Multiple sequence alignment - TraesCS2D01G165000

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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 TraesCS2D01G165000 chr2D 100.000 1683 0 0 903 2585 109401977 109403659 0.000000e+00 3109.0
1 TraesCS2D01G165000 chr2D 100.000 386 0 0 1 386 109401075 109401460 0.000000e+00 713.0
2 TraesCS2D01G165000 chr2D 92.629 407 26 2 1852 2255 293215483 293215078 1.330000e-162 582.0
3 TraesCS2D01G165000 chr2D 92.346 405 26 3 1852 2255 100123954 100124354 2.890000e-159 571.0
4 TraesCS2D01G165000 chr2D 92.515 334 23 2 2254 2585 276962471 276962138 6.470000e-131 477.0
5 TraesCS2D01G165000 chr2D 92.492 333 21 4 2251 2581 293215006 293214676 8.370000e-130 473.0
6 TraesCS2D01G165000 chr2D 92.216 334 24 2 2254 2585 327678587 327678920 3.010000e-129 472.0
7 TraesCS2D01G165000 chr2D 92.661 327 23 1 2254 2579 483921952 483922278 1.080000e-128 470.0
8 TraesCS2D01G165000 chr7D 92.147 955 55 12 904 1851 464033590 464034531 0.000000e+00 1330.0
9 TraesCS2D01G165000 chr7D 90.820 915 62 13 941 1848 582089014 582089913 0.000000e+00 1205.0
10 TraesCS2D01G165000 chr7D 91.964 336 23 4 2254 2585 480242555 480242890 3.890000e-128 468.0
11 TraesCS2D01G165000 chr7D 90.504 337 23 4 42 378 376527805 376528132 1.100000e-118 436.0
12 TraesCS2D01G165000 chr5D 91.295 919 62 10 945 1854 432179392 432178483 0.000000e+00 1238.0
13 TraesCS2D01G165000 chr5D 89.872 938 70 16 927 1851 84452266 84453191 0.000000e+00 1182.0
14 TraesCS2D01G165000 chr5D 89.744 936 75 13 926 1851 84407578 84408502 0.000000e+00 1177.0
15 TraesCS2D01G165000 chr5D 92.574 404 25 4 1852 2255 469983764 469984162 2.230000e-160 575.0
16 TraesCS2D01G165000 chr5D 92.216 334 24 2 2254 2585 384504525 384504192 3.010000e-129 472.0
17 TraesCS2D01G165000 chr5D 90.533 338 31 1 42 378 53755586 53755923 1.820000e-121 446.0
18 TraesCS2D01G165000 chr5D 89.489 333 24 4 53 378 326743007 326743335 6.660000e-111 411.0
19 TraesCS2D01G165000 chr5D 93.431 274 18 0 42 315 444747592 444747319 8.610000e-110 407.0
20 TraesCS2D01G165000 chr5D 91.815 281 22 1 40 319 287812150 287811870 8.670000e-105 390.0
21 TraesCS2D01G165000 chr5D 91.636 275 23 0 45 319 294578390 294578116 5.220000e-102 381.0
22 TraesCS2D01G165000 chr3D 91.167 917 59 13 950 1851 486147193 486146284 0.000000e+00 1225.0
23 TraesCS2D01G165000 chr3D 93.069 404 25 1 1852 2255 52777324 52777724 2.870000e-164 588.0
24 TraesCS2D01G165000 chr3D 92.892 408 20 5 1852 2255 482290383 482289981 3.710000e-163 584.0
25 TraesCS2D01G165000 chr3D 92.593 405 29 1 1852 2255 399998511 399998915 4.790000e-162 580.0
26 TraesCS2D01G165000 chr3D 92.574 404 25 3 1852 2255 188653272 188652874 2.230000e-160 575.0
27 TraesCS2D01G165000 chr3D 92.058 277 21 1 40 316 545071961 545071686 3.120000e-104 388.0
28 TraesCS2D01G165000 chr3D 90.169 295 24 2 42 335 486147831 486147541 1.880000e-101 379.0
29 TraesCS2D01G165000 chr7A 90.084 948 75 13 919 1851 700256674 700257617 0.000000e+00 1212.0
30 TraesCS2D01G165000 chr5B 90.919 914 65 11 947 1851 297042230 297043134 0.000000e+00 1212.0
31 TraesCS2D01G165000 chr5B 89.854 956 66 10 908 1851 56361516 56362452 0.000000e+00 1199.0
32 TraesCS2D01G165000 chr5B 86.310 336 41 5 42 372 56360635 56360970 6.800000e-96 361.0
33 TraesCS2D01G165000 chr4A 92.701 411 22 4 1852 2255 580463733 580463324 1.030000e-163 586.0
34 TraesCS2D01G165000 chr1D 92.195 410 25 3 1852 2255 273505000 273505408 8.020000e-160 573.0
35 TraesCS2D01G165000 chr1D 91.150 339 29 1 39 376 441580054 441580392 2.340000e-125 459.0
36 TraesCS2D01G165000 chr1D 93.750 272 16 1 40 310 13229704 13229433 8.610000e-110 407.0
37 TraesCS2D01G165000 chr1D 90.747 281 19 6 42 319 396219898 396219622 4.060000e-98 368.0
38 TraesCS2D01G165000 chr6D 92.515 334 23 2 2254 2585 143719039 143718706 6.470000e-131 477.0
39 TraesCS2D01G165000 chr6D 91.916 334 25 2 2254 2585 132479231 132479564 1.400000e-127 466.0
40 TraesCS2D01G165000 chr6D 91.916 334 25 2 2254 2585 324876084 324875751 1.400000e-127 466.0
41 TraesCS2D01G165000 chr6D 93.133 233 16 0 40 272 427314847 427315079 2.460000e-90 342.0
42 TraesCS2D01G165000 chr6D 89.015 264 28 1 42 305 42044641 42044379 2.480000e-85 326.0
43 TraesCS2D01G165000 chr6D 91.775 231 19 0 38 268 192187978 192188208 3.210000e-84 322.0
44 TraesCS2D01G165000 chr6D 91.026 234 20 1 46 278 18144372 18144139 5.370000e-82 315.0
45 TraesCS2D01G165000 chr6D 89.700 233 21 3 40 272 46861960 46862189 7.000000e-76 294.0
46 TraesCS2D01G165000 chr6D 92.593 189 13 1 44 232 308329429 308329242 1.180000e-68 270.0
47 TraesCS2D01G165000 chr6D 87.281 228 27 2 46 272 472984017 472983791 2.550000e-65 259.0
48 TraesCS2D01G165000 chr6D 85.714 217 26 5 46 260 31806190 31805977 9.310000e-55 224.0
49 TraesCS2D01G165000 chr6D 100.000 44 0 0 1 44 112551093 112551136 5.930000e-12 82.4
50 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 26560835 26560877 2.130000e-11 80.5
51 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 115406103 115406145 2.130000e-11 80.5
52 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 143247293 143247251 2.130000e-11 80.5
53 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 161508393 161508351 2.130000e-11 80.5
54 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 209735304 209735346 2.130000e-11 80.5
55 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 210743517 210743475 2.130000e-11 80.5
56 TraesCS2D01G165000 chr6D 100.000 43 0 0 1 43 261891385 261891343 2.130000e-11 80.5
57 TraesCS2D01G165000 chr6A 91.691 337 28 0 40 376 9522130 9522466 3.890000e-128 468.0
58 TraesCS2D01G165000 chr3A 91.964 336 24 1 40 372 9515437 9515772 3.890000e-128 468.0
59 TraesCS2D01G165000 chr3B 92.806 278 19 1 40 316 794530649 794530926 4.010000e-108 401.0
60 TraesCS2D01G165000 chr4D 89.577 307 26 6 39 342 92671989 92671686 4.040000e-103 385.0
61 TraesCS2D01G165000 chr4D 93.724 239 14 1 40 278 76607765 76608002 8.800000e-95 357.0
62 TraesCS2D01G165000 chr4D 93.103 232 15 1 42 272 210460224 210460455 3.190000e-89 339.0
63 TraesCS2D01G165000 chr4D 91.803 244 19 1 40 282 490104287 490104044 3.190000e-89 339.0
64 TraesCS2D01G165000 chr4D 87.636 275 29 3 42 316 439785586 439785855 5.370000e-82 315.0
65 TraesCS2D01G165000 chr7B 88.217 314 34 2 37 350 201004743 201004433 3.140000e-99 372.0
66 TraesCS2D01G165000 chr4B 90.545 275 26 0 42 316 577064128 577063854 5.260000e-97 364.0
67 TraesCS2D01G165000 chr1A 88.043 276 28 5 44 316 586521464 586521737 3.210000e-84 322.0
68 TraesCS2D01G165000 chrUn 87.732 269 29 4 42 309 91675873 91675608 6.950000e-81 311.0
69 TraesCS2D01G165000 chrUn 87.361 269 30 4 42 309 441250332 441250597 3.230000e-79 305.0
70 TraesCS2D01G165000 chrUn 100.000 43 0 0 1 43 25823170 25823128 2.130000e-11 80.5
71 TraesCS2D01G165000 chrUn 100.000 43 0 0 1 43 173174961 173174919 2.130000e-11 80.5
72 TraesCS2D01G165000 chrUn 100.000 30 0 0 39 68 298579844 298579873 3.590000e-04 56.5
73 TraesCS2D01G165000 chrUn 100.000 30 0 0 39 68 298584700 298584729 3.590000e-04 56.5
74 TraesCS2D01G165000 chrUn 100.000 30 0 0 39 68 377457006 377456977 3.590000e-04 56.5
75 TraesCS2D01G165000 chrUn 96.774 31 1 0 37 67 141014738 141014768 5.000000e-03 52.8
76 TraesCS2D01G165000 chrUn 100.000 28 0 0 40 67 180989429 180989402 5.000000e-03 52.8


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 TraesCS2D01G165000 chr2D 109401075 109403659 2584 False 1911.0 3109 100.0000 1 2585 2 chr2D.!!$F4 2584
1 TraesCS2D01G165000 chr2D 293214676 293215483 807 True 527.5 582 92.5605 1852 2581 2 chr2D.!!$R2 729
2 TraesCS2D01G165000 chr7D 464033590 464034531 941 False 1330.0 1330 92.1470 904 1851 1 chr7D.!!$F2 947
3 TraesCS2D01G165000 chr7D 582089014 582089913 899 False 1205.0 1205 90.8200 941 1848 1 chr7D.!!$F4 907
4 TraesCS2D01G165000 chr5D 432178483 432179392 909 True 1238.0 1238 91.2950 945 1854 1 chr5D.!!$R4 909
5 TraesCS2D01G165000 chr5D 84452266 84453191 925 False 1182.0 1182 89.8720 927 1851 1 chr5D.!!$F3 924
6 TraesCS2D01G165000 chr5D 84407578 84408502 924 False 1177.0 1177 89.7440 926 1851 1 chr5D.!!$F2 925
7 TraesCS2D01G165000 chr3D 486146284 486147831 1547 True 802.0 1225 90.6680 42 1851 2 chr3D.!!$R4 1809
8 TraesCS2D01G165000 chr7A 700256674 700257617 943 False 1212.0 1212 90.0840 919 1851 1 chr7A.!!$F1 932
9 TraesCS2D01G165000 chr5B 297042230 297043134 904 False 1212.0 1212 90.9190 947 1851 1 chr5B.!!$F1 904
10 TraesCS2D01G165000 chr5B 56360635 56362452 1817 False 780.0 1199 88.0820 42 1851 2 chr5B.!!$F2 1809

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
101 102 0.955919 CTTTTGGACCGTCTGAGGCC 60.956 60.0 0.0 0.0 33.69 5.19 F
263 265 0.962356 CAGCCGCCACTTCATTTCCT 60.962 55.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1092 1134 0.174845 CGATCCACCAACGCCTTCTA 59.825 55.0 0.0 0.0 0.0 2.1 R
2230 2301 0.399949 ATGGAGGTGGGGCGATAAGA 60.400 55.0 0.0 0.0 0.0 2.1 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
26 27 8.879227 TCCATTCTGTATATGTGGATGATAACA 58.121 33.333 0.00 0.00 34.23 2.41
27 28 9.506018 CCATTCTGTATATGTGGATGATAACAA 57.494 33.333 0.00 0.00 31.59 2.83
38 39 9.685276 ATGTGGATGATAACAACTAGATTCAAA 57.315 29.630 0.00 0.00 0.00 2.69
39 40 9.685276 TGTGGATGATAACAACTAGATTCAAAT 57.315 29.630 0.00 0.00 0.00 2.32
76 77 7.975616 CCAATAGATGGTCCAAATGTAAAAGTG 59.024 37.037 0.00 0.00 44.85 3.16
97 98 3.385433 TGACTAACTTTTGGACCGTCTGA 59.615 43.478 0.00 0.00 0.00 3.27
101 102 0.955919 CTTTTGGACCGTCTGAGGCC 60.956 60.000 0.00 0.00 33.69 5.19
110 111 1.781025 CGTCTGAGGCCAAAAACGCA 61.781 55.000 5.01 0.00 0.00 5.24
133 134 2.168521 CTCCAACAGACGGTCCATATGT 59.831 50.000 4.14 0.00 0.00 2.29
159 161 1.789576 AATTGGACCGTGGCCTCCTT 61.790 55.000 3.32 0.00 0.00 3.36
172 174 4.947388 GTGGCCTCCTTGTGATGTAAAATA 59.053 41.667 3.32 0.00 0.00 1.40
185 187 5.410132 TGATGTAAAATACAACACCTCGTGG 59.590 40.000 0.99 0.99 42.76 4.94
202 204 2.289274 CGTGGTGCAAACTTACATCACA 59.711 45.455 7.13 0.00 46.10 3.58
205 207 3.317711 TGGTGCAAACTTACATCACAAGG 59.682 43.478 0.00 0.00 0.00 3.61
223 225 1.133513 AGGTGCATCTGGTCCAAAACA 60.134 47.619 0.00 0.00 0.00 2.83
263 265 0.962356 CAGCCGCCACTTCATTTCCT 60.962 55.000 0.00 0.00 0.00 3.36
272 274 1.203001 ACTTCATTTCCTTTCCCGCCA 60.203 47.619 0.00 0.00 0.00 5.69
276 278 3.879180 TTTCCTTTCCCGCCAGCCC 62.879 63.158 0.00 0.00 0.00 5.19
365 375 4.996434 CCCGCATCAGATCCGGCC 62.996 72.222 7.32 0.00 40.65 6.13
367 377 4.996434 CGCATCAGATCCGGCCCC 62.996 72.222 0.00 0.00 0.00 5.80
1005 1047 4.147449 CACCGCTCTCCGATGGCA 62.147 66.667 0.00 0.00 40.02 4.92
1092 1134 0.885196 GAGTGGAGTTCTCTGACGCT 59.115 55.000 0.00 0.00 0.00 5.07
1115 1157 2.824041 GCGTTGGTGGATCGGCAT 60.824 61.111 0.00 0.00 0.00 4.40
1194 1236 4.473520 CCTCGGGCGCACCTCAAT 62.474 66.667 10.83 0.00 36.97 2.57
1217 1261 0.464735 CCAGAGATCGAGAGTCGGGT 60.465 60.000 0.00 0.00 40.88 5.28
1264 1308 3.065655 GGCATCAAGATGAAGGAGATCG 58.934 50.000 13.93 0.00 41.20 3.69
1475 1529 0.390860 GTGATCCCCATCGAGTCCTG 59.609 60.000 0.00 0.00 0.00 3.86
1521 1578 2.015726 GGAGGAGGAGGAGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
1525 1588 1.235696 GAGGAGGAGGAGGGATGCT 59.764 63.158 0.00 0.00 0.00 3.79
1548 1611 0.178900 ACCCGGAGAAGGAGGAGTTT 60.179 55.000 0.73 0.00 0.00 2.66
1595 1658 7.041916 CGACGATGAGGAGTAGTTTATCTAGTT 60.042 40.741 0.00 0.00 32.96 2.24
1987 2058 8.910944 ACGTGATGATACTTAACTACTTGGTAT 58.089 33.333 0.00 0.00 0.00 2.73
2097 2168 2.746277 GCGGCGTCTTCCCATTGT 60.746 61.111 9.37 0.00 0.00 2.71
2099 2170 2.877691 GGCGTCTTCCCATTGTGC 59.122 61.111 0.00 0.00 0.00 4.57
2111 2182 1.089920 CATTGTGCAGGCAGTACTCC 58.910 55.000 0.00 0.00 33.54 3.85
2146 2217 2.470821 GTAGCGCTTGATGTACCGATT 58.529 47.619 18.68 0.00 0.00 3.34
2150 2221 1.396648 CGCTTGATGTACCGATTTGCA 59.603 47.619 0.00 0.00 0.00 4.08
2162 2233 0.526954 GATTTGCATCTTGCTGGCGG 60.527 55.000 0.75 0.00 45.31 6.13
2167 2238 4.393155 ATCTTGCTGGCGGACGCA 62.393 61.111 18.95 4.03 44.11 5.24
2230 2301 4.760047 GTCGGTGGCACGCTGGAT 62.760 66.667 12.17 0.00 46.74 3.41
2238 2309 1.560860 GGCACGCTGGATCTTATCGC 61.561 60.000 0.00 0.00 0.00 4.58
2249 2320 0.399949 TCTTATCGCCCCACCTCCAT 60.400 55.000 0.00 0.00 0.00 3.41
2286 2432 2.359975 CCGCCGCCTCCTTTTTCT 60.360 61.111 0.00 0.00 0.00 2.52
2295 2441 1.613255 CCTCCTTTTTCTAGGCGGCAA 60.613 52.381 13.08 0.00 33.64 4.52
2296 2442 2.369394 CTCCTTTTTCTAGGCGGCAAT 58.631 47.619 13.08 0.00 35.15 3.56
2333 2479 0.970937 CCTCGTACCTGGCTTCCTCA 60.971 60.000 0.00 0.00 0.00 3.86
2355 2501 1.339055 CCGCCATCTCCTTCTTGAACA 60.339 52.381 0.00 0.00 0.00 3.18
2402 2549 1.002033 GCAGCAACTTCCACAGACAAG 60.002 52.381 0.00 0.00 0.00 3.16
2428 2575 2.407340 ACTGGCCCCAAAACCAATTA 57.593 45.000 0.00 0.00 34.96 1.40
2491 2638 0.179108 GGTCCTCGTCGCTGCTATTT 60.179 55.000 0.00 0.00 0.00 1.40
2492 2639 0.924090 GTCCTCGTCGCTGCTATTTG 59.076 55.000 0.00 0.00 0.00 2.32
2529 2677 2.811317 GGCAACTCCTCGTCAGCG 60.811 66.667 0.00 0.00 39.92 5.18
2581 2729 2.435372 TTGAGAGAGAGAGAGAGGGC 57.565 55.000 0.00 0.00 0.00 5.19
2582 2730 0.180171 TGAGAGAGAGAGAGAGGGCG 59.820 60.000 0.00 0.00 0.00 6.13
2583 2731 0.468226 GAGAGAGAGAGAGAGGGCGA 59.532 60.000 0.00 0.00 0.00 5.54
2584 2732 0.469917 AGAGAGAGAGAGAGGGCGAG 59.530 60.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.685276 TTTGAATCTAGTTGTTATCATCCACAT 57.315 29.630 0.00 0.00 0.00 3.21
13 14 9.685276 ATTTGAATCTAGTTGTTATCATCCACA 57.315 29.630 0.00 0.00 0.00 4.17
23 24 9.678260 AGATGCTCTAATTTGAATCTAGTTGTT 57.322 29.630 3.24 0.00 0.00 2.83
26 27 8.489489 TGGAGATGCTCTAATTTGAATCTAGTT 58.511 33.333 4.68 0.00 0.00 2.24
27 28 8.027524 TGGAGATGCTCTAATTTGAATCTAGT 57.972 34.615 4.68 0.00 0.00 2.57
30 31 9.504708 CTATTGGAGATGCTCTAATTTGAATCT 57.495 33.333 10.57 4.42 38.24 2.40
31 32 9.499479 TCTATTGGAGATGCTCTAATTTGAATC 57.501 33.333 10.57 0.00 38.24 2.52
74 75 3.493503 CAGACGGTCCAAAAGTTAGTCAC 59.506 47.826 4.14 0.00 0.00 3.67
76 77 3.986277 TCAGACGGTCCAAAAGTTAGTC 58.014 45.455 4.14 0.00 0.00 2.59
97 98 2.564721 GGAGCTGCGTTTTTGGCCT 61.565 57.895 3.32 0.00 0.00 5.19
101 102 1.065401 TCTGTTGGAGCTGCGTTTTTG 59.935 47.619 0.00 0.00 0.00 2.44
110 111 1.194781 ATGGACCGTCTGTTGGAGCT 61.195 55.000 0.00 0.00 0.00 4.09
183 185 3.317711 CCTTGTGATGTAAGTTTGCACCA 59.682 43.478 0.00 0.00 0.00 4.17
185 187 4.290155 CACCTTGTGATGTAAGTTTGCAC 58.710 43.478 0.00 0.00 35.23 4.57
192 194 3.376234 CCAGATGCACCTTGTGATGTAAG 59.624 47.826 0.00 0.00 35.23 2.34
193 195 3.244875 ACCAGATGCACCTTGTGATGTAA 60.245 43.478 0.00 0.00 35.23 2.41
202 204 1.963515 GTTTTGGACCAGATGCACCTT 59.036 47.619 0.00 0.00 0.00 3.50
205 207 2.863704 GCTTGTTTTGGACCAGATGCAC 60.864 50.000 0.00 0.00 0.00 4.57
246 248 0.603065 AAAGGAAATGAAGTGGCGGC 59.397 50.000 0.00 0.00 0.00 6.53
973 1015 4.803426 GTGAGAGCGGTGGAGCGG 62.803 72.222 0.00 0.00 43.00 5.52
974 1016 4.803426 GGTGAGAGCGGTGGAGCG 62.803 72.222 0.00 0.00 43.00 5.03
975 1017 4.803426 CGGTGAGAGCGGTGGAGC 62.803 72.222 0.00 0.00 35.16 4.70
976 1018 4.803426 GCGGTGAGAGCGGTGGAG 62.803 72.222 0.00 0.00 39.82 3.86
981 1023 4.200283 GGAGAGCGGTGAGAGCGG 62.200 72.222 0.00 0.00 39.82 5.52
982 1024 4.544689 CGGAGAGCGGTGAGAGCG 62.545 72.222 0.00 0.00 42.73 5.03
983 1025 2.485795 ATCGGAGAGCGGTGAGAGC 61.486 63.158 0.00 0.00 43.63 4.09
984 1026 1.358402 CATCGGAGAGCGGTGAGAG 59.642 63.158 0.00 0.00 43.63 3.20
985 1027 2.121538 CCATCGGAGAGCGGTGAGA 61.122 63.158 0.00 0.00 43.63 3.27
986 1028 2.415010 CCATCGGAGAGCGGTGAG 59.585 66.667 0.00 0.00 43.63 3.51
987 1029 3.838271 GCCATCGGAGAGCGGTGA 61.838 66.667 0.00 0.00 43.63 4.02
1005 1047 1.080705 CTTCGGCGTCTTCTTCGGT 60.081 57.895 6.85 0.00 0.00 4.69
1092 1134 0.174845 CGATCCACCAACGCCTTCTA 59.825 55.000 0.00 0.00 0.00 2.10
1194 1236 2.017782 CGACTCTCGATCTCTGGGAAA 58.982 52.381 0.00 0.00 43.74 3.13
1264 1308 1.579808 CATCGTCTTCTTCTTCGTCGC 59.420 52.381 0.00 0.00 0.00 5.19
1475 1529 3.020237 GCCCAGTCCTCCTCGGAAC 62.020 68.421 0.00 0.00 45.32 3.62
1521 1578 1.392710 CCTTCTCCGGGTCGTAGCAT 61.393 60.000 0.00 0.00 0.00 3.79
1525 1588 1.077212 CCTCCTTCTCCGGGTCGTA 60.077 63.158 0.00 0.00 0.00 3.43
1678 1741 9.039165 AGATGGTCCAAAATGAAGATGTAAATT 57.961 29.630 0.00 0.00 0.00 1.82
1714 1782 5.243730 GTCCAAATTGATGGTCCAAAAGAGA 59.756 40.000 0.00 0.00 41.46 3.10
2040 2111 2.590092 GGGCTGCCGGAATACTGT 59.410 61.111 13.40 0.00 0.00 3.55
2094 2165 1.005037 CGGAGTACTGCCTGCACAA 60.005 57.895 8.99 0.00 0.00 3.33
2127 2198 2.863740 CAAATCGGTACATCAAGCGCTA 59.136 45.455 12.05 0.00 40.07 4.26
2150 2221 4.393155 TGCGTCCGCCAGCAAGAT 62.393 61.111 9.43 0.00 40.78 2.40
2162 2233 0.635731 CAAGATCGTTCTCGTGCGTC 59.364 55.000 0.00 0.00 38.33 5.19
2167 2238 2.386661 AATGGCAAGATCGTTCTCGT 57.613 45.000 0.00 0.00 38.33 4.18
2170 2241 2.699954 ACGAAATGGCAAGATCGTTCT 58.300 42.857 16.47 0.00 45.33 3.01
2198 2269 2.435059 GACAAGGAGCTCCGGTGC 60.435 66.667 30.09 20.71 42.08 5.01
2230 2301 0.399949 ATGGAGGTGGGGCGATAAGA 60.400 55.000 0.00 0.00 0.00 2.10
2238 2309 4.828296 GGCTGCATGGAGGTGGGG 62.828 72.222 16.65 0.00 0.00 4.96
2268 2414 2.530958 TAGAAAAAGGAGGCGGCGGG 62.531 60.000 9.78 0.00 0.00 6.13
2286 2432 2.653953 GAAGCCCGTATTGCCGCCTA 62.654 60.000 0.00 0.00 0.00 3.93
2295 2441 2.590092 GGCCTGTGAAGCCCGTAT 59.410 61.111 0.00 0.00 45.16 3.06
2317 2463 0.105039 GGATGAGGAAGCCAGGTACG 59.895 60.000 0.00 0.00 0.00 3.67
2333 2479 1.500474 TCAAGAAGGAGATGGCGGAT 58.500 50.000 0.00 0.00 0.00 4.18
2355 2501 1.073897 GAGAAGCCAGGCAAGTGGT 59.926 57.895 15.80 0.00 40.09 4.16
2387 2534 4.170468 ACAATCCTTGTCTGTGGAAGTT 57.830 40.909 0.00 0.00 40.56 2.66
2402 2549 1.548719 GTTTTGGGGCCAGTACAATCC 59.451 52.381 4.39 0.00 0.00 3.01
2414 2561 4.824537 CCCAACTTTTAATTGGTTTTGGGG 59.175 41.667 14.50 4.25 45.45 4.96
2491 2638 3.062466 CCCGAGGACGCTCACTCA 61.062 66.667 0.00 0.00 38.29 3.41
2492 2639 3.827898 CCCCGAGGACGCTCACTC 61.828 72.222 0.00 0.00 38.29 3.51
2512 2660 2.811317 CGCTGACGAGGAGTTGCC 60.811 66.667 0.00 0.00 43.93 4.52
2515 2663 3.671411 ACGCGCTGACGAGGAGTT 61.671 61.111 5.73 0.00 44.04 3.01


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

AutoCloner maintained by Alex Coulton.