Multiple sequence alignment - TraesCS2A01G196500

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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 TraesCS2A01G196500 chr2A 100.000 3539 0 0 1 3539 166260604 166257066 0.000000e+00 6536
1 TraesCS2A01G196500 chr2A 79.302 430 55 17 2850 3273 166631690 166631289 1.620000e-68 270
2 TraesCS2A01G196500 chr2D 94.179 3281 139 24 300 3539 156598346 156595077 0.000000e+00 4953
3 TraesCS2A01G196500 chr2D 79.953 429 56 15 2850 3273 156711074 156710671 4.470000e-74 289
4 TraesCS2A01G196500 chr2D 91.099 191 14 3 95 285 156598812 156598625 4.530000e-64 255
5 TraesCS2A01G196500 chr2D 93.269 104 6 1 1 103 156600523 156600420 6.120000e-33 152
6 TraesCS2A01G196500 chr2B 92.803 3029 167 31 1 2990 214287762 214284746 0.000000e+00 4338


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 TraesCS2A01G196500 chr2A 166257066 166260604 3538 True 6536.000000 6536 100.000 1 3539 1 chr2A.!!$R1 3538
1 TraesCS2A01G196500 chr2D 156595077 156600523 5446 True 1786.666667 4953 92.849 1 3539 3 chr2D.!!$R2 3538
2 TraesCS2A01G196500 chr2B 214284746 214287762 3016 True 4338.000000 4338 92.803 1 2990 1 chr2B.!!$R1 2989

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
996 2902 0.526739 CCACGTATCATTCGGTCGCA 60.527 55.0 0.0 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 4482 0.037326 TAAGAGGCAAGACACGGCTG 60.037 55.0 0.0 0.0 39.76 4.85 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
77 79 1.227853 ACTGGAAGCACAACCGTCC 60.228 57.895 0.00 0.00 37.60 4.79
86 88 2.511600 CAACCGTCCGGCATCTCC 60.512 66.667 5.47 0.00 39.32 3.71
155 1775 5.189180 GTGCCAAGAAGAGATAAAGGATGT 58.811 41.667 0.00 0.00 0.00 3.06
187 1807 2.035066 ACAGCAGAACTTTGTTGATGGC 59.965 45.455 0.00 0.00 32.84 4.40
193 1813 3.259123 AGAACTTTGTTGATGGCATTCCC 59.741 43.478 0.00 0.00 0.00 3.97
214 1834 4.580580 CCCTATTTCTAGCAATGGTTCCAC 59.419 45.833 0.00 0.00 0.00 4.02
216 1836 5.297776 CCTATTTCTAGCAATGGTTCCACTG 59.702 44.000 0.00 0.00 0.00 3.66
217 1837 3.788227 TTCTAGCAATGGTTCCACTGT 57.212 42.857 2.38 0.00 0.00 3.55
218 1838 4.901197 TTCTAGCAATGGTTCCACTGTA 57.099 40.909 2.38 0.00 0.00 2.74
262 1882 5.046014 AGAGAATTTCTACATGGTCAGCAGT 60.046 40.000 0.00 0.00 33.23 4.40
273 1893 2.698274 TGGTCAGCAGTAAAGTCACAGA 59.302 45.455 0.00 0.00 0.00 3.41
304 2188 9.905713 AGCATTTCTGGTGATTATTAGTTAGAA 57.094 29.630 0.00 0.00 0.00 2.10
373 2260 2.108514 CCTCATCGGCAACATGCGT 61.109 57.895 0.00 0.00 46.21 5.24
457 2357 6.316640 GCATATCATCCATGAGGAAGATCTTG 59.683 42.308 14.00 0.00 46.56 3.02
463 2363 3.433314 CCATGAGGAAGATCTTGTCCTGG 60.433 52.174 18.87 18.01 44.57 4.45
468 2368 2.859273 AAGATCTTGTCCTGGGCGCG 62.859 60.000 7.30 0.00 0.00 6.86
499 2403 5.685728 AGGTAGCAAGATTCTAATTCACCC 58.314 41.667 0.00 0.00 0.00 4.61
538 2442 3.432051 CTAGAGGCGGGTGGAAGCG 62.432 68.421 0.00 0.00 33.03 4.68
553 2457 1.416772 GAAGCGGTAGGGGCTAAGATT 59.583 52.381 0.00 0.00 40.53 2.40
586 2491 1.226211 CGAATGAGGCAAGCAAGCG 60.226 57.895 0.00 0.00 34.64 4.68
614 2519 1.690985 GTGGGGGAGGAGGAAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
726 2631 2.282958 TCGCGGTTCTCCCAGTCT 60.283 61.111 6.13 0.00 0.00 3.24
886 2791 0.687354 AAGTCGCTTCTGTCCATGGT 59.313 50.000 12.58 0.00 0.00 3.55
887 2792 0.687354 AGTCGCTTCTGTCCATGGTT 59.313 50.000 12.58 0.00 0.00 3.67
888 2793 1.899814 AGTCGCTTCTGTCCATGGTTA 59.100 47.619 12.58 0.80 0.00 2.85
889 2794 2.000447 GTCGCTTCTGTCCATGGTTAC 59.000 52.381 12.58 3.89 0.00 2.50
959 2865 3.135530 GGCAATCTACTTCCACATCCTCT 59.864 47.826 0.00 0.00 0.00 3.69
960 2866 4.376146 GCAATCTACTTCCACATCCTCTC 58.624 47.826 0.00 0.00 0.00 3.20
961 2867 4.742138 GCAATCTACTTCCACATCCTCTCC 60.742 50.000 0.00 0.00 0.00 3.71
963 2869 5.671463 ATCTACTTCCACATCCTCTCCTA 57.329 43.478 0.00 0.00 0.00 2.94
964 2870 5.671463 TCTACTTCCACATCCTCTCCTAT 57.329 43.478 0.00 0.00 0.00 2.57
965 2871 6.781857 TCTACTTCCACATCCTCTCCTATA 57.218 41.667 0.00 0.00 0.00 1.31
966 2872 7.162973 TCTACTTCCACATCCTCTCCTATAA 57.837 40.000 0.00 0.00 0.00 0.98
996 2902 0.526739 CCACGTATCATTCGGTCGCA 60.527 55.000 0.00 0.00 0.00 5.10
1270 3184 2.642254 ATTCCCTCGCCGTCGTTCA 61.642 57.895 0.00 0.00 36.96 3.18
1507 3421 4.357947 ACATGGACGACGCACGCT 62.358 61.111 0.00 0.00 46.94 5.07
1623 3537 2.341257 GTGTTCGACATGATGCTCAGT 58.659 47.619 0.00 0.00 0.00 3.41
1630 3544 1.478105 ACATGATGCTCAGTGCTCGTA 59.522 47.619 0.00 0.00 43.37 3.43
1732 3646 1.816537 GCTCTCATCACCGCTACCA 59.183 57.895 0.00 0.00 0.00 3.25
1748 3662 1.071471 CCACCGGTAGGATGGATGC 59.929 63.158 6.87 0.00 41.02 3.91
1749 3663 1.300931 CACCGGTAGGATGGATGCG 60.301 63.158 6.87 0.00 41.02 4.73
1782 3696 0.462581 CGCTGGTGGACATGTATGCT 60.463 55.000 0.00 0.00 0.00 3.79
1793 3707 2.093181 ACATGTATGCTAAGTGCGGGAA 60.093 45.455 0.00 0.00 46.63 3.97
1881 3795 1.288439 CATGATCTCGGGGCTCTCG 59.712 63.158 0.00 0.00 0.00 4.04
1922 3836 2.664851 CGTTGAGCTGTTCGGCCA 60.665 61.111 2.24 0.00 0.00 5.36
1928 3842 2.747460 GCTGTTCGGCCAGATGCA 60.747 61.111 2.24 0.00 43.89 3.96
1934 3848 4.100084 CGGCCAGATGCAGGACCA 62.100 66.667 2.24 0.00 43.89 4.02
1965 3879 1.676014 CCCAACGAGGTCACCTTCATC 60.676 57.143 0.00 0.00 31.76 2.92
1975 3889 0.534412 CACCTTCATCTGCGTCCTCT 59.466 55.000 0.00 0.00 0.00 3.69
1978 3892 0.108472 CTTCATCTGCGTCCTCTGCA 60.108 55.000 0.00 0.00 40.70 4.41
1980 3894 1.217511 CATCTGCGTCCTCTGCACT 59.782 57.895 0.00 0.00 37.44 4.40
2018 3932 3.378552 GCTTGTCAGCGTCGCTAG 58.621 61.111 21.25 14.75 36.40 3.42
2029 3943 0.594110 CGTCGCTAGGGAGATCTTCC 59.406 60.000 12.77 12.77 46.00 3.46
2088 4002 1.147153 GCACTATGGGAGCCTGGTC 59.853 63.158 0.00 0.00 0.00 4.02
2094 4008 4.436998 GGGAGCCTGGTCGACGTG 62.437 72.222 9.92 4.44 0.00 4.49
2247 4161 1.127567 AGCAGGTTGTGGAGTGGCTA 61.128 55.000 0.00 0.00 0.00 3.93
2253 4167 1.476845 TTGTGGAGTGGCTAGCGGAA 61.477 55.000 9.00 0.00 0.00 4.30
2540 4454 1.134491 GCTATCCAACTTGGCGTAGGT 60.134 52.381 15.99 0.00 37.47 3.08
2547 4462 2.381725 ACTTGGCGTAGGTTTAGAGC 57.618 50.000 0.00 0.00 0.00 4.09
2567 4482 2.087009 CGTTTCCGTCTCAGGTCGC 61.087 63.158 0.00 0.00 0.00 5.19
2568 4483 1.006571 GTTTCCGTCTCAGGTCGCA 60.007 57.895 0.00 0.00 0.00 5.10
2571 4486 4.803426 CCGTCTCAGGTCGCAGCC 62.803 72.222 0.00 0.00 0.00 4.85
2573 4488 4.057428 GTCTCAGGTCGCAGCCGT 62.057 66.667 0.00 0.00 35.54 5.68
2574 4489 4.056125 TCTCAGGTCGCAGCCGTG 62.056 66.667 0.00 0.00 35.54 4.94
2576 4491 4.357947 TCAGGTCGCAGCCGTGTC 62.358 66.667 0.00 0.00 35.54 3.67
2578 4493 3.616721 AGGTCGCAGCCGTGTCTT 61.617 61.111 0.00 0.00 35.54 3.01
2604 4524 4.571919 TCTTATAAGTTGGAACACCACGG 58.428 43.478 12.19 0.00 39.29 4.94
2617 4543 1.301087 CCACGGCTCGTACCACAAA 60.301 57.895 0.00 0.00 38.32 2.83
2686 4616 3.036091 TCAGATGACATGCTCATGGAGA 58.964 45.455 13.69 7.30 39.96 3.71
2876 4807 9.133627 CTTACAGAGATGTATGGAATGATTACG 57.866 37.037 0.00 0.00 0.00 3.18
2882 4813 7.810658 AGATGTATGGAATGATTACGAAATGC 58.189 34.615 0.00 0.00 0.00 3.56
2898 4829 2.910688 ATGCGATTTATCTCCACGGT 57.089 45.000 0.00 0.00 0.00 4.83
2976 4907 1.273606 AGATTGATCCCCGTAGCATCG 59.726 52.381 0.00 0.00 0.00 3.84
2990 4921 4.031426 CGTAGCATCGACTAACAGGTTTTC 59.969 45.833 0.00 0.00 0.00 2.29
2991 4922 4.002906 AGCATCGACTAACAGGTTTTCA 57.997 40.909 0.00 0.00 0.00 2.69
2992 4923 4.579869 AGCATCGACTAACAGGTTTTCAT 58.420 39.130 0.00 0.00 0.00 2.57
3075 5007 5.278266 GCTTAATGTGCCAGTTTGTCAGTTA 60.278 40.000 0.00 0.00 0.00 2.24
3078 5010 2.294074 GTGCCAGTTTGTCAGTTACCA 58.706 47.619 0.00 0.00 0.00 3.25
3092 5024 8.322906 TGTCAGTTACCATAATCAGAAACTTG 57.677 34.615 0.00 0.00 0.00 3.16
3111 5043 5.428253 ACTTGTCAAGTTCTTCAGCACTTA 58.572 37.500 12.62 0.00 39.04 2.24
3113 5045 6.543831 ACTTGTCAAGTTCTTCAGCACTTATT 59.456 34.615 12.62 0.00 39.04 1.40
3114 5046 7.715249 ACTTGTCAAGTTCTTCAGCACTTATTA 59.285 33.333 12.62 0.00 39.04 0.98
3177 5109 5.163943 GCACTTTTCGACTTATCCTTCAGTC 60.164 44.000 0.00 0.00 36.78 3.51
3192 5124 4.344448 CTTCAGTCGTCGACCTATCTTTC 58.656 47.826 21.40 0.00 32.18 2.62
3193 5125 3.607741 TCAGTCGTCGACCTATCTTTCT 58.392 45.455 21.40 0.00 32.18 2.52
3194 5126 4.008330 TCAGTCGTCGACCTATCTTTCTT 58.992 43.478 21.40 0.00 32.18 2.52
3209 5141 6.749923 ATCTTTCTTGCAGTTCATCCTAAC 57.250 37.500 0.00 0.00 0.00 2.34
3270 5203 4.141135 TCCTCAGATTACTAGCAGCTACCT 60.141 45.833 0.00 0.00 0.00 3.08
3312 5245 0.602638 CAGCACGCTACCCTGTTCAA 60.603 55.000 0.00 0.00 0.00 2.69
3314 5247 1.165270 GCACGCTACCCTGTTCAAAT 58.835 50.000 0.00 0.00 0.00 2.32
3321 5254 0.188342 ACCCTGTTCAAATGGTGGCT 59.812 50.000 0.00 0.00 0.00 4.75
3322 5255 1.341080 CCCTGTTCAAATGGTGGCTT 58.659 50.000 0.00 0.00 0.00 4.35
3330 5263 3.420893 TCAAATGGTGGCTTCCTAAGTG 58.579 45.455 1.63 0.00 0.00 3.16
3354 5294 0.671472 TGATGGTGTTGAGCAGCTCG 60.671 55.000 17.81 0.00 45.23 5.03
3358 5298 2.031012 TGTTGAGCAGCTCGGTGG 59.969 61.111 17.81 0.00 32.35 4.61
3409 5350 4.271696 TGGAGTTCTCCATGTTAGTGTG 57.728 45.455 16.47 0.00 34.33 3.82
3424 5365 1.065491 AGTGTGACCTTGCTGTTCACA 60.065 47.619 6.57 6.57 38.74 3.58
3441 5382 2.034179 TCACAGACAACCACTACGACAG 59.966 50.000 0.00 0.00 0.00 3.51
3444 5385 1.137513 GACAACCACTACGACAGCAC 58.862 55.000 0.00 0.00 0.00 4.40
3450 5391 0.172803 CACTACGACAGCACCTACCC 59.827 60.000 0.00 0.00 0.00 3.69
3465 5406 1.546476 CTACCCATAGATCTCCCGTGC 59.454 57.143 0.00 0.00 0.00 5.34
3466 5407 1.290324 CCCATAGATCTCCCGTGCG 59.710 63.158 0.00 0.00 0.00 5.34
3491 5433 7.096065 CGGAAATTGAACAGATTTTTGTCTTCC 60.096 37.037 0.00 0.00 0.00 3.46
3498 5440 7.922278 TGAACAGATTTTTGTCTTCCAGAAATG 59.078 33.333 0.00 0.00 37.83 2.32
3502 5444 7.383300 CAGATTTTTGTCTTCCAGAAATGGAAC 59.617 37.037 5.62 0.00 42.51 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 2.409870 GCAAACCTGGGAGATGCCG 61.410 63.158 0.00 0.00 37.63 5.69
155 1775 5.661056 AAGTTCTGCTGTAGTATGTGCTA 57.339 39.130 0.00 0.00 0.00 3.49
172 1792 3.259123 AGGGAATGCCATCAACAAAGTTC 59.741 43.478 0.00 0.00 35.15 3.01
187 1807 6.015940 GGAACCATTGCTAGAAATAGGGAATG 60.016 42.308 6.79 0.00 38.11 2.67
193 1813 5.882557 ACAGTGGAACCATTGCTAGAAATAG 59.117 40.000 14.62 0.00 37.80 1.73
235 1855 5.877012 GCTGACCATGTAGAAATTCTCTTGA 59.123 40.000 0.00 0.00 35.41 3.02
244 1864 5.865085 ACTTTACTGCTGACCATGTAGAAA 58.135 37.500 0.00 0.00 0.00 2.52
246 1866 4.526650 TGACTTTACTGCTGACCATGTAGA 59.473 41.667 0.00 0.00 0.00 2.59
273 1893 9.686683 ACTAATAATCACCAGAAATGCTAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
304 2188 2.912025 CAACGGTGCTTTGCCCCT 60.912 61.111 0.00 0.00 0.00 4.79
373 2260 0.975556 TGCCATAGCCGACTTCCTCA 60.976 55.000 0.00 0.00 38.69 3.86
449 2349 1.078143 GCGCCCAGGACAAGATCTT 60.078 57.895 0.88 0.88 0.00 2.40
463 2363 3.486252 CTACCTACCTGCTCGCGCC 62.486 68.421 0.00 0.00 34.43 6.53
468 2368 3.386402 AGAATCTTGCTACCTACCTGCTC 59.614 47.826 0.00 0.00 0.00 4.26
481 2384 4.614946 GCATGGGTGAATTAGAATCTTGC 58.385 43.478 0.00 0.00 0.00 4.01
499 2403 3.378112 AGGTGTGATTTATTCCACGCATG 59.622 43.478 0.00 0.00 43.40 4.06
538 2442 2.234168 GGATCGAATCTTAGCCCCTACC 59.766 54.545 0.00 0.00 0.00 3.18
570 2474 1.930908 GCTCGCTTGCTTGCCTCATT 61.931 55.000 0.00 0.00 0.00 2.57
614 2519 0.468771 CCCATTTCCCTCCCTGCATC 60.469 60.000 0.00 0.00 0.00 3.91
829 2734 2.830370 GAGGGGAGCCAATTGCCG 60.830 66.667 0.00 0.00 42.71 5.69
834 2739 3.023735 GTGGGGAGGGGAGCCAAT 61.024 66.667 0.00 0.00 0.00 3.16
886 2791 4.338879 AGCGTAGAGTGGAAGGTAAGTAA 58.661 43.478 0.00 0.00 0.00 2.24
887 2792 3.960571 AGCGTAGAGTGGAAGGTAAGTA 58.039 45.455 0.00 0.00 0.00 2.24
888 2793 2.805194 AGCGTAGAGTGGAAGGTAAGT 58.195 47.619 0.00 0.00 0.00 2.24
889 2794 3.731264 CGAAGCGTAGAGTGGAAGGTAAG 60.731 52.174 0.00 0.00 0.00 2.34
959 2865 4.331906 GCCTGGGCCCTTATAGGA 57.668 61.111 26.56 2.63 37.67 2.94
1503 3417 1.541310 TTCCATCGAACAGGGAGCGT 61.541 55.000 0.00 0.00 31.19 5.07
1507 3421 0.107214 GGCATTCCATCGAACAGGGA 60.107 55.000 0.00 0.00 0.00 4.20
1589 3503 2.835701 GAACACCTCGAGCGCATCCA 62.836 60.000 11.47 0.00 0.00 3.41
1732 3646 2.507854 CCGCATCCATCCTACCGGT 61.508 63.158 13.98 13.98 0.00 5.28
1782 3696 2.097825 GAGTCTAGGTTCCCGCACTTA 58.902 52.381 0.00 0.00 0.00 2.24
1793 3707 1.608717 CTGCCTTGCCGAGTCTAGGT 61.609 60.000 0.56 0.00 32.63 3.08
1881 3795 3.883744 CTGGCAGTGACCGTGGTCC 62.884 68.421 16.12 7.82 43.97 4.46
1908 3822 1.078918 CATCTGGCCGAACAGCTCA 60.079 57.895 0.00 0.00 38.36 4.26
1922 3836 2.693864 CCCCCTGGTCCTGCATCT 60.694 66.667 0.00 0.00 0.00 2.90
1965 3879 1.301244 ACAAGTGCAGAGGACGCAG 60.301 57.895 0.00 0.00 40.78 5.18
2018 3932 1.767681 ACATGCTCTGGAAGATCTCCC 59.232 52.381 0.00 0.00 45.62 4.30
2061 3975 2.586079 CCATAGTGCTCCACGCCG 60.586 66.667 0.00 0.00 39.64 6.46
2163 4077 1.226974 CAGCGCACCTAGCACGTAT 60.227 57.895 11.47 0.00 46.13 3.06
2247 4161 3.311110 TCGAGCCCAAGTTCCGCT 61.311 61.111 0.00 0.00 34.97 5.52
2253 4167 2.743718 CTGTGGTCGAGCCCAAGT 59.256 61.111 12.85 0.00 35.92 3.16
2567 4482 0.037326 TAAGAGGCAAGACACGGCTG 60.037 55.000 0.00 0.00 39.76 4.85
2568 4483 0.905357 ATAAGAGGCAAGACACGGCT 59.095 50.000 0.00 0.00 42.85 5.52
2571 4486 4.330074 CCAACTTATAAGAGGCAAGACACG 59.670 45.833 19.38 0.00 0.00 4.49
2572 4487 5.488341 TCCAACTTATAAGAGGCAAGACAC 58.512 41.667 19.38 0.00 0.00 3.67
2573 4488 5.755409 TCCAACTTATAAGAGGCAAGACA 57.245 39.130 19.38 1.45 0.00 3.41
2574 4489 5.938125 TGTTCCAACTTATAAGAGGCAAGAC 59.062 40.000 19.38 14.39 0.00 3.01
2576 4491 5.123979 GGTGTTCCAACTTATAAGAGGCAAG 59.876 44.000 19.38 2.17 0.00 4.01
2578 4493 4.042311 TGGTGTTCCAACTTATAAGAGGCA 59.958 41.667 19.38 8.02 41.25 4.75
2604 4524 3.063452 CCATGTGTATTTGTGGTACGAGC 59.937 47.826 0.00 0.00 0.00 5.03
2617 4543 5.465532 TGAACAATGTTTGCCATGTGTAT 57.534 34.783 0.00 0.00 32.82 2.29
2652 4579 2.548904 GTCATCTGAGCAATGGATCTGC 59.451 50.000 0.00 0.00 40.24 4.26
2686 4616 1.527370 GCCGGCAGGTAGGAGAAAT 59.473 57.895 24.80 0.00 40.50 2.17
2843 4774 5.544176 TCCATACATCTCTGTAAGGATTCCC 59.456 44.000 5.80 0.00 45.93 3.97
2876 4807 3.560068 ACCGTGGAGATAAATCGCATTTC 59.440 43.478 0.00 0.00 33.82 2.17
2882 4813 3.793559 AGGAAACCGTGGAGATAAATCG 58.206 45.455 0.00 0.00 0.00 3.34
2898 4829 6.549364 TCAACTTCTTAAATGCCTGAAGGAAA 59.451 34.615 0.00 0.00 39.90 3.13
2976 4907 9.744468 AAACAAACATATGAAAACCTGTTAGTC 57.256 29.630 10.38 0.00 31.88 2.59
2990 4921 7.228840 CGGAATTGCAGAAAAACAAACATATG 58.771 34.615 0.00 0.00 0.00 1.78
2991 4922 6.368516 CCGGAATTGCAGAAAAACAAACATAT 59.631 34.615 0.00 0.00 0.00 1.78
2992 4923 5.694006 CCGGAATTGCAGAAAAACAAACATA 59.306 36.000 0.00 0.00 0.00 2.29
3092 5024 9.587772 TCTATAATAAGTGCTGAAGAACTTGAC 57.412 33.333 13.12 0.00 43.51 3.18
3130 5062 9.301153 GTGCTTTCTCAATGTTTTCTTTTAGAA 57.699 29.630 0.00 0.00 30.63 2.10
3132 5064 8.862550 AGTGCTTTCTCAATGTTTTCTTTTAG 57.137 30.769 0.00 0.00 0.00 1.85
3138 5070 6.472163 TCGAAAAGTGCTTTCTCAATGTTTTC 59.528 34.615 0.00 0.00 41.23 2.29
3141 5073 5.066505 AGTCGAAAAGTGCTTTCTCAATGTT 59.933 36.000 0.00 0.00 41.23 2.71
3143 5075 5.100751 AGTCGAAAAGTGCTTTCTCAATG 57.899 39.130 0.00 0.00 41.23 2.82
3144 5076 5.757850 AAGTCGAAAAGTGCTTTCTCAAT 57.242 34.783 0.00 0.00 41.23 2.57
3145 5077 6.073222 GGATAAGTCGAAAAGTGCTTTCTCAA 60.073 38.462 0.00 0.00 41.23 3.02
3146 5078 5.408604 GGATAAGTCGAAAAGTGCTTTCTCA 59.591 40.000 0.00 0.00 41.23 3.27
3149 5081 5.864628 AGGATAAGTCGAAAAGTGCTTTC 57.135 39.130 0.00 0.00 40.17 2.62
3152 5084 4.894784 TGAAGGATAAGTCGAAAAGTGCT 58.105 39.130 0.00 0.00 0.00 4.40
3153 5085 4.691216 ACTGAAGGATAAGTCGAAAAGTGC 59.309 41.667 0.00 0.00 0.00 4.40
3162 5094 3.487209 GGTCGACGACTGAAGGATAAGTC 60.487 52.174 25.87 2.38 39.57 3.01
3177 5109 2.854777 CTGCAAGAAAGATAGGTCGACG 59.145 50.000 9.92 0.00 34.07 5.12
3181 5113 5.295540 GGATGAACTGCAAGAAAGATAGGTC 59.704 44.000 0.00 0.00 37.43 3.85
3192 5124 4.940046 ACATGAGTTAGGATGAACTGCAAG 59.060 41.667 0.00 0.00 39.79 4.01
3193 5125 4.910195 ACATGAGTTAGGATGAACTGCAA 58.090 39.130 0.00 0.00 39.79 4.08
3194 5126 4.558226 ACATGAGTTAGGATGAACTGCA 57.442 40.909 0.00 0.00 39.79 4.41
3232 5164 3.625764 TCTGAGGAAAACCAAAACTGACG 59.374 43.478 0.00 0.00 0.00 4.35
3242 5175 4.572795 GCTGCTAGTAATCTGAGGAAAACC 59.427 45.833 0.00 0.00 0.00 3.27
3270 5203 0.035317 GCACCACTGTGACATCTCCA 59.965 55.000 9.86 0.00 45.76 3.86
3312 5245 1.075374 TGCACTTAGGAAGCCACCATT 59.925 47.619 0.00 0.00 0.00 3.16
3314 5247 0.036732 CTGCACTTAGGAAGCCACCA 59.963 55.000 0.00 0.00 0.00 4.17
3321 5254 3.264193 ACACCATCATCTGCACTTAGGAA 59.736 43.478 0.00 0.00 0.00 3.36
3322 5255 2.840038 ACACCATCATCTGCACTTAGGA 59.160 45.455 0.00 0.00 0.00 2.94
3330 5263 1.400846 CTGCTCAACACCATCATCTGC 59.599 52.381 0.00 0.00 0.00 4.26
3409 5350 1.953559 TGTCTGTGAACAGCAAGGTC 58.046 50.000 5.55 0.00 43.46 3.85
3424 5365 1.037493 TGCTGTCGTAGTGGTTGTCT 58.963 50.000 0.00 0.00 0.00 3.41
3441 5382 1.903183 GGGAGATCTATGGGTAGGTGC 59.097 57.143 0.00 0.00 0.00 5.01
3444 5385 2.171840 CACGGGAGATCTATGGGTAGG 58.828 57.143 0.00 0.00 0.00 3.18
3450 5391 2.341452 TCCGCACGGGAGATCTATG 58.659 57.895 9.58 0.00 40.94 2.23
3465 5406 7.096065 GGAAGACAAAAATCTGTTCAATTTCCG 60.096 37.037 0.00 0.00 0.00 4.30
3466 5407 7.710475 TGGAAGACAAAAATCTGTTCAATTTCC 59.290 33.333 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.