Multiple sequence alignment - TraesCS5A01G361300

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 TraesCS5A01G361300 chr5A 100.000 6231 0 0 1 6231 562535404 562541634 0.000000e+00 11507.0
1 TraesCS5A01G361300 chr5B 96.571 5453 134 20 342 5776 542926693 542932110 0.000000e+00 8985.0
2 TraesCS5A01G361300 chr5B 94.915 59 3 0 5918 5976 542932439 542932497 6.650000e-15 93.5
3 TraesCS5A01G361300 chr5D 97.779 4773 89 9 1470 6231 445199903 445204669 0.000000e+00 8211.0
4 TraesCS5A01G361300 chr5D 95.302 1192 24 15 310 1480 445198701 445199881 0.000000e+00 1862.0
5 TraesCS5A01G361300 chr5D 87.613 331 30 9 1 329 445198437 445198758 2.120000e-99 374.0
6 TraesCS5A01G361300 chr3B 83.314 3476 547 25 1688 5148 80167902 80164445 0.000000e+00 3175.0
7 TraesCS5A01G361300 chr3B 86.194 536 64 7 760 1287 80168871 80168338 7.010000e-159 571.0
8 TraesCS5A01G361300 chr3A 84.020 1990 298 15 1688 3670 63563411 63561435 0.000000e+00 1895.0
9 TraesCS5A01G361300 chr3A 83.414 1441 233 5 3720 5155 63561416 63559977 0.000000e+00 1332.0
10 TraesCS5A01G361300 chr3A 84.888 536 71 8 760 1287 63564319 63563786 3.310000e-147 532.0
11 TraesCS5A01G361300 chr3D 82.095 1279 224 4 3881 5155 50552479 50551202 0.000000e+00 1088.0
12 TraesCS5A01G361300 chr3D 83.453 417 59 8 760 1168 50552889 50552475 4.560000e-101 379.0


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 TraesCS5A01G361300 chr5A 562535404 562541634 6230 False 11507.000000 11507 100.000000 1 6231 1 chr5A.!!$F1 6230
1 TraesCS5A01G361300 chr5B 542926693 542932497 5804 False 4539.250000 8985 95.743000 342 5976 2 chr5B.!!$F1 5634
2 TraesCS5A01G361300 chr5D 445198437 445204669 6232 False 3482.333333 8211 93.564667 1 6231 3 chr5D.!!$F1 6230
3 TraesCS5A01G361300 chr3B 80164445 80168871 4426 True 1873.000000 3175 84.754000 760 5148 2 chr3B.!!$R1 4388
4 TraesCS5A01G361300 chr3A 63559977 63564319 4342 True 1253.000000 1895 84.107333 760 5155 3 chr3A.!!$R1 4395
5 TraesCS5A01G361300 chr3D 50551202 50552889 1687 True 733.500000 1088 82.774000 760 5155 2 chr3D.!!$R1 4395

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
487 496 0.105760 TCTCTCAGATCCAGCCCCTC 60.106 60.000 0.00 0.00 0.00 4.30 F
488 497 0.398239 CTCTCAGATCCAGCCCCTCA 60.398 60.000 0.00 0.00 0.00 3.86 F
1780 1928 2.501610 GATGAGGTCGGAGGTGGC 59.498 66.667 0.00 0.00 0.00 5.01 F
2467 2615 0.330604 AGCATCATGGGCAGACAGTT 59.669 50.000 11.89 0.00 0.00 3.16 F
3686 3843 2.165030 AGCAAGCTTGGTTCATATGCAC 59.835 45.455 24.96 4.84 34.89 4.57 F
4472 4629 1.937546 GCAGTTTGCAGAATCCCGGG 61.938 60.000 16.85 16.85 44.26 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2132 0.981183 ACTTTGGGTGCCTGTCGATA 59.019 50.000 0.00 0.0 0.00 2.92 R
1988 2136 1.109323 AGCAACTTTGGGTGCCTGTC 61.109 55.000 2.24 0.0 0.00 3.51 R
2941 3089 0.458543 AATACGACAGCACCAGAGCG 60.459 55.000 0.00 0.0 40.15 5.03 R
3764 3921 4.187694 GACCTTGGTTCTTCAGCATCTAG 58.812 47.826 0.00 0.0 31.27 2.43 R
4597 4754 2.435410 CGCAGCCACATCTCAGCA 60.435 61.111 0.00 0.0 0.00 4.41 R
5750 5913 3.302161 AGGCCTACAACCATATACGTCA 58.698 45.455 1.29 0.0 0.00 4.35 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
32 33 3.243737 ACGATATATTGAAGGCGTGCTCA 60.244 43.478 6.98 0.00 0.00 4.26
54 55 5.481824 TCACTGTCTTCTTCTGTCATACCAT 59.518 40.000 0.00 0.00 0.00 3.55
81 82 8.958119 TGGTTAAGCTAAATATCGAGTCAAAT 57.042 30.769 6.19 0.00 0.00 2.32
85 86 5.289595 AGCTAAATATCGAGTCAAATCGCA 58.710 37.500 0.00 0.00 42.43 5.10
94 95 4.213270 TCGAGTCAAATCGCAATTCAAACT 59.787 37.500 0.00 0.00 42.43 2.66
104 105 3.941483 CGCAATTCAAACTCTATCCCACT 59.059 43.478 0.00 0.00 0.00 4.00
113 114 6.012858 TCAAACTCTATCCCACTACAAACCAT 60.013 38.462 0.00 0.00 0.00 3.55
131 132 7.989741 ACAAACCATAATTTTCAACACATCCAA 59.010 29.630 0.00 0.00 0.00 3.53
143 144 8.572855 TTCAACACATCCAATCACATACATAA 57.427 30.769 0.00 0.00 0.00 1.90
154 155 8.916654 CCAATCACATACATAAACTCGATCTAC 58.083 37.037 0.00 0.00 0.00 2.59
184 185 0.837272 TAAAGGCTCCGGGGAATCAG 59.163 55.000 4.80 0.00 0.00 2.90
195 196 1.064463 GGGGAATCAGTGCCAATCTCA 60.064 52.381 0.00 0.00 40.26 3.27
214 215 4.329801 TCTCAACACATATGATGTTCGTGC 59.670 41.667 10.38 0.00 42.70 5.34
228 229 4.056050 TGTTCGTGCTAAACCTTCTTCTC 58.944 43.478 0.00 0.00 0.00 2.87
230 231 2.295349 TCGTGCTAAACCTTCTTCTCGT 59.705 45.455 0.00 0.00 0.00 4.18
233 234 2.295349 TGCTAAACCTTCTTCTCGTCGT 59.705 45.455 0.00 0.00 0.00 4.34
234 235 2.662156 GCTAAACCTTCTTCTCGTCGTG 59.338 50.000 0.00 0.00 0.00 4.35
237 238 2.418983 ACCTTCTTCTCGTCGTGAAC 57.581 50.000 5.67 0.00 0.00 3.18
268 269 7.128331 CCGTTGAGCTACATAAATCAATTCAG 58.872 38.462 0.00 0.00 34.45 3.02
269 270 7.011389 CCGTTGAGCTACATAAATCAATTCAGA 59.989 37.037 0.00 0.00 34.45 3.27
272 273 9.671279 TTGAGCTACATAAATCAATTCAGAAGA 57.329 29.630 0.00 0.00 0.00 2.87
279 280 9.525826 ACATAAATCAATTCAGAAGACCTCTTT 57.474 29.630 0.00 0.00 36.11 2.52
280 281 9.784680 CATAAATCAATTCAGAAGACCTCTTTG 57.215 33.333 0.00 0.00 36.11 2.77
281 282 9.745018 ATAAATCAATTCAGAAGACCTCTTTGA 57.255 29.630 0.00 0.00 34.46 2.69
282 283 8.647256 AAATCAATTCAGAAGACCTCTTTGAT 57.353 30.769 1.58 1.58 39.34 2.57
283 284 8.647256 AATCAATTCAGAAGACCTCTTTGATT 57.353 30.769 10.76 10.76 40.80 2.57
284 285 7.678947 TCAATTCAGAAGACCTCTTTGATTC 57.321 36.000 0.00 0.00 36.11 2.52
285 286 6.369890 TCAATTCAGAAGACCTCTTTGATTCG 59.630 38.462 0.00 0.00 36.11 3.34
286 287 5.468540 TTCAGAAGACCTCTTTGATTCGA 57.531 39.130 0.00 0.00 36.11 3.71
287 288 4.810790 TCAGAAGACCTCTTTGATTCGAC 58.189 43.478 0.00 0.00 36.11 4.20
288 289 3.610242 CAGAAGACCTCTTTGATTCGACG 59.390 47.826 0.00 0.00 36.11 5.12
289 290 2.656560 AGACCTCTTTGATTCGACGG 57.343 50.000 0.00 0.00 0.00 4.79
290 291 2.168496 AGACCTCTTTGATTCGACGGA 58.832 47.619 0.00 0.00 0.00 4.69
291 292 2.561419 AGACCTCTTTGATTCGACGGAA 59.439 45.455 0.00 0.00 36.41 4.30
292 293 3.195825 AGACCTCTTTGATTCGACGGAAT 59.804 43.478 0.00 0.00 45.43 3.01
293 294 3.933332 GACCTCTTTGATTCGACGGAATT 59.067 43.478 0.00 0.00 42.86 2.17
294 295 4.324267 ACCTCTTTGATTCGACGGAATTT 58.676 39.130 0.00 0.00 42.86 1.82
295 296 4.760204 ACCTCTTTGATTCGACGGAATTTT 59.240 37.500 0.00 0.00 42.86 1.82
296 297 5.935789 ACCTCTTTGATTCGACGGAATTTTA 59.064 36.000 0.00 0.00 42.86 1.52
297 298 6.598064 ACCTCTTTGATTCGACGGAATTTTAT 59.402 34.615 0.00 0.00 42.86 1.40
298 299 6.907212 CCTCTTTGATTCGACGGAATTTTATG 59.093 38.462 0.00 0.00 42.86 1.90
299 300 7.201609 CCTCTTTGATTCGACGGAATTTTATGA 60.202 37.037 0.00 0.00 42.86 2.15
300 301 8.035165 TCTTTGATTCGACGGAATTTTATGAA 57.965 30.769 0.00 0.00 42.86 2.57
301 302 8.508062 TCTTTGATTCGACGGAATTTTATGAAA 58.492 29.630 0.00 0.00 42.86 2.69
302 303 9.123709 CTTTGATTCGACGGAATTTTATGAAAA 57.876 29.630 0.00 0.00 42.86 2.29
303 304 9.464714 TTTGATTCGACGGAATTTTATGAAAAA 57.535 25.926 0.00 0.00 42.86 1.94
304 305 8.667987 TGATTCGACGGAATTTTATGAAAAAG 57.332 30.769 0.00 0.00 42.86 2.27
305 306 7.753132 TGATTCGACGGAATTTTATGAAAAAGG 59.247 33.333 0.00 0.00 42.86 3.11
306 307 6.804770 TCGACGGAATTTTATGAAAAAGGA 57.195 33.333 0.00 0.00 37.97 3.36
307 308 7.204496 TCGACGGAATTTTATGAAAAAGGAA 57.796 32.000 0.00 0.00 37.97 3.36
308 309 7.822658 TCGACGGAATTTTATGAAAAAGGAAT 58.177 30.769 0.00 0.00 37.97 3.01
309 310 7.753132 TCGACGGAATTTTATGAAAAAGGAATG 59.247 33.333 0.00 0.00 37.97 2.67
310 311 7.009174 CGACGGAATTTTATGAAAAAGGAATGG 59.991 37.037 0.00 0.00 37.97 3.16
311 312 6.593770 ACGGAATTTTATGAAAAAGGAATGGC 59.406 34.615 0.00 0.00 37.97 4.40
312 313 6.037062 CGGAATTTTATGAAAAAGGAATGGCC 59.963 38.462 0.00 0.00 37.97 5.36
322 323 3.496675 GGAATGGCCTACTCCCAAC 57.503 57.895 3.32 0.00 35.67 3.77
327 328 1.367346 TGGCCTACTCCCAACATGAA 58.633 50.000 3.32 0.00 0.00 2.57
335 336 6.624423 CCTACTCCCAACATGAAGAAATTTG 58.376 40.000 0.00 0.00 0.00 2.32
337 338 6.729690 ACTCCCAACATGAAGAAATTTGAA 57.270 33.333 0.00 0.00 0.00 2.69
374 378 0.974010 CTGCCCCCAACATGAAGCAT 60.974 55.000 0.00 0.00 0.00 3.79
467 476 3.409026 ACTAGGAGTTGAGCTTTGGTG 57.591 47.619 0.00 0.00 0.00 4.17
483 492 0.463620 GGTGTCTCTCAGATCCAGCC 59.536 60.000 0.00 0.00 0.00 4.85
484 493 0.463620 GTGTCTCTCAGATCCAGCCC 59.536 60.000 0.00 0.00 0.00 5.19
485 494 0.689080 TGTCTCTCAGATCCAGCCCC 60.689 60.000 0.00 0.00 0.00 5.80
486 495 0.398381 GTCTCTCAGATCCAGCCCCT 60.398 60.000 0.00 0.00 0.00 4.79
487 496 0.105760 TCTCTCAGATCCAGCCCCTC 60.106 60.000 0.00 0.00 0.00 4.30
488 497 0.398239 CTCTCAGATCCAGCCCCTCA 60.398 60.000 0.00 0.00 0.00 3.86
493 502 4.369591 ATCCAGCCCCTCACCCCA 62.370 66.667 0.00 0.00 0.00 4.96
1436 1476 5.965922 AGTTTAACTTGCAGTGCTCTTTTT 58.034 33.333 17.60 5.11 0.00 1.94
1543 1615 3.229293 TGTCATTCCAGCAATTTGACCA 58.771 40.909 0.00 0.00 36.68 4.02
1666 1771 6.339587 CCAAGTTTGGTGTATTAATGTGGT 57.660 37.500 2.66 0.00 43.43 4.16
1780 1928 2.501610 GATGAGGTCGGAGGTGGC 59.498 66.667 0.00 0.00 0.00 5.01
1962 2110 4.263905 TGCTCTGGGGTTGATAAATTCTGT 60.264 41.667 0.00 0.00 0.00 3.41
1984 2132 2.890808 TTGAGTTGTCAGCTTCGTCT 57.109 45.000 0.00 0.00 32.98 4.18
1988 2136 3.102276 GAGTTGTCAGCTTCGTCTATCG 58.898 50.000 0.00 0.00 41.41 2.92
2371 2519 3.081804 CCCTGTAAACAGTCCATTGTCC 58.918 50.000 9.17 0.00 42.27 4.02
2383 2531 2.824936 TCCATTGTCCGCATTGAATGTT 59.175 40.909 7.05 0.00 0.00 2.71
2467 2615 0.330604 AGCATCATGGGCAGACAGTT 59.669 50.000 11.89 0.00 0.00 3.16
2941 3089 3.848726 CATGTTTGTTAACAGGGATGCC 58.151 45.455 8.56 0.00 46.71 4.40
3103 3251 6.757010 TCTTGTCGGAGCTGTTTTATTCTATC 59.243 38.462 0.00 0.00 0.00 2.08
3686 3843 2.165030 AGCAAGCTTGGTTCATATGCAC 59.835 45.455 24.96 4.84 34.89 4.57
3742 3899 3.403228 AAAACATATGGGCTGATGGGT 57.597 42.857 7.80 0.00 0.00 4.51
3764 3921 4.548451 AGGTTTAGCCAACTACTGTACC 57.452 45.455 0.00 0.00 40.61 3.34
4472 4629 1.937546 GCAGTTTGCAGAATCCCGGG 61.938 60.000 16.85 16.85 44.26 5.73
4597 4754 5.136105 GCAGACAGGATATTGGAAGGAATT 58.864 41.667 0.00 0.00 0.00 2.17
4819 4976 7.725844 AGTTACTCACCAAAGGATTTCAGAAAT 59.274 33.333 8.20 8.20 35.03 2.17
4919 5076 0.318445 CAGTTTCAGCAAGCTGTGGC 60.318 55.000 20.34 11.74 43.96 5.01
5059 5219 4.275936 GCAAATGGTGTACTGTCAAAGACT 59.724 41.667 0.00 0.00 33.15 3.24
5232 5392 1.453155 CAAACTGCCGAGCAATAGGT 58.547 50.000 0.35 0.00 38.41 3.08
5351 5511 5.355350 AGAGCAAGCTGGTGTATTGTAATTC 59.645 40.000 0.00 0.00 0.00 2.17
5687 5849 5.125900 TGCATATTGAGTGAATTGGGTTGAG 59.874 40.000 0.00 0.00 0.00 3.02
5699 5862 0.322816 GGGTTGAGCATGGCTTGAGA 60.323 55.000 4.32 0.00 39.88 3.27
5717 5880 6.375455 GCTTGAGAATTTTTGTAGGATCTGGA 59.625 38.462 0.00 0.00 0.00 3.86
5718 5881 7.094205 GCTTGAGAATTTTTGTAGGATCTGGAA 60.094 37.037 0.00 0.00 0.00 3.53
5750 5913 2.316108 ACCTTTTCGCCTTGATTGGTT 58.684 42.857 0.00 0.00 0.00 3.67
5777 5983 5.121768 CGTATATGGTTGTAGGCCTATTTGC 59.878 44.000 17.38 3.16 0.00 3.68
5812 6018 3.680937 TCGAAAATTCTACGGCGTGAATT 59.319 39.130 28.28 28.28 42.52 2.17
5983 6333 8.103305 ACATATTCTGGTAATCAACAGACTTGT 58.897 33.333 0.00 0.00 42.91 3.16
6093 6443 6.040209 TGCAATTTTCATGATAAAGGTGCT 57.960 33.333 23.38 3.93 34.01 4.40
6109 6459 4.781934 AGGTGCTTAAATAGATGGGTCAC 58.218 43.478 0.00 0.00 0.00 3.67
6204 6558 8.407064 CGTACCATAGCTTTATATAAGAGAGGG 58.593 40.741 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.418368 CCATATGGTATGACAGAAGAAGACAGT 60.418 40.741 14.09 0.00 0.00 3.55
64 65 8.275632 TGAATTGCGATTTGACTCGATATTTAG 58.724 33.333 0.00 0.00 41.12 1.85
71 72 4.213270 AGTTTGAATTGCGATTTGACTCGA 59.787 37.500 0.00 0.00 41.12 4.04
81 82 3.938963 GTGGGATAGAGTTTGAATTGCGA 59.061 43.478 0.00 0.00 0.00 5.10
85 86 7.393515 GGTTTGTAGTGGGATAGAGTTTGAATT 59.606 37.037 0.00 0.00 0.00 2.17
94 95 9.403583 GAAAATTATGGTTTGTAGTGGGATAGA 57.596 33.333 0.00 0.00 0.00 1.98
104 105 8.642432 TGGATGTGTTGAAAATTATGGTTTGTA 58.358 29.630 0.00 0.00 0.00 2.41
113 114 9.853555 GTATGTGATTGGATGTGTTGAAAATTA 57.146 29.630 0.00 0.00 0.00 1.40
143 144 5.359194 ACCATTCCATTGTAGATCGAGTT 57.641 39.130 0.00 0.00 0.00 3.01
154 155 2.358898 CGGAGCCTTTACCATTCCATTG 59.641 50.000 0.00 0.00 0.00 2.82
156 157 1.133792 CCGGAGCCTTTACCATTCCAT 60.134 52.381 0.00 0.00 0.00 3.41
184 185 5.066893 ACATCATATGTGTTGAGATTGGCAC 59.933 40.000 7.44 0.00 43.01 5.01
195 196 6.403200 GGTTTAGCACGAACATCATATGTGTT 60.403 38.462 17.83 17.83 44.07 3.32
214 215 4.156664 TCACGACGAGAAGAAGGTTTAG 57.843 45.455 0.00 0.00 0.00 1.85
233 234 3.334751 CTCAACGGCGTGCGTTCA 61.335 61.111 15.70 0.00 0.00 3.18
234 235 4.719616 GCTCAACGGCGTGCGTTC 62.720 66.667 15.70 0.00 0.00 3.95
237 238 3.838795 GTAGCTCAACGGCGTGCG 61.839 66.667 15.70 8.56 37.29 5.34
239 240 1.635844 TTATGTAGCTCAACGGCGTG 58.364 50.000 15.70 8.32 37.29 5.34
241 242 2.863740 TGATTTATGTAGCTCAACGGCG 59.136 45.455 4.80 4.80 37.29 6.46
242 243 4.875544 TTGATTTATGTAGCTCAACGGC 57.124 40.909 0.00 0.00 0.00 5.68
243 244 7.011389 TCTGAATTGATTTATGTAGCTCAACGG 59.989 37.037 0.00 0.00 31.00 4.44
244 245 7.909267 TCTGAATTGATTTATGTAGCTCAACG 58.091 34.615 0.00 0.00 31.00 4.10
245 246 9.713740 CTTCTGAATTGATTTATGTAGCTCAAC 57.286 33.333 0.00 0.00 31.00 3.18
246 247 9.671279 TCTTCTGAATTGATTTATGTAGCTCAA 57.329 29.630 0.00 0.00 32.63 3.02
249 250 8.270744 AGGTCTTCTGAATTGATTTATGTAGCT 58.729 33.333 0.00 0.00 0.00 3.32
268 269 2.924290 CCGTCGAATCAAAGAGGTCTTC 59.076 50.000 0.00 0.00 34.61 2.87
269 270 2.561419 TCCGTCGAATCAAAGAGGTCTT 59.439 45.455 0.00 0.00 37.91 3.01
272 273 3.611766 ATTCCGTCGAATCAAAGAGGT 57.388 42.857 0.00 0.00 33.15 3.85
279 280 7.753132 CCTTTTTCATAAAATTCCGTCGAATCA 59.247 33.333 0.00 0.00 37.76 2.57
280 281 7.966204 TCCTTTTTCATAAAATTCCGTCGAATC 59.034 33.333 0.00 0.00 37.76 2.52
281 282 7.822658 TCCTTTTTCATAAAATTCCGTCGAAT 58.177 30.769 0.00 0.00 40.58 3.34
282 283 7.204496 TCCTTTTTCATAAAATTCCGTCGAA 57.796 32.000 0.00 0.00 33.05 3.71
283 284 6.804770 TCCTTTTTCATAAAATTCCGTCGA 57.195 33.333 0.00 0.00 33.05 4.20
284 285 7.009174 CCATTCCTTTTTCATAAAATTCCGTCG 59.991 37.037 0.00 0.00 33.05 5.12
285 286 7.201522 GCCATTCCTTTTTCATAAAATTCCGTC 60.202 37.037 0.00 0.00 33.05 4.79
286 287 6.593770 GCCATTCCTTTTTCATAAAATTCCGT 59.406 34.615 0.00 0.00 33.05 4.69
287 288 6.037062 GGCCATTCCTTTTTCATAAAATTCCG 59.963 38.462 0.00 0.00 33.05 4.30
288 289 7.112122 AGGCCATTCCTTTTTCATAAAATTCC 58.888 34.615 5.01 0.00 44.75 3.01
289 290 9.098355 GTAGGCCATTCCTTTTTCATAAAATTC 57.902 33.333 5.01 0.00 44.75 2.17
290 291 8.825774 AGTAGGCCATTCCTTTTTCATAAAATT 58.174 29.630 5.01 0.00 44.75 1.82
291 292 8.379428 AGTAGGCCATTCCTTTTTCATAAAAT 57.621 30.769 5.01 0.00 44.75 1.82
292 293 7.093509 GGAGTAGGCCATTCCTTTTTCATAAAA 60.094 37.037 5.01 0.00 44.75 1.52
293 294 6.379988 GGAGTAGGCCATTCCTTTTTCATAAA 59.620 38.462 5.01 0.00 44.75 1.40
294 295 5.891551 GGAGTAGGCCATTCCTTTTTCATAA 59.108 40.000 5.01 0.00 44.75 1.90
295 296 5.445964 GGAGTAGGCCATTCCTTTTTCATA 58.554 41.667 5.01 0.00 44.75 2.15
296 297 4.281657 GGAGTAGGCCATTCCTTTTTCAT 58.718 43.478 5.01 0.00 44.75 2.57
297 298 3.563479 GGGAGTAGGCCATTCCTTTTTCA 60.563 47.826 16.77 0.00 44.75 2.69
298 299 3.024547 GGGAGTAGGCCATTCCTTTTTC 58.975 50.000 16.77 0.54 44.75 2.29
299 300 2.381961 TGGGAGTAGGCCATTCCTTTTT 59.618 45.455 16.77 0.00 44.75 1.94
300 301 2.000048 TGGGAGTAGGCCATTCCTTTT 59.000 47.619 16.77 0.00 44.75 2.27
301 302 1.681229 TGGGAGTAGGCCATTCCTTT 58.319 50.000 16.77 0.00 44.75 3.11
302 303 1.285078 GTTGGGAGTAGGCCATTCCTT 59.715 52.381 16.77 0.00 44.75 3.36
304 305 0.623723 TGTTGGGAGTAGGCCATTCC 59.376 55.000 5.01 8.70 32.20 3.01
305 306 2.092429 TCATGTTGGGAGTAGGCCATTC 60.092 50.000 5.01 0.00 0.00 2.67
306 307 1.922447 TCATGTTGGGAGTAGGCCATT 59.078 47.619 5.01 0.00 0.00 3.16
307 308 1.595311 TCATGTTGGGAGTAGGCCAT 58.405 50.000 5.01 0.00 0.00 4.40
308 309 1.281867 CTTCATGTTGGGAGTAGGCCA 59.718 52.381 5.01 0.00 0.00 5.36
309 310 1.559682 TCTTCATGTTGGGAGTAGGCC 59.440 52.381 0.00 0.00 0.00 5.19
310 311 3.350219 TTCTTCATGTTGGGAGTAGGC 57.650 47.619 0.00 0.00 0.00 3.93
311 312 6.434028 TCAAATTTCTTCATGTTGGGAGTAGG 59.566 38.462 0.00 0.00 0.00 3.18
312 313 7.452880 TCAAATTTCTTCATGTTGGGAGTAG 57.547 36.000 0.00 0.00 0.00 2.57
313 314 7.831691 TTCAAATTTCTTCATGTTGGGAGTA 57.168 32.000 0.00 0.00 0.00 2.59
314 315 6.729690 TTCAAATTTCTTCATGTTGGGAGT 57.270 33.333 0.00 0.00 0.00 3.85
315 316 8.436046 TTTTTCAAATTTCTTCATGTTGGGAG 57.564 30.769 0.00 0.00 0.00 4.30
345 346 4.529731 GGGGGCAGGCCATTCCTC 62.530 72.222 16.36 1.71 45.52 3.71
357 358 1.035139 CTATGCTTCATGTTGGGGGC 58.965 55.000 0.00 0.00 0.00 5.80
358 359 2.734755 TCTATGCTTCATGTTGGGGG 57.265 50.000 0.00 0.00 0.00 5.40
467 476 0.398381 AGGGGCTGGATCTGAGAGAC 60.398 60.000 0.00 0.00 0.00 3.36
484 493 3.253838 TTCGGGGTTGGGGTGAGG 61.254 66.667 0.00 0.00 0.00 3.86
485 494 2.221299 TCTTCGGGGTTGGGGTGAG 61.221 63.158 0.00 0.00 0.00 3.51
486 495 2.122324 TCTTCGGGGTTGGGGTGA 60.122 61.111 0.00 0.00 0.00 4.02
487 496 2.033602 GTCTTCGGGGTTGGGGTG 59.966 66.667 0.00 0.00 0.00 4.61
488 497 3.254617 GGTCTTCGGGGTTGGGGT 61.255 66.667 0.00 0.00 0.00 4.95
493 502 1.152138 GGGTTTGGTCTTCGGGGTT 59.848 57.895 0.00 0.00 0.00 4.11
1400 1439 8.039603 TGCAAGTTAAACTATCACAATACTGG 57.960 34.615 0.00 0.00 0.00 4.00
1436 1476 8.863086 AGTATAGTTACTTCAGTACACAAACCA 58.137 33.333 0.00 0.00 34.99 3.67
1543 1615 1.806542 GAGTCGGTTTCATGTGCACAT 59.193 47.619 26.61 26.61 36.96 3.21
1780 1928 1.021202 TGTCTTGAACGGCACCAAAG 58.979 50.000 0.00 0.00 0.00 2.77
1909 2057 4.083643 GGCACGTCCTCATCATAATCAATG 60.084 45.833 0.00 0.00 36.88 2.82
1962 2110 3.059884 GACGAAGCTGACAACTCAATGA 58.940 45.455 0.00 0.00 0.00 2.57
1984 2132 0.981183 ACTTTGGGTGCCTGTCGATA 59.019 50.000 0.00 0.00 0.00 2.92
1988 2136 1.109323 AGCAACTTTGGGTGCCTGTC 61.109 55.000 2.24 0.00 0.00 3.51
2309 2457 9.171877 CAGAAGATTAGCTAGGTCTTCAAAAAT 57.828 33.333 31.45 19.11 46.40 1.82
2371 2519 3.061563 CCAATGCAAGAACATTCAATGCG 59.938 43.478 14.04 4.48 41.93 4.73
2383 2531 2.607499 ACCAAACCATCCAATGCAAGA 58.393 42.857 0.00 0.00 0.00 3.02
2941 3089 0.458543 AATACGACAGCACCAGAGCG 60.459 55.000 0.00 0.00 40.15 5.03
3103 3251 4.002982 TGGTTTTGATCTCATTCCGACAG 58.997 43.478 0.00 0.00 0.00 3.51
3742 3899 5.336102 AGGTACAGTAGTTGGCTAAACCTA 58.664 41.667 0.00 0.00 39.85 3.08
3764 3921 4.187694 GACCTTGGTTCTTCAGCATCTAG 58.812 47.826 0.00 0.00 31.27 2.43
4468 4625 1.192146 TCTCTGAAGACCCAACCCGG 61.192 60.000 0.00 0.00 0.00 5.73
4472 4629 5.010617 GGATAGATCTCTCTGAAGACCCAAC 59.989 48.000 0.00 0.00 32.66 3.77
4481 4638 4.401048 AGGCATGGATAGATCTCTCTGA 57.599 45.455 0.00 0.00 32.66 3.27
4597 4754 2.435410 CGCAGCCACATCTCAGCA 60.435 61.111 0.00 0.00 0.00 4.41
4919 5076 3.885901 TCTATCATGTCGAGGACTTCCAG 59.114 47.826 0.00 0.00 38.89 3.86
5059 5219 2.754254 TTCTCCTCGCTGGCGCTA 60.754 61.111 7.64 0.00 39.59 4.26
5232 5392 2.542020 TCGATGTTCAGCAGTTTGGA 57.458 45.000 0.00 0.00 0.00 3.53
5687 5849 4.866486 CCTACAAAAATTCTCAAGCCATGC 59.134 41.667 0.00 0.00 0.00 4.06
5717 5880 5.479027 AGGCGAAAAGGTTACCATGTATTTT 59.521 36.000 3.51 0.87 0.00 1.82
5718 5881 5.014202 AGGCGAAAAGGTTACCATGTATTT 58.986 37.500 3.51 0.00 0.00 1.40
5750 5913 3.302161 AGGCCTACAACCATATACGTCA 58.698 45.455 1.29 0.00 0.00 4.35
5777 5983 9.573102 CGTAGAATTTTCGATATGATTGTGAAG 57.427 33.333 0.00 0.00 0.00 3.02
5925 6275 8.677300 GCTTTAGATTGAATATCCAAACAGACA 58.323 33.333 0.00 0.00 0.00 3.41
6008 6358 4.860072 ACTTCTCATTCAAAACCTTTCGC 58.140 39.130 0.00 0.00 0.00 4.70
6117 6467 3.421919 TGCATGAGAATCTGGTCACAA 57.578 42.857 0.00 0.00 34.92 3.33
6134 6485 8.669946 AAAATCAATTTATCATCATGCATGCA 57.330 26.923 25.04 25.04 31.70 3.96
6200 6554 7.755373 GCACTTTTATCTTGTACATTTTCCCTC 59.245 37.037 0.00 0.00 0.00 4.30
6204 6558 9.624697 TGATGCACTTTTATCTTGTACATTTTC 57.375 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.