Multiple sequence alignment - TraesCS4A01G490000

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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 TraesCS4A01G490000 chr4A 100.000 2363 0 0 1 2363 740451580 740453942 0.000000e+00 4364.0
1 TraesCS4A01G490000 chr4A 88.541 1693 155 19 1 1678 740941563 740939895 0.000000e+00 2015.0
2 TraesCS4A01G490000 chr4A 86.091 1819 182 42 530 2317 739870909 739869131 0.000000e+00 1892.0
3 TraesCS4A01G490000 chr4A 83.871 1829 225 44 529 2312 741593746 741591943 0.000000e+00 1679.0
4 TraesCS4A01G490000 chr4A 87.649 1093 114 12 529 1609 742134140 742133057 0.000000e+00 1251.0
5 TraesCS4A01G490000 chr4A 87.523 1098 116 12 529 1614 739737617 739736529 0.000000e+00 1249.0
6 TraesCS4A01G490000 chr4A 86.482 1117 120 12 508 1614 741812279 741813374 0.000000e+00 1197.0
7 TraesCS4A01G490000 chr4A 86.422 1009 109 13 741 1732 741791509 741792506 0.000000e+00 1079.0
8 TraesCS4A01G490000 chr4A 89.120 625 54 3 1689 2312 740939715 740939104 0.000000e+00 765.0
9 TraesCS4A01G490000 chr4A 90.637 502 42 4 1811 2308 741482218 741482718 0.000000e+00 662.0
10 TraesCS4A01G490000 chr4A 90.457 503 46 2 1811 2312 741813602 741814103 0.000000e+00 662.0
11 TraesCS4A01G490000 chr4A 89.861 503 49 2 1811 2312 740581092 740580591 0.000000e+00 645.0
12 TraesCS4A01G490000 chr4A 88.294 504 57 2 1810 2312 739654093 739653591 9.340000e-169 603.0
13 TraesCS4A01G490000 chr4A 85.526 76 8 2 1685 1757 741813444 741813519 2.520000e-10 76.8
14 TraesCS4A01G490000 chr7A 87.050 1807 173 39 531 2309 1993200 1994973 0.000000e+00 1984.0
15 TraesCS4A01G490000 chr7A 86.608 1822 182 36 529 2312 2114212 2116009 0.000000e+00 1956.0
16 TraesCS4A01G490000 chr7A 86.489 1310 138 24 463 1757 3204624 3205909 0.000000e+00 1402.0
17 TraesCS4A01G490000 chr7A 84.737 1330 153 15 457 1761 3316080 3314776 0.000000e+00 1286.0
18 TraesCS4A01G490000 chr7A 92.644 503 35 2 1811 2312 3205984 3206485 0.000000e+00 723.0
19 TraesCS4A01G490000 chr7D 83.576 2131 220 66 211 2312 2560529 2562558 0.000000e+00 1877.0
20 TraesCS4A01G490000 chr7D 87.074 1261 115 19 529 1761 3783623 3784863 0.000000e+00 1382.0
21 TraesCS4A01G490000 chr7D 86.778 1263 118 20 529 1761 3629822 3631065 0.000000e+00 1362.0
22 TraesCS4A01G490000 chr7D 86.407 1258 105 27 529 1761 2354355 2355571 0.000000e+00 1315.0
23 TraesCS4A01G490000 chr7D 85.903 1135 125 19 515 1632 2606541 2607657 0.000000e+00 1177.0
24 TraesCS4A01G490000 chr7D 86.957 920 107 3 452 1364 2499961 2500874 0.000000e+00 1022.0


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 TraesCS4A01G490000 chr4A 740451580 740453942 2362 False 4364.000000 4364 100.000000 1 2363 1 chr4A.!!$F1 2362
1 TraesCS4A01G490000 chr4A 739869131 739870909 1778 True 1892.000000 1892 86.091000 530 2317 1 chr4A.!!$R3 1787
2 TraesCS4A01G490000 chr4A 741591943 741593746 1803 True 1679.000000 1679 83.871000 529 2312 1 chr4A.!!$R5 1783
3 TraesCS4A01G490000 chr4A 740939104 740941563 2459 True 1390.000000 2015 88.830500 1 2312 2 chr4A.!!$R7 2311
4 TraesCS4A01G490000 chr4A 742133057 742134140 1083 True 1251.000000 1251 87.649000 529 1609 1 chr4A.!!$R6 1080
5 TraesCS4A01G490000 chr4A 739736529 739737617 1088 True 1249.000000 1249 87.523000 529 1614 1 chr4A.!!$R2 1085
6 TraesCS4A01G490000 chr4A 741791509 741792506 997 False 1079.000000 1079 86.422000 741 1732 1 chr4A.!!$F3 991
7 TraesCS4A01G490000 chr4A 741482218 741482718 500 False 662.000000 662 90.637000 1811 2308 1 chr4A.!!$F2 497
8 TraesCS4A01G490000 chr4A 741812279 741814103 1824 False 645.266667 1197 87.488333 508 2312 3 chr4A.!!$F4 1804
9 TraesCS4A01G490000 chr4A 740580591 740581092 501 True 645.000000 645 89.861000 1811 2312 1 chr4A.!!$R4 501
10 TraesCS4A01G490000 chr4A 739653591 739654093 502 True 603.000000 603 88.294000 1810 2312 1 chr4A.!!$R1 502
11 TraesCS4A01G490000 chr7A 1993200 1994973 1773 False 1984.000000 1984 87.050000 531 2309 1 chr7A.!!$F1 1778
12 TraesCS4A01G490000 chr7A 2114212 2116009 1797 False 1956.000000 1956 86.608000 529 2312 1 chr7A.!!$F2 1783
13 TraesCS4A01G490000 chr7A 3314776 3316080 1304 True 1286.000000 1286 84.737000 457 1761 1 chr7A.!!$R1 1304
14 TraesCS4A01G490000 chr7A 3204624 3206485 1861 False 1062.500000 1402 89.566500 463 2312 2 chr7A.!!$F3 1849
15 TraesCS4A01G490000 chr7D 2560529 2562558 2029 False 1877.000000 1877 83.576000 211 2312 1 chr7D.!!$F3 2101
16 TraesCS4A01G490000 chr7D 3783623 3784863 1240 False 1382.000000 1382 87.074000 529 1761 1 chr7D.!!$F6 1232
17 TraesCS4A01G490000 chr7D 3629822 3631065 1243 False 1362.000000 1362 86.778000 529 1761 1 chr7D.!!$F5 1232
18 TraesCS4A01G490000 chr7D 2354355 2355571 1216 False 1315.000000 1315 86.407000 529 1761 1 chr7D.!!$F1 1232
19 TraesCS4A01G490000 chr7D 2606541 2607657 1116 False 1177.000000 1177 85.903000 515 1632 1 chr7D.!!$F4 1117
20 TraesCS4A01G490000 chr7D 2499961 2500874 913 False 1022.000000 1022 86.957000 452 1364 1 chr7D.!!$F2 912

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
915 961 0.032117 TGTCGATGACCCTCCAGGAT 60.032 55.0 0.0 0.0 39.89 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2727 0.108945 CTCTCGACACAGCTGCATCA 60.109 55.0 15.27 2.2 0.0 3.07 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
21 22 1.064389 ACTTGAGAATAAGGCCCAGGC 60.064 52.381 0.00 0.00 41.06 4.85
22 23 0.998928 TTGAGAATAAGGCCCAGGCA 59.001 50.000 11.50 0.00 44.11 4.75
25 26 1.423161 GAGAATAAGGCCCAGGCAGAT 59.577 52.381 11.50 0.00 44.11 2.90
30 31 2.440980 GGCCCAGGCAGATGTTCC 60.441 66.667 11.50 0.00 44.11 3.62
31 32 2.679716 GCCCAGGCAGATGTTCCT 59.320 61.111 3.12 0.00 41.49 3.36
61 62 6.726230 CACTGCATGGAAATATGAAGAGAAG 58.274 40.000 0.91 0.00 36.02 2.85
78 79 2.351726 AGAAGCACAACGTCAGTCAAAC 59.648 45.455 0.00 0.00 0.00 2.93
84 85 2.162809 ACAACGTCAGTCAAACAAACCC 59.837 45.455 0.00 0.00 0.00 4.11
95 96 3.120041 CAAACAAACCCACAAATCGACC 58.880 45.455 0.00 0.00 0.00 4.79
112 113 2.872245 CGACCATCACAAGTTCACAACT 59.128 45.455 0.00 0.00 45.46 3.16
119 120 7.554835 ACCATCACAAGTTCACAACTAAAACTA 59.445 33.333 0.00 0.00 41.91 2.24
193 194 4.445452 AGCAATTATTCACAACCAGCAG 57.555 40.909 0.00 0.00 0.00 4.24
198 199 6.215121 CAATTATTCACAACCAGCAGAACAA 58.785 36.000 0.00 0.00 0.00 2.83
248 253 9.846248 GATAACAGAACTGAACAAAAGCATATT 57.154 29.630 8.87 0.00 0.00 1.28
321 338 7.948278 ACGCACCTTATTGATAATAGAGAAC 57.052 36.000 0.00 0.00 0.00 3.01
328 345 9.276590 CCTTATTGATAATAGAGAACACATGCA 57.723 33.333 0.00 0.00 0.00 3.96
370 387 2.035066 AGCATCAACAGTGAAAAGCCAC 59.965 45.455 0.00 0.00 37.30 5.01
432 449 2.408050 ACACGTCAAATCTCAGCAGAC 58.592 47.619 0.00 0.00 0.00 3.51
464 482 9.227777 GATGTCCAGTTAATACAAACTAAGGTT 57.772 33.333 0.00 0.00 37.61 3.50
485 503 6.318900 AGGTTTGAAACTCGTCAGAAATCTTT 59.681 34.615 8.09 0.00 0.00 2.52
492 510 9.695884 GAAACTCGTCAGAAATCTTTATTCATC 57.304 33.333 0.00 0.00 0.00 2.92
538 566 2.672961 TATTCCGTGGACTCAGCAAG 57.327 50.000 0.00 0.00 0.00 4.01
557 585 1.351707 CCATCACGGCGCACATAAC 59.648 57.895 10.83 0.00 0.00 1.89
686 726 1.288932 AGGCCCAATAACAATCAGCCT 59.711 47.619 0.00 0.00 44.25 4.58
708 748 1.101049 CACCACACGCTTGGAAACCT 61.101 55.000 9.82 0.00 39.24 3.50
725 771 1.771255 ACCTATGTCCCAGCCATCTTC 59.229 52.381 0.00 0.00 0.00 2.87
727 773 1.688735 CTATGTCCCAGCCATCTTCGA 59.311 52.381 0.00 0.00 0.00 3.71
752 798 5.248477 TCTTAGACTGTACAGGCAATTTCCT 59.752 40.000 30.11 10.45 39.50 3.36
861 907 3.267860 GCAATGAGCGGAGGAGCG 61.268 66.667 0.00 0.00 43.00 5.03
863 909 1.153568 CAATGAGCGGAGGAGCGAA 60.154 57.895 0.00 0.00 43.00 4.70
912 958 0.608130 TGTTGTCGATGACCCTCCAG 59.392 55.000 0.00 0.00 0.00 3.86
915 961 0.032117 TGTCGATGACCCTCCAGGAT 60.032 55.000 0.00 0.00 39.89 3.24
919 965 1.383109 ATGACCCTCCAGGATCGCA 60.383 57.895 0.00 0.00 39.89 5.10
921 967 1.758514 GACCCTCCAGGATCGCAGA 60.759 63.158 0.00 0.00 39.80 4.26
925 971 0.319383 CCTCCAGGATCGCAGATTCG 60.319 60.000 0.00 0.00 45.12 3.34
970 1019 1.676746 TACCTCGTGGCTACTGCTAG 58.323 55.000 2.76 0.00 39.59 3.42
1094 1143 3.318557 TCATACATCTCTGCAGAGCTCAG 59.681 47.826 34.48 24.68 41.80 3.35
1295 1359 3.456431 CTACAGCGAGCGACTCCCG 62.456 68.421 0.00 0.00 42.21 5.14
1343 1416 2.152602 TTGGGCACATGGATCCAGCA 62.153 55.000 21.33 0.47 0.00 4.41
1353 1426 4.176404 ATCCAGCACCCAGTGGAT 57.824 55.556 11.95 0.00 46.56 3.41
1460 1536 0.828022 TAGATGTCCCCGTTGCGAAT 59.172 50.000 0.00 0.00 0.00 3.34
1513 1589 2.555547 GCGCCATATTCCCACCTGC 61.556 63.158 0.00 0.00 0.00 4.85
1597 1700 0.177604 GACCTCTCCACCATCTGCAG 59.822 60.000 7.63 7.63 0.00 4.41
1785 2165 4.882671 AGAGTTACAACAGCAACAACAG 57.117 40.909 0.00 0.00 0.00 3.16
1786 2166 3.065371 AGAGTTACAACAGCAACAACAGC 59.935 43.478 0.00 0.00 0.00 4.40
1801 2181 2.557924 CAACAGCCATTTAGCTTGGACA 59.442 45.455 7.13 0.00 42.61 4.02
1826 2209 8.529476 CAAGTACTGTACTACCTTTTATCACCT 58.471 37.037 19.97 0.00 38.26 4.00
1868 2254 7.769044 ACTAGTTGCACGTCAATTATAGGATTT 59.231 33.333 0.00 0.00 36.99 2.17
1871 2257 7.985184 AGTTGCACGTCAATTATAGGATTTCTA 59.015 33.333 0.00 0.00 36.99 2.10
1920 2306 5.639139 TGGAGACATACTCTAGATCAGCAT 58.361 41.667 0.00 0.00 44.37 3.79
2054 2440 1.914263 TCGTTGGTCCATTCGGGGA 60.914 57.895 14.22 0.00 37.22 4.81
2207 2605 9.799106 CCAAAGGTTATCTTAATATCAGGTGAT 57.201 33.333 0.00 0.00 35.47 3.06
2214 2612 9.929180 TTATCTTAATATCAGGTGATTTCTCCG 57.071 33.333 0.00 0.00 36.05 4.63
2233 2631 1.732405 CGCATACAACGACAGAGCAGA 60.732 52.381 0.00 0.00 0.00 4.26
2280 2678 8.683615 AGATACGAACATCATTTACTGACAGTA 58.316 33.333 11.37 11.37 36.48 2.74
2283 2681 6.926826 ACGAACATCATTTACTGACAGTACAA 59.073 34.615 14.96 12.30 36.48 2.41
2317 2715 7.792374 TCTTCAGAATGCATAGGTTATCAAC 57.208 36.000 0.00 0.00 34.76 3.18
2318 2716 7.337938 TCTTCAGAATGCATAGGTTATCAACA 58.662 34.615 0.00 0.00 34.76 3.33
2319 2717 7.496920 TCTTCAGAATGCATAGGTTATCAACAG 59.503 37.037 0.00 0.00 34.76 3.16
2320 2718 6.057533 TCAGAATGCATAGGTTATCAACAGG 58.942 40.000 0.00 0.00 34.76 4.00
2321 2719 5.240183 CAGAATGCATAGGTTATCAACAGGG 59.760 44.000 0.00 0.00 0.00 4.45
2322 2720 5.132648 AGAATGCATAGGTTATCAACAGGGA 59.867 40.000 0.00 0.00 0.00 4.20
2323 2721 4.150897 TGCATAGGTTATCAACAGGGAC 57.849 45.455 0.00 0.00 0.00 4.46
2324 2722 3.521531 TGCATAGGTTATCAACAGGGACA 59.478 43.478 0.00 0.00 0.00 4.02
2325 2723 4.018870 TGCATAGGTTATCAACAGGGACAA 60.019 41.667 0.00 0.00 0.00 3.18
2326 2724 4.947388 GCATAGGTTATCAACAGGGACAAA 59.053 41.667 0.00 0.00 0.00 2.83
2327 2725 5.594317 GCATAGGTTATCAACAGGGACAAAT 59.406 40.000 0.00 0.00 0.00 2.32
2328 2726 6.770785 GCATAGGTTATCAACAGGGACAAATA 59.229 38.462 0.00 0.00 0.00 1.40
2329 2727 7.448469 GCATAGGTTATCAACAGGGACAAATAT 59.552 37.037 0.00 0.00 0.00 1.28
2330 2728 8.786898 CATAGGTTATCAACAGGGACAAATATG 58.213 37.037 0.00 0.00 0.00 1.78
2331 2729 6.969043 AGGTTATCAACAGGGACAAATATGA 58.031 36.000 0.00 0.00 0.00 2.15
2332 2730 7.586349 AGGTTATCAACAGGGACAAATATGAT 58.414 34.615 0.00 0.00 0.00 2.45
2333 2731 7.503566 AGGTTATCAACAGGGACAAATATGATG 59.496 37.037 0.00 0.00 0.00 3.07
2334 2732 5.779529 ATCAACAGGGACAAATATGATGC 57.220 39.130 0.00 0.00 0.00 3.91
2335 2733 4.598022 TCAACAGGGACAAATATGATGCA 58.402 39.130 0.00 0.00 0.00 3.96
2336 2734 4.641541 TCAACAGGGACAAATATGATGCAG 59.358 41.667 0.00 0.00 0.00 4.41
2337 2735 2.954318 ACAGGGACAAATATGATGCAGC 59.046 45.455 0.00 0.00 0.00 5.25
2338 2736 3.220110 CAGGGACAAATATGATGCAGCT 58.780 45.455 2.53 0.00 0.00 4.24
2339 2737 3.004419 CAGGGACAAATATGATGCAGCTG 59.996 47.826 10.11 10.11 0.00 4.24
2340 2738 2.954318 GGGACAAATATGATGCAGCTGT 59.046 45.455 16.64 0.00 0.00 4.40
2341 2739 3.243301 GGGACAAATATGATGCAGCTGTG 60.243 47.826 16.64 4.57 0.00 3.66
2342 2740 3.379372 GGACAAATATGATGCAGCTGTGT 59.621 43.478 16.64 8.08 0.00 3.72
2343 2741 4.497006 GGACAAATATGATGCAGCTGTGTC 60.497 45.833 16.64 16.24 33.70 3.67
2344 2742 3.064408 ACAAATATGATGCAGCTGTGTCG 59.936 43.478 16.64 3.00 0.00 4.35
2345 2743 2.896745 ATATGATGCAGCTGTGTCGA 57.103 45.000 16.64 6.49 0.00 4.20
2346 2744 2.214387 TATGATGCAGCTGTGTCGAG 57.786 50.000 16.64 0.00 0.00 4.04
2347 2745 0.533951 ATGATGCAGCTGTGTCGAGA 59.466 50.000 16.64 0.00 0.00 4.04
2348 2746 0.108945 TGATGCAGCTGTGTCGAGAG 60.109 55.000 16.64 0.00 0.00 3.20
2349 2747 1.419874 GATGCAGCTGTGTCGAGAGC 61.420 60.000 16.64 0.00 38.81 4.09
2350 2748 2.048784 GCAGCTGTGTCGAGAGCA 60.049 61.111 16.64 0.38 41.05 4.26
2351 2749 1.447489 GCAGCTGTGTCGAGAGCAT 60.447 57.895 16.64 0.00 41.05 3.79
2352 2750 1.018226 GCAGCTGTGTCGAGAGCATT 61.018 55.000 16.64 0.00 41.05 3.56
2353 2751 0.997932 CAGCTGTGTCGAGAGCATTC 59.002 55.000 5.25 0.00 41.05 2.67
2354 2752 0.605083 AGCTGTGTCGAGAGCATTCA 59.395 50.000 12.26 0.00 41.05 2.57
2355 2753 1.001293 AGCTGTGTCGAGAGCATTCAA 59.999 47.619 12.26 0.00 41.05 2.69
2356 2754 1.800586 GCTGTGTCGAGAGCATTCAAA 59.199 47.619 6.21 0.00 38.39 2.69
2357 2755 2.417933 GCTGTGTCGAGAGCATTCAAAT 59.582 45.455 6.21 0.00 38.39 2.32
2358 2756 3.484886 GCTGTGTCGAGAGCATTCAAATC 60.485 47.826 6.21 0.00 38.39 2.17
2359 2757 3.930336 TGTGTCGAGAGCATTCAAATCT 58.070 40.909 0.00 0.00 0.00 2.40
2360 2758 3.928992 TGTGTCGAGAGCATTCAAATCTC 59.071 43.478 0.00 0.00 36.85 2.75
2361 2759 4.180057 GTGTCGAGAGCATTCAAATCTCT 58.820 43.478 0.00 0.00 39.66 3.10
2362 2760 4.032672 GTGTCGAGAGCATTCAAATCTCTG 59.967 45.833 8.48 0.00 37.32 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.000396 GAACATCTGCCTGGGCCTT 60.000 57.895 4.53 0.00 41.09 4.35
21 22 0.322277 AGTGGCTGCAGGAACATCTG 60.322 55.000 17.12 0.00 37.79 2.90
22 23 0.322277 CAGTGGCTGCAGGAACATCT 60.322 55.000 17.12 0.00 0.00 2.90
56 57 1.852942 TGACTGACGTTGTGCTTCTC 58.147 50.000 0.00 0.00 0.00 2.87
61 62 2.535934 TTGTTTGACTGACGTTGTGC 57.464 45.000 0.00 0.00 0.00 4.57
78 79 2.556189 TGATGGTCGATTTGTGGGTTTG 59.444 45.455 0.00 0.00 0.00 2.93
84 85 4.024133 TGAACTTGTGATGGTCGATTTGTG 60.024 41.667 0.00 0.00 0.00 3.33
95 96 9.781834 TTTAGTTTTAGTTGTGAACTTGTGATG 57.218 29.630 0.00 0.00 42.81 3.07
136 137 6.375589 GCATGTGCTACAGGATTAACCTTGA 61.376 44.000 5.35 0.00 41.97 3.02
149 150 6.293571 GCTATTTATGATGTGCATGTGCTACA 60.294 38.462 6.55 9.14 42.66 2.74
152 153 4.581409 TGCTATTTATGATGTGCATGTGCT 59.419 37.500 6.55 0.00 42.66 4.40
153 154 4.862350 TGCTATTTATGATGTGCATGTGC 58.138 39.130 0.00 0.00 37.87 4.57
154 155 7.940178 AATTGCTATTTATGATGTGCATGTG 57.060 32.000 0.00 0.00 37.87 3.21
193 194 9.941664 CTTCTGAATGGTATTGATATGTTGTTC 57.058 33.333 0.00 0.00 0.00 3.18
198 199 7.805163 TCACCTTCTGAATGGTATTGATATGT 58.195 34.615 10.01 0.00 34.79 2.29
248 253 4.534500 TCTCTTTACCCAGTTTGCTCCATA 59.466 41.667 0.00 0.00 0.00 2.74
328 345 5.114081 GCTTCATCTTTGGCTGCAATAAAT 58.886 37.500 0.50 0.00 0.00 1.40
380 397 1.796617 GCATTTGGATCAACAGCTCGC 60.797 52.381 0.00 0.00 0.00 5.03
432 449 9.823647 AGTTTGTATTAACTGGACATCTATCTG 57.176 33.333 0.00 0.00 37.00 2.90
464 482 9.051679 TGAATAAAGATTTCTGACGAGTTTCAA 57.948 29.630 0.00 0.00 0.00 2.69
485 503 4.523943 GCAGTGGGCATTTATGGATGAATA 59.476 41.667 0.00 0.00 43.97 1.75
557 585 1.153168 CCATACAGGGGCGGACTTG 60.153 63.158 0.00 0.00 0.00 3.16
588 622 0.958822 AACCGCCTGTGTGGAATTTC 59.041 50.000 0.00 0.00 45.51 2.17
615 649 1.002069 AGCTTCATTCATGGACCCCA 58.998 50.000 0.00 0.00 38.19 4.96
686 726 0.393132 TTTCCAAGCGTGTGGTGACA 60.393 50.000 0.00 0.00 39.88 3.58
708 748 1.788229 TCGAAGATGGCTGGGACATA 58.212 50.000 0.00 0.00 38.20 2.29
725 771 4.371855 TTGCCTGTACAGTCTAAGATCG 57.628 45.455 21.18 4.06 0.00 3.69
727 773 6.069963 AGGAAATTGCCTGTACAGTCTAAGAT 60.070 38.462 21.18 6.58 36.76 2.40
752 798 3.181458 GGACAACAAGTGGACCACTCTTA 60.181 47.826 27.28 0.00 44.62 2.10
861 907 2.369394 CTCAACCATACAAGCCCCTTC 58.631 52.381 0.00 0.00 0.00 3.46
863 909 0.034089 GCTCAACCATACAAGCCCCT 60.034 55.000 0.00 0.00 0.00 4.79
912 958 2.430546 ATGACTCGAATCTGCGATCC 57.569 50.000 0.00 0.00 39.85 3.36
915 961 2.290916 GGAGTATGACTCGAATCTGCGA 59.709 50.000 0.00 0.00 45.96 5.10
919 965 3.886505 GGTGAGGAGTATGACTCGAATCT 59.113 47.826 0.00 0.00 45.96 2.40
921 967 2.619177 CGGTGAGGAGTATGACTCGAAT 59.381 50.000 0.73 0.00 45.96 3.34
925 971 1.103803 TGCGGTGAGGAGTATGACTC 58.896 55.000 0.00 0.00 44.32 3.36
970 1019 4.124851 AGTTCTATGTGATCGGTGGTTC 57.875 45.455 0.00 0.00 0.00 3.62
1094 1143 4.025647 GCGCTGATTCTTCTGGTAATGTAC 60.026 45.833 0.00 0.00 0.00 2.90
1383 1456 4.520874 TGGATCTATCTCTCTTGCGGTAAG 59.479 45.833 0.00 0.00 37.76 2.34
1460 1536 2.773487 ACCGTGATTTCAATTCCGTGA 58.227 42.857 0.00 0.00 0.00 4.35
1513 1589 3.335356 ATTGCCTCCACCGCCTCTG 62.335 63.158 0.00 0.00 0.00 3.35
1785 2165 4.010349 AGTACTTGTCCAAGCTAAATGGC 58.990 43.478 6.94 0.00 41.99 4.40
1786 2166 5.003804 ACAGTACTTGTCCAAGCTAAATGG 58.996 41.667 6.94 0.00 41.99 3.16
1801 2181 8.661752 AGGTGATAAAAGGTAGTACAGTACTT 57.338 34.615 18.56 2.22 40.14 2.24
1826 2209 3.256704 ACTAGTGGATTCTGGTTCCCAA 58.743 45.455 0.00 0.00 30.80 4.12
1868 2254 8.721133 TTGGCATAGTTAGTAATCATCCTAGA 57.279 34.615 0.00 0.00 0.00 2.43
1871 2257 7.238514 AGGATTGGCATAGTTAGTAATCATCCT 59.761 37.037 3.33 3.33 0.00 3.24
1920 2306 0.396060 GCAAAATTTGGGGGTGCAGA 59.604 50.000 7.89 0.00 35.28 4.26
2054 2440 5.622233 GCTCAGGCTCGTTTTTAATTCCATT 60.622 40.000 0.00 0.00 35.22 3.16
2207 2605 2.029739 TCTGTCGTTGTATGCGGAGAAA 60.030 45.455 0.00 0.00 0.00 2.52
2214 2612 1.923204 CTCTGCTCTGTCGTTGTATGC 59.077 52.381 0.00 0.00 0.00 3.14
2233 2631 0.251077 CAGAAAGTTGCCTGCCCTCT 60.251 55.000 0.00 0.00 0.00 3.69
2247 2645 9.653287 AGTAAATGATGTTCGTATCTTCAGAAA 57.347 29.630 0.00 0.00 0.00 2.52
2248 2646 9.087424 CAGTAAATGATGTTCGTATCTTCAGAA 57.913 33.333 0.00 0.00 0.00 3.02
2254 2652 7.548097 ACTGTCAGTAAATGATGTTCGTATCT 58.452 34.615 2.87 0.00 40.92 1.98
2260 2658 7.172532 TGGTTGTACTGTCAGTAAATGATGTTC 59.827 37.037 14.33 0.01 40.92 3.18
2280 2678 3.213206 TCTGAAGATTGCAGTGGTTGT 57.787 42.857 0.00 0.00 34.98 3.32
2283 2681 2.490903 GCATTCTGAAGATTGCAGTGGT 59.509 45.455 17.87 0.00 45.53 4.16
2312 2710 5.202765 TGCATCATATTTGTCCCTGTTGAT 58.797 37.500 0.00 0.00 0.00 2.57
2317 2715 3.004419 CAGCTGCATCATATTTGTCCCTG 59.996 47.826 0.00 0.00 0.00 4.45
2318 2716 3.220110 CAGCTGCATCATATTTGTCCCT 58.780 45.455 0.00 0.00 0.00 4.20
2319 2717 2.954318 ACAGCTGCATCATATTTGTCCC 59.046 45.455 15.27 0.00 0.00 4.46
2320 2718 3.379372 ACACAGCTGCATCATATTTGTCC 59.621 43.478 15.27 0.00 0.00 4.02
2321 2719 4.595116 GACACAGCTGCATCATATTTGTC 58.405 43.478 15.27 12.72 0.00 3.18
2322 2720 3.064408 CGACACAGCTGCATCATATTTGT 59.936 43.478 15.27 7.11 0.00 2.83
2323 2721 3.310501 TCGACACAGCTGCATCATATTTG 59.689 43.478 15.27 3.43 0.00 2.32
2324 2722 3.534554 TCGACACAGCTGCATCATATTT 58.465 40.909 15.27 0.00 0.00 1.40
2325 2723 3.129109 CTCGACACAGCTGCATCATATT 58.871 45.455 15.27 0.00 0.00 1.28
2326 2724 2.363359 TCTCGACACAGCTGCATCATAT 59.637 45.455 15.27 0.00 0.00 1.78
2327 2725 1.750778 TCTCGACACAGCTGCATCATA 59.249 47.619 15.27 1.94 0.00 2.15
2328 2726 0.533951 TCTCGACACAGCTGCATCAT 59.466 50.000 15.27 0.00 0.00 2.45
2329 2727 0.108945 CTCTCGACACAGCTGCATCA 60.109 55.000 15.27 2.20 0.00 3.07
2330 2728 1.419874 GCTCTCGACACAGCTGCATC 61.420 60.000 15.27 10.75 32.48 3.91
2331 2729 1.447489 GCTCTCGACACAGCTGCAT 60.447 57.895 15.27 0.73 32.48 3.96
2332 2730 2.048784 GCTCTCGACACAGCTGCA 60.049 61.111 15.27 0.00 32.48 4.41
2333 2731 1.018226 AATGCTCTCGACACAGCTGC 61.018 55.000 15.27 0.00 36.53 5.25
2334 2732 0.997932 GAATGCTCTCGACACAGCTG 59.002 55.000 13.48 13.48 36.53 4.24
2335 2733 0.605083 TGAATGCTCTCGACACAGCT 59.395 50.000 7.57 0.00 36.53 4.24
2336 2734 1.432514 TTGAATGCTCTCGACACAGC 58.567 50.000 0.20 0.20 36.08 4.40
2337 2735 3.931468 AGATTTGAATGCTCTCGACACAG 59.069 43.478 0.00 0.00 0.00 3.66
2338 2736 3.928992 GAGATTTGAATGCTCTCGACACA 59.071 43.478 0.00 0.00 0.00 3.72
2339 2737 4.032672 CAGAGATTTGAATGCTCTCGACAC 59.967 45.833 0.00 0.00 40.26 3.67
2340 2738 4.179298 CAGAGATTTGAATGCTCTCGACA 58.821 43.478 0.00 0.00 40.26 4.35
2341 2739 4.775440 CAGAGATTTGAATGCTCTCGAC 57.225 45.455 0.00 0.00 40.26 4.20


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

AutoCloner maintained by Alex Coulton.