Multiple sequence alignment - TraesCS2D01G594800

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 TraesCS2D01G594800 chr2D 100.000 4871 0 0 1 4871 648351414 648356284 0.000000e+00 8996
1 TraesCS2D01G594800 chr2D 86.256 1477 172 13 833 2307 648115431 648113984 0.000000e+00 1574
2 TraesCS2D01G594800 chr2D 84.557 1580 186 30 743 2305 648126776 648125238 0.000000e+00 1513
3 TraesCS2D01G594800 chr2D 83.254 1469 175 34 2342 3761 648113985 648112539 0.000000e+00 1284
4 TraesCS2D01G594800 chr2D 86.467 835 89 8 2343 3174 648125236 648124423 0.000000e+00 894
5 TraesCS2D01G594800 chr2D 81.545 466 67 8 3211 3662 648124269 648123809 2.770000e-97 366
6 TraesCS2D01G594800 chr2D 86.667 255 33 1 4598 4852 648387441 648387188 1.030000e-71 281
7 TraesCS2D01G594800 chr2D 84.615 156 19 3 3733 3884 648112495 648112341 3.040000e-32 150
8 TraesCS2D01G594800 chr2D 82.993 147 23 2 3733 3878 648123597 648123452 1.100000e-26 132
9 TraesCS2D01G594800 chr2B 93.776 4322 204 23 286 4583 784272989 784277269 0.000000e+00 6431
10 TraesCS2D01G594800 chr2B 86.703 1474 164 19 844 2307 781801099 781802550 0.000000e+00 1607
11 TraesCS2D01G594800 chr2B 84.635 1562 196 20 764 2305 781790026 781791563 0.000000e+00 1515
12 TraesCS2D01G594800 chr2B 83.014 1460 179 31 2342 3753 781802549 781803987 0.000000e+00 1258
13 TraesCS2D01G594800 chr2B 86.260 837 91 8 2343 3176 781791565 781792380 0.000000e+00 887
14 TraesCS2D01G594800 chr2B 91.176 238 16 3 38 270 784272773 784273010 7.870000e-83 318
15 TraesCS2D01G594800 chr2B 83.974 156 20 3 3733 3884 781804039 781804193 1.410000e-30 145
16 TraesCS2D01G594800 chr2B 84.354 147 18 3 3733 3875 781793264 781793409 6.570000e-29 139
17 TraesCS2D01G594800 chrUn 95.343 3994 159 12 326 4305 31092261 31088281 0.000000e+00 6320
18 TraesCS2D01G594800 chrUn 84.207 1659 209 30 668 2307 31320506 31322130 0.000000e+00 1563
19 TraesCS2D01G594800 chrUn 86.405 1199 145 6 1113 2305 31306603 31307789 0.000000e+00 1295
20 TraesCS2D01G594800 chrUn 83.322 1469 174 34 2342 3761 31322129 31323575 0.000000e+00 1290
21 TraesCS2D01G594800 chrUn 96.309 569 20 1 4304 4871 31088231 31087663 0.000000e+00 933
22 TraesCS2D01G594800 chrUn 87.070 843 85 8 2343 3182 31307791 31308612 0.000000e+00 931
23 TraesCS2D01G594800 chrUn 82.227 467 64 11 3210 3662 31308757 31309218 7.650000e-103 385
24 TraesCS2D01G594800 chrUn 91.144 271 18 3 1 270 31092535 31092270 3.580000e-96 363
25 TraesCS2D01G594800 chrUn 83.217 286 35 9 876 1150 31306318 31306601 2.910000e-62 250
26 TraesCS2D01G594800 chrUn 84.615 156 19 3 3733 3884 31323619 31323773 3.040000e-32 150
27 TraesCS2D01G594800 chr2A 92.777 443 20 5 195 625 110868150 110867708 8.900000e-177 630
28 TraesCS2D01G594800 chr7A 92.278 259 17 2 324 581 280226250 280225994 9.960000e-97 364
29 TraesCS2D01G594800 chr7A 83.122 237 21 12 23 240 280226524 280226288 1.070000e-46 198


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 TraesCS2D01G594800 chr2D 648351414 648356284 4870 False 8996.000000 8996 100.000000 1 4871 1 chr2D.!!$F1 4870
1 TraesCS2D01G594800 chr2D 648112341 648115431 3090 True 1002.666667 1574 84.708333 833 3884 3 chr2D.!!$R2 3051
2 TraesCS2D01G594800 chr2D 648123452 648126776 3324 True 726.250000 1513 83.890500 743 3878 4 chr2D.!!$R3 3135
3 TraesCS2D01G594800 chr2B 784272773 784277269 4496 False 3374.500000 6431 92.476000 38 4583 2 chr2B.!!$F3 4545
4 TraesCS2D01G594800 chr2B 781801099 781804193 3094 False 1003.333333 1607 84.563667 844 3884 3 chr2B.!!$F2 3040
5 TraesCS2D01G594800 chr2B 781790026 781793409 3383 False 847.000000 1515 85.083000 764 3875 3 chr2B.!!$F1 3111
6 TraesCS2D01G594800 chrUn 31087663 31092535 4872 True 2538.666667 6320 94.265333 1 4871 3 chrUn.!!$R1 4870
7 TraesCS2D01G594800 chrUn 31320506 31323773 3267 False 1001.000000 1563 84.048000 668 3884 3 chrUn.!!$F2 3216
8 TraesCS2D01G594800 chrUn 31306318 31309218 2900 False 715.250000 1295 84.729750 876 3662 4 chrUn.!!$F1 2786
9 TraesCS2D01G594800 chr7A 280225994 280226524 530 True 281.000000 364 87.700000 23 581 2 chr7A.!!$R1 558

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
306 331 0.031585 CACATTGTGCAGTGCAGCTT 59.968 50.000 20.42 2.59 40.08 3.74 F
1450 1575 0.317479 GTCCAGTACCGTGCAGACTT 59.683 55.000 0.00 0.00 0.00 3.01 F
2064 2201 0.787787 CAAAGGAAATCGACGCGACA 59.212 50.000 15.93 0.00 39.18 4.35 F
3177 3338 1.004361 AGGCCTTCCTAATCCCGGT 59.996 57.895 0.00 0.00 42.06 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2414 0.031585 TGTCAGACAACCGAACCTCG 59.968 55.0 0.00 0.0 40.07 4.63 R
2588 2725 0.403271 AAGGCCTGCAACTCTGACAT 59.597 50.0 5.69 0.0 0.00 3.06 R
3790 4287 0.322546 GGCTGGGAAGGTTTCATCGT 60.323 55.0 0.00 0.0 0.00 3.73 R
4310 4808 0.248012 TGGTGGTGATGCGACGTAAT 59.752 50.0 0.00 0.0 0.00 1.89 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
55 56 2.680312 TGTAGCTCTTGATCTGCACC 57.320 50.000 0.00 0.00 0.00 5.01
136 137 7.607991 ACCTTCTGATATCACTTAAAACCACAG 59.392 37.037 0.00 0.00 0.00 3.66
152 153 1.000955 CACAGGGAGACTACTTGCGTT 59.999 52.381 0.00 0.00 0.00 4.84
270 295 1.267533 CACATTGTGCAGTGCAGCTTA 59.732 47.619 20.42 4.38 40.08 3.09
271 296 1.267806 ACATTGTGCAGTGCAGCTTAC 59.732 47.619 20.42 6.91 40.08 2.34
272 297 1.267533 CATTGTGCAGTGCAGCTTACA 59.732 47.619 20.42 9.86 40.08 2.41
273 298 0.662619 TTGTGCAGTGCAGCTTACAC 59.337 50.000 20.42 5.28 40.08 2.90
275 300 1.069978 TGTGCAGTGCAGCTTACACTA 59.930 47.619 20.42 2.59 46.44 2.74
277 302 0.723981 GCAGTGCAGCTTACACTAGC 59.276 55.000 16.74 17.12 46.44 3.42
304 329 4.238385 CACATTGTGCAGTGCAGC 57.762 55.556 20.42 13.96 40.08 5.25
305 330 1.658114 CACATTGTGCAGTGCAGCT 59.342 52.632 20.42 2.80 40.08 4.24
306 331 0.031585 CACATTGTGCAGTGCAGCTT 59.968 50.000 20.42 2.59 40.08 3.74
307 332 1.267533 CACATTGTGCAGTGCAGCTTA 59.732 47.619 20.42 4.38 40.08 3.09
308 333 2.094906 CACATTGTGCAGTGCAGCTTAT 60.095 45.455 20.42 6.71 40.08 1.73
309 334 2.559668 ACATTGTGCAGTGCAGCTTATT 59.440 40.909 20.42 0.00 40.08 1.40
310 335 3.758023 ACATTGTGCAGTGCAGCTTATTA 59.242 39.130 20.42 0.00 40.08 0.98
311 336 4.400251 ACATTGTGCAGTGCAGCTTATTAT 59.600 37.500 20.42 1.59 40.08 1.28
312 337 5.105635 ACATTGTGCAGTGCAGCTTATTATT 60.106 36.000 20.42 0.00 40.08 1.40
313 338 6.095300 ACATTGTGCAGTGCAGCTTATTATTA 59.905 34.615 20.42 0.00 40.08 0.98
314 339 5.739752 TGTGCAGTGCAGCTTATTATTAG 57.260 39.130 20.42 0.00 40.08 1.73
315 340 4.035558 TGTGCAGTGCAGCTTATTATTAGC 59.964 41.667 20.42 2.05 40.08 3.09
316 341 4.035558 GTGCAGTGCAGCTTATTATTAGCA 59.964 41.667 20.42 0.00 40.08 3.49
317 342 4.274214 TGCAGTGCAGCTTATTATTAGCAG 59.726 41.667 15.37 0.00 41.11 4.24
318 343 4.274459 GCAGTGCAGCTTATTATTAGCAGT 59.726 41.667 11.09 0.00 41.11 4.40
319 344 5.745514 CAGTGCAGCTTATTATTAGCAGTG 58.254 41.667 10.64 10.64 43.98 3.66
320 345 5.674525 AGTGCAGCTTATTATTAGCAGTGA 58.325 37.500 5.99 0.00 41.11 3.41
321 346 6.115446 AGTGCAGCTTATTATTAGCAGTGAA 58.885 36.000 5.99 0.00 41.11 3.18
322 347 6.769822 AGTGCAGCTTATTATTAGCAGTGAAT 59.230 34.615 5.99 0.00 41.11 2.57
339 364 8.531982 AGCAGTGAATATTAAGAGTGTAGACAA 58.468 33.333 0.00 0.00 0.00 3.18
360 385 4.616181 ACACTTTGTGCAACTTACACTC 57.384 40.909 0.00 0.00 38.86 3.51
581 617 4.124910 ACGTGAGTGCCAACTGTG 57.875 55.556 0.00 0.00 46.97 3.66
634 670 0.619832 TCCTGGGCTCTGCATCTCTT 60.620 55.000 0.00 0.00 0.00 2.85
639 675 1.427592 GGCTCTGCATCTCTTGACGC 61.428 60.000 0.00 0.00 31.27 5.19
681 721 6.928492 TGATTATGCAAGTTCCTTTTGGTTTC 59.072 34.615 0.00 0.00 41.38 2.78
686 726 4.432712 CAAGTTCCTTTTGGTTTCTGTGG 58.567 43.478 0.00 0.00 41.38 4.17
694 734 4.846779 TTTGGTTTCTGTGGCTATCAAC 57.153 40.909 0.00 0.00 0.00 3.18
709 750 5.973565 GGCTATCAACATTGCAACTTGATAC 59.026 40.000 24.61 21.31 36.33 2.24
1079 1144 4.194640 TCTGCTGAATATGAAGAAGGCAC 58.805 43.478 0.00 0.00 0.00 5.01
1319 1441 2.307768 TGAGGAAGAAGACAGTGACGT 58.692 47.619 0.00 0.00 0.00 4.34
1450 1575 0.317479 GTCCAGTACCGTGCAGACTT 59.683 55.000 0.00 0.00 0.00 3.01
1453 1578 1.429463 CAGTACCGTGCAGACTTTCC 58.571 55.000 0.00 0.00 0.00 3.13
1485 1610 9.157104 GAACAAAATAAGAGAGAGGTCCTAAAG 57.843 37.037 0.00 0.00 0.00 1.85
1508 1633 3.025924 CACTGAGAAAGGGCAGCAA 57.974 52.632 0.00 0.00 35.57 3.91
1534 1659 1.671054 CACAAGGCGGTACCAGTGG 60.671 63.158 13.54 7.91 40.90 4.00
1541 1666 1.024579 GCGGTACCAGTGGTTGATGG 61.025 60.000 22.49 7.12 42.60 3.51
1568 1693 4.499019 GGAAATGAAGCCGTTGAAGAAACA 60.499 41.667 0.00 0.00 38.84 2.83
1704 1829 2.159653 GCGTAAGAGGCAAGAACACATG 60.160 50.000 0.00 0.00 43.02 3.21
1726 1851 3.223435 CTCTCCTCGCTTAAGGATGGTA 58.777 50.000 4.29 0.00 44.43 3.25
1848 1973 1.974265 TTGTCCGATCAAAAGTGGCA 58.026 45.000 0.00 0.00 0.00 4.92
2021 2158 2.223971 CCAATCCATCCAAGCAATCTGC 60.224 50.000 0.00 0.00 45.46 4.26
2063 2200 1.059264 CTCAAAGGAAATCGACGCGAC 59.941 52.381 15.93 5.54 39.18 5.19
2064 2201 0.787787 CAAAGGAAATCGACGCGACA 59.212 50.000 15.93 0.00 39.18 4.35
2172 2309 4.447138 AAAGGTACCCAAAGATCACACA 57.553 40.909 8.74 0.00 0.00 3.72
2182 2319 5.243730 CCCAAAGATCACACAACAGGTTTAT 59.756 40.000 0.00 0.00 0.00 1.40
2220 2357 1.584308 GTGAAGTACGCTGATTCTCGC 59.416 52.381 0.00 0.00 0.00 5.03
2277 2414 7.308649 GGACTTCTTGTTGAGGGTAAAAAGATC 60.309 40.741 0.00 0.00 0.00 2.75
2373 2510 3.191162 TCAAGGAAATCGACATGGCAAAG 59.809 43.478 0.00 0.00 0.00 2.77
2412 2549 5.581126 TTCCTGCATCCATTGATACAAAC 57.419 39.130 0.00 0.00 0.00 2.93
2460 2597 1.541233 GGTAAGATCACCCATGCGAGG 60.541 57.143 0.00 0.00 31.91 4.63
2586 2723 2.224867 ACTGGTTGAAGGGGAGACATTG 60.225 50.000 0.00 0.00 0.00 2.82
2588 2725 2.445145 TGGTTGAAGGGGAGACATTGAA 59.555 45.455 0.00 0.00 0.00 2.69
2625 2765 3.552875 CCTTTCATCATCAGCATCCAGT 58.447 45.455 0.00 0.00 0.00 4.00
2775 2915 2.295253 AAGTCGTGATCAATCCGGAC 57.705 50.000 6.12 0.00 0.00 4.79
3021 3173 3.872027 GTCGAGCTTTTCCGACCC 58.128 61.111 13.17 0.00 46.54 4.46
3177 3338 1.004361 AGGCCTTCCTAATCCCGGT 59.996 57.895 0.00 0.00 42.06 5.28
3200 3385 1.913778 TGTCTAACACTACCGGAGCA 58.086 50.000 9.46 0.00 0.00 4.26
3243 3521 8.469200 CAAATTGACATGACCAACCTATATGTT 58.531 33.333 0.00 0.00 32.58 2.71
3333 3611 3.499338 TCAAGCAAAGGTGGTCATTGAT 58.501 40.909 0.00 0.00 33.24 2.57
3704 4066 3.499737 GTCAAGCCATGTCGCCGG 61.500 66.667 0.00 0.00 0.00 6.13
3785 4282 1.632965 GCCCCCAAGAAGGATACCGT 61.633 60.000 0.00 0.00 41.22 4.83
3790 4287 1.553248 CCAAGAAGGATACCGTCACCA 59.447 52.381 6.51 0.00 41.22 4.17
4021 4519 7.479980 TGGTGAAATTTGCTATGTGCTATTAC 58.520 34.615 0.00 0.00 43.37 1.89
4043 4541 9.778741 ATTACTTCAGTTCAAGTATCAGTTCAA 57.221 29.630 0.00 0.00 38.40 2.69
4139 4637 6.381994 AGGATTCATGCCATTGTTACTCATTT 59.618 34.615 0.00 0.00 0.00 2.32
4302 4800 5.928264 AGCATGTAGGCAAACAATCTTTTTC 59.072 36.000 0.00 0.00 35.83 2.29
4305 4803 4.651503 TGTAGGCAAACAATCTTTTTCCCA 59.348 37.500 0.00 0.00 0.00 4.37
4307 4805 6.495181 TGTAGGCAAACAATCTTTTTCCCATA 59.505 34.615 0.00 0.00 0.00 2.74
4308 4806 5.793817 AGGCAAACAATCTTTTTCCCATAC 58.206 37.500 0.00 0.00 0.00 2.39
4309 4807 5.543790 AGGCAAACAATCTTTTTCCCATACT 59.456 36.000 0.00 0.00 0.00 2.12
4310 4808 6.723977 AGGCAAACAATCTTTTTCCCATACTA 59.276 34.615 0.00 0.00 0.00 1.82
4392 4943 6.146837 GGAGAACCGTGAAGATTCATATCATG 59.853 42.308 0.00 0.00 39.73 3.07
4597 5155 4.637977 GGAAGGAAAGGATGATTCAGACAC 59.362 45.833 0.00 0.00 0.00 3.67
4701 5259 1.227263 CCGTGATACCGGGAAGCAG 60.227 63.158 6.32 0.00 44.32 4.24
4742 5300 2.236959 AAAGGCCACAACCCCACTGT 62.237 55.000 5.01 0.00 0.00 3.55
4790 5348 0.178068 GGCCTGCATCGAACCTAGAA 59.822 55.000 0.00 0.00 0.00 2.10
4851 5409 5.414454 TGTCAAAGCAAATGGTAGATACACC 59.586 40.000 0.00 0.00 39.20 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.500559 ACTGATCAAAAGCCAAATCCTAGATAC 59.499 37.037 0.00 0.00 0.00 2.24
16 17 4.922206 ACATCCTACTGATCAAAAGCCAA 58.078 39.130 0.00 0.00 0.00 4.52
20 21 6.815089 AGAGCTACATCCTACTGATCAAAAG 58.185 40.000 0.00 0.00 0.00 2.27
55 56 1.153208 GCAGAGCAGAGGGGATGTG 60.153 63.158 0.00 0.00 0.00 3.21
119 120 5.546499 AGTCTCCCTGTGGTTTTAAGTGATA 59.454 40.000 0.00 0.00 0.00 2.15
152 153 3.610040 ACAATCGGTATGACTGCAGAA 57.390 42.857 23.35 8.67 0.00 3.02
287 312 0.031585 AAGCTGCACTGCACAATGTG 59.968 50.000 9.36 9.36 33.79 3.21
288 313 1.608055 TAAGCTGCACTGCACAATGT 58.392 45.000 0.00 0.00 33.79 2.71
289 314 2.933495 ATAAGCTGCACTGCACAATG 57.067 45.000 0.00 0.00 33.79 2.82
290 315 5.587388 AATAATAAGCTGCACTGCACAAT 57.413 34.783 0.00 0.00 33.79 2.71
291 316 5.449041 GCTAATAATAAGCTGCACTGCACAA 60.449 40.000 0.00 0.00 37.01 3.33
292 317 4.035558 GCTAATAATAAGCTGCACTGCACA 59.964 41.667 0.00 0.00 37.01 4.57
293 318 4.035558 TGCTAATAATAAGCTGCACTGCAC 59.964 41.667 0.00 0.00 40.73 4.57
294 319 4.198530 TGCTAATAATAAGCTGCACTGCA 58.801 39.130 3.11 3.11 40.73 4.41
295 320 4.274459 ACTGCTAATAATAAGCTGCACTGC 59.726 41.667 1.02 0.00 41.19 4.40
296 321 5.525012 TCACTGCTAATAATAAGCTGCACTG 59.475 40.000 1.02 0.00 41.19 3.66
297 322 5.674525 TCACTGCTAATAATAAGCTGCACT 58.325 37.500 1.02 0.00 41.19 4.40
298 323 5.991328 TCACTGCTAATAATAAGCTGCAC 57.009 39.130 1.02 0.00 41.19 4.57
299 324 8.853077 ATATTCACTGCTAATAATAAGCTGCA 57.147 30.769 1.02 0.00 41.19 4.41
312 337 9.185680 TGTCTACACTCTTAATATTCACTGCTA 57.814 33.333 0.00 0.00 0.00 3.49
313 338 8.067751 TGTCTACACTCTTAATATTCACTGCT 57.932 34.615 0.00 0.00 0.00 4.24
314 339 8.596380 GTTGTCTACACTCTTAATATTCACTGC 58.404 37.037 0.00 0.00 0.00 4.40
315 340 9.639601 TGTTGTCTACACTCTTAATATTCACTG 57.360 33.333 0.00 0.00 0.00 3.66
339 364 3.063452 CGAGTGTAAGTTGCACAAAGTGT 59.937 43.478 23.54 4.13 39.17 3.55
360 385 5.201910 CAGTAGAGACTTCGAATTCTAGCG 58.798 45.833 16.99 6.78 31.73 4.26
550 582 1.131693 CTCACGTGCGTATACCACAGA 59.868 52.381 11.67 15.06 32.85 3.41
681 721 3.192001 AGTTGCAATGTTGATAGCCACAG 59.808 43.478 0.59 0.00 0.00 3.66
686 726 5.678483 CGTATCAAGTTGCAATGTTGATAGC 59.322 40.000 29.51 24.37 41.55 2.97
694 734 2.097466 GGACCCGTATCAAGTTGCAATG 59.903 50.000 0.59 0.00 0.00 2.82
709 750 4.643784 ACTAGTAAGTAATCACTGGACCCG 59.356 45.833 0.00 0.00 34.36 5.28
1057 1122 4.080695 AGTGCCTTCTTCATATTCAGCAGA 60.081 41.667 0.00 0.00 0.00 4.26
1079 1144 5.616424 CGTTCAAATGGCTCTTCTTCTTCAG 60.616 44.000 0.00 0.00 0.00 3.02
1319 1441 1.611977 CCGGATAATACGAGTCCTGCA 59.388 52.381 0.00 0.00 0.00 4.41
1453 1578 7.164803 ACCTCTCTCTTATTTTGTTCCTTCTG 58.835 38.462 0.00 0.00 0.00 3.02
1472 1597 1.144276 GCCCGCTTTAGGACCTCTC 59.856 63.158 0.00 0.00 0.00 3.20
1485 1610 2.747855 CCCTTTCTCAGTGCCCGC 60.748 66.667 0.00 0.00 0.00 6.13
1508 1633 0.036164 TACCGCCTTGTGCTCATTGT 59.964 50.000 0.00 0.00 38.05 2.71
1534 1659 4.498009 CGGCTTCATTTCCATACCATCAAC 60.498 45.833 0.00 0.00 0.00 3.18
1541 1666 4.394920 TCTTCAACGGCTTCATTTCCATAC 59.605 41.667 0.00 0.00 0.00 2.39
1568 1693 4.516698 CAGTAGCAAACCTGACAGACAATT 59.483 41.667 3.32 0.00 0.00 2.32
1726 1851 2.645838 TCCACTTCTTTCAGCTTGCT 57.354 45.000 0.00 0.00 0.00 3.91
1848 1973 3.685139 ACACCAGTGAAACGATCATCT 57.315 42.857 4.48 0.00 45.86 2.90
1890 2015 3.859961 CACTACGAGGTTCAGCATACTTG 59.140 47.826 0.00 0.00 0.00 3.16
2063 2200 1.812571 GGTGGCTGACATACAGGTTTG 59.187 52.381 0.00 0.00 45.82 2.93
2064 2201 1.705186 AGGTGGCTGACATACAGGTTT 59.295 47.619 0.00 0.00 45.82 3.27
2172 2309 5.163416 GCCATATCCTTTGCATAAACCTGTT 60.163 40.000 0.00 0.00 0.00 3.16
2182 2319 4.436113 TCACATAGCCATATCCTTTGCA 57.564 40.909 0.00 0.00 0.00 4.08
2254 2391 6.426937 TCGATCTTTTTACCCTCAACAAGAAG 59.573 38.462 0.00 0.00 0.00 2.85
2277 2414 0.031585 TGTCAGACAACCGAACCTCG 59.968 55.000 0.00 0.00 40.07 4.63
2460 2597 3.842925 TTCTTGGTCTGCCGCCACC 62.843 63.158 2.18 2.18 35.46 4.61
2481 2618 4.504864 CCATATCCTTTACCGGAATGAGCA 60.505 45.833 9.46 0.00 36.49 4.26
2586 2723 0.807496 GGCCTGCAACTCTGACATTC 59.193 55.000 0.00 0.00 0.00 2.67
2588 2725 0.403271 AAGGCCTGCAACTCTGACAT 59.597 50.000 5.69 0.00 0.00 3.06
2625 2765 1.270839 GGTGAGCCTTGTACAGCTGAA 60.271 52.381 23.35 3.06 40.11 3.02
2775 2915 6.825944 TCTGCATAGAACACTAGGCTATAG 57.174 41.667 13.38 0.00 42.15 1.31
2932 3084 5.662208 TGGCCATATCAATTTCTTTCATGGT 59.338 36.000 0.00 0.00 35.07 3.55
3021 3173 5.865552 CCTAGATTGCACAATTTGTCCAAAG 59.134 40.000 9.80 3.71 33.32 2.77
3177 3338 3.119245 GCTCCGGTAGTGTTAGACAATCA 60.119 47.826 0.00 0.00 0.00 2.57
3200 3385 1.841302 TTGCCTCTGCTCGTTCCCAT 61.841 55.000 0.00 0.00 38.71 4.00
3243 3521 2.377810 ATGGAGCGGGAGATGGCAA 61.378 57.895 0.00 0.00 0.00 4.52
3704 4066 3.251729 TGAAGAATGTTGCTGAGAACTGC 59.748 43.478 0.00 0.00 40.53 4.40
3785 4282 1.271163 GGGAAGGTTTCATCGTGGTGA 60.271 52.381 0.00 0.00 0.00 4.02
3790 4287 0.322546 GGCTGGGAAGGTTTCATCGT 60.323 55.000 0.00 0.00 0.00 3.73
4021 4519 8.997323 AGAATTGAACTGATACTTGAACTGAAG 58.003 33.333 0.00 0.00 0.00 3.02
4302 4800 3.918591 GTGATGCGACGTAATAGTATGGG 59.081 47.826 0.00 0.00 0.00 4.00
4305 4803 4.543692 GTGGTGATGCGACGTAATAGTAT 58.456 43.478 0.00 0.00 0.00 2.12
4307 4805 2.480759 GGTGGTGATGCGACGTAATAGT 60.481 50.000 0.00 0.00 0.00 2.12
4308 4806 2.124903 GGTGGTGATGCGACGTAATAG 58.875 52.381 0.00 0.00 0.00 1.73
4309 4807 1.477295 TGGTGGTGATGCGACGTAATA 59.523 47.619 0.00 0.00 0.00 0.98
4310 4808 0.248012 TGGTGGTGATGCGACGTAAT 59.752 50.000 0.00 0.00 0.00 1.89
4314 4812 1.741401 ACATGGTGGTGATGCGACG 60.741 57.895 0.00 0.00 0.00 5.12
4371 4922 5.528690 CCACATGATATGAATCTTCACGGTT 59.471 40.000 0.00 0.00 40.49 4.44
4374 4925 4.453478 CCCCACATGATATGAATCTTCACG 59.547 45.833 0.00 0.00 40.49 4.35
4392 4943 0.467290 TTGCACTCCACTTTCCCCAC 60.467 55.000 0.00 0.00 0.00 4.61
4597 5155 1.135859 GCTGCTTGACTCAAACGATGG 60.136 52.381 0.00 0.00 0.00 3.51
4646 5204 2.163815 AGTGACGGTGAAATCGAGTAGG 59.836 50.000 0.00 0.00 0.00 3.18
4652 5210 1.068474 GGACAGTGACGGTGAAATCG 58.932 55.000 0.00 0.00 0.00 3.34
4742 5300 1.342174 GGGTGTAGGTGTCGTCAAAGA 59.658 52.381 0.00 0.00 0.00 2.52
4790 5348 1.732259 CGAGTTACGCTTGGAGCAATT 59.268 47.619 0.50 0.00 42.58 2.32


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

AutoCloner maintained by Alex Coulton.