Multiple sequence alignment - TraesCS5D01G242700

Loading Multiple Alignment...

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 TraesCS5D01G242700 chr5D 100.000 3367 0 0 1 3367 351001125 350997759 0.000000e+00 6218.0
1 TraesCS5D01G242700 chr5B 94.001 2934 112 13 398 3294 411815822 411812916 0.000000e+00 4385.0
2 TraesCS5D01G242700 chr5B 91.163 215 17 2 49 262 411816087 411815874 1.180000e-74 291.0
3 TraesCS5D01G242700 chr5B 100.000 51 0 0 1 51 411816158 411816108 9.950000e-16 95.3
4 TraesCS5D01G242700 chr5A 95.619 1438 55 5 1936 3367 451468649 451467214 0.000000e+00 2300.0
5 TraesCS5D01G242700 chr5A 92.320 1237 52 15 687 1884 451469898 451468666 0.000000e+00 1718.0


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 TraesCS5D01G242700 chr5D 350997759 351001125 3366 True 6218.000000 6218 100.000000 1 3367 1 chr5D.!!$R1 3366
1 TraesCS5D01G242700 chr5B 411812916 411816158 3242 True 1590.433333 4385 95.054667 1 3294 3 chr5B.!!$R1 3293
2 TraesCS5D01G242700 chr5A 451467214 451469898 2684 True 2009.000000 2300 93.969500 687 3367 2 chr5A.!!$R1 2680

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
276 301 0.030101 CATCTTCGAGAGACCGAGCC 59.970 60.0 0.35 0.0 41.84 4.70 F
313 338 0.108709 CCATGGAAATGTTGCCACGG 60.109 55.0 5.56 0.0 36.92 4.94 F
1249 1314 0.179018 GGGCATAACAGGTAGGCAGG 60.179 60.0 4.19 0.0 41.39 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1970 0.106819 AGATCATCAGGCCAACCAGC 60.107 55.0 5.01 0.0 39.06 4.85 R
2159 2248 1.009829 CTTCTGGGCGTTGCATACTC 58.990 55.0 0.00 0.0 0.00 2.59 R
2789 2881 0.684535 TCAATGCACTTCTCCGGTCA 59.315 50.0 0.00 0.0 0.00 4.02 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
53 77 0.393537 CCTCCACATCCTGGACTTGC 60.394 60.000 0.00 0.00 44.99 4.01
66 90 2.155279 GGACTTGCTTCTCCCTGTTTC 58.845 52.381 0.00 0.00 0.00 2.78
110 134 4.349365 TGTCCAAGGAGAAAACAAAAGGT 58.651 39.130 0.00 0.00 0.00 3.50
112 136 3.630312 TCCAAGGAGAAAACAAAAGGTCG 59.370 43.478 0.00 0.00 0.00 4.79
114 138 3.292492 AGGAGAAAACAAAAGGTCGGT 57.708 42.857 0.00 0.00 0.00 4.69
138 163 4.849111 TTGTGCCGTGAAAATGAAAAAC 57.151 36.364 0.00 0.00 0.00 2.43
146 171 5.164196 CCGTGAAAATGAAAAACTGTATGCG 60.164 40.000 0.00 0.00 0.00 4.73
147 172 5.398122 CGTGAAAATGAAAAACTGTATGCGT 59.602 36.000 0.00 0.00 0.00 5.24
213 238 2.104770 CTCACAACACGCGCACACAT 62.105 55.000 5.73 0.00 0.00 3.21
214 239 1.298264 CACAACACGCGCACACATT 60.298 52.632 5.73 0.00 0.00 2.71
217 242 0.385849 CAACACGCGCACACATTCAT 60.386 50.000 5.73 0.00 0.00 2.57
222 247 2.539688 CACGCGCACACATTCATATACT 59.460 45.455 5.73 0.00 0.00 2.12
224 249 3.001228 ACGCGCACACATTCATATACTTG 59.999 43.478 5.73 0.00 0.00 3.16
239 264 2.399396 ACTTGTAAACACATGCACGC 57.601 45.000 0.00 0.00 0.00 5.34
251 276 0.767375 ATGCACGCAATCCTATCCCT 59.233 50.000 0.00 0.00 0.00 4.20
262 287 5.383476 CAATCCTATCCCTTTGAGCATCTT 58.617 41.667 0.00 0.00 34.92 2.40
264 289 3.070159 TCCTATCCCTTTGAGCATCTTCG 59.930 47.826 0.00 0.00 34.92 3.79
265 290 3.070159 CCTATCCCTTTGAGCATCTTCGA 59.930 47.826 0.00 0.00 34.92 3.71
266 291 2.680312 TCCCTTTGAGCATCTTCGAG 57.320 50.000 0.00 0.00 34.92 4.04
267 292 2.179427 TCCCTTTGAGCATCTTCGAGA 58.821 47.619 0.00 0.00 34.92 4.04
268 293 2.167281 TCCCTTTGAGCATCTTCGAGAG 59.833 50.000 0.00 0.00 34.92 3.20
269 294 2.167281 CCCTTTGAGCATCTTCGAGAGA 59.833 50.000 0.79 0.79 39.13 3.10
270 295 3.186119 CCTTTGAGCATCTTCGAGAGAC 58.814 50.000 0.35 0.00 41.84 3.36
271 296 2.949451 TTGAGCATCTTCGAGAGACC 57.051 50.000 0.35 0.00 41.84 3.85
272 297 0.735471 TGAGCATCTTCGAGAGACCG 59.265 55.000 0.35 0.00 41.84 4.79
273 298 1.018148 GAGCATCTTCGAGAGACCGA 58.982 55.000 0.35 0.00 41.84 4.69
274 299 1.002900 GAGCATCTTCGAGAGACCGAG 60.003 57.143 0.35 0.00 41.84 4.63
275 300 0.593773 GCATCTTCGAGAGACCGAGC 60.594 60.000 0.35 0.00 41.84 5.03
276 301 0.030101 CATCTTCGAGAGACCGAGCC 59.970 60.000 0.35 0.00 41.84 4.70
277 302 0.394488 ATCTTCGAGAGACCGAGCCA 60.394 55.000 0.35 0.00 41.84 4.75
278 303 1.027255 TCTTCGAGAGACCGAGCCAG 61.027 60.000 0.00 0.00 41.84 4.85
279 304 1.002502 TTCGAGAGACCGAGCCAGA 60.003 57.895 0.00 0.00 41.84 3.86
280 305 0.394488 TTCGAGAGACCGAGCCAGAT 60.394 55.000 0.00 0.00 41.84 2.90
281 306 0.468648 TCGAGAGACCGAGCCAGATA 59.531 55.000 0.00 0.00 34.19 1.98
282 307 0.589223 CGAGAGACCGAGCCAGATAC 59.411 60.000 0.00 0.00 0.00 2.24
283 308 0.589223 GAGAGACCGAGCCAGATACG 59.411 60.000 0.00 0.00 0.00 3.06
297 322 4.574828 GCCAGATACGTAATTGTTCACCAT 59.425 41.667 0.00 0.00 0.00 3.55
304 329 5.708948 ACGTAATTGTTCACCATGGAAATG 58.291 37.500 21.47 6.62 0.00 2.32
306 331 6.155827 CGTAATTGTTCACCATGGAAATGTT 58.844 36.000 21.47 10.42 0.00 2.71
307 332 6.089283 CGTAATTGTTCACCATGGAAATGTTG 59.911 38.462 21.47 4.91 0.00 3.33
308 333 3.383620 TGTTCACCATGGAAATGTTGC 57.616 42.857 21.47 2.43 0.00 4.17
309 334 2.036992 TGTTCACCATGGAAATGTTGCC 59.963 45.455 21.47 0.00 0.00 4.52
310 335 2.006805 TCACCATGGAAATGTTGCCA 57.993 45.000 21.47 0.00 38.78 4.92
311 336 1.617850 TCACCATGGAAATGTTGCCAC 59.382 47.619 21.47 0.00 36.92 5.01
312 337 0.602562 ACCATGGAAATGTTGCCACG 59.397 50.000 21.47 0.00 36.92 4.94
313 338 0.108709 CCATGGAAATGTTGCCACGG 60.109 55.000 5.56 0.00 36.92 4.94
314 339 0.887247 CATGGAAATGTTGCCACGGA 59.113 50.000 0.00 0.00 36.92 4.69
315 340 1.271934 CATGGAAATGTTGCCACGGAA 59.728 47.619 0.00 0.00 36.92 4.30
316 341 1.403814 TGGAAATGTTGCCACGGAAA 58.596 45.000 0.00 0.00 0.00 3.13
317 342 1.967066 TGGAAATGTTGCCACGGAAAT 59.033 42.857 0.00 0.00 0.00 2.17
318 343 2.366916 TGGAAATGTTGCCACGGAAATT 59.633 40.909 0.00 0.00 0.00 1.82
319 344 3.181461 TGGAAATGTTGCCACGGAAATTT 60.181 39.130 0.00 0.00 0.00 1.82
320 345 3.186205 GGAAATGTTGCCACGGAAATTTG 59.814 43.478 0.00 0.00 0.00 2.32
321 346 3.467374 AATGTTGCCACGGAAATTTGT 57.533 38.095 0.00 0.00 0.00 2.83
322 347 4.592485 AATGTTGCCACGGAAATTTGTA 57.408 36.364 0.00 0.00 0.00 2.41
323 348 3.357166 TGTTGCCACGGAAATTTGTAC 57.643 42.857 0.00 0.00 0.00 2.90
324 349 2.952978 TGTTGCCACGGAAATTTGTACT 59.047 40.909 0.00 0.00 0.00 2.73
325 350 4.135306 TGTTGCCACGGAAATTTGTACTA 58.865 39.130 0.00 0.00 0.00 1.82
326 351 4.023878 TGTTGCCACGGAAATTTGTACTAC 60.024 41.667 0.00 0.00 0.00 2.73
327 352 3.741249 TGCCACGGAAATTTGTACTACA 58.259 40.909 0.00 0.00 0.00 2.74
328 353 4.328536 TGCCACGGAAATTTGTACTACAT 58.671 39.130 0.00 0.00 0.00 2.29
329 354 4.393680 TGCCACGGAAATTTGTACTACATC 59.606 41.667 0.00 0.00 0.00 3.06
330 355 4.201881 GCCACGGAAATTTGTACTACATCC 60.202 45.833 0.00 0.00 0.00 3.51
331 356 4.938832 CCACGGAAATTTGTACTACATCCA 59.061 41.667 0.00 0.00 0.00 3.41
351 376 8.150945 ACATCCATACTTCATCCTACAATGTAC 58.849 37.037 0.00 0.00 0.00 2.90
352 377 7.914427 TCCATACTTCATCCTACAATGTACT 57.086 36.000 0.00 0.00 0.00 2.73
353 378 9.601810 ATCCATACTTCATCCTACAATGTACTA 57.398 33.333 0.00 0.00 0.00 1.82
354 379 9.078990 TCCATACTTCATCCTACAATGTACTAG 57.921 37.037 0.00 0.00 0.00 2.57
355 380 8.861086 CCATACTTCATCCTACAATGTACTAGT 58.139 37.037 0.00 0.00 0.00 2.57
358 383 8.596781 ACTTCATCCTACAATGTACTAGTTCT 57.403 34.615 0.00 0.00 0.00 3.01
359 384 8.470805 ACTTCATCCTACAATGTACTAGTTCTG 58.529 37.037 0.00 0.00 0.00 3.02
360 385 7.956328 TCATCCTACAATGTACTAGTTCTGT 57.044 36.000 0.00 0.00 0.00 3.41
361 386 9.470399 TTCATCCTACAATGTACTAGTTCTGTA 57.530 33.333 0.00 1.25 0.00 2.74
362 387 9.642343 TCATCCTACAATGTACTAGTTCTGTAT 57.358 33.333 0.00 0.00 0.00 2.29
389 414 8.940768 TTTTCTTCTTTGGAATTTGTACAAGG 57.059 30.769 8.56 0.00 0.00 3.61
390 415 7.654022 TTCTTCTTTGGAATTTGTACAAGGT 57.346 32.000 8.56 0.43 0.00 3.50
391 416 8.754991 TTCTTCTTTGGAATTTGTACAAGGTA 57.245 30.769 8.56 0.00 0.00 3.08
392 417 8.754991 TCTTCTTTGGAATTTGTACAAGGTAA 57.245 30.769 8.56 0.00 0.00 2.85
393 418 8.626526 TCTTCTTTGGAATTTGTACAAGGTAAC 58.373 33.333 8.56 1.00 0.00 2.50
394 419 7.883391 TCTTTGGAATTTGTACAAGGTAACA 57.117 32.000 8.56 3.54 41.41 2.41
395 420 8.472007 TCTTTGGAATTTGTACAAGGTAACAT 57.528 30.769 8.56 0.00 41.41 2.71
396 421 8.356657 TCTTTGGAATTTGTACAAGGTAACATG 58.643 33.333 8.56 0.00 42.18 3.21
412 437 2.057922 ACATGGTCTTTGTCCCAGACT 58.942 47.619 0.00 0.00 40.60 3.24
428 453 4.160626 CCCAGACTAAGTTGGACTAAGAGG 59.839 50.000 0.00 0.00 36.55 3.69
439 464 5.916661 TGGACTAAGAGGATTACACACTC 57.083 43.478 0.00 0.00 0.00 3.51
445 470 9.303537 GACTAAGAGGATTACACACTCATTAAC 57.696 37.037 0.00 0.00 33.76 2.01
446 471 9.036980 ACTAAGAGGATTACACACTCATTAACT 57.963 33.333 0.00 0.00 33.76 2.24
453 478 7.716998 GGATTACACACTCATTAACTGGATCAT 59.283 37.037 0.00 0.00 0.00 2.45
476 501 4.907269 TCATATGGCCTAGGTTCAGATTGA 59.093 41.667 11.31 10.39 0.00 2.57
486 511 8.568794 GCCTAGGTTCAGATTGATTTAATTACC 58.431 37.037 11.31 0.00 0.00 2.85
506 531 3.118223 ACCTGCATTCCCTAGAAGCTAAC 60.118 47.826 0.00 0.00 34.86 2.34
529 554 3.610911 AGGGCTTAAAAGTCAAGATCCG 58.389 45.455 0.00 0.00 30.55 4.18
591 616 1.339055 TGCTGAGTAGGGCAACACATC 60.339 52.381 0.00 0.00 35.40 3.06
610 635 1.499007 TCTGCCTCCTGGTTTCCTTTT 59.501 47.619 0.00 0.00 35.27 2.27
682 711 5.599999 TCCTTCAGGAATGCTTAGTACTC 57.400 43.478 0.00 0.00 42.18 2.59
745 774 2.198827 ATTCACATTCCGTCCAAGCA 57.801 45.000 0.00 0.00 0.00 3.91
834 893 1.432807 TCCCCTTTCCTTTCCATTGCT 59.567 47.619 0.00 0.00 0.00 3.91
853 912 1.827344 CTCCCTTTTCTGGCCAATTCC 59.173 52.381 7.01 0.00 0.00 3.01
885 944 0.340208 TCCTTTCTCCTCCCCTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
1056 1121 0.814457 ACGAGTGCAGAGAGATCCAC 59.186 55.000 0.00 0.00 0.00 4.02
1059 1124 0.323816 AGTGCAGAGAGATCCACGGA 60.324 55.000 0.00 0.00 33.62 4.69
1062 1127 1.670949 GCAGAGAGATCCACGGAGCA 61.671 60.000 3.85 0.00 32.23 4.26
1216 1281 5.424757 CCAATCAGGACAACGAGGTAATAA 58.575 41.667 0.00 0.00 41.22 1.40
1217 1282 6.055588 CCAATCAGGACAACGAGGTAATAAT 58.944 40.000 0.00 0.00 41.22 1.28
1218 1283 7.214381 CCAATCAGGACAACGAGGTAATAATA 58.786 38.462 0.00 0.00 41.22 0.98
1249 1314 0.179018 GGGCATAACAGGTAGGCAGG 60.179 60.000 4.19 0.00 41.39 4.85
1358 1435 2.278792 CGAGACGCGATCATGGCA 60.279 61.111 15.93 0.00 44.57 4.92
1532 1609 3.658709 GCACCCTTATCAGAGAGTATGC 58.341 50.000 0.00 0.00 0.00 3.14
1539 1621 2.836636 TCAGAGAGTATGCCTGTCCT 57.163 50.000 0.00 0.00 33.98 3.85
1540 1622 3.953542 TCAGAGAGTATGCCTGTCCTA 57.046 47.619 0.00 0.00 33.98 2.94
1541 1623 4.461450 TCAGAGAGTATGCCTGTCCTAT 57.539 45.455 0.00 0.00 33.98 2.57
1542 1624 4.402829 TCAGAGAGTATGCCTGTCCTATC 58.597 47.826 0.00 0.00 33.98 2.08
1543 1625 3.509575 CAGAGAGTATGCCTGTCCTATCC 59.490 52.174 0.00 0.00 33.98 2.59
1547 1629 1.348036 GTATGCCTGTCCTATCCACCC 59.652 57.143 0.00 0.00 0.00 4.61
1563 1645 0.252103 ACCCCCTGCTTCTCGTTCTA 60.252 55.000 0.00 0.00 0.00 2.10
1571 1653 3.318017 TGCTTCTCGTTCTAGTTTCAGC 58.682 45.455 0.00 0.00 0.00 4.26
1574 1656 3.299340 TCTCGTTCTAGTTTCAGCCAC 57.701 47.619 0.00 0.00 0.00 5.01
1624 1707 0.537371 CTCACTCCTTGCCGGGTTTT 60.537 55.000 2.18 0.00 0.00 2.43
1887 1970 0.323178 AAGCAGACTCAATGGCCTGG 60.323 55.000 3.32 0.00 0.00 4.45
1913 1996 2.763039 TGGCCTGATGATCTCCACTTA 58.237 47.619 3.32 0.00 0.00 2.24
1916 1999 3.118261 GGCCTGATGATCTCCACTTAACA 60.118 47.826 0.00 0.00 0.00 2.41
1917 2000 4.125703 GCCTGATGATCTCCACTTAACAG 58.874 47.826 0.00 0.00 0.00 3.16
1918 2001 4.141846 GCCTGATGATCTCCACTTAACAGA 60.142 45.833 0.00 0.00 0.00 3.41
1928 2011 4.703897 TCCACTTAACAGAAGAACACTGG 58.296 43.478 0.00 0.00 39.38 4.00
1933 2016 5.585047 ACTTAACAGAAGAACACTGGTGAAC 59.415 40.000 7.78 1.56 39.38 3.18
1961 2048 4.338964 TGGCCAATCATGAATGTGTATGTC 59.661 41.667 0.61 0.00 0.00 3.06
1990 2077 2.560105 ACTGAAGAAGAATTTGGCTGGC 59.440 45.455 0.00 0.00 0.00 4.85
2053 2140 6.952358 TCTACACTCCTTCCAAGTATTACTGT 59.048 38.462 0.00 0.00 0.00 3.55
2084 2172 2.047679 CAGAAAGCAAGCAGTTCTGC 57.952 50.000 18.99 15.88 41.16 4.26
2131 2220 4.026744 CTGGTCCCTGACTCATTCTTCTA 58.973 47.826 0.00 0.00 32.47 2.10
2159 2248 2.693069 CCTTGTCAGTTACTGCAGAGG 58.307 52.381 23.35 9.42 0.00 3.69
2162 2251 2.598565 TGTCAGTTACTGCAGAGGAGT 58.401 47.619 23.35 5.49 0.00 3.85
2180 2269 1.026718 GTATGCAACGCCCAGAAGCT 61.027 55.000 0.00 0.00 0.00 3.74
2264 2353 4.196971 AGTTGGCGTTCAAGAGTAACTTT 58.803 39.130 0.00 0.00 36.61 2.66
2444 2533 5.053145 CAGCAGTACCATCTTATCTGAACC 58.947 45.833 0.00 0.00 0.00 3.62
2474 2563 5.627182 AGGTGAGAACATGCTATCATTCT 57.373 39.130 0.00 0.00 0.00 2.40
2475 2564 6.737720 AGGTGAGAACATGCTATCATTCTA 57.262 37.500 0.00 0.00 0.00 2.10
2789 2881 9.775854 TTGGTATCAACAAAATTGATGAAACAT 57.224 25.926 9.68 0.00 42.11 2.71
2840 2933 1.060266 CTCAGCACGAGCAGATTTTCG 59.940 52.381 7.77 0.00 45.49 3.46
2903 2996 4.079253 GTGCAACTCCCTATTCAGGAAAA 58.921 43.478 0.00 0.00 45.91 2.29
2905 2998 5.185828 GTGCAACTCCCTATTCAGGAAAATT 59.814 40.000 0.00 0.00 45.91 1.82
3077 3170 3.117284 ACCACCAAACCCTTGTTATCACT 60.117 43.478 0.00 0.00 33.30 3.41
3132 3225 5.047164 TGCTTCTGATGTGGTAAATGCAAAT 60.047 36.000 0.00 0.00 0.00 2.32
3141 3234 3.900601 TGGTAAATGCAAATTGGTCCACT 59.099 39.130 0.00 0.00 0.00 4.00
3145 3238 4.789012 AATGCAAATTGGTCCACTGTAG 57.211 40.909 0.00 0.00 0.00 2.74
3238 3331 6.797033 CGGATACAAATGAGTCAAGAAAACAC 59.203 38.462 0.00 0.00 0.00 3.32
3331 3424 1.217183 AGGAAGCCTAGTGACGGGATA 59.783 52.381 2.11 0.00 28.47 2.59
3332 3425 1.340568 GGAAGCCTAGTGACGGGATAC 59.659 57.143 2.11 0.00 0.00 2.24
3363 3456 0.472044 TTCTACTGCCCTTGCACACA 59.528 50.000 0.00 0.00 44.23 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 77 7.448469 TCATAAAGAAAAGGAAACAGGGAGAAG 59.552 37.037 0.00 0.00 0.00 2.85
66 90 6.507023 ACAGTTGCAGTTCATAAAGAAAAGG 58.493 36.000 0.00 0.00 38.13 3.11
112 136 3.190874 TCATTTTCACGGCACAAAAACC 58.809 40.909 0.00 0.00 0.00 3.27
114 138 5.862924 TTTTCATTTTCACGGCACAAAAA 57.137 30.435 0.00 0.00 0.00 1.94
122 146 5.164196 CGCATACAGTTTTTCATTTTCACGG 60.164 40.000 0.00 0.00 0.00 4.94
126 150 8.502161 AGTTACGCATACAGTTTTTCATTTTC 57.498 30.769 0.00 0.00 0.00 2.29
138 163 0.928229 GCCGGAAGTTACGCATACAG 59.072 55.000 5.05 0.00 0.00 2.74
146 171 5.873164 TCAGAAAGAATAAGCCGGAAGTTAC 59.127 40.000 5.05 0.00 0.00 2.50
147 172 6.045072 TCAGAAAGAATAAGCCGGAAGTTA 57.955 37.500 5.05 0.00 0.00 2.24
213 238 7.460296 CGTGCATGTGTTTACAAGTATATGAA 58.540 34.615 0.00 0.00 40.84 2.57
214 239 6.456315 GCGTGCATGTGTTTACAAGTATATGA 60.456 38.462 7.93 0.00 40.84 2.15
217 242 4.691216 TGCGTGCATGTGTTTACAAGTATA 59.309 37.500 7.93 0.00 40.84 1.47
222 247 2.851805 TTGCGTGCATGTGTTTACAA 57.148 40.000 7.93 0.00 40.84 2.41
224 249 2.095263 AGGATTGCGTGCATGTGTTTAC 60.095 45.455 7.93 0.00 0.00 2.01
239 264 4.983053 AGATGCTCAAAGGGATAGGATTG 58.017 43.478 0.00 0.00 0.00 2.67
251 276 2.416027 CGGTCTCTCGAAGATGCTCAAA 60.416 50.000 0.00 0.00 36.11 2.69
262 287 0.468648 TATCTGGCTCGGTCTCTCGA 59.531 55.000 0.00 0.00 37.60 4.04
264 289 0.589223 CGTATCTGGCTCGGTCTCTC 59.411 60.000 0.00 0.00 0.00 3.20
265 290 0.107116 ACGTATCTGGCTCGGTCTCT 60.107 55.000 0.00 0.00 0.00 3.10
266 291 1.590932 TACGTATCTGGCTCGGTCTC 58.409 55.000 0.00 0.00 0.00 3.36
267 292 2.048444 TTACGTATCTGGCTCGGTCT 57.952 50.000 0.00 0.00 0.00 3.85
268 293 3.050619 CAATTACGTATCTGGCTCGGTC 58.949 50.000 0.00 0.00 0.00 4.79
269 294 2.429610 ACAATTACGTATCTGGCTCGGT 59.570 45.455 0.00 0.00 0.00 4.69
270 295 3.093717 ACAATTACGTATCTGGCTCGG 57.906 47.619 0.00 0.00 0.00 4.63
271 296 4.026804 GTGAACAATTACGTATCTGGCTCG 60.027 45.833 0.00 0.00 0.00 5.03
272 297 4.270325 GGTGAACAATTACGTATCTGGCTC 59.730 45.833 0.00 0.00 0.00 4.70
273 298 4.189231 GGTGAACAATTACGTATCTGGCT 58.811 43.478 0.00 0.00 0.00 4.75
274 299 3.936453 TGGTGAACAATTACGTATCTGGC 59.064 43.478 0.00 0.00 0.00 4.85
275 300 5.007626 CCATGGTGAACAATTACGTATCTGG 59.992 44.000 2.57 0.00 0.00 3.86
276 301 5.815222 TCCATGGTGAACAATTACGTATCTG 59.185 40.000 12.58 0.00 0.00 2.90
277 302 5.984725 TCCATGGTGAACAATTACGTATCT 58.015 37.500 12.58 0.00 0.00 1.98
278 303 6.671614 TTCCATGGTGAACAATTACGTATC 57.328 37.500 12.58 0.00 0.00 2.24
279 304 7.122055 ACATTTCCATGGTGAACAATTACGTAT 59.878 33.333 12.58 0.00 34.27 3.06
280 305 6.431543 ACATTTCCATGGTGAACAATTACGTA 59.568 34.615 12.58 0.00 34.27 3.57
281 306 5.242838 ACATTTCCATGGTGAACAATTACGT 59.757 36.000 12.58 0.00 34.27 3.57
282 307 5.708948 ACATTTCCATGGTGAACAATTACG 58.291 37.500 12.58 0.00 34.27 3.18
304 329 3.636282 AGTACAAATTTCCGTGGCAAC 57.364 42.857 0.00 0.00 0.00 4.17
306 331 3.741249 TGTAGTACAAATTTCCGTGGCA 58.259 40.909 0.00 0.00 0.00 4.92
307 332 4.201881 GGATGTAGTACAAATTTCCGTGGC 60.202 45.833 7.16 0.00 0.00 5.01
308 333 4.938832 TGGATGTAGTACAAATTTCCGTGG 59.061 41.667 7.16 0.00 28.59 4.94
309 334 6.677781 ATGGATGTAGTACAAATTTCCGTG 57.322 37.500 12.59 0.00 28.59 4.94
310 335 7.562135 AGTATGGATGTAGTACAAATTTCCGT 58.438 34.615 16.13 16.13 28.59 4.69
311 336 8.433421 AAGTATGGATGTAGTACAAATTTCCG 57.567 34.615 7.16 0.00 28.59 4.30
312 337 9.391006 TGAAGTATGGATGTAGTACAAATTTCC 57.609 33.333 7.16 10.12 0.00 3.13
315 340 9.561069 GGATGAAGTATGGATGTAGTACAAATT 57.439 33.333 7.16 0.00 0.00 1.82
316 341 8.938883 AGGATGAAGTATGGATGTAGTACAAAT 58.061 33.333 7.16 4.62 0.00 2.32
317 342 8.319057 AGGATGAAGTATGGATGTAGTACAAA 57.681 34.615 7.16 0.00 0.00 2.83
318 343 7.914427 AGGATGAAGTATGGATGTAGTACAA 57.086 36.000 7.16 0.00 0.00 2.41
319 344 8.002459 TGTAGGATGAAGTATGGATGTAGTACA 58.998 37.037 5.24 5.24 0.00 2.90
320 345 8.405418 TGTAGGATGAAGTATGGATGTAGTAC 57.595 38.462 0.00 0.00 0.00 2.73
321 346 9.601810 ATTGTAGGATGAAGTATGGATGTAGTA 57.398 33.333 0.00 0.00 0.00 1.82
322 347 7.914427 TTGTAGGATGAAGTATGGATGTAGT 57.086 36.000 0.00 0.00 0.00 2.73
323 348 8.370940 ACATTGTAGGATGAAGTATGGATGTAG 58.629 37.037 0.00 0.00 0.00 2.74
324 349 8.262601 ACATTGTAGGATGAAGTATGGATGTA 57.737 34.615 0.00 0.00 0.00 2.29
325 350 7.141758 ACATTGTAGGATGAAGTATGGATGT 57.858 36.000 0.00 0.00 0.00 3.06
326 351 8.370940 AGTACATTGTAGGATGAAGTATGGATG 58.629 37.037 0.00 0.00 0.00 3.51
327 352 8.497910 AGTACATTGTAGGATGAAGTATGGAT 57.502 34.615 0.00 0.00 0.00 3.41
328 353 7.914427 AGTACATTGTAGGATGAAGTATGGA 57.086 36.000 0.00 0.00 0.00 3.41
329 354 8.861086 ACTAGTACATTGTAGGATGAAGTATGG 58.139 37.037 0.00 0.00 0.00 2.74
363 388 9.377312 CCTTGTACAAATTCCAAAGAAGAAAAA 57.623 29.630 10.03 0.00 34.86 1.94
364 389 8.536175 ACCTTGTACAAATTCCAAAGAAGAAAA 58.464 29.630 10.03 0.00 34.86 2.29
365 390 8.073467 ACCTTGTACAAATTCCAAAGAAGAAA 57.927 30.769 10.03 0.00 34.86 2.52
366 391 7.654022 ACCTTGTACAAATTCCAAAGAAGAA 57.346 32.000 10.03 0.00 34.86 2.52
367 392 8.626526 GTTACCTTGTACAAATTCCAAAGAAGA 58.373 33.333 10.03 0.00 34.86 2.87
368 393 8.410141 TGTTACCTTGTACAAATTCCAAAGAAG 58.590 33.333 10.03 0.00 34.86 2.85
369 394 8.294954 TGTTACCTTGTACAAATTCCAAAGAA 57.705 30.769 10.03 0.00 36.15 2.52
370 395 7.883391 TGTTACCTTGTACAAATTCCAAAGA 57.117 32.000 10.03 0.00 0.00 2.52
371 396 7.598493 CCATGTTACCTTGTACAAATTCCAAAG 59.402 37.037 10.03 0.00 0.00 2.77
372 397 7.070074 ACCATGTTACCTTGTACAAATTCCAAA 59.930 33.333 10.03 0.00 0.00 3.28
373 398 6.551601 ACCATGTTACCTTGTACAAATTCCAA 59.448 34.615 10.03 0.00 0.00 3.53
374 399 6.071984 ACCATGTTACCTTGTACAAATTCCA 58.928 36.000 10.03 3.75 0.00 3.53
375 400 6.433093 AGACCATGTTACCTTGTACAAATTCC 59.567 38.462 10.03 0.00 0.00 3.01
376 401 7.448748 AGACCATGTTACCTTGTACAAATTC 57.551 36.000 10.03 0.20 0.00 2.17
377 402 7.833285 AAGACCATGTTACCTTGTACAAATT 57.167 32.000 10.03 1.90 0.00 1.82
378 403 7.286775 ACAAAGACCATGTTACCTTGTACAAAT 59.713 33.333 10.03 3.59 0.00 2.32
379 404 6.603997 ACAAAGACCATGTTACCTTGTACAAA 59.396 34.615 10.03 0.00 0.00 2.83
380 405 6.123651 ACAAAGACCATGTTACCTTGTACAA 58.876 36.000 8.28 8.28 0.00 2.41
381 406 5.686753 ACAAAGACCATGTTACCTTGTACA 58.313 37.500 0.00 0.00 0.00 2.90
382 407 5.180680 GGACAAAGACCATGTTACCTTGTAC 59.819 44.000 0.00 0.00 0.00 2.90
383 408 5.310451 GGACAAAGACCATGTTACCTTGTA 58.690 41.667 0.00 0.00 0.00 2.41
384 409 4.142038 GGACAAAGACCATGTTACCTTGT 58.858 43.478 0.00 0.00 0.00 3.16
385 410 3.506067 GGGACAAAGACCATGTTACCTTG 59.494 47.826 0.00 0.00 0.00 3.61
386 411 3.139397 TGGGACAAAGACCATGTTACCTT 59.861 43.478 0.00 0.00 31.92 3.50
387 412 2.714250 TGGGACAAAGACCATGTTACCT 59.286 45.455 0.00 0.00 31.92 3.08
388 413 3.081804 CTGGGACAAAGACCATGTTACC 58.918 50.000 0.00 0.00 38.70 2.85
389 414 3.751698 GTCTGGGACAAAGACCATGTTAC 59.248 47.826 0.00 0.00 38.70 2.50
390 415 3.650942 AGTCTGGGACAAAGACCATGTTA 59.349 43.478 0.11 0.00 44.27 2.41
391 416 2.443255 AGTCTGGGACAAAGACCATGTT 59.557 45.455 0.11 0.00 44.27 2.71
392 417 2.057922 AGTCTGGGACAAAGACCATGT 58.942 47.619 0.11 0.00 44.27 3.21
393 418 2.867109 AGTCTGGGACAAAGACCATG 57.133 50.000 0.11 0.00 44.27 3.66
394 419 3.910627 ACTTAGTCTGGGACAAAGACCAT 59.089 43.478 0.11 0.00 44.27 3.55
395 420 3.314693 ACTTAGTCTGGGACAAAGACCA 58.685 45.455 0.11 0.00 44.27 4.02
396 421 4.065789 CAACTTAGTCTGGGACAAAGACC 58.934 47.826 0.11 0.00 44.27 3.85
412 437 7.453752 AGTGTGTAATCCTCTTAGTCCAACTTA 59.546 37.037 0.00 0.00 0.00 2.24
428 453 8.668510 ATGATCCAGTTAATGAGTGTGTAATC 57.331 34.615 0.00 0.00 0.00 1.75
439 464 6.185511 AGGCCATATGATGATCCAGTTAATG 58.814 40.000 5.01 0.00 0.00 1.90
445 470 3.779183 ACCTAGGCCATATGATGATCCAG 59.221 47.826 9.30 0.00 0.00 3.86
446 471 3.806975 ACCTAGGCCATATGATGATCCA 58.193 45.455 9.30 0.00 0.00 3.41
453 478 4.907269 TCAATCTGAACCTAGGCCATATGA 59.093 41.667 9.30 8.91 0.00 2.15
476 501 7.231519 GCTTCTAGGGAATGCAGGTAATTAAAT 59.768 37.037 0.00 0.00 0.00 1.40
486 511 4.142609 TGTTAGCTTCTAGGGAATGCAG 57.857 45.455 0.00 0.00 32.26 4.41
506 531 4.142600 CGGATCTTGACTTTTAAGCCCTTG 60.143 45.833 0.00 0.00 0.00 3.61
529 554 2.202479 GGTTTTCGGCGCTCATGC 60.202 61.111 7.64 0.00 0.00 4.06
591 616 1.889170 GAAAAGGAAACCAGGAGGCAG 59.111 52.381 0.00 0.00 39.06 4.85
610 635 8.547967 AATTTAGTCAGAAAAGTAAGCGATGA 57.452 30.769 0.00 0.00 0.00 2.92
682 711 3.766068 AGTCATGTCCTATGATGGCAG 57.234 47.619 0.00 0.00 0.00 4.85
834 893 1.148867 TGGAATTGGCCAGAAAAGGGA 59.851 47.619 5.11 0.00 33.10 4.20
853 912 6.821160 GGAGGAGAAAGGAAGAAAGTTATCTG 59.179 42.308 0.00 0.00 0.00 2.90
885 944 5.467035 TGTTCTTGGCTTCCTTTTAATGG 57.533 39.130 0.00 0.00 0.00 3.16
954 1013 1.069227 GGCTTTCGATGTGTGAACCAC 60.069 52.381 0.00 0.00 44.78 4.16
1035 1100 1.474478 TGGATCTCTCTGCACTCGTTC 59.526 52.381 0.00 0.00 0.00 3.95
1216 1281 7.839200 ACCTGTTATGCCCTTTGTTTATCTTAT 59.161 33.333 0.00 0.00 0.00 1.73
1217 1282 7.179269 ACCTGTTATGCCCTTTGTTTATCTTA 58.821 34.615 0.00 0.00 0.00 2.10
1218 1283 6.016555 ACCTGTTATGCCCTTTGTTTATCTT 58.983 36.000 0.00 0.00 0.00 2.40
1358 1435 3.082579 GCTCTCGATGGCGTCCCTT 62.083 63.158 0.14 0.00 38.98 3.95
1532 1609 1.056700 CAGGGGGTGGATAGGACAGG 61.057 65.000 0.00 0.00 0.00 4.00
1539 1621 1.048724 CGAGAAGCAGGGGGTGGATA 61.049 60.000 0.00 0.00 0.00 2.59
1540 1622 2.370445 CGAGAAGCAGGGGGTGGAT 61.370 63.158 0.00 0.00 0.00 3.41
1541 1623 3.003173 CGAGAAGCAGGGGGTGGA 61.003 66.667 0.00 0.00 0.00 4.02
1542 1624 2.804828 GAACGAGAAGCAGGGGGTGG 62.805 65.000 0.00 0.00 0.00 4.61
1543 1625 1.376037 GAACGAGAAGCAGGGGGTG 60.376 63.158 0.00 0.00 0.00 4.61
1547 1629 3.254892 GAAACTAGAACGAGAAGCAGGG 58.745 50.000 0.00 0.00 0.00 4.45
1563 1645 2.618709 CGGAAGAAAAGTGGCTGAAACT 59.381 45.455 0.00 0.00 0.00 2.66
1571 1653 4.522722 AGTAGAGACGGAAGAAAAGTGG 57.477 45.455 0.00 0.00 0.00 4.00
1574 1656 5.710984 TGCTAAGTAGAGACGGAAGAAAAG 58.289 41.667 0.00 0.00 0.00 2.27
1624 1707 1.393603 CTGCTCAGACCACGATAGGA 58.606 55.000 0.00 0.00 43.77 2.94
1832 1915 5.122869 GTCATGCCCATATATGTGCTTGTAG 59.877 44.000 24.91 11.29 37.50 2.74
1873 1956 1.751927 CCAGCCAGGCCATTGAGTC 60.752 63.158 8.22 0.00 0.00 3.36
1887 1970 0.106819 AGATCATCAGGCCAACCAGC 60.107 55.000 5.01 0.00 39.06 4.85
1913 1996 3.054361 AGGTTCACCAGTGTTCTTCTGTT 60.054 43.478 0.00 0.00 38.89 3.16
1916 1999 3.041946 AGAGGTTCACCAGTGTTCTTCT 58.958 45.455 0.00 1.71 38.89 2.85
1917 2000 3.477210 AGAGGTTCACCAGTGTTCTTC 57.523 47.619 0.00 0.00 38.89 2.87
1918 2001 3.545703 CAAGAGGTTCACCAGTGTTCTT 58.454 45.455 0.00 0.00 38.89 2.52
1928 2011 1.909700 TGATTGGCCAAGAGGTTCAC 58.090 50.000 24.94 7.82 37.19 3.18
1933 2016 3.028850 ACATTCATGATTGGCCAAGAGG 58.971 45.455 24.94 14.46 38.23 3.69
1961 2048 1.888215 TTCTTCTTCAGTGCCTGCAG 58.112 50.000 6.78 6.78 0.00 4.41
1990 2077 5.708948 ACTCTCAGAGACTCTTCAAAATCG 58.291 41.667 9.27 0.00 33.32 3.34
2053 2140 4.396166 GCTTGCTTTCTGCTATTCACCTTA 59.604 41.667 0.00 0.00 43.37 2.69
2064 2151 2.047679 CAGAACTGCTTGCTTTCTGC 57.952 50.000 17.76 0.00 39.75 4.26
2080 2168 7.438564 TGTAGTAGTACAAATTCAAGTGCAGA 58.561 34.615 7.99 0.00 36.15 4.26
2084 2172 7.275779 AGCGATGTAGTAGTACAAATTCAAGTG 59.724 37.037 14.26 0.00 42.54 3.16
2131 2220 4.074970 CAGTAACTGACAAGGCCAAGAAT 58.925 43.478 5.01 0.00 32.44 2.40
2159 2248 1.009829 CTTCTGGGCGTTGCATACTC 58.990 55.000 0.00 0.00 0.00 2.59
2162 2251 1.026182 CAGCTTCTGGGCGTTGCATA 61.026 55.000 0.00 0.00 37.29 3.14
2180 2269 4.581868 CCCTCGTAACCAACCTTTTATCA 58.418 43.478 0.00 0.00 0.00 2.15
2264 2353 2.859165 AATCTGCGAGGTTCTTTCCA 57.141 45.000 0.00 0.00 0.00 3.53
2353 2442 8.836413 GCAAGTACCAATTTTATGATGCTACTA 58.164 33.333 0.00 0.00 0.00 1.82
2408 2497 0.689055 ACTGCTGCCACTCTTCATGA 59.311 50.000 0.00 0.00 0.00 3.07
2444 2533 3.118112 AGCATGTTCTCACCTAATCCCAG 60.118 47.826 0.00 0.00 0.00 4.45
2538 2630 5.640783 TCTGCAGCATACATACATTCTATGC 59.359 40.000 9.47 0.00 42.06 3.14
2742 2834 6.183360 ACCAAAAGGTTTAACTACTCCGTTTG 60.183 38.462 12.06 12.06 43.51 2.93
2757 2849 9.054922 CATCAATTTTGTTGATACCAAAAGGTT 57.945 29.630 3.23 0.00 42.96 3.50
2758 2850 8.428063 TCATCAATTTTGTTGATACCAAAAGGT 58.572 29.630 3.23 0.00 42.96 3.50
2789 2881 0.684535 TCAATGCACTTCTCCGGTCA 59.315 50.000 0.00 0.00 0.00 4.02
2840 2933 7.615582 TGATGAATCTGTCCAAACAATCTAC 57.384 36.000 0.00 0.00 34.24 2.59
2903 2996 4.819105 TCCTCGTTTGGATGACAGTAAT 57.181 40.909 0.00 0.00 0.00 1.89
2905 2998 4.610605 TTTCCTCGTTTGGATGACAGTA 57.389 40.909 0.00 0.00 35.83 2.74
3077 3170 5.123227 ACTTAGCTTGCTTTACAGTTGACA 58.877 37.500 0.00 0.00 0.00 3.58
3132 3225 3.450904 AGATAAGGCTACAGTGGACCAA 58.549 45.455 0.00 0.00 0.00 3.67
3141 3234 7.047891 CCATACACAAGAAAGATAAGGCTACA 58.952 38.462 0.00 0.00 0.00 2.74
3145 3238 7.173390 GGATACCATACACAAGAAAGATAAGGC 59.827 40.741 0.00 0.00 0.00 4.35
3304 3397 0.608640 CACTAGGCTTCCTTCCACGT 59.391 55.000 0.00 0.00 34.61 4.49


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

AutoCloner maintained by Alex Coulton.