Multiple sequence alignment - TraesCS2D01G159800

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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 TraesCS2D01G159800 chr2D 100.000 5272 0 0 1 5272 102855738 102861009 0.000000e+00 9736.0
1 TraesCS2D01G159800 chr2B 93.845 3103 124 25 2205 5272 154234792 154237862 0.000000e+00 4610.0
2 TraesCS2D01G159800 chr2B 90.818 2102 84 32 122 2149 154232475 154234541 0.000000e+00 2712.0
3 TraesCS2D01G159800 chr2B 98.438 64 1 0 1 64 154232240 154232303 4.320000e-21 113.0
4 TraesCS2D01G159800 chr2B 100.000 30 0 0 2171 2200 154234603 154234632 7.380000e-04 56.5
5 TraesCS2D01G159800 chr2A 91.111 2025 130 25 2371 4379 101888184 101890174 0.000000e+00 2697.0
6 TraesCS2D01G159800 chr2A 86.776 2019 128 49 1 1958 101885927 101887867 0.000000e+00 2121.0
7 TraesCS2D01G159800 chr2A 88.210 687 56 16 4599 5272 101890245 101890919 0.000000e+00 797.0
8 TraesCS2D01G159800 chr2A 92.336 274 17 4 1 271 101883282 101883554 2.300000e-103 387.0
9 TraesCS2D01G159800 chr2A 91.606 274 20 3 1 271 101885118 101885391 4.980000e-100 375.0
10 TraesCS2D01G159800 chr2A 91.353 266 16 5 1 262 101884087 101884349 1.810000e-94 357.0
11 TraesCS2D01G159800 chr2A 88.406 207 21 2 4393 4599 101890570 101890773 4.080000e-61 246.0
12 TraesCS2D01G159800 chr2A 96.364 55 0 1 2149 2201 101888052 101888106 7.270000e-14 89.8
13 TraesCS2D01G159800 chr3A 83.844 359 34 15 90 433 42215319 42215668 2.370000e-83 320.0
14 TraesCS2D01G159800 chr3A 80.628 382 50 17 90 460 708985701 708986069 1.870000e-69 274.0
15 TraesCS2D01G159800 chr6D 82.216 388 41 15 90 460 91846788 91846412 5.130000e-80 309.0
16 TraesCS2D01G159800 chr4A 80.429 373 55 16 93 460 516584667 516585026 8.700000e-68 268.0


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 TraesCS2D01G159800 chr2D 102855738 102861009 5271 False 9736.000 9736 100.00000 1 5272 1 chr2D.!!$F1 5271
1 TraesCS2D01G159800 chr2B 154232240 154237862 5622 False 1872.875 4610 95.77525 1 5272 4 chr2B.!!$F1 5271
2 TraesCS2D01G159800 chr2A 101883282 101890919 7637 False 883.725 2697 90.77025 1 5272 8 chr2A.!!$F1 5271

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
684 3355 1.072489 TCACCGCAATCCACACCTAAA 59.928 47.619 0.00 0.0 0.00 1.85 F
1222 3941 0.811616 GTCCGATGATCTTTGCGGCT 60.812 55.000 0.00 0.0 43.26 5.52 F
2781 5805 0.307760 GTGTTCGGCACAAGAACCTG 59.692 55.000 6.63 0.0 46.91 4.00 F
2817 5841 0.331278 ATTGTGCCGAGGGGAATCAA 59.669 50.000 0.00 0.0 34.06 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 5224 0.379669 GATGAACGCAATCCAGCAGG 59.620 55.0 0.0 0.0 0.0 4.85 R
2888 5913 0.179225 GCAACACTTACATCGCCACG 60.179 55.0 0.0 0.0 0.0 4.94 R
3662 6693 0.036875 CCACAACCCCCTCAGAGTTC 59.963 60.0 0.0 0.0 0.0 3.01 R
4614 7648 2.095617 GGTTATTTGTACACGGGCACAC 60.096 50.0 0.0 0.0 0.0 3.82 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
222 1027 8.185505 TGTACTTGTAAGAAAAATTCCACACAC 58.814 33.333 0.00 0.00 0.00 3.82
534 3205 5.982890 AACGTTCATGAAAGGATCCAAAT 57.017 34.783 22.66 0.00 0.00 2.32
635 3306 2.899339 GCTCCTTCGGCAGATGGC 60.899 66.667 13.04 0.00 40.43 4.40
654 3325 2.139118 GCGGAAAGGATATCAGCAGAC 58.861 52.381 4.83 0.00 37.83 3.51
684 3355 1.072489 TCACCGCAATCCACACCTAAA 59.928 47.619 0.00 0.00 0.00 1.85
727 3408 5.445069 TCCTTCTTCCACACTTTGAATTCA 58.555 37.500 3.38 3.38 0.00 2.57
737 3418 2.470801 TTTGAATTCACGCTGCGCCC 62.471 55.000 23.51 5.54 0.00 6.13
738 3419 4.520846 GAATTCACGCTGCGCCCG 62.521 66.667 23.51 14.80 0.00 6.13
755 3450 1.451504 CGGCTTCCTCCCATGCATA 59.548 57.895 0.00 0.00 0.00 3.14
812 3507 1.684049 CTCGCTCCCACCCTCTTCT 60.684 63.158 0.00 0.00 0.00 2.85
1100 3819 3.376078 CACATTGCTGCGGCCCTT 61.376 61.111 16.57 0.00 37.74 3.95
1163 3882 3.798511 CTCCCCGCTCCCTTTCCC 61.799 72.222 0.00 0.00 0.00 3.97
1196 3915 3.430862 GCATCTGGCCGTTTGCGA 61.431 61.111 7.71 0.00 42.61 5.10
1222 3941 0.811616 GTCCGATGATCTTTGCGGCT 60.812 55.000 0.00 0.00 43.26 5.52
1237 3956 3.880846 GCTTGATTGCTCCGGGCG 61.881 66.667 0.00 0.00 45.43 6.13
1255 3974 2.586245 CGGCCAGAGATCCAGCAA 59.414 61.111 2.24 0.00 0.00 3.91
1257 3976 0.883814 CGGCCAGAGATCCAGCAATC 60.884 60.000 2.24 0.00 0.00 2.67
1262 3981 1.047002 AGAGATCCAGCAATCCGAGG 58.953 55.000 0.00 0.00 0.00 4.63
1326 4045 2.037772 CTCCCTCCCATAAATGTCGGAG 59.962 54.545 7.80 7.80 41.41 4.63
1362 4081 4.988598 ACGGTGCTGTTCGGGCTG 62.989 66.667 0.00 0.00 0.00 4.85
1452 4171 4.742201 TGCTTCCTCGGCTCACGC 62.742 66.667 0.00 0.00 43.86 5.34
1946 4677 6.674066 TGCTTAACAACAGGTATTTTACAGC 58.326 36.000 0.00 0.00 0.00 4.40
1978 4710 3.942829 TCATGGAACTCGCTCTGAAAAT 58.057 40.909 0.00 0.00 0.00 1.82
1984 4716 5.529430 TGGAACTCGCTCTGAAAATTTTACA 59.471 36.000 2.75 3.51 0.00 2.41
1994 4726 9.730420 GCTCTGAAAATTTTACAGTAACTTGAA 57.270 29.630 20.24 6.91 33.93 2.69
2013 4745 6.093219 ACTTGAAATTGTCATCTCGGATGAAG 59.907 38.462 15.34 10.40 35.70 3.02
2020 4752 1.667724 CATCTCGGATGAAGGTGTTGC 59.332 52.381 7.82 0.00 0.00 4.17
2077 4811 3.301794 TTGCATTGGCTATGGATCACT 57.698 42.857 10.82 0.00 41.91 3.41
2250 5224 2.094659 CCCACGTGATCAGTGTCGC 61.095 63.158 19.30 0.00 37.88 5.19
2271 5245 1.329906 CTGCTGGATTGCGTTCATCTC 59.670 52.381 0.00 0.00 35.36 2.75
2274 5248 2.208431 CTGGATTGCGTTCATCTCCTC 58.792 52.381 0.00 0.00 0.00 3.71
2342 5334 1.139853 GGGAGGAGTAAGTGCAGATGG 59.860 57.143 0.00 0.00 0.00 3.51
2353 5345 2.821366 CAGATGGCGAGGTGGTGC 60.821 66.667 0.00 0.00 0.00 5.01
2354 5346 4.457496 AGATGGCGAGGTGGTGCG 62.457 66.667 0.00 0.00 0.00 5.34
2394 5387 2.483106 CTGCTCGATGAAATGCCTATGG 59.517 50.000 0.00 0.00 0.00 2.74
2396 5389 2.430465 CTCGATGAAATGCCTATGGGG 58.570 52.381 0.00 0.00 38.36 4.96
2397 5390 1.073763 TCGATGAAATGCCTATGGGGG 59.926 52.381 0.00 0.00 35.12 5.40
2398 5391 1.073763 CGATGAAATGCCTATGGGGGA 59.926 52.381 0.00 0.00 40.52 4.81
2399 5392 2.800250 GATGAAATGCCTATGGGGGAG 58.200 52.381 0.00 0.00 39.29 4.30
2400 5393 1.905839 TGAAATGCCTATGGGGGAGA 58.094 50.000 0.00 0.00 39.29 3.71
2401 5394 1.776667 TGAAATGCCTATGGGGGAGAG 59.223 52.381 0.00 0.00 39.29 3.20
2437 5450 4.572978 AGGACAGAGGGTAGAGAGAGATA 58.427 47.826 0.00 0.00 0.00 1.98
2438 5451 5.170198 AGGACAGAGGGTAGAGAGAGATAT 58.830 45.833 0.00 0.00 0.00 1.63
2439 5452 5.615261 AGGACAGAGGGTAGAGAGAGATATT 59.385 44.000 0.00 0.00 0.00 1.28
2440 5453 5.710099 GGACAGAGGGTAGAGAGAGATATTG 59.290 48.000 0.00 0.00 0.00 1.90
2441 5454 5.076873 ACAGAGGGTAGAGAGAGATATTGC 58.923 45.833 0.00 0.00 0.00 3.56
2442 5455 4.462483 CAGAGGGTAGAGAGAGATATTGCC 59.538 50.000 0.00 0.00 0.00 4.52
2443 5456 4.107149 AGAGGGTAGAGAGAGATATTGCCA 59.893 45.833 0.00 0.00 0.00 4.92
2444 5457 4.415596 AGGGTAGAGAGAGATATTGCCAG 58.584 47.826 0.00 0.00 0.00 4.85
2445 5458 3.513515 GGGTAGAGAGAGATATTGCCAGG 59.486 52.174 0.00 0.00 0.00 4.45
2448 5461 3.652055 AGAGAGAGATATTGCCAGGTGT 58.348 45.455 0.00 0.00 0.00 4.16
2471 5484 0.512952 GTGTGCGATGACCTGTCAAC 59.487 55.000 3.79 0.65 43.58 3.18
2481 5494 1.004277 GACCTGTCAACCCCATGCTTA 59.996 52.381 0.00 0.00 0.00 3.09
2482 5495 1.004745 ACCTGTCAACCCCATGCTTAG 59.995 52.381 0.00 0.00 0.00 2.18
2556 5576 1.995376 AGTGCAAGTTTCCCGGATTT 58.005 45.000 0.73 0.00 0.00 2.17
2567 5587 0.626916 CCCGGATTTGGGGTTAAGGA 59.373 55.000 0.73 0.00 46.17 3.36
2575 5595 4.757019 TTTGGGGTTAAGGAACAAAACC 57.243 40.909 0.00 0.00 42.34 3.27
2673 5693 5.703978 TGGATTGGTCAATGTTTAGTGTG 57.296 39.130 0.43 0.00 0.00 3.82
2676 5696 6.773200 TGGATTGGTCAATGTTTAGTGTGTTA 59.227 34.615 0.43 0.00 0.00 2.41
2685 5705 9.602568 TCAATGTTTAGTGTGTTACTCAAACTA 57.397 29.630 0.00 0.00 42.28 2.24
2760 5784 1.200020 GTTGAGGTCGAAGCAATTGGG 59.800 52.381 7.72 0.00 0.00 4.12
2781 5805 0.307760 GTGTTCGGCACAAGAACCTG 59.692 55.000 6.63 0.00 46.91 4.00
2817 5841 0.331278 ATTGTGCCGAGGGGAATCAA 59.669 50.000 0.00 0.00 34.06 2.57
2825 5849 3.181448 GCCGAGGGGAATCAAAGGTATTA 60.181 47.826 0.00 0.00 34.06 0.98
2835 5860 8.749354 GGGAATCAAAGGTATTATCTTGTTGTT 58.251 33.333 0.00 0.00 0.00 2.83
2843 5868 3.513462 TTATCTTGTTGTTCGTGCACG 57.487 42.857 32.76 32.76 41.45 5.34
2856 5881 5.177881 TGTTCGTGCACGTTATTTGATTACT 59.822 36.000 35.74 0.00 40.80 2.24
2860 5885 5.282778 CGTGCACGTTATTTGATTACTTTGG 59.717 40.000 30.50 0.00 34.11 3.28
2867 5892 8.073768 ACGTTATTTGATTACTTTGGTGAGTTG 58.926 33.333 0.00 0.00 0.00 3.16
2893 5918 4.836125 ATCAACAATTATGGATCGTGGC 57.164 40.909 0.00 0.00 0.00 5.01
2901 5926 2.154854 ATGGATCGTGGCGATGTAAG 57.845 50.000 8.82 0.00 47.00 2.34
2912 5937 2.420022 GGCGATGTAAGTGTTGCTCATT 59.580 45.455 0.00 0.00 0.00 2.57
2913 5938 3.485877 GGCGATGTAAGTGTTGCTCATTC 60.486 47.826 0.00 0.00 0.00 2.67
2914 5939 3.372206 GCGATGTAAGTGTTGCTCATTCT 59.628 43.478 0.00 0.00 0.00 2.40
2921 5949 8.165239 TGTAAGTGTTGCTCATTCTGTTATTT 57.835 30.769 0.00 0.00 0.00 1.40
2983 6011 2.438434 CAATGGCTCCACGGGGAC 60.438 66.667 0.00 0.00 38.64 4.46
3064 6092 2.280797 GGGTGCGTGTTGCTCAGA 60.281 61.111 0.00 0.00 46.63 3.27
3121 6149 5.700722 AGTCACGTAAACATCTCACACTA 57.299 39.130 0.00 0.00 0.00 2.74
3159 6187 1.941377 ATTTGCATGAGGGGCTTGAA 58.059 45.000 0.00 0.00 0.00 2.69
3162 6190 1.304381 GCATGAGGGGCTTGAACCA 60.304 57.895 0.00 0.00 0.00 3.67
3259 6287 2.613223 GGACTTGCGAAACTCTTAGGCT 60.613 50.000 0.00 0.00 0.00 4.58
3393 6421 4.764679 TGTTGTTGATCATTGCAGGTAC 57.235 40.909 0.00 0.00 0.00 3.34
3848 6879 7.680730 ACAACAGAGATGTAGGTCAATAAAGT 58.319 34.615 0.00 0.00 0.00 2.66
3891 6922 9.169592 GGATTTTCATTTGATTTGGACATTCAT 57.830 29.630 0.00 0.00 0.00 2.57
3905 6936 6.169800 TGGACATTCATGATCGTAAAGACAA 58.830 36.000 0.00 0.00 0.00 3.18
4183 7217 2.787473 TTTAGTGTCAGCCATGGAGG 57.213 50.000 18.40 6.31 41.84 4.30
4372 7406 4.033894 GTGACTTGCACTGACGCT 57.966 55.556 0.00 0.00 44.27 5.07
4400 7434 8.637986 ACACCATTTAAAGAAGCTTCACATTTA 58.362 29.630 27.57 19.23 0.00 1.40
4430 7464 8.747538 AGTTTGACTTAAGACAATACCAAACT 57.252 30.769 18.69 18.66 44.06 2.66
4484 7518 6.672266 AGTACTGGAGATCAAAGAAGAACA 57.328 37.500 0.00 0.00 0.00 3.18
4549 7583 4.866508 AATCCGGGTTTCTTTTTCCTTC 57.133 40.909 0.00 0.00 0.00 3.46
4565 7599 3.631250 TCCTTCTGTTGCCTTCTTGTTT 58.369 40.909 0.00 0.00 0.00 2.83
4636 7670 2.152830 GTGCCCGTGTACAAATAACCA 58.847 47.619 0.00 0.00 0.00 3.67
4754 7788 7.015877 AGTCAGTACACCCACTGTTCTAAATTA 59.984 37.037 0.00 0.00 45.11 1.40
4804 7849 8.311109 AGTCAAACTTGTTTAACTTTGACCAAT 58.689 29.630 24.59 12.81 43.28 3.16
4990 8035 7.848875 TCAATTAATTTGGAAATGGGGGAGTAT 59.151 33.333 0.00 0.00 35.92 2.12
4996 8041 3.031013 GGAAATGGGGGAGTATTTGGTG 58.969 50.000 0.00 0.00 0.00 4.17
4998 8043 0.261696 ATGGGGGAGTATTTGGTGCC 59.738 55.000 0.00 0.00 0.00 5.01
5252 8299 1.103803 AGCTGATATGTCGTGACCGT 58.896 50.000 0.00 0.00 35.01 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 1033 1.420430 TCGGGAAGAAGTCAACAGGT 58.580 50.000 0.00 0.00 0.00 4.00
229 1034 2.543777 TTCGGGAAGAAGTCAACAGG 57.456 50.000 0.00 0.00 34.26 4.00
230 1035 4.893424 TTTTTCGGGAAGAAGTCAACAG 57.107 40.909 0.00 0.00 40.40 3.16
438 3077 6.678411 ACCCATATACACCCTATATGAGCAAT 59.322 38.462 8.36 0.00 39.19 3.56
441 3080 7.857404 ATACCCATATACACCCTATATGAGC 57.143 40.000 8.36 0.00 39.19 4.26
468 3124 3.494924 CCAATAGCGGTGAATGATCTGGA 60.495 47.826 0.00 0.00 0.00 3.86
534 3205 4.686191 ATCATTTGTTTTTGCAGGGTGA 57.314 36.364 0.00 0.00 0.00 4.02
574 3245 3.751698 GGTTGCGACTTTTCTAATCCTGT 59.248 43.478 3.59 0.00 0.00 4.00
635 3306 3.126831 GTGTCTGCTGATATCCTTTCCG 58.873 50.000 0.00 0.00 0.00 4.30
636 3307 4.141846 TGAGTGTCTGCTGATATCCTTTCC 60.142 45.833 0.00 0.00 0.00 3.13
654 3325 0.036952 ATTGCGGTGAGGAGTGAGTG 60.037 55.000 0.00 0.00 0.00 3.51
684 3355 4.017130 AGGAGAAGGGAGGCAAATGTTTAT 60.017 41.667 0.00 0.00 0.00 1.40
737 3418 0.886490 GTATGCATGGGAGGAAGCCG 60.886 60.000 10.16 0.00 0.00 5.52
738 3419 0.886490 CGTATGCATGGGAGGAAGCC 60.886 60.000 10.16 0.00 0.00 4.35
812 3507 5.576563 TGACAATTGAAGGGAAGAAGGTA 57.423 39.130 13.59 0.00 0.00 3.08
1100 3819 0.404040 ATCGGGTGCAAAAGGGAAGA 59.596 50.000 0.00 0.00 0.00 2.87
1196 3915 1.786937 AAGATCATCGGACTCTGCCT 58.213 50.000 0.00 0.00 0.00 4.75
1237 3956 2.955022 ATTGCTGGATCTCTGGCCGC 62.955 60.000 0.00 0.00 0.00 6.53
1252 3971 1.821332 CTTGCTCCCCTCGGATTGC 60.821 63.158 0.00 0.00 37.60 3.56
1255 3974 1.977293 GCTTCTTGCTCCCCTCGGAT 61.977 60.000 0.00 0.00 37.60 4.18
1257 3976 2.124942 GCTTCTTGCTCCCCTCGG 60.125 66.667 0.00 0.00 38.95 4.63
1310 4029 1.411246 CCGACTCCGACATTTATGGGA 59.589 52.381 0.00 0.00 38.22 4.37
1620 4351 2.185350 CGCTGCTCCTTGACCGAT 59.815 61.111 0.00 0.00 0.00 4.18
1782 4513 2.351276 GTGTACCAGTGGCCCCAG 59.649 66.667 9.78 0.00 0.00 4.45
1911 4642 5.163663 CCTGTTGTTAAGCAAGTTCTTGACA 60.164 40.000 15.52 8.31 39.69 3.58
1946 4677 5.812642 AGCGAGTTCCATGAATAGTAAGTTG 59.187 40.000 0.00 0.00 0.00 3.16
1984 4716 6.464222 TCCGAGATGACAATTTCAAGTTACT 58.536 36.000 0.00 0.00 37.92 2.24
1994 4726 4.194640 CACCTTCATCCGAGATGACAATT 58.805 43.478 13.90 0.62 0.00 2.32
2013 4745 5.849564 ATGATATTTCAACGTTGGCAACACC 60.850 40.000 28.12 12.12 40.69 4.16
2020 4752 8.064222 GTGACAGATATGATATTTCAACGTTGG 58.936 37.037 27.02 9.69 34.96 3.77
2091 4826 8.842777 CAAATTCAAATTCAAATTCAAATCGGC 58.157 29.630 0.08 0.00 0.00 5.54
2250 5224 0.379669 GATGAACGCAATCCAGCAGG 59.620 55.000 0.00 0.00 0.00 4.85
2271 5245 4.803426 GCACCAGAGCCGACGAGG 62.803 72.222 0.00 0.00 44.97 4.63
2357 5349 2.736236 AGTTGCAGTGCGCTCTCG 60.736 61.111 9.42 6.77 43.06 4.04
2368 5361 1.135603 GCATTTCATCGAGCAGTTGCA 60.136 47.619 6.90 0.00 45.16 4.08
2394 5387 4.222588 CCTTGTCATCATATCTCTCTCCCC 59.777 50.000 0.00 0.00 0.00 4.81
2396 5389 5.538053 TGTCCTTGTCATCATATCTCTCTCC 59.462 44.000 0.00 0.00 0.00 3.71
2397 5390 6.489700 TCTGTCCTTGTCATCATATCTCTCTC 59.510 42.308 0.00 0.00 0.00 3.20
2398 5391 6.372104 TCTGTCCTTGTCATCATATCTCTCT 58.628 40.000 0.00 0.00 0.00 3.10
2399 5392 6.294675 CCTCTGTCCTTGTCATCATATCTCTC 60.295 46.154 0.00 0.00 0.00 3.20
2400 5393 5.539574 CCTCTGTCCTTGTCATCATATCTCT 59.460 44.000 0.00 0.00 0.00 3.10
2401 5394 5.279406 CCCTCTGTCCTTGTCATCATATCTC 60.279 48.000 0.00 0.00 0.00 2.75
2437 5450 0.538057 CACACCTGACACCTGGCAAT 60.538 55.000 0.00 0.00 35.04 3.56
2438 5451 1.152984 CACACCTGACACCTGGCAA 60.153 57.895 0.00 0.00 35.04 4.52
2439 5452 2.510411 CACACCTGACACCTGGCA 59.490 61.111 0.00 0.00 35.04 4.92
2440 5453 2.980233 GCACACCTGACACCTGGC 60.980 66.667 0.00 0.00 35.04 4.85
2441 5454 2.454832 ATCGCACACCTGACACCTGG 62.455 60.000 0.00 0.00 37.41 4.45
2442 5455 1.004560 ATCGCACACCTGACACCTG 60.005 57.895 0.00 0.00 0.00 4.00
2443 5456 1.004560 CATCGCACACCTGACACCT 60.005 57.895 0.00 0.00 0.00 4.00
2444 5457 1.005037 TCATCGCACACCTGACACC 60.005 57.895 0.00 0.00 0.00 4.16
2445 5458 1.291877 GGTCATCGCACACCTGACAC 61.292 60.000 4.52 0.00 40.80 3.67
2448 5461 3.791640 AGGTCATCGCACACCTGA 58.208 55.556 0.00 0.00 41.79 3.86
2481 5494 0.671781 CTAGCCAAAGCGTGCTGACT 60.672 55.000 0.00 0.00 46.67 3.41
2482 5495 1.639298 CCTAGCCAAAGCGTGCTGAC 61.639 60.000 0.00 0.00 46.67 3.51
2567 5587 4.729227 ATCGACAAGTTTGGGTTTTGTT 57.271 36.364 0.00 0.00 35.35 2.83
2575 5595 4.377022 CCGTCAACTAATCGACAAGTTTGG 60.377 45.833 10.67 9.53 33.72 3.28
2576 5596 4.446385 TCCGTCAACTAATCGACAAGTTTG 59.554 41.667 10.67 7.70 33.72 2.93
2577 5597 4.446719 GTCCGTCAACTAATCGACAAGTTT 59.553 41.667 10.67 0.00 33.72 2.66
2623 5643 7.677982 GCCGGTCCTAAAAAGTTGAACATATAC 60.678 40.741 1.90 0.00 0.00 1.47
2692 5712 7.272244 CCCCTAACAAGTCAAGAAAACAAAAT 58.728 34.615 0.00 0.00 0.00 1.82
2781 5805 2.224305 ACAATATCCTAGAAGGCGCACC 60.224 50.000 10.83 0.00 34.61 5.01
2817 5841 5.703592 TGCACGAACAACAAGATAATACCTT 59.296 36.000 0.00 0.00 0.00 3.50
2825 5849 1.295792 ACGTGCACGAACAACAAGAT 58.704 45.000 42.94 16.00 43.02 2.40
2835 5860 5.849357 AAGTAATCAAATAACGTGCACGA 57.151 34.783 42.94 24.35 43.02 4.35
2856 5881 7.581213 ATTGTTGATTCTACAACTCACCAAA 57.419 32.000 14.43 0.00 46.79 3.28
2860 5885 8.946085 TCCATAATTGTTGATTCTACAACTCAC 58.054 33.333 14.43 0.00 46.79 3.51
2867 5892 7.576236 CCACGATCCATAATTGTTGATTCTAC 58.424 38.462 0.00 0.00 28.71 2.59
2888 5913 0.179225 GCAACACTTACATCGCCACG 60.179 55.000 0.00 0.00 0.00 4.94
2893 5918 4.389992 ACAGAATGAGCAACACTTACATCG 59.610 41.667 0.00 0.00 39.69 3.84
2901 5926 8.296713 TCCTAAAAATAACAGAATGAGCAACAC 58.703 33.333 0.00 0.00 39.69 3.32
2912 5937 7.759489 ACACAAGCATCCTAAAAATAACAGA 57.241 32.000 0.00 0.00 0.00 3.41
2913 5938 7.692291 CGTACACAAGCATCCTAAAAATAACAG 59.308 37.037 0.00 0.00 0.00 3.16
2914 5939 7.388224 TCGTACACAAGCATCCTAAAAATAACA 59.612 33.333 0.00 0.00 0.00 2.41
2921 5949 4.530710 ACTCGTACACAAGCATCCTAAA 57.469 40.909 0.00 0.00 0.00 1.85
2983 6011 1.376812 GGGGCTTACAGGTCCAACG 60.377 63.158 0.00 0.00 31.57 4.10
3052 6080 3.935203 AGTTATCCAATCTGAGCAACACG 59.065 43.478 0.00 0.00 0.00 4.49
3121 6149 9.627123 ATGCAAATACAATAACCTACACTACAT 57.373 29.630 0.00 0.00 0.00 2.29
3136 6164 2.496871 CAAGCCCCTCATGCAAATACAA 59.503 45.455 0.00 0.00 0.00 2.41
3259 6287 4.452114 TGTAGTTACGTAACTTCGCTCTGA 59.548 41.667 37.78 19.73 43.57 3.27
3393 6421 1.148157 CCGCATACTCTGGAGCAACG 61.148 60.000 0.00 0.00 0.00 4.10
3546 6574 7.408756 AAATGCATTAACAAGCTCATAAGGA 57.591 32.000 13.39 0.00 0.00 3.36
3662 6693 0.036875 CCACAACCCCCTCAGAGTTC 59.963 60.000 0.00 0.00 0.00 3.01
3877 6908 7.852945 GTCTTTACGATCATGAATGTCCAAATC 59.147 37.037 0.00 0.00 0.00 2.17
3880 6911 6.169800 TGTCTTTACGATCATGAATGTCCAA 58.830 36.000 0.00 0.00 0.00 3.53
3891 6922 9.377312 TCATATGTTTCATTGTCTTTACGATCA 57.623 29.630 1.90 0.00 0.00 2.92
3925 6956 9.412460 TCCTGAAATTAGCAATAAGATGATGTT 57.588 29.630 0.00 0.00 0.00 2.71
4282 7316 8.740123 TCTGTTGTTAACTTAAAAGGATCACA 57.260 30.769 7.22 0.00 0.00 3.58
4372 7406 5.592282 TGTGAAGCTTCTTTAAATGGTGTCA 59.408 36.000 26.09 0.00 0.00 3.58
4400 7434 9.403583 TGGTATTGTCTTAAGTCAAACTTCTTT 57.596 29.630 17.11 4.09 39.51 2.52
4430 7464 5.069781 CCCCACAGTTCCAAATTAAGTGAAA 59.930 40.000 2.05 0.00 32.66 2.69
4549 7583 4.108699 TGTTCAAACAAGAAGGCAACAG 57.891 40.909 0.00 0.00 35.67 3.16
4565 7599 2.622942 GCCAAAGTTCCTCACATGTTCA 59.377 45.455 0.00 0.00 0.00 3.18
4614 7648 2.095617 GGTTATTTGTACACGGGCACAC 60.096 50.000 0.00 0.00 0.00 3.82
4636 7670 7.054124 TGCCCTTCAAACGAGAAATATCTTAT 58.946 34.615 0.00 0.00 35.54 1.73
4754 7788 8.543774 ACTTCAGACATATCTACAACTCCAATT 58.456 33.333 0.00 0.00 32.25 2.32


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

AutoCloner maintained by Alex Coulton.