Multiple sequence alignment - TraesCS3B01G505300

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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 TraesCS3B01G505300 chr3B 100.000 2315 0 0 1 2315 749504609 749502295 0.000000e+00 4276
1 TraesCS3B01G505300 chr3B 95.475 884 34 2 1433 2315 715062040 715061162 0.000000e+00 1406
2 TraesCS3B01G505300 chr3A 90.102 1273 74 20 196 1432 697514833 697513577 0.000000e+00 1605
3 TraesCS3B01G505300 chr3A 93.789 322 20 0 997 1318 697461638 697461317 3.460000e-133 484
4 TraesCS3B01G505300 chr3A 85.286 367 50 4 996 1360 697628056 697628420 2.170000e-100 375
5 TraesCS3B01G505300 chr3D 88.329 1388 77 35 85 1432 562216155 562214813 0.000000e+00 1587
6 TraesCS3B01G505300 chr3D 93.789 322 20 0 997 1318 561728876 561728555 3.460000e-133 484
7 TraesCS3B01G505300 chr4A 96.840 886 27 1 1431 2315 643931594 643930709 0.000000e+00 1480
8 TraesCS3B01G505300 chr4A 96.731 887 26 3 1428 2313 642985676 642986560 0.000000e+00 1474
9 TraesCS3B01G505300 chr4A 96.380 884 29 3 1431 2313 643798593 643797712 0.000000e+00 1452
10 TraesCS3B01G505300 chr4A 96.154 884 31 3 1431 2313 643702831 643701950 0.000000e+00 1441
11 TraesCS3B01G505300 chrUn 96.833 884 25 3 1431 2313 314693316 314692435 0.000000e+00 1474
12 TraesCS3B01G505300 chr2B 95.701 884 32 2 1433 2315 140112948 140113826 0.000000e+00 1417
13 TraesCS3B01G505300 chr7B 95.265 887 34 4 1432 2315 572387589 572386708 0.000000e+00 1399
14 TraesCS3B01G505300 chr6A 95.039 887 41 3 1432 2315 18640173 18639287 0.000000e+00 1391
15 TraesCS3B01G505300 chr6D 90.909 88 7 1 1 88 5904676 5904762 1.450000e-22 117
16 TraesCS3B01G505300 chr5A 90.909 55 5 0 1 55 14270599 14270545 8.870000e-10 75


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 TraesCS3B01G505300 chr3B 749502295 749504609 2314 True 4276 4276 100.000 1 2315 1 chr3B.!!$R2 2314
1 TraesCS3B01G505300 chr3B 715061162 715062040 878 True 1406 1406 95.475 1433 2315 1 chr3B.!!$R1 882
2 TraesCS3B01G505300 chr3A 697513577 697514833 1256 True 1605 1605 90.102 196 1432 1 chr3A.!!$R2 1236
3 TraesCS3B01G505300 chr3D 562214813 562216155 1342 True 1587 1587 88.329 85 1432 1 chr3D.!!$R2 1347
4 TraesCS3B01G505300 chr4A 643930709 643931594 885 True 1480 1480 96.840 1431 2315 1 chr4A.!!$R3 884
5 TraesCS3B01G505300 chr4A 642985676 642986560 884 False 1474 1474 96.731 1428 2313 1 chr4A.!!$F1 885
6 TraesCS3B01G505300 chr4A 643797712 643798593 881 True 1452 1452 96.380 1431 2313 1 chr4A.!!$R2 882
7 TraesCS3B01G505300 chr4A 643701950 643702831 881 True 1441 1441 96.154 1431 2313 1 chr4A.!!$R1 882
8 TraesCS3B01G505300 chrUn 314692435 314693316 881 True 1474 1474 96.833 1431 2313 1 chrUn.!!$R1 882
9 TraesCS3B01G505300 chr2B 140112948 140113826 878 False 1417 1417 95.701 1433 2315 1 chr2B.!!$F1 882
10 TraesCS3B01G505300 chr7B 572386708 572387589 881 True 1399 1399 95.265 1432 2315 1 chr7B.!!$R1 883
11 TraesCS3B01G505300 chr6A 18639287 18640173 886 True 1391 1391 95.039 1432 2315 1 chr6A.!!$R1 883

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
158 159 0.035820 TCCGGTATGGAAGTGGCAAC 60.036 55.0 0.0 0.0 46.38 4.17 F
198 199 0.037419 GATGGCCGCAATGGTTGTTT 60.037 50.0 0.0 0.0 41.21 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1037 1088 1.884075 CGTCCCGAAGATCACCACCA 61.884 60.0 0.00 0.0 0.00 4.17 R
1856 1922 2.499756 TTCGCGTAGGAGCATGTGCA 62.500 55.0 5.77 0.0 45.16 4.57 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
31 32 2.413837 CGCTAAAAGTGCTACAGTGGT 58.586 47.619 0.00 0.00 0.00 4.16
32 33 2.157668 CGCTAAAAGTGCTACAGTGGTG 59.842 50.000 0.00 0.00 0.00 4.17
33 34 2.095718 GCTAAAAGTGCTACAGTGGTGC 60.096 50.000 0.00 0.00 0.00 5.01
34 35 2.348411 AAAAGTGCTACAGTGGTGCT 57.652 45.000 10.24 0.00 0.00 4.40
35 36 1.884235 AAAGTGCTACAGTGGTGCTC 58.116 50.000 10.24 7.20 0.00 4.26
36 37 1.051812 AAGTGCTACAGTGGTGCTCT 58.948 50.000 10.24 9.04 32.87 4.09
37 38 1.924731 AGTGCTACAGTGGTGCTCTA 58.075 50.000 10.88 0.00 0.00 2.43
38 39 2.248248 AGTGCTACAGTGGTGCTCTAA 58.752 47.619 10.88 0.00 0.00 2.10
39 40 2.632996 AGTGCTACAGTGGTGCTCTAAA 59.367 45.455 10.88 0.00 0.00 1.85
40 41 3.071023 AGTGCTACAGTGGTGCTCTAAAA 59.929 43.478 10.88 0.00 0.00 1.52
41 42 3.186613 GTGCTACAGTGGTGCTCTAAAAC 59.813 47.826 10.24 0.00 0.00 2.43
42 43 3.071023 TGCTACAGTGGTGCTCTAAAACT 59.929 43.478 10.24 0.00 0.00 2.66
43 44 4.282449 TGCTACAGTGGTGCTCTAAAACTA 59.718 41.667 10.24 0.00 0.00 2.24
44 45 5.046591 TGCTACAGTGGTGCTCTAAAACTAT 60.047 40.000 10.24 0.00 0.00 2.12
45 46 5.875359 GCTACAGTGGTGCTCTAAAACTATT 59.125 40.000 0.00 0.00 0.00 1.73
46 47 6.371825 GCTACAGTGGTGCTCTAAAACTATTT 59.628 38.462 0.00 0.00 0.00 1.40
47 48 7.094762 GCTACAGTGGTGCTCTAAAACTATTTT 60.095 37.037 0.00 0.00 36.67 1.82
48 49 9.431887 CTACAGTGGTGCTCTAAAACTATTTTA 57.568 33.333 0.00 0.00 34.19 1.52
66 67 9.289303 ACTATTTTAGCACTCAATATTTTTGCG 57.711 29.630 6.92 0.00 38.26 4.85
67 68 6.388259 TTTTAGCACTCAATATTTTTGCGC 57.612 33.333 0.00 0.00 38.26 6.09
68 69 2.879826 AGCACTCAATATTTTTGCGCC 58.120 42.857 4.18 0.00 38.26 6.53
69 70 2.493278 AGCACTCAATATTTTTGCGCCT 59.507 40.909 4.18 0.00 38.26 5.52
70 71 2.854185 GCACTCAATATTTTTGCGCCTC 59.146 45.455 4.18 0.00 0.00 4.70
71 72 3.428045 GCACTCAATATTTTTGCGCCTCT 60.428 43.478 4.18 0.00 0.00 3.69
72 73 4.100529 CACTCAATATTTTTGCGCCTCTG 58.899 43.478 4.18 0.00 0.00 3.35
73 74 3.758554 ACTCAATATTTTTGCGCCTCTGT 59.241 39.130 4.18 0.00 0.00 3.41
74 75 4.218417 ACTCAATATTTTTGCGCCTCTGTT 59.782 37.500 4.18 0.00 0.00 3.16
75 76 4.484236 TCAATATTTTTGCGCCTCTGTTG 58.516 39.130 4.18 1.80 0.00 3.33
76 77 3.508744 ATATTTTTGCGCCTCTGTTGG 57.491 42.857 4.18 0.00 0.00 3.77
77 78 1.327303 ATTTTTGCGCCTCTGTTGGA 58.673 45.000 4.18 0.00 0.00 3.53
78 79 0.667993 TTTTTGCGCCTCTGTTGGAG 59.332 50.000 4.18 0.00 41.51 3.86
79 80 0.179032 TTTTGCGCCTCTGTTGGAGA 60.179 50.000 4.18 0.00 44.45 3.71
80 81 0.036732 TTTGCGCCTCTGTTGGAGAT 59.963 50.000 4.18 0.00 44.45 2.75
81 82 0.036732 TTGCGCCTCTGTTGGAGATT 59.963 50.000 4.18 0.00 44.45 2.40
82 83 0.391661 TGCGCCTCTGTTGGAGATTC 60.392 55.000 4.18 0.00 44.45 2.52
83 84 0.107945 GCGCCTCTGTTGGAGATTCT 60.108 55.000 0.00 0.00 44.45 2.40
94 95 3.066208 TGGAGATTCTCTTAGGGGCAT 57.934 47.619 13.22 0.00 0.00 4.40
95 96 2.707791 TGGAGATTCTCTTAGGGGCATG 59.292 50.000 13.22 0.00 0.00 4.06
97 98 3.495806 GGAGATTCTCTTAGGGGCATGTG 60.496 52.174 13.22 0.00 0.00 3.21
98 99 2.158696 AGATTCTCTTAGGGGCATGTGC 60.159 50.000 0.00 0.00 41.14 4.57
113 114 0.884259 TGTGCACGAACACATCCTGG 60.884 55.000 13.13 0.00 45.36 4.45
116 117 0.391130 GCACGAACACATCCTGGCTA 60.391 55.000 0.00 0.00 0.00 3.93
129 130 1.506493 CTGGCTATCATCGACAAGGC 58.494 55.000 0.00 0.00 35.26 4.35
136 137 1.191489 TCATCGACAAGGCCAGGTCA 61.191 55.000 22.02 12.25 33.66 4.02
148 149 1.443407 CAGGTCAGCTCCGGTATGG 59.557 63.158 0.00 0.00 40.09 2.74
157 158 2.378211 TCCGGTATGGAAGTGGCAA 58.622 52.632 0.00 0.00 46.38 4.52
158 159 0.035820 TCCGGTATGGAAGTGGCAAC 60.036 55.000 0.00 0.00 46.38 4.17
159 160 0.322098 CCGGTATGGAAGTGGCAACA 60.322 55.000 0.00 0.00 43.96 3.33
189 190 1.677300 ATCGGTTTGATGGCCGCAA 60.677 52.632 6.75 6.75 46.79 4.85
198 199 0.037419 GATGGCCGCAATGGTTGTTT 60.037 50.000 0.00 0.00 41.21 2.83
205 206 1.864565 GCAATGGTTGTTTGGTGGTC 58.135 50.000 0.00 0.00 0.00 4.02
317 320 9.866798 TGATAAGAGATGCATCAAGTATACATC 57.133 33.333 27.81 16.98 38.27 3.06
319 322 6.047511 AGAGATGCATCAAGTATACATCCC 57.952 41.667 27.81 0.00 38.63 3.85
320 323 5.545335 AGAGATGCATCAAGTATACATCCCA 59.455 40.000 27.81 0.00 38.63 4.37
321 324 5.555017 AGATGCATCAAGTATACATCCCAC 58.445 41.667 27.81 0.00 38.63 4.61
323 326 5.109500 TGCATCAAGTATACATCCCACAA 57.891 39.130 5.50 0.00 0.00 3.33
460 479 3.797039 CCGACATTCACATGGTATCAGT 58.203 45.455 0.00 0.00 34.27 3.41
560 587 3.595173 ACGTGGAAATTCATGATGACGA 58.405 40.909 7.43 0.00 0.00 4.20
563 590 4.285292 GTGGAAATTCATGATGACGATGC 58.715 43.478 0.00 0.00 0.00 3.91
601 632 0.947244 CATGGTAGCCCGATTCAAGC 59.053 55.000 0.00 0.00 0.00 4.01
632 663 9.669353 CGAATATTAATTCACCTCCATTTTCAG 57.331 33.333 0.00 0.00 41.44 3.02
645 676 6.801862 CCTCCATTTTCAGTTATTCGAAACAC 59.198 38.462 0.00 1.56 31.09 3.32
677 708 1.777461 GAACCATATCGCGTACGTCAC 59.223 52.381 17.90 0.00 41.18 3.67
697 728 6.398621 CGTCACACTCATCGTACAAAGTTTAG 60.399 42.308 0.00 0.00 0.00 1.85
699 730 7.592533 GTCACACTCATCGTACAAAGTTTAGTA 59.407 37.037 0.00 0.00 0.00 1.82
701 732 8.922676 CACACTCATCGTACAAAGTTTAGTAAT 58.077 33.333 0.00 0.00 0.00 1.89
705 736 9.671521 CTCATCGTACAAAGTTTAGTAATTTCG 57.328 33.333 0.00 0.00 0.00 3.46
706 737 8.164153 TCATCGTACAAAGTTTAGTAATTTCGC 58.836 33.333 0.00 0.00 0.00 4.70
707 738 6.515882 TCGTACAAAGTTTAGTAATTTCGCG 58.484 36.000 0.00 0.00 0.00 5.87
711 742 9.956797 GTACAAAGTTTAGTAATTTCGCGAATA 57.043 29.630 24.05 10.40 0.00 1.75
736 767 2.073816 AGGTAACCGTGAGATTTTGCG 58.926 47.619 0.00 0.00 37.17 4.85
864 902 2.814913 CTAACGGTCCACTTGCCCCC 62.815 65.000 0.00 0.00 0.00 5.40
866 904 4.722700 CGGTCCACTTGCCCCCAG 62.723 72.222 0.00 0.00 0.00 4.45
867 905 3.580319 GGTCCACTTGCCCCCAGT 61.580 66.667 0.00 0.00 0.00 4.00
868 906 2.034221 GTCCACTTGCCCCCAGTC 59.966 66.667 0.00 0.00 0.00 3.51
869 907 2.449518 TCCACTTGCCCCCAGTCA 60.450 61.111 0.00 0.00 0.00 3.41
895 933 7.667557 TCATCTATAAATAGCTAGCACCGTTT 58.332 34.615 18.83 13.43 0.00 3.60
896 934 7.813148 TCATCTATAAATAGCTAGCACCGTTTC 59.187 37.037 18.83 0.00 0.00 2.78
926 969 6.462552 TCTCATCACCATCACAAACAAAAA 57.537 33.333 0.00 0.00 0.00 1.94
939 982 5.565259 CACAAACAAAAACATCGCTAGCTAG 59.435 40.000 16.84 16.84 0.00 3.42
943 986 4.567159 ACAAAAACATCGCTAGCTAGCTAC 59.433 41.667 36.02 15.46 46.85 3.58
944 987 3.372660 AAACATCGCTAGCTAGCTACC 57.627 47.619 36.02 13.40 46.85 3.18
946 989 2.156098 ACATCGCTAGCTAGCTACCTC 58.844 52.381 36.02 12.95 46.85 3.85
948 991 1.885560 TCGCTAGCTAGCTACCTCAG 58.114 55.000 36.02 22.11 46.85 3.35
950 993 1.543650 CGCTAGCTAGCTACCTCAGGA 60.544 57.143 36.02 0.00 46.85 3.86
962 1009 5.708230 AGCTACCTCAGGATAGTTAAGATCG 59.292 44.000 0.00 0.00 0.00 3.69
1215 1266 2.185867 GTGCCGGCGGTCTTCATA 59.814 61.111 28.82 0.00 0.00 2.15
1218 1269 2.280186 CCGGCGGTCTTCATAGGC 60.280 66.667 19.97 0.00 0.00 3.93
1379 1430 5.336531 GGAGTACTAGCTTGCAGTTACAGAA 60.337 44.000 0.00 0.00 0.00 3.02
1384 1435 7.545362 ACTAGCTTGCAGTTACAGAATTATG 57.455 36.000 0.00 0.00 0.00 1.90
1394 1457 7.306051 GCAGTTACAGAATTATGCTACACTACG 60.306 40.741 0.00 0.00 0.00 3.51
1416 1479 6.577103 ACGTGTGATCACAATATGAGAATCT 58.423 36.000 29.42 1.55 43.77 2.40
1725 1791 0.763035 AGTAACCAAACGCTCCCTGT 59.237 50.000 0.00 0.00 0.00 4.00
1838 1904 4.612264 AGCCAAATCATTTCTGCAGTTT 57.388 36.364 14.67 2.57 0.00 2.66
1856 1922 5.412286 GCAGTTTCAAATTGCCCATAACAAT 59.588 36.000 6.35 0.00 39.38 2.71
2161 2227 4.149598 AGCGGAACCTTAACTTTCCAAAT 58.850 39.130 9.88 0.00 41.35 2.32
2198 2264 7.629157 TGGGAATAACACTAGAATTGATGACA 58.371 34.615 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.449525 TAGCACTTTTAGCGCGCCG 61.450 57.895 30.33 13.74 37.01 6.46
7 8 1.060465 GTAGCACTTTTAGCGCGCC 59.940 57.895 30.33 9.85 37.01 6.53
8 9 0.247301 CTGTAGCACTTTTAGCGCGC 60.247 55.000 26.66 26.66 37.01 6.86
9 10 1.068474 ACTGTAGCACTTTTAGCGCG 58.932 50.000 0.00 0.00 37.01 6.86
10 11 1.128692 CCACTGTAGCACTTTTAGCGC 59.871 52.381 0.00 0.00 37.01 5.92
11 12 2.157668 CACCACTGTAGCACTTTTAGCG 59.842 50.000 0.00 0.00 37.01 4.26
12 13 2.095718 GCACCACTGTAGCACTTTTAGC 60.096 50.000 0.00 0.00 0.00 3.09
13 14 3.403038 AGCACCACTGTAGCACTTTTAG 58.597 45.455 0.00 0.00 0.00 1.85
14 15 3.071023 AGAGCACCACTGTAGCACTTTTA 59.929 43.478 0.00 0.00 0.00 1.52
15 16 2.158755 AGAGCACCACTGTAGCACTTTT 60.159 45.455 0.00 0.00 0.00 2.27
16 17 1.417890 AGAGCACCACTGTAGCACTTT 59.582 47.619 0.00 0.00 0.00 2.66
17 18 1.051812 AGAGCACCACTGTAGCACTT 58.948 50.000 0.00 0.00 0.00 3.16
18 19 1.924731 TAGAGCACCACTGTAGCACT 58.075 50.000 0.00 0.00 33.82 4.40
19 20 2.743636 TTAGAGCACCACTGTAGCAC 57.256 50.000 0.00 0.00 0.00 4.40
20 21 3.071023 AGTTTTAGAGCACCACTGTAGCA 59.929 43.478 0.00 0.00 0.00 3.49
21 22 3.665190 AGTTTTAGAGCACCACTGTAGC 58.335 45.455 0.00 0.00 0.00 3.58
22 23 7.907214 AAATAGTTTTAGAGCACCACTGTAG 57.093 36.000 0.00 0.00 0.00 2.74
40 41 9.289303 CGCAAAAATATTGAGTGCTAAAATAGT 57.711 29.630 13.38 0.00 32.99 2.12
41 42 8.261908 GCGCAAAAATATTGAGTGCTAAAATAG 58.738 33.333 0.30 1.97 32.99 1.73
42 43 7.221838 GGCGCAAAAATATTGAGTGCTAAAATA 59.778 33.333 10.83 0.00 33.72 1.40
43 44 6.035975 GGCGCAAAAATATTGAGTGCTAAAAT 59.964 34.615 10.83 0.00 33.72 1.82
44 45 5.347364 GGCGCAAAAATATTGAGTGCTAAAA 59.653 36.000 10.83 0.00 33.72 1.52
45 46 4.862018 GGCGCAAAAATATTGAGTGCTAAA 59.138 37.500 10.83 0.00 33.72 1.85
46 47 4.157656 AGGCGCAAAAATATTGAGTGCTAA 59.842 37.500 10.83 0.00 33.72 3.09
47 48 3.694072 AGGCGCAAAAATATTGAGTGCTA 59.306 39.130 10.83 0.00 33.72 3.49
48 49 2.493278 AGGCGCAAAAATATTGAGTGCT 59.507 40.909 10.83 0.00 33.72 4.40
49 50 2.854185 GAGGCGCAAAAATATTGAGTGC 59.146 45.455 10.83 10.43 32.94 4.40
50 51 4.100529 CAGAGGCGCAAAAATATTGAGTG 58.899 43.478 10.83 0.00 0.00 3.51
51 52 3.758554 ACAGAGGCGCAAAAATATTGAGT 59.241 39.130 10.83 0.00 0.00 3.41
52 53 4.361451 ACAGAGGCGCAAAAATATTGAG 57.639 40.909 10.83 0.00 0.00 3.02
53 54 4.484236 CAACAGAGGCGCAAAAATATTGA 58.516 39.130 10.83 0.00 0.00 2.57
54 55 3.613737 CCAACAGAGGCGCAAAAATATTG 59.386 43.478 10.83 4.43 0.00 1.90
55 56 3.509575 TCCAACAGAGGCGCAAAAATATT 59.490 39.130 10.83 0.00 0.00 1.28
56 57 3.088532 TCCAACAGAGGCGCAAAAATAT 58.911 40.909 10.83 0.00 0.00 1.28
57 58 2.487762 CTCCAACAGAGGCGCAAAAATA 59.512 45.455 10.83 0.00 39.13 1.40
58 59 1.270550 CTCCAACAGAGGCGCAAAAAT 59.729 47.619 10.83 0.00 39.13 1.82
59 60 0.667993 CTCCAACAGAGGCGCAAAAA 59.332 50.000 10.83 0.00 39.13 1.94
60 61 0.179032 TCTCCAACAGAGGCGCAAAA 60.179 50.000 10.83 0.00 43.44 2.44
61 62 0.036732 ATCTCCAACAGAGGCGCAAA 59.963 50.000 10.83 0.00 43.44 3.68
62 63 0.036732 AATCTCCAACAGAGGCGCAA 59.963 50.000 10.83 0.00 43.44 4.85
63 64 0.391661 GAATCTCCAACAGAGGCGCA 60.392 55.000 10.83 0.00 43.44 6.09
64 65 0.107945 AGAATCTCCAACAGAGGCGC 60.108 55.000 0.00 0.00 43.44 6.53
65 66 1.933247 GAGAATCTCCAACAGAGGCG 58.067 55.000 0.00 0.00 43.44 5.52
76 77 4.054235 GCACATGCCCCTAAGAGAATCTC 61.054 52.174 1.19 1.19 39.15 2.75
77 78 2.158696 GCACATGCCCCTAAGAGAATCT 60.159 50.000 0.00 0.00 41.24 2.40
78 79 2.225467 GCACATGCCCCTAAGAGAATC 58.775 52.381 0.00 0.00 34.31 2.52
79 80 1.565759 TGCACATGCCCCTAAGAGAAT 59.434 47.619 0.49 0.00 41.18 2.40
80 81 0.991146 TGCACATGCCCCTAAGAGAA 59.009 50.000 0.49 0.00 41.18 2.87
81 82 0.253044 GTGCACATGCCCCTAAGAGA 59.747 55.000 13.17 0.00 41.18 3.10
82 83 1.091771 CGTGCACATGCCCCTAAGAG 61.092 60.000 18.64 0.00 41.18 2.85
83 84 1.078497 CGTGCACATGCCCCTAAGA 60.078 57.895 18.64 0.00 41.18 2.10
95 96 1.868997 CCAGGATGTGTTCGTGCAC 59.131 57.895 6.82 6.82 38.61 4.57
97 98 0.391130 TAGCCAGGATGTGTTCGTGC 60.391 55.000 0.00 0.00 38.61 5.34
98 99 2.205074 GATAGCCAGGATGTGTTCGTG 58.795 52.381 0.00 0.00 39.44 4.35
103 104 2.036475 GTCGATGATAGCCAGGATGTGT 59.964 50.000 0.00 0.00 0.00 3.72
104 105 2.036346 TGTCGATGATAGCCAGGATGTG 59.964 50.000 0.00 0.00 0.00 3.21
113 114 1.506493 CTGGCCTTGTCGATGATAGC 58.494 55.000 3.32 0.00 0.00 2.97
116 117 0.179000 GACCTGGCCTTGTCGATGAT 59.821 55.000 3.32 0.00 0.00 2.45
129 130 1.443407 CATACCGGAGCTGACCTGG 59.557 63.158 9.46 0.00 0.00 4.45
143 144 6.918022 GCTAATTAATGTTGCCACTTCCATAC 59.082 38.462 0.00 0.00 0.00 2.39
148 149 6.194796 TGAGCTAATTAATGTTGCCACTTC 57.805 37.500 0.00 0.00 0.00 3.01
150 151 5.008019 CGATGAGCTAATTAATGTTGCCACT 59.992 40.000 0.00 0.00 0.00 4.00
151 152 5.207768 CGATGAGCTAATTAATGTTGCCAC 58.792 41.667 0.00 0.00 0.00 5.01
154 155 5.424121 ACCGATGAGCTAATTAATGTTGC 57.576 39.130 0.00 0.00 0.00 4.17
155 156 7.471721 TCAAACCGATGAGCTAATTAATGTTG 58.528 34.615 0.00 0.00 0.00 3.33
157 158 7.807977 ATCAAACCGATGAGCTAATTAATGT 57.192 32.000 0.00 0.00 31.20 2.71
186 187 1.412343 AGACCACCAAACAACCATTGC 59.588 47.619 0.00 0.00 0.00 3.56
189 190 3.650942 TCTCTAGACCACCAAACAACCAT 59.349 43.478 0.00 0.00 0.00 3.55
276 279 7.776933 TCTCTTATCATCCATCAAAAGTTCG 57.223 36.000 0.00 0.00 0.00 3.95
317 320 7.592164 CCGTACAAAAGTAGTAAAATTTGTGGG 59.408 37.037 11.72 9.30 43.59 4.61
319 322 9.719279 TTCCGTACAAAAGTAGTAAAATTTGTG 57.281 29.630 11.72 0.00 43.59 3.33
320 323 9.940166 CTTCCGTACAAAAGTAGTAAAATTTGT 57.060 29.630 7.72 7.72 45.18 2.83
321 324 9.389570 CCTTCCGTACAAAAGTAGTAAAATTTG 57.610 33.333 0.00 0.00 38.42 2.32
323 326 7.446319 AGCCTTCCGTACAAAAGTAGTAAAATT 59.554 33.333 0.00 0.00 0.00 1.82
362 376 9.787435 TTCCACTCTGTAAACATTAAGTACAAT 57.213 29.630 0.00 0.00 0.00 2.71
397 411 1.098050 GGCAGCCTGAACCATGTAAG 58.902 55.000 3.29 0.00 0.00 2.34
403 422 1.073722 CAGAAGGCAGCCTGAACCA 59.926 57.895 17.05 0.00 32.13 3.67
460 479 4.933400 GGTACTCAAAGAATAAAGCGTCCA 59.067 41.667 0.00 0.00 0.00 4.02
501 528 3.482436 AGTAGGCAACGAAATTCCAACA 58.518 40.909 0.00 0.00 46.39 3.33
560 587 2.126463 CTCGACGTGTCACCGCAT 60.126 61.111 0.00 0.00 0.00 4.73
563 590 1.135888 TGTATTCTCGACGTGTCACCG 60.136 52.381 0.00 0.00 0.00 4.94
601 632 7.786178 TGGAGGTGAATTAATATTCGACTTG 57.214 36.000 0.00 0.00 42.55 3.16
656 687 1.672363 TGACGTACGCGATATGGTTCT 59.328 47.619 15.93 0.00 42.00 3.01
699 730 7.599998 ACGGTTACCTATATTATTCGCGAAATT 59.400 33.333 27.23 13.21 0.00 1.82
701 732 6.363088 CACGGTTACCTATATTATTCGCGAAA 59.637 38.462 27.23 11.10 0.00 3.46
703 734 5.181056 TCACGGTTACCTATATTATTCGCGA 59.819 40.000 3.71 3.71 0.00 5.87
704 735 5.393124 TCACGGTTACCTATATTATTCGCG 58.607 41.667 0.00 0.00 0.00 5.87
705 736 6.615088 TCTCACGGTTACCTATATTATTCGC 58.385 40.000 0.00 0.00 0.00 4.70
706 737 9.635520 AAATCTCACGGTTACCTATATTATTCG 57.364 33.333 0.00 0.00 0.00 3.34
711 742 6.202188 CGCAAAATCTCACGGTTACCTATATT 59.798 38.462 0.00 0.00 0.00 1.28
736 767 4.452114 CACTTTTATTGCTTTTTGGGAGGC 59.548 41.667 0.00 0.00 0.00 4.70
784 821 7.562135 GTGGCTAATCGGGGAAGAATATATAA 58.438 38.462 0.00 0.00 0.00 0.98
864 902 9.299963 GTGCTAGCTATTTATAGATGATGACTG 57.700 37.037 17.23 0.00 30.67 3.51
865 903 8.474025 GGTGCTAGCTATTTATAGATGATGACT 58.526 37.037 17.23 0.00 30.67 3.41
866 904 7.433719 CGGTGCTAGCTATTTATAGATGATGAC 59.566 40.741 17.23 0.00 30.67 3.06
867 905 7.122799 ACGGTGCTAGCTATTTATAGATGATGA 59.877 37.037 17.23 0.00 30.67 2.92
868 906 7.261325 ACGGTGCTAGCTATTTATAGATGATG 58.739 38.462 17.23 0.00 30.67 3.07
869 907 7.411486 ACGGTGCTAGCTATTTATAGATGAT 57.589 36.000 17.23 0.00 30.67 2.45
895 933 1.056125 ATGGTGATGAGATGGCCCGA 61.056 55.000 0.00 0.00 0.00 5.14
896 934 0.604780 GATGGTGATGAGATGGCCCG 60.605 60.000 0.00 0.00 0.00 6.13
898 936 1.134007 TGTGATGGTGATGAGATGGCC 60.134 52.381 0.00 0.00 0.00 5.36
899 937 2.336945 TGTGATGGTGATGAGATGGC 57.663 50.000 0.00 0.00 0.00 4.40
900 938 4.011698 TGTTTGTGATGGTGATGAGATGG 58.988 43.478 0.00 0.00 0.00 3.51
939 982 5.706369 TCGATCTTAACTATCCTGAGGTAGC 59.294 44.000 0.00 0.00 0.00 3.58
943 986 6.825944 TGATCGATCTTAACTATCCTGAGG 57.174 41.667 25.02 0.00 0.00 3.86
944 987 8.909708 GATTGATCGATCTTAACTATCCTGAG 57.090 38.462 25.02 0.00 0.00 3.35
962 1009 5.013547 TCCTTCCCTAGATCTCGATTGATC 58.986 45.833 0.00 6.56 42.18 2.92
979 1026 0.750249 GCTGGTAGCTCTCTCCTTCC 59.250 60.000 0.00 0.00 38.45 3.46
1037 1088 1.884075 CGTCCCGAAGATCACCACCA 61.884 60.000 0.00 0.00 0.00 4.17
1206 1257 2.967615 GCGCCGCCTATGAAGACC 60.968 66.667 0.00 0.00 0.00 3.85
1394 1457 8.147058 AGGTAGATTCTCATATTGTGATCACAC 58.853 37.037 27.88 12.26 46.09 3.82
1447 1512 3.991924 ATGCAGAGGCCGGGAGTCT 62.992 63.158 2.18 0.00 40.13 3.24
1448 1513 3.453070 GATGCAGAGGCCGGGAGTC 62.453 68.421 2.18 0.00 40.13 3.36
1449 1514 3.474570 GATGCAGAGGCCGGGAGT 61.475 66.667 2.18 0.00 40.13 3.85
1450 1515 3.457625 CTGATGCAGAGGCCGGGAG 62.458 68.421 2.18 0.00 40.13 4.30
1451 1516 3.473647 CTGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.00 40.13 5.14
1838 1904 4.252073 GTGCATTGTTATGGGCAATTTGA 58.748 39.130 0.00 0.00 38.10 2.69
1856 1922 2.499756 TTCGCGTAGGAGCATGTGCA 62.500 55.000 5.77 0.00 45.16 4.57
1980 2046 4.323477 CCCGTTGGCGAGGGTTCA 62.323 66.667 12.31 0.00 42.67 3.18
2161 2227 7.446106 AGTGTTATTCCCAGTTCCATACATA 57.554 36.000 0.00 0.00 0.00 2.29
2198 2264 4.220821 ACAGTCAAGTCGATGTACCTTGAT 59.779 41.667 15.79 5.66 44.43 2.57
2261 2327 1.002544 GTTCAGCTTACTCACCAGCCT 59.997 52.381 0.00 0.00 36.62 4.58


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

AutoCloner maintained by Alex Coulton.