Multiple sequence alignment - TraesCS2D01G136300

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 TraesCS2D01G136300 chr2D 100.000 3958 0 0 808 4765 79990425 79986468 0.000000e+00 7310.0
1 TraesCS2D01G136300 chr2D 100.000 392 0 0 1 392 79991232 79990841 0.000000e+00 725.0
2 TraesCS2D01G136300 chr2D 89.041 73 2 5 308 378 638752012 638752080 8.500000e-13 86.1
3 TraesCS2D01G136300 chr2D 89.362 47 4 1 309 355 194676943 194676988 1.850000e-04 58.4
4 TraesCS2D01G136300 chr2B 95.694 3971 142 12 808 4765 131577153 131573199 0.000000e+00 6359.0
5 TraesCS2D01G136300 chr2B 86.880 343 25 13 1 332 131577548 131577215 2.710000e-97 366.0
6 TraesCS2D01G136300 chr2B 94.595 37 1 1 319 355 740737854 740737889 6.660000e-04 56.5
7 TraesCS2D01G136300 chr2A 96.912 3789 105 2 987 4765 80595796 80592010 0.000000e+00 6338.0
8 TraesCS2D01G136300 chr2A 93.048 187 9 1 808 994 80598786 80598604 2.190000e-68 270.0
9 TraesCS2D01G136300 chr4D 99.499 599 3 0 987 1585 30752060 30751462 0.000000e+00 1090.0
10 TraesCS2D01G136300 chr5D 96.540 607 13 5 987 1585 425666139 425665533 0.000000e+00 998.0
11 TraesCS2D01G136300 chr3A 83.133 83 3 8 307 381 724485535 724485456 1.110000e-06 65.8
12 TraesCS2D01G136300 chr1D 93.023 43 3 0 307 349 475961970 475962012 3.980000e-06 63.9
13 TraesCS2D01G136300 chr5B 100.000 28 0 0 351 378 466774717 466774690 9.000000e-03 52.8
14 TraesCS2D01G136300 chr5A 92.105 38 2 1 318 355 508874950 508874986 9.000000e-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 TraesCS2D01G136300 chr2D 79986468 79991232 4764 True 4017.5 7310 100.000 1 4765 2 chr2D.!!$R1 4764
1 TraesCS2D01G136300 chr2B 131573199 131577548 4349 True 3362.5 6359 91.287 1 4765 2 chr2B.!!$R1 4764
2 TraesCS2D01G136300 chr2A 80592010 80598786 6776 True 3304.0 6338 94.980 808 4765 2 chr2A.!!$R1 3957
3 TraesCS2D01G136300 chr4D 30751462 30752060 598 True 1090.0 1090 99.499 987 1585 1 chr4D.!!$R1 598
4 TraesCS2D01G136300 chr5D 425665533 425666139 606 True 998.0 998 96.540 987 1585 1 chr5D.!!$R1 598

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
105 116 0.179000 GGTGCTGTAGGGAGGATGTG 59.821 60.0 0.0 0.0 0.00 3.21 F
263 274 0.588252 GCATGCGAGTTTGTGTCTGT 59.412 50.0 0.0 0.0 0.00 3.41 F
1952 4793 0.911769 TGGAGGCTTTCGATGTCCAT 59.088 50.0 0.0 0.0 32.21 3.41 F
3291 6132 0.108756 GTACACCGCTGACTTCTCCC 60.109 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 5136 0.312102 TCCGTCATCGCATAGCTCAG 59.688 55.0 0.0 0.0 35.54 3.35 R
2357 5198 0.674581 CGACCAGATCTTGCAGCCAA 60.675 55.0 0.0 0.0 0.00 4.52 R
3596 6437 0.189822 TTCCCCTTCCCAACCCAAAG 59.810 55.0 0.0 0.0 0.00 2.77 R
4226 7077 0.107459 GGAAGAGGCTGATGGACACC 60.107 60.0 0.0 0.0 0.00 4.16 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
56 60 2.097791 AGTGTCGCTCCGAAGATCTAAC 59.902 50.000 0.00 0.00 37.72 2.34
59 63 1.033574 CGCTCCGAAGATCTAACCCT 58.966 55.000 0.00 0.00 0.00 4.34
105 116 0.179000 GGTGCTGTAGGGAGGATGTG 59.821 60.000 0.00 0.00 0.00 3.21
114 125 1.299976 GGAGGATGTGGCGGTTTCT 59.700 57.895 0.00 0.00 0.00 2.52
117 128 2.106683 GGATGTGGCGGTTTCTCGG 61.107 63.158 0.00 0.00 0.00 4.63
128 139 4.400845 GCGGTTTCTCGGTTTTTATTCTC 58.599 43.478 0.00 0.00 0.00 2.87
132 143 5.049886 GGTTTCTCGGTTTTTATTCTCGTGT 60.050 40.000 0.00 0.00 0.00 4.49
216 227 7.336475 TCTTCTAGCTGGAATCCTCTATCTA 57.664 40.000 13.40 0.00 0.00 1.98
237 248 4.090057 GGCGCTTGCTTCGGTCAC 62.090 66.667 7.64 0.00 39.13 3.67
249 260 0.955428 TCGGTCACCAAAGAGCATGC 60.955 55.000 10.51 10.51 35.83 4.06
260 271 1.151668 AGAGCATGCGAGTTTGTGTC 58.848 50.000 13.01 0.45 0.00 3.67
261 272 1.151668 GAGCATGCGAGTTTGTGTCT 58.848 50.000 13.01 0.00 0.00 3.41
263 274 0.588252 GCATGCGAGTTTGTGTCTGT 59.412 50.000 0.00 0.00 0.00 3.41
266 277 1.279840 GCGAGTTTGTGTCTGTGCC 59.720 57.895 0.00 0.00 0.00 5.01
270 281 2.904866 TTTGTGTCTGTGCCGGCC 60.905 61.111 26.77 16.24 0.00 6.13
288 299 1.269778 GCCGCTACAGACATGCATAGA 60.270 52.381 0.00 0.00 0.00 1.98
289 300 2.803133 GCCGCTACAGACATGCATAGAA 60.803 50.000 0.00 0.00 0.00 2.10
292 303 4.053983 CGCTACAGACATGCATAGAATGT 58.946 43.478 0.00 5.10 40.93 2.71
299 310 7.105588 ACAGACATGCATAGAATGTTCACTTA 58.894 34.615 0.00 0.00 38.37 2.24
305 316 9.229784 CATGCATAGAATGTTCACTTACAATTC 57.770 33.333 0.00 0.00 0.00 2.17
314 325 7.062749 TGTTCACTTACAATTCACTACTCCT 57.937 36.000 0.00 0.00 0.00 3.69
315 326 7.152645 TGTTCACTTACAATTCACTACTCCTC 58.847 38.462 0.00 0.00 0.00 3.71
316 327 5.950883 TCACTTACAATTCACTACTCCTCG 58.049 41.667 0.00 0.00 0.00 4.63
317 328 4.563184 CACTTACAATTCACTACTCCTCGC 59.437 45.833 0.00 0.00 0.00 5.03
332 343 2.035449 TCCTCGCGTCCCATAATGTAAG 59.965 50.000 5.77 0.00 0.00 2.34
334 345 3.309388 CTCGCGTCCCATAATGTAAGAG 58.691 50.000 5.77 0.00 0.00 2.85
335 346 1.792949 CGCGTCCCATAATGTAAGAGC 59.207 52.381 0.00 0.00 0.00 4.09
336 347 1.792949 GCGTCCCATAATGTAAGAGCG 59.207 52.381 0.00 0.00 0.00 5.03
337 348 2.802057 GCGTCCCATAATGTAAGAGCGT 60.802 50.000 0.00 0.00 0.00 5.07
338 349 3.454375 CGTCCCATAATGTAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
339 350 3.869246 CGTCCCATAATGTAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
340 351 4.331717 CGTCCCATAATGTAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
341 352 5.163794 CGTCCCATAATGTAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
342 353 6.036300 CGTCCCATAATGTAAGAGCGTTTTTA 59.964 38.462 0.00 0.00 0.00 1.52
343 354 7.413219 CGTCCCATAATGTAAGAGCGTTTTTAA 60.413 37.037 0.00 0.00 0.00 1.52
344 355 7.695201 GTCCCATAATGTAAGAGCGTTTTTAAC 59.305 37.037 0.00 0.00 0.00 2.01
345 356 7.390996 TCCCATAATGTAAGAGCGTTTTTAACA 59.609 33.333 0.00 0.00 0.00 2.41
346 357 7.483691 CCCATAATGTAAGAGCGTTTTTAACAC 59.516 37.037 0.00 0.00 0.00 3.32
347 358 8.234546 CCATAATGTAAGAGCGTTTTTAACACT 58.765 33.333 0.00 0.00 0.00 3.55
350 361 7.718272 ATGTAAGAGCGTTTTTAACACTACA 57.282 32.000 0.00 0.00 0.00 2.74
351 362 6.936374 TGTAAGAGCGTTTTTAACACTACAC 58.064 36.000 0.00 0.00 0.00 2.90
352 363 6.757947 TGTAAGAGCGTTTTTAACACTACACT 59.242 34.615 0.00 0.00 0.00 3.55
353 364 6.673154 AAGAGCGTTTTTAACACTACACTT 57.327 33.333 0.00 0.00 0.00 3.16
367 378 6.561614 ACACTACACTTACATTATGAGACGG 58.438 40.000 0.00 0.00 0.00 4.79
370 381 5.263968 ACACTTACATTATGAGACGGAGG 57.736 43.478 0.00 0.00 0.00 4.30
840 856 7.964545 ACAAACAAATCAACGTCTTACTTTC 57.035 32.000 0.00 0.00 0.00 2.62
889 905 2.485814 TCACAGTCTCACAGATCTCACG 59.514 50.000 0.00 0.00 0.00 4.35
899 917 1.596477 GATCTCACGCATCCAGGCC 60.596 63.158 0.00 0.00 0.00 5.19
900 918 2.315781 GATCTCACGCATCCAGGCCA 62.316 60.000 5.01 0.00 0.00 5.36
901 919 2.599645 ATCTCACGCATCCAGGCCAC 62.600 60.000 5.01 0.00 0.00 5.01
902 920 3.610619 CTCACGCATCCAGGCCACA 62.611 63.158 5.01 0.00 0.00 4.17
952 970 2.112507 AGCAGCACAGCTCAGCAA 59.887 55.556 0.00 0.00 42.18 3.91
1724 4565 2.809601 CAGTACAGCCACGCCGAC 60.810 66.667 0.00 0.00 0.00 4.79
1949 4790 2.356069 GGAAATGGAGGCTTTCGATGTC 59.644 50.000 0.00 0.00 34.19 3.06
1952 4793 0.911769 TGGAGGCTTTCGATGTCCAT 59.088 50.000 0.00 0.00 32.21 3.41
2051 4892 4.760047 CCGGCGTTCTGGGGTCTG 62.760 72.222 6.01 0.00 35.00 3.51
2295 5136 4.033817 CACTCTTTGAGCGGATTCTTGATC 59.966 45.833 0.00 0.00 32.04 2.92
2321 5162 4.593864 GCGATGACGGAGGAGGGC 62.594 72.222 0.00 0.00 40.15 5.19
2357 5198 2.419574 GGATTTGCATTTCATGGCTGCT 60.420 45.455 13.61 0.00 36.84 4.24
2423 5264 1.182667 TGTCATTGGAGATCGACCGT 58.817 50.000 0.00 0.00 0.00 4.83
2432 5273 2.437895 ATCGACCGTCCGAGAGCA 60.438 61.111 0.00 0.00 42.21 4.26
2512 5353 2.386935 GGGTGGAGGAGATTGGGGG 61.387 68.421 0.00 0.00 0.00 5.40
2612 5453 2.383245 CTGTGGACCGGACTGCACTT 62.383 60.000 9.46 0.00 0.00 3.16
2627 5468 1.943507 GCACTTGAGTGGAGGCTTCTC 60.944 57.143 12.65 1.55 45.72 2.87
2751 5592 4.890158 TCAGCTTGATCTGTAACCTTGA 57.110 40.909 0.00 0.00 35.63 3.02
2759 5600 7.329471 GCTTGATCTGTAACCTTGAAATTTTCC 59.671 37.037 6.68 0.00 0.00 3.13
2770 5611 6.327365 ACCTTGAAATTTTCCTCATGTTTCCT 59.673 34.615 6.68 0.00 0.00 3.36
2773 5614 9.196552 CTTGAAATTTTCCTCATGTTTCCTTAC 57.803 33.333 6.68 0.00 0.00 2.34
2824 5665 5.120674 GCTTCATTTGCTTGGATACCAAAAC 59.879 40.000 4.78 1.42 43.44 2.43
2829 5670 5.699097 TTGCTTGGATACCAAAACTGTAC 57.301 39.130 4.78 0.00 43.44 2.90
2835 5676 6.019779 TGGATACCAAAACTGTACAATTGC 57.980 37.500 5.05 0.00 0.00 3.56
3029 5870 5.043248 GTCCTGGTTTGTGAAATTTGTGAG 58.957 41.667 0.00 0.00 0.00 3.51
3230 6071 8.635765 ACAAAAGAAGCATAGGTGAAGATAAA 57.364 30.769 0.00 0.00 0.00 1.40
3291 6132 0.108756 GTACACCGCTGACTTCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
3308 6149 5.750352 TCTCCCACCTCGTTAAAGTTATT 57.250 39.130 0.00 0.00 0.00 1.40
3348 6189 0.396139 CACCATTGGAGTCCCCATGG 60.396 60.000 26.11 26.11 46.10 3.66
3386 6227 3.482436 TGTACCGAGCAATTTTGAACCT 58.518 40.909 0.00 0.00 0.00 3.50
3429 6270 1.974265 TCGGACAAACTTGCCATCAA 58.026 45.000 0.00 0.00 0.00 2.57
3434 6275 4.320861 CGGACAAACTTGCCATCAAATACA 60.321 41.667 0.00 0.00 0.00 2.29
3470 6311 4.694760 ATATACTCCTGAAGCACATGCA 57.305 40.909 6.64 0.00 45.16 3.96
3636 6477 7.300320 GGGAAACAAAACTACGATCGTTAAAT 58.700 34.615 27.88 8.25 0.00 1.40
3742 6583 7.274033 CACATGATCACATTAACACCATTGTTC 59.726 37.037 0.00 0.00 39.55 3.18
3747 6588 5.708230 TCACATTAACACCATTGTTCCCTAC 59.292 40.000 0.00 0.00 42.67 3.18
3764 6605 6.697641 TCCCTACTGTGAAATCTTTACCTT 57.302 37.500 0.00 0.00 0.00 3.50
3771 6612 6.040504 ACTGTGAAATCTTTACCTTTTGGACC 59.959 38.462 0.00 0.00 44.07 4.46
3798 6639 8.690840 GTTGCAGTTCAATGTAAAGATAACAAC 58.309 33.333 0.00 0.00 36.99 3.32
3824 6665 8.840867 CGAAGAATGCTAAACTTCAAATGTTAC 58.159 33.333 0.00 0.00 39.64 2.50
3972 6823 6.149474 CACCCTCTTTGTTAAAGGTCTGTATG 59.851 42.308 1.88 0.00 39.01 2.39
4033 6884 1.606480 CGACTCAGCAAGGCAGAAGAA 60.606 52.381 0.00 0.00 29.11 2.52
4034 6885 2.709213 GACTCAGCAAGGCAGAAGAAT 58.291 47.619 0.00 0.00 30.88 2.40
4172 7023 0.755686 CTGATGTCTCCCAGTAGCCC 59.244 60.000 0.00 0.00 0.00 5.19
4205 7056 4.646572 CTTCTAGGAAGGTTTGAAGCAGT 58.353 43.478 0.00 0.00 0.00 4.40
4223 7074 2.228822 CAGTTTCCTGAACGAATTGGGG 59.771 50.000 0.00 0.00 43.20 4.96
4226 7077 1.904287 TCCTGAACGAATTGGGGTTG 58.096 50.000 0.00 0.00 0.00 3.77
4262 7113 5.363292 CCTCTTCCTCATCTCTTCATCTTCA 59.637 44.000 0.00 0.00 0.00 3.02
4571 7422 1.476891 TCGAAGTAGTGGCTGACATCC 59.523 52.381 0.00 0.00 0.00 3.51
4589 7440 0.378962 CCGTCAGTGAGATCTCCGAC 59.621 60.000 20.03 19.78 0.00 4.79
4688 7539 1.354040 CTGGAGCATCACTGTCGAAC 58.646 55.000 0.00 0.00 36.25 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 18 5.895534 CACTAGGGTATAGAGTGGTGGTTAA 59.104 44.000 0.00 0.00 37.52 2.01
29 33 0.035152 TTCGGAGCGACACTAGGGTA 60.035 55.000 0.00 0.00 34.89 3.69
56 60 0.908198 CTGAGGGTGGAAGAGAAGGG 59.092 60.000 0.00 0.00 0.00 3.95
59 63 0.473694 TGGCTGAGGGTGGAAGAGAA 60.474 55.000 0.00 0.00 0.00 2.87
94 105 2.198304 GAAACCGCCACATCCTCCCT 62.198 60.000 0.00 0.00 0.00 4.20
105 116 3.189910 AGAATAAAAACCGAGAAACCGCC 59.810 43.478 0.00 0.00 0.00 6.13
114 125 4.930405 TGCATACACGAGAATAAAAACCGA 59.070 37.500 0.00 0.00 0.00 4.69
117 128 8.895932 ATTCTTGCATACACGAGAATAAAAAC 57.104 30.769 7.18 0.00 45.13 2.43
159 170 8.801299 TGAAGATAACACCATTATCAAAGCAAA 58.199 29.630 8.86 0.00 34.66 3.68
190 201 7.248237 AGATAGAGGATTCCAGCTAGAAGATT 58.752 38.462 5.29 0.00 0.00 2.40
203 214 2.094442 GCGCCACCTAGATAGAGGATTC 60.094 54.545 0.00 0.00 39.15 2.52
237 248 1.267806 ACAAACTCGCATGCTCTTTGG 59.732 47.619 24.02 12.82 0.00 3.28
249 260 1.564622 CGGCACAGACACAAACTCG 59.435 57.895 0.00 0.00 0.00 4.18
266 277 3.264897 GCATGTCTGTAGCGGCCG 61.265 66.667 24.05 24.05 0.00 6.13
270 281 4.053983 ACATTCTATGCATGTCTGTAGCG 58.946 43.478 10.16 0.00 27.99 4.26
271 282 5.525012 TGAACATTCTATGCATGTCTGTAGC 59.475 40.000 10.16 4.85 33.54 3.58
272 283 6.760298 AGTGAACATTCTATGCATGTCTGTAG 59.240 38.462 10.16 0.00 33.54 2.74
273 284 6.643388 AGTGAACATTCTATGCATGTCTGTA 58.357 36.000 10.16 0.00 33.54 2.74
274 285 5.494724 AGTGAACATTCTATGCATGTCTGT 58.505 37.500 10.16 4.89 33.54 3.41
275 286 6.432607 AAGTGAACATTCTATGCATGTCTG 57.567 37.500 10.16 4.25 33.54 3.51
276 287 7.105588 TGTAAGTGAACATTCTATGCATGTCT 58.894 34.615 10.16 0.00 33.54 3.41
277 288 7.307493 TGTAAGTGAACATTCTATGCATGTC 57.693 36.000 10.16 0.00 33.54 3.06
288 299 8.157476 AGGAGTAGTGAATTGTAAGTGAACATT 58.843 33.333 0.00 0.00 0.00 2.71
289 300 7.680730 AGGAGTAGTGAATTGTAAGTGAACAT 58.319 34.615 0.00 0.00 0.00 2.71
292 303 6.387465 CGAGGAGTAGTGAATTGTAAGTGAA 58.613 40.000 0.00 0.00 0.00 3.18
299 310 1.544691 ACGCGAGGAGTAGTGAATTGT 59.455 47.619 15.93 0.00 0.00 2.71
305 316 1.384989 ATGGGACGCGAGGAGTAGTG 61.385 60.000 15.93 0.00 0.00 2.74
314 325 2.545113 GCTCTTACATTATGGGACGCGA 60.545 50.000 15.93 0.00 0.00 5.87
315 326 1.792949 GCTCTTACATTATGGGACGCG 59.207 52.381 3.53 3.53 0.00 6.01
316 327 1.792949 CGCTCTTACATTATGGGACGC 59.207 52.381 0.00 0.00 0.00 5.19
317 328 3.093717 ACGCTCTTACATTATGGGACG 57.906 47.619 0.00 2.61 0.00 4.79
334 345 9.815936 ATAATGTAAGTGTAGTGTTAAAAACGC 57.184 29.630 0.00 0.00 42.10 4.84
340 351 9.563898 CGTCTCATAATGTAAGTGTAGTGTTAA 57.436 33.333 0.00 0.00 0.00 2.01
341 352 8.186163 CCGTCTCATAATGTAAGTGTAGTGTTA 58.814 37.037 0.00 0.00 0.00 2.41
342 353 7.033791 CCGTCTCATAATGTAAGTGTAGTGTT 58.966 38.462 0.00 0.00 0.00 3.32
343 354 6.376299 TCCGTCTCATAATGTAAGTGTAGTGT 59.624 38.462 0.00 0.00 0.00 3.55
344 355 6.792326 TCCGTCTCATAATGTAAGTGTAGTG 58.208 40.000 0.00 0.00 0.00 2.74
345 356 6.039493 CCTCCGTCTCATAATGTAAGTGTAGT 59.961 42.308 0.00 0.00 0.00 2.73
346 357 6.439599 CCTCCGTCTCATAATGTAAGTGTAG 58.560 44.000 0.00 0.00 0.00 2.74
347 358 5.301045 CCCTCCGTCTCATAATGTAAGTGTA 59.699 44.000 0.00 0.00 0.00 2.90
348 359 4.099573 CCCTCCGTCTCATAATGTAAGTGT 59.900 45.833 0.00 0.00 0.00 3.55
349 360 4.341235 TCCCTCCGTCTCATAATGTAAGTG 59.659 45.833 0.00 0.00 0.00 3.16
350 361 4.543689 TCCCTCCGTCTCATAATGTAAGT 58.456 43.478 0.00 0.00 0.00 2.24
351 362 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
352 363 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
353 364 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
362 373 2.025226 TGATTGACTACTCCCTCCGTCT 60.025 50.000 0.00 0.00 0.00 4.18
363 374 2.376109 TGATTGACTACTCCCTCCGTC 58.624 52.381 0.00 0.00 0.00 4.79
817 828 6.140108 CCGAAAGTAAGACGTTGATTTGTTTG 59.860 38.462 0.00 0.00 0.00 2.93
840 856 1.204941 ACTCGTTTGAATCCCTCTCCG 59.795 52.381 0.00 0.00 0.00 4.63
871 887 1.200948 TGCGTGAGATCTGTGAGACTG 59.799 52.381 0.00 0.00 0.00 3.51
889 905 2.282391 TGTGTGTGGCCTGGATGC 60.282 61.111 3.32 0.00 0.00 3.91
899 917 0.466189 AAGGGCTCAACCTGTGTGTG 60.466 55.000 0.00 0.00 40.87 3.82
900 918 0.258774 AAAGGGCTCAACCTGTGTGT 59.741 50.000 0.00 0.00 40.87 3.72
901 919 0.954452 GAAAGGGCTCAACCTGTGTG 59.046 55.000 0.00 0.00 40.87 3.82
902 920 0.846693 AGAAAGGGCTCAACCTGTGT 59.153 50.000 0.00 0.00 40.87 3.72
952 970 4.692475 CGTTTCGGACCGGGCCTT 62.692 66.667 27.76 0.00 0.00 4.35
2295 5136 0.312102 TCCGTCATCGCATAGCTCAG 59.688 55.000 0.00 0.00 35.54 3.35
2321 5162 3.350833 CAAATCCTTCTCCCACCAGAAG 58.649 50.000 3.61 3.61 46.33 2.85
2357 5198 0.674581 CGACCAGATCTTGCAGCCAA 60.675 55.000 0.00 0.00 0.00 4.52
2423 5264 2.244117 GACCAATGGCTGCTCTCGGA 62.244 60.000 0.00 0.00 0.00 4.55
2512 5353 2.977914 TGCCAATCTCAGTGCTTACTC 58.022 47.619 0.00 0.00 0.00 2.59
2612 5453 2.292521 ACCATAGAGAAGCCTCCACTCA 60.293 50.000 0.00 0.00 40.30 3.41
2648 5489 4.156739 CCTTGCTCTGAAAGAATAACCACC 59.843 45.833 0.00 0.00 46.34 4.61
2751 5592 8.314021 GGATGTAAGGAAACATGAGGAAAATTT 58.686 33.333 0.00 0.00 40.17 1.82
2759 5600 6.644347 ACAGTAGGATGTAAGGAAACATGAG 58.356 40.000 0.00 0.00 40.17 2.90
2770 5611 5.045942 TGGATGAAGCAACAGTAGGATGTAA 60.046 40.000 0.00 0.00 31.70 2.41
2773 5614 3.875727 CTGGATGAAGCAACAGTAGGATG 59.124 47.826 0.00 0.00 0.00 3.51
2824 5665 7.172532 TCAGTAAGTGGTTAAGCAATTGTACAG 59.827 37.037 25.62 15.52 0.00 2.74
2829 5670 8.730680 ACTTATCAGTAAGTGGTTAAGCAATTG 58.269 33.333 25.62 13.27 46.65 2.32
2857 5698 1.702401 TGGGCAAGTACCTGTGATGAA 59.298 47.619 0.00 0.00 0.00 2.57
2858 5699 1.357137 TGGGCAAGTACCTGTGATGA 58.643 50.000 0.00 0.00 0.00 2.92
3057 5898 6.986817 TGAGAACCAGAGAAGTTAGTTTTGAG 59.013 38.462 0.00 0.00 0.00 3.02
3230 6071 6.710597 ATCTCACTGCTGCAATGAATTATT 57.289 33.333 15.07 0.00 0.00 1.40
3280 6121 0.969894 AACGAGGTGGGAGAAGTCAG 59.030 55.000 0.00 0.00 0.00 3.51
3291 6132 6.206048 AGGTTTCCAATAACTTTAACGAGGTG 59.794 38.462 0.00 0.00 0.00 4.00
3308 6149 3.843619 TGTGATGGATGTCTAGGTTTCCA 59.156 43.478 9.82 9.82 42.18 3.53
3348 6189 3.119495 GGTACATCCATTGCAAGGAACAC 60.119 47.826 13.66 13.16 38.93 3.32
3386 6227 5.351948 AAGCAAGTTTTCCCAAAGCTTTA 57.648 34.783 12.25 0.00 39.48 1.85
3429 6270 8.521176 AGTATATATCGCCGAGAAAGTTGTATT 58.479 33.333 0.00 0.00 0.00 1.89
3434 6275 5.711036 AGGAGTATATATCGCCGAGAAAGTT 59.289 40.000 0.00 0.00 0.00 2.66
3470 6311 4.684724 TCTCAACCTTCATAGGGTACACT 58.315 43.478 1.68 1.68 40.45 3.55
3512 6353 4.378774 CTGAAGCCATGACTCTGATTAGG 58.621 47.826 0.00 0.00 0.00 2.69
3581 6422 9.245481 CCCAACCCAAAGTATACAATTTTAGTA 57.755 33.333 5.50 0.00 0.00 1.82
3596 6437 0.189822 TTCCCCTTCCCAACCCAAAG 59.810 55.000 0.00 0.00 0.00 2.77
3642 6483 4.293368 AGGGAGGATGAAGAGGAACAAAAT 59.707 41.667 0.00 0.00 0.00 1.82
3695 6536 5.831525 TGTGAGACTACTGACAAGGTAAGAA 59.168 40.000 0.00 0.00 37.32 2.52
3697 6538 5.707242 TGTGAGACTACTGACAAGGTAAG 57.293 43.478 0.00 0.00 37.32 2.34
3705 6546 5.316327 TGTGATCATGTGAGACTACTGAC 57.684 43.478 0.00 0.00 0.00 3.51
3742 6583 7.309194 CCAAAAGGTAAAGATTTCACAGTAGGG 60.309 40.741 0.00 0.00 0.00 3.53
3747 6588 6.447162 GGTCCAAAAGGTAAAGATTTCACAG 58.553 40.000 0.00 0.00 0.00 3.66
3764 6605 1.464734 TTGAACTGCAACGGTCCAAA 58.535 45.000 0.00 0.00 0.00 3.28
3771 6612 7.075121 TGTTATCTTTACATTGAACTGCAACG 58.925 34.615 0.00 0.00 39.78 4.10
3798 6639 7.858052 AACATTTGAAGTTTAGCATTCTTCG 57.142 32.000 0.00 0.00 39.97 3.79
3972 6823 9.632807 TGTGATTTATAAAAGTTGTAACATGCC 57.367 29.630 1.21 0.00 0.00 4.40
4014 6865 2.175878 TTCTTCTGCCTTGCTGAGTC 57.824 50.000 0.00 0.00 37.75 3.36
4033 6884 6.664816 TCCAGCATTTGACCAAGAAGAAATAT 59.335 34.615 0.00 0.00 0.00 1.28
4034 6885 6.009589 TCCAGCATTTGACCAAGAAGAAATA 58.990 36.000 0.00 0.00 0.00 1.40
4205 7056 2.625790 CAACCCCAATTCGTTCAGGAAA 59.374 45.455 0.00 0.00 0.00 3.13
4223 7074 0.326264 AGAGGCTGATGGACACCAAC 59.674 55.000 0.00 0.00 36.95 3.77
4226 7077 0.107459 GGAAGAGGCTGATGGACACC 60.107 60.000 0.00 0.00 0.00 4.16
4262 7113 5.163622 CGAGGAAGCAAATACCACATTCATT 60.164 40.000 0.00 0.00 0.00 2.57
4472 7323 1.795768 ACATAGCAGACACAACCACG 58.204 50.000 0.00 0.00 0.00 4.94
4571 7422 3.907927 GTCGGAGATCTCACTGACG 57.092 57.895 23.85 16.83 40.67 4.35


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

AutoCloner maintained by Alex Coulton.