Multiple sequence alignment - TraesCS6D01G286300

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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 TraesCS6D01G286300 chr6D 100.000 4324 0 0 1 4324 394829197 394824874 0.000000e+00 7986
1 TraesCS6D01G286300 chr6B 93.483 3253 158 24 971 4209 591127302 591124090 0.000000e+00 4783
2 TraesCS6D01G286300 chr6B 94.848 951 32 8 1 942 591128245 591127303 0.000000e+00 1469
3 TraesCS6D01G286300 chr6A 96.255 1869 48 11 1 1854 541240761 541238900 0.000000e+00 3044
4 TraesCS6D01G286300 chr6A 93.885 1897 98 11 1840 3730 541238818 541236934 0.000000e+00 2844
5 TraesCS6D01G286300 chr6A 88.502 287 22 3 3940 4215 541236815 541236529 1.930000e-88 337
6 TraesCS6D01G286300 chr5B 79.570 279 55 2 1946 2222 522408946 522409224 9.480000e-47 198
7 TraesCS6D01G286300 chr2D 91.071 56 3 2 4253 4306 616062136 616062081 1.670000e-09 75


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 TraesCS6D01G286300 chr6D 394824874 394829197 4323 True 7986 7986 100.000000 1 4324 1 chr6D.!!$R1 4323
1 TraesCS6D01G286300 chr6B 591124090 591128245 4155 True 3126 4783 94.165500 1 4209 2 chr6B.!!$R1 4208
2 TraesCS6D01G286300 chr6A 541236529 541240761 4232 True 2075 3044 92.880667 1 4215 3 chr6A.!!$R1 4214

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
717 730 0.035152 TGCATGCCAGTAGTTCCCTG 60.035 55.0 16.68 0.0 0.0 4.45 F
832 845 0.417437 TGATCCCTCTTCCACCTCCA 59.583 55.0 0.00 0.0 0.0 3.86 F
1620 1638 0.467844 AACTGCATGCACCTTGACCA 60.468 50.0 18.46 0.0 0.0 4.02 F
2737 2858 0.343372 TCTCCTCCCTTACCCAGCAT 59.657 55.0 0.00 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2313 0.833287 AAGGATCGGTGAGTGATGGG 59.167 55.000 0.00 0.00 0.00 4.00 R
2213 2328 1.003355 CTTCTGCGGCAAGGAAGGA 60.003 57.895 18.98 4.06 34.55 3.36 R
3178 3299 0.037605 GATGGACCGTTGAGTTCCGT 60.038 55.000 0.00 0.00 0.00 4.69 R
4264 4406 0.095935 GAGCGCTTGCATGTACTGTG 59.904 55.000 13.26 0.00 42.66 3.66 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
40 41 7.392393 ACCGTTTAGCAGTTATCCTTAAAACAT 59.608 33.333 0.00 0.00 0.00 2.71
41 42 8.885722 CCGTTTAGCAGTTATCCTTAAAACATA 58.114 33.333 0.00 0.00 0.00 2.29
42 43 9.698617 CGTTTAGCAGTTATCCTTAAAACATAC 57.301 33.333 0.00 0.00 0.00 2.39
160 163 4.164988 GGGGAGGGGATATAGATGTTGATG 59.835 50.000 0.00 0.00 0.00 3.07
180 183 8.755018 GTTGATGCCAATGTAAAATATAGTTGC 58.245 33.333 0.00 0.00 34.39 4.17
273 283 6.261381 TGTCTTGGGAATTGTTACTTACACAC 59.739 38.462 0.00 0.00 36.21 3.82
477 490 5.091431 GCAGCAGAATTTGTACAGTTCATC 58.909 41.667 19.18 12.52 0.00 2.92
609 622 4.094294 GTGTGAACAATAAGCCGAATAGCA 59.906 41.667 0.00 0.00 34.23 3.49
688 701 2.022764 GCTTGAGCTTCCTTCTCTCC 57.977 55.000 0.00 0.00 38.21 3.71
707 720 1.945394 CCTTAAGTAGCTGCATGCCAG 59.055 52.381 16.68 13.51 44.23 4.85
717 730 0.035152 TGCATGCCAGTAGTTCCCTG 60.035 55.000 16.68 0.00 0.00 4.45
774 787 2.545731 GCAGTGCTTAGAGCTAGGTTC 58.454 52.381 8.18 0.00 42.97 3.62
832 845 0.417437 TGATCCCTCTTCCACCTCCA 59.583 55.000 0.00 0.00 0.00 3.86
835 848 1.089978 TCCCTCTTCCACCTCCAGTA 58.910 55.000 0.00 0.00 0.00 2.74
994 1008 1.268640 CCGGTTTGTTTTACGGTGGTG 60.269 52.381 0.00 0.00 41.34 4.17
1038 1052 3.373439 GTGATGACATGGAGAAGCAAGAC 59.627 47.826 0.00 0.00 0.00 3.01
1125 1139 4.331108 AGAGAAAAATCCAGCAGAAGTCC 58.669 43.478 0.00 0.00 0.00 3.85
1505 1523 1.132643 CCACGAGTAGACAGCACCTAC 59.867 57.143 0.00 0.00 37.38 3.18
1620 1638 0.467844 AACTGCATGCACCTTGACCA 60.468 50.000 18.46 0.00 0.00 4.02
1677 1695 6.039047 CCCATCTTTGAGTTTACATGATCCTG 59.961 42.308 0.00 0.00 0.00 3.86
1686 1705 7.093509 TGAGTTTACATGATCCTGCTACTGTAA 60.094 37.037 0.00 0.00 0.00 2.41
1694 1713 4.402056 TCCTGCTACTGTAATGCTTACC 57.598 45.455 1.52 0.00 35.25 2.85
1702 1721 5.924475 ACTGTAATGCTTACCGAATATGC 57.076 39.130 0.00 0.00 35.25 3.14
2171 2286 0.744281 CGGCCAAAGGTGTCAAAACT 59.256 50.000 2.24 0.00 0.00 2.66
2198 2313 1.372582 TGATGCATGAGTTTCGGCTC 58.627 50.000 2.46 0.00 36.12 4.70
2213 2328 1.690219 GGCTCCCATCACTCACCGAT 61.690 60.000 0.00 0.00 0.00 4.18
2219 2334 1.202580 CCATCACTCACCGATCCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
2299 2414 6.579666 TGCTGCAACTTTGAGAGAAAATAT 57.420 33.333 0.00 0.00 0.00 1.28
2335 2450 5.589855 TCACTGAACATGTGAAGTTGAATGT 59.410 36.000 10.25 0.00 40.89 2.71
2337 2452 6.852853 CACTGAACATGTGAAGTTGAATGTAC 59.147 38.462 10.25 0.00 37.60 2.90
2338 2453 6.767902 ACTGAACATGTGAAGTTGAATGTACT 59.232 34.615 0.00 0.00 33.04 2.73
2340 2455 8.669946 TGAACATGTGAAGTTGAATGTACTTA 57.330 30.769 0.00 0.00 36.04 2.24
2353 2469 5.606749 TGAATGTACTTATGTAGGATGCCCT 59.393 40.000 0.00 0.00 46.62 5.19
2389 2507 7.930513 AGAACATTGCTGCTACTTTAAAAAC 57.069 32.000 0.00 0.00 0.00 2.43
2394 2512 7.382218 ACATTGCTGCTACTTTAAAAACACATC 59.618 33.333 0.00 0.00 0.00 3.06
2496 2616 8.363390 GCCTAGCAGATATATATAGCACAATGA 58.637 37.037 17.27 0.00 0.00 2.57
2737 2858 0.343372 TCTCCTCCCTTACCCAGCAT 59.657 55.000 0.00 0.00 0.00 3.79
2765 2886 2.124411 GCCTACATTCCTCCCCACTTA 58.876 52.381 0.00 0.00 0.00 2.24
2790 2911 0.846401 CACACACAGAAGTCGACACG 59.154 55.000 19.50 5.17 0.00 4.49
2807 2928 0.969149 ACGCCTCAGAGAACACATCA 59.031 50.000 0.00 0.00 0.00 3.07
2810 2931 2.200067 GCCTCAGAGAACACATCATCG 58.800 52.381 0.00 0.00 0.00 3.84
2874 2995 5.825507 GCAGTGGCTATTTTCCTTCAATAG 58.174 41.667 0.00 0.00 37.30 1.73
2891 3012 5.087323 TCAATAGTTTCCTCCTGTCAGAGT 58.913 41.667 0.00 0.00 31.53 3.24
3041 3162 1.597195 GCATCGATGGTTATGAACGCA 59.403 47.619 26.00 0.00 0.00 5.24
3101 3222 2.859526 TGAACATTGAGTTTGCGCAA 57.140 40.000 21.02 21.02 41.51 4.85
3144 3265 1.404035 GCAACATGATCAGCAGATGCA 59.596 47.619 17.20 0.00 45.16 3.96
3174 3295 1.378531 GCCTGATATCGGCAACAACA 58.621 50.000 24.50 0.00 46.77 3.33
3177 3298 3.205338 CCTGATATCGGCAACAACATCA 58.795 45.455 5.98 0.00 0.00 3.07
3178 3299 3.627123 CCTGATATCGGCAACAACATCAA 59.373 43.478 5.98 0.00 0.00 2.57
3183 3304 0.309302 CGGCAACAACATCAACGGAA 59.691 50.000 0.00 0.00 0.00 4.30
3187 3308 2.032799 GCAACAACATCAACGGAACTCA 59.967 45.455 0.00 0.00 0.00 3.41
3197 3318 0.037605 ACGGAACTCAACGGTCCATC 60.038 55.000 0.00 0.00 0.00 3.51
3223 3344 1.688197 CCCATTCAACAACCTGCAAGT 59.312 47.619 0.00 0.00 0.00 3.16
3249 3370 0.820226 TTCTGATGACTGGAGAGCGG 59.180 55.000 0.00 0.00 0.00 5.52
3371 3492 7.554959 TTTGGTTTTAGAGTGGAGTAGAGAT 57.445 36.000 0.00 0.00 0.00 2.75
3469 3590 4.328440 GCTAACAGAACTGATGTGTGCTAG 59.672 45.833 8.87 0.00 35.36 3.42
3472 3593 4.810790 ACAGAACTGATGTGTGCTAGTAC 58.189 43.478 8.87 3.70 33.59 2.73
3473 3594 4.524714 ACAGAACTGATGTGTGCTAGTACT 59.475 41.667 12.42 0.00 33.59 2.73
3474 3595 5.710567 ACAGAACTGATGTGTGCTAGTACTA 59.289 40.000 12.42 1.89 33.59 1.82
3475 3596 6.378564 ACAGAACTGATGTGTGCTAGTACTAT 59.621 38.462 12.42 6.74 33.59 2.12
3476 3597 6.694844 CAGAACTGATGTGTGCTAGTACTATG 59.305 42.308 12.42 0.00 0.00 2.23
3480 3601 6.073327 TGATGTGTGCTAGTACTATGTAGC 57.927 41.667 12.42 5.72 41.81 3.58
3481 3602 5.828328 TGATGTGTGCTAGTACTATGTAGCT 59.172 40.000 14.76 0.00 41.94 3.32
3704 3825 3.645975 GGGTTGTCGGTGCACGTG 61.646 66.667 12.28 12.28 44.69 4.49
3735 3857 9.073475 GTGTAAGAGGATCACTAGTATCAGAAT 57.927 37.037 0.00 0.00 37.82 2.40
3736 3858 9.647918 TGTAAGAGGATCACTAGTATCAGAATT 57.352 33.333 0.00 0.00 37.82 2.17
3738 3860 8.774546 AAGAGGATCACTAGTATCAGAATTCA 57.225 34.615 8.44 0.00 37.82 2.57
3739 3861 8.408043 AGAGGATCACTAGTATCAGAATTCAG 57.592 38.462 8.44 0.00 37.82 3.02
3740 3862 8.224025 AGAGGATCACTAGTATCAGAATTCAGA 58.776 37.037 8.44 5.51 37.82 3.27
3741 3863 8.774546 AGGATCACTAGTATCAGAATTCAGAA 57.225 34.615 8.44 0.00 0.00 3.02
3742 3864 8.859090 AGGATCACTAGTATCAGAATTCAGAAG 58.141 37.037 8.44 2.21 0.00 2.85
3798 3920 1.073025 TCCGCTTGCCTGACAACAT 59.927 52.632 0.00 0.00 33.68 2.71
3800 3922 1.236616 CCGCTTGCCTGACAACATGA 61.237 55.000 0.00 0.00 33.68 3.07
3808 3930 0.647410 CTGACAACATGATCGTCCGC 59.353 55.000 0.00 0.00 0.00 5.54
3811 3933 2.890474 AACATGATCGTCCGCCGC 60.890 61.111 0.00 0.00 36.19 6.53
3856 3978 0.530650 CTGGCGGCGATTCATACAGT 60.531 55.000 12.98 0.00 0.00 3.55
3870 3992 0.902531 TACAGTCTGCCCTGGTTAGC 59.097 55.000 0.00 0.00 36.75 3.09
3975 4105 3.314331 CCTGGCAGTCTCGGTGGT 61.314 66.667 14.43 0.00 0.00 4.16
4084 4219 1.144565 CTGTCTCTTGCTCGCATCGG 61.145 60.000 0.00 0.00 0.00 4.18
4090 4225 0.249197 CTTGCTCGCATCGGATCTGA 60.249 55.000 6.72 6.72 0.00 3.27
4104 4239 1.098712 ATCTGAGGTCTCGACGGAGC 61.099 60.000 0.00 1.13 40.26 4.70
4187 4329 1.672356 GCCAGAAGCTGCGGAGAAA 60.672 57.895 8.65 0.00 38.99 2.52
4205 4347 6.310467 CGGAGAAATTGACGTTTCAGATTAGA 59.690 38.462 0.00 0.00 39.88 2.10
4209 4351 7.661847 AGAAATTGACGTTTCAGATTAGAACCT 59.338 33.333 0.00 0.00 39.88 3.50
4215 4357 1.860641 TCAGATTAGAACCTGGCCGA 58.139 50.000 0.00 0.00 0.00 5.54
4216 4358 2.398588 TCAGATTAGAACCTGGCCGAT 58.601 47.619 0.00 0.00 0.00 4.18
4217 4359 3.572642 TCAGATTAGAACCTGGCCGATA 58.427 45.455 0.00 0.00 0.00 2.92
4218 4360 3.574396 TCAGATTAGAACCTGGCCGATAG 59.426 47.826 0.00 0.00 0.00 2.08
4219 4361 2.300437 AGATTAGAACCTGGCCGATAGC 59.700 50.000 0.00 0.00 42.60 2.97
4220 4362 0.387929 TTAGAACCTGGCCGATAGCG 59.612 55.000 0.00 0.00 45.17 4.26
4221 4363 2.083835 TAGAACCTGGCCGATAGCGC 62.084 60.000 0.00 0.00 45.17 5.92
4222 4364 3.447025 GAACCTGGCCGATAGCGCT 62.447 63.158 17.26 17.26 45.17 5.92
4223 4365 2.925162 GAACCTGGCCGATAGCGCTT 62.925 60.000 18.68 2.89 45.17 4.68
4224 4366 2.203070 CCTGGCCGATAGCGCTTT 60.203 61.111 18.68 8.03 45.17 3.51
4225 4367 1.819632 CCTGGCCGATAGCGCTTTT 60.820 57.895 18.68 3.01 45.17 2.27
4226 4368 1.376609 CCTGGCCGATAGCGCTTTTT 61.377 55.000 18.68 0.00 45.17 1.94
4250 4392 2.961522 TTTTAAGAAACGGCTGCGAG 57.038 45.000 0.00 0.00 0.00 5.03
4251 4393 0.515564 TTTAAGAAACGGCTGCGAGC 59.484 50.000 0.00 0.11 41.46 5.03
4252 4394 0.320421 TTAAGAAACGGCTGCGAGCT 60.320 50.000 7.85 0.00 41.99 4.09
4253 4395 0.736325 TAAGAAACGGCTGCGAGCTC 60.736 55.000 2.73 2.73 41.99 4.09
4254 4396 2.433318 GAAACGGCTGCGAGCTCT 60.433 61.111 12.85 0.00 41.99 4.09
4255 4397 2.433318 AAACGGCTGCGAGCTCTC 60.433 61.111 12.85 4.04 41.99 3.20
4256 4398 2.827383 GAAACGGCTGCGAGCTCTCT 62.827 60.000 12.85 0.00 41.99 3.10
4257 4399 2.441822 AAACGGCTGCGAGCTCTCTT 62.442 55.000 12.85 0.00 41.99 2.85
4258 4400 2.125753 CGGCTGCGAGCTCTCTTT 60.126 61.111 12.85 0.00 41.99 2.52
4259 4401 1.739562 CGGCTGCGAGCTCTCTTTT 60.740 57.895 12.85 0.00 41.99 2.27
4260 4402 1.294659 CGGCTGCGAGCTCTCTTTTT 61.295 55.000 12.85 0.00 41.99 1.94
4280 4422 3.804518 TTAACACAGTACATGCAAGCG 57.195 42.857 0.00 0.00 0.00 4.68
4281 4423 0.238289 AACACAGTACATGCAAGCGC 59.762 50.000 0.00 0.00 39.24 5.92
4282 4424 0.603707 ACACAGTACATGCAAGCGCT 60.604 50.000 2.64 2.64 39.64 5.92
4283 4425 0.095935 CACAGTACATGCAAGCGCTC 59.904 55.000 12.06 0.00 39.64 5.03
4284 4426 0.320683 ACAGTACATGCAAGCGCTCA 60.321 50.000 12.06 5.63 39.64 4.26
4285 4427 1.012086 CAGTACATGCAAGCGCTCAT 58.988 50.000 12.06 8.31 39.64 2.90
4286 4428 2.204237 CAGTACATGCAAGCGCTCATA 58.796 47.619 12.06 0.00 39.64 2.15
4287 4429 2.804527 CAGTACATGCAAGCGCTCATAT 59.195 45.455 12.06 2.09 39.64 1.78
4288 4430 3.989817 CAGTACATGCAAGCGCTCATATA 59.010 43.478 12.06 0.91 39.64 0.86
4289 4431 4.628766 CAGTACATGCAAGCGCTCATATAT 59.371 41.667 12.06 2.84 39.64 0.86
4290 4432 5.807011 CAGTACATGCAAGCGCTCATATATA 59.193 40.000 12.06 1.87 39.64 0.86
4291 4433 5.807520 AGTACATGCAAGCGCTCATATATAC 59.192 40.000 12.06 13.29 39.64 1.47
4292 4434 3.614176 ACATGCAAGCGCTCATATATACG 59.386 43.478 12.06 0.26 39.64 3.06
4301 4443 6.756189 GCGCTCATATATACGCGTATATAC 57.244 41.667 40.60 31.08 46.56 1.47
4302 4444 6.532311 GCGCTCATATATACGCGTATATACT 58.468 40.000 40.60 30.66 46.56 2.12
4303 4445 6.677828 GCGCTCATATATACGCGTATATACTC 59.322 42.308 40.60 30.55 46.56 2.59
4304 4446 7.620806 GCGCTCATATATACGCGTATATACTCA 60.621 40.741 40.60 30.19 46.56 3.41
4305 4447 7.683270 CGCTCATATATACGCGTATATACTCAC 59.317 40.741 40.60 31.59 41.27 3.51
4306 4448 8.710551 GCTCATATATACGCGTATATACTCACT 58.289 37.037 40.60 29.25 41.27 3.41
4308 4450 9.978044 TCATATATACGCGTATATACTCACTCT 57.022 33.333 40.60 28.22 41.27 3.24
4312 4454 9.978044 ATATACGCGTATATACTCACTCTATGA 57.022 33.333 37.76 17.20 37.07 2.15
4313 4455 8.713737 ATACGCGTATATACTCACTCTATGAA 57.286 34.615 29.34 0.00 36.69 2.57
4314 4456 6.829703 ACGCGTATATACTCACTCTATGAAC 58.170 40.000 11.67 0.00 36.69 3.18
4315 4457 6.649973 ACGCGTATATACTCACTCTATGAACT 59.350 38.462 11.67 0.00 36.69 3.01
4316 4458 7.172875 ACGCGTATATACTCACTCTATGAACTT 59.827 37.037 11.67 0.00 36.69 2.66
4317 4459 8.654215 CGCGTATATACTCACTCTATGAACTTA 58.346 37.037 11.05 0.00 36.69 2.24
4323 4465 6.694877 ACTCACTCTATGAACTTATACGCA 57.305 37.500 0.00 0.00 36.69 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 163 7.479980 TGACAGCAACTATATTTTACATTGGC 58.520 34.615 0.00 0.00 0.00 4.52
180 183 4.130286 GGAGTGTAATTCCCTCTGACAG 57.870 50.000 0.00 0.00 36.60 3.51
273 283 2.290896 TGGCTTCCTTGTCCATAGTTGG 60.291 50.000 0.00 0.00 45.15 3.77
609 622 2.913617 CCTTTGTAGGGTCTTCCTTCCT 59.086 50.000 0.00 0.00 45.47 3.36
672 685 4.421131 ACTTAAGGAGAGAAGGAAGCTCA 58.579 43.478 7.53 0.00 34.85 4.26
688 701 2.636830 ACTGGCATGCAGCTACTTAAG 58.363 47.619 21.36 0.00 44.79 1.85
707 720 4.876679 GCAGGAAAACTATCAGGGAACTAC 59.123 45.833 0.00 0.00 40.21 2.73
717 730 3.729163 GCAAAGCGAGCAGGAAAACTATC 60.729 47.826 0.00 0.00 0.00 2.08
774 787 9.199982 TGAACGTAAGATTGAACTAACCTAAAG 57.800 33.333 0.00 0.00 43.62 1.85
794 807 4.223514 GCTCGACGACTTGAACGT 57.776 55.556 0.00 0.00 46.58 3.99
832 845 7.272144 AGGATTTGGGTTTCTACTGATTACT 57.728 36.000 0.00 0.00 0.00 2.24
835 848 6.603599 GCTAAGGATTTGGGTTTCTACTGATT 59.396 38.462 0.00 0.00 0.00 2.57
994 1008 5.185635 CACTCCTGATCTCCTCCATATCTTC 59.814 48.000 0.00 0.00 0.00 2.87
1038 1052 4.250464 TGAAGCCAGGTAACATAACTTCG 58.750 43.478 0.00 0.00 37.33 3.79
1107 1121 3.532641 AGGGACTTCTGCTGGATTTTT 57.467 42.857 0.00 0.00 27.25 1.94
1125 1139 3.397482 CCTGATAAGCTCAATCGGAAGG 58.603 50.000 15.99 8.63 32.40 3.46
1264 1278 7.081526 AGCAAGTAATGTTCTTATTGCAGAG 57.918 36.000 10.00 0.00 44.11 3.35
1304 1318 1.451927 GCTTCATCCCGGTCATGCA 60.452 57.895 0.00 0.00 0.00 3.96
1686 1705 4.357918 AGAAGGCATATTCGGTAAGCAT 57.642 40.909 0.00 0.00 34.27 3.79
1694 1713 4.693283 TGAACCACTAGAAGGCATATTCG 58.307 43.478 0.00 0.00 34.27 3.34
1702 1721 6.540189 CCTTAACATGATGAACCACTAGAAGG 59.460 42.308 0.00 0.00 0.00 3.46
1876 1991 3.242123 GCGTCTATTAAGCAACTCAGTGC 60.242 47.826 0.00 0.00 45.28 4.40
2171 2286 3.639672 AACTCATGCATCATCCAGTCA 57.360 42.857 0.00 0.00 0.00 3.41
2198 2313 0.833287 AAGGATCGGTGAGTGATGGG 59.167 55.000 0.00 0.00 0.00 4.00
2213 2328 1.003355 CTTCTGCGGCAAGGAAGGA 60.003 57.895 18.98 4.06 34.55 3.36
2219 2334 1.968017 TGGCTTCTTCTGCGGCAAG 60.968 57.895 3.44 0.00 0.00 4.01
2299 2414 7.282901 TCACATGTTCAGTGAAAAATTCAGAGA 59.717 33.333 7.25 0.00 42.57 3.10
2327 2442 6.204882 GGGCATCCTACATAAGTACATTCAAC 59.795 42.308 0.00 0.00 0.00 3.18
2335 2450 6.621394 AGTTAGAGGGCATCCTACATAAGTA 58.379 40.000 0.00 0.00 45.05 2.24
2337 2452 5.777732 AGAGTTAGAGGGCATCCTACATAAG 59.222 44.000 0.00 0.00 45.05 1.73
2338 2453 5.716979 AGAGTTAGAGGGCATCCTACATAA 58.283 41.667 0.00 0.00 45.05 1.90
2340 2455 4.206244 AGAGTTAGAGGGCATCCTACAT 57.794 45.455 0.00 0.00 45.05 2.29
2353 2469 5.180117 GCAGCAATGTTCTTCAAGAGTTAGA 59.820 40.000 0.00 0.00 0.00 2.10
2455 2573 3.826157 TGCTAGGCATTTGCAGTTTTACT 59.174 39.130 4.74 0.00 44.36 2.24
2586 2706 7.920682 GTGTTGGTTAGTGATTTTCTTGTGAAT 59.079 33.333 0.00 0.00 31.56 2.57
2620 2741 4.202545 CCTGCTCATGAGGGGAAAATAGAT 60.203 45.833 23.89 0.00 0.00 1.98
2737 2858 3.394606 GGGAGGAATGTAGGCTCCATTTA 59.605 47.826 6.76 0.00 36.01 1.40
2765 2886 1.202417 CGACTTCTGTGTGTGGTCTGT 60.202 52.381 0.00 0.00 0.00 3.41
2790 2911 2.200067 CGATGATGTGTTCTCTGAGGC 58.800 52.381 4.59 0.00 0.00 4.70
2807 2928 2.127271 TGATGTTGGTCATTGCCGAT 57.873 45.000 0.00 0.00 36.83 4.18
2810 2931 2.360165 GGAGATGATGTTGGTCATTGCC 59.640 50.000 0.00 0.00 38.88 4.52
2874 2995 4.083565 AGAGTACTCTGACAGGAGGAAAC 58.916 47.826 24.62 0.00 38.75 2.78
2891 3012 5.151297 TGCTGTCAATGATGTTGAGAGTA 57.849 39.130 13.99 8.61 40.62 2.59
3041 3162 1.956869 TGGAGAGTGTGATGGGTGAT 58.043 50.000 0.00 0.00 0.00 3.06
3144 3265 2.288457 CGATATCAGGCAAGTCGACCAT 60.288 50.000 13.01 0.00 34.46 3.55
3174 3295 1.607251 GGACCGTTGAGTTCCGTTGAT 60.607 52.381 0.00 0.00 0.00 2.57
3177 3298 0.395312 ATGGACCGTTGAGTTCCGTT 59.605 50.000 0.00 0.00 0.00 4.44
3178 3299 0.037605 GATGGACCGTTGAGTTCCGT 60.038 55.000 0.00 0.00 0.00 4.69
3183 3304 3.081804 GGAAATTGATGGACCGTTGAGT 58.918 45.455 0.00 0.00 0.00 3.41
3187 3308 2.595750 TGGGAAATTGATGGACCGTT 57.404 45.000 0.00 0.00 0.00 4.44
3197 3318 3.747529 GCAGGTTGTTGAATGGGAAATTG 59.252 43.478 0.00 0.00 0.00 2.32
3223 3344 0.674581 CCAGTCATCAGAAAGCGGCA 60.675 55.000 1.45 0.00 0.00 5.69
3371 3492 1.762957 GCAGATGGAGGTAGGTGCTAA 59.237 52.381 0.00 0.00 0.00 3.09
3469 3590 5.518847 TGCACGAATTCAAGCTACATAGTAC 59.481 40.000 16.98 0.00 0.00 2.73
3472 3593 5.063944 AGTTGCACGAATTCAAGCTACATAG 59.936 40.000 24.35 3.29 35.66 2.23
3473 3594 4.935205 AGTTGCACGAATTCAAGCTACATA 59.065 37.500 24.35 4.89 35.66 2.29
3474 3595 3.753272 AGTTGCACGAATTCAAGCTACAT 59.247 39.130 24.35 13.45 35.66 2.29
3475 3596 3.138304 AGTTGCACGAATTCAAGCTACA 58.862 40.909 24.35 6.51 35.66 2.74
3476 3597 3.813529 AGTTGCACGAATTCAAGCTAC 57.186 42.857 18.90 18.90 33.90 3.58
3480 3601 5.088739 GGTGATTAGTTGCACGAATTCAAG 58.911 41.667 6.22 0.00 35.91 3.02
3481 3602 4.083003 GGGTGATTAGTTGCACGAATTCAA 60.083 41.667 6.22 0.00 35.91 2.69
3704 3825 3.618690 AGTGATCCTCTTACACAAGGC 57.381 47.619 0.00 0.00 37.05 4.35
3735 3857 5.220586 CGTGTAAGCAAACTGTTCTTCTGAA 60.221 40.000 0.00 0.00 0.00 3.02
3736 3858 4.270084 CGTGTAAGCAAACTGTTCTTCTGA 59.730 41.667 0.00 0.00 0.00 3.27
3737 3859 4.270084 TCGTGTAAGCAAACTGTTCTTCTG 59.730 41.667 0.00 0.00 0.00 3.02
3738 3860 4.270325 GTCGTGTAAGCAAACTGTTCTTCT 59.730 41.667 0.00 0.00 0.00 2.85
3739 3861 4.033587 TGTCGTGTAAGCAAACTGTTCTTC 59.966 41.667 0.00 0.00 0.00 2.87
3740 3862 3.936453 TGTCGTGTAAGCAAACTGTTCTT 59.064 39.130 0.00 0.00 0.00 2.52
3741 3863 3.527533 TGTCGTGTAAGCAAACTGTTCT 58.472 40.909 0.00 0.00 0.00 3.01
3742 3864 3.936902 TGTCGTGTAAGCAAACTGTTC 57.063 42.857 0.00 0.00 0.00 3.18
3818 3940 1.903183 AGTTCAGAGCCAAGTCCTACC 59.097 52.381 0.00 0.00 0.00 3.18
3856 3978 1.888436 CGTGAGCTAACCAGGGCAGA 61.888 60.000 0.00 0.00 0.00 4.26
3960 4090 4.314440 GCACCACCGAGACTGCCA 62.314 66.667 0.00 0.00 0.00 4.92
4016 4147 0.870393 CATACATAGCAGGCCGCAAG 59.130 55.000 19.30 11.60 46.13 4.01
4060 4195 2.947532 CGAGCAAGAGACAGGGGCA 61.948 63.158 0.00 0.00 0.00 5.36
4070 4205 0.249197 CAGATCCGATGCGAGCAAGA 60.249 55.000 0.57 0.05 0.00 3.02
4084 4219 0.941542 CTCCGTCGAGACCTCAGATC 59.058 60.000 0.00 0.00 38.52 2.75
4090 4225 2.282251 TGTGCTCCGTCGAGACCT 60.282 61.111 0.00 0.00 38.52 3.85
4104 4239 2.121116 ACGTCAAGAACTCTCGTGTG 57.879 50.000 0.00 0.00 33.29 3.82
4187 4329 5.643777 CCAGGTTCTAATCTGAAACGTCAAT 59.356 40.000 4.52 0.00 39.54 2.57
4205 4347 2.536997 AAAGCGCTATCGGCCAGGTT 62.537 55.000 12.05 0.00 37.74 3.50
4209 4351 4.312052 AAAAAGCGCTATCGGCCA 57.688 50.000 12.05 0.00 37.74 5.36
4230 4372 2.603652 GCTCGCAGCCGTTTCTTAAAAA 60.604 45.455 0.00 0.00 34.48 1.94
4231 4373 1.069500 GCTCGCAGCCGTTTCTTAAAA 60.069 47.619 0.00 0.00 34.48 1.52
4232 4374 0.515564 GCTCGCAGCCGTTTCTTAAA 59.484 50.000 0.00 0.00 34.48 1.52
4233 4375 0.320421 AGCTCGCAGCCGTTTCTTAA 60.320 50.000 4.77 0.00 43.77 1.85
4234 4376 0.736325 GAGCTCGCAGCCGTTTCTTA 60.736 55.000 0.00 0.00 43.77 2.10
4235 4377 2.029844 GAGCTCGCAGCCGTTTCTT 61.030 57.895 0.00 0.00 43.77 2.52
4236 4378 2.433318 GAGCTCGCAGCCGTTTCT 60.433 61.111 0.00 0.00 43.77 2.52
4237 4379 2.433318 AGAGCTCGCAGCCGTTTC 60.433 61.111 8.37 0.00 43.77 2.78
4238 4380 2.433318 GAGAGCTCGCAGCCGTTT 60.433 61.111 13.06 0.00 43.77 3.60
4239 4381 2.441822 AAAGAGAGCTCGCAGCCGTT 62.442 55.000 20.08 1.58 43.77 4.44
4240 4382 2.441822 AAAAGAGAGCTCGCAGCCGT 62.442 55.000 20.08 0.00 43.77 5.68
4241 4383 1.294659 AAAAAGAGAGCTCGCAGCCG 61.295 55.000 20.08 0.00 43.77 5.52
4242 4384 2.549332 AAAAAGAGAGCTCGCAGCC 58.451 52.632 20.08 2.92 43.77 4.85
4257 4399 4.973051 CGCTTGCATGTACTGTGTTAAAAA 59.027 37.500 1.14 0.00 0.00 1.94
4258 4400 4.532276 CGCTTGCATGTACTGTGTTAAAA 58.468 39.130 1.14 0.00 0.00 1.52
4259 4401 3.608241 GCGCTTGCATGTACTGTGTTAAA 60.608 43.478 0.00 0.00 38.92 1.52
4260 4402 2.095969 GCGCTTGCATGTACTGTGTTAA 60.096 45.455 0.00 0.00 38.92 2.01
4261 4403 1.463056 GCGCTTGCATGTACTGTGTTA 59.537 47.619 0.00 0.00 38.92 2.41
4262 4404 0.238289 GCGCTTGCATGTACTGTGTT 59.762 50.000 0.00 0.00 38.92 3.32
4263 4405 0.603707 AGCGCTTGCATGTACTGTGT 60.604 50.000 2.64 0.00 42.66 3.72
4264 4406 0.095935 GAGCGCTTGCATGTACTGTG 59.904 55.000 13.26 0.00 42.66 3.66
4265 4407 0.320683 TGAGCGCTTGCATGTACTGT 60.321 50.000 13.26 0.00 42.66 3.55
4266 4408 1.012086 ATGAGCGCTTGCATGTACTG 58.988 50.000 13.26 0.00 42.66 2.74
4267 4409 2.602257 TATGAGCGCTTGCATGTACT 57.398 45.000 13.26 0.00 42.66 2.73
4268 4410 5.275927 CGTATATATGAGCGCTTGCATGTAC 60.276 44.000 13.26 15.32 42.66 2.90
4269 4411 4.798387 CGTATATATGAGCGCTTGCATGTA 59.202 41.667 13.26 14.34 42.66 2.29
4270 4412 3.614176 CGTATATATGAGCGCTTGCATGT 59.386 43.478 13.26 12.44 42.66 3.21
4271 4413 3.542875 GCGTATATATGAGCGCTTGCATG 60.543 47.826 13.26 0.00 45.48 4.06
4272 4414 2.604914 GCGTATATATGAGCGCTTGCAT 59.395 45.455 13.26 14.41 45.48 3.96
4273 4415 1.992667 GCGTATATATGAGCGCTTGCA 59.007 47.619 13.26 6.25 45.48 4.08
4274 4416 1.007011 CGCGTATATATGAGCGCTTGC 60.007 52.381 13.26 0.00 46.56 4.01
4275 4417 2.959586 CGCGTATATATGAGCGCTTG 57.040 50.000 13.26 7.35 46.56 4.01
4280 4422 8.710551 AGTGAGTATATACGCGTATATATGAGC 58.289 37.037 40.31 31.77 40.83 4.26
4282 4424 9.978044 AGAGTGAGTATATACGCGTATATATGA 57.022 33.333 40.31 29.75 40.83 2.15
4286 4428 9.978044 TCATAGAGTGAGTATATACGCGTATAT 57.022 33.333 39.01 39.01 36.38 0.86
4287 4429 9.807649 TTCATAGAGTGAGTATATACGCGTATA 57.192 33.333 33.99 33.99 38.29 1.47
4288 4430 8.602328 GTTCATAGAGTGAGTATATACGCGTAT 58.398 37.037 32.13 32.13 38.29 3.06
4289 4431 7.816513 AGTTCATAGAGTGAGTATATACGCGTA 59.183 37.037 22.94 22.94 38.29 4.42
4290 4432 6.649973 AGTTCATAGAGTGAGTATATACGCGT 59.350 38.462 19.17 19.17 38.29 6.01
4291 4433 7.062906 AGTTCATAGAGTGAGTATATACGCG 57.937 40.000 3.53 3.53 38.29 6.01
4297 4439 9.498176 TGCGTATAAGTTCATAGAGTGAGTATA 57.502 33.333 0.00 0.00 38.29 1.47
4298 4440 8.392372 TGCGTATAAGTTCATAGAGTGAGTAT 57.608 34.615 0.00 0.00 38.29 2.12
4299 4441 7.797038 TGCGTATAAGTTCATAGAGTGAGTA 57.203 36.000 0.00 0.00 38.29 2.59
4300 4442 6.694877 TGCGTATAAGTTCATAGAGTGAGT 57.305 37.500 0.00 0.00 38.29 3.41


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

AutoCloner maintained by Alex Coulton.