Multiple sequence alignment - TraesCS1A01G211900

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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 TraesCS1A01G211900 chr1A 100.000 4769 0 0 1 4769 374565679 374570447 0.000000e+00 8807
1 TraesCS1A01G211900 chr1A 92.342 901 62 4 1 894 445887683 445886783 0.000000e+00 1275
2 TraesCS1A01G211900 chr1D 96.717 3229 94 6 895 4119 300062251 300065471 0.000000e+00 5365
3 TraesCS1A01G211900 chr1D 88.196 898 91 11 1 890 219711366 219710476 0.000000e+00 1057
4 TraesCS1A01G211900 chr1D 93.151 657 36 7 4119 4767 300065570 300066225 0.000000e+00 955
5 TraesCS1A01G211900 chr1D 84.641 905 121 12 1 896 209473557 209472662 0.000000e+00 885
6 TraesCS1A01G211900 chr1B 97.041 3109 85 3 984 4087 405181461 405184567 0.000000e+00 5225
7 TraesCS1A01G211900 chr1B 90.854 656 37 7 4119 4767 405184929 405185568 0.000000e+00 857
8 TraesCS1A01G211900 chr1B 91.954 261 20 1 3859 4119 405184571 405184830 9.750000e-97 364
9 TraesCS1A01G211900 chr6A 87.929 903 99 6 1 896 352811566 352812465 0.000000e+00 1055
10 TraesCS1A01G211900 chr7D 87.265 903 75 17 1 896 186812670 186813539 0.000000e+00 994
11 TraesCS1A01G211900 chr4B 86.489 903 111 8 1 896 166648903 166648005 0.000000e+00 981
12 TraesCS1A01G211900 chr2D 86.157 903 98 16 1 894 460367357 460366473 0.000000e+00 950
13 TraesCS1A01G211900 chr3B 84.573 901 107 19 1 893 650020539 650021415 0.000000e+00 865
14 TraesCS1A01G211900 chr5D 90.455 660 56 5 1 654 540844995 540844337 0.000000e+00 863
15 TraesCS1A01G211900 chr2B 90.535 243 16 4 658 896 113195737 113195976 9.960000e-82 315


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 TraesCS1A01G211900 chr1A 374565679 374570447 4768 False 8807.000000 8807 100.000 1 4769 1 chr1A.!!$F1 4768
1 TraesCS1A01G211900 chr1A 445886783 445887683 900 True 1275.000000 1275 92.342 1 894 1 chr1A.!!$R1 893
2 TraesCS1A01G211900 chr1D 300062251 300066225 3974 False 3160.000000 5365 94.934 895 4767 2 chr1D.!!$F1 3872
3 TraesCS1A01G211900 chr1D 219710476 219711366 890 True 1057.000000 1057 88.196 1 890 1 chr1D.!!$R2 889
4 TraesCS1A01G211900 chr1D 209472662 209473557 895 True 885.000000 885 84.641 1 896 1 chr1D.!!$R1 895
5 TraesCS1A01G211900 chr1B 405181461 405185568 4107 False 2148.666667 5225 93.283 984 4767 3 chr1B.!!$F1 3783
6 TraesCS1A01G211900 chr6A 352811566 352812465 899 False 1055.000000 1055 87.929 1 896 1 chr6A.!!$F1 895
7 TraesCS1A01G211900 chr7D 186812670 186813539 869 False 994.000000 994 87.265 1 896 1 chr7D.!!$F1 895
8 TraesCS1A01G211900 chr4B 166648005 166648903 898 True 981.000000 981 86.489 1 896 1 chr4B.!!$R1 895
9 TraesCS1A01G211900 chr2D 460366473 460367357 884 True 950.000000 950 86.157 1 894 1 chr2D.!!$R1 893
10 TraesCS1A01G211900 chr3B 650020539 650021415 876 False 865.000000 865 84.573 1 893 1 chr3B.!!$F1 892
11 TraesCS1A01G211900 chr5D 540844337 540844995 658 True 863.000000 863 90.455 1 654 1 chr5D.!!$R1 653

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
619 634 0.033991 AGAGGGAGACAGCGAGCTAA 60.034 55.0 0.00 0.00 0.00 3.09 F
1804 1827 0.627986 ATTTGCTAGGCTGGCTCCTT 59.372 50.0 23.69 3.56 37.66 3.36 F
2772 2795 0.673437 TGCCAGGCACAGCTAAAAAC 59.327 50.0 11.22 0.00 31.71 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2129 0.034186 TAAGGTGCAATGCCTCCCTG 60.034 55.000 1.53 0.0 34.81 4.45 R
3278 3301 1.139058 GATCATTGGCACGAGGGTAGT 59.861 52.381 0.00 0.0 0.00 2.73 R
4256 4615 0.038166 CAGCCCTAAAGGTCAGCCAA 59.962 55.000 0.00 0.0 38.26 4.52 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
134 140 1.065636 GGGGAGAAAGAACCCTAACCG 60.066 57.143 0.00 0.00 44.97 4.44
140 146 3.325716 AGAAAGAACCCTAACCGCTACAA 59.674 43.478 0.00 0.00 0.00 2.41
147 153 3.518303 ACCCTAACCGCTACAAATCTCTT 59.482 43.478 0.00 0.00 0.00 2.85
206 213 2.041620 ACAGGAAGCAGCCCTATTTTGA 59.958 45.455 0.00 0.00 31.64 2.69
245 253 7.175104 TCATCAAGAAACTGCTAAAACCCTAT 58.825 34.615 0.00 0.00 0.00 2.57
263 271 2.837031 ATCACCCACACCCAATCCGC 62.837 60.000 0.00 0.00 0.00 5.54
267 275 2.751436 CACACCCAATCCGCCAGG 60.751 66.667 0.00 0.00 39.46 4.45
313 322 0.645355 CTCGTACGCGCAATTGATGT 59.355 50.000 11.24 6.27 38.14 3.06
390 399 1.658931 CGACAACGACGTACCGTACAA 60.659 52.381 0.00 0.00 41.37 2.41
534 543 0.318275 GCGACGAGCTTAGAGGATGG 60.318 60.000 0.00 0.00 44.04 3.51
582 597 3.947173 CGGGAGCAGAGGAGACAT 58.053 61.111 0.00 0.00 0.00 3.06
619 634 0.033991 AGAGGGAGACAGCGAGCTAA 60.034 55.000 0.00 0.00 0.00 3.09
625 640 2.875786 GACAGCGAGCTAATGCGGC 61.876 63.158 0.00 0.00 45.42 6.53
702 721 6.326583 CCAAATGGACTAGTATTCACCCTAGA 59.673 42.308 0.00 0.00 37.39 2.43
882 905 2.415512 CGGCTCAAGTTTAACCTACAGC 59.584 50.000 0.00 0.00 0.00 4.40
917 940 5.045012 TCGCTATTCTAACTAGGTCCTCA 57.955 43.478 0.00 0.00 0.00 3.86
938 961 1.067213 TCGTTGCAATGAGATCGACCA 60.067 47.619 17.41 0.00 0.00 4.02
1155 1178 2.725008 CTCTCCGAGATCCACCGC 59.275 66.667 0.00 0.00 0.00 5.68
1749 1772 5.220662 CCTTTACAATCTGCTAACCACATCG 60.221 44.000 0.00 0.00 0.00 3.84
1804 1827 0.627986 ATTTGCTAGGCTGGCTCCTT 59.372 50.000 23.69 3.56 37.66 3.36
1818 1841 0.734253 CTCCTTTGGAGTCGCGTCTG 60.734 60.000 11.38 0.00 44.25 3.51
2094 2117 0.986527 TGTCACTGGGTGATGCTGAT 59.013 50.000 3.67 0.00 44.63 2.90
2106 2129 2.097954 TGATGCTGATTCAAACATCCGC 59.902 45.455 19.21 6.05 38.49 5.54
2292 2315 6.313658 TGTCAGATTTTGATTGGTATGTCTCG 59.686 38.462 0.00 0.00 38.29 4.04
2298 2321 4.307443 TGATTGGTATGTCTCGCTACTG 57.693 45.455 0.00 0.00 0.00 2.74
2300 2323 2.430248 TGGTATGTCTCGCTACTGGA 57.570 50.000 0.00 0.00 0.00 3.86
2322 2345 2.911636 AGATATGGCTAGGAGCTTGCAT 59.088 45.455 0.00 0.00 41.99 3.96
2327 2350 1.457346 GCTAGGAGCTTGCATTGTGT 58.543 50.000 0.00 0.00 38.45 3.72
2400 2423 2.980233 GCACGGCCAGAGCTTGTT 60.980 61.111 2.24 0.00 39.73 2.83
2583 2606 2.344950 CCAATGTCAGTGAGAGCTGTC 58.655 52.381 3.38 3.38 37.70 3.51
2706 2729 4.756084 AGCTGTTGATCAAACTGTTAGC 57.244 40.909 10.35 12.48 39.70 3.09
2714 2737 3.806949 TCAAACTGTTAGCAGGGGAAT 57.193 42.857 11.56 0.00 46.62 3.01
2729 2752 4.095483 CAGGGGAATCAAGTCTGAAATTCG 59.905 45.833 0.00 0.00 34.49 3.34
2730 2753 4.010349 GGGGAATCAAGTCTGAAATTCGT 58.990 43.478 0.00 0.00 34.49 3.85
2772 2795 0.673437 TGCCAGGCACAGCTAAAAAC 59.327 50.000 11.22 0.00 31.71 2.43
2832 2855 1.835494 TGGTTGAAACAACGGTTGGA 58.165 45.000 23.51 3.32 37.30 3.53
2965 2988 3.055021 TCATAACAAGCATAACCGGGTCA 60.055 43.478 6.32 0.00 0.00 4.02
3116 3139 8.988934 TGACATTTTAAGTGAAGATGACACTAC 58.011 33.333 0.00 0.00 46.01 2.73
3132 3155 6.582636 TGACACTACTCTGTCAACTTCAATT 58.417 36.000 0.00 0.00 46.04 2.32
3278 3301 3.266510 AGCTGAGGATGACGCAAATAA 57.733 42.857 0.00 0.00 0.00 1.40
3311 3334 4.263639 TGCCAATGATCCTCTTCTTTCTGT 60.264 41.667 0.00 0.00 0.00 3.41
3438 3461 3.606687 TGGCGAAGATTTCCTAAGTTCC 58.393 45.455 0.00 0.00 0.00 3.62
3480 3503 4.046938 TCTAAAGGCTGCAGATAAGTCG 57.953 45.455 20.43 0.00 0.00 4.18
3485 3508 1.576356 GCTGCAGATAAGTCGGAAGG 58.424 55.000 20.43 0.00 0.00 3.46
3594 3617 6.115448 AGTTCTAGGACAAGTAAGCAACAT 57.885 37.500 3.42 0.00 0.00 2.71
3629 3655 1.277557 GAAGAGCACACCTCCTGACAT 59.722 52.381 0.00 0.00 41.74 3.06
3635 3661 3.118482 AGCACACCTCCTGACATTGATAG 60.118 47.826 0.00 0.00 0.00 2.08
3643 3669 5.454471 CCTCCTGACATTGATAGGAAAGAGG 60.454 48.000 12.41 8.06 39.93 3.69
3656 3682 3.055094 AGGAAAGAGGCGAGAAAGCATAA 60.055 43.478 0.00 0.00 39.27 1.90
3778 3804 0.749649 CCTTCTGTAGCTGCCGAGAT 59.250 55.000 0.00 0.00 0.00 2.75
3779 3805 1.137872 CCTTCTGTAGCTGCCGAGATT 59.862 52.381 0.00 0.00 0.00 2.40
3970 3996 9.349713 TCTAAGAAAATGTGGTACATGAAAGTT 57.650 29.630 0.00 0.00 44.52 2.66
3979 4005 5.049405 GTGGTACATGAAAGTTCCAGTGAAG 60.049 44.000 0.00 0.00 44.52 3.02
3987 4013 6.356556 TGAAAGTTCCAGTGAAGATCAAAGA 58.643 36.000 0.00 0.00 0.00 2.52
4040 4068 8.522178 AAAAGAGTATTTTGACTAGAGACGTG 57.478 34.615 0.00 0.00 0.00 4.49
4041 4069 6.197364 AGAGTATTTTGACTAGAGACGTGG 57.803 41.667 0.00 0.00 0.00 4.94
4053 4312 8.242053 TGACTAGAGACGTGGTAAATAAAAGAG 58.758 37.037 0.00 0.00 0.00 2.85
4083 4342 7.458397 AGTGGGAAGTGATAGATGTTTGTTTA 58.542 34.615 0.00 0.00 0.00 2.01
4110 4369 8.272889 GTGAGGAAAAATAACCTATAGACCCTT 58.727 37.037 0.00 0.00 36.57 3.95
4122 4381 9.462606 AACCTATAGACCCTTTATTTCTGTTTG 57.537 33.333 0.00 0.00 0.00 2.93
4123 4382 8.612145 ACCTATAGACCCTTTATTTCTGTTTGT 58.388 33.333 0.00 0.00 0.00 2.83
4124 4383 8.893727 CCTATAGACCCTTTATTTCTGTTTGTG 58.106 37.037 0.00 0.00 0.00 3.33
4129 4488 5.048991 ACCCTTTATTTCTGTTTGTGTAGCG 60.049 40.000 0.00 0.00 0.00 4.26
4133 4492 6.854496 TTATTTCTGTTTGTGTAGCGTTCT 57.146 33.333 0.00 0.00 0.00 3.01
4168 4527 4.863491 CACAGCTAATTTCTGTTGTGCTT 58.137 39.130 9.50 0.00 42.38 3.91
4202 4561 2.720688 CAAGAAATGCTGCGCACTG 58.279 52.632 5.66 0.00 43.04 3.66
4256 4615 7.885399 AGCAGTATAGTTTCTCAGGATTTTTGT 59.115 33.333 0.00 0.00 0.00 2.83
4274 4633 0.038310 GTTGGCTGACCTTTAGGGCT 59.962 55.000 2.78 0.00 45.91 5.19
4276 4635 1.077429 GGCTGACCTTTAGGGCTGG 60.077 63.158 10.16 1.52 45.91 4.85
4294 4653 4.304939 GCTGGTATACATAGACGAAACCC 58.695 47.826 5.01 0.00 0.00 4.11
4421 4781 2.152016 GGCTGTGAACTTGGTAGGTTC 58.848 52.381 0.00 0.00 42.17 3.62
4453 4818 4.345257 AGGACTGAGCTCTGTTTTGTTCTA 59.655 41.667 24.88 0.00 0.00 2.10
4465 4830 8.519799 TCTGTTTTGTTCTATTTGAGGTCTTT 57.480 30.769 0.00 0.00 0.00 2.52
4473 4838 8.786898 TGTTCTATTTGAGGTCTTTGAGAATTG 58.213 33.333 0.00 0.00 0.00 2.32
4501 4866 3.023832 CTCCTGTGGTGTTTTGGTTCTT 58.976 45.455 0.00 0.00 0.00 2.52
4534 4899 2.551270 AGCTGTAGGATGGTTTGGAGA 58.449 47.619 0.00 0.00 0.00 3.71
4578 4943 0.250901 GTGCCACCTGACAGAATGGT 60.251 55.000 20.62 3.42 43.62 3.55
4634 4999 6.445451 TTTCATGGAAATGAAAATTGGGGA 57.555 33.333 10.60 0.00 44.64 4.81
4656 5021 0.900182 GGAGGCCCTTGGGTTGAAAG 60.900 60.000 0.00 0.00 0.00 2.62
4687 5053 5.344665 CGTTGATGTGTTGTTCACTTTTTGT 59.655 36.000 0.00 0.00 46.27 2.83
4767 5138 4.016706 CGCCCCGAGGAGTTGGTT 62.017 66.667 0.00 0.00 33.47 3.67
4768 5139 2.359975 GCCCCGAGGAGTTGGTTG 60.360 66.667 0.00 0.00 33.47 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 59 6.038271 CAGTAAAGGTTGCTTTTAGTGTCAGT 59.962 38.462 9.16 0.00 36.98 3.41
86 92 2.657352 ATGGGTCCAGGGGCCTAGA 61.657 63.158 9.17 0.00 0.00 2.43
111 117 2.581246 GTTAGGGTTCTTTCTCCCCCAT 59.419 50.000 0.00 0.00 44.40 4.00
134 140 5.098211 GCCATGTTTGAAGAGATTTGTAGC 58.902 41.667 0.00 0.00 0.00 3.58
140 146 4.346730 TGATGGCCATGTTTGAAGAGATT 58.653 39.130 26.56 0.00 0.00 2.40
147 153 1.273048 GCAGTTGATGGCCATGTTTGA 59.727 47.619 26.56 0.55 0.00 2.69
191 197 1.957113 GCAGGTCAAAATAGGGCTGCT 60.957 52.381 0.00 0.00 34.23 4.24
206 213 3.327757 TCTTGATGAACTTAGTGGCAGGT 59.672 43.478 0.00 0.00 0.00 4.00
245 253 2.753701 CGGATTGGGTGTGGGTGA 59.246 61.111 0.00 0.00 0.00 4.02
263 271 0.234884 GCGTTCGTTCAACTTCCTGG 59.765 55.000 0.00 0.00 32.09 4.45
267 275 0.658897 TTGGGCGTTCGTTCAACTTC 59.341 50.000 0.00 0.00 32.09 3.01
330 339 4.646945 TCGATCTGTCCAATTTAGCTCTCT 59.353 41.667 0.00 0.00 0.00 3.10
510 519 1.978712 CTCTAAGCTCGTCGCCGTCA 61.979 60.000 0.00 0.00 40.39 4.35
543 555 0.459934 CCCTCTCTACTCGTCGTCGT 60.460 60.000 1.33 0.00 38.33 4.34
554 566 2.442272 GCTCCCGCACCCTCTCTA 60.442 66.667 0.00 0.00 35.78 2.43
619 634 4.552365 CACCTGATCGGGCCGCAT 62.552 66.667 23.83 15.82 36.97 4.73
625 640 4.181010 CCAGCCCACCTGATCGGG 62.181 72.222 19.66 19.66 44.64 5.14
671 686 7.039293 GGTGAATACTAGTCCATTTGGGTTTTT 60.039 37.037 0.00 0.00 38.11 1.94
672 687 6.436218 GGTGAATACTAGTCCATTTGGGTTTT 59.564 38.462 0.00 0.00 38.11 2.43
680 699 6.441222 TGTCTAGGGTGAATACTAGTCCATT 58.559 40.000 0.00 0.00 38.24 3.16
702 721 3.249189 ACCGCCACCTGGTCATGT 61.249 61.111 0.00 0.00 33.35 3.21
785 805 1.744320 GCAAGGGGTTCGCTTTGGTT 61.744 55.000 11.98 0.00 34.44 3.67
793 813 0.738389 ATATTTGCGCAAGGGGTTCG 59.262 50.000 23.68 0.00 38.28 3.95
917 940 2.205074 GGTCGATCTCATTGCAACGAT 58.795 47.619 0.00 4.23 32.78 3.73
1341 1364 3.731766 GAGGAGGGAGAGCGAGGCT 62.732 68.421 0.00 0.00 43.88 4.58
1620 1643 2.434359 GGGTCGGACGAAGCAAGG 60.434 66.667 1.43 0.00 0.00 3.61
1804 1827 4.373116 GGCCAGACGCGACTCCAA 62.373 66.667 15.93 0.00 38.94 3.53
1818 1841 2.322999 GATCAACAATCCGTGCGGCC 62.323 60.000 5.64 0.00 34.68 6.13
1926 1949 4.099170 GCAAGGCTCACTGCAGCG 62.099 66.667 15.27 3.95 45.15 5.18
1929 1952 1.228644 AATGGCAAGGCTCACTGCA 60.229 52.632 11.44 0.00 45.15 4.41
2094 2117 0.322456 CCTCCCTGCGGATGTTTGAA 60.322 55.000 0.00 0.00 37.60 2.69
2106 2129 0.034186 TAAGGTGCAATGCCTCCCTG 60.034 55.000 1.53 0.00 34.81 4.45
2292 2315 4.090090 TCCTAGCCATATCTTCCAGTAGC 58.910 47.826 0.00 0.00 0.00 3.58
2298 2321 3.867984 GCAAGCTCCTAGCCATATCTTCC 60.868 52.174 0.00 0.00 43.77 3.46
2300 2323 2.707791 TGCAAGCTCCTAGCCATATCTT 59.292 45.455 0.00 0.00 43.77 2.40
2322 2345 1.133181 TCTCATCCCCCTGCACACAA 61.133 55.000 0.00 0.00 0.00 3.33
2327 2350 0.920763 ACCAATCTCATCCCCCTGCA 60.921 55.000 0.00 0.00 0.00 4.41
2400 2423 1.018148 GGAGAGATCGAGCTGAACGA 58.982 55.000 8.50 0.00 43.65 3.85
2583 2606 5.812642 CACTTTAAGTACTGCCTGGATGTAG 59.187 44.000 0.00 0.00 0.00 2.74
2668 2691 7.161404 TCAACAGCTAACTCATCAAACACTAT 58.839 34.615 0.00 0.00 0.00 2.12
2706 2729 4.095483 CGAATTTCAGACTTGATTCCCCTG 59.905 45.833 0.00 0.00 32.27 4.45
2714 2737 3.067106 GCAGGACGAATTTCAGACTTGA 58.933 45.455 0.00 0.00 0.00 3.02
2729 2752 2.808543 ACGATTTGTTCTTCAGCAGGAC 59.191 45.455 0.00 0.00 0.00 3.85
2730 2753 3.126001 ACGATTTGTTCTTCAGCAGGA 57.874 42.857 0.00 0.00 0.00 3.86
2772 2795 4.314740 TGATTTGTTTGAAAAGGGGTCG 57.685 40.909 0.00 0.00 0.00 4.79
2815 2838 1.473278 TGGTCCAACCGTTGTTTCAAC 59.527 47.619 10.34 2.95 42.58 3.18
2832 2855 1.843851 TCCTTGGACTCAACAAGTGGT 59.156 47.619 0.00 0.00 42.84 4.16
2965 2988 7.720957 TGTTTGCATACTATTAATGAGCTCCAT 59.279 33.333 12.15 2.09 36.99 3.41
3132 3155 5.538118 TGACAGTTGCGAGAGATAAAAGAA 58.462 37.500 0.00 0.00 0.00 2.52
3237 3260 4.876679 GCTTTTCCTGTTGGGAGATAGTAC 59.123 45.833 0.00 0.00 46.01 2.73
3278 3301 1.139058 GATCATTGGCACGAGGGTAGT 59.861 52.381 0.00 0.00 0.00 2.73
3311 3334 1.546923 CCATGGCACTTGCATTCTCAA 59.453 47.619 0.00 0.00 44.36 3.02
3509 3532 6.749139 TGTATCCATTGAGAACTAGATTCGG 58.251 40.000 0.00 0.00 42.69 4.30
3594 3617 7.316640 GTGTGCTCTTCTCTTTAGTAAGATCA 58.683 38.462 0.00 0.00 39.58 2.92
3629 3655 4.759782 CTTTCTCGCCTCTTTCCTATCAA 58.240 43.478 0.00 0.00 0.00 2.57
3635 3661 1.743996 ATGCTTTCTCGCCTCTTTCC 58.256 50.000 0.00 0.00 0.00 3.13
3643 3669 4.393371 AGAAGAGGTTTTATGCTTTCTCGC 59.607 41.667 0.00 0.00 0.00 5.03
3656 3682 1.909986 GCCCACTCCTAGAAGAGGTTT 59.090 52.381 0.00 0.00 46.76 3.27
3844 3870 4.713824 TGTACACCTATGTTCTTCCTCG 57.286 45.455 0.00 0.00 40.48 4.63
3916 3942 7.328737 GTCATCTAGTTTAACTAGCCTTTGGA 58.671 38.462 23.14 12.56 45.93 3.53
3940 3966 7.402054 TCATGTACCACATTTTCTTAGATGGT 58.598 34.615 9.12 9.12 42.90 3.55
3945 3971 9.612620 GAACTTTCATGTACCACATTTTCTTAG 57.387 33.333 0.00 0.00 36.53 2.18
4040 4068 4.948004 CCCACTCCACCTCTTTTATTTACC 59.052 45.833 0.00 0.00 0.00 2.85
4041 4069 5.812286 TCCCACTCCACCTCTTTTATTTAC 58.188 41.667 0.00 0.00 0.00 2.01
4053 4312 2.467880 TCTATCACTTCCCACTCCACC 58.532 52.381 0.00 0.00 0.00 4.61
4083 4342 7.628101 AGGGTCTATAGGTTATTTTTCCTCACT 59.372 37.037 0.00 0.00 35.51 3.41
4098 4357 8.893727 CACAAACAGAAATAAAGGGTCTATAGG 58.106 37.037 0.00 0.00 0.00 2.57
4110 4369 6.854496 AGAACGCTACACAAACAGAAATAA 57.146 33.333 0.00 0.00 0.00 1.40
4119 4378 5.047164 TCCTTACCATAGAACGCTACACAAA 60.047 40.000 0.00 0.00 0.00 2.83
4120 4379 4.463539 TCCTTACCATAGAACGCTACACAA 59.536 41.667 0.00 0.00 0.00 3.33
4121 4380 4.018490 TCCTTACCATAGAACGCTACACA 58.982 43.478 0.00 0.00 0.00 3.72
4122 4381 4.644103 TCCTTACCATAGAACGCTACAC 57.356 45.455 0.00 0.00 0.00 2.90
4123 4382 4.500887 GCATCCTTACCATAGAACGCTACA 60.501 45.833 0.00 0.00 0.00 2.74
4124 4383 3.988517 GCATCCTTACCATAGAACGCTAC 59.011 47.826 0.00 0.00 0.00 3.58
4129 4488 3.561725 GCTGTGCATCCTTACCATAGAAC 59.438 47.826 0.00 0.00 0.00 3.01
4133 4492 5.567037 ATTAGCTGTGCATCCTTACCATA 57.433 39.130 0.00 0.00 0.00 2.74
4168 4527 2.596346 TCTTGCTTTCAGATTGCCCAA 58.404 42.857 0.00 0.00 0.00 4.12
4226 4585 7.661536 ATCCTGAGAAACTATACTGCTGTAA 57.338 36.000 7.59 0.00 31.80 2.41
4256 4615 0.038166 CAGCCCTAAAGGTCAGCCAA 59.962 55.000 0.00 0.00 38.26 4.52
4274 4633 3.243501 GCGGGTTTCGTCTATGTATACCA 60.244 47.826 0.00 0.00 41.72 3.25
4276 4635 3.968649 TGCGGGTTTCGTCTATGTATAC 58.031 45.455 0.00 0.00 41.72 1.47
4325 4685 5.924475 TTTCAACTGCTACTAGCTGAAAC 57.076 39.130 18.87 0.00 41.94 2.78
4326 4686 6.467677 AGATTTCAACTGCTACTAGCTGAAA 58.532 36.000 18.86 18.86 42.79 2.69
4340 4700 4.188247 TCGACGATGGAAGATTTCAACT 57.812 40.909 0.00 0.00 0.00 3.16
4421 4781 3.030291 AGAGCTCAGTCCTACCATCAAG 58.970 50.000 17.77 0.00 0.00 3.02
4453 4818 7.255730 CCAACTCAATTCTCAAAGACCTCAAAT 60.256 37.037 0.00 0.00 0.00 2.32
4465 4830 2.373169 ACAGGAGCCAACTCAATTCTCA 59.627 45.455 0.00 0.00 45.42 3.27
4473 4838 0.179018 AACACCACAGGAGCCAACTC 60.179 55.000 0.00 0.00 42.66 3.01
4501 4866 2.095461 CTACAGCTACACTCAGCCTCA 58.905 52.381 0.00 0.00 42.84 3.86
4534 4899 0.681733 ACACAGACTGACCTCGCAAT 59.318 50.000 10.08 0.00 0.00 3.56
4578 4943 6.068010 ACAACCAAGTTCCACATCAAGATAA 58.932 36.000 0.00 0.00 0.00 1.75
4651 5016 6.481976 ACAACACATCAACGTATTCTCTTTCA 59.518 34.615 0.00 0.00 0.00 2.69
4656 5021 6.223138 TGAACAACACATCAACGTATTCTC 57.777 37.500 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.