Multiple sequence alignment - TraesCS4D01G197300

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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 TraesCS4D01G197300 chr4D 100.000 5382 0 0 1 5382 342091931 342086550 0.000000e+00 9939
1 TraesCS4D01G197300 chr4A 91.687 4956 179 62 1 4804 124204370 124209244 0.000000e+00 6654
2 TraesCS4D01G197300 chr4B 92.200 4372 123 55 582 4804 424290255 424285953 0.000000e+00 5984
3 TraesCS4D01G197300 chr4B 87.726 554 38 11 2 541 424290798 424290261 2.130000e-173 619
4 TraesCS4D01G197300 chr7A 90.756 595 49 6 4791 5382 163155695 163155104 0.000000e+00 789
5 TraesCS4D01G197300 chr7A 91.156 441 31 7 4804 5242 552968062 552968496 4.640000e-165 592
6 TraesCS4D01G197300 chrUn 90.172 580 53 3 4804 5382 293730459 293731035 0.000000e+00 752
7 TraesCS4D01G197300 chrUn 90.172 580 53 3 4804 5382 469618202 469617626 0.000000e+00 752
8 TraesCS4D01G197300 chr2D 88.512 531 52 8 4805 5330 80193948 80193422 7.600000e-178 634
9 TraesCS4D01G197300 chr2D 87.902 529 58 4 4805 5330 572126989 572127514 7.660000e-173 617
10 TraesCS4D01G197300 chr2D 91.480 446 30 6 4800 5242 531323639 531324079 1.660000e-169 606
11 TraesCS4D01G197300 chr3D 91.136 440 32 5 4805 5242 29994498 29994932 1.670000e-164 590
12 TraesCS4D01G197300 chr3D 95.633 229 9 1 5154 5382 420002562 420002789 3.060000e-97 366
13 TraesCS4D01G197300 chr1D 91.136 440 32 5 4805 5242 449685587 449686021 1.670000e-164 590


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 TraesCS4D01G197300 chr4D 342086550 342091931 5381 True 9939.0 9939 100.000 1 5382 1 chr4D.!!$R1 5381
1 TraesCS4D01G197300 chr4A 124204370 124209244 4874 False 6654.0 6654 91.687 1 4804 1 chr4A.!!$F1 4803
2 TraesCS4D01G197300 chr4B 424285953 424290798 4845 True 3301.5 5984 89.963 2 4804 2 chr4B.!!$R1 4802
3 TraesCS4D01G197300 chr7A 163155104 163155695 591 True 789.0 789 90.756 4791 5382 1 chr7A.!!$R1 591
4 TraesCS4D01G197300 chrUn 293730459 293731035 576 False 752.0 752 90.172 4804 5382 1 chrUn.!!$F1 578
5 TraesCS4D01G197300 chrUn 469617626 469618202 576 True 752.0 752 90.172 4804 5382 1 chrUn.!!$R1 578
6 TraesCS4D01G197300 chr2D 80193422 80193948 526 True 634.0 634 88.512 4805 5330 1 chr2D.!!$R1 525
7 TraesCS4D01G197300 chr2D 572126989 572127514 525 False 617.0 617 87.902 4805 5330 1 chr2D.!!$F2 525

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
349 353 1.037493 TATAGATGTCGCGGCCAAGT 58.963 50.000 8.89 0.0 0.0 3.16 F
1725 1750 1.268899 CTCCCAGCAGCAAAGTGAAAG 59.731 52.381 0.00 0.0 0.0 2.62 F
2418 2503 0.030908 CGAGGAATCCGAGCCAGTAC 59.969 60.000 0.00 0.0 0.0 2.73 F
3339 3499 0.602905 CCGACAAGTCCCAGGTCAAC 60.603 60.000 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2022 0.254747 TTTAATGGGGAGGGTGAGCG 59.745 55.0 0.00 0.00 0.00 5.03 R
3168 3328 0.104672 TCAGGTCCCTGGAGAACCAA 60.105 55.0 13.24 1.58 46.32 3.67 R
3879 4119 0.397535 CCCCTCCCCACCAAATCATG 60.398 60.0 0.00 0.00 0.00 3.07 R
5332 5610 0.249398 CGGTGGTTCTTCTTCCGGAT 59.751 55.0 4.15 0.00 37.92 4.18 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
31 32 1.078497 CGGGCTAATCTGTGCACCA 60.078 57.895 15.69 0.34 0.00 4.17
170 172 3.708631 ACTCCACATCTTACTCTCCCATG 59.291 47.826 0.00 0.00 0.00 3.66
173 175 4.162320 TCCACATCTTACTCTCCCATGAAC 59.838 45.833 0.00 0.00 0.00 3.18
339 343 9.547753 TTTTATGACTTGGAGCTTATAGATGTC 57.452 33.333 0.00 0.00 0.00 3.06
349 353 1.037493 TATAGATGTCGCGGCCAAGT 58.963 50.000 8.89 0.00 0.00 3.16
451 456 8.784043 GGTCAAACCATATCTACATTTGGATAC 58.216 37.037 0.00 0.00 38.42 2.24
521 538 6.096001 ACATTAATGTTGAGAGAGGGAAATGC 59.904 38.462 15.47 0.00 37.90 3.56
542 559 1.539388 TGTAGTGCGGCTTGATTTTGG 59.461 47.619 0.00 0.00 0.00 3.28
545 562 1.812571 AGTGCGGCTTGATTTTGGTAG 59.187 47.619 0.00 0.00 0.00 3.18
607 624 2.095461 TCAGCTAGACTGCATTCGTCT 58.905 47.619 11.39 11.39 46.76 4.18
619 636 2.926200 GCATTCGTCTGATATCCATCCG 59.074 50.000 0.00 0.00 0.00 4.18
666 683 5.407502 CCCGTGCATATAGATTTCGATGTA 58.592 41.667 0.00 0.00 0.00 2.29
789 806 4.847444 GCCGCTTCCTCCCTCTGC 62.847 72.222 0.00 0.00 0.00 4.26
857 874 1.356527 AAATTCGCGTCCGCCACTAC 61.357 55.000 5.77 0.00 37.98 2.73
886 903 3.199880 CCTAACCAGGCTACAATCAGG 57.800 52.381 0.00 0.00 34.35 3.86
1023 1043 3.605749 CTCCGCCATGGACCACGTT 62.606 63.158 18.40 0.00 43.74 3.99
1278 1298 4.796495 GCCGCAAGAATCGGGGGT 62.796 66.667 11.30 0.00 46.51 4.95
1725 1750 1.268899 CTCCCAGCAGCAAAGTGAAAG 59.731 52.381 0.00 0.00 0.00 2.62
1756 1781 5.303747 TCACTCGAGCAAAACAAGAAAAA 57.696 34.783 13.61 0.00 0.00 1.94
1871 1922 2.690653 TTTGTCAGGTTGCCCCGAGG 62.691 60.000 0.00 0.00 38.74 4.63
1970 2021 1.099879 GCCATGTGATGTGAGGAGGC 61.100 60.000 0.00 0.00 0.00 4.70
1971 2022 0.465097 CCATGTGATGTGAGGAGGCC 60.465 60.000 0.00 0.00 0.00 5.19
2093 2167 1.228988 TCAGTCAGGCTGGAGCAGA 60.229 57.895 15.73 5.27 45.08 4.26
2094 2168 1.218585 CAGTCAGGCTGGAGCAGAG 59.781 63.158 15.73 0.00 44.36 3.35
2097 2171 2.219164 TCAGGCTGGAGCAGAGCAA 61.219 57.895 15.73 0.00 44.36 3.91
2098 2172 1.745864 CAGGCTGGAGCAGAGCAAG 60.746 63.158 6.61 0.00 44.36 4.01
2099 2173 3.132801 GGCTGGAGCAGAGCAAGC 61.133 66.667 0.20 0.00 44.36 4.01
2100 2174 3.497932 GCTGGAGCAGAGCAAGCG 61.498 66.667 0.00 0.00 41.59 4.68
2101 2175 2.818714 CTGGAGCAGAGCAAGCGG 60.819 66.667 0.00 0.00 37.01 5.52
2102 2176 3.602513 CTGGAGCAGAGCAAGCGGT 62.603 63.158 0.00 0.00 37.01 5.68
2103 2177 2.359230 GGAGCAGAGCAAGCGGTT 60.359 61.111 0.00 0.00 37.01 4.44
2104 2178 2.394563 GGAGCAGAGCAAGCGGTTC 61.395 63.158 0.00 0.00 37.01 3.62
2105 2179 1.669115 GAGCAGAGCAAGCGGTTCA 60.669 57.895 0.00 0.00 37.01 3.18
2106 2180 1.002868 AGCAGAGCAAGCGGTTCAT 60.003 52.632 0.00 0.00 37.01 2.57
2107 2181 0.607489 AGCAGAGCAAGCGGTTCATT 60.607 50.000 0.00 0.00 37.01 2.57
2108 2182 0.455633 GCAGAGCAAGCGGTTCATTG 60.456 55.000 0.00 0.00 0.00 2.82
2247 2323 0.324645 ATGATTGGCACCCCTCAACC 60.325 55.000 0.00 0.00 0.00 3.77
2308 2384 2.436646 AGGGAAACATGAGCGCGG 60.437 61.111 8.83 0.00 0.00 6.46
2309 2385 3.508840 GGGAAACATGAGCGCGGG 61.509 66.667 8.83 0.00 0.00 6.13
2310 2386 3.508840 GGAAACATGAGCGCGGGG 61.509 66.667 8.83 0.00 0.00 5.73
2311 2387 2.435938 GAAACATGAGCGCGGGGA 60.436 61.111 8.83 0.00 0.00 4.81
2312 2388 2.436646 AAACATGAGCGCGGGGAG 60.437 61.111 8.83 0.00 0.00 4.30
2360 2436 4.338379 AACTGTCAAACTGGGAGTACTC 57.662 45.455 14.87 14.87 0.00 2.59
2402 2487 2.743938 CATGTTCTATTCGGGGTCGAG 58.256 52.381 0.00 0.00 46.75 4.04
2416 2501 1.379977 TCGAGGAATCCGAGCCAGT 60.380 57.895 0.00 0.00 0.00 4.00
2417 2502 0.106868 TCGAGGAATCCGAGCCAGTA 60.107 55.000 0.00 0.00 0.00 2.74
2418 2503 0.030908 CGAGGAATCCGAGCCAGTAC 59.969 60.000 0.00 0.00 0.00 2.73
2495 2605 3.708563 TCAGTTCGCCAAAAAGGAAAG 57.291 42.857 0.00 0.00 41.22 2.62
2695 2808 2.717580 TGTCTGTAACACGCCAGTAG 57.282 50.000 0.00 0.00 31.20 2.57
2948 3102 2.558617 GCAGCATGACATGGACACA 58.441 52.632 17.03 0.00 39.69 3.72
3061 3221 3.120683 CGAGAATCTGTTGCTTTTACGCA 60.121 43.478 0.00 0.00 38.31 5.24
3168 3328 1.977544 CTCGTCCAAGGTCCTCGGT 60.978 63.158 0.00 0.00 0.00 4.69
3338 3498 1.752198 CCGACAAGTCCCAGGTCAA 59.248 57.895 0.00 0.00 0.00 3.18
3339 3499 0.602905 CCGACAAGTCCCAGGTCAAC 60.603 60.000 0.00 0.00 0.00 3.18
3348 3508 0.960364 CCCAGGTCAACCAACCATCG 60.960 60.000 1.33 0.00 42.12 3.84
3375 3535 2.029380 TCATTGCGCAGTACAGTACAGT 60.029 45.455 11.31 0.00 0.00 3.55
3476 3641 2.173669 CATGCACGCCCGGAACTAG 61.174 63.158 0.73 0.00 0.00 2.57
3530 3718 2.589492 CGATGTCGCGGAGGCAATC 61.589 63.158 6.13 0.07 38.34 2.67
3683 3895 1.144969 TGTCACGCGTCCTTCAATTC 58.855 50.000 9.86 0.00 0.00 2.17
3727 3945 4.265073 CCTCCTTCGTTTCATCAGGAAAT 58.735 43.478 0.00 0.00 46.55 2.17
3731 3949 4.622740 CCTTCGTTTCATCAGGAAATTTGC 59.377 41.667 0.68 0.68 46.55 3.68
3838 4078 1.000884 AATGCAAATGCCAAATCGCG 58.999 45.000 0.00 0.00 41.18 5.87
3961 4201 3.030652 CTCGGTGTTGGTGGTTGC 58.969 61.111 0.00 0.00 0.00 4.17
4018 4271 4.083802 GGCTAATAGCTAATGCCGTTCTTG 60.084 45.833 12.41 0.00 41.99 3.02
4096 4349 0.253327 CCACTAAAGCACCCCCTCTC 59.747 60.000 0.00 0.00 0.00 3.20
4402 4659 2.243736 AGAGGAGGTAGAAGGGAGAGTG 59.756 54.545 0.00 0.00 0.00 3.51
4573 4830 0.822944 TCCCGGGCAATATCGTCGTA 60.823 55.000 18.49 0.00 0.00 3.43
4710 4982 2.871096 TACATGACACCCCTTGAACC 57.129 50.000 0.00 0.00 0.00 3.62
4741 5013 6.409524 AAGAATGAAATGAACAGAAGGCAA 57.590 33.333 0.00 0.00 0.00 4.52
4742 5014 6.022163 AGAATGAAATGAACAGAAGGCAAG 57.978 37.500 0.00 0.00 0.00 4.01
4743 5015 4.796038 ATGAAATGAACAGAAGGCAAGG 57.204 40.909 0.00 0.00 0.00 3.61
4744 5016 2.297033 TGAAATGAACAGAAGGCAAGGC 59.703 45.455 0.00 0.00 0.00 4.35
4745 5017 1.999648 AATGAACAGAAGGCAAGGCA 58.000 45.000 0.00 0.00 0.00 4.75
4746 5018 1.251251 ATGAACAGAAGGCAAGGCAC 58.749 50.000 0.00 0.00 0.00 5.01
4765 5037 4.444720 GGCACGTACAAGCTGAAGATATAC 59.555 45.833 6.50 0.00 0.00 1.47
4780 5053 8.306313 TGAAGATATACCTTTTGCTCTCTACA 57.694 34.615 0.00 0.00 0.00 2.74
4819 5092 4.163427 GGGGATCTGTTAGGATGATCTCA 58.837 47.826 0.00 0.00 38.93 3.27
4921 5196 3.840666 CCCCTGTCACCTGCACTATATAT 59.159 47.826 0.00 0.00 0.00 0.86
4923 5198 5.483937 CCCCTGTCACCTGCACTATATATAA 59.516 44.000 0.00 0.00 0.00 0.98
4926 5201 7.039011 CCCTGTCACCTGCACTATATATAAAGA 60.039 40.741 0.00 0.00 0.00 2.52
4927 5202 8.031864 CCTGTCACCTGCACTATATATAAAGAG 58.968 40.741 0.00 0.00 0.00 2.85
4929 5204 7.509318 TGTCACCTGCACTATATATAAAGAGGT 59.491 37.037 0.00 0.00 0.00 3.85
4950 5225 4.060038 GTCGGCGGTTCGGAGGAA 62.060 66.667 7.21 0.00 0.00 3.36
4996 5271 1.329256 CACCTACATCCCCTACCGAG 58.671 60.000 0.00 0.00 0.00 4.63
5040 5315 3.546714 AAGCACCGCCACCACTACC 62.547 63.158 0.00 0.00 0.00 3.18
5051 5326 0.043334 ACCACTACCCTCTGCCATCT 59.957 55.000 0.00 0.00 0.00 2.90
5054 5329 0.339859 ACTACCCTCTGCCATCTCCA 59.660 55.000 0.00 0.00 0.00 3.86
5062 5338 4.101448 GCCATCTCCAGCACCGGT 62.101 66.667 0.00 0.00 0.00 5.28
5063 5339 2.124983 CCATCTCCAGCACCGGTG 60.125 66.667 30.66 30.66 0.00 4.94
5131 5407 4.188937 ACCTATCACCACTACCGGAATA 57.811 45.455 9.46 0.00 0.00 1.75
5242 5520 2.375509 CCCAAAGAACCCTAGAACAGGT 59.624 50.000 0.00 0.00 43.80 4.00
5243 5521 3.412386 CCAAAGAACCCTAGAACAGGTG 58.588 50.000 0.00 0.00 43.80 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.688197 CCCAAAATCAGTGGTGCACTT 59.312 47.619 17.98 0.00 42.59 3.16
41 42 2.767394 TCATCCAATGGCCCAAAATCAG 59.233 45.455 0.00 0.00 0.00 2.90
145 147 2.159028 GGAGAGTAAGATGTGGAGTGCC 60.159 54.545 0.00 0.00 0.00 5.01
251 254 9.878599 CGTCGAAATAAAGATTATAGCCAAAAT 57.121 29.630 0.00 0.00 0.00 1.82
269 272 5.073311 TCTTCCAAAGATCTCGTCGAAAT 57.927 39.130 0.00 0.00 31.20 2.17
339 343 0.526524 TGTTTTGAAACTTGGCCGCG 60.527 50.000 0.00 0.00 39.59 6.46
489 505 9.050601 CCCTCTCTCAACATTAATGTAGATTTC 57.949 37.037 21.07 0.00 40.80 2.17
521 538 2.414559 CCAAAATCAAGCCGCACTACAG 60.415 50.000 0.00 0.00 0.00 2.74
542 559 1.714794 ACAATGCTCTCACGCACTAC 58.285 50.000 0.00 0.00 43.61 2.73
545 562 3.373020 CAACAATGCTCTCACGCAC 57.627 52.632 0.00 0.00 43.61 5.34
607 624 0.879090 CGACCGTCGGATGGATATCA 59.121 55.000 22.75 0.00 36.00 2.15
619 636 2.093783 CACCAAGCTATTTTCGACCGTC 59.906 50.000 0.00 0.00 0.00 4.79
642 659 2.683968 TCGAAATCTATATGCACGGGC 58.316 47.619 0.34 0.34 41.68 6.13
1196 1216 2.014093 GATCACTTGCGGCGTCTTCG 62.014 60.000 9.37 0.00 40.37 3.79
1725 1750 5.050091 TGTTTTGCTCGAGTGAAAGATCTTC 60.050 40.000 15.13 3.35 0.00 2.87
1743 1768 7.113264 CACAAGGCAAAAGTTTTTCTTGTTTTG 59.887 33.333 27.32 19.24 40.34 2.44
1756 1781 1.405391 GCACCAACACAAGGCAAAAGT 60.405 47.619 0.00 0.00 0.00 2.66
1970 2021 1.632018 TTAATGGGGAGGGTGAGCGG 61.632 60.000 0.00 0.00 0.00 5.52
1971 2022 0.254747 TTTAATGGGGAGGGTGAGCG 59.745 55.000 0.00 0.00 0.00 5.03
2066 2131 2.435372 AGCCTGACTGACTAGAGAGG 57.565 55.000 0.00 0.00 0.00 3.69
2094 2168 4.972591 AAGCAATGAACCGCTTGC 57.027 50.000 0.00 0.00 46.41 4.01
2097 2171 1.408702 ACACAAAAGCAATGAACCGCT 59.591 42.857 0.00 0.00 41.20 5.52
2098 2172 1.851658 ACACAAAAGCAATGAACCGC 58.148 45.000 0.00 0.00 0.00 5.68
2099 2173 6.523676 AAATAACACAAAAGCAATGAACCG 57.476 33.333 0.00 0.00 0.00 4.44
2100 2174 9.040939 AGTAAAATAACACAAAAGCAATGAACC 57.959 29.630 0.00 0.00 0.00 3.62
2103 2177 9.906660 CCTAGTAAAATAACACAAAAGCAATGA 57.093 29.630 0.00 0.00 0.00 2.57
2104 2178 9.906660 TCCTAGTAAAATAACACAAAAGCAATG 57.093 29.630 0.00 0.00 0.00 2.82
2105 2179 9.908152 GTCCTAGTAAAATAACACAAAAGCAAT 57.092 29.630 0.00 0.00 0.00 3.56
2106 2180 8.071368 CGTCCTAGTAAAATAACACAAAAGCAA 58.929 33.333 0.00 0.00 0.00 3.91
2107 2181 7.308109 CCGTCCTAGTAAAATAACACAAAAGCA 60.308 37.037 0.00 0.00 0.00 3.91
2108 2182 7.019418 CCGTCCTAGTAAAATAACACAAAAGC 58.981 38.462 0.00 0.00 0.00 3.51
2109 2183 7.019418 GCCGTCCTAGTAAAATAACACAAAAG 58.981 38.462 0.00 0.00 0.00 2.27
2110 2184 6.347563 CGCCGTCCTAGTAAAATAACACAAAA 60.348 38.462 0.00 0.00 0.00 2.44
2128 2202 4.404654 ACCGTTACGTCGCCGTCC 62.405 66.667 0.00 0.00 46.28 4.79
2360 2436 4.505217 GCGTCTGCCGTGATTGCG 62.505 66.667 0.00 0.00 39.32 4.85
2402 2487 1.001597 CGTAGTACTGGCTCGGATTCC 60.002 57.143 5.39 0.00 0.00 3.01
2416 2501 1.392168 GTGCCGTGTACGTACGTAGTA 59.608 52.381 27.48 16.88 42.24 1.82
2417 2502 0.165944 GTGCCGTGTACGTACGTAGT 59.834 55.000 27.48 5.15 42.24 2.73
2418 2503 0.853224 CGTGCCGTGTACGTACGTAG 60.853 60.000 27.48 16.78 42.24 3.51
2470 2580 3.115554 CCTTTTTGGCGAACTGAACAAG 58.884 45.455 0.00 0.00 0.00 3.16
2695 2808 9.202273 CCCGTATATATATACTCGGAGAAGTAC 57.798 40.741 25.86 9.47 37.10 2.73
2946 3100 5.865085 TGAAAAGATGCTGGTAAGTAGTGT 58.135 37.500 0.00 0.00 0.00 3.55
2948 3102 8.176185 AAGCTTGAAAAGATGCTGGTAAGTAGT 61.176 37.037 0.00 0.00 45.10 2.73
3061 3221 5.920273 CACCGAATGTACTGCAAAAGATTTT 59.080 36.000 0.00 0.00 0.00 1.82
3168 3328 0.104672 TCAGGTCCCTGGAGAACCAA 60.105 55.000 13.24 1.58 46.32 3.67
3237 3397 2.762234 GCCGTGGACGTCGATCTCT 61.762 63.158 9.92 0.00 37.74 3.10
3338 3498 0.991920 ATGAAGGGTCGATGGTTGGT 59.008 50.000 0.00 0.00 0.00 3.67
3339 3499 1.745087 CAATGAAGGGTCGATGGTTGG 59.255 52.381 0.00 0.00 0.00 3.77
3348 3508 0.727398 GTACTGCGCAATGAAGGGTC 59.273 55.000 13.05 0.00 0.00 4.46
3375 3535 2.223502 GCTACTGCTACTGCGATGTGTA 60.224 50.000 0.00 0.00 43.34 2.90
3476 3641 1.604693 GGCCATATGAATGCTTGCTGC 60.605 52.381 3.65 0.00 43.25 5.25
3801 4041 3.293337 CATTGCCATTTCCAGATCCTCA 58.707 45.455 0.00 0.00 0.00 3.86
3879 4119 0.397535 CCCCTCCCCACCAAATCATG 60.398 60.000 0.00 0.00 0.00 3.07
4018 4271 4.218635 CCTAAAAGAAGCCCTGGTTTTCTC 59.781 45.833 9.52 0.00 31.16 2.87
4296 4553 1.489649 CCATGATCTCCAGGCAGTCTT 59.510 52.381 0.00 0.00 0.00 3.01
4300 4557 0.545171 ACACCATGATCTCCAGGCAG 59.455 55.000 0.00 0.00 0.00 4.85
4352 4609 2.427506 GGAGTTTGTTGCGAGGAAGAT 58.572 47.619 0.00 0.00 0.00 2.40
4402 4659 4.082845 TGGATCCGATGATCTCTTCTACC 58.917 47.826 7.39 0.00 45.62 3.18
4573 4830 9.498176 AAAGAAAAGGTAAGTACGATGTACAAT 57.502 29.630 0.00 0.00 0.00 2.71
4710 4982 8.244494 TCTGTTCATTTCATTCTTTAGAGACG 57.756 34.615 0.00 0.00 0.00 4.18
4741 5013 0.679505 TCTTCAGCTTGTACGTGCCT 59.320 50.000 0.00 0.00 0.00 4.75
4742 5014 1.726853 ATCTTCAGCTTGTACGTGCC 58.273 50.000 0.00 0.00 0.00 5.01
4743 5015 4.444720 GGTATATCTTCAGCTTGTACGTGC 59.555 45.833 0.00 0.00 0.00 5.34
4744 5016 5.833082 AGGTATATCTTCAGCTTGTACGTG 58.167 41.667 0.00 0.00 0.00 4.49
4745 5017 6.466885 AAGGTATATCTTCAGCTTGTACGT 57.533 37.500 0.00 0.00 31.60 3.57
4746 5018 7.621991 CAAAAGGTATATCTTCAGCTTGTACG 58.378 38.462 0.00 0.00 33.05 3.67
4765 5037 9.399403 GTAAAGAAAAATGTAGAGAGCAAAAGG 57.601 33.333 0.00 0.00 0.00 3.11
4780 5053 7.292356 ACAGATCCCCCTTTTGTAAAGAAAAAT 59.708 33.333 0.89 0.00 0.00 1.82
4819 5092 2.600173 CATTGGGCCCACACGGTT 60.600 61.111 28.70 1.86 0.00 4.44
4883 5156 1.339644 GGGGCCCGTCAACCATAGTA 61.340 60.000 17.79 0.00 0.00 1.82
4921 5196 2.652095 CGCCGACCCCACCTCTTTA 61.652 63.158 0.00 0.00 0.00 1.85
4941 5216 0.886563 GACGAACCTCTTCCTCCGAA 59.113 55.000 0.00 0.00 0.00 4.30
4945 5220 1.514443 CGCGACGAACCTCTTCCTC 60.514 63.158 0.00 0.00 0.00 3.71
4947 5222 1.800713 GTCGCGACGAACCTCTTCC 60.801 63.158 25.19 0.00 37.72 3.46
4948 5223 1.081641 TGTCGCGACGAACCTCTTC 60.082 57.895 31.88 6.92 37.72 2.87
4950 5225 2.254651 GTGTCGCGACGAACCTCT 59.745 61.111 31.88 0.00 37.72 3.69
4996 5271 0.250513 AGCACTGCACTAACCCTAGC 59.749 55.000 3.30 0.00 0.00 3.42
5040 5315 1.153208 GTGCTGGAGATGGCAGAGG 60.153 63.158 0.00 0.00 39.22 3.69
5131 5407 1.508667 TTGATCCAGTGGGCATGGGT 61.509 55.000 9.92 0.00 38.44 4.51
5187 5463 3.745799 TCTGTTGCTACCGAAAATCCAA 58.254 40.909 0.00 0.00 0.00 3.53
5291 5569 2.119655 CCGGATCGAGAGGAACGGT 61.120 63.158 0.00 0.00 41.56 4.83
5332 5610 0.249398 CGGTGGTTCTTCTTCCGGAT 59.751 55.000 4.15 0.00 37.92 4.18
5335 5613 0.389948 CTCCGGTGGTTCTTCTTCCG 60.390 60.000 0.00 0.00 40.72 4.30


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

AutoCloner maintained by Alex Coulton.