Multiple sequence alignment - TraesCS6D01G111300

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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 TraesCS6D01G111300 chr6D 100.000 3530 0 0 1 3530 77865745 77862216 0.000000e+00 6519.0
1 TraesCS6D01G111300 chr6D 93.208 265 17 1 3267 3530 336536625 336536361 4.270000e-104 388.0
2 TraesCS6D01G111300 chr6D 90.385 52 2 1 2068 2119 77863621 77863573 8.180000e-07 65.8
3 TraesCS6D01G111300 chr6A 96.212 1584 47 5 1318 2891 93632633 93631053 0.000000e+00 2580.0
4 TraesCS6D01G111300 chr6A 90.226 1105 62 14 234 1305 93633874 93632783 0.000000e+00 1400.0
5 TraesCS6D01G111300 chr6A 82.558 688 64 25 2876 3529 93623880 93623215 3.980000e-154 555.0
6 TraesCS6D01G111300 chr6A 95.102 245 12 0 1 245 93762689 93762445 1.540000e-103 387.0
7 TraesCS6D01G111300 chr6B 88.704 1080 79 27 2170 3242 150665404 150664361 0.000000e+00 1279.0
8 TraesCS6D01G111300 chr6B 92.048 830 47 6 1269 2091 150666261 150665444 0.000000e+00 1149.0
9 TraesCS6D01G111300 chr6B 89.852 877 72 11 315 1183 150667163 150666296 0.000000e+00 1110.0
10 TraesCS6D01G111300 chr6B 81.884 414 45 19 1 408 150667533 150667144 4.400000e-84 322.0
11 TraesCS6D01G111300 chr6B 82.353 136 16 4 3071 3202 173662121 173662252 1.040000e-20 111.0
12 TraesCS6D01G111300 chr7D 95.885 243 10 0 3260 3502 138304565 138304807 9.180000e-106 394.0
13 TraesCS6D01G111300 chr7D 81.102 127 11 4 3079 3203 21009226 21009341 4.850000e-14 89.8
14 TraesCS6D01G111300 chrUn 87.591 274 29 5 3260 3530 342264402 342264131 2.650000e-81 313.0
15 TraesCS6D01G111300 chrUn 93.443 122 3 5 3260 3378 342264863 342264744 3.620000e-40 176.0
16 TraesCS6D01G111300 chrUn 93.333 120 7 1 3260 3378 342265324 342265205 3.620000e-40 176.0
17 TraesCS6D01G111300 chrUn 93.333 120 7 1 3260 3378 342265785 342265666 3.620000e-40 176.0
18 TraesCS6D01G111300 chrUn 93.333 120 7 1 3260 3378 417836421 417836302 3.620000e-40 176.0
19 TraesCS6D01G111300 chr4B 86.594 276 28 9 3260 3530 369519243 369519514 2.660000e-76 296.0
20 TraesCS6D01G111300 chr1D 92.199 141 10 1 3390 3530 218273603 218273742 7.730000e-47 198.0
21 TraesCS6D01G111300 chr7B 93.333 120 7 1 3260 3378 666558742 666558861 3.620000e-40 176.0
22 TraesCS6D01G111300 chr5D 85.976 164 22 1 3066 3229 457266711 457266549 1.300000e-39 174.0
23 TraesCS6D01G111300 chr4A 80.120 166 26 5 3066 3228 570454529 570454368 2.230000e-22 117.0
24 TraesCS6D01G111300 chr1A 85.882 85 10 2 3071 3154 432515318 432515235 4.850000e-14 89.8
25 TraesCS6D01G111300 chr1A 83.824 68 10 1 3087 3154 520762241 520762175 2.940000e-06 63.9
26 TraesCS6D01G111300 chr3B 90.476 63 4 2 3070 3131 169240799 169240860 8.120000e-12 82.4


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 TraesCS6D01G111300 chr6D 77862216 77865745 3529 True 3292.40 6519 95.1925 1 3530 2 chr6D.!!$R2 3529
1 TraesCS6D01G111300 chr6A 93631053 93633874 2821 True 1990.00 2580 93.2190 234 2891 2 chr6A.!!$R3 2657
2 TraesCS6D01G111300 chr6A 93623215 93623880 665 True 555.00 555 82.5580 2876 3529 1 chr6A.!!$R1 653
3 TraesCS6D01G111300 chr6B 150664361 150667533 3172 True 965.00 1279 88.1220 1 3242 4 chr6B.!!$R1 3241
4 TraesCS6D01G111300 chrUn 342264131 342265785 1654 True 210.25 313 91.9250 3260 3530 4 chrUn.!!$R2 270

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
89 90 0.254178 CTCACCTTGGGGATCTGTGG 59.746 60.000 0.00 0.0 36.25 4.17 F
750 847 0.330604 ACATGAGCACTTGAGGCCAT 59.669 50.000 5.01 0.0 0.00 4.40 F
1099 1205 0.961358 CGGTTATTTGGCCCGGTTGA 60.961 55.000 0.00 0.0 38.09 3.18 F
1429 1677 1.193874 CGTCTTACGGTTGTCCTTTGC 59.806 52.381 0.00 0.0 38.08 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1194 0.110678 TATGTGTTTCAACCGGGCCA 59.889 50.0 6.32 0.0 0.00 5.36 R
2033 2281 0.373716 CTTCGGCGAGTTATTGTGCC 59.626 55.0 10.46 0.0 44.09 5.01 R
2106 2354 0.818296 CGACGTCCTCCATCTCCTTT 59.182 55.0 10.58 0.0 0.00 3.11 R
3144 3436 0.754472 GGGCATTGCATGTGGCTTAT 59.246 50.0 20.47 0.0 45.15 1.73 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
31 32 2.166459 TCGAAGGTAGAGCATGTTGAGG 59.834 50.000 0.00 0.00 0.00 3.86
40 41 4.293494 AGAGCATGTTGAGGGAGAAGATA 58.707 43.478 0.00 0.00 0.00 1.98
45 46 5.512060 GCATGTTGAGGGAGAAGATATAGCA 60.512 44.000 0.00 0.00 0.00 3.49
48 49 4.477536 TGAGGGAGAAGATATAGCAGGT 57.522 45.455 0.00 0.00 0.00 4.00
51 52 2.027653 GGGAGAAGATATAGCAGGTGCC 60.028 54.545 0.00 0.00 43.38 5.01
86 87 2.406559 AGATCTCACCTTGGGGATCTG 58.593 52.381 4.83 0.00 41.95 2.90
89 90 0.254178 CTCACCTTGGGGATCTGTGG 59.746 60.000 0.00 0.00 36.25 4.17
94 95 0.549950 CTTGGGGATCTGTGGAGCAT 59.450 55.000 0.00 0.00 0.00 3.79
146 147 1.415200 GTAGGAGGATGTGAGGGGTC 58.585 60.000 0.00 0.00 0.00 4.46
157 158 1.079336 GAGGGGTCGGAGGAAAACG 60.079 63.158 0.00 0.00 0.00 3.60
163 164 2.639970 TCGGAGGAAAACGACGGTA 58.360 52.632 0.00 0.00 33.69 4.02
173 174 2.159327 AACGACGGTAGGGTTTGAAG 57.841 50.000 0.00 0.00 0.00 3.02
222 226 4.112634 GGAAACTTCCAAACAACTGAAGC 58.887 43.478 3.50 0.00 46.76 3.86
279 283 7.164122 AGATATGGCAAACTGGTGTAGATATG 58.836 38.462 0.00 0.00 0.00 1.78
440 521 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
722 819 4.026052 CCTAAAATTCCTCCAAGCCATGT 58.974 43.478 0.00 0.00 0.00 3.21
750 847 0.330604 ACATGAGCACTTGAGGCCAT 59.669 50.000 5.01 0.00 0.00 4.40
765 862 1.275856 GGCCATGCATGAACTTTTCCA 59.724 47.619 28.31 0.00 0.00 3.53
1060 1166 9.225201 CAATTTATGATGTTCCGAGTAACAATG 57.775 33.333 2.76 0.00 42.33 2.82
1063 1169 4.250464 TGATGTTCCGAGTAACAATGTCC 58.750 43.478 2.76 0.00 42.33 4.02
1066 1172 3.259902 GTTCCGAGTAACAATGTCCTCC 58.740 50.000 7.24 0.00 0.00 4.30
1093 1199 1.249407 TGTTGTCGGTTATTTGGCCC 58.751 50.000 0.00 0.00 0.00 5.80
1099 1205 0.961358 CGGTTATTTGGCCCGGTTGA 60.961 55.000 0.00 0.00 38.09 3.18
1176 1282 9.950496 AGTATCAGTTCTTTTGATTAGACATGT 57.050 29.630 0.00 0.00 36.68 3.21
1180 1286 9.119418 TCAGTTCTTTTGATTAGACATGTTTCA 57.881 29.630 0.00 0.00 0.00 2.69
1186 1294 9.695526 CTTTTGATTAGACATGTTTCAAATCCA 57.304 29.630 19.11 9.08 36.50 3.41
1234 1342 4.356289 ACAAACAACTCCAAAATACACGC 58.644 39.130 0.00 0.00 0.00 5.34
1244 1352 7.081976 ACTCCAAAATACACGCTCAAAAATAC 58.918 34.615 0.00 0.00 0.00 1.89
1246 1354 7.426410 TCCAAAATACACGCTCAAAAATACAA 58.574 30.769 0.00 0.00 0.00 2.41
1247 1355 7.593273 TCCAAAATACACGCTCAAAAATACAAG 59.407 33.333 0.00 0.00 0.00 3.16
1248 1356 7.381139 CCAAAATACACGCTCAAAAATACAAGT 59.619 33.333 0.00 0.00 0.00 3.16
1251 1359 8.944212 AATACACGCTCAAAAATACAAGTAAC 57.056 30.769 0.00 0.00 0.00 2.50
1253 1361 6.966021 ACACGCTCAAAAATACAAGTAACAT 58.034 32.000 0.00 0.00 0.00 2.71
1257 1365 9.389570 ACGCTCAAAAATACAAGTAACATTTAC 57.610 29.630 0.00 0.00 0.00 2.01
1258 1366 9.388346 CGCTCAAAAATACAAGTAACATTTACA 57.612 29.630 0.00 0.00 0.00 2.41
1267 1375 5.944007 ACAAGTAACATTTACATCCTGGACC 59.056 40.000 0.00 0.00 0.00 4.46
1429 1677 1.193874 CGTCTTACGGTTGTCCTTTGC 59.806 52.381 0.00 0.00 38.08 3.68
1443 1691 2.637382 TCCTTTGCGGATCTATATGCCA 59.363 45.455 0.00 0.00 36.69 4.92
1800 2048 2.680913 CCGGCGCAAGAAGAACCTG 61.681 63.158 10.83 0.00 43.02 4.00
1869 2117 3.382832 AAGGGGTCCGACGCTGAG 61.383 66.667 14.60 0.00 33.55 3.35
2033 2281 1.893786 CAGAGGAACAGGACGAGGG 59.106 63.158 0.00 0.00 0.00 4.30
2114 2362 1.028868 GCTGCCGCTGAAAAGGAGAT 61.029 55.000 0.73 0.00 0.00 2.75
2168 2422 2.733301 CGCCGCTGAGATGGAGAT 59.267 61.111 0.00 0.00 0.00 2.75
2178 2432 3.574749 TGAGATGGAGATGGAGAAGGAG 58.425 50.000 0.00 0.00 0.00 3.69
2494 2748 4.531426 ACAACCAAAGCCCCGCCA 62.531 61.111 0.00 0.00 0.00 5.69
2535 2795 1.153823 CCTCCACGCCTGAACTACG 60.154 63.158 0.00 0.00 0.00 3.51
2536 2796 1.592400 CCTCCACGCCTGAACTACGA 61.592 60.000 0.00 0.00 0.00 3.43
2537 2797 0.179161 CTCCACGCCTGAACTACGAG 60.179 60.000 0.00 0.00 0.00 4.18
2538 2798 0.892358 TCCACGCCTGAACTACGAGT 60.892 55.000 0.00 0.00 0.00 4.18
2539 2799 0.806868 CCACGCCTGAACTACGAGTA 59.193 55.000 0.00 0.00 0.00 2.59
2540 2800 1.467035 CCACGCCTGAACTACGAGTAC 60.467 57.143 0.00 0.00 0.00 2.73
2545 2805 3.445857 GCCTGAACTACGAGTACATTCC 58.554 50.000 0.00 0.00 0.00 3.01
2548 2808 4.421948 CTGAACTACGAGTACATTCCACC 58.578 47.826 0.00 0.00 0.00 4.61
2588 2848 1.367840 CGCCTCCTCCTTTATCCCG 59.632 63.158 0.00 0.00 0.00 5.14
2739 3002 5.684704 TCATGGAGGAAGATGGTGTATTTC 58.315 41.667 0.00 0.00 0.00 2.17
2745 3008 7.110155 GGAGGAAGATGGTGTATTTCACTTTA 58.890 38.462 0.00 0.00 45.50 1.85
2799 3062 2.415512 CCTACTAGCTTTGCGTTTCACC 59.584 50.000 0.00 0.00 0.00 4.02
2965 3235 8.751242 TGAAGGCATAGATTGAATGAAAAATCA 58.249 29.630 0.00 0.00 35.63 2.57
3000 3290 0.695347 CTCCCTGGGCTTGAAACTCT 59.305 55.000 8.22 0.00 0.00 3.24
3006 3296 3.244561 CCTGGGCTTGAAACTCTGAGTAA 60.245 47.826 11.30 1.00 0.00 2.24
3060 3350 5.215252 TCAATTTTGACTCGGTCTTCTCT 57.785 39.130 5.77 0.00 33.15 3.10
3075 3365 7.656948 TCGGTCTTCTCTCGGTTTTTATTTTTA 59.343 33.333 0.00 0.00 0.00 1.52
3144 3436 3.458118 ACATAAGGGATCATCGGGTTGAA 59.542 43.478 0.00 0.00 0.00 2.69
3176 3468 3.582208 TGCAATGCCCCTGAACTAAATTT 59.418 39.130 1.53 0.00 0.00 1.82
3245 3537 4.261322 CCTTCATGTAGCATCGATTTTGGG 60.261 45.833 0.00 0.00 0.00 4.12
3249 3541 1.604278 GTAGCATCGATTTTGGGGAGC 59.396 52.381 0.00 0.00 0.00 4.70
3250 3542 0.257039 AGCATCGATTTTGGGGAGCT 59.743 50.000 0.00 0.00 0.00 4.09
3251 3543 0.665298 GCATCGATTTTGGGGAGCTC 59.335 55.000 4.71 4.71 0.00 4.09
3252 3544 1.312815 CATCGATTTTGGGGAGCTCC 58.687 55.000 25.59 25.59 0.00 4.70
3376 3669 1.770957 GTGCAGGAAAGGAAAAAGCG 58.229 50.000 0.00 0.00 0.00 4.68
3383 3707 4.457257 CAGGAAAGGAAAAAGCGAGAGAAT 59.543 41.667 0.00 0.00 0.00 2.40
3407 3732 4.838046 TCGAACTGCGACAACCAA 57.162 50.000 0.00 0.00 45.59 3.67
3430 3756 3.000727 GTGAATGCCTACAAGCGTTACT 58.999 45.455 0.00 0.00 41.99 2.24
3431 3757 3.000041 TGAATGCCTACAAGCGTTACTG 59.000 45.455 0.00 0.00 41.99 2.74
3450 3776 1.014564 GCTGGGACACGCTCAGTTAC 61.015 60.000 0.00 0.00 31.61 2.50
3467 3793 7.275999 GCTCAGTTACTTGATTACTAGTGGAAC 59.724 40.741 5.39 0.42 34.40 3.62
3468 3794 8.185506 TCAGTTACTTGATTACTAGTGGAACA 57.814 34.615 5.39 0.00 41.43 3.18
3504 3830 4.083271 GCCACTCATTCAGTACAAACCTTC 60.083 45.833 0.00 0.00 32.21 3.46
3507 3833 6.039270 CCACTCATTCAGTACAAACCTTCAAA 59.961 38.462 0.00 0.00 32.21 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.449018 TCTTCTCCCTCAACATGCTCTAC 59.551 47.826 0.00 0.00 0.00 2.59
31 32 2.903135 AGGCACCTGCTATATCTTCTCC 59.097 50.000 0.00 0.00 41.70 3.71
40 41 1.214305 TCCCCAAAGGCACCTGCTAT 61.214 55.000 0.00 0.00 41.70 2.97
45 46 0.332972 GATCTTCCCCAAAGGCACCT 59.667 55.000 0.00 0.00 35.54 4.00
48 49 2.845659 TCTAGATCTTCCCCAAAGGCA 58.154 47.619 0.00 0.00 35.54 4.75
86 87 1.448540 CACTCCGTCCATGCTCCAC 60.449 63.158 0.00 0.00 0.00 4.02
89 90 2.512515 GGCACTCCGTCCATGCTC 60.513 66.667 0.00 0.00 39.38 4.26
94 95 3.096852 CCTATATATGGCACTCCGTCCA 58.903 50.000 0.00 0.00 36.70 4.02
117 118 3.118000 CACATCCTCCTACCCTTAAACCC 60.118 52.174 0.00 0.00 0.00 4.11
146 147 0.457337 CCTACCGTCGTTTTCCTCCG 60.457 60.000 0.00 0.00 0.00 4.63
157 158 0.978907 TCCCTTCAAACCCTACCGTC 59.021 55.000 0.00 0.00 0.00 4.79
159 160 2.572209 TTTCCCTTCAAACCCTACCG 57.428 50.000 0.00 0.00 0.00 4.02
201 202 3.791353 CGCTTCAGTTGTTTGGAAGTTTC 59.209 43.478 0.00 0.00 40.06 2.78
208 212 1.007387 GCCCGCTTCAGTTGTTTGG 60.007 57.895 0.00 0.00 0.00 3.28
211 215 1.039856 AATTGCCCGCTTCAGTTGTT 58.960 45.000 0.00 0.00 0.00 2.83
217 221 0.033228 CAACCAAATTGCCCGCTTCA 59.967 50.000 0.00 0.00 0.00 3.02
220 224 1.532794 TCCAACCAAATTGCCCGCT 60.533 52.632 0.00 0.00 36.93 5.52
222 226 1.080839 CGTCCAACCAAATTGCCCG 60.081 57.895 0.00 0.00 36.93 6.13
279 283 4.560128 GTTTCCTTTCATGAAAAGAGGCC 58.440 43.478 20.82 8.85 46.18 5.19
306 310 4.600111 ACACCCAACCTAAGATCTAAACCA 59.400 41.667 0.00 0.00 0.00 3.67
382 459 1.757699 ACGCCCAACCTAAGATCTCTC 59.242 52.381 0.00 0.00 0.00 3.20
687 783 7.447545 GGAGGAATTTTAGGAGCCGTATTTTAT 59.552 37.037 0.00 0.00 0.00 1.40
722 819 3.008266 TCAAGTGCTCATGTCCAGAATCA 59.992 43.478 0.00 0.00 0.00 2.57
750 847 4.734398 AAGTTGTGGAAAAGTTCATGCA 57.266 36.364 0.00 0.00 0.00 3.96
765 862 3.896272 AGAGAGGAAACCGAGTAAGTTGT 59.104 43.478 0.00 0.00 0.00 3.32
952 1049 6.346279 CGACGCGATGGATTTTTAGCTATAAA 60.346 38.462 15.93 11.12 0.00 1.40
1049 1155 3.056107 TCCAAGGAGGACATTGTTACTCG 60.056 47.826 13.10 3.91 43.07 4.18
1063 1169 1.270839 ACCGACAACATGTCCAAGGAG 60.271 52.381 14.65 0.00 44.20 3.69
1066 1172 5.153513 CAAATAACCGACAACATGTCCAAG 58.846 41.667 0.00 0.00 44.20 3.61
1088 1194 0.110678 TATGTGTTTCAACCGGGCCA 59.889 50.000 6.32 0.00 0.00 5.36
1093 1199 4.921470 ACTCGATTATGTGTTTCAACCG 57.079 40.909 0.00 0.00 0.00 4.44
1099 1205 6.611381 CACATGGAAACTCGATTATGTGTTT 58.389 36.000 0.00 3.75 40.06 2.83
1148 1254 8.256611 TGTCTAATCAAAAGAACTGATACTGC 57.743 34.615 0.00 0.00 33.13 4.40
1176 1282 9.709495 CCATCAGAACTTAAATTGGATTTGAAA 57.291 29.630 0.00 0.00 33.82 2.69
1198 1306 9.921637 TGGAGTTGTTTGTAATTAAATTCCATC 57.078 29.630 6.87 0.00 0.00 3.51
1244 1352 5.357032 GGGTCCAGGATGTAAATGTTACTTG 59.643 44.000 0.00 0.00 0.00 3.16
1246 1354 4.079958 GGGGTCCAGGATGTAAATGTTACT 60.080 45.833 0.00 0.00 0.00 2.24
1247 1355 4.079958 AGGGGTCCAGGATGTAAATGTTAC 60.080 45.833 0.00 0.00 0.00 2.50
1248 1356 4.080015 CAGGGGTCCAGGATGTAAATGTTA 60.080 45.833 0.00 0.00 0.00 2.41
1251 1359 2.423373 CCAGGGGTCCAGGATGTAAATG 60.423 54.545 0.00 0.00 31.24 2.32
1253 1361 1.295020 CCAGGGGTCCAGGATGTAAA 58.705 55.000 0.00 0.00 31.24 2.01
1257 1365 3.324713 GACCAGGGGTCCAGGATG 58.675 66.667 4.00 0.00 46.19 3.51
1267 1375 2.504585 GGGAACTAAGTAAGGACCAGGG 59.495 54.545 0.00 0.00 0.00 4.45
1340 1587 4.553938 GCGTCCAATAATTACATCCAACGG 60.554 45.833 0.00 0.00 0.00 4.44
1352 1600 2.706890 ACGAACAAGGCGTCCAATAAT 58.293 42.857 0.00 0.00 37.42 1.28
1443 1691 2.190578 GAGGCCCTACGCTGCATT 59.809 61.111 0.00 0.00 37.74 3.56
1530 1778 1.379309 GGAGGAGGAGACGCTGAGT 60.379 63.158 0.00 0.00 0.00 3.41
1869 2117 0.449388 CCATGGAAAAGACGCTGCTC 59.551 55.000 5.56 0.00 0.00 4.26
2016 2264 1.305381 CCCCTCGTCCTGTTCCTCT 60.305 63.158 0.00 0.00 0.00 3.69
2033 2281 0.373716 CTTCGGCGAGTTATTGTGCC 59.626 55.000 10.46 0.00 44.09 5.01
2106 2354 0.818296 CGACGTCCTCCATCTCCTTT 59.182 55.000 10.58 0.00 0.00 3.11
2114 2362 3.733960 CAGCGACGACGTCCTCCA 61.734 66.667 21.63 0.00 41.98 3.86
2168 2422 0.972983 CTCGGGCTTCTCCTTCTCCA 60.973 60.000 0.00 0.00 34.39 3.86
2178 2432 2.188207 GCCTCCTTCTCGGGCTTC 59.812 66.667 0.00 0.00 42.31 3.86
2535 2795 3.266510 TCATGCTGGTGGAATGTACTC 57.733 47.619 0.00 0.00 32.78 2.59
2536 2796 3.614092 CTTCATGCTGGTGGAATGTACT 58.386 45.455 0.00 0.00 32.78 2.73
2537 2797 2.098117 GCTTCATGCTGGTGGAATGTAC 59.902 50.000 0.00 0.00 38.95 2.90
2538 2798 2.368439 GCTTCATGCTGGTGGAATGTA 58.632 47.619 0.00 0.00 38.95 2.29
2539 2799 1.180029 GCTTCATGCTGGTGGAATGT 58.820 50.000 0.00 0.00 38.95 2.71
2588 2848 5.036117 TGATGGGTGATTAAAGAGTAGCC 57.964 43.478 0.00 0.00 0.00 3.93
2799 3062 7.376435 ACACACAAAATTCCCAAAAGAAAAG 57.624 32.000 0.00 0.00 0.00 2.27
2905 3175 4.021016 AGAGTCGGAATTGTGCTTCTTAGT 60.021 41.667 0.00 0.00 0.00 2.24
2906 3176 4.499183 AGAGTCGGAATTGTGCTTCTTAG 58.501 43.478 0.00 0.00 0.00 2.18
2907 3177 4.537135 AGAGTCGGAATTGTGCTTCTTA 57.463 40.909 0.00 0.00 0.00 2.10
2965 3235 4.827284 CCAGGGAGTACATGTTTTTCAACT 59.173 41.667 2.30 0.00 33.58 3.16
3060 3350 8.639761 TGTTCATCCCTTAAAAATAAAAACCGA 58.360 29.630 0.00 0.00 0.00 4.69
3075 3365 8.230472 GATGAATAAAGTCATGTTCATCCCTT 57.770 34.615 17.47 0.00 45.53 3.95
3144 3436 0.754472 GGGCATTGCATGTGGCTTAT 59.246 50.000 20.47 0.00 45.15 1.73
3176 3468 6.717289 TCATAGCTTAGCAAAGTTTTCCCTA 58.283 36.000 7.07 0.00 34.99 3.53
3259 3551 2.202676 CGCCGAACAGGAGCTCTC 60.203 66.667 14.64 3.76 45.00 3.20
3354 3647 2.223711 GCTTTTTCCTTTCCTGCACGAA 60.224 45.455 0.00 0.00 0.00 3.85
3357 3650 1.336755 TCGCTTTTTCCTTTCCTGCAC 59.663 47.619 0.00 0.00 0.00 4.57
3358 3651 1.608590 CTCGCTTTTTCCTTTCCTGCA 59.391 47.619 0.00 0.00 0.00 4.41
3360 3653 3.403038 TCTCTCGCTTTTTCCTTTCCTG 58.597 45.455 0.00 0.00 0.00 3.86
3399 3723 3.505680 TGTAGGCATTCACATTGGTTGTC 59.494 43.478 0.00 0.00 36.00 3.18
3405 3730 2.162208 ACGCTTGTAGGCATTCACATTG 59.838 45.455 0.00 0.00 0.00 2.82
3407 3732 2.113860 ACGCTTGTAGGCATTCACAT 57.886 45.000 0.00 0.00 0.00 3.21
3430 3756 1.468506 TAACTGAGCGTGTCCCAGCA 61.469 55.000 0.00 0.00 35.48 4.41
3431 3757 1.014564 GTAACTGAGCGTGTCCCAGC 61.015 60.000 0.00 0.00 0.00 4.85
3450 3776 9.442047 AGAGATTTTGTTCCACTAGTAATCAAG 57.558 33.333 12.52 0.00 0.00 3.02
3467 3793 4.589216 TGAGTGGCCAAAAGAGATTTTG 57.411 40.909 7.24 6.50 40.57 2.44
3468 3794 5.305128 TGAATGAGTGGCCAAAAGAGATTTT 59.695 36.000 7.24 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.