Multiple sequence alignment - TraesCS2A01G414100

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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 TraesCS2A01G414100 chr2A 100.000 2930 0 0 1 2930 671281227 671284156 0.000000e+00 5411
1 TraesCS2A01G414100 chr2A 77.604 384 72 11 118 494 451014736 451014360 1.370000e-53 220
2 TraesCS2A01G414100 chr2D 91.992 2435 82 32 528 2930 526344801 526347154 0.000000e+00 3312
3 TraesCS2A01G414100 chr2D 73.922 464 104 14 3 455 304335169 304335626 1.400000e-38 171
4 TraesCS2A01G414100 chr2B 90.652 2118 125 32 1 2086 622656051 622658127 0.000000e+00 2747
5 TraesCS2A01G414100 chr2B 94.892 744 28 4 2153 2895 622673325 622674059 0.000000e+00 1155
6 TraesCS2A01G414100 chr2B 74.138 522 109 19 20 532 641651923 641652427 2.980000e-45 193
7 TraesCS2A01G414100 chr2B 74.058 451 108 6 65 510 681736643 681736197 3.000000e-40 176
8 TraesCS2A01G414100 chr6A 90.909 374 31 2 1558 1928 464538478 464538851 1.570000e-137 499
9 TraesCS2A01G414100 chr6A 76.042 384 81 8 117 494 497996713 497996335 3.850000e-44 189
10 TraesCS2A01G414100 chr6A 89.922 129 13 0 1001 1129 464537913 464538041 1.810000e-37 167
11 TraesCS2A01G414100 chr6D 90.374 374 33 2 1558 1928 325756235 325756608 3.390000e-134 488
12 TraesCS2A01G414100 chr6D 88.372 129 15 0 1001 1129 325755666 325755794 3.910000e-34 156
13 TraesCS2A01G414100 chr6B 89.655 377 36 2 1558 1931 497216207 497215831 7.350000e-131 477
14 TraesCS2A01G414100 chr7D 85.870 276 39 0 1601 1876 433876570 433876845 7.940000e-76 294
15 TraesCS2A01G414100 chr7D 74.451 501 113 11 3 494 80326966 80326472 4.950000e-48 202
16 TraesCS2A01G414100 chr7B 84.828 290 44 0 1601 1890 451289912 451290201 2.860000e-75 292
17 TraesCS2A01G414100 chr7B 82.143 168 29 1 3 170 394807046 394806880 3.040000e-30 143
18 TraesCS2A01G414100 chr7A 85.612 278 40 0 1599 1876 484525275 484525552 2.860000e-75 292
19 TraesCS2A01G414100 chr4D 76.160 474 96 13 22 487 499254065 499253601 1.760000e-57 233
20 TraesCS2A01G414100 chr4D 74.614 453 102 10 4 455 375155729 375155289 1.390000e-43 187
21 TraesCS2A01G414100 chr4B 75.373 536 103 21 3 521 29706186 29705663 6.310000e-57 231
22 TraesCS2A01G414100 chr4A 74.164 538 122 11 3 534 89417962 89418488 1.060000e-49 207
23 TraesCS2A01G414100 chr3B 80.435 276 46 6 1606 1877 826725618 826725889 1.380000e-48 204
24 TraesCS2A01G414100 chr1B 75.121 414 90 9 124 531 32419838 32420244 6.450000e-42 182
25 TraesCS2A01G414100 chr1A 75.781 384 79 10 117 493 532632105 532632481 6.450000e-42 182


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 TraesCS2A01G414100 chr2A 671281227 671284156 2929 False 5411 5411 100.0000 1 2930 1 chr2A.!!$F1 2929
1 TraesCS2A01G414100 chr2D 526344801 526347154 2353 False 3312 3312 91.9920 528 2930 1 chr2D.!!$F2 2402
2 TraesCS2A01G414100 chr2B 622656051 622658127 2076 False 2747 2747 90.6520 1 2086 1 chr2B.!!$F1 2085
3 TraesCS2A01G414100 chr2B 622673325 622674059 734 False 1155 1155 94.8920 2153 2895 1 chr2B.!!$F2 742
4 TraesCS2A01G414100 chr6A 464537913 464538851 938 False 333 499 90.4155 1001 1928 2 chr6A.!!$F1 927
5 TraesCS2A01G414100 chr6D 325755666 325756608 942 False 322 488 89.3730 1001 1928 2 chr6D.!!$F1 927
6 TraesCS2A01G414100 chr4B 29705663 29706186 523 True 231 231 75.3730 3 521 1 chr4B.!!$R1 518
7 TraesCS2A01G414100 chr4A 89417962 89418488 526 False 207 207 74.1640 3 534 1 chr4A.!!$F1 531

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
166 169 0.242825 GGTGTGTCTCCGACGAATCA 59.757 55.0 0.0 0.0 34.95 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2242 0.249868 TCACAAGCAACCGTCAGAGG 60.25 55.0 0.0 0.0 37.3 3.69 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
58 61 2.475155 TCCTGCTCATGAAGGAGATGT 58.525 47.619 11.47 0.00 45.87 3.06
105 108 1.988846 AGGTTCTTCCTAGCAAGCCTT 59.011 47.619 0.00 0.00 46.10 4.35
166 169 0.242825 GGTGTGTCTCCGACGAATCA 59.757 55.000 0.00 0.00 34.95 2.57
225 229 6.654582 TCCGTATGGACCAATATTCATTCATG 59.345 38.462 0.00 0.00 40.17 3.07
226 230 6.317088 CGTATGGACCAATATTCATTCATGC 58.683 40.000 0.00 0.00 0.00 4.06
245 249 4.270245 TGCATGTTCATGTGTCTACAGA 57.730 40.909 13.24 0.00 40.79 3.41
274 279 4.761739 TCATTCTGATCCACGCTTTTCTTT 59.238 37.500 0.00 0.00 0.00 2.52
279 284 4.500127 TGATCCACGCTTTTCTTTATCGA 58.500 39.130 0.00 0.00 0.00 3.59
299 304 2.610374 GACGACAGTTGCTGTTTTGGTA 59.390 45.455 3.16 0.00 45.44 3.25
302 307 3.308530 GACAGTTGCTGTTTTGGTATGC 58.691 45.455 3.16 0.00 45.44 3.14
309 314 1.468520 CTGTTTTGGTATGCTGGTCCG 59.531 52.381 0.00 0.00 0.00 4.79
341 346 5.394883 CCTTAGCACAATAACTTCCCGTCTA 60.395 44.000 0.00 0.00 0.00 2.59
349 354 8.794553 CACAATAACTTCCCGTCTATCTACTAT 58.205 37.037 0.00 0.00 0.00 2.12
375 380 2.084546 GATTTGCCTTAGCTTCGGTGT 58.915 47.619 0.00 0.00 40.80 4.16
381 386 0.895530 CTTAGCTTCGGTGTGGGAGA 59.104 55.000 0.00 0.00 0.00 3.71
418 427 0.736325 GTCTTCGGCTCGCTTGCTTA 60.736 55.000 0.00 0.00 0.00 3.09
427 436 2.794981 GCTCGCTTGCTTATAGTCGTCA 60.795 50.000 0.00 0.00 0.00 4.35
443 452 3.884091 GTCGTCACTAGGTGGTCTATGAT 59.116 47.826 0.00 0.00 33.87 2.45
498 507 8.201554 TGTTCTTTATACTGACATGATGCTTC 57.798 34.615 0.00 0.00 0.00 3.86
555 567 6.695292 AACATTCGCAAGTTCAAATCATTC 57.305 33.333 0.00 0.00 39.48 2.67
576 588 8.615211 TCATTCAAATGATCTCACCTAATTTCG 58.385 33.333 1.30 0.00 40.32 3.46
593 605 1.170442 TCGATAGACGCAAGGACACA 58.830 50.000 0.00 0.00 42.67 3.72
685 697 1.869767 CTTCTCCACACTGTCTTGTGC 59.130 52.381 0.00 0.00 44.79 4.57
728 740 4.937620 TGCCTAAACAATTGCAACAAACAA 59.062 33.333 0.00 0.00 0.00 2.83
735 747 7.620397 AACAATTGCAACAAACAAAAAGTTG 57.380 28.000 0.00 0.00 44.01 3.16
742 754 6.487689 CAACAAACAAAAAGTTGCCCTAAA 57.512 33.333 0.00 0.00 41.19 1.85
743 755 6.903419 CAACAAACAAAAAGTTGCCCTAAAA 58.097 32.000 0.00 0.00 41.19 1.52
744 756 7.363431 CAACAAACAAAAAGTTGCCCTAAAAA 58.637 30.769 0.00 0.00 41.19 1.94
1381 1463 1.975327 CCACGTCACCATCCTCACT 59.025 57.895 0.00 0.00 0.00 3.41
1517 1599 1.501169 GTGCAACAAATCTTGCCACC 58.499 50.000 0.00 0.00 45.13 4.61
1523 1605 1.956477 ACAAATCTTGCCACCTCACAC 59.044 47.619 0.00 0.00 0.00 3.82
1554 1665 5.731591 AGTACTCACTGGCCTTTTATGTAC 58.268 41.667 3.32 10.37 32.25 2.90
1932 2046 0.178941 ACCAGGAGTACCCGTGAAGT 60.179 55.000 0.00 0.00 40.87 3.01
1937 2051 0.669625 GAGTACCCGTGAAGTGCACC 60.670 60.000 14.63 0.00 44.85 5.01
1947 2061 0.669318 GAAGTGCACCGATCCGAACA 60.669 55.000 14.63 0.00 0.00 3.18
1948 2062 0.250124 AAGTGCACCGATCCGAACAA 60.250 50.000 14.63 0.00 0.00 2.83
1949 2063 0.949105 AGTGCACCGATCCGAACAAC 60.949 55.000 14.63 0.00 0.00 3.32
1950 2064 1.669760 TGCACCGATCCGAACAACC 60.670 57.895 0.00 0.00 0.00 3.77
1951 2065 1.375523 GCACCGATCCGAACAACCT 60.376 57.895 0.00 0.00 0.00 3.50
1952 2066 0.108520 GCACCGATCCGAACAACCTA 60.109 55.000 0.00 0.00 0.00 3.08
1953 2067 1.922570 CACCGATCCGAACAACCTAG 58.077 55.000 0.00 0.00 0.00 3.02
1955 2069 0.460311 CCGATCCGAACAACCTAGCT 59.540 55.000 0.00 0.00 0.00 3.32
1957 2071 2.194271 CGATCCGAACAACCTAGCTTC 58.806 52.381 0.00 0.00 0.00 3.86
2000 2118 4.503123 CCCTTGTGTGAATTTCCCTTTTCC 60.503 45.833 0.00 0.00 0.00 3.13
2012 2139 9.685276 GAATTTCCCTTTTCCATTTTAATCCAT 57.315 29.630 0.00 0.00 0.00 3.41
2017 2144 7.677745 TCCCTTTTCCATTTTAATCCATCTCAA 59.322 33.333 0.00 0.00 0.00 3.02
2018 2145 8.320617 CCCTTTTCCATTTTAATCCATCTCAAA 58.679 33.333 0.00 0.00 0.00 2.69
2019 2146 9.895138 CCTTTTCCATTTTAATCCATCTCAAAT 57.105 29.630 0.00 0.00 0.00 2.32
2090 2218 2.724174 GCGTTTTCCGAAATCTTTGTGG 59.276 45.455 0.00 0.00 39.56 4.17
2107 2235 1.678970 GGCAAATTCGTGGAGGCCT 60.679 57.895 3.86 3.86 38.37 5.19
2109 2237 1.508088 CAAATTCGTGGAGGCCTGC 59.492 57.895 18.95 18.95 0.00 4.85
2110 2238 1.678970 AAATTCGTGGAGGCCTGCC 60.679 57.895 22.95 17.17 0.00 4.85
2111 2239 2.424842 AAATTCGTGGAGGCCTGCCA 62.425 55.000 22.95 19.60 38.92 4.92
2125 2253 4.681978 GCCACGCCTCTGACGGTT 62.682 66.667 0.00 0.00 34.00 4.44
2126 2254 2.738521 CCACGCCTCTGACGGTTG 60.739 66.667 0.00 0.00 34.00 3.77
2127 2255 3.414700 CACGCCTCTGACGGTTGC 61.415 66.667 0.00 0.00 34.00 4.17
2128 2256 3.616721 ACGCCTCTGACGGTTGCT 61.617 61.111 0.00 0.00 34.00 3.91
2129 2257 2.357517 CGCCTCTGACGGTTGCTT 60.358 61.111 0.00 0.00 0.00 3.91
2130 2258 2.671177 CGCCTCTGACGGTTGCTTG 61.671 63.158 0.00 0.00 0.00 4.01
2131 2259 1.598130 GCCTCTGACGGTTGCTTGT 60.598 57.895 0.00 0.00 0.00 3.16
2132 2260 1.845809 GCCTCTGACGGTTGCTTGTG 61.846 60.000 0.00 0.00 0.00 3.33
2133 2261 0.249868 CCTCTGACGGTTGCTTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
2134 2262 1.581934 CTCTGACGGTTGCTTGTGAA 58.418 50.000 0.00 0.00 0.00 3.18
2135 2263 1.261619 CTCTGACGGTTGCTTGTGAAC 59.738 52.381 0.00 0.00 0.00 3.18
2217 2345 3.610619 TACGGTCGCGTCCCTCTCA 62.611 63.158 16.75 0.00 0.00 3.27
2317 2446 2.896243 GAGACGCTCGAACTTGTAGA 57.104 50.000 0.00 0.00 0.00 2.59
2334 2463 0.673644 AGAAATGGCGTCCAACCTCG 60.674 55.000 2.68 0.00 36.95 4.63
2341 2470 3.499737 GTCCAACCTCGGCATGCG 61.500 66.667 12.44 7.41 0.00 4.73
2456 2585 2.669229 TCCGCCAGTACGTCGACA 60.669 61.111 17.16 0.00 0.00 4.35
2457 2586 1.989966 CTCCGCCAGTACGTCGACAT 61.990 60.000 17.16 1.85 0.00 3.06
2461 2590 1.202110 CGCCAGTACGTCGACATACTT 60.202 52.381 20.83 4.92 28.91 2.24
2507 2636 0.642800 GAGTTCATGCTCTCGTTCGC 59.357 55.000 0.00 0.00 32.99 4.70
2523 2652 1.163420 TCGCACGTGCTCATGGTTTT 61.163 50.000 35.27 0.00 39.32 2.43
2772 2901 2.031012 CAACTGCTCGGCTCCACA 59.969 61.111 0.00 0.00 0.00 4.17
2843 2972 1.001268 ACCATCGATCGATCACTTCCG 60.001 52.381 27.20 14.09 31.62 4.30
2845 2974 0.668535 ATCGATCGATCACTTCCGCA 59.331 50.000 24.60 0.00 0.00 5.69
2847 2976 0.848942 CGATCGATCACTTCCGCAAG 59.151 55.000 24.40 0.96 35.50 4.01
2848 2977 1.799181 CGATCGATCACTTCCGCAAGT 60.799 52.381 24.40 0.00 44.26 3.16
2849 2978 2.540973 CGATCGATCACTTCCGCAAGTA 60.541 50.000 24.40 0.00 41.24 2.24
2850 2979 3.643763 GATCGATCACTTCCGCAAGTAT 58.356 45.455 20.52 0.00 41.24 2.12
2851 2980 2.809446 TCGATCACTTCCGCAAGTATG 58.191 47.619 0.00 0.00 41.24 2.39
2866 2995 5.980698 CAAGTATGCAACTCCTAGTCATG 57.019 43.478 0.00 0.00 37.50 3.07
2868 2997 1.945387 ATGCAACTCCTAGTCATGCG 58.055 50.000 0.00 0.00 35.34 4.73
2884 3013 2.563427 CGTCTCAGAGTGCTCGCA 59.437 61.111 0.00 0.00 34.09 5.10
2902 3033 1.019278 CACCCGTGTGTGCCTATGTC 61.019 60.000 0.00 0.00 37.72 3.06
2906 3037 1.070821 CGTGTGTGCCTATGTCTGTG 58.929 55.000 0.00 0.00 0.00 3.66
2908 3039 1.800586 GTGTGTGCCTATGTCTGTGTG 59.199 52.381 0.00 0.00 0.00 3.82
2910 3041 2.069273 GTGTGCCTATGTCTGTGTGTC 58.931 52.381 0.00 0.00 0.00 3.67
2916 3047 0.613260 TATGTCTGTGTGTCCAGGCC 59.387 55.000 0.00 0.00 36.21 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 56 1.198713 AGGAAGCCGACATCACATCT 58.801 50.000 0.00 0.00 0.00 2.90
58 61 4.346709 TCCATATTTAGGAAGCCGACATCA 59.653 41.667 0.00 0.00 30.71 3.07
119 122 0.242286 CCCTCCGACGATGCTAGATG 59.758 60.000 0.00 0.00 0.00 2.90
120 123 1.528292 GCCCTCCGACGATGCTAGAT 61.528 60.000 0.00 0.00 0.00 1.98
166 169 4.199310 CAAACACCTATCGAATCCCACAT 58.801 43.478 0.00 0.00 0.00 3.21
180 183 0.834612 TCCACCGAAGACAAACACCT 59.165 50.000 0.00 0.00 0.00 4.00
225 229 5.448225 CCAATCTGTAGACACATGAACATGC 60.448 44.000 13.71 0.00 42.39 4.06
226 230 5.876460 TCCAATCTGTAGACACATGAACATG 59.124 40.000 12.43 12.43 44.15 3.21
269 274 3.673338 CAGCAACTGTCGTCGATAAAGAA 59.327 43.478 0.00 0.00 0.00 2.52
274 279 2.717580 AACAGCAACTGTCGTCGATA 57.282 45.000 0.00 0.00 44.62 2.92
279 284 1.459450 ACCAAAACAGCAACTGTCGT 58.541 45.000 0.00 0.00 44.62 4.34
299 304 4.047125 CCCCCAACGGACCAGCAT 62.047 66.667 0.00 0.00 0.00 3.79
309 314 0.614697 ATTGTGCTAAGGCCCCCAAC 60.615 55.000 0.00 0.00 37.74 3.77
349 354 6.260050 CACCGAAGCTAAGGCAAATCTTATTA 59.740 38.462 7.25 0.00 41.70 0.98
364 369 0.970937 CCTCTCCCACACCGAAGCTA 60.971 60.000 0.00 0.00 0.00 3.32
366 371 2.266055 CCTCTCCCACACCGAAGC 59.734 66.667 0.00 0.00 0.00 3.86
375 380 2.134287 GCTATCACCGCCTCTCCCA 61.134 63.158 0.00 0.00 0.00 4.37
381 386 4.530857 GTGCCGCTATCACCGCCT 62.531 66.667 0.00 0.00 0.00 5.52
386 391 1.472276 CGAAGACGTGCCGCTATCAC 61.472 60.000 0.00 0.00 34.56 3.06
418 427 3.648507 AGACCACCTAGTGACGACTAT 57.351 47.619 0.00 0.00 35.23 2.12
427 436 3.467483 TCCAGGATCATAGACCACCTAGT 59.533 47.826 0.00 0.00 0.00 2.57
443 452 6.023603 AGTAAGAGAAACCTTACATCCAGGA 58.976 40.000 13.99 0.00 46.65 3.86
555 567 9.481340 TCTATCGAAATTAGGTGAGATCATTTG 57.519 33.333 0.00 0.00 0.00 2.32
576 588 2.415512 GGTTTGTGTCCTTGCGTCTATC 59.584 50.000 0.00 0.00 0.00 2.08
593 605 9.349713 TGATGAACTGTTTTCTATGTAAGGTTT 57.650 29.630 0.00 0.00 0.00 3.27
685 697 3.384668 CAGGAGCCACGTTATGATACAG 58.615 50.000 0.00 0.00 0.00 2.74
743 755 4.276926 CCACTCTGCTCTGCTAAACTTTTT 59.723 41.667 0.00 0.00 0.00 1.94
744 756 3.817647 CCACTCTGCTCTGCTAAACTTTT 59.182 43.478 0.00 0.00 0.00 2.27
745 757 3.181450 ACCACTCTGCTCTGCTAAACTTT 60.181 43.478 0.00 0.00 0.00 2.66
746 758 2.370189 ACCACTCTGCTCTGCTAAACTT 59.630 45.455 0.00 0.00 0.00 2.66
747 759 1.974236 ACCACTCTGCTCTGCTAAACT 59.026 47.619 0.00 0.00 0.00 2.66
748 760 2.464157 ACCACTCTGCTCTGCTAAAC 57.536 50.000 0.00 0.00 0.00 2.01
749 761 2.550855 CCAACCACTCTGCTCTGCTAAA 60.551 50.000 0.00 0.00 0.00 1.85
750 762 1.002430 CCAACCACTCTGCTCTGCTAA 59.998 52.381 0.00 0.00 0.00 3.09
756 768 1.374758 CCGACCAACCACTCTGCTC 60.375 63.158 0.00 0.00 0.00 4.26
1381 1463 0.970937 CGACCCAGTAGAAGAGCCCA 60.971 60.000 0.00 0.00 0.00 5.36
1477 1559 2.719426 CGTGGTTCGTAGAAGGTTCT 57.281 50.000 0.00 0.00 45.90 3.01
1512 1594 1.098712 TTTTCACGGTGTGAGGTGGC 61.099 55.000 8.17 0.00 43.69 5.01
1513 1595 0.944386 CTTTTCACGGTGTGAGGTGG 59.056 55.000 8.17 0.00 43.69 4.61
1517 1599 3.489785 GTGAGTACTTTTCACGGTGTGAG 59.510 47.826 8.17 7.22 43.69 3.51
1920 2034 2.025418 CGGTGCACTTCACGGGTAC 61.025 63.158 17.98 0.00 46.56 3.34
1932 2046 1.669760 GGTTGTTCGGATCGGTGCA 60.670 57.895 0.00 0.00 0.00 4.57
1937 2051 2.194271 GAAGCTAGGTTGTTCGGATCG 58.806 52.381 12.82 0.00 0.00 3.69
1947 2061 0.250513 CGAGCCAAGGAAGCTAGGTT 59.749 55.000 6.94 6.94 41.75 3.50
1948 2062 0.905337 ACGAGCCAAGGAAGCTAGGT 60.905 55.000 0.00 0.00 41.75 3.08
1949 2063 0.250513 AACGAGCCAAGGAAGCTAGG 59.749 55.000 0.00 0.00 41.75 3.02
1950 2064 1.363744 CAACGAGCCAAGGAAGCTAG 58.636 55.000 0.00 0.00 41.75 3.42
1951 2065 0.673644 GCAACGAGCCAAGGAAGCTA 60.674 55.000 0.00 0.00 41.75 3.32
1952 2066 1.968540 GCAACGAGCCAAGGAAGCT 60.969 57.895 0.00 0.00 45.23 3.74
1953 2067 2.563427 GCAACGAGCCAAGGAAGC 59.437 61.111 0.00 0.00 37.23 3.86
2044 2171 5.356190 AGAACCGTTCATGTAAGATCGAGTA 59.644 40.000 13.69 0.00 33.72 2.59
2090 2218 1.508088 CAGGCCTCCACGAATTTGC 59.492 57.895 0.00 0.00 0.00 3.68
2109 2237 2.738521 CAACCGTCAGAGGCGTGG 60.739 66.667 0.00 0.00 33.69 4.94
2110 2238 3.414700 GCAACCGTCAGAGGCGTG 61.415 66.667 0.00 0.00 33.69 5.34
2111 2239 3.165160 AAGCAACCGTCAGAGGCGT 62.165 57.895 0.00 0.00 33.69 5.68
2113 2241 1.598130 ACAAGCAACCGTCAGAGGC 60.598 57.895 0.00 0.00 33.69 4.70
2114 2242 0.249868 TCACAAGCAACCGTCAGAGG 60.250 55.000 0.00 0.00 37.30 3.69
2115 2243 1.261619 GTTCACAAGCAACCGTCAGAG 59.738 52.381 0.00 0.00 0.00 3.35
2116 2244 1.134521 AGTTCACAAGCAACCGTCAGA 60.135 47.619 0.00 0.00 0.00 3.27
2117 2245 1.299541 AGTTCACAAGCAACCGTCAG 58.700 50.000 0.00 0.00 0.00 3.51
2118 2246 1.400142 CAAGTTCACAAGCAACCGTCA 59.600 47.619 0.00 0.00 0.00 4.35
2119 2247 1.268539 CCAAGTTCACAAGCAACCGTC 60.269 52.381 0.00 0.00 0.00 4.79
2120 2248 0.738389 CCAAGTTCACAAGCAACCGT 59.262 50.000 0.00 0.00 0.00 4.83
2121 2249 1.002468 CTCCAAGTTCACAAGCAACCG 60.002 52.381 0.00 0.00 0.00 4.44
2122 2250 1.269257 GCTCCAAGTTCACAAGCAACC 60.269 52.381 0.00 0.00 33.21 3.77
2123 2251 1.597937 CGCTCCAAGTTCACAAGCAAC 60.598 52.381 0.00 0.00 33.21 4.17
2124 2252 0.662619 CGCTCCAAGTTCACAAGCAA 59.337 50.000 0.00 0.00 33.21 3.91
2125 2253 1.165907 CCGCTCCAAGTTCACAAGCA 61.166 55.000 0.00 0.00 33.21 3.91
2126 2254 1.576421 CCGCTCCAAGTTCACAAGC 59.424 57.895 0.00 0.00 0.00 4.01
2127 2255 1.856265 GCCCGCTCCAAGTTCACAAG 61.856 60.000 0.00 0.00 0.00 3.16
2128 2256 1.896660 GCCCGCTCCAAGTTCACAA 60.897 57.895 0.00 0.00 0.00 3.33
2129 2257 2.281484 GCCCGCTCCAAGTTCACA 60.281 61.111 0.00 0.00 0.00 3.58
2130 2258 3.423154 CGCCCGCTCCAAGTTCAC 61.423 66.667 0.00 0.00 0.00 3.18
2315 2444 0.673644 CGAGGTTGGACGCCATTTCT 60.674 55.000 0.00 0.00 31.53 2.52
2317 2446 1.674322 CCGAGGTTGGACGCCATTT 60.674 57.895 0.00 0.00 31.53 2.32
2456 2585 1.153901 CGTGGACGCGGTGAAGTAT 60.154 57.895 12.47 0.00 0.00 2.12
2457 2586 2.256158 CGTGGACGCGGTGAAGTA 59.744 61.111 12.47 0.00 0.00 2.24
2483 2612 1.615883 ACGAGAGCATGAACTCACACT 59.384 47.619 15.98 0.00 39.26 3.55
2507 2636 4.378046 GGTTAGTAAAACCATGAGCACGTG 60.378 45.833 12.28 12.28 40.03 4.49
2523 2652 0.388907 AAAGAAGCGCGCGGTTAGTA 60.389 50.000 42.26 0.00 35.84 1.82
2818 2947 4.179926 AGTGATCGATCGATGGTAATGG 57.820 45.455 33.86 0.00 34.60 3.16
2845 2974 4.446371 GCATGACTAGGAGTTGCATACTT 58.554 43.478 0.00 0.00 37.17 2.24
2847 2976 2.797156 CGCATGACTAGGAGTTGCATAC 59.203 50.000 0.00 0.00 32.90 2.39
2848 2977 2.430694 ACGCATGACTAGGAGTTGCATA 59.569 45.455 0.00 0.00 32.90 3.14
2849 2978 1.208052 ACGCATGACTAGGAGTTGCAT 59.792 47.619 0.00 0.00 32.90 3.96
2850 2979 0.608130 ACGCATGACTAGGAGTTGCA 59.392 50.000 0.00 0.00 32.90 4.08
2851 2980 1.134965 AGACGCATGACTAGGAGTTGC 60.135 52.381 0.00 0.00 30.68 4.17
2852 2981 2.164422 TGAGACGCATGACTAGGAGTTG 59.836 50.000 0.00 0.00 0.00 3.16
2853 2982 2.425312 CTGAGACGCATGACTAGGAGTT 59.575 50.000 0.00 0.00 0.00 3.01
2854 2983 2.020720 CTGAGACGCATGACTAGGAGT 58.979 52.381 0.00 0.00 0.00 3.85
2855 2984 2.290367 CTCTGAGACGCATGACTAGGAG 59.710 54.545 0.00 0.64 0.00 3.69
2866 2995 2.878520 GCGAGCACTCTGAGACGC 60.879 66.667 12.44 16.89 39.33 5.19
2868 2997 1.445238 GGTGCGAGCACTCTGAGAC 60.445 63.158 24.79 5.54 45.52 3.36
2884 3013 1.192146 AGACATAGGCACACACGGGT 61.192 55.000 0.00 0.00 0.00 5.28
2895 3024 1.406069 GCCTGGACACACAGACATAGG 60.406 57.143 0.00 0.00 40.97 2.57
2896 3025 1.406069 GGCCTGGACACACAGACATAG 60.406 57.143 0.00 0.00 40.97 2.23
2902 3033 2.666190 CACGGCCTGGACACACAG 60.666 66.667 0.00 0.00 38.21 3.66


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

AutoCloner maintained by Alex Coulton.