Multiple sequence alignment - TraesCS5D01G324300

Loading Multiple Alignment...

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 TraesCS5D01G324300 chr5D 100.000 3860 0 0 1 3860 416171688 416175547 0.000000e+00 7129.0
1 TraesCS5D01G324300 chr5D 86.471 1604 189 18 1280 2860 468340494 468342092 0.000000e+00 1735.0
2 TraesCS5D01G324300 chr5D 85.183 1586 203 18 1279 2849 415746235 415747803 0.000000e+00 1598.0
3 TraesCS5D01G324300 chr5D 84.956 1602 197 31 1279 2848 415768217 415769806 0.000000e+00 1583.0
4 TraesCS5D01G324300 chr5D 86.928 918 105 10 1246 2155 416199522 416200432 0.000000e+00 1016.0
5 TraesCS5D01G324300 chr5B 91.489 2761 169 18 1087 3796 503077599 503080344 0.000000e+00 3736.0
6 TraesCS5D01G324300 chr5B 85.402 1603 195 26 1280 2848 502376272 502377869 0.000000e+00 1628.0
7 TraesCS5D01G324300 chr5B 85.229 1591 196 21 1279 2849 502264842 502266413 0.000000e+00 1600.0
8 TraesCS5D01G324300 chr5B 94.212 622 32 2 1 621 503076785 503077403 0.000000e+00 946.0
9 TraesCS5D01G324300 chr5B 80.296 609 118 2 2232 2839 503085917 503086524 3.510000e-125 459.0
10 TraesCS5D01G324300 chr5B 98.352 182 3 0 876 1057 503077419 503077600 1.730000e-83 320.0
11 TraesCS5D01G324300 chr5B 75.075 333 69 9 280 603 662644032 662643705 4.020000e-30 143.0
12 TraesCS5D01G324300 chr5B 75.159 157 35 4 2537 2691 473609150 473608996 1.920000e-08 71.3
13 TraesCS5D01G324300 chr5A 96.851 2191 45 12 819 2988 528890339 528892526 0.000000e+00 3642.0
14 TraesCS5D01G324300 chr5A 84.035 1591 213 31 1288 2848 528490068 528488489 0.000000e+00 1493.0
15 TraesCS5D01G324300 chr5A 92.203 590 27 2 1 590 528889454 528890024 0.000000e+00 817.0
16 TraesCS5D01G324300 chr5A 83.509 855 90 20 2978 3796 528894874 528895713 0.000000e+00 750.0
17 TraesCS5D01G324300 chr5A 97.810 274 3 2 550 822 528890027 528890298 1.620000e-128 470.0
18 TraesCS5D01G324300 chr5A 82.621 351 59 2 2232 2581 528912290 528912639 3.750000e-80 309.0
19 TraesCS5D01G324300 chr5A 77.122 271 55 4 289 558 311913570 311913834 2.400000e-32 150.0
20 TraesCS5D01G324300 chr5A 74.684 158 34 5 2537 2691 495727609 495727455 8.950000e-07 65.8
21 TraesCS5D01G324300 chr5A 100.000 32 0 0 2660 2691 495587015 495586984 4.160000e-05 60.2
22 TraesCS5D01G324300 chr7D 77.391 345 58 13 279 609 498537252 498536914 1.830000e-43 187.0
23 TraesCS5D01G324300 chr7D 86.301 73 9 1 3292 3364 214991469 214991540 1.150000e-10 78.7
24 TraesCS5D01G324300 chr3D 79.853 273 39 11 291 558 583322076 583321815 6.590000e-43 185.0
25 TraesCS5D01G324300 chr1D 78.723 282 52 6 279 558 472292470 472292195 8.520000e-42 182.0
26 TraesCS5D01G324300 chr1D 73.700 327 69 6 296 609 490573781 490574103 1.130000e-20 111.0
27 TraesCS5D01G324300 chr4D 78.378 259 50 4 289 545 484092556 484092302 3.090000e-36 163.0
28 TraesCS5D01G324300 chr4B 77.947 263 51 5 279 539 591910423 591910166 1.440000e-34 158.0
29 TraesCS5D01G324300 chr7A 91.837 49 4 0 128 176 719970014 719969966 6.920000e-08 69.4
30 TraesCS5D01G324300 chr4A 89.091 55 6 0 128 182 738403321 738403267 6.920000e-08 69.4


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 TraesCS5D01G324300 chr5D 416171688 416175547 3859 False 7129.000000 7129 100.000000 1 3860 1 chr5D.!!$F3 3859
1 TraesCS5D01G324300 chr5D 468340494 468342092 1598 False 1735.000000 1735 86.471000 1280 2860 1 chr5D.!!$F5 1580
2 TraesCS5D01G324300 chr5D 415746235 415747803 1568 False 1598.000000 1598 85.183000 1279 2849 1 chr5D.!!$F1 1570
3 TraesCS5D01G324300 chr5D 415768217 415769806 1589 False 1583.000000 1583 84.956000 1279 2848 1 chr5D.!!$F2 1569
4 TraesCS5D01G324300 chr5D 416199522 416200432 910 False 1016.000000 1016 86.928000 1246 2155 1 chr5D.!!$F4 909
5 TraesCS5D01G324300 chr5B 503076785 503080344 3559 False 1667.333333 3736 94.684333 1 3796 3 chr5B.!!$F4 3795
6 TraesCS5D01G324300 chr5B 502376272 502377869 1597 False 1628.000000 1628 85.402000 1280 2848 1 chr5B.!!$F2 1568
7 TraesCS5D01G324300 chr5B 502264842 502266413 1571 False 1600.000000 1600 85.229000 1279 2849 1 chr5B.!!$F1 1570
8 TraesCS5D01G324300 chr5B 503085917 503086524 607 False 459.000000 459 80.296000 2232 2839 1 chr5B.!!$F3 607
9 TraesCS5D01G324300 chr5A 528488489 528490068 1579 True 1493.000000 1493 84.035000 1288 2848 1 chr5A.!!$R3 1560
10 TraesCS5D01G324300 chr5A 528889454 528895713 6259 False 1419.750000 3642 92.593250 1 3796 4 chr5A.!!$F3 3795

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
118 119 0.598158 TTAAGCGCCTCGAACACGTT 60.598 50.0 2.29 0.0 0.0 3.99 F
604 649 0.753262 CGAATCCCCTGAGATCCGTT 59.247 55.0 0.00 0.0 0.0 4.44 F
1326 1428 0.965866 TCGTCATCAGGAAGGCTCGT 60.966 55.0 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2131 1.452399 GTCGTCACGCTTCTTCTCAAC 59.548 52.381 0.00 0.0 0.0 3.18 R
2204 2351 1.332195 CGGACATGGAGCAGAGGATA 58.668 55.000 0.00 0.0 0.0 2.59 R
3281 5819 0.385473 CGCAACAATGACCGGACAAC 60.385 55.000 9.46 0.0 0.0 3.32 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
24 25 2.436646 AGTTCCTTGCGCATCCCG 60.437 61.111 12.75 0.00 40.75 5.14
43 44 3.480133 CCATCCCAGTCCCCGGAC 61.480 72.222 0.73 5.70 44.86 4.79
70 71 0.760567 TGATGCCTCCATAGTCGGCT 60.761 55.000 0.00 0.00 44.09 5.52
96 97 1.685224 GTCAACTCCTCCATGGGCA 59.315 57.895 13.02 0.00 36.20 5.36
118 119 0.598158 TTAAGCGCCTCGAACACGTT 60.598 50.000 2.29 0.00 0.00 3.99
334 335 9.236006 CCAAAAATTACTCCCATATCCATAGAG 57.764 37.037 0.00 0.00 0.00 2.43
339 340 3.181402 ACTCCCATATCCATAGAGCACCT 60.181 47.826 0.00 0.00 0.00 4.00
340 341 4.045974 ACTCCCATATCCATAGAGCACCTA 59.954 45.833 0.00 0.00 0.00 3.08
341 342 4.614475 TCCCATATCCATAGAGCACCTAG 58.386 47.826 0.00 0.00 0.00 3.02
404 405 1.729470 CGTCATCGTCCCTCCCTCAG 61.729 65.000 0.00 0.00 0.00 3.35
426 428 3.064931 CGGAGACAGGTAAACCTTGTTC 58.935 50.000 0.00 0.00 46.09 3.18
438 440 7.039853 AGGTAAACCTTGTTCTAGTAGACAGTC 60.040 40.741 0.00 0.00 46.09 3.51
501 503 4.816385 AGAACAACAACTGTCGTCAATGAT 59.184 37.500 0.00 0.00 37.23 2.45
604 649 0.753262 CGAATCCCCTGAGATCCGTT 59.247 55.000 0.00 0.00 0.00 4.44
786 832 3.502920 AGTCTTGATCATGTCGTTCGTC 58.497 45.455 8.33 0.00 0.00 4.20
1326 1428 0.965866 TCGTCATCAGGAAGGCTCGT 60.966 55.000 0.00 0.00 0.00 4.18
2023 2131 1.278172 CGAGATAATGGCCGAGCACG 61.278 60.000 0.00 0.00 39.43 5.34
2055 2175 4.415332 GACGACGGCGCAGAGGAA 62.415 66.667 12.58 0.00 42.48 3.36
2220 2368 2.441001 CCCTTTATCCTCTGCTCCATGT 59.559 50.000 0.00 0.00 0.00 3.21
2534 2690 1.805539 CGGCGCTCTTCATCAACGA 60.806 57.895 7.64 0.00 0.00 3.85
3042 5562 7.088589 GATTTCAATCCTCGAAATTCCTTGA 57.911 36.000 0.00 0.00 41.87 3.02
3043 5563 5.880054 TTCAATCCTCGAAATTCCTTGAC 57.120 39.130 0.00 0.00 0.00 3.18
3044 5564 4.905429 TCAATCCTCGAAATTCCTTGACA 58.095 39.130 0.00 0.00 0.00 3.58
3046 5566 5.412594 TCAATCCTCGAAATTCCTTGACAAG 59.587 40.000 8.31 8.31 0.00 3.16
3051 5589 5.239525 CCTCGAAATTCCTTGACAAGAACTT 59.760 40.000 16.99 5.45 0.00 2.66
3081 5619 2.514458 TGAGAAGAATTGCCCCTTCC 57.486 50.000 0.00 0.00 39.54 3.46
3100 5638 5.339200 CCTTCCTCCTAATTTGAGTAGCCAA 60.339 44.000 4.55 0.00 0.00 4.52
3101 5639 5.772393 TCCTCCTAATTTGAGTAGCCAAA 57.228 39.130 0.00 0.00 39.93 3.28
3124 5662 7.565323 AAGCTCATTCTCATTACAAGATTCC 57.435 36.000 0.00 0.00 0.00 3.01
3125 5663 6.060788 AGCTCATTCTCATTACAAGATTCCC 58.939 40.000 0.00 0.00 0.00 3.97
3126 5664 6.060788 GCTCATTCTCATTACAAGATTCCCT 58.939 40.000 0.00 0.00 0.00 4.20
3127 5665 6.204495 GCTCATTCTCATTACAAGATTCCCTC 59.796 42.308 0.00 0.00 0.00 4.30
3128 5666 6.595682 TCATTCTCATTACAAGATTCCCTCC 58.404 40.000 0.00 0.00 0.00 4.30
3129 5667 6.388100 TCATTCTCATTACAAGATTCCCTCCT 59.612 38.462 0.00 0.00 0.00 3.69
3130 5668 5.878406 TCTCATTACAAGATTCCCTCCTC 57.122 43.478 0.00 0.00 0.00 3.71
3136 5674 3.173965 ACAAGATTCCCTCCTCGAGAAA 58.826 45.455 15.71 0.04 0.00 2.52
3160 5698 3.039202 GCGCCTCATGTTGGTTCCG 62.039 63.158 0.00 5.82 0.00 4.30
3211 5749 2.968156 CCCGACCGTTGACGCAAA 60.968 61.111 0.00 0.00 38.18 3.68
3212 5750 2.535788 CCCGACCGTTGACGCAAAA 61.536 57.895 0.00 0.00 38.18 2.44
3215 5753 1.009335 GACCGTTGACGCAAAACCC 60.009 57.895 0.00 0.00 38.18 4.11
3226 5764 3.370231 AAAACCCCATCGCCACGC 61.370 61.111 0.00 0.00 0.00 5.34
3249 5787 1.846124 ATCACGGTTCCACCCCACT 60.846 57.895 0.00 0.00 33.75 4.00
3252 5790 0.326927 CACGGTTCCACCCCACTAAT 59.673 55.000 0.00 0.00 33.75 1.73
3253 5791 1.555992 CACGGTTCCACCCCACTAATA 59.444 52.381 0.00 0.00 33.75 0.98
3256 5794 2.704065 CGGTTCCACCCCACTAATATCT 59.296 50.000 0.00 0.00 33.75 1.98
3258 5796 3.714798 GGTTCCACCCCACTAATATCTGA 59.285 47.826 0.00 0.00 30.04 3.27
3271 5809 9.922305 CCACTAATATCTGACGAAATTTTTCTC 57.078 33.333 0.00 0.29 35.07 2.87
3279 5817 7.940850 TCTGACGAAATTTTTCTCCAATTTCT 58.059 30.769 13.49 4.25 43.82 2.52
3281 5819 6.855914 TGACGAAATTTTTCTCCAATTTCTCG 59.144 34.615 13.49 7.06 43.82 4.04
3282 5820 6.735130 ACGAAATTTTTCTCCAATTTCTCGT 58.265 32.000 13.49 7.55 43.82 4.18
3283 5821 7.200455 ACGAAATTTTTCTCCAATTTCTCGTT 58.800 30.769 13.49 0.00 43.82 3.85
3284 5822 7.167468 ACGAAATTTTTCTCCAATTTCTCGTTG 59.833 33.333 13.49 3.77 43.82 4.10
3306 5844 1.577328 CGGTCATTGTTGCGCTCCTT 61.577 55.000 9.73 0.00 0.00 3.36
3317 5855 2.125633 GCTCCTTCCCGTCGTTCC 60.126 66.667 0.00 0.00 0.00 3.62
3318 5856 2.577593 CTCCTTCCCGTCGTTCCC 59.422 66.667 0.00 0.00 0.00 3.97
3321 5859 3.688159 CTTCCCGTCGTTCCCGGT 61.688 66.667 0.00 0.00 43.98 5.28
3325 5863 3.980989 CCGTCGTTCCCGGTCACA 61.981 66.667 0.00 0.00 40.59 3.58
3366 5904 2.202932 CGACCATGGGCGGAGAAG 60.203 66.667 33.24 2.09 0.00 2.85
3367 5905 2.721167 CGACCATGGGCGGAGAAGA 61.721 63.158 33.24 0.00 0.00 2.87
3401 5939 3.859443 ACAACACGTACACAACAACCTA 58.141 40.909 0.00 0.00 0.00 3.08
3425 5963 3.067106 CAAAGCGACCTAGAGAAAAGCA 58.933 45.455 0.00 0.00 0.00 3.91
3453 5991 4.357918 AAGGAGCACTTACATGACAACT 57.642 40.909 0.00 0.00 37.74 3.16
3454 5992 5.483685 AAGGAGCACTTACATGACAACTA 57.516 39.130 0.00 0.00 37.74 2.24
3458 5996 4.836825 AGCACTTACATGACAACTAGCAT 58.163 39.130 0.00 0.00 0.00 3.79
3460 5998 4.259970 GCACTTACATGACAACTAGCATCG 60.260 45.833 0.00 0.00 0.00 3.84
3478 6016 0.368907 CGTCGCCGATTTCAACGAAT 59.631 50.000 0.00 0.00 36.14 3.34
3497 6035 3.343421 GTGTGTTCCGGACCACGC 61.343 66.667 26.80 26.80 42.52 5.34
3514 6052 1.204704 ACGCCATCGAGTCAAATGAGA 59.795 47.619 4.46 0.00 39.41 3.27
3538 6076 3.364964 CGAAAAGGGGAAGAACACATTCG 60.365 47.826 0.00 0.00 40.04 3.34
3600 6138 2.857483 TCGCCAAATTTCTGAACTCCA 58.143 42.857 0.00 0.00 0.00 3.86
3606 6160 4.161333 CAAATTTCTGAACTCCATCACGC 58.839 43.478 0.00 0.00 0.00 5.34
3608 6162 2.839486 TTCTGAACTCCATCACGCTT 57.161 45.000 0.00 0.00 0.00 4.68
3629 6183 6.868430 GCTTACAGAGCGTCTATCAAATTAC 58.132 40.000 0.00 0.00 42.46 1.89
3635 6189 6.684555 CAGAGCGTCTATCAAATTACTTTTGC 59.315 38.462 0.00 0.00 43.68 3.68
3662 6217 1.359474 TCCATCCTAGGCCCTAGCTAG 59.641 57.143 12.62 14.20 39.73 3.42
3664 6219 0.787084 ATCCTAGGCCCTAGCTAGCA 59.213 55.000 18.83 1.89 39.73 3.49
3666 6221 1.188871 CCTAGGCCCTAGCTAGCACC 61.189 65.000 18.83 17.15 39.73 5.01
3692 6247 3.251245 ACATCATCTACGCCTAGAAGTCG 59.749 47.826 0.00 0.00 32.49 4.18
3702 6257 1.336517 CCTAGAAGTCGTTGTTCGCCA 60.337 52.381 0.00 0.00 39.67 5.69
3708 6263 1.227704 TCGTTGTTCGCCATGTGGT 60.228 52.632 0.35 0.00 39.67 4.16
3712 6267 2.673862 CGTTGTTCGCCATGTGGTAATA 59.326 45.455 0.35 0.00 37.57 0.98
3713 6268 3.125487 CGTTGTTCGCCATGTGGTAATAA 59.875 43.478 0.35 0.00 37.57 1.40
3714 6269 4.658071 GTTGTTCGCCATGTGGTAATAAG 58.342 43.478 0.35 0.00 37.57 1.73
3720 6275 4.873827 TCGCCATGTGGTAATAAGAAGAAC 59.126 41.667 0.35 0.00 37.57 3.01
3727 6282 7.884816 TGTGGTAATAAGAAGAACGAAGAAG 57.115 36.000 0.00 0.00 0.00 2.85
3736 6291 9.810545 ATAAGAAGAACGAAGAAGGAATAAGAG 57.189 33.333 0.00 0.00 0.00 2.85
3739 6294 4.162509 AGAACGAAGAAGGAATAAGAGGGG 59.837 45.833 0.00 0.00 0.00 4.79
3766 6321 4.020128 AGACTTCATGTGGGGTCTAGTTTC 60.020 45.833 9.50 0.00 37.29 2.78
3768 6323 4.020128 ACTTCATGTGGGGTCTAGTTTCTC 60.020 45.833 0.00 0.00 0.00 2.87
3770 6325 4.942944 TCATGTGGGGTCTAGTTTCTCTA 58.057 43.478 0.00 0.00 0.00 2.43
3772 6327 5.422331 TCATGTGGGGTCTAGTTTCTCTAAG 59.578 44.000 0.00 0.00 0.00 2.18
3777 6332 4.646040 GGGGTCTAGTTTCTCTAAGGAGTC 59.354 50.000 0.00 0.00 40.29 3.36
3791 6346 3.953542 AGGAGTCAAGTTTGAGGGTTT 57.046 42.857 0.00 0.00 37.98 3.27
3796 6351 3.699538 AGTCAAGTTTGAGGGTTTGGTTC 59.300 43.478 0.00 0.00 37.98 3.62
3797 6352 3.028130 TCAAGTTTGAGGGTTTGGTTCC 58.972 45.455 0.00 0.00 32.50 3.62
3798 6353 2.763448 CAAGTTTGAGGGTTTGGTTCCA 59.237 45.455 0.00 0.00 0.00 3.53
3799 6354 2.384828 AGTTTGAGGGTTTGGTTCCAC 58.615 47.619 0.00 0.00 0.00 4.02
3800 6355 1.411246 GTTTGAGGGTTTGGTTCCACC 59.589 52.381 0.00 0.00 39.22 4.61
3801 6356 0.930726 TTGAGGGTTTGGTTCCACCT 59.069 50.000 0.02 0.02 39.58 4.00
3802 6357 0.184933 TGAGGGTTTGGTTCCACCTG 59.815 55.000 4.54 0.00 39.58 4.00
3803 6358 0.476771 GAGGGTTTGGTTCCACCTGA 59.523 55.000 4.54 0.00 39.58 3.86
3804 6359 0.930726 AGGGTTTGGTTCCACCTGAA 59.069 50.000 0.00 0.00 39.58 3.02
3805 6360 1.133482 AGGGTTTGGTTCCACCTGAAG 60.133 52.381 0.00 0.00 39.58 3.02
3809 6364 3.655481 GGTTCCACCTGAAGCGTG 58.345 61.111 0.00 0.00 41.23 5.34
3813 6368 4.157607 CCACCTGAAGCGTGGTTT 57.842 55.556 8.85 0.00 44.87 3.27
3814 6369 3.315765 CCACCTGAAGCGTGGTTTA 57.684 52.632 8.85 0.00 44.87 2.01
3815 6370 1.156736 CCACCTGAAGCGTGGTTTAG 58.843 55.000 8.85 0.00 44.87 1.85
3816 6371 1.156736 CACCTGAAGCGTGGTTTAGG 58.843 55.000 17.85 17.85 38.79 2.69
3817 6372 0.036306 ACCTGAAGCGTGGTTTAGGG 59.964 55.000 21.78 10.72 37.48 3.53
3818 6373 0.323629 CCTGAAGCGTGGTTTAGGGA 59.676 55.000 13.17 0.00 31.04 4.20
3819 6374 1.439679 CTGAAGCGTGGTTTAGGGAC 58.560 55.000 0.00 0.00 0.00 4.46
3820 6375 0.759959 TGAAGCGTGGTTTAGGGACA 59.240 50.000 0.00 0.00 0.00 4.02
3821 6376 1.154197 GAAGCGTGGTTTAGGGACAC 58.846 55.000 0.00 0.00 0.00 3.67
3822 6377 0.250597 AAGCGTGGTTTAGGGACACC 60.251 55.000 0.00 0.00 0.00 4.16
3823 6378 1.673337 GCGTGGTTTAGGGACACCC 60.673 63.158 0.00 0.00 45.90 4.61
3836 6391 4.770874 CACCCGGGCCGAACGAAT 62.771 66.667 30.79 2.29 0.00 3.34
3837 6392 4.462280 ACCCGGGCCGAACGAATC 62.462 66.667 30.79 0.00 0.00 2.52
3851 6406 3.357504 GAATCGTTCGGTACTGGGG 57.642 57.895 0.85 0.00 0.00 4.96
3852 6407 0.179092 GAATCGTTCGGTACTGGGGG 60.179 60.000 0.85 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.811616 GGCATCAGTAGCAAGTCCGG 60.812 60.000 0.00 0.00 0.00 5.14
40 41 1.474143 GGAGGCATCAGTAGCAAGTCC 60.474 57.143 0.00 0.00 0.00 3.85
43 44 2.634815 ATGGAGGCATCAGTAGCAAG 57.365 50.000 0.00 0.00 0.00 4.01
70 71 0.991920 GGAGGAGTTGACCCATGGAA 59.008 55.000 15.22 0.00 0.00 3.53
96 97 1.014564 GTGTTCGAGGCGCTTAAGCT 61.015 55.000 24.33 6.65 39.32 3.74
118 119 0.390124 GGTGGTGACGGTGTCTAACA 59.610 55.000 0.00 0.00 33.15 2.41
319 320 3.567375 AGGTGCTCTATGGATATGGGA 57.433 47.619 0.00 0.00 0.00 4.37
426 428 5.501092 CGACAATGTCTCGACTGTCTACTAG 60.501 48.000 11.92 0.00 32.65 2.57
438 440 1.321743 GCTTAGCACGACAATGTCTCG 59.678 52.381 11.92 2.26 37.17 4.04
501 503 3.014623 TCCTTCTTATCGACGCTTCTCA 58.985 45.455 0.00 0.00 0.00 3.27
604 649 6.039415 ACTTCCCTCCTATATACAACTCCA 57.961 41.667 0.00 0.00 0.00 3.86
762 808 5.651530 ACGAACGACATGATCAAGACTATT 58.348 37.500 4.68 0.00 0.00 1.73
763 809 5.250235 ACGAACGACATGATCAAGACTAT 57.750 39.130 4.68 0.00 0.00 2.12
1524 1632 1.978542 CGAGGTCGTGGTTCTTGTAG 58.021 55.000 0.00 0.00 34.11 2.74
1929 2037 1.483415 GTCGCCCACCTAACCATCTTA 59.517 52.381 0.00 0.00 0.00 2.10
2023 2131 1.452399 GTCGTCACGCTTCTTCTCAAC 59.548 52.381 0.00 0.00 0.00 3.18
2204 2351 1.332195 CGGACATGGAGCAGAGGATA 58.668 55.000 0.00 0.00 0.00 2.59
2220 2368 3.055458 TGTCCTGCATATCAAGAAACGGA 60.055 43.478 0.00 0.00 0.00 4.69
2534 2690 2.343475 ATCCCTCGCGATTGCCCAAT 62.343 55.000 10.36 0.00 38.08 3.16
2866 3027 2.489751 GTGGCACCGCTAAATGGC 59.510 61.111 6.29 0.00 41.57 4.40
2867 3028 2.760159 CCGTGGCACCGCTAAATGG 61.760 63.158 12.86 0.37 0.00 3.16
3025 5545 5.165961 TCTTGTCAAGGAATTTCGAGGAT 57.834 39.130 12.66 0.00 0.00 3.24
3081 5619 5.491635 GCTTTGGCTACTCAAATTAGGAG 57.508 43.478 5.70 5.70 36.24 3.69
3100 5638 6.545298 GGGAATCTTGTAATGAGAATGAGCTT 59.455 38.462 0.00 0.00 0.00 3.74
3101 5639 6.060788 GGGAATCTTGTAATGAGAATGAGCT 58.939 40.000 0.00 0.00 0.00 4.09
3124 5662 2.184579 GGGCGTTTCTCGAGGAGG 59.815 66.667 13.56 8.63 42.86 4.30
3125 5663 2.202623 CGGGCGTTTCTCGAGGAG 60.203 66.667 13.56 2.90 42.86 3.69
3126 5664 4.430765 GCGGGCGTTTCTCGAGGA 62.431 66.667 13.56 0.00 42.86 3.71
3188 5726 3.998672 TCAACGGTCGGGGCACTC 61.999 66.667 0.00 0.00 0.00 3.51
3196 5734 1.368374 GGTTTTGCGTCAACGGTCG 60.368 57.895 4.54 0.00 40.23 4.79
3252 5790 9.840427 GAAATTGGAGAAAAATTTCGTCAGATA 57.160 29.630 6.02 0.00 41.56 1.98
3253 5791 8.748380 GAAATTGGAGAAAAATTTCGTCAGAT 57.252 30.769 6.02 0.00 41.56 2.90
3281 5819 0.385473 CGCAACAATGACCGGACAAC 60.385 55.000 9.46 0.00 0.00 3.32
3282 5820 1.945522 CGCAACAATGACCGGACAA 59.054 52.632 9.46 0.00 0.00 3.18
3283 5821 2.612567 GCGCAACAATGACCGGACA 61.613 57.895 9.46 9.50 0.00 4.02
3284 5822 2.175811 GCGCAACAATGACCGGAC 59.824 61.111 9.46 1.07 0.00 4.79
3321 5859 3.695606 GGAGGAGCGTGGCTGTGA 61.696 66.667 0.00 0.00 39.88 3.58
3363 5901 4.862574 GTGTTGTTGTGGGTCTTTTTCTTC 59.137 41.667 0.00 0.00 0.00 2.87
3364 5902 4.617298 CGTGTTGTTGTGGGTCTTTTTCTT 60.617 41.667 0.00 0.00 0.00 2.52
3366 5904 3.175929 CGTGTTGTTGTGGGTCTTTTTC 58.824 45.455 0.00 0.00 0.00 2.29
3367 5905 2.559231 ACGTGTTGTTGTGGGTCTTTTT 59.441 40.909 0.00 0.00 0.00 1.94
3401 5939 3.746045 TTTCTCTAGGTCGCTTTGTGT 57.254 42.857 0.00 0.00 0.00 3.72
3425 5963 6.109359 GTCATGTAAGTGCTCCTTTGTAGAT 58.891 40.000 0.00 0.00 34.46 1.98
3460 5998 2.072990 GATTCGTTGAAATCGGCGAC 57.927 50.000 13.76 0.00 32.89 5.19
3473 6011 0.665369 GTCCGGAACACACGATTCGT 60.665 55.000 5.23 5.75 42.36 3.85
3474 6012 1.349259 GGTCCGGAACACACGATTCG 61.349 60.000 16.61 4.14 0.00 3.34
3497 6035 3.511699 TCGTTCTCATTTGACTCGATGG 58.488 45.455 0.00 0.00 0.00 3.51
3514 6052 3.007473 TGTGTTCTTCCCCTTTTCGTT 57.993 42.857 0.00 0.00 0.00 3.85
3538 6076 5.397240 CGACGTTTTGGGTAATTCTTTGTTC 59.603 40.000 0.00 0.00 0.00 3.18
3585 6123 4.074970 AGCGTGATGGAGTTCAGAAATTT 58.925 39.130 0.00 0.00 0.00 1.82
3587 6125 3.340814 AGCGTGATGGAGTTCAGAAAT 57.659 42.857 0.00 0.00 0.00 2.17
3593 6131 3.182967 CTCTGTAAGCGTGATGGAGTTC 58.817 50.000 0.00 0.00 0.00 3.01
3606 6160 8.635877 AAGTAATTTGATAGACGCTCTGTAAG 57.364 34.615 0.00 0.00 0.00 2.34
3608 6162 8.997621 AAAAGTAATTTGATAGACGCTCTGTA 57.002 30.769 0.00 0.00 0.00 2.74
3629 6183 2.731572 AGGATGGATGACCTGCAAAAG 58.268 47.619 0.00 0.00 34.99 2.27
3635 6189 0.689623 GGCCTAGGATGGATGACCTG 59.310 60.000 14.75 0.00 37.68 4.00
3662 6217 1.858091 CGTAGATGATGTCCAGGTGC 58.142 55.000 0.00 0.00 0.00 5.01
3664 6219 0.753262 GGCGTAGATGATGTCCAGGT 59.247 55.000 0.00 0.00 0.00 4.00
3666 6221 3.149981 TCTAGGCGTAGATGATGTCCAG 58.850 50.000 12.02 0.00 29.69 3.86
3692 6247 4.393680 TCTTATTACCACATGGCGAACAAC 59.606 41.667 0.00 0.00 39.32 3.32
3702 6257 7.549488 CCTTCTTCGTTCTTCTTATTACCACAT 59.451 37.037 0.00 0.00 0.00 3.21
3712 6267 7.100409 CCTCTTATTCCTTCTTCGTTCTTCTT 58.900 38.462 0.00 0.00 0.00 2.52
3713 6268 6.351456 CCCTCTTATTCCTTCTTCGTTCTTCT 60.351 42.308 0.00 0.00 0.00 2.85
3714 6269 5.813157 CCCTCTTATTCCTTCTTCGTTCTTC 59.187 44.000 0.00 0.00 0.00 2.87
3720 6275 3.039011 TCCCCCTCTTATTCCTTCTTCG 58.961 50.000 0.00 0.00 0.00 3.79
3727 6282 3.338110 AGTCTCTCCCCCTCTTATTCC 57.662 52.381 0.00 0.00 0.00 3.01
3736 6291 0.543749 CCACATGAAGTCTCTCCCCC 59.456 60.000 0.00 0.00 0.00 5.40
3739 6294 1.208293 GACCCCACATGAAGTCTCTCC 59.792 57.143 0.00 0.00 0.00 3.71
3766 6321 4.284746 ACCCTCAAACTTGACTCCTTAGAG 59.715 45.833 0.00 0.00 46.36 2.43
3768 6323 4.625607 ACCCTCAAACTTGACTCCTTAG 57.374 45.455 0.00 0.00 32.90 2.18
3770 6325 3.953542 AACCCTCAAACTTGACTCCTT 57.046 42.857 0.00 0.00 32.90 3.36
3772 6327 2.623416 CCAAACCCTCAAACTTGACTCC 59.377 50.000 0.00 0.00 32.90 3.85
3777 6332 2.763448 TGGAACCAAACCCTCAAACTTG 59.237 45.455 0.00 0.00 0.00 3.16
3797 6352 1.156736 CCTAAACCACGCTTCAGGTG 58.843 55.000 0.00 0.00 38.37 4.00
3798 6353 0.036306 CCCTAAACCACGCTTCAGGT 59.964 55.000 0.00 0.00 40.61 4.00
3799 6354 0.323629 TCCCTAAACCACGCTTCAGG 59.676 55.000 0.00 0.00 0.00 3.86
3800 6355 1.270625 TGTCCCTAAACCACGCTTCAG 60.271 52.381 0.00 0.00 0.00 3.02
3801 6356 0.759959 TGTCCCTAAACCACGCTTCA 59.240 50.000 0.00 0.00 0.00 3.02
3802 6357 1.154197 GTGTCCCTAAACCACGCTTC 58.846 55.000 0.00 0.00 0.00 3.86
3803 6358 0.250597 GGTGTCCCTAAACCACGCTT 60.251 55.000 0.00 0.00 36.41 4.68
3804 6359 1.373812 GGTGTCCCTAAACCACGCT 59.626 57.895 0.00 0.00 36.41 5.07
3805 6360 1.673337 GGGTGTCCCTAAACCACGC 60.673 63.158 0.00 0.00 41.34 5.34
3806 6361 1.375013 CGGGTGTCCCTAAACCACG 60.375 63.158 3.25 0.00 42.67 4.94
3807 6362 1.002990 CCGGGTGTCCCTAAACCAC 60.003 63.158 0.00 0.00 42.67 4.16
3808 6363 2.225596 CCCGGGTGTCCCTAAACCA 61.226 63.158 14.18 0.00 42.67 3.67
3809 6364 2.672908 CCCGGGTGTCCCTAAACC 59.327 66.667 14.18 0.00 42.67 3.27
3810 6365 2.045634 GCCCGGGTGTCCCTAAAC 60.046 66.667 24.63 0.00 42.67 2.01
3811 6366 3.332385 GGCCCGGGTGTCCCTAAA 61.332 66.667 24.63 0.00 42.67 1.85
3819 6374 4.770874 ATTCGTTCGGCCCGGGTG 62.771 66.667 24.63 15.79 0.00 4.61
3820 6375 4.462280 GATTCGTTCGGCCCGGGT 62.462 66.667 24.63 0.00 0.00 5.28
3833 6388 0.179092 CCCCCAGTACCGAACGATTC 60.179 60.000 0.00 0.00 0.00 2.52
3834 6389 1.902556 CCCCCAGTACCGAACGATT 59.097 57.895 0.00 0.00 0.00 3.34
3835 6390 3.625099 CCCCCAGTACCGAACGAT 58.375 61.111 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.