Multiple sequence alignment - TraesCS5D01G511800

Loading Multiple Alignment...

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 TraesCS5D01G511800 chr5D 100.000 3610 0 0 1 3610 536255880 536252271 0.000000e+00 6667.0
1 TraesCS5D01G511800 chr5D 83.019 2385 236 75 817 3115 536025007 536027308 0.000000e+00 2004.0
2 TraesCS5D01G511800 chr5D 82.706 2365 258 68 817 3115 536280349 536278070 0.000000e+00 1962.0
3 TraesCS5D01G511800 chr5D 88.661 926 92 10 2027 2942 536048214 536049136 0.000000e+00 1116.0
4 TraesCS5D01G511800 chr5D 88.168 524 42 9 1 508 536036762 536037281 1.110000e-169 606.0
5 TraesCS5D01G511800 chr5D 90.521 211 14 5 653 863 536037526 536037730 1.280000e-69 274.0
6 TraesCS5D01G511800 chr5D 82.099 324 34 17 999 1316 535996615 535996920 4.630000e-64 255.0
7 TraesCS5D01G511800 chr5D 79.379 354 48 17 925 1260 536003524 536003870 3.630000e-55 226.0
8 TraesCS5D01G511800 chr5D 89.130 46 4 1 2629 2674 535998262 535998306 5.040000e-04 56.5
9 TraesCS5D01G511800 chr5B 91.488 2373 131 35 653 2982 676538371 676536027 0.000000e+00 3197.0
10 TraesCS5D01G511800 chr5B 81.449 2388 273 96 817 3115 676549648 676547342 0.000000e+00 1799.0
11 TraesCS5D01G511800 chr5B 87.107 636 63 8 1 621 676539101 676538470 0.000000e+00 702.0
12 TraesCS5D01G511800 chr5B 84.738 439 26 19 3199 3610 676535907 676535483 5.610000e-108 401.0
13 TraesCS5D01G511800 chr5B 78.851 435 57 25 896 1315 676461258 676461672 9.940000e-66 261.0
14 TraesCS5D01G511800 chr5B 79.083 349 47 19 925 1259 676466559 676466895 2.180000e-52 217.0
15 TraesCS5D01G511800 chr4A 90.069 2034 141 29 738 2729 635275949 635273935 0.000000e+00 2580.0
16 TraesCS5D01G511800 chr4A 85.387 2053 205 48 924 2942 635744833 635742842 0.000000e+00 2041.0
17 TraesCS5D01G511800 chr4A 82.791 2365 249 73 821 3115 635303490 635301214 0.000000e+00 1967.0
18 TraesCS5D01G511800 chr4A 89.714 525 18 6 3110 3610 635273136 635272624 3.930000e-179 638.0
19 TraesCS5D01G511800 chr4A 95.103 388 14 3 2733 3115 635273615 635273228 1.110000e-169 606.0
20 TraesCS5D01G511800 chr4A 79.884 865 123 26 1789 2622 635863434 635862590 1.440000e-163 586.0
21 TraesCS5D01G511800 chr4A 87.400 500 52 7 2212 2706 635300335 635299842 6.770000e-157 564.0
22 TraesCS5D01G511800 chr4A 87.179 78 6 3 653 730 580661662 580661735 6.420000e-13 86.1


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 TraesCS5D01G511800 chr5D 536252271 536255880 3609 True 6667.000000 6667 100.000000 1 3610 1 chr5D.!!$R1 3609
1 TraesCS5D01G511800 chr5D 536025007 536027308 2301 False 2004.000000 2004 83.019000 817 3115 1 chr5D.!!$F2 2298
2 TraesCS5D01G511800 chr5D 536278070 536280349 2279 True 1962.000000 1962 82.706000 817 3115 1 chr5D.!!$R2 2298
3 TraesCS5D01G511800 chr5D 536048214 536049136 922 False 1116.000000 1116 88.661000 2027 2942 1 chr5D.!!$F3 915
4 TraesCS5D01G511800 chr5D 536036762 536037730 968 False 440.000000 606 89.344500 1 863 2 chr5D.!!$F5 862
5 TraesCS5D01G511800 chr5B 676547342 676549648 2306 True 1799.000000 1799 81.449000 817 3115 1 chr5B.!!$R1 2298
6 TraesCS5D01G511800 chr5B 676535483 676539101 3618 True 1433.333333 3197 87.777667 1 3610 3 chr5B.!!$R2 3609
7 TraesCS5D01G511800 chr4A 635742842 635744833 1991 True 2041.000000 2041 85.387000 924 2942 1 chr4A.!!$R1 2018
8 TraesCS5D01G511800 chr4A 635272624 635275949 3325 True 1274.666667 2580 91.628667 738 3610 3 chr4A.!!$R3 2872
9 TraesCS5D01G511800 chr4A 635299842 635303490 3648 True 1265.500000 1967 85.095500 821 3115 2 chr4A.!!$R4 2294
10 TraesCS5D01G511800 chr4A 635862590 635863434 844 True 586.000000 586 79.884000 1789 2622 1 chr4A.!!$R2 833

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
900 1037 0.169672 TCGTCTCGTTTCGACATCCC 59.830 55.0 0.0 0.0 0.00 3.85 F
1491 1707 0.394488 TCCCTCGCAGTAGTCTCTGG 60.394 60.0 0.0 0.0 36.12 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2207 0.454600 GATCCGACTGGTACGAGCAA 59.545 55.0 4.6 0.0 36.3 3.91 R
3482 4925 0.107831 TGCGTCCCTTGTTGCTACTT 59.892 50.0 0.0 0.0 0.0 2.24 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
26 27 2.203182 AGACCCCTCAACCCGTGA 59.797 61.111 0.00 0.00 34.17 4.35
59 60 2.627933 AGGAGCCTAAACCCTAACACA 58.372 47.619 0.00 0.00 0.00 3.72
90 91 0.179081 GAACCCTACCCGCAGTCATC 60.179 60.000 0.00 0.00 0.00 2.92
110 111 1.404315 CCCCGAAGAAGAAAGAGACGG 60.404 57.143 0.00 0.00 38.83 4.79
129 144 2.139118 GGATCAAGCATAGAAGGACGC 58.861 52.381 0.00 0.00 0.00 5.19
167 182 1.939785 GTATCAGGCAGACGACGCG 60.940 63.158 3.53 3.53 0.00 6.01
207 222 1.074248 GAAAGCCCCTCCCAAACGA 59.926 57.895 0.00 0.00 0.00 3.85
216 231 1.361668 CTCCCAAACGACGCAGATGG 61.362 60.000 0.00 0.00 0.00 3.51
217 232 2.480555 CCAAACGACGCAGATGGC 59.519 61.111 0.00 0.00 39.90 4.40
249 267 1.780503 TCCGATGAAGAGCTCATGGA 58.219 50.000 17.77 10.16 45.23 3.41
251 269 1.411977 CCGATGAAGAGCTCATGGAGT 59.588 52.381 17.77 0.00 45.23 3.85
259 277 2.278206 CTCATGGAGTCGTCGCCG 60.278 66.667 0.00 0.00 36.30 6.46
305 323 4.778143 GACCACCTCGGCGGCAAT 62.778 66.667 10.53 0.00 39.03 3.56
315 333 2.354510 CTCGGCGGCAATGAAGAAATAA 59.645 45.455 10.53 0.00 0.00 1.40
321 339 4.096382 GCGGCAATGAAGAAATAAGGAAGA 59.904 41.667 0.00 0.00 0.00 2.87
322 340 5.393027 GCGGCAATGAAGAAATAAGGAAGAA 60.393 40.000 0.00 0.00 0.00 2.52
325 343 7.479150 GGCAATGAAGAAATAAGGAAGAAGAG 58.521 38.462 0.00 0.00 0.00 2.85
334 352 0.333312 AGGAAGAAGAGAGCGAGGGA 59.667 55.000 0.00 0.00 0.00 4.20
340 358 0.916086 AAGAGAGCGAGGGAGAGAGA 59.084 55.000 0.00 0.00 0.00 3.10
365 383 1.554583 GGAGAAGAGGGGTGTGGTCC 61.555 65.000 0.00 0.00 0.00 4.46
382 400 0.532115 TCCGGTCGCTAGGGTTTTAC 59.468 55.000 0.00 0.00 0.00 2.01
392 410 4.390909 CGCTAGGGTTTTACTTTTGTCGAT 59.609 41.667 0.00 0.00 0.00 3.59
393 411 5.445540 CGCTAGGGTTTTACTTTTGTCGATC 60.446 44.000 0.00 0.00 0.00 3.69
474 494 1.135199 GTCAACGCTAGGTGGATCGAA 60.135 52.381 0.00 0.00 35.31 3.71
563 619 5.240121 TGACAAGTTTAGGGACCGTATTTC 58.760 41.667 0.00 0.00 0.00 2.17
572 628 5.446260 AGGGACCGTATTTCAGGTATTTT 57.554 39.130 0.00 0.00 41.51 1.82
602 658 4.160439 CAGATACTAAAGTGAGTCCCAGCA 59.840 45.833 0.00 0.00 0.00 4.41
611 667 3.118038 AGTGAGTCCCAGCACAAGTTTAA 60.118 43.478 0.00 0.00 37.48 1.52
616 672 3.057526 GTCCCAGCACAAGTTTAATGACC 60.058 47.826 0.00 0.00 0.00 4.02
621 677 2.550606 GCACAAGTTTAATGACCGTGGA 59.449 45.455 0.00 0.00 0.00 4.02
622 678 3.608474 GCACAAGTTTAATGACCGTGGAC 60.608 47.826 0.00 0.00 0.00 4.02
623 679 2.803956 ACAAGTTTAATGACCGTGGACG 59.196 45.455 0.00 0.00 39.44 4.79
624 680 3.061322 CAAGTTTAATGACCGTGGACGA 58.939 45.455 0.00 0.00 43.02 4.20
625 681 2.680577 AGTTTAATGACCGTGGACGAC 58.319 47.619 0.00 0.00 43.02 4.34
626 682 2.036217 AGTTTAATGACCGTGGACGACA 59.964 45.455 0.00 1.43 43.02 4.35
627 683 2.997986 GTTTAATGACCGTGGACGACAT 59.002 45.455 0.00 3.72 43.02 3.06
659 782 9.487442 TTTAAACTATGGCCCAAAATAGATTCT 57.513 29.630 13.35 0.00 31.93 2.40
661 784 7.978099 AACTATGGCCCAAAATAGATTCTTT 57.022 32.000 13.35 0.00 31.93 2.52
669 792 9.836864 GGCCCAAAATAGATTCTTTCATTTTAT 57.163 29.630 0.00 0.00 31.26 1.40
758 881 1.234821 TGATTCGAAGCACAACCACC 58.765 50.000 12.91 0.00 0.00 4.61
863 990 0.794981 CTCGTGCTCACACTAGTCGC 60.795 60.000 0.00 0.00 45.10 5.19
876 1013 2.194388 TAGTCGCCTCTCCGTCCTGT 62.194 60.000 0.00 0.00 0.00 4.00
900 1037 0.169672 TCGTCTCGTTTCGACATCCC 59.830 55.000 0.00 0.00 0.00 3.85
908 1045 1.004394 GTTTCGACATCCCCCTTCCTT 59.996 52.381 0.00 0.00 0.00 3.36
910 1047 0.981277 TCGACATCCCCCTTCCTTCC 60.981 60.000 0.00 0.00 0.00 3.46
968 1114 1.118356 GCCATCCTCAGATCCCGAGT 61.118 60.000 8.51 0.00 0.00 4.18
1088 1247 3.849951 GCCCCGATTCGAGCTCCA 61.850 66.667 8.47 0.00 0.00 3.86
1090 1249 2.278857 CCCGATTCGAGCTCCACG 60.279 66.667 8.47 8.63 0.00 4.94
1331 1516 3.712655 CGTATTGCGCATTCCCGA 58.287 55.556 12.75 0.00 0.00 5.14
1367 1581 1.944234 TAGCATGCTTCACTCCGCGA 61.944 55.000 28.02 0.00 0.00 5.87
1491 1707 0.394488 TCCCTCGCAGTAGTCTCTGG 60.394 60.000 0.00 0.00 36.12 3.86
1529 1751 1.893808 CGGCTAATCGGGCTGCAAT 60.894 57.895 0.50 0.00 0.00 3.56
1539 1761 1.220749 GGCTGCAATGTCCTCCGTA 59.779 57.895 0.50 0.00 0.00 4.02
1554 1776 2.201022 CGTAGGTCGCCAGCCCTAT 61.201 63.158 0.00 0.00 35.82 2.57
1560 1782 0.828343 GTCGCCAGCCCTATCTACCT 60.828 60.000 0.00 0.00 0.00 3.08
1581 1815 2.183409 CCCCCATTTCAGTTCAGCG 58.817 57.895 0.00 0.00 0.00 5.18
1602 1845 1.758936 TAGCAGTAACCGCTAGCTCA 58.241 50.000 13.93 0.00 40.96 4.26
1665 1908 1.016653 GGTGGAGAAGCTCTTCGTGC 61.017 60.000 4.19 0.42 43.97 5.34
1840 2098 3.799366 AGAGCATGAAGAATCAGAGCAG 58.201 45.455 0.00 0.00 40.84 4.24
1865 2123 5.747248 GCAGAAGACATATAAGGGGCTCAAT 60.747 44.000 0.00 0.00 0.00 2.57
1874 2132 2.503895 AGGGGCTCAATGTGAAGAAG 57.496 50.000 0.00 0.00 0.00 2.85
1949 2207 1.834263 GTGAGTCAGCCCAACTCCTAT 59.166 52.381 0.00 0.00 42.03 2.57
1961 2219 3.448686 CAACTCCTATTGCTCGTACCAG 58.551 50.000 0.00 0.00 0.00 4.00
2009 2273 2.359967 GCCACGTAGGAAGAGGCCT 61.360 63.158 3.86 3.86 41.22 5.19
2092 2356 1.567537 GCACGTTAAGCAGCGACAA 59.432 52.632 0.00 0.00 32.08 3.18
2198 2465 1.600957 CAAGCAGCGAATGAATCCGAT 59.399 47.619 0.00 0.00 0.00 4.18
2311 2590 0.958822 GTGCCGGAATTTTCAGTGGT 59.041 50.000 5.05 0.00 0.00 4.16
2385 2679 1.065926 CAGGTCAGGCACAAGCTGATA 60.066 52.381 7.05 0.00 41.99 2.15
2483 2777 3.151022 GGCTGGGACGAGGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
2643 2952 7.321153 TCTCATTGGTTTAGTAGTTAGCTCAC 58.679 38.462 0.00 0.00 0.00 3.51
2644 2953 7.178628 TCTCATTGGTTTAGTAGTTAGCTCACT 59.821 37.037 5.75 5.75 0.00 3.41
2683 2992 0.512952 GTGCTGAGTTGCAAGGTACG 59.487 55.000 0.00 0.00 45.12 3.67
2791 3420 6.700960 TGTCTTAAAAGGTGTCGTTTAATCGA 59.299 34.615 4.54 4.54 36.66 3.59
3201 4618 7.840716 TGGATTTTCTGTGATTTATTCCATCCT 59.159 33.333 0.00 0.00 0.00 3.24
3334 4756 0.821711 CGGCTGAAACTTTGGGTGGA 60.822 55.000 0.00 0.00 0.00 4.02
3353 4775 1.795286 GAGTCAGCTCTTTCACGTTGG 59.205 52.381 0.00 0.00 38.66 3.77
3385 4827 2.026636 AGCAAATACTACCCTTTCGCCA 60.027 45.455 0.00 0.00 0.00 5.69
3520 4963 2.509336 CCCTGCACGAAGCTACCG 60.509 66.667 6.86 6.86 45.94 4.02
3521 4964 2.261671 CCTGCACGAAGCTACCGT 59.738 61.111 8.09 8.09 45.94 4.83
3522 4965 1.509463 CCTGCACGAAGCTACCGTA 59.491 57.895 12.76 0.00 45.94 4.02
3524 4967 0.801067 CTGCACGAAGCTACCGTACC 60.801 60.000 12.76 8.47 45.94 3.34
3570 5050 1.080569 CGCTGGACACCCAAAATGC 60.081 57.895 0.00 0.00 42.98 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.783365 AGGCTCCTTCTCCCTTTTTGT 59.217 47.619 0.00 0.00 0.00 2.83
59 60 2.890945 GGTAGGGTTCAATTGCACAAGT 59.109 45.455 10.41 0.00 0.00 3.16
90 91 1.404315 CCGTCTCTTTCTTCTTCGGGG 60.404 57.143 0.00 0.00 34.05 5.73
110 111 2.541762 GTGCGTCCTTCTATGCTTGATC 59.458 50.000 0.00 0.00 32.39 2.92
129 144 2.129146 TCACGGCCCCTATACGGTG 61.129 63.158 0.00 0.00 38.17 4.94
144 159 0.450583 TCGTCTGCCTGATACGTCAC 59.549 55.000 0.00 0.00 37.83 3.67
167 182 4.477975 CGTCCGTCTCGCTCCCAC 62.478 72.222 0.00 0.00 0.00 4.61
176 191 1.371389 GCTTTCGTGACGTCCGTCT 60.371 57.895 19.30 0.00 44.80 4.18
179 194 3.110178 GGGCTTTCGTGACGTCCG 61.110 66.667 14.12 15.86 0.00 4.79
181 196 1.737008 GAGGGGCTTTCGTGACGTC 60.737 63.158 9.11 9.11 0.00 4.34
235 253 1.474478 GACGACTCCATGAGCTCTTCA 59.526 52.381 16.19 0.00 40.85 3.02
300 318 7.337942 TCTCTTCTTCCTTATTTCTTCATTGCC 59.662 37.037 0.00 0.00 0.00 4.52
303 321 7.279758 CGCTCTCTTCTTCCTTATTTCTTCATT 59.720 37.037 0.00 0.00 0.00 2.57
305 323 6.071334 TCGCTCTCTTCTTCCTTATTTCTTCA 60.071 38.462 0.00 0.00 0.00 3.02
315 333 0.333312 TCCCTCGCTCTCTTCTTCCT 59.667 55.000 0.00 0.00 0.00 3.36
321 339 0.916086 TCTCTCTCCCTCGCTCTCTT 59.084 55.000 0.00 0.00 0.00 2.85
322 340 0.469917 CTCTCTCTCCCTCGCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
325 343 0.107410 TCACTCTCTCTCCCTCGCTC 60.107 60.000 0.00 0.00 0.00 5.03
334 352 3.373001 CCCTCTTCTCCATCACTCTCTCT 60.373 52.174 0.00 0.00 0.00 3.10
340 358 1.203364 ACACCCCTCTTCTCCATCACT 60.203 52.381 0.00 0.00 0.00 3.41
365 383 2.375173 AAGTAAAACCCTAGCGACCG 57.625 50.000 0.00 0.00 0.00 4.79
370 388 5.642491 AGATCGACAAAAGTAAAACCCTAGC 59.358 40.000 0.00 0.00 0.00 3.42
405 423 4.722361 ACTTAGACATTCGAGGGTTCTC 57.278 45.455 0.00 0.00 36.69 2.87
444 464 2.612972 CCTAGCGTTGACTGGACACATT 60.613 50.000 0.00 0.00 0.00 2.71
474 494 2.282887 GGTTTGGCACCGGTCCAT 60.283 61.111 21.56 0.00 35.12 3.41
572 628 8.475639 GGGACTCACTTTAGTATCTGTATTTCA 58.524 37.037 0.00 0.00 0.00 2.69
590 646 1.680338 AAACTTGTGCTGGGACTCAC 58.320 50.000 0.00 0.00 34.30 3.51
596 652 2.095263 CGGTCATTAAACTTGTGCTGGG 60.095 50.000 0.00 0.00 0.00 4.45
602 658 2.803956 CGTCCACGGTCATTAAACTTGT 59.196 45.455 0.00 0.00 35.37 3.16
611 667 2.178912 AAAATGTCGTCCACGGTCAT 57.821 45.000 0.00 2.61 40.29 3.06
634 690 9.487442 AAGAATCTATTTTGGGCCATAGTTTAA 57.513 29.630 7.26 0.00 0.00 1.52
636 692 7.978099 AAGAATCTATTTTGGGCCATAGTTT 57.022 32.000 7.26 7.84 0.00 2.66
637 693 7.619302 TGAAAGAATCTATTTTGGGCCATAGTT 59.381 33.333 7.26 3.85 0.00 2.24
638 694 7.125391 TGAAAGAATCTATTTTGGGCCATAGT 58.875 34.615 7.26 1.22 0.00 2.12
639 695 7.587037 TGAAAGAATCTATTTTGGGCCATAG 57.413 36.000 7.26 6.69 0.00 2.23
640 696 8.551682 AATGAAAGAATCTATTTTGGGCCATA 57.448 30.769 7.26 0.00 0.00 2.74
642 698 6.872585 AATGAAAGAATCTATTTTGGGCCA 57.127 33.333 0.00 0.00 0.00 5.36
643 699 9.836864 ATAAAATGAAAGAATCTATTTTGGGCC 57.163 29.630 10.75 0.00 34.07 5.80
706 829 9.857957 CTTCCTCCGTTCCTATAAATATAAGTC 57.142 37.037 0.00 0.00 0.00 3.01
707 830 9.377238 ACTTCCTCCGTTCCTATAAATATAAGT 57.623 33.333 0.00 0.00 0.00 2.24
717 840 9.716556 AATCATATATACTTCCTCCGTTCCTAT 57.283 33.333 0.00 0.00 0.00 2.57
720 843 6.973474 CGAATCATATATACTTCCTCCGTTCC 59.027 42.308 0.00 0.00 0.00 3.62
725 848 7.489757 GTGCTTCGAATCATATATACTTCCTCC 59.510 40.741 4.82 0.00 0.00 4.30
758 881 2.738521 ACGGCAAGCTAGTGTGCG 60.739 61.111 11.97 10.18 41.85 5.34
863 990 3.775654 GGCCACAGGACGGAGAGG 61.776 72.222 0.00 0.00 0.00 3.69
876 1013 2.257371 CGAAACGAGACGAGGCCA 59.743 61.111 5.01 0.00 0.00 5.36
900 1037 2.026169 GGGAGTAAACAGGAAGGAAGGG 60.026 54.545 0.00 0.00 0.00 3.95
908 1045 4.597507 AGATTTGTGAGGGAGTAAACAGGA 59.402 41.667 0.00 0.00 0.00 3.86
910 1047 5.551233 TGAGATTTGTGAGGGAGTAAACAG 58.449 41.667 0.00 0.00 0.00 3.16
1124 1289 1.304134 GATTCGTGGGCTGGGGTTT 60.304 57.895 0.00 0.00 0.00 3.27
1126 1291 3.728373 GGATTCGTGGGCTGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
1430 1646 3.170810 CTAGACCTCGACGCGGCTC 62.171 68.421 11.76 0.00 0.00 4.70
1431 1647 3.203412 CTAGACCTCGACGCGGCT 61.203 66.667 11.76 5.02 0.00 5.52
1432 1648 4.908877 GCTAGACCTCGACGCGGC 62.909 72.222 12.47 6.41 0.00 6.53
1546 1768 1.484444 GGGGCAGGTAGATAGGGCTG 61.484 65.000 0.00 0.00 0.00 4.85
1581 1815 2.293677 TGAGCTAGCGGTTACTGCTATC 59.706 50.000 23.96 20.10 43.50 2.08
1591 1825 1.359848 CAACGAAATGAGCTAGCGGT 58.640 50.000 9.55 0.00 0.00 5.68
1602 1845 5.427036 AAATACACGTCAACCAACGAAAT 57.573 34.783 3.16 0.00 45.37 2.17
1665 1908 5.471456 AGGAAACACTAATGAAGCAAGTCTG 59.529 40.000 0.00 0.00 0.00 3.51
1679 1922 1.822990 CTACCTCGCCAGGAAACACTA 59.177 52.381 3.62 0.00 43.65 2.74
1840 2098 2.373502 AGCCCCTTATATGTCTTCTGCC 59.626 50.000 0.00 0.00 0.00 4.85
1865 2123 1.416401 GTCCACACTCCCTTCTTCACA 59.584 52.381 0.00 0.00 0.00 3.58
1874 2132 2.357517 CTGCACGTCCACACTCCC 60.358 66.667 0.00 0.00 0.00 4.30
1935 2193 1.673168 GAGCAATAGGAGTTGGGCTG 58.327 55.000 0.00 0.00 0.00 4.85
1949 2207 0.454600 GATCCGACTGGTACGAGCAA 59.545 55.000 4.60 0.00 36.30 3.91
1961 2219 2.506472 GGGGGCTTCTGATCCGAC 59.494 66.667 0.00 0.00 0.00 4.79
2009 2273 1.101635 CCTCGCCTAGGTCGATGTCA 61.102 60.000 22.72 6.35 40.94 3.58
2198 2465 1.296392 CGGGAGCACCACTTGATGA 59.704 57.895 1.58 0.00 40.22 2.92
2218 2485 4.145876 TCGTCAACAATGTTTGCTGATC 57.854 40.909 0.00 0.00 37.98 2.92
2261 2540 1.005630 GCTCTCCTTGTCACACGCT 60.006 57.895 0.00 0.00 0.00 5.07
2311 2590 2.105134 TCCTCTTTCGGTGGTTTAGCAA 59.895 45.455 0.00 0.00 0.00 3.91
2385 2679 3.144506 CTGCTTCTTGATGGTCTGTGTT 58.855 45.455 0.00 0.00 0.00 3.32
2643 2952 4.023707 CACCAAAACTGGAGCAGACTAAAG 60.024 45.833 0.00 0.00 35.18 1.85
2644 2953 3.882888 CACCAAAACTGGAGCAGACTAAA 59.117 43.478 0.00 0.00 35.18 1.85
2683 2992 5.519927 ACAAAAGATGCTACAAACAGTTTGC 59.480 36.000 23.53 12.08 44.39 3.68
2791 3420 1.077212 GGCTGCATCTCACCCATGT 60.077 57.895 0.50 0.00 0.00 3.21
3060 3741 1.761244 GCGCAACAAAACCACTTGGC 61.761 55.000 0.30 0.00 39.32 4.52
3130 4547 4.279043 GGTGCCGCCAACCAACAC 62.279 66.667 0.00 0.00 37.17 3.32
3201 4618 8.372459 TCTCCTACTACAAGAACATTGCTAAAA 58.628 33.333 0.00 0.00 0.00 1.52
3315 4736 0.821711 TCCACCCAAAGTTTCAGCCG 60.822 55.000 0.00 0.00 0.00 5.52
3334 4756 1.412710 TCCAACGTGAAAGAGCTGACT 59.587 47.619 0.00 0.00 0.00 3.41
3353 4775 6.873605 AGGGTAGTATTTGCTGCAAAATTTTC 59.126 34.615 29.05 18.79 36.90 2.29
3468 4911 4.808414 TGCTACTTGCTACTGATCTTGT 57.192 40.909 0.00 0.00 43.37 3.16
3469 4912 4.931601 TGTTGCTACTTGCTACTGATCTTG 59.068 41.667 0.00 0.00 45.30 3.02
3470 4913 5.152623 TGTTGCTACTTGCTACTGATCTT 57.847 39.130 0.00 0.00 45.30 2.40
3472 4915 4.331168 CCTTGTTGCTACTTGCTACTGATC 59.669 45.833 0.00 0.00 45.30 2.92
3474 4917 3.557054 CCCTTGTTGCTACTTGCTACTGA 60.557 47.826 0.00 0.00 45.30 3.41
3476 4919 2.637872 TCCCTTGTTGCTACTTGCTACT 59.362 45.455 0.00 0.00 45.30 2.57
3477 4920 2.742589 GTCCCTTGTTGCTACTTGCTAC 59.257 50.000 0.00 0.00 45.29 3.58
3480 4923 0.517316 CGTCCCTTGTTGCTACTTGC 59.483 55.000 0.00 0.00 43.25 4.01
3481 4924 0.517316 GCGTCCCTTGTTGCTACTTG 59.483 55.000 0.00 0.00 0.00 3.16
3482 4925 0.107831 TGCGTCCCTTGTTGCTACTT 59.892 50.000 0.00 0.00 0.00 2.24
3520 4963 3.381590 GCCATTTCTCCATTCAAGGGTAC 59.618 47.826 0.00 0.00 0.00 3.34
3521 4964 3.627237 GGCCATTTCTCCATTCAAGGGTA 60.627 47.826 0.00 0.00 0.00 3.69
3522 4965 2.460669 GCCATTTCTCCATTCAAGGGT 58.539 47.619 0.00 0.00 0.00 4.34
3524 4967 2.459644 TGGCCATTTCTCCATTCAAGG 58.540 47.619 0.00 0.00 0.00 3.61
3570 5050 2.124193 TGGAATCGGCATGCCTGG 60.124 61.111 33.07 19.53 0.00 4.45


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

AutoCloner maintained by Alex Coulton.