Multiple sequence alignment - TraesCS6A01G120900

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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 TraesCS6A01G120900 chr6A 100.000 3173 0 0 1 3173 93204411 93207583 0.000000e+00 5860.0
1 TraesCS6A01G120900 chr6A 93.048 1237 70 10 877 2103 93271528 93272758 0.000000e+00 1794.0
2 TraesCS6A01G120900 chr6A 92.066 668 30 2 2107 2751 93283832 93284499 0.000000e+00 918.0
3 TraesCS6A01G120900 chr6A 97.134 314 8 1 2754 3067 93310185 93310497 2.170000e-146 529.0
4 TraesCS6A01G120900 chr6A 97.134 314 8 1 2754 3067 93344322 93344634 2.170000e-146 529.0
5 TraesCS6A01G120900 chr6A 97.541 122 3 0 3052 3173 93311961 93312082 3.210000e-50 209.0
6 TraesCS6A01G120900 chr6A 97.541 122 3 0 3052 3173 93346096 93346217 3.210000e-50 209.0
7 TraesCS6A01G120900 chr6B 87.713 1937 139 37 877 2751 150222273 150224172 0.000000e+00 2167.0
8 TraesCS6A01G120900 chr6B 75.137 366 82 6 2390 2751 204111652 204112012 2.530000e-36 163.0
9 TraesCS6A01G120900 chr6B 92.063 63 5 0 2753 2815 150663567 150663629 4.360000e-14 89.8
10 TraesCS6A01G120900 chr6D 90.548 1132 62 17 877 1994 77624044 77625144 0.000000e+00 1456.0
11 TraesCS6A01G120900 chr6D 84.912 1246 143 25 879 2104 56928407 56927187 0.000000e+00 1218.0
12 TraesCS6A01G120900 chr6D 92.075 694 29 3 1990 2657 77625830 77626523 0.000000e+00 953.0
13 TraesCS6A01G120900 chr6D 84.724 851 103 21 7 839 281655470 281654629 0.000000e+00 826.0
14 TraesCS6A01G120900 chr6D 97.381 420 10 1 2754 3173 77663421 77663839 0.000000e+00 713.0
15 TraesCS6A01G120900 chr6D 94.681 94 5 0 2658 2751 77647744 77647837 2.550000e-31 147.0
16 TraesCS6A01G120900 chr6D 79.787 94 19 0 2658 2751 464067445 464067538 5.680000e-08 69.4
17 TraesCS6A01G120900 chr7A 87.925 853 85 12 1 839 534512860 534513708 0.000000e+00 989.0
18 TraesCS6A01G120900 chr7A 83.503 885 85 32 1 839 681427625 681428494 0.000000e+00 769.0
19 TraesCS6A01G120900 chr7A 74.217 415 77 15 2363 2751 37838919 37839329 2.550000e-31 147.0
20 TraesCS6A01G120900 chr7A 93.023 86 6 0 1 86 131036310 131036225 3.320000e-25 126.0
21 TraesCS6A01G120900 chr5A 87.251 855 89 13 1 839 92955299 92956149 0.000000e+00 957.0
22 TraesCS6A01G120900 chr5A 93.421 76 5 0 1 76 249778876 249778801 2.590000e-21 113.0
23 TraesCS6A01G120900 chr1A 86.698 842 90 17 11 839 502974957 502975789 0.000000e+00 915.0
24 TraesCS6A01G120900 chr1A 84.696 856 97 26 1 839 308680936 308681774 0.000000e+00 824.0
25 TraesCS6A01G120900 chr3D 84.696 856 94 28 6 836 346389845 346390688 0.000000e+00 821.0
26 TraesCS6A01G120900 chr4A 84.543 854 98 26 6 839 68164523 68165362 0.000000e+00 815.0
27 TraesCS6A01G120900 chr4A 87.500 56 7 0 2458 2513 189665396 189665451 7.350000e-07 65.8
28 TraesCS6A01G120900 chr5B 84.266 858 102 24 6 836 323303553 323304404 0.000000e+00 806.0
29 TraesCS6A01G120900 chr1D 84.229 856 92 26 9 839 366661430 366660593 0.000000e+00 793.0
30 TraesCS6A01G120900 chr2D 77.424 1258 230 37 889 2104 610404219 610402974 0.000000e+00 701.0
31 TraesCS6A01G120900 chr2D 77.218 1251 237 34 889 2104 610377778 610376541 0.000000e+00 688.0
32 TraesCS6A01G120900 chrUn 97.134 314 8 1 2754 3067 367858371 367858059 2.170000e-146 529.0
33 TraesCS6A01G120900 chr2A 80.032 626 114 6 1490 2104 743265932 743265307 1.340000e-123 453.0
34 TraesCS6A01G120900 chr2A 92.366 131 10 0 1 131 614151591 614151461 1.500000e-43 187.0
35 TraesCS6A01G120900 chr2A 84.524 84 13 0 2658 2741 154411071 154410988 2.030000e-12 84.2
36 TraesCS6A01G120900 chr2A 84.524 84 13 0 2658 2741 677807547 677807630 2.030000e-12 84.2
37 TraesCS6A01G120900 chr2B 77.614 612 115 17 1493 2088 41473328 41472723 5.040000e-93 351.0
38 TraesCS6A01G120900 chr7D 84.332 217 34 0 2442 2658 34745723 34745507 2.480000e-51 213.0
39 TraesCS6A01G120900 chr7D 81.122 196 34 2 2460 2655 79267168 79267360 1.520000e-33 154.0
40 TraesCS6A01G120900 chr7D 81.313 198 30 4 2460 2655 79301340 79301532 1.520000e-33 154.0
41 TraesCS6A01G120900 chr7D 79.695 197 36 3 2460 2655 79210054 79210247 4.270000e-29 139.0
42 TraesCS6A01G120900 chr7D 80.899 89 17 0 2658 2746 538898516 538898604 1.580000e-08 71.3
43 TraesCS6A01G120900 chr4B 85.965 57 8 0 2457 2513 369183715 369183659 9.500000e-06 62.1


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 TraesCS6A01G120900 chr6A 93204411 93207583 3172 False 5860.0 5860 100.0000 1 3173 1 chr6A.!!$F1 3172
1 TraesCS6A01G120900 chr6A 93271528 93272758 1230 False 1794.0 1794 93.0480 877 2103 1 chr6A.!!$F2 1226
2 TraesCS6A01G120900 chr6A 93283832 93284499 667 False 918.0 918 92.0660 2107 2751 1 chr6A.!!$F3 644
3 TraesCS6A01G120900 chr6A 93310185 93312082 1897 False 369.0 529 97.3375 2754 3173 2 chr6A.!!$F4 419
4 TraesCS6A01G120900 chr6A 93344322 93346217 1895 False 369.0 529 97.3375 2754 3173 2 chr6A.!!$F5 419
5 TraesCS6A01G120900 chr6B 150222273 150224172 1899 False 2167.0 2167 87.7130 877 2751 1 chr6B.!!$F1 1874
6 TraesCS6A01G120900 chr6D 56927187 56928407 1220 True 1218.0 1218 84.9120 879 2104 1 chr6D.!!$R1 1225
7 TraesCS6A01G120900 chr6D 77624044 77626523 2479 False 1204.5 1456 91.3115 877 2657 2 chr6D.!!$F4 1780
8 TraesCS6A01G120900 chr6D 281654629 281655470 841 True 826.0 826 84.7240 7 839 1 chr6D.!!$R2 832
9 TraesCS6A01G120900 chr7A 534512860 534513708 848 False 989.0 989 87.9250 1 839 1 chr7A.!!$F2 838
10 TraesCS6A01G120900 chr7A 681427625 681428494 869 False 769.0 769 83.5030 1 839 1 chr7A.!!$F3 838
11 TraesCS6A01G120900 chr5A 92955299 92956149 850 False 957.0 957 87.2510 1 839 1 chr5A.!!$F1 838
12 TraesCS6A01G120900 chr1A 502974957 502975789 832 False 915.0 915 86.6980 11 839 1 chr1A.!!$F2 828
13 TraesCS6A01G120900 chr1A 308680936 308681774 838 False 824.0 824 84.6960 1 839 1 chr1A.!!$F1 838
14 TraesCS6A01G120900 chr3D 346389845 346390688 843 False 821.0 821 84.6960 6 836 1 chr3D.!!$F1 830
15 TraesCS6A01G120900 chr4A 68164523 68165362 839 False 815.0 815 84.5430 6 839 1 chr4A.!!$F1 833
16 TraesCS6A01G120900 chr5B 323303553 323304404 851 False 806.0 806 84.2660 6 836 1 chr5B.!!$F1 830
17 TraesCS6A01G120900 chr1D 366660593 366661430 837 True 793.0 793 84.2290 9 839 1 chr1D.!!$R1 830
18 TraesCS6A01G120900 chr2D 610402974 610404219 1245 True 701.0 701 77.4240 889 2104 1 chr2D.!!$R2 1215
19 TraesCS6A01G120900 chr2D 610376541 610377778 1237 True 688.0 688 77.2180 889 2104 1 chr2D.!!$R1 1215
20 TraesCS6A01G120900 chr2A 743265307 743265932 625 True 453.0 453 80.0320 1490 2104 1 chr2A.!!$R3 614
21 TraesCS6A01G120900 chr2B 41472723 41473328 605 True 351.0 351 77.6140 1493 2088 1 chr2B.!!$R1 595

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
875 942 0.100146 GACGCCGACCTTCGATACTT 59.9 55.0 0.0 0.0 43.74 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 3424 1.226575 GGATGACGATGCGACGACA 60.227 57.895 0.0 9.22 41.1 4.35 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
65 66 8.043113 GCACTATGGATGGAATAGAATGTGATA 58.957 37.037 0.00 0.00 32.85 2.15
116 122 3.928992 GAGAAAGTCTCACATTGATGCGA 59.071 43.478 0.32 0.00 42.90 5.10
133 139 4.882842 TGCGACTAATCAATGGGCTATA 57.117 40.909 0.00 0.00 0.00 1.31
134 140 5.222079 TGCGACTAATCAATGGGCTATAA 57.778 39.130 0.00 0.00 0.00 0.98
141 147 7.465116 ACTAATCAATGGGCTATAAAGATGCT 58.535 34.615 0.00 0.00 0.00 3.79
176 183 3.266772 TCAATGCAAGGAGTAGGGATTGT 59.733 43.478 0.00 0.00 40.09 2.71
204 211 4.506886 ACGGATGCACTAGAGCTATAAC 57.493 45.455 13.47 1.03 34.99 1.89
236 244 5.869579 AGCTCATCAAAGGAAACTAAGTGA 58.130 37.500 0.00 0.00 42.68 3.41
296 305 3.454719 TTTGAGGAAGCCCATCATTGA 57.545 42.857 0.00 0.00 33.88 2.57
445 456 5.896073 TGTCCCTTCTCTCTTTTTCTCTT 57.104 39.130 0.00 0.00 0.00 2.85
448 462 8.666129 TGTCCCTTCTCTCTTTTTCTCTTATA 57.334 34.615 0.00 0.00 0.00 0.98
493 512 3.393800 GCCTTTCTTTTGGCCTCTTTTC 58.606 45.455 3.32 0.00 43.11 2.29
497 516 4.937201 TTCTTTTGGCCTCTTTTCTTCC 57.063 40.909 3.32 0.00 0.00 3.46
498 517 3.230976 TCTTTTGGCCTCTTTTCTTCCC 58.769 45.455 3.32 0.00 0.00 3.97
501 520 3.328535 TTGGCCTCTTTTCTTCCCTTT 57.671 42.857 3.32 0.00 0.00 3.11
532 589 5.957842 GAGAATCATAGTCTCCATCGTCT 57.042 43.478 0.00 0.00 36.33 4.18
536 594 7.560368 AGAATCATAGTCTCCATCGTCTTTTT 58.440 34.615 0.00 0.00 0.00 1.94
668 732 0.390124 GGTGTACCGGGATTGCGATA 59.610 55.000 6.32 0.00 0.00 2.92
798 865 9.974980 ATAATAAATGAAACGGTGAAAAGTTGT 57.025 25.926 0.00 0.00 0.00 3.32
802 869 6.627395 ATGAAACGGTGAAAAGTTGTATGA 57.373 33.333 0.00 0.00 0.00 2.15
832 899 4.780815 TCTCGAAATGGCTATGGAAATGT 58.219 39.130 0.00 0.00 0.00 2.71
839 906 7.752239 CGAAATGGCTATGGAAATGTCATAATC 59.248 37.037 0.00 0.00 0.00 1.75
840 907 8.481492 AAATGGCTATGGAAATGTCATAATCA 57.519 30.769 0.00 0.00 0.00 2.57
841 908 8.660295 AATGGCTATGGAAATGTCATAATCAT 57.340 30.769 0.00 0.00 0.00 2.45
842 909 7.457024 TGGCTATGGAAATGTCATAATCATG 57.543 36.000 0.00 0.00 0.00 3.07
843 910 6.434965 TGGCTATGGAAATGTCATAATCATGG 59.565 38.462 0.00 0.00 32.61 3.66
844 911 6.127535 GGCTATGGAAATGTCATAATCATGGG 60.128 42.308 0.00 0.00 32.61 4.00
845 912 5.733620 ATGGAAATGTCATAATCATGGGC 57.266 39.130 0.00 0.00 32.61 5.36
846 913 3.569277 TGGAAATGTCATAATCATGGGCG 59.431 43.478 0.00 0.00 32.61 6.13
847 914 3.820467 GGAAATGTCATAATCATGGGCGA 59.180 43.478 0.00 0.00 32.61 5.54
848 915 4.460382 GGAAATGTCATAATCATGGGCGAT 59.540 41.667 0.00 0.00 32.61 4.58
849 916 5.392380 GGAAATGTCATAATCATGGGCGATC 60.392 44.000 0.00 0.00 32.61 3.69
850 917 3.767902 TGTCATAATCATGGGCGATCA 57.232 42.857 0.00 0.00 32.61 2.92
851 918 4.084011 TGTCATAATCATGGGCGATCAA 57.916 40.909 0.00 0.00 32.61 2.57
852 919 3.814842 TGTCATAATCATGGGCGATCAAC 59.185 43.478 0.00 0.00 32.61 3.18
853 920 3.189287 GTCATAATCATGGGCGATCAACC 59.811 47.826 0.00 0.00 32.61 3.77
854 921 1.877637 TAATCATGGGCGATCAACCG 58.122 50.000 0.00 0.00 0.00 4.44
855 922 0.180171 AATCATGGGCGATCAACCGA 59.820 50.000 0.00 0.00 0.00 4.69
856 923 0.250038 ATCATGGGCGATCAACCGAG 60.250 55.000 0.00 0.00 0.00 4.63
857 924 1.143838 CATGGGCGATCAACCGAGA 59.856 57.895 0.00 0.00 0.00 4.04
858 925 1.144057 ATGGGCGATCAACCGAGAC 59.856 57.895 0.00 0.00 0.00 3.36
859 926 2.582498 GGGCGATCAACCGAGACG 60.582 66.667 0.00 0.00 0.00 4.18
860 927 3.255379 GGCGATCAACCGAGACGC 61.255 66.667 0.00 0.00 44.50 5.19
861 928 3.255379 GCGATCAACCGAGACGCC 61.255 66.667 0.00 0.00 41.66 5.68
862 929 2.949678 CGATCAACCGAGACGCCG 60.950 66.667 0.00 0.00 0.00 6.46
863 930 2.488355 GATCAACCGAGACGCCGA 59.512 61.111 0.00 0.00 0.00 5.54
864 931 1.872679 GATCAACCGAGACGCCGAC 60.873 63.158 0.00 0.00 0.00 4.79
865 932 3.352338 ATCAACCGAGACGCCGACC 62.352 63.158 0.00 0.00 0.00 4.79
866 933 4.052229 CAACCGAGACGCCGACCT 62.052 66.667 0.00 0.00 0.00 3.85
867 934 3.300765 AACCGAGACGCCGACCTT 61.301 61.111 0.00 0.00 0.00 3.50
868 935 3.278592 AACCGAGACGCCGACCTTC 62.279 63.158 0.00 0.00 0.00 3.46
869 936 4.831307 CCGAGACGCCGACCTTCG 62.831 72.222 0.00 0.00 40.07 3.79
870 937 3.796443 CGAGACGCCGACCTTCGA 61.796 66.667 0.00 0.00 43.74 3.71
871 938 2.799371 GAGACGCCGACCTTCGAT 59.201 61.111 0.00 0.00 43.74 3.59
872 939 1.769098 CGAGACGCCGACCTTCGATA 61.769 60.000 0.00 0.00 43.74 2.92
873 940 0.316854 GAGACGCCGACCTTCGATAC 60.317 60.000 0.00 0.00 43.74 2.24
874 941 0.747283 AGACGCCGACCTTCGATACT 60.747 55.000 0.00 0.00 43.74 2.12
875 942 0.100146 GACGCCGACCTTCGATACTT 59.900 55.000 0.00 0.00 43.74 2.24
884 951 2.022195 CCTTCGATACTTCCACTCGGA 58.978 52.381 0.00 0.00 40.60 4.55
929 996 3.528370 GCTCTTCTCGGCGCCCTA 61.528 66.667 23.46 8.64 0.00 3.53
997 1064 0.615331 GGACAATCTGCTCCAGGACA 59.385 55.000 0.00 0.00 31.51 4.02
1075 1151 1.230635 GGTGCTGAACGTGATGCTGT 61.231 55.000 0.00 0.00 0.00 4.40
1077 1153 0.532640 TGCTGAACGTGATGCTGTGT 60.533 50.000 0.00 0.00 0.00 3.72
1121 1197 2.742372 CGACTTGGGCAGGTTCCG 60.742 66.667 0.00 0.00 0.00 4.30
1149 1225 2.351157 CGTCGAGGAGTCGTTTAAGGTT 60.351 50.000 0.00 0.00 46.85 3.50
1190 1266 2.032528 CTTCTTCCCGGCACTGCA 59.967 61.111 2.82 0.00 0.00 4.41
1374 1468 1.671979 CCGATCCCGAGTACTACACA 58.328 55.000 0.00 0.00 38.22 3.72
1445 1605 6.564709 TGCTTCATCCAACATGAATATAGC 57.435 37.500 0.00 0.00 37.40 2.97
1446 1606 6.301486 TGCTTCATCCAACATGAATATAGCT 58.699 36.000 0.00 0.00 37.40 3.32
1447 1607 6.774170 TGCTTCATCCAACATGAATATAGCTT 59.226 34.615 0.00 0.00 37.40 3.74
1448 1608 7.938490 TGCTTCATCCAACATGAATATAGCTTA 59.062 33.333 0.00 0.00 37.40 3.09
1449 1609 8.786898 GCTTCATCCAACATGAATATAGCTTAA 58.213 33.333 0.00 0.00 37.40 1.85
1451 1611 8.310406 TCATCCAACATGAATATAGCTTAACG 57.690 34.615 0.00 0.00 0.00 3.18
1452 1612 7.931407 TCATCCAACATGAATATAGCTTAACGT 59.069 33.333 0.00 0.00 0.00 3.99
1453 1613 9.203421 CATCCAACATGAATATAGCTTAACGTA 57.797 33.333 0.00 0.00 0.00 3.57
1454 1614 9.944376 ATCCAACATGAATATAGCTTAACGTAT 57.056 29.630 0.00 0.00 0.00 3.06
1541 1701 2.125512 GGCGCTGACCATCGAGTT 60.126 61.111 7.64 0.00 0.00 3.01
1608 1768 1.009900 GGACGAGATAGACGCCGTG 60.010 63.158 0.00 0.00 34.31 4.94
1609 1769 1.654743 GACGAGATAGACGCCGTGC 60.655 63.158 0.00 0.00 34.31 5.34
1610 1770 2.353607 CGAGATAGACGCCGTGCC 60.354 66.667 0.00 0.00 0.00 5.01
1645 1813 0.037303 AGTCTGACATGGCCAACCTG 59.963 55.000 10.96 6.36 36.63 4.00
1677 1845 2.182030 CGTCGTGAAGGAGAGCCC 59.818 66.667 0.00 0.00 33.31 5.19
1774 1942 2.421314 CGCGGCACCATGATCCTA 59.579 61.111 0.00 0.00 0.00 2.94
1886 2063 2.124736 CCATGATGCCGTTCGGGT 60.125 61.111 13.16 0.00 38.44 5.28
1969 2146 2.310233 GCTCGTGCAGTGCTTCGAA 61.310 57.895 26.04 15.61 39.41 3.71
2131 2998 4.017499 ACATATGGAGTAAGGGCAGGTTTT 60.017 41.667 7.80 0.00 0.00 2.43
2195 3063 2.628178 CCTATGTTAGGGCATCTCACGA 59.372 50.000 0.00 0.00 42.42 4.35
2257 3125 0.906775 TAAATGTCCGGTCAGGTCCC 59.093 55.000 7.60 0.00 41.99 4.46
2468 3364 1.933021 TCTTGGTCGCCTCCTTCTTA 58.067 50.000 0.00 0.00 0.00 2.10
2528 3424 1.451927 ATGGATGGCGTGCACGATT 60.452 52.632 41.19 24.26 43.02 3.34
2561 3457 3.432749 CGTCATCCAACTCATCCATCCTT 60.433 47.826 0.00 0.00 0.00 3.36
2614 3510 1.323412 GCGAGCTCATCCCTTCTCTA 58.677 55.000 15.40 0.00 0.00 2.43
2741 3660 3.812167 GCCAAGATGTCCTCAAACCTCTT 60.812 47.826 0.00 0.00 35.37 2.85
2746 3665 2.317040 TGTCCTCAAACCTCTTCGTCT 58.683 47.619 0.00 0.00 0.00 4.18
2751 3670 4.101119 TCCTCAAACCTCTTCGTCTTCTTT 59.899 41.667 0.00 0.00 0.00 2.52
2752 3671 5.303589 TCCTCAAACCTCTTCGTCTTCTTTA 59.696 40.000 0.00 0.00 0.00 1.85
2800 3719 7.646314 AGCATTTCTCTTTTCAATATGGATCG 58.354 34.615 0.00 0.00 0.00 3.69
2864 3783 2.870435 GCACAACAACCTATCGTCCAGT 60.870 50.000 0.00 0.00 0.00 4.00
3094 5492 5.048434 TGTCATAATCATCAAAACGGTTGCA 60.048 36.000 0.00 0.00 0.00 4.08
3159 5557 9.294030 GCAATTCTTTAGAAAACCTGACATATG 57.706 33.333 0.00 0.00 37.61 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.956435 TCTATTCCATCCATAGTGCTATGTCT 59.044 38.462 15.52 2.84 40.90 3.41
48 49 9.872684 AACCTCAATTATCACATTCTATTCCAT 57.127 29.630 0.00 0.00 0.00 3.41
65 66 4.780815 TGTCTTCTCACACAACCTCAATT 58.219 39.130 0.00 0.00 0.00 2.32
112 118 3.769739 ATAGCCCATTGATTAGTCGCA 57.230 42.857 0.00 0.00 0.00 5.10
116 122 7.465116 AGCATCTTTATAGCCCATTGATTAGT 58.535 34.615 0.00 0.00 0.00 2.24
204 211 9.118300 AGTTTCCTTTGATGAGCTTTCATATAG 57.882 33.333 1.61 1.43 0.00 1.31
236 244 1.338973 CAAGCAAGTTGGATGCACACT 59.661 47.619 4.75 0.00 46.22 3.55
353 362 8.806429 TGATCTTCATGATAGAGTCTCCTATC 57.194 38.462 0.00 0.00 43.21 2.08
381 392 2.034124 ACTTGTGCTTCAAAGTGGCAT 58.966 42.857 0.00 0.00 38.27 4.40
385 396 2.423185 TCCACACTTGTGCTTCAAAGTG 59.577 45.455 12.66 12.66 44.34 3.16
411 422 7.129425 AGAGAGAAGGGACAATGTTACTATCT 58.871 38.462 0.00 0.00 0.00 1.98
473 487 4.944619 AGAAAAGAGGCCAAAAGAAAGG 57.055 40.909 5.01 0.00 0.00 3.11
511 568 6.723298 AAAGACGATGGAGACTATGATTCT 57.277 37.500 0.00 0.00 0.00 2.40
529 586 5.464168 CATTGTCCCATGTGAGAAAAAGAC 58.536 41.667 0.00 0.00 0.00 3.01
532 589 3.896888 AGCATTGTCCCATGTGAGAAAAA 59.103 39.130 0.00 0.00 0.00 1.94
536 594 2.885135 AAGCATTGTCCCATGTGAGA 57.115 45.000 0.00 0.00 0.00 3.27
580 641 9.244799 GGGTTGTAATTTTTGAGTTGTAAGAAG 57.755 33.333 0.00 0.00 0.00 2.85
802 869 7.851228 TCCATAGCCATTTCGAGATATATTGT 58.149 34.615 0.00 0.00 0.00 2.71
815 882 8.481492 TGATTATGACATTTCCATAGCCATTT 57.519 30.769 0.00 0.00 0.00 2.32
832 899 3.411446 GGTTGATCGCCCATGATTATGA 58.589 45.455 0.00 0.00 36.36 2.15
839 906 1.143838 TCTCGGTTGATCGCCCATG 59.856 57.895 1.86 0.00 0.00 3.66
840 907 1.144057 GTCTCGGTTGATCGCCCAT 59.856 57.895 1.86 0.00 0.00 4.00
841 908 2.577059 GTCTCGGTTGATCGCCCA 59.423 61.111 1.86 0.00 0.00 5.36
842 909 2.582498 CGTCTCGGTTGATCGCCC 60.582 66.667 1.16 0.00 0.00 6.13
843 910 3.255379 GCGTCTCGGTTGATCGCC 61.255 66.667 0.00 0.00 39.61 5.54
844 911 3.255379 GGCGTCTCGGTTGATCGC 61.255 66.667 0.00 0.00 42.45 4.58
845 912 2.949678 CGGCGTCTCGGTTGATCG 60.950 66.667 0.00 0.00 0.00 3.69
846 913 1.872679 GTCGGCGTCTCGGTTGATC 60.873 63.158 6.85 0.00 0.00 2.92
847 914 2.181021 GTCGGCGTCTCGGTTGAT 59.819 61.111 6.85 0.00 0.00 2.57
848 915 4.047059 GGTCGGCGTCTCGGTTGA 62.047 66.667 6.85 0.00 0.00 3.18
849 916 3.569049 AAGGTCGGCGTCTCGGTTG 62.569 63.158 6.85 0.00 0.00 3.77
850 917 3.278592 GAAGGTCGGCGTCTCGGTT 62.279 63.158 6.85 0.00 0.00 4.44
851 918 3.745803 GAAGGTCGGCGTCTCGGT 61.746 66.667 6.85 0.00 0.00 4.69
852 919 4.831307 CGAAGGTCGGCGTCTCGG 62.831 72.222 6.85 0.00 36.00 4.63
853 920 1.769098 TATCGAAGGTCGGCGTCTCG 61.769 60.000 6.85 8.12 40.88 4.04
854 921 0.316854 GTATCGAAGGTCGGCGTCTC 60.317 60.000 6.85 0.00 40.88 3.36
855 922 0.747283 AGTATCGAAGGTCGGCGTCT 60.747 55.000 6.85 2.96 40.88 4.18
856 923 0.100146 AAGTATCGAAGGTCGGCGTC 59.900 55.000 6.85 0.00 40.88 5.19
857 924 0.100146 GAAGTATCGAAGGTCGGCGT 59.900 55.000 6.85 0.00 40.88 5.68
858 925 0.594284 GGAAGTATCGAAGGTCGGCG 60.594 60.000 0.00 0.00 40.88 6.46
859 926 0.458669 TGGAAGTATCGAAGGTCGGC 59.541 55.000 0.00 0.00 40.88 5.54
860 927 1.749634 AGTGGAAGTATCGAAGGTCGG 59.250 52.381 0.00 0.00 40.88 4.79
861 928 2.539142 CGAGTGGAAGTATCGAAGGTCG 60.539 54.545 0.00 0.00 42.10 4.79
862 929 2.223525 CCGAGTGGAAGTATCGAAGGTC 60.224 54.545 0.00 0.00 38.72 3.85
863 930 1.749634 CCGAGTGGAAGTATCGAAGGT 59.250 52.381 0.00 0.00 38.72 3.50
864 931 2.022195 TCCGAGTGGAAGTATCGAAGG 58.978 52.381 0.00 0.00 42.85 3.46
884 951 2.227089 GAGGAACCGACGCAGGACAT 62.227 60.000 3.59 0.00 34.73 3.06
928 995 1.138036 CCGTGCGTTCATCGAGGTA 59.862 57.895 0.00 0.00 42.86 3.08
929 996 2.126071 CCGTGCGTTCATCGAGGT 60.126 61.111 0.00 0.00 42.86 3.85
1054 1130 0.534877 AGCATCACGTTCAGCACCAA 60.535 50.000 5.77 0.00 0.00 3.67
1101 1177 3.842925 GAACCTGCCCAAGTCGCCA 62.843 63.158 0.00 0.00 0.00 5.69
1121 1197 1.801983 GACTCCTCGACGAACTCCC 59.198 63.158 0.00 0.00 0.00 4.30
1190 1266 2.043248 ATAGGCGGTCGACCCACT 60.043 61.111 28.52 25.92 0.00 4.00
1326 1420 1.355563 CGCCAAGAGCTCGTCGATA 59.644 57.895 8.37 0.00 40.39 2.92
1374 1468 0.468226 TGCCTTTGAGGACGTTGTCT 59.532 50.000 0.00 0.00 37.67 3.41
1445 1605 6.355638 GTTGCAGCAGCTTATATACGTTAAG 58.644 40.000 1.76 0.00 42.74 1.85
1446 1606 5.051307 CGTTGCAGCAGCTTATATACGTTAA 60.051 40.000 7.73 0.00 42.74 2.01
1447 1607 4.443063 CGTTGCAGCAGCTTATATACGTTA 59.557 41.667 7.73 0.00 42.74 3.18
1448 1608 3.245284 CGTTGCAGCAGCTTATATACGTT 59.755 43.478 7.73 0.00 42.74 3.99
1449 1609 2.794910 CGTTGCAGCAGCTTATATACGT 59.205 45.455 7.73 0.00 42.74 3.57
1450 1610 2.794910 ACGTTGCAGCAGCTTATATACG 59.205 45.455 7.73 8.89 42.74 3.06
1451 1611 5.900339 TTACGTTGCAGCAGCTTATATAC 57.100 39.130 7.73 0.00 42.74 1.47
1452 1612 5.989168 ACATTACGTTGCAGCAGCTTATATA 59.011 36.000 7.73 0.00 42.74 0.86
1453 1613 4.816385 ACATTACGTTGCAGCAGCTTATAT 59.184 37.500 7.73 0.00 42.74 0.86
1454 1614 4.188462 ACATTACGTTGCAGCAGCTTATA 58.812 39.130 7.73 0.00 42.74 0.98
1455 1615 3.009723 ACATTACGTTGCAGCAGCTTAT 58.990 40.909 7.73 0.00 42.74 1.73
1456 1616 2.415168 GACATTACGTTGCAGCAGCTTA 59.585 45.455 7.73 0.00 42.74 3.09
1457 1617 1.197721 GACATTACGTTGCAGCAGCTT 59.802 47.619 7.73 0.09 42.74 3.74
1458 1618 0.798776 GACATTACGTTGCAGCAGCT 59.201 50.000 7.73 0.00 42.74 4.24
1459 1619 0.179189 GGACATTACGTTGCAGCAGC 60.179 55.000 0.24 0.00 42.57 5.25
1460 1620 1.155889 TGGACATTACGTTGCAGCAG 58.844 50.000 0.24 0.00 0.00 4.24
1587 1747 0.602106 CGGCGTCTATCTCGTCCCTA 60.602 60.000 0.00 0.00 0.00 3.53
1645 1813 1.523938 GACGCATTGGAGGTAGGGC 60.524 63.158 0.00 0.00 0.00 5.19
1969 2146 3.501911 CCTTCCCCGGCATCCCAT 61.502 66.667 0.00 0.00 0.00 4.00
2195 3063 3.372025 GGCTCTTACATTTCAGGGGATGT 60.372 47.826 0.00 0.00 39.62 3.06
2292 3160 8.085296 TGCTATGTAAACCACAATTTAACTTGG 58.915 33.333 9.99 0.78 41.55 3.61
2468 3364 2.722201 GGACGAGATGGAGGCGGTT 61.722 63.158 0.00 0.00 0.00 4.44
2528 3424 1.226575 GGATGACGATGCGACGACA 60.227 57.895 0.00 9.22 41.10 4.35
2561 3457 6.761242 CGAAGGATACAAAGATGTTGACCATA 59.239 38.462 0.00 0.00 41.05 2.74
2614 3510 2.096248 AGAAGGAGACGAAGCTCGAAT 58.904 47.619 11.64 1.12 43.74 3.34
2741 3660 5.468746 CCACAAGGACAAATAAAGAAGACGA 59.531 40.000 0.00 0.00 36.89 4.20
2746 3665 6.361433 TCTGACCACAAGGACAAATAAAGAA 58.639 36.000 0.00 0.00 39.06 2.52
2751 3670 4.072131 GCTTCTGACCACAAGGACAAATA 58.928 43.478 0.00 0.00 39.06 1.40
2752 3671 2.887152 GCTTCTGACCACAAGGACAAAT 59.113 45.455 0.00 0.00 39.06 2.32
3094 5492 8.404000 CAGAAAGAAAGATCCGATCAATTGATT 58.596 33.333 21.57 6.23 34.37 2.57


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

AutoCloner maintained by Alex Coulton.