Multiple sequence alignment - TraesCS2D01G309400

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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 TraesCS2D01G309400 chr2D 100.000 4783 0 0 1 4783 396673315 396668533 0.000000e+00 8833.0
1 TraesCS2D01G309400 chr2D 92.771 83 5 1 1 83 340755717 340755636 8.410000e-23 119.0
2 TraesCS2D01G309400 chr2D 89.247 93 8 2 1 91 347707584 347707492 1.090000e-21 115.0
3 TraesCS2D01G309400 chr2A 97.495 3234 77 2 1547 4777 534633927 534630695 0.000000e+00 5520.0
4 TraesCS2D01G309400 chr2A 92.152 446 19 5 1049 1485 534634384 534633946 2.450000e-172 616.0
5 TraesCS2D01G309400 chr2A 92.672 232 12 4 738 968 534634792 534634565 3.570000e-86 329.0
6 TraesCS2D01G309400 chr2A 81.423 253 35 8 73 314 95264108 95264359 3.780000e-46 196.0
7 TraesCS2D01G309400 chr2B 93.329 2983 133 32 1594 4562 470067883 470064953 0.000000e+00 4346.0
8 TraesCS2D01G309400 chr2B 90.000 330 25 5 1001 1330 470068485 470068164 2.060000e-113 420.0
9 TraesCS2D01G309400 chr2B 96.970 231 6 1 4547 4777 470064906 470064677 2.090000e-103 387.0
10 TraesCS2D01G309400 chr2B 94.737 95 3 2 875 968 470068738 470068645 3.860000e-31 147.0
11 TraesCS2D01G309400 chr2B 92.233 103 6 2 750 851 470068973 470068872 1.390000e-30 145.0
12 TraesCS2D01G309400 chr3D 95.441 680 30 1 65 744 387256336 387257014 0.000000e+00 1083.0
13 TraesCS2D01G309400 chr3D 92.683 82 3 3 1 82 475961497 475961419 1.090000e-21 115.0
14 TraesCS2D01G309400 chr6D 86.300 781 96 8 2935 3706 411616114 411615336 0.000000e+00 839.0
15 TraesCS2D01G309400 chr6D 88.277 708 47 9 65 746 19521086 19520389 0.000000e+00 815.0
16 TraesCS2D01G309400 chr6D 81.157 605 78 17 4034 4625 411615087 411614506 2.030000e-123 453.0
17 TraesCS2D01G309400 chr6D 79.898 393 65 11 2370 2754 411616925 411616539 4.720000e-70 276.0
18 TraesCS2D01G309400 chr6D 85.714 224 22 5 1839 2053 411617427 411617205 1.340000e-55 228.0
19 TraesCS2D01G309400 chr6D 90.683 161 15 0 2175 2335 411617207 411617047 1.040000e-51 215.0
20 TraesCS2D01G309400 chr6D 90.566 53 5 0 3775 3827 411615172 411615120 2.390000e-08 71.3
21 TraesCS2D01G309400 chr6B 89.173 665 43 10 65 701 482468514 482469177 0.000000e+00 802.0
22 TraesCS2D01G309400 chr6B 86.047 731 97 4 2968 3693 618943154 618942424 0.000000e+00 780.0
23 TraesCS2D01G309400 chr6B 81.402 328 56 4 2430 2754 618943976 618943651 3.670000e-66 263.0
24 TraesCS2D01G309400 chr6B 76.723 537 60 24 73 550 37050745 37050215 6.190000e-59 239.0
25 TraesCS2D01G309400 chr6B 90.000 180 15 2 1876 2053 618944472 618944294 3.720000e-56 230.0
26 TraesCS2D01G309400 chr6B 91.411 163 14 0 2175 2337 618944296 618944134 1.730000e-54 224.0
27 TraesCS2D01G309400 chr6B 83.333 162 20 5 3759 3914 618942152 618941992 4.990000e-30 143.0
28 TraesCS2D01G309400 chr6A 84.248 838 115 10 2872 3693 556532211 556531375 0.000000e+00 800.0
29 TraesCS2D01G309400 chr6A 82.537 607 72 18 4031 4620 556531076 556530487 1.990000e-138 503.0
30 TraesCS2D01G309400 chr6A 80.457 394 64 10 2370 2754 556532942 556532553 6.060000e-74 289.0
31 TraesCS2D01G309400 chr6A 87.302 189 20 2 1869 2053 556533402 556533214 3.750000e-51 213.0
32 TraesCS2D01G309400 chr6A 88.415 164 15 3 2175 2337 556533216 556533056 1.360000e-45 195.0
33 TraesCS2D01G309400 chr6A 87.879 132 9 5 3787 3914 556531209 556531081 1.070000e-31 148.0
34 TraesCS2D01G309400 chr4D 85.835 593 55 11 182 746 372833112 372832521 1.900000e-168 603.0
35 TraesCS2D01G309400 chr4D 87.255 510 37 9 67 549 372833837 372833329 1.500000e-154 556.0
36 TraesCS2D01G309400 chr4D 84.843 508 29 15 67 549 372835099 372834615 7.250000e-128 468.0
37 TraesCS2D01G309400 chr4D 85.326 184 25 2 83 265 12150820 12150638 6.320000e-44 189.0
38 TraesCS2D01G309400 chr5D 77.206 544 61 26 65 550 493686430 493686968 4.750000e-65 259.0
39 TraesCS2D01G309400 chr5D 90.698 86 7 1 1 85 479272282 479272197 3.910000e-21 113.0
40 TraesCS2D01G309400 chr5D 89.130 92 4 4 1 92 389333669 389333584 5.060000e-20 110.0
41 TraesCS2D01G309400 chr5B 76.493 536 61 30 73 550 382364224 382363696 1.040000e-56 231.0
42 TraesCS2D01G309400 chr5B 92.683 82 4 2 1 81 549430191 549430111 3.020000e-22 117.0
43 TraesCS2D01G309400 chr5B 92.683 82 4 2 1 81 549463852 549463772 3.020000e-22 117.0
44 TraesCS2D01G309400 chr7A 96.053 76 3 0 1 76 729764362 729764437 1.810000e-24 124.0
45 TraesCS2D01G309400 chr4A 95.833 72 3 0 1 72 438263624 438263695 3.020000e-22 117.0
46 TraesCS2D01G309400 chr4A 100.000 29 0 0 718 746 357696207 357696179 2.000000e-03 54.7
47 TraesCS2D01G309400 chr1A 97.222 36 0 1 715 749 312863476 312863511 5.170000e-05 60.2


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 TraesCS2D01G309400 chr2D 396668533 396673315 4782 True 8833.000000 8833 100.000000 1 4783 1 chr2D.!!$R3 4782
1 TraesCS2D01G309400 chr2A 534630695 534634792 4097 True 2155.000000 5520 94.106333 738 4777 3 chr2A.!!$R1 4039
2 TraesCS2D01G309400 chr2B 470064677 470068973 4296 True 1089.000000 4346 93.453800 750 4777 5 chr2B.!!$R1 4027
3 TraesCS2D01G309400 chr3D 387256336 387257014 678 False 1083.000000 1083 95.441000 65 744 1 chr3D.!!$F1 679
4 TraesCS2D01G309400 chr6D 19520389 19521086 697 True 815.000000 815 88.277000 65 746 1 chr6D.!!$R1 681
5 TraesCS2D01G309400 chr6D 411614506 411617427 2921 True 347.050000 839 85.719667 1839 4625 6 chr6D.!!$R2 2786
6 TraesCS2D01G309400 chr6B 482468514 482469177 663 False 802.000000 802 89.173000 65 701 1 chr6B.!!$F1 636
7 TraesCS2D01G309400 chr6B 618941992 618944472 2480 True 328.000000 780 86.438600 1876 3914 5 chr6B.!!$R2 2038
8 TraesCS2D01G309400 chr6B 37050215 37050745 530 True 239.000000 239 76.723000 73 550 1 chr6B.!!$R1 477
9 TraesCS2D01G309400 chr6A 556530487 556533402 2915 True 358.000000 800 85.139667 1869 4620 6 chr6A.!!$R1 2751
10 TraesCS2D01G309400 chr4D 372832521 372835099 2578 True 542.333333 603 85.977667 67 746 3 chr4D.!!$R2 679
11 TraesCS2D01G309400 chr5D 493686430 493686968 538 False 259.000000 259 77.206000 65 550 1 chr5D.!!$F1 485
12 TraesCS2D01G309400 chr5B 382363696 382364224 528 True 231.000000 231 76.493000 73 550 1 chr5B.!!$R1 477

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
898 2945 0.252239 TGTGGCCAGCTCTTCCTCTA 60.252 55.000 5.11 0.0 0.00 2.43 F
1103 3286 0.037232 CTTTCCCACAGGTCCGTCTC 60.037 60.000 0.00 0.0 0.00 3.36 F
1399 3586 0.105778 GTCTGGATACTGCTGCCCTC 59.894 60.000 0.00 0.0 35.12 4.30 F
1789 4052 1.202818 GGGATATGGGAAGGAGTGTGC 60.203 57.143 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 4032 1.202818 GCACACTCCTTCCCATATCCC 60.203 57.143 0.00 0.0 0.0 3.85 R
1919 4193 1.669115 CTCCCTTGTCAGTGGTGCG 60.669 63.158 0.00 0.0 0.0 5.34 R
2654 5026 3.707102 GCCTAGGAGTTGAGATTGTAGGT 59.293 47.826 14.75 0.0 0.0 3.08 R
3785 6736 1.686052 TGTGTGGGATTGGCAAGAAAC 59.314 47.619 5.96 2.3 0.0 2.78 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
51 52 7.839680 AACCATTTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53
334 1623 6.739331 TTTTCTTTTGGATAGCTTTTGGGA 57.261 33.333 0.00 0.00 0.00 4.37
501 1825 2.215942 AAACTGGGGGAAAAGGATCG 57.784 50.000 0.00 0.00 0.00 3.69
602 2538 1.771565 TGGGTCGAGAATACCGTCAT 58.228 50.000 0.00 0.00 37.93 3.06
609 2545 7.394077 TGGGTCGAGAATACCGTCATATATAAA 59.606 37.037 0.00 0.00 37.93 1.40
640 2576 7.461749 ACTTCTCCTGGATGATTTTGTAAAGA 58.538 34.615 0.00 0.00 0.00 2.52
729 2665 2.680312 AGTCTAGACGTGCATTGCAT 57.320 45.000 15.49 0.00 41.91 3.96
749 2685 6.481954 GCATGTGCAAACTTACTAGTACTT 57.518 37.500 0.00 0.00 41.59 2.24
750 2686 6.534934 GCATGTGCAAACTTACTAGTACTTC 58.465 40.000 0.00 0.00 41.59 3.01
751 2687 6.369065 GCATGTGCAAACTTACTAGTACTTCT 59.631 38.462 0.00 0.00 41.59 2.85
752 2688 7.544566 GCATGTGCAAACTTACTAGTACTTCTA 59.455 37.037 0.00 0.00 41.59 2.10
822 2759 0.463204 CGCTGGATCTGGATGACTGT 59.537 55.000 0.00 0.00 0.00 3.55
897 2944 1.537397 TGTGGCCAGCTCTTCCTCT 60.537 57.895 5.11 0.00 0.00 3.69
898 2945 0.252239 TGTGGCCAGCTCTTCCTCTA 60.252 55.000 5.11 0.00 0.00 2.43
1080 3263 2.092375 CCCCTACAAGATGGGAAGGTTC 60.092 54.545 0.00 0.00 46.15 3.62
1103 3286 0.037232 CTTTCCCACAGGTCCGTCTC 60.037 60.000 0.00 0.00 0.00 3.36
1116 3299 2.085320 TCCGTCTCTTCTTCTTCCGAG 58.915 52.381 0.00 0.00 0.00 4.63
1176 3363 3.120095 AGCCGCCGATTTTTGTTAGTAAC 60.120 43.478 6.06 6.06 0.00 2.50
1184 3371 4.571372 TTTTTGTTAGTAACCGCCCAAG 57.429 40.909 10.51 0.00 0.00 3.61
1185 3372 3.488778 TTTGTTAGTAACCGCCCAAGA 57.511 42.857 10.51 0.00 0.00 3.02
1186 3373 3.488778 TTGTTAGTAACCGCCCAAGAA 57.511 42.857 10.51 0.00 0.00 2.52
1187 3374 3.706600 TGTTAGTAACCGCCCAAGAAT 57.293 42.857 10.51 0.00 0.00 2.40
1188 3375 3.602483 TGTTAGTAACCGCCCAAGAATC 58.398 45.455 10.51 0.00 0.00 2.52
1231 3418 1.039233 ATTTGGGGCGATTCCTGCAG 61.039 55.000 6.78 6.78 34.39 4.41
1261 3448 1.818674 CCAATTCGGGTGCTAAAGCTT 59.181 47.619 3.26 0.00 42.66 3.74
1374 3561 3.614092 TCCTGCTTTTTATCAGAGGCTG 58.386 45.455 0.00 0.00 32.26 4.85
1399 3586 0.105778 GTCTGGATACTGCTGCCCTC 59.894 60.000 0.00 0.00 35.12 4.30
1409 3596 2.328099 GCTGCCCTCCTGTTGTTCG 61.328 63.158 0.00 0.00 0.00 3.95
1445 3637 2.352388 TCAAGAACCGAATTTAGCCCG 58.648 47.619 0.00 0.00 0.00 6.13
1487 3679 4.963318 AATCGAGGAAGGAAGCATCATA 57.037 40.909 0.00 0.00 0.00 2.15
1488 3680 4.963318 ATCGAGGAAGGAAGCATCATAA 57.037 40.909 0.00 0.00 0.00 1.90
1489 3681 4.060038 TCGAGGAAGGAAGCATCATAAC 57.940 45.455 0.00 0.00 0.00 1.89
1516 3708 9.342308 CAGGTCCTATGCTGAAATCTTTTATTA 57.658 33.333 0.00 0.00 0.00 0.98
1564 3756 8.118893 ACGAAAATTAGCATGCATTTTGTATC 57.881 30.769 25.14 14.33 33.62 2.24
1591 3785 2.162608 ACAAGAGAAGTGTCGATCCGAG 59.837 50.000 0.00 0.00 36.23 4.63
1622 3885 4.892345 TGTTTCTGAATGAACATGTGGGAA 59.108 37.500 0.00 0.00 33.88 3.97
1632 3895 7.722949 ATGAACATGTGGGAAGATATTTGTT 57.277 32.000 0.00 0.00 0.00 2.83
1644 3907 7.979537 GGGAAGATATTTGTTAACCCAAATCAC 59.020 37.037 2.48 2.53 42.49 3.06
1657 3920 4.042809 ACCCAAATCACCTGTCATTACTGA 59.957 41.667 0.00 0.00 0.00 3.41
1680 3943 9.347240 CTGAACAATTATTCCATCAATAGACCT 57.653 33.333 0.00 0.00 0.00 3.85
1681 3944 9.123902 TGAACAATTATTCCATCAATAGACCTG 57.876 33.333 0.00 0.00 0.00 4.00
1750 4013 8.257306 AGTAAGTGTGGTCAACAATCAATTTTT 58.743 29.630 0.00 0.00 41.57 1.94
1769 4032 8.422457 CAATTTTTCGTCTGATGAATTTCTGTG 58.578 33.333 12.73 4.31 0.00 3.66
1771 4034 3.599343 TCGTCTGATGAATTTCTGTGGG 58.401 45.455 0.00 0.00 0.00 4.61
1789 4052 1.202818 GGGATATGGGAAGGAGTGTGC 60.203 57.143 0.00 0.00 0.00 4.57
1820 4083 2.388735 TCTTCGACTGTGCCTATGGAT 58.611 47.619 0.00 0.00 0.00 3.41
2132 4407 6.206829 AGTTTCCTCTTTGCAGTTGTATTACC 59.793 38.462 0.00 0.00 0.00 2.85
2754 5126 2.192664 TGCAATTGAAGCCGGTAAGA 57.807 45.000 10.34 0.00 0.00 2.10
3157 5856 5.135508 TGGAAGTAGTTCAAGCTGTAGTC 57.864 43.478 12.31 0.00 33.93 2.59
3643 6347 1.130054 ATCCCCACCCCATCAGATCG 61.130 60.000 0.00 0.00 0.00 3.69
3712 6660 2.355444 TCAATGCTCATGTGTATTGGCG 59.645 45.455 27.25 11.37 39.42 5.69
3769 6717 8.872845 CAATTTAAGAAGTGCAAACTGAAAAGT 58.127 29.630 0.00 0.00 0.00 2.66
3923 6878 4.842574 AGAACTTTGGTTTTGGCATGTTT 58.157 34.783 0.00 0.00 35.58 2.83
3954 6909 6.811253 AAACACGCCATCTCTTGTAAATAA 57.189 33.333 0.00 0.00 0.00 1.40
4100 7068 8.515473 ACAGAAAACTTCAGTTGTTGTTTAAC 57.485 30.769 0.00 0.00 38.44 2.01
4299 7283 9.072294 GCTTATCGTAAAAGTAATTGTGCAATT 57.928 29.630 13.68 13.68 42.95 2.32
4343 7327 5.923114 CCTGATATTACCTGACATTGTCTCG 59.077 44.000 17.26 9.65 33.15 4.04
4627 7674 5.241403 TCAAGGAAGAGCTTTCAATACCA 57.759 39.130 9.75 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
26 27 8.934023 CCCTAGAGGCAATAATAAAATGGTTA 57.066 34.615 0.00 0.00 0.00 2.85
27 28 7.839680 CCCTAGAGGCAATAATAAAATGGTT 57.160 36.000 0.00 0.00 0.00 3.67
43 44 7.823745 AATTGTTGTAAATATGCCCTAGAGG 57.176 36.000 0.00 0.00 39.47 3.69
44 45 8.902806 TCAAATTGTTGTAAATATGCCCTAGAG 58.097 33.333 0.00 0.00 36.07 2.43
45 46 8.815565 TCAAATTGTTGTAAATATGCCCTAGA 57.184 30.769 0.00 0.00 36.07 2.43
46 47 9.520204 CTTCAAATTGTTGTAAATATGCCCTAG 57.480 33.333 0.00 0.00 36.07 3.02
47 48 9.249053 TCTTCAAATTGTTGTAAATATGCCCTA 57.751 29.630 0.00 0.00 36.07 3.53
48 49 8.133024 TCTTCAAATTGTTGTAAATATGCCCT 57.867 30.769 0.00 0.00 36.07 5.19
49 50 8.947055 ATCTTCAAATTGTTGTAAATATGCCC 57.053 30.769 0.00 0.00 36.07 5.36
50 51 9.034544 GGATCTTCAAATTGTTGTAAATATGCC 57.965 33.333 0.00 0.00 36.07 4.40
51 52 9.807649 AGGATCTTCAAATTGTTGTAAATATGC 57.192 29.630 0.00 0.00 36.07 3.14
56 57 8.573035 GGTGTAGGATCTTCAAATTGTTGTAAA 58.427 33.333 0.00 0.00 36.07 2.01
57 58 7.721842 TGGTGTAGGATCTTCAAATTGTTGTAA 59.278 33.333 0.00 0.00 36.07 2.41
58 59 7.227873 TGGTGTAGGATCTTCAAATTGTTGTA 58.772 34.615 0.00 0.00 36.07 2.41
59 60 6.068010 TGGTGTAGGATCTTCAAATTGTTGT 58.932 36.000 0.00 0.00 36.07 3.32
60 61 6.430925 TCTGGTGTAGGATCTTCAAATTGTTG 59.569 38.462 0.00 0.00 35.95 3.33
61 62 6.542821 TCTGGTGTAGGATCTTCAAATTGTT 58.457 36.000 0.00 0.00 0.00 2.83
62 63 6.126863 TCTGGTGTAGGATCTTCAAATTGT 57.873 37.500 0.00 0.00 0.00 2.71
63 64 6.176183 ACTCTGGTGTAGGATCTTCAAATTG 58.824 40.000 0.00 0.00 0.00 2.32
348 1637 3.721087 ATCAGGTCCTCACGGAAAAAT 57.279 42.857 0.00 0.00 42.08 1.82
501 1825 4.045636 ACATGACCAAGTTTGAAAGCAC 57.954 40.909 0.00 0.00 0.00 4.40
564 2500 7.340743 TCGACCCAATAATTGTTGATATGGTTT 59.659 33.333 15.75 0.00 0.00 3.27
609 2545 6.882768 AAATCATCCAGGAGAAGTAGAAGT 57.117 37.500 0.00 0.00 0.00 3.01
640 2576 6.866010 TGCGTGCTATTTTCAATATCTCAT 57.134 33.333 0.00 0.00 0.00 2.90
729 2665 9.820725 TTTTAGAAGTACTAGTAAGTTTGCACA 57.179 29.630 3.61 0.00 37.15 4.57
822 2759 2.229062 CACTTCTTCGAGGTCACTGCTA 59.771 50.000 0.00 0.00 0.00 3.49
873 2811 0.536006 AAGAGCTGGCCACACACTTC 60.536 55.000 0.00 0.00 0.00 3.01
897 2944 4.554526 CGTTTTGCTTGCAAGATCACAGTA 60.555 41.667 30.39 7.46 0.00 2.74
898 2945 3.709987 GTTTTGCTTGCAAGATCACAGT 58.290 40.909 30.39 0.00 0.00 3.55
1016 3199 2.161211 GCAGTGTTGCTCATCTTCCTTC 59.839 50.000 0.00 0.00 46.95 3.46
1080 3263 0.460284 CGGACCTGTGGGAAAGATCG 60.460 60.000 0.00 0.00 36.25 3.69
1103 3286 0.610687 AGTGGGCTCGGAAGAAGAAG 59.389 55.000 0.00 0.00 41.32 2.85
1116 3299 1.339535 CCAAGGAAAGAGAGAGTGGGC 60.340 57.143 0.00 0.00 0.00 5.36
1176 3363 0.529773 TCGATTCGATTCTTGGGCGG 60.530 55.000 4.29 0.00 0.00 6.13
1231 3418 0.246360 CCCGAATTGGTTTTCCCTGC 59.754 55.000 0.00 0.00 39.73 4.85
1237 3424 3.554129 GCTTTAGCACCCGAATTGGTTTT 60.554 43.478 0.00 0.00 41.59 2.43
1293 3480 4.514401 AGTCATGTCCGGGATTAGAAAAC 58.486 43.478 0.00 0.00 0.00 2.43
1374 3561 2.675348 GCAGCAGTATCCAGACAAGAAC 59.325 50.000 0.00 0.00 0.00 3.01
1399 3586 6.017770 TGGTAAAACAAGATACGAACAACAGG 60.018 38.462 0.00 0.00 0.00 4.00
1409 3596 7.118680 TCGGTTCTTGATGGTAAAACAAGATAC 59.881 37.037 0.00 0.00 45.62 2.24
1469 3661 3.134458 GGTTATGATGCTTCCTTCCTCG 58.866 50.000 0.00 0.00 0.00 4.63
1487 3679 3.525199 AGATTTCAGCATAGGACCTGGTT 59.475 43.478 3.53 0.00 0.00 3.67
1488 3680 3.118531 AGATTTCAGCATAGGACCTGGT 58.881 45.455 3.53 0.00 0.00 4.00
1489 3681 3.853355 AGATTTCAGCATAGGACCTGG 57.147 47.619 3.53 0.00 0.00 4.45
1530 3722 5.601582 CATGCTAATTTTCGTTGTTTGCAG 58.398 37.500 0.00 0.00 37.11 4.41
1531 3723 4.084641 GCATGCTAATTTTCGTTGTTTGCA 60.085 37.500 11.37 0.00 37.81 4.08
1532 3724 4.084641 TGCATGCTAATTTTCGTTGTTTGC 60.085 37.500 20.33 0.00 0.00 3.68
1533 3725 5.573296 TGCATGCTAATTTTCGTTGTTTG 57.427 34.783 20.33 0.00 0.00 2.93
1534 3726 6.783892 AATGCATGCTAATTTTCGTTGTTT 57.216 29.167 20.33 0.00 0.00 2.83
1535 3727 6.783892 AAATGCATGCTAATTTTCGTTGTT 57.216 29.167 20.33 0.00 0.00 2.83
1536 3728 6.202570 ACAAAATGCATGCTAATTTTCGTTGT 59.797 30.769 20.13 15.04 34.55 3.32
1540 3732 8.343974 AGATACAAAATGCATGCTAATTTTCG 57.656 30.769 20.13 17.61 34.55 3.46
1564 3756 6.415280 CGGATCGACACTTCTCTTGTAAATAG 59.585 42.308 0.00 0.00 0.00 1.73
1591 3785 9.199982 ACATGTTCATTCAGAAACATCAAAATC 57.800 29.630 0.00 0.00 38.13 2.17
1632 3895 5.943416 CAGTAATGACAGGTGATTTGGGTTA 59.057 40.000 0.00 0.00 0.00 2.85
1644 3907 8.279970 TGGAATAATTGTTCAGTAATGACAGG 57.720 34.615 15.72 0.00 0.00 4.00
1657 3920 9.699410 TTCAGGTCTATTGATGGAATAATTGTT 57.301 29.630 0.00 0.00 0.00 2.83
1750 4013 3.260632 TCCCACAGAAATTCATCAGACGA 59.739 43.478 0.00 0.00 0.00 4.20
1769 4032 1.202818 GCACACTCCTTCCCATATCCC 60.203 57.143 0.00 0.00 0.00 3.85
1771 4034 1.202818 GGGCACACTCCTTCCCATATC 60.203 57.143 0.00 0.00 38.62 1.63
1789 4052 3.189287 CACAGTCGAAGAAATTTCAGGGG 59.811 47.826 19.99 6.59 39.69 4.79
1820 4083 4.243793 TGACTCCTTTTTCAGGGACAAA 57.756 40.909 0.00 0.00 44.12 2.83
1841 4104 3.679389 AGATGAGTGGCAGAATTCGTTT 58.321 40.909 0.00 0.00 0.00 3.60
1919 4193 1.669115 CTCCCTTGTCAGTGGTGCG 60.669 63.158 0.00 0.00 0.00 5.34
2251 4526 8.744568 ATCTGACAGAAAAATATTCCTCCTTC 57.255 34.615 9.70 0.00 0.00 3.46
2505 4875 3.933861 ACAAGGATGACTATGGGGTTC 57.066 47.619 0.00 0.00 0.00 3.62
2654 5026 3.707102 GCCTAGGAGTTGAGATTGTAGGT 59.293 47.826 14.75 0.00 0.00 3.08
2754 5126 5.284861 GGTTCATTACCAACCAAAAGGTT 57.715 39.130 0.00 0.00 46.92 3.50
2847 5223 4.836125 TTTGGTTGAATGAGAAGTCTGC 57.164 40.909 0.00 0.00 0.00 4.26
3157 5856 3.806521 CCTTATCAGCTCCAACTTCATCG 59.193 47.826 0.00 0.00 0.00 3.84
3568 6267 4.564821 GGCAGAAATGGGTAGTCAGTGTAA 60.565 45.833 0.00 0.00 0.00 2.41
3643 6347 8.624367 ACATAGTACTGATACATGAGGTAGAC 57.376 38.462 5.39 0.00 34.92 2.59
3769 6717 7.504238 TGGCAAGAAACCAGACTTCTTAATTTA 59.496 33.333 0.00 0.00 40.37 1.40
3785 6736 1.686052 TGTGTGGGATTGGCAAGAAAC 59.314 47.619 5.96 2.30 0.00 2.78
3923 6878 4.331968 AGAGATGGCGTGTTTTTAATGGA 58.668 39.130 0.00 0.00 0.00 3.41
3954 6909 8.924511 TCATTAAGAGACAAGAGAAACCAAAT 57.075 30.769 0.00 0.00 0.00 2.32
3968 6923 3.437049 ACGCTGCCTTTTCATTAAGAGAC 59.563 43.478 0.00 0.00 0.00 3.36
4343 7327 7.816995 CCTAATCTGTGAGCCTGATATTTACTC 59.183 40.741 0.00 0.00 32.05 2.59
4627 7674 7.453393 TCTGAACCTCACTTTTGATACAGAAT 58.547 34.615 0.00 0.00 30.65 2.40


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

AutoCloner maintained by Alex Coulton.