Multiple sequence alignment - TraesCS2A01G509000

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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 TraesCS2A01G509000 chr2A 100.000 2829 0 0 1 2829 735136790 735139618 0.000000e+00 5225
1 TraesCS2A01G509000 chr2A 98.595 2705 35 3 123 2826 605912755 605910053 0.000000e+00 4782
2 TraesCS2A01G509000 chrUn 98.671 2708 34 2 123 2829 223706812 223704106 0.000000e+00 4800
3 TraesCS2A01G509000 chrUn 98.117 2709 47 4 123 2829 40085981 40088687 0.000000e+00 4717
4 TraesCS2A01G509000 chr7B 98.486 2708 38 3 123 2829 698140282 698142987 0.000000e+00 4771
5 TraesCS2A01G509000 chr1B 98.449 2708 38 3 123 2829 683734020 683731316 0.000000e+00 4765
6 TraesCS2A01G509000 chr1B 97.897 2710 53 4 123 2829 338892939 338895647 0.000000e+00 4686
7 TraesCS2A01G509000 chr1B 97.896 2709 52 4 123 2829 583536649 583533944 0.000000e+00 4682
8 TraesCS2A01G509000 chr5B 98.043 2708 47 4 123 2829 713082096 713079394 0.000000e+00 4702
9 TraesCS2A01G509000 chr3B 97.970 2709 49 6 123 2829 92261978 92264682 0.000000e+00 4693
10 TraesCS2A01G509000 chr5A 100.000 124 0 0 1 124 63991264 63991141 2.190000e-56 230
11 TraesCS2A01G509000 chr5A 100.000 124 0 0 1 124 194300753 194300876 2.190000e-56 230
12 TraesCS2A01G509000 chr5A 98.438 128 2 0 1 128 63999104 63998977 2.840000e-55 226
13 TraesCS2A01G509000 chr5A 99.200 125 1 0 1 125 71906725 71906601 2.840000e-55 226
14 TraesCS2A01G509000 chr5A 100.000 122 0 0 1 122 194292678 194292799 2.840000e-55 226
15 TraesCS2A01G509000 chr3A 100.000 122 0 0 1 122 223431196 223431317 2.840000e-55 226
16 TraesCS2A01G509000 chr3A 100.000 122 0 0 1 122 223439166 223439287 2.840000e-55 226
17 TraesCS2A01G509000 chr3A 99.194 124 1 0 1 124 254411326 254411449 1.020000e-54 224
18 TraesCS2A01G509000 chr2B 100.000 122 0 0 1 122 263525711 263525590 2.840000e-55 226


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 TraesCS2A01G509000 chr2A 735136790 735139618 2828 False 5225 5225 100.000 1 2829 1 chr2A.!!$F1 2828
1 TraesCS2A01G509000 chr2A 605910053 605912755 2702 True 4782 4782 98.595 123 2826 1 chr2A.!!$R1 2703
2 TraesCS2A01G509000 chrUn 223704106 223706812 2706 True 4800 4800 98.671 123 2829 1 chrUn.!!$R1 2706
3 TraesCS2A01G509000 chrUn 40085981 40088687 2706 False 4717 4717 98.117 123 2829 1 chrUn.!!$F1 2706
4 TraesCS2A01G509000 chr7B 698140282 698142987 2705 False 4771 4771 98.486 123 2829 1 chr7B.!!$F1 2706
5 TraesCS2A01G509000 chr1B 683731316 683734020 2704 True 4765 4765 98.449 123 2829 1 chr1B.!!$R2 2706
6 TraesCS2A01G509000 chr1B 338892939 338895647 2708 False 4686 4686 97.897 123 2829 1 chr1B.!!$F1 2706
7 TraesCS2A01G509000 chr1B 583533944 583536649 2705 True 4682 4682 97.896 123 2829 1 chr1B.!!$R1 2706
8 TraesCS2A01G509000 chr5B 713079394 713082096 2702 True 4702 4702 98.043 123 2829 1 chr5B.!!$R1 2706
9 TraesCS2A01G509000 chr3B 92261978 92264682 2704 False 4693 4693 97.970 123 2829 1 chr3B.!!$F1 2706

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
90 91 0.038159 AAACTCGGAGTCGCTGGAAG 60.038 55.0 11.71 0.0 36.13 3.46 F
95 96 0.456995 CGGAGTCGCTGGAAGTCTTC 60.457 60.0 3.80 3.8 35.30 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1825 0.035152 AATCAGAGTTCATGCCGCCA 60.035 50.0 0.0 0.0 0.0 5.69 R
2061 2068 0.242825 CGACCTCTCTTTGCGTACCA 59.757 55.0 0.0 0.0 0.0 3.25 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
24 25 6.812879 TTTATGAGATGATGGCATGATGAC 57.187 37.500 3.81 0.00 34.11 3.06
25 26 3.849563 TGAGATGATGGCATGATGACA 57.150 42.857 2.18 2.18 41.29 3.58
32 33 2.593026 ATGGCATGATGACATGATGCA 58.407 42.857 31.93 21.63 46.11 3.96
33 34 2.962421 ATGGCATGATGACATGATGCAA 59.038 40.909 31.93 25.60 46.11 4.08
34 35 3.578282 ATGGCATGATGACATGATGCAAT 59.422 39.130 31.93 26.49 46.11 3.56
35 36 4.561326 ATGGCATGATGACATGATGCAATG 60.561 41.667 31.93 11.07 46.11 2.82
38 39 4.664150 ATGATGACATGATGCAATGCAA 57.336 36.364 13.45 0.00 37.45 4.08
39 40 4.457834 TGATGACATGATGCAATGCAAA 57.542 36.364 13.45 3.94 43.62 3.68
40 41 5.017294 TGATGACATGATGCAATGCAAAT 57.983 34.783 13.45 6.47 43.62 2.32
41 42 4.808364 TGATGACATGATGCAATGCAAATG 59.192 37.500 23.88 23.88 43.62 2.32
42 43 4.457834 TGACATGATGCAATGCAAATGA 57.542 36.364 29.04 13.42 43.62 2.57
43 44 5.017294 TGACATGATGCAATGCAAATGAT 57.983 34.783 29.04 18.31 43.62 2.45
44 45 4.808364 TGACATGATGCAATGCAAATGATG 59.192 37.500 29.04 19.24 43.62 3.07
60 61 7.792383 CAAATGATGCAACAAACAAAACAAA 57.208 28.000 0.00 0.00 0.00 2.83
61 62 8.395940 CAAATGATGCAACAAACAAAACAAAT 57.604 26.923 0.00 0.00 0.00 2.32
62 63 8.525071 CAAATGATGCAACAAACAAAACAAATC 58.475 29.630 0.00 0.00 0.00 2.17
63 64 6.732531 TGATGCAACAAACAAAACAAATCA 57.267 29.167 0.00 0.00 0.00 2.57
64 65 6.541086 TGATGCAACAAACAAAACAAATCAC 58.459 32.000 0.00 0.00 0.00 3.06
65 66 5.929697 TGCAACAAACAAAACAAATCACA 57.070 30.435 0.00 0.00 0.00 3.58
66 67 5.683859 TGCAACAAACAAAACAAATCACAC 58.316 33.333 0.00 0.00 0.00 3.82
67 68 4.780524 GCAACAAACAAAACAAATCACACG 59.219 37.500 0.00 0.00 0.00 4.49
68 69 5.388890 GCAACAAACAAAACAAATCACACGA 60.389 36.000 0.00 0.00 0.00 4.35
69 70 5.755330 ACAAACAAAACAAATCACACGAC 57.245 34.783 0.00 0.00 0.00 4.34
70 71 4.322274 ACAAACAAAACAAATCACACGACG 59.678 37.500 0.00 0.00 0.00 5.12
71 72 4.343811 AACAAAACAAATCACACGACGA 57.656 36.364 0.00 0.00 0.00 4.20
72 73 4.343811 ACAAAACAAATCACACGACGAA 57.656 36.364 0.00 0.00 0.00 3.85
73 74 4.724303 ACAAAACAAATCACACGACGAAA 58.276 34.783 0.00 0.00 0.00 3.46
74 75 4.555747 ACAAAACAAATCACACGACGAAAC 59.444 37.500 0.00 0.00 0.00 2.78
75 76 4.609691 AAACAAATCACACGACGAAACT 57.390 36.364 0.00 0.00 0.00 2.66
76 77 3.854286 ACAAATCACACGACGAAACTC 57.146 42.857 0.00 0.00 0.00 3.01
77 78 2.217847 ACAAATCACACGACGAAACTCG 59.782 45.455 0.00 0.00 46.93 4.18
78 79 1.415374 AATCACACGACGAAACTCGG 58.585 50.000 0.00 0.00 45.59 4.63
79 80 0.594602 ATCACACGACGAAACTCGGA 59.405 50.000 0.00 0.00 45.59 4.55
80 81 0.040692 TCACACGACGAAACTCGGAG 60.041 55.000 0.00 2.83 45.59 4.63
81 82 0.317603 CACACGACGAAACTCGGAGT 60.318 55.000 4.45 4.45 45.59 3.85
82 83 0.040603 ACACGACGAAACTCGGAGTC 60.041 55.000 11.71 0.00 45.59 3.36
83 84 4.038036 CGACGAAACTCGGAGTCG 57.962 61.111 11.71 13.79 45.59 4.18
84 85 3.751470 GACGAAACTCGGAGTCGC 58.249 61.111 11.71 5.68 45.59 5.19
85 86 1.209640 GACGAAACTCGGAGTCGCT 59.790 57.895 11.71 0.00 45.59 4.93
86 87 1.066114 GACGAAACTCGGAGTCGCTG 61.066 60.000 11.71 4.77 45.59 5.18
87 88 1.801913 CGAAACTCGGAGTCGCTGG 60.802 63.158 11.71 0.00 36.00 4.85
88 89 1.585006 GAAACTCGGAGTCGCTGGA 59.415 57.895 11.71 0.00 36.13 3.86
89 90 0.038526 GAAACTCGGAGTCGCTGGAA 60.039 55.000 11.71 0.00 36.13 3.53
90 91 0.038159 AAACTCGGAGTCGCTGGAAG 60.038 55.000 11.71 0.00 36.13 3.46
91 92 1.179814 AACTCGGAGTCGCTGGAAGT 61.180 55.000 11.71 0.00 35.30 3.01
92 93 1.137825 CTCGGAGTCGCTGGAAGTC 59.862 63.158 0.00 0.00 35.30 3.01
93 94 1.303398 TCGGAGTCGCTGGAAGTCT 60.303 57.895 0.00 0.00 35.30 3.24
94 95 0.894184 TCGGAGTCGCTGGAAGTCTT 60.894 55.000 0.00 0.00 35.30 3.01
95 96 0.456995 CGGAGTCGCTGGAAGTCTTC 60.457 60.000 3.80 3.80 35.30 2.87
96 97 0.892063 GGAGTCGCTGGAAGTCTTCT 59.108 55.000 12.31 0.00 35.30 2.85
97 98 1.403514 GGAGTCGCTGGAAGTCTTCTG 60.404 57.143 12.31 7.07 35.30 3.02
98 99 0.605589 AGTCGCTGGAAGTCTTCTGG 59.394 55.000 12.31 6.74 35.30 3.86
99 100 0.603569 GTCGCTGGAAGTCTTCTGGA 59.396 55.000 12.31 2.68 35.30 3.86
100 101 0.891373 TCGCTGGAAGTCTTCTGGAG 59.109 55.000 12.31 7.33 35.30 3.86
101 102 0.739112 CGCTGGAAGTCTTCTGGAGC 60.739 60.000 12.31 14.52 35.30 4.70
102 103 0.739112 GCTGGAAGTCTTCTGGAGCG 60.739 60.000 12.31 0.00 35.30 5.03
103 104 0.605589 CTGGAAGTCTTCTGGAGCGT 59.394 55.000 12.31 0.00 0.00 5.07
104 105 0.603569 TGGAAGTCTTCTGGAGCGTC 59.396 55.000 12.31 0.00 0.00 5.19
105 106 0.456995 GGAAGTCTTCTGGAGCGTCG 60.457 60.000 12.31 0.00 0.00 5.12
106 107 0.456995 GAAGTCTTCTGGAGCGTCGG 60.457 60.000 5.27 0.00 0.00 4.79
107 108 1.179814 AAGTCTTCTGGAGCGTCGGT 61.180 55.000 0.00 0.00 0.00 4.69
108 109 1.153997 GTCTTCTGGAGCGTCGGTC 60.154 63.158 15.95 15.95 0.00 4.79
109 110 1.303398 TCTTCTGGAGCGTCGGTCT 60.303 57.895 22.48 0.00 0.00 3.85
110 111 1.137825 CTTCTGGAGCGTCGGTCTC 59.862 63.158 22.48 13.69 0.00 3.36
111 112 2.585170 CTTCTGGAGCGTCGGTCTCG 62.585 65.000 22.48 14.05 37.82 4.04
112 113 4.180946 CTGGAGCGTCGGTCTCGG 62.181 72.222 22.48 14.09 36.95 4.63
119 120 3.443045 GTCGGTCTCGGGGCGTTA 61.443 66.667 0.00 0.00 36.95 3.18
120 121 3.443045 TCGGTCTCGGGGCGTTAC 61.443 66.667 0.00 0.00 36.95 2.50
121 122 3.751246 CGGTCTCGGGGCGTTACA 61.751 66.667 0.00 0.00 0.00 2.41
345 346 3.677121 GCTGGTAATCACTGATATGCTCG 59.323 47.826 0.00 0.00 0.00 5.03
450 451 8.712285 AGCTGTAATTGTACGTACATGTAAAT 57.288 30.769 27.82 15.57 35.89 1.40
1106 1109 3.632333 TCGTCAGTAGAGATGTTCCCAT 58.368 45.455 0.00 0.00 0.00 4.00
1236 1240 1.334869 GTGGAGTGTTGGTCAAAGCAG 59.665 52.381 0.00 0.00 0.00 4.24
1310 1314 5.622770 ATGCTTTATTTCGTTTCGTTCCT 57.377 34.783 0.00 0.00 0.00 3.36
1379 1383 2.497675 AGAATCTTTCTGCGGTCTGCTA 59.502 45.455 5.01 0.00 46.63 3.49
1396 1400 7.360861 CGGTCTGCTATGTTTACAATTCTTTCA 60.361 37.037 0.00 0.00 0.00 2.69
1506 1510 4.873817 TGAGCAACAAAATGACAAGATGG 58.126 39.130 0.00 0.00 0.00 3.51
1818 1825 5.163152 CCTCCTATTCTATTTGTTCAGGGCT 60.163 44.000 0.00 0.00 0.00 5.19
1874 1881 1.078918 CCGCCACTGAGATGCTCAA 60.079 57.895 0.00 0.00 40.18 3.02
2192 2199 4.105553 CTGCTAGCAGGCCAGCCA 62.106 66.667 33.06 6.95 40.17 4.75
2261 2269 0.846693 GGGTCAGCATAGAATGGGGT 59.153 55.000 0.00 0.00 0.00 4.95
2490 2498 5.339200 GGACTGGGATGGAATAGAAAGAACA 60.339 44.000 0.00 0.00 0.00 3.18
2514 2522 0.964358 GCAGCAAGCAAGGGATGAGT 60.964 55.000 0.00 0.00 44.79 3.41
2583 2591 3.434039 GGGGGTGGGGCAATAAGA 58.566 61.111 0.00 0.00 0.00 2.10
2623 2631 3.646715 CCGCCCCCTTTCCTGTCA 61.647 66.667 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.946009 TGTCATCATGCCATCATCTCATAAAT 59.054 34.615 0.00 0.00 0.00 1.40
1 2 6.300703 TGTCATCATGCCATCATCTCATAAA 58.699 36.000 0.00 0.00 0.00 1.40
2 3 5.871834 TGTCATCATGCCATCATCTCATAA 58.128 37.500 0.00 0.00 0.00 1.90
3 4 5.492855 TGTCATCATGCCATCATCTCATA 57.507 39.130 0.00 0.00 0.00 2.15
4 5 4.367039 TGTCATCATGCCATCATCTCAT 57.633 40.909 0.00 0.00 0.00 2.90
5 6 3.849563 TGTCATCATGCCATCATCTCA 57.150 42.857 0.00 0.00 0.00 3.27
6 7 4.686839 CATGTCATCATGCCATCATCTC 57.313 45.455 0.00 0.00 43.66 2.75
14 15 6.817434 TGCATTGCATCATGTCATCATGCC 62.817 45.833 17.82 4.29 41.34 4.40
15 16 3.798548 TGCATTGCATCATGTCATCATGC 60.799 43.478 14.26 14.26 41.34 4.06
16 17 3.976169 TGCATTGCATCATGTCATCATG 58.024 40.909 7.38 0.00 42.12 3.07
17 18 4.664150 TTGCATTGCATCATGTCATCAT 57.336 36.364 12.95 0.00 38.76 2.45
18 19 4.457834 TTTGCATTGCATCATGTCATCA 57.542 36.364 12.95 0.00 38.76 3.07
19 20 5.047188 TCATTTGCATTGCATCATGTCATC 58.953 37.500 21.74 0.00 38.76 2.92
20 21 5.017294 TCATTTGCATTGCATCATGTCAT 57.983 34.783 21.74 3.94 38.76 3.06
21 22 4.457834 TCATTTGCATTGCATCATGTCA 57.542 36.364 21.74 8.80 38.76 3.58
22 23 5.328886 CATCATTTGCATTGCATCATGTC 57.671 39.130 21.74 0.00 38.76 3.06
36 37 7.792383 TTTGTTTTGTTTGTTGCATCATTTG 57.208 28.000 0.00 0.00 0.00 2.32
37 38 8.242053 TGATTTGTTTTGTTTGTTGCATCATTT 58.758 25.926 0.00 0.00 0.00 2.32
38 39 7.697291 GTGATTTGTTTTGTTTGTTGCATCATT 59.303 29.630 0.00 0.00 0.00 2.57
39 40 7.148289 TGTGATTTGTTTTGTTTGTTGCATCAT 60.148 29.630 0.00 0.00 0.00 2.45
40 41 6.148315 TGTGATTTGTTTTGTTTGTTGCATCA 59.852 30.769 0.00 0.00 0.00 3.07
41 42 6.465465 GTGTGATTTGTTTTGTTTGTTGCATC 59.535 34.615 0.00 0.00 0.00 3.91
42 43 6.313252 GTGTGATTTGTTTTGTTTGTTGCAT 58.687 32.000 0.00 0.00 0.00 3.96
43 44 5.613360 CGTGTGATTTGTTTTGTTTGTTGCA 60.613 36.000 0.00 0.00 0.00 4.08
44 45 4.780524 CGTGTGATTTGTTTTGTTTGTTGC 59.219 37.500 0.00 0.00 0.00 4.17
45 46 6.006482 GTCGTGTGATTTGTTTTGTTTGTTG 58.994 36.000 0.00 0.00 0.00 3.33
46 47 5.164138 CGTCGTGTGATTTGTTTTGTTTGTT 60.164 36.000 0.00 0.00 0.00 2.83
47 48 4.322274 CGTCGTGTGATTTGTTTTGTTTGT 59.678 37.500 0.00 0.00 0.00 2.83
48 49 4.555360 TCGTCGTGTGATTTGTTTTGTTTG 59.445 37.500 0.00 0.00 0.00 2.93
49 50 4.724303 TCGTCGTGTGATTTGTTTTGTTT 58.276 34.783 0.00 0.00 0.00 2.83
50 51 4.343811 TCGTCGTGTGATTTGTTTTGTT 57.656 36.364 0.00 0.00 0.00 2.83
51 52 4.343811 TTCGTCGTGTGATTTGTTTTGT 57.656 36.364 0.00 0.00 0.00 2.83
52 53 4.791163 AGTTTCGTCGTGTGATTTGTTTTG 59.209 37.500 0.00 0.00 0.00 2.44
53 54 4.976987 AGTTTCGTCGTGTGATTTGTTTT 58.023 34.783 0.00 0.00 0.00 2.43
54 55 4.584394 GAGTTTCGTCGTGTGATTTGTTT 58.416 39.130 0.00 0.00 0.00 2.83
55 56 3.302221 CGAGTTTCGTCGTGTGATTTGTT 60.302 43.478 0.00 0.00 34.72 2.83
56 57 2.217847 CGAGTTTCGTCGTGTGATTTGT 59.782 45.455 0.00 0.00 34.72 2.83
57 58 2.409752 CCGAGTTTCGTCGTGTGATTTG 60.410 50.000 0.00 0.00 38.40 2.32
58 59 1.790623 CCGAGTTTCGTCGTGTGATTT 59.209 47.619 0.00 0.00 38.40 2.17
59 60 1.001048 TCCGAGTTTCGTCGTGTGATT 60.001 47.619 0.00 0.00 38.40 2.57
60 61 0.594602 TCCGAGTTTCGTCGTGTGAT 59.405 50.000 0.00 0.00 38.40 3.06
61 62 0.040692 CTCCGAGTTTCGTCGTGTGA 60.041 55.000 0.00 0.00 38.40 3.58
62 63 0.317603 ACTCCGAGTTTCGTCGTGTG 60.318 55.000 0.00 0.00 38.40 3.82
63 64 0.040603 GACTCCGAGTTTCGTCGTGT 60.041 55.000 1.71 0.00 38.40 4.49
64 65 1.058590 CGACTCCGAGTTTCGTCGTG 61.059 60.000 1.71 0.00 42.89 4.35
65 66 1.206072 CGACTCCGAGTTTCGTCGT 59.794 57.895 1.71 0.00 42.89 4.34
66 67 4.038036 CGACTCCGAGTTTCGTCG 57.962 61.111 1.71 0.00 42.39 5.12
67 68 1.066114 CAGCGACTCCGAGTTTCGTC 61.066 60.000 1.71 0.25 38.40 4.20
68 69 1.081376 CAGCGACTCCGAGTTTCGT 60.081 57.895 1.71 0.00 38.40 3.85
69 70 1.801913 CCAGCGACTCCGAGTTTCG 60.802 63.158 1.71 3.93 40.07 3.46
70 71 0.038526 TTCCAGCGACTCCGAGTTTC 60.039 55.000 1.71 0.00 38.22 2.78
71 72 0.038159 CTTCCAGCGACTCCGAGTTT 60.038 55.000 1.71 0.00 38.22 2.66
72 73 1.179814 ACTTCCAGCGACTCCGAGTT 61.180 55.000 1.71 0.00 38.22 3.01
73 74 1.587933 GACTTCCAGCGACTCCGAGT 61.588 60.000 0.00 0.00 38.22 4.18
74 75 1.137825 GACTTCCAGCGACTCCGAG 59.862 63.158 0.00 0.00 38.22 4.63
75 76 0.894184 AAGACTTCCAGCGACTCCGA 60.894 55.000 0.00 0.00 38.22 4.55
76 77 0.456995 GAAGACTTCCAGCGACTCCG 60.457 60.000 3.63 0.00 39.16 4.63
77 78 0.892063 AGAAGACTTCCAGCGACTCC 59.108 55.000 11.67 0.00 0.00 3.85
78 79 1.403514 CCAGAAGACTTCCAGCGACTC 60.404 57.143 11.67 0.00 0.00 3.36
79 80 0.605589 CCAGAAGACTTCCAGCGACT 59.394 55.000 11.67 0.00 0.00 4.18
80 81 0.603569 TCCAGAAGACTTCCAGCGAC 59.396 55.000 11.67 0.00 0.00 5.19
81 82 0.891373 CTCCAGAAGACTTCCAGCGA 59.109 55.000 11.67 1.96 0.00 4.93
82 83 0.739112 GCTCCAGAAGACTTCCAGCG 60.739 60.000 11.67 0.13 0.00 5.18
83 84 0.739112 CGCTCCAGAAGACTTCCAGC 60.739 60.000 11.67 14.50 0.00 4.85
84 85 0.605589 ACGCTCCAGAAGACTTCCAG 59.394 55.000 11.67 6.79 0.00 3.86
85 86 0.603569 GACGCTCCAGAAGACTTCCA 59.396 55.000 11.67 0.00 0.00 3.53
86 87 0.456995 CGACGCTCCAGAAGACTTCC 60.457 60.000 11.67 0.00 0.00 3.46
87 88 0.456995 CCGACGCTCCAGAAGACTTC 60.457 60.000 7.14 7.14 0.00 3.01
88 89 1.179814 ACCGACGCTCCAGAAGACTT 61.180 55.000 0.00 0.00 0.00 3.01
89 90 1.587933 GACCGACGCTCCAGAAGACT 61.588 60.000 0.00 0.00 0.00 3.24
90 91 1.153997 GACCGACGCTCCAGAAGAC 60.154 63.158 0.00 0.00 0.00 3.01
91 92 1.303398 AGACCGACGCTCCAGAAGA 60.303 57.895 0.00 0.00 0.00 2.87
92 93 1.137825 GAGACCGACGCTCCAGAAG 59.862 63.158 0.00 0.00 0.00 2.85
93 94 2.687805 CGAGACCGACGCTCCAGAA 61.688 63.158 0.00 0.00 38.22 3.02
94 95 3.125573 CGAGACCGACGCTCCAGA 61.126 66.667 0.00 0.00 38.22 3.86
95 96 4.180946 CCGAGACCGACGCTCCAG 62.181 72.222 0.00 0.00 38.22 3.86
102 103 3.443045 TAACGCCCCGAGACCGAC 61.443 66.667 0.00 0.00 38.22 4.79
103 104 3.443045 GTAACGCCCCGAGACCGA 61.443 66.667 0.00 0.00 38.22 4.69
104 105 3.751246 TGTAACGCCCCGAGACCG 61.751 66.667 0.00 0.00 0.00 4.79
105 106 2.125793 GTGTAACGCCCCGAGACC 60.126 66.667 0.00 0.00 0.00 3.85
106 107 2.125793 GGTGTAACGCCCCGAGAC 60.126 66.667 0.00 0.00 38.12 3.36
107 108 1.546589 ATTGGTGTAACGCCCCGAGA 61.547 55.000 0.00 0.00 38.12 4.04
108 109 1.078708 ATTGGTGTAACGCCCCGAG 60.079 57.895 0.00 0.00 38.12 4.63
109 110 1.078988 GATTGGTGTAACGCCCCGA 60.079 57.895 0.00 0.00 38.12 5.14
110 111 0.675522 AAGATTGGTGTAACGCCCCG 60.676 55.000 0.00 0.00 38.12 5.73
111 112 1.092348 GAAGATTGGTGTAACGCCCC 58.908 55.000 0.00 0.00 38.12 5.80
112 113 2.007608 GAGAAGATTGGTGTAACGCCC 58.992 52.381 0.00 0.00 38.12 6.13
113 114 1.659098 CGAGAAGATTGGTGTAACGCC 59.341 52.381 0.00 0.00 38.12 5.68
114 115 2.602878 TCGAGAAGATTGGTGTAACGC 58.397 47.619 0.00 0.00 38.12 4.84
115 116 3.482472 CGATCGAGAAGATTGGTGTAACG 59.518 47.826 10.26 0.00 40.26 3.18
116 117 4.669318 TCGATCGAGAAGATTGGTGTAAC 58.331 43.478 15.15 0.00 40.26 2.50
117 118 4.976224 TCGATCGAGAAGATTGGTGTAA 57.024 40.909 15.15 0.00 40.26 2.41
118 119 4.157105 TGTTCGATCGAGAAGATTGGTGTA 59.843 41.667 18.54 0.00 40.26 2.90
119 120 3.056821 TGTTCGATCGAGAAGATTGGTGT 60.057 43.478 18.54 0.00 40.26 4.16
120 121 3.511699 TGTTCGATCGAGAAGATTGGTG 58.488 45.455 18.54 0.00 40.26 4.17
121 122 3.868757 TGTTCGATCGAGAAGATTGGT 57.131 42.857 18.54 0.00 40.26 3.67
345 346 5.086058 CAGCAACAATAACGTCACCAATAC 58.914 41.667 0.00 0.00 0.00 1.89
450 451 2.891112 ACCGTTGTCACGTTTGAGTTA 58.109 42.857 0.00 0.00 45.62 2.24
821 824 4.721132 ACTTTCCCTATGGTTTTCGAACA 58.279 39.130 0.00 0.00 0.00 3.18
984 987 2.625790 GACCATCTGCTCTATCCGTTCT 59.374 50.000 0.00 0.00 0.00 3.01
1106 1109 2.517959 CATTGGAAGAAGAGGCACCAA 58.482 47.619 0.00 0.00 43.23 3.67
1236 1240 1.626825 TGGTAATAGAATAGGGCGGCC 59.373 52.381 22.67 22.67 0.00 6.13
1396 1400 4.201930 CGCGTGGTAAAGAGAAGAGAGTAT 60.202 45.833 0.00 0.00 0.00 2.12
1695 1702 8.455903 TCCATGTGAAATAGAAAGATTCATCC 57.544 34.615 0.00 0.00 35.70 3.51
1818 1825 0.035152 AATCAGAGTTCATGCCGCCA 60.035 50.000 0.00 0.00 0.00 5.69
1861 1868 3.518705 AGGAGTCAATTGAGCATCTCAGT 59.481 43.478 19.66 8.33 41.75 3.41
1874 1881 7.403231 TCTTCCTATCAAGGTTAAGGAGTCAAT 59.597 37.037 0.00 0.00 44.09 2.57
2061 2068 0.242825 CGACCTCTCTTTGCGTACCA 59.757 55.000 0.00 0.00 0.00 3.25
2100 2107 2.034532 TCCACGAGGAGCGGTACA 59.965 61.111 0.00 0.00 46.49 2.90
2261 2269 0.322098 CACAACATTAGGGCCGTCCA 60.322 55.000 0.00 0.00 38.24 4.02
2490 2498 2.263741 CCCTTGCTTGCTGCTTCGT 61.264 57.895 0.00 0.00 43.37 3.85
2570 2578 3.026694 AGAAGCAATCTTATTGCCCCAC 58.973 45.455 18.37 9.36 45.98 4.61


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

AutoCloner maintained by Alex Coulton.