Multiple sequence alignment - TraesCS1A01G268700

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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 TraesCS1A01G268700 chr1A 100.000 3425 0 0 1000 4424 463403089 463399665 0.000000e+00 6325
1 TraesCS1A01G268700 chr1A 100.000 672 0 0 1 672 463404088 463403417 0.000000e+00 1242
2 TraesCS1A01G268700 chr1D 94.580 3450 122 28 1000 4424 364387138 364383729 0.000000e+00 5275
3 TraesCS1A01G268700 chr1D 86.561 692 48 26 1 672 364387896 364387230 0.000000e+00 721
4 TraesCS1A01G268700 chr1D 90.123 81 8 0 4141 4221 364384070 364383990 6.050000e-19 106
5 TraesCS1A01G268700 chr1B 95.971 2780 83 13 1083 3842 487682191 487679421 0.000000e+00 4486
6 TraesCS1A01G268700 chr1B 88.323 471 42 9 3961 4424 487679067 487678603 1.800000e-153 553
7 TraesCS1A01G268700 chr1B 85.060 502 48 17 172 672 487682989 487682514 1.850000e-133 486
8 TraesCS1A01G268700 chr1B 89.041 146 8 1 1 146 487683124 487682987 1.640000e-39 174
9 TraesCS1A01G268700 chr1B 87.611 113 11 1 3849 3958 487679358 487679246 1.290000e-25 128
10 TraesCS1A01G268700 chr6B 94.872 1950 97 2 1101 3048 500525863 500523915 0.000000e+00 3044
11 TraesCS1A01G268700 chr5A 93.846 1950 96 3 1101 3048 396680471 396682398 0.000000e+00 2915
12 TraesCS1A01G268700 chr3B 90.909 99 9 0 1696 1794 627615397 627615299 2.780000e-27 134


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 TraesCS1A01G268700 chr1A 463399665 463404088 4423 True 3783.5 6325 100.000000 1 4424 2 chr1A.!!$R1 4423
1 TraesCS1A01G268700 chr1D 364383729 364387896 4167 True 2034.0 5275 90.421333 1 4424 3 chr1D.!!$R1 4423
2 TraesCS1A01G268700 chr1B 487678603 487683124 4521 True 1165.4 4486 89.201200 1 4424 5 chr1B.!!$R1 4423
3 TraesCS1A01G268700 chr6B 500523915 500525863 1948 True 3044.0 3044 94.872000 1101 3048 1 chr6B.!!$R1 1947
4 TraesCS1A01G268700 chr5A 396680471 396682398 1927 False 2915.0 2915 93.846000 1101 3048 1 chr5A.!!$F1 1947

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
481 519 0.043310 CGTAGCGCCTTTTATCGTGC 60.043 55.0 2.29 0.0 35.72 5.34 F
605 643 0.189822 AGATCCCTCTCTACCCTGCC 59.810 60.0 0.00 0.0 0.00 4.85 F
2211 2255 0.477597 TTGGGATCCTTGAGGTGGGT 60.478 55.0 12.58 0.0 36.34 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2261 0.871722 GTATCAAGTTGCGTGCACCA 59.128 50.000 12.15 7.62 0.00 4.17 R
2235 2279 1.620524 CCATCCTTGGCCTTCATTGGT 60.621 52.381 3.32 0.00 35.85 3.67 R
4073 4375 0.036952 AGCGCACATTCAGTAGCTGT 60.037 50.000 11.47 0.00 40.43 4.40 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
36 37 0.179092 CCGTCCTTGGGGTTCGTATC 60.179 60.000 0.00 0.00 32.78 2.24
49 50 4.271687 GGTTCGTATCAAACATGATTCGC 58.728 43.478 0.00 1.68 38.42 4.70
55 56 0.798009 CAAACATGATTCGCGGCACC 60.798 55.000 6.13 0.00 0.00 5.01
146 178 2.030946 GCACGTAAATGGCTAGCAAGAG 59.969 50.000 18.24 3.28 0.00 2.85
147 179 2.030946 CACGTAAATGGCTAGCAAGAGC 59.969 50.000 18.24 0.00 42.05 4.09
157 189 2.203126 GCAAGAGCTCCGATGGGG 60.203 66.667 10.93 0.00 37.91 4.96
158 190 3.036429 GCAAGAGCTCCGATGGGGT 62.036 63.158 10.93 0.00 37.91 4.95
159 191 1.686325 GCAAGAGCTCCGATGGGGTA 61.686 60.000 10.93 0.00 37.91 3.69
160 192 0.390860 CAAGAGCTCCGATGGGGTAG 59.609 60.000 10.93 0.00 37.00 3.18
161 193 0.760945 AAGAGCTCCGATGGGGTAGG 60.761 60.000 10.93 0.00 37.00 3.18
162 194 2.122813 AGCTCCGATGGGGTAGGG 60.123 66.667 0.00 0.00 37.00 3.53
163 195 3.942439 GCTCCGATGGGGTAGGGC 61.942 72.222 0.00 0.00 37.00 5.19
164 196 3.616721 CTCCGATGGGGTAGGGCG 61.617 72.222 0.00 0.00 37.00 6.13
165 197 4.468769 TCCGATGGGGTAGGGCGT 62.469 66.667 0.00 0.00 37.00 5.68
166 198 2.522436 CCGATGGGGTAGGGCGTA 60.522 66.667 0.00 0.00 0.00 4.42
167 199 2.571216 CCGATGGGGTAGGGCGTAG 61.571 68.421 0.00 0.00 0.00 3.51
168 200 2.571216 CGATGGGGTAGGGCGTAGG 61.571 68.421 0.00 0.00 0.00 3.18
200 232 2.260434 GAACAGCACGCTCGGGTA 59.740 61.111 0.00 0.00 0.00 3.69
224 261 4.767255 CCACAGCGGAGACCCAGC 62.767 72.222 0.00 0.00 36.56 4.85
263 300 2.847441 CATGGGTGATGGATCTCACAG 58.153 52.381 14.90 1.37 45.95 3.66
264 301 2.252535 TGGGTGATGGATCTCACAGA 57.747 50.000 14.90 0.84 45.95 3.41
265 302 1.833630 TGGGTGATGGATCTCACAGAC 59.166 52.381 14.90 6.95 45.95 3.51
266 303 1.833630 GGGTGATGGATCTCACAGACA 59.166 52.381 14.90 0.00 45.95 3.41
310 347 0.900182 TCGAGCTGTCCACCACATCT 60.900 55.000 0.00 0.00 33.98 2.90
313 350 2.544694 CGAGCTGTCCACCACATCTATC 60.545 54.545 0.00 0.00 31.30 2.08
317 354 0.765510 GTCCACCACATCTATCCCCC 59.234 60.000 0.00 0.00 0.00 5.40
481 519 0.043310 CGTAGCGCCTTTTATCGTGC 60.043 55.000 2.29 0.00 35.72 5.34
505 543 3.484547 CGGGCCGTCACGCTTTAC 61.485 66.667 19.97 0.00 0.00 2.01
537 575 7.148689 CCTTTTTGTTAGATACGGATATACGCC 60.149 40.741 7.41 0.00 37.37 5.68
574 612 2.889018 GACGGCCGGGATTCGTTC 60.889 66.667 31.76 11.54 37.25 3.95
596 634 0.825840 AGGCGCTACAGATCCCTCTC 60.826 60.000 7.64 0.00 0.00 3.20
597 635 0.825840 GGCGCTACAGATCCCTCTCT 60.826 60.000 7.64 0.00 0.00 3.10
598 636 1.545875 GGCGCTACAGATCCCTCTCTA 60.546 57.143 7.64 0.00 0.00 2.43
599 637 1.538075 GCGCTACAGATCCCTCTCTAC 59.462 57.143 0.00 0.00 0.00 2.59
600 638 2.156098 CGCTACAGATCCCTCTCTACC 58.844 57.143 0.00 0.00 0.00 3.18
601 639 2.521126 GCTACAGATCCCTCTCTACCC 58.479 57.143 0.00 0.00 0.00 3.69
602 640 2.109304 GCTACAGATCCCTCTCTACCCT 59.891 54.545 0.00 0.00 0.00 4.34
603 641 2.765689 ACAGATCCCTCTCTACCCTG 57.234 55.000 0.00 0.00 0.00 4.45
604 642 1.337118 CAGATCCCTCTCTACCCTGC 58.663 60.000 0.00 0.00 0.00 4.85
605 643 0.189822 AGATCCCTCTCTACCCTGCC 59.810 60.000 0.00 0.00 0.00 4.85
606 644 0.834261 GATCCCTCTCTACCCTGCCC 60.834 65.000 0.00 0.00 0.00 5.36
607 645 1.307976 ATCCCTCTCTACCCTGCCCT 61.308 60.000 0.00 0.00 0.00 5.19
608 646 1.764054 CCCTCTCTACCCTGCCCTG 60.764 68.421 0.00 0.00 0.00 4.45
609 647 1.764054 CCTCTCTACCCTGCCCTGG 60.764 68.421 0.00 0.00 0.00 4.45
633 675 4.742201 CACACACGCTCCCCTCCG 62.742 72.222 0.00 0.00 0.00 4.63
1581 1623 1.953138 CGGCGAGATCATGCTGTCC 60.953 63.158 0.00 0.00 32.78 4.02
1635 1677 2.514824 GAGGCCTGGCATTCCGAC 60.515 66.667 22.05 0.33 34.14 4.79
2139 2183 1.986378 CATGTTCTTGACGAGTCGACC 59.014 52.381 21.50 10.96 0.00 4.79
2211 2255 0.477597 TTGGGATCCTTGAGGTGGGT 60.478 55.000 12.58 0.00 36.34 4.51
2217 2261 1.518367 TCCTTGAGGTGGGTGTTCTT 58.482 50.000 0.00 0.00 36.34 2.52
2235 2279 1.535028 CTTGGTGCACGCAACTTGATA 59.465 47.619 11.45 0.00 34.17 2.15
2238 2282 0.871722 GTGCACGCAACTTGATACCA 59.128 50.000 0.00 0.00 0.00 3.25
2429 2473 0.255318 AGCCAGATTGGGAGCAAGAG 59.745 55.000 0.00 0.00 38.19 2.85
2571 2615 2.575461 GGTGAGCTGCATTTGGCC 59.425 61.111 1.02 0.00 43.89 5.36
2670 2714 5.008980 TCACAACCAATATCAGTGATGCAA 58.991 37.500 16.15 0.00 34.59 4.08
2733 2777 2.265739 CTTAGCCGTGCTGAGCCA 59.734 61.111 0.23 0.00 40.10 4.75
2787 2831 0.895100 ATGTGGGCTCGCACATGTTT 60.895 50.000 25.18 8.07 40.16 2.83
2790 2834 1.305219 TGGGCTCGCACATGTTTAGC 61.305 55.000 13.11 13.11 0.00 3.09
3214 3258 2.581354 GTGAGAGAGCCCATGCGT 59.419 61.111 0.00 0.00 44.33 5.24
3321 3365 1.270550 CAGGTTTTGCTGGTCATCACC 59.729 52.381 0.00 0.00 44.10 4.02
3434 3498 9.650371 CGATTCGCTTATTTGAAGATAAAATGA 57.350 29.630 0.00 0.00 0.00 2.57
3500 3564 4.953667 TGGTTAGCATCAGATCAGATGTC 58.046 43.478 24.08 17.54 45.58 3.06
3535 3599 7.814264 ATGAGTTGATTAATTTAGAGCCAGG 57.186 36.000 0.00 0.00 0.00 4.45
3536 3600 5.590259 TGAGTTGATTAATTTAGAGCCAGGC 59.410 40.000 1.84 1.84 0.00 4.85
3537 3601 5.509498 AGTTGATTAATTTAGAGCCAGGCA 58.491 37.500 15.80 0.00 0.00 4.75
3538 3602 5.591877 AGTTGATTAATTTAGAGCCAGGCAG 59.408 40.000 15.80 0.00 0.00 4.85
3608 3673 2.162681 AGGCAGAAAACGAAGGAATGG 58.837 47.619 0.00 0.00 0.00 3.16
3637 3702 3.343941 TCCCTTCGTAGTTTTGGATGG 57.656 47.619 0.00 0.00 0.00 3.51
3779 3844 4.202631 TGTTACCTGCCCCTAATCTTGTTT 60.203 41.667 0.00 0.00 0.00 2.83
3837 3902 9.717942 CCCTTTTCTCCAGAAATATATCTACTG 57.282 37.037 2.59 0.00 42.83 2.74
3842 3907 7.474445 TCTCCAGAAATATATCTACTGCTCCT 58.526 38.462 0.00 0.00 0.00 3.69
3843 3908 8.615705 TCTCCAGAAATATATCTACTGCTCCTA 58.384 37.037 0.00 0.00 0.00 2.94
3844 3909 9.420118 CTCCAGAAATATATCTACTGCTCCTAT 57.580 37.037 0.00 0.00 0.00 2.57
3845 3910 9.775539 TCCAGAAATATATCTACTGCTCCTATT 57.224 33.333 0.00 0.00 0.00 1.73
3958 4082 4.039973 TGGGTATATCGGTGAAGTTCATCC 59.960 45.833 9.18 10.99 0.00 3.51
3959 4083 4.235360 GGTATATCGGTGAAGTTCATCCG 58.765 47.826 27.14 27.14 40.14 4.18
4032 4332 2.033299 CGTGGTTCAGTGCAGAATTGTT 59.967 45.455 0.00 0.00 0.00 2.83
4039 4339 2.095059 CAGTGCAGAATTGTTGTAGCCC 60.095 50.000 0.00 0.00 0.00 5.19
4046 4346 3.332485 AGAATTGTTGTAGCCCTTACCCA 59.668 43.478 0.00 0.00 0.00 4.51
4055 4355 3.156288 AGCCCTTACCCAACTTTTCTC 57.844 47.619 0.00 0.00 0.00 2.87
4056 4356 2.716969 AGCCCTTACCCAACTTTTCTCT 59.283 45.455 0.00 0.00 0.00 3.10
4073 4375 2.034939 TCTCTTTGTCGTAGCGGTTGAA 59.965 45.455 0.00 0.00 0.00 2.69
4090 4392 2.068519 TGAACAGCTACTGAATGTGCG 58.931 47.619 0.78 0.00 35.18 5.34
4111 4413 2.031069 GCTAATCCAGCGTGATCTCGTA 60.031 50.000 17.55 1.70 41.37 3.43
4113 4415 4.142665 GCTAATCCAGCGTGATCTCGTATA 60.143 45.833 17.55 3.22 41.37 1.47
4135 4437 1.045407 TTACTCCGTGGTTCAGTGCT 58.955 50.000 0.00 0.00 0.00 4.40
4148 4450 2.959516 TCAGTGCTGAATTGTCGTAGG 58.040 47.619 0.00 0.00 36.53 3.18
4149 4451 2.002586 CAGTGCTGAATTGTCGTAGGG 58.997 52.381 0.00 0.00 0.00 3.53
4150 4452 1.066143 AGTGCTGAATTGTCGTAGGGG 60.066 52.381 0.00 0.00 0.00 4.79
4151 4453 0.981183 TGCTGAATTGTCGTAGGGGT 59.019 50.000 0.00 0.00 0.00 4.95
4152 4454 1.349688 TGCTGAATTGTCGTAGGGGTT 59.650 47.619 0.00 0.00 0.00 4.11
4153 4455 2.224670 TGCTGAATTGTCGTAGGGGTTT 60.225 45.455 0.00 0.00 0.00 3.27
4154 4456 3.008157 TGCTGAATTGTCGTAGGGGTTTA 59.992 43.478 0.00 0.00 0.00 2.01
4155 4457 4.196971 GCTGAATTGTCGTAGGGGTTTAT 58.803 43.478 0.00 0.00 0.00 1.40
4156 4458 4.272748 GCTGAATTGTCGTAGGGGTTTATC 59.727 45.833 0.00 0.00 0.00 1.75
4157 4459 5.423704 TGAATTGTCGTAGGGGTTTATCA 57.576 39.130 0.00 0.00 0.00 2.15
4158 4460 5.424757 TGAATTGTCGTAGGGGTTTATCAG 58.575 41.667 0.00 0.00 0.00 2.90
4159 4461 2.973694 TGTCGTAGGGGTTTATCAGC 57.026 50.000 0.00 0.00 0.00 4.26
4160 4462 2.463752 TGTCGTAGGGGTTTATCAGCT 58.536 47.619 0.00 0.00 0.00 4.24
4161 4463 3.634504 TGTCGTAGGGGTTTATCAGCTA 58.365 45.455 0.00 0.00 0.00 3.32
4162 4464 3.382546 TGTCGTAGGGGTTTATCAGCTAC 59.617 47.826 0.00 0.00 0.00 3.58
4163 4465 3.635836 GTCGTAGGGGTTTATCAGCTACT 59.364 47.826 0.00 0.00 0.00 2.57
4164 4466 3.635373 TCGTAGGGGTTTATCAGCTACTG 59.365 47.826 0.00 0.00 0.00 2.74
4211 4536 0.250124 TGCCAGTTACTCCGTGGTTG 60.250 55.000 0.00 0.00 33.51 3.77
4231 4556 0.386478 GGTGCAGAAAAGAAGCAGCG 60.386 55.000 0.00 0.00 45.13 5.18
4285 4610 1.203287 CTGATCCGCACTGAGAGAACA 59.797 52.381 0.00 0.00 0.00 3.18
4286 4611 1.203287 TGATCCGCACTGAGAGAACAG 59.797 52.381 0.00 0.00 42.78 3.16
4298 4623 6.777526 CTGAGAGAACAGTTAGAAAGGTTG 57.222 41.667 0.00 0.00 33.73 3.77
4299 4624 6.235231 TGAGAGAACAGTTAGAAAGGTTGT 57.765 37.500 0.00 0.00 0.00 3.32
4303 4628 5.506708 AGAACAGTTAGAAAGGTTGTGGTT 58.493 37.500 0.00 0.00 0.00 3.67
4320 4645 1.002142 GGTTGTACCCACGCTTTTGAC 60.002 52.381 0.00 0.00 30.04 3.18
4398 4723 5.067936 TCCTTGTCGGCAACAAAAAGATAAA 59.932 36.000 0.00 0.00 46.95 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.798009 GGTGCCGCGAATCATGTTTG 60.798 55.000 8.23 0.00 0.00 2.93
49 50 1.370414 CAGCGAAACTTTGGTGCCG 60.370 57.895 0.00 0.00 33.78 5.69
55 56 1.401931 CCATCCTGCAGCGAAACTTTG 60.402 52.381 8.66 2.40 0.00 2.77
80 81 5.589192 GCCCAAAGATGATTGAGAGAATTG 58.411 41.667 0.00 0.00 31.84 2.32
124 156 1.064060 CTTGCTAGCCATTTACGTGCC 59.936 52.381 13.29 0.00 0.00 5.01
146 178 3.942439 GCCCTACCCCATCGGAGC 61.942 72.222 0.00 0.00 34.64 4.70
147 179 2.989173 TACGCCCTACCCCATCGGAG 62.989 65.000 0.00 0.00 34.64 4.63
148 180 2.989173 CTACGCCCTACCCCATCGGA 62.989 65.000 0.00 0.00 34.64 4.55
150 182 2.571216 CCTACGCCCTACCCCATCG 61.571 68.421 0.00 0.00 0.00 3.84
151 183 2.880380 GCCTACGCCCTACCCCATC 61.880 68.421 0.00 0.00 0.00 3.51
155 187 3.603671 CTCGCCTACGCCCTACCC 61.604 72.222 0.00 0.00 39.84 3.69
156 188 1.669999 TTTCTCGCCTACGCCCTACC 61.670 60.000 0.00 0.00 39.84 3.18
157 189 0.248949 CTTTCTCGCCTACGCCCTAC 60.249 60.000 0.00 0.00 39.84 3.18
158 190 0.682209 ACTTTCTCGCCTACGCCCTA 60.682 55.000 0.00 0.00 39.84 3.53
159 191 1.982938 ACTTTCTCGCCTACGCCCT 60.983 57.895 0.00 0.00 39.84 5.19
160 192 1.810030 CACTTTCTCGCCTACGCCC 60.810 63.158 0.00 0.00 39.84 6.13
161 193 0.389426 TTCACTTTCTCGCCTACGCC 60.389 55.000 0.00 0.00 39.84 5.68
162 194 1.126296 GTTTCACTTTCTCGCCTACGC 59.874 52.381 0.00 0.00 39.84 4.42
163 195 1.385743 CGTTTCACTTTCTCGCCTACG 59.614 52.381 0.00 0.00 42.01 3.51
164 196 2.669364 TCGTTTCACTTTCTCGCCTAC 58.331 47.619 0.00 0.00 0.00 3.18
165 197 3.054878 GTTCGTTTCACTTTCTCGCCTA 58.945 45.455 0.00 0.00 0.00 3.93
166 198 1.865340 GTTCGTTTCACTTTCTCGCCT 59.135 47.619 0.00 0.00 0.00 5.52
167 199 1.595794 TGTTCGTTTCACTTTCTCGCC 59.404 47.619 0.00 0.00 0.00 5.54
168 200 2.892613 CTGTTCGTTTCACTTTCTCGC 58.107 47.619 0.00 0.00 0.00 5.03
169 201 2.284150 TGCTGTTCGTTTCACTTTCTCG 59.716 45.455 0.00 0.00 0.00 4.04
170 202 3.608456 GTGCTGTTCGTTTCACTTTCTC 58.392 45.455 0.00 0.00 0.00 2.87
171 203 2.030457 CGTGCTGTTCGTTTCACTTTCT 59.970 45.455 0.00 0.00 0.00 2.52
172 204 2.363220 CGTGCTGTTCGTTTCACTTTC 58.637 47.619 0.00 0.00 0.00 2.62
173 205 1.531058 GCGTGCTGTTCGTTTCACTTT 60.531 47.619 0.00 0.00 0.00 2.66
174 206 0.027586 GCGTGCTGTTCGTTTCACTT 59.972 50.000 0.00 0.00 0.00 3.16
175 207 0.810031 AGCGTGCTGTTCGTTTCACT 60.810 50.000 0.00 0.00 0.00 3.41
176 208 0.383124 GAGCGTGCTGTTCGTTTCAC 60.383 55.000 0.00 0.00 0.00 3.18
177 209 1.817217 CGAGCGTGCTGTTCGTTTCA 61.817 55.000 0.00 0.00 45.05 2.69
178 210 1.154836 CGAGCGTGCTGTTCGTTTC 60.155 57.895 0.00 0.00 45.05 2.78
207 239 4.767255 GCTGGGTCTCCGCTGTGG 62.767 72.222 0.00 0.00 40.09 4.17
249 286 3.434309 TCTGTGTCTGTGAGATCCATCA 58.566 45.455 0.00 0.00 0.00 3.07
250 287 3.181477 CCTCTGTGTCTGTGAGATCCATC 60.181 52.174 0.00 0.00 0.00 3.51
251 288 2.765135 CCTCTGTGTCTGTGAGATCCAT 59.235 50.000 0.00 0.00 0.00 3.41
252 289 2.174360 CCTCTGTGTCTGTGAGATCCA 58.826 52.381 0.00 0.00 0.00 3.41
253 290 2.451490 TCCTCTGTGTCTGTGAGATCC 58.549 52.381 0.00 0.00 0.00 3.36
254 291 3.068024 GGATCCTCTGTGTCTGTGAGATC 59.932 52.174 3.84 0.00 0.00 2.75
255 292 3.030291 GGATCCTCTGTGTCTGTGAGAT 58.970 50.000 3.84 0.00 0.00 2.75
256 293 2.451490 GGATCCTCTGTGTCTGTGAGA 58.549 52.381 3.84 0.00 0.00 3.27
257 294 1.133982 CGGATCCTCTGTGTCTGTGAG 59.866 57.143 10.75 0.00 0.00 3.51
258 295 1.177401 CGGATCCTCTGTGTCTGTGA 58.823 55.000 10.75 0.00 0.00 3.58
259 296 1.135257 GTCGGATCCTCTGTGTCTGTG 60.135 57.143 10.75 0.00 0.00 3.66
260 297 1.178276 GTCGGATCCTCTGTGTCTGT 58.822 55.000 10.75 0.00 0.00 3.41
261 298 0.099613 CGTCGGATCCTCTGTGTCTG 59.900 60.000 10.75 0.00 0.00 3.51
262 299 1.658686 GCGTCGGATCCTCTGTGTCT 61.659 60.000 10.75 0.00 0.00 3.41
263 300 1.226717 GCGTCGGATCCTCTGTGTC 60.227 63.158 10.75 0.00 0.00 3.67
264 301 1.977009 TGCGTCGGATCCTCTGTGT 60.977 57.895 10.75 0.00 0.00 3.72
265 302 1.517257 GTGCGTCGGATCCTCTGTG 60.517 63.158 10.75 0.00 0.00 3.66
266 303 2.711922 GGTGCGTCGGATCCTCTGT 61.712 63.158 10.75 0.00 0.00 3.41
402 440 2.022129 GTCAGTGACGTTGGAGGCG 61.022 63.158 7.68 0.00 0.00 5.52
443 481 0.109873 GTCACCGACGTGTAGGTCAG 60.110 60.000 1.49 0.00 41.09 3.51
444 482 1.951510 GTCACCGACGTGTAGGTCA 59.048 57.895 1.49 0.00 41.09 4.02
445 483 4.855596 GTCACCGACGTGTAGGTC 57.144 61.111 1.49 0.00 41.09 3.85
469 507 1.721487 CAGCCCGCACGATAAAAGG 59.279 57.895 0.00 0.00 0.00 3.11
505 543 5.104817 TCCGTATCTAACAAAAAGGGGTAGG 60.105 44.000 0.00 0.00 0.00 3.18
574 612 2.336809 GGATCTGTAGCGCCTCGG 59.663 66.667 2.29 2.34 0.00 4.63
596 634 3.801997 CAGGCCAGGGCAGGGTAG 61.802 72.222 16.94 0.00 44.11 3.18
619 661 4.003788 CAACGGAGGGGAGCGTGT 62.004 66.667 0.00 0.00 0.00 4.49
1836 1880 2.359354 CACATCGGGTTGGGCGAA 60.359 61.111 0.00 0.00 0.00 4.70
1837 1881 4.402528 CCACATCGGGTTGGGCGA 62.403 66.667 0.00 0.00 0.00 5.54
2139 2183 3.243367 GCTGGAGATCACTGCTGTAGTAG 60.243 52.174 0.00 0.00 37.60 2.57
2211 2255 1.029408 AGTTGCGTGCACCAAGAACA 61.029 50.000 17.58 2.87 0.00 3.18
2217 2261 0.871722 GTATCAAGTTGCGTGCACCA 59.128 50.000 12.15 7.62 0.00 4.17
2235 2279 1.620524 CCATCCTTGGCCTTCATTGGT 60.621 52.381 3.32 0.00 35.85 3.67
2271 2315 1.665679 CCATACTTGGCAACGCAGTAG 59.334 52.381 0.00 0.00 36.13 2.57
2429 2473 2.516930 CATCCCGGGCATCACCAC 60.517 66.667 18.49 0.00 42.05 4.16
2571 2615 4.433102 GTGCATGTAAACCGCACG 57.567 55.556 8.44 0.00 45.69 5.34
2670 2714 0.912486 GGTGCCTCAGGTAGTCCAAT 59.088 55.000 0.00 0.00 35.89 3.16
3186 3230 2.811317 CTCTCACCTTGCGTCGCC 60.811 66.667 15.88 0.00 0.00 5.54
3214 3258 2.596851 GGTCCCTCCAGCTCAGCAA 61.597 63.158 0.00 0.00 35.97 3.91
3434 3498 3.421844 GGACAATGTTACAAGCTTCCCT 58.578 45.455 0.00 0.00 0.00 4.20
3535 3599 2.843912 ATTACAGGGCCACCAGCTGC 62.844 60.000 8.66 0.00 43.05 5.25
3536 3600 0.546122 TATTACAGGGCCACCAGCTG 59.454 55.000 6.78 6.78 43.05 4.24
3537 3601 1.212935 CTTATTACAGGGCCACCAGCT 59.787 52.381 6.18 0.00 43.05 4.24
3538 3602 1.680338 CTTATTACAGGGCCACCAGC 58.320 55.000 6.18 0.00 40.13 4.85
3624 3689 5.408299 GCCAACATTTTCCATCCAAAACTAC 59.592 40.000 0.00 0.00 0.00 2.73
3637 3702 2.928801 ACCCCAAAGCCAACATTTTC 57.071 45.000 0.00 0.00 0.00 2.29
3786 3851 8.314751 GGAAGGAACAGCACATATACTACATAT 58.685 37.037 0.00 0.00 0.00 1.78
3787 3852 7.256190 GGGAAGGAACAGCACATATACTACATA 60.256 40.741 0.00 0.00 0.00 2.29
3788 3853 6.464465 GGGAAGGAACAGCACATATACTACAT 60.464 42.308 0.00 0.00 0.00 2.29
3789 3854 5.163343 GGGAAGGAACAGCACATATACTACA 60.163 44.000 0.00 0.00 0.00 2.74
3790 3855 5.070580 AGGGAAGGAACAGCACATATACTAC 59.929 44.000 0.00 0.00 0.00 2.73
3791 3856 5.216622 AGGGAAGGAACAGCACATATACTA 58.783 41.667 0.00 0.00 0.00 1.82
3792 3857 4.040755 AGGGAAGGAACAGCACATATACT 58.959 43.478 0.00 0.00 0.00 2.12
3793 3858 4.423625 AGGGAAGGAACAGCACATATAC 57.576 45.455 0.00 0.00 0.00 1.47
3794 3859 5.450818 AAAGGGAAGGAACAGCACATATA 57.549 39.130 0.00 0.00 0.00 0.86
3795 3860 4.322057 AAAGGGAAGGAACAGCACATAT 57.678 40.909 0.00 0.00 0.00 1.78
3845 3910 2.292292 GGTAAGCGCCTCAGAACAAAAA 59.708 45.455 2.29 0.00 0.00 1.94
3846 3911 1.877443 GGTAAGCGCCTCAGAACAAAA 59.123 47.619 2.29 0.00 0.00 2.44
3880 4001 0.790814 GTGAAACTACCTCAGCGTGC 59.209 55.000 0.00 0.00 0.00 5.34
3958 4082 0.924090 GCACATTCGTAGGCTCTTCG 59.076 55.000 0.00 0.00 0.00 3.79
3959 4083 0.924090 CGCACATTCGTAGGCTCTTC 59.076 55.000 0.00 0.00 0.00 2.87
4032 4332 3.396611 AGAAAAGTTGGGTAAGGGCTACA 59.603 43.478 0.00 0.00 31.45 2.74
4039 4339 5.296035 ACGACAAAGAGAAAAGTTGGGTAAG 59.704 40.000 0.00 0.00 0.00 2.34
4046 4346 3.493503 CCGCTACGACAAAGAGAAAAGTT 59.506 43.478 0.00 0.00 0.00 2.66
4055 4355 1.862201 TGTTCAACCGCTACGACAAAG 59.138 47.619 0.00 0.00 0.00 2.77
4056 4356 1.862201 CTGTTCAACCGCTACGACAAA 59.138 47.619 0.00 0.00 0.00 2.83
4073 4375 0.036952 AGCGCACATTCAGTAGCTGT 60.037 50.000 11.47 0.00 40.43 4.40
4105 4407 4.517285 ACCACGGAGTAACTTATACGAGA 58.483 43.478 0.00 0.00 41.61 4.04
4108 4410 4.985413 TGAACCACGGAGTAACTTATACG 58.015 43.478 0.00 0.00 41.61 3.06
4111 4413 4.817517 CACTGAACCACGGAGTAACTTAT 58.182 43.478 0.00 0.00 41.61 1.73
4113 4415 2.805657 GCACTGAACCACGGAGTAACTT 60.806 50.000 0.00 0.00 41.61 2.66
4135 4437 5.423704 TGATAAACCCCTACGACAATTCA 57.576 39.130 0.00 0.00 0.00 2.57
4142 4444 3.635373 CAGTAGCTGATAAACCCCTACGA 59.365 47.826 0.00 0.00 34.94 3.43
4147 4449 4.576463 CACATTCAGTAGCTGATAAACCCC 59.424 45.833 0.00 0.00 40.39 4.95
4148 4450 4.035675 GCACATTCAGTAGCTGATAAACCC 59.964 45.833 0.00 0.00 40.39 4.11
4149 4451 4.635765 TGCACATTCAGTAGCTGATAAACC 59.364 41.667 0.00 0.00 40.39 3.27
4150 4452 5.352569 AGTGCACATTCAGTAGCTGATAAAC 59.647 40.000 21.04 0.00 40.39 2.01
4151 4453 5.491070 AGTGCACATTCAGTAGCTGATAAA 58.509 37.500 21.04 0.00 40.39 1.40
4152 4454 5.089970 AGTGCACATTCAGTAGCTGATAA 57.910 39.130 21.04 0.00 40.39 1.75
4153 4455 4.743057 AGTGCACATTCAGTAGCTGATA 57.257 40.909 21.04 0.00 40.39 2.15
4154 4456 3.623906 AGTGCACATTCAGTAGCTGAT 57.376 42.857 21.04 0.00 40.39 2.90
4155 4457 4.535526 TTAGTGCACATTCAGTAGCTGA 57.464 40.909 21.04 0.00 38.87 4.26
4156 4458 4.272018 GGATTAGTGCACATTCAGTAGCTG 59.728 45.833 21.04 0.00 0.00 4.24
4157 4459 4.080919 TGGATTAGTGCACATTCAGTAGCT 60.081 41.667 21.04 0.00 0.00 3.32
4158 4460 4.191544 TGGATTAGTGCACATTCAGTAGC 58.808 43.478 21.04 0.00 0.00 3.58
4159 4461 4.272018 GCTGGATTAGTGCACATTCAGTAG 59.728 45.833 21.04 9.74 0.00 2.57
4160 4462 4.191544 GCTGGATTAGTGCACATTCAGTA 58.808 43.478 21.04 0.00 0.00 2.74
4161 4463 3.012518 GCTGGATTAGTGCACATTCAGT 58.987 45.455 21.04 0.00 0.00 3.41
4162 4464 2.031314 CGCTGGATTAGTGCACATTCAG 59.969 50.000 21.04 18.85 0.00 3.02
4163 4465 2.009051 CGCTGGATTAGTGCACATTCA 58.991 47.619 21.04 8.80 0.00 2.57
4164 4466 2.009774 ACGCTGGATTAGTGCACATTC 58.990 47.619 21.04 12.02 40.64 2.67
4211 4536 0.038801 GCTGCTTCTTTTCTGCACCC 60.039 55.000 0.00 0.00 32.91 4.61
4241 4566 0.319211 CGGGAACTGCTCACGTACAA 60.319 55.000 0.00 0.00 46.39 2.41
4254 4579 3.195698 GGATCAGCGCACGGGAAC 61.196 66.667 11.47 0.00 0.00 3.62
4285 4610 5.128205 GGTACAACCACAACCTTTCTAACT 58.872 41.667 0.00 0.00 38.42 2.24
4286 4611 4.276678 GGGTACAACCACAACCTTTCTAAC 59.723 45.833 0.00 0.00 41.02 2.34
4287 4612 4.079901 TGGGTACAACCACAACCTTTCTAA 60.080 41.667 0.00 0.00 41.02 2.10
4288 4613 3.458857 TGGGTACAACCACAACCTTTCTA 59.541 43.478 0.00 0.00 41.02 2.10
4289 4614 2.242708 TGGGTACAACCACAACCTTTCT 59.757 45.455 0.00 0.00 41.02 2.52
4299 4624 1.025812 CAAAAGCGTGGGTACAACCA 58.974 50.000 0.00 0.00 41.02 3.67
4303 4628 0.535553 GGGTCAAAAGCGTGGGTACA 60.536 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.