Multiple sequence alignment - TraesCS5A01G248000

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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 TraesCS5A01G248000 chr5A 100.000 3002 0 0 1 3002 461913647 461910646 0.000000e+00 5544
1 TraesCS5A01G248000 chr5D 91.922 2909 152 37 130 2999 361150013 361147149 0.000000e+00 3993
2 TraesCS5A01G248000 chr5B 91.673 2726 134 46 309 2998 426622436 426619768 0.000000e+00 3690
3 TraesCS5A01G248000 chr5B 80.997 321 35 13 1 315 426625126 426624826 6.470000e-57 231
4 TraesCS5A01G248000 chr3D 95.906 171 7 0 1738 1908 443602314 443602144 8.200000e-71 278
5 TraesCS5A01G248000 chr7D 96.774 62 1 1 1738 1798 555876845 555876784 5.290000e-18 102


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 TraesCS5A01G248000 chr5A 461910646 461913647 3001 True 5544.0 5544 100.000 1 3002 1 chr5A.!!$R1 3001
1 TraesCS5A01G248000 chr5D 361147149 361150013 2864 True 3993.0 3993 91.922 130 2999 1 chr5D.!!$R1 2869
2 TraesCS5A01G248000 chr5B 426619768 426625126 5358 True 1960.5 3690 86.335 1 2998 2 chr5B.!!$R1 2997

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
767 3182 0.11456 TCTTCCTTCTCCCAGACGGT 59.885 55.0 0.0 0.0 35.36 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 4859 0.305922 GGTGCGTGCTATCAGATTGC 59.694 55.0 9.67 9.67 0.0 3.56 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
17 18 4.919653 CACACTCCTCCATCGTGG 57.080 61.111 0.00 0.00 39.43 4.94
23 24 2.225791 CTCCTCCATCGTGGTTGCGA 62.226 60.000 4.33 0.00 45.32 5.10
44 46 1.342975 TGATGACTTCCCCGAGGATGA 60.343 52.381 5.83 0.00 43.54 2.92
51 53 1.952621 TCCCCGAGGATGACTTCTTT 58.047 50.000 0.00 0.00 37.19 2.52
56 58 1.476891 CGAGGATGACTTCTTTCCCGA 59.523 52.381 0.00 0.00 0.00 5.14
60 62 3.118592 AGGATGACTTCTTTCCCGACATC 60.119 47.826 0.00 0.00 34.06 3.06
61 63 3.369471 GGATGACTTCTTTCCCGACATCA 60.369 47.826 0.00 0.00 35.75 3.07
67 69 1.616865 TCTTTCCCGACATCAACGACT 59.383 47.619 0.00 0.00 0.00 4.18
86 88 4.862018 CGACTGTCTCTTCTTGAATTCTCC 59.138 45.833 7.05 0.00 0.00 3.71
87 89 5.336372 CGACTGTCTCTTCTTGAATTCTCCT 60.336 44.000 7.05 0.00 0.00 3.69
93 99 6.148645 GTCTCTTCTTGAATTCTCCTTTCACC 59.851 42.308 7.05 0.00 33.03 4.02
123 129 8.501580 CCATATGTCATATGTGTGTCATTTCTC 58.498 37.037 24.70 0.00 40.76 2.87
151 157 0.618458 TGCTGAGGTGGTAATGACCC 59.382 55.000 0.00 0.00 46.32 4.46
171 177 2.286359 CCGATTGTGATATTGTGCGTGG 60.286 50.000 0.00 0.00 0.00 4.94
193 199 6.698329 GTGGGAATAATTTTATTTACGGGCAC 59.302 38.462 0.00 0.00 33.72 5.01
209 215 3.075884 GGGCACCGTGTCAATAAAGTTA 58.924 45.455 5.31 0.00 40.86 2.24
210 216 3.692593 GGGCACCGTGTCAATAAAGTTAT 59.307 43.478 5.31 0.00 40.86 1.89
211 217 4.877251 GGGCACCGTGTCAATAAAGTTATA 59.123 41.667 5.31 0.00 40.86 0.98
212 218 5.220719 GGGCACCGTGTCAATAAAGTTATAC 60.221 44.000 5.31 0.00 40.86 1.47
213 219 5.220719 GGCACCGTGTCAATAAAGTTATACC 60.221 44.000 0.00 0.00 0.00 2.73
214 220 5.352016 GCACCGTGTCAATAAAGTTATACCA 59.648 40.000 0.00 0.00 0.00 3.25
215 221 6.673796 GCACCGTGTCAATAAAGTTATACCAC 60.674 42.308 0.00 0.00 0.00 4.16
233 239 5.535753 ACCACTACAGTAAGTTTACCGTT 57.464 39.130 0.00 0.00 34.19 4.44
280 286 1.803366 CGCCCTATGGAGACCCGTAC 61.803 65.000 0.00 0.00 32.25 3.67
292 298 2.104331 CCGTACGGGCTACTGCAG 59.896 66.667 27.00 13.48 41.91 4.41
373 2776 1.003355 CTGTCACGGGGCAGATGTT 60.003 57.895 15.96 0.00 34.87 2.71
431 2842 0.460459 GGACCTCCAGCTACTTTCGC 60.460 60.000 0.00 0.00 35.64 4.70
469 2880 1.349627 CTGCGAATGCCGACATGAC 59.650 57.895 0.00 0.00 41.78 3.06
529 2943 3.926616 ACGATGTGAGGTTTCCTTGTAG 58.073 45.455 0.00 0.00 31.76 2.74
530 2944 2.673368 CGATGTGAGGTTTCCTTGTAGC 59.327 50.000 0.00 0.00 31.76 3.58
553 2968 6.606796 AGCCCTAGAAGTAAAGAAGGTACTAC 59.393 42.308 0.00 0.00 38.49 2.73
554 2969 6.606796 GCCCTAGAAGTAAAGAAGGTACTACT 59.393 42.308 0.00 0.00 38.49 2.57
588 3003 2.402305 TGCATTTTTACGCTTGCTTGG 58.598 42.857 0.00 0.00 36.10 3.61
608 3023 3.927481 GAAGAGGTGCCACCCCTGC 62.927 68.421 11.06 0.00 39.75 4.85
643 3058 6.717997 AGAAATACCGTTGGACCAAAAGTAAT 59.282 34.615 8.94 4.22 0.00 1.89
648 3063 3.124636 CGTTGGACCAAAAGTAATCGAGG 59.875 47.826 8.94 0.00 0.00 4.63
725 3140 2.761208 GACCTCCTCCGATGAAGAAGAA 59.239 50.000 0.00 0.00 0.00 2.52
726 3141 2.763448 ACCTCCTCCGATGAAGAAGAAG 59.237 50.000 0.00 0.00 0.00 2.85
727 3142 3.027412 CCTCCTCCGATGAAGAAGAAGA 58.973 50.000 0.00 0.00 0.00 2.87
730 3145 2.482839 CCTCCGATGAAGAAGAAGAGGC 60.483 54.545 0.00 0.00 33.59 4.70
766 3181 0.820871 CTCTTCCTTCTCCCAGACGG 59.179 60.000 0.00 0.00 35.16 4.79
767 3182 0.114560 TCTTCCTTCTCCCAGACGGT 59.885 55.000 0.00 0.00 35.36 4.83
768 3183 0.247736 CTTCCTTCTCCCAGACGGTG 59.752 60.000 0.00 0.00 35.36 4.94
769 3184 1.827399 TTCCTTCTCCCAGACGGTGC 61.827 60.000 0.00 0.00 35.36 5.01
770 3185 2.583441 CCTTCTCCCAGACGGTGCA 61.583 63.158 0.00 0.00 29.74 4.57
771 3186 1.374758 CTTCTCCCAGACGGTGCAC 60.375 63.158 8.80 8.80 0.00 4.57
926 3341 0.539438 TGACCGCTTCCTGCCAATTT 60.539 50.000 0.00 0.00 38.78 1.82
949 3364 3.489513 CCCCGATCCCCAACCTCC 61.490 72.222 0.00 0.00 0.00 4.30
958 3373 2.359169 CCCAACCTCCTCGCAGCTA 61.359 63.158 0.00 0.00 0.00 3.32
959 3374 1.690219 CCCAACCTCCTCGCAGCTAT 61.690 60.000 0.00 0.00 0.00 2.97
961 3376 1.269831 CCAACCTCCTCGCAGCTATAC 60.270 57.143 0.00 0.00 0.00 1.47
962 3377 1.409064 CAACCTCCTCGCAGCTATACA 59.591 52.381 0.00 0.00 0.00 2.29
963 3378 1.033574 ACCTCCTCGCAGCTATACAC 58.966 55.000 0.00 0.00 0.00 2.90
964 3379 1.032794 CCTCCTCGCAGCTATACACA 58.967 55.000 0.00 0.00 0.00 3.72
965 3380 1.615883 CCTCCTCGCAGCTATACACAT 59.384 52.381 0.00 0.00 0.00 3.21
966 3381 2.352225 CCTCCTCGCAGCTATACACATC 60.352 54.545 0.00 0.00 0.00 3.06
967 3382 1.613925 TCCTCGCAGCTATACACATCC 59.386 52.381 0.00 0.00 0.00 3.51
968 3383 1.337260 CCTCGCAGCTATACACATCCC 60.337 57.143 0.00 0.00 0.00 3.85
969 3384 1.341209 CTCGCAGCTATACACATCCCA 59.659 52.381 0.00 0.00 0.00 4.37
970 3385 1.068588 TCGCAGCTATACACATCCCAC 59.931 52.381 0.00 0.00 0.00 4.61
971 3386 1.873903 CGCAGCTATACACATCCCACC 60.874 57.143 0.00 0.00 0.00 4.61
972 3387 1.140852 GCAGCTATACACATCCCACCA 59.859 52.381 0.00 0.00 0.00 4.17
1725 4145 2.887568 GACGCGATGGAGCTGGTG 60.888 66.667 15.93 0.00 34.40 4.17
2031 4451 2.271497 GATGCCTGTGCCTGCTCT 59.729 61.111 0.00 0.00 36.33 4.09
2036 4456 1.220206 CCTGTGCCTGCTCTACTGG 59.780 63.158 0.00 0.00 40.30 4.00
2158 4578 5.427036 GAAGATCGATTCGAAGTAGGAGT 57.573 43.478 13.47 0.00 39.99 3.85
2161 4581 5.366460 AGATCGATTCGAAGTAGGAGTACA 58.634 41.667 13.47 0.00 39.99 2.90
2162 4582 5.821470 AGATCGATTCGAAGTAGGAGTACAA 59.179 40.000 13.47 0.00 39.99 2.41
2163 4583 5.227238 TCGATTCGAAGTAGGAGTACAAC 57.773 43.478 6.24 0.00 31.06 3.32
2166 4586 6.072286 TCGATTCGAAGTAGGAGTACAACTTT 60.072 38.462 6.24 0.00 33.72 2.66
2167 4587 6.585322 CGATTCGAAGTAGGAGTACAACTTTT 59.415 38.462 3.35 0.00 33.72 2.27
2168 4588 7.201333 CGATTCGAAGTAGGAGTACAACTTTTC 60.201 40.741 3.35 0.75 33.72 2.29
2169 4589 6.645790 TCGAAGTAGGAGTACAACTTTTCT 57.354 37.500 0.00 0.00 33.72 2.52
2209 4629 0.040958 CTGCTTGCTGGTTTCACGAC 60.041 55.000 0.00 0.00 0.00 4.34
2285 4705 1.073199 CTTGACAAGCCCCTTCCGT 59.927 57.895 1.43 0.00 0.00 4.69
2452 4872 4.198530 TCCAATTTCGCAATCTGATAGCA 58.801 39.130 0.00 0.00 0.00 3.49
2510 4930 2.503331 CAAGATGTGCAGGTGGTGTAA 58.497 47.619 0.00 0.00 0.00 2.41
2526 4946 5.761234 GTGGTGTAAACAATGAGGTCACTTA 59.239 40.000 0.00 0.00 0.00 2.24
2583 5005 1.538849 GGGGCTTGTGCTTTTGACTTG 60.539 52.381 0.00 0.00 39.59 3.16
2597 5019 5.518848 TTTGACTTGTTCATTCATGTGCT 57.481 34.783 0.00 0.00 32.84 4.40
2603 5025 2.563620 TGTTCATTCATGTGCTTGGCAT 59.436 40.909 0.00 0.00 41.91 4.40
2612 5034 4.276678 TCATGTGCTTGGCATTCTATTAGC 59.723 41.667 0.00 0.00 41.91 3.09
2615 5037 1.537202 GCTTGGCATTCTATTAGCGGG 59.463 52.381 0.00 0.00 0.00 6.13
2749 5180 4.036027 TCGTACCTAAAAGAGATACCGCAG 59.964 45.833 0.00 0.00 0.00 5.18
2751 5182 4.657436 ACCTAAAAGAGATACCGCAGAG 57.343 45.455 0.00 0.00 0.00 3.35
2758 5189 1.878522 GATACCGCAGAGCACACCG 60.879 63.158 0.00 0.00 0.00 4.94
2760 5191 1.317431 ATACCGCAGAGCACACCGTA 61.317 55.000 0.00 0.00 0.00 4.02
2819 5252 2.078392 GTTCTTTGTTATCCCGCGGAA 58.922 47.619 30.73 6.63 34.34 4.30
2830 5263 3.615224 TCCCGCGGAAAACTAGTTATT 57.385 42.857 30.73 5.71 0.00 1.40
2873 5306 2.185350 CATGTTCGGCTCCTCGCT 59.815 61.111 0.00 0.00 39.13 4.93
2884 5317 0.108424 CTCCTCGCTGTTCAGGGAAG 60.108 60.000 17.58 13.05 0.00 3.46
2891 5324 2.095567 CGCTGTTCAGGGAAGTTGATTG 60.096 50.000 10.66 0.00 0.00 2.67
2920 5353 6.020971 GTAAGGGACGGAAATTGACAAAAT 57.979 37.500 0.00 0.00 0.00 1.82
2921 5354 5.545063 AAGGGACGGAAATTGACAAAATT 57.455 34.783 0.00 0.00 0.00 1.82
2974 5426 1.272147 GCAGGGATGAGGGAAAAGTGT 60.272 52.381 0.00 0.00 0.00 3.55
2986 5438 4.893524 AGGGAAAAGTGTGGAAAGTTAAGG 59.106 41.667 0.00 0.00 0.00 2.69
2999 5451 5.511373 GGAAAGTTAAGGCTCAAGGCAAAAT 60.511 40.000 6.34 0.00 44.01 1.82
3000 5452 4.525912 AGTTAAGGCTCAAGGCAAAATG 57.474 40.909 6.34 0.00 44.01 2.32
3001 5453 3.259123 AGTTAAGGCTCAAGGCAAAATGG 59.741 43.478 6.34 0.00 44.01 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.296715 GCAACCACGATGGAGGAGT 59.703 57.895 10.46 0.00 40.96 3.85
17 18 1.017387 GGGGAAGTCATCATCGCAAC 58.983 55.000 0.00 0.00 0.00 4.17
23 24 1.696336 CATCCTCGGGGAAGTCATCAT 59.304 52.381 8.88 0.00 45.78 2.45
24 25 1.123077 CATCCTCGGGGAAGTCATCA 58.877 55.000 8.88 0.00 45.78 3.07
25 26 1.069358 GTCATCCTCGGGGAAGTCATC 59.931 57.143 8.88 0.00 45.78 2.92
26 27 1.123928 GTCATCCTCGGGGAAGTCAT 58.876 55.000 8.88 0.00 45.78 3.06
27 28 0.041238 AGTCATCCTCGGGGAAGTCA 59.959 55.000 8.88 0.00 45.78 3.41
28 29 1.137282 GAAGTCATCCTCGGGGAAGTC 59.863 57.143 8.88 0.63 45.78 3.01
44 46 2.036733 TCGTTGATGTCGGGAAAGAAGT 59.963 45.455 0.00 0.00 0.00 3.01
51 53 0.242825 GACAGTCGTTGATGTCGGGA 59.757 55.000 0.00 0.00 36.76 5.14
56 58 4.038042 TCAAGAAGAGACAGTCGTTGATGT 59.962 41.667 0.00 0.00 0.00 3.06
60 62 5.694006 AGAATTCAAGAAGAGACAGTCGTTG 59.306 40.000 8.44 0.00 0.00 4.10
61 63 5.848406 AGAATTCAAGAAGAGACAGTCGTT 58.152 37.500 8.44 0.00 0.00 3.85
67 69 6.708054 GTGAAAGGAGAATTCAAGAAGAGACA 59.292 38.462 8.44 0.00 38.44 3.41
86 88 2.355197 TGACATATGGTGCGGTGAAAG 58.645 47.619 7.80 0.00 0.00 2.62
87 89 2.481289 TGACATATGGTGCGGTGAAA 57.519 45.000 7.80 0.00 0.00 2.69
93 99 3.809279 ACACACATATGACATATGGTGCG 59.191 43.478 31.48 24.19 45.36 5.34
151 157 2.286359 CCCACGCACAATATCACAATCG 60.286 50.000 0.00 0.00 0.00 3.34
171 177 5.916320 CGGTGCCCGTAAATAAAATTATTCC 59.084 40.000 5.56 0.00 42.73 3.01
193 199 7.760794 TGTAGTGGTATAACTTTATTGACACGG 59.239 37.037 0.00 0.00 31.29 4.94
228 234 5.105635 TCGTCCTAATCTGAACATTAACGGT 60.106 40.000 0.00 0.00 29.36 4.83
233 239 9.261180 GATTTGATCGTCCTAATCTGAACATTA 57.739 33.333 0.00 0.00 0.00 1.90
292 298 6.321181 TGGATATAGTTTTCATTGACCCAAGC 59.679 38.462 0.00 0.00 0.00 4.01
298 304 7.865706 ACCTGTGGATATAGTTTTCATTGAC 57.134 36.000 0.00 0.00 0.00 3.18
373 2776 0.183492 GCTGTATCCCCATTGCCAGA 59.817 55.000 0.00 0.00 0.00 3.86
502 2913 4.759782 AGGAAACCTCACATCGTAATCAG 58.240 43.478 0.00 0.00 0.00 2.90
510 2921 3.010420 GGCTACAAGGAAACCTCACATC 58.990 50.000 0.00 0.00 30.89 3.06
529 2943 5.936187 AGTACCTTCTTTACTTCTAGGGC 57.064 43.478 0.00 0.00 0.00 5.19
530 2944 9.692325 TTAGTAGTACCTTCTTTACTTCTAGGG 57.308 37.037 0.00 0.00 33.52 3.53
554 2969 9.332301 GCGTAAAAATGCAACTACTAATTGTTA 57.668 29.630 0.00 0.00 0.00 2.41
557 2972 8.365210 CAAGCGTAAAAATGCAACTACTAATTG 58.635 33.333 0.00 0.00 0.00 2.32
558 2973 7.061789 GCAAGCGTAAAAATGCAACTACTAATT 59.938 33.333 0.00 0.00 38.63 1.40
559 2974 6.526674 GCAAGCGTAAAAATGCAACTACTAAT 59.473 34.615 0.00 0.00 38.63 1.73
560 2975 5.854338 GCAAGCGTAAAAATGCAACTACTAA 59.146 36.000 0.00 0.00 38.63 2.24
561 2976 5.180492 AGCAAGCGTAAAAATGCAACTACTA 59.820 36.000 0.00 0.00 41.18 1.82
562 2977 4.023193 AGCAAGCGTAAAAATGCAACTACT 60.023 37.500 0.00 0.00 41.18 2.57
563 2978 4.226761 AGCAAGCGTAAAAATGCAACTAC 58.773 39.130 0.00 0.00 41.18 2.73
588 3003 2.034221 GGGGTGGCACCTCTTCAC 59.966 66.667 33.87 17.27 35.29 3.18
608 3023 4.985044 AACGGTATTTCTCGTTGTTCTG 57.015 40.909 0.00 0.00 46.03 3.02
643 3058 0.319900 GCTCTTCTGTTGCACCTCGA 60.320 55.000 0.00 0.00 0.00 4.04
648 3063 2.096516 CGAGAAAGCTCTTCTGTTGCAC 60.097 50.000 13.60 1.40 39.06 4.57
725 3140 0.318762 GAGTCAACTTGTCCGCCTCT 59.681 55.000 0.00 0.00 0.00 3.69
726 3141 1.009389 CGAGTCAACTTGTCCGCCTC 61.009 60.000 0.00 0.00 0.00 4.70
727 3142 1.006102 CGAGTCAACTTGTCCGCCT 60.006 57.895 0.00 0.00 0.00 5.52
768 3183 3.527360 GAACGGTGCAGTGCAGTGC 62.527 63.158 34.65 34.65 40.08 4.40
769 3184 2.633657 GAACGGTGCAGTGCAGTG 59.366 61.111 20.42 17.56 40.08 3.66
770 3185 2.591715 GGAACGGTGCAGTGCAGT 60.592 61.111 20.42 11.45 40.08 4.40
811 3226 5.536554 TTGACTCGATCAATTTGCTTCTC 57.463 39.130 6.28 0.00 42.62 2.87
949 3364 1.341209 TGGGATGTGTATAGCTGCGAG 59.659 52.381 0.00 0.00 0.00 5.03
958 3373 0.623723 GGTGGTGGTGGGATGTGTAT 59.376 55.000 0.00 0.00 0.00 2.29
959 3374 0.474854 AGGTGGTGGTGGGATGTGTA 60.475 55.000 0.00 0.00 0.00 2.90
961 3376 1.002134 GAGGTGGTGGTGGGATGTG 60.002 63.158 0.00 0.00 0.00 3.21
962 3377 2.231380 GGAGGTGGTGGTGGGATGT 61.231 63.158 0.00 0.00 0.00 3.06
963 3378 1.915078 GAGGAGGTGGTGGTGGGATG 61.915 65.000 0.00 0.00 0.00 3.51
964 3379 1.616628 GAGGAGGTGGTGGTGGGAT 60.617 63.158 0.00 0.00 0.00 3.85
965 3380 2.203938 GAGGAGGTGGTGGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
966 3381 3.706373 CGAGGAGGTGGTGGTGGG 61.706 72.222 0.00 0.00 0.00 4.61
967 3382 4.394712 GCGAGGAGGTGGTGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
968 3383 4.742201 CGCGAGGAGGTGGTGGTG 62.742 72.222 0.00 0.00 0.00 4.17
1707 4127 4.148825 ACCAGCTCCATCGCGTCC 62.149 66.667 5.77 0.00 34.40 4.79
1722 4142 4.374702 CGCTTCAGCACGCACACC 62.375 66.667 0.00 0.00 42.21 4.16
2031 4451 5.590530 ATGTTTGAAACTTGCAACCAGTA 57.409 34.783 9.69 0.00 0.00 2.74
2084 4504 1.788258 TCTGCTCAGCTTCTTCAACG 58.212 50.000 0.00 0.00 0.00 4.10
2167 4587 9.357652 GCAGCACATAATTTAATCAAGAAAAGA 57.642 29.630 0.00 0.00 0.00 2.52
2168 4588 9.362539 AGCAGCACATAATTTAATCAAGAAAAG 57.637 29.630 0.00 0.00 0.00 2.27
2169 4589 9.709495 AAGCAGCACATAATTTAATCAAGAAAA 57.291 25.926 0.00 0.00 0.00 2.29
2209 4629 1.399440 CATCACGGCTCTCATGTTTGG 59.601 52.381 0.00 0.00 0.00 3.28
2214 4634 1.793258 GGATCATCACGGCTCTCATG 58.207 55.000 0.00 0.00 0.00 3.07
2285 4705 0.881118 GTCATTTTCCAGCGCAGGAA 59.119 50.000 28.27 28.27 45.61 3.36
2352 4772 1.138047 CATCCGGAGAACGCGTGTAC 61.138 60.000 14.98 7.97 42.52 2.90
2353 4773 1.138036 CATCCGGAGAACGCGTGTA 59.862 57.895 14.98 0.00 42.52 2.90
2354 4774 2.126071 CATCCGGAGAACGCGTGT 60.126 61.111 14.98 2.32 42.52 4.49
2355 4775 2.126071 ACATCCGGAGAACGCGTG 60.126 61.111 14.98 3.51 42.52 5.34
2356 4776 2.126071 CACATCCGGAGAACGCGT 60.126 61.111 11.34 5.58 42.52 6.01
2402 4822 4.521130 ATTCGTGCGTGATATGATAGGT 57.479 40.909 0.00 0.00 0.00 3.08
2435 4855 1.327460 GCGTGCTATCAGATTGCGAAA 59.673 47.619 11.57 0.00 33.65 3.46
2436 4856 0.930310 GCGTGCTATCAGATTGCGAA 59.070 50.000 11.57 0.00 33.65 4.70
2439 4859 0.305922 GGTGCGTGCTATCAGATTGC 59.694 55.000 9.67 9.67 0.00 3.56
2452 4872 4.038642 ACAAATTGTTTATGAAGGGTGCGT 59.961 37.500 0.00 0.00 0.00 5.24
2507 4927 6.371389 GCAACTAAGTGACCTCATTGTTTAC 58.629 40.000 0.00 0.00 0.00 2.01
2510 4930 3.498397 CGCAACTAAGTGACCTCATTGTT 59.502 43.478 0.00 0.00 0.00 2.83
2526 4946 1.144496 ACGTACACCCAACGCAACT 59.856 52.632 0.00 0.00 44.04 3.16
2583 5005 2.728690 TGCCAAGCACATGAATGAAC 57.271 45.000 0.00 0.00 31.71 3.18
2597 5019 2.948979 CAACCCGCTAATAGAATGCCAA 59.051 45.455 0.00 0.00 0.00 4.52
2603 5025 2.389962 AACGCAACCCGCTAATAGAA 57.610 45.000 0.00 0.00 41.76 2.10
2612 5034 0.791610 GCATTACGAAACGCAACCCG 60.792 55.000 0.00 0.00 44.21 5.28
2615 5037 2.412089 AGAGAGCATTACGAAACGCAAC 59.588 45.455 0.00 0.00 0.00 4.17
2749 5180 2.369870 CCGAACATACGGTGTGCTC 58.630 57.895 4.68 1.57 46.70 4.26
2758 5189 5.465390 TGCTACTATGAAATGCCGAACATAC 59.535 40.000 0.00 0.00 38.34 2.39
2760 5191 4.450976 TGCTACTATGAAATGCCGAACAT 58.549 39.130 0.00 0.00 42.30 2.71
2796 5229 3.118702 TCCGCGGGATAACAAAGAACATA 60.119 43.478 27.83 0.00 0.00 2.29
2819 5252 8.020861 TCGCGTTAAACATCAATAACTAGTTT 57.979 30.769 14.49 0.00 36.49 2.66
2873 5306 3.138304 CGACAATCAACTTCCCTGAACA 58.862 45.455 0.00 0.00 0.00 3.18
2884 5317 2.665052 GTCCCTTACGTCGACAATCAAC 59.335 50.000 17.16 0.78 0.00 3.18
2920 5353 9.360093 CCTCACAAATTACTACAACAAACAAAA 57.640 29.630 0.00 0.00 0.00 2.44
2921 5354 7.489757 GCCTCACAAATTACTACAACAAACAAA 59.510 33.333 0.00 0.00 0.00 2.83
2926 5359 5.825679 ACAGCCTCACAAATTACTACAACAA 59.174 36.000 0.00 0.00 0.00 2.83
2929 5380 4.759693 CCACAGCCTCACAAATTACTACAA 59.240 41.667 0.00 0.00 0.00 2.41
2933 5384 2.162681 GCCACAGCCTCACAAATTACT 58.837 47.619 0.00 0.00 0.00 2.24
2936 5387 1.959085 CGCCACAGCCTCACAAATT 59.041 52.632 0.00 0.00 34.57 1.82
2974 5426 2.158534 TGCCTTGAGCCTTAACTTTCCA 60.159 45.455 0.00 0.00 42.71 3.53


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

AutoCloner maintained by Alex Coulton.