Multiple sequence alignment - TraesCS6A01G170400

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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 TraesCS6A01G170400 chr6A 100.000 6300 0 0 1 6300 180919157 180925456 0.000000e+00 11635
1 TraesCS6A01G170400 chr6B 95.941 6331 182 36 6 6300 237695377 237701668 0.000000e+00 10198
2 TraesCS6A01G170400 chr6B 89.498 219 23 0 2575 2793 514607429 514607211 1.730000e-70 278
3 TraesCS6A01G170400 chr6D 96.736 5423 133 21 6 5398 138358320 138363728 0.000000e+00 8994
4 TraesCS6A01G170400 chr6D 91.522 979 41 14 5329 6300 138363702 138364645 0.000000e+00 1310
5 TraesCS6A01G170400 chr7A 94.614 427 18 3 5287 5710 475840852 475840428 0.000000e+00 656
6 TraesCS6A01G170400 chr5A 93.911 427 14 5 5287 5710 509964951 509964534 8.910000e-178 634
7 TraesCS6A01G170400 chr2A 87.136 412 46 6 2717 3124 339109702 339110110 1.600000e-125 460
8 TraesCS6A01G170400 chr7D 91.603 131 10 1 2575 2704 175877287 175877417 5.020000e-41 180


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 TraesCS6A01G170400 chr6A 180919157 180925456 6299 False 11635 11635 100.000 1 6300 1 chr6A.!!$F1 6299
1 TraesCS6A01G170400 chr6B 237695377 237701668 6291 False 10198 10198 95.941 6 6300 1 chr6B.!!$F1 6294
2 TraesCS6A01G170400 chr6D 138358320 138364645 6325 False 5152 8994 94.129 6 6300 2 chr6D.!!$F1 6294

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
94 95 0.447011 GAGATCGGTCGAACGTGACT 59.553 55.000 24.03 19.08 38.91 3.41 F
150 161 0.478507 AGGGGCTTATAATTGGCGCT 59.521 50.000 7.64 10.65 44.60 5.92 F
152 163 0.598065 GGGCTTATAATTGGCGCTGG 59.402 55.000 7.64 0.00 36.28 4.85 F
391 413 0.614979 TGGTGGTCTGAGAGGCCTAC 60.615 60.000 4.42 3.40 41.63 3.18 F
538 560 1.056700 AGGAGATCCCATCCGGTTGG 61.057 60.000 22.69 22.69 42.02 3.77 F
1622 1650 1.537776 CCATACGAGCAGAAGAGGCAG 60.538 57.143 0.00 0.00 0.00 4.85 F
2640 2670 1.456296 AATCTGCTTGATTCGCTGCA 58.544 45.000 0.00 0.00 41.17 4.41 F
3796 3834 2.039084 GGAAGTCTGCCTCAGGAGAAAA 59.961 50.000 0.00 0.00 31.51 2.29 F
4776 4816 0.250901 AGCAGAGTGCCAACCGAATT 60.251 50.000 0.00 0.00 46.52 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1112 0.882042 CGCCTCCATTCTCAATCCCG 60.882 60.000 0.00 0.0 0.00 5.14 R
1202 1230 1.241990 CGAAGAGGTGGTCGAGGACA 61.242 60.000 0.00 0.0 39.64 4.02 R
1508 1536 1.303561 GTGCTGGCAGGTTGATGGA 60.304 57.895 17.64 0.0 0.00 3.41 R
2144 2174 2.222227 AAGGCATCCCTGGAAGAAAC 57.778 50.000 0.00 0.0 41.90 2.78 R
2461 2491 5.640147 TGATTAAAATGGTCACAGAAGGGT 58.360 37.500 0.00 0.0 0.00 4.34 R
3339 3370 2.053244 AGAAGAGGCATAGACATGGGG 58.947 52.381 0.00 0.0 32.36 4.96 R
3820 3858 2.291741 GAGGGCTATTGCAAGAAATCCG 59.708 50.000 4.94 0.0 41.91 4.18 R
4989 5029 0.179018 GTTGTGGTTCCAGCCAGAGT 60.179 55.000 0.00 0.0 39.53 3.24 R
5762 5859 0.405198 TCAAAAGATGGCCAGGAGCA 59.595 50.000 13.05 0.0 46.50 4.26 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
94 95 0.447011 GAGATCGGTCGAACGTGACT 59.553 55.000 24.03 19.08 38.91 3.41
130 141 4.645921 GGGTGCACTGCAAACGGC 62.646 66.667 17.98 0.00 41.47 5.68
141 152 0.750182 GCAAACGGCAGGGGCTTATA 60.750 55.000 0.00 0.00 43.97 0.98
150 161 0.478507 AGGGGCTTATAATTGGCGCT 59.521 50.000 7.64 10.65 44.60 5.92
152 163 0.598065 GGGCTTATAATTGGCGCTGG 59.402 55.000 7.64 0.00 36.28 4.85
161 172 2.628696 TTGGCGCTGGCAATGACAG 61.629 57.895 12.63 12.63 42.98 3.51
183 194 3.556213 GGCCACCTATCGTAATGCACATA 60.556 47.826 0.00 0.00 0.00 2.29
273 285 3.389925 AAACACAATGCATGAACCAGG 57.610 42.857 0.00 0.00 0.00 4.45
303 315 3.552132 TGTGTTGAACTCCTACAAGCA 57.448 42.857 0.00 0.00 32.63 3.91
312 324 7.202016 TGAACTCCTACAAGCAAGTTAATTG 57.798 36.000 0.00 0.00 42.20 2.32
391 413 0.614979 TGGTGGTCTGAGAGGCCTAC 60.615 60.000 4.42 3.40 41.63 3.18
435 457 1.132913 CATCCATCCTCCTCTCCCTCA 60.133 57.143 0.00 0.00 0.00 3.86
442 464 1.075970 TCCTCTCCCTCACATCCGG 60.076 63.158 0.00 0.00 0.00 5.14
538 560 1.056700 AGGAGATCCCATCCGGTTGG 61.057 60.000 22.69 22.69 42.02 3.77
573 595 5.534207 TTTCATTCCACAAGTGAGCAATT 57.466 34.783 0.94 0.00 0.00 2.32
574 596 4.508461 TCATTCCACAAGTGAGCAATTG 57.492 40.909 8.88 8.88 41.61 2.32
631 659 6.839124 ATGTCAATCATGTTGTACATTGGT 57.161 33.333 0.00 0.00 36.53 3.67
643 671 6.545666 TGTTGTACATTGGTCAAGAATTCTGT 59.454 34.615 9.17 3.40 0.00 3.41
718 746 6.173427 AGGTTGTTCATTTGCCAAAGTATT 57.827 33.333 0.00 0.00 0.00 1.89
761 789 6.086765 GTTCTCTACGAATTTGCACAAATGTG 59.913 38.462 9.26 9.17 40.57 3.21
861 889 4.260990 CGGCATCCATCTATTACGCAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
1018 1046 2.892640 CGCCTGATTCCCACTCGA 59.107 61.111 0.00 0.00 0.00 4.04
1026 1054 2.521958 ATTCCCACTCGAACCTGCCG 62.522 60.000 0.00 0.00 0.00 5.69
1092 1120 2.856628 CGATCGAGGCCGGGATTGA 61.857 63.158 10.26 1.71 36.24 2.57
1552 1580 4.072131 TCTTTTTCCAGCAAGCTAATCGT 58.928 39.130 0.00 0.00 0.00 3.73
1622 1650 1.537776 CCATACGAGCAGAAGAGGCAG 60.538 57.143 0.00 0.00 0.00 4.85
1687 1715 1.546923 TCTTCGGATTCAAGGTGCGTA 59.453 47.619 0.00 0.00 0.00 4.42
1690 1718 2.980568 TCGGATTCAAGGTGCGTAAAT 58.019 42.857 0.00 0.00 0.00 1.40
1691 1719 2.675844 TCGGATTCAAGGTGCGTAAATG 59.324 45.455 0.00 0.00 0.00 2.32
1692 1720 2.418628 CGGATTCAAGGTGCGTAAATGT 59.581 45.455 0.00 0.00 0.00 2.71
1693 1721 3.727673 CGGATTCAAGGTGCGTAAATGTG 60.728 47.826 0.00 0.00 0.00 3.21
1939 1969 8.432013 TGAGCATATCAACTAACCATCTATGTT 58.568 33.333 0.00 0.00 34.02 2.71
2144 2174 9.859427 ACAAATGTTGAATCTTACATTATGGTG 57.141 29.630 12.25 10.10 42.47 4.17
2251 2281 7.649533 TTTGAAGCAACCAGATCATGATTAT 57.350 32.000 10.14 0.00 0.00 1.28
2345 2375 4.466726 TGTTTCATGATTGATGCCATTGGA 59.533 37.500 6.95 0.00 31.32 3.53
2640 2670 1.456296 AATCTGCTTGATTCGCTGCA 58.544 45.000 0.00 0.00 41.17 4.41
2903 2934 8.995027 ATCTTATTAAGTATGGAAACCATGCA 57.005 30.769 17.90 0.00 46.60 3.96
2992 3023 6.936335 TCAGATCATTCAAGTTTCTGCACTTA 59.064 34.615 0.00 0.00 35.10 2.24
3264 3295 3.475575 TGAGCAGCACTGTAATGTTTCA 58.524 40.909 0.00 0.00 0.00 2.69
3275 3306 7.518161 CACTGTAATGTTTCATATTGTCACGT 58.482 34.615 0.00 0.00 0.00 4.49
3307 3338 6.423182 TGTGCATTACCTAAAATCTAAGCCT 58.577 36.000 0.00 0.00 0.00 4.58
3336 3367 6.455360 AGCTTACCAATCACCAATAATGTG 57.545 37.500 0.00 0.00 35.01 3.21
3615 3652 5.240183 ACACTGACTGGTTTCATTCTCAATG 59.760 40.000 0.00 0.00 40.28 2.82
3796 3834 2.039084 GGAAGTCTGCCTCAGGAGAAAA 59.961 50.000 0.00 0.00 31.51 2.29
3917 3956 9.897744 TTGTGTGATCTAATTTGAGATGTTTTC 57.102 29.630 0.00 0.00 36.27 2.29
3918 3957 9.288576 TGTGTGATCTAATTTGAGATGTTTTCT 57.711 29.630 0.00 0.00 36.27 2.52
4159 4198 5.362430 ACCTTTCCTATTTTTGTGCAGTTCA 59.638 36.000 0.00 0.00 0.00 3.18
4339 4378 1.363744 CTCATTCGCCAAGTGAGTCC 58.636 55.000 0.00 0.00 35.72 3.85
4416 4455 5.476599 TGGTGCTAACATTATGTGCTTTCTT 59.523 36.000 0.00 0.00 0.00 2.52
4722 4761 1.311859 CAGCTGAGGCAGTTGTTCAA 58.688 50.000 8.42 0.00 37.79 2.69
4770 4809 2.772287 AGTTTCTAGCAGAGTGCCAAC 58.228 47.619 0.00 0.00 46.52 3.77
4776 4816 0.250901 AGCAGAGTGCCAACCGAATT 60.251 50.000 0.00 0.00 46.52 2.17
4819 4859 1.580845 ATTTGTCGCAGAGTGCCAGC 61.581 55.000 0.00 0.00 41.12 4.85
4989 5029 5.580661 CCATATGTTCGAATTGTGCATTGA 58.419 37.500 0.00 0.00 0.00 2.57
5020 5060 5.366460 TGGAACCACAACGTACTTTTATCA 58.634 37.500 0.00 0.00 0.00 2.15
5021 5061 5.998981 TGGAACCACAACGTACTTTTATCAT 59.001 36.000 0.00 0.00 0.00 2.45
5043 5083 7.041721 TCATAGTGTTGGTCAGACATATGTTC 58.958 38.462 10.30 3.64 0.00 3.18
5082 5122 2.972021 TCACCCTCATCAAGAACAGTCA 59.028 45.455 0.00 0.00 0.00 3.41
5083 5123 3.584406 TCACCCTCATCAAGAACAGTCAT 59.416 43.478 0.00 0.00 0.00 3.06
5249 5289 4.617762 GCCAGACCAGTACTGTACAACTAC 60.618 50.000 21.18 0.00 34.04 2.73
5270 5310 3.182341 CAGCTCTGGATCTTTGAGAGG 57.818 52.381 12.08 2.63 34.87 3.69
5300 5340 6.207691 ACAATCAAGGGATAATTTGAACCG 57.792 37.500 0.00 0.00 36.93 4.44
5475 5559 9.341078 ACAGATGCTTTGACCATTTTTATTTTT 57.659 25.926 0.00 0.00 0.00 1.94
5615 5702 2.364647 TGCATCAGTGGTGCATTTTGAA 59.635 40.909 27.04 2.25 46.76 2.69
5680 5767 0.326264 CTGCTGAGCTTACCTTGGGT 59.674 55.000 5.83 0.00 40.16 4.51
5681 5768 1.555075 CTGCTGAGCTTACCTTGGGTA 59.445 52.381 5.83 0.00 37.09 3.69
5756 5853 3.524541 AGAAAAACAAAAGGCTGTGCTG 58.475 40.909 0.00 0.00 0.00 4.41
5757 5854 3.055891 AGAAAAACAAAAGGCTGTGCTGT 60.056 39.130 0.00 0.00 0.00 4.40
5758 5855 2.298411 AAACAAAAGGCTGTGCTGTG 57.702 45.000 0.00 0.00 0.00 3.66
5759 5856 0.179103 AACAAAAGGCTGTGCTGTGC 60.179 50.000 0.00 0.00 0.00 4.57
5760 5857 1.039233 ACAAAAGGCTGTGCTGTGCT 61.039 50.000 0.00 0.00 0.00 4.40
5761 5858 0.103572 CAAAAGGCTGTGCTGTGCTT 59.896 50.000 0.00 0.00 0.00 3.91
5762 5859 0.826062 AAAAGGCTGTGCTGTGCTTT 59.174 45.000 0.00 0.00 0.00 3.51
5763 5860 0.103572 AAAGGCTGTGCTGTGCTTTG 59.896 50.000 0.00 0.00 0.00 2.77
5764 5861 2.355481 GGCTGTGCTGTGCTTTGC 60.355 61.111 0.00 0.00 0.00 3.68
5765 5862 2.726274 GCTGTGCTGTGCTTTGCT 59.274 55.556 0.00 0.00 0.00 3.91
5869 5966 5.692204 AGTATTGTAAGCAGCGATGTCATAC 59.308 40.000 1.22 4.24 0.00 2.39
6059 6157 9.856488 ACGAGATCATATATAATTAAGCACGTT 57.144 29.630 0.00 0.00 0.00 3.99
6169 6269 5.356751 TGGTCCATCATTTTATTGACTTCGG 59.643 40.000 0.00 0.00 0.00 4.30
6179 6279 2.028484 GACTTCGGTGGTGCGTCA 59.972 61.111 0.00 0.00 0.00 4.35
6180 6280 2.279918 ACTTCGGTGGTGCGTCAC 60.280 61.111 1.92 1.92 36.95 3.67
6186 6286 1.509463 GGTGGTGCGTCACGATCTA 59.491 57.895 0.00 0.00 38.46 1.98
6212 6313 6.957920 TTTTTGAAAGACTGATCCATCACA 57.042 33.333 0.00 0.00 32.50 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250727 CCTACCACCACCCTGTGTTG 60.251 60.000 0.00 0.00 34.35 3.33
1 2 0.696485 ACCTACCACCACCCTGTGTT 60.696 55.000 0.00 0.00 34.35 3.32
2 3 1.074014 ACCTACCACCACCCTGTGT 60.074 57.895 0.00 0.00 34.35 3.72
3 4 1.125093 TCACCTACCACCACCCTGTG 61.125 60.000 0.00 0.00 35.98 3.66
4 5 0.836400 CTCACCTACCACCACCCTGT 60.836 60.000 0.00 0.00 0.00 4.00
94 95 1.965930 GCCCGCAGACAATCACACA 60.966 57.895 0.00 0.00 0.00 3.72
122 133 0.750182 TATAAGCCCCTGCCGTTTGC 60.750 55.000 0.00 0.00 38.69 3.68
128 139 0.969149 GCCAATTATAAGCCCCTGCC 59.031 55.000 0.00 0.00 38.69 4.85
130 141 0.598065 GCGCCAATTATAAGCCCCTG 59.402 55.000 0.00 0.00 0.00 4.45
141 152 1.216178 GTCATTGCCAGCGCCAATT 59.784 52.632 2.29 0.00 0.00 2.32
152 163 1.312815 GATAGGTGGCCTGTCATTGC 58.687 55.000 3.32 0.00 40.73 3.56
161 172 1.226746 GTGCATTACGATAGGTGGCC 58.773 55.000 0.00 0.00 43.77 5.36
247 259 6.286758 TGGTTCATGCATTGTGTTTTTGTAT 58.713 32.000 0.00 0.00 0.00 2.29
256 268 2.494471 ACATCCTGGTTCATGCATTGTG 59.506 45.455 0.00 0.00 0.00 3.33
258 270 2.756207 TCACATCCTGGTTCATGCATTG 59.244 45.455 0.00 0.00 0.00 2.82
303 315 5.826643 TGGAACTAGGATGGCAATTAACTT 58.173 37.500 0.00 0.00 0.00 2.66
312 324 2.099756 GCATGTTTGGAACTAGGATGGC 59.900 50.000 0.00 0.00 0.00 4.40
316 328 4.032960 ACATGCATGTTTGGAACTAGGA 57.967 40.909 26.61 0.00 37.90 2.94
317 329 4.096382 GGTACATGCATGTTTGGAACTAGG 59.904 45.833 35.45 3.90 41.97 3.02
372 394 0.614979 GTAGGCCTCTCAGACCACCA 60.615 60.000 9.68 0.00 0.00 4.17
391 413 0.537653 GGAAAGGACGAGAGGGGAAG 59.462 60.000 0.00 0.00 0.00 3.46
435 457 1.071699 ACCATAAATAGCGCCGGATGT 59.928 47.619 5.05 0.00 0.00 3.06
442 464 5.748592 CAAGAACCTAACCATAAATAGCGC 58.251 41.667 0.00 0.00 0.00 5.92
553 575 3.890756 ACAATTGCTCACTTGTGGAATGA 59.109 39.130 5.05 0.00 33.72 2.57
573 595 0.179004 AAACCAGGTCGGATGCAACA 60.179 50.000 0.00 0.00 38.63 3.33
574 596 0.958822 AAAACCAGGTCGGATGCAAC 59.041 50.000 0.00 0.00 38.63 4.17
575 597 1.243902 GAAAACCAGGTCGGATGCAA 58.756 50.000 0.00 0.00 38.63 4.08
665 693 6.656693 CACAGAGGAAGGAGTAAATCATGTTT 59.343 38.462 0.00 0.00 0.00 2.83
761 789 8.549777 TCGTACAAATTTCATACAAACACAAC 57.450 30.769 8.95 0.00 0.00 3.32
789 817 3.258372 TCCAGCTCTAAACAGTTCGACAT 59.742 43.478 0.00 0.00 0.00 3.06
861 889 0.465460 ACATGGTGCCAGTCAACGTT 60.465 50.000 0.00 0.00 34.29 3.99
862 890 1.148273 ACATGGTGCCAGTCAACGT 59.852 52.632 0.00 0.00 34.29 3.99
870 898 2.598099 CACAGCCACATGGTGCCA 60.598 61.111 0.00 0.00 46.55 4.92
1018 1046 3.066190 TCGATCGTCCGGCAGGTT 61.066 61.111 15.94 0.00 39.05 3.50
1026 1054 2.413765 GGAGCAGGTCGATCGTCC 59.586 66.667 21.72 21.72 0.00 4.79
1084 1112 0.882042 CGCCTCCATTCTCAATCCCG 60.882 60.000 0.00 0.00 0.00 5.14
1202 1230 1.241990 CGAAGAGGTGGTCGAGGACA 61.242 60.000 0.00 0.00 39.64 4.02
1508 1536 1.303561 GTGCTGGCAGGTTGATGGA 60.304 57.895 17.64 0.00 0.00 3.41
1552 1580 2.536365 GTCAAGCGACATGGACGATTA 58.464 47.619 15.12 4.91 42.13 1.75
1622 1650 4.101942 GCTGCTCGACTATAGATATGCAC 58.898 47.826 6.78 3.92 0.00 4.57
1687 1715 8.641498 AATAATCCTGAAGACACTTCACATTT 57.359 30.769 9.67 6.67 0.00 2.32
1690 1718 7.522073 GCAAAATAATCCTGAAGACACTTCACA 60.522 37.037 9.67 1.63 0.00 3.58
1691 1719 6.803807 GCAAAATAATCCTGAAGACACTTCAC 59.196 38.462 9.67 0.00 0.00 3.18
1692 1720 6.071952 GGCAAAATAATCCTGAAGACACTTCA 60.072 38.462 12.53 12.53 0.00 3.02
1693 1721 6.071952 TGGCAAAATAATCCTGAAGACACTTC 60.072 38.462 0.00 0.00 0.00 3.01
1759 1788 5.924254 CACTCGTCTTTACACCAGTGATTTA 59.076 40.000 4.48 0.00 32.72 1.40
2050 2080 8.946085 GTGACAAATTCAGTGTTATCCTTATCA 58.054 33.333 0.00 0.00 33.71 2.15
2144 2174 2.222227 AAGGCATCCCTGGAAGAAAC 57.778 50.000 0.00 0.00 41.90 2.78
2461 2491 5.640147 TGATTAAAATGGTCACAGAAGGGT 58.360 37.500 0.00 0.00 0.00 4.34
2462 2492 6.588719 TTGATTAAAATGGTCACAGAAGGG 57.411 37.500 0.00 0.00 0.00 3.95
2640 2670 2.438392 TCCTCTTCATCATCAGCATGCT 59.562 45.455 16.30 16.30 34.76 3.79
2992 3023 9.658799 AATCGCTGCATGTAATAGATAAAGTAT 57.341 29.630 0.00 0.00 0.00 2.12
3001 3032 7.177498 TGTAAAGAATCGCTGCATGTAATAG 57.823 36.000 0.00 0.00 0.00 1.73
3003 3034 6.435430 TTGTAAAGAATCGCTGCATGTAAT 57.565 33.333 0.00 0.00 0.00 1.89
3307 3338 2.169561 TGGTGATTGGTAAGCTCGCATA 59.830 45.455 0.00 0.00 0.00 3.14
3336 3367 2.264455 AGAGGCATAGACATGGGGATC 58.736 52.381 0.00 0.00 32.36 3.36
3339 3370 2.053244 AGAAGAGGCATAGACATGGGG 58.947 52.381 0.00 0.00 32.36 4.96
3615 3652 7.694367 GCAAGTAAAGAATTCTGCTTAGCTTAC 59.306 37.037 9.17 11.51 0.00 2.34
3820 3858 2.291741 GAGGGCTATTGCAAGAAATCCG 59.708 50.000 4.94 0.00 41.91 4.18
3900 3938 8.578308 TGCAACAAGAAAACATCTCAAATTAG 57.422 30.769 0.00 0.00 37.42 1.73
3997 4036 3.415457 TCAATGTGTGTGAGTATGCCA 57.585 42.857 0.00 0.00 0.00 4.92
4159 4198 9.905713 TCAGCTTAAAAATGTACAGGATCTTAT 57.094 29.630 0.33 0.00 0.00 1.73
4339 4378 8.322906 TGGATGTAGAATACTTGTGAAAACTG 57.677 34.615 0.00 0.00 43.54 3.16
4416 4455 3.865164 CACGCATCTGCAGTTACATTAGA 59.135 43.478 14.67 0.00 42.21 2.10
4719 4758 7.624360 AACTTTAGATAATGCCAACGATTGA 57.376 32.000 0.00 0.00 0.00 2.57
4722 4761 7.120579 TGTCAAACTTTAGATAATGCCAACGAT 59.879 33.333 0.00 0.00 0.00 3.73
4757 4796 0.250901 AATTCGGTTGGCACTCTGCT 60.251 50.000 0.00 0.00 44.28 4.24
4770 4809 7.265673 TGGAAGTATCTGTCTTTAGAATTCGG 58.734 38.462 0.00 0.00 0.00 4.30
4776 4816 7.733773 TTGGATGGAAGTATCTGTCTTTAGA 57.266 36.000 0.00 0.00 0.00 2.10
4819 4859 7.307632 CCTGAAACTCACTGTCACTAATCAAAG 60.308 40.741 0.00 0.00 0.00 2.77
4950 4990 0.541296 ATGGCACTTCCTTGCTTGCT 60.541 50.000 0.00 0.00 42.56 3.91
4989 5029 0.179018 GTTGTGGTTCCAGCCAGAGT 60.179 55.000 0.00 0.00 39.53 3.24
5020 5060 6.042777 CGAACATATGTCTGACCAACACTAT 58.957 40.000 9.23 0.00 0.00 2.12
5021 5061 5.047590 ACGAACATATGTCTGACCAACACTA 60.048 40.000 9.23 0.00 0.00 2.74
5082 5122 7.220741 ACATAGATACAGAATACACGAGCAT 57.779 36.000 0.00 0.00 0.00 3.79
5083 5123 6.635030 ACATAGATACAGAATACACGAGCA 57.365 37.500 0.00 0.00 0.00 4.26
5300 5340 2.540931 CACAGCAATTCAGCACAAAACC 59.459 45.455 0.00 0.00 36.85 3.27
5475 5559 3.290710 GCTAATCCCCTCATCTGCAAAA 58.709 45.455 0.00 0.00 0.00 2.44
5548 5632 4.438148 TGGTGCAAAAGCTTTTCTTAACC 58.562 39.130 21.45 22.37 33.88 2.85
5555 5639 3.384816 GCCTGGTGCAAAAGCTTTT 57.615 47.368 18.74 18.74 40.77 2.27
5566 5650 1.753930 TACATGCAGATTGCCTGGTG 58.246 50.000 10.32 2.53 44.23 4.17
5615 5702 0.629058 GTCTCCTCTGTCCCTCTCCT 59.371 60.000 0.00 0.00 0.00 3.69
5680 5767 8.384693 AGAGGAAAGGCATGATCATACATATA 57.615 34.615 8.15 0.00 0.00 0.86
5681 5768 7.268212 AGAGGAAAGGCATGATCATACATAT 57.732 36.000 8.15 0.00 0.00 1.78
5756 5853 1.941999 GATGGCCAGGAGCAAAGCAC 61.942 60.000 13.05 0.00 46.50 4.40
5757 5854 1.679977 GATGGCCAGGAGCAAAGCA 60.680 57.895 13.05 0.00 46.50 3.91
5758 5855 0.969409 AAGATGGCCAGGAGCAAAGC 60.969 55.000 13.05 0.00 46.50 3.51
5759 5856 1.553706 AAAGATGGCCAGGAGCAAAG 58.446 50.000 13.05 0.00 46.50 2.77
5760 5857 1.619827 CAAAAGATGGCCAGGAGCAAA 59.380 47.619 13.05 0.00 46.50 3.68
5761 5858 1.203038 TCAAAAGATGGCCAGGAGCAA 60.203 47.619 13.05 0.00 46.50 3.91
5762 5859 0.405198 TCAAAAGATGGCCAGGAGCA 59.595 50.000 13.05 0.00 46.50 4.26
5763 5860 1.475682 CTTCAAAAGATGGCCAGGAGC 59.524 52.381 13.05 0.00 42.60 4.70
5764 5861 1.475682 GCTTCAAAAGATGGCCAGGAG 59.524 52.381 13.05 0.69 0.00 3.69
5765 5862 1.203038 TGCTTCAAAAGATGGCCAGGA 60.203 47.619 13.05 0.00 0.00 3.86
5869 5966 4.268405 GGTGTGTTGCTGTTCAAGATTTTG 59.732 41.667 0.00 0.00 34.91 2.44
6059 6157 7.509141 TGATGTTAGTTTTCTCTTTGCATGA 57.491 32.000 0.00 0.00 0.00 3.07
6142 6240 6.624352 AGTCAATAAAATGATGGACCATCG 57.376 37.500 25.89 11.63 43.14 3.84
6169 6269 1.922570 AATAGATCGTGACGCACCAC 58.077 50.000 0.00 0.00 0.00 4.16
6194 6295 6.998968 AAGATTGTGATGGATCAGTCTTTC 57.001 37.500 0.00 0.00 37.51 2.62
6212 6313 2.746472 GCCCTCAACCGCTGATAAGATT 60.746 50.000 0.00 0.00 32.14 2.40


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

AutoCloner maintained by Alex Coulton.