Multiple sequence alignment - TraesCS1D01G001000

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 TraesCS1D01G001000 chr1D 100.000 3052 0 0 1 3052 252430 249379 0.000000e+00 5637
1 TraesCS1D01G001000 chr1D 90.078 1935 153 14 315 2227 261317 259400 0.000000e+00 2473
2 TraesCS1D01G001000 chr1D 98.906 823 9 0 2230 3052 238857 238035 0.000000e+00 1471
3 TraesCS1D01G001000 chr1D 98.544 824 12 0 2229 3052 9429683 9430506 0.000000e+00 1456
4 TraesCS1D01G001000 chr1D 88.022 1102 102 10 395 1487 323555 322475 0.000000e+00 1277
5 TraesCS1D01G001000 chr1D 88.707 1036 96 17 1207 2227 322683 321654 0.000000e+00 1245
6 TraesCS1D01G001000 chr1D 85.679 1222 119 33 159 1370 383055 381880 0.000000e+00 1236
7 TraesCS1D01G001000 chr1D 86.395 882 82 17 1343 2223 381528 380684 0.000000e+00 929
8 TraesCS1D01G001000 chr1B 93.919 2072 99 9 159 2229 5141136 5143181 0.000000e+00 3103
9 TraesCS1D01G001000 chr1B 85.180 2112 204 47 159 2235 4993521 4991484 0.000000e+00 2065
10 TraesCS1D01G001000 chr1B 91.589 1177 73 7 335 1488 5136323 5137496 0.000000e+00 1602
11 TraesCS1D01G001000 chr1B 87.102 1132 113 14 386 1487 5098629 5099757 0.000000e+00 1251
12 TraesCS1D01G001000 chr1B 87.120 1118 124 11 387 1492 5056250 5057359 0.000000e+00 1249
13 TraesCS1D01G001000 chr1B 88.928 569 61 2 1164 1731 4965801 4966368 0.000000e+00 701
14 TraesCS1D01G001000 chr1B 87.524 513 57 6 1717 2227 5057749 5058256 1.220000e-163 586
15 TraesCS1D01G001000 chr1B 85.770 513 67 5 1717 2228 5137860 5138367 3.460000e-149 538
16 TraesCS1D01G001000 chr1B 87.310 197 21 3 159 353 4962109 4962303 3.960000e-54 222
17 TraesCS1D01G001000 chr1B 98.413 63 1 0 97 159 618554746 618554684 8.950000e-21 111
18 TraesCS1D01G001000 chr1B 93.056 72 5 0 87 158 588004599 588004528 4.160000e-19 106
19 TraesCS1D01G001000 chr1A 86.488 1532 130 32 220 1731 4040503 4041977 0.000000e+00 1611
20 TraesCS1D01G001000 chr1A 86.358 1532 132 32 220 1731 4032518 4033992 0.000000e+00 1600
21 TraesCS1D01G001000 chr1A 85.648 1505 163 24 245 1732 3909600 3911068 0.000000e+00 1533
22 TraesCS1D01G001000 chr1A 86.442 1158 124 16 239 1387 3847965 3846832 0.000000e+00 1238
23 TraesCS1D01G001000 chr1A 83.956 910 113 15 1324 2227 3846409 3845527 0.000000e+00 841
24 TraesCS1D01G001000 chr1A 85.036 421 59 3 1798 2218 4034026 4034442 2.810000e-115 425
25 TraesCS1D01G001000 chr7D 98.665 824 11 0 2229 3052 596696942 596696119 0.000000e+00 1461
26 TraesCS1D01G001000 chr7D 98.545 825 12 0 2228 3052 577304257 577303433 0.000000e+00 1458
27 TraesCS1D01G001000 chr7D 98.542 823 12 0 2230 3052 596689528 596688706 0.000000e+00 1454
28 TraesCS1D01G001000 chr3D 98.663 823 11 0 2230 3052 399822911 399822089 0.000000e+00 1459
29 TraesCS1D01G001000 chr3D 98.542 823 12 0 2230 3052 614945549 614944727 0.000000e+00 1454
30 TraesCS1D01G001000 chr3D 98.438 64 1 0 97 160 61053076 61053139 2.490000e-21 113
31 TraesCS1D01G001000 chr5D 98.542 823 12 0 2230 3052 502391650 502390828 0.000000e+00 1454
32 TraesCS1D01G001000 chr2D 98.422 824 13 0 2229 3052 580152321 580151498 0.000000e+00 1450
33 TraesCS1D01G001000 chr6A 93.506 77 3 2 98 172 602356569 602356493 2.490000e-21 113
34 TraesCS1D01G001000 chr7B 94.366 71 2 2 97 166 675631390 675631459 1.160000e-19 108
35 TraesCS1D01G001000 chr5A 93.151 73 3 2 98 168 450435684 450435612 4.160000e-19 106
36 TraesCS1D01G001000 chr7A 91.139 79 4 3 98 175 439630408 439630484 1.500000e-18 104
37 TraesCS1D01G001000 chr2B 95.385 65 3 0 94 158 79524866 79524802 1.500000e-18 104
38 TraesCS1D01G001000 chr3B 89.873 79 6 1 81 159 108895681 108895757 1.940000e-17 100


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 TraesCS1D01G001000 chr1D 249379 252430 3051 True 5637.000000 5637 100.0000 1 3052 1 chr1D.!!$R2 3051
1 TraesCS1D01G001000 chr1D 259400 261317 1917 True 2473.000000 2473 90.0780 315 2227 1 chr1D.!!$R3 1912
2 TraesCS1D01G001000 chr1D 238035 238857 822 True 1471.000000 1471 98.9060 2230 3052 1 chr1D.!!$R1 822
3 TraesCS1D01G001000 chr1D 9429683 9430506 823 False 1456.000000 1456 98.5440 2229 3052 1 chr1D.!!$F1 823
4 TraesCS1D01G001000 chr1D 321654 323555 1901 True 1261.000000 1277 88.3645 395 2227 2 chr1D.!!$R4 1832
5 TraesCS1D01G001000 chr1D 380684 383055 2371 True 1082.500000 1236 86.0370 159 2223 2 chr1D.!!$R5 2064
6 TraesCS1D01G001000 chr1B 4991484 4993521 2037 True 2065.000000 2065 85.1800 159 2235 1 chr1B.!!$R1 2076
7 TraesCS1D01G001000 chr1B 5136323 5143181 6858 False 1747.666667 3103 90.4260 159 2229 3 chr1B.!!$F4 2070
8 TraesCS1D01G001000 chr1B 5098629 5099757 1128 False 1251.000000 1251 87.1020 386 1487 1 chr1B.!!$F1 1101
9 TraesCS1D01G001000 chr1B 5056250 5058256 2006 False 917.500000 1249 87.3220 387 2227 2 chr1B.!!$F3 1840
10 TraesCS1D01G001000 chr1B 4962109 4966368 4259 False 461.500000 701 88.1190 159 1731 2 chr1B.!!$F2 1572
11 TraesCS1D01G001000 chr1A 4040503 4041977 1474 False 1611.000000 1611 86.4880 220 1731 1 chr1A.!!$F2 1511
12 TraesCS1D01G001000 chr1A 3909600 3911068 1468 False 1533.000000 1533 85.6480 245 1732 1 chr1A.!!$F1 1487
13 TraesCS1D01G001000 chr1A 3845527 3847965 2438 True 1039.500000 1238 85.1990 239 2227 2 chr1A.!!$R1 1988
14 TraesCS1D01G001000 chr1A 4032518 4034442 1924 False 1012.500000 1600 85.6970 220 2218 2 chr1A.!!$F3 1998
15 TraesCS1D01G001000 chr7D 596696119 596696942 823 True 1461.000000 1461 98.6650 2229 3052 1 chr7D.!!$R3 823
16 TraesCS1D01G001000 chr7D 577303433 577304257 824 True 1458.000000 1458 98.5450 2228 3052 1 chr7D.!!$R1 824
17 TraesCS1D01G001000 chr7D 596688706 596689528 822 True 1454.000000 1454 98.5420 2230 3052 1 chr7D.!!$R2 822
18 TraesCS1D01G001000 chr3D 399822089 399822911 822 True 1459.000000 1459 98.6630 2230 3052 1 chr3D.!!$R1 822
19 TraesCS1D01G001000 chr3D 614944727 614945549 822 True 1454.000000 1454 98.5420 2230 3052 1 chr3D.!!$R2 822
20 TraesCS1D01G001000 chr5D 502390828 502391650 822 True 1454.000000 1454 98.5420 2230 3052 1 chr5D.!!$R1 822
21 TraesCS1D01G001000 chr2D 580151498 580152321 823 True 1450.000000 1450 98.4220 2229 3052 1 chr2D.!!$R1 823

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
136 137 0.755686 AACCGATCTCCATGGAGCTC 59.244 55.0 33.39 30.73 41.71 4.09 F
886 8269 0.800300 GTGCCACCAAACACAACACG 60.800 55.0 0.00 0.00 36.77 4.49 F
1341 9447 0.905357 CCCCCAACAACCACAACAAA 59.095 50.0 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 8814 0.116940 AATGGTTGTTGGGGCTGGAT 59.883 50.0 0.00 0.0 0.00 3.41 R
1878 10021 0.309302 TACACGTTGCACATGGTTGC 59.691 50.0 0.00 0.0 43.31 4.17 R
2470 10616 1.015607 GCCCTCAAAATTGCTTGGCG 61.016 55.0 5.19 0.0 0.00 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
22 23 3.554342 CTCCCGGGAGCCATGGAG 61.554 72.222 36.90 12.91 36.38 3.86
105 106 9.986833 AAAAATTTGTGCAAGTAGACAAAATTC 57.013 25.926 0.00 0.00 43.39 2.17
107 108 8.715191 AATTTGTGCAAGTAGACAAAATTCAA 57.285 26.923 0.00 0.00 43.39 2.69
108 109 8.715191 ATTTGTGCAAGTAGACAAAATTCAAA 57.285 26.923 0.00 0.00 43.39 2.69
109 110 8.539770 TTTGTGCAAGTAGACAAAATTCAAAA 57.460 26.923 0.00 0.00 38.73 2.44
110 111 8.715191 TTGTGCAAGTAGACAAAATTCAAAAT 57.285 26.923 0.00 0.00 0.00 1.82
112 113 9.160496 TGTGCAAGTAGACAAAATTCAAAATTT 57.840 25.926 0.00 0.00 0.00 1.82
113 114 9.986833 GTGCAAGTAGACAAAATTCAAAATTTT 57.013 25.926 0.00 0.00 0.00 1.82
121 122 9.553418 AGACAAAATTCAAAATTTTCAAAACCG 57.447 25.926 0.00 0.00 0.00 4.44
127 128 7.707774 TTCAAAATTTTCAAAACCGATCTCC 57.292 32.000 0.00 0.00 0.00 3.71
128 129 6.810911 TCAAAATTTTCAAAACCGATCTCCA 58.189 32.000 0.00 0.00 0.00 3.86
130 131 7.384660 TCAAAATTTTCAAAACCGATCTCCATG 59.615 33.333 0.00 0.00 0.00 3.66
131 132 4.782019 TTTTCAAAACCGATCTCCATGG 57.218 40.909 4.97 4.97 0.00 3.66
132 133 3.712016 TTCAAAACCGATCTCCATGGA 57.288 42.857 15.27 15.27 0.00 3.41
133 134 3.266510 TCAAAACCGATCTCCATGGAG 57.733 47.619 32.60 32.60 43.21 3.86
134 135 1.672881 CAAAACCGATCTCCATGGAGC 59.327 52.381 33.39 20.74 41.71 4.70
136 137 0.755686 AACCGATCTCCATGGAGCTC 59.244 55.000 33.39 30.73 41.71 4.09
139 140 1.005156 GATCTCCATGGAGCTCGGC 60.005 63.158 33.39 17.38 41.71 5.54
140 141 2.447586 GATCTCCATGGAGCTCGGCC 62.448 65.000 33.39 15.55 41.71 6.13
141 142 2.961559 ATCTCCATGGAGCTCGGCCT 62.962 60.000 33.39 11.04 41.71 5.19
142 143 3.157252 TCCATGGAGCTCGGCCTC 61.157 66.667 11.44 0.00 0.00 4.70
148 149 2.982130 GAGCTCGGCCTCCAAAGA 59.018 61.111 0.00 0.00 0.00 2.52
149 150 1.448717 GAGCTCGGCCTCCAAAGAC 60.449 63.158 0.00 0.00 0.00 3.01
151 152 1.302511 GCTCGGCCTCCAAAGACAA 60.303 57.895 0.00 0.00 0.00 3.18
153 154 1.406887 GCTCGGCCTCCAAAGACAATA 60.407 52.381 0.00 0.00 0.00 1.90
154 155 2.746472 GCTCGGCCTCCAAAGACAATAT 60.746 50.000 0.00 0.00 0.00 1.28
155 156 3.134458 CTCGGCCTCCAAAGACAATATC 58.866 50.000 0.00 0.00 0.00 1.63
156 157 2.158813 TCGGCCTCCAAAGACAATATCC 60.159 50.000 0.00 0.00 0.00 2.59
190 4847 8.661352 ATGCCACTATTTATTTTGTAAATGCC 57.339 30.769 3.89 0.00 0.00 4.40
191 4848 7.044798 TGCCACTATTTATTTTGTAAATGCCC 58.955 34.615 3.89 0.00 0.00 5.36
223 4880 8.717821 CATTCTCGGAAATCTTAGTAACAACAA 58.282 33.333 0.00 0.00 0.00 2.83
308 4966 9.515226 AGTTCAATAAGTTAACCTATTGAAGCA 57.485 29.630 33.14 20.58 44.50 3.91
362 7711 7.172532 AGTGAATCAATTAAGACGTGTAAAGCA 59.827 33.333 0.00 0.00 0.00 3.91
468 7817 6.746822 TGATAACGTGTACAACATTACTACCG 59.253 38.462 0.00 0.00 0.00 4.02
494 7843 9.387123 GTTGACATAAAAAGAGAAGTTGATGAC 57.613 33.333 0.00 0.00 0.00 3.06
499 7848 9.985318 CATAAAAAGAGAAGTTGATGACTCATC 57.015 33.333 11.59 11.59 40.88 2.92
819 8200 7.384439 TCCTCACTCTTAGATAATATGAGCG 57.616 40.000 0.00 0.00 32.53 5.03
857 8240 3.369756 TGTTGATCACTCCGAAATTACGC 59.630 43.478 0.00 0.00 0.00 4.42
886 8269 0.800300 GTGCCACCAAACACAACACG 60.800 55.000 0.00 0.00 36.77 4.49
893 8276 2.069273 CCAAACACAACACGCCAAAAA 58.931 42.857 0.00 0.00 0.00 1.94
1090 8476 4.080919 CACCATGAAGACCTTACTCATCCA 60.081 45.833 0.00 0.00 0.00 3.41
1100 8486 5.501156 ACCTTACTCATCCAAACAATCCTC 58.499 41.667 0.00 0.00 0.00 3.71
1102 8488 3.703001 ACTCATCCAAACAATCCTCGT 57.297 42.857 0.00 0.00 0.00 4.18
1159 8545 2.307611 GACCCTAGCGGCCAAGTACC 62.308 65.000 2.24 0.00 33.26 3.34
1272 8784 4.880696 CCCATCAACCACAACAACAATTTT 59.119 37.500 0.00 0.00 0.00 1.82
1280 8792 2.771372 ACAACAACAATTTTCCCAGCCT 59.229 40.909 0.00 0.00 0.00 4.58
1302 8814 5.330455 TCAGCAACCACAACAACAATTTA 57.670 34.783 0.00 0.00 0.00 1.40
1341 9447 0.905357 CCCCCAACAACCACAACAAA 59.095 50.000 0.00 0.00 0.00 2.83
1354 9460 2.091541 ACAACAAACATATCCCCAGCG 58.908 47.619 0.00 0.00 0.00 5.18
1738 9845 3.543494 CAGCAAGAACAACAAGAACAACG 59.457 43.478 0.00 0.00 0.00 4.10
1784 9927 3.111853 CTGTCTCAACAGCAACAGGTA 57.888 47.619 0.00 0.00 46.01 3.08
2006 10150 9.878737 AGCTATACTAAAAGGTAGATAGGTCAA 57.121 33.333 0.00 0.00 0.00 3.18
2083 10228 1.198094 ATCATGTGTGACCCCGACCA 61.198 55.000 0.00 0.00 37.14 4.02
2141 10287 4.510038 AGTTCTTGTTTGCTAGCATTGG 57.490 40.909 20.13 7.70 0.00 3.16
2156 10302 3.059166 GCATTGGTTGTCATTGTTCCAC 58.941 45.455 0.00 0.00 0.00 4.02
2159 10305 2.217750 TGGTTGTCATTGTTCCACTCG 58.782 47.619 0.00 0.00 0.00 4.18
2163 10309 0.166814 GTCATTGTTCCACTCGCTGC 59.833 55.000 0.00 0.00 0.00 5.25
2179 10325 2.472861 CGCTGCGTATTTAGATGTCTGG 59.527 50.000 14.93 0.00 0.00 3.86
2206 10352 2.536365 TCGTAATTCTAGCCTTGCACG 58.464 47.619 0.00 0.00 0.00 5.34
2211 10357 1.725641 TTCTAGCCTTGCACGTCATG 58.274 50.000 0.00 0.00 0.00 3.07
2540 10686 4.131649 TCGACCCGAATTGATGTTATGT 57.868 40.909 0.00 0.00 31.06 2.29
2643 10789 1.806542 TCGAGTTTCTTCATGCTTGCC 59.193 47.619 0.00 0.00 0.00 4.52
2749 10895 6.701145 AAGTGACTTGATAGCTCGAGATTA 57.299 37.500 18.75 8.11 36.52 1.75
2807 10953 0.316204 CCTCTCGGTGTTACGGTGTT 59.684 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.554342 CTCCATGGCTCCCGGGAG 61.554 72.222 41.29 41.29 44.56 4.30
79 80 9.986833 GAATTTTGTCTACTTGCACAAATTTTT 57.013 25.926 0.00 0.00 41.10 1.94
80 81 9.160496 TGAATTTTGTCTACTTGCACAAATTTT 57.840 25.926 0.00 0.00 41.10 1.82
84 85 8.539770 TTTTGAATTTTGTCTACTTGCACAAA 57.460 26.923 0.00 0.00 40.05 2.83
85 86 8.715191 ATTTTGAATTTTGTCTACTTGCACAA 57.285 26.923 0.00 0.00 0.00 3.33
86 87 8.715191 AATTTTGAATTTTGTCTACTTGCACA 57.285 26.923 0.00 0.00 0.00 4.57
96 97 9.548208 TCGGTTTTGAAAATTTTGAATTTTGTC 57.452 25.926 8.47 4.23 32.03 3.18
101 102 8.773645 GGAGATCGGTTTTGAAAATTTTGAATT 58.226 29.630 8.47 0.00 0.00 2.17
104 105 6.810911 TGGAGATCGGTTTTGAAAATTTTGA 58.189 32.000 8.47 0.00 0.00 2.69
105 106 7.360269 CCATGGAGATCGGTTTTGAAAATTTTG 60.360 37.037 5.56 0.00 0.00 2.44
107 108 6.014669 TCCATGGAGATCGGTTTTGAAAATTT 60.015 34.615 11.44 0.00 0.00 1.82
108 109 5.480073 TCCATGGAGATCGGTTTTGAAAATT 59.520 36.000 11.44 0.00 0.00 1.82
109 110 5.016173 TCCATGGAGATCGGTTTTGAAAAT 58.984 37.500 11.44 0.00 0.00 1.82
110 111 4.402829 TCCATGGAGATCGGTTTTGAAAA 58.597 39.130 11.44 0.00 0.00 2.29
112 113 3.609853 CTCCATGGAGATCGGTTTTGAA 58.390 45.455 34.54 0.00 44.53 2.69
113 114 2.680805 GCTCCATGGAGATCGGTTTTGA 60.681 50.000 40.29 3.23 44.53 2.69
115 116 1.561542 AGCTCCATGGAGATCGGTTTT 59.438 47.619 40.29 14.38 44.53 2.43
116 117 1.139853 GAGCTCCATGGAGATCGGTTT 59.860 52.381 40.29 17.82 45.66 3.27
117 118 0.755686 GAGCTCCATGGAGATCGGTT 59.244 55.000 40.29 19.41 45.66 4.44
118 119 2.435418 GAGCTCCATGGAGATCGGT 58.565 57.895 40.29 22.83 45.66 4.69
123 124 3.157252 GGCCGAGCTCCATGGAGA 61.157 66.667 40.29 9.63 44.53 3.71
124 125 3.160047 AGGCCGAGCTCCATGGAG 61.160 66.667 33.73 33.73 44.56 3.86
126 127 4.247380 GGAGGCCGAGCTCCATGG 62.247 72.222 4.97 4.97 39.45 3.66
127 128 3.473647 TGGAGGCCGAGCTCCATG 61.474 66.667 8.47 0.00 44.02 3.66
130 131 2.124942 CTTTGGAGGCCGAGCTCC 60.125 66.667 8.47 0.00 40.05 4.70
131 132 1.448717 GTCTTTGGAGGCCGAGCTC 60.449 63.158 2.73 2.73 0.00 4.09
132 133 1.768684 TTGTCTTTGGAGGCCGAGCT 61.769 55.000 0.00 0.00 0.00 4.09
133 134 0.678048 ATTGTCTTTGGAGGCCGAGC 60.678 55.000 0.00 0.00 0.00 5.03
134 135 2.691409 TATTGTCTTTGGAGGCCGAG 57.309 50.000 0.00 0.00 0.00 4.63
136 137 2.222027 GGATATTGTCTTTGGAGGCCG 58.778 52.381 0.00 0.00 0.00 6.13
137 138 2.222027 CGGATATTGTCTTTGGAGGCC 58.778 52.381 0.00 0.00 0.00 5.19
138 139 2.919228 ACGGATATTGTCTTTGGAGGC 58.081 47.619 0.00 0.00 0.00 4.70
139 140 5.018539 TGTACGGATATTGTCTTTGGAGG 57.981 43.478 0.00 0.00 0.00 4.30
140 141 6.978343 TTTGTACGGATATTGTCTTTGGAG 57.022 37.500 0.00 0.00 0.00 3.86
141 142 9.051679 CATATTTGTACGGATATTGTCTTTGGA 57.948 33.333 0.00 0.00 0.00 3.53
142 143 7.803189 GCATATTTGTACGGATATTGTCTTTGG 59.197 37.037 0.00 0.00 0.00 3.28
143 144 7.803189 GGCATATTTGTACGGATATTGTCTTTG 59.197 37.037 0.00 0.00 0.00 2.77
146 147 6.426937 GTGGCATATTTGTACGGATATTGTCT 59.573 38.462 0.00 0.00 0.00 3.41
147 148 6.426937 AGTGGCATATTTGTACGGATATTGTC 59.573 38.462 0.00 0.00 0.00 3.18
148 149 6.296026 AGTGGCATATTTGTACGGATATTGT 58.704 36.000 0.00 0.00 0.00 2.71
149 150 6.801539 AGTGGCATATTTGTACGGATATTG 57.198 37.500 0.00 0.00 0.00 1.90
153 154 9.515226 AATAAATAGTGGCATATTTGTACGGAT 57.485 29.630 17.57 6.38 36.33 4.18
154 155 8.911918 AATAAATAGTGGCATATTTGTACGGA 57.088 30.769 17.57 4.98 36.33 4.69
155 156 9.959749 AAAATAAATAGTGGCATATTTGTACGG 57.040 29.630 17.57 0.00 36.33 4.02
191 4848 7.470289 ACTAAGATTTCCGAGAATGATTTCG 57.530 36.000 0.00 3.79 36.93 3.46
292 4950 8.865590 TTGTTTTCTTGCTTCAATAGGTTAAC 57.134 30.769 0.00 0.00 0.00 2.01
312 4970 9.185680 ACTCTAAGTACATTTCAAGGTTTGTTT 57.814 29.630 0.00 0.00 0.00 2.83
409 7758 7.993183 ACTCATCATATTCCCTTTTTACGTCAT 59.007 33.333 0.00 0.00 0.00 3.06
468 7817 9.387123 GTCATCAACTTCTCTTTTTATGTCAAC 57.613 33.333 0.00 0.00 0.00 3.18
509 7858 7.158697 ACAAGCTGATAGTAATGTTGTACACA 58.841 34.615 0.00 0.00 40.71 3.72
819 8200 6.019075 GTGATCAACAAAGTTGCCTTTTTACC 60.019 38.462 0.00 0.00 38.87 2.85
837 8220 3.857052 AGCGTAATTTCGGAGTGATCAA 58.143 40.909 6.60 0.00 0.00 2.57
857 8240 1.246649 TTGGTGGCACTGCATACAAG 58.753 50.000 18.45 0.00 0.00 3.16
1090 8476 2.198827 TGCCATCACGAGGATTGTTT 57.801 45.000 0.00 0.00 32.57 2.83
1159 8545 0.463204 TGGTTGTTGTTGTGGCCATG 59.537 50.000 9.72 0.00 0.00 3.66
1272 8784 2.853542 TGGTTGCTGAGGCTGGGA 60.854 61.111 0.00 0.00 39.59 4.37
1280 8792 3.883830 AATTGTTGTTGTGGTTGCTGA 57.116 38.095 0.00 0.00 0.00 4.26
1302 8814 0.116940 AATGGTTGTTGGGGCTGGAT 59.883 50.000 0.00 0.00 0.00 3.41
1341 9447 0.980754 TGTGGTCGCTGGGGATATGT 60.981 55.000 0.00 0.00 0.00 2.29
1354 9460 0.966179 GGGGAATGGTTGTTGTGGTC 59.034 55.000 0.00 0.00 0.00 4.02
1738 9845 0.883833 CAGGATTTGCACACCCTGTC 59.116 55.000 4.94 0.00 40.84 3.51
1853 9996 3.561143 AGTTTGCAACACCAATGACCTA 58.439 40.909 0.00 0.00 0.00 3.08
1878 10021 0.309302 TACACGTTGCACATGGTTGC 59.691 50.000 0.00 0.00 43.31 4.17
2000 10144 2.256117 AAGCTAAGCAACGTTGACCT 57.744 45.000 31.62 16.89 0.00 3.85
2002 10146 3.120338 TGCATAAGCTAAGCAACGTTGAC 60.120 43.478 31.62 21.18 42.74 3.18
2006 10150 1.737793 GGTGCATAAGCTAAGCAACGT 59.262 47.619 8.94 0.00 40.35 3.99
2083 10228 4.640771 TCCCAATCTTGAACTAGCACTT 57.359 40.909 0.00 0.00 0.00 3.16
2141 10287 1.873591 AGCGAGTGGAACAATGACAAC 59.126 47.619 0.00 0.00 44.16 3.32
2156 10302 3.423536 CAGACATCTAAATACGCAGCGAG 59.576 47.826 24.65 8.09 0.00 5.03
2159 10305 2.221981 GCCAGACATCTAAATACGCAGC 59.778 50.000 0.00 0.00 0.00 5.25
2163 10309 3.753294 AGGGCCAGACATCTAAATACG 57.247 47.619 6.18 0.00 0.00 3.06
2179 10325 4.538746 AGGCTAGAATTACGATTAGGGC 57.461 45.455 0.00 0.00 0.00 5.19
2470 10616 1.015607 GCCCTCAAAATTGCTTGGCG 61.016 55.000 5.19 0.00 0.00 5.69
2511 10657 3.403968 TCAATTCGGGTCGATTCAACAA 58.596 40.909 0.00 0.00 35.23 2.83
2643 10789 4.670896 AACAAACCCCAAAGTTCATGAG 57.329 40.909 0.00 0.00 0.00 2.90
3011 11157 7.886446 CCCCTATACCCACACGAATAAATATTT 59.114 37.037 5.89 5.89 0.00 1.40


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

AutoCloner maintained by Alex Coulton.