Multiple sequence alignment - TraesCS7A01G448900

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 TraesCS7A01G448900 chr7A 100.000 3806 0 0 1 3806 643074781 643078586 0.000000e+00 7029
1 TraesCS7A01G448900 chr7D 92.174 3169 128 49 5 3108 557573801 557576914 0.000000e+00 4368
2 TraesCS7A01G448900 chr7D 83.146 712 50 25 3124 3806 557577053 557577723 1.520000e-163 586
3 TraesCS7A01G448900 chr7B 92.633 2484 109 30 649 3107 605643564 605645998 0.000000e+00 3506
4 TraesCS7A01G448900 chr7B 86.910 657 39 18 7 641 605642513 605643144 0.000000e+00 693
5 TraesCS7A01G448900 chr7B 85.366 328 34 10 3434 3755 605646639 605646958 1.020000e-85 327
6 TraesCS7A01G448900 chr7B 89.744 156 10 3 3127 3281 605646154 605646304 1.080000e-45 195
7 TraesCS7A01G448900 chr3B 93.248 622 23 10 2490 3108 607414697 607414092 0.000000e+00 898
8 TraesCS7A01G448900 chr5D 86.364 242 18 6 2785 3020 168233719 168233487 2.270000e-62 250
9 TraesCS7A01G448900 chr5D 83.824 136 11 7 3303 3430 168233365 168233233 6.680000e-23 119
10 TraesCS7A01G448900 chr3D 87.952 83 10 0 1602 1684 479117462 479117380 8.700000e-17 99
11 TraesCS7A01G448900 chr2A 86.022 93 12 1 1593 1684 712968527 712968619 8.700000e-17 99


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 TraesCS7A01G448900 chr7A 643074781 643078586 3805 False 7029.00 7029 100.00000 1 3806 1 chr7A.!!$F1 3805
1 TraesCS7A01G448900 chr7D 557573801 557577723 3922 False 2477.00 4368 87.66000 5 3806 2 chr7D.!!$F1 3801
2 TraesCS7A01G448900 chr7B 605642513 605646958 4445 False 1180.25 3506 88.66325 7 3755 4 chr7B.!!$F1 3748
3 TraesCS7A01G448900 chr3B 607414092 607414697 605 True 898.00 898 93.24800 2490 3108 1 chr3B.!!$R1 618

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
196 214 0.179084 GCAGCTTCCATGCATGCATT 60.179 50.0 30.32 12.5 43.31 3.56 F
258 276 0.179108 CGGGAGGAGGAAGCGTAAAG 60.179 60.0 0.00 0.0 0.00 1.85 F
411 430 0.231534 CGCATGCACGATGATCTCAC 59.768 55.0 19.57 0.0 33.31 3.51 F
2161 2644 0.250234 CGTGAGGGAAGAAGCCATCA 59.750 55.0 0.00 0.0 45.54 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1572 1.587933 AAGACGACGCCAGAGTCTCC 61.588 60.0 0.00 0.0 43.60 3.71 R
2244 2727 0.034670 AGCAGAAGAACCAGATGGCC 60.035 55.0 0.00 0.0 39.32 5.36 R
2355 2838 1.086634 GGATCTTGAGCGTGCAGTCC 61.087 60.0 0.00 0.0 0.00 3.85 R
3783 4634 0.111832 ATGCAGGCCATTCATCGGAT 59.888 50.0 5.01 0.0 0.00 4.18 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
20 21 3.357079 GCCTCGGCACACAACCAG 61.357 66.667 2.41 0.00 41.49 4.00
21 22 3.357079 CCTCGGCACACAACCAGC 61.357 66.667 0.00 0.00 0.00 4.85
22 23 2.281070 CTCGGCACACAACCAGCT 60.281 61.111 0.00 0.00 0.00 4.24
23 24 1.005037 CTCGGCACACAACCAGCTA 60.005 57.895 0.00 0.00 0.00 3.32
25 26 0.882927 TCGGCACACAACCAGCTAAC 60.883 55.000 0.00 0.00 0.00 2.34
26 27 1.163420 CGGCACACAACCAGCTAACA 61.163 55.000 0.00 0.00 0.00 2.41
28 29 1.613437 GGCACACAACCAGCTAACAAT 59.387 47.619 0.00 0.00 0.00 2.71
29 30 2.817258 GGCACACAACCAGCTAACAATA 59.183 45.455 0.00 0.00 0.00 1.90
40 41 4.800993 CCAGCTAACAATAGAACAGACGAG 59.199 45.833 0.00 0.00 0.00 4.18
65 71 0.747255 GATCAGAGCAGGGCGAGTTA 59.253 55.000 0.00 0.00 0.00 2.24
118 136 4.464951 ACCTTCACACAAGTATCATACGGA 59.535 41.667 0.00 0.00 0.00 4.69
137 155 1.218316 CCTACGGCTGAGGTTGGTC 59.782 63.158 0.00 0.00 0.00 4.02
192 210 0.179137 CACAGCAGCTTCCATGCATG 60.179 55.000 20.19 20.19 46.31 4.06
194 212 1.680989 AGCAGCTTCCATGCATGCA 60.681 52.632 25.04 25.04 46.31 3.96
195 213 1.043116 AGCAGCTTCCATGCATGCAT 61.043 50.000 27.46 27.46 46.31 3.96
196 214 0.179084 GCAGCTTCCATGCATGCATT 60.179 50.000 30.32 12.50 43.31 3.56
208 226 2.760799 TGCATTGCATCCCCAGCC 60.761 61.111 7.38 0.00 31.71 4.85
209 227 2.760799 GCATTGCATCCCCAGCCA 60.761 61.111 3.15 0.00 0.00 4.75
242 260 4.637483 TCGTGGAGTACTTAATAACGGG 57.363 45.455 0.00 0.00 0.00 5.28
258 276 0.179108 CGGGAGGAGGAAGCGTAAAG 60.179 60.000 0.00 0.00 0.00 1.85
304 322 2.367567 TCAGGGAAAGGTACACACACTC 59.632 50.000 0.00 0.00 0.00 3.51
305 323 1.343465 AGGGAAAGGTACACACACTCG 59.657 52.381 0.00 0.00 0.00 4.18
306 324 1.342174 GGGAAAGGTACACACACTCGA 59.658 52.381 0.00 0.00 0.00 4.04
333 351 1.588239 TGCCCTCACAGATCCTGAAT 58.412 50.000 0.45 0.00 35.18 2.57
411 430 0.231534 CGCATGCACGATGATCTCAC 59.768 55.000 19.57 0.00 33.31 3.51
412 431 1.579698 GCATGCACGATGATCTCACT 58.420 50.000 14.21 0.00 33.31 3.41
413 432 1.526041 GCATGCACGATGATCTCACTC 59.474 52.381 14.21 0.00 33.31 3.51
414 433 2.802415 GCATGCACGATGATCTCACTCT 60.802 50.000 14.21 0.00 33.31 3.24
415 434 2.859526 TGCACGATGATCTCACTCTC 57.140 50.000 0.00 0.00 0.00 3.20
416 435 2.094675 TGCACGATGATCTCACTCTCA 58.905 47.619 0.00 0.00 0.00 3.27
427 446 4.397481 TCTCACTCTCAGGCATATGTTG 57.603 45.455 4.29 3.96 0.00 3.33
432 451 3.181467 ACTCTCAGGCATATGTTGAGCTC 60.181 47.826 23.53 6.82 38.52 4.09
434 453 1.141657 TCAGGCATATGTTGAGCTCCC 59.858 52.381 12.15 1.97 0.00 4.30
437 456 1.602311 GCATATGTTGAGCTCCCCTG 58.398 55.000 12.15 1.61 0.00 4.45
438 457 1.141657 GCATATGTTGAGCTCCCCTGA 59.858 52.381 12.15 0.00 0.00 3.86
440 459 3.672808 CATATGTTGAGCTCCCCTGATC 58.327 50.000 12.15 0.00 0.00 2.92
442 461 0.615331 TGTTGAGCTCCCCTGATCAC 59.385 55.000 12.15 0.00 31.72 3.06
470 489 1.000896 CCCACCCAACCCACTGATC 60.001 63.158 0.00 0.00 0.00 2.92
559 579 6.029346 ACCAAATGAGATTGTTGGCTTAAG 57.971 37.500 0.00 0.00 44.75 1.85
574 608 4.220382 TGGCTTAAGAAATGATGTTGTGGG 59.780 41.667 6.67 0.00 0.00 4.61
656 1108 2.234296 AAGTTGGGGCAGGAGGAGG 61.234 63.158 0.00 0.00 0.00 4.30
850 1321 5.128827 TCCATTAATAGTTGAAGCTCTCCGT 59.871 40.000 0.00 0.00 0.00 4.69
865 1336 1.077212 CCGTCGAGTTCCCTCCCTA 60.077 63.158 0.00 0.00 33.93 3.53
973 1447 3.009115 TACAGGGCTGGGGAGTGC 61.009 66.667 0.00 0.00 34.19 4.40
1026 1500 0.530211 CAGAGATGGGAGAAGCAGCG 60.530 60.000 0.00 0.00 0.00 5.18
1045 1519 2.274645 CCGGCAGCAATGGTGGAAA 61.275 57.895 14.61 0.00 0.00 3.13
1050 1524 1.340889 GCAGCAATGGTGGAAACAGAA 59.659 47.619 14.61 0.00 44.46 3.02
1179 1653 2.383527 CGTCAAGGACAAGCTCCGC 61.384 63.158 0.00 0.00 45.10 5.54
1210 1684 4.748679 GCCTCAGTTTGCTGCGCG 62.749 66.667 0.00 0.00 42.29 6.86
1242 1716 2.835895 GGCGAGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1246 1720 1.916738 GAGGAGGAGGAGGACGAGA 59.083 63.158 0.00 0.00 0.00 4.04
1254 1734 1.758906 GGAGGACGAGAAGGGGGAG 60.759 68.421 0.00 0.00 0.00 4.30
1258 1738 0.691413 GGACGAGAAGGGGGAGGAAT 60.691 60.000 0.00 0.00 0.00 3.01
1271 1754 2.107204 GGGAGGAATATCATGTGCTGGT 59.893 50.000 0.00 0.00 0.00 4.00
1393 1876 3.315142 GACATGGACGGCCTGAGCA 62.315 63.158 9.82 0.00 42.56 4.26
1989 2472 3.764466 AGCTCCTCCTTCGCCGTG 61.764 66.667 0.00 0.00 0.00 4.94
2154 2637 2.654877 GCCGACGTGAGGGAAGAA 59.345 61.111 0.00 0.00 0.00 2.52
2161 2644 0.250234 CGTGAGGGAAGAAGCCATCA 59.750 55.000 0.00 0.00 45.54 3.07
2292 2775 1.357334 GAGCTCCATCGACGACCTC 59.643 63.158 0.87 0.00 0.00 3.85
2813 3296 3.838244 ATGGAGCGCCTAAGTTATTCA 57.162 42.857 8.34 0.00 34.31 2.57
2814 3297 3.179443 TGGAGCGCCTAAGTTATTCAG 57.821 47.619 8.34 0.00 34.31 3.02
2815 3298 2.500098 TGGAGCGCCTAAGTTATTCAGT 59.500 45.455 8.34 0.00 34.31 3.41
2816 3299 3.055385 TGGAGCGCCTAAGTTATTCAGTT 60.055 43.478 8.34 0.00 34.31 3.16
2817 3300 3.939592 GGAGCGCCTAAGTTATTCAGTTT 59.060 43.478 2.29 0.00 0.00 2.66
2818 3301 4.395231 GGAGCGCCTAAGTTATTCAGTTTT 59.605 41.667 2.29 0.00 0.00 2.43
2819 3302 5.296813 AGCGCCTAAGTTATTCAGTTTTG 57.703 39.130 2.29 0.00 0.00 2.44
2933 3427 1.538047 ACATCCAACCATCAGTGTGC 58.462 50.000 0.00 0.00 0.00 4.57
3037 3540 8.143835 AGTTGTAAATTCCAGTTGAAATTCAGG 58.856 33.333 0.00 0.00 36.33 3.86
3069 3572 3.756963 GGGGGTTTCAGACATCTTGTAAC 59.243 47.826 0.00 0.00 0.00 2.50
3108 3611 3.253188 TGACAAGTCCAGCAAATTACAGC 59.747 43.478 0.00 0.00 0.00 4.40
3110 3613 3.004734 ACAAGTCCAGCAAATTACAGCAC 59.995 43.478 0.00 0.00 0.00 4.40
3112 3615 2.162681 GTCCAGCAAATTACAGCACCT 58.837 47.619 0.00 0.00 0.00 4.00
3113 3616 2.095059 GTCCAGCAAATTACAGCACCTG 60.095 50.000 0.00 0.00 37.52 4.00
3114 3617 1.403249 CCAGCAAATTACAGCACCTGC 60.403 52.381 0.00 0.00 42.49 4.85
3145 3785 8.777865 TGTCAGATAAATACCAAGACAAGAAG 57.222 34.615 0.00 0.00 32.26 2.85
3219 3859 2.368655 TATCATCCCGTGATGCATCG 57.631 50.000 21.34 11.30 46.85 3.84
3220 3860 0.681175 ATCATCCCGTGATGCATCGA 59.319 50.000 21.34 12.71 45.76 3.59
3221 3861 0.032540 TCATCCCGTGATGCATCGAG 59.967 55.000 21.34 16.58 46.60 4.04
3222 3862 0.032540 CATCCCGTGATGCATCGAGA 59.967 55.000 21.34 14.68 41.81 4.04
3223 3863 0.972134 ATCCCGTGATGCATCGAGAT 59.028 50.000 21.34 16.12 0.00 2.75
3224 3864 0.032540 TCCCGTGATGCATCGAGATG 59.967 55.000 21.34 9.64 41.60 2.90
3240 3880 3.715495 GAGATGAGATGAGCACGTGAAT 58.285 45.455 22.23 9.23 0.00 2.57
3242 3882 3.131755 AGATGAGATGAGCACGTGAATCA 59.868 43.478 22.23 21.74 0.00 2.57
3250 3890 1.959899 GCACGTGAATCACTCCAGCG 61.960 60.000 22.23 0.00 31.34 5.18
3295 4097 3.317711 TGTTTGTATTTGTGCTCTGTGGG 59.682 43.478 0.00 0.00 0.00 4.61
3305 4107 4.211125 TGTGCTCTGTGGGTCAAATTTAA 58.789 39.130 0.00 0.00 0.00 1.52
3325 4127 1.078214 CCTGGAGCCAAAGCGATCA 60.078 57.895 0.00 0.00 46.67 2.92
3326 4128 1.372087 CCTGGAGCCAAAGCGATCAC 61.372 60.000 0.00 0.00 46.67 3.06
3350 4152 0.031585 TCTTGGTTCACGTGTCTCCG 59.968 55.000 16.51 5.45 0.00 4.63
3365 4167 2.880890 GTCTCCGGCAATGCTGAATTAT 59.119 45.455 16.76 0.00 37.02 1.28
3366 4168 4.065088 GTCTCCGGCAATGCTGAATTATA 58.935 43.478 16.76 0.00 37.02 0.98
3389 4211 6.089249 AGTGAATTTTCAGTGGATTTGGAC 57.911 37.500 0.00 0.00 39.29 4.02
3395 4217 2.715046 TCAGTGGATTTGGACTCATGC 58.285 47.619 0.00 0.00 0.00 4.06
3396 4218 2.306805 TCAGTGGATTTGGACTCATGCT 59.693 45.455 0.00 0.00 0.00 3.79
3397 4219 3.087031 CAGTGGATTTGGACTCATGCTT 58.913 45.455 0.00 0.00 0.00 3.91
3398 4220 4.019411 TCAGTGGATTTGGACTCATGCTTA 60.019 41.667 0.00 0.00 0.00 3.09
3429 4251 3.555547 GTCCATCTTTTGGTTGTTGTTGC 59.444 43.478 0.00 0.00 46.52 4.17
3430 4252 3.196469 TCCATCTTTTGGTTGTTGTTGCA 59.804 39.130 0.00 0.00 46.52 4.08
3431 4253 3.556775 CCATCTTTTGGTTGTTGTTGCAG 59.443 43.478 0.00 0.00 40.99 4.41
3432 4254 2.615869 TCTTTTGGTTGTTGTTGCAGC 58.384 42.857 0.00 0.00 0.00 5.25
3448 4294 1.072159 AGCTGCAGTGAACCTCCAC 59.928 57.895 16.64 0.00 37.32 4.02
3527 4373 5.050227 CAGCACTGGACGTACTATAGTACTC 60.050 48.000 30.80 25.85 46.43 2.59
3591 4440 6.618287 TGAAACAATGACTAGGAAACACTG 57.382 37.500 0.00 0.00 0.00 3.66
3592 4441 6.119536 TGAAACAATGACTAGGAAACACTGT 58.880 36.000 0.00 0.00 0.00 3.55
3599 4448 2.612212 ACTAGGAAACACTGTTTGCACG 59.388 45.455 23.37 16.67 0.00 5.34
3600 4449 1.459450 AGGAAACACTGTTTGCACGT 58.541 45.000 23.37 5.07 0.00 4.49
3601 4450 1.132262 AGGAAACACTGTTTGCACGTG 59.868 47.619 23.37 12.28 33.26 4.49
3602 4451 1.131504 GGAAACACTGTTTGCACGTGA 59.868 47.619 22.23 1.04 32.23 4.35
3603 4452 2.414824 GGAAACACTGTTTGCACGTGAA 60.415 45.455 22.23 5.66 32.23 3.18
3604 4453 2.999507 AACACTGTTTGCACGTGAAA 57.000 40.000 22.23 13.66 32.23 2.69
3605 4454 2.542766 ACACTGTTTGCACGTGAAAG 57.457 45.000 22.23 5.87 32.23 2.62
3606 4455 1.132262 ACACTGTTTGCACGTGAAAGG 59.868 47.619 22.23 11.65 32.23 3.11
3607 4456 1.400142 CACTGTTTGCACGTGAAAGGA 59.600 47.619 22.23 4.35 0.00 3.36
3610 4459 2.354510 CTGTTTGCACGTGAAAGGAGAA 59.645 45.455 22.23 0.00 0.00 2.87
3611 4460 2.948979 TGTTTGCACGTGAAAGGAGAAT 59.051 40.909 22.23 0.00 0.00 2.40
3619 4469 6.016693 TGCACGTGAAAGGAGAATTATTTCAA 60.017 34.615 22.23 0.00 42.70 2.69
3637 4487 2.999355 TCAACAAGCTTTGCAAACAACC 59.001 40.909 8.05 0.00 34.87 3.77
3677 4528 2.070262 GCAAACAGCAGGTTTCATCC 57.930 50.000 3.80 0.00 46.61 3.51
3695 4546 1.902508 TCCAAGGACGCAGAGAGAAAT 59.097 47.619 0.00 0.00 0.00 2.17
3711 4562 8.735315 CAGAGAGAAATAACAGAGTACTTCTCA 58.265 37.037 15.71 0.00 44.98 3.27
3722 4573 6.102663 CAGAGTACTTCTCACCCAAGTTATG 58.897 44.000 0.00 0.00 44.98 1.90
3759 4610 8.584157 TGCCATGTTTAATAATGCTAATAAGGG 58.416 33.333 0.00 0.00 0.00 3.95
3760 4611 8.034804 GCCATGTTTAATAATGCTAATAAGGGG 58.965 37.037 0.00 0.00 0.00 4.79
3761 4612 9.308000 CCATGTTTAATAATGCTAATAAGGGGA 57.692 33.333 0.00 0.00 0.00 4.81
3778 4629 4.593956 AGGGGATTCTTGTCTCAAATGAC 58.406 43.478 0.00 0.00 37.47 3.06
3782 4633 4.142513 GGATTCTTGTCTCAAATGACAGGC 60.143 45.833 0.00 0.00 46.02 4.85
3783 4634 3.490439 TCTTGTCTCAAATGACAGGCA 57.510 42.857 0.00 0.00 46.02 4.75
3784 4635 4.025040 TCTTGTCTCAAATGACAGGCAT 57.975 40.909 0.00 0.00 46.02 4.40
3787 4639 1.667724 GTCTCAAATGACAGGCATCCG 59.332 52.381 0.00 0.00 35.78 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.357079 CTGGTTGTGTGCCGAGGC 61.357 66.667 7.26 7.26 42.35 4.70
19 20 4.158764 AGCTCGTCTGTTCTATTGTTAGCT 59.841 41.667 0.00 0.00 0.00 3.32
20 21 4.425520 AGCTCGTCTGTTCTATTGTTAGC 58.574 43.478 0.00 0.00 0.00 3.09
21 22 5.641709 TGAGCTCGTCTGTTCTATTGTTAG 58.358 41.667 9.64 0.00 0.00 2.34
22 23 5.638596 TGAGCTCGTCTGTTCTATTGTTA 57.361 39.130 9.64 0.00 0.00 2.41
23 24 4.521130 TGAGCTCGTCTGTTCTATTGTT 57.479 40.909 9.64 0.00 0.00 2.83
25 26 4.676546 TCATGAGCTCGTCTGTTCTATTG 58.323 43.478 5.16 0.00 0.00 1.90
26 27 4.991153 TCATGAGCTCGTCTGTTCTATT 57.009 40.909 5.16 0.00 0.00 1.73
28 29 3.947834 TGATCATGAGCTCGTCTGTTCTA 59.052 43.478 12.92 0.00 0.00 2.10
29 30 2.757314 TGATCATGAGCTCGTCTGTTCT 59.243 45.455 12.92 0.00 0.00 3.01
146 164 4.284550 GCCAGTGCTGTTGGGGGA 62.285 66.667 0.00 0.00 36.19 4.81
192 210 2.760799 TGGCTGGGGATGCAATGC 60.761 61.111 0.00 0.00 0.00 3.56
194 212 2.440796 CGTGGCTGGGGATGCAAT 60.441 61.111 0.00 0.00 0.00 3.56
195 213 3.645660 TCGTGGCTGGGGATGCAA 61.646 61.111 0.00 0.00 0.00 4.08
196 214 4.408821 GTCGTGGCTGGGGATGCA 62.409 66.667 0.00 0.00 0.00 3.96
199 217 2.363276 TACGTCGTGGCTGGGGAT 60.363 61.111 8.47 0.00 0.00 3.85
200 218 3.376078 GTACGTCGTGGCTGGGGA 61.376 66.667 8.47 0.00 0.00 4.81
201 219 3.642778 CTGTACGTCGTGGCTGGGG 62.643 68.421 8.47 0.00 0.00 4.96
202 220 2.126071 CTGTACGTCGTGGCTGGG 60.126 66.667 8.47 0.00 0.00 4.45
203 221 1.006571 AACTGTACGTCGTGGCTGG 60.007 57.895 8.47 1.86 0.00 4.85
204 222 1.334992 CGAACTGTACGTCGTGGCTG 61.335 60.000 8.47 7.51 0.00 4.85
205 223 1.081641 CGAACTGTACGTCGTGGCT 60.082 57.895 8.47 0.00 0.00 4.75
206 224 1.370900 ACGAACTGTACGTCGTGGC 60.371 57.895 15.59 1.35 39.87 5.01
207 225 4.929198 ACGAACTGTACGTCGTGG 57.071 55.556 15.59 0.77 39.87 4.94
209 227 0.236711 CTCCACGAACTGTACGTCGT 59.763 55.000 11.84 11.84 42.07 4.34
242 260 0.537653 AGGCTTTACGCTTCCTCCTC 59.462 55.000 0.00 0.00 39.13 3.71
304 322 0.032540 TGTGAGGGCATCATCGATCG 59.967 55.000 9.36 9.36 40.92 3.69
305 323 1.342496 TCTGTGAGGGCATCATCGATC 59.658 52.381 4.69 0.00 40.92 3.69
306 324 1.417288 TCTGTGAGGGCATCATCGAT 58.583 50.000 4.69 0.00 40.92 3.59
333 351 3.882102 ATGCACTAGCCCATTATGGAA 57.118 42.857 13.63 0.00 38.13 3.53
411 430 3.391965 GAGCTCAACATATGCCTGAGAG 58.608 50.000 27.63 17.37 39.15 3.20
412 431 2.103771 GGAGCTCAACATATGCCTGAGA 59.896 50.000 27.63 9.99 39.15 3.27
413 432 2.492012 GGAGCTCAACATATGCCTGAG 58.508 52.381 22.52 22.52 39.69 3.35
414 433 1.141657 GGGAGCTCAACATATGCCTGA 59.858 52.381 17.19 5.32 0.00 3.86
415 434 1.602311 GGGAGCTCAACATATGCCTG 58.398 55.000 17.19 0.62 0.00 4.85
416 435 0.475906 GGGGAGCTCAACATATGCCT 59.524 55.000 17.19 0.00 0.00 4.75
427 446 0.463620 GTGAGTGATCAGGGGAGCTC 59.536 60.000 4.71 4.71 0.00 4.09
432 451 1.686052 GAGCTAGTGAGTGATCAGGGG 59.314 57.143 0.00 0.00 0.00 4.79
434 453 1.686052 GGGAGCTAGTGAGTGATCAGG 59.314 57.143 0.00 0.00 0.00 3.86
437 456 1.410882 GGTGGGAGCTAGTGAGTGATC 59.589 57.143 0.00 0.00 0.00 2.92
438 457 1.490574 GGTGGGAGCTAGTGAGTGAT 58.509 55.000 0.00 0.00 0.00 3.06
440 459 0.904865 TGGGTGGGAGCTAGTGAGTG 60.905 60.000 0.00 0.00 0.00 3.51
442 461 0.250513 GTTGGGTGGGAGCTAGTGAG 59.749 60.000 0.00 0.00 0.00 3.51
470 489 3.023119 TCGATTTGGAATGATGGGGTTG 58.977 45.455 0.00 0.00 0.00 3.77
528 547 8.819974 GCCAACAATCTCATTTGGTAAAATATG 58.180 33.333 1.79 0.00 41.69 1.78
549 569 5.634859 CCACAACATCATTTCTTAAGCCAAC 59.365 40.000 0.00 0.00 0.00 3.77
559 579 2.496871 TCCATGCCCACAACATCATTTC 59.503 45.455 0.00 0.00 0.00 2.17
574 608 2.305009 CTCCCTCCAAAATCTCCATGC 58.695 52.381 0.00 0.00 0.00 4.06
656 1108 3.963428 TCTGTCTTCTTGTTAGCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
809 1280 3.887335 GAGGCGTTGGTGCGGGTAA 62.887 63.158 0.00 0.00 35.06 2.85
865 1336 0.260523 GAGTAGGAGGAGGAGCTGGT 59.739 60.000 0.00 0.00 0.00 4.00
954 1428 2.285442 ACTCCCCAGCCCTGTACC 60.285 66.667 0.00 0.00 0.00 3.34
981 1455 2.244382 GCGACGAACCAACACACG 59.756 61.111 0.00 0.00 0.00 4.49
1031 1505 2.624838 ACTTCTGTTTCCACCATTGCTG 59.375 45.455 0.00 0.00 0.00 4.41
1045 1519 2.833913 CCCCTGGCACCACTTCTGT 61.834 63.158 0.00 0.00 0.00 3.41
1098 1572 1.587933 AAGACGACGCCAGAGTCTCC 61.588 60.000 0.00 0.00 43.60 3.71
1222 1696 3.522731 CTCCTCCTCCTCGCCGTG 61.523 72.222 0.00 0.00 0.00 4.94
1242 1716 2.609747 TGATATTCCTCCCCCTTCTCG 58.390 52.381 0.00 0.00 0.00 4.04
1246 1720 2.108952 GCACATGATATTCCTCCCCCTT 59.891 50.000 0.00 0.00 0.00 3.95
1254 1734 4.202441 ACTGAACCAGCACATGATATTCC 58.798 43.478 0.00 0.00 34.37 3.01
1258 1738 4.696877 CAGAAACTGAACCAGCACATGATA 59.303 41.667 0.00 0.00 34.37 2.15
2161 2644 1.620589 ACTGGATCACCCCCATGCT 60.621 57.895 0.00 0.00 32.49 3.79
2244 2727 0.034670 AGCAGAAGAACCAGATGGCC 60.035 55.000 0.00 0.00 39.32 5.36
2292 2775 4.363990 AGCACGTCGGAGCTGGTG 62.364 66.667 12.77 0.00 38.73 4.17
2355 2838 1.086634 GGATCTTGAGCGTGCAGTCC 61.087 60.000 0.00 0.00 0.00 3.85
2619 3102 2.413765 GTGACGGCGGAGAGGATC 59.586 66.667 13.24 0.00 0.00 3.36
2778 3261 3.186001 CGCTCCATATCTTGCTGAACATC 59.814 47.826 0.00 0.00 0.00 3.06
2813 3296 3.270877 AGAAACGAGTGTCAGCAAAACT 58.729 40.909 0.00 0.00 0.00 2.66
2814 3297 3.675467 AGAAACGAGTGTCAGCAAAAC 57.325 42.857 0.00 0.00 0.00 2.43
2815 3298 4.873827 AGTAAGAAACGAGTGTCAGCAAAA 59.126 37.500 0.00 0.00 0.00 2.44
2816 3299 4.439057 AGTAAGAAACGAGTGTCAGCAAA 58.561 39.130 0.00 0.00 0.00 3.68
2817 3300 4.049186 GAGTAAGAAACGAGTGTCAGCAA 58.951 43.478 0.00 0.00 0.00 3.91
2818 3301 3.067601 TGAGTAAGAAACGAGTGTCAGCA 59.932 43.478 0.00 0.00 0.00 4.41
2819 3302 3.639538 TGAGTAAGAAACGAGTGTCAGC 58.360 45.455 0.00 0.00 0.00 4.26
2827 3310 7.883217 AGTAAAGACATCTGAGTAAGAAACGA 58.117 34.615 0.00 0.00 38.79 3.85
2933 3427 2.095059 GCAATGTACAGCACAAGGGAAG 60.095 50.000 0.33 0.00 41.55 3.46
3037 3540 2.962421 TCTGAAACCCCCATGACAAAAC 59.038 45.455 0.00 0.00 0.00 2.43
3069 3572 2.030562 AGGGTTGACGGTTCAGCG 59.969 61.111 0.00 0.00 33.87 5.18
3110 3613 1.725641 TTATCTGACAACAGCGCAGG 58.274 50.000 11.47 3.29 43.17 4.85
3112 3615 3.621268 GGTATTTATCTGACAACAGCGCA 59.379 43.478 11.47 0.00 43.17 6.09
3113 3616 3.621268 TGGTATTTATCTGACAACAGCGC 59.379 43.478 0.00 0.00 43.17 5.92
3114 3617 5.580691 TCTTGGTATTTATCTGACAACAGCG 59.419 40.000 0.00 0.00 43.17 5.18
3115 3618 6.371548 TGTCTTGGTATTTATCTGACAACAGC 59.628 38.462 0.00 0.00 43.17 4.40
3116 3619 7.905604 TGTCTTGGTATTTATCTGACAACAG 57.094 36.000 0.00 0.00 44.66 3.16
3118 3621 8.547967 TCTTGTCTTGGTATTTATCTGACAAC 57.452 34.615 0.00 0.00 37.82 3.32
3120 3623 8.593679 TCTTCTTGTCTTGGTATTTATCTGACA 58.406 33.333 0.00 0.00 0.00 3.58
3121 3624 9.606631 ATCTTCTTGTCTTGGTATTTATCTGAC 57.393 33.333 0.00 0.00 0.00 3.51
3122 3625 9.605275 CATCTTCTTGTCTTGGTATTTATCTGA 57.395 33.333 0.00 0.00 0.00 3.27
3145 3785 5.996513 TCTAGGTCGATAGTAGGACAACATC 59.003 44.000 0.00 0.00 34.87 3.06
3219 3859 2.859526 TCACGTGCTCATCTCATCTC 57.140 50.000 11.67 0.00 0.00 2.75
3220 3860 3.131755 TGATTCACGTGCTCATCTCATCT 59.868 43.478 11.67 0.00 0.00 2.90
3221 3861 3.244814 GTGATTCACGTGCTCATCTCATC 59.755 47.826 19.24 8.20 0.00 2.92
3222 3862 3.118847 AGTGATTCACGTGCTCATCTCAT 60.119 43.478 19.24 6.36 39.64 2.90
3223 3863 2.232208 AGTGATTCACGTGCTCATCTCA 59.768 45.455 19.24 9.59 39.64 3.27
3224 3864 2.857152 GAGTGATTCACGTGCTCATCTC 59.143 50.000 19.24 19.98 39.64 2.75
3258 3898 2.079925 CAAACAGCTAGAAGCCTGGAC 58.920 52.381 0.00 0.00 43.77 4.02
3295 4097 3.161866 TGGCTCCAGGGTTAAATTTGAC 58.838 45.455 4.57 4.57 0.00 3.18
3305 4107 2.543067 GATCGCTTTGGCTCCAGGGT 62.543 60.000 0.00 0.00 36.09 4.34
3325 4127 1.416401 ACACGTGAACCAAGATCCAGT 59.584 47.619 25.01 0.00 0.00 4.00
3326 4128 2.069273 GACACGTGAACCAAGATCCAG 58.931 52.381 25.01 0.00 0.00 3.86
3350 4152 8.652810 AAAATTCACTATAATTCAGCATTGCC 57.347 30.769 4.70 0.00 0.00 4.52
3365 4167 7.004086 AGTCCAAATCCACTGAAAATTCACTA 58.996 34.615 0.00 0.00 32.90 2.74
3366 4168 5.835280 AGTCCAAATCCACTGAAAATTCACT 59.165 36.000 0.00 0.00 32.90 3.41
3389 4211 4.832248 TGGACCAAGTAAGTAAGCATGAG 58.168 43.478 0.00 0.00 0.00 2.90
3429 4251 1.071987 TGGAGGTTCACTGCAGCTG 59.928 57.895 15.27 10.11 43.13 4.24
3430 4252 3.567308 TGGAGGTTCACTGCAGCT 58.433 55.556 15.27 1.30 43.13 4.24
3591 4440 3.626028 ATTCTCCTTTCACGTGCAAAC 57.374 42.857 11.67 0.00 0.00 2.93
3592 4441 5.957842 ATAATTCTCCTTTCACGTGCAAA 57.042 34.783 11.67 11.29 0.00 3.68
3599 4448 8.084684 AGCTTGTTGAAATAATTCTCCTTTCAC 58.915 33.333 0.00 0.00 38.30 3.18
3600 4449 8.181904 AGCTTGTTGAAATAATTCTCCTTTCA 57.818 30.769 0.00 0.00 37.17 2.69
3601 4450 9.481340 AAAGCTTGTTGAAATAATTCTCCTTTC 57.519 29.630 0.00 0.00 36.48 2.62
3602 4451 9.264719 CAAAGCTTGTTGAAATAATTCTCCTTT 57.735 29.630 0.00 0.00 36.48 3.11
3603 4452 7.386025 GCAAAGCTTGTTGAAATAATTCTCCTT 59.614 33.333 0.00 0.00 36.48 3.36
3604 4453 6.870439 GCAAAGCTTGTTGAAATAATTCTCCT 59.130 34.615 0.00 0.00 36.48 3.69
3605 4454 6.646240 TGCAAAGCTTGTTGAAATAATTCTCC 59.354 34.615 0.00 0.00 36.48 3.71
3606 4455 7.642071 TGCAAAGCTTGTTGAAATAATTCTC 57.358 32.000 0.00 0.00 36.48 2.87
3607 4456 8.337532 GTTTGCAAAGCTTGTTGAAATAATTCT 58.662 29.630 13.26 0.00 36.48 2.40
3610 4459 7.551035 TGTTTGCAAAGCTTGTTGAAATAAT 57.449 28.000 13.26 0.00 0.00 1.28
3611 4460 6.974932 TGTTTGCAAAGCTTGTTGAAATAA 57.025 29.167 13.26 0.00 0.00 1.40
3619 4469 4.159506 TCTTAGGTTGTTTGCAAAGCTTGT 59.840 37.500 13.26 0.26 36.22 3.16
3670 4521 1.623311 TCTCTGCGTCCTTGGATGAAA 59.377 47.619 12.65 0.00 0.00 2.69
3677 4528 4.245660 TGTTATTTCTCTCTGCGTCCTTG 58.754 43.478 0.00 0.00 0.00 3.61
3695 4546 5.145564 ACTTGGGTGAGAAGTACTCTGTTA 58.854 41.667 0.00 0.00 45.13 2.41
3711 4562 8.886369 TGGCATATAAGTATACATAACTTGGGT 58.114 33.333 5.50 0.00 37.71 4.51
3755 4606 5.012893 GTCATTTGAGACAAGAATCCCCTT 58.987 41.667 0.00 0.00 38.40 3.95
3756 4607 4.043310 TGTCATTTGAGACAAGAATCCCCT 59.957 41.667 0.00 0.00 44.92 4.79
3757 4608 4.335416 TGTCATTTGAGACAAGAATCCCC 58.665 43.478 0.00 0.00 44.92 4.81
3758 4609 4.397417 CCTGTCATTTGAGACAAGAATCCC 59.603 45.833 0.00 0.00 46.90 3.85
3759 4610 4.142513 GCCTGTCATTTGAGACAAGAATCC 60.143 45.833 0.00 0.00 46.90 3.01
3760 4611 4.456911 TGCCTGTCATTTGAGACAAGAATC 59.543 41.667 0.00 0.00 46.90 2.52
3761 4612 4.401022 TGCCTGTCATTTGAGACAAGAAT 58.599 39.130 0.00 0.00 46.90 2.40
3762 4613 3.819368 TGCCTGTCATTTGAGACAAGAA 58.181 40.909 0.00 0.00 46.90 2.52
3763 4614 3.490439 TGCCTGTCATTTGAGACAAGA 57.510 42.857 0.00 0.00 46.90 3.02
3778 4629 1.521450 GGCCATTCATCGGATGCCTG 61.521 60.000 13.15 11.72 35.99 4.85
3782 4633 0.820482 TGCAGGCCATTCATCGGATG 60.820 55.000 11.79 11.79 0.00 3.51
3783 4634 0.111832 ATGCAGGCCATTCATCGGAT 59.888 50.000 5.01 0.00 0.00 4.18
3784 4635 0.820482 CATGCAGGCCATTCATCGGA 60.820 55.000 5.01 0.00 29.71 4.55
3787 4639 2.426651 AGCATGCAGGCCATTCATC 58.573 52.632 21.42 0.00 29.71 2.92


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

AutoCloner maintained by Alex Coulton.