Multiple sequence alignment - TraesCS7D01G498400

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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 TraesCS7D01G498400 chr7D 100.000 6117 0 0 1 6117 605089117 605083001 0.000000e+00 11297.0
1 TraesCS7D01G498400 chr7D 100.000 513 0 0 6444 6956 605082674 605082162 0.000000e+00 948.0
2 TraesCS7D01G498400 chr7D 85.632 348 35 9 6623 6956 604905232 604904886 1.110000e-92 351.0
3 TraesCS7D01G498400 chr7D 93.269 104 4 2 6444 6545 604905553 604905451 4.350000e-32 150.0
4 TraesCS7D01G498400 chr7D 97.222 36 1 0 6521 6556 604905453 604905418 2.090000e-05 62.1
5 TraesCS7D01G498400 chr3D 96.928 6119 174 12 1 6117 606146373 606140267 0.000000e+00 10246.0
6 TraesCS7D01G498400 chr1A 92.453 6122 448 14 1 6117 405541595 405547707 0.000000e+00 8733.0
7 TraesCS7D01G498400 chr1A 86.122 6103 821 25 1 6092 461263899 461257812 0.000000e+00 6554.0
8 TraesCS7D01G498400 chr7A 92.051 5900 446 14 219 6109 78843067 78848952 0.000000e+00 8275.0
9 TraesCS7D01G498400 chr4A 87.049 6123 765 24 1 6108 531310359 531304250 0.000000e+00 6889.0
10 TraesCS7D01G498400 chr4D 96.017 3841 144 8 2282 6117 73417235 73421071 0.000000e+00 6237.0
11 TraesCS7D01G498400 chr4D 94.444 1206 48 8 1 1206 73406275 73407461 0.000000e+00 1838.0
12 TraesCS7D01G498400 chr2D 92.767 4106 291 4 43 4148 11503052 11498953 0.000000e+00 5932.0
13 TraesCS7D01G498400 chr6B 88.406 4761 538 12 1 4757 15778669 15773919 0.000000e+00 5722.0
14 TraesCS7D01G498400 chr6B 92.857 42 2 1 6516 6556 75040704 75040745 7.530000e-05 60.2
15 TraesCS7D01G498400 chr1D 83.314 6161 927 67 3 6112 72461441 72467551 0.000000e+00 5589.0
16 TraesCS7D01G498400 chr5B 87.214 1877 216 11 1 1857 396818039 396819911 0.000000e+00 2115.0
17 TraesCS7D01G498400 chr7B 87.440 414 38 8 6555 6956 686139240 686139651 1.370000e-126 464.0
18 TraesCS7D01G498400 chr7B 81.493 335 31 15 6635 6956 687479440 687479124 5.390000e-61 246.0
19 TraesCS7D01G498400 chr7B 92.308 117 4 3 6445 6557 686138940 686139055 2.010000e-35 161.0
20 TraesCS7D01G498400 chr7B 92.135 89 4 2 6470 6556 686139113 686139200 9.470000e-24 122.0
21 TraesCS7D01G498400 chr7B 88.119 101 5 2 6463 6556 687481124 687481024 5.700000e-21 113.0
22 TraesCS7D01G498400 chr7B 88.372 86 8 2 6554 6638 687480940 687480856 1.230000e-17 102.0


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 TraesCS7D01G498400 chr7D 605082162 605089117 6955 True 6122.5 11297 100.000000 1 6956 2 chr7D.!!$R2 6955
1 TraesCS7D01G498400 chr3D 606140267 606146373 6106 True 10246.0 10246 96.928000 1 6117 1 chr3D.!!$R1 6116
2 TraesCS7D01G498400 chr1A 405541595 405547707 6112 False 8733.0 8733 92.453000 1 6117 1 chr1A.!!$F1 6116
3 TraesCS7D01G498400 chr1A 461257812 461263899 6087 True 6554.0 6554 86.122000 1 6092 1 chr1A.!!$R1 6091
4 TraesCS7D01G498400 chr7A 78843067 78848952 5885 False 8275.0 8275 92.051000 219 6109 1 chr7A.!!$F1 5890
5 TraesCS7D01G498400 chr4A 531304250 531310359 6109 True 6889.0 6889 87.049000 1 6108 1 chr4A.!!$R1 6107
6 TraesCS7D01G498400 chr4D 73417235 73421071 3836 False 6237.0 6237 96.017000 2282 6117 1 chr4D.!!$F2 3835
7 TraesCS7D01G498400 chr4D 73406275 73407461 1186 False 1838.0 1838 94.444000 1 1206 1 chr4D.!!$F1 1205
8 TraesCS7D01G498400 chr2D 11498953 11503052 4099 True 5932.0 5932 92.767000 43 4148 1 chr2D.!!$R1 4105
9 TraesCS7D01G498400 chr6B 15773919 15778669 4750 True 5722.0 5722 88.406000 1 4757 1 chr6B.!!$R1 4756
10 TraesCS7D01G498400 chr1D 72461441 72467551 6110 False 5589.0 5589 83.314000 3 6112 1 chr1D.!!$F1 6109
11 TraesCS7D01G498400 chr5B 396818039 396819911 1872 False 2115.0 2115 87.214000 1 1857 1 chr5B.!!$F1 1856
12 TraesCS7D01G498400 chr7B 686138940 686139651 711 False 249.0 464 90.627667 6445 6956 3 chr7B.!!$F1 511

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
516 550 0.252239 TCCTCCTCCTGCTGCTACAA 60.252 55.000 0.00 0.0 0.00 2.41 F
817 852 0.877743 GTTTCTGCCTCAGAGTTGCC 59.122 55.000 0.00 0.0 41.75 4.52 F
1081 1118 1.902918 TGGTGTGCATGGAAGGTGC 60.903 57.895 0.00 0.0 42.81 5.01 F
2347 2397 1.004745 GGCCAGACTGGGAAGAATCAA 59.995 52.381 23.09 0.0 38.19 2.57 F
2952 3004 1.002888 CTGTTGTGACAGCTCTCCCAT 59.997 52.381 0.29 0.0 46.08 4.00 F
3397 3450 3.805207 AGAACAACGCTTACTTCCAAGT 58.195 40.909 0.00 0.0 42.91 3.16 F
4348 4408 4.388575 CCCAATATAATTCCAGGGGGTGTT 60.389 45.833 0.00 0.0 34.93 3.32 F
5310 5372 2.171659 TGTTGAGGGTTGTTCAGCAGTA 59.828 45.455 0.00 0.0 32.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1512 2.097825 GGAATTCCACTGCAGAAGCAT 58.902 47.619 23.35 3.79 42.59 3.79 R
2347 2397 4.910458 ACTAACAAAGTCACCTAGGCAT 57.090 40.909 9.30 0.00 30.33 4.40 R
2952 3004 1.134521 GGTATGATCGCTCCCAACACA 60.135 52.381 0.00 0.00 0.00 3.72 R
3621 3680 1.799933 ATCGCCTCCTTGATCTCCTT 58.200 50.000 0.00 0.00 0.00 3.36 R
4776 4836 3.181467 CCAAAAGAAGTGTGCCATTTGGA 60.181 43.478 8.95 0.00 46.05 3.53 R
5117 5179 1.701847 GACCCAGGTATCATGCCAGAT 59.298 52.381 0.00 0.00 0.00 2.90 R
5557 5619 0.716108 CACAGATTCGAACTCCGCAC 59.284 55.000 0.00 0.00 38.37 5.34 R
6648 6925 0.030369 ATCCGATCCGTGTCGTAAGC 59.970 55.000 6.05 0.00 39.89 3.09 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
125 126 1.412074 CCTAGCCTTGCAATCCCCAAT 60.412 52.381 0.00 0.00 0.00 3.16
181 182 7.766278 GGATAGAAAATTCTCAGCACAAGACTA 59.234 37.037 0.00 0.00 38.70 2.59
292 293 0.910338 GAGGTGGTTAAGGGAGGGAC 59.090 60.000 0.00 0.00 0.00 4.46
367 368 2.438763 CTGCTCCTCAAGATGGGAAGAT 59.561 50.000 0.00 0.00 0.00 2.40
379 380 2.504519 GAAGATAACGGCCCCGCT 59.495 61.111 6.63 0.00 44.19 5.52
516 550 0.252239 TCCTCCTCCTGCTGCTACAA 60.252 55.000 0.00 0.00 0.00 2.41
550 584 5.307976 TGGATCCAAGGTACAAGGATATGAG 59.692 44.000 13.46 0.00 42.76 2.90
697 731 0.974383 ACCTACTTTGGTAGCGCAGT 59.026 50.000 11.47 5.48 42.85 4.40
775 810 5.107491 GGCTTAACTACAAAAATTGTGCAGC 60.107 40.000 6.01 5.92 45.03 5.25
817 852 0.877743 GTTTCTGCCTCAGAGTTGCC 59.122 55.000 0.00 0.00 41.75 4.52
864 901 3.678529 GCAAAAACAAAGAGTGGCCTTGA 60.679 43.478 3.32 0.00 0.00 3.02
898 935 5.320277 ACTTGGGAGAGAAGAAATTCTTGG 58.680 41.667 13.55 0.00 36.73 3.61
1081 1118 1.902918 TGGTGTGCATGGAAGGTGC 60.903 57.895 0.00 0.00 42.81 5.01
1475 1512 5.111989 CAGTCAGTCAAACTCACAGAAAGA 58.888 41.667 0.00 0.00 0.00 2.52
1616 1660 3.711190 ACTCCTGCAAAACCATTTCCTTT 59.289 39.130 0.00 0.00 0.00 3.11
1931 1975 5.768662 ACAAAGCAGCTGCATATATGAAGAT 59.231 36.000 38.24 15.04 45.16 2.40
2347 2397 1.004745 GGCCAGACTGGGAAGAATCAA 59.995 52.381 23.09 0.00 38.19 2.57
2676 2728 5.413833 AGTTTATTGCTGAACTCCATGACAG 59.586 40.000 0.00 0.00 30.64 3.51
2757 2809 5.583854 CGGCTGATGATAAGAATAATGGGAG 59.416 44.000 0.00 0.00 0.00 4.30
2952 3004 1.002888 CTGTTGTGACAGCTCTCCCAT 59.997 52.381 0.29 0.00 46.08 4.00
2991 3043 8.612486 TCATACCCCTTTACTTATTGACACTA 57.388 34.615 0.00 0.00 0.00 2.74
2997 3049 6.879458 CCCTTTACTTATTGACACTAGTGCTT 59.121 38.462 22.90 4.01 0.00 3.91
3347 3400 4.157958 GCTTTCTGGCAGCGCTCG 62.158 66.667 7.13 4.46 0.00 5.03
3397 3450 3.805207 AGAACAACGCTTACTTCCAAGT 58.195 40.909 0.00 0.00 42.91 3.16
3614 3673 6.766467 AGAATGAACGTCTCCAAAGTAACTTT 59.234 34.615 0.00 0.00 33.58 2.66
3621 3680 5.983720 CGTCTCCAAAGTAACTTTTCTGAGA 59.016 40.000 0.00 0.00 32.58 3.27
3822 3881 6.954684 AGTCCTTATTCCTAAAGAGTCTGACA 59.045 38.462 10.88 0.00 0.00 3.58
4348 4408 4.388575 CCCAATATAATTCCAGGGGGTGTT 60.389 45.833 0.00 0.00 34.93 3.32
4840 4900 7.807977 ACACAAATACCATCTAGCTAATTGG 57.192 36.000 16.48 16.48 35.31 3.16
5117 5179 4.017958 TGGGGAATGGTGAGTTAATTAGCA 60.018 41.667 1.97 0.00 0.00 3.49
5310 5372 2.171659 TGTTGAGGGTTGTTCAGCAGTA 59.828 45.455 0.00 0.00 32.00 2.74
5642 5704 6.264518 GGGGCTTTATATCCGATTTCTTTGAA 59.735 38.462 0.00 0.00 0.00 2.69
5847 5911 1.623811 GCACCAGTGGAAGGTTCTCTA 59.376 52.381 18.40 0.00 37.23 2.43
6046 6132 8.075761 AGTACCTAGATTTCGTTCCTGTTATT 57.924 34.615 0.00 0.00 0.00 1.40
6082 6169 2.165845 TGCTCTCGAACTTTAGGTAGCC 59.834 50.000 0.00 0.00 0.00 3.93
6519 6753 7.226720 TGTGTCCTTAGAGTGAAGTTGATTTTC 59.773 37.037 0.00 0.00 0.00 2.29
6525 6761 5.514279 AGAGTGAAGTTGATTTTCTTTGCG 58.486 37.500 0.00 0.00 0.00 4.85
6558 6794 9.832445 ATAGATGTTTATTCCATCAAAGTACGT 57.168 29.630 0.00 0.00 40.93 3.57
6559 6795 8.197988 AGATGTTTATTCCATCAAAGTACGTC 57.802 34.615 0.00 0.00 40.93 4.34
6560 6796 7.822334 AGATGTTTATTCCATCAAAGTACGTCA 59.178 33.333 0.00 0.00 40.93 4.35
6561 6797 7.915293 TGTTTATTCCATCAAAGTACGTCAT 57.085 32.000 0.00 0.00 0.00 3.06
6562 6798 9.607988 ATGTTTATTCCATCAAAGTACGTCATA 57.392 29.630 0.00 0.00 0.00 2.15
6563 6799 9.093970 TGTTTATTCCATCAAAGTACGTCATAG 57.906 33.333 0.00 0.00 0.00 2.23
6564 6800 8.548721 GTTTATTCCATCAAAGTACGTCATAGG 58.451 37.037 0.00 0.00 0.00 2.57
6565 6801 4.665833 TCCATCAAAGTACGTCATAGGG 57.334 45.455 0.00 0.00 0.00 3.53
6579 6856 1.632409 CATAGGGCTGGGCTATGTCAT 59.368 52.381 0.00 0.00 0.00 3.06
6583 6860 1.073897 GCTGGGCTATGTCATCCCC 59.926 63.158 12.53 12.53 39.30 4.81
6638 6915 8.693625 AGTTGATTAACTAAGCCGACTACTAAT 58.306 33.333 0.14 0.00 45.07 1.73
6647 6924 2.980568 CCGACTACTAATTGTTGGCCA 58.019 47.619 0.00 0.00 31.76 5.36
6648 6925 2.936498 CCGACTACTAATTGTTGGCCAG 59.064 50.000 5.11 0.00 31.76 4.85
6655 6932 1.904287 AATTGTTGGCCAGCTTACGA 58.096 45.000 21.11 9.44 0.00 3.43
6679 6956 0.962489 GATCGGATCCACCTCACGAT 59.038 55.000 13.41 6.52 45.70 3.73
6741 7018 8.784994 TGTTTTTACAACACGGACATATATTGT 58.215 29.630 0.00 0.00 42.79 2.71
6742 7019 9.057365 GTTTTTACAACACGGACATATATTGTG 57.943 33.333 0.00 0.00 39.18 3.33
6743 7020 8.549338 TTTTACAACACGGACATATATTGTGA 57.451 30.769 9.79 0.00 39.18 3.58
6744 7021 8.725405 TTTACAACACGGACATATATTGTGAT 57.275 30.769 9.79 0.00 39.18 3.06
6748 7025 9.168451 ACAACACGGACATATATTGTGATAAAA 57.832 29.630 9.79 0.00 39.18 1.52
6797 7085 3.058016 CGAGTGTTTTCAACATGAGCCAT 60.058 43.478 0.00 0.00 44.35 4.40
6799 7087 5.334802 CGAGTGTTTTCAACATGAGCCATTA 60.335 40.000 0.00 0.00 44.35 1.90
6818 7106 1.818642 ATGAGCTCAGAGGTTTGCAC 58.181 50.000 22.96 0.00 0.00 4.57
6822 7110 1.571460 CTCAGAGGTTTGCACGCAC 59.429 57.895 0.00 0.00 0.00 5.34
6826 7114 0.748005 AGAGGTTTGCACGCACACTT 60.748 50.000 8.11 0.48 0.00 3.16
6830 7118 0.024873 GTTTGCACGCACACTTTTGC 59.975 50.000 1.12 0.00 39.28 3.68
6835 7123 1.558741 CACGCACACTTTTGCAACAT 58.441 45.000 0.00 0.00 43.15 2.71
6843 7131 3.501828 ACACTTTTGCAACATGAGCGATA 59.498 39.130 0.00 0.00 33.85 2.92
6844 7132 4.156556 ACACTTTTGCAACATGAGCGATAT 59.843 37.500 0.00 0.00 33.85 1.63
6851 7139 3.310774 GCAACATGAGCGATATTGTCACT 59.689 43.478 0.00 0.00 0.00 3.41
6852 7140 4.784394 GCAACATGAGCGATATTGTCACTG 60.784 45.833 0.00 0.00 0.00 3.66
6856 7144 2.672874 TGAGCGATATTGTCACTGCAAC 59.327 45.455 0.00 0.00 0.00 4.17
6859 7147 4.441792 AGCGATATTGTCACTGCAACATA 58.558 39.130 0.00 0.00 0.00 2.29
6875 7163 5.469760 TGCAACATACCCTCATTAATCGATG 59.530 40.000 0.00 0.00 0.00 3.84
6933 7221 3.213506 CCTCCACAACATTGACTCACAA 58.786 45.455 0.00 0.00 42.95 3.33
6943 7231 5.311265 ACATTGACTCACAACACATGAGAT 58.689 37.500 8.92 0.00 45.46 2.75
6944 7232 6.466812 ACATTGACTCACAACACATGAGATA 58.533 36.000 8.92 0.00 45.46 1.98
6946 7234 7.609146 ACATTGACTCACAACACATGAGATATT 59.391 33.333 8.92 0.00 45.46 1.28
6947 7235 6.973229 TGACTCACAACACATGAGATATTG 57.027 37.500 8.92 0.00 45.46 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.168291 GGCGGCTGGGAGAAGGAG 62.168 72.222 0.00 0.00 0.00 3.69
111 112 4.023021 CCAAAACAAATTGGGGATTGCAAG 60.023 41.667 4.94 0.00 45.03 4.01
125 126 6.609616 ACAGATCCTTTCTAACCCAAAACAAA 59.390 34.615 0.00 0.00 31.77 2.83
270 271 1.282157 CCCTCCCTTAACCACCTCAAG 59.718 57.143 0.00 0.00 0.00 3.02
516 550 0.465097 CTTGGATCCAGCGCCTGAAT 60.465 55.000 15.53 0.00 32.44 2.57
550 584 2.095212 GGCCAACTACAGTTAAAGCAGC 60.095 50.000 0.00 0.00 36.32 5.25
697 731 2.474268 TAAAACCCCAGGCCAGCCA 61.474 57.895 12.03 0.00 38.92 4.75
775 810 4.319177 CTCACCCTTAACCACTTTGAGAG 58.681 47.826 0.00 0.00 32.42 3.20
841 877 1.830477 AGGCCACTCTTTGTTTTTGCA 59.170 42.857 5.01 0.00 0.00 4.08
864 901 3.012959 TCTCTCCCAAGTCCCTAATCTGT 59.987 47.826 0.00 0.00 0.00 3.41
970 1007 4.370049 CATTCGCAGATCTTGACAGAGAT 58.630 43.478 0.00 1.30 39.04 2.75
1081 1118 1.133790 GCAAGCTGTAATCTGGGCAAG 59.866 52.381 0.00 0.00 0.00 4.01
1475 1512 2.097825 GGAATTCCACTGCAGAAGCAT 58.902 47.619 23.35 3.79 42.59 3.79
1616 1660 5.356190 GCTGACATGGAATCAGATCTTTCAA 59.644 40.000 14.28 0.00 45.46 2.69
2347 2397 4.910458 ACTAACAAAGTCACCTAGGCAT 57.090 40.909 9.30 0.00 30.33 4.40
2445 2497 6.916909 TGCCATATAAATTCCTCCTTACCAA 58.083 36.000 0.00 0.00 0.00 3.67
2553 2605 5.701290 ACAGTAGCCACAATACAAAACTCTC 59.299 40.000 0.00 0.00 0.00 3.20
2898 2950 8.491045 AATTTAAAATCCCAAGAACCAGAAGA 57.509 30.769 0.00 0.00 0.00 2.87
2952 3004 1.134521 GGTATGATCGCTCCCAACACA 60.135 52.381 0.00 0.00 0.00 3.72
2991 3043 3.182105 AGGTAACCCTCCAAGCACT 57.818 52.632 0.00 0.00 35.62 4.40
3143 3195 4.652822 TCCAGCCTTTTACTTTCTTCCTC 58.347 43.478 0.00 0.00 0.00 3.71
3347 3400 3.784701 TCAACAATCTAGCGGTCTCTC 57.215 47.619 0.00 0.00 0.00 3.20
3357 3410 8.946085 GTTGTTCTTATCACCATCAACAATCTA 58.054 33.333 0.00 0.00 36.44 1.98
3525 3580 4.240096 CCAAGATGCACATGAGGTTTTTC 58.760 43.478 0.00 0.00 0.00 2.29
3614 3673 4.029520 CCTCCTTGATCTCCTTCTCAGAA 58.970 47.826 0.00 0.00 0.00 3.02
3621 3680 1.799933 ATCGCCTCCTTGATCTCCTT 58.200 50.000 0.00 0.00 0.00 3.36
3822 3881 7.508977 TGGTCTAAATTTCTTCAAATCCTTGGT 59.491 33.333 0.00 0.00 30.37 3.67
4348 4408 3.934457 TCTGCGTATTGAAGACTCACA 57.066 42.857 0.00 0.00 0.00 3.58
4650 4710 3.718434 TGTGAGATATCTCCCAAGCCATT 59.282 43.478 26.33 0.00 42.20 3.16
4776 4836 3.181467 CCAAAAGAAGTGTGCCATTTGGA 60.181 43.478 8.95 0.00 46.05 3.53
4840 4900 6.098552 ACTCTTTTCTCCTAGTAACATAGCCC 59.901 42.308 0.00 0.00 0.00 5.19
5117 5179 1.701847 GACCCAGGTATCATGCCAGAT 59.298 52.381 0.00 0.00 0.00 2.90
5372 5434 9.860898 GTTTATGCTTTTGTAGAAGGATTTCAT 57.139 29.630 0.00 0.00 38.44 2.57
5395 5457 4.089361 CAGAAGCTATTCCCCCAAAGTTT 58.911 43.478 0.00 0.00 35.94 2.66
5557 5619 0.716108 CACAGATTCGAACTCCGCAC 59.284 55.000 0.00 0.00 38.37 5.34
5588 5650 2.818130 GTGCCACCACACAATCAAAT 57.182 45.000 0.00 0.00 41.67 2.32
5642 5704 8.579850 TGTCAAAGCTGGTAATTCTATCAATT 57.420 30.769 0.00 0.00 0.00 2.32
6046 6132 4.264460 GAGAGCAGAAGTTCTCTCCAAA 57.736 45.455 19.93 0.00 45.46 3.28
6082 6169 8.528044 AATAAAACTACTCTCCAGGAGACTAG 57.472 38.462 22.67 22.67 44.45 2.57
6487 6574 3.154710 TCACTCTAAGGACACATGACGT 58.845 45.455 0.00 0.00 0.00 4.34
6488 6575 3.850122 TCACTCTAAGGACACATGACG 57.150 47.619 0.00 0.00 0.00 4.35
6489 6576 5.140747 ACTTCACTCTAAGGACACATGAC 57.859 43.478 0.00 0.00 0.00 3.06
6519 6753 9.591404 GAATAAACATCTATTGATCTCGCAAAG 57.409 33.333 0.00 0.00 0.00 2.77
6552 6788 1.400530 GCCCAGCCCTATGACGTACT 61.401 60.000 0.00 0.00 0.00 2.73
6556 6792 0.036952 CATAGCCCAGCCCTATGACG 60.037 60.000 3.01 0.00 42.95 4.35
6557 6793 1.002544 GACATAGCCCAGCCCTATGAC 59.997 57.143 13.55 5.55 42.95 3.06
6558 6794 1.352083 GACATAGCCCAGCCCTATGA 58.648 55.000 13.55 0.00 42.95 2.15
6559 6795 1.059098 TGACATAGCCCAGCCCTATG 58.941 55.000 6.82 6.82 44.80 2.23
6560 6796 1.912043 GATGACATAGCCCAGCCCTAT 59.088 52.381 0.00 0.00 0.00 2.57
6561 6797 1.352083 GATGACATAGCCCAGCCCTA 58.648 55.000 0.00 0.00 0.00 3.53
6562 6798 1.422161 GGATGACATAGCCCAGCCCT 61.422 60.000 0.00 0.00 33.03 5.19
6563 6799 1.073897 GGATGACATAGCCCAGCCC 59.926 63.158 0.00 0.00 33.03 5.19
6564 6800 4.809070 GGATGACATAGCCCAGCC 57.191 61.111 0.00 0.00 0.00 4.85
6592 6869 3.265791 CTTCACTCTAAGGGCACATGAC 58.734 50.000 0.00 0.00 0.00 3.06
6638 6915 0.179043 TGTCGTAAGCTGGCCAACAA 60.179 50.000 7.01 0.00 37.18 2.83
6647 6924 1.028330 TCCGATCCGTGTCGTAAGCT 61.028 55.000 6.05 0.00 39.89 3.74
6648 6925 0.030369 ATCCGATCCGTGTCGTAAGC 59.970 55.000 6.05 0.00 39.89 3.09
6673 6950 1.750206 CAAATTGGATGGCCATCGTGA 59.250 47.619 33.95 23.69 45.46 4.35
6679 6956 3.724624 GCCCAAATTGGATGGCCA 58.275 55.556 14.62 8.56 40.96 5.36
6748 7025 4.022416 TGCAAACCTTCGAGTGCAATATTT 60.022 37.500 7.16 0.00 43.65 1.40
6750 7027 3.081061 TGCAAACCTTCGAGTGCAATAT 58.919 40.909 7.16 0.00 43.65 1.28
6751 7028 2.499197 TGCAAACCTTCGAGTGCAATA 58.501 42.857 7.16 0.00 43.65 1.90
6752 7029 1.317613 TGCAAACCTTCGAGTGCAAT 58.682 45.000 7.16 0.00 43.65 3.56
6753 7030 2.787191 TGCAAACCTTCGAGTGCAA 58.213 47.368 7.16 0.00 43.65 4.08
6754 7031 0.662619 CTTGCAAACCTTCGAGTGCA 59.337 50.000 0.00 5.92 44.85 4.57
6755 7032 0.944386 TCTTGCAAACCTTCGAGTGC 59.056 50.000 0.00 0.00 37.51 4.40
6756 7033 1.070577 CGTCTTGCAAACCTTCGAGTG 60.071 52.381 0.00 0.00 0.00 3.51
6757 7034 1.202486 TCGTCTTGCAAACCTTCGAGT 60.202 47.619 0.00 0.00 0.00 4.18
6758 7035 1.457303 CTCGTCTTGCAAACCTTCGAG 59.543 52.381 17.11 17.11 37.55 4.04
6766 7054 4.427096 TTGAAAACACTCGTCTTGCAAA 57.573 36.364 0.00 0.00 0.00 3.68
6797 7085 3.338249 GTGCAAACCTCTGAGCTCATAA 58.662 45.455 18.63 7.83 0.00 1.90
6799 7087 1.818642 GTGCAAACCTCTGAGCTCAT 58.181 50.000 18.63 0.00 0.00 2.90
6822 7110 2.404265 TCGCTCATGTTGCAAAAGTG 57.596 45.000 0.00 3.73 0.00 3.16
6826 7114 4.155644 TGACAATATCGCTCATGTTGCAAA 59.844 37.500 0.00 0.00 37.15 3.68
6830 7118 4.784394 GCAGTGACAATATCGCTCATGTTG 60.784 45.833 0.00 1.84 45.43 3.33
6835 7123 2.671130 TGCAGTGACAATATCGCTCA 57.329 45.000 0.00 0.00 45.43 4.26
6843 7131 3.244875 TGAGGGTATGTTGCAGTGACAAT 60.245 43.478 0.00 0.00 0.00 2.71
6844 7132 2.105649 TGAGGGTATGTTGCAGTGACAA 59.894 45.455 0.00 0.00 0.00 3.18
6851 7139 5.029807 TCGATTAATGAGGGTATGTTGCA 57.970 39.130 0.00 0.00 0.00 4.08
6852 7140 5.470098 ACATCGATTAATGAGGGTATGTTGC 59.530 40.000 0.00 0.00 0.00 4.17
6856 7144 6.467677 AGGAACATCGATTAATGAGGGTATG 58.532 40.000 0.00 0.00 0.00 2.39
6859 7147 4.202367 GGAGGAACATCGATTAATGAGGGT 60.202 45.833 0.00 0.00 0.00 4.34
6922 7210 7.609146 ACAATATCTCATGTGTTGTGAGTCAAT 59.391 33.333 0.00 0.00 42.82 2.57
6933 7221 4.226427 ACTGCCACAATATCTCATGTGT 57.774 40.909 5.32 0.00 44.21 3.72


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

AutoCloner maintained by Alex Coulton.