Multiple sequence alignment - TraesCS3A01G288900

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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 TraesCS3A01G288900 chr3A 100.000 5073 0 0 1 5073 517075377 517080449 0.000000e+00 9369.0
1 TraesCS3A01G288900 chr3A 96.296 108 4 0 3727 3834 368533783 368533890 1.450000e-40 178.0
2 TraesCS3A01G288900 chr3A 97.436 39 1 0 3968 4006 368533888 368533926 3.280000e-07 67.6
3 TraesCS3A01G288900 chr3D 91.197 3226 151 58 1 3127 397778362 397781553 0.000000e+00 4261.0
4 TraesCS3A01G288900 chr3D 90.448 1539 81 27 3136 4660 397781744 397783230 0.000000e+00 1967.0
5 TraesCS3A01G288900 chr3D 87.132 272 22 7 4811 5073 397783452 397783719 3.840000e-76 296.0
6 TraesCS3A01G288900 chr3B 88.773 2111 126 47 3 2023 523558955 523561044 0.000000e+00 2483.0
7 TraesCS3A01G288900 chr3B 91.694 1541 89 19 3200 4736 523562394 523563899 0.000000e+00 2100.0
8 TraesCS3A01G288900 chr3B 92.642 897 51 6 2066 2958 523561130 523562015 0.000000e+00 1277.0
9 TraesCS3A01G288900 chr3B 91.045 201 6 5 4812 5003 523568718 523568915 1.400000e-65 261.0
10 TraesCS3A01G288900 chr3B 81.609 87 13 2 2531 2614 124387297 124387211 9.110000e-08 69.4
11 TraesCS3A01G288900 chr7B 88.778 499 32 12 90 569 304271730 304272223 1.570000e-164 590.0
12 TraesCS3A01G288900 chr7B 100.000 32 0 0 2540 2571 704263023 704262992 5.490000e-05 60.2
13 TraesCS3A01G288900 chr6B 100.000 31 0 0 2541 2571 222858938 222858968 1.970000e-04 58.4


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 TraesCS3A01G288900 chr3A 517075377 517080449 5072 False 9369.000000 9369 100.000000 1 5073 1 chr3A.!!$F1 5072
1 TraesCS3A01G288900 chr3D 397778362 397783719 5357 False 2174.666667 4261 89.592333 1 5073 3 chr3D.!!$F1 5072
2 TraesCS3A01G288900 chr3B 523558955 523563899 4944 False 1953.333333 2483 91.036333 3 4736 3 chr3B.!!$F2 4733

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
809 837 0.107017 CCATCCCATCGCCTTCACTT 60.107 55.0 0.00 0.0 0.00 3.16 F
1257 1314 0.963225 TTGCTGCTCAACATGCACAT 59.037 45.0 0.00 0.0 36.37 3.21 F
2700 2868 0.318107 GCCATGCGTGTGGAATATGC 60.318 55.0 11.69 0.0 42.02 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2391 2.695359 GTGGAAGTTCATGTCGCCTAA 58.305 47.619 5.01 0.0 0.00 2.69 R
2857 3027 1.153647 CAGGAGCGACGCATTACCA 60.154 57.895 23.70 0.0 0.00 3.25 R
4213 4680 0.110486 AATGAAGGACAACCACGGCT 59.890 50.000 0.00 0.0 38.94 5.52 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
29 32 6.535963 TCGTAGATCCTATCATACGTCCTA 57.464 41.667 0.00 0.00 37.50 2.94
66 69 6.599244 TGAACTGGCAACTTATATCCTTCTTG 59.401 38.462 0.00 0.00 37.61 3.02
98 101 3.255642 GTGCTGTTCTGGCTAATCCAAAA 59.744 43.478 0.00 0.00 46.01 2.44
99 102 3.507233 TGCTGTTCTGGCTAATCCAAAAG 59.493 43.478 0.00 0.00 46.01 2.27
101 104 4.700213 GCTGTTCTGGCTAATCCAAAAGTA 59.300 41.667 0.00 0.00 46.01 2.24
103 106 5.007682 TGTTCTGGCTAATCCAAAAGTACC 58.992 41.667 0.00 0.00 46.01 3.34
104 107 4.919774 TCTGGCTAATCCAAAAGTACCA 57.080 40.909 0.00 0.00 46.01 3.25
105 108 5.450818 TCTGGCTAATCCAAAAGTACCAT 57.549 39.130 0.00 0.00 46.01 3.55
106 109 5.192927 TCTGGCTAATCCAAAAGTACCATG 58.807 41.667 0.00 0.00 46.01 3.66
116 119 0.328258 AAGTACCATGGACACTGGGC 59.672 55.000 21.47 0.00 38.14 5.36
213 233 4.932200 TGCTTTTGTTTTCGTTCACCAATT 59.068 33.333 0.00 0.00 0.00 2.32
217 237 7.958025 GCTTTTGTTTTCGTTCACCAATTAAAA 59.042 29.630 0.00 0.00 0.00 1.52
218 238 9.813080 CTTTTGTTTTCGTTCACCAATTAAAAA 57.187 25.926 0.00 0.00 0.00 1.94
275 298 5.048434 AGGGCTCATTCTCGAAAAGAAAAAG 60.048 40.000 0.00 0.00 46.85 2.27
292 315 6.406370 AGAAAAAGAAAAACAAGGTTGAGGG 58.594 36.000 0.00 0.00 0.00 4.30
305 328 3.519913 AGGTTGAGGGGAAACTATCACTC 59.480 47.826 0.00 0.00 35.38 3.51
308 331 5.179533 GTTGAGGGGAAACTATCACTCTTC 58.820 45.833 0.00 0.00 35.67 2.87
313 336 5.894964 AGGGGAAACTATCACTCTTCTAGAC 59.105 44.000 0.00 0.00 0.00 2.59
351 374 5.465056 GCATCCTAGTTAAAGAGAGCATGTC 59.535 44.000 0.00 0.00 0.00 3.06
353 376 5.023452 TCCTAGTTAAAGAGAGCATGTCCA 58.977 41.667 0.00 0.00 0.00 4.02
411 434 5.633182 CGTGCAGCATTGGTTACTAATTTTT 59.367 36.000 0.00 0.00 0.00 1.94
484 512 5.582269 TCAATGATGCTGCTTCACTAGTTAC 59.418 40.000 18.87 0.00 0.00 2.50
666 694 4.142556 TGTTTGGACAAGTTTCTTCCGTTC 60.143 41.667 0.00 0.00 31.49 3.95
723 751 6.947464 TCCTTGTAATCTGACTTCTTAAGGG 58.053 40.000 1.85 0.00 34.42 3.95
800 828 4.456911 CCTTATCATGAAACCATCCCATCG 59.543 45.833 0.00 0.00 0.00 3.84
809 837 0.107017 CCATCCCATCGCCTTCACTT 60.107 55.000 0.00 0.00 0.00 3.16
883 911 1.448922 GCCAGCACCACGGTAAAACA 61.449 55.000 0.00 0.00 0.00 2.83
985 1013 3.373439 CAGCTCACAATCCAGCTAGTTTC 59.627 47.826 0.00 0.00 44.47 2.78
1121 1178 3.325293 TTCCTCTGTGACTGCATTCTC 57.675 47.619 5.59 2.47 0.00 2.87
1173 1230 2.692557 ACTTGCAGGTATTTGTGTTGCA 59.307 40.909 0.00 0.00 42.44 4.08
1227 1284 2.983030 GACATGGGTGCCGTGCAA 60.983 61.111 0.00 0.00 43.81 4.08
1257 1314 0.963225 TTGCTGCTCAACATGCACAT 59.037 45.000 0.00 0.00 36.37 3.21
1403 1460 9.201989 GTATGGGTATGTCCTATTATCTCATGA 57.798 37.037 0.00 0.00 38.39 3.07
1407 1464 7.397476 GGGTATGTCCTATTATCTCATGAGTCA 59.603 40.741 21.92 8.60 36.25 3.41
1625 1699 5.823209 TGCATTCATATTCTCAGTGGTTG 57.177 39.130 0.00 0.00 0.00 3.77
1712 1786 7.970061 TGTTGTTTATGCTGCTATTTGAATCTC 59.030 33.333 0.00 0.00 0.00 2.75
1772 1848 6.371548 TGTGCTGATTCAAGGACACTATTAAC 59.628 38.462 6.43 0.00 42.74 2.01
1802 1886 5.977725 CGGTATGTTGGGAGCTATAATATCG 59.022 44.000 0.00 0.00 0.00 2.92
1914 2031 6.311200 GCATGTAAGGTTTTCCACAAATGATC 59.689 38.462 0.00 0.00 43.73 2.92
2023 2140 7.415592 TGGGAGCTGTAATATCATGAGATAG 57.584 40.000 2.67 0.00 39.94 2.08
2024 2141 7.184862 TGGGAGCTGTAATATCATGAGATAGA 58.815 38.462 2.67 0.00 39.94 1.98
2025 2142 7.675619 TGGGAGCTGTAATATCATGAGATAGAA 59.324 37.037 2.67 0.00 39.94 2.10
2029 2170 8.310382 AGCTGTAATATCATGAGATAGAACACC 58.690 37.037 2.67 1.41 39.94 4.16
2066 2207 6.790285 GAACCGTTGTTCTATTTCTTGGTA 57.210 37.500 0.00 0.00 46.03 3.25
2432 2600 7.986085 AGTCATTGCTTCATAAAAGTAGTGT 57.014 32.000 0.00 0.00 0.00 3.55
2441 2609 8.780249 GCTTCATAAAAGTAGTGTTTTCCTGTA 58.220 33.333 0.00 0.00 31.96 2.74
2454 2622 6.311935 GTGTTTTCCTGTATAGCGTCAATGTA 59.688 38.462 0.00 0.00 0.00 2.29
2459 2627 6.389906 TCCTGTATAGCGTCAATGTATCATG 58.610 40.000 0.00 0.00 0.00 3.07
2604 2772 3.835395 TCCAGTTTTGGGTGTTTTGTCTT 59.165 39.130 0.00 0.00 45.10 3.01
2700 2868 0.318107 GCCATGCGTGTGGAATATGC 60.318 55.000 11.69 0.00 42.02 3.14
2842 3012 2.095461 GGTGGCAGGGAGAATTTCTTC 58.905 52.381 0.00 0.00 0.00 2.87
2857 3027 5.796424 ATTTCTTCCACTGCTCAAAATGT 57.204 34.783 0.00 0.00 0.00 2.71
2870 3040 1.910819 CAAAATGTGGTAATGCGTCGC 59.089 47.619 11.10 11.10 0.00 5.19
2873 3043 0.810031 ATGTGGTAATGCGTCGCTCC 60.810 55.000 19.50 14.92 0.00 4.70
2889 3059 2.744202 CGCTCCTGTGTCTAAAATTGCT 59.256 45.455 0.00 0.00 0.00 3.91
2941 3111 0.107312 ATGTAGGAGGCTTGCTGCAG 60.107 55.000 13.70 10.11 40.37 4.41
2963 3133 5.360213 GCATGTTTGTGCACGTATATTTG 57.640 39.130 13.13 5.13 44.43 2.32
2975 3245 7.477422 GTGCACGTATATTTGTTTGTAGACTTG 59.523 37.037 0.00 0.00 0.00 3.16
3031 3303 7.060383 TGATTTGGCCAGAAAATAACAAGAA 57.940 32.000 5.11 0.00 0.00 2.52
3058 3330 9.630098 TTGTTCTCAGAGATATTTTCATTTTGC 57.370 29.630 0.00 0.00 0.00 3.68
3062 3337 8.456471 TCTCAGAGATATTTTCATTTTGCTGTG 58.544 33.333 0.00 0.00 0.00 3.66
3127 3402 4.568152 ACTTTCAACTCCAAAATCCACG 57.432 40.909 0.00 0.00 0.00 4.94
3129 3404 4.642885 ACTTTCAACTCCAAAATCCACGAA 59.357 37.500 0.00 0.00 0.00 3.85
3133 3408 6.885952 TCAACTCCAAAATCCACGAATTTA 57.114 33.333 0.00 0.00 0.00 1.40
3134 3409 7.461182 TCAACTCCAAAATCCACGAATTTAT 57.539 32.000 0.00 0.00 0.00 1.40
3162 3619 9.041354 AGTCTATTCCTCAAGTTCTTTAGTCAT 57.959 33.333 0.00 0.00 0.00 3.06
3230 3695 6.534079 AGAGTGTACATTTTATTCGTGCTACC 59.466 38.462 0.00 0.00 0.00 3.18
3611 4078 6.817641 TGGTCATACAATTCATGAAAAATGCC 59.182 34.615 13.09 16.11 34.32 4.40
3822 4289 3.310246 GACTCTGTCAAACTCCTTCGAC 58.690 50.000 0.00 0.00 32.09 4.20
3829 4296 4.921515 TGTCAAACTCCTTCGACGATAAAG 59.078 41.667 0.00 0.00 0.00 1.85
3861 4328 2.528125 TCGTTTCACGTCGTTTTCTCA 58.472 42.857 0.00 0.00 43.14 3.27
3899 4366 4.038042 TCGGCACATTGTTAACCAATTTCA 59.962 37.500 2.48 0.00 41.93 2.69
4128 4595 2.300152 CTGGAAGTTGGTGAGAGTGCTA 59.700 50.000 0.00 0.00 0.00 3.49
4133 4600 2.202623 GGTGAGAGTGCTACGGCG 60.203 66.667 4.80 4.80 42.25 6.46
4144 4611 1.813859 CTACGGCGGTGGAGATTCA 59.186 57.895 13.24 0.00 0.00 2.57
4148 4615 0.461870 CGGCGGTGGAGATTCATTCA 60.462 55.000 0.00 0.00 0.00 2.57
4182 4649 1.792301 CTGCGAAGGCACATCACTG 59.208 57.895 0.00 0.00 46.21 3.66
4221 4688 2.358737 GCAGTTAGCAGCCGTGGT 60.359 61.111 0.00 0.00 44.79 4.16
4222 4689 1.966451 GCAGTTAGCAGCCGTGGTT 60.966 57.895 0.00 0.00 44.79 3.67
4223 4690 1.868997 CAGTTAGCAGCCGTGGTTG 59.131 57.895 0.00 0.00 35.51 3.77
4224 4691 0.884704 CAGTTAGCAGCCGTGGTTGT 60.885 55.000 4.63 0.00 35.51 3.32
4225 4692 0.602905 AGTTAGCAGCCGTGGTTGTC 60.603 55.000 4.63 0.00 35.51 3.18
4226 4693 1.302192 TTAGCAGCCGTGGTTGTCC 60.302 57.895 4.63 0.00 35.51 4.02
4227 4694 1.764571 TTAGCAGCCGTGGTTGTCCT 61.765 55.000 4.63 0.00 35.51 3.85
4228 4695 1.764571 TAGCAGCCGTGGTTGTCCTT 61.765 55.000 4.63 0.00 35.51 3.36
4229 4696 2.617274 GCAGCCGTGGTTGTCCTTC 61.617 63.158 4.63 0.00 34.23 3.46
4230 4697 1.227823 CAGCCGTGGTTGTCCTTCA 60.228 57.895 0.00 0.00 34.23 3.02
4231 4698 0.606401 CAGCCGTGGTTGTCCTTCAT 60.606 55.000 0.00 0.00 34.23 2.57
4232 4699 0.110486 AGCCGTGGTTGTCCTTCATT 59.890 50.000 0.00 0.00 34.23 2.57
4233 4700 1.349688 AGCCGTGGTTGTCCTTCATTA 59.650 47.619 0.00 0.00 34.23 1.90
4234 4701 1.737793 GCCGTGGTTGTCCTTCATTAG 59.262 52.381 0.00 0.00 34.23 1.73
4235 4702 2.874457 GCCGTGGTTGTCCTTCATTAGT 60.874 50.000 0.00 0.00 34.23 2.24
4236 4703 3.408634 CCGTGGTTGTCCTTCATTAGTT 58.591 45.455 0.00 0.00 34.23 2.24
4237 4704 3.818773 CCGTGGTTGTCCTTCATTAGTTT 59.181 43.478 0.00 0.00 34.23 2.66
4240 4707 5.238650 CGTGGTTGTCCTTCATTAGTTTCTT 59.761 40.000 0.00 0.00 34.23 2.52
4283 4752 3.365976 TGTGTAACAGTTTCCGCGT 57.634 47.368 4.92 0.00 45.67 6.01
4284 4753 1.654317 TGTGTAACAGTTTCCGCGTT 58.346 45.000 4.92 0.00 45.67 4.84
4313 4782 2.449464 AGCCTTGCATATTTCAGCACA 58.551 42.857 0.00 0.00 41.05 4.57
4314 4783 2.827322 AGCCTTGCATATTTCAGCACAA 59.173 40.909 0.00 0.00 41.05 3.33
4315 4784 2.925563 GCCTTGCATATTTCAGCACAAC 59.074 45.455 0.00 0.00 41.05 3.32
4316 4785 3.173599 CCTTGCATATTTCAGCACAACG 58.826 45.455 0.00 0.00 41.05 4.10
4352 4821 2.010145 TTGTGCTCTACTCGATTGGC 57.990 50.000 0.00 0.00 0.00 4.52
4364 4833 2.212652 TCGATTGGCATCATTTCCTCG 58.787 47.619 0.00 0.00 0.00 4.63
4365 4834 1.265095 CGATTGGCATCATTTCCTCGG 59.735 52.381 0.00 0.00 0.00 4.63
4372 4841 2.026641 CATCATTTCCTCGGCATTGGT 58.973 47.619 0.00 0.00 0.00 3.67
4480 4950 7.494952 TGCAAAATGTCTTGATCAACAATTTCA 59.505 29.630 3.38 6.58 37.88 2.69
4508 4978 0.883833 GATCACCAAGTTGGGCTGTG 59.116 55.000 25.59 14.51 43.37 3.66
4518 4988 3.140814 GGGCTGTGATTTCCGGGC 61.141 66.667 0.00 0.00 0.00 6.13
4529 4999 2.296073 TTTCCGGGCCTACATTGTTT 57.704 45.000 0.84 0.00 0.00 2.83
4530 5000 1.540267 TTCCGGGCCTACATTGTTTG 58.460 50.000 0.84 0.00 0.00 2.93
4531 5001 0.963355 TCCGGGCCTACATTGTTTGC 60.963 55.000 0.84 0.00 0.00 3.68
4532 5002 1.247419 CCGGGCCTACATTGTTTGCA 61.247 55.000 0.84 0.00 0.00 4.08
4535 5005 0.890683 GGCCTACATTGTTTGCAGCT 59.109 50.000 0.00 0.00 0.00 4.24
4559 5029 6.724694 TTTTCATTCAGTTTATTGCATGCC 57.275 33.333 16.68 0.00 0.00 4.40
4561 5031 5.664294 TCATTCAGTTTATTGCATGCCTT 57.336 34.783 16.68 4.86 0.00 4.35
4614 5085 4.789807 AGGATTGTTATCTGAGCAATGCT 58.210 39.130 7.79 7.79 43.20 3.79
4685 5186 0.974010 TAGGTTCCTCGAATGGCGGT 60.974 55.000 0.00 0.00 41.33 5.68
4717 5219 2.881111 AGTTAGGGTTCTTGGGCTTC 57.119 50.000 0.00 0.00 0.00 3.86
4719 5221 2.649816 AGTTAGGGTTCTTGGGCTTCAT 59.350 45.455 0.00 0.00 0.00 2.57
4721 5223 4.080299 AGTTAGGGTTCTTGGGCTTCATAG 60.080 45.833 0.00 0.00 0.00 2.23
4728 5230 5.189180 GTTCTTGGGCTTCATAGAGATGTT 58.811 41.667 0.00 0.00 34.41 2.71
4730 5232 6.753913 TCTTGGGCTTCATAGAGATGTTAT 57.246 37.500 0.00 0.00 34.41 1.89
4737 5239 8.157476 GGGCTTCATAGAGATGTTATTTTAGGA 58.843 37.037 0.00 0.00 34.41 2.94
4739 5241 9.771534 GCTTCATAGAGATGTTATTTTAGGACT 57.228 33.333 0.00 0.00 34.41 3.85
4772 5282 9.691362 ATTTGTTTAATCGTATGCAACTCTTTT 57.309 25.926 0.00 0.00 0.00 2.27
4773 5283 8.722342 TTGTTTAATCGTATGCAACTCTTTTC 57.278 30.769 0.00 0.00 0.00 2.29
4775 5285 8.564574 TGTTTAATCGTATGCAACTCTTTTCTT 58.435 29.630 0.00 0.00 0.00 2.52
4778 5288 9.647797 TTAATCGTATGCAACTCTTTTCTTAGA 57.352 29.630 0.00 0.00 0.00 2.10
4814 5357 9.719355 TGTATAAGTATTTCAGCTCAGTTGAAA 57.281 29.630 17.88 17.88 44.17 2.69
4823 5366 8.571461 TTTCAGCTCAGTTGAAATTATGAGAT 57.429 30.769 12.32 0.00 41.35 2.75
4838 5381 2.123589 TGAGATAGATTTCCCCCGCAA 58.876 47.619 0.00 0.00 0.00 4.85
4842 5385 3.954258 AGATAGATTTCCCCCGCAAAAAG 59.046 43.478 0.00 0.00 0.00 2.27
4846 5389 2.900716 TTTCCCCCGCAAAAAGAAAG 57.099 45.000 0.00 0.00 0.00 2.62
4847 5390 2.074729 TTCCCCCGCAAAAAGAAAGA 57.925 45.000 0.00 0.00 0.00 2.52
4848 5391 2.074729 TCCCCCGCAAAAAGAAAGAA 57.925 45.000 0.00 0.00 0.00 2.52
4853 5396 4.021456 CCCCCGCAAAAAGAAAGAAGTTAT 60.021 41.667 0.00 0.00 0.00 1.89
4855 5398 5.278758 CCCCGCAAAAAGAAAGAAGTTATGA 60.279 40.000 0.00 0.00 0.00 2.15
4857 5400 6.293955 CCCGCAAAAAGAAAGAAGTTATGAGA 60.294 38.462 0.00 0.00 0.00 3.27
5003 5552 9.117145 CAACACACATGTTCATGTCTTTTATAC 57.883 33.333 14.43 0.00 46.46 1.47
5005 5554 7.172532 ACACACATGTTCATGTCTTTTATACGT 59.827 33.333 14.43 0.00 34.46 3.57
5006 5555 7.478355 CACACATGTTCATGTCTTTTATACGTG 59.522 37.037 14.43 12.07 35.58 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.839817 TTCAATCCAAAAATATAGGACGTATGA 57.160 29.630 0.00 0.00 33.57 2.15
29 32 7.008021 AGTTGCCAGTTCAATCCAAAAATAT 57.992 32.000 0.00 0.00 0.00 1.28
98 101 1.562672 GGCCCAGTGTCCATGGTACT 61.563 60.000 12.58 14.44 35.96 2.73
99 102 1.077716 GGCCCAGTGTCCATGGTAC 60.078 63.158 12.58 12.34 35.96 3.34
101 104 2.858476 TGGCCCAGTGTCCATGGT 60.858 61.111 12.58 0.00 35.96 3.55
103 106 1.676635 CAGTGGCCCAGTGTCCATG 60.677 63.158 10.59 0.00 34.47 3.66
104 107 2.759114 CAGTGGCCCAGTGTCCAT 59.241 61.111 10.59 0.00 34.47 3.41
105 108 4.269523 GCAGTGGCCCAGTGTCCA 62.270 66.667 19.51 0.00 37.16 4.02
106 109 3.574074 ATGCAGTGGCCCAGTGTCC 62.574 63.158 19.51 4.93 40.13 4.02
218 238 9.040939 GTTTTTACAAGCATATCCACTGTTTTT 57.959 29.630 0.00 0.00 0.00 1.94
241 261 1.880027 GAATGAGCCCTCAACACGTTT 59.120 47.619 1.62 0.00 43.58 3.60
271 291 4.780554 TCCCCTCAACCTTGTTTTTCTTTT 59.219 37.500 0.00 0.00 0.00 2.27
275 298 4.161565 AGTTTCCCCTCAACCTTGTTTTTC 59.838 41.667 0.00 0.00 0.00 2.29
292 315 7.832769 ACTTGTCTAGAAGAGTGATAGTTTCC 58.167 38.462 8.13 0.00 0.00 3.13
308 331 8.773619 TAGGATGCCTGAAGGTAACTTGTCTAG 61.774 44.444 0.00 0.00 46.54 2.43
313 336 4.080863 ACTAGGATGCCTGAAGGTAACTTG 60.081 45.833 0.00 1.30 46.54 3.16
351 374 1.288127 GCAAGTTGCTGCCTTCTGG 59.712 57.895 20.71 0.00 40.96 3.86
370 393 1.649171 CACGCAGCAAGTAAGTAGTCG 59.351 52.381 0.00 0.00 0.00 4.18
484 512 4.457603 CCTACTGAATAGGGATCGTCTCAG 59.542 50.000 7.14 7.14 46.32 3.35
666 694 3.190878 GCCACCGGCTTCATCTTG 58.809 61.111 0.00 0.00 46.69 3.02
723 751 8.073768 TGAATGTTTTTATCGAACAGAAAGGTC 58.926 33.333 0.00 0.00 40.04 3.85
883 911 2.504585 ACACAGTGATCCATCTGCATCT 59.495 45.455 7.81 0.00 35.37 2.90
985 1013 5.590530 AACCTCATAGTCACAGCTAGAAG 57.409 43.478 0.00 0.00 0.00 2.85
1023 1067 2.978010 CCAAAGCAACGCCGGACT 60.978 61.111 5.05 0.00 0.00 3.85
1121 1178 6.147492 GCATTTAGCAGGATGACTCTCAATAG 59.853 42.308 0.00 0.00 44.79 1.73
1173 1230 2.916716 CAAAAGCTATCGCGTTGCAAAT 59.083 40.909 18.66 0.00 42.32 2.32
1195 1252 0.036164 ATGTCGGCTGTTTGGTAGCA 59.964 50.000 0.00 0.00 42.88 3.49
1227 1284 0.038709 GAGCAGCAACAGACTCGAGT 60.039 55.000 20.18 20.18 0.00 4.18
1257 1314 5.500234 AGTGAATCCACATTTAGCTTAGCA 58.500 37.500 7.07 0.00 45.54 3.49
1403 1460 5.411831 TCATTACTGTGAGCAGATTGACT 57.588 39.130 1.30 0.00 45.28 3.41
1625 1699 4.510571 TCAATTCTAGTTTCCGGCCTTAC 58.489 43.478 0.00 0.00 0.00 2.34
1712 1786 8.458843 ACTAAATCAGATTATTTTTCCACCGTG 58.541 33.333 0.00 0.00 31.63 4.94
1741 1815 5.124457 GTGTCCTTGAATCAGCACATAACAT 59.876 40.000 0.00 0.00 0.00 2.71
1772 1848 3.541632 AGCTCCCAACATACCGTTAATG 58.458 45.455 0.00 0.00 35.52 1.90
1802 1886 8.387354 TGTTAATGATGTTTCGACATATCACAC 58.613 33.333 12.44 10.29 32.90 3.82
1881 1966 4.462483 GGAAAACCTTACATGCATCCAGAA 59.538 41.667 0.00 0.00 0.00 3.02
1883 1968 3.763360 TGGAAAACCTTACATGCATCCAG 59.237 43.478 0.00 0.00 32.29 3.86
1884 1969 3.509575 GTGGAAAACCTTACATGCATCCA 59.490 43.478 0.00 0.00 33.54 3.41
1885 1970 3.509575 TGTGGAAAACCTTACATGCATCC 59.490 43.478 0.00 0.00 0.00 3.51
1886 1971 4.782019 TGTGGAAAACCTTACATGCATC 57.218 40.909 0.00 0.00 0.00 3.91
1887 1972 5.543507 TTTGTGGAAAACCTTACATGCAT 57.456 34.783 0.00 0.00 0.00 3.96
1976 2093 6.765036 CCAACATGCTGTTAATATGACTCTCT 59.235 38.462 0.00 0.00 38.77 3.10
1977 2094 6.017605 CCCAACATGCTGTTAATATGACTCTC 60.018 42.308 0.00 0.00 38.77 3.20
1978 2095 5.824624 CCCAACATGCTGTTAATATGACTCT 59.175 40.000 0.00 0.00 38.77 3.24
1979 2096 5.822519 TCCCAACATGCTGTTAATATGACTC 59.177 40.000 0.00 0.00 38.77 3.36
2047 2188 7.545965 AGAGATGTACCAAGAAATAGAACAACG 59.454 37.037 0.00 0.00 0.00 4.10
2112 2272 4.119442 ACCGTAACAGAACGCATAATCT 57.881 40.909 0.00 0.00 41.51 2.40
2231 2391 2.695359 GTGGAAGTTCATGTCGCCTAA 58.305 47.619 5.01 0.00 0.00 2.69
2432 2600 7.269316 TGATACATTGACGCTATACAGGAAAA 58.731 34.615 0.00 0.00 0.00 2.29
2604 2772 3.554934 ACTGCCACAACTTGATCAAAGA 58.445 40.909 9.88 0.00 39.38 2.52
2734 2903 8.888419 AGAGAGATACATCCATACAATTCCAAT 58.112 33.333 0.00 0.00 0.00 3.16
2801 2971 5.796935 CACCAATTCTGCAAAGATAAGAACG 59.203 40.000 0.00 0.00 33.01 3.95
2857 3027 1.153647 CAGGAGCGACGCATTACCA 60.154 57.895 23.70 0.00 0.00 3.25
2870 3040 6.566197 AGAAAGCAATTTTAGACACAGGAG 57.434 37.500 0.00 0.00 0.00 3.69
2873 3043 8.633075 TTTCAAGAAAGCAATTTTAGACACAG 57.367 30.769 0.00 0.00 0.00 3.66
2924 3094 2.111582 GCTGCAGCAAGCCTCCTAC 61.112 63.158 33.36 0.00 44.83 3.18
2941 3111 4.856487 ACAAATATACGTGCACAAACATGC 59.144 37.500 18.64 0.00 46.32 4.06
2951 3121 7.477422 CACAAGTCTACAAACAAATATACGTGC 59.523 37.037 0.00 0.00 0.00 5.34
2956 3126 6.651643 ACCGCACAAGTCTACAAACAAATATA 59.348 34.615 0.00 0.00 0.00 0.86
2959 3129 3.630312 ACCGCACAAGTCTACAAACAAAT 59.370 39.130 0.00 0.00 0.00 2.32
2963 3133 3.556775 TGTAACCGCACAAGTCTACAAAC 59.443 43.478 0.00 0.00 0.00 2.93
2975 3245 2.286536 ACGAAACATTGTGTAACCGCAC 60.287 45.455 0.00 0.00 39.65 5.34
2993 3263 3.496884 GCCAAATCAACTACAAGTCACGA 59.503 43.478 0.00 0.00 0.00 4.35
3034 3306 9.286946 CAGCAAAATGAAAATATCTCTGAGAAC 57.713 33.333 12.00 0.88 0.00 3.01
3037 3309 7.220300 GCACAGCAAAATGAAAATATCTCTGAG 59.780 37.037 0.00 0.00 0.00 3.35
3050 3322 8.240682 AGTAATTTATAACGCACAGCAAAATGA 58.759 29.630 0.00 0.00 0.00 2.57
3055 3327 6.819649 ACCTAGTAATTTATAACGCACAGCAA 59.180 34.615 0.00 0.00 0.00 3.91
3058 3330 7.997107 TCACCTAGTAATTTATAACGCACAG 57.003 36.000 0.00 0.00 0.00 3.66
3100 3375 7.333174 GTGGATTTTGGAGTTGAAAGTTGAAAA 59.667 33.333 0.00 0.00 0.00 2.29
3189 3646 7.526608 TGTACACTCTTTCAAAAACAGAAGTG 58.473 34.615 0.00 0.00 0.00 3.16
3192 3649 9.921637 AAAATGTACACTCTTTCAAAAACAGAA 57.078 25.926 0.00 0.00 0.00 3.02
3201 3666 7.172532 AGCACGAATAAAATGTACACTCTTTCA 59.827 33.333 0.00 0.00 0.00 2.69
3202 3667 7.519002 AGCACGAATAAAATGTACACTCTTTC 58.481 34.615 0.00 0.00 0.00 2.62
3205 3670 6.534079 GGTAGCACGAATAAAATGTACACTCT 59.466 38.462 0.00 0.00 0.00 3.24
3519 3986 0.545171 ATCATGACAGGGTCAGCCAG 59.455 55.000 0.00 0.00 46.04 4.85
3611 4078 4.201930 GCAATGCTCCTTCATCTCTTTCAG 60.202 45.833 0.00 0.00 0.00 3.02
3822 4289 6.642683 AACGAGAACATTACCACTTTATCG 57.357 37.500 0.00 0.00 0.00 2.92
3925 4392 2.098934 CAGCAGCGGCCAACATATTTAA 59.901 45.455 4.82 0.00 42.56 1.52
4096 4563 4.455877 CACCAACTTCCAGGAAGAATGTAC 59.544 45.833 32.59 0.00 41.71 2.90
4128 4595 0.462047 GAATGAATCTCCACCGCCGT 60.462 55.000 0.00 0.00 0.00 5.68
4133 4600 4.747108 CACGTAGATGAATGAATCTCCACC 59.253 45.833 0.00 0.00 37.98 4.61
4148 4615 1.660607 CGCAGCAAACATCACGTAGAT 59.339 47.619 0.00 0.00 37.48 1.98
4165 4632 1.672030 CCAGTGATGTGCCTTCGCA 60.672 57.895 0.00 0.00 44.78 5.10
4213 4680 0.110486 AATGAAGGACAACCACGGCT 59.890 50.000 0.00 0.00 38.94 5.52
4217 4684 6.262273 TGAAGAAACTAATGAAGGACAACCAC 59.738 38.462 0.00 0.00 38.94 4.16
4218 4685 6.361433 TGAAGAAACTAATGAAGGACAACCA 58.639 36.000 0.00 0.00 38.94 3.67
4219 4686 6.877611 TGAAGAAACTAATGAAGGACAACC 57.122 37.500 0.00 0.00 0.00 3.77
4220 4687 7.095187 ACGATGAAGAAACTAATGAAGGACAAC 60.095 37.037 0.00 0.00 0.00 3.32
4221 4688 6.934645 ACGATGAAGAAACTAATGAAGGACAA 59.065 34.615 0.00 0.00 0.00 3.18
4222 4689 6.464222 ACGATGAAGAAACTAATGAAGGACA 58.536 36.000 0.00 0.00 0.00 4.02
4223 4690 6.969828 ACGATGAAGAAACTAATGAAGGAC 57.030 37.500 0.00 0.00 0.00 3.85
4224 4691 7.878127 AGAAACGATGAAGAAACTAATGAAGGA 59.122 33.333 0.00 0.00 0.00 3.36
4225 4692 7.959651 CAGAAACGATGAAGAAACTAATGAAGG 59.040 37.037 0.00 0.00 0.00 3.46
4226 4693 8.499162 ACAGAAACGATGAAGAAACTAATGAAG 58.501 33.333 0.00 0.00 0.00 3.02
4227 4694 8.378172 ACAGAAACGATGAAGAAACTAATGAA 57.622 30.769 0.00 0.00 0.00 2.57
4228 4695 7.962964 ACAGAAACGATGAAGAAACTAATGA 57.037 32.000 0.00 0.00 0.00 2.57
4229 4696 9.746711 CTAACAGAAACGATGAAGAAACTAATG 57.253 33.333 0.00 0.00 0.00 1.90
4230 4697 9.490379 ACTAACAGAAACGATGAAGAAACTAAT 57.510 29.630 0.00 0.00 0.00 1.73
4231 4698 8.882415 ACTAACAGAAACGATGAAGAAACTAA 57.118 30.769 0.00 0.00 0.00 2.24
4232 4699 8.882415 AACTAACAGAAACGATGAAGAAACTA 57.118 30.769 0.00 0.00 0.00 2.24
4233 4700 7.494625 TGAACTAACAGAAACGATGAAGAAACT 59.505 33.333 0.00 0.00 0.00 2.66
4234 4701 7.627340 TGAACTAACAGAAACGATGAAGAAAC 58.373 34.615 0.00 0.00 0.00 2.78
4235 4702 7.780008 TGAACTAACAGAAACGATGAAGAAA 57.220 32.000 0.00 0.00 0.00 2.52
4236 4703 7.780008 TTGAACTAACAGAAACGATGAAGAA 57.220 32.000 0.00 0.00 0.00 2.52
4237 4704 7.780008 TTTGAACTAACAGAAACGATGAAGA 57.220 32.000 0.00 0.00 0.00 2.87
4240 4707 7.908082 CACTTTTTGAACTAACAGAAACGATGA 59.092 33.333 0.00 0.00 0.00 2.92
4283 4752 1.327303 ATGCAAGGCTTGAACGGAAA 58.673 45.000 30.45 6.62 0.00 3.13
4284 4753 2.192664 TATGCAAGGCTTGAACGGAA 57.807 45.000 30.45 8.31 0.00 4.30
4313 4782 1.045407 TTCTACCAGTCTGCCACGTT 58.955 50.000 0.00 0.00 0.00 3.99
4314 4783 1.267121 ATTCTACCAGTCTGCCACGT 58.733 50.000 0.00 0.00 0.00 4.49
4315 4784 2.002586 CAATTCTACCAGTCTGCCACG 58.997 52.381 0.00 0.00 0.00 4.94
4316 4785 2.744202 CACAATTCTACCAGTCTGCCAC 59.256 50.000 0.00 0.00 0.00 5.01
4352 4821 2.026641 ACCAATGCCGAGGAAATGATG 58.973 47.619 0.00 0.00 0.00 3.07
4364 4833 3.455469 GCAGGCCTGACCAATGCC 61.455 66.667 37.21 12.12 45.70 4.40
4365 4834 2.277591 TTGCAGGCCTGACCAATGC 61.278 57.895 37.21 20.27 43.14 3.56
4372 4841 1.522092 CTATCCGTTGCAGGCCTGA 59.478 57.895 37.21 18.42 0.00 3.86
4440 4909 5.789521 ACATTTTGCAACCATAAACCCTAC 58.210 37.500 0.00 0.00 0.00 3.18
4480 4950 4.281688 CCCAACTTGGTGATCACTGAAATT 59.718 41.667 24.50 11.49 35.17 1.82
4508 4978 2.052782 ACAATGTAGGCCCGGAAATC 57.947 50.000 0.73 0.00 0.00 2.17
4518 4988 5.049167 TGAAAAAGCTGCAAACAATGTAGG 58.951 37.500 1.02 0.00 41.60 3.18
4529 4999 6.073657 GCAATAAACTGAATGAAAAAGCTGCA 60.074 34.615 1.02 0.00 0.00 4.41
4530 5000 6.073657 TGCAATAAACTGAATGAAAAAGCTGC 60.074 34.615 0.00 0.00 0.00 5.25
4531 5001 7.410800 TGCAATAAACTGAATGAAAAAGCTG 57.589 32.000 0.00 0.00 0.00 4.24
4532 5002 7.360607 GCATGCAATAAACTGAATGAAAAAGCT 60.361 33.333 14.21 0.00 34.63 3.74
4535 5005 6.935771 AGGCATGCAATAAACTGAATGAAAAA 59.064 30.769 21.36 0.00 34.63 1.94
4559 5029 1.472480 CCAGGAACATTAACCGGCAAG 59.528 52.381 0.00 0.00 0.00 4.01
4561 5031 0.963355 GCCAGGAACATTAACCGGCA 60.963 55.000 0.00 0.00 41.59 5.69
4663 5164 1.653151 GCCATTCGAGGAACCTACAC 58.347 55.000 0.00 0.00 0.00 2.90
4685 5186 3.112263 ACCCTAACTAGCATTGGCAGTA 58.888 45.455 0.00 0.00 44.61 2.74
4749 5251 8.094798 AGAAAAGAGTTGCATACGATTAAACA 57.905 30.769 0.00 0.00 0.00 2.83
4750 5252 8.950403 AAGAAAAGAGTTGCATACGATTAAAC 57.050 30.769 0.00 0.00 0.00 2.01
4752 5254 9.647797 TCTAAGAAAAGAGTTGCATACGATTAA 57.352 29.630 0.00 0.00 0.00 1.40
4753 5255 9.302345 CTCTAAGAAAAGAGTTGCATACGATTA 57.698 33.333 0.00 0.00 38.57 1.75
4754 5256 8.035394 TCTCTAAGAAAAGAGTTGCATACGATT 58.965 33.333 0.00 0.00 43.02 3.34
4755 5257 7.548097 TCTCTAAGAAAAGAGTTGCATACGAT 58.452 34.615 0.00 0.00 43.02 3.73
4814 5357 4.536090 TGCGGGGGAAATCTATCTCATAAT 59.464 41.667 0.00 0.00 0.00 1.28
4823 5366 3.443145 TCTTTTTGCGGGGGAAATCTA 57.557 42.857 0.00 0.00 0.00 1.98
4828 5371 2.074729 TCTTTCTTTTTGCGGGGGAA 57.925 45.000 0.00 0.00 0.00 3.97
4897 5440 8.906867 CCCTCTTGTGTACAATATGATTGAAAT 58.093 33.333 0.00 0.00 35.02 2.17
4909 5452 4.157656 GCATAATTGCCCTCTTGTGTACAA 59.842 41.667 0.00 0.00 43.38 2.41
5003 5552 5.494618 TCTTCACGAAATTTTGTGTACACG 58.505 37.500 29.34 17.59 42.08 4.49
5005 5554 7.306213 TGTTTCTTCACGAAATTTTGTGTACA 58.694 30.769 29.34 22.85 43.08 2.90
5006 5555 7.728580 TGTTTCTTCACGAAATTTTGTGTAC 57.271 32.000 29.34 21.29 43.08 2.90


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

AutoCloner maintained by Alex Coulton.