Multiple sequence alignment - TraesCS4D01G174800

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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 TraesCS4D01G174800 chr4D 100.000 6357 0 0 1 6357 303061875 303068231 0.000000e+00 11740.0
1 TraesCS4D01G174800 chr4D 96.970 33 0 1 703 734 503522037 503522069 3.000000e-03 54.7
2 TraesCS4D01G174800 chr4A 95.776 6226 179 43 1 6185 176601929 176595747 0.000000e+00 9963.0
3 TraesCS4D01G174800 chr4A 86.179 123 13 2 6169 6291 176595363 176595245 5.170000e-26 130.0
4 TraesCS4D01G174800 chr4B 95.616 6159 150 39 1 6111 377786050 377792136 0.000000e+00 9768.0
5 TraesCS4D01G174800 chr2D 78.000 1000 205 14 3866 4857 39828337 39829329 1.170000e-171 614.0
6 TraesCS4D01G174800 chr2D 77.678 999 210 12 3866 4857 55371373 55370381 1.180000e-166 597.0
7 TraesCS4D01G174800 chr2B 77.778 999 209 12 3866 4857 87845084 87844092 2.540000e-168 603.0
8 TraesCS4D01G174800 chr2A 77.767 1003 202 14 3866 4857 56920461 56919469 1.180000e-166 597.0
9 TraesCS4D01G174800 chr1A 90.370 135 13 0 1861 1995 6707021 6707155 1.820000e-40 178.0


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 TraesCS4D01G174800 chr4D 303061875 303068231 6356 False 11740.0 11740 100.0000 1 6357 1 chr4D.!!$F1 6356
1 TraesCS4D01G174800 chr4A 176595245 176601929 6684 True 5046.5 9963 90.9775 1 6291 2 chr4A.!!$R1 6290
2 TraesCS4D01G174800 chr4B 377786050 377792136 6086 False 9768.0 9768 95.6160 1 6111 1 chr4B.!!$F1 6110
3 TraesCS4D01G174800 chr2D 39828337 39829329 992 False 614.0 614 78.0000 3866 4857 1 chr2D.!!$F1 991
4 TraesCS4D01G174800 chr2D 55370381 55371373 992 True 597.0 597 77.6780 3866 4857 1 chr2D.!!$R1 991
5 TraesCS4D01G174800 chr2B 87844092 87845084 992 True 603.0 603 77.7780 3866 4857 1 chr2B.!!$R1 991
6 TraesCS4D01G174800 chr2A 56919469 56920461 992 True 597.0 597 77.7670 3866 4857 1 chr2A.!!$R1 991

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
82 88 0.178929 AGACGAGGAGAAACCCCTGT 60.179 55.000 0.00 0.00 40.05 4.00 F
775 808 1.269361 TGTCTTCTCGCGCACACTAAA 60.269 47.619 8.75 0.00 0.00 1.85 F
2298 2352 1.342174 AGCCACCAATTCAAACAGCTG 59.658 47.619 13.48 13.48 0.00 4.24 F
2837 2892 0.173481 TCACCATCTTCGGCTCTTCG 59.827 55.000 0.00 0.00 0.00 3.79 F
2873 2929 0.528249 GTGCACACCTTTTGCCACTG 60.528 55.000 13.17 0.00 39.39 3.66 F
3641 3700 3.715628 ATTCGGCATGCTTGTTATTCC 57.284 42.857 18.92 0.00 0.00 3.01 F
4712 4776 2.689983 CAAGTTTTGTGGCCTGAGACTT 59.310 45.455 3.32 5.32 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1281 0.322975 ACACCAGAAGCCAGCACTAG 59.677 55.000 0.0 0.0 0.00 2.57 R
2614 2668 0.310854 GTAACAGTGTTGCAGCCACC 59.689 55.000 18.9 0.0 33.20 4.61 R
3641 3700 1.463674 AATGCTAAACGGGGCAAGAG 58.536 50.000 0.0 0.0 41.90 2.85 R
3844 3905 2.936202 AGCACAGGTCAAGTGTCATTT 58.064 42.857 0.0 0.0 39.17 2.32 R
4712 4776 3.751518 GAGAAGGTTTCTTAGTTGGCCA 58.248 45.455 0.0 0.0 40.87 5.36 R
5131 5199 7.454380 AGAGGATATACAAGATTCTGGAAGGAG 59.546 40.741 0.0 0.0 0.00 3.69 R
6294 6777 0.390209 CTTGAAAATGCCCTTGCCGG 60.390 55.000 0.0 0.0 36.33 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
20 21 3.790089 AATCCCTTCAAAGTCGTCCTT 57.210 42.857 0.00 0.00 33.79 3.36
26 27 4.384208 CCCTTCAAAGTCGTCCTTCCATAT 60.384 45.833 0.00 0.00 31.27 1.78
39 45 3.560068 CCTTCCATATTTGTCACCGTAGC 59.440 47.826 0.00 0.00 0.00 3.58
40 46 4.442706 CTTCCATATTTGTCACCGTAGCT 58.557 43.478 0.00 0.00 0.00 3.32
41 47 4.054780 TCCATATTTGTCACCGTAGCTC 57.945 45.455 0.00 0.00 0.00 4.09
42 48 2.794910 CCATATTTGTCACCGTAGCTCG 59.205 50.000 0.00 0.00 39.52 5.03
43 49 3.490249 CCATATTTGTCACCGTAGCTCGA 60.490 47.826 7.07 0.00 42.86 4.04
82 88 0.178929 AGACGAGGAGAAACCCCTGT 60.179 55.000 0.00 0.00 40.05 4.00
98 104 4.131088 GTGGTCGAGAGGGGTCGC 62.131 72.222 0.00 0.00 39.90 5.19
131 138 3.697439 ATTCCGCCCCACACCATCG 62.697 63.158 0.00 0.00 0.00 3.84
172 179 3.223157 CATTAACGTCACAAGGCGAAAC 58.777 45.455 0.00 0.00 0.00 2.78
307 314 4.081476 ACATGTCTCTCATCGGAAATGACA 60.081 41.667 0.00 0.00 37.37 3.58
370 378 5.195001 TGTTGGAACTAATTTGAAGTGCC 57.805 39.130 0.00 0.00 42.40 5.01
401 409 1.303561 TGCCACAGCAGATTGTCCC 60.304 57.895 0.00 0.00 46.52 4.46
431 439 4.389992 CACTGATATCCATCACAATACGGC 59.610 45.833 0.00 0.00 36.22 5.68
527 548 6.686679 CGAAAACAGCATAGCAAATCGAATTA 59.313 34.615 0.00 0.00 0.00 1.40
775 808 1.269361 TGTCTTCTCGCGCACACTAAA 60.269 47.619 8.75 0.00 0.00 1.85
776 809 1.790623 GTCTTCTCGCGCACACTAAAA 59.209 47.619 8.75 0.00 0.00 1.52
1146 1179 3.400054 CCGTCCCTCTTGTCCCCC 61.400 72.222 0.00 0.00 0.00 5.40
1158 1191 3.018805 TCCCCCACCCGGATTTCC 61.019 66.667 0.73 0.00 0.00 3.13
1248 1281 5.495502 AGTGTTGTTTCGTTAATTGTCGTC 58.504 37.500 0.00 0.00 0.00 4.20
1258 1291 1.726853 AATTGTCGTCTAGTGCTGGC 58.273 50.000 0.00 0.00 0.00 4.85
1344 1377 4.148825 GTGACGGATGAGCGCCCT 62.149 66.667 2.29 0.00 0.00 5.19
1411 1449 3.690139 TGCAGACGTTTGTCCAAGTTTTA 59.310 39.130 8.00 0.00 46.74 1.52
1500 1538 5.178096 TCATTTGTGCTGGATTTAGGAGA 57.822 39.130 0.00 0.00 0.00 3.71
1536 1574 3.965292 TCGATCGCTTAGTGGTAGAAG 57.035 47.619 11.09 0.00 0.00 2.85
1653 1703 5.988287 TGGCAGTGATGAACTCATATAACA 58.012 37.500 0.00 0.00 36.83 2.41
1788 1838 3.786656 TGCCTACTAGCATGCCTTG 57.213 52.632 15.66 7.37 38.00 3.61
1816 1866 8.262227 TGTAACTAAAAGATACAGTACCCCATG 58.738 37.037 0.00 0.00 30.04 3.66
1972 2022 3.795688 TTTCTGCCACTCTTCCTCATT 57.204 42.857 0.00 0.00 0.00 2.57
2070 2120 6.991938 TGCTAAAAGGAAATTGTGCATAAGT 58.008 32.000 1.43 0.00 0.00 2.24
2246 2300 1.609555 CCTCTCTTCGACCGAATAGGG 59.390 57.143 14.58 12.16 46.96 3.53
2283 2337 5.682862 CGCATACAGAAATAATTCAAGCCAC 59.317 40.000 0.00 0.00 38.06 5.01
2298 2352 1.342174 AGCCACCAATTCAAACAGCTG 59.658 47.619 13.48 13.48 0.00 4.24
2404 2458 8.613060 TTCATGATTATGAACTATGAAGGCTC 57.387 34.615 8.73 0.00 45.77 4.70
2479 2533 7.064134 TGCATAGATTACTAGTGTTTTCCGTTG 59.936 37.037 5.39 0.00 31.78 4.10
2770 2825 4.677673 ACGTTGTAGGAAACCAGTTACT 57.322 40.909 0.00 0.00 0.00 2.24
2830 2885 0.742281 CAGCACCTCACCATCTTCGG 60.742 60.000 0.00 0.00 0.00 4.30
2831 2886 2.109126 GCACCTCACCATCTTCGGC 61.109 63.158 0.00 0.00 0.00 5.54
2832 2887 1.599047 CACCTCACCATCTTCGGCT 59.401 57.895 0.00 0.00 0.00 5.52
2833 2888 0.460987 CACCTCACCATCTTCGGCTC 60.461 60.000 0.00 0.00 0.00 4.70
2834 2889 0.616111 ACCTCACCATCTTCGGCTCT 60.616 55.000 0.00 0.00 0.00 4.09
2835 2890 0.539051 CCTCACCATCTTCGGCTCTT 59.461 55.000 0.00 0.00 0.00 2.85
2836 2891 1.472376 CCTCACCATCTTCGGCTCTTC 60.472 57.143 0.00 0.00 0.00 2.87
2837 2892 0.173481 TCACCATCTTCGGCTCTTCG 59.827 55.000 0.00 0.00 0.00 3.79
2860 2915 3.348119 TGTTACTTGTTTCCAGTGCACA 58.652 40.909 21.04 0.00 0.00 4.57
2873 2929 0.528249 GTGCACACCTTTTGCCACTG 60.528 55.000 13.17 0.00 39.39 3.66
2922 2978 4.942761 ATTCTGAACAAATGCTGGTGTT 57.057 36.364 0.00 0.04 40.61 3.32
3030 3086 7.125507 ACCTGATTCTCTTCTCATGATGTACTT 59.874 37.037 0.00 0.00 0.00 2.24
3641 3700 3.715628 ATTCGGCATGCTTGTTATTCC 57.284 42.857 18.92 0.00 0.00 3.01
3744 3803 7.870445 GGGTTGAAATGCTTTGTTACATCTTAA 59.130 33.333 0.00 0.00 0.00 1.85
3844 3905 9.672086 GACTGTGCATTTAATTGTTTGTTACTA 57.328 29.630 0.00 0.00 0.00 1.82
4616 4680 4.918810 AAAGAAGGTGATTGTGTTGGAC 57.081 40.909 0.00 0.00 0.00 4.02
4712 4776 2.689983 CAAGTTTTGTGGCCTGAGACTT 59.310 45.455 3.32 5.32 0.00 3.01
5384 5458 5.069119 ACTTTGGAAACCAGAAGATTTGACC 59.931 40.000 14.50 0.00 33.81 4.02
5822 5904 9.574516 AAAGTTATGTGGATGGGAAGTATATTC 57.425 33.333 0.00 0.00 0.00 1.75
5892 5974 5.527214 CGGTGGATATCTTTGCACATTCTTA 59.473 40.000 2.05 0.00 39.47 2.10
6081 6164 3.692257 AATATTGCTGAGATCCCGAGG 57.308 47.619 0.00 0.00 0.00 4.63
6145 6228 5.248477 GGTAGGGATAATAGAAGTGCCATCA 59.752 44.000 0.00 0.00 0.00 3.07
6161 6244 9.643693 AAGTGCCATCAGTATTTGAAAATAAAG 57.356 29.630 0.00 0.00 39.77 1.85
6182 6665 0.321671 AGTTGGTGATCTGGTGGACG 59.678 55.000 0.00 0.00 0.00 4.79
6184 6667 0.034756 TTGGTGATCTGGTGGACGTG 59.965 55.000 0.00 0.00 0.00 4.49
6189 6672 0.179161 GATCTGGTGGACGTGTCTCG 60.179 60.000 0.00 0.00 46.00 4.04
6214 6697 2.050077 GTGCAGCCAGCCGTTTTC 60.050 61.111 0.00 0.00 44.83 2.29
6215 6698 2.203337 TGCAGCCAGCCGTTTTCT 60.203 55.556 0.00 0.00 44.83 2.52
6218 6701 0.811281 GCAGCCAGCCGTTTTCTTAT 59.189 50.000 0.00 0.00 37.23 1.73
6219 6702 2.014128 GCAGCCAGCCGTTTTCTTATA 58.986 47.619 0.00 0.00 37.23 0.98
6220 6703 2.032178 GCAGCCAGCCGTTTTCTTATAG 59.968 50.000 0.00 0.00 37.23 1.31
6221 6704 3.270877 CAGCCAGCCGTTTTCTTATAGT 58.729 45.455 0.00 0.00 0.00 2.12
6222 6705 4.439057 CAGCCAGCCGTTTTCTTATAGTA 58.561 43.478 0.00 0.00 0.00 1.82
6279 6762 2.609183 CTAGCTACGCACGGACACCC 62.609 65.000 0.00 0.00 0.00 4.61
6311 6794 3.375438 CCGGCAAGGGCATTTTCA 58.625 55.556 0.00 0.00 43.71 2.69
6312 6795 1.670590 CCGGCAAGGGCATTTTCAA 59.329 52.632 0.00 0.00 43.71 2.69
6313 6796 0.390209 CCGGCAAGGGCATTTTCAAG 60.390 55.000 0.00 0.00 43.71 3.02
6314 6797 0.602562 CGGCAAGGGCATTTTCAAGA 59.397 50.000 0.00 0.00 43.71 3.02
6315 6798 1.669795 CGGCAAGGGCATTTTCAAGAC 60.670 52.381 0.00 0.00 43.71 3.01
6316 6799 1.669795 GGCAAGGGCATTTTCAAGACG 60.670 52.381 0.00 0.00 43.71 4.18
6317 6800 1.669795 GCAAGGGCATTTTCAAGACGG 60.670 52.381 0.00 0.00 40.72 4.79
6318 6801 1.885887 CAAGGGCATTTTCAAGACGGA 59.114 47.619 0.00 0.00 0.00 4.69
6319 6802 2.493278 CAAGGGCATTTTCAAGACGGAT 59.507 45.455 0.00 0.00 0.00 4.18
6320 6803 2.807676 AGGGCATTTTCAAGACGGATT 58.192 42.857 0.00 0.00 0.00 3.01
6321 6804 2.755103 AGGGCATTTTCAAGACGGATTC 59.245 45.455 0.00 0.00 0.00 2.52
6322 6805 2.477863 GGGCATTTTCAAGACGGATTCG 60.478 50.000 0.00 0.00 43.02 3.34
6338 6821 5.035443 CGGATTCGTAAACTAGAGACAAGG 58.965 45.833 0.00 0.00 0.00 3.61
6339 6822 5.163683 CGGATTCGTAAACTAGAGACAAGGA 60.164 44.000 0.00 0.00 0.00 3.36
6340 6823 6.267070 GGATTCGTAAACTAGAGACAAGGAG 58.733 44.000 0.00 0.00 0.00 3.69
6341 6824 6.127675 GGATTCGTAAACTAGAGACAAGGAGT 60.128 42.308 0.00 0.00 0.00 3.85
6342 6825 6.645790 TTCGTAAACTAGAGACAAGGAGTT 57.354 37.500 0.00 0.00 33.60 3.01
6343 6826 6.645790 TCGTAAACTAGAGACAAGGAGTTT 57.354 37.500 0.00 4.47 42.96 2.66
6344 6827 7.047460 TCGTAAACTAGAGACAAGGAGTTTT 57.953 36.000 0.00 0.00 41.25 2.43
6345 6828 6.921857 TCGTAAACTAGAGACAAGGAGTTTTG 59.078 38.462 0.00 0.00 41.25 2.44
6346 6829 6.700520 CGTAAACTAGAGACAAGGAGTTTTGT 59.299 38.462 0.00 0.00 43.61 2.83
6347 6830 6.927294 AAACTAGAGACAAGGAGTTTTGTG 57.073 37.500 0.00 0.00 41.15 3.33
6348 6831 5.871396 ACTAGAGACAAGGAGTTTTGTGA 57.129 39.130 0.00 0.00 41.15 3.58
6349 6832 5.848406 ACTAGAGACAAGGAGTTTTGTGAG 58.152 41.667 0.00 0.00 41.15 3.51
6350 6833 5.598830 ACTAGAGACAAGGAGTTTTGTGAGA 59.401 40.000 0.00 0.00 41.15 3.27
6351 6834 4.954875 AGAGACAAGGAGTTTTGTGAGAG 58.045 43.478 0.00 0.00 41.15 3.20
6352 6835 4.407296 AGAGACAAGGAGTTTTGTGAGAGT 59.593 41.667 0.00 0.00 41.15 3.24
6353 6836 4.698575 AGACAAGGAGTTTTGTGAGAGTC 58.301 43.478 0.00 0.00 41.15 3.36
6354 6837 3.809905 ACAAGGAGTTTTGTGAGAGTCC 58.190 45.455 0.00 0.00 39.68 3.85
6355 6838 2.802816 CAAGGAGTTTTGTGAGAGTCCG 59.197 50.000 0.00 0.00 39.79 4.79
6356 6839 1.344763 AGGAGTTTTGTGAGAGTCCGG 59.655 52.381 0.00 0.00 39.79 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.490249 CGAGCTACGGTGACAAATATGGA 60.490 47.826 0.00 0.00 38.46 3.41
26 27 1.336517 CCTTCGAGCTACGGTGACAAA 60.337 52.381 5.87 0.00 42.82 2.83
39 45 1.376037 GTTGCCTCCCACCTTCGAG 60.376 63.158 0.00 0.00 0.00 4.04
40 46 2.747686 GTTGCCTCCCACCTTCGA 59.252 61.111 0.00 0.00 0.00 3.71
41 47 2.742372 CGTTGCCTCCCACCTTCG 60.742 66.667 0.00 0.00 0.00 3.79
42 48 3.056328 GCGTTGCCTCCCACCTTC 61.056 66.667 0.00 0.00 0.00 3.46
43 49 4.660938 GGCGTTGCCTCCCACCTT 62.661 66.667 0.00 0.00 46.69 3.50
111 117 3.697439 ATGGTGTGGGGCGGAATCG 62.697 63.158 0.00 0.00 39.81 3.34
146 153 2.066262 CCTTGTGACGTTAATGCGAGT 58.934 47.619 0.00 0.00 35.59 4.18
172 179 2.358737 GAAGGTGGTGGTGAGGCG 60.359 66.667 0.00 0.00 0.00 5.52
244 251 2.672996 CCGCCAGTGACCCCAAAG 60.673 66.667 0.00 0.00 0.00 2.77
307 314 7.508687 AGAAATTTAAAACTCTTTGGGTGCAT 58.491 30.769 0.00 0.00 0.00 3.96
350 358 3.305064 GCGGCACTTCAAATTAGTTCCAA 60.305 43.478 0.00 0.00 29.56 3.53
388 396 1.001764 TGCTGGGGACAATCTGCTG 60.002 57.895 0.00 0.00 42.06 4.41
401 409 2.105306 TGATGGATATCAGTGGTGCTGG 59.895 50.000 4.83 0.00 45.08 4.85
431 439 3.014623 GGGACGGAGGGAATAAAACTTG 58.985 50.000 0.00 0.00 0.00 3.16
775 808 2.125673 CGGACGCTCGGATTGGTT 60.126 61.111 0.00 0.00 0.00 3.67
801 834 2.746277 GCGTGGCGATTTGGGAGT 60.746 61.111 0.00 0.00 0.00 3.85
1248 1281 0.322975 ACACCAGAAGCCAGCACTAG 59.677 55.000 0.00 0.00 0.00 2.57
1258 1291 5.582689 AAGAAGGACAAAAACACCAGAAG 57.417 39.130 0.00 0.00 0.00 2.85
1386 1422 2.806244 ACTTGGACAAACGTCTGCATAC 59.194 45.455 0.00 0.00 33.65 2.39
1392 1430 5.591067 TCCATTAAAACTTGGACAAACGTCT 59.409 36.000 0.00 0.00 37.10 4.18
1411 1449 8.732531 CACCATTTTCATAAAAAGCAATCCATT 58.267 29.630 0.00 0.00 37.76 3.16
1500 1538 4.260784 GCGATCGAATGAAGGCAAAGTAAT 60.261 41.667 21.57 0.00 0.00 1.89
1536 1574 4.872691 CACTTCATGTACAATCCTGTCTCC 59.127 45.833 0.00 0.00 36.96 3.71
1632 1682 5.525012 TGCTGTTATATGAGTTCATCACTGC 59.475 40.000 15.95 15.95 41.91 4.40
1653 1703 3.234353 TCCGTGGAATGATCTAGATGCT 58.766 45.455 10.74 0.00 0.00 3.79
1713 1763 3.431415 GGAGAACAAACAGGGGCTAAAT 58.569 45.455 0.00 0.00 0.00 1.40
1786 1836 9.492973 GGGTACTGTATCTTTTAGTTACAACAA 57.507 33.333 0.00 0.00 32.03 2.83
1787 1837 8.096414 GGGGTACTGTATCTTTTAGTTACAACA 58.904 37.037 0.00 0.00 32.03 3.33
1788 1838 8.096414 TGGGGTACTGTATCTTTTAGTTACAAC 58.904 37.037 0.00 0.00 32.03 3.32
1816 1866 6.915544 TCATGCTAGTGAACATCAAAGATC 57.084 37.500 0.00 0.00 0.00 2.75
1972 2022 6.233434 AGTCTGAAACATGCTGATAGACAAA 58.767 36.000 15.52 0.00 36.45 2.83
2023 2073 6.295688 GCATAGGCCTAAACTAGCTGGTATTA 60.296 42.308 18.42 4.20 0.00 0.98
2246 2300 5.168526 TCTGTATGCGTTTTCCATATTGC 57.831 39.130 0.00 0.00 0.00 3.56
2283 2337 2.545106 GGTTTGCAGCTGTTTGAATTGG 59.455 45.455 16.64 0.00 0.00 3.16
2404 2458 9.314321 ACCGATTCTACAACATATACTTTTCAG 57.686 33.333 0.00 0.00 0.00 3.02
2479 2533 5.910614 AGGATTCAAATTATCCAAAGCTGC 58.089 37.500 8.18 0.00 43.33 5.25
2614 2668 0.310854 GTAACAGTGTTGCAGCCACC 59.689 55.000 18.90 0.00 33.20 4.61
2750 2804 4.212636 CCAAGTAACTGGTTTCCTACAACG 59.787 45.833 0.00 0.00 0.00 4.10
2759 2813 4.497291 TCAGTGTCCAAGTAACTGGTTT 57.503 40.909 2.50 0.00 41.34 3.27
2770 2825 4.038642 GGCCAACTATTTTTCAGTGTCCAA 59.961 41.667 0.00 0.00 0.00 3.53
2830 2885 5.796846 TGGAAACAAGTAACAGCGAAGAGC 61.797 45.833 0.00 0.00 42.27 4.09
2831 2886 3.807622 TGGAAACAAGTAACAGCGAAGAG 59.192 43.478 0.00 0.00 37.44 2.85
2832 2887 3.799366 TGGAAACAAGTAACAGCGAAGA 58.201 40.909 0.00 0.00 37.44 2.87
2833 2888 3.560068 ACTGGAAACAAGTAACAGCGAAG 59.440 43.478 0.00 0.00 42.06 3.79
2834 2889 3.311322 CACTGGAAACAAGTAACAGCGAA 59.689 43.478 0.00 0.00 42.06 4.70
2835 2890 2.869801 CACTGGAAACAAGTAACAGCGA 59.130 45.455 0.00 0.00 42.06 4.93
2836 2891 2.602217 GCACTGGAAACAAGTAACAGCG 60.602 50.000 0.00 0.00 42.06 5.18
2837 2892 2.357637 TGCACTGGAAACAAGTAACAGC 59.642 45.455 0.00 0.00 42.06 4.40
2860 2915 6.969993 TTTTAAGATACAGTGGCAAAAGGT 57.030 33.333 0.00 0.00 0.00 3.50
3030 3086 4.650734 TCAGCATGACCAACTGAAACATA 58.349 39.130 0.00 0.00 42.56 2.29
3094 3150 3.003378 GGTACTGGCTTCACTTGTTCAAC 59.997 47.826 0.00 0.00 0.00 3.18
3306 3362 1.667724 GTCACTGAAATCCTGGCATCG 59.332 52.381 0.00 0.00 0.00 3.84
3641 3700 1.463674 AATGCTAAACGGGGCAAGAG 58.536 50.000 0.00 0.00 41.90 2.85
3844 3905 2.936202 AGCACAGGTCAAGTGTCATTT 58.064 42.857 0.00 0.00 39.17 2.32
4616 4680 4.083820 CACGTTGAACAATGACATCATCG 58.916 43.478 12.75 13.01 40.35 3.84
4712 4776 3.751518 GAGAAGGTTTCTTAGTTGGCCA 58.248 45.455 0.00 0.00 40.87 5.36
5131 5199 7.454380 AGAGGATATACAAGATTCTGGAAGGAG 59.546 40.741 0.00 0.00 0.00 3.69
5822 5904 2.286184 CCGACAAGTTTCTGACAAACCG 60.286 50.000 0.00 0.00 0.00 4.44
5892 5974 2.032030 CCGTGACGCAAGAAAATGAACT 60.032 45.455 0.00 0.00 43.62 3.01
6081 6164 4.027572 TGTAAATATTTCGGCAGCAAGC 57.972 40.909 3.39 0.00 44.65 4.01
6120 6203 4.562767 TGGCACTTCTATTATCCCTACCA 58.437 43.478 0.00 0.00 0.00 3.25
6130 6213 8.579850 TTTCAAATACTGATGGCACTTCTATT 57.420 30.769 0.00 0.00 32.78 1.73
6161 6244 2.674177 CGTCCACCAGATCACCAACTAC 60.674 54.545 0.00 0.00 0.00 2.73
6166 6249 1.118965 ACACGTCCACCAGATCACCA 61.119 55.000 0.00 0.00 0.00 4.17
6182 6665 2.680913 GCACATGGCCACGAGACAC 61.681 63.158 8.16 0.00 36.11 3.67
6184 6667 2.358615 TGCACATGGCCACGAGAC 60.359 61.111 8.16 0.00 43.89 3.36
6194 6677 2.424705 AAAACGGCTGGCTGCACATG 62.425 55.000 18.32 7.08 45.15 3.21
6195 6678 2.146073 GAAAACGGCTGGCTGCACAT 62.146 55.000 18.32 0.00 45.15 3.21
6218 6701 7.325694 CGATGGTCTCCCTTTAAAAAGTACTA 58.674 38.462 0.00 0.00 34.20 1.82
6219 6702 6.171213 CGATGGTCTCCCTTTAAAAAGTACT 58.829 40.000 0.00 0.00 34.20 2.73
6220 6703 5.163784 GCGATGGTCTCCCTTTAAAAAGTAC 60.164 44.000 2.03 0.00 34.20 2.73
6221 6704 4.939439 GCGATGGTCTCCCTTTAAAAAGTA 59.061 41.667 2.03 0.00 34.20 2.24
6222 6705 3.756963 GCGATGGTCTCCCTTTAAAAAGT 59.243 43.478 2.03 0.00 34.20 2.66
6232 6715 3.622514 AGACAGCGATGGTCTCCC 58.377 61.111 5.32 0.00 41.63 4.30
6238 6721 1.329906 GCTTTCATGAGACAGCGATGG 59.670 52.381 5.32 0.00 37.77 3.51
6294 6777 0.390209 CTTGAAAATGCCCTTGCCGG 60.390 55.000 0.00 0.00 36.33 6.13
6295 6778 0.602562 TCTTGAAAATGCCCTTGCCG 59.397 50.000 0.00 0.00 36.33 5.69
6296 6779 1.669795 CGTCTTGAAAATGCCCTTGCC 60.670 52.381 0.00 0.00 36.33 4.52
6297 6780 1.669795 CCGTCTTGAAAATGCCCTTGC 60.670 52.381 0.00 0.00 38.26 4.01
6298 6781 1.885887 TCCGTCTTGAAAATGCCCTTG 59.114 47.619 0.00 0.00 0.00 3.61
6299 6782 2.286365 TCCGTCTTGAAAATGCCCTT 57.714 45.000 0.00 0.00 0.00 3.95
6300 6783 2.514458 ATCCGTCTTGAAAATGCCCT 57.486 45.000 0.00 0.00 0.00 5.19
6301 6784 2.477863 CGAATCCGTCTTGAAAATGCCC 60.478 50.000 0.00 0.00 0.00 5.36
6302 6785 2.785679 CGAATCCGTCTTGAAAATGCC 58.214 47.619 0.00 0.00 0.00 4.40
6315 6798 5.035443 CCTTGTCTCTAGTTTACGAATCCG 58.965 45.833 0.00 0.00 42.50 4.18
6316 6799 6.127675 ACTCCTTGTCTCTAGTTTACGAATCC 60.128 42.308 0.00 0.00 0.00 3.01
6317 6800 6.854778 ACTCCTTGTCTCTAGTTTACGAATC 58.145 40.000 0.00 0.00 0.00 2.52
6318 6801 6.837471 ACTCCTTGTCTCTAGTTTACGAAT 57.163 37.500 0.00 0.00 0.00 3.34
6319 6802 6.645790 AACTCCTTGTCTCTAGTTTACGAA 57.354 37.500 0.00 0.00 0.00 3.85
6320 6803 6.645790 AAACTCCTTGTCTCTAGTTTACGA 57.354 37.500 0.00 0.00 39.67 3.43
6321 6804 6.700520 ACAAAACTCCTTGTCTCTAGTTTACG 59.299 38.462 0.00 0.00 40.35 3.18
6322 6805 7.709613 TCACAAAACTCCTTGTCTCTAGTTTAC 59.290 37.037 0.00 0.00 40.35 2.01
6323 6806 7.788026 TCACAAAACTCCTTGTCTCTAGTTTA 58.212 34.615 0.00 0.00 40.35 2.01
6324 6807 6.650120 TCACAAAACTCCTTGTCTCTAGTTT 58.350 36.000 0.00 0.00 42.40 2.66
6325 6808 6.098409 TCTCACAAAACTCCTTGTCTCTAGTT 59.902 38.462 0.00 0.00 37.43 2.24
6326 6809 5.598830 TCTCACAAAACTCCTTGTCTCTAGT 59.401 40.000 0.00 0.00 37.43 2.57
6327 6810 6.090483 TCTCACAAAACTCCTTGTCTCTAG 57.910 41.667 0.00 0.00 37.43 2.43
6328 6811 5.598830 ACTCTCACAAAACTCCTTGTCTCTA 59.401 40.000 0.00 0.00 37.43 2.43
6329 6812 4.407296 ACTCTCACAAAACTCCTTGTCTCT 59.593 41.667 0.00 0.00 37.43 3.10
6330 6813 4.698575 ACTCTCACAAAACTCCTTGTCTC 58.301 43.478 0.00 0.00 37.43 3.36
6331 6814 4.443598 GGACTCTCACAAAACTCCTTGTCT 60.444 45.833 0.00 0.00 37.43 3.41
6332 6815 3.810386 GGACTCTCACAAAACTCCTTGTC 59.190 47.826 0.00 0.00 37.43 3.18
6333 6816 3.741388 CGGACTCTCACAAAACTCCTTGT 60.741 47.826 0.00 0.00 40.17 3.16
6334 6817 2.802816 CGGACTCTCACAAAACTCCTTG 59.197 50.000 0.00 0.00 0.00 3.61
6335 6818 2.224305 CCGGACTCTCACAAAACTCCTT 60.224 50.000 0.00 0.00 0.00 3.36
6336 6819 1.344763 CCGGACTCTCACAAAACTCCT 59.655 52.381 0.00 0.00 0.00 3.69
6337 6820 1.797025 CCGGACTCTCACAAAACTCC 58.203 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.