Multiple sequence alignment - TraesCS3A01G434200

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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 TraesCS3A01G434200 chr3A 100.000 1689 0 0 862 2550 676072151 676070463 0.000000e+00 3120.0
1 TraesCS3A01G434200 chr3A 100.000 340 0 0 1 340 676073012 676072673 1.670000e-176 628.0
2 TraesCS3A01G434200 chr3D 95.650 1701 45 9 862 2550 540903982 540902299 0.000000e+00 2704.0
3 TraesCS3A01G434200 chr3D 89.256 242 13 8 99 340 540905386 540905158 8.920000e-75 291.0
4 TraesCS3A01G434200 chr3D 94.872 39 2 0 1 39 540905414 540905376 7.620000e-06 62.1


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 TraesCS3A01G434200 chr3A 676070463 676073012 2549 True 1874.000000 3120 100.000000 1 2550 2 chr3A.!!$R1 2549
1 TraesCS3A01G434200 chr3D 540902299 540905414 3115 True 1019.033333 2704 93.259333 1 2550 3 chr3D.!!$R1 2549

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
87 88 0.107703 GCTCATTCGATCCACCACCA 60.108 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2432 0.030369 GAGTACACGATAGGCCACGG 59.97 60.0 18.1 11.04 43.77 4.94 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
28 29 5.183140 TGATGCTCTTACTTTGCCCTTTTAC 59.817 40.000 0.00 0.00 0.00 2.01
34 35 5.410439 TCTTACTTTGCCCTTTTACGTGATC 59.590 40.000 0.00 0.00 0.00 2.92
35 36 3.751518 ACTTTGCCCTTTTACGTGATCT 58.248 40.909 0.00 0.00 0.00 2.75
36 37 4.142038 ACTTTGCCCTTTTACGTGATCTT 58.858 39.130 0.00 0.00 0.00 2.40
37 38 4.583073 ACTTTGCCCTTTTACGTGATCTTT 59.417 37.500 0.00 0.00 0.00 2.52
38 39 5.068591 ACTTTGCCCTTTTACGTGATCTTTT 59.931 36.000 0.00 0.00 0.00 2.27
39 40 6.263617 ACTTTGCCCTTTTACGTGATCTTTTA 59.736 34.615 0.00 0.00 0.00 1.52
40 41 5.873179 TGCCCTTTTACGTGATCTTTTAG 57.127 39.130 0.00 0.00 0.00 1.85
41 42 5.553123 TGCCCTTTTACGTGATCTTTTAGA 58.447 37.500 0.00 0.00 0.00 2.10
42 43 5.998981 TGCCCTTTTACGTGATCTTTTAGAA 59.001 36.000 0.00 0.00 0.00 2.10
43 44 6.657541 TGCCCTTTTACGTGATCTTTTAGAAT 59.342 34.615 0.00 0.00 0.00 2.40
44 45 7.175990 TGCCCTTTTACGTGATCTTTTAGAATT 59.824 33.333 0.00 0.00 0.00 2.17
45 46 8.027189 GCCCTTTTACGTGATCTTTTAGAATTT 58.973 33.333 0.00 0.00 0.00 1.82
46 47 9.341899 CCCTTTTACGTGATCTTTTAGAATTTG 57.658 33.333 0.00 0.00 0.00 2.32
47 48 9.341899 CCTTTTACGTGATCTTTTAGAATTTGG 57.658 33.333 0.00 0.00 0.00 3.28
48 49 9.893305 CTTTTACGTGATCTTTTAGAATTTGGT 57.107 29.630 0.00 0.00 0.00 3.67
49 50 9.887406 TTTTACGTGATCTTTTAGAATTTGGTC 57.113 29.630 0.00 0.00 0.00 4.02
50 51 8.610248 TTACGTGATCTTTTAGAATTTGGTCA 57.390 30.769 0.00 0.00 0.00 4.02
51 52 6.899114 ACGTGATCTTTTAGAATTTGGTCAC 58.101 36.000 0.00 0.00 0.00 3.67
52 53 6.015504 CGTGATCTTTTAGAATTTGGTCACG 58.984 40.000 11.61 11.61 46.41 4.35
53 54 6.347402 CGTGATCTTTTAGAATTTGGTCACGT 60.347 38.462 15.88 0.00 46.42 4.49
54 55 7.360361 GTGATCTTTTAGAATTTGGTCACGTT 58.640 34.615 0.00 0.00 0.00 3.99
55 56 7.860872 GTGATCTTTTAGAATTTGGTCACGTTT 59.139 33.333 0.00 0.00 0.00 3.60
56 57 8.410141 TGATCTTTTAGAATTTGGTCACGTTTT 58.590 29.630 0.00 0.00 0.00 2.43
57 58 9.244799 GATCTTTTAGAATTTGGTCACGTTTTT 57.755 29.630 0.00 0.00 0.00 1.94
58 59 8.401046 TCTTTTAGAATTTGGTCACGTTTTTG 57.599 30.769 0.00 0.00 0.00 2.44
59 60 7.489757 TCTTTTAGAATTTGGTCACGTTTTTGG 59.510 33.333 0.00 0.00 0.00 3.28
60 61 4.729227 AGAATTTGGTCACGTTTTTGGT 57.271 36.364 0.00 0.00 0.00 3.67
61 62 5.838531 AGAATTTGGTCACGTTTTTGGTA 57.161 34.783 0.00 0.00 0.00 3.25
62 63 6.210287 AGAATTTGGTCACGTTTTTGGTAA 57.790 33.333 0.00 0.00 0.00 2.85
63 64 6.631962 AGAATTTGGTCACGTTTTTGGTAAA 58.368 32.000 0.00 0.00 0.00 2.01
64 65 6.754675 AGAATTTGGTCACGTTTTTGGTAAAG 59.245 34.615 0.00 0.00 0.00 1.85
65 66 5.388408 TTTGGTCACGTTTTTGGTAAAGT 57.612 34.783 0.00 0.00 0.00 2.66
66 67 4.358494 TGGTCACGTTTTTGGTAAAGTG 57.642 40.909 0.00 0.00 38.37 3.16
67 68 3.128938 TGGTCACGTTTTTGGTAAAGTGG 59.871 43.478 0.00 0.00 37.85 4.00
68 69 3.489568 GGTCACGTTTTTGGTAAAGTGGG 60.490 47.826 0.00 0.00 37.85 4.61
69 70 2.099427 TCACGTTTTTGGTAAAGTGGGC 59.901 45.455 0.00 0.00 37.85 5.36
70 71 2.100087 CACGTTTTTGGTAAAGTGGGCT 59.900 45.455 0.00 0.00 34.99 5.19
71 72 2.359848 ACGTTTTTGGTAAAGTGGGCTC 59.640 45.455 0.00 0.00 0.00 4.70
72 73 2.359531 CGTTTTTGGTAAAGTGGGCTCA 59.640 45.455 0.00 0.00 0.00 4.26
73 74 3.005367 CGTTTTTGGTAAAGTGGGCTCAT 59.995 43.478 0.00 0.00 0.00 2.90
74 75 4.500716 CGTTTTTGGTAAAGTGGGCTCATT 60.501 41.667 0.00 0.00 0.00 2.57
75 76 4.864704 TTTTGGTAAAGTGGGCTCATTC 57.135 40.909 0.00 0.00 0.00 2.67
76 77 2.107950 TGGTAAAGTGGGCTCATTCG 57.892 50.000 0.00 0.00 0.00 3.34
77 78 1.626321 TGGTAAAGTGGGCTCATTCGA 59.374 47.619 0.00 0.00 0.00 3.71
78 79 2.238646 TGGTAAAGTGGGCTCATTCGAT 59.761 45.455 0.00 0.00 0.00 3.59
79 80 2.872858 GGTAAAGTGGGCTCATTCGATC 59.127 50.000 0.00 0.00 0.00 3.69
80 81 2.044123 AAAGTGGGCTCATTCGATCC 57.956 50.000 0.00 0.00 0.00 3.36
81 82 0.911769 AAGTGGGCTCATTCGATCCA 59.088 50.000 0.00 0.00 0.00 3.41
82 83 0.179000 AGTGGGCTCATTCGATCCAC 59.821 55.000 0.00 0.00 41.76 4.02
83 84 0.815615 GTGGGCTCATTCGATCCACC 60.816 60.000 0.00 0.00 38.45 4.61
84 85 1.271127 TGGGCTCATTCGATCCACCA 61.271 55.000 0.00 0.00 0.00 4.17
85 86 0.815615 GGGCTCATTCGATCCACCAC 60.816 60.000 0.00 0.00 0.00 4.16
86 87 0.815615 GGCTCATTCGATCCACCACC 60.816 60.000 0.00 0.00 0.00 4.61
87 88 0.107703 GCTCATTCGATCCACCACCA 60.108 55.000 0.00 0.00 0.00 4.17
88 89 1.656652 CTCATTCGATCCACCACCAC 58.343 55.000 0.00 0.00 0.00 4.16
89 90 0.980423 TCATTCGATCCACCACCACA 59.020 50.000 0.00 0.00 0.00 4.17
90 91 1.559219 TCATTCGATCCACCACCACAT 59.441 47.619 0.00 0.00 0.00 3.21
91 92 2.026356 TCATTCGATCCACCACCACATT 60.026 45.455 0.00 0.00 0.00 2.71
92 93 1.819928 TTCGATCCACCACCACATTG 58.180 50.000 0.00 0.00 0.00 2.82
93 94 0.690192 TCGATCCACCACCACATTGT 59.310 50.000 0.00 0.00 0.00 2.71
94 95 0.804364 CGATCCACCACCACATTGTG 59.196 55.000 9.92 9.92 35.98 3.33
117 118 5.126869 TGGTGAGTGATTTTTCTTTTCAGCA 59.873 36.000 0.00 0.00 38.70 4.41
119 120 6.460123 GGTGAGTGATTTTTCTTTTCAGCAGA 60.460 38.462 0.00 0.00 33.27 4.26
237 238 5.161358 CGAGTTACGCATGTATGGTGATAT 58.839 41.667 0.00 0.00 34.51 1.63
262 263 0.463620 CTCTTGGGGAGCAGAGTAGC 59.536 60.000 0.00 0.00 35.08 3.58
264 265 0.615331 CTTGGGGAGCAGAGTAGCAA 59.385 55.000 0.00 0.00 36.85 3.91
265 266 1.211457 CTTGGGGAGCAGAGTAGCAAT 59.789 52.381 0.00 0.00 36.85 3.56
266 267 1.289160 TGGGGAGCAGAGTAGCAATT 58.711 50.000 0.00 0.00 36.85 2.32
268 269 2.019984 GGGGAGCAGAGTAGCAATTTG 58.980 52.381 0.00 0.00 36.85 2.32
269 270 1.403323 GGGAGCAGAGTAGCAATTTGC 59.597 52.381 13.55 13.55 45.46 3.68
282 283 4.972286 GCAATTTGCTTTCCTACACAAC 57.028 40.909 14.11 0.00 40.96 3.32
283 284 3.740832 GCAATTTGCTTTCCTACACAACC 59.259 43.478 14.11 0.00 40.96 3.77
284 285 4.739137 GCAATTTGCTTTCCTACACAACCA 60.739 41.667 14.11 0.00 40.96 3.67
285 286 4.584327 ATTTGCTTTCCTACACAACCAC 57.416 40.909 0.00 0.00 0.00 4.16
310 311 3.243839 GCAAACAGCAATTCCTGGAAGAA 60.244 43.478 15.34 0.00 44.79 2.52
315 316 2.165998 GCAATTCCTGGAAGAACAGCT 58.834 47.619 15.34 0.00 37.16 4.24
320 321 1.151668 CCTGGAAGAACAGCTCAACG 58.848 55.000 0.00 0.00 37.16 4.10
890 1545 1.202463 AGTAGATCATCGTGGCTGCAC 60.202 52.381 0.50 0.00 0.00 4.57
891 1546 0.823460 TAGATCATCGTGGCTGCACA 59.177 50.000 0.50 0.00 0.00 4.57
911 1566 5.221342 GCACACTAGCTATCAAGGATGTACT 60.221 44.000 0.00 0.00 0.00 2.73
919 1574 3.981071 TCAAGGATGTACTGGTTCCAG 57.019 47.619 16.25 16.25 39.74 3.86
924 1579 0.844661 ATGTACTGGTTCCAGGGGCA 60.845 55.000 20.88 15.88 38.30 5.36
1121 1776 0.605319 GGAGTTGACGGCACAATGGA 60.605 55.000 0.00 0.00 32.36 3.41
1156 1811 5.009854 ACAAACAATGTTTGAGGAAGGTG 57.990 39.130 36.28 14.77 40.06 4.00
1197 1852 5.897050 TCTGAACACGGCTTTAAAATGTTT 58.103 33.333 7.72 0.00 33.76 2.83
1244 1899 7.092668 ACAAATGAGAAGCTAGTATCTTTCCCT 60.093 37.037 0.00 0.00 0.00 4.20
1245 1900 6.664428 ATGAGAAGCTAGTATCTTTCCCTC 57.336 41.667 0.00 0.00 0.00 4.30
1360 2015 2.102420 TCATTATGCTGGTGAGGGTACG 59.898 50.000 0.00 0.00 0.00 3.67
1383 2038 2.539547 CCAGTGCAAGAAACACTCAACG 60.540 50.000 0.00 0.00 45.06 4.10
1410 2068 3.893326 AATGCAAATAAGGCTTGACCC 57.107 42.857 10.69 0.00 40.58 4.46
1412 2070 0.179137 GCAAATAAGGCTTGACCCGC 60.179 55.000 10.69 2.42 40.58 6.13
1447 2105 4.552365 ATGGTGGATGGCGAGCCG 62.552 66.667 9.78 0.00 39.42 5.52
1523 2181 8.360390 ACCTTCAAGTTCACATTATCCTTTTTC 58.640 33.333 0.00 0.00 0.00 2.29
1565 2223 0.460284 ATGAACTCGATGGGTGACGC 60.460 55.000 0.00 0.00 0.00 5.19
1596 2254 3.438087 GCACGCCTAGATAAATGCATGAT 59.562 43.478 0.00 0.00 33.27 2.45
1633 2291 8.713708 TGTTTTCTCTTTTAAATATGGTCCCA 57.286 30.769 0.00 0.00 0.00 4.37
1634 2292 9.320295 TGTTTTCTCTTTTAAATATGGTCCCAT 57.680 29.630 3.94 3.94 40.19 4.00
1649 2307 3.497942 GGTCCCATAATAGCCCATCGTTT 60.498 47.826 0.00 0.00 0.00 3.60
1662 2320 4.036262 GCCCATCGTTTCAATAATAGCACA 59.964 41.667 0.00 0.00 0.00 4.57
1691 2349 7.281549 GGGTATATGTCTTGTGAAAATACGGTT 59.718 37.037 0.00 0.00 0.00 4.44
1725 2383 6.699575 AGAAAAATACTTCAGCAAGTGTGT 57.300 33.333 0.00 0.00 43.17 3.72
1726 2384 7.100458 AGAAAAATACTTCAGCAAGTGTGTT 57.900 32.000 0.00 0.00 43.17 3.32
1727 2385 8.220755 AGAAAAATACTTCAGCAAGTGTGTTA 57.779 30.769 0.00 0.00 43.17 2.41
1728 2386 8.129211 AGAAAAATACTTCAGCAAGTGTGTTAC 58.871 33.333 0.00 0.00 43.17 2.50
1765 2423 8.420374 TTCATAAATATCGACAACAGAAGACC 57.580 34.615 0.00 0.00 0.00 3.85
1774 2432 4.677378 CGACAACAGAAGACCGATATCATC 59.323 45.833 3.12 0.00 0.00 2.92
1785 2443 2.223829 CCGATATCATCCGTGGCCTATC 60.224 54.545 3.32 0.00 0.00 2.08
2048 2715 0.913451 ACCTCAATGGCTGCCTCTCT 60.913 55.000 21.03 0.00 40.22 3.10
2193 2860 3.216944 CTTGGCTGCTGGTGGTTGC 62.217 63.158 0.00 0.00 0.00 4.17
2306 2973 2.266055 CTGCTCTGTTCCGTCCCC 59.734 66.667 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.276878 ACCAAAAACGTGACCAAATTCTAAAAG 59.723 33.333 0.00 0.00 0.00 2.27
35 36 7.097834 ACCAAAAACGTGACCAAATTCTAAAA 58.902 30.769 0.00 0.00 0.00 1.52
36 37 6.631962 ACCAAAAACGTGACCAAATTCTAAA 58.368 32.000 0.00 0.00 0.00 1.85
37 38 6.210287 ACCAAAAACGTGACCAAATTCTAA 57.790 33.333 0.00 0.00 0.00 2.10
38 39 5.838531 ACCAAAAACGTGACCAAATTCTA 57.161 34.783 0.00 0.00 0.00 2.10
39 40 4.729227 ACCAAAAACGTGACCAAATTCT 57.271 36.364 0.00 0.00 0.00 2.40
40 41 6.532302 ACTTTACCAAAAACGTGACCAAATTC 59.468 34.615 0.00 0.00 0.00 2.17
41 42 6.311690 CACTTTACCAAAAACGTGACCAAATT 59.688 34.615 0.00 0.00 0.00 1.82
42 43 5.808030 CACTTTACCAAAAACGTGACCAAAT 59.192 36.000 0.00 0.00 0.00 2.32
43 44 5.162075 CACTTTACCAAAAACGTGACCAAA 58.838 37.500 0.00 0.00 0.00 3.28
44 45 4.380655 CCACTTTACCAAAAACGTGACCAA 60.381 41.667 0.00 0.00 0.00 3.67
45 46 3.128938 CCACTTTACCAAAAACGTGACCA 59.871 43.478 0.00 0.00 0.00 4.02
46 47 3.489568 CCCACTTTACCAAAAACGTGACC 60.490 47.826 0.00 0.00 0.00 4.02
47 48 3.697982 CCCACTTTACCAAAAACGTGAC 58.302 45.455 0.00 0.00 0.00 3.67
48 49 2.099427 GCCCACTTTACCAAAAACGTGA 59.901 45.455 0.00 0.00 0.00 4.35
49 50 2.100087 AGCCCACTTTACCAAAAACGTG 59.900 45.455 0.00 0.00 0.00 4.49
50 51 2.359848 GAGCCCACTTTACCAAAAACGT 59.640 45.455 0.00 0.00 0.00 3.99
51 52 2.359531 TGAGCCCACTTTACCAAAAACG 59.640 45.455 0.00 0.00 0.00 3.60
52 53 4.600692 ATGAGCCCACTTTACCAAAAAC 57.399 40.909 0.00 0.00 0.00 2.43
53 54 4.261825 CGAATGAGCCCACTTTACCAAAAA 60.262 41.667 0.00 0.00 0.00 1.94
54 55 3.254657 CGAATGAGCCCACTTTACCAAAA 59.745 43.478 0.00 0.00 0.00 2.44
55 56 2.817258 CGAATGAGCCCACTTTACCAAA 59.183 45.455 0.00 0.00 0.00 3.28
56 57 2.039216 TCGAATGAGCCCACTTTACCAA 59.961 45.455 0.00 0.00 0.00 3.67
57 58 1.626321 TCGAATGAGCCCACTTTACCA 59.374 47.619 0.00 0.00 0.00 3.25
58 59 2.396590 TCGAATGAGCCCACTTTACC 57.603 50.000 0.00 0.00 0.00 2.85
59 60 2.872858 GGATCGAATGAGCCCACTTTAC 59.127 50.000 0.00 0.00 45.19 2.01
60 61 3.194005 GGATCGAATGAGCCCACTTTA 57.806 47.619 0.00 0.00 45.19 1.85
61 62 2.044123 GGATCGAATGAGCCCACTTT 57.956 50.000 0.00 0.00 45.19 2.66
62 63 3.788672 GGATCGAATGAGCCCACTT 57.211 52.632 0.00 0.00 45.19 3.16
68 69 0.107703 TGGTGGTGGATCGAATGAGC 60.108 55.000 0.00 0.00 0.00 4.26
69 70 1.066215 TGTGGTGGTGGATCGAATGAG 60.066 52.381 0.00 0.00 0.00 2.90
70 71 0.980423 TGTGGTGGTGGATCGAATGA 59.020 50.000 0.00 0.00 0.00 2.57
71 72 2.042686 ATGTGGTGGTGGATCGAATG 57.957 50.000 0.00 0.00 0.00 2.67
72 73 2.290896 ACAATGTGGTGGTGGATCGAAT 60.291 45.455 0.00 0.00 0.00 3.34
73 74 1.073125 ACAATGTGGTGGTGGATCGAA 59.927 47.619 0.00 0.00 0.00 3.71
74 75 0.690192 ACAATGTGGTGGTGGATCGA 59.310 50.000 0.00 0.00 0.00 3.59
75 76 0.804364 CACAATGTGGTGGTGGATCG 59.196 55.000 5.29 0.00 35.13 3.69
86 87 5.835257 AGAAAAATCACTCACCACAATGTG 58.165 37.500 6.37 6.37 37.59 3.21
87 88 6.469782 AAGAAAAATCACTCACCACAATGT 57.530 33.333 0.00 0.00 0.00 2.71
88 89 7.492020 TGAAAAGAAAAATCACTCACCACAATG 59.508 33.333 0.00 0.00 0.00 2.82
89 90 7.555087 TGAAAAGAAAAATCACTCACCACAAT 58.445 30.769 0.00 0.00 0.00 2.71
90 91 6.929625 TGAAAAGAAAAATCACTCACCACAA 58.070 32.000 0.00 0.00 0.00 3.33
91 92 6.522625 TGAAAAGAAAAATCACTCACCACA 57.477 33.333 0.00 0.00 0.00 4.17
92 93 5.460091 GCTGAAAAGAAAAATCACTCACCAC 59.540 40.000 0.00 0.00 0.00 4.16
93 94 5.126869 TGCTGAAAAGAAAAATCACTCACCA 59.873 36.000 0.00 0.00 0.00 4.17
94 95 5.591099 TGCTGAAAAGAAAAATCACTCACC 58.409 37.500 0.00 0.00 0.00 4.02
95 96 6.498304 TCTGCTGAAAAGAAAAATCACTCAC 58.502 36.000 0.00 0.00 0.00 3.51
96 97 6.698008 TCTGCTGAAAAGAAAAATCACTCA 57.302 33.333 0.00 0.00 0.00 3.41
97 98 9.852091 ATAATCTGCTGAAAAGAAAAATCACTC 57.148 29.630 0.00 0.00 0.00 3.51
98 99 9.635520 CATAATCTGCTGAAAAGAAAAATCACT 57.364 29.630 0.00 0.00 0.00 3.41
99 100 8.866956 CCATAATCTGCTGAAAAGAAAAATCAC 58.133 33.333 0.00 0.00 0.00 3.06
100 101 8.587608 ACCATAATCTGCTGAAAAGAAAAATCA 58.412 29.630 0.00 0.00 0.00 2.57
101 102 8.866956 CACCATAATCTGCTGAAAAGAAAAATC 58.133 33.333 0.00 0.00 0.00 2.17
102 103 8.587608 TCACCATAATCTGCTGAAAAGAAAAAT 58.412 29.630 0.00 0.00 0.00 1.82
103 104 7.950512 TCACCATAATCTGCTGAAAAGAAAAA 58.049 30.769 0.00 0.00 0.00 1.94
104 105 7.231317 ACTCACCATAATCTGCTGAAAAGAAAA 59.769 33.333 0.00 0.00 0.00 2.29
105 106 6.716628 ACTCACCATAATCTGCTGAAAAGAAA 59.283 34.615 0.00 0.00 0.00 2.52
108 109 5.645067 TCACTCACCATAATCTGCTGAAAAG 59.355 40.000 0.00 0.00 0.00 2.27
237 238 4.362677 ACTCTGCTCCCCAAGAGTTTATA 58.637 43.478 0.00 0.00 45.21 0.98
262 263 4.744631 GTGGTTGTGTAGGAAAGCAAATTG 59.255 41.667 0.00 0.00 35.72 2.32
264 265 4.215109 AGTGGTTGTGTAGGAAAGCAAAT 58.785 39.130 0.00 0.00 35.72 2.32
265 266 3.626930 AGTGGTTGTGTAGGAAAGCAAA 58.373 40.909 0.00 0.00 35.72 3.68
266 267 3.290948 AGTGGTTGTGTAGGAAAGCAA 57.709 42.857 0.00 0.00 35.72 3.91
268 269 2.742589 GCTAGTGGTTGTGTAGGAAAGC 59.257 50.000 0.00 0.00 0.00 3.51
269 270 4.002906 TGCTAGTGGTTGTGTAGGAAAG 57.997 45.455 0.00 0.00 0.00 2.62
270 271 4.425180 TTGCTAGTGGTTGTGTAGGAAA 57.575 40.909 0.00 0.00 0.00 3.13
271 272 4.131596 GTTTGCTAGTGGTTGTGTAGGAA 58.868 43.478 0.00 0.00 0.00 3.36
272 273 3.134985 TGTTTGCTAGTGGTTGTGTAGGA 59.865 43.478 0.00 0.00 0.00 2.94
273 274 3.472652 TGTTTGCTAGTGGTTGTGTAGG 58.527 45.455 0.00 0.00 0.00 3.18
274 275 3.058914 GCTGTTTGCTAGTGGTTGTGTAG 60.059 47.826 0.00 0.00 38.95 2.74
275 276 2.875933 GCTGTTTGCTAGTGGTTGTGTA 59.124 45.455 0.00 0.00 38.95 2.90
276 277 1.676006 GCTGTTTGCTAGTGGTTGTGT 59.324 47.619 0.00 0.00 38.95 3.72
277 278 1.675483 TGCTGTTTGCTAGTGGTTGTG 59.325 47.619 0.00 0.00 43.37 3.33
278 279 2.051334 TGCTGTTTGCTAGTGGTTGT 57.949 45.000 0.00 0.00 43.37 3.32
279 280 3.648339 ATTGCTGTTTGCTAGTGGTTG 57.352 42.857 0.00 0.00 43.37 3.77
280 281 3.005791 GGAATTGCTGTTTGCTAGTGGTT 59.994 43.478 0.00 0.00 43.37 3.67
281 282 2.558359 GGAATTGCTGTTTGCTAGTGGT 59.442 45.455 0.00 0.00 43.37 4.16
282 283 2.821969 AGGAATTGCTGTTTGCTAGTGG 59.178 45.455 0.00 0.00 43.37 4.00
283 284 3.366679 CCAGGAATTGCTGTTTGCTAGTG 60.367 47.826 23.38 3.34 43.37 2.74
284 285 2.821969 CCAGGAATTGCTGTTTGCTAGT 59.178 45.455 23.38 0.00 43.37 2.57
285 286 3.084039 TCCAGGAATTGCTGTTTGCTAG 58.916 45.455 23.38 8.24 43.37 3.42
304 305 1.531578 GGTTCGTTGAGCTGTTCTTCC 59.468 52.381 0.00 0.00 0.00 3.46
310 311 0.034059 CTCAGGGTTCGTTGAGCTGT 59.966 55.000 0.00 0.00 34.94 4.40
870 1525 1.114627 TGCAGCCACGATGATCTACT 58.885 50.000 0.00 0.00 0.00 2.57
890 1545 5.303078 ACCAGTACATCCTTGATAGCTAGTG 59.697 44.000 0.00 0.00 0.00 2.74
891 1546 5.459505 ACCAGTACATCCTTGATAGCTAGT 58.540 41.667 0.00 0.00 0.00 2.57
911 1566 3.970410 CTGCTGCCCCTGGAACCA 61.970 66.667 0.00 0.00 0.00 3.67
919 1574 2.057137 TCATACATTTCTGCTGCCCC 57.943 50.000 0.00 0.00 0.00 5.80
924 1579 5.738909 ACTGTAGCTTCATACATTTCTGCT 58.261 37.500 0.00 0.00 35.21 4.24
1121 1776 4.466015 ACATTGTTTGTCCTCCAAGTTGTT 59.534 37.500 1.45 0.00 30.89 2.83
1156 1811 3.055094 TCAGAGAAGCCATTGTAAGGGTC 60.055 47.826 0.00 0.00 35.44 4.46
1197 1852 7.959689 TTGTGCAAAAGTTAATACGTACCTA 57.040 32.000 0.00 0.00 0.00 3.08
1214 1869 6.409704 AGATACTAGCTTCTCATTTGTGCAA 58.590 36.000 0.00 0.00 0.00 4.08
1251 1906 6.434028 TGATGGTGCAAAGATACTAGCTTTTT 59.566 34.615 0.00 0.00 33.56 1.94
1252 1907 5.945784 TGATGGTGCAAAGATACTAGCTTTT 59.054 36.000 0.00 0.00 33.56 2.27
1253 1908 5.500234 TGATGGTGCAAAGATACTAGCTTT 58.500 37.500 0.00 0.00 36.07 3.51
1255 1910 4.163078 ACTGATGGTGCAAAGATACTAGCT 59.837 41.667 0.00 0.00 0.00 3.32
1256 1911 4.446371 ACTGATGGTGCAAAGATACTAGC 58.554 43.478 0.00 0.00 0.00 3.42
1360 2015 2.288666 TGAGTGTTTCTTGCACTGGAC 58.711 47.619 2.49 0.00 45.99 4.02
1378 2033 3.822594 ATTTGCATTAACTCGCGTTGA 57.177 38.095 5.77 0.00 34.59 3.18
1383 2038 4.292977 AGCCTTATTTGCATTAACTCGC 57.707 40.909 0.00 0.00 0.00 5.03
1410 2068 5.637810 ACCATCTTGTAATATATGTTCGGCG 59.362 40.000 0.00 0.00 0.00 6.46
1412 2070 7.158697 TCCACCATCTTGTAATATATGTTCGG 58.841 38.462 0.00 0.00 0.00 4.30
1447 2105 8.514330 TGTCCATATTTCCTAATAACACCAAC 57.486 34.615 0.00 0.00 30.38 3.77
1523 2181 8.347771 TCATTCATTGTTGTTCAGAAGAAGAAG 58.652 33.333 8.38 2.39 37.65 2.85
1579 2237 9.976511 ACAAAAATCATCATGCATTTATCTAGG 57.023 29.630 0.00 0.00 0.00 3.02
1620 2278 6.979018 TGGGCTATTATGGGACCATATTTA 57.021 37.500 11.59 6.62 38.52 1.40
1630 2288 3.750371 TGAAACGATGGGCTATTATGGG 58.250 45.455 0.00 0.00 0.00 4.00
1631 2289 5.964958 ATTGAAACGATGGGCTATTATGG 57.035 39.130 0.00 0.00 0.00 2.74
1633 2291 8.893727 GCTATTATTGAAACGATGGGCTATTAT 58.106 33.333 0.00 0.00 0.00 1.28
1634 2292 7.880713 TGCTATTATTGAAACGATGGGCTATTA 59.119 33.333 0.00 0.00 0.00 0.98
1635 2293 6.714810 TGCTATTATTGAAACGATGGGCTATT 59.285 34.615 0.00 0.00 0.00 1.73
1636 2294 6.149474 GTGCTATTATTGAAACGATGGGCTAT 59.851 38.462 0.00 0.00 0.00 2.97
1637 2295 5.468746 GTGCTATTATTGAAACGATGGGCTA 59.531 40.000 0.00 0.00 0.00 3.93
1638 2296 4.275936 GTGCTATTATTGAAACGATGGGCT 59.724 41.667 0.00 0.00 0.00 5.19
1649 2307 9.502091 GACATATACCCTTTGTGCTATTATTGA 57.498 33.333 0.00 0.00 0.00 2.57
1662 2320 8.889717 CGTATTTTCACAAGACATATACCCTTT 58.110 33.333 0.00 0.00 0.00 3.11
1765 2423 2.541794 CGATAGGCCACGGATGATATCG 60.542 54.545 5.01 8.96 35.11 2.92
1774 2432 0.030369 GAGTACACGATAGGCCACGG 59.970 60.000 18.10 11.04 43.77 4.94
1785 2443 4.483311 GAACTGGAAACTAGGAGTACACG 58.517 47.826 0.00 0.00 0.00 4.49
1831 2489 4.826274 TGTTGAGTGGAGGATAAGGAAG 57.174 45.455 0.00 0.00 0.00 3.46
1862 2520 9.745018 TTCTTCTTGATTGATGAAGAAACCTAT 57.255 29.630 12.95 0.00 45.24 2.57
1990 2657 2.635229 ATCTGAAGCTTCGCGCCGAT 62.635 55.000 21.11 13.64 40.39 4.18
2182 2849 2.126346 GAATGCGCAACCACCAGC 60.126 61.111 17.11 0.00 0.00 4.85
2193 2860 2.593468 ATCCTCCACCCACGAATGCG 62.593 60.000 0.00 0.00 44.79 4.73
2425 3092 2.989253 CACCGGGAAAACCAGCCC 60.989 66.667 6.32 0.00 40.22 5.19


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

AutoCloner maintained by Alex Coulton.