTCCAAA 59.865 47.619 0.00 0.00 46.39 3.28
3225 3729 4.243008 TCCACCGCCGCTTTGTCA 62.243 61.111 0.00 0.00 0.00 3.58
3322 3826 6.974048 GCAACAACACATCATATTCTGCATAA 59.026 34.615 0.00 0.00 0.00 1.90
3347 3851 3.186909 CTGAGCACATGCATTTTCCATG 58.813 45.455 6.64 0.00 45.16 3.66
3348 3852 2.167693 CCTGAGCACATGCATTTTCCAT 59.832 45.455 6.64 0.00 45.16 3.41
3386 3890 1.453015 AGAGATCGCCGCTCTCACT 60.453 57.895 18.90 0.00 41.34 3.41
3534 4038 1.395954 GTCCAGGTTACCGAATTTCGC 59.604 52.381 13.26 0.00 38.82 4.70
3539 4043 3.071892 TGAAACTGTCCAGGTTACCGAAT 59.928 43.478 0.00 0.00 38.71 3.34
3624 4128 4.342862 AAGACACAACACTAGCTCACAT 57.657 40.909 0.00 0.00 0.00 3.21
3646 4150 8.798975 TTCACTACCATCTATTATCCCTTCTT 57.201 34.615 0.00 0.00 0.00 2.52
3664 4168 6.127563 TGGTTTGTTCCTTTTCCTTTCACTAC 60.128 38.462 0.00 0.00 0.00 2.73
3694 4198 4.817517 TCGGTCTAGGTGACTTCAAATTC 58.182 43.478 0.00 0.00 44.74 2.17
3789 4293 3.991773 CCAACTGCAATGGAATTCTTGTG 59.008 43.478 11.89 2.28 40.56 3.33
3816 4320 4.094294 TCTTGCATAACCGATACACAAAGC 59.906 41.667 0.00 0.00 0.00 3.51
3852 4356 4.114015 TCCCCCTCCTTTTCTCTTTTTC 57.886 45.455 0.00 0.00 0.00 2.29
3868 4372 6.187682 TGAGAACAATCTTTAGATTTCCCCC 58.812 40.000 2.27 0.00 42.41 5.40
3948 4452 0.892755 GGACCCACGTATCACAGTGA 59.107 55.000 5.50 5.50 40.56 3.41
3958 4462 1.537889 TGGAATCCTGGACCCACGT 60.538 57.895 13.79 0.00 0.00 4.49
4016 4529 2.010145 ACGGCAATGCTACACTAGTG 57.990 50.000 21.44 21.44 0.00 2.74
4083 4597 4.147133 GCTAACGAAAAGAAGCAAAAGCTG 59.853 41.667 0.00 0.00 34.27 4.24
4094 4608 2.487762 CCAATGCCAGCTAACGAAAAGA 59.512 45.455 0.00 0.00 0.00 2.52
4101 4615 1.826385 AGACACCAATGCCAGCTAAC 58.174 50.000 0.00 0.00 0.00 2.34
4141 4655 8.677148 AAAGAATAACACTCTACTCAAGCAAA 57.323 30.769 0.00 0.00 0.00 3.68
4176 4690 2.010497 CAGCAGCACTCTACTCGACTA 58.990 52.381 0.00 0.00 0.00 2.59
4212 4729 5.142639 ACATGGGATATTGGGATTTCACAG 58.857 41.667 0.00 0.00 31.52 3.66
4299 4875 4.946157 AGACTCAGCAATTTCACCCTATTG 59.054 41.667 0.00 0.00 35.39 1.90
4300 4876 5.184892 AGACTCAGCAATTTCACCCTATT 57.815 39.130 0.00 0.00 0.00 1.73
4301 4877 4.851639 AGACTCAGCAATTTCACCCTAT 57.148 40.909 0.00 0.00 0.00 2.57
4317 4893 1.153469 GCTGTGCCCTGCTAGACTC 60.153 63.158 0.00 0.00 33.16 3.36
4341 4917 5.449041 CGCTATGAAGCCACATTACAATTGT 60.449 40.000 16.68 16.68 46.68 2.71
4342 4918 4.971830 CGCTATGAAGCCACATTACAATTG 59.028 41.667 3.24 3.24 46.68 2.32
4343 4919 4.036734 CCGCTATGAAGCCACATTACAATT 59.963 41.667 0.00 0.00 46.68 2.32
4346 4922 2.560504 CCGCTATGAAGCCACATTACA 58.439 47.619 0.00 0.00 46.68 2.41
4347 4923 1.873591 CCCGCTATGAAGCCACATTAC 59.126 52.381 0.00 0.00 46.68 1.89
4348 4924 1.813862 GCCCGCTATGAAGCCACATTA 60.814 52.381 0.00 0.00 46.68 1.90
4349 4925 1.103398 GCCCGCTATGAAGCCACATT 61.103 55.000 0.00 0.00 46.68 2.71
4351 4927 2.124736 GCCCGCTATGAAGCCACA 60.125 61.111 0.00 0.00 46.68 4.17
4356 4940 3.508744 AAAACAATGCCCGCTATGAAG 57.491 42.857 0.38 0.00 0.00 3.02
4364 4948 6.072673 GGGAGTATTATCTAAAACAATGCCCG 60.073 42.308 0.00 0.00 0.00 6.13
4382 4966 3.406512 AAGTAGACCTGCTGGGAGTAT 57.593 47.619 14.82 0.00 38.76 2.12
4383 4967 2.921834 AAGTAGACCTGCTGGGAGTA 57.078 50.000 14.82 0.00 38.76 2.59
4389 4974 4.213564 AGATGGAAAAGTAGACCTGCTG 57.786 45.455 0.00 0.00 0.00 4.41
4392 4977 7.979444 TTTTGTAGATGGAAAAGTAGACCTG 57.021 36.000 0.00 0.00 0.00 4.00
4412 4997 5.179929 GCTTGGGATGTTTGGAAAGATTTTG 59.820 40.000 0.00 0.00 0.00 2.44
4422 5007 1.753073 GGATCTGCTTGGGATGTTTGG 59.247 52.381 0.00 0.00 0.00 3.28
4470 5055 1.073025 TAGTGTGTTGCCTGCTGGG 59.927 57.895 12.06 1.66 38.36 4.45
4472 5057 1.002468 GTTGTAGTGTGTTGCCTGCTG 60.002 52.381 0.00 0.00 0.00 4.41
4549 5135 3.835378 TCAGATCTTGTACACGCGTTA 57.165 42.857 10.22 2.66 0.00 3.18
4552 5138 1.321743 GCTTCAGATCTTGTACACGCG 59.678 52.381 3.53 3.53 0.00 6.01
4572 5159 8.867112 TTACTTGTTCTATATGTAAAGAGCGG 57.133 34.615 0.00 0.00 0.00 5.52
4585 5172 9.778741 TTCTGATCACAGTTTTACTTGTTCTAT 57.221 29.630 0.00 0.00 43.81 1.98
4586 5173 9.778741 ATTCTGATCACAGTTTTACTTGTTCTA 57.221 29.630 0.00 0.00 43.81 2.10
4587 5174 8.562892 CATTCTGATCACAGTTTTACTTGTTCT 58.437 33.333 0.00 0.00 43.81 3.01
4607 5194 1.136252 CGTCGGTGCTGTTTCATTCTG 60.136 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.