Multiple sequence alignment - TraesCS1D01G199200

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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 TraesCS1D01G199200 chr1D 100.000 4748 0 0 1 4748 281406486 281401739 0.000000e+00 8769.0
1 TraesCS1D01G199200 chr1B 95.434 4052 137 24 4 4035 382214605 382218628 0.000000e+00 6414.0
2 TraesCS1D01G199200 chr1B 91.873 283 11 2 4464 4746 382219094 382219364 7.450000e-103 385.0
3 TraesCS1D01G199200 chr1B 84.926 272 13 12 4108 4361 382218647 382218908 2.840000e-62 250.0
4 TraesCS1D01G199200 chr1A 96.339 3906 97 23 161 4047 353252793 353256671 0.000000e+00 6379.0
5 TraesCS1D01G199200 chr1A 95.324 278 10 1 4474 4748 353257255 353257532 5.640000e-119 438.0
6 TraesCS1D01G199200 chr1A 96.914 162 5 0 1 162 353252564 353252725 6.050000e-69 272.0
7 TraesCS1D01G199200 chr1A 90.355 197 7 5 4166 4361 353256872 353257057 1.020000e-61 248.0
8 TraesCS1D01G199200 chr5A 95.238 42 1 1 2799 2840 646897103 646897143 1.100000e-06 65.8


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 TraesCS1D01G199200 chr1D 281401739 281406486 4747 True 8769.000000 8769 100.000000 1 4748 1 chr1D.!!$R1 4747
1 TraesCS1D01G199200 chr1B 382214605 382219364 4759 False 2349.666667 6414 90.744333 4 4746 3 chr1B.!!$F1 4742
2 TraesCS1D01G199200 chr1A 353252564 353257532 4968 False 1834.250000 6379 94.733000 1 4748 4 chr1A.!!$F1 4747

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
557 640 1.079888 CCCTTCAACAAATGGCGGC 60.080 57.895 0.00 0.0 0.0 6.53 F
659 742 1.735571 AGTTCGTTGTTTGTCGTGCTT 59.264 42.857 0.00 0.0 0.0 3.91 F
1113 1198 2.046507 GCCTGCCACACCTCTCAG 60.047 66.667 0.00 0.0 0.0 3.35 F
2855 2941 1.594293 AAGTTCGGCCGACAGTGTG 60.594 57.895 31.19 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 2540 1.285641 CAACCCGGCACAACATCAC 59.714 57.895 0.00 0.00 0.00 3.06 R
2804 2890 4.196971 CCAGTGAAGCATCAGATGAATCA 58.803 43.478 15.12 13.43 35.88 2.57 R
3143 3229 3.885297 CCTGTTTCCACACAGAAGAACAT 59.115 43.478 2.32 0.00 46.29 2.71 R
4160 4343 0.035056 AGGATGTACACAAGCCTGCC 60.035 55.000 0.00 0.00 34.68 4.85 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
178 248 4.976116 TGAATACATGATAGTTCTGCGTCG 59.024 41.667 0.00 0.00 0.00 5.12
189 259 5.160699 AGTTCTGCGTCGTAATCGTAATA 57.839 39.130 0.00 0.00 38.33 0.98
199 269 4.157289 TCGTAATCGTAATATCTGAGCCCC 59.843 45.833 0.00 0.00 38.33 5.80
309 381 5.334395 CGTTTTTCGCGCTTAGATGAATATG 59.666 40.000 5.56 0.00 0.00 1.78
557 640 1.079888 CCCTTCAACAAATGGCGGC 60.080 57.895 0.00 0.00 0.00 6.53
659 742 1.735571 AGTTCGTTGTTTGTCGTGCTT 59.264 42.857 0.00 0.00 0.00 3.91
805 890 2.419673 TGTTCGTCGCTTATAAGACCGA 59.580 45.455 16.85 15.09 34.10 4.69
1113 1198 2.046507 GCCTGCCACACCTCTCAG 60.047 66.667 0.00 0.00 0.00 3.35
1551 1636 5.067936 TGTCTATGTTAGAGCTGAGCCTAAC 59.932 44.000 25.54 25.54 39.90 2.34
1574 1659 2.477189 GGGCACGTGAAATAAATGACCG 60.477 50.000 22.23 0.00 0.00 4.79
1730 1815 4.137543 GGAGAGAATGAACCACACACTTT 58.862 43.478 0.00 0.00 0.00 2.66
2195 2281 4.132122 ACTCCCCTCCATCATTTTTGTT 57.868 40.909 0.00 0.00 0.00 2.83
2196 2282 4.492646 ACTCCCCTCCATCATTTTTGTTT 58.507 39.130 0.00 0.00 0.00 2.83
2855 2941 1.594293 AAGTTCGGCCGACAGTGTG 60.594 57.895 31.19 0.00 0.00 3.82
3056 3142 7.275779 TCGAGCTGATTGTAGTCTTAATGTTTC 59.724 37.037 0.00 0.00 0.00 2.78
3141 3227 4.096382 GTGAGTCACAAAACACCAGTTGAT 59.904 41.667 18.54 0.00 34.57 2.57
3143 3229 5.883115 TGAGTCACAAAACACCAGTTGATAA 59.117 36.000 0.00 0.00 38.17 1.75
3281 3367 5.226194 TGCCTTTTTCCATGTTATTTGCT 57.774 34.783 0.00 0.00 0.00 3.91
3293 3379 6.020440 CCATGTTATTTGCTGCTATTTCAACG 60.020 38.462 0.00 0.00 0.00 4.10
3376 3462 6.939730 TGCTATTCATCAGTTCTTGGTTGTTA 59.060 34.615 0.00 0.00 0.00 2.41
3378 3464 9.109393 GCTATTCATCAGTTCTTGGTTGTTATA 57.891 33.333 0.00 0.00 0.00 0.98
3419 3505 1.304464 CCCCTTCTTGTTGGAGCCC 60.304 63.158 0.00 0.00 0.00 5.19
3441 3527 4.472286 CGAGTTGACTTGTGTTTGTGTTT 58.528 39.130 0.00 0.00 0.00 2.83
3445 3531 7.906010 CGAGTTGACTTGTGTTTGTGTTTATAA 59.094 33.333 0.00 0.00 0.00 0.98
3591 3677 4.371786 CGCTGTTAGCTCCTGATTCATTA 58.628 43.478 0.00 0.00 39.60 1.90
3923 4014 3.739401 ACCTAAGATGGTTTCAAGGGG 57.261 47.619 0.00 0.00 36.89 4.79
3953 4044 4.661709 TCCTTGTTTACCCTCCTAGTTTGT 59.338 41.667 0.00 0.00 0.00 2.83
4016 4111 9.815936 GCCATTTTCTGTTAATTTTCTTGATTG 57.184 29.630 0.00 0.00 0.00 2.67
4042 4137 2.425578 TATTCTTGCGTGTGTGTCGA 57.574 45.000 0.00 0.00 0.00 4.20
4047 4142 0.179121 TTGCGTGTGTGTCGACTTCT 60.179 50.000 17.92 0.00 0.00 2.85
4048 4143 0.869880 TGCGTGTGTGTCGACTTCTG 60.870 55.000 17.92 3.11 0.00 3.02
4066 4229 2.483441 GCTCAGTGGTAGAGAGCGA 58.517 57.895 0.00 0.00 44.37 4.93
4067 4230 0.099791 GCTCAGTGGTAGAGAGCGAC 59.900 60.000 0.00 0.00 44.37 5.19
4069 4232 0.680280 TCAGTGGTAGAGAGCGACCC 60.680 60.000 0.00 0.00 38.86 4.46
4070 4233 0.681564 CAGTGGTAGAGAGCGACCCT 60.682 60.000 0.00 0.00 38.86 4.34
4071 4234 0.681564 AGTGGTAGAGAGCGACCCTG 60.682 60.000 0.00 0.00 38.86 4.45
4072 4235 0.680280 GTGGTAGAGAGCGACCCTGA 60.680 60.000 0.00 0.00 38.86 3.86
4073 4236 0.259065 TGGTAGAGAGCGACCCTGAT 59.741 55.000 0.00 0.00 38.86 2.90
4075 4238 2.092049 TGGTAGAGAGCGACCCTGATAA 60.092 50.000 0.00 0.00 38.86 1.75
4077 4240 3.574826 GGTAGAGAGCGACCCTGATAATT 59.425 47.826 0.00 0.00 34.09 1.40
4078 4241 3.742433 AGAGAGCGACCCTGATAATTG 57.258 47.619 0.00 0.00 0.00 2.32
4079 4242 2.139118 GAGAGCGACCCTGATAATTGC 58.861 52.381 0.00 0.00 0.00 3.56
4080 4243 1.486310 AGAGCGACCCTGATAATTGCA 59.514 47.619 0.00 0.00 0.00 4.08
4081 4244 2.105477 AGAGCGACCCTGATAATTGCAT 59.895 45.455 0.00 0.00 0.00 3.96
4082 4245 2.481952 GAGCGACCCTGATAATTGCATC 59.518 50.000 0.00 0.00 0.00 3.91
4083 4246 1.195448 GCGACCCTGATAATTGCATCG 59.805 52.381 0.00 0.00 0.00 3.84
4084 4247 2.483876 CGACCCTGATAATTGCATCGT 58.516 47.619 0.00 0.00 0.00 3.73
4087 4250 2.951642 ACCCTGATAATTGCATCGTTGG 59.048 45.455 0.00 0.00 0.00 3.77
4088 4251 3.213506 CCCTGATAATTGCATCGTTGGA 58.786 45.455 0.00 0.00 0.00 3.53
4089 4252 3.822735 CCCTGATAATTGCATCGTTGGAT 59.177 43.478 0.00 0.00 0.00 3.41
4090 4253 4.083110 CCCTGATAATTGCATCGTTGGATC 60.083 45.833 0.00 0.00 0.00 3.36
4091 4254 4.377738 CCTGATAATTGCATCGTTGGATCG 60.378 45.833 0.00 0.00 0.00 3.69
4098 4262 1.006832 CATCGTTGGATCGGGTGAAC 58.993 55.000 0.00 0.00 0.00 3.18
4105 4269 2.656002 TGGATCGGGTGAACTAGAGAG 58.344 52.381 0.00 0.00 0.00 3.20
4147 4330 9.449719 TCTTGGTCCTGAATAAGAGTATTTTTC 57.550 33.333 0.00 0.00 29.69 2.29
4148 4331 8.575649 TTGGTCCTGAATAAGAGTATTTTTCC 57.424 34.615 0.00 0.00 29.69 3.13
4150 4333 6.260271 GGTCCTGAATAAGAGTATTTTTCCCG 59.740 42.308 0.00 0.00 29.69 5.14
4151 4334 5.820947 TCCTGAATAAGAGTATTTTTCCCGC 59.179 40.000 0.00 0.00 29.69 6.13
4152 4335 5.823045 CCTGAATAAGAGTATTTTTCCCGCT 59.177 40.000 0.00 0.00 29.69 5.52
4153 4336 6.318900 CCTGAATAAGAGTATTTTTCCCGCTT 59.681 38.462 0.00 0.00 29.69 4.68
4154 4337 7.148069 CCTGAATAAGAGTATTTTTCCCGCTTT 60.148 37.037 0.00 0.00 29.69 3.51
4155 4338 7.535139 TGAATAAGAGTATTTTTCCCGCTTTG 58.465 34.615 0.00 0.00 29.69 2.77
4156 4339 3.850122 AGAGTATTTTTCCCGCTTTGC 57.150 42.857 0.00 0.00 0.00 3.68
4158 4341 3.057526 AGAGTATTTTTCCCGCTTTGCAC 60.058 43.478 0.00 0.00 0.00 4.57
4179 4370 0.035056 GGCAGGCTTGTGTACATCCT 60.035 55.000 0.00 0.92 31.97 3.24
4189 4380 3.331150 TGTGTACATCCTTAAGCAACGG 58.669 45.455 0.00 0.00 0.00 4.44
4361 4561 0.541764 TTCCCTGCCATTCCAACACC 60.542 55.000 0.00 0.00 0.00 4.16
4362 4562 1.228831 CCCTGCCATTCCAACACCA 60.229 57.895 0.00 0.00 0.00 4.17
4363 4563 0.831288 CCCTGCCATTCCAACACCAA 60.831 55.000 0.00 0.00 0.00 3.67
4364 4564 1.047002 CCTGCCATTCCAACACCAAA 58.953 50.000 0.00 0.00 0.00 3.28
4365 4565 1.624813 CCTGCCATTCCAACACCAAAT 59.375 47.619 0.00 0.00 0.00 2.32
4366 4566 2.354003 CCTGCCATTCCAACACCAAATC 60.354 50.000 0.00 0.00 0.00 2.17
4367 4567 2.299582 CTGCCATTCCAACACCAAATCA 59.700 45.455 0.00 0.00 0.00 2.57
4368 4568 2.299582 TGCCATTCCAACACCAAATCAG 59.700 45.455 0.00 0.00 0.00 2.90
4369 4569 2.299867 GCCATTCCAACACCAAATCAGT 59.700 45.455 0.00 0.00 0.00 3.41
4370 4570 3.861886 GCCATTCCAACACCAAATCAGTG 60.862 47.826 0.00 0.00 41.15 3.66
4371 4571 3.306225 CCATTCCAACACCAAATCAGTGG 60.306 47.826 0.00 0.00 44.92 4.00
4372 4572 1.327303 TCCAACACCAAATCAGTGGC 58.673 50.000 0.00 0.00 43.00 5.01
4373 4573 1.039068 CCAACACCAAATCAGTGGCA 58.961 50.000 0.00 0.00 43.00 4.92
4374 4574 1.411977 CCAACACCAAATCAGTGGCAA 59.588 47.619 0.00 0.00 43.00 4.52
4375 4575 2.158986 CCAACACCAAATCAGTGGCAAA 60.159 45.455 0.00 0.00 43.00 3.68
4376 4576 3.494749 CCAACACCAAATCAGTGGCAAAT 60.495 43.478 0.00 0.00 43.00 2.32
4377 4577 4.128643 CAACACCAAATCAGTGGCAAATT 58.871 39.130 0.00 0.00 43.00 1.82
4378 4578 4.420522 ACACCAAATCAGTGGCAAATTT 57.579 36.364 0.00 0.00 43.00 1.82
4379 4579 4.779696 ACACCAAATCAGTGGCAAATTTT 58.220 34.783 0.00 0.00 43.00 1.82
4380 4580 4.575645 ACACCAAATCAGTGGCAAATTTTG 59.424 37.500 4.72 4.72 43.00 2.44
4381 4581 4.575645 CACCAAATCAGTGGCAAATTTTGT 59.424 37.500 10.65 0.00 43.00 2.83
4382 4582 4.815846 ACCAAATCAGTGGCAAATTTTGTC 59.184 37.500 6.79 6.79 43.00 3.18
4383 4583 5.058490 CCAAATCAGTGGCAAATTTTGTCT 58.942 37.500 14.34 6.56 35.94 3.41
4384 4584 5.049954 CCAAATCAGTGGCAAATTTTGTCTG 60.050 40.000 14.34 15.90 35.94 3.51
4385 4585 3.096489 TCAGTGGCAAATTTTGTCTGC 57.904 42.857 14.34 7.76 35.94 4.26
4386 4586 2.694628 TCAGTGGCAAATTTTGTCTGCT 59.305 40.909 14.34 9.66 35.94 4.24
4387 4587 3.888323 TCAGTGGCAAATTTTGTCTGCTA 59.112 39.130 14.34 0.00 35.94 3.49
4388 4588 4.022935 TCAGTGGCAAATTTTGTCTGCTAG 60.023 41.667 14.34 7.98 35.94 3.42
4389 4589 3.256631 AGTGGCAAATTTTGTCTGCTAGG 59.743 43.478 14.34 0.00 35.94 3.02
4390 4590 3.005791 GTGGCAAATTTTGTCTGCTAGGT 59.994 43.478 14.34 0.00 35.94 3.08
4391 4591 3.640967 TGGCAAATTTTGTCTGCTAGGTT 59.359 39.130 14.34 0.00 35.94 3.50
4392 4592 4.100808 TGGCAAATTTTGTCTGCTAGGTTT 59.899 37.500 14.34 0.00 35.94 3.27
4393 4593 4.686091 GGCAAATTTTGTCTGCTAGGTTTC 59.314 41.667 10.65 0.00 36.32 2.78
4394 4594 5.509670 GGCAAATTTTGTCTGCTAGGTTTCT 60.510 40.000 10.65 0.00 36.32 2.52
4395 4595 5.985530 GCAAATTTTGTCTGCTAGGTTTCTT 59.014 36.000 10.65 0.00 33.20 2.52
4396 4596 7.145323 GCAAATTTTGTCTGCTAGGTTTCTTA 58.855 34.615 10.65 0.00 33.20 2.10
4397 4597 7.114953 GCAAATTTTGTCTGCTAGGTTTCTTAC 59.885 37.037 10.65 0.00 33.20 2.34
4409 4609 4.727235 GGTTTCTTACCAAACACTCGAG 57.273 45.455 11.84 11.84 46.92 4.04
4441 4641 6.441093 TTTTTCTTGCAGATATGCACCTAG 57.559 37.500 15.91 10.35 45.32 3.02
4457 4657 5.013704 TGCACCTAGTGAAAGGGAATCTAAA 59.986 40.000 0.00 0.00 41.32 1.85
4458 4658 6.122964 GCACCTAGTGAAAGGGAATCTAAAT 58.877 40.000 0.00 0.00 41.32 1.40
4459 4659 6.038714 GCACCTAGTGAAAGGGAATCTAAATG 59.961 42.308 0.00 0.00 41.32 2.32
4460 4660 7.112779 CACCTAGTGAAAGGGAATCTAAATGT 58.887 38.462 0.00 0.00 41.32 2.71
4461 4661 8.265055 CACCTAGTGAAAGGGAATCTAAATGTA 58.735 37.037 0.00 0.00 41.32 2.29
4462 4662 8.487028 ACCTAGTGAAAGGGAATCTAAATGTAG 58.513 37.037 0.00 0.00 41.32 2.74
4463 4663 8.487028 CCTAGTGAAAGGGAATCTAAATGTAGT 58.513 37.037 0.00 0.00 32.55 2.73
4464 4664 9.319143 CTAGTGAAAGGGAATCTAAATGTAGTG 57.681 37.037 0.00 0.00 0.00 2.74
4465 4665 7.112779 AGTGAAAGGGAATCTAAATGTAGTGG 58.887 38.462 0.00 0.00 0.00 4.00
4466 4666 6.884836 GTGAAAGGGAATCTAAATGTAGTGGT 59.115 38.462 0.00 0.00 0.00 4.16
4467 4667 6.884295 TGAAAGGGAATCTAAATGTAGTGGTG 59.116 38.462 0.00 0.00 0.00 4.17
4468 4668 6.388619 AAGGGAATCTAAATGTAGTGGTGT 57.611 37.500 0.00 0.00 0.00 4.16
4470 4670 6.180472 AGGGAATCTAAATGTAGTGGTGTTG 58.820 40.000 0.00 0.00 0.00 3.33
4471 4671 5.163652 GGGAATCTAAATGTAGTGGTGTTGC 60.164 44.000 0.00 0.00 0.00 4.17
4585 4931 0.250858 CCAGCTTCACCACCACATCA 60.251 55.000 0.00 0.00 0.00 3.07
4685 5034 0.325933 ACAGCATAGCAGCAGGTCAA 59.674 50.000 0.00 0.00 36.85 3.18
4689 5038 1.541147 GCATAGCAGCAGGTCAACAAA 59.459 47.619 0.00 0.00 0.00 2.83
4699 5048 3.243201 GCAGGTCAACAAAGAAGAACCAG 60.243 47.826 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 2.330440 ATCATGTATTCACCTGCGCA 57.670 45.000 10.98 10.98 0.00 6.09
178 248 4.082354 ACGGGGCTCAGATATTACGATTAC 60.082 45.833 0.00 0.00 0.00 1.89
297 369 7.453126 ACCCCAAACAAACACATATTCATCTAA 59.547 33.333 0.00 0.00 0.00 2.10
298 370 6.951198 ACCCCAAACAAACACATATTCATCTA 59.049 34.615 0.00 0.00 0.00 1.98
309 381 9.930693 TTTATAATTATCACCCCAAACAAACAC 57.069 29.630 0.00 0.00 0.00 3.32
557 640 5.704515 CCCATAAAGTCCTCATATGCAGAAG 59.295 44.000 0.00 0.00 0.00 2.85
646 729 5.467063 TCATGTTACATAAGCACGACAAACA 59.533 36.000 0.00 0.00 0.00 2.83
650 733 6.569780 ACTATCATGTTACATAAGCACGACA 58.430 36.000 0.00 0.00 0.00 4.35
659 742 9.707957 AATTCCCCAAAACTATCATGTTACATA 57.292 29.630 0.00 0.00 0.00 2.29
805 890 5.313506 AGGAAACCTGAAAAGGGAAGATAGT 59.686 40.000 0.00 0.00 29.57 2.12
1113 1198 3.976339 AGTAGGATGCTGATGCGAC 57.024 52.632 0.00 0.00 43.34 5.19
1185 1270 5.473066 AAATCTGCTTGTTAAAGTGGCAT 57.527 34.783 0.00 0.00 35.69 4.40
1551 1636 1.740585 TCATTTATTTCACGTGCCCCG 59.259 47.619 11.67 0.00 44.03 5.73
1574 1659 3.244044 GGAACTCTCTGATGCTCCATACC 60.244 52.174 0.00 0.00 0.00 2.73
2365 2451 4.599047 TTTTTGCAATGGTTAGGGACAG 57.401 40.909 0.00 0.00 0.00 3.51
2454 2540 1.285641 CAACCCGGCACAACATCAC 59.714 57.895 0.00 0.00 0.00 3.06
2804 2890 4.196971 CCAGTGAAGCATCAGATGAATCA 58.803 43.478 15.12 13.43 35.88 2.57
2855 2941 4.067972 TGTAAAGAACCTCACCTGTGAC 57.932 45.455 0.00 0.00 35.46 3.67
3141 3227 5.530915 CCTGTTTCCACACAGAAGAACATTA 59.469 40.000 2.32 0.00 46.29 1.90
3143 3229 3.885297 CCTGTTTCCACACAGAAGAACAT 59.115 43.478 2.32 0.00 46.29 2.71
3281 3367 4.151689 CGAGGAAGTTTCGTTGAAATAGCA 59.848 41.667 0.00 0.00 33.97 3.49
3293 3379 4.755123 TCCATTTTCTCACGAGGAAGTTTC 59.245 41.667 0.00 0.00 0.00 2.78
3305 3391 8.680001 CAGTTATTGATCATGTCCATTTTCTCA 58.320 33.333 0.00 0.00 0.00 3.27
3376 3462 5.440610 AGGCCAGTTTTCAATCGAGAATAT 58.559 37.500 5.01 0.00 0.00 1.28
3378 3464 3.690460 AGGCCAGTTTTCAATCGAGAAT 58.310 40.909 5.01 0.00 0.00 2.40
3419 3505 3.740044 ACACAAACACAAGTCAACTCG 57.260 42.857 0.00 0.00 0.00 4.18
3441 3527 7.116075 TCTGCTTATTTTCTTGGCCTGTTATA 58.884 34.615 3.32 0.00 0.00 0.98
3445 3531 3.766545 TCTGCTTATTTTCTTGGCCTGT 58.233 40.909 3.32 0.00 0.00 4.00
3591 3677 2.264005 TGTGTGTTAAACGGGCAGAT 57.736 45.000 0.00 0.00 0.00 2.90
3701 3788 1.926511 ATTTGCTGCTTCCCGCTTCG 61.927 55.000 0.00 0.00 40.11 3.79
3889 3980 8.147244 ACCATCTTAGGTTCACAAGTATACTT 57.853 34.615 12.50 12.50 39.34 2.24
3923 4014 4.018324 AGGAGGGTAAACAAGGATTCTTCC 60.018 45.833 0.00 0.00 42.96 3.46
3988 4082 8.954950 TCAAGAAAATTAACAGAAAATGGCAA 57.045 26.923 0.00 0.00 0.00 4.52
3990 4084 9.815936 CAATCAAGAAAATTAACAGAAAATGGC 57.184 29.630 0.00 0.00 0.00 4.40
4012 4107 5.115472 CACACGCAAGAATAAACACACAATC 59.885 40.000 0.00 0.00 43.62 2.67
4016 4111 3.723764 CACACACGCAAGAATAAACACAC 59.276 43.478 0.00 0.00 43.62 3.82
4029 4124 0.869880 CAGAAGTCGACACACACGCA 60.870 55.000 19.50 0.00 0.00 5.24
4042 4137 3.088532 CTCTCTACCACTGAGCAGAAGT 58.911 50.000 4.21 3.79 0.00 3.01
4048 4143 0.099791 GTCGCTCTCTACCACTGAGC 59.900 60.000 0.00 0.00 46.73 4.26
4064 4227 2.483876 ACGATGCAATTATCAGGGTCG 58.516 47.619 0.00 0.00 0.00 4.79
4066 4229 2.951642 CCAACGATGCAATTATCAGGGT 59.048 45.455 0.00 0.00 0.00 4.34
4067 4230 3.213506 TCCAACGATGCAATTATCAGGG 58.786 45.455 0.00 0.00 0.00 4.45
4069 4232 4.377738 CCGATCCAACGATGCAATTATCAG 60.378 45.833 0.00 0.00 35.09 2.90
4070 4233 3.498018 CCGATCCAACGATGCAATTATCA 59.502 43.478 0.00 0.00 35.09 2.15
4071 4234 3.120199 CCCGATCCAACGATGCAATTATC 60.120 47.826 0.00 0.00 35.09 1.75
4072 4235 2.813754 CCCGATCCAACGATGCAATTAT 59.186 45.455 0.00 0.00 35.09 1.28
4073 4236 2.217750 CCCGATCCAACGATGCAATTA 58.782 47.619 0.00 0.00 35.09 1.40
4075 4238 0.107214 ACCCGATCCAACGATGCAAT 60.107 50.000 0.00 0.00 35.09 3.56
4077 4240 1.449423 CACCCGATCCAACGATGCA 60.449 57.895 0.00 0.00 35.09 3.96
4078 4241 0.742990 TTCACCCGATCCAACGATGC 60.743 55.000 0.00 0.00 35.09 3.91
4079 4242 1.006832 GTTCACCCGATCCAACGATG 58.993 55.000 0.00 0.00 35.09 3.84
4080 4243 0.902531 AGTTCACCCGATCCAACGAT 59.097 50.000 0.00 0.00 35.09 3.73
4081 4244 1.475280 CTAGTTCACCCGATCCAACGA 59.525 52.381 0.00 0.00 35.09 3.85
4082 4245 1.475280 TCTAGTTCACCCGATCCAACG 59.525 52.381 0.00 0.00 0.00 4.10
4083 4246 2.758979 TCTCTAGTTCACCCGATCCAAC 59.241 50.000 0.00 0.00 0.00 3.77
4084 4247 3.024547 CTCTCTAGTTCACCCGATCCAA 58.975 50.000 0.00 0.00 0.00 3.53
4087 4250 4.425520 CAAACTCTCTAGTTCACCCGATC 58.574 47.826 0.00 0.00 45.37 3.69
4088 4251 3.195825 CCAAACTCTCTAGTTCACCCGAT 59.804 47.826 0.00 0.00 45.37 4.18
4089 4252 2.561419 CCAAACTCTCTAGTTCACCCGA 59.439 50.000 0.00 0.00 45.37 5.14
4090 4253 2.931320 GCCAAACTCTCTAGTTCACCCG 60.931 54.545 0.00 0.00 45.37 5.28
4091 4254 2.038557 TGCCAAACTCTCTAGTTCACCC 59.961 50.000 0.00 0.00 45.37 4.61
4098 4262 7.271511 AGAGTATGAAATGCCAAACTCTCTAG 58.728 38.462 0.00 0.00 39.48 2.43
4105 4269 5.391312 ACCAAGAGTATGAAATGCCAAAC 57.609 39.130 0.00 0.00 0.00 2.93
4143 4326 2.725008 CCGTGCAAAGCGGGAAAA 59.275 55.556 6.35 0.00 44.98 2.29
4156 4339 2.031919 TACACAAGCCTGCCCGTG 59.968 61.111 6.91 6.91 35.48 4.94
4158 4341 1.369091 GATGTACACAAGCCTGCCCG 61.369 60.000 0.00 0.00 0.00 6.13
4160 4343 0.035056 AGGATGTACACAAGCCTGCC 60.035 55.000 0.00 0.00 34.68 4.85
4161 4344 1.826385 AAGGATGTACACAAGCCTGC 58.174 50.000 0.00 0.00 35.68 4.85
4163 4346 3.009033 TGCTTAAGGATGTACACAAGCCT 59.991 43.478 17.91 11.74 38.04 4.58
4167 4358 3.749088 CCGTTGCTTAAGGATGTACACAA 59.251 43.478 4.29 0.00 0.00 3.33
4179 4370 7.499321 TTCAAGACTTTATTCCGTTGCTTAA 57.501 32.000 0.00 0.00 0.00 1.85
4361 4561 5.559417 GCAGACAAAATTTGCCACTGATTTG 60.559 40.000 22.15 5.02 34.19 2.32
4362 4562 4.512571 GCAGACAAAATTTGCCACTGATTT 59.487 37.500 22.15 0.00 34.19 2.17
4363 4563 4.060205 GCAGACAAAATTTGCCACTGATT 58.940 39.130 22.15 0.00 34.19 2.57
4364 4564 3.322828 AGCAGACAAAATTTGCCACTGAT 59.677 39.130 22.15 16.89 38.58 2.90
4365 4565 2.694628 AGCAGACAAAATTTGCCACTGA 59.305 40.909 22.15 0.00 38.58 3.41
4366 4566 3.102052 AGCAGACAAAATTTGCCACTG 57.898 42.857 17.20 17.20 38.58 3.66
4367 4567 3.256631 CCTAGCAGACAAAATTTGCCACT 59.743 43.478 5.52 0.00 38.58 4.00
4368 4568 3.005791 ACCTAGCAGACAAAATTTGCCAC 59.994 43.478 5.52 0.00 38.58 5.01
4369 4569 3.230134 ACCTAGCAGACAAAATTTGCCA 58.770 40.909 5.52 0.00 38.58 4.92
4370 4570 3.942130 ACCTAGCAGACAAAATTTGCC 57.058 42.857 5.52 0.00 38.58 4.52
4371 4571 5.532557 AGAAACCTAGCAGACAAAATTTGC 58.467 37.500 5.52 0.00 38.09 3.68
4372 4572 7.595130 GGTAAGAAACCTAGCAGACAAAATTTG 59.405 37.037 3.89 3.89 45.75 2.32
4373 4573 7.658261 GGTAAGAAACCTAGCAGACAAAATTT 58.342 34.615 0.00 0.00 45.75 1.82
4374 4574 7.215719 GGTAAGAAACCTAGCAGACAAAATT 57.784 36.000 0.00 0.00 45.75 1.82
4375 4575 6.819397 GGTAAGAAACCTAGCAGACAAAAT 57.181 37.500 0.00 0.00 45.75 1.82
4385 4585 8.679767 CACTCGAGTGTTTGGTAAGAAACCTAG 61.680 44.444 32.77 4.71 43.73 3.02
4386 4586 6.957525 CACTCGAGTGTTTGGTAAGAAACCTA 60.958 42.308 32.77 0.00 43.73 3.08
4387 4587 6.196649 CACTCGAGTGTTTGGTAAGAAACCT 61.197 44.000 32.77 0.00 43.73 3.50
4388 4588 4.025145 CACTCGAGTGTTTGGTAAGAAACC 60.025 45.833 32.77 0.00 43.69 3.27
4389 4589 4.807304 TCACTCGAGTGTTTGGTAAGAAAC 59.193 41.667 37.21 0.00 45.76 2.78
4390 4590 5.013568 TCACTCGAGTGTTTGGTAAGAAA 57.986 39.130 37.21 16.55 45.76 2.52
4391 4591 4.659111 TCACTCGAGTGTTTGGTAAGAA 57.341 40.909 37.21 17.03 45.76 2.52
4392 4592 4.556233 CATCACTCGAGTGTTTGGTAAGA 58.444 43.478 37.21 20.15 45.76 2.10
4393 4593 3.123621 GCATCACTCGAGTGTTTGGTAAG 59.876 47.826 37.21 20.59 45.76 2.34
4394 4594 3.064207 GCATCACTCGAGTGTTTGGTAA 58.936 45.455 37.21 21.49 45.76 2.85
4395 4595 2.611971 GGCATCACTCGAGTGTTTGGTA 60.612 50.000 37.21 22.16 45.76 3.25
4396 4596 1.512926 GCATCACTCGAGTGTTTGGT 58.487 50.000 37.21 20.18 45.76 3.67
4397 4597 0.798776 GGCATCACTCGAGTGTTTGG 59.201 55.000 37.21 26.35 45.76 3.28
4398 4598 1.511850 TGGCATCACTCGAGTGTTTG 58.488 50.000 37.21 33.09 45.76 2.93
4399 4599 2.479566 ATGGCATCACTCGAGTGTTT 57.520 45.000 37.21 25.82 45.76 2.83
4400 4600 2.479566 AATGGCATCACTCGAGTGTT 57.520 45.000 37.21 29.33 45.76 3.32
4401 4601 2.479566 AAATGGCATCACTCGAGTGT 57.520 45.000 37.21 24.84 45.76 3.55
4402 4602 3.438087 AGAAAAATGGCATCACTCGAGTG 59.562 43.478 34.76 34.76 46.91 3.51
4403 4603 3.679389 AGAAAAATGGCATCACTCGAGT 58.321 40.909 13.58 13.58 0.00 4.18
4404 4604 4.409570 CAAGAAAAATGGCATCACTCGAG 58.590 43.478 11.84 11.84 0.00 4.04
4405 4605 3.366273 GCAAGAAAAATGGCATCACTCGA 60.366 43.478 0.00 0.00 0.00 4.04
4406 4606 2.919229 GCAAGAAAAATGGCATCACTCG 59.081 45.455 0.00 0.00 0.00 4.18
4407 4607 3.916761 TGCAAGAAAAATGGCATCACTC 58.083 40.909 0.00 0.00 0.00 3.51
4408 4608 3.575256 TCTGCAAGAAAAATGGCATCACT 59.425 39.130 0.00 0.00 42.31 3.41
4409 4609 3.916761 TCTGCAAGAAAAATGGCATCAC 58.083 40.909 0.00 0.00 42.31 3.06
4441 4641 6.884836 ACCACTACATTTAGATTCCCTTTCAC 59.115 38.462 0.00 0.00 0.00 3.18
4457 4657 1.621814 AGGTACGCAACACCACTACAT 59.378 47.619 1.64 0.00 38.62 2.29
4458 4658 1.042229 AGGTACGCAACACCACTACA 58.958 50.000 1.64 0.00 38.62 2.74
4459 4659 1.425412 CAGGTACGCAACACCACTAC 58.575 55.000 1.64 0.00 38.62 2.73
4460 4660 0.320073 GCAGGTACGCAACACCACTA 60.320 55.000 1.64 0.00 38.62 2.74
4461 4661 1.597027 GCAGGTACGCAACACCACT 60.597 57.895 1.64 0.00 38.62 4.00
4462 4662 0.320073 TAGCAGGTACGCAACACCAC 60.320 55.000 1.64 0.00 38.62 4.16
4463 4663 0.037697 CTAGCAGGTACGCAACACCA 60.038 55.000 1.64 0.00 38.62 4.17
4464 4664 1.359459 GCTAGCAGGTACGCAACACC 61.359 60.000 10.63 0.00 36.22 4.16
4465 4665 0.389948 AGCTAGCAGGTACGCAACAC 60.390 55.000 18.83 0.00 0.00 3.32
4466 4666 0.320374 AAGCTAGCAGGTACGCAACA 59.680 50.000 18.83 0.00 0.00 3.33
4467 4667 1.000145 GAAGCTAGCAGGTACGCAAC 59.000 55.000 18.83 0.00 0.00 4.17
4468 4668 0.895530 AGAAGCTAGCAGGTACGCAA 59.104 50.000 18.83 0.00 0.00 4.85
4470 4670 1.281899 CAAGAAGCTAGCAGGTACGC 58.718 55.000 18.83 0.00 0.00 4.42
4471 4671 2.164624 AGACAAGAAGCTAGCAGGTACG 59.835 50.000 18.83 3.00 0.00 3.67
4648 4994 2.124403 GCTGGGGGTGCAGATGAG 60.124 66.667 0.00 0.00 0.00 2.90
4685 5034 6.064060 TGATGATTGTCTGGTTCTTCTTTGT 58.936 36.000 0.00 0.00 0.00 2.83
4689 5038 5.006386 GGTTGATGATTGTCTGGTTCTTCT 58.994 41.667 0.00 0.00 0.00 2.85
4699 5048 3.829886 TTCGCTTGGTTGATGATTGTC 57.170 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.