Multiple sequence alignment - TraesCS2A01G168400

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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 TraesCS2A01G168400 chr2A 100.000 4663 0 0 1 4663 121228782 121224120 0.000000e+00 8612.0
1 TraesCS2A01G168400 chr2D 93.752 3345 116 38 668 3971 119302331 119299039 0.000000e+00 4933.0
2 TraesCS2A01G168400 chr2D 92.308 702 20 12 3 682 119303689 119303000 0.000000e+00 966.0
3 TraesCS2A01G168400 chr2D 94.679 545 25 4 4121 4663 119298950 119298408 0.000000e+00 843.0
4 TraesCS2A01G168400 chr2D 97.561 41 1 0 3968 4008 119299023 119298983 2.330000e-08 71.3
5 TraesCS2A01G168400 chr2B 92.504 2041 106 21 1 2008 171465216 171463190 0.000000e+00 2878.0
6 TraesCS2A01G168400 chr2B 92.735 1872 66 32 2135 3971 171462851 171461015 0.000000e+00 2639.0
7 TraesCS2A01G168400 chr2B 95.310 533 25 0 4121 4653 171460901 171460369 0.000000e+00 846.0
8 TraesCS2A01G168400 chr2B 97.561 41 1 0 3968 4008 171460999 171460959 2.330000e-08 71.3
9 TraesCS2A01G168400 chr5D 83.899 1149 136 28 814 1947 377474953 377476067 0.000000e+00 1051.0
10 TraesCS2A01G168400 chr5D 80.889 450 62 19 2822 3255 377476731 377477172 2.690000e-87 333.0
11 TraesCS2A01G168400 chr5D 92.432 185 13 1 3479 3663 377482493 377482676 3.580000e-66 263.0
12 TraesCS2A01G168400 chr5D 92.308 117 9 0 3369 3485 377482144 377482260 2.890000e-37 167.0
13 TraesCS2A01G168400 chr5D 85.075 134 17 2 692 822 377474799 377474932 2.930000e-27 134.0
14 TraesCS2A01G168400 chr5D 89.412 85 9 0 3171 3255 488863899 488863983 1.770000e-19 108.0
15 TraesCS2A01G168400 chr5A 85.686 1006 113 19 904 1897 478005454 478006440 0.000000e+00 1031.0
16 TraesCS2A01G168400 chr5A 80.580 448 61 20 2825 3255 478007199 478007637 5.820000e-84 322.0
17 TraesCS2A01G168400 chr5A 93.514 185 11 1 3479 3663 478013298 478013481 1.650000e-69 274.0
18 TraesCS2A01G168400 chr5A 93.966 116 7 0 3370 3485 478013001 478013116 4.800000e-40 176.0
19 TraesCS2A01G168400 chr5A 82.895 152 18 4 2012 2158 478006506 478006654 3.790000e-26 130.0
20 TraesCS2A01G168400 chr5B 82.216 1119 141 33 843 1947 450758732 450759806 0.000000e+00 911.0
21 TraesCS2A01G168400 chr5B 79.956 454 59 22 2825 3255 450760437 450760881 5.860000e-79 305.0
22 TraesCS2A01G168400 chr5B 94.054 185 10 1 3479 3663 450767235 450767418 3.550000e-71 279.0
23 TraesCS2A01G168400 chr5B 93.578 109 7 0 3377 3485 450767048 450767156 3.730000e-36 163.0


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 TraesCS2A01G168400 chr2A 121224120 121228782 4662 True 8612.000000 8612 100.000000 1 4663 1 chr2A.!!$R1 4662
1 TraesCS2A01G168400 chr2D 119298408 119303689 5281 True 1703.325000 4933 94.575000 3 4663 4 chr2D.!!$R1 4660
2 TraesCS2A01G168400 chr2B 171460369 171465216 4847 True 1608.575000 2878 94.527500 1 4653 4 chr2B.!!$R1 4652
3 TraesCS2A01G168400 chr5D 377474799 377477172 2373 False 506.000000 1051 83.287667 692 3255 3 chr5D.!!$F2 2563
4 TraesCS2A01G168400 chr5D 377482144 377482676 532 False 215.000000 263 92.370000 3369 3663 2 chr5D.!!$F3 294
5 TraesCS2A01G168400 chr5A 478005454 478007637 2183 False 494.333333 1031 83.053667 904 3255 3 chr5A.!!$F1 2351
6 TraesCS2A01G168400 chr5B 450758732 450760881 2149 False 608.000000 911 81.086000 843 3255 2 chr5B.!!$F1 2412

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
299 300 2.288640 GCATCATCATAAAAGGCCTGGC 60.289 50.000 5.69 11.05 0.00 4.85 F
1644 2398 1.202348 GTTGCCTCCAGTTGTAATGCC 59.798 52.381 0.00 0.00 0.00 4.40 F
3064 4212 0.940991 GTCGGTAAACGCTGTTCGGT 60.941 55.000 0.00 0.00 43.86 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 2546 1.599047 CCATGACTCTCAGCCCGTT 59.401 57.895 0.0 0.0 0.00 4.44 R
3265 4447 0.035439 AATGGAAGACGACGGGCATT 60.035 50.000 0.0 0.0 0.00 3.56 R
3959 5391 0.984230 TGCTAGGGTTGGGAACAGAG 59.016 55.000 0.0 0.0 44.54 3.35 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
27 28 4.688879 CGGAACTGTACTCTTGTTGCATTA 59.311 41.667 0.00 0.00 32.79 1.90
193 194 3.264998 AGTTTGGCACTGCAAATGTTT 57.735 38.095 2.82 0.00 32.83 2.83
198 199 2.954989 TGGCACTGCAAATGTTTGTCTA 59.045 40.909 2.82 0.00 40.24 2.59
286 287 7.552330 TGTTTTATTAGTACAGCTGCATCATCA 59.448 33.333 15.27 0.00 0.00 3.07
289 290 9.777297 TTTATTAGTACAGCTGCATCATCATAA 57.223 29.630 15.27 5.56 0.00 1.90
290 291 9.777297 TTATTAGTACAGCTGCATCATCATAAA 57.223 29.630 15.27 0.00 0.00 1.40
292 293 6.615264 AGTACAGCTGCATCATCATAAAAG 57.385 37.500 15.27 0.00 0.00 2.27
293 294 4.913335 ACAGCTGCATCATCATAAAAGG 57.087 40.909 15.27 0.00 0.00 3.11
294 295 3.067742 ACAGCTGCATCATCATAAAAGGC 59.932 43.478 15.27 0.00 0.00 4.35
295 296 2.626743 AGCTGCATCATCATAAAAGGCC 59.373 45.455 1.02 0.00 0.00 5.19
297 298 3.552273 GCTGCATCATCATAAAAGGCCTG 60.552 47.826 5.69 0.00 0.00 4.85
298 299 2.960384 TGCATCATCATAAAAGGCCTGG 59.040 45.455 5.69 0.00 0.00 4.45
299 300 2.288640 GCATCATCATAAAAGGCCTGGC 60.289 50.000 5.69 11.05 0.00 4.85
301 302 4.401022 CATCATCATAAAAGGCCTGGCTA 58.599 43.478 19.68 2.96 0.00 3.93
302 303 4.729552 TCATCATAAAAGGCCTGGCTAT 57.270 40.909 19.68 5.47 0.00 2.97
420 447 4.884744 TCAGACCTTTTTGGATTTGACGAA 59.115 37.500 0.00 0.00 39.71 3.85
550 578 2.679082 GGCCTCCAGTCCTACAATAGA 58.321 52.381 0.00 0.00 0.00 1.98
724 1437 7.862512 AAAAACAAATTGGCTCAAAGATCAA 57.137 28.000 0.00 0.00 0.00 2.57
868 1610 8.931385 ATGTGTAAAAGATGTAATGATTTGGC 57.069 30.769 0.00 0.00 0.00 4.52
987 1734 5.877012 TCAGCTGAATGACCTCTAAACATTC 59.123 40.000 15.67 0.00 45.46 2.67
1280 2032 4.270245 TGTCAGCAACATAGACATGTCA 57.730 40.909 27.02 13.67 44.83 3.58
1532 2286 8.077991 GTCAACTGACAATTCATGATCTTTCAA 58.922 33.333 4.96 0.00 44.18 2.69
1620 2374 1.952990 TCAGCCAGTTGCAAAATCGAA 59.047 42.857 0.00 0.00 44.83 3.71
1644 2398 1.202348 GTTGCCTCCAGTTGTAATGCC 59.798 52.381 0.00 0.00 0.00 4.40
1656 2410 6.088883 CCAGTTGTAATGCCATTCGTTTTTAC 59.911 38.462 0.00 0.00 0.00 2.01
1787 2546 7.066163 CAGAGATATTTCAGCAACATTGGTACA 59.934 37.037 0.00 0.00 37.09 2.90
1806 2565 1.903877 AACGGGCTGAGAGTCATGGG 61.904 60.000 0.00 0.00 0.00 4.00
1976 2739 1.541147 CGGCAAACCACATGACAAGAT 59.459 47.619 0.00 0.00 34.57 2.40
2287 3353 9.812347 AGATATTTATATGGCCTTTGAATGTCA 57.188 29.630 3.32 0.00 0.00 3.58
2409 3475 4.986622 TGCCAATAGATGATCTCGATACG 58.013 43.478 0.00 0.00 0.00 3.06
2514 3583 9.274065 GAACAAAATAGTTTATGACATTCGGAC 57.726 33.333 0.00 0.00 0.00 4.79
2523 3592 3.245518 TGACATTCGGACACTACATGG 57.754 47.619 0.00 0.00 0.00 3.66
2568 3654 4.150274 GCTCATATTTCTCATCTGCAGACG 59.850 45.833 20.97 11.99 0.00 4.18
2642 3728 4.661222 TCATGGAAGGTACAGCAAAATCA 58.339 39.130 0.00 0.00 0.00 2.57
2705 3849 3.243737 TGCGCCAGTACTCCATAAGTATG 60.244 47.826 4.18 0.00 42.38 2.39
2737 3881 5.750352 AATTTCAAGGACAATTCTGCCAT 57.250 34.783 0.00 0.00 0.00 4.40
3064 4212 0.940991 GTCGGTAAACGCTGTTCGGT 60.941 55.000 0.00 0.00 43.86 4.69
3072 4220 2.279582 ACGCTGTTCGGTATCTTCAG 57.720 50.000 0.00 0.00 43.86 3.02
3074 4222 2.186076 CGCTGTTCGGTATCTTCAGTC 58.814 52.381 0.00 0.00 33.78 3.51
3075 4223 2.415491 CGCTGTTCGGTATCTTCAGTCA 60.415 50.000 0.00 0.00 33.78 3.41
3076 4224 3.735208 CGCTGTTCGGTATCTTCAGTCAT 60.735 47.826 0.00 0.00 33.78 3.06
3265 4447 1.070786 GAAGAGGTTCACCGCACCA 59.929 57.895 2.32 0.00 42.08 4.17
3295 4477 5.578776 GTCGTCTTCCATTTTGTTCAAAGT 58.421 37.500 0.00 0.00 0.00 2.66
3307 4489 2.881513 TGTTCAAAGTGTGTGTGTGTGT 59.118 40.909 0.00 0.00 0.00 3.72
3308 4490 3.233578 GTTCAAAGTGTGTGTGTGTGTG 58.766 45.455 0.00 0.00 0.00 3.82
3309 4491 2.499197 TCAAAGTGTGTGTGTGTGTGT 58.501 42.857 0.00 0.00 0.00 3.72
3310 4492 2.225255 TCAAAGTGTGTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
3311 4493 1.890876 AAGTGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 0.00 3.72
3312 4494 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
3313 4495 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3314 4496 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3315 4497 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3316 4498 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3317 4499 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3318 4500 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3319 4501 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3320 4502 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3321 4503 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3322 4504 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3323 4505 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3339 4521 3.317430 TGTGTGTGTGCAGCATCATAAAA 59.683 39.130 0.00 0.00 0.00 1.52
3348 4530 6.150809 TGTGCAGCATCATAAAACACATTCTA 59.849 34.615 0.00 0.00 32.06 2.10
3725 5152 2.906388 ACACGCTGCATGTGCCAA 60.906 55.556 16.62 0.00 41.03 4.52
3730 5157 4.764336 CTGCATGTGCCAACGCCG 62.764 66.667 2.07 0.00 41.18 6.46
3758 5185 5.378292 GATCATTCGAGATGCTGGTAGTA 57.622 43.478 0.00 0.00 0.00 1.82
3784 5211 6.831976 ACTAGCTAAGGATCTGTAAAATGGG 58.168 40.000 0.00 0.00 0.00 4.00
3796 5223 9.671279 GATCTGTAAAATGGGAAATTGGATTTT 57.329 29.630 0.00 0.00 33.64 1.82
3869 5297 4.799564 GATTTTATCCAAACACCCAGCA 57.200 40.909 0.00 0.00 0.00 4.41
3870 5298 5.343307 GATTTTATCCAAACACCCAGCAT 57.657 39.130 0.00 0.00 0.00 3.79
3871 5299 6.463995 GATTTTATCCAAACACCCAGCATA 57.536 37.500 0.00 0.00 0.00 3.14
3872 5300 7.054491 GATTTTATCCAAACACCCAGCATAT 57.946 36.000 0.00 0.00 0.00 1.78
3909 5341 8.801882 TTTATCCAAAGAATCGTATGAGGTTT 57.198 30.769 0.00 0.00 0.00 3.27
3959 5391 2.095213 TGAATGGACGCGCTTGTATTTC 59.905 45.455 5.73 1.31 0.00 2.17
3999 5450 5.188555 AGCACTCTGGTTGATCTATTCAAGA 59.811 40.000 0.00 0.00 44.89 3.02
4008 5459 8.762645 TGGTTGATCTATTCAAGACATCTACTT 58.237 33.333 0.00 0.00 44.89 2.24
4010 5461 9.255304 GTTGATCTATTCAAGACATCTACTTCC 57.745 37.037 0.00 0.00 44.89 3.46
4011 5462 8.774546 TGATCTATTCAAGACATCTACTTCCT 57.225 34.615 0.00 0.00 36.93 3.36
4012 5463 8.855110 TGATCTATTCAAGACATCTACTTCCTC 58.145 37.037 0.00 0.00 36.93 3.71
4013 5464 7.589958 TCTATTCAAGACATCTACTTCCTCC 57.410 40.000 0.00 0.00 0.00 4.30
4014 5465 4.720649 TTCAAGACATCTACTTCCTCCG 57.279 45.455 0.00 0.00 0.00 4.63
4015 5466 3.698289 TCAAGACATCTACTTCCTCCGT 58.302 45.455 0.00 0.00 0.00 4.69
4016 5467 4.087182 TCAAGACATCTACTTCCTCCGTT 58.913 43.478 0.00 0.00 0.00 4.44
4017 5468 4.158025 TCAAGACATCTACTTCCTCCGTTC 59.842 45.833 0.00 0.00 0.00 3.95
4018 5469 3.025262 AGACATCTACTTCCTCCGTTCC 58.975 50.000 0.00 0.00 0.00 3.62
4019 5470 3.025262 GACATCTACTTCCTCCGTTCCT 58.975 50.000 0.00 0.00 0.00 3.36
4021 5472 4.607239 ACATCTACTTCCTCCGTTCCTAA 58.393 43.478 0.00 0.00 0.00 2.69
4022 5473 5.021458 ACATCTACTTCCTCCGTTCCTAAA 58.979 41.667 0.00 0.00 0.00 1.85
4023 5474 5.482878 ACATCTACTTCCTCCGTTCCTAAAA 59.517 40.000 0.00 0.00 0.00 1.52
4024 5475 6.156429 ACATCTACTTCCTCCGTTCCTAAAAT 59.844 38.462 0.00 0.00 0.00 1.82
4025 5476 7.343833 ACATCTACTTCCTCCGTTCCTAAAATA 59.656 37.037 0.00 0.00 0.00 1.40
4027 5478 8.315220 TCTACTTCCTCCGTTCCTAAAATATT 57.685 34.615 0.00 0.00 0.00 1.28
4028 5479 8.765517 TCTACTTCCTCCGTTCCTAAAATATTT 58.234 33.333 0.00 0.00 0.00 1.40
4029 5480 7.860918 ACTTCCTCCGTTCCTAAAATATTTC 57.139 36.000 0.10 0.00 0.00 2.17
4030 5481 7.399634 ACTTCCTCCGTTCCTAAAATATTTCA 58.600 34.615 0.10 0.00 0.00 2.69
4031 5482 7.886446 ACTTCCTCCGTTCCTAAAATATTTCAA 59.114 33.333 0.10 0.00 0.00 2.69
4032 5483 8.817092 TTCCTCCGTTCCTAAAATATTTCAAT 57.183 30.769 0.10 0.00 0.00 2.57
4033 5484 9.908747 TTCCTCCGTTCCTAAAATATTTCAATA 57.091 29.630 0.10 0.00 0.00 1.90
4037 5488 9.854668 TCCGTTCCTAAAATATTTCAATATGGA 57.145 29.630 0.10 4.59 32.17 3.41
4038 5489 9.893305 CCGTTCCTAAAATATTTCAATATGGAC 57.107 33.333 0.10 0.00 32.17 4.02
4052 5503 9.908152 TTTCAATATGGACTACGACTACATATG 57.092 33.333 0.00 0.00 35.56 1.78
4053 5504 8.631480 TCAATATGGACTACGACTACATATGT 57.369 34.615 13.93 13.93 35.56 2.29
4054 5505 9.729281 TCAATATGGACTACGACTACATATGTA 57.271 33.333 14.75 14.75 35.56 2.29
4074 5525 6.918892 TGTAGTCCATATTGAAATCAACGG 57.081 37.500 0.00 0.50 38.86 4.44
4075 5526 6.645306 TGTAGTCCATATTGAAATCAACGGA 58.355 36.000 0.00 2.81 38.86 4.69
4076 5527 6.761242 TGTAGTCCATATTGAAATCAACGGAG 59.239 38.462 9.75 0.00 38.86 4.63
4077 5528 5.126067 AGTCCATATTGAAATCAACGGAGG 58.874 41.667 9.75 5.63 38.86 4.30
4078 5529 4.275936 GTCCATATTGAAATCAACGGAGGG 59.724 45.833 9.75 5.43 38.86 4.30
4079 5530 4.165180 TCCATATTGAAATCAACGGAGGGA 59.835 41.667 0.00 1.62 38.86 4.20
4080 5531 4.516698 CCATATTGAAATCAACGGAGGGAG 59.483 45.833 0.00 0.00 38.86 4.30
4095 5546 5.221783 ACGGAGGGAGTACTACAAAACAATT 60.222 40.000 7.57 0.00 0.00 2.32
4096 5547 5.121768 CGGAGGGAGTACTACAAAACAATTG 59.878 44.000 7.57 3.24 0.00 2.32
4097 5548 6.235664 GGAGGGAGTACTACAAAACAATTGA 58.764 40.000 13.59 0.00 0.00 2.57
4099 5550 7.065923 GGAGGGAGTACTACAAAACAATTGATC 59.934 40.741 13.59 0.00 0.00 2.92
4100 5551 7.690256 AGGGAGTACTACAAAACAATTGATCT 58.310 34.615 13.59 0.00 0.00 2.75
4101 5552 8.822805 AGGGAGTACTACAAAACAATTGATCTA 58.177 33.333 13.59 0.00 0.00 1.98
4102 5553 9.614792 GGGAGTACTACAAAACAATTGATCTAT 57.385 33.333 13.59 0.00 0.00 1.98
4132 5583 7.116376 AGTCATCTACTACAAAATGTGAACACG 59.884 37.037 0.57 0.00 36.36 4.49
4195 5646 7.834046 AGGAGGTTAGAGTAGGGTATTCATTA 58.166 38.462 0.00 0.00 0.00 1.90
4462 5913 0.803768 CCTCCACAATGAGCTCGTCG 60.804 60.000 9.35 0.00 0.00 5.12
4492 5943 5.817816 CCAGTCCTCGTAGCTATTTCAAAAT 59.182 40.000 0.00 0.00 0.00 1.82
4535 5987 9.929180 CTATAGTACATAATAGCCAGCAAAGAA 57.071 33.333 0.00 0.00 0.00 2.52
4543 5995 2.165998 AGCCAGCAAAGAAAGGTGATC 58.834 47.619 0.00 0.00 36.64 2.92
4549 6001 4.219070 CAGCAAAGAAAGGTGATCATTGGA 59.781 41.667 0.00 0.00 36.64 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.015584 ACTCAGCCAAGATGGTTAAAAATTCTT 59.984 33.333 0.00 0.00 40.46 2.52
70 71 4.522789 GGACTCAGCCAAGATGGTTAAAAA 59.477 41.667 0.00 0.00 40.46 1.94
127 128 9.499585 CAAAAGCTTACTGACAATCTAATCATG 57.500 33.333 0.00 0.00 0.00 3.07
193 194 2.629137 TGGAGTAAAGTGCCGTTAGACA 59.371 45.455 0.00 0.00 0.00 3.41
198 199 5.560966 CATTTATGGAGTAAAGTGCCGTT 57.439 39.130 0.00 0.00 35.83 4.44
550 578 0.252284 AGCCCTACTGCTACCACTGT 60.252 55.000 0.00 0.00 40.56 3.55
629 657 2.012937 TTACATGCGTAAACCGGGAG 57.987 50.000 6.32 0.00 34.63 4.30
724 1437 3.821033 GACAACCTATTGCTTGTGTTCCT 59.179 43.478 0.00 0.00 39.66 3.36
868 1610 9.167311 AGATGCCTATTTTTCAGTACTTTAGTG 57.833 33.333 0.00 0.00 0.00 2.74
888 1633 2.290323 ACCAACTGTCCAACTAGATGCC 60.290 50.000 0.00 0.00 0.00 4.40
995 1745 8.772250 TGACTGGTAGATTATTCTCCATTTCTT 58.228 33.333 6.38 0.00 32.37 2.52
1027 1777 2.560981 TGGCGAGTTCTTGATACTCACA 59.439 45.455 0.00 0.00 41.64 3.58
1280 2032 8.806146 GGCATGTCATATCCCAATAAGTTTATT 58.194 33.333 0.00 0.00 33.82 1.40
1573 2327 5.001232 GGATAGCACCTGTACTTGACAAAA 58.999 41.667 0.00 0.00 37.70 2.44
1787 2546 1.599047 CCATGACTCTCAGCCCGTT 59.401 57.895 0.00 0.00 0.00 4.44
1788 2547 2.362369 CCCATGACTCTCAGCCCGT 61.362 63.158 0.00 0.00 0.00 5.28
1806 2565 4.869861 ACTGTCAAAACAATTGCCTTGAAC 59.130 37.500 19.11 14.80 38.29 3.18
2124 3178 7.200434 AGATGGTACTAACATCACCAGATTT 57.800 36.000 15.18 0.00 45.15 2.17
2287 3353 3.084039 CTGTGCCATGGTGTCTGTTTAT 58.916 45.455 14.67 0.00 0.00 1.40
2409 3475 0.524862 CAAGCAGGCATTGACTCACC 59.475 55.000 0.00 0.00 0.00 4.02
2514 3583 9.350357 CAGAAAGAAAAATGAATCCATGTAGTG 57.650 33.333 0.00 0.00 32.36 2.74
2523 3592 7.869429 TGAGCCTTTCAGAAAGAAAAATGAATC 59.131 33.333 22.55 8.26 45.11 2.52
2568 3654 1.446272 CTCAAGCTTCGACCCGTCC 60.446 63.158 0.00 0.00 0.00 4.79
2642 3728 4.406649 AGCTTTAATTTGCATATGGGTGCT 59.593 37.500 4.56 0.00 45.27 4.40
2705 3849 8.871686 AATTGTCCTTGAAATTACTGTTGAAC 57.128 30.769 0.00 0.00 0.00 3.18
2737 3881 2.702478 CCTCTAGATGGGTCATGCAGAA 59.298 50.000 0.00 0.00 0.00 3.02
2802 3946 3.762288 TGTAAGGCACGTTCTCTACTGAT 59.238 43.478 0.00 0.00 0.00 2.90
3128 4305 2.432510 GTTTGTTCCCCATGGTGTTCAA 59.567 45.455 11.73 8.12 0.00 2.69
3265 4447 0.035439 AATGGAAGACGACGGGCATT 60.035 50.000 0.00 0.00 0.00 3.56
3295 4477 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3307 4489 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3308 4490 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
3309 4491 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
3310 4492 0.179192 CTGCACACACACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
3311 4493 1.921045 GCTGCACACACACACACACA 61.921 55.000 0.00 0.00 0.00 3.72
3312 4494 1.226379 GCTGCACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
3313 4495 1.031029 ATGCTGCACACACACACACA 61.031 50.000 3.57 0.00 0.00 3.72
3314 4496 0.317269 GATGCTGCACACACACACAC 60.317 55.000 3.57 0.00 0.00 3.82
3315 4497 0.747283 TGATGCTGCACACACACACA 60.747 50.000 3.57 0.00 0.00 3.72
3316 4498 0.594602 ATGATGCTGCACACACACAC 59.405 50.000 3.57 0.00 0.00 3.82
3317 4499 2.181954 TATGATGCTGCACACACACA 57.818 45.000 3.57 0.00 0.00 3.72
3318 4500 3.557577 TTTATGATGCTGCACACACAC 57.442 42.857 3.57 0.00 0.00 3.82
3319 4501 3.317430 TGTTTTATGATGCTGCACACACA 59.683 39.130 3.57 3.78 0.00 3.72
3320 4502 3.670055 GTGTTTTATGATGCTGCACACAC 59.330 43.478 3.57 6.05 34.48 3.82
3321 4503 3.317430 TGTGTTTTATGATGCTGCACACA 59.683 39.130 3.57 9.40 40.45 3.72
3322 4504 3.899734 TGTGTTTTATGATGCTGCACAC 58.100 40.909 3.57 6.64 34.83 3.82
3323 4505 4.787260 ATGTGTTTTATGATGCTGCACA 57.213 36.364 3.57 5.91 39.25 4.57
3339 4521 1.165270 GCACCGCCTTTAGAATGTGT 58.835 50.000 0.00 0.00 0.00 3.72
3348 4530 2.203153 ACACGAAGCACCGCCTTT 60.203 55.556 0.00 0.00 0.00 3.11
3467 4653 4.722700 ACCATGACTGCCCGTGCC 62.723 66.667 0.00 0.00 36.33 5.01
3470 4656 4.033776 CCCACCATGACTGCCCGT 62.034 66.667 0.00 0.00 0.00 5.28
3690 5117 2.738846 GTGTCCTTCACAGTATGCAGTG 59.261 50.000 0.00 0.00 45.51 3.66
3725 5152 1.956170 GAATGATCGATGCCGGCGT 60.956 57.895 24.16 24.16 36.24 5.68
3737 5164 5.791336 TTACTACCAGCATCTCGAATGAT 57.209 39.130 10.52 2.99 0.00 2.45
3758 5185 7.775561 CCCATTTTACAGATCCTTAGCTAGTTT 59.224 37.037 0.00 0.00 0.00 2.66
3784 5211 6.081693 GCACAAAGCATCAAAATCCAATTTC 58.918 36.000 0.00 0.00 44.79 2.17
3913 5345 8.770828 CAAACCTTAATACGAACTCTCAAAAGA 58.229 33.333 0.00 0.00 0.00 2.52
3930 5362 1.198178 GCGCGTCCATTCAAACCTTAA 59.802 47.619 8.43 0.00 0.00 1.85
3959 5391 0.984230 TGCTAGGGTTGGGAACAGAG 59.016 55.000 0.00 0.00 44.54 3.35
3999 5450 3.103080 AGGAACGGAGGAAGTAGATGT 57.897 47.619 0.00 0.00 0.00 3.06
4011 5462 9.854668 TCCATATTGAAATATTTTAGGAACGGA 57.145 29.630 1.43 1.79 29.35 4.69
4012 5463 9.893305 GTCCATATTGAAATATTTTAGGAACGG 57.107 33.333 1.43 0.00 29.35 4.44
4027 5478 9.074576 ACATATGTAGTCGTAGTCCATATTGAA 57.925 33.333 6.56 0.00 28.79 2.69
4028 5479 8.631480 ACATATGTAGTCGTAGTCCATATTGA 57.369 34.615 6.56 0.00 28.79 2.57
4029 5480 9.989869 CTACATATGTAGTCGTAGTCCATATTG 57.010 37.037 27.86 4.11 42.22 1.90
4049 5500 8.425703 TCCGTTGATTTCAATATGGACTACATA 58.574 33.333 0.00 0.00 45.60 2.29
4050 5501 7.279615 TCCGTTGATTTCAATATGGACTACAT 58.720 34.615 0.00 0.00 43.68 2.29
4051 5502 6.645306 TCCGTTGATTTCAATATGGACTACA 58.355 36.000 0.00 0.00 38.24 2.74
4052 5503 6.202954 CCTCCGTTGATTTCAATATGGACTAC 59.797 42.308 0.00 0.00 38.24 2.73
4053 5504 6.288294 CCTCCGTTGATTTCAATATGGACTA 58.712 40.000 0.00 0.00 38.24 2.59
4054 5505 5.126067 CCTCCGTTGATTTCAATATGGACT 58.874 41.667 0.00 0.00 38.24 3.85
4055 5506 4.275936 CCCTCCGTTGATTTCAATATGGAC 59.724 45.833 0.00 0.00 38.24 4.02
4056 5507 4.165180 TCCCTCCGTTGATTTCAATATGGA 59.835 41.667 9.87 9.87 38.24 3.41
4057 5508 4.460263 TCCCTCCGTTGATTTCAATATGG 58.540 43.478 0.00 0.49 38.24 2.74
4058 5509 5.126067 ACTCCCTCCGTTGATTTCAATATG 58.874 41.667 0.00 0.00 38.24 1.78
4059 5510 5.373812 ACTCCCTCCGTTGATTTCAATAT 57.626 39.130 0.00 0.00 38.24 1.28
4060 5511 4.837093 ACTCCCTCCGTTGATTTCAATA 57.163 40.909 0.00 0.00 38.24 1.90
4061 5512 3.721087 ACTCCCTCCGTTGATTTCAAT 57.279 42.857 0.00 0.00 38.24 2.57
4062 5513 3.581332 AGTACTCCCTCCGTTGATTTCAA 59.419 43.478 0.00 0.00 0.00 2.69
4063 5514 3.170717 AGTACTCCCTCCGTTGATTTCA 58.829 45.455 0.00 0.00 0.00 2.69
4064 5515 3.889520 AGTACTCCCTCCGTTGATTTC 57.110 47.619 0.00 0.00 0.00 2.17
4065 5516 4.091549 TGTAGTACTCCCTCCGTTGATTT 58.908 43.478 0.00 0.00 0.00 2.17
4066 5517 3.705051 TGTAGTACTCCCTCCGTTGATT 58.295 45.455 0.00 0.00 0.00 2.57
4067 5518 3.377253 TGTAGTACTCCCTCCGTTGAT 57.623 47.619 0.00 0.00 0.00 2.57
4068 5519 2.885135 TGTAGTACTCCCTCCGTTGA 57.115 50.000 0.00 0.00 0.00 3.18
4069 5520 3.947910 TTTGTAGTACTCCCTCCGTTG 57.052 47.619 0.00 0.00 0.00 4.10
4070 5521 3.642848 TGTTTTGTAGTACTCCCTCCGTT 59.357 43.478 0.00 0.00 0.00 4.44
4071 5522 3.233507 TGTTTTGTAGTACTCCCTCCGT 58.766 45.455 0.00 0.00 0.00 4.69
4072 5523 3.947910 TGTTTTGTAGTACTCCCTCCG 57.052 47.619 0.00 0.00 0.00 4.63
4073 5524 6.235664 TCAATTGTTTTGTAGTACTCCCTCC 58.764 40.000 0.00 0.00 0.00 4.30
4074 5525 7.824779 AGATCAATTGTTTTGTAGTACTCCCTC 59.175 37.037 0.00 0.00 0.00 4.30
4075 5526 7.690256 AGATCAATTGTTTTGTAGTACTCCCT 58.310 34.615 0.00 0.00 0.00 4.20
4076 5527 7.923414 AGATCAATTGTTTTGTAGTACTCCC 57.077 36.000 0.00 0.00 0.00 4.30
4101 5552 9.725019 TCACATTTTGTAGTAGATGACTTGAAT 57.275 29.630 0.00 0.00 39.81 2.57
4102 5553 9.554395 TTCACATTTTGTAGTAGATGACTTGAA 57.446 29.630 0.00 0.00 39.81 2.69
4103 5554 8.988934 GTTCACATTTTGTAGTAGATGACTTGA 58.011 33.333 0.00 0.00 39.81 3.02
4104 5555 8.773645 TGTTCACATTTTGTAGTAGATGACTTG 58.226 33.333 0.00 0.00 39.81 3.16
4106 5557 7.116376 CGTGTTCACATTTTGTAGTAGATGACT 59.884 37.037 3.87 0.00 42.69 3.41
4107 5558 7.115805 TCGTGTTCACATTTTGTAGTAGATGAC 59.884 37.037 3.87 0.00 0.00 3.06
4108 5559 7.149307 TCGTGTTCACATTTTGTAGTAGATGA 58.851 34.615 3.87 0.00 0.00 2.92
4110 5561 7.956420 TTCGTGTTCACATTTTGTAGTAGAT 57.044 32.000 3.87 0.00 0.00 1.98
4111 5562 7.773864 TTTCGTGTTCACATTTTGTAGTAGA 57.226 32.000 3.87 0.00 0.00 2.59
4114 5565 9.607285 GATTATTTCGTGTTCACATTTTGTAGT 57.393 29.630 3.87 0.00 0.00 2.73
4115 5566 8.775884 CGATTATTTCGTGTTCACATTTTGTAG 58.224 33.333 3.87 0.00 43.01 2.74
4116 5567 7.746916 CCGATTATTTCGTGTTCACATTTTGTA 59.253 33.333 3.87 0.00 46.65 2.41
4117 5568 6.580791 CCGATTATTTCGTGTTCACATTTTGT 59.419 34.615 3.87 0.00 46.65 2.83
4118 5569 6.452350 GCCGATTATTTCGTGTTCACATTTTG 60.452 38.462 3.87 0.00 46.65 2.44
4119 5570 5.571357 GCCGATTATTTCGTGTTCACATTTT 59.429 36.000 3.87 0.00 46.65 1.82
4125 5576 3.591023 TCTGCCGATTATTTCGTGTTCA 58.409 40.909 0.00 0.00 46.65 3.18
4132 5583 5.100751 CAGGACATTCTGCCGATTATTTC 57.899 43.478 0.00 0.00 0.00 2.17
4340 5791 3.873952 GCCCTAGTAGCTATATGCAATGC 59.126 47.826 0.00 0.00 45.94 3.56
4462 5913 1.385756 GCTACGAGGACTGGGGAGTC 61.386 65.000 0.00 0.00 38.04 3.36
4515 5966 6.318648 CACCTTTCTTTGCTGGCTATTATGTA 59.681 38.462 0.00 0.00 0.00 2.29
4535 5987 6.940430 AAAGGAAAATCCAATGATCACCTT 57.060 33.333 0.00 0.00 39.61 3.50
4543 5995 8.534496 AGGTGAGATTTAAAGGAAAATCCAATG 58.466 33.333 5.86 0.00 43.78 2.82
4549 6001 8.670521 ATGGAAGGTGAGATTTAAAGGAAAAT 57.329 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.