Multiple sequence alignment - TraesCS3D01G487100

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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 TraesCS3D01G487100 chr3D 100.000 2320 0 0 1 2320 582796856 582799175 0.000000e+00 4285
1 TraesCS3D01G487100 chr4D 96.560 2209 73 3 115 2320 496006354 496008562 0.000000e+00 3655
2 TraesCS3D01G487100 chr7D 95.993 2221 86 3 103 2320 463977694 463979914 0.000000e+00 3605
3 TraesCS3D01G487100 chr2D 95.905 2222 86 5 103 2320 63681806 63684026 0.000000e+00 3594
4 TraesCS3D01G487100 chr6D 95.801 2215 89 4 103 2314 80672920 80670707 0.000000e+00 3572
5 TraesCS3D01G487100 chr6D 96.190 105 4 0 6 110 356602625 356602729 3.060000e-39 172
6 TraesCS3D01G487100 chr6D 95.283 106 5 0 8 113 467773478 467773583 3.960000e-38 169
7 TraesCS3D01G487100 chr5D 95.504 2224 92 7 103 2320 60521530 60519309 0.000000e+00 3546
8 TraesCS3D01G487100 chr5D 98.020 101 2 0 7 107 266749453 266749353 2.370000e-40 176
9 TraesCS3D01G487100 chr5D 95.327 107 5 0 6 112 565043190 565043084 1.100000e-38 171
10 TraesCS3D01G487100 chr7A 95.050 2222 106 4 103 2320 89990516 89988295 0.000000e+00 3491
11 TraesCS3D01G487100 chr3A 94.509 2222 117 5 103 2320 328922764 328924984 0.000000e+00 3422
12 TraesCS3D01G487100 chr5B 94.163 2227 118 9 103 2320 415774198 415771975 0.000000e+00 3382
13 TraesCS3D01G487100 chr5B 94.545 110 4 2 8 116 625959558 625959450 3.960000e-38 169
14 TraesCS3D01G487100 chr2B 94.163 2227 119 8 103 2320 631382466 631380242 0.000000e+00 3382
15 TraesCS3D01G487100 chr2B 94.545 110 4 2 4 113 766523843 766523736 3.960000e-38 169
16 TraesCS3D01G487100 chr4B 98.020 101 2 0 7 107 581064814 581064914 2.370000e-40 176
17 TraesCS3D01G487100 chr6B 97.030 101 3 0 7 107 633054017 633054117 1.100000e-38 171
18 TraesCS3D01G487100 chr6A 94.545 110 6 0 8 117 11165152 11165043 1.100000e-38 171


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 TraesCS3D01G487100 chr3D 582796856 582799175 2319 False 4285 4285 100.000 1 2320 1 chr3D.!!$F1 2319
1 TraesCS3D01G487100 chr4D 496006354 496008562 2208 False 3655 3655 96.560 115 2320 1 chr4D.!!$F1 2205
2 TraesCS3D01G487100 chr7D 463977694 463979914 2220 False 3605 3605 95.993 103 2320 1 chr7D.!!$F1 2217
3 TraesCS3D01G487100 chr2D 63681806 63684026 2220 False 3594 3594 95.905 103 2320 1 chr2D.!!$F1 2217
4 TraesCS3D01G487100 chr6D 80670707 80672920 2213 True 3572 3572 95.801 103 2314 1 chr6D.!!$R1 2211
5 TraesCS3D01G487100 chr5D 60519309 60521530 2221 True 3546 3546 95.504 103 2320 1 chr5D.!!$R1 2217
6 TraesCS3D01G487100 chr7A 89988295 89990516 2221 True 3491 3491 95.050 103 2320 1 chr7A.!!$R1 2217
7 TraesCS3D01G487100 chr3A 328922764 328924984 2220 False 3422 3422 94.509 103 2320 1 chr3A.!!$F1 2217
8 TraesCS3D01G487100 chr5B 415771975 415774198 2223 True 3382 3382 94.163 103 2320 1 chr5B.!!$R1 2217
9 TraesCS3D01G487100 chr2B 631380242 631382466 2224 True 3382 3382 94.163 103 2320 1 chr2B.!!$R1 2217

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
906 912 0.037232 AGCCTTCTTGTACCGTCAGC 60.037 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2053 0.038526 CGTTTCTCTACCAGGTGCGT 60.039 55.0 0.76 0.0 0.0 5.24 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
20 21 0.831307 AAAGCATACTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
21 22 1.049289 AAGCATACTCCCTCCGTCCC 61.049 60.000 0.00 0.00 0.00 4.46
22 23 1.760875 GCATACTCCCTCCGTCCCA 60.761 63.158 0.00 0.00 0.00 4.37
23 24 1.335132 GCATACTCCCTCCGTCCCAA 61.335 60.000 0.00 0.00 0.00 4.12
24 25 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
25 26 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
26 27 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
27 28 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
28 29 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
29 30 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
30 31 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
31 32 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
32 33 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
33 34 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
34 35 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
35 36 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
36 37 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
37 38 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
38 39 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
39 40 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
40 41 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
41 42 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
42 43 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
43 44 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
55 56 9.857957 GTGACTCAACTTTATACTAGCTTTAGT 57.142 33.333 0.00 0.00 0.00 2.24
73 74 9.828039 AGCTTTAGTACAAAGTTAGTACAAACT 57.172 29.630 14.90 0.00 43.24 2.66
79 80 9.310716 AGTACAAAGTTAGTACAAACTTGAGTC 57.689 33.333 2.97 0.00 46.40 3.36
80 81 9.090692 GTACAAAGTTAGTACAAACTTGAGTCA 57.909 33.333 2.97 0.00 46.40 3.41
81 82 7.971455 ACAAAGTTAGTACAAACTTGAGTCAC 58.029 34.615 2.97 0.00 46.40 3.67
82 83 7.822822 ACAAAGTTAGTACAAACTTGAGTCACT 59.177 33.333 2.97 0.00 46.40 3.41
83 84 8.665685 CAAAGTTAGTACAAACTTGAGTCACTT 58.334 33.333 2.97 0.00 46.40 3.16
84 85 9.880157 AAAGTTAGTACAAACTTGAGTCACTTA 57.120 29.630 2.97 0.00 46.40 2.24
90 91 8.621286 AGTACAAACTTGAGTCACTTATTTTGG 58.379 33.333 9.57 0.00 29.00 3.28
91 92 6.805713 ACAAACTTGAGTCACTTATTTTGGG 58.194 36.000 9.57 0.00 0.00 4.12
92 93 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
93 94 6.635030 AACTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
94 95 4.755123 ACTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
95 96 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
96 97 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
97 98 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
98 99 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
99 100 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
100 101 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
101 102 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
193 194 5.784177 TGATTATTACGAGGAGAAGCATCC 58.216 41.667 0.00 0.00 39.89 3.51
217 218 1.992557 TGTGCTAATGGAAAGAGGGGT 59.007 47.619 0.00 0.00 0.00 4.95
237 238 7.918076 AGGGGTGGTAATTATGTATCTACATG 58.082 38.462 12.10 0.00 45.77 3.21
255 260 8.893219 TCTACATGGTTGATTCTCATATTGTC 57.107 34.615 0.00 0.00 0.00 3.18
445 451 1.079819 CATGGCTGAACTCGACGGT 60.080 57.895 0.00 0.00 0.00 4.83
548 554 2.544685 GATATTGCGATGATCTCCGGG 58.455 52.381 0.00 0.00 0.00 5.73
574 580 0.472734 ATCGAGGGCAGGGCTCTTAT 60.473 55.000 0.00 0.00 40.72 1.73
677 683 2.037385 AGAAGGATCCTAGGCCATCC 57.963 55.000 16.55 18.10 39.24 3.51
701 707 2.869801 TGTTTTGTTCTCGTGGCTACAG 59.130 45.455 0.00 0.00 0.00 2.74
720 726 3.880490 ACAGGAACATTTTTACGAGTGCA 59.120 39.130 0.00 0.00 0.00 4.57
847 853 2.356227 GGATGTTCTTGGACCCTCTTCC 60.356 54.545 0.00 0.00 36.03 3.46
906 912 0.037232 AGCCTTCTTGTACCGTCAGC 60.037 55.000 0.00 0.00 0.00 4.26
1035 1043 5.049828 CCAAAATCTTGTCTTGGTGGTTTC 58.950 41.667 0.00 0.00 35.80 2.78
1100 1108 2.699954 CCGTAACTTCACCATTGCTCT 58.300 47.619 0.00 0.00 0.00 4.09
1110 1118 1.089920 CCATTGCTCTGGAAGAACCG 58.910 55.000 0.00 0.00 46.34 4.44
1124 1132 1.833787 GAACCGTGGGAGTGGCCTTA 61.834 60.000 3.32 0.00 36.66 2.69
1156 1164 1.147191 AGGAGCGGTATCCCACTATCA 59.853 52.381 0.00 0.00 40.53 2.15
1280 1288 5.818678 ATCAAATGCCTTGCCATCATTAT 57.181 34.783 0.00 0.00 34.76 1.28
1324 1334 3.618594 GCGAGTGACATGTTGTGATGTAT 59.381 43.478 0.00 0.00 36.67 2.29
1404 1414 0.387239 GACCAACATCTTTGGCGTGC 60.387 55.000 2.85 0.00 43.23 5.34
1410 1420 3.308878 ATCTTTGGCGTGCGCGTTC 62.309 57.895 22.18 14.20 43.06 3.95
1422 1433 2.516486 CGCGTTCGCCATGATATGA 58.484 52.632 11.51 0.00 0.00 2.15
1490 1503 0.250166 GGAGTACAACAACGCACCCT 60.250 55.000 0.00 0.00 0.00 4.34
1502 1516 2.555547 GCACCCTGCCGGATTATGC 61.556 63.158 5.05 3.68 37.42 3.14
1511 1525 2.288666 GCCGGATTATGCTGAGACAAA 58.711 47.619 5.05 0.00 0.00 2.83
1539 1553 5.344884 GTGCTACATAGGTGAGAGTTTCTC 58.655 45.833 0.00 0.00 43.65 2.87
1540 1554 5.126384 GTGCTACATAGGTGAGAGTTTCTCT 59.874 44.000 7.52 0.00 43.73 3.10
1567 1582 7.062322 ACCATATGTTGATCAATGTGTACCAT 58.938 34.615 12.12 10.54 34.36 3.55
1621 1637 2.102109 TTGTAGGACGAGCCGGCAAA 62.102 55.000 31.54 0.00 43.43 3.68
1681 1697 1.146774 TGTGGGTGGACATGTGGAATT 59.853 47.619 1.15 0.00 0.00 2.17
1752 1768 3.903714 AGGGGGCATATTTAAGGCATTTC 59.096 43.478 0.00 0.00 0.00 2.17
1811 1827 1.298859 GCTTGGACTCGTGCCGATTT 61.299 55.000 0.00 0.00 34.61 2.17
1995 2011 6.010219 ACTTATGTTTTATTCAGGGCACAGT 58.990 36.000 0.00 0.00 0.00 3.55
2037 2053 0.112218 AGTAATGTGGTGCTTGGCCA 59.888 50.000 0.00 0.00 0.00 5.36
2112 2130 6.995091 AGAGGCCTTCTTAATATGAACATGTC 59.005 38.462 6.77 0.00 29.61 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.037144 GGACGGAGGGAGTATGCTTTA 58.963 52.381 0.00 0.00 0.00 1.85
1 2 0.831307 GGACGGAGGGAGTATGCTTT 59.169 55.000 0.00 0.00 0.00 3.51
2 3 1.049289 GGGACGGAGGGAGTATGCTT 61.049 60.000 0.00 0.00 0.00 3.91
3 4 1.457831 GGGACGGAGGGAGTATGCT 60.458 63.158 0.00 0.00 0.00 3.79
4 5 1.335132 TTGGGACGGAGGGAGTATGC 61.335 60.000 0.00 0.00 0.00 3.14
5 6 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
6 7 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
7 8 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
8 9 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
9 10 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
10 11 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
11 12 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
12 13 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
13 14 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
14 15 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
15 16 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
16 17 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
17 18 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
18 19 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
29 30 9.857957 ACTAAAGCTAGTATAAAGTTGAGTCAC 57.142 33.333 0.00 0.00 36.56 3.67
47 48 9.828039 AGTTTGTACTAACTTTGTACTAAAGCT 57.172 29.630 15.68 7.77 40.44 3.74
53 54 9.310716 GACTCAAGTTTGTACTAACTTTGTACT 57.689 33.333 26.14 11.72 43.85 2.73
54 55 9.090692 TGACTCAAGTTTGTACTAACTTTGTAC 57.909 33.333 26.14 19.04 43.85 2.90
55 56 9.090692 GTGACTCAAGTTTGTACTAACTTTGTA 57.909 33.333 26.14 16.32 43.85 2.41
56 57 7.822822 AGTGACTCAAGTTTGTACTAACTTTGT 59.177 33.333 26.14 25.01 43.85 2.83
57 58 8.197988 AGTGACTCAAGTTTGTACTAACTTTG 57.802 34.615 26.14 22.84 43.85 2.77
58 59 8.788325 AAGTGACTCAAGTTTGTACTAACTTT 57.212 30.769 26.14 15.97 43.85 2.66
64 65 8.621286 CCAAAATAAGTGACTCAAGTTTGTACT 58.379 33.333 15.07 0.00 35.68 2.73
65 66 7.860872 CCCAAAATAAGTGACTCAAGTTTGTAC 59.139 37.037 15.07 0.00 0.00 2.90
66 67 7.776030 TCCCAAAATAAGTGACTCAAGTTTGTA 59.224 33.333 15.07 5.29 0.00 2.41
67 68 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
68 69 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
69 70 6.238648 CGTCCCAAAATAAGTGACTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
70 71 5.238650 CGTCCCAAAATAAGTGACTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
71 72 4.755123 CGTCCCAAAATAAGTGACTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
72 73 4.154195 CCGTCCCAAAATAAGTGACTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
73 74 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
74 75 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
75 76 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
76 77 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
77 78 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
78 79 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
79 80 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
80 81 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
81 82 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
82 83 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
83 84 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
84 85 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
85 86 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
86 87 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
87 88 2.178325 TGATATACTCCCTCCGTCCCAA 59.822 50.000 0.00 0.00 0.00 4.12
88 89 1.784593 TGATATACTCCCTCCGTCCCA 59.215 52.381 0.00 0.00 0.00 4.37
89 90 2.599408 TGATATACTCCCTCCGTCCC 57.401 55.000 0.00 0.00 0.00 4.46
90 91 4.645588 CCTTATGATATACTCCCTCCGTCC 59.354 50.000 0.00 0.00 0.00 4.79
91 92 5.507637 TCCTTATGATATACTCCCTCCGTC 58.492 45.833 0.00 0.00 0.00 4.79
92 93 5.531753 TCCTTATGATATACTCCCTCCGT 57.468 43.478 0.00 0.00 0.00 4.69
93 94 6.041069 GGATTCCTTATGATATACTCCCTCCG 59.959 46.154 0.00 0.00 0.00 4.63
94 95 6.903534 TGGATTCCTTATGATATACTCCCTCC 59.096 42.308 3.95 0.00 0.00 4.30
95 96 7.979786 TGGATTCCTTATGATATACTCCCTC 57.020 40.000 3.95 0.00 0.00 4.30
96 97 8.776119 CAATGGATTCCTTATGATATACTCCCT 58.224 37.037 3.95 0.00 0.00 4.20
97 98 8.772250 TCAATGGATTCCTTATGATATACTCCC 58.228 37.037 3.95 0.00 0.00 4.30
98 99 9.606631 GTCAATGGATTCCTTATGATATACTCC 57.393 37.037 3.95 0.00 0.00 3.85
99 100 9.606631 GGTCAATGGATTCCTTATGATATACTC 57.393 37.037 3.95 0.00 0.00 2.59
100 101 9.343994 AGGTCAATGGATTCCTTATGATATACT 57.656 33.333 3.95 2.01 0.00 2.12
101 102 9.965902 AAGGTCAATGGATTCCTTATGATATAC 57.034 33.333 3.95 0.00 38.34 1.47
164 165 7.148641 GCTTCTCCTCGTAATAATCATCAAGA 58.851 38.462 0.00 0.00 0.00 3.02
193 194 2.681848 CCTCTTTCCATTAGCACAGCAG 59.318 50.000 0.00 0.00 0.00 4.24
204 205 5.195756 ACATAATTACCACCCCTCTTTCCAT 59.804 40.000 0.00 0.00 0.00 3.41
341 347 1.065701 CGACGGTCATACTTCAGGGAG 59.934 57.143 9.10 0.00 0.00 4.30
548 554 2.279784 CTGCCCTCGATCGGAAGC 60.280 66.667 16.41 15.29 0.00 3.86
574 580 1.257743 CTCAGACTTCACCTTCCCGA 58.742 55.000 0.00 0.00 0.00 5.14
677 683 0.316689 GCCACGAGAACAAAACACCG 60.317 55.000 0.00 0.00 0.00 4.94
701 707 4.024387 TCTGTGCACTCGTAAAAATGTTCC 60.024 41.667 19.41 0.00 0.00 3.62
720 726 1.599047 CCGGACTGGCATTCTCTGT 59.401 57.895 0.00 0.00 0.00 3.41
847 853 5.422214 ACTCCACTTAACATCCCAGTTAG 57.578 43.478 0.00 0.00 35.57 2.34
1035 1043 1.472480 CAAATCTGTAGGGCCCAAACG 59.528 52.381 27.56 16.80 0.00 3.60
1073 1081 0.322187 GGTGAAGTTACGGCCCACAT 60.322 55.000 0.00 0.00 0.00 3.21
1100 1108 1.752198 CACTCCCACGGTTCTTCCA 59.248 57.895 0.00 0.00 35.57 3.53
1110 1118 0.462047 CGTCATAAGGCCACTCCCAC 60.462 60.000 5.01 0.00 34.51 4.61
1124 1132 2.502492 CGCTCCTCATCCCCGTCAT 61.502 63.158 0.00 0.00 0.00 3.06
1156 1164 1.203994 GACAGTAGCCCACGTGTATGT 59.796 52.381 15.65 9.22 0.00 2.29
1304 1314 6.486253 AACATACATCACAACATGTCACTC 57.514 37.500 0.00 0.00 38.07 3.51
1324 1334 3.275143 CATGTACGGCCTCCAATTAACA 58.725 45.455 0.00 0.00 0.00 2.41
1404 1414 1.070821 ATCATATCATGGCGAACGCG 58.929 50.000 3.53 3.53 43.06 6.01
1490 1503 0.829990 TGTCTCAGCATAATCCGGCA 59.170 50.000 0.00 0.00 0.00 5.69
1497 1511 3.191162 GCACCACATTTGTCTCAGCATAA 59.809 43.478 0.00 0.00 0.00 1.90
1502 1516 3.402110 TGTAGCACCACATTTGTCTCAG 58.598 45.455 0.00 0.00 0.00 3.35
1511 1525 3.374764 TCTCACCTATGTAGCACCACAT 58.625 45.455 4.36 4.36 41.88 3.21
1539 1553 8.559536 GGTACACATTGATCAACATATGGTAAG 58.440 37.037 11.07 0.72 0.00 2.34
1540 1554 8.049721 TGGTACACATTGATCAACATATGGTAA 58.950 33.333 11.07 0.00 0.00 2.85
1567 1582 8.746052 AGTATCGGTATCAATTTCATTTTCCA 57.254 30.769 0.00 0.00 0.00 3.53
1621 1637 6.549364 TCCCAATTAGTGACATTCTTGTTGTT 59.451 34.615 0.00 0.00 35.79 2.83
1681 1697 0.324738 ACTCGGGCATTCCTCTGAGA 60.325 55.000 6.17 0.00 33.44 3.27
1880 1896 1.699634 GAGGGCCATAATCTAGGTGCA 59.300 52.381 6.18 0.00 0.00 4.57
1943 1959 4.074970 ACCACTCATGAAGAAATGACACC 58.925 43.478 0.00 0.00 33.08 4.16
1995 2011 8.371571 ACTATCATTGATACATCTCCATAGCA 57.628 34.615 2.14 0.00 0.00 3.49
2037 2053 0.038526 CGTTTCTCTACCAGGTGCGT 60.039 55.000 0.76 0.00 0.00 5.24
2148 2166 3.146618 GCAGAGGCAAAGACATTGATG 57.853 47.619 0.00 0.00 41.85 3.07
2196 2214 1.443802 GCAAGAGAGTAAAGCGGCTT 58.556 50.000 9.94 9.94 0.00 4.35


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

AutoCloner maintained by Alex Coulton.