Multiple sequence alignment - TraesCS3A01G345200

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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 TraesCS3A01G345200 chr3A 100.000 2977 0 0 1 2977 594666049 594669025 0.000000e+00 5498
1 TraesCS3A01G345200 chr3D 93.546 2324 116 18 678 2977 452416266 452418579 0.000000e+00 3430
2 TraesCS3A01G345200 chr3D 91.912 544 42 2 92 635 452414852 452415393 0.000000e+00 760
3 TraesCS3A01G345200 chr3D 92.708 96 7 0 1 96 452413204 452413299 4.000000e-29 139
4 TraesCS3A01G345200 chr3B 92.630 2266 110 33 740 2977 594409856 594412092 0.000000e+00 3206


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 TraesCS3A01G345200 chr3A 594666049 594669025 2976 False 5498 5498 100.000 1 2977 1 chr3A.!!$F1 2976
1 TraesCS3A01G345200 chr3D 452413204 452418579 5375 False 1443 3430 92.722 1 2977 3 chr3D.!!$F1 2976
2 TraesCS3A01G345200 chr3B 594409856 594412092 2236 False 3206 3206 92.630 740 2977 1 chr3B.!!$F1 2237

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
305 1863 0.248377 GATGATGGCGTGCTTGAAGC 60.248 55.0 10.84 10.84 42.82 3.86 F
1038 3433 0.250338 GCGGTGAAGGAGAACCAACT 60.250 55.0 0.00 0.00 36.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 3560 0.106708 CTGCTTTCGCATAGGCCCTA 59.893 55.0 0.0 0.0 46.74 3.53 R
2096 4518 0.108138 GGCCTCTGTTCGTGTGCTAT 60.108 55.0 0.0 0.0 0.00 2.97 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
27 28 1.993956 TGACCCATGTTGTCCCTTTG 58.006 50.000 9.41 0.00 31.60 2.77
35 36 3.006112 TGTTGTCCCTTTGCAACACTA 57.994 42.857 0.00 0.00 46.58 2.74
44 45 3.181507 CCTTTGCAACACTATCATCGGTG 60.182 47.826 0.00 0.00 39.13 4.94
45 46 2.760634 TGCAACACTATCATCGGTGT 57.239 45.000 0.00 0.00 46.84 4.16
49 50 3.797256 GCAACACTATCATCGGTGTAGTC 59.203 47.826 7.65 0.00 44.54 2.59
51 52 3.276857 ACACTATCATCGGTGTAGTCGT 58.723 45.455 7.65 7.39 43.66 4.34
53 54 2.543012 ACTATCATCGGTGTAGTCGTCG 59.457 50.000 0.00 0.00 0.00 5.12
101 102 2.594592 GCCTTTGCGACACCAGGT 60.595 61.111 0.00 0.00 0.00 4.00
102 103 2.617274 GCCTTTGCGACACCAGGTC 61.617 63.158 0.00 0.00 43.36 3.85
203 1761 4.052229 ACTTCGAGTGGCCCGACG 62.052 66.667 0.00 2.15 35.61 5.12
222 1780 2.664185 CCTGCCCGCATCATCTCG 60.664 66.667 0.00 0.00 0.00 4.04
227 1785 2.721859 CCGCATCATCTCGACCGA 59.278 61.111 0.00 0.00 0.00 4.69
237 1795 3.376914 CTCGACCGACGCGTGATCA 62.377 63.158 20.70 0.00 42.26 2.92
245 1803 1.664302 CGACGCGTGATCATAGCTGAT 60.664 52.381 20.70 8.57 44.93 2.90
305 1863 0.248377 GATGATGGCGTGCTTGAAGC 60.248 55.000 10.84 10.84 42.82 3.86
374 1932 2.287251 CGAGGGGGAAGGAGGGAT 59.713 66.667 0.00 0.00 0.00 3.85
393 1951 5.014202 GGGATGTTAGAGAGATAGGAGACC 58.986 50.000 0.00 0.00 0.00 3.85
411 1969 1.076350 ACCAGAGGATAGGGAGATCGG 59.924 57.143 0.00 0.00 0.00 4.18
422 1980 1.110518 GGAGATCGGGGGAGAGTCAC 61.111 65.000 0.00 0.00 0.00 3.67
423 1981 0.395862 GAGATCGGGGGAGAGTCACA 60.396 60.000 0.00 0.00 0.00 3.58
436 1994 1.668751 GAGTCACAACGTTCCAGCAAA 59.331 47.619 0.00 0.00 0.00 3.68
450 2008 1.135689 CAGCAAACGATAAGGTGCACC 60.136 52.381 29.22 29.22 37.43 5.01
464 2022 2.696759 GCACCACATACGGGCCAAC 61.697 63.158 4.39 0.00 0.00 3.77
499 2057 3.733960 GCCCGAGGCGGTTGAAAC 61.734 66.667 5.06 0.00 46.80 2.78
517 2075 0.800631 ACGAGCGTGTAATCAGTCGA 59.199 50.000 0.00 0.00 0.00 4.20
537 2095 3.865745 CGATAGAACAAAAGCGTCTCCAT 59.134 43.478 0.00 0.00 39.76 3.41
556 2114 7.795047 TCTCCATGAGACTAATGCTTTCAATA 58.205 34.615 0.00 0.00 33.35 1.90
560 2118 9.674824 CCATGAGACTAATGCTTTCAATAATTC 57.325 33.333 0.00 0.00 0.00 2.17
569 2127 6.330004 TGCTTTCAATAATTCTCAGCAACA 57.670 33.333 0.00 0.00 32.96 3.33
581 2139 5.902613 TCTCAGCAACATATTCAAAAGGG 57.097 39.130 0.00 0.00 0.00 3.95
612 2170 4.518278 AAAAACCCCAAAAGCCAATTCT 57.482 36.364 0.00 0.00 0.00 2.40
614 2172 2.397044 ACCCCAAAAGCCAATTCTCA 57.603 45.000 0.00 0.00 0.00 3.27
680 2987 7.677276 GCACACGAATAAAAGAAGCTGACATAT 60.677 37.037 0.00 0.00 0.00 1.78
683 2990 8.177663 CACGAATAAAAGAAGCTGACATATGTT 58.822 33.333 10.30 0.00 0.00 2.71
685 2992 8.607459 CGAATAAAAGAAGCTGACATATGTTCT 58.393 33.333 10.30 5.50 0.00 3.01
695 3082 6.815641 AGCTGACATATGTTCTCACTTAACAG 59.184 38.462 10.30 9.29 40.00 3.16
724 3111 9.358872 GCCTGAGTTTTAATTATTTTTCCTGAG 57.641 33.333 0.00 0.00 0.00 3.35
853 3247 1.513158 CAACGCCGTCCTCTCATCT 59.487 57.895 0.00 0.00 0.00 2.90
1038 3433 0.250338 GCGGTGAAGGAGAACCAACT 60.250 55.000 0.00 0.00 36.14 3.16
1137 3534 1.035932 CATGCCCTCCTTCAAGCCAG 61.036 60.000 0.00 0.00 0.00 4.85
1163 3560 1.484240 GCCAGTCCTGCTAGATCAGTT 59.516 52.381 0.00 0.00 32.32 3.16
1347 3744 2.572104 AGGATGACAAGGGAACAGGTAC 59.428 50.000 0.00 0.00 0.00 3.34
1349 3746 3.054361 GGATGACAAGGGAACAGGTACAT 60.054 47.826 0.00 0.00 0.00 2.29
1353 3750 6.877668 TGACAAGGGAACAGGTACATATAA 57.122 37.500 0.00 0.00 0.00 0.98
1354 3751 7.446106 TGACAAGGGAACAGGTACATATAAT 57.554 36.000 0.00 0.00 0.00 1.28
1355 3752 7.506114 TGACAAGGGAACAGGTACATATAATC 58.494 38.462 0.00 0.00 0.00 1.75
1356 3753 6.522054 ACAAGGGAACAGGTACATATAATCG 58.478 40.000 0.00 0.00 0.00 3.34
1357 3754 6.325545 ACAAGGGAACAGGTACATATAATCGA 59.674 38.462 0.00 0.00 0.00 3.59
1358 3755 7.016268 ACAAGGGAACAGGTACATATAATCGAT 59.984 37.037 0.00 0.00 0.00 3.59
1360 3757 6.724441 AGGGAACAGGTACATATAATCGATCA 59.276 38.462 0.00 0.00 0.00 2.92
1361 3758 6.812160 GGGAACAGGTACATATAATCGATCAC 59.188 42.308 0.00 0.00 0.00 3.06
1364 3761 9.256477 GAACAGGTACATATAATCGATCACAAA 57.744 33.333 0.00 0.00 0.00 2.83
1365 3762 9.607988 AACAGGTACATATAATCGATCACAAAA 57.392 29.630 0.00 0.00 0.00 2.44
1366 3763 9.778741 ACAGGTACATATAATCGATCACAAAAT 57.221 29.630 0.00 0.00 0.00 1.82
1370 3767 9.318041 GTACATATAATCGATCACAAAATGCAC 57.682 33.333 0.00 0.00 0.00 4.57
1386 3791 8.027771 ACAAAATGCACAACAATTTTGAACAAT 58.972 25.926 21.60 2.79 43.04 2.71
1388 3793 8.983307 AAATGCACAACAATTTTGAACAATTT 57.017 23.077 0.00 0.00 0.00 1.82
1427 3832 5.574443 GCAAGTTTTCCTTATGCTGATGAAC 59.426 40.000 0.00 0.00 0.00 3.18
1439 3844 2.227388 GCTGATGAACTTCTGGTTGGTG 59.773 50.000 0.00 0.00 38.41 4.17
1586 3992 6.672266 TTGTCTACTCTTGATTTCTCAGGT 57.328 37.500 0.00 0.00 31.68 4.00
1590 3996 7.094162 TGTCTACTCTTGATTTCTCAGGTAGTG 60.094 40.741 0.00 0.00 35.17 2.74
1602 4008 7.843490 TTCTCAGGTAGTGCAATATTTGTAC 57.157 36.000 0.00 0.88 45.13 2.90
1605 4011 5.878116 TCAGGTAGTGCAATATTTGTACACC 59.122 40.000 10.37 13.27 46.85 4.16
1617 4023 1.275666 TGTACACCACTGCTAGGCAT 58.724 50.000 0.00 0.00 38.13 4.40
1627 4033 4.023707 CCACTGCTAGGCATAATAAACTGC 60.024 45.833 0.00 0.00 38.13 4.40
1648 4054 5.563592 TGCCAGGATTAATATGACCTCATG 58.436 41.667 0.00 0.00 37.15 3.07
1774 4182 4.742438 TTCTGAAAATACAGTTGACGGC 57.258 40.909 0.00 0.00 38.79 5.68
1921 4329 6.146347 CGAAACCAACAAACTTCTTTTCCAAA 59.854 34.615 0.00 0.00 0.00 3.28
1955 4363 7.524912 CAGATGAACTTCTTTTGTACCATCAG 58.475 38.462 0.00 0.00 33.80 2.90
2057 4479 6.289834 TGTGAAATGGTTTTTGATGAGCATT 58.710 32.000 0.00 0.00 43.50 3.56
2078 4500 9.017509 AGCATTTATACACATTCCATTATCCAG 57.982 33.333 0.00 0.00 0.00 3.86
2091 4513 6.053005 TCCATTATCCAGTTTCGTTGGTATC 58.947 40.000 0.00 0.00 37.02 2.24
2096 4518 4.963373 TCCAGTTTCGTTGGTATCTCAAA 58.037 39.130 0.00 0.00 37.02 2.69
2104 4526 4.868171 TCGTTGGTATCTCAAATAGCACAC 59.132 41.667 0.00 0.28 32.52 3.82
2267 4689 4.889995 AGAAGCTTAACAGAAACTTTGGCT 59.110 37.500 0.00 0.00 0.00 4.75
2283 4705 7.425224 ACTTTGGCTGACAGACTTACTATAT 57.575 36.000 10.32 0.00 0.00 0.86
2285 4707 8.634444 ACTTTGGCTGACAGACTTACTATATAG 58.366 37.037 10.32 8.27 0.00 1.31
2314 4736 2.332063 TCTGCTTACCTAATGGCTGC 57.668 50.000 0.00 0.00 36.63 5.25
2364 4786 7.611821 GCGTTAAGCTTACACAAATAAACAA 57.388 32.000 5.45 0.00 44.04 2.83
2408 4830 0.034863 TCTTAAACCCCGGCATGACC 60.035 55.000 0.00 0.00 0.00 4.02
2432 4854 2.640316 ACCCAACACTGAACTTCTCC 57.360 50.000 0.00 0.00 0.00 3.71
2436 4858 3.181450 CCCAACACTGAACTTCTCCTCTT 60.181 47.826 0.00 0.00 0.00 2.85
2437 4859 4.061596 CCAACACTGAACTTCTCCTCTTC 58.938 47.826 0.00 0.00 0.00 2.87
2438 4860 4.202305 CCAACACTGAACTTCTCCTCTTCT 60.202 45.833 0.00 0.00 0.00 2.85
2439 4861 4.864704 ACACTGAACTTCTCCTCTTCTC 57.135 45.455 0.00 0.00 0.00 2.87
2440 4862 3.576550 ACACTGAACTTCTCCTCTTCTCC 59.423 47.826 0.00 0.00 0.00 3.71
2446 4868 5.125739 TGAACTTCTCCTCTTCTCCGATAAC 59.874 44.000 0.00 0.00 0.00 1.89
2456 4878 0.815615 CTCCGATAACCTTGGCTGGC 60.816 60.000 0.00 0.00 0.00 4.85
2471 4893 0.447801 CTGGCGTACTTTCCATGTGC 59.552 55.000 0.00 0.00 0.00 4.57
2519 4941 8.078596 GTCTTGACATAAAACATTTCAGCTCTT 58.921 33.333 0.00 0.00 0.00 2.85
2561 4983 2.035449 TGCGAGTAGTGCCCATGTATAC 59.965 50.000 0.00 0.00 0.00 1.47
2606 5028 1.185315 AAAATGGCGTCCTTGGATGG 58.815 50.000 10.50 0.00 0.00 3.51
2608 5030 2.215451 AATGGCGTCCTTGGATGGCT 62.215 55.000 27.81 15.48 37.51 4.75
2785 5207 1.352352 ACAGTCAACTGAATCCAGGGG 59.648 52.381 16.71 0.00 46.59 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.782046 ACTACACCGATGATAGTGTTGC 58.218 45.455 6.11 0.00 44.65 4.17
35 36 1.376543 ACGACGACTACACCGATGAT 58.623 50.000 0.00 0.00 0.00 2.45
44 45 2.598205 GGTTTTGCACAACGACGACTAC 60.598 50.000 9.50 0.00 0.00 2.73
45 46 1.593933 GGTTTTGCACAACGACGACTA 59.406 47.619 9.50 0.00 0.00 2.59
49 50 1.833860 ATTGGTTTTGCACAACGACG 58.166 45.000 9.50 0.00 0.00 5.12
51 52 2.796383 CGGAATTGGTTTTGCACAACGA 60.796 45.455 9.50 2.93 0.00 3.85
53 54 2.794350 CTCGGAATTGGTTTTGCACAAC 59.206 45.455 7.21 7.21 0.00 3.32
97 98 4.427394 GCGAGTAGCCATGACCTG 57.573 61.111 0.00 0.00 40.81 4.00
163 1721 2.292559 GCTACCCAACCCACCGGTA 61.293 63.158 6.87 0.00 43.71 4.02
186 1744 4.052229 CGTCGGGCCACTCGAAGT 62.052 66.667 4.39 0.00 38.42 3.01
203 1761 4.575973 AGATGATGCGGGCAGGGC 62.576 66.667 0.00 0.00 0.00 5.19
211 1769 2.006062 CGTCGGTCGAGATGATGCG 61.006 63.158 0.00 0.00 42.86 4.73
215 1773 3.122971 ACGCGTCGGTCGAGATGA 61.123 61.111 5.58 0.00 41.61 2.92
222 1780 1.269444 GCTATGATCACGCGTCGGTC 61.269 60.000 9.86 11.92 0.00 4.79
227 1785 1.603931 CCATCAGCTATGATCACGCGT 60.604 52.381 5.58 5.58 44.58 6.01
237 1795 1.755179 GGTTGTGCACCATCAGCTAT 58.245 50.000 15.69 0.00 46.42 2.97
290 1848 3.434319 CGGCTTCAAGCACGCCAT 61.434 61.111 12.53 0.00 44.75 4.40
327 1885 2.676471 GGGGATGTTGTGCCGCTT 60.676 61.111 0.00 0.00 39.69 4.68
374 1932 5.163141 CCTCTGGTCTCCTATCTCTCTAACA 60.163 48.000 0.00 0.00 0.00 2.41
393 1951 1.618345 CCCCGATCTCCCTATCCTCTG 60.618 61.905 0.00 0.00 0.00 3.35
411 1969 0.320508 GGAACGTTGTGACTCTCCCC 60.321 60.000 5.00 0.00 0.00 4.81
436 1994 2.737359 CGTATGTGGTGCACCTTATCGT 60.737 50.000 34.75 23.35 36.82 3.73
450 2008 2.822255 CCCGTTGGCCCGTATGTG 60.822 66.667 0.00 0.00 0.00 3.21
491 2049 2.477375 TGATTACACGCTCGTTTCAACC 59.523 45.455 0.00 0.00 0.00 3.77
499 2057 2.106750 ATCGACTGATTACACGCTCG 57.893 50.000 0.00 0.00 0.00 5.03
517 2075 4.832248 TCATGGAGACGCTTTTGTTCTAT 58.168 39.130 0.00 0.00 0.00 1.98
537 2095 9.671279 TGAGAATTATTGAAAGCATTAGTCTCA 57.329 29.630 0.00 0.00 34.59 3.27
556 2114 7.178983 TCCCTTTTGAATATGTTGCTGAGAATT 59.821 33.333 0.00 0.00 0.00 2.17
560 2118 5.902613 TCCCTTTTGAATATGTTGCTGAG 57.097 39.130 0.00 0.00 0.00 3.35
574 2132 6.540914 GGGGTTTTTAAAGAACTTCCCTTTTG 59.459 38.462 13.79 0.00 35.65 2.44
579 2137 5.617528 TTGGGGTTTTTAAAGAACTTCCC 57.382 39.130 13.99 13.99 32.35 3.97
580 2138 6.037830 GCTTTTGGGGTTTTTAAAGAACTTCC 59.962 38.462 0.00 11.94 30.97 3.46
581 2139 6.037830 GGCTTTTGGGGTTTTTAAAGAACTTC 59.962 38.462 0.00 6.44 30.97 3.01
595 2153 2.397044 TGAGAATTGGCTTTTGGGGT 57.603 45.000 0.00 0.00 0.00 4.95
657 2964 7.688372 ACATATGTCAGCTTCTTTTATTCGTG 58.312 34.615 1.41 0.00 0.00 4.35
668 2975 7.331934 TGTTAAGTGAGAACATATGTCAGCTTC 59.668 37.037 9.23 2.48 30.90 3.86
695 3082 8.094548 AGGAAAAATAATTAAAACTCAGGCCAC 58.905 33.333 5.01 0.00 0.00 5.01
724 3111 5.996669 TTCTCCTGGAACGAAACTAAAAC 57.003 39.130 0.00 0.00 0.00 2.43
730 3117 3.190744 GGGATTTTCTCCTGGAACGAAAC 59.809 47.826 9.83 2.05 44.28 2.78
853 3247 1.867233 GCAACGAGAGCAGAGTTTTCA 59.133 47.619 0.00 0.00 0.00 2.69
1038 3433 2.646930 CATGGCTTTGATCAGCTGGTA 58.353 47.619 15.13 0.00 39.97 3.25
1086 3483 1.743252 CAAACGAGGAGCTCTGGGC 60.743 63.158 14.64 0.00 42.19 5.36
1100 3497 4.404691 CTCTGGTGGAGCCCAAAC 57.595 61.111 0.00 0.00 34.18 2.93
1163 3560 0.106708 CTGCTTTCGCATAGGCCCTA 59.893 55.000 0.00 0.00 46.74 3.53
1347 3744 8.684655 GTTGTGCATTTTGTGATCGATTATATG 58.315 33.333 0.00 0.43 0.00 1.78
1349 3746 7.756558 TGTTGTGCATTTTGTGATCGATTATA 58.243 30.769 0.00 0.00 0.00 0.98
1353 3750 4.502171 TGTTGTGCATTTTGTGATCGAT 57.498 36.364 0.00 0.00 0.00 3.59
1354 3751 3.978718 TGTTGTGCATTTTGTGATCGA 57.021 38.095 0.00 0.00 0.00 3.59
1355 3752 5.579384 AATTGTTGTGCATTTTGTGATCG 57.421 34.783 0.00 0.00 0.00 3.69
1356 3753 7.408123 TCAAAATTGTTGTGCATTTTGTGATC 58.592 30.769 16.43 0.00 41.84 2.92
1357 3754 7.317842 TCAAAATTGTTGTGCATTTTGTGAT 57.682 28.000 16.43 0.00 41.84 3.06
1358 3755 6.732531 TCAAAATTGTTGTGCATTTTGTGA 57.267 29.167 16.43 1.27 41.84 3.58
1360 3757 6.906659 TGTTCAAAATTGTTGTGCATTTTGT 58.093 28.000 16.43 0.00 41.84 2.83
1361 3758 7.792383 TTGTTCAAAATTGTTGTGCATTTTG 57.208 28.000 12.59 12.59 42.25 2.44
1364 3761 8.983307 AAAATTGTTCAAAATTGTTGTGCATT 57.017 23.077 0.00 0.00 30.21 3.56
1365 3762 8.983307 AAAAATTGTTCAAAATTGTTGTGCAT 57.017 23.077 0.00 0.00 27.99 3.96
1399 3804 3.256631 CAGCATAAGGAAAACTTGCAGGT 59.743 43.478 0.00 0.00 40.37 4.00
1400 3805 3.507233 TCAGCATAAGGAAAACTTGCAGG 59.493 43.478 0.00 0.00 40.37 4.85
1427 3832 5.163519 ACTGAATTGAAACACCAACCAGAAG 60.164 40.000 0.00 0.00 35.49 2.85
1439 3844 3.445096 AGGGCTGCATACTGAATTGAAAC 59.555 43.478 0.50 0.00 0.00 2.78
1586 3992 5.123186 GCAGTGGTGTACAAATATTGCACTA 59.877 40.000 13.96 0.00 31.04 2.74
1590 3996 4.701956 AGCAGTGGTGTACAAATATTGC 57.298 40.909 0.00 5.93 0.00 3.56
1602 4008 5.008019 CAGTTTATTATGCCTAGCAGTGGTG 59.992 44.000 4.76 0.00 43.65 4.17
1605 4011 5.100751 GCAGTTTATTATGCCTAGCAGTG 57.899 43.478 0.00 0.00 43.65 3.66
1617 4023 9.515226 GGTCATATTAATCCTGGCAGTTTATTA 57.485 33.333 14.43 11.13 0.00 0.98
1627 4033 7.000472 ACAACATGAGGTCATATTAATCCTGG 59.000 38.462 0.00 0.00 34.26 4.45
1628 4034 9.730705 ATACAACATGAGGTCATATTAATCCTG 57.269 33.333 0.00 0.00 34.26 3.86
1680 4086 1.751924 CAGAGGAAGGACGGGTAGAAG 59.248 57.143 0.00 0.00 0.00 2.85
1774 4182 2.268298 CAACCTTCCTCCACGTATTCG 58.732 52.381 0.00 0.00 43.34 3.34
1921 4329 2.564947 AGAAGTTCATCTGCCGAAGAGT 59.435 45.455 5.50 0.00 38.67 3.24
1955 4363 7.963532 TCTATTTATCTAACCATGAGTGGGTC 58.036 38.462 0.00 0.00 43.92 4.46
2057 4479 9.051679 CGAAACTGGATAATGGAATGTGTATAA 57.948 33.333 0.00 0.00 0.00 0.98
2078 4500 6.128391 TGTGCTATTTGAGATACCAACGAAAC 60.128 38.462 0.00 0.00 0.00 2.78
2091 4513 3.369147 CCTCTGTTCGTGTGCTATTTGAG 59.631 47.826 0.00 0.00 0.00 3.02
2096 4518 0.108138 GGCCTCTGTTCGTGTGCTAT 60.108 55.000 0.00 0.00 0.00 2.97
2104 4526 2.874701 CCATAAATCAGGCCTCTGTTCG 59.125 50.000 0.00 0.00 41.59 3.95
2211 4633 3.571590 CCTAGGAGTTGAGGAGCACTAT 58.428 50.000 1.05 0.00 34.46 2.12
2283 4705 9.494271 CATTAGGTAAGCAGAATCAAATAGCTA 57.506 33.333 0.00 0.00 34.66 3.32
2285 4707 7.588512 CCATTAGGTAAGCAGAATCAAATAGC 58.411 38.462 0.00 0.00 0.00 2.97
2314 4736 6.990341 TGGACTTCTGAACACATCATATTG 57.010 37.500 0.00 0.00 37.44 1.90
2353 4775 7.604549 TGTCATCAGATGCATTGTTTATTTGT 58.395 30.769 5.41 0.00 0.00 2.83
2363 4785 2.718563 TGCACTGTCATCAGATGCATT 58.281 42.857 5.41 0.00 44.74 3.56
2364 4786 2.413310 TGCACTGTCATCAGATGCAT 57.587 45.000 0.00 0.00 44.74 3.96
2408 4830 3.875134 AGAAGTTCAGTGTTGGGTTTACG 59.125 43.478 5.50 0.00 0.00 3.18
2432 4854 2.432510 AGCCAAGGTTATCGGAGAAGAG 59.567 50.000 0.00 0.00 43.58 2.85
2436 4858 0.830648 CCAGCCAAGGTTATCGGAGA 59.169 55.000 0.00 0.00 45.75 3.71
2437 4859 0.815615 GCCAGCCAAGGTTATCGGAG 60.816 60.000 0.00 0.00 0.00 4.63
2438 4860 1.223487 GCCAGCCAAGGTTATCGGA 59.777 57.895 0.00 0.00 0.00 4.55
2439 4861 2.180204 CGCCAGCCAAGGTTATCGG 61.180 63.158 0.00 0.00 0.00 4.18
2440 4862 0.179094 TACGCCAGCCAAGGTTATCG 60.179 55.000 0.00 0.00 0.00 2.92
2446 4868 1.305930 GGAAAGTACGCCAGCCAAGG 61.306 60.000 0.00 0.00 0.00 3.61
2456 4878 2.386661 AGGAGCACATGGAAAGTACG 57.613 50.000 0.00 0.00 0.00 3.67
2471 4893 2.143925 GGTGTTCAGTTTCGGAAGGAG 58.856 52.381 0.00 0.00 0.00 3.69
2493 4915 7.588512 AGAGCTGAAATGTTTTATGTCAAGAC 58.411 34.615 0.00 0.00 0.00 3.01
2519 4941 0.321346 TTGCTCGTGCTCTGAATCCA 59.679 50.000 11.19 0.00 40.48 3.41
2530 4952 0.387367 ACTACTCGCAGTTGCTCGTG 60.387 55.000 2.29 0.00 39.32 4.35
2561 4983 3.512724 AGAAATTTGTGAGGATGGCAAGG 59.487 43.478 0.00 0.00 0.00 3.61
2614 5036 2.084610 TCACAGAGCATTTGTCGAGG 57.915 50.000 0.00 0.00 0.00 4.63
2618 5040 3.755378 ACTTGGATCACAGAGCATTTGTC 59.245 43.478 0.00 0.00 0.00 3.18
2785 5207 3.452474 GCAGACAGAGATGACCATACAC 58.548 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.