Multiple sequence alignment - TraesCS3A01G344400

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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 TraesCS3A01G344400 chr3A 100.000 4700 0 0 1 4700 594003889 593999190 0.000000e+00 8680
1 TraesCS3A01G344400 chr3B 93.101 2783 114 22 1 2729 592613450 592610692 0.000000e+00 4004
2 TraesCS3A01G344400 chr3B 95.376 1276 44 10 2920 4188 592610284 592609017 0.000000e+00 2015
3 TraesCS3A01G344400 chr3B 91.971 411 15 6 4281 4691 592608883 592608491 1.140000e-155 560
4 TraesCS3A01G344400 chr3B 98.101 158 2 1 2768 2925 592610478 592610322 1.670000e-69 274
5 TraesCS3A01G344400 chr3D 94.118 1938 72 12 260 2175 450482378 450480461 0.000000e+00 2909
6 TraesCS3A01G344400 chr3D 97.349 1358 31 3 2920 4277 450479215 450477863 0.000000e+00 2303
7 TraesCS3A01G344400 chr3D 94.875 761 19 5 2178 2925 450480035 450479282 0.000000e+00 1171
8 TraesCS3A01G344400 chr3D 91.529 425 32 2 4276 4700 450477780 450477360 2.440000e-162 582
9 TraesCS3A01G344400 chr3D 92.760 221 16 0 1 221 450483170 450482950 2.110000e-83 320


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 TraesCS3A01G344400 chr3A 593999190 594003889 4699 True 8680.00 8680 100.00000 1 4700 1 chr3A.!!$R1 4699
1 TraesCS3A01G344400 chr3B 592608491 592613450 4959 True 1713.25 4004 94.63725 1 4691 4 chr3B.!!$R1 4690
2 TraesCS3A01G344400 chr3D 450477360 450483170 5810 True 1457.00 2909 94.12620 1 4700 5 chr3D.!!$R1 4699

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
200 201 0.032267 CGGAGGCTTAGGATTCGTCC 59.968 60.0 0.00 0.00 0.00 4.79 F
630 1176 0.324943 TCTTTGGTCCTAGCTGGTGC 59.675 55.0 0.00 0.00 37.07 5.01 F
1134 1695 0.461516 ATGTGCCATCTCTGCAGTCG 60.462 55.0 14.67 6.52 39.87 4.18 F
2344 3339 0.330941 TTGCCACCTACATGCCATGA 59.669 50.0 12.53 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1881 0.389817 GGGGCAGCGGATTTGAAAAC 60.390 55.0 0.0 0.0 0.00 2.43 R
1907 2477 0.548510 ATTTCTACAGGGGGCAGAGC 59.451 55.0 0.0 0.0 0.00 4.09 R
2849 4019 0.947244 CATATCCCGACAGCTTTGCC 59.053 55.0 0.0 0.0 0.00 4.52 R
4134 5426 0.031994 AGGTCAACAATTGCAACGGC 59.968 50.0 0.0 0.0 41.68 5.68 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
52 53 0.884514 GCTTCTTCAGCCCCTTGTTC 59.115 55.000 0.00 0.00 43.65 3.18
55 56 2.282180 TTCAGCCCCTTGTTCGCC 60.282 61.111 0.00 0.00 0.00 5.54
63 64 1.234615 CCCTTGTTCGCCGTTCATGT 61.235 55.000 0.00 0.00 0.00 3.21
98 99 2.866726 GCTCGGCCTGGATCTCTCC 61.867 68.421 0.00 0.00 42.45 3.71
198 199 0.745468 GACGGAGGCTTAGGATTCGT 59.255 55.000 0.00 0.00 0.00 3.85
200 201 0.032267 CGGAGGCTTAGGATTCGTCC 59.968 60.000 0.00 0.00 0.00 4.79
230 252 3.820467 TGATTCTTGAGCGTTTTGGTGAT 59.180 39.130 0.00 0.00 0.00 3.06
235 257 1.304134 AGCGTTTTGGTGATCCCCC 60.304 57.895 0.00 0.00 0.00 5.40
252 274 0.897621 CCCCTTGGTGATTTTCAGCC 59.102 55.000 4.43 0.00 43.72 4.85
355 895 2.492010 GGGTTTGGTGGGGTCAATTACT 60.492 50.000 0.00 0.00 0.00 2.24
356 896 3.236047 GGTTTGGTGGGGTCAATTACTT 58.764 45.455 0.00 0.00 0.00 2.24
364 904 4.941873 GTGGGGTCAATTACTTAGTTGAGG 59.058 45.833 0.00 0.00 33.46 3.86
366 906 5.311121 TGGGGTCAATTACTTAGTTGAGGAA 59.689 40.000 0.00 0.00 33.46 3.36
486 1026 8.414778 GTGGCTTGATAGATAGTAGTTGTAGTT 58.585 37.037 0.00 0.00 0.00 2.24
488 1028 7.382759 GGCTTGATAGATAGTAGTTGTAGTTGC 59.617 40.741 0.00 0.00 0.00 4.17
489 1029 7.382759 GCTTGATAGATAGTAGTTGTAGTTGCC 59.617 40.741 0.00 0.00 0.00 4.52
608 1154 3.254024 AACCAGCCAGGCCACGTAG 62.254 63.158 8.22 0.00 43.14 3.51
610 1156 2.355986 CCAGCCAGGCCACGTAGTA 61.356 63.158 8.22 0.00 41.61 1.82
630 1176 0.324943 TCTTTGGTCCTAGCTGGTGC 59.675 55.000 0.00 0.00 37.07 5.01
761 1319 4.242475 TCAGTTCATAGGCGTTGTACTTG 58.758 43.478 0.00 0.00 0.00 3.16
852 1411 9.461312 TGTACTGGATTAATCTTTAAGCAACAT 57.539 29.630 14.95 0.00 0.00 2.71
853 1412 9.722056 GTACTGGATTAATCTTTAAGCAACATG 57.278 33.333 14.95 0.00 0.00 3.21
858 1417 8.416329 GGATTAATCTTTAAGCAACATGGATGT 58.584 33.333 14.95 0.00 44.20 3.06
941 1502 5.638234 CAGGACCAGTTACTTTTGCTACTAC 59.362 44.000 0.00 0.00 0.00 2.73
942 1503 5.543020 AGGACCAGTTACTTTTGCTACTACT 59.457 40.000 0.00 0.00 0.00 2.57
943 1504 6.723052 AGGACCAGTTACTTTTGCTACTACTA 59.277 38.462 0.00 0.00 0.00 1.82
1126 1687 1.307097 GGAAGCTCATGTGCCATCTC 58.693 55.000 15.81 7.89 0.00 2.75
1134 1695 0.461516 ATGTGCCATCTCTGCAGTCG 60.462 55.000 14.67 6.52 39.87 4.18
1233 1794 2.042404 CTGCTCCCTCCAGCCTGATC 62.042 65.000 0.00 0.00 38.80 2.92
1269 1830 0.586802 GCCTTCCGTATGCCGAATTC 59.413 55.000 0.00 0.00 39.56 2.17
1285 1846 3.677121 CGAATTCGATGATCAGGATGACC 59.323 47.826 23.29 0.00 46.45 4.02
1320 1881 1.071605 GAGCTATTAAGGCGCATCGG 58.928 55.000 10.83 0.00 34.52 4.18
1332 1893 1.534028 CGCATCGGTTTTCAAATCCG 58.466 50.000 12.69 12.69 44.76 4.18
1548 2109 2.726760 CTCGGAAACTCAGACTTTGACG 59.273 50.000 0.00 0.00 0.00 4.35
1554 2115 5.869888 GGAAACTCAGACTTTGACGTCATAT 59.130 40.000 20.80 7.80 36.38 1.78
1599 2160 5.514274 TTGTTGAACCAAAGAAGATGGAC 57.486 39.130 0.00 0.00 40.56 4.02
1814 2384 7.031415 TGCCTATCCACCATGAATGTATTAT 57.969 36.000 0.00 0.00 0.00 1.28
1889 2459 4.034510 GCTGTTTACATCTAGGCATGTGAC 59.965 45.833 7.21 6.63 37.57 3.67
1907 2477 4.818005 TGTGACCTATGCTTATTGATGCAG 59.182 41.667 0.00 0.00 42.74 4.41
1970 2540 8.129211 GCAAATACAACTTAGGACCATAACATC 58.871 37.037 0.00 0.00 0.00 3.06
1971 2541 8.335356 CAAATACAACTTAGGACCATAACATCG 58.665 37.037 0.00 0.00 0.00 3.84
1972 2542 4.766375 ACAACTTAGGACCATAACATCGG 58.234 43.478 0.00 0.00 0.00 4.18
1973 2543 4.224370 ACAACTTAGGACCATAACATCGGT 59.776 41.667 0.00 0.00 38.56 4.69
1974 2544 4.402056 ACTTAGGACCATAACATCGGTG 57.598 45.455 0.00 0.00 34.99 4.94
1975 2545 3.134081 ACTTAGGACCATAACATCGGTGG 59.866 47.826 0.00 0.00 34.99 4.61
1976 2546 0.837272 AGGACCATAACATCGGTGGG 59.163 55.000 0.00 0.00 37.33 4.61
1977 2547 0.544697 GGACCATAACATCGGTGGGT 59.455 55.000 0.00 0.00 37.33 4.51
1978 2548 1.064979 GGACCATAACATCGGTGGGTT 60.065 52.381 0.00 0.00 37.33 4.11
1979 2549 2.171027 GGACCATAACATCGGTGGGTTA 59.829 50.000 0.00 0.00 37.33 2.85
1980 2550 3.370739 GGACCATAACATCGGTGGGTTAA 60.371 47.826 0.00 0.00 37.33 2.01
1981 2551 3.875134 GACCATAACATCGGTGGGTTAAG 59.125 47.826 0.00 0.00 37.33 1.85
1982 2552 3.264964 ACCATAACATCGGTGGGTTAAGT 59.735 43.478 0.00 0.00 37.33 2.24
1987 2557 2.504175 ACATCGGTGGGTTAAGTAGCAT 59.496 45.455 0.00 0.00 0.00 3.79
1998 2568 4.700213 GGTTAAGTAGCATGCTTTGAAGGA 59.300 41.667 28.02 2.00 38.02 3.36
2001 2571 3.350833 AGTAGCATGCTTTGAAGGAAGG 58.649 45.455 28.02 0.00 0.00 3.46
2002 2572 2.592102 AGCATGCTTTGAAGGAAGGA 57.408 45.000 16.30 0.00 0.00 3.36
2015 2585 6.331369 TGAAGGAAGGAAATGTGTTTGATC 57.669 37.500 0.00 0.00 0.00 2.92
2090 2660 4.022849 GGCTTTATCACTTGTGAGCTGTTT 60.023 41.667 9.39 0.00 0.00 2.83
2150 2720 2.660236 GCTTTCTCTTGCAAGCGATTTG 59.340 45.455 21.99 13.81 36.33 2.32
2295 3288 8.840200 AGATTGTTGGTTAGACCTTCTAGATA 57.160 34.615 0.00 0.00 39.58 1.98
2302 3296 7.363031 TGGTTAGACCTTCTAGATAACTGGAT 58.637 38.462 11.21 1.33 39.58 3.41
2324 3318 7.829211 TGGATACCTTTCACCATTTTAGAGAAG 59.171 37.037 0.00 0.00 0.00 2.85
2336 3331 4.967084 TTTAGAGAAGTTGCCACCTACA 57.033 40.909 0.00 0.00 0.00 2.74
2344 3339 0.330941 TTGCCACCTACATGCCATGA 59.669 50.000 12.53 0.00 0.00 3.07
2365 3360 7.225538 CCATGACTACTATGTTTCTTGGATCAC 59.774 40.741 0.00 0.00 36.04 3.06
2367 3362 6.440647 TGACTACTATGTTTCTTGGATCACCT 59.559 38.462 0.00 0.00 37.04 4.00
2452 3447 6.183360 TGCAGAGTTTCAAAGAATTTAAGGCA 60.183 34.615 0.00 0.00 35.03 4.75
2545 3540 8.599624 ATGAATCTAATGAAAGGATGTTGGTT 57.400 30.769 0.00 0.00 0.00 3.67
2734 3742 3.758554 ACATGACCAAGAAGTTACCATGC 59.241 43.478 0.00 0.00 34.84 4.06
2753 3761 2.099592 TGCTCTCTTGCACTTTGTTTGG 59.900 45.455 0.00 0.00 38.12 3.28
2756 3764 4.555511 GCTCTCTTGCACTTTGTTTGGTAG 60.556 45.833 0.00 0.00 0.00 3.18
2849 4019 7.978982 ACATCCAAATAGAGAAAGATTTCACG 58.021 34.615 7.97 0.00 39.61 4.35
3213 4496 2.401017 GTTCCACCAAAGAAGAACGC 57.599 50.000 0.00 0.00 30.33 4.84
3231 4514 1.202290 CGCAATATTGTCAAGTGGGGC 60.202 52.381 16.61 0.00 0.00 5.80
3333 4616 1.209019 AGGACTGTGGCAGACATCATC 59.791 52.381 2.91 0.00 35.18 2.92
3552 4835 3.121030 CCTCCTTCGCGCAACCAG 61.121 66.667 8.75 0.00 0.00 4.00
3586 4869 1.265462 GAGATCATCGACGTCTGCGC 61.265 60.000 14.70 0.00 42.83 6.09
3588 4871 1.535636 GATCATCGACGTCTGCGCTG 61.536 60.000 14.70 8.88 42.83 5.18
3614 4897 1.528129 CCAAGGAACTGCTCTTCCAC 58.472 55.000 13.52 0.00 42.16 4.02
3792 5075 6.379703 AGTGATCTCAGTGCTATGGGATATAC 59.620 42.308 4.35 7.05 40.57 1.47
3793 5076 6.379703 GTGATCTCAGTGCTATGGGATATACT 59.620 42.308 4.35 0.00 40.57 2.12
3794 5077 7.558081 GTGATCTCAGTGCTATGGGATATACTA 59.442 40.741 4.35 0.00 40.57 1.82
3830 5113 1.956477 TGAAAAAGGGCAGAGTGAAGC 59.044 47.619 0.00 0.00 0.00 3.86
3879 5162 4.248859 ACTTGTCGTTCTCTGATTGGATG 58.751 43.478 0.00 0.00 0.00 3.51
3992 5278 5.036737 CGTCAAACATTTCAGCTGTTTCTT 58.963 37.500 14.67 0.00 43.15 2.52
3993 5279 5.516339 CGTCAAACATTTCAGCTGTTTCTTT 59.484 36.000 14.67 3.74 43.15 2.52
3994 5280 6.291269 CGTCAAACATTTCAGCTGTTTCTTTC 60.291 38.462 14.67 0.00 43.15 2.62
3995 5281 6.753744 GTCAAACATTTCAGCTGTTTCTTTCT 59.246 34.615 14.67 0.00 43.15 2.52
4131 5423 5.964958 TTCCTTTCTGTGGAATGTTGATC 57.035 39.130 0.00 0.00 38.53 2.92
4134 5426 4.093998 CCTTTCTGTGGAATGTTGATCTCG 59.906 45.833 0.00 0.00 0.00 4.04
4153 5445 0.031994 GCCGTTGCAATTGTTGACCT 59.968 50.000 0.59 0.00 37.47 3.85
4238 5530 2.812011 GCGTTTTGTAGATTGGACTGGT 59.188 45.455 0.00 0.00 0.00 4.00
4262 5554 8.182227 GGTACAGTAATAAAATGCCAAGAAGAC 58.818 37.037 0.00 0.00 0.00 3.01
4300 5676 5.532032 ACAAAAGCCTTGGAATTCCATTTTG 59.468 36.000 35.60 35.60 46.83 2.44
4312 5689 8.838365 TGGAATTCCATTTTGTTCATCTTTTTG 58.162 29.630 23.63 0.00 42.01 2.44
4353 5730 4.023963 TCTGACGTCTGAAACACTAGTGAG 60.024 45.833 29.30 15.60 0.00 3.51
4366 5743 4.941263 ACACTAGTGAGCTGTTTTGTTCAA 59.059 37.500 29.30 0.00 0.00 2.69
4368 5745 5.065218 CACTAGTGAGCTGTTTTGTTCAACT 59.935 40.000 18.45 0.00 0.00 3.16
4395 5772 3.983044 ATGTTTCTTCTAGCGTTCCCT 57.017 42.857 0.00 0.00 0.00 4.20
4573 5950 0.731417 CTGCGGAAAGATGGCTTGAG 59.269 55.000 0.00 0.00 33.79 3.02
4595 5972 4.039124 AGTTTTCAACCCGAAATCTTGCAT 59.961 37.500 0.00 0.00 43.12 3.96
4624 6001 0.960861 GGGCTCACCTAAGTGCAACC 60.961 60.000 0.00 0.00 44.16 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.902063 CTCGCGACATGAACGGCG 61.902 66.667 3.71 4.80 34.08 6.46
55 56 1.702299 GGAACTCGCGACATGAACG 59.298 57.895 3.71 6.19 0.00 3.95
63 64 4.116328 CAGCTCCGGAACTCGCGA 62.116 66.667 9.26 9.26 37.59 5.87
198 199 2.640184 CTCAAGAATCAGCATGCAGGA 58.360 47.619 21.98 17.23 34.76 3.86
200 201 1.268083 CGCTCAAGAATCAGCATGCAG 60.268 52.381 21.98 12.90 35.15 4.41
235 257 1.067354 GCAGGCTGAAAATCACCAAGG 60.067 52.381 20.86 0.00 0.00 3.61
241 263 4.001248 CCGGCAGGCTGAAAATCA 57.999 55.556 20.86 0.00 0.00 2.57
281 815 3.737172 ATTTGACCAGCACGCGGC 61.737 61.111 12.47 11.61 45.30 6.53
333 873 0.565674 AATTGACCCCACCAAACCCT 59.434 50.000 0.00 0.00 0.00 4.34
355 895 7.833285 AAAATAAGCAACCTTCCTCAACTAA 57.167 32.000 0.00 0.00 32.47 2.24
356 896 7.120726 GCTAAAATAAGCAACCTTCCTCAACTA 59.879 37.037 0.00 0.00 42.30 2.24
364 904 5.416013 AGACCAGCTAAAATAAGCAACCTTC 59.584 40.000 0.00 0.00 45.30 3.46
366 906 4.923415 AGACCAGCTAAAATAAGCAACCT 58.077 39.130 0.00 0.00 45.30 3.50
411 951 1.127343 AGAGCCCTCACCTAATCTGC 58.873 55.000 0.00 0.00 0.00 4.26
532 1075 7.090953 TCCAAACACCGTCCATTATTAATTC 57.909 36.000 0.00 0.00 0.00 2.17
608 1154 3.798202 CACCAGCTAGGACCAAAGATAC 58.202 50.000 8.91 0.00 41.22 2.24
609 1155 2.170607 GCACCAGCTAGGACCAAAGATA 59.829 50.000 8.91 0.00 41.22 1.98
610 1156 1.065126 GCACCAGCTAGGACCAAAGAT 60.065 52.381 8.91 0.00 41.22 2.40
630 1176 0.398664 AGAACTGATCTACCCCCGGG 60.399 60.000 15.80 15.80 36.32 5.73
675 1221 2.754552 CTCCAAAAATCATTGCCGGAGA 59.245 45.455 5.05 0.00 0.00 3.71
761 1319 4.137543 ACCCAGCTATGATTTTTCCGATC 58.862 43.478 0.00 0.00 0.00 3.69
858 1417 3.290948 AGAAAAAGCTGTGGTGTACCA 57.709 42.857 0.00 0.00 45.30 3.25
942 1503 9.585369 TGAAATGGGTTGATGAATTAGCATATA 57.415 29.630 0.00 0.00 0.00 0.86
943 1504 8.481492 TGAAATGGGTTGATGAATTAGCATAT 57.519 30.769 0.00 0.00 0.00 1.78
962 1523 4.451629 AGCTCCTGCAGAATTTGAAATG 57.548 40.909 17.39 0.00 42.74 2.32
1053 1614 1.804326 GCCATGCTTCTTGCTTGCG 60.804 57.895 0.00 0.00 43.09 4.85
1134 1695 1.153349 CCTGAAACTAGGAGGCGCC 60.153 63.158 21.89 21.89 40.42 6.53
1285 1846 1.768077 CTCCTCCCTTGCCCCTAGG 60.768 68.421 0.06 0.06 0.00 3.02
1291 1852 2.224646 CCTTAATAGCTCCTCCCTTGCC 60.225 54.545 0.00 0.00 0.00 4.52
1320 1881 0.389817 GGGGCAGCGGATTTGAAAAC 60.390 55.000 0.00 0.00 0.00 2.43
1332 1893 2.273776 GGAAGAGGAAGGGGCAGC 59.726 66.667 0.00 0.00 0.00 5.25
1455 2016 2.860735 CGAGAAGTTCTTAAGCCCATCG 59.139 50.000 6.88 0.00 0.00 3.84
1548 2109 3.997021 CCCTGAACGATGCCTTATATGAC 59.003 47.826 0.00 0.00 0.00 3.06
1554 2115 2.115427 TCATCCCTGAACGATGCCTTA 58.885 47.619 0.00 0.00 37.60 2.69
1731 2300 2.969950 AGTAGGTGTGCCAGAAAGTGTA 59.030 45.455 0.00 0.00 37.19 2.90
1782 2352 5.022122 TCATGGTGGATAGGCAAATTTCAA 58.978 37.500 0.00 0.00 0.00 2.69
1783 2353 4.608269 TCATGGTGGATAGGCAAATTTCA 58.392 39.130 0.00 0.00 0.00 2.69
1814 2384 6.540551 TGTAAACAGAACAGATACTGCAAACA 59.459 34.615 0.00 0.00 37.61 2.83
1889 2459 4.154375 CAGAGCTGCATCAATAAGCATAGG 59.846 45.833 1.02 0.00 40.42 2.57
1907 2477 0.548510 ATTTCTACAGGGGGCAGAGC 59.451 55.000 0.00 0.00 0.00 4.09
1970 2540 1.014352 GCATGCTACTTAACCCACCG 58.986 55.000 11.37 0.00 0.00 4.94
1971 2541 2.420058 AGCATGCTACTTAACCCACC 57.580 50.000 21.21 0.00 0.00 4.61
1972 2542 3.756434 TCAAAGCATGCTACTTAACCCAC 59.244 43.478 23.00 0.00 0.00 4.61
1973 2543 4.027674 TCAAAGCATGCTACTTAACCCA 57.972 40.909 23.00 0.00 0.00 4.51
1974 2544 4.142381 CCTTCAAAGCATGCTACTTAACCC 60.142 45.833 23.00 0.00 0.00 4.11
1975 2545 4.700213 TCCTTCAAAGCATGCTACTTAACC 59.300 41.667 23.00 0.00 0.00 2.85
1976 2546 5.880054 TCCTTCAAAGCATGCTACTTAAC 57.120 39.130 23.00 0.00 0.00 2.01
1977 2547 5.415701 CCTTCCTTCAAAGCATGCTACTTAA 59.584 40.000 23.00 12.02 0.00 1.85
1978 2548 4.943705 CCTTCCTTCAAAGCATGCTACTTA 59.056 41.667 23.00 6.48 0.00 2.24
1979 2549 3.760684 CCTTCCTTCAAAGCATGCTACTT 59.239 43.478 23.00 10.03 0.00 2.24
1980 2550 3.009473 TCCTTCCTTCAAAGCATGCTACT 59.991 43.478 23.00 8.68 0.00 2.57
1981 2551 3.347216 TCCTTCCTTCAAAGCATGCTAC 58.653 45.455 23.00 0.00 0.00 3.58
1982 2552 3.719268 TCCTTCCTTCAAAGCATGCTA 57.281 42.857 23.00 1.69 0.00 3.49
1987 2557 3.960102 ACACATTTCCTTCCTTCAAAGCA 59.040 39.130 0.00 0.00 0.00 3.91
1998 2568 4.398319 AGGACGATCAAACACATTTCCTT 58.602 39.130 0.00 0.00 0.00 3.36
2001 2571 5.108385 ACAAGGACGATCAAACACATTTC 57.892 39.130 0.00 0.00 0.00 2.17
2002 2572 5.299279 AGAACAAGGACGATCAAACACATTT 59.701 36.000 0.00 0.00 0.00 2.32
2015 2585 5.060662 TCATAGTGAAGAGAACAAGGACG 57.939 43.478 0.00 0.00 0.00 4.79
2090 2660 5.221224 CCCAAAAGAACATTGCTAGTGAACA 60.221 40.000 0.00 0.00 0.00 3.18
2254 3247 8.211629 ACCAACAATCTCAGACTACTAGTTTTT 58.788 33.333 0.00 0.00 0.00 1.94
2295 3288 7.466804 TCTAAAATGGTGAAAGGTATCCAGTT 58.533 34.615 0.00 0.00 39.39 3.16
2302 3296 7.040686 GCAACTTCTCTAAAATGGTGAAAGGTA 60.041 37.037 0.00 0.00 0.00 3.08
2336 3331 5.824624 CCAAGAAACATAGTAGTCATGGCAT 59.175 40.000 0.00 0.00 0.00 4.40
2344 3339 6.875972 AGGTGATCCAAGAAACATAGTAGT 57.124 37.500 0.00 0.00 35.89 2.73
2452 3447 5.001232 AGTGATGCCAACGTATTTACTTGT 58.999 37.500 0.00 0.00 0.00 3.16
2545 3540 1.271001 CCATGATGGAGCCGCTCATAA 60.271 52.381 21.76 7.36 40.96 1.90
2734 3742 4.576463 ACTACCAAACAAAGTGCAAGAGAG 59.424 41.667 0.00 0.00 0.00 3.20
2849 4019 0.947244 CATATCCCGACAGCTTTGCC 59.053 55.000 0.00 0.00 0.00 4.52
3213 4496 2.428171 CCTGCCCCACTTGACAATATTG 59.572 50.000 14.01 14.01 0.00 1.90
3258 4541 2.776536 GGGATCCATGATGAGGGATAGG 59.223 54.545 15.23 0.00 43.00 2.57
3552 4835 2.172483 ATCTCGGTGACACCAGGTGC 62.172 60.000 24.18 12.81 38.47 5.01
3614 4897 1.345715 GGGGTAGTCCAGGGTGATGG 61.346 65.000 0.00 0.00 42.11 3.51
3792 5075 5.375417 TTTCACATGTCCTTGCAACATAG 57.625 39.130 0.00 0.00 35.62 2.23
3793 5076 5.781210 TTTTCACATGTCCTTGCAACATA 57.219 34.783 0.00 0.00 35.62 2.29
3794 5077 4.669206 TTTTCACATGTCCTTGCAACAT 57.331 36.364 0.00 0.00 37.85 2.71
3830 5113 5.502153 ACAAGCTGGTTCTACTATCTACG 57.498 43.478 0.00 0.00 0.00 3.51
3879 5162 0.698818 ACACTTCTTCCATGACCCCC 59.301 55.000 0.00 0.00 0.00 5.40
3992 5278 8.225603 ACAAAACTTAGCATTCAAGAGAAGAA 57.774 30.769 0.00 0.00 37.14 2.52
3993 5279 7.807977 ACAAAACTTAGCATTCAAGAGAAGA 57.192 32.000 0.00 0.00 37.14 2.87
3994 5280 7.096312 GCAACAAAACTTAGCATTCAAGAGAAG 60.096 37.037 0.00 0.00 37.14 2.85
3995 5281 6.697019 GCAACAAAACTTAGCATTCAAGAGAA 59.303 34.615 0.00 0.00 38.31 2.87
4131 5423 0.040514 TCAACAATTGCAACGGCGAG 60.041 50.000 16.62 6.85 45.35 5.03
4134 5426 0.031994 AGGTCAACAATTGCAACGGC 59.968 50.000 0.00 0.00 41.68 5.68
4153 5445 2.656947 AAAGCAAGTAGGCTGGTCAA 57.343 45.000 0.00 0.00 45.07 3.18
4187 5479 4.454678 TCACCCTAATCAAGCACATCATC 58.545 43.478 0.00 0.00 0.00 2.92
4238 5530 7.604927 ACGTCTTCTTGGCATTTTATTACTGTA 59.395 33.333 0.00 0.00 0.00 2.74
4248 5540 3.411446 TCATCACGTCTTCTTGGCATTT 58.589 40.909 0.00 0.00 0.00 2.32
4300 5676 3.049912 GACCGCCAACAAAAAGATGAAC 58.950 45.455 0.00 0.00 0.00 3.18
4312 5689 0.109919 GAAACATTCCGACCGCCAAC 60.110 55.000 0.00 0.00 0.00 3.77
4366 5743 5.125739 ACGCTAGAAGAAACATAGCTGTAGT 59.874 40.000 0.00 0.00 39.80 2.73
4368 5745 5.578005 ACGCTAGAAGAAACATAGCTGTA 57.422 39.130 0.00 0.00 39.80 2.74
4395 5772 6.403200 CGAACAGGAAACACAAGAGAAAGAAA 60.403 38.462 0.00 0.00 0.00 2.52
4441 5818 4.285517 AGGACTAATATCATCCACCAGCTG 59.714 45.833 6.78 6.78 34.73 4.24
4595 5972 1.568504 AGGTGAGCCCGATCAAACTA 58.431 50.000 0.00 0.00 38.74 2.24
4624 6001 4.318831 GCAAAAAGTAACACGACAGAGAGG 60.319 45.833 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.