Multiple sequence alignment - TraesCS1B01G026800

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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 TraesCS1B01G026800 chr1B 100.000 2059 0 0 1 2059 13008836 13010894 0.000000e+00 3803
1 TraesCS1B01G026800 chr1B 94.809 1175 60 1 853 2027 13497262 13498435 0.000000e+00 1831
2 TraesCS1B01G026800 chr1B 92.175 869 62 6 511 1378 12491426 12492289 0.000000e+00 1223
3 TraesCS1B01G026800 chr1B 92.060 869 63 6 511 1378 12561489 12562352 0.000000e+00 1218
4 TraesCS1B01G026800 chr1B 84.891 503 45 12 1370 1852 12492478 12492969 1.790000e-131 479
5 TraesCS1B01G026800 chr1B 84.891 503 45 12 1370 1852 12562541 12563032 1.790000e-131 479
6 TraesCS1B01G026800 chr1B 76.605 919 174 30 518 1410 13565639 13564736 3.880000e-128 468
7 TraesCS1B01G026800 chr1B 85.127 316 35 10 966 1276 12764362 12764054 1.920000e-81 313
8 TraesCS1B01G026800 chr1B 81.529 314 49 7 1088 1397 13560066 13559758 1.530000e-62 250
9 TraesCS1B01G026800 chr1B 100.000 102 0 0 2472 2573 13011307 13011408 3.380000e-44 189
10 TraesCS1B01G026800 chr1B 94.382 89 4 1 2486 2573 13498687 13498775 4.470000e-28 135
11 TraesCS1B01G026800 chr1A 88.796 1312 99 16 548 1833 10696211 10697500 0.000000e+00 1565
12 TraesCS1B01G026800 chr1D 81.281 1015 141 24 1030 2017 9426806 9427798 0.000000e+00 776
13 TraesCS1B01G026800 chr1D 77.472 799 125 37 514 1278 9425598 9426375 6.580000e-116 427
14 TraesCS1B01G026800 chr1D 84.211 342 40 9 1127 1459 9402120 9402456 1.150000e-83 320
15 TraesCS1B01G026800 chr6A 85.475 537 45 22 1 518 7585109 7585631 1.750000e-146 529
16 TraesCS1B01G026800 chr3D 89.151 212 21 2 309 519 8315319 8315109 1.960000e-66 263
17 TraesCS1B01G026800 chr3D 80.460 174 18 10 1 171 8315718 8315558 4.500000e-23 119
18 TraesCS1B01G026800 chr7B 95.570 158 5 2 63 219 617523614 617523458 4.250000e-63 252
19 TraesCS1B01G026800 chr7B 85.119 168 8 8 239 391 617510980 617510815 3.430000e-34 156
20 TraesCS1B01G026800 chr5B 84.651 215 26 5 309 518 703182353 703182565 9.330000e-50 207
21 TraesCS1B01G026800 chr4B 84.651 215 25 6 309 518 590042968 590043179 9.330000e-50 207
22 TraesCS1B01G026800 chr4B 83.756 197 28 4 309 504 553751860 553752053 1.570000e-42 183
23 TraesCS1B01G026800 chr3B 80.435 230 34 11 293 518 528122129 528121907 5.700000e-37 165
24 TraesCS1B01G026800 chr3B 79.888 179 29 7 345 518 525636453 525636277 9.670000e-25 124
25 TraesCS1B01G026800 chr5D 80.093 216 35 7 293 504 211364909 211365120 1.230000e-33 154
26 TraesCS1B01G026800 chr4D 89.744 117 10 2 403 518 6065697 6065812 5.740000e-32 148


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 TraesCS1B01G026800 chr1B 13008836 13011408 2572 False 1996.0 3803 100.0000 1 2573 2 chr1B.!!$F3 2572
1 TraesCS1B01G026800 chr1B 13497262 13498775 1513 False 983.0 1831 94.5955 853 2573 2 chr1B.!!$F4 1720
2 TraesCS1B01G026800 chr1B 12491426 12492969 1543 False 851.0 1223 88.5330 511 1852 2 chr1B.!!$F1 1341
3 TraesCS1B01G026800 chr1B 12561489 12563032 1543 False 848.5 1218 88.4755 511 1852 2 chr1B.!!$F2 1341
4 TraesCS1B01G026800 chr1B 13564736 13565639 903 True 468.0 468 76.6050 518 1410 1 chr1B.!!$R3 892
5 TraesCS1B01G026800 chr1A 10696211 10697500 1289 False 1565.0 1565 88.7960 548 1833 1 chr1A.!!$F1 1285
6 TraesCS1B01G026800 chr1D 9425598 9427798 2200 False 601.5 776 79.3765 514 2017 2 chr1D.!!$F2 1503
7 TraesCS1B01G026800 chr6A 7585109 7585631 522 False 529.0 529 85.4750 1 518 1 chr6A.!!$F1 517

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
290 315 0.172803 GCACGTACAGGACTACAGGG 59.827 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2954 2.436911 GTTATGGGATGTAGGTCGGGTT 59.563 50.0 0.0 0.0 0.0 4.11 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
46 47 8.446599 AATTATGTATCTTTTTCCCTGTACCG 57.553 34.615 0.00 0.00 0.00 4.02
47 48 3.602483 TGTATCTTTTTCCCTGTACCGC 58.398 45.455 0.00 0.00 0.00 5.68
148 150 9.118236 GTGTAGAAAACAATCTTGCTAAATGAC 57.882 33.333 0.00 0.00 40.63 3.06
156 158 8.635765 ACAATCTTGCTAAATGACTTCCTTAA 57.364 30.769 0.00 0.00 0.00 1.85
157 159 8.734386 ACAATCTTGCTAAATGACTTCCTTAAG 58.266 33.333 0.00 0.00 38.77 1.85
160 162 8.691661 TCTTGCTAAATGACTTCCTTAAGTTT 57.308 30.769 0.97 0.00 46.09 2.66
161 163 8.567948 TCTTGCTAAATGACTTCCTTAAGTTTG 58.432 33.333 0.97 0.00 46.09 2.93
162 164 8.458573 TTGCTAAATGACTTCCTTAAGTTTGA 57.541 30.769 0.97 0.00 46.09 2.69
163 165 8.635765 TGCTAAATGACTTCCTTAAGTTTGAT 57.364 30.769 0.97 0.00 46.09 2.57
189 193 2.076863 GTTCGCCTACAATGCTTCAGT 58.923 47.619 0.00 0.00 0.00 3.41
219 223 9.825972 CCATTAAGCAAGTGGATAAAATATACG 57.174 33.333 0.00 0.00 34.94 3.06
237 241 9.847706 AAATATACGTAGATCAGAGCACATAAG 57.152 33.333 2.67 0.00 0.00 1.73
238 242 6.885952 ATACGTAGATCAGAGCACATAAGT 57.114 37.500 0.08 0.00 0.00 2.24
258 283 8.655970 CATAAGTATGATTCTTGACACGTTGAA 58.344 33.333 0.00 0.00 35.75 2.69
264 289 3.040147 TCTTGACACGTTGAAGGGATC 57.960 47.619 0.00 0.00 0.00 3.36
265 290 2.632996 TCTTGACACGTTGAAGGGATCT 59.367 45.455 0.00 0.00 0.00 2.75
268 293 4.819105 TGACACGTTGAAGGGATCTAAT 57.181 40.909 0.00 0.00 0.00 1.73
269 294 4.503910 TGACACGTTGAAGGGATCTAATG 58.496 43.478 0.00 0.00 0.00 1.90
270 295 3.270877 ACACGTTGAAGGGATCTAATGC 58.729 45.455 0.00 0.00 0.00 3.56
271 296 2.285220 CACGTTGAAGGGATCTAATGCG 59.715 50.000 0.00 0.00 0.00 4.73
272 297 1.261619 CGTTGAAGGGATCTAATGCGC 59.738 52.381 0.00 0.00 0.00 6.09
274 299 1.953559 TGAAGGGATCTAATGCGCAC 58.046 50.000 14.90 0.00 0.00 5.34
275 300 0.861837 GAAGGGATCTAATGCGCACG 59.138 55.000 14.90 4.20 0.00 5.34
277 302 1.037493 AGGGATCTAATGCGCACGTA 58.963 50.000 14.90 7.44 0.00 3.57
279 304 1.537348 GGGATCTAATGCGCACGTACA 60.537 52.381 14.90 0.00 0.00 2.90
281 306 1.787155 GATCTAATGCGCACGTACAGG 59.213 52.381 14.90 0.00 0.00 4.00
283 308 0.921347 CTAATGCGCACGTACAGGAC 59.079 55.000 14.90 0.00 0.00 3.85
284 309 0.528924 TAATGCGCACGTACAGGACT 59.471 50.000 14.90 0.00 0.00 3.85
285 310 0.528924 AATGCGCACGTACAGGACTA 59.471 50.000 14.90 0.00 0.00 2.59
286 311 0.179145 ATGCGCACGTACAGGACTAC 60.179 55.000 14.90 0.00 0.00 2.73
287 312 1.210931 GCGCACGTACAGGACTACA 59.789 57.895 0.30 0.00 0.00 2.74
289 314 0.179171 CGCACGTACAGGACTACAGG 60.179 60.000 0.00 0.00 0.00 4.00
290 315 0.172803 GCACGTACAGGACTACAGGG 59.827 60.000 0.00 0.00 0.00 4.45
291 316 1.830279 CACGTACAGGACTACAGGGA 58.170 55.000 0.00 0.00 0.00 4.20
292 317 2.376109 CACGTACAGGACTACAGGGAT 58.624 52.381 0.00 0.00 0.00 3.85
293 318 2.099263 CACGTACAGGACTACAGGGATG 59.901 54.545 0.00 0.00 0.00 3.51
294 319 1.067212 CGTACAGGACTACAGGGATGC 59.933 57.143 0.00 0.00 0.00 3.91
295 320 2.108168 GTACAGGACTACAGGGATGCA 58.892 52.381 0.00 0.00 0.00 3.96
298 323 2.092753 ACAGGACTACAGGGATGCAATG 60.093 50.000 0.00 0.00 0.00 2.82
299 324 1.133976 AGGACTACAGGGATGCAATGC 60.134 52.381 0.00 0.00 0.00 3.56
300 325 1.408683 GGACTACAGGGATGCAATGCA 60.409 52.381 11.44 11.44 44.86 3.96
301 326 2.368439 GACTACAGGGATGCAATGCAA 58.632 47.619 13.45 0.00 43.62 4.08
302 327 2.094675 ACTACAGGGATGCAATGCAAC 58.905 47.619 13.45 9.92 43.62 4.17
303 328 2.093890 CTACAGGGATGCAATGCAACA 58.906 47.619 13.45 0.00 43.62 3.33
304 329 1.563924 ACAGGGATGCAATGCAACAT 58.436 45.000 13.45 2.98 43.62 2.71
305 330 2.737544 ACAGGGATGCAATGCAACATA 58.262 42.857 13.45 0.00 43.62 2.29
306 331 3.098377 ACAGGGATGCAATGCAACATAA 58.902 40.909 13.45 0.00 43.62 1.90
307 332 3.514706 ACAGGGATGCAATGCAACATAAA 59.485 39.130 13.45 0.00 43.62 1.40
314 339 5.340439 TGCAATGCAACATAAATGATGGA 57.660 34.783 5.01 0.00 34.92 3.41
345 370 1.199789 CACTTACATGCATGCAACCGT 59.800 47.619 26.68 22.75 0.00 4.83
346 371 1.468520 ACTTACATGCATGCAACCGTC 59.531 47.619 26.68 0.00 0.00 4.79
387 412 4.101114 TGGATCTTAGTGTAGGGCTTTCA 58.899 43.478 0.00 0.00 0.00 2.69
415 440 4.495422 CACATCGGGTGGCTATTATAGAC 58.505 47.826 3.04 0.00 44.04 2.59
465 490 4.730949 ATTTTGATGATGTGGCTCAAGG 57.269 40.909 0.00 0.00 31.11 3.61
484 509 7.214460 TCAAGGAGAGAGTAGAGAATTCCTA 57.786 40.000 0.65 0.84 33.44 2.94
485 510 7.821566 TCAAGGAGAGAGTAGAGAATTCCTAT 58.178 38.462 0.65 0.00 33.44 2.57
490 515 9.010029 GGAGAGAGTAGAGAATTCCTATTAGTG 57.990 40.741 0.65 0.00 0.00 2.74
492 517 8.729047 AGAGAGTAGAGAATTCCTATTAGTGGA 58.271 37.037 0.65 0.00 0.00 4.02
600 625 2.357034 GCGTTTGGGCAGTCGAGA 60.357 61.111 0.00 0.00 0.00 4.04
615 640 4.922103 CAGTCGAGAGTACAGTTTAAACCC 59.078 45.833 14.72 1.28 0.00 4.11
631 656 3.508840 CCGATGCAGCCGGGTTTC 61.509 66.667 19.21 0.00 43.05 2.78
701 728 6.936900 TCATGAGAAAGAAACGAGAAGGAAAT 59.063 34.615 0.00 0.00 0.00 2.17
743 770 4.156664 CAGAATGTGCCAACTTTCTCTG 57.843 45.455 4.54 0.00 44.65 3.35
758 785 8.427774 CAACTTTCTCTGAAAGACAAAAACAAC 58.572 33.333 22.03 0.00 38.67 3.32
772 799 5.882557 ACAAAAACAACATGCCAATTAACCA 59.117 32.000 0.00 0.00 0.00 3.67
787 815 7.493971 GCCAATTAACCAAACATGTGCATTATA 59.506 33.333 0.00 0.00 0.00 0.98
900 929 3.951306 TGTTTTGTGAGCAAACGATCTG 58.049 40.909 0.00 0.00 43.47 2.90
1012 1769 3.659092 CAACCACACCGCACGCAT 61.659 61.111 0.00 0.00 0.00 4.73
1176 1936 2.050144 GAGGTGCTCCAGATTGGGATA 58.950 52.381 7.70 0.00 38.32 2.59
1313 2073 0.763652 CTGAGGAGGCTACATGGCAT 59.236 55.000 0.00 0.00 44.55 4.40
1428 2396 6.135454 TGGCTTGGTGAATGGTTTCATATAT 58.865 36.000 0.00 0.00 43.49 0.86
1433 2401 9.683069 CTTGGTGAATGGTTTCATATATTAAGC 57.317 33.333 0.00 0.00 43.49 3.09
1534 2524 7.475299 TGATATCTTTTCCTTTACCCCTTGTT 58.525 34.615 3.98 0.00 0.00 2.83
1874 2867 3.876914 GGTGTCATGTGTGAAGTTGAGAA 59.123 43.478 0.00 0.00 35.80 2.87
1961 2954 5.495926 AAATTTATGCCCAATTGTGGTCA 57.504 34.783 4.43 8.21 44.30 4.02
1981 2974 2.436542 CAACCCGACCTACATCCCATAA 59.563 50.000 0.00 0.00 0.00 1.90
1988 2981 4.142026 CGACCTACATCCCATAACAACTCA 60.142 45.833 0.00 0.00 0.00 3.41
1994 2987 3.350219 TCCCATAACAACTCAGCTTCC 57.650 47.619 0.00 0.00 0.00 3.46
1996 2989 3.012518 CCCATAACAACTCAGCTTCCTG 58.987 50.000 0.00 0.00 40.54 3.86
2002 2995 3.825328 ACAACTCAGCTTCCTGTTCATT 58.175 40.909 0.00 0.00 40.09 2.57
2047 3055 3.315142 GAGAGTGGCGATGGGTGCA 62.315 63.158 0.00 0.00 0.00 4.57
2048 3056 2.124570 GAGTGGCGATGGGTGCAT 60.125 61.111 0.00 0.00 0.00 3.96
2049 3057 2.438975 AGTGGCGATGGGTGCATG 60.439 61.111 0.00 0.00 0.00 4.06
2050 3058 3.520862 GTGGCGATGGGTGCATGG 61.521 66.667 0.00 0.00 0.00 3.66
2051 3059 4.818863 TGGCGATGGGTGCATGGG 62.819 66.667 0.00 0.00 0.00 4.00
2052 3060 4.504596 GGCGATGGGTGCATGGGA 62.505 66.667 0.00 0.00 0.00 4.37
2053 3061 3.211963 GCGATGGGTGCATGGGAC 61.212 66.667 0.00 0.00 0.00 4.46
2489 3497 2.462301 TCATGGAGCTGTCAACCCA 58.538 52.632 0.00 0.00 0.00 4.51
2490 3498 0.770499 TCATGGAGCTGTCAACCCAA 59.230 50.000 0.00 0.00 31.77 4.12
2510 3518 1.669115 CAGGGCCGCGAGATATTGG 60.669 63.158 8.23 0.00 0.00 3.16
2558 3567 1.212751 GCTCAAACGTGCAATCCCC 59.787 57.895 0.00 0.00 0.00 4.81
2567 3576 3.908081 GCAATCCCCGCTGCCATG 61.908 66.667 0.00 0.00 32.18 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.606272 CGCGGTACAGGGAAAAAGATAC 59.394 50.000 3.98 0.00 0.00 2.24
31 32 1.728425 GTACGCGGTACAGGGAAAAAG 59.272 52.381 16.57 0.00 38.71 2.27
39 40 0.519999 GAGTCACGTACGCGGTACAG 60.520 60.000 16.72 9.46 43.45 2.74
41 42 0.790866 GTGAGTCACGTACGCGGTAC 60.791 60.000 16.72 9.82 43.45 3.34
42 43 0.950555 AGTGAGTCACGTACGCGGTA 60.951 55.000 16.72 0.00 43.45 4.02
43 44 2.180131 GAGTGAGTCACGTACGCGGT 62.180 60.000 16.72 0.00 43.45 5.68
44 45 1.511464 GAGTGAGTCACGTACGCGG 60.511 63.158 16.72 8.28 43.45 6.46
45 46 0.179197 ATGAGTGAGTCACGTACGCG 60.179 55.000 16.72 3.53 38.28 6.01
46 47 2.819422 TATGAGTGAGTCACGTACGC 57.181 50.000 16.72 0.00 38.28 4.42
47 48 4.966249 TCTTTATGAGTGAGTCACGTACG 58.034 43.478 17.40 15.01 38.28 3.67
148 150 7.007697 CGAACACGTAATCAAACTTAAGGAAG 58.992 38.462 7.53 0.00 38.76 3.46
156 158 2.762745 AGGCGAACACGTAATCAAACT 58.237 42.857 0.00 0.00 0.00 2.66
157 159 3.429543 TGTAGGCGAACACGTAATCAAAC 59.570 43.478 0.00 0.00 0.00 2.93
158 160 3.651206 TGTAGGCGAACACGTAATCAAA 58.349 40.909 0.00 0.00 0.00 2.69
160 162 3.300852 TTGTAGGCGAACACGTAATCA 57.699 42.857 0.00 0.00 0.00 2.57
161 163 3.543460 GCATTGTAGGCGAACACGTAATC 60.543 47.826 0.00 0.00 0.00 1.75
162 164 2.350498 GCATTGTAGGCGAACACGTAAT 59.650 45.455 0.00 0.00 0.00 1.89
163 165 1.727880 GCATTGTAGGCGAACACGTAA 59.272 47.619 0.00 0.00 0.00 3.18
189 193 5.708736 TTATCCACTTGCTTAATGGGAGA 57.291 39.130 0.00 0.00 34.03 3.71
218 222 6.903419 TCATACTTATGTGCTCTGATCTACG 58.097 40.000 0.00 0.00 35.26 3.51
219 223 9.352784 GAATCATACTTATGTGCTCTGATCTAC 57.647 37.037 0.00 0.00 35.26 2.59
220 224 9.306777 AGAATCATACTTATGTGCTCTGATCTA 57.693 33.333 0.00 0.00 35.26 1.98
221 225 8.192743 AGAATCATACTTATGTGCTCTGATCT 57.807 34.615 0.00 0.00 35.26 2.75
234 238 7.330946 CCTTCAACGTGTCAAGAATCATACTTA 59.669 37.037 0.00 0.00 0.00 2.24
236 240 5.639506 CCTTCAACGTGTCAAGAATCATACT 59.360 40.000 0.00 0.00 0.00 2.12
237 241 5.163854 CCCTTCAACGTGTCAAGAATCATAC 60.164 44.000 0.00 0.00 0.00 2.39
238 242 4.935205 CCCTTCAACGTGTCAAGAATCATA 59.065 41.667 0.00 0.00 0.00 2.15
258 283 1.037493 TACGTGCGCATTAGATCCCT 58.963 50.000 15.91 0.00 0.00 4.20
264 289 0.921347 GTCCTGTACGTGCGCATTAG 59.079 55.000 15.91 11.37 0.00 1.73
265 290 0.528924 AGTCCTGTACGTGCGCATTA 59.471 50.000 15.91 5.33 0.00 1.90
268 293 1.210931 GTAGTCCTGTACGTGCGCA 59.789 57.895 5.66 5.66 0.00 6.09
269 294 0.797249 CTGTAGTCCTGTACGTGCGC 60.797 60.000 0.00 0.00 0.00 6.09
270 295 0.179171 CCTGTAGTCCTGTACGTGCG 60.179 60.000 0.00 0.00 0.00 5.34
271 296 0.172803 CCCTGTAGTCCTGTACGTGC 59.827 60.000 0.00 0.00 0.00 5.34
272 297 1.830279 TCCCTGTAGTCCTGTACGTG 58.170 55.000 0.00 0.00 0.00 4.49
274 299 1.067212 GCATCCCTGTAGTCCTGTACG 59.933 57.143 0.00 0.00 0.00 3.67
275 300 2.108168 TGCATCCCTGTAGTCCTGTAC 58.892 52.381 0.00 0.00 0.00 2.90
277 302 1.656587 TTGCATCCCTGTAGTCCTGT 58.343 50.000 0.00 0.00 0.00 4.00
279 304 1.133976 GCATTGCATCCCTGTAGTCCT 60.134 52.381 3.15 0.00 0.00 3.85
281 306 2.042686 TGCATTGCATCCCTGTAGTC 57.957 50.000 7.38 0.00 31.71 2.59
283 308 2.093890 TGTTGCATTGCATCCCTGTAG 58.906 47.619 12.95 0.00 38.76 2.74
284 309 2.212812 TGTTGCATTGCATCCCTGTA 57.787 45.000 12.95 0.00 38.76 2.74
285 310 1.563924 ATGTTGCATTGCATCCCTGT 58.436 45.000 12.95 0.00 38.76 4.00
286 311 3.804786 TTATGTTGCATTGCATCCCTG 57.195 42.857 12.95 0.00 38.76 4.45
287 312 4.406326 TCATTTATGTTGCATTGCATCCCT 59.594 37.500 12.95 4.87 38.76 4.20
289 314 5.178623 CCATCATTTATGTTGCATTGCATCC 59.821 40.000 12.95 7.00 33.68 3.51
290 315 5.986741 TCCATCATTTATGTTGCATTGCATC 59.013 36.000 12.95 12.34 33.68 3.91
291 316 5.919755 TCCATCATTTATGTTGCATTGCAT 58.080 33.333 12.95 0.00 33.68 3.96
292 317 5.340439 TCCATCATTTATGTTGCATTGCA 57.660 34.783 7.38 7.38 32.63 4.08
293 318 6.854496 ATTCCATCATTTATGTTGCATTGC 57.146 33.333 0.46 0.46 33.34 3.56
314 339 9.650539 TGCATGCATGTAAGTGTATTTTAAATT 57.349 25.926 26.79 0.00 0.00 1.82
323 348 2.418280 CGGTTGCATGCATGTAAGTGTA 59.582 45.455 27.61 6.24 33.11 2.90
330 355 0.890542 ACTGACGGTTGCATGCATGT 60.891 50.000 26.79 19.85 0.00 3.21
375 400 0.759959 TGGACGTTGAAAGCCCTACA 59.240 50.000 0.00 0.00 0.00 2.74
415 440 5.804692 AGCCGTTCGATATACTAGATCAG 57.195 43.478 0.00 0.00 0.00 2.90
465 490 9.010029 CCACTAATAGGAATTCTCTACTCTCTC 57.990 40.741 5.23 0.00 0.00 3.20
479 504 4.200447 AGCTAGCCTCCACTAATAGGAA 57.800 45.455 12.13 0.00 34.58 3.36
484 509 9.722317 ATATCTAAATAGCTAGCCTCCACTAAT 57.278 33.333 12.13 0.00 0.00 1.73
561 586 5.691305 CGCATTCCACCACATATTAATTTGG 59.309 40.000 10.17 9.16 38.66 3.28
593 618 4.320788 CGGGTTTAAACTGTACTCTCGACT 60.321 45.833 17.50 0.00 0.00 4.18
600 625 4.000988 CTGCATCGGGTTTAAACTGTACT 58.999 43.478 17.50 0.00 0.00 2.73
615 640 3.508840 GGAAACCCGGCTGCATCG 61.509 66.667 0.50 0.00 0.00 3.84
690 715 8.202745 AGCAAAGTTAGATTATTTCCTTCTCG 57.797 34.615 0.00 0.00 0.00 4.04
723 750 4.090761 TCAGAGAAAGTTGGCACATTCT 57.909 40.909 7.98 7.98 42.40 2.40
740 767 5.108517 GGCATGTTGTTTTTGTCTTTCAGA 58.891 37.500 0.00 0.00 0.00 3.27
743 770 5.793026 TTGGCATGTTGTTTTTGTCTTTC 57.207 34.783 0.00 0.00 0.00 2.62
758 785 4.142859 GCACATGTTTGGTTAATTGGCATG 60.143 41.667 0.00 0.00 38.41 4.06
823 852 1.807814 ATTCGGGAGGACCTTATGCT 58.192 50.000 0.00 0.00 36.97 3.79
900 929 3.057946 GCTCCAATGTTTCACTTCTGGAC 60.058 47.826 0.00 0.00 0.00 4.02
950 988 5.529060 GGATTTATAGGCTAGCATGCATACC 59.471 44.000 21.98 17.03 31.96 2.73
1176 1936 2.846532 CCAGGTGGGCTTGGACTT 59.153 61.111 0.00 0.00 43.81 3.01
1428 2396 6.468333 TTGTATACTGGACCATACGCTTAA 57.532 37.500 4.17 0.00 31.52 1.85
1534 2524 8.275015 TGCTTTCGTATGATGATTTTCCTTTA 57.725 30.769 0.00 0.00 0.00 1.85
1806 2799 2.939756 TGCTTGTCTTAACGTGCTTGAA 59.060 40.909 0.00 0.00 0.00 2.69
1810 2803 4.537015 GAAAATGCTTGTCTTAACGTGCT 58.463 39.130 0.00 0.00 0.00 4.40
1856 2849 6.507958 TGTTTTTCTCAACTTCACACATGA 57.492 33.333 0.00 0.00 0.00 3.07
1961 2954 2.436911 GTTATGGGATGTAGGTCGGGTT 59.563 50.000 0.00 0.00 0.00 4.11
1981 2974 3.498774 ATGAACAGGAAGCTGAGTTGT 57.501 42.857 0.00 0.00 0.00 3.32
1988 2981 6.959639 TTTAAGTGAAATGAACAGGAAGCT 57.040 33.333 0.00 0.00 0.00 3.74
2002 2995 7.338449 CCTCCCGATTCCTTTTATTTAAGTGAA 59.662 37.037 0.00 0.00 0.00 3.18
2023 3016 2.444895 ATCGCCACTCTCCCTCCC 60.445 66.667 0.00 0.00 0.00 4.30
2471 3479 0.770499 TTGGGTTGACAGCTCCATGA 59.230 50.000 0.00 0.00 0.00 3.07
2472 3480 0.883833 GTTGGGTTGACAGCTCCATG 59.116 55.000 0.00 0.00 0.00 3.66
2473 3481 0.251341 GGTTGGGTTGACAGCTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
2474 3482 1.150536 GGTTGGGTTGACAGCTCCA 59.849 57.895 0.00 0.00 0.00 3.86
2475 3483 0.890996 CTGGTTGGGTTGACAGCTCC 60.891 60.000 0.00 0.00 0.00 4.70
2476 3484 0.890996 CCTGGTTGGGTTGACAGCTC 60.891 60.000 0.00 0.00 0.00 4.09
2477 3485 1.151450 CCTGGTTGGGTTGACAGCT 59.849 57.895 0.00 0.00 0.00 4.24
2478 3486 3.763671 CCTGGTTGGGTTGACAGC 58.236 61.111 0.00 0.00 0.00 4.40
2488 3496 2.383245 ATATCTCGCGGCCCTGGTTG 62.383 60.000 6.13 0.00 0.00 3.77
2489 3497 1.696097 AATATCTCGCGGCCCTGGTT 61.696 55.000 6.13 0.00 0.00 3.67
2490 3498 2.140792 AATATCTCGCGGCCCTGGT 61.141 57.895 6.13 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.