Multiple sequence alignment - TraesCS3B01G292500

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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 TraesCS3B01G292500 chr3B 100.000 3575 0 0 1 3575 470862325 470858751 0.000000 6602.0
1 TraesCS3B01G292500 chr5B 97.370 3004 77 2 123 3126 24137525 24140526 0.000000 5108.0
2 TraesCS3B01G292500 chr5B 98.022 455 9 0 3121 3575 24141207 24141661 0.000000 791.0
3 TraesCS3B01G292500 chr5A 93.578 3348 183 16 118 3458 647573860 647570538 0.000000 4963.0
4 TraesCS3B01G292500 chr5A 96.119 2345 87 2 782 3126 650157119 650154779 0.000000 3823.0
5 TraesCS3B01G292500 chr5A 97.143 455 13 0 3121 3575 650154098 650153644 0.000000 769.0
6 TraesCS3B01G292500 chr2A 95.716 3011 115 7 123 3126 769243464 769240461 0.000000 4833.0
7 TraesCS3B01G292500 chr2A 94.083 1369 75 2 123 1485 115136887 115135519 0.000000 2074.0
8 TraesCS3B01G292500 chr2A 96.484 455 16 0 3121 3575 769239779 769239325 0.000000 752.0
9 TraesCS3B01G292500 chr2A 95.824 455 16 3 3121 3575 115133555 115133104 0.000000 732.0
10 TraesCS3B01G292500 chr3A 95.580 3009 119 8 123 3124 636526818 636529819 0.000000 4807.0
11 TraesCS3B01G292500 chr3A 96.484 455 16 0 3121 3575 636530527 636530981 0.000000 752.0
12 TraesCS3B01G292500 chr3A 97.297 37 1 0 69 105 481879035 481878999 0.000003 63.9
13 TraesCS3B01G292500 chr3D 95.548 3010 103 10 122 3126 523407677 523404694 0.000000 4787.0
14 TraesCS3B01G292500 chr3D 95.824 455 19 0 3121 3575 160920527 160920073 0.000000 736.0
15 TraesCS3B01G292500 chr4D 95.147 3029 120 11 104 3126 498698629 498701636 0.000000 4754.0
16 TraesCS3B01G292500 chr5D 95.183 3010 107 10 123 3126 494238227 494241204 0.000000 4721.0
17 TraesCS3B01G292500 chr5D 88.481 790 80 4 123 911 114464973 114465752 0.000000 944.0
18 TraesCS3B01G292500 chr6A 95.048 3009 129 5 123 3126 162661645 162658652 0.000000 4713.0
19 TraesCS3B01G292500 chr6A 96.264 455 17 0 3121 3575 162657970 162657516 0.000000 747.0
20 TraesCS3B01G292500 chr4A 92.188 832 59 5 123 951 521957235 521956407 0.000000 1171.0
21 TraesCS3B01G292500 chr7A 88.213 806 77 9 122 911 563217811 563218614 0.000000 946.0
22 TraesCS3B01G292500 chr1B 91.853 626 46 2 123 748 94929387 94930007 0.000000 869.0
23 TraesCS3B01G292500 chr1D 96.044 455 18 0 3121 3575 30070305 30070759 0.000000 741.0
24 TraesCS3B01G292500 chr6D 95.824 455 19 0 3121 3575 61155051 61155505 0.000000 736.0


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 TraesCS3B01G292500 chr3B 470858751 470862325 3574 True 6602.0 6602 100.0000 1 3575 1 chr3B.!!$R1 3574
1 TraesCS3B01G292500 chr5B 24137525 24141661 4136 False 2949.5 5108 97.6960 123 3575 2 chr5B.!!$F1 3452
2 TraesCS3B01G292500 chr5A 647570538 647573860 3322 True 4963.0 4963 93.5780 118 3458 1 chr5A.!!$R1 3340
3 TraesCS3B01G292500 chr5A 650153644 650157119 3475 True 2296.0 3823 96.6310 782 3575 2 chr5A.!!$R2 2793
4 TraesCS3B01G292500 chr2A 769239325 769243464 4139 True 2792.5 4833 96.1000 123 3575 2 chr2A.!!$R2 3452
5 TraesCS3B01G292500 chr2A 115133104 115136887 3783 True 1403.0 2074 94.9535 123 3575 2 chr2A.!!$R1 3452
6 TraesCS3B01G292500 chr3A 636526818 636530981 4163 False 2779.5 4807 96.0320 123 3575 2 chr3A.!!$F1 3452
7 TraesCS3B01G292500 chr3D 523404694 523407677 2983 True 4787.0 4787 95.5480 122 3126 1 chr3D.!!$R2 3004
8 TraesCS3B01G292500 chr4D 498698629 498701636 3007 False 4754.0 4754 95.1470 104 3126 1 chr4D.!!$F1 3022
9 TraesCS3B01G292500 chr5D 494238227 494241204 2977 False 4721.0 4721 95.1830 123 3126 1 chr5D.!!$F2 3003
10 TraesCS3B01G292500 chr5D 114464973 114465752 779 False 944.0 944 88.4810 123 911 1 chr5D.!!$F1 788
11 TraesCS3B01G292500 chr6A 162657516 162661645 4129 True 2730.0 4713 95.6560 123 3575 2 chr6A.!!$R1 3452
12 TraesCS3B01G292500 chr4A 521956407 521957235 828 True 1171.0 1171 92.1880 123 951 1 chr4A.!!$R1 828
13 TraesCS3B01G292500 chr7A 563217811 563218614 803 False 946.0 946 88.2130 122 911 1 chr7A.!!$F1 789
14 TraesCS3B01G292500 chr1B 94929387 94930007 620 False 869.0 869 91.8530 123 748 1 chr1B.!!$F1 625

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
397 422 0.543174 ACACACTCTCTCACTCCCCC 60.543 60.000 0.0 0.0 0.0 5.40 F
666 691 1.815003 CGCATCCACGCTGATCCAA 60.815 57.895 0.0 0.0 0.0 3.53 F
2255 2338 0.037303 CCTGGAGCTGGTGTTGACAT 59.963 55.000 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1355 0.902531 GCACTAGAGGCAGGGTACAA 59.097 55.000 0.0 0.0 0.0 2.41 R
2394 2477 2.288273 GCCAGGGTTAGTATCTAGCACG 60.288 54.545 0.0 0.0 0.0 5.34 R
3455 4258 1.053835 TTGAGAGGTGGTGGTGCTGA 61.054 55.000 0.0 0.0 0.0 4.26 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
31 32 8.942338 AGAAATAGAACTGTAATTATGCGTGA 57.058 30.769 0.00 0.00 0.00 4.35
32 33 9.035607 AGAAATAGAACTGTAATTATGCGTGAG 57.964 33.333 0.00 0.00 0.00 3.51
33 34 8.718102 AAATAGAACTGTAATTATGCGTGAGT 57.282 30.769 0.00 0.00 0.00 3.41
34 35 8.718102 AATAGAACTGTAATTATGCGTGAGTT 57.282 30.769 0.00 0.00 0.00 3.01
35 36 6.408858 AGAACTGTAATTATGCGTGAGTTG 57.591 37.500 0.00 0.00 0.00 3.16
36 37 4.600012 ACTGTAATTATGCGTGAGTTGC 57.400 40.909 0.00 0.00 0.00 4.17
46 47 4.598406 TGCGTGAGTTGCATATAACTTG 57.402 40.909 0.00 0.00 40.78 3.16
47 48 3.373748 TGCGTGAGTTGCATATAACTTGG 59.626 43.478 0.00 0.00 40.78 3.61
48 49 3.374058 GCGTGAGTTGCATATAACTTGGT 59.626 43.478 0.00 0.00 40.78 3.67
49 50 4.727734 GCGTGAGTTGCATATAACTTGGTG 60.728 45.833 0.00 0.00 40.78 4.17
50 51 4.391830 CGTGAGTTGCATATAACTTGGTGT 59.608 41.667 0.00 0.00 40.78 4.16
51 52 5.106712 CGTGAGTTGCATATAACTTGGTGTT 60.107 40.000 0.00 0.00 40.78 3.32
52 53 6.086222 GTGAGTTGCATATAACTTGGTGTTG 58.914 40.000 0.00 0.00 40.78 3.33
53 54 5.182950 TGAGTTGCATATAACTTGGTGTTGG 59.817 40.000 0.00 0.00 40.78 3.77
54 55 5.076873 AGTTGCATATAACTTGGTGTTGGT 58.923 37.500 0.00 0.00 37.62 3.67
55 56 6.242396 AGTTGCATATAACTTGGTGTTGGTA 58.758 36.000 0.00 0.00 37.62 3.25
56 57 6.717540 AGTTGCATATAACTTGGTGTTGGTAA 59.282 34.615 0.00 0.00 37.62 2.85
57 58 6.503589 TGCATATAACTTGGTGTTGGTAAC 57.496 37.500 0.00 0.00 39.55 2.50
76 77 8.777578 TGGTAACAGATGGTCAGTAATATACT 57.222 34.615 0.00 0.00 46.17 2.12
77 78 9.209048 TGGTAACAGATGGTCAGTAATATACTT 57.791 33.333 0.00 0.00 46.17 2.24
78 79 9.694137 GGTAACAGATGGTCAGTAATATACTTC 57.306 37.037 0.00 0.00 36.76 3.01
81 82 9.823647 AACAGATGGTCAGTAATATACTTCTTG 57.176 33.333 0.00 0.00 36.76 3.02
82 83 9.201989 ACAGATGGTCAGTAATATACTTCTTGA 57.798 33.333 0.00 0.00 36.76 3.02
83 84 9.689976 CAGATGGTCAGTAATATACTTCTTGAG 57.310 37.037 0.00 0.00 36.76 3.02
84 85 8.364142 AGATGGTCAGTAATATACTTCTTGAGC 58.636 37.037 0.00 0.00 36.76 4.26
85 86 7.661536 TGGTCAGTAATATACTTCTTGAGCT 57.338 36.000 0.00 0.00 36.76 4.09
86 87 8.762481 TGGTCAGTAATATACTTCTTGAGCTA 57.238 34.615 0.00 0.00 36.76 3.32
87 88 9.197306 TGGTCAGTAATATACTTCTTGAGCTAA 57.803 33.333 0.00 0.00 36.76 3.09
88 89 9.685828 GGTCAGTAATATACTTCTTGAGCTAAG 57.314 37.037 0.00 0.00 36.76 2.18
96 97 7.719871 ATACTTCTTGAGCTAAGTACAAGGA 57.280 36.000 8.62 1.61 40.10 3.36
97 98 6.031751 ACTTCTTGAGCTAAGTACAAGGAG 57.968 41.667 15.54 15.54 46.56 3.69
98 99 5.775701 ACTTCTTGAGCTAAGTACAAGGAGA 59.224 40.000 21.42 5.83 45.03 3.71
99 100 6.439058 ACTTCTTGAGCTAAGTACAAGGAGAT 59.561 38.462 21.42 7.95 45.03 2.75
100 101 7.616150 ACTTCTTGAGCTAAGTACAAGGAGATA 59.384 37.037 21.42 0.00 45.03 1.98
101 102 7.956328 TCTTGAGCTAAGTACAAGGAGATAA 57.044 36.000 11.07 0.00 40.60 1.75
102 103 8.540507 TCTTGAGCTAAGTACAAGGAGATAAT 57.459 34.615 11.07 0.00 40.60 1.28
103 104 8.417106 TCTTGAGCTAAGTACAAGGAGATAATG 58.583 37.037 11.07 0.00 40.60 1.90
104 105 7.661536 TGAGCTAAGTACAAGGAGATAATGT 57.338 36.000 0.00 0.00 0.00 2.71
105 106 8.762481 TGAGCTAAGTACAAGGAGATAATGTA 57.238 34.615 0.00 0.00 0.00 2.29
106 107 8.630917 TGAGCTAAGTACAAGGAGATAATGTAC 58.369 37.037 7.10 7.10 46.11 2.90
107 108 7.953752 AGCTAAGTACAAGGAGATAATGTACC 58.046 38.462 10.67 0.00 46.65 3.34
108 109 7.563924 AGCTAAGTACAAGGAGATAATGTACCA 59.436 37.037 10.67 1.03 46.65 3.25
109 110 8.368668 GCTAAGTACAAGGAGATAATGTACCAT 58.631 37.037 10.67 4.70 46.65 3.55
110 111 9.698309 CTAAGTACAAGGAGATAATGTACCATG 57.302 37.037 10.67 0.00 46.65 3.66
111 112 7.676683 AGTACAAGGAGATAATGTACCATGT 57.323 36.000 10.67 0.00 46.65 3.21
112 113 7.500992 AGTACAAGGAGATAATGTACCATGTG 58.499 38.462 10.67 0.00 46.65 3.21
113 114 6.313519 ACAAGGAGATAATGTACCATGTGT 57.686 37.500 0.00 0.00 33.97 3.72
114 115 6.349300 ACAAGGAGATAATGTACCATGTGTC 58.651 40.000 0.00 0.00 33.97 3.67
115 116 6.070251 ACAAGGAGATAATGTACCATGTGTCA 60.070 38.462 0.00 0.00 33.97 3.58
116 117 6.753913 AGGAGATAATGTACCATGTGTCAT 57.246 37.500 0.00 0.00 0.00 3.06
117 118 7.855784 AGGAGATAATGTACCATGTGTCATA 57.144 36.000 0.00 0.00 0.00 2.15
118 119 7.901029 AGGAGATAATGTACCATGTGTCATAG 58.099 38.462 0.00 0.00 0.00 2.23
296 298 3.080641 CCCATCTGTCAGCCCACA 58.919 61.111 0.00 0.00 0.00 4.17
397 422 0.543174 ACACACTCTCTCACTCCCCC 60.543 60.000 0.00 0.00 0.00 5.40
666 691 1.815003 CGCATCCACGCTGATCCAA 60.815 57.895 0.00 0.00 0.00 3.53
845 875 8.426489 TGGTTAAGTCAGTGTATAAGAAAGTGT 58.574 33.333 0.00 0.00 0.00 3.55
875 918 6.861055 CGTTAGTTCATTTGGTTAGTGCATTT 59.139 34.615 0.00 0.00 0.00 2.32
1306 1355 5.010282 ACAGAGTTTCACAAGAAGGTGTTT 58.990 37.500 0.00 0.00 39.76 2.83
1404 1453 4.729227 TTTGAACAAGGGGAAAACAGTC 57.271 40.909 0.00 0.00 0.00 3.51
1405 1454 3.374042 TGAACAAGGGGAAAACAGTCA 57.626 42.857 0.00 0.00 0.00 3.41
1676 1758 7.122048 TCTGAAGATGAAGAAGTAGAGGATCA 58.878 38.462 0.00 0.00 37.82 2.92
1770 1852 0.801251 GTGAGCCTGAGCACATCAAC 59.199 55.000 0.00 0.00 41.77 3.18
1901 1983 3.299503 AGCAGAAGAAGGAGAGGAGATC 58.700 50.000 0.00 0.00 0.00 2.75
2114 2197 1.137872 AGTTGCCTCCAAGATAGCTCG 59.862 52.381 0.00 0.00 0.00 5.03
2148 2231 8.816894 ACTTTCAGTATCAAGAAGATGAACCTA 58.183 33.333 0.00 0.00 37.57 3.08
2189 2272 3.117131 AGTGGGGAGAAAACAAAGGTGAT 60.117 43.478 0.00 0.00 0.00 3.06
2255 2338 0.037303 CCTGGAGCTGGTGTTGACAT 59.963 55.000 0.00 0.00 0.00 3.06
2554 2639 8.792633 GCATGCCATTTATAGGTAAGTATTCAA 58.207 33.333 6.36 0.00 0.00 2.69
2739 2824 5.775195 TGTTGATAAGGAAGAGACAGACAGA 59.225 40.000 0.00 0.00 0.00 3.41
2743 2828 2.465813 AGGAAGAGACAGACAGATGGG 58.534 52.381 0.00 0.00 0.00 4.00
2962 3047 8.605065 TGAATGCAATAGATGATGTATTCCCTA 58.395 33.333 12.01 0.00 43.61 3.53
2976 3061 5.783360 TGTATTCCCTAACTCTCCACAAAGA 59.217 40.000 0.00 0.00 0.00 2.52
3051 3136 8.937884 GGAGAGGAACTTAAGAAACATTTAGAC 58.062 37.037 10.09 0.00 41.55 2.59
3111 3196 8.782339 ATTTAGGCATGGAGAATTTGAAAAAG 57.218 30.769 0.00 0.00 0.00 2.27
3335 4138 4.211125 TGGTTCTTCAATGGTTGCAACTA 58.789 39.130 27.64 23.36 0.00 2.24
3420 4223 2.554142 TGAGTCAACACAGACAGCTTG 58.446 47.619 0.00 0.00 40.98 4.01
3455 4258 2.305927 AGGGCAACACTAGCTACAACAT 59.694 45.455 0.00 0.00 39.74 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.942338 TCACGCATAATTACAGTTCTATTTCT 57.058 30.769 0.00 0.00 0.00 2.52
7 8 8.818057 ACTCACGCATAATTACAGTTCTATTTC 58.182 33.333 0.00 0.00 0.00 2.17
9 10 8.604035 CAACTCACGCATAATTACAGTTCTATT 58.396 33.333 0.00 0.00 0.00 1.73
12 13 5.163854 GCAACTCACGCATAATTACAGTTCT 60.164 40.000 0.00 0.00 0.00 3.01
13 14 5.022021 GCAACTCACGCATAATTACAGTTC 58.978 41.667 0.00 0.00 0.00 3.01
14 15 4.454161 TGCAACTCACGCATAATTACAGTT 59.546 37.500 0.00 0.00 33.55 3.16
15 16 4.000325 TGCAACTCACGCATAATTACAGT 59.000 39.130 0.00 0.00 33.55 3.55
16 17 4.598406 TGCAACTCACGCATAATTACAG 57.402 40.909 0.00 0.00 33.55 2.74
25 26 3.373748 CCAAGTTATATGCAACTCACGCA 59.626 43.478 0.00 0.00 44.94 5.24
26 27 3.374058 ACCAAGTTATATGCAACTCACGC 59.626 43.478 0.00 0.00 37.78 5.34
27 28 4.391830 ACACCAAGTTATATGCAACTCACG 59.608 41.667 0.00 0.00 37.78 4.35
28 29 5.880054 ACACCAAGTTATATGCAACTCAC 57.120 39.130 0.00 0.00 37.78 3.51
29 30 5.182950 CCAACACCAAGTTATATGCAACTCA 59.817 40.000 0.00 0.00 38.74 3.41
30 31 5.183140 ACCAACACCAAGTTATATGCAACTC 59.817 40.000 0.00 0.00 38.74 3.01
31 32 5.076873 ACCAACACCAAGTTATATGCAACT 58.923 37.500 0.00 0.00 38.74 3.16
32 33 5.385509 ACCAACACCAAGTTATATGCAAC 57.614 39.130 0.00 0.00 38.74 4.17
33 34 6.490381 TGTTACCAACACCAAGTTATATGCAA 59.510 34.615 0.00 0.00 38.74 4.08
34 35 6.004574 TGTTACCAACACCAAGTTATATGCA 58.995 36.000 0.00 0.00 38.74 3.96
35 36 6.373216 TCTGTTACCAACACCAAGTTATATGC 59.627 38.462 0.00 0.00 38.74 3.14
36 37 7.915293 TCTGTTACCAACACCAAGTTATATG 57.085 36.000 0.00 0.00 38.74 1.78
37 38 7.556275 CCATCTGTTACCAACACCAAGTTATAT 59.444 37.037 0.00 0.00 38.74 0.86
38 39 6.882140 CCATCTGTTACCAACACCAAGTTATA 59.118 38.462 0.00 0.00 38.74 0.98
39 40 5.710099 CCATCTGTTACCAACACCAAGTTAT 59.290 40.000 0.00 0.00 38.74 1.89
40 41 5.067273 CCATCTGTTACCAACACCAAGTTA 58.933 41.667 0.00 0.00 38.74 2.24
41 42 3.888930 CCATCTGTTACCAACACCAAGTT 59.111 43.478 0.00 0.00 42.42 2.66
42 43 3.117663 ACCATCTGTTACCAACACCAAGT 60.118 43.478 0.00 0.00 36.25 3.16
43 44 3.486383 ACCATCTGTTACCAACACCAAG 58.514 45.455 0.00 0.00 36.25 3.61
44 45 3.117851 TGACCATCTGTTACCAACACCAA 60.118 43.478 0.00 0.00 36.25 3.67
45 46 2.439880 TGACCATCTGTTACCAACACCA 59.560 45.455 0.00 0.00 36.25 4.17
46 47 3.074412 CTGACCATCTGTTACCAACACC 58.926 50.000 0.00 0.00 36.25 4.16
47 48 3.740115 ACTGACCATCTGTTACCAACAC 58.260 45.455 0.00 0.00 36.25 3.32
48 49 5.554437 TTACTGACCATCTGTTACCAACA 57.446 39.130 0.00 0.00 39.52 3.33
49 50 9.257651 GTATATTACTGACCATCTGTTACCAAC 57.742 37.037 0.00 0.00 31.00 3.77
50 51 9.209048 AGTATATTACTGACCATCTGTTACCAA 57.791 33.333 0.00 0.00 37.69 3.67
51 52 8.777578 AGTATATTACTGACCATCTGTTACCA 57.222 34.615 0.00 0.00 37.69 3.25
52 53 9.694137 GAAGTATATTACTGACCATCTGTTACC 57.306 37.037 0.00 0.00 39.39 2.85
55 56 9.823647 CAAGAAGTATATTACTGACCATCTGTT 57.176 33.333 0.00 0.00 39.39 3.16
56 57 9.201989 TCAAGAAGTATATTACTGACCATCTGT 57.798 33.333 0.00 0.00 39.39 3.41
57 58 9.689976 CTCAAGAAGTATATTACTGACCATCTG 57.310 37.037 0.00 0.00 39.39 2.90
58 59 8.364142 GCTCAAGAAGTATATTACTGACCATCT 58.636 37.037 0.00 0.00 39.39 2.90
59 60 8.364142 AGCTCAAGAAGTATATTACTGACCATC 58.636 37.037 0.00 0.00 39.39 3.51
60 61 8.256356 AGCTCAAGAAGTATATTACTGACCAT 57.744 34.615 0.00 0.00 39.39 3.55
61 62 7.661536 AGCTCAAGAAGTATATTACTGACCA 57.338 36.000 0.00 0.00 39.39 4.02
62 63 9.685828 CTTAGCTCAAGAAGTATATTACTGACC 57.314 37.037 0.00 0.00 39.39 4.02
70 71 9.422681 TCCTTGTACTTAGCTCAAGAAGTATAT 57.577 33.333 12.40 0.00 39.63 0.86
71 72 8.818622 TCCTTGTACTTAGCTCAAGAAGTATA 57.181 34.615 12.40 6.58 39.63 1.47
72 73 7.616150 TCTCCTTGTACTTAGCTCAAGAAGTAT 59.384 37.037 12.40 0.00 39.63 2.12
73 74 6.946583 TCTCCTTGTACTTAGCTCAAGAAGTA 59.053 38.462 12.40 7.95 40.35 2.24
74 75 5.775701 TCTCCTTGTACTTAGCTCAAGAAGT 59.224 40.000 12.40 8.87 40.35 3.01
75 76 6.274157 TCTCCTTGTACTTAGCTCAAGAAG 57.726 41.667 12.40 3.32 40.35 2.85
76 77 6.859112 ATCTCCTTGTACTTAGCTCAAGAA 57.141 37.500 12.40 0.00 40.35 2.52
77 78 7.956328 TTATCTCCTTGTACTTAGCTCAAGA 57.044 36.000 12.40 0.00 40.35 3.02
78 79 8.200792 ACATTATCTCCTTGTACTTAGCTCAAG 58.799 37.037 5.36 5.36 40.38 3.02
79 80 8.079211 ACATTATCTCCTTGTACTTAGCTCAA 57.921 34.615 0.00 0.00 0.00 3.02
80 81 7.661536 ACATTATCTCCTTGTACTTAGCTCA 57.338 36.000 0.00 0.00 0.00 4.26
81 82 8.083462 GGTACATTATCTCCTTGTACTTAGCTC 58.917 40.741 11.04 0.00 43.25 4.09
82 83 7.563924 TGGTACATTATCTCCTTGTACTTAGCT 59.436 37.037 11.04 0.00 43.25 3.32
83 84 7.723324 TGGTACATTATCTCCTTGTACTTAGC 58.277 38.462 11.04 0.00 43.25 3.09
103 104 7.569639 TTACTCTCTCTATGACACATGGTAC 57.430 40.000 0.00 0.00 0.00 3.34
104 105 8.768501 ATTTACTCTCTCTATGACACATGGTA 57.231 34.615 0.00 0.00 0.00 3.25
105 106 7.667575 ATTTACTCTCTCTATGACACATGGT 57.332 36.000 0.00 0.00 0.00 3.55
106 107 7.812191 GCTATTTACTCTCTCTATGACACATGG 59.188 40.741 0.00 0.00 0.00 3.66
107 108 8.355913 TGCTATTTACTCTCTCTATGACACATG 58.644 37.037 0.00 0.00 0.00 3.21
108 109 8.470657 TGCTATTTACTCTCTCTATGACACAT 57.529 34.615 0.00 0.00 0.00 3.21
109 110 7.881775 TGCTATTTACTCTCTCTATGACACA 57.118 36.000 0.00 0.00 0.00 3.72
275 277 4.864334 GGCTGACAGATGGGCCCG 62.864 72.222 19.37 4.81 38.77 6.13
397 422 2.612251 GAGAGGAGGGGGAGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
446 471 3.982424 GACGACATTTGGCTGCGCG 62.982 63.158 0.00 0.00 0.00 6.86
845 875 8.231837 GCACTAACCAAATGAACTAACGAAATA 58.768 33.333 0.00 0.00 0.00 1.40
850 880 5.351233 TGCACTAACCAAATGAACTAACG 57.649 39.130 0.00 0.00 0.00 3.18
1051 1100 2.170166 GCCATCCAACTCAACCAATGA 58.830 47.619 0.00 0.00 36.38 2.57
1306 1355 0.902531 GCACTAGAGGCAGGGTACAA 59.097 55.000 0.00 0.00 0.00 2.41
1404 1453 5.183969 TCTTCTGCATCTTCTTCTTCCATG 58.816 41.667 0.00 0.00 0.00 3.66
1405 1454 5.432680 TCTTCTGCATCTTCTTCTTCCAT 57.567 39.130 0.00 0.00 0.00 3.41
1613 1695 4.041691 CCTCCCAAAACTCAGAAGGTTCTA 59.958 45.833 0.00 0.00 35.34 2.10
1676 1758 3.820467 TGCTTTTGTAGTTACAGCAGCAT 59.180 39.130 17.05 0.00 42.86 3.79
1770 1852 5.884792 AGCTTCAGGGACATAATCTTCAAAG 59.115 40.000 0.00 0.00 0.00 2.77
1901 1983 3.278574 TCAGGCCTTTTTGGATCATACG 58.721 45.455 0.00 0.00 38.35 3.06
2053 2136 5.227569 TGTTTTCTATCAGAGCACCAAGA 57.772 39.130 0.00 0.00 0.00 3.02
2172 2255 5.998363 ACTGACTATCACCTTTGTTTTCTCC 59.002 40.000 0.00 0.00 0.00 3.71
2189 2272 2.976882 ACCTTAGCAACCCAACTGACTA 59.023 45.455 0.00 0.00 0.00 2.59
2394 2477 2.288273 GCCAGGGTTAGTATCTAGCACG 60.288 54.545 0.00 0.00 0.00 5.34
2570 2655 8.630054 AGTGCCTAAGTACATCAATGTTTAAA 57.370 30.769 0.20 0.00 41.97 1.52
2739 2824 1.203038 TGTGTGAGAAACCATGCCCAT 60.203 47.619 0.00 0.00 0.00 4.00
2743 2828 2.618241 TCAACTGTGTGAGAAACCATGC 59.382 45.455 0.00 0.00 0.00 4.06
2927 3012 5.302568 TCATCTATTGCATTCAACAATCCCC 59.697 40.000 0.00 0.00 38.62 4.81
2962 3047 7.993183 TCTAAGACAAAATCTTTGTGGAGAGTT 59.007 33.333 9.39 0.00 46.05 3.01
3051 3136 2.576615 GTAAAGGAATAGGCAGCCTGG 58.423 52.381 25.59 0.00 34.61 4.45
3111 3196 2.890945 TGCCCTTGCTTCTAAACTTTCC 59.109 45.455 0.00 0.00 38.71 3.13
3294 4097 2.289945 CCAGCCTCAGAGTAGTTTGCTT 60.290 50.000 0.00 0.00 0.00 3.91
3335 4138 1.457455 CCCTTGGTGGCCTTTGTGT 60.457 57.895 3.32 0.00 0.00 3.72
3381 4184 4.202609 ACTCATTTGTTGTTGGAGGAGGAT 60.203 41.667 0.00 0.00 0.00 3.24
3420 4223 3.055094 TGTTGCCCTCTTCCTTGATCTAC 60.055 47.826 0.00 0.00 0.00 2.59
3455 4258 1.053835 TTGAGAGGTGGTGGTGCTGA 61.054 55.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.