Multiple sequence alignment - TraesCS2A01G281900

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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 TraesCS2A01G281900 chr2A 100.000 2591 0 0 1 2591 471006798 471004208 0.000000e+00 4785
1 TraesCS2A01G281900 chr2A 92.553 94 7 0 5 98 678161262 678161355 4.500000e-28 135
2 TraesCS2A01G281900 chr2A 91.579 95 6 2 4 97 693445802 693445709 2.090000e-26 130
3 TraesCS2A01G281900 chr2B 89.037 2545 132 62 99 2591 419323429 419320980 0.000000e+00 3018
4 TraesCS2A01G281900 chr2D 91.937 1848 69 25 96 1924 352906370 352904584 0.000000e+00 2514
5 TraesCS2A01G281900 chr2D 91.857 614 35 4 1986 2591 352904563 352903957 0.000000e+00 843
6 TraesCS2A01G281900 chr4A 95.455 88 4 0 10 97 547197698 547197785 9.670000e-30 141
7 TraesCS2A01G281900 chr4A 91.579 95 6 2 9 102 215349613 215349706 2.090000e-26 130
8 TraesCS2A01G281900 chr5A 94.382 89 5 0 9 97 347461274 347461362 1.250000e-28 137
9 TraesCS2A01G281900 chr1D 91.089 101 8 1 9 108 364730869 364730769 4.500000e-28 135
10 TraesCS2A01G281900 chr1D 89.320 103 8 3 8 108 463456973 463456872 2.710000e-25 126
11 TraesCS2A01G281900 chr3B 91.489 94 8 0 8 101 697073838 697073745 2.090000e-26 130
12 TraesCS2A01G281900 chr3D 86.726 113 13 2 5 116 54783319 54783430 9.740000e-25 124


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 TraesCS2A01G281900 chr2A 471004208 471006798 2590 True 4785.0 4785 100.000 1 2591 1 chr2A.!!$R1 2590
1 TraesCS2A01G281900 chr2B 419320980 419323429 2449 True 3018.0 3018 89.037 99 2591 1 chr2B.!!$R1 2492
2 TraesCS2A01G281900 chr2D 352903957 352906370 2413 True 1678.5 2514 91.897 96 2591 2 chr2D.!!$R1 2495


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
234 236 0.035247 TTTATTTGGCCCGCTACGGT 60.035 50.0 0.0 0.0 46.80 4.83 F
823 847 0.179134 CCACCGTCTGCTACTGCTAC 60.179 60.0 0.0 0.0 40.48 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1364 0.105555 CTCCTCCTCCTCCTGCTCAT 60.106 60.0 0.00 0.0 0.00 2.90 R
2402 2483 0.757188 CAGGTATCTCGGGCAGGAGT 60.757 60.0 4.96 0.0 35.52 3.85 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
25 26 8.104838 ACTCTATAGTACTCCCTCTGTAAACT 57.895 38.462 0.00 0.00 32.84 2.66
26 27 9.223291 ACTCTATAGTACTCCCTCTGTAAACTA 57.777 37.037 0.00 0.00 32.84 2.24
36 37 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
37 38 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
38 39 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
39 40 9.106070 CCCTCTGTAAACTAATATAAAAGCGTT 57.894 33.333 0.00 0.00 0.00 4.84
57 58 8.728088 AAAGCGTTTAGATCACTGTTTTAATG 57.272 30.769 0.00 0.00 0.00 1.90
58 59 7.667043 AGCGTTTAGATCACTGTTTTAATGA 57.333 32.000 0.00 0.00 0.00 2.57
59 60 8.268850 AGCGTTTAGATCACTGTTTTAATGAT 57.731 30.769 0.00 0.00 35.77 2.45
60 61 8.391106 AGCGTTTAGATCACTGTTTTAATGATC 58.609 33.333 7.60 7.60 46.04 2.92
127 128 8.923270 AGAAGAAGAGCTGCTTAATCTATAGTT 58.077 33.333 2.53 0.00 36.83 2.24
138 139 6.362820 GCTTAATCTATAGTTGTACTCGTGGC 59.637 42.308 0.00 0.00 0.00 5.01
217 219 6.461509 CCAGCTGAGATTTACCAAACACTTTT 60.462 38.462 17.39 0.00 0.00 2.27
232 234 1.741145 ACTTTTATTTGGCCCGCTACG 59.259 47.619 0.00 0.00 0.00 3.51
234 236 0.035247 TTTATTTGGCCCGCTACGGT 60.035 50.000 0.00 0.00 46.80 4.83
235 237 0.829333 TTATTTGGCCCGCTACGGTA 59.171 50.000 0.00 0.00 46.80 4.02
236 238 1.050204 TATTTGGCCCGCTACGGTAT 58.950 50.000 0.00 0.00 46.80 2.73
325 333 5.718724 TGTTGATGGCATCACAATTTACA 57.281 34.783 28.83 24.14 39.39 2.41
441 458 2.689553 AAAAGGCCACAAACTTGGTG 57.310 45.000 5.01 0.00 39.09 4.17
454 471 7.039882 CACAAACTTGGTGGTACTAGTATAGG 58.960 42.308 5.75 0.00 36.40 2.57
455 472 6.955851 ACAAACTTGGTGGTACTAGTATAGGA 59.044 38.462 5.75 0.00 44.97 2.94
456 473 7.123847 ACAAACTTGGTGGTACTAGTATAGGAG 59.876 40.741 5.75 3.22 44.97 3.69
489 506 3.882888 TGAACACCTCACCATGAACTTTC 59.117 43.478 0.00 0.00 0.00 2.62
500 517 6.704493 TCACCATGAACTTTCTTACTACACAC 59.296 38.462 0.00 0.00 0.00 3.82
564 581 2.621526 TCTTTGAAAGGAAAGAACCCGC 59.378 45.455 4.94 0.00 38.69 6.13
568 585 4.717313 AGGAAAGAACCCGCCCGC 62.717 66.667 0.00 0.00 0.00 6.13
615 632 0.838987 TTACCCACGAGGAGCCCTTT 60.839 55.000 0.00 0.00 39.89 3.11
616 633 1.550130 TACCCACGAGGAGCCCTTTG 61.550 60.000 0.00 0.00 39.89 2.77
617 634 2.747855 CCACGAGGAGCCCTTTGC 60.748 66.667 0.00 0.00 41.71 3.68
618 635 2.032528 CACGAGGAGCCCTTTGCA 59.967 61.111 0.00 0.00 44.83 4.08
694 712 1.339711 CTGCGGCACTTGTTAATTGC 58.660 50.000 0.00 0.00 36.45 3.56
714 738 2.143122 CTACACACACACACACCCATC 58.857 52.381 0.00 0.00 0.00 3.51
716 740 1.891919 ACACACACACACCCATCGC 60.892 57.895 0.00 0.00 0.00 4.58
771 795 0.512518 TCGTGCGATGCTGAAACTTG 59.487 50.000 0.00 0.00 0.00 3.16
813 837 4.394712 GCTCACCCCCACCGTCTG 62.395 72.222 0.00 0.00 0.00 3.51
814 838 4.394712 CTCACCCCCACCGTCTGC 62.395 72.222 0.00 0.00 0.00 4.26
815 839 4.954118 TCACCCCCACCGTCTGCT 62.954 66.667 0.00 0.00 0.00 4.24
816 840 3.000819 CACCCCCACCGTCTGCTA 61.001 66.667 0.00 0.00 0.00 3.49
817 841 3.001406 ACCCCCACCGTCTGCTAC 61.001 66.667 0.00 0.00 0.00 3.58
818 842 2.683933 CCCCCACCGTCTGCTACT 60.684 66.667 0.00 0.00 0.00 2.57
819 843 2.579201 CCCCACCGTCTGCTACTG 59.421 66.667 0.00 0.00 0.00 2.74
820 844 2.125512 CCCACCGTCTGCTACTGC 60.126 66.667 0.00 0.00 40.20 4.40
821 845 2.650116 CCCACCGTCTGCTACTGCT 61.650 63.158 0.00 0.00 40.48 4.24
822 846 1.320344 CCCACCGTCTGCTACTGCTA 61.320 60.000 0.00 0.00 40.48 3.49
823 847 0.179134 CCACCGTCTGCTACTGCTAC 60.179 60.000 0.00 0.00 40.48 3.58
824 848 0.811915 CACCGTCTGCTACTGCTACT 59.188 55.000 0.00 0.00 40.48 2.57
825 849 0.811915 ACCGTCTGCTACTGCTACTG 59.188 55.000 0.00 0.00 40.48 2.74
826 850 0.526524 CCGTCTGCTACTGCTACTGC 60.527 60.000 0.00 0.00 40.48 4.40
827 851 0.453793 CGTCTGCTACTGCTACTGCT 59.546 55.000 0.00 0.00 40.48 4.24
828 852 1.671328 CGTCTGCTACTGCTACTGCTA 59.329 52.381 0.00 0.00 40.48 3.49
829 853 2.286713 CGTCTGCTACTGCTACTGCTAG 60.287 54.545 0.00 0.00 40.48 3.42
909 933 1.336887 ACACCTTGCGCTACTGTACAG 60.337 52.381 21.44 21.44 0.00 2.74
913 943 0.669318 TTGCGCTACTGTACAGCCAC 60.669 55.000 22.90 10.77 35.53 5.01
918 948 1.673033 GCTACTGTACAGCCACCACAG 60.673 57.143 22.90 9.31 44.20 3.66
970 1024 5.863397 CCACATACACACCTTTATTTTGCAG 59.137 40.000 0.00 0.00 0.00 4.41
991 1045 5.677598 GCAGGCTAGTTAGAGTAGTGAACTG 60.678 48.000 0.00 0.00 39.07 3.16
1006 1060 8.037758 AGTAGTGAACTGTAATCAAGATGAAGG 58.962 37.037 0.00 0.00 36.93 3.46
1056 1110 4.124351 TCCACCATCGTCGCCGTC 62.124 66.667 0.00 0.00 35.01 4.79
1071 1125 2.372690 CGTCGTCAAGGCCAAGTCG 61.373 63.158 5.01 6.64 0.00 4.18
1101 1155 2.671177 CGCCAAGACGAGCACCTTG 61.671 63.158 0.00 0.00 39.43 3.61
1238 1292 4.072088 CCAACAAGACGACGGCGC 62.072 66.667 12.58 3.05 42.48 6.53
1242 1296 4.072088 CAAGACGACGGCGCCAAC 62.072 66.667 28.98 18.23 42.48 3.77
1299 1353 4.838486 GAGCGCGACGTGGAGGAG 62.838 72.222 12.10 0.00 0.00 3.69
1368 1422 4.280494 ACGCACTCGCTGTTCCGT 62.280 61.111 0.00 0.00 39.84 4.69
1383 1437 4.436653 CGTGAGGAAGACGACGAC 57.563 61.111 0.00 0.00 39.21 4.34
1426 1480 2.388232 GGGTCGGTGATTGACGTGC 61.388 63.158 0.00 0.00 37.22 5.34
1551 1605 4.492955 CTGCAGAAGCTCGAGTCC 57.507 61.111 15.13 3.57 42.74 3.85
1600 1654 2.244117 GAGCGCTTGATCCACCTCCA 62.244 60.000 13.26 0.00 0.00 3.86
1602 1656 1.442526 GCGCTTGATCCACCTCCATG 61.443 60.000 0.00 0.00 0.00 3.66
1636 1690 5.256474 CACCTCCAGTCCAGTGATTTATTT 58.744 41.667 0.00 0.00 31.79 1.40
1694 1748 7.227512 CACTCCTTAAGCCAGGATTATGTTTAG 59.772 40.741 0.00 1.55 42.42 1.85
1739 1795 4.773323 AAAGAAGGAAAAGATGAAGCCG 57.227 40.909 0.00 0.00 0.00 5.52
1796 1852 1.694696 GGGGATGCCAAGGTCTACTAG 59.305 57.143 5.30 0.00 0.00 2.57
1797 1853 2.399580 GGGATGCCAAGGTCTACTAGT 58.600 52.381 0.00 0.00 0.00 2.57
1798 1854 2.365941 GGGATGCCAAGGTCTACTAGTC 59.634 54.545 0.00 0.00 0.00 2.59
1799 1855 2.365941 GGATGCCAAGGTCTACTAGTCC 59.634 54.545 0.00 0.00 0.00 3.85
1800 1856 2.921834 TGCCAAGGTCTACTAGTCCT 57.078 50.000 0.00 0.00 35.24 3.85
1801 1857 4.471548 GATGCCAAGGTCTACTAGTCCTA 58.528 47.826 0.00 0.00 32.56 2.94
1821 1883 8.921205 AGTCCTACGTGGTACTTTAATCATTAT 58.079 33.333 0.00 0.00 37.07 1.28
1924 1986 9.448438 TGAAGCAAATAAATAGACGGCATATAT 57.552 29.630 0.00 0.00 0.00 0.86
1925 1987 9.922305 GAAGCAAATAAATAGACGGCATATATC 57.078 33.333 0.00 0.00 0.00 1.63
2040 2107 6.839657 AGATTTTCTTCTAATCCCCGAGAGTA 59.160 38.462 0.00 0.00 33.45 2.59
2045 2112 3.474600 TCTAATCCCCGAGAGTAGAACG 58.525 50.000 9.28 0.00 46.38 3.95
2075 2142 5.220228 CGTACTAACATACAGTTCAAGCAGC 60.220 44.000 0.00 0.00 41.64 5.25
2079 2146 4.220693 ACATACAGTTCAAGCAGCCATA 57.779 40.909 0.00 0.00 0.00 2.74
2080 2147 4.588899 ACATACAGTTCAAGCAGCCATAA 58.411 39.130 0.00 0.00 0.00 1.90
2081 2148 4.637534 ACATACAGTTCAAGCAGCCATAAG 59.362 41.667 0.00 0.00 0.00 1.73
2112 2187 4.672024 GCAGAATCAAGCTCACATGACAAG 60.672 45.833 0.00 0.00 0.00 3.16
2139 2214 2.706190 AGGGCTCGCTAGTTTTATGGAT 59.294 45.455 0.00 0.00 0.00 3.41
2145 2220 5.290493 TCGCTAGTTTTATGGATGGATGT 57.710 39.130 0.00 0.00 0.00 3.06
2165 2240 2.030451 GTCTCTGCTTTTGGCCAAGAAG 60.030 50.000 24.46 24.46 40.92 2.85
2170 2245 2.624838 TGCTTTTGGCCAAGAAGAGAAG 59.375 45.455 29.20 23.99 40.92 2.85
2212 2287 1.131504 CGTAGGATCGGATCAGCTAGC 59.868 57.143 18.99 6.62 0.00 3.42
2220 2295 1.642215 GATCAGCTAGCGTCGTCGA 59.358 57.895 9.55 0.00 39.71 4.20
2236 2311 1.369930 CGACGTTTTGCATTGCGGT 60.370 52.632 3.84 0.00 0.00 5.68
2270 2351 0.909610 TCGGCCTCCTCCAACTTGAT 60.910 55.000 0.00 0.00 0.00 2.57
2285 2366 1.198094 TTGATGTCCTTGGCGAGGGA 61.198 55.000 20.82 8.33 46.31 4.20
2289 2370 3.068691 TCCTTGGCGAGGGAGACG 61.069 66.667 20.82 0.00 46.31 4.18
2321 2402 2.270205 CATTGCCTCCTGCTCGGT 59.730 61.111 0.00 0.00 42.00 4.69
2402 2483 1.213296 GGCCTCTGTTCCCTATTGGA 58.787 55.000 0.00 0.00 43.18 3.53
2480 2561 1.026718 GCTGCCGCAACTCCTATGTT 61.027 55.000 0.00 0.00 35.78 2.71
2486 2567 3.741388 GCCGCAACTCCTATGTTGTAGAT 60.741 47.826 8.78 0.00 46.33 1.98
2492 2573 5.646577 ACTCCTATGTTGTAGATATCGCC 57.353 43.478 0.00 0.00 0.00 5.54
2541 2622 0.455815 TGGATGACGATGAGGACGTG 59.544 55.000 0.00 0.00 43.97 4.49
2547 2628 1.032657 ACGATGAGGACGTGGAGGAG 61.033 60.000 0.00 0.00 42.37 3.69
2566 2647 1.951130 CCGATCGGATTGTCCTGCG 60.951 63.158 30.62 0.00 37.50 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.104838 AGTTTACAGAGGGAGTACTATAGAGT 57.895 38.462 6.78 0.00 39.92 3.24
10 11 9.833917 GCTTTTATATTAGTTTACAGAGGGAGT 57.166 33.333 0.00 0.00 0.00 3.85
11 12 8.979574 CGCTTTTATATTAGTTTACAGAGGGAG 58.020 37.037 0.00 0.00 0.00 4.30
12 13 8.480501 ACGCTTTTATATTAGTTTACAGAGGGA 58.519 33.333 0.00 0.00 0.00 4.20
13 14 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
31 32 9.180678 CATTAAAACAGTGATCTAAACGCTTTT 57.819 29.630 0.00 0.00 0.00 2.27
32 33 8.564574 TCATTAAAACAGTGATCTAAACGCTTT 58.435 29.630 0.00 0.00 0.00 3.51
33 34 8.094798 TCATTAAAACAGTGATCTAAACGCTT 57.905 30.769 0.00 0.00 0.00 4.68
34 35 7.667043 TCATTAAAACAGTGATCTAAACGCT 57.333 32.000 0.00 0.00 0.00 5.07
35 36 8.535066 GATCATTAAAACAGTGATCTAAACGC 57.465 34.615 0.00 0.00 42.98 4.84
72 73 9.202273 CGTAGTACTCTCTCCGTAAACTAATAT 57.798 37.037 0.00 0.00 0.00 1.28
73 74 8.198109 ACGTAGTACTCTCTCCGTAAACTAATA 58.802 37.037 0.00 0.00 41.94 0.98
74 75 7.044798 ACGTAGTACTCTCTCCGTAAACTAAT 58.955 38.462 0.00 0.00 41.94 1.73
75 76 6.398918 ACGTAGTACTCTCTCCGTAAACTAA 58.601 40.000 0.00 0.00 41.94 2.24
76 77 5.967088 ACGTAGTACTCTCTCCGTAAACTA 58.033 41.667 0.00 0.00 41.94 2.24
77 78 4.826556 ACGTAGTACTCTCTCCGTAAACT 58.173 43.478 0.00 0.00 41.94 2.66
78 79 6.531948 TCTTACGTAGTACTCTCTCCGTAAAC 59.468 42.308 17.31 2.13 45.76 2.01
79 80 6.631016 TCTTACGTAGTACTCTCTCCGTAAA 58.369 40.000 17.31 10.61 45.76 2.01
80 81 6.208988 TCTTACGTAGTACTCTCTCCGTAA 57.791 41.667 0.00 10.60 45.76 3.18
81 82 5.836821 TCTTACGTAGTACTCTCTCCGTA 57.163 43.478 0.00 3.32 45.76 4.02
82 83 4.727507 TCTTACGTAGTACTCTCTCCGT 57.272 45.455 0.00 4.30 45.76 4.69
83 84 5.347342 TCTTCTTACGTAGTACTCTCTCCG 58.653 45.833 0.00 0.00 45.76 4.63
84 85 7.041107 TCTTCTTCTTACGTAGTACTCTCTCC 58.959 42.308 0.00 0.00 45.76 3.71
85 86 7.254218 GCTCTTCTTCTTACGTAGTACTCTCTC 60.254 44.444 0.00 0.00 45.76 3.20
86 87 6.536224 GCTCTTCTTCTTACGTAGTACTCTCT 59.464 42.308 0.00 0.00 45.76 3.10
87 88 6.536224 AGCTCTTCTTCTTACGTAGTACTCTC 59.464 42.308 0.00 0.00 45.76 3.20
88 89 6.314400 CAGCTCTTCTTCTTACGTAGTACTCT 59.686 42.308 0.00 0.00 45.76 3.24
89 90 6.480285 CAGCTCTTCTTCTTACGTAGTACTC 58.520 44.000 0.00 0.00 45.76 2.59
90 91 5.163733 GCAGCTCTTCTTCTTACGTAGTACT 60.164 44.000 0.00 0.00 45.76 2.73
91 92 5.029654 GCAGCTCTTCTTCTTACGTAGTAC 58.970 45.833 0.00 0.00 45.76 2.73
92 93 4.942483 AGCAGCTCTTCTTCTTACGTAGTA 59.058 41.667 0.00 0.00 45.11 1.82
93 94 5.415077 TAAGCAGCTCTTCTTCTTACGTAGT 59.585 40.000 0.00 0.00 39.50 2.73
94 95 4.364415 AGCAGCTCTTCTTCTTACGTAG 57.636 45.455 0.00 0.00 0.00 3.51
127 128 0.541063 TTCTGGGAGCCACGAGTACA 60.541 55.000 0.00 0.00 0.00 2.90
232 234 7.224297 ACACATGAGATTTACCATACCATACC 58.776 38.462 0.00 0.00 0.00 2.73
233 235 8.677148 AACACATGAGATTTACCATACCATAC 57.323 34.615 0.00 0.00 0.00 2.39
234 236 8.713971 AGAACACATGAGATTTACCATACCATA 58.286 33.333 0.00 0.00 0.00 2.74
235 237 7.577303 AGAACACATGAGATTTACCATACCAT 58.423 34.615 0.00 0.00 0.00 3.55
236 238 6.957631 AGAACACATGAGATTTACCATACCA 58.042 36.000 0.00 0.00 0.00 3.25
291 299 3.827876 TGCCATCAACAACACATGAGATT 59.172 39.130 0.00 0.00 0.00 2.40
292 300 3.423749 TGCCATCAACAACACATGAGAT 58.576 40.909 0.00 0.00 0.00 2.75
293 301 2.861274 TGCCATCAACAACACATGAGA 58.139 42.857 0.00 0.00 0.00 3.27
294 302 3.191791 TGATGCCATCAACAACACATGAG 59.808 43.478 4.55 0.00 36.11 2.90
295 303 3.057386 GTGATGCCATCAACAACACATGA 60.057 43.478 9.36 0.00 41.69 3.07
325 333 1.366319 AGTGAGAGATGGGGCTGTTT 58.634 50.000 0.00 0.00 0.00 2.83
489 506 8.547967 AGTTATTTCCATGTGTGTGTAGTAAG 57.452 34.615 0.00 0.00 0.00 2.34
534 551 7.832503 TCTTTCCTTTCAAAGAAAAAGCTTG 57.167 32.000 15.18 0.00 39.06 4.01
564 581 1.605165 TTTTGGCTAACTGGGCGGG 60.605 57.895 0.00 0.00 34.31 6.13
568 585 3.317603 CCAATGTTTTGGCTAACTGGG 57.682 47.619 5.04 1.36 45.71 4.45
676 694 3.488048 GCAATTAACAAGTGCCGCA 57.512 47.368 0.08 0.00 45.96 5.69
682 700 5.355630 TGTGTGTGTGTAGCAATTAACAAGT 59.644 36.000 0.00 0.00 0.00 3.16
683 701 5.681105 GTGTGTGTGTGTAGCAATTAACAAG 59.319 40.000 0.00 0.00 0.00 3.16
694 712 2.143122 GATGGGTGTGTGTGTGTGTAG 58.857 52.381 0.00 0.00 0.00 2.74
771 795 1.335496 GCGAGTGGATGTCTCCTAGAC 59.665 57.143 0.01 0.01 45.26 2.59
813 837 1.407258 AGCACTAGCAGTAGCAGTAGC 59.593 52.381 0.00 0.00 45.49 3.58
814 838 6.751514 ATATAGCACTAGCAGTAGCAGTAG 57.248 41.667 0.00 0.00 45.49 2.57
815 839 9.327628 GTATATATAGCACTAGCAGTAGCAGTA 57.672 37.037 0.00 0.00 45.49 2.74
816 840 7.283580 GGTATATATAGCACTAGCAGTAGCAGT 59.716 40.741 15.49 0.00 45.49 4.40
817 841 7.255312 GGGTATATATAGCACTAGCAGTAGCAG 60.255 44.444 20.52 0.00 45.49 4.24
818 842 6.546403 GGGTATATATAGCACTAGCAGTAGCA 59.454 42.308 20.52 0.00 45.49 3.49
819 843 6.546403 TGGGTATATATAGCACTAGCAGTAGC 59.454 42.308 20.52 2.89 45.49 3.58
820 844 8.572185 CATGGGTATATATAGCACTAGCAGTAG 58.428 40.741 20.52 3.70 45.49 2.57
821 845 7.505923 CCATGGGTATATATAGCACTAGCAGTA 59.494 40.741 20.52 0.14 45.49 2.74
822 846 6.325028 CCATGGGTATATATAGCACTAGCAGT 59.675 42.308 20.52 1.42 45.49 4.40
823 847 6.739843 GCCATGGGTATATATAGCACTAGCAG 60.740 46.154 20.52 6.32 45.49 4.24
824 848 5.070446 GCCATGGGTATATATAGCACTAGCA 59.930 44.000 20.52 10.96 45.49 3.49
825 849 5.070446 TGCCATGGGTATATATAGCACTAGC 59.930 44.000 20.52 17.06 42.56 3.42
826 850 6.731292 TGCCATGGGTATATATAGCACTAG 57.269 41.667 20.52 9.56 32.63 2.57
827 851 6.270000 GGATGCCATGGGTATATATAGCACTA 59.730 42.308 20.52 9.03 32.63 2.74
828 852 5.072329 GGATGCCATGGGTATATATAGCACT 59.928 44.000 20.52 6.90 32.63 4.40
829 853 5.308825 GGATGCCATGGGTATATATAGCAC 58.691 45.833 20.52 11.98 32.63 4.40
909 933 4.927782 TGCGTGGACTGTGGTGGC 62.928 66.667 0.00 0.00 0.00 5.01
913 943 2.591429 TTGCTGCGTGGACTGTGG 60.591 61.111 0.00 0.00 0.00 4.17
918 948 2.482374 GATGCTTGCTGCGTGGAC 59.518 61.111 1.93 0.00 46.63 4.02
970 1024 5.900865 ACAGTTCACTACTCTAACTAGCC 57.099 43.478 0.00 0.00 33.85 3.93
991 1045 3.067320 GCCTTGGCCTTCATCTTGATTAC 59.933 47.826 3.32 0.00 0.00 1.89
1006 1060 1.203287 GAAGAATGTGGAAGCCTTGGC 59.797 52.381 2.97 2.97 0.00 4.52
1056 1110 2.372690 CGTCGACTTGGCCTTGACG 61.373 63.158 16.30 16.30 45.06 4.35
1099 1153 2.261671 GAGGAGGCGCGTCTTCAA 59.738 61.111 29.95 0.00 0.00 2.69
1101 1155 4.117661 ACGAGGAGGCGCGTCTTC 62.118 66.667 26.60 26.60 35.59 2.87
1238 1292 1.926511 GAGCACGATGGCCTTGTTGG 61.927 60.000 3.32 0.00 39.35 3.77
1242 1296 0.108186 TGTAGAGCACGATGGCCTTG 60.108 55.000 3.32 0.00 0.00 3.61
1310 1364 0.105555 CTCCTCCTCCTCCTGCTCAT 60.106 60.000 0.00 0.00 0.00 2.90
1311 1365 1.309347 CTCCTCCTCCTCCTGCTCA 59.691 63.158 0.00 0.00 0.00 4.26
1312 1366 1.457455 CCTCCTCCTCCTCCTGCTC 60.457 68.421 0.00 0.00 0.00 4.26
1313 1367 1.938596 TCCTCCTCCTCCTCCTGCT 60.939 63.158 0.00 0.00 0.00 4.24
1314 1368 1.457455 CTCCTCCTCCTCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
1315 1369 0.185901 CTCTCCTCCTCCTCCTCCTG 59.814 65.000 0.00 0.00 0.00 3.86
1368 1422 1.864862 GTCGTCGTCGTCTTCCTCA 59.135 57.895 1.33 0.00 38.33 3.86
1383 1437 2.081212 GTTCACCAGCTCGTCGTCG 61.081 63.158 0.00 0.00 38.55 5.12
1439 1493 2.787866 CCTCCCCCTCCTTCTCCA 59.212 66.667 0.00 0.00 0.00 3.86
1551 1605 2.732412 TCTCGCAGAACCTCTTGAAG 57.268 50.000 0.00 0.00 34.09 3.02
1602 1656 2.103941 GACTGGAGGTGGATCTGATTCC 59.896 54.545 0.00 0.00 36.24 3.01
1614 1668 5.520748 AAATAAATCACTGGACTGGAGGT 57.479 39.130 0.00 0.00 0.00 3.85
1636 1690 4.155826 GGCGCCATTGCATACTTATGAATA 59.844 41.667 24.80 0.00 37.32 1.75
1694 1748 1.518903 GCATGGGCCTCCGATTAAGC 61.519 60.000 4.53 0.00 35.24 3.09
1796 1852 8.975439 CATAATGATTAAAGTACCACGTAGGAC 58.025 37.037 10.46 0.00 41.22 3.85
1797 1853 8.698210 ACATAATGATTAAAGTACCACGTAGGA 58.302 33.333 10.46 0.00 41.22 2.94
1798 1854 8.882415 ACATAATGATTAAAGTACCACGTAGG 57.118 34.615 0.00 0.00 45.67 3.18
1801 1857 9.525409 GAGTACATAATGATTAAAGTACCACGT 57.475 33.333 19.08 8.15 34.19 4.49
1924 1986 2.225491 GTGTTACATTTCGGCTTGCTGA 59.775 45.455 0.00 0.00 0.00 4.26
1925 1987 2.584791 GTGTTACATTTCGGCTTGCTG 58.415 47.619 0.00 0.00 0.00 4.41
2024 2091 3.474600 CGTTCTACTCTCGGGGATTAGA 58.525 50.000 1.14 1.14 35.38 2.10
2045 2112 5.403166 TGAACTGTATGTTAGTACGTGTTGC 59.597 40.000 0.00 0.00 39.30 4.17
2075 2142 6.750963 GCTTGATTCTGCTTTTCTTCTTATGG 59.249 38.462 0.00 0.00 0.00 2.74
2079 2146 5.533903 TGAGCTTGATTCTGCTTTTCTTCTT 59.466 36.000 6.28 0.00 39.91 2.52
2080 2147 5.048852 GTGAGCTTGATTCTGCTTTTCTTCT 60.049 40.000 6.28 0.00 39.91 2.85
2081 2148 5.152804 GTGAGCTTGATTCTGCTTTTCTTC 58.847 41.667 6.28 0.00 39.91 2.87
2112 2187 1.822506 AACTAGCGAGCCCTTTTTCC 58.177 50.000 0.00 0.00 0.00 3.13
2139 2214 1.538047 GCCAAAAGCAGAGACATCCA 58.462 50.000 0.00 0.00 42.97 3.41
2145 2220 2.158623 TCTTCTTGGCCAAAAGCAGAGA 60.159 45.455 20.91 8.40 46.50 3.10
2165 2240 3.181485 ACTGGTATGCGTTAGCTCTTCTC 60.181 47.826 0.00 0.00 45.42 2.87
2170 2245 3.988517 GGATTACTGGTATGCGTTAGCTC 59.011 47.826 0.00 0.00 45.42 4.09
2220 2295 1.948635 GCACCGCAATGCAAAACGT 60.949 52.632 5.91 0.00 45.39 3.99
2321 2402 1.107114 GAGATTCTCCCTGCGTCTCA 58.893 55.000 1.97 0.00 36.28 3.27
2402 2483 0.757188 CAGGTATCTCGGGCAGGAGT 60.757 60.000 4.96 0.00 35.52 3.85
2480 2561 2.264124 GGCGAGGGCGATATCTACA 58.736 57.895 0.34 0.00 41.24 2.74
2492 2573 4.072088 GCGACACAAACGGCGAGG 62.072 66.667 16.62 4.60 0.00 4.63
2517 2598 1.114627 CCTCATCGTCATCCACCTCA 58.885 55.000 0.00 0.00 0.00 3.86
2541 2622 1.005630 CAATCCGATCGGCTCCTCC 60.006 63.158 29.62 0.00 34.68 4.30
2547 2628 2.247437 GCAGGACAATCCGATCGGC 61.247 63.158 29.62 14.55 42.75 5.54
2566 2647 1.078759 CACATCTCTTCGTCGGCACC 61.079 60.000 0.00 0.00 0.00 5.01



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

AutoCloner maintained by Alex Coulton.