Multiple sequence alignment - TraesCS3B01G208600

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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 TraesCS3B01G208600 chr3B 100.000 4853 0 0 1 4853 244657626 244662478 0.000000e+00 8962
1 TraesCS3B01G208600 chr3D 93.578 3270 142 39 888 4108 169789039 169792289 0.000000e+00 4813
2 TraesCS3B01G208600 chr3D 88.032 869 86 10 1 855 16264836 16265700 0.000000e+00 1013
3 TraesCS3B01G208600 chr3D 96.757 185 6 0 4669 4853 169792289 169792473 4.720000e-80 309
4 TraesCS3B01G208600 chr3D 73.579 651 118 31 4243 4851 144250651 144250013 2.960000e-47 200
5 TraesCS3B01G208600 chr3A 94.809 3063 97 29 888 3901 197433102 197436151 0.000000e+00 4719
6 TraesCS3B01G208600 chr3A 94.043 940 32 7 3909 4839 197436361 197437285 0.000000e+00 1404
7 TraesCS3B01G208600 chr3A 75.372 471 86 22 4243 4691 163910589 163910127 2.960000e-47 200
8 TraesCS3B01G208600 chr7B 93.515 879 42 8 3849 4722 568391161 568390293 0.000000e+00 1293
9 TraesCS3B01G208600 chr7B 88.404 802 79 10 1 798 6084391 6083600 0.000000e+00 953
10 TraesCS3B01G208600 chr6D 89.064 887 87 9 1 879 86597237 86598121 0.000000e+00 1092
11 TraesCS3B01G208600 chr1D 88.345 858 86 10 4 853 287469524 287468673 0.000000e+00 1018
12 TraesCS3B01G208600 chr5D 89.106 817 77 9 1 814 480843294 480842487 0.000000e+00 1005
13 TraesCS3B01G208600 chr5D 86.987 853 97 10 1 851 226454349 226453509 0.000000e+00 948
14 TraesCS3B01G208600 chr1B 87.925 853 89 8 1 850 619213040 619213881 0.000000e+00 992
15 TraesCS3B01G208600 chr6B 87.500 824 87 9 3 816 182378615 182377798 0.000000e+00 937
16 TraesCS3B01G208600 chr7D 86.030 859 107 8 1 853 592476367 592475516 0.000000e+00 909
17 TraesCS3B01G208600 chr2B 84.706 170 20 5 688 853 653616892 653617059 1.080000e-36 165


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 TraesCS3B01G208600 chr3B 244657626 244662478 4852 False 8962.0 8962 100.0000 1 4853 1 chr3B.!!$F1 4852
1 TraesCS3B01G208600 chr3D 169789039 169792473 3434 False 2561.0 4813 95.1675 888 4853 2 chr3D.!!$F2 3965
2 TraesCS3B01G208600 chr3D 16264836 16265700 864 False 1013.0 1013 88.0320 1 855 1 chr3D.!!$F1 854
3 TraesCS3B01G208600 chr3A 197433102 197437285 4183 False 3061.5 4719 94.4260 888 4839 2 chr3A.!!$F1 3951
4 TraesCS3B01G208600 chr7B 568390293 568391161 868 True 1293.0 1293 93.5150 3849 4722 1 chr7B.!!$R2 873
5 TraesCS3B01G208600 chr7B 6083600 6084391 791 True 953.0 953 88.4040 1 798 1 chr7B.!!$R1 797
6 TraesCS3B01G208600 chr6D 86597237 86598121 884 False 1092.0 1092 89.0640 1 879 1 chr6D.!!$F1 878
7 TraesCS3B01G208600 chr1D 287468673 287469524 851 True 1018.0 1018 88.3450 4 853 1 chr1D.!!$R1 849
8 TraesCS3B01G208600 chr5D 480842487 480843294 807 True 1005.0 1005 89.1060 1 814 1 chr5D.!!$R2 813
9 TraesCS3B01G208600 chr5D 226453509 226454349 840 True 948.0 948 86.9870 1 851 1 chr5D.!!$R1 850
10 TraesCS3B01G208600 chr1B 619213040 619213881 841 False 992.0 992 87.9250 1 850 1 chr1B.!!$F1 849
11 TraesCS3B01G208600 chr6B 182377798 182378615 817 True 937.0 937 87.5000 3 816 1 chr6B.!!$R1 813
12 TraesCS3B01G208600 chr7D 592475516 592476367 851 True 909.0 909 86.0300 1 853 1 chr7D.!!$R1 852

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
32 33 0.036858 GCCGAGAAAGAGAGTTGGCT 60.037 55.000 0.00 0.0 38.00 4.75 F
1183 1227 0.100861 CTCCGTTCTACCGCTTCTCC 59.899 60.000 0.00 0.0 0.00 3.71 F
1232 1276 0.892358 AGACCACTCCGTCGCTGTAA 60.892 55.000 0.00 0.0 37.85 2.41 F
2739 2818 1.813178 CGAGCTGGATCTATCGGCTTA 59.187 52.381 5.41 0.0 36.93 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1510 1.172812 ACGGTGCTTGAAAGAAGGGC 61.173 55.000 0.0 0.0 0.0 5.19 R
2687 2766 0.110486 AACCATCCTTGTTCAGCGGT 59.890 50.000 0.0 0.0 0.0 5.68 R
3135 3216 1.618837 TCCCTCAACTTCTGTCTTCGG 59.381 52.381 0.0 0.0 0.0 4.30 R
4084 4394 1.479323 TGTACTCCAACATACTCCGGC 59.521 52.381 0.0 0.0 0.0 6.13 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
32 33 0.036858 GCCGAGAAAGAGAGTTGGCT 60.037 55.000 0.00 0.00 38.00 4.75
51 52 0.986527 TGCAGCAATCCCTTCTCAGA 59.013 50.000 0.00 0.00 0.00 3.27
99 100 3.030291 TCCCTCCATAATGCGCAAAAAT 58.970 40.909 17.11 5.29 0.00 1.82
105 106 6.869913 CCTCCATAATGCGCAAAAATAATGAT 59.130 34.615 17.11 0.00 0.00 2.45
141 143 0.462047 GGCGACGAAACCATGGATCT 60.462 55.000 21.47 1.05 0.00 2.75
182 184 3.253188 GGAGCAAAGTAGTCATTGTGCAA 59.747 43.478 0.00 0.00 34.44 4.08
243 245 4.927267 TCTTCCTTTGATTGAGCCCTTA 57.073 40.909 0.00 0.00 0.00 2.69
267 269 5.171339 AGTTGAGAATATGCTCCACTTGT 57.829 39.130 11.02 0.00 37.55 3.16
322 324 2.248248 TCATGTCCACTTCTTCGTCCT 58.752 47.619 0.00 0.00 0.00 3.85
323 325 2.632996 TCATGTCCACTTCTTCGTCCTT 59.367 45.455 0.00 0.00 0.00 3.36
326 328 4.884668 TGTCCACTTCTTCGTCCTTATT 57.115 40.909 0.00 0.00 0.00 1.40
370 373 2.749076 TGAATCATTTGGTCAAGCTCCG 59.251 45.455 0.00 0.00 0.00 4.63
371 374 2.496899 ATCATTTGGTCAAGCTCCGT 57.503 45.000 0.00 0.00 0.00 4.69
427 430 8.962679 TGGAATCCATAATGTACCTAACAAAAC 58.037 33.333 0.00 0.00 42.70 2.43
564 572 3.453679 GGAGCGCTCTTCCGGAGT 61.454 66.667 34.46 0.00 43.62 3.85
682 692 2.043652 CCGGTAACTCGGGAGGGA 60.044 66.667 0.00 0.00 45.78 4.20
694 717 0.327576 GGGAGGGAGGAGGGATTTGA 60.328 60.000 0.00 0.00 0.00 2.69
723 747 2.652095 GGTGGGATCGGGTTGTCGA 61.652 63.158 0.00 0.00 43.61 4.20
773 811 2.916269 TCCATATCCGCCCCATATTTGA 59.084 45.455 0.00 0.00 0.00 2.69
791 830 0.320247 GAGCTGGATATGGGAGTGCG 60.320 60.000 0.00 0.00 0.00 5.34
819 858 3.740513 AACGTTTGAGGGCCGTTC 58.259 55.556 0.00 0.00 40.46 3.95
826 865 3.069318 GAGGGCCGTTCGAGAGGT 61.069 66.667 0.00 0.00 0.00 3.85
827 866 2.603776 AGGGCCGTTCGAGAGGTT 60.604 61.111 0.00 0.00 0.00 3.50
842 881 4.593956 GAGAGGTTCATCTGGGTCAAAAT 58.406 43.478 0.00 0.00 0.00 1.82
855 895 5.928976 TGGGTCAAAATATCATGATCGAGT 58.071 37.500 12.53 0.00 0.00 4.18
856 896 5.991606 TGGGTCAAAATATCATGATCGAGTC 59.008 40.000 12.53 0.00 0.00 3.36
857 897 6.183361 TGGGTCAAAATATCATGATCGAGTCT 60.183 38.462 12.53 0.00 0.00 3.24
858 898 6.146837 GGGTCAAAATATCATGATCGAGTCTG 59.853 42.308 12.53 4.03 0.00 3.51
862 906 1.322442 ATCATGATCGAGTCTGCCGA 58.678 50.000 1.18 0.00 40.53 5.54
871 915 1.347817 GAGTCTGCCGAGCGTTTGAG 61.348 60.000 0.00 0.00 0.00 3.02
883 927 2.928416 GTTTGAGACGGGTTGAGGG 58.072 57.895 0.00 0.00 0.00 4.30
884 928 0.108019 GTTTGAGACGGGTTGAGGGT 59.892 55.000 0.00 0.00 0.00 4.34
885 929 0.841289 TTTGAGACGGGTTGAGGGTT 59.159 50.000 0.00 0.00 0.00 4.11
886 930 0.395312 TTGAGACGGGTTGAGGGTTC 59.605 55.000 0.00 0.00 0.00 3.62
920 964 1.338973 ACAGCGGAAGAACAGTCGTTA 59.661 47.619 0.00 0.00 34.75 3.18
923 967 2.035576 AGCGGAAGAACAGTCGTTAGTT 59.964 45.455 0.00 0.00 34.75 2.24
972 1016 4.036262 CGAAACAGAACACAGAAATCCCAA 59.964 41.667 0.00 0.00 0.00 4.12
1183 1227 0.100861 CTCCGTTCTACCGCTTCTCC 59.899 60.000 0.00 0.00 0.00 3.71
1232 1276 0.892358 AGACCACTCCGTCGCTGTAA 60.892 55.000 0.00 0.00 37.85 2.41
1254 1298 2.535331 CGGTTCCCCAACTCCCCTT 61.535 63.158 0.00 0.00 32.50 3.95
1387 1431 2.328099 CCAGTGCCGCCAAGAAGAC 61.328 63.158 0.00 0.00 0.00 3.01
1466 1510 2.860735 CGGCTTATTTCCTCTGTTCTCG 59.139 50.000 0.00 0.00 0.00 4.04
1514 1561 2.820059 CGGAGCACTTGCCAGATATA 57.180 50.000 0.00 0.00 43.38 0.86
1524 1571 9.745018 AGCACTTGCCAGATATAAATAATACAT 57.255 29.630 0.00 0.00 43.38 2.29
1525 1572 9.778993 GCACTTGCCAGATATAAATAATACATG 57.221 33.333 0.00 0.00 34.31 3.21
1651 1723 8.237949 TCTCGTTTGTTTTCTGTTGAACATAAA 58.762 29.630 0.00 1.22 35.85 1.40
1683 1756 4.018484 TGCAGGCCAAAATATTTGCTTT 57.982 36.364 5.01 0.00 33.00 3.51
1687 1760 6.072783 TGCAGGCCAAAATATTTGCTTTAAAC 60.073 34.615 5.01 0.00 33.00 2.01
1717 1790 9.442047 AGTGAAGTCAATCTTTGGAACTAATAG 57.558 33.333 0.00 0.00 36.40 1.73
1952 2031 8.088365 TCATACATGAATCTTTATGTCTACGGG 58.912 37.037 0.00 0.00 38.41 5.28
1954 2033 4.746535 TGAATCTTTATGTCTACGGGCA 57.253 40.909 0.00 0.00 0.00 5.36
1957 2036 5.527214 TGAATCTTTATGTCTACGGGCAATG 59.473 40.000 0.00 0.00 0.00 2.82
1975 2054 6.295292 GGGCAATGTCCTTTTCTGATTACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2092 2171 4.760878 TGTACGTTGCCAATTATCTGCTA 58.239 39.130 0.00 0.00 0.00 3.49
2314 2393 2.634982 TTGATTGACAGCATTTCGGC 57.365 45.000 0.00 0.00 0.00 5.54
2330 2409 3.410631 TCGGCAGTTTCCATTTCACTA 57.589 42.857 0.00 0.00 0.00 2.74
2687 2766 7.502895 AGAGCGAGTCTTCCAAGTTAAGATATA 59.497 37.037 0.00 0.00 35.53 0.86
2739 2818 1.813178 CGAGCTGGATCTATCGGCTTA 59.187 52.381 5.41 0.00 36.93 3.09
2954 3035 8.896744 TGACTGCTTTGGATTTTATCATAGAAG 58.103 33.333 0.00 0.00 0.00 2.85
3002 3083 4.935352 TGGTTGGAAGATTTGTTCAAGG 57.065 40.909 0.00 0.00 0.00 3.61
3083 3164 4.892655 TGTTTCGTATTTGTGATGATCGC 58.107 39.130 0.00 0.00 0.00 4.58
3135 3216 7.990314 ACCATAGCTAAGAGAAAATCTTCTTCC 59.010 37.037 0.00 0.00 45.50 3.46
3171 3252 1.343465 AGGGAGTCCAAACAGTACACG 59.657 52.381 12.30 0.00 34.83 4.49
3189 3270 3.420943 GCACGTATCCATGTGGCC 58.579 61.111 0.00 0.00 41.27 5.36
3306 3390 4.209452 TGAGTCTTCACGCAATTTTCAC 57.791 40.909 0.00 0.00 27.98 3.18
3389 3474 6.869388 GTCCTCTTCGTTTGTATTTCTCTCTT 59.131 38.462 0.00 0.00 0.00 2.85
3472 3557 5.079406 CCGTGTGTTCAACTTCATATTTCG 58.921 41.667 0.00 0.00 0.00 3.46
3475 3560 6.077838 GTGTGTTCAACTTCATATTTCGGTC 58.922 40.000 0.00 0.00 0.00 4.79
3543 3643 7.222031 TCAGTATAATCGAGAAAAATGACCGTG 59.778 37.037 0.00 0.00 0.00 4.94
3547 3647 3.591023 TCGAGAAAAATGACCGTGCATA 58.409 40.909 0.00 0.00 0.00 3.14
3569 3669 8.012241 GCATACGAAGACAGATAATTGATTTCC 58.988 37.037 0.00 0.00 0.00 3.13
3570 3670 9.045223 CATACGAAGACAGATAATTGATTTCCA 57.955 33.333 0.00 0.00 0.00 3.53
3572 3672 7.752695 ACGAAGACAGATAATTGATTTCCAAC 58.247 34.615 0.00 0.00 37.63 3.77
3585 3686 7.470289 TTGATTTCCAACGTTTAACCATTTG 57.530 32.000 0.00 0.00 0.00 2.32
3687 3788 8.789767 TGATAGAGAAAAGATACCCTGATCTT 57.210 34.615 0.00 0.00 46.02 2.40
3767 3868 5.425630 GGTATCTAATGGTCGGTTGAAACT 58.574 41.667 0.00 0.00 0.00 2.66
3774 3875 1.594331 GTCGGTTGAAACTGGAGCTT 58.406 50.000 2.29 0.00 35.96 3.74
3939 4246 1.205179 ACGATACCGCACATTGTACCA 59.795 47.619 0.00 0.00 39.95 3.25
3942 4249 3.527533 GATACCGCACATTGTACCAGAA 58.472 45.455 0.00 0.00 0.00 3.02
3985 4292 4.285863 TCCCAAGGAATATTTTGCCGAAT 58.714 39.130 0.00 0.00 0.00 3.34
3986 4293 4.099266 TCCCAAGGAATATTTTGCCGAATG 59.901 41.667 0.00 0.00 0.00 2.67
3987 4294 4.141959 CCCAAGGAATATTTTGCCGAATGT 60.142 41.667 0.00 0.00 0.00 2.71
3988 4295 5.068460 CCCAAGGAATATTTTGCCGAATGTA 59.932 40.000 0.00 0.00 0.00 2.29
4084 4394 8.366401 ACTAGATGTCCATTGAATCAGTAGATG 58.634 37.037 0.00 0.00 33.90 2.90
4092 4402 3.562182 TGAATCAGTAGATGCCGGAGTA 58.438 45.455 5.05 0.00 33.90 2.59
4119 4429 4.039488 TGGAGTACAAAGACGAAGCCTAAA 59.961 41.667 0.00 0.00 0.00 1.85
4170 4480 1.488393 GCCAGAGAGGGAGCAATTACT 59.512 52.381 0.00 0.00 38.09 2.24
4171 4481 2.092699 GCCAGAGAGGGAGCAATTACTT 60.093 50.000 0.00 0.00 38.09 2.24
4201 4511 8.745590 GGGAAAATGAAAATAACCTACAGCTAA 58.254 33.333 0.00 0.00 0.00 3.09
4220 4530 9.012161 ACAGCTAACTACTACTAGTATATTGGC 57.988 37.037 2.33 14.68 35.40 4.52
4221 4531 8.460428 CAGCTAACTACTACTAGTATATTGGCC 58.540 40.741 16.90 0.00 35.58 5.36
4222 4532 8.168725 AGCTAACTACTACTAGTATATTGGCCA 58.831 37.037 0.00 0.00 35.58 5.36
4223 4533 8.800332 GCTAACTACTACTAGTATATTGGCCAA 58.200 37.037 23.00 23.00 32.23 4.52
4371 4681 4.504596 TAATGCCAGCCCGCCCAG 62.505 66.667 0.00 0.00 0.00 4.45
4747 5063 2.022902 CGACGTCGACGGAGATGG 59.977 66.667 37.89 17.24 44.95 3.51
4751 5067 3.823330 GTCGACGGAGATGGCGGT 61.823 66.667 0.00 0.00 0.00 5.68
4813 5129 1.302033 CAGAAGGCGTGGAAGCAGT 60.302 57.895 0.00 0.00 39.27 4.40
4814 5130 1.004440 AGAAGGCGTGGAAGCAGTC 60.004 57.895 0.00 0.00 39.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.986527 TCTGAGAAGGGATTGCTGCA 59.013 50.000 0.00 0.00 0.00 4.41
51 52 2.325761 GCACACGACGACTACTTCAAT 58.674 47.619 0.00 0.00 0.00 2.57
141 143 1.028905 CCACACCTGCTTTTTCGGAA 58.971 50.000 0.00 0.00 0.00 4.30
182 184 2.836981 AGAGTGTCTGGAGCAAAGCTAT 59.163 45.455 0.00 0.00 39.88 2.97
267 269 0.690192 TGCAAGAGGAAATGGACCGA 59.310 50.000 0.00 0.00 0.00 4.69
326 328 3.374367 AGATGAGTTCTTCGATTCGTCGA 59.626 43.478 5.89 0.00 40.66 4.20
370 373 2.073037 GACGAGGAGTATGGCCCGAC 62.073 65.000 0.00 0.00 0.00 4.79
371 374 1.826921 GACGAGGAGTATGGCCCGA 60.827 63.158 0.00 0.00 0.00 5.14
401 404 8.962679 GTTTTGTTAGGTACATTATGGATTCCA 58.037 33.333 8.08 8.08 36.44 3.53
427 430 1.937899 GACCGACCGGAATTATTGTGG 59.062 52.381 16.07 0.00 38.96 4.17
546 554 3.452786 CTCCGGAAGAGCGCTCCA 61.453 66.667 32.94 9.87 35.31 3.86
622 630 4.200283 CCTCCTCTGCGCCGTCTC 62.200 72.222 4.18 0.00 0.00 3.36
623 631 4.742649 TCCTCCTCTGCGCCGTCT 62.743 66.667 4.18 0.00 0.00 4.18
678 688 0.849417 GCATCAAATCCCTCCTCCCT 59.151 55.000 0.00 0.00 0.00 4.20
682 692 4.897670 CCTAAATTGCATCAAATCCCTCCT 59.102 41.667 0.00 0.00 0.00 3.69
694 717 2.586425 CGATCCCACCCTAAATTGCAT 58.414 47.619 0.00 0.00 0.00 3.96
773 811 1.750930 CGCACTCCCATATCCAGCT 59.249 57.895 0.00 0.00 0.00 4.24
819 858 1.186200 TGACCCAGATGAACCTCTCG 58.814 55.000 0.00 0.00 0.00 4.04
826 865 7.173735 CGATCATGATATTTTGACCCAGATGAA 59.826 37.037 8.54 0.00 0.00 2.57
827 866 6.652062 CGATCATGATATTTTGACCCAGATGA 59.348 38.462 8.54 0.00 0.00 2.92
842 881 2.485814 CTCGGCAGACTCGATCATGATA 59.514 50.000 8.54 0.00 36.01 2.15
855 895 1.372997 GTCTCAAACGCTCGGCAGA 60.373 57.895 0.00 0.00 0.00 4.26
856 896 2.720758 CGTCTCAAACGCTCGGCAG 61.721 63.158 0.00 0.00 45.76 4.85
857 897 2.733218 CGTCTCAAACGCTCGGCA 60.733 61.111 0.00 0.00 45.76 5.69
871 915 1.302271 GTGGAACCCTCAACCCGTC 60.302 63.158 0.00 0.00 0.00 4.79
896 940 1.160329 ACTGTTCTTCCGCTGTGCAC 61.160 55.000 10.75 10.75 0.00 4.57
920 964 2.890808 TCGTCACTGCAGAGAAAACT 57.109 45.000 23.35 0.00 0.00 2.66
923 967 1.686587 TCCTTCGTCACTGCAGAGAAA 59.313 47.619 23.35 9.36 0.00 2.52
1183 1227 1.344942 CGACGCCGGTCAAAGAGAAG 61.345 60.000 1.90 0.00 43.61 2.85
1387 1431 2.507992 CCAGCAACTCGAGCTCCG 60.508 66.667 13.61 3.57 41.14 4.63
1466 1510 1.172812 ACGGTGCTTGAAAGAAGGGC 61.173 55.000 0.00 0.00 0.00 5.19
1524 1571 7.630082 ACAACCATTTTTAGCTAGACTATCCA 58.370 34.615 0.00 0.00 0.00 3.41
1525 1572 9.262358 CTACAACCATTTTTAGCTAGACTATCC 57.738 37.037 0.00 0.00 0.00 2.59
1527 1574 7.715686 GCCTACAACCATTTTTAGCTAGACTAT 59.284 37.037 0.00 0.00 0.00 2.12
1528 1575 7.046033 GCCTACAACCATTTTTAGCTAGACTA 58.954 38.462 0.00 0.00 0.00 2.59
1601 1673 4.321452 GCTTCATTCACCTTTTCAGATGCA 60.321 41.667 0.00 0.00 0.00 3.96
1683 1756 6.238731 CCAAAGATTGACTTCACTGCAGTTTA 60.239 38.462 18.94 5.47 37.93 2.01
1687 1760 3.817084 TCCAAAGATTGACTTCACTGCAG 59.183 43.478 13.48 13.48 37.93 4.41
1952 2031 7.116805 CCAAAAGTAATCAGAAAAGGACATTGC 59.883 37.037 0.00 0.00 0.00 3.56
1954 2033 7.015584 AGCCAAAAGTAATCAGAAAAGGACATT 59.984 33.333 0.00 0.00 0.00 2.71
1957 2036 6.152379 CAGCCAAAAGTAATCAGAAAAGGAC 58.848 40.000 0.00 0.00 0.00 3.85
1995 2074 3.842732 TGCAAAGCATGAAGATCTGTG 57.157 42.857 0.00 0.00 31.71 3.66
1996 2075 4.077108 TCTTGCAAAGCATGAAGATCTGT 58.923 39.130 0.00 0.00 45.70 3.41
2061 2140 0.743345 GGCAACGTACAGGATCACCC 60.743 60.000 0.00 0.00 36.73 4.61
2092 2171 6.233434 TCAAGTGAAGCATACTGAATTGAGT 58.767 36.000 2.35 2.35 0.00 3.41
2687 2766 0.110486 AACCATCCTTGTTCAGCGGT 59.890 50.000 0.00 0.00 0.00 5.68
2739 2818 6.697641 ATATCCCACCCAAACGAAGTATAT 57.302 37.500 0.00 0.00 45.00 0.86
2954 3035 6.261603 TCATCTCTATCACATTGTTTGATGGC 59.738 38.462 0.00 0.00 35.31 4.40
3002 3083 6.437094 GGTATCAGGACGTATAAACAGTCTC 58.563 44.000 0.00 0.00 35.42 3.36
3083 3164 2.228138 AGCACTGCAACAACAAATGG 57.772 45.000 3.30 0.00 0.00 3.16
3135 3216 1.618837 TCCCTCAACTTCTGTCTTCGG 59.381 52.381 0.00 0.00 0.00 4.30
3472 3557 6.979238 GTGACTAGAACATGTATGGTAAGACC 59.021 42.308 0.00 0.00 39.22 3.85
3475 3560 6.561614 ACGTGACTAGAACATGTATGGTAAG 58.438 40.000 0.00 0.00 36.01 2.34
3528 3628 3.670203 CGTATGCACGGTCATTTTTCTC 58.330 45.455 0.00 0.00 44.59 2.87
3543 3643 8.012241 GGAAATCAATTATCTGTCTTCGTATGC 58.988 37.037 0.00 0.00 0.00 3.14
3547 3647 7.413000 CGTTGGAAATCAATTATCTGTCTTCGT 60.413 37.037 0.00 0.00 37.73 3.85
3550 3650 7.687941 ACGTTGGAAATCAATTATCTGTCTT 57.312 32.000 0.00 0.00 37.73 3.01
3555 3655 8.798402 TGGTTAAACGTTGGAAATCAATTATCT 58.202 29.630 0.00 0.00 37.73 1.98
3569 3669 4.747108 TGGCATTCAAATGGTTAAACGTTG 59.253 37.500 0.00 0.00 36.90 4.10
3570 3670 4.950050 TGGCATTCAAATGGTTAAACGTT 58.050 34.783 0.00 0.00 36.90 3.99
3572 3672 3.925913 CCTGGCATTCAAATGGTTAAACG 59.074 43.478 4.98 0.00 36.90 3.60
3585 3686 6.072286 CCACATTGTATATCTTCCTGGCATTC 60.072 42.308 0.00 0.00 0.00 2.67
3767 3868 2.046314 GCCTAACGCCAAGCTCCA 60.046 61.111 0.00 0.00 0.00 3.86
4084 4394 1.479323 TGTACTCCAACATACTCCGGC 59.521 52.381 0.00 0.00 0.00 6.13
4092 4402 3.746492 GCTTCGTCTTTGTACTCCAACAT 59.254 43.478 0.00 0.00 31.20 2.71
4201 4511 7.783596 ACTGTTGGCCAATATACTAGTAGTAGT 59.216 37.037 23.66 14.57 42.49 2.73
4205 4515 7.948357 TGTACTGTTGGCCAATATACTAGTAG 58.052 38.462 23.66 6.87 0.00 2.57
4206 4516 7.901283 TGTACTGTTGGCCAATATACTAGTA 57.099 36.000 23.66 18.22 0.00 1.82
4208 4518 8.677148 AAATGTACTGTTGGCCAATATACTAG 57.323 34.615 23.66 14.77 0.00 2.57
4210 4520 7.954666 AAAATGTACTGTTGGCCAATATACT 57.045 32.000 23.66 6.93 0.00 2.12
4211 4521 8.899771 ACTAAAATGTACTGTTGGCCAATATAC 58.100 33.333 23.66 22.11 0.00 1.47
4212 4522 8.898761 CACTAAAATGTACTGTTGGCCAATATA 58.101 33.333 23.66 11.62 0.00 0.86
4213 4523 7.613801 TCACTAAAATGTACTGTTGGCCAATAT 59.386 33.333 23.66 12.69 0.00 1.28
4215 4525 5.772672 TCACTAAAATGTACTGTTGGCCAAT 59.227 36.000 23.66 8.57 0.00 3.16
4216 4526 5.133941 TCACTAAAATGTACTGTTGGCCAA 58.866 37.500 16.05 16.05 0.00 4.52
4220 4530 7.630242 ATCCATCACTAAAATGTACTGTTGG 57.370 36.000 0.00 0.00 0.00 3.77
4221 4531 9.345517 CAAATCCATCACTAAAATGTACTGTTG 57.654 33.333 0.00 0.00 0.00 3.33
4222 4532 9.077885 ACAAATCCATCACTAAAATGTACTGTT 57.922 29.630 0.00 0.00 0.00 3.16
4223 4533 8.635765 ACAAATCCATCACTAAAATGTACTGT 57.364 30.769 0.00 0.00 0.00 3.55
4371 4681 4.107051 GCGCAGTGTCATGCCCAC 62.107 66.667 0.30 7.12 43.49 4.61
4604 4920 2.669569 GCACGGGCTGCAAGAAGA 60.670 61.111 0.00 0.00 46.29 2.87
4728 5044 3.122971 ATCTCCGTCGACGTCGCA 61.123 61.111 33.49 18.37 39.60 5.10
4751 5067 4.178169 ACCGTGGGCCGTTTCACA 62.178 61.111 10.04 0.00 33.83 3.58
4813 5129 2.596851 GGGACAGCTTCTGCCTGGA 61.597 63.158 0.00 0.00 40.80 3.86
4814 5130 2.045536 GGGACAGCTTCTGCCTGG 60.046 66.667 0.00 0.00 40.80 4.45


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

AutoCloner maintained by Alex Coulton.