Multiple sequence alignment - TraesCS2D01G162400

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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 TraesCS2D01G162400 chr2D 100.000 2179 0 0 1 2179 106950519 106952697 0.000000e+00 4024.0
1 TraesCS2D01G162400 chr2D 100.000 94 0 0 2438 2531 106952956 106953049 9.310000e-40 174.0
2 TraesCS2D01G162400 chr2B 92.584 1780 90 20 316 2057 157242617 157244392 0.000000e+00 2518.0
3 TraesCS2D01G162400 chr2B 95.695 302 11 2 1 302 157242056 157242355 3.790000e-133 484.0
4 TraesCS2D01G162400 chr2B 90.769 65 5 1 2037 2100 157244104 157244168 4.490000e-13 86.1
5 TraesCS2D01G162400 chr2A 91.397 1825 101 23 311 2118 103224802 103226587 0.000000e+00 2449.0
6 TraesCS2D01G162400 chr2A 95.410 305 9 4 1 302 103224439 103224741 4.900000e-132 481.0
7 TraesCS2D01G162400 chr2A 100.000 28 0 0 2143 2170 103227190 103227217 5.000000e-03 52.8


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 TraesCS2D01G162400 chr2D 106950519 106953049 2530 False 2099.000000 4024 100.000000 1 2531 2 chr2D.!!$F1 2530
1 TraesCS2D01G162400 chr2B 157242056 157244392 2336 False 1029.366667 2518 93.016000 1 2100 3 chr2B.!!$F1 2099
2 TraesCS2D01G162400 chr2A 103224439 103227217 2778 False 994.266667 2449 95.602333 1 2170 3 chr2A.!!$F1 2169

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
303 307 0.878086 GCTCCATGAAGCCGACTAGC 60.878 60.0 0.0 0.0 36.22 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2227 0.467804 TCCGCCACTTATATGCTGCA 59.532 50.0 4.13 4.13 0.0 4.41 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
126 129 2.093500 TGTGAGAATTCATGCTACGGCT 60.093 45.455 8.44 0.00 39.59 5.52
302 306 3.280920 GCTCCATGAAGCCGACTAG 57.719 57.895 0.00 0.00 36.22 2.57
303 307 0.878086 GCTCCATGAAGCCGACTAGC 60.878 60.000 0.00 0.00 36.22 3.42
317 569 2.223294 CGACTAGCTTCCGGAACTGTAG 60.223 54.545 14.35 15.57 0.00 2.74
406 658 6.363896 TGTCAGAAAAAGAAAACAACGGAAAC 59.636 34.615 0.00 0.00 0.00 2.78
407 659 6.584942 GTCAGAAAAAGAAAACAACGGAAACT 59.415 34.615 0.00 0.00 0.00 2.66
408 660 7.115805 GTCAGAAAAAGAAAACAACGGAAACTT 59.884 33.333 0.00 0.00 0.00 2.66
520 776 7.707624 AATGTCATCATTTGGTTATGTCAGT 57.292 32.000 0.00 0.00 40.88 3.41
587 843 9.865321 CTAGCTAGTTGTAATTGTTAACCTACA 57.135 33.333 12.92 5.77 0.00 2.74
906 1165 4.068599 GGCTCAGCCTCCAAGAATATAAC 58.931 47.826 9.09 0.00 46.69 1.89
919 1178 9.502091 TCCAAGAATATAACATACCAGCAATAC 57.498 33.333 0.00 0.00 0.00 1.89
952 1214 1.535015 GCAGACGAGCTAAGCTACCTG 60.535 57.143 0.00 0.00 39.88 4.00
1131 1396 2.535984 CGTCTGTGTCTTCATAATCGCC 59.464 50.000 0.00 0.00 0.00 5.54
1533 1798 1.448540 GGTGCCTCCTGTGTGATCG 60.449 63.158 0.00 0.00 0.00 3.69
1546 1811 2.604914 GTGTGATCGATGCGAGATTTGT 59.395 45.455 0.54 0.00 39.91 2.83
1571 1836 6.400579 CAGAGTTTTCTGTGCTATGTACTG 57.599 41.667 0.00 0.00 44.74 2.74
1573 1838 7.090808 CAGAGTTTTCTGTGCTATGTACTGTA 58.909 38.462 0.00 0.00 44.74 2.74
1574 1839 7.274468 CAGAGTTTTCTGTGCTATGTACTGTAG 59.726 40.741 0.00 0.00 44.74 2.74
1575 1840 5.869888 AGTTTTCTGTGCTATGTACTGTAGC 59.130 40.000 18.22 18.22 43.73 3.58
1658 1930 3.003378 GCACCAAACTAGTTTCACCTGTC 59.997 47.826 18.00 1.16 0.00 3.51
1761 2036 3.074390 TGGTTGATCCAGTCTGATTGGTT 59.926 43.478 17.45 10.37 41.93 3.67
1776 2059 8.734386 GTCTGATTGGTTCTGACATAAAAATCT 58.266 33.333 7.49 0.00 46.81 2.40
1811 2094 9.645059 TTCTTGACATTGACTTGTAATAGAGAG 57.355 33.333 0.00 0.00 0.00 3.20
1830 2114 4.677584 AGAGTCATCTTCATAGTCAACGC 58.322 43.478 0.00 0.00 28.57 4.84
1836 2120 3.840468 TCTTCATAGTCAACGCGCTTTA 58.160 40.909 5.73 0.00 0.00 1.85
1837 2121 4.430007 TCTTCATAGTCAACGCGCTTTAT 58.570 39.130 5.73 0.00 0.00 1.40
1841 2125 5.556470 TCATAGTCAACGCGCTTTATTTTC 58.444 37.500 5.73 0.00 0.00 2.29
1850 2134 6.663944 ACGCGCTTTATTTTCTTCTAATCT 57.336 33.333 5.73 0.00 0.00 2.40
1853 2137 7.692705 ACGCGCTTTATTTTCTTCTAATCTTTC 59.307 33.333 5.73 0.00 0.00 2.62
1879 2163 7.452880 TTTTTGACAAGAAATCATCTCCGAT 57.547 32.000 0.00 0.00 37.42 4.18
1881 2165 3.873361 TGACAAGAAATCATCTCCGATGC 59.127 43.478 0.00 0.00 37.42 3.91
1885 2169 2.374504 AGAAATCATCTCCGATGCCCAT 59.625 45.455 0.00 0.00 30.46 4.00
1898 2182 2.902705 TGCCCATACTATTGGTCGAC 57.097 50.000 7.13 7.13 34.77 4.20
1899 2183 2.112190 TGCCCATACTATTGGTCGACA 58.888 47.619 18.91 0.00 34.77 4.35
1904 2188 4.202212 CCCATACTATTGGTCGACATCACA 60.202 45.833 18.91 2.69 34.77 3.58
1905 2189 5.356426 CCATACTATTGGTCGACATCACAA 58.644 41.667 18.91 12.39 31.74 3.33
1907 2191 4.801330 ACTATTGGTCGACATCACAAGA 57.199 40.909 18.91 8.51 0.00 3.02
1931 2215 2.356135 GGTGTTGACCACGAATGCTAT 58.644 47.619 0.00 0.00 45.52 2.97
1936 2220 3.751479 TGACCACGAATGCTATATGCT 57.249 42.857 0.00 0.00 43.37 3.79
1937 2221 3.392882 TGACCACGAATGCTATATGCTG 58.607 45.455 0.00 0.00 43.37 4.41
1940 2224 2.420642 CACGAATGCTATATGCTGCCT 58.579 47.619 0.00 0.00 43.37 4.75
1941 2225 2.414481 CACGAATGCTATATGCTGCCTC 59.586 50.000 0.00 0.00 43.37 4.70
1943 2227 3.244353 ACGAATGCTATATGCTGCCTCTT 60.244 43.478 0.00 0.00 43.37 2.85
1971 2255 2.631160 TAAGTGGCGGATAACCCATG 57.369 50.000 0.00 0.00 32.95 3.66
1980 2264 0.598065 GATAACCCATGGGCGATTGC 59.402 55.000 31.73 11.74 39.32 3.56
1990 2274 1.283793 GGCGATTGCGATTGGGATG 59.716 57.895 3.23 0.00 44.10 3.51
2001 2285 0.766674 ATTGGGATGGCGGCCTAGTA 60.767 55.000 21.46 0.00 0.00 1.82
2036 2328 3.183237 GCGGGAATACATAAACGCATC 57.817 47.619 0.00 0.00 45.57 3.91
2102 2394 1.676006 AGTCAACGTGCTTTCTTTGGG 59.324 47.619 0.00 0.00 0.00 4.12
2138 2430 4.323477 CCCGGCGAGGTCAACCAA 62.323 66.667 9.30 0.00 38.74 3.67
2139 2431 3.047877 CCGGCGAGGTCAACCAAC 61.048 66.667 9.30 0.00 38.89 3.77
2140 2432 2.280524 CGGCGAGGTCAACCAACA 60.281 61.111 0.00 0.00 38.89 3.33
2170 3040 1.336887 TGTTAGGAGCACGAGAGTTGC 60.337 52.381 0.00 0.00 46.40 4.17
2171 3041 0.246635 TTAGGAGCACGAGAGTTGCC 59.753 55.000 0.00 0.00 46.40 4.52
2172 3042 0.612174 TAGGAGCACGAGAGTTGCCT 60.612 55.000 0.00 0.00 46.40 4.75
2173 3043 1.004440 GGAGCACGAGAGTTGCCTT 60.004 57.895 0.00 0.00 46.40 4.35
2174 3044 0.246635 GGAGCACGAGAGTTGCCTTA 59.753 55.000 0.00 0.00 46.40 2.69
2175 3045 1.634702 GAGCACGAGAGTTGCCTTAG 58.365 55.000 0.00 0.00 46.40 2.18
2176 3046 1.202582 GAGCACGAGAGTTGCCTTAGA 59.797 52.381 0.00 0.00 46.40 2.10
2177 3047 1.827969 AGCACGAGAGTTGCCTTAGAT 59.172 47.619 0.00 0.00 46.40 1.98
2178 3048 2.234908 AGCACGAGAGTTGCCTTAGATT 59.765 45.455 0.00 0.00 46.40 2.40
2456 3326 1.737838 GTTGACCTCAATGATCCGCA 58.262 50.000 0.00 0.00 38.24 5.69
2457 3327 2.083774 GTTGACCTCAATGATCCGCAA 58.916 47.619 0.00 0.00 38.24 4.85
2458 3328 2.487762 GTTGACCTCAATGATCCGCAAA 59.512 45.455 0.00 0.00 38.24 3.68
2459 3329 2.789213 TGACCTCAATGATCCGCAAAA 58.211 42.857 0.00 0.00 0.00 2.44
2460 3330 3.355378 TGACCTCAATGATCCGCAAAAT 58.645 40.909 0.00 0.00 0.00 1.82
2461 3331 4.522114 TGACCTCAATGATCCGCAAAATA 58.478 39.130 0.00 0.00 0.00 1.40
2462 3332 5.132502 TGACCTCAATGATCCGCAAAATAT 58.867 37.500 0.00 0.00 0.00 1.28
2463 3333 5.239306 TGACCTCAATGATCCGCAAAATATC 59.761 40.000 0.00 0.00 0.00 1.63
2464 3334 5.380043 ACCTCAATGATCCGCAAAATATCT 58.620 37.500 0.00 0.00 0.00 1.98
2465 3335 5.471456 ACCTCAATGATCCGCAAAATATCTC 59.529 40.000 0.00 0.00 0.00 2.75
2466 3336 5.390251 CCTCAATGATCCGCAAAATATCTCG 60.390 44.000 0.00 0.00 0.00 4.04
2467 3337 5.296748 TCAATGATCCGCAAAATATCTCGA 58.703 37.500 0.00 0.00 0.00 4.04
2468 3338 5.757808 TCAATGATCCGCAAAATATCTCGAA 59.242 36.000 0.00 0.00 0.00 3.71
2469 3339 5.597813 ATGATCCGCAAAATATCTCGAAC 57.402 39.130 0.00 0.00 0.00 3.95
2470 3340 4.693283 TGATCCGCAAAATATCTCGAACT 58.307 39.130 0.00 0.00 0.00 3.01
2471 3341 5.838529 TGATCCGCAAAATATCTCGAACTA 58.161 37.500 0.00 0.00 0.00 2.24
2472 3342 5.920840 TGATCCGCAAAATATCTCGAACTAG 59.079 40.000 0.00 0.00 0.00 2.57
2473 3343 5.509716 TCCGCAAAATATCTCGAACTAGA 57.490 39.130 0.00 0.00 0.00 2.43
2474 3344 5.898174 TCCGCAAAATATCTCGAACTAGAA 58.102 37.500 0.00 0.00 0.00 2.10
2475 3345 5.977725 TCCGCAAAATATCTCGAACTAGAAG 59.022 40.000 0.00 0.00 0.00 2.85
2476 3346 5.977725 CCGCAAAATATCTCGAACTAGAAGA 59.022 40.000 0.00 0.00 0.00 2.87
2477 3347 6.074782 CCGCAAAATATCTCGAACTAGAAGAC 60.075 42.308 0.00 0.00 0.00 3.01
2478 3348 6.472486 CGCAAAATATCTCGAACTAGAAGACA 59.528 38.462 0.00 0.00 0.00 3.41
2479 3349 7.009265 CGCAAAATATCTCGAACTAGAAGACAA 59.991 37.037 0.00 0.00 0.00 3.18
2480 3350 8.656849 GCAAAATATCTCGAACTAGAAGACAAA 58.343 33.333 0.00 0.00 0.00 2.83
2483 3353 9.796120 AAATATCTCGAACTAGAAGACAAAGAG 57.204 33.333 0.00 0.00 0.00 2.85
2484 3354 6.827586 ATCTCGAACTAGAAGACAAAGAGT 57.172 37.500 0.00 0.00 0.00 3.24
2485 3355 6.636562 TCTCGAACTAGAAGACAAAGAGTT 57.363 37.500 0.00 0.00 33.14 3.01
2486 3356 6.439599 TCTCGAACTAGAAGACAAAGAGTTG 58.560 40.000 0.00 0.00 40.84 3.16
2487 3357 5.529791 TCGAACTAGAAGACAAAGAGTTGG 58.470 41.667 0.00 0.00 39.22 3.77
2488 3358 5.301045 TCGAACTAGAAGACAAAGAGTTGGA 59.699 40.000 0.00 0.00 39.22 3.53
2489 3359 5.402867 CGAACTAGAAGACAAAGAGTTGGAC 59.597 44.000 0.00 0.00 39.22 4.02
2490 3360 4.872664 ACTAGAAGACAAAGAGTTGGACG 58.127 43.478 0.00 0.00 39.22 4.79
2491 3361 3.113260 AGAAGACAAAGAGTTGGACGG 57.887 47.619 0.00 0.00 39.22 4.79
2492 3362 1.531578 GAAGACAAAGAGTTGGACGGC 59.468 52.381 0.00 0.00 39.22 5.68
2493 3363 0.600255 AGACAAAGAGTTGGACGGCG 60.600 55.000 4.80 4.80 39.22 6.46
2494 3364 0.878961 GACAAAGAGTTGGACGGCGT 60.879 55.000 14.65 14.65 39.22 5.68
2495 3365 0.463116 ACAAAGAGTTGGACGGCGTT 60.463 50.000 16.19 0.00 39.22 4.84
2496 3366 0.661020 CAAAGAGTTGGACGGCGTTT 59.339 50.000 16.19 0.00 0.00 3.60
2497 3367 1.064952 CAAAGAGTTGGACGGCGTTTT 59.935 47.619 16.19 5.82 0.00 2.43
2498 3368 1.385528 AAGAGTTGGACGGCGTTTTT 58.614 45.000 16.19 0.00 0.00 1.94
2499 3369 0.942252 AGAGTTGGACGGCGTTTTTC 59.058 50.000 16.19 8.33 0.00 2.29
2500 3370 0.942252 GAGTTGGACGGCGTTTTTCT 59.058 50.000 16.19 11.10 0.00 2.52
2501 3371 1.332686 GAGTTGGACGGCGTTTTTCTT 59.667 47.619 16.19 0.00 0.00 2.52
2502 3372 1.064952 AGTTGGACGGCGTTTTTCTTG 59.935 47.619 16.19 0.00 0.00 3.02
2503 3373 0.248702 TTGGACGGCGTTTTTCTTGC 60.249 50.000 16.19 0.00 0.00 4.01
2504 3374 1.724581 GGACGGCGTTTTTCTTGCG 60.725 57.895 16.19 0.00 0.00 4.85
2505 3375 1.277440 GACGGCGTTTTTCTTGCGA 59.723 52.632 16.19 0.00 0.00 5.10
2506 3376 0.316360 GACGGCGTTTTTCTTGCGAA 60.316 50.000 16.19 0.00 0.00 4.70
2507 3377 0.316689 ACGGCGTTTTTCTTGCGAAG 60.317 50.000 6.77 0.00 0.00 3.79
2508 3378 0.996727 CGGCGTTTTTCTTGCGAAGG 60.997 55.000 0.00 0.00 0.00 3.46
2509 3379 1.275471 GGCGTTTTTCTTGCGAAGGC 61.275 55.000 0.00 0.00 40.52 4.35
2510 3380 0.317854 GCGTTTTTCTTGCGAAGGCT 60.318 50.000 0.00 0.00 40.82 4.58
2511 3381 1.398595 CGTTTTTCTTGCGAAGGCTG 58.601 50.000 0.00 0.00 40.82 4.85
2512 3382 1.002900 CGTTTTTCTTGCGAAGGCTGA 60.003 47.619 0.00 0.00 40.82 4.26
2513 3383 2.350772 CGTTTTTCTTGCGAAGGCTGAT 60.351 45.455 0.00 0.00 40.82 2.90
2514 3384 2.982470 GTTTTTCTTGCGAAGGCTGATG 59.018 45.455 0.00 0.00 40.82 3.07
2515 3385 1.896220 TTTCTTGCGAAGGCTGATGT 58.104 45.000 0.00 0.00 40.82 3.06
2516 3386 1.159285 TTCTTGCGAAGGCTGATGTG 58.841 50.000 0.00 0.00 40.82 3.21
2517 3387 0.674581 TCTTGCGAAGGCTGATGTGG 60.675 55.000 0.00 0.00 40.82 4.17
2518 3388 0.674581 CTTGCGAAGGCTGATGTGGA 60.675 55.000 0.00 0.00 40.82 4.02
2519 3389 0.035152 TTGCGAAGGCTGATGTGGAT 60.035 50.000 0.00 0.00 40.82 3.41
2520 3390 0.462581 TGCGAAGGCTGATGTGGATC 60.463 55.000 0.00 0.00 40.82 3.36
2521 3391 0.462581 GCGAAGGCTGATGTGGATCA 60.463 55.000 0.00 0.00 37.07 2.92
2522 3392 1.813092 GCGAAGGCTGATGTGGATCAT 60.813 52.381 0.00 0.00 37.97 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 129 4.245660 CGAAAGTCTGCTTCAAGACCATA 58.754 43.478 0.84 0.00 46.51 2.74
175 178 5.537295 ACATGAACATGATGTTGGGATATGG 59.463 40.000 16.52 0.00 41.28 2.74
216 219 1.004277 TGTTGTTGCCCCTGTAGATCC 59.996 52.381 0.00 0.00 0.00 3.36
302 306 2.202566 GCATACTACAGTTCCGGAAGC 58.797 52.381 19.50 10.43 0.00 3.86
303 307 2.431057 AGGCATACTACAGTTCCGGAAG 59.569 50.000 19.50 9.76 0.00 3.46
304 308 2.463752 AGGCATACTACAGTTCCGGAA 58.536 47.619 14.35 14.35 0.00 4.30
305 309 2.154567 AGGCATACTACAGTTCCGGA 57.845 50.000 0.00 0.00 0.00 5.14
307 311 5.196341 TCATTAGGCATACTACAGTTCCG 57.804 43.478 0.00 0.00 0.00 4.30
430 686 5.163343 TGTGTAGTAGGTCAATGGAATAGGC 60.163 44.000 0.00 0.00 0.00 3.93
484 740 3.753815 TGATGACATTTGGCAACTCTGA 58.246 40.909 0.00 0.00 36.16 3.27
849 1105 5.228220 CGCTATATATGCAACGCTAGAAGTC 59.772 44.000 0.00 0.00 0.00 3.01
906 1165 4.497006 GCTTTGAGCTGTATTGCTGGTATG 60.497 45.833 0.00 0.00 44.17 2.39
952 1214 3.130693 AGTTTCTAGCCGTGTCACCTATC 59.869 47.826 0.00 0.00 0.00 2.08
1116 1381 4.279922 TCGAATAGGGCGATTATGAAGACA 59.720 41.667 0.00 0.00 32.09 3.41
1131 1396 1.600957 CAGCACAGGCAATCGAATAGG 59.399 52.381 0.00 0.00 44.61 2.57
1374 1639 1.566298 CCTCCCCTTCCTTCACCAGG 61.566 65.000 0.00 0.00 45.64 4.45
1533 1798 2.005451 ACTCTGCACAAATCTCGCATC 58.995 47.619 0.00 0.00 34.63 3.91
1546 1811 3.743521 ACATAGCACAGAAAACTCTGCA 58.256 40.909 2.05 0.00 41.19 4.41
1658 1930 4.467795 TCCAGAGAAAGGGTAGAGAACATG 59.532 45.833 0.00 0.00 0.00 3.21
1773 2048 8.105829 AGTCAATGTCAAGAACCAATAAGAGAT 58.894 33.333 0.00 0.00 0.00 2.75
1776 2059 7.502226 ACAAGTCAATGTCAAGAACCAATAAGA 59.498 33.333 0.00 0.00 0.00 2.10
1811 2094 2.034507 GCGCGTTGACTATGAAGATGAC 60.035 50.000 8.43 0.00 0.00 3.06
1860 2144 3.249559 GGCATCGGAGATGATTTCTTGTC 59.750 47.826 13.56 0.00 45.12 3.18
1861 2145 3.209410 GGCATCGGAGATGATTTCTTGT 58.791 45.455 13.56 0.00 45.12 3.16
1871 2155 3.198635 CCAATAGTATGGGCATCGGAGAT 59.801 47.826 0.00 0.00 37.93 2.75
1873 2157 2.303022 ACCAATAGTATGGGCATCGGAG 59.697 50.000 3.16 0.00 45.18 4.63
1874 2158 2.334977 ACCAATAGTATGGGCATCGGA 58.665 47.619 3.16 0.00 45.18 4.55
1875 2159 2.859165 ACCAATAGTATGGGCATCGG 57.141 50.000 3.16 0.00 45.18 4.18
1881 2165 4.202212 TGTGATGTCGACCAATAGTATGGG 60.202 45.833 14.12 1.55 45.18 4.00
1885 2169 5.417894 ACTCTTGTGATGTCGACCAATAGTA 59.582 40.000 14.12 0.00 0.00 1.82
1898 2182 3.003689 GGTCAACACCAACTCTTGTGATG 59.996 47.826 0.00 0.00 43.17 3.07
1899 2183 3.214328 GGTCAACACCAACTCTTGTGAT 58.786 45.455 0.00 0.00 43.17 3.06
1937 2221 2.551459 CCACTTATATGCTGCAAGAGGC 59.449 50.000 6.36 0.00 45.13 4.70
1940 2224 2.212652 CGCCACTTATATGCTGCAAGA 58.787 47.619 6.36 0.00 34.07 3.02
1941 2225 1.265095 CCGCCACTTATATGCTGCAAG 59.735 52.381 6.36 1.37 0.00 4.01
1943 2227 0.467804 TCCGCCACTTATATGCTGCA 59.532 50.000 4.13 4.13 0.00 4.41
1971 2255 1.898574 ATCCCAATCGCAATCGCCC 60.899 57.895 0.00 0.00 35.26 6.13
1980 2264 3.177194 TAGGCCGCCATCCCAATCG 62.177 63.158 13.15 0.00 0.00 3.34
2019 2311 6.017109 ACCAATCAGATGCGTTTATGTATTCC 60.017 38.462 0.00 0.00 0.00 3.01
2020 2312 6.959361 ACCAATCAGATGCGTTTATGTATTC 58.041 36.000 0.00 0.00 0.00 1.75
2021 2313 6.942532 ACCAATCAGATGCGTTTATGTATT 57.057 33.333 0.00 0.00 0.00 1.89
2032 2324 5.356190 TCAATCTCAAGAACCAATCAGATGC 59.644 40.000 0.00 0.00 0.00 3.91
2036 2328 6.206243 ACAAGTCAATCTCAAGAACCAATCAG 59.794 38.462 0.00 0.00 0.00 2.90
2078 2370 4.466828 CAAAGAAAGCACGTTGACTATGG 58.533 43.478 0.00 0.00 32.69 2.74
2088 2380 2.116366 CGAAAACCCAAAGAAAGCACG 58.884 47.619 0.00 0.00 0.00 5.34
2122 2414 3.047877 GTTGGTTGACCTCGCCGG 61.048 66.667 0.00 0.00 36.82 6.13
2123 2415 1.671054 ATGTTGGTTGACCTCGCCG 60.671 57.895 1.34 0.00 36.82 6.46
2124 2416 1.586154 CCATGTTGGTTGACCTCGCC 61.586 60.000 1.34 0.00 36.82 5.54
2126 2418 1.270839 ACTCCATGTTGGTTGACCTCG 60.271 52.381 1.34 0.00 39.03 4.63
2127 2419 2.568623 ACTCCATGTTGGTTGACCTC 57.431 50.000 1.34 0.00 39.03 3.85
2137 2429 3.821033 GCTCCTAACAACAACTCCATGTT 59.179 43.478 0.00 0.00 44.08 2.71
2138 2430 3.181445 TGCTCCTAACAACAACTCCATGT 60.181 43.478 0.00 0.00 34.24 3.21
2139 2431 3.189287 GTGCTCCTAACAACAACTCCATG 59.811 47.826 0.00 0.00 0.00 3.66
2140 2432 3.412386 GTGCTCCTAACAACAACTCCAT 58.588 45.455 0.00 0.00 0.00 3.41
2437 3307 1.737838 TGCGGATCATTGAGGTCAAC 58.262 50.000 0.00 0.00 38.86 3.18
2438 3308 2.488204 TTGCGGATCATTGAGGTCAA 57.512 45.000 0.00 0.00 40.51 3.18
2439 3309 2.488204 TTTGCGGATCATTGAGGTCA 57.512 45.000 0.00 0.00 0.00 4.02
2440 3310 5.471456 AGATATTTTGCGGATCATTGAGGTC 59.529 40.000 0.00 0.00 0.00 3.85
2441 3311 5.380043 AGATATTTTGCGGATCATTGAGGT 58.620 37.500 0.00 0.00 0.00 3.85
2442 3312 5.390251 CGAGATATTTTGCGGATCATTGAGG 60.390 44.000 0.00 0.00 0.00 3.86
2443 3313 5.406477 TCGAGATATTTTGCGGATCATTGAG 59.594 40.000 0.00 0.00 0.00 3.02
2444 3314 5.296748 TCGAGATATTTTGCGGATCATTGA 58.703 37.500 0.00 0.00 0.00 2.57
2445 3315 5.596268 TCGAGATATTTTGCGGATCATTG 57.404 39.130 0.00 0.00 0.00 2.82
2446 3316 5.760253 AGTTCGAGATATTTTGCGGATCATT 59.240 36.000 0.00 0.00 0.00 2.57
2447 3317 5.300752 AGTTCGAGATATTTTGCGGATCAT 58.699 37.500 0.00 0.00 0.00 2.45
2448 3318 4.693283 AGTTCGAGATATTTTGCGGATCA 58.307 39.130 0.00 0.00 0.00 2.92
2449 3319 6.150318 TCTAGTTCGAGATATTTTGCGGATC 58.850 40.000 0.00 0.00 0.00 3.36
2450 3320 6.085555 TCTAGTTCGAGATATTTTGCGGAT 57.914 37.500 0.00 0.00 0.00 4.18
2451 3321 5.509716 TCTAGTTCGAGATATTTTGCGGA 57.490 39.130 0.00 0.00 0.00 5.54
2452 3322 5.977725 TCTTCTAGTTCGAGATATTTTGCGG 59.022 40.000 0.00 0.00 0.00 5.69
2453 3323 6.472486 TGTCTTCTAGTTCGAGATATTTTGCG 59.528 38.462 0.00 0.00 0.00 4.85
2454 3324 7.757097 TGTCTTCTAGTTCGAGATATTTTGC 57.243 36.000 0.00 0.00 0.00 3.68
2457 3327 9.796120 CTCTTTGTCTTCTAGTTCGAGATATTT 57.204 33.333 0.00 0.00 0.00 1.40
2458 3328 8.962679 ACTCTTTGTCTTCTAGTTCGAGATATT 58.037 33.333 0.00 0.00 0.00 1.28
2459 3329 8.514330 ACTCTTTGTCTTCTAGTTCGAGATAT 57.486 34.615 0.00 0.00 0.00 1.63
2460 3330 7.925043 ACTCTTTGTCTTCTAGTTCGAGATA 57.075 36.000 0.00 0.00 0.00 1.98
2461 3331 6.827586 ACTCTTTGTCTTCTAGTTCGAGAT 57.172 37.500 0.00 0.00 0.00 2.75
2462 3332 6.439599 CAACTCTTTGTCTTCTAGTTCGAGA 58.560 40.000 0.00 0.00 0.00 4.04
2463 3333 5.631512 CCAACTCTTTGTCTTCTAGTTCGAG 59.368 44.000 0.00 0.00 0.00 4.04
2464 3334 5.301045 TCCAACTCTTTGTCTTCTAGTTCGA 59.699 40.000 0.00 0.00 0.00 3.71
2465 3335 5.402867 GTCCAACTCTTTGTCTTCTAGTTCG 59.597 44.000 0.00 0.00 0.00 3.95
2466 3336 5.402867 CGTCCAACTCTTTGTCTTCTAGTTC 59.597 44.000 0.00 0.00 0.00 3.01
2467 3337 5.290386 CGTCCAACTCTTTGTCTTCTAGTT 58.710 41.667 0.00 0.00 0.00 2.24
2468 3338 4.262079 CCGTCCAACTCTTTGTCTTCTAGT 60.262 45.833 0.00 0.00 0.00 2.57
2469 3339 4.238514 CCGTCCAACTCTTTGTCTTCTAG 58.761 47.826 0.00 0.00 0.00 2.43
2470 3340 3.554337 GCCGTCCAACTCTTTGTCTTCTA 60.554 47.826 0.00 0.00 0.00 2.10
2471 3341 2.807108 GCCGTCCAACTCTTTGTCTTCT 60.807 50.000 0.00 0.00 0.00 2.85
2472 3342 1.531578 GCCGTCCAACTCTTTGTCTTC 59.468 52.381 0.00 0.00 0.00 2.87
2473 3343 1.594331 GCCGTCCAACTCTTTGTCTT 58.406 50.000 0.00 0.00 0.00 3.01
2474 3344 0.600255 CGCCGTCCAACTCTTTGTCT 60.600 55.000 0.00 0.00 0.00 3.41
2475 3345 0.878961 ACGCCGTCCAACTCTTTGTC 60.879 55.000 0.00 0.00 0.00 3.18
2476 3346 0.463116 AACGCCGTCCAACTCTTTGT 60.463 50.000 0.00 0.00 0.00 2.83
2477 3347 0.661020 AAACGCCGTCCAACTCTTTG 59.339 50.000 0.00 0.00 0.00 2.77
2478 3348 1.385528 AAAACGCCGTCCAACTCTTT 58.614 45.000 0.00 0.00 0.00 2.52
2479 3349 1.332686 GAAAAACGCCGTCCAACTCTT 59.667 47.619 0.00 0.00 0.00 2.85
2480 3350 0.942252 GAAAAACGCCGTCCAACTCT 59.058 50.000 0.00 0.00 0.00 3.24
2481 3351 0.942252 AGAAAAACGCCGTCCAACTC 59.058 50.000 0.00 0.00 0.00 3.01
2482 3352 1.064952 CAAGAAAAACGCCGTCCAACT 59.935 47.619 0.00 0.00 0.00 3.16
2483 3353 1.472990 CAAGAAAAACGCCGTCCAAC 58.527 50.000 0.00 0.00 0.00 3.77
2484 3354 0.248702 GCAAGAAAAACGCCGTCCAA 60.249 50.000 0.00 0.00 0.00 3.53
2485 3355 1.357334 GCAAGAAAAACGCCGTCCA 59.643 52.632 0.00 0.00 0.00 4.02
2486 3356 1.724581 CGCAAGAAAAACGCCGTCC 60.725 57.895 0.00 0.00 43.02 4.79
2487 3357 3.809990 CGCAAGAAAAACGCCGTC 58.190 55.556 0.00 0.00 43.02 4.79
2499 3369 0.674581 TCCACATCAGCCTTCGCAAG 60.675 55.000 0.00 0.00 37.52 4.01
2500 3370 0.035152 ATCCACATCAGCCTTCGCAA 60.035 50.000 0.00 0.00 37.52 4.85
2501 3371 0.462581 GATCCACATCAGCCTTCGCA 60.463 55.000 0.00 0.00 37.52 5.10
2502 3372 0.462581 TGATCCACATCAGCCTTCGC 60.463 55.000 0.00 0.00 33.80 4.70
2503 3373 2.251409 ATGATCCACATCAGCCTTCG 57.749 50.000 0.00 0.00 42.53 3.79


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

AutoCloner maintained by Alex Coulton.