Multiple sequence alignment - TraesCS6A01G014900

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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 TraesCS6A01G014900 chr6A 100.000 2726 0 0 1 2726 7186372 7183647 0.000000e+00 5035.0
1 TraesCS6A01G014900 chr6A 89.394 1716 169 11 12 1719 7175526 7173816 0.000000e+00 2148.0
2 TraesCS6A01G014900 chr6A 90.081 1351 88 15 664 2012 7091335 7092641 0.000000e+00 1711.0
3 TraesCS6A01G014900 chr6A 87.333 821 50 16 1716 2501 7081795 7082596 0.000000e+00 891.0
4 TraesCS6A01G014900 chr6A 91.566 83 7 0 2009 2091 7081864 7081946 6.170000e-22 115.0
5 TraesCS6A01G014900 chr6A 93.056 72 5 0 2009 2080 7092414 7092485 3.710000e-19 106.0
6 TraesCS6A01G014900 chr6A 93.056 72 5 0 1785 1856 7184364 7184293 3.710000e-19 106.0
7 TraesCS6A01G014900 chr6A 93.056 72 5 0 2009 2080 7184588 7184517 3.710000e-19 106.0
8 TraesCS6A01G014900 chr6A 93.220 59 4 0 1785 1843 7082071 7082129 1.340000e-13 87.9
9 TraesCS6A01G014900 chrUn 91.846 1717 133 7 1 1714 79937534 79939246 0.000000e+00 2388.0
10 TraesCS6A01G014900 chrUn 90.139 1724 164 5 1 1719 80036712 80034990 0.000000e+00 2237.0
11 TraesCS6A01G014900 chr6B 91.667 1716 138 5 1 1714 12887012 12888724 0.000000e+00 2372.0
12 TraesCS6A01G014900 chr6B 90.692 1719 151 8 1 1714 26862233 26863947 0.000000e+00 2279.0
13 TraesCS6A01G014900 chr6B 90.278 1728 156 8 1 1719 13653494 13651770 0.000000e+00 2250.0
14 TraesCS6A01G014900 chr6B 95.238 42 2 0 2685 2726 13651062 13651021 1.750000e-07 67.6
15 TraesCS6A01G014900 chr5B 90.909 1716 153 3 1 1714 432983113 432984827 0.000000e+00 2302.0
16 TraesCS6A01G014900 chr5B 82.178 303 32 10 1712 2013 432984861 432985142 9.750000e-60 241.0
17 TraesCS6A01G014900 chr7D 91.027 1694 147 4 30 1719 597676676 597674984 0.000000e+00 2281.0
18 TraesCS6A01G014900 chr6D 90.501 1716 155 8 1 1712 7359076 7357365 0.000000e+00 2259.0
19 TraesCS6A01G014900 chr6D 86.667 855 71 11 1714 2541 7357327 7356489 0.000000e+00 907.0
20 TraesCS6A01G014900 chr6D 89.535 86 7 1 2008 2091 7357257 7357172 1.030000e-19 108.0
21 TraesCS6A01G014900 chr6D 87.778 90 6 3 2009 2095 7343648 7343561 1.730000e-17 100.0


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 TraesCS6A01G014900 chr6A 7183647 7186372 2725 True 1749.000000 5035 95.370667 1 2726 3 chr6A.!!$R2 2725
1 TraesCS6A01G014900 chr6A 7173816 7175526 1710 True 2148.000000 2148 89.394000 12 1719 1 chr6A.!!$R1 1707
2 TraesCS6A01G014900 chr6A 7091335 7092641 1306 False 908.500000 1711 91.568500 664 2080 2 chr6A.!!$F2 1416
3 TraesCS6A01G014900 chr6A 7081795 7082596 801 False 364.633333 891 90.706333 1716 2501 3 chr6A.!!$F1 785
4 TraesCS6A01G014900 chrUn 79937534 79939246 1712 False 2388.000000 2388 91.846000 1 1714 1 chrUn.!!$F1 1713
5 TraesCS6A01G014900 chrUn 80034990 80036712 1722 True 2237.000000 2237 90.139000 1 1719 1 chrUn.!!$R1 1718
6 TraesCS6A01G014900 chr6B 12887012 12888724 1712 False 2372.000000 2372 91.667000 1 1714 1 chr6B.!!$F1 1713
7 TraesCS6A01G014900 chr6B 26862233 26863947 1714 False 2279.000000 2279 90.692000 1 1714 1 chr6B.!!$F2 1713
8 TraesCS6A01G014900 chr6B 13651021 13653494 2473 True 1158.800000 2250 92.758000 1 2726 2 chr6B.!!$R1 2725
9 TraesCS6A01G014900 chr5B 432983113 432985142 2029 False 1271.500000 2302 86.543500 1 2013 2 chr5B.!!$F1 2012
10 TraesCS6A01G014900 chr7D 597674984 597676676 1692 True 2281.000000 2281 91.027000 30 1719 1 chr7D.!!$R1 1689
11 TraesCS6A01G014900 chr6D 7356489 7359076 2587 True 1091.333333 2259 88.901000 1 2541 3 chr6D.!!$R2 2540

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
289 293 0.315886 CTGGCATGTGCAAAGCTCAA 59.684 50.0 7.36 0.0 44.36 3.02 F
1083 1091 0.250901 ACATGGGTGTGAAGCCTGAC 60.251 55.0 0.00 0.0 37.14 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1285 0.037605 AACAGACGGCTTACCCTTCG 60.038 55.0 0.00 0.0 36.98 3.79 R
2300 2450 0.929824 CACAGCGCACACGGAAAAAG 60.930 55.0 11.47 0.0 40.57 2.27 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
28 29 5.279256 GCCCATGTTTAACTGTGTACCAAAT 60.279 40.000 0.00 0.00 0.00 2.32
47 48 7.775120 ACCAAATATTTTCTCCTACAGCATTG 58.225 34.615 0.00 0.00 0.00 2.82
204 208 1.771854 TGAGGTGGACCAAGCTTACAA 59.228 47.619 0.00 0.00 38.89 2.41
285 289 0.815734 ATCTCTGGCATGTGCAAAGC 59.184 50.000 7.36 0.00 44.36 3.51
289 293 0.315886 CTGGCATGTGCAAAGCTCAA 59.684 50.000 7.36 0.00 44.36 3.02
290 294 0.970640 TGGCATGTGCAAAGCTCAAT 59.029 45.000 7.36 0.00 44.36 2.57
293 297 2.259618 GCATGTGCAAAGCTCAATCAG 58.740 47.619 0.00 0.00 41.59 2.90
305 309 2.355108 GCTCAATCAGTGGACAAGGCTA 60.355 50.000 0.00 0.00 0.00 3.93
379 383 8.314751 ACCACATATAATAGTCTGATACAAGGC 58.685 37.037 0.00 0.00 0.00 4.35
414 418 0.321564 CGGTGCAAAGAGGTGGATCA 60.322 55.000 0.00 0.00 0.00 2.92
435 439 8.156165 GGATCAGATTTTCAAGGAGATGACTAT 58.844 37.037 0.00 0.00 0.00 2.12
499 503 2.945668 GGATTATCTTTGCAAGAGCGGT 59.054 45.455 0.00 0.00 46.23 5.68
500 504 3.002759 GGATTATCTTTGCAAGAGCGGTC 59.997 47.826 6.48 6.48 46.23 4.79
501 505 2.760634 TATCTTTGCAAGAGCGGTCA 57.239 45.000 18.15 0.00 46.23 4.02
505 509 1.267806 CTTTGCAAGAGCGGTCAATGT 59.732 47.619 18.15 0.00 46.23 2.71
553 557 3.683365 ATGATCAGTTTGGGCCAAAAC 57.317 42.857 31.94 25.93 39.80 2.43
561 565 3.680786 GGGCCAAAACCCGACTGC 61.681 66.667 4.39 0.00 40.98 4.40
652 656 9.252962 CTTATTGATTTGATGGTAGAAAATGGC 57.747 33.333 0.00 0.00 0.00 4.40
661 665 4.415596 TGGTAGAAAATGGCATTTCACCT 58.584 39.130 30.70 25.37 40.89 4.00
697 701 9.347934 GTCTACAACATACTCATATCTGCATAC 57.652 37.037 0.00 0.00 0.00 2.39
891 896 4.351407 TCCTGGTACCATAGTTTTCAACCA 59.649 41.667 16.75 0.00 34.52 3.67
952 957 8.924511 AGAAGGTTCATGAACTATTTTCTGAA 57.075 30.769 31.81 0.00 40.94 3.02
975 981 2.106938 GGATCGCGCATCTGTCCA 59.893 61.111 8.75 0.00 0.00 4.02
1031 1039 4.754618 CCTTTGCAAAAATGGAAGGGTTAC 59.245 41.667 13.84 0.00 33.01 2.50
1050 1058 0.543749 CGGAAGCCCAGGATCTCTTT 59.456 55.000 0.00 0.00 0.00 2.52
1083 1091 0.250901 ACATGGGTGTGAAGCCTGAC 60.251 55.000 0.00 0.00 37.14 3.51
1277 1285 4.142049 TGTTTTCAGGGAAATGTTGGACAC 60.142 41.667 0.00 0.00 31.34 3.67
1283 1291 1.539827 GGAAATGTTGGACACGAAGGG 59.460 52.381 0.00 0.00 0.00 3.95
1290 1298 1.447314 GGACACGAAGGGTAAGCCG 60.447 63.158 0.00 0.00 34.97 5.52
1301 1309 2.431057 AGGGTAAGCCGTCTGTTATCAG 59.569 50.000 0.00 0.00 38.11 2.90
1338 1346 2.632028 TGGTGCATTGCTTAAATGTGGT 59.368 40.909 10.49 0.00 46.37 4.16
1383 1391 3.299503 GTTTGATGGTATCTGGGCCAAT 58.700 45.455 8.04 7.05 38.38 3.16
1478 1486 9.077885 AGAGTCTGATGATCTATTCCTTTCTAC 57.922 37.037 0.00 0.00 0.00 2.59
1511 1520 3.449227 TGCTGCCGACTCCCGTAG 61.449 66.667 0.00 0.00 36.31 3.51
1554 1563 4.538089 AGCTTACTTCAGAAAGGGGAGATT 59.462 41.667 0.00 0.00 36.78 2.40
1557 1566 3.536287 ACTTCAGAAAGGGGAGATTCCT 58.464 45.455 0.00 0.00 36.78 3.36
1650 1659 2.416107 CTGCACTTGCTTCAGGGGGA 62.416 60.000 2.33 0.00 42.66 4.81
1665 1674 1.688311 GGGGGAAAAGGCCAGGAATAC 60.688 57.143 5.01 0.00 0.00 1.89
1721 1766 2.031870 GGAACAGGGCACTTTGAACTT 58.968 47.619 0.00 0.00 0.00 2.66
1730 1775 4.636206 GGGCACTTTGAACTTCTAATCGAT 59.364 41.667 0.00 0.00 0.00 3.59
1777 1912 9.974980 GTTACATCTCCCAACATTTTCTTTTTA 57.025 29.630 0.00 0.00 0.00 1.52
1837 1972 1.263356 TCTGGGAGGAACTTGTACCG 58.737 55.000 0.00 0.00 41.55 4.02
1858 1993 4.082408 CCGGTAGTAAATGTCTGACTGTGA 60.082 45.833 9.51 0.00 0.00 3.58
1937 2072 0.675083 TGTGCATTTGGCCTCAACTG 59.325 50.000 3.32 0.00 43.89 3.16
2028 2164 5.123979 CCTTGTCTAAAATGTAGGCCACTTC 59.876 44.000 5.01 0.00 0.00 3.01
2076 2212 7.997773 ACTTGTACTAGTAGTGAATGTCTGA 57.002 36.000 13.29 0.00 0.00 3.27
2080 2216 5.317733 ACTAGTAGTGAATGTCTGACTGC 57.682 43.478 9.51 0.00 0.00 4.40
2086 2234 2.417933 GTGAATGTCTGACTGCACCATC 59.582 50.000 9.51 0.00 0.00 3.51
2152 2300 7.693969 AACTTCGGCTAGTAGTAAACTTCTA 57.306 36.000 0.00 0.00 39.80 2.10
2168 2316 3.573967 ACTTCTAACTGGCACCATTTTGG 59.426 43.478 0.00 0.00 45.02 3.28
2196 2346 4.449068 CGACTGTGTTTCATCTATATGGCC 59.551 45.833 0.00 0.00 33.61 5.36
2215 2365 4.113354 GGCCGAGTACTACTTCTTCAATG 58.887 47.826 0.00 0.00 0.00 2.82
2221 2371 6.748198 CGAGTACTACTTCTTCAATGGAGTTC 59.252 42.308 0.00 0.00 0.00 3.01
2248 2398 1.247567 GGCCTGAACTAAGCTGCAAA 58.752 50.000 1.02 0.00 0.00 3.68
2325 2477 3.957535 GTGTGCGCTGTGCTGCTT 61.958 61.111 14.92 0.00 46.63 3.91
2332 2484 0.095935 CGCTGTGCTGCTTGACATAC 59.904 55.000 0.00 0.00 0.00 2.39
2333 2485 1.446907 GCTGTGCTGCTTGACATACT 58.553 50.000 0.00 0.00 0.00 2.12
2334 2486 2.621338 GCTGTGCTGCTTGACATACTA 58.379 47.619 0.00 0.00 0.00 1.82
2378 2532 2.225167 TGGGATAACCTTGGGACCAAAC 60.225 50.000 5.17 0.00 41.11 2.93
2388 2542 1.328279 GGGACCAAACCCTTTGACAG 58.672 55.000 0.00 0.00 45.90 3.51
2415 2569 6.403866 TTGTCAATATCCAGCAAGTTGTTT 57.596 33.333 4.48 0.00 0.00 2.83
2434 2607 8.853126 AGTTGTTTATGATATGATGACCATTGG 58.147 33.333 0.00 0.00 36.71 3.16
2458 2631 8.423349 TGGAGTTGTTAGCAGTAAGTTAGTTTA 58.577 33.333 0.00 0.00 0.00 2.01
2513 2686 4.511527 ACATGCAGTTCTCGAAGAATCAT 58.488 39.130 0.00 0.00 36.50 2.45
2520 2693 5.409520 CAGTTCTCGAAGAATCATTGTTCCA 59.590 40.000 1.78 0.00 36.50 3.53
2542 2715 6.328934 TCCATCCACCACTTAGCATTCTATAA 59.671 38.462 0.00 0.00 0.00 0.98
2544 2717 7.667219 CCATCCACCACTTAGCATTCTATAATT 59.333 37.037 0.00 0.00 0.00 1.40
2546 2719 8.677148 TCCACCACTTAGCATTCTATAATTTC 57.323 34.615 0.00 0.00 0.00 2.17
2547 2720 7.719633 TCCACCACTTAGCATTCTATAATTTCC 59.280 37.037 0.00 0.00 0.00 3.13
2548 2721 7.721399 CCACCACTTAGCATTCTATAATTTCCT 59.279 37.037 0.00 0.00 0.00 3.36
2549 2722 9.125026 CACCACTTAGCATTCTATAATTTCCTT 57.875 33.333 0.00 0.00 0.00 3.36
2550 2723 9.700831 ACCACTTAGCATTCTATAATTTCCTTT 57.299 29.630 0.00 0.00 0.00 3.11
2562 2735 8.726988 TCTATAATTTCCTTTGTTTTCTCGGTG 58.273 33.333 0.00 0.00 0.00 4.94
2563 2736 5.592104 AATTTCCTTTGTTTTCTCGGTGT 57.408 34.783 0.00 0.00 0.00 4.16
2564 2737 4.625972 TTTCCTTTGTTTTCTCGGTGTC 57.374 40.909 0.00 0.00 0.00 3.67
2565 2738 3.269538 TCCTTTGTTTTCTCGGTGTCA 57.730 42.857 0.00 0.00 0.00 3.58
2566 2739 3.815809 TCCTTTGTTTTCTCGGTGTCAT 58.184 40.909 0.00 0.00 0.00 3.06
2567 2740 4.204012 TCCTTTGTTTTCTCGGTGTCATT 58.796 39.130 0.00 0.00 0.00 2.57
2568 2741 5.369833 TCCTTTGTTTTCTCGGTGTCATTA 58.630 37.500 0.00 0.00 0.00 1.90
2569 2742 6.001460 TCCTTTGTTTTCTCGGTGTCATTAT 58.999 36.000 0.00 0.00 0.00 1.28
2570 2743 6.072728 TCCTTTGTTTTCTCGGTGTCATTATG 60.073 38.462 0.00 0.00 0.00 1.90
2572 2745 5.856126 TGTTTTCTCGGTGTCATTATGTC 57.144 39.130 0.00 0.00 0.00 3.06
2573 2746 4.693566 TGTTTTCTCGGTGTCATTATGTCC 59.306 41.667 0.00 0.00 0.00 4.02
2575 2748 4.819105 TTCTCGGTGTCATTATGTCCTT 57.181 40.909 0.00 0.00 0.00 3.36
2576 2749 4.819105 TCTCGGTGTCATTATGTCCTTT 57.181 40.909 0.00 0.00 0.00 3.11
2577 2750 5.925506 TCTCGGTGTCATTATGTCCTTTA 57.074 39.130 0.00 0.00 0.00 1.85
2579 2752 5.421056 TCTCGGTGTCATTATGTCCTTTAGT 59.579 40.000 0.00 0.00 0.00 2.24
2580 2753 5.657474 TCGGTGTCATTATGTCCTTTAGTC 58.343 41.667 0.00 0.00 0.00 2.59
2581 2754 5.421056 TCGGTGTCATTATGTCCTTTAGTCT 59.579 40.000 0.00 0.00 0.00 3.24
2582 2755 5.520288 CGGTGTCATTATGTCCTTTAGTCTG 59.480 44.000 0.00 0.00 0.00 3.51
2585 2758 7.278868 GGTGTCATTATGTCCTTTAGTCTGAAG 59.721 40.741 0.00 0.00 0.00 3.02
2586 2759 7.819900 GTGTCATTATGTCCTTTAGTCTGAAGT 59.180 37.037 3.88 0.00 0.00 3.01
2588 2761 8.254508 GTCATTATGTCCTTTAGTCTGAAGTCT 58.745 37.037 3.88 0.00 0.00 3.24
2589 2762 8.816894 TCATTATGTCCTTTAGTCTGAAGTCTT 58.183 33.333 3.88 0.00 0.00 3.01
2595 2768 8.429641 TGTCCTTTAGTCTGAAGTCTTATTGTT 58.570 33.333 3.88 0.00 0.00 2.83
2596 2769 8.927721 GTCCTTTAGTCTGAAGTCTTATTGTTC 58.072 37.037 3.88 0.00 0.00 3.18
2597 2770 8.647796 TCCTTTAGTCTGAAGTCTTATTGTTCA 58.352 33.333 3.88 0.00 0.00 3.18
2598 2771 9.442047 CCTTTAGTCTGAAGTCTTATTGTTCAT 57.558 33.333 3.88 0.00 30.03 2.57
2604 2777 9.907576 GTCTGAAGTCTTATTGTTCATTATTCG 57.092 33.333 0.00 0.00 30.03 3.34
2605 2778 9.653287 TCTGAAGTCTTATTGTTCATTATTCGT 57.347 29.630 0.00 0.00 30.03 3.85
2628 2801 9.214957 TCGTATAACTTCTTTTCATGTCATTGT 57.785 29.630 0.00 0.00 0.00 2.71
2643 2816 7.666804 TCATGTCATTGTATATTTGCTGGCTAT 59.333 33.333 0.00 0.00 0.00 2.97
2655 2828 6.832520 TTTGCTGGCTATATGTTTTCTGAA 57.167 33.333 0.00 0.00 0.00 3.02
2656 2829 6.832520 TTGCTGGCTATATGTTTTCTGAAA 57.167 33.333 0.00 0.00 0.00 2.69
2657 2830 6.441093 TGCTGGCTATATGTTTTCTGAAAG 57.559 37.500 2.75 0.00 0.00 2.62
2658 2831 6.179756 TGCTGGCTATATGTTTTCTGAAAGA 58.820 36.000 2.75 0.00 44.68 2.52
2673 2846 3.074412 TGAAAGACAGGAAAATCGGAGC 58.926 45.455 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.402798 TGAAAACAATGCTGTAGGAGAAAATA 57.597 30.769 0.00 0.00 33.45 1.40
47 48 2.287009 CGTTGCAGAGACCCTTGAAAAC 60.287 50.000 0.00 0.00 0.00 2.43
204 208 3.758554 ACGCAGCATTTCAGAAAATAGGT 59.241 39.130 0.00 0.00 33.27 3.08
285 289 2.486472 AGCCTTGTCCACTGATTGAG 57.514 50.000 0.00 0.00 0.00 3.02
289 293 2.503356 CTCCTTAGCCTTGTCCACTGAT 59.497 50.000 0.00 0.00 0.00 2.90
290 294 1.902508 CTCCTTAGCCTTGTCCACTGA 59.097 52.381 0.00 0.00 0.00 3.41
293 297 0.984995 ACCTCCTTAGCCTTGTCCAC 59.015 55.000 0.00 0.00 0.00 4.02
305 309 4.713792 ACATCTGTTGAAGAACCTCCTT 57.286 40.909 0.00 0.00 38.79 3.36
376 380 5.794894 CACCGTCCTAATGAATAATAGCCT 58.205 41.667 0.00 0.00 0.00 4.58
379 383 7.441157 TCTTTGCACCGTCCTAATGAATAATAG 59.559 37.037 0.00 0.00 0.00 1.73
499 503 3.261643 TCTTCCTAGCTTCTGCACATTGA 59.738 43.478 0.00 0.00 42.74 2.57
500 504 3.603532 TCTTCCTAGCTTCTGCACATTG 58.396 45.455 0.00 0.00 42.74 2.82
501 505 3.988976 TCTTCCTAGCTTCTGCACATT 57.011 42.857 0.00 0.00 42.74 2.71
505 509 5.316167 TCAAAAATCTTCCTAGCTTCTGCA 58.684 37.500 0.00 0.00 42.74 4.41
553 557 1.948145 CTGTAGGTAGTAGCAGTCGGG 59.052 57.143 1.58 0.00 0.00 5.14
561 565 7.569639 TGAAGCAGAATACTGTAGGTAGTAG 57.430 40.000 0.00 0.00 45.04 2.57
628 632 8.303780 TGCCATTTTCTACCATCAAATCAATA 57.696 30.769 0.00 0.00 0.00 1.90
652 656 8.667076 TGTAGACATAATGATCAGGTGAAATG 57.333 34.615 0.09 1.45 0.00 2.32
697 701 4.215399 TCACCAACCATTTCTTCTTTAGCG 59.785 41.667 0.00 0.00 0.00 4.26
891 896 8.626526 CACAAGTACAAAAACCACTAATAAGGT 58.373 33.333 0.00 0.00 40.61 3.50
907 912 2.890311 CTCCCATTTGCCACAAGTACAA 59.110 45.455 0.00 0.00 0.00 2.41
911 916 2.242043 CTTCTCCCATTTGCCACAAGT 58.758 47.619 0.00 0.00 0.00 3.16
952 957 0.659427 CAGATGCGCGATCCAACATT 59.341 50.000 12.10 0.00 0.00 2.71
1031 1039 0.543749 AAAGAGATCCTGGGCTTCCG 59.456 55.000 0.00 0.00 0.00 4.30
1050 1058 5.203557 CACCCATGTGTACCATCAGGTCA 62.204 52.174 10.32 0.00 39.94 4.02
1107 1115 2.081462 CCAACGAACAAGTATCCACCC 58.919 52.381 0.00 0.00 0.00 4.61
1277 1285 0.037605 AACAGACGGCTTACCCTTCG 60.038 55.000 0.00 0.00 36.98 3.79
1283 1291 5.857822 AAAACTGATAACAGACGGCTTAC 57.142 39.130 7.05 0.00 46.03 2.34
1338 1346 5.520748 AATCTTTGGCTTCTTCCTTCCTA 57.479 39.130 0.00 0.00 0.00 2.94
1383 1391 1.340088 TAACGTCAGGCACTAACCCA 58.660 50.000 0.00 0.00 36.02 4.51
1478 1486 1.938577 CAGCACATCCATTCTTCTCCG 59.061 52.381 0.00 0.00 0.00 4.63
1554 1563 1.866943 AGATAAGTCCCAGCCCTAGGA 59.133 52.381 11.48 0.00 0.00 2.94
1557 1566 2.247635 AGACAGATAAGTCCCAGCCCTA 59.752 50.000 0.00 0.00 39.34 3.53
1650 1659 3.076032 ACTCCTTGTATTCCTGGCCTTTT 59.924 43.478 3.32 0.00 0.00 2.27
1721 1766 5.734720 AGAAAAGTTCAGGCATCGATTAGA 58.265 37.500 0.00 0.00 0.00 2.10
1730 1775 2.430332 CCCACAAAGAAAAGTTCAGGCA 59.570 45.455 0.00 0.00 0.00 4.75
1777 1912 7.159372 AGTGACCTTCATTTTAGACGTACAAT 58.841 34.615 0.00 0.00 0.00 2.71
1837 1972 6.456501 AGTTCACAGTCAGACATTTACTACC 58.543 40.000 2.66 0.00 0.00 3.18
1858 1993 8.001881 ACAGATAGTCGTTCATCAGAATAGTT 57.998 34.615 0.00 0.00 35.92 2.24
2028 2164 7.562088 AGTTCCTCCCAGAATTACTAGTAAGAG 59.438 40.741 19.58 17.20 0.00 2.85
2076 2212 2.592102 ACATTTCAGGATGGTGCAGT 57.408 45.000 0.00 0.00 36.16 4.40
2080 2216 3.941483 GTGACCTACATTTCAGGATGGTG 59.059 47.826 0.00 0.00 36.61 4.17
2086 2234 5.413309 AGAGAAGTGACCTACATTTCAGG 57.587 43.478 0.00 0.00 44.20 3.86
2120 2268 3.764237 ACTAGCCGAAGTTTCTCCAAA 57.236 42.857 0.00 0.00 0.00 3.28
2133 2281 6.264088 CCAGTTAGAAGTTTACTACTAGCCG 58.736 44.000 0.00 0.00 35.54 5.52
2168 2316 7.254117 CCATATAGATGAAACACAGTCGTTCAC 60.254 40.741 0.00 0.00 34.73 3.18
2196 2346 6.197364 ACTCCATTGAAGAAGTAGTACTCG 57.803 41.667 2.58 0.00 0.00 4.18
2215 2365 2.238521 TCAGGCCAAATGTTGAACTCC 58.761 47.619 5.01 0.00 0.00 3.85
2221 2371 3.256631 AGCTTAGTTCAGGCCAAATGTTG 59.743 43.478 5.01 0.00 0.00 3.33
2262 2412 9.784531 ATTTATCAGGTCAAATCGAATACTGAT 57.215 29.630 16.74 16.74 41.25 2.90
2271 2421 9.056005 TCAAGGATAATTTATCAGGTCAAATCG 57.944 33.333 16.27 0.00 36.91 3.34
2300 2450 0.929824 CACAGCGCACACGGAAAAAG 60.930 55.000 11.47 0.00 40.57 2.27
2308 2460 3.957535 AAGCAGCACAGCGCACAC 61.958 61.111 11.47 0.00 46.13 3.82
2388 2542 6.183360 ACAACTTGCTGGATATTGACAATAGC 60.183 38.462 13.85 13.85 0.00 2.97
2415 2569 7.748677 ACAACTCCAATGGTCATCATATCATA 58.251 34.615 0.00 0.00 34.44 2.15
2458 2631 4.641396 TGCAAAGGAGCTACGCAATATAT 58.359 39.130 0.00 0.00 34.99 0.86
2467 2640 2.289002 CCATTCGATGCAAAGGAGCTAC 59.711 50.000 0.00 0.00 34.99 3.58
2483 2656 3.436704 TCGAGAACTGCATGTTTCCATTC 59.563 43.478 0.00 0.00 39.30 2.67
2520 2693 9.289782 GAAATTATAGAATGCTAAGTGGTGGAT 57.710 33.333 0.00 0.00 0.00 3.41
2542 2715 4.642885 TGACACCGAGAAAACAAAGGAAAT 59.357 37.500 0.00 0.00 0.00 2.17
2544 2717 3.611970 TGACACCGAGAAAACAAAGGAA 58.388 40.909 0.00 0.00 0.00 3.36
2546 2719 4.568152 AATGACACCGAGAAAACAAAGG 57.432 40.909 0.00 0.00 0.00 3.11
2547 2720 6.668323 ACATAATGACACCGAGAAAACAAAG 58.332 36.000 0.00 0.00 0.00 2.77
2548 2721 6.293735 GGACATAATGACACCGAGAAAACAAA 60.294 38.462 0.00 0.00 0.00 2.83
2549 2722 5.180492 GGACATAATGACACCGAGAAAACAA 59.820 40.000 0.00 0.00 0.00 2.83
2550 2723 4.693566 GGACATAATGACACCGAGAAAACA 59.306 41.667 0.00 0.00 0.00 2.83
2552 2725 5.160607 AGGACATAATGACACCGAGAAAA 57.839 39.130 0.00 0.00 0.00 2.29
2553 2726 4.819105 AGGACATAATGACACCGAGAAA 57.181 40.909 0.00 0.00 0.00 2.52
2554 2727 4.819105 AAGGACATAATGACACCGAGAA 57.181 40.909 0.00 0.00 0.00 2.87
2555 2728 4.819105 AAAGGACATAATGACACCGAGA 57.181 40.909 0.00 0.00 0.00 4.04
2556 2729 5.661458 ACTAAAGGACATAATGACACCGAG 58.339 41.667 0.00 0.00 0.00 4.63
2557 2730 5.421056 AGACTAAAGGACATAATGACACCGA 59.579 40.000 0.00 0.00 0.00 4.69
2558 2731 5.520288 CAGACTAAAGGACATAATGACACCG 59.480 44.000 0.00 0.00 0.00 4.94
2559 2732 6.640518 TCAGACTAAAGGACATAATGACACC 58.359 40.000 0.00 0.00 0.00 4.16
2560 2733 7.819900 ACTTCAGACTAAAGGACATAATGACAC 59.180 37.037 0.00 0.00 0.00 3.67
2562 2735 8.254508 AGACTTCAGACTAAAGGACATAATGAC 58.745 37.037 0.00 0.00 0.00 3.06
2563 2736 8.367660 AGACTTCAGACTAAAGGACATAATGA 57.632 34.615 0.00 0.00 0.00 2.57
2568 2741 8.598041 ACAATAAGACTTCAGACTAAAGGACAT 58.402 33.333 0.00 0.00 0.00 3.06
2569 2742 7.963532 ACAATAAGACTTCAGACTAAAGGACA 58.036 34.615 0.00 0.00 0.00 4.02
2570 2743 8.834749 AACAATAAGACTTCAGACTAAAGGAC 57.165 34.615 0.00 0.00 0.00 3.85
2572 2745 8.833231 TGAACAATAAGACTTCAGACTAAAGG 57.167 34.615 0.00 0.00 0.00 3.11
2579 2752 9.653287 ACGAATAATGAACAATAAGACTTCAGA 57.347 29.630 0.00 0.00 0.00 3.27
2602 2775 9.214957 ACAATGACATGAAAAGAAGTTATACGA 57.785 29.630 0.00 0.00 0.00 3.43
2612 2785 9.791820 CAGCAAATATACAATGACATGAAAAGA 57.208 29.630 0.00 0.00 0.00 2.52
2613 2786 9.027129 CCAGCAAATATACAATGACATGAAAAG 57.973 33.333 0.00 0.00 0.00 2.27
2614 2787 7.492020 GCCAGCAAATATACAATGACATGAAAA 59.508 33.333 0.00 0.00 0.00 2.29
2615 2788 6.979817 GCCAGCAAATATACAATGACATGAAA 59.020 34.615 0.00 0.00 0.00 2.69
2616 2789 6.321945 AGCCAGCAAATATACAATGACATGAA 59.678 34.615 0.00 0.00 0.00 2.57
2617 2790 5.829391 AGCCAGCAAATATACAATGACATGA 59.171 36.000 0.00 0.00 0.00 3.07
2618 2791 6.080648 AGCCAGCAAATATACAATGACATG 57.919 37.500 0.00 0.00 0.00 3.21
2619 2792 9.690913 ATATAGCCAGCAAATATACAATGACAT 57.309 29.630 0.00 0.00 0.00 3.06
2620 2793 8.949177 CATATAGCCAGCAAATATACAATGACA 58.051 33.333 0.00 0.00 0.00 3.58
2621 2794 8.950210 ACATATAGCCAGCAAATATACAATGAC 58.050 33.333 0.00 0.00 0.00 3.06
2622 2795 9.519191 AACATATAGCCAGCAAATATACAATGA 57.481 29.630 0.00 0.00 0.00 2.57
2626 2799 9.573166 AGAAAACATATAGCCAGCAAATATACA 57.427 29.630 0.00 0.00 0.00 2.29
2627 2800 9.831737 CAGAAAACATATAGCCAGCAAATATAC 57.168 33.333 0.00 0.00 0.00 1.47
2628 2801 9.791801 TCAGAAAACATATAGCCAGCAAATATA 57.208 29.630 0.00 0.00 0.00 0.86
2631 2804 7.408756 TTCAGAAAACATATAGCCAGCAAAT 57.591 32.000 0.00 0.00 0.00 2.32
2643 2816 8.289618 CGATTTTCCTGTCTTTCAGAAAACATA 58.710 33.333 9.80 2.60 46.27 2.29
2655 2828 3.425162 AAGCTCCGATTTTCCTGTCTT 57.575 42.857 0.00 0.00 0.00 3.01
2656 2829 3.425162 AAAGCTCCGATTTTCCTGTCT 57.575 42.857 0.00 0.00 0.00 3.41
2657 2830 4.254492 AGTAAAGCTCCGATTTTCCTGTC 58.746 43.478 0.00 0.00 0.00 3.51
2658 2831 4.287766 AGTAAAGCTCCGATTTTCCTGT 57.712 40.909 0.00 0.00 0.00 4.00
2659 2832 5.412904 AGAAAGTAAAGCTCCGATTTTCCTG 59.587 40.000 0.00 0.00 0.00 3.86
2668 2841 2.779506 ACCCAAGAAAGTAAAGCTCCG 58.220 47.619 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.