Multiple sequence alignment - TraesCS5A01G397100

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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 TraesCS5A01G397100 chr5A 100.000 4541 0 0 1 4541 591494200 591489660 0.000000e+00 8386
1 TraesCS5A01G397100 chr5D 96.479 4005 95 15 512 4482 472289692 472285700 0.000000e+00 6573
2 TraesCS5A01G397100 chr5D 78.495 465 50 19 1 428 472290282 472289831 4.510000e-65 259
3 TraesCS5A01G397100 chr5D 98.361 61 1 0 4481 4541 472285492 472285432 1.730000e-19 108
4 TraesCS5A01G397100 chr5B 95.677 3493 136 10 513 3996 578608715 578605229 0.000000e+00 5600
5 TraesCS5A01G397100 chr5B 82.767 412 42 15 4141 4534 578604820 578604420 1.560000e-89 340
6 TraesCS5A01G397100 chr5B 82.895 228 27 9 42 265 578609217 578608998 1.290000e-45 195
7 TraesCS5A01G397100 chr5B 87.402 127 11 3 4012 4134 578604980 578604855 1.700000e-29 141


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 TraesCS5A01G397100 chr5A 591489660 591494200 4540 True 8386.000000 8386 100.000000 1 4541 1 chr5A.!!$R1 4540
1 TraesCS5A01G397100 chr5D 472285432 472290282 4850 True 2313.333333 6573 91.111667 1 4541 3 chr5D.!!$R1 4540
2 TraesCS5A01G397100 chr5B 578604420 578609217 4797 True 1569.000000 5600 87.185250 42 4534 4 chr5B.!!$R1 4492

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
928 1058 0.174617 CTGCGTCCTTTCCCTCTCTC 59.825 60.000 0.00 0.00 0.00 3.20 F
1224 1360 0.102120 GCTCTGATCCTGAGTCGGTG 59.898 60.000 12.47 0.00 33.06 4.94 F
1227 1363 1.177401 CTGATCCTGAGTCGGTGTCA 58.823 55.000 0.00 1.23 0.00 3.58 F
2538 2674 2.204463 TCCAGTGCTTATGGATTGGGA 58.796 47.619 10.82 0.00 41.96 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 2674 1.200716 TCGACGAAGGTGAAATAGCGT 59.799 47.619 0.0 0.0 34.39 5.07 R
2730 2866 1.962306 GTGGCGGTGGCGAAGTTTA 60.962 57.895 0.0 0.0 41.24 2.01 R
3180 3316 2.496291 GGCTGGATTGATGGCTGGC 61.496 63.158 0.0 0.0 0.00 4.85 R
4417 4837 0.315251 GTTGAACTTCCCCAAGCTGC 59.685 55.000 0.0 0.0 32.09 5.25 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
23 24 1.369091 GGGCTGCCACTTACGTGATG 61.369 60.000 22.05 0.00 43.97 3.07
88 101 1.805945 CGTCTACAGTTCAGCGCCC 60.806 63.158 2.29 0.00 0.00 6.13
89 102 1.805945 GTCTACAGTTCAGCGCCCG 60.806 63.158 2.29 0.00 0.00 6.13
90 103 2.261671 CTACAGTTCAGCGCCCGT 59.738 61.111 2.29 0.00 0.00 5.28
91 104 1.805945 CTACAGTTCAGCGCCCGTC 60.806 63.158 2.29 0.00 0.00 4.79
92 105 3.620300 TACAGTTCAGCGCCCGTCG 62.620 63.158 2.29 0.00 42.12 5.12
93 106 4.717629 CAGTTCAGCGCCCGTCGA 62.718 66.667 2.29 0.00 41.67 4.20
94 107 3.760035 AGTTCAGCGCCCGTCGAT 61.760 61.111 2.29 0.00 41.67 3.59
95 108 2.103538 GTTCAGCGCCCGTCGATA 59.896 61.111 2.29 0.00 41.67 2.92
96 109 2.103538 TTCAGCGCCCGTCGATAC 59.896 61.111 2.29 0.00 41.67 2.24
103 117 1.469126 CGCCCGTCGATACAAGAACG 61.469 60.000 0.00 0.00 41.67 3.95
110 124 3.062707 CGTCGATACAAGAACGAATCGTG 60.063 47.826 9.74 0.00 39.99 4.35
159 176 5.741011 ACAACATATGGCCTATTATACCCG 58.259 41.667 3.32 0.00 0.00 5.28
165 182 2.635915 TGGCCTATTATACCCGTCTTGG 59.364 50.000 3.32 0.00 37.55 3.61
169 186 4.321824 GCCTATTATACCCGTCTTGGAGAC 60.322 50.000 0.00 0.00 42.00 3.36
176 193 1.599047 CGTCTTGGAGACATGGCCT 59.401 57.895 3.32 0.00 45.30 5.19
182 199 2.254152 TGGAGACATGGCCTAGAACT 57.746 50.000 3.32 2.01 33.40 3.01
198 215 2.137523 GAACTTGGGCAGCACAATTTG 58.862 47.619 17.14 5.66 0.00 2.32
217 234 3.354948 TGCTGGAACAATACTGATGCT 57.645 42.857 0.00 0.00 38.70 3.79
220 237 3.881688 GCTGGAACAATACTGATGCTCAT 59.118 43.478 0.00 0.00 38.70 2.90
221 238 4.261072 GCTGGAACAATACTGATGCTCATG 60.261 45.833 0.00 0.00 38.70 3.07
222 239 3.628942 TGGAACAATACTGATGCTCATGC 59.371 43.478 0.00 0.00 35.53 4.06
223 240 3.004106 GGAACAATACTGATGCTCATGCC 59.996 47.826 0.00 0.00 38.71 4.40
224 241 3.286329 ACAATACTGATGCTCATGCCA 57.714 42.857 0.00 0.00 38.71 4.92
225 242 3.623703 ACAATACTGATGCTCATGCCAA 58.376 40.909 0.00 0.00 38.71 4.52
226 243 4.018490 ACAATACTGATGCTCATGCCAAA 58.982 39.130 0.00 0.00 38.71 3.28
227 244 4.647853 ACAATACTGATGCTCATGCCAAAT 59.352 37.500 0.00 0.00 38.71 2.32
237 254 3.675228 GCTCATGCCAAATTGACAAGGAG 60.675 47.826 8.98 8.98 0.00 3.69
241 258 2.036217 TGCCAAATTGACAAGGAGCAAG 59.964 45.455 0.00 0.00 0.00 4.01
243 260 3.056322 GCCAAATTGACAAGGAGCAAGAT 60.056 43.478 0.00 0.00 0.00 2.40
253 270 5.075493 ACAAGGAGCAAGATCAGTGAAAAT 58.925 37.500 0.00 0.00 0.00 1.82
265 282 5.047566 TCAGTGAAAATGTTCTTCTGGGA 57.952 39.130 15.90 2.28 37.20 4.37
276 304 7.855784 ATGTTCTTCTGGGAAAGGTTAATTT 57.144 32.000 0.00 0.00 0.00 1.82
298 326 0.325933 TTGATGCCAGGACTGACAGG 59.674 55.000 7.51 0.00 0.00 4.00
300 328 2.883267 GATGCCAGGACTGACAGGCC 62.883 65.000 20.78 20.78 46.64 5.19
309 337 3.471680 GGACTGACAGGCCAGAATATTC 58.528 50.000 23.37 7.41 45.15 1.75
311 339 4.376146 GACTGACAGGCCAGAATATTCTC 58.624 47.826 15.24 5.38 37.59 2.87
312 340 3.776969 ACTGACAGGCCAGAATATTCTCA 59.223 43.478 15.24 7.88 37.59 3.27
318 354 5.767168 ACAGGCCAGAATATTCTCAAATAGC 59.233 40.000 15.24 10.70 34.74 2.97
319 355 5.182760 CAGGCCAGAATATTCTCAAATAGCC 59.817 44.000 15.24 17.66 35.46 3.93
334 370 0.179020 TAGCCCCGCATGATTTCTGG 60.179 55.000 0.00 0.00 0.00 3.86
337 373 0.740737 CCCCGCATGATTTCTGGAAC 59.259 55.000 0.00 0.00 0.00 3.62
345 381 4.322953 GCATGATTTCTGGAACCAAACCAT 60.323 41.667 0.00 0.00 36.79 3.55
348 384 6.773976 TGATTTCTGGAACCAAACCATATC 57.226 37.500 0.00 0.00 36.79 1.63
354 390 2.430694 GGAACCAAACCATATCCAAGGC 59.569 50.000 0.00 0.00 0.00 4.35
356 392 3.182887 ACCAAACCATATCCAAGGCAA 57.817 42.857 0.00 0.00 0.00 4.52
357 393 3.515562 ACCAAACCATATCCAAGGCAAA 58.484 40.909 0.00 0.00 0.00 3.68
358 394 3.906846 ACCAAACCATATCCAAGGCAAAA 59.093 39.130 0.00 0.00 0.00 2.44
359 395 4.349342 ACCAAACCATATCCAAGGCAAAAA 59.651 37.500 0.00 0.00 0.00 1.94
428 465 3.153919 GTTTAGAGCAATGGTGGGACAA 58.846 45.455 0.00 0.00 44.16 3.18
432 503 4.046286 AGAGCAATGGTGGGACAATTAA 57.954 40.909 0.00 0.00 44.16 1.40
465 537 3.145233 AGCTGTGCTGAGTGCTGA 58.855 55.556 0.00 0.00 43.37 4.26
477 549 0.610687 AGTGCTGACAACCTAGCCTC 59.389 55.000 0.00 0.00 39.15 4.70
478 550 0.737715 GTGCTGACAACCTAGCCTCG 60.738 60.000 0.00 0.00 39.15 4.63
489 561 4.347360 ACCTAGCCTCGTTGTTAAAAGT 57.653 40.909 0.00 0.00 0.00 2.66
498 570 7.646526 AGCCTCGTTGTTAAAAGTGTTTATTTC 59.353 33.333 0.00 0.00 0.00 2.17
530 631 7.670605 AATATACTGTTAGTCTGCCCACTAA 57.329 36.000 1.38 1.38 36.66 2.24
553 654 7.687941 AATTTAATATCCTACATCAAGCCCG 57.312 36.000 0.00 0.00 0.00 6.13
615 716 5.050769 CGGAGATCGAATTGAATAACCACTG 60.051 44.000 0.00 0.00 42.43 3.66
868 972 1.131126 CGTGCATCCAACCAACATCTC 59.869 52.381 0.00 0.00 0.00 2.75
873 977 3.118261 GCATCCAACCAACATCTCCTCTA 60.118 47.826 0.00 0.00 0.00 2.43
928 1058 0.174617 CTGCGTCCTTTCCCTCTCTC 59.825 60.000 0.00 0.00 0.00 3.20
1053 1189 3.114616 CCGTGCAAGAGAGTGCCG 61.115 66.667 0.00 0.00 44.26 5.69
1087 1223 6.240549 TCCTCTTCATCCTTTCCATTACTC 57.759 41.667 0.00 0.00 0.00 2.59
1224 1360 0.102120 GCTCTGATCCTGAGTCGGTG 59.898 60.000 12.47 0.00 33.06 4.94
1227 1363 1.177401 CTGATCCTGAGTCGGTGTCA 58.823 55.000 0.00 1.23 0.00 3.58
1241 1377 2.810400 CGGTGTCATTTCTGTCAACCCT 60.810 50.000 0.00 0.00 0.00 4.34
2082 2218 2.351253 CCTTGATCTATCGAGCCTGACG 60.351 54.545 2.12 0.00 37.06 4.35
2152 2288 3.067742 CAGCATCATCAATTCCACCCTTC 59.932 47.826 0.00 0.00 0.00 3.46
2295 2431 6.406692 ACAAGCTCAGAAGTTAGTAAGACA 57.593 37.500 0.00 0.00 0.00 3.41
2538 2674 2.204463 TCCAGTGCTTATGGATTGGGA 58.796 47.619 10.82 0.00 41.96 4.37
3006 3142 4.130286 TGAAAATTTTGTCGCCAAGGTT 57.870 36.364 8.47 0.00 0.00 3.50
3285 3421 9.563748 CTTGGCAAAATAATTGATCCCAATATT 57.436 29.630 0.00 0.00 41.84 1.28
3301 3437 4.403432 CCAATATTGCAGGACAAATCAGGT 59.597 41.667 10.11 0.00 42.86 4.00
3333 3469 0.251033 AGATGTTTGCTGAGGCTGCA 60.251 50.000 0.50 0.00 39.59 4.41
3554 3690 4.971282 AGGAAGATGAAGATACCATGGTGA 59.029 41.667 28.17 11.79 0.00 4.02
3615 3751 2.573009 TCTTGTCTGATCCCATGCAGAA 59.427 45.455 2.76 0.00 42.27 3.02
3623 3759 5.011840 TCTGATCCCATGCAGAAATCTCTAG 59.988 44.000 0.00 0.00 38.14 2.43
3625 3761 5.840693 TGATCCCATGCAGAAATCTCTAGTA 59.159 40.000 0.00 0.00 0.00 1.82
3626 3762 5.537300 TCCCATGCAGAAATCTCTAGTAC 57.463 43.478 0.00 0.00 0.00 2.73
3795 3931 4.947388 GCAATTAGGGGACATTGTAAGACA 59.053 41.667 0.00 0.00 33.58 3.41
3822 3958 4.704540 TGTAAACTAAACCATGCCATCAGG 59.295 41.667 0.00 0.00 38.23 3.86
3895 4031 8.715998 CCATCATCAGCTGAATGTAAGTAATAC 58.284 37.037 22.50 0.00 37.44 1.89
3989 4128 6.328714 CACACAGCTACCTATATCAGCATAG 58.671 44.000 0.00 0.00 37.78 2.23
4053 4424 7.559590 ACAACTATGGCATCATACTCTTTTC 57.440 36.000 1.65 0.00 34.96 2.29
4061 4432 5.591877 GGCATCATACTCTTTTCAGGTTCAT 59.408 40.000 0.00 0.00 0.00 2.57
4094 4465 2.607635 GGTGACATGGTGTTATGTAGCG 59.392 50.000 0.00 0.00 41.15 4.26
4186 4589 6.542005 ACATCCAAGAACGATATTGCAACATA 59.458 34.615 0.00 0.00 0.00 2.29
4220 4623 1.067635 CACAATAGTGCCAAACAGCCC 60.068 52.381 0.00 0.00 39.21 5.19
4299 4702 4.038162 CACTACCAGACAGCTAGGGAATAC 59.962 50.000 0.00 0.00 0.00 1.89
4417 4837 3.698040 AGCCCTCAATAACTGCTTCAATG 59.302 43.478 0.00 0.00 0.00 2.82
4478 4898 5.582269 CGAGTATATGGCATGGTAATTGGAG 59.418 44.000 10.98 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 101 3.062707 CACGATTCGTTCTTGTATCGACG 60.063 47.826 9.40 0.00 40.30 5.12
89 102 3.850273 ACACGATTCGTTCTTGTATCGAC 59.150 43.478 9.40 0.00 40.30 4.20
90 103 4.087510 ACACGATTCGTTCTTGTATCGA 57.912 40.909 9.40 0.00 40.30 3.59
91 104 4.817987 AACACGATTCGTTCTTGTATCG 57.182 40.909 9.40 0.00 42.54 2.92
92 105 7.272948 AGACTAAACACGATTCGTTCTTGTATC 59.727 37.037 9.40 2.86 38.32 2.24
93 106 7.088905 AGACTAAACACGATTCGTTCTTGTAT 58.911 34.615 9.40 0.34 38.32 2.29
94 107 6.441274 AGACTAAACACGATTCGTTCTTGTA 58.559 36.000 9.40 0.00 38.32 2.41
95 108 5.287226 AGACTAAACACGATTCGTTCTTGT 58.713 37.500 9.40 1.39 38.32 3.16
96 109 5.824243 AGACTAAACACGATTCGTTCTTG 57.176 39.130 9.40 0.70 38.32 3.02
103 117 9.408069 TCTAAGAAGAAAGACTAAACACGATTC 57.592 33.333 0.00 0.00 0.00 2.52
140 154 5.871396 AGACGGGTATAATAGGCCATATG 57.129 43.478 5.01 0.00 0.00 1.78
145 162 2.901839 TCCAAGACGGGTATAATAGGCC 59.098 50.000 0.00 0.00 34.36 5.19
159 176 2.111384 TCTAGGCCATGTCTCCAAGAC 58.889 52.381 5.01 0.08 45.26 3.01
165 182 2.420687 CCCAAGTTCTAGGCCATGTCTC 60.421 54.545 5.01 0.00 0.00 3.36
169 186 0.034186 TGCCCAAGTTCTAGGCCATG 60.034 55.000 5.01 0.00 46.55 3.66
176 193 2.584835 ATTGTGCTGCCCAAGTTCTA 57.415 45.000 3.59 0.00 0.00 2.10
198 215 3.273434 TGAGCATCAGTATTGTTCCAGC 58.727 45.455 0.00 0.00 42.56 4.85
217 234 2.231964 GCTCCTTGTCAATTTGGCATGA 59.768 45.455 16.05 9.98 29.04 3.07
220 237 1.702182 TGCTCCTTGTCAATTTGGCA 58.298 45.000 0.00 0.00 0.00 4.92
221 238 2.297033 TCTTGCTCCTTGTCAATTTGGC 59.703 45.455 0.00 0.00 0.00 4.52
222 239 4.219070 TGATCTTGCTCCTTGTCAATTTGG 59.781 41.667 0.00 0.00 0.00 3.28
223 240 5.048224 ACTGATCTTGCTCCTTGTCAATTTG 60.048 40.000 0.00 0.00 0.00 2.32
224 241 5.048224 CACTGATCTTGCTCCTTGTCAATTT 60.048 40.000 0.00 0.00 0.00 1.82
225 242 4.458295 CACTGATCTTGCTCCTTGTCAATT 59.542 41.667 0.00 0.00 0.00 2.32
226 243 4.008330 CACTGATCTTGCTCCTTGTCAAT 58.992 43.478 0.00 0.00 0.00 2.57
227 244 3.071457 TCACTGATCTTGCTCCTTGTCAA 59.929 43.478 0.00 0.00 0.00 3.18
237 254 6.581542 CAGAAGAACATTTTCACTGATCTTGC 59.418 38.462 11.00 0.00 39.05 4.01
241 258 5.707298 TCCCAGAAGAACATTTTCACTGATC 59.293 40.000 15.47 0.00 39.05 2.92
243 260 5.047566 TCCCAGAAGAACATTTTCACTGA 57.952 39.130 15.47 0.92 39.05 3.41
253 270 6.609616 ACAAATTAACCTTTCCCAGAAGAACA 59.390 34.615 0.00 0.00 0.00 3.18
265 282 5.997129 CCTGGCATCAAACAAATTAACCTTT 59.003 36.000 0.00 0.00 0.00 3.11
276 304 1.142667 TGTCAGTCCTGGCATCAAACA 59.857 47.619 0.00 0.00 40.71 2.83
298 326 4.460731 GGGGCTATTTGAGAATATTCTGGC 59.539 45.833 22.61 17.17 37.73 4.85
300 328 4.154918 GCGGGGCTATTTGAGAATATTCTG 59.845 45.833 22.61 8.14 37.73 3.02
301 329 4.202461 TGCGGGGCTATTTGAGAATATTCT 60.202 41.667 17.96 17.96 41.00 2.40
304 332 3.788227 TGCGGGGCTATTTGAGAATAT 57.212 42.857 0.00 0.00 0.00 1.28
305 333 3.072330 TCATGCGGGGCTATTTGAGAATA 59.928 43.478 0.00 0.00 0.00 1.75
306 334 2.158623 TCATGCGGGGCTATTTGAGAAT 60.159 45.455 0.00 0.00 0.00 2.40
307 335 1.211703 TCATGCGGGGCTATTTGAGAA 59.788 47.619 0.00 0.00 0.00 2.87
309 337 1.901591 ATCATGCGGGGCTATTTGAG 58.098 50.000 0.00 0.00 0.00 3.02
311 339 2.624838 AGAAATCATGCGGGGCTATTTG 59.375 45.455 0.00 0.00 0.00 2.32
312 340 2.624838 CAGAAATCATGCGGGGCTATTT 59.375 45.455 0.00 0.00 0.00 1.40
318 354 0.740737 GTTCCAGAAATCATGCGGGG 59.259 55.000 0.00 0.00 0.00 5.73
319 355 0.740737 GGTTCCAGAAATCATGCGGG 59.259 55.000 0.00 0.00 0.00 6.13
334 370 3.096092 TGCCTTGGATATGGTTTGGTTC 58.904 45.455 0.00 0.00 0.00 3.62
337 373 4.550076 TTTTGCCTTGGATATGGTTTGG 57.450 40.909 0.00 0.00 0.00 3.28
370 406 9.062524 TGCCATATGGTGTAGTATGTTTTTATC 57.937 33.333 22.79 0.40 37.57 1.75
372 408 7.829706 TGTGCCATATGGTGTAGTATGTTTTTA 59.170 33.333 22.79 0.00 37.57 1.52
398 434 0.322456 TTGCTCTAAACGCCATGGCT 60.322 50.000 33.07 18.25 39.32 4.75
405 441 0.451783 CCCACCATTGCTCTAAACGC 59.548 55.000 0.00 0.00 0.00 4.84
414 451 5.353956 GGAATTTTAATTGTCCCACCATTGC 59.646 40.000 0.00 0.00 0.00 3.56
459 531 0.737715 CGAGGCTAGGTTGTCAGCAC 60.738 60.000 0.00 0.00 39.63 4.40
460 532 1.185618 ACGAGGCTAGGTTGTCAGCA 61.186 55.000 0.00 0.00 39.63 4.41
461 533 0.037232 AACGAGGCTAGGTTGTCAGC 60.037 55.000 0.00 0.00 37.05 4.26
462 534 1.714794 CAACGAGGCTAGGTTGTCAG 58.285 55.000 18.00 0.00 38.89 3.51
463 535 3.906660 CAACGAGGCTAGGTTGTCA 57.093 52.632 18.00 0.00 38.89 3.58
477 549 8.259194 CAGCTGAAATAAACACTTTTAACAACG 58.741 33.333 8.42 0.00 30.86 4.10
478 550 9.083080 ACAGCTGAAATAAACACTTTTAACAAC 57.917 29.630 23.35 0.00 30.86 3.32
498 570 7.169982 GGCAGACTAACAGTATATTTACAGCTG 59.830 40.741 13.48 13.48 0.00 4.24
508 580 7.670605 AATTAGTGGGCAGACTAACAGTATA 57.329 36.000 9.72 0.00 40.41 1.47
520 621 9.167311 GATGTAGGATATTAAATTAGTGGGCAG 57.833 37.037 0.00 0.00 0.00 4.85
521 622 8.664992 TGATGTAGGATATTAAATTAGTGGGCA 58.335 33.333 0.00 0.00 0.00 5.36
530 631 5.648092 GCGGGCTTGATGTAGGATATTAAAT 59.352 40.000 0.00 0.00 0.00 1.40
553 654 1.789464 CTGACGATATCTTTCGCTGGC 59.211 52.381 0.34 0.00 42.82 4.85
648 749 1.139654 AGTCAAGCAGAACTGTGCAGA 59.860 47.619 6.17 0.00 46.60 4.26
928 1058 2.232208 GGGAAGTGCTCTTTTGGATTGG 59.768 50.000 2.00 0.00 33.64 3.16
1036 1166 2.842394 ATCGGCACTCTCTTGCACGG 62.842 60.000 0.00 0.00 44.94 4.94
1037 1167 1.446792 ATCGGCACTCTCTTGCACG 60.447 57.895 0.00 0.00 44.94 5.34
1053 1189 5.927819 AGGATGAAGAGGATCAAGAACATC 58.072 41.667 0.00 0.00 37.82 3.06
1241 1377 0.179111 GGCGATCTTGATGTCCGTCA 60.179 55.000 0.00 0.00 0.00 4.35
1899 2035 9.661563 AATCTTGCATTTGTGATATTTGTTGAT 57.338 25.926 0.00 0.00 0.00 2.57
1956 2092 2.633481 GCGGATAAGGTACCTGAATCCT 59.367 50.000 33.46 17.10 37.32 3.24
2082 2218 3.833304 GCTACTGCAAGCCCCATC 58.167 61.111 0.00 0.00 37.60 3.51
2295 2431 2.795231 ATGCTATGCCAGTCAGTGTT 57.205 45.000 0.00 0.00 0.00 3.32
2378 2514 1.202976 AGCTGTTTGTCCTCTGCCATT 60.203 47.619 0.00 0.00 0.00 3.16
2538 2674 1.200716 TCGACGAAGGTGAAATAGCGT 59.799 47.619 0.00 0.00 34.39 5.07
2730 2866 1.962306 GTGGCGGTGGCGAAGTTTA 60.962 57.895 0.00 0.00 41.24 2.01
3006 3142 4.771577 TCTTTTGATAGGCCAAAATCAGCA 59.228 37.500 5.01 0.00 42.81 4.41
3180 3316 2.496291 GGCTGGATTGATGGCTGGC 61.496 63.158 0.00 0.00 0.00 4.85
3264 3400 8.995220 CCTGCAATATTGGGATCAATTATTTTG 58.005 33.333 17.02 0.00 42.90 2.44
3285 3421 1.699083 TCAGACCTGATTTGTCCTGCA 59.301 47.619 0.00 0.00 34.14 4.41
3301 3437 5.180680 CAGCAAACATCTCAAGTGAATCAGA 59.819 40.000 0.00 0.00 0.00 3.27
3333 3469 2.875094 AGTCAGCAAGGCATTTCTCT 57.125 45.000 0.00 0.00 0.00 3.10
3432 3568 1.667830 ATCACTGGTGCCGTCAACG 60.668 57.895 0.00 0.00 39.44 4.10
3442 3578 0.548031 ATTGCGATCCCATCACTGGT 59.452 50.000 0.00 0.00 41.37 4.00
3554 3690 8.429641 CCTTAATACCCTTACATACTGTGATGT 58.570 37.037 0.00 0.00 42.68 3.06
3615 3751 9.411189 CCCTTCTACTAAAGTGTACTAGAGATT 57.589 37.037 0.00 0.00 0.00 2.40
3623 3759 7.148289 GGCAAAATCCCTTCTACTAAAGTGTAC 60.148 40.741 0.00 0.00 0.00 2.90
3625 3761 5.710567 GGCAAAATCCCTTCTACTAAAGTGT 59.289 40.000 0.00 0.00 0.00 3.55
3626 3762 5.946377 AGGCAAAATCCCTTCTACTAAAGTG 59.054 40.000 0.00 0.00 0.00 3.16
3710 3846 8.121305 TGGATGCTCAAGTAAAACAAATACAT 57.879 30.769 0.00 0.00 0.00 2.29
3718 3854 2.819608 TGGCTGGATGCTCAAGTAAAAC 59.180 45.455 0.00 0.00 42.39 2.43
3895 4031 4.998788 TCTACGTTGGAATGATCTGACAG 58.001 43.478 0.00 0.00 0.00 3.51
4102 4473 2.637872 ACAACTACCTAGCTTCCTGCAA 59.362 45.455 0.00 0.00 45.94 4.08
4112 4487 7.156673 TGGCTTTACAAGTTACAACTACCTAG 58.843 38.462 0.00 0.00 38.57 3.02
4253 4656 7.829211 AGTGTTCAATTGCAGTTATATGGTAGT 59.171 33.333 0.00 0.00 0.00 2.73
4254 4657 8.213518 AGTGTTCAATTGCAGTTATATGGTAG 57.786 34.615 0.00 0.00 0.00 3.18
4255 4658 9.104965 GTAGTGTTCAATTGCAGTTATATGGTA 57.895 33.333 0.00 0.00 0.00 3.25
4417 4837 0.315251 GTTGAACTTCCCCAAGCTGC 59.685 55.000 0.00 0.00 32.09 5.25
4460 4880 3.591695 TGCTCCAATTACCATGCCATA 57.408 42.857 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.