Multiple sequence alignment - TraesCS2A01G281900
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
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 primersListed 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. |
---|
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.
AutoCloner maintained by Alex Coulton.