Multiple sequence alignment - TraesCS2A01G100900

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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 TraesCS2A01G100900 chr2A 100.000 2272 0 0 965 3236 53928541 53926270 0.000000e+00 4196.0
1 TraesCS2A01G100900 chr2A 100.000 622 0 0 1 622 53929505 53928884 0.000000e+00 1149.0
2 TraesCS2A01G100900 chr2A 86.364 88 12 0 2634 2721 12396599 12396512 2.660000e-16 97.1
3 TraesCS2A01G100900 chr2A 85.882 85 12 0 2634 2718 449370765 449370849 1.240000e-14 91.6
4 TraesCS2A01G100900 chr2D 90.878 2313 120 32 965 3236 52559280 52557018 0.000000e+00 3018.0
5 TraesCS2A01G100900 chr2D 88.070 570 39 9 64 622 52559897 52559346 0.000000e+00 649.0
6 TraesCS2A01G100900 chr2B 90.795 1510 90 25 965 2446 82061453 82059965 0.000000e+00 1973.0
7 TraesCS2A01G100900 chr2B 92.480 492 23 7 2758 3236 82055456 82054966 0.000000e+00 691.0
8 TraesCS2A01G100900 chr2B 91.127 417 22 6 2749 3150 82059887 82059471 4.720000e-153 551.0
9 TraesCS2A01G100900 chr2B 83.276 586 49 17 74 622 82062100 82061527 8.070000e-136 494.0
10 TraesCS2A01G100900 chr2B 95.556 90 3 1 3147 3236 82056582 82056494 3.370000e-30 143.0
11 TraesCS2A01G100900 chr4D 86.932 176 21 2 1683 1857 305379796 305379970 2.550000e-46 196.0
12 TraesCS2A01G100900 chr4D 86.047 86 10 2 2634 2718 507733525 507733609 1.240000e-14 91.6
13 TraesCS2A01G100900 chr5A 86.364 88 12 0 2634 2721 604640177 604640090 2.660000e-16 97.1
14 TraesCS2A01G100900 chr5A 85.882 85 12 0 2634 2718 518617779 518617863 1.240000e-14 91.6
15 TraesCS2A01G100900 chr5A 96.154 52 1 1 1710 1760 44885913 44885862 2.070000e-12 84.2
16 TraesCS2A01G100900 chr3D 85.870 92 11 1 2629 2718 232875579 232875670 2.660000e-16 97.1
17 TraesCS2A01G100900 chr1A 87.059 85 11 0 2634 2718 222516911 222516995 2.660000e-16 97.1
18 TraesCS2A01G100900 chr7A 85.882 85 12 0 2634 2718 69838480 69838564 1.240000e-14 91.6


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 TraesCS2A01G100900 chr2A 53926270 53929505 3235 True 2672.5 4196 100.0000 1 3236 2 chr2A.!!$R2 3235
1 TraesCS2A01G100900 chr2D 52557018 52559897 2879 True 1833.5 3018 89.4740 64 3236 2 chr2D.!!$R1 3172
2 TraesCS2A01G100900 chr2B 82054966 82062100 7134 True 770.4 1973 90.6468 74 3236 5 chr2B.!!$R1 3162

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
325 336 0.478507 CCCTGACCTTGAACACCCTT 59.521 55.0 0.0 0.0 0.0 3.95 F
992 1029 0.901124 TCCTGCTCTTCCTTCTGCTC 59.099 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1519 0.179026 CGGACTCGACCTCCCTCATA 60.179 60.0 0.0 0.0 39.00 2.15 R
2516 2605 0.108329 TTTCCGCCTCCGACAATCTC 60.108 55.0 0.0 0.0 36.29 2.75 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
23 24 5.746307 TCTTCTCTAATGCAATGACATGC 57.254 39.130 0.00 0.00 46.58 4.06
33 34 2.475111 GCAATGACATGCATGCTTATGC 59.525 45.455 26.53 24.66 45.70 3.14
43 44 3.996032 GCATGCTTATGCGTATTCTAGC 58.004 45.455 11.37 0.00 43.34 3.42
212 220 1.072505 CTGTGGTAACCGGCCAACT 59.927 57.895 0.00 0.00 37.81 3.16
222 230 1.576421 CGGCCAACTGCTTGAGTTC 59.424 57.895 2.24 0.00 43.52 3.01
245 253 4.272489 TCTCCATTTTTACCATGCTCCAG 58.728 43.478 0.00 0.00 0.00 3.86
281 289 2.675423 GACCCACGCCCTTTTCCC 60.675 66.667 0.00 0.00 0.00 3.97
282 290 4.295199 ACCCACGCCCTTTTCCCC 62.295 66.667 0.00 0.00 0.00 4.81
289 300 2.989253 CCCTTTTCCCCGTGTGGC 60.989 66.667 0.00 0.00 0.00 5.01
325 336 0.478507 CCCTGACCTTGAACACCCTT 59.521 55.000 0.00 0.00 0.00 3.95
475 508 1.300233 GATGCCTGATCCGACGGAC 60.300 63.158 21.02 13.67 32.98 4.79
477 510 3.515286 GCCTGATCCGACGGACGA 61.515 66.667 21.02 7.66 45.77 4.20
480 513 1.226323 CTGATCCGACGGACGACAC 60.226 63.158 21.02 9.07 45.77 3.67
507 540 2.549282 CCACGTGAAAGCCGTTCG 59.451 61.111 19.30 0.00 39.30 3.95
585 622 3.125573 GGGCGGCGACCTTTTCTC 61.126 66.667 27.98 0.00 0.00 2.87
992 1029 0.901124 TCCTGCTCTTCCTTCTGCTC 59.099 55.000 0.00 0.00 0.00 4.26
1610 1660 2.074576 GTAGGAGTTCTTGGCCGAAAC 58.925 52.381 0.00 2.10 0.00 2.78
1620 1670 2.675423 GCCGAAACCCCCTGTTCC 60.675 66.667 0.00 0.00 35.67 3.62
1621 1671 2.359478 CCGAAACCCCCTGTTCCG 60.359 66.667 0.00 0.00 35.67 4.30
1623 1673 1.228033 CGAAACCCCCTGTTCCGTT 60.228 57.895 0.00 0.00 35.67 4.44
1625 1675 0.892358 GAAACCCCCTGTTCCGTTCC 60.892 60.000 0.00 0.00 35.67 3.62
1626 1676 2.685804 AAACCCCCTGTTCCGTTCCG 62.686 60.000 0.00 0.00 35.67 4.30
1639 1689 1.656652 CGTTCCGGCAATCTGATTCT 58.343 50.000 0.00 0.00 0.00 2.40
1640 1690 1.328680 CGTTCCGGCAATCTGATTCTG 59.671 52.381 0.00 1.55 0.00 3.02
1642 1693 3.009723 GTTCCGGCAATCTGATTCTGAA 58.990 45.455 0.00 0.00 0.00 3.02
1648 1699 3.423571 GCAATCTGATTCTGAAACTGCG 58.576 45.455 0.00 0.00 0.00 5.18
1864 1916 0.602638 TGCAACCGTAAGCCTCACTG 60.603 55.000 0.00 0.00 0.00 3.66
1867 1919 2.699954 CAACCGTAAGCCTCACTGATT 58.300 47.619 0.00 0.00 0.00 2.57
1868 1920 3.857052 CAACCGTAAGCCTCACTGATTA 58.143 45.455 0.00 0.00 0.00 1.75
1869 1921 4.442706 CAACCGTAAGCCTCACTGATTAT 58.557 43.478 0.00 0.00 0.00 1.28
1870 1922 4.060038 ACCGTAAGCCTCACTGATTATG 57.940 45.455 0.00 0.00 0.00 1.90
1872 1924 4.081087 ACCGTAAGCCTCACTGATTATGTT 60.081 41.667 0.00 0.00 0.00 2.71
1874 1926 5.006746 CCGTAAGCCTCACTGATTATGTTTC 59.993 44.000 0.00 0.00 0.00 2.78
1875 1927 5.812642 CGTAAGCCTCACTGATTATGTTTCT 59.187 40.000 0.00 0.00 0.00 2.52
1876 1928 6.313905 CGTAAGCCTCACTGATTATGTTTCTT 59.686 38.462 0.00 0.00 0.00 2.52
1877 1929 6.749923 AAGCCTCACTGATTATGTTTCTTC 57.250 37.500 0.00 0.00 0.00 2.87
1878 1930 6.059787 AGCCTCACTGATTATGTTTCTTCT 57.940 37.500 0.00 0.00 0.00 2.85
1879 1931 6.479884 AGCCTCACTGATTATGTTTCTTCTT 58.520 36.000 0.00 0.00 0.00 2.52
1884 1936 9.604626 CTCACTGATTATGTTTCTTCTTTTGTC 57.395 33.333 0.00 0.00 0.00 3.18
1886 1938 8.352201 CACTGATTATGTTTCTTCTTTTGTCCA 58.648 33.333 0.00 0.00 0.00 4.02
1887 1939 8.352942 ACTGATTATGTTTCTTCTTTTGTCCAC 58.647 33.333 0.00 0.00 0.00 4.02
1888 1940 8.463930 TGATTATGTTTCTTCTTTTGTCCACT 57.536 30.769 0.00 0.00 0.00 4.00
1889 1941 9.567776 TGATTATGTTTCTTCTTTTGTCCACTA 57.432 29.630 0.00 0.00 0.00 2.74
1890 1942 9.827411 GATTATGTTTCTTCTTTTGTCCACTAC 57.173 33.333 0.00 0.00 0.00 2.73
1891 1943 8.740123 TTATGTTTCTTCTTTTGTCCACTACA 57.260 30.769 0.00 0.00 35.88 2.74
1892 1944 7.639113 ATGTTTCTTCTTTTGTCCACTACAA 57.361 32.000 0.00 0.00 46.41 2.41
2169 2235 2.513259 CCCATGGATGCCATTGCCC 61.513 63.158 15.22 0.00 42.23 5.36
2226 2292 3.934962 GGCTCGCTGATCCCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
2256 2322 2.156051 AACTCGAGACCAGGCCGAAC 62.156 60.000 21.68 0.00 31.59 3.95
2281 2347 4.438744 CGGCCATTTCTGTACAGATTTTCC 60.439 45.833 25.68 19.64 37.29 3.13
2305 2372 6.692681 CCTCTTTTGTTGTGTGTTGTATTGAG 59.307 38.462 0.00 0.00 0.00 3.02
2388 2457 0.819259 ATCGTGTTGCTGCAACCAGT 60.819 50.000 34.79 19.44 42.96 4.00
2457 2541 1.419387 CTCCCCAGATCCTTCATGACC 59.581 57.143 0.00 0.00 0.00 4.02
2460 2544 1.202580 CCCAGATCCTTCATGACCGAC 60.203 57.143 0.00 0.00 0.00 4.79
2488 2577 8.830915 TCTCCATGAATTCTAGTTACTCTCTT 57.169 34.615 7.05 0.00 0.00 2.85
2515 2604 7.961351 TCTTTCTCTGAGATTGTTCTTTCTCT 58.039 34.615 8.42 0.00 39.30 3.10
2516 2605 7.871973 TCTTTCTCTGAGATTGTTCTTTCTCTG 59.128 37.037 8.42 0.00 39.30 3.35
2522 2611 7.818446 TCTGAGATTGTTCTTTCTCTGAGATTG 59.182 37.037 8.42 4.79 40.11 2.67
2523 2612 7.448420 TGAGATTGTTCTTTCTCTGAGATTGT 58.552 34.615 8.42 0.00 39.30 2.71
2524 2613 7.601886 TGAGATTGTTCTTTCTCTGAGATTGTC 59.398 37.037 8.42 0.18 39.30 3.18
2525 2614 6.589523 AGATTGTTCTTTCTCTGAGATTGTCG 59.410 38.462 8.42 0.00 0.00 4.35
2526 2615 4.560128 TGTTCTTTCTCTGAGATTGTCGG 58.440 43.478 8.42 0.00 0.00 4.79
2532 2621 1.227089 CTGAGATTGTCGGAGGCGG 60.227 63.158 0.00 0.00 32.51 6.13
2540 2629 0.250553 TGTCGGAGGCGGAAAAATGT 60.251 50.000 0.00 0.00 28.88 2.71
2543 2632 1.215382 GGAGGCGGAAAAATGTGGC 59.785 57.895 0.00 0.00 0.00 5.01
2568 2657 2.375174 TGAGGCCTAATGACAAGGTTGT 59.625 45.455 4.42 0.00 45.65 3.32
2575 2664 5.619981 GCCTAATGACAAGGTTGTGTGATTC 60.620 44.000 0.00 0.00 42.43 2.52
2577 2666 5.695851 AATGACAAGGTTGTGTGATTCTC 57.304 39.130 0.00 0.00 42.43 2.87
2581 2670 6.295249 TGACAAGGTTGTGTGATTCTCAATA 58.705 36.000 0.00 0.00 42.43 1.90
2586 2675 6.725364 AGGTTGTGTGATTCTCAATAGGATT 58.275 36.000 0.00 0.00 33.19 3.01
2587 2676 6.600822 AGGTTGTGTGATTCTCAATAGGATTG 59.399 38.462 0.00 0.00 33.19 2.67
2591 2680 6.070021 TGTGTGATTCTCAATAGGATTGGAGT 60.070 38.462 0.00 0.00 0.00 3.85
2598 2687 7.870509 TCTCAATAGGATTGGAGTTTTGATG 57.129 36.000 0.00 0.00 0.00 3.07
2599 2688 6.830324 TCTCAATAGGATTGGAGTTTTGATGG 59.170 38.462 0.00 0.00 0.00 3.51
2602 2691 3.509442 AGGATTGGAGTTTTGATGGCAA 58.491 40.909 0.00 0.00 0.00 4.52
2607 2696 4.038271 TGGAGTTTTGATGGCAAGATCT 57.962 40.909 0.00 0.00 35.04 2.75
2608 2697 4.410099 TGGAGTTTTGATGGCAAGATCTT 58.590 39.130 0.88 0.88 35.04 2.40
2609 2698 4.460382 TGGAGTTTTGATGGCAAGATCTTC 59.540 41.667 4.57 0.75 35.04 2.87
2610 2699 4.460382 GGAGTTTTGATGGCAAGATCTTCA 59.540 41.667 4.57 1.81 35.04 3.02
2611 2700 5.382618 AGTTTTGATGGCAAGATCTTCAC 57.617 39.130 4.57 1.88 35.04 3.18
2612 2701 5.075493 AGTTTTGATGGCAAGATCTTCACT 58.925 37.500 4.57 0.00 35.04 3.41
2613 2702 6.240894 AGTTTTGATGGCAAGATCTTCACTA 58.759 36.000 4.57 0.00 35.04 2.74
2614 2703 6.150140 AGTTTTGATGGCAAGATCTTCACTAC 59.850 38.462 4.57 1.65 35.04 2.73
2615 2704 4.142609 TGATGGCAAGATCTTCACTACC 57.857 45.455 4.57 3.27 0.00 3.18
2616 2705 3.519107 TGATGGCAAGATCTTCACTACCA 59.481 43.478 4.57 8.81 0.00 3.25
2617 2706 3.616956 TGGCAAGATCTTCACTACCAG 57.383 47.619 4.57 0.00 0.00 4.00
2618 2707 2.237143 TGGCAAGATCTTCACTACCAGG 59.763 50.000 4.57 0.00 0.00 4.45
2619 2708 2.501723 GGCAAGATCTTCACTACCAGGA 59.498 50.000 4.57 0.00 0.00 3.86
2620 2709 3.135530 GGCAAGATCTTCACTACCAGGAT 59.864 47.826 4.57 0.00 0.00 3.24
2621 2710 4.376146 GCAAGATCTTCACTACCAGGATC 58.624 47.826 4.57 0.00 34.69 3.36
2622 2711 4.615949 CAAGATCTTCACTACCAGGATCG 58.384 47.826 4.57 0.00 38.15 3.69
2623 2712 3.226777 AGATCTTCACTACCAGGATCGG 58.773 50.000 0.00 0.00 38.15 4.18
2624 2713 2.820728 TCTTCACTACCAGGATCGGA 57.179 50.000 0.00 0.00 0.00 4.55
2625 2714 3.314307 TCTTCACTACCAGGATCGGAT 57.686 47.619 0.00 0.00 0.00 4.18
2626 2715 3.643237 TCTTCACTACCAGGATCGGATT 58.357 45.455 0.00 0.00 0.00 3.01
2627 2716 3.637229 TCTTCACTACCAGGATCGGATTC 59.363 47.826 0.00 0.00 0.00 2.52
2628 2717 3.314307 TCACTACCAGGATCGGATTCT 57.686 47.619 0.00 0.00 0.00 2.40
2629 2718 2.959030 TCACTACCAGGATCGGATTCTG 59.041 50.000 17.82 17.82 0.00 3.02
2630 2719 2.959030 CACTACCAGGATCGGATTCTGA 59.041 50.000 24.83 7.55 0.00 3.27
2631 2720 3.384789 CACTACCAGGATCGGATTCTGAA 59.615 47.826 24.83 12.87 0.00 3.02
2632 2721 4.039730 CACTACCAGGATCGGATTCTGAAT 59.960 45.833 24.83 15.57 0.00 2.57
2646 2735 7.710907 TCGGATTCTGAATCAAATCGTAGAATT 59.289 33.333 26.60 0.00 39.07 2.17
2650 2739 9.708222 ATTCTGAATCAAATCGTAGAATTTTCG 57.292 29.630 0.00 0.00 43.58 3.46
2660 2749 4.082081 TCGTAGAATTTTCGCTACCAGGAA 60.082 41.667 0.00 0.00 34.84 3.36
2661 2750 4.809426 CGTAGAATTTTCGCTACCAGGAAT 59.191 41.667 0.00 0.00 34.84 3.01
2664 2753 4.636206 AGAATTTTCGCTACCAGGAATGTC 59.364 41.667 0.00 0.00 0.00 3.06
2673 2762 5.116882 GCTACCAGGAATGTCGAAAAGTAT 58.883 41.667 0.00 0.00 0.00 2.12
2675 2764 6.929606 GCTACCAGGAATGTCGAAAAGTATAT 59.070 38.462 0.00 0.00 0.00 0.86
2714 2803 6.853720 TCGTAGAATCAGAGGAGTTAGTTTG 58.146 40.000 0.00 0.00 0.00 2.93
2716 2805 6.127703 CGTAGAATCAGAGGAGTTAGTTTGGA 60.128 42.308 0.00 0.00 0.00 3.53
2756 2845 9.793259 AACCTTGTAATGAGAACTTTGAATCTA 57.207 29.630 0.00 0.00 0.00 1.98
2871 2965 2.989253 TCGGCGTTGCTGAGAGGA 60.989 61.111 6.85 0.00 39.19 3.71
2911 3005 0.533085 TGTTCCGTTGCATCAACCGA 60.533 50.000 4.35 1.21 40.82 4.69
2986 3097 1.138859 CACCATCATCCTTGTCGCCTA 59.861 52.381 0.00 0.00 0.00 3.93
2987 3098 1.414181 ACCATCATCCTTGTCGCCTAG 59.586 52.381 0.00 0.00 0.00 3.02
2988 3099 1.414181 CCATCATCCTTGTCGCCTAGT 59.586 52.381 0.00 0.00 0.00 2.57
2989 3100 2.158900 CCATCATCCTTGTCGCCTAGTT 60.159 50.000 0.00 0.00 0.00 2.24
2990 3101 3.535561 CATCATCCTTGTCGCCTAGTTT 58.464 45.455 0.00 0.00 0.00 2.66
2991 3102 3.247006 TCATCCTTGTCGCCTAGTTTC 57.753 47.619 0.00 0.00 0.00 2.78
2992 3103 2.832129 TCATCCTTGTCGCCTAGTTTCT 59.168 45.455 0.00 0.00 0.00 2.52
2993 3104 4.021229 TCATCCTTGTCGCCTAGTTTCTA 58.979 43.478 0.00 0.00 0.00 2.10
2994 3105 3.863142 TCCTTGTCGCCTAGTTTCTAC 57.137 47.619 0.00 0.00 0.00 2.59
2995 3106 2.494870 TCCTTGTCGCCTAGTTTCTACC 59.505 50.000 0.00 0.00 0.00 3.18
2996 3107 2.232941 CCTTGTCGCCTAGTTTCTACCA 59.767 50.000 0.00 0.00 0.00 3.25
2997 3108 3.118738 CCTTGTCGCCTAGTTTCTACCAT 60.119 47.826 0.00 0.00 0.00 3.55
2998 3109 4.098960 CCTTGTCGCCTAGTTTCTACCATA 59.901 45.833 0.00 0.00 0.00 2.74
2999 3110 5.221461 CCTTGTCGCCTAGTTTCTACCATAT 60.221 44.000 0.00 0.00 0.00 1.78
3010 3121 9.838339 CTAGTTTCTACCATATCCACTGAAAAT 57.162 33.333 0.00 0.00 0.00 1.82
3034 3145 2.476185 GCAAACGGTGTGTAGATGATGC 60.476 50.000 0.00 0.00 0.00 3.91
3098 3211 0.323725 ATTGGCGTTGGAATCAGGCT 60.324 50.000 0.00 0.00 0.00 4.58
3190 7732 1.235724 ACTGGTACAAAAAGAGCGGC 58.764 50.000 0.00 0.00 38.70 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.749620 GCATGTCATTGCATTAGAGAAGAG 58.250 41.667 0.00 0.00 42.31 2.85
1 2 5.746307 GCATGTCATTGCATTAGAGAAGA 57.254 39.130 0.00 0.00 42.31 2.87
23 24 5.596268 TTGCTAGAATACGCATAAGCATG 57.404 39.130 0.00 0.00 39.50 4.06
24 25 6.618287 TTTTGCTAGAATACGCATAAGCAT 57.382 33.333 0.00 0.00 39.50 3.79
25 26 6.429791 TTTTTGCTAGAATACGCATAAGCA 57.570 33.333 0.00 0.00 42.27 3.91
57 58 9.221933 TCAACTCGTAACCATACATATTTTTGT 57.778 29.630 0.00 0.00 32.02 2.83
62 63 9.221933 TGTTTTCAACTCGTAACCATACATATT 57.778 29.630 0.00 0.00 32.02 1.28
190 198 2.436115 GCCGGTTACCACAGCTCC 60.436 66.667 1.90 0.00 0.00 4.70
212 220 5.473504 GGTAAAAATGGAGAGAACTCAAGCA 59.526 40.000 4.64 0.00 44.22 3.91
222 230 4.272489 TGGAGCATGGTAAAAATGGAGAG 58.728 43.478 0.00 0.00 0.00 3.20
289 300 1.597027 GGTGTCTGTCAACGTGGGG 60.597 63.158 0.00 0.00 0.00 4.96
296 307 1.140852 CAAGGTCAGGGTGTCTGTCAA 59.859 52.381 0.00 0.00 43.76 3.18
297 308 0.758734 CAAGGTCAGGGTGTCTGTCA 59.241 55.000 0.00 0.00 43.76 3.58
299 310 1.141053 GTTCAAGGTCAGGGTGTCTGT 59.859 52.381 0.00 0.00 43.76 3.41
325 336 1.500512 GGTTAAAGCGCCACGTGTGA 61.501 55.000 15.65 0.00 0.00 3.58
360 384 2.561478 TTGGATAAGATTAGGGCCGC 57.439 50.000 0.00 0.00 0.00 6.53
362 386 7.122799 GGATATGTTTTGGATAAGATTAGGGCC 59.877 40.741 0.00 0.00 0.00 5.80
462 495 1.226323 GTGTCGTCCGTCGGATCAG 60.226 63.158 18.75 12.20 40.32 2.90
475 508 1.623081 CGTGGGGTGAATTCGTGTCG 61.623 60.000 0.04 0.00 0.00 4.35
477 510 1.448497 ACGTGGGGTGAATTCGTGT 59.552 52.632 0.04 0.00 33.55 4.49
507 540 2.931246 TTTTTACCGTCTTCGCCCC 58.069 52.632 0.00 0.00 35.54 5.80
543 577 0.599204 AACGAAGCGAGGAAAAGCGA 60.599 50.000 0.00 0.00 38.61 4.93
1185 1222 4.767255 CCGACCTGTCCAGCAGCC 62.767 72.222 0.00 0.00 43.71 4.85
1248 1285 5.890334 ACTGAAATCTCAAGATCTCGTCTC 58.110 41.667 0.00 0.00 35.67 3.36
1321 1359 7.547722 CACCAGCTAAAAACCAAAACTAAAACT 59.452 33.333 0.00 0.00 0.00 2.66
1322 1360 7.201574 CCACCAGCTAAAAACCAAAACTAAAAC 60.202 37.037 0.00 0.00 0.00 2.43
1323 1361 6.819146 CCACCAGCTAAAAACCAAAACTAAAA 59.181 34.615 0.00 0.00 0.00 1.52
1333 1375 2.003937 TTCCCCACCAGCTAAAAACC 57.996 50.000 0.00 0.00 0.00 3.27
1469 1519 0.179026 CGGACTCGACCTCCCTCATA 60.179 60.000 0.00 0.00 39.00 2.15
1594 1644 1.241990 GGGGTTTCGGCCAAGAACTC 61.242 60.000 2.24 3.70 0.00 3.01
1596 1646 2.273179 GGGGGTTTCGGCCAAGAAC 61.273 63.158 2.24 3.79 0.00 3.01
1621 1671 2.632377 TCAGAATCAGATTGCCGGAAC 58.368 47.619 5.05 0.00 0.00 3.62
1623 1673 3.009723 GTTTCAGAATCAGATTGCCGGA 58.990 45.455 5.05 0.00 0.00 5.14
1625 1675 3.730061 GCAGTTTCAGAATCAGATTGCCG 60.730 47.826 0.00 0.00 0.00 5.69
1626 1676 3.730061 CGCAGTTTCAGAATCAGATTGCC 60.730 47.826 0.00 0.00 0.00 4.52
1627 1677 3.125829 TCGCAGTTTCAGAATCAGATTGC 59.874 43.478 0.00 0.00 0.00 3.56
1628 1678 4.645956 GTCGCAGTTTCAGAATCAGATTG 58.354 43.478 0.00 0.00 0.00 2.67
1630 1680 2.926200 CGTCGCAGTTTCAGAATCAGAT 59.074 45.455 0.00 0.00 0.00 2.90
1639 1689 3.835378 TGAGTATACGTCGCAGTTTCA 57.165 42.857 0.00 0.00 0.00 2.69
1640 1690 3.000971 GCTTGAGTATACGTCGCAGTTTC 60.001 47.826 0.00 0.00 0.00 2.78
1642 1693 2.527100 GCTTGAGTATACGTCGCAGTT 58.473 47.619 0.00 0.00 0.00 3.16
1648 1699 3.421231 CCGAATTCGCTTGAGTATACGTC 59.579 47.826 22.36 0.00 38.18 4.34
1677 1728 1.297378 CTGCGCAATCTGCACATCG 60.297 57.895 13.05 0.00 45.36 3.84
1842 1894 1.539827 GTGAGGCTTACGGTTGCATTT 59.460 47.619 0.00 0.00 0.00 2.32
1857 1909 8.571336 ACAAAAGAAGAAACATAATCAGTGAGG 58.429 33.333 0.00 0.00 0.00 3.86
1864 1916 9.827411 GTAGTGGACAAAAGAAGAAACATAATC 57.173 33.333 0.00 0.00 0.00 1.75
1867 1919 8.740123 TTGTAGTGGACAAAAGAAGAAACATA 57.260 30.769 0.00 0.00 45.23 2.29
1868 1920 7.639113 TTGTAGTGGACAAAAGAAGAAACAT 57.361 32.000 0.00 0.00 45.23 2.71
1884 1936 8.783093 TGTCTGAAGAACATATTTTTGTAGTGG 58.217 33.333 0.00 0.00 0.00 4.00
1886 1938 8.495949 CGTGTCTGAAGAACATATTTTTGTAGT 58.504 33.333 0.00 0.00 0.00 2.73
1887 1939 8.495949 ACGTGTCTGAAGAACATATTTTTGTAG 58.504 33.333 0.00 0.00 0.00 2.74
1888 1940 8.373048 ACGTGTCTGAAGAACATATTTTTGTA 57.627 30.769 0.00 0.00 0.00 2.41
1889 1941 7.259290 ACGTGTCTGAAGAACATATTTTTGT 57.741 32.000 0.00 0.00 0.00 2.83
1890 1942 8.560576 AAACGTGTCTGAAGAACATATTTTTG 57.439 30.769 0.00 0.00 0.00 2.44
1892 1944 9.878599 CTTAAACGTGTCTGAAGAACATATTTT 57.121 29.630 0.00 0.00 0.00 1.82
1896 1954 8.085909 TCATCTTAAACGTGTCTGAAGAACATA 58.914 33.333 0.00 0.00 30.41 2.29
2058 2121 0.251787 ATTCCAGGTCCCTGTTTGCC 60.252 55.000 12.20 0.00 42.15 4.52
2121 2187 1.696336 GAGGCAGCTTCCATCTGGATA 59.304 52.381 4.85 0.00 44.98 2.59
2226 2292 3.875727 TGGTCTCGAGTTACTATCTTCCG 59.124 47.826 13.13 0.00 0.00 4.30
2256 2322 0.251916 TCTGTACAGAAATGGCCGGG 59.748 55.000 23.24 0.00 33.91 5.73
2281 2347 7.250569 ACTCAATACAACACACAACAAAAGAG 58.749 34.615 0.00 0.00 0.00 2.85
2305 2372 0.458543 TGCGATTCTGCCTCTCGAAC 60.459 55.000 0.00 0.00 34.41 3.95
2388 2457 3.134623 AGGATTACCATGATGAGCAACGA 59.865 43.478 0.00 0.00 38.94 3.85
2457 2541 5.207110 ACTAGAATTCATGGAGATGGTCG 57.793 43.478 8.44 0.00 0.00 4.79
2460 2544 7.961351 AGAGTAACTAGAATTCATGGAGATGG 58.039 38.462 8.44 0.00 0.00 3.51
2488 2577 8.970859 AGAAAGAACAATCTCAGAGAAAGAAA 57.029 30.769 3.63 0.00 33.77 2.52
2515 2604 1.254975 TTCCGCCTCCGACAATCTCA 61.255 55.000 0.00 0.00 36.29 3.27
2516 2605 0.108329 TTTCCGCCTCCGACAATCTC 60.108 55.000 0.00 0.00 36.29 2.75
2522 2611 0.168128 CACATTTTTCCGCCTCCGAC 59.832 55.000 0.00 0.00 36.29 4.79
2523 2612 0.958382 CCACATTTTTCCGCCTCCGA 60.958 55.000 0.00 0.00 36.29 4.55
2524 2613 1.506262 CCACATTTTTCCGCCTCCG 59.494 57.895 0.00 0.00 0.00 4.63
2525 2614 1.215382 GCCACATTTTTCCGCCTCC 59.785 57.895 0.00 0.00 0.00 4.30
2526 2615 1.132453 GTAGCCACATTTTTCCGCCTC 59.868 52.381 0.00 0.00 0.00 4.70
2532 2621 3.494045 GCCTCAGTAGCCACATTTTTC 57.506 47.619 0.00 0.00 0.00 2.29
2543 2632 3.452627 ACCTTGTCATTAGGCCTCAGTAG 59.547 47.826 9.68 0.00 36.17 2.57
2575 2664 6.460676 GCCATCAAAACTCCAATCCTATTGAG 60.461 42.308 1.23 0.00 0.00 3.02
2577 2666 5.127519 TGCCATCAAAACTCCAATCCTATTG 59.872 40.000 0.00 0.00 0.00 1.90
2581 2670 3.173953 TGCCATCAAAACTCCAATCCT 57.826 42.857 0.00 0.00 0.00 3.24
2586 2675 4.038271 AGATCTTGCCATCAAAACTCCA 57.962 40.909 0.00 0.00 0.00 3.86
2587 2676 4.460382 TGAAGATCTTGCCATCAAAACTCC 59.540 41.667 14.00 0.00 0.00 3.85
2591 2680 5.415701 GGTAGTGAAGATCTTGCCATCAAAA 59.584 40.000 14.00 0.00 0.00 2.44
2598 2687 2.501723 TCCTGGTAGTGAAGATCTTGCC 59.498 50.000 14.00 2.19 0.00 4.52
2599 2688 3.895232 TCCTGGTAGTGAAGATCTTGC 57.105 47.619 14.00 5.61 0.00 4.01
2602 2691 3.117474 TCCGATCCTGGTAGTGAAGATCT 60.117 47.826 0.00 0.00 32.87 2.75
2607 2696 3.384789 CAGAATCCGATCCTGGTAGTGAA 59.615 47.826 0.00 0.00 0.00 3.18
2608 2697 2.959030 CAGAATCCGATCCTGGTAGTGA 59.041 50.000 0.00 0.00 0.00 3.41
2609 2698 2.959030 TCAGAATCCGATCCTGGTAGTG 59.041 50.000 0.00 0.00 0.00 2.74
2610 2699 3.314307 TCAGAATCCGATCCTGGTAGT 57.686 47.619 0.00 0.00 0.00 2.73
2611 2700 4.281941 TGATTCAGAATCCGATCCTGGTAG 59.718 45.833 18.80 0.00 37.09 3.18
2612 2701 4.223144 TGATTCAGAATCCGATCCTGGTA 58.777 43.478 18.80 0.00 37.09 3.25
2613 2702 3.041211 TGATTCAGAATCCGATCCTGGT 58.959 45.455 18.80 0.00 37.09 4.00
2614 2703 3.758755 TGATTCAGAATCCGATCCTGG 57.241 47.619 18.80 0.00 37.09 4.45
2615 2704 5.107182 CGATTTGATTCAGAATCCGATCCTG 60.107 44.000 18.80 7.95 37.09 3.86
2616 2705 4.993584 CGATTTGATTCAGAATCCGATCCT 59.006 41.667 18.80 0.25 37.09 3.24
2617 2706 4.752101 ACGATTTGATTCAGAATCCGATCC 59.248 41.667 18.80 5.46 37.09 3.36
2618 2707 5.914085 ACGATTTGATTCAGAATCCGATC 57.086 39.130 18.80 18.24 37.09 3.69
2619 2708 6.749139 TCTACGATTTGATTCAGAATCCGAT 58.251 36.000 18.80 12.77 37.09 4.18
2620 2709 6.144078 TCTACGATTTGATTCAGAATCCGA 57.856 37.500 18.80 8.90 37.09 4.55
2621 2710 6.828502 TTCTACGATTTGATTCAGAATCCG 57.171 37.500 18.80 16.38 37.09 4.18
2624 2713 9.708222 CGAAAATTCTACGATTTGATTCAGAAT 57.292 29.630 0.00 0.00 34.95 2.40
2625 2714 7.692291 GCGAAAATTCTACGATTTGATTCAGAA 59.308 33.333 0.00 0.00 30.06 3.02
2626 2715 7.064609 AGCGAAAATTCTACGATTTGATTCAGA 59.935 33.333 0.00 0.00 30.06 3.27
2627 2716 7.182761 AGCGAAAATTCTACGATTTGATTCAG 58.817 34.615 0.00 0.00 30.06 3.02
2628 2717 7.072177 AGCGAAAATTCTACGATTTGATTCA 57.928 32.000 0.00 0.00 30.06 2.57
2629 2718 7.583040 GGTAGCGAAAATTCTACGATTTGATTC 59.417 37.037 0.00 0.00 36.82 2.52
2630 2719 7.065324 TGGTAGCGAAAATTCTACGATTTGATT 59.935 33.333 0.00 0.00 36.82 2.57
2631 2720 6.537301 TGGTAGCGAAAATTCTACGATTTGAT 59.463 34.615 0.00 0.00 36.82 2.57
2632 2721 5.870433 TGGTAGCGAAAATTCTACGATTTGA 59.130 36.000 0.00 0.00 36.82 2.69
2646 2735 1.546923 TCGACATTCCTGGTAGCGAAA 59.453 47.619 0.00 0.00 0.00 3.46
2650 2739 3.335579 ACTTTTCGACATTCCTGGTAGC 58.664 45.455 0.00 0.00 0.00 3.58
2687 2776 7.648039 ACTAACTCCTCTGATTCTACGATTT 57.352 36.000 0.00 0.00 0.00 2.17
2701 2790 6.881602 AGAATCACAATCCAAACTAACTCCTC 59.118 38.462 0.00 0.00 0.00 3.71
2703 2792 6.655003 TCAGAATCACAATCCAAACTAACTCC 59.345 38.462 0.00 0.00 0.00 3.85
2714 2803 4.520492 ACAAGGTTGTCAGAATCACAATCC 59.480 41.667 0.00 0.00 35.75 3.01
2716 2805 7.448161 TCATTACAAGGTTGTCAGAATCACAAT 59.552 33.333 0.00 0.00 42.35 2.71
2858 2947 1.301677 GGCCTTTCCTCTCAGCAACG 61.302 60.000 0.00 0.00 0.00 4.10
2869 2963 2.094026 CACAGCTTTTATGGGCCTTTCC 60.094 50.000 4.53 0.00 0.00 3.13
2871 2965 2.888212 TCACAGCTTTTATGGGCCTTT 58.112 42.857 4.53 0.00 0.00 3.11
2911 3005 2.627515 ATGCTTATCGTCACCATGCT 57.372 45.000 0.00 0.00 0.00 3.79
2986 3097 8.328758 TCATTTTCAGTGGATATGGTAGAAACT 58.671 33.333 2.41 0.00 0.00 2.66
2987 3098 8.506168 TCATTTTCAGTGGATATGGTAGAAAC 57.494 34.615 2.41 0.00 0.00 2.78
2988 3099 7.283127 GCTCATTTTCAGTGGATATGGTAGAAA 59.717 37.037 2.41 0.00 0.00 2.52
2989 3100 6.767902 GCTCATTTTCAGTGGATATGGTAGAA 59.232 38.462 2.41 0.00 0.00 2.10
2990 3101 6.126796 TGCTCATTTTCAGTGGATATGGTAGA 60.127 38.462 2.41 0.00 0.00 2.59
2991 3102 6.057533 TGCTCATTTTCAGTGGATATGGTAG 58.942 40.000 2.41 0.00 0.00 3.18
2992 3103 6.000246 TGCTCATTTTCAGTGGATATGGTA 58.000 37.500 2.41 0.00 0.00 3.25
2993 3104 4.858850 TGCTCATTTTCAGTGGATATGGT 58.141 39.130 2.41 0.00 0.00 3.55
2994 3105 5.840243 TTGCTCATTTTCAGTGGATATGG 57.160 39.130 2.41 0.00 0.00 2.74
2995 3106 5.740569 CGTTTGCTCATTTTCAGTGGATATG 59.259 40.000 0.00 0.00 0.00 1.78
2996 3107 5.163622 CCGTTTGCTCATTTTCAGTGGATAT 60.164 40.000 0.00 0.00 0.00 1.63
2997 3108 4.155826 CCGTTTGCTCATTTTCAGTGGATA 59.844 41.667 0.00 0.00 0.00 2.59
2998 3109 3.057315 CCGTTTGCTCATTTTCAGTGGAT 60.057 43.478 0.00 0.00 0.00 3.41
2999 3110 2.293122 CCGTTTGCTCATTTTCAGTGGA 59.707 45.455 0.00 0.00 0.00 4.02
3010 3121 2.036604 TCATCTACACACCGTTTGCTCA 59.963 45.455 0.00 0.00 0.00 4.26
3034 3145 1.650912 GTTAGCGCATGGGCATGAG 59.349 57.895 33.01 0.00 41.20 2.90
3084 3197 1.081892 CTGTGAGCCTGATTCCAACG 58.918 55.000 0.00 0.00 0.00 4.10
3098 3211 3.270027 CCGATTTCCTATGCAACTGTGA 58.730 45.455 0.00 0.00 0.00 3.58
3181 7723 1.451028 GCTCATCTGGCCGCTCTTT 60.451 57.895 0.00 0.00 0.00 2.52
3182 7724 1.908340 AAGCTCATCTGGCCGCTCTT 61.908 55.000 0.00 0.00 31.30 2.85


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

AutoCloner maintained by Alex Coulton.