Multiple sequence alignment - TraesCS5B01G273600

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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 TraesCS5B01G273600 chr5B 100.000 4263 0 0 1 4263 458901165 458896903 0.000000e+00 7873.0
1 TraesCS5B01G273600 chr5B 94.231 52 2 1 2365 2416 458898758 458898708 1.270000e-10 78.7
2 TraesCS5B01G273600 chr5B 94.231 52 2 1 2408 2458 458898801 458898750 1.270000e-10 78.7
3 TraesCS5B01G273600 chr5A 96.126 1265 39 3 653 1907 482904924 482903660 0.000000e+00 2056.0
4 TraesCS5B01G273600 chr5A 96.861 924 26 1 3343 4263 482903276 482902353 0.000000e+00 1543.0
5 TraesCS5B01G273600 chr5A 81.602 337 27 17 3021 3343 482903656 482903341 3.290000e-61 246.0
6 TraesCS5B01G273600 chr5D 94.531 1353 35 10 555 1907 382490791 382489478 0.000000e+00 2052.0
7 TraesCS5B01G273600 chr5D 97.937 921 19 0 3343 4263 382489068 382488148 0.000000e+00 1596.0
8 TraesCS5B01G273600 chr5D 92.551 980 50 4 855 1834 382521094 382520138 0.000000e+00 1384.0
9 TraesCS5B01G273600 chr5D 88.174 575 32 11 2 560 382491454 382490900 0.000000e+00 652.0
10 TraesCS5B01G273600 chr5D 84.286 350 16 13 3026 3343 382489477 382489135 5.360000e-79 305.0
11 TraesCS5B01G273600 chr5D 89.151 212 12 5 648 859 382535272 382535072 1.970000e-63 254.0
12 TraesCS5B01G273600 chr1B 99.385 650 3 1 2365 3014 584481766 584482414 0.000000e+00 1177.0
13 TraesCS5B01G273600 chr1B 98.152 541 10 0 1918 2458 584481276 584481816 0.000000e+00 944.0
14 TraesCS5B01G273600 chr1B 94.231 52 2 1 2408 2458 584481723 584481774 1.270000e-10 78.7
15 TraesCS5B01G273600 chr1B 95.833 48 2 0 2369 2416 584481811 584481858 1.270000e-10 78.7
16 TraesCS5B01G273600 chr2B 80.600 433 66 10 1907 2338 33667282 33667697 6.880000e-83 318.0
17 TraesCS5B01G273600 chr2A 78.541 466 64 17 1972 2416 21181460 21181910 1.510000e-69 274.0
18 TraesCS5B01G273600 chr4D 90.741 54 2 3 4117 4169 388927635 388927686 7.650000e-08 69.4
19 TraesCS5B01G273600 chr4A 90.741 54 2 3 4117 4169 70311037 70311088 7.650000e-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 TraesCS5B01G273600 chr5B 458896903 458901165 4262 True 2676.800000 7873 96.154000 1 4263 3 chr5B.!!$R1 4262
1 TraesCS5B01G273600 chr5A 482902353 482904924 2571 True 1281.666667 2056 91.529667 653 4263 3 chr5A.!!$R1 3610
2 TraesCS5B01G273600 chr5D 382520138 382521094 956 True 1384.000000 1384 92.551000 855 1834 1 chr5D.!!$R1 979
3 TraesCS5B01G273600 chr5D 382488148 382491454 3306 True 1151.250000 2052 91.232000 2 4263 4 chr5D.!!$R3 4261
4 TraesCS5B01G273600 chr1B 584481276 584482414 1138 False 569.600000 1177 96.900250 1918 3014 4 chr1B.!!$F1 1096

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
205 213 0.110486 GCCAAGTCCTCTCCCAAACA 59.890 55.0 0.00 0.00 0.00 2.83 F
278 286 0.522495 GAGCAAGACGAGACGAGCTC 60.522 60.0 2.73 2.73 41.21 4.09 F
1907 2064 0.531200 GGCTGCAACGGTACTACTCT 59.469 55.0 0.50 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2175 0.102481 GCACGAGCCGAGGATAGAAA 59.898 55.000 0.0 0.0 33.58 2.52 R
2199 2356 1.394917 GTTCAGGCATAGCTGACGTTG 59.605 52.381 0.0 0.0 34.62 4.10 R
3289 3520 0.672342 ACCTAACGACTGAAGCGTGT 59.328 50.000 0.0 0.0 41.75 4.49 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
38 39 3.430790 CCTCACCTCGAGCACATCATTTA 60.431 47.826 6.99 0.00 40.78 1.40
45 46 3.251487 TCGAGCACATCATTTATGGCATG 59.749 43.478 10.98 0.00 40.16 4.06
64 65 2.750948 TGAATAGATAAGGCGGCGAAC 58.249 47.619 12.98 1.56 0.00 3.95
102 110 2.749839 CCCGCCGCCAGAAAATCA 60.750 61.111 0.00 0.00 0.00 2.57
122 130 5.576563 TCATGTAAAAGAGGGGTCTTTGA 57.423 39.130 1.25 0.00 39.59 2.69
205 213 0.110486 GCCAAGTCCTCTCCCAAACA 59.890 55.000 0.00 0.00 0.00 2.83
207 215 2.819348 GCCAAGTCCTCTCCCAAACAAT 60.819 50.000 0.00 0.00 0.00 2.71
215 223 3.319972 CCTCTCCCAAACAATGCATATGG 59.680 47.826 0.00 6.69 0.00 2.74
228 236 2.515979 ATATGGGGGCGCATCGACA 61.516 57.895 10.83 4.16 36.10 4.35
255 263 2.094803 AGACAAGCTCATCTCACTGTCG 60.095 50.000 5.51 0.00 0.00 4.35
257 265 1.991264 CAAGCTCATCTCACTGTCGTG 59.009 52.381 0.00 0.00 42.59 4.35
271 279 1.602605 TCGTGGGAGCAAGACGAGA 60.603 57.895 0.00 0.00 37.21 4.04
272 280 1.444553 CGTGGGAGCAAGACGAGAC 60.445 63.158 0.00 0.00 35.05 3.36
274 282 1.602605 TGGGAGCAAGACGAGACGA 60.603 57.895 0.00 0.00 0.00 4.20
275 283 1.137825 GGGAGCAAGACGAGACGAG 59.862 63.158 0.00 0.00 0.00 4.18
276 284 1.515304 GGAGCAAGACGAGACGAGC 60.515 63.158 0.00 0.00 0.00 5.03
277 285 1.504446 GAGCAAGACGAGACGAGCT 59.496 57.895 0.00 0.00 34.61 4.09
278 286 0.522495 GAGCAAGACGAGACGAGCTC 60.522 60.000 2.73 2.73 41.21 4.09
310 318 1.635663 CGCCTCATGTTTCGACACCC 61.636 60.000 0.00 0.00 0.00 4.61
334 344 2.607771 CCGAACAAAGGCAAAGGACATG 60.608 50.000 0.00 0.00 0.00 3.21
347 357 1.295292 AGGACATGGGTAGGAGTGGAT 59.705 52.381 0.00 0.00 0.00 3.41
348 358 2.127708 GGACATGGGTAGGAGTGGATT 58.872 52.381 0.00 0.00 0.00 3.01
354 364 3.533146 TGGGTAGGAGTGGATTGGTTAA 58.467 45.455 0.00 0.00 0.00 2.01
364 374 3.438781 GTGGATTGGTTAATGTGCGAAGA 59.561 43.478 0.00 0.00 0.00 2.87
367 377 3.410631 TTGGTTAATGTGCGAAGAGGA 57.589 42.857 0.00 0.00 0.00 3.71
368 378 2.695359 TGGTTAATGTGCGAAGAGGAC 58.305 47.619 0.00 0.00 41.99 3.85
381 391 3.684788 CGAAGAGGACAGTGGGTTTTATG 59.315 47.826 0.00 0.00 0.00 1.90
382 392 3.073274 AGAGGACAGTGGGTTTTATGC 57.927 47.619 0.00 0.00 0.00 3.14
383 393 2.375174 AGAGGACAGTGGGTTTTATGCA 59.625 45.455 0.00 0.00 0.00 3.96
384 394 3.153919 GAGGACAGTGGGTTTTATGCAA 58.846 45.455 0.00 0.00 0.00 4.08
385 395 3.571590 AGGACAGTGGGTTTTATGCAAA 58.428 40.909 0.00 0.00 0.00 3.68
386 396 3.964031 AGGACAGTGGGTTTTATGCAAAA 59.036 39.130 0.00 0.00 0.00 2.44
407 417 1.024579 GTTCACGCCATTCGGTCCAT 61.025 55.000 0.00 0.00 43.86 3.41
415 425 1.153369 ATTCGGTCCATGCTGTCCG 60.153 57.895 8.89 8.89 43.65 4.79
451 464 7.574217 CGCCCATGTATAGCGGTTAAAATATTT 60.574 37.037 0.00 0.00 45.88 1.40
525 538 6.707273 ATAGTGAACAACTTAAACCCCCTA 57.293 37.500 0.00 0.00 40.56 3.53
526 539 4.722220 AGTGAACAACTTAAACCCCCTAC 58.278 43.478 0.00 0.00 34.57 3.18
527 540 3.822735 GTGAACAACTTAAACCCCCTACC 59.177 47.826 0.00 0.00 0.00 3.18
528 541 3.462579 TGAACAACTTAAACCCCCTACCA 59.537 43.478 0.00 0.00 0.00 3.25
529 542 3.513909 ACAACTTAAACCCCCTACCAC 57.486 47.619 0.00 0.00 0.00 4.16
548 564 4.215613 ACCACGCAAGAATAAAAACCTCTC 59.784 41.667 0.00 0.00 43.62 3.20
553 569 7.693951 CACGCAAGAATAAAAACCTCTCTAATG 59.306 37.037 0.00 0.00 43.62 1.90
588 718 4.062991 AGTTAAAATCGAGCGACCAAAGT 58.937 39.130 0.00 0.00 0.00 2.66
595 725 3.777478 TCGAGCGACCAAAGTAATAAGG 58.223 45.455 0.00 0.00 0.00 2.69
598 728 3.007635 AGCGACCAAAGTAATAAGGCAC 58.992 45.455 0.00 0.00 0.00 5.01
599 729 2.745281 GCGACCAAAGTAATAAGGCACA 59.255 45.455 0.00 0.00 0.00 4.57
600 730 3.189702 GCGACCAAAGTAATAAGGCACAA 59.810 43.478 0.00 0.00 0.00 3.33
601 731 4.671766 GCGACCAAAGTAATAAGGCACAAG 60.672 45.833 0.00 0.00 0.00 3.16
602 732 4.671766 CGACCAAAGTAATAAGGCACAAGC 60.672 45.833 0.00 0.00 41.10 4.01
603 733 4.407365 ACCAAAGTAATAAGGCACAAGCT 58.593 39.130 0.00 0.00 41.70 3.74
623 753 3.985925 GCTCAAGCTCAATTTGAAGTTGG 59.014 43.478 15.37 10.09 34.41 3.77
634 764 9.219603 CTCAATTTGAAGTTGGAGTACTATTGA 57.780 33.333 0.00 2.97 32.57 2.57
635 765 8.999431 TCAATTTGAAGTTGGAGTACTATTGAC 58.001 33.333 0.00 0.00 30.33 3.18
636 766 9.003658 CAATTTGAAGTTGGAGTACTATTGACT 57.996 33.333 0.00 0.00 28.57 3.41
637 767 9.574516 AATTTGAAGTTGGAGTACTATTGACTT 57.425 29.630 11.13 11.13 0.00 3.01
641 771 9.653287 TGAAGTTGGAGTACTATTGACTTATTG 57.347 33.333 0.00 0.00 0.00 1.90
642 772 9.871238 GAAGTTGGAGTACTATTGACTTATTGA 57.129 33.333 0.00 0.00 0.00 2.57
644 774 9.877178 AGTTGGAGTACTATTGACTTATTGAAG 57.123 33.333 0.00 0.00 38.76 3.02
645 775 8.604890 GTTGGAGTACTATTGACTTATTGAAGC 58.395 37.037 0.00 0.00 35.97 3.86
646 776 7.847096 TGGAGTACTATTGACTTATTGAAGCA 58.153 34.615 0.00 0.00 35.97 3.91
647 777 8.486210 TGGAGTACTATTGACTTATTGAAGCAT 58.514 33.333 0.00 0.00 35.97 3.79
648 778 9.331282 GGAGTACTATTGACTTATTGAAGCATT 57.669 33.333 0.00 0.00 35.97 3.56
690 820 4.619227 GGCCCGCAGCGCCTATTA 62.619 66.667 10.07 0.00 45.17 0.98
702 832 2.286772 GCGCCTATTAACCATTTCCACG 60.287 50.000 0.00 0.00 0.00 4.94
817 974 4.376450 GAATAATGGTTCGATGTCTCGC 57.624 45.455 0.00 0.00 44.65 5.03
818 975 2.218953 TAATGGTTCGATGTCTCGCC 57.781 50.000 0.00 0.00 44.65 5.54
819 976 0.806102 AATGGTTCGATGTCTCGCCG 60.806 55.000 0.00 0.00 44.65 6.46
820 977 1.945354 ATGGTTCGATGTCTCGCCGT 61.945 55.000 0.00 0.00 44.65 5.68
821 978 2.158959 GGTTCGATGTCTCGCCGTG 61.159 63.158 0.00 0.00 44.65 4.94
822 979 2.506217 TTCGATGTCTCGCCGTGC 60.506 61.111 0.00 0.00 44.65 5.34
881 1038 1.712977 CTTCCATTGCCGCTCTCTGC 61.713 60.000 0.00 0.00 38.57 4.26
1319 1476 4.735132 CTCCGGCCGCGTTCTTGA 62.735 66.667 22.85 8.91 0.00 3.02
1539 1696 3.628646 GAGCAACATCCCGCTGGGT 62.629 63.158 12.46 0.00 44.74 4.51
1848 2005 2.186903 CCGGGCTACGTCTGCAAT 59.813 61.111 14.06 0.00 42.24 3.56
1907 2064 0.531200 GGCTGCAACGGTACTACTCT 59.469 55.000 0.50 0.00 0.00 3.24
1908 2065 1.747355 GGCTGCAACGGTACTACTCTA 59.253 52.381 0.50 0.00 0.00 2.43
1909 2066 2.223525 GGCTGCAACGGTACTACTCTAG 60.224 54.545 0.50 0.00 0.00 2.43
1910 2067 2.795331 GCTGCAACGGTACTACTCTAGC 60.795 54.545 0.00 0.00 0.00 3.42
1911 2068 2.683867 CTGCAACGGTACTACTCTAGCT 59.316 50.000 0.00 0.00 0.00 3.32
1912 2069 2.681848 TGCAACGGTACTACTCTAGCTC 59.318 50.000 0.00 0.00 0.00 4.09
1913 2070 2.286301 GCAACGGTACTACTCTAGCTCG 60.286 54.545 0.00 0.00 0.00 5.03
1914 2071 2.237393 ACGGTACTACTCTAGCTCGG 57.763 55.000 0.00 0.00 0.00 4.63
1915 2072 1.759445 ACGGTACTACTCTAGCTCGGA 59.241 52.381 0.00 0.00 0.00 4.55
1916 2073 2.169352 ACGGTACTACTCTAGCTCGGAA 59.831 50.000 0.00 0.00 0.00 4.30
1919 2076 4.095483 CGGTACTACTCTAGCTCGGAAAAA 59.905 45.833 0.00 0.00 0.00 1.94
2565 2764 9.009327 GTAATTGTGTTGTATCATCGAATTTGG 57.991 33.333 0.00 0.00 0.00 3.28
3083 3282 0.674581 TCTTGCTCATCGGTGGCTTG 60.675 55.000 9.95 4.03 0.00 4.01
3085 3284 0.955428 TTGCTCATCGGTGGCTTGTC 60.955 55.000 9.95 0.00 0.00 3.18
3093 3292 0.742281 CGGTGGCTTGTCATCCTCTG 60.742 60.000 0.00 0.00 0.00 3.35
3288 3519 2.025418 GGCCGTCACAGGTACAACG 61.025 63.158 0.00 0.00 35.01 4.10
3289 3520 1.007038 GCCGTCACAGGTACAACGA 60.007 57.895 0.00 0.00 37.31 3.85
3290 3521 1.280206 GCCGTCACAGGTACAACGAC 61.280 60.000 0.00 0.00 37.31 4.34
3291 3522 0.031043 CCGTCACAGGTACAACGACA 59.969 55.000 0.00 0.00 37.31 4.35
3292 3523 1.126079 CGTCACAGGTACAACGACAC 58.874 55.000 0.00 0.00 37.31 3.67
3297 3529 0.782384 CAGGTACAACGACACGCTTC 59.218 55.000 0.00 0.00 0.00 3.86
3316 3548 4.733405 GCTTCAGTCGTTAGGTTTTGTTTG 59.267 41.667 0.00 0.00 0.00 2.93
3318 3550 5.728351 TCAGTCGTTAGGTTTTGTTTGAG 57.272 39.130 0.00 0.00 0.00 3.02
3321 3553 6.540914 TCAGTCGTTAGGTTTTGTTTGAGAAT 59.459 34.615 0.00 0.00 0.00 2.40
3324 3556 7.713942 AGTCGTTAGGTTTTGTTTGAGAATACT 59.286 33.333 0.00 0.00 0.00 2.12
3326 3558 8.981647 TCGTTAGGTTTTGTTTGAGAATACTAC 58.018 33.333 0.00 0.00 0.00 2.73
3362 3658 2.985896 TGTTCAGGTGTAAGCATAGGC 58.014 47.619 0.00 0.00 41.61 3.93
3422 3718 5.458451 TGAGTCTTCAGAAGAGGAGGATA 57.542 43.478 13.53 0.00 38.41 2.59
3467 3763 2.656069 GCAGAACGGTGGGCTCCTA 61.656 63.158 0.00 0.00 0.00 2.94
3566 3862 2.357034 GGCAACTTCGACGAGGCA 60.357 61.111 6.92 0.00 0.00 4.75
3665 3961 3.322466 AAGAGGTCCAGGGTGGCG 61.322 66.667 0.00 0.00 37.47 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.204704 TGAGGACTATGCAGGACAACG 59.795 52.381 0.00 0.00 0.00 4.10
15 16 0.611896 TGATGTGCTCGAGGTGAGGA 60.612 55.000 15.58 0.00 45.38 3.71
38 39 3.614092 CCGCCTTATCTATTCATGCCAT 58.386 45.455 0.00 0.00 0.00 4.40
45 46 2.475487 GTGTTCGCCGCCTTATCTATTC 59.525 50.000 0.00 0.00 0.00 1.75
64 65 3.089284 GAGGGAAACATTGGTTAGGGTG 58.911 50.000 0.00 0.00 35.82 4.61
96 104 7.508977 TCAAAGACCCCTCTTTTACATGATTTT 59.491 33.333 0.00 0.00 43.10 1.82
102 110 7.010160 TGATTTCAAAGACCCCTCTTTTACAT 58.990 34.615 0.00 0.00 43.10 2.29
122 130 7.984422 TCATCACCGCTTTATGATATGATTT 57.016 32.000 0.00 0.00 33.73 2.17
186 194 0.110486 TGTTTGGGAGAGGACTTGGC 59.890 55.000 0.00 0.00 0.00 4.52
192 200 2.905415 ATGCATTGTTTGGGAGAGGA 57.095 45.000 0.00 0.00 0.00 3.71
194 202 4.579454 CCATATGCATTGTTTGGGAGAG 57.421 45.455 3.54 0.00 0.00 3.20
205 213 1.228956 ATGCGCCCCCATATGCATT 60.229 52.632 3.54 0.00 45.16 3.56
207 215 2.282391 GATGCGCCCCCATATGCA 60.282 61.111 4.18 0.00 42.22 3.96
215 223 3.585990 CCAATGTCGATGCGCCCC 61.586 66.667 4.18 0.00 0.00 5.80
228 236 4.019501 AGTGAGATGAGCTTGTCTTCCAAT 60.020 41.667 3.66 0.00 30.98 3.16
255 263 1.444553 CGTCTCGTCTTGCTCCCAC 60.445 63.158 0.00 0.00 0.00 4.61
257 265 1.137825 CTCGTCTCGTCTTGCTCCC 59.862 63.158 0.00 0.00 0.00 4.30
271 279 1.205893 GATCAAGTTGGAGGAGCTCGT 59.794 52.381 9.04 9.04 0.00 4.18
272 280 1.800655 CGATCAAGTTGGAGGAGCTCG 60.801 57.143 7.83 0.00 0.00 5.03
274 282 0.107945 GCGATCAAGTTGGAGGAGCT 60.108 55.000 2.34 0.00 0.00 4.09
275 283 1.092345 GGCGATCAAGTTGGAGGAGC 61.092 60.000 2.34 2.54 0.00 4.70
276 284 0.539051 AGGCGATCAAGTTGGAGGAG 59.461 55.000 2.34 0.00 0.00 3.69
277 285 0.537188 GAGGCGATCAAGTTGGAGGA 59.463 55.000 2.34 0.00 0.00 3.71
278 286 0.250234 TGAGGCGATCAAGTTGGAGG 59.750 55.000 2.34 0.00 34.02 4.30
310 318 1.665442 CTTTGCCTTTGTTCGGGGG 59.335 57.895 0.00 0.00 0.00 5.40
321 331 0.625849 CCTACCCATGTCCTTTGCCT 59.374 55.000 0.00 0.00 0.00 4.75
334 344 4.079958 ACATTAACCAATCCACTCCTACCC 60.080 45.833 0.00 0.00 0.00 3.69
347 357 3.071479 GTCCTCTTCGCACATTAACCAA 58.929 45.455 0.00 0.00 0.00 3.67
348 358 2.037902 TGTCCTCTTCGCACATTAACCA 59.962 45.455 0.00 0.00 0.00 3.67
354 364 0.036952 CCACTGTCCTCTTCGCACAT 60.037 55.000 0.00 0.00 0.00 3.21
364 374 2.969821 TGCATAAAACCCACTGTCCT 57.030 45.000 0.00 0.00 0.00 3.85
381 391 0.775861 GAATGGCGTGAACGTTTTGC 59.224 50.000 0.46 7.03 42.22 3.68
382 392 1.041726 CGAATGGCGTGAACGTTTTG 58.958 50.000 0.46 0.00 42.22 2.44
383 393 0.040781 CCGAATGGCGTGAACGTTTT 60.041 50.000 0.46 0.00 42.22 2.43
384 394 1.161563 ACCGAATGGCGTGAACGTTT 61.162 50.000 0.46 0.00 42.22 3.60
385 395 1.562575 GACCGAATGGCGTGAACGTT 61.563 55.000 0.00 0.00 42.22 3.99
386 396 2.025418 GACCGAATGGCGTGAACGT 61.025 57.895 4.59 0.00 42.22 3.99
387 397 2.736682 GGACCGAATGGCGTGAACG 61.737 63.158 0.00 0.00 39.70 3.95
388 398 1.024579 ATGGACCGAATGGCGTGAAC 61.025 55.000 0.00 0.00 39.70 3.18
389 399 1.024046 CATGGACCGAATGGCGTGAA 61.024 55.000 0.00 0.00 39.70 3.18
390 400 1.449423 CATGGACCGAATGGCGTGA 60.449 57.895 0.00 0.00 39.70 4.35
391 401 3.101209 CATGGACCGAATGGCGTG 58.899 61.111 0.00 0.00 39.70 5.34
392 402 2.824041 GCATGGACCGAATGGCGT 60.824 61.111 0.00 0.00 39.70 5.68
393 403 2.514592 AGCATGGACCGAATGGCG 60.515 61.111 0.00 0.00 39.70 5.69
407 417 3.825160 GACACTTGGCCGGACAGCA 62.825 63.158 11.51 0.00 0.00 4.41
451 464 4.905429 TCTGCTAACTTGGCATAAAGTGA 58.095 39.130 0.00 0.00 40.28 3.41
525 538 4.142038 AGAGGTTTTTATTCTTGCGTGGT 58.858 39.130 0.00 0.00 0.00 4.16
526 539 4.455877 AGAGAGGTTTTTATTCTTGCGTGG 59.544 41.667 0.00 0.00 0.00 4.94
527 540 5.613358 AGAGAGGTTTTTATTCTTGCGTG 57.387 39.130 0.00 0.00 0.00 5.34
528 541 7.148239 CCATTAGAGAGGTTTTTATTCTTGCGT 60.148 37.037 0.00 0.00 0.00 5.24
529 542 7.148239 ACCATTAGAGAGGTTTTTATTCTTGCG 60.148 37.037 0.00 0.00 33.39 4.85
553 569 8.554528 GCTCGATTTTAACTTACCCTAATTACC 58.445 37.037 0.00 0.00 0.00 2.85
557 573 6.478016 GTCGCTCGATTTTAACTTACCCTAAT 59.522 38.462 0.00 0.00 0.00 1.73
601 731 3.985925 CCAACTTCAAATTGAGCTTGAGC 59.014 43.478 13.21 0.00 42.49 4.26
602 732 5.009410 ACTCCAACTTCAAATTGAGCTTGAG 59.991 40.000 13.21 10.95 34.41 3.02
603 733 4.889409 ACTCCAACTTCAAATTGAGCTTGA 59.111 37.500 13.21 0.00 0.00 3.02
637 767 9.720667 CGAGTAAAATTGATCAATGCTTCAATA 57.279 29.630 21.39 5.17 40.70 1.90
638 768 8.246180 ACGAGTAAAATTGATCAATGCTTCAAT 58.754 29.630 21.39 0.00 42.77 2.57
639 769 7.592938 ACGAGTAAAATTGATCAATGCTTCAA 58.407 30.769 21.39 3.34 36.38 2.69
640 770 7.144722 ACGAGTAAAATTGATCAATGCTTCA 57.855 32.000 21.39 0.00 0.00 3.02
641 771 9.722056 AATACGAGTAAAATTGATCAATGCTTC 57.278 29.630 21.39 13.13 0.00 3.86
649 779 9.314501 GCCGAATAAATACGAGTAAAATTGATC 57.685 33.333 0.00 0.00 0.00 2.92
690 820 1.896660 ACTGCGCGTGGAAATGGTT 60.897 52.632 8.43 0.00 0.00 3.67
822 979 2.809601 CTTCGTTGACGGGGAGCG 60.810 66.667 3.48 0.00 40.29 5.03
823 980 3.119096 GCTTCGTTGACGGGGAGC 61.119 66.667 3.48 7.52 40.29 4.70
824 981 1.738099 CAGCTTCGTTGACGGGGAG 60.738 63.158 3.48 1.68 40.29 4.30
881 1038 4.271049 TGTCAAGAAAAGAAACGCAGAGAG 59.729 41.667 0.00 0.00 0.00 3.20
1803 1960 2.433318 GAGTCCAGGCACACGCTC 60.433 66.667 0.00 0.00 38.60 5.03
1848 2005 3.932580 CTCGTAGCCGCTGGTGCAA 62.933 63.158 2.16 0.00 39.64 4.08
1975 2132 0.972983 CATCGGGAGGACAGGTGTCT 60.973 60.000 9.90 0.00 44.20 3.41
2018 2175 0.102481 GCACGAGCCGAGGATAGAAA 59.898 55.000 0.00 0.00 33.58 2.52
2090 2247 1.539929 CGGGGAGATGAGATTGTCAGC 60.540 57.143 0.00 0.00 42.33 4.26
2199 2356 1.394917 GTTCAGGCATAGCTGACGTTG 59.605 52.381 0.00 0.00 34.62 4.10
2565 2764 3.428045 CGGGAATTTCTTCAATGGAGCAC 60.428 47.826 0.00 0.00 32.70 4.40
3014 3213 6.877322 GGGAACAGAGTATACTAGAGCTAGAG 59.123 46.154 5.09 0.00 36.97 2.43
3015 3214 6.329460 TGGGAACAGAGTATACTAGAGCTAGA 59.671 42.308 5.09 0.00 34.86 2.43
3016 3215 6.535540 TGGGAACAGAGTATACTAGAGCTAG 58.464 44.000 5.09 3.06 36.06 3.42
3017 3216 6.511017 TGGGAACAGAGTATACTAGAGCTA 57.489 41.667 5.09 0.00 35.01 3.32
3018 3217 5.390087 TGGGAACAGAGTATACTAGAGCT 57.610 43.478 5.09 0.00 35.01 4.09
3019 3218 6.466885 TTTGGGAACAGAGTATACTAGAGC 57.533 41.667 5.09 0.00 44.54 4.09
3104 3303 3.869246 TCTTCCGTTTGAGTCAGTTTCAC 59.131 43.478 0.00 0.00 0.00 3.18
3105 3304 4.131649 TCTTCCGTTTGAGTCAGTTTCA 57.868 40.909 0.00 0.00 0.00 2.69
3106 3305 4.511826 ACATCTTCCGTTTGAGTCAGTTTC 59.488 41.667 0.00 0.00 0.00 2.78
3186 3417 3.384532 CCCTTGGGGCATGTGCAC 61.385 66.667 10.75 10.75 45.53 4.57
3288 3519 1.335689 ACCTAACGACTGAAGCGTGTC 60.336 52.381 0.00 0.00 41.75 3.67
3289 3520 0.672342 ACCTAACGACTGAAGCGTGT 59.328 50.000 0.00 0.00 41.75 4.49
3290 3521 1.779569 AACCTAACGACTGAAGCGTG 58.220 50.000 0.00 0.00 41.75 5.34
3291 3522 2.521105 AAACCTAACGACTGAAGCGT 57.479 45.000 0.00 0.00 44.94 5.07
3292 3523 2.542595 ACAAAACCTAACGACTGAAGCG 59.457 45.455 0.00 0.00 0.00 4.68
3297 3529 5.728351 TCTCAAACAAAACCTAACGACTG 57.272 39.130 0.00 0.00 0.00 3.51
3324 3556 9.349713 ACCTGAACATTTCTGTCAAATAAAGTA 57.650 29.630 0.00 0.00 33.36 2.24
3326 3558 8.137437 ACACCTGAACATTTCTGTCAAATAAAG 58.863 33.333 0.00 0.00 33.36 1.85
3330 3562 7.581213 TTACACCTGAACATTTCTGTCAAAT 57.419 32.000 0.00 0.00 33.36 2.32
3331 3563 6.459573 GCTTACACCTGAACATTTCTGTCAAA 60.460 38.462 0.00 0.00 33.36 2.69
3332 3564 5.008613 GCTTACACCTGAACATTTCTGTCAA 59.991 40.000 0.00 0.00 33.36 3.18
3333 3565 4.515191 GCTTACACCTGAACATTTCTGTCA 59.485 41.667 0.00 0.00 33.36 3.58
3336 3568 5.633830 ATGCTTACACCTGAACATTTCTG 57.366 39.130 0.00 0.00 0.00 3.02
3338 3570 5.449177 GCCTATGCTTACACCTGAACATTTC 60.449 44.000 0.00 0.00 33.53 2.17
3339 3571 4.399303 GCCTATGCTTACACCTGAACATTT 59.601 41.667 0.00 0.00 33.53 2.32
3340 3572 3.947834 GCCTATGCTTACACCTGAACATT 59.052 43.478 0.00 0.00 33.53 2.71
3362 3658 1.372582 CCAGGATCACCATGAACACG 58.627 55.000 0.00 0.00 38.94 4.49
3422 3718 0.897863 ACCTCTGCTTCGCTCTGAGT 60.898 55.000 6.53 0.00 0.00 3.41
3503 3799 3.428045 CGGAAAAGATCTTGAATGCCACC 60.428 47.826 9.17 3.63 0.00 4.61
3665 3961 1.209019 TCCTTGAGCTGCTTCTCATCC 59.791 52.381 2.53 0.00 42.12 3.51
4239 4538 1.725557 ATGATCTCCCGGTGTCGTCG 61.726 60.000 0.00 0.00 33.95 5.12


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

AutoCloner maintained by Alex Coulton.