Multiple sequence alignment - TraesCS4A01G193300

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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 TraesCS4A01G193300 chr4A 100.000 3428 0 0 1 3428 474745402 474741975 0.000000e+00 6331
1 TraesCS4A01G193300 chr4D 95.478 2167 66 14 1274 3428 101021832 101023978 0.000000e+00 3430
2 TraesCS4A01G193300 chr4D 91.842 809 36 8 470 1273 101020989 101021772 0.000000e+00 1101
3 TraesCS4A01G193300 chr4D 93.122 189 6 1 1 182 101020471 101020659 1.570000e-68 270
4 TraesCS4A01G193300 chr4D 95.370 108 5 0 374 481 101020861 101020968 4.550000e-39 172
5 TraesCS4A01G193300 chr4B 94.288 2171 87 19 1274 3428 144745672 144747821 0.000000e+00 3288
6 TraesCS4A01G193300 chr4B 91.568 925 44 11 374 1273 144744695 144745610 0.000000e+00 1245
7 TraesCS4A01G193300 chr4B 95.139 288 11 3 1 287 144744161 144744446 5.220000e-123 451


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 TraesCS4A01G193300 chr4A 474741975 474745402 3427 True 6331.000000 6331 100.000 1 3428 1 chr4A.!!$R1 3427
1 TraesCS4A01G193300 chr4D 101020471 101023978 3507 False 1243.250000 3430 93.953 1 3428 4 chr4D.!!$F1 3427
2 TraesCS4A01G193300 chr4B 144744161 144747821 3660 False 1661.333333 3288 93.665 1 3428 3 chr4B.!!$F1 3427

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
346 356 0.106769 TGCAGACAAACCAAGCCTGA 60.107 50.0 0.00 0.0 0.0 3.86 F
353 363 0.185901 AAACCAAGCCTGAGGAAGCA 59.814 50.0 0.65 0.0 0.0 3.91 F
1279 1574 0.255890 GTACCCACATCCCACTGCAT 59.744 55.0 0.00 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1724 0.808755 TTGCGCGTCTCATCAGTCTA 59.191 50.000 8.43 0.0 0.0 2.59 R
1438 1744 1.134788 CAGGGAAGTTACACTAGGCCG 60.135 57.143 0.00 0.0 0.0 6.13 R
3047 3359 0.811616 GGAGCGGCTTGTCATACTGG 60.812 60.000 2.97 0.0 0.0 4.00 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
72 80 6.575162 AATCATTTGTCCCTTGACTGTAAC 57.425 37.500 0.00 0.00 42.28 2.50
136 144 1.630369 TGGTTGGACCTCCTGAAGATG 59.370 52.381 7.57 0.00 39.58 2.90
151 159 5.902613 TGAAGATGTTCAGGGCTTAATTG 57.097 39.130 0.23 0.00 37.79 2.32
158 166 2.446435 TCAGGGCTTAATTGGTGCTTC 58.554 47.619 0.00 0.00 0.00 3.86
173 181 0.818040 GCTTCGTGGACCCTGTGTTT 60.818 55.000 0.00 0.00 0.00 2.83
207 215 1.134371 CAAACTAGCTCTAGTGGGGGC 60.134 57.143 10.05 0.00 44.96 5.80
208 216 0.340208 AACTAGCTCTAGTGGGGGCT 59.660 55.000 10.05 0.00 44.96 5.19
209 217 0.397816 ACTAGCTCTAGTGGGGGCTG 60.398 60.000 8.64 0.00 44.11 4.85
210 218 1.753368 CTAGCTCTAGTGGGGGCTGC 61.753 65.000 0.00 0.00 36.40 5.25
211 219 2.243774 TAGCTCTAGTGGGGGCTGCT 62.244 60.000 0.00 0.00 36.40 4.24
214 222 0.393537 CTCTAGTGGGGGCTGCTTTG 60.394 60.000 0.00 0.00 0.00 2.77
231 240 3.799917 GCTTTGTGTTGGACCATTTGGAG 60.800 47.826 3.01 0.00 38.94 3.86
281 291 4.836125 AAAATACCCGATGATCATGCAC 57.164 40.909 14.30 0.00 0.00 4.57
287 297 2.036346 CCCGATGATCATGCACTAGTCA 59.964 50.000 14.30 0.00 0.00 3.41
288 298 3.306571 CCCGATGATCATGCACTAGTCAT 60.307 47.826 14.30 0.00 32.59 3.06
289 299 4.313282 CCGATGATCATGCACTAGTCATT 58.687 43.478 14.30 0.00 30.24 2.57
290 300 4.753610 CCGATGATCATGCACTAGTCATTT 59.246 41.667 14.30 0.00 30.24 2.32
291 301 5.237996 CCGATGATCATGCACTAGTCATTTT 59.762 40.000 14.30 0.00 30.24 1.82
292 302 6.361114 CGATGATCATGCACTAGTCATTTTC 58.639 40.000 14.30 0.00 30.24 2.29
293 303 5.723492 TGATCATGCACTAGTCATTTTCG 57.277 39.130 0.00 0.00 0.00 3.46
294 304 4.571984 TGATCATGCACTAGTCATTTTCGG 59.428 41.667 0.00 0.00 0.00 4.30
295 305 2.677836 TCATGCACTAGTCATTTTCGGC 59.322 45.455 0.00 0.00 0.00 5.54
296 306 1.448985 TGCACTAGTCATTTTCGGCC 58.551 50.000 0.00 0.00 0.00 6.13
300 310 2.416547 CACTAGTCATTTTCGGCCTGTG 59.583 50.000 0.00 0.00 0.00 3.66
304 314 1.812571 GTCATTTTCGGCCTGTGTCAT 59.187 47.619 0.00 0.00 0.00 3.06
306 316 3.438781 GTCATTTTCGGCCTGTGTCATTA 59.561 43.478 0.00 0.00 0.00 1.90
307 317 3.438781 TCATTTTCGGCCTGTGTCATTAC 59.561 43.478 0.00 0.00 0.00 1.89
308 318 1.816074 TTTCGGCCTGTGTCATTACC 58.184 50.000 0.00 0.00 0.00 2.85
310 320 0.535335 TCGGCCTGTGTCATTACCTC 59.465 55.000 0.00 0.00 0.00 3.85
311 321 0.806102 CGGCCTGTGTCATTACCTCG 60.806 60.000 0.00 0.00 0.00 4.63
312 322 1.090052 GGCCTGTGTCATTACCTCGC 61.090 60.000 0.00 0.00 0.00 5.03
313 323 1.090052 GCCTGTGTCATTACCTCGCC 61.090 60.000 0.00 0.00 0.00 5.54
314 324 0.249120 CCTGTGTCATTACCTCGCCA 59.751 55.000 0.00 0.00 0.00 5.69
315 325 1.338674 CCTGTGTCATTACCTCGCCAA 60.339 52.381 0.00 0.00 0.00 4.52
316 326 2.632377 CTGTGTCATTACCTCGCCAAT 58.368 47.619 0.00 0.00 0.00 3.16
317 327 3.009723 CTGTGTCATTACCTCGCCAATT 58.990 45.455 0.00 0.00 0.00 2.32
318 328 4.188462 CTGTGTCATTACCTCGCCAATTA 58.812 43.478 0.00 0.00 0.00 1.40
319 329 4.188462 TGTGTCATTACCTCGCCAATTAG 58.812 43.478 0.00 0.00 0.00 1.73
320 330 3.560068 GTGTCATTACCTCGCCAATTAGG 59.440 47.826 0.00 0.00 41.84 2.69
333 343 2.360165 CCAATTAGGCCATCTTGCAGAC 59.640 50.000 5.01 0.00 0.00 3.51
335 345 2.877097 TTAGGCCATCTTGCAGACAA 57.123 45.000 5.01 0.00 0.00 3.18
336 346 2.877097 TAGGCCATCTTGCAGACAAA 57.123 45.000 5.01 0.00 34.74 2.83
337 347 1.251251 AGGCCATCTTGCAGACAAAC 58.749 50.000 5.01 0.00 34.74 2.93
338 348 0.244721 GGCCATCTTGCAGACAAACC 59.755 55.000 0.00 0.00 34.74 3.27
339 349 0.961019 GCCATCTTGCAGACAAACCA 59.039 50.000 0.00 0.00 34.74 3.67
340 350 1.340889 GCCATCTTGCAGACAAACCAA 59.659 47.619 0.00 0.00 34.74 3.67
341 351 2.608752 GCCATCTTGCAGACAAACCAAG 60.609 50.000 0.00 0.00 37.80 3.61
343 353 1.032014 TCTTGCAGACAAACCAAGCC 58.968 50.000 0.00 0.00 36.72 4.35
344 354 1.035139 CTTGCAGACAAACCAAGCCT 58.965 50.000 0.00 0.00 34.74 4.58
345 355 0.746063 TTGCAGACAAACCAAGCCTG 59.254 50.000 0.00 0.00 31.21 4.85
346 356 0.106769 TGCAGACAAACCAAGCCTGA 60.107 50.000 0.00 0.00 0.00 3.86
347 357 0.595095 GCAGACAAACCAAGCCTGAG 59.405 55.000 0.00 0.00 0.00 3.35
348 358 1.242076 CAGACAAACCAAGCCTGAGG 58.758 55.000 0.00 0.00 0.00 3.86
349 359 1.140312 AGACAAACCAAGCCTGAGGA 58.860 50.000 0.65 0.00 0.00 3.71
350 360 1.494721 AGACAAACCAAGCCTGAGGAA 59.505 47.619 0.65 0.00 0.00 3.36
351 361 1.882623 GACAAACCAAGCCTGAGGAAG 59.117 52.381 0.65 0.00 0.00 3.46
352 362 0.600057 CAAACCAAGCCTGAGGAAGC 59.400 55.000 0.65 0.00 0.00 3.86
353 363 0.185901 AAACCAAGCCTGAGGAAGCA 59.814 50.000 0.65 0.00 0.00 3.91
354 364 0.407139 AACCAAGCCTGAGGAAGCAT 59.593 50.000 0.65 0.00 0.00 3.79
355 365 0.407139 ACCAAGCCTGAGGAAGCATT 59.593 50.000 0.65 0.00 0.00 3.56
356 366 0.815734 CCAAGCCTGAGGAAGCATTG 59.184 55.000 0.65 0.00 0.00 2.82
357 367 1.615116 CCAAGCCTGAGGAAGCATTGA 60.615 52.381 0.65 0.00 0.00 2.57
358 368 2.165167 CAAGCCTGAGGAAGCATTGAA 58.835 47.619 0.65 0.00 0.00 2.69
359 369 2.125773 AGCCTGAGGAAGCATTGAAG 57.874 50.000 0.65 0.00 0.00 3.02
361 371 2.015587 GCCTGAGGAAGCATTGAAGAG 58.984 52.381 0.65 0.00 0.00 2.85
362 372 2.641305 CCTGAGGAAGCATTGAAGAGG 58.359 52.381 0.00 0.00 0.00 3.69
363 373 2.015587 CTGAGGAAGCATTGAAGAGGC 58.984 52.381 0.00 0.00 34.64 4.70
364 374 1.352017 TGAGGAAGCATTGAAGAGGCA 59.648 47.619 0.00 0.00 37.56 4.75
365 375 2.025605 TGAGGAAGCATTGAAGAGGCAT 60.026 45.455 0.00 0.00 37.56 4.40
366 376 3.022406 GAGGAAGCATTGAAGAGGCATT 58.978 45.455 0.00 0.00 37.56 3.56
367 377 2.758979 AGGAAGCATTGAAGAGGCATTG 59.241 45.455 0.00 0.00 37.56 2.82
368 378 2.756760 GGAAGCATTGAAGAGGCATTGA 59.243 45.455 0.00 0.00 37.56 2.57
370 380 4.421948 GAAGCATTGAAGAGGCATTGAAG 58.578 43.478 0.00 0.00 37.56 3.02
371 381 2.165845 AGCATTGAAGAGGCATTGAAGC 59.834 45.455 0.00 0.00 37.56 3.86
415 587 2.105128 GAGGTGTCCGATCGGCAG 59.895 66.667 29.62 6.38 34.68 4.85
453 625 3.028850 CTGATCATTCCAGGTTGGCATT 58.971 45.455 0.00 0.00 37.47 3.56
467 639 4.923281 GGTTGGCATTCATGTGTTTTCTAC 59.077 41.667 0.00 0.00 0.00 2.59
468 640 4.418013 TGGCATTCATGTGTTTTCTACG 57.582 40.909 0.00 0.00 0.00 3.51
553 763 5.934935 ATAAAGGACAAAACACGTGTAGG 57.065 39.130 23.69 16.31 0.00 3.18
572 782 1.446907 GACAACCCTGAGTGATGCAG 58.553 55.000 0.00 0.00 0.00 4.41
600 810 2.926200 CAGAGACACCAATTCTAGTGCG 59.074 50.000 0.00 0.00 37.51 5.34
601 811 2.563179 AGAGACACCAATTCTAGTGCGT 59.437 45.455 0.00 0.00 37.51 5.24
602 812 3.762288 AGAGACACCAATTCTAGTGCGTA 59.238 43.478 0.00 0.00 37.51 4.42
603 813 3.846360 AGACACCAATTCTAGTGCGTAC 58.154 45.455 0.00 0.00 37.51 3.67
604 814 3.257375 AGACACCAATTCTAGTGCGTACA 59.743 43.478 6.38 0.00 37.51 2.90
607 817 4.219070 ACACCAATTCTAGTGCGTACAGTA 59.781 41.667 6.38 0.00 37.51 2.74
612 822 7.145985 CCAATTCTAGTGCGTACAGTACATAT 58.854 38.462 11.37 0.00 37.96 1.78
697 910 3.758088 CTCCATCGACCGGCTCACG 62.758 68.421 0.00 2.59 43.80 4.35
711 924 2.844281 GCTCACGCTGAGTCAATTTTC 58.156 47.619 13.91 0.00 45.94 2.29
817 1051 4.081309 CAGGTGATTTTCCTGCATTTGGAT 60.081 41.667 0.00 0.00 44.46 3.41
882 1116 3.859386 GCCAATGCTTCTGGAAATAAACG 59.141 43.478 3.78 0.00 35.85 3.60
926 1160 6.238786 CCTCGCCTATATAAATAGCTCGTCAT 60.239 42.308 0.00 0.00 34.78 3.06
936 1170 2.717639 AGCTCGTCATTAAAGGGCAT 57.282 45.000 0.00 0.00 0.00 4.40
955 1189 1.324383 TGCAACCGCGGATAGATAGA 58.676 50.000 35.90 3.61 42.97 1.98
966 1200 2.352225 GGATAGATAGACAGGCGCACAG 60.352 54.545 10.83 0.00 0.00 3.66
977 1211 0.736325 GGCGCACAGACAATCGTAGT 60.736 55.000 10.83 0.00 0.00 2.73
978 1212 0.366871 GCGCACAGACAATCGTAGTG 59.633 55.000 0.30 0.00 35.44 2.74
979 1213 0.992072 CGCACAGACAATCGTAGTGG 59.008 55.000 0.00 0.00 33.83 4.00
1140 1374 4.373116 TCCTGCGTCGACCTTGCC 62.373 66.667 10.58 0.00 0.00 4.52
1269 1503 3.369052 CGACAGTAACCATGTACCCACAT 60.369 47.826 0.00 0.00 46.58 3.21
1279 1574 0.255890 GTACCCACATCCCACTGCAT 59.744 55.000 0.00 0.00 0.00 3.96
1280 1575 0.546122 TACCCACATCCCACTGCATC 59.454 55.000 0.00 0.00 0.00 3.91
1301 1596 2.028567 CACTCTTTCAGTCTCAGGGGAC 60.029 54.545 0.00 0.00 30.26 4.46
1394 1700 7.968405 ACTTATTTTGCGTTGCTCTTTATTAGG 59.032 33.333 0.00 0.00 0.00 2.69
1418 1724 6.434340 GGAAACCACTTTCTATGACTTCCAAT 59.566 38.462 0.00 0.00 36.71 3.16
1430 1736 8.001292 TCTATGACTTCCAATAGACTGATGAGA 58.999 37.037 0.00 0.00 0.00 3.27
1434 1740 2.033424 TCCAATAGACTGATGAGACGCG 59.967 50.000 3.53 3.53 0.00 6.01
1438 1744 0.734253 AGACTGATGAGACGCGCAAC 60.734 55.000 5.73 0.00 0.00 4.17
1531 1837 8.721133 AAGAAATTGTGTACCTTAGGGAAATT 57.279 30.769 2.32 0.00 36.25 1.82
1640 1949 7.993821 AATCTCGTGTTACTGATTGATACTG 57.006 36.000 0.00 0.00 0.00 2.74
1747 2056 4.107363 TGCAATGCATTTATTCAGCGAA 57.893 36.364 9.83 0.00 31.71 4.70
1925 2234 6.718454 TCTTCCTTTCAAGAATTTCAGCTGAT 59.282 34.615 19.04 1.77 29.01 2.90
2181 2490 3.207669 GCGCTTGCCTCCATCCTG 61.208 66.667 0.00 0.00 0.00 3.86
2451 2760 1.814394 CTTGTACACCATGCATGCACT 59.186 47.619 25.37 9.74 0.00 4.40
2459 2768 0.678684 CATGCATGCACTGTCTGGGA 60.679 55.000 25.37 0.00 0.00 4.37
2643 2955 1.064505 TCCGATAAGTTAGCACGTCCG 59.935 52.381 0.00 0.00 0.00 4.79
2645 2957 2.107178 CGATAAGTTAGCACGTCCGTC 58.893 52.381 0.00 0.00 0.00 4.79
2845 3157 1.191535 CCCGGTGATTGGTACAGAGA 58.808 55.000 0.00 0.00 42.39 3.10
2846 3158 1.137086 CCCGGTGATTGGTACAGAGAG 59.863 57.143 0.00 0.00 42.39 3.20
2856 3168 6.384015 TGATTGGTACAGAGAGGTAATGATGT 59.616 38.462 0.00 0.00 42.39 3.06
2872 3184 8.531982 GGTAATGATGTACTCAATAGGCAGATA 58.468 37.037 0.00 0.00 37.44 1.98
2900 3212 1.619807 GCATGGCAGGGGAGCATTTT 61.620 55.000 0.00 0.00 35.83 1.82
2921 3233 0.482446 TGCTTGTTCATGGGGAAGGT 59.518 50.000 0.00 0.00 35.82 3.50
2978 3290 3.541713 GAGGGCTCCGGCTACCAG 61.542 72.222 0.00 0.00 38.73 4.00
2999 3311 1.065854 GTGACCTGCATAGACCTTGCT 60.066 52.381 0.00 0.00 40.77 3.91
3003 3315 2.408271 CTGCATAGACCTTGCTGGAA 57.592 50.000 3.40 0.00 40.77 3.53
3005 3317 1.630369 TGCATAGACCTTGCTGGAAGT 59.370 47.619 8.14 0.00 40.77 3.01
3035 3347 1.597027 CACCGACCCCAACACTGTC 60.597 63.158 0.00 0.00 0.00 3.51
3047 3359 0.038526 ACACTGTCCGGTCATTCGAC 60.039 55.000 0.00 0.00 41.80 4.20
3184 3496 5.127031 AGGTAGTTTGTTGCTTTGTTGTGAT 59.873 36.000 0.00 0.00 0.00 3.06
3185 3497 5.810074 GGTAGTTTGTTGCTTTGTTGTGATT 59.190 36.000 0.00 0.00 0.00 2.57
3186 3498 5.783100 AGTTTGTTGCTTTGTTGTGATTG 57.217 34.783 0.00 0.00 0.00 2.67
3189 3501 4.446994 TGTTGCTTTGTTGTGATTGTGA 57.553 36.364 0.00 0.00 0.00 3.58
3190 3502 4.814147 TGTTGCTTTGTTGTGATTGTGAA 58.186 34.783 0.00 0.00 0.00 3.18
3191 3503 4.863689 TGTTGCTTTGTTGTGATTGTGAAG 59.136 37.500 0.00 0.00 0.00 3.02
3192 3504 3.446799 TGCTTTGTTGTGATTGTGAAGC 58.553 40.909 0.00 0.00 38.69 3.86
3193 3505 3.130869 TGCTTTGTTGTGATTGTGAAGCT 59.869 39.130 0.00 0.00 38.92 3.74
3195 3507 2.780065 TGTTGTGATTGTGAAGCTGC 57.220 45.000 0.00 0.00 0.00 5.25
3196 3508 2.300433 TGTTGTGATTGTGAAGCTGCT 58.700 42.857 0.00 0.00 0.00 4.24
3197 3509 2.689471 TGTTGTGATTGTGAAGCTGCTT 59.311 40.909 15.92 15.92 0.00 3.91
3200 3512 5.704978 TGTTGTGATTGTGAAGCTGCTTATA 59.295 36.000 15.95 4.77 0.00 0.98
3201 3513 6.206438 TGTTGTGATTGTGAAGCTGCTTATAA 59.794 34.615 15.95 10.88 0.00 0.98
3202 3514 7.094248 TGTTGTGATTGTGAAGCTGCTTATAAT 60.094 33.333 15.95 14.89 0.00 1.28
3203 3515 7.395190 TGTGATTGTGAAGCTGCTTATAATT 57.605 32.000 15.95 0.54 0.00 1.40
3204 3516 8.504812 TGTGATTGTGAAGCTGCTTATAATTA 57.495 30.769 15.95 9.82 0.00 1.40
3205 3517 8.615211 TGTGATTGTGAAGCTGCTTATAATTAG 58.385 33.333 15.95 0.00 0.00 1.73
3206 3518 8.072567 GTGATTGTGAAGCTGCTTATAATTAGG 58.927 37.037 15.95 0.00 0.00 2.69
3207 3519 6.942532 TTGTGAAGCTGCTTATAATTAGGG 57.057 37.500 15.95 0.00 0.00 3.53
3208 3520 6.247229 TGTGAAGCTGCTTATAATTAGGGA 57.753 37.500 15.95 0.00 0.00 4.20
3209 3521 6.055588 TGTGAAGCTGCTTATAATTAGGGAC 58.944 40.000 15.95 0.00 0.00 4.46
3210 3522 6.055588 GTGAAGCTGCTTATAATTAGGGACA 58.944 40.000 15.95 1.38 0.00 4.02
3244 3556 3.181469 TGGCGAAGAGTTATAGGCGATTT 60.181 43.478 0.00 0.00 0.00 2.17
3257 3569 4.948341 AGGCGATTTGGTTTACCTTTTT 57.052 36.364 0.00 0.00 36.82 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 76 2.293399 CAGGTGAACTTGGCAAGGTTAC 59.707 50.000 26.80 26.80 34.23 2.50
72 80 0.178992 TCCAGGTGAACTTGGCAAGG 60.179 55.000 29.26 11.49 42.26 3.61
136 144 2.171003 AGCACCAATTAAGCCCTGAAC 58.829 47.619 0.00 0.00 0.00 3.18
151 159 2.358737 CAGGGTCCACGAAGCACC 60.359 66.667 0.00 0.00 0.00 5.01
158 166 0.602905 GGAGAAACACAGGGTCCACG 60.603 60.000 0.00 0.00 0.00 4.94
173 181 1.896660 GTTTGCGTTGGCCAGGAGA 60.897 57.895 5.11 0.00 38.85 3.71
207 215 3.125316 CAAATGGTCCAACACAAAGCAG 58.875 45.455 0.00 0.00 0.00 4.24
208 216 2.158986 CCAAATGGTCCAACACAAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
209 217 2.102252 TCCAAATGGTCCAACACAAAGC 59.898 45.455 0.00 0.00 36.34 3.51
210 218 3.243839 CCTCCAAATGGTCCAACACAAAG 60.244 47.826 0.00 0.00 36.34 2.77
211 219 2.697751 CCTCCAAATGGTCCAACACAAA 59.302 45.455 0.00 0.00 36.34 2.83
214 222 1.886542 GTCCTCCAAATGGTCCAACAC 59.113 52.381 0.00 0.00 36.34 3.32
231 240 6.049149 TCAAAATATGTCGATTCTCTGGTCC 58.951 40.000 0.00 0.00 0.00 4.46
281 291 2.673368 GACACAGGCCGAAAATGACTAG 59.327 50.000 0.00 0.00 0.00 2.57
287 297 2.752903 GGTAATGACACAGGCCGAAAAT 59.247 45.455 0.00 0.00 0.00 1.82
288 298 2.156098 GGTAATGACACAGGCCGAAAA 58.844 47.619 0.00 0.00 0.00 2.29
289 299 1.349688 AGGTAATGACACAGGCCGAAA 59.650 47.619 0.00 0.00 0.00 3.46
290 300 0.981183 AGGTAATGACACAGGCCGAA 59.019 50.000 0.00 0.00 0.00 4.30
291 301 0.535335 GAGGTAATGACACAGGCCGA 59.465 55.000 0.00 0.00 0.00 5.54
292 302 0.806102 CGAGGTAATGACACAGGCCG 60.806 60.000 0.00 0.00 0.00 6.13
293 303 1.090052 GCGAGGTAATGACACAGGCC 61.090 60.000 0.00 0.00 0.00 5.19
294 304 1.090052 GGCGAGGTAATGACACAGGC 61.090 60.000 0.00 0.00 0.00 4.85
295 305 0.249120 TGGCGAGGTAATGACACAGG 59.751 55.000 0.00 0.00 0.00 4.00
296 306 2.093306 TTGGCGAGGTAATGACACAG 57.907 50.000 0.00 0.00 0.00 3.66
312 322 2.658285 TCTGCAAGATGGCCTAATTGG 58.342 47.619 3.32 0.00 38.67 3.16
325 335 1.035139 AGGCTTGGTTTGTCTGCAAG 58.965 50.000 0.00 0.00 35.82 4.01
326 336 0.746063 CAGGCTTGGTTTGTCTGCAA 59.254 50.000 0.00 0.00 30.16 4.08
327 337 0.106769 TCAGGCTTGGTTTGTCTGCA 60.107 50.000 0.00 0.00 37.11 4.41
328 338 0.595095 CTCAGGCTTGGTTTGTCTGC 59.405 55.000 0.00 0.00 37.11 4.26
329 339 1.202806 TCCTCAGGCTTGGTTTGTCTG 60.203 52.381 0.00 0.00 38.39 3.51
331 341 1.882623 CTTCCTCAGGCTTGGTTTGTC 59.117 52.381 0.00 0.00 0.00 3.18
333 343 0.600057 GCTTCCTCAGGCTTGGTTTG 59.400 55.000 0.00 0.00 0.00 2.93
335 345 0.407139 ATGCTTCCTCAGGCTTGGTT 59.593 50.000 0.00 0.00 0.00 3.67
336 346 0.407139 AATGCTTCCTCAGGCTTGGT 59.593 50.000 0.00 0.00 0.00 3.67
337 347 0.815734 CAATGCTTCCTCAGGCTTGG 59.184 55.000 0.00 0.00 0.00 3.61
338 348 1.830279 TCAATGCTTCCTCAGGCTTG 58.170 50.000 0.00 0.00 0.00 4.01
339 349 2.040813 TCTTCAATGCTTCCTCAGGCTT 59.959 45.455 0.00 0.00 0.00 4.35
340 350 1.632409 TCTTCAATGCTTCCTCAGGCT 59.368 47.619 0.00 0.00 0.00 4.58
341 351 2.015587 CTCTTCAATGCTTCCTCAGGC 58.984 52.381 0.00 0.00 0.00 4.85
343 353 2.015587 GCCTCTTCAATGCTTCCTCAG 58.984 52.381 0.00 0.00 0.00 3.35
344 354 1.352017 TGCCTCTTCAATGCTTCCTCA 59.648 47.619 0.00 0.00 0.00 3.86
345 355 2.119801 TGCCTCTTCAATGCTTCCTC 57.880 50.000 0.00 0.00 0.00 3.71
346 356 2.758979 CAATGCCTCTTCAATGCTTCCT 59.241 45.455 0.00 0.00 0.00 3.36
347 357 2.756760 TCAATGCCTCTTCAATGCTTCC 59.243 45.455 0.00 0.00 0.00 3.46
348 358 4.421948 CTTCAATGCCTCTTCAATGCTTC 58.578 43.478 0.00 0.00 0.00 3.86
349 359 3.368116 GCTTCAATGCCTCTTCAATGCTT 60.368 43.478 0.00 0.00 0.00 3.91
350 360 2.165845 GCTTCAATGCCTCTTCAATGCT 59.834 45.455 0.00 0.00 0.00 3.79
351 361 2.537401 GCTTCAATGCCTCTTCAATGC 58.463 47.619 0.00 0.00 0.00 3.56
362 372 0.108945 GCTTGTCCAGGCTTCAATGC 60.109 55.000 0.00 0.00 0.00 3.56
363 373 0.529378 GGCTTGTCCAGGCTTCAATG 59.471 55.000 1.30 0.00 45.03 2.82
364 374 2.967270 GGCTTGTCCAGGCTTCAAT 58.033 52.632 1.30 0.00 45.03 2.57
365 375 4.500265 GGCTTGTCCAGGCTTCAA 57.500 55.556 1.30 0.00 45.03 2.69
371 381 2.800250 AGAATCAAAGGCTTGTCCAGG 58.200 47.619 0.00 0.00 37.29 4.45
372 382 4.142513 GCTAAGAATCAAAGGCTTGTCCAG 60.143 45.833 0.00 0.00 37.29 3.86
415 587 3.208747 TCAGGTGGTTTGACTCTTTCC 57.791 47.619 0.00 0.00 0.00 3.13
453 625 4.699637 ACTTCACCGTAGAAAACACATGA 58.300 39.130 0.00 0.00 0.00 3.07
467 639 2.108514 ATGCATGCCGACTTCACCG 61.109 57.895 16.68 0.00 0.00 4.94
468 640 1.308069 ACATGCATGCCGACTTCACC 61.308 55.000 26.53 0.00 0.00 4.02
507 711 1.561542 CTGGGTGGATTTCTAGTGCCT 59.438 52.381 0.00 0.00 0.00 4.75
553 763 1.446907 CTGCATCACTCAGGGTTGTC 58.553 55.000 0.00 0.00 0.00 3.18
572 782 2.338577 ATTGGTGTCTCTGCATAGCC 57.661 50.000 0.00 0.00 0.00 3.93
574 784 5.752472 CACTAGAATTGGTGTCTCTGCATAG 59.248 44.000 0.00 0.00 0.00 2.23
580 790 2.563179 ACGCACTAGAATTGGTGTCTCT 59.437 45.455 0.00 0.00 36.03 3.10
584 794 3.006537 ACTGTACGCACTAGAATTGGTGT 59.993 43.478 0.00 0.00 36.03 4.16
587 797 4.740268 TGTACTGTACGCACTAGAATTGG 58.260 43.478 12.87 0.00 0.00 3.16
601 811 7.870445 TCACGTACGGTATGTATATGTACTGTA 59.130 37.037 21.06 11.92 40.09 2.74
602 812 6.705825 TCACGTACGGTATGTATATGTACTGT 59.294 38.462 21.06 13.32 41.77 3.55
603 813 7.011773 GTCACGTACGGTATGTATATGTACTG 58.988 42.308 21.06 2.65 35.02 2.74
604 814 6.705825 TGTCACGTACGGTATGTATATGTACT 59.294 38.462 21.06 0.00 35.02 2.73
607 817 6.375945 TTGTCACGTACGGTATGTATATGT 57.624 37.500 21.06 0.00 35.02 2.29
612 822 4.422840 CCATTTGTCACGTACGGTATGTA 58.577 43.478 21.06 0.93 0.00 2.29
697 910 5.491982 TCCTAAGGAGAAAATTGACTCAGC 58.508 41.667 12.18 0.00 35.17 4.26
711 924 8.484575 TCACGTCCTATATACTATCCTAAGGAG 58.515 40.741 0.00 0.00 34.05 3.69
784 1015 1.972588 AAATCACCTGCTACCTCCCT 58.027 50.000 0.00 0.00 0.00 4.20
814 1048 2.493713 ACATCAGTAGTCGCGAATCC 57.506 50.000 14.32 0.00 0.00 3.01
817 1051 3.754955 CACTTACATCAGTAGTCGCGAA 58.245 45.455 12.06 0.00 0.00 4.70
882 1116 2.036346 AGGCCAAGCAATTTGTCTTGTC 59.964 45.455 21.35 14.44 38.33 3.18
926 1160 1.589113 GCGGTTGCATGCCCTTTAA 59.411 52.632 16.68 0.00 42.15 1.52
936 1170 1.000607 GTCTATCTATCCGCGGTTGCA 60.001 52.381 27.15 5.72 42.97 4.08
955 1189 2.029288 CGATTGTCTGTGCGCCTGT 61.029 57.895 4.18 0.00 0.00 4.00
977 1211 6.822667 TCTCGTCAATAACTTGTAGTACCA 57.177 37.500 0.00 0.00 33.87 3.25
978 1212 6.696148 CCATCTCGTCAATAACTTGTAGTACC 59.304 42.308 0.00 0.00 33.87 3.34
979 1213 7.431668 GTCCATCTCGTCAATAACTTGTAGTAC 59.568 40.741 0.00 0.00 33.87 2.73
1230 1464 2.664436 CGTCACCTTTTCGCCGTCC 61.664 63.158 0.00 0.00 0.00 4.79
1269 1503 1.699083 TGAAAGAGTGATGCAGTGGGA 59.301 47.619 0.00 0.00 0.00 4.37
1279 1574 2.158310 TCCCCTGAGACTGAAAGAGTGA 60.158 50.000 0.00 0.00 37.43 3.41
1280 1575 2.028567 GTCCCCTGAGACTGAAAGAGTG 60.029 54.545 0.00 0.00 37.43 3.51
1353 1650 9.507280 CGCAAAATAAGTCTGATCATAAAACAT 57.493 29.630 0.00 0.00 0.00 2.71
1367 1673 7.796958 AATAAAGAGCAACGCAAAATAAGTC 57.203 32.000 0.00 0.00 0.00 3.01
1377 1683 4.155280 TGGTTTCCTAATAAAGAGCAACGC 59.845 41.667 0.00 0.00 0.00 4.84
1394 1700 6.877611 TTGGAAGTCATAGAAAGTGGTTTC 57.122 37.500 0.00 0.00 42.25 2.78
1418 1724 0.808755 TTGCGCGTCTCATCAGTCTA 59.191 50.000 8.43 0.00 0.00 2.59
1434 1740 1.730612 GAAGTTACACTAGGCCGTTGC 59.269 52.381 0.00 0.00 0.00 4.17
1438 1744 1.134788 CAGGGAAGTTACACTAGGCCG 60.135 57.143 0.00 0.00 0.00 6.13
1494 1800 8.241367 GGTACACAATTTCTTATTTCGATGGTT 58.759 33.333 0.00 0.00 0.00 3.67
1495 1801 7.610305 AGGTACACAATTTCTTATTTCGATGGT 59.390 33.333 0.00 0.00 0.00 3.55
1581 1890 9.831737 ATTGTGAGTAAATTTCTTTGATTCTCG 57.168 29.630 0.00 0.00 0.00 4.04
1640 1949 6.530181 GCTACCATTAGTTTTGTTATTGTGCC 59.470 38.462 0.00 0.00 0.00 5.01
1747 2056 4.603131 TGAAGATTGCCTGCTTAATCCTT 58.397 39.130 0.00 0.00 34.60 3.36
1865 2174 4.689071 TGCTACTGTAACCGGACATAATG 58.311 43.478 9.46 0.00 0.00 1.90
2341 2650 2.658422 CATGGCCACAACCTTGCC 59.342 61.111 8.16 0.00 45.56 4.52
2451 2760 2.052690 GCTAGGCGTCTCCCAGACA 61.053 63.158 0.00 0.00 45.30 3.41
2459 2768 2.043450 AGGAGCAGCTAGGCGTCT 60.043 61.111 0.00 0.00 39.27 4.18
2665 2977 1.283321 GGTTTCTCTCCTCCCTGCATT 59.717 52.381 0.00 0.00 0.00 3.56
2748 3060 6.360370 TGAGGTCTACTATAAATGGATGCC 57.640 41.667 0.00 0.00 0.00 4.40
2845 3157 6.554982 TCTGCCTATTGAGTACATCATTACCT 59.445 38.462 0.00 0.00 37.89 3.08
2846 3158 6.759272 TCTGCCTATTGAGTACATCATTACC 58.241 40.000 0.00 0.00 37.89 2.85
2856 3168 5.009710 CCGTTCAGTATCTGCCTATTGAGTA 59.990 44.000 0.00 0.00 0.00 2.59
2872 3184 2.360350 CTGCCATGCCCGTTCAGT 60.360 61.111 0.00 0.00 0.00 3.41
2900 3212 1.619654 CTTCCCCATGAACAAGCACA 58.380 50.000 0.00 0.00 0.00 4.57
2921 3233 2.605607 CCAGCACCACCCTCCATGA 61.606 63.158 0.00 0.00 0.00 3.07
2978 3290 2.014068 GCAAGGTCTATGCAGGTCACC 61.014 57.143 0.00 0.00 43.29 4.02
2999 3311 2.288025 GGGGTCTACGCCACTTCCA 61.288 63.158 11.06 0.00 46.98 3.53
3047 3359 0.811616 GGAGCGGCTTGTCATACTGG 60.812 60.000 2.97 0.00 0.00 4.00
3184 3496 6.542370 GTCCCTAATTATAAGCAGCTTCACAA 59.458 38.462 12.07 4.71 0.00 3.33
3185 3497 6.055588 GTCCCTAATTATAAGCAGCTTCACA 58.944 40.000 12.07 0.00 0.00 3.58
3186 3498 6.055588 TGTCCCTAATTATAAGCAGCTTCAC 58.944 40.000 12.07 0.00 0.00 3.18
3189 3501 6.488006 CACATGTCCCTAATTATAAGCAGCTT 59.512 38.462 13.46 13.46 0.00 3.74
3190 3502 6.000219 CACATGTCCCTAATTATAAGCAGCT 59.000 40.000 0.00 0.00 0.00 4.24
3191 3503 5.765182 ACACATGTCCCTAATTATAAGCAGC 59.235 40.000 0.00 0.00 0.00 5.25
3192 3504 7.426929 GACACATGTCCCTAATTATAAGCAG 57.573 40.000 0.00 0.00 39.07 4.24
3207 3519 1.539388 TCGCCATTTTGGACACATGTC 59.461 47.619 0.00 3.27 40.96 3.06
3208 3520 1.614996 TCGCCATTTTGGACACATGT 58.385 45.000 0.00 0.00 40.96 3.21
3209 3521 2.228582 TCTTCGCCATTTTGGACACATG 59.771 45.455 0.00 0.00 40.96 3.21
3210 3522 2.489329 CTCTTCGCCATTTTGGACACAT 59.511 45.455 0.00 0.00 40.96 3.21
3224 3536 3.184581 CCAAATCGCCTATAACTCTTCGC 59.815 47.826 0.00 0.00 0.00 4.70
3225 3537 4.369182 ACCAAATCGCCTATAACTCTTCG 58.631 43.478 0.00 0.00 0.00 3.79
3257 3569 8.792633 ACCTGAAATTCGATCAAAATGAGTTTA 58.207 29.630 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.