Multiple sequence alignment - TraesCS6D01G163200

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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 TraesCS6D01G163200 chr6D 100.000 7401 0 0 1 7401 142743814 142751214 0.000000e+00 13668
1 TraesCS6D01G163200 chr6B 97.118 3192 66 10 3431 6599 248354169 248357357 0.000000e+00 5361
2 TraesCS6D01G163200 chr6B 93.477 2928 85 35 562 3431 248351034 248353913 0.000000e+00 4252
3 TraesCS6D01G163200 chr6B 93.657 804 30 12 6607 7401 248359634 248360425 0.000000e+00 1182
4 TraesCS6D01G163200 chr6B 86.837 509 26 20 1 508 248350551 248351019 1.410000e-146 531
5 TraesCS6D01G163200 chr6A 97.415 3134 60 9 3491 6613 187739002 187742125 0.000000e+00 5319
6 TraesCS6D01G163200 chr6A 93.584 3460 108 50 1 3408 187735289 187738686 0.000000e+00 5055
7 TraesCS6D01G163200 chr6A 94.674 751 29 6 6658 7401 187762290 187763036 0.000000e+00 1155
8 TraesCS6D01G163200 chr1A 75.274 639 129 26 3808 4431 536936617 536937241 2.030000e-70 278
9 TraesCS6D01G163200 chr1B 75.118 635 133 23 3808 4429 598903676 598903054 2.630000e-69 274
10 TraesCS6D01G163200 chr1D 74.803 635 135 23 3808 4429 441078340 441077718 5.690000e-66 263
11 TraesCS6D01G163200 chr1D 90.291 103 10 0 3455 3557 487335664 487335562 1.300000e-27 135
12 TraesCS6D01G163200 chr5D 94.792 96 5 0 3458 3553 220199922 220199827 4.630000e-32 150
13 TraesCS6D01G163200 chr5B 93.939 99 4 1 3455 3553 243141711 243141615 1.660000e-31 148
14 TraesCS6D01G163200 chr7D 89.908 109 10 1 3453 3560 426726669 426726777 1.000000e-28 139
15 TraesCS6D01G163200 chr3B 91.176 102 9 0 3455 3556 560765974 560765873 1.000000e-28 139
16 TraesCS6D01G163200 chr2D 90.385 104 10 0 3455 3558 152871118 152871221 3.600000e-28 137
17 TraesCS6D01G163200 chr4A 90.909 99 9 0 3455 3553 586273696 586273794 4.660000e-27 134


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 TraesCS6D01G163200 chr6D 142743814 142751214 7400 False 13668.0 13668 100.00000 1 7401 1 chr6D.!!$F1 7400
1 TraesCS6D01G163200 chr6B 248350551 248360425 9874 False 2831.5 5361 92.77225 1 7401 4 chr6B.!!$F1 7400
2 TraesCS6D01G163200 chr6A 187735289 187742125 6836 False 5187.0 5319 95.49950 1 6613 2 chr6A.!!$F2 6612
3 TraesCS6D01G163200 chr6A 187762290 187763036 746 False 1155.0 1155 94.67400 6658 7401 1 chr6A.!!$F1 743
4 TraesCS6D01G163200 chr1A 536936617 536937241 624 False 278.0 278 75.27400 3808 4431 1 chr1A.!!$F1 623
5 TraesCS6D01G163200 chr1B 598903054 598903676 622 True 274.0 274 75.11800 3808 4429 1 chr1B.!!$R1 621
6 TraesCS6D01G163200 chr1D 441077718 441078340 622 True 263.0 263 74.80300 3808 4429 1 chr1D.!!$R1 621

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
386 389 0.321021 GTGGCACCATCCATTTGCAA 59.679 50.000 6.29 0.0 38.57 4.08 F
1120 1177 0.468214 TCAATCAAAACACCGCCCCA 60.468 50.000 0.00 0.0 0.00 4.96 F
1128 1185 0.675522 AACACCGCCCCATTAGTTCG 60.676 55.000 0.00 0.0 0.00 3.95 F
1134 1191 0.814010 GCCCCATTAGTTCGTCGCAT 60.814 55.000 0.00 0.0 0.00 4.73 F
2683 2765 0.886490 CATTCCCATGAGTAGGGCGC 60.886 60.000 0.00 0.0 46.36 6.53 F
3713 4063 1.734465 CCTGTTGCTTGATCGTTCCTC 59.266 52.381 0.00 0.0 0.00 3.71 F
4237 4588 0.250513 CTTGCTCCCACCTACCAGTC 59.749 60.000 0.00 0.0 0.00 3.51 F
6131 6495 1.219664 CTGGAACCCGCCGATGTTA 59.780 57.895 0.00 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2299 0.179169 GAGGTAAGTCGGCGTGTCTC 60.179 60.000 6.85 3.49 0.00 3.36 R
2890 2972 0.756903 GTACCACAGACCCACACAGT 59.243 55.000 0.00 0.00 0.00 3.55 R
3285 3378 2.223272 GCTAGCTCCCGTGCAAAATAAC 60.223 50.000 7.70 0.00 34.99 1.89 R
3288 3381 0.035056 AGCTAGCTCCCGTGCAAAAT 60.035 50.000 12.68 0.00 34.99 1.82 R
4237 4588 1.135199 GGCATGTGCATCTTTGACCAG 60.135 52.381 7.36 0.00 44.36 4.00 R
5760 6123 0.249120 TTCCATCGACGACCAATGCT 59.751 50.000 0.00 0.00 0.00 3.79 R
6233 6597 0.326264 CCAGTTGCTACCAGGAAGCT 59.674 55.000 0.00 0.00 40.73 3.74 R
7080 9736 0.741326 GAGGCTACAGCGATGAGTCA 59.259 55.000 8.12 0.00 43.26 3.41 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 3.817647 GACCTGAGAGCTTTGAACATGTT 59.182 43.478 11.78 11.78 0.00 2.71
113 114 4.293415 GAGCCAACATGAGTGTTCAAAAG 58.707 43.478 0.00 0.00 45.14 2.27
114 115 3.953612 AGCCAACATGAGTGTTCAAAAGA 59.046 39.130 0.00 0.00 45.14 2.52
119 120 3.256631 ACATGAGTGTTCAAAAGATGGGC 59.743 43.478 0.00 0.00 36.78 5.36
120 121 1.879380 TGAGTGTTCAAAAGATGGGCG 59.121 47.619 0.00 0.00 0.00 6.13
121 122 1.880027 GAGTGTTCAAAAGATGGGCGT 59.120 47.619 0.00 0.00 0.00 5.68
122 123 3.071479 GAGTGTTCAAAAGATGGGCGTA 58.929 45.455 0.00 0.00 0.00 4.42
123 124 2.812011 AGTGTTCAAAAGATGGGCGTAC 59.188 45.455 0.00 0.00 0.00 3.67
124 125 2.095415 GTGTTCAAAAGATGGGCGTACC 60.095 50.000 0.00 0.00 40.81 3.34
171 172 3.512033 AGAGTTTCTCGTCCATGTAGC 57.488 47.619 0.00 0.00 35.36 3.58
251 253 2.503331 TGCGGTGACATTTCAGATTGT 58.497 42.857 0.00 0.00 30.10 2.71
254 256 4.517075 TGCGGTGACATTTCAGATTGTTTA 59.483 37.500 0.00 0.00 30.10 2.01
255 257 5.009110 TGCGGTGACATTTCAGATTGTTTAA 59.991 36.000 0.00 0.00 30.10 1.52
257 259 6.586082 GCGGTGACATTTCAGATTGTTTAATT 59.414 34.615 0.00 0.00 30.10 1.40
258 260 7.116233 GCGGTGACATTTCAGATTGTTTAATTT 59.884 33.333 0.00 0.00 30.10 1.82
259 261 8.977505 CGGTGACATTTCAGATTGTTTAATTTT 58.022 29.630 0.00 0.00 30.10 1.82
281 283 3.147595 CCCCTCGCAGACGGATCA 61.148 66.667 0.00 0.00 40.63 2.92
338 341 0.385223 CGCTCTGCAACTGAACAAGC 60.385 55.000 0.00 0.00 0.00 4.01
382 385 4.459199 GGGTGGCACCATCCATTT 57.541 55.556 35.69 0.00 46.13 2.32
383 386 1.899617 GGGTGGCACCATCCATTTG 59.100 57.895 35.69 0.00 46.13 2.32
384 387 1.218854 GGTGGCACCATCCATTTGC 59.781 57.895 31.26 0.00 38.42 3.68
385 388 1.543065 GGTGGCACCATCCATTTGCA 61.543 55.000 31.26 0.00 38.42 4.08
386 389 0.321021 GTGGCACCATCCATTTGCAA 59.679 50.000 6.29 0.00 38.57 4.08
443 446 1.226547 GTCGAGAGAAGCGAGGCAG 60.227 63.158 0.00 0.00 45.01 4.85
491 495 1.115930 ATCCCGATTCCACTCCGAGG 61.116 60.000 0.00 0.00 0.00 4.63
541 545 4.821589 CGCCGCCCTCTTCACTCC 62.822 72.222 0.00 0.00 0.00 3.85
551 555 3.649277 CTTCACTCCGGACGCTGGG 62.649 68.421 0.00 0.00 0.00 4.45
552 556 4.988716 TCACTCCGGACGCTGGGT 62.989 66.667 0.00 0.00 0.00 4.51
553 557 4.436998 CACTCCGGACGCTGGGTC 62.437 72.222 15.72 15.72 45.31 4.46
576 580 2.359169 CCTGCTCCCTCGCAACCTA 61.359 63.158 0.00 0.00 39.80 3.08
713 754 1.405661 GGGGTGAGAGCCGTTAAGAAG 60.406 57.143 0.00 0.00 36.39 2.85
726 767 4.563993 CCGTTAAGAAGTGTTACCATCCCA 60.564 45.833 0.00 0.00 0.00 4.37
870 926 1.587933 GCTAGATAGACGGGGCCTCG 61.588 65.000 27.07 27.07 0.00 4.63
1116 1173 4.083324 TCTCTCAATCAATCAAAACACCGC 60.083 41.667 0.00 0.00 0.00 5.68
1120 1177 0.468214 TCAATCAAAACACCGCCCCA 60.468 50.000 0.00 0.00 0.00 4.96
1123 1180 2.223803 ATCAAAACACCGCCCCATTA 57.776 45.000 0.00 0.00 0.00 1.90
1124 1181 1.540267 TCAAAACACCGCCCCATTAG 58.460 50.000 0.00 0.00 0.00 1.73
1128 1185 0.675522 AACACCGCCCCATTAGTTCG 60.676 55.000 0.00 0.00 0.00 3.95
1129 1186 1.078708 CACCGCCCCATTAGTTCGT 60.079 57.895 0.00 0.00 0.00 3.85
1130 1187 1.087771 CACCGCCCCATTAGTTCGTC 61.088 60.000 0.00 0.00 0.00 4.20
1131 1188 1.881252 CCGCCCCATTAGTTCGTCG 60.881 63.158 0.00 0.00 0.00 5.12
1132 1189 2.522638 CGCCCCATTAGTTCGTCGC 61.523 63.158 0.00 0.00 0.00 5.19
1133 1190 1.448893 GCCCCATTAGTTCGTCGCA 60.449 57.895 0.00 0.00 0.00 5.10
1134 1191 0.814010 GCCCCATTAGTTCGTCGCAT 60.814 55.000 0.00 0.00 0.00 4.73
1245 1309 4.093408 ACTTGTGCAGCTACATTACATTCG 59.907 41.667 0.00 0.00 0.00 3.34
1263 1327 3.299340 TCGTCTTTCCTTGTAGCAGAC 57.701 47.619 0.00 0.00 0.00 3.51
1439 1507 9.492973 CCTTGTAAACAAATCCAAATGATTCTT 57.507 29.630 0.00 0.00 42.97 2.52
1442 1510 7.930325 TGTAAACAAATCCAAATGATTCTTGCA 59.070 29.630 0.00 0.00 42.97 4.08
1547 1619 3.906218 TGATCCTCATACTCCTTCATGGG 59.094 47.826 0.00 0.00 36.20 4.00
1682 1754 2.064434 TTTTGATCTGCCACCACACA 57.936 45.000 0.00 0.00 0.00 3.72
1693 1765 1.531365 ACCACACAGGCCATGTTGG 60.531 57.895 21.06 21.06 41.41 3.77
1958 2030 2.356695 ACAAAACGTACAAGCTGGGTTC 59.643 45.455 0.00 0.00 0.00 3.62
2224 2298 5.477984 TGCCATTTGAGCTCTTTTAAGATGT 59.522 36.000 16.19 0.00 33.93 3.06
2225 2299 5.803967 GCCATTTGAGCTCTTTTAAGATGTG 59.196 40.000 16.19 1.53 33.93 3.21
2356 2430 5.827666 AGTTCTTGTTCATGTTAAAACGGG 58.172 37.500 0.00 0.00 0.00 5.28
2636 2718 7.779326 TGGCATCCAAAAAGAATATCTGTGATA 59.221 33.333 0.00 0.00 0.00 2.15
2683 2765 0.886490 CATTCCCATGAGTAGGGCGC 60.886 60.000 0.00 0.00 46.36 6.53
3036 3128 4.083377 GGGGTTAGCGAACGAAAAATTACA 60.083 41.667 3.50 0.00 36.32 2.41
3285 3378 3.387397 AGTCCGAAGAAAACCTAACACG 58.613 45.455 0.00 0.00 0.00 4.49
3288 3381 4.744631 GTCCGAAGAAAACCTAACACGTTA 59.255 41.667 0.00 0.00 0.00 3.18
3293 3387 7.112426 CCGAAGAAAACCTAACACGTTATTTTG 59.888 37.037 6.16 0.00 0.00 2.44
3713 4063 1.734465 CCTGTTGCTTGATCGTTCCTC 59.266 52.381 0.00 0.00 0.00 3.71
3759 4109 2.431419 CCCAAGCACATTTGATGCCATA 59.569 45.455 0.00 0.00 44.53 2.74
4237 4588 0.250513 CTTGCTCCCACCTACCAGTC 59.749 60.000 0.00 0.00 0.00 3.51
4431 4785 1.355066 GAGCTGTCGGTAAGCACTGC 61.355 60.000 0.00 0.00 43.37 4.40
4953 5314 6.475402 CCACTTTCATGACAAAAGTTGTTACC 59.525 38.462 8.28 0.00 45.52 2.85
5042 5403 6.183360 ACCTTGAAACGTAAAGAACAGAACAG 60.183 38.462 7.04 0.00 0.00 3.16
5205 5566 4.457949 TCTTTACTTTGCCCGAATTCCTTC 59.542 41.667 0.00 0.00 0.00 3.46
5266 5627 6.116806 TCGAGATAGAGGTAGCATATCCTTC 58.883 44.000 11.44 5.52 33.83 3.46
5270 5631 7.651607 AGATAGAGGTAGCATATCCTTCTCAT 58.348 38.462 11.44 0.00 33.83 2.90
5304 5667 4.431416 TTGCTCATGTTATCCCCGTAAT 57.569 40.909 0.00 0.00 0.00 1.89
5442 5805 2.144482 GCAAGCAGCAAGTGTTCATT 57.856 45.000 0.00 0.00 44.79 2.57
5569 5932 1.442769 TGAGATCAAGGAGTTTGCGC 58.557 50.000 0.00 0.00 36.70 6.09
5760 6123 2.224314 CGAGATCGCTACATACTCTGCA 59.776 50.000 0.00 0.00 0.00 4.41
6131 6495 1.219664 CTGGAACCCGCCGATGTTA 59.780 57.895 0.00 0.00 0.00 2.41
6233 6597 4.082523 GCTCCAGTGCCGGCAGTA 62.083 66.667 35.35 20.77 0.00 2.74
6248 6612 1.066143 GCAGTAGCTTCCTGGTAGCAA 60.066 52.381 24.53 0.00 41.11 3.91
6301 6665 3.251245 GCCATTGATCATCTCTTGCTGAG 59.749 47.826 0.00 1.66 43.96 3.35
6437 6802 4.965119 ACACACCTTCAGAAAGTTTCAC 57.035 40.909 17.65 0.00 0.00 3.18
6461 6826 3.444916 CATGCATGCTTGAATCTGAACC 58.555 45.455 25.15 0.00 0.00 3.62
6483 6849 5.376854 CCTCAAATGTTTAGGGAACTGTG 57.623 43.478 0.00 0.00 43.88 3.66
6651 9298 8.174733 AGACTTGAAAGTTTCACAATGATCAT 57.825 30.769 17.85 1.18 39.88 2.45
6652 9299 8.080417 AGACTTGAAAGTTTCACAATGATCATG 58.920 33.333 17.85 6.30 39.88 3.07
6653 9300 7.149973 ACTTGAAAGTTTCACAATGATCATGG 58.850 34.615 17.85 9.03 39.87 3.66
6654 9301 5.472148 TGAAAGTTTCACAATGATCATGGC 58.528 37.500 14.35 0.00 34.08 4.40
6655 9302 5.010820 TGAAAGTTTCACAATGATCATGGCA 59.989 36.000 14.35 0.00 34.08 4.92
6656 9303 5.670792 AAGTTTCACAATGATCATGGCAT 57.329 34.783 9.46 0.00 0.00 4.40
6783 9432 1.226802 CACCGCATCCTCTCAGACG 60.227 63.158 0.00 0.00 0.00 4.18
6932 9581 0.689412 GGGTTCTCCTCCTCCTCCTG 60.689 65.000 0.00 0.00 0.00 3.86
6933 9582 0.689412 GGTTCTCCTCCTCCTCCTGG 60.689 65.000 0.00 0.00 0.00 4.45
6934 9583 0.336737 GTTCTCCTCCTCCTCCTGGA 59.663 60.000 0.00 0.00 40.69 3.86
6950 9606 2.109128 CCTGGAGCTCCCTCTGATAGTA 59.891 54.545 29.95 6.10 38.21 1.82
6951 9607 3.420893 CTGGAGCTCCCTCTGATAGTAG 58.579 54.545 29.95 12.38 38.21 2.57
6980 9636 1.228533 GTTCGAGGGTGGCGTTTTTA 58.771 50.000 0.00 0.00 0.00 1.52
6981 9637 1.603326 GTTCGAGGGTGGCGTTTTTAA 59.397 47.619 0.00 0.00 0.00 1.52
7080 9736 3.617263 CGACGCTTTCTTACCAATAGCTT 59.383 43.478 0.00 0.00 0.00 3.74
7124 9780 9.083422 TCTGTAGATTAGATTAGATGTTCCCAG 57.917 37.037 0.00 0.00 0.00 4.45
7176 9832 1.963515 ACAATCTGTGGGTTTTCTGCC 59.036 47.619 0.00 0.00 0.00 4.85
7232 9888 1.908299 GAAGGGTGTGCTTTGGGGG 60.908 63.158 0.00 0.00 0.00 5.40
7239 9895 1.367471 GTGCTTTGGGGGAAACTGC 59.633 57.895 0.00 0.00 0.00 4.40
7378 10035 0.387202 AAGCGGGTGAGATCATCGAG 59.613 55.000 11.06 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.594303 ACCGACGACCCGTACACA 60.594 61.111 0.00 0.00 41.37 3.72
119 120 2.037511 TCAAACAACTGGGTAGGGTACG 59.962 50.000 0.00 0.00 0.00 3.67
120 121 3.775261 TCAAACAACTGGGTAGGGTAC 57.225 47.619 0.00 0.00 0.00 3.34
121 122 5.786457 TCTATTCAAACAACTGGGTAGGGTA 59.214 40.000 0.00 0.00 0.00 3.69
122 123 3.895704 ATTCAAACAACTGGGTAGGGT 57.104 42.857 0.00 0.00 0.00 4.34
123 124 5.174037 TCTATTCAAACAACTGGGTAGGG 57.826 43.478 0.00 0.00 0.00 3.53
124 125 6.001460 TGTTCTATTCAAACAACTGGGTAGG 58.999 40.000 0.00 0.00 33.86 3.18
125 126 7.687941 ATGTTCTATTCAAACAACTGGGTAG 57.312 36.000 0.00 0.00 39.84 3.18
198 199 8.755977 AGGCATGTTTCTTTCTTCATTCATATT 58.244 29.630 0.00 0.00 0.00 1.28
258 260 1.302192 CGTCTGCGAGGGGGAAAAA 60.302 57.895 0.00 0.00 41.33 1.94
259 261 2.345991 CGTCTGCGAGGGGGAAAA 59.654 61.111 0.00 0.00 41.33 2.29
333 336 2.244651 GCACTCCGTTGTCGCTTGT 61.245 57.895 0.00 0.00 35.54 3.16
334 337 2.162921 CTGCACTCCGTTGTCGCTTG 62.163 60.000 0.00 0.00 35.54 4.01
338 341 2.029073 ACCTGCACTCCGTTGTCG 59.971 61.111 0.00 0.00 0.00 4.35
382 385 3.682885 CGGTGGCCTTGCATTGCA 61.683 61.111 7.38 7.38 36.47 4.08
383 386 4.440127 CCGGTGGCCTTGCATTGC 62.440 66.667 3.32 0.46 0.00 3.56
384 387 4.440127 GCCGGTGGCCTTGCATTG 62.440 66.667 3.32 0.00 44.06 2.82
443 446 1.393883 GAACTCTTCCGCCACGATTTC 59.606 52.381 0.00 0.00 0.00 2.17
560 564 2.656069 GGTAGGTTGCGAGGGAGCA 61.656 63.158 0.00 0.00 46.54 4.26
567 571 1.597797 CCGGTAGTGGTAGGTTGCGA 61.598 60.000 0.00 0.00 0.00 5.10
694 735 1.275573 ACTTCTTAACGGCTCTCACCC 59.724 52.381 0.00 0.00 0.00 4.61
726 767 0.845102 ATTGAAACGGGAGGGGGAGT 60.845 55.000 0.00 0.00 0.00 3.85
870 926 7.907563 GTGCTTGCTTAATTTAGATTCAGAGAC 59.092 37.037 0.00 0.00 0.00 3.36
914 970 3.181483 GGCTCTAAAATTAGGACGACGGA 60.181 47.826 0.00 0.00 0.00 4.69
1095 1152 3.057596 GGCGGTGTTTTGATTGATTGAGA 60.058 43.478 0.00 0.00 0.00 3.27
1112 1169 1.219935 GACGAACTAATGGGGCGGT 59.780 57.895 0.00 0.00 0.00 5.68
1116 1173 2.519377 TATGCGACGAACTAATGGGG 57.481 50.000 0.00 0.00 0.00 4.96
1120 1177 6.740110 AGAAGAAGATATGCGACGAACTAAT 58.260 36.000 0.00 0.00 0.00 1.73
1123 1180 4.640789 AGAAGAAGATATGCGACGAACT 57.359 40.909 0.00 0.00 0.00 3.01
1124 1181 5.108179 GCTAAGAAGAAGATATGCGACGAAC 60.108 44.000 0.00 0.00 0.00 3.95
1128 1185 5.176590 CCAAGCTAAGAAGAAGATATGCGAC 59.823 44.000 0.00 0.00 0.00 5.19
1129 1186 5.292765 CCAAGCTAAGAAGAAGATATGCGA 58.707 41.667 0.00 0.00 0.00 5.10
1130 1187 4.450419 CCCAAGCTAAGAAGAAGATATGCG 59.550 45.833 0.00 0.00 0.00 4.73
1131 1188 5.615289 TCCCAAGCTAAGAAGAAGATATGC 58.385 41.667 0.00 0.00 0.00 3.14
1132 1189 9.434420 CTAATCCCAAGCTAAGAAGAAGATATG 57.566 37.037 0.00 0.00 0.00 1.78
1133 1190 9.386122 TCTAATCCCAAGCTAAGAAGAAGATAT 57.614 33.333 0.00 0.00 0.00 1.63
1134 1191 8.783660 TCTAATCCCAAGCTAAGAAGAAGATA 57.216 34.615 0.00 0.00 0.00 1.98
1221 1279 5.390885 CGAATGTAATGTAGCTGCACAAGTT 60.391 40.000 6.66 0.00 30.84 2.66
1222 1280 4.093408 CGAATGTAATGTAGCTGCACAAGT 59.907 41.667 6.66 0.00 30.84 3.16
1224 1282 4.000325 ACGAATGTAATGTAGCTGCACAA 59.000 39.130 6.66 0.00 30.84 3.33
1245 1309 2.303311 AGGGTCTGCTACAAGGAAAGAC 59.697 50.000 0.00 0.00 37.20 3.01
1263 1327 3.754965 TGTGAAACAGAAGATGGAAGGG 58.245 45.455 0.00 0.00 45.67 3.95
1439 1507 1.678635 CCCCGGAGAAGCAATTGCA 60.679 57.895 30.89 0.00 45.16 4.08
1442 1510 1.077429 GAGCCCCGGAGAAGCAATT 60.077 57.895 0.73 0.00 0.00 2.32
1693 1765 6.814506 ATGATAGGATGATTAGCACTTTGC 57.185 37.500 0.00 0.00 45.46 3.68
1958 2030 5.450965 GCAAACCACCCATGAATATCTTCTG 60.451 44.000 0.00 0.00 32.29 3.02
2092 2165 2.535934 TTACCATTGCAAATCGTCGC 57.464 45.000 1.71 0.00 0.00 5.19
2224 2298 0.892358 AGGTAAGTCGGCGTGTCTCA 60.892 55.000 6.85 0.00 0.00 3.27
2225 2299 0.179169 GAGGTAAGTCGGCGTGTCTC 60.179 60.000 6.85 3.49 0.00 3.36
2309 2383 3.923461 GCTATAAGCTAGTGGAATGCTCG 59.077 47.826 0.00 0.00 38.45 5.03
2356 2430 8.847196 GGGATAATTAGGTCCATAAACAACTTC 58.153 37.037 7.30 0.00 36.19 3.01
2477 2551 4.256920 GCAAGAGAAAAGGTATGCTGAGA 58.743 43.478 0.00 0.00 0.00 3.27
2636 2718 7.071572 AGGGGGTACACGTTATGTAAAGATAAT 59.928 37.037 0.00 0.00 45.51 1.28
2706 2788 1.228552 ACCCTGCGCCTTGTTCAAT 60.229 52.632 4.18 0.00 0.00 2.57
2734 2816 2.310647 GGTAGTTTGGGGAGAAATGGGA 59.689 50.000 0.00 0.00 0.00 4.37
2890 2972 0.756903 GTACCACAGACCCACACAGT 59.243 55.000 0.00 0.00 0.00 3.55
3285 3378 2.223272 GCTAGCTCCCGTGCAAAATAAC 60.223 50.000 7.70 0.00 34.99 1.89
3288 3381 0.035056 AGCTAGCTCCCGTGCAAAAT 60.035 50.000 12.68 0.00 34.99 1.82
3293 3387 0.664767 CGATTAGCTAGCTCCCGTGC 60.665 60.000 23.26 5.26 0.00 5.34
3759 4109 5.620206 TCATCAAGCGTATACATTCCCATT 58.380 37.500 3.32 0.00 0.00 3.16
4237 4588 1.135199 GGCATGTGCATCTTTGACCAG 60.135 52.381 7.36 0.00 44.36 4.00
4431 4785 6.092092 TGCATTTTCAACATGGAATAGTTCG 58.908 36.000 0.00 0.00 0.00 3.95
4505 4866 7.618502 TGCGTAATGTGATAATTAACCTGTT 57.381 32.000 0.00 0.00 0.00 3.16
5067 5428 6.370994 ACAAGATGTTAGTGCATGAGAAAGAG 59.629 38.462 0.00 0.00 0.00 2.85
5266 5627 8.671921 ACATGAGCAAATAGTAACTTCAATGAG 58.328 33.333 0.00 0.00 0.00 2.90
5304 5667 5.450412 GCCAAGAATGTTCAGTTCAACAGAA 60.450 40.000 0.00 0.00 39.63 3.02
5569 5932 1.939974 CGGGTCACCATCACTACATG 58.060 55.000 0.00 0.00 36.13 3.21
5667 6030 4.430765 GGACCGACGTGCACCGAT 62.431 66.667 15.81 0.00 40.70 4.18
5760 6123 0.249120 TTCCATCGACGACCAATGCT 59.751 50.000 0.00 0.00 0.00 3.79
6178 6542 0.391228 TGTCAGCTACTTTCGGTGCA 59.609 50.000 0.00 0.00 0.00 4.57
6233 6597 0.326264 CCAGTTGCTACCAGGAAGCT 59.674 55.000 0.00 0.00 40.73 3.74
6437 6802 1.068588 CAGATTCAAGCATGCATGGGG 59.931 52.381 27.34 3.29 0.00 4.96
6461 6826 4.827284 ACACAGTTCCCTAAACATTTGAGG 59.173 41.667 0.00 0.00 40.56 3.86
6640 9287 2.159028 TGCCAATGCCATGATCATTGTG 60.159 45.455 25.28 20.33 45.57 3.33
6642 9289 2.900716 TGCCAATGCCATGATCATTG 57.099 45.000 22.79 22.79 46.20 2.82
6645 9292 2.232696 GCATATGCCAATGCCATGATCA 59.767 45.455 17.26 0.00 45.31 2.92
6671 9318 1.563435 GGAGGATGATGATGCGTGCG 61.563 60.000 0.00 0.00 0.00 5.34
6766 9415 3.069980 GCGTCTGAGAGGATGCGGT 62.070 63.158 6.31 0.00 38.27 5.68
6932 9581 3.686016 CTCTACTATCAGAGGGAGCTCC 58.314 54.545 25.59 25.59 38.74 4.70
6980 9636 2.226330 TGCAACAAACGCCTACTGATT 58.774 42.857 0.00 0.00 0.00 2.57
6981 9637 1.806542 CTGCAACAAACGCCTACTGAT 59.193 47.619 0.00 0.00 0.00 2.90
7044 9700 1.269998 AGCGTCGTTTCTTCTAGCAGT 59.730 47.619 0.00 0.00 0.00 4.40
7080 9736 0.741326 GAGGCTACAGCGATGAGTCA 59.259 55.000 8.12 0.00 43.26 3.41
7124 9780 5.112686 GTGAGGAACATATGAGACTTGACC 58.887 45.833 10.38 1.24 0.00 4.02
7176 9832 5.817816 AGCCCTAAATCTACAAAAGATGACG 59.182 40.000 0.00 0.00 44.56 4.35
7232 9888 5.967088 TCAGACATCTAACCTAGCAGTTTC 58.033 41.667 0.00 0.00 0.00 2.78
7239 9895 9.145865 GAAAGAAGTTTCAGACATCTAACCTAG 57.854 37.037 0.00 0.00 41.64 3.02
7363 10020 1.006805 CGCCTCGATGATCTCACCC 60.007 63.158 0.00 0.00 0.00 4.61
7378 10035 1.833787 TAGGTTCCACTTCCACCGCC 61.834 60.000 0.00 0.00 35.54 6.13


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

AutoCloner maintained by Alex Coulton.