Multiple sequence alignment - TraesCS2D01G395000

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 TraesCS2D01G395000 chr2D 100.000 5519 0 0 1 5519 506407481 506401963 0.000000e+00 10192
1 TraesCS2D01G395000 chr2D 92.143 280 21 1 6 285 593231886 593232164 1.440000e-105 394
2 TraesCS2D01G395000 chr2D 90.875 263 23 1 545 806 76002727 76002989 8.800000e-93 351
3 TraesCS2D01G395000 chr2A 94.181 4623 163 49 987 5519 651085251 651080645 0.000000e+00 6950
4 TraesCS2D01G395000 chr2A 90.805 261 24 0 546 806 413179095 413178835 3.160000e-92 350
5 TraesCS2D01G395000 chr2B 95.151 4372 146 33 986 5330 594100342 594096010 0.000000e+00 6839
6 TraesCS2D01G395000 chr2B 96.606 766 24 2 1 766 594102612 594101849 0.000000e+00 1269
7 TraesCS2D01G395000 chr2B 91.525 413 32 3 4923 5334 402120331 402120741 2.890000e-157 566
8 TraesCS2D01G395000 chr2B 97.126 174 5 0 775 948 594101280 594101107 1.500000e-75 294
9 TraesCS2D01G395000 chr2B 89.950 199 10 4 5327 5519 594095984 594095790 1.190000e-61 248
10 TraesCS2D01G395000 chr3B 92.989 271 18 1 547 816 77005271 77005541 1.440000e-105 394
11 TraesCS2D01G395000 chr3B 90.909 264 23 1 543 806 738505644 738505906 2.450000e-93 353
12 TraesCS2D01G395000 chr5A 91.459 281 22 2 5 285 649571403 649571681 8.670000e-103 385
13 TraesCS2D01G395000 chr5A 91.221 262 21 2 546 806 566367239 566366979 6.800000e-94 355
14 TraesCS2D01G395000 chr5A 87.004 277 32 2 10 283 657391183 657390908 5.370000e-80 309
15 TraesCS2D01G395000 chr5B 90.508 295 18 7 14 304 376813876 376813588 1.120000e-101 381
16 TraesCS2D01G395000 chr5B 91.103 281 24 1 5 285 529577363 529577642 4.040000e-101 379
17 TraesCS2D01G395000 chr5B 90.942 276 24 1 8 283 565532006 565531732 2.430000e-98 370
18 TraesCS2D01G395000 chr6A 91.538 260 22 0 547 806 78486937 78486678 5.260000e-95 359
19 TraesCS2D01G395000 chr6A 91.188 261 23 0 546 806 6294752 6295012 6.800000e-94 355
20 TraesCS2D01G395000 chr5D 90.875 263 24 0 544 806 473469982 473469720 2.450000e-93 353
21 TraesCS2D01G395000 chr5D 86.738 279 31 4 6 284 438970373 438970101 6.950000e-79 305
22 TraesCS2D01G395000 chr3A 85.765 281 40 0 6 286 726238222 726237942 1.160000e-76 298


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 TraesCS2D01G395000 chr2D 506401963 506407481 5518 True 10192.0 10192 100.00000 1 5519 1 chr2D.!!$R1 5518
1 TraesCS2D01G395000 chr2A 651080645 651085251 4606 True 6950.0 6950 94.18100 987 5519 1 chr2A.!!$R2 4532
2 TraesCS2D01G395000 chr2B 594095790 594102612 6822 True 2162.5 6839 94.70825 1 5519 4 chr2B.!!$R1 5518

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
144 145 0.178973 AGTTGGCCCACCTTACAACC 60.179 55.000 2.72 0.00 43.02 3.77 F
165 166 0.868406 CACAAAGCGTCTTGGGTCTC 59.132 55.000 4.08 0.00 0.00 3.36 F
293 294 0.988832 ATTTGCTCTAACACGGGGGA 59.011 50.000 0.00 0.00 0.00 4.81 F
565 566 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94 F
958 1519 2.603776 GTCTCACCCGTCCACCCT 60.604 66.667 0.00 0.00 0.00 4.34 F
2592 3879 0.538057 TTGGCAGCCTTCTGAACCTG 60.538 55.000 14.15 8.28 42.95 4.00 F
3156 4443 0.176449 GCATCCCTGTTTCATTGGCC 59.824 55.000 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2769 1.219393 GAGGTTGGCGAGGAAGGAG 59.781 63.158 0.00 0.00 0.00 3.69 R
1485 2772 1.376037 GGTGAGGTTGGCGAGGAAG 60.376 63.158 0.00 0.00 0.00 3.46 R
2052 3339 2.933287 AGCCATGTGGGGAACGGA 60.933 61.111 0.54 0.00 37.04 4.69 R
2583 3870 1.686587 TCAAGAACTCGCAGGTTCAGA 59.313 47.619 17.26 12.68 45.52 3.27 R
2640 3927 0.664466 GCAAACCGAAAAGCTCTGCC 60.664 55.000 0.00 0.00 0.00 4.85 R
3754 5041 0.535102 AGGTTTCTGTGCTTCACCCG 60.535 55.000 0.00 0.00 32.73 5.28 R
4631 5932 0.909623 GCTACTTCCCCCACTTGCTA 59.090 55.000 0.00 0.00 0.00 3.49 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
85 86 1.602323 CCAACCTTGTAGCCGGCAA 60.602 57.895 31.54 13.85 0.00 4.52
89 90 0.909623 ACCTTGTAGCCGGCAAGTAT 59.090 50.000 31.54 10.27 41.08 2.12
136 137 3.279434 CTTCATTAGTAGTTGGCCCACC 58.721 50.000 2.72 0.00 0.00 4.61
144 145 0.178973 AGTTGGCCCACCTTACAACC 60.179 55.000 2.72 0.00 43.02 3.77
165 166 0.868406 CACAAAGCGTCTTGGGTCTC 59.132 55.000 4.08 0.00 0.00 3.36
218 219 4.494484 GCTTCTCTTCTCTCTTCTCCAAC 58.506 47.826 0.00 0.00 0.00 3.77
272 273 7.047891 TCTAACCTGCTTATGTCACCTTATTG 58.952 38.462 0.00 0.00 0.00 1.90
293 294 0.988832 ATTTGCTCTAACACGGGGGA 59.011 50.000 0.00 0.00 0.00 4.81
327 328 2.632377 CTTCTTGATTGGGCGAGCTAA 58.368 47.619 0.00 0.00 0.00 3.09
374 375 2.107950 TCAAATTCGGCCACCTACTG 57.892 50.000 2.24 0.00 0.00 2.74
507 508 7.065894 CACAACATCAGTTTTTACTCTCTTCG 58.934 38.462 0.00 0.00 35.28 3.79
565 566 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
588 589 3.069729 ACTCCGCATATTAGAGTTGGGTC 59.930 47.826 0.00 0.00 37.60 4.46
602 603 4.441792 AGTTGGGTCAAGTCAAATTTTGC 58.558 39.130 4.19 0.57 0.00 3.68
755 756 9.979578 CTATAAGCTTGATGAAAGTAGAGATGT 57.020 33.333 9.86 0.00 38.25 3.06
766 767 8.370493 TGAAAGTAGAGATGTTTTGACTTCAG 57.630 34.615 0.00 0.00 0.00 3.02
768 769 7.954788 AAGTAGAGATGTTTTGACTTCAGAC 57.045 36.000 0.00 0.00 0.00 3.51
769 770 7.055667 AGTAGAGATGTTTTGACTTCAGACA 57.944 36.000 1.48 1.48 0.00 3.41
770 771 7.500992 AGTAGAGATGTTTTGACTTCAGACAA 58.499 34.615 2.77 0.00 31.08 3.18
796 1357 5.240844 ACTTATGTGCACACTAAAAAGGACC 59.759 40.000 24.37 0.00 0.00 4.46
847 1408 8.712285 TCGAGTGTAAGGGAGTATTATTTTTG 57.288 34.615 0.00 0.00 0.00 2.44
893 1454 5.437946 AGCTCAGTGTAGTACTATAGCACA 58.562 41.667 18.92 7.84 44.26 4.57
956 1517 4.736896 GCGTCTCACCCGTCCACC 62.737 72.222 0.00 0.00 0.00 4.61
957 1518 4.065281 CGTCTCACCCGTCCACCC 62.065 72.222 0.00 0.00 0.00 4.61
958 1519 2.603776 GTCTCACCCGTCCACCCT 60.604 66.667 0.00 0.00 0.00 4.34
960 1521 4.394712 CTCACCCGTCCACCCTGC 62.395 72.222 0.00 0.00 0.00 4.85
2583 3870 1.675641 GTCGACCATTGGCAGCCTT 60.676 57.895 14.15 0.00 0.00 4.35
2592 3879 0.538057 TTGGCAGCCTTCTGAACCTG 60.538 55.000 14.15 8.28 42.95 4.00
2898 4185 1.717032 ACCTCACTGTGCTTGACCTA 58.283 50.000 2.12 0.00 0.00 3.08
2903 4190 2.146342 CACTGTGCTTGACCTAAGTGG 58.854 52.381 0.00 0.00 38.70 4.00
2934 4221 1.640670 ACTGGCCCAATACCAAGTGAT 59.359 47.619 0.00 0.00 36.56 3.06
2940 4227 3.118261 GCCCAATACCAAGTGATCTCTCA 60.118 47.826 0.00 0.00 0.00 3.27
3090 4377 3.993535 GCCTCTCTTGCCAACCTG 58.006 61.111 0.00 0.00 0.00 4.00
3156 4443 0.176449 GCATCCCTGTTTCATTGGCC 59.824 55.000 0.00 0.00 0.00 5.36
3216 4503 1.964223 GATCTTGCCGGAGAGATACCA 59.036 52.381 17.00 0.00 32.96 3.25
3516 4803 4.600576 TCGAGCGGCACAAGCACA 62.601 61.111 1.45 0.00 44.61 4.57
3657 4944 2.554032 CAAGGCTTGTTACAGTGAAGGG 59.446 50.000 19.07 0.00 0.00 3.95
3909 5196 1.379916 CCACATCCTCAACTGGCCA 59.620 57.895 4.71 4.71 0.00 5.36
4011 5298 3.449018 AGCCACAGAACATACTCTTCGAT 59.551 43.478 0.00 0.00 0.00 3.59
4041 5328 2.079925 GAGCCACACCTGTCTGATTTC 58.920 52.381 0.00 0.00 0.00 2.17
4206 5493 1.890876 ACAGCTTTGGCATCGTGTTA 58.109 45.000 0.00 0.00 41.70 2.41
4212 5499 2.552599 TTGGCATCGTGTTACTGGAA 57.447 45.000 0.00 0.00 0.00 3.53
4314 5601 4.828925 GCAGTGGCCGAGCTCCTC 62.829 72.222 8.47 0.00 0.00 3.71
4335 5622 4.154347 CCGGGTCTGCTGGAGCTC 62.154 72.222 4.71 4.71 41.70 4.09
4386 5673 2.276740 CTGGGGATCAAGGTGGGC 59.723 66.667 0.00 0.00 0.00 5.36
4571 5866 5.578727 CAGATTCAGTTCAGTAGCTTGTACC 59.421 44.000 0.00 0.00 0.00 3.34
4618 5919 9.607988 TTTCTTAGTTCAGATTAGTGTTTGTCA 57.392 29.630 0.00 0.00 0.00 3.58
4619 5920 8.818141 TCTTAGTTCAGATTAGTGTTTGTCAG 57.182 34.615 0.00 0.00 0.00 3.51
4620 5921 8.638873 TCTTAGTTCAGATTAGTGTTTGTCAGA 58.361 33.333 0.00 0.00 0.00 3.27
4622 5923 9.778741 TTAGTTCAGATTAGTGTTTGTCAGATT 57.221 29.630 0.00 0.00 0.00 2.40
4623 5924 8.316640 AGTTCAGATTAGTGTTTGTCAGATTC 57.683 34.615 0.00 0.00 0.00 2.52
4624 5925 7.933577 AGTTCAGATTAGTGTTTGTCAGATTCA 59.066 33.333 0.00 0.00 0.00 2.57
4625 5926 7.895975 TCAGATTAGTGTTTGTCAGATTCAG 57.104 36.000 0.00 0.00 0.00 3.02
4630 5931 4.063689 AGTGTTTGTCAGATTCAGCTCAG 58.936 43.478 0.00 0.00 0.00 3.35
4631 5932 3.812053 GTGTTTGTCAGATTCAGCTCAGT 59.188 43.478 0.00 0.00 0.00 3.41
4632 5933 4.991056 GTGTTTGTCAGATTCAGCTCAGTA 59.009 41.667 0.00 0.00 0.00 2.74
4655 5969 1.376812 GTGGGGGAAGTAGCCGTTG 60.377 63.158 0.00 0.00 0.00 4.10
4866 6189 5.643777 ACTCTGTTAGGAAATTGATTCGTGG 59.356 40.000 0.00 0.00 39.05 4.94
4960 6290 5.576774 CAGATCTTTGTAATGTCGTGCTGTA 59.423 40.000 0.00 0.00 0.00 2.74
4966 6297 5.933187 TGTAATGTCGTGCTGTACATTTT 57.067 34.783 13.65 0.00 42.22 1.82
4967 6298 5.684850 TGTAATGTCGTGCTGTACATTTTG 58.315 37.500 13.65 0.00 42.22 2.44
4968 6299 4.829064 AATGTCGTGCTGTACATTTTGT 57.171 36.364 0.00 0.00 42.22 2.83
4969 6300 3.870723 TGTCGTGCTGTACATTTTGTC 57.129 42.857 0.00 0.00 0.00 3.18
4970 6301 3.462982 TGTCGTGCTGTACATTTTGTCT 58.537 40.909 0.00 0.00 0.00 3.41
4971 6302 3.493129 TGTCGTGCTGTACATTTTGTCTC 59.507 43.478 0.00 0.00 0.00 3.36
4973 6304 4.025229 GTCGTGCTGTACATTTTGTCTCAA 60.025 41.667 0.00 0.00 0.00 3.02
4974 6305 4.754618 TCGTGCTGTACATTTTGTCTCAAT 59.245 37.500 0.00 0.00 0.00 2.57
4975 6306 5.082059 CGTGCTGTACATTTTGTCTCAATC 58.918 41.667 0.00 0.00 0.00 2.67
4977 6308 6.566564 CGTGCTGTACATTTTGTCTCAATCTT 60.567 38.462 0.00 0.00 0.00 2.40
4978 6309 6.580041 GTGCTGTACATTTTGTCTCAATCTTG 59.420 38.462 0.00 0.00 0.00 3.02
4986 6320 7.609146 ACATTTTGTCTCAATCTTGCTATCTCA 59.391 33.333 0.00 0.00 0.00 3.27
4987 6321 8.622157 CATTTTGTCTCAATCTTGCTATCTCAT 58.378 33.333 0.00 0.00 0.00 2.90
5030 6364 5.163663 GGAAATGATGCTTCATGACCGTTAA 60.164 40.000 15.21 0.00 41.83 2.01
5140 6475 2.621668 GGCCCTGCTTATCCTTTGTCTT 60.622 50.000 0.00 0.00 0.00 3.01
5308 6649 0.599558 CTCCACCGTCGTACTTTCCA 59.400 55.000 0.00 0.00 0.00 3.53
5330 6671 6.042897 TCCATGAGCATCTAAATCTCATCAGT 59.957 38.462 0.00 0.00 43.44 3.41
5368 6738 4.214971 GCACAATCAGGACCTGCATTATAG 59.785 45.833 17.33 10.60 0.00 1.31
5369 6739 5.371526 CACAATCAGGACCTGCATTATAGT 58.628 41.667 17.33 8.81 0.00 2.12
5370 6740 6.524734 CACAATCAGGACCTGCATTATAGTA 58.475 40.000 17.33 0.00 0.00 1.82
5371 6741 6.425114 CACAATCAGGACCTGCATTATAGTAC 59.575 42.308 17.33 0.00 0.00 2.73
5439 6810 1.408702 GAGGACAGCCAGTTTTGCAAA 59.591 47.619 8.05 8.05 36.29 3.68
5483 6854 5.121811 AGTAGCTGAAATGAGCCACAATAG 58.878 41.667 0.00 0.00 40.08 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 3.131396 AGACGCTTTGTGAGGTTGTAAG 58.869 45.455 0.00 0.00 0.00 2.34
144 145 0.868406 GACCCAAGACGCTTTGTGAG 59.132 55.000 0.00 0.00 0.00 3.51
165 166 1.164662 TAGTAGCCGGCTCTAGCACG 61.165 60.000 36.73 5.23 44.36 5.34
245 246 5.091261 AGGTGACATAAGCAGGTTAGAAG 57.909 43.478 0.00 0.00 0.00 2.85
247 248 6.808321 ATAAGGTGACATAAGCAGGTTAGA 57.192 37.500 0.00 0.00 0.00 2.10
248 249 6.823689 ACAATAAGGTGACATAAGCAGGTTAG 59.176 38.462 0.00 0.00 0.00 2.34
249 250 6.717289 ACAATAAGGTGACATAAGCAGGTTA 58.283 36.000 0.00 0.00 0.00 2.85
250 251 5.570320 ACAATAAGGTGACATAAGCAGGTT 58.430 37.500 0.00 0.00 0.00 3.50
251 252 5.179452 ACAATAAGGTGACATAAGCAGGT 57.821 39.130 0.00 0.00 0.00 4.00
272 273 2.093341 TCCCCCGTGTTAGAGCAAATAC 60.093 50.000 0.00 0.00 0.00 1.89
293 294 2.766263 TCAAGAAGCGATACCACCATCT 59.234 45.455 0.00 0.00 0.00 2.90
327 328 0.768622 TGGGACATTCTCGGGTGTTT 59.231 50.000 0.00 0.00 0.00 2.83
437 438 6.374333 TGAGCAAACCTCCTAATACACAATTC 59.626 38.462 0.00 0.00 39.98 2.17
440 441 5.221843 ACTGAGCAAACCTCCTAATACACAA 60.222 40.000 0.00 0.00 39.98 3.33
443 444 5.482526 TGTACTGAGCAAACCTCCTAATACA 59.517 40.000 0.00 0.00 39.98 2.29
444 445 5.974108 TGTACTGAGCAAACCTCCTAATAC 58.026 41.667 0.00 0.00 39.98 1.89
527 528 9.357161 AGGGAGTACATTAAAGTAGTGATCTAG 57.643 37.037 3.01 0.00 0.00 2.43
565 566 4.220724 ACCCAACTCTAATATGCGGAGTA 58.779 43.478 6.10 0.00 39.09 2.59
588 589 8.233190 TGGTTAAACTTTGCAAAATTTGACTTG 58.767 29.630 28.37 12.45 0.00 3.16
632 633 6.681729 ATATTCGGTATGGTAGGTGTTGAT 57.318 37.500 0.00 0.00 0.00 2.57
729 730 9.979578 ACATCTCTACTTTCATCAAGCTTATAG 57.020 33.333 0.00 0.00 35.65 1.31
755 756 7.487829 GCACATAAGTTTTGTCTGAAGTCAAAA 59.512 33.333 10.19 10.19 39.44 2.44
766 767 7.979115 TTTTAGTGTGCACATAAGTTTTGTC 57.021 32.000 24.69 5.70 0.00 3.18
768 769 7.704472 TCCTTTTTAGTGTGCACATAAGTTTTG 59.296 33.333 24.69 9.62 0.00 2.44
769 770 7.704899 GTCCTTTTTAGTGTGCACATAAGTTTT 59.295 33.333 24.69 5.69 0.00 2.43
770 771 7.200455 GTCCTTTTTAGTGTGCACATAAGTTT 58.800 34.615 24.69 7.41 0.00 2.66
773 1334 5.616866 CGGTCCTTTTTAGTGTGCACATAAG 60.617 44.000 24.69 18.77 0.00 1.73
796 1357 2.744202 CAAAAACATCTCACTCCCTCCG 59.256 50.000 0.00 0.00 0.00 4.63
808 1369 2.286772 ACACTCGAACCGCAAAAACATC 60.287 45.455 0.00 0.00 0.00 3.06
847 1408 1.478288 CCAAATGGCCTCTCCCTCATC 60.478 57.143 3.32 0.00 0.00 2.92
893 1454 2.486982 GAGCTGATGAAATGTGTGCAGT 59.513 45.455 0.00 0.00 0.00 4.40
961 1522 3.920093 AAGAAAAGGAGCGGGCGGG 62.920 63.158 0.00 0.00 0.00 6.13
964 1525 1.027255 GGAGAAGAAAAGGAGCGGGC 61.027 60.000 0.00 0.00 0.00 6.13
1482 2769 1.219393 GAGGTTGGCGAGGAAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
1485 2772 1.376037 GGTGAGGTTGGCGAGGAAG 60.376 63.158 0.00 0.00 0.00 3.46
1633 2920 3.760035 GAGCTTGGTCGCCGAGGA 61.760 66.667 13.08 0.00 35.62 3.71
2052 3339 2.933287 AGCCATGTGGGGAACGGA 60.933 61.111 0.54 0.00 37.04 4.69
2583 3870 1.686587 TCAAGAACTCGCAGGTTCAGA 59.313 47.619 17.26 12.68 45.52 3.27
2592 3879 2.165437 ACCAGAGAGATCAAGAACTCGC 59.835 50.000 0.00 3.52 38.08 5.03
2640 3927 0.664466 GCAAACCGAAAAGCTCTGCC 60.664 55.000 0.00 0.00 0.00 4.85
2641 3928 0.664466 GGCAAACCGAAAAGCTCTGC 60.664 55.000 0.00 0.00 0.00 4.26
2856 4143 1.915614 AACAATTGGCGAGCTCTGCG 61.916 55.000 19.37 6.69 0.00 5.18
2898 4185 1.546323 CCAGTCAGATGGTTGCCACTT 60.546 52.381 0.00 0.00 35.80 3.16
2903 4190 2.048603 GGGCCAGTCAGATGGTTGC 61.049 63.158 4.39 0.00 42.75 4.17
2934 4221 1.964223 AGTTCGTCAAGCCTTGAGAGA 59.036 47.619 7.55 7.87 41.01 3.10
2940 4227 1.416401 TCTTCCAGTTCGTCAAGCCTT 59.584 47.619 0.00 0.00 0.00 4.35
3060 4347 3.224324 GAGGCCGGTATCTCGCCA 61.224 66.667 1.90 0.00 0.00 5.69
3090 4377 2.431601 AGCGTCTGCAGCTTCGAC 60.432 61.111 22.53 10.53 43.24 4.20
3156 4443 2.290514 TGACAGAAGGCTTGGAATCTGG 60.291 50.000 15.50 1.19 42.76 3.86
3198 4485 1.112113 GTGGTATCTCTCCGGCAAGA 58.888 55.000 7.90 7.90 0.00 3.02
3252 4539 0.886490 AGTCTCGGTTGGCAGCAAAG 60.886 55.000 3.14 0.00 0.00 2.77
3516 4803 1.603236 CCAGCTTCGTCTGGCTCTCT 61.603 60.000 7.86 0.00 46.11 3.10
3642 4929 1.764134 ACGGTCCCTTCACTGTAACAA 59.236 47.619 0.00 0.00 33.87 2.83
3657 4944 1.090052 GTAAGATGGCCAGCACGGTC 61.090 60.000 25.38 8.91 41.21 4.79
3754 5041 0.535102 AGGTTTCTGTGCTTCACCCG 60.535 55.000 0.00 0.00 32.73 5.28
4011 5298 1.891919 GTGTGGCTCAAAGTCGGCA 60.892 57.895 0.00 0.00 0.00 5.69
4206 5493 2.743718 CCGGTGAGCAGTTCCAGT 59.256 61.111 0.00 0.00 0.00 4.00
4528 5817 2.194056 CAATGCCGGCTGAGGGAT 59.806 61.111 29.70 8.67 44.57 3.85
4610 5911 4.077300 ACTGAGCTGAATCTGACAAACA 57.923 40.909 0.00 0.00 0.00 2.83
4630 5931 1.407025 GCTACTTCCCCCACTTGCTAC 60.407 57.143 0.00 0.00 0.00 3.58
4631 5932 0.909623 GCTACTTCCCCCACTTGCTA 59.090 55.000 0.00 0.00 0.00 3.49
4632 5933 1.685820 GCTACTTCCCCCACTTGCT 59.314 57.895 0.00 0.00 0.00 3.91
4635 5936 1.131928 AACGGCTACTTCCCCCACTT 61.132 55.000 0.00 0.00 0.00 3.16
4636 5937 1.538135 AACGGCTACTTCCCCCACT 60.538 57.895 0.00 0.00 0.00 4.00
4655 5969 1.558294 ACCACGAGATTAGAAACCCCC 59.442 52.381 0.00 0.00 0.00 5.40
4933 6263 2.930040 ACGACATTACAAAGATCTGGCG 59.070 45.455 0.00 0.00 43.76 5.69
4960 6290 7.609146 TGAGATAGCAAGATTGAGACAAAATGT 59.391 33.333 0.00 0.00 0.00 2.71
4966 6297 7.333323 TCAAATGAGATAGCAAGATTGAGACA 58.667 34.615 0.00 0.00 0.00 3.41
4967 6298 7.783090 TCAAATGAGATAGCAAGATTGAGAC 57.217 36.000 0.00 0.00 0.00 3.36
4968 6299 7.660617 GGATCAAATGAGATAGCAAGATTGAGA 59.339 37.037 0.00 0.00 0.00 3.27
4969 6300 7.444487 TGGATCAAATGAGATAGCAAGATTGAG 59.556 37.037 0.00 0.00 0.00 3.02
4970 6301 7.284820 TGGATCAAATGAGATAGCAAGATTGA 58.715 34.615 0.00 0.00 0.00 2.57
4971 6302 7.506328 TGGATCAAATGAGATAGCAAGATTG 57.494 36.000 0.00 0.00 0.00 2.67
4973 6304 7.515586 TCTTGGATCAAATGAGATAGCAAGAT 58.484 34.615 0.00 0.00 0.00 2.40
4974 6305 6.892485 TCTTGGATCAAATGAGATAGCAAGA 58.108 36.000 0.00 0.00 0.00 3.02
4975 6306 6.205076 CCTCTTGGATCAAATGAGATAGCAAG 59.795 42.308 9.60 0.00 34.57 4.01
4977 6308 5.367644 TCCTCTTGGATCAAATGAGATAGCA 59.632 40.000 9.60 0.00 37.46 3.49
4978 6309 5.862845 TCCTCTTGGATCAAATGAGATAGC 58.137 41.667 9.60 0.00 37.46 2.97
5030 6364 3.088532 TGTGCAGAGGAAAACAACAAGT 58.911 40.909 0.00 0.00 0.00 3.16
5098 6433 1.271054 CCCTTCTCATTATCCAGGGCG 60.271 57.143 0.00 0.00 37.98 6.13
5140 6475 1.486310 AGAAAGCGTATCCATCCAGCA 59.514 47.619 0.00 0.00 0.00 4.41
5197 6532 3.119245 CCACTGCTCCAAATCATTTCCTG 60.119 47.826 0.00 0.00 0.00 3.86
5240 6581 2.006888 TGCCAAATAAGCGTACAGAGC 58.993 47.619 0.00 0.00 0.00 4.09
5330 6671 1.515020 GTGCAACAACAGTGGCCAA 59.485 52.632 7.24 0.00 36.32 4.52
5368 6738 8.336801 AGTTTCCAGATTTCATTAACTGGTAC 57.663 34.615 0.00 0.00 46.68 3.34
5369 6739 8.934023 AAGTTTCCAGATTTCATTAACTGGTA 57.066 30.769 0.00 0.00 46.68 3.25
5370 6740 7.839680 AAGTTTCCAGATTTCATTAACTGGT 57.160 32.000 0.00 0.00 46.68 4.00
5454 6825 4.714802 TGGCTCATTTCAGCTACTACCTTA 59.285 41.667 0.00 0.00 39.58 2.69
5462 6833 4.080356 ACCTATTGTGGCTCATTTCAGCTA 60.080 41.667 0.00 0.00 39.58 3.32
5463 6834 3.285484 CCTATTGTGGCTCATTTCAGCT 58.715 45.455 0.00 0.00 39.58 4.24


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

AutoCloner maintained by Alex Coulton.