Multiple sequence alignment - TraesCS3D01G071200

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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 TraesCS3D01G071200 chr3D 100.000 2825 0 0 1 2825 31851209 31848385 0.000000e+00 5217
1 TraesCS3D01G071200 chr3D 87.826 1265 118 13 864 2100 31895697 31896953 0.000000e+00 1450
2 TraesCS3D01G071200 chr3D 86.957 759 62 20 72 805 31876687 31877433 0.000000e+00 819
3 TraesCS3D01G071200 chr3D 85.459 784 83 19 89 865 31887662 31888421 0.000000e+00 787
4 TraesCS3D01G071200 chr3D 81.742 356 37 20 409 742 31877296 31877645 3.590000e-69 272
5 TraesCS3D01G071200 chr3D 79.259 405 52 23 415 814 31876798 31877175 1.300000e-63 254
6 TraesCS3D01G071200 chr3D 90.643 171 15 1 2497 2666 31804672 31804502 2.830000e-55 226
7 TraesCS3D01G071200 chr3D 85.116 215 21 4 2432 2635 31964870 31965084 2.850000e-50 209
8 TraesCS3D01G071200 chr3D 90.299 134 8 3 2679 2812 31803349 31803221 1.350000e-38 171
9 TraesCS3D01G071200 chr3D 84.615 169 24 2 961 1128 31909607 31909774 1.740000e-37 167
10 TraesCS3D01G071200 chr3D 95.522 67 3 0 2183 2249 31904020 31904086 1.070000e-19 108
11 TraesCS3D01G071200 chr2A 95.725 1661 36 4 1050 2675 528101513 528103173 0.000000e+00 2641
12 TraesCS3D01G071200 chr2A 88.538 253 18 4 2425 2666 528106515 528106767 2.130000e-76 296
13 TraesCS3D01G071200 chr3B 90.494 263 21 4 2422 2681 54503612 54503351 7.490000e-91 344
14 TraesCS3D01G071200 chr3B 90.511 137 12 1 2529 2664 54325925 54325789 2.240000e-41 180
15 TraesCS3D01G071200 chr3B 90.323 124 7 3 2679 2802 54502227 54502109 1.050000e-34 158
16 TraesCS3D01G071200 chr3A 90.667 150 14 0 982 1131 44442056 44441907 1.720000e-47 200
17 TraesCS3D01G071200 chr2B 83.945 218 14 11 2425 2625 227311336 227311549 3.720000e-44 189


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 TraesCS3D01G071200 chr3D 31848385 31851209 2824 True 5217.000000 5217 100.000000 1 2825 1 chr3D.!!$R1 2824
1 TraesCS3D01G071200 chr3D 31895697 31896953 1256 False 1450.000000 1450 87.826000 864 2100 1 chr3D.!!$F2 1236
2 TraesCS3D01G071200 chr3D 31887662 31888421 759 False 787.000000 787 85.459000 89 865 1 chr3D.!!$F1 776
3 TraesCS3D01G071200 chr3D 31876687 31877645 958 False 448.333333 819 82.652667 72 814 3 chr3D.!!$F6 742
4 TraesCS3D01G071200 chr2A 528101513 528106767 5254 False 1468.500000 2641 92.131500 1050 2675 2 chr2A.!!$F1 1625
5 TraesCS3D01G071200 chr3B 54502109 54503612 1503 True 251.000000 344 90.408500 2422 2802 2 chr3B.!!$R2 380

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
30 31 0.393820 ATGTGTGCCTTTTGCCAAGG 59.606 50.0 7.32 7.32 40.16 3.61 F
1257 1329 0.535102 GCTATACCCATTGCTGCGGT 60.535 55.0 2.58 2.58 31.18 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1518 0.801872 TGATTTCACCGGCATTGTCG 59.198 50.000 0.00 3.1 0.00 4.35 R
2743 7044 1.279271 CCAAACAGCTGTACCTAGCCT 59.721 52.381 22.01 0.0 44.76 4.58 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
25 26 3.302365 ACATGTATGTGTGCCTTTTGC 57.698 42.857 0.00 0.00 40.03 3.68
26 27 2.029110 ACATGTATGTGTGCCTTTTGCC 60.029 45.455 0.00 0.00 40.03 4.52
27 28 1.697284 TGTATGTGTGCCTTTTGCCA 58.303 45.000 0.00 0.00 40.16 4.92
28 29 2.034878 TGTATGTGTGCCTTTTGCCAA 58.965 42.857 0.00 0.00 40.16 4.52
29 30 2.035704 TGTATGTGTGCCTTTTGCCAAG 59.964 45.455 0.00 0.00 40.16 3.61
30 31 0.393820 ATGTGTGCCTTTTGCCAAGG 59.606 50.000 7.32 7.32 40.16 3.61
31 32 0.685785 TGTGTGCCTTTTGCCAAGGA 60.686 50.000 14.63 0.00 39.81 3.36
32 33 0.681175 GTGTGCCTTTTGCCAAGGAT 59.319 50.000 14.63 0.00 39.81 3.24
33 34 1.070601 GTGTGCCTTTTGCCAAGGATT 59.929 47.619 14.63 0.00 39.81 3.01
34 35 1.344114 TGTGCCTTTTGCCAAGGATTC 59.656 47.619 14.63 5.53 39.81 2.52
35 36 1.344114 GTGCCTTTTGCCAAGGATTCA 59.656 47.619 14.63 2.14 39.81 2.57
36 37 2.045524 TGCCTTTTGCCAAGGATTCAA 58.954 42.857 14.63 0.00 39.81 2.69
37 38 2.037511 TGCCTTTTGCCAAGGATTCAAG 59.962 45.455 14.63 0.00 39.81 3.02
38 39 2.299867 GCCTTTTGCCAAGGATTCAAGA 59.700 45.455 14.63 0.00 39.81 3.02
39 40 3.244181 GCCTTTTGCCAAGGATTCAAGAA 60.244 43.478 14.63 0.00 39.81 2.52
40 41 4.743348 GCCTTTTGCCAAGGATTCAAGAAA 60.743 41.667 14.63 0.00 39.81 2.52
41 42 5.367302 CCTTTTGCCAAGGATTCAAGAAAA 58.633 37.500 5.97 0.00 39.81 2.29
42 43 5.999600 CCTTTTGCCAAGGATTCAAGAAAAT 59.000 36.000 5.97 0.00 39.81 1.82
43 44 6.148315 CCTTTTGCCAAGGATTCAAGAAAATC 59.852 38.462 5.97 0.00 39.81 2.17
55 56 8.647143 GATTCAAGAAAATCCAAGAAACAACA 57.353 30.769 0.00 0.00 30.82 3.33
56 57 9.097257 GATTCAAGAAAATCCAAGAAACAACAA 57.903 29.630 0.00 0.00 30.82 2.83
57 58 9.617523 ATTCAAGAAAATCCAAGAAACAACAAT 57.382 25.926 0.00 0.00 0.00 2.71
58 59 8.422973 TCAAGAAAATCCAAGAAACAACAATG 57.577 30.769 0.00 0.00 0.00 2.82
59 60 6.849588 AGAAAATCCAAGAAACAACAATGC 57.150 33.333 0.00 0.00 0.00 3.56
60 61 6.347696 AGAAAATCCAAGAAACAACAATGCA 58.652 32.000 0.00 0.00 0.00 3.96
61 62 5.989551 AAATCCAAGAAACAACAATGCAC 57.010 34.783 0.00 0.00 0.00 4.57
62 63 4.942761 ATCCAAGAAACAACAATGCACT 57.057 36.364 0.00 0.00 0.00 4.40
63 64 4.305989 TCCAAGAAACAACAATGCACTC 57.694 40.909 0.00 0.00 0.00 3.51
64 65 3.698539 TCCAAGAAACAACAATGCACTCA 59.301 39.130 0.00 0.00 0.00 3.41
65 66 4.159321 TCCAAGAAACAACAATGCACTCAA 59.841 37.500 0.00 0.00 0.00 3.02
66 67 4.869297 CCAAGAAACAACAATGCACTCAAA 59.131 37.500 0.00 0.00 0.00 2.69
67 68 5.350914 CCAAGAAACAACAATGCACTCAAAA 59.649 36.000 0.00 0.00 0.00 2.44
68 69 6.455913 CCAAGAAACAACAATGCACTCAAAAG 60.456 38.462 0.00 0.00 0.00 2.27
69 70 5.111293 AGAAACAACAATGCACTCAAAAGG 58.889 37.500 0.00 0.00 0.00 3.11
70 71 4.734398 AACAACAATGCACTCAAAAGGA 57.266 36.364 0.00 0.00 0.00 3.36
95 96 1.580059 AAGGCGGGAGGTAGAATCAA 58.420 50.000 0.00 0.00 0.00 2.57
109 110 6.071391 AGGTAGAATCAAACGCCAAATTTCAT 60.071 34.615 0.00 0.00 0.00 2.57
131 132 7.381766 CATCAAGTGATGTTTGGTCTATGAA 57.618 36.000 12.30 0.00 45.10 2.57
216 218 7.332557 TCTACACCTAGAAGTGAAAACAACAA 58.667 34.615 6.18 0.00 40.34 2.83
219 221 6.433093 ACACCTAGAAGTGAAAACAACAAACT 59.567 34.615 6.18 0.00 40.34 2.66
226 228 8.087750 AGAAGTGAAAACAACAAACTGATTTCA 58.912 29.630 5.29 5.29 42.40 2.69
254 266 9.872684 ATCATTGATTATTGTTAAGATCTGGGT 57.127 29.630 0.00 0.00 0.00 4.51
335 348 9.000486 CGATGAGTAATATGTACACCTAGAAGA 58.000 37.037 0.00 0.00 0.00 2.87
347 366 9.403583 TGTACACCTAGAAGAAAAAGACAATTT 57.596 29.630 0.00 0.00 0.00 1.82
367 386 7.926018 ACAATTTTTCTACCATTGGTTCTTGTC 59.074 33.333 14.78 0.00 37.09 3.18
576 595 6.565234 TCAGTAAGATCTTCACCTCGAAATC 58.435 40.000 12.24 0.00 31.71 2.17
586 605 4.065088 TCACCTCGAAATCAAAACCAGAG 58.935 43.478 0.00 0.00 0.00 3.35
591 610 3.064207 CGAAATCAAAACCAGAGACCGA 58.936 45.455 0.00 0.00 0.00 4.69
929 983 2.907042 ACTCTTCTTCTCGTCCCCAAAT 59.093 45.455 0.00 0.00 0.00 2.32
930 984 3.328050 ACTCTTCTTCTCGTCCCCAAATT 59.672 43.478 0.00 0.00 0.00 1.82
931 985 3.935828 CTCTTCTTCTCGTCCCCAAATTC 59.064 47.826 0.00 0.00 0.00 2.17
932 986 2.781681 TCTTCTCGTCCCCAAATTCC 57.218 50.000 0.00 0.00 0.00 3.01
933 987 1.066430 TCTTCTCGTCCCCAAATTCCG 60.066 52.381 0.00 0.00 0.00 4.30
934 988 0.675522 TTCTCGTCCCCAAATTCCGC 60.676 55.000 0.00 0.00 0.00 5.54
935 989 2.045731 TCGTCCCCAAATTCCGCC 60.046 61.111 0.00 0.00 0.00 6.13
936 990 3.505184 CGTCCCCAAATTCCGCCG 61.505 66.667 0.00 0.00 0.00 6.46
937 991 2.360726 GTCCCCAAATTCCGCCGT 60.361 61.111 0.00 0.00 0.00 5.68
938 992 1.974875 GTCCCCAAATTCCGCCGTT 60.975 57.895 0.00 0.00 0.00 4.44
939 993 1.974343 TCCCCAAATTCCGCCGTTG 60.974 57.895 0.00 0.00 0.00 4.10
940 994 2.126110 CCCAAATTCCGCCGTTGC 60.126 61.111 0.00 0.00 0.00 4.17
941 995 2.126110 CCAAATTCCGCCGTTGCC 60.126 61.111 0.00 0.00 0.00 4.52
942 996 2.635443 CCAAATTCCGCCGTTGCCT 61.635 57.895 0.00 0.00 0.00 4.75
943 997 1.154035 CAAATTCCGCCGTTGCCTC 60.154 57.895 0.00 0.00 0.00 4.70
944 998 1.602323 AAATTCCGCCGTTGCCTCA 60.602 52.632 0.00 0.00 0.00 3.86
949 1003 3.121030 CGCCGTTGCCTCAGGAAG 61.121 66.667 0.00 0.00 0.00 3.46
974 1028 2.185310 GAACAGATGTCCCAGCCGGT 62.185 60.000 1.90 0.00 0.00 5.28
1013 1067 2.845797 TCCTCATGGAGATCCTGGC 58.154 57.895 0.00 0.00 37.46 4.85
1016 1070 2.664185 CATGGAGATCCTGGCGCG 60.664 66.667 0.00 0.00 36.82 6.86
1017 1071 3.933722 ATGGAGATCCTGGCGCGG 61.934 66.667 8.83 0.00 36.82 6.46
1039 1093 2.732619 CCCTACCGTTCCCTCTGCC 61.733 68.421 0.00 0.00 0.00 4.85
1104 1158 2.050350 CGGCCTCCTTAGACGGTCA 61.050 63.158 11.27 0.00 0.00 4.02
1180 1234 0.885196 TTTCCTCAATTTTCCGGCCG 59.115 50.000 21.04 21.04 0.00 6.13
1257 1329 0.535102 GCTATACCCATTGCTGCGGT 60.535 55.000 2.58 2.58 31.18 5.68
1424 1496 2.932130 GATCCCTCCTGCTTCGTGGC 62.932 65.000 0.00 0.00 0.00 5.01
1438 1510 1.374252 GTGGCCTTCGTGATCGTGT 60.374 57.895 3.32 0.00 38.33 4.49
1446 1518 1.990799 TCGTGATCGTGTTGGATGAC 58.009 50.000 0.00 0.00 38.33 3.06
1499 1575 7.125792 AGATATACTTGTCGGAAACCAGAAT 57.874 36.000 0.00 0.00 0.00 2.40
1822 1898 9.950496 ACACTGTAAATCTTTCAGAACTGATAT 57.050 29.630 5.34 0.00 39.64 1.63
1880 1956 2.893215 ATCGGTATCCATCCGGACTA 57.107 50.000 6.12 0.00 46.79 2.59
2013 2109 2.029290 TCGTCTTTACACTCCCTGCTTC 60.029 50.000 0.00 0.00 0.00 3.86
2068 2164 2.032681 AACTCGTGCCTGCCTTCC 59.967 61.111 0.00 0.00 0.00 3.46
2283 2391 2.148768 CAAGTCACTTCATGAGCTGCA 58.851 47.619 1.02 0.00 38.28 4.41
2288 2396 2.148768 CACTTCATGAGCTGCACTGAA 58.851 47.619 1.02 6.87 0.00 3.02
2353 2461 8.724229 CAAAATACACATGAGATTTCTCTGTGA 58.276 33.333 27.76 18.89 44.89 3.58
2697 6945 0.179089 CAGGATTGCGAGGACAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2699 6947 0.537188 GGATTGCGAGGACAGGAGAA 59.463 55.000 0.00 0.00 0.00 2.87
2700 6948 1.139853 GGATTGCGAGGACAGGAGAAT 59.860 52.381 0.00 0.00 0.00 2.40
2702 6950 2.386661 TTGCGAGGACAGGAGAATTC 57.613 50.000 0.00 0.00 0.00 2.17
2705 6953 2.275318 GCGAGGACAGGAGAATTCAAG 58.725 52.381 8.44 0.00 0.00 3.02
2706 6954 2.898705 CGAGGACAGGAGAATTCAAGG 58.101 52.381 8.44 0.00 0.00 3.61
2708 6956 2.238395 GAGGACAGGAGAATTCAAGGCT 59.762 50.000 8.44 0.00 0.00 4.58
2709 6957 2.238395 AGGACAGGAGAATTCAAGGCTC 59.762 50.000 8.44 0.00 0.00 4.70
2710 6958 2.637947 GACAGGAGAATTCAAGGCTCC 58.362 52.381 8.44 5.41 46.75 4.70
2786 7087 9.693739 TTGGTTGTATAACTGGAATGACAATAT 57.306 29.630 2.17 0.00 36.99 1.28
2814 7115 9.781834 TCAATCAACTAACTAAAACACTTGTTG 57.218 29.630 0.00 0.00 38.44 3.33
2815 7116 8.531530 CAATCAACTAACTAAAACACTTGTTGC 58.468 33.333 0.00 0.00 38.44 4.17
2816 7117 7.385778 TCAACTAACTAAAACACTTGTTGCT 57.614 32.000 0.00 0.00 38.44 3.91
2817 7118 7.247728 TCAACTAACTAAAACACTTGTTGCTG 58.752 34.615 0.00 0.00 38.44 4.41
2818 7119 6.131544 ACTAACTAAAACACTTGTTGCTGG 57.868 37.500 0.00 0.00 38.44 4.85
2819 7120 3.436700 ACTAAAACACTTGTTGCTGGC 57.563 42.857 0.00 0.00 38.44 4.85
2820 7121 2.757868 ACTAAAACACTTGTTGCTGGCA 59.242 40.909 0.00 0.00 38.44 4.92
2821 7122 2.758736 AAAACACTTGTTGCTGGCAA 57.241 40.000 3.72 3.72 38.44 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.299867 TCTTGAATCCTTGGCAAAAGGC 59.700 45.455 11.63 0.87 43.74 4.35
18 19 4.605640 TTCTTGAATCCTTGGCAAAAGG 57.394 40.909 10.47 10.47 38.78 3.11
19 20 7.125536 GATTTTCTTGAATCCTTGGCAAAAG 57.874 36.000 0.00 0.86 31.33 2.27
30 31 8.647143 TGTTGTTTCTTGGATTTTCTTGAATC 57.353 30.769 0.00 0.00 35.71 2.52
31 32 9.617523 ATTGTTGTTTCTTGGATTTTCTTGAAT 57.382 25.926 0.00 0.00 0.00 2.57
32 33 8.881743 CATTGTTGTTTCTTGGATTTTCTTGAA 58.118 29.630 0.00 0.00 0.00 2.69
33 34 7.011295 GCATTGTTGTTTCTTGGATTTTCTTGA 59.989 33.333 0.00 0.00 0.00 3.02
34 35 7.127686 GCATTGTTGTTTCTTGGATTTTCTTG 58.872 34.615 0.00 0.00 0.00 3.02
35 36 6.822676 TGCATTGTTGTTTCTTGGATTTTCTT 59.177 30.769 0.00 0.00 0.00 2.52
36 37 6.258507 GTGCATTGTTGTTTCTTGGATTTTCT 59.741 34.615 0.00 0.00 0.00 2.52
37 38 6.258507 AGTGCATTGTTGTTTCTTGGATTTTC 59.741 34.615 0.00 0.00 0.00 2.29
38 39 6.114767 AGTGCATTGTTGTTTCTTGGATTTT 58.885 32.000 0.00 0.00 0.00 1.82
39 40 5.673514 AGTGCATTGTTGTTTCTTGGATTT 58.326 33.333 0.00 0.00 0.00 2.17
40 41 5.163426 TGAGTGCATTGTTGTTTCTTGGATT 60.163 36.000 0.00 0.00 0.00 3.01
41 42 4.341806 TGAGTGCATTGTTGTTTCTTGGAT 59.658 37.500 0.00 0.00 0.00 3.41
42 43 3.698539 TGAGTGCATTGTTGTTTCTTGGA 59.301 39.130 0.00 0.00 0.00 3.53
43 44 4.044336 TGAGTGCATTGTTGTTTCTTGG 57.956 40.909 0.00 0.00 0.00 3.61
44 45 6.406093 TTTTGAGTGCATTGTTGTTTCTTG 57.594 33.333 0.00 0.00 0.00 3.02
45 46 5.581874 CCTTTTGAGTGCATTGTTGTTTCTT 59.418 36.000 0.00 0.00 0.00 2.52
46 47 5.105392 TCCTTTTGAGTGCATTGTTGTTTCT 60.105 36.000 0.00 0.00 0.00 2.52
47 48 5.108517 TCCTTTTGAGTGCATTGTTGTTTC 58.891 37.500 0.00 0.00 0.00 2.78
48 49 5.083533 TCCTTTTGAGTGCATTGTTGTTT 57.916 34.783 0.00 0.00 0.00 2.83
49 50 4.734398 TCCTTTTGAGTGCATTGTTGTT 57.266 36.364 0.00 0.00 0.00 2.83
50 51 4.734398 TTCCTTTTGAGTGCATTGTTGT 57.266 36.364 0.00 0.00 0.00 3.32
51 52 6.419980 TTTTTCCTTTTGAGTGCATTGTTG 57.580 33.333 0.00 0.00 0.00 3.33
84 85 5.242838 TGAAATTTGGCGTTTGATTCTACCT 59.757 36.000 0.00 0.00 0.00 3.08
95 96 4.582701 TCACTTGATGAAATTTGGCGTT 57.417 36.364 0.00 0.00 33.02 4.84
109 110 7.815840 TTTTCATAGACCAAACATCACTTGA 57.184 32.000 0.00 0.00 0.00 3.02
176 178 4.512198 AGGTGTAGATCTTACTCGTCGATG 59.488 45.833 0.00 0.00 0.00 3.84
335 348 9.679661 AACCAATGGTAGAAAAATTGTCTTTTT 57.320 25.926 4.88 0.00 33.12 1.94
347 366 6.361433 TCTTGACAAGAACCAATGGTAGAAA 58.639 36.000 15.58 0.00 33.12 2.52
353 372 4.379813 CCGAATCTTGACAAGAACCAATGG 60.380 45.833 21.29 13.11 41.63 3.16
553 572 6.333416 TGATTTCGAGGTGAAGATCTTACTG 58.667 40.000 8.25 3.46 37.99 2.74
570 589 3.064207 TCGGTCTCTGGTTTTGATTTCG 58.936 45.455 0.00 0.00 0.00 3.46
576 595 6.017440 TGTTAGAAAATCGGTCTCTGGTTTTG 60.017 38.462 4.58 0.00 0.00 2.44
586 605 8.237267 ACAAGAATCAATGTTAGAAAATCGGTC 58.763 33.333 0.00 0.00 0.00 4.79
898 952 6.869388 GGACGAGAAGAAGAGTTGTTTTCTAT 59.131 38.462 0.00 0.00 33.49 1.98
901 955 4.211584 GGGACGAGAAGAAGAGTTGTTTTC 59.788 45.833 0.00 0.00 0.00 2.29
912 966 2.614481 CGGAATTTGGGGACGAGAAGAA 60.614 50.000 0.00 0.00 0.00 2.52
929 983 4.697756 CCTGAGGCAACGGCGGAA 62.698 66.667 13.24 0.00 46.39 4.30
931 985 4.697756 TTCCTGAGGCAACGGCGG 62.698 66.667 13.24 0.00 46.39 6.13
932 986 3.121030 CTTCCTGAGGCAACGGCG 61.121 66.667 4.80 4.80 46.39 6.46
933 987 2.747855 CCTTCCTGAGGCAACGGC 60.748 66.667 0.00 0.00 46.39 5.68
934 988 0.035056 ATTCCTTCCTGAGGCAACGG 60.035 55.000 0.00 0.00 45.87 4.44
935 989 1.089920 CATTCCTTCCTGAGGCAACG 58.910 55.000 0.00 0.00 45.87 4.10
936 990 1.004745 TCCATTCCTTCCTGAGGCAAC 59.995 52.381 0.00 0.00 45.87 4.17
937 991 1.371467 TCCATTCCTTCCTGAGGCAA 58.629 50.000 0.00 0.00 45.87 4.52
938 992 1.004745 GTTCCATTCCTTCCTGAGGCA 59.995 52.381 0.00 0.00 45.87 4.75
939 993 1.004745 TGTTCCATTCCTTCCTGAGGC 59.995 52.381 0.00 0.00 45.87 4.70
941 995 3.988976 TCTGTTCCATTCCTTCCTGAG 57.011 47.619 0.00 0.00 0.00 3.35
942 996 3.588842 ACATCTGTTCCATTCCTTCCTGA 59.411 43.478 0.00 0.00 0.00 3.86
943 997 3.944015 GACATCTGTTCCATTCCTTCCTG 59.056 47.826 0.00 0.00 0.00 3.86
944 998 3.054065 GGACATCTGTTCCATTCCTTCCT 60.054 47.826 0.00 0.00 0.00 3.36
958 1012 2.124983 CACCGGCTGGGACATCTG 60.125 66.667 18.00 0.00 40.75 2.90
1028 1082 2.436824 GGAAGCGGCAGAGGGAAC 60.437 66.667 1.45 0.00 0.00 3.62
1081 1135 2.682494 TCTAAGGAGGCCGCGGTT 60.682 61.111 28.70 16.06 0.00 4.44
1257 1329 2.203983 TTGCAGAGGAGGAGGCCA 60.204 61.111 5.01 0.00 0.00 5.36
1424 1496 1.660607 CATCCAACACGATCACGAAGG 59.339 52.381 0.00 0.00 42.66 3.46
1438 1510 1.024046 CCGGCATTGTCGTCATCCAA 61.024 55.000 10.10 0.00 0.00 3.53
1446 1518 0.801872 TGATTTCACCGGCATTGTCG 59.198 50.000 0.00 3.10 0.00 4.35
1499 1575 3.826157 CCCAGTTTGCTTTGAAGTCCATA 59.174 43.478 0.00 0.00 0.00 2.74
1822 1898 6.929606 TCATCAAATTTGTGAACATGCATTCA 59.070 30.769 17.47 0.00 36.23 2.57
1880 1956 8.472413 CCATGTCTACCAAGAAAATCAAATCAT 58.528 33.333 0.00 0.00 32.16 2.45
1917 1993 8.071967 CGGCTATCCATATCGTACGATATAAAA 58.928 37.037 37.26 27.88 43.59 1.52
1923 2019 2.617308 CCGGCTATCCATATCGTACGAT 59.383 50.000 31.40 31.40 38.54 3.73
1925 2021 2.011947 TCCGGCTATCCATATCGTACG 58.988 52.381 9.53 9.53 0.00 3.67
2013 2109 3.470709 ACCATCTGATAACCATTCAGCG 58.529 45.455 0.00 0.00 40.35 5.18
2068 2164 8.954950 ACTCATACTCAACATCTGGATTTTAG 57.045 34.615 0.00 0.00 0.00 1.85
2554 2663 8.697507 ATTTGTCTAGAGTTTCCACTGAAAAT 57.302 30.769 0.00 0.00 41.92 1.82
2555 2664 9.793259 ATATTTGTCTAGAGTTTCCACTGAAAA 57.207 29.630 0.00 0.00 41.92 2.29
2677 2788 1.817099 CCTGTCCTCGCAATCCTGC 60.817 63.158 0.00 0.00 45.75 4.85
2725 6973 8.903820 ACCTAGCCTGTTATATTGAATTTGAAC 58.096 33.333 0.00 0.00 0.00 3.18
2743 7044 1.279271 CCAAACAGCTGTACCTAGCCT 59.721 52.381 22.01 0.00 44.76 4.58
2746 7047 3.740115 ACAACCAAACAGCTGTACCTAG 58.260 45.455 22.01 11.31 0.00 3.02
2802 7103 2.758736 TTGCCAGCAACAAGTGTTTT 57.241 40.000 0.00 0.00 35.83 2.43


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

AutoCloner maintained by Alex Coulton.