Multiple sequence alignment - TraesCS6A01G288500

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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 TraesCS6A01G288500 chr6A 100.000 5850 0 0 1 5850 520710193 520716042 0.000000e+00 10804.0
1 TraesCS6A01G288500 chr6A 100.000 30 0 0 5323 5352 520715455 520715484 8.190000e-04 56.5
2 TraesCS6A01G288500 chr6A 100.000 30 0 0 5263 5292 520715515 520715544 8.190000e-04 56.5
3 TraesCS6A01G288500 chr6A 100.000 29 0 0 5056 5084 520715182 520715210 3.000000e-03 54.7
4 TraesCS6A01G288500 chr6A 100.000 29 0 0 4990 5018 520715248 520715276 3.000000e-03 54.7
5 TraesCS6A01G288500 chr6D 96.289 5039 133 27 1 4993 380149635 380144605 0.000000e+00 8220.0
6 TraesCS6A01G288500 chr6D 95.161 558 27 0 5293 5850 380143543 380142986 0.000000e+00 881.0
7 TraesCS6A01G288500 chr6D 91.244 217 9 6 5034 5243 380144604 380144391 2.670000e-73 287.0
8 TraesCS6A01G288500 chr6D 98.361 61 1 0 5262 5322 380143544 380143484 2.230000e-19 108.0
9 TraesCS6A01G288500 chr6D 100.000 30 0 0 5263 5292 380143513 380143484 8.190000e-04 56.5
10 TraesCS6A01G288500 chr6B 96.518 2585 79 4 1 2585 566142782 566145355 0.000000e+00 4265.0
11 TraesCS6A01G288500 chr6B 96.043 1971 70 6 3026 4991 566145909 566147876 0.000000e+00 3201.0
12 TraesCS6A01G288500 chr6B 91.803 610 36 7 5246 5850 566148356 566148956 0.000000e+00 837.0
13 TraesCS6A01G288500 chr6B 97.556 450 9 2 2582 3030 566145435 566145883 0.000000e+00 769.0
14 TraesCS6A01G288500 chr6B 100.000 42 0 0 5281 5322 566148412 566148453 1.750000e-10 78.7
15 TraesCS6A01G288500 chr6B 100.000 30 0 0 5263 5292 566148424 566148453 8.190000e-04 56.5


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 TraesCS6A01G288500 chr6A 520710193 520716042 5849 False 2205.280000 10804 100.000000 1 5850 5 chr6A.!!$F1 5849
1 TraesCS6A01G288500 chr6D 380142986 380149635 6649 True 1910.500000 8220 96.211000 1 5850 5 chr6D.!!$R1 5849
2 TraesCS6A01G288500 chr6B 566142782 566148956 6174 False 1534.533333 4265 96.986667 1 5850 6 chr6B.!!$F1 5849

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
924 933 1.244019 GGGTGCTGTTCTGGCGAAAT 61.244 55.0 0.00 0.0 0.00 2.17 F
1838 1848 0.609957 AGCACTTGGCAGCAATGCTA 60.610 50.0 7.70 0.0 44.59 3.49 F
2331 2341 1.261097 GCGCTCTCTTTGTCGACTAC 58.739 55.0 17.92 0.0 0.00 2.73 F
3829 3955 0.464554 GGCTGCTCATTACCCTGTCC 60.465 60.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2341 0.031857 CTCGAGCACCATAGCCTCAG 59.968 60.0 0.00 0.0 34.23 3.35 R
3235 3361 0.107312 CCATCTGCACCTCTTCTGGG 60.107 60.0 0.00 0.0 0.00 4.45 R
3892 4018 0.109597 CGTGGCTGATGCTTTTGACC 60.110 55.0 0.00 0.0 39.59 4.02 R
5330 6529 0.107459 CTTAACTGGGCCAGCTCTCC 60.107 60.0 33.04 0.0 34.37 3.71 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
75 76 2.537639 CGTCCCTCGGTTTAATTTGC 57.462 50.000 0.00 0.00 35.71 3.68
116 121 4.761739 TCTATCCCTTTGTTTCACAAGCTG 59.238 41.667 0.00 0.00 39.53 4.24
207 212 9.793259 AATTCTGAAGACATTAGTTCAAACCTA 57.207 29.630 0.00 0.00 32.36 3.08
494 503 5.706916 AGCTATCACTTTTGAATTGCTGTG 58.293 37.500 0.00 0.00 35.59 3.66
535 544 1.755959 TGCAACATCCAATGGCATACC 59.244 47.619 0.00 0.00 33.60 2.73
547 556 3.862877 TGGCATACCTCATAACAGCAT 57.137 42.857 0.00 0.00 36.63 3.79
573 582 1.689258 GGAGGGGCATGCTTACCAATT 60.689 52.381 18.92 2.34 0.00 2.32
757 766 4.993584 AGACTGTCACTCATTGATTGTGTC 59.006 41.667 10.88 10.04 36.32 3.67
836 845 7.335627 CAGTATTAAAAGGGGTCACATAGTGA 58.664 38.462 0.00 0.00 40.50 3.41
924 933 1.244019 GGGTGCTGTTCTGGCGAAAT 61.244 55.000 0.00 0.00 0.00 2.17
1054 1063 6.442952 TGTAATCTTCATTCGTTTGTTTGGG 58.557 36.000 0.00 0.00 0.00 4.12
1231 1240 8.466798 TGTCTTTTGTGATCGATATACTTCAGA 58.533 33.333 0.00 1.67 0.00 3.27
1290 1299 6.366332 AGTCAGTTAGAAAAATAGTCACGCTG 59.634 38.462 0.00 0.00 0.00 5.18
1308 1317 3.683281 CGCTGTAAGAGGACTAGAGGAGT 60.683 52.174 0.00 0.00 37.30 3.85
1309 1318 3.630312 GCTGTAAGAGGACTAGAGGAGTG 59.370 52.174 0.00 0.00 34.88 3.51
1360 1369 4.641094 AGGTCTACTCTGAGTAATCGTTGG 59.359 45.833 17.52 5.51 29.00 3.77
1500 1510 8.484575 AGCATGTAATTATCTCCCATATCTGAG 58.515 37.037 0.00 0.00 0.00 3.35
1838 1848 0.609957 AGCACTTGGCAGCAATGCTA 60.610 50.000 7.70 0.00 44.59 3.49
1918 1928 1.441738 TGAATGCAGTGACCGACATG 58.558 50.000 0.00 0.00 0.00 3.21
2083 2093 2.029020 TGGATTCTTCTGTCCACTGACG 60.029 50.000 0.00 0.00 44.86 4.35
2166 2176 5.070981 CCATAGAGGAGCATTTTGAGAGGTA 59.929 44.000 0.00 0.00 41.22 3.08
2170 2180 2.289002 GGAGCATTTTGAGAGGTATGCG 59.711 50.000 0.00 0.00 46.00 4.73
2331 2341 1.261097 GCGCTCTCTTTGTCGACTAC 58.739 55.000 17.92 0.00 0.00 2.73
2858 2951 9.281371 TGAAGATTAATGATTCTGATGATCCAC 57.719 33.333 0.00 0.00 0.00 4.02
3084 3208 9.626045 GAACCACCTAGATTTTCAAAAAGTATG 57.374 33.333 0.00 0.00 0.00 2.39
3235 3361 4.022068 TGACATGAAGATTCCAAAACAGGC 60.022 41.667 0.00 0.00 0.00 4.85
3348 3474 1.405933 CGTCCTCATCAAGATGGTGCA 60.406 52.381 9.96 0.00 39.24 4.57
3568 3694 1.340405 GGCATTGATCCAGACACCACT 60.340 52.381 0.00 0.00 0.00 4.00
3627 3753 7.133891 AGTATTGCATCTACAACTTTGTGTC 57.866 36.000 4.82 0.00 42.31 3.67
3685 3811 0.533755 GCATCATCCGCCTACTGCTT 60.534 55.000 0.00 0.00 38.05 3.91
3730 3856 2.419713 CCTGGATGTCATGGTCTCAGTG 60.420 54.545 0.00 0.00 0.00 3.66
3736 3862 1.895798 GTCATGGTCTCAGTGGTCAGA 59.104 52.381 0.00 0.00 0.00 3.27
3823 3949 0.872021 CGACGAGGCTGCTCATTACC 60.872 60.000 0.00 0.00 0.00 2.85
3829 3955 0.464554 GGCTGCTCATTACCCTGTCC 60.465 60.000 0.00 0.00 0.00 4.02
3967 4093 1.439644 GCTCCTCTCAAGGCTACCG 59.560 63.158 0.00 0.00 43.02 4.02
4158 4284 1.014564 CCGACCGTTCTGAAGGAAGC 61.015 60.000 11.39 0.46 34.23 3.86
4199 4325 0.681733 GGTGCTGACTGAACTCCTCA 59.318 55.000 0.00 0.00 0.00 3.86
4414 4540 3.626924 GTGCACCGGGGAGTCTGT 61.627 66.667 8.67 0.00 0.00 3.41
4567 4693 2.336478 CGTGGAGAGGAGCGTGTCT 61.336 63.158 0.00 0.00 0.00 3.41
4579 4705 4.329545 GTGTCTGCCCTCGCCCAA 62.330 66.667 0.00 0.00 0.00 4.12
4666 4792 0.961019 GCTTCTGCATGGTGGACAAA 59.039 50.000 0.00 0.00 39.41 2.83
4853 4979 7.340743 CCTATATGTCCGTGGAGATTTAGAGAT 59.659 40.741 18.71 4.33 34.11 2.75
4867 4993 8.239038 AGATTTAGAGATTCCTTGTCATACGA 57.761 34.615 0.00 0.00 0.00 3.43
4874 5000 3.728076 TCCTTGTCATACGATACTGCC 57.272 47.619 0.00 0.00 0.00 4.85
4882 5008 1.977056 TACGATACTGCCGGTGATCT 58.023 50.000 1.90 0.00 0.00 2.75
4900 5026 6.914757 GGTGATCTATTAAAACAGAAGCATGC 59.085 38.462 10.51 10.51 0.00 4.06
4910 5037 4.256920 AACAGAAGCATGCTGGTACTTAG 58.743 43.478 23.48 9.88 42.84 2.18
4919 5046 5.437060 CATGCTGGTACTTAGGGTGTTTAT 58.563 41.667 0.00 0.00 0.00 1.40
4923 5050 5.708697 GCTGGTACTTAGGGTGTTTATTTGT 59.291 40.000 0.00 0.00 0.00 2.83
4925 5052 7.255695 GCTGGTACTTAGGGTGTTTATTTGTTT 60.256 37.037 0.00 0.00 0.00 2.83
4936 5065 7.254624 GGGTGTTTATTTGTTTGTCATTTCCAC 60.255 37.037 0.00 0.00 0.00 4.02
4939 5068 7.989741 TGTTTATTTGTTTGTCATTTCCACCAT 59.010 29.630 0.00 0.00 0.00 3.55
4954 5083 5.199024 TCCACCATTGTGAATTTGTGAAG 57.801 39.130 0.00 0.00 45.76 3.02
4971 5102 7.843490 TTGTGAAGCTGGTTCTTGTATATAC 57.157 36.000 19.08 5.89 35.99 1.47
4993 5124 2.095567 GCACATGTGAATCAAACGAGCT 60.096 45.455 29.80 0.00 0.00 4.09
4994 5125 3.485633 CACATGTGAATCAAACGAGCTG 58.514 45.455 21.64 0.00 0.00 4.24
4995 5126 2.095567 ACATGTGAATCAAACGAGCTGC 60.096 45.455 0.00 0.00 0.00 5.25
4997 5128 1.800586 TGTGAATCAAACGAGCTGCTC 59.199 47.619 19.53 19.53 0.00 4.26
4998 5129 1.800586 GTGAATCAAACGAGCTGCTCA 59.199 47.619 27.46 9.64 0.00 4.26
4999 5130 1.800586 TGAATCAAACGAGCTGCTCAC 59.199 47.619 27.46 4.35 0.00 3.51
5000 5131 2.072298 GAATCAAACGAGCTGCTCACT 58.928 47.619 27.46 12.08 0.00 3.41
5001 5132 3.254060 GAATCAAACGAGCTGCTCACTA 58.746 45.455 27.46 9.59 0.00 2.74
5002 5133 2.065993 TCAAACGAGCTGCTCACTAC 57.934 50.000 27.46 2.83 0.00 2.73
5003 5134 1.071605 CAAACGAGCTGCTCACTACC 58.928 55.000 27.46 2.08 0.00 3.18
5004 5135 0.679505 AAACGAGCTGCTCACTACCA 59.320 50.000 27.46 0.00 0.00 3.25
5005 5136 0.898320 AACGAGCTGCTCACTACCAT 59.102 50.000 27.46 4.08 0.00 3.55
5006 5137 0.174389 ACGAGCTGCTCACTACCATG 59.826 55.000 27.46 12.08 0.00 3.66
5007 5138 1.150567 CGAGCTGCTCACTACCATGC 61.151 60.000 27.46 0.00 0.00 4.06
5008 5139 0.813210 GAGCTGCTCACTACCATGCC 60.813 60.000 24.02 0.00 0.00 4.40
5009 5140 1.078214 GCTGCTCACTACCATGCCA 60.078 57.895 0.00 0.00 0.00 4.92
5010 5141 0.465097 GCTGCTCACTACCATGCCAT 60.465 55.000 0.00 0.00 0.00 4.40
5011 5142 1.590932 CTGCTCACTACCATGCCATC 58.409 55.000 0.00 0.00 0.00 3.51
5012 5143 1.140452 CTGCTCACTACCATGCCATCT 59.860 52.381 0.00 0.00 0.00 2.90
5013 5144 1.561076 TGCTCACTACCATGCCATCTT 59.439 47.619 0.00 0.00 0.00 2.40
5014 5145 1.945394 GCTCACTACCATGCCATCTTG 59.055 52.381 0.00 0.00 0.00 3.02
5015 5146 2.681976 GCTCACTACCATGCCATCTTGT 60.682 50.000 0.00 0.00 0.00 3.16
5016 5147 2.941064 CTCACTACCATGCCATCTTGTG 59.059 50.000 0.00 0.00 0.00 3.33
5017 5148 2.305635 TCACTACCATGCCATCTTGTGT 59.694 45.455 0.00 0.00 0.00 3.72
5018 5149 3.517500 TCACTACCATGCCATCTTGTGTA 59.482 43.478 0.00 0.00 0.00 2.90
5019 5150 4.164030 TCACTACCATGCCATCTTGTGTAT 59.836 41.667 0.00 0.00 0.00 2.29
5020 5151 4.274214 CACTACCATGCCATCTTGTGTATG 59.726 45.833 0.00 0.00 0.00 2.39
5021 5152 2.026641 ACCATGCCATCTTGTGTATGC 58.973 47.619 0.00 0.00 0.00 3.14
5022 5153 2.025898 CCATGCCATCTTGTGTATGCA 58.974 47.619 0.00 0.00 0.00 3.96
5023 5154 2.626266 CCATGCCATCTTGTGTATGCAT 59.374 45.455 3.79 3.79 0.00 3.96
5024 5155 3.552068 CCATGCCATCTTGTGTATGCATG 60.552 47.826 10.16 13.70 37.91 4.06
5025 5156 1.406180 TGCCATCTTGTGTATGCATGC 59.594 47.619 11.82 11.82 0.00 4.06
5026 5157 1.406180 GCCATCTTGTGTATGCATGCA 59.594 47.619 25.04 25.04 0.00 3.96
5027 5158 2.797087 GCCATCTTGTGTATGCATGCAC 60.797 50.000 33.15 33.15 42.66 4.57
5133 5472 9.512588 AAGCAGAATCCATTCTAATTACTATGG 57.487 33.333 12.14 12.14 44.84 2.74
5301 6500 1.560923 CAGTTAAGTCGAGCGGATGG 58.439 55.000 0.00 0.00 0.00 3.51
5302 6501 1.134367 CAGTTAAGTCGAGCGGATGGA 59.866 52.381 0.00 0.00 0.00 3.41
5303 6502 1.405821 AGTTAAGTCGAGCGGATGGAG 59.594 52.381 0.00 0.00 0.00 3.86
5304 6503 1.404391 GTTAAGTCGAGCGGATGGAGA 59.596 52.381 0.00 0.00 0.00 3.71
5305 6504 1.309950 TAAGTCGAGCGGATGGAGAG 58.690 55.000 0.00 0.00 0.00 3.20
5306 6505 2.010582 AAGTCGAGCGGATGGAGAGC 62.011 60.000 0.00 0.00 0.00 4.09
5307 6506 2.124109 TCGAGCGGATGGAGAGCT 60.124 61.111 0.00 0.00 44.80 4.09
5308 6507 2.027314 CGAGCGGATGGAGAGCTG 59.973 66.667 0.00 0.00 41.84 4.24
5309 6508 2.420890 GAGCGGATGGAGAGCTGG 59.579 66.667 0.00 0.00 41.84 4.85
5310 6509 3.805891 GAGCGGATGGAGAGCTGGC 62.806 68.421 0.00 0.00 41.84 4.85
5311 6510 4.925861 GCGGATGGAGAGCTGGCC 62.926 72.222 0.00 0.00 0.00 5.36
5312 6511 4.247380 CGGATGGAGAGCTGGCCC 62.247 72.222 0.00 0.00 0.00 5.80
5313 6512 3.092511 GGATGGAGAGCTGGCCCA 61.093 66.667 0.00 0.00 0.00 5.36
5314 6513 2.509916 GATGGAGAGCTGGCCCAG 59.490 66.667 6.32 6.32 32.90 4.45
5315 6514 2.285969 ATGGAGAGCTGGCCCAGT 60.286 61.111 13.35 0.00 33.43 4.00
5316 6515 1.919600 GATGGAGAGCTGGCCCAGTT 61.920 60.000 13.35 6.11 33.43 3.16
5317 6516 0.621571 ATGGAGAGCTGGCCCAGTTA 60.622 55.000 13.35 0.00 33.43 2.24
5318 6517 0.840288 TGGAGAGCTGGCCCAGTTAA 60.840 55.000 13.35 0.00 33.43 2.01
5319 6518 0.107459 GGAGAGCTGGCCCAGTTAAG 60.107 60.000 13.35 0.00 33.43 1.85
5320 6519 0.615850 GAGAGCTGGCCCAGTTAAGT 59.384 55.000 13.35 0.00 33.43 2.24
5321 6520 0.615850 AGAGCTGGCCCAGTTAAGTC 59.384 55.000 13.35 2.16 33.43 3.01
5322 6521 0.741221 GAGCTGGCCCAGTTAAGTCG 60.741 60.000 13.35 0.00 33.43 4.18
5323 6522 1.192146 AGCTGGCCCAGTTAAGTCGA 61.192 55.000 13.35 0.00 33.43 4.20
5324 6523 0.741221 GCTGGCCCAGTTAAGTCGAG 60.741 60.000 13.35 0.00 33.43 4.04
5325 6524 0.741221 CTGGCCCAGTTAAGTCGAGC 60.741 60.000 1.39 0.00 0.00 5.03
5326 6525 1.810030 GGCCCAGTTAAGTCGAGCG 60.810 63.158 0.00 0.00 0.00 5.03
5327 6526 1.810030 GCCCAGTTAAGTCGAGCGG 60.810 63.158 0.00 0.00 0.00 5.52
5328 6527 1.888018 CCCAGTTAAGTCGAGCGGA 59.112 57.895 0.00 0.00 0.00 5.54
5329 6528 0.460311 CCCAGTTAAGTCGAGCGGAT 59.540 55.000 0.00 0.00 0.00 4.18
5330 6529 1.560923 CCAGTTAAGTCGAGCGGATG 58.439 55.000 0.00 0.00 0.00 3.51
5364 6563 4.689345 CCAGTTAAGTCCAAAGTCGTAAGG 59.311 45.833 0.00 0.00 38.47 2.69
5410 6609 2.003548 GTTCCCTCCCCATCCTGCT 61.004 63.158 0.00 0.00 0.00 4.24
5491 6690 1.956620 GCGACAGCTTAGCGGAACAC 61.957 60.000 11.87 0.00 41.01 3.32
5543 6745 1.778591 GTTTGTTCATCGCGTTTGGTG 59.221 47.619 5.77 0.00 0.00 4.17
5670 6872 0.603569 GCTCTGTTGAGGTTCGGAGA 59.396 55.000 5.36 0.00 40.53 3.71
5696 6898 3.724732 AAACTGCGGGAAAAGGGTATA 57.275 42.857 0.00 0.00 0.00 1.47
5767 6969 2.472909 GGCAGCGATTTTCCTCGGG 61.473 63.158 0.00 0.00 39.05 5.14
5772 6974 1.417890 AGCGATTTTCCTCGGGATCAT 59.582 47.619 0.00 0.00 39.05 2.45
5796 6998 3.576078 TTCTGTCCACATTCACCTTGT 57.424 42.857 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 6.306987 AGATTATTCCATAGTCCCGCAAATT 58.693 36.000 0.00 0.00 0.00 1.82
75 76 6.041069 GGGATAGAGATTATTCCATAGTCCCG 59.959 46.154 0.00 0.00 31.99 5.14
116 121 5.626955 GCACAAGCTACTTCTCACAAATTTC 59.373 40.000 0.00 0.00 37.91 2.17
494 503 4.437239 CAGTGGAATGTCATACTCAGGTC 58.563 47.826 0.00 0.00 0.00 3.85
535 544 4.818546 CCCTCCAAAGTATGCTGTTATGAG 59.181 45.833 0.00 0.00 0.00 2.90
547 556 0.704076 AAGCATGCCCCTCCAAAGTA 59.296 50.000 15.66 0.00 0.00 2.24
573 582 5.690865 AGCGTAGATTAATGGGAAATTGGA 58.309 37.500 0.00 0.00 0.00 3.53
757 766 7.446319 TGATGATGCTATCCACATAAAAGAAGG 59.554 37.037 0.00 0.00 0.00 3.46
1054 1063 3.809905 AGCCTCCAAACGAATAATCTCC 58.190 45.455 0.00 0.00 0.00 3.71
1290 1299 2.953648 GGCACTCCTCTAGTCCTCTTAC 59.046 54.545 0.00 0.00 35.76 2.34
1330 1339 9.053840 CGATTACTCAGAGTAGACCTGTATTTA 57.946 37.037 10.27 0.00 31.47 1.40
1360 1369 5.697178 GCATAAGTAGAAGGCTTAAGCTACC 59.303 44.000 25.88 14.69 38.97 3.18
1479 1489 6.975772 GTCGCTCAGATATGGGAGATAATTAC 59.024 42.308 0.00 0.00 32.87 1.89
1500 1510 3.001127 ACAACAACAATGCAAATTGTCGC 59.999 39.130 12.38 0.00 43.29 5.19
1711 1721 0.108615 GTTGCAGCGCTCTTCCTCTA 60.109 55.000 7.13 0.00 0.00 2.43
1830 1840 1.135972 CCACGTCAGTGTTAGCATTGC 60.136 52.381 0.00 0.00 46.56 3.56
1838 1848 1.603802 CTTCATTGCCACGTCAGTGTT 59.396 47.619 0.00 0.00 46.56 3.32
1918 1928 1.501582 AGACAGACCTCCTATTGGGC 58.498 55.000 0.00 0.00 34.39 5.36
2083 2093 4.081198 ACAGGATCAGTCATCACCTCTTTC 60.081 45.833 0.00 0.00 32.33 2.62
2166 2176 0.110486 AGGTTCCAAACTGTCCGCAT 59.890 50.000 0.00 0.00 0.00 4.73
2331 2341 0.031857 CTCGAGCACCATAGCCTCAG 59.968 60.000 0.00 0.00 34.23 3.35
2573 2583 8.418662 AGCCGATCAGTTATTTACTTGTGTATA 58.581 33.333 0.00 0.00 33.85 1.47
2585 2595 2.292267 CCAAGCAGCCGATCAGTTATT 58.708 47.619 0.00 0.00 0.00 1.40
2586 2596 1.959042 CCAAGCAGCCGATCAGTTAT 58.041 50.000 0.00 0.00 0.00 1.89
2613 2706 6.822667 TTCCATTATAATATGCAGCACAGG 57.177 37.500 0.00 0.00 0.00 4.00
2644 2737 6.361481 CGATTTCCTGTAATATGCAGCAATTG 59.639 38.462 0.00 0.00 32.93 2.32
2743 2836 3.502191 AGCTCTAGCAAGAAAGAGACG 57.498 47.619 4.54 0.00 41.51 4.18
2858 2951 2.678836 CTCCAGATTTCTCAGCAGCAAG 59.321 50.000 0.00 0.00 0.00 4.01
3024 3118 5.978919 CAGACTTGCAAGAAAACAATAGCAA 59.021 36.000 32.50 0.00 39.38 3.91
3084 3208 8.336801 ACAACTATTAAATGACAAGAGGGTTC 57.663 34.615 0.00 0.00 0.00 3.62
3235 3361 0.107312 CCATCTGCACCTCTTCTGGG 60.107 60.000 0.00 0.00 0.00 4.45
3348 3474 1.373590 GACCACCGTGTTGCAACTGT 61.374 55.000 28.61 19.68 0.00 3.55
3568 3694 0.467290 GGCCTTCCTTGTTCACCACA 60.467 55.000 0.00 0.00 0.00 4.17
3616 3742 3.067180 ACTTGAGCATGGACACAAAGTTG 59.933 43.478 0.00 0.00 0.00 3.16
3627 3753 2.357009 GGTATGAAGCACTTGAGCATGG 59.643 50.000 0.00 0.00 36.85 3.66
3730 3856 1.079750 GCGGTGGTTCTCTCTGACC 60.080 63.158 0.00 0.00 0.00 4.02
3823 3949 3.803082 CCAATGTGCGCGGACAGG 61.803 66.667 35.57 28.21 0.00 4.00
3892 4018 0.109597 CGTGGCTGATGCTTTTGACC 60.110 55.000 0.00 0.00 39.59 4.02
3949 4075 1.439644 CGGTAGCCTTGAGAGGAGC 59.560 63.158 0.00 0.00 46.74 4.70
4016 4142 4.069232 CCCGCTCAGCAGAACCGA 62.069 66.667 0.00 0.00 0.00 4.69
4158 4284 3.895025 CCAAGCTGTGGTCCATCG 58.105 61.111 0.00 0.00 43.20 3.84
4357 4483 1.228124 TTGGAGGGTCTTGTTGCCG 60.228 57.895 0.00 0.00 0.00 5.69
4735 4861 0.109342 CCTTGTGGAAGGCACTCACT 59.891 55.000 0.00 0.00 42.60 3.41
4741 4867 3.565214 TCGCCCTTGTGGAAGGCA 61.565 61.111 0.70 0.00 46.89 4.75
4853 4979 3.490249 CGGCAGTATCGTATGACAAGGAA 60.490 47.826 0.00 0.00 0.00 3.36
4867 4993 6.588204 TGTTTTAATAGATCACCGGCAGTAT 58.412 36.000 0.00 0.00 0.00 2.12
4874 5000 6.662414 TGCTTCTGTTTTAATAGATCACCG 57.338 37.500 0.00 0.00 0.00 4.94
4882 5008 6.884295 AGTACCAGCATGCTTCTGTTTTAATA 59.116 34.615 19.98 0.00 31.97 0.98
4900 5026 7.754851 AACAAATAAACACCCTAAGTACCAG 57.245 36.000 0.00 0.00 0.00 4.00
4903 5029 8.623030 TGACAAACAAATAAACACCCTAAGTAC 58.377 33.333 0.00 0.00 0.00 2.73
4910 5037 6.763610 TGGAAATGACAAACAAATAAACACCC 59.236 34.615 0.00 0.00 0.00 4.61
4919 5046 5.583854 CACAATGGTGGAAATGACAAACAAA 59.416 36.000 0.00 0.00 41.45 2.83
4923 5050 5.604758 TTCACAATGGTGGAAATGACAAA 57.395 34.783 0.00 0.00 45.32 2.83
4925 5052 5.804944 AATTCACAATGGTGGAAATGACA 57.195 34.783 0.00 0.00 45.32 3.58
4936 5065 3.991773 CCAGCTTCACAAATTCACAATGG 59.008 43.478 0.00 0.00 0.00 3.16
4939 5068 4.402155 AGAACCAGCTTCACAAATTCACAA 59.598 37.500 0.00 0.00 0.00 3.33
4954 5083 4.116961 TGTGCGTATATACAAGAACCAGC 58.883 43.478 13.22 6.03 0.00 4.85
4971 5102 2.498905 CTCGTTTGATTCACATGTGCG 58.501 47.619 21.38 15.96 0.00 5.34
4993 5124 1.206878 AGATGGCATGGTAGTGAGCA 58.793 50.000 3.81 0.00 37.51 4.26
4994 5125 1.945394 CAAGATGGCATGGTAGTGAGC 59.055 52.381 3.81 0.00 0.00 4.26
4995 5126 2.941064 CACAAGATGGCATGGTAGTGAG 59.059 50.000 3.81 0.00 0.00 3.51
4997 5128 2.715046 ACACAAGATGGCATGGTAGTG 58.285 47.619 3.81 10.73 0.00 2.74
4998 5129 4.454678 CATACACAAGATGGCATGGTAGT 58.545 43.478 3.81 0.00 0.00 2.73
4999 5130 3.251729 GCATACACAAGATGGCATGGTAG 59.748 47.826 3.81 0.00 0.00 3.18
5000 5131 3.213506 GCATACACAAGATGGCATGGTA 58.786 45.455 3.81 0.00 0.00 3.25
5001 5132 2.026641 GCATACACAAGATGGCATGGT 58.973 47.619 3.81 0.00 0.00 3.55
5002 5133 2.025898 TGCATACACAAGATGGCATGG 58.974 47.619 3.81 0.00 0.00 3.66
5003 5134 3.638484 CATGCATACACAAGATGGCATG 58.362 45.455 3.81 9.62 35.03 4.06
5004 5135 2.035449 GCATGCATACACAAGATGGCAT 59.965 45.455 14.21 0.00 0.00 4.40
5005 5136 1.406180 GCATGCATACACAAGATGGCA 59.594 47.619 14.21 0.00 0.00 4.92
5006 5137 1.406180 TGCATGCATACACAAGATGGC 59.594 47.619 18.46 0.00 0.00 4.40
5007 5138 2.424246 TGTGCATGCATACACAAGATGG 59.576 45.455 26.80 0.00 43.48 3.51
5008 5139 3.768468 TGTGCATGCATACACAAGATG 57.232 42.857 26.80 1.97 43.48 2.90
5014 5145 3.119743 ACTCACAATGTGCATGCATACAC 60.120 43.478 25.64 21.07 37.31 2.90
5015 5146 3.083293 ACTCACAATGTGCATGCATACA 58.917 40.909 25.64 18.55 32.98 2.29
5016 5147 3.770263 ACTCACAATGTGCATGCATAC 57.230 42.857 25.64 12.77 32.98 2.39
5017 5148 4.787260 AAACTCACAATGTGCATGCATA 57.213 36.364 25.64 22.69 32.98 3.14
5018 5149 3.671008 AAACTCACAATGTGCATGCAT 57.329 38.095 25.64 5.67 32.98 3.96
5019 5150 3.455990 AAAACTCACAATGTGCATGCA 57.544 38.095 18.46 18.46 32.98 3.96
5127 5466 6.601217 GGAGAAAAGAGCTCATTTTCCATAGT 59.399 38.462 28.55 18.94 44.21 2.12
5133 5472 6.324561 ACAAGGAGAAAAGAGCTCATTTTC 57.675 37.500 26.83 26.83 43.72 2.29
5240 5589 8.898761 CGCTCTTATACCTGTGATATATTCTCT 58.101 37.037 0.00 0.00 0.00 3.10
5241 5590 8.132362 CCGCTCTTATACCTGTGATATATTCTC 58.868 40.741 0.00 0.00 0.00 2.87
5242 5591 7.834681 TCCGCTCTTATACCTGTGATATATTCT 59.165 37.037 0.00 0.00 0.00 2.40
5243 5592 7.997482 TCCGCTCTTATACCTGTGATATATTC 58.003 38.462 0.00 0.00 0.00 1.75
5301 6500 0.615850 ACTTAACTGGGCCAGCTCTC 59.384 55.000 33.04 0.00 34.37 3.20
5302 6501 0.615850 GACTTAACTGGGCCAGCTCT 59.384 55.000 33.04 19.66 34.37 4.09
5303 6502 0.741221 CGACTTAACTGGGCCAGCTC 60.741 60.000 33.04 17.40 34.37 4.09
5304 6503 1.192146 TCGACTTAACTGGGCCAGCT 61.192 55.000 33.04 24.11 34.37 4.24
5305 6504 0.741221 CTCGACTTAACTGGGCCAGC 60.741 60.000 33.04 14.63 34.37 4.85
5306 6505 0.741221 GCTCGACTTAACTGGGCCAG 60.741 60.000 31.62 31.62 37.52 4.85
5307 6506 1.295423 GCTCGACTTAACTGGGCCA 59.705 57.895 5.85 5.85 0.00 5.36
5308 6507 1.810030 CGCTCGACTTAACTGGGCC 60.810 63.158 0.00 0.00 0.00 5.80
5309 6508 1.810030 CCGCTCGACTTAACTGGGC 60.810 63.158 0.00 0.00 0.00 5.36
5310 6509 0.460311 ATCCGCTCGACTTAACTGGG 59.540 55.000 0.00 0.00 0.00 4.45
5311 6510 1.560923 CATCCGCTCGACTTAACTGG 58.439 55.000 0.00 0.00 0.00 4.00
5312 6511 1.134367 TCCATCCGCTCGACTTAACTG 59.866 52.381 0.00 0.00 0.00 3.16
5313 6512 1.405821 CTCCATCCGCTCGACTTAACT 59.594 52.381 0.00 0.00 0.00 2.24
5314 6513 1.404391 TCTCCATCCGCTCGACTTAAC 59.596 52.381 0.00 0.00 0.00 2.01
5315 6514 1.676529 CTCTCCATCCGCTCGACTTAA 59.323 52.381 0.00 0.00 0.00 1.85
5316 6515 1.309950 CTCTCCATCCGCTCGACTTA 58.690 55.000 0.00 0.00 0.00 2.24
5317 6516 2.010582 GCTCTCCATCCGCTCGACTT 62.011 60.000 0.00 0.00 0.00 3.01
5318 6517 2.485795 GCTCTCCATCCGCTCGACT 61.486 63.158 0.00 0.00 0.00 4.18
5319 6518 2.026879 GCTCTCCATCCGCTCGAC 59.973 66.667 0.00 0.00 0.00 4.20
5320 6519 2.124109 AGCTCTCCATCCGCTCGA 60.124 61.111 0.00 0.00 0.00 4.04
5321 6520 2.027314 CAGCTCTCCATCCGCTCG 59.973 66.667 0.00 0.00 0.00 5.03
5322 6521 2.420890 CCAGCTCTCCATCCGCTC 59.579 66.667 0.00 0.00 0.00 5.03
5323 6522 3.859414 GCCAGCTCTCCATCCGCT 61.859 66.667 0.00 0.00 0.00 5.52
5324 6523 4.925861 GGCCAGCTCTCCATCCGC 62.926 72.222 0.00 0.00 0.00 5.54
5325 6524 4.247380 GGGCCAGCTCTCCATCCG 62.247 72.222 4.39 0.00 0.00 4.18
5326 6525 3.092511 TGGGCCAGCTCTCCATCC 61.093 66.667 0.00 0.00 0.00 3.51
5327 6526 1.919600 AACTGGGCCAGCTCTCCATC 61.920 60.000 33.04 0.00 34.37 3.51
5328 6527 0.621571 TAACTGGGCCAGCTCTCCAT 60.622 55.000 33.04 9.26 34.37 3.41
5329 6528 0.840288 TTAACTGGGCCAGCTCTCCA 60.840 55.000 33.04 8.83 34.37 3.86
5330 6529 0.107459 CTTAACTGGGCCAGCTCTCC 60.107 60.000 33.04 0.00 34.37 3.71
5364 6563 3.507622 GTCCAAGATATAAATGGGCTGGC 59.492 47.826 0.00 0.00 35.93 4.85
5410 6609 1.408969 TGCCTCTGCGGTACATATCA 58.591 50.000 0.00 0.00 41.78 2.15
5491 6690 3.533547 CAAAAGCTGGAGATCTGAGAGG 58.466 50.000 0.00 0.00 0.00 3.69
5653 6855 1.618837 CCTTCTCCGAACCTCAACAGA 59.381 52.381 0.00 0.00 0.00 3.41
5670 6872 1.686587 CTTTTCCCGCAGTTTTCCCTT 59.313 47.619 0.00 0.00 0.00 3.95
5696 6898 3.893200 CTGGATTGATGTTGCACCCATAT 59.107 43.478 0.00 0.00 0.00 1.78
5750 6952 0.815615 ATCCCGAGGAAAATCGCTGC 60.816 55.000 0.00 0.00 41.37 5.25
5796 6998 9.715121 ACTAAACGAATCCAAACTATAGAACAA 57.285 29.630 6.78 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.