Multiple sequence alignment - TraesCS3D01G123600

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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 TraesCS3D01G123600 chr3D 100.000 4147 0 0 1 4147 81372008 81367862 0.000000e+00 7659.0
1 TraesCS3D01G123600 chr3A 93.513 2451 110 22 1384 3805 95533844 95531414 0.000000e+00 3600.0
2 TraesCS3D01G123600 chr3A 84.691 1424 96 53 25 1389 95535587 95534227 0.000000e+00 1310.0
3 TraesCS3D01G123600 chr3B 94.413 1933 79 12 1586 3506 127296514 127294599 0.000000e+00 2944.0
4 TraesCS3D01G123600 chr3B 88.235 1547 100 43 1 1525 127298031 127296545 0.000000e+00 1773.0
5 TraesCS3D01G123600 chr3B 93.548 248 13 1 3560 3804 127294600 127294353 2.360000e-97 366.0
6 TraesCS3D01G123600 chr3B 89.024 246 21 4 3849 4089 127294032 127293788 2.420000e-77 300.0
7 TraesCS3D01G123600 chr3B 97.959 49 1 0 4099 4147 127293690 127293642 7.390000e-13 86.1
8 TraesCS3D01G123600 chr5A 100.000 28 0 0 3505 3532 48464242 48464269 7.000000e-03 52.8


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 TraesCS3D01G123600 chr3D 81367862 81372008 4146 True 7659.00 7659 100.0000 1 4147 1 chr3D.!!$R1 4146
1 TraesCS3D01G123600 chr3A 95531414 95535587 4173 True 2455.00 3600 89.1020 25 3805 2 chr3A.!!$R1 3780
2 TraesCS3D01G123600 chr3B 127293642 127298031 4389 True 1093.82 2944 92.6358 1 4147 5 chr3B.!!$R1 4146

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
147 148 0.251787 GCCCTGAAGAAATGGGTGGT 60.252 55.0 0.00 0.00 42.77 4.16 F
726 772 0.399949 ATATCAAGGTGGGCCCTCGA 60.400 55.0 25.70 12.83 45.47 4.04 F
1215 1285 0.601558 TTCCTTCTCCGTTGGACTCG 59.398 55.0 0.00 0.00 0.00 4.18 F
2756 3234 0.249953 TTGGGCTTGCATTTGTGCTG 60.250 50.0 1.86 0.00 35.49 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1312 0.034896 GAACCTGCAAAGACCCGAGA 59.965 55.000 0.0 0.0 0.00 4.04 R
1656 2124 0.663153 AACGTTTTCCACTCAGCAGC 59.337 50.000 0.0 0.0 0.00 5.25 R
2837 3315 2.388735 TCGATCAGGCTTCCACATAGT 58.611 47.619 0.0 0.0 0.00 2.12 R
3860 4645 0.036022 GAGCAAGAGTTCCAGCAGGT 59.964 55.000 0.0 0.0 35.89 4.00 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
46 47 7.487829 CACTGGTCCGGAAATATTGTTTTATTG 59.512 37.037 5.23 0.00 0.00 1.90
49 50 8.030106 TGGTCCGGAAATATTGTTTTATTGAAC 58.970 33.333 5.23 0.00 0.00 3.18
63 64 1.732941 TTGAACGGCTATGCGATGTT 58.267 45.000 0.00 0.00 0.00 2.71
98 99 1.533033 TGACCTCAGAGGCCGAACA 60.533 57.895 17.31 6.59 39.63 3.18
147 148 0.251787 GCCCTGAAGAAATGGGTGGT 60.252 55.000 0.00 0.00 42.77 4.16
162 163 2.041755 GGGTGGTGGGAGAAGAGATTTT 59.958 50.000 0.00 0.00 0.00 1.82
221 222 3.625853 GAAGCAGGGGAAGATTTTAGCT 58.374 45.455 0.00 0.00 0.00 3.32
256 257 7.885009 ACTGTATTTTCTCTAGGGTACTCTC 57.115 40.000 0.00 0.00 0.00 3.20
318 322 6.479006 TGATGATCATCACCTTTTGAAGAGT 58.521 36.000 30.27 0.00 42.42 3.24
360 364 6.773638 TGGTCATCTTAAAAGCTTCTCTCTT 58.226 36.000 0.00 0.00 0.00 2.85
372 376 9.598517 AAAAGCTTCTCTCTTTAGTATCTGATG 57.401 33.333 0.00 0.00 33.77 3.07
373 377 8.532186 AAGCTTCTCTCTTTAGTATCTGATGA 57.468 34.615 0.00 0.00 0.00 2.92
374 378 8.710749 AGCTTCTCTCTTTAGTATCTGATGAT 57.289 34.615 0.00 0.00 36.74 2.45
375 379 8.579006 AGCTTCTCTCTTTAGTATCTGATGATG 58.421 37.037 0.00 0.00 34.32 3.07
376 380 8.575589 GCTTCTCTCTTTAGTATCTGATGATGA 58.424 37.037 0.00 0.00 34.32 2.92
379 383 9.804977 TCTCTCTTTAGTATCTGATGATGATGA 57.195 33.333 0.00 0.00 34.32 2.92
381 385 9.022884 TCTCTTTAGTATCTGATGATGATGAGG 57.977 37.037 0.00 0.00 34.32 3.86
382 386 8.946797 TCTTTAGTATCTGATGATGATGAGGA 57.053 34.615 0.00 0.00 34.32 3.71
383 387 9.544579 TCTTTAGTATCTGATGATGATGAGGAT 57.455 33.333 0.00 0.00 34.32 3.24
384 388 9.589111 CTTTAGTATCTGATGATGATGAGGATG 57.411 37.037 0.00 0.00 34.32 3.51
389 393 6.875972 TCTGATGATGATGAGGATGATGAT 57.124 37.500 0.00 0.00 0.00 2.45
391 395 5.186198 TGATGATGATGAGGATGATGATGC 58.814 41.667 0.00 0.00 0.00 3.91
399 403 6.156256 TGATGAGGATGATGATGCTGATGATA 59.844 38.462 0.00 0.00 28.67 2.15
516 525 6.112058 ACAAGGCAAACAACATGTGTATTTT 58.888 32.000 0.00 0.00 40.60 1.82
525 534 7.060383 ACAACATGTGTATTTTCCATGGAAA 57.940 32.000 31.75 31.75 39.29 3.13
629 638 8.612619 TGATGACTTGTTACTTCTTCTGTTTTC 58.387 33.333 0.00 0.00 0.00 2.29
665 694 8.994429 AAACTTGTTTTGTATTTCATGTGACA 57.006 26.923 0.00 0.00 0.00 3.58
724 770 1.215423 ACAATATCAAGGTGGGCCCTC 59.785 52.381 25.70 20.64 45.47 4.30
726 772 0.399949 ATATCAAGGTGGGCCCTCGA 60.400 55.000 25.70 12.83 45.47 4.04
736 782 2.618709 GTGGGCCCTCGATGAAAAATAG 59.381 50.000 25.70 0.00 0.00 1.73
740 786 2.230660 CCCTCGATGAAAAATAGGGGC 58.769 52.381 0.00 0.00 42.79 5.80
742 789 2.618709 CCTCGATGAAAAATAGGGGCAC 59.381 50.000 0.00 0.00 0.00 5.01
745 792 2.650322 GATGAAAAATAGGGGCACGGA 58.350 47.619 0.00 0.00 0.00 4.69
747 794 3.935818 TGAAAAATAGGGGCACGGATA 57.064 42.857 0.00 0.00 0.00 2.59
757 804 1.702491 GGCACGGATAACAACTCGGC 61.702 60.000 0.00 0.00 0.00 5.54
811 858 5.440685 CAAAACATAACGATATTCTCCGGC 58.559 41.667 0.00 0.00 0.00 6.13
843 890 5.805728 TCTTAAACCTGAAGGAATCTCACC 58.194 41.667 2.62 0.00 38.94 4.02
847 906 1.649664 CTGAAGGAATCTCACCAGCG 58.350 55.000 0.00 0.00 0.00 5.18
971 1037 3.083600 GAATCGGCGGCGAGTTGTG 62.084 63.158 36.74 5.78 0.00 3.33
1215 1285 0.601558 TTCCTTCTCCGTTGGACTCG 59.398 55.000 0.00 0.00 0.00 4.18
1235 1312 3.138798 CGTGACGGGGATCTCGGT 61.139 66.667 5.32 5.32 33.17 4.69
1350 1427 2.637947 GATCCTGAGTTCAAAGAGGGC 58.362 52.381 0.00 0.00 0.00 5.19
1396 1861 1.807573 GCTCCTTCCGTTGCTCTCG 60.808 63.158 0.00 0.00 0.00 4.04
1407 1872 3.243877 CCGTTGCTCTCGTTTATCATCTG 59.756 47.826 0.00 0.00 0.00 2.90
1409 1874 4.027295 CGTTGCTCTCGTTTATCATCTGTC 60.027 45.833 0.00 0.00 0.00 3.51
1424 1890 7.623999 ATCATCTGTCCCAATTATACTCTGT 57.376 36.000 0.00 0.00 0.00 3.41
1448 1916 1.152368 GGATGGGCAGATCTTGGGG 59.848 63.158 0.00 0.00 0.00 4.96
1468 1936 3.010420 GGAGCTGGTCTTGGTATTGTTC 58.990 50.000 6.83 0.00 0.00 3.18
1487 1955 2.483876 TCGGGATGCTTGATTTCGATC 58.516 47.619 0.00 0.00 0.00 3.69
1497 1965 5.753438 TGCTTGATTTCGATCATGTACTACC 59.247 40.000 0.00 0.00 0.00 3.18
1660 2128 3.187227 TCTGTCAAAAGAGAATTCGCTGC 59.813 43.478 12.75 2.52 0.00 5.25
1679 2147 2.159448 TGCTGAGTGGAAAACGTTTGTG 60.159 45.455 15.46 0.63 0.00 3.33
1790 2265 7.543756 TGATGATTACGTGATAGACAGAAACA 58.456 34.615 0.00 0.00 0.00 2.83
1791 2266 8.197439 TGATGATTACGTGATAGACAGAAACAT 58.803 33.333 0.00 0.00 0.00 2.71
1806 2281 8.575589 AGACAGAAACATGTGTTAATTTGCATA 58.424 29.630 0.00 0.00 37.25 3.14
1905 2380 6.325919 TGTGAATAGCAAACTTTGGTTAGG 57.674 37.500 11.31 0.00 42.20 2.69
1919 2394 4.911514 TGGTTAGGACAAAAGCAACTTC 57.088 40.909 0.00 0.00 31.82 3.01
1946 2421 7.697352 TCTATAGAGAACGTCGAGAACTTAG 57.303 40.000 0.00 0.00 0.00 2.18
2048 2523 1.689984 TGGTTGCTGCATCAAGTTGA 58.310 45.000 8.27 8.27 0.00 3.18
2049 2524 2.030371 TGGTTGCTGCATCAAGTTGAA 58.970 42.857 10.14 0.00 0.00 2.69
2050 2525 2.034939 TGGTTGCTGCATCAAGTTGAAG 59.965 45.455 10.14 6.70 0.00 3.02
2051 2526 2.035066 GGTTGCTGCATCAAGTTGAAGT 59.965 45.455 10.14 0.00 0.00 3.01
2052 2527 3.047796 GTTGCTGCATCAAGTTGAAGTG 58.952 45.455 10.14 5.88 0.00 3.16
2053 2528 2.300433 TGCTGCATCAAGTTGAAGTGT 58.700 42.857 10.14 0.00 0.00 3.55
2054 2529 2.689471 TGCTGCATCAAGTTGAAGTGTT 59.311 40.909 10.14 0.00 0.00 3.32
2055 2530 3.047796 GCTGCATCAAGTTGAAGTGTTG 58.952 45.455 10.14 4.35 0.00 3.33
2137 2612 2.356135 CAATCTGTTACACCTTCCCCG 58.644 52.381 0.00 0.00 0.00 5.73
2220 2696 7.389232 TCAACATATCTAATGAGATGCGGAAT 58.611 34.615 2.42 0.00 43.52 3.01
2282 2758 3.056107 TGACCTCCGTTGTTGAGATAAGG 60.056 47.826 0.00 0.00 31.26 2.69
2580 3057 7.376866 CGAATTATCACAACATTCAAGGTATGC 59.623 37.037 0.00 0.00 0.00 3.14
2582 3059 7.643569 TTATCACAACATTCAAGGTATGCAT 57.356 32.000 3.79 3.79 0.00 3.96
2583 3060 5.313520 TCACAACATTCAAGGTATGCATG 57.686 39.130 10.16 0.00 38.46 4.06
2599 3076 9.466497 AGGTATGCATGAAATCTTCTTTTCTAA 57.534 29.630 10.16 0.00 36.71 2.10
2756 3234 0.249953 TTGGGCTTGCATTTGTGCTG 60.250 50.000 1.86 0.00 35.49 4.41
2876 3354 0.732571 ATTCATTACTGGGCGCAACG 59.267 50.000 10.83 0.00 0.00 4.10
2927 3405 4.072131 GCAAGAAGGTATGACACTCCAAA 58.928 43.478 1.42 0.00 0.00 3.28
2957 3436 9.146984 TGTAGATTGCTATATGTTAAATACCGC 57.853 33.333 0.00 0.00 0.00 5.68
2964 3443 8.450180 TGCTATATGTTAAATACCGCAATCATG 58.550 33.333 0.00 0.00 0.00 3.07
2970 3449 7.542890 TGTTAAATACCGCAATCATGTTTGAT 58.457 30.769 18.58 7.03 44.62 2.57
3276 3755 9.562408 TTTATTTACTATTGGTGATATTGGCGA 57.438 29.630 0.00 0.00 0.00 5.54
3290 3769 2.823196 TGGCGATTGTTGATTTAGCG 57.177 45.000 0.00 0.00 0.00 4.26
3300 3781 7.201149 CGATTGTTGATTTAGCGTTAGTGTTTG 60.201 37.037 0.00 0.00 0.00 2.93
3406 3888 5.324409 TGGTTCTGCCAGAATATTGTTTCT 58.676 37.500 10.87 0.00 43.61 2.52
3512 3996 5.989777 TCGCTTATTTAATTGCTACTCCCTC 59.010 40.000 0.00 0.00 0.00 4.30
3514 3998 6.146347 CGCTTATTTAATTGCTACTCCCTCTC 59.854 42.308 0.00 0.00 0.00 3.20
3519 4003 8.966069 ATTTAATTGCTACTCCCTCTCTAAAC 57.034 34.615 0.00 0.00 0.00 2.01
3520 4004 7.735326 TTAATTGCTACTCCCTCTCTAAACT 57.265 36.000 0.00 0.00 0.00 2.66
3704 4210 6.316390 CACATAAAGATAGTTGGACCCAGTTC 59.684 42.308 0.00 0.00 0.00 3.01
3735 4241 9.715121 AATGTACAAAATCTCAAGAATGCATTT 57.285 25.926 14.33 0.77 0.00 2.32
3738 4244 9.362539 GTACAAAATCTCAAGAATGCATTTCAT 57.637 29.630 14.33 0.00 36.75 2.57
3804 4313 9.823647 TCACAAGGCATTTAATTAAACTCAAAA 57.176 25.926 12.74 0.00 0.00 2.44
3823 4588 8.859090 ACTCAAAAATACAATGAATTCACTGGA 58.141 29.630 20.06 13.05 0.00 3.86
3851 4636 9.638239 CTAGAGCTCTTGAATGAATATAGGTTC 57.362 37.037 23.84 0.00 0.00 3.62
3880 4665 1.018226 CCTGCTGGAACTCTTGCTCG 61.018 60.000 2.92 0.00 34.57 5.03
3886 4671 3.390135 CTGGAACTCTTGCTCGTGTAAA 58.610 45.455 0.00 0.00 0.00 2.01
3888 4673 2.157863 GGAACTCTTGCTCGTGTAAAGC 59.842 50.000 0.00 0.00 40.26 3.51
3906 4691 1.807886 CAGAAATCAGGCAGGCTGC 59.192 57.895 30.93 30.93 44.08 5.25
3934 4719 9.629878 AGAAGAAAATTATACTCTCTCGGTCTA 57.370 33.333 0.00 0.00 0.00 2.59
3952 4737 6.787085 GGTCTATCCGATCCAAAATAAGTG 57.213 41.667 0.00 0.00 0.00 3.16
3953 4738 5.701290 GGTCTATCCGATCCAAAATAAGTGG 59.299 44.000 0.00 0.00 37.51 4.00
3955 4740 2.285083 TCCGATCCAAAATAAGTGGCG 58.715 47.619 0.00 0.00 35.99 5.69
3963 4748 3.738791 CCAAAATAAGTGGCGTGGTTTTC 59.261 43.478 0.00 0.00 0.00 2.29
3964 4749 4.363999 CAAAATAAGTGGCGTGGTTTTCA 58.636 39.130 0.00 0.00 0.00 2.69
3976 4763 6.367422 TGGCGTGGTTTTCATTCAATTATTTC 59.633 34.615 0.00 0.00 0.00 2.17
3982 4769 7.700234 TGGTTTTCATTCAATTATTTCGGATCG 59.300 33.333 0.00 0.00 0.00 3.69
4027 4817 7.535997 TCAGTATTATCACCATACGCATAGAC 58.464 38.462 0.00 0.00 33.07 2.59
4068 4858 2.809861 CTTCTGGACATGGCCGCAGT 62.810 60.000 14.43 0.00 0.00 4.40
4131 5008 0.948678 TTTCACCGCAACTACAAGGC 59.051 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.394352 ATTTCCGGACCAGTGGATGC 60.394 55.000 18.40 4.64 33.42 3.91
46 47 2.825086 AAAACATCGCATAGCCGTTC 57.175 45.000 0.00 0.00 0.00 3.95
49 50 2.539547 CCTGAAAAACATCGCATAGCCG 60.540 50.000 0.00 0.00 0.00 5.52
84 85 1.079543 CAGGTGTTCGGCCTCTGAG 60.080 63.158 0.00 0.00 33.31 3.35
98 99 1.271325 TGAACATGTTCATCCGCAGGT 60.271 47.619 32.36 0.00 46.49 4.00
147 148 2.501723 CCCTCGAAAATCTCTTCTCCCA 59.498 50.000 0.00 0.00 0.00 4.37
202 203 2.578021 TGAGCTAAAATCTTCCCCTGCT 59.422 45.455 0.00 0.00 0.00 4.24
237 238 7.136203 AGATTGGAGAGTACCCTAGAGAAAAT 58.864 38.462 0.00 0.00 0.00 1.82
242 243 5.450453 TGAAGATTGGAGAGTACCCTAGAG 58.550 45.833 0.00 0.00 0.00 2.43
244 245 5.450453 TCTGAAGATTGGAGAGTACCCTAG 58.550 45.833 0.00 0.00 0.00 3.02
256 257 2.295885 GCCACCATCTCTGAAGATTGG 58.704 52.381 7.54 7.54 40.38 3.16
315 319 2.022195 TCATGACACTACCGCCTACTC 58.978 52.381 0.00 0.00 0.00 2.59
318 322 1.686587 CCATCATGACACTACCGCCTA 59.313 52.381 0.00 0.00 0.00 3.93
360 364 8.890410 TCATCCTCATCATCATCAGATACTAA 57.110 34.615 0.00 0.00 31.88 2.24
369 373 5.295540 CAGCATCATCATCCTCATCATCATC 59.704 44.000 0.00 0.00 0.00 2.92
370 374 5.045578 TCAGCATCATCATCCTCATCATCAT 60.046 40.000 0.00 0.00 0.00 2.45
371 375 4.286032 TCAGCATCATCATCCTCATCATCA 59.714 41.667 0.00 0.00 0.00 3.07
372 376 4.833390 TCAGCATCATCATCCTCATCATC 58.167 43.478 0.00 0.00 0.00 2.92
373 377 4.910458 TCAGCATCATCATCCTCATCAT 57.090 40.909 0.00 0.00 0.00 2.45
374 378 4.286032 TCATCAGCATCATCATCCTCATCA 59.714 41.667 0.00 0.00 0.00 3.07
375 379 4.833390 TCATCAGCATCATCATCCTCATC 58.167 43.478 0.00 0.00 0.00 2.92
376 380 4.910458 TCATCAGCATCATCATCCTCAT 57.090 40.909 0.00 0.00 0.00 2.90
377 381 4.910458 ATCATCAGCATCATCATCCTCA 57.090 40.909 0.00 0.00 0.00 3.86
378 382 5.585445 GGTTATCATCAGCATCATCATCCTC 59.415 44.000 0.00 0.00 0.00 3.71
379 383 5.251005 AGGTTATCATCAGCATCATCATCCT 59.749 40.000 0.00 0.00 0.00 3.24
380 384 5.498393 AGGTTATCATCAGCATCATCATCC 58.502 41.667 0.00 0.00 0.00 3.51
381 385 7.450124 AAAGGTTATCATCAGCATCATCATC 57.550 36.000 0.00 0.00 0.00 2.92
382 386 7.834881 AAAAGGTTATCATCAGCATCATCAT 57.165 32.000 0.00 0.00 0.00 2.45
383 387 8.623903 GTTAAAAGGTTATCATCAGCATCATCA 58.376 33.333 0.00 0.00 0.00 3.07
384 388 8.844244 AGTTAAAAGGTTATCATCAGCATCATC 58.156 33.333 0.00 0.00 0.00 2.92
389 393 8.635765 AAAGAGTTAAAAGGTTATCATCAGCA 57.364 30.769 0.00 0.00 0.00 4.41
421 425 3.466836 TCAGAGTGAAACGAACATGCTT 58.533 40.909 0.00 0.00 45.86 3.91
422 426 3.062763 CTCAGAGTGAAACGAACATGCT 58.937 45.455 0.00 0.00 45.86 3.79
423 427 2.802816 ACTCAGAGTGAAACGAACATGC 59.197 45.455 0.91 0.00 45.86 4.06
475 482 3.066760 CCTTGTTTCTGAACCCTTGACAC 59.933 47.826 0.00 0.00 34.80 3.67
683 712 7.959658 TTGTTCAGAATATCATGTGGGATTT 57.040 32.000 0.00 0.00 0.00 2.17
696 730 5.827797 GCCCACCTTGATATTGTTCAGAATA 59.172 40.000 0.00 0.00 0.00 1.75
724 770 1.333619 CCGTGCCCCTATTTTTCATCG 59.666 52.381 0.00 0.00 0.00 3.84
726 772 2.818751 TCCGTGCCCCTATTTTTCAT 57.181 45.000 0.00 0.00 0.00 2.57
736 782 1.087771 CGAGTTGTTATCCGTGCCCC 61.088 60.000 0.00 0.00 0.00 5.80
740 786 0.719465 GTGCCGAGTTGTTATCCGTG 59.281 55.000 0.00 0.00 0.00 4.94
742 789 1.127951 GTTGTGCCGAGTTGTTATCCG 59.872 52.381 0.00 0.00 0.00 4.18
745 792 1.796459 GACGTTGTGCCGAGTTGTTAT 59.204 47.619 0.00 0.00 0.00 1.89
747 794 0.741574 TGACGTTGTGCCGAGTTGTT 60.742 50.000 0.00 0.00 0.00 2.83
757 804 0.661020 GGAACCACCTTGACGTTGTG 59.339 55.000 0.00 0.00 35.41 3.33
802 849 3.199880 AGAATTCATTCGCCGGAGAAT 57.800 42.857 25.64 25.64 41.56 2.40
811 858 7.377766 TCCTTCAGGTTTAAGAATTCATTCG 57.622 36.000 8.44 0.00 37.90 3.34
898 957 1.228398 TGGGTTCGATTTGGCTGCA 60.228 52.632 0.50 0.00 0.00 4.41
901 960 0.953960 GTCGTGGGTTCGATTTGGCT 60.954 55.000 0.00 0.00 41.78 4.75
902 961 1.500396 GTCGTGGGTTCGATTTGGC 59.500 57.895 0.00 0.00 41.78 4.52
985 1051 3.257561 CATTGCGGCGACTCCTCG 61.258 66.667 12.98 0.00 43.28 4.63
986 1052 2.650813 ATCCATTGCGGCGACTCCTC 62.651 60.000 12.98 0.00 33.14 3.71
987 1053 2.650813 GATCCATTGCGGCGACTCCT 62.651 60.000 12.98 0.00 33.14 3.69
988 1054 2.203070 ATCCATTGCGGCGACTCC 60.203 61.111 12.98 0.00 33.14 3.85
989 1055 2.247437 GGATCCATTGCGGCGACTC 61.247 63.158 12.98 0.00 33.14 3.36
990 1056 2.203070 GGATCCATTGCGGCGACT 60.203 61.111 12.98 0.00 33.14 4.18
991 1057 3.640000 CGGATCCATTGCGGCGAC 61.640 66.667 12.98 2.02 35.23 5.19
1101 1167 1.737008 GAAGACGGCGGTGAAGTCC 60.737 63.158 13.24 0.00 35.65 3.85
1215 1285 1.226603 CGAGATCCCCGTCACGAAC 60.227 63.158 0.00 0.00 34.75 3.95
1235 1312 0.034896 GAACCTGCAAAGACCCGAGA 59.965 55.000 0.00 0.00 0.00 4.04
1269 1346 0.179094 ACGCCGTGAAGAAGAACACA 60.179 50.000 0.00 0.00 36.91 3.72
1314 1391 1.735376 GATCGAGGGCACGCTTCCTA 61.735 60.000 0.00 0.00 32.74 2.94
1326 1403 3.430098 CCTCTTTGAACTCAGGATCGAGG 60.430 52.174 0.00 0.00 37.34 4.63
1407 1872 5.368989 CCCTCAACAGAGTATAATTGGGAC 58.631 45.833 0.00 0.00 33.14 4.46
1409 1874 4.412199 TCCCCTCAACAGAGTATAATTGGG 59.588 45.833 0.00 0.00 0.00 4.12
1424 1890 0.327867 AGATCTGCCCATCCCCTCAA 60.328 55.000 0.00 0.00 0.00 3.02
1448 1916 2.673368 CGAACAATACCAAGACCAGCTC 59.327 50.000 0.00 0.00 0.00 4.09
1468 1936 2.212652 TGATCGAAATCAAGCATCCCG 58.787 47.619 0.00 0.00 38.97 5.14
1487 1955 3.795623 AAGCACTACGGGTAGTACATG 57.204 47.619 10.91 0.00 43.98 3.21
1497 1965 4.688879 TGTTACTGAATCAAAGCACTACGG 59.311 41.667 0.00 0.00 0.00 4.02
1656 2124 0.663153 AACGTTTTCCACTCAGCAGC 59.337 50.000 0.00 0.00 0.00 5.25
1660 2128 4.552166 ATCACAAACGTTTTCCACTCAG 57.448 40.909 11.66 0.00 0.00 3.35
1774 2249 5.845985 AACACATGTTTCTGTCTATCACG 57.154 39.130 0.00 0.00 33.93 4.35
1779 2254 7.935520 TGCAAATTAACACATGTTTCTGTCTA 58.064 30.769 1.98 0.00 39.31 2.59
1806 2281 8.317679 ACACTAGCTCTTCTGTAAAATGAATCT 58.682 33.333 0.00 0.00 0.00 2.40
1905 2380 7.819900 TCTCTATAGAAGGAAGTTGCTTTTGTC 59.180 37.037 11.24 0.00 0.00 3.18
1957 2432 4.739195 TCGCCAAATTAAACCAGCATAAC 58.261 39.130 0.00 0.00 0.00 1.89
2048 2523 6.469782 AAGTTCATTCATGGTTCAACACTT 57.530 33.333 0.00 0.00 0.00 3.16
2049 2524 6.469782 AAAGTTCATTCATGGTTCAACACT 57.530 33.333 0.00 0.00 0.00 3.55
2050 2525 6.509997 GCAAAAGTTCATTCATGGTTCAACAC 60.510 38.462 0.00 0.00 0.00 3.32
2051 2526 5.523188 GCAAAAGTTCATTCATGGTTCAACA 59.477 36.000 0.00 0.00 0.00 3.33
2052 2527 5.754890 AGCAAAAGTTCATTCATGGTTCAAC 59.245 36.000 0.00 0.00 0.00 3.18
2053 2528 5.916318 AGCAAAAGTTCATTCATGGTTCAA 58.084 33.333 0.00 0.00 0.00 2.69
2054 2529 5.534207 AGCAAAAGTTCATTCATGGTTCA 57.466 34.783 0.00 0.00 0.00 3.18
2055 2530 6.913170 TCTAGCAAAAGTTCATTCATGGTTC 58.087 36.000 0.00 0.00 0.00 3.62
2282 2758 3.609103 TTTTCTGAAGCTGAAAGACGC 57.391 42.857 0.00 0.00 34.02 5.19
2756 3234 7.201565 GCACACTGAGTTGTTAAGAATCCTATC 60.202 40.741 0.00 0.00 0.00 2.08
2837 3315 2.388735 TCGATCAGGCTTCCACATAGT 58.611 47.619 0.00 0.00 0.00 2.12
2876 3354 3.430779 GTACCCGCTGTACTGAACC 57.569 57.895 3.61 0.00 45.32 3.62
2970 3449 7.571026 CGCCAAACAAACAATCAAATTATGAA 58.429 30.769 0.00 0.00 42.54 2.57
3259 3738 5.825151 TCAACAATCGCCAATATCACCAATA 59.175 36.000 0.00 0.00 0.00 1.90
3262 3741 3.615155 TCAACAATCGCCAATATCACCA 58.385 40.909 0.00 0.00 0.00 4.17
3274 3753 5.854157 ACACTAACGCTAAATCAACAATCG 58.146 37.500 0.00 0.00 0.00 3.34
3276 3755 7.589954 GTCAAACACTAACGCTAAATCAACAAT 59.410 33.333 0.00 0.00 0.00 2.71
3290 3769 7.871463 AGTCTATACTTGGTGTCAAACACTAAC 59.129 37.037 9.83 0.00 43.19 2.34
3333 3815 6.357367 ACATCTGAATGGGATAACTACAACC 58.643 40.000 0.00 0.00 37.19 3.77
3704 4210 9.265938 CATTCTTGAGATTTTGTACATTACACG 57.734 33.333 0.00 0.00 38.63 4.49
3767 4273 9.723601 ATTAAATGCCTTGTGATTGTTTGTATT 57.276 25.926 0.00 0.00 0.00 1.89
3804 4313 7.568349 TCTAGCTCCAGTGAATTCATTGTATT 58.432 34.615 24.26 12.48 32.48 1.89
3805 4314 7.129457 TCTAGCTCCAGTGAATTCATTGTAT 57.871 36.000 24.26 12.51 32.48 2.29
3860 4645 0.036022 GAGCAAGAGTTCCAGCAGGT 59.964 55.000 0.00 0.00 35.89 4.00
3880 4665 3.119708 CCTGCCTGATTTCTGCTTTACAC 60.120 47.826 0.00 0.00 0.00 2.90
3886 4671 0.680280 CAGCCTGCCTGATTTCTGCT 60.680 55.000 0.00 0.00 44.64 4.24
3888 4673 1.807886 GCAGCCTGCCTGATTTCTG 59.192 57.895 5.06 0.00 44.64 3.02
3906 4691 7.493367 ACCGAGAGAGTATAATTTTCTTCTGG 58.507 38.462 0.00 0.00 0.00 3.86
3907 4692 8.410141 AGACCGAGAGAGTATAATTTTCTTCTG 58.590 37.037 0.00 0.00 0.00 3.02
3934 4719 2.878406 CGCCACTTATTTTGGATCGGAT 59.122 45.455 0.00 0.00 36.02 4.18
3950 4735 2.500509 TTGAATGAAAACCACGCCAC 57.499 45.000 0.00 0.00 0.00 5.01
3952 4737 6.453659 CGAAATAATTGAATGAAAACCACGCC 60.454 38.462 0.00 0.00 0.00 5.68
3953 4738 6.453659 CCGAAATAATTGAATGAAAACCACGC 60.454 38.462 0.00 0.00 0.00 5.34
3955 4740 8.702163 ATCCGAAATAATTGAATGAAAACCAC 57.298 30.769 0.00 0.00 0.00 4.16
3963 4748 6.204688 TCCCTTCGATCCGAAATAATTGAATG 59.795 38.462 3.38 0.00 45.23 2.67
3964 4749 6.296026 TCCCTTCGATCCGAAATAATTGAAT 58.704 36.000 3.38 0.00 45.23 2.57
3976 4763 0.962489 ATGCTACTCCCTTCGATCCG 59.038 55.000 0.00 0.00 0.00 4.18
3982 4769 7.416964 ACTGATATCATATGCTACTCCCTTC 57.583 40.000 5.72 0.00 0.00 3.46
4089 4887 4.971924 AGCTTGGGAGATGTATAACCTTCT 59.028 41.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.