Multiple sequence alignment - TraesCS5D01G168900

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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 TraesCS5D01G168900 chr5D 100.000 2864 0 0 1 2864 264794313 264797176 0.000000e+00 5289.0
1 TraesCS5D01G168900 chr5A 93.426 2890 137 28 1 2859 351473215 351476082 0.000000e+00 4235.0
2 TraesCS5D01G168900 chr5A 94.872 39 2 0 1262 1300 470194386 470194424 8.570000e-06 62.1
3 TraesCS5D01G168900 chr5B 92.605 2096 82 27 426 2479 297105350 297107414 0.000000e+00 2944.0
4 TraesCS5D01G168900 chr5B 96.154 390 9 1 2472 2861 297112871 297113254 1.450000e-177 632.0
5 TraesCS5D01G168900 chr5B 81.928 415 51 14 1 405 297096894 297097294 2.130000e-86 329.0
6 TraesCS5D01G168900 chr5B 92.308 39 3 0 1262 1300 436257242 436257280 3.990000e-04 56.5
7 TraesCS5D01G168900 chr4B 85.246 305 43 2 57 361 311376873 311377175 2.140000e-81 313.0
8 TraesCS5D01G168900 chr4B 94.286 35 2 0 12 46 395663355 395663389 1.000000e-03 54.7
9 TraesCS5D01G168900 chr4A 97.297 37 0 1 194 230 585702354 585702389 8.570000e-06 62.1
10 TraesCS5D01G168900 chr7B 92.683 41 2 1 6 46 515185537 515185498 1.110000e-04 58.4
11 TraesCS5D01G168900 chr6D 100.000 31 0 0 13 43 103202671 103202641 1.110000e-04 58.4
12 TraesCS5D01G168900 chr6D 96.875 32 0 1 16 46 221269000 221268969 5.000000e-03 52.8
13 TraesCS5D01G168900 chr2A 94.737 38 1 1 194 230 195833687 195833724 1.110000e-04 58.4
14 TraesCS5D01G168900 chr1B 97.059 34 0 1 14 46 178378849 178378882 3.990000e-04 56.5
15 TraesCS5D01G168900 chr6A 100.000 29 0 0 13 41 442079276 442079248 1.000000e-03 54.7
16 TraesCS5D01G168900 chr2D 96.970 33 0 1 15 46 498231623 498231591 1.000000e-03 54.7
17 TraesCS5D01G168900 chr2B 100.000 29 0 0 18 46 479239814 479239786 1.000000e-03 54.7
18 TraesCS5D01G168900 chr6B 96.875 32 0 1 16 46 374455900 374455869 5.000000e-03 52.8


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 TraesCS5D01G168900 chr5D 264794313 264797176 2863 False 5289 5289 100.000 1 2864 1 chr5D.!!$F1 2863
1 TraesCS5D01G168900 chr5A 351473215 351476082 2867 False 4235 4235 93.426 1 2859 1 chr5A.!!$F1 2858
2 TraesCS5D01G168900 chr5B 297105350 297107414 2064 False 2944 2944 92.605 426 2479 1 chr5B.!!$F2 2053

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
555 558 0.106967 GATTTGAGACCAGGGGCCTC 60.107 60.0 0.84 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2426 0.994247 TGGGAGCACACCATCTGATT 59.006 50.0 0.0 0.0 31.83 2.57 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
34 35 4.164221 ACACAAATACTACCTCCATCCTGG 59.836 45.833 0.00 0.00 39.43 4.45
43 44 2.310538 CCTCCATCCTGGTTTATTGGC 58.689 52.381 0.00 0.00 39.03 4.52
49 50 1.065272 TCCTGGTTTATTGGCCCGTAC 60.065 52.381 0.00 0.00 0.00 3.67
54 55 0.612229 TTTATTGGCCCGTACCGTGA 59.388 50.000 0.00 0.00 0.00 4.35
72 74 3.508793 CGTGAGGGGAGTTACTCTAACAA 59.491 47.826 12.41 0.00 41.07 2.83
73 75 4.159879 CGTGAGGGGAGTTACTCTAACAAT 59.840 45.833 12.41 0.00 41.07 2.71
74 76 5.359009 CGTGAGGGGAGTTACTCTAACAATA 59.641 44.000 12.41 0.00 41.07 1.90
79 81 8.303780 AGGGGAGTTACTCTAACAATAAGTAC 57.696 38.462 12.41 0.00 41.07 2.73
111 113 2.716217 ACAAGGGCTAGATCAAGCAAC 58.284 47.619 0.00 0.00 44.64 4.17
114 116 1.440145 GGGCTAGATCAAGCAACGGC 61.440 60.000 0.00 0.00 44.64 5.68
138 140 4.261994 GCAAGTGTGACACATGGGTTTTAT 60.262 41.667 20.60 0.00 36.74 1.40
173 176 5.374921 CTCTCGGAGGAGGTAATAACACTA 58.625 45.833 4.96 0.00 40.85 2.74
183 186 5.181748 AGGTAATAACACTACGTCTCGAGT 58.818 41.667 13.13 0.00 0.00 4.18
185 188 6.150140 AGGTAATAACACTACGTCTCGAGTTT 59.850 38.462 13.13 0.30 0.00 2.66
189 192 2.620115 ACACTACGTCTCGAGTTTTGGA 59.380 45.455 13.13 0.00 0.00 3.53
194 197 2.295349 ACGTCTCGAGTTTTGGAAGCTA 59.705 45.455 13.13 0.00 0.00 3.32
197 200 4.246458 GTCTCGAGTTTTGGAAGCTATGT 58.754 43.478 13.13 0.00 0.00 2.29
201 204 5.757886 TCGAGTTTTGGAAGCTATGTTTTG 58.242 37.500 0.00 0.00 0.00 2.44
202 205 5.298276 TCGAGTTTTGGAAGCTATGTTTTGT 59.702 36.000 0.00 0.00 0.00 2.83
215 218 6.651225 AGCTATGTTTTGTTTCTCTAGTGTCC 59.349 38.462 0.00 0.00 0.00 4.02
216 219 6.426937 GCTATGTTTTGTTTCTCTAGTGTCCA 59.573 38.462 0.00 0.00 0.00 4.02
238 241 7.940178 CCAATGATTACAATGGATGTGAATG 57.060 36.000 0.00 0.00 46.68 2.67
261 264 2.901051 CTTACTGTGCTACGGGGCGG 62.901 65.000 0.00 0.00 34.52 6.13
273 276 0.179108 CGGGGCGGCTTATATAGAGC 60.179 60.000 9.56 7.84 39.41 4.09
275 278 0.531200 GGGCGGCTTATATAGAGCGT 59.469 55.000 9.56 0.00 41.03 5.07
276 279 1.630148 GGCGGCTTATATAGAGCGTG 58.370 55.000 0.00 6.93 41.03 5.34
313 316 5.161943 AGCTACGTTACAAAGAGGGATTT 57.838 39.130 0.00 0.00 0.00 2.17
342 345 7.618502 AACATGAATTATTACAGGCGTTACA 57.381 32.000 0.00 0.00 0.00 2.41
363 366 6.985188 ACACATGGTAACTGATGTATTGAC 57.015 37.500 0.00 0.00 31.46 3.18
365 368 7.847096 ACACATGGTAACTGATGTATTGACTA 58.153 34.615 0.00 0.00 31.46 2.59
366 369 7.981789 ACACATGGTAACTGATGTATTGACTAG 59.018 37.037 0.00 0.00 31.46 2.57
367 370 7.981789 CACATGGTAACTGATGTATTGACTAGT 59.018 37.037 0.00 0.00 31.46 2.57
368 371 9.197306 ACATGGTAACTGATGTATTGACTAGTA 57.803 33.333 0.00 0.00 30.86 1.82
389 392 2.357327 TGAACGCTAGTAATGCACGT 57.643 45.000 0.00 0.00 38.88 4.49
408 411 1.254975 TAGGCGTGCACCTCTTAGCA 61.255 55.000 12.15 0.00 41.50 3.49
443 446 1.347050 CGGACCGTCTATCTCCCTCTA 59.653 57.143 5.48 0.00 0.00 2.43
446 449 3.181441 GGACCGTCTATCTCCCTCTAACT 60.181 52.174 0.00 0.00 0.00 2.24
452 455 5.106869 CGTCTATCTCCCTCTAACTGAATCG 60.107 48.000 0.00 0.00 0.00 3.34
530 533 3.054802 GGATGGAACCTTGACTGATGTCT 60.055 47.826 0.00 0.00 43.29 3.41
547 550 4.639078 TGTCTGAATGGATTTGAGACCA 57.361 40.909 0.00 0.00 40.57 4.02
548 551 4.582869 TGTCTGAATGGATTTGAGACCAG 58.417 43.478 0.00 0.00 39.62 4.00
549 552 3.944015 GTCTGAATGGATTTGAGACCAGG 59.056 47.826 0.00 0.00 39.62 4.45
550 553 3.054139 TCTGAATGGATTTGAGACCAGGG 60.054 47.826 0.00 0.00 39.62 4.45
551 554 2.025037 TGAATGGATTTGAGACCAGGGG 60.025 50.000 0.00 0.00 39.62 4.79
552 555 0.259938 ATGGATTTGAGACCAGGGGC 59.740 55.000 0.00 0.00 39.62 5.80
554 557 1.575447 GGATTTGAGACCAGGGGCCT 61.575 60.000 0.84 0.00 0.00 5.19
555 558 0.106967 GATTTGAGACCAGGGGCCTC 60.107 60.000 0.84 0.00 0.00 4.70
556 559 0.846427 ATTTGAGACCAGGGGCCTCA 60.846 55.000 4.79 0.00 35.38 3.86
587 591 3.181459 CGTTGTGGGTCCCATGTATGATA 60.181 47.826 15.49 0.00 35.28 2.15
621 626 5.354792 CCTCTCGTACTCTACCTATAATGGC 59.645 48.000 0.00 0.00 0.00 4.40
637 642 1.063070 TGGCTAACCCCAACAGTCCA 61.063 55.000 0.00 0.00 33.59 4.02
715 720 6.237969 GCGTGTCACCAAAAATTACATTGTTT 60.238 34.615 0.00 0.00 0.00 2.83
828 846 1.840635 AGAGGGACTAATCAACCAGGC 59.159 52.381 0.00 0.00 41.55 4.85
1503 1530 3.917760 CCCATCCCCGACGAGCTC 61.918 72.222 2.73 2.73 0.00 4.09
1704 1731 4.776322 CCAATGCGAGGCCACGGA 62.776 66.667 24.15 22.25 38.05 4.69
1902 1939 1.399714 CTGATGCCGGTGGTACTCTA 58.600 55.000 1.90 0.00 0.00 2.43
1903 1940 1.067212 CTGATGCCGGTGGTACTCTAC 59.933 57.143 1.90 0.00 0.00 2.59
1904 1941 1.108776 GATGCCGGTGGTACTCTACA 58.891 55.000 1.90 0.00 0.00 2.74
1905 1942 1.067212 GATGCCGGTGGTACTCTACAG 59.933 57.143 1.90 0.00 0.00 2.74
1906 1943 0.038599 TGCCGGTGGTACTCTACAGA 59.961 55.000 1.90 0.00 0.00 3.41
1907 1944 1.341679 TGCCGGTGGTACTCTACAGAT 60.342 52.381 1.90 0.00 0.00 2.90
1908 1945 1.067212 GCCGGTGGTACTCTACAGATG 59.933 57.143 1.90 0.00 0.00 2.90
2151 2195 3.650942 TCTTCTCTTTCAGCTTGGGGTAA 59.349 43.478 0.00 0.00 0.00 2.85
2152 2196 3.703001 TCTCTTTCAGCTTGGGGTAAG 57.297 47.619 0.00 0.00 39.49 2.34
2153 2197 2.979678 TCTCTTTCAGCTTGGGGTAAGT 59.020 45.455 0.00 0.00 38.70 2.24
2154 2198 4.164981 TCTCTTTCAGCTTGGGGTAAGTA 58.835 43.478 0.00 0.00 38.70 2.24
2155 2199 4.783227 TCTCTTTCAGCTTGGGGTAAGTAT 59.217 41.667 0.00 0.00 38.70 2.12
2156 2200 5.250774 TCTCTTTCAGCTTGGGGTAAGTATT 59.749 40.000 0.00 0.00 38.70 1.89
2157 2201 6.442564 TCTCTTTCAGCTTGGGGTAAGTATTA 59.557 38.462 0.00 0.00 38.70 0.98
2204 2252 0.173708 CGACCCTCTGGAGTTAGTGC 59.826 60.000 0.00 0.00 34.81 4.40
2230 2278 0.741915 GAGAGGGACAGAGTTAGGCG 59.258 60.000 0.00 0.00 0.00 5.52
2456 2505 7.428826 CATCCCCTTTTGATAAGCTGAAATAC 58.571 38.462 0.00 0.00 0.00 1.89
2457 2506 6.731467 TCCCCTTTTGATAAGCTGAAATACT 58.269 36.000 0.00 0.00 0.00 2.12
2458 2507 7.867921 TCCCCTTTTGATAAGCTGAAATACTA 58.132 34.615 0.00 0.00 0.00 1.82
2470 2519 4.153475 GCTGAAATACTAGAAAACACGGCA 59.847 41.667 0.00 0.00 0.00 5.69
2513 2562 1.848652 AGCAAGGCATGAATGAAGCT 58.151 45.000 0.00 0.00 0.00 3.74
2537 2586 0.314935 AAAATTGCGTGAGTGGCAGG 59.685 50.000 0.00 0.00 42.12 4.85
2708 2760 1.374947 CTTCCGTGTGGGTGTGGAT 59.625 57.895 0.00 0.00 37.00 3.41
2811 2866 3.057946 GTGTGAAGTTCCCATCAGCTTTC 60.058 47.826 0.00 0.00 0.00 2.62
2859 2914 3.173965 ACCCGGGATGATAATAGACAGG 58.826 50.000 32.02 0.00 0.00 4.00
2860 2915 3.181410 ACCCGGGATGATAATAGACAGGA 60.181 47.826 32.02 0.00 0.00 3.86
2861 2916 3.449018 CCCGGGATGATAATAGACAGGAG 59.551 52.174 18.48 0.00 0.00 3.69
2862 2917 3.118956 CCGGGATGATAATAGACAGGAGC 60.119 52.174 0.00 0.00 0.00 4.70
2863 2918 3.511540 CGGGATGATAATAGACAGGAGCA 59.488 47.826 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.720046 TGGAGGTAGTATTTGTGTTGCAA 58.280 39.130 0.00 0.00 34.87 4.08
8 9 4.335594 GGATGGAGGTAGTATTTGTGTTGC 59.664 45.833 0.00 0.00 0.00 4.17
9 10 5.586243 CAGGATGGAGGTAGTATTTGTGTTG 59.414 44.000 0.00 0.00 0.00 3.33
49 50 2.426381 GTTAGAGTAACTCCCCTCACGG 59.574 54.545 0.00 0.00 35.81 4.94
54 55 8.121185 AGTACTTATTGTTAGAGTAACTCCCCT 58.879 37.037 0.00 0.00 39.38 4.79
72 74 7.418712 GCCCTTGTTCATACACCTAGTACTTAT 60.419 40.741 0.00 0.00 35.05 1.73
73 75 6.127253 GCCCTTGTTCATACACCTAGTACTTA 60.127 42.308 0.00 0.00 35.05 2.24
74 76 5.338137 GCCCTTGTTCATACACCTAGTACTT 60.338 44.000 0.00 0.00 35.05 2.24
79 81 3.914426 AGCCCTTGTTCATACACCTAG 57.086 47.619 0.00 0.00 32.98 3.02
84 86 5.674525 CTTGATCTAGCCCTTGTTCATACA 58.325 41.667 0.00 0.00 0.00 2.29
111 113 2.606961 ATGTGTCACACTTGCGCCG 61.607 57.895 8.08 0.00 35.11 6.46
114 116 1.165907 ACCCATGTGTCACACTTGCG 61.166 55.000 16.63 11.69 37.92 4.85
120 122 4.724399 ACTCATAAAACCCATGTGTCACA 58.276 39.130 8.40 8.40 0.00 3.58
138 140 3.998156 CGAGAGGGTCCGAACTCA 58.002 61.111 0.00 0.00 36.20 3.41
173 176 1.068741 AGCTTCCAAAACTCGAGACGT 59.931 47.619 21.68 0.23 0.00 4.34
183 186 7.781056 AGAGAAACAAAACATAGCTTCCAAAA 58.219 30.769 0.00 0.00 0.00 2.44
185 188 6.959639 AGAGAAACAAAACATAGCTTCCAA 57.040 33.333 0.00 0.00 0.00 3.53
189 192 7.173390 GGACACTAGAGAAACAAAACATAGCTT 59.827 37.037 0.00 0.00 0.00 3.74
194 197 7.502226 TCATTGGACACTAGAGAAACAAAACAT 59.498 33.333 0.00 0.00 0.00 2.71
197 200 8.463930 AATCATTGGACACTAGAGAAACAAAA 57.536 30.769 0.00 0.00 0.00 2.44
201 204 8.547967 TTGTAATCATTGGACACTAGAGAAAC 57.452 34.615 0.00 0.00 0.00 2.78
202 205 9.166173 CATTGTAATCATTGGACACTAGAGAAA 57.834 33.333 0.00 0.00 0.00 2.52
215 218 6.422701 GGCATTCACATCCATTGTAATCATTG 59.577 38.462 0.00 0.00 36.57 2.82
216 219 6.325545 AGGCATTCACATCCATTGTAATCATT 59.674 34.615 0.00 0.00 36.57 2.57
233 236 3.676049 CGTAGCACAGTAAGAGGCATTCA 60.676 47.826 0.00 0.00 0.00 2.57
237 240 0.530744 CCGTAGCACAGTAAGAGGCA 59.469 55.000 0.00 0.00 0.00 4.75
238 241 0.179108 CCCGTAGCACAGTAAGAGGC 60.179 60.000 0.00 0.00 0.00 4.70
275 278 3.785859 CTAGCTCAAGGGGCGGCA 61.786 66.667 12.47 0.00 34.52 5.69
293 296 7.611213 AATCAAATCCCTCTTTGTAACGTAG 57.389 36.000 0.00 0.00 37.39 3.51
313 316 8.445275 ACGCCTGTAATAATTCATGTTAATCA 57.555 30.769 0.00 0.00 0.00 2.57
342 345 8.079211 ACTAGTCAATACATCAGTTACCATGT 57.921 34.615 0.00 3.50 37.08 3.21
363 366 6.129431 CGTGCATTACTAGCGTTCATTACTAG 60.129 42.308 0.00 0.00 39.44 2.57
365 368 4.503007 CGTGCATTACTAGCGTTCATTACT 59.497 41.667 0.00 0.00 33.85 2.24
366 369 4.266976 ACGTGCATTACTAGCGTTCATTAC 59.733 41.667 0.00 0.00 31.37 1.89
367 370 4.426416 ACGTGCATTACTAGCGTTCATTA 58.574 39.130 0.00 0.00 31.37 1.90
368 371 3.259064 ACGTGCATTACTAGCGTTCATT 58.741 40.909 0.00 0.00 31.37 2.57
369 372 2.888594 ACGTGCATTACTAGCGTTCAT 58.111 42.857 0.00 0.00 31.37 2.57
370 373 2.357327 ACGTGCATTACTAGCGTTCA 57.643 45.000 0.00 0.00 31.37 3.18
371 374 2.787680 CCTACGTGCATTACTAGCGTTC 59.212 50.000 0.00 0.00 37.05 3.95
372 375 2.805845 CCTACGTGCATTACTAGCGTT 58.194 47.619 0.00 0.00 37.05 4.84
373 376 1.535437 GCCTACGTGCATTACTAGCGT 60.535 52.381 0.00 0.00 39.23 5.07
374 377 1.129326 GCCTACGTGCATTACTAGCG 58.871 55.000 0.00 0.00 33.85 4.26
389 392 1.254975 TGCTAAGAGGTGCACGCCTA 61.255 55.000 11.45 0.00 39.34 3.93
408 411 2.356313 CCGCGCAGACACTGAAGT 60.356 61.111 8.75 0.00 32.44 3.01
418 421 2.353607 GATAGACGGTCCGCGCAG 60.354 66.667 12.28 0.00 0.00 5.18
419 422 2.827190 AGATAGACGGTCCGCGCA 60.827 61.111 12.28 0.00 0.00 6.09
422 425 1.517210 GAGGGAGATAGACGGTCCGC 61.517 65.000 12.28 4.24 0.00 5.54
443 446 0.981183 TACCCCACAGCGATTCAGTT 59.019 50.000 0.00 0.00 0.00 3.16
446 449 0.035820 GGTTACCCCACAGCGATTCA 60.036 55.000 0.00 0.00 0.00 2.57
452 455 0.035820 TCATTCGGTTACCCCACAGC 60.036 55.000 0.00 0.00 0.00 4.40
484 487 1.548719 CGGACACCACTGATCCACTTA 59.451 52.381 0.00 0.00 32.35 2.24
493 496 0.390340 CATCCACTCGGACACCACTG 60.390 60.000 0.00 0.00 46.79 3.66
494 497 1.544825 CCATCCACTCGGACACCACT 61.545 60.000 0.00 0.00 46.79 4.00
530 533 2.025037 CCCCTGGTCTCAAATCCATTCA 60.025 50.000 0.00 0.00 33.01 2.57
547 550 2.988839 GCCAGACATTGAGGCCCCT 61.989 63.158 0.00 0.00 42.58 4.79
548 551 2.440980 GCCAGACATTGAGGCCCC 60.441 66.667 0.00 0.00 42.58 5.80
549 552 2.825836 CGCCAGACATTGAGGCCC 60.826 66.667 0.00 0.00 45.56 5.80
550 553 1.675641 AACGCCAGACATTGAGGCC 60.676 57.895 0.00 0.00 45.56 5.19
551 554 1.237285 ACAACGCCAGACATTGAGGC 61.237 55.000 8.71 8.71 44.89 4.70
552 555 0.518636 CACAACGCCAGACATTGAGG 59.481 55.000 0.00 0.00 0.00 3.86
554 557 0.888736 CCCACAACGCCAGACATTGA 60.889 55.000 0.00 0.00 0.00 2.57
555 558 1.172180 ACCCACAACGCCAGACATTG 61.172 55.000 0.00 0.00 0.00 2.82
556 559 0.889186 GACCCACAACGCCAGACATT 60.889 55.000 0.00 0.00 0.00 2.71
603 607 6.154192 GGGGTTAGCCATTATAGGTAGAGTAC 59.846 46.154 1.94 0.00 36.17 2.73
621 626 3.496331 ACAAATGGACTGTTGGGGTTAG 58.504 45.455 0.00 0.00 0.00 2.34
660 665 8.217131 ACGTTTTGTTAGTTAAATCTCTGGTT 57.783 30.769 0.00 0.00 0.00 3.67
678 683 2.717011 GGTGACACGCATTAACGTTTTG 59.283 45.455 5.91 6.33 45.75 2.44
683 688 2.672188 TTTGGTGACACGCATTAACG 57.328 45.000 0.00 0.00 42.67 3.18
792 800 7.403312 AGTCCCTCTATCATATTTCGATCAG 57.597 40.000 0.00 0.00 0.00 2.90
798 806 9.660180 GGTTGATTAGTCCCTCTATCATATTTC 57.340 37.037 0.00 0.00 0.00 2.17
807 815 3.039011 GCCTGGTTGATTAGTCCCTCTA 58.961 50.000 0.00 0.00 0.00 2.43
828 846 0.617820 TTTTCTCCTCCCTCCTCCGG 60.618 60.000 0.00 0.00 0.00 5.14
861 887 1.449778 GACCCGTGGCTTTAGGCTC 60.450 63.158 4.87 0.33 41.69 4.70
1101 1128 1.956170 CAGGCACAGCTCGTCGTTT 60.956 57.895 0.00 0.00 0.00 3.60
1704 1731 3.649277 GATGGCGAGCACGGACAGT 62.649 63.158 5.52 0.00 40.15 3.55
1746 1773 1.175347 TGAGCACGAGACTGAGCAGT 61.175 55.000 2.20 2.20 45.84 4.40
1755 1782 1.886585 GGAGAAGCTGAGCACGAGA 59.113 57.895 7.39 0.00 0.00 4.04
1902 1939 4.315588 GCAAGGAGCTGCATCTGT 57.684 55.556 8.35 0.00 42.17 3.41
1908 1945 1.023513 AACTCGATGCAAGGAGCTGC 61.024 55.000 15.12 0.00 45.94 5.25
2183 2230 1.893801 CACTAACTCCAGAGGGTCGTT 59.106 52.381 0.00 0.00 34.75 3.85
2204 2252 1.000771 TCTGTCCCTCTCCCTCACG 60.001 63.158 0.00 0.00 0.00 4.35
2377 2426 0.994247 TGGGAGCACACCATCTGATT 59.006 50.000 0.00 0.00 31.83 2.57
2384 2433 3.177884 AAGGCTGGGAGCACACCA 61.178 61.111 0.00 0.00 44.75 4.17
2456 2505 3.502211 ACAAAGGATGCCGTGTTTTCTAG 59.498 43.478 0.00 0.00 0.00 2.43
2457 2506 3.482436 ACAAAGGATGCCGTGTTTTCTA 58.518 40.909 0.00 0.00 0.00 2.10
2458 2507 2.306847 ACAAAGGATGCCGTGTTTTCT 58.693 42.857 0.00 0.00 0.00 2.52
2470 2519 3.411446 TCTTGTGATCGCAACAAAGGAT 58.589 40.909 17.57 0.00 0.00 3.24
2513 2562 3.753797 TGCCACTCACGCAATTTTATACA 59.246 39.130 0.00 0.00 32.05 2.29
2660 2712 2.396590 ACGATGATTTTACGTGGGCT 57.603 45.000 0.00 0.00 38.79 5.19
2708 2760 5.278414 CCCACTTGCGCATTCATATTTCATA 60.278 40.000 12.75 0.00 0.00 2.15
2811 2866 2.038975 TCCTCGGTGGAAGGGAGG 59.961 66.667 0.00 0.00 46.99 4.30


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

AutoCloner maintained by Alex Coulton.