Multiple sequence alignment - TraesCS3D01G131100

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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 TraesCS3D01G131100 chr3D 100.000 6333 0 0 1 6333 91217758 91224090 0.000000e+00 11695
1 TraesCS3D01G131100 chr3D 75.623 361 78 10 3104 3459 248535603 248535958 3.040000e-38 171
2 TraesCS3D01G131100 chr3B 94.334 5454 178 55 419 5812 140849686 140855068 0.000000e+00 8239
3 TraesCS3D01G131100 chr3B 87.667 300 24 7 3 299 782743689 782743978 2.830000e-88 337
4 TraesCS3D01G131100 chr3B 90.821 207 14 3 6093 6297 140855609 140855812 8.090000e-69 272
5 TraesCS3D01G131100 chr3A 94.476 4562 118 50 370 4863 107397063 107401558 0.000000e+00 6905
6 TraesCS3D01G131100 chr3A 98.095 630 11 1 5183 5812 107401944 107402572 0.000000e+00 1096
7 TraesCS3D01G131100 chr3A 90.248 564 22 5 5800 6333 107402594 107403154 0.000000e+00 706
8 TraesCS3D01G131100 chr3A 95.473 243 11 0 4862 5104 107401662 107401904 7.700000e-104 388
9 TraesCS3D01G131100 chr6D 85.830 988 95 20 2809 3785 83040639 83041592 0.000000e+00 1007
10 TraesCS3D01G131100 chr6D 84.291 261 24 9 60 312 790705 790454 8.210000e-59 239
11 TraesCS3D01G131100 chr4D 97.778 360 6 2 1 359 63785590 63785948 2.510000e-173 619
12 TraesCS3D01G131100 chr5D 97.205 322 1 3 1 320 266077439 266077124 7.220000e-149 538
13 TraesCS3D01G131100 chr5D 97.205 322 1 3 1 320 266078239 266077924 7.220000e-149 538
14 TraesCS3D01G131100 chr6B 89.691 388 27 6 2809 3193 157860141 157860518 3.430000e-132 483
15 TraesCS3D01G131100 chr6B 85.032 314 39 5 3479 3785 158066323 158066635 4.770000e-81 313
16 TraesCS3D01G131100 chr6B 85.390 308 34 5 3 306 112891268 112891568 6.170000e-80 309
17 TraesCS3D01G131100 chr6B 86.364 286 27 6 2928 3212 157948997 157949271 1.030000e-77 302
18 TraesCS3D01G131100 chr6A 89.123 285 22 4 3 285 428676016 428675739 4.700000e-91 346
19 TraesCS3D01G131100 chr6A 85.333 300 28 10 3 295 85148954 85148664 4.800000e-76 296
20 TraesCS3D01G131100 chr6A 85.563 284 35 6 2995 3274 99966905 99967186 6.210000e-75 292
21 TraesCS3D01G131100 chr6A 96.273 161 6 0 2809 2969 99972895 99973055 1.350000e-66 265
22 TraesCS3D01G131100 chr6A 89.796 98 7 2 2889 2983 99966702 99966799 8.620000e-24 122
23 TraesCS3D01G131100 chr1B 88.571 280 24 4 3 280 476907346 476907619 3.660000e-87 333


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 TraesCS3D01G131100 chr3D 91217758 91224090 6332 False 11695.00 11695 100.0000 1 6333 1 chr3D.!!$F1 6332
1 TraesCS3D01G131100 chr3B 140849686 140855812 6126 False 4255.50 8239 92.5775 419 6297 2 chr3B.!!$F2 5878
2 TraesCS3D01G131100 chr3A 107397063 107403154 6091 False 2273.75 6905 94.5730 370 6333 4 chr3A.!!$F1 5963
3 TraesCS3D01G131100 chr6D 83040639 83041592 953 False 1007.00 1007 85.8300 2809 3785 1 chr6D.!!$F1 976
4 TraesCS3D01G131100 chr5D 266077124 266078239 1115 True 538.00 538 97.2050 1 320 2 chr5D.!!$R1 319

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
371 374 0.110192 CTCGTCCTTTGCTTTTCCGC 60.110 55.0 0.00 0.0 0.00 5.54 F
376 379 0.110192 CCTTTGCTTTTCCGCGAGAC 60.110 55.0 8.23 0.0 0.00 3.36 F
377 380 0.451135 CTTTGCTTTTCCGCGAGACG 60.451 55.0 8.23 0.0 43.15 4.18 F
1399 1550 0.167251 GTTGGTTTGTCGCATACCGG 59.833 55.0 0.00 0.0 38.09 5.28 F
1628 1780 0.037160 TTCTTTCGGCAACCTACCCC 59.963 55.0 0.00 0.0 0.00 4.95 F
2012 2178 0.473755 AATGTCACAGGAGTGCCACA 59.526 50.0 0.00 0.0 45.49 4.17 F
3984 4183 0.798776 GTGCACTGACAATCCTTCCG 59.201 55.0 10.32 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1440 0.483770 GGGACTAAAAACCCCCACCA 59.516 55.000 0.00 0.00 40.19 4.17 R
1290 1441 0.781920 AGGGACTAAAAACCCCCACC 59.218 55.000 0.00 0.00 46.64 4.61 R
1449 1600 1.002069 ACCCCAGCTCCAAATGATCA 58.998 50.000 0.00 0.00 0.00 2.92 R
2625 2809 2.677902 GCTTGCTGCACCTGTAGACATA 60.678 50.000 0.00 0.00 42.31 2.29 R
3053 3241 6.533723 CAGTATTCTGTTACGGCTGTATCAAA 59.466 38.462 15.55 12.84 36.97 2.69 R
3997 4196 7.039993 GGAAATCATAGTTAACAACAACCCTGT 60.040 37.037 8.61 0.00 37.39 4.00 R
5893 6256 0.544833 TGGCAGCCAACCAAATGGAT 60.545 50.000 13.33 0.00 43.54 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
337 340 1.699730 AAAAACCAGACGAAAGGGGG 58.300 50.000 0.00 0.00 0.00 5.40
359 362 4.141914 GGGACTATTCAATCAACTCGTCCT 60.142 45.833 0.00 0.00 39.58 3.85
362 365 6.183360 GGACTATTCAATCAACTCGTCCTTTG 60.183 42.308 0.00 0.00 37.34 2.77
363 366 3.896648 TTCAATCAACTCGTCCTTTGC 57.103 42.857 0.00 0.00 0.00 3.68
364 367 3.126001 TCAATCAACTCGTCCTTTGCT 57.874 42.857 0.00 0.00 0.00 3.91
365 368 3.476552 TCAATCAACTCGTCCTTTGCTT 58.523 40.909 0.00 0.00 0.00 3.91
366 369 3.882888 TCAATCAACTCGTCCTTTGCTTT 59.117 39.130 0.00 0.00 0.00 3.51
368 371 3.963383 TCAACTCGTCCTTTGCTTTTC 57.037 42.857 0.00 0.00 0.00 2.29
369 372 2.616842 TCAACTCGTCCTTTGCTTTTCC 59.383 45.455 0.00 0.00 0.00 3.13
370 373 1.226746 ACTCGTCCTTTGCTTTTCCG 58.773 50.000 0.00 0.00 0.00 4.30
371 374 0.110192 CTCGTCCTTTGCTTTTCCGC 60.110 55.000 0.00 0.00 0.00 5.54
372 375 1.440353 CGTCCTTTGCTTTTCCGCG 60.440 57.895 0.00 0.00 0.00 6.46
373 376 1.837538 CGTCCTTTGCTTTTCCGCGA 61.838 55.000 8.23 0.00 0.00 5.87
374 377 0.110192 GTCCTTTGCTTTTCCGCGAG 60.110 55.000 8.23 0.00 0.00 5.03
375 378 0.250124 TCCTTTGCTTTTCCGCGAGA 60.250 50.000 8.23 0.00 0.00 4.04
376 379 0.110192 CCTTTGCTTTTCCGCGAGAC 60.110 55.000 8.23 0.00 0.00 3.36
377 380 0.451135 CTTTGCTTTTCCGCGAGACG 60.451 55.000 8.23 0.00 43.15 4.18
417 420 2.229784 GCTGGAATTAGCAAAGCACAGT 59.770 45.455 0.00 0.00 43.17 3.55
563 644 1.922369 AGCTGGCCACCTGTCATCT 60.922 57.895 0.00 0.00 0.00 2.90
682 784 2.389962 TACTTTTCAATCGGACGGGG 57.610 50.000 0.00 0.00 0.00 5.73
684 786 1.977594 CTTTTCAATCGGACGGGGCG 61.978 60.000 0.00 0.00 0.00 6.13
685 787 2.451928 TTTTCAATCGGACGGGGCGA 62.452 55.000 0.00 0.00 0.00 5.54
686 788 2.451928 TTTCAATCGGACGGGGCGAA 62.452 55.000 0.00 0.00 0.00 4.70
878 1018 1.722636 GATCGCTAGGGTTCGTCCGT 61.723 60.000 6.70 0.00 37.00 4.69
901 1049 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1268 1418 1.117150 GACCAGCCCGAGGTATAACA 58.883 55.000 0.00 0.00 40.09 2.41
1289 1440 4.901250 ACACCAAAATCATCTCCCACTTTT 59.099 37.500 0.00 0.00 0.00 2.27
1290 1441 5.221501 ACACCAAAATCATCTCCCACTTTTG 60.222 40.000 0.00 0.00 36.84 2.44
1291 1442 4.824289 CCAAAATCATCTCCCACTTTTGG 58.176 43.478 9.83 9.83 45.32 3.28
1326 1477 0.457851 CCTCTCCCGTAGCTTCTGTG 59.542 60.000 0.00 0.00 0.00 3.66
1383 1534 5.015733 CGAGATTTCCTTTTCGATTCGTTG 58.984 41.667 5.89 0.00 35.19 4.10
1396 1547 2.953640 TTCGTTGGTTTGTCGCATAC 57.046 45.000 0.00 0.00 0.00 2.39
1397 1548 1.149987 TCGTTGGTTTGTCGCATACC 58.850 50.000 10.79 10.79 36.31 2.73
1398 1549 0.179235 CGTTGGTTTGTCGCATACCG 60.179 55.000 12.19 0.00 38.09 4.02
1399 1550 0.167251 GTTGGTTTGTCGCATACCGG 59.833 55.000 0.00 0.00 38.09 5.28
1400 1551 1.579084 TTGGTTTGTCGCATACCGGC 61.579 55.000 0.00 0.00 38.09 6.13
1405 1556 2.817834 GTCGCATACCGGCAGCAA 60.818 61.111 0.00 0.00 42.23 3.91
1406 1557 2.511373 TCGCATACCGGCAGCAAG 60.511 61.111 0.00 0.00 37.59 4.01
1449 1600 4.087892 AGAATGCGTGCGCCTCCT 62.088 61.111 14.16 5.17 41.09 3.69
1462 1614 1.316651 GCCTCCTGATCATTTGGAGC 58.683 55.000 19.48 13.10 44.32 4.70
1497 1649 1.419387 CTCCCCACCTTCTCATCATCC 59.581 57.143 0.00 0.00 0.00 3.51
1554 1706 4.518217 GCGTTGTATCTGTGTCATAATGC 58.482 43.478 0.00 0.00 0.00 3.56
1582 1734 3.312421 AGCATGGTATACAACACGAATGC 59.688 43.478 5.01 7.78 37.12 3.56
1628 1780 0.037160 TTCTTTCGGCAACCTACCCC 59.963 55.000 0.00 0.00 0.00 4.95
1639 1791 0.916809 ACCTACCCCAATGCCACTAC 59.083 55.000 0.00 0.00 0.00 2.73
1652 1804 0.539051 CCACTACCCAGGAAGCAGAG 59.461 60.000 0.00 0.00 0.00 3.35
1664 1816 5.066593 CAGGAAGCAGAGAGTTTAGGTTTT 58.933 41.667 0.00 0.00 0.00 2.43
1795 1954 7.595130 GGAAATTTCAGTTTGTTAAGCCTACTG 59.405 37.037 19.49 0.00 38.00 2.74
2012 2178 0.473755 AATGTCACAGGAGTGCCACA 59.526 50.000 0.00 0.00 45.49 4.17
2254 2420 1.277326 TGTTATGCGCGATGTGACTC 58.723 50.000 12.10 0.00 0.00 3.36
2578 2751 9.816787 ACCTTTTCCTTTTTGTCCTATTGTATA 57.183 29.630 0.00 0.00 0.00 1.47
2890 3076 6.182627 AGCAATCAAGTTTGGTAGATCATCA 58.817 36.000 0.00 0.00 35.67 3.07
3011 3199 7.012704 CCACATTGCTAGATGCTAATGTTACTT 59.987 37.037 0.00 0.00 43.67 2.24
3984 4183 0.798776 GTGCACTGACAATCCTTCCG 59.201 55.000 10.32 0.00 0.00 4.30
3994 4193 6.072452 ACTGACAATCCTTCCGAAATCTTTTC 60.072 38.462 0.00 0.00 0.00 2.29
3997 4196 3.799432 TCCTTCCGAAATCTTTTCCCA 57.201 42.857 0.00 0.00 0.00 4.37
4356 4555 5.300969 TGAATACTTCATTCAGCACTTGC 57.699 39.130 0.00 0.00 46.48 4.01
4386 4585 5.237127 CCTGATGAATTATCGTTTGCAGCTA 59.763 40.000 0.00 0.00 38.71 3.32
4387 4586 6.072838 CCTGATGAATTATCGTTTGCAGCTAT 60.073 38.462 0.00 0.00 38.71 2.97
4436 4635 2.048603 GGCGCTCCAAGCTTCCATT 61.049 57.895 7.64 0.00 39.60 3.16
4704 4906 7.346471 ACTGTATCCCTAAAATGTGCTTGTAT 58.654 34.615 0.00 0.00 0.00 2.29
4750 4952 1.421268 TCCACAGAGAAGCACATGGTT 59.579 47.619 0.00 0.00 38.61 3.67
4795 4997 1.382522 CATGCTATGCCGTGTCCTTT 58.617 50.000 0.00 0.00 0.00 3.11
4869 5176 4.961438 TGCTCTTAGATCATATGTGGCA 57.039 40.909 1.90 0.00 0.00 4.92
4897 5204 6.491062 TGGATGGATTGCCTAGTTGAATTATG 59.509 38.462 0.00 0.00 34.31 1.90
5107 5414 7.122948 ACAAATTGAGTTAACCACCACTTTACA 59.877 33.333 0.00 0.00 0.00 2.41
5113 5420 7.994334 TGAGTTAACCACCACTTTACATTAAGT 59.006 33.333 0.88 0.00 38.87 2.24
5140 5450 3.573967 ACATGTCTGTTTTGTTCCATCCC 59.426 43.478 0.00 0.00 28.70 3.85
5403 5713 9.442062 TTCCCTAACCAAATCATAGTATCAGTA 57.558 33.333 0.00 0.00 0.00 2.74
5464 5775 2.572191 TAGGTTAAGCGTGTCGGATG 57.428 50.000 0.00 0.00 0.00 3.51
5528 5839 1.739929 TGTCCGTATGCTGGCGTTG 60.740 57.895 0.00 0.00 0.00 4.10
5697 6008 1.606668 GTTGAACTGAAATGCCCGACA 59.393 47.619 0.00 0.00 0.00 4.35
5893 6256 4.215827 CCAATTGCTAGCAAAATTTTGGCA 59.784 37.500 32.22 24.47 36.32 4.92
5913 6276 1.186917 TCCATTTGGTTGGCTGCCAG 61.187 55.000 22.17 8.16 37.31 4.85
5932 6295 3.515104 CCAGAATTTTGGTTGCCTATGGT 59.485 43.478 6.85 0.00 33.38 3.55
6040 6429 6.648879 TGGCACAAGCTATCTTTTTAAGTT 57.351 33.333 0.00 0.00 41.70 2.66
6297 6921 9.535878 CTAATCCTCTATCTCAAAAACCTGTAC 57.464 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 2.029666 GAGGATACGCAGCCGCAT 59.970 61.111 0.00 0.00 46.39 4.73
116 117 3.214250 CTCCCGAGGATACGCAGCC 62.214 68.421 0.00 0.00 46.39 4.85
117 118 2.194212 TCTCCCGAGGATACGCAGC 61.194 63.158 0.00 0.00 46.39 5.25
118 119 1.655329 GTCTCCCGAGGATACGCAG 59.345 63.158 0.00 0.00 46.39 5.18
119 120 2.184830 CGTCTCCCGAGGATACGCA 61.185 63.158 14.51 0.00 43.18 5.24
120 121 1.890979 TCGTCTCCCGAGGATACGC 60.891 63.158 19.15 1.78 46.86 4.42
336 339 4.120589 GGACGAGTTGATTGAATAGTCCC 58.879 47.826 0.00 0.00 40.54 4.46
337 340 5.012328 AGGACGAGTTGATTGAATAGTCC 57.988 43.478 3.35 3.35 45.12 3.85
342 345 4.074970 AGCAAAGGACGAGTTGATTGAAT 58.925 39.130 0.00 0.00 0.00 2.57
348 351 2.616842 GGAAAAGCAAAGGACGAGTTGA 59.383 45.455 0.00 0.00 0.00 3.18
359 362 0.876777 TCGTCTCGCGGAAAAGCAAA 60.877 50.000 6.13 0.00 41.72 3.68
362 365 0.442699 ATTTCGTCTCGCGGAAAAGC 59.557 50.000 6.13 0.00 41.98 3.51
363 366 2.281762 CCTATTTCGTCTCGCGGAAAAG 59.718 50.000 6.13 8.14 41.98 2.27
364 367 2.264813 CCTATTTCGTCTCGCGGAAAA 58.735 47.619 6.13 1.75 41.98 2.29
365 368 1.917273 CCTATTTCGTCTCGCGGAAA 58.083 50.000 6.13 8.59 41.98 3.13
366 369 0.526954 GCCTATTTCGTCTCGCGGAA 60.527 55.000 6.13 0.00 42.98 4.30
368 371 2.293627 CGCCTATTTCGTCTCGCGG 61.294 63.158 6.13 0.00 41.72 6.46
369 372 1.262824 CTCGCCTATTTCGTCTCGCG 61.263 60.000 0.00 0.00 40.88 5.87
370 373 0.029035 TCTCGCCTATTTCGTCTCGC 59.971 55.000 0.00 0.00 0.00 5.03
371 374 1.922444 GCTCTCGCCTATTTCGTCTCG 60.922 57.143 0.00 0.00 0.00 4.04
372 375 1.761206 GCTCTCGCCTATTTCGTCTC 58.239 55.000 0.00 0.00 0.00 3.36
373 376 0.029567 CGCTCTCGCCTATTTCGTCT 59.970 55.000 0.00 0.00 0.00 4.18
374 377 2.496718 CGCTCTCGCCTATTTCGTC 58.503 57.895 0.00 0.00 0.00 4.20
375 378 4.711980 CGCTCTCGCCTATTTCGT 57.288 55.556 0.00 0.00 0.00 3.85
496 533 2.203684 AAAGGTGCAAGGCCCAGG 60.204 61.111 0.00 0.00 0.00 4.45
497 534 2.629656 CGAAAGGTGCAAGGCCCAG 61.630 63.158 0.00 0.00 0.00 4.45
498 535 2.597217 CGAAAGGTGCAAGGCCCA 60.597 61.111 0.00 0.00 0.00 5.36
563 644 3.071206 GAGCCAGCGAGGAGTGGA 61.071 66.667 2.12 0.00 41.22 4.02
684 786 0.672711 GTAGGGTGGGTGCGTTCTTC 60.673 60.000 0.00 0.00 0.00 2.87
685 787 1.125711 AGTAGGGTGGGTGCGTTCTT 61.126 55.000 0.00 0.00 0.00 2.52
686 788 1.125711 AAGTAGGGTGGGTGCGTTCT 61.126 55.000 0.00 0.00 0.00 3.01
892 1040 4.862823 GGGACGGAGGGAGGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
949 1097 1.600058 AGGAAATCAGATCAGGGCCA 58.400 50.000 6.18 0.00 0.00 5.36
1244 1394 2.856039 TACCTCGGGCTGGTCTCTGG 62.856 65.000 0.00 0.00 38.88 3.86
1268 1418 5.473066 CAAAAGTGGGAGATGATTTTGGT 57.527 39.130 0.00 0.00 37.26 3.67
1284 1435 3.707611 GACTAAAAACCCCCACCAAAAGT 59.292 43.478 0.00 0.00 0.00 2.66
1289 1440 0.483770 GGGACTAAAAACCCCCACCA 59.516 55.000 0.00 0.00 40.19 4.17
1290 1441 0.781920 AGGGACTAAAAACCCCCACC 59.218 55.000 0.00 0.00 46.64 4.61
1291 1442 1.709115 AGAGGGACTAAAAACCCCCAC 59.291 52.381 0.00 0.00 46.64 4.61
1326 1477 4.341487 ACTTACACCCCAGAAATTAAGCC 58.659 43.478 0.00 0.00 0.00 4.35
1383 1534 1.977594 CTGCCGGTATGCGACAAACC 61.978 60.000 1.90 0.00 0.00 3.27
1449 1600 1.002069 ACCCCAGCTCCAAATGATCA 58.998 50.000 0.00 0.00 0.00 2.92
1497 1649 1.624487 TGATGTAACAGTAGCGTGCG 58.376 50.000 0.00 0.00 0.00 5.34
1554 1706 3.551890 GTGTTGTATACCATGCTCGTCTG 59.448 47.826 0.00 0.00 0.00 3.51
1628 1780 1.755179 CTTCCTGGGTAGTGGCATTG 58.245 55.000 0.00 0.00 0.00 2.82
1639 1791 2.093235 CCTAAACTCTCTGCTTCCTGGG 60.093 54.545 0.00 0.00 0.00 4.45
1664 1816 3.576982 ACCTCAACACGAGATAGGTCAAA 59.423 43.478 0.00 0.00 45.45 2.69
1677 1835 4.981794 AGCGCATAATTTAACCTCAACAC 58.018 39.130 11.47 0.00 0.00 3.32
1795 1954 7.509546 TGAAATAGATTCCCCAGTTACAGATC 58.490 38.462 0.00 0.00 37.22 2.75
2012 2178 6.827251 AGAACAAGATATGCATCACAGTTGAT 59.173 34.615 0.19 0.00 43.80 2.57
2203 2369 4.383010 GGATTGGGGGCATAAAAGAAGTTG 60.383 45.833 0.00 0.00 0.00 3.16
2562 2735 7.836685 TCAAGCCCAATATACAATAGGACAAAA 59.163 33.333 0.00 0.00 0.00 2.44
2578 2751 7.025520 AGTATAGCTGATATTCAAGCCCAAT 57.974 36.000 0.00 0.00 0.00 3.16
2625 2809 2.677902 GCTTGCTGCACCTGTAGACATA 60.678 50.000 0.00 0.00 42.31 2.29
2890 3076 9.965902 AAGGAACATACAGTAGATGAAATTCTT 57.034 29.630 0.00 0.00 0.00 2.52
3011 3199 8.801882 AACGGAAATTCCATTTCTTAGATACA 57.198 30.769 13.04 0.00 46.03 2.29
3053 3241 6.533723 CAGTATTCTGTTACGGCTGTATCAAA 59.466 38.462 15.55 12.84 36.97 2.69
3997 4196 7.039993 GGAAATCATAGTTAACAACAACCCTGT 60.040 37.037 8.61 0.00 37.39 4.00
4350 4549 2.749044 ATCAGGCTGGCGCAAGTG 60.749 61.111 14.59 4.73 38.10 3.16
4356 4555 1.462283 CGATAATTCATCAGGCTGGCG 59.538 52.381 15.73 6.19 32.71 5.69
4386 4585 3.003394 TGCCACTGCTGCTGTTATTAT 57.997 42.857 9.60 0.00 38.71 1.28
4387 4586 2.488204 TGCCACTGCTGCTGTTATTA 57.512 45.000 9.60 0.00 38.71 0.98
4750 4952 1.972795 AGGTGAACGGCAAAGTAGGTA 59.027 47.619 0.00 0.00 0.00 3.08
4869 5176 4.870636 TCAACTAGGCAATCCATCCAATT 58.129 39.130 0.00 0.00 33.74 2.32
4926 5233 1.885887 GCCTCTATCGAGTGAGATGCT 59.114 52.381 16.14 0.00 35.43 3.79
5023 5330 8.090214 CCAAAAGTTTCACCAATACAATCAGAT 58.910 33.333 0.00 0.00 0.00 2.90
5064 5371 8.755696 TCAATTTGTCAACCATAAAATACAGC 57.244 30.769 0.00 0.00 0.00 4.40
5392 5702 9.899661 TGCTTAAACCAACATTACTGATACTAT 57.100 29.630 0.00 0.00 0.00 2.12
5403 5713 3.801594 CACGCTTTGCTTAAACCAACATT 59.198 39.130 0.00 0.00 0.00 2.71
5464 5775 4.236935 CCACCACATCAACATAGCAAAAC 58.763 43.478 0.00 0.00 0.00 2.43
5528 5839 4.470304 AGGTTCCAGGTTTCATAGAGTACC 59.530 45.833 0.00 0.00 0.00 3.34
5697 6008 3.054875 TGCAGGATAGTTCAGCAGTTCAT 60.055 43.478 0.00 0.00 32.68 2.57
5747 6060 4.485163 CCCCTTATGCTTTGAGAAAAACG 58.515 43.478 0.00 0.00 0.00 3.60
5751 6064 3.168035 TGCCCCTTATGCTTTGAGAAA 57.832 42.857 0.00 0.00 0.00 2.52
5879 6242 4.218852 CCAAATGGATGCCAAAATTTTGCT 59.781 37.500 22.90 11.06 36.95 3.91
5893 6256 0.544833 TGGCAGCCAACCAAATGGAT 60.545 50.000 13.33 0.00 43.54 3.41
5913 6276 6.715347 AGATACCATAGGCAACCAAAATTC 57.285 37.500 0.00 0.00 37.17 2.17
6056 6445 2.092968 TGCCATGAGAATACCACACTCC 60.093 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.