Multiple sequence alignment - TraesCS1B01G050300

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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 TraesCS1B01G050300 chr1B 100.000 2844 0 0 1 2844 30529310 30532153 0.000000e+00 5252
1 TraesCS1B01G050300 chr1B 88.521 906 61 16 1968 2844 663658095 663657204 0.000000e+00 1057
2 TraesCS1B01G050300 chr4A 98.310 2248 17 2 617 2844 3252926 3255172 0.000000e+00 3921
3 TraesCS1B01G050300 chr4A 95.850 506 21 0 2339 2844 705571052 705570547 0.000000e+00 819
4 TraesCS1B01G050300 chr5B 97.438 2264 20 2 619 2844 448586418 448588681 0.000000e+00 3825
5 TraesCS1B01G050300 chr1A 97.345 2260 28 6 617 2844 485328195 485330454 0.000000e+00 3812
6 TraesCS1B01G050300 chr1A 97.969 1723 14 2 619 2320 507989878 507991600 0.000000e+00 2968
7 TraesCS1B01G050300 chr1A 84.855 449 63 4 173 618 17006181 17006627 5.590000e-122 448
8 TraesCS1B01G050300 chr7A 97.174 2265 26 2 618 2844 705281554 705283818 0.000000e+00 3794
9 TraesCS1B01G050300 chr7A 97.132 2266 26 3 617 2844 556141849 556139585 0.000000e+00 3788
10 TraesCS1B01G050300 chr2B 97.849 1953 16 2 912 2844 629109272 629111218 0.000000e+00 3350
11 TraesCS1B01G050300 chr2B 99.096 1328 10 1 619 1944 90434083 90435410 0.000000e+00 2385
12 TraesCS1B01G050300 chr5A 98.129 1603 12 1 619 2203 666315906 666317508 0.000000e+00 2778
13 TraesCS1B01G050300 chr4B 92.882 1714 54 21 619 2269 134586678 134584970 0.000000e+00 2427
14 TraesCS1B01G050300 chr4B 95.850 506 21 0 2339 2844 134584937 134584432 0.000000e+00 819
15 TraesCS1B01G050300 chr3A 96.245 506 19 0 2339 2844 11578954 11579459 0.000000e+00 830
16 TraesCS1B01G050300 chr1D 89.279 513 49 4 110 618 16608417 16608927 3.090000e-179 638
17 TraesCS1B01G050300 chr3B 97.019 369 10 1 617 985 457636052 457636419 1.120000e-173 619


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 TraesCS1B01G050300 chr1B 30529310 30532153 2843 False 5252 5252 100.000 1 2844 1 chr1B.!!$F1 2843
1 TraesCS1B01G050300 chr1B 663657204 663658095 891 True 1057 1057 88.521 1968 2844 1 chr1B.!!$R1 876
2 TraesCS1B01G050300 chr4A 3252926 3255172 2246 False 3921 3921 98.310 617 2844 1 chr4A.!!$F1 2227
3 TraesCS1B01G050300 chr4A 705570547 705571052 505 True 819 819 95.850 2339 2844 1 chr4A.!!$R1 505
4 TraesCS1B01G050300 chr5B 448586418 448588681 2263 False 3825 3825 97.438 619 2844 1 chr5B.!!$F1 2225
5 TraesCS1B01G050300 chr1A 485328195 485330454 2259 False 3812 3812 97.345 617 2844 1 chr1A.!!$F2 2227
6 TraesCS1B01G050300 chr1A 507989878 507991600 1722 False 2968 2968 97.969 619 2320 1 chr1A.!!$F3 1701
7 TraesCS1B01G050300 chr7A 705281554 705283818 2264 False 3794 3794 97.174 618 2844 1 chr7A.!!$F1 2226
8 TraesCS1B01G050300 chr7A 556139585 556141849 2264 True 3788 3788 97.132 617 2844 1 chr7A.!!$R1 2227
9 TraesCS1B01G050300 chr2B 629109272 629111218 1946 False 3350 3350 97.849 912 2844 1 chr2B.!!$F2 1932
10 TraesCS1B01G050300 chr2B 90434083 90435410 1327 False 2385 2385 99.096 619 1944 1 chr2B.!!$F1 1325
11 TraesCS1B01G050300 chr5A 666315906 666317508 1602 False 2778 2778 98.129 619 2203 1 chr5A.!!$F1 1584
12 TraesCS1B01G050300 chr4B 134584432 134586678 2246 True 1623 2427 94.366 619 2844 2 chr4B.!!$R1 2225
13 TraesCS1B01G050300 chr3A 11578954 11579459 505 False 830 830 96.245 2339 2844 1 chr3A.!!$F1 505
14 TraesCS1B01G050300 chr1D 16608417 16608927 510 False 638 638 89.279 110 618 1 chr1D.!!$F1 508

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
455 458 0.107848 ATAAGCCGTATATGCCCCGC 60.108 55.0 0.0 0.0 0.00 6.13 F
515 520 0.323302 TTCACCGAAGCAGGCACATA 59.677 50.0 0.0 0.0 33.69 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1711 2.239150 AGAGCCACATTCTCTTCAGCAT 59.761 45.455 0.0 0.0 37.63 3.79 R
2292 2462 4.201657 CTGAATGTGCCCATGTTGATCTA 58.798 43.478 0.0 0.0 0.00 1.98 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
32 33 8.809159 TGAACAATATGTTTATGTTTGGTGTG 57.191 30.769 0.00 0.00 41.28 3.82
33 34 8.633561 TGAACAATATGTTTATGTTTGGTGTGA 58.366 29.630 0.00 0.00 41.28 3.58
34 35 9.469807 GAACAATATGTTTATGTTTGGTGTGAA 57.530 29.630 0.00 0.00 41.28 3.18
35 36 9.995003 AACAATATGTTTATGTTTGGTGTGAAT 57.005 25.926 0.00 0.00 37.26 2.57
36 37 9.995003 ACAATATGTTTATGTTTGGTGTGAATT 57.005 25.926 0.00 0.00 0.00 2.17
39 40 9.995003 ATATGTTTATGTTTGGTGTGAATTTGT 57.005 25.926 0.00 0.00 0.00 2.83
40 41 8.729805 ATGTTTATGTTTGGTGTGAATTTGTT 57.270 26.923 0.00 0.00 0.00 2.83
41 42 7.968246 TGTTTATGTTTGGTGTGAATTTGTTG 58.032 30.769 0.00 0.00 0.00 3.33
42 43 7.065085 TGTTTATGTTTGGTGTGAATTTGTTGG 59.935 33.333 0.00 0.00 0.00 3.77
43 44 3.866651 TGTTTGGTGTGAATTTGTTGGG 58.133 40.909 0.00 0.00 0.00 4.12
44 45 3.261897 TGTTTGGTGTGAATTTGTTGGGT 59.738 39.130 0.00 0.00 0.00 4.51
45 46 4.466370 TGTTTGGTGTGAATTTGTTGGGTA 59.534 37.500 0.00 0.00 0.00 3.69
46 47 5.129485 TGTTTGGTGTGAATTTGTTGGGTAT 59.871 36.000 0.00 0.00 0.00 2.73
47 48 4.862902 TGGTGTGAATTTGTTGGGTATG 57.137 40.909 0.00 0.00 0.00 2.39
48 49 4.219115 TGGTGTGAATTTGTTGGGTATGT 58.781 39.130 0.00 0.00 0.00 2.29
49 50 4.651503 TGGTGTGAATTTGTTGGGTATGTT 59.348 37.500 0.00 0.00 0.00 2.71
50 51 5.221342 TGGTGTGAATTTGTTGGGTATGTTC 60.221 40.000 0.00 0.00 0.00 3.18
51 52 5.221342 GGTGTGAATTTGTTGGGTATGTTCA 60.221 40.000 0.00 0.00 0.00 3.18
52 53 6.276847 GTGTGAATTTGTTGGGTATGTTCAA 58.723 36.000 0.00 0.00 0.00 2.69
53 54 6.200097 GTGTGAATTTGTTGGGTATGTTCAAC 59.800 38.462 0.00 0.00 42.38 3.18
54 55 6.097554 TGTGAATTTGTTGGGTATGTTCAACT 59.902 34.615 0.00 0.00 42.48 3.16
55 56 6.983890 GTGAATTTGTTGGGTATGTTCAACTT 59.016 34.615 0.00 0.00 42.48 2.66
56 57 7.494298 GTGAATTTGTTGGGTATGTTCAACTTT 59.506 33.333 0.00 0.00 42.48 2.66
57 58 7.493971 TGAATTTGTTGGGTATGTTCAACTTTG 59.506 33.333 0.00 0.00 42.48 2.77
58 59 5.923733 TTGTTGGGTATGTTCAACTTTGT 57.076 34.783 0.00 0.00 42.48 2.83
59 60 5.923733 TGTTGGGTATGTTCAACTTTGTT 57.076 34.783 0.00 0.00 42.48 2.83
60 61 5.655488 TGTTGGGTATGTTCAACTTTGTTG 58.345 37.500 4.25 4.25 42.48 3.33
61 62 4.927978 TGGGTATGTTCAACTTTGTTGG 57.072 40.909 10.05 0.00 0.00 3.77
62 63 4.537751 TGGGTATGTTCAACTTTGTTGGA 58.462 39.130 10.05 0.00 0.00 3.53
63 64 4.339814 TGGGTATGTTCAACTTTGTTGGAC 59.660 41.667 13.28 13.28 0.00 4.02
64 65 4.339814 GGGTATGTTCAACTTTGTTGGACA 59.660 41.667 21.93 21.93 0.00 4.02
65 66 5.010617 GGGTATGTTCAACTTTGTTGGACAT 59.989 40.000 28.87 28.87 0.00 3.06
66 67 5.920273 GGTATGTTCAACTTTGTTGGACATG 59.080 40.000 31.51 0.00 0.00 3.21
67 68 5.596836 ATGTTCAACTTTGTTGGACATGT 57.403 34.783 26.88 12.32 0.00 3.21
68 69 6.707440 ATGTTCAACTTTGTTGGACATGTA 57.293 33.333 26.88 8.66 0.00 2.29
69 70 6.707440 TGTTCAACTTTGTTGGACATGTAT 57.293 33.333 17.53 0.00 0.00 2.29
70 71 6.502652 TGTTCAACTTTGTTGGACATGTATG 58.497 36.000 17.53 0.00 0.00 2.39
71 72 5.703978 TCAACTTTGTTGGACATGTATGG 57.296 39.130 0.00 0.00 0.00 2.74
72 73 5.380900 TCAACTTTGTTGGACATGTATGGA 58.619 37.500 0.00 0.00 0.00 3.41
73 74 6.009589 TCAACTTTGTTGGACATGTATGGAT 58.990 36.000 0.00 0.00 0.00 3.41
74 75 5.902613 ACTTTGTTGGACATGTATGGATG 57.097 39.130 0.00 0.00 0.00 3.51
75 76 5.324409 ACTTTGTTGGACATGTATGGATGT 58.676 37.500 0.00 0.00 39.34 3.06
76 77 5.774690 ACTTTGTTGGACATGTATGGATGTT 59.225 36.000 0.00 0.00 36.67 2.71
77 78 5.641783 TTGTTGGACATGTATGGATGTTG 57.358 39.130 0.00 0.00 36.67 3.33
78 79 4.916183 TGTTGGACATGTATGGATGTTGA 58.084 39.130 0.00 0.00 36.67 3.18
79 80 5.320277 TGTTGGACATGTATGGATGTTGAA 58.680 37.500 0.00 0.00 36.67 2.69
80 81 5.182950 TGTTGGACATGTATGGATGTTGAAC 59.817 40.000 0.00 0.00 36.67 3.18
81 82 5.178096 TGGACATGTATGGATGTTGAACT 57.822 39.130 0.00 0.00 36.67 3.01
82 83 5.569355 TGGACATGTATGGATGTTGAACTT 58.431 37.500 0.00 0.00 36.67 2.66
83 84 6.009589 TGGACATGTATGGATGTTGAACTTT 58.990 36.000 0.00 0.00 36.67 2.66
84 85 6.072008 TGGACATGTATGGATGTTGAACTTTG 60.072 38.462 0.00 0.00 36.67 2.77
85 86 6.071952 GGACATGTATGGATGTTGAACTTTGT 60.072 38.462 0.00 0.00 36.67 2.83
86 87 7.288810 ACATGTATGGATGTTGAACTTTGTT 57.711 32.000 0.00 0.00 32.38 2.83
87 88 7.725251 ACATGTATGGATGTTGAACTTTGTTT 58.275 30.769 0.00 0.00 32.38 2.83
88 89 8.855110 ACATGTATGGATGTTGAACTTTGTTTA 58.145 29.630 0.00 0.00 32.38 2.01
89 90 9.859427 CATGTATGGATGTTGAACTTTGTTTAT 57.141 29.630 0.00 0.00 0.00 1.40
91 92 9.689976 TGTATGGATGTTGAACTTTGTTTATTG 57.310 29.630 0.00 0.00 0.00 1.90
92 93 9.691362 GTATGGATGTTGAACTTTGTTTATTGT 57.309 29.630 0.00 0.00 0.00 2.71
93 94 8.592105 ATGGATGTTGAACTTTGTTTATTGTG 57.408 30.769 0.00 0.00 0.00 3.33
94 95 7.551585 TGGATGTTGAACTTTGTTTATTGTGT 58.448 30.769 0.00 0.00 0.00 3.72
95 96 7.704472 TGGATGTTGAACTTTGTTTATTGTGTC 59.296 33.333 0.00 0.00 0.00 3.67
96 97 7.704472 GGATGTTGAACTTTGTTTATTGTGTCA 59.296 33.333 0.00 0.00 0.00 3.58
97 98 8.633075 ATGTTGAACTTTGTTTATTGTGTCAG 57.367 30.769 0.00 0.00 0.00 3.51
98 99 6.529829 TGTTGAACTTTGTTTATTGTGTCAGC 59.470 34.615 0.00 0.00 0.00 4.26
99 100 5.587289 TGAACTTTGTTTATTGTGTCAGCC 58.413 37.500 0.00 0.00 0.00 4.85
100 101 4.584327 ACTTTGTTTATTGTGTCAGCCC 57.416 40.909 0.00 0.00 0.00 5.19
101 102 3.320826 ACTTTGTTTATTGTGTCAGCCCC 59.679 43.478 0.00 0.00 0.00 5.80
102 103 1.529226 TGTTTATTGTGTCAGCCCCG 58.471 50.000 0.00 0.00 0.00 5.73
103 104 1.202830 TGTTTATTGTGTCAGCCCCGT 60.203 47.619 0.00 0.00 0.00 5.28
104 105 1.199097 GTTTATTGTGTCAGCCCCGTG 59.801 52.381 0.00 0.00 0.00 4.94
105 106 0.322098 TTATTGTGTCAGCCCCGTGG 60.322 55.000 0.00 0.00 0.00 4.94
123 124 3.059597 CGTGGCACAACAAACAAACAAAA 60.060 39.130 19.09 0.00 44.16 2.44
124 125 4.552767 CGTGGCACAACAAACAAACAAAAA 60.553 37.500 19.09 0.00 44.16 1.94
171 173 7.094762 GCCCAATGTAATACTTAGCTTACCATC 60.095 40.741 0.00 0.00 0.00 3.51
187 190 0.674895 CATCTATAAGCCGGCTGCCC 60.675 60.000 33.60 0.00 42.71 5.36
197 200 3.661648 GGCTGCCCAGGGGAAAGA 61.662 66.667 7.66 0.00 37.50 2.52
204 207 1.377333 CCAGGGGAAAGAACTCGGC 60.377 63.158 0.00 0.00 0.00 5.54
213 216 2.205307 AAGAACTCGGCGTATACTGC 57.795 50.000 6.85 10.11 0.00 4.40
215 218 1.197910 GAACTCGGCGTATACTGCAC 58.802 55.000 6.85 8.90 0.00 4.57
224 227 1.006832 GTATACTGCACAAGCCGTGG 58.993 55.000 6.05 0.00 46.45 4.94
242 245 2.785258 CGCCCAGTTAAAGCGCTC 59.215 61.111 12.06 0.00 43.72 5.03
256 259 0.808453 GCGCTCGGCTTACATAACCA 60.808 55.000 0.00 0.00 39.11 3.67
271 274 5.755849 ACATAACCATAAGCCATATAGCCC 58.244 41.667 0.00 0.00 0.00 5.19
293 296 4.208460 CCAGAAAATACACACGGCGTATAG 59.792 45.833 14.22 8.20 0.00 1.31
305 308 2.606272 CGGCGTATAGAAACCAAAGGAC 59.394 50.000 0.00 0.00 0.00 3.85
334 337 7.198306 TGGTATCTGCCGATGTATATATACG 57.802 40.000 16.29 6.38 36.06 3.06
338 341 2.944349 TGCCGATGTATATATACGCCGA 59.056 45.455 25.41 12.58 36.06 5.54
413 416 2.358737 CTTGCCCGAGAAAGCCGT 60.359 61.111 0.00 0.00 0.00 5.68
419 422 0.108138 CCCGAGAAAGCCGTGAGAAT 60.108 55.000 0.00 0.00 0.00 2.40
421 424 2.224066 CCCGAGAAAGCCGTGAGAATAT 60.224 50.000 0.00 0.00 0.00 1.28
422 425 2.797156 CCGAGAAAGCCGTGAGAATATG 59.203 50.000 0.00 0.00 0.00 1.78
453 456 1.838077 AGGATAAGCCGTATATGCCCC 59.162 52.381 0.00 0.00 43.43 5.80
455 458 0.107848 ATAAGCCGTATATGCCCCGC 60.108 55.000 0.00 0.00 0.00 6.13
473 476 3.241177 GGCACACGACGTTCTTCC 58.759 61.111 0.00 0.00 0.00 3.46
478 481 2.925306 GCACACGACGTTCTTCCAGTAT 60.925 50.000 0.00 0.00 0.00 2.12
480 483 3.850273 CACACGACGTTCTTCCAGTATAC 59.150 47.826 0.00 0.00 0.00 1.47
488 491 4.439153 CGTTCTTCCAGTATACGGCTTACA 60.439 45.833 8.38 0.00 0.00 2.41
507 512 2.357034 GAGCCGTTCACCGAAGCA 60.357 61.111 0.00 0.00 39.56 3.91
509 514 3.423154 GCCGTTCACCGAAGCAGG 61.423 66.667 0.00 0.00 39.56 4.85
512 517 2.946762 GTTCACCGAAGCAGGCAC 59.053 61.111 0.00 0.00 33.69 5.01
514 519 1.073025 TTCACCGAAGCAGGCACAT 59.927 52.632 0.00 0.00 33.69 3.21
515 520 0.323302 TTCACCGAAGCAGGCACATA 59.677 50.000 0.00 0.00 33.69 2.29
535 540 1.517694 CGTACAATGACGTCCCGGG 60.518 63.158 16.85 16.85 38.04 5.73
548 553 2.426522 GTCCCGGGTTACTTGTAAACC 58.573 52.381 22.86 15.55 44.75 3.27
575 580 1.487231 CACTGCGCACACGACTTAC 59.513 57.895 5.66 0.00 43.93 2.34
579 584 1.212455 TGCGCACACGACTTACTGTG 61.212 55.000 5.66 0.00 43.93 3.66
655 660 7.937394 ACTATTCATACATAAACTTGTAGGGGC 59.063 37.037 0.00 0.00 35.24 5.80
708 713 2.582052 CACAAAACTAGCCCTCCAACA 58.418 47.619 0.00 0.00 0.00 3.33
1635 1711 0.469705 AGGCAGGTGATTGGCAAACA 60.470 50.000 3.01 4.71 45.32 2.83
2222 2392 2.346803 CACAAAGTGCGCACCTAGTAT 58.653 47.619 35.51 14.67 0.00 2.12
2292 2462 2.632028 TGGGCACATGCAAATTAACAGT 59.368 40.909 6.15 0.00 44.36 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.421806 CACACCAAACATAAACATATTGTTCAT 57.578 29.630 0.00 0.00 40.14 2.57
7 8 8.633561 TCACACCAAACATAAACATATTGTTCA 58.366 29.630 0.00 0.00 40.14 3.18
8 9 9.469807 TTCACACCAAACATAAACATATTGTTC 57.530 29.630 0.00 0.00 40.14 3.18
9 10 9.995003 ATTCACACCAAACATAAACATATTGTT 57.005 25.926 0.00 0.00 43.41 2.83
10 11 9.995003 AATTCACACCAAACATAAACATATTGT 57.005 25.926 0.00 0.00 0.00 2.71
13 14 9.995003 ACAAATTCACACCAAACATAAACATAT 57.005 25.926 0.00 0.00 0.00 1.78
14 15 9.823647 AACAAATTCACACCAAACATAAACATA 57.176 25.926 0.00 0.00 0.00 2.29
15 16 8.610896 CAACAAATTCACACCAAACATAAACAT 58.389 29.630 0.00 0.00 0.00 2.71
16 17 7.065085 CCAACAAATTCACACCAAACATAAACA 59.935 33.333 0.00 0.00 0.00 2.83
17 18 7.405769 CCAACAAATTCACACCAAACATAAAC 58.594 34.615 0.00 0.00 0.00 2.01
18 19 6.540189 CCCAACAAATTCACACCAAACATAAA 59.460 34.615 0.00 0.00 0.00 1.40
19 20 6.051717 CCCAACAAATTCACACCAAACATAA 58.948 36.000 0.00 0.00 0.00 1.90
20 21 5.129485 ACCCAACAAATTCACACCAAACATA 59.871 36.000 0.00 0.00 0.00 2.29
21 22 4.080638 ACCCAACAAATTCACACCAAACAT 60.081 37.500 0.00 0.00 0.00 2.71
22 23 3.261897 ACCCAACAAATTCACACCAAACA 59.738 39.130 0.00 0.00 0.00 2.83
23 24 3.867857 ACCCAACAAATTCACACCAAAC 58.132 40.909 0.00 0.00 0.00 2.93
24 25 5.129485 ACATACCCAACAAATTCACACCAAA 59.871 36.000 0.00 0.00 0.00 3.28
25 26 4.651503 ACATACCCAACAAATTCACACCAA 59.348 37.500 0.00 0.00 0.00 3.67
26 27 4.219115 ACATACCCAACAAATTCACACCA 58.781 39.130 0.00 0.00 0.00 4.17
27 28 4.864704 ACATACCCAACAAATTCACACC 57.135 40.909 0.00 0.00 0.00 4.16
28 29 5.837437 TGAACATACCCAACAAATTCACAC 58.163 37.500 0.00 0.00 0.00 3.82
29 30 6.097554 AGTTGAACATACCCAACAAATTCACA 59.902 34.615 0.00 0.00 43.60 3.58
30 31 6.512297 AGTTGAACATACCCAACAAATTCAC 58.488 36.000 0.00 0.00 43.60 3.18
31 32 6.723298 AGTTGAACATACCCAACAAATTCA 57.277 33.333 0.00 0.00 43.60 2.57
32 33 7.494298 ACAAAGTTGAACATACCCAACAAATTC 59.506 33.333 0.00 0.00 43.60 2.17
33 34 7.334858 ACAAAGTTGAACATACCCAACAAATT 58.665 30.769 0.00 0.00 43.60 1.82
34 35 6.883744 ACAAAGTTGAACATACCCAACAAAT 58.116 32.000 0.00 0.00 43.60 2.32
35 36 6.287589 ACAAAGTTGAACATACCCAACAAA 57.712 33.333 0.00 0.00 43.60 2.83
36 37 5.923733 ACAAAGTTGAACATACCCAACAA 57.076 34.783 0.00 0.00 43.60 2.83
37 38 5.394663 CCAACAAAGTTGAACATACCCAACA 60.395 40.000 11.19 0.00 43.60 3.33
38 39 5.047188 CCAACAAAGTTGAACATACCCAAC 58.953 41.667 11.19 0.00 42.02 3.77
39 40 4.956700 TCCAACAAAGTTGAACATACCCAA 59.043 37.500 11.19 0.00 0.00 4.12
40 41 4.339814 GTCCAACAAAGTTGAACATACCCA 59.660 41.667 11.19 0.00 0.00 4.51
41 42 4.339814 TGTCCAACAAAGTTGAACATACCC 59.660 41.667 11.19 0.00 0.00 3.69
42 43 5.508200 TGTCCAACAAAGTTGAACATACC 57.492 39.130 11.19 0.00 0.00 2.73
43 44 6.503524 ACATGTCCAACAAAGTTGAACATAC 58.496 36.000 13.14 4.26 0.00 2.39
44 45 6.707440 ACATGTCCAACAAAGTTGAACATA 57.293 33.333 13.14 0.00 0.00 2.29
45 46 5.596836 ACATGTCCAACAAAGTTGAACAT 57.403 34.783 8.63 8.63 0.00 2.71
46 47 6.460814 CCATACATGTCCAACAAAGTTGAACA 60.461 38.462 0.00 7.87 0.00 3.18
47 48 5.920273 CCATACATGTCCAACAAAGTTGAAC 59.080 40.000 0.00 1.89 0.00 3.18
48 49 5.830457 TCCATACATGTCCAACAAAGTTGAA 59.170 36.000 0.00 0.00 0.00 2.69
49 50 5.380900 TCCATACATGTCCAACAAAGTTGA 58.619 37.500 0.00 0.00 0.00 3.18
50 51 5.703978 TCCATACATGTCCAACAAAGTTG 57.296 39.130 0.00 3.00 0.00 3.16
51 52 5.774690 ACATCCATACATGTCCAACAAAGTT 59.225 36.000 0.00 0.00 30.76 2.66
52 53 5.324409 ACATCCATACATGTCCAACAAAGT 58.676 37.500 0.00 0.00 30.76 2.66
53 54 5.902613 ACATCCATACATGTCCAACAAAG 57.097 39.130 0.00 0.00 30.76 2.77
54 55 5.772169 TCAACATCCATACATGTCCAACAAA 59.228 36.000 0.00 0.00 35.87 2.83
55 56 5.320277 TCAACATCCATACATGTCCAACAA 58.680 37.500 0.00 0.00 35.87 2.83
56 57 4.916183 TCAACATCCATACATGTCCAACA 58.084 39.130 0.00 0.00 35.87 3.33
57 58 5.415701 AGTTCAACATCCATACATGTCCAAC 59.584 40.000 0.00 0.00 35.87 3.77
58 59 5.569355 AGTTCAACATCCATACATGTCCAA 58.431 37.500 0.00 0.00 35.87 3.53
59 60 5.178096 AGTTCAACATCCATACATGTCCA 57.822 39.130 0.00 0.00 35.87 4.02
60 61 6.071952 ACAAAGTTCAACATCCATACATGTCC 60.072 38.462 0.00 0.00 35.87 4.02
61 62 6.913170 ACAAAGTTCAACATCCATACATGTC 58.087 36.000 0.00 0.00 35.87 3.06
62 63 6.899393 ACAAAGTTCAACATCCATACATGT 57.101 33.333 2.69 2.69 38.74 3.21
63 64 9.859427 ATAAACAAAGTTCAACATCCATACATG 57.141 29.630 0.00 0.00 0.00 3.21
65 66 9.689976 CAATAAACAAAGTTCAACATCCATACA 57.310 29.630 0.00 0.00 0.00 2.29
66 67 9.691362 ACAATAAACAAAGTTCAACATCCATAC 57.309 29.630 0.00 0.00 0.00 2.39
67 68 9.689976 CACAATAAACAAAGTTCAACATCCATA 57.310 29.630 0.00 0.00 0.00 2.74
68 69 8.203485 ACACAATAAACAAAGTTCAACATCCAT 58.797 29.630 0.00 0.00 0.00 3.41
69 70 7.551585 ACACAATAAACAAAGTTCAACATCCA 58.448 30.769 0.00 0.00 0.00 3.41
70 71 7.704472 TGACACAATAAACAAAGTTCAACATCC 59.296 33.333 0.00 0.00 0.00 3.51
71 72 8.627487 TGACACAATAAACAAAGTTCAACATC 57.373 30.769 0.00 0.00 0.00 3.06
72 73 7.222611 GCTGACACAATAAACAAAGTTCAACAT 59.777 33.333 0.00 0.00 0.00 2.71
73 74 6.529829 GCTGACACAATAAACAAAGTTCAACA 59.470 34.615 0.00 0.00 0.00 3.33
74 75 6.019881 GGCTGACACAATAAACAAAGTTCAAC 60.020 38.462 0.00 0.00 0.00 3.18
75 76 6.039616 GGCTGACACAATAAACAAAGTTCAA 58.960 36.000 0.00 0.00 0.00 2.69
76 77 5.451242 GGGCTGACACAATAAACAAAGTTCA 60.451 40.000 0.00 0.00 0.00 3.18
77 78 4.982295 GGGCTGACACAATAAACAAAGTTC 59.018 41.667 0.00 0.00 0.00 3.01
78 79 4.202212 GGGGCTGACACAATAAACAAAGTT 60.202 41.667 0.00 0.00 0.00 2.66
79 80 3.320826 GGGGCTGACACAATAAACAAAGT 59.679 43.478 0.00 0.00 0.00 2.66
80 81 3.611530 CGGGGCTGACACAATAAACAAAG 60.612 47.826 0.00 0.00 0.00 2.77
81 82 2.294791 CGGGGCTGACACAATAAACAAA 59.705 45.455 0.00 0.00 0.00 2.83
82 83 1.883275 CGGGGCTGACACAATAAACAA 59.117 47.619 0.00 0.00 0.00 2.83
83 84 1.202830 ACGGGGCTGACACAATAAACA 60.203 47.619 0.00 0.00 0.00 2.83
84 85 1.199097 CACGGGGCTGACACAATAAAC 59.801 52.381 0.00 0.00 0.00 2.01
85 86 1.529226 CACGGGGCTGACACAATAAA 58.471 50.000 0.00 0.00 0.00 1.40
86 87 0.322098 CCACGGGGCTGACACAATAA 60.322 55.000 0.00 0.00 0.00 1.40
87 88 1.298340 CCACGGGGCTGACACAATA 59.702 57.895 0.00 0.00 0.00 1.90
88 89 2.034066 CCACGGGGCTGACACAAT 59.966 61.111 0.00 0.00 0.00 2.71
98 99 1.949847 TTGTTTGTTGTGCCACGGGG 61.950 55.000 0.00 0.00 37.18 5.73
99 100 0.108615 TTTGTTTGTTGTGCCACGGG 60.109 50.000 0.00 0.00 0.00 5.28
100 101 0.995728 GTTTGTTTGTTGTGCCACGG 59.004 50.000 0.00 0.00 0.00 4.94
101 102 1.702886 TGTTTGTTTGTTGTGCCACG 58.297 45.000 0.00 0.00 0.00 4.94
102 103 4.474226 TTTTGTTTGTTTGTTGTGCCAC 57.526 36.364 0.00 0.00 0.00 5.01
138 140 9.672673 AGCTAAGTATTACATTGGGCTTATATG 57.327 33.333 0.00 0.00 0.00 1.78
171 173 1.302033 CTGGGCAGCCGGCTTATAG 60.302 63.158 30.60 17.58 44.01 1.31
173 175 4.195334 CCTGGGCAGCCGGCTTAT 62.195 66.667 30.60 2.44 44.01 1.73
187 190 1.741770 CGCCGAGTTCTTTCCCCTG 60.742 63.158 0.00 0.00 0.00 4.45
197 200 0.528924 TGTGCAGTATACGCCGAGTT 59.471 50.000 14.28 0.00 0.00 3.01
204 207 0.645355 CACGGCTTGTGCAGTATACG 59.355 55.000 0.00 0.00 45.29 3.06
239 242 3.186613 GCTTATGGTTATGTAAGCCGAGC 59.813 47.826 5.97 3.55 44.30 5.03
256 259 7.611855 GTGTATTTTCTGGGCTATATGGCTTAT 59.388 37.037 11.16 0.00 41.48 1.73
271 274 5.038683 TCTATACGCCGTGTGTATTTTCTG 58.961 41.667 0.00 3.51 39.51 3.02
322 325 4.439700 GGCACACTCGGCGTATATATACAT 60.440 45.833 20.24 0.00 32.87 2.29
390 393 3.567579 TTTCTCGGGCAAGCTGGGG 62.568 63.158 0.00 0.00 0.00 4.96
402 405 2.219674 GCATATTCTCACGGCTTTCTCG 59.780 50.000 0.00 0.00 0.00 4.04
413 416 3.243873 CCTGTAAGCCGAGCATATTCTCA 60.244 47.826 3.25 0.00 33.41 3.27
419 422 3.306088 GCTTATCCTGTAAGCCGAGCATA 60.306 47.826 8.26 0.00 42.88 3.14
421 424 1.202533 GCTTATCCTGTAAGCCGAGCA 60.203 52.381 8.26 0.00 42.88 4.26
422 425 1.503294 GCTTATCCTGTAAGCCGAGC 58.497 55.000 8.26 0.00 42.88 5.03
455 458 2.654912 GGAAGAACGTCGTGTGCCG 61.655 63.158 0.00 0.00 38.13 5.69
464 467 2.097825 AGCCGTATACTGGAAGAACGT 58.902 47.619 15.19 0.00 36.76 3.99
488 491 1.741770 GCTTCGGTGAACGGCTCAT 60.742 57.895 0.00 0.00 44.45 2.90
507 512 2.550978 GTCATTGTACGCTATGTGCCT 58.449 47.619 0.00 0.00 38.78 4.75
509 514 1.924524 ACGTCATTGTACGCTATGTGC 59.075 47.619 8.05 0.00 46.71 4.57
512 517 2.124903 GGGACGTCATTGTACGCTATG 58.875 52.381 18.91 0.00 46.71 2.23
515 520 4.904466 GGGACGTCATTGTACGCT 57.096 55.556 18.91 0.00 46.71 5.07
535 540 2.031769 GGCCACACGGTTTACAAGTAAC 60.032 50.000 0.00 0.00 33.28 2.50
575 580 2.143122 ACAATAAGCCGTGTGTCACAG 58.857 47.619 5.74 0.00 33.40 3.66
579 584 1.126113 CGTGACAATAAGCCGTGTGTC 59.874 52.381 0.00 0.00 40.64 3.67
606 611 3.681417 GGTATTAACTCAACGGTGACACC 59.319 47.826 15.13 15.13 34.05 4.16
655 660 5.827666 AGTTTTTGTATGAAACTGTTCCCG 58.172 37.500 1.80 0.00 43.58 5.14
708 713 7.686438 TGTATGAATTTGTTACAGCAGACAT 57.314 32.000 0.00 0.00 0.00 3.06
1635 1711 2.239150 AGAGCCACATTCTCTTCAGCAT 59.761 45.455 0.00 0.00 37.63 3.79
2292 2462 4.201657 CTGAATGTGCCCATGTTGATCTA 58.798 43.478 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.