Multiple sequence alignment - TraesCS3D01G316100

Loading Multiple Alignment...

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 TraesCS3D01G316100 chr3D 100.000 2336 0 0 1 2336 429600108 429597773 0.000000e+00 4314
1 TraesCS3D01G316100 chr3D 98.925 93 1 0 1 93 1039928 1039836 1.440000e-37 167
2 TraesCS3D01G316100 chr3D 96.939 98 2 1 1 98 321937558 321937654 1.860000e-36 163
3 TraesCS3D01G316100 chr3B 91.943 2296 107 36 94 2336 561542179 561539909 0.000000e+00 3144
4 TraesCS3D01G316100 chr3A 90.999 2222 130 23 159 2336 556458086 556460281 0.000000e+00 2931
5 TraesCS3D01G316100 chr2D 97.980 99 2 0 1 99 487266559 487266461 3.090000e-39 172
6 TraesCS3D01G316100 chr2D 98.947 95 1 0 1 95 125441482 125441388 1.110000e-38 171
7 TraesCS3D01G316100 chr5D 97.938 97 2 0 1 97 184091385 184091289 3.990000e-38 169
8 TraesCS3D01G316100 chr5D 96.117 103 3 1 1 103 16921276 16921175 1.440000e-37 167
9 TraesCS3D01G316100 chr5D 96.040 101 2 2 1 100 523458459 523458360 1.860000e-36 163
10 TraesCS3D01G316100 chr4D 98.925 93 1 0 1 93 105300060 105299968 1.440000e-37 167
11 TraesCS3D01G316100 chr4D 96.078 102 4 0 1 102 493896666 493896565 1.440000e-37 167


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 TraesCS3D01G316100 chr3D 429597773 429600108 2335 True 4314 4314 100.000 1 2336 1 chr3D.!!$R2 2335
1 TraesCS3D01G316100 chr3B 561539909 561542179 2270 True 3144 3144 91.943 94 2336 1 chr3B.!!$R1 2242
2 TraesCS3D01G316100 chr3A 556458086 556460281 2195 False 2931 2931 90.999 159 2336 1 chr3A.!!$F1 2177

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
34 35 0.109153 GGTACAAACCGACTTGGGGT 59.891 55.0 0.0 0.0 44.64 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1774 0.87439 GCAGACAACATTTCTCGGCA 59.126 50.0 0.0 0.0 0.0 5.69 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
33 34 2.936928 GGTACAAACCGACTTGGGG 58.063 57.895 0.00 0.00 44.64 4.96
34 35 0.109153 GGTACAAACCGACTTGGGGT 59.891 55.000 0.00 0.00 44.64 4.95
35 36 1.347378 GGTACAAACCGACTTGGGGTA 59.653 52.381 0.00 0.00 44.64 3.69
36 37 2.613725 GGTACAAACCGACTTGGGGTAG 60.614 54.545 0.00 0.00 44.64 3.18
37 38 1.426751 ACAAACCGACTTGGGGTAGA 58.573 50.000 0.00 0.00 44.64 2.59
38 39 1.346722 ACAAACCGACTTGGGGTAGAG 59.653 52.381 0.00 0.00 44.64 2.43
39 40 0.981943 AAACCGACTTGGGGTAGAGG 59.018 55.000 0.00 0.00 44.64 3.69
40 41 0.178912 AACCGACTTGGGGTAGAGGT 60.179 55.000 0.00 0.00 44.64 3.85
41 42 0.706433 ACCGACTTGGGGTAGAGGTA 59.294 55.000 0.00 0.00 44.64 3.08
42 43 1.109609 CCGACTTGGGGTAGAGGTAC 58.890 60.000 0.00 0.00 0.00 3.34
43 44 1.617804 CCGACTTGGGGTAGAGGTACA 60.618 57.143 0.00 0.00 0.00 2.90
44 45 2.173519 CGACTTGGGGTAGAGGTACAA 58.826 52.381 0.00 0.00 0.00 2.41
45 46 2.564062 CGACTTGGGGTAGAGGTACAAA 59.436 50.000 0.00 0.00 0.00 2.83
46 47 3.007182 CGACTTGGGGTAGAGGTACAAAA 59.993 47.826 0.00 0.00 0.00 2.44
47 48 4.321718 GACTTGGGGTAGAGGTACAAAAC 58.678 47.826 0.00 0.00 0.00 2.43
48 49 3.978672 ACTTGGGGTAGAGGTACAAAACT 59.021 43.478 0.00 0.00 0.00 2.66
49 50 4.202430 ACTTGGGGTAGAGGTACAAAACTG 60.202 45.833 0.00 0.00 0.00 3.16
50 51 3.589641 TGGGGTAGAGGTACAAAACTGA 58.410 45.455 0.00 0.00 0.00 3.41
51 52 3.325716 TGGGGTAGAGGTACAAAACTGAC 59.674 47.826 0.00 0.00 0.00 3.51
52 53 3.581770 GGGGTAGAGGTACAAAACTGACT 59.418 47.826 0.00 0.00 0.00 3.41
53 54 4.041321 GGGGTAGAGGTACAAAACTGACTT 59.959 45.833 0.00 0.00 0.00 3.01
54 55 4.995487 GGGTAGAGGTACAAAACTGACTTG 59.005 45.833 0.00 0.00 0.00 3.16
55 56 4.995487 GGTAGAGGTACAAAACTGACTTGG 59.005 45.833 0.00 0.00 0.00 3.61
56 57 5.221581 GGTAGAGGTACAAAACTGACTTGGA 60.222 44.000 0.00 0.00 0.00 3.53
57 58 4.704965 AGAGGTACAAAACTGACTTGGAC 58.295 43.478 0.00 1.73 36.96 4.02
58 59 4.409247 AGAGGTACAAAACTGACTTGGACT 59.591 41.667 0.00 0.00 37.69 3.85
59 60 5.601313 AGAGGTACAAAACTGACTTGGACTA 59.399 40.000 0.00 0.00 37.69 2.59
60 61 5.855045 AGGTACAAAACTGACTTGGACTAG 58.145 41.667 0.00 0.00 37.69 2.57
61 62 5.601313 AGGTACAAAACTGACTTGGACTAGA 59.399 40.000 0.00 0.00 37.69 2.43
62 63 6.099269 AGGTACAAAACTGACTTGGACTAGAA 59.901 38.462 0.00 0.00 37.69 2.10
63 64 6.424207 GGTACAAAACTGACTTGGACTAGAAG 59.576 42.308 0.00 0.00 37.69 2.85
64 65 5.990668 ACAAAACTGACTTGGACTAGAAGT 58.009 37.500 0.00 0.00 36.33 3.01
65 66 6.049790 ACAAAACTGACTTGGACTAGAAGTC 58.950 40.000 13.36 13.36 46.45 3.01
72 73 6.058827 GACTTGGACTAGAAGTCGTATACC 57.941 45.833 6.96 0.00 45.96 2.73
73 74 5.503927 ACTTGGACTAGAAGTCGTATACCA 58.496 41.667 0.00 0.00 45.96 3.25
74 75 6.127793 ACTTGGACTAGAAGTCGTATACCAT 58.872 40.000 0.00 0.00 45.96 3.55
75 76 7.285566 ACTTGGACTAGAAGTCGTATACCATA 58.714 38.462 0.00 0.00 45.96 2.74
76 77 7.776969 ACTTGGACTAGAAGTCGTATACCATAA 59.223 37.037 0.00 0.00 45.96 1.90
77 78 8.701908 TTGGACTAGAAGTCGTATACCATAAT 57.298 34.615 0.00 0.00 45.96 1.28
78 79 8.107399 TGGACTAGAAGTCGTATACCATAATG 57.893 38.462 0.00 0.00 45.96 1.90
79 80 7.940688 TGGACTAGAAGTCGTATACCATAATGA 59.059 37.037 0.00 0.00 45.96 2.57
80 81 8.235905 GGACTAGAAGTCGTATACCATAATGAC 58.764 40.741 0.00 0.00 45.96 3.06
81 82 8.921353 ACTAGAAGTCGTATACCATAATGACT 57.079 34.615 0.00 0.39 42.40 3.41
84 85 8.921353 AGAAGTCGTATACCATAATGACTACT 57.079 34.615 8.63 0.00 40.29 2.57
85 86 9.001542 AGAAGTCGTATACCATAATGACTACTC 57.998 37.037 8.63 5.22 40.29 2.59
86 87 8.921353 AAGTCGTATACCATAATGACTACTCT 57.079 34.615 8.63 0.00 40.29 3.24
90 91 9.783081 TCGTATACCATAATGACTACTCTAACA 57.217 33.333 0.00 0.00 0.00 2.41
91 92 9.823098 CGTATACCATAATGACTACTCTAACAC 57.177 37.037 0.00 0.00 0.00 3.32
92 93 9.823098 GTATACCATAATGACTACTCTAACACG 57.177 37.037 0.00 0.00 0.00 4.49
98 99 2.738846 TGACTACTCTAACACGGTCGTC 59.261 50.000 0.00 0.00 0.00 4.20
101 102 1.888215 ACTCTAACACGGTCGTCTCA 58.112 50.000 0.00 0.00 0.00 3.27
109 110 0.612229 ACGGTCGTCTCAGGACTCTA 59.388 55.000 0.00 0.00 40.10 2.43
111 112 1.600013 CGGTCGTCTCAGGACTCTATG 59.400 57.143 0.00 0.00 40.10 2.23
189 195 1.198408 CGTCGCTTACAGTAGTGTGGA 59.802 52.381 13.66 2.93 37.52 4.02
192 198 3.673809 GTCGCTTACAGTAGTGTGGAAAG 59.326 47.826 13.66 9.94 37.52 2.62
193 199 2.412089 CGCTTACAGTAGTGTGGAAAGC 59.588 50.000 19.99 19.99 37.52 3.51
195 201 3.859627 GCTTACAGTAGTGTGGAAAGCGA 60.860 47.826 16.88 0.00 37.52 4.93
198 204 2.364324 ACAGTAGTGTGGAAAGCGAGAA 59.636 45.455 1.37 0.00 34.75 2.87
199 205 2.731976 CAGTAGTGTGGAAAGCGAGAAC 59.268 50.000 0.00 0.00 0.00 3.01
200 206 1.719780 GTAGTGTGGAAAGCGAGAACG 59.280 52.381 0.00 0.00 42.93 3.95
201 207 0.600255 AGTGTGGAAAGCGAGAACGG 60.600 55.000 0.00 0.00 40.15 4.44
360 368 2.711978 GGAATCCGAAAACTAGGCCT 57.288 50.000 11.78 11.78 0.00 5.19
362 370 1.671328 GAATCCGAAAACTAGGCCTGC 59.329 52.381 17.99 0.00 0.00 4.85
379 387 5.105187 AGGCCTGCAAAATTCTCTTTAATCC 60.105 40.000 3.11 0.00 0.00 3.01
390 399 6.422776 TTCTCTTTAATCCTCATCGCAAAC 57.577 37.500 0.00 0.00 0.00 2.93
478 487 0.370273 CGGAAATTTCCTGCGAGTCG 59.630 55.000 29.85 8.54 45.33 4.18
479 488 1.722011 GGAAATTTCCTGCGAGTCGA 58.278 50.000 26.94 0.26 44.11 4.20
480 489 1.661112 GGAAATTTCCTGCGAGTCGAG 59.339 52.381 26.94 10.62 44.11 4.04
481 490 2.338500 GAAATTTCCTGCGAGTCGAGT 58.662 47.619 18.61 0.00 0.00 4.18
482 491 1.997669 AATTTCCTGCGAGTCGAGTC 58.002 50.000 18.61 10.37 0.00 3.36
514 523 0.110238 CACGTCAAAATGCCGTCCAG 60.110 55.000 0.00 0.00 31.46 3.86
574 583 6.711194 CCTCGAGATCACCTCAGTTTATACTA 59.289 42.308 15.71 0.00 42.06 1.82
575 584 7.094975 CCTCGAGATCACCTCAGTTTATACTAG 60.095 44.444 15.71 0.00 42.06 2.57
576 585 7.281098 TCGAGATCACCTCAGTTTATACTAGT 58.719 38.462 0.00 0.00 42.06 2.57
578 587 9.053840 CGAGATCACCTCAGTTTATACTAGTTA 57.946 37.037 0.00 0.00 42.06 2.24
613 622 1.002888 CACATTGACCTGACTCTGCCT 59.997 52.381 0.00 0.00 0.00 4.75
615 624 3.110705 ACATTGACCTGACTCTGCCTAT 58.889 45.455 0.00 0.00 0.00 2.57
616 625 3.521126 ACATTGACCTGACTCTGCCTATT 59.479 43.478 0.00 0.00 0.00 1.73
652 673 6.913170 TCATAAAGAAAAAGAGGCACACATC 58.087 36.000 0.00 0.00 0.00 3.06
653 674 6.489700 TCATAAAGAAAAAGAGGCACACATCA 59.510 34.615 0.00 0.00 0.00 3.07
654 675 5.796424 AAAGAAAAAGAGGCACACATCAT 57.204 34.783 0.00 0.00 0.00 2.45
655 676 5.382618 AAGAAAAAGAGGCACACATCATC 57.617 39.130 0.00 0.00 0.00 2.92
656 677 4.401022 AGAAAAAGAGGCACACATCATCA 58.599 39.130 0.00 0.00 0.00 3.07
941 1005 1.955778 CTCCATTCACCACTGTTGCAA 59.044 47.619 0.00 0.00 0.00 4.08
942 1006 1.955778 TCCATTCACCACTGTTGCAAG 59.044 47.619 0.00 0.00 0.00 4.01
943 1007 1.603678 CCATTCACCACTGTTGCAAGC 60.604 52.381 0.00 0.00 0.00 4.01
944 1008 1.338973 CATTCACCACTGTTGCAAGCT 59.661 47.619 0.00 0.00 0.00 3.74
956 1025 4.974721 CAAGCTGGGCCGGGTGTT 62.975 66.667 19.48 0.00 0.00 3.32
966 1040 0.322546 GCCGGGTGTTCTTGATCCTT 60.323 55.000 2.18 0.00 0.00 3.36
967 1041 1.886655 GCCGGGTGTTCTTGATCCTTT 60.887 52.381 2.18 0.00 0.00 3.11
985 1059 2.127118 GTTCTTCGCCGTCGACGA 60.127 61.111 37.65 16.87 45.43 4.20
1243 1317 3.006728 GGGACATGGACGGGGACA 61.007 66.667 0.00 0.00 0.00 4.02
1406 1480 5.012871 CCAGTGATACAGAGATCCAATCCAT 59.987 44.000 0.00 0.00 0.00 3.41
1409 1483 6.100859 AGTGATACAGAGATCCAATCCATTGT 59.899 38.462 0.00 0.00 36.06 2.71
1437 1515 6.480320 GTGCACTCCCTACTGAAACATAATAG 59.520 42.308 10.32 0.00 0.00 1.73
1440 1518 7.652507 GCACTCCCTACTGAAACATAATAGTAC 59.347 40.741 0.00 0.00 0.00 2.73
1490 1568 4.502962 ACCAACACACAATTTTTGGACAG 58.497 39.130 6.22 0.00 40.97 3.51
1493 1571 3.784338 ACACACAATTTTTGGACAGCAG 58.216 40.909 0.00 0.00 34.12 4.24
1680 1759 8.668353 TGACAGAATCAACATACTAAAAGATGC 58.332 33.333 0.00 0.00 33.02 3.91
1695 1774 6.575162 AAAAGATGCCATCTCGTTTACTTT 57.425 33.333 7.84 0.18 39.08 2.66
1872 1951 1.457346 CTGCATCCCAGTCAAACCTC 58.543 55.000 0.00 0.00 36.79 3.85
1925 2004 5.946377 ACCCCTTTCAGATAAGAATCAACAC 59.054 40.000 0.00 0.00 34.28 3.32
1938 2017 5.120399 AGAATCAACACGTAACAGACCAAA 58.880 37.500 0.00 0.00 0.00 3.28
1939 2018 5.236478 AGAATCAACACGTAACAGACCAAAG 59.764 40.000 0.00 0.00 0.00 2.77
1945 2024 4.093850 ACACGTAACAGACCAAAGTTGAAC 59.906 41.667 0.00 0.00 0.00 3.18
1962 2041 3.897239 TGAACAGCTTATGGGTAATGGG 58.103 45.455 0.00 0.00 0.00 4.00
1968 2047 2.623416 GCTTATGGGTAATGGGCAGTTC 59.377 50.000 0.00 0.00 0.00 3.01
2032 2111 7.946381 AAGAGTGGGATCTTTTAAGGAAATC 57.054 36.000 0.00 0.00 36.05 2.17
2059 2138 4.391523 CGTTGGGGAAAATTTAAAGCCATG 59.608 41.667 0.00 0.00 0.00 3.66
2150 2229 9.722184 ATACTCTTCTTAAACTGAAAAGGTACC 57.278 33.333 2.73 2.73 0.00 3.34
2201 2280 4.438148 TCAGCGTAACATAATAGCAAGCA 58.562 39.130 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.781693 TCGGTTTGTACCCTCTTATATACTCTT 59.218 37.037 0.00 0.00 41.75 2.85
1 2 7.230309 GTCGGTTTGTACCCTCTTATATACTCT 59.770 40.741 0.00 0.00 41.75 3.24
2 3 7.230309 AGTCGGTTTGTACCCTCTTATATACTC 59.770 40.741 0.00 0.00 41.75 2.59
3 4 7.065504 AGTCGGTTTGTACCCTCTTATATACT 58.934 38.462 0.00 0.00 41.75 2.12
4 5 7.282332 AGTCGGTTTGTACCCTCTTATATAC 57.718 40.000 0.00 0.00 41.75 1.47
5 6 7.201938 CCAAGTCGGTTTGTACCCTCTTATATA 60.202 40.741 0.00 0.00 41.75 0.86
6 7 6.407752 CCAAGTCGGTTTGTACCCTCTTATAT 60.408 42.308 0.00 0.00 41.75 0.86
7 8 5.105228 CCAAGTCGGTTTGTACCCTCTTATA 60.105 44.000 0.00 0.00 41.75 0.98
8 9 4.323257 CCAAGTCGGTTTGTACCCTCTTAT 60.323 45.833 0.00 0.00 41.75 1.73
9 10 3.007182 CCAAGTCGGTTTGTACCCTCTTA 59.993 47.826 0.00 0.00 41.75 2.10
10 11 2.224450 CCAAGTCGGTTTGTACCCTCTT 60.224 50.000 0.00 0.00 41.75 2.85
11 12 1.346722 CCAAGTCGGTTTGTACCCTCT 59.653 52.381 0.00 0.00 41.75 3.69
12 13 1.609841 CCCAAGTCGGTTTGTACCCTC 60.610 57.143 0.00 0.00 41.75 4.30
13 14 0.399075 CCCAAGTCGGTTTGTACCCT 59.601 55.000 0.00 0.00 41.75 4.34
14 15 0.607217 CCCCAAGTCGGTTTGTACCC 60.607 60.000 0.00 0.00 41.75 3.69
15 16 0.109153 ACCCCAAGTCGGTTTGTACC 59.891 55.000 0.00 0.00 41.33 3.34
16 17 2.299867 TCTACCCCAAGTCGGTTTGTAC 59.700 50.000 0.00 0.00 34.66 2.90
17 18 2.564062 CTCTACCCCAAGTCGGTTTGTA 59.436 50.000 0.00 0.00 34.66 2.41
18 19 1.346722 CTCTACCCCAAGTCGGTTTGT 59.653 52.381 0.00 0.00 34.66 2.83
19 20 1.338769 CCTCTACCCCAAGTCGGTTTG 60.339 57.143 0.00 0.00 34.66 2.93
20 21 0.981943 CCTCTACCCCAAGTCGGTTT 59.018 55.000 0.00 0.00 34.66 3.27
21 22 0.178912 ACCTCTACCCCAAGTCGGTT 60.179 55.000 0.00 0.00 34.66 4.44
22 23 0.706433 TACCTCTACCCCAAGTCGGT 59.294 55.000 0.00 0.00 37.40 4.69
23 24 1.109609 GTACCTCTACCCCAAGTCGG 58.890 60.000 0.00 0.00 0.00 4.79
24 25 1.843368 TGTACCTCTACCCCAAGTCG 58.157 55.000 0.00 0.00 0.00 4.18
25 26 4.041321 AGTTTTGTACCTCTACCCCAAGTC 59.959 45.833 0.00 0.00 0.00 3.01
26 27 3.978672 AGTTTTGTACCTCTACCCCAAGT 59.021 43.478 0.00 0.00 0.00 3.16
27 28 4.041198 TCAGTTTTGTACCTCTACCCCAAG 59.959 45.833 0.00 0.00 0.00 3.61
28 29 3.975312 TCAGTTTTGTACCTCTACCCCAA 59.025 43.478 0.00 0.00 0.00 4.12
29 30 3.325716 GTCAGTTTTGTACCTCTACCCCA 59.674 47.826 0.00 0.00 0.00 4.96
30 31 3.581770 AGTCAGTTTTGTACCTCTACCCC 59.418 47.826 0.00 0.00 0.00 4.95
31 32 4.886496 AGTCAGTTTTGTACCTCTACCC 57.114 45.455 0.00 0.00 0.00 3.69
32 33 4.995487 CCAAGTCAGTTTTGTACCTCTACC 59.005 45.833 0.00 0.00 0.00 3.18
33 34 5.695363 GTCCAAGTCAGTTTTGTACCTCTAC 59.305 44.000 0.00 0.00 0.00 2.59
34 35 5.601313 AGTCCAAGTCAGTTTTGTACCTCTA 59.399 40.000 0.00 0.00 0.00 2.43
35 36 4.409247 AGTCCAAGTCAGTTTTGTACCTCT 59.591 41.667 0.00 0.00 0.00 3.69
36 37 4.704965 AGTCCAAGTCAGTTTTGTACCTC 58.295 43.478 0.00 0.00 0.00 3.85
37 38 4.772886 AGTCCAAGTCAGTTTTGTACCT 57.227 40.909 0.00 0.00 0.00 3.08
38 39 5.850614 TCTAGTCCAAGTCAGTTTTGTACC 58.149 41.667 0.00 0.00 0.00 3.34
39 40 6.985059 ACTTCTAGTCCAAGTCAGTTTTGTAC 59.015 38.462 0.00 0.00 27.00 2.90
40 41 7.120923 ACTTCTAGTCCAAGTCAGTTTTGTA 57.879 36.000 0.00 0.00 27.00 2.41
41 42 5.990668 ACTTCTAGTCCAAGTCAGTTTTGT 58.009 37.500 0.00 0.00 27.00 2.83
42 43 5.175856 CGACTTCTAGTCCAAGTCAGTTTTG 59.824 44.000 18.00 2.79 46.99 2.44
43 44 5.163437 ACGACTTCTAGTCCAAGTCAGTTTT 60.163 40.000 18.00 0.57 46.99 2.43
44 45 4.341520 ACGACTTCTAGTCCAAGTCAGTTT 59.658 41.667 18.00 2.39 46.99 2.66
45 46 3.890147 ACGACTTCTAGTCCAAGTCAGTT 59.110 43.478 18.00 4.22 46.99 3.16
46 47 3.488363 ACGACTTCTAGTCCAAGTCAGT 58.512 45.455 18.00 14.31 46.99 3.41
47 48 5.821516 ATACGACTTCTAGTCCAAGTCAG 57.178 43.478 18.00 13.87 46.99 3.51
48 49 5.587844 GGTATACGACTTCTAGTCCAAGTCA 59.412 44.000 18.00 5.06 46.99 3.41
49 50 5.587844 TGGTATACGACTTCTAGTCCAAGTC 59.412 44.000 11.14 11.14 42.12 3.01
50 51 5.503927 TGGTATACGACTTCTAGTCCAAGT 58.496 41.667 0.00 0.00 42.12 3.16
51 52 6.636562 ATGGTATACGACTTCTAGTCCAAG 57.363 41.667 0.00 0.00 42.12 3.61
52 53 8.573885 CATTATGGTATACGACTTCTAGTCCAA 58.426 37.037 0.00 0.00 42.12 3.53
53 54 7.940688 TCATTATGGTATACGACTTCTAGTCCA 59.059 37.037 0.00 0.00 42.12 4.02
54 55 8.235905 GTCATTATGGTATACGACTTCTAGTCC 58.764 40.741 0.00 0.00 42.12 3.85
55 56 9.001542 AGTCATTATGGTATACGACTTCTAGTC 57.998 37.037 3.78 0.00 41.71 2.59
56 57 8.921353 AGTCATTATGGTATACGACTTCTAGT 57.079 34.615 3.78 0.00 29.68 2.57
59 60 8.921353 AGTAGTCATTATGGTATACGACTTCT 57.079 34.615 12.23 10.29 35.47 2.85
60 61 9.001542 AGAGTAGTCATTATGGTATACGACTTC 57.998 37.037 12.23 8.65 35.47 3.01
61 62 8.921353 AGAGTAGTCATTATGGTATACGACTT 57.079 34.615 12.23 0.00 35.47 3.01
64 65 9.783081 TGTTAGAGTAGTCATTATGGTATACGA 57.217 33.333 0.00 0.00 0.00 3.43
65 66 9.823098 GTGTTAGAGTAGTCATTATGGTATACG 57.177 37.037 0.00 0.00 0.00 3.06
66 67 9.823098 CGTGTTAGAGTAGTCATTATGGTATAC 57.177 37.037 0.00 0.00 0.00 1.47
67 68 9.006839 CCGTGTTAGAGTAGTCATTATGGTATA 57.993 37.037 0.00 0.00 0.00 1.47
68 69 7.504911 ACCGTGTTAGAGTAGTCATTATGGTAT 59.495 37.037 0.00 0.00 0.00 2.73
69 70 6.830324 ACCGTGTTAGAGTAGTCATTATGGTA 59.170 38.462 0.00 0.00 0.00 3.25
70 71 5.655532 ACCGTGTTAGAGTAGTCATTATGGT 59.344 40.000 0.00 1.95 0.00 3.55
71 72 6.145338 ACCGTGTTAGAGTAGTCATTATGG 57.855 41.667 0.00 1.37 0.00 2.74
72 73 5.907945 CGACCGTGTTAGAGTAGTCATTATG 59.092 44.000 0.00 0.00 0.00 1.90
73 74 5.587844 ACGACCGTGTTAGAGTAGTCATTAT 59.412 40.000 0.00 0.00 0.00 1.28
74 75 4.937620 ACGACCGTGTTAGAGTAGTCATTA 59.062 41.667 0.00 0.00 0.00 1.90
75 76 3.755378 ACGACCGTGTTAGAGTAGTCATT 59.245 43.478 0.00 0.00 0.00 2.57
76 77 3.341823 ACGACCGTGTTAGAGTAGTCAT 58.658 45.455 0.00 0.00 0.00 3.06
77 78 2.738846 GACGACCGTGTTAGAGTAGTCA 59.261 50.000 0.00 0.00 36.51 3.41
78 79 2.999355 AGACGACCGTGTTAGAGTAGTC 59.001 50.000 0.00 0.00 36.68 2.59
79 80 2.999355 GAGACGACCGTGTTAGAGTAGT 59.001 50.000 0.00 0.00 0.00 2.73
80 81 2.998670 TGAGACGACCGTGTTAGAGTAG 59.001 50.000 0.00 0.00 0.00 2.57
81 82 2.998670 CTGAGACGACCGTGTTAGAGTA 59.001 50.000 5.74 0.00 28.64 2.59
82 83 1.805345 CTGAGACGACCGTGTTAGAGT 59.195 52.381 5.74 0.00 28.64 3.24
83 84 1.130749 CCTGAGACGACCGTGTTAGAG 59.869 57.143 11.89 1.63 28.64 2.43
84 85 1.162698 CCTGAGACGACCGTGTTAGA 58.837 55.000 11.89 0.00 28.64 2.10
85 86 1.135746 GTCCTGAGACGACCGTGTTAG 60.136 57.143 0.00 2.04 32.18 2.34
86 87 0.877071 GTCCTGAGACGACCGTGTTA 59.123 55.000 0.00 0.00 32.18 2.41
87 88 1.658673 GTCCTGAGACGACCGTGTT 59.341 57.895 0.00 0.00 32.18 3.32
88 89 3.352524 GTCCTGAGACGACCGTGT 58.647 61.111 0.00 0.00 32.18 4.49
134 138 8.501580 CGACTGCATGTGAATTAATCAATAGAT 58.498 33.333 0.00 0.00 40.50 1.98
143 147 3.006940 GACCCGACTGCATGTGAATTAA 58.993 45.455 0.00 0.00 0.00 1.40
144 148 2.627945 GACCCGACTGCATGTGAATTA 58.372 47.619 0.00 0.00 0.00 1.40
155 159 4.477975 GACGAGCCGACCCGACTG 62.478 72.222 1.50 0.00 0.00 3.51
189 195 1.605712 CCTCTCAACCGTTCTCGCTTT 60.606 52.381 0.00 0.00 35.54 3.51
192 198 0.733223 GTCCTCTCAACCGTTCTCGC 60.733 60.000 0.00 0.00 35.54 5.03
193 199 0.454620 CGTCCTCTCAACCGTTCTCG 60.455 60.000 0.00 0.00 0.00 4.04
195 201 1.811359 CTACGTCCTCTCAACCGTTCT 59.189 52.381 0.00 0.00 34.95 3.01
198 204 1.593296 GCCTACGTCCTCTCAACCGT 61.593 60.000 0.00 0.00 37.33 4.83
199 205 1.139095 GCCTACGTCCTCTCAACCG 59.861 63.158 0.00 0.00 0.00 4.44
200 206 0.606604 TTGCCTACGTCCTCTCAACC 59.393 55.000 0.00 0.00 0.00 3.77
201 207 2.450609 TTTGCCTACGTCCTCTCAAC 57.549 50.000 0.00 0.00 0.00 3.18
202 208 3.695830 AATTTGCCTACGTCCTCTCAA 57.304 42.857 0.00 0.00 0.00 3.02
203 209 3.512329 TGTAATTTGCCTACGTCCTCTCA 59.488 43.478 0.00 0.00 0.00 3.27
204 210 4.119442 TGTAATTTGCCTACGTCCTCTC 57.881 45.455 0.00 0.00 0.00 3.20
205 211 4.020485 ACTTGTAATTTGCCTACGTCCTCT 60.020 41.667 0.00 0.00 0.00 3.69
247 255 1.122019 ATCGTAGACATGGGAGGGCC 61.122 60.000 0.00 0.00 42.51 5.80
352 360 3.728385 AGAGAATTTTGCAGGCCTAGT 57.272 42.857 3.98 0.00 0.00 2.57
360 368 7.475015 CGATGAGGATTAAAGAGAATTTTGCA 58.525 34.615 0.00 0.00 0.00 4.08
362 370 7.475015 TGCGATGAGGATTAAAGAGAATTTTG 58.525 34.615 0.00 0.00 0.00 2.44
379 387 2.485426 ACACTTGATGGTTTGCGATGAG 59.515 45.455 0.00 0.00 0.00 2.90
390 399 4.067192 TCAGTTGTGATCACACTTGATGG 58.933 43.478 27.88 14.53 42.95 3.51
478 487 5.168569 TGACGTGGTCATCTTAAATGACTC 58.831 41.667 20.37 14.41 45.60 3.36
479 488 5.147330 TGACGTGGTCATCTTAAATGACT 57.853 39.130 20.37 8.89 45.60 3.41
480 489 5.856126 TTGACGTGGTCATCTTAAATGAC 57.144 39.130 16.22 16.22 42.40 3.06
481 490 6.869315 TTTTGACGTGGTCATCTTAAATGA 57.131 33.333 0.00 0.00 42.40 2.57
482 491 6.033831 GCATTTTGACGTGGTCATCTTAAATG 59.966 38.462 19.43 19.43 42.99 2.32
514 523 3.764885 ATTTCCGATTTGTGTAGCTGC 57.235 42.857 0.00 0.00 0.00 5.25
521 530 5.454232 GTGGCGTATTTATTTCCGATTTGTG 59.546 40.000 0.00 0.00 0.00 3.33
574 583 5.876651 TGTGTCTGGCTGATCATATAACT 57.123 39.130 0.00 0.00 0.00 2.24
575 584 6.707608 TCAATGTGTCTGGCTGATCATATAAC 59.292 38.462 0.00 0.00 0.00 1.89
576 585 6.707608 GTCAATGTGTCTGGCTGATCATATAA 59.292 38.462 0.00 3.35 0.00 0.98
578 587 5.061853 GTCAATGTGTCTGGCTGATCATAT 58.938 41.667 0.00 7.48 0.00 1.78
591 600 2.072298 GCAGAGTCAGGTCAATGTGTC 58.928 52.381 0.00 0.00 0.00 3.67
652 673 2.172082 AGGGGTCTCATGTGATGTGATG 59.828 50.000 0.02 0.00 35.53 3.07
653 674 2.172082 CAGGGGTCTCATGTGATGTGAT 59.828 50.000 0.02 0.00 35.53 3.06
654 675 1.556451 CAGGGGTCTCATGTGATGTGA 59.444 52.381 0.02 0.00 0.00 3.58
655 676 2.015588 GCAGGGGTCTCATGTGATGTG 61.016 57.143 0.02 0.00 0.00 3.21
656 677 0.254178 GCAGGGGTCTCATGTGATGT 59.746 55.000 0.02 0.00 0.00 3.06
755 799 2.126071 TCTAGGACGTTGCTGCGC 60.126 61.111 0.00 0.00 34.88 6.09
942 1006 4.660938 AAGAACACCCGGCCCAGC 62.661 66.667 0.00 0.00 0.00 4.85
943 1007 2.484287 ATCAAGAACACCCGGCCCAG 62.484 60.000 0.00 0.00 0.00 4.45
944 1008 2.478335 GATCAAGAACACCCGGCCCA 62.478 60.000 0.00 0.00 0.00 5.36
952 1021 5.444122 CGAAGAACAAAGGATCAAGAACAC 58.556 41.667 0.00 0.00 0.00 3.32
956 1025 3.074412 GGCGAAGAACAAAGGATCAAGA 58.926 45.455 0.00 0.00 0.00 3.02
958 1027 1.804151 CGGCGAAGAACAAAGGATCAA 59.196 47.619 0.00 0.00 0.00 2.57
985 1059 2.191375 CATGCTGTGCCCGATCCT 59.809 61.111 0.00 0.00 0.00 3.24
995 1069 3.939837 CTGTCGACGCCCATGCTGT 62.940 63.158 11.62 0.00 34.43 4.40
997 1071 4.457496 CCTGTCGACGCCCATGCT 62.457 66.667 11.62 0.00 34.43 3.79
1007 1081 4.316823 AGGTGCTCCCCCTGTCGA 62.317 66.667 0.00 0.00 0.00 4.20
1074 1148 1.074623 CTCCTGGATCAGCCCCTCT 60.075 63.158 0.00 0.00 34.97 3.69
1243 1317 3.474570 GGTCTGATCCAGGGCGCT 61.475 66.667 7.64 0.00 31.51 5.92
1385 1459 6.294473 ACAATGGATTGGATCTCTGTATCAC 58.706 40.000 4.45 0.00 41.96 3.06
1406 1480 2.171659 TCAGTAGGGAGTGCACAAACAA 59.828 45.455 21.04 0.00 0.00 2.83
1409 1483 3.211045 GTTTCAGTAGGGAGTGCACAAA 58.789 45.455 21.04 4.32 0.00 2.83
1437 1515 3.320541 AGCATGATCAGCCAGACTAGTAC 59.679 47.826 0.09 0.00 0.00 2.73
1440 1518 4.804868 ATAGCATGATCAGCCAGACTAG 57.195 45.455 0.09 0.00 0.00 2.57
1443 1521 3.736720 TCAATAGCATGATCAGCCAGAC 58.263 45.455 0.09 0.00 0.00 3.51
1444 1522 4.426736 TTCAATAGCATGATCAGCCAGA 57.573 40.909 0.09 0.00 0.00 3.86
1572 1650 1.641577 ATAAGTCGTCTGGCTTTCGC 58.358 50.000 0.00 0.00 0.00 4.70
1680 1759 2.343101 TCGGCAAAGTAAACGAGATGG 58.657 47.619 0.00 0.00 0.00 3.51
1695 1774 0.874390 GCAGACAACATTTCTCGGCA 59.126 50.000 0.00 0.00 0.00 5.69
1773 1852 1.142748 GATCGGTGAGCTCTGTGGG 59.857 63.158 16.19 0.00 0.00 4.61
1925 2004 4.785341 GCTGTTCAACTTTGGTCTGTTACG 60.785 45.833 0.00 0.00 0.00 3.18
1938 2017 4.949856 CCATTACCCATAAGCTGTTCAACT 59.050 41.667 0.00 0.00 0.00 3.16
1939 2018 4.097892 CCCATTACCCATAAGCTGTTCAAC 59.902 45.833 0.00 0.00 0.00 3.18
1945 2024 2.233271 CTGCCCATTACCCATAAGCTG 58.767 52.381 0.00 0.00 0.00 4.24
1962 2041 7.064016 TCCAAGTGTTTGTTTAAATTGAACTGC 59.936 33.333 2.43 0.00 32.21 4.40
2026 2105 1.253100 TTCCCCAACGCTTGATTTCC 58.747 50.000 0.15 0.00 0.00 3.13
2032 2111 4.084066 GCTTTAAATTTTCCCCAACGCTTG 60.084 41.667 0.00 0.00 0.00 4.01
2059 2138 4.463559 GCTATGGCTTTGTGCTTTTCAGC 61.464 47.826 0.00 0.00 42.39 4.26
2255 2334 6.203808 TGCTCGTTTGATGTGTATACTACT 57.796 37.500 4.17 0.00 0.00 2.57
2273 2352 3.433274 TGTCTTGTCTTATTTGCTGCTCG 59.567 43.478 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.