Multiple sequence alignment - TraesCS1D01G114000

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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 TraesCS1D01G114000 chr1D 100.000 3617 0 0 1 3617 110054790 110051174 0.000000e+00 6680
1 TraesCS1D01G114000 chr1D 84.854 515 55 12 1531 2040 258388933 258389429 6.970000e-137 497
2 TraesCS1D01G114000 chr1D 89.247 93 7 2 2237 2326 77013454 77013362 2.950000e-21 113
3 TraesCS1D01G114000 chr1B 93.896 1458 68 8 1569 3013 167109759 167108310 0.000000e+00 2180
4 TraesCS1D01G114000 chr1B 92.118 609 46 2 3010 3617 661570271 661569664 0.000000e+00 857
5 TraesCS1D01G114000 chr1B 93.814 485 29 1 1037 1521 167110254 167109771 0.000000e+00 728
6 TraesCS1D01G114000 chr1B 88.247 502 31 13 293 779 167111240 167110752 3.130000e-160 575
7 TraesCS1D01G114000 chr1B 95.053 283 5 1 1 274 167112603 167112321 1.540000e-118 436
8 TraesCS1D01G114000 chr1B 90.278 216 7 4 832 1039 167110737 167110528 1.660000e-68 270
9 TraesCS1D01G114000 chr1A 97.243 1197 26 4 1801 2992 114061514 114060320 0.000000e+00 2021
10 TraesCS1D01G114000 chr1A 90.210 1093 73 13 734 1798 114062769 114061683 0.000000e+00 1395
11 TraesCS1D01G114000 chr1A 93.770 610 34 2 3008 3617 355589232 355589837 0.000000e+00 913
12 TraesCS1D01G114000 chr1A 90.227 706 21 15 1 694 114063440 114062771 0.000000e+00 878
13 TraesCS1D01G114000 chr1A 80.902 377 28 16 1873 2239 104830808 104830466 1.290000e-64 257
14 TraesCS1D01G114000 chr5B 97.311 595 16 0 3023 3617 405525585 405524991 0.000000e+00 1011
15 TraesCS1D01G114000 chr2A 96.242 612 23 0 3006 3617 345483602 345484213 0.000000e+00 1003
16 TraesCS1D01G114000 chr2A 96.339 601 21 1 3017 3617 227832443 227831844 0.000000e+00 987
17 TraesCS1D01G114000 chr2A 90.526 95 5 3 2229 2319 593655900 593655994 4.900000e-24 122
18 TraesCS1D01G114000 chr2A 87.879 99 8 3 2238 2332 4969536 4969438 2.950000e-21 113
19 TraesCS1D01G114000 chr2A 88.660 97 6 4 2227 2319 376082529 376082434 2.950000e-21 113
20 TraesCS1D01G114000 chr3A 96.179 602 22 1 3016 3617 41951302 41950702 0.000000e+00 983
21 TraesCS1D01G114000 chr2D 96.013 602 23 1 3016 3617 618381820 618381220 0.000000e+00 977
22 TraesCS1D01G114000 chr2D 90.722 97 4 4 2227 2319 299891114 299891019 1.360000e-24 124
23 TraesCS1D01G114000 chr3B 95.175 601 27 2 3017 3617 436516572 436515974 0.000000e+00 948
24 TraesCS1D01G114000 chr3B 94.527 603 32 1 3015 3617 43838482 43839083 0.000000e+00 929
25 TraesCS1D01G114000 chr3B 86.667 105 6 6 2235 2332 1611951 1612054 3.820000e-20 110
26 TraesCS1D01G114000 chr5A 80.637 377 25 19 1873 2239 105256725 105256387 7.760000e-62 248
27 TraesCS1D01G114000 chr4A 91.860 86 4 2 2238 2320 590111631 590111546 2.280000e-22 117


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 TraesCS1D01G114000 chr1D 110051174 110054790 3616 True 6680.000000 6680 100.0000 1 3617 1 chr1D.!!$R2 3616
1 TraesCS1D01G114000 chr1B 661569664 661570271 607 True 857.000000 857 92.1180 3010 3617 1 chr1B.!!$R1 607
2 TraesCS1D01G114000 chr1B 167108310 167112603 4293 True 837.800000 2180 92.2576 1 3013 5 chr1B.!!$R2 3012
3 TraesCS1D01G114000 chr1A 114060320 114063440 3120 True 1431.333333 2021 92.5600 1 2992 3 chr1A.!!$R2 2991
4 TraesCS1D01G114000 chr1A 355589232 355589837 605 False 913.000000 913 93.7700 3008 3617 1 chr1A.!!$F1 609
5 TraesCS1D01G114000 chr5B 405524991 405525585 594 True 1011.000000 1011 97.3110 3023 3617 1 chr5B.!!$R1 594
6 TraesCS1D01G114000 chr2A 345483602 345484213 611 False 1003.000000 1003 96.2420 3006 3617 1 chr2A.!!$F1 611
7 TraesCS1D01G114000 chr2A 227831844 227832443 599 True 987.000000 987 96.3390 3017 3617 1 chr2A.!!$R2 600
8 TraesCS1D01G114000 chr3A 41950702 41951302 600 True 983.000000 983 96.1790 3016 3617 1 chr3A.!!$R1 601
9 TraesCS1D01G114000 chr2D 618381220 618381820 600 True 977.000000 977 96.0130 3016 3617 1 chr2D.!!$R2 601
10 TraesCS1D01G114000 chr3B 436515974 436516572 598 True 948.000000 948 95.1750 3017 3617 1 chr3B.!!$R1 600
11 TraesCS1D01G114000 chr3B 43838482 43839083 601 False 929.000000 929 94.5270 3015 3617 1 chr3B.!!$F2 602

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
784 1871 0.323725 GCATCCAGTTGTGATGGGGT 60.324 55.0 0.0 0.0 39.97 4.95 F
1445 2875 0.107214 TTGGCGAGGATGTGGGAATC 60.107 55.0 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 4021 2.158623 TGGAAGCATCAGAACAACCTGT 60.159 45.455 0.00 0.0 35.71 4.00 R
2901 4510 0.035056 AGGCAGCCCTGAACACATAC 60.035 55.000 8.22 0.0 40.94 2.39 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
118 119 2.102588 AGAATATTCCACGTCCCTTCCG 59.897 50.000 11.92 0.00 0.00 4.30
280 300 2.279069 ACACCACCGGAGAGCTCTG 61.279 63.158 23.91 9.72 35.77 3.35
291 1366 2.613223 GGAGAGCTCTGCCTTTTACGTT 60.613 50.000 23.91 0.00 0.00 3.99
302 1377 6.035650 TCTGCCTTTTACGTTAATCAATCGAG 59.964 38.462 0.00 0.00 0.00 4.04
375 1450 3.203412 CCGTCTCCTCCGACCTCG 61.203 72.222 0.00 0.00 39.44 4.63
436 1511 0.546598 AAAATCCCCGCTTCCGATCT 59.453 50.000 0.00 0.00 36.29 2.75
465 1540 1.380403 CCTCTCGCTGATCTGGTCGT 61.380 60.000 1.46 0.00 0.00 4.34
568 1654 0.387565 GGATTTTTGTGTGCGGGTGT 59.612 50.000 0.00 0.00 0.00 4.16
576 1662 2.822255 GTGCGGGTGTGTGTGTGT 60.822 61.111 0.00 0.00 0.00 3.72
577 1663 2.512745 TGCGGGTGTGTGTGTGTC 60.513 61.111 0.00 0.00 0.00 3.67
578 1664 3.636043 GCGGGTGTGTGTGTGTCG 61.636 66.667 0.00 0.00 0.00 4.35
579 1665 2.964925 CGGGTGTGTGTGTGTCGG 60.965 66.667 0.00 0.00 0.00 4.79
580 1666 2.188469 GGGTGTGTGTGTGTCGGT 59.812 61.111 0.00 0.00 0.00 4.69
581 1667 2.177580 GGGTGTGTGTGTGTCGGTG 61.178 63.158 0.00 0.00 0.00 4.94
582 1668 2.177580 GGTGTGTGTGTGTCGGTGG 61.178 63.158 0.00 0.00 0.00 4.61
583 1669 2.177580 GTGTGTGTGTGTCGGTGGG 61.178 63.158 0.00 0.00 0.00 4.61
584 1670 2.188469 GTGTGTGTGTCGGTGGGT 59.812 61.111 0.00 0.00 0.00 4.51
701 1787 2.114616 AGAATTCCGACCTCTGCATCT 58.885 47.619 0.65 0.00 0.00 2.90
744 1830 3.848019 CGTAGCTCATCACAATTGCAAAC 59.152 43.478 1.71 0.00 0.00 2.93
750 1836 4.239304 TCATCACAATTGCAAACAGATGC 58.761 39.130 20.52 0.00 46.58 3.91
775 1862 2.271800 GTAGTTCCTCGCATCCAGTTG 58.728 52.381 0.00 0.00 0.00 3.16
776 1863 0.687354 AGTTCCTCGCATCCAGTTGT 59.313 50.000 0.00 0.00 0.00 3.32
777 1864 0.798776 GTTCCTCGCATCCAGTTGTG 59.201 55.000 0.00 0.00 0.00 3.33
778 1865 0.684535 TTCCTCGCATCCAGTTGTGA 59.315 50.000 0.00 0.00 35.04 3.58
779 1866 0.904649 TCCTCGCATCCAGTTGTGAT 59.095 50.000 0.00 0.00 35.70 3.06
780 1867 1.012086 CCTCGCATCCAGTTGTGATG 58.988 55.000 0.00 0.00 42.01 3.07
781 1868 1.012086 CTCGCATCCAGTTGTGATGG 58.988 55.000 0.00 0.00 39.97 3.51
782 1869 2.100846 CGCATCCAGTTGTGATGGG 58.899 57.895 3.43 3.43 43.68 4.00
783 1870 1.378882 CGCATCCAGTTGTGATGGGG 61.379 60.000 8.84 0.00 44.75 4.96
784 1871 0.323725 GCATCCAGTTGTGATGGGGT 60.324 55.000 0.00 0.00 39.97 4.95
785 1872 1.064758 GCATCCAGTTGTGATGGGGTA 60.065 52.381 0.00 0.00 39.97 3.69
811 1909 6.287589 GAGAAAAATACTCTCCTCAGTCCA 57.712 41.667 0.00 0.00 34.42 4.02
812 1910 6.882768 AGAAAAATACTCTCCTCAGTCCAT 57.117 37.500 0.00 0.00 0.00 3.41
813 1911 7.264294 AGAAAAATACTCTCCTCAGTCCATT 57.736 36.000 0.00 0.00 0.00 3.16
814 1912 7.694093 AGAAAAATACTCTCCTCAGTCCATTT 58.306 34.615 0.00 0.00 0.00 2.32
815 1913 7.609532 AGAAAAATACTCTCCTCAGTCCATTTG 59.390 37.037 0.00 0.00 0.00 2.32
816 1914 6.627087 AAATACTCTCCTCAGTCCATTTGA 57.373 37.500 0.00 0.00 0.00 2.69
817 1915 3.971245 ACTCTCCTCAGTCCATTTGAC 57.029 47.619 0.00 0.00 44.82 3.18
830 1928 5.858475 GTCCATTTGACGACAAGTTATCTG 58.142 41.667 0.00 0.00 37.32 2.90
831 1929 5.408604 GTCCATTTGACGACAAGTTATCTGT 59.591 40.000 0.00 0.00 37.32 3.41
945 2081 7.345653 AGTTTCCTTCTGATAGACCATGACATA 59.654 37.037 0.00 0.00 0.00 2.29
946 2082 7.862274 TTCCTTCTGATAGACCATGACATAT 57.138 36.000 0.00 0.00 0.00 1.78
948 2084 7.901029 TCCTTCTGATAGACCATGACATATTC 58.099 38.462 0.00 0.00 0.00 1.75
968 2104 8.926710 CATATTCTACTATTGTTTAGGCCTTCG 58.073 37.037 12.58 0.00 0.00 3.79
973 2109 2.891191 TTGTTTAGGCCTTCGGGAAT 57.109 45.000 12.58 0.00 37.25 3.01
1068 2498 3.127895 TGTGTTTTGTTCTTGAACTCCCG 59.872 43.478 13.65 0.00 0.00 5.14
1072 2502 2.526304 TGTTCTTGAACTCCCGAGTG 57.474 50.000 13.65 0.00 41.58 3.51
1089 2519 6.990349 TCCCGAGTGATTTTTATGTAATCCTC 59.010 38.462 0.00 0.00 32.29 3.71
1119 2549 0.535335 TTGGTCAGGGTCGTAGCATC 59.465 55.000 0.00 0.00 0.00 3.91
1260 2690 8.810427 GCAATTTGTTACAATGGATTACAGATG 58.190 33.333 0.00 0.00 0.00 2.90
1305 2735 9.821662 GTTTGGTATGAACTACTTGATGTTTAC 57.178 33.333 0.00 0.00 0.00 2.01
1307 2737 6.311935 TGGTATGAACTACTTGATGTTTACGC 59.688 38.462 0.00 0.00 0.00 4.42
1359 2789 8.549731 TGAGAATAGGTCTAAGAAGTCTGTCTA 58.450 37.037 0.00 0.00 36.41 2.59
1367 2797 4.323553 AAGAAGTCTGTCTACACACACC 57.676 45.455 0.00 0.00 0.00 4.16
1378 2808 2.380064 ACACACACCAATTCCACCAT 57.620 45.000 0.00 0.00 0.00 3.55
1411 2841 5.161943 AGCCTGTAAAATAAGTCCGTTCT 57.838 39.130 0.00 0.00 0.00 3.01
1429 2859 4.572985 TTCTTGCAAGAGAACACATTGG 57.427 40.909 27.02 0.00 36.22 3.16
1430 2860 2.294233 TCTTGCAAGAGAACACATTGGC 59.706 45.455 25.16 0.00 0.00 4.52
1434 2864 1.466167 CAAGAGAACACATTGGCGAGG 59.534 52.381 0.00 0.00 0.00 4.63
1441 2871 1.077501 ACATTGGCGAGGATGTGGG 60.078 57.895 0.00 0.00 35.31 4.61
1445 2875 0.107214 TTGGCGAGGATGTGGGAATC 60.107 55.000 0.00 0.00 0.00 2.52
1534 2964 1.351017 TGAAGGTCCTTAGCTGTTGGG 59.649 52.381 3.42 0.00 32.57 4.12
1566 2996 6.127310 ACTGTAGAAAGCCTGTAGTGATTAGG 60.127 42.308 0.00 0.00 34.67 2.69
1626 3056 8.442374 TGGACAGGTTAACTAAACTATTTTCCT 58.558 33.333 5.42 0.00 38.23 3.36
1852 3448 7.141363 ACAACTAACAATTCTTGATGCAGTTC 58.859 34.615 0.00 0.00 0.00 3.01
2172 3777 4.391405 ACCTTTCAGCCAAACTTCAAAG 57.609 40.909 0.00 0.00 0.00 2.77
2415 4021 7.809546 TGGTTGATAACACTGTGATTAACAA 57.190 32.000 15.86 15.29 38.67 2.83
2823 4430 4.142381 CCCTGCTGGTAAAATGCTAGTTTC 60.142 45.833 9.00 0.00 0.00 2.78
2892 4501 5.064198 TGTTTCTGTGTTGAGAAAACGTAGG 59.936 40.000 0.00 0.00 42.27 3.18
2901 4510 1.003233 AGAAAACGTAGGCCTTCCTGG 59.997 52.381 12.58 0.00 44.08 4.45
2925 4536 4.704833 TTCAGGGCTGCCTCGTGC 62.705 66.667 19.68 0.61 41.77 5.34
2956 4567 5.554070 CAATTGCTTCTTCCCCTTTGATTT 58.446 37.500 0.00 0.00 0.00 2.17
2983 4594 9.232473 GTAGGGTTTTCAGAGAAATGTTCTTAT 57.768 33.333 0.00 0.00 40.87 1.73
3125 4737 1.264020 GACACACGCACACACATCATT 59.736 47.619 0.00 0.00 0.00 2.57
3162 4774 2.496817 GCGAGGAGGTGCTACCAG 59.503 66.667 7.86 0.00 41.95 4.00
3224 4836 1.671054 AACCATGAACGGCGAGGTG 60.671 57.895 16.62 6.63 31.86 4.00
3284 4896 1.302511 GGCGCCTCCAAAGAAGACA 60.303 57.895 22.15 0.00 34.01 3.41
3305 4917 0.979709 CATCTCCAGGGCTGTCCAGA 60.980 60.000 0.00 0.00 38.24 3.86
3398 5010 1.097547 CCATCGTCTTGGACATGCCC 61.098 60.000 0.00 0.00 39.25 5.36
3464 5076 1.434622 CCCTCATCACAGCATCGCAC 61.435 60.000 0.00 0.00 0.00 5.34
3513 5126 2.673523 GCCACCATCTCCAGCTGT 59.326 61.111 13.81 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.742201 TGCTTCTGGAGGCGACGC 62.742 66.667 12.43 12.43 36.05 5.19
227 240 4.736896 GGGTCGTCTGGTGGTCGC 62.737 72.222 0.00 0.00 0.00 5.19
280 300 4.962151 GCTCGATTGATTAACGTAAAAGGC 59.038 41.667 0.00 0.00 0.00 4.35
291 1366 5.984725 TCTTTAACTGGGCTCGATTGATTA 58.015 37.500 0.00 0.00 0.00 1.75
302 1377 6.621613 CAATTAAGAGGTTCTTTAACTGGGC 58.378 40.000 0.00 0.00 37.89 5.36
342 1417 1.757699 GACGGAGAAGATAAGCCTGGT 59.242 52.381 0.00 0.00 0.00 4.00
465 1540 1.277326 CGCATCGGACAAATCGAAGA 58.723 50.000 0.00 0.00 45.75 2.87
568 1654 2.188207 CACCCACCGACACACACA 59.812 61.111 0.00 0.00 0.00 3.72
576 1662 3.485346 GAAAGCACCCACCCACCGA 62.485 63.158 0.00 0.00 0.00 4.69
577 1663 2.976494 AAGAAAGCACCCACCCACCG 62.976 60.000 0.00 0.00 0.00 4.94
578 1664 0.759060 AAAGAAAGCACCCACCCACC 60.759 55.000 0.00 0.00 0.00 4.61
579 1665 0.673985 GAAAGAAAGCACCCACCCAC 59.326 55.000 0.00 0.00 0.00 4.61
580 1666 0.469144 GGAAAGAAAGCACCCACCCA 60.469 55.000 0.00 0.00 0.00 4.51
581 1667 1.185618 GGGAAAGAAAGCACCCACCC 61.186 60.000 0.00 0.00 41.72 4.61
582 1668 1.185618 GGGGAAAGAAAGCACCCACC 61.186 60.000 0.00 0.00 43.67 4.61
583 1669 1.185618 GGGGGAAAGAAAGCACCCAC 61.186 60.000 0.00 0.00 43.30 4.61
584 1670 1.155155 GGGGGAAAGAAAGCACCCA 59.845 57.895 0.00 0.00 43.30 4.51
627 1713 9.459640 GAACCTGAACCTGATTTTAAACTAAAC 57.540 33.333 0.00 0.00 0.00 2.01
744 1830 0.176680 AGGAACTACCGCTGCATCTG 59.823 55.000 0.00 0.00 44.74 2.90
775 1862 3.732048 TTTTTCTCCCTACCCCATCAC 57.268 47.619 0.00 0.00 0.00 3.06
776 1863 5.043762 AGTATTTTTCTCCCTACCCCATCA 58.956 41.667 0.00 0.00 0.00 3.07
777 1864 5.369993 AGAGTATTTTTCTCCCTACCCCATC 59.630 44.000 0.00 0.00 32.93 3.51
778 1865 5.297799 AGAGTATTTTTCTCCCTACCCCAT 58.702 41.667 0.00 0.00 32.93 4.00
779 1866 4.706616 AGAGTATTTTTCTCCCTACCCCA 58.293 43.478 0.00 0.00 32.93 4.96
780 1867 5.293319 GAGAGTATTTTTCTCCCTACCCC 57.707 47.826 0.00 0.00 36.01 4.95
805 1903 5.639506 AGATAACTTGTCGTCAAATGGACTG 59.360 40.000 0.00 0.00 44.68 3.51
806 1904 5.639506 CAGATAACTTGTCGTCAAATGGACT 59.360 40.000 0.00 0.00 44.68 3.85
807 1905 5.408604 ACAGATAACTTGTCGTCAAATGGAC 59.591 40.000 0.00 0.00 43.36 4.02
808 1906 5.547465 ACAGATAACTTGTCGTCAAATGGA 58.453 37.500 0.00 0.00 32.87 3.41
809 1907 5.862924 ACAGATAACTTGTCGTCAAATGG 57.137 39.130 0.00 0.00 32.87 3.16
810 1908 9.901724 GTATAACAGATAACTTGTCGTCAAATG 57.098 33.333 0.00 0.00 32.87 2.32
811 1909 9.871238 AGTATAACAGATAACTTGTCGTCAAAT 57.129 29.630 0.00 0.00 32.87 2.32
812 1910 9.135843 CAGTATAACAGATAACTTGTCGTCAAA 57.864 33.333 0.00 0.00 32.87 2.69
813 1911 7.274904 GCAGTATAACAGATAACTTGTCGTCAA 59.725 37.037 0.00 0.00 0.00 3.18
814 1912 6.750501 GCAGTATAACAGATAACTTGTCGTCA 59.249 38.462 0.00 0.00 0.00 4.35
815 1913 6.973474 AGCAGTATAACAGATAACTTGTCGTC 59.027 38.462 0.00 0.00 0.00 4.20
816 1914 6.864342 AGCAGTATAACAGATAACTTGTCGT 58.136 36.000 0.00 0.00 0.00 4.34
817 1915 9.464714 AATAGCAGTATAACAGATAACTTGTCG 57.535 33.333 0.00 0.00 0.00 4.35
826 1924 9.445878 CATGATGGAAATAGCAGTATAACAGAT 57.554 33.333 0.00 0.00 0.00 2.90
827 1925 7.879677 CCATGATGGAAATAGCAGTATAACAGA 59.120 37.037 5.27 0.00 40.96 3.41
828 1926 7.879677 TCCATGATGGAAATAGCAGTATAACAG 59.120 37.037 12.63 0.00 45.00 3.16
829 1927 7.744733 TCCATGATGGAAATAGCAGTATAACA 58.255 34.615 12.63 0.00 45.00 2.41
849 1975 6.757897 TTTCAGCAAGGTATTTACTCCATG 57.242 37.500 0.00 0.00 0.00 3.66
907 2035 5.941058 TCAGAAGGAAACTGTGTTTGTAACA 59.059 36.000 0.10 0.00 42.68 2.41
945 2081 6.289064 CCGAAGGCCTAAACAATAGTAGAAT 58.711 40.000 5.16 0.00 46.14 2.40
946 2082 5.667466 CCGAAGGCCTAAACAATAGTAGAA 58.333 41.667 5.16 0.00 46.14 2.10
968 2104 1.075970 GAAAGGCCCCCTGATTCCC 60.076 63.158 0.00 0.00 32.13 3.97
973 2109 0.783206 TTCAATGAAAGGCCCCCTGA 59.217 50.000 0.00 0.00 32.13 3.86
1068 2498 8.738645 ACAGGAGGATTACATAAAAATCACTC 57.261 34.615 0.00 0.00 35.46 3.51
1072 2502 8.214364 AGAGGACAGGAGGATTACATAAAAATC 58.786 37.037 0.00 0.00 33.44 2.17
1119 2549 4.858935 TGAAATCAAGCTTTTCTTCCACG 58.141 39.130 10.02 0.00 34.80 4.94
1260 2690 6.206829 ACCAAACACTATAAGAAGCAAAGGAC 59.793 38.462 0.00 0.00 0.00 3.85
1298 2728 5.583457 GGTGTAAACTGATAGGCGTAAACAT 59.417 40.000 0.00 0.00 0.00 2.71
1305 2735 7.320399 TCATATATGGTGTAAACTGATAGGCG 58.680 38.462 12.78 0.00 0.00 5.52
1359 2789 1.962807 CATGGTGGAATTGGTGTGTGT 59.037 47.619 0.00 0.00 0.00 3.72
1367 2797 0.538118 CAAGGGGCATGGTGGAATTG 59.462 55.000 0.00 0.00 0.00 2.32
1378 2808 1.068948 TTACAGGCTAACAAGGGGCA 58.931 50.000 0.00 0.00 0.00 5.36
1411 2841 1.001487 CGCCAATGTGTTCTCTTGCAA 60.001 47.619 0.00 0.00 0.00 4.08
1429 2859 1.303309 CTTGATTCCCACATCCTCGC 58.697 55.000 0.00 0.00 0.00 5.03
1430 2860 1.303309 GCTTGATTCCCACATCCTCG 58.697 55.000 0.00 0.00 0.00 4.63
1434 2864 3.940209 TTTGTGCTTGATTCCCACATC 57.060 42.857 0.00 0.00 39.03 3.06
1441 2871 7.864379 TCTCTCAAAGAAATTTGTGCTTGATTC 59.136 33.333 0.00 0.00 33.82 2.52
1445 2875 5.689068 GGTCTCTCAAAGAAATTTGTGCTTG 59.311 40.000 0.00 0.00 35.21 4.01
1534 2964 3.118592 ACAGGCTTTCTACAGTCTATGCC 60.119 47.826 0.00 0.00 39.40 4.40
1566 2996 7.200455 AGTGCACAACTAAGAAAATAAACACC 58.800 34.615 21.04 0.00 37.36 4.16
1852 3448 5.068329 TGAGTACATCAGATGCAACTCTAGG 59.932 44.000 29.41 0.42 42.51 3.02
2172 3777 3.066342 TGAGAAGCTACGGTACTGCATAC 59.934 47.826 0.23 0.00 0.00 2.39
2250 3855 8.818057 CATGGACTCTAAAAACGTCTTATAAGG 58.182 37.037 12.54 0.17 0.00 2.69
2377 3983 9.638239 GTGTTATCAACCAAACATGTTATTCAT 57.362 29.630 12.39 1.92 37.87 2.57
2415 4021 2.158623 TGGAAGCATCAGAACAACCTGT 60.159 45.455 0.00 0.00 35.71 4.00
2823 4430 0.738762 CCCAGCAGATGACACTCACG 60.739 60.000 0.00 0.00 0.00 4.35
2892 4501 2.359900 CTGAACACATACCAGGAAGGC 58.640 52.381 0.00 0.00 43.14 4.35
2901 4510 0.035056 AGGCAGCCCTGAACACATAC 60.035 55.000 8.22 0.00 40.94 2.39
2925 4536 2.159142 GGAAGAAGCAATTGCATGGAGG 60.159 50.000 30.89 0.00 45.16 4.30
2956 4567 6.601332 AGAACATTTCTCTGAAAACCCTACA 58.399 36.000 0.00 0.00 34.07 2.74
2983 4594 3.267812 AGATTTCCCTGCTCCAAAGATCA 59.732 43.478 0.00 0.00 0.00 2.92
3021 4633 3.861569 ACTCTTTTGCGTTTTCTCGAG 57.138 42.857 5.93 5.93 0.00 4.04
3125 4737 0.249868 CTGCTCGTTTGGTGAGGACA 60.250 55.000 0.00 0.00 33.99 4.02
3162 4774 2.631418 TCGTAGTTGCAGTCTGTAGC 57.369 50.000 0.93 0.00 0.00 3.58
3224 4836 2.687935 CCTTGAGGCTCTGAGTCTAGTC 59.312 54.545 12.49 0.72 24.78 2.59
3249 4861 2.591429 CTGGCAACGGCTGTGACA 60.591 61.111 0.00 0.74 40.87 3.58
3284 4896 2.373707 GGACAGCCCTGGAGATGCT 61.374 63.158 0.00 0.00 35.25 3.79
3305 4917 1.055551 TGGGTGGAAGGTACGTTGGT 61.056 55.000 5.36 0.00 0.00 3.67
3431 5043 1.871418 TGAGGGCTTCAGCATAGAGT 58.129 50.000 0.00 0.00 44.36 3.24
3464 5076 2.512515 GGCGAGGCTTGCTGGTAG 60.513 66.667 25.21 0.00 0.00 3.18
3513 5126 2.682136 TTGGAGTCCCCGATGCGA 60.682 61.111 6.74 0.00 37.93 5.10


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

AutoCloner maintained by Alex Coulton.