Multiple sequence alignment - TraesCS5A01G457300

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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 TraesCS5A01G457300 chr5A 100.000 3385 0 0 1 3385 637095954 637092570 0.000000e+00 6252.0
1 TraesCS5A01G457300 chr5A 98.980 980 9 1 1 980 69227303 69226325 0.000000e+00 1753.0
2 TraesCS5A01G457300 chr5A 87.013 77 10 0 3309 3385 330730434 330730358 1.670000e-13 87.9
3 TraesCS5A01G457300 chr5D 90.722 1843 59 23 981 2770 509590505 509588722 0.000000e+00 2353.0
4 TraesCS5A01G457300 chr3A 99.082 980 8 1 1 980 23451315 23452293 0.000000e+00 1759.0
5 TraesCS5A01G457300 chr3B 98.982 982 9 1 1 982 344140905 344139925 0.000000e+00 1757.0
6 TraesCS5A01G457300 chr7B 98.882 984 9 2 1 983 122630955 122631937 0.000000e+00 1755.0
7 TraesCS5A01G457300 chr4A 98.784 987 10 2 1 986 162151025 162152010 0.000000e+00 1755.0
8 TraesCS5A01G457300 chr4A 98.683 987 11 2 1 986 162138900 162139885 0.000000e+00 1749.0
9 TraesCS5A01G457300 chr4A 98.683 987 11 2 1 986 162142799 162143784 0.000000e+00 1749.0
10 TraesCS5A01G457300 chr4A 98.480 987 13 2 1 986 162147149 162148134 0.000000e+00 1738.0
11 TraesCS5A01G457300 chr4A 94.969 477 24 0 2909 3385 102994267 102994743 0.000000e+00 749.0
12 TraesCS5A01G457300 chr4B 98.878 980 10 1 1 980 451444991 451444013 0.000000e+00 1748.0
13 TraesCS5A01G457300 chr5B 91.854 712 38 7 1850 2543 640425638 640424929 0.000000e+00 976.0
14 TraesCS5A01G457300 chr5B 92.671 423 12 7 981 1403 640427410 640427007 2.910000e-165 592.0
15 TraesCS5A01G457300 chr5B 92.982 342 24 0 1416 1757 640427024 640426683 1.810000e-137 499.0
16 TraesCS5A01G457300 chr5B 89.655 203 17 1 2544 2746 640424569 640424371 4.330000e-64 255.0
17 TraesCS5A01G457300 chr5B 89.000 100 9 2 2669 2768 640420415 640420318 4.590000e-24 122.0
18 TraesCS5A01G457300 chr3D 96.673 571 18 1 2815 3385 455950386 455949817 0.000000e+00 948.0
19 TraesCS5A01G457300 chr3D 82.867 572 95 3 2815 3385 399672962 399672393 8.380000e-141 510.0
20 TraesCS5A01G457300 chr6A 93.296 358 24 0 2815 3172 13693341 13692984 2.310000e-146 529.0
21 TraesCS5A01G457300 chr6A 94.969 159 8 0 3187 3345 13691968 13691810 2.020000e-62 250.0
22 TraesCS5A01G457300 chr6A 74.103 390 98 3 2997 3385 22436688 22436301 1.260000e-34 158.0
23 TraesCS5A01G457300 chr4D 74.849 497 113 8 2893 3385 477858287 477858775 7.360000e-52 215.0


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 TraesCS5A01G457300 chr5A 637092570 637095954 3384 True 6252.00 6252 100.0000 1 3385 1 chr5A.!!$R3 3384
1 TraesCS5A01G457300 chr5A 69226325 69227303 978 True 1753.00 1753 98.9800 1 980 1 chr5A.!!$R1 979
2 TraesCS5A01G457300 chr5D 509588722 509590505 1783 True 2353.00 2353 90.7220 981 2770 1 chr5D.!!$R1 1789
3 TraesCS5A01G457300 chr3A 23451315 23452293 978 False 1759.00 1759 99.0820 1 980 1 chr3A.!!$F1 979
4 TraesCS5A01G457300 chr3B 344139925 344140905 980 True 1757.00 1757 98.9820 1 982 1 chr3B.!!$R1 981
5 TraesCS5A01G457300 chr7B 122630955 122631937 982 False 1755.00 1755 98.8820 1 983 1 chr7B.!!$F1 982
6 TraesCS5A01G457300 chr4A 162138900 162152010 13110 False 1747.75 1755 98.6575 1 986 4 chr4A.!!$F2 985
7 TraesCS5A01G457300 chr4B 451444013 451444991 978 True 1748.00 1748 98.8780 1 980 1 chr4B.!!$R1 979
8 TraesCS5A01G457300 chr5B 640420318 640427410 7092 True 488.80 976 91.2324 981 2768 5 chr5B.!!$R1 1787
9 TraesCS5A01G457300 chr3D 455949817 455950386 569 True 948.00 948 96.6730 2815 3385 1 chr3D.!!$R2 570
10 TraesCS5A01G457300 chr3D 399672393 399672962 569 True 510.00 510 82.8670 2815 3385 1 chr3D.!!$R1 570
11 TraesCS5A01G457300 chr6A 13691810 13693341 1531 True 389.50 529 94.1325 2815 3345 2 chr6A.!!$R2 530

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
999 13124 3.801129 GCTAGCGCCAAGAAGGTC 58.199 61.111 2.29 0.0 40.61 3.85 F
1630 13762 0.689623 AAACTGGACTGGGCAGAGAG 59.310 55.000 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 15039 0.464452 GGATCTTACCCTGGACCGTG 59.536 60.0 0.0 0.0 0.00 4.94 R
3260 20291 0.764890 TTCAGGTCAAGGACACCCAG 59.235 55.0 0.0 0.0 33.96 4.45 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
999 13124 3.801129 GCTAGCGCCAAGAAGGTC 58.199 61.111 2.29 0.00 40.61 3.85
1301 13426 4.701651 CCATGTTGGAGAGCTTCATGTAAA 59.298 41.667 0.00 0.00 40.96 2.01
1313 13438 9.064706 AGAGCTTCATGTAAATCATCATTAAGG 57.935 33.333 0.00 0.00 34.09 2.69
1340 13468 2.163815 AGAGTACAACGTCCAAGATCGG 59.836 50.000 0.00 0.00 0.00 4.18
1345 13473 0.892755 AACGTCCAAGATCGGCACTA 59.107 50.000 0.00 0.00 0.00 2.74
1401 13529 8.967218 CAATTGTTTAGTTCATCGACAAATTGT 58.033 29.630 0.00 0.00 34.34 2.71
1402 13530 9.528018 AATTGTTTAGTTCATCGACAAATTGTT 57.472 25.926 0.00 0.00 34.34 2.83
1403 13531 8.918961 TTGTTTAGTTCATCGACAAATTGTTT 57.081 26.923 0.00 0.00 0.00 2.83
1404 13532 8.918961 TGTTTAGTTCATCGACAAATTGTTTT 57.081 26.923 0.00 0.00 0.00 2.43
1405 13533 9.360093 TGTTTAGTTCATCGACAAATTGTTTTT 57.640 25.926 0.00 0.00 0.00 1.94
1406 13534 9.829637 GTTTAGTTCATCGACAAATTGTTTTTC 57.170 29.630 0.00 0.00 0.00 2.29
1407 13535 9.796120 TTTAGTTCATCGACAAATTGTTTTTCT 57.204 25.926 0.00 0.00 0.00 2.52
1408 13536 9.796120 TTAGTTCATCGACAAATTGTTTTTCTT 57.204 25.926 0.00 0.00 0.00 2.52
1409 13537 8.702163 AGTTCATCGACAAATTGTTTTTCTTT 57.298 26.923 0.00 0.00 0.00 2.52
1410 13538 9.150348 AGTTCATCGACAAATTGTTTTTCTTTT 57.850 25.926 0.00 0.00 0.00 2.27
1414 13542 9.631639 CATCGACAAATTGTTTTTCTTTTAACC 57.368 29.630 0.00 0.00 0.00 2.85
1415 13543 7.886696 TCGACAAATTGTTTTTCTTTTAACCG 58.113 30.769 0.00 0.00 0.00 4.44
1416 13544 7.541437 TCGACAAATTGTTTTTCTTTTAACCGT 59.459 29.630 0.00 0.00 0.00 4.83
1417 13545 8.163516 CGACAAATTGTTTTTCTTTTAACCGTT 58.836 29.630 0.00 0.00 0.00 4.44
1418 13546 9.467990 GACAAATTGTTTTTCTTTTAACCGTTC 57.532 29.630 0.00 0.00 0.00 3.95
1419 13547 8.989980 ACAAATTGTTTTTCTTTTAACCGTTCA 58.010 25.926 0.00 0.00 0.00 3.18
1420 13548 9.980780 CAAATTGTTTTTCTTTTAACCGTTCAT 57.019 25.926 0.00 0.00 0.00 2.57
1422 13550 7.439204 TTGTTTTTCTTTTAACCGTTCATCG 57.561 32.000 0.00 0.00 39.52 3.84
1423 13551 6.783162 TGTTTTTCTTTTAACCGTTCATCGA 58.217 32.000 0.00 0.00 42.86 3.59
1424 13552 6.687958 TGTTTTTCTTTTAACCGTTCATCGAC 59.312 34.615 0.00 0.00 42.86 4.20
1425 13553 5.987777 TTTCTTTTAACCGTTCATCGACA 57.012 34.783 0.00 0.00 42.86 4.35
1426 13554 5.987777 TTCTTTTAACCGTTCATCGACAA 57.012 34.783 0.00 0.00 42.86 3.18
1427 13555 5.987777 TCTTTTAACCGTTCATCGACAAA 57.012 34.783 0.00 0.00 42.86 2.83
1428 13556 6.548441 TCTTTTAACCGTTCATCGACAAAT 57.452 33.333 0.00 0.00 42.86 2.32
1429 13557 7.655236 TCTTTTAACCGTTCATCGACAAATA 57.345 32.000 0.00 0.00 42.86 1.40
1430 13558 7.735500 TCTTTTAACCGTTCATCGACAAATAG 58.264 34.615 0.00 0.00 42.86 1.73
1434 13562 8.531622 TTAACCGTTCATCGACAAATAGTTAA 57.468 30.769 0.00 1.85 42.86 2.01
1526 13658 1.001406 CGAGAGTTCTTCAGGTTGCCT 59.999 52.381 0.00 0.00 0.00 4.75
1529 13661 3.511477 AGAGTTCTTCAGGTTGCCTCTA 58.489 45.455 0.00 0.00 0.00 2.43
1562 13694 2.511600 GTGGGGATCGTCAAGGCG 60.512 66.667 0.00 0.00 0.00 5.52
1629 13761 1.623811 GTAAACTGGACTGGGCAGAGA 59.376 52.381 0.00 0.00 0.00 3.10
1630 13762 0.689623 AAACTGGACTGGGCAGAGAG 59.310 55.000 0.00 0.00 0.00 3.20
1712 13844 4.917385 TGCCAACATTTAGGTGAGTACAT 58.083 39.130 0.00 0.00 36.95 2.29
1747 13879 5.212194 AGAATGCATACGTTTTTGTGTGTC 58.788 37.500 0.00 0.00 33.94 3.67
1757 13892 4.607557 CGTTTTTGTGTGTCCGTCTATGTC 60.608 45.833 0.00 0.00 0.00 3.06
1758 13893 3.737032 TTTGTGTGTCCGTCTATGTCA 57.263 42.857 0.00 0.00 0.00 3.58
1761 13896 5.592104 TTGTGTGTCCGTCTATGTCATAT 57.408 39.130 0.00 0.00 0.00 1.78
1762 13897 5.183014 TGTGTGTCCGTCTATGTCATATC 57.817 43.478 0.00 0.00 0.00 1.63
1764 13899 5.008712 TGTGTGTCCGTCTATGTCATATCTC 59.991 44.000 0.00 0.00 0.00 2.75
1765 13900 5.239744 GTGTGTCCGTCTATGTCATATCTCT 59.760 44.000 0.00 0.00 0.00 3.10
1766 13901 5.470437 TGTGTCCGTCTATGTCATATCTCTC 59.530 44.000 0.00 0.00 0.00 3.20
1767 13902 5.004448 TGTCCGTCTATGTCATATCTCTCC 58.996 45.833 0.00 0.00 0.00 3.71
1768 13903 4.093703 GTCCGTCTATGTCATATCTCTCCG 59.906 50.000 0.00 0.00 0.00 4.63
1769 13904 4.004314 CCGTCTATGTCATATCTCTCCGT 58.996 47.826 0.00 0.00 0.00 4.69
1770 13905 5.046807 TCCGTCTATGTCATATCTCTCCGTA 60.047 44.000 0.00 0.00 0.00 4.02
1771 13906 5.818336 CCGTCTATGTCATATCTCTCCGTAT 59.182 44.000 0.00 0.00 0.00 3.06
1772 13907 6.018588 CCGTCTATGTCATATCTCTCCGTATC 60.019 46.154 0.00 0.00 0.00 2.24
1773 13908 6.535508 CGTCTATGTCATATCTCTCCGTATCA 59.464 42.308 0.00 0.00 0.00 2.15
1774 13909 7.064728 CGTCTATGTCATATCTCTCCGTATCAA 59.935 40.741 0.00 0.00 0.00 2.57
1775 13910 8.731605 GTCTATGTCATATCTCTCCGTATCAAA 58.268 37.037 0.00 0.00 0.00 2.69
1776 13911 9.297037 TCTATGTCATATCTCTCCGTATCAAAA 57.703 33.333 0.00 0.00 0.00 2.44
1786 13921 8.988064 TCTCTCCGTATCAAAATATAAGATGC 57.012 34.615 0.00 0.00 0.00 3.91
1787 13922 8.807118 TCTCTCCGTATCAAAATATAAGATGCT 58.193 33.333 0.00 0.00 0.00 3.79
1788 13923 8.988064 TCTCCGTATCAAAATATAAGATGCTC 57.012 34.615 0.00 0.00 0.00 4.26
1789 13924 8.807118 TCTCCGTATCAAAATATAAGATGCTCT 58.193 33.333 0.00 0.00 0.00 4.09
1828 13967 3.355378 TGATTTGCTGTAACAGGGATGG 58.645 45.455 0.00 0.00 31.21 3.51
1895 15009 2.800736 GCGTCCATGGCCATTGAC 59.199 61.111 31.03 31.03 32.09 3.18
1925 15039 1.587933 AACCAGAGACGCTCCTCGAC 61.588 60.000 3.66 0.00 41.67 4.20
1928 15042 2.098680 GAGACGCTCCTCGACACG 59.901 66.667 0.00 0.00 41.67 4.49
1937 15051 2.989824 CTCGACACGGTCCAGGGT 60.990 66.667 0.00 0.00 0.00 4.34
2083 15197 2.684881 CTGGCTTACAGGTTAGCAATGG 59.315 50.000 11.89 0.00 43.70 3.16
2123 15237 3.093835 CCATTGCCGGGGTCCCTA 61.094 66.667 8.15 0.00 0.00 3.53
2135 15249 0.172127 GGTCCCTAACCGTCTTCGTC 59.828 60.000 0.00 0.00 38.58 4.20
2387 15501 3.628032 TCGATAGCCTCAAGATATAGCCG 59.372 47.826 0.00 0.00 0.00 5.52
2392 15506 2.072298 CCTCAAGATATAGCCGCAAGC 58.928 52.381 0.00 0.00 44.25 4.01
2436 15568 1.304796 TGAAATTCATGCCGGGCCA 60.305 52.632 17.97 4.99 0.00 5.36
2441 15573 1.039233 ATTCATGCCGGGCCAAAGAG 61.039 55.000 17.97 0.00 0.00 2.85
2463 15595 0.935196 ACGAACGAAGACAAGGTTGC 59.065 50.000 0.14 0.00 0.00 4.17
2496 15628 5.003778 GCGTCTATTTTGCTTGCATGTTTAG 59.996 40.000 1.14 0.00 0.00 1.85
2528 15663 5.666969 TTTCAGTTGTGTACCGAAGATTG 57.333 39.130 0.00 0.00 0.00 2.67
2596 16094 7.548196 TTCCTTTTGTAATAATCTAGCCGTG 57.452 36.000 0.00 0.00 0.00 4.94
2645 16143 0.392461 TGTTCAGGCCAGGCGTATTC 60.392 55.000 6.25 0.79 0.00 1.75
2730 16228 9.662947 GTACAAGGTTACACAAGGAAGTATATT 57.337 33.333 0.00 0.00 0.00 1.28
2757 16255 6.198966 GTCGAAAATGCAATTCAGTTTGAAGT 59.801 34.615 13.91 0.00 42.29 3.01
2761 16259 7.846644 AAATGCAATTCAGTTTGAAGTCAAA 57.153 28.000 2.32 2.32 40.05 2.69
2794 16292 8.710749 TTTAGGGTAGTCAAACTAGTTGTAGA 57.289 34.615 9.34 5.28 38.47 2.59
2795 16293 8.710749 TTAGGGTAGTCAAACTAGTTGTAGAA 57.289 34.615 9.34 0.00 38.47 2.10
2797 16295 7.838884 AGGGTAGTCAAACTAGTTGTAGAATC 58.161 38.462 9.34 0.00 38.47 2.52
2798 16296 7.040494 GGGTAGTCAAACTAGTTGTAGAATCC 58.960 42.308 9.34 9.90 38.47 3.01
2800 16298 6.681729 AGTCAAACTAGTTGTAGAATCCCA 57.318 37.500 9.34 0.00 38.47 4.37
2801 16299 7.074653 AGTCAAACTAGTTGTAGAATCCCAA 57.925 36.000 9.34 0.00 38.47 4.12
2802 16300 7.690256 AGTCAAACTAGTTGTAGAATCCCAAT 58.310 34.615 9.34 0.00 38.47 3.16
2803 16301 8.164070 AGTCAAACTAGTTGTAGAATCCCAATT 58.836 33.333 9.34 0.00 38.47 2.32
2805 16303 9.010029 TCAAACTAGTTGTAGAATCCCAATTTC 57.990 33.333 9.34 0.00 38.47 2.17
2806 16304 7.611213 AACTAGTTGTAGAATCCCAATTTCG 57.389 36.000 7.48 0.00 0.00 3.46
2807 16305 6.942976 ACTAGTTGTAGAATCCCAATTTCGA 58.057 36.000 0.00 0.00 0.00 3.71
2808 16306 6.817140 ACTAGTTGTAGAATCCCAATTTCGAC 59.183 38.462 0.00 0.00 31.70 4.20
2809 16307 5.556915 AGTTGTAGAATCCCAATTTCGACA 58.443 37.500 0.00 0.00 37.07 4.35
2810 16308 6.001460 AGTTGTAGAATCCCAATTTCGACAA 58.999 36.000 7.65 7.65 42.49 3.18
2811 16309 6.149474 AGTTGTAGAATCCCAATTTCGACAAG 59.851 38.462 10.84 0.00 44.07 3.16
2812 16310 4.394920 TGTAGAATCCCAATTTCGACAAGC 59.605 41.667 0.00 0.00 36.30 4.01
2813 16311 3.420893 AGAATCCCAATTTCGACAAGCA 58.579 40.909 0.00 0.00 0.00 3.91
2821 16728 6.431543 TCCCAATTTCGACAAGCACTAATTTA 59.568 34.615 0.00 0.00 0.00 1.40
2862 17534 3.817647 GTGACAAACTTGGAGAAGAGCAT 59.182 43.478 0.00 0.00 32.98 3.79
2901 17668 1.407618 TGATGGTATCAACCTCGACGG 59.592 52.381 0.00 0.03 46.91 4.79
2961 18575 1.915078 ATGCGCTACCTTGGCCTTCT 61.915 55.000 9.73 0.00 0.00 2.85
3005 18740 5.546499 AGGAAGATTGACCTACAACACCTAA 59.454 40.000 0.00 0.00 41.52 2.69
3131 19059 9.277783 CCTTTCATGCTACTGTAATTAAGCTAT 57.722 33.333 8.05 0.00 35.95 2.97
3201 20232 4.843728 TGGGCGAGATTTGATAAAGTCTT 58.156 39.130 0.00 0.00 0.00 3.01
3298 20329 3.618594 TGAATATGTTTGCTCGTGCTCTC 59.381 43.478 11.19 1.80 40.48 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 4057 6.707440 TTACTGTTGCTCTCCAAAATTTGA 57.293 33.333 7.37 0.00 34.68 2.69
997 13122 0.749649 ATCTCGTCCCTCAGCATGAC 59.250 55.000 0.00 0.00 42.56 3.06
999 13124 0.749049 TGATCTCGTCCCTCAGCATG 59.251 55.000 0.00 0.00 37.54 4.06
1340 13468 5.539582 TTTGACGATGTAATGGTTAGTGC 57.460 39.130 0.00 0.00 34.53 4.40
1345 13473 6.817765 AGACATTTTGACGATGTAATGGTT 57.182 33.333 0.00 0.00 34.53 3.67
1401 13529 6.783162 TGTCGATGAACGGTTAAAAGAAAAA 58.217 32.000 0.00 0.00 42.82 1.94
1402 13530 6.360844 TGTCGATGAACGGTTAAAAGAAAA 57.639 33.333 0.00 0.00 42.82 2.29
1403 13531 5.987777 TGTCGATGAACGGTTAAAAGAAA 57.012 34.783 0.00 0.00 42.82 2.52
1404 13532 5.987777 TTGTCGATGAACGGTTAAAAGAA 57.012 34.783 0.00 0.00 42.82 2.52
1405 13533 5.987777 TTTGTCGATGAACGGTTAAAAGA 57.012 34.783 0.00 0.00 42.82 2.52
1406 13534 7.515643 ACTATTTGTCGATGAACGGTTAAAAG 58.484 34.615 0.00 0.00 42.82 2.27
1407 13535 7.424227 ACTATTTGTCGATGAACGGTTAAAA 57.576 32.000 0.00 0.00 42.82 1.52
1408 13536 7.424227 AACTATTTGTCGATGAACGGTTAAA 57.576 32.000 0.00 0.00 42.82 1.52
1409 13537 8.531622 TTAACTATTTGTCGATGAACGGTTAA 57.468 30.769 0.00 4.25 42.82 2.01
1410 13538 8.706492 ATTAACTATTTGTCGATGAACGGTTA 57.294 30.769 0.00 0.00 42.82 2.85
1411 13539 7.201582 GGATTAACTATTTGTCGATGAACGGTT 60.202 37.037 0.00 0.00 42.82 4.44
1412 13540 6.257193 GGATTAACTATTTGTCGATGAACGGT 59.743 38.462 0.00 0.00 42.82 4.83
1413 13541 6.479001 AGGATTAACTATTTGTCGATGAACGG 59.521 38.462 0.00 0.00 42.82 4.44
1414 13542 7.222031 TCAGGATTAACTATTTGTCGATGAACG 59.778 37.037 0.00 0.00 44.09 3.95
1415 13543 8.420374 TCAGGATTAACTATTTGTCGATGAAC 57.580 34.615 0.00 0.00 0.00 3.18
1434 13562 9.007901 GTTTCTTAGCTGCATAATTATCAGGAT 57.992 33.333 18.47 5.90 0.00 3.24
1526 13658 4.221703 CCCACTGCTTTCTTCTTCTCTAGA 59.778 45.833 0.00 0.00 0.00 2.43
1529 13661 2.039613 CCCCACTGCTTTCTTCTTCTCT 59.960 50.000 0.00 0.00 0.00 3.10
1629 13761 2.995872 GCGTTCCGAGGAGCAGACT 61.996 63.158 6.78 0.00 0.00 3.24
1630 13762 2.507324 GCGTTCCGAGGAGCAGAC 60.507 66.667 6.78 0.00 0.00 3.51
1655 13787 1.073923 AGGTCCATGTTTCTGTGTCCC 59.926 52.381 0.00 0.00 0.00 4.46
1729 13861 2.286536 ACGGACACACAAAAACGTATGC 60.287 45.455 0.00 0.00 32.30 3.14
1747 13879 4.004314 ACGGAGAGATATGACATAGACGG 58.996 47.826 0.98 0.00 0.00 4.79
1761 13896 8.807118 AGCATCTTATATTTTGATACGGAGAGA 58.193 33.333 0.00 0.00 0.00 3.10
1762 13897 8.994429 AGCATCTTATATTTTGATACGGAGAG 57.006 34.615 0.00 0.00 0.00 3.20
1828 13967 5.747342 TCTCTAGGGAGTACTTCTCAACTC 58.253 45.833 0.01 0.00 44.40 3.01
1895 15009 2.716217 GTCTCTGGTTTGATCCCAAGG 58.284 52.381 0.00 0.00 33.23 3.61
1925 15039 0.464452 GGATCTTACCCTGGACCGTG 59.536 60.000 0.00 0.00 0.00 4.94
1928 15042 2.170817 GTTCTGGATCTTACCCTGGACC 59.829 54.545 0.00 0.00 0.00 4.46
2135 15249 1.433879 GACCTCGAGGATGTCACCG 59.566 63.158 37.69 8.26 38.94 4.94
2387 15501 1.607628 CATAGGCAATGGAGAGCTTGC 59.392 52.381 0.00 0.00 45.46 4.01
2392 15506 3.681593 CCTCTCATAGGCAATGGAGAG 57.318 52.381 14.30 14.30 38.97 3.20
2417 15549 1.141665 GGCCCGGCATGAATTTCAC 59.858 57.895 12.58 0.00 0.00 3.18
2436 15568 1.202486 TGTCTTCGTTCGTGGCTCTTT 60.202 47.619 0.00 0.00 0.00 2.52
2441 15573 0.878961 ACCTTGTCTTCGTTCGTGGC 60.879 55.000 0.00 0.00 0.00 5.01
2463 15595 6.506827 GCAAGCAAAATAGACGCATACATTTG 60.507 38.462 0.00 0.00 0.00 2.32
2474 15606 7.809806 AGAACTAAACATGCAAGCAAAATAGAC 59.190 33.333 0.00 1.76 0.00 2.59
2496 15628 6.564125 CGGTACACAACTGAAATCAGAAGAAC 60.564 42.308 16.93 7.01 46.59 3.01
2528 15663 4.862018 ACAGTACAAACATGCACAAACAAC 59.138 37.500 0.00 0.00 0.00 3.32
2707 16205 9.010029 ACAAATATACTTCCTTGTGTAACCTTG 57.990 33.333 0.00 0.00 34.36 3.61
2730 16228 6.038985 TCAAACTGAATTGCATTTTCGACAA 58.961 32.000 0.00 0.00 28.10 3.18
2770 16268 8.710749 TTCTACAACTAGTTTGACTACCCTAA 57.289 34.615 5.07 0.00 38.73 2.69
2771 16269 8.890410 ATTCTACAACTAGTTTGACTACCCTA 57.110 34.615 5.07 0.00 38.73 3.53
2772 16270 7.093421 GGATTCTACAACTAGTTTGACTACCCT 60.093 40.741 5.07 0.00 38.73 4.34
2773 16271 7.040494 GGATTCTACAACTAGTTTGACTACCC 58.960 42.308 5.07 0.00 38.73 3.69
2774 16272 7.040494 GGGATTCTACAACTAGTTTGACTACC 58.960 42.308 5.07 5.76 38.73 3.18
2775 16273 7.609056 TGGGATTCTACAACTAGTTTGACTAC 58.391 38.462 5.07 0.42 38.73 2.73
2776 16274 7.786046 TGGGATTCTACAACTAGTTTGACTA 57.214 36.000 5.07 0.00 38.73 2.59
2778 16276 7.923414 ATTGGGATTCTACAACTAGTTTGAC 57.077 36.000 5.07 0.00 38.73 3.18
2780 16278 7.962918 CGAAATTGGGATTCTACAACTAGTTTG 59.037 37.037 5.07 4.54 41.49 2.93
2781 16279 7.881232 TCGAAATTGGGATTCTACAACTAGTTT 59.119 33.333 5.07 0.62 0.00 2.66
2782 16280 7.333672 GTCGAAATTGGGATTCTACAACTAGTT 59.666 37.037 1.12 1.12 0.00 2.24
2783 16281 6.817140 GTCGAAATTGGGATTCTACAACTAGT 59.183 38.462 0.00 0.00 0.00 2.57
2785 16283 6.703319 TGTCGAAATTGGGATTCTACAACTA 58.297 36.000 0.00 0.00 31.86 2.24
2786 16284 5.556915 TGTCGAAATTGGGATTCTACAACT 58.443 37.500 0.00 0.00 31.86 3.16
2789 16287 4.394920 GCTTGTCGAAATTGGGATTCTACA 59.605 41.667 0.00 0.00 32.62 2.74
2790 16288 4.394920 TGCTTGTCGAAATTGGGATTCTAC 59.605 41.667 0.00 0.00 0.00 2.59
2791 16289 4.394920 GTGCTTGTCGAAATTGGGATTCTA 59.605 41.667 0.00 0.00 0.00 2.10
2792 16290 3.191371 GTGCTTGTCGAAATTGGGATTCT 59.809 43.478 0.00 0.00 0.00 2.40
2794 16292 3.157087 AGTGCTTGTCGAAATTGGGATT 58.843 40.909 0.00 0.00 0.00 3.01
2795 16293 2.795329 AGTGCTTGTCGAAATTGGGAT 58.205 42.857 0.00 0.00 0.00 3.85
2797 16295 4.701956 ATTAGTGCTTGTCGAAATTGGG 57.298 40.909 0.00 0.00 0.00 4.12
2798 16296 6.747280 CCTAAATTAGTGCTTGTCGAAATTGG 59.253 38.462 0.00 0.00 0.00 3.16
2800 16298 6.127730 CCCCTAAATTAGTGCTTGTCGAAATT 60.128 38.462 0.00 0.00 0.00 1.82
2801 16299 5.357032 CCCCTAAATTAGTGCTTGTCGAAAT 59.643 40.000 0.00 0.00 0.00 2.17
2802 16300 4.698304 CCCCTAAATTAGTGCTTGTCGAAA 59.302 41.667 0.00 0.00 0.00 3.46
2803 16301 4.020039 TCCCCTAAATTAGTGCTTGTCGAA 60.020 41.667 0.00 0.00 0.00 3.71
2805 16303 3.869065 TCCCCTAAATTAGTGCTTGTCG 58.131 45.455 0.00 0.00 0.00 4.35
2806 16304 4.200092 CCTCCCCTAAATTAGTGCTTGTC 58.800 47.826 0.00 0.00 0.00 3.18
2807 16305 3.591977 ACCTCCCCTAAATTAGTGCTTGT 59.408 43.478 0.00 0.00 0.00 3.16
2808 16306 4.200092 GACCTCCCCTAAATTAGTGCTTG 58.800 47.826 0.00 0.00 0.00 4.01
2809 16307 3.850173 TGACCTCCCCTAAATTAGTGCTT 59.150 43.478 0.00 0.00 0.00 3.91
2810 16308 3.200165 GTGACCTCCCCTAAATTAGTGCT 59.800 47.826 0.00 0.00 0.00 4.40
2811 16309 3.200165 AGTGACCTCCCCTAAATTAGTGC 59.800 47.826 0.00 0.00 0.00 4.40
2812 16310 4.384208 CCAGTGACCTCCCCTAAATTAGTG 60.384 50.000 0.00 0.00 0.00 2.74
2813 16311 3.780850 CCAGTGACCTCCCCTAAATTAGT 59.219 47.826 0.00 0.00 0.00 2.24
2821 16728 3.947041 AGGCCAGTGACCTCCCCT 61.947 66.667 5.01 0.00 28.76 4.79
2862 17534 3.511595 ACCGAATAGGCGCGACGA 61.512 61.111 12.10 2.21 46.52 4.20
3005 18740 2.424842 TTTCCTGCGGCCTTGTCCAT 62.425 55.000 0.00 0.00 0.00 3.41
3077 18813 3.259902 GGGACACGAGGACAGATTTAAC 58.740 50.000 0.00 0.00 0.00 2.01
3131 19059 2.184322 GCCGATTGTGCTCTCCGA 59.816 61.111 0.00 0.00 0.00 4.55
3201 20232 2.676121 CCTTGCATTGCCCACCGA 60.676 61.111 6.12 0.00 0.00 4.69
3260 20291 0.764890 TTCAGGTCAAGGACACCCAG 59.235 55.000 0.00 0.00 33.96 4.45
3298 20329 1.153289 CCAGAGCCACCTCAATCGG 60.153 63.158 0.00 0.00 40.68 4.18


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

AutoCloner maintained by Alex Coulton.